If you are doing curation on Google Sheets, you can copy the sheet identifier
and use the `--google-sheet` option like in:
.. code-block:: shell
$ python -m bioregistry.curation.bulk_google_import --google-sheet 10MPt-H6My33mOa1V_VkLh4YG8609N7B_Dey0CBnfTL4
"""
import sys
from collections import defaultdict
from typing import Any, DefaultDict, Dict, Mapping, Optional
import click
import pandas as pd
from bioregistry import Resource
from bioregistry.schema_utils import add_resource
from bioregistry.utils import norm
NESTED = {"contact", "contributor"}
def _resource_from_row(row: Mapping[str, Any]) -> Resource:
kwargs = {}
nested: DefaultDict[str, Dict[str, str]] = defaultdict(dict)
for key, value in row.items():
if pd.isna(value):
continue
key = key.split(" ")[0] # get rid of all of the "(optional)" labels
subkeys = key.split("_")
if subkeys[0] in NESTED:
k1, k2 = subkeys
nested[k1][k2] = value
else:
kwargs[key] = value
kwargs.update(nested)
prefix = kwargs.pop("prefix")
prefix_norm = norm(prefix)
if prefix == prefix_norm:
kwargs["prefix"] = prefix
else:
kwargs["prefix"] = prefix_norm
kwargs.setdefault("synonyms", []).append(prefix)
kwargs["synonyms"] = sorted(kwargs["synonyms"])
return Resource(**kwargs)
def _bulk_import_df(df: pd.DataFrame):
for _, row in df.iterrows():
resource = _resource_from_row(row.to_dict())
try:
add_resource(resource)
except KeyError as e:
click.secho(str(e).strip("'"))
continue
@click.command()
@click.option("--google-sheet")
@click.option("--google-sheet-gid", type=int, default=0)
@click.option("--path")
def main(google_sheet: Optional[str], google_sheet_gid: int, path: Optional[str]):
"""Import prefixes from a google sheet in bulk."""
# google_sheet = "10MPt-H6My33mOa1V_VkLh4YG8609N7B_Dey0CBnfTL4"
if google_sheet:
url = f"https://docs.google.com/spreadsheets/d/{google_sheet}/export?format=tsv&gid={google_sheet_gid}"
df = pd.read_csv(url, sep="\t")
elif path:
df = pd.read_csv(path, sep="," if path.endswith("csv") else "\t")
else:
click.secho("no sheet provided", fg="red")
return sys.exit(1)
_bulk_import_df(df)
if __name__ == "__main__":
main()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/curation/clean_licenses.py 0000644 0001751 0000177 00000001153 14655542206 024132 0 ustar 00runner docker """Standardize licenses."""
import click
from tqdm import tqdm
from bioregistry import manager
from bioregistry.license_standardizer import standardize_license
__all__ = [
"main",
]
@click.command(name="standardize-licenses")
def main():
"""Standardize manually curated licenses."""
licensed = [resource for resource in manager.registry.values() if resource.license]
for resource in tqdm(licensed, unit="resource", desc="Standardizing manually curated licenses"):
resource.license = standardize_license(resource.license)
manager.write_registry()
if __name__ == "__main__":
main()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/curation/clean_name_suffixes.py 0000644 0001751 0000177 00000001247 14655542206 025165 0 ustar 00runner docker """Remove uninformative suffixes in names of resources."""
import click
from tabulate import tabulate
import bioregistry
suffixes = ["id", "accession"]
@click.command()
def _main():
rows = []
registry = bioregistry.read_registry()
for prefix, resource in registry.items():
name = bioregistry.get_name(prefix)
for suffix in suffixes:
if name.lower().endswith(f" {suffix}"):
resource.name = name[: -len(suffix) - 1]
rows.append((prefix, name))
click.echo(tabulate(rows, headers=["prefix", "name"], tablefmt="github"))
bioregistry.write_registry(registry)
if __name__ == "__main__":
_main()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/curation/clean_publications.py 0000644 0001751 0000177 00000001300 14655542206 025013 0 ustar 00runner docker """Clean up the publications.
1. Remove duplications
2. Remove publications missing key metadat (e.g., title)
"""
from tqdm import tqdm
import bioregistry
from bioregistry.schema.struct import deduplicate_publications
def _main():
for resource in tqdm(bioregistry.manager.registry.values()):
if resource.publications:
new = []
for p in deduplicate_publications(resource.publications):
if not p.title:
continue
p.title = p.title.rstrip(".").replace(" ", " ")
new.append(p)
resource.publications = new
bioregistry.manager.write_registry()
if __name__ == "__main__":
_main()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/curation/cleanup_authors.py 0000644 0001751 0000177 00000003752 14655542206 024366 0 ustar 00runner docker """Add ragged ORCID, email, and GitHub."""
from collections import defaultdict
from bioregistry import manager
from bioregistry.schema import Attributable
def _main():
githubs, emails = {}, {}
names = defaultdict(set)
for resource in manager.registry.values():
authors = [
resource.contributor,
resource.contributor,
resource.contact,
resource.reviewer,
*(resource.contributor_extras or []),
]
for author in authors:
if author is None:
continue
orcid = author.orcid
if orcid is None:
continue
if author.name:
names[orcid].add(author.name)
if author.github:
githubs[orcid] = author.github
if author.email:
emails[orcid] = author.email
# Chose the longest name, assuming that contains the least abbreviations and most initials
orcid_to_name = {orcid: max(all_names, key=len) for orcid, all_names in names.items()}
def _new(orcid_: str) -> Attributable:
return Attributable(
orcid=orcid_,
name=orcid_to_name[orcid_],
email=emails.get(orcid_),
github=githubs.get(orcid_),
)
for resource in manager.registry.values():
if resource.contributor and resource.contributor.orcid:
resource.contributor = _new(resource.contributor.orcid)
if resource.reviewer and resource.reviewer.orcid:
resource.reviewer = _new(resource.reviewer.orcid)
if resource.contact and resource.contact.orcid:
resource.contact = _new(resource.contact.orcid)
if resource.contributor_extras:
resource.contributor_extras = [
_new(contributor.orcid) if contributor.orcid else contributor
for contributor in resource.contributor_extras
]
manager.write_registry()
if __name__ == "__main__":
_main()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/curation/curated_papers.csv 0000644 0001751 0000177 00000000045 14655542206 024326 0 ustar 00runner docker pmid, relevant, relevancy_type, notes ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/curation/deprecation_diff.py 0000644 0001751 0000177 00000003044 14655542206 024451 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Show discrepancies between Bioregistry and OBO Foundry deprecation status."""
import click
import pandas as pd
import bioregistry
@click.command()
def main():
"""Show discrepancies between Bioregistry and OBO Foundry deprecation status."""
rows = []
for prefix, resource in bioregistry.read_registry().items():
if resource.obofoundry is None and resource.miriam:
continue
# no additional judgement was passed in curation of the Bioregistry
if resource.deprecated is None:
continue
obo_deprecation = (
None if resource.obofoundry is None else resource.obofoundry.get("deprecated", False)
)
miriam_deprecation = (resource.miriam or {}).get("deprecated")
if obo_deprecation is not None and miriam_deprecation is not None:
if resource.deprecated != obo_deprecation or resource.deprecated != miriam_deprecation:
rows.append((prefix, resource.deprecated, obo_deprecation, miriam_deprecation))
elif obo_deprecation is not None:
if resource.deprecated != obo_deprecation:
rows.append((prefix, resource.deprecated, obo_deprecation, "-"))
elif miriam_deprecation is not None:
if resource.deprecated != miriam_deprecation:
rows.append((prefix, resource.deprecated, "-", miriam_deprecation))
df = pd.DataFrame(rows, columns=["prefix", "bioregistry", "obo", "miriam"])
click.echo(df.to_markdown())
if __name__ == "__main__":
main()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/curation/enrich_publications.py 0000644 0001751 0000177 00000012156 14655542206 025214 0 ustar 00runner docker """Add titles and missing xrefs for publications.
Run this script with python -m bioregistry.curation.clean_publications.
"""
from functools import lru_cache
from typing import Optional, cast
from manubot.cite.doi import get_doi_csl_item
from manubot.cite.pubmed import get_pmid_for_doi, get_pubmed_csl_item
from tqdm import tqdm
from bioregistry import manager
from bioregistry.schema.struct import Publication, deduplicate_publications
from bioregistry.utils import removeprefix
@lru_cache(None)
def _get_pubmed_csl_item(pmid):
try:
return get_pubmed_csl_item(pmid)
except Exception:
return None
@lru_cache(None)
def _get_doi_csl_item(pmid):
return get_doi_csl_item(pmid)
@lru_cache(None)
def _get_pubmed_from_doi(doi: str) -> Optional[str]:
doi = cast(str, removeprefix(doi, "https://doi.org/"))
return get_pmid_for_doi(doi)
def _main() -> None: # noqa:C901
c = 0
resource_dois = []
resources = []
it = tqdm(manager.registry.values(), unit="resource", unit_scale=True, desc="caching PMIDs")
for resource in it:
it.set_postfix(prefix=resource.prefix)
resource_publications = resource.get_publications()
pubmed_ids = set()
dois = set()
for publication in resource_publications:
if publication.pubmed:
pubmed_ids.add(publication.pubmed)
elif publication.doi:
doi = publication.doi.lower()
doi = removeprefix(doi, "https://doi.org/")
doi = removeprefix(doi, "http://doi.org/")
doi = removeprefix(doi, "doi:")
tqdm.write(f"getting pubmed from DOI:{doi}")
pubmed = _get_pubmed_from_doi(doi)
if pubmed:
pubmed_ids.add(pubmed)
else:
dois.add(doi.lower())
if pubmed_ids:
resources.append((resource, pubmed_ids))
if dois:
resource_dois.append((resource, dois))
if not pubmed_ids and not dois and resource.publications:
resource.publications = deduplicate_publications(resource.publications)
tqdm.write(f"looked up {len(resource_dois):,} DOIs")
for resource, dois in tqdm(resource_dois):
new_publications = []
for doi in dois:
csl_item = _get_doi_csl_item(doi)
if not csl_item:
continue
title = csl_item.get("title", "").strip().rstrip(".") or None
pubmed = csl_item.get("PMID") or None
pmc = csl_item.get("PMCID") or None
year = csl_item.get("issued", {}).get("date-parts", [[None]])[0][0]
if not title:
tqdm.write(f"No title available for pubmed:{pubmed} / doi:{doi} / pmc:{pmc}")
continue
new_publications.append(
Publication(
pubmed=pubmed,
title=title,
doi=doi,
pmc=pmc,
year=year,
)
)
_pubs = [
*(new_publications or []),
*(resource.publications or []),
]
if len(_pubs) == 1:
resource.publications = _pubs
else:
resource.publications = deduplicate_publications(_pubs)
c += 1
if c > 7:
# output every so often in case of failure
manager.write_registry()
c = 0
for resource, pubmed_ids in tqdm(
resources, desc="resources with pubmeds to update", unit="resource"
):
new_publications = []
for pubmed in pubmed_ids:
csl_item = _get_pubmed_csl_item(pubmed)
if not csl_item:
continue
title = csl_item.get("title", "").strip().rstrip(".") or None
doi = csl_item.get("DOI") or None
if doi:
doi = doi.lower()
doi = removeprefix(doi, "https://doi.org/")
doi = removeprefix(doi, "http://doi.org/")
doi = removeprefix(doi, "doi:")
pmc = csl_item.get("PMCID") or None
year = csl_item.get("issued", {}).get("date-parts", [[None]])[0][0]
if not title:
tqdm.write(f"No title available for pubmed:{pubmed} / doi:{doi} / pmc:{pmc}")
continue
new_publications.append(
Publication(
pubmed=pubmed,
title=title,
doi=doi,
pmc=pmc,
year=year,
)
)
if not resource.publications and not new_publications:
tqdm.write(f"error on {resource.prefix}")
continue
_pubs = [
*(new_publications or []),
*(resource.publications or []),
]
if len(_pubs) == 1:
resource.publications = _pubs
else:
resource.publications = deduplicate_publications(_pubs)
c += 1
if c > 7:
# output every so often in case of failure
manager.write_registry()
c = 0
if __name__ == "__main__":
_main()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/curation/fix_obo_purls.py 0000644 0001751 0000177 00000001075 14655542206 024040 0 ustar 00runner docker """Fix OBO PURLs as default URI prefixes."""
import click
from bioregistry import manager
__all__ = [
"main",
]
@click.command(name="standardize-obo-uris")
def main():
"""Fix OBO PURLs as default URI prefixes."""
for resource in manager.registry.values():
if (
not resource.get_obofoundry_prefix()
or resource.is_deprecated()
or resource.no_own_terms
):
continue
resource.uri_format = resource.get_rdf_uri_format()
manager.write_registry()
if __name__ == "__main__":
main()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/curation/import_pc_semiautomatic.py 0000644 0001751 0000177 00000006475 14655542206 026117 0 ustar 00runner docker """A script for semi-automatically importing part of Prefix Commons."""
import json
import click
import requests
from tqdm import tqdm
import bioregistry
from bioregistry import Resource, manager
from bioregistry.constants import BIOREGISTRY_MODULE
from bioregistry.external import get_prefixcommons
from bioregistry.schema_utils import add_resource
skip = {
"pharmgkb",
"pdb",
"panther",
"intenz", # already mapped via "enzyme"
"explorenz", # already mapped via "enzyme"
"geisha", # resolution is broken
"gopad", # doesn't exist anymore
"genomereviews", # doesn't exist anymore
"integr8", # same as genome reviews, doesn't exist anymore
"hdbase", # doesn't exist anymore, silent redirect
"mirortho", # redirects to new site
"hagr", # nonsense
"recode", # dead
"pathwayontology", # duplicate of pw
"pdbe", # duplicate
}
def norm(s: str) -> str:
"""Normalize a string for dictionary key usage."""
return s.lower().replace("-", "_").replace(" ", "")
@click.command()
def main():
"""Run semi-automated import of Prefix Commons."""
dead_stuff_path = BIOREGISTRY_MODULE.join(name="pc_dead_prefixes.json")
if dead_stuff_path.is_file():
dead_prefixes = set(json.loads(dead_stuff_path.read_text()))
else:
dead_prefixes = set()
click.echo(f"see {dead_stuff_path}")
uniprot_pattern = bioregistry.get_resource("uniprot").get_pattern_re()
pc = get_prefixcommons(force_download=False)
prefixes = manager.get_registry_invmap("prefixcommons")
c = 0
for prefix, data in tqdm(pc.items(), unit="prefix", desc="Checking PC prefixes"):
if prefix in prefixes or prefix in skip or prefix in dead_prefixes or len(prefix) < 4:
continue
if bioregistry.normalize_prefix(prefix):
tqdm.write(f"[{prefix:15}] duplicate alignment")
continue
uri_format = data.get("uri_format")
if uri_format is None:
continue
if not uri_format.endswith("$1"):
tqdm.write(f"[{prefix:15}] URI format: {uri_format}")
continue
if not all(data.get(k) for k in ["name", "description", "homepage", "pattern", "example"]):
continue
example = data["example"]
if uniprot_pattern.match(example):
tqdm.write(f"[{prefix:15}] skipping duplicate of UniProt: {example}")
continue
example_url = uri_format.replace("$1", data["example"])
tqdm.write(f"checking {prefix}")
homepage_res = _works(data["homepage"])
entry_res = _works(example_url)
if homepage_res and entry_res:
c += 1
tqdm.write("adding " + click.style(prefix, fg="green"))
add_resource(
Resource(
prefix=norm(prefix),
mappings=dict(prefixcommons=prefix),
prefixcommons=data,
)
)
else:
dead_prefixes.add(prefix)
dead_stuff_path.write_text(json.dumps(sorted(dead_prefixes), indent=2))
click.echo(c)
def _works(url: str) -> bool:
try:
homepage_res = requests.head(url, timeout=3, allow_redirects=True)
except IOError:
return False
else:
return homepage_res.status_code == 200
if __name__ == "__main__":
main()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/curation/make_description_curation_sheet.py 0000644 0001751 0000177 00000005326 14655542206 027605 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Make a curation sheet for the bioregistry."""
import click
import pandas as pd
import bioregistry
from bioregistry.constants import BIOREGISTRY_MODULE
def descriptions():
"""Make a curation sheet for descriptions."""
columns = [
"prefix",
"name",
"homepage",
"description",
]
path = BIOREGISTRY_MODULE.join("curation", name="descriptions.tsv")
rows = []
for prefix in bioregistry.read_registry():
if bioregistry.get_description(prefix):
continue
if bioregistry.is_deprecated(prefix):
continue
rows.append(
(
prefix,
bioregistry.get_name(prefix),
bioregistry.get_homepage(prefix),
"",
)
)
df = pd.DataFrame(rows, columns=columns)
click.echo(f"Writing {len(df.index)} description rows to {path}")
df.to_csv(path, sep="\t", index=False)
def examples():
"""Make a curation sheet for examples."""
columns = [
"prefix",
"name",
"homepage",
"deprecated",
"example",
]
rows = []
for prefix in bioregistry.read_registry():
if bioregistry.get_example(prefix):
continue
homepage = bioregistry.get_homepage(prefix)
if homepage is None:
continue
deprecated = bioregistry.is_deprecated(prefix)
rows.append(
(
prefix,
bioregistry.get_name(prefix),
homepage,
"x" if deprecated else "",
"",
)
)
df = pd.DataFrame(rows, columns=columns)
path = BIOREGISTRY_MODULE.join("curation", name="examples.tsv")
click.echo(f"Outputting {len(df.index)} example rows to {path}")
df.to_csv(path, sep="\t", index=False)
def homepages():
"""Make a curation sheet for homepages."""
columns = [
"prefix",
"name",
"deprecated",
"homepage",
]
path = BIOREGISTRY_MODULE.join("curation", name="homepages.tsv")
rows = []
for prefix in bioregistry.read_registry():
homepage = bioregistry.get_homepage(prefix)
if homepage is not None:
continue
deprecated = bioregistry.is_deprecated(prefix)
rows.append(
(
prefix,
bioregistry.get_name(prefix),
"x" if deprecated else "",
homepage,
)
)
df = pd.DataFrame(rows, columns=columns)
click.echo(f"Outputting {len(df.index)} homepage rows to {path}")
df.to_csv(path, sep="\t", index=False)
if __name__ == "__main__":
descriptions()
examples()
homepages()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/curation/make_health_report_curation_sheet.py 0000644 0001751 0000177 00000003113 14655542206 030112 0 ustar 00runner docker """Get a curation sheet for recently failing prefixes from the Bioregistry Health Report.
.. seealso:: https://biopragmatics.github.io/bioregistry/health/
"""
from pathlib import Path
import click
import pandas as pd
import yaml
import bioregistry
HERE = Path(__file__).parent.resolve()
ROOT = HERE.parent
HEALTH = ROOT.joinpath("docs", "_data", "health.yaml")
OUTPUT_PATH = Path("~/Desktop/bioregistry_health_report_failures.tsv").expanduser()
def _get_df() -> pd.DataFrame:
"""Get the curation dataframe for recently failing prefixes via the health report."""
data = yaml.safe_load(HEALTH.read_text())
most_recent_run = data["runs"][0]
rows = []
for result in most_recent_run["results"]:
if not result["failed"]:
continue
prefix = result["prefix"]
rows.append(
(
prefix,
bioregistry.get_name(prefix),
bioregistry.get_homepage(prefix),
result["url"],
# The following columns are to fill in by the curator
"", # call
"", # date
"", # curator orcid
"", # notes
)
)
columns = ["prefix", "name", "homepage", "url", "call", "date", "curator_orcid", "notes"]
return pd.DataFrame(rows, columns=columns)
@click.command()
@click.option("--path", type=click.Path(), default=OUTPUT_PATH, show_default=True)
def main(path: Path):
"""Write the curation sheet."""
df = _get_df()
df.to_csv(path, sep="\t", index=False)
if __name__ == "__main__":
main()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/curation/map_bartoc_via_wikidata.py 0000644 0001751 0000177 00000001534 14655542206 026011 0 ustar 00runner docker """Add bartoc mappings via wikidata."""
import bioregistry
from bioregistry import manager
from bioregistry.external.bartoc import get_bartoc
def _main():
wikidata_database_to_bioregistry = {
resource.wikidata["database"]: resource.prefix
for resource in bioregistry.resources()
if resource.wikidata and "database" in resource.wikidata
}
wikidata_database_to_bartoc = {
value["wikidata_database"]: key
for key, value in get_bartoc(force_download=False).items()
if "wikidata_database" in value
}
for wikidata_id, prefix in wikidata_database_to_bioregistry.items():
bartoc_id = wikidata_database_to_bartoc.get(wikidata_id)
if bartoc_id:
manager.registry[prefix].mappings["bartoc"] = bartoc_id
manager.write_registry()
if __name__ == "__main__":
_main()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/curation/map_re3data_via_fairsharing.py 0000644 0001751 0000177 00000001425 14655542206 026561 0 ustar 00runner docker """Add re3data mappings via FAIRsharing."""
from bioregistry import manager
from bioregistry.external.re3data import get_re3data
def _main():
fairsharing_invmap = manager.get_registry_invmap("fairsharing")
re3data_map = manager.get_registry_map("re3data")
fairsharing_to_re3data = {
value["xrefs"]["fairsharing"]: key
for key, value in get_re3data(force_download=False).items()
if "fairsharing" in value.get("xrefs", {})
}
for fairsharing_id, prefix in fairsharing_invmap.items():
re3data_id = fairsharing_to_re3data.get(fairsharing_id)
if re3data_id and re3data_id not in re3data_map:
manager.registry[prefix].mappings["re3data"] = re3data_id
manager.write_registry()
if __name__ == "__main__":
_main()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/curation/rename_metaprefix.py 0000644 0001751 0000177 00000001544 14655542206 024662 0 ustar 00runner docker """A script for renaming a metaprefix in the Bioregistry."""
import json
import click
from bioregistry import Resource, write_registry
from bioregistry.constants import BIOREGISTRY_PATH
@click.command()
@click.argument("old_metaprefix")
@click.argument("new_metaprefix")
def main(old_metaprefix: str, new_metaprefix: str):
"""Rename a metaprefix."""
registry = json.loads(BIOREGISTRY_PATH.read_text())
for value in registry.values():
if old_metaprefix in value:
value[new_metaprefix] = value.pop(old_metaprefix)
mappings = value.get("mappings")
if mappings and old_metaprefix in mappings:
mappings[new_metaprefix] = mappings.pop(old_metaprefix)
write_registry(
{prefix: Resource(prefix=prefix, **values) for prefix, values in registry.items()}
)
if __name__ == "__main__":
main()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/curation/review_pc.py 0000644 0001751 0000177 00000004165 14655542206 023154 0 ustar 00runner docker """Help review prefix commons imports."""
import webbrowser
import click
import pandas
from bioregistry import Author, manager
from bioregistry.constants import BIOREGISTRY_MODULE
@click.command()
def main():
"""Run the prefix commons import reviewer workflow."""
reviewed_count = 0
rows = []
for prefix, resource in sorted(manager.registry.items()):
if set(resource.get_mappings()) != {"prefixcommons"}:
continue
if resource.contributor:
continue
if resource.reviewer:
reviewed_count += 1
rows.append(
(prefix, resource.is_deprecated(), resource.provides, resource.get_example_iri())
)
continue
homepage = resource.get_homepage()
example_iri = resource.get_example_iri()
if example_iri is None or homepage is None:
continue
webbrowser.open_new_tab(example_iri)
res = input(f"[{prefix}] type y or yes to accept, anything else to continue: ")
if res.lower() in {"yes", "y"}:
resource.reviewer = Author(
name="Charles Tapley Hoyt",
orcid="0000-0003-4423-4370",
email="cthoyt@gmail.com",
github="cthoyt",
)
manager.write_registry()
reviewed_count += 1
elif res.lower() in {"n", "no"}:
resource.deprecated = True
resource.comment = "This resource doesn't exist on the web anymore"
resource.reviewer = Author(
name="Charles Tapley Hoyt",
orcid="0000-0003-4423-4370",
email="cthoyt@gmail.com",
github="cthoyt",
)
manager.write_registry()
reviewed_count += 1
else:
continue
click.echo(f"{reviewed_count} were reviewed")
df = pandas.DataFrame(rows, columns=["prefix", "deprecated", "provides", "example_url"])
path = BIOREGISTRY_MODULE.join(name="pc_results.tsv")
df.to_csv(path, sep="\t", index=False)
click.echo(f"Output results to {path}")
if __name__ == "__main__":
main()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/curation/suggest_author_curation.py 0000644 0001751 0000177 00000004412 14655542206 026133 0 ustar 00runner docker """Suggest curation of authors missing orcid/github."""
from collections import defaultdict
import click
from tabulate import tabulate
import bioregistry
# This keeps a list of group emails that are explicitly inappropriate
# for the bioregistry since we want single responsibility
EMAIL_BLACKLIST = {
"agrovoc@fao.org",
"swisslipids@isb-sib.ch",
"Intellectual.PropertyServices@ama-assn.org",
"ordo.orphanet@inserm.fr",
"help@emdatabank.org",
"biomodels-net-support@lists.sf.net",
"support@bioontology.org",
"chebi-help@ebi.ac.uk",
"helpdesk@cropontology-curationtool.org",
"ncictcaehelp@mail.nih.gov",
"eugenes@iubio.bio.indiana.edu",
"helpdesk@eionet.europa.eu",
"faldo@googlegroups.com",
"cs@firstdatabank.com",
"itiswebmaster@itis.gov",
"depod@embl.de",
"datasubs@ebi.ac.uk",
"curator@inoh.org",
"support@bel.bio",
"loinc@regenstrief.org",
"info@who.int",
"admin@envipath.org",
"interhelp@ebi.ac.uk",
"datex@efsa.europa.eu",
"secretariat@eol.org",
"whocc@fhi.no",
"info@casrai.org",
"ppdb@gifu-u.ac.jp",
}
def _main():
rows = defaultdict(set)
for resource in bioregistry.resources():
if resource.is_deprecated():
continue
contact = resource.get_contact()
if not contact:
continue
if contact.email in EMAIL_BLACKLIST:
contact.email = None
contact.name = contact.name.removeprefix("Dr. ").strip()
contact.name = contact.name.removeprefix("Dr ").strip()
contact.name = contact.name.removesuffix("MD").strip()
if contact.orcid and contact.email and contact.github:
continue
rows[
contact.name or "", contact.orcid or "", contact.email or "", contact.github or ""
].add(resource.prefix)
click.echo(
tabulate(
[
(name, orcid, email, github, ", ".join(sorted(prefixes)))
for (name, orcid, email, github), prefixes in sorted(
rows.items(), key=lambda t: (t[0][0].casefold(), t[0][0])
)
],
tablefmt="github",
headers=["name", "orcid", "email", "github", "prefixes"],
)
)
if __name__ == "__main__":
_main()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/curation/suggest_uniprot_providers.py 0000644 0001751 0000177 00000001473 14655542206 026526 0 ustar 00runner docker """This script suggests prefixes that might be providers for uniprot."""
import click
from tabulate import tabulate
import bioregistry
FALSE_POSITIVES = {
"panther.pathway",
"panther.pthcmp",
"protclustdb",
}
@click.command()
def _main():
rows = []
for prefix, resource in bioregistry.read_registry().items():
if prefix == "uniprot" or prefix in FALSE_POSITIVES:
continue
example = resource.get_example()
if example is None:
continue
if resource.provides:
continue
if bioregistry.is_standardizable_identifier("uniprot", example):
rows.append((prefix, example, bioregistry.get_uri_format(prefix)))
click.echo(tabulate(rows, headers=["prefix", "example", "uri_format"]))
if __name__ == "__main__":
_main()
././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9459667
bioregistry-0.11.12/src/bioregistry/data/ 0000755 0001751 0000177 00000000000 14655546227 017705 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/data/README.md 0000644 0001751 0000177 00000003404 14655542206 021156 0 ustar 00runner docker # Bioregisty Data
This is the folder that holds the manually curated, single source of truth JSON
files that power the Bioregistry. It also has a directory `external/`
where the processed content from external registries gets stored.
## Main Database Files
### [`bioregistry.json`](bioregistry.json)
This is the main file that supports the Bioregistry's registry. It has three
goals:
1. Support novel curation
2. Support import and alignment of prefixes and metadata from external
registries
3. Enable overriding of metadata from external registries when they are wrong
All edits to the registry should be made through this file. However, you'll
notice that for some entries, there are no top-level fields like "name". This
is because the associated Python package for the Bioregistry has logic baked in
for accessing metadata through the mapped registries. This reduces the curation
burden and enables the Bioregistry to benefit from upstream changes in external
registries.
Several exports to YAML, TSV, and RDF, including consensus views over the
registry, are built on a weekly basis and can be downloaded via the
[`exports/`](https://github.com/biopragmatics/bioregistry/tree/main/exports)
directory.
### [`metaregistry.json`](metaregistry.json)
The metaregistry contains information about external registries.
### [`collections.json`](collections.json)
This file contains manually curated collections of prefixes/resources for
various purposes.
### [`mismatch.json`](metaregistry.json)
This file contains the mismatch dictionary, so the alignment algorithm doesn't
accidentally create resources that are chimera of two different ones. Its keys
correspond to bioregistry prefixes and its values are dictionaries mapping from
metaprefixes to wrong external prefixes to avoid.
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/data/__init__.py 0000644 0001751 0000177 00000000070 14655542206 022004 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Data in the bioregistry."""
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723255146.0
bioregistry-0.11.12/src/bioregistry/data/bioregistry.json 0000644 0001751 0000177 00023536345 14655544552 023166 0 ustar 00runner docker {
"3dmet": {
"biocontext": {
"prefix": "3DMET"
},
"edam": {
"description": "Identifier of a metabolite from the 3DMET database.",
"name": "Compound ID (3DMET)",
"obsolete": false,
"prefix": "2635"
},
"fairsharing": {
"abbreviation": "3DMET",
"description": "3DMET is a database of three-dimensional structures of natural metabolites.",
"homepage": "http://www.3dmet.dna.affrc.go.jp/",
"name": "Three-Dimensional Structure Database of Natural Metabolites",
"prefix": "FAIRsharing.5ab0n7",
"publications": [
{
"doi": "10.1021/ci300309k",
"pubmed_id": 23293959,
"title": "Three-Dimensional Structure Database of Natural Metabolites (3DMET): A Novel Database of Curated 3D Structures."
}
],
"subjects": [
"Life Science",
"Metabolomics"
]
},
"integbio": {
"alt_name": "A three-dimensional-structure database of natural metabolites",
"description": "This database is composed of three-dimensional structures and physical properties of natural metabolites, mainly those useful in agriculture (design of chemicals used in agriculture, compositional analysis of food). Compounds with similar structures and physical properties can be searched through an easy interface.",
"fairsharing": "biodbcore-000465",
"homepage": "http://www.3dmet.dna.affrc.go.jp/",
"information_keywords": [
"3D structure"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "3DMET",
"prefix": "nbdc00351",
"status": "Inactive",
"target_keywords": [
"Metabolite",
"Chemical compound"
]
},
"mappings": {
"biocontext": "3DMET",
"edam": "2635",
"fairsharing": "FAIRsharing.5ab0n7",
"integbio": "nbdc00351",
"miriam": "3dmet",
"n2t": "3dmet",
"prefixcommons": "3dmet",
"wikidata": "P2796"
},
"miriam": {
"deprecated": true,
"description": "3DMET is a database collecting three-dimensional structures of natural metabolites.",
"homepage": "http://www.3dmet.dna.affrc.go.jp/",
"id": "00000066",
"name": "3DMET",
"namespaceEmbeddedInLui": false,
"pattern": "^B\\d{5}$",
"prefix": "3dmet",
"sampleId": "B00162",
"uri_format": "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1"
},
"n2t": {
"description": "3DMET is a database collecting three-dimensional structures of natural metabolites.",
"example": "B00162",
"homepage": "http://www.3dmet.dna.affrc.go.jp/",
"name": "3DMET database",
"namespaceEmbeddedInLui": false,
"pattern": "^B\\d{5}$",
"prefix": "3dmet",
"uri_format": "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1"
},
"name": "3D Metabolites",
"prefixcommons": {
"description": "3DMET is a database of three-dimensional structures of natural metabolites.",
"example": "B00162",
"homepage": "http://www.3dmet.dna.affrc.go.jp",
"keywords": [
"chemical",
"metabolite",
"structure"
],
"miriam": "3dmet",
"name": "Three-Dimensional Structure Database of Natural Metabolites",
"pattern": "^B\\d{5}$",
"prefix": "3dmet",
"pubmed_ids": [
"23293959",
"29892514"
]
},
"publications": [
{
"doi": "10.2142/biophysico.15.0_87",
"pmc": "PMC5992871",
"pubmed": "29892514",
"title": "Chemical curation to improve data accuracy: recent development of the 3DMET database",
"year": 2018
},
{
"doi": "10.1021/ci300309k",
"pubmed": "23293959",
"title": "Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures",
"year": 2013
}
],
"wikidata": {
"description": "identifier of chemical compounds in 3DMet database",
"example": [
"B01253",
"B01305"
],
"name": "3DMet ID",
"pattern": "^B\\d{5}$",
"prefix": "P2796",
"uri_format": "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1"
}
},
"4dn.biosource": {
"cellosaurus": {
"category": "Biological sample resources",
"homepage": "https://data.4dnucleome.org/",
"name": "4D Nucleome Data Portal",
"prefix": "4DN",
"uri_format": "https://data.4dnucleome.org/biosources/$1"
},
"contact": {
"email": "Job.Dekker@umassmed.edu",
"name": "Job Dekker",
"orcid": "0000-0001-5631-0698"
},
"example": "4DNSR73BT2A2",
"fairsharing": {
"abbreviation": "4DN",
"description": "The 4D Nucleome Data Portal (4DN) hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization. It is a platform to search, visualize, and download nucleomics data.",
"homepage": "https://data.4dnucleome.org/",
"name": "4DNucleome Data Portal",
"prefix": "FAIRsharing.CugtbQ",
"publications": [
{
"doi": "10.1038/nature23884",
"pubmed_id": 28905911,
"title": "The 4D nucleome project."
}
],
"subjects": [
"Life Science"
],
"twitter": "4dn_dcic"
},
"homepage": "https://data.4dnucleome.org/biosources",
"mappings": {
"cellosaurus": "4DN",
"fairsharing": "FAIRsharing.CugtbQ",
"miriam": "4dn",
"prefixcommons": "4dn"
},
"miriam": {
"deprecated": false,
"description": "The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases.",
"homepage": "https://data.4dnucleome.org/",
"id": "00000833",
"name": "4D Nucleome",
"namespaceEmbeddedInLui": false,
"pattern": "^4DN[A-Z]{2}[A-Z0-9]{7}$",
"prefix": "4dn",
"sampleId": "4DNES265ETYQ",
"uri_format": "https://data.4dnucleome.org/$1"
},
"name": "4D Nucleome Data Portal Biosource",
"prefixcommons": {
"description": "The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases.",
"example": "4DNESBOY2QLJ",
"homepage": "https://data.4dnucleome.org/",
"keywords": [
"DNA",
"protein"
],
"miriam": "4dn",
"name": "4D Nucleome",
"pattern": "^4DN[A-Z]{2}[A-Z0-9]{7}$",
"prefix": "4dn",
"pubmed_ids": [
"28905911"
],
"uri_format": "https://data.4dnucleome.org/$1"
},
"publications": [
{
"doi": "10.1038/nature23884",
"pmc": "PMC5617335",
"pubmed": "28905911",
"title": "The 4D nucleome project",
"year": 2017
}
],
"synonyms": [
"4DN"
],
"uri_format": "https://data.4dnucleome.org/biosources/$1",
"wikidata": {
"database": "Q110613621"
}
},
"4dn.replicate": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor_extras": [
{
"email": "laylamichan@ciencias.unam.mx",
"github": "lmichan",
"name": "Layla MichΓ‘n Aguirre",
"orcid": "0000-0002-5798-662X"
},
{
"email": "mineromero2901@ciencias.unam.mx",
"github": "MinRo60",
"name": "Minerva MarΓa Romero PΓ©rez",
"orcid": "0000-0002-6240-9325"
},
{
"email": "victorinolavida@ciencias.unam.mx",
"github": "Victorinolavida",
"name": "JosΓ© Victorino Ruiz Lavida",
"orcid": "0000-0001-5130-7705"
}
],
"description": "Database portal containing replicate experiments of different assays and samples",
"example": "4DNESWX1J3QU",
"homepage": "https://data.4dnucleome.org/experiment-set-replicates/",
"name": "4D Nucleome Data Portal Experiment Replicate",
"uri_format": "https://data.4dnucleome.org/experiment-set-replicates/$1",
"wikidata": {
"database": "Q110613797"
}
},
"aaindex": {
"contact": {
"email": "shuichi@hgc.jp",
"github": "skwsm",
"name": "Shuichi Kawashima",
"orcid": "0000-0001-7883-3756"
},
"contributor_extras": [
{
"email": "sumirp77@gmail.com",
"github": "sumirp",
"name": "Sumir H Pandit",
"orcid": "0000-0002-1216-4761"
}
],
"edam": {
"description": "Identifier of an entry from the AAindex database.",
"name": "AAindex",
"obsolete": false,
"prefix": "1128"
},
"integbio": {
"alt_name": "Amino acid indices, substitution matrices and pair-wise contact potentials",
"description": "The AAindex database collects and organizes amino acid properties. Users can search from dozens of studies summarizing multiple biophysical parameters for three types of information:\n- AAindex1: Biophysical properties of individual amino acids. All indexed studies have been compared to other studies in the database and pairwise correlation coefficients between related studies are provided. \n- AAindex2: Substitution indices indicating amino acid similarity.\n- AAindex3: Pairwise contact potentials between amino acids in various contexts.\nAll three databases can be searched either by study or keyword using DBGET.",
"homepage": "http://www.genome.jp/aaindex/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "AAindex",
"prefix": "nbdc00004",
"pubmeds": [
"17998252",
"9847231",
"10592278",
"3244698",
"9053899"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"mappings": {
"edam": "1128",
"integbio": "nbdc00004",
"prefixcommons": "aaindex"
},
"prefixcommons": {
"description": "AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. AAindex consists of three sections now: AAindex1 for the amino acid index of 20 numerical values, AAindex2 for the amino acid mutation matrix and AAindex3 for the statistical protein contact potentials.",
"example": "BUNA790102",
"homepage": "http://www.genome.ad.jp/aaindex/",
"keywords": [
"protein"
],
"name": "Amino acid indices, substitution matrices and pair-wise contact potentials",
"pattern": "^[A-Z]+\\d+$",
"prefix": "aaindex",
"pubmed_ids": [
"17998252"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?aaindex:$1"
},
"publications": [
{
"doi": "10.1093/nar/gkm998",
"pmc": "PMC2238890",
"pubmed": "17998252",
"title": "AAindex: amino acid index database, progress report 2008",
"year": 2007
}
],
"references": [
"https://github.com/biopragmatics/bioregistry/pull/1098"
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"wikidata": {
"database": "Q85738825"
}
},
"aao": {
"agroportal": {
"contact": {
"email": "cavoc@ml.affrc.go.jp",
"name": "Akane Takezaki"
},
"description": "Agriculture Activity ontology (AAO) is an ontology that describes agricultural work using attributes such as purpose, behavior, objective, and its attribute values.",
"name": "Agriculture Activity Ontology",
"prefix": "AAO"
},
"biocontext": {
"prefix": "AAO"
},
"description": "A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon.",
"example": "0000138",
"fairsharing": {
"abbreviation": "AAO",
"contact": {
"email": "david.c.blackburn@gmail.com",
"name": "David Blackburn",
"orcid": "0000-0002-1810-9886"
},
"description": "A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO has been integrated into Uberon.",
"homepage": "http://bioportal.bioontology.org/ontologies/AAO",
"name": "Amphibian gross Anatomy Ontology",
"prefix": "FAIRsharing.mxx5rp",
"publications": [
{
"doi": "10.1186/2041-1480-5-21",
"pubmed": "25009735",
"title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon",
"year": 2014
},
{
"doi": "10.1142/9789812772435_0035",
"title": "AN ANATOMICAL ONTOLOGY FOR AMPHIBIANS",
"year": 2006
}
],
"subjects": [
"Anatomy"
]
},
"mappings": {
"agroportal": "AAO",
"biocontext": "AAO",
"fairsharing": "FAIRsharing.mxx5rp",
"obofoundry": "aao",
"prefixcommons": "aao"
},
"obofoundry": {
"contact": "david.c.blackburn@gmail.com",
"contact.label": "David Blackburn",
"contact.orcid": "0000-0002-1810-9886",
"deprecated": true,
"domain": "anatomy and development",
"homepage": "http://github.com/seger/aao",
"name": "Amphibian gross anatomy",
"prefix": "aao"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1090",
"description": "The Amphibian Anatomical Ontology (AmphibAnat) is an NSF-sponsored project dedicated to constructing semi-automatically a draft ontology of amphibian anatomy. In this project, small, subset ontologies are constructed manually, and data-mining software (that we develop) is used to mine electronic media for instances of concepts and properties to be added to the ontologies.",
"example": "ASD:0000138",
"homepage": "http://www.amphibanat.org",
"keywords": [
"obo",
"anatomy"
],
"name": "Amphibian Anatomical Ontology",
"pattern": "^[A-Z]+:\\d+$",
"prefix": "aao",
"pubmed_ids": [
"17992749"
]
},
"publications": [
{
"doi": "10.1186/2041-1480-5-21",
"pmc": "PMC4089931",
"pubmed": "25009735",
"title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon",
"year": 2014
},
{
"doi": "10.1142/9789812772435_0035",
"pubmed": "17992749",
"title": "An anatomical ontology for amphibians",
"year": 2007
}
]
},
"abcam": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.abcam.com/nav/cell-lines-and-lysates",
"name": "Abcam cell line products",
"prefix": "Abcam",
"uri_format": "https://www.abcam.com/$1.html"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor_extras": [
{
"email": "sumirp77@gmail.com",
"github": "sumirp",
"name": "Sumir H Pandit",
"orcid": "0000-0002-1216-4761"
}
],
"description": "Vendor for assays, cells, and antibodies",
"example": "ab275461",
"homepage": "https://www.abcam.com",
"mappings": {
"cellosaurus": "Abcam"
},
"name": "Abcam",
"references": [
"https://github.com/biopragmatics/bioregistry/pull/1098"
],
"uri_format": "https://www.abcam.com/$1.html",
"wikidata": {
"database": "Q29123382"
}
},
"abcd": {
"cellosaurus": {
"category": "Biological sample resources",
"homepage": "https://web.expasy.org/abcd/",
"name": "AntiBodies Chemically Defined database",
"prefix": "ABCD",
"uri_format": "https://web.expasy.org/abcd/$1"
},
"contact": {
"email": "Pierre.Cosson@unige.ch",
"name": "Pierre Cosson",
"orcid": "0000-0002-4881-0358"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor_extras": [
{
"email": "sumirp77@gmail.com",
"github": "sumirp",
"name": "Sumir H Pandit",
"orcid": "0000-0002-1216-4761"
}
],
"description": "The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies",
"example": "AD834",
"fairsharing": {
"abbreviation": "ABCD",
"description": "The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies.",
"homepage": "https://web.expasy.org/abcd/",
"name": "ABCD database",
"prefix": "FAIRsharing.Z8OKi5",
"publications": [
{
"doi": "10.1093/nar/gkz714",
"pubmed_id": 31410491,
"title": "The ABCD database: a repository for chemically defined antibodies."
}
],
"subjects": [
"Molecular biology",
"Immunology"
]
},
"homepage": "https://web.expasy.org/abcd/",
"mappings": {
"cellosaurus": "ABCD",
"fairsharing": "FAIRsharing.Z8OKi5",
"uniprot": "DB-0236"
},
"name": "AntiBodies Chemically Defined database",
"publications": [
{
"doi": "10.1093/nar/gkz714",
"pmc": "PMC6943046",
"pubmed": "31410491",
"title": "The ABCD database: a repository for chemically defined antibodies",
"year": 2020
}
],
"references": [
"https://github.com/biopragmatics/bioregistry/pull/1098"
],
"uniprot": {
"abbreviation": "ABCD",
"category": "Protocols and materials databases",
"homepage": "https://web.expasy.org/abcd",
"name": "ABCD curated depository of sequenced antibodies",
"prefix": "DB-0236",
"uri_format": "https://web.expasy.org/cgi-bin/abcd/search_abcd.pl?input=$1"
},
"uri_format": "https://web.expasy.org/abcd/ABCD_$1",
"wikidata": {
"database": "Q110998933"
}
},
"abm": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.abmgood.com/Cell-Biology.html",
"name": "Applied Biological Materials cell line products",
"prefix": "ABM",
"uri_format": "https://www.abmgood.com/catalogsearch/result/?cat=&q=$1"
},
"contributor_extras": [
{
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
}
],
"example": "T0599",
"mappings": {
"cellosaurus": "ABM"
},
"uri_format": "https://www.abmgood.com/search?query=$1"
},
"abs": {
"biocontext": {
"prefix": "ABS"
},
"edam": {
"description": "Identifier of an entry (promoter) from the ABS database.",
"name": "ABS",
"obsolete": false,
"prefix": "2741"
},
"fairsharing": {
"abbreviation": "ABS",
"contact": {
"email": "enrique.blanco@crg.eu",
"name": "Enrique Blanco",
"orcid": "0000-0001-6261-7370"
},
"description": "ABS is a database of Annotated regulatory Binding Sites from known binding sites identified in promoters of orthologous vertebrate genes.",
"homepage": "https://genome.crg.es/datasets/abs2005/",
"name": "Annotated regulatory Binding Sites from Orthologous Promoters",
"prefix": "FAIRsharing.7mnebr",
"publications": [
{
"doi": "10.1093/nar/gkj116",
"pubmed_id": 16381947,
"title": "ABS: a database of Annotated regulatory Binding Sites from orthologous promoters."
}
],
"subjects": [
"Biology"
]
},
"mappings": {
"biocontext": "ABS",
"edam": "2741",
"fairsharing": "FAIRsharing.7mnebr",
"miriam": "abs",
"n2t": "abs",
"pathguide": "217",
"prefixcommons": "abs"
},
"miriam": {
"deprecated": false,
"description": "The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography.",
"homepage": "http://genome.crg.es/datasets/abs2005/",
"id": "00000277",
"name": "ABS",
"namespaceEmbeddedInLui": false,
"pattern": "^A\\d+$",
"prefix": "abs",
"sampleId": "A0014",
"uri_format": "http://genome.crg.es/datasets/abs2005/entries/$1.html"
},
"n2t": {
"description": "The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography.",
"example": "A0014",
"homepage": "http://genome.crg.es/datasets/abs2005/",
"name": "ABS at IMIM",
"namespaceEmbeddedInLui": false,
"pattern": "^A\\d+$",
"prefix": "abs",
"uri_format": "http://genome.crg.es/datasets/abs2005/entries/$1.html"
},
"name": "Annotated Regulatory Binding Sites",
"pathguide": {
"abbreviation": "ABS",
"homepage": "http://genome.crg.es/datasets/abs2005/",
"name": "Annotated regulatory Binding Sites",
"prefix": "217"
},
"prefixcommons": {
"description": "ABS: A database of Annotated regulatory Binding Sites from known binding sites identified in promoters of orthologous vertebrate genes.",
"example": "A0014",
"homepage": "http://genome.imim.es/datasets/abs2005/",
"keywords": [
"interaction",
"gene",
"regulation"
],
"miriam": "abs",
"name": "ABS: a database of Annotated regulatory Binding Sites from Orthologous Promoters",
"pattern": "^A\\d+$",
"prefix": "abs",
"pubmed_ids": [
"16381947"
],
"uri_format": "http://genome.crg.es/datasets/abs2005/entries/$1.html"
},
"publications": [
{
"doi": "10.1093/nar/gkj116",
"pmc": "PMC1347478",
"pubmed": "16381947",
"title": "ABS: a database of Annotated regulatory Binding Sites from orthologous promoters",
"year": 2006
}
],
"wikidata": {
"database": "Q111134507"
}
},
"ac": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor_extras": [
{
"email": "sumirp77@gmail.com",
"github": "sumirp",
"name": "Sumir H Pandit",
"orcid": "0000-0002-1216-4761"
}
],
"description": "Activity Streams is an open format specification for activity stream protocols, which are used to syndicate activities taken in social web applications and services, similar to those in Facebook's, Instagram's, and Twitter's. The standard provides a general way to represent activities.",
"example": "Add",
"homepage": "http://www.w3.org/ns/activitystreams",
"keywords": [
"semantic web",
"social media"
],
"name": "Activity Streams",
"preferred_prefix": "ac",
"references": [
"https://github.com/biopragmatics/bioregistry/pull/1098"
],
"uri_format": "http://www.w3.org/ns/activitystreams#$1",
"wikidata": {
"database": "Q4677626"
}
},
"aceview.worm": {
"biocontext": {
"prefix": "ACEVIEW.WORM"
},
"contact": {
"email": "mieg@ncbi.nlm.nih.gov",
"name": "Danielle Thierry-Mieg",
"orcid": "0000-0001-9568-4211"
},
"mappings": {
"biocontext": "ACEVIEW.WORM",
"miriam": "aceview.worm",
"n2t": "aceview.worm",
"prefixcommons": "aceview.worm"
},
"miriam": {
"deprecated": false,
"description": "AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression.",
"homepage": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm",
"id": "00000282",
"name": "Aceview Worm",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z0-9-]+$",
"prefix": "aceview.worm",
"sampleId": "aap-1",
"uri_format": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1"
},
"n2t": {
"description": "AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression.",
"example": "aap-1",
"homepage": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm",
"name": "AceView Worm at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z0-9-]+$",
"prefix": "aceview.worm",
"uri_format": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1"
},
"prefixcommons": {
"description": "AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes.",
"example": "AP2B1",
"homepage": "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/",
"keywords": [
"RNA",
"DNA",
"gene"
],
"miriam": "aceview.worm",
"name": "AceView Worm Genome",
"pattern": "^[a-z0-9-]+$",
"prefix": "aceview.worm",
"pubmed_ids": [
"16925834"
],
"synonyms": [
"aceview_wormgenes"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=[?species_database]&c=Gene&l=$1"
},
"publications": [
{
"doi": "10.1186/gb-2006-7-s1-s12",
"pmc": "PMC1810549",
"pubmed": "16925834",
"title": "AceView: a comprehensive cDNA-supported gene and transcripts annotation",
"year": 2006
}
]
},
"adcad": {
"aberowl": {
"description": "Ontology to support disciplinary annotation of datasets housed at the Arctic Data Center (https://arcticdata.io)",
"download_owl": "http://aber-owl.net/media/ontologies/ADCAD/1/adcad.owl",
"homepage": "https://github.com/NCEAS/adc-disciplines",
"name": "Arctic Data Center Academic Disciplines Ontology",
"prefix": "ADCAD",
"version": "Version 1.0.0"
},
"bioportal": {
"contact": {
"email": "mecum@nceas.ucsb.edu",
"name": "Bryce Mecum"
},
"description": "Ontology to support disciplinary annotation of datasets housed at the Arctic Data Center (https://arcticdata.io)",
"homepage": "https://github.com/NCEAS/adc-disciplines",
"name": "Arctic Data Center Academic Disciplines Ontology",
"prefix": "ADCAD",
"version": "Version 1.0.0"
},
"contact": {
"email": "brycemecum@gmail.com",
"github": "amoeba",
"name": "Bryce Mecum",
"orcid": "0000-0002-0381-3766"
},
"contributor": {
"email": "j.harry.caufield@gmail.com",
"github": "caufieldjh",
"name": "Harry Caufield",
"orcid": "0000-0001-5705-7831"
},
"description": "An ontology to support disciplinary annotation of Arctic Data Center datasets.",
"download_rdf": "https://github.com/NCEAS/adc-disciplines/raw/main/ADCAD.ttl",
"example": "00000",
"github_request_issue": 827,
"homepage": "https://arcticdata.io/",
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "ADCAD",
"bioportal": "ADCAD"
},
"name": "Arctic Data Center Academic Disciplines Ontology",
"pattern": "^\\d{5}$",
"repository": "https://github.com/NCEAS/adc-disciplines",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://purl.dataone.org/odo/ADCAD_$1"
},
"addexbio": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.addexbio.com/productshow?id=4",
"name": "AddexBio cell line products",
"prefix": "AddexBio",
"uri_format": "https://www.addexbio.com/productdetail?pid=$1"
},
"example": "C0020004/4992",
"mappings": {
"cellosaurus": "AddexBio"
}
},
"addgene": {
"contact": {
"email": "joanne.kamens@addgene.org",
"name": "Joanne Kamens",
"orcid": "0000-0002-7000-1477"
},
"fairsharing": {
"abbreviation": "Addgene",
"description": "Addgene is a non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Addgene are working with thousands of laboratories to assemble a high-quality library of published plasmids for use in research and discovery. By linking plasmids with articles, scientists can always find data related to the materials they request.",
"homepage": "http://www.addgene.org/",
"license": "https://www.addgene.org/terms-of-use",
"name": "Addgene",
"prefix": "FAIRsharing.8hcczk",
"publications": [
{
"doi": "10.1038/nbt.2177",
"pubmed_id": 22491276,
"title": "Addgene provides an open forum for plasmid sharing."
},
{
"doi": "10.1038/505272a",
"pubmed_id": null,
"title": "Repositories share key research tools"
},
{
"doi": "10.1093/nar/gku893",
"pubmed_id": 25392412,
"title": "The Addgene repository: an international nonprofit plasmid and data resource"
}
],
"subjects": [
"Life Science"
],
"twitter": "Addgene"
},
"integbio": {
"description": "Addgene is a non-profit organization providing plasmids to researchers. It is a collaboration with several hundred research teams, creating a high quality plasmid library and repository used for publications. By linking the plasmid to its publications, researchers always have access to necessary plasmid and associated data. The site contains links to deposit plasmids, request plasmids, access sequence information on plasmids, as well as links to a vector database and associated protocols. They provide Viral service, CRISPR tools, Fluorescent proteins, Cancer resources as special colections.",
"fairsharing": "biodbcore-000196",
"homepage": "http://www.addgene.org/",
"information_keywords": [
"Bioresource",
"Method",
"Sequence",
"Repository"
],
"maintainer": "Addgene",
"name": "addgene",
"prefix": "nbdc00356",
"status": "Active",
"target_keywords": [
"DNA"
]
},
"mappings": {
"fairsharing": "FAIRsharing.8hcczk",
"integbio": "nbdc00356",
"miriam": "addgene",
"n2t": "addgene",
"prefixcommons": "addgene",
"re3data": "r3d100010741",
"rrid": "Addgene"
},
"miriam": {
"deprecated": false,
"description": "Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world.",
"homepage": "http://addgene.org/",
"id": "00000675",
"name": "Addgene Plasmid Repository",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$",
"prefix": "addgene",
"sampleId": "50943",
"uri_format": "http://addgene.org/$1"
},
"n2t": {
"description": "Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world.",
"example": "50943",
"homepage": "http://addgene.org/",
"name": "Addgene Plasmid Repository",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$",
"prefix": "addgene",
"uri_format": "http://addgene.org/$1"
},
"prefixcommons": {
"description": "Addgene is a global, nonprofit repository that was created to help scientists share plasmids.",
"example": "41816",
"homepage": "http://www.addgene.org",
"keywords": [
"plasmid"
],
"miriam": "addgene",
"name": "Addgene",
"pattern": "^\\d+$",
"prefix": "addgene",
"pubmed_ids": [
"25392412"
],
"uri_format": "http://www.addgene.org/$1"
},
"publications": [
{
"doi": "10.1093/nar/gku893",
"pmc": "PMC4384007",
"pubmed": "25392412",
"title": "The Addgene repository: an international nonprofit plasmid and data resource",
"year": 2014
},
{
"doi": "10.1038/505272a",
"pubmed": "24429608",
"title": "Repositories share key research tools",
"year": 2014
},
{
"doi": "10.1038/nbt.2177",
"pubmed": "22491276",
"title": "Addgene provides an open forum for plasmid sharing",
"year": 2012
}
],
"re3data": {
"description": "Addgene archives and distributes plasmids for researchers around the globe. They are working with thousands of laboratories to assemble a high-quality library of published plasmids for use in research and discovery. By linking plasmids with articles, scientists can always find data related to the materials they request.",
"homepage": "https://www.addgene.org/",
"name": "Addgene",
"prefix": "r3d100010741",
"xrefs": {
"fairsharing": "FAIRsharing.8hcczk",
"miriam": "00000675",
"nif": "0000-11872",
"scr": "002037"
}
},
"rrid": {
"homepage": "http://www.addgene.org",
"keywords": [
"FASEB list",
"bio.tools",
"molecular biology",
"plasmid",
"repository",
"sequence alignment"
],
"name": "Addgene",
"prefix": "Addgene",
"scr": "002037",
"twitter": "Addgene"
}
},
"adms": {
"contact": {
"email": "bert.van.nuffelen@tenforce.com",
"github": "bertvannuffelen",
"name": "Bert Van Nuffelen"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A vocabulary for describing semantic assets, defined as highly reusable metadata (e.g. XML1 schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies).",
"example": "Asset",
"homepage": "http://www.w3.org/ns/adms",
"license": "CC-BY-4.0",
"lov": {
"description": "ADMS is a profile of DCAT, used to describe semantic assets (or just 'Assets'), defined as highly reusable metadata (e.g. xml schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies) that are used for eGovernment system development.",
"homepage": "http://www.w3.org/TR/vocab-adms/",
"keywords": [
"Metadata"
],
"modified": "2015-07-22",
"name": "Asset Description Metadata Schema",
"prefix": "adms",
"uri_prefix": "http://www.w3.org/ns/adms#$1"
},
"mappings": {
"lov": "adms"
},
"name": "Asset Description Metadata Schema Vocabulary",
"repository": "https://github.com/SEMICeu/ADMS/",
"uri_format": "http://www.w3.org/ns/adms#$1"
},
"ado": {
"aberowl": {
"description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining.",
"download_owl": "http://aber-owl.net/media/ontologies/ADO/8/ado.owl",
"homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO",
"name": "Alzheimer's Disease Ontology",
"prefix": "ADO"
},
"bioportal": {
"contact": {
"email": "alpha.tom.kodamullil@scai.fraunhofer.de",
"name": "Alpha Tom Kodamullil"
},
"description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer's Disease, structured by upper level Basic Formal Ontology (BFO). This ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining.",
"homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO",
"name": "Alzheimer's Disease Ontology",
"prefix": "ADO",
"publication": "https://pubmed.ncbi.nlm.nih.gov/23830913/",
"version": "2.0.1"
},
"contributor_extras": [
{
"email": "sumirp77@gmail.com",
"github": "sumirp",
"name": "Sumir H Pandit",
"orcid": "0000-0002-1216-4761"
}
],
"example": "0000001",
"fairsharing": {
"abbreviation": "ADO",
"description": "The Alzheimer's Disease Ontology (ADO) is an ontology representing relevant knowledge on Alzheimerβs disease. ADO was developed with the purpose of containing information relevant to four main biological viewsβpreclinical, clinical, etiological, and molecular/cellular mechanismsβand contains synonyms and references.",
"homepage": "https://bioportal.bioontology.org/ontologies/ADO",
"name": "Alzheimer's Disease Ontology",
"prefix": "FAIRsharing.ckd4rf",
"publications": [
{
"doi": "10.1016/j.jalz.2013.02.009",
"pubmed": "23830913",
"title": "ADO: a disease ontology representing the domain knowledge specific to Alzheimer's disease",
"year": 2013
}
],
"subjects": [
"Health Science"
],
"user_defined_tags": [
"Alzheimerβs disease"
]
},
"mappings": {
"aberowl": "ADO",
"bioportal": "ADO",
"fairsharing": "FAIRsharing.ckd4rf",
"obofoundry": "ado",
"ols": "ado",
"ontobee": "ADO"
},
"obofoundry": {
"contact": "alpha.tom.kodamullil@scai.fraunhofer.de",
"contact.github": "akodamullil",
"contact.label": "Alpha Tom Kodamullil",
"contact.orcid": "0000-0001-9896-3531",
"depends_on": [
"bfo"
],
"deprecated": false,
"description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/ado.owl",
"homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Alzheimer's Disease Ontology",
"preferredPrefix": "ADO",
"prefix": "ado",
"repository": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO"
},
"ols": {
"description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining.",
"download_owl": "http://purl.obolibrary.org/obo/ado.owl",
"homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO",
"name": "Alzheimer's Disease Ontology (ADO)",
"prefix": "ado",
"version": "2023-09-20",
"version.iri": "http://purl.obolibrary.org/obo/ado/releases/2023-09-20/ado.owl"
},
"ontobee": {
"library": "Library",
"name": "Alzheimer's Disease Ontology",
"prefix": "ADO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1016/j.jalz.2013.02.009",
"pubmed": "23830913",
"title": "ADO: a disease ontology representing the domain knowledge specific to Alzheimer's disease",
"year": 2013
}
],
"references": [
"https://github.com/biopragmatics/bioregistry/pull/1098"
],
"uri_format": "http://purl.obolibrary.org/obo/ADO_$1",
"wikidata": {
"database": "Q54887745"
}
},
"adw": {
"aberowl": {
"description": "An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.",
"download_owl": "http://aber-owl.net/media/ontologies/ADW/2/adw.owl",
"homepage": "http://www.animaldiversity.org",
"name": "Animal Natural History and Life History Ontology",
"prefix": "ADW",
"version": "10/11/04"
},
"agroportal": {
"contact": {
"email": "adw.staff@umich.edu",
"name": "Animal Diversity Web technical staff"
},
"description": "An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.",
"homepage": "https://bioportal.bioontology.org/ontologies/ADW",
"name": "Animal Natural History and Life History Ontology",
"prefix": "ADW"
},
"biocontext": {
"prefix": "ADW"
},
"bioportal": {
"contact": {
"email": "adw.staff@umich.edu",
"name": "Animal Diversity Web technical staff"
},
"description": "An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.",
"homepage": "http://www.animaldiversity.org",
"name": "Animal Natural History and Life History Ontology",
"prefix": "ADW",
"version": "10/11/04"
},
"contributor_extras": [
{
"email": "sumirp77@gmail.com",
"github": "sumirp",
"name": "Sumir H Pandit",
"orcid": "0000-0002-1216-4761"
}
],
"fairsharing": {
"abbreviation": "ADW",
"description": "An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.",
"domains": [
"Taxonomic classification"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1530",
"name": "Animal natural history and life history",
"prefix": "FAIRsharing.t9fvdn",
"subjects": [
"Anatomy",
"Life Science"
]
},
"mappings": {
"aberowl": "ADW",
"agroportal": "ADW",
"biocontext": "ADW",
"bioportal": "ADW",
"fairsharing": "FAIRsharing.t9fvdn",
"miriam": "adw",
"n2t": "adw",
"obofoundry": "adw"
},
"miriam": {
"deprecated": false,
"description": "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology.",
"homepage": "https://animaldiversity.org/",
"id": "00000492",
"name": "Animal Diversity Web",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z_a-z]+$",
"prefix": "adw",
"sampleId": "Lycalopex_vetulus",
"uri_format": "https://animaldiversity.org/accounts/$1/"
},
"n2t": {
"description": "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology.",
"example": "Lycalopex_vetulus",
"homepage": "https://animaldiversity.org/",
"name": "Animal Diversity Web at University of Michigan",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z_a-z]+$",
"prefix": "adw",
"uri_format": "https://animaldiversity.org/accounts/$1/"
},
"obofoundry": {
"contact": "adw_geeks@umich.edu",
"contact.label": "Animal Diversity Web technical staff",
"deprecated": true,
"domain": "organisms",
"homepage": "http://www.animaldiversity.org",
"name": "Animal natural history and life history",
"prefix": "adw"
},
"references": [
"https://github.com/biopragmatics/bioregistry/pull/1098"
],
"uri_format": "https://animaldiversity.org/accounts/$1",
"wikidata": {
"database": "Q114677837"
}
},
"aeo": {
"aberowl": {
"description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology",
"download_owl": "http://aber-owl.net/media/ontologies/AEO/8/aeo.owl",
"homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology/",
"name": "Anatomical Entity Ontology",
"prefix": "AEO"
},
"bartoc": {
"abbreviation": "AEO",
"description": "The AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology, to about 160 classes using the is_a relationship; it thus provides a detailed type classification for tissues. The ~100 new classes were chosen for their use in categorizing the major vertebrate and invertebrate anatomy ontologies at a granularity adequate for tissues of a single cell type.\n\nThe AEO is intended to be useful in increasing the amount of knowledge in anatomy ontologies, facilitating annotation and enabling interoperability across anatomy ontologies.\n\nAn important subcategory of the AEO is simple tissue (a synonym of the CARO portion of tissue), a recognisable anatomical entity composed predominantly to a single cell type. CARO had a only few epithelial classes here and these are inadequate for capturing the richness of anatomical tissue knowledge. The AEO has ~70 simple tissues and these are linked to their cell types (~100) as detailed in the cell type ontology through a has_part relationship. The AEO thus includes a subset of the cell type ontology.\n\nThe AEO has been refined through its use in annotating the ~2500 terms of the new version of the Ontology of Developing Human Anatomy and, while this has improved the ontology, it may have given it a mammalian bias.\n\nThe ontology can be used to classify most organisms as its terms are appropriate for most plant and fungal tissues. I plan to improve the ontology to include more non-animal anatomical terms.",
"name": "Ontology of Anatomical Entities",
"prefix": "181"
},
"biocontext": {
"prefix": "AEO"
},
"bioportal": {
"contact": {
"email": "J.Bard@ed.ac.uk",
"name": "Jonathan Bard"
},
"description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology, to about 200 classes using the is_a relationship; it thus provides a detailed type classification for tissues. The new classes were chosen for their use in categorizing the major vertebrate and invertebrate anatomy ontologies at a granularity adequate for tissues of a single cell type. The ontology should be useful in increasing the amount of knowledge in anatomy ontologies, facilitating annotation and enabling interoperability across anatomy ontologies",
"homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology/",
"name": "Anatomical Entity Ontology",
"prefix": "AEO"
},
"contributor_extras": [
{
"email": "sumirp77@gmail.com",
"github": "sumirp",
"name": "Sumir H Pandit",
"orcid": "0000-0002-1216-4761"
}
],
"download_obo": "http://purl.obolibrary.org/obo/aeo.obo",
"example": "0001017",
"fairsharing": {
"abbreviation": "AEO",
"description": "The AEO ontology of anatomical structures is a resource to facilitate the increase in knowledge in anatomy ontologies, supporting annotation and enabling compatibility with other anatomy ontologies. The ontology can be used to classify most organisms as its terms are appropriate for most plant and fungal tissues. It is envisaged that in future the ontology will include more non-animal anatomical terms.",
"homepage": "http://www.obofoundry.org/ontology/aeo.html",
"name": "Anatomical Entity Ontology",
"prefix": "FAIRsharing.93ee19",
"publications": [
{
"doi": "10.3389/fgene.2012.00018",
"pubmed": "22347883",
"title": "The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs",
"year": 2012
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"mappings": {
"aberowl": "AEO",
"bartoc": "181",
"biocontext": "AEO",
"bioportal": "AEO",
"fairsharing": "FAIRsharing.93ee19",
"obofoundry": "aeo",
"ols": "aeo",
"ontobee": "AEO"
},
"obofoundry": {
"appears_in": [
"ehdaa2"
],
"contact": "J.Bard@ed.ac.uk",
"contact.label": "Jonathan Bard",
"deprecated": true,
"description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology",
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/aeo.owl",
"homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology/",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Anatomical Entity Ontology",
"preferredPrefix": "AEO",
"prefix": "aeo",
"repository": "https://github.com/obophenotype/human-developmental-anatomy-ontology"
},
"ols": {
"description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology",
"download_owl": "http://purl.obolibrary.org/obo/aeo.owl",
"homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology/",
"name": "Anatomical Entity Ontology",
"prefix": "aeo",
"version": "2014-12-05",
"version.iri": "http://purl.obolibrary.org/obo/aeo/releases/2014-12-05/aeo.owl"
},
"ontobee": {
"library": "Library",
"name": "Anatomical Entity Ontology",
"prefix": "AEO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.3389/fgene.2012.00018",
"pmc": "PMC3278863",
"pubmed": "22347883",
"title": "The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs",
"year": 2012
}
],
"references": [
"https://github.com/biopragmatics/bioregistry/pull/1098"
],
"synonyms": [
"AEO_RETIRED"
],
"wikidata": {
"database": "Q81661532"
}
},
"aeon": {
"contact": {
"email": "Philip.Stroemert@tib.eu",
"github": "StroemPhi",
"name": "Philip StrΓΆmert",
"orcid": "0000-0002-1595-3213"
},
"contributor": {
"email": "Philip.Stroemert@tib.eu",
"github": "StroemPhi",
"name": "Philip StrΓΆmert",
"orcid": "0000-0002-1595-3213"
},
"description": "The academic event ontology, currently still in development and thus unstable, is an OBO compliant reference ontology for describing academic events such as conferences, workshops or seminars and their series. It is being developed as part of the [ConfIDent project](https://projects.tib.eu/confident/) to allow RDF representations of the academic events and series stored and curated in the [ConfIDent platform](https://www.confident-conference.org/index.php/main_page).",
"download_owl": "https://raw.githubusercontent.com/tibonto/aeon/main/aeon.owl",
"example": "0000001",
"github_request_issue": 617,
"homepage": "https://tibonto.github.io/aeon/",
"license": "CC-BY-4.0",
"name": "Academic Event Ontology",
"pattern": "^\\d{7}$",
"repository": "https://github.com/tibonto/aeon",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://purl.obolibrary.org/obo/AEON_$1"
},
"aero": {
"aberowl": {
"description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events.",
"download_owl": "http://aber-owl.net/media/ontologies/AERO/45/aero.owl",
"homepage": "http://purl.obolibrary.org/obo/aero",
"name": "Adverse Event Reporting Ontology",
"prefix": "AERO",
"version": "unknown"
},
"biocontext": {
"prefix": "AERO"
},
"bioportal": {
"contact": {
"email": "mcourtot@gmail.com",
"name": "Melanie Courtot"
},
"description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events.",
"homepage": "http://purl.obolibrary.org/obo/aero",
"name": "Adverse Event Reporting Ontology",
"prefix": "AERO",
"version": "unknown"
},
"contributor_extras": [
{
"github": "sumirp",
"name": "Sumir H Pandit",
"orcid": "0000-0002-1216-4761"
}
],
"example": "0000125",
"fairsharing": {
"abbreviation": "AERO",
"contact": {
"email": "mcourtot@gmail.com",
"name": "Melanie Courtot",
"orcid": "0000-0002-9551-6370"
},
"description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events.",
"domains": [
"Electronic health record",
"Adverse Reaction"
],
"homepage": "http://purl.obolibrary.org/obo/aero",
"license": "CC-BY-3.0",
"name": "Adverse Event Reporting ontology",
"prefix": "FAIRsharing.rycy2x",
"subjects": [
"Medicine",
"Health Science",
"Biomedical Science",
"Preclinical Studies"
]
},
"mappings": {
"aberowl": "AERO",
"biocontext": "AERO",
"bioportal": "AERO",
"fairsharing": "FAIRsharing.rycy2x",
"obofoundry": "aero",
"ols": "aero"
},
"obofoundry": {
"contact": "mcourtot@gmail.com",
"contact.label": "Melanie Courtot",
"contact.orcid": "0000-0002-9551-6370",
"deprecated": true,
"description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/aero.owl",
"homepage": "http://purl.obolibrary.org/obo/aero",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Adverse Event Reporting Ontology",
"prefix": "aero"
},
"ols": {
"description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events",
"homepage": "http://purl.obolibrary.org/obo/aero",
"name": "Adverse Event Reporting Ontology",
"prefix": "aero"
},
"pattern": "^\\d{7}$",
"references": [
"https://github.com/biopragmatics/bioregistry/pull/1098"
],
"wikidata": {
"database": "Q55118235"
}
},
"affy.probeset": {
"biocontext": {
"prefix": "AFFY.PROBESET"
},
"mappings": {
"biocontext": "AFFY.PROBESET",
"miriam": "affy.probeset",
"n2t": "affy.probeset",
"togoid": "AffyProbeset"
},
"miriam": {
"deprecated": false,
"description": "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration.",
"homepage": "http://www.affymetrix.com/",
"id": "00000394",
"name": "Affymetrix Probeset",
"namespaceEmbeddedInLui": false,
"pattern": "\\d{4,}((_[asx])?_at)?",
"prefix": "affy.probeset",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "Bio2RDF",
"homepage": "http://cu.affymetrix.bio2rdf.org/fct/",
"name": "Bio2RDF",
"uri_format": "http://cu.affymetrix.bio2rdf.org/describe/?url=http://bio2rdf.org/affymetrix:$1"
}
],
"sampleId": "243002_at",
"uri_format": "https://www.affymetrix.com/LinkServlet?probeset=$1"
},
"n2t": {
"description": "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration.",
"example": "243002_at",
"homepage": "http://www.affymetrix.com/",
"name": "Affymetrix ProbeSet in Santa Clara",
"namespaceEmbeddedInLui": false,
"pattern": "\\d{4,}((_[asx])?_at)?",
"prefix": "affy.probeset",
"uri_format": "https://www.affymetrix.com/LinkServlet?probeset=$1"
},
"togoid": {
"examples": [
"1553582_a_at",
"211531_x_at",
"202573_at",
"201640_x_at",
"205117_at",
"201017_at",
"205099_s_at",
"200614_at",
"201895_at",
"202666_s_at"
],
"keywords": [
"Probe"
],
"name": "Affymetrix probeset",
"pattern": "^(?\\d{3,}(?:_[a-z])?_at)$",
"prefix": "AffyProbeset",
"uri_format": "http://identifiers.org/affy.probeset/$1"
}
},
"afo": {
"aberowl": {
"description": "Allotrope Merged Ontology Suite
The AFO is an ontology suite that provides a standard vocabulary and semantic model for the representation of laboratory analytical processes. The AFO suite is aligned at the upper layer to the Basic Formal Ontology (BFO). The core domains modeled include: Equipment, Material, Process, and Results.
This version of Allotrope Foundation Ontology (AFO) has been prepared specifically for publication on the NCBO platform.
license: http://purl.allotrope.org/voc/creative-commons-attribution-license
rights: http://purl.allotrope.org/voc/copyright
Please get the latest version of AFO from http://purl.allotrope.org
",
"download_owl": "http://aber-owl.net/media/ontologies/AFO/38/afo.owl",
"homepage": "http://purl.allotrope.org",
"name": "Allotrope Merged Ontology Suite",
"prefix": "AFO",
"version": "REC/2024/06"
},
"bioportal": {
"contact": {
"email": "more.info@allotrope.org",
"name": "Allotrope Foundation"
},
"description": "Allotrope Merged Ontology Suite
The AFO is an ontology suite that provides a standard vocabulary and semantic model for the representation of laboratory analytical processes. The AFO suite is aligned at the upper layer to the Basic Formal Ontology (BFO). The core domains modeled include: Equipment, Material, Process, and Results.
This version of Allotrope Foundation Ontology (AFO) has been prepared specifically for publication on the NCBO platform.
license: http://purl.allotrope.org/voc/creative-commons-attribution-license
rights: http://purl.allotrope.org/voc/copyright
Please get the latest version of AFO from http://purl.allotrope.org
",
"homepage": "http://purl.allotrope.org",
"name": "Allotrope Merged Ontology Suite",
"prefix": "AFO",
"publication": "http://www.allotrope.org",
"version": "REC/2024/06"
},
"fairsharing": {
"abbreviation": "AFO",
"description": "The Agriculture and Forestry Ontology (AFO), also known as the Agriforest Ontology, combines the concepts of the Agriforest Thesaurus with The Finnish General Upper Ontology (YSO). This combination of ontologies can be used for describing resources especially in domain of agriculture, forestry, veterinary medicine, food science, environmental science and biology.",
"domains": [
"Food"
],
"homepage": "https://seco.cs.aalto.fi/ontologies/afo/",
"license": "CC-BY-4.0",
"name": "Agriculture and Forestry Ontology",
"prefix": "FAIRsharing.595710",
"subjects": [
"Environmental Science",
"Forest Management",
"Agricultural Engineering",
"Agriculture",
"Veterinary Medicine",
"Food Chemistry",
"Biology"
]
},
"homepage": "https://www.allotrope.org/",
"mappings": {
"aberowl": "AFO",
"bioportal": "AFO",
"fairsharing": "FAIRsharing.595710",
"ols": "afo",
"ontobee": "AFO"
},
"no_own_terms": true,
"ols": {
"description": "Allotrope Merged Ontology Suite",
"name": "Allotrope Merged Ontology Suite",
"prefix": "afo",
"version": "2024/06",
"version.iri": "http://purl.allotrope.org/voc/afo/merged/REC/2024/06/merged-without-qudt-and-inferred"
},
"ontobee": {
"library": "Not Specified/No",
"name": "Allotrope Foundation Ontology",
"prefix": "AFO"
}
},
"afpo": {
"aberowl": {
"description": "AfPO is a tool which enables to annotate the African individuals, and brings together knowledge accumulated about existing populations with their genetic fingerprint in a standardized format.",
"download_owl": "http://aber-owl.net/media/ontologies/AFPO/1/afpo.owl",
"homepage": "https://github.com/h3abionet/afpo",
"name": "African Population Ontology",
"prefix": "AFPO"
},
"bioportal": {
"contact": {
"email": "mcmelek@msn.com",
"name": "Melek Chaouch"
},
"description": "AfPO is a tool which enables to annotate the African individuals, and brings together knowledge accumulated about existing populations with their genetic fingerprint in a standardized format.",
"homepage": "https://github.com/h3abionet/afpo",
"name": "African Population Ontology",
"prefix": "AFPO",
"version": "2024-03-21"
},
"example": "0000440",
"mappings": {
"aberowl": "AFPO",
"bioportal": "AFPO",
"obofoundry": "afpo",
"ontobee": "AfPO"
},
"obofoundry": {
"contact": "mcmelek@msn.com",
"contact.github": "Melek-C",
"contact.label": "Melek Chaouch",
"contact.orcid": "0000-0001-5868-4204",
"deprecated": false,
"description": "AfPO is an ontology that can be used in the study of diverse populations across Africa. It brings together publicly available demographic, anthropological and genetic data relating to African people in a standardised and structured format. The AfPO can be employed to classify African study participants comprehensively in prospective research studies. It can also be used to classify past study participants by mapping them using a language or ethnicity identifier or synonyms.",
"domain": "organisms",
"download.json": "http://purl.obolibrary.org/obo/afpo.json",
"download.obo": "http://purl.obolibrary.org/obo/afpo.obo",
"download.owl": "http://purl.obolibrary.org/obo/afpo.owl",
"homepage": "https://github.com/h3abionet/afpo",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "African Population Ontology",
"preferredPrefix": "AfPO",
"prefix": "afpo",
"repository": "https://github.com/h3abionet/afpo"
},
"ontobee": {
"library": "Library",
"name": "African Population Ontology",
"prefix": "AfPO"
}
},
"aftol.category": {
"contact": {
"email": "davem@umn.edu",
"name": "David J. McLaughlin"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Categories in the AFTOL database",
"example": "229",
"homepage": "https://aftol.umn.edu",
"name": "Assembling the Fungal Tree of Life - Category",
"uri_format": "https://aftol.umn.edu/glossary?category=$1"
},
"aftol.taxonomy": {
"biocontext": {
"prefix": "AFTOL.TAXONOMY"
},
"contact": {
"email": "davem@umn.edu",
"name": "David J. McLaughlin"
},
"contributor_extras": [
{
"email": "laylamichan@ciencias.unam.mx",
"github": "lmichan",
"name": "Layla MichΓ‘n Aguirre",
"orcid": "0000-0002-5798-662X"
}
],
"homepage": "https://aftol.umn.edu",
"mappings": {
"biocontext": "AFTOL.TAXONOMY",
"miriam": "aftol.taxonomy",
"n2t": "aftol.taxonomy"
},
"miriam": {
"deprecated": false,
"description": "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species.",
"homepage": "http://aftol.org/data.php",
"id": "00000411",
"name": "AFTOL",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "aftol.taxonomy",
"sampleId": "959",
"uri_format": "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1"
},
"n2t": {
"description": "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species.",
"example": "959",
"homepage": "http://aftol.org/data.php",
"name": "AFTOL at University of Minnesota",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "aftol.taxonomy",
"uri_format": "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1"
},
"name": "Assembling the Fungal Tree of Life - Taxonomy"
},
"agilent.probe": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699.",
"example": "A_24_P98555",
"homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt",
"keywords": [
"transcriptomics"
],
"name": "Agilent Probe",
"pattern": "^A_\\d+_.+$",
"references": [
"http://www.cs.tau.ac.il/cgi-bin/cgiwrap/click/get.cgi/conversionFiles/conversion_human_14850_agilent2entrez.txt"
]
},
"agricola": {
"biocontext": {
"prefix": "AGRICOLA"
},
"contact": {
"email": "judith.blake@jax.org",
"github": "judyblake",
"name": "Judith A Blake",
"orcid": "0000-0001-8522-334X"
},
"contributor_extras": [
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
{
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
{
"email": "sumirp77@gmail.com",
"github": "sumirp",
"name": "Sumir H Pandit",
"orcid": "0000-0002-1216-4761"
}
],
"go": {
"homepage": "http://agricola.nal.usda.gov/",
"name": "AGRICultural OnLine Access",
"prefix": "AGRICOLA_ID"
},
"mappings": {
"biocontext": "AGRICOLA",
"go": "AGRICOLA_ID",
"miriam": "agricola",
"n2t": "agricola",
"uniprot": "DB-0266"
},
"miriam": {
"deprecated": false,
"description": "AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century.",
"homepage": "http://agricola.nal.usda.gov/",
"id": "00000589",
"name": "AGRICOLA",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "agricola",
"sampleId": "50018",
"uri_format": "http://ddr.nal.usda.gov/dspace/handle/10113/$1"
},
"n2t": {
"description": "AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century.",
"example": "50018",
"homepage": "http://agricola.nal.usda.gov/",
"name": "AGRICOLA at National Agricultural Library",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "agricola",
"uri_format": "http://ddr.nal.usda.gov/dspace/handle/10113/$1"
},
"name": "Agricultural Online Access",
"publications": [
{
"doi": "10.1093/nar/gkz813",
"pmc": "PMC6943066",
"pubmed": "31552413",
"title": "Alliance of Genome Resources Portal: unified model organism research platform",
"year": 2020
}
],
"references": [
"https://github.com/biopragmatics/bioregistry/pull/1098"
],
"synonyms": [
"AGR",
"AGRICOLA_ID"
],
"uniprot": {
"abbreviation": "AGR",
"category": "Organism-specific databases",
"homepage": "https://alliancegenome.org/",
"name": "The Alliance of Genome Resources",
"prefix": "DB-0266",
"publications": [
{
"doi": "10.1093/nar/gkz813",
"pubmed": "31552413"
}
],
"uri_format": "https://alliancegenome.org/gene/$1"
},
"uri_format": "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1",
"wikidata": {
"database": "Q4651693"
}
},
"agrkb": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "AGRKB",
"uri_format": "https://www.alliancegenome.org/$1"
},
"contact": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"contributor": {
"github": "sierra-moxon",
"name": "Sierra Moxon",
"orcid": "0000-0002-8719-7760"
},
"description": "The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations.\n\nThe Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location:\n\n- [ZFIN](https://zfin.org) - Zebrafish Information Network\n- [WormBase](https://wormbase.org)\n- [MGI](https://www.mgi.org) - Mouse Genome Informatics\n- [RGD](https://rgd.mcw.edu) - Rat Genome Database\n- [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database\n- [FlyBase](https://flybase.org)\n- [Xenbase](https://www.xenbase.org)",
"example": "100000000000001",
"github_request_issue": 359,
"homepage": "https://www.alliancegenome.org",
"keywords": [
"model organism database"
],
"mappings": {
"biolink": "AGRKB"
},
"name": "Alliance of Genome Resources Knowledge Base",
"pattern": "^[1-9][0-9]{14}$",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://www.alliancegenome.org/accession/$1"
},
"agro": {
"aberowl": {
"description": "Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments",
"download_owl": "http://aber-owl.net/media/ontologies/AGRO/7/agro.owl",
"homepage": "https://github.com/AgriculturalSemantics/agro",
"name": "Agronomy Ontology",
"prefix": "AGRO"
},
"agroportal": {
"contact": {
"email": "c.aubert@cgiar.org",
"name": "CΓ©line Aubert"
},
"description": "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities",
"example_uri": "http://purl.obolibrary.org/obo/AGRO_00000002",
"homepage": "https://bigdata.cgiar.org/resources/agronomy-ontology/",
"license": "CC-BY-4.0",
"name": "Agronomy Ontology",
"prefix": "AGRO",
"publication": "http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf",
"repository": "https://github.com/AgriculturalSemantics/agro",
"version": "1.0"
},
"biocontext": {
"prefix": "AGRO"
},
"bioportal": {
"contact": {
"email": "m.a.laporte@cgiar.org",
"name": "Marie-AngΓ©lique Laporte"
},
"description": "AGRO, the AGRonomy Ontology, describes agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments. AGRO is being built using traits identified by agronomists, the ICASA variables, and other existing ontologies such as ENVO, UO, and PATO, IAO, and CHEBI. Further, AGRO will power an Agronomy Management System and fieldbook modeled on a CGIAR Breeding Management System to capture agronomic data.",
"homepage": "https://github.com/AgriculturalSemantics/agro",
"name": "AGRonomy Ontology",
"prefix": "AGRO"
},
"contributor_extras": [
{
"email": "sumirp77@gmail.com",
"github": "sumirp",
"name": "Sumir H Pandit",
"orcid": "0000-0002-1216-4761"
}
],
"download_obo": "https://raw.githubusercontent.com/KrishnaTO/agro/master/agro.obo",
"example": "00020007",
"fairsharing": {
"abbreviation": "AgrO",
"description": "AgrO, the Agronomy Ontology, describes agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments. AgrO is being built by CGIAR using traits identified by agronomists, the ICASA variables, and other existing ontologies such as ENVO, UO, and PATO. It will complement existing crop, livestock, and fish ontologies to enable harmonized approaches to data collection, facilitating easier data sharing and reuse. A key use case for AgrO is the Agronomy Field Information Management System (AgroFIMS). AgroFIMS enables digital collection of agronomic data that is semantically described a priori with agronomic terms from AgrO.",
"domains": [
"Cropping systems"
],
"homepage": "https://bigdata.cgiar.org/resources/agronomy-ontology/",
"license": "CC-BY-4.0",
"name": "Agronomy Ontology",
"prefix": "FAIRsharing.m40bhw",
"repository": "https://github.com/AgriculturalSemantics/agro/issues/",
"subjects": [
"Farming Systems Research",
"Plant Breeding",
"Agronomy",
"Agriculture"
]
},
"mappings": {
"aberowl": "AGRO",
"agroportal": "AGRO",
"biocontext": "AGRO",
"bioportal": "AGRO",
"fairsharing": "FAIRsharing.m40bhw",
"obofoundry": "agro",
"ols": "agro",
"ontobee": "AGRO"
},
"obofoundry": {
"contact": "m.a.laporte@cgiar.org",
"contact.github": "marieALaporte",
"contact.label": "Marie-AngΓ©lique Laporte",
"contact.orcid": "0000-0002-8461-9745",
"depends_on": [
"bfo",
"envo",
"foodon",
"go",
"iao",
"ncbitaxon",
"obi",
"pato",
"peco",
"po",
"ro",
"to",
"uo",
"xco"
],
"deprecated": false,
"description": "Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments",
"domain": "agriculture",
"download.owl": "http://purl.obolibrary.org/obo/agro.owl",
"homepage": "https://github.com/AgriculturalSemantics/agro",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Agronomy Ontology",
"preferredPrefix": "AGRO",
"prefix": "agro",
"publications": [
{
"id": "http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf",
"title": "Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics."
}
],
"repository": "https://github.com/AgriculturalSemantics/agro"
},
"ols": {
"description": "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities",
"download_owl": "http://purl.obolibrary.org/obo/agro.owl",
"homepage": "https://github.com/AgriculturalSemantics/agro",
"name": "Agronomy Ontology",
"prefix": "agro",
"version": "2022-11-02",
"version.iri": "http://purl.obolibrary.org/obo/agro/releases/2022-11-02/agro.owl"
},
"ontobee": {
"library": "Library",
"name": "Agronomy Ontology",
"prefix": "AGRO"
},
"pattern": "^\\d{8}$",
"references": [
"https://github.com/biopragmatics/bioregistry/pull/1098"
],
"uri_format": "http://purl.obolibrary.org/obo/AGRO_$1",
"wikidata": {
"database": "Q81661533"
}
},
"agrovoc": {
"agroportal": {
"contact": {
"email": "AGROVOC@fao.org",
"name": "AGROVOC"
},
"description": "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is a large Linked Open Data set about agriculture, available for public use, and its highest impact is through facilitating the access and visibility of data across domains and languages.",
"example_uri": "http://aims.fao.org/aos/agrovoc/c_38445",
"homepage": "http://www.fao.org/agrovoc/",
"license": "CC-BY-4.0",
"name": "AGROVOC",
"prefix": "AGROVOC",
"publication": "https://www.fao.org/agrovoc/publications",
"version": "2024-04"
},
"banana": "c_",
"banana_peel": "",
"bartoc": {
"description": "AGROVOC is a controlled vocabulary covering all areas of interest of the Food and Agriculture Organization (FAO) of the United Nations, including food, nutrition, agriculture, fisheries, forestry, environment etc. It is published by FAO and edited by a community of experts.\n\nAGROVOC consists of over 40,900 concepts available in up to 42 languages: Arabic, Belarusian, Chinese, Czech, English, Estonian, French, German, Hindi, Hungarian, Italian, Japanese, Korean, Lao, Malay, Norwegian BokmΓ₯l, Persian, Polish, Portuguese, Russian, Slovak, Spanish, Swahili, Telugu, Thai, Turkish, Ukrainian and others.\n\nYou can use AGROVOC to look up the common name of a plant in a language that you do not master, or to find relations between a commodity and the crop from which it is produced. Your library can use AGROVOC to index its documents, or you can use it from inside your content management system (e.g., Drupal) to organize your documents or web site. You can also use AGROVOC as an hub to access many other vocabularies available on the web.\n\nTo date, AGROVOC is used by researchers, librarians and information managers for indexing, retrieving and organizing data in agricultural information systems and Web pages. Currently, AGROVOC is an SKOS-XL concept scheme and a Linked Open Data (LOD) set aligned with 16 other multilingual knowledge organization systems related to agriculture.\n\nYou may download AGROVOC, access its Web Services or SPARQL endpoint.",
"homepage": "http://www.fao.org/agrovoc/",
"license": "CC BY-SA 3.0",
"name": "AGROVOC",
"prefix": "305",
"wikidata_database": "Q292649"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages.",
"ecoportal": {
"contact": {
"email": "agrovoc@fao.org",
"name": "AGROVOC Team"
},
"description": "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is a large Linked Open Data set about agriculture, available for public use, and its highest impact is through facilitating the access and visibility of data across domains and languages.",
"homepage": "http://www.fao.org/agrovoc/",
"license": "CC-BY-4.0",
"name": "AGROVOC",
"prefix": "AGROVOC",
"publication": "https://www.fao.org/agrovoc/publications",
"version": "2024-04"
},
"example": "2842",
"fairsharing": {
"abbreviation": "AGROVOC",
"description": "AGROVOC is a controlled vocabulary covering all areas of interest of the Food and Agriculture Organization (FAO) of the United Nations, including food, nutrition, agriculture, fisheries, forestry, environment etc. It is published by FAO and edited by a community of experts. AGROVOC consists of over 41,000 concepts available in up to 42 languages. AGROVOC uses semantic web technologies, linking to other multilingual knowledge organization systems and building bridges between datasets. Your library can use AGROVOC to index its documents or datasets, or you can use it from inside your content management system (e.g., Drupal) to organize your documents or web site. You can also use AGROVOC as an hub to access many other vocabularies available on the web. To date, AGROVOC is used by researchers, librarians and information managers for indexing, retrieving and organizing data in agricultural information systems and Web pages. Currently, AGROVOC is an SKOS-XL concept scheme and a Linked Open Data (LOD*) set aligned with over 20 other multilingual knowledge organization systems related to agriculture. You may browse AGROVOC, access its Web Services or SPARQL endpoint.",
"domains": [
"Food"
],
"homepage": "http://www.fao.org/agrovoc/",
"license": "CC-BY-3.0-IGO",
"name": "AGROVOC",
"prefix": "FAIRsharing.anpj91",
"publications": [
{
"doi": "10.3390/engproc2021009017",
"title": "How Agricultural Digital Innovation Can Benefit from Semantics: The Case of the AGROVOC Multilingual Thesaurus",
"year": 2021
},
{
"doi": "10.4060/cb2838en",
"title": "AGROVOC β Semantic data interoperability on food and agriculture",
"year": 2021
},
{
"doi": "10.1016/j.compag.2020.105965",
"title": "AGROVOC: The linked data concept hub for food and agriculture",
"year": 2022
}
],
"subjects": [
"Botany",
"Fisheries Science",
"Environmental Science",
"Forest Management",
"Data Management",
"Agriculture",
"Nutritional Science"
],
"twitter": "FAOAIMS",
"user_defined_tags": [
"thesaurus"
]
},
"homepage": "https://data.apps.fao.org/catalog/organization/agrovoc",
"mappings": {
"agroportal": "AGROVOC",
"bartoc": "305",
"ecoportal": "AGROVOC",
"fairsharing": "FAIRsharing.anpj91",
"wikidata": "P8061"
},
"name": "Agronomy Vocabulary",
"pattern": "^[a-z0-9]+$",
"publications": [
{
"doi": "10.4060/cb2838en",
"title": "AGROVOC",
"year": 2021
},
{
"doi": "10.3390/engproc2021009017",
"title": "How Agricultural Digital Innovation Can Benefit from Semantics: The Case of the AGROVOC Multilingual Thesaurus",
"year": 2021
},
{
"doi": "10.1016/j.compag.2020.105965",
"title": "AGROVOC: The linked data concept hub for food and agriculture",
"year": 2022
}
],
"references": [
"http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_core.nt.zip",
"http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_lod.nt.zip",
"https://en.wikipedia.org/wiki/AGROVOC"
],
"uri_format": "http://aims.fao.org/aos/agrovoc/c_$1",
"wikidata": {
"database": "Q292649",
"description": "identifier for a subject in AGROVOC thesaurus",
"example": [
"c_00824893",
"c_10",
"c_33507"
],
"name": "AGROVOC ID",
"prefix": "P8061",
"uri_format": "http://aims.fao.org/aos/agrovoc/$1",
"uri_format_rdf": "http://aims.fao.org/aos/agrovoc/$1"
}
},
"agsc": {
"contact": {
"email": "srvoss@uky.edu",
"name": "Stephen Randal Voss",
"orcid": "0000-0002-8332-3176"
},
"description": "The Ambystoma Genetic Stock Center (AGSC) maintains a breeding colony of Mexican axolotls (Ambystoma mexicanum) and distributes axolotl embryos, larvae, and adults to laboratories and classrooms throughout the United States and abroad. [from homepage]",
"example": "100E",
"mappings": {
"rrid": "AGSC"
},
"rrid": {
"homepage": "https://ambystoma.uky.edu/genetic-stock-center/",
"keywords": [
"adult",
"ambystoma",
"embryo",
"k-12 teacher",
"larvae",
"salamander"
],
"name": "Ambystoma Genetic Stock Center",
"prefix": "AGSC",
"pubmeds": [
"16359543"
],
"scr": "006372"
},
"uri_format": "https://scicrunch.org/resolver/RRID:AGSC_$1"
},
"agsd": {
"contributor_extras": [
{
"email": "sumirp77@gmail.com",
"github": "sumirp",
"name": "Sumir H Pandit",
"orcid": "0000-0002-1216-4761"
}
],
"fairsharing": {
"abbreviation": "AGSD",
"description": "A comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources.",
"homepage": "http://www.genomesize.com",
"name": "Animal Genome Size Database",
"prefix": "FAIRsharing.efp5v2",
"publications": [],
"subjects": [
"Life Science"
]
},
"mappings": {
"fairsharing": "FAIRsharing.efp5v2",
"prefixcommons": "agsd",
"re3data": "r3d100012517"
},
"prefixcommons": {
"description": "The Animal Genome Size Database (AGSD) is a comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources.",
"example": "4779",
"homepage": "http://www.genomesize.com",
"keywords": [
"DNA",
"genome"
],
"name": "Animal Genome Size Database",
"pattern": "^\\d+$",
"prefix": "agsd",
"uri_format": "http://www.genomesize.com/result_species.php?id=$1"
},
"re3data": {
"description": "Welcome to the Animal Genome Size Database, Release 2.0, a comprehensive catalogue of animal genome size data.",
"homepage": "https://www.genomesize.com/",
"name": "Animal Genome Size Database",
"prefix": "r3d100012517",
"xrefs": {
"fairsharing": "FAIRsharing.efp5v2",
"nif": "0000-02548",
"omics": "16749",
"scr": "007551"
}
},
"references": [
"https://github.com/biopragmatics/bioregistry/pull/1098"
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"wikidata": {
"database": "Q4764809"
}
},
"aio": {
"aberowl": {
"description": "This ontology models classes and relationships describing deep learning networks, their component layers and activation functions, as well as potential biases.",
"download_owl": "http://aber-owl.net/media/ontologies/AIO/17/aio.owl",
"homepage": "https://github.com/berkeleybop/artificial-intelligence-ontology",
"name": "Artificial Intelligence Ontology",
"prefix": "AIO",
"version": "2024-08-02"
},
"bioportal": {
"contact": {
"email": "MJoachimiak@lbl.gov",
"name": "marcin pawel joachimiak"
},
"description": "This ontology models classes and relationships describing deep learning networks, their component layers and activation functions, as well as potential biases.",
"homepage": "https://github.com/berkeleybop/artificial-intelligence-ontology",
"name": "Artificial Intelligence Ontology",
"prefix": "AIO",
"publication": "https://arxiv.org/abs/2404.03044",
"version": "2024-08-09"
},
"contact": {
"email": "MJoachimiak@lbl.gov",
"github": "realmarcin",
"name": "Marcin Pawel Joachimiak",
"orcid": "0000-0001-8175-045X"
},
"contributor": {
"email": "lindsey.anderson@pnnl.gov",
"github": "lnanderson",
"name": "Lindsey N. Anderson",
"orcid": "0000-0002-8741-7823"
},
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"download_obo": "https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.obo",
"download_owl": "https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.owl",
"example": "Causal_Graphical_Model",
"fairsharing": {
"abbreviation": "AIO",
"contact": {
"email": "MJoachimiak@lbl.gov",
"name": "Marcin P. Joachimiak",
"orcid": "0000-0001-8175-045X"
},
"description": "The Artificial Intelligence Ontology (AIO) is a systematized collection of terms covering artificial intelligence (AI) concepts, methodologies, and interrelations aimed to address the rapidly evolving landscape of AI terminolgy by providing a comprehensive framework that encompasses both technical and ethical aspects of AI technologies. The primary audience for this collection includes AI researchers, developers, and educators seeking to standardize terminology and concepts within the AI domain.",
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"Hidden Markov model",
"Network model",
"Natural language processing",
"Machine learning",
"Knowledge representation"
],
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"license": "CC-BY-4.0",
"name": "Artificial Intelligence Ontology",
"prefix": "FAIRsharing.8d6247",
"publications": [
{
"doi": "10.48550/arxiv.2404.03044",
"title": "The Artificial Intelligence Ontology: LLM-assisted construction of AI concept hierarchies",
"year": 2024
}
],
"repository": "https://github.com/berkeleybop/artificial-intelligence-ontology",
"subjects": [
"Artificial Intelligence",
"Computational Biology"
]
},
"github_request_issue": 884,
"homepage": "https://github.com/berkeleybop/artificial-intelligence-ontology",
"mappings": {
"aberowl": "AIO",
"bioportal": "AIO",
"fairsharing": "FAIRsharing.8d6247"
},
"name": "The Artificial Intelligence Ontology",
"repository": "https://github.com/berkeleybop",
"reviewer": {
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"uri_format": "https://w3id.org/aio/$1"
},
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"description": "The AISM contains terms used in insect biodiversity research for describing structures of the exoskeleton and the skeletomuscular system. It aims to serve as the basic backbone of generalized terms to be expanded with order-specific terminology.",
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"homepage": "https://github.com/insect-morphology/aism",
"name": "Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)",
"prefix": "AISM"
},
"bioportal": {
"contact": {
"email": "entiminae@gmail.com",
"name": "Jennifer C. GirΓ³n"
},
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"publication": "GirΓ³n, J. C., S. Tarasov, L. A. GonzΓ‘lez MontaΓ±a, N. Matentzoglu, A. D. Smith, M. Koch, B. E. Boudinot, P. Bouchard, R. Burks, L. Vogt, M. Yoder, D. Osumi-Sutherland, F. Friedrich, R. Beutel, I. MikΓ³ (2022) Formalizing insect morphological data: a model-based, extensible insect anatomy ontology and its potential applications in biodiversity research and informatics. Preprints. https://doi.org/10.20944/preprints202201.0254.v1",
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{
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"github": "sumirp",
"name": "Sumir H Pandit",
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"ols": "aism",
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],
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"contact.label": "Jennifer C. GirΓ³n",
"contact.orcid": "0000-0002-0851-6883",
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"license": "CC BY 4.0",
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},
"alfred": {
"comment": "This resource doesn't exist on the web anymore",
"contributor_extras": [
{
"email": "sumirp77@gmail.com",
"github": "sumirp",
"name": "Sumir H Pandit",
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"references": [
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},
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},
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},
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}
],
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"description": "Allergome aims to supply information on Allergenic Molecules (Allergens) causing an IgE-mediated (allergic, atopic) disease (anaphylaxis, asthma, atopic dermatitis, conjunctivitis, rhinitis, urticaria).",
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"pubmed": "19671381",
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},
{
"doi": "10.1016/j.cellimm.2007.02.012",
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{
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],
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"genes",
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},
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],
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],
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"prefix": "amoebadb",
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"prefix": "amoebadb",
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}
],
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"name": "AmoebaDB",
"prefix": "r3d100012457",
"xrefs": {
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}
},
"references": [
"https://github.com/biopragmatics/bioregistry/pull/1098"
],
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}
},
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"homepage": "https://github.com/EBISPOT/amphx_ontology",
"name": "The Amphioxus Development and Anatomy Ontology",
"prefix": "AMPHX"
},
"bioportal": {
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"name": "Hector Escriva"
},
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"name": "The Amphioxus Development and Anatomy Ontology",
"prefix": "AMPHX"
},
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"github": "sumirp",
"name": "Sumir H Pandit",
"orcid": "0000-0002-1216-4761"
}
],
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},
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],
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"description": "APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.",
"example": "P01116",
"homepage": "http://cicblade.dep.usal.es:8080/APID/",
"name": "APID at Salamanca",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$",
"prefix": "apid.interactions",
"uri_format": "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1"
},
"provides": "uniprot",
"references": [
"https://github.com/biopragmatics/bioregistry/pull/1098"
],
"wikidata": {
"database": "Q111047825"
}
},
"apo": {
"aberowl": {
"description": "A structured controlled vocabulary for the phenotypes of Ascomycete fungi",
"download_owl": "http://aber-owl.net/media/ontologies/APO/57/apo.owl",
"homepage": "http://www.yeastgenome.org/",
"name": "Ascomycete phenotype ontology",
"prefix": "APO"
},
"biocontext": {
"prefix": "APO"
},
"bioportal": {
"contact": {
"email": "sgd-helpdesk@lists.stanford.edu",
"name": "Saccharomyces Genome Database"
},
"description": "A structured controlled vocabulary for the phenotypes of Ascomycete fungi",
"homepage": "http://www.yeastgenome.org/",
"name": "Ascomycete Phenotype Ontology",
"prefix": "APO",
"version": "releases/2024-08-03"
},
"contributor_extras": [
{
"email": "sumirp77@gmail.com",
"github": "sumirp",
"name": "Sumir H Pandit",
"orcid": "0000-0002-1216-4761"
}
],
"example": "0000184",
"fairsharing": {
"abbreviation": "APO",
"contact": {
"email": "cherry@stanford.edu",
"name": "J. Michael Cherry",
"orcid": "0000-0001-9163-5180"
},
"description": "Ascomycete Phenotype Ontology is a structured controlled vocabulary for the phenotypes of Ascomycete fungi.",
"domains": [
"Mutation",
"Study design",
"Phenotype",
"Morphology",
"Life cycle stage"
],
"homepage": "http://bioportal.bioontology.org/ontologies/APO?p=summary",
"name": "Ascomycete Phenotype Ontology",
"prefix": "FAIRsharing.dyqz3y",
"subjects": [
"Life Science",
"Cell Biology"
],
"twitter": "yeastgenome"
},
"mappings": {
"aberowl": "APO",
"biocontext": "APO",
"bioportal": "APO",
"fairsharing": "FAIRsharing.dyqz3y",
"obofoundry": "apo",
"ols": "apo",
"ontobee": "APO"
},
"obofoundry": {
"contact": "stacia@stanford.edu",
"contact.github": "srengel",
"contact.label": "Stacia R Engel",
"contact.orcid": "0000-0001-5472-917X",
"deprecated": false,
"description": "A structured controlled vocabulary for the phenotypes of Ascomycete fungi",
"domain": "phenotype",
"download.obo": "http://purl.obolibrary.org/obo/apo.obo",
"download.owl": "http://purl.obolibrary.org/obo/apo.owl",
"homepage": "http://www.yeastgenome.org/",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Ascomycete phenotype ontology",
"preferredPrefix": "APO",
"prefix": "apo",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/20157474",
"title": "New mutant phenotype data curation system in the Saccharomyces Genome Database"
}
],
"repository": "https://github.com/obophenotype/ascomycete-phenotype-ontology"
},
"ols": {
"description": "A structured controlled vocabulary for the phenotypes of Ascomycete fungi.",
"download_owl": "http://purl.obolibrary.org/obo/apo.owl",
"homepage": "http://www.yeastgenome.org/",
"name": "Ascomycete Phenotype Ontology (APO)",
"prefix": "apo",
"version": "2024-08-03",
"version.iri": "http://purl.obolibrary.org/obo/apo/releases/2024-08-03/apo.owl"
},
"ontobee": {
"library": "Library",
"name": "Ascomycete phenotype ontology",
"prefix": "APO"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "APO",
"publications": [
{
"doi": "10.1093/database/bap001",
"pmc": "PMC2790299",
"pubmed": "20157474",
"title": "New mutant phenotype data curation system in the Saccharomyces Genome Database",
"year": 2009
}
],
"references": [
"https://github.com/biopragmatics/bioregistry/pull/1098"
],
"uri_format": "http://purl.obolibrary.org/obo/APO_$1",
"wikidata": {
"database": "Q81661535"
}
},
"apollosv": {
"aberowl": {
"description": "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.",
"download_owl": "http://aber-owl.net/media/ontologies/APOLLO_SV/24/apollo_sv.owl",
"homepage": "https://github.com/ApolloDev/apollo-sv",
"name": "Apollo Structured Vocabulary",
"prefix": "APOLLO_SV"
},
"bioportal": {
"contact": {
"email": "hoganwr@gmail.com",
"name": "William Hogan"
},
"description": "Apollo-SV, developed as an OWL specification, defines the terms and relations necessary for interoperation between epidemic simulators and public health application software that interface with these simulators.",
"homepage": "https://github.com/ApolloDev/apollo-sv",
"name": "Apollo Structured Vocabulary",
"prefix": "APOLLO-SV",
"version": "2024-04-19"
},
"example": "00000443",
"fairsharing": {
"abbreviation": "Apollo-SV",
"contact": {
"email": "hoganwr@gmail.com",
"name": "William Hogan",
"orcid": "0000-0002-9881-1017"
},
"description": "An ontology of infectious disease epidemiology and ecology (a.k.a. population biology).",
"domains": [
"Pathogen",
"Infection"
],
"homepage": "http://purl.obolibrary.org/obo/apollo_sv.owl",
"license": "CC-BY-3.0",
"name": "Apollo-SV",
"prefix": "FAIRsharing.ngv2xx",
"publications": [
{
"pubmed": "24551417",
"title": "Apollo: giving application developers a single point of access to public health models using structured vocabularies and Web services",
"year": 2014
},
{
"doi": "10.1186/s13326-016-0092-y",
"pubmed": "27538448",
"title": "The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation",
"year": 2016
}
],
"repository": "https://github.com/ApolloDev/apollo-sv",
"subjects": [
"Ecology",
"Biomedical Science",
"Epidemiology",
"Population Genetics"
]
},
"mappings": {
"aberowl": "APOLLO_SV",
"bioportal": "APOLLO-SV",
"fairsharing": "FAIRsharing.ngv2xx",
"obofoundry": "apollo_sv",
"ols": "apollo_sv",
"ontobee": "APOLLO_SV"
},
"obofoundry": {
"appears_in": [
"scdo"
],
"contact": "hoganwr@gmail.com",
"contact.github": "hoganwr",
"contact.label": "William Hogan",
"contact.orcid": "0000-0002-9881-1017",
"deprecated": false,
"description": "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/apollo_sv.owl",
"homepage": "https://github.com/ApolloDev/apollo-sv",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Apollo Structured Vocabulary",
"preferredPrefix": "APOLLO_SV",
"prefix": "apollo_sv",
"publications": [
{
"id": "https://doi.org/10.1186/s13326-016-0092-y",
"title": "The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation"
}
],
"repository": "https://github.com/ApolloDev/apollo-sv"
},
"ols": {
"description": "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.",
"download_owl": "http://purl.obolibrary.org/obo/apollo_sv.owl",
"homepage": "https://github.com/ApolloDev/apollo-sv",
"name": "Apollo Structured Vocabulary (Apollo-SV)",
"prefix": "apollo_sv",
"version": "2024-04-19",
"version.iri": "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-04-19/apollo_sv.owl"
},
"ontobee": {
"library": "Library",
"name": "Apollo Structured Vocabulary",
"prefix": "APOLLO_SV"
},
"pattern": "^\\d{8}$",
"providers": [
{
"code": "conflated",
"description": "This might be resulting from properties in Apollo SV actually trying to use appropriate identifiers",
"homepage": "http://purl.obolibrary.org",
"name": "OBO PURL in Parts",
"uri_format": "http://purl.obolibrary.org/obo/apollo_sv/dev/apollo_sv.owl#APOLLO_SV_$1"
}
],
"publications": [
{
"doi": "10.1186/s13326-016-0092-y",
"pmc": "PMC4989460",
"pubmed": "27538448",
"title": "The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation",
"year": 2016
},
{
"pmc": "PMC3900155",
"pubmed": "24551417",
"title": "Apollo: giving application developers a single point of access to public health models using structured vocabularies and Web services",
"year": 2013
}
],
"uri_format": "http://purl.obolibrary.org/obo/APOLLO_SV_$1"
},
"arachnoserver": {
"biocontext": {
"prefix": "ARACHNOSERVER"
},
"contact": {
"email": "glenn.king@imb.uq.edu.au",
"name": "Glenn King",
"orcid": "0000-0002-2308-2200"
},
"contributor_extras": [
{
"email": "sumirp77@gmail.com",
"github": "sumirp",
"name": "Sumir H Pandit",
"orcid": "0000-0002-1216-4761"
}
],
"edam": {
"description": "Unique identifier of a toxin from the ArachnoServer database.",
"name": "ArachnoServer",
"obsolete": false,
"prefix": "2578"
},
"fairsharing": {
"abbreviation": "ArachnoServer",
"description": "ArachnoServer is a manually curated database containing information on the sequence, three-dimensional structure, and biological activity of protein toxins derived from spider venom.",
"homepage": "http://www.arachnoserver.org",
"name": "ArachnoServer: Spider toxin database",
"prefix": "FAIRsharing.c54ywe",
"publications": [
{
"doi": "10.1093/nar/gkq1058",
"pubmed_id": 21036864,
"title": "ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures."
}
],
"subjects": [
"Life Science"
]
},
"integbio": {
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"fairsharing": "biodbcore-000504",
"homepage": "http://www.arachnoserver.org/mainMenu.html",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "QFAB (Queensland Facility for Advanced Bioinformatics)",
"name": "ArachnoServer",
"prefix": "nbdc01221",
"pubmeds": [
"19674480",
"19674480"
],
"status": "Suspended",
"target_keywords": [
"Protein"
]
},
"mappings": {
"biocontext": "ARACHNOSERVER",
"edam": "2578",
"fairsharing": "FAIRsharing.c54ywe",
"integbio": "nbdc01221",
"miriam": "arachnoserver",
"n2t": "arachnoserver",
"prefixcommons": "arachnoserver",
"re3data": "r3d100012902",
"uniprot": "DB-0145"
},
"miriam": {
"deprecated": false,
"description": "ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information.",
"homepage": "http://www.arachnoserver.org/",
"id": "00000193",
"name": "ArachnoServer",
"namespaceEmbeddedInLui": false,
"pattern": "^AS\\d{6}$",
"prefix": "arachnoserver",
"sampleId": "AS000060",
"uri_format": "http://www.arachnoserver.org/toxincard.html?id=$1"
},
"n2t": {
"description": "ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information.",
"example": "AS000060",
"homepage": "http://www.arachnoserver.org/",
"name": "ArachnoServer at Brisbane",
"namespaceEmbeddedInLui": false,
"pattern": "^AS\\d{6}$",
"prefix": "arachnoserver",
"uri_format": "http://www.arachnoserver.org/toxincard.html?id=$1"
},
"prefixcommons": {
"description": "ArachnoServer is a manually curated database containing information on the sequence, three-dimensional structure, and biological activity of protein toxins derived from spider venom.",
"example": "AS000060",
"homepage": "http://www.arachnoserver.org",
"keywords": [
"drug",
"protein"
],
"miriam": "arachnoserver",
"name": "ArachnoServer: Spider toxin database",
"pattern": "^AS\\d{6}$",
"prefix": "arachnoserver",
"pubmed_ids": [
"21036864",
"29069336"
],
"uri_format": "http://www.arachnoserver.org/toxincard.html?id=$1"
},
"publications": [
{
"doi": "10.1093/bioinformatics/btx661",
"pubmed": "29069336",
"title": "ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins",
"year": 2018
},
{
"doi": "10.1093/nar/gkq1058",
"pmc": "PMC3013666",
"pubmed": "21036864",
"title": "ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures",
"year": 2010
}
],
"re3data": {
"description": "ArachnoServer is a manually curated database containing information on the sequence, three-dimensional structure, and biological activity of protein toxins derived from spider venom. Spiders are the largest group of venomous animals and they are predicted to contain by far the largest number of pharmacologically active peptide toxins (Escoubas et al., 2006). ArachnoServer has been custom-built so that a wide range of biological scientists, including neuroscientists, pharmacologists, and toxinologists, can readily access key data relevant to their discipline without being overwhelmed by extraneous information.",
"homepage": "https://arachnoserver.qfab.org/mainMenu.html",
"name": "ArachnoServer",
"prefix": "r3d100012902",
"xrefs": {
"fairsharing": "FAIRsharing.c54ywe",
"miriam": "00000193",
"omics": "03117"
}
},
"references": [
"https://github.com/biopragmatics/bioregistry/pull/1141"
],
"uniprot": {
"abbreviation": "ArachnoServer",
"category": "Organism-specific databases",
"homepage": "http://www.arachnoserver.org",
"name": "ArachnoServer",
"prefix": "DB-0145",
"publications": [
{
"doi": "10.1093/bioinformatics/btx661",
"pubmed": "29069336"
}
]
},
"wikidata": {
"database": "Q4783563"
}
},
"araport": {
"contact": {
"email": "hello@vivekkrish.com",
"github": "vivekkrish",
"name": "Vivek Krishnakuma",
"orcid": "0000-0002-5227-0200"
},
"description": "Website with general information about Arabidopsis and functionalities such as a genomic viewer",
"homepage": "https://www.araport.org/",
"integbio": {
"alt_name": "Arabidopsis Information Portal",
"description": "Araport is an open-access online community resource for Arabidopsis research. It hosts the Araport11, updated Arabidopsis genome annotation from TAIR10. Araport offers two core web applications: ThaleMine for data mining and JBrowse for genome browsing. The site also hosts 'science apps,' that use dynamic web pages to present data obtained on-demand from third-party servers. The Araport11 data are also available by bulk download and web services.",
"fairsharing": "biodbcore-001076/",
"homepage": "https://www.araport.org/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway",
"Portal"
],
"maintainer": "JCVI (J. Craig Venter Institute)||Texas Advanced Computing Center, The University of Texas at Austin||University of Cambridge",
"name": "Araport",
"prefix": "nbdc02433",
"pubmeds": [
"28013278",
"27862469",
"25414324"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"RNA",
"Protein"
]
},
"mappings": {
"integbio": "nbdc02433",
"miriam": "tair.name",
"ncbi": "Araport",
"pathguide": "768",
"uniprot": "DB-0221"
},
"miriam": {
"deprecated": false,
"description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS.",
"homepage": "https://www.arabidopsis.org/index.jsp",
"id": "00000976",
"name": "TAIR gene name",
"namespaceEmbeddedInLui": false,
"pattern": "^AT.G[0-9]{5}$",
"prefix": "tair.name",
"sampleId": "AT5G05330",
"uri_format": "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1"
},
"name": "Arabidopsis Information Portal",
"ncbi": {
"example": "AT1G01010",
"homepage": "https://www.araport.org/",
"name": "Arabidopsis Information Portal",
"prefix": "Araport"
},
"pathguide": {
"abbreviation": "Araport",
"homepage": "https://www.araport.org/",
"name": "Arabidopsis Information Portal",
"prefix": "768"
},
"publications": [
{
"doi": "10.1093/nar/gku1200",
"pmc": "PMC4383980",
"pubmed": "25414324",
"title": "Araport: the Arabidopsis information portal",
"year": 2014
}
],
"uniprot": {
"abbreviation": "Araport",
"category": "Organism-specific databases",
"homepage": "https://bar.utoronto.ca/thalemine/begin.do",
"name": "Arabidopsis Information Portal",
"prefix": "DB-0221",
"publications": [
{
"doi": "10.1093/nar/gku1200",
"pubmed": "25414324"
}
],
"uri_format": "https://bar.utoronto.ca/thalemine/portal.do?externalids=$1"
},
"uri_format": "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1"
},
"archdb": {
"fairsharing": {
"abbreviation": "ArchDB",
"contact": {
"email": "narcis.fernandez@gmail.com",
"name": "Narcis Fernandez-Fuentes",
"orcid": "0000-0002-6421-1080"
},
"contributor_extras": [
{
"email": "sumirp77@gmail.com",
"github": "sumirp",
"name": "Sumir H Pandit",
"orcid": "0000-0002-1216-4761"
}
],
"description": "ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al.",
"homepage": "http://sbi.imim.es/archdb",
"name": "ArchDB",
"prefix": "FAIRsharing.tp9z4q",
"publications": [
{
"doi": "10.1093/nar/gkh002",
"pubmed_id": 14681390,
"title": "ArchDB: automated protein loop classification as a tool for structural genomics."
},
{
"doi": "10.1093/nar/gkt1189",
"pubmed_id": 24265221,
"title": "ArchDB 2014: structural classification of loops in proteins."
}
],
"subjects": [
"Life Science"
]
},
"integbio": {
"description": "ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al.",
"fairsharing": "FAIRsharing.tp9z4q",
"homepage": "http://sbi.imim.es/archdb",
"information_keywords": [
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"Sequence",
"3D structure"
],
"maintainer": "LMGM (Laboratoire de Microbiologie et Genetique Moleculaires)||SBI (The Structural Bioinformatics Laboratory)||bioinsilico.org",
"name": "ArchDB",
"prefix": "nbdc01795",
"pubmeds": [
"14681390",
"24265221"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"mappings": {
"fairsharing": "FAIRsharing.tp9z4q",
"integbio": "nbdc01795",
"prefixcommons": "archdb"
},
"prefixcommons": {
"description": "ArchDB is a compilation of structural classifications of loops extracted from known protein structures. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al..",
"example": "39421",
"homepage": "http://sbi.imim.es/archdb",
"keywords": [
"classification",
"protein"
],
"name": "ArchDB",
"pattern": "^\\d+$",
"prefix": "archdb",
"pubmed_ids": [
"24265221"
],
"uri_format": "http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkt1189",
"pmc": "PMC3964960",
"pubmed": "24265221",
"title": "ArchDB 2014: structural classification of loops in proteins",
"year": 2013
},
{
"doi": "10.1093/nar/gkh002",
"pmc": "PMC308737",
"pubmed": "14681390",
"title": "ArchDB: automated protein loop classification as a tool for structural genomics",
"year": 2004
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"ardb": {
"biocontext": {
"prefix": "ARDB"
},
"mappings": {
"biocontext": "ARDB",
"miriam": "ardb",
"n2t": "ardb"
},
"miriam": {
"deprecated": false,
"description": "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes.",
"homepage": "http://ardb.cbcb.umd.edu/",
"id": "00000522",
"name": "Antibiotic Resistance Genes Database",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z_]{3}[0-9]{4,}$",
"prefix": "ardb",
"sampleId": "CAE46076",
"uri_format": "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1"
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"fairsharing": {
"abbreviation": "arrayMap",
"contact": {
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"name": "Michael Baudis",
"orcid": "0000-0002-9903-4248"
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"description": "Part of the Progenetix project, the arrayMap database facilitates the study of the genetics of human cancer. The Progenetix project provides the data customisation and visualization tools to mine the available data. The arrayMap database is developed by the group \"Theoretical Cytogenetics and Oncogenomics\" at the Department of Molecular Life Sciences of the University of Zurich.",
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"twitter": "progenetix"
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"miriam": {
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"description": "arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome.",
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"id": "00000621",
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],
"name": "Anatomical Therapeutic Chemical",
"pattern": "^\\w(\\d+)?(\\w{1,2})?(\\d+)?$",
"prefix": "atc",
"synonyms": [
"uatc"
],
"uri_format": "http://www.whocc.no/atc_ddd_index/?code=$1"
},
"publications": [
{
"pubmed": "7368387",
"title": "[New classification of drugs. The Medical list and the Drug catalogue are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code) in 1981]",
"year": 1980
},
{
"doi": "10.1007/s002280000200",
"pubmed": "11214783",
"title": "Different versions of the anatomical therapeutic chemical classification system and the defined daily dose--are drug utilisation data comparable?",
"year": 2000
}
],
"synonyms": [
"ATC_code",
"ATTC"
],
"togoid": {
"examples": [
"J01DD11",
"B02BA02",
"A03AD30",
"R03AC17",
"J01CA05",
"D07AB07",
"D07XB03",
"G04CA01",
"S01BC11",
"G03DB05"
],
"keywords": [
"Drug"
],
"name": "ATC classification",
"pattern": "^(?[A-Z]\\d{2}[A-Z]{2}\\d{2})$",
"prefix": "Atc",
"uri_format": "http://identifiers.org/atc/$1"
},
"wikidata": {
"description": "therapeutic chemical identification code per ATC",
"example": [
"A02BC04",
"D08AX08"
],
"homepage": "https://www.whocc.no/",
"name": "ATC code",
"pattern": "^[A-V]([0-9][0-9]([A-Z]([A-Z]([0-9][0-9])?)?)?)[0-9]$",
"prefix": "P267",
"uri_format": "https://www.whocc.no/atc_ddd_index/?code=$1"
}
},
"atcc": {
"biocontext": {
"prefix": "ATCC"
},
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.atcc.org/",
"name": "American Type Culture Collection",
"prefix": "ATCC",
"uri_format": "https://www.atcc.org/Products/$1"
},
"example_extras": [
"ccl-1.4",
"ccl-1"
],
"fairsharing": {
"abbreviation": "ATCC",
"description": "ATCC authenticates microorganisms and cell lines and manages logistics of long-term preservation and distribution of cultures for the scientific community. ATCC supports the cultures it acquires and authenticates with expert technical support, intellectual property management and characterization data.",
"homepage": "http://www.atcc.org/",
"name": "American Type Culture Collection database",
"prefix": "FAIRsharing.j0ezpm",
"publications": [],
"subjects": [
"Virology",
"Life Science",
"Epidemiology"
]
},
"hl7": {
"description": "American Type Culture Collection",
"name": "ATC",
"preferred_prefix": "ATC",
"prefix": "2.16.840.1.113883.6.77",
"status": "Pending"
},
"homepage": "https://www.lgcstandards-atcc.org",
"mappings": {
"biocontext": "ATCC",
"cellosaurus": "ATCC",
"fairsharing": "FAIRsharing.j0ezpm",
"hl7": "2.16.840.1.113883.6.77",
"miriam": "atcc",
"n2t": "atcc",
"ncbi": "ATCC"
},
"miriam": {
"deprecated": false,
"description": "The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences.",
"homepage": "http://www.atcc.org/",
"id": "00000284",
"name": "ATCC",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "atcc",
"sampleId": "11303",
"uri_format": "https://www.atcc.org/products/$1"
},
"n2t": {
"description": "The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences.",
"example": "11303",
"homepage": "http://www.atcc.org/",
"name": "ATCC in Virginia",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "atcc",
"uri_format": "http://www.lgcstandards-atcc.org/Products/All/$1.aspx"
},
"name": "American Type Culture Collection",
"ncbi": {
"example": "123456",
"homepage": "http://www.atcc.org/",
"name": "American Type Culture Collection database",
"prefix": "ATCC"
},
"pattern": "^([a-zA-Z]+-)?\\d+(\\.\\d)?$",
"synonyms": [
"ATCC",
"ATCC number",
"ATCC(dna)",
"ATCC(in host)"
],
"uri_format": "https://www.atcc.org/products/$1"
},
"atcvet": {
"biocontext": {
"prefix": "ATCVET"
},
"mappings": {
"biocontext": "ATCVET",
"miriam": "atcvet",
"n2t": "atcvet"
},
"miriam": {
"deprecated": false,
"description": "The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use.",
"homepage": "http://www.whocc.no/atcvet/atcvet_index/",
"id": "00000267",
"name": "Anatomical Therapeutic Chemical Vetinary",
"namespaceEmbeddedInLui": false,
"pattern": "^Q[A-Z0-9]+$",
"prefix": "atcvet",
"sampleId": "QJ51RV02",
"uri_format": "http://www.whocc.no/atcvet/atcvet_index/?code=$1"
},
"n2t": {
"description": "The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use.",
"example": "QJ51RV02",
"homepage": "http://www.whocc.no/atcvet/atcvet_index/",
"name": "Anatomical Therapeutic Chemical Vet Index at WHO",
"namespaceEmbeddedInLui": false,
"pattern": "^Q[A-Z0-9]+$",
"prefix": "atcvet",
"uri_format": "http://www.whocc.no/atcvet/atcvet_index/?code=$1"
}
},
"atfdb.family": {
"biocontext": {
"prefix": "ATFDB.FAMILY"
},
"mappings": {
"biocontext": "ATFDB.FAMILY",
"miriam": "atfdb.family",
"n2t": "atfdb.family"
},
"miriam": {
"deprecated": false,
"description": "The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found.",
"homepage": "http://www.bioguo.org/AnimalTFDB/family_index.php",
"id": "00000316",
"name": "Animal TFDB Family",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "atfdb.family",
"sampleId": "CUT",
"uri_format": "http://www.bioguo.org/AnimalTFDB/family.php?fam=$1"
},
"n2t": {
"description": "The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found.",
"example": "CUT",
"homepage": "http://www.bioguo.org/AnimalTFDB/family_index.php",
"name": "Animal TFDB at Hubei Bioinformatics & Molecular Imaging Key Laboratory",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "atfdb.family",
"uri_format": "http://www.bioguo.org/AnimalTFDB/family.php?fam=$1"
}
},
"ato": {
"aberowl": {
"description": "A taxonomy of Amphibia",
"download_obo": "http://aber-owl.net/media/ontologies/ATO/2/ato.obo",
"homepage": "http://www.amphibanat.org",
"name": "Amphibian Taxonomy Ontology",
"prefix": "ATO",
"version": "See Remote Site"
},
"biocontext": {
"prefix": "ATO"
},
"bioportal": {
"contact": {
"email": "sbhdbe@mst.edu",
"name": "AmphiAnat list"
},
"description": "A taxonomy of Amphibia",
"homepage": "http://www.amphibanat.org",
"name": "Amphibian Taxonomy Ontology",
"prefix": "ATO",
"version": "See Remote Site"
},
"contact": {
"email": "david.c.blackburn@gmail.com",
"name": "David Blackburn",
"orcid": "0000-0002-1810-9886"
},
"example": "0000000",
"fairsharing": {
"abbreviation": "ATO",
"description": "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource",
"domains": [
"Taxonomic classification"
],
"homepage": "http://purl.bioontology.org/ontology/ATO",
"name": "Amphibian Taxonomy Ontology",
"prefix": "FAIRsharing.ayjdsm",
"subjects": [
"Taxonomy"
]
},
"mappings": {
"aberowl": "ATO",
"biocontext": "ATO",
"bioportal": "ATO",
"fairsharing": "FAIRsharing.ayjdsm",
"obofoundry": "ato"
},
"obofoundry": {
"contact": "david.c.blackburn@gmail.com",
"contact.label": "David Blackburn",
"contact.orcid": "0000-0002-1810-9886",
"deprecated": true,
"domain": "organisms",
"homepage": "http://www.amphibanat.org",
"name": "Amphibian taxonomy",
"prefix": "ato"
},
"pattern": "^\\d{7}$"
},
"atol": {
"aberowl": {
"description": "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientific and educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production",
"download_owl": "http://aber-owl.net/media/ontologies/ATOL/1/atol.owl",
"homepage": "www.atol-ontology.com",
"name": "Animal Trait Ontology for Livestock",
"prefix": "ATOL"
},
"agroportal": {
"contact": {
"email": "matthieu.reichstadt@inrae.fr",
"name": "Matthieu Reichstadt"
},
"description": "ATOL dΓ©finit et organise les caractΓ¨res phΓ©notypiques des animaux dβΓ©levage, en prenant en compte les prΓ©occupations sociΓ©tales et les grands types de production (lait, Εuf, viande, fertilitΓ©, alimentation)., ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientific and educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production",
"example_uri": "http://opendata.inra.fr/ATOL/ATOL_0000455",
"homepage": "http://www.atol-ontology.com/",
"license": "CC-BY-4.0",
"name": "Animal Trait Ontology for Livestock",
"prefix": "ATOL",
"publication": "http://www.atol-ontology.com/rb/fr/6",
"version": "6.0"
},
"bioportal": {
"contact": {
"email": "matthieu.reichstadt@clermont.inra.fr",
"name": "Reichstadt Matthieu"
},
"description": "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientific and educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production",
"homepage": "www.atol-ontology.com",
"name": "Animal Trait Ontology for Livestock",
"prefix": "ATOL",
"version": "6.0"
},
"contact": {
"email": "pylebail@rennes.inra.fr",
"name": "Pierre-Yves LeBail",
"orcid": "0000-0002-8310-5195"
},
"download_owl": "http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=atol.owl",
"example": "0002233",
"fairsharing": {
"abbreviation": "ATOL",
"description": "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment. ATOL aims to: provide a reference ontology of phenotypic traits of farm animals for the international scientific and educational - communities, farmers, etc.; deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; represent traits as generic as possible for livestock vertebrates; make the ATOL ontology as operational as possible and closely related to measurement techniques; and structure the ontology in relation to animal production.",
"domains": [
"Phenotype"
],
"homepage": "http://www.atol-ontology.com/en/atol-2/",
"license": "CC-BY-4.0",
"name": "Animal Trait Ontology for Livestock",
"prefix": "FAIRsharing.wsfk5z",
"subjects": [
"Animal Husbandry",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Livestock"
]
},
"mappings": {
"aberowl": "ATOL",
"agroportal": "ATOL",
"bioportal": "ATOL",
"fairsharing": "FAIRsharing.wsfk5z",
"ols": "atol"
},
"ols": {
"contact": "pylebail@rennes.inra.fr",
"description": "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production.",
"download": "http://www.atol-ontology.com/public/telechargement/atol.owl",
"homepage": "http://www.atol-ontology.com",
"name": "Animal Trait Ontology for Livestock",
"prefix": "atol",
"version": "2018-09-13"
},
"pattern": "^\\d{7}$",
"uri_format": "http://opendata.inra.fr/ATOL/ATOL_$1"
},
"autdb": {
"biocontext": {
"prefix": "AUTDB"
},
"mappings": {
"biocontext": "AUTDB",
"miriam": "autdb",
"n2t": "autdb"
},
"miriam": {
"deprecated": false,
"description": "AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder.",
"homepage": "http://autism.mindspec.org/autdb/",
"id": "00000415",
"name": "AutDB",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]+[A-Z-0-9]{2,}$",
"prefix": "autdb",
"sampleId": "ADA",
"uri_format": "http://autism.mindspec.org/GeneDetail/$1"
},
"n2t": {
"description": "AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder.",
"example": "ADA",
"homepage": "http://autism.mindspec.org/autdb/",
"name": "AutDB at MindSpec",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]+[A-Z-0-9]{2,}$",
"prefix": "autdb",
"uri_format": "http://autism.mindspec.org/GeneDetail/$1"
}
},
"authorea.author": {
"example": "229233",
"mappings": {
"wikidata": "P5039"
},
"wikidata": {
"description": "identifier for an author on the Authorea writing service",
"example": [
"106",
"229233"
],
"homepage": "https://www.authorea.com",
"name": "Authorea author ID",
"pattern": "^[1-9]\\d*$",
"prefix": "P5039",
"uri_format": "https://www.authorea.com/users/$1"
}
},
"babelon": {
"contact": {
"email": "nicolas.matentzoglu@gmail.com",
"github": "matentzn",
"name": "Nicolas Matentzoglu",
"orcid": "0000-0002-7356-1779"
},
"contributor": {
"email": "nicolas.matentzoglu@gmail.com",
"github": "matentzn",
"name": "Nicolas Matentzoglu",
"orcid": "0000-0002-7356-1779"
},
"description": "Babelon is a simple standard for managing ontology translations and language profiles. Profiles are managed as TSV files, see for example https://github.com/obophenotype/hpo-translations/tree/main/babelon. The goal of Babelon as a data model and vocabulary is to capture the minimum data required to capture important metadata such as confidence and precision of translation.",
"example": "translation_language",
"github_request_issue": 903,
"homepage": "https://monarch-initiative.github.io/babelon/",
"license": "MIT",
"name": "Babelon",
"pattern": "^[a-z][a-z0-9_]+[a-z0-9]$",
"repository": "https://github.com/monarch-initiative/babelon",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://w3id.org/babelon/$1"
},
"bacdive": {
"fairsharing": {
"abbreviation": "BacDive",
"contact": {
"email": "contact@bacdive.de",
"name": "Lorenz Reimer",
"orcid": "0000-0002-7805-0660"
},
"description": "BacDiveβthe Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. BacDive contains entries for over 63,000 strains and provides information on their taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.",
"homepage": "https://bacdive.dsmz.de/",
"license": "CC BY-NC 4.0",
"name": "Bacterial Diversity Metadatabase",
"prefix": "FAIRsharing.aSszvY",
"publications": [
{
"doi": "10.1093/nar/gkv983",
"pubmed_id": 26424852,
"title": "BacDive--The Bacterial Diversity Metadatabase in 2016."
},
{
"doi": "10.1016/j.jbiotec.2017.05.004",
"pubmed_id": 28487186,
"title": "Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase."
},
{
"doi": "10.1093/nar/gkt1058",
"pubmed_id": 24214959,
"title": "BacDive--the Bacterial Diversity Metadatabase."
},
{
"doi": "10.1093/nar/gky879",
"pubmed_id": 30256983,
"title": "BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis."
}
],
"subjects": [
"Biodiversity",
"Life Science",
"Microbiology"
]
},
"mappings": {
"fairsharing": "FAIRsharing.aSszvY",
"miriam": "bacdive",
"n2t": "bacdive",
"re3data": "r3d100013060",
"wikidata": "P2946"
},
"miriam": {
"deprecated": false,
"description": "BacDiveβthe Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity.",
"homepage": "https://bacdive.dsmz.de/",
"id": "00000676",
"name": "Bacterial Diversity Metadatabase",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "bacdive",
"sampleId": "131392",
"uri_format": "https://bacdive.dsmz.de/strain/$1"
},
"n2t": {
"description": "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity.",
"example": "131392",
"homepage": "https://bacdive.dsmz.de/",
"name": "Bacterial Diversity Metadatabase",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "bacdive",
"uri_format": "https://bacdive.dsmz.de/strain/$1"
},
"name": "BacDive",
"publications": [
{
"doi": "10.1093/nar/gky879",
"pmc": "PMC6323973",
"pubmed": "30256983",
"title": "BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis",
"year": 2019
},
{
"doi": "10.1016/j.jbiotec.2017.05.004",
"pubmed": "28487186",
"title": "Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase",
"year": 2017
},
{
"doi": "10.1093/nar/gkv983",
"pmc": "PMC4702946",
"pubmed": "26424852",
"title": "BacDive--The Bacterial Diversity Metadatabase in 2016",
"year": 2015
},
{
"doi": "10.1093/nar/gkt1058",
"pmc": "PMC3965005",
"pubmed": "24214959",
"title": "BacDive--the Bacterial Diversity Metadatabase",
"year": 2013
}
],
"re3data": {
"description": "BacDive is a bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity. The database is a resource for different kind of phenotypic data like taxonomy, morphology, physiology, environment and molecular-biology. The majority of data is manually annotated and curated. With the release in April 2019 BacDive offers information for 80,584 strains. The database is hosted by the Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH and is part of de.NBI the German Network for Bioinformatics Infrastructure.",
"homepage": "https://bacdive.dsmz.de/",
"name": "BacDive",
"prefix": "r3d100013060",
"synonyms": [
"Bacterial Diversity Metadatabase"
],
"xrefs": {
"fairsharing": "FAIRsharing.aSszvY",
"miriam": "00000676",
"omics": "10161"
}
},
"wikidata": {
"description": "identifier for a microorganism, in the BacDive database",
"example": [
"1419",
"2631",
"8607"
],
"name": "BacDive ID",
"pattern": "^\\d{1,6}$",
"prefix": "P2946",
"uri_format": "https://bacdive.dsmz.de/strain/$1"
}
},
"bacmap.biog": {
"biocontext": {
"prefix": "BACMAP.BIOG"
},
"mappings": {
"biocontext": "BACMAP.BIOG",
"miriam": "bacmap.biog",
"n2t": "bacmap.biog"
},
"miriam": {
"deprecated": false,
"description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information.",
"homepage": "http://bacmap.wishartlab.com/",
"id": "00000361",
"name": "BacMap Biography",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "bacmap.biog",
"sampleId": "1050",
"uri_format": "http://bacmap.wishartlab.com/organisms/$1"
},
"n2t": {
"description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information.",
"example": "1050",
"homepage": "http://bacmap.wishartlab.com/",
"name": "BacMap Biography at University of Alberta",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "bacmap.biog",
"uri_format": "http://bacmap.wishartlab.com/organisms/$1"
}
},
"bacmap.map": {
"biocontext": {
"prefix": "BACMAP.MAP"
},
"mappings": {
"biocontext": "BACMAP.MAP",
"miriam": "bacmap.map",
"n2t": "bacmap.map"
},
"miriam": {
"deprecated": false,
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"homepage": "http://bacmap.wishartlab.com/",
"id": "00000416",
"name": "BacMap Map",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$",
"prefix": "bacmap.map",
"sampleId": "AP011135",
"uri_format": "http://bacmap.wishartlab.com/maps/$1/index.html"
},
"n2t": {
"description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information.",
"example": "AP011135",
"homepage": "http://bacmap.wishartlab.com/",
"name": "BacMap Genome Map at University of Alberta",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$",
"prefix": "bacmap.map",
"uri_format": "http://bacmap.wishartlab.com/maps/$1/index.html"
}
},
"bactibase": {
"contact": {
"email": "ismail.fliss@fsaa.ulaval.ca",
"name": "Ismail Fliss",
"orcid": "0000-0002-8467-9414"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria.",
"example": "BAC045",
"fairsharing": {
"abbreviation": "BACTIBASE",
"description": "BACTIBASE contains calculated or predicted physicochemical properties of bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships structure/function and target organisms of these peptides and therefore better exploitation of their biological activity in both the medical and food sectors.",
"homepage": "http://bactibase.hammamilab.org/main.php",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "Bactibase: database dedicated to bacteriocins",
"prefix": "FAIRsharing.5f5mfm",
"publications": [
{
"doi": "10.1186/1471-2180-10-22",
"pubmed_id": 20105292,
"title": "BACTIBASE second release: a database and tool platform for bacteriocin characterization."
},
{
"doi": "10.1186/1471-2180-7-89",
"pubmed_id": 17941971,
"title": "BACTIBASE: a new web-accessible database for bacteriocin characterization."
}
],
"subjects": [
"Life Science"
]
},
"homepage": "http://bactibase.hammamilab.org",
"mappings": {
"fairsharing": "FAIRsharing.5f5mfm",
"prefixcommons": "bactibase",
"re3data": "r3d100012755"
},
"name": "Bactibase",
"prefixcommons": {
"description": "BACTIBASE contains calculated or predicted physicochemical properties of 177 bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships structure/function and target organisms of these peptides and therefore better exploitation of their biological activity in both the medical and food sectors.",
"example": "BAC152",
"homepage": "http://bactibase.pfba-lab-tun.org/main.php",
"keywords": [
"protein"
],
"name": "Bactibase: database dedicated to bacteriocins",
"pattern": "^BA\\d+$",
"prefix": "bactibase",
"uri_format": "http://bactibase.pfba-lab-tun.org/$1"
},
"publications": [
{
"doi": "10.1186/1471-2180-10-22",
"pmc": "PMC2824694",
"pubmed": "20105292",
"title": "BACTIBASE second release: a database and tool platform for bacteriocin characterization",
"year": 2010
},
{
"doi": "10.1186/1471-2180-7-89",
"pmc": "PMC2211298",
"pubmed": "17941971",
"title": "BACTIBASE: a new web-accessible database for bacteriocin characterization",
"year": 2007
}
],
"re3data": {
"description": "BACTIBASE contains calculated or predicted physicochemical properties of bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships structure/function and target organisms of these peptides and therefore better exploitation of their biological activity in both the medical and food sectors.",
"homepage": "http://bactibase.hammamilab.org/main.php",
"name": "BACTIBASE",
"prefix": "r3d100012755",
"synonyms": [
"a database dedicated to bacteriocins"
],
"xrefs": {
"fairsharing": "FAIRsharing.5f5mfm",
"nlx": "54530",
"omics": "05726",
"scr": "006694"
}
},
"uri_format": "http://bactibase.hammamilab.org/$1"
},
"bams": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"description": "BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions.",
"homepage": "https://bams1.org",
"name": "Brain Architecture Knowledge Management System Neuroanatomical Ontology",
"references": [
"https://www.frontiersin.org/articles/10.3389/neuro.11.002.2008/full"
]
},
"bao": {
"aberowl": {
"description": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 1000 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc.). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation.",
"download_owl": "http://aber-owl.net/media/ontologies/BAO/32/bao.owl",
"homepage": "http://www.bioassayontology.org/",
"name": "BioAssay Ontology",
"prefix": "BAO",
"version": "2.3.3"
},
"biocontext": {
"prefix": "BAO"
},
"bioportal": {
"contact": {
"email": "sschurer@med.miami.edu",
"name": "Stephan Schurer"
},
"description": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 1000 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc.). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation.",
"homepage": "http://www.bioassayontology.org/",
"name": "BioAssay Ontology",
"prefix": "BAO",
"publication": "http://www.bioassayontology.org/",
"version": "2.8.11"
},
"download_owl": "http://www.bioassayontology.org/bao/bao_complete.owl",
"fairsharing": {
"abbreviation": "BAO",
"description": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.",
"domains": [
"Molecular entity",
"Chemical entity",
"Reagent",
"Cell",
"Biological process",
"Assay",
"Protein",
"Target"
],
"homepage": "http://bioassayontology.org",
"license": "CC-BY-4.0",
"name": "BioAssay Ontology",
"prefix": "FAIRsharing.mye76w",
"publications": [
{
"doi": "10.1186/2041-1480-5-s1-s5",
"pubmed": "25093074",
"title": "Evolving BioAssay Ontology (BAO): modularization, integration and applications",
"year": 2014
},
{
"doi": "10:1371/journal.pone.0049198",
"pubmed": "10",
"title": "Digitoxin metabolism by rat liver microsomes",
"year": 1975
},
{
"doi": "10.1371/journal.pone.0049198",
"pubmed": "23155465",
"title": "Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO)",
"year": 2012
},
{
"doi": "10.1186/1471-2105-12-257",
"pubmed": "21702939",
"title": "BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results",
"year": 2011
}
],
"repository": "https://github.com/BioAssayOntology/BAO/wiki",
"subjects": [
"Biochemistry",
"Life Science",
"Biomedical Science"
]
},
"mappings": {
"aberowl": "BAO",
"biocontext": "BAO",
"bioportal": "BAO",
"fairsharing": "FAIRsharing.mye76w",
"miriam": "bao",
"n2t": "bao",
"ols": "bao",
"ontobee": "BAO"
},
"miriam": {
"deprecated": false,
"description": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.",
"homepage": "http://bioportal.bioontology.org/ontologies/BAO/",
"id": "00000597",
"name": "BioAssay Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{7}$",
"prefix": "bao",
"sampleId": "0002989",
"uri_format": "http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1"
},
"n2t": {
"description": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.",
"example": "0002989",
"homepage": "http://bioportal.bioontology.org/ontologies/BAO/",
"name": "BioAssay Ontology through BioPortal",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{7}$",
"prefix": "bao",
"uri_format": "http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1"
},
"ols": {
"description": "The BioAssay Ontology (BAO) describes biological screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 700 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation.",
"homepage": "http://bioassayontology.org",
"name": "BioAssay Ontology",
"prefix": "bao",
"version": "2.8.11",
"version.iri": "http://www.bioassayontology.org/bao/bao_complete.owl"
},
"ontobee": {
"library": "Not Specified/No",
"name": "BioAssay Ontology",
"prefix": "BAO"
},
"publications": [
{
"doi": "10.1186/2041-1480-5-s1-s5",
"pmc": "PMC4108877",
"pubmed": "25093074",
"title": "Evolving BioAssay Ontology (BAO): modularization, integration and applications",
"year": 2014
},
{
"doi": "10.1371/journal.pone.0049198",
"pmc": "PMC3498356",
"pubmed": "23155465",
"title": "Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO)",
"year": 2012
},
{
"doi": "10.1186/1471-2105-12-257",
"pmc": "PMC3149580",
"pubmed": "21702939",
"title": "BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results",
"year": 2011
},
{
"doi": "10:1371/journal.pone.0049198",
"pubmed": "10",
"title": "Digitoxin metabolism by rat liver microsomes",
"year": 1975
}
],
"repository": "https://github.com/BioAssayOntology/BAO",
"synonyms": [
"BAO"
],
"uri_format": "http://www.bioassayontology.org/bao#BAO_$1"
},
"bartoc": {
"contact": {
"email": "voss@gbv.de",
"github": "nichtich",
"name": "Jakob VoΓ",
"orcid": "0000-0002-7613-4123"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor_extras": [
{
"email": "voss@gbv.de",
"github": "nichtich",
"name": "Jakob VoΓ",
"orcid": "0000-0002-7613-4123"
}
],
"description": "The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries.\nThe main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOCβs search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO).",
"example": "241",
"fairsharing": {
"abbreviation": "BARTOC",
"description": "The Basel Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems (KOS) and KOS -related registries. Its main goal is to list as many KOS as possible in one place in order to achieve greater visibility, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOCβs search interface is available in 20 European languages.",
"homepage": "https://bartoc.org/",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "Basel Register of Thesauri, Ontologies and Classifications",
"prefix": "FAIRsharing.f1777e",
"publications": [],
"repository": "https://github.com/gbv/bartoc.org",
"subjects": [
"Knowledge and Information Systems",
"Ontology and Terminology"
]
},
"homepage": "https://bartoc.org",
"license": "PDDL 1.0",
"mappings": {
"bartoc": "2054",
"fairsharing": "FAIRsharing.f1777e",
"wikidata": "P2689"
},
"name": "Basic Register of Thesauri, Ontologies & Classifications",
"owners": [
{
"name": "Verbundzentrale des GBV",
"partnered": false,
"ror": "048vdhs48"
}
],
"pattern": "^[1-9][0-9]*$",
"references": [
"https://github.com/biopragmatics/bioregistry/issues/783"
],
"repository": "https://github.com/gbv/bartoc.org",
"uri_format": "https://bartoc.org/en/node/$1",
"wikidata": {
"description": "identifier in the BARTOC Terminology Registry",
"example": [
"18801",
"241"
],
"homepage": "https://bartoc.org/",
"name": "BARTOC ID",
"pattern": "^[1-9][0-9]*$",
"prefix": "P2689",
"uri_format": "https://bartoc.org/en/node/$1",
"uri_format_rdf": "http://bartoc.org/en/node/$1"
}
},
"bbkg": {
"mappings": {
"miriam": "bbkg"
},
"miriam": {
"deprecated": false,
"description": "Blue Brain Project's published data as knowledge graphs and Web Studios.",
"homepage": "https://portal.bluebrain.epfl.ch",
"id": "00000903",
"name": "Blue Brain Project Knowledge Graph",
"namespaceEmbeddedInLui": false,
"pattern": "^[-\\w]+(?:\\/[-\\w]+)(?:\\/\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b)$",
"prefix": "bbkg",
"sampleId": "topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a",
"uri_format": "https://bbp.epfl.ch/nexus/web/studios/public/$1"
}
},
"bbtp": {
"mappings": {
"miriam": "bbtp"
},
"miriam": {
"deprecated": false,
"description": "Input data and analysis results for the paper \"Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 ).",
"homepage": "https://portal.bluebrain.epfl.ch",
"id": "00000889",
"name": "Blue Brain Project Topological sampling Knowledge Graph",
"namespaceEmbeddedInLui": false,
"pattern": "\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b",
"prefix": "bbtp",
"sampleId": "f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a",
"uri_format": "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1"
}
},
"bcbc": {
"description": "One of the many goals of the BCBC was to develop and maintain databases of useful research resources. A total of 813 different scientific resources were generated and submitted by BCBC investigators over the 14 years it existed. Information pertaining to 495 selected resources, judged to be the most scientifically-useful, has been converted into a static catalog, as shown below. In addition, the metadata for these 495 resources have been transferred to dkNET in the form of RDF descriptors, and all genomics data have been deposited to either ArrayExpress or GEO. [from homepage]",
"example": "4623",
"integbio": {
"alt_name": "Beta Cell Biology Consortium",
"description": "The Beta Cell Biology Consortium was to advance understanding associated with the development and function of the islets of Langerhans through functional genomics research data and distribution of resources; however, they have stopped operations as of August 1, 2015. The database contains information about antibodies, genomics study, mouse ECS lines, and mouse strains as screenshots.",
"homepage": "http://www.betacell.org/",
"information_keywords": [
"Bioresource",
"Method"
],
"maintainer": "Beta Cell Biology Consortium",
"name": "BCBC",
"prefix": "nbdc00375",
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"mappings": {
"integbio": "nbdc00375",
"rrid": "BCBC"
},
"pattern": "^\\d+$",
"rrid": {
"homepage": "http://www.betacell.org/",
"keywords": [
"adenovirus",
"antibody",
"basic research",
"basic science",
"beta cell",
"cell line",
"cell regeneration",
"cell replacement",
"cell reprogramming",
"data set",
"data sharing",
"embryonic stem cell",
"embryonic stem cell line",
"functional genomics",
"gene",
"gene expression",
"genomics",
"mouse",
"mouse embryonic stem cell line",
"mouse strain",
"pancreas",
"pancreatic development",
"pancreatic islet",
"pancreatic islet development",
"pancreatic islet function",
"protocol"
],
"name": "Beta Cell Biology Consortium",
"prefix": "BCBC",
"scr": "005136"
},
"uri_format": "https://scicrunch.org/resolver/RRID:BCBC_$1"
},
"bcgo": {
"aberowl": {
"description": "An application ontology built for beta cell genomics studies.",
"download_owl": "http://aber-owl.net/media/ontologies/BCGO/3/bcgo.owl",
"homepage": "https://github.com/obi-bcgo/bcgo",
"name": "Beta Cell Genomics Ontology",
"prefix": "BCGO"
},
"biocontext": {
"prefix": "BCGO"
},
"bioportal": {
"contact": {
"email": "alex27bulzan@yahoo.com",
"name": "Alexandra Bulzan"
},
"description": "assigns a grade to a tumor starting from the 3 criteria of the NGS",
"name": "Breast Cancer Grading Ontology",
"prefix": "BCGO",
"version": "1.5"
},
"cellosaurus": {
"category": "Anatomy/cell type resources",
"homepage": "https://github.com/obi-bcgo/bcgo",
"name": "Beta Cell Genomics Ontology",
"prefix": "BCGO",
"uri_format": "http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/$1"
},
"download_owl": "https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl",
"example": "0000015",
"mappings": {
"aberowl": "BCGO",
"biocontext": "BCGO",
"bioportal": "BCGO",
"cellosaurus": "BCGO",
"obofoundry": "bcgo",
"ols": "bcgo",
"ontobee": "BCGO"
},
"obofoundry": {
"contact": "jiezheng@pennmedicine.upenn.edu",
"contact.github": "zhengj2007",
"contact.label": "Jie Zheng",
"contact.orcid": "0000-0002-2999-0103",
"deprecated": true,
"description": "An application ontology built for beta cell genomics studies.",
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/bcgo.owl",
"homepage": "https://github.com/obi-bcgo/bcgo",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Beta Cell Genomics Ontology",
"prefix": "bcgo",
"repository": "https://github.com/obi-bcgo/bcgo"
},
"ols": {
"description": "An application ontology built for beta cell genomics studies.",
"homepage": "https://github.com/obi-bcgo/bcgo",
"name": "Beta Cell Genomics Ontology",
"prefix": "bcgo",
"version": "2015-07-08",
"version.iri": "http://purl.obolibrary.org/obo/bcgo/2015-07-08/bcgo.owl"
},
"ontobee": {
"library": "Library",
"name": "Beta Cell Genomics Ontology",
"prefix": "BCGO"
},
"pattern": "^\\d{7}$"
},
"bcio": {
"aberowl": {
"description": "The BCI ontology specifies a foundational metadata model set for real-world multimodal Brain-Computer Interaction (BCI) data capture activities. Its structure depicts a conceptual framework that BCI applications can extend and use in their implementations, to define core concepts that capture a relevant and interoperable metadata vocabulary. This ontology is aligned to the Semantic Sensor Network Ontology (SSN): a domain-independent and end-to-end model for sensor/actuator applications. Hence, its structure has been normalized to assist its use in conjunction with other ontologies or linked data resources to specify any particular definitions (such as units of measurement, time and time series, and location and mobility), that specialized applications in the BCI domain might need. Its spec provides general alignment data modeling guidelines for core concepts, to help BCI applications in their design.",
"download_owl": "http://aber-owl.net/media/ontologies/BCI-O/6/bci-o.owl",
"homepage": "http://lov.okfn.org/dataset/lov/vocabs/bci",
"name": "Brain-Computer Interaction (BCI) Ontology",
"prefix": "BCI-O",
"version": "0.9.6"
},
"bioportal": {
"contact": {
"email": "srodriguez@pet.cs.nctu.edu.tw",
"name": "Sergio JosΓ© RodrΓguez MΓ©ndez"
},
"description": "The BCI ontology specifies a foundational metadata model set for real-world multimodal Brain-Computer Interaction (BCI) data capture activities. Its structure depicts a conceptual framework that BCI applications can extend and use in their implementations, to define core concepts that capture a relevant and interoperable metadata vocabulary. This ontology is aligned to the Semantic Sensor Network Ontology (SSN): a domain-independent and end-to-end model for sensor/actuator applications. Hence, its structure has been normalized to assist its use in conjunction with other ontologies or linked data resources to specify any particular definitions (such as units of measurement, time and time series, and location and mobility), that specialized applications in the BCI domain might need. Its spec provides general alignment data modeling guidelines for core concepts, to help BCI applications in their design.",
"homepage": "http://lov.okfn.org/dataset/lov/vocabs/bci",
"name": "Brain-Computer Interaction (BCI) Ontology",
"prefix": "BCI-O",
"publication": "https://github.com/perma-id/w3id.org/tree/master/BCI-ontology",
"version": "0.9.6"
},
"contact": {
"email": "srodriguez142857@gmail.com",
"name": "Sergio JosΓ© RodrΓguez MΓ©ndez",
"orcid": "0000-0001-7203-8399"
},
"download_owl": "http://humanbehaviourchange.org/ontology/bcio.owl",
"example": "040000",
"mappings": {
"aberowl": "BCI-O",
"bioportal": "BCI-O",
"ols": "bcio"
},
"ols": {
"description": "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation.",
"download_owl": "http://humanbehaviourchange.org/ontology/bcio.owl",
"homepage": "https://www.humanbehaviourchange.org/",
"name": "The Behaviour Change Intervention Ontology",
"prefix": "bcio",
"version": "2024-07-03",
"version.iri": "http://humanbehaviourchange.org/ontology/bcio.owl/2024-07-03"
},
"pattern": "^\\d{6}$",
"uri_format": "https://w3id.org/BCI-ontology#$1"
},
"bco": {
"aberowl": {
"description": "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.",
"download_owl": "http://aber-owl.net/media/ontologies/BCO/12/bco.owl",
"homepage": "https://github.com/tucotuco/bco",
"name": "Biological Collections Ontology",
"prefix": "BCO"
},
"agroportal": {
"contact": {
"email": "rwalls2008@gmail.com",
"name": "Ramona Walls"
},
"description": "The goal of the BCO is to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. The BCO covers distinctions between individuals, organisms, voucher specimens, lots, samples, the relations between these entities, and the processes governing the creation and use of \"samples\". Also within scope are properties including collector, location, time, storage environment, containers, institution, and collection identifiers.",
"example_uri": "http://purl.obolibrary.org/obo/bco_0000036",
"homepage": "https://github.com/BiodiversityOntologies",
"license": "CC0-1.0",
"name": "Biological Collections Ontology",
"prefix": "BCO",
"repository": "https://github.com/BiodiversityOntologies/bco"
},
"biocontext": {
"prefix": "BCO"
},
"bioportal": {
"contact": {
"email": "bco-discuss@googlegroups.com",
"name": "bco-discuss list"
},
"description": "BCO supports the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. A key feature of BCO is an ontological interpretation of Darwin Core terms.",
"homepage": "https://github.com/BiodiversityOntologies/bcom/p/bco/",
"name": "Biological Collections Ontology",
"prefix": "BCO",
"version": "2021-11-14"
},
"ecoportal": {
"contact": {
"email": "rlwalls2008@gmail.com",
"name": "Ramona Walls"
},
"description": "The BCO supports the interoperability of biodiversity and biodiversity related data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. A key aspect of the BCO is distinguishing among material samples (i.e. specimens), observing processes, and data about either of those entities.",
"homepage": "https://github.com/BiodiversityOntologies/bco",
"name": "BioCollections Ontology",
"prefix": "BCO",
"publication": "https://github.com/BiodiversityOntologies/bco",
"version": "2021-11-14"
},
"example": "0000081",
"fairsharing": {
"abbreviation": "BCO",
"description": "The Biological Collections Ontology (BCO) supports the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. The BCO covers distinctions between individuals, organisms, voucher specimens, lots, samples, the relations between these entities, and the processes governing the creation and use of \"samples\". Also within scope are properties including collector, location, time, storage environment, containers, institution, and collection identifiers.",
"domains": [
"Taxonomic classification",
"Biological sample annotation",
"Environmental material",
"Biological sample"
],
"homepage": "https://github.com/BiodiversityOntologies/bco",
"license": "CC0-1.0",
"name": "Biological Collections Ontology",
"prefix": "FAIRsharing.8ktkqy",
"publications": [
{
"doi": "10.1371/journal.pone.0089606",
"pubmed": "24595056",
"title": "Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies",
"year": 2014
}
],
"subjects": [
"Metagenomics",
"Taxonomy",
"Ecology",
"Biodiversity"
]
},
"mappings": {
"aberowl": "BCO",
"agroportal": "BCO",
"biocontext": "BCO",
"bioportal": "BCO",
"ecoportal": "BCO",
"fairsharing": "FAIRsharing.8ktkqy",
"obofoundry": "bco",
"ols": "bco",
"ontobee": "BCO"
},
"obofoundry": {
"appears_in": [
"fovt"
],
"contact": "rlwalls2008@gmail.com",
"contact.github": "ramonawalls",
"contact.label": "Ramona Walls",
"contact.orcid": "0000-0001-8815-0078",
"deprecated": false,
"description": "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.",
"domain": "organisms",
"download.owl": "http://purl.obolibrary.org/obo/bco.owl",
"homepage": "https://github.com/BiodiversityOntologies/bco",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Biological Collections Ontology",
"preferredPrefix": "BCO",
"prefix": "bco",
"publications": [
{
"id": "https://doi.org/10.1371/journal.pone.0089606",
"title": "Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies"
}
],
"repository": "https://github.com/BiodiversityOntologies/bco"
},
"ols": {
"description": "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.",
"download_owl": "http://purl.obolibrary.org/obo/bco.owl",
"homepage": "https://github.com/BiodiversityOntologies/bco",
"name": "Biological Collections Ontology",
"prefix": "bco",
"version": "2021-11-14",
"version.iri": "http://purl.obolibrary.org/obo/bco/releases/2021-11-14/bco.owl"
},
"ontobee": {
"library": "Library",
"name": "Biological Collections Ontology",
"prefix": "BCO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1371/journal.pone.0089606",
"pmc": "PMC3940615",
"pubmed": "24595056",
"title": "Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies",
"year": 2014
}
],
"uri_format": "http://purl.obolibrary.org/obo/BCO_$1"
},
"bcrc": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://catalog.bcrc.firdi.org.tw/",
"name": "Taiwan Bioresource Collection and Research Center",
"prefix": "BCRC",
"uri_format": "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"example": "60316",
"homepage": "https://catalog.bcrc.firdi.org.tw",
"keywords": [
"cell lines"
],
"mappings": {
"cellosaurus": "BCRC"
},
"name": "BCRC Strain Collection Catalog",
"pattern": "^\\d+$",
"uri_format": "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1"
},
"bcrj": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://bcrj.org.br/pesquisa/",
"name": "Banco de Celulas do Rio de Janeiro",
"prefix": "BCRJ",
"uri_format": "http://bcrj.org.br/celula/$1"
},
"example": "0278",
"mappings": {
"cellosaurus": "BCRJ"
},
"pattern": "^\\d{4}$"
},
"bdgp.est": {
"biocontext": {
"prefix": "BDGP.EST"
},
"has_canonical": "dbest",
"mappings": {
"biocontext": "BDGP.EST",
"miriam": "bdgp.est",
"n2t": "bdgp.est",
"ncbi": "BDGP_EST",
"prefixcommons": "flybase.est"
},
"miriam": {
"deprecated": false,
"description": "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI).",
"homepage": "https://www.ncbi.nlm.nih.gov/dbEST/index.html",
"id": "00000285",
"name": "BDGP EST",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\.)?(\\d+)?$",
"prefix": "bdgp.est",
"sampleId": "EY223054.1",
"uri_format": "https://www.ncbi.nlm.nih.gov/nucest/$1"
},
"n2t": {
"description": "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI).",
"example": "EY223054.1",
"homepage": "https://www.ncbi.nlm.nih.gov/dbEST/index.html",
"name": "BDGP EST at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\.)?(\\d+)?$",
"prefix": "bdgp.est",
"uri_format": "https://www.ncbi.nlm.nih.gov/nucest/$1"
},
"ncbi": {
"example": "123456",
"homepage": "http://www.fruitfly.org/EST/index.shtml",
"name": "Berkeley Drosophila Genome Project EST database",
"prefix": "BDGP_EST"
},
"prefixcommons": {
"description": "The goals of the Drosophila Genome Center are to finish the sequence of the euchromatic genome of Drosophila melanogaster to high quality and to generate and maintain biological annotations of this sequence.",
"example": "123456",
"homepage": "http://www.fruitfly.org/EST/index.shtml",
"keywords": [
"genome"
],
"name": "Berkeley Drosophila Genome Project EST database",
"pattern": "^\\d+$",
"prefix": "flybase.est",
"synonyms": [
"bdgp_est"
]
}
},
"bdgp.insertion": {
"biocontext": {
"prefix": "BDGP.INSERTION"
},
"contact": {
"email": "spradling@ciwemb.edu",
"name": "Allan Spradling",
"orcid": "0000-0002-5251-1801"
},
"mappings": {
"biocontext": "BDGP.INSERTION",
"miriam": "bdgp.insertion",
"n2t": "bdgp.insertion",
"prefixcommons": "bdgp"
},
"miriam": {
"deprecated": false,
"description": "BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element.",
"homepage": "http://flypush.imgen.bcm.tmc.edu/pscreen/",
"id": "00000156",
"name": "BDGP insertion DB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "bdgp.insertion",
"sampleId": "KG09531",
"uri_format": "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1"
},
"n2t": {
"description": "BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element.",
"example": "KG09531",
"homepage": "http://flypush.imgen.bcm.tmc.edu/pscreen/",
"name": "BDGP Gene Disruption Project",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "bdgp.insertion",
"uri_format": "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1"
},
"prefixcommons": {
"description": "BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element.",
"example": "KG09531",
"keywords": [
"gene",
"sequence"
],
"name": "Drosphila Gene Disruption Database",
"pattern": "^\\w+$",
"prefix": "bdgp",
"pubmed_ids": [
"15238527"
],
"synonyms": [
"BDGP.insertion"
],
"uri_format": "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1"
},
"publications": [
{
"doi": "10.1534/genetics.104.026427",
"pmc": "PMC1470905",
"pubmed": "15238527",
"title": "The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes",
"year": 2004
}
]
},
"bdsc": {
"mappings": {
"miriam": "bdsc",
"n2t": "bdsc",
"rrid": "BDSC"
},
"miriam": {
"deprecated": false,
"description": "The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research.",
"homepage": "https://bdsc.indiana.edu/about/mission.html",
"id": "00000332",
"name": "Bloomington Drosophila Stock Center",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "bdsc",
"sampleId": "33607",
"uri_format": "https://bdsc.indiana.edu/stocks/$1"
},
"n2t": {
"description": "The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research.",
"example": "33607",
"homepage": "https://bdsc.indiana.edu/about/mission.html",
"name": "BDSC at Indiana University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "bdsc",
"uri_format": "https://bdsc.indiana.edu/stocks/$1"
},
"rrid": {
"homepage": "https://bdsc.indiana.edu/",
"keywords": [
"FASEB list",
"database",
"deficiency",
"deletion",
"disease model",
"duplication",
"fly",
"gene",
"genetic",
"genetic analysis",
"genetic construct",
"germline",
"human disease model",
"insertion",
"invertebrate",
"mutation",
"protein trap",
"scientist",
"sequenced strain",
"somatic",
"stock",
"transposon",
"transposon insertion"
],
"name": "Bloomington Drosophila Stock Center",
"prefix": "BDSC",
"scr": "006457"
}
},
"beetlebase": {
"biocontext": {
"prefix": "BEETLEBASE"
},
"contact": {
"email": "sjbrown@ksu.edu",
"name": "Susan J. Brown",
"orcid": "0000-0002-7984-0445"
},
"fairsharing": {
"abbreviation": "BeetleBase",
"description": "BeetleBase is a community resource for Tribolium genetics, genomics and developmental biology. The database is built on the Chado generic data model, and is able to store various types of data, ranging from genome sequences to mutant phenotypes.",
"homepage": "http://www.beetlebase.org/",
"name": "BeetleBase",
"prefix": "FAIRsharing.h5f091",
"publications": [
{
"doi": "10.1093/nar/gkp807",
"pubmed_id": 19820115,
"title": "BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum."
}
],
"subjects": [
"Computational Biology",
"Life Science"
]
},
"integbio": {
"description": "BeetleBase is a community resource for Tribolium genetics, genomics and developmental biology. The database is built on the Chado generic data model, and is able to store various types of data, ranging from genome sequences to mutant phenotypes.",
"fairsharing": "FAIRsharing.h5f091",
"homepage": "http://www.beetlebase.org/",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Kansas State University",
"name": "BeetleBase",
"prefix": "nbdc01820",
"pubmeds": [
"19820115"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein"
]
},
"mappings": {
"biocontext": "BEETLEBASE",
"fairsharing": "FAIRsharing.h5f091",
"integbio": "nbdc01820",
"miriam": "beetlebase",
"n2t": "beetlebase",
"ncbi": "BEETLEBASE",
"prefixcommons": "beetlebase",
"re3data": "r3d100010921"
},
"miriam": {
"deprecated": false,
"description": "BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications.",
"homepage": "http://beetlebase.org/",
"id": "00000157",
"name": "BeetleBase",
"namespaceEmbeddedInLui": false,
"pattern": "^TC\\d+$",
"prefix": "beetlebase",
"sampleId": "TC010103",
"uri_format": "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1"
},
"n2t": {
"description": "BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications.",
"example": "TC010103",
"homepage": "http://beetlebase.org/",
"name": "BeetleBase at Kansas State University",
"namespaceEmbeddedInLui": false,
"pattern": "^TC\\d+$",
"prefix": "beetlebase",
"uri_format": "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1"
},
"ncbi": {
"example": "TC030551",
"homepage": "http://www.beetlebase.org/",
"name": "Tribolium Genome Database -- Insertion",
"prefix": "BEETLEBASE"
},
"prefixcommons": {
"description": "BeetleBase is being developed as an important community resource for Tribolium genetics, genomics and developmental biology.The database is built on the Chado generic data model, and is able to store various types of data, ranging from genome sequences to mutant phenotypes.",
"example": "TC010103",
"homepage": "http://www.beetlebase.org/",
"keywords": [
"genome"
],
"name": "BeetleBase",
"pattern": "^TC\\d+$",
"prefix": "beetlebase",
"pubmed_ids": [
"19820115"
],
"uri_format": "http://www.beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkp807",
"pmc": "PMC2808946",
"pubmed": "19820115",
"title": "BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum",
"year": 2009
}
],
"re3data": {
"description": "<<>>!!!>>>",
"homepage": "http://beetlebase.org/",
"name": "BeetleBase",
"prefix": "r3d100010921",
"xrefs": {
"fairsharing": "FAIRsharing.h5f091",
"nif": "0000-02599",
"omics": "03118"
}
}
},
"begdb": {
"biocontext": {
"prefix": "BEGDB"
},
"contact": {
"email": "pavel.hobza@uochb.cas.cz",
"name": "Pavel Hobza",
"orcid": "0000-0001-5292-6719"
},
"fairsharing": {
"abbreviation": "BEGDB",
"description": "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate QM calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods.",
"homepage": "http://www.begdb.org/",
"name": "The Benchmark Energy & Geometry Database",
"prefix": "FAIRsharing.nbe4fq",
"publications": [
{
"doi": "10.1135/cccc20081261",
"pubmed_id": null,
"title": "Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples"
}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"biocontext": "BEGDB",
"fairsharing": "FAIRsharing.nbe4fq",
"miriam": "begdb",
"n2t": "begdb",
"re3data": "r3d100011166"
},
"miriam": {
"deprecated": false,
"description": "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods.",
"homepage": "http://www.begdb.com",
"id": "00000622",
"name": "Benchmark Energy & Geometry Database",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "begdb",
"sampleId": "4214",
"uri_format": "http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1"
},
"n2t": {
"description": "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods.",
"example": "4214",
"homepage": "http://www.begdb.com",
"name": "Benchmark Energy & Geometry Database",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "begdb",
"uri_format": "http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1"
},
"publications": [
{
"doi": "10.1135/cccc20081261",
"title": "Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples",
"year": 2008
}
],
"re3data": {
"description": "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate QM calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods.",
"homepage": "http://www.begdb.org/",
"name": "Benchmark Energy & Geometry Database",
"prefix": "r3d100011166",
"synonyms": [
"BEGDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.nbe4fq"
}
}
},
"beiresources": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.beiresources.org/Home.aspx",
"name": "BEI Resources cell line products",
"prefix": "BEI_Resources",
"uri_format": "https://www.beiresources.org/Catalog/cellBanks/$1.aspx"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"example": "MRA-253",
"homepage": "https://www.beiresources.org",
"keywords": [
"cell lines"
],
"mappings": {
"cellosaurus": "BEI_Resources"
},
"name": "BEI Resources",
"synonyms": [
"BEI_Resources"
],
"uri_format": "https://www.beiresources.org/Catalog/cellBanks/$1.aspx"
},
"bel": {
"comment": "INDRA uses bel as a catch-all for scomp/sfam",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents.",
"example": "9-1-1 Complex",
"fairsharing": {
"abbreviation": "BEL",
"contact": {
"email": "support@bel.bio",
"name": "William Hayes",
"orcid": "0000-0003-0728-781X"
},
"description": "BEL is a language for representing scientific findings in the life sciences in a reusable, shareable, and computable form. BEL is designed to represent scientific findings by capturing causal and correlative relationships in context, where context can include information about the biological and experimental system in which the relationships were observed, the supporting publications cited and the process of curation. BEL is intended as a knowledge capture and interchange medium, supporting the operation of systems that integrate knowledge derived from independent efforts. The language is designed to be use-neutral, facilitating the storage and use of structured knowledge for inference by applications through a knowledge assembly process that can create computable biological networks. While BEL does not prescribe any particular assembly process or any particular knowledge format for the output of an assembly process, a suite of software components called the BEL Framework provides everything necessary to create, compile, assemble, and deliver computable knowledge models to BEL-aware applications. The current version of BEL provides the means to describe biological interactions qualitatively but not to quantify the magnitude or rate of these interactions. This limitation is by design because this quantitative information has significant variability and is not consistently reported in the literature. It is our hope that future versions of BEL can accommodate these additional data.",
"homepage": "https://bel.bio",
"license": "CC-BY-4.0",
"name": "Biological Expression Language",
"prefix": "FAIRsharing.dp0jvd",
"publications": [],
"subjects": [
"Biology"
]
},
"homepage": "https://biological-expression-language.github.io/",
"mappings": {
"fairsharing": "FAIRsharing.dp0jvd"
},
"name": "Biological Expression Language"
},
"bfo": {
"aberowl": {
"description": "The upper level ontology upon which OBO Foundry ontologies are built.",
"download_owl": "http://aber-owl.net/media/ontologies/BFO/5/bfo.owl",
"homepage": "http://ifomis.org/bfo/",
"name": "Basic Formal Ontology",
"prefix": "BFO"
},
"agroportal": {
"contact": {
"email": "phismith@buffalo.edu",
"name": "Barry Smith"
},
"description": "BFO grows out of a philosophical orientation which overlaps with that of DOLCE and SUMO. Unlike these, however, it is narrowly focused on the task of providing a genuine upper ontology which can be used in support of domain ontologies developed for scientific research, as for example in biomedicine within the framework of the OBO Foundry. Thus BFO does not contain physical, chemical, biological or other terms which would properly fall within the special sciences domains. BFO is the upper level ontology upon which OBO Foundry ontologies are built.",
"example_uri": "http://purl.obolibrary.org/obo/BFO_0000140",
"homepage": "http://ifomis.org/bfo",
"license": "CC-BY-4.0",
"name": "Basic Formal Ontology",
"prefix": "BFO",
"publication": "http://ifomis.uni-saarland.de/bfo/publications",
"repository": "https://github.com/BFO-ontology/BFO",
"version": "1.1"
},
"biocontext": {
"prefix": "BFO"
},
"bioportal": {
"contact": {
"email": "phismith@buffalo.edu",
"name": "Barry Smith"
},
"description": "BFO grows out of a philosophical orientation which overlaps with that of DOLCE and SUMO. Unlike these, however, it is narrowly focused on the task of providing a genuine upper ontology which can be used in support of domain ontologies developed for scientific research, as for example in biomedicine within the framework of the OBO Foundry. Thus BFO does not contain physical, chemical, biological or other terms which would properly fall within the special sciences domains.",
"homepage": "http://www.ifomis.org/bfo",
"name": "Basic Formal Ontology",
"prefix": "BFO",
"version": "2.0"
},
"example": "0000001",
"fairsharing": {
"abbreviation": "BFO",
"description": "The Basic Formal Ontology (BFO, also known via its ISO label as 'ISO/IEC 21838-2:2021 Information technology β Top-level ontologies (TLO) β Part 2: Basic Formal Ontology (BFO)') is an ontology that is conformant to the requirements specified for top-level ontologies in ISO/IEC 21838β1. BFO is a small, upper level ontology that is designed for use in supporting information retrieval, analysis and integration in scientific and other domains. BFO is a genuine upper ontology. Thus it does not contain physical, chemical, biological or other terms which would properly fall within the coverage domains of the special sciences. BFO is used by more than 250 ontology-driven endeavors throughout the world. ",
"domains": [
"Data retrieval"
],
"homepage": "https://www.iso.org/standard/74572.html",
"license": "CC-BY-4.0",
"name": "Basic Formal Ontology",
"prefix": "FAIRsharing.wcpd6f",
"repository": "https://github.com/bfo-ontology/BFO",
"subjects": [
"Subject Agnostic"
]
},
"go": {
"description": "An upper ontology used by Open Bio Ontologies (OBO) Foundry. BFO contains upper-level classes as well as core relations such as part_of (BFO_0000050)",
"name": "Basic Formal Ontology",
"prefix": "BFO"
},
"mappings": {
"aberowl": "BFO",
"agroportal": "BFO",
"biocontext": "BFO",
"bioportal": "BFO",
"fairsharing": "FAIRsharing.wcpd6f",
"go": "BFO",
"obofoundry": "bfo",
"ols": "bfo",
"ontobee": "BFO"
},
"obofoundry": {
"appears_in": [
"ado",
"agro",
"aism",
"cdno",
"colao",
"duo",
"ecocore",
"epio",
"foodon",
"fovt",
"hso",
"lepao",
"mco",
"ons",
"pcl",
"pco",
"psdo",
"rbo",
"uberon",
"xpo",
"zp"
],
"contact": "phismith@buffalo.edu",
"contact.github": "phismith",
"contact.label": "Barry Smith",
"contact.orcid": "0000-0003-1384-116X",
"deprecated": false,
"description": "The upper level ontology upon which OBO Foundry ontologies are built.",
"domain": "upper",
"download.obo": "http://purl.obolibrary.org/obo/bfo.obo",
"download.owl": "http://purl.obolibrary.org/obo/bfo.owl",
"homepage": "http://ifomis.org/bfo/",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"logo": "https://avatars2.githubusercontent.com/u/12972134?v=3&s=200",
"name": "Basic Formal Ontology",
"preferredPrefix": "BFO",
"prefix": "bfo",
"repository": "https://github.com/BFO-ontology/BFO"
},
"ols": {
"description": "The upper level ontology upon which OBO Foundry ontologies are built.",
"download_owl": "http://purl.obolibrary.org/obo/bfo.owl",
"homepage": "http://ifomis.org/bfo/",
"name": "Basic Formal Ontology",
"prefix": "bfo",
"version": "2019-08-26",
"version.iri": "http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl"
},
"ontobee": {
"library": "Foundry",
"name": "Basic Formal Ontology",
"prefix": "BFO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/BFO_$1"
},
"bgee.family": {
"biocontext": {
"prefix": "BGEE.FAMILY"
},
"contributor_extras": [
{
"github": "smoretti",
"name": "SΓ©bastien Moretti",
"orcid": "0000-0003-3947-488X"
}
],
"deprecated": true,
"mappings": {
"biocontext": "BGEE.FAMILY",
"miriam": "bgee.family",
"n2t": "bgee.family"
},
"miriam": {
"deprecated": true,
"description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species.",
"homepage": "http://bgee.unil.ch/bgee/bgee",
"id": "00000417",
"name": "Bgee family",
"namespaceEmbeddedInLui": false,
"pattern": "^(ENSFM|ENSGTV:)\\d+$",
"prefix": "bgee.family",
"sampleId": "ENSFM00500000270089",
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1"
},
"n2t": {
"description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species.",
"example": "ENSFM00500000270089",
"homepage": "http://bgee.unil.ch/bgee/bgee",
"name": "Bgee at Lausanne",
"namespaceEmbeddedInLui": false,
"pattern": "^(ENSFM|ENSGTV:)\\d+$",
"prefix": "bgee.family",
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1"
},
"references": [
"https://github.com/biopragmatics/bioregistry/issues/889"
]
},
"bgee.gene": {
"biocontext": {
"prefix": "BGEE.GENE"
},
"contact": {
"email": "sebastien.moretti@sib.swiss",
"github": "smoretti",
"name": "Sebastien Moretti",
"orcid": "0000-0003-3947-488X"
},
"contributor_extras": [
{
"email": "sebastien.moretti@sib.swiss",
"github": "smoretti",
"name": "Sebastien Moretti",
"orcid": "0000-0003-3947-488X"
}
],
"description": "Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee.",
"homepage": "https://www.bgee.org",
"mappings": {
"biocontext": "BGEE.GENE",
"miriam": "bgee.gene",
"n2t": "bgee.gene",
"prefixcommons": "bgee"
},
"miriam": {
"deprecated": false,
"description": "Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee.",
"homepage": "https://www.bgee.org/",
"id": "00000418",
"name": "Bgee gene",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9]+$",
"prefix": "bgee.gene",
"sampleId": "FBgn0000015",
"uri_format": "https://www.bgee.org/gene/$1"
},
"n2t": {
"description": "Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee.",
"example": "FBgn0000015",
"homepage": "https://bgee.org/",
"name": "Bgee gene",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z]+\\d+$",
"prefix": "bgee.gene",
"uri_format": "https://bgee.org/?page=gene&gene_id=$1"
},
"pattern": "^[A-Za-z0-9]+$",
"prefixcommons": {
"description": "Bgee is a database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently EST, Affymetrix, and in situ hybridization data) on anatomical and developmental ontologies. Then, in order to perform automated cross species comparisons, homology relationships across anatomical ontologies, and comparison criteria between developmental ontologies, are designed.",
"example": "FBgn0041195",
"homepage": "http://bgee.unil.ch",
"keywords": [
"gene expression"
],
"name": "Bgee DataBase for Gene Expression Evolution",
"pattern": "^[A-Z]+\\d+$",
"prefix": "bgee",
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=gene&action=expression&gene_id=$1"
},
"references": [
"https://github.com/biopragmatics/bioregistry/issues/890"
],
"uri_format": "https://www.bgee.org/gene/$1"
},
"bgee.organ": {
"biocontext": {
"prefix": "BGEE.ORGAN"
},
"contributor_extras": [
{
"github": "smoretti",
"name": "SΓ©bastien Moretti",
"orcid": "0000-0003-3947-488X"
}
],
"deprecated": true,
"mappings": {
"biocontext": "BGEE.ORGAN",
"miriam": "bgee.organ",
"n2t": "bgee.organ"
},
"miriam": {
"deprecated": true,
"description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures.",
"homepage": "http://bgee.unil.ch/bgee/bgee",
"id": "00000420",
"name": "Bgee organ",
"namespaceEmbeddedInLui": false,
"pattern": "^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\\:\\d+$",
"prefix": "bgee.organ",
"sampleId": "EHDAA:2185",
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_id=$1&organ_children=on"
},
"n2t": {
"description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures.",
"example": "EHDAA:2185",
"homepage": "http://bgee.unil.ch/bgee/bgee",
"name": "Bgee at Lausanne",
"namespaceEmbeddedInLui": false,
"pattern": "^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\\:\\d+$",
"prefix": "bgee.organ",
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_id=$1&organ_children=on"
},
"references": [
"https://github.com/biopragmatics/bioregistry/issues/889"
],
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1"
},
"bgee.stage": {
"biocontext": {
"prefix": "BGEE.STAGE"
},
"contributor_extras": [
{
"github": "smoretti",
"name": "SΓ©bastien Moretti",
"orcid": "0000-0003-3947-488X"
}
],
"deprecated": true,
"mappings": {
"biocontext": "BGEE.STAGE",
"miriam": "bgee.stage",
"n2t": "bgee.stage"
},
"miriam": {
"deprecated": true,
"description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages.",
"homepage": "http://bgee.unil.ch/bgee/bgee",
"id": "00000419",
"name": "Bgee stage",
"namespaceEmbeddedInLui": false,
"pattern": "^(FBvd|XtroDO|HsapDO|MmusDO)\\:\\d+$",
"prefix": "bgee.stage",
"sampleId": "HsapDO:0000004",
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_id=$1&stage_children=on"
},
"n2t": {
"description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages.",
"example": "HsapDO:0000004",
"homepage": "http://bgee.unil.ch/bgee/bgee",
"name": "Bgee at Lausanne",
"namespaceEmbeddedInLui": false,
"pattern": "^(FBvd|XtroDO|HsapDO|MmusDO)\\:\\d+$",
"prefix": "bgee.stage",
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_id=$1&stage_children=on"
},
"references": [
"https://github.com/biopragmatics/bioregistry/issues/889"
],
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1"
},
"bibo": {
"contact": {
"email": "fred@fgiasson.com",
"github": "fgiasson",
"name": "FrΓ©dΓ©rick Giasson"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Bibliographic Ontology Specification provides main concepts and properties for describing citations and bibliographic references (i.e. quotes, books, articles, etc) on the Semantic Web.",
"example": "authorList",
"homepage": "https://bibliontology.com/",
"keywords": [
"bibliometrics"
],
"lov": {
"description": "The Bibliographic Ontology Specification provides main concepts and properties for describing citations and bibliographic references (i.e. quotes, books, articles, etc) on the Semantic Web.",
"homepage": "http://purl.org/ontology/bibo/",
"keywords": [
"Catalogs"
],
"modified": "2009-11-04",
"name": "The Bibliographic Ontology",
"prefix": "bibo",
"uri_prefix": "http://purl.org/ontology/bibo/$1"
},
"mappings": {
"lov": "bibo",
"zazuko": "bibo"
},
"name": "The Bibliographic Ontology",
"preferred_prefix": "bibo",
"uri_format": "http://purl.org/ontology/bibo/$1",
"zazuko": {
"prefix": "bibo",
"uri_format": "http://purl.org/ontology/bibo/$1"
}
},
"bido": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF.",
"example": "CategorialBibliometricData",
"fairsharing": {
"abbreviation": "BiDO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Bibliometric Data Ontology (BiDO) is a modular ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/bido",
"license": "CC-BY-4.0",
"name": "Bibliometric Data Ontology ",
"prefix": "FAIRsharing.d7f0a9",
"repository": "https://github.com/sparontologies/bido",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"homepage": "http://www.sparontologies.net/ontologies/bido",
"mappings": {
"fairsharing": "FAIRsharing.d7f0a9"
},
"name": "Bibliometric Data Ontology",
"preferred_prefix": "BiDO",
"repository": "https://github.com/sparontologies/bido",
"uri_format": "http://purl.org/spar/bido/$1"
},
"bigg.compartment": {
"biocontext": {
"prefix": "BIGG.COMPARTMENT"
},
"mappings": {
"biocontext": "BIGG.COMPARTMENT",
"miriam": "bigg.compartment",
"n2t": "bigg.compartment"
},
"miriam": {
"deprecated": false,
"description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments.",
"homepage": "http://bigg.ucsd.edu/compartments/",
"id": "00000555",
"name": "BiGG Compartment",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z_A-Z]+$",
"prefix": "bigg.compartment",
"sampleId": "c",
"uri_format": "http://bigg.ucsd.edu/compartments/$1"
},
"n2t": {
"description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments.",
"example": "c",
"homepage": "http://bigg.ucsd.edu/compartments/",
"name": "BiGG Compartment at University of California",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z_A-Z]+$",
"prefix": "bigg.compartment",
"uri_format": "http://bigg.ucsd.edu/compartments/$1"
}
},
"bigg.metabolite": {
"biocontext": {
"prefix": "BIGG.METABOLITE"
},
"mappings": {
"biocontext": "BIGG.METABOLITE",
"miriam": "bigg.metabolite",
"n2t": "bigg.metabolite"
},
"miriam": {
"deprecated": false,
"description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolites.",
"homepage": "http://bigg.ucsd.edu/universal/metabolites",
"id": "00000556",
"name": "BiGG Metabolite",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z_A-Z0-9]+$",
"prefix": "bigg.metabolite",
"sampleId": "12dgr161",
"uri_format": "http://bigg.ucsd.edu/models/universal/metabolites/$1"
},
"n2t": {
"description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes.",
"example": "12dgr161",
"homepage": "http://bigg.ucsd.edu/universal/metabolites",
"name": "BiGG Metabolite at University of Cakifornia",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z_A-Z0-9]+$",
"prefix": "bigg.metabolite",
"uri_format": "http://bigg.ucsd.edu/models/universal/metabolites/$1"
}
},
"bigg.model": {
"biocontext": {
"prefix": "BIGG.MODEL"
},
"mappings": {
"biocontext": "BIGG.MODEL",
"miriam": "bigg.model",
"n2t": "bigg.model"
},
"miriam": {
"deprecated": false,
"description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models.",
"homepage": "http://bigg.ucsd.edu/models",
"id": "00000554",
"name": "BiGG Model",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z_A-Z0-9]+$",
"prefix": "bigg.model",
"sampleId": "iECABU_c1320",
"uri_format": "http://bigg.ucsd.edu/models/$1"
},
"n2t": {
"description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models.",
"example": "iECABU_c1320",
"homepage": "http://bigg.ucsd.edu/models",
"name": "BiGG Model at University of California",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z_A-Z0-9]+$",
"prefix": "bigg.model",
"uri_format": "http://bigg.ucsd.edu/models/$1"
}
},
"bigg.reaction": {
"biocontext": {
"prefix": "BIGG.REACTION"
},
"mappings": {
"biocontext": "BIGG.REACTION",
"miriam": "bigg.reaction",
"n2t": "bigg.reaction"
},
"miriam": {
"deprecated": false,
"description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions.",
"homepage": "http://bigg.ucsd.edu/universal/reactions",
"id": "00000557",
"name": "BiGG Reaction",
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"homepage": "http://teddyontology.sourceforge.net/",
"id": "00000107",
"name": "TEDDY",
"namespaceEmbeddedInLui": false,
"pattern": "^TEDDY_\\d{7}$",
"prefix": "biomodels.teddy",
"sampleId": "TEDDY_0000066",
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},
"n2t": {
"description": "The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.",
"example": "TEDDY_0000066",
"homepage": "http://teddyontology.sourceforge.net/",
"name": "TEDDY through BioPortal",
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"pattern": "^TEDDY_\\d{7}$",
"prefix": "biomodels.teddy",
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},
"ols": {
"description": "TEDDY is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems and Synthetic Biology.",
"download_owl": "file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/teddy-inferred-fixed.owl",
"name": "Terminology for Description of Dynamics",
"prefix": "teddy",
"version": "2014-04-24",
"version.iri": "http://identifiers.org/combine.specifications/teddy.rel-2014-04-24"
},
"pattern": "^\\d+$",
"prefixcommons": {
"alt_uri_formats": [
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"http://biomodels.net/teddy/TEDDY#$1"
],
"bioportal": "1407",
"description": "The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.",
"example": "TEDDY_0000066",
"homepage": "http://teddyontology.sourceforge.net/",
"keywords": [
"ontology"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Terminology for the Description of Dynamics",
"pattern": "^TEDDY_\\d{7}$",
"prefix": "teddy",
"synonyms": [
"biomodels.teddy"
]
},
"publications": [
{
"doi": "10.1038/msb.2011.77",
"pmc": "PMC3261705",
"pubmed": "22027554",
"title": "Controlled vocabularies and semantics in systems biology",
"year": 2011
}
],
"synonyms": [
"teddy"
],
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1"
},
"biomodels.vocabulary": {
"biocontext": {
"prefix": "BIOMODELS.VOCABULARY"
},
"mappings": {
"biocontext": "BIOMODELS.VOCABULARY",
"miriam": "biomodels.vocabulary",
"n2t": "biomodels.vocabulary"
},
"miriam": {
"deprecated": false,
"description": "Vocabulary used in the RDF representation of SBML models.",
"homepage": "http://biomodels.net/rdf/vocabulary.rdf",
"id": "00000514",
"name": "SBML RDF Vocabulary",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z]+$",
"prefix": "biomodels.vocabulary",
"sampleId": "rateRule",
"uri_format": "http://biomodels.net/rdf/vocabulary.rdf#$1"
},
"n2t": {
"description": "Vocabulary used in the RDF representation of SBML models.",
"example": "rateRule",
"homepage": "http://biomodels.net/rdf/vocabulary.rdf",
"name": "Vocabulary via BioModels.net",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z]+$",
"prefix": "biomodels.vocabulary",
"uri_format": "http://biomodels.net/rdf/vocabulary.rdf#$1"
}
},
"bionumbers": {
"biocontext": {
"prefix": "BIONUMBERS"
},
"edam": {
"description": "Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology.",
"name": "BioNumbers",
"obsolete": false,
"prefix": "2660"
},
"mappings": {
"biocontext": "BIONUMBERS",
"edam": "2660",
"miriam": "bionumbers",
"n2t": "bionumbers",
"prefixcommons": "bionumbers"
},
"miriam": {
"deprecated": false,
"description": "BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data.",
"homepage": "https://bionumbers.hms.harvard.edu",
"id": "00000101",
"name": "BioNumbers",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "bionumbers",
"sampleId": "104674",
"uri_format": "https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1"
},
"n2t": {
"description": "BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data.",
"example": "104674",
"homepage": "https://bionumbers.hms.harvard.edu",
"name": "BioNumbers database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "bionumbers",
"uri_format": "https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1"
},
"prefixcommons": {
"description": "BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data.",
"example": "104674",
"homepage": "http://www.bionumbers.hms.harvard.edu/search.aspx",
"name": "The Database of Useful Biological Numbers",
"pattern": "^\\d+$",
"prefix": "bionumbers",
"uri_format": "http://www.bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=$1&ver=1"
}
},
"biopixie": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"mappings": {
"prefixcommons": "biopixie"
},
"prefixcommons": {
"description": "bioPIXIE is a novel system for biological data integration and visualization. It allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate.",
"example": "12",
"homepage": "http://pixie.princeton.edu/pixie/",
"keywords": [
"gene",
"interaction"
],
"name": "biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology",
"pattern": "^\\d+$",
"prefix": "biopixie",
"synonyms": [
"biopixie_mefit"
],
"uri_format": "http://avis.princeton.edu/pixie/viewgraph.php?graphID=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"bioportal": {
"biocontext": {
"prefix": "BIOPORTAL"
},
"example_extras": [
"SEPIO",
"pseudo",
"FBBi"
],
"fairsharing": {
"abbreviation": "BioPortal",
"contact": {
"email": "support@bioontology.org",
"name": "John Graybeal",
"orcid": "0000-0001-6875-5360"
},
"description": "BioPortal is a library of biomedical ontologies and terminologies developed in Web Ontology Language (OWL), Resource Description Framework (RDF)(S), Open Biological and Biomedical Ontologies (OBO) format, and ProtΓ©gΓ© frames and Rich Release Format. BioPortal groups ontologies by domain to aid discoverability and allows users to browse, search and visualize the content of ontologies. BioPortal also provides ontology recommendation, text annotation, ontology mapping, and a reference index to resources like PubMed.",
"homepage": "http://bioportal.bioontology.org/",
"name": "BioPortal",
"prefix": "FAIRsharing.4m97ah",
"publications": [
{
"doi": "10.1093/nar/gkr469",
"pubmed_id": 21672956,
"title": "BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications."
}
],
"repository": "http://github.com/ncbo",
"subjects": [
"Life Science",
"Ontology and Terminology"
],
"twitter": "bioontology"
},
"integbio": {
"description": "BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in Web Ontology Language (OWL), Resource Description Framework (RDF)(S), Open Biological and Biomedical Ontologies (OBO) format, and ProtΓ©gΓ© frames and Rich Release Format. BioPortal has a service-oriented architecture; the NCBO Web services provide the functionality found in BioPortal and these Web services can be incorporated into other software applications to access and use ontology content. BioPortal groups ontologies by domain to ease finding relevant ontologies and allows users to browse, search and visualize the content of ontologies. BioPortal also provides value-added features like ontology recommendation, text annotation, ontology mapping, and a reference index to resources like PubMed.",
"fairsharing": "FAIRsharing.4m97ah",
"homepage": "http://bioportal.bioontology.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Bibliography/Documents",
"Portal"
],
"maintainer": "Stanford Center for Biomedical Informatics Research",
"name": "BioPortal",
"prefix": "nbdc02144",
"pubmeds": [
"21672956"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"mappings": {
"biocontext": "BIOPORTAL",
"fairsharing": "FAIRsharing.4m97ah",
"integbio": "nbdc02144",
"miriam": "bioportal",
"n2t": "bioportal",
"prefixcommons": "bioportal",
"re3data": "r3d100012344"
},
"miriam": {
"deprecated": false,
"description": "BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and ProtΓ©gΓ© frames. BioPortal functionality includes the ability to browse, search and visualize ontologies.",
"homepage": "http://bioportal.bioontology.org/",
"id": "00000187",
"name": "BioPortal",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "bioportal",
"sampleId": "1046",
"uri_format": "http://bioportal.bioontology.org/ontologies/$1"
},
"n2t": {
"description": "BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies.",
"example": "1046",
"homepage": "http://bioportal.bioontology.org/",
"name": "BioPortal at National Center for Biomedical Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "bioportal",
"uri_format": "http://bioportal.bioontology.org/ontologies/$1"
},
"pattern": "^(\\d+)|(\\w+)$",
"prefixcommons": {
"description": "BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protege frames. BioPortal functionality includes the ability to browse, search and visualize ontologies.",
"example": "1046",
"homepage": "http://bioportal.bioontology.org/",
"keywords": [
"ontology"
],
"name": "BioPortal",
"pattern": "^\\d+$",
"prefix": "bioportal",
"pubmed_ids": [
"19483092"
],
"uri_format": "http://bioportal.bioontology.org/ontologies/$1"
},
"publications": [
{
"doi": "10.1093/nar/gkr469",
"pmc": "PMC3125807",
"pubmed": "21672956",
"title": "BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications",
"year": 2011
},
{
"doi": "10.1093/nar/gkp440",
"pmc": "PMC2703982",
"pubmed": "19483092",
"title": "BioPortal: ontologies and integrated data resources at the click of a mouse",
"year": 2009
}
],
"re3data": {
"description": "BioPortal is an open repository of biomedical ontologies, a service that provides access to those ontologies, and a set of tools for working with them. BioPortal provides a wide range of such tools, either directly via the BioPortal web site, or using the BioPortal web service REST API. BioPortal also includes community features for adding notes, reviews, and even mappings to specific ontologies.\nBioPortal has four major product components: the web application; the API services; widgets, or applets, that can be installed on your own site; and a Virtual Appliance version that is available for download or through Amazon Web Services machine instance (AMI). There is also a beta release SPARQL endpoint.",
"homepage": "https://bioportal.bioontology.org/",
"name": "BioPortal",
"prefix": "r3d100012344",
"xrefs": {
"fairsharing": "FAIRsharing.4m97ah",
"miriam": "00000187",
"nif": "0000-23346",
"scr": "002713"
}
}
},
"bioproject": {
"biocontext": {
"prefix": "BIOPROJECT"
},
"contact": {
"email": "mizrachi@ncbi.nlm.nih.gov",
"name": "Ilene Karsch-Mizrachi",
"orcid": "0000-0002-0289-7101"
},
"fairsharing": {
"abbreviation": "BioProject",
"description": "A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. The BioProject database is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms.",
"homepage": "https://www.ncbi.nlm.nih.gov/bioproject/",
"name": "NCBI BioProject",
"prefix": "FAIRsharing.aqhv1y",
"publications": [
{
"doi": "10.1093/nar/gkr1163",
"pubmed_id": 22139929,
"title": "BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata."
}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"biocontext": "BIOPROJECT",
"fairsharing": "FAIRsharing.aqhv1y",
"miriam": "bioproject",
"n2t": "bioproject",
"re3data": "r3d100013330",
"togoid": "Bioproject"
},
"miriam": {
"deprecated": false,
"description": "BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a projectβs scope, material, objectives, funding source and general relevance categories.",
"homepage": "https://www.ncbi.nlm.nih.gov/bioproject",
"id": "00000349",
"name": "BioProject",
"namespaceEmbeddedInLui": false,
"pattern": "^PRJ[DEN][A-Z]\\d+$",
"prefix": "bioproject",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "BioProject at DNA Data Bank of Japan",
"homepage": "http://trace.ddbj.nig.ac.jp/bioproject/",
"name": "BioProject at DNA Data Bank of Japan",
"uri_format": "http://trace.ddbj.nig.ac.jp/BPSearch/bioproject?acc=$1"
}
],
"sampleId": "PRJDB3",
"uri_format": "https://www.ncbi.nlm.nih.gov/bioproject?term=$1"
},
"n2t": {
"description": "BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories.",
"example": "PRJDB3",
"homepage": "https://www.ncbi.nlm.nih.gov/bioproject",
"name": "BioProject at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^PRJ[DEN][A-Z]\\d+$",
"prefix": "bioproject",
"uri_format": "https://www.ncbi.nlm.nih.gov/bioproject?term=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkr1163",
"pmc": "PMC3245069",
"pubmed": "22139929",
"title": "BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata",
"year": 2011
}
],
"re3data": {
"description": "The BioProject database is a searcheable collection of complete and incomplete (in-progress) large-scale molecular projects including genome sequencing and assembly, transcriptome, metagenomic, annotation, expression and mapping projects. BioProject provides a central point to link to all data associated with a project in the NCBI molecular and literature databases.",
"homepage": "https://www.ncbi.nlm.nih.gov/bioproject/",
"name": "BioProject",
"prefix": "r3d100013330",
"xrefs": {
"fairsharing": "FAIRsharing.aqhv1y",
"nlx": "143909",
"scr": "004801"
}
},
"togoid": {
"catalog": "nbdc00476",
"examples": [
"PRJDB575",
"PRJDB1880",
"PRJDB478",
"PRJDA45949",
"PRJEB6285",
"PRJEA28961",
"PRJEB2222",
"PRJNA30641",
"PRJNA68235",
"PRJNA42549"
],
"keywords": [
"Project"
],
"name": "BioProject",
"pattern": "^(?PRJ[DEN][A-Z]\\d+)$",
"prefix": "Bioproject",
"uri_format": "http://identifiers.org/bioproject/$1"
},
"uri_format": "https://www.ncbi.nlm.nih.gov/bioproject/?term=$1"
},
"bioregistry": {
"contact": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database.",
"example": "bioregistry",
"fairsharing": {
"abbreviation": "bioregistry",
"contact": {
"email": "cthoyt@gmail.com",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Bioregistry is an open source, community curated registry, meta-registry, and compact identifier resolver.",
"homepage": "https://bioregistry.io",
"license": "CC0-1.0",
"name": "Bioregistry",
"prefix": "FAIRsharing.250a8c",
"publications": [
{
"doi": "10.1101/2022.07.08.499378",
"pubmed_id": null,
"title": "Unifying the Identification of Biomedical Entities with the Bioregistry"
}
],
"repository": "https://github.com/biopragmatics/bioregistry",
"subjects": [
"Cheminformatics",
"Bioinformatics",
"Computational Biology",
"Life Science",
"Ontology and Terminology",
"Computational Chemistry"
],
"twitter": "bioregistry"
},
"homepage": "https://bioregistry.io",
"mappings": {
"bartoc": "18951",
"fairsharing": "FAIRsharing.250a8c"
},
"mastodon": "bioregistry@fosstodon.org",
"name": "Bioregistry",
"publications": [
{
"doi": "10.1101/2022.07.08.499378",
"title": "Unifying the Identification of Biomedical Entities with the Bioregistry",
"year": 2022
}
],
"repository": "https://github.com/biopragmatics/bioregistry",
"uri_format": "https://bioregistry.io/registry/$1"
},
"bioregistry.collection": {
"contact": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Manually curated collections of resources stored in the bioregistry",
"example": "0000001",
"homepage": "https://bioregistry.io/collection",
"keywords": [
"registry"
],
"name": "Bioregistry Collections",
"pattern": "^\\d{7}$",
"uri_format": "https://bioregistry.io/collection/$1"
},
"bioregistry.registry": {
"contact": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Bioregistry's meta-registry",
"example": "miriam",
"homepage": "https://bioregistry.io/metaregistry/",
"keywords": [
"data integration",
"data science",
"metaregistry",
"registry"
],
"name": "Bioregistry Metaregistry",
"uri_format": "https://bioregistry.io/metaregistry/$1"
},
"bioregistry.schema": {
"contact": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Schema for the export of the Bioregistry as RDF",
"example": "0000001",
"homepage": "https://bioregistry.io/schema",
"keywords": [
"registry"
],
"name": "Bioregistry Schema",
"pattern": "^\\d{7}$",
"uri_format": "https://bioregistry.io/schema/#$1"
},
"biorxiv": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The bioRxiv is a preprint server for biology",
"example": "2022.07.08.499378",
"example_extras": [
"000091",
"000091v1",
"2022.07.08.499378v2"
],
"go": {
"homepage": "https://www.biorxiv.org/",
"name": "bioRxiv",
"prefix": "bioRxiv",
"synonyms": [
"BIORXIV"
],
"uri_format": "https://www.biorxiv.org/content/$1"
},
"homepage": "https://biorxiv.org",
"keywords": [
"preprints",
"publishing"
],
"mappings": {
"go": "bioRxiv",
"wikidata": "P3951"
},
"name": "bioRxiv",
"pattern": "^(\\d{4}\\.\\d{2}\\.\\d{2}\\.)?\\d{6,8}(v\\d{1,3})?$",
"providers": [
{
"code": "scholia",
"description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.",
"homepage": "https://scholia.toolforge.org/",
"name": "Scholia",
"uri_format": "https://scholia.toolforge.org/biorxiv/$1"
}
],
"uri_format": "https://www.biorxiv.org/content/10.1101/$1",
"wikidata": {
"description": "identifier of a document in BioRxiv, a preprint repository for the biological sciences launched in November 2013",
"example": [
"028522",
"2021.09.10.459803"
],
"homepage": "http://biorxiv.org/search/limit_from:2010-01-01%20limit_to:2017-02-16%20numresults:10%20sort:relevance-rank%20format_result:standard",
"name": "BioRxiv ID",
"pattern": "^(\\d{4}\\.\\d{2}\\.\\d{2}\\.)?\\d{6}$",
"prefix": "P3951",
"uri_format": "https://doi.org/10.1101/$1",
"uri_format_rdf": "http://dx.doi.org/10.1101/$1"
}
},
"biosample": {
"biocontext": {
"prefix": "BIOSAMPLE"
},
"cellosaurus": {
"category": "Biological sample resources",
"homepage": "https://www.ebi.ac.uk/biosamples/",
"name": "BioSamples database",
"prefix": "BioSamples",
"uri_format": "https://www.ebi.ac.uk/biosamples/samples/$1"
},
"contact": {
"email": "mizrachi@ncbi.nlm.nih.gov",
"name": "Ilene Karsch-Mizrachi",
"orcid": "0000-0002-0289-7101"
},
"fairsharing": {
"abbreviation": "BioSample",
"description": "The NCBI BioSample database stores submitter-supplied descriptive information, or metadata, about the biological materials from which data stored in NCBIβs primary data archives are derived. NCBIβs archives host data from diverse types of samples from any species, so the BioSample database is similarly diverse; typical examples of a BioSample include a cell line, a primary tissue biopsy, an individual organism or an environmental isolate. The BioSample database promotes the use of structured and consistent attribute names and values that describe what the samples are as well as information about their provenance, where appropriate.",
"homepage": "https://www.ncbi.nlm.nih.gov/biosample",
"name": "NCBI BioSample",
"prefix": "FAIRsharing.qr6pqk",
"publications": [
{
"doi": "10.1093/nar/gkr1163",
"pubmed_id": 22139929,
"title": "BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata."
}
],
"subjects": [
"Biology"
]
},
"mappings": {
"biocontext": "BIOSAMPLE",
"cellosaurus": "BioSamples",
"fairsharing": "FAIRsharing.qr6pqk",
"miriam": "biosample",
"n2t": "biosample",
"re3data": "r3d100012828",
"rrid": "SAMN",
"togoid": "Biosample"
},
"miriam": {
"deprecated": false,
"description": "The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation.",
"homepage": "https://www.ebi.ac.uk/biosamples/",
"id": "00000350",
"name": "BioSample",
"namespaceEmbeddedInLui": false,
"pattern": "^SAM[NED](\\w)?\\d+$",
"prefix": "biosample",
"providers": [
{
"code": "ncbi",
"description": "BioSample at NCBI",
"homepage": "http://www.ncbi.nlm.nih.gov/biosample",
"name": "BioSample at NCBI",
"uri_format": "http://www.ncbi.nlm.nih.gov/biosample?term=$1"
},
{
"code": "ddbj",
"description": "BioSample at DNA Data Bank of Japan",
"homepage": "http://trace.ddbj.nig.ac.jp/biosample/",
"name": "BioSample at DNA Data Bank of Japan",
"uri_format": "http://trace.ddbj.nig.ac.jp/BSSearch/biosample?acc=$1"
}
],
"sampleId": "SAMEA2397676",
"uri_format": "https://www.ebi.ac.uk/biosamples/sample/$1"
},
"n2t": {
"description": "The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation.",
"example": "SAMEA2397676",
"homepage": "https://www.ebi.ac.uk/biosamples/",
"name": "BioSamples Database at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^SAM[NED](\\w)?\\d+$",
"prefix": "biosample",
"uri_format": "https://www.ebi.ac.uk/biosamples/sample/$1"
},
"publications": [
{
"doi": "10.1093/nar/gkr1163",
"pmc": "PMC3245069",
"pubmed": "22139929",
"title": "BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata",
"year": 2011
}
],
"re3data": {
"description": "The BioSample database contains descriptions of biological source materials used in experimental assays.",
"homepage": "https://www.ncbi.nlm.nih.gov/biosample/",
"name": "BioSample",
"prefix": "r3d100012828",
"synonyms": [
"BioSample at the NCBI"
],
"xrefs": {
"fairsharing": "FAIRsharing.qr6pqk",
"nlx": "143929",
"scr": "004854"
}
},
"rrid": {
"abbreviation": "BioSample",
"homepage": "http://www.ncbi.nlm.nih.gov/biosample",
"keywords": [
"biomaterial",
"cell",
"cell line",
"dna",
"gold standard",
"rna",
"stem cell"
],
"name": "NCBI BioSample",
"prefix": "SAMN",
"pubmeds": [
"22139929"
],
"scr": "004854"
},
"synonyms": [
"biosamples"
],
"togoid": {
"catalog": "nbdc01983",
"examples": [
"SAMD00003683",
"SAMD00006315",
"SAMD00003741",
"SAMD00011226",
"SAMN13091859",
"SAMN05877962",
"SAMN05877838",
"SAMEA104232303",
"SAMEA4760552",
"SAMEA1572228"
],
"keywords": [
"Sample"
],
"name": "BioSample",
"pattern": "^(?SAM[NED]\\w?\\d+)$",
"prefix": "Biosample",
"uri_format": "http://identifiers.org/biosample/$1"
}
},
"bioschemas": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "bioschemas",
"uri_format": "https://bioschemas.org/$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. It does this by encouraging people in the life sciences to use Schema.org markup in their websites so that they are indexable by search engines and other services. Bioschemas encourages the consistent use of markup to ease the consumption of the contained markup across many sites. This structured information then makes it easier to discover, collate, and analyse distributed resources. [from BioSchemas.org]",
"example": "Dataset",
"homepage": "https://bioschemas.org",
"mappings": {
"biolink": "bioschemas"
},
"name": "BioSchemas",
"repository": "https://github.com/BioSchemas/specifications",
"synonyms": [
"bioschema"
],
"twitter": "bioschemas",
"uri_format": "https://bioschemas.org/profiles/$1"
},
"biosimulations": {
"mappings": {
"miriam": "biosimulations",
"re3data": "r3d100013361"
},
"miriam": {
"deprecated": false,
"description": "BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools.",
"homepage": "https://icahn.mssm.edu/",
"id": "00000880",
"name": "biosimulations",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-zA-Z0-9_-]{3,}$",
"prefix": "biosimulations",
"sampleId": "Yeast-cell-cycle-Irons-J-Theor-Biol-2009",
"uri_format": "https://biosimulations.org/projects/$1"
},
"re3data": {
"description": "BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and simulation tools (e.g., COPASI, libRoadRunner/tellurium, NFSim, VCell). BioSimulations aims to help researchers discover published models that might be useful for their research and quickly try them via a simple web-based interface.",
"homepage": "https://biosimulations.org/",
"name": "BioSimulations",
"prefix": "r3d100013361",
"xrefs": {
"fairsharing.legacy": "3208",
"scr": "018733"
}
}
},
"biosimulators": {
"fairsharing": {
"abbreviation": "BioSimulators",
"contact": {
"email": "karr@mssm.edu",
"name": "Jonathan Karr",
"orcid": "0000-0002-2605-5080"
},
"description": "BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms, and modeling formats) needed for specific modeling projects.",
"homepage": "https://biosimulators.org",
"name": "BioSimulators",
"prefix": "FAIRsharing.pwEima",
"publications": [],
"repository": "https://github.com/biosimulators/Biosimulators/issues/new/choose",
"subjects": [
"Computational Biology",
"Systems Biology"
]
},
"mappings": {
"fairsharing": "FAIRsharing.pwEima",
"miriam": "biosimulators",
"re3data": "r3d100013432"
},
"miriam": {
"deprecated": false,
"description": "BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML).",
"homepage": "https://biosimulators.org/",
"id": "00000767",
"name": "BioSimulators",
"namespaceEmbeddedInLui": false,
"pattern": "[a-zA-Z0-9-_]+",
"prefix": "biosimulators",
"sampleId": "vcell",
"uri_format": "https://biosimulators.org/simulators/$1"
},
"re3data": {
"description": "BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms, and modeling formats) needed for specific modeling projects.",
"homepage": "https://biosimulators.org",
"name": "BioSimulators",
"prefix": "r3d100013432",
"xrefs": {
"fairsharing": "FAIRsharing.pwEima"
}
}
},
"biostudies": {
"contact": {
"email": "ugis@ebi.ac.uk",
"name": "Ugis Sarkans",
"orcid": "0000-0001-9227-8488"
},
"fairsharing": {
"abbreviation": "BioStudies",
"description": "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.",
"homepage": "https://www.ebi.ac.uk/biostudies/",
"name": "BioStudies",
"prefix": "FAIRsharing.mtjvme",
"publications": [
{
"doi": "10.1093/nar/gkx965",
"pubmed_id": 29069414,
"title": "The BioStudies database-one stop shop for all data supporting a life sciences study."
},
{
"doi": "10.15252/msb.20156658",
"pubmed_id": 26700850,
"title": "The BioStudies database."
}
],
"subjects": [
"Life Science",
"Biomedical Science"
]
},
"integbio": {
"description": "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.",
"fairsharing": "FAIRsharing.mtjvme",
"homepage": "https://www.ebi.ac.uk/biostudies/",
"information_keywords": [
"Portal"
],
"maintainer": "European Commission FP7||EMBL (European Molecular Biology Laboratory)",
"name": "BioStudies",
"prefix": "nbdc02279",
"pubmeds": [
"26700850",
"29069414"
],
"status": "Active"
},
"mappings": {
"fairsharing": "FAIRsharing.mtjvme",
"integbio": "nbdc02279",
"miriam": "biostudies",
"n2t": "biostudies",
"re3data": "r3d100012627"
},
"miriam": {
"deprecated": false,
"description": "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.",
"homepage": "https://www.ebi.ac.uk/biostudies/",
"id": "00000694",
"name": "BioStudies database",
"namespaceEmbeddedInLui": false,
"pattern": "^S-[A-Z]{4}[\\-\\_A-Z\\d]+$",
"prefix": "biostudies",
"sampleId": "S-EPMC6266652",
"uri_format": "https://www.ebi.ac.uk/biostudies/studies/$1"
},
"n2t": {
"description": "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.",
"example": "S-EPMC6266652",
"homepage": "https://www.ebi.ac.uk/biostudies/",
"name": "BioStudies database",
"namespaceEmbeddedInLui": false,
"pattern": "^S-[A-Z]{4}[A-Z\\d\\-]+$",
"prefix": "biostudies",
"uri_format": "https://www.ebi.ac.uk/biostudies/studies/$1"
},
"publications": [
{
"doi": "10.1093/nar/gkx965",
"pmc": "PMC5753238",
"pubmed": "29069414",
"title": "The BioStudies database-one stop shop for all data supporting a life sciences study",
"year": 2018
},
{
"doi": "10.15252/msb.20156658",
"pmc": "PMC4704487",
"pubmed": "26700850",
"title": "The BioStudies database",
"year": 2015
}
],
"re3data": {
"description": "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database accepts submissions via an online tool, or in a simple tab-delimited format. It also enables authors to submit supplementary information and link to it from the publication.",
"homepage": "https://www.ebi.ac.uk/biostudies/",
"name": "BioStudies",
"prefix": "r3d100012627",
"xrefs": {
"fairsharing": "FAIRsharing.mtjvme"
}
}
},
"biosystems": {
"biocontext": {
"prefix": "BIOSYSTEMS"
},
"contact": {
"email": "lewis.geer@nih.gov",
"name": "Aron Marchler-Bauer",
"orcid": "0000-0003-1516-0712"
},
"contributor_extras": [
{
"email": "egon.willighagen@gmail.com",
"github": "egonw",
"name": "Egon Willighagen",
"orcid": "0000-0001-7542-0286"
}
],
"fairsharing": {
"abbreviation": "BioSystems",
"description": "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. The resource provides categorical information on genes, proteins and small molecules of biosystems.",
"homepage": "https://www.ncbi.nlm.nih.gov/biosystems/",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "NCBI BioSystems Database",
"prefix": "FAIRsharing.w2eeqr",
"publications": [
{
"doi": "10.1093/nar/gkp858",
"pubmed_id": 19854944,
"title": "The NCBI BioSystems database."
}
],
"subjects": [
"Biology",
"Systems Biology"
]
},
"homepage": "https://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html",
"integbio": {
"description": "This database is a collection of metabolic and signaling pathways in organisms, as well as interaction sets between biological molecules associated with disease and other biological processes. Each entry contains information including pathway maps, relevant citations, genes, proteins sequences, and data on compounds.",
"fairsharing": "biodbcore-000430",
"homepage": "http://www.ncbi.nlm.nih.gov/biosystems/",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "BioSystems",
"prefix": "nbdc00379",
"pubmeds": [
"19854944"
],
"status": "Closed",
"target_keywords": [
"Protein",
"Health/Disease",
"Metabolite",
"Cell/Organelle"
]
},
"mappings": {
"biocontext": "BIOSYSTEMS",
"fairsharing": "FAIRsharing.w2eeqr",
"integbio": "nbdc00379",
"miriam": "biosystems",
"n2t": "biosystems",
"prefixcommons": "biosystems",
"re3data": "r3d100011033"
},
"miriam": {
"deprecated": false,
"description": "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources.",
"homepage": "https://www.ncbi.nlm.nih.gov/biosystems/",
"id": "00000097",
"name": "BioSystems",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "biosystems",
"sampleId": "001",
"uri_format": "https://www.ncbi.nlm.nih.gov/biosystems/$1"
},
"n2t": {
"description": "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources.",
"example": "001",
"homepage": "https://www.ncbi.nlm.nih.gov/biosystems/",
"name": "BioSystems database at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "biosystems",
"uri_format": "https://www.ncbi.nlm.nih.gov/biosystems/$1"
},
"prefixcommons": {
"description": "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources.",
"example": "1",
"homepage": "http://www.ncbi.nlm.nih.gov/biosystems/",
"keywords": [
"molecules",
"pathways"
],
"license": "http://www.nlm.nih.gov/copyright.html",
"name": "BioSystems",
"pattern": "^\\d+$",
"prefix": "biosystems",
"pubmed_ids": [
"19854944"
],
"synonyms": [
"bsid"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/biosystems/$1"
},
"publications": [
{
"doi": "10.1093/nar/gkp858",
"pmc": "PMC2808896",
"pubmed": "19854944",
"title": "The NCBI BioSystems database",
"year": 2009
}
],
"re3data": {
"description": "<<>>!!!>>>\nThis retirement includes the representation of BioSystems records in the NCBI Entrez system and viewers of BioSystems content. \nNCBI now provides metabolic pathway and other biosystems data through the regularly updated PubChem Pathways resource (https://pubchemdocs.ncbi.nlm.nih.gov/pathways) that offers a fresh, extended, and more modern interface.",
"homepage": "https://www.ncbi.nlm.nih.gov/biosystems/",
"name": "NCBI BioSystems Database",
"prefix": "r3d100011033",
"synonyms": [
"NCBI BioSystems"
],
"xrefs": {
"fairsharing": "FAIRsharing.w2eeqr",
"miriam": "00000097",
"nlx": "69646",
"scr": "004690"
}
}
},
"biotools": {
"biocontext": {
"prefix": "BIOTOOLS"
},
"contact": {
"email": "haiiu@dtu.dk",
"github": "hansioan",
"name": "Hans Ienasescu",
"orcid": "0000-0001-9727-2544"
},
"description": "BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research.",
"example": "bioregistry",
"fairsharing": {
"abbreviation": "bio.tools",
"description": "bio.tools is a registry of information about bioinformatics software and data services. It was created to help researchers in biological and biomedical science to find and use such resources.",
"homepage": "https://bio.tools/",
"license": "CC-BY-4.0",
"name": "bio.tools",
"prefix": "FAIRsharing.63520c",
"publications": [
{
"doi": "10.1093/nar/gkv1116",
"pubmed_id": 26538599,
"title": "Tools and data services registry: a community effort to document bioinformatics resources."
}
],
"repository": "http://github.com/bio-tools/biotoolsregistry/",
"subjects": [
"Bioinformatics",
"Biomedical Science",
"Biology"
]
},
"mappings": {
"biocontext": "BIOTOOLS",
"fairsharing": "FAIRsharing.63520c",
"miriam": "biotools",
"n2t": "biotools",
"re3data": "r3d100013668"
},
"miriam": {
"deprecated": false,
"description": "Tool and data services registry.",
"homepage": "https://bio.tools/",
"id": "00000616",
"name": "BioTools",
"namespaceEmbeddedInLui": false,
"pattern": "^[-A-Za-z0-9\\_]*$",
"prefix": "biotools",
"sampleId": "uniprotkb",
"uri_format": "https://bio.tools/$1"
},
"n2t": {
"description": "Tool and data services registry.",
"example": "uniprotkb",
"homepage": "https://bio.tools/",
"name": "BioTools",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9\\_]*$",
"prefix": "biotools",
"uri_format": "https://bio.tools/$1"
},
"pattern": "^[-A-Za-z0-9\\_]*$",
"publications": [
{
"doi": "10.1093/nar/gkv1116",
"pmc": "PMC4702812",
"pubmed": "26538599",
"title": "Tools and data services registry: a community effort to document bioinformatics resources",
"year": 2015
}
],
"re3data": {
"description": "bio.tools is a software registry for bioinformatics and the life sciences.",
"homepage": "https://bio.tools",
"name": "bio.tools",
"prefix": "r3d100013668",
"xrefs": {
"biodbcore": "001815"
}
}
},
"biozil": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Redistributor of bilogics and biomedical supplies",
"example": "ls-c35719-120",
"homepage": "https://www.biozol.de/en",
"keywords": [
"biologics",
"life sciences",
"vendor"
],
"name": "BIOZIL",
"uri_format": "https://www.biozol.de/en/product/$1"
},
"birnlex": {
"aberowl": {
"description": "The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design.",
"download_owl": "http://aber-owl.net/media/ontologies/BIRNLEX/1/birnlex.owl",
"homepage": "http://xwiki.nbirn.net:8080/xwiki/bin/view/%20BIRN-OTF-Public/Home",
"name": "Biomedical Informatics Research Network Project Lexicon",
"prefix": "BIRNLEX",
"version": "1.3.1"
},
"bioportal": {
"contact": {
"email": "wbug@ncmir.ucsd.edu",
"name": "William Bug"
},
"description": "The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design.",
"homepage": "http://xwiki.nbirn.net:8080/xwiki/bin/view/%20BIRN-OTF-Public/Home",
"name": "Biomedical Informatics Research Network Project Lexicon",
"prefix": "BIRNLEX",
"version": "1.3.1"
},
"comment": "Part of the NeuroLex namespace now",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design.",
"example": "2023",
"fairsharing": {
"abbreviation": "BIRNLEX",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Study design",
"Disease"
],
"homepage": "http://xwiki.nbirn.net:8080/xwiki/bin/view/%20BIRN-OTF-Public/Home",
"name": "Biomedical Informatics Research Network Project Lexicon",
"prefix": "FAIRsharing.jedbbt",
"subjects": [
"Anatomy",
"Biomedical Science"
]
},
"homepage": "https://bioportal.bioontology.org/ontologies/BIRNLEX",
"mappings": {
"aberowl": "BIRNLEX",
"bioportal": "BIRNLEX",
"fairsharing": "FAIRsharing.jedbbt"
},
"name": "Biomedical Informatics Research Network Lexicon",
"pattern": "^\\d+$",
"uri_format": "http://uri.neuinfo.org/nif/nifstd/birnlex_$1"
},
"biro": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively.",
"example": "BibliographicRecord",
"fairsharing": {
"abbreviation": "BiRO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "the Bibliographic Reference Ontology (BiRO) is an ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively.\n\n",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/biro",
"license": "CC-BY-4.0",
"name": "Bibliographic Reference Ontology ",
"prefix": "FAIRsharing.99da5f",
"repository": "https://github.com/sparontologies/biro",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"homepage": "http://www.sparontologies.net/ontologies/biro",
"lov": {
"description": "BiRO, the Bibliographic Reference Ontology, is an ontology structured according to the FRBR model to define bibliographic records (as subclasses of frbr:Work) and bibliographic references (as subclasses of frbr:Expression), and their compilations into bibliographic collections such as library catalogues, and into bibliographic lists such as reference lists in journal articles, respectively.",
"homepage": "http://purl.org/spar/biro",
"keywords": [
"SPAR"
],
"modified": "2013-05-11",
"name": "The Bibliographic Reference Ontology",
"prefix": "biro",
"uri_prefix": "http://purl.org/spar/biro/$1"
},
"mappings": {
"fairsharing": "FAIRsharing.99da5f",
"lov": "biro"
},
"name": "Bibliographic Reference Ontology",
"preferred_prefix": "BiRO",
"repository": "https://github.com/sparontologies/biro",
"uri_format": "http://purl.org/spar/biro/$1"
},
"bitbucket": {
"fairsharing": {
"abbreviation": "Bitbucket",
"description": "Bitbucket is a Git-based source code repository hosting service owned by Atlassian. It provides a number of different access levels, from free through to premium paid services. Users can create public or private repositories, the latter of which is restricted to 5 users under the free plan.",
"homepage": "https://bitbucket.org/",
"name": "Bitbucket",
"prefix": "FAIRsharing.fc3431",
"publications": [],
"subjects": [
"Knowledge and Information Systems",
"Subject Agnostic",
"Software Engineering"
]
},
"mappings": {
"fairsharing": "FAIRsharing.fc3431",
"miriam": "bitbucket",
"re3data": "r3d100013478"
},
"miriam": {
"deprecated": false,
"description": "Bitbucket is a Git-based source code repository hosting service owned by Atlassian.",
"homepage": "https://www.atlassian.com/",
"id": "00000899",
"name": "Bitbucket",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9A-Za-z-_\\.]+/[0-9A-Za-z-_\\.]+$",
"prefix": "bitbucket",
"sampleId": "andreadega/systems-biology-compiler",
"uri_format": "https://bitbucket.org/$1"
},
"re3data": {
"description": "Bitbucket is a web-based version control repository hosting service owned by Atlassian, for source code and development projects that use either Mercurial or Git revision control systems.",
"homepage": "https://bitbucket.org/",
"name": "Bitbucket",
"prefix": "r3d100013478",
"synonyms": [
"Atlassian Bitbucket"
],
"xrefs": {
"fairsharing": "FAIRsharing.fc3431",
"nlx": "158615",
"scr": "000502"
}
}
},
"bitterdb.cpd": {
"biocontext": {
"prefix": "BITTERDB.CPD"
},
"mappings": {
"biocontext": "BITTERDB.CPD",
"miriam": "bitterdb.cpd",
"n2t": "bitterdb.cpd"
},
"miriam": {
"deprecated": false,
"description": "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds.",
"homepage": "http://bitterdb.agri.huji.ac.il/dbbitter.php",
"id": "00000348",
"name": "BitterDB Compound",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "bitterdb.cpd",
"sampleId": "46",
"uri_format": "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1"
},
"n2t": {
"description": "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds.",
"example": "46",
"homepage": "http://bitterdb.agri.huji.ac.il/dbbitter.php",
"name": "BitterDB Compound at The Hebrew University of Jerusalem",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "bitterdb.cpd",
"uri_format": "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1"
}
},
"bitterdb.rec": {
"biocontext": {
"prefix": "BITTERDB.REC"
},
"mappings": {
"biocontext": "BITTERDB.REC",
"miriam": "bitterdb.rec",
"n2t": "bitterdb.rec"
},
"miriam": {
"deprecated": false,
"description": "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors.",
"homepage": "http://bitterdb.agri.huji.ac.il/dbbitter.php",
"id": "00000347",
"name": "BitterDB Receptor",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "bitterdb.rec",
"sampleId": "1",
"uri_format": "http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1"
},
"n2t": {
"description": "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors.",
"example": "1",
"homepage": "http://bitterdb.agri.huji.ac.il/dbbitter.php",
"name": "BitterDB Receptor at The Hebrew University of Jerusalem",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "bitterdb.rec",
"uri_format": "http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1"
}
},
"bko": {
"aberowl": {
"description": "The BricKs Ontology (BKO) provides Systems Biology Graphical Notation representations of recurring concepts in molecular networks. These representations, called bricks, are associated in the ontology with terms describing the concepts. Part of these terms are borrowed from the Gene Ontology and the Systems Biology Ontology. The bricks can be used for both the template-based construction of molecular networks maps as well as for their annotation.",
"download_owl": "http://aber-owl.net/media/ontologies/BKO/1/bko.owl",
"homepage": "http://sbgnbricks.org",
"name": "Bricks ontology",
"prefix": "BKO",
"version": "13:07:2018 10:45"
},
"bioportal": {
"contact": {
"email": "adrienrougny@gmail.com",
"name": "Adrien Rougny"
},
"description": "The BricKs Ontology (BKO) provides Systems Biology Graphical Notation representations of recurring concepts in molecular networks. These representations, called bricks, are associated in the ontology with terms describing the concepts. Part of these terms are borrowed from the Gene Ontology and the Systems Biology Ontology. The bricks can be used for both the template-based construction of molecular networks maps as well as for their annotation.",
"homepage": "http://sbgnbricks.org",
"name": "Bricks ontology",
"prefix": "BKO",
"version": "13:07:2018 10:45"
},
"comment": "This resource also uses SBO terms and resolves them, e.g., http://www.sbgnbricks.org/BKO/full/entry/all/SBO:0000177/.",
"contact": {
"email": "adrienrougny@gmail.com",
"github": "adrienrougny",
"name": "Adrien Rougny",
"orcid": "0000-0002-2118-035X"
},
"contributor": {
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"description": "SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way.",
"example": "0000204",
"github_request_issue": 283,
"homepage": "http://www.sbgnbricks.org/",
"mappings": {
"aberowl": "BKO",
"bioportal": "BKO"
},
"name": "SBGN Bricks data and ontology",
"pattern": "^\\d+$",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1"
},
"bmrb": {
"contact": {
"email": "markley@nmrfam.wisc.edu",
"name": "John L. Markley",
"orcid": "0000-0003-1799-6134"
},
"fairsharing": {
"abbreviation": "BMRB",
"description": "BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. Its goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy.",
"homepage": "https://bmrb.io/",
"license": "CC0-1.0",
"name": "Biological Magnetic Resonance Data Bank",
"prefix": "FAIRsharing.p06nme",
"publications": [
{
"doi": "10.1007/s10858-008-9221-y",
"pubmed_id": 18288446,
"title": "BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions."
},
{
"doi": "10.1093/nar/gkm957",
"pubmed_id": 17984079,
"title": "BioMagResBank."
}
],
"subjects": [
"Structural Biology"
]
},
"integbio": {
"alt_name": "Biological Magnetic Resonance Data Bank",
"description": "BMRB is a database of biomolecular magnetic resonance data. Proteins, peptides, and nucleic acids, and other molecules are represented in NMR and PDB data form. Several search functions are supported and users can upload or download data.",
"fairsharing": "biodbcore-000584",
"homepage": "http://www.bmrb.wisc.edu/",
"information_keywords": [
"3D structure",
"Repository"
],
"maintainer": "University of Wisconsin System Board of Regents",
"name": "BMRB",
"prefix": "nbdc00380",
"pubmeds": [
"17984079"
],
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Protein"
]
},
"mappings": {
"fairsharing": "FAIRsharing.p06nme",
"integbio": "nbdc00380",
"miriam": "bmrb",
"re3data": "r3d100010191",
"uniprot": "DB-0256"
},
"miriam": {
"deprecated": false,
"description": "BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy.",
"homepage": "http://www.bmrb.wisc.edu/",
"id": "00000716",
"name": "Biological Magnetic Resonance Data Bank",
"namespaceEmbeddedInLui": false,
"pattern": "^(bmr|bmse|bmst)?[0-9]{1,6}$",
"prefix": "bmrb",
"sampleId": "15000",
"uri_format": "http://rest.bmrb.wisc.edu/bmrb/$1/html"
},
"publications": [
{
"doi": "10.1007/s10858-008-9221-y",
"pmc": "PMC2268728",
"pubmed": "18288446",
"title": "BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions",
"year": 2008
},
{
"doi": "10.1093/nar/gkm957",
"pmc": "PMC2238925",
"pubmed": "17984079",
"title": "BioMagResBank",
"year": 2007
}
],
"re3data": {
"description": "BioMagResBank (BMRB) is the publicly-accessible depository for NMR results from peptides, proteins, and nucleic acids recognized by the International Society of Magnetic Resonance and by the IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy. In addition, BMRB provides reference information and maintains a collection of NMR pulse sequences and computer software for biomolecular NMR",
"homepage": "https://bmrb.io/",
"name": "Biological Magnetic Resonance Data Bank",
"prefix": "r3d100010191",
"synonyms": [
"BMRB",
"BioMagResBank",
"Biological Magnetic Resonance Databank"
],
"xrefs": {
"fairsharing": "FAIRsharing.p06nme",
"nif": "0000-21058",
"omics": "02858",
"scr": "002296"
}
},
"uniprot": {
"abbreviation": "BMRB",
"category": "3D structure databases",
"homepage": "https://bmrb.io/",
"name": "Biological Magnetic Resonance Data Bank",
"prefix": "DB-0256",
"publications": [
{
"doi": "10.1093/nar/gkm957",
"pubmed": "17984079"
}
],
"uri_format": "https://bmrb.io/data_library/summary/protein.php?uniprot=$1"
}
},
"bmrb.restraint": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively.",
"example": "28789",
"homepage": "https://restraintsgrid.bmrb.io/NRG/MRGridServlet",
"keywords": [
"chemistry",
"nmr",
"spectrometry"
],
"name": "NMR Restraints Grid",
"pattern": "^\\d+$",
"uri_format": "https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1"
},
"bold.taxonomy": {
"biocontext": {
"prefix": "BOLD.TAXONOMY"
},
"contact": {
"email": "phebert@uoguelph.ca",
"name": "Paul David Neil Hebert",
"orcid": "0000-0002-3081-6700"
},
"mappings": {
"biocontext": "BOLD.TAXONOMY",
"miriam": "bold.taxonomy",
"n2t": "bold.taxonomy",
"ncbi": "BOLD",
"prefixcommons": "bold",
"wikidata": "P3606"
},
"miriam": {
"deprecated": false,
"description": "The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information.",
"homepage": "http://www.boldsystems.org/",
"id": "00000158",
"name": "BOLD Taxonomy",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "bold.taxonomy",
"sampleId": "27267",
"uri_format": "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1"
},
"n2t": {
"description": "The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information.",
"example": "27267",
"homepage": "http://www.boldsystems.org/",
"name": "BOLD taxonomy browser",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "bold.taxonomy",
"uri_format": "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1"
},
"name": "BOLD Systems taxon",
"ncbi": {
"example": "EPAF263",
"homepage": "http://www.barcodinglife.com",
"name": "Barcode of Life database",
"prefix": "BOLD"
},
"prefixcommons": {
"description": "The Barcode of Life Data Systems (BOLD) is an online workbench that aids collection, management, analysis, and use of DNA barcodes. It consists of 3 components (MAS, IDS, and ECS) that each address the needs of various groups in the barcoding community.",
"example": "27267",
"homepage": "http://www.barcodinglife.com",
"keywords": [
"DNA"
],
"name": "The Barcode of Life Data Systems",
"pattern": "^\\d+$",
"prefix": "bold",
"pubmed_ids": [
"18784790"
],
"synonyms": [
"bold.taxonomy"
],
"uri_format": "http://www.barcodinglife.com/views/taxbrowser.php?taxid=$1"
},
"publications": [
{
"doi": "10.1111/j.1471-8286.2007.01678.x",
"pmc": "PMC1890991",
"pubmed": "18784790",
"title": "bold: The Barcode of Life Data System (http://www.barcodinglife.org)",
"year": 2007
}
],
"wikidata": {
"description": "identifier for a taxon in boldsystems.org",
"example": [
"286001",
"38074"
],
"name": "BOLD Systems taxon ID",
"prefix": "P3606",
"uri_format": "http://www.boldsystems.org/index.php/TaxBrowser_TaxonPage?taxid=$1"
}
},
"bootstrep": {
"biocontext": {
"prefix": "BOOTSTREP"
},
"mappings": {
"biocontext": "BOOTSTREP",
"obofoundry": "bootstrep"
},
"obofoundry": {
"contact": "vlee@ebi.ac.uk",
"contact.label": "Vivian Lee",
"deprecated": true,
"domain": "chemistry and biochemistry",
"homepage": "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html",
"name": "Gene Regulation Ontology",
"prefix": "bootstrep"
}
},
"bpdb": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Database of biopesticides maintained by the University of Hertfordshire ",
"example": "2404",
"homepage": "https://sitem.herts.ac.uk/aeru/bpdb/index.htm",
"keywords": [
"biology",
"biopesticides",
"pesticides"
],
"name": "Bio-Pesticides DataBase",
"pattern": "^\\d+$",
"uri_format": "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm"
},
"brenda": {
"biocontext": {
"prefix": "BRENDA"
},
"contact": {
"email": "D.Schomburg@tu-braunschweig.de",
"name": "Dietmar Schomburg",
"orcid": "0000-0002-3354-822X"
},
"fairsharing": {
"abbreviation": "BRENDA",
"description": "BRENDA is the main collection of enzyme functional data available to the scientific community.",
"homepage": "https://www.brenda-enzymes.org/",
"license": "CC-BY-4.0",
"name": "BRENDA Enzyme Database",
"prefix": "FAIRsharing.etp533",
"publications": [
{
"doi": "10.1016/S0968-0004(01)02027-8",
"pubmed_id": 11796225,
"title": "BRENDA: a resource for enzyme data and metabolic information."
},
{
"doi": "10.1093/nar/30.1.47",
"pubmed_id": 11752250,
"title": "BRENDA, enzyme data and metabolic information."
},
{
"doi": "10.1093/nar/gkh081",
"pubmed_id": 14681450,
"title": "BRENDA, the enzyme database: updates and major new developments."
},
{
"doi": "10.1016/S1096-7176(03)00008-9",
"pubmed_id": 12850129,
"title": "Review of the BRENDA Database."
},
{
"doi": "10.1093/nar/gku1068",
"pubmed_id": 25378310,
"title": "BRENDA in 2015: exciting developments in its 25th year of existence."
},
{
"doi": "10.1093/nar/gkl972",
"pubmed_id": 17202167,
"title": "BRENDA, AMENDA and FRENDA: the enzyme information system in 2007."
},
{
"doi": "10.1093/nar/gkn820",
"pubmed_id": 18984617,
"title": "BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009."
},
{
"doi": "10.1093/nar/gks1049",
"pubmed_id": 23203881,
"title": "BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA."
},
{
"doi": "10.1093/nar/gkq1089",
"pubmed_id": 21062828,
"title": "BRENDA, the enzyme information system in 2011."
},
{
"doi": "S0168-1656(17)30183-9",
"pubmed_id": 28438579,
"title": "The BRENDA enzyme information system-From a database to an expert system."
}
],
"subjects": [
"Life Science"
]
},
"go": {
"homepage": "http://www.brenda-enzymes.info",
"name": "BRENDA, The Comprehensive Enzyme Information System",
"prefix": "BRENDA",
"uri_format": "https://www.brenda-enzymes.info/enzyme.php?ecno=$1"
},
"mappings": {
"biocontext": "BRENDA",
"fairsharing": "FAIRsharing.etp533",
"go": "BRENDA",
"miriam": "brenda",
"n2t": "brenda",
"pathguide": "51",
"prefixcommons": "brenda",
"re3data": "r3d100010616"
},
"miriam": {
"deprecated": false,
"description": "BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data.",
"homepage": "https://www.brenda-enzymes.org/",
"id": "00000071",
"name": "BRENDA",
"namespaceEmbeddedInLui": false,
"pattern": "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$",
"prefix": "brenda",
"sampleId": "1.1.1.1",
"uri_format": "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1"
},
"n2t": {
"description": "BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data.",
"example": "1.1.1.1",
"homepage": "https://www.brenda-enzymes.org/",
"name": "Brenda enzyme database",
"namespaceEmbeddedInLui": false,
"pattern": "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$",
"prefix": "brenda",
"uri_format": "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1"
},
"name": "BRENDA Enzyme",
"pathguide": {
"abbreviation": "BRENDA",
"homepage": "http://www.brenda-enzymes.info/",
"keywords": [
"SBML"
],
"name": "BRaunschweig ENzyme DAtabase",
"prefix": "51"
},
"prefixcommons": {
"description": "BRENDA is the main collection of enzyme functional data available to the scientific community.",
"example": "1.1.1.1",
"homepage": "http://www.brenda-enzymes.org",
"keywords": [
"enzyme"
],
"license": "http://www.brenda-enzymes.org",
"name": "The Comprehensive Enzyme Information System",
"pattern": "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$",
"prefix": "brenda",
"pubmed_ids": [
"18984617"
],
"uri_format": "http://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1"
},
"provides": "eccode",
"publications": [
{
"doi": "10.1016/j.jbiotec.2017.04.020",
"pubmed": "28438579",
"title": "The BRENDA enzyme information system-From a database to an expert system",
"year": 2017
},
{
"doi": "10.1093/nar/gku1068",
"pmc": "PMC4383907",
"pubmed": "25378310",
"title": "BRENDA in 2015: exciting developments in its 25th year of existence",
"year": 2014
},
{
"doi": "10.1093/nar/gks1049",
"pmc": "PMC3531171",
"pubmed": "23203881",
"title": "BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA",
"year": 2012
},
{
"doi": "10.1093/nar/gkq1089",
"pmc": "PMC3013686",
"pubmed": "21062828",
"title": "BRENDA, the enzyme information system in 2011",
"year": 2010
},
{
"doi": "10.1093/nar/gkn820",
"pmc": "PMC2686525",
"pubmed": "18984617",
"title": "BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009",
"year": 2008
},
{
"doi": "10.1093/nar/gkl972",
"pmc": "PMC1899097",
"pubmed": "17202167",
"title": "BRENDA, AMENDA and FRENDA: the enzyme information system in 2007",
"year": 2007
},
{
"doi": "10.1093/nar/gkh081",
"pmc": "PMC308815",
"pubmed": "14681450",
"title": "BRENDA, the enzyme database: updates and major new developments",
"year": 2004
},
{
"doi": "10.1016/s1096-7176(03)00008-9",
"pubmed": "12850129",
"title": "Review of the BRENDA Database",
"year": 2003
},
{
"doi": "10.1016/s0968-0004(01)02027-8",
"pubmed": "11796225",
"title": "BRENDA: a resource for enzyme data and metabolic information",
"year": 2002
},
{
"doi": "10.1093/nar/30.1.47",
"pmc": "PMC99121",
"pubmed": "11752250",
"title": "BRENDA, enzyme data and metabolic information",
"year": 2002
}
],
"re3data": {
"description": "BRENDA is the main collection of enzyme functional data available to the scientific community worldwide. The enzymes are classified according to the Enzyme Commission list of enzymes. It is available free of charge for via the internet (http://www.brenda-enzymes.org/) and as an in-house database for commercial users (requests to our distributor Biobase). The enzymes are classified according to the Enzyme Commission list of enzymes. Some 5000 \"different\" enzymes are covered. Frequently enzymes with very different properties are included under the same EC number. BRENDA includes biochemical and molecular information on classification, nomenclature, reaction, specificity, functional parameters, occurrence, enzyme structure, application, engineering, stability, disease, isolation, and preparation. The database also provides additional information on ligands, which function as natural or in vitro substrates/products, inhibitors, activating compounds, cofactors, bound metals, and other attributes.",
"homepage": "https://www.brenda-enzymes.org",
"name": "BRENDA",
"prefix": "r3d100010616",
"synonyms": [
"BRENDA Enzyme Database",
"BRaunschweig ENzyme DAtabase"
],
"xrefs": {
"fairsharing": "FAIRsharing.etp533",
"nif": "0000-30222",
"omics": "02681",
"scr": "002997"
}
}
},
"brenda.ligand": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Information for ligands in the BRENDA database.",
"example": "278",
"homepage": "https://www.brenda-enzymes.de/ligand.php",
"keywords": [
"chemistry",
"structrual bioinformatics"
],
"name": "BRENDA Ligand",
"pattern": "^\\d+$",
"uri_format": "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1"
},
"brenda.ligandgroup": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Information for ligand groups (chemical classes).",
"example": "18030",
"homepage": "https://www.brenda-enzymes.de/ligand.php",
"keywords": [
"chemistry",
"grouping",
"structrual bioinformatics"
],
"name": "BRENDA Ligand Group",
"pattern": "^\\d+$",
"uri_format": "https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1"
},
"bridgedb": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A vocabulary about resources, similar to bioregistry.schema, venn, idot, etc.",
"example": "hasPrimaryUriPattern",
"homepage": "https://bridgedb.org",
"name": "BridgeDb Vocabulary",
"references": [
"https://github.com/bridgedb/BridgeDb/blob/master/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl"
],
"uri_format": "http://vocabularies.bridgedb.org/ops#$1"
},
"broad": {
"biocontext": {
"prefix": "BROAD"
},
"mappings": {
"biocontext": "BROAD",
"miriam": "broad",
"n2t": "broad"
},
"miriam": {
"deprecated": false,
"description": "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae.",
"homepage": "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/",
"id": "00000438",
"name": "Broad Fungal Genome Initiative",
"namespaceEmbeddedInLui": false,
"pattern": "^S\\d+$",
"prefix": "broad",
"sampleId": "S7000002168151102",
"uri_format": "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1"
},
"n2t": {
"description": "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae.",
"example": "S7000002168151102",
"homepage": "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/",
"name": "Broad Fungal Genome Initiative at Broad Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^S\\d+$",
"prefix": "broad",
"uri_format": "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1"
}
},
"bs": {
"comment": "An alernative vocabulary that has been aligned and integrated in Sequence Ontology (SO).",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library.",
"download_obo": "https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/subsets/biosapiens.obo",
"example": "00042",
"homepage": "https://github.com/The-Sequence-Ontology/SO-Ontologies",
"name": "Biosapiens Protein Feature Ontology",
"pattern": "^\\d+$",
"repository": "https://github.com/The-Sequence-Ontology/SO-Ontologies",
"uri_format": "https://biopragmatics.github.io/providers/bs/$1"
},
"bspo": {
"aberowl": {
"description": "An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces",
"download_owl": "http://aber-owl.net/media/ontologies/BSPO/31/bspo.owl",
"homepage": "https://github.com/obophenotype/biological-spatial-ontology",
"name": "Biological Spatial Ontology",
"prefix": "BSPO"
},
"biocontext": {
"prefix": "BSPO"
},
"bioportal": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies.",
"homepage": "https://github.com/obophenotype/biological-spatial-ontology",
"name": "Spatial Ontology",
"prefix": "BSPO",
"version": "2023-05-27"
},
"download_json": "http://purl.obolibrary.org/obo/bspo.json",
"download_obo": "https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo",
"example": "0000029",
"fairsharing": {
"abbreviation": "BSPO",
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"description": "This ontology represents spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies.",
"homepage": "http://bioportal.bioontology.org/ontologies/BSPO",
"license": "CC-BY-3.0",
"name": "Biological SPatial Ontology",
"prefix": "FAIRsharing.newa3z",
"publications": [
{
"doi": "10.1186/2041-1480-5-34",
"pubmed": "25140222",
"title": "Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology",
"year": 2014
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"mappings": {
"aberowl": "BSPO",
"biocontext": "BSPO",
"bioportal": "BSPO",
"fairsharing": "FAIRsharing.newa3z",
"obofoundry": "bspo",
"ols": "bspo",
"ontobee": "BSPO"
},
"obofoundry": {
"appears_in": [
"aism",
"colao",
"fovt",
"lepao",
"uberon",
"zp"
],
"contact": "cjmungall@lbl.gov",
"contact.github": "cmungall",
"contact.label": "Chris Mungall",
"contact.orcid": "0000-0002-6601-2165",
"deprecated": false,
"description": "An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/bspo.obo",
"download.owl": "http://purl.obolibrary.org/obo/bspo.owl",
"homepage": "https://github.com/obophenotype/biological-spatial-ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Biological Spatial Ontology",
"preferredPrefix": "BSPO",
"prefix": "bspo",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/25140222",
"title": "Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology."
}
],
"repository": "https://github.com/obophenotype/biological-spatial-ontology"
},
"ols": {
"description": "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies.",
"download_owl": "http://purl.obolibrary.org/obo/bspo.owl",
"homepage": "https://github.com/obophenotype/biological-spatial-ontology",
"name": "Biological Spatial Ontology",
"prefix": "bspo",
"version": "2023-05-27",
"version.iri": "http://purl.obolibrary.org/obo/bspo/releases/2023-05-27/bspo.owl"
},
"ontobee": {
"library": "Library",
"name": "Biological Spatial Ontology",
"prefix": "BSPO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1186/2041-1480-5-34",
"pmc": "PMC4137724",
"pubmed": "25140222",
"title": "Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology",
"year": 2014
}
],
"uri_format": "http://purl.obolibrary.org/obo/BSPO_$1"
},
"bto": {
"aberowl": {
"description": "A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.",
"download_owl": "http://aber-owl.net/media/ontologies/BTO/39/bto.owl",
"homepage": "http://www.brenda-enzymes.org",
"name": "BRENDA tissue / enzyme source",
"prefix": "BTO"
},
"biocontext": {
"prefix": "BTO"
},
"bioportal": {
"contact": {
"email": "a.chang@tu-bs.de",
"name": "BrendaTissue Administrators"
},
"description": "A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.",
"homepage": "http://www.brenda-enzymes.info",
"name": "BRENDA Tissue and Enzyme Source Ontology",
"prefix": "BTO",
"version": "releases/2021-10-26"
},
"cellosaurus": {
"category": "Anatomy/cell type resources",
"homepage": "https://bioportal.bioontology.org/ontologies/BTO",
"name": "BRENDA Tissue Ontology",
"prefix": "BTO",
"uri_format": "https://bioportal.bioontology.org/ontologies/BTO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_$1"
},
"example": "0000590",
"fairsharing": {
"abbreviation": "BTO",
"description": "A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.",
"domains": [
"Reaction data",
"Cell",
"Enzyme",
"Organ"
],
"homepage": "http://www.brenda-enzymes.info",
"name": "BRENDA tissue / enzyme source",
"prefix": "FAIRsharing.1414v8",
"publications": [
{
"doi": "10.1093/nar/gkq968",
"pubmed": "21030441",
"title": "The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources",
"year": 2010
},
{
"doi": "10.1093/nar/gky1048",
"pubmed": "30395242",
"title": "BRENDA in 2019: a European ELIXIR core data resource",
"year": 2018
},
{
"doi": "10.1093/nar/gkh081",
"pubmed": "14681450",
"title": "BRENDA, the enzyme database: updates and major new developments",
"year": 2003
},
{
"doi": "10.1093/nar/gku1068",
"pubmed": "25378310",
"title": "BRENDA in 2015: exciting developments in its 25th year of existence",
"year": 2014
},
{
"doi": "10.1093/nar/gks1049",
"pubmed": "23203881",
"title": "BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA",
"year": 2012
}
],
"subjects": [
"Enzymology",
"Life Science"
]
},
"go": {
"description": "A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.",
"name": "BRENDA tissue / enzyme ontology",
"prefix": "BTO"
},
"mappings": {
"aberowl": "BTO",
"biocontext": "BTO",
"bioportal": "BTO",
"cellosaurus": "BTO",
"fairsharing": "FAIRsharing.1414v8",
"go": "BTO",
"miriam": "bto",
"n2t": "bto",
"obofoundry": "bto",
"ols": "bto",
"ontobee": "BTO",
"prefixcommons": "bto",
"wikidata": "P5501"
},
"miriam": {
"deprecated": false,
"description": "The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.",
"homepage": "http://bioportal.bioontology.org/ontologies/BTO",
"id": "00000111",
"name": "Brenda Tissue Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^BTO:\\d{7}$",
"prefix": "bto",
"sampleId": "0000146",
"uri_format": "http://purl.bioontology.org/ontology/BTO/BTO:$1"
},
"n2t": {
"description": "The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.",
"example": "0000146",
"homepage": "http://bioportal.bioontology.org/ontologies/BTO",
"name": "Brenda Tissue Ontology through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^BTO:\\d{7}$",
"prefix": "bto",
"uri_format": "http://purl.bioontology.org/ontology/BTO/BTO:$1"
},
"name": "BRENDA Tissue Ontology",
"obofoundry": {
"contact": "c.dudek@tu-braunschweig.de",
"contact.github": "chdudek",
"contact.label": "Christian-Alexander Dudek",
"contact.orcid": "0000-0001-9117-7909",
"deprecated": false,
"description": "A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.",
"domain": "anatomy and development",
"download.json": "http://purl.obolibrary.org/obo/bto.json",
"download.obo": "http://purl.obolibrary.org/obo/bto.obo",
"download.owl": "http://purl.obolibrary.org/obo/bto.owl",
"homepage": "http://www.brenda-enzymes.org",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "BRENDA tissue / enzyme source",
"preferredPrefix": "BTO",
"prefix": "bto",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/21030441",
"title": "The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources"
}
],
"repository": "https://github.com/BRENDA-Enzymes/BTO"
},
"ols": {
"description": "A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.",
"download_owl": "http://purl.obolibrary.org/obo/bto.owl",
"homepage": "http://www.brenda-enzymes.org",
"name": "The BRENDA Tissue Ontology (BTO)",
"prefix": "bto",
"version": "2021-10-26",
"version.iri": "http://purl.obolibrary.org/obo/bto/releases/2021-10-26/bto.owl"
},
"ontobee": {
"library": "Library",
"name": "BRENDA tissue / enzyme source",
"prefix": "BTO"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"alt_uri_formats": [
"http://purl.org/obo/owl/BTO#$1"
],
"bioportal": "1005",
"description": "The Brenda tissue ontology is a structured controlled vocabulary established to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.",
"example": "BTO:0000146",
"homepage": "http://www.brenda-enzymes.info",
"keywords": [
"obo",
"tissue"
],
"name": "BRENDA Tissue Ontology",
"pattern": "^BTO:\\d{7}$",
"prefix": "bto",
"synonyms": [
"brendatissueontology",
"obo.bto"
]
},
"providers": [
{
"code": "miriam_obo_legacy",
"description": "An old URI style for MIRIAM",
"homepage": "https://identifiers.org/",
"name": "MIRIAM OBO Legacy",
"uri_format": "http://identifiers.org/obo.bto/BTO:$1"
}
],
"publications": [
{
"doi": "10.1093/nar/gky1048",
"pmc": "PMC6323942",
"pubmed": "30395242",
"title": "BRENDA in 2019: a European ELIXIR core data resource",
"year": 2019
},
{
"doi": "10.1093/nar/gku1068",
"pmc": "PMC4383907",
"pubmed": "25378310",
"title": "BRENDA in 2015: exciting developments in its 25th year of existence",
"year": 2014
},
{
"doi": "10.1093/nar/gks1049",
"pmc": "PMC3531171",
"pubmed": "23203881",
"title": "BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA",
"year": 2012
},
{
"doi": "10.1093/nar/gkq968",
"pmc": "PMC3013802",
"pubmed": "21030441",
"title": "The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources",
"year": 2010
},
{
"doi": "10.1093/nar/gkh081",
"pmc": "PMC308815",
"pubmed": "14681450",
"title": "BRENDA, the enzyme database: updates and major new developments",
"year": 2004
}
],
"synonyms": [
"BTO"
],
"uri_format": "http://purl.obolibrary.org/obo/BTO_$1",
"wikidata": {
"database": "Q81661549",
"description": "identifier in the Brenda Tissue Ontology",
"example": [
"BTO:0000562",
"BTO:0001172"
],
"homepage": "https://www.brenda-enzymes.org/ontology.php?ontology_id=3",
"name": "Brenda Tissue Ontology ID",
"pattern": "^BTO:\\d+$",
"prefix": "P5501",
"uri_format": "https://www.brenda-enzymes.org/ontology.php?ontology_id=3&id_go=$1"
}
},
"bugbase.expt": {
"biocontext": {
"prefix": "BUGBASE.EXPT"
},
"mappings": {
"biocontext": "BUGBASE.EXPT",
"miriam": "bugbase.expt",
"n2t": "bugbase.expt"
},
"miriam": {
"deprecated": false,
"description": "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments.",
"homepage": "http://bugs.sgul.ac.uk/E-BUGS",
"id": "00000404",
"name": "BugBase Expt",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "bugbase.expt",
"sampleId": "288",
"uri_format": "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view"
},
"n2t": {
"description": "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments.",
"example": "288",
"homepage": "http://bugs.sgul.ac.uk/E-BUGS",
"name": "BugBase Expt at University of London",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "bugbase.expt",
"uri_format": "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view"
},
"uri_format": "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?action=view&expt_id=$1"
},
"bugbase.protocol": {
"biocontext": {
"prefix": "BUGBASE.PROTOCOL"
},
"mappings": {
"biocontext": "BUGBASE.PROTOCOL",
"miriam": "bugbase.protocol",
"n2t": "bugbase.protocol"
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"description": "The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features.",
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"homepage": "http://www.cazy.org/",
"name": "CAZy at CNRS",
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"pattern": "^(GT|GH|PL|CE|CBM)\\d+(\\_\\d+)?$",
"prefix": "cazy",
"uri_format": "http://www.cazy.org/$1.html"
},
"prefixcommons": {
"description": "The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.",
"example": "GT10",
"homepage": "http://www.cazy.org/",
"keywords": [
"classification",
"polysaccharide"
],
"name": "The Carbohydrate-Active enZYmes Database",
"pattern": "^GT\\d+$",
"prefix": "cazy",
"pubmed_ids": [
"18838391"
],
"uri_format": "http://www.cazy.org/$1.html"
},
"publications": [
{
"doi": "10.1093/nar/gkt1178",
"pmc": "PMC3965031",
"pubmed": "24270786",
"title": "The carbohydrate-active enzymes database (CAZy) in 2013",
"year": 2013
},
{
"doi": "10.1093/nar/gkn663",
"pmc": "PMC2686590",
"pubmed": "18838391",
"title": "The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics",
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}
],
"re3data": {
"description": "CAZy is a specialist database dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description.",
"homepage": "http://www.cazy.org/",
"name": "Carbohydrate-Active enZYmes Database",
"prefix": "r3d100012321",
"synonyms": [
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"omics": "01677",
"scr": "012909"
}
},
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"category": "Protein family/group databases",
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"name": "Carbohydrate-Active enZymes",
"prefix": "DB-0136",
"publications": [
{
"doi": "10.1093/nar/gkab1045",
"pubmed": "34850161"
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],
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"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE.",
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"homepage": "http://www.cba.ac.cn",
"keywords": [
"bibliography"
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"name": "Chinese Biological Abstracts",
"pattern": "^\\d+$",
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"name": "Jianjiong Gao",
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"abbreviation": "cBioPortal",
"description": "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.",
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"name": "cBioPortal for Cancer Genomics",
"prefix": "FAIRsharing.6L6MjA",
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"title": "The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data."
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{
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"pmc": "PMC3956037",
"pubmed": "22588877",
"title": "The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data",
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}
],
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},
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"download_rdf": "https://creativecommons.org/schema.rdf",
"example": "Work",
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"license": "CC0-1.0",
"lov": {
"description": "The Creative Commons Rights Expression Language (CC REL) lets you describe copyright licenses in RDF",
"homepage": "http://creativecommons.org/ns",
"keywords": [
"Metadata"
],
"modified": "2008-03-03",
"name": "Creative Commons Rights Expression Language",
"prefix": "cc",
"uri_prefix": "http://creativecommons.org/ns#$1"
},
"mappings": {
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},
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}
],
"subjects": [
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]
},
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"Protein"
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"example": "4824",
"homepage": "http://www.ncbi.nlm.nih.gov/CCDS/",
"keywords": [
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"gene"
],
"name": "The Consensus CDS",
"pattern": "^\\d+$",
"prefix": "ccds",
"pubmed_ids": [
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"year": 2009
}
],
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"catalog": "nbdc00023",
"examples": [
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"CCDS10913",
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"CCDS35175",
"CCDS2395",
"CCDS58412",
"CCDS55555",
"CCDS34401",
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],
"keywords": [
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},
"uniprot": {
"abbreviation": "CCDS",
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"homepage": "https://www.ncbi.nlm.nih.gov/CCDS",
"name": "The Consensus CDS (CCDS) project",
"prefix": "DB-0187",
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{
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"pubmed": "29126148"
}
],
"uri_format": "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=$1"
}
},
"ccf": {
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"download_owl": "http://aber-owl.net/media/ontologies/CCF/16/ccf.owl",
"homepage": "https://lod.humanatlas.io/vocab/ccf/latest",
"name": "Human Reference Atlas Common Coordinate Framework Ontology",
"prefix": "CCF",
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},
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"homepage": "https://lod.humanatlas.io/vocab/ccf/latest",
"name": "Human Reference Atlas Common Coordinate Framework Ontology",
"prefix": "CCF",
"publication": "https://hubmapconsortium.github.io/ccf/",
"version": "3.0.0"
},
"contact": {
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"github": "katyb",
"name": "Katy BΓΆrner",
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},
"contributor": {
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"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"example": "extraction_set",
"github_request_issue": 879,
"homepage": "https://bioportal.bioontology.org/ontologies/CCF",
"license": "CC-BY-4.0",
"mappings": {
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"bioportal": "CCF",
"ols": "ccf",
"re3data": "r3d100012657"
},
"name": "Human Reference Atlas Common Coordinate Framework Ontology",
"ols": {
"contact": "infoccf@indiana.edu",
"description": "The Common Coordinate Framework (CCF) Ontology is an application ontology built to support the development of the Human Reference Atlas (HRA). It unifies vocabulary for HRA construction and usageβmaking it possible to ingest external data sources; supporting uniform tissue sample registration that includes the spatial positioning and semantic annotations within 3D reference organs; and supporting user-formulated cross-domain queries over tissue donor properties, anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology consists of three major ontologies. The Biological Structure Ontology records anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships between them. The ASCT+B tables are authored by human experts using templated Google Sheets. The biomarkers, cell types, and anatomical structures are mapped to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible. All relationships between anatomical structures and from cell types to anatomical structures are valid Uberon and CL relationships. The Spatial Ontology defines the shape, size, location, and rotation of experimental tissue and data major anatomical structures in the 3D Reference Object Library. The Specimen Ontology captures the sex, age, and other information on donors that provided tissue data used in the construction of the HRA.",
"download_owl": "https://purl.org/ccf/2.0/ccf.owl",
"homepage": "https://hubmapconsortium.github.io/ccf/pages/ccf-ontology.html",
"name": "Human Reference Atlas Common Coordinate Framework Ontology",
"prefix": "ccf",
"version": "2.3.0",
"version.iri": "http://purl.org/ccf/releases/2.3.0/ccf.owl"
},
"pattern": "^\\S+$",
"rdf_uri_format": "http://purl.org/ccf/$1",
"re3data": {
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"homepage": "https://nda.nih.gov/ccf",
"name": "CCF",
"prefix": "r3d100012657",
"synonyms": [
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]
},
"repository": "https://github.com/hubmapconsortium/ccf-ontology",
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
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},
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},
"ccle": {
"cellosaurus": {
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"name": "Cancer Cell Line Encyclopedia",
"prefix": "CCLE",
"uri_format": "https://portals.broadinstitute.org/ccle/page?cell_line=$1"
},
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"name": "Charles Tapley Hoyt",
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},
"description": "Datasets around different cancer cell lines generated by the Broad Institute and Novartis",
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"license": "ODbL-1.0",
"mappings": {
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},
"name": "Cancer Cell Line Encyclopedia Cells",
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"name": "Cell Cycle Ontology",
"prefix": "CCO",
"version": "2015"
},
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"description": "A manual to help you describe, document, and catalog cultural artifacts (like art and architecture) and visual media that represent them.",
"homepage": "https://www.vraweb.org/cco",
"license": "CC BY-NC-SA 3.0",
"name": "Cataloging Cultural Objects",
"prefix": "20461"
},
"biocontext": {
"prefix": "CCO"
},
"bioportal": {
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"name": "Vladimir Mironov"
},
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"name": "Cell Cycle Ontology",
"prefix": "CCO",
"publication": "http://genomebiology.com/2009/10/5/R58",
"version": "2.10"
},
"contact": {
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"github": "makuintnu",
"name": "Martin Kuiper",
"orcid": "0000-0002-1171-9876"
},
"download_obo": "https://www.bio.ntnu.no/ontology/CCO/cco.obo",
"download_owl": "https://www.bio.ntnu.no/ontology/CCO/cco.owl",
"fairsharing": {
"abbreviation": "CCO",
"contact": {
"email": "kuiper@bio.ntnu.no",
"name": "Martin Kuiper",
"orcid": "0000-0002-1171-9876"
},
"description": "CCO contains genes, proteins, interactions (comprising genes or proteins that participate in them), processes from the cell cycle subtree of GO, molecular functions (GO), taxa, and ontological constructs (like an upper level ontology and relationships) to stick everything together.",
"domains": [
"Cell",
"Molecular function",
"Cell cycle"
],
"homepage": "https://www.biogateway.eu/tools/#CCO",
"name": "Cell Cycle Ontology",
"prefix": "FAIRsharing.xhwrnr",
"publications": [
{
"doi": "10.1186/gb-2009-10-5-r58",
"pubmed": "19480664",
"title": "The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process",
"year": 2009
}
],
"subjects": [
"Functional Genomics",
"Genomics",
"Proteomics",
"Life Science"
]
},
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"bartoc": "20461",
"biocontext": "CCO",
"bioportal": "CCO",
"fairsharing": "FAIRsharing.xhwrnr",
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"n2t": "cco",
"ols": "cco",
"prefixcommons": "cco"
},
"miriam": {
"deprecated": false,
"description": "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process.",
"homepage": "https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CCO",
"id": "00000234",
"name": "Cell Cycle Ontology",
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"pattern": "^CCO:\\w+$",
"prefix": "cco",
"sampleId": "0000003",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:$1"
},
"n2t": {
"description": "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process.",
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"homepage": "https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CCO",
"name": "Cell Cycle Ontology through OLS",
"namespaceEmbeddedInLui": true,
"pattern": "^CCO\\:\\w+$",
"prefix": "cco",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1"
},
"ols": {
"contact": "vladimir.n.mironov@gmail.com",
"description": "The Cell Cycle Ontology extends existing ontologies for cell cycle knowledge building a resource that integrates and manages knowledge about the cell cycle components and regulatory aspects.",
"download_owl": "http://www.bio.ntnu.no/ontology/CCO/cco.owl",
"homepage": "http://www.semantic-systems-biology.org/apo",
"name": "Cell Cycle Ontology",
"prefix": "cco"
},
"pattern": "^\\w+$",
"prefixcommons": {
"alt_uri_formats": [
"http://purl.org/obo/owl/CCO#$1"
],
"bioportal": "1507",
"description": "An application ontology integrating knowledge about the eukaryotic cell cycle.",
"example": "CCO:P0000023",
"homepage": "http://www.semantic-systems-biology.org/cco/",
"keywords": [
"obo",
"cell cycle"
],
"name": "Cell Cycle Ontology",
"pattern": "^CCO\\:\\w+$",
"prefix": "cco",
"pubmed_ids": [
"19480664"
]
},
"publications": [
{
"doi": "10.1186/gb-2009-10-5-r58",
"pmc": "PMC2718524",
"pubmed": "19480664",
"title": "The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process",
"year": 2009
}
]
},
"ccrid": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "http://cellresource.cn/",
"name": "Chinese Cell Resource Information Database",
"prefix": "CCRID",
"uri_format": "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"example": "4201PAT-CCTCC00348",
"homepage": "http://www.cellresource.cn",
"mappings": {
"cellosaurus": "CCRID"
},
"name": "National Experimental Cell Resource Sharing Platform",
"uri_format": "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1"
},
"cdao": {
"aberowl": {
"description": "a formalization of concepts and relations relevant to evolutionary comparative analysis",
"download_owl": "http://aber-owl.net/media/ontologies/CDAO/11/cdao.owl",
"homepage": "https://github.com/evoinfo/cdao",
"name": "Comparative Data Analysis Ontology",
"prefix": "CDAO"
},
"agroportal": {
"contact": {
"email": "balhoff@nescent.org",
"name": "Jim Balhoff"
},
"description": "The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character.",
"example_uri": "http://purl.obolibrary.org/obo/CDAO_0000098",
"homepage": "http://www.evolutionaryontology.org/",
"license": "CC0-1.0",
"name": "Comparative Data Analysis Ontology",
"prefix": "CDAO",
"publication": "http://www.evolutionaryontology.org",
"repository": "https://sourceforge.net/projects/cdao/",
"version": "2013-02-01"
},
"biocontext": {
"prefix": "CDAO"
},
"bioportal": {
"contact": {
"email": "balhoff@renci.org",
"name": "Jim Balhoff"
},
"description": "A formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science.",
"homepage": "https://github.com/evoinfo/cdao",
"name": "Comparative Data Analysis Ontology",
"prefix": "CDAO",
"version": "$Revision$"
},
"example": "0000072",
"fairsharing": {
"abbreviation": "CDAO",
"contact": {
"email": "balhoff@gmail.com",
"name": "Jim Balhoff",
"orcid": "0000-0002-8688-6599"
},
"description": "Comparative Data Analysis Ontology (CDAO) is a formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types).",
"domains": [
"Evolution"
],
"homepage": "https://github.com/evoinfo/cdao",
"license": "CC0-1.0",
"name": "Comparative Data Analysis Ontology",
"prefix": "FAIRsharing.kay31r",
"publications": [
{
"doi": "10.4137/ebo.s2320",
"pubmed": "19812726",
"title": "Initial implementation of a comparative data analysis ontology",
"year": 2009
}
],
"repository": "https://github.com/evoinfo/cdao/issues",
"subjects": [
"Molecular biology",
"Bioinformatics",
"Taxonomy",
"Phylogenetics",
"Evolutionary Biology",
"Life Science",
"Biomedical Science"
]
},
"mappings": {
"aberowl": "CDAO",
"agroportal": "CDAO",
"biocontext": "CDAO",
"bioportal": "CDAO",
"fairsharing": "FAIRsharing.kay31r",
"obofoundry": "cdao",
"ols": "cdao",
"ontobee": "CDAO"
},
"obofoundry": {
"contact": "balhoff@renci.org",
"contact.github": "balhoff",
"contact.label": "Jim Balhoff",
"contact.orcid": "0000-0002-8688-6599",
"deprecated": false,
"description": "a formalization of concepts and relations relevant to evolutionary comparative analysis",
"domain": "organisms",
"download.owl": "http://purl.obolibrary.org/obo/cdao.owl",
"homepage": "https://github.com/evoinfo/cdao",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Comparative Data Analysis Ontology",
"preferredPrefix": "CDAO",
"prefix": "cdao",
"publications": [
{
"id": "https://doi.org/10.4137/EBO.S2320",
"title": "Initial Implementation of a Comparative Data Analysis Ontology"
}
],
"repository": "https://github.com/evoinfo/cdao"
},
"ols": {
"description": "a formalization of concepts and relations relevant to evolutionary comparative analysis",
"download_owl": "http://purl.obolibrary.org/obo/cdao.owl",
"homepage": "https://github.com/evoinfo/cdao",
"name": "Comparative Data Analysis Ontology",
"prefix": "cdao",
"version": "2024-01-25",
"version.iri": "http://purl.obolibrary.org/obo/cdao/2024-01-25/cdao.owl"
},
"ontobee": {
"library": "Library",
"name": "Comparative Data Analysis Ontology",
"prefix": "CDAO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.4137/ebo.s2320",
"pmc": "PMC2747124",
"pubmed": "19812726",
"title": "Initial implementation of a comparative data analysis ontology",
"year": 2009
}
],
"uri_format": "http://purl.obolibrary.org/obo/CDAO_$1"
},
"cdd": {
"biocontext": {
"prefix": "CDD"
},
"edam": {
"description": "Identifier of a conserved domain from the Conserved Domain Database.",
"name": "CDD",
"obsolete": false,
"prefix": "2666"
},
"fairsharing": {
"abbreviation": "CDD",
"description": "The Canadian Disaster Database (CDD) contains detailed disaster information on more than 1000 natural, technological and conflict events (excluding war) that have happened since 1900 at home or abroad and that have directly affected Canadians. The database describes where and when a disaster occurred, the number of injuries, evacuations, and fatalities, as well as a rough estimate of the costs. As much as possible, the CDD contains primary data that is valid, current and supported by reliable and traceable sources, including federal institutions, provincial/territorial governments, non-governmental organizations and media sources. Data is updated and reviewed on a semi-annual basis.",
"homepage": "https://www.publicsafety.gc.ca/cnt/rsrcs/cndn-dsstr-dtbs/index-en.aspx",
"name": "Canadian Disaster Database",
"prefix": "FAIRsharing.ea287c",
"publications": [],
"subjects": [
"Geology",
"Earth Science"
]
},
"go": {
"homepage": "https://www.ncbi.nlm.nih.gov/cdd",
"name": "Conserved Domain Database at NCBI",
"prefix": "CDD",
"uri_format": "http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"
},
"integbio": {
"alt_name": "Conserved Domain Database",
"description": "This is a collection of muliple sequence alignment models for ancient domains and full-length proteins, for the purpose of giving annotations for proteins. This database includes domain information curated by NCBI as well as those imported from the external sources; Pfam, SMART, COG, PRK, and TIGRFAM.",
"homepage": "http://www.ncbi.nlm.nih.gov/cdd",
"information_keywords": [
"Sequence",
"Image/Movie",
"Classification"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "CDD",
"prefix": "nbdc00401",
"pubmeds": [
"18984618",
"17135202",
"15215404",
"12368255"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"mappings": {
"biocontext": "CDD",
"edam": "2666",
"fairsharing": "FAIRsharing.ea287c",
"go": "CDD",
"integbio": "nbdc00401",
"miriam": "cdd",
"n2t": "cdd",
"ncbi": "CDD",
"prefixcommons": "cdd",
"re3data": "r3d100012041",
"uniprot": "DB-0214"
},
"miriam": {
"deprecated": false,
"description": "The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution.",
"homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd",
"id": "00000119",
"name": "Conserved Domain Database",
"namespaceEmbeddedInLui": false,
"pattern": "^(cd)?\\d{5}$",
"prefix": "cdd",
"sampleId": "cd00400",
"uri_format": "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"
},
"n2t": {
"description": "The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution.",
"example": "cd00400",
"homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd",
"name": "Conserved Domain Database at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^(cd)?\\d{5}$",
"prefix": "cdd",
"uri_format": "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"
},
"ncbi": {
"example": "02194",
"homepage": "https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml",
"name": "Conserved Domain Database",
"prefix": "CDD"
},
"prefixcommons": {
"description": "The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, including NCBI-curated domains, which use 3D-structure information to explicitly to define domain boundaries and provide insights into sequence/structure/function relationships, as well as domain models imported from a number of external source databases (Pfam, SMART, COG, PRK, TIGRFAM).",
"example": "cd00400",
"homepage": "http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml",
"keywords": [
"protein",
"structure"
],
"license": "http://www.nlm.nih.gov/copyright.html",
"name": "Conserved Domain Database",
"pattern": "^cd\\d{5}$",
"prefix": "cdd",
"pubmed_ids": [
"18984618"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"
},
"publications": [
{
"doi": "10.1093/nar/gku1221",
"pmc": "PMC4383992",
"pubmed": "25414356",
"title": "CDD: NCBI's conserved domain database",
"year": 2014
},
{
"doi": "10.1093/nar/gkn845",
"pmc": "PMC2686570",
"pubmed": "18984618",
"title": "CDD: specific functional annotation with the Conserved Domain Database",
"year": 2008
}
],
"re3data": {
"description": "The Canadian Disaster Database (CDD) contains detailed disaster information on more than 1000 natural, technological and conflict events (excluding war) that have happened since 1900 at home or abroad and that have directly affected Canadians.\nMessage since 2022-01: The Canadian Disaster Database geospatial view is temporarily out of service. We apologize for the inconvenience. The standard view of the database is still available.",
"homepage": "https://www.publicsafety.gc.ca/cnt/rsrcs/cndn-dsstr-dtbs/index-en.aspx",
"name": "Canadian Disaster Database",
"prefix": "r3d100012041",
"synonyms": [
"BDC",
"Base de donnΓ©es canadienne sur les catastrophes",
"CDD"
],
"xrefs": {
"fairsharing": "FAIRsharing.ea287c"
}
},
"uniprot": {
"abbreviation": "CDD",
"category": "Family and domain databases",
"homepage": "https://www.ncbi.nlm.nih.gov/cdd",
"name": "Conserved Domains Database",
"prefix": "DB-0214",
"publications": [
{
"doi": "10.1093/nar/gkac1096",
"pubmed": "36477806"
}
],
"uri_format": "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"
}
},
"cdno": {
"aberowl": {
"description": "CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet.",
"download_owl": "http://aber-owl.net/media/ontologies/CDNO/15/cdno.owl",
"homepage": "https://cdno.info/",
"name": "Compositional Dietary Nutrition Ontology",
"prefix": "CDNO"
},
"agroportal": {
"contact": {
"email": "landreshdz@gmail.com",
"name": "Liliana AndrΓ©sβHernΓ‘ndez"
},
"description": "The CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. These terms are intended primarily to be associated with datasets that quantify concentration of chemical nutritional components derived from samples taken from any stage in the production of food raw materials (including from crops, livestock, fisheries) and through processing and supply chains. Additional knowledge associated with these dietary sources may be represented by terms that describe functional, physical and other attributes. Whilst recognising that dietary nutrients within food substrates may be present as complex and dynamic physical and chemical structures or mixtures, CDNO focuses on components typically quantified in an analytical chemistry laboratory. The primary CDNO class βdietary nutritional componentβ contains hierarchical sets of terms organised to reflect commonly used classifications of chemical food composition. This class does not represent an exhaustive classification of chemical components, but focuses on structuring terms according to widely accepted categories. This class is independent of, but may be used in conjunction with, classes that describe βanalytical methodsβ for quantification, βphysical propertiesβ or βdietary functionβ. Quantification data may be used and reported in research literature, to inform food composition tables and labelling, or for supply chain quality assurance and control. More specifically, terms within the βnutritional component concentrationβ class may be used to represent quantification of components described in the βdietary nutritional componentβ class. Concentration data are intended to be described in conjunction with post-composed metadata concepts, such as represented by the Food Ontology (FoodOn) βFood product by organismβ, which derives from some food or anatomical entity and a NCBI organismal classification ontology (NCBITaxon) entity. The common vocabulary and relationships defined within CDNO should facilitate description, communication and exchange of material entity-derived nutritional composition datasets typically generated by analytical laboratories. The organisation of the vocabulary is structured to reflect common categories variously used by those involved in crop, livestock or other organismal production, associated R&D and breeding, as well as the food processing and supply sector, and nutritionists, inlcuding compilers and users of food composition databases. The CDNO therefore supports characterisation of genetic diversity and management of biodiversity collections, as well as sharing of knowledge relating to dietary composition between a wider set of researchers, breeders, farmers, processors and other stakeholders. Further development of the functional class should also assist in understanding how interactions between organismal genetic and environmental variation contribute to human diet and health in the farm to fork continuum., None",
"example_uri": "http://purl.obolibrary.org/obo/CDNO_0200815",
"homepage": "https://cdno.info/",
"license": "CC-BY-3.0",
"name": "Compositional Dietary Nutrition Ontology",
"prefix": "CDNO",
"repository": "https://github.com/Southern-Cross-Plant-Science/cdno"
},
"bioportal": {
"contact": {
"email": "l.andres.hernandez.18@student.scu.edu.au",
"name": "Liliana Andres Hernandez"
},
"description": "CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet.",
"homepage": "https://github.com/Southern-Cross-Plant-Science/cdno",
"name": "Compositional Dietary Nutrition Ontology",
"prefix": "CDNO"
},
"example": "0000013",
"mappings": {
"aberowl": "CDNO",
"agroportal": "CDNO",
"bioportal": "CDNO",
"obofoundry": "cdno",
"ols": "cdno",
"ontobee": "CDNO"
},
"obofoundry": {
"contact": "landreshdz@gmail.com",
"contact.github": "LilyAndres",
"contact.label": "Liliana Andres Hernandez",
"contact.orcid": "0000-0002-7696-731X",
"depends_on": [
"bfo",
"chebi",
"envo",
"pato",
"ro"
],
"deprecated": false,
"description": "CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet.",
"domain": "diet, metabolomics, and nutrition",
"download.obo": "http://purl.obolibrary.org/obo/cdno.obo",
"download.owl": "http://purl.obolibrary.org/obo/cdno.owl",
"homepage": "https://cdno.info/",
"license": "CC BY 3.0",
"license.url": "https://creativecommons.org/licenses/by/3.0/",
"name": "Compositional Dietary Nutrition Ontology",
"preferredPrefix": "CDNO",
"prefix": "cdno",
"publications": [
{
"id": "https://doi.org/10.3389/fnut.2022.928837",
"title": "Establishing a Common Nutritional Vocabulary - From Food Production to Diet"
}
],
"repository": "https://github.com/CompositionalDietaryNutritionOntology/cdno"
},
"ols": {
"description": "The CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. These terms are intended primarily to be associated with datasets that quantify concentration of chemical nutritional components derived from samples taken from any stage in the production of food raw materials (including from crops, livestock, fisheries) and through processing and supply chains. Additional knowledge associated with these dietary sources may be represented by terms that describe functional, physical and other attributes. Whilst recognising that dietary nutrients within food substrates may be present as complex and dynamic physical and chemical structures or mixtures, CDNO focuses on components typically quantified in an analytical chemistry laboratory. The primary CDNO class βdietary nutritional componentβ contains hierarchical sets of terms organised to reflect commonly used classifications of chemical food composition. This class does not represent an exhaustive classification of chemical components, but focuses on structuring terms according to widely accepted categories. This class is independent of, but may be used in conjunction with, classes that describe βanalytical methodsβ for quantification, βphysical propertiesβ or βdietary functionβ. Quantification data may be used and reported in research literature, to inform food composition tables and labelling, or for supply chain quality assurance and control. More specifically, terms within the βnutritional component concentrationβ class may be used to represent quantification of components described in the βdietary nutritional componentβ class. Concentration data are intended to be described in conjunction with post-composed metadata concepts, such as represented by the Food Ontology (FoodOn) βFood product by organismβ, which derives from some food or anatomical entity and a NCBI organismal classification ontology (NCBITaxon) entity. The common vocabulary and relationships defined within CDNO should facilitate description, communication and exchange of material entity-derived nutritional composition datasets typically generated by analytical laboratories. The organisation of the vocabulary is structured to reflect common categories variously used by those involved in crop, livestock or other organismal production, associated R&D and breeding, as well as the food processing and supply sector, and nutritionists, inlcuding compilers and users of food composition databases. The CDNO therefore supports characterisation of genetic diversity and management of biodiversity collections, as well as sharing of knowledge relating to dietary composition between a wider set of researchers, breeders, farmers, processors and other stakeholders. Further development of the functional class should also assist in understanding how interactions between organismal genetic and environmental variation contribute to human diet and health in the farm to fork continuum.",
"download_owl": "http://purl.obolibrary.org/obo/cdno.owl",
"homepage": "https://cdno.info/",
"name": "Compositional Dietary Nutrition Ontology",
"prefix": "cdno",
"version": "2024-06-21",
"version.iri": "http://purl.obolibrary.org/obo/cdno/releases/2024-06-21/cdno.owl"
},
"ontobee": {
"library": "Library",
"name": "Compositional Dietary Nutrition Ontology",
"prefix": "CDNO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1002/csc2.20092",
"title": "Knowledge representation and data sharing to unlock crop variation for nutritional food security",
"year": 2020
}
],
"uri_format": "http://purl.obolibrary.org/obo/CDNO_$1"
},
"cdpd": {
"biocontext": {
"prefix": "CDPD"
},
"mappings": {
"biocontext": "CDPD",
"miriam": "cdpd",
"n2t": "cdpd"
},
"miriam": {
"deprecated": false,
"description": "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN).",
"homepage": "http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp",
"id": "00000272",
"name": "Canadian Drug Product Database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "cdpd",
"sampleId": "63250",
"uri_format": "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1"
},
"n2t": {
"description": "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN).",
"example": "63250",
"homepage": "http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp",
"name": "Canadian Drug Identification Number at Health Canada",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "cdpd",
"uri_format": "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1"
}
},
"cdt": {
"appears_in": [
"ohd"
],
"bartoc": {
"abbreviation": "CDT",
"description": "The Code on Dental Procedures and Nomenclature is used to provide for the efficient processing of dental claims, and to populate an Electronic Health Record.",
"homepage": "http://www.ada.org/en/publications/cdt",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Code on Dental Procedures and Nomenclature",
"prefix": "20299"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment.\n\nNote that CDT codes should look like D2150 but for some reason the ontology conversion that is reused across OBO rewrites them as CPT_000 + the four numbers without the leading D.",
"download_owl": "https://raw.githubusercontent.com/oral-health-and-disease-ontologies/ohd-ontology/f19378ff192b6f9ea16133e85671e8359fc371cd/src/ontology/archive/CDTCodes%20as%20Classes_pruned.owl",
"example": "1000001",
"hl7": {
"description": "Version of Current Dental Terminology (CDT) version 4, included in the Healthcare Common Procedure Coding System (HCPCS).Request rejected. This is a duplicate of OID 2.16.840.1.113883.6.13",
"name": "Current Dental Terminology",
"preferred_prefix": "CDT",
"prefix": "2.16.840.1.113883.6.116",
"status": "Rejected"
},
"homepage": "https://www.ada.org/publications/CDT",
"mappings": {
"bartoc": "20299",
"hl7": "2.16.840.1.113883.6.116"
},
"name": "Current Dental Terminology",
"pattern": "^\\d{7}$"
},
"cell_biolabs": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.cellbiolabs.com",
"name": "Cell Biolabs cell line products",
"prefix": "Cell_Biolabs",
"uri_format": "https://www.cellbiolabs.com/search?keywords=$1"
},
"example": "AKR-270",
"mappings": {
"cellosaurus": "Cell_Biolabs"
}
},
"cell_model_passport": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://cellmodelpassports.sanger.ac.uk/",
"name": "Sanger Cell Model Passports",
"prefix": "Cell_Model_Passport",
"uri_format": "https://cellmodelpassports.sanger.ac.uk/passports/$1"
},
"example": "SIDM01262",
"mappings": {
"cellosaurus": "Cell_Model_Passport"
}
},
"cellbank.australia": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/",
"name": "CellBank Australia",
"prefix": "CBA",
"uri_format": "https://www.cellbankaustralia.com/$1"
},
"description": "CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world.",
"example": "ab-1-ha",
"mappings": {
"cellosaurus": "CBA"
},
"uri_format": "https://www.cellbankaustralia.com/$1.html"
},
"cellimage": {
"biocontext": {
"prefix": "CELLIMAGE"
},
"contact": {
"email": "dorloff@ncmir.ucsd.edu",
"name": "David N. Orloff",
"orcid": "0000-0001-7594-0820"
},
"fairsharing": {
"abbreviation": null,
"description": "This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The purpose of this database is to advance research on cellular activity, with the ultimate goal of improving human health. It is a repository for images, movies, and animations of cells from a variety of organisms that demonstrate cellular architecture and functions. This comprehensive library is designed as a public resource first and foremost for research, and secondarily as a tool for education. The long-term goal is the construction of a library of images that will serve as primary data for research.",
"homepage": "http://www.cellimagelibrary.org",
"name": "Cell Image Library",
"prefix": "FAIRsharing.8t18te",
"publications": [
{
"doi": "10.1093/nar/gks1257",
"pubmed_id": 23203874,
"title": "The cell: an image library-CCDB: a curated repository of microscopy data."
}
],
"subjects": [
"Life Science",
"Cell Biology"
],
"twitter": "CellImageLibrar"
},
"mappings": {
"biocontext": "CELLIMAGE",
"fairsharing": "FAIRsharing.8t18te",
"miriam": "cellimage",
"n2t": "cellimage",
"prefixcommons": "cellimage",
"re3data": "r3d100000023"
},
"miriam": {
"deprecated": false,
"description": "The Cell: An Image Libraryβ’ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.",
"homepage": "http://cellimagelibrary.org/",
"id": "00000257",
"name": "Cell Image Library",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "cellimage",
"sampleId": "24801",
"uri_format": "http://cellimagelibrary.org/images/$1"
},
"n2t": {
"description": "The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.",
"example": "24801",
"homepage": "http://cellimagelibrary.org/",
"name": "Cell Image Library at American Society for Cell Biology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "cellimage",
"uri_format": "http://cellimagelibrary.org/images/$1"
},
"prefixcommons": {
"description": "The Cell: An Image Libraryβ’ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.",
"example": "24801",
"keywords": [
"image"
],
"name": "The Cell: An Image Library",
"pattern": "^\\d+$",
"prefix": "cellimage",
"uri_format": "http://cellimagelibrary.org/images/$1"
},
"publications": [
{
"doi": "10.1093/nar/gks1257",
"pmc": "PMC3531121",
"pubmed": "23203874",
"title": "The cell: an image library-CCDB: a curated repository of microscopy data",
"year": 2012
}
],
"re3data": {
"description": "This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The Cell Image Library has been merged with \"Cell Centered Database\" in 2017. The purpose of the database is to advance research on cellular activity, with the ultimate goal of improving human health.",
"homepage": "http://www.cellimagelibrary.org/home",
"name": "The Cell Image Library",
"prefix": "r3d100000023",
"synonyms": [
"CIL",
"The Cell"
],
"xrefs": {
"fairsharing": "FAIRsharing.8t18te",
"nif": "0000-37639",
"scr": "003510"
}
}
},
"cellopub": {
"cellosaurus": {
"category": "Reference resources",
"homepage": "https://www.cellosaurus.org/",
"name": "Cellosaurus Publication",
"prefix": "CelloPub",
"uri_format": "https://www.cellosaurus.org/cellopub/$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Cellosaurus identifeirs for publications, like Pubmed",
"example": "CLPUB00496",
"homepage": "https://web.expasy.org/cellosaurus/",
"mappings": {
"cellosaurus": "CelloPub"
},
"name": "Cellosaurus Publication",
"pattern": "^CLPUB\\d+$",
"uri_format": "https://web.expasy.org/cellosaurus/cellopub/$1"
},
"cellosaurus": {
"banana": "CVCL",
"banana_peel": "_",
"biocontext": {
"prefix": "CELLOSAURUS"
},
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://www.cellosaurus.org/",
"name": "Cellosaurus - a knowledge resource on cell lines",
"prefix": "Cellosaurus",
"uri_format": "https://www.cellosaurus.org/$1"
},
"contact": {
"email": "Amos.Bairoch@sib.swiss",
"github": "AmosBairoch",
"name": "Amos Bairoch",
"orcid": "0000-0003-2826-6444"
},
"download_obo": "https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo",
"example": "0440",
"fairsharing": {
"abbreviation": "Cellosaurus",
"contact": {
"email": "Amos.Bairoch@sib.swiss",
"name": "Amos Bairoch",
"orcid": "0000-0003-2826-6444"
},
"description": "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.",
"homepage": "https://www.cellosaurus.org",
"license": "CC-BY-4.0",
"name": "Cellosaurus",
"prefix": "FAIRsharing.hkk309",
"publications": [
{
"doi": "10.1002/ijc.32639",
"pubmed_id": 31444973,
"title": "CLASTR: The Cellosaurus STR similarity search tool - A precious help for cell line authentication."
},
{
"doi": "10.7171/jbt.18-2902-002",
"pubmed_id": 29805321,
"title": "The Cellosaurus, a Cell-Line Knowledge Resource."
}
],
"subjects": [
"Life Science"
]
},
"homepage": "https://cellosaurus.org",
"integbio": {
"description": "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research.\nIts scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.",
"fairsharing": "FAIRsharing.hkk309",
"homepage": "http://web.expasy.org/cellosaurus/",
"information_keywords": [
"Bioresource"
],
"maintainer": "CALIPHO (Computer and Laboratory Investigation of Proteins of Human Origin Group, Swiss Institute of Bioinformatics)",
"name": "Cellosaurus",
"prefix": "nbdc02180",
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"Organism"
]
},
"license": "CC-BY-4.0",
"mappings": {
"biocontext": "CELLOSAURUS",
"cellosaurus": "Cellosaurus",
"fairsharing": "FAIRsharing.hkk309",
"integbio": "nbdc02180",
"miriam": "cellosaurus",
"n2t": "cellosaurus",
"re3data": "r3d100013293",
"rrid": "CVCL",
"togoid": "Cellosaurus",
"wikidata": "P3289"
},
"mastodon": "cellosaurus@fediscience.org",
"miriam": {
"deprecated": false,
"description": "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.",
"homepage": "https://www.cellosaurus.org/",
"id": "00000598",
"name": "Cellosaurus",
"namespaceEmbeddedInLui": false,
"pattern": "^CVCL_[A-Z0-9]{4}(\\.txt)?$",
"prefix": "cellosaurus",
"sampleId": "CVCL_0030",
"uri_format": "https://www.cellosaurus.org/$1"
},
"n2t": {
"description": "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.",
"example": "CVCL_0030",
"homepage": "https://web.expasy.org/cellosaurus/",
"name": "Cellosaurus through SIB",
"namespaceEmbeddedInLui": false,
"pattern": "CVCL_[A-Z0-9]{4}",
"prefix": "cellosaurus",
"uri_format": "https://web.expasy.org/cellosaurus/$1"
},
"name": "Cellosaurus",
"pattern": "^[A-Z0-9]{4}$",
"providers": [
{
"code": "legacy",
"description": "The legacy URI for the Cellosaurus website, updated on August 30, 2022 [ref](https://twitter.com/Cellosaurus/status/1564658792691810305).",
"homepage": "https://web.expasy.org/cellosaurus",
"name": "Legacy Endpoint",
"uri_format": "https://web.expasy.org/cellosaurus/CVCL_$1"
},
{
"code": "nextprot",
"description": "The neXtProt endpoint for exploring Cellosaurus",
"homepage": "https://www.nextprot.org/",
"name": "neXtProt Cellosaurus Browser",
"uri_format": "https://www.nextprot.org/term/CVCL_$1"
}
],
"publications": [
{
"doi": "10.1002/ijc.32639",
"pubmed": "31444973",
"title": "CLASTR: The Cellosaurus STR similarity search tool - A precious help for cell line authentication",
"year": 2019
},
{
"doi": "10.7171/jbt.18-2902-002",
"pmc": "PMC5945021",
"pubmed": "29805321",
"title": "The Cellosaurus, a Cell-Line Knowledge Resource",
"year": 2018
}
],
"re3data": {
"description": "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines, Naturally immortal cell lines (example: stem cell lines), Finite life cell lines when those are distributed and used widely, Vertebrate cell line with an emphasis on human, mouse and rat cell lines, Invertebrate (insects and ticks) cell lines. Its scope does not include: Primary cell lines (with the exception of the finite life cell lines described above), Plant cell lines. Cellosaurus was initiated to be used as a cell line controlled vocabulary in the context of the neXtProt knowledgebase, but it quickly become apparent that there was a need for a cell line knowledge resource that would serve the needs of individual researchers, cell line distributors and bioinformatic resources. This leads to an increase of the scope and depth of the content of the Cellosaurus. The Cellosaurus is a participant of the Resource Identification Initiative and contributes actively to the work of the International Cell Line Authentication Committee (ICLAC). It is a Global Core Biodata Resource, an ELIXIR Core Data Resource and an IRDiRC Recognized Resource.",
"homepage": "https://www.cellosaurus.org/",
"name": "Cellosaurus",
"prefix": "r3d100013293",
"synonyms": [
"Cellosaurus - a knowledge resource on cell lines"
],
"xrefs": {
"fairsharing": "FAIRsharing.hkk309",
"scr": "013869"
}
},
"repository": "https://github.com/calipho-sib/cellosaurus",
"rrid": {
"homepage": "https://web.expasy.org/cellosaurus/",
"keywords": [
"cell lines",
"controlled vocabularies",
"ontologies",
"thesaurus"
],
"name": "Cellosaurus",
"prefix": "CVCL",
"pubmeds": [
"29805321"
],
"scr": "013869",
"twitter": "Cellosaurus"
},
"synonyms": [
"CVCL"
],
"togoid": {
"catalog": "nbdc02180",
"examples": [
"CVCL:7T24",
"CVCL:SE45",
"CVCL:XG73",
"CVCL:B6HT",
"CVCL:WM34",
"CVCL:7891",
"CVCL:FV52",
"CVCL:0367",
"CVCL:9Z18",
"CVCL:CG19"
],
"keywords": [
"CellLine"
],
"name": "Cellosaurus",
"pattern": "^CVCL[:_](?[A-Z0-9]{4})$",
"prefix": "Cellosaurus",
"uri_format": "http://www.cellosaurus.org/CVCL_$1"
},
"twitter": "cellosaurus",
"uri_format": "https://www.cellosaurus.org/CVCL_$1",
"wikidata": {
"database": "Q21014462",
"description": "Cellosaurus cell line identifier",
"example": [
"CVCL_0030",
"CVCL_0440"
],
"name": "Cellosaurus ID",
"pattern": "^CVCL_[A-Z\\d][A-Z\\d][A-Z\\d][A-Z\\d]$",
"prefix": "P3289",
"uri_format": "https://www.cellosaurus.org/$1"
}
},
"cellosaurus.resource": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The set of prefixes used in the Cellosaurus resource",
"example": "4DN",
"homepage": "https://web.expasy.org/cellosaurus/",
"keywords": [
"cell lines",
"cells",
"registry"
],
"name": "Cellosaurus Registry",
"uri_format": "https://bioregistry.io/metaregistry/cellosaurus/$1"
},
"cellrepo": {
"mappings": {
"miriam": "cellrepo"
},
"miriam": {
"deprecated": false,
"description": "The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines",
"homepage": "https://www.cellrepo.com/",
"id": "00000829",
"name": "Cell Version Control Repository",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "cellrepo",
"sampleId": "82",
"uri_format": "https://www.cellrepo.com/repositories/$1"
}
},
"cemo": {
"contact": {
"email": "n.queralt_rosinach@lumc.nl",
"github": "NuriaQueralt",
"name": "NΓΊria Queralt Rosinach",
"orcid": "0000-0003-0169-8159"
},
"contributor": {
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"description": "The covid-19 epidemiology and monitoring ontology (cemo) provides a common ontological model to make epidemiological quantitative data for monitoring the covid-19 outbreak machine-readable and interoperable to facilitate its exchange, integration and analysis, to eventually support evidence-based rapid response.",
"download_json": "https://raw.githubusercontent.com/cthoyt/covid19-epidemiology-ontology/add-artifacts/owl/cemo.json",
"download_owl": "https://raw.githubusercontent.com/NuriaQueralt/covid19-epidemiology-ontology/main/owl/cemo.owl",
"example": "secondary_attack_rate",
"github_request_issue": 593,
"homepage": "https://github.com/NuriaQueralt/covid19-epidemiology-ontology",
"license": "CC0-1.0",
"name": "The COVID-19 epidemiology and monitoring ontology",
"pattern": "^[0-9a-z_-]+$",
"providers": [
{
"code": "obo",
"description": "This represents misconfigured base IRIs, even though this ontology isn't an OBO Foundry ontology",
"homepage": "http://purl.obolibrary.org/obo/",
"name": "Legacy OBO PURL",
"uri_format": "http://purl.obolibrary.org/obo/cemo.owl#$1"
}
],
"repository": "https://github.com/NuriaQueralt/covid19-epidemiology-ontology",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://biopragmatics.github.io/providers/cemo/$1"
},
"ceph": {
"aberowl": {
"description": "An anatomical and developmental ontology for cephalopods",
"download_owl": "http://aber-owl.net/media/ontologies/CEPH/2/ceph.owl",
"homepage": "https://github.com/obophenotype/cephalopod-ontology",
"name": "Cephalopod Ontology",
"prefix": "CEPH"
},
"biocontext": {
"prefix": "CEPH"
},
"bioportal": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "An anatomical and developmental ontology for cephalopods",
"homepage": "https://github.com/obophenotype/cephalopod-ontology",
"name": "Cephalopod Ontology",
"prefix": "CEPH"
},
"download_obo": "https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo",
"example": "0000109",
"fairsharing": {
"abbreviation": "CEPH",
"description": "An anatomical and developmental ontology for cephalopods",
"domains": [
"Life cycle"
],
"homepage": "https://github.com/obophenotype/cephalopod-ontology",
"name": "Cephalopod Ontology",
"prefix": "FAIRsharing.p58bm4",
"subjects": [
"Fisheries Science",
"Anatomy",
"Zoology"
]
},
"mappings": {
"aberowl": "CEPH",
"biocontext": "CEPH",
"bioportal": "CEPH",
"fairsharing": "FAIRsharing.p58bm4",
"obofoundry": "ceph",
"ols": "ceph",
"ontobee": "CEPH"
},
"obofoundry": {
"contact": "cjmungall@lbl.gov",
"contact.github": "cmungall",
"contact.label": "Chris Mungall",
"contact.orcid": "0000-0002-6601-2165",
"deprecated": true,
"description": "An anatomical and developmental ontology for cephalopods",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/ceph.obo",
"download.owl": "http://purl.obolibrary.org/obo/ceph.owl",
"homepage": "https://github.com/obophenotype/cephalopod-ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Cephalopod Ontology",
"prefix": "ceph",
"repository": "https://github.com/obophenotype/cephalopod-ontology"
},
"ols": {
"description": "An anatomical and developmental ontology for cephalopods",
"download_owl": "http://purl.obolibrary.org/obo/ceph.owl",
"homepage": "https://github.com/obophenotype/cephalopod-ontology",
"name": "Cephalopod Ontology",
"prefix": "ceph",
"version": "2016-01-12",
"version.iri": "http://purl.obolibrary.org/obo/ceph/releases/2016-01-12/ceph.owl"
},
"ontobee": {
"library": "Library",
"name": "Cephalopod Ontology",
"prefix": "CEPH"
},
"pattern": "^\\d{7}$"
},
"cgd": {
"biocontext": {
"prefix": "CGD"
},
"contact": {
"email": "gsherloc@stanford.edu",
"name": "Gavin Sherlock",
"orcid": "0000-0002-1692-4983"
},
"fairsharing": {
"abbreviation": "CGD",
"description": "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.",
"homepage": "http://www.candidagenome.org/",
"name": "Candida Genome Database",
"prefix": "FAIRsharing.j7j53",
"publications": [
{
"doi": "10.1093/nar/gki003",
"pubmed_id": 15608216,
"title": "The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information."
},
{
"doi": "10.1093/nar/gkr945",
"pubmed_id": 22064862,
"title": "The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata."
}
],
"subjects": [
"Life Science"
]
},
"go": {
"homepage": "http://www.candidagenome.org/",
"name": "Candida Genome Database",
"prefix": "CGD",
"synonyms": [
"CGDID"
],
"uri_format": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"
},
"integbio": {
"alt_name": "Candida Genome Database",
"description": "This database is a genome database for Candida. It contains manually curated annotations on genes and proteins, as well as genomic sequences of the human pathogen Candida. Users can view the information of four strains of Candida, including C. albicans, C. dubliniensis, C. glabrata, and C. parapsilosis, which are metabolic pathways, experimental data, and full text of publications as well as genomic information.",
"fairsharing": "biodbcore-000276",
"homepage": "http://www.candidagenome.org",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Bibliography/Documents",
"Repository"
],
"maintainer": "Stanford University",
"name": "CGD",
"prefix": "nbdc00391",
"pubmeds": [
"19808938",
"19577928",
"19465905",
"17090582",
"16879419",
"15608216",
"22064862"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"Protein",
"Health/Disease"
]
},
"mappings": {
"biocontext": "CGD",
"fairsharing": "FAIRsharing.j7j53",
"go": "CGD",
"integbio": "nbdc00391",
"miriam": "cgd",
"n2t": "cgd",
"ncbi": "CGD",
"prefixcommons": "cgd",
"re3data": "r3d100010617",
"uniprot": "DB-0126"
},
"miriam": {
"deprecated": false,
"description": "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.",
"homepage": "http://www.candidagenome.org/",
"id": "00000145",
"name": "Candida Genome Database",
"namespaceEmbeddedInLui": false,
"pattern": "^CAL\\d{7}$",
"prefix": "cgd",
"sampleId": "CAL0003079",
"uri_format": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"
},
"n2t": {
"description": "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.",
"example": "CAL0003079",
"homepage": "http://www.candidagenome.org/",
"name": "Candida Genome Database at Stanford University",
"namespaceEmbeddedInLui": false,
"pattern": "^CAL\\d{7}$",
"prefix": "cgd",
"uri_format": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"
},
"ncbi": {
"example": "CAL0005934",
"homepage": "http://www.candidagenome.org/",
"name": "Candida Genome Database",
"prefix": "CGD"
},
"prefixcommons": {
"description": "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.",
"example": "CAL0003079",
"homepage": "http://www.candidagenome.org/",
"keywords": [
"eukaryotic",
"genome",
"nucleotide"
],
"name": "Candida Genome Database",
"pattern": "^CAL\\d{7}$",
"prefix": "cgd",
"pubmed_ids": [
"15608216"
],
"uri_format": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkw924",
"pmc": "PMC5210628",
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],
"name": "ChemBank",
"pattern": "^\\d+$",
"prefix": "chembank",
"pubmed_ids": [
"17947324"
],
"uri_format": "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkm843",
"pmc": "PMC2238881",
"pubmed": "17947324",
"title": "ChemBank: a small-molecule screening and cheminformatics resource database",
"year": 2007
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"chembl": {
"cheminf": {
"description": "Identifier used by the ChEMBL database for compounds, assays, target, etc.",
"name": "ChEMBL",
"obsolete": false,
"prefix": "000412"
},
"contact": {
"email": "dmendez@ebi.ac.uk",
"github": "nclopezo",
"name": "David Mendez Lopez",
"orcid": "0000-0002-0294-5484"
},
"fairsharing": {
"abbreviation": "ChEMBL",
"description": "ChEMBL is an open, manually-curated, large-scale bioactivity database integrating data records extracted from medicinal chemistry literature, from deposited data sets, as well as other public data sources. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. Information regarding the compounds tested (including their chemical structures), the biological or physicochemical assays performed on these and the targets of these assays are recorded in a structured form, standardized, and annotated with controlled vocabularies to allow users to address a broad range of drug discovery questions.",
"homepage": "https://www.ebi.ac.uk/chembl",
"license": "CC BY-SA 3.0",
"name": "ChEMBL",
"prefix": "FAIRsharing.m3jtpg",
"publications": [
{
"doi": "10.1093/nar/gkr777",
"pubmed_id": 21948594,
"title": "ChEMBL: a large-scale bioactivity database for drug discovery."
},
{
"doi": "10.1093/nar/gky1075",
"pubmed_id": 30398643,
"title": "ChEMBL: towards direct deposition of bioassay data."
},
{
"doi": "10.1093/nar/gkt1031",
"pubmed_id": 24214965,
"title": "The ChEMBL bioactivity database: an update"
},
{
"doi": "10.1093/nar/gkw1074",
"pubmed_id": 27899562,
"title": "The ChEMBL database in 2017."
}
],
"repository": "https://github.com/chembl/GLaDOS",
"subjects": [
"Drug Discovery",
"Biochemistry",
"Genomics",
"Medicinal Chemistry"
],
"twitter": "chembl"
},
"homepage": "https://www.ebi.ac.uk/chembl",
"integbio": {
"description": "ChEMBL is a database for bioactive molecules. It collects information of small molecules, such as calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data), and the target information. Metadata of assays for small molecule activities or assays for binding activities between small molecules and its targets are also provided.",
"fairsharing": "FAIRsharing.m3jtpg",
"homepage": "https://www.ebi.ac.uk/chembl/",
"information_keywords": [
"Chemical structure",
"Interaction/Pathway",
"Repository"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "ChEMBL",
"prefix": "nbdc02555",
"pubmeds": [
"33507738",
"30398643",
"25883136"
],
"status": "Active",
"target_keywords": [
"Chemical compound",
"Drug",
"Protein"
]
},
"license": "CC-BY-SA-3.0",
"mappings": {
"cheminf": "000412",
"fairsharing": "FAIRsharing.m3jtpg",
"integbio": "nbdc02555",
"miriam": "chembl",
"prefixcommons": "chembl",
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"uniprot": "DB-0174"
},
"miriam": {
"deprecated": false,
"description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.",
"homepage": "https://www.ebi.ac.uk/chembl",
"id": "00000799",
"name": "ChEMBL",
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"pattern": "^CHEMBL\\d+$",
"prefix": "chembl",
"sampleId": "CHEMBL4303805",
"uri_format": "https://www.ebi.ac.uk/chembl/entity/$1"
},
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"description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.",
"example": "210313",
"homepage": "https://www.ebi.ac.uk/chembldb/",
"keywords": [
"molecules"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "chEMBL",
"pattern": "^\\d+$",
"prefix": "chembl",
"synonyms": [
"chembldb"
],
"uri_format": "https://www.ebi.ac.uk/chembldb/index.php/compound/inspect/$1"
},
"publications": [
{
"doi": "10.1093/nar/gky1075",
"pmc": "PMC6323927",
"pubmed": "30398643",
"title": "ChEMBL: towards direct deposition of bioassay data",
"year": 2019
},
{
"doi": "10.1093/nar/gkw1074",
"pmc": "PMC5210557",
"pubmed": "27899562",
"title": "The ChEMBL database in 2017",
"year": 2016
},
{
"doi": "10.1093/nar/gkt1031",
"pmc": "PMC3965067",
"pubmed": "24214965",
"title": "The ChEMBL bioactivity database: an update",
"year": 2013
},
{
"doi": "10.1093/nar/gkr777",
"pmc": "PMC3245175",
"pubmed": "21948594",
"title": "ChEMBL: a large-scale bioactivity database for drug discovery",
"year": 2011
}
],
"re3data": {
"description": "ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data).\nThe data is abstracted and curated from the primary scientific literature, and cover a significant fraction of the SAR and discovery of modern drugs\nWe attempt to normalise the bioactivities into a uniform set of end-points and units where possible, and also to tag the links between a molecular target and a published assay with a set of varying confidence levels. Additional data on clinical progress of compounds is being integrated into ChEMBL at the current time.",
"homepage": "https://www.ebi.ac.uk/chembl/",
"name": "ChEMBL",
"prefix": "r3d100010539",
"xrefs": {
"fairsharing": "fairsharing.m3jtpg",
"omics": "02731",
"scr": "014042"
}
},
"synonyms": [
"ChEMBL",
"ChEMBL_ID",
"chembl"
],
"uniprot": {
"abbreviation": "ChEMBL",
"category": "Chemistry databases",
"homepage": "https://www.ebi.ac.uk/chembl",
"name": "ChEMBL database of bioactive drug-like small molecules",
"prefix": "DB-0174",
"publications": [
{
"doi": "10.1093/nar/gky1075",
"pubmed": "30398643"
}
],
"uri_format": "https://www.ebi.ac.uk/chembl/target/inspect/$1"
}
},
"chembl.cell": {
"cellosaurus": {
"category": "Chemistry resources",
"homepage": "https://www.ebi.ac.uk/chembldb",
"name": "ChEMBL database of bioactive drug-like small molecules - Cell lines section",
"prefix": "ChEMBL-Cells",
"uri_format": "https://www.ebi.ac.uk/chembldb/cell/inspect/$1"
},
"contact": {
"email": "dmendez@ebi.ac.uk",
"github": "nclopezo",
"name": "David Mendez Lopez",
"orcid": "0000-0002-0294-5484"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"example": "CHEMBL3307800",
"keywords": [
"bioactivities",
"cell lines"
],
"license": "CC-BY-SA-3.0",
"mappings": {
"cellosaurus": "ChEMBL-Cells"
},
"part_of": "chembl",
"pattern": "^CHEMBL\\d+$",
"synonyms": [
"ChEMBL-Cells"
],
"uri_format": "https://www.ebi.ac.uk/chembl/cell_line_report_card/$1"
},
"chembl.compound": {
"biocontext": {
"prefix": "CHEMBL.COMPOUND"
},
"contact": {
"email": "dmendez@ebi.ac.uk",
"github": "nclopezo",
"name": "David Mendez Lopez",
"orcid": "0000-0002-0294-5484"
},
"edam": {
"description": "Identifier of a small molecular from the ChEMBL database.",
"name": "Compound ID (ChEMBL)",
"obsolete": false,
"prefix": "2646"
},
"example": "CHEMBL465070",
"license": "CC-BY-SA-3.0",
"mappings": {
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"edam": "2646",
"miriam": "chembl.compound",
"n2t": "chembl.compound",
"togoid": "ChemblCompound",
"wikidata": "P592"
},
"miriam": {
"deprecated": false,
"description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.",
"homepage": "https://www.ebi.ac.uk/chembldb/",
"id": "00000084",
"name": "ChEMBL compound",
"namespaceEmbeddedInLui": false,
"pattern": "^CHEMBL\\d+$",
"prefix": "chembl.compound",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "ChEMBL compound RDF",
"homepage": "https://github.com/egonw/chembl.rdf",
"name": "ChEMBL compound RDF",
"uri_format": "http://linkedchemistry.info/chembl/chemblid/$1"
},
{
"code": "CURATOR_REVIEW",
"description": "ChEMBL compound RDF through EBI RDF Platform",
"homepage": "https://www.ebi.ac.uk/rdf/services/chembl/",
"name": "ChEMBL compound RDF through EBI RDF Platform",
"uri_format": "https://rdf.ebi.ac.uk/resource/chembl/molecule/$1"
}
],
"sampleId": "CHEMBL308052",
"uri_format": "https://www.ebi.ac.uk/chembl/compound/inspect/$1"
},
"n2t": {
"description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.",
"example": "CHEMBL308052",
"homepage": "https://www.ebi.ac.uk/chembldb/",
"name": "ChEMBL compound database at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^CHEMBL\\d+$",
"prefix": "chembl.compound",
"uri_format": "https://www.ebi.ac.uk/chembl/compound/inspect/$1"
},
"name": "ChEMBL",
"part_of": "chembl",
"pattern": "^CHEMBL\\d+$",
"togoid": {
"catalog": "nbdc02555",
"examples": [
"CHEMBL121649",
"CHEMBL190334",
"CHEMBL3103282",
"CHEMBL69329",
"CHEMBL2105131",
"CHEMBL2177390",
"CHEMBL3091820",
"CHEMBL1200335",
"CHEMBL3094412",
"CHEMBL67367"
],
"keywords": [
"Compound"
],
"name": "ChEMBL compound",
"pattern": "^(?CHEMBL\\d+)$",
"prefix": "ChemblCompound",
"uri_format": "http://identifiers.org/chembl.compound/$1"
},
"wikidata": {
"description": "identifier from a chemical database of bioactive molecules with drug-like properties",
"example": [
"CHEMBL113",
"CHEMBL1200604",
"CHEMBL417016"
],
"homepage": "https://www.ebi.ac.uk/chembl",
"miriam": "chembl",
"name": "ChEMBL ID",
"pattern": "^CHEMBL\\d+$",
"prefix": "P592",
"uri_format": "https://www.ebi.ac.uk/chembl/compound_report_card/$1/",
"uri_format_rdf": "http://rdf.ebi.ac.uk/resource/chembl/molecule/$1"
}
},
"chembl.target": {
"biocontext": {
"prefix": "CHEMBL.TARGET"
},
"cellosaurus": {
"category": "Chemistry resources",
"homepage": "https://www.ebi.ac.uk/chembldb",
"name": "ChEMBL database of bioactive drug-like small molecules - Targets section",
"prefix": "ChEMBL-Targets",
"uri_format": "https://www.ebi.ac.uk/chembldb/target/inspect/$1"
},
"contact": {
"email": "dmendez@ebi.ac.uk",
"github": "nclopezo",
"name": "David Mendez Lopez",
"orcid": "0000-0002-0294-5484"
},
"license": "CC-BY-SA-3.0",
"mappings": {
"biocontext": "CHEMBL.TARGET",
"cellosaurus": "ChEMBL-Targets",
"miriam": "chembl.target",
"n2t": "chembl.target",
"togoid": "ChemblTarget"
},
"miriam": {
"deprecated": false,
"description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.",
"homepage": "https://www.ebi.ac.uk/chembldb/",
"id": "00000085",
"name": "ChEMBL target",
"namespaceEmbeddedInLui": false,
"pattern": "^CHEMBL\\d+$",
"prefix": "chembl.target",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "ChEMBL target RDF",
"homepage": "https://github.com/egonw/chembl.rdf",
"name": "ChEMBL target RDF",
"uri_format": "http://linkedchemistry.info/chembl/chemblid/$1"
},
{
"code": "CURATOR_REVIEW",
"description": "ChEMBL target RDF through EBI RDF Platform",
"homepage": "https://rdf.ebi.ac.uk/resource/chembl/",
"name": "ChEMBL target RDF through EBI RDF Platform",
"uri_format": "https://rdf.ebi.ac.uk/resource/chembl/target/$1"
}
],
"sampleId": "CHEMBL3467",
"uri_format": "https://www.ebi.ac.uk/chembl/target/inspect/$1"
},
"n2t": {
"description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.",
"example": "CHEMBL3467",
"homepage": "https://www.ebi.ac.uk/chembldb/",
"name": "ChEMBL targets database at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^CHEMBL\\d+$",
"prefix": "chembl.target",
"uri_format": "https://www.ebi.ac.uk/chembl/target/inspect/$1"
},
"part_of": "chembl",
"synonyms": [
"ChEMBL-Targets"
],
"togoid": {
"catalog": "nbdc02555",
"examples": [
"CHEMBL2788",
"CHEMBL3091264",
"CHEMBL3831324",
"CHEMBL5524",
"CHEMBL5597",
"CHEMBL3983",
"CHEMBL4187",
"CHEMBL3391681",
"CHEMBL5135",
"CHEMBL1255130"
],
"keywords": [
"Protein"
],
"name": "ChEMBL target",
"pattern": "^(?CHEMBL\\d+)$",
"prefix": "ChemblTarget",
"uri_format": "http://identifiers.org/chembl.target/$1"
}
},
"chemdb": {
"biocontext": {
"prefix": "CHEMDB"
},
"contact": {
"email": "pfbaldi@uci.edu",
"name": "Pierre Baldi",
"orcid": "0000-0001-8752-4664"
},
"fairsharing": {
"abbreviation": "ChemDB",
"description": "ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds.",
"homepage": "http://cdb.ics.uci.edu",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "The UC Irvine ChemDB",
"prefix": "FAIRsharing.dstf7h",
"publications": [
{
"doi": "10.1093/bioinformatics/bti683",
"pubmed_id": 16174682,
"title": "ChemDB: a public database of small molecules and related chemoinformatics resources."
},
{
"doi": "10.1093/bioinformatics/btm341",
"pubmed_id": 17599932,
"title": "ChemDB update--full-text search and virtual chemical space."
}
],
"subjects": [
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"Life Science",
"Biomedical Science",
"Systems Biology",
"Preclinical Studies"
]
},
"mappings": {
"biocontext": "CHEMDB",
"fairsharing": "FAIRsharing.dstf7h",
"miriam": "chemdb",
"n2t": "chemdb",
"prefixcommons": "chemdb"
},
"miriam": {
"deprecated": false,
"description": "ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds.",
"homepage": "http://cdb.ics.uci.edu/",
"id": "00000279",
"name": "ChemDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "chemdb",
"sampleId": "3966782",
"uri_format": "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1"
},
"n2t": {
"description": "ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds.",
"example": "3966782",
"homepage": "http://cdb.ics.uci.edu/",
"name": "ChemDB at UC Irvine",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "chemdb",
"uri_format": "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1"
},
"prefixcommons": {
"description": "ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds.",
"example": "3965223",
"homepage": "http://cdb.ics.uci.edu",
"keywords": [
"small molecule"
],
"name": "The UC Irvine ChemDB",
"pattern": "^\\d+$",
"prefix": "chemdb",
"pubmed_ids": [
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],
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},
"publications": [
{
"doi": "10.1093/bioinformatics/btm341",
"pubmed": "17599932",
"title": "ChemDB update--full-text search and virtual chemical space",
"year": 2007
},
{
"doi": "10.1093/bioinformatics/bti683",
"pubmed": "16174682",
"title": "ChemDB: a public database of small molecules and related chemoinformatics resources",
"year": 2005
}
]
},
"chemidplus": {
"biocontext": {
"prefix": "CHEMIDPLUS"
},
"edam": {
"description": "Identifier of a chemical from the ChemIDplus database.",
"name": "Compound ID (ChemIDplus)",
"obsolete": false,
"prefix": "2658"
},
"fairsharing": {
"abbreviation": "ChemIDplus",
"description": "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.",
"homepage": "https://chem.nlm.nih.gov/chemidplus/",
"name": "ChemIDplus",
"prefix": "FAIRsharing.5949vn",
"publications": [
{
"doi": "10.1300/J115v21n01_04",
"pubmed_id": 11989279,
"title": "ChemIDplus-super source for chemical and drug information."
}
],
"subjects": [
"Chemistry",
"Biomedical Science"
]
},
"integbio": {
"description": "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.",
"fairsharing": "FAIRsharing.5949vn",
"homepage": "https://chem.nlm.nih.gov/chemidplus/",
"information_keywords": [
"3D structure",
"Image/Movie",
"Chemical structure"
],
"maintainer": "NLM (National Library of Medicine)",
"name": "ChemIDplus",
"prefix": "nbdc01837",
"pubmeds": [
"11989279"
],
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"mappings": {
"biocontext": "CHEMIDPLUS",
"edam": "2658",
"fairsharing": "FAIRsharing.5949vn",
"integbio": "nbdc01837",
"miriam": "chemidplus",
"n2t": "chemidplus",
"prefixcommons": "chemidplus"
},
"miriam": {
"deprecated": false,
"description": "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.",
"homepage": "https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp",
"id": "00000096",
"name": "ChemIDplus",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+\\-\\d+\\-\\d+$",
"prefix": "chemidplus",
"sampleId": "57-27-2",
"uri_format": "https://chem.nlm.nih.gov/chemidplus/rn/$1"
},
"n2t": {
"description": "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.",
"example": "57-27-2",
"homepage": "https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp",
"name": "ChemIDplus at National Library of Medicine",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+\\-\\d+\\-\\d+$",
"prefix": "chemidplus",
"uri_format": "https://chem.nlm.nih.gov/chemidplus/rn/$1"
},
"prefixcommons": {
"description": "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.",
"example": "000057272",
"homepage": "http://chem.sis.nlm.nih.gov/chemidplus/chemidheavy.jsp",
"keywords": [
"structure",
"molecules"
],
"license": "http://www.nlm.nih.gov/copyright.html",
"name": "ChemIDplus",
"pattern": "^\\d+$",
"prefix": "chemidplus",
"uri_format": "http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$1"
},
"publications": [
{
"doi": "10.1300/j115v21n01_04",
"pubmed": "11989279",
"title": "ChemIDplus-super source for chemical and drug information",
"year": 2002
}
],
"synonyms": [
"ChemIDplus"
]
},
"cheminf": {
"aberowl": {
"description": "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.",
"download_owl": "http://aber-owl.net/media/ontologies/CHEMINF/49/cheminf.owl",
"homepage": "https://github.com/semanticchemistry/semanticchemistry",
"name": "Chemical Information Ontology",
"prefix": "CHEMINF"
},
"biocontext": {
"prefix": "CHEMINF"
},
"bioportal": {
"contact": {
"email": "egon.willighagen@maastrichtuniversity.nl",
"name": "Egon Willighagen"
},
"description": "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.",
"homepage": "https://github.com/semanticchemistry/semanticchemistry",
"name": "Chemical Information Ontology",
"prefix": "CHEMINF",
"publication": "https://github.com/semanticchemistry/semanticchemistry",
"version": "2.1.0"
},
"download_owl": "https://github.com/semanticchemistry/semanticchemistry/raw/master/ontology/cheminf.owl",
"example": "000410",
"fairsharing": {
"abbreviation": "CHEMINF",
"contact": {
"email": "egon.willighagen@gmail.com",
"name": "Egon Willighagen",
"orcid": "0000-0001-7542-0286"
},
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],
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"name": "CHEMical INFormation Ontology",
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{
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"pubmed": "21991315",
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}
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"obofoundry": "cheminf",
"ols": "cheminf",
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],
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"domain": "chemistry and biochemistry",
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"homepage": "https://github.com/semanticchemistry/semanticchemistry",
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],
"subjects": [
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],
"twitter": "ChemSpider"
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"prefix": "P661",
"uri_format": "https://www.chemspider.com/Chemical-Structure.$1.html",
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},
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"description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs.",
"homepage": "https://www.animalgenome.org/QTLdb",
"id": "00000505",
"name": "Animal Genome Chicken QTL",
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},
"bioportal": {
"contact": {
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"name": "Nicole Vasilevsky"
},
"description": "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.",
"homepage": "https://github.com/obophenotype/chiro",
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"prefix": "CHIRO"
},
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"no_own_terms": true,
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"contact": "vasilevs@ohsu.edu",
"contact.github": "nicolevasilevsky",
"contact.label": "Nicole Vasilevsky",
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"ncbitaxon",
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],
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"description": "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.",
"domain": "chemistry and biochemistry",
"download.obo": "http://purl.obolibrary.org/obo/chiro.obo",
"download.owl": "http://purl.obolibrary.org/obo/chiro.owl",
"homepage": "https://github.com/obophenotype/chiro",
"license": "CC0 1.0",
"license.url": "http://creativecommons.org/publicdomain/zero/1.0/",
"name": "CHEBI Integrated Role Ontology",
"preferredPrefix": "CHIRO",
"prefix": "chiro",
"publications": [
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"title": "Extension of Roles in the ChEBI Ontology"
}
],
"repository": "https://github.com/obophenotype/chiro"
},
"ols": {
"description": "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.",
"download_owl": "http://purl.obolibrary.org/obo/chiro.owl",
"homepage": "https://github.com/obophenotype/chiro",
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"prefix": "chiro",
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}
]
},
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"name": "Chemical Methods Ontology",
"prefix": "CHMO"
},
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"homepage": "https://github.com/rsc-ontologies/rsc-cmo",
"license": "CC-BY-4.0",
"name": "Chemical Methods Ontology",
"prefix": "20509"
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"biocontext": {
"prefix": "CHMO"
},
"bioportal": {
"contact": {
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},
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"name": "Chemical Methods Ontology",
"prefix": "CHMO",
"version": "releases/2014-11-20"
},
"download_obo": "http://purl.obolibrary.org/obo/chmo.obo",
"example": "0002902",
"fairsharing": {
"abbreviation": "CHMO",
"description": "CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy; prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis; and synthesise materials such as epitaxy and continuous vapour deposition. It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI).",
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"Electron microscopy",
"Assay",
"Mass spectrometry assay"
],
"homepage": "https://github.com/rsc-ontologies/rsc-cmo",
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"name": "Chemical Methods Ontology",
"prefix": "FAIRsharing.9j4wh2",
"repository": "https://github.com/rsc-ontologies/rsc-cmo/issues",
"subjects": [
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},
"mappings": {
"aberowl": "CHMO",
"bartoc": "20509",
"biocontext": "CHMO",
"bioportal": "CHMO",
"fairsharing": "FAIRsharing.9j4wh2",
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},
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],
"contact": "batchelorc@rsc.org",
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"description": "CHMO, the chemical methods ontology, describes methods used to",
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"download.owl": "http://purl.obolibrary.org/obo/chmo.owl",
"homepage": "https://github.com/rsc-ontologies/rsc-cmo",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Chemical Methods Ontology",
"preferredPrefix": "CHMO",
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"repository": "https://github.com/rsc-ontologies/rsc-cmo"
},
"ols": {
"contact": "chemistry-ontologies@googlegroups.com",
"description": "CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI).",
"download_owl": "http://purl.obolibrary.org/obo/chmo.owl",
"homepage": "https://github.com/rsc-ontologies/rsc-cmo",
"name": "Chemical Methods Ontology",
"prefix": "chmo",
"version": "2022-04-19",
"version.iri": "http://purl.obolibrary.org/obo/chmo/releases/2022-04-19/chmo.owl"
},
"ontobee": {
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"name": "Chemical Methods Ontology",
"prefix": "CHMO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/CHMO_$1"
},
"cido": {
"aberowl": {
"description": "The Coronavirus Infectious Disease Ontology (CIDO) aims to ontologically represent and standardize various aspects of coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment.",
"download_owl": "http://aber-owl.net/media/ontologies/CIDO/35/cido.owl",
"homepage": "https://github.com/cido-ontology/cido",
"name": "Coronavirus Infectious Disease Ontology",
"prefix": "CIDO"
},
"bioportal": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun Oliver He"
},
"description": "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.",
"homepage": "https://github.com/CIDO-ontology/cido",
"name": "Coronavirus Infectious Disease Ontology",
"prefix": "CIDO",
"publication": "He Y, Yu H, Ong E, Wang Y, Liu Y, Huffman A, Huang H, Beverley J, Hur J, Yang X, Chen L, Omenn GS, Athey B, Smith B. CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. Scientific Data. (2020) 7:181 | https://doi.org/10.1038/s41597-020-0523-6.",
"version": "2024-02-16"
},
"download_owl": "https://github.com/CIDO-ontology/cido/raw/master/cido.owl",
"example": "0000005",
"fairsharing": {
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"description": "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment. Its development follows the OBO Foundry Principles.",
"domains": [
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"Infection",
"Disease"
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"homepage": "https://github.com/cido-ontology/cido",
"license": "CC-BY-4.0",
"name": "Coronavirus Infectious Disease Ontology",
"prefix": "FAIRsharing.aVmpKl",
"publications": [
{
"doi": "10.1038/s41597-020-0523-6",
"pubmed": "32533075",
"title": "CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis",
"year": 2020
}
],
"repository": "https://github.com/CIDO-ontology/cido/issues",
"subjects": [
"Drug Discovery",
"Bioinformatics",
"Drug Repositioning",
"Virology",
"Epidemiology"
],
"user_defined_tags": [
"COVID-19"
]
},
"mappings": {
"aberowl": "CIDO",
"bioportal": "CIDO",
"fairsharing": "FAIRsharing.aVmpKl",
"obofoundry": "cido",
"ols": "cido",
"ontobee": "CIDO"
},
"obofoundry": {
"contact": "yongqunh@med.umich.edu",
"contact.github": "yongqunh",
"contact.label": "Yongqun Oliver He",
"contact.orcid": "0000-0001-9189-9661",
"deprecated": false,
"description": "The Coronavirus Infectious Disease Ontology (CIDO) aims to ontologically represent and standardize various aspects of coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/cido.owl",
"homepage": "https://github.com/cido-ontology/cido",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Coronavirus Infectious Disease Ontology",
"preferredPrefix": "CIDO",
"prefix": "cido",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/36271389",
"title": "A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology"
}
],
"repository": "https://github.com/cido-ontology/cido"
},
"ols": {
"contact": "cido-discuss@googlegroups.com",
"description": "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.",
"download_owl": "http://purl.obolibrary.org/obo/cido.owl",
"homepage": "https://github.com/cido-ontology/cido",
"name": "CIDO: Ontology of Coronavirus Infectious Disease",
"prefix": "cido",
"version": "2024-02-16",
"version.iri": "http://purl.obolibrary.org/obo/cido/releases/2024-02-16/cido.owl"
},
"ontobee": {
"library": "Library",
"name": "Coronavirus Infectious Disease Ontology",
"prefix": "CIDO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1186/s13326-022-00279-z",
"pmc": "PMC9585694",
"pubmed": "36271389",
"title": "A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology",
"year": 2022
},
{
"doi": "10.1038/s41597-020-0523-6",
"pmc": "PMC7293349",
"pubmed": "32533075",
"title": "CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis",
"year": 2020
}
],
"uri_format": "http://purl.obolibrary.org/obo/CIDO_$1"
},
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"aberowl": {
"description": "An ontology to capture confidence information about annotations.",
"download_owl": "http://aber-owl.net/media/ontologies/CIO/2/cio.owl",
"homepage": "https://github.com/BgeeDB/confidence-information-ontology",
"name": "Confidence Information Ontology",
"prefix": "CIO"
},
"biocontext": {
"prefix": "CIO"
},
"bioportal": {
"contact": {
"email": "frederic.bastian@unil.ch",
"name": "Frederic Bastian"
},
"description": "An ontology to capture confidence information about annotations",
"homepage": "https://github.com/BgeeDB/confidence-information-ontology",
"name": "Confidence Information Ontology",
"prefix": "CIO"
},
"example": "0000040",
"fairsharing": {
"abbreviation": "CIO",
"description": "The Confidence Information Ontology (CIO) is an ontology to capture confidence information about annotations. Please note that the last update to the ontology files were in 2015.",
"domains": [
"Annotation"
],
"homepage": "https://github.com/BgeeDB/confidence-information-ontology",
"license": "CC0-1.0",
"name": "Confidence Information Ontology",
"prefix": "FAIRsharing.e3t0yw",
"publications": [
{
"doi": "10.1093/database/bav043",
"title": "The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations",
"year": 2015
}
],
"subjects": [
"Biology"
]
},
"mappings": {
"aberowl": "CIO",
"biocontext": "CIO",
"bioportal": "CIO",
"fairsharing": "FAIRsharing.e3t0yw",
"obofoundry": "cio",
"ols": "cio",
"ontobee": "CIO"
},
"obofoundry": {
"contact": "frederic.bastian@unil.ch",
"contact.github": "fbastian",
"contact.label": "FrΓ©dΓ©ric Bastian",
"contact.orcid": "0000-0002-9415-5104",
"deprecated": false,
"description": "An ontology to capture confidence information about annotations.",
"domain": "information",
"download.obo": "http://purl.obolibrary.org/obo/cio.obo",
"download.owl": "http://purl.obolibrary.org/obo/cio.owl",
"homepage": "https://github.com/BgeeDB/confidence-information-ontology",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Confidence Information Ontology",
"preferredPrefix": "CIO",
"prefix": "cio",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/25957950",
"title": "The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations"
}
],
"repository": "https://github.com/BgeeDB/confidence-information-ontology"
},
"ols": {
"description": "An ontology to capture confidence information about annotations.",
"download_owl": "http://purl.obolibrary.org/obo/cio.owl",
"homepage": "https://github.com/BgeeDB/confidence-information-ontology",
"name": "Confidence Information Ontology",
"prefix": "cio",
"version": "2015-03-10",
"version.iri": "http://purl.obolibrary.org/obo/cio/releases/2015-03-10/cio.owl"
},
"ontobee": {
"library": "Library",
"name": "Confidence Information Ontology",
"prefix": "CIO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1093/database/bav043",
"pmc": "PMC4425939",
"pubmed": "25957950",
"title": "The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations",
"year": 2015
}
],
"uri_format": "http://purl.obolibrary.org/obo/CIO_$1"
},
"citexplore": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes.",
"example": "C6155",
"fairsharing": {
"abbreviation": "CTX",
"contact": {
"email": "maria.taboada@usc.es",
"name": "Maria Taboada",
"orcid": "0000-0002-2353-596X"
},
"description": "The ontology represents CTX phenotypes, genetic variants, and bidirectional relationships between them though a patient model. The CTX ontology was build reusing the Human Phenotype Ontology (HPO) and the Snomed ct ontologies. A set of temporal clinical manifestations are semantically annotated with a domain phenotype ontology and registered with a time-stamped value.",
"domains": [
"Lipid",
"Phenotype",
"Disease",
"Brain"
],
"homepage": "http://bioportal.bioontology.org/ontologies/CTX",
"name": "Cerebrotendinous Xanthomatosis Ontology",
"prefix": "FAIRsharing.619eqr",
"publications": [
{
"doi": "10.1097/mol.0b013e328362df13",
"pubmed": "23759795",
"title": "Cerebrotendinous xanthomatosis",
"year": 2013
}
],
"subjects": [
"Genetics",
"Biomedical Science",
"Preclinical Studies"
]
},
"homepage": "https://www.ebi.ac.uk/citexplore/",
"mappings": {
"fairsharing": "FAIRsharing.619eqr",
"prefixcommons": "citexplore"
},
"name": "CiteXplore",
"prefixcommons": {
"description": "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.",
"example": "16333295",
"homepage": "http://www.ebi.ac.uk/citexplore/",
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "CiteXplore",
"pattern": "^\\d+$",
"prefix": "citexplore",
"uri_format": "http://www.ebi.ac.uk/citexplore/citationDetails.do?dataSource=MED&externalId=$1"
},
"publications": [
{
"doi": "10.1097/mol.0b013e328362df13",
"pubmed": "23759795",
"title": "Cerebrotendinous xanthomatosis",
"year": 2013
}
],
"references": [
"https://www.embl.de/aboutus/communication_outreach/media_relations/2006/061127_hinxton/"
],
"synonyms": [
"CTX"
],
"uri_format": "https://europepmc.org/article/CTX/$1"
},
"cito": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology that enables characterization of the nature or type of citations, both factually and rhetorically.",
"example": "sharesAuthorInstitutionWith",
"fairsharing": {
"abbreviation": "CiTO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Citation Typing Ontology (CiTO) is an ontology that enables the characterization of the nature or type of citations, both factually and rhetorically. It is intended to allow authors (or others) to mark citation links and to capture citation intent when someone cites a particular publication. In particular, CiTO allows the creation of metadata describing citations that are distinct from metadata describing the cited works themselves, and permits the motives of an author when referring to another document to be captured.\n",
"domains": [
"Citation",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/cito",
"license": "CC-BY-4.0",
"name": "Citation Typing Ontology ",
"prefix": "FAIRsharing.b220d4",
"publications": [
{
"doi": "10.1016/j.websem.2012.08.001",
"title": "FaBiO and CiTO: Ontologies for describing bibliographic resources and citations",
"year": 2012
}
],
"repository": "https://github.com/sparontologies/cito",
"subjects": [
"Knowledge and Information Systems"
],
"twitter": "sparontologies"
},
"homepage": "http://www.sparontologies.net/ontologies/cito",
"lov": {
"description": "The Citation Typing Ontology enables characterization of the nature or type of citations",
"homepage": "http://www.sparontologies.net/ontologies/cito",
"keywords": [
"SPAR"
],
"modified": "2018-02-16",
"name": "CiTO, the Citation Typing Ontology",
"prefix": "cito",
"uri_prefix": "http://purl.org/spar/cito/$1"
},
"mappings": {
"fairsharing": "FAIRsharing.b220d4",
"lov": "cito"
},
"name": "Citation Typing Ontology",
"preferred_prefix": "CiTO",
"publications": [
{
"doi": "10.1016/j.websem.2012.08.001",
"title": "FaBiO and CiTO: Ontologies for describing bibliographic resources and citations",
"year": 2012
}
],
"repository": "https://github.com/sparontologies/cito",
"uri_format": "http://purl.org/spar/cito/$1"
},
"civic.aid": {
"contact": {
"email": "mgriffit@wustl.edu",
"github": "malachig",
"name": "Malachi Griffith",
"orcid": "0000-0002-6388-446X"
},
"license": "CC0-1.0",
"mappings": {
"miriam": "civic.aid"
},
"miriam": {
"deprecated": false,
"description": "A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC.",
"homepage": "https://civicdb.org/",
"id": "00000835",
"name": "CIViC Assertion",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "civic.aid",
"sampleId": "3",
"uri_format": "https://civicdb.org/links/assertions/$1"
},
"part_of": "civic",
"synonyms": [
"civic.assertion"
]
},
"civic.did": {
"contact": {
"email": "mgriffit@wustl.edu",
"github": "malachig",
"name": "Malachi Griffith",
"orcid": "0000-0002-6388-446X"
},
"license": "CC0-1.0",
"mappings": {
"miriam": "civic.did"
},
"miriam": {
"deprecated": false,
"description": "Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement.",
"homepage": "https://civicdb.org/",
"id": "00000957",
"name": "CIViC Disease",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "civic.did",
"sampleId": "46",
"uri_format": "https://civicdb.org/links/diseases/$1"
},
"part_of": "civic",
"synonyms": [
"civic.disease"
]
},
"civic.eid": {
"contact": {
"email": "mgriffit@wustl.edu",
"github": "malachig",
"name": "Malachi Griffith",
"orcid": "0000-0002-6388-446X"
},
"license": "CC0-1.0",
"mappings": {
"miriam": "civic.eid"
},
"miriam": {
"deprecated": false,
"description": "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic βeventβ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract).",
"homepage": "https://civicdb.org/",
"id": "00000839",
"name": "CIViC Evidence",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "civic.eid",
"sampleId": "1199",
"uri_format": "https://civicdb.org/links/evidence/$1"
},
"part_of": "civic",
"synonyms": [
"civic.evidence"
]
},
"civic.gid": {
"contact": {
"email": "mgriffit@wustl.edu",
"github": "malachig",
"name": "Malachi Griffith",
"orcid": "0000-0002-6388-446X"
},
"license": "CC0-1.0",
"mappings": {
"miriam": "civic.gid",
"wikidata": "P11277"
},
"miriam": {
"deprecated": false,
"description": "A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus on emphasizing the clinical relevance from a molecular perspective rather than describing the biological function of the gene unless necessary to contextualize its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes, specific treatments for the geneβs associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis",
"homepage": "https://civicdb.org/",
"id": "00000907",
"name": "CIViC Gene",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "civic.gid",
"sampleId": "272",
"uri_format": "https://civicdb.org/links/gene/$1"
},
"name": "CIViC gene",
"part_of": "civic",
"synonyms": [
"civic.gene"
],
"wikidata": {
"description": "identifier for a human gene in the CIViC database",
"example": [
"1134",
"14221",
"2",
"3",
"4"
],
"homepage": "https://civic.genome.wustl.edu/#/home",
"name": "CIViC gene ID",
"pattern": "^[1-9]\\d*$",
"prefix": "P11277",
"uri_format": "https://civicdb.org/genes/$1/summary"
}
},
"civic.mpid": {
"contact": {
"email": "mgriffit@wustl.edu",
"github": "malachig",
"name": "Malachi Griffith",
"orcid": "0000-0002-6388-446X"
},
"license": "CC0-1.0",
"mappings": {
"miriam": "civic.mpid"
},
"miriam": {
"deprecated": false,
"description": "CIViC Molecular Profiles are combinations of one or more CIViC variants. Most Molecular Profiles are βSimpleβ Molecular Profiles comprised of a single variant. In most cases, these can be considered equivalent to the CIViC concept of a Variant. However, increasingly clinical significance must be considered in the context of multiple variants simultaneously. Complex Molecular Profiles in CIViC allow for curation of such variant combinations. Regardless of the nature of the Molecular Profile (Simple or Complex), it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional clinical relevance to be entered in CIViC.",
"homepage": "https://civicdb.org/",
"id": "00000981",
"name": "CIViC Molecular Profile",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "civic.mpid",
"sampleId": "559",
"uri_format": "https://civicdb.org/links/molecular_profile/$1"
},
"synonyms": [
"civic.molecularprofile"
]
},
"civic.sid": {
"contact": {
"email": "mgriffit@wustl.edu",
"github": "malachig",
"name": "Malachi Griffith",
"orcid": "0000-0002-6388-446X"
},
"license": "CC0-1.0",
"mappings": {
"miriam": "civic.sid"
},
"miriam": {
"deprecated": false,
"description": "In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source.",
"homepage": "https://civicdb.org/",
"id": "00000953",
"name": "CIViC Source",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "civic.sid",
"sampleId": "62",
"uri_format": "https://civicdb.org/links/sources/$1"
},
"part_of": "civic",
"synonyms": [
"civic.source"
]
},
"civic.tid": {
"contact": {
"email": "mgriffit@wustl.edu",
"github": "malachig",
"name": "Malachi Griffith",
"orcid": "0000-0002-6388-446X"
},
"license": "CC0-1.0",
"mappings": {
"miriam": "civic.tid"
},
"miriam": {
"deprecated": false,
"description": "Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant.",
"homepage": "https://civicdb.org/",
"id": "00000955",
"name": "CIViC Therapy",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "civic.tid",
"sampleId": "14",
"uri_format": "https://civicdb.org/links/drugs/$1"
},
"part_of": "civic",
"synonyms": [
"civic.therapy"
]
},
"civic.vgid": {
"contact": {
"email": "mgriffit@wustl.edu",
"github": "malachig",
"name": "Malachi Griffith",
"orcid": "0000-0002-6388-446X"
},
"license": "CC0-1.0",
"mappings": {
"miriam": "civic.vgid"
},
"miriam": {
"deprecated": false,
"description": "Variant Groups in CIViC provide user-defined grouping of Variants within and between genes based on unifying characteristics. CIViC curators are required to define a cohesive rationale for grouping these variants together, summarize their relevance to cancer diagnosis, prognosis or treatment and highlight any treatments or cancers of particular relevance",
"homepage": "https://civicdb.org/",
"id": "00000979",
"name": "CIViC Variant Group",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "civic.vgid",
"sampleId": "16",
"uri_format": "https://civicdb.org/links/variant_group/$1"
},
"synonyms": [
"civic.variantgroup"
]
},
"civic.vid": {
"contact": {
"email": "mgriffit@wustl.edu",
"github": "malachig",
"name": "Malachi Griffith",
"orcid": "0000-0002-6388-446X"
},
"license": "CC0-1.0",
"mappings": {
"miriam": "civic.vid",
"wikidata": "P3329"
},
"miriam": {
"deprecated": false,
"description": "CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNVβs such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the βnormalβ genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, βexpressionβ or βover-expressionβ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making.",
"homepage": "https://civicdb.org/",
"id": "00000909",
"name": "CIViC Variant",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "civic.vid",
"sampleId": "12",
"uri_format": "https://civicdb.org/links/variant/$1"
},
"name": "CIViC variant",
"part_of": "civic",
"synonyms": [
"civic.variant"
],
"wikidata": {
"description": "identifier used in the CIViC database to identify specific variant",
"example": [
"12",
"2416",
"2979"
],
"homepage": "https://civic.genome.wustl.edu/#/home",
"name": "CIViC variant ID",
"pattern": "^[1-9]\\d*$",
"prefix": "P3329",
"uri_format": "https://civic.genome.wustl.edu/links/variants/$1"
}
},
"cl": {
"aberowl": {
"description": "The Cell Ontology is a structured controlled vocabulary for cell types in animals.",
"download_owl": "http://aber-owl.net/media/ontologies/CL/107/cl.owl",
"homepage": "https://obophenotype.github.io/cell-ontology/",
"name": "Cell Ontology",
"prefix": "CL"
},
"agroportal": {
"contact": {
"email": "addiehl@buffalo.edu",
"name": "Alex Diehl"
},
"description": "An ontology of cell types.",
"example_uri": "http://purl.obolibrary.org/obo/CL_0000000",
"homepage": "https://cell-ontology.github.io/",
"license": "CC-BY-4.0",
"name": "Cell Ontology",
"prefix": "CL",
"repository": "https://github.com/obophenotype/cell-ontology",
"version": "2024-07-10"
},
"biocontext": {
"prefix": "CL"
},
"bioportal": {
"contact": {
"email": "addiehl@buffalo.edu",
"name": "Alexander Diehl"
},
"description": "The Cell Ontology is a structured controlled vocabulary for cell types in animals. The Cell Ontology is designed as a structured controlled vocabulary for cell types. This ontology was constructed for use by the model organism and other bioinformatics databases, where there is a need for a controlled vocabulary of cell types. This ontology is not organism specific. It covers cell types from prokaryotes to mammals. However, it excludes plant cell types, which are covered by PO.",
"homepage": "https://obophenotype.github.io/cell-ontology/",
"name": "Cell Ontology",
"prefix": "CL",
"publication": "https://www.ncbi.nlm.nih.gov/pubmed/27377652",
"version": "2024-07-10"
},
"cellosaurus": {
"category": "Anatomy/cell type resources",
"homepage": "https://obophenotype.github.io/cell-ontology/",
"name": "Cell Ontology",
"prefix": "CL",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http://purl.obolibrary.org/obo/$1"
},
"contributor_extras": [
{
"github": "anitacaron",
"name": "Anita Caron",
"orcid": "0000-0002-6523-4866"
}
],
"download_obo": "https://github.com/obophenotype/cell-ontology/raw/master/cl.obo",
"example": "0000062",
"fairsharing": {
"abbreviation": "CL",
"contact": {
"email": "addiehl@buffalo.edu",
"name": "Alexander Diehl",
"orcid": "0000-0001-9990-8331"
},
"description": "The Cell Ontology (CL) is a candidate OBO Foundry ontology for the representation of cell types. First described in 2005, the CL integrates cell types from the prokaryotic, fungal, and eukaryotic organisms. As a core component of the OBO Foundry, the CL merges information contained in species-specific anatomical ontologies as well as referencing other OBO Foundry ontologies such as the Protein Ontology (PR) for uniquely expressed biomarkers and the Gene Ontology (GO) for the biological processes a cell type participates in. The CL is under continuous revision to expand representation of cell types and to better integrate with other biomedical ontologies.",
"domains": [
"Annotation",
"Cell",
"Morphology"
],
"homepage": "https://github.com/obophenotype/cell-ontology",
"license": "CC-BY-3.0",
"name": "Cell Ontology",
"prefix": "FAIRsharing.j9y503",
"publications": [
{
"doi": "10.1186/1471-2105-12-6",
"pubmed": "21208450",
"title": "Logical development of the cell ontology",
"year": 2011
},
{
"doi": "10.1186/s13326-016-0088-7",
"pubmed": "27377652",
"title": "The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability",
"year": 2016
}
],
"repository": "https://github.com/obophenotype/cell-ontology/blob/master/src/ontology/README.txt",
"subjects": [
"Anatomy",
"Life Science",
"Cell Biology"
]
},
"go": {
"homepage": "http://cellontology.org",
"name": "Cell Type Ontology",
"prefix": "CL"
},
"mappings": {
"aberowl": "CL",
"agroportal": "CL",
"biocontext": "CL",
"bioportal": "CL",
"cellosaurus": "CL",
"fairsharing": "FAIRsharing.j9y503",
"go": "CL",
"miriam": "cl",
"n2t": "cl",
"obofoundry": "cl",
"ols": "cl",
"ontobee": "CL",
"prefixcommons": "cl",
"wikidata": "P7963"
},
"miriam": {
"deprecated": false,
"description": "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.",
"homepage": "http://bioportal.bioontology.org/ontologies/CL",
"id": "00000110",
"name": "Cell Type Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^CL:\\d{7}$",
"prefix": "cl",
"sampleId": "0000232",
"uri_format": "http://purl.bioontology.org/ontology/CL/CL:$1"
},
"n2t": {
"description": "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.",
"example": "0000232",
"homepage": "http://bioportal.bioontology.org/ontologies/CL",
"name": "Cell Type Ontology through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^CL:\\d{7}$",
"prefix": "cl",
"uri_format": "http://purl.bioontology.org/ontology/CL/CL:$1"
},
"obofoundry": {
"appears_in": [
"clo",
"ecao",
"go",
"mco",
"pcl",
"uberon",
"xpo",
"ehdaa2"
],
"contact": "addiehl@buffalo.edu",
"contact.github": "addiehl",
"contact.label": "Alexander Diehl",
"contact.orcid": "0000-0001-9990-8331",
"depends_on": [
"chebi",
"go",
"ncbitaxon",
"pato",
"pr",
"ro",
"uberon"
],
"deprecated": false,
"description": "The Cell Ontology is a structured controlled vocabulary for cell types in animals.",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/cl.obo",
"download.owl": "http://purl.obolibrary.org/obo/cl.owl",
"homepage": "https://obophenotype.github.io/cell-ontology/",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"logo": "https://obofoundry.org/images/CL-logo.jpg",
"name": "Cell Ontology",
"preferredPrefix": "CL",
"prefix": "cl",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/27377652",
"title": "The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability."
}
],
"repository": "https://github.com/obophenotype/cell-ontology",
"twitter": "CellOntology"
},
"ols": {
"description": "An ontology of cell types.",
"download_owl": "http://purl.obolibrary.org/obo/cl.owl",
"homepage": "https://obophenotype.github.io/cell-ontology/",
"name": "Cell Ontology",
"prefix": "cl",
"version": "2024-07-10",
"version.iri": "http://purl.obolibrary.org/obo/cl/releases/2024-07-10/cl.owl"
},
"ontobee": {
"library": "Library",
"name": "Cell Ontology",
"prefix": "CL"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1006",
"description": "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.",
"example": "CL:0000232",
"homepage": "http://lists.sourceforge.net/lists/listinfo/obo-cell-type",
"keywords": [
"obo",
"cell"
],
"name": "Cell Ontology",
"pattern": "^CL:\\d+$",
"prefix": "cl"
},
"providers": [
{
"code": "cellxgene",
"description": "Explore single cell data through the CZ CELLxGENE portal",
"homepage": "https://onto.cellxgene-labs.prod.si.czi.technology",
"name": "CELLxGENE",
"uri_format": "https://onto.cellxgene-labs.prod.si.czi.technology/a/ontology/CL/CL:$1"
},
{
"code": "cellguide",
"description": "CellGuide is a comprehensive resource for knowledge about cell types.",
"homepage": "https://cellxgene.cziscience.com/cellguide",
"name": "Cell Guide",
"uri_format": "https://cellxgene.cziscience.com/cellguide/CL_$1"
}
],
"publications": [
{
"doi": "10.1186/s13326-016-0088-7",
"pmc": "PMC4932724",
"pubmed": "27377652",
"title": "The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability",
"year": 2016
},
{
"doi": "10.1186/1471-2105-12-6",
"pmc": "PMC3024222",
"pubmed": "21208450",
"title": "Logical development of the cell ontology",
"year": 2011
}
],
"uri_format": "http://purl.obolibrary.org/obo/CL_$1",
"wikidata": {
"description": "ID in the Cell Ontology",
"example": [
"CL_0000148",
"CL_0000232",
"CL_0000235",
"CL_0000540",
"CL_0002328"
],
"homepage": "https://github.com/obophenotype/cell-ontology",
"miriam": "cl",
"name": "Cell Ontology ID",
"pattern": "^CL_[0-9]{7}$",
"prefix": "P7963"
}
},
"clao": {
"aberowl": {
"description": "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).",
"download_owl": "http://aber-owl.net/media/ontologies/CLAO/2/clao.owl",
"homepage": "https://github.com/luis-gonzalez-m/Collembola",
"name": "Collembola Anatomy Ontology",
"prefix": "CLAO"
},
"bioportal": {
"contact": {
"email": "lagonzalezmo@unal.edu.co",
"name": "Luis A. GonzΓ‘lez-MontaΓ±a"
},
"description": "Collembola Anatomy Ontology (CLAO) includes anatomical terms to refer to sclerites, anatomical systems, cell components, and chaetotaxy. CLAO is directed towards building semantic annotations or the production of morphological data employing a standardized language. CLAO is intended as a complementary tool to morhological descriptions during taxonomic work, before obtaining phylogenetic characters.",
"homepage": "http://github/luis-gonzalez-m",
"name": "Collembola Anatomy Ontology",
"prefix": "CLAO",
"version": "2021-09-27"
},
"example": "0000088",
"mappings": {
"aberowl": "CLAO",
"bioportal": "CLAO",
"obofoundry": "clao",
"ols": "clao",
"ontobee": "CLAO"
},
"obofoundry": {
"contact": "lagonzalezmo@unal.edu.co",
"contact.github": "luis-gonzalez-m",
"contact.label": "Luis GonzΓ‘lez-MontaΓ±a",
"contact.orcid": "0000-0002-9136-9932",
"depends_on": [
"ro"
],
"deprecated": false,
"description": "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/clao.obo",
"download.owl": "http://purl.obolibrary.org/obo/clao.owl",
"homepage": "https://github.com/luis-gonzalez-m/Collembola",
"license": "CC0 1.0",
"license.url": "http://creativecommons.org/publicdomain/zero/1.0/",
"name": "Collembola Anatomy Ontology",
"preferredPrefix": "CLAO",
"prefix": "clao",
"repository": "https://github.com/luis-gonzalez-m/Collembola"
},
"ols": {
"description": "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).",
"download_owl": "http://purl.obolibrary.org/obo/clao.owl",
"homepage": "https://github.com/luis-gonzalez-m/Collembola",
"name": "Collembola Anatomy Ontology",
"prefix": "clao",
"version": "2021-09-27",
"version.iri": "http://purl.obolibrary.org/obo/clao/releases/2021-09-27/clao.owl"
},
"ontobee": {
"library": "Library",
"name": "Collembola Anatomy Ontology",
"prefix": "CLAO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/CLAO_$1"
},
"classyfire": {
"banana": "C",
"banana_peel": "",
"comment": "There's a mismatch between the MIRIAM URI format string, which has a C prefix in front of class identifiers and the ontology which does not use them.",
"download_obo": "http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip",
"example": "0004828",
"mappings": {
"miriam": "classyfire"
},
"miriam": {
"deprecated": false,
"description": "ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API.",
"homepage": "http://classyfire.wishartlab.com/",
"id": "00000770",
"name": "ClassyFire",
"namespaceEmbeddedInLui": false,
"pattern": "^C[0-9]{7}$",
"prefix": "classyfire",
"sampleId": "C0004828",
"uri_format": "http://classyfire.wishartlab.com/tax_nodes/$1"
},
"pattern": "^\\d{7}$",
"synonyms": [
"CHEMONTID"
],
"uri_format": "http://classyfire.wishartlab.com/tax_nodes/C$1"
},
"clb": {
"mappings": {
"miriam": "clb"
},
"miriam": {
"deprecated": false,
"description": "ChecklistBank is an index and repository for taxonomic and nomenclatural datasets",
"homepage": "https://www.checklistbank.org",
"id": "00000964",
"name": "ChecklistBank",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+(LR)?$",
"prefix": "clb",
"sampleId": "1010",
"uri_format": "https://www.checklistbank.org/dataset/$1"
}
},
"cldb": {
"biocontext": {
"prefix": "CLDB"
},
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "http://bioinformatics.hsanmartino.it/cldb/",
"name": "Cell Line Data Base",
"prefix": "CLDB",
"uri_format": "http://bioinformatics.hsanmartino.it/cldb/$1.html"
},
"mappings": {
"biocontext": "CLDB",
"cellosaurus": "CLDB",
"miriam": "cldb",
"n2t": "cldb"
},
"miriam": {
"deprecated": false,
"description": "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories.",
"homepage": "http://bioinformatics.hsanmartino.it/hypercldb/indexes.html",
"id": "00000390",
"name": "CLDB",
"namespaceEmbeddedInLui": false,
"pattern": "^(cl|tum)\\d+$",
"prefix": "cldb",
"sampleId": "cl3603",
"uri_format": "http://bioinformatics.hsanmartino.it/hypercldb/$1.html"
},
"n2t": {
"description": "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories.",
"example": "cl3603",
"homepage": "http://bioinformatics.hsanmartino.it/hypercldb/indexes.html",
"name": "CLDB at Genova",
"namespaceEmbeddedInLui": false,
"pattern": "^(cl|tum)\\d+$",
"prefix": "cldb",
"uri_format": "http://bioinformatics.hsanmartino.it/hypercldb/$1.html"
},
"name": "Cell Line Database",
"synonyms": [
"hypercldb"
]
},
"clingene": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "CAID",
"uri_format": "http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor_extras": [
{
"github": "sierra-moxon",
"name": "Sierra Moxon",
"orcid": "0000-0002-8719-7760"
}
],
"description": "The allele registry provides and maintains identifiers for genetic variants",
"example": "CA981206459",
"homepage": "https://reg.clinicalgenome.org",
"keywords": [
"alleles",
"genetics",
"mutations"
],
"mappings": {
"biolink": "CAID"
},
"name": "ClinGen Allele Registry",
"pattern": "^CA\\d+$",
"references": [
"https://github.com/biopragmatics/bioregistry/issues/647"
],
"synonyms": [
"CAID"
],
"uri_format": "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1"
},
"clinicaltrials": {
"biocontext": {
"prefix": "CLINICALTRIALS"
},
"mappings": {
"biocontext": "CLINICALTRIALS",
"miriam": "clinicaltrials",
"n2t": "clinicaltrials",
"prefixcommons": "clinicaltrials",
"wikidata": "P3098"
},
"miriam": {
"deprecated": false,
"description": "ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries",
"homepage": "https://clinicaltrials.gov/",
"id": "00000137",
"name": "ClinicalTrials.gov",
"namespaceEmbeddedInLui": false,
"pattern": "^NCT\\d{8}$",
"prefix": "clinicaltrials",
"sampleId": "NCT00222573",
"uri_format": "https://clinicaltrials.gov/ct2/show/$1"
},
"n2t": {
"description": "ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries",
"example": "NCT00222573",
"homepage": "https://clinicaltrials.gov/",
"name": "ClinicalTrials.gov at NIH",
"namespaceEmbeddedInLui": false,
"pattern": "^NCT\\d{8}$",
"prefix": "clinicaltrials",
"uri_format": "https://clinicaltrials.gov/ct2/show/$1"
},
"name": "ClinicalTrials.gov",
"prefixcommons": {
"description": "ClinicalTrials.gov is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world.",
"example": "NCT00050895",
"homepage": "http://clinicaltrials.gov/",
"keywords": [
"disease",
"drug",
"human"
],
"license": "http://www.nlm.nih.gov/copyright.html",
"name": "ClinicalTrials.gov",
"pattern": "^NCT\\d{8}$",
"prefix": "clinicaltrials",
"uri_format": "http://clinicaltrials.gov/ct2/show/$1"
},
"providers": [
{
"code": "smartpatients",
"description": "Smart Patients is an online community for patients and their families. Join us to talk with other patients about the latest research for your condition.",
"homepage": "https://www.smartpatients.com",
"name": "Smart Patients",
"uri_format": "https://www.smartpatients.com/trials/$1"
}
],
"synonyms": [
"NCT",
"clinicaltrial",
"ctgov"
],
"uri_format": "https://www.clinicaltrials.gov/study/$1",
"wikidata": {
"description": "identifier in the ClinicalTrials.gov database",
"example": [
"NCT00243178",
"NCT04315948"
],
"name": "ClinicalTrials.gov ID",
"pattern": "^NCT(\\d{8})$",
"prefix": "P3098",
"uri_format": "https://clinicaltrials.gov/show/$1"
}
},
"clinvar": {
"biocontext": {
"prefix": "ClinVarVariant",
"uri_format": "http://www.ncbi.nlm.nih.gov/clinvar/variation/$1"
},
"biolink": {
"is_identifiers": true,
"is_obo": false,
"prefix": "CLINVAR",
"uri_format": "http://identifiers.org/clinvar$1"
},
"cellosaurus": {
"category": "Polymorphism and mutation databases",
"homepage": "https://www.ncbi.nlm.nih.gov/clinvar/",
"name": "ClinVar",
"prefix": "ClinVar",
"uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1"
},
"contact": {
"email": "maglott@ncbi.nlm.nih.gov",
"name": "Donna R. Maglott",
"orcid": "0000-0001-7451-4467"
},
"fairsharing": {
"abbreviation": "ClinVar",
"description": "ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works in collaboration with interested organizations to meet the needs of the medical genetics community as efficiently and effectively as possible.",
"homepage": "http://www.ncbi.nlm.nih.gov/clinvar/",
"license": "https://www.ncbi.nlm.nih.gov/home/about/policies",
"name": "ClinVar",
"prefix": "FAIRsharing.wx5r6f",
"publications": [
{
"doi": "10.1093/nar/gkt1113",
"pubmed_id": 24234437,
"title": "ClinVar: public archive of relationships among sequence variation and human phenotype."
}
],
"subjects": [
"Genomics",
"Clinical Studies",
"Biomedical Science",
"Preclinical Studies"
]
},
"hl7": {
"description": "ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. The ClinVar records have a field for Allele ID and for Variant ID. All simple variants have an Allele ID. At present, all complex and most simple variants also have a Variant ID, and by the end of 2016, all variants will have a variant ID. This coding system uses the variant ID as the code and the variant name ( field TBD) from the \"variant_summary\" file as the code print string. The \"variant_summary\" file caries more than 20 fields , including the seperate components of the variant nane, the cytogenomic locatiaon, the genomic reference etc. Many of these attributes have been indexed to assist users and applications that need to find the ID for a particular variant. ",
"homepage": "https://lhncbc.nlm.nih.gov/",
"name": "ClinVar Variant ID",
"organization": "National Lister Hill Center of Biomedical Communications, National Library of Medicine",
"preferred_prefix": "clinVar-V",
"prefix": "2.16.840.1.113883.6.319",
"status": "Complete"
},
"integbio": {
"description": "ClinVar is a freely available archive describing relationships between medically important variants and phenotypes. Submissions report human variation, interpretations of the relationship of that variation to human health, and the evidence supporting each interpretation. ClinVar is tightly coupled with dbSNP and dbVar, which maintain information about locations of variations on human assemblies, and also based on the phenotypic descriptions maintained in MedGen (http://www.ncbi.nlm.nih.gov/medgen). Each record contains the submitter, the variation and the phenotype. Furthermore, to facilitate evaluation of the medical importance of each variant, ClinVar aggregates submissions with the same variation/phenotype combination, adds value from other NCBI databases, and reports if there are conflicting clinical interpretations. Data in ClinVar are available in multiple formats, including html, download as XML, VCF or tab-delimited subsets.",
"fairsharing": "biodbcore-000739",
"homepage": "http://www.ncbi.nlm.nih.gov/clinvar/",
"information_keywords": [
"Phenotype",
"Bibliography/Documents",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "ClinVar",
"prefix": "nbdc01514",
"pubmeds": [
"24234437"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"mappings": {
"biocontext": "ClinVarVariant",
"biolink": "CLINVAR",
"cellosaurus": "ClinVar",
"fairsharing": "FAIRsharing.wx5r6f",
"hl7": "2.16.840.1.113883.6.319",
"integbio": "nbdc01514",
"miriam": "clinvar",
"n2t": "clinvar",
"re3data": "r3d100013331",
"togoid": "Clinvar",
"wikidata": "P1929"
},
"miriam": {
"deprecated": false,
"description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier.",
"homepage": "http://www.ncbi.nlm.nih.gov/clinvar/",
"id": "00000596",
"name": "ClinVar Variant",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "clinvar",
"sampleId": "12345",
"uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1"
},
"n2t": {
"description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier.",
"example": "12345",
"homepage": "http://www.ncbi.nlm.nih.gov/clinvar/",
"name": "ClinVar Variant at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "clinvar",
"uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1"
},
"name": "ClinVar Variation",
"publications": [
{
"doi": "10.1093/nar/gkt1113",
"pmc": "PMC3965032",
"pubmed": "24234437",
"title": "ClinVar: public archive of relationships among sequence variation and human phenotype",
"year": 2013
}
],
"re3data": {
"description": "ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works in collaboration with interested organizations to meet the needs of the medical genetics community as efficiently and effectively as possible",
"homepage": "https://www.ncbi.nlm.nih.gov/clinvar/",
"name": "ClinVar",
"prefix": "r3d100013331",
"xrefs": {
"fairsharing": "FAIRsharing.wx5r6f",
"nlx": "151671",
"scr": "006169"
}
},
"synonyms": [
"clinvar.variant",
"clinvar.variation"
],
"togoid": {
"catalog": "nbdc01514",
"examples": [
"658761",
"619209",
"745342",
"11955",
"731668",
"724289",
"725734",
"743127",
"789913",
"5302"
],
"keywords": [
"Variant"
],
"name": "ClinVar variant",
"pattern": "^(VCV0*)?(?(\\d{1,9}))$",
"prefix": "Clinvar",
"uri_format": "http://identifiers.org/clinvar/$1"
},
"wikidata": {
"description": "identifier in the ClinVar database for human genomic variation",
"example": [
"13961",
"586",
"7105"
],
"homepage": "https://www.ncbi.nlm.nih.gov/clinvar/",
"name": "ClinVar Variation ID",
"prefix": "P1929",
"uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1/"
}
},
"clinvar.record": {
"biocontext": {
"prefix": "CLINVAR.RECORD"
},
"mappings": {
"biocontext": "CLINVAR.RECORD",
"miriam": "clinvar.record",
"n2t": "clinvar.record"
},
"miriam": {
"deprecated": false,
"description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession.",
"homepage": "http://www.ncbi.nlm.nih.gov/clinvar/",
"id": "00000534",
"name": "ClinVar Record",
"namespaceEmbeddedInLui": false,
"pattern": "^RCV\\d+(\\.\\d+)?$",
"prefix": "clinvar.record",
"sampleId": "RCV000033555.3",
"uri_format": "http://www.ncbi.nlm.nih.gov/clinvar/$1/"
},
"n2t": {
"description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession.",
"example": "RCV000033555.3",
"homepage": "http://www.ncbi.nlm.nih.gov/clinvar/",
"name": "ClinVar Record at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^RCV\\d+(\\.\\d+)?$",
"prefix": "clinvar.record",
"uri_format": "http://www.ncbi.nlm.nih.gov/clinvar/$1/"
},
"part_of": "clinvar",
"uri_format": "http://www.ncbi.nlm.nih.gov/clinvar/$1"
},
"clinvar.submission": {
"biocontext": {
"prefix": "CLINVAR.SUBMISSION"
},
"mappings": {
"biocontext": "CLINVAR.SUBMISSION",
"miriam": "clinvar.submission",
"n2t": "clinvar.submission"
},
"miriam": {
"deprecated": false,
"description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession.",
"homepage": "http://www.ncbi.nlm.nih.gov/clinvar/",
"id": "00000595",
"name": "ClinVar Submission",
"namespaceEmbeddedInLui": false,
"pattern": "^SCV\\d+(\\.\\d+)?$",
"prefix": "clinvar.submission",
"sampleId": "SCV000151292",
"uri_format": "http://www.ncbi.nlm.nih.gov/clinvar?term=$1"
},
"n2t": {
"description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession.",
"example": "SCV000151292",
"homepage": "http://www.ncbi.nlm.nih.gov/clinvar/",
"name": "ClinVar Submission at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^SCV\\d+(\\.\\d+)?$",
"prefix": "clinvar.submission",
"uri_format": "http://www.ncbi.nlm.nih.gov/clinvar?term=$1"
}
},
"clinvar.submitter": {
"mappings": {
"miriam": "clinvar.submitter"
},
"miriam": {
"deprecated": false,
"description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs).",
"homepage": "https://www.ncbi.nlm.nih.gov/clinvar/",
"id": "00000769",
"name": "ClinVar Submitter",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "clinvar.submitter",
"sampleId": "26957",
"uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1"
}
},
"clo": {
"aberowl": {
"description": "An ontology to standardize and integrate cell line information and to support computer-assisted reasoning.",
"download_owl": "http://aber-owl.net/media/ontologies/CLO/7/clo.owl",
"homepage": "https://github.com/CLO-Ontology/CLO",
"name": "Cell Line Ontology",
"prefix": "CLO"
},
"biocontext": {
"prefix": "CLO"
},
"bioportal": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "The Cell Line Ontology (CLO) is a community-based ontology in domain of biological cell lines with a focus on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications.",
"homepage": "http://www.clo-ontology.org/",
"name": "Cell Line Ontology",
"prefix": "CLO",
"publication": "http://www.jbiomedsem.com/content/5/1/37",
"version": "2.1.188"
},
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "http://www.clo-ontology.org",
"name": "Cell Line Ontology",
"prefix": "CLO",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/clo/terms?iri=http://purl.obolibrary.org/obo/$1"
},
"example": "0000091",
"fairsharing": {
"abbreviation": "CLO",
"contact": {
"email": "Sirarat.Sarntivijai@fda.hhs.gov",
"name": "Sirarat Sarntivijai",
"orcid": "0000-0002-2548-641X"
},
"description": "The Cell Line Ontology (CLO) is a community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. Thousands of cell lines have been artificially developed and used for different applications. Integration of data from multiple sources is a challenge, confounded by lack of consistent naming conventions, contamination of cell lines, and provision of the same cell lines by multiple commercial sources but with different biological attributes. CLO is a community-based effort to represent all cell lines in a standard ontology approach.",
"domains": [
"Cell line",
"Cell",
"Morphology"
],
"homepage": "https://github.com/CLO-ontology/CLO",
"license": "CC-BY-3.0",
"name": "Cell Line Ontology",
"prefix": "FAIRsharing.4dvtcz",
"publications": [
{
"doi": "10.1186/2041-1480-5-37",
"pubmed": "25852852",
"title": "CLO: The cell line ontology",
"year": 2014
}
],
"repository": "https://github.com/CLO-ontology/CLO/issues",
"subjects": [
"Life Science",
"Cell Biology"
]
},
"mappings": {
"aberowl": "CLO",
"biocontext": "CLO",
"bioportal": "CLO",
"cellosaurus": "CLO",
"fairsharing": "FAIRsharing.4dvtcz",
"miriam": "clo",
"obofoundry": "clo",
"ols": "clo",
"ontobee": "CLO",
"prefixcommons": "clo",
"wikidata": "P2158"
},
"miriam": {
"deprecated": false,
"description": "The Cell Line Ontology is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/clo",
"id": "00000983",
"name": "Cell Line Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{7}$",
"prefix": "clo",
"providers": [
{
"code": "bioportal",
"description": "Our vision is that all biomedical knowledge and data are disseminated on the Internet using principled ontologies in such a way that the knowledge and data are semantically interoperable and useful for furthering biomedical science and clinical care. Our mission is to create software and support services for the application of principled ontologies in biomedical science and clinical care, ranging from tools for application developers to software for end-users.",
"homepage": "https://bioportal.bioontology.org",
"name": "Center for Biomedical Informatics Research, Stanford",
"uri_format": "https://bioportal.bioontology.org/ontologies/CLO/?p=classes&conceptid=http://purl.obolibrary.org/obo/CLO_$1"
}
],
"sampleId": "0000091",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/clo/terms?short_form=CLO_$1"
},
"obofoundry": {
"appears_in": [
"mco"
],
"contact": "zhengj2007@gmail.com",
"contact.github": "zhengj2007",
"contact.label": "Jie Zheng",
"contact.orcid": "0000-0002-2999-0103",
"depends_on": [
"cl",
"doid",
"ncbitaxon",
"uberon"
],
"deprecated": false,
"description": "An ontology to standardize and integrate cell line information and to support computer-assisted reasoning.",
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/clo.owl",
"homepage": "https://github.com/CLO-Ontology/CLO",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Cell Line Ontology",
"preferredPrefix": "CLO",
"prefix": "clo",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/25852852",
"title": "CLO: The Cell Line Ontology"
}
],
"repository": "https://github.com/CLO-Ontology/CLO"
},
"ols": {
"description": "The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.",
"download_owl": "http://purl.obolibrary.org/obo/clo.owl",
"homepage": "https://github.com/CLO-Ontology/CLO",
"name": "CLO: Cell Line Ontology",
"prefix": "clo",
"version": "2.1.188"
},
"ontobee": {
"library": "Library",
"name": "Cell Line Ontology",
"prefix": "CLO"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"alt_uri_formats": [
"http://purl.org/obo/owl/CL#$1",
"http://purl.org/obo/owl/CLO#$1"
],
"bioportal": "1314",
"description": "The Cell Line Ontology (CLO) is a community-based ontology in domain of biological cell lines with a focus on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications.",
"example": "CL:0000232",
"homepage": "http://sourceforge.net/projects/clo-ontology/",
"keywords": [
"ontology"
],
"name": "Cell Line Ontology",
"pattern": "^CL:\\d{7}$",
"prefix": "clo",
"pubmed_ids": [
"15693950"
],
"synonyms": [
"obo.clo"
]
},
"publications": [
{
"doi": "10.1186/2041-1480-5-37",
"pmc": "PMC4387853",
"pubmed": "25852852",
"title": "CLO: The cell line ontology",
"year": 2014
},
{
"doi": "10.1186/gb-2005-6-2-r21",
"pmc": "PMC551541",
"pubmed": "15693950",
"title": "An ontology for cell types",
"year": 2005
}
],
"synonyms": [
"CLO"
],
"uri_format": "http://purl.obolibrary.org/obo/CLO_$1",
"wikidata": {
"description": "identifier for the Cell Line Ontology which describes anatomic origin and nature of eukaryotic cell lines",
"example": [
"CLO_0004283",
"CLO_0007043",
"CLO_0008177"
],
"homepage": "http://www.clo-ontology.org/",
"name": "Cell Line Ontology ID",
"pattern": "^CLO_\\d{7}$",
"prefix": "P2158"
}
},
"cls": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.cytion.com/",
"name": "Cell Lines Service",
"prefix": "CLS",
"uri_format": "https://www.cytion.com/$1"
},
"example": "300108/p3934_A-172",
"mappings": {
"cellosaurus": "CLS"
}
},
"clyh": {
"aberowl": {
"description": "The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle.",
"download_owl": "http://aber-owl.net/media/ontologies/CLYH/3/clyh.owl",
"homepage": "https://github.com/EBISPOT/clyh_ontology",
"name": "Clytia hemisphaerica Development and Anatomy Ontology",
"prefix": "CLYH"
},
"bioportal": {
"contact": {
"email": "lucas.leclere@obs-vlfr.fr",
"name": "Lucas Leclere"
},
"description": "The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle.",
"homepage": "https://github.com/EBISPOT/clyh_ontology",
"name": "Clytia hemisphaerica Development and Anatomy Ontology",
"prefix": "CLYH"
},
"example": "1000100",
"mappings": {
"aberowl": "CLYH",
"bioportal": "CLYH",
"obofoundry": "clyh",
"ols": "clyh",
"ontobee": "CLYH"
},
"obofoundry": {
"contact": "lucas.leclere@obs-vlfr.fr",
"contact.github": "L-Leclere",
"contact.label": "Lucas Leclere",
"contact.orcid": "0000-0002-7440-0467",
"depends_on": [
"iao",
"ro",
"uberon"
],
"deprecated": false,
"description": "The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle.",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/clyh.obo",
"download.owl": "http://purl.obolibrary.org/obo/clyh.owl",
"homepage": "https://github.com/EBISPOT/clyh_ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Clytia hemisphaerica Development and Anatomy Ontology",
"preferredPrefix": "CLYH",
"prefix": "clyh",
"repository": "https://github.com/EBISPOT/clyh_ontology"
},
"ols": {
"description": "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica.",
"download_owl": "http://purl.obolibrary.org/obo/clyh.owl",
"homepage": "https://github.com/EBISPOT/clyh_ontology",
"name": "Clytia hemisphaerica Development and Anatomy Ontology (CLYH)",
"prefix": "clyh",
"version": "2020-05-29",
"version.iri": "http://purl.obolibrary.org/obo/clyh/releases/2020-05-29/clyh.owl"
},
"ontobee": {
"library": "Library",
"name": "Clytia hemisphaerica Development and Anatomy Ontology",
"prefix": "CLYH"
},
"pattern": "^\\d+$",
"uri_format": "http://purl.obolibrary.org/obo/CLYH_$1"
},
"cmecs": {
"aberowl": {
"description": "The Coastal and Marine Ecological Classification Standard (CMECS, FGDC-STD-018-2012) is collection of defined terms (\"units\") used to describe and classify marine ecological data. It is a national scheme for classifying and integrating observational data collected in coastal, marine, and lacustrine environments in U.S. waters. CMECS was published by the U.S. Federal Geographic Data Committee (FGDC) in 2012.",
"download_owl": "http://aber-owl.net/media/ontologies/CMECS/2/cmecs.owl",
"homepage": "https://github.com/NCEI-NOAAGov/cmecs",
"name": "Coastal and Marine Ecological Classification Standard Catalog",
"prefix": "CMECS",
"version": "1.1.0"
},
"bioportal": {
"contact": {
"email": "kate.rose@noaa.gov",
"name": "Kate Rose"
},
"description": "The Coastal and Marine Ecological Classification Standard (CMECS, FGDC-STD-018-2012) is collection of defined terms (\"units\") used to describe and classify marine ecological data. It is a national scheme for classifying and integrating observational data collected in coastal, marine, and lacustrine environments in U.S. waters. CMECS was published by the U.S. Federal Geographic Data Committee (FGDC) in 2012.",
"homepage": "https://github.com/NCEI-NOAAGov/cmecs",
"name": "Coastal and Marine Ecological Classification Standard Catalog",
"prefix": "CMECS",
"version": "1.1.0"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard.",
"example": "595",
"homepage": "https://cmecscatalog.org/cmecs",
"keywords": [
"ecology",
"marine ecology"
],
"mappings": {
"aberowl": "CMECS",
"bioportal": "CMECS"
},
"name": "Costal and Marine Ecological Classification Standard",
"pattern": "^\\d+$",
"references": [
"http://www.natureserve.org/sites/default/files/publications/files/cmecs_version_06-2012_final.pdf"
],
"uri_format": "https://cmecscatalog.org/cmecs/classification/unit/$1.html"
},
"cmf": {
"aberowl": {
"name": "CranioMaxilloFacial ontology",
"prefix": "CMF"
},
"biocontext": {
"prefix": "CMF"
},
"deprecated": true,
"description": "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain",
"mappings": {
"aberowl": "CMF",
"biocontext": "CMF",
"obofoundry": "cmf",
"ontobee": "CMF"
},
"obofoundry": {
"contact": "engelsta@ohsu.edu",
"contact.label": "Mark Engelstad",
"contact.orcid": "0000-0001-5889-4463",
"deprecated": true,
"domain": "health",
"homepage": "https://code.google.com/p/craniomaxillofacial-ontology/",
"name": "CranioMaxilloFacial ontology",
"prefix": "cmf"
},
"ontobee": {
"library": "Library",
"name": "CranioMaxilloFacial ontology",
"prefix": "CMF"
}
},
"cmo": {
"aberowl": {
"description": "Morphological and physiological measurement records generated from clinical and model organism research and health programs.",
"download_owl": "http://aber-owl.net/media/ontologies/CMO/127/cmo.owl",
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
"name": "Clinical measurement ontology",
"prefix": "CMO"
},
"biocontext": {
"prefix": "CMO"
},
"bioportal": {
"contact": {
"email": "akwitek@mcw.edu",
"name": "Anne Kwitek"
},
"description": "The Clinical Measurement Ontology is designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs.",
"homepage": "https://rgd.mcw.edu/rgdweb/ontology/search.html",
"name": "Clinical Measurement Ontology",
"prefix": "CMO",
"publication": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361058/",
"version": "2.221"
},
"example": "0001350",
"fairsharing": {
"abbreviation": "CMO",
"contact": {
"email": "shimoyama@mcw.edu",
"name": "Mary Shimoyama",
"orcid": "0000-0003-1176-0796"
},
"description": "The Clinical Measurement Ontology is designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs.",
"domains": [
"Model organism",
"Electronic health record",
"Phenotype",
"Disease"
],
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=CMO:0000000",
"license": "CC0-1.0",
"name": "Clinical Measurement Ontology",
"prefix": "FAIRsharing.dq78pn",
"publications": [
{
"doi": "10.3389/fgene.2012.00087",
"pubmed": "22654893",
"title": "Three ontologies to define phenotype measurement data",
"year": 2012
},
{
"doi": "10.1186/2041-1480-4-26",
"pubmed": "24103152",
"title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications",
"year": 2013
}
],
"subjects": [
"Life Science",
"Biomedical Science",
"Preclinical Studies"
]
},
"mappings": {
"aberowl": "CMO",
"biocontext": "CMO",
"bioportal": "CMO",
"fairsharing": "FAIRsharing.dq78pn",
"obofoundry": "cmo",
"ols": "cmo",
"ontobee": "CMO"
},
"obofoundry": {
"appears_in": [
"scdo"
],
"contact": "jrsmith@mcw.edu",
"contact.github": "jrsjrs",
"contact.label": "Jennifer Smith",
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"description": "Morphological and physiological measurement records generated from clinical and model organism research and health programs.",
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"download.obo": "http://purl.obolibrary.org/obo/cmo.obo",
"download.owl": "http://purl.obolibrary.org/obo/cmo.owl",
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
"license": "CC0 1.0",
"license.url": "http://creativecommons.org/publicdomain/zero/1.0/",
"logo": "http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif",
"name": "Clinical measurement ontology",
"preferredPrefix": "CMO",
"prefix": "cmo",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/22654893",
"title": "Three ontologies to define phenotype measurement data."
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{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/24103152",
"title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications."
}
],
"repository": "https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology"
},
"ols": {
"description": "Morphological and physiological measurement records generated from clinical and model organism research and health programs.",
"download_owl": "http://purl.obolibrary.org/obo/cmo.owl",
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
"name": "Clinical measurement ontology",
"prefix": "cmo",
"version": "2.221",
"version.iri": "http://purl.obolibrary.org/obo/cmo/2.221/cmo.owl"
},
"ontobee": {
"library": "Library",
"name": "Clinical measurement ontology",
"prefix": "CMO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1186/2041-1480-4-26",
"pmc": "PMC3882879",
"pubmed": "24103152",
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"year": 2013
},
{
"doi": "10.3389/fgene.2012.00087",
"pmc": "PMC3361058",
"pubmed": "22654893",
"title": "Three ontologies to define phenotype measurement data",
"year": 2012
}
],
"twitter": "ratgenome",
"uri_format": "http://purl.obolibrary.org/obo/CMO_$1"
},
"cmpo": {
"aberowl": {
"description": "The Cellular Microscopy Phenotype Ontology (CMPO) is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is an application ontology developed in OWL that contains precomposed phenotypes descriptions that are defined using the Gene Ontology (GO) and the Phenotype Trait Ontology (PATO).",
"download_owl": "http://aber-owl.net/media/ontologies/CMPO/14/cmpo.owl",
"homepage": "https://github.com/EBISPOT/CMPO",
"name": "Cellular microscopy phenotype ontology",
"prefix": "CMPO",
"version": "1.3"
},
"bioportal": {
"contact": {
"email": "jupp@ebi.ac.uk",
"name": "Simon Jupp"
},
"description": "The Cellular Microscopy Phenotype Ontology (CMPO) is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is an application ontology developed in OWL that contains precomposed phenotypes descriptions that are defined using the Gene Ontology (GO) and the Phenotype Trait Ontology (PATO).",
"homepage": "https://github.com/EBISPOT/CMPO",
"name": "Cellular microscopy phenotype ontology",
"prefix": "CMPO",
"version": "1.3"
},
"contact": {
"email": "jupp@ebi.ac.uk",
"name": "Simon Jupp",
"orcid": "0000-0002-0643-3144"
},
"example": "0000435",
"fairsharing": {
"abbreviation": "CMPO",
"description": "Cellular Microscopy Phenotype Ontology (CMPO) is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations",
"domains": [
"Cell",
"Microscopy",
"Cellular component",
"Phenotype"
],
"homepage": "http://www.ebi.ac.uk/cmpo/",
"license": "Apache 2.0 License",
"name": "Cellular Microscopy Phenotype Ontology",
"prefix": "FAIRsharing.knp11s",
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{
"doi": "10.1186/s13326-016-0074-0",
"pubmed": "27195102",
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}
],
"repository": "https://github.com/EBISPOT/CMPO",
"subjects": [
"Cell Biology"
]
},
"mappings": {
"aberowl": "CMPO",
"bioportal": "CMPO",
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"ols": "cmpo"
},
"ols": {
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"description": "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations.",
"download_owl": "http://www.ebi.ac.uk/cmpo/cmpo.owl",
"homepage": "http://www.ebi.ac.uk/cmpo",
"name": "Cellular Microscopy Phenotype Ontology",
"prefix": "cmpo",
"version": "2017-12-19",
"version.iri": "http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1186/s13326-016-0074-0",
"pmc": "PMC4870745",
"pubmed": "27195102",
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],
"repository": "https://github.com/EBISPOT/CMPO",
"twitter": "EBIOLS",
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},
"cnrs": {
"comment": "Motivated to add because of appearance in ROR",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
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"example": "UMR7315",
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"wikidata": "P4550"
},
"name": "French National Center for Scientific Research - Research Group Identifier",
"pattern": "^(UMR|UMS|UMI|UPR|URA|USR|GDR|EA|FR|SNC|ERL|FRC|FRE|IFR|MOY)\\d+$",
"uri_format": "https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin?&p_lab=$1&p_origine_appel=u",
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"UMR7315",
"UMR7318",
"UMR8627"
],
"name": "CNRS research group ID",
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"prefix": "P4550",
"uri_format": "https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin?&p_lab=$1&p_origine_appel=u"
}
},
"co_320": {
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"contact": {
"email": "j.detras@cgiar.org",
"name": "Jeffrey A. Detras"
},
"description": "Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables",
"example_uri": "http://www.cropontology.org/rdf/CO_320:0000600/5",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Rice Ontology",
"prefix": "CO_320",
"repository": "https://github.com/Planteome/CO_320-rice-traits",
"version": "March 2016"
},
"contact": {
"email": "j.detras@cgiar.org",
"name": "Jeffrey A. Detras",
"orcid": "0000-0002-6680-578X"
},
"cropoct": {
"description": "Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables",
"download_owl": "http://cropontology.org/rdf/CO_320.owl",
"homepage": "http://cropontology.org/term/CO_320:ROOT",
"name": "Rice ontology",
"prefix": "CO_320"
},
"example": "0000618",
"fairsharing": {
"abbreviation": "CO_320",
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The IBP Rice Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology. Based on SES, Rice Descriptor and IRIS DB.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_320:ROOT",
"license": "CC-BY-4.0",
"name": "Rice Ontology",
"prefix": "FAIRsharing.2jkxp5",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
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"mappings": {
"agroportal": "CO_320",
"cropoct": "CO_320",
"fairsharing": "FAIRsharing.2jkxp5",
"ols": "co_320"
},
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"description": "Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables",
"download": "https://cropontology.org/ontology/CO_320/Rice/owl",
"homepage": "https://cropontology.org/ontology/CO_320/Rice",
"name": "Rice ontology",
"prefix": "co_320",
"version": "2019-10-09"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_320",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_320:$1"
},
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"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Wheat Trait Dictionary in template v5.",
"example_uri": "http://www.cropontology.org/rdf/CO_321:0000238",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Wheat Ontology",
"prefix": "CO_321",
"repository": "https://github.com/Planteome/CO_321-wheat-traits",
"version": "Feb 2016"
},
"cropoct": {
"description": "July 2018",
"download_owl": "http://cropontology.org/rdf/CO_321.owl",
"homepage": "http://cropontology.org/term/CO_321:ROOT",
"name": "Wheat ontology",
"prefix": "CO_321"
},
"example": "0000449",
"fairsharing": {
"abbreviation": "CO_321",
"contact": {
"email": "R.Shrestha2@cgiar.org",
"name": "Rosemary Shrestha",
"orcid": "0000-0002-9399-8003"
},
"description": "This ontology defines traits of the International Wheat Information System (IWIS) database and wheat descriptor. The Wheat Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_321:ROOT",
"license": "CC-BY-4.0",
"name": "Wheat Ontology",
"prefix": "FAIRsharing.czzmpg",
"publications": [
{
"doi": "10.1093/aobpla/plq008",
"pubmed": "22476066",
"title": "Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature",
"year": 2010
}
],
"subjects": [
"Agriculture",
"Life Science"
]
},
"license": "CC-BY-4.0",
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"agroportal": "CO_321",
"cropoct": "CO_321",
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"ols": "co_321"
},
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"contact": "helpdesk@cropontology-curationtool.org",
"description": "July 2018",
"download": "https://cropontology.org/ontology/CO_321/Wheat/owl",
"homepage": "https://cropontology.org/ontology/CO_321/Wheat",
"name": "Wheat ontology",
"prefix": "co_321",
"version": "2019-10-09"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_321",
"publications": [
{
"doi": "10.1093/aobpla/plq008",
"pmc": "PMC3000699",
"pubmed": "22476066",
"title": "Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature",
"year": 2010
}
],
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_321:$1"
},
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"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project (http://www.cropontology.org),as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_322:0000850",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Maize Ontology",
"prefix": "CO_322",
"repository": "https://github.com/Planteome/CO_322-maize-traits",
"version": "September 2016"
},
"cropoct": {
"description": "Maize Trait Dictionary in template 5 - CIMMYT- September 2016- Updated nov 2023 Updated Nov 2023 with the traits and variables for on farm comparative ranking of varieties",
"download_owl": "http://cropontology.org/rdf/CO_322.owl",
"homepage": "http://cropontology.org/term/CO_322:ROOT",
"name": "Maize ontology",
"prefix": "CO_322"
},
"example": "0000773",
"fairsharing": {
"abbreviation": "CO_322",
"description": "The Maize Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_322:ROOT",
"license": "CC-BY-4.0",
"name": "Maize Ontology",
"prefix": "FAIRsharing.eeyne8",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_322",
"cropoct": "CO_322",
"fairsharing": "FAIRsharing.eeyne8",
"ols": "co_322"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Maize Trait Dictionary in template 5 - CIMMYT- September 2016",
"download": "https://cropontology.org/ontology/CO_322/Maize/owl",
"homepage": "https://cropontology.org/ontology/CO_322/Maize",
"name": "Maize ontology",
"prefix": "co_322",
"version": "2019-10-09"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_322",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_322:$1"
},
"co_323": {
"agroportal": {
"contact": {
"email": "r.verma@cgiar.org",
"name": "Ramesh Verna"
},
"description": "Reference Plant Ontologies are being developed in the context of the Plantome project and are being integrated with the Crop Ontology, which provides harmonized breeder's trait names, measurement methods, scales, and standard variables for many crops. The barley Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"example_uri": "http://www.cropontology.org/rdf/CO_323:0000005/4",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Barley Ontology",
"prefix": "CO_323",
"repository": "https://github.com/Planteome/CO_323-barley-traits",
"version": "1.2"
},
"cropoct": {
"description": "ICARDA - TDv5 - Sept 2018",
"download_owl": "http://cropontology.org/rdf/CO_323.owl",
"homepage": "http://cropontology.org/term/CO_323:ROOT",
"name": "Barley ontology",
"prefix": "CO_323"
},
"example": "0000252",
"fairsharing": {
"abbreviation": "CO_323",
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Barley Ontology is one of these reference plant ontologies integrated within the Crop Ontology. Its focus is on traits and variable used in field trials for breeding.",
"domains": [
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_323:ROOT",
"license": "CC-BY-4.0",
"name": "Barley Ontology",
"prefix": "FAIRsharing.f69084",
"subjects": [
"Botany",
"Agriculture"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_323",
"cropoct": "CO_323",
"fairsharing": "FAIRsharing.f69084",
"ols": "co_323"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "ICARDA - TDv5 - Sept 2018",
"download": "https://cropontology.org/ontology/CO_323/Barley/owl",
"homepage": "https://cropontology.org/ontology/CO_323/Barley",
"name": "Barley ontology",
"prefix": "co_323",
"version": "2019-11-20"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_323",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_323:$1"
},
"co_324": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Sorghum TDv5 Ontology",
"example_uri": "http://www.cropontology.org/rdf/CO_324:0000660",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Sorghum Ontology",
"prefix": "CO_324",
"repository": "https://github.com/Planteome/CO_324-sorghum-traits",
"version": "1.0"
},
"cropoct": {
"description": "Sorghum TDv5 - Oct 2019- Updated January 2024 with the Traits of 1000Farms project trials using comparative ranking by farmers method",
"download_owl": "http://cropontology.org/rdf/CO_324.owl",
"homepage": "http://cropontology.org/term/CO_324:ROOT",
"name": "Sorghum ontology",
"prefix": "CO_324"
},
"example": "0000111",
"fairsharing": {
"abbreviation": "CO_324",
"description": "The Sorghum Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_324:ROOT",
"license": "CC-BY-4.0",
"name": "Sorghum Ontology",
"prefix": "FAIRsharing.dxx0c",
"subjects": [
"Botany",
"Agriculture"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_324",
"cropoct": "CO_324",
"fairsharing": "FAIRsharing.dxx0c",
"ols": "co_324"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Sorghum TDv5 - Oct 2019",
"download": "https://cropontology.org/ontology/CO_324/Sorghum/owl",
"homepage": "https://cropontology.org/ontology/CO_324/Sorghum",
"name": "Sorghum ontology",
"prefix": "co_324",
"version": "2019-10-09"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_324",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_324:$1"
},
"co_325": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Banana Trait Dictionary in template 5 - characterization and breeding variables, drought experiment variables.",
"example_uri": "http://www.cropontology.org/rdf/CO_325:0000267",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Banana Ontology",
"prefix": "CO_325",
"repository": "https://github.com/Planteome/CO_325-banana-traits",
"version": "April 2019"
},
"cropoct": {
"description": "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019",
"download_owl": "http://cropontology.org/rdf/CO_325.owl",
"homepage": "http://cropontology.org/term/CO_325:ROOT",
"name": "Banana ontology",
"prefix": "CO_325"
},
"example": "0000519",
"fairsharing": {
"abbreviation": "CO_325",
"contact": {
"email": "e.arnaud@cgiar.org",
"name": "Elizabeth Arnaud",
"orcid": "0000-0002-6020-5919"
},
"description": "The Banana Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_325:ROOT",
"license": "CC-BY-4.0",
"name": "Banana Ontology",
"prefix": "FAIRsharing.gdszhh",
"subjects": [
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_325",
"cropoct": "CO_325",
"fairsharing": "FAIRsharing.gdszhh",
"ols": "co_325"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019",
"download": "https://cropontology.org/ontology/CO_325/Banana/owl",
"homepage": "https://cropontology.org/ontology/CO_325/Banana",
"name": "Banana ontology",
"prefix": "co_325",
"version": "2019-10-09"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_325",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_325:$1"
},
"co_326": {
"agroportal": {
"contact": {
"email": "coming@coming.com",
"name": "Stephanie Bocs Sidibe"
},
"description": "Coconut Ontology v1.0 - Coconut trait dictionary started by CIRAD, based on the \"Guidelines for collecting coconut germplasm characterisation data during prospecting missions\", COGENT (to be published); the \"Descriptors for Coconut, (Cocos nucifera L.)\", IPGRI (1995); and the \"Manual on standardized research techniques in coconut breeding\", IPGRI (1996).",
"homepage": "https://cropontology.org/term/CO_326:ROOT",
"license": "CC-BY-4.0",
"name": "Coconut Ontology",
"prefix": "CO_326",
"version": "1.0"
},
"cropoct": {
"download_owl": "http://cropontology.org/rdf/CO_326.owl",
"homepage": "http://cropontology.org/term/CO_326:ROOT",
"name": "Coconut ontology",
"prefix": "CO_326"
},
"example": "0000254",
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_326",
"cropoct": "CO_326",
"ols": "co_326"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Draft version",
"download": "https://cropontology.org/ontology/CO_326/Coconut/owl",
"homepage": "https://cropontology.org/ontology/CO_326/Coconut",
"name": "Coconut ontology",
"prefix": "co_326"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_326",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_326:$1"
},
"co_327": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Pearl millet Trait Dictionary in template 5.",
"example_uri": "http://www.cropontology.org/rdf/CO_327:0000185",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Pearl Millet Ontology",
"prefix": "CO_327",
"repository": "https://github.com/Planteome/CO_327-pearl-millet-traits",
"version": "April 2016"
},
"cropoct": {
"description": "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016 - Updated with onfarm trial traits from 1000Farms project, 2024",
"download_owl": "http://cropontology.org/rdf/CO_327.owl",
"homepage": "http://cropontology.org/term/CO_327:ROOT",
"name": "Pearl millet ontology",
"prefix": "CO_327"
},
"example": "0000095",
"fairsharing": {
"abbreviation": "CO_327",
"description": "The goal of the CGIAR Pearl Millet Ontology is to help improve food security for subsistence smallholder farmers in East and West Africa with productive and nutritious pearl millet food and fodder production technologies.",
"domains": [
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_327:ROOT",
"license": "CC-BY-4.0",
"name": "Pearl Millet Ontology",
"prefix": "FAIRsharing.4e3qh9",
"subjects": [
"Botany",
"Agriculture"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_327",
"cropoct": "CO_327",
"fairsharing": "FAIRsharing.4e3qh9",
"ols": "co_327"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016",
"download": "http://www.cropontology.org/ontology/CO_327/Pearl%20millet/owl",
"homepage": "http://www.cropontology.org/ontology/CO_327/Pearl%20millet",
"name": "Pearl millet ontology",
"prefix": "co_327"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_327",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_327:$1"
},
"co_330": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "(to come)",
"example_uri": "http://www.cropontology.org/rdf/CO_330:0000056/2",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Potato Ontology",
"prefix": "CO_330",
"repository": "https://github.com/Planteome/CO_330-potato-traits",
"version": "december 2017"
},
"cropoct": {
"description": "CIP - potato ontology - december 2018",
"download_owl": "http://cropontology.org/rdf/CO_330.owl",
"homepage": "http://cropontology.org/term/CO_330:ROOT",
"name": "Potato ontology",
"prefix": "CO_330"
},
"example": "0000106",
"fairsharing": {
"abbreviation": "CO_330",
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Potato Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_330:ROOT",
"license": "CC-BY-4.0",
"name": "Potato Ontology",
"prefix": "FAIRsharing.4fa657",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_330",
"cropoct": "CO_330",
"fairsharing": "FAIRsharing.4fa657",
"ols": "co_330"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "CIP - potato ontology - december 2018",
"download": "https://cropontology.org/ontology/CO_330/Potato/owl",
"homepage": "https://cropontology.org/ontology/CO_330/Potato",
"name": "Potato ontology",
"prefix": "co_330",
"version": "2019-10-09"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_330",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_330:$1"
},
"co_331": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Sweet Potato Trait Dictionary in template v5",
"example_uri": "http://www.cropontology.org/rdf/CO_331:0000601/1",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Sweet Potato Ontology",
"prefix": "CO_331",
"repository": "https://github.com/Planteome/CO_331-sweetpotato-traits",
"version": "June 2016"
},
"cropoct": {
"description": "Sweetpotato Trait Dictionary in template v5 - CIP - November 2019",
"download_owl": "http://cropontology.org/rdf/CO_331.owl",
"homepage": "http://cropontology.org/term/CO_331:ROOT",
"name": "Sweet Potato ontology",
"prefix": "CO_331"
},
"example": "0000088",
"fairsharing": {
"abbreviation": "CO_331",
"contact": {
"email": "V.Hualla@cgiar.org",
"name": "Vilma Hualla Mamani",
"orcid": "0000-0003-0595-5271"
},
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Sweet Potato Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Food"
],
"homepage": "https://cropontology.org/term/CO_331:ROOT",
"license": "CC-BY-4.0",
"name": "Sweet Potato Ontology",
"prefix": "FAIRsharing.4g5qcw",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_331",
"cropoct": "CO_331",
"fairsharing": "FAIRsharing.4g5qcw",
"ols": "co_331"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019",
"download": "http://www.cropontology.org/ontology/CO_331/Sweet%20Potato/owl",
"homepage": "http://www.cropontology.org/ontology/CO_331/Sweet%20Potato",
"name": "Sweet Potato ontology",
"prefix": "co_331"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_331",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_331:$1"
},
"co_333": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRA, Geves, ITB, UnversitΓ© d'Angers) and breeding companies (Florimond Desprez).",
"example_uri": "http://www.cropontology.org/rdf/CO_333:0001137",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Beet Ontology",
"prefix": "CO_333",
"repository": "https://forgemia.inra.fr/urgi-is/ontologies/-/tree/develop/Beet",
"version": "November 2017"
},
"cropoct": {
"description": "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017.",
"download_owl": "http://cropontology.org/rdf/CO_333.owl",
"homepage": "http://cropontology.org/term/CO_333:ROOT",
"name": "Beet Ontology ontology",
"prefix": "CO_333"
},
"example": "3000045",
"fairsharing": {
"abbreviation": "CO_333",
"description": "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution and breeding company within the project. Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Beet Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_333:ROOT",
"license": "CC-BY-4.0",
"name": "Beet Ontology",
"prefix": "FAIRsharing.af5655",
"subjects": [
"Botany",
"Plant Breeding",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_333",
"cropoct": "CO_333",
"fairsharing": "FAIRsharing.af5655",
"ols": "co_333"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017.",
"download": "http://www.cropontology.org/ontology/CO_333/Beet%20Ontology/owl",
"homepage": "http://www.cropontology.org/ontology/CO_333/Beet%20Ontology",
"name": "Beet Ontology ontology",
"prefix": "co_333"
},
"pattern": "^\\d+$",
"preferred_prefix": "CO_333",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_333:$1"
},
"co_334": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project, as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_334:0100676",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Cassava Ontology",
"prefix": "CO_334",
"publication": "http://www.cropontology.org/",
"repository": "https://github.com/Planteome/CO_334-cassava-traits",
"version": "February 2016"
},
"cropoct": {
"description": "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016, and in 2023 for the traits from on farm trials",
"download_owl": "http://cropontology.org/rdf/CO_334.owl",
"homepage": "http://cropontology.org/term/CO_334:ROOT",
"name": "Cassava ontology",
"prefix": "CO_334"
},
"example": "0000070",
"fairsharing": {
"abbreviation": "CO_334",
"description": "Crop-specific trait ontologies enhance the interoperability and effectiveness of data exchange between the data sources which adopt it, by providing standard concepts that are use to describe phenotypes stored in those sources. As one of them, the Cassava Ontology is actively used and shared in different databases such as the BMS (Breeding Management system) of the IBP or the CassavaBase. Cassava, a major staple crop, is the main source of calories for 500 million people across the globe. A perennial woody shrub native to Latin America, cassava is primarily grown as an annual crop in the humid tropics. A cash crop as well as a subsistence crop, cassava's large edible starchy roots are a source of low-cost carbohydrates for millions. Cassava end products range from fresh roots cooked, boiled, baked or fried at the household level, to highly processed starch as a food additive.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_334:ROOT",
"license": "CC-BY-4.0",
"name": "IBP Cassava Trait Ontology",
"prefix": "FAIRsharing.v06c4q",
"repository": "https://github.com/Planteome/ibp-cassava-traits",
"subjects": [
"Botany",
"Agriculture",
"Nutritional Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_334",
"cropoct": "CO_334",
"fairsharing": "FAIRsharing.v06c4q",
"ols": "co_334"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016",
"download": "https://cropontology.org/ontology/CO_334/Cassava/owl",
"homepage": "https://cropontology.org/ontology/CO_334/Cassava",
"name": "Cassava ontology",
"prefix": "co_334",
"version": "2019-10-09"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_334",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_334:$1"
},
"co_335": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project, as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_335:0000475/4",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Common Bean Ontology",
"prefix": "CO_335",
"repository": "https://github.com/Planteome/CO_335-common-bean-traits",
"version": "August 2014"
},
"cropoct": {
"description": "CIAT Common bean trait dictionary - Updated version Nov. 2023, with the traits and variables for on farm comparative ranking of varieties",
"download_owl": "http://cropontology.org/rdf/CO_335.owl",
"homepage": "http://cropontology.org/term/CO_335:ROOT",
"name": "Common bean ontology",
"prefix": "CO_335"
},
"example": "0000189",
"fairsharing": {
"abbreviation": "CO_335",
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Common Bean Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Food"
],
"homepage": "https://cropontology.org/term/CO_335:ROOT",
"license": "CC-BY-4.0",
"name": "Common Bean Ontology",
"prefix": "FAIRsharing.a14123",
"subjects": [
"Botany",
"Agriculture"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_335",
"cropoct": "CO_335",
"fairsharing": "FAIRsharing.a14123",
"ols": "co_335"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "CIAT Common bean trait dictionary - version August 2014",
"download": "http://www.cropontology.org/ontology/CO_335/Common%20Bean/owl",
"homepage": "http://www.cropontology.org/ontology/CO_335/Common%20Bean",
"name": "Common Bean ontology",
"prefix": "co_335"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_335",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_335:$1"
},
"co_336": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Soybean Trait Dictionary in template v5",
"example_uri": "http://www.cropontology.org/rdf/CO_336:0000230/2",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Soybean Ontology",
"prefix": "CO_336",
"repository": "https://github.com/Planteome/CO_336-soybean-traits",
"version": "July 2015"
},
"cropoct": {
"description": "Soybean Trait Dictionary in template v5 - IITA - July 2015",
"download_owl": "http://cropontology.org/rdf/CO_336.owl",
"homepage": "http://cropontology.org/term/CO_336:ROOT",
"name": "Soybean ontology",
"prefix": "CO_336"
},
"example": "0000339",
"fairsharing": {
"abbreviation": "CO_336",
"contact": {
"email": "e.arnaud@cgiar.org",
"name": "Elizabeth Arnaud",
"orcid": "0000-0002-6020-5919"
},
"description": "The Soybean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_336:ROOT",
"license": "CC-BY-4.0",
"name": "Soybean Ontology",
"prefix": "FAIRsharing.j75srj",
"subjects": [
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_336",
"cropoct": "CO_336",
"fairsharing": "FAIRsharing.j75srj",
"ols": "co_336"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Soybean Trait Dictionary in template v5 - IITA - July 2015",
"download": "https://cropontology.org/ontology/CO_336/Soybean/owl",
"homepage": "https://cropontology.org/ontology/CO_336/Soybean",
"name": "Soybean ontology",
"prefix": "co_336"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_336",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_336:$1"
},
"co_337": {
"agroportal": {
"contact": {
"email": "tm.shah@cgiar.org",
"name": "Trushar Shah"
},
"description": "This ontology is a part of the the Crop Ontology project , as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_337:0000006",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Groundnut Ontology",
"prefix": "CO_337",
"repository": "https://github.com/Planteome/CO_337-groundnut-traits",
"version": "Sept 2015"
},
"contact": {
"email": "tm.shah@cgiar.org",
"name": "Trushar Shah",
"orcid": "0000-0002-0091-7981"
},
"cropoct": {
"description": "Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015 -Updated Nov 2023 with traits from the on farm trials for the comparative ranking of varieties",
"download_owl": "http://cropontology.org/rdf/CO_337.owl",
"homepage": "http://cropontology.org/term/CO_337:ROOT",
"name": "Groundnut ontology",
"prefix": "CO_337"
},
"example": "0000054",
"fairsharing": {
"abbreviation": "CO_337",
"description": "The Groundnut Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_337:ROOT",
"license": "CC-BY-4.0",
"name": "Groundnut Ontology",
"prefix": "FAIRsharing.ge8y23",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_337",
"cropoct": "CO_337",
"fairsharing": "FAIRsharing.ge8y23",
"ols": "co_337"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015",
"download": "https://cropontology.org/ontology/CO_337/Groundnut/owl",
"homepage": "https://cropontology.org/ontology/CO_337/Groundnut",
"name": "Groundnut ontology",
"prefix": "co_337",
"version": "2019-10-09"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_337",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_337:$1"
},
"co_338": {
"agroportal": {
"contact": {
"email": "tm.shah@cgiar.org",
"name": "Trushar Shah"
},
"description": "This ontology is a part of the the Crop Ontology project, as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_338:0000344",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Chickpea Ontology",
"prefix": "CO_338",
"repository": "https://github.com/Planteome/CO_338-chickpea-traits",
"version": "July 2015"
},
"contact": {
"email": "tm.shah@cgiar.org",
"name": "Trushar Shah",
"orcid": "0000-0002-0091-7981"
},
"cropoct": {
"description": "Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015",
"download_owl": "http://cropontology.org/rdf/CO_338.owl",
"homepage": "http://cropontology.org/term/CO_338:ROOT",
"name": "Chickpea ontology",
"prefix": "CO_338"
},
"example": "0000138",
"fairsharing": {
"abbreviation": "CO_338",
"description": "Development of crop-specific trait ontologies including the Chickpea Ontology began in 2008 as part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_338:ROOT",
"license": "CC-BY-4.0",
"name": "Chickpea Ontology",
"prefix": "FAIRsharing.js20q3",
"subjects": [
"Botany",
"Agriculture"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_338",
"cropoct": "CO_338",
"fairsharing": "FAIRsharing.js20q3",
"ols": "co_338"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015",
"download": "https://cropontology.org/ontology/CO_338/Chickpea/owl",
"homepage": "https://cropontology.org/ontology/CO_338/Chickpea",
"name": "Chickpea ontology",
"prefix": "co_338",
"version": "2019-10-09"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_338",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_338:$1"
},
"co_339": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project, as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_339:0000117",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Lentil Ontology",
"prefix": "CO_339",
"repository": "https://github.com/Planteome/CO_339-lentil-traits",
"version": "July 2015"
},
"cropoct": {
"description": "Lentil Trait Dictionary in template v5 - ICARDA - July 2015",
"download_owl": "http://cropontology.org/rdf/CO_339.owl",
"homepage": "http://cropontology.org/term/CO_339:ROOT",
"name": "Lentil ontology",
"prefix": "CO_339"
},
"example": "0000032",
"fairsharing": {
"abbreviation": "CO_339",
"description": "The Lentil Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_339:ROOT",
"license": "CC-BY-4.0",
"name": "Lentil Ontology",
"prefix": "FAIRsharing.ry1ezg",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_339",
"cropoct": "CO_339",
"fairsharing": "FAIRsharing.ry1ezg",
"ols": "co_339"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Lentil Trait Dictionary in template v5 - ICARDA - July 2015",
"download": "https://cropontology.org/ontology/CO_339/Lentil/owl",
"homepage": "https://cropontology.org/ontology/CO_339/Lentil",
"name": "Lentil ontology",
"prefix": "co_339",
"version": "2019-10-09"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_339",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_339:$1"
},
"co_340": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project (http://www.cropontology.org), created in 2008 by the CGIAR, as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_340:0000388/4",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Cowpea Ontology",
"prefix": "CO_340",
"publication": "http://www.cropontology.org/",
"repository": "https://github.com/Planteome/CO_340-cowpea-traits",
"version": "August 2015"
},
"cropoct": {
"description": "Cowpea Trait Dictionary - IITA - August 2015 - Updated Nov 2023 with the traits and variables for on farm comparative ranking of varieties",
"download_owl": "http://cropontology.org/rdf/CO_340.owl",
"homepage": "http://cropontology.org/term/CO_340:ROOT",
"name": "Cowpea ontology",
"prefix": "CO_340"
},
"example": "0000639",
"fairsharing": {
"abbreviation": "CO_340",
"description": "The Cowpea Trait Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_340:ROOT",
"license": "CC-BY-4.0",
"name": "IBP Cowpea Trait Ontology",
"prefix": "FAIRsharing.31apg2",
"publications": [
{
"doi": "10.3389/fphys.2012.00326",
"pubmed": "22934074",
"title": "Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice",
"year": 2012
}
],
"subjects": [
"Botany",
"Agriculture"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_340",
"cropoct": "CO_340",
"fairsharing": "FAIRsharing.31apg2",
"ols": "co_340"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Cowpea Trait Dictionary in template v5 - IITA - August 2015",
"download": "https://cropontology.org/ontology/CO_340/Cowpea/owl",
"homepage": "https://cropontology.org/ontology/CO_340/Cowpea",
"name": "Cowpea ontology",
"prefix": "co_340",
"version": "2019-10-09"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_340",
"publications": [
{
"doi": "10.3389/fphys.2012.00326",
"pmc": "PMC3429094",
"pubmed": "22934074",
"title": "Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice",
"year": 2012
}
],
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_340:$1"
},
"co_341": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Pigeonpea Trait Dictionary in template v5",
"example_uri": "http://www.cropontology.org/rdf/CO_341:0000015",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Pigeon Pea Ontology",
"prefix": "CO_341",
"repository": "https://github.com/Planteome/CO_341-pigeonpea-traits",
"version": "July 2015"
},
"cropoct": {
"description": "Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015",
"download_owl": "http://cropontology.org/rdf/CO_341.owl",
"homepage": "http://cropontology.org/term/CO_341:ROOT",
"name": "Pigeonpea ontology",
"prefix": "CO_341"
},
"example": "0000140",
"fairsharing": {
"abbreviation": "CO_341",
"contact": {
"email": "e.arnaud@cgiar.org",
"name": "Elizabeth Arnaud",
"orcid": "0000-0002-6020-5919"
},
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Pigeon Pea Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_341:ROOT",
"license": "CC-BY-4.0",
"name": "Pigeon Pea Ontology",
"prefix": "FAIRsharing.ehe3yp",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_341",
"cropoct": "CO_341",
"fairsharing": "FAIRsharing.ehe3yp",
"ols": "co_341"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015",
"download": "https://cropontology.org/ontology/CO_341/Pigeonpea/owl",
"homepage": "https://cropontology.org/ontology/CO_341/Pigeonpea",
"name": "Pigeonpea ontology",
"prefix": "co_341",
"version": "2019-11-18"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_341",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_341:$1"
},
"co_343": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Yam trait ontology",
"example_uri": "http://www.cropontology.org/rdf/CO_343:0000357",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Yam Ontology",
"prefix": "CO_343",
"repository": "https://github.com/Planteome/CO_343-yam-traits",
"version": "Feb 2017"
},
"cropoct": {
"description": "version 2019 - pvs",
"download_owl": "http://cropontology.org/rdf/CO_343.owl",
"homepage": "http://cropontology.org/term/CO_343:ROOT",
"name": "Yam ontology",
"prefix": "CO_343"
},
"example": "0100010",
"fairsharing": {
"abbreviation": "CO_343",
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Yam Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_343:ROOT",
"license": "CC-BY-4.0",
"name": "Yam Ontology",
"prefix": "FAIRsharing.7e9cff",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_343",
"cropoct": "CO_343",
"fairsharing": "FAIRsharing.7e9cff",
"ols": "co_343"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "version 2019 - pvs",
"download": "https://cropontology.org/ontology/CO_343/Yam/owl",
"homepage": "https://cropontology.org/ontology/CO_343/Yam",
"name": "Yam ontology",
"prefix": "co_343",
"version": "2019-10-09"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_343",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_343:$1"
},
"co_345": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project (http://www.cropontology.org), as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_345:0000044",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Brachiaria Ontology",
"prefix": "CO_345",
"repository": "https://github.com/Planteome/CO_345-brachiaria-traits",
"version": "Oct 2016"
},
"cropoct": {
"description": "Brachiaria (forages) ontology TD v5 - Version Oct 2016",
"download_owl": "http://cropontology.org/rdf/CO_345.owl",
"homepage": "http://cropontology.org/term/CO_345:ROOT",
"name": "Brachiaria ontology",
"prefix": "CO_345"
},
"example": "0000127",
"fairsharing": {
"abbreviation": "CO_345",
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Brachiaria Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_345:ROOT",
"license": "CC-BY-4.0",
"name": "Brachiaria Ontology",
"prefix": "FAIRsharing.9e9683",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_345",
"cropoct": "CO_345",
"fairsharing": "FAIRsharing.9e9683",
"ols": "co_345"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Brachiaria (forages) ontology TD v5 - Version Oct 2016",
"download": "https://cropontology.org/ontology/CO_345/Brachiaria/owl",
"homepage": "https://cropontology.org/ontology/CO_345/Brachiaria",
"name": "Brachiaria ontology",
"prefix": "co_345",
"version": "2019-10-09"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_345",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_345:$1"
},
"co_346": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project , as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_346:0000095",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Mungbean Ontology",
"prefix": "CO_346",
"repository": "https://agroportal.lirmm.fr/ontologies/CO_346",
"version": "Oct 2016"
},
"cropoct": {
"description": "oct 2016",
"download_owl": "http://cropontology.org/rdf/CO_346.owl",
"homepage": "http://cropontology.org/term/CO_346:ROOT",
"name": "Mungbean ontology",
"prefix": "CO_346"
},
"example": "0000199",
"fairsharing": {
"abbreviation": "CO_346",
"description": "The Mungbean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe data.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_346:ROOT",
"license": "CC-BY-4.0",
"name": "Mungbean Ontology",
"prefix": "FAIRsharing.fgd5gq",
"subjects": [
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_346",
"cropoct": "CO_346",
"fairsharing": "FAIRsharing.fgd5gq",
"ols": "co_346"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "oct 2016",
"download": "https://cropontology.org/ontology/CO_346/Mungbean/owl",
"homepage": "https://cropontology.org/ontology/CO_346/Mungbean",
"name": "Mungbean ontology",
"prefix": "co_346",
"version": "2019-10-09"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_346",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_346:$1"
},
"co_347": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project, as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_347:0000108",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Castor Bean Ontology",
"prefix": "CO_347",
"repository": "https://github.com/Planteome/CO_347-castorbean-traits",
"version": "March 2017"
},
"cropoct": {
"description": "March 2017 version ",
"download_owl": "http://cropontology.org/rdf/CO_347.owl",
"homepage": "http://cropontology.org/term/CO_347:ROOT",
"name": "Castor bean ontology",
"prefix": "CO_347"
},
"example": "0000108",
"fairsharing": {
"abbreviation": "CO_347",
"description": "The Castor Bean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe data.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_347:ROOT",
"license": "CC-BY-4.0",
"name": "Castor Bean Ontology",
"prefix": "FAIRsharing.qrrvyk",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_347",
"cropoct": "CO_347",
"fairsharing": "FAIRsharing.qrrvyk",
"ols": "co_347"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "March 2017 version ",
"download": "http://www.cropontology.org/ontology/CO_347/Castor%20bean/owl",
"homepage": "http://www.cropontology.org/ontology/CO_347/Castor%20bean",
"name": "Castor bean ontology",
"prefix": "co_347"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_347",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_347:$1"
},
"co_348": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "helpdesk cropontology"
},
"description": "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France).",
"example_uri": "http://www.cropontology.org/rdf/CO_348:1000012",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Brassica Ontology",
"prefix": "CO_348",
"repository": "https://github.com/Brassica-Trait-Ontology/brato",
"version": "November 2017"
},
"cropoct": {
"description": "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France).",
"download_owl": "http://cropontology.org/rdf/CO_348.owl",
"homepage": "http://cropontology.org/term/CO_348:ROOT",
"name": "Brassica ontology",
"prefix": "CO_348"
},
"example": "1100107",
"fairsharing": {
"abbreviation": "CO_348",
"description": "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Brassica Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_348:ROOT",
"license": "CC-BY-4.0",
"name": "Brassica Ontology",
"prefix": "FAIRsharing.af7a2d",
"repository": "https://github.com/Brassica-Trait-Ontology/brato",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_348",
"cropoct": "CO_348",
"fairsharing": "FAIRsharing.af7a2d",
"ols": "co_348"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France).",
"download": "https://cropontology.org/ontology/CO_348/Brassica/owl",
"homepage": "https://cropontology.org/ontology/CO_348/Brassica",
"name": "Brassica ontology",
"prefix": "co_348",
"version": "2019-11-29"
},
"pattern": "^\\d+$",
"preferred_prefix": "CO_348",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_348:$1"
},
"co_350": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Oat trait dictionary commissioned by Oat Global (http://oatglobal.org/) to hold the traits used in the T3/Oat database (http://triticeaetoolbox.org/oat/).",
"example_uri": "http://www.cropontology.org/rdf/CO_350:0000091",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Oat Ontology",
"prefix": "CO_350",
"repository": "https://github.com/Planteome/CO_350-oat-traits",
"version": "1.0"
},
"cropoct": {
"description": "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo",
"download_owl": "http://cropontology.org/rdf/CO_350.owl",
"homepage": "http://cropontology.org/term/CO_350:ROOT",
"name": "Oat ontology",
"prefix": "CO_350"
},
"example": "0000215",
"fairsharing": {
"abbreviation": "CO_350",
"contact": {
"email": "jeanluc.work@gmail.com",
"name": "Jean-Luc Jannink",
"orcid": "0000-0003-4849-628X"
},
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Oat Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology. The Oat Trait Dictionary was commissioned by Oat Global (http://oatglobal.org/) to hold the traits used in the T3/Oat database (http://triticeaetoolbox.org/oat/).",
"domains": [
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_350:ROOT",
"license": "CC-BY-4.0",
"name": "Oat Trait Ontology",
"prefix": "FAIRsharing.35e1c3",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_350",
"cropoct": "CO_350",
"fairsharing": "FAIRsharing.35e1c3",
"ols": "co_350"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo",
"download": "https://cropontology.org/ontology/CO_350/Oat/owl",
"homepage": "https://cropontology.org/ontology/CO_350/Oat",
"name": "Oat ontology",
"prefix": "co_350",
"version": "2019-10-09"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_350",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_350:$1"
},
"co_356": {
"agroportal": {
"contact": {
"email": "cyril.pommier@inrae.fr",
"name": "Cyril Pommier"
},
"description": "Grape Ontology including OIV and bioversity descriptors.",
"example_uri": "http://www.cropontology.org/rdf/CO_356:1000182",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Vitis Ontology",
"prefix": "CO_356",
"repository": "https://forgemia.inra.fr/urgi-is/ontologies/-/tree/develop/Vitis"
},
"cropoct": {
"description": "Grape Ontology including OIV and bioversity descriptors. INRA July 2017",
"download_owl": "http://cropontology.org/rdf/CO_356.owl",
"homepage": "http://cropontology.org/term/CO_356:ROOT",
"name": "Vitis ontology",
"prefix": "CO_356"
},
"example": "4000027",
"fairsharing": {
"abbreviation": "CO_356",
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Vitis Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_356:ROOT",
"license": "CC BY-SA 4.0",
"name": "Vitis Ontology",
"prefix": "FAIRsharing.c7f4d7",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_356",
"cropoct": "CO_356",
"fairsharing": "FAIRsharing.c7f4d7",
"ols": "co_356"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Grape Ontology including OIV and bioversity descriptors. INRA July 2017",
"download": "https://cropontology.org/ontology/CO_356/Vitis/owl",
"homepage": "https://cropontology.org/ontology/CO_356/Vitis",
"name": "Vitis ontology",
"prefix": "co_356",
"version": "2019-11-29"
},
"pattern": "^\\d+$",
"preferred_prefix": "CO_356",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_356:$1"
},
"co_357": {
"agroportal": {
"name": "Woody Plant Ontology",
"prefix": "CO_357"
},
"contact": {
"email": "celia.michotey@inrae.fr",
"name": "CΓ©lia Michotey",
"orcid": "0000-0003-1877-1703"
},
"cropoct": {
"description": "This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (ITQB NOVA/IBET) - Version 2 submitted on Jun 2020 by INRAE.",
"download_owl": "http://cropontology.org/rdf/CO_357.owl",
"homepage": "http://cropontology.org/term/CO_357:ROOT",
"name": "Woody Plant Ontology ontology",
"prefix": "CO_357"
},
"example": "1000290",
"fairsharing": {
"abbreviation": "CO_357",
"description": "The Woody Plant Ontology lists reference variables used for experimentations and observations on woody plants (forest trees and shrubs, and possibly fruit trees). It is an international initiative based on various communities (French, Portuguese and European). Terms are collected from various sources and organized following the Crop Ontology standard which provides harmonized variables composed by a triplet: (i) a trait, the studied character, (ii) a method, the measurement protocol and (iii) a scale, the unit of measurement or scoring scale. ",
"domains": [
"Phenotype"
],
"homepage": "https://doi.org/10.15454/JB2WCE",
"license": "CC-BY-4.0",
"name": "Woody Plant Ontology",
"prefix": "FAIRsharing.2b04ae",
"subjects": [
"Botany",
"Life Science"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_357",
"cropoct": "CO_357",
"fairsharing": "FAIRsharing.2b04ae",
"ols": "co_357"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE.",
"download": "http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology/owl",
"homepage": "http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology",
"name": "Woody Plant Ontology ontology",
"prefix": "co_357"
},
"pattern": "^\\d+$",
"preferred_prefix": "CO_357",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_357:$1"
},
"co_358": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project, as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_358:0000215",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Cotton Ontology",
"prefix": "CO_358",
"repository": "https://github.com/Planteome/CO_358-cotton-traits",
"version": "2020-01-03"
},
"cropoct": {
"description": "Cotton ontology from CottonGen database - June 2019",
"download_owl": "http://cropontology.org/rdf/CO_358.owl",
"homepage": "http://cropontology.org/term/CO_358:ROOT",
"name": "Cotton ontology",
"prefix": "CO_358"
},
"example": "0000139",
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_358",
"cropoct": "CO_358",
"ols": "co_358"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Cotton ontology from CottonGen database - June 2019",
"download": "https://cropontology.org/ontology/CO_358/Cotton/owl",
"homepage": "https://cropontology.org/ontology/CO_358/Cotton",
"name": "Cotton ontology",
"prefix": "co_358",
"version": "2020-01-03"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_358",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_358:$1"
},
"co_359": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "To add",
"example_uri": "https://cropontology.org/rdf/CO_359:0000568",
"homepage": "https://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Sunflower Ontology",
"prefix": "CO_359",
"repository": "https://github.com/Planteome/CO_359-sunflower-traits",
"version": "2019-12-16"
},
"cropoct": {
"description": "December 2019",
"download_owl": "http://cropontology.org/rdf/CO_359.owl",
"homepage": "http://cropontology.org/term/CO_359:ROOT",
"name": "Sunflower ontology",
"prefix": "CO_359"
},
"example": "0000947",
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_359",
"cropoct": "CO_359",
"ols": "co_359"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "December 2019",
"download": "https://cropontology.org/ontology/CO_359/Sunflower/owl",
"homepage": "https://cropontology.org/ontology/CO_359/Sunflower",
"name": "Sunflower ontology",
"prefix": "co_359"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_359",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_359:$1"
},
"co_360": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Sugar Kelp trait ontology",
"example_uri": "http://www.cropontology.org/rdf/CO_360:0000085",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Sugar Kelp Ontology",
"prefix": "CO_360",
"repository": "https://github.com/Planteome/CO_360-sugar-kelp-traits",
"version": "June 2019"
},
"cropoct": {
"description": "Sugar Kelp trait ontology",
"download_owl": "http://cropontology.org/rdf/CO_360.owl",
"homepage": "http://cropontology.org/term/CO_360:ROOT",
"name": "Sugar Kelp trait ontology",
"prefix": "CO_360"
},
"example": "0000071",
"fairsharing": {
"abbreviation": "CO_360",
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Sugar Kelp Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Marine environment",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_360:ROOT",
"license": "CC-BY-4.0",
"name": "Sugar Kelp Trait Ontology",
"prefix": "FAIRsharing.1c1738",
"subjects": [
"Botany",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_360",
"cropoct": "CO_360",
"fairsharing": "FAIRsharing.1c1738",
"ols": "co_360"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "Sugar Kelp trait ontology",
"download": "http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait/owl",
"homepage": "http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait",
"name": "Sugar Kelp trait ontology",
"prefix": "co_360"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_360",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_360:$1"
},
"co_365": {
"agroportal": {
"contact": {
"email": "ICARDA-ethiopia@cgiar.org",
"name": "ICARDA Ethiopia"
},
"description": "to add",
"example_uri": "http://www.cropontology.org/rdf/CO_365:0000146",
"homepage": "http://www.cropontology.org",
"license": "CC-BY-4.0",
"name": "Fababean Ontology",
"prefix": "CO_365",
"repository": "https://github.com/Planteome/CO_365-faba-bean-traits",
"version": "2019-10-15"
},
"cropoct": {
"description": "developed by ICARDA - Dec 2018",
"download_owl": "http://cropontology.org/rdf/CO_365.owl",
"homepage": "http://cropontology.org/term/CO_365:ROOT",
"name": "Fababean ontology",
"prefix": "CO_365"
},
"example": "0000205",
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_365",
"cropoct": "CO_365",
"ols": "co_365"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "developed by ICARDA - Dec 2018",
"download": "https://cropontology.org/ontology/CO_365/Fababean/owl",
"homepage": "https://cropontology.org/ontology/CO_365/Fababean",
"name": "Fababean ontology",
"prefix": "co_365",
"version": "2019-10-15"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_365",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_365:$1"
},
"co_366": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project , as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_366:0000253/9",
"homepage": "http://www.cropontology.org",
"license": "CC-BY-4.0",
"name": "Bambara Groundnut Ontology",
"prefix": "CO_366",
"repository": "https://github.com/Planteome/CO_366-bambara-goundnut-traits",
"version": "2019-12-23"
},
"cropoct": {
"description": "version Dec 2019",
"download_owl": "http://cropontology.org/rdf/CO_366.owl",
"homepage": "http://cropontology.org/term/CO_366:ROOT",
"name": "Bambara groundnut ontology",
"prefix": "CO_366"
},
"example": "0000072",
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_366",
"cropoct": "CO_366",
"ols": "co_366"
},
"ols": {
"contact": "helpdesk@cropontology-curationtool.org",
"description": "version Dec 2019",
"download": "http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut/owl",
"homepage": "http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut",
"name": "Bambara groundnut ontology",
"prefix": "co_366"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_366",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_366:$1"
},
"co_367": {
"agroportal": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Quinoa Ontology database of the Crop Ontology (CO_367) of the Generation Challenge Program (GCP) describe traits variables of Quinoa Germinate Database http://germinate.quinoadb.org. Quinoa Phenotyping Consortium Creation Date 23.05.2021",
"homepage": "https://cropontology.org/term/CO_367:ROOT",
"license": "CC-BY-4.0",
"name": "Quinoa Ontology",
"prefix": "CO_367",
"publication": "https://doi.org/10.3390/plants10091759"
},
"cropoct": {
"description": "Curator name: Clara S. Stanschewski; Curator Affiliation: King Abdullah University of Science and Technology; Contributing Scientists or Crop expert group: The Salt Lab and the Quinoa Phenotyping Consortium Creation Date: 23.05.2021",
"download_owl": "http://cropontology.org/rdf/CO_367.owl",
"homepage": "http://cropontology.org/term/CO_367:ROOT",
"name": "Quinoa Ontology ontology",
"prefix": "CO_367"
},
"example": "0000004",
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_367",
"cropoct": "CO_367"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_367",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_367:$1"
},
"co_370": {
"agroportal": {
"contact": {
"email": "ekaterina.chuprikova@eurac.edu",
"name": "Ekaterina Chuprikova"
},
"description": "Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales.",
"example_uri": "https://cropontology.org/rdf/CO_370:0001028",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Apple Ontology",
"prefix": "CO_370",
"publication": "https://doi.org/10.5194/egusphere-egu21-15804",
"repository": "https://github.com/echuprikova/AppleCropOntology",
"version": "1.1"
},
"contact": {
"email": "ekaterina.chuprikova@eurac.edu",
"name": "Ekaterina Chuprikova",
"orcid": "0000-0002-8981-0442"
},
"cropoct": {
"description": "Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales.",
"download_owl": "http://cropontology.org/rdf/CO_370.owl",
"homepage": "http://cropontology.org/term/CO_370:ROOT",
"name": "Apple ontology",
"prefix": "CO_370"
},
"example": "0000890",
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_370",
"cropoct": "CO_370"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_370",
"repository": "https://github.com/bioversity/Crop-Ontology",
"uri_format": "https://cropontology.org/rdf/CO_370:$1"
},
"cob": {
"aberowl": {
"description": "COB brings together key terms from a wide range of OBO projects to improve interoperability.",
"download_owl": "http://aber-owl.net/media/ontologies/COB/11/cob.owl",
"homepage": "https://obofoundry.org/COB/",
"name": "Core Ontology for Biology and Biomedicine",
"prefix": "COB"
},
"bioportal": {
"contact": {
"email": "bpeters@lji.org",
"name": "Bjoern Peters"
},
"description": "The Core Ontology for Biology and Biomedicine (COB) brings together key terms from a wide range of OBO projects into a single, small ontology. The goal is to improve interoperabilty and reuse across the OBO community through better coordination of key terms.",
"homepage": "https://github.com/OBOFoundry/COB",
"name": "Core Ontology for Biology and Biomedicine",
"prefix": "COB",
"version": "2023-11-16"
},
"example": "0000080",
"mappings": {
"aberowl": "COB",
"bioportal": "COB",
"obofoundry": "cob",
"ols": "cob",
"ontobee": "COB"
},
"obofoundry": {
"contact": "bpeters@lji.org",
"contact.github": "bpeters42",
"contact.label": "Bjoern Peters",
"contact.orcid": "0000-0002-8457-6693",
"deprecated": false,
"description": "COB brings together key terms from a wide range of OBO projects to improve interoperability.",
"domain": "upper",
"download.owl": "http://purl.obolibrary.org/obo/cob.owl",
"homepage": "https://obofoundry.org/COB/",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Core Ontology for Biology and Biomedicine",
"preferredPrefix": "COB",
"prefix": "cob",
"repository": "https://github.com/OBOFoundry/COB"
},
"ols": {
"description": "COB brings together key terms from a wide range of OBO projects to improve interoperability.",
"download_owl": "http://purl.obolibrary.org/obo/cob.owl",
"homepage": "https://obofoundry.org/COB/",
"name": "Core Ontology for Biology and Biomedicine",
"prefix": "cob",
"version": "2023-11-16",
"version.iri": "http://purl.obolibrary.org/obo/cob/releases/2023-11-16/cob.owl"
},
"ontobee": {
"library": "Library",
"name": "Core Ontology for Biology and Biomedicine",
"prefix": "COB"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/COB_$1"
},
"coconut": {
"comment": "@mSorok is the dev of the resource, hope I got it right!",
"contributor": {
"email": "adriano.rutz@ik.me",
"github": "adafede",
"name": "Adriano Rutz",
"orcid": "0000-0003-0443-9902"
},
"description": "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a \"flat\" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties.",
"example": "CNP0171505",
"github_request_issue": 221,
"homepage": "https://coconut.naturalproducts.net",
"keywords": [
"chemistry",
"natural producs",
"organic chemistry"
],
"name": "COlleCtion of Open Natural ProdUcTs",
"pattern": "^CNP\\d{7}$",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://coconut.naturalproducts.net/compound/coconut_id/$1"
},
"codelink": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release).",
"example": "GE86325",
"homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt",
"keywords": [
"microarray",
"transcriptomics"
],
"name": "GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray",
"pattern": "^GE\\d+$",
"references": [
"https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-8060/A-GEOD-8060.adf.txt",
"https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt"
]
},
"cog": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "COG",
"uri_format": "https://www.ncbi.nlm.nih.gov/research/cog-project/$1"
},
"contact": {
"email": "cogs@ncbi.nlm.nih.gov",
"name": "Michael Y Galperin",
"orcid": "0000-0002-2265-5572"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems.",
"example": "COG0001",
"fairsharing": {
"abbreviation": "COG",
"contact": {
"email": "koonin@ncbi.nlm.nih.gov",
"name": "Eugene V Koonin",
"orcid": "0000-0003-3943-8299"
},
"description": "Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.",
"homepage": "https://www.ncbi.nlm.nih.gov/research/cog/",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes",
"prefix": "FAIRsharing.djsbw2",
"publications": [
{
"doi": "10.1126/science.278.5338.631",
"pubmed_id": 9381173,
"title": "A genomic perspective on protein families."
},
{
"doi": "10.1093/nar/gku1223",
"pubmed_id": 25428365,
"title": "Expanded microbial genome coverage and improved protein family annotation in the COG database."
}
],
"subjects": [
"Life Science"
]
},
"go": {
"homepage": "http://www.ncbi.nlm.nih.gov/COG/",
"name": "NCBI COG cluster",
"prefix": "COG_Cluster",
"uri_format": "http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=$1"
},
"homepage": "https://www.ncbi.nlm.nih.gov/research/cog/",
"mappings": {
"biolink": "COG",
"fairsharing": "FAIRsharing.djsbw2",
"go": "COG_Cluster",
"miriam": "cog",
"prefixcommons": "cog",
"togoid": "Cog"
},
"miriam": {
"deprecated": false,
"description": "Database of Clusters of Orthologous Genes (COGs). This database defines all orthologs of protein sequences coded by known genomes. The species name, protein name, and phylogenetic tree of orthologous clusters can be viewed through this site. Each cluster is comprised of individual proteins and its paralogs, matched to evolutionarily conserved molecular domains.",
"homepage": "https://www.ncbi.nlm.nih.gov/",
"id": "00000930",
"name": "COG",
"namespaceEmbeddedInLui": false,
"pattern": "^COG[0-9]+$",
"prefix": "cog",
"sampleId": "COG1806",
"uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1/"
},
"name": "Cluster of orthologous genes",
"pattern": "^COG\\d+$",
"prefixcommons": {
"description": "Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.",
"example": "145262",
"homepage": "http://www.ncbi.nlm.nih.gov/COG",
"keywords": [
"protein",
"genome"
],
"name": "Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes",
"pattern": "^\\d+$",
"prefix": "cog",
"uri_format": "http://www.ncbi.nlm.nih.gov/COG/grace/cogenome.cgi?g=$1"
},
"publications": [
{
"doi": "10.1126/science.278.5338.631",
"pubmed": "9381173",
"title": "A genomic perspective on protein families",
"year": 1997
},
{
"doi": "10.1093/nar/gku1223",
"pmc": "PMC4383993",
"pubmed": "25428365",
"title": "Expanded microbial genome coverage and improved protein family annotation in the COG database",
"year": 2014
}
],
"synonyms": [
"COG_Cluster"
],
"togoid": {
"catalog": "nbdc00397",
"examples": [
"COG0130",
"COG0663",
"COG0762",
"COG1186",
"COG1285",
"COG1390",
"COG3079",
"COG3354",
"COG4957",
"COG5379"
],
"keywords": [
"Ortholog"
],
"name": "COG",
"pattern": "^(?COG\\d{4})$",
"prefix": "Cog",
"uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1"
},
"uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1"
},
"cog.category": {
"contact": {
"email": "cogs@ncbi.nlm.nih.gov",
"name": "Michael Y Galperin",
"orcid": "0000-0002-2265-5572"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Higher-level classifications of COG Pathways",
"example": "K",
"homepage": "https://www.ncbi.nlm.nih.gov/research/cog/",
"keywords": [
"pathways"
],
"name": "COG Categories",
"part_of": "cog",
"uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1"
},
"cog.pathway": {
"contact": {
"email": "cogs@ncbi.nlm.nih.gov",
"name": "Michael Y Galperin",
"orcid": "0000-0002-2265-5572"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera.",
"example": "NAD%20biosynthesis",
"go": {
"homepage": "http://www.ncbi.nlm.nih.gov/COG/",
"name": "NCBI COG pathway",
"prefix": "COG_Pathway",
"uri_format": "http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=$1"
},
"homepage": "https://www.ncbi.nlm.nih.gov/research/cog/pathways",
"mappings": {
"go": "COG_Pathway"
},
"name": "COG Pathways",
"part_of": "cog",
"uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1"
},
"cohd": {
"comment": "not really sure where the source is. this also links to a system called athena. I was not able to figure out what COHD stands for.",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012",
"homepage": "https://github.com/MIT-LCP/mimic-omop",
"keywords": [
"clinical data",
"clinical trials",
"health",
"health sciences"
],
"name": "MIMIC III Database",
"no_own_terms": true,
"repository": "https://github.com/MIT-LCP/mimic-omop"
},
"coi": {
"contact": {
"email": "coi@bot.uc.pt",
"name": "COI Catalogue"
},
"contributor": {
"email": "shah.tanay2@northeastern.edu",
"github": "tanayshah2",
"name": "Tanay Shah",
"orcid": "0009-0001-1912-5132"
},
"description": "COI Catalogue is a herbarium with c. 800.000 specimens, organised in separate collections due to the research priorities over the years.",
"example": "63812",
"homepage": "https://coicatalogue.uc.pt/index.php",
"name": "COI Catalogue",
"publications": [
{
"doi": "10.1038/s41597-024-03520-9",
"pmc": "PMC11193818",
"pubmed": "38909064",
"title": "O armΓ‘rio: Fruiting phenology data for 4,462 plant taxa in Portugal (1926-2013)",
"year": 2024
}
],
"reviewer": {
"email": "b.gyori@northeastern.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"uri_format": "https://coicatalogue.uc.pt/index.php?t=specimen&COINumber=$1"
},
"col": {
"bartoc": {
"abbreviation": "CoL",
"description": "The Catalogue of Life (CoL) is the nearest thing to a comprehensive catalogue of all known species of organisms on Earth. Continuous progress is made towards completion, and this edition contains 1,639,016 living and 5,763 extinct species. Please note that this is probably just over three quarters of the world's known species. This means that for many groups it continues to be deficient, and users will notice that many species are still missing from the Catalogue.\n\nThe present Catalogue is compiled with sectors provided by 157 taxonomic databases from around the world. Many of these contain taxonomic data and opinions from extensive networks of specialists, so that the complete work contains contributions from more than 3,000 specialists from throughout the taxonomic profession. Species 2000 and ITIS teams peer review databases, select appropriate sectors and integrate the sectors into a single coherent catalogue with a single hierarchical classification.",
"homepage": "http://www.catalogueoflife.org/col/",
"name": "Catalogue of Life",
"prefix": "1915",
"wikidata_database": "Q38840"
},
"mappings": {
"bartoc": "1915",
"miriam": "col"
},
"miriam": {
"deprecated": false,
"description": "Identifier of a taxon or synonym in the Catalogue of Life",
"homepage": "https://www.checklistbank.org",
"id": "00000969",
"name": "Catalogue of Life",
"namespaceEmbeddedInLui": false,
"pattern": "^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$",
"prefix": "col",
"providers": [
{
"code": "col",
"description": "The Catalogue of Life website providing a view onto the latest release of the COL Checklist.",
"homepage": "https://www.catalogueoflife.org",
"name": "Catalogue of Life (COL)",
"uri_format": "https://www.catalogueoflife.org/data/taxon/$1"
}
],
"sampleId": "4QHKG",
"uri_format": "https://www.checklistbank.org/dataset/3LR/taxon/$1"
}
},
"col.taiwan": {
"contributor": {
"email": "meghan.balk@gmail.com",
"github": "megbalk",
"name": "Meghan Balk",
"orcid": "0000-0003-2699-3066"
},
"description": "Identifier (name code) for a taxon in the catalogue of life in taiwan",
"example": "431472",
"github_request_issue": 466,
"homepage": "http://taibnet.sinica.edu.tw/home.php",
"mappings": {
"wikidata": "P3088"
},
"name": "Catalogue of Life in Taiwan",
"pattern": "^[1-9]\\d{5}$",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1",
"wikidata": {
"description": "identifier (name code) for a taxon in the Catalogue of Life in Taiwan",
"example": [
"421738",
"431472"
],
"homepage": "https://taibnet.sinica.edu.tw/home_eng.php",
"name": "Catalogue of Life in Taiwan ID (old version)",
"pattern": "^([1-9]\\d{5})$",
"prefix": "P3088",
"uri_format": "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1"
}
},
"colao": {
"aberowl": {
"description": "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. It has been built using the Ontology Develoment Kit, with the Ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM) as a backbone.",
"download_owl": "http://aber-owl.net/media/ontologies/COLAO/10/colao.owl",
"homepage": "https://github.com/insect-morphology/colao",
"name": "Coleoptera Anatomy Ontology (COLAO)",
"prefix": "COLAO"
},
"bioportal": {
"contact": {
"email": "entiminae@gmail.com",
"name": "Jennifer C. GirΓ³n"
},
"description": "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. It has been built using the Ontology Develoment Kit with the Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) as a backbone. The project is open for collaboration.",
"homepage": "https://github.com/insect-morphology/colao",
"name": "Coleoptera Anatomy Ontology",
"prefix": "COLAO",
"version": "2024-06-21"
},
"example": "0000000",
"mappings": {
"aberowl": "COLAO",
"bioportal": "COLAO",
"obofoundry": "colao",
"ols": "colao",
"ontobee": "COLAO"
},
"name": "Coleoptera Anatomy Ontology",
"obofoundry": {
"contact": "entiminae@gmail.com",
"contact.github": "JCGiron",
"contact.label": "Jennifer C. Giron",
"contact.orcid": "0000-0002-0851-6883",
"depends_on": [
"aism",
"bfo",
"bspo",
"caro",
"pato",
"ro",
"uberon"
],
"deprecated": false,
"description": "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. It has been built using the Ontology Develoment Kit, with the Ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM) as a backbone.",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/colao.obo",
"download.owl": "http://purl.obolibrary.org/obo/colao.owl",
"homepage": "https://github.com/insect-morphology/colao",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Coleoptera Anatomy Ontology (COLAO)",
"preferredPrefix": "COLAO",
"prefix": "colao",
"repository": "https://github.com/insect-morphology/colao"
},
"ols": {
"description": "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research.",
"download_owl": "http://purl.obolibrary.org/obo/colao.owl",
"homepage": "https://github.com/insect-morphology/colao",
"name": "Coleoptera Anatomy Ontology",
"prefix": "colao",
"version": "2024-06-21",
"version.iri": "http://purl.obolibrary.org/obo/colao/releases/2024-06-21/colao.owl"
},
"ontobee": {
"library": "Library",
"name": "Coleoptera Anatomy Ontology (COLAO)",
"prefix": "COLAO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/COLAO_$1"
},
"collagenmutdb": {
"mappings": {
"prefixcommons": "cmd"
},
"prefixcommons": {
"description": "This database aims to record all published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP, FKBP10, LEPRE1 and PPIB genes.",
"example": "COL3A1",
"homepage": "http://www.le.ac.uk/genetics/collagen/",
"keywords": [
"gene"
],
"name": "Collagen Mutation Database",
"pattern": "^[A-Z,0-9]+$",
"prefix": "cmd",
"uri_format": "https://eds.gene.le.ac.uk/home.php?select_db=$1"
},
"provides": "hgnc.symbol",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"colonatlas": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "http://www.coloncanceratlas.org",
"name": "Colorectal Cancer Atlas",
"prefix": "ColonAtlas",
"uri_format": "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1"
},
"example": "ALA",
"mappings": {
"cellosaurus": "ColonAtlas"
}
},
"combine.specifications": {
"biocontext": {
"prefix": "COMBINE.SPECIFICATIONS"
},
"mappings": {
"biocontext": "COMBINE.SPECIFICATIONS",
"miriam": "combine.specifications",
"n2t": "combine.specifications"
},
"miriam": {
"deprecated": false,
"description": "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network.",
"homepage": "https://co.mbine.org/standards/",
"id": "00000258",
"name": "COMBINE specifications",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\-|\\.|\\w)*$",
"prefix": "combine.specifications",
"sampleId": "sed-ml.level-1.version-1",
"uri_format": "https://github.com/combine-org/combine-specifications/blob/main/specifications/$1.md"
},
"n2t": {
"description": "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network.",
"example": "sbgn.er.level-1.version-1.2",
"homepage": "https://co.mbine.org/standards/",
"name": "COMBINE at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\-|\\.|\\w)*$",
"prefix": "combine.specifications",
"uri_format": "https://co.mbine.org/specifications/$1"
}
},
"come": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif.",
"example": "MOL000160",
"homepage": "https://www.flymine.org/come",
"mappings": {
"prefixcommons": "come"
},
"name": "The Bioinorganic Motif Database",
"prefixcommons": {
"description": "COMe is an attempt to classify metalloproteins and some other complex proteins using the concept of bioinorganic motif.",
"example": "BIM000347",
"homepage": "http://www.flymine.org/come/",
"keywords": [
"protein"
],
"name": "COMe",
"pattern": "^BIM\\d+$",
"prefix": "come",
"uri_format": "http://www.flymine.org/come/entry?gn=$1"
},
"uri_format": "https://www.flymine.org/come/entry?gn=$1"
},
"commoncoreontology": {
"contact": {
"email": "mpjensen@buffalo.edu",
"github": "mark-jensen",
"name": "Mark Jensen",
"orcid": "0000-0001-9228-8838"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Common Core Ontologies (CCO) comprise twelve ontologies that are designed to represent and integrate taxonomies of generic classes and relations across all domains of interest.\n\nCCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained by the BFO framework, from which it inherits much of its basic semantic relationships.",
"example": "DirectiveInformationContentEntity",
"homepage": "http://www.ontologyrepository.com",
"keywords": [
"ontology",
"upper-level ontology"
],
"license": "CC-BY-4.0",
"name": "Common Core Ontologies",
"repository": "https://github.com/CommonCoreOntology/CommonCoreOntologies",
"uri_format": "http://www.ontologyrepository.com/CommonCoreOntologies/$1"
},
"complexportal": {
"biocontext": {
"prefix": "COMPLEXPORTAL"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "ComplexPortal",
"uri_format": "https://www.ebi.ac.uk/complexportal/complex/$1"
},
"contact": {
"email": "bmeldal@ebi.ac.uk",
"github": "bmeldal-eg",
"name": "Birgit Meldal",
"orcid": "0000-0003-4062-6158"
},
"example": "CPX-263",
"go": {
"homepage": "https://www.ebi.ac.uk/complexportal",
"name": "Complex Portal database of macromolecular complexes",
"prefix": "ComplexPortal",
"uri_format": "https://www.ebi.ac.uk/complexportal/complex/$1"
},
"license": "CC0-1.0",
"mappings": {
"biocontext": "COMPLEXPORTAL",
"biolink": "ComplexPortal",
"go": "ComplexPortal",
"miriam": "complexportal",
"n2t": "complexportal",
"re3data": "r3d100013295",
"uniprot": "DB-0228",
"wikidata": "P7718"
},
"miriam": {
"deprecated": false,
"description": "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases.",
"homepage": "https://www.ebi.ac.uk/complexportal",
"id": "00000657",
"name": "Complex Portal",
"namespaceEmbeddedInLui": false,
"pattern": "^CPX-[0-9]+$",
"prefix": "complexportal",
"sampleId": "CPX-2158",
"uri_format": "https://www.ebi.ac.uk/complexportal/complex/$1"
},
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"description": "The conference-ontology is a new self-contained ontology for modelleing knowledge about conferences. The conference-ontology adopts best ontology design practices (e.g., Ontology Design Patterns, ontology reuse and interlinking) and guarantees interoperability with SWC ontology and all other pertinent vocabularies. (from homepage)",
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"name": "Conference Ontology",
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"fairsharing": {
"abbreviation": "ConoServer",
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"name": "David Craik",
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},
"description": "ConoServer is a database specializing in sequences and structures of peptides expressed by marine cone snails. The database gives access to protein sequences, nucleic acid sequences and structural information on conopeptides. ConoServer's data are first collected from the peer reviewed literature and from publicly available databases, including UniProtKB/Swiss-Prot, NCBI nucleotide (nt), and the World Wide Protein Data Bank. The data are then curated manually, which include the addition of references, the analysis of sequence regions, the identification of cysteine frameworks and gene superfamilies, and the identification of mature peptides in the precusor sequences.",
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"license": "http://www.conoserver.org",
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"prefix": "FAIRsharing.y00hz4",
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{
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{
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},
{
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},
{
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},
{
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],
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}
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"description": "An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases.",
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"description": "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).",
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"name": "CORDIS Project",
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},
"cellosaurus": {
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"subjects": [
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"Genetics",
"Life Science",
"Systems Biology"
]
},
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"description": "CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). Each protein complex is described by a protein complex name, subunit composition, function as well as the literature reference that characterizes the respective protein complex.",
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],
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]
},
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"biocontext": "CST",
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"pathguide": "193"
},
"miriam": {
"deprecated": false,
"description": "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways.",
"homepage": "http://www.cellsignal.com/pathways/index.html",
"id": "00000429",
"name": "Cell Signaling Technology Pathways",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9_-]+$",
"prefix": "cst",
"sampleId": "Akt_PKB",
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},
"n2t": {
"description": "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways.",
"example": "Akt_PKB",
"homepage": "http://www.cellsignal.com/pathways/index.html",
"name": "CST Pathways at Cell Signaling Technology",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9_-]+$",
"prefix": "cst",
"uri_format": "http://www.cellsignal.com/reference/pathway/$1.html"
},
"pathguide": {
"abbreviation": "CST",
"homepage": "https://www.cellsignal.com/common/content/content.jsp?id=science-pathways",
"name": "Cell Signaling Technology Pathway Database",
"prefix": "193"
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},
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"n2t": "cst.ab",
"prefixcommons": "cst"
},
"miriam": {
"deprecated": false,
"description": "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products.",
"homepage": "http://www.cellsignal.com/catalog/index.html",
"id": "00000430",
"name": "Cell Signaling Technology Antibody",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "cst.ab",
"sampleId": "3305",
"uri_format": "http://www.cellsignal.com/products/$1.html"
},
"n2t": {
"description": "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products.",
"example": "3305",
"homepage": "http://www.cellsignal.com/catalog/index.html",
"name": "CST Antibody at Cell Signaling Technology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "cst.ab",
"uri_format": "http://www.cellsignal.com/products/$1.html"
},
"prefixcommons": {
"description": "A small pathway portal for showcasing Cell Signaling Technology phospho-antibody products. Contains pathway diagrams that are clickable and link to more information about each protein and the commercial products that are available for that protein.",
"example": "3762",
"homepage": "http://www.cellsignal.com/",
"keywords": [
"pathway"
],
"name": "Cell Signaling Technology Pathway Database",
"pattern": "^\\d+$",
"prefix": "cst",
"uri_format": "http://www.cellsignal.com/products/$1.html"
}
},
"cstr": {
"mappings": {
"miriam": "cstr"
},
"miriam": {
"deprecated": false,
"description": "CSTR is an identifier for Common Science and Technology Resources, to provide persistent identification services for the positioning, traceability, citation, statistics and evaluation of science and technology resources. ",
"homepage": "https://www.cstr.cn/en/",
"id": "00000998",
"name": "CSTR",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{5}\\.\\d{2}\\..*$",
"prefix": "cstr",
"sampleId": "31253.11.sciencedb.j00001.00123",
"uri_format": "https://cstr.cn/$1"
},
"name": "Common Science and Technology Resources"
},
"ctcae": {
"aberowl": {
"description": "A coding system for reporting adverse events that occur in the course of cancer therapy. It was derived from the Common Toxicity Criteria (CTC) v2.0 and is maintained by the Cancer Therapy Evaluation Program (CTEP) at the National Cancer Institution (NCI).",
"download_owl": "http://aber-owl.net/media/ontologies/CTCAE/2/ctcae.owl",
"name": "Common Terminology Criteria for Adverse Events",
"prefix": "CTCAE",
"version": "4.03"
},
"appears_in": [
"oae"
],
"bioportal": {
"contact": {
"email": "ncictcaehelp@mail.nih.gov",
"name": "CTCAE Help"
},
"description": "Common Terminology Criteria for Adverse Events (CTCAE) is widely accepted throughout the oncology community as the standard classification and severity grading scale for adverse events in cancer therapy clinical trials and other oncology settings. Version 5 was published by the NCI Cancer Therapy Evaluation Program (CTEP) in November 2017. It is organized by MedDRA System Organ Class and mapped to MedDRA LLTs with corresponding MedDRA codes, and harmonized with MedDRA at the Adverse Event (AE) level including revised AE terms and severity indicators to reflect clinical effects identified with current oncology interventions.Severity grades are assigned and most are defined to clarify the meaning of the term. CTCAE is designed to integrate into information networks for safety data exchange, and is the primary standard for data management for AE data collection, analysis, and patient outcomes associated with cancer research and care.",
"homepage": "https://nciterms.nci.nih.gov/ncitbrowser/pages/vocabulary.jsf?dictionary=CTCAE_v5&version=5.0",
"name": "Common Terminology Criteria for Adverse Events",
"prefix": "CTCAE",
"version": "5.0"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"description": "The Common Terminology Criteria for Adverse Events (CTCAE),[1] formerly called the Common Toxicity Criteria (CTC or NCI-CTC), are a set of criteria for the standardized classification of adverse effects of drugs used in cancer therapy. The CTCAE system is a product of the US National Cancer Institute (NCI).",
"example": "E12768",
"homepage": "https://evs.nci.nih.gov/ftp1/CTCAE/About.html",
"mappings": {
"aberowl": "CTCAE",
"bioportal": "CTCAE"
},
"name": "Common Terminology Criteria for Adverse Events",
"pattern": "^E\\d+$",
"publications": [
{
"pmc": "PMC5977606",
"pubmed": "29854250",
"title": "Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs",
"year": 2018
}
],
"references": [
"https://github.com/OAE-ontology/OAE/issues/8",
"https://en.wikipedia.org/wiki/Common_Terminology_Criteria_for_Adverse_Events"
],
"synonyms": [
"CTCAE"
]
},
"ctd.chemical": {
"biocontext": {
"prefix": "CTD.CHEMICAL"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "CTD.CHEMICAL",
"uri_format": "http://ctdbase.org/detail.go?type=chem&acc=$1"
},
"mappings": {
"biocontext": "CTD.CHEMICAL",
"biolink": "CTD.CHEMICAL",
"miriam": "ctd.chemical",
"n2t": "ctd.chemical"
},
"miriam": {
"deprecated": false,
"description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.",
"homepage": "http://ctdbase.org/",
"id": "00000098",
"name": "CTD Chemical",
"namespaceEmbeddedInLui": false,
"pattern": "^[CD]\\d+$",
"prefix": "ctd.chemical",
"sampleId": "D001151",
"uri_format": "http://ctdbase.org/detail.go?type=chem&acc=$1"
},
"n2t": {
"description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.",
"example": "D001151",
"homepage": "http://ctdbase.org/",
"name": "Comparative Toxicogenomics Database (Chemical)",
"namespaceEmbeddedInLui": false,
"pattern": "^[CD]\\d+$",
"prefix": "ctd.chemical",
"uri_format": "http://ctdbase.org/detail.go?type=chem&acc=$1"
},
"part_of": "ctd",
"provides": "mesh"
},
"ctd.disease": {
"biocontext": {
"prefix": "CTD.DISEASE"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "CTD.DISEASE",
"uri_format": "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1"
},
"mappings": {
"biocontext": "CTD.DISEASE",
"biolink": "CTD.DISEASE",
"miriam": "ctd.disease",
"n2t": "ctd.disease"
},
"miriam": {
"deprecated": false,
"description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.",
"homepage": "http://ctdbase.org/",
"id": "00000099",
"name": "CTD Disease",
"namespaceEmbeddedInLui": false,
"pattern": "^D\\d+$",
"prefix": "ctd.disease",
"sampleId": "D053716",
"uri_format": "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1"
},
"n2t": {
"description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.",
"example": "D053716",
"homepage": "http://ctdbase.org/",
"name": "Comparative Toxicogenomics Database (Disease)",
"namespaceEmbeddedInLui": false,
"pattern": "^D\\d+$",
"prefix": "ctd.disease",
"uri_format": "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1"
},
"part_of": "ctd",
"provides": "mesh"
},
"ctd.gene": {
"biocontext": {
"prefix": "CTD.GENE"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "CTD.GENE",
"uri_format": "http://ctdbase.org/detail.go?type=gene&acc=$1"
},
"contact": {
"email": "apdavis3@ncsu.edu",
"name": "Allan Peter Davis",
"orcid": "0000-0002-5741-7128"
},
"mappings": {
"biocontext": "CTD.GENE",
"biolink": "CTD.GENE",
"miriam": "ctd.gene",
"n2t": "ctd.gene",
"uniprot": "DB-0140"
},
"miriam": {
"deprecated": false,
"description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.",
"homepage": "http://ctdbase.org/",
"id": "00000100",
"name": "CTD Gene",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "ctd.gene",
"sampleId": "101",
"uri_format": "http://ctdbase.org/detail.go?type=gene&acc=$1"
},
"n2t": {
"description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.",
"example": "101",
"homepage": "http://ctdbase.org/",
"name": "Comparative Toxicogenomics Database (Gene)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "ctd.gene",
"uri_format": "http://ctdbase.org/detail.go?type=gene&acc=$1"
},
"part_of": "ctd",
"provides": "ncbigene",
"publications": [
{
"doi": "10.1093/nar/gkaa891",
"pmc": "PMC7779006",
"pubmed": "33068428",
"title": "Comparative Toxicogenomics Database (CTD): update 2021",
"year": 2021
}
],
"uniprot": {
"abbreviation": "CTD",
"category": "Organism-specific databases",
"homepage": "https://ctdbase.org/",
"name": "Comparative Toxicogenomics Database",
"prefix": "DB-0140",
"publications": [
{
"doi": "10.1093/nar/gkaa891",
"pubmed": "33068428"
}
],
"uri_format": "https://ctdbase.org/detail.go?type=gene&db=GENE&acc=$1"
}
},
"cteno": {
"aberowl": {
"description": "An anatomical and developmental ontology for ctenophores (Comb Jellies)",
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"homepage": "https://github.com/obophenotype/ctenophore-ontology",
"name": "Ctenophore Ontology",
"prefix": "CTENO"
},
"biocontext": {
"prefix": "CTENO"
},
"bioportal": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "An anatomical and developmental ontology for ctenophores (Comb Jellies)",
"homepage": "https://github.com/obophenotype/ctenophore-ontology",
"name": "Ctenophore Ontology",
"prefix": "CTENO"
},
"download_obo": "https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo",
"example": "0000047",
"fairsharing": {
"abbreviation": "CTENO",
"description": "An anatomical and developmental ontology for ctenophores (Comb Jellies). Please note that, while available, this ontology has not been updated since 2016.",
"homepage": "https://github.com/obophenotype/ctenophore-ontology",
"license": "CC-BY-3.0",
"name": "Ctenophore Ontology",
"prefix": "FAIRsharing.mgxgza",
"subjects": [
"Anatomy",
"Developmental Biology"
]
},
"mappings": {
"aberowl": "CTENO",
"biocontext": "CTENO",
"bioportal": "CTENO",
"fairsharing": "FAIRsharing.mgxgza",
"obofoundry": "cteno",
"ols": "cteno",
"ontobee": "CTENO"
},
"obofoundry": {
"contact": "cjmungall@lbl.gov",
"contact.github": "cmungall",
"contact.label": "Chris Mungall",
"contact.orcid": "0000-0002-6601-2165",
"depends_on": [
"ro",
"uberon"
],
"deprecated": false,
"description": "An anatomical and developmental ontology for ctenophores (Comb Jellies)",
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/cteno.owl",
"homepage": "https://github.com/obophenotype/ctenophore-ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Ctenophore Ontology",
"preferredPrefix": "CTENO",
"prefix": "cteno",
"repository": "https://github.com/obophenotype/ctenophore-ontology"
},
"ols": {
"description": "An anatomical and developmental ontology for ctenophores (Comb Jellies)",
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"homepage": "https://github.com/obophenotype/ctenophore-ontology",
"name": "Ctenophore Ontology",
"prefix": "cteno",
"version": "2016-10-19",
"version.iri": "http://purl.obolibrary.org/obo/cteno/releases/2016-10-19/cteno.owl"
},
"ontobee": {
"library": "Library",
"name": "Ctenophore Ontology",
"prefix": "CTENO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/CTENO_$1"
},
"ctis": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "This website supports the undertaking and oversight of clinical trials in the European Union (EU) and European Economic Area (EEA). It is part of a broad initiative to transform the EU/EEA clinical trials environment in support of large clinical trials in multiple European countries, to the benefit of medical innovation and patients. (from homepage)",
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"uri_format": "https://euclinicaltrials.eu/app/#/view/$1"
},
"cto": {
"aberowl": {
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"download_owl": "http://aber-owl.net/media/ontologies/CTO/5/cto.owl",
"homepage": "https://github.com/ClinicalTrialOntology/CTO/",
"name": "CTO: Core Ontology of Clinical Trials",
"prefix": "CTO"
},
"bioportal": {
"contact": {
"email": "alpha.tom.kodamullil@scai.fraunhofer.de",
"name": "Alpha Tom Kodamullil"
},
"description": "Clinical Trial Ontology (CTO) is designed to formally represent and integrate all terms used to describe and register the clinical trials. The development of CTO was done as a collaborative project among Fraunhofer SCAI, Germany; University of Michigan; Center for Devices and Radiological Health, FDA; and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda. Respective related projects are described below: At Fraunhofer SCAI, the work was supported and funded from the EUβs Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 785907 (Human Brain Project SGA2 by the HBP Medical Informatics Platform) and No. 826421 (VirtualBrainCloud), and a Fraunhofer internal funding MAVO project \"Human Brain Pharmacome\". At University of Michigan, the work was supported by the NIH-NIDDK U2C Project (1U2CDK114886) and a grant from the Michigan MedicineβPeking University Health Sciences Center Joint Institute for Clinical and Translational Research (U063430). At NCBI side, thhe work of QL and EB was supported by the Intramural Research Program of the National Library of Medicine, National Institutes of Health.",
"name": "Clinical Trials Ontology",
"prefix": "CTO",
"version": "Version Release: 1.0.0"
},
"example": "0000022",
"fairsharing": {
"abbreviation": "CTO",
"contact": {
"email": "erfan.younesi@scai.fraunhofer.de",
"name": "Erfan Younesi",
"orcid": "0000-0001-8793-2692"
},
"description": "The Clinical Trials Ontology (CTO) is also known as the Clinical Trial Ontology-Neurodegenerative Diseases (CTO-NDD), and describes clinical trials in the field of neurodegeneration. This resource has been created for use in the IMI-funded AETIONOMY project (www.aetionomy.org).",
"domains": [
"Disease"
],
"homepage": "http://bioportal.bioontology.org/ontologies/CTO",
"name": "Clinical Trials Ontology",
"prefix": "FAIRsharing.qp211a",
"subjects": [
"Neurobiology",
"Biomedical Science",
"Preclinical Studies"
]
},
"mappings": {
"aberowl": "CTO",
"bioportal": "CTO",
"fairsharing": "FAIRsharing.qp211a",
"obofoundry": "cto",
"ols": "cto",
"ontobee": "CTO"
},
"name": "Clinical Trials Ontology",
"obofoundry": {
"contact": "alpha.tom.kodamullil@scai.fraunhofer.de",
"contact.github": "akodamullil",
"contact.label": "Dr. Alpha Tom Kodamullil",
"contact.orcid": "0000-0001-9896-3531",
"deprecated": false,
"description": "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/cto.owl",
"homepage": "https://github.com/ClinicalTrialOntology/CTO/",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "CTO: Core Ontology of Clinical Trials",
"preferredPrefix": "CTO",
"prefix": "cto",
"repository": "https://github.com/ClinicalTrialOntology/CTO"
},
"ols": {
"description": "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials.",
"download": "http://purl.obolibrary.org/obo/cto.owl",
"homepage": "https://github.com/BFO-ontology/BFO",
"name": "CTO: Core Ontology of Clinical Trials",
"prefix": "cto",
"version": "1.0.0"
},
"ontobee": {
"library": "Library",
"name": "CTO: Core Ontology of Clinical Trials",
"prefix": "CTO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/CTO_$1"
},
"ctri": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The mission of the Clinical Trials Registry-India (CTRI) is to ensure that all clinical trials conducted in India are prospectively registered, i.e. before the enrolment of the first participant. Additionally, post-marketing surveillance studies, BA/BE studies as well as clinical studies as part of PG thesis are also expected to be registered in the CTRI. (from homepage)\n\nNote that the identifier in this semantic space is not the one used in the webpages",
"example": "CTRI/2023/04/052053",
"homepage": "https://ctri.nic.in",
"name": "India Clinical Trials Registry",
"pattern": "^CTRI/\\d{4}/\\d{2,3}/\\d+$",
"references": [
"https://www.ctri.nic.in/Clinicaltrials/pmaindet2.php?trialid=82487"
],
"uri_format": "https://trialsearch.who.int/Trial2.aspx?TrialID=$1"
},
"cubedb": {
"biocontext": {
"prefix": "CUBEDB"
},
"comment": "website down as of 2021-10-04",
"deprecated": true,
"integbio": {
"description": "Detection of functional divergence in human protein families. Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family classification follows (largely) the classification suggested by HUGO Gene Nomenclature Committee. Sets of orthologous protein sequences were generated by mutual-best-hit strategy using full vertebrate genomes available in Ensembl. The scores, described on documentation page, are assigned to each individual residue in a protein, and presented in the form of a table (html or downloadable xls formats) and mapped, when appropriate, onto the related structure (Jmol, Pymol, Chimera).",
"fairsharing": "FAIRsharing.aqb4ne",
"homepage": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Evolution of Protein Structure and Function Group, Biomolecular Modelling and Design Division, Bioinformatics Institute",
"name": "CUBE-DB",
"prefix": "nbdc02094",
"pubmeds": [
"21931701",
"22139934"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"mappings": {
"biocontext": "CUBEDB",
"integbio": "nbdc02094",
"miriam": "cubedb",
"n2t": "cubedb"
},
"miriam": {
"deprecated": false,
"description": "Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available.",
"homepage": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html",
"id": "00000397",
"name": "Cube db",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z_0-9]+$",
"prefix": "cubedb",
"sampleId": "AKR",
"uri_format": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/"
},
"n2t": {
"description": "Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available.",
"example": "AKR",
"homepage": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html",
"name": "Cube db at Bioinformatics Institute (Singapore)",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z_0-9]+$",
"prefix": "cubedb",
"uri_format": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/"
}
},
"cutg": {
"mappings": {
"prefixcommons": "cutg"
},
"prefixcommons": {
"description": "Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank.",
"example": "9606",
"homepage": "http://www.kazusa.or.jp/codon/",
"keywords": [
"gene",
"DNA"
],
"name": "Codon Usage Tabulated from GenBank",
"pattern": "^\\d+$",
"prefix": "cutg",
"uri_format": "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=$1"
},
"provides": "ncbitaxon",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"cvdo": {
"aberowl": {
"description": "An ontology to describe entities related to cardiovascular diseases",
"download_owl": "http://aber-owl.net/media/ontologies/CVDO/6/cvdo.owl",
"homepage": "https://github.com/OpenLHS/CVDO",
"name": "Cardiovascular Disease Ontology",
"prefix": "CVDO"
},
"biocontext": {
"prefix": "CVDO"
},
"bioportal": {
"contact": {
"email": "adrien.barton@gmail.com",
"name": "Adrien Barton"
},
"description": "CVDO is an ontology based on the OGMS model of disease, designed to describe entities related to cardiovascular diseases (including the diseases themselves, the underlying disorders, and the related pathological processes). It is being developed at Sherbrooke University (Canada) and the INSERM research institute (Institut National de la SantΓ© et de la Recherche MΓ©dicale).",
"homepage": "https://github.com/OpenLHS/CVDO",
"name": "Cardiovascular Disease Ontology",
"prefix": "CVDO",
"version": "2024-05-17"
},
"example": "0000546",
"fairsharing": {
"abbreviation": "CVDO",
"description": "CVDO is an ontology based on the OGMS model of disease, designed to describe entities related to cardiovascular diseases (including the diseases themselves, the underlying disorders, and the related pathological processes).",
"domains": [
"Cardiovascular disease"
],
"homepage": "https://github.com/OpenLHS/CVDO",
"license": "CC-BY-4.0",
"name": "Cardiovascular Disease Ontology",
"prefix": "FAIRsharing.2basyz",
"subjects": [
"Cardiology"
]
},
"mappings": {
"aberowl": "CVDO",
"biocontext": "CVDO",
"bioportal": "CVDO",
"fairsharing": "FAIRsharing.2basyz",
"obofoundry": "cvdo",
"ols": "cvdo",
"ontobee": "CVDO"
},
"obofoundry": {
"contact": "paul.fabry@usherbrooke.ca",
"contact.github": "pfabry",
"contact.label": "Paul Fabry",
"contact.orcid": "0000-0002-3336-2476",
"deprecated": false,
"description": "An ontology to describe entities related to cardiovascular diseases",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/cvdo.owl",
"homepage": "https://github.com/OpenLHS/CVDO",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Cardiovascular Disease Ontology",
"preferredPrefix": "CVDO",
"prefix": "cvdo",
"repository": "https://github.com/OpenLHS/CVDO"
},
"ols": {
"description": "An ontology to describe entities related to cardiovascular diseases",
"download_owl": "http://purl.obolibrary.org/obo/cvdo.owl",
"homepage": "https://github.com/OpenLHS/CVDO",
"name": "Cardiovascular Disease Ontology",
"prefix": "cvdo",
"version": "2024-05-17",
"version.iri": "http://purl.obolibrary.org/obo/cvdo/2024-05-17/cvdo.owl"
},
"ontobee": {
"library": "Library",
"name": "Cardiovascular Disease Ontology",
"prefix": "CVDO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/CVDO_$1"
},
"cvx": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The CDC's National Center of Immunization and Respiratory Diseases (NCIRD) developed and maintains the CVX (vaccine administered) code set. The table below has the most up to date values. It includes both active and inactive vaccines available in the US. CVX codes for inactive vaccines allow transmission of historical immunization records.",
"example": "54",
"hl7": {
"description": "CDC Vaccine Codes used in the 1999 RRF research project at HL7.DO NOT USEThis OID has been retired as it only identifies the set of codes used in the RRF research project.",
"name": "CVX",
"preferred_prefix": "cvx",
"prefix": "2.16.840.1.113883.6.59",
"status": "Retired"
},
"homepage": "https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx",
"mappings": {
"hl7": "2.16.840.1.113883.6.59"
},
"name": "Vaccine administered code set",
"pattern": "^\\d+$",
"uri_format": "https://biopragmatics.github.io/providers/cvx/$1"
},
"d1id": {
"biocontext": {
"prefix": "D1ID"
},
"mappings": {
"biocontext": "D1ID",
"miriam": "d1id",
"n2t": "d1id"
},
"miriam": {
"deprecated": false,
"description": "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences.",
"homepage": "https://www.dataone.org",
"id": "00000611",
"name": "DataONE",
"namespaceEmbeddedInLui": false,
"pattern": "\\S+",
"prefix": "d1id",
"sampleId": "00030692-0FE1-4A1B-955E-A2E55D659267",
"uri_format": "https://cn.dataone.org/cn/v2/resolve/{$1}"
},
"n2t": {
"description": "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences.",
"example": "00030692-0FE1-4A1B-955E-A2E55D659267",
"homepage": "https://www.dataone.org",
"name": "DataONE",
"namespaceEmbeddedInLui": false,
"pattern": "\\S+",
"prefix": "d1id",
"uri_format": "https://cn.dataone.org/cn/v2/resolve/{$1}"
}
},
"dailymed": {
"biocontext": {
"prefix": "DAILYMED"
},
"mappings": {
"biocontext": "DAILYMED",
"miriam": "dailymed",
"n2t": "dailymed",
"prefixcommons": "dailymed"
},
"miriam": {
"deprecated": false,
"description": "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read.",
"homepage": "https://dailymed.nlm.nih.gov/dailymed/",
"id": "00000434",
"name": "DailyMed",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9-]+",
"prefix": "dailymed",
"sampleId": "973a9333-fec7-46dd-8eb5-25738f06ee54",
"uri_format": "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1"
},
"n2t": {
"description": "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read.",
"example": "973a9333-fec7-46dd-8eb5-25738f06ee54",
"homepage": "https://dailymed.nlm.nih.gov/dailymed/",
"name": "DailyMed at NLM",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9-]+",
"prefix": "dailymed",
"uri_format": "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1"
},
"prefixcommons": {
"description": "DailyMed provides high quality information about marketed drugs including FDA labels (package inserts).",
"example": "3be94523-f6d6-4b25-82b0-3e0d021594c5",
"homepage": "http://dailymed.nlm.nih.gov/dailymed/",
"name": "Dailymed",
"pattern": "^[A-Za-z0-9]{8}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{12}$",
"prefix": "dailymed",
"uri_format": "http://dailymed.nlm.nih.gov/dailymed/lookup.cfm?setid=$1"
}
},
"dandi": {
"fairsharing": {
"abbreviation": "DANDI",
"contact": {
"email": "yoh@dartmouth.edu",
"name": "Yaroslav Halchenko",
"orcid": "0000-0003-3456-2493"
},
"description": "The Distributed Archives for Neurophysiology Data Integration (DANDI) is a platform for publishing, sharing, and processing neurophysiology data funded by the BRAIN Initiative. The archive accepts cellular neurophysiology data including electrophysiology, optophysiology, and behavioral time-series, and images from immunostaining experiments.",
"homepage": "https://www.dandiarchive.org",
"license": "CC0-1.0",
"name": "Distributed Archives for Neurophysiology Data Integration",
"prefix": "FAIRsharing.f2c119",
"publications": [],
"repository": "https://github.com/dandi/dandiarchive",
"subjects": [
"Neurophysiology"
],
"twitter": "dandiarchive"
},
"mappings": {
"fairsharing": "FAIRsharing.f2c119",
"miriam": "dandi",
"re3data": "r3d100013638"
},
"miriam": {
"deprecated": false,
"description": "DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable).\nDANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data.\nThese data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.",
"homepage": "https://dandiarchive.org/",
"id": "00000786",
"name": "DANDI: Distributed Archives for Neurophysiology Data Integration",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{6}(\\/\\d+\\.\\d+\\.\\d+)?$",
"prefix": "dandi",
"sampleId": "000017",
"uri_format": "https://dandiarchive.org/dandiset/$1"
},
"name": "Distributed Archives for Neurophysiology Data Integration",
"re3data": {
"description": "The US BRAIN Initiative archive for publishing and sharing neurophysiology data including electrophysiology, optophysiology, and behavioral time-series, and images from immunostaining experiments.",
"homepage": "https://dandiarchive.org/",
"name": "DANDI",
"prefix": "r3d100013638",
"synonyms": [
"DANDI Archive",
"Distributed Archives for Neurophysiology Data Integration"
],
"xrefs": {
"fairsharing": "FAIRsharing.f2c119",
"scr": "017571"
}
}
},
"darc": {
"biocontext": {
"prefix": "DARC"
},
"contact": {
"email": "daniel.wilson@uni-hamburg.de",
"name": "Daniel N. Wilson",
"orcid": "0000-0003-3816-3828"
},
"fairsharing": {
"abbreviation": "DARC",
"description": "The Database for Aligned Ribosomal Complexes (DARC) site provides a resource for directly comparing the structures of available ribosomal complexes.",
"homepage": "http://darcsite.genzentrum.lmu.de/darc/",
"name": "Database of Aligned Ribosomal Complexes",
"prefix": "FAIRsharing.evfe2s",
"publications": [
{
"doi": "10.1093/nar/gkr824",
"pubmed_id": 22009674,
"title": "The DARC site: a database of aligned ribosomal complexes."
}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"biocontext": "DARC",
"fairsharing": "FAIRsharing.evfe2s",
"miriam": "darc",
"n2t": "darc"
},
"miriam": {
"deprecated": false,
"description": "DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.",
"homepage": "http://darcsite.genzentrum.lmu.de/darc/index.php",
"id": "00000366",
"name": "DARC",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "darc",
"sampleId": "1250",
"uri_format": "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1"
},
"n2t": {
"description": "DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.",
"example": "1250",
"homepage": "http://darcsite.genzentrum.lmu.de/darc/index.php",
"name": "DARC at University of Munich",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "darc",
"uri_format": "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1"
},
"name": "Database of Aligned Ribosomal Complexes",
"publications": [
{
"doi": "10.1093/nar/gkr824",
"pmc": "PMC3245104",
"pubmed": "22009674",
"title": "The DARC site: a database of aligned ribosomal complexes",
"year": 2011
}
]
},
"dashr": {
"biocontext": {
"prefix": "DASHR"
},
"fairsharing": {
"abbreviation": "DASHR",
"contact": {
"email": "dashr@lisanwanglab.org",
"name": "Li-San Wang",
"orcid": "0000-0002-3684-0031"
},
"description": "Integrated annotation and sequencing-based expression data for all major classes of human small non-coding RNAs (sncRNAs) for both full sncRNA transcripts and mature sncRNA products derived from these larger RNAs.",
"homepage": "http://lisanwanglab.org/DASHR",
"name": "Database of small human non-coding RNAs",
"prefix": "FAIRsharing.ztvs34",
"publications": [
{
"doi": "10.1093/nar/gkv1188",
"pubmed_id": 26553799,
"title": "DASHR: database of small human noncoding RNAs."
}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"biocontext": "DASHR",
"fairsharing": "FAIRsharing.ztvs34",
"miriam": "dashr",
"n2t": "dashr"
},
"miriam": {
"deprecated": false,
"description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records.",
"homepage": "http://lisanwanglab.org/DASHR/",
"id": "00000564",
"name": "DASHR",
"namespaceEmbeddedInLui": false,
"pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$",
"prefix": "dashr",
"sampleId": "hsa-mir-200a",
"uri_format": "http://lisanwanglab.org/DASHR/entry/$1"
},
"n2t": {
"description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records.",
"example": "hsa-mir-200a",
"homepage": "http://lisanwanglab.org/DASHR/",
"name": "DASHR at University of Pennsylvania",
"namespaceEmbeddedInLui": false,
"pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$",
"prefix": "dashr",
"uri_format": "http://lisanwanglab.org/DASHR/entry/$1"
},
"name": "Database of small human noncoding RNAs",
"publications": [
{
"doi": "10.1093/nar/gkv1188",
"pmc": "PMC4702848",
"pubmed": "26553799",
"title": "DASHR: database of small human noncoding RNAs",
"year": 2015
}
]
},
"dashr.expression": {
"biocontext": {
"prefix": "DASHR.EXPRESSION"
},
"mappings": {
"biocontext": "DASHR.EXPRESSION",
"miriam": "dashr.expression",
"n2t": "dashr.expression"
},
"miriam": {
"deprecated": false,
"description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression.",
"homepage": "https://dashr1.lisanwanglab.org/show-expression-table.php?start=0",
"id": "00000565",
"name": "DASHR expression",
"namespaceEmbeddedInLui": false,
"pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$",
"prefix": "dashr.expression",
"sampleId": "hsa-mir-200a",
"uri_format": "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable"
},
"n2t": {
"description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression.",
"example": "hsa-mir-200a",
"homepage": "https://dashr1.lisanwanglab.org/show-expression-table.php?start=0",
"name": "DASHR expression at University of Pennsylvania",
"namespaceEmbeddedInLui": false,
"pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$",
"prefix": "dashr.expression",
"uri_format": "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable"
}
},
"datacite": {
"aberowl": {
"description": "The DataCite Ontology (DataCite) is an ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF.",
"download_owl": "http://aber-owl.net/media/ontologies/DATACITE/2/datacite.owl",
"homepage": "http://www.sparontologies.net/ontologies/datacite",
"name": "SPAR DataCite Ontology",
"prefix": "DATACITE",
"version": "1.2"
},
"bioportal": {
"contact": {
"email": "sparontologies@gmail.com",
"name": "SPAR Ontologies"
},
"description": "The DataCite Ontology (DataCite) is an ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF.",
"homepage": "http://www.sparontologies.net/ontologies/datacite",
"name": "SPAR DataCite Ontology",
"prefix": "DATACITE",
"publication": "http://dx.doi.org/10.6084/m9.figshare.2075356",
"version": "1.2"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF.",
"example": "AgentIdentifierScheme",
"fairsharing": {
"abbreviation": "DataCite",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The DataCite Ontology (DataCite) is an ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/datacite",
"license": "CC-BY-4.0",
"name": "DataCite Ontology ",
"prefix": "FAIRsharing.c06f1e",
"repository": "https://github.com/sparontologies/datacite",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"homepage": "http://www.sparontologies.net/ontologies/datacite",
"mappings": {
"aberowl": "DATACITE",
"bioportal": "DATACITE",
"fairsharing": "FAIRsharing.c06f1e"
},
"name": "DataCite Ontology",
"preferred_prefix": "DataCite",
"repository": "https://github.com/sparontologies/datacite",
"twitter": "datacite",
"uri_format": "http://purl.org/spar/datacite/$1"
},
"datacommons": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "dcid",
"uri_format": "https://datacommons.org/browser/$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A large RDF store built from American governmental data. This semantic space has a mixture of direct terms and subspaces.",
"example": "Gene",
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"homepage": "https://icahn.mssm.edu/",
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"prefixcommons": "datf"
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"miriam": {
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"example": "AT1G01030.1",
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"name": "Database of Arabidopsis Transcription Factors",
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"abbreviation": "DATF",
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"name": "Database of Arabidopsis Transcription Factors",
"prefix": "518"
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"description": "The Database of Arabidopsis Transcription Factors (DATF) collects all Arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families.The Version 2 of DATF was updated at July 2006. It is based on the Arabidopsis Sequence of TAIR http://www.pdb.org, predicted Nuclear Location Signals, UniGene information, as well as links to literature reference.",
"example": "AT1G08970.3",
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"keywords": [
"regulation"
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"name": "Database of Arabidopsis Transcription Factors",
"pattern": "^AT\\d[A-Z]\\d+$",
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}
},
"dbd": {
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"prefix": "DBD"
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"edam": {
"description": "Identifier of a predicted transcription factor from the DBD database.",
"name": "DBD",
"obsolete": false,
"prefix": "2716"
},
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"miriam": {
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"homepage": "http://www.transcriptionfactor.org/",
"id": "00000455",
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"pattern": "^\\d+$",
"prefix": "dbd",
"sampleId": "0045310",
"uri_format": "http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD"
},
"n2t": {
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"example": "0045310",
"homepage": "http://www.transcriptionfactor.org/",
"name": "DBD at MRC Laboratory of Molecular Biology",
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"pattern": "^\\d+$",
"prefix": "dbd",
"uri_format": "http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD"
},
"name": "Transcription Factor Database",
"pathguide": {
"abbreviation": "DBD",
"homepage": "http://www.transcriptionfactor.org/index.cgi?Home",
"name": "DNA-Binding Domain: Transcription Factor Predictor Database",
"prefix": "496"
},
"prefixcommons": {
"description": "DBD provides transcription factor predictions for more than 150 completely sequenced genomes available for browsing and download. Predictions are based on presence of sequence specific DNA binding domain assignments using hidden Markov models from the SUPERFAMILY and PFAM databases",
"example": "0035306",
"homepage": "http://www.transcriptionfactor.org",
"keywords": [
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"genome"
],
"name": "DBD",
"pattern": "^\\d+$",
"prefix": "dbd",
"uri_format": "http://dbd.mrc-lmb.cam.ac.uk/DBD/index.cgi?Search/Domain+domain:$1"
}
},
"dbest": {
"biocontext": {
"prefix": "DBEST"
},
"contact": {
"email": "tmjlowe@ucsc.edu",
"name": "Todd M Lowe",
"orcid": "0000-0003-3253-6021"
},
"edam": {
"description": "Identifier of a dbEST database entry.",
"name": "dbEST",
"obsolete": false,
"prefix": "1105"
},
"fairsharing": {
"abbreviation": "dbEST",
"description": "The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms. NCBI is in the process of merging EST and GSS records into the Nucleotide database, and the process is expected to be completed 2019. Accession.version and GI identifiers will not change during this process. For more information please see https://ncbiinsights.ncbi.nlm.nih.gov/2018/07/30/upcoming-changes-est-gss-databases/",
"homepage": "https://www.ncbi.nlm.nih.gov/genbank/dbest/",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "Expressed Sequence Tags database",
"prefix": "FAIRsharing.v9fya8",
"publications": [
{
"doi": "10.1038/ng0893-332",
"pubmed_id": 8401577,
"title": "dbEST--database for \"expressed sequence tags\"."
}
],
"subjects": [
"Bioinformatics",
"Life Science"
]
},
"integbio": {
"alt_name": "Expressed Sequence Tags database",
"description": "This is one of the world's largest repository for EST with information on multiple species. Users can also submit their own data.",
"fairsharing": "biodbcore-000435",
"homepage": "https://www.ncbi.nlm.nih.gov/genbank/dbest/",
"information_keywords": [
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"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "dbEST",
"prefix": "nbdc00413",
"pubmeds": [
"8401577"
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"status": "Active",
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"cDNA/EST"
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},
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"homepage": "https://www.ncbi.nlm.nih.gov/nucest",
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{
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},
{
"code": "CURATOR_REVIEW",
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"name": "dbEST through DNA Data Bank of Japan (DDBJ)",
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}
],
"sampleId": "BP100000",
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},
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"year": 1993
}
],
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"description": "dbEST is a division of GenBank that contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms. Expressed Sequence Tags (ESTs) are short (usually about 300-500 bp), single-pass sequence reads from mRNA (cDNA). Typically they are produced in large batches. They represent a snapshot of genes expressed in a given tissue and/or at a given developmental stage. They are tags (some coding, others not) of expression for a given cDNA library.\nMost EST projects develop large numbers of sequences. These are commonly submitted to GenBank and dbEST as batches of dozens to thousands of entries, with a great deal of redundancy in the citation, submitter and library information. To improve the efficiency of the submission process for this type of data, we have designed a special streamlined submission process and data format.\ndbEST also includes sequences that are longer than the traditional ESTs, or are produced as single sequences or in small batches. Among these sequences are products of differential display experiments and RACE experiments. The thing that these sequences have in common with traditional ESTs, regardless of length, quality, or quantity, is that there is little information that can be annotated in the record.\nIf a sequence is later characterized and annotated with biological features such as a coding region, 5'UTR, or 3'UTR, it should be submitted through the regular GenBank submissions procedure (via BankIt or Sequin), even if part of the sequence is already in dbEST.\ndbEST is reserved for single-pass reads. Assembled sequences should not be submitted to dbEST. GenBank will accept assembled EST submissions for the forthcoming TSA (Transcriptome Shotgun Assembly) division. The individual reads which make up the assembly should be submitted to dbEST, the Trace archive or the Short Read Archive (SRA) prior to the submission of the assemblies.",
"homepage": "https://www.ncbi.nlm.nih.gov/genbank/dbest/",
"name": "Expressed Sequence Tags database",
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"synonyms": [
"NCBI EST",
"dbEST"
],
"xrefs": {
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"miriam": "00000159",
"scr": "016578"
}
}
},
"dbg2introns": {
"biocontext": {
"prefix": "DBG2INTRONS"
},
"contact": {
"email": "zimmerly@ucalgary.ca",
"name": "Steven John Zimmerly"
},
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},
"miriam": {
"deprecated": false,
"description": "The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank.",
"homepage": "http://webapps2.ucalgary.ca/~groupii/",
"id": "00000318",
"name": "DBG2 Introns",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$",
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"sampleId": "Cu.me.I1",
"uri_format": "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1"
},
"n2t": {
"description": "The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank.",
"example": "Cu.me.I1",
"homepage": "http://webapps2.ucalgary.ca/~groupii/",
"name": "Bacterial Group II Introns at University of Calgary",
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"pattern": "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$",
"prefix": "dbg2introns",
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},
"prefixcommons": {
"description": "Many newly sequenced bacterial group II introns are incorrectly identified or annotated. A major goal of this database is to be a resource in helping to identify and catalog group II introns in the databases.",
"example": "Cu.me.I1",
"homepage": "http://www.fp.ucalgary.ca/group2introns/",
"keywords": [
"DNA"
],
"name": "Mobile group II introns database",
"pattern": "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$",
"prefix": "mgiid",
"pubmed_ids": [
"22080509"
],
"synonyms": [
"dbg2introns"
],
"uri_format": "http://www.fp.ucalgary.ca/group2introns/$1.htm"
},
"publications": [
{
"doi": "10.1093/nar/gkr1043",
"pmc": "PMC3245105",
"pubmed": "22080509",
"title": "Database for bacterial group II introns",
"year": 2011
}
]
},
"dbgap": {
"biocontext": {
"prefix": "DBGAP"
},
"cellosaurus": {
"category": "Sequence databases",
"homepage": "https://www.ncbi.nlm.nih.gov/gap/",
"name": "Database of Genotypes and Phenotypes",
"prefix": "dbGAP",
"uri_format": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1"
},
"contact": {
"email": "feolo@ncbi.nlm.nih.gov",
"github": "mfeolo",
"name": "Michael Feolo",
"orcid": "0000-0002-1650-5156"
},
"fairsharing": {
"abbreviation": "dbGaP",
"description": "The Database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits.",
"homepage": "https://www.ncbi.nlm.nih.gov/gap/",
"name": "Database of Genotypes and Phenotypes",
"prefix": "FAIRsharing.88v2k0",
"publications": [
{
"doi": "10.1038/ng1007-1181",
"pubmed_id": 17898773,
"title": "The NCBI dbGaP database of genotypes and phenotypes."
},
{
"doi": "10.1093/nar/gkt1211",
"pubmed_id": 24297256,
"title": "NCBI's Database of Genotypes and Phenotypes: dbGaP."
}
],
"subjects": [
"Epigenetics",
"Genetics",
"Biomedical Science"
]
},
"integbio": {
"alt_name": "Genotypes and Phenotypes",
"description": "This is a database for research on genotypes and phenotypes in humans, including genome-wide association studies (GWAS), medical sequencing, and molecular diagnostic assays. The dataset is classified into public data and controlled-access data, and an application procedure is required for access to controlled-access data.",
"fairsharing": "biodbcore-000462",
"homepage": "http://www.ncbi.nlm.nih.gov/gap",
"information_keywords": [
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"Bibliography/Documents",
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],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "dbGaP",
"prefix": "nbdc00414",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"mappings": {
"biocontext": "DBGAP",
"cellosaurus": "dbGAP",
"fairsharing": "FAIRsharing.88v2k0",
"integbio": "nbdc00414",
"miriam": "dbgap",
"n2t": "dbgap"
},
"miriam": {
"deprecated": false,
"description": "The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype.",
"homepage": "https://www.ncbi.nlm.nih.gov/gap/",
"id": "00000602",
"name": "dbGaP",
"namespaceEmbeddedInLui": false,
"pattern": "^phs[0-9]{6}(.v\\d+.p\\d+)?$",
"prefix": "dbgap",
"sampleId": "phs000768.v2.p1",
"uri_format": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1"
},
"n2t": {
"description": "The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype.",
"example": "phs000768.v2.p1",
"homepage": "https://www.ncbi.nlm.nih.gov/projects/gap",
"name": "dbGaP through NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^phs[0-9]{6}(.v\\d+.p\\d+)?$",
"prefix": "dbgap",
"uri_format": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1"
},
"name": "Database of Genotypes and Phenotypes",
"publications": [
{
"doi": "10.1093/nar/gkt1211",
"pmc": "PMC3965052",
"pubmed": "24297256",
"title": "NCBI's Database of Genotypes and Phenotypes: dbGaP",
"year": 2013
},
{
"doi": "10.1038/ng1007-1181",
"pmc": "PMC2031016",
"pubmed": "17898773",
"title": "The NCBI dbGaP database of genotypes and phenotypes",
"year": 2007
}
]
},
"dblp.author": {
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"mappings": {
"wikidata": "P2456"
},
"wikidata": {
"description": "identifier for author entries in the DBLP computer science bibliography (use portion of DBLP person key after pid/)",
"example": [
"181/8944",
"d/JeffreyDean",
"z/LixiaZhang1"
],
"homepage": "https://dblp.org/",
"name": "DBLP author ID",
"prefix": "P2456",
"uri_format": "https://dblp.org/pid/$1",
"uri_format_rdf": "https://dblp.org/pid/$1.rdf"
}
},
"dbmhc": {
"appears_in": [
"cellosaurus"
],
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://www.ncbi.nlm.nih.gov/gv/mhc/",
"name": "dbMHC database",
"prefix": "dbMHC"
},
"deprecated": true,
"example": "48439",
"integbio": {
"description": "dbMHC provides access to HLA sequences, tools to support genetic testing of HLA loci, HLA allele and haplotype frequencies of over 90 populations worldwide, as well as clinical datasets on nematopoietic stem cell transplantation, and insulin dependant diabetes mellitus (IDDM), Rheumatoid Arthritis (RA), Narcolepsy and Spondyloarthropathy. All clinical datasets housed at the dbMHC provide access to genotypic and phenotypic data on anonimyzed samples with aggregate query functions, and complete download capability.",
"fairsharing": "FAIRsharing.r90425",
"homepage": "http://www.ncbi.nlm.nih.gov/mhc/",
"information_keywords": [
"Sequence",
"Expression"
],
"name": "dbMHC",
"prefix": "nbdc01831",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Protein"
]
},
"mappings": {
"cellosaurus": "dbMHC",
"integbio": "nbdc01831"
},
"name": "Database of human Major Histocompatibility Complex",
"pattern": "^\\d+$"
},
"dbo": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki.",
"example": "careerPrizeMoney",
"github_request_issue": 515,
"homepage": "https://dbpedia.org/ontology",
"keywords": [
"dbpedia",
"ontology"
],
"mappings": {
"zazuko": "dbo"
},
"name": "DBPedia Ontology",
"uri_format": "https://dbpedia.org/ontology/$1",
"zazuko": {
"prefix": "dbo",
"uri_format": "http://dbpedia.org/ontology/$1"
}
},
"dbprobe": {
"biocontext": {
"prefix": "DBPROBE"
},
"edam": {
"description": "Identifier of an oligonucleotide probe from the dbProbe database.",
"name": "dbProbe",
"obsolete": false,
"prefix": "2719"
},
"mappings": {
"biocontext": "DBPROBE",
"edam": "2719",
"miriam": "dbprobe",
"n2t": "dbprobe",
"ncbi": "dbProbe",
"prefixcommons": "dbprobe"
},
"miriam": {
"deprecated": false,
"description": "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.",
"homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe",
"id": "00000160",
"name": "dbProbe",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "dbprobe",
"sampleId": "1000000",
"uri_format": "https://www.ncbi.nlm.nih.gov/probe/?term=$1"
},
"n2t": {
"description": "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.",
"example": "1000000",
"homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe",
"name": "dbProbe at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "dbprobe",
"uri_format": "https://www.ncbi.nlm.nih.gov/probe/?term=$1"
},
"ncbi": {
"example": "38",
"homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe",
"name": "NCBI Probe database Public registry of nucleic acid reagents",
"prefix": "dbProbe"
},
"prefixcommons": {
"description": "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.",
"example": "1000000",
"homepage": "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=probe",
"keywords": [
"nucleotide"
],
"name": "NCBI Probe database Public registry of nucleic acid reagents",
"pattern": "^\\d+$",
"prefix": "dbprobe",
"uri_format": "http://www.ncbi.nlm.nih.gov/genome/probe/reports/probereport.cgi?uid=$1"
}
},
"dbsnp": {
"biocontext": {
"prefix": "dbSNP",
"uri_format": "http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$1"
},
"cellosaurus": {
"category": "Polymorphism and mutation databases",
"homepage": "https://www.ncbi.nlm.nih.gov/snp/",
"name": "Single Nucleotide Polymorphism database",
"prefix": "dbSNP",
"uri_format": "https://www.ncbi.nlm.nih.gov/snp/$1"
},
"contact": {
"email": "pruitt@ncbi.nlm.nih.gov",
"name": "Kim Dixon Pruitt",
"orcid": "0000-0001-7950-1374"
},
"edam": {
"description": "Identifier of a dbSNP database entry.",
"name": "dbSNP",
"obsolete": false,
"prefix": "1106"
},
"fairsharing": {
"abbreviation": "dbSNP",
"description": "dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations.",
"homepage": "https://www.ncbi.nlm.nih.gov/snp/",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "Database of Single Nucleotide Polymorphism",
"prefix": "FAIRsharing.edxb58",
"publications": [
{
"doi": "10.1093/nar/29.1.308",
"pubmed_id": 11125122,
"title": "dbSNP: the NCBI database of genetic variation."
}
],
"repository": "https://github.com/ncbi/dbsnp/tree/master/tutorials",
"subjects": [
"Life Science"
]
},
"go": {
"homepage": "http://www.ncbi.nlm.nih.gov/projects/SNP",
"name": "NCBI dbSNP",
"prefix": "dbSNP",
"uri_format": "http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$1"
},
"hl7": {
"description": "In collaboration with the National Human Genome Research Institute, The National Center for Biotechnology Information has established the dbSNP database to serve as a central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. The entries in the dbSNP database can be used with the HL7 coded data type. For example, in the HL7 messages specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model, dbSNP entries can be used to as the observation values for DNA sequence variation identifiers. For example, OBX|1|CWE|48004-6^DNA Sequence Variation Identifier^LN||rs55538123^^dbSNPVersioning is identified by the build id. A new build is released approximately every six months or every year. The latest build id is 130, and the dbSNP web query for built 130 was available on Apr 30, 2009.dbSNP is a database that can be used freely by the public.More information may be fouond at: http://www.ncbi.nlm.nih.gov/projects/SNP/",
"homepage": "https://lhncbc.nlm.nih.gov/",
"name": "The Short Genetic Variations database",
"organization": "National Center for Biotechnology Information,National Center for Biotechnology Information",
"preferred_prefix": "dbSNP",
"prefix": "2.16.840.1.113883.6.284",
"status": "Complete"
},
"integbio": {
"alt_name": "The Single Nucleotide Polymorphism Database (dbSNP)",
"description": "dbSNP collects information on polymorphisms based on single and small-scale multi-base substitutions, including insertions and deletions, microsatelites, and non-polymorphic variants. Differences in the frequency of polymorphisms in a population can be visually compared for each SNP.",
"fairsharing": "biodbcore-000438",
"homepage": "http://www.ncbi.nlm.nih.gov/snp/",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "dbSNP",
"prefix": "nbdc00206",
"pubmeds": [
"11125122",
"10592272"
],
"status": "Active",
"target_keywords": [
"Genetic variation"
]
},
"mappings": {
"biocontext": "dbSNP",
"cellosaurus": "dbSNP",
"edam": "1106",
"fairsharing": "FAIRsharing.edxb58",
"go": "dbSNP",
"hl7": "2.16.840.1.113883.6.284",
"integbio": "nbdc00206",
"miriam": "dbsnp",
"n2t": "dbsnp",
"ncbi": "dbSNP",
"prefixcommons": "dbsnp",
"re3data": "r3d100010652",
"togoid": "Dbsnp",
"uniprot": "DB-0013",
"wikidata": "P6861"
},
"miriam": {
"deprecated": false,
"description": "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.",
"homepage": "https://www.ncbi.nlm.nih.gov/snp/",
"id": "00000161",
"name": "dbSNP",
"namespaceEmbeddedInLui": false,
"pattern": "^rs\\d+$",
"prefix": "dbsnp",
"providers": [
{
"code": "sib",
"description": "SNP2TFBS",
"homepage": "https://ccg.epfl.ch/snp2tfbs/",
"name": "SNP2TFBS",
"uri_format": "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1"
}
],
"sampleId": "rs121909098",
"uri_format": "https://www.ncbi.nlm.nih.gov/snp/$1"
},
"n2t": {
"description": "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.",
"example": "rs121909098",
"homepage": "https://www.ncbi.nlm.nih.gov/snp/",
"name": "dbSNP at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^rs\\d+$",
"prefix": "dbsnp",
"uri_format": "https://www.ncbi.nlm.nih.gov/snp/$1"
},
"ncbi": {
"example": "4647",
"homepage": "https://www.ncbi.nlm.nih.gov/snp",
"name": "Variation database maintained at the NCBI.",
"prefix": "dbSNP"
},
"prefixcommons": {
"description": "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.",
"example": "rs199422184",
"homepage": "http://www.ncbi.nlm.nih.gov/SNP/",
"keywords": [
"genome"
],
"name": "Database of single nucleotide polymorphism",
"pattern": "^rs\\d+$",
"prefix": "dbsnp",
"pubmed_ids": [
"11125122"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkl1031",
"pmc": "PMC1781113",
"pubmed": "17170002",
"title": "Database resources of the National Center for Biotechnology Information",
"year": 2006
},
{
"doi": "10.1093/nar/29.1.308",
"pmc": "PMC29783",
"pubmed": "11125122",
"title": "dbSNP: the NCBI database of genetic variation",
"year": 2001
}
],
"re3data": {
"description": "The NCBI Short Genetic Variations database, commonly known as dbSNP, catalogs short variations in nucleotide sequences from a wide range of organisms. These variations include single nucleotide variations, short nucleotide insertions and deletions, short tandem repeats and microsatellites. Short Genetic Variations may be common, thus representing true polymorphisms, or they may be rare. Some rare human entries have additional information associated withthem, including disease associations, genotype information and allele origin, as some variations are somatic rather than germline events.\n***NCBI will phase out support for non-human organism data in dbSNP and dbVar beginning on September 1, 2017***",
"homepage": "https://www.ncbi.nlm.nih.gov/snp/",
"name": "dbSNP",
"prefix": "r3d100010652",
"synonyms": [
"Database for short genetic variations",
"SNV"
],
"xrefs": {
"fairsharing": "FAIRsharing.edxb58",
"nif": "0000-02734",
"omics": "00264",
"scr": "002338"
}
},
"togoid": {
"catalog": "nbdc00206",
"examples": [
"rs746303788",
"rs1407020249",
"rs374003162",
"rs4647297",
"rs549539526",
"rs1387864740",
"rs1177577242",
"rs769848663",
"rs16961655",
"rs79135400"
],
"keywords": [
"Variant"
],
"name": "dbSNP",
"pattern": "^(?rs\\d+)$",
"prefix": "Dbsnp",
"uri_format": "http://identifiers.org/dbsnp/$1"
},
"uniprot": {
"abbreviation": "dbSNP",
"category": "Genetic variation databases",
"homepage": "https://www.ncbi.nlm.nih.gov/snp/",
"name": "Database of single nucleotide polymorphism",
"prefix": "DB-0013",
"publications": [
{
"doi": "10.1093/nar/gkaa892",
"pubmed": "33095870"
}
],
"uri_format": "https://www.ncbi.nlm.nih.gov/snp/$1"
},
"wikidata": {
"description": "identifier used in dbSNP to uniquely identify a genetic variant",
"example": [
"rs113488022",
"rs121913355",
"rs1488384581"
],
"homepage": "https://civicdb.org/home",
"miriam": "dbsnp",
"name": "dbSNP Reference SNP number",
"prefix": "P6861",
"uri_format": "https://www.ncbi.nlm.nih.gov/snp/$1"
}
},
"dbvar.study": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Studies in dbVar.",
"example": "nstd102",
"homepage": "https://www.ncbi.nlm.nih.gov/dbvar",
"name": "Database of Genomic Structural Variation - Study",
"synonyms": [
"dbvar.studies"
],
"uri_format": "https://www.ncbi.nlm.nih.gov/dbvar/studies/$1"
},
"dbvar.variant": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Variants in dbVar.",
"example": "nsv3875336",
"homepage": "https://www.ncbi.nlm.nih.gov/dbvar",
"name": "Database of Genomic Structural Variation - Variant",
"synonyms": [
"dbvar.variants"
],
"uri_format": "https://www.ncbi.nlm.nih.gov/dbvar/variants/$1"
},
"dc": {
"aberowl": {
"description": "This file is imported by vivo-core-public-1.5.owl. It contains selected terms from the \thttp://purl.org/dc/elements/1.1/ namespace that are included in the vivo core ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/dcelements/1/dcelements.owl",
"homepage": "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology",
"name": "dcelements",
"prefix": "dcelements",
"version": "1.5"
},
"biocontext": {
"prefix": "dc",
"uri_format": "http://purl.org/dc/elements/1.1/$1"
},
"bioportal": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kim Durante"
},
"description": "The Dublin Core Schema is a small set of vocabulary terms that can be used to describe several kinds of resources. Dublin Core Metadata may be used for multiple purposes, from simple resource description, to combining metadata vocabularies of different metadata standards, to providing interoperability for metadata vocabularies in the Linked Data cloud and Semantic Web implementations.",
"homepage": "http://dublincore.org",
"name": "Dublin Core",
"prefix": "DC"
},
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kim Durante",
"orcid": "0000-0001-9052-2854"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"description": "Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.\n\n**Deprecation Notice**: While the `/elements/1.1/` namespace will be supported indefinitely, DCMI gently encourages use of the `/terms/` namespace (i.e., `dcterms`) ([source](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3)).",
"example": "contributor",
"fairsharing": {
"abbreviation": "DCES",
"description": "The Dublin Metadata Element Set, which is often called Dublin Core (DC), is a standardized metadata scheme for description of any kind of resource such as documents in electronic and non-electronic form, digital materials (such as video, sound, images, etc) and composite media like web pages. Dublin Core Metadata may be used for multiple purposes, from simple resource description, to combining metadata vocabularies of different metadata standards, to providing interoperability for metadata vocabularies in the Linked Data cloud and Semantic Web implementations. Please note that this version of the specification for the Dublin Core Element Set 1.1 is somewhat out of date, although it is not officially deprecated. The DCMI Metadata Terms specification is linked to this record and is the current documentation that should be used for the Dublin Core Element Set 1.1. This document, an excerpt from the more comprehensive document \"DCMI Metadata Terms\" [DCTERMS] provides an abbreviated reference version of the fifteen element descriptions that have been formally endorsed in the following standards: ISO Standard 15836:2009 of February 2009 [ISO15836], ANSI/NISO Standard Z39.85-2012 of February 2013 [NISOZ3985], and IETF RFC 5013 of August 2007 [RFC5013].",
"domains": [
"Resource metadata",
"Annotation"
],
"homepage": "https://www.dublincore.org/specifications/dublin-core/dces/",
"license": "CC-BY-3.0",
"name": "Dublin Core Metadata Element Set",
"prefix": "FAIRsharing.3nx7t",
"subjects": [
"Life Science",
"Subject Agnostic",
"Biomedical Science"
],
"user_defined_tags": [
"Metadata standardization"
]
},
"homepage": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/",
"lov": {
"description": "The Dublin Core Metadata Element Set is a vocabulary of fifteen properties for use in resource description. The name \"Dublin\" is due to its origin at a 1995 invitational workshop in Dublin, Ohio; \"core\" because its elements are broad and generic, usable for describing a wide range of resources.",
"homepage": "http://dublincore.org/documents/dces",
"keywords": [
"Metadata"
],
"modified": "2012-06-14",
"name": "Dublin Core Metadata Element Set",
"prefix": "dce",
"uri_prefix": "http://purl.org/dc/elements/1.1/$1"
},
"mappings": {
"aberowl": "dcelements",
"biocontext": "dc",
"bioportal": "DC",
"fairsharing": "FAIRsharing.3nx7t",
"lov": "dce",
"ols": "dc",
"zazuko": "dc11"
},
"name": "Dublin Core Elements (1.1)",
"ols": {
"download_rdf": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_elements.rdf",
"prefix": "dc"
},
"preferred_prefix": "dc",
"synonyms": [
"dc.elements",
"dc11",
"dce"
],
"uri_format": "http://purl.org/dc/elements/1.1/$1",
"zazuko": {
"prefix": "dc11",
"uri_format": "http://purl.org/dc/elements/1.1/$1"
}
},
"dc_cl": {
"biocontext": {
"prefix": "DC_CL"
},
"example": "0000003",
"mappings": {
"biocontext": "DC_CL",
"obofoundry": "dc_cl"
},
"obofoundry": {
"contact": "Lindsay.Cowell@utsouthwestern.edu",
"contact.label": "Lindsay Cowell",
"contact.orcid": "0000-0003-1617-8244",
"deprecated": true,
"domain": "anatomy and development",
"homepage": "http://www.dukeontologygroup.org/Projects.html",
"name": "Dendritic cell",
"prefix": "dc_cl"
},
"pattern": "^\\d{7}$"
},
"dcat": {
"aberowl": {
"description": "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web.",
"download_owl": "http://aber-owl.net/media/ontologies/DCAT/2/dcat.owl",
"homepage": "https://www.w3.org/TR/vocab-dcat/",
"name": "Data Catalog Vocabulary",
"prefix": "DCAT"
},
"biocontext": {
"prefix": "dcat",
"uri_format": "http://www.w3.org/ns/dcat#$1"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "dcat",
"uri_format": "http://www.w3.org/ns/dcat#$1"
},
"bioportal": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "kdurante"
},
"description": "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web.",
"homepage": "https://www.w3.org/TR/vocab-dcat/",
"name": "Data Catalog Vocabulary",
"prefix": "DCAT"
},
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kim Durante",
"orcid": "0000-0001-9052-2854"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web",
"example": "Dataset",
"fairsharing": {
"abbreviation": "DCAT",
"contact": {
"email": "phila@w3.org",
"name": "Phil Archer",
"orcid": "0000-0002-4989-0601"
},
"description": "An RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web. By using DCAT to describe datasets in data catalogs, publishers increase discoverability and enable applications easily to consume metadata from multiple catalogs. It further enables decentralized publishing of catalogs and facilitates federated dataset search across sites. Aggregated DCAT metadata can serve as a manifest file to facilitate digital preservation.",
"homepage": "https://www.w3.org/TR/vocab-dcat/",
"name": "Data Catalog Vocabulary",
"prefix": "FAIRsharing.h4j3qm",
"publications": [],
"repository": "https://github.com/w3c/dxwg/",
"subjects": [
"Data Management",
"Subject Agnostic"
]
},
"homepage": "https://www.w3.org/ns/dcat",
"lov": {
"description": "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web",
"homepage": "http://www.w3.org/TR/vocab-dcat/",
"keywords": [
"W3C Rec"
],
"modified": "2020-02-04",
"name": "Data Catalog Vocabulary",
"prefix": "dcat",
"uri_prefix": "http://www.w3.org/ns/dcat#$1"
},
"mappings": {
"aberowl": "DCAT",
"biocontext": "dcat",
"biolink": "dcat",
"bioportal": "DCAT",
"fairsharing": "FAIRsharing.h4j3qm",
"lov": "dcat",
"zazuko": "dcat"
},
"name": "Data Catalog",
"preferred_prefix": "dcat",
"uri_format": "http://www.w3.org/ns/dcat#$1",
"zazuko": {
"prefix": "dcat",
"uri_format": "http://www.w3.org/ns/dcat#$1"
}
},
"dcterms": {
"aberowl": {
"description": "This file is imported by vivo-core-public-1.5.owl. It contains terms from the http://purl.org/dc/terms/ namespace that are included in the vivo ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/dcterms/1/dcterms.owl",
"homepage": "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology",
"name": "dcterms",
"prefix": "dcterms",
"version": "1.5"
},
"biocontext": {
"prefix": "dcterms",
"uri_format": "http://purl.org/dc/terms/$1"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "dct",
"uri_format": "http://purl.org/dc/terms/$1"
},
"bioportal": {
"contact": {
"email": "futo@stanford.edu",
"name": "Michelle Futornick"
},
"description": "DCMI properties in the /terms/ namespace",
"homepage": "http://dublincore.org/documents/dcmi-terms/",
"name": "DCMI Metadata Terms: properties in /terms/ namespace",
"prefix": "DCTERMS"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.",
"example": "title",
"fairsharing": {
"abbreviation": "DCMI Metadata Terms",
"description": "This document is an up-to-date, authoritative specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. Included are the fifteen terms of the Dublin Core Metadata Element Set, which have also been published as a separate specification.",
"domains": [
"Resource metadata"
],
"homepage": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/",
"license": "CC-BY-3.0",
"name": "Dublin Core Metadata Initiative Terms",
"prefix": "FAIRsharing.9vtwjs",
"subjects": [
"Subject Agnostic"
],
"user_defined_tags": [
"Metadata standardization"
]
},
"homepage": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/",
"lov": {
"description": "an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.",
"homepage": "http://dublincore.org/documents/dcmi-terms",
"keywords": [
"Metadata"
],
"modified": "2012-06-14",
"name": "DCMI Metadata Terms",
"prefix": "dcterms",
"uri_prefix": "http://purl.org/dc/terms/$1"
},
"mappings": {
"aberowl": "dcterms",
"biocontext": "dcterms",
"biolink": "dct",
"bioportal": "DCTERMS",
"fairsharing": "FAIRsharing.9vtwjs",
"lov": "dcterms",
"ols": "dcterms",
"zazuko": "dcterms"
},
"name": "Dublin Core Metadata Initiative Terms",
"ols": {
"download_rdf": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_terms.rdf",
"prefix": "dcterms"
},
"preferred_prefix": "dcterms",
"synonyms": [
"dc.terms",
"dct"
],
"uri_format": "http://purl.org/dc/terms/$1",
"zazuko": {
"prefix": "dcterms",
"uri_format": "http://purl.org/dc/terms/$1"
}
},
"dctypes": {
"biocontext": {
"prefix": "dctypes",
"uri_format": "http://purl.org/dc/dcmitype/$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.",
"example": "Collection",
"homepage": "https://dublincore.org/specifications/dublin-core/dcmi-terms/",
"mappings": {
"biocontext": "dctypes"
},
"name": "Dublin Core Types",
"preferred_prefix": "dctypes",
"uri_format": "http://purl.org/dc/dcmitype/$1"
},
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"description": "A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum",
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"homepage": "http://dictybase.org/",
"name": "Dictyostelium discoideum anatomy",
"prefix": "DDANAT"
},
"biocontext": {
"prefix": "DDANAT"
},
"bioportal": {
"contact": {
"email": "pfey@northwestern.edu",
"name": "Petra Fey"
},
"description": "A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum.",
"homepage": "http://dictybase.org/",
"name": "Dictyostelium Discoideum Anatomy Ontology",
"prefix": "DDANAT",
"publication": "http://www.biomedcentral.com/1471-2164/9/130",
"version": "1.19"
},
"example": "0000006",
"fairsharing": {
"abbreviation": "DDANAT",
"contact": {
"email": "pgaudet@northwestern.edu",
"name": "Pascale Gaudet",
"orcid": "0000-0003-1813-6857"
},
"description": "The Dictyostelium Anatomy Ontology ontology describes the anatomy of the slime mold. It defines the structural makeup of Dictyostelium and its composing parts including the different cell types, throughout its life cycle. It has two main goals: (1) promote the consistent annotation of Dictyostelium-specific events, such as phenotypes and gene expression information; and (2) encourage researchers to use the same terms with the same intended meaning.",
"domains": [
"Cell"
],
"homepage": "http://dictybase.org/Dicty_Info/dicty_anatomy_ontology.html",
"name": "Dictyostelium Anatomy Ontology",
"prefix": "FAIRsharing.z656ab",
"publications": [
{
"doi": "10.1186/1471-2164-9-130",
"pubmed": "18366659",
"title": "An anatomy ontology to represent biological knowledge in Dictyostelium discoideum",
"year": 2008
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"go": {
"homepage": "http://dictybase.org/Dicty_Info/dicty_anatomy_ontology.html",
"name": "Dictyostelium discoideum anatomy",
"prefix": "DDANAT"
},
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"aberowl": "DDANAT",
"biocontext": "DDANAT",
"bioportal": "DDANAT",
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"go": "DDANAT",
"obofoundry": "ddanat",
"ols": "ddanat",
"ontobee": "DDANAT",
"prefixcommons": "ddanat"
},
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"contact": "pfey@northwestern.edu",
"contact.github": "pfey03",
"contact.label": "Petra Fey",
"contact.orcid": "0000-0002-4532-2703",
"deprecated": false,
"description": "A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum",
"domain": "anatomy and development",
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"download.owl": "http://purl.obolibrary.org/obo/ddanat.owl",
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"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Dictyostelium discoideum anatomy",
"preferredPrefix": "DDANAT",
"prefix": "ddanat",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/18366659",
"title": "An anatomy ontology to represent biological knowledge in Dictyostelium discoideum"
}
],
"repository": "https://github.com/dictyBase/migration-data",
"twitter": "dictybase"
},
"ols": {
"description": "A structured controlled vocabulary of anatomies of the slime-mold Dictyostelium discoideum.",
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"homepage": "http://dictybase.org/",
"name": "Dicty Anatomy Ontology (DDANAT)",
"prefix": "ddanat"
},
"ontobee": {
"library": "Library",
"name": "Dictyostelium discoideum anatomy",
"prefix": "DDANAT"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1008",
"description": "A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum.",
"example": "DDANAT_0010081",
"homepage": "http://dictybase.org/",
"keywords": [
"obo",
"anatomy",
"slime-mould"
],
"name": "Dictyostelium discoideum anatomy",
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"prefix": "ddanat",
"synonyms": [
"ddana"
]
},
"publications": [
{
"doi": "10.1186/1471-2164-9-130",
"pmc": "PMC2323390",
"pubmed": "18366659",
"title": "An anatomy ontology to represent biological knowledge in Dictyostelium discoideum",
"year": 2008
}
],
"uri_format": "http://purl.obolibrary.org/obo/DDANAT_$1"
},
"ddc": {
"bartoc": {
"abbreviation": "DDC",
"description": "The Dewey Decimal Classification (DDC) system, devised by library pioneer Melvil Dewey in the 1870s and owned by OCLC since 1988, provides a dynamic structure for the organization of library collections. Now in its 23rd edition, and available in print and Web versions, the DDC is the world's most widely used library classification system.",
"homepage": "http://www.oclc.org/dewey/",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Dewey Decimal Classification",
"pattern": "^(([0-9][0-9]?|[0-9]{3}(-[0-9]{3})?|[0-9]{3}(-[0-9]{3}(:[0-9]+)?)?|[0-9]{3}\\.[0-9]+(-[0-9]{3}\\.[0-9]+(:[0-9]+)?)?|T[1-9][A-Z]?--[0-9]+(-T[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?|[1-9][A-Z]?--[0-9]+(-[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?)?)$",
"prefix": "241",
"uri_format": "http://dewey.info/class/$1/e23/",
"wikidata_database": "Q48460"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"example": "325.4",
"example_extras": [
"325.4-325.9",
"325",
"32",
"3"
],
"mappings": {
"bartoc": "241"
}
},
"ddinter.drug": {
"contact": {
"email": "oriental-cds@163.com",
"name": "Dongsheng Cao",
"orcid": "0000-0003-3604-3785"
},
"contributor": {
"github": "sierra-moxon",
"name": "Sierra Moxon",
"orcid": "0000-0002-8719-7760"
},
"description": "Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety.",
"example": "DDInter20",
"github_request_issue": 492,
"homepage": "http://ddinter.scbdd.com",
"keywords": [
"chemistry",
"drugs",
"relationships"
],
"license": "CC-BY-NC-SA-4.0",
"name": "Curated Drug-Drug Interactions Database - Drug",
"pattern": "^DDInter\\d+$",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://ddinter.scbdd.com/ddinter/drug-detail/$1"
},
"ddinter.interaction": {
"contact": {
"email": "oriental-cds@163.com",
"name": "Dongsheng Cao",
"orcid": "0000-0003-3604-3785"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety.",
"example": "1122888",
"github_request_issue": 492,
"homepage": "http://ddinter.scbdd.com",
"keywords": [
"chemistry",
"drug-drug interactions",
"drugs",
"relationships"
],
"license": "CC-BY-NC-SA-4.0",
"name": "Curated Drug-Drug Interactions Database - Interaction",
"pattern": "^\\d+$",
"uri_format": "http://ddinter.scbdd.com/ddinter/interact/$1"
},
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"aberowl": {
"description": "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum.",
"download_owl": "http://aber-owl.net/media/ontologies/DDPHENO/165/ddpheno.owl",
"homepage": "http://dictybase.org/",
"name": "Dictyostelium discoideum phenotype ontology",
"prefix": "DDPHENO"
},
"biocontext": {
"prefix": "DDPHENO"
},
"bioportal": {
"contact": {
"email": "pfey@northwestern.edu",
"name": "Petra Fey"
},
"description": "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum.",
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"name": "Dictyostelium Discoideum Phenotype Ontology",
"prefix": "DDPHENO"
},
"download_json": "http://purl.obolibrary.org/obo/ddpheno.json",
"download_obo": "https://raw.githubusercontent.com/obophenotype/dicty-phenotype-ontology/master/ddpheno.obo",
"example": "0001417",
"fairsharing": {
"abbreviation": "DDPHENO",
"contact": {
"email": "pfey@northwestern.edu",
"name": "Petra Fey",
"orcid": "0000-0002-4532-2703"
},
"description": "A structured controlled vocabulary of phenotypes of the social amoeba Dictyostelium discoideum. The Dicty Phenotype Ontology is a hierarchical controlled vocabulary used for annotating strains with phenotypes. Terms from the Dicty Phenotype Ontology are required when annotating phenotypes within dictyBase. The phenotype ontology consists of two composite terms: (1) the anatomical part or the biological process changed in the mutant, and (2) a quality describing that modification. For example, a βdelayed aggregationβ phenotype qualifies the βaggregationβ (biological process) as being βdelayedβ, or the βdecreased spore sizeβ qualifies the βsporeβ to be of βdecreased sizeβ.",
"domains": [
"Phenotype"
],
"homepage": "https://github.com/dictyBase/migration-data/blob/master/ontologies/dicty_phenotypes.obo",
"name": "Dictyostelium Phenotype Ontology",
"prefix": "FAIRsharing.9c1p18",
"publications": [
{
"doi": "10.1007/978-1-62703-302-2_4",
"pubmed": "23494302",
"title": "One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012",
"year": 2013
}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"aberowl": "DDPHENO",
"biocontext": "DDPHENO",
"bioportal": "DDPHENO",
"fairsharing": "FAIRsharing.9c1p18",
"obofoundry": "ddpheno",
"ols": "ddpheno",
"ontobee": "DDPHENO"
},
"obofoundry": {
"contact": "pfey@northwestern.edu",
"contact.github": "pfey03",
"contact.label": "Petra Fey",
"contact.orcid": "0000-0002-4532-2703",
"deprecated": false,
"description": "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum.",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/ddpheno.obo",
"download.owl": "http://purl.obolibrary.org/obo/ddpheno.owl",
"homepage": "http://dictybase.org/",
"license": "CC0 1.0",
"license.url": "http://creativecommons.org/publicdomain/zero/1.0/",
"name": "Dictyostelium discoideum phenotype ontology",
"preferredPrefix": "DDPHENO",
"prefix": "ddpheno",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/31840793",
"title": "dictyBase and the Dicty Stock Center (version 2.0) - a progress report"
}
],
"repository": "https://github.com/obophenotype/dicty-phenotype-ontology",
"twitter": "dictybase"
},
"ols": {
"description": "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum.",
"download_owl": "http://purl.obolibrary.org/obo/ddpheno.owl",
"homepage": "http://dictybase.org/",
"name": "Dicty Phenotype Ontology (DDPHENO)",
"prefix": "ddpheno",
"version": "2023-08-26",
"version.iri": "http://purl.obolibrary.org/obo/ddpheno/releases/2023-08-26/ddpheno.owl"
},
"ontobee": {
"library": "Library",
"name": "Dictyostelium discoideum phenotype ontology",
"prefix": "DDPHENO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1387/ijdb.190226pf",
"pmc": "PMC7409682",
"pubmed": "31840793",
"title": "dictyBase and the Dicty Stock Center (version 2.0) - a progress report",
"year": 2019
},
{
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"pmc": "PMC3762881",
"pubmed": "23494302",
"title": "One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012",
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}
],
"uri_format": "http://purl.obolibrary.org/obo/DDPHENO_$1"
},
"debio": {
"contact": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor": {
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON.",
"download_json": "https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.json",
"download_obo": "https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.obo",
"download_owl": "https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.owl",
"example": "0000001",
"homepage": "https://biopragmatics.github.io/debio",
"name": "Decentralized Biomedical Ontology",
"pattern": "^\\d{7}$",
"providers": [
{
"code": "obo2",
"description": "Because it's not possible to configure the base URI with ROBOT/OWLAPI, this pops out",
"homepage": "http://purl.obolibrary.org",
"name": "Placeholder OBO PURL",
"uri_format": "http://purl.obolibrary.org/obo/debio_$1"
}
],
"synonyms": [
"DeBiO"
],
"uri_format": "https://biopragmatics.github.io/debio/$1"
},
"decipher": {
"biocontext": {
"prefix": "DECIPHER"
},
"contact": {
"email": "ganesh.swaminathan@sanger.ac.uk",
"name": "Jawahar Swaminathan",
"orcid": "0000-0002-0215-4084"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms",
"example": "1",
"fairsharing": {
"abbreviation": "DECIPHER",
"description": "DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources) is an interactive web-based resource that incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance, inversions, and translocations.",
"homepage": "https://decipher.sanger.ac.uk/",
"name": "DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources",
"prefix": "FAIRsharing.l8Sf5x",
"publications": [
{
"doi": "10.1093/nar/gkt937",
"pubmed_id": 24150940,
"title": "DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation."
},
{
"doi": "10.1016/j.ajhg.2009.03.010",
"pubmed_id": 19344873,
"title": "DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources."
}
],
"subjects": [
"Life Science",
"Biomedical Science"
]
},
"homepage": "https://www.deciphergenomics.org/",
"mappings": {
"biocontext": "DECIPHER",
"fairsharing": "FAIRsharing.l8Sf5x"
},
"name": "DECIPHER CNV Syndromes",
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1093/nar/gkt937",
"pmc": "PMC3965078",
"pubmed": "24150940",
"title": "DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation",
"year": 2013
},
{
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"pmc": "PMC2667985",
"pubmed": "19344873",
"title": "DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources",
"year": 2009
}
],
"uri_format": "https://www.deciphergenomics.org/syndrome/$1"
},
"degradome": {
"biocontext": {
"prefix": "DEGRADOME"
},
"mappings": {
"biocontext": "DEGRADOME",
"miriam": "degradome",
"n2t": "degradome"
},
"miriam": {
"deprecated": false,
"description": "The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced.",
"homepage": "http://degradome.uniovi.es/",
"id": "00000454",
"name": "Degradome Database",
"namespaceEmbeddedInLui": false,
"pattern": "^[AMCST][0-9x][0-9]$",
"prefix": "degradome",
"sampleId": "Ax1",
"uri_format": "http://degradome.uniovi.es/cgi-bin/protease/$1"
},
"n2t": {
"description": "The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced.",
"example": "Ax1",
"homepage": "http://degradome.uniovi.es/",
"name": "Degradome Database at",
"namespaceEmbeddedInLui": false,
"pattern": "^[AMCST][0-9x][0-9]$",
"prefix": "degradome",
"uri_format": "http://degradome.uniovi.es/cgi-bin/protease/$1"
}
},
"deo": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology that provides a structured vocabulary for rhetorical elements within documents (e.g., Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix). It is imported by DoCO.",
"example": "Reference",
"fairsharing": {
"abbreviation": "DEO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Discourse Elements Ontology (DEO) is an ontology that provides a structured vocabulary for rhetorical elements within documents (e.g., Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix). It is imported by DoCO.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/deo",
"license": "CC-BY-4.0",
"name": "Discourse Elements Ontology",
"prefix": "FAIRsharing.39fd58",
"publications": [
{
"doi": "10.3233/sw-150177",
"title": "The Document Components Ontology (DoCO)",
"year": 2016
}
],
"repository": "https://github.com/sparontologies/deo",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"homepage": "http://www.sparontologies.net/ontologies/deo",
"lov": {
"description": "The Discourse Elements Ontology is an ontology for describing the major rhetorical elements of a document such as a journal article. It is a subsidiary ontology that is imported into the Document Components Ontology, itself part of SPAR, the Semantic Publishing and Referencing Ontologies",
"homepage": "http://www.essepuntato.it/lode/http://purl.org/spar/deo",
"keywords": [
"SPAR"
],
"modified": "2015-07-03",
"name": "The Discourse Elements Ontology",
"prefix": "deo",
"uri_prefix": "http://purl.org/spar/deo/$1"
},
"mappings": {
"fairsharing": "FAIRsharing.39fd58",
"lov": "deo"
},
"name": "Discourse Elements Ontology",
"preferred_prefix": "DEO",
"publications": [
{
"doi": "10.3233/sw-150177",
"title": "TheΒ DocumentΒ ComponentsΒ OntologyΒ (DoCO)",
"year": 2016
}
],
"repository": "https://github.com/sparontologies/deo",
"uri_format": "http://purl.org/spar/deo/$1"
},
"depmap": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://depmap.org/portal/",
"name": "Cancer Dependency Map",
"prefix": "DepMap",
"uri_format": "https://depmap.org/portal/cell_line/$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells.",
"example": "ACH-000001",
"homepage": "https://depmap.org/portal",
"license": "CC-BY-4.0",
"mappings": {
"cellosaurus": "DepMap"
},
"name": "DepMap Cell Lines",
"pattern": "^ACH-\\d+$",
"uri_format": "https://depmap.org/portal/cell_line/$1"
},
"depod": {
"biocontext": {
"prefix": "DEPOD"
},
"fairsharing": {
"abbreviation": "DEPOD",
"contact": {
"email": "depod@embl.de",
"name": "General Enquiries",
"orcid": "0000-0003-3562-7869"
},
"description": "DEPOD - the human DEPhOsphorylation Database is a manually curated database collecting human active and inactive phosphatases, their experimentally verified protein and non-protein substrates, and dephosphorylation site information, and pathways in which they are involved. It also provides links to popular kinase databases and protein-protein interaction databases for these phosphatases and substrates.",
"homepage": "http://www.depod.org/",
"name": "The human DEPhOsphorylation Database",
"prefix": "FAIRsharing.q9j2e3",
"publications": [
{
"doi": "10.1093/nar/gku1009",
"pubmed_id": 25332398,
"title": "The human DEPhOsphorylation database DEPOD: a 2015 update."
},
{
"doi": "10.1126/scisignal.2003203",
"pubmed_id": 23674824,
"title": "Elucidating human phosphatase-substrate networks."
}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"biocontext": "DEPOD",
"fairsharing": "FAIRsharing.q9j2e3",
"miriam": "depod",
"n2t": "depod",
"pathguide": "584",
"re3data": "r3d100011936",
"uniprot": "DB-0190"
},
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"description": "DICOM Controlled Terminology (PS3.16 2024 Annex D)",
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"contact": {
"email": "lynn.schriml@gmail.com",
"name": "Lynn Schriml"
},
"description": "Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. Built in collaboration with EnvO, ExO, ECTO and ChEBI.",
"homepage": "https://disease-ontology.org/",
"name": "Disease Drivers Ontology",
"prefix": "DISDRIV"
},
"example": "0000000",
"mappings": {
"aberowl": "DISDRIV",
"bioportal": "DISDRIV",
"obofoundry": "disdriv",
"ols": "disdriv",
"ontobee": "DISDRIV"
},
"obofoundry": {
"contact": "lynn.schriml@gmail.com",
"contact.github": "lschriml",
"contact.label": "Lynn Schriml",
"contact.orcid": "0000-0001-8910-9851",
"deprecated": false,
"description": "Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. Built in collaboration with EnvO, ExO, ECTO and ChEBI.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/disdriv.owl",
"homepage": "http://www.disease-ontology.org",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Disease Drivers Ontology",
"preferredPrefix": "DISDRIV",
"prefix": "disdriv",
"repository": "https://github.com/DiseaseOntology/DiseaseDriversOntology",
"twitter": "diseaseontology"
},
"ols": {
"description": "Drivers of human diseases including environmental, maternal and social exposures.",
"download_owl": "http://purl.obolibrary.org/obo/disdriv.owl",
"homepage": "http://www.disease-ontology.org",
"name": "Disease Drivers",
"prefix": "disdriv",
"version": "2023-12-15",
"version.iri": "http://purl.obolibrary.org/obo/disdriv/releases/2023-12-15/disdriv.owl"
},
"ontobee": {
"library": "Library",
"name": "Disease Drivers Ontology",
"prefix": "DISDRIV"
},
"pattern": "^\\d+$",
"uri_format": "http://purl.obolibrary.org/obo/DISDRIV_$1"
},
"diseaseclass": {
"appears_in": [
"efo"
],
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"description": "Legacy disease classes that later became MONDO",
"download_obo": "https://github.com/obophenotype/human-disease-ontology/raw/master/src/experimental/missing-omc.obo",
"example": "0000598",
"name": "Disease Class",
"pattern": "^\\d{7}$",
"uri_format": "https://biopragmatics.github.io/providers/diseaseclass/$1"
},
"diseasesdb": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities.",
"example": "1784",
"homepage": "http://www.diseasesdatabase.com/",
"mappings": {
"wikidata": "P557"
},
"name": "Diseases Database",
"pattern": "^\\d+$",
"uri_format": "https://www.diseasesdatabase.com/ddb$1.htm",
"wikidata": {
"description": "identifier sourced on the Diseases Database",
"example": [
"10166",
"8664"
],
"homepage": "http://www.diseasesdatabase.com",
"name": "DiseasesDB",
"pattern": "^\\d{2,5}$",
"prefix": "P557",
"uri_format": "http://www.diseasesdatabase.com/ddb$1.htm"
}
},
"disprot": {
"biocontext": {
"prefix": "DISPROT"
},
"edam": {
"description": "Unique identifier for a protein from the DisProt database.",
"name": "Protein ID (DisProt)",
"obsolete": false,
"prefix": "2723"
},
"fairsharing": {
"abbreviation": "DisProt",
"contact": {
"email": "silvio.tosatto@unipd.it",
"name": "Silvio C.E. Tosatto",
"orcid": "0000-0003-4525-7793"
},
"description": "The Database of Protein Disorder (DisProt) is a curated database that provides information about intrinsically disordered proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. Disordered regions are manually curated from literature. DisProt annotations cover both structural and functional aspects of disorder detected by specific experimental methods.",
"homepage": "https://disprot.org/",
"license": "CC-BY-4.0",
"name": "DisProt",
"prefix": "FAIRsharing.dt9z89",
"publications": [
{
"doi": "10.1093/nar/gkl893",
"pubmed_id": 17145717,
"title": "DisProt: the Database of Disordered Proteins."
},
{
"doi": "10.1093/nar/gkw1056",
"pubmed_id": 27899601,
"title": "DisProt 7.0: a major update of the database of disordered proteins."
},
{
"doi": "10.1093/nar/gkz975",
"pubmed_id": 31713636,
"title": "DisProt: intrinsic protein disorder annotation in 2020."
},
{
"doi": "10.1093/nar/gkab1082",
"pubmed_id": null,
"title": "DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation"
}
],
"repository": "https://disprot.github.io/",
"subjects": [
"Structural Biology",
"Biomedical Science",
"Biology"
],
"twitter": "disprot_db"
},
"go": {
"description": "Database of intrinsically disordered proteins",
"homepage": "https://www.disprot.org",
"name": "DisProt",
"prefix": "DisProt",
"uri_format": "https://www.disprot.org/$1"
},
"mappings": {
"biocontext": "DISPROT",
"edam": "2723",
"fairsharing": "FAIRsharing.dt9z89",
"go": "DisProt",
"miriam": "disprot",
"n2t": "disprot",
"prefixcommons": "disprot",
"re3data": "r3d100010561",
"uniprot": "DB-0017"
},
"miriam": {
"deprecated": false,
"description": "DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature.",
"homepage": "https://disprot.org/",
"id": "00000199",
"name": "DisProt",
"namespaceEmbeddedInLui": false,
"pattern": "^DP\\d{5}$",
"prefix": "disprot",
"sampleId": "DP00003",
"uri_format": "https://disprot.org/$1"
},
"n2t": {
"description": "The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part.",
"example": "DP00003",
"homepage": "http://www.disprot.org/",
"name": "DisProt at Indiana University",
"namespaceEmbeddedInLui": false,
"pattern": "^DP\\d{5}$",
"prefix": "disprot",
"uri_format": "http://www.disprot.org/$1"
},
"prefixcommons": {
"description": "The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part.",
"example": "DP00001",
"homepage": "http://www.disprot.org/",
"keywords": [
"protein",
"structure"
],
"name": "Database of protein disorder",
"pattern": "^DP\\d{5}$",
"prefix": "disprot",
"pubmed_ids": [
"17145717"
],
"uri_format": "http://www.disprot.org/protein.php?id=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkab1082",
"pmc": "PMC8728214",
"pubmed": "34850135",
"title": "DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation",
"year": 2022
},
{
"doi": "10.1093/nar/gkz975",
"pmc": "PMC7145575",
"pubmed": "31713636",
"title": "DisProt: intrinsic protein disorder annotation in 2020",
"year": 2020
},
{
"doi": "10.1093/nar/gkw1056",
"pmc": "PMC5210544",
"pubmed": "27899601",
"title": "DisProt 7.0: a major update of the database of disordered proteins",
"year": 2016
},
{
"doi": "10.1093/nar/gkl893",
"pmc": "PMC1751543",
"pubmed": "17145717",
"title": "DisProt: the Database of Disordered Proteins",
"year": 2006
},
{
"doi": "10.1093/bioinformatics/bth476",
"pubmed": "15310560",
"title": "DisProt: a database of protein disorder",
"year": 2004
}
],
"re3data": {
"description": "The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. DisProt is a community resource annotating protein sequences for intrinsically disorder regions from the literature.\nIt classifies intrinsic disorder based on experimental methods and three ontologies for molecular function, transition and binding partner.",
"homepage": "https://www.disprot.org/",
"name": "DisProt",
"prefix": "r3d100010561",
"synonyms": [
"Database of Protein Disorder"
],
"xrefs": {
"fairsharing": "FAIRsharing.dt9z89",
"nif": "0000-02754",
"scr": "007097"
}
},
"uniprot": {
"abbreviation": "DisProt",
"category": "Family and domain databases",
"homepage": "https://disprot.org",
"name": "Database of protein disorder",
"prefix": "DB-0017",
"publications": [
{
"doi": "10.1093/nar/gkab1082",
"pubmed": "34850135"
}
],
"uri_format": "https://disprot.org/$1"
}
},
"disprot.region": {
"mappings": {
"miriam": "disprot.region"
},
"miriam": {
"deprecated": false,
"description": "DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature.",
"homepage": "https://www.disprot.org",
"id": "00000745",
"name": "DisProt region",
"namespaceEmbeddedInLui": false,
"pattern": "^DP\\d{5}r\\d{3}$",
"prefix": "disprot.region",
"sampleId": "DP00086r013",
"uri_format": "https://www.disprot.org/$1"
},
"part_of": "disprot"
},
"dlxb": {
"mappings": {
"miriam": "dlxb"
},
"miriam": {
"deprecated": false,
"description": "DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences.",
"homepage": "https://doulix.com",
"id": "00000747",
"name": "Linear double stranded DNA sequences",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]{6,7}$",
"prefix": "dlxb",
"sampleId": "6VDC956",
"uri_format": "https://doulix.com/biomodules/$1/"
},
"part_of": "dlx",
"uri_format": "https://doulix.com/biomodules/$1"
},
"dlxc": {
"mappings": {
"miriam": "dlxc"
},
"miriam": {
"deprecated": false,
"description": "DOULIX lab-tested standard biological parts, in this case, full length constructs.",
"homepage": "https://doulix.com",
"id": "00000742",
"name": "Circular double stranded DNA sequences composed",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]{6,7}$",
"prefix": "dlxc",
"sampleId": "M77F7JM",
"uri_format": "https://doulix.com/constructs/$1/"
},
"part_of": "dlx",
"uri_format": "https://doulix.com/constructs/$1"
},
"dmba": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A controlled vocabulary to support the study of transcription in the developing mouse brain",
"download_obo": "https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dmba.obo",
"example": "15567",
"homepage": "https://developingmouse.brain-map.org/",
"name": "Developing Mouse Brain Atlas",
"pattern": "^\\d+$",
"preferred_prefix": "DMBA",
"uri_format": "https://biopragmatics.github.io/providers/dmba/$1"
},
"doap": {
"contact": {
"email": "edd@usefulinc.com",
"github": "ewilderj",
"name": "Edd Wilder-James"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "DOAP is a project to create an XML/RDF vocabulary to describe software projects, and in particular open source projects.",
"download_rdf": "http://usefulinc.com/ns/doap",
"example": "Project",
"homepage": "https://github.com/ewilderj/doap/wiki",
"keywords": [
"metadata",
"rdf",
"semantic web"
],
"lov": {
"description": "The Description of a Project (DOAP) vocabulary, described using W3C RDF Schema and the Web Ontology Language.",
"homepage": "https://github.com/edumbill/doap/wiki",
"keywords": [
"Society"
],
"modified": "2012-01-04",
"name": "Description of a Project vocabulary",
"prefix": "doap",
"uri_prefix": "http://usefulinc.com/ns/doap#$1"
},
"mappings": {
"lov": "doap",
"zazuko": "doap"
},
"name": "Description of a Project",
"preferred_prefix": "doap",
"references": [
"https://en.wikipedia.org/wiki/DOAP"
],
"repository": "https://github.com/ewilderj/doap",
"uri_format": "http://usefulinc.com/ns/doap#$1",
"zazuko": {
"prefix": "doap",
"uri_format": "http://usefulinc.com/ns/doap#$1"
}
},
"doco": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology that provides a structured vocabulary written of document components, both structural (e.g., block, inline, paragraph, section, chapter) and rhetorical (e.g., introduction, discussion, acknowledgements, reference list, figure, appendix).",
"example": "Paragraph",
"fairsharing": {
"abbreviation": "DoCO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Document Components Ontology (DoCO) is an ontology that provides a structured vocabulary written of document components, both structural (e.g., block, inline, paragraph, section, chapter) and rhetorical (e.g., introduction, discussion, acknowledgements, reference list, figure, appendix).",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/doco",
"license": "CC-BY-4.0",
"name": "Document Components Ontology ",
"prefix": "FAIRsharing.162003",
"publications": [
{
"doi": "10.3233/sw-150177",
"title": "The Document Components Ontology (DoCO)",
"year": 2016
}
],
"repository": "https://github.com/sparontologies/doco",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"homepage": "http://www.sparontologies.net/ontologies/doco",
"lov": {
"description": "An ontology for describing the component parts of a bibliographic document",
"homepage": "https://sparontologies.github.io/doco/current/doco.html",
"keywords": [
"SPAR"
],
"modified": "2015-07-03",
"name": "DoCO, the Document Components Ontology",
"prefix": "doco",
"uri_prefix": "http://purl.org/spar/doco/$1"
},
"mappings": {
"fairsharing": "FAIRsharing.162003",
"lov": "doco"
},
"name": "Document Components Ontology",
"preferred_prefix": "DoCO",
"publications": [
{
"doi": "10.3233/sw-150177",
"title": "TheΒ DocumentΒ ComponentsΒ OntologyΒ (DoCO)",
"year": 2016
}
],
"repository": "https://github.com/sparontologies/doco",
"uri_format": "http://purl.org/spar/doco/$1"
},
"doi": {
"banana": "doi",
"biocontext": {
"prefix": "DOI",
"uri_format": "http://dx.doi.org/$1"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "doi",
"uri_format": "https://doi.org/$1"
},
"cellosaurus": {
"category": "Reference resources",
"homepage": "https://dx.doi.org",
"name": "Digital Object Identifier",
"prefix": "DOI",
"uri_format": "https://dx.doi.org/$1"
},
"comment": "The [DOI resolution factsheet](https://www.doi.org/factsheets/DOIProxy.html) specifies that `https://doi.org/DOI` is the preferred format:\n\n> Users may resolve DOI names that are structured to use the DOI system Proxy Server (https://doi.org (preferred)). The resolution of the DOI name in this case depends on the use of URL syntax: the example DOI name doi:10.10.123/456 would be resolved from the address: \"https://doi.org/10.123/456\". Any standard browser encountering a DOI name in this form will be able to resolve it. The proxy service (both doi.org and the **earlier but no longer preferred** dx.doi.org) is accessible over IPv6, and supports DNSSEC. The proxy servers respond to HTTPS (**preferred**) as well as HTTP requests.",
"contributor_extras": [
{
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
{
"github": "dhimmel",
"name": "Daniel Himmelstein",
"orcid": "0000-0002-3012-7446"
}
],
"edam": {
"description": "Digital Object Identifier (DOI) of a published article.",
"name": "DOI",
"obsolete": false,
"prefix": "1188"
},
"example": "10.1038/s41597-022-01807-3",
"example_extras": [
"10.21/FQSQT4T3",
"10.1333/s00897980202a",
"10.1139/z02-135",
"10.1016/j.foodchem.2008.11.065",
"10.1093/acprof:oso/9780195159561.001.1"
],
"fairsharing": {
"abbreviation": "DOI",
"description": "The digital object identifier (DOI) system originated in a joint initiative of three trade associations in the publishing industry (International Publishers Association; International Association of Scientific, Technical and Medical Publishers; Association of American Publishers). The system was announced at the Frankfurt Book Fair 1997. The International DOIΒ Foundation (IDF) was created to develop and manage the DOI system, also in 1997. The DOI system was adopted as International Standard ISO 26324 in 2012. The DOI system implements the Handle System and adds a number of new features. The DOI system provides an infrastructure for persistent unique identification of objects of any type. The DOI system is designed to work over the Internet. A DOI name is permanently assigned to an object to provide a resolvable persistent network link to current information about that object, including where the object, or information about it, can be found on the Internet. While information about an object can change over time, its DOI name will not change. A DOI name can be resolved within the DOI system to values of one or more types of data relating to the object identified by that DOI name, such as a URL, an e-mail address, other identifiers and descriptive metadata. The DOI system enables the construction of automated services and transactions. Applications of the DOI system include but are not limited to managing information and documentation location and access; managing metadata; facilitating electronic transactions; persistent unique identification of any form of any data; and commercial and non-commercial transactions. The content of an object associated with a DOI name is described unambiguously by DOI metadata, based on a structured extensible data model that enables the object to be associated with metadata of any desired degree of precision and granularity to support description and services. The data model supports interoperability between DOI applications. The scope of the DOI system is not defined by reference to the type of content (format, etc.) of the referent, but by reference to the functionalities it provides and the context of use. The DOI system provides, within networks of DOI applications, for unique identification, persistence, resolution, metadata and semantic interoperability.",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://www.doi.org",
"name": "Digital Object Identifier",
"prefix": "FAIRsharing.hFLKCn",
"subjects": [
"Knowledge and Information Systems"
]
},
"go": {
"homepage": "http://dx.doi.org/",
"name": "Digital Object Identifier",
"prefix": "DOI",
"uri_format": "http://dx.doi.org/$1"
},
"mappings": {
"biocontext": "DOI",
"biolink": "doi",
"cellosaurus": "DOI",
"edam": "1188",
"fairsharing": "FAIRsharing.hFLKCn",
"go": "DOI",
"miriam": "doi",
"n2t": "doi",
"prefixcommons": "doi",
"wikidata": "P356"
},
"miriam": {
"deprecated": false,
"description": "The Digital Object Identifier System is for identifying content objects in the digital environment.",
"homepage": "https://www.doi.org/",
"id": "00000019",
"name": "DOI",
"namespaceEmbeddedInLui": false,
"pattern": "^(doi\\:)?10\\.\\d+/.*$",
"prefix": "doi",
"providers": [
{
"code": "scholia",
"description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.",
"homepage": "https://scholia.toolforge.org/",
"name": "Scholia",
"uri_format": "https://scholia.toolforge.org/doi/$1"
}
],
"sampleId": "10.1038/nbt1156",
"uri_format": "https://doi.org/$1"
},
"n2t": {
"description": "The Digital Object Identifier System is for identifying content objects in the digital environment.",
"example": "10.1038/nbt1156",
"homepage": "https://www.doi.org/",
"name": "Digital Object Identifier",
"namespaceEmbeddedInLui": false,
"pattern": "^(doi\\:)?\\d{2}\\.\\d{4}.*$",
"prefix": "doi",
"uri_format": "https://doi.org/$1"
},
"name": "Digital Object Identifier",
"pattern": "^10.\\d{2,9}/.*$",
"prefixcommons": {
"alt_uri_formats": [
"http://hdl.handle.net/#$1"
],
"description": "The Digital Object Identifier System is for identifying content objects in the digital environment.",
"example": "10.1038/nbt1156",
"homepage": "http://www.doi.org/",
"keywords": [
"bibliography"
],
"name": "Digital Object Identifier",
"pattern": "^(doi\\:)?\\d{2}\\.\\d{4}.*$",
"prefix": "doi",
"uri_format": "http://dx.doi.org/$1"
},
"providers": [
{
"code": "dx_doi_http",
"description": "An alternate provider from the DOI website using HTTP",
"homepage": "https://www.doi.org",
"name": "Digital Object Identifier",
"uri_format": "http://dx.doi.org/$1"
},
{
"code": "dx_doi_https",
"description": "An alternate provider from the DOI website using HTTPS",
"homepage": "https://www.doi.org",
"name": "Digital Object Identifier",
"uri_format": "https://dx.doi.org/$1"
},
{
"code": "doi_http",
"description": "An alternate provider from the DOI website using HTTP",
"homepage": "https://www.doi.org",
"name": "Digital Object Identifier",
"uri_format": "http://doi.org/$1"
},
{
"code": "miriam_legacy",
"description": "A legacy MIRIAM URI that does not follow the standard pattern",
"homepage": "https://identifiers.org",
"name": "Legacy MIRIAM URI",
"uri_format": "http://identifiers.org/DOI/$1"
}
],
"references": [
"https://github.com/biopragmatics/bioregistry/issues/287",
"https://github.com/biopragmatics/bioregistry/pull/316"
],
"uri_format": "https://doi.org/$1",
"wikidata": {
"database": "Q25670",
"description": "serial code used to uniquely identify digital objects like academic papers (use upper case letters only)",
"example": [
"10.12987/YALE/9780300197051.003.0010",
"10.1371/JOURNAL.PONE.0029797"
],
"name": "DOI",
"pattern": "^(?i)10.\\d{4,9}/[^\\s]+$",
"prefix": "P356",
"uri_format": "https://doi.org/$1",
"uri_format_rdf": "http://dx.doi.org/$1"
}
},
"doid": {
"aberowl": {
"description": "An ontology for describing the classification of human diseases organized by etiology.",
"download_owl": "http://aber-owl.net/media/ontologies/DOID/684/doid.owl",
"homepage": "http://www.disease-ontology.org",
"name": "Human Disease Ontology",
"prefix": "DOID"
},
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"contact": {
"email": "bhalla@ncbs.res.in",
"github": "upibhalla",
"name": "Upinder S. Bhalla",
"orcid": "0000-0003-1722-5188"
},
"mappings": {
"biocontext": "DOQCS.PATHWAY",
"miriam": "doqcs.pathway",
"n2t": "doqcs.pathway",
"prefixcommons": "doqcs.pathway"
},
"miriam": {
"deprecated": false,
"description": "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways.",
"homepage": "http://doqcs.ncbs.res.in/",
"id": "00000135",
"name": "Database of Quantitative Cellular Signaling: Pathway",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "doqcs.pathway",
"sampleId": "131",
"uri_format": "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1"
},
"n2t": {
"description": "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways.",
"example": "131",
"homepage": "http://doqcs.ncbs.res.in/",
"name": "Database of Quantitative Cellular Signaling (DOQCS) - Pathway Access",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "doqcs.pathway",
"uri_format": "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1"
},
"part_of": "doqcs",
"prefixcommons": {
"description": "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions.",
"example": "38",
"homepage": "http://doqcs.ncbs.res.in/",
"keywords": [
"pathway"
],
"license": "http://doqcs.ncbs.res.in/template.php?&y=faq#q2",
"name": "Database of Quantitative Cellular Signaling: Pathway",
"pattern": "^\\d+$",
"prefix": "doqcs.pathway",
"pubmed_ids": [
"12584128"
],
"uri_format": "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1"
},
"publications": [
{
"doi": "10.1093/bioinformatics/btf860",
"pubmed": "12584128",
"title": "The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks",
"year": 2003
}
]
},
"dpo": {
"aberowl": {
"description": "An ontology of commonly encountered and/or high level Drosophila phenotypes.",
"download_owl": "http://aber-owl.net/media/ontologies/DPO/33/dpo.owl",
"homepage": "http://purl.obolibrary.org/obo/fbcv",
"name": "Drosophila Phenotype Ontology",
"prefix": "DPO"
},
"bioportal": {
"contact": {
"email": "cp390@cam.ac.uk",
"name": "Clare Pilgrim"
},
"description": "An ontology of commonly encountered and/or high level Drosophila phenotypes. It has significant formalisation - utilising terms from GO, CL, PATO and the Drosophila anatomy ontology. It has been used by FlyBase for > 159000 annotations of phenotype.",
"homepage": "http://purl.obolibrary.org/obo/fbcv",
"name": "Drosophila Phenotype Ontology",
"prefix": "DPO",
"version": "2024-08-08"
},
"comment": "DPO is a subset of terms from FBcv",
"mappings": {
"aberowl": "DPO",
"bioportal": "DPO",
"obofoundry": "dpo",
"ols": "dpo",
"ontobee": "DPO"
},
"no_own_terms": true,
"obofoundry": {
"contact": "cp390@cam.ac.uk",
"contact.github": "Clare72",
"contact.label": "Clare Pilgrim",
"contact.orcid": "0000-0002-1373-1705",
"deprecated": false,
"description": "An ontology of commonly encountered and/or high level Drosophila phenotypes.",
"domain": "phenotype",
"download.json": "http://purl.obolibrary.org/obo/dpo.json",
"download.obo": "http://purl.obolibrary.org/obo/dpo.obo",
"download.owl": "http://purl.obolibrary.org/obo/dpo.owl",
"homepage": "http://purl.obolibrary.org/obo/fbcv",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Drosophila Phenotype Ontology",
"preferredPrefix": "FBcv",
"prefix": "dpo",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/24138933",
"title": "The Drosophila phenotype ontology."
}
],
"repository": "https://github.com/FlyBase/drosophila-phenotype-ontology"
},
"ols": {
"description": "An ontology for the description of Drosophila melanogaster phenotypes.",
"download_owl": "http://purl.obolibrary.org/obo/dpo.owl",
"homepage": "http://purl.obolibrary.org/obo/fbcv",
"name": "Drosophila Phenotype Ontology (DPO)",
"prefix": "dpo",
"version": "2024-06-13",
"version.iri": "http://purl.obolibrary.org/obo/dpo/releases/2024-06-13/dpo.owl"
},
"ontobee": {
"library": "Library",
"name": "Drosophila Phenotype Ontology",
"prefix": "DPO"
},
"part_of": "fbcv",
"preferred_prefix": "DPO",
"publications": [
{
"doi": "10.1186/2041-1480-4-30",
"pmc": "PMC3816596",
"pubmed": "24138933",
"title": "The Drosophila phenotype ontology",
"year": 2013
}
]
},
"dpv": {
"biocontext": {
"prefix": "DPV"
},
"contact": {
"email": "mike.adams@bbsrc.ac.uk",
"name": "Michael J. Adams"
},
"integbio": {
"alt_name": "Database of Pathogenic Variants",
"description": "DPV provides information on germline pathogenic mutations in the Japanese population. The data of mutations were curated from published papers regarding Japanese patients with rare diseases and research activities in Japan. All registered variants can be downloaded as an aggregated single VCF file to use in laboratories.",
"homepage": "http://dpv.cmg.med.keio.ac.jp/dpv-pub/top",
"information_keywords": [
"Phenotype",
"Sequence",
"Bibliography/Documents"
],
"maintainer": "Center for Medical Genetics, Keio University School of Medicine",
"name": "DPV",
"prefix": "nbdc02410",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"lov": {
"description": "The Data Privacy Vocabulary (DPV) provides terms (classes and properties) to represent information about processing of personal data, for example - purposes, processing operations, personal data, technical and organisational measures.",
"homepage": "https://github.com/w3c/dpv/",
"keywords": [
"People",
"Security"
],
"modified": "2022-08-18",
"name": "Data Privacy Vocabulary (DPV)",
"prefix": "dpv",
"uri_prefix": "https://w3id.org/dpv#$1"
},
"mappings": {
"biocontext": "DPV",
"integbio": "nbdc02410",
"lov": "dpv",
"miriam": "dpv",
"n2t": "dpv",
"prefixcommons": "dpvweb"
},
"miriam": {
"deprecated": false,
"description": "Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene.",
"homepage": "http://www.dpvweb.net/",
"id": "00000280",
"name": "DPV",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "dpv",
"sampleId": "100",
"uri_format": "http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1"
},
"n2t": {
"description": "Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene.",
"example": "100",
"homepage": "http://www.dpvweb.net/",
"name": "DPV at Rothamsted",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "dpv",
"uri_format": "http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1"
},
"name": "Description of Plant Viruses",
"prefixcommons": {
"description": "DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene (currently, n~9000).",
"example": "100",
"homepage": "http://www.dpvweb.net",
"keywords": [
"classification",
"gene"
],
"name": "Description of Plant Viruses",
"pattern": "^\\d+$",
"prefix": "dpvweb",
"pubmed_ids": [
"16381892"
],
"uri_format": "http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkj023",
"pmc": "PMC1347386",
"pubmed": "16381892",
"title": "DPVweb: a comprehensive database of plant and fungal virus genes and genomes",
"year": 2006
}
]
},
"dragondb.allele": {
"biocontext": {
"prefix": "DRAGONDB.ALLELE"
},
"comment": "Deprecated because the website is dead",
"deprecated": true,
"mappings": {
"biocontext": "DRAGONDB.ALLELE",
"miriam": "dragondb.allele",
"n2t": "dragondb.allele"
},
"miriam": {
"deprecated": false,
"description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information.",
"homepage": "http://www.antirrhinum.net/",
"id": "00000300",
"name": "DragonDB Allele",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "dragondb.allele",
"sampleId": "cho",
"uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele"
},
"n2t": {
"description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information.",
"example": "cho",
"homepage": "http://www.antirrhinum.net/",
"name": "DragonDB Allele at University of British Columbia",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "dragondb.allele",
"uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele"
},
"part_of": "dragondb"
},
"dragondb.dna": {
"biocontext": {
"prefix": "DRAGONDB.DNA"
},
"comment": "Deprecated because the website is dead",
"deprecated": true,
"mappings": {
"biocontext": "DRAGONDB.DNA",
"miriam": "dragondb.dna",
"n2t": "dragondb.dna"
},
"miriam": {
"deprecated": false,
"description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information.",
"homepage": "http://www.antirrhinum.net/",
"id": "00000297",
"name": "DragonDB DNA",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d\\w+$",
"prefix": "dragondb.dna",
"sampleId": "3hB06",
"uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA"
},
"n2t": {
"description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information.",
"example": "3hB06",
"homepage": "http://www.antirrhinum.net/",
"name": "DragonDB DNA at University of British Columbia",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d\\w+$",
"prefix": "dragondb.dna",
"uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA"
},
"part_of": "dragondb"
},
"dragondb.locus": {
"biocontext": {
"prefix": "DRAGONDB.LOCUS"
},
"comment": "Deprecated because the website is dead",
"deprecated": true,
"mappings": {
"biocontext": "DRAGONDB.LOCUS",
"miriam": "dragondb.locus",
"n2t": "dragondb.locus"
},
"miriam": {
"deprecated": false,
"description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information.",
"homepage": "http://www.antirrhinum.net/",
"id": "00000299",
"name": "DragonDB Locus",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "dragondb.locus",
"sampleId": "DEF",
"uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus"
},
"n2t": {
"description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information.",
"example": "DEF",
"homepage": "http://www.antirrhinum.net/",
"name": "DragonDB Locus at University of British Columbia",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "dragondb.locus",
"uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus"
},
"part_of": "dragondb"
},
"dragondb.protein": {
"biocontext": {
"prefix": "DRAGONDB.PROTEIN"
},
"comment": "Deprecated because the website is dead",
"deprecated": true,
"mappings": {
"biocontext": "DRAGONDB.PROTEIN",
"miriam": "dragondb.protein",
"n2t": "dragondb.protein"
},
"miriam": {
"deprecated": false,
"description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information.",
"homepage": "http://www.antirrhinum.net/",
"id": "00000298",
"name": "DragonDB Protein",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "dragondb.protein",
"sampleId": "AMDEFA",
"uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide"
},
"n2t": {
"description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information.",
"example": "AMDEFA",
"homepage": "http://www.antirrhinum.net/",
"name": "DragonDB Protein at University of British Columbia",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "dragondb.protein",
"uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide"
},
"part_of": "dragondb"
},
"drduke": {
"mappings": {
"wikidata": "P10074"
},
"name": "Dr. Duke's Phytochemical and Ethnobotanical Databases chemical",
"wikidata": {
"description": "identifier for chemicals linked to information on occurrence in plants",
"example": [
"19",
"32"
],
"homepage": "https://phytochem.nal.usda.gov/phytochem/search/list",
"name": "Dr. Duke's Phytochemical and Ethnobotanical Databases chemical ID",
"prefix": "P10074",
"uri_format": "https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1"
}
},
"drks": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The German Clinical Trials Register (DRKS) is the German WHO primary registry. It is competent for the registration of all patient-oriented clinical trials conducted in Germany. The DRKS now contains well over 14,000 studies. Currently, around 2,000 studies are added annually. (from website)",
"example": "DRKS00031815",
"homepage": "http://drks.de",
"name": "German Clinical Trials Register",
"pattern": "^DRKS\\d+$",
"providers": [
{
"code": "alt1",
"description": "German Language Provider",
"first_party": true,
"homepage": "http://drks.de",
"name": "German Language Provider",
"uri_format": "https://drks.de/search/de/trial/$1"
},
{
"code": "alt2",
"description": "Legacy Provider",
"first_party": true,
"homepage": "http://drks.de",
"name": "Legacy Provider",
"uri_format": "http://drks.de/en/trial/$1"
}
],
"uri_format": "https://drks.de/search/en/trial/$1"
},
"dron": {
"aberowl": {
"description": "An ontology to support comparative effectiveness researchers studying claims data.",
"download_owl": "http://aber-owl.net/media/ontologies/DRON/25/dron.owl",
"homepage": "https://github.com/ufbmi/dron",
"name": "The Drug Ontology",
"prefix": "DRON"
},
"biocontext": {
"prefix": "DRON"
},
"bioportal": {
"contact": {
"email": "hoganwr@gmail.com",
"name": "William Hogan"
},
"description": "We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive).",
"homepage": "https://github.com/ufbmi/dron",
"name": "The Drug Ontology",
"prefix": "DRON",
"version": "2024-08-05"
},
"download_json": "http://purl.obolibrary.org/obo/dron.json",
"download_obo": "http://purl.obolibrary.org/obo/dron.obo",
"example": "00023232",
"fairsharing": {
"abbreviation": "DrOn",
"contact": {
"email": "hoganwr@gmail.com",
"name": "William Hogan",
"orcid": "0000-0002-9881-1017"
},
"description": "An ontology of drug products and packaged drug products.",
"domains": [
"Drug",
"Small molecule",
"Approved drug"
],
"homepage": "https://github.com/mcwdsi/dron",
"license": "CC-BY-4.0",
"name": "The Drug Ontology",
"prefix": "FAIRsharing.w5ntfd",
"publications": [
{
"doi": "10.1186/s13326-016-0048-2",
"pubmed": "27096073",
"title": "An accurate and precise representation of drug ingredients",
"year": 2016
},
{
"doi": "10.1186/s13326-017-0121-5",
"pubmed": "28253937",
"title": "Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request",
"year": 2017
},
{
"doi": "10.1186/2041-1480-4-44",
"pubmed": "24345026",
"title": "Building a drug ontology based on RxNorm and other sources",
"year": 2013
}
],
"subjects": [
"Biomedical Science"
]
},
"mappings": {
"aberowl": "DRON",
"biocontext": "DRON",
"bioportal": "DRON",
"fairsharing": "FAIRsharing.w5ntfd",
"obofoundry": "dron",
"ols": "dron",
"ontobee": "DRON"
},
"obofoundry": {
"appears_in": [
"scdo"
],
"contact": "hoganwr@gmail.com",
"contact.github": "hoganwr",
"contact.label": "William Hogan",
"contact.orcid": "0000-0002-9881-1017",
"deprecated": false,
"description": "An ontology to support comparative effectiveness researchers studying claims data.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/dron.owl",
"homepage": "https://github.com/ufbmi/dron",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "The Drug Ontology",
"preferredPrefix": "DRON",
"prefix": "dron",
"publications": [
{
"id": "https://doi.org/10.1186/s13326-017-0121-5",
"title": "Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request"
}
],
"repository": "https://github.com/ufbmi/dron"
},
"ols": {
"description": "An ontology to support comparative effectiveness researchers studying claims data.",
"download_owl": "http://purl.obolibrary.org/obo/dron.owl",
"homepage": "https://github.com/ufbmi/dron",
"name": "The Drug Ontology",
"prefix": "dron",
"version": "2024-08-05",
"version.iri": "http://purl.obolibrary.org/obo/dron/releases/2024-08-05/dron.owl"
},
"ontobee": {
"library": "Library",
"name": "The Drug Ontology",
"prefix": "DRON"
},
"pattern": "^\\d{8}$",
"publications": [
{
"doi": "10.1186/s13326-017-0121-5",
"pmc": "PMC5335794",
"pubmed": "28253937",
"title": "Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request",
"year": 2017
},
{
"doi": "10.1186/s13326-016-0048-2",
"pmc": "PMC4836073",
"pubmed": "27096073",
"title": "An accurate and precise representation of drug ingredients",
"year": 2016
},
{
"doi": "10.1186/2041-1480-4-44",
"pmc": "PMC3931349",
"pubmed": "24345026",
"title": "Building a drug ontology based on RxNorm and other sources",
"year": 2013
}
],
"uri_format": "http://purl.obolibrary.org/obo/DRON_$1"
},
"drsanv0": {
"mappings": {
"miriam": "drs.anv0"
},
"miriam": {
"deprecated": false,
"description": "This namespace is used for GA4GH Data Repository Service (DRS) access to the USA National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI), Genomic Analysis, Visualization and Informatics Lab-space (AnVIL) program data. AnVIL is a cloud-based genomic data sharing and analysis platform which facilitates integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by the National Institutes of Health (NIH) or by other agencies that support human genomics research. ",
"homepage": "https://www.genome.gov/",
"id": "00001014",
"name": "AnVIL DRS",
"namespaceEmbeddedInLui": false,
"pattern": "^v2_[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$",
"prefix": "drs.anv0",
"sampleId": "v2_1b0f158a-86e2-3887-b990-89e3cf2d9082",
"uri_format": "https://data.terra.bio/ga4gh/drs/v1/objects/$1"
}
},
"drsc": {
"biocontext": {
"prefix": "DRSC"
},
"mappings": {
"biocontext": "DRSC",
"miriam": "drsc",
"n2t": "drsc"
},
"miriam": {
"deprecated": false,
"description": "The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene.",
"homepage": "http://flyrnai.org/",
"id": "00000367",
"name": "DRSC",
"namespaceEmbeddedInLui": false,
"pattern": "^DRSC\\d+$",
"prefix": "drsc",
"sampleId": "DRSC05221",
"uri_format": "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1"
},
"n2t": {
"description": "The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene.",
"example": "DRSC05221",
"homepage": "http://flyrnai.org/",
"name": "DRSC at Harvard Medical School",
"namespaceEmbeddedInLui": false,
"pattern": "^DRSC\\d+$",
"prefix": "drsc",
"uri_format": "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1"
},
"name": "Drosophila RNAi Screening Center"
},
"drugbank": {
"bartoc": {
"description": "The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains 8246 drug entries including 2012 FDA-approved small molecule drugs, 229 FDA-approved biotech (protein/peptide) drugs, 94 nutraceuticals and over 6000 experimental drugs. Additionally, 4344 non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences are linked to these drug entries. Each DrugCard entry contains more than 200 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data.",
"homepage": "http://www.drugbank.ca/",
"license": "CC BY-NC 3.0",
"name": "DrugBank",
"prefix": "18377",
"wikidata_database": "Q1122544"
},
"biocontext": {
"prefix": "DrugBank",
"uri_format": "http://www.drugbank.ca/drugs/$1"
},
"cellosaurus": {
"category": "Chemistry resources",
"homepage": "https://go.drugbank.com/",
"name": "DrugBank database",
"prefix": "DrugBank",
"uri_format": "https://go.drugbank.com/drugs/$1"
},
"cheminf": {
"description": "Database identifier used by DrugBank.",
"name": "DrugBank",
"obsolete": false,
"prefix": "000406"
},
"edam": {
"description": "Unique identifier of a drug from the DrugBank database.",
"name": "DrugBank",
"obsolete": false,
"prefix": "2326"
},
"example": "DB14938",
"fairsharing": {
"abbreviation": "DrugBank",
"contact": {
"email": "david.wishart@ualberta.ca",
"name": "David Wishart",
"orcid": "0000-0002-3207-2434"
},
"description": "The DrugBank database is a freely available bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.",
"homepage": "http://www.drugbank.ca/",
"name": "DrugBank",
"prefix": "FAIRsharing.353yat",
"publications": [
{
"doi": "10.1093/nar/gkt1068",
"pubmed_id": 24203711,
"title": "DrugBank 4.0: shedding new light on drug metabolism."
},
{
"doi": "10.1093/nar/gkq1126",
"pubmed_id": 21059682,
"title": "DrugBank 3.0: a comprehensive resource for 'omics' research on drugs."
},
{
"doi": "10.1093/nar/gkm958",
"pubmed_id": 18048412,
"title": "DrugBank: a knowledgebase for drugs, drug actions and drug targets."
},
{
"doi": "10.1093/nar/gkj067",
"pubmed_id": 16381955,
"title": "DrugBank: a comprehensive resource for in silico drug discovery and exploration."
}
],
"subjects": [
"Life Science",
"Biomedical Science"
],
"twitter": "DrugBankDB"
},
"homepage": "http://www.drugbank.ca",
"integbio": {
"description": "DrugBank is a database of detailed informatics resources on approved and experimental drugs. The database contains informaiton on drug targets as well as the results of experiments resulting in extensive bioinformatics and chemoinformatics data. Users can browse or search by drug or target. Data is available for download.",
"fairsharing": "biodbcore-000304",
"homepage": "http://www.drugbank.ca/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Chemical structure"
],
"maintainer": "University of Alberta/Department of Computing Science",
"name": "DrugBank",
"prefix": "nbdc01071",
"pubmeds": [
"18048412",
"16381955"
],
"status": "Active",
"target_keywords": [
"Protein",
"Drug"
]
},
"mappings": {
"bartoc": "18377",
"biocontext": "DrugBank",
"cellosaurus": "DrugBank",
"cheminf": "000406",
"edam": "2326",
"fairsharing": "FAIRsharing.353yat",
"integbio": "nbdc01071",
"miriam": "drugbank",
"n2t": "drugbank",
"pathguide": "221",
"prefixcommons": "drugbank",
"re3data": "r3d100010544",
"togoid": "Drugbank",
"uniprot": "DB-0019",
"wikidata": "P715"
},
"miriam": {
"deprecated": false,
"description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information.",
"homepage": "http://www.drugbank.ca/",
"id": "00000102",
"name": "DrugBank",
"namespaceEmbeddedInLui": false,
"pattern": "^DB\\d{5}$",
"prefix": "drugbank",
"sampleId": "DB00001",
"uri_format": "http://www.drugbank.ca/drugs/$1"
},
"n2t": {
"description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information.",
"example": "DB00001",
"homepage": "http://www.drugbank.ca/",
"name": "DrugBank drug information",
"namespaceEmbeddedInLui": false,
"pattern": "^DB\\d{5}$",
"prefix": "drugbank",
"uri_format": "http://www.drugbank.ca/drugs/$1"
},
"name": "DrugBank",
"pathguide": {
"abbreviation": "DrugBank",
"homepage": "http://www.drugbank.ca/",
"name": "DrugBank",
"prefix": "221"
},
"prefixcommons": {
"description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.",
"example": "DB00001",
"homepage": "http://www.drugbank.ca/",
"keywords": [
"drug",
"protein"
],
"license": "http://www.drugbank.ca/about",
"name": "DrugBank",
"pattern": "^DB\\d{5}$",
"prefix": "drugbank",
"pubmed_ids": [
"24203711",
"21059682",
"18048412",
"16381955"
],
"uri_format": "http://www.drugbank.ca/drugs/$1"
},
"publications": [
{
"doi": "10.1093/nar/gkt1068",
"pmc": "PMC3965102",
"pubmed": "24203711",
"title": "DrugBank 4.0: shedding new light on drug metabolism",
"year": 2013
},
{
"doi": "10.1093/nar/gkq1126",
"pmc": "PMC3013709",
"pubmed": "21059682",
"title": "DrugBank 3.0: a comprehensive resource for 'omics' research on drugs",
"year": 2010
},
{
"doi": "10.1093/nar/gkm958",
"pmc": "PMC2238889",
"pubmed": "18048412",
"title": "DrugBank: a knowledgebase for drugs, drug actions and drug targets",
"year": 2007
},
{
"doi": "10.1093/nar/gkj067",
"pmc": "PMC1347430",
"pubmed": "16381955",
"title": "DrugBank: a comprehensive resource for in silico drug discovery and exploration",
"year": 2006
}
],
"re3data": {
"description": "The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The latest release of DrugBank (version 5.1.1, released 2018-07-03) contains 11,881 drug entries including 2,526 approved small molecule drugs, 1,184 approved biotech (protein/peptide) drugs, 129 nutraceuticals and over 5,751 experimental drugs. Additionally, 5,132 non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences are linked to these drug entries. Each DrugCard entry contains more than 200 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data.",
"homepage": "https://go.drugbank.com/",
"name": "DrugBank",
"prefix": "r3d100010544",
"synonyms": [
"DrugBank Online",
"Open Data Drug & Drug Target Database"
],
"xrefs": {
"fairsharing": "fairsharing.353yat",
"miriam": "00000102",
"nif": "0000-00417",
"scr": "002700"
}
},
"synonyms": [
"DRUGBANK_ID",
"DrugBank"
],
"togoid": {
"catalog": "nbdc01071",
"examples": [
"DB15589",
"DB13471",
"DB05830",
"DB07423",
"DB07074",
"DB08912",
"DB02908",
"DB05088",
"DB05229",
"DB08910"
],
"keywords": [
"Drug"
],
"name": "DrugBank",
"pattern": "^(?DB\\d{5})$",
"prefix": "Drugbank",
"uri_format": "http://identifiers.org/drugbank/$1"
},
"uniprot": {
"abbreviation": "DrugBank",
"category": "Chemistry databases",
"homepage": "https://www.drugbank.ca/",
"name": "Drug and drug target database",
"prefix": "DB-0019",
"publications": [
{
"doi": "10.1093/nar/gkx1037",
"pubmed": "29126136"
}
],
"uri_format": "https://www.drugbank.ca/drugs/$1"
},
"wikidata": {
"description": "identifier in the bioinformatics and cheminformatics database from the University of Alberta",
"example": [
"00126",
"CAT005101"
],
"homepage": "https://www.drugbank.ca",
"name": "DrugBank ID",
"pattern": "^DB(SALT\\d|CAT\\d)?\\d{5}$",
"prefix": "P715",
"uri_format": "https://go.drugbank.com/drugs/$1"
}
},
"drugbank.bioentity": {
"biocontext": {
"prefix": "DRUGBANKV4.TARGET"
},
"mappings": {
"biocontext": "DRUGBANKV4.TARGET",
"miriam": "drugbankv4.target",
"n2t": "drugbankv4.target"
},
"miriam": {
"deprecated": false,
"description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database.",
"homepage": "http://www.drugbank.ca/targets",
"id": "00000528",
"name": "DrugBank Target v4",
"namespaceEmbeddedInLui": false,
"pattern": "^BE\\d{7}$",
"prefix": "drugbankv4.target",
"sampleId": "BE0000048",
"uri_format": "http://www.drugbank.ca/biodb/bio_entities/$1"
},
"n2t": {
"description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database.",
"example": "BE0000048",
"homepage": "http://www.drugbank.ca/targets",
"name": "DrugBank Target information version 4",
"namespaceEmbeddedInLui": false,
"pattern": "^BE\\d{7}$",
"prefix": "drugbankv4.target",
"uri_format": "http://www.drugbank.ca/biodb/bio_entities/$1"
},
"part_of": "drugbank",
"synonyms": [
"drugbank.target",
"drugbankv4.target"
],
"uri_format": "https://go.drugbank.com/bio_entities/$1"
},
"drugbank.category": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Close to 5K Categorizations for drugs, similar to ATCC.",
"example": "DBCAT000600",
"homepage": "https://go.drugbank.com/categories",
"keywords": [
"chemistry",
"drugs",
"metascience",
"topics"
],
"name": "DrugBank Drug Category",
"part_of": "drugbank",
"pattern": "^DBCAT\\d+$",
"uri_format": "https://www.drugbank.ca/categories/$1"
},
"drugbank.condition": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Indications and other conditions in drugbank",
"example": "DBCOND0066902",
"homepage": "https://go.drugbank.com",
"name": "DrugBank Condition",
"pattern": "^DBCOND\\d+$",
"uri_format": "https://go.drugbank.com/indications/$1"
},
"drugbank.metabolite": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Metabolites in drugbank",
"example": "DBMET02292",
"homepage": "https://go.drugbank.com",
"name": "DrugBank Metabolite",
"pattern": "^DBMET\\d+$",
"uri_format": "https://go.drugbank.com/metabolites/$1"
},
"drugbank.reaction": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Reactions in drugbank",
"example": "1537",
"homepage": "https://go.drugbank.com",
"name": "DrugBank Reaction",
"pattern": "^\\d+$",
"uri_format": "https://go.drugbank.com/reactions/$1"
},
"drugbank.salt": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets.",
"example": "DBSALT001211",
"homepage": "http://www.drugbank.ca",
"name": "DrugBank Salts",
"part_of": "drugbank",
"pattern": "^DBSALT\\d{6}$",
"uri_format": "https://go.drugbank.com/salts/$1"
},
"drugcentral": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "DrugCentral",
"uri_format": "http://drugcentral.org/drugcard/$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action.",
"example": "307",
"fairsharing": {
"abbreviation": "DrugCentral",
"contact": {
"email": "toprea@salud.unm.edu",
"name": "Tudor Oprea",
"orcid": "0000-0002-6195-6976"
},
"description": "DrugCentral is online drug information that provides information on active ingredients, chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic mode of action. DrugCentral monitors FDA, EMA, and PMDA for new drug approval on regular basis to ensure currency of the resource. This resource was created and is maintained by the Division of Translational Informatics at the University of New Mexico School of Medicine.",
"homepage": "http://drugcentral.org/",
"license": "CC BY-SA 4.0",
"name": "DrugCentral",
"prefix": "FAIRsharing.3me82d",
"publications": [
{
"doi": "10.1093/nar/gkw993",
"pubmed_id": 27789690,
"title": "DrugCentral: online drug compendium."
}
],
"subjects": [
"Drug Discovery",
"Drug Repositioning",
"Drug Development",
"Pharmacy",
"Pharmacology",
"Biomedical Science"
]
},
"homepage": "http://drugcentral.org",
"integbio": {
"description": "DrugCentral is online drug information that provides information on active ingredients, chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic mode of action. DrugCentral monitors FDA, EMA, and PMDA for new drug approval on regular basis to ensure currency of the resource. This resource was created and is maintained by the Division of Translational Informatics at the University of New Mexico School of Medicine.",
"fairsharing": "FAIRsharing.3me82d",
"homepage": "http://drugcentral.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Chemical structure",
"Interaction/Pathway",
"Phenotype"
],
"maintainer": "UNM School of Medicine",
"name": "DrugCentral",
"prefix": "nbdc02192",
"pubmeds": [
"27789690"
],
"status": "Active",
"target_keywords": [
"Chemical compound",
"Drug"
]
},
"license": "CC-BY-SA-4.0",
"mappings": {
"biolink": "DrugCentral",
"fairsharing": "FAIRsharing.3me82d",
"integbio": "nbdc02192",
"miriam": "drugcentral",
"uniprot": "DB-0239",
"wikidata": "P11198"
},
"miriam": {
"deprecated": false,
"description": "DrugCentral (http://drugcentral.org) is an open-access online drug compendium. DrugCentral integrates structure, bioactivity, regulatory, pharmacologic actions and indications for active pharmaceutical ingredients approved by FDA and other regulatory agencies. Monitoring of regulatory agencies for new drugs approvals ensures the resource is up-to-date. DrugCentral integrates content for active ingredients with pharmaceutical formulations, indexing drugs and drug label annotations, complementing similar resources available online. Its complementarity with other online resources is facilitated by cross referencing to external resources. At the molecular level, DrugCentral bridges drug-target interactions with pharmacological action and indications. The integration with FDA drug labels enables text mining applications for drug adverse events and clinical trial information. Chemical structure overlap between DrugCentral and five online drug resources, and the overlap between DrugCentral FDA-approved drugs and their presence in four different chemical collections, are discussed. DrugCentral can be accessed via the web application or downloaded in relational database format.",
"homepage": "http://www.unm.edu/",
"id": "00000966",
"name": "DrugCentral",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "drugcentral",
"sampleId": "257",
"uri_format": "https://drugcentral.org/drugcard/$1"
},
"name": "Drug Central",
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1093/nar/gky963",
"pmc": "PMC6323925",
"pubmed": "30371892",
"title": "DrugCentral 2018: an update",
"year": 2019
},
{
"doi": "10.1093/nar/gkw993",
"pmc": "PMC5210665",
"pubmed": "27789690",
"title": "DrugCentral: online drug compendium",
"year": 2016
}
],
"synonyms": [
"Drug_Central"
],
"uniprot": {
"abbreviation": "DrugCentral",
"category": "Chemistry databases",
"homepage": "https://drugcentral.org/",
"name": "DrugCentral",
"prefix": "DB-0239",
"publications": [
{
"doi": "10.1093/nar/gkac1085",
"pubmed": "36484092"
}
],
"uri_format": "https://drugcentral.org?q=$1"
},
"uri_format": "http://drugcentral.org/drugcard/$1",
"wikidata": {
"description": "ID of a chemical compound in DrugCentral",
"example": [
"158",
"21",
"947"
],
"homepage": "https://drugcentral.org/",
"name": "DrugCentral ID",
"pattern": "^\\d+$",
"prefix": "P11198",
"uri_format": "https://drugcentral.org/drugcard/$1"
}
},
"dsm4": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]",
"example": "315.1",
"example_extras": [
"291.89"
],
"hl7": {
"description": "Diagnostic and Statistical Manual of Mental Disorders (DSM-IV). 4th ed. Washington (DC): American Psychiatric Association, 1994.",
"homepage": "http://www.psych.org",
"name": "DSM-IV",
"organization": "American Psychiatric Association",
"preferred_prefix": "dsm4",
"prefix": "2.16.840.1.113883.6.126",
"status": "Complete"
},
"homepage": "https://en.wikipedia.org/wiki/Diagnostic_and_Statistical_Manual_of_Mental_Disorders#DSM-IV-TR_(2000)",
"mappings": {
"hl7": "2.16.840.1.113883.6.126",
"wikidata": "P663"
},
"name": "Diagnostic and Statistical Manual of Mental Disorders (4th Edition)",
"pattern": "^\\d+\\.\\d+$",
"synonyms": [
"dsm-iv"
],
"wikidata": {
"database": "Q3078495",
"description": "identifier for a mental disorder in the 4th edition of Diagnostic and Statistical Manual of Mental Disorders",
"example": [
"291.89",
"315.1"
],
"homepage": "https://en.wikipedia.org/wiki/DSM-IV_codes",
"name": "DSM-IV classification",
"pattern": "^\\d+\\.\\d+$",
"prefix": "P663"
}
},
"dsm5": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]",
"example": "312.33",
"hl7": {
"description": "The Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) is the 2013 update to the Diagnostic and Statistical Manual of Mental Disorders, the taxonomic and diagnostic tool published by the American Psychiatric Association (APA). In the United States, the DSM serves as a universal authority for psychiatric diagnoses. Treatment recommendations, as well as payment by health care providers, are often determined by DSM classifications, so the appearance of a new version has significant practical importance.The DSM-5 was published on May 18, 2013, superseding the DSM-IV-TR, which was published in 2000.",
"homepage": "https://www.psychiatry.org",
"name": "DSM-5",
"organization": "American Psychiatry Association",
"preferred_prefix": "dsm5",
"prefix": "2.16.840.1.113883.6.344",
"status": "Complete"
},
"homepage": "https://en.wikipedia.org/wiki/DSM-5",
"mappings": {
"hl7": "2.16.840.1.113883.6.344",
"wikidata": "P1930"
},
"name": "Diagnostic and Statistical Manual of Mental Disorders (5th Edition)",
"pattern": "^\\d{3}\\.\\d{2}$",
"references": [
"https://archive.org/details/diagnosticstatis0005unse"
],
"synonyms": [
"dsm-v"
],
"wikidata": {
"description": "identifier for a mental disorder in the 5th edition of Diagnostic and Statistical Manual of Mental Disorders",
"example": [
"312.33"
],
"name": "DSM-5 classification",
"pattern": "^\\d\\d\\d\\.\\d\\d?$",
"prefix": "P1930"
}
},
"dsmz": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://celldive.dsmz.de/",
"name": "DSMZ Tools for Diving into Cell Line Data",
"prefix": "DSMZCellDive",
"uri_format": "https://celldive.dsmz.de/celllines/$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). The following designations are used as part of local unique identifiers:\n\n- `PC`: positive control\n- `NC`: negative control\n- `AS`: antiserum\n- `PV`: plant viruses\n- `RT`: recommended test\n- `ACC`: human or animal cell line\n- `DSM`: microorganism cell line",
"example": "ACC-1",
"example_extras": [
"DSM-2",
"RT-0753",
"PC-0754",
"AS-0753",
"PV-0998"
],
"homepage": "https://www.dsmz.de",
"mappings": {
"cellosaurus": "DSMZCellDive",
"re3data": "r3d100010219"
},
"name": "Deutsche Sammlung von Mikroorganismen und Zellkulturen",
"pattern": "^(ACC|DSM|NC|PC|RT|AS|PV)-\\d+$",
"re3data": {
"description": "The DSMZ is the most comprehensive biological resource center worldwide. Being one of the world's largest collections, the DSMZ currently comprises more than 73,700 items, including about 31,900 different bacterial and 6,600 fungal strains, 840 human and animal cell lines, 1,500 plant viruses and antisera, 700 bacteriophages and 19,000 different types of bacterial genomic DNA. All biological materials accepted in the DSMZ collection are subject to extensive quality control and physiological and molecular characterization by our central services. In addition, DSMZ provides an extensive documentation and detailed diagnostic information on the biological materials. The unprecedented diversity and quality management of its bioresources render the DSMZ an internationally renowned supplier for science, diagnostic laboratories, national reference centers, as well as industrial partners.",
"homepage": "https://www.dsmz.de/",
"name": "DSMZ",
"prefix": "r3d100010219",
"synonyms": [
"Deutsche Sammlung von Mikroorganismen und Zellkulturen",
"Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures",
"Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen"
],
"xrefs": {
"nif": "0000-10209",
"scr": "001711"
}
},
"synonyms": [
"DSMZCellDive"
],
"uri_format": "https://www.dsmz.de/collection/catalogue/details/culture/$1"
},
"dso": {
"contact": {
"email": "evan@epatters.org",
"github": "epatters",
"name": "Evan Patterson",
"orcid": "0000-0002-8600-949X"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Data Science Ontology is a research project of IBM Research AI and Stanford University Statistics. Its long-term objective is to improve the efficiency and transparency of collaborative, data-driven science.",
"example": "classification-model",
"homepage": "https://www.datascienceontology.org/",
"keywords": [
"data science",
"ontology"
],
"name": "Data Science Ontology",
"repository": "https://github.com/IBM/datascienceontology",
"uri_format": "https://www.datascienceontology.org/concept/$1"
},
"dto": {
"aberowl": {
"description": "Drug Target Ontology (DTO) is being developed at the University of Miami in the research group of Stephan SchΓΌrer. DTO is supported by grant U54CA189205 (Illuminating the Druggable Genome Knowledge Management Center, Tudor Oprea, PI) awarded by the NCI through the NIH Common Fund. It is a component of the Illuminating the Druggable Genome (IDG) project (https://commonfund.nih.gov/idg). The DTO project develops a novel semantic framework to formalize knowledge about drug targets with a focus on the current IDG protein families. The DTO is developed as a reference for drug targets with the longer-term goal to create a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The first version of the DTO consists of asserted class hierarchies of the four IDG protein families, GPCRs, kinases, ion channels, and nuclear hormone receptors. Protein classes are linked to tissue and disease via different levels of confidence. DTO also contains drug target development level classifications developed in the IDG project (http://targetcentral.ws/), and functional and qualitative annotations and classifications for kinase proteins, GPCR ligands and ion channels. DTO is modeled in OWL2-DL to enable further classification by inference reasoning and SPARQL queries. DTO is implemented following a modularization approach. DTO is used as the organizational framework for drug targets in the IDG PHAROS User Interface Portal (https://pharos.nih.gov) and also the Tin-X Target Importance and Novelty Explorer (http://newdrugtargets.org).",
"download_owl": "http://aber-owl.net/media/ontologies/DTO/4/dto.owl",
"homepage": "http://drugtargetontology.org/",
"name": "Drug Target Ontology",
"prefix": "DTO",
"version": "1.1"
},
"appears_in": [
"pr"
],
"bioportal": {
"contact": {
"email": "sschurer@med.miami.edu",
"name": "Stephan Schurer"
},
"description": "Drug Target Ontology (DTO) is being developed at the University of Miami in the research group of Stephan SchΓΌrer. DTO is supported by grant U54CA189205 (Illuminating the Druggable Genome Knowledge Management Center, Tudor Oprea, PI) awarded by the NCI through the NIH Common Fund. It is a component of the Illuminating the Druggable Genome (IDG) project (https://commonfund.nih.gov/idg). The DTO project develops a novel semantic framework to formalize knowledge about drug targets with a focus on the current IDG protein families. The DTO is developed as a reference for drug targets with the longer-term goal to create a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The first version of the DTO consists of asserted class hierarchies of the four IDG protein families, GPCRs, kinases, ion channels, and nuclear hormone receptors. Protein classes are linked to tissue and disease via different levels of confidence. DTO also contains drug target development level classifications developed in the IDG project (http://targetcentral.ws/), and functional and qualitative annotations and classifications for kinase proteins, GPCR ligands and ion channels. DTO is modeled in OWL2-DL to enable further classification by inference reasoning and SPARQL queries. DTO is implemented following a modularization approach. DTO is used as the organizational framework for drug targets in the IDG PHAROS User Interface Portal (https://pharos.nih.gov) and also the Tin-X Target Importance and Novelty Explorer (http://newdrugtargets.org).",
"homepage": "http://drugtargetontology.org/",
"name": "Drug Target Ontology",
"prefix": "DTO",
"publication": "http://drugtargetontology.org/",
"version": "1.1.1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.",
"example": "90000018",
"fairsharing": {
"abbreviation": "DTO",
"description": "Drug Target Ontology (DTO) is developed as a reference for drug targets with the longer-term goal to create a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The first version of the DTO consists of asserted class hierarchies of the four IDG protein families, GPCRs, kinases, ion channels, and nuclear hormone receptors. Protein classes are linked to tissue and disease via different levels of confidence. DTO also contains drug target development classifications, a large collection of cell lines from the LINCS project and relevant cell-disease and cell-tissue relations. DTO is modeled in OWL2-DL to enable further classification by inference reasoning and SPARQL queries. DTO is implemented following a modularization approach. DTO will serve as the organizational framework for drug targets in the IDG PHAROS User Interface Portal (https://pharos.nih.gov).",
"domains": [
"Disease",
"Protein"
],
"homepage": "http://drugtargetontology.org/",
"license": "CC-BY-3.0",
"name": "Drug Target Ontology",
"prefix": "FAIRsharing.tke3y2",
"publications": [
{
"doi": "10.1186/s13326-017-0161-x",
"pubmed": "29122012",
"title": "Drug target ontology to classify and integrate drug discovery data",
"year": 2017
}
],
"repository": "https://github.com/DrugTargetOntology/DTO",
"subjects": [
"Drug Discovery",
"Biomedical Science"
],
"user_defined_tags": [
"Drug Target"
]
},
"homepage": "https://github.com/DrugTargetOntology/DTO",
"mappings": {
"aberowl": "DTO",
"bioportal": "DTO",
"fairsharing": "FAIRsharing.tke3y2"
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"name": "Drug Target Ontology",
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1186/s13326-017-0161-x",
"pmc": "PMC5679337",
"pubmed": "29122012",
"title": "Drug target ontology to classify and integrate drug discovery data",
"year": 2017
}
],
"repository": "https://github.com/DrugTargetOntology/DTO",
"uri_format": "http://www.drugtargetontology.org/dto/DTO_$1"
},
"duo": {
"aberowl": {
"description": "DUO is an ontology which represent data use conditions.",
"download_owl": "http://aber-owl.net/media/ontologies/DUO/9/duo.owl",
"homepage": "https://github.com/EBISPOT/DUO",
"name": "Data Use Ontology",
"prefix": "DUO"
},
"biocontext": {
"prefix": "DUO"
},
"bioportal": {
"contact": {
"email": "mcourtot@ebi.ac.uk",
"name": "Melanie Courtot"
},
"description": "An ontology based on the consent codes decsription from the Dyke et al. paper at http://dx.doi.org/10.1371/journal.pgen.1005772. It allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage. This resource is based on the OBO Foundry principles, and its use is under review by the Broad Institute ad the European Genome-phenome Archive (EGA) at EMBL-EBI.",
"homepage": "https://github.com/EBISPOT/DUO",
"name": "The Data Use Ontology",
"prefix": "DUO"
},
"example": "0000046",
"fairsharing": {
"abbreviation": "DUO",
"description": "The Data Use Ontology (DUO) describes data use requirements and limitations. DUO allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage. This resource is based on the OBO Foundry principles, and developed using the W3C Web Ontology Language. It is used in production by the European Genome-phenome Archive (EGA) at EMBL-EBI and CRG as well as the Broad Institute for the Data Use Oversight System (DUOS).",
"homepage": "https://raw.githubusercontent.com/EBISPOT/DUO/master/duo.owl",
"license": "CC-BY-3.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdmdCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--9a42083efa91d79ee5c7ed8e7868db0f7faf0b76/DUO_logo_white_background.png?disposition=inline",
"name": "The Data Use Ontology",
"prefix": "FAIRsharing.5dnjs2",
"publications": [
{
"doi": "10.1016/j.xgen.2021.100028",
"title": "The Data Use Ontology to streamline responsible access to human biomedical datasets",
"year": 2021
}
],
"repository": "https://github.com/EBISPOT/duo/issues",
"subjects": [
"Subject Agnostic",
"Biomedical Science"
],
"user_defined_tags": [
"Metadata standardization"
]
},
"mappings": {
"aberowl": "DUO",
"biocontext": "DUO",
"bioportal": "DUO",
"fairsharing": "FAIRsharing.5dnjs2",
"obofoundry": "duo",
"ols": "duo",
"ontobee": "DUO"
},
"obofoundry": {
"appears_in": [
"scdo"
],
"contact": "mcourtot@gmail.com",
"contact.github": "mcourtot",
"contact.label": "Melanie Courtot",
"contact.orcid": "0000-0002-9551-6370",
"depends_on": [
"bfo",
"iao"
],
"deprecated": false,
"description": "DUO is an ontology which represent data use conditions.",
"domain": "information",
"download.owl": "http://purl.obolibrary.org/obo/duo.owl",
"homepage": "https://github.com/EBISPOT/DUO",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Data Use Ontology",
"preferredPrefix": "DUO",
"prefix": "duo",
"repository": "https://github.com/EBISPOT/DUO"
},
"ols": {
"description": "DUO is an ontology which represent data use conditions.",
"download_owl": "http://purl.obolibrary.org/obo/duo.owl",
"homepage": "https://github.com/EBISPOT/DUO",
"name": "Data Use Ontology",
"prefix": "duo",
"version": "2021-02-23",
"version.iri": "http://purl.obolibrary.org/obo/duo/releases/2021-02-23/duo.owl"
},
"ontobee": {
"library": "Library",
"name": "Data Use Ontology",
"prefix": "DUO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1016/j.xgen.2021.100028",
"pmc": "PMC8591903",
"pubmed": "34820659",
"title": "The Data Use Ontology to streamline responsible access to human biomedical datasets",
"year": 2021
}
],
"repository": "https://github.com/EBISPOT/DUO",
"uri_format": "http://purl.obolibrary.org/obo/DUO_$1"
},
"eaglei": {
"cellosaurus": {
"category": "Biological sample resources",
"homepage": "https://www.eagle-i.net/",
"name": "eagle-i resource discovery tool",
"prefix": "eagle-i"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Discovery tool for biomedical research resources available at institutions throughout the U.S.",
"example": "0000012b-5661-2f63-2f73-b43980000000",
"homepage": "https://hawaii.eagle-i.net",
"mappings": {
"cellosaurus": "eagle-i",
"re3data": "r3d100011564"
},
"name": "eagle-i",
"re3data": {
"description": ">>>!!!<<< The repository is no longer available. >>>!!!<<< The eagle-i National Network and eagle-i resource search at www.eagle-.net was retired on November 4, 2021.!!! Groundbreaking biomedical research requires access to cutting edge scientific resources; however such resources are often invisible beyond the laboratories or universities where they were developed. eagle-i is a discovery platform that helps biomedical scientists find previously invisible, but highly valuable, resources.",
"homepage": "https://open.catalyst.harvard.edu/products/eagle-i/",
"name": "eagle-i",
"prefix": "r3d100011564",
"xrefs": {
"nlx": "143592",
"scr": "013153"
}
},
"uri_format": "http://hawaii.eagle-i.net/i/$1"
},
"easychair.cfp": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Conferences in EasyChair",
"example": "SysBioCancer2022",
"homepage": "https://easychair.org/cfp/",
"keywords": [
"conferences",
"metascience"
],
"name": "EasyChair Call for Paper",
"uri_format": "https://easychair.org/cfp/$1"
},
"easychair.topic": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Call for paper topics in EasyChair",
"example": "27106865",
"homepage": "https://easychair.org/cfp/",
"keywords": [
"metascience",
"topics"
],
"name": "EasyChair Topic",
"pattern": "^\\d+$",
"uri_format": "https://easychair.org/cfp/topic.cgi?tid=$1"
},
"ebisc": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.ebisc.org",
"name": "European Bank for induced pluripotent Stem Cells",
"prefix": "EBiSC",
"uri_format": "https://cells.ebisc.org/$1"
},
"example": "ESi007-A",
"example_extras": [
"EDi008-B"
],
"mappings": {
"cellosaurus": "EBiSC"
},
"pattern": "^E(S|D)i\\d+-\\w$"
},
"ecacc": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.culturecollections.org.uk/about-us/ecacc/",
"name": "European Collection of Cell Cultures",
"prefix": "ECACC",
"uri_format": "https://www.culturecollections.org.uk/products/celllines/detail.jsp?refId=$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs).",
"example": "90062901",
"homepage": "https://www.phe-culturecollections.org.uk/collections/ecacc.aspx",
"mappings": {
"cellosaurus": "ECACC"
},
"name": "European Collection of Authenticated Cell Culture",
"pattern": "^\\d+$",
"uri_format": "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1"
},
"ecao": {
"aberowl": {
"description": "An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586).",
"download_owl": "http://aber-owl.net/media/ontologies/ECAO/3/ecao.owl",
"homepage": "https://github.com/echinoderm-ontology/ecao_ontology",
"name": "The Echinoderm Anatomy and Development Ontology",
"prefix": "ECAO"
},
"bioportal": {
"contact": {
"email": "ettensohn@cmu.edu",
"name": "Charles Ettensohn"
},
"description": "An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586).",
"homepage": "https://github.com/echinoderm-ontology/ecao_ontology",
"name": "The Echinoderm Anatomy and Development Ontology",
"prefix": "ECAO"
},
"example": "0107180",
"mappings": {
"aberowl": "ECAO",
"bioportal": "ECAO",
"obofoundry": "ecao",
"ols": "ecao",
"ontobee": "ECAO"
},
"obofoundry": {
"contact": "ettensohn@cmu.edu",
"contact.github": "ettensohn",
"contact.label": "Charles Ettensohn",
"contact.orcid": "0000-0002-3625-0955",
"depends_on": [
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"ro",
"uberon"
],
"deprecated": false,
"description": "An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586).",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/ecao.obo",
"download.owl": "http://purl.obolibrary.org/obo/ecao.owl",
"homepage": "https://github.com/echinoderm-ontology/ecao_ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "The Echinoderm Anatomy and Development Ontology",
"preferredPrefix": "ECAO",
"prefix": "ecao",
"repository": "https://github.com/echinoderm-ontology/ecao_ontology"
},
"ols": {
"description": "None",
"download_owl": "http://purl.obolibrary.org/obo/ecao.owl",
"homepage": "https://github.com/echinoderm-ontology/ecao_ontology",
"name": "Echinoderm Anatomy and Development Ontology",
"prefix": "ecao",
"version.iri": "http://purl.obolibrary.org/obo/ecao/releases/2024-07-28/ecao-simple.owl"
},
"ontobee": {
"library": "Library",
"name": "The Echinoderm Anatomy and Development Ontology",
"prefix": "ECAO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/ECAO_$1"
},
"eccode": {
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"description": "By the late 1950's it had become evident that the nomenclature of enzymology, in the absence of any guiding authority, in a period when the number of known enzymes was increasing rapidly, was getting out of hand. The naming of enzymes by individual workers had proved far from satisfactory in practice. In many cases the same enzymes became known by several different names, while conversely the same name was sometimes given to different enzymes. Many of the names conveyed little or no idea of the nature of the reactions catalysed, and similar names were sometimes given to enzymes of quite different types. To meet this situation, various attempts to bring order into the general nomenclature of enzymes, or into that of particular groups of enzymes, were made by individuals or small groups of specialists, but none of the resulting nomenclatures met with general approval. (...) The Enzyme List in the sixth edition (1992) contains 3540 entries, of which 178 record enzymes which are now transferred elsewhere in the list, and 166 have been deleted completely. Thus the number of enzymes actually listed is 3196, an increase of 29% on the 1984 edition.",
"homepage": "https://www.abbexa.com/enzyme-commission-number",
"name": "Enzyme Nomenclature",
"prefix": "671",
"wikidata_database": "Q741108"
},
"biocontext": {
"prefix": "EC-CODE"
},
"contact": {
"email": "kristian.axelsen@sib.swiss",
"github": "kaxelsen",
"name": "Kristian Axelsen",
"orcid": "0000-0003-3889-2879"
},
"edam": {
"description": "An Enzyme Commission (EC) number of an enzyme.",
"name": "EC number",
"obsolete": false,
"prefix": "1011"
},
"example_decoys": [
"100",
"2.",
"2.n1",
"2.3.",
"2.3.n1",
"2.3.1.",
"2.3.1.n",
"2.3.4.1."
],
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"2.3",
"2.3.1",
"2.3.1.n12",
"3.1.26.n2"
],
"fairsharing": {
"abbreviation": "EC Number",
"description": "In its report in 1961, the first Enzyme Commission devised a system for enzyme classification that also serves as a basis for assigning code numbers. These code numbers, prefixed by EC, contain four elements separated by points / full stops and are now widely in use. The first number shows to which of the six main divisions (classes) the enzyme belongs and therefore identifies the class of reaction catalysed. The second number indicates the subclass, and generally contains information about the type of compound or group involved. The third figure gives the sub-subclass, which further specifies the type of reaction involved. The fourth figure is the serial number of the enzyme in its sub-subclass.",
"domains": [
"Enzyme Commission number",
"Centrally registered identifier",
"Enzyme",
"Classification"
],
"homepage": "https://www.qmul.ac.uk/sbcs/iubmb/enzyme/rules.html",
"name": "Enzyme Commission Number",
"prefix": "FAIRsharing.rfLD2u",
"subjects": [
"Biochemistry",
"Enzymology"
]
},
"go": {
"homepage": "http://enzyme.expasy.org/",
"name": "Enzyme Commission",
"prefix": "EC",
"uri_format": "https://enzyme.expasy.org/EC/$1"
},
"homepage": "https://www.enzyme-database.org/",
"integbio": {
"alt_name": "Integrated relational Enzyme database",
"description": "IntEnz is a resource for enzymatic nomenclature. The site contains information on naming conventions based on the interantional standards for enzyme classification. Users can browse classifications by type, access standard definitions, submit entries, and download entry data in several formats.",
"fairsharing": "biodbcore-000314",
"homepage": "http://www.ebi.ac.uk/intenz/index.jsp",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Repository"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "IntEnz",
"prefix": "nbdc00508",
"pubmeds": [
"14681451"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"license": "CC-BY-4.0",
"mappings": {
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"biocontext": "EC-CODE",
"edam": "1011",
"fairsharing": "FAIRsharing.rfLD2u",
"go": "EC",
"integbio": "nbdc00508",
"miriam": "ec-code",
"n2t": "ec-code",
"pathguide": "106",
"prefixcommons": "intenz",
"re3data": "r3d100010803",
"togoid": "Ec",
"uniprot": "DB-0024",
"wikidata": "P591"
},
"miriam": {
"deprecated": false,
"description": "The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions.",
"homepage": "https://www.ebi.ac.uk/intenz/",
"id": "00000004",
"name": "Enzyme Nomenclature",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+\\.-\\.-\\.-|\\d+\\.\\d+\\.-\\.-|\\d+\\.\\d+\\.\\d+\\.-|\\d+\\.\\d+\\.\\d+\\.(n)?\\d+$",
"prefix": "ec-code",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "KEGG Ligand Database for Enzyme Nomenclature",
"homepage": "https://www.genome.jp/dbget-bin/www_bfind?enzyme",
"name": "KEGG Ligand Database for Enzyme Nomenclature",
"uri_format": "https://www.genome.jp/dbget-bin/www_bget?ec:$1"
},
{
"code": "expenz",
"description": "ExploreEnz at Trinity College",
"homepage": "http://www.enzyme-database.org/",
"name": "ExploreEnz at Trinity College",
"uri_format": "http://www.enzyme-database.org/query.php?ec=$1"
},
{
"code": "enzymeportal",
"description": "Enzyme Portal through EMBL-EBI",
"homepage": "https://www.ebi.ac.uk/enzymeportal",
"name": "Enzyme Portal through EMBL-EBI",
"uri_format": "https://www.ebi.ac.uk/enzymeportal/ec/$1"
},
{
"code": "expasy",
"description": "Enzyme nomenclature database, ExPASy (Expert Protein Analysis System)",
"homepage": "https://enzyme.expasy.org/",
"name": "Enzyme nomenclature database, ExPASy (Expert Protein Analysis System)",
"uri_format": "https://enzyme.expasy.org/EC/$1"
}
],
"sampleId": "1.1.1.1",
"uri_format": "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1"
},
"n2t": {
"description": "The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions.",
"example": "1.1.1.1",
"homepage": "https://www.ebi.ac.uk/intenz/",
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"description": "Echinobase supports the international research community by providing a centralized, integrated and easy to use web based resource to access the diverse and rich, functional genomics data of echinoderm species.",
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"contact": {
"email": "gavin.thomas@york.ac.uk",
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}
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},
"name": "E. coli Metabolite Database",
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"name": "E. Coli Metabolome Database",
"prefix": "386"
},
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},
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"name": "Evidence and Conclusion Ontology",
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"homepage": "http://code.google.com/p/evidenceontology/",
"name": "Evidence Codes Ontology",
"prefix": "1028"
},
"biocontext": {
"prefix": "ECO"
},
"bioportal": {
"contact": {
"email": "mgiglio@som.umaryland.edu",
"name": "Michelle Giglio"
},
"description": "An ontology of evidence types for supporting conclusions in scientific research",
"homepage": "https://github.com/evidenceontology/evidenceontology",
"name": "Evidence and Conclusion Ontology",
"prefix": "ECO",
"publication": "https://github.com/evidenceontology/evidenceontology",
"version": "releases/2024-07-19"
},
"example": "0007807",
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"abbreviation": "ECO",
"contact": {
"email": "mchibucos@som.umaryland.edu",
"name": "Marcos Chibucos",
"orcid": "0000-0001-9586-0780"
},
"description": "The Evidence and Conclusion Ontology (ECO) contains terms that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has function Y as supported by evidence Z). Capture of this information allows tracking of annotation provenance, establishment of quality control measures, and query of eviden",
"domains": [
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"Resource metadata",
"Biological sample annotation",
"Text mining",
"Assay",
"Curated information",
"Digital curation",
"Study design",
"Literature curation",
"Biocuration"
],
"homepage": "https://evidenceontology.org/",
"license": "CC0-1.0",
"name": "Evidence and Conclusion Ontology",
"prefix": "FAIRsharing.wvpgwn",
"publications": [
{
"doi": "10.1142/9789812704856_0019",
"pubmed": "14992503",
"title": "An evidence ontology for use in pathway/genome databases",
"year": 2004
},
{
"doi": "10.1093/nar/gky1036",
"pubmed": "30407590",
"title": "ECO, the Evidence & Conclusion Ontology: community standard for evidence information",
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},
{
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"pubmed": "27812948",
"title": "The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations",
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}
],
"repository": "https://github.com/evidenceontology/evidenceontology",
"subjects": [
"Computational Biology",
"Life Science"
]
},
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"homepage": "http://www.evidenceontology.org/",
"name": "Evidence Code Ontology",
"prefix": "ECO",
"uri_format": "http://www.evidenceontology.org/browse/#ECO_$1"
},
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"biocontext": "ECO",
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"ontobee": "ECO",
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"miriam": {
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"description": "Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity.",
"homepage": "http://bioportal.bioontology.org/ontologies/ECO",
"id": "00000055",
"name": "Evidence Code Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "ECO:\\d{7}$",
"prefix": "eco",
"sampleId": "0000006",
"uri_format": "http://purl.bioontology.org/ontology/ECO/ECO:$1"
},
"n2t": {
"description": "Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity.",
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"homepage": "http://bioportal.bioontology.org/ontologies/ECO",
"name": "Evidence Code Ontology through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "ECO:\\d{7}$",
"prefix": "eco",
"uri_format": "http://purl.bioontology.org/ontology/ECO/ECO:$1"
},
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"domain": "investigations",
"download.obo": "http://purl.obolibrary.org/obo/eco.obo",
"download.owl": "http://purl.obolibrary.org/obo/eco.owl",
"homepage": "https://www.evidenceontology.org",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"logo": "https://avatars1.githubusercontent.com/u/12802432",
"name": "Evidence and Conclusion Ontology",
"preferredPrefix": "ECO",
"prefix": "eco",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/34986598",
"preferred": true,
"title": "ECO: the Evidence and Conclusion Ontology, an update for 2022."
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/30407590",
"title": "ECO, the Evidence & Conclusion Ontology: community standard for evidence information."
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/25052702",
"title": "Standardized description of scientific evidence using the Evidence Ontology (ECO)"
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],
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},
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"description": "The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the biological research domain that arise from laboratory experiments, computational methods, literature curation, or other means.",
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"homepage": "https://www.evidenceontology.org",
"name": "Evidence & Conclusion Ontology (ECO)",
"prefix": "eco",
"version": "2024-07-19",
"version.iri": "http://purl.obolibrary.org/obo/eco/releases/2024-07-19/eco.owl"
},
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"library": "Library",
"name": "Evidence and Conclusion Ontology",
"prefix": "ECO"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"alt_uri_formats": [
"http://purl.org/obo/owl/ECO#$1"
],
"bioportal": "1012",
"description": "Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity.",
"example": "ECO:0000006",
"keywords": [
"obo",
"ontology"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Evidence Code Ontology",
"pattern": "^ECO:\\d{7}$",
"prefix": "eco",
"synonyms": [
"obo.eco"
]
},
"publications": [
{
"doi": "10.1093/nar/gkab1025",
"pmc": "PMC8728134",
"pubmed": "34986598",
"title": "ECO: the Evidence and Conclusion Ontology, an update for 2022",
"year": 2022
},
{
"doi": "10.1093/nar/gky1036",
"pmc": "PMC6323956",
"pubmed": "30407590",
"title": "ECO, the Evidence & Conclusion Ontology: community standard for evidence information",
"year": 2019
},
{
"doi": "10.1007/978-1-4939-3743-1_18",
"pmc": "PMC6377151",
"pubmed": "27812948",
"title": "The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations",
"year": 2017
},
{
"doi": "10.1093/database/bau075",
"pmc": "PMC4105709",
"pubmed": "25052702",
"title": "Standardized description of scientific evidence using the Evidence Ontology (ECO)",
"year": 2014
},
{
"doi": "10.1142/9789812704856_0019",
"pubmed": "14992503",
"title": "An evidence ontology for use in pathway/genome databases",
"year": 2004
}
],
"uri_format": "http://purl.obolibrary.org/obo/ECO_$1",
"wikidata": {
"description": "identifier in the Evidence & Conclusion Ontology for capturing evidence in biological research",
"homepage": "http://evidenceontology.org/",
"name": "Evidence & Conclusion Ontology ID",
"pattern": "^ECO_[0-9]{7}$",
"prefix": "P3811"
}
},
"ecocore": {
"aberowl": {
"description": "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.",
"download_owl": "http://aber-owl.net/media/ontologies/ECOCORE/8/ecocore.owl",
"homepage": "https://github.com/EcologicalSemantics/ecocore",
"name": "An ontology of core ecological entities",
"prefix": "ECOCORE"
},
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"name": "An ontology of core ecological entities",
"prefix": "ECOCORE",
"version": "2022-03-09"
},
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"ols": "ecocore",
"ontobee": "ECOCORE"
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"contact": "p.buttigieg@gmail.com",
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"contact.label": "Pier Luigi Buttigieg",
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"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "An ontology of core ecological entities",
"preferredPrefix": "ECOCORE",
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"prefix": "ecocore",
"version": "2022-03-09",
"version.iri": "http://purl.obolibrary.org/obo/ecocore/releases/2022-03-09/ecocore.owl"
},
"ontobee": {
"library": "Library",
"name": "An ontology of core ecological entities",
"prefix": "ECOCORE"
},
"pattern": "^\\d+$",
"uri_format": "http://purl.obolibrary.org/obo/ECOCORE_$1"
},
"ecocyc": {
"contact": {
"email": "pkarp@ai.sri.com",
"github": "pkarp111",
"name": "Peter Karp",
"orcid": "0000-0002-5876-6418"
},
"contributor_extras": [
{
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
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],
"description": "EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways.",
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"name": "EcoCyc E. coli Database",
"prefix": "FAIRsharing.65dmtr",
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"subjects": [
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"prefix": "EcoGene",
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"prefix": "FAIRsharing.tx95wa",
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"name": "The Ecosystem Ontology",
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},
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"description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities.",
"example": "23",
"homepage": "http://www.e-cyanobacterium.org/bcs/entity/",
"name": "e-cyanobacterium entity at Masaryk University Brno",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "ecyano.entity",
"uri_format": "http://e-cyanobacterium.org/bcs/entity/$1/"
},
"part_of": "ecyano",
"uri_format": "https://www.e-cyanobacterium.org/bcs/entity/$1"
},
"ecyano.experiment": {
"mappings": {
"miriam": "ecyano.experiment"
},
"miriam": {
"deprecated": false,
"description": "E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments.",
"homepage": "https://www.e-cyanobacterium.org/experiments-repository/",
"id": "00000760",
"name": "E-cyanobacterium Experimental Data",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "ecyano.experiment",
"sampleId": "18",
"uri_format": "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1"
},
"part_of": "ecyano"
},
"ecyano.model": {
"biocontext": {
"prefix": "ECYANO.MODEL"
},
"mappings": {
"biocontext": "ECYANO.MODEL",
"miriam": "ecyano.model",
"n2t": "ecyano.model"
},
"miriam": {
"deprecated": false,
"description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction β as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models.",
"homepage": "http://e-cyanobacterium.org/models/",
"id": "00000586",
"name": "E-cyanobacterium model",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "ecyano.model",
"sampleId": "26",
"uri_format": "http://e-cyanobacterium.org/models/model/$1/"
},
"n2t": {
"description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models.",
"example": "26",
"homepage": "http://e-cyanobacterium.org/models/",
"name": "e-cyanobacterium entity at Masaryk University Brno",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "ecyano.model",
"uri_format": "http://e-cyanobacterium.org/models/model/$1/"
},
"uri_format": "https://e-cyanobacterium.org/models/model/$1"
},
"ecyano.rule": {
"biocontext": {
"prefix": "ECYANO.RULE"
},
"mappings": {
"biocontext": "ECYANO.RULE",
"miriam": "ecyano.rule",
"n2t": "ecyano.rule"
},
"miriam": {
"deprecated": false,
"description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction β as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules.",
"homepage": "http://www.e-cyanobacterium.org/bcs/rule/",
"id": "00000587",
"name": "E-cyanobacterium rule",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "ecyano.rule",
"sampleId": "56",
"uri_format": "http://e-cyanobacterium.org/bcs/rule/$1/"
},
"n2t": {
"description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules.",
"example": "56",
"homepage": "http://www.e-cyanobacterium.org/bcs/rule/",
"name": "e-cyanobacterium entity at Masaryk University Brno",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "ecyano.rule",
"uri_format": "http://e-cyanobacterium.org/bcs/rule/$1/"
},
"part_of": "ecyano",
"uri_format": "https://e-cyanobacterium.org/bcs/rule/$1"
},
"edam": {
"aberowl": {
"description": "EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within bioinformatics and computational biology, including types of data and data identifiers, data formats, operations and topics. EDAM is a simply-structured ontology - essentially a set of concepts with preferred terms and synonyms, definitions, and some additional information - organised into a simple and intuitive hierarchy for convenient use by information curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries.",
"download_owl": "http://aber-owl.net/media/ontologies/EDAM/36/edam.owl",
"homepage": "http://edamontology.org",
"name": "EDAM bioinformatics operations, types of data, data formats, identifiers, and topics",
"prefix": "EDAM",
"version": "1.19"
},
"agroportal": {
"name": "EDAM bioinformatics operations, data types, formats, identifiers and topics",
"prefix": "EDAM"
},
"biocontext": {
"prefix": "EDAM"
},
"bioportal": {
"contact": {
"email": "matus.kalas@uib.no",
"name": "MatΓΊΕ‘ KalaΕ‘"
},
"description": "EDAM is a domain ontology of data analysis and data management in bio- and other sciences, and science-based applications. It comprises concepts related to analysis, modelling, optimisation, and data life-cycle. Targetting usability by diverse users, the structure of EDAM is relatively simple, divided into 4 main sections: Topic, Operation, Data (incl. Identifier), and Format. EDAM is particularly suitable for semantic annotations and categorisation of diverse resources related to data analysis and management: e.g. tools, workflows, learning materials, or standards. EDAM is also useful in data management itself, for recording provenance metadata of processed data. As a reference article (citation), please use https://doi.org/10.7490/f1000research.1118900.1",
"homepage": "http://edamontology.org",
"name": "EDAM - Bioscientific data analysis ontology",
"prefix": "EDAM",
"publication": "https://doi.org/10.7490/f1000research.1118900.1",
"version": "unstable(1.26_dev)"
},
"contact": {
"email": "matus.kalas@uib.no",
"github": "matuskalas",
"name": "MatΓΊΕ‘ KalaΕ‘",
"orcid": "0000-0002-1509-4981"
},
"download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo",
"fairsharing": {
"abbreviation": "EDAM",
"description": "EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within bioscientific data analysis and data management (including computational biology, bioinformatics, and bioimage informatics). EDAM includes topics, operations, types of data and data identifiers, and data formats, relevant in data analysis and data management in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use. EDAM is particularly suitable for semantic annotations and categorisation of diverse resources related to data analysis and management: e.g. tools, workflows, learning materials, or standards. EDAM is also useful in data management itself, for recording provenance metadata of processed bioscientific data.",
"domains": [
"Analysis",
"Data acquisition",
"Data transformation"
],
"homepage": "http://edamontology.org",
"license": "CC BY-SA 4.0",
"name": "The bioscientific data analysis and management ontology",
"prefix": "FAIRsharing.a6r7zs",
"publications": [
{
"doi": "10.1093/bioinformatics/btt113",
"pubmed": "23479348",
"title": "EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats",
"year": 2013
},
{
"doi": "10.7490/f1000research.1118900.1",
"title": "EDAM: the bioscientific data analysis ontology (update 2021)",
"year": 2021
},
{
"doi": "10.5281/zenodo.3899895",
"title": "edamontology/edamontology: EDAM 1.25",
"year": 2020
}
],
"repository": "https://github.com/edamontology/edamontology",
"subjects": [
"Bioinformatics",
"Life Science",
"Subject Agnostic"
],
"twitter": "edamontology"
},
"mappings": {
"aberowl": "EDAM",
"agroportal": "EDAM",
"biocontext": "EDAM",
"bioportal": "EDAM",
"fairsharing": "FAIRsharing.a6r7zs",
"miriam": "edam",
"n2t": "edam",
"ols": "edam",
"ontobee": "EDAM",
"prefixcommons": "edam"
},
"miriam": {
"deprecated": false,
"description": "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).",
"homepage": "http://bioportal.bioontology.org/ontologies/EDAM",
"id": "00000189",
"name": "EDAM Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^(data|topic|operation|format)\\_\\d{4}$",
"prefix": "edam",
"sampleId": "data_1664",
"uri_format": "http://purl.bioontology.org/ontology/EDAM/$1"
},
"n2t": {
"description": "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).",
"example": "data_1664",
"homepage": "http://bioportal.bioontology.org/ontologies/EDAM",
"name": "EDAM through BioPortal",
"namespaceEmbeddedInLui": false,
"pattern": "^(data|topic|operation|format)\\_\\d{4}$",
"prefix": "edam",
"uri_format": "http://purl.bioontology.org/ontology/EDAM/$1"
},
"name": "EDAM Ontology",
"ols": {
"contact": "edam@elixir-dk.org",
"description": "EDAM is a simple ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM provides a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use.",
"download_owl": "https://raw.githubusercontent.com/edamontology/edamontology/master/releases/EDAM.owl",
"homepage": "http://edamontology.org",
"name": "Bioinformatics operations, data types, formats, identifiers and topics",
"prefix": "edam"
},
"ontobee": {
"library": "Not Specified/No",
"name": "EMBRACE Data and Methods",
"prefix": "EDAM"
},
"prefixcommons": {
"bioportal": "1498",
"description": "EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. The applications of EDAM are within organising tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web.",
"example": "EDAM_data:1664",
"homepage": "https://sourceforge.net/projects/edamontology/",
"keywords": [
"obo",
"ontology"
],
"name": "Bioinformatics operations, types of data, data formats and topics",
"pattern": "^EDAM_(data|topic)\\:\\d{4}$",
"prefix": "edam"
},
"publications": [
{
"doi": "10.1093/bioinformatics/btt113",
"pmc": "PMC3654706",
"pubmed": "23479348",
"title": "EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats",
"year": 2013
}
],
"rdf_uri_format": "http://edamontology.org/$1",
"repository": "https://github.com/edamontology/edamontology",
"twitter": "edamontology",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1"
},
"edam.data": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "EDAM-DATA",
"uri_format": "http://edamontology.org/data_$1"
},
"contact": {
"email": "matus.kalas@uib.no",
"github": "matuskalas",
"name": "MatΓΊΕ‘ KalaΕ‘",
"orcid": "0000-0002-1509-4981"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.",
"download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo",
"example": "1664",
"homepage": "http://edamontology.org",
"mappings": {
"biolink": "EDAM-DATA"
},
"name": "EDAM Data",
"part_of": "edam",
"pattern": "^\\d+$",
"repository": "https://github.com/edamontology/edamontology",
"twitter": "edamontology",
"uri_format": "http://edamontology.org/data_$1"
},
"edam.format": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "EDAM-FORMAT",
"uri_format": "http://edamontology.org/format_$1"
},
"contact": {
"email": "matus.kalas@uib.no",
"github": "matuskalas",
"name": "MatΓΊΕ‘ KalaΕ‘",
"orcid": "0000-0002-1509-4981"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data.",
"download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo",
"example": "1915",
"homepage": "http://edamontology.org",
"mappings": {
"biolink": "EDAM-FORMAT"
},
"name": "EDAM Format",
"part_of": "edam",
"pattern": "^\\d+$",
"repository": "https://github.com/edamontology/edamontology",
"twitter": "edamontology",
"uri_format": "http://edamontology.org/format_$1"
},
"edam.operation": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "EDAM-OPERATION",
"uri_format": "http://edamontology.org/operation_$1"
},
"contact": {
"email": "matus.kalas@uib.no",
"github": "matuskalas",
"name": "MatΓΊΕ‘ KalaΕ‘",
"orcid": "0000-0002-1509-4981"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.",
"download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo",
"example": "0004",
"homepage": "http://edamontology.org",
"mappings": {
"biolink": "EDAM-OPERATION"
},
"name": "EDAM Operation",
"part_of": "edam",
"pattern": "^\\d+$",
"repository": "https://github.com/edamontology/edamontology",
"twitter": "edamontology",
"uri_format": "http://edamontology.org/operation_$1"
},
"edam.topic": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "EDAM-TOPIC",
"uri_format": "http://edamontology.org/topic_$1"
},
"contact": {
"email": "matus.kalas@uib.no",
"github": "matuskalas",
"name": "MatΓΊΕ‘ KalaΕ‘",
"orcid": "0000-0002-1509-4981"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.",
"download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo",
"example": "0003",
"homepage": "http://edamontology.org",
"mappings": {
"biolink": "EDAM-TOPIC"
},
"name": "EDAM Topic",
"part_of": "edam",
"pattern": "^\\d+$",
"repository": "https://github.com/edamontology/edamontology",
"twitter": "edamontology",
"uri_format": "http://edamontology.org/topic_$1"
},
"edda": {
"aberowl": {
"description": "The EDDA Study Designs Taxonomy (v2.0) was developed by the Evidence in Documents, Discovery, and Analytics (EDDA) Group: Tanja Bekhuis (Principal Scientist); Eugene Tseytlin (Systems Developer); Ashleigh Faith (Taxonomist); Faina Linkov (Epidemiologist). The EDDA Group is a division of TCB Research & Indexing LLC. This work was made possible, in part, by the US National Library of Medicine, National Institutes of Health, grant no. R00LM010943. Foundational research is described in Bekhuis T, Demner Fushman D, Crowley RS. Comparative effectiveness research designs: an analysis of terms and coverage in Medical Subject Headings (MeSH) and Emtree. Journal of the Medical Library Association (JMLA). 2013 April;101(2):92-100. PMC3634392. Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries. A PDF of this taxonomy is available in ResearchGate DOI: 10.13140/RG.2.1.3769.2406/1. The EDDA Study Designs Taxonomy by Tanja Bekhuis and Eugene Tseytlin is licensed under a Creative Commons AttributionβNonCommercialβShareAlike 4.0 International License (CC BY-NC-SA 4.0). For information about this license, see https://creativecommons.org/licenses/by-nc-sa/4.0/.",
"download_owl": "http://aber-owl.net/media/ontologies/EDDA/11/edda.owl",
"name": "EDDA Study Designs Taxonomy",
"prefix": "EDDA",
"version": "2.0"
},
"bioportal": {
"contact": {
"email": "tanja.bekhuis@tcbinfosci.com",
"name": "Tanja Bekhuis"
},
"description": "The EDDA Study Designs Taxonomy (v2.0) was developed by the Evidence in Documents, Discovery, and Analytics (EDDA) Group: Tanja Bekhuis (Principal Scientist); Eugene Tseytlin (Systems Developer); Ashleigh Faith (Taxonomist); Faina Linkov (Epidemiologist). The EDDA Group is a division of TCB Research & Indexing LLC. This work was made possible, in part, by the US National Library of Medicine, National Institutes of Health, grant no. R00LM010943. Foundational research is described in Bekhuis T, Demner Fushman D, Crowley RS. Comparative effectiveness research designs: an analysis of terms and coverage in Medical Subject Headings (MeSH) and Emtree. Journal of the Medical Library Association (JMLA). 2013 April;101(2):92-100. PMC3634392. Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries. A PDF of this taxonomy is available in ResearchGate DOI: 10.13140/RG.2.1.3769.2406/1. The EDDA Study Designs Taxonomy by Tanja Bekhuis and Eugene Tseytlin is licensed under a Creative Commons AttributionβNonCommercialβShareAlike 4.0 International License (CC BY-NC-SA 4.0). For information about this license, see https://creativecommons.org/licenses/by-nc-sa/4.0/.",
"name": "EDDA Study Designs Taxonomy",
"prefix": "EDDA",
"version": "2.0"
},
"contact": {
"email": "tanja.bekhuis@tcbinfosci.com",
"name": "Tanja Bekhuis",
"orcid": "0000-0002-8537-9077"
},
"description": "Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries.",
"example": "health_care_quality_assessment",
"fairsharing": {
"abbreviation": "EDDA",
"description": "Terminology of study designs and publication types (beta version). Developed by the Evidence in Documents, Discovery, and Analysis (EDDA) Group. Tanja Bekhuis (PI); Eugene Tseytlin (Systems Developer); Ashleigh Faith (Taxonomist). Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pennsylvania, US. This work was made possible, in part, by the US National Library of Medicine, National Institutes of Health, grant no. R00LM010943. Based on research described in Bekhuis T, Demner-Fushman D, Crowley RS. Comparative effectiveness research designs: an analysis of terms and coverage in Medical Subject Headings (MeSH) and Emtree. Journal of the Medical Library Association (JMLA). 2013 April;101(2):92-100. PMC3634392. The terminology appearing in JMLA has been enriched with terms from MeSH, NCI Thesaurus (NCIT), and Emtree, the controlled vocabularies for MEDLINE, the National Cancer Institute, and Embase, respectively, as well as from published research literature. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCIT, Emtree, and medical dictionaries. A class for Publication Type is included because investigators consider type and design when screening reports for inclusion in comparative effectiveness research. EDDA Study Designs and Publications by Tanja Bekhuis is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.",
"homepage": "http://edda.dbmi.pitt.edu/",
"name": "EDDA Study Designs Taxonomy",
"prefix": "FAIRsharing.2ffmsb",
"subjects": [
"Medicine"
]
},
"homepage": "https://bioportal.bioontology.org/ontologies/EDDA",
"mappings": {
"aberowl": "EDDA",
"bioportal": "EDDA",
"fairsharing": "FAIRsharing.2ffmsb"
},
"uri_format": "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1"
},
"efo": {
"aberowl": {
"description": "The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental variables in multiple resources at the EBI and Open Targets. The ontology has been developed to increase the richness of the annotations that are currently made in resources and to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology pulls together classes from reference ontologies such as disease, cell line, cell type and anatomy and adds axiomatisation as necessary to connect areas such as disease to phenotype. Contact EFO users list for information: efo-users@lists.sourceforge.net",
"download_owl": "http://aber-owl.net/media/ontologies/EFO/168/efo.owl",
"homepage": "http://www.ebi.ac.uk/efo",
"name": "Experimental Factor Ontology",
"prefix": "EFO",
"version": "2.89"
},
"agroportal": {
"contact": {
"email": "efo-users@lists.sourceforge.net",
"name": "EFO User List"
},
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"example_uri": "http://www.orpha.net/ORDO/Orphanet_1390",
"homepage": "http://www.ebi.ac.uk/efo/",
"license": "Apache 2.0 License",
"name": "Experimental Factor Ontology",
"prefix": "EFO",
"repository": "https://github.com/EBISPOT/efo",
"version": "3.68.0"
},
"biocontext": {
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},
"biolink": {
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},
"bioportal": {
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"name": "EFO User List"
},
"description": "The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental variables in multiple resources at the EBI and Open Targets. The ontology has been developed to increase the richness of the annotations that are currently made in resources and to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology pulls together classes from reference ontologies such as disease, cell line, cell type and anatomy and adds axiomatisation as necessary to connect areas such as disease to phenotype. Contact EFO users list for information: efo-users@ebi.ac.uk.",
"homepage": "http://www.ebi.ac.uk/efo",
"name": "Experimental Factor Ontology",
"prefix": "EFO",
"version": "3.68.0"
},
"cellosaurus": {
"category": "Experimental variables resources",
"homepage": "https://www.ebi.ac.uk/efo/",
"name": "Experimental Factor Ontology",
"prefix": "EFO",
"uri_format": "https://www.ebi.ac.uk/efo/$1"
},
"contact": {
"email": "plwhetzel@gmail.com",
"github": "twhetzel",
"name": "Trish Whetzel",
"orcid": "0000-0002-3458-4839"
},
"download_obo": "http://www.ebi.ac.uk/efo/efo.obo",
"download_owl": "http://www.ebi.ac.uk/efo/efo.owl",
"example": "0005147",
"fairsharing": {
"abbreviation": "EFO",
"contact": {
"email": "siiraa@ebi.ac.uk",
"name": "Sirarat Sarntivijai",
"orcid": "0000-0002-2548-641X"
},
"description": "The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental variables in multiple resources at the EBI and the Centre for Therapeutic Target Validation. The ontology has been developed to increase the richness of the annotations that are currently made in resources and to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology pulls together classes from reference ontologies such as disease, cell line, cell type and anatomy and adds axiomatisation as necessary to connect areas such as disease to phenotype.",
"domains": [
"Experimental measurement",
"Assay",
"Independent variable",
"Study design",
"Genome-wide association study"
],
"homepage": "https://www.ebi.ac.uk/efo/",
"license": "Apache 2.0 License",
"name": "Experimental Factor Ontology",
"prefix": "FAIRsharing.1gr4tz",
"publications": [
{
"doi": "10.1093/bioinformatics/btq099",
"pubmed": "20200009",
"title": "Modeling sample variables with an Experimental Factor Ontology",
"year": 2010
}
],
"repository": "https://github.com/EBISPOT/efo",
"subjects": [
"Functional Genomics"
],
"user_defined_tags": [
"Experimental condition"
]
},
"license": "Apache-2.0",
"mappings": {
"aberowl": "EFO",
"agroportal": "EFO",
"biocontext": "EFO",
"biolink": "EFO",
"bioportal": "EFO",
"cellosaurus": "EFO",
"fairsharing": "FAIRsharing.1gr4tz",
"miriam": "efo",
"n2t": "efo",
"ols": "efo",
"ontobee": "EFO",
"wikidata": "P11956"
},
"miriam": {
"deprecated": false,
"description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.",
"homepage": "http://bioportal.bioontology.org/ontologies/EFO",
"id": "00000391",
"name": "Experimental Factor Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{7}$",
"prefix": "efo",
"providers": [
{
"code": "ebi",
"description": "EFO through Functional Genomics Group (EBI)",
"homepage": "https://www.ebi.ac.uk/efo/",
"name": "EFO through Functional Genomics Group (EBI)",
"uri_format": "https://www.ebi.ac.uk/efo/EFO_$1"
}
],
"sampleId": "0004859",
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},
"n2t": {
"description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.",
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"homepage": "http://bioportal.bioontology.org/ontologies/EFO",
"name": "EFO through BioPortal",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{7}$",
"prefix": "efo",
"uri_format": "http://purl.bioontology.org/ontology/EFO/efo:EFO_$1"
},
"ols": {
"contact": "efo-users@lists.sourceforge.net",
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"download_owl": "http://www.ebi.ac.uk/efo/efo.owl",
"homepage": "http://www.ebi.ac.uk/efo",
"name": "Experimental Factor Ontology",
"prefix": "efo",
"version": "3.68.0",
"version.iri": "http://www.ebi.ac.uk/efo/releases/v3.68.0/efo.owl"
},
"ontobee": {
"library": "Not Specified/No",
"name": "Experimental Factor Ontology",
"prefix": "EFO"
},
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{
"name": "European Bioinformatics Institute",
"partnered": false,
"ror": "02catss52"
}
],
"preferred_prefix": "EFO",
"publications": [
{
"doi": "10.1093/bioinformatics/btq099",
"pmc": "PMC2853691",
"pubmed": "20200009",
"title": "Modeling sample variables with an Experimental Factor Ontology",
"year": 2010
}
],
"repository": "https://github.com/EBISPOT/efo/",
"uri_format": "http://www.ebi.ac.uk/efo/EFO_$1",
"wikidata": {
"description": "identifier for an experimental factor in the Experimental Factor Ontology",
"example": [
"0000408",
"0003894",
"0008559"
],
"homepage": "https://www.ebi.ac.uk/efo/",
"name": "Experimental Factor Ontology ID",
"prefix": "P11956",
"uri_format": "http://www.ebi.ac.uk/efo/EFO_$1"
}
},
"ega.dataset": {
"biocontext": {
"prefix": "EGA.DATASET"
},
"contact": {
"email": "tk2@ebi.ac.uk",
"github": "tk2",
"name": "Thomas Keane",
"orcid": "0000-0001-7532-6898"
},
"fairsharing": {
"abbreviation": "EGA",
"description": "The European Genome-phenome Archive (EGA) is a service for permanent archiving and sharing of personally identifiable genetic, phenotypic, and clinical data generated for the purposes of biomedical research projects or in the context of research-focused healthcare systems. Access to data must be approved by the specified Data Access Committee (DAC).",
"homepage": "https://ega-archive.org/",
"name": "The European Genome-phenome Archive",
"prefix": "FAIRsharing.mya1ff",
"publications": [
{
"doi": "10.1038/ng.3312",
"pubmed_id": 26111507,
"title": "The European Genome-phenome Archive of human data consented for biomedical research."
},
{
"doi": "10.1093/nar/gkab1059",
"pubmed_id": null,
"title": "The European Genome-phenome Archive in 2021"
}
],
"subjects": [
"Genomics",
"Clinical Studies",
"Phenomics",
"Biomedical Science",
"Biology"
],
"twitter": "EGAarchive"
},
"homepage": "https://ega-archive.org/",
"mappings": {
"biocontext": "EGA.DATASET",
"fairsharing": "FAIRsharing.mya1ff",
"miriam": "ega.dataset",
"n2t": "ega.dataset",
"re3data": "r3d100011242"
},
"miriam": {
"deprecated": false,
"description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.",
"homepage": "https://www.ebi.ac.uk/ega/dataset",
"id": "00000512",
"name": "European Genome-phenome Archive Dataset",
"namespaceEmbeddedInLui": false,
"pattern": "^EGAD\\d{11}$",
"prefix": "ega.dataset",
"providers": [
{
"code": "omicsdi",
"description": "EGA Dataset through OmicsDI",
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"name": "EGA Dataset through OmicsDI",
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}
],
"sampleId": "EGAD00000000001",
"uri_format": "https://www.ebi.ac.uk/ega/datasets/$1"
},
"n2t": {
"description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.",
"example": "EGAD00000000001",
"homepage": "https://www.ebi.ac.uk/ega/dataset",
"name": "EGA Dataset at European Bioinformatics Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^EGAD\\d{11}$",
"prefix": "ega.dataset",
"uri_format": "https://www.ebi.ac.uk/ega/datasets/$1"
},
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{
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"partnered": false,
"ror": "02catss52"
}
],
"publications": [
{
"doi": "10.1093/nar/gkab1059",
"pmc": "PMC8728218",
"pubmed": "34791407",
"title": "The European Genome-phenome Archive in 2021",
"year": 2022
},
{
"doi": "10.1038/ng.3312",
"pmc": "PMC5426533",
"pubmed": "26111507",
"title": "The European Genome-phenome Archive of human data consented for biomedical research",
"year": 2015
}
],
"re3data": {
"description": "The European Genome-phenome Archive (EGA) is designed to be a repository for all types of sequence and genotype experiments, including case-control, population, and family studies. We will include SNP and CNV genotypes from array based methods and genotyping done with re-sequencing methods. \nThe EGA will serve as a permanent archive that will archive several levels of data including the raw data (which could, for example, be re-analysed in the future by other algorithms) as well as the genotype calls provided by the submitters. We are developing data mining and access tools for the database.\nFor controlled access data, the EGA will provide the necessary security required to control access, and maintain patient confidentiality, while providing access to those researchers and clinicians authorised to view the data. In all cases, data access decisions will be made by the appropriate data access-granting organisation (DAO) and not by the EGA. The DAO will normally be the same organisation that approved and monitored the initial study protocol or a designate of this approving organisation. The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).",
"homepage": "https://ega-archive.org/",
"name": "The European Genome-phenome Archive",
"prefix": "r3d100011242",
"synonyms": [
"EGA"
],
"xrefs": {
"fairsharing": "FAIRsharing.mya1ff",
"miriam": "00000512",
"nlx": "91316",
"scr": "004944"
}
}
},
"ega.study": {
"biocontext": {
"prefix": "EGA.STUDY"
},
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"biocontext": "EGA.STUDY",
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"n2t": "ega.study"
},
"miriam": {
"deprecated": false,
"description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.",
"homepage": "https://www.ebi.ac.uk/ega/studies",
"id": "00000511",
"name": "European Genome-phenome Archive Study",
"namespaceEmbeddedInLui": false,
"pattern": "^EGAS\\d{11}$",
"prefix": "ega.study",
"sampleId": "EGAS00000000001",
"uri_format": "https://www.ebi.ac.uk/ega/studies/$1"
},
"n2t": {
"description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.",
"example": "EGAS00000000001",
"homepage": "https://www.ebi.ac.uk/ega/studies",
"name": "EGA Study at European Bioinformatics Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^EGAS\\d{11}$",
"prefix": "ega.study",
"uri_format": "https://www.ebi.ac.uk/ega/studies/$1"
}
},
"eggnog": {
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},
"contact": {
"email": "j.huerta@csic.es",
"github": "jhcepas",
"name": "Jaime Huerta-Cepas",
"orcid": "0000-0003-4195-5025"
},
"fairsharing": {
"abbreviation": "eggNOG",
"description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).",
"homepage": "http://eggnog.embl.de",
"name": "Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups",
"prefix": "FAIRsharing.j1wj7d",
"publications": [
{
"doi": "10.1093/nar/gkp951",
"pubmed_id": 19900971,
"title": "eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations."
},
{
"doi": "10.1093/nar/gkm796",
"pubmed_id": 17942413,
"title": "eggNOG: automated construction and annotation of orthologous groups of genes."
}
],
"subjects": [
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]
},
"mappings": {
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"fairsharing": "FAIRsharing.j1wj7d",
"miriam": "eggnog",
"n2t": "eggnog",
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"uniprot": "DB-0152"
},
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"deprecated": false,
"description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).",
"homepage": "http://eggnog.embl.de/version_3.0/",
"id": "00000201",
"name": "eggNOG",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "eggnog",
"sampleId": "veNOG12876",
"uri_format": "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1"
},
"n2t": {
"description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).",
"example": "veNOG12876",
"homepage": "http://eggnog.embl.de/version_3.0/",
"name": "eggNOG Version 3 at European Molecular Biology Laboratory",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "eggnog",
"uri_format": "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1"
},
"prefixcommons": {
"description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).",
"example": "NOG80852",
"homepage": "http://eggnog.embl.de",
"keywords": [
"gene"
],
"name": "Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups",
"pattern": "^\\w+$",
"prefix": "eggnog",
"pubmed_ids": [
"19900971"
],
"uri_format": "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkp951",
"pmc": "PMC2808932",
"pubmed": "19900971",
"title": "eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations",
"year": 2009
},
{
"doi": "10.1093/nar/gkm796",
"pmc": "PMC2238944",
"pubmed": "17942413",
"title": "eggNOG: automated construction and annotation of orthologous groups of genes",
"year": 2007
}
],
"uniprot": {
"abbreviation": "eggNOG",
"category": "Phylogenomic databases",
"homepage": "http://eggnogdb.embl.de/",
"name": "evolutionary genealogy of genes",
"prefix": "DB-0152",
"publications": [
{
"doi": "10.1093/nar/gkac1022",
"pubmed": "36399505"
}
],
"uri_format": "http://eggnog.embl.de/search/ogs/$1"
}
},
"ehda": {
"aberowl": {
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once.",
"download_obo": "http://aber-owl.net/media/ontologies/EHDA/6/ehda.obo",
"homepage": "http://genex.hgu.mrc.ac.uk/",
"name": "Human Developmental Anatomy Ontology, timed version",
"prefix": "EHDA",
"version": "unknown"
},
"biocontext": {
"prefix": "EHDA"
},
"bioportal": {
"contact": {
"email": "J.Bard@ed.ac.uk",
"name": "Jonathan Bard"
},
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once.",
"homepage": "http://obofoundry.org/ontology/ehda.html",
"name": "Human Developmental Anatomy Ontology, timed version",
"prefix": "EHDA",
"version": "unknown"
},
"example": "1",
"mappings": {
"aberowl": "EHDA",
"biocontext": "EHDA",
"bioportal": "EHDA",
"obofoundry": "ehda",
"prefixcommons": "ehda"
},
"obofoundry": {
"contact": "J.Bard@ed.ac.uk",
"contact.label": "Jonathan Bard",
"deprecated": true,
"domain": "anatomy and development",
"homepage": "http://genex.hgu.mrc.ac.uk/",
"name": "Human developmental anatomy, timed version",
"prefix": "ehda"
},
"pattern": "^\\d+$",
"prefixcommons": {
"bioportal": "1022",
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20).",
"example": "EHDAA_1",
"homepage": "http://genex.hgu.mrc.ac.uk/",
"keywords": [
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"anatomy",
"development",
"human"
],
"name": "Human developmental anatomy, timed version",
"pattern": "^EHDA_\\d+$",
"prefix": "ehda"
}
},
"ehdaa": {
"aberowl": {
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release.",
"download_obo": "http://aber-owl.net/media/ontologies/EHDAA/6/ehdaa.obo",
"homepage": "http://genex.hgu.mrc.ac.uk/",
"name": "Human Developmental Anatomy Ontology, abstract version 1",
"prefix": "EHDAA",
"version": "unknown"
},
"biocontext": {
"prefix": "EHDAA"
},
"bioportal": {
"contact": {
"email": "J.Bard@ed.ac.uk",
"name": "Jonathan Bard"
},
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release.",
"homepage": "http://obofoundry.org/ontology/ehdaa.html",
"name": "Human Developmental Anatomy Ontology, abstract version 1",
"prefix": "EHDAA",
"version": "unknown"
},
"example": "1",
"mappings": {
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"biocontext": "EHDAA",
"bioportal": "EHDAA",
"obofoundry": "ehdaa",
"prefixcommons": "ehdaa"
},
"obofoundry": {
"contact": "J.Bard@ed.ac.uk",
"contact.label": "Jonathan Bard",
"deprecated": true,
"domain": "anatomy and development",
"name": "Human developmental anatomy, abstract version",
"prefix": "ehdaa"
},
"pattern": "^\\d+$",
"prefixcommons": {
"bioportal": "1021",
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20).",
"example": "EHDAA_573",
"homepage": "http://genex.hgu.mrc.ac.uk/",
"keywords": [
"obo",
"anatomy",
"development",
"human"
],
"name": "Human developmental anatomy, abstract version",
"pattern": "^EHDAA_\\d+$",
"prefix": "ehdaa",
"synonyms": [
"hdaa"
]
}
},
"ehdaa2": {
"aberowl": {
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the developing human.",
"download_owl": "http://aber-owl.net/media/ontologies/EHDAA2/33/ehdaa2.owl",
"homepage": "http://genex.hgu.mrc.ac.uk/",
"name": "Human developmental anatomy, abstract",
"prefix": "EHDAA2"
},
"biocontext": {
"prefix": "EHDAA2"
},
"bioportal": {
"contact": {
"email": "J.Bard@ed.ac.uk",
"name": "EMAP Administrators"
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"name": "Matthieu Reichstadt"
},
"description": "L'ontologie EOL décrit les conditions d'environnement des élevages d'animaux domestiques. Elle décrit plus particulièrement les modalités de l'alimentation, de l'environnement, de la structure des élevages et des systèmes d'élevage., The EOL ontology describes environmental conditions of livestock breeding. It includes feeding modalities, the structure of breeding systems and their environment.",
"example_uri": "http://opendata.inra.fr/EOL/EOL_0000301",
"homepage": "http://www.atol-ontology.com/",
"license": "CC-BY-4.0",
"name": "Environment Ontology for Livestock",
"prefix": "EOL",
"publication": "http://www.atol-ontology.com/rb/fr/6"
},
"bioportal": {
"contact": {
"email": "matthieu.reichstadt@clermont.inra.fr",
"name": "Reichstadt Matthieu"
},
"description": "L'ontologie EOL décrit les conditions d'environnement des élevages d'animaux domestiques. Elle décrit plus particulièrement les modalités de l'alimentation, de l'environnement, de la structure des élevages et des systèmes d'élevage",
"name": "Environment Ontology for Livestock",
"prefix": "EOL"
},
"contact": {
"email": "pylebail@rennes.inra.fr",
"name": "Pierre-Yves LeBail",
"orcid": "0000-0002-8310-5195"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems.",
"download_owl": "http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=eol.owl",
"example": "0001927",
"fairsharing": {
"abbreviation": "EOL",
"description": "The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems.",
"homepage": "http://www.atol-ontology.com/en/eol-2/",
"license": "CC-BY-4.0",
"name": "Environment Ontology for Livestock",
"prefix": "FAIRsharing.w7bw2y",
"subjects": [
"Environmental Science",
"Animal Husbandry",
"Agriculture"
],
"user_defined_tags": [
"Livestock",
"Species-environment interaction"
]
},
"mappings": {
"aberowl": "EOL",
"agroportal": "EOL",
"bioportal": "EOL",
"fairsharing": "FAIRsharing.w7bw2y",
"ols": "eol",
"re3data": "r3d100011663"
},
"ols": {
"contact": "pylebail@rennes.inra.fr",
"description": "L'ontologie EOL décrit les conditions d'environnement des élevages d'animaux domestiques. Elle décrit plus particulièrement les modalités de l'alimentation, de l'environnement, de la structure des élevages et des systèmes d'élevage",
"download": "http://www.atol-ontology.com/public/telechargement/eol.owl",
"homepage": "http://www.atol-ontology.com",
"name": "Environment Ontology for Livestock",
"prefix": "eol",
"version": "2018-09-13"
},
"pattern": "^\\d{7}$",
"re3data": {
"description": "EOLβs platforms and instruments collect large and often unique data sets that must be validated, archived and made available to the research community. The goal of EOL data services is to advance science through delivering high-quality project data and metadata in ways that are as transparent, secure, and easily accessible as possible - today and into the future. By adhering to accepted standards in data formats and data services, EOL provides infrastructure to facilitate discovery and direct access to data and software from state-of-the-art commercial and locally-developed applications. EOLβs data services are committed to the highest standard of data stewardship from collection to validation to archival.",
"homepage": "https://www.eol.ucar.edu/",
"name": "EOL",
"prefix": "r3d100011663",
"synonyms": [
"Earth Observing Laboratory"
]
},
"uri_format": "http://purl.org/obo/owlEOL_$1"
},
"eolife": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A collaborative project intended to create an encyclopedia documenting all living species known to science",
"example": "1044544",
"fairsharing": {
"abbreviation": "EOL",
"contact": {
"email": "secretariat@eol.org",
"name": "EOL Secretariat",
"orcid": "0000-0002-9943-2342"
},
"description": "The Encyclopedia of Life (EOL) is a collaborative encyclopedia to describe all known living species. It identifies sources of biodiversity knowledge that are legally and practically shareable; integrates them with other sources and adds metadata; provides searching and other services; and collaborates with other projects to support data sharing.",
"homepage": "https://eol.org/",
"license": "https://creativecommons.org/licenses",
"name": "Encyclopedia of Life",
"prefix": "FAIRsharing.3J6NYn",
"publications": [],
"subjects": [
"Taxonomy",
"Ecology",
"Biodiversity",
"Biology"
],
"twitter": "eol"
},
"homepage": "https://eol.org",
"mappings": {
"fairsharing": "FAIRsharing.3J6NYn",
"re3data": "r3d100010229",
"wikidata": "P830"
},
"name": "Encyclopedia of Life",
"pattern": "^\\d+$",
"re3data": {
"description": "Our knowledge of the many life-forms on Earth - of animals, plants, fungi, protists and bacteria - is scattered around the world in books, journals, databases, websites, specimen collections, and in the minds of people everywhere. Imagine what it would mean if this information could be gathered together and made available to everyone β anywhere β at a momentβs notice. This dream is becoming a reality through the Encyclopedia of Life.",
"homepage": "https://eol.org/",
"name": "Encyclopedia of Life",
"prefix": "r3d100010229",
"synonyms": [
"Global access to knowledge about life on earth",
"eol"
],
"xrefs": {
"fairsharing": "FAIRsharing.3J6NYn",
"nlx": "149476",
"scr": "005905"
}
},
"uri_format": "https://eol.org/pages/$1",
"wikidata": {
"description": "eol.org item reference number",
"example": [
"1044544",
"110747",
"1174823",
"20831",
"327419"
],
"homepage": "http://eol.org/api/docs/pages",
"name": "Encyclopedia of Life ID",
"pattern": "^[1-9]\\d{0,7}$",
"prefix": "P830",
"uri_format": "https://eol.org/pages/$1"
}
},
"epcc": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Collection of European paediatric cardiac coding files",
"homepage": "https://www.aepc.org/european-paediatric-cardiac-coding",
"name": "European Paediatric Cardiac Codes",
"proprietary": true,
"references": [
"https://www.cambridge.org/core/journals/cardiology-in-the-young/article/abs/european-paediatric-cardiac-codes-the-long-list-with-icd9-icd10-crossmapping-and-crossmap-to-epcc-short-list/FCA4DFCCB661298294A3D113FC79D5BE"
]
},
"epd": {
"biocontext": {
"prefix": "EPD"
},
"contact": {
"email": "Philipp.Bucher@sib.swiss",
"name": "Philipp Bucher",
"orcid": "0000-0002-0816-7775"
},
"contributor_extras": [
{
"email": "sebastien.moretti@sib.swiss",
"github": "smoretti",
"name": "Sebastien Moretti",
"orcid": "0000-0003-3947-488X"
}
],
"edam": {
"description": "Identifier of an entry (promoter) from the EPD database.",
"name": "EPD",
"obsolete": false,
"prefix": "2386"
},
"fairsharing": {
"abbreviation": "EPD",
"contact": {
"email": "ask-epd@googlegroups.com",
"name": "Philipp Bucher",
"orcid": "0000-0002-0816-7775"
},
"description": "The Eukaryotic Promoter Database (EPD) provides accurate transcription start site (TSS) information for promoters of 15 model organisms, from human to yeast to the malaria parasite Plasmodium falciparum. While the original database was a manually curated database based on published experiments, new promoter collections are now produced entirely automatically (under the name βEPDnewβ) based on high-throughput transcript mapping data and high-quality gene annotation resources. Corresponding functional genomics data can be viewed in a genome browser, queried or analyzed via web interfaces, or exported in standard formats like FASTA or BED for subsequent analysis with other tools; of note, EPD is tightly integrated with two tool suites developed by our group: ChIP-Seq and Signal Search Analysis, for analysis of chromatin context and sequence motif respectively. EPD provides promoter viewers, designed with the aim of integrating and displaying information from different sources about, for instance, histone marks, transcription factor-binding sites or SNPs with known phenotypes. These viewers rely upon the UCSC genome browser as a visualization platform, which enables users to view data tracks from EPD jointly with tracks from UCSC or public track hubs.",
"homepage": "https://epd.epfl.ch/",
"name": "Eukaryotic Promoter Database",
"prefix": "FAIRsharing.yk1krv",
"publications": [
{
"doi": "10.1093/nar/26.1.353",
"pubmed_id": 9399872,
"title": "The Eukaryotic Promoter Database EPD."
},
{
"doi": "10.1093/nar/28.1.302",
"pubmed_id": 10592254,
"title": "The eukaryotic promoter database (EPD)."
},
{
"doi": "10.1093/nar/27.1.307",
"pubmed_id": 9847211,
"title": "The Eukaryotic Promoter Database (EPD): recent developments."
},
{
"doi": "10.1093/nar/14.24.10009",
"pubmed_id": 3808945,
"title": "Compilation and analysis of eukaryotic POL II promoter sequences"
},
{
"doi": "10.1093/nar/gku1111",
"pubmed_id": 25378343,
"title": "The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools."
},
{
"doi": "10.1093/nar/gks1233",
"pubmed_id": 23193273,
"title": "EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era."
},
{
"doi": "10.1093/nar/gkj146",
"pubmed_id": 16381980,
"title": "EPD in its twentieth year: towards complete promoter coverage of selected model organisms."
},
{
"doi": "10.1093/nar/gkh122",
"pubmed_id": 14681364,
"title": "The Eukaryotic Promoter Database EPD: the impact of in silico primer extension."
},
{
"doi": "10.1093/nar/30.1.322",
"pubmed_id": 11752326,
"title": "The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data."
},
{
"doi": "10.1093/nar/gkw1069",
"pubmed_id": 27899657,
"title": "The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms."
}
],
"subjects": [
"Bioinformatics",
"Biology"
]
},
"homepage": "https://epd.expasy.org/epd/",
"integbio": {
"alt_name": "The Eukaryotic Promoter Database",
"description": "EPD is a satabase of unique gene promoters. The database contains non-redundant sequences of promoters for genes transcribed by RNA polymerase II. Users can search the database, browse promoter elements, or download sequences via HTTP or FTP.",
"fairsharing": "biodbcore-000653",
"homepage": "https://epd.expasy.org/epd/",
"information_keywords": [
"Sequence"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "EPD",
"prefix": "nbdc00438",
"pubmeds": [
"16381980",
"14681364",
"11752326",
"10592254",
"9847211",
"9399872"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"mappings": {
"biocontext": "EPD",
"edam": "2386",
"fairsharing": "FAIRsharing.yk1krv",
"integbio": "nbdc00438",
"miriam": "epd",
"n2t": "epd",
"ncbi": "EPD",
"uniprot": "DB-0205"
},
"miriam": {
"deprecated": false,
"description": "The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.",
"homepage": "https://epd.expasy.org/epd",
"id": "00000408",
"name": "EPD",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z-_0-9]+$",
"prefix": "epd",
"sampleId": "TA_H3",
"uri_format": "https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0=$1"
},
"n2t": {
"description": "The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.",
"example": "TA_H3",
"homepage": "http://epd.vital-it.ch/",
"name": "EPD at Swiss Institute of Bioinformatics",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z-_0-9]+$",
"prefix": "epd",
"uri_format": "http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1"
},
"ncbi": {
"example": "EP00576",
"homepage": "http://epd.vital-it.ch/",
"name": "Eukaryotic Promoter Database",
"prefix": "EPD"
},
"publications": [
{
"doi": "10.1093/nar/27.1.307",
"pmc": "PMC148166",
"pubmed": "9847211",
"title": "The Eukaryotic Promoter Database (EPD): recent developments",
"year": 1999
},
{
"doi": "10.1093/nar/26.1.353",
"pmc": "PMC147208",
"pubmed": "9399872",
"title": "The Eukaryotic Promoter Database EPD",
"year": 1998
},
{
"doi": "10.1093/nar/14.24.10009",
"pmc": "PMC341352",
"pubmed": "3808945",
"title": "Compilation and analysis of eukaryotic POL II promoter sequences",
"year": 1986
},
{
"doi": "10.1093/nar/gkx807",
"pmc": "PMC5753345",
"pubmed": "28981707",
"title": "The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics",
"year": 2018
},
{
"doi": "10.1093/nar/gkw1069",
"pmc": "PMC5210552",
"pubmed": "27899657",
"title": "The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms",
"year": 2016
},
{
"doi": "10.1093/nar/gku1111",
"pmc": "PMC4383928",
"pubmed": "25378343",
"title": "The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools",
"year": 2014
},
{
"doi": "10.1093/nar/gks1233",
"pmc": "PMC3531148",
"pubmed": "23193273",
"title": "EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era",
"year": 2012
},
{
"doi": "10.1093/nar/gkj146",
"pmc": "PMC1347508",
"pubmed": "16381980",
"title": "EPD in its twentieth year: towards complete promoter coverage of selected model organisms",
"year": 2006
},
{
"doi": "10.1093/nar/gkh122",
"pmc": "PMC308856",
"pubmed": "14681364",
"title": "The Eukaryotic Promoter Database EPD: the impact of in silico primer extension",
"year": 2004
},
{
"doi": "10.1093/nar/30.1.322",
"pmc": "PMC99099",
"pubmed": "11752326",
"title": "The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data",
"year": 2002
},
{
"doi": "10.1093/nar/28.1.302",
"pmc": "PMC102462",
"pubmed": "10592254",
"title": "The eukaryotic promoter database (EPD)",
"year": 2000
}
],
"uniprot": {
"abbreviation": "EPD",
"category": "Proteomic databases",
"homepage": "https://www.peptracker.com/epd/analytics/",
"name": "Encyclopedia of Proteome Dynamics",
"prefix": "DB-0205",
"publications": [
{
"doi": "10.1093/nar/gkx807",
"pubmed": "28981707"
}
],
"uri_format": "https://www.peptracker.com/epd/analytics/?protein_id=$1"
},
"uri_format": "https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0=$1"
},
"epio": {
"aberowl": {
"description": "A application driven Epilepsy Ontology with official terms from the ILAE.",
"download_owl": "http://aber-owl.net/media/ontologies/EPIO/3/epio.owl",
"homepage": "https://github.com/SCAI-BIO/EpilepsyOntology",
"name": "Epilepsy Ontology",
"prefix": "EPIO"
},
"bioportal": {
"contact": {
"email": "alpha.tom.kodamullil@scai.fraunhofer.de",
"name": "Alpha Tom Kodanullil"
},
"description": "The Epilepsy Ontology (EPO) is an assembly of structured knowledge on various aspects of epilepsy, developed according to basic formal ontology (BFO) and Open Biological and Biomedical Ontology (OBO) Foundry principles. Entities and definitions are collected from the latest International League against Epilepsy (ILAE) classification, as well as from domain-specific ontologies such as Epilepsy Ontology (EPILONT), Epilepsy Syndrome Seizure Ontology (ESSO), Epilepsy Semiology(EPISEM) and Epilepsy and Seizure Ontology (EPSO) and scientific literature. This ontology is intended to be used for data management and for text mining purposes. The current release of the ontology is publicly available and is a community based effort to assemble various facets of the complex disease Epilepsy.",
"name": "EpilepsyOntology",
"prefix": "EPIO",
"version": "Version Release: 1.0.0"
},
"example": "0000011",
"mappings": {
"aberowl": "EPIO",
"bioportal": "EPIO",
"obofoundry": "epio",
"ontobee": "EPIO"
},
"obofoundry": {
"contact": "alpha.tom.kodamullil@scai.fraunhofer.de",
"contact.github": "akodamullil",
"contact.label": "Alpha Tom Kodamullil",
"contact.orcid": "0000-0001-9896-3531",
"depends_on": [
"bfo"
],
"deprecated": false,
"description": "A application driven Epilepsy Ontology with official terms from the ILAE.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/epio.owl",
"homepage": "https://github.com/SCAI-BIO/EpilepsyOntology",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Epilepsy Ontology",
"preferredPrefix": "EPIO",
"prefix": "epio",
"repository": "https://github.com/SCAI-BIO/EpilepsyOntology"
},
"ontobee": {
"library": "Library",
"name": "Epilepsy Ontology",
"prefix": "EPIO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/EPIO_$1"
},
"epo": {
"biocontext": {
"prefix": "EPO"
},
"contributor_extras": [
{
"github": "djinnome",
"name": "Jeremy Zucker",
"orcid": "0000-0002-7276-9009"
}
],
"download_owl": "https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/epidemiology-ontology/epo.owl",
"mappings": {
"biocontext": "EPO",
"obofoundry": "epo",
"ontobee": "EPO"
},
"obofoundry": {
"deprecated": true,
"description": "An ontology designed to support the semantic annotation of epidemiology resources",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/epo.owl",
"homepage": "https://code.google.com/p/epidemiology-ontology/",
"name": "Epidemiology Ontology",
"prefix": "epo"
},
"ontobee": {
"library": "Library",
"name": "Epidemiology Ontology",
"prefix": "EPO"
}
},
"epso": {
"aberowl": {
"description": "A application driven Epilepsy Ontology sith official terms from the ILAE.",
"download_owl": "http://aber-owl.net/media/ontologies/EPSO/3/epso.owl",
"name": "Epilepsy Ontology",
"prefix": "EPSO"
},
"bioportal": {
"contact": {
"email": "satyasahoo@ieee.org",
"name": "Satya Sahoo"
},
"description": "The Epilepsy Ontology (BioPortal ID: EpSO) is an application ontology developed to support epilepsy research, patient care, and health system management. The updated version of the Epilepsy Ontology adds Dravet Syndrome (DS) related terms covering both model systems and patients with DS. This version expands on the prior version of the ontology, which focused on neuropathology terms, including immunohistochemistry, microscopy, and anatomical description, related to epilepsy. This work has been funded in part by the Dravet Syndrome Foundation (DSF), International League Against Epilepsy (ILAE), and the US National Institutes of Health (NIH). Some of the funding agencies retain intellectual ownership of the ontology, together with the Case Western Reserve University and other collaborating institutions. Contributors: Satya S. Sahoo, Jeffrey Buchhalter, Samden D. Lhatoo, Katja Kobow, Deepak K. Gupta, Alireza Bozorgi, Aman Dabir, Bilal Gonen, Hans O. Luders, Kenneth Loparo, Veronica Hood",
"homepage": "https://bmhinformatics.case.edu/",
"name": "Epilepsy and Seizure Ontology",
"prefix": "EPSO",
"publication": "https://bmhinformatics.case.edu/",
"version": "3"
},
"contact": {
"email": "satyasahoo@ieee.org",
"name": "Satya S. Sahoo",
"orcid": "0000-0001-9190-4256"
},
"example": "0000400",
"fairsharing": {
"abbreviation": "EPSO",
"description": "The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. ",
"domains": [
"Epilepsy",
"Patient care"
],
"homepage": "https://bioportal.bioontology.org/ontologies/EPSO",
"license": "CC BY-SA 3.0",
"name": "Epilepsy and Seizure Ontology",
"prefix": "FAIRsharing.ttprgy",
"publications": [
{
"doi": "10.1136/amiajnl-2013-001696",
"title": "Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care",
"year": 2013
}
],
"subjects": [
"Neurology"
]
},
"homepage": "http://prism.case.edu/prism/index.php/EpilepsyOntology",
"mappings": {
"aberowl": "EPSO",
"bioportal": "EPSO",
"fairsharing": "FAIRsharing.ttprgy",
"ontobee": "EPSO"
},
"ontobee": {
"library": "Library",
"name": "Epilepsy Ontology",
"prefix": "EPSO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1136/amiajnl-2013-001696",
"pmc": "PMC3912711",
"pubmed": "23686934",
"title": "Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care",
"year": 2013
}
],
"uri_format": "http://www.case.edu/EpilepsyOntology.owl#$1"
},
"erm": {
"cheminf": {
"description": "Identifier used by the European Registry of Materials (https://nanocommons.github.io/identifiers/).",
"name": "European Registry of Materials",
"obsolete": false,
"prefix": "000569"
},
"contact": {
"email": "egon.willighagen@gmail.com",
"github": "egonw",
"name": "Egon Willighagen",
"orcid": "0000-0001-7542-0286"
},
"download_rdf": "https://nanocommons.github.io/identifiers/registry",
"fairsharing": {
"abbreviation": "ERM Identifier",
"contact": {
"email": "egon.willighagen@maastrichtuniversity.nl",
"name": "Egon Willighagen",
"orcid": "0000-0001-7542-0286"
},
"description": "Identifier project to uniquely identify nanomaterials, allowing them to identify materials in experimental designs, data, reports, project deliverables, and scholarly publications.",
"domains": [
"Chemical entity"
],
"homepage": "https://nanocommons.github.io/identifiers/",
"license": "CC0-1.0",
"name": "European Registry of Materials Identifier",
"prefix": "FAIRsharing.c26a4e",
"publications": [
{
"doi": "10.1186/s13321-022-00614-7",
"title": "European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials",
"year": 2022
}
],
"subjects": [
"Nanotechnology",
"Materials Informatics"
]
},
"mappings": {
"cheminf": "000569",
"fairsharing": "FAIRsharing.c26a4e",
"miriam": "erm",
"n2t": "erm"
},
"miriam": {
"deprecated": false,
"description": "The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project.",
"homepage": "https://nanocommons.github.io/identifiers/",
"id": "00000763",
"name": "European Registry of Materials",
"namespaceEmbeddedInLui": false,
"pattern": "^ERM[0-9]{8}$",
"prefix": "erm",
"sampleId": "ERM00000044",
"uri_format": "https://nanocommons.github.io/identifiers/registry#$1"
},
"n2t": {
"description": "The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project.",
"example": "ERM00000044",
"homepage": "https://nanocommons.github.io/identifiers/",
"name": "European Registry of Materials",
"namespaceEmbeddedInLui": false,
"pattern": "^ERM[0-9]{8}$",
"prefix": "erm",
"uri_format": "https://nanocommons.github.io/identifiers/registry#$1"
},
"providers": [
{
"code": "erm.database",
"description": "Database that provides links to onlnie information about materials with an European Registry of Materials (ERM) identifier",
"homepage": "https://nanocommons.github.io/erm-database/",
"name": "ERM Identifier Database",
"uri_format": "https://nanocommons.github.io/erm-database/substance/erm/$1"
}
],
"publications": [
{
"doi": "10.1186/s13321-022-00614-7",
"pmc": "PMC9400299",
"pubmed": "36002868",
"title": "European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials",
"year": 2022
}
],
"twitter": "nanocommons"
},
"ero": {
"aberowl": {
"description": "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.",
"download_owl": "http://aber-owl.net/media/ontologies/ERO/15/ero.owl",
"homepage": "https://open.med.harvard.edu/wiki/display/eaglei/Ontology",
"name": "eagle-i resource ontology",
"prefix": "ERO"
},
"biocontext": {
"prefix": "ERO"
},
"bioportal": {
"contact": {
"email": "carlotorniai@gmail.com",
"name": "Carlo Torniai"
},
"description": "This ontology models research resources such instruments. protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/).",
"homepage": "http://code.google.com/p/eagle-i/",
"name": "Eagle-I Research Resource Ontology",
"prefix": "ERO",
"publication": "http://code.google.com/p/eagle-i/wiki/Publications",
"version": "2013-08-02"
},
"example": "0001655",
"fairsharing": {
"abbreviation": "ERO",
"contact": {
"email": "carlotorniai@gmail.com",
"name": "Carlo Torniai",
"orcid": "0000-0002-3734-1859"
},
"description": "A unique feature of the eagle-i software is that the data collection and search tools are completely driven by ontologies. These ontologies are a set of modules that are written in the OWL language and edited and managed using ProtΓ©gΓ©. Beginning in 2009, the eagle-i Research Resource Ontology (ERO) was developed alongside the eagle-i applications to model various biomedical research resources such as instruments, Core Facilities, protocols, reagents, animal models and biospecimens. It has now been integrated into the VIVO-ISF Ontology, which leverages and expands upon both the eagle-i and VIVO ontologies to create a semantic framework that describes not only scientific resources but research activities and clinical activities.",
"domains": [
"Reagent",
"Biological sample",
"Protocol",
"Study design"
],
"homepage": "https://open.catalyst.harvard.edu/wiki/display/eaglei/Ontology",
"name": "eagle-i Research Resource Ontology",
"prefix": "FAIRsharing.nwgynk",
"publications": [
{
"doi": "10.1109/jcdl.2017.7991571",
"pubmed": "29599662",
"title": "Automating data citation: the eagle-i experience",
"year": 2018
},
{
"doi": "10.1093/database/bar067",
"pubmed": "22434835",
"title": "Research resources: curating the new eagle-i discovery system",
"year": 2012
}
],
"subjects": [
"Life Science",
"Biomedical Science"
]
},
"mappings": {
"aberowl": "ERO",
"biocontext": "ERO",
"bioportal": "ERO",
"fairsharing": "FAIRsharing.nwgynk",
"obofoundry": "ero",
"ols": "ero",
"ontobee": "ERO"
},
"obofoundry": {
"contact": "Marc_Ciriello@hms.harvard.edu",
"contact.label": "Marc Ciriello",
"deprecated": true,
"description": "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.",
"domain": "information",
"download.owl": "http://purl.obolibrary.org/obo/ero.owl",
"homepage": "https://open.med.harvard.edu/wiki/display/eaglei/Ontology",
"license": "CC BY 2.0",
"license.url": "https://creativecommons.org/licenses/by/2.0/",
"name": "eagle-i resource ontology",
"prefix": "ero"
},
"ols": {
"description": "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.",
"download": "http://purl.obolibrary.org/obo/ero.owl",
"homepage": "https://open.med.harvard.edu/wiki/display/eaglei/Ontology",
"name": "eagle-i resource ontology",
"prefix": "ero",
"version": "2016-07-27"
},
"ontobee": {
"library": "Library",
"name": "eagle-i resource ontology",
"prefix": "ERO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1109/jcdl.2017.7991571",
"pmc": "PMC5868434",
"pubmed": "29599662",
"title": "Automating data citation: the eagle-i experience",
"year": 2017
},
{
"doi": "10.1093/database/bar067",
"pmc": "PMC3308157",
"pubmed": "22434835",
"title": "Research resources: curating the new eagle-i discovery system",
"year": 2012
}
]
},
"eropmoscow": {
"integbio": {
"alt_name": "Endogenous Regulatory OligoPeptide knowledgebase",
"description": "EROP(Endogenous Regulatory OligoPeptide)-Moscow is a database that provides information on a collection of oligopeptide sequences. \nThese sequences contain any number of amino acid residues, from 2 to 50.\nAnnotations of a high level of accuracy, such as an oligopeptide's source, function, structure and post-translational modifications are provided.\nThis database contains information on 10,229 sequences. \nInformation can be retrieved by entering the EROP-accession ID, the name of the oligopeptide, its function, the family name and/or the biological classification (oligopeptide source). \nThe database may also be searched by entering physicochemical features, for instance, the amino acid number, its sequence or molecular mass.\nThis version was released on 21 August 2010.",
"homepage": "http://erop.inbi.ras.ru/",
"information_keywords": [
"Sequence"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "EROP-Moscow",
"prefix": "nbdc00265",
"pubmeds": [
"16381860"
],
"status": "Active",
"target_keywords": [
"Protein",
"Carbohydrate"
]
},
"mappings": {
"integbio": "nbdc00265",
"prefixcommons": "eropmoscow"
},
"prefixcommons": {
"description": "EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence database which strives to provide a high level of annotations (such as descriptions of the structure of an oligopeptide, its source and function, post-translational modifications, etc.).",
"example": "E00002",
"homepage": "http://erop.inbi.ras.ru",
"keywords": [
"protein"
],
"name": "Endogenous Regulatory OligoPeptide knowledgebase-Moscow",
"pattern": "^E\\d+$",
"prefix": "eropmoscow",
"uri_format": "http://erop.inbi.ras.ru/result2.php?PepName=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"erv": {
"biocontext": {
"prefix": "ERV"
},
"mappings": {
"biocontext": "ERV",
"miriam": "erv",
"n2t": "erv"
},
"miriam": {
"deprecated": false,
"description": "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features.",
"homepage": "https://herv.img.cas.cz/",
"id": "00000619",
"name": "Human Endogenous Retrovirus Database",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9\\-\\_]+$",
"prefix": "erv",
"sampleId": "THE1B",
"uri_format": "https://herv.img.cas.cz/s/$1"
},
"n2t": {
"description": "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features.",
"example": "THE1B",
"homepage": "https://herv.img.cas.cz/",
"name": "Human Endogenous Retrovirus Database",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9\\-\\_]+$",
"prefix": "erv",
"uri_format": "https://herv.img.cas.cz/s/$1"
}
},
"esldb": {
"mappings": {
"prefixcommons": "esldb"
},
"prefixcommons": {
"description": "eSLDB is a database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.",
"example": "HS000015122",
"homepage": "http://gpcr.biocomp.unibo.it/esldb",
"keywords": [
"protein"
],
"name": "eukaryotic Subcellular Localization database",
"pattern": "^[A-Z]+\\d+$",
"prefix": "esldb",
"uri_format": "http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"estdab": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://www.ebi.ac.uk/ipd/estdab/",
"name": "European Searchable Tumour Line Database",
"prefix": "ESTDAB"
},
"comment": "Website is dead",
"deprecated": true,
"example": "046",
"mappings": {
"cellosaurus": "ESTDAB"
},
"owners": [
{
"name": "European Bioinformatics Institute",
"partnered": false,
"ror": "02catss52"
}
],
"pattern": "^\\d{3}$",
"uri_format": "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1"
},
"eu89h": {
"biocontext": {
"prefix": "EU89H"
},
"mappings": {
"biocontext": "EU89H",
"miriam": "eu89h",
"n2t": "eu89h"
},
"miriam": {
"deprecated": false,
"description": "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union.",
"homepage": "http://data.jrc.ec.europa.eu/",
"id": "00000644",
"name": "JRC Data Catalogue",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z0-9\\-_]+$",
"prefix": "eu89h",
"sampleId": "jrc-eurl-ecvam-chemagora",
"uri_format": "http://data.europa.eu/89h/$1"
},
"n2t": {
"description": "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union.",
"example": "jrc-eurl-ecvam-chemagora",
"homepage": "http://data.jrc.ec.europa.eu/",
"name": "JRC Data Catalogue",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z0-9\\-_]+$",
"prefix": "eu89h",
"uri_format": "http://data.europa.eu/89h/$1"
}
},
"euclinicaltrials": {
"biocontext": {
"prefix": "EUCLINICALTRIALS"
},
"mappings": {
"biocontext": "EUCLINICALTRIALS",
"miriam": "euclinicaltrials",
"n2t": "euclinicaltrials"
},
"miriam": {
"deprecated": false,
"description": "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.",
"homepage": "https://www.clinicaltrialsregister.eu/",
"id": "00000536",
"name": "EU Clinical Trials",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{4}\\-\\d{6}\\-\\d{2}$",
"prefix": "euclinicaltrials",
"sampleId": "2008-005144-16",
"uri_format": "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1"
},
"n2t": {
"description": "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004. It also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.",
"example": "2008-005144-16",
"homepage": "https://www.clinicaltrialsregister.eu/",
"name": "EU Clinical Trials at European Medicines Agency",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{4}\\-\\d{6}\\-\\d{2}$",
"prefix": "euclinicaltrials",
"uri_format": "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1"
},
"synonyms": [
"EUCTR"
]
},
"eugenes": {
"fairsharing": {
"abbreviation": "euGenes",
"contact": {
"email": "eugenes@iubio.bio.indiana.edu",
"name": "Don Gilbert",
"orcid": "0000-0002-6646-7274"
},
"description": "euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information.",
"homepage": "http://eugenes.org/",
"name": "Eukaryotic Genes",
"prefix": "FAIRsharing.7fc5y6",
"publications": [
{
"doi": "10.1093/nar/30.1.145",
"pubmed_id": 11752277,
"title": "euGenes: a eukaryote genome information system."
}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"fairsharing": "FAIRsharing.7fc5y6",
"prefixcommons": "eugenes"
},
"prefixcommons": {
"description": "euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information.",
"example": "MGgn0008978",
"homepage": "http://eugenes.org/",
"keywords": [
"genome",
"ontology"
],
"name": "Eukaryotic Genes",
"pattern": "^[A-Z]+\\d+$",
"prefix": "eugenes",
"synonyms": [
"eugenes:"
],
"uri_format": "http://eugenes.org:7072/.bin/fbidq.html?$1"
},
"publications": [
{
"doi": "10.1093/nar/30.1.145",
"pmc": "PMC99146",
"pubmed": "11752277",
"title": "euGenes: a eukaryote genome information system",
"year": 2002
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"eupath": {
"aberowl": {
"description": "An ontology is developed to support Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org).",
"download_owl": "http://aber-owl.net/media/ontologies/EUPATH/20/eupath.owl",
"homepage": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology",
"name": "VEuPathDB ontology",
"prefix": "EUPATH"
},
"biocontext": {
"prefix": "EUPATH"
},
"bioportal": {
"contact": {
"email": "stoeckrt@pennmedicine.upenn.edu",
"name": "Chris Stoeckert"
},
"description": "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.",
"homepage": "https://github.com/EuPath-ontology/EuPath-ontology",
"name": "VEuPathDB Ontology",
"prefix": "EUPATH",
"publication": "https://pdfs.semanticscholar.org/888e/a51dbb138122d39c42f863f2a1ada7976db4.pdf",
"version": "2023-05-30"
},
"example": "0010316",
"fairsharing": {
"abbreviation": "VEuPathDB Ontology",
"description": "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource. The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.",
"domains": [
"Microbiome"
],
"homepage": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology",
"license": "CC-BY-4.0",
"name": "Eukaryotic Pathogen, Host & Vector Genomics Resource Ontology",
"prefix": "FAIRsharing.9rhr9j",
"repository": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology",
"subjects": [
"Functional Genomics",
"Biomedical Science",
"Epidemiology",
"Population Genetics"
]
},
"mappings": {
"aberowl": "EUPATH",
"biocontext": "EUPATH",
"bioportal": "EUPATH",
"fairsharing": "FAIRsharing.9rhr9j",
"obofoundry": "eupath",
"ols": "eupath",
"ontobee": "EUPATH"
},
"obofoundry": {
"appears_in": [
"scdo"
],
"contact": "jiezhen@med.umich.edu",
"contact.github": "zhengj2007",
"contact.label": "Jie Zheng",
"contact.orcid": "0000-0002-2999-0103",
"deprecated": true,
"description": "An ontology is developed to support Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org).",
"domain": "organisms",
"download.owl": "http://purl.obolibrary.org/obo/eupath.owl",
"homepage": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"logo": "https://raw.githubusercontent.com/EuPathDB/communitysite/master/assets/images/VEuPathDB-logo-s.png",
"name": "VEuPathDB ontology",
"preferredPrefix": "EUPATH",
"prefix": "eupath",
"publications": [
{
"id": "https://doi.org/10.5281/zenodo.6685957",
"title": "Malaria study data integration and information retrieval based on OBO Foundry ontologies."
}
],
"repository": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology"
},
"ols": {
"description": "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.",
"download_owl": "http://purl.obolibrary.org/obo/eupath.owl",
"homepage": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology",
"name": "VEuPathDB Ontology",
"prefix": "eupath",
"version": "2023-05-30",
"version.iri": "http://purl.obolibrary.org/obo/eupath/2023-05-30/eupath.owl"
},
"ontobee": {
"library": "Library",
"name": "VEuPathDB ontology",
"prefix": "EUPATH"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.5281/zenodo.6685957",
"title": "Malaria study data integration and information retrieval based on OBO Foundry ontologies",
"year": 2016
}
],
"uri_format": "http://purl.obolibrary.org/obo/EUPATH_$1"
},
"eurofir": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries.",
"homepage": "https://www.eurofir.org",
"name": "European Food Information Resource Network",
"proprietary": true
},
"ev": {
"appears_in": [
"cl"
],
"biocontext": {
"prefix": "EV"
},
"example": "0100011",
"mappings": {
"biocontext": "EV",
"obofoundry": "ev",
"prefixcommons": "evoc"
},
"obofoundry": {
"contact": "evoc@sanbi.ac.za",
"contact.label": "eVOC mailing list",
"deprecated": true,
"domain": "anatomy and development",
"name": "eVOC (Expressed Sequence Annotation for Humans)",
"prefix": "ev"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1013",
"description": "Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment.",
"example": "EV_0100011",
"homepage": "http://www.evocontology.org/",
"keywords": [
"obo",
"anatomy",
"cell",
"development",
"experiment"
],
"name": "eVOC (Expressed Sequence Annotation for Humans)",
"pattern": "^EV_\\d+$",
"prefix": "evoc",
"synonyms": [
"ev"
],
"uri_format": "http://www.evocontology.org/site/Main/BrowseEvoc?x_termid=$1"
},
"references": [
"https://twitter.com/Bgeedb/status/1350124337815281664"
]
},
"evm": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"name": "eVOC mouse development stage",
"references": [
"https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r229"
]
},
"exac.gene": {
"biocontext": {
"prefix": "EXAC.GENE"
},
"mappings": {
"biocontext": "EXAC.GENE",
"miriam": "exac.gene",
"n2t": "exac.gene"
},
"miriam": {
"deprecated": false,
"description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information.",
"homepage": "http://exac.broadinstitute.org/",
"id": "00000548",
"name": "ExAC Gene",
"namespaceEmbeddedInLui": false,
"pattern": "^ENSG\\d{11}$",
"prefix": "exac.gene",
"sampleId": "ENSG00000169174",
"uri_format": "http://exac.broadinstitute.org/gene/$1"
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"n2t": {
"description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information.",
"example": "ENSG00000169174",
"homepage": "http://exac.broadinstitute.org/",
"name": "ExAC Gene at Exome Aggregation Consortium",
"namespaceEmbeddedInLui": false,
"pattern": "^ENSG\\d{11}$",
"prefix": "exac.gene",
"uri_format": "http://exac.broadinstitute.org/gene/$1"
}
},
"exac.transcript": {
"biocontext": {
"prefix": "EXAC.TRANSCRIPT"
},
"mappings": {
"biocontext": "EXAC.TRANSCRIPT",
"miriam": "exac.transcript",
"n2t": "exac.transcript"
},
"miriam": {
"deprecated": false,
"description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information.",
"homepage": "http://exac.broadinstitute.org/",
"id": "00000547",
"name": "ExAC Transcript",
"namespaceEmbeddedInLui": false,
"pattern": "^ENST\\d{11}$",
"prefix": "exac.transcript",
"sampleId": "ENST00000407236",
"uri_format": "http://exac.broadinstitute.org/transcript/$1"
},
"n2t": {
"description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information.",
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"name": "ExAC Transcript at Exome Aggregation Consortium",
"namespaceEmbeddedInLui": false,
"pattern": "^ENST\\d{11}$",
"prefix": "exac.transcript",
"uri_format": "http://exac.broadinstitute.org/transcript/$1"
}
},
"exac.variant": {
"biocontext": {
"prefix": "EXAC.VARIANT"
},
"mappings": {
"biocontext": "EXAC.VARIANT",
"miriam": "exac.variant",
"n2t": "exac.variant"
},
"miriam": {
"deprecated": false,
"description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information.",
"homepage": "http://exac.broadinstitute.org/",
"id": "00000541",
"name": "ExAC Variant",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$",
"prefix": "exac.variant",
"sampleId": "22-46615880-T-C",
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},
"n2t": {
"description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information.",
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"name": "ExAC Variant at Exome Aggregation Consortium",
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"pattern": "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$",
"prefix": "exac.variant",
"uri_format": "http://exac.broadinstitute.org/variant/$1"
}
},
"exo": {
"aberowl": {
"description": "Vocabularies for describing exposure data to inform understanding of environmental health.",
"download_owl": "http://aber-owl.net/media/ontologies/EXO/15/exo.owl",
"homepage": "https://github.com/CTDbase/exposure-ontology",
"name": "Exposure ontology",
"prefix": "EXO"
},
"biocontext": {
"prefix": "EXO"
},
"biolink": {
"is_identifiers": false,
"is_obo": true,
"prefix": "ExO",
"uri_format": "http://purl.obolibrary.org/obo/ExO_$1"
},
"bioportal": {
"contact": {
"email": "annethessen@gmail.com",
"name": "Anne Thessen"
},
"description": "Significant progress has been made over the last several years in collecting and improving access to genomic, toxicology, and health data to promote understanding about environmental influences on human health. The resulting information resources, however, lack extensive and reliable exposure data, which are required to translate molecular insights, elucidate environmental contributions to diseases, and assess human health risks at the individual and population levels. We report our development of an Exposure Ontology, ExO, designed to address this information gap by facilitating centralization and integration of exposure data to inform understanding of environmental health. Like other widely used ontologies, ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics.",
"homepage": "https://github.com/CTDbase/exposure-ontology",
"name": "Exposure Ontology",
"prefix": "EXO",
"version": "releases/2022-06-29"
},
"example": "0000078",
"fairsharing": {
"abbreviation": "ExO",
"description": "Exposure Ontology (ExO) is designed to facilitate the centralization and integration of exposure data to inform understanding of environmental health. ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics.",
"domains": [
"Disease",
"Exposure"
],
"homepage": "https://github.com/CTDbase/exposure-ontology",
"license": "CC-BY-4.0",
"name": "Exposure Ontology",
"prefix": "FAIRsharing.6hna78",
"publications": [
{
"doi": "10.1021/es2033857",
"pubmed": "22324457",
"title": "Providing the missing link: the exposure science ontology ExO",
"year": 2012
}
],
"repository": "https://github.com/CTDbase/exposure-ontology",
"subjects": [
"Environmental Science",
"Epigenetics",
"Toxicology"
]
},
"mappings": {
"aberowl": "EXO",
"biocontext": "EXO",
"biolink": "ExO",
"bioportal": "EXO",
"fairsharing": "FAIRsharing.6hna78",
"obofoundry": "exo",
"ols": "exo",
"ontobee": "ExO"
},
"obofoundry": {
"appears_in": [
"ecto",
"scdo"
],
"contact": "annethessen@gmail.com",
"contact.github": "diatomsRcool",
"contact.label": "Anne Thessen",
"contact.orcid": "0000-0002-2908-3327",
"deprecated": false,
"description": "Vocabularies for describing exposure data to inform understanding of environmental health.",
"domain": "health",
"download.obo": "http://purl.obolibrary.org/obo/exo.obo",
"download.owl": "http://purl.obolibrary.org/obo/exo.owl",
"homepage": "https://github.com/CTDbase/exposure-ontology",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Exposure ontology",
"preferredPrefix": "ExO",
"prefix": "exo",
"repository": "https://github.com/CTDbase/exposure-ontology"
},
"ols": {
"description": "ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics.",
"download_owl": "http://purl.obolibrary.org/obo/exo.owl",
"homepage": "https://github.com/CTDbase/exposure-ontology",
"name": "Exposure ontology (ExO)",
"prefix": "exo",
"version": "2022-06-29",
"version.iri": "http://purl.obolibrary.org/obo/exo/releases/2022-06-29/exo.owl"
},
"ontobee": {
"library": "Library",
"name": "Exposure ontology",
"prefix": "ExO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1021/es2033857",
"pmc": "PMC3314380",
"pubmed": "22324457",
"title": "Providing the missing link: the exposure science ontology ExO",
"year": 2012
}
],
"synonyms": [
"ExO"
],
"uri_format": "http://purl.obolibrary.org/obo/ExO_$1"
},
"fabio": {
"aberowl": {
"description": "This file is imported by the vivo-core-public-1.5.owl file. It contains terms relating to documents from the http://purl.org/spar/fabio/ namespace that are included in the VIVO ontology. FaBiO is a FRBR-aligned Bibliographic Ontology that is part of the Semantic Publishing and Referencing (SPAR) suite of ontologies.",
"download_owl": "http://aber-owl.net/media/ontologies/FaBiO/1/fabio.owl",
"homepage": "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology",
"name": "FaBiO (bibliographic)",
"prefix": "FaBiO",
"version": "1.5"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "fabio",
"uri_format": "http://purl.org/spar/fabio/$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references.",
"example": "d4e2515",
"fairsharing": {
"abbreviation": "FaBiO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "FaBiO, the FRBR-aligned Bibliographic Ontology, is an ontology for recording and publishing on the Semantic Web descriptions of entities that are published or potentially publishable, and that contain or are referred to by bibliographic references, or entities used to define such bibliographic references. FaBiO entities are primarily textual publications such as books, magazines, newspapers and journals, and items of their content such as poems, conference papers and editorials. However, they also include blogs, web pages, datasets, computer algorithms, experimental protocols, formal specifications and vocabularies, legal records, governmental papers, technical and commercial reports and similar publications, and also anthologies, catalogues and similar collections.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Publication",
"Protocol",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/fabio",
"license": "CC-BY-4.0",
"name": "FRBR-aligned Bibliographic Ontology",
"prefix": "FAIRsharing.2f3180",
"publications": [
{
"doi": "10.1016/j.websem.2012.08.001",
"title": "FaBiO and CiTO: Ontologies for describing bibliographic resources and citations",
"year": 2012
}
],
"repository": "https://github.com/sparontologies/fabio",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"homepage": "https://github.com/sparontologies/fabio",
"lov": {
"description": "FaBiO, the FRBR-aligned Bibliographic Ontology, is an ontology for recording and publishing on the Semantic Web bibliographic records of scholarly endeavours. It forms part of SPAR, a suite of Semantic Publishing and Referencing Ontologies.",
"homepage": "https://github.com/SPAROntologies/fabio",
"keywords": [
"SPAR"
],
"modified": "2019-02-19",
"name": "FRBR-aligned Bibliographic Ontology",
"prefix": "fabio",
"uri_prefix": "http://purl.org/spar/fabio/$1"
},
"mappings": {
"aberowl": "FaBiO",
"biolink": "fabio",
"fairsharing": "FAIRsharing.2f3180",
"lov": "fabio"
},
"name": "FaBiO, the FRBR-aligned Bibliographic Ontology",
"publications": [
{
"doi": "10.1016/j.websem.2012.08.001",
"title": "FaBiO and CiTO: Ontologies for describing bibliographic resources and citations",
"year": 2012
}
],
"rdf_uri_format": "http://purl.org/spar/fabio/$1",
"repository": "https://github.com/sparontologies/fabio",
"uri_format": "https://sparontologies.github.io/fabio/current/fabio.html#$1"
},
"facebase": {
"biocontext": {
"prefix": "FACEBASE"
},
"contact": {
"email": "ychai@usc.edu",
"name": "Yang Chai",
"orcid": "0000-0003-2477-7247"
},
"fairsharing": {
"abbreviation": "FaceBase",
"description": "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.",
"homepage": "https://www.facebase.org/",
"license": "https://www.facebase.org/methods/policies",
"name": "FaceBase",
"prefix": "FAIRsharing.mqvqde",
"publications": [
{
"doi": "10.1242/dev.191213",
"pubmed_id": null,
"title": "FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research"
}
],
"subjects": [
"Anatomy",
"Medicine",
"Epigenetics",
"Genetics",
"Developmental Biology"
]
},
"integbio": {
"description": "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.",
"fairsharing": "FAIRsharing.mqvqde",
"homepage": "https://www.facebase.org/",
"information_keywords": [
"Interaction/Pathway",
"Expression",
"Phenotype",
"Image/Movie",
"Method",
"Bibliography/Documents"
],
"maintainer": "USC (University of Southern California)",
"name": "FaceBase",
"prefix": "nbdc02022",
"status": "Active",
"target_keywords": [
"Protein",
"Genome/Gene",
"RNA",
"Health/Disease"
]
},
"mappings": {
"biocontext": "FACEBASE",
"fairsharing": "FAIRsharing.mqvqde",
"integbio": "nbdc02022",
"miriam": "facebase",
"n2t": "facebase",
"re3data": "r3d100013263"
},
"miriam": {
"deprecated": false,
"description": "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.",
"homepage": "https://www.facebase.org",
"id": "00000642",
"name": "FaceBase Data Repository",
"namespaceEmbeddedInLui": false,
"pattern": "^FB\\d{8}$",
"prefix": "facebase",
"sampleId": "FB00000917",
"uri_format": "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1"
},
"n2t": {
"description": "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.",
"example": "FB00000917",
"homepage": "https://www.facebase.org",
"name": "FaceBase Data Repository",
"namespaceEmbeddedInLui": false,
"pattern": "^FB\\d{8}$",
"prefix": "facebase",
"uri_format": "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1"
},
"publications": [
{
"doi": "10.1242/dev.191213",
"pmc": "PMC7522026",
"pubmed": "32958507",
"title": "FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research",
"year": 2020
}
],
"re3data": {
"description": "FaceBase is a collaborative NIDCR-funded project that houses comprehensive data in support of advancing research into craniofacial development and malformation. It serves as a community resource by curating large datasets of a variety of types from the craniofacial research community and sharing them via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this project is to facilitate cooperation and collaboration between the central coordinating center (ie, the Hub) and the craniofacial research community.",
"homepage": "https://www.facebase.org",
"name": "FaceBase",
"prefix": "r3d100013263",
"xrefs": {
"fairsharing": "FAIRsharing.mqvqde",
"nlx": "151372",
"scr": "005998"
}
}
},
"fairsharing": {
"biocontext": {
"prefix": "FAIRSHARING"
},
"example_extras": [
"FAIRsharing.CugtbQ"
],
"fairsharing": {
"abbreviation": "FAIRsharing",
"contact": {
"email": "allyson.lister@oerc.ox.ac.uk",
"github": "allysonlister",
"name": "Allyson Lister",
"orcid": "0000-0002-7702-4495"
},
"description": "FAIRsharing is a FAIR-supporting resource that provides an informative and educational registry on data standards, databases, repositories and policy, alongside search and visualization tools and services that interoperate with other FAIR-enabling resources. FAIRsharing guides consumers to discover, select and use standards, databases, repositories and policy with confidence, and producers to make their resources more discoverable, more widely adopted and cited. Each record in FAIRsharing is curated in collaboration with the maintainers of the resource themselves, ensuring that the metadata in the FAIRsharing registry is accurate and timely. Every record is manually reviewed at least once a year. Records can be collated into collections, based on a project, society or organisation, or Recommendations, where they are collated around a policy, such as a journal or funder data policy.",
"homepage": "https://www.FAIRsharing.org",
"license": "CC-BY-4.0",
"name": "FAIRsharing",
"prefix": "FAIRsharing.2abjs5",
"publications": [
{
"doi": "10.1038/s41587-019-0080-8",
"pubmed_id": 30940948,
"title": "FAIRsharing as a community approach to standards, repositories and policies."
},
{
"doi": "10.1093/database/baw075",
"pubmed_id": 27189610,
"title": "BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences."
},
{
"doi": "10.5281/zenodo.5106255",
"pubmed_id": null,
"title": "FAIRsharing, a FAIR-enabling service for repositories, standards and policies"
}
],
"repository": "https://github.com/FAIRsharing",
"subjects": [
"Environmental Science",
"Policy",
"Humanities",
"Data Governance",
"Natural Science",
"Earth Science",
"Agriculture",
"Life Science",
"Database Management",
"Biomedical Science",
"Ontology and Terminology"
],
"twitter": "fairsharing_org"
},
"mappings": {
"biocontext": "FAIRSHARING",
"fairsharing": "FAIRsharing.2abjs5",
"miriam": "fairsharing",
"n2t": "fairsharing",
"re3data": "r3d100010142"
},
"mastodon": "fairsharing@fediscience.org",
"miriam": {
"deprecated": false,
"description": "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies.",
"homepage": "https://fairsharing.org/",
"id": "00000364",
"name": "FAIRsharing",
"namespaceEmbeddedInLui": false,
"pattern": "^bsg-[dscp]?\\d{6}$",
"prefix": "fairsharing",
"sampleId": "bsg-000052",
"uri_format": "https://fairsharing.org/$1"
},
"n2t": {
"description": "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies.",
"example": "bsg-000052",
"homepage": "https://fairsharing.org/",
"name": "FAIRSharing at University of Oxford",
"namespaceEmbeddedInLui": false,
"pattern": "^bsg-[dscp]?\\d{6}$",
"prefix": "fairsharing",
"uri_format": "https://fairsharing.org/$1"
},
"pattern": "^(bsg-[dscp]?\\d{6})|(FAIRsharing\\.\\w+)$",
"publications": [
{
"doi": "10.1038/s41587-019-0080-8",
"pmc": "PMC6785156",
"pubmed": "30940948",
"title": "FAIRsharing as a community approach to standards, repositories and policies",
"year": 2019
},
{
"doi": "10.1093/database/baw075",
"pmc": "PMC4869797",
"pubmed": "27189610",
"title": "BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences",
"year": 2016
},
{
"doi": "10.5281/zenodo.5106255",
"title": "FAIRsharing, a FAIR-enabling service for repositories, standards and policies",
"year": 2021
}
],
"re3data": {
"description": "FAIRsharing is a web-based, searchable portal of three interlinked registries, containing both in-house and crowdsourced manually curated descriptions of standards, databases and data policies, combined with an integrated view across all three types of resource. By registering your resource on FAIRsharing, you not only gain credit for your work, but you increase its visibility outside of your direct domain, so reducing the potential for unnecessary reinvention and proliferation of standards and databases.",
"homepage": "https://fairsharing.org/",
"name": "FAIRsharing",
"prefix": "r3d100010142",
"synonyms": [
"formerly: biosharing"
],
"xrefs": {
"fairsharing": "FAIRsharing.2abjs5",
"miriam": "00100463",
"nlx": "143602",
"omics": "17902",
"scr": "004177"
}
}
},
"fairsharing.organization": {
"contact": {
"email": "allyson.lister@oerc.ox.ac.uk",
"github": "allysonlister",
"name": "Allyson Lister",
"orcid": "0000-0002-7702-4495"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An organization in FAIRsharing, including universities, labs, etc.",
"example": "3851",
"homepage": "https://fairsharing.org",
"name": "FAIRsharing Organization",
"part_of": "fairsharing",
"pattern": "^\\d+$",
"uri_format": "https://fairsharing.org/organisations/$1"
},
"fairsharing.user": {
"contact": {
"email": "allyson.lister@oerc.ox.ac.uk",
"github": "allysonlister",
"name": "Allyson Lister",
"orcid": "0000-0002-7702-4495"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A user of FAIRsharing",
"example": "5112",
"homepage": "https://fairsharing.org",
"name": "FAIRsharing User",
"part_of": "fairsharing",
"pattern": "^\\d+$",
"uri_format": "https://fairsharing.org/users/$1"
},
"faldo": {
"aberowl": {
"description": "FALDO is the Feature Annotation Location Description Ontology. It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources. The aim of this ontology is to describe the position of a sequence region or a feature. It does not aim to describe features or regions itself, but instead depends on resources such as the Sequence Ontology or the UniProt core ontolgy.",
"download_owl": "http://aber-owl.net/media/ontologies/FALDO/1/faldo.owl",
"homepage": "http://biohackathon.org/resource/faldo",
"name": "Feature Annotation Location Description Ontology ",
"prefix": "FALDO",
"version": "Created at the Biohackathon 2012 and 2013"
},
"agroportal": {
"contact": {
"email": "jerven.bolleman@isb-sib.ch",
"name": "Jerven Bolleman"
},
"description": "FALDO is the Feature Annotation Location Description Ontology. It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources. The aim of this ontology is to describe the position of a sequence region or a feature. It does not aim to describe features or regions itself, but instead depends on resources such as the Sequence Ontology or the UniProt core ontolgy.",
"example_uri": "http://biohackathon.org/resource/faldo#CollectionOfRegions",
"homepage": "http://aber-owl.net/ontology/FALDO/#/",
"license": "CC0-1.0",
"name": "Feature Annotation Location Description Ontology",
"prefix": "FALDO",
"repository": "https://github.com/OBF/FALDO",
"version": "Created at the Biohackathon 2012 and 2013"
},
"biocontext": {
"prefix": "faldo",
"uri_format": "http://biohackathon.org/resource/faldo#$1"
},
"bioportal": {
"contact": {
"email": "faldo@googlegroups.com",
"name": "FALDO group"
},
"description": "FALDO is the Feature Annotation Location Description Ontology. It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources. The aim of this ontology is to describe the position of a sequence region or a feature. It does not aim to describe features or regions itself, but instead depends on resources such as the Sequence Ontology or the UniProt core ontolgy.",
"homepage": "http://biohackathon.org/resource/faldo",
"name": "Feature Annotation Location Description Ontology",
"prefix": "FALDO",
"publication": "https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0067-z",
"version": "Created at the Biohackathon 2012 and 2013"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources",
"example": "ForwardStrandPosition",
"fairsharing": {
"abbreviation": "FALDO",
"description": "The Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences for data resources represented in RDF and/or OWL. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned βomicsβ areas. Using the same data format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types.",
"domains": [
"Nucleic acid sequence",
"Sequence annotation",
"Gene feature",
"Sequence feature",
"Binding site"
],
"homepage": "http://biohackathon.org/resource/faldo",
"license": "CC0-1.0",
"name": "Feature Annotation Location Description Ontology",
"prefix": "FAIRsharing.haxp7g",
"publications": [
{
"doi": "10.1186/s13326-016-0067-z",
"pubmed": "27296299",
"title": "FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation",
"year": 2016
}
],
"repository": "https://github.com/OBF/FALDO",
"subjects": [
"Genetics"
]
},
"homepage": "http://biohackathon.org/resource/faldo",
"lov": {
"description": "Used to describe a location that consists of a number of Regions but where the order is not known. e.g. the oddly named order() keyword in a INSDC file.",
"homepage": "http://biohackathon.org/resource/faldo",
"keywords": [
"Geography"
],
"modified": "2012-09-07",
"name": "Feature Annotation Location Description Ontology",
"prefix": "faldo",
"uri_prefix": "http://biohackathon.org/resource/faldo#$1"
},
"mappings": {
"aberowl": "FALDO",
"agroportal": "FALDO",
"biocontext": "faldo",
"bioportal": "FALDO",
"fairsharing": "FAIRsharing.haxp7g",
"lov": "faldo"
},
"name": "Feature Annotation Location Description Ontology ",
"preferred_prefix": "faldo",
"publications": [
{
"doi": "10.1186/s13326-016-0067-z",
"pmc": "PMC4907002",
"pubmed": "27296299",
"title": "FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation",
"year": 2016
}
],
"uri_format": "http://biohackathon.org/resource/faldo#$1"
},
"fao": {
"aberowl": {
"description": "A structured controlled vocabulary for the anatomy of fungi.",
"download_owl": "http://aber-owl.net/media/ontologies/FAO/28/fao.owl",
"homepage": "https://github.com/obophenotype/fungal-anatomy-ontology/",
"name": "Fungal gross anatomy",
"prefix": "FAO"
},
"biocontext": {
"prefix": "FAO"
},
"bioportal": {
"contact": {
"email": "dinglis@stanford.edu",
"name": "Diane Inglis"
},
"description": "A structured controlled vocabulary for the anatomy of fungi.",
"homepage": "https://github.com/obophenotype/fungal-anatomy-ontology",
"name": "Fungal Gross Anatomy Ontology",
"prefix": "FAO"
},
"example": "0000001",
"fairsharing": {
"abbreviation": "FAO",
"contact": {
"email": "dinglis@stanford.edu",
"name": "Diane Inglis",
"orcid": "0000-0003-3166-4638"
},
"description": "A structured controlled vocabulary for the anatomy of fungi.",
"homepage": "https://github.com/obophenotype/fungal-anatomy-ontology",
"name": "Fungal Gross Anatomy Ontology",
"prefix": "FAIRsharing.xs6t67",
"subjects": [
"Anatomy",
"Life Science",
"Microbiology"
]
},
"mappings": {
"aberowl": "FAO",
"biocontext": "FAO",
"bioportal": "FAO",
"fairsharing": "FAIRsharing.xs6t67",
"obofoundry": "fao",
"ols": "fao",
"ontobee": "FAO",
"prefixcommons": "fao"
},
"obofoundry": {
"contact": "vw253@cam.ac.uk",
"contact.github": "ValWood",
"contact.label": "Val Wood",
"contact.orcid": "0000-0001-6330-7526",
"deprecated": false,
"description": "A structured controlled vocabulary for the anatomy of fungi.",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/fao.obo",
"download.owl": "http://purl.obolibrary.org/obo/fao.owl",
"homepage": "https://github.com/obophenotype/fungal-anatomy-ontology/",
"license": "CC0 1.0",
"license.url": "http://creativecommons.org/publicdomain/zero/1.0/",
"name": "Fungal gross anatomy",
"preferredPrefix": "FAO",
"prefix": "fao",
"repository": "https://github.com/obophenotype/fungal-anatomy-ontology"
},
"ols": {
"description": "A structured controlled vocabulary for the anatomy of fungi.",
"download_owl": "http://purl.obolibrary.org/obo/fao.owl",
"homepage": "https://github.com/obophenotype/fungal-anatomy-ontology/",
"name": "Fungal gross anatomy",
"prefix": "fao",
"version": "2020-05-07",
"version.iri": "http://purl.obolibrary.org/obo/fao/releases/2020-05-07/fao.owl"
},
"ontobee": {
"library": "Library",
"name": "Fungal gross anatomy",
"prefix": "FAO"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1019",
"description": "The project aims to develop a controlled vocabulary to describe the 'anatomy' of fungi and other microbes, called the fungal anatomy ontology (FAO).",
"example": "FAO_0000001",
"homepage": "http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/",
"keywords": [
"obo",
"anatomy",
"fungi"
],
"name": "Fungal Anatomy Ontology",
"pattern": "^FAO_\\d+$",
"prefix": "fao"
},
"uri_format": "http://purl.obolibrary.org/obo/FAO_$1"
},
"fao.asfis": {
"comment": "This resource is offered freely by FAO for download but no obvious licensing is indicated, and no caution about appropriate reuse.",
"contributor": {
"github": "ddooley",
"name": "Damion Dooley",
"orcid": "0000-0002-8844-9165"
},
"description": "The FAO Statistics Team (NFISS) of Fisheries and Aquaculture Division collates world capture and aquaculture production statistics at either the species, genus, family, or higher taxonomic levels in 3,169 statistical categories (2022 data release) referred to as species items. ASFIS list of species includes 13,417 species items selected according to their interest or relation to fisheries and aquaculture. For each species item stored in a record, codes (ISSCAAP group, taxonomic and 3-alpha) and taxonomic information (scientific name, author(s), family, and higher taxonomic classification) are provided. An English name is available for most of the records, and about one third of them have also a French and Spanish name. Information is also provided about the availability of fishery production statistics on the species item in the FAO databases. (from homepage)",
"example": "20560",
"github_request_issue": 872,
"homepage": "https://www.fao.org/fishery/en/collection/asfis/en",
"name": "Aquatic Sciences and Fisheries Information System",
"pattern": "^\\d+$",
"repository": "bioregistry",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"synonyms": [
"asfis"
],
"uri_format": "https://www.fao.org/fishery/en/species/$1"
},
"fbbi": {
"aberowl": {
"description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.",
"download_obo": "http://aber-owl.net/media/ontologies/FBbi/14/fbbi.obo",
"homepage": "http://cellimagelibrary.org/",
"name": "Biological Imaging Methods Ontology",
"prefix": "FBbi",
"version": "unknown"
},
"biocontext": {
"prefix": "FBbi"
},
"bioportal": {
"contact": {
"email": "chris@bio.umass.edu",
"name": "Chris Woodcock"
},
"description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.",
"homepage": "http://cellimagelibrary.org/",
"name": "Biological Imaging Methods Ontology",
"prefix": "FBbi"
},
"example": "00000268",
"fairsharing": {
"abbreviation": "FBbi",
"description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.",
"domains": [
"Imaging",
"Image",
"Assay"
],
"homepage": "http://flybase.org/vocabularies",
"name": "Biological Imaging methods Ontology",
"prefix": "FAIRsharing.ny3z9j",
"subjects": [
"Life Science",
"Biomedical Science"
]
},
"mappings": {
"aberowl": "FBbi",
"biocontext": "FBbi",
"bioportal": "FBbi",
"fairsharing": "FAIRsharing.ny3z9j",
"obofoundry": "fbbi",
"ols": "fbbi",
"ontobee": "FBbi",
"prefixcommons": "fbbi"
},
"obofoundry": {
"contact": "wawong@gmail.com",
"contact.github": "wawong",
"contact.label": "Willy Wong",
"contact.orcid": "0000-0002-8841-5870",
"deprecated": true,
"description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.",
"domain": "investigations",
"download.owl": "http://purl.obolibrary.org/obo/fbbi.owl",
"homepage": "http://cellimagelibrary.org/",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Biological Imaging Methods Ontology",
"preferredPrefix": "FBbi",
"prefix": "fbbi",
"repository": "https://github.com/CRBS/Biological_Imaging_Methods_Ontology"
},
"ols": {
"description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.",
"download_owl": "http://purl.obolibrary.org/obo/fbbi.owl",
"homepage": "http://cellimagelibrary.org/",
"name": "Biological Imaging Methods Ontology",
"prefix": "fbbi",
"version": "2020-11-06",
"version.iri": "http://purl.obolibrary.org/obo/fbbi/releases/2020-11-06/fbbi.owl"
},
"ontobee": {
"library": "Library",
"name": "Biological Imaging Methods Ontology",
"prefix": "FBbi"
},
"pattern": "^\\d+$",
"prefixcommons": {
"bioportal": "1023",
"description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.",
"example": "FBbi_00000222",
"homepage": "http://cellimagelibrary.org/",
"keywords": [
"obo",
"experiment",
"imaging"
],
"name": "Biological imaging methods",
"pattern": "^FBbi_\\d+$",
"prefix": "fbbi",
"synonyms": [
"fbbi.root"
]
},
"synonyms": [
"FBbi"
],
"uri_format": "http://purl.obolibrary.org/obo/FBbi_$1"
},
"fbbt": {
"aberowl": {
"description": "An ontology representing the gross anatomy of Drosophila melanogaster.",
"download_owl": "http://aber-owl.net/media/ontologies/FBBT/41/fbbt.owl",
"homepage": "http://purl.obolibrary.org/obo/fbbt",
"name": "Drosophila gross anatomy",
"prefix": "FBBT"
},
"biocontext": {
"prefix": "FBbt"
},
"bioportal": {
"contact": {
"email": "cp390@cam.ac.uk",
"name": "Claire Pilgrim"
},
"description": "An ontology representing the gross anatomy of Drosophila melanogaster",
"homepage": "http://purl.obolibrary.org/obo/fbbt",
"name": "Drosophila Gross Anatomy Ontology",
"prefix": "FB-BT",
"version": "fbbt/releases/2024-08-08"
},
"example": "00007294",
"fairsharing": {
"abbreviation": "FBbt",
"contact": {
"email": "cp390@cam.ac.uk",
"name": "Clare Pilgrim",
"orcid": "0000-0002-1373-1705"
},
"description": "An ontology of the anatomy of Drosophila melanogaster. It can be used for annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotype and images. It was originally developed by FlyBase, who continue to maintain it and use it for curation.",
"domains": [
"Gene expression",
"Image",
"Phenotype",
"Life cycle stage"
],
"homepage": "http://flybase.org/vocabularies",
"license": "CC-BY-4.0",
"name": "Drosophila anatomy ontology",
"prefix": "FAIRsharing.y2qkst",
"publications": [
{
"doi": "10.1093/nar/gkj068",
"pubmed": "16381917",
"title": "FlyBase: anatomical data, images and queries",
"year": 2005
},
{
"doi": "10.1186/2041-1480-4-32",
"pubmed": "24139062",
"title": "The Drosophila anatomy ontology",
"year": 2013
},
{
"doi": "10.1093/bioinformatics/bts113",
"pubmed": "22402613",
"title": "A strategy for building neuro-anatomy ontologies",
"year": 2012
},
{
"doi": "10.1093/bioinformatics/btr677",
"pubmed": "22180411",
"title": "The Virtual Fly Brain Browser and Query Interface",
"year": 2011
}
],
"repository": "https://github.com/FlyBase/drosophila-anatomy-developmental-ontology",
"subjects": [
"Anatomy",
"Developmental Biology",
"Life Science"
]
},
"go": {
"homepage": "http://flybase.org/",
"name": "Drosophila gross anatomy",
"prefix": "FBbt"
},
"mappings": {
"aberowl": "FBBT",
"biocontext": "FBbt",
"bioportal": "FB-BT",
"fairsharing": "FAIRsharing.y2qkst",
"go": "FBbt",
"obofoundry": "fbbt",
"ols": "fbbt",
"ontobee": "FBbt",
"prefixcommons": "fbbt"
},
"obofoundry": {
"contact": "cp390@cam.ac.uk",
"contact.github": "Clare72",
"contact.label": "Clare Pilgrim",
"contact.orcid": "0000-0002-1373-1705",
"deprecated": false,
"description": "An ontology representing the gross anatomy of Drosophila melanogaster.",
"domain": "anatomy and development",
"download.json": "http://purl.obolibrary.org/obo/fbbt.json",
"download.obo": "http://purl.obolibrary.org/obo/fbbt.obo",
"download.owl": "http://purl.obolibrary.org/obo/fbbt.owl",
"homepage": "http://purl.obolibrary.org/obo/fbbt",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Drosophila gross anatomy",
"preferredPrefix": "FBbt",
"prefix": "fbbt",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/24139062",
"preferred": true,
"title": "The Drosophila anatomy ontology"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/22402613",
"title": "A strategy for building neuroanatomy ontologies"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/22180411",
"title": "The Virtual Fly Brain Browser and Query Interface"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/16381917",
"title": "FlyBase: anatomical data, images and queries"
}
],
"repository": "https://github.com/FlyBase/drosophila-anatomy-developmental-ontology"
},
"ols": {
"description": "An ontology representing the gross anatomy of Drosophila melanogaster.",
"download_owl": "http://purl.obolibrary.org/obo/fbbt.owl",
"homepage": "http://purl.obolibrary.org/obo/fbbt",
"name": "Drosophila gross anatomy",
"prefix": "fbbt",
"version": "2024-06-13",
"version.iri": "http://purl.obolibrary.org/obo/fbbt/releases/2024-06-13/fbbt.owl"
},
"ontobee": {
"library": "Library",
"name": "Drosophila gross anatomy",
"prefix": "FBbt"
},
"pattern": "^\\d{8}$",
"prefixcommons": {
"bioportal": "1015",
"description": "A structured controlled vocabulary of the anatomy of Drosophila melanogaster",
"example": "FBbt_00005835",
"homepage": "http://www.flybase.org/",
"keywords": [
"obo",
"anatomy",
"fly"
],
"name": "Drosophila gross anatomy",
"pattern": "^FBbt_\\d{8}$",
"prefix": "fbbt",
"synonyms": [
"fly_anatomy",
"fbbt_root"
]
},
"publications": [
{
"doi": "10.1186/2041-1480-4-32",
"pmc": "PMC4015547",
"pubmed": "24139062",
"title": "The Drosophila anatomy ontology",
"year": 2013
},
{
"doi": "10.1093/bioinformatics/bts113",
"pubmed": "22402613",
"title": "A strategy for building neuroanatomy ontologies",
"year": 2012
},
{
"doi": "10.1093/bioinformatics/btr677",
"pubmed": "22180411",
"title": "The Virtual Fly Brain browser and query interface",
"year": 2011
},
{
"doi": "10.1093/nar/gkj068",
"pmc": "PMC1347431",
"pubmed": "16381917",
"title": "FlyBase: anatomical data, images and queries",
"year": 2006
}
],
"synonyms": [
"FBbt",
"FBbt_root"
],
"uri_format": "http://purl.obolibrary.org/obo/FBbt_$1"
},
"fbcv": {
"aberowl": {
"description": "A structured controlled vocabulary used for various aspects of annotation by FlyBase.",
"download_owl": "http://aber-owl.net/media/ontologies/FBCV/34/fbcv.owl",
"homepage": "http://purl.obolibrary.org/obo/fbcv",
"name": "FlyBase Controlled Vocabulary",
"prefix": "FBCV"
},
"biocontext": {
"prefix": "FBcv"
},
"bioportal": {
"contact": {
"email": "cp390@cam.ac.uk",
"name": "Clare Pilgrim"
},
"description": "A structured controlled vocabulary used for various aspects of annotation by FlyBase. It includes the Drosophila Phenotype Ontology (DPO) which is also released separately. This ontology is maintained by FlyBase for various aspects of annotation not covered, or not yet covered, by other OBO ontologies. If and when community ontologies are available for the domains here covered FlyBase will use them.",
"homepage": "http://purl.obolibrary.org/obo/fbcv",
"name": "FlyBase Controlled Vocabulary",
"prefix": "FB-CV",
"version": "2024-08-08"
},
"download_obo": "https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/fbcv.obo",
"example": "0000586",
"fairsharing": {
"abbreviation": "FBcv",
"contact": {
"email": "cp390@cam.ac.uk",
"name": "Clare Pilgrim",
"orcid": "0000-0002-1373-1705"
},
"description": "A structured controlled vocabulary developed and used by FlyBase, including the Drosophila phenotype ontology. It is used in annotation and classification of data related to Drosophila, including phenotypes and expression.",
"domains": [
"Expression data",
"Phenotype"
],
"homepage": "https://github.com/FlyBase/flybase-controlled-vocabulary",
"license": "CC-BY-4.0",
"name": "FlyBase Controlled Vocabulary",
"prefix": "FAIRsharing.6tgyxf",
"publications": [
{
"doi": "10.1186/2041-1480-4-30",
"pubmed": "24138933",
"title": "The Drosophila phenotype ontology",
"year": 2013
}
],
"repository": "https://github.com/FlyBase/flybase-controlled-vocabulary",
"subjects": [
"Life Science"
]
},
"mappings": {
"aberowl": "FBCV",
"biocontext": "FBcv",
"bioportal": "FB-CV",
"fairsharing": "FAIRsharing.6tgyxf",
"obofoundry": "fbcv",
"ols": "fbcv",
"ontobee": "FBcv",
"prefixcommons": "fbcv"
},
"obofoundry": {
"appears_in": [
"ontoavida"
],
"contact": "cp390@cam.ac.uk",
"contact.github": "Clare72",
"contact.label": "Clare Pilgrim",
"contact.orcid": "0000-0002-1373-1705",
"deprecated": false,
"description": "A structured controlled vocabulary used for various aspects of annotation by FlyBase.",
"domain": "organisms",
"download.json": "http://purl.obolibrary.org/obo/fbcv.json",
"download.obo": "http://purl.obolibrary.org/obo/fbcv.obo",
"download.owl": "http://purl.obolibrary.org/obo/fbcv.owl",
"homepage": "http://purl.obolibrary.org/obo/fbcv",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "FlyBase Controlled Vocabulary",
"preferredPrefix": "FBcv",
"prefix": "fbcv",
"repository": "https://github.com/FlyBase/flybase-controlled-vocabulary"
},
"ols": {
"description": "A miscellaneous ontology of terms used for curation in FlyBase, including the DPO.",
"download_owl": "http://purl.obolibrary.org/obo/fbcv.owl",
"homepage": "http://purl.obolibrary.org/obo/fbcv",
"name": "FlyBase Controlled Vocabulary (FBcv)",
"prefix": "fbcv",
"version": "2024-06-13",
"version.iri": "http://purl.obolibrary.org/obo/fbcv/releases/2024-06-13/fbcv.owl"
},
"ontobee": {
"library": "Library",
"name": "Drosophila Phenotype Ontology",
"prefix": "FBcv"
},
"part_of": "flybase",
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1017",
"description": "A structured controlled vocabulary used for various aspects of annotation by FlyBase. This ontology is maintained by FlyBase for various aspects of annotation not covered, or not yet covered, by other OBO ontologies. If and when community ontologies are available for the domains here covered FlyBase will use them.",
"example": "FBcv_0000013",
"homepage": "http://www.flybase.org/",
"keywords": [
"obo",
"descriptor",
"fly"
],
"name": "FlyBase Controlled Vocabulary",
"pattern": "^FBcv_\\d{7}$",
"prefix": "fbcv"
},
"publications": [
{
"doi": "10.1186/2041-1480-4-30",
"pmc": "PMC3816596",
"pubmed": "24138933",
"title": "The Drosophila phenotype ontology",
"year": 2013
}
],
"synonyms": [
"FBcv"
],
"uri_format": "http://purl.obolibrary.org/obo/FBcv_$1"
},
"fbdv": {
"aberowl": {
"description": "A structured controlled vocabulary of the development of Drosophila melanogaster.",
"download_owl": "http://aber-owl.net/media/ontologies/FBDV/37/fbdv.owl",
"homepage": "http://purl.obolibrary.org/obo/fbdv",
"name": "Drosophila development",
"prefix": "FBDV"
},
"biocontext": {
"prefix": "FBdv"
},
"bioportal": {
"contact": {
"email": "mmc46@gen.cam.ac.uk",
"name": "Marta Costa"
},
"description": "A structured controlled vocabulary of the development of Drosophila melanogaster.",
"homepage": "http://sourceforge.net/p/fbbtdv/wiki/Home/",
"name": "Drosophila Development Ontology",
"prefix": "FB-DV",
"version": "fbdv/releases/2024-08-07"
},
"example": "00000000",
"fairsharing": {
"abbreviation": "FBdv",
"contact": {
"email": "cp390@cam.ac.uk",
"name": "Clare Pilgrim",
"orcid": "0000-0002-1373-1705"
},
"description": "An ontology of the developmental stages of Drosophila melanogaster. It provides a controlled vocabulary for use in annotation and classification of data related to Drosophila, such as gene expression, phenotypes and images.",
"domains": [
"Life cycle",
"Life cycle stage"
],
"homepage": "http://flybase.org/vocabularies",
"license": "CC-BY-4.0",
"name": "Drosophila developmental ontology",
"prefix": "FAIRsharing.p52pzj",
"repository": "https://github.com/FlyBase/drosophila-anatomy-developmental-ontology",
"subjects": [
"Developmental Biology",
"Life Science"
]
},
"go": {
"homepage": "http://flybase.org/",
"name": "Drosophila development",
"prefix": "FBdv",
"uri_format": "http://flybase.org/cgi-bin/fbcvq.html?query=FBdv:$1"
},
"mappings": {
"aberowl": "FBDV",
"biocontext": "FBdv",
"bioportal": "FB-DV",
"fairsharing": "FAIRsharing.p52pzj",
"go": "FBdv",
"obofoundry": "fbdv",
"ols": "fbdv",
"ontobee": "FBdv",
"prefixcommons": "fbdv"
},
"obofoundry": {
"contact": "cp390@cam.ac.uk",
"contact.github": "Clare72",
"contact.label": "Clare Pilgrim",
"contact.orcid": "0000-0002-1373-1705",
"deprecated": false,
"description": "A structured controlled vocabulary of the development of Drosophila melanogaster.",
"domain": "anatomy and development",
"download.json": "http://purl.obolibrary.org/obo/fbdv.json",
"download.obo": "http://purl.obolibrary.org/obo/fbdv.obo",
"download.owl": "http://purl.obolibrary.org/obo/fbdv.owl",
"homepage": "http://purl.obolibrary.org/obo/fbdv",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Drosophila development",
"preferredPrefix": "FBdv",
"prefix": "fbdv",
"repository": "https://github.com/FlyBase/drosophila-developmental-ontology"
},
"ols": {
"description": "An ontology of Drosophila melanogaster developmental stages.",
"download_owl": "http://purl.obolibrary.org/obo/fbdv.owl",
"homepage": "http://purl.obolibrary.org/obo/fbdv",
"name": "Drosophila Developmental Ontology",
"prefix": "fbdv",
"version": "2024-06-13",
"version.iri": "http://purl.obolibrary.org/obo/fbdv/releases/2024-06-13/fbdv.owl"
},
"ontobee": {
"library": "Library",
"name": "Drosophila development",
"prefix": "FBdv"
},
"pattern": "^\\d{8}$",
"prefixcommons": {
"alt_uri_formats": [
"http://purl.org/obo/owl/FBDV#$1"
],
"bioportal": "1016",
"description": "A structured controlled vocabulary of the development of Drosophila melanogaster.",
"example": "FBdv_00005291",
"homepage": "http://www.flybase.org/",
"keywords": [
"obo",
"development",
"fly"
],
"name": "Drosophila development",
"pattern": "^FBdv_\\d{8}$",
"prefix": "fbdv",
"synonyms": [
"fbdv.root"
]
},
"synonyms": [
"FBdv"
],
"uri_format": "http://purl.obolibrary.org/obo/FBdv_$1"
},
"fbol": {
"biocontext": {
"prefix": "FBOL"
},
"comment": "Website down, checked on 2021-10-07",
"deprecated": true,
"mappings": {
"biocontext": "FBOL",
"miriam": "fbol",
"n2t": "fbol",
"ncbi": "FBOL"
},
"miriam": {
"deprecated": false,
"description": "DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms.",
"homepage": "http://www.fungalbarcoding.org/",
"id": "00000410",
"name": "Fungal Barcode",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "fbol",
"sampleId": "2224",
"uri_format": "http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T"
},
"n2t": {
"description": "DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms.",
"example": "2224",
"homepage": "http://www.fungalbarcoding.org/",
"name": "Fungal Barcode at Fungal Biodiversity Centre",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "fbol",
"uri_format": "http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T"
},
"ncbi": {
"example": "2224",
"homepage": "http://www.fungalbarcoding.org/",
"name": "International Fungal Working Group Fungal Barcoding.",
"prefix": "FBOL"
}
},
"fbql": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"example": "00005254",
"name": "FlyBase Qualifiers",
"pattern": "^\\d+$"
},
"fbrf": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "FlyBase internal citation identifiers",
"example": "0187632",
"homepage": "https://flybase.org",
"name": "FlyBase Reference Report",
"part_of": "flybase",
"pattern": "^\\d{7}$",
"uri_format": "https://flybase.org/reports/FBrf$1"
},
"fbsp": {
"aberowl": {
"description": "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.",
"download_obo": "http://aber-owl.net/media/ontologies/FB-SP/7/fb-sp.obo",
"homepage": "http://www.flybase.org/",
"name": "Fly Taxonomy",
"prefix": "FB-SP",
"version": "unknown"
},
"biocontext": {
"prefix": "FBSP"
},
"bioportal": {
"contact": {
"email": "mmc46@gen.cam.ac.uk",
"name": "Marta Costa"
},
"description": "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.",
"homepage": "http://www.flybase.org/",
"name": "Fly Taxonomy",
"prefix": "FB-SP"
},
"example": "00000000",
"mappings": {
"aberowl": "FB-SP",
"biocontext": "FBSP",
"bioportal": "FB-SP",
"obofoundry": "fbsp",
"ols": "fbsp"
},
"obofoundry": {
"contact": "cp390@cam.ac.uk",
"contact.github": "Clare72",
"contact.label": "Clare Pilgrim",
"contact.orcid": "0000-0002-1373-1705",
"deprecated": true,
"description": "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.",
"domain": "organisms",
"download.owl": "http://purl.obolibrary.org/obo/fbsp.owl",
"homepage": "http://www.flybase.org/",
"name": "Fly taxonomy",
"prefix": "fbsp"
},
"ols": {
"description": "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.",
"homepage": "http://www.flybase.org/",
"name": "Fly taxonomy",
"prefix": "fbsp",
"version": "2017-11-19",
"version.iri": "http://purl.obolibrary.org/obo/fbsp/releases/2017-11-19/fbsp.owl"
},
"part_of": "flybase",
"pattern": "^\\d{8}$"
},
"fbtc": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://flybase.org/cgi-bin/cvreport.pl?id=FBbt%3A00005329",
"name": "Drosophila genome database; cell line entry",
"prefix": "FlyBase_Cell_line",
"uri_format": "https://flybase.org/reports/$1.html"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The cell line vocabulary inside FlyBase",
"example": "0000190",
"homepage": "https://flybase.org",
"mappings": {
"cellosaurus": "FlyBase_Cell_line"
},
"name": "Flybase Cell Line",
"part_of": "flybase",
"pattern": "^\\d{7}$",
"synonyms": [
"FlyBase_Cell_line"
],
"uri_format": "https://flybase.org/reports/FBtc$1"
},
"fcb": {
"mappings": {
"miriam": "fcb"
},
"miriam": {
"deprecated": false,
"description": "Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR).\n\n",
"homepage": "https://w3id.org",
"id": "00000891",
"name": "the FAIR Cookbook",
"namespaceEmbeddedInLui": false,
"pattern": "^FCB\\d{3}",
"prefix": "fcb",
"sampleId": "FCB005",
"uri_format": "https://w3id.org/faircookbook/$1"
}
},
"fcsfree": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://fcs-free.org/",
"name": "Fetal Calf Serum-Free Database",
"prefix": "FCS-free",
"uri_format": "https://fcs-free.org/fcs-database?$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"example": "240-17-488-3-4-12",
"homepage": "https://fcs-free.org",
"mappings": {
"cellosaurus": "FCS-free"
},
"name": "Fetal Calf Serum-Free Database",
"uri_format": "https://fcs-free.org/fcs-database?$1"
},
"ferroliganddb": {
"contact": {
"email": "guqiong@mail.sysu.edu.cn",
"name": "Qiong Gu"
},
"contributor": {
"email": "shah.tanay2@northeastern.edu",
"github": "tanayshah2",
"name": "Tanay Shah",
"orcid": "0009-0001-1912-5132"
},
"description": "FerroLigandDB is a meticulously curated, high-quality database of ferroptosis regulators, including inducers and inhibitors.",
"example": "486",
"homepage": "https://ferr.gulab.org.cn/",
"name": "FerroLigandDB",
"publications": [
{
"doi": "10.1021/acs.jcim.4c00525",
"pubmed": "38885636",
"title": "FerroLigandDB: A Ferroptosis Ligand Database of Structure-Activity Relations",
"year": 2024
}
],
"reviewer": {
"email": "b.gyori@northeastern.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"uri_format": "https://ferr.gulab.org.cn/browse/$1"
},
"fhir.implementation": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A set of guides on implementing various processes within hospitals or healthcare systems.",
"example": "immds",
"homepage": "https://hl7.org/fhir/us/",
"name": "FHIR United States Implementation Guides",
"uri_format": "https://hl7.org/fhir/us/$1"
},
"fideo": {
"aberowl": {
"description": "Food-Drug interactions automatically extracted from scientific literature",
"download_owl": "http://aber-owl.net/media/ontologies/FIDEO/9/fideo.owl",
"homepage": "https://gitub.u-bordeaux.fr/erias/fideo",
"name": "Food Interactions with Drugs Evidence Ontology",
"prefix": "FIDEO"
},
"bioportal": {
"contact": {
"email": "georgeta.bordea@u-bordeaux.fr",
"name": "Georgeta Bordea"
},
"description": "The Food Interactions with Drugs Evidence Ontology (FIDEO) is an ontology used for annotation and retrieval of scientific articles about food-drug interactions.",
"homepage": "https://gitub.u-bordeaux.fr/erias/fideo",
"name": "Food Interactions with Drugs Evidence Ontology",
"prefix": "FIDEO",
"publication": "http://www.informatik.uni-leipzig.de/~loebe/tmp/ICBO2020/paperL.pdf",
"version": "2023-12-18"
},
"example": "00000021",
"mappings": {
"aberowl": "FIDEO",
"bioportal": "FIDEO",
"obofoundry": "fideo",
"ols": "fideo",
"ontobee": "FIDEO"
},
"obofoundry": {
"contact": "georgeta.bordea@u-bordeaux.fr",
"contact.github": "getbordea",
"contact.label": "Georgeta Bordea",
"contact.orcid": "0000-0001-9921-8234",
"deprecated": false,
"description": "Food-Drug interactions automatically extracted from scientific literature",
"domain": "diet, metabolomics, and nutrition",
"download.owl": "http://purl.obolibrary.org/obo/fideo.owl",
"homepage": "https://gitub.u-bordeaux.fr/erias/fideo",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Food Interactions with Drugs Evidence Ontology",
"preferredPrefix": "FIDEO",
"prefix": "fideo",
"repository": "https://gitub.u-bordeaux.fr/erias/fideo"
},
"ols": {
"description": "Food-Drug interactions automatically extracted from scientific literature",
"download_owl": "http://purl.obolibrary.org/obo/fideo.owl",
"homepage": "https://gitub.u-bordeaux.fr/erias/fideo",
"name": "Food Interactions with Drugs Evidence Ontology",
"prefix": "fideo",
"version": "2023-12-18",
"version.iri": "http://purl.obolibrary.org/obo/fideo/releases/2023-12-18/fideo.owl"
},
"ontobee": {
"library": "Library",
"name": "Food Interactions with Drugs Evidence Ontology",
"prefix": "FIDEO"
},
"pattern": "^\\d{8}$",
"uri_format": "http://purl.obolibrary.org/obo/FIDEO_$1"
},
"fishbase.species": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years.",
"example": "6472",
"homepage": "http://fishbase.org",
"integbio": {
"description": "FishBase is a relational database containing information about fish around the world to cater to different professionals such as research scientists, fisheries managers, zoologists and many more. Each entry contains scientific names, common names , pictures, links to other tables, links to internet sources, etc. Moreover, various genetic data are available for many species. All items are referenced, with full citation. Scientific names are verified against Eschmeyer's Catalog of Fishes. Users enter FishBase through common names which classified by country and language. Full academic course with exercises in Ichthyology is available in Fish-On-Line.",
"homepage": "http://www.fishbase.org/search.php?lang=English",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie"
],
"maintainer": "FishBase Consortium",
"name": "FishBase",
"prefix": "nbdc00270",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"mappings": {
"integbio": "nbdc00270",
"re3data": "r3d100010912",
"wikidata": "P938"
},
"name": "FishBase",
"pattern": "^\\d+$",
"re3data": {
"description": "Fishbase is a global species database and encyclopedia of over 30,000 species and subspecies of fishes that is searchable by common name, genus, species, geography, family, ecosystem, references literature, tools, etc. Links to other, related databases such as the Catalog of Fishes, GenBack, and LarvalBase. Associated with a partner journal, Acta Ichthyologica et Piscatoria. With mirror sites in English, German, French Spanish, Portuguese, French, Swedish, Chinese and Arabian language.",
"homepage": "https://www.fishbase.se/home.php",
"name": "Fishbase",
"prefix": "r3d100010912",
"xrefs": {
"nlx": "39009",
"scr": "004376"
}
},
"synonyms": [
"fishbase"
],
"uri_format": "https://www.fishbase.ca/summary/$1",
"wikidata": {
"description": "identifier for a species in FishBase",
"example": [
"1234",
"19053",
"5918"
],
"name": "FishBase species ID",
"pattern": "^[1-9]\\d{0,4}$",
"prefix": "P938",
"uri_format": "https://www.fishbase.ca/summary/$1"
}
},
"fivestars": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata.",
"example": "hasOpenAccessRating",
"fairsharing": {
"abbreviation": "FiveStars",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Five Stars of Online Research Articles Ontology (FiveStars) is an ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/fivestars",
"license": "CC-BY-4.0",
"name": "Five Stars of Online Research Articles Ontology ",
"prefix": "FAIRsharing.6dfe9b",
"publications": [
{
"doi": "10.1045/january2012-shotton",
"title": "The Five Stars of Online Journal Articles - a Framework for Article Evaluation",
"year": 2012
}
],
"repository": "https://github.com/sparontologies/fivestars",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"homepage": "http://www.sparontologies.net/ontologies/fivestars",
"mappings": {
"fairsharing": "FAIRsharing.6dfe9b"
},
"name": "Five Stars of Online Research Articles Ontology",
"preferred_prefix": "FiveStars",
"publications": [
{
"doi": "10.1045/january2012-shotton",
"title": "The Five Stars of Online Journal Articles - a Framework for Article Evaluation",
"year": 2012
}
],
"repository": "https://github.com/sparontologies/fivestars"
},
"fix": {
"aberowl": {
"description": "An ontology of physico-chemical methods and properties.",
"download_owl": "http://aber-owl.net/media/ontologies/FIX/119/fix.owl",
"name": "Physico-chemical methods and properties",
"prefix": "FIX"
},
"biocontext": {
"prefix": "FIX"
},
"bioportal": {
"contact": {
"email": "chebi-help@ebi.ac.uk",
"name": "Chebi Administrators"
},
"description": "FIX consists of two ontologies: methods and properties (but not objects, which are subject of the chemical ontology). The methods are applied to study the properties.",
"name": "Physico-Chemical Methods and Properties",
"prefix": "FIX",
"version": "1.2"
},
"example": "0000390",
"fairsharing": {
"abbreviation": "FIX",
"description": "FIX consists of two ontologies: methods and properties (but not objects, which are subject of the chemical ontology). The methods are applied to study the properties. While this ontology is available via BioPortal and the OBO Foundry, we cannot find a home page or a publication for the resource, and the resource itself is no longer maintained.",
"domains": [
"Experimental measurement",
"Protocol"
],
"homepage": "http://purl.bioontology.org/ontology/FIX",
"name": "Physico-chemical methods and properties",
"prefix": "FAIRsharing.wwy1ns",
"subjects": [
"Chemistry"
]
},
"homepage": "https://www.ebi.ac.uk/chebi/",
"mappings": {
"aberowl": "FIX",
"biocontext": "FIX",
"bioportal": "FIX",
"fairsharing": "FAIRsharing.wwy1ns",
"obofoundry": "fix",
"ols": "fix",
"ontobee": "FIX",
"prefixcommons": "fix"
},
"obofoundry": {
"contact.label": "chEBI",
"deprecated": true,
"description": "An ontology of physico-chemical methods and properties.",
"domain": "chemistry and biochemistry",
"download.obo": "http://purl.obolibrary.org/obo/fix.obo",
"download.owl": "http://purl.obolibrary.org/obo/fix.owl",
"homepage": "http://www.ebi.ac.uk/chebi",
"name": "Physico-chemical methods and properties",
"prefix": "fix"
},
"ols": {
"description": "An ontology of physico-chemical methods and properties.",
"download_owl": "http://purl.obolibrary.org/obo/fix.owl",
"homepage": "http://www.ebi.ac.uk/chebi",
"name": "Physico-chemical methods and properties",
"prefix": "fix",
"version": "2020-04-13",
"version.iri": "http://purl.obolibrary.org/obo/fix/releases/2020-04-13/fix.owl"
},
"ontobee": {
"library": "Library",
"name": "Physico-chemical methods and properties",
"prefix": "FIX"
},
"owners": [
{
"name": "European Bioinformatics Institute",
"partnered": false,
"ror": "02catss52"
}
],
"part_of": "chebi",
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1014",
"description": "FIX consists of two ontologies: methods and properties (but not objects, which are subject of the chemical ontology). The methods are applied to study the properties.",
"example": "FIX_0000000",
"keywords": [
"obo",
"property",
"experiment"
],
"name": "Physico-chemical methods and properties",
"pattern": "^FIX_\\d{7}$",
"prefix": "fix"
}
},
"flopo": {
"aberowl": {
"description": "Traits and phenotypes of flowering plants occurring in digitized Floras",
"download_owl": "http://aber-owl.net/media/ontologies/FLOPO/10/flopo.owl",
"homepage": "https://github.com/flora-phenotype-ontology/flopoontology",
"name": "Flora Phenotype Ontology",
"prefix": "FLOPO"
},
"agroportal": {
"contact": {
"email": "robert.hoehndorf@kaust.edu.sa",
"name": "Robert Hoehndorf"
},
"description": "The Flora Phenotype Ontology (FLOPO) is an ontology of phenotypes reported in Floras. The original version was developed at the pro-iBiosphere Hackathon in Leiden. This is the pre-classified version of the ontology. The Flora Phenotype Ontology is generated from the Flora Malesiana, Flora Gabon, Flora of Central Africa, and a collection of Kew's African Floras. Every class in the ontology has at least one taxon annotation. The (draft) taxon annotation are available at http://jagannath.pdn.cam.ac.uk/plant/flora/clean-rerun/",
"example_uri": "http://purl.obolibrary.org/obo/FLOPO_0000003",
"homepage": "https://github.com/flora-phenotype-ontology",
"license": "CC0-1.0",
"name": "Flora Phenotype Ontology",
"prefix": "FLOPO",
"repository": "https://github.com/flora-phenotype-ontology/flopoontology/",
"version": "0.9"
},
"biocontext": {
"prefix": "FLOPO"
},
"bioportal": {
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}
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}
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],
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"name": "Rafael Gonçalves"
},
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},
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"github": "cthoyt",
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"keywords": [
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],
"modified": "2014-01-14",
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},
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},
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},
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},
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"version": "1.0.0"
},
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"name": "Pol Castellano Escuder"
},
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"homepage": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology",
"name": "FOBI (Food-Biomarker Ontology)",
"prefix": "FOBI"
},
"example": "030719",
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],
"homepage": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology",
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},
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"contact.github": "pcastellanoescuder",
"contact.label": "Pol Castellano Escuder",
"contact.orcid": "0000-0001-6466-877X",
"depends_on": [
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],
"deprecated": false,
"description": "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data",
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"homepage": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Food-Biomarker Ontology",
"preferredPrefix": "FOBI",
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"publications": [
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"id": "https://www.ncbi.nlm.nih.gov/pubmed/32556148",
"title": "FOBI: an ontology to represent food intake data and associate it with metabolomic data"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/34601570",
"title": "The fobitools framework: the first steps towards food enrichment analysis"
}
],
"repository": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology"
},
"ols": {
"description": "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data",
"download_owl": "http://purl.obolibrary.org/obo/fobi.owl",
"homepage": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology",
"name": "Food-Biomarker Ontology",
"prefix": "fobi",
"version.iri": "http://purl.obolibrary.org/obo/fobi/fobi.owl"
},
"ontobee": {
"library": "Library",
"name": "Food-Biomarker Ontology",
"prefix": "FOBI"
},
"pattern": "^\\d{4,6}$",
"providers": [
{
"code": "fobi.legacy",
"description": "An incorrect encoding of OBO purls",
"homepage": "http://purl.obolibrary.org/obo/fobi",
"name": "FOBI Hash",
"uri_format": "http://purl.obolibrary.org/obo/fobi.owl#FOBI:$1"
}
],
"publications": [
{
"doi": "10.1093/bioinformatics/btab626",
"pubmed": "34601570",
"title": "The fobitools framework: the first steps towards food enrichment analysis",
"year": 2021
},
{
"doi": "10.1093/databa/baaa033",
"pmc": "PMC7298227",
"pubmed": "32556148",
"title": "FOBI: an ontology to represent food intake data and associate it with metabolomic data",
"year": 2020
}
],
"uri_format": "http://purl.obolibrary.org/obo/FOBI_$1"
},
"foodb.compound": {
"biocontext": {
"prefix": "FOODB.COMPOUND"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "foodb.compound",
"uri_format": "http://foodb.ca/compounds/$1"
},
"homepage": "https://foodb.ca/",
"mappings": {
"biocontext": "FOODB.COMPOUND",
"biolink": "foodb.compound",
"miriam": "foodb.compound",
"n2t": "foodb.compound",
"re3data": "r3d100012152",
"wikidata": "P8117"
},
"miriam": {
"deprecated": false,
"description": "FooDB is resource on food and its constituent compounds. It includes data on the compoundβs nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds.",
"homepage": "http://foodb.ca/foods",
"id": "00000530",
"name": "FooDB Compound",
"namespaceEmbeddedInLui": false,
"pattern": "^FDB\\d+$",
"prefix": "foodb.compound",
"sampleId": "FDB002100",
"uri_format": "http://foodb.ca/compounds/$1"
},
"n2t": {
"description": "FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds.",
"example": "FDB002100",
"homepage": "http://foodb.ca/foods",
"name": "FooDB database of food additives at University of Alberta",
"namespaceEmbeddedInLui": false,
"pattern": "^FDB\\d+$",
"prefix": "foodb.compound",
"uri_format": "http://foodb.ca/compounds/$1"
},
"name": "FooDB compound",
"re3data": {
"description": "FooDB is the worldβs largest and most comprehensive resource on food constituents, chemistry and biology. It provides information on both macronutrients and micronutrients, including many of the constituents that give foods their flavor, color, taste, texture and aroma.",
"homepage": "https://foodb.ca/",
"name": "FooDB",
"prefix": "r3d100012152",
"synonyms": [
"Food Database"
]
},
"synonyms": [
"foodb"
],
"wikidata": {
"description": "ID of chemical compound in FooDB",
"example": [
"FDB000082",
"FDB000316",
"FDB002100"
],
"name": "FooDB compound ID",
"prefix": "P8117",
"uri_format": "https://foodb.ca/compounds/$1"
}
},
"foodb.food": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "foodb.food",
"uri_format": "http://foodb.ca/foods/$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Foods in FooDB",
"example": "FOOD00020",
"homepage": "https://foodb.ca/foods",
"mappings": {
"biolink": "foodb.food"
},
"name": "FooDB Food",
"pattern": "^FOOD\\d+$",
"uri_format": "https://foodb.ca/foods/$1"
},
"foodex2": {
"agroportal": {
"contact": {
"email": "data@food.gov.uk",
"name": "UK Food Standard Agency"
},
"description": "Food Type identifiers, supporting codes and vocabularies based on the EFSA FoodEx2 (https://www.efsa.europa.eu/en/data/data-standardisation) that are being tested in the development of the FSA's code and data standards repository. These codes may be used within FSA data.",
"example_uri": "http://data.food.gov.uk/codes/foodtype/id/A0TMC",
"homepage": "https://data.food.gov.uk/codes/_foodtype",
"name": "Food Classification and Description System (from FSA Food Type identifiers)",
"prefix": "FOODEX2",
"version": "2"
},
"example": "A0TMC",
"mappings": {
"agroportal": "FOODEX2"
},
"uri_format": "http://data.food.gov.uk/codes/foodtype/id/$1"
},
"foodon": {
"aberowl": {
"description": "A broadly scoped ontology representing entities which bear a βfood roleβ. It encompasses materials in natural ecosystems and agriculture that are consumed by humans and domesticated animals. This includes any generic (unbranded) raw or processed food material found in processing plants, markets, stores or food distribution points. FoodOn also imports nutritional component and dietary pattern terms from other OBO Foundry ontologies to support interoperability in diet and nutrition research",
"download_owl": "http://aber-owl.net/media/ontologies/FOODON/86/foodon.owl",
"homepage": "https://foodon.org/",
"name": "Food Ontology",
"prefix": "FOODON"
},
"agroportal": {
"contact": {
"email": "damion_dooley@sfu.ca",
"name": "Damion Dooley"
},
"description": "FoodOn is a consortium-driven project to build a comprehensive and easily accessible global farm-to-fork ontology about food, that accurately and consistently describes foods commonly known in cultures from around the world., that accurately and consistently describes foods commonly known in cultures from around the world. See https://foodon.org for more details.",
"example_uri": "http://purl.obolibrary.org/obo/FOODON_03412974",
"homepage": "https://foodon.org",
"license": "CC-BY-3.0",
"name": "FoodOn",
"prefix": "FOODON",
"repository": "https://github.com/FoodOntology/foodon",
"version": "2024-07-12"
},
"biocontext": {
"prefix": "FOODON"
},
"bioportal": {
"contact": {
"email": "damion_dooley@sfu.ca",
"name": "Damion Dooley"
},
"description": "FoodOn is an ontology built to represent entities which bear a βfood roleβ and is initially focused on categorizing and processing of food for humans. We aim to develop semantics for food safety, food security, the agricultural and animal husbandry practices linked to food production, culinary, nutritional and chemical ingredients and processes. FoodOn belongs to the OBOFoundry.org family of ontologies.",
"homepage": "http://foodon.org",
"name": "The FoodOn Food Ontology",
"prefix": "FOODON",
"publication": "https://www.nature.com/articles/s41538-018-0032-6",
"version": "2024-06-17"
},
"download_obo": "http://purl.obolibrary.org/obo/foodon.obo",
"fairsharing": {
"abbreviation": "FOODON",
"contact": {
"email": "damion.dooley@bccdc.ca",
"name": "Damion Dooley",
"orcid": "0000-0002-8844-9165"
},
"description": "The need to represent knowledge about food is central to many human activities including agriculture, medicine, food safety inspection, shopping patterns, and sustainable development. FoodOn is built to interoperate with the OBO Library and to represent entities which bear a food role. Initially the ontology will focus on the human-centric categorization and handling of food, but in the future it will also encompass materials in natural ecosystems and food webs. We aim to develop semantics for food safety, food security, the agricultural and animal husbandry practices linked to food production, culinary, nutritional and chemical ingredients and processes.",
"domains": [
"Sustainability",
"Food",
"Disease"
],
"homepage": "https://foodon.org/",
"license": "CC-BY-3.0",
"name": "Food Ontology",
"prefix": "FAIRsharing.dzxae",
"publications": [
{
"doi": "10.3389/fmicb.2017.01068",
"pubmed": "28694792",
"title": "Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance",
"year": 2017
},
{
"doi": "10.1038/s41538-018-0032-6",
"pubmed": "31304272",
"title": "FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration",
"year": 2019
}
],
"repository": "https://github.com/FoodOntology/foodon",
"subjects": [
"Botany",
"Environmental Science",
"Medicine",
"Agriculture"
]
},
"mappings": {
"aberowl": "FOODON",
"agroportal": "FOODON",
"biocontext": "FOODON",
"bioportal": "FOODON",
"fairsharing": "FAIRsharing.dzxae",
"miriam": "foodon",
"n2t": "foodon",
"obofoundry": "foodon",
"ols": "foodon",
"ontobee": "FOODON"
},
"miriam": {
"deprecated": false,
"description": "FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies.",
"homepage": "https://foodon.org",
"id": "00000661",
"name": "FoodOn Food Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^FOODON:[0-9]{8}$",
"prefix": "foodon",
"sampleId": "03307879",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/foodon/terms?obo_id=FOODON:$1"
},
"n2t": {
"description": "FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies.",
"example": "03307879",
"homepage": "https://foodon.org",
"name": "FoodOn Food Ontology through OLS",
"namespaceEmbeddedInLui": true,
"pattern": "^FOODON:[0-9]{8}$",
"prefix": "foodon",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1"
},
"name": "The Food Ontology",
"obofoundry": {
"appears_in": [
"agro",
"envo",
"fobi",
"maxo",
"one",
"ons"
],
"contact": "damion_dooley@sfu.ca",
"contact.github": "ddooley",
"contact.label": "Damion Dooley",
"contact.orcid": "0000-0002-8844-9165",
"depends_on": [
"bfo",
"chebi",
"envo",
"eo",
"ncbitaxon",
"obi",
"ro",
"uberon"
],
"deprecated": false,
"description": "A broadly scoped ontology representing entities which bear a βfood roleβ. It encompasses materials in natural ecosystems and agriculture that are consumed by humans and domesticated animals. This includes any generic (unbranded) raw or processed food material found in processing plants, markets, stores or food distribution points. FoodOn also imports nutritional component and dietary pattern terms from other OBO Foundry ontologies to support interoperability in diet and nutrition research",
"domain": "diet, metabolomics, and nutrition",
"download.owl": "http://purl.obolibrary.org/obo/foodon.owl",
"homepage": "https://foodon.org/",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Food Ontology",
"preferredPrefix": "FOODON",
"prefix": "foodon",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/31304272",
"title": "FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration"
}
],
"repository": "https://github.com/FoodOntology/foodon"
},
"ols": {
"description": "A broadly scoped ontology representing entities which bear a βfood roleβ. It encompasses materials in natural ecosystems and agriculture that are consumed by humans and domesticated animals. This includes any generic (unbranded) raw or processed food material found in processing plants, markets, stores or food distribution points. FoodOn also imports nutritional component and dietary pattern terms from other OBO Foundry ontologies to support interoperability in diet and nutrition research",
"download_owl": "http://purl.obolibrary.org/obo/foodon.owl",
"homepage": "https://foodon.org/",
"name": "Food Ontology",
"prefix": "foodon",
"version": "2024-07-12",
"version.iri": "https://github.com/FoodOntology/foodon/releases/download/v2024-07-12/foodon.owl"
},
"ontobee": {
"library": "Library",
"name": "Food Ontology",
"prefix": "FOODON"
},
"pattern": "^[0-9]{8}$",
"publications": [
{
"doi": "10.1038/s41538-018-0032-6",
"pmc": "PMC6550238",
"pubmed": "31304272",
"title": "FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration",
"year": 2018
},
{
"doi": "10.3389/fmicb.2017.01068",
"pmc": "PMC5483436",
"pubmed": "28694792",
"title": "Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance",
"year": 2017
}
],
"uri_format": "http://purl.obolibrary.org/obo/FOODON_$1"
},
"fossilworks.journal": {
"contributor": {
"email": "meghan.balk@gmail.com",
"github": "megbalk",
"name": "Meghan Balk",
"orcid": "0000-0003-2699-3066"
},
"description": "Identifier for a journal article in the fossilworks website",
"example": "61467",
"github_request_issue": 468,
"homepage": "http://fossilworks.org",
"mappings": {
"wikidata": "P7720"
},
"name": "Fossilworks Journal",
"part_of": "fossilworks",
"pattern": "^\\d+$",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://fossilworks.org/?a=referenceInfo&reference_no=$1",
"wikidata": {
"description": "identifier for a journal article in the Fossilworks database",
"example": [
"55763",
"61467",
"65044"
],
"homepage": "http://www.fossilworks.org",
"name": "Fossilworks ID for this journal article",
"pattern": "^\\d+$",
"prefix": "P7720",
"uri_format": "http://www.fossilworks.org/cgi-bin/bridge.pl?a=displayReference&reference_no=$1"
}
},
"fossilworks.taxon": {
"contributor": {
"email": "meghan.balk@gmail.com",
"github": "megbalk",
"name": "Meghan Balk",
"orcid": "0000-0003-2699-3066"
},
"description": "Identifier for an animal, plant, or microorganism from the fossilworks website",
"example": "40565",
"github_request_issue": 469,
"homepage": "http://www.fossilworks.org",
"mappings": {
"wikidata": "P842"
},
"name": "Fossilworks Taxon",
"part_of": "fossilworks",
"pattern": "^[1-9]\\d{0,5}$",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1",
"wikidata": {
"description": "identifier for an animal, plant, or microorganism in the Fossilworks database",
"example": [
"40565",
"49734"
],
"homepage": "http://www.fossilworks.org",
"name": "Fossilworks taxon ID",
"pattern": "^([1-9]\\d{0,5})$",
"prefix": "P842",
"uri_format": "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1"
}
},
"fovt": {
"aberowl": {
"description": "FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA).",
"download_owl": "http://aber-owl.net/media/ontologies/FOVT/7/fovt.owl",
"homepage": "https://github.com/futres/fovt",
"name": "FuTRES Ontology of Vertebrate Traits",
"prefix": "FOVT"
},
"bioportal": {
"contact": {
"email": "rlwalls2008@gmail.com",
"name": "Ramona Walls"
},
"description": "FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA).",
"homepage": "https://github.com/futres/fovt",
"name": "FuTRES Ontology of Vertebrate Traits",
"prefix": "FOVT",
"version": "2023-05-31"
},
"example": "0000009",
"mappings": {
"aberowl": "FOVT",
"bioportal": "FOVT",
"obofoundry": "fovt",
"ols": "fovt",
"ontobee": "FOVT"
},
"obofoundry": {
"contact": "meghan.balk@gmail.com",
"contact.github": "megbalk",
"contact.label": "Meghan Balk",
"contact.orcid": "0000-0003-2699-3066",
"depends_on": [
"bco",
"bfo",
"bspo",
"iao",
"oba",
"pato",
"ro",
"uberon"
],
"deprecated": false,
"description": "FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA).",
"domain": "phenotype",
"download.obo": "http://purl.obolibrary.org/obo/fovt.obo",
"download.owl": "http://purl.obolibrary.org/obo/fovt.owl",
"homepage": "https://github.com/futres/fovt",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "FuTRES Ontology of Vertebrate Traits",
"preferredPrefix": "FOVT",
"prefix": "fovt",
"repository": "https://github.com/futres/fovt"
},
"ols": {
"description": "These are the terms that are improted for FOVT to describe vertebrate traits.",
"download_owl": "http://purl.obolibrary.org/obo/fovt.owl",
"homepage": "https://github.com/futres/fovt",
"name": "FuTRES Ontology of Vertebrate Traits",
"prefix": "fovt",
"version": "2023-05-31",
"version.iri": "http://purl.obolibrary.org/obo/fovt/releases/2023-05-31/fovt.owl"
},
"ontobee": {
"library": "Library",
"name": "FuTRES Ontology of Vertebrate Traits",
"prefix": "FOVT"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/FOVT_$1"
},
"fplx": {
"aberowl": {
"name": "FamPlex",
"prefix": "FPLX"
},
"biocontext": {
"prefix": "FPLX"
},
"bioportal": {
"homepage": "https://github.com/sorgerlab/famplex",
"name": "FamPlex",
"prefix": "FPLX",
"publication": "https://www.biorxiv.org/content/early/2018/03/26/225698",
"version": "1.0"
},
"contact": {
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"example": "GPIb_IX_V",
"homepage": "https://sorgerlab.github.io/famplex/",
"license": "CC0-1.0",
"mappings": {
"aberowl": "FPLX",
"biocontext": "FPLX",
"bioportal": "FPLX",
"miriam": "fplx",
"n2t": "fplx"
},
"miriam": {
"deprecated": false,
"description": "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships.",
"homepage": "https://sorgerlab.github.io/famplex",
"id": "00000651",
"name": "FamPlex",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-zA-Z0-9][A-Za-z0-9_]+$",
"prefix": "fplx",
"sampleId": "RAS",
"uri_format": "https://sorgerlab.github.io/famplex/$1"
},
"n2t": {
"description": "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships.",
"example": "RAS",
"homepage": "http://bioportal.bioontology.org/ontologies/FPLX/",
"name": "FPLX through BioPortal",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-zA-Z0-9][A-Za-z0-9_]+$",
"prefix": "fplx",
"uri_format": "http://bioportal.bioontology.org/ontologies/FPLX/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FFPLX%23_$1"
},
"name": "FamPlex",
"publications": [
{
"doi": "10.1186/s12859-018-2211-5",
"pmc": "PMC6022344",
"pubmed": "29954318",
"title": "FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining",
"year": 2018
}
],
"synonyms": [
"famplex"
],
"uri_format": "https://sorgerlab.github.io/famplex/$1",
"wikidata": {
"paper": "Q55505864"
}
},
"fr": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology that enables the description of reviews of scientific articles and other scholarly resources.",
"example": "ReviewVersion",
"fairsharing": {
"abbreviation": "FR",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The FAIR* Reviews Ontology (FR) enables the description of reviews of scientific articles and other scholarly resources.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/fr",
"license": "CC-BY-4.0",
"name": "FAIR* Reviews Ontology ",
"prefix": "FAIRsharing.e7e609",
"repository": "https://github.com/sparontologies/fr",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"homepage": "http://www.sparontologies.net/ontologies/fr",
"mappings": {
"fairsharing": "FAIRsharing.e7e609"
},
"name": "FAIR* Reviews Ontology",
"preferred_prefix": "FR",
"repository": "https://github.com/sparontologies/fr"
},
"frapo": {
"aberowl": {
"name": "Funding, Research Administration and Projects Ontology",
"prefix": "FRAPO"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc.",
"example": "Grant",
"fairsharing": {
"abbreviation": "FRAPO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Funding, Research Administration and Projects Ontology (FRAPO) is an ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc.",
"domains": [
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/frapo",
"license": "CC-BY-4.0",
"name": "Funding, Research Administration and Projects Ontology ",
"prefix": "FAIRsharing.0a2576",
"repository": "https://github.com/sparontologies/frapo",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies",
"user_defined_tags": [
"Funding bodies",
"grant application",
"research project"
]
},
"homepage": "http://www.sparontologies.net/ontologies/frapo",
"lov": {
"description": "FRAPO, the Funding, Research Administration and Projects Ontology, is a CERIF-compliant ontology written in OWL 2 DL for describing research project administrative information.",
"homepage": "http://purl.org/cerif/frapo/",
"keywords": [
"Academy"
],
"modified": "2014-01-31",
"name": "Funding, Research Administration and Projects Ontology",
"prefix": "frapo",
"uri_prefix": "http://purl.org/cerif/frapo/$1"
},
"mappings": {
"aberowl": "FRAPO",
"fairsharing": "FAIRsharing.0a2576",
"lov": "frapo"
},
"name": "Funding, Research Administration and Projects Ontology",
"preferred_prefix": "FRAPO",
"repository": "https://github.com/sparontologies/frapo",
"uri_format": "http://purl.org/cerif/frapo/$1"
},
"frbr": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO.",
"example": "Expression",
"fairsharing": {
"abbreviation": "FRBR",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/frbr",
"license": "CC-BY-4.0",
"name": "Essential FRBR in OWL2 DL Ontology ",
"prefix": "FAIRsharing.b34b43",
"repository": "https://github.com/sparontologies/frbr",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"homepage": "http://www.sparontologies.net/ontologies/frbr",
"lov": {
"description": "An expression in RDF of the concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR)",
"homepage": "http://vocab.org/frbr/core.html",
"keywords": [
"FRBR"
],
"modified": "2009-05-16",
"name": "Expression of Core FRBR Concepts in RDF",
"prefix": "frbr",
"uri_prefix": "http://purl.org/vocab/frbr/core#$1"
},
"mappings": {
"fairsharing": "FAIRsharing.b34b43",
"lov": "frbr",
"zazuko": "frbr"
},
"name": "Functional Requirements for Bibliographic Records",
"preferred_prefix": "FRBR",
"repository": "https://github.com/sparontologies/frbr",
"uri_format": "http://purl.org/vocab/frbr/core#$1",
"zazuko": {
"prefix": "frbr",
"uri_format": "http://purl.org/vocab/frbr/core#$1"
}
},
"frbrer": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "This is the element set of native RDF classes and properties described in the current text (Feb 2009) of the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model. (from https://www.iflastandards.info/fr/frbr/frbrer.html)",
"download_rdf": "http://iflastandards.info/ns/fr/frbr/frbrer.jsonld",
"example": "1001",
"homepage": "https://www.iflastandards.info/fr/frbr/frbrer",
"lov": {
"description": "This is the element set of native RDF classes and properties described in the current text (Feb 2009) of the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model.",
"homepage": "http://iflastandards.info/ns/fr/frbr/frbrer/",
"keywords": [
"FRBR"
],
"modified": "2015-07-14",
"name": "FRBRer model",
"prefix": "frbrer",
"uri_prefix": "http://iflastandards.info/ns/fr/frbr/frbrer/$1"
},
"mappings": {
"lov": "frbrer"
},
"name": "Functional Requirements for Bibliographic Records Entity-Relationship Model",
"part_of": "frbr",
"uri_format": "http://iflastandards.info/ns/fr/frbr/frbrer/$1"
},
"fsnp": {
"biocontext": {
"prefix": "FSNP"
},
"mappings": {
"biocontext": "FSNP",
"miriam": "fsnp",
"n2t": "fsnp",
"prefixcommons": "fsnp"
},
"miriam": {
"deprecated": false,
"description": "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.",
"homepage": "http://compbio.cs.queensu.ca/F-SNP/",
"id": "00000496",
"name": "F-SNP",
"namespaceEmbeddedInLui": false,
"pattern": "^rs\\d+$",
"prefix": "fsnp",
"sampleId": "rs17852708",
"uri_format": "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1"
},
"n2t": {
"description": "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.",
"example": "rs17852708",
"homepage": "http://compbio.cs.queensu.ca/F-SNP/",
"name": "F-SNP at Queen's University (Canada)",
"namespaceEmbeddedInLui": false,
"pattern": "^rs\\d+$",
"prefix": "fsnp",
"uri_format": "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1"
},
"prefixcommons": {
"description": "F-SNP database provides integrated information about the functional effects of SNPs obtained from 16 bioinformatics tools and databases. The functional effects are predicted and indicated at the splicing, transcriptional, translational, and post-translational level. As such, the F-SNP database helps identify and focus on SNPs with potential pathological effect to human health.",
"example": "rs36095613",
"homepage": "http://compbio.cs.queensu.ca/F-SNP/",
"keywords": [
"DNA",
"protein"
],
"name": "F-SNP: a collection of functional SNPs, specifically prioritized for disease association studies",
"pattern": "^rs\\d+$",
"prefix": "fsnp"
}
},
"ftt": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific.",
"example": "273",
"homepage": "https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3",
"name": "Feature Type Thesaurus",
"pattern": "^\\d+$",
"references": [
"https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200",
"https://github.com/EnvironmentOntology/envo/issues/1130"
],
"uri_format": "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1"
},
"funcbase.fly": {
"biocontext": {
"prefix": "FUNCBASE.FLY"
},
"mappings": {
"biocontext": "FUNCBASE.FLY",
"miriam": "funcbase.fly",
"n2t": "funcbase.fly"
},
"miriam": {
"deprecated": false,
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data.",
"homepage": "http://func.mshri.on.ca/fly",
"id": "00000461",
"name": "FuncBase Fly",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "funcbase.fly",
"sampleId": "10194",
"uri_format": "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1"
},
"n2t": {
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data.",
"example": "10194",
"homepage": "http://func.mshri.on.ca/fly",
"name": "FuncBase Fly at Harvard Medical School",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "funcbase.fly",
"uri_format": "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1"
}
},
"funcbase.human": {
"biocontext": {
"prefix": "FUNCBASE.HUMAN"
},
"mappings": {
"biocontext": "FUNCBASE.HUMAN",
"miriam": "funcbase.human",
"n2t": "funcbase.human"
},
"miriam": {
"deprecated": false,
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data.",
"homepage": "http://func.mshri.on.ca/human/",
"id": "00000462",
"name": "FuncBase Human",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "funcbase.human",
"sampleId": "119514",
"uri_format": "http://func.mshri.on.ca/human/genes/list_functional_scores/$1"
},
"n2t": {
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data.",
"example": "119514",
"homepage": "http://func.mshri.on.ca/human/",
"name": "FuncBase Human at Harvard Medical School",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "funcbase.human",
"uri_format": "http://func.mshri.on.ca/human/genes/list_functional_scores/$1"
}
},
"funcbase.mouse": {
"biocontext": {
"prefix": "FUNCBASE.MOUSE"
},
"mappings": {
"biocontext": "FUNCBASE.MOUSE",
"miriam": "funcbase.mouse",
"n2t": "funcbase.mouse"
},
"miriam": {
"deprecated": false,
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse.",
"homepage": "http://func.mshri.on.ca/mouse/",
"id": "00000463",
"name": "FuncBase Mouse",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "funcbase.mouse",
"sampleId": "1351341",
"uri_format": "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1"
},
"n2t": {
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse.",
"example": "1351341",
"homepage": "http://func.mshri.on.ca/mouse/",
"name": "FuncBase Mouse at Harvard Medical School",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "funcbase.mouse",
"uri_format": "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1"
}
},
"funcbase.yeast": {
"biocontext": {
"prefix": "FUNCBASE.YEAST"
},
"mappings": {
"biocontext": "FUNCBASE.YEAST",
"miriam": "funcbase.yeast",
"n2t": "funcbase.yeast"
},
"miriam": {
"deprecated": false,
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast.",
"homepage": "http://func.mshri.on.ca/yeast",
"id": "00000464",
"name": "FuncBase Yeast",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "funcbase.yeast",
"sampleId": "2701",
"uri_format": "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1"
},
"n2t": {
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast.",
"example": "2701",
"homepage": "http://func.mshri.on.ca/yeast",
"name": "FuncBase Yeast at Harvard Medical School",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "funcbase.yeast",
"uri_format": "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1"
}
},
"funderregistry": {
"mappings": {
"miriam": "funderregistry"
},
"miriam": {
"deprecated": false,
"description": "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world.",
"homepage": "https://www.crossref.org/",
"id": "00000847",
"name": "FunderRegistry",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{9,9}$",
"prefix": "funderregistry",
"sampleId": "100000001",
"uri_format": "http://data.crossref.org/fundingdata/funder/10.13039/$1"
},
"providers": [
{
"code": "crossref.api",
"description": "Access funder data through the Crossref API",
"homepage": "https://api.crossref.org",
"name": "Crossref API",
"uri_format": "https://api.crossref.org/funders/$1"
},
{
"code": "doi",
"description": "Access funder data through a DOI for crossref funders.",
"homepage": "https://doi.org",
"name": "DOI",
"uri_format": "https://dx.doi.org/10.13039/501100000995"
}
],
"synonyms": [
"FundRef",
"crossref.funder"
]
},
"fungidb": {
"biocontext": {
"prefix": "FUNGIDB"
},
"fairsharing": {
"abbreviation": "FungiDB",
"contact": {
"email": "jason.stajich@ucr.edu",
"name": "Jason E. Stajich",
"orcid": "0000-0002-7591-0020"
},
"description": "FungiDB is an integrated genomic and functional genomic database for the kingdom Fungi. The database integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining.",
"homepage": "http://fungidb.org",
"name": "Fungal and Oomycete genomics resource",
"prefix": "FAIRsharing.xf30yc",
"publications": [
{
"doi": "10.1016/j.fgb.2016.04.002",
"pubmed_id": 27259951,
"title": "Database whiplash, crowdsourcing, and FungiDB."
},
{
"doi": "10.1093/nar/gkr918",
"pubmed_id": 22064857,
"title": "FungiDB: an integrated functional genomics database for fungi."
},
{
"doi": "10.1128/EC.00083-14",
"pubmed_id": 24813190,
"title": "Literature-based gene curation and proposed genetic nomenclature for cryptococcus."
}
],
"subjects": [
"Genomics"
],
"twitter": "fungidb"
},
"mappings": {
"biocontext": "FUNGIDB",
"fairsharing": "FAIRsharing.xf30yc",
"miriam": "fungidb",
"n2t": "fungidb",
"re3data": "r3d100011906"
},
"miriam": {
"deprecated": false,
"description": "FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina.",
"homepage": "https://fungidb.org/fungidb",
"id": "00000365",
"name": "FungiDB",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z_0-9]+$",
"prefix": "fungidb",
"sampleId": "CNBG_0001",
"uri_format": "https://fungidb.org/fungidb/app/record/gene/$1"
},
"n2t": {
"description": "FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina.",
"example": "CNBG_0001",
"homepage": "https://fungidb.org/fungidb",
"name": "FungiDB at University of California",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z_0-9]+$",
"prefix": "fungidb",
"uri_format": "https://fungidb.org/fungidb/app/record/gene/$1"
},
"publications": [
{
"doi": "10.1016/j.fgb.2016.04.002",
"pubmed": "27259951",
"title": "Database whiplash, crowdsourcing, and FungiDB",
"year": 2016
},
{
"doi": "10.1128/ec.00083-14",
"pmc": "PMC4135733",
"pubmed": "24813190",
"title": "Literature-based gene curation and proposed genetic nomenclature for cryptococcus",
"year": 2014
},
{
"doi": "10.1093/nar/gkr918",
"pmc": "PMC3245123",
"pubmed": "22064857",
"title": "FungiDB: an integrated functional genomics database for fungi",
"year": 2011
}
],
"re3data": {
"description": "FungiDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for the kingdom Fungi. FungiDB was first released in early 2011 as a collaborative project between EuPathDB and the group of Jason Stajich (University of California, Riverside). At the end of 2015, FungiDB was integrated into the EuPathDB bioinformatic resource center. FungiDB integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining.",
"homepage": "https://fungidb.org/fungidb/app",
"name": "FungiDB",
"prefix": "r3d100011906",
"synonyms": [
"The Fungal and Oomycete Genomics Resource"
],
"xrefs": {
"fairsharing": "FAIRsharing.xf30yc",
"nlx": "151401",
"omics": "03103",
"scr": "006013"
}
}
},
"fungorum": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "identifier for a fungus taxon in Index Fungorum",
"example": "154022",
"homepage": "http://www.indexfungorum.org",
"mappings": {
"ncbi": "Fungorum",
"wikidata": "P1391"
},
"name": "Index Fungorum",
"ncbi": {
"example": "ID550186",
"homepage": "http://www.indexfungorum.org",
"name": "Index Fungorum",
"prefix": "Fungorum"
},
"pattern": "^[1-9]\\d{0,5}$",
"uri_format": "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1",
"wikidata": {
"description": "identifier for a fungus taxon in Index Fungorum",
"example": [
"154022",
"17030",
"90345"
],
"name": "Index Fungorum taxon ID",
"pattern": "^[1-9]\\d{0,5}|$",
"prefix": "P1391",
"uri_format": "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1"
}
},
"fyeco": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "FYECO",
"uri_format": "https://www.pombase.org/term/$1"
},
"comment": "Rather than admitting FYECO to the OBO foundry, we secure the prefix here at bioregistry. The FYECO namespace shows up in a lot of ingests (basically anywhere you ingest PomBase gene-phenotype data). Future work includes mapping FYECO to other OBO ontologies, but this is way ahead in the future.",
"contact": {
"email": "vw253@cam.ac.uk",
"github": "ValWood",
"name": "Val Wood",
"orcid": "0000-0001-6330-7526"
},
"contributor": {
"email": "vw253@cam.ac.uk",
"github": "ValWood",
"name": "Val Wood",
"orcid": "0000-0001-6330-7526"
},
"description": "PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase.",
"example": "0000003",
"github_request_issue": 268,
"homepage": "https://github.com/pombase/fypo",
"mappings": {
"biolink": "FYECO"
},
"name": "Fission Yeast Experimental Conditions Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "FYECO",
"repository": "https://github.com/pombase/fypo",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"fyler": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A hierarchical classification of congenital heart disease ",
"example": "4447",
"homepage": "https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906",
"name": "Fyler",
"pattern": "^\\d+$",
"references": [
"https://github.com/obophenotype/human-phenotype-ontology/issues/2568",
"https://github.com/obophenotype/human-phenotype-ontology/issues/2511"
]
},
"fypo": {
"aberowl": {
"description": "FYPO is a formal ontology of phenotypes observed in fission yeast.",
"download_owl": "http://aber-owl.net/media/ontologies/FYPO/464/fypo.owl",
"homepage": "https://github.com/pombase/fypo",
"name": "Fission Yeast Phenotype Ontology",
"prefix": "FYPO"
},
"biocontext": {
"prefix": "FYPO"
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},
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"contact": {
"email": "vw253@cam.ac.uk",
"name": "Valerie Wood"
},
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"name": "Fission Yeast Phenotype Ontology",
"prefix": "FYPO",
"version": "2024-08-01"
},
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"abbreviation": "FYPO",
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"name": "Valerie Wood",
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},
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"Phenotype"
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}
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"Phylogenetics",
"Life Science"
]
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"obofoundry": "fypo",
"ols": "fypo",
"ontobee": "FYPO"
},
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"contact.github": "ValWood",
"contact.label": "Val Wood",
"contact.orcid": "0000-0001-6330-7526",
"deprecated": false,
"description": "FYPO is a formal ontology of phenotypes observed in fission yeast.",
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"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"logo": "https://github.com/pombase/website/blob/master/src/assets/FYPO_logo_tiny.png",
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{
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],
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},
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"homepage": "https://github.com/pombase/fypo",
"name": "Fission Yeast Phenotype Ontology (FYPO)",
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"prefix": "FYPO"
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{
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},
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},
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"n2t": "gabi",
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"sampleId": "2679240",
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"name": "GABI at Max Planck",
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"homepage": "http://www.gabipd.org/information/about.shtml",
"name": "Network of Different Plant Genomic Research Projects",
"prefix": "GABI"
},
"prefixcommons": {
"description": "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'.",
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"homepage": "http://www.gabi.de/",
"keywords": [
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"genome",
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],
"name": "Network of Different Plant Genomic Research Projects",
"pattern": "^\\w+$",
"prefix": "gabi",
"pubmed_ids": [
"18812395"
],
"uri_format": "http://gabi.rzpd.de/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject"
},
"publications": [
{
"doi": "10.1093/nar/gkn611",
"pmc": "PMC2686513",
"pubmed": "18812395",
"title": "GabiPD: the GABI primary database--a plant integrative 'omics' database",
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}
]
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"gainesville.core": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Describes typical Computational Chemistry experiments, including Molecular Publications, Molecular Systems, Molecular Calculations",
"download_owl": "http://ontologies.makolab.com/gc06/gc.owl",
"example": "Aromatic",
"homepage": "http://ontologies.makolab.com/gc06/gc.html",
"license": "CC-BY-3.0",
"name": "Gainesville Core Ontology",
"references": [
"http://ontologies.makolab.com/gc/"
],
"uri_format": "http://purl.org/gc/$1"
},
"galen": {
"aberowl": {
"description": "A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.",
"download_owl": "http://aber-owl.net/media/ontologies/GALEN/1/galen.owl",
"homepage": "http://www.co-ode.org/galen/",
"name": "Galen Ontology",
"prefix": "GALEN",
"version": "1.1"
},
"bioportal": {
"contact": {
"email": "j@deltaflow.com",
"name": "Julian Seidenberg"
},
"description": "A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.",
"homepage": "http://www.co-ode.org/galen/",
"name": "Galen Ontology",
"prefix": "GALEN",
"version": "1.1"
},
"comment": "I really tried, but could not figure out what GALEN stands for",
"deprecated": true,
"example": "MagnitudeValueType",
"homepage": "https://www.opengalen.org",
"mappings": {
"aberowl": "GALEN",
"bioportal": "GALEN"
},
"name": "GALEN",
"uri_format": "http://www.co-ode.org/ontologies/galen#$1"
},
"gallont": {
"aberowl": {
"description": "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls.",
"download_owl": "http://aber-owl.net/media/ontologies/GALLONT/5/gallont.owl",
"homepage": "https://adeans.github.io/gallont/",
"name": "Plant Gall Ontology",
"prefix": "GALLONT"
},
"agroportal": {
"contact": {
"email": "adeans@psu.edu",
"name": "Andy Deans"
},
"description": "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls., None",
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"homepage": "https://adeans.github.io/gallont/",
"license": "CC0-1.0",
"name": "Plant Gall Ontology",
"prefix": "GALLONT",
"publication": "https://doi.org/10.3897/arphapreprints.e128953",
"repository": "https://github.com/adeans/gallont",
"version": "2024-04-19"
},
"bioportal": {
"contact": {
"email": "adeans@psu.edu",
"name": "Andy Deans"
},
"description": "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls.",
"homepage": "https://adeans.github.io/gallont/",
"name": "Plant Gall Ontology",
"prefix": "GALLONT",
"version": "2024-04-19"
},
"example": "0000001",
"mappings": {
"aberowl": "GALLONT",
"agroportal": "GALLONT",
"bioportal": "GALLONT",
"obofoundry": "gallont",
"ontobee": "GALLONT"
},
"obofoundry": {
"contact": "adeans@psu.edu",
"contact.github": "adeans",
"contact.label": "Andy Deans",
"contact.orcid": "0000-0002-2119-4663",
"depends_on": [
"caro",
"flopo",
"ncbitaxon",
"obi",
"pato",
"po",
"poro",
"ro"
],
"deprecated": false,
"description": "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls.",
"domain": "phenotype",
"download.json": "http://purl.obolibrary.org/obo/gallont.json",
"download.obo": "http://purl.obolibrary.org/obo/gallont.obo",
"download.owl": "http://purl.obolibrary.org/obo/gallont.owl",
"homepage": "https://adeans.github.io/gallont/",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Plant Gall Ontology",
"preferredPrefix": "GALLONT",
"prefix": "gallont",
"repository": "https://github.com/adeans/gallont"
},
"ontobee": {
"library": "Library",
"name": "Plant Gall Ontology",
"prefix": "GALLONT"
},
"pattern": "^\\d{7}$"
},
"gard": {
"contact": {
"email": "eric.sid@nih.gov",
"github": "ericsid",
"name": "Eric Sid",
"orcid": "0000-0001-7697-3026"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease.",
"example": "6038",
"homepage": "https://rarediseases.info.nih.gov/diseases",
"mappings": {
"wikidata": "P4317"
},
"name": "Genetic and Rare Diseases Information Center",
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1080/02763869.2022.2131143",
"pubmed": "36394913",
"title": "Genetic and Rare Diseases Information Center (GARD)",
"year": 2022
},
{
"doi": "10.3233/trd-170011",
"pmc": "PMC5685198",
"pubmed": "29152459",
"title": "Marking 15 years of the Genetic and Rare Diseases Information Center",
"year": 2017
}
],
"synonyms": [
"GARD",
"Genetic and Rare Diseases Information Center"
],
"uri_format": "https://rarediseases.info.nih.gov/diseases/$1/index",
"wikidata": {
"description": "identifier for a rare disease in the United States National Institutes of Health's Genetic and Rare Diseases (GARD) Information Center database",
"example": [
"1062",
"10716",
"12136"
],
"homepage": "https://rarediseases.info.nih.gov/diseases/",
"name": "GARD rare disease ID",
"pattern": "^[1-9]\\d*$",
"prefix": "P4317",
"uri_format": "https://rarediseases.info.nih.gov/diseases/$1/index"
}
},
"gateway": {
"mappings": {
"miriam": "gateway"
},
"miriam": {
"deprecated": false,
"description": "The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access.",
"homepage": "https://www.hdruk.ac.uk",
"id": "00000796",
"name": "gateway",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$",
"prefix": "gateway",
"sampleId": "fd8d0743-344a-4758-bb97-f8ad84a37357",
"uri_format": "https://web.www.healthdatagateway.org/dataset/$1"
},
"name": "Health Data Research Innovation Gateway"
},
"gaz": {
"aberowl": {
"description": "Gazetteer",
"download_obo": "http://aber-owl.net/media/ontologies/GAZ/14/gaz.obo",
"homepage": "http://gensc.org/gc_wiki/index.php/GAZ_Project",
"name": "Gazetteer",
"prefix": "GAZ",
"version": "$Revision: 1.512 $"
},
"biocontext": {
"prefix": "GAZ"
},
"bioportal": {
"contact": {
"email": "lschriml@som.umaryland.edu",
"name": "Lynne Schriml"
},
"description": "GAZ is a large, ontologically-oriented resource listing place names which can be treated as instances of environments.",
"homepage": "http://environmentontology.github.io/gaz/",
"name": "Gazetteer",
"prefix": "GAZ",
"version": "$Revision: 1.512 $"
},
"download_obo": "http://purl.obolibrary.org/obo/gaz.obo",
"example": "00620027",
"fairsharing": {
"abbreviation": "GAZ",
"description": "A controlled vocabulary following ontological rules that describes named geographical locations. GAZ represents a first step towards an open source gazetteer, constructed on ontological principles, that describes places and place names and the relations between them.",
"domains": [
"Geographical location"
],
"homepage": "http://environmentontology.github.io/gaz/",
"license": "CC0-1.0",
"name": "Gazetteer",
"prefix": "FAIRsharing.wkdjpb",
"subjects": [
"Environmental Science"
]
},
"mappings": {
"aberowl": "GAZ",
"biocontext": "GAZ",
"bioportal": "GAZ",
"fairsharing": "FAIRsharing.wkdjpb",
"obofoundry": "gaz",
"ols": "gaz",
"ontobee": "GAZ",
"wikidata": "P6778"
},
"obofoundry": {
"appears_in": [
"scdo"
],
"contact": "lschriml@som.umaryland.edu",
"contact.github": "lschriml",
"contact.label": "Lynn Schriml",
"contact.orcid": "0000-0001-8910-9851",
"deprecated": true,
"description": "A gazetteer constructed on ontological principles. The countries are actively maintained.",
"domain": "environment",
"download.obo": "http://purl.obolibrary.org/obo/gaz.obo",
"download.owl": "http://purl.obolibrary.org/obo/gaz.owl",
"homepage": "http://environmentontology.github.io/gaz/",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Gazetteer",
"prefix": "gaz",
"repository": "https://github.com/EnvironmentOntology/gaz"
},
"ols": {
"description": "A gazetteer constructed on ontological principles. The countries are actively maintained.",
"download_owl": "http://purl.obolibrary.org/obo/gaz.owl",
"homepage": "http://environmentontology.github.io/gaz/",
"name": "Gazetteer",
"prefix": "gaz"
},
"ontobee": {
"library": "Library",
"name": "Gazetteer",
"prefix": "GAZ"
},
"pattern": "^\\d{8}$",
"wikidata": {
"description": "identifier from the Open Bio Ontologies Gazetteer (GAZ) (without prefix)",
"example": [
"00000005",
"00001460",
"00008990"
],
"homepage": "http://obofoundry.org/ontology/gaz",
"name": "OBO Gazetteer ID",
"pattern": "^\\d{8}$",
"prefix": "P6778",
"uri_format": "http://purl.obolibrary.org/obo/GAZ_$1",
"uri_format_rdf": "http://purl.obolibrary.org/obo/GAZ_$1"
}
},
"gbif": {
"contact": {
"email": "timrobertson100@gmail.com",
"github": "timrobertson100",
"name": "Tim Robertson",
"orcid": "0000-0001-6215-3617"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Database of living organisms, taxonomic. \n The GBIFβthe Global Biodiversity Information Facilityβis international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth.",
"example": "4238",
"fairsharing": {
"abbreviation": "GBIF.org",
"description": "GBIFβthe Global Biodiversity Information Facilityβis an international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth.\n\nStrictly speaking, GBIF is not a data repository. Rather, GBIF indexes thousands of datasets through a distributed infrastructure involving more than 100 formal participants that supports hundreds of data-publishing institutions worldwide. GBIF.org makes the FAIR and open data discoverable and citable, assigning each download a DOI and storing it for an extended period of time. More than three peer-reviewed research articles make use of data from the GBIF network every day, in studies spanning the impacts of climate change, the spread of pests and diseases, priority areas for conservation and food security. \n\nTo share data with GBIF, follow this quick guide: http://www.gbif.org/publishing-data/quick-guide. To deposit or host data, we suggest using one of the trusted data hosting centres (DHC) listed in FAIRsharing.org that uses GBIF's IPT (Integrated Publishing Toolkit) software. The DHC provides data publishers with a hosted IPT account enabling them to manage and publish datasets through GBIF.org.",
"homepage": "https://www.gbif.org",
"license": "CC0-1.0",
"name": "GBIF.org",
"prefix": "FAIRsharing.zv11j3",
"publications": [
{
"doi": "10.1371/journal.pone.0102623",
"pubmed_id": 25099149,
"title": "The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet."
}
],
"repository": "https://github.com/gbif/",
"subjects": [
"Metagenomics",
"Bioinformatics",
"Taxonomy",
"Marine Biology",
"Biodiversity",
"Natural Science",
"Natural History"
],
"twitter": "GBIF"
},
"homepage": "https://www.gbif.org/species",
"integbio": {
"alt_name": "Global Biodiversity Information Facility free and open access to biodiversity data",
"description": "GBIF (Global Biodiversity Information Facility) is a database of information on Biodiversity and its global effect.\nA network of countries across the globe has access to, and participates in supplying, information to the database. \nThere are 38 countries that support the facility financially and are therefore members of the voting governing board.\nThe database contains 396,026,747 indexed records and 10,004 sets of data provided by 464 publishers.\nIt is imperative that the users of any data obtained by means of the GBIF Portal will always give credit to the original data publishers. \nA keyword search option is provided whereby the facility can be searched for information on a specific group of organisms of a specific country or as displayed in a specific set of data.",
"fairsharing": "biodbcore-000635",
"homepage": "http://www.gbif.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Repository"
],
"maintainer": "GBIF Secretariat",
"name": "GBIF",
"prefix": "nbdc00069",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"mappings": {
"fairsharing": "FAIRsharing.zv11j3",
"integbio": "nbdc00069",
"re3data": "r3d100000039",
"wikidata": "P846"
},
"name": "Global Biodiversity Information Facility",
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1371/journal.pone.0102623",
"pmc": "PMC4123864",
"pubmed": "25099149",
"title": "The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet",
"year": 2014
}
],
"re3data": {
"description": "GBIF is an international organisation that is working to make the world's biodiversity data accessible everywhere in the world. GBIF and its many partners work to mobilize the data, and to improve search mechanisms, data and metadata standards, web services, and the other components of an Internet-based information infrastructure for biodiversity.\nGBIF makes available data that are shared by hundreds of data publishers from around the world. These data are shared according to the GBIF Data Use Agreement, which includes the provision that users of any data accessed through or retrieved via the GBIF Portal will always give credit to the original data publishers.",
"homepage": "https://www.gbif.org/",
"name": "Global Biodiversity Information Facility",
"prefix": "r3d100000039",
"synonyms": [
"Data index of the Global Biodiversity Information Facility",
"GBIF.org"
],
"xrefs": {
"fairsharing": "FAIRsharing.zv11j3",
"nlx": "149475",
"ror": "05fjyn938",
"scr": "005904"
}
},
"twitter": "GBIF",
"uri_format": "https://www.gbif.org/species/$1",
"wikidata": {
"description": "taxon identifier in GBIF",
"example": [
"1948418",
"3239598",
"4656467",
"5963040"
],
"name": "GBIF taxon ID",
"pattern": "^([1-9]\\d{0,8}|)$",
"prefix": "P846",
"uri_format": "https://www.gbif.org/species/$1"
}
},
"gc": {
"comment": "see comment here: https://github.com/obophenotype/ncbitaxon/issues/47",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries.",
"example": "11",
"homepage": "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html",
"name": "Genetic Code",
"pattern": "^\\d+$",
"references": [
"https://github.com/obophenotype/ncbitaxon/issues/47"
],
"synonyms": [
"gc_id"
],
"uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1"
},
"gcst": {
"mappings": {
"miriam": "gcst",
"n2t": "gcst"
},
"miriam": {
"deprecated": false,
"description": "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide.",
"homepage": "https://www.ebi.ac.uk",
"id": "00000715",
"name": "GWAS Catalog",
"namespaceEmbeddedInLui": false,
"pattern": "^GCST\\d{6}\\d*$",
"prefix": "gcst",
"sampleId": "GCST000035",
"uri_format": "https://www.ebi.ac.uk/gwas/studies/$1"
},
"n2t": {
"description": "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide.",
"example": "GCST000035",
"homepage": "https://www.ebi.ac.uk/gwas/studies",
"name": "GWAS Catalog",
"namespaceEmbeddedInLui": false,
"pattern": "^GCST\\d{6}$",
"prefix": "gcst",
"uri_format": "https://www.ebi.ac.uk/gwas/studies/$1"
},
"owners": [
{
"name": "European Bioinformatics Institute",
"partnered": false,
"ror": "02catss52"
}
]
},
"gdc": {
"biocontext": {
"prefix": "GDC"
},
"mappings": {
"biocontext": "GDC",
"miriam": "gdc",
"n2t": "gdc"
},
"miriam": {
"deprecated": false,
"description": "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis.",
"homepage": "https://gdc.cancer.gov",
"id": "00000604",
"name": "Genomic Data Commons Data Portal",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$",
"prefix": "gdc",
"sampleId": "ae8c77fe-e6c8-44d5-8265-4a38c637bbef",
"uri_format": "https://portal.gdc.cancer.gov/cases/$1"
},
"n2t": {
"description": "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis.",
"example": "ae8c77fe-e6c8-44d5-8265-4a38c637bbef",
"homepage": "https://gdc.cancer.gov",
"name": "Genomic Data Commons",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$",
"prefix": "gdc",
"uri_format": "https://portal.gdc.cancer.gov/cases/$1"
}
},
"gdsc": {
"cellosaurus": {
"category": "Chemistry resources",
"homepage": "https://www.cancerrxgene.org",
"name": "Genomics of Drug Sensitivity in Cancer Project",
"prefix": "GDSC",
"uri_format": "https://www.cancerrxgene.org/translation/CellLine/$1"
},
"mappings": {
"cellosaurus": "GDSC",
"miriam": "gdsc",
"n2t": "gdsc"
},
"miriam": {
"deprecated": false,
"description": "The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies.",
"homepage": "https://www.cancerrxgene.org",
"id": "00000678",
"name": "Genomics of Drug Sensitivity in Cancer",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "gdsc",
"sampleId": "1242",
"uri_format": "https://www.cancerrxgene.org/translation/Drug/$1"
},
"n2t": {
"description": "The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies.",
"example": "1242",
"homepage": "https://www.cancerrxgene.org",
"name": "Genomics of Drug Sensitivity in Cancer",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "gdsc",
"uri_format": "https://www.cancerrxgene.org/translation/Drug/$1"
}
},
"gear": {
"contact": {
"email": "jorvis@gmail.com",
"github": "jorvis",
"name": "Joshua Orvis",
"orcid": "0000-0002-5705-5710"
},
"contributor": {
"email": "jorvis@gmail.com",
"github": "jorvis",
"name": "Joshua Orvis",
"orcid": "0000-0002-5705-5710"
},
"description": "The gEAR portal is a website for visualization and analysis of multi-omic data both in public and private domains.",
"example": "d.a59037e8",
"example_extras": [
"p.bfd178f5"
],
"github_request_issue": 728,
"homepage": "https://umgear.org",
"license": "AGPL-3.0-only",
"name": "Gene Expression Analysis Resource",
"pattern": "^[dp]\\.[a-z0-9]{8}$",
"repository": "https://github.com/IGS/gEAR",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://umgear.org/p?id=$1"
},
"gecko": {
"aberowl": {
"description": "An ontology to represent genomics cohort attributes",
"download_owl": "http://aber-owl.net/media/ontologies/GECKO/10/gecko.owl",
"homepage": "https://github.com/IHCC-cohorts/GECKO",
"name": "Genomics Cohorts Knowledge Ontology",
"prefix": "GECKO"
},
"bioportal": {
"contact": {
"email": "rbca.jackson@gmail.com",
"name": "Rebecca Jackson"
},
"description": "An ontology to represent genomics cohort attributes.",
"homepage": "https://github.com/IHCC-cohorts/GECKO",
"name": "Genomics Cohorts Knowledge Ontology",
"prefix": "GECKO"
},
"example": "0000044",
"fairsharing": {
"abbreviation": "GECKO",
"contact": {
"email": "mcourtot@gmail.com",
"name": "MΓ©lanie Courtot",
"orcid": "0000-0002-9551-6370"
},
"description": "GECKO is an ontology to represent genomics cohort attributes. The GECKO is maintained by the CINECA project, and standardises attributes commonly used for genomics cohort description as well as individual-level data items.",
"domains": [
"Experimental measurement",
"Biological sample"
],
"homepage": "https://github.com/IHCC-cohorts/GECKO",
"license": "CC-BY-4.0",
"name": "Genomics Cohorts Knowledge Ontology",
"prefix": "FAIRsharing.3da56b",
"subjects": [
"Genomics",
"Statistics",
"Life Science"
],
"user_defined_tags": [
"Survey"
]
},
"mappings": {
"aberowl": "GECKO",
"bioportal": "GECKO",
"fairsharing": "FAIRsharing.3da56b",
"obofoundry": "gecko",
"ols": "gecko",
"ontobee": "GECKO"
},
"obofoundry": {
"contact": "rbca.jackson@gmail.com",
"contact.github": "beckyjackson",
"contact.label": "Rebecca Jackson",
"contact.orcid": "0000-0003-4871-5569",
"deprecated": false,
"description": "An ontology to represent genomics cohort attributes",
"domain": "organisms",
"download.owl": "http://purl.obolibrary.org/obo/gecko.owl",
"homepage": "https://github.com/IHCC-cohorts/GECKO",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Genomics Cohorts Knowledge Ontology",
"preferredPrefix": "GECKO",
"prefix": "gecko",
"repository": "https://github.com/IHCC-cohorts/GECKO"
},
"ols": {
"description": "An ontology to represent genomics cohort attributes.",
"download_owl": "http://purl.obolibrary.org/obo/gecko.owl",
"homepage": "https://github.com/IHCC-cohorts/GECKO",
"name": "Genomics Cohorts Knowledge Ontology",
"prefix": "gecko",
"version": "2021-01-18",
"version.iri": "http://purl.obolibrary.org/obo/gecko/releases/2021-01-18/gecko.owl"
},
"ontobee": {
"library": "Library",
"name": "Genomics Cohorts Knowledge Ontology",
"prefix": "GECKO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/GECKO_$1"
},
"gemet": {
"agroportal": {
"contact": {
"email": "helpdesk@eionet.europa.eu",
"name": "Eionet Helpdesk"
},
"description": "The basic idea for the development of GEMET was to use the best of the presently available excellent multilingual thesauri, in order to save time, energy and funds. GEMET was conceived as a βgeneralβ thesaurus, aimed to define a common general language, a core of general terminology for the environment. Specific thesauri and descriptor systems (e.g. on Nature Conservation, on Wastes, on Energy, etc.) have been excluded from the first step of development of the thesaurus and have been taken into account only for their structure and upper level terminology.",
"example_uri": "http://www.eionet.europa.eu/gemet/concept/5580",
"homepage": "http://www.eionet.europa.eu/gemet/en/about/",
"license": "http://creativecommons.org/licenses/by/2.5/dk",
"name": "GEneral Multilingual Environmental Thesaurus",
"prefix": "GEMET",
"publication": "http://www.eionet.europa.eu/gemet/en/about/#chapter-VII",
"version": "4.2.3"
},
"bartoc": {
"abbreviation": "GEMET",
"description": "The basic idea for the development of GEMET was to use the best of the presently available excellent multilingual thesauri, in order to save time, energy and funds. GEMET was conceived as a 'general' thesaurus, aimed to define a common general language, a core of general terminology for the environment. Specific thesauri and descriptor systems (e.g. on Nature Conservation, on Wastes, on Energy, etc.) have been excluded from the first step of development of the thesaurus and have been taken into account only for their structure and upper level terminology. The merging has been performed both on conceptual and formal basis. Coinciding concepts in the different thesauri have been identified and scored. Like in other multilingual thesauri, e. g. Infoterra EnVoc, a neutral alphanumerical notation allows the identification of a concept independently on the user's language.\n\nThe links with the original thesauri are ensured by the respective identifiers or code notations. Following the identification of the coinciding concepts, a selection was made by the experts of the National Focal Points of the organisations involved. The resulting 6.562 terms have been arranged in a classification scheme made of 3 super-groups, 30 groups plus 5 accessory, instrumental groups. Each descriptor has been arranged in a hierarchical structure headed by a Top Term. The level of poly-hierarchy, i.e. the allocation of a descriptor to more than one group, has been kept to a minimum. Further, to allow a thematic retrieval of terms thematically related but scattered in different groups, a set of 40 themes have been agreed upon with the EEA and each descriptor has been assigned to as many themes as necessary. Thus, the user can access the thesaurus through the group- hierarchical list, through the thematic list or through the alphabetical list. As a complement to the hierarchical 'vertical' relations, an exhaustive series of strong 'horizontal' relations between terms (RT, Related Terms) have been introduced. A progressive Line Number has been assigned to each descriptor of the systematic list, in order to help the user of the lists to identify the descriptor in the different lists. The Line Number is merely a neutral identifier for the present version. The GEMET size, formerly figured at about 200000 descriptors, rose to more than 5.000 in the course of merging, due to the limited overlapping between the different thesauri, to constraints of the selection work carried out by the parental organisations and to a few new additions, mainly from CDS indexing work. The present version 2001* of GEMET is the result of a close collaboration between CNR and UBA under contract and supervision of the ETC/CDS. It presents 5.298 descriptors, including 109 Top Terms, and 1.264 synonyms in English. The 5.524 terms belonging to the parental thesauri and not included in GEMET, constitute an accessory alphabetical list of free terms. GEMET has been developed as an indexing, retrieval and control tool for the European Topic Centre on Catalogue of Data Sources (ETC/CDS) and the European Environment Agency (EEA), Copenhagen.",
"homepage": "http://www.eionet.europa.eu/gemet/",
"license": "CC-BY-3.0",
"name": "General Multilingual Environmental Thesaurus",
"prefix": "16",
"wikidata_database": "Q1485161"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts.",
"example": "627",
"fairsharing": {
"abbreviation": "GEMET",
"description": "The GEneral Multilingual Environmental Thesaurus (GEMET) was created as a βgeneralβ environmental thesaurus, aimed to define a common general language with a core of general terminology for the environment. It is the reference vocabulary of the European Environment Agency (EEA) and its Network (Eionet).",
"homepage": "https://www.eionet.europa.eu/gemet/en/themes/",
"name": "GEneral Multilingual Environmental Thesaurus",
"prefix": "FAIRsharing.9091d9",
"subjects": [
"Environmental Science",
"Ecology",
"Biodiversity"
]
},
"homepage": "https://www.eionet.europa.eu/gemet/en/themes/",
"mappings": {
"agroportal": "GEMET",
"bartoc": "16",
"fairsharing": "FAIRsharing.9091d9"
},
"name": "General Multilingual Environmental Thesaurus",
"pattern": "^\\d+$",
"uri_format": "https://www.eionet.europa.eu/gemet/en/concept/$1"
},
"genatlas": {
"biocontext": {
"prefix": "GENATLAS"
},
"fairsharing": {
"abbreviation": "GenAtlas",
"description": "GenAtlas is a database containing information on human genes, markers and phenotypes.",
"homepage": "http://www.genatlas.org/",
"name": "GenAtlas",
"prefix": "FAIRsharing.pmg2vd",
"publications": [
{
"doi": "10.1016/s0764-4469(99)80021-3",
"pubmed_id": 9835018,
"title": "Genatlas database, genes and development defects"
},
{
"doi": "10.1006/mgme.1999.2867",
"pubmed_id": 10444337,
"title": "Human genes involved in chromatin remodeling in transcription initiation, and associated diseases: An overview using the GENAtlas database"
}
],
"subjects": [
"Life Science"
]
},
"integbio": {
"description": "Genatlas is a collection of information on gene mapping and the diseases they are genetically related to. \nThe data is obtained by scanning available literature on a regular basis.\nThis database contains information on 22,723 genes, 5,065 phenotypes and 113,755 citations.\nNew information is available immediately after the site is updated and this is done daily.\nSeveral search options are available. \nA search for all genes involved with one disease, called a phenotype search, reveals information pertaining to chromosomal diseases.\nA full search of the gene Database, on the basis of DNA characteristics, RNA characteristics, protein characteristics, expression, and/or pathology gives information about all diseases related to one gene.\nA search of the Citation Database leads to a list of all citations about a particular gene or disease.",
"fairsharing": "biodbcore-000377",
"homepage": "http://genatlas.medecine.univ-paris5.fr/",
"information_keywords": [
"Phenotype",
"Sequence",
"Expression",
"Bibliography/Documents"
],
"maintainer": "Universite Rene Descartes",
"name": "GENATLAS",
"prefix": "nbdc00275",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein",
"Health/Disease"
]
},
"mappings": {
"biocontext": "GENATLAS",
"fairsharing": "FAIRsharing.pmg2vd",
"integbio": "nbdc00275",
"miriam": "genatlas",
"n2t": "genatlas",
"prefixcommons": "genatlas",
"uniprot": "DB-0027"
},
"miriam": {
"deprecated": false,
"description": "GenAtlas is a database containing information on human genes, markers and phenotypes.",
"homepage": "http://genatlas.medecine.univ-paris5.fr/",
"id": "00000208",
"name": "Genatlas",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "genatlas",
"sampleId": "HBB",
"uri_format": "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1"
},
"n2t": {
"description": "GenAtlas is a database containing information on human genes, markers and phenotypes.",
"example": "HBB",
"homepage": "http://genatlas.medecine.univ-paris5.fr/",
"name": "Genatlas at Paris Descartes University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "genatlas",
"uri_format": "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1"
},
"prefixcommons": {
"description": "GenAtlas is a database containing information on human genes, markers and phenotypes.",
"example": "HBB",
"homepage": "http://www.genatlas.org/",
"keywords": [
"disorder",
"gene",
"human"
],
"name": "GenAtlas: human gene database",
"pattern": "^\\w+$",
"prefix": "genatlas",
"pubmed_ids": [
"9835018"
],
"uri_format": "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1"
},
"publications": [
{
"doi": "10.1016/s0764-4469(99)80021-3",
"pubmed": "9835018",
"title": "Genatlas database, genes and development defects",
"year": 1998
},
{
"doi": "10.1006/mgme.1999.2867",
"pubmed": "10444337",
"title": "Human genes involved in chromatin remodeling in transcription initiation, and associated diseases: An overview using the GENATLAS database",
"year": 1999
}
],
"uniprot": {
"abbreviation": "GenAtlas",
"category": "Organism-specific databases",
"homepage": "http://genatlas.medecine.univ-paris5.fr/",
"name": "GenAtlas",
"prefix": "DB-0027",
"publications": [
{
"doi": "10.1016/s0764-4469(99)80021-3",
"pubmed": "9835018"
}
],
"uri_format": "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1"
}
},
"genbank": {
"biocontext": {
"prefix": "GenBank",
"uri_format": "http://www.ncbi.nlm.nih.gov/nuccore/$1"
},
"cheminf": {
"description": [],
"name": "GenBank Nucleotide Identifier",
"obsolete": false,
"prefix": "000304"
},
"contact": {
"email": "nawrocke@ncbi.nlm.nih.gov",
"github": "nawrockie",
"name": "Eric P. Nawrocki",
"orcid": "0000-0002-2497-3427"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "GenBank Β is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42).",
"edam": {
"description": "Accession number of an entry from the GenBank sequence database.",
"name": "GenBank",
"obsolete": false,
"prefix": "2292"
},
"example": "U49845",
"fairsharing": {
"abbreviation": "GenBank",
"description": "GenBank Β is the NIH genetic sequence database of annotated collections of all publicly available DNA sequences. GenBank is part of an International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI. The GenBank database is designed to provide and encourage access within the scientific community to the most up-to-date and comprehensive DNA sequence information, and release available versioned collections every two months from the ftp site. As part of the International Nucleotide Sequence Database Collaboration (INSDC), a long-standing foundational initiative (operating between DDBJ, EMBL-EBI and NCBI), the INSDC covers the spectrum of data raw reads, through alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations. GenBank data submission types include: mRNA sequences, Prokaryotic genes, Eukaryotic genes, rRNA and/or ITS, viral sequences, transposon or insertion sequences, microsatellite sequences, pseudogenes, cloning vectors, phylogenetic or population sets, and non-coding RNAs.\n",
"homepage": "https://www.ncbi.nlm.nih.gov/genbank/",
"license": "https://www.insdc.org/policy",
"name": "GenBank Nucleotide Sequence Database",
"prefix": "FAIRsharing.9kahy4",
"publications": [
{
"doi": "10.1093/nar/gkr1202",
"pubmed_id": 22144687,
"title": "GenBank."
},
{
"doi": "10.1093/nar/gkq1079",
"pubmed_id": 21071399,
"title": "GenBank."
},
{
"doi": "10.1093/nar/gkm929",
"pubmed_id": 18073190,
"title": "GenBank."
},
{
"doi": "10.1093/nar/gkn723",
"pubmed_id": 18940867,
"title": "GenBank."
},
{
"doi": "10.1093/nar/gks1195",
"pubmed_id": 23193287,
"title": "GenBank."
},
{
"doi": "10.1093/nar/gkt1030",
"pubmed_id": 24217914,
"title": "GenBank."
},
{
"doi": "10.1093/nar/gkx1094",
"pubmed_id": 29140468,
"title": "GenBank"
},
{
"doi": "10.1093/nar/gkz956",
"pubmed_id": 31665464,
"title": "GenBank."
},
{
"doi": "10.1093/nar/gky989",
"pubmed_id": 30365038,
"title": "GenBank."
},
{
"doi": "10.1093/nar/gkw1070",
"pubmed_id": 27899564,
"title": "GenBank."
},
{
"doi": "10.1093/nar/gkv1276",
"pubmed_id": 26590407,
"title": "GenBank."
},
{
"doi": "10.1093/nar/gku1216",
"pubmed_id": 25414350,
"title": "GenBank."
},
{
"doi": "10.1186/s12859-020-3537-3",
"pubmed_id": null,
"title": "VADR: validation and annotation of virus sequence submissions to GenBank"
},
{
"doi": "10.1093/nar/gks1195",
"pubmed_id": 23193287,
"title": "GenBank"
}
],
"subjects": [
"Functional Genomics",
"Metagenomics",
"Genomics",
"Bioinformatics",
"Data Management",
"Virology",
"Transcriptomics",
"Epidemiology"
]
},
"go": {
"description": "The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.",
"homepage": "http://www.ncbi.nlm.nih.gov/Genbank/",
"name": "GenBank",
"prefix": "GenBank",
"synonyms": [
"GB"
]
},
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},
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{
"doi": "10.1093/glycob/cwx066",
"pmc": "PMC5881658",
"pubmed": "28922742",
"title": "GlyTouCan: an accessible glycan structure repository",
"year": 2017
},
{
"doi": "10.1093/nar/gkv1041",
"pmc": "PMC4702779",
"pubmed": "26476458",
"title": "GlyTouCan 1.0--The international glycan structure repository",
"year": 2015
}
],
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"name": "GlyTouCan",
"prefix": "r3d100012388",
"synonyms": [
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],
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}
},
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"G81263BG",
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],
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"Glycan"
],
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"prefix": "Glytoucan",
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}
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},
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"name": "Joachim Kopka",
"orcid": "0000-0001-9675-4883"
},
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"abbreviation": "GMD",
"description": "The Golm Metabolome Database (GMD) provides gas chromatography (GC) mass spectrometry (MS) reference spectra, reference metabolite profiles and tools for one of the most widespread routine technologies applied to the large scale screening and discovery of novel metabolic biomarkers.",
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"name": "Golm Metabolome Database",
"prefix": "FAIRsharing.jykmkw",
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],
"subjects": [
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"Metabolomics"
]
},
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"name": "Golm Metabolome Database",
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"description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena.",
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"homepage": "http://gmd.mpimp-golm.mpg.de/",
"name": "Golm Metabolome Database at Max Planck Institute of Molecular Plant Physiology",
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"publications": [
{
"doi": "10.1007/s11306-010-0198-7",
"pmc": "PMC2874469",
"pubmed": "20526350",
"title": "Decision tree supported substructure prediction of metabolites from GC-MS profiles",
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}
],
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"name": "Golm Metabolome Database",
"prefix": "r3d100011046",
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],
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"id": "00000426",
"name": "Golm Metabolome Database Analyte",
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},
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"id": "00000425",
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},
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s.",
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"obsolete": false,
"prefix": "1004"
},
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"homepage": "https://link.springer.com/bookseries/562",
"mappings": {
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},
"name": "Gmelins Handbuch der anorganischen Chemie",
"pattern": "^[1-9][0-9]{3,6}$",
"proprietary": true,
"references": [
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],
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"349",
"917"
],
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"prefix": "P1578"
}
},
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"homepage": "http://www.dnb.de/gnd",
"license": "CC0-1.0",
"name": "Integrated Authority File",
"pattern": "^[0-9X]+(-[0-9X])?$",
"prefix": "430",
"wikidata_database": "Q36578"
},
"fairsharing": {
"abbreviation": "GND",
"description": "The Integrated Authority File (GND) is a service facilitating the collaborative use and administration of authority data. These authority data represent and describe entities, i.e. persons, corporate bodies, conferences and events, geographic entities, topics and works relating to cultural and academic collections. Libraries in particular use the GND to catalogue publications. However, archives, museums, cultural and academic institutions, and researchers involved in research projects are also increasingly working with the GND. Authority data make cataloguing easier, offer definitive search entries and forge links between different information resources. Every entity in the GND features a unique and stable identifier (GND ID). This makes it possible to link the authority data with both each other and external data sets and web resources. This results in a cross-organisational, machine-readable data network.",
"domains": [
"Publication"
],
"homepage": "https://www.dnb.de/EN/Professionell/Standardisierung/GND/gnd_node.html",
"license": "CC0-1.0",
"name": "Integrated Authority File",
"prefix": "FAIRsharing.8337e2",
"subjects": [
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"Culture",
"Social Science"
],
"twitter": "gndnet"
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"mappings": {
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"homepage": "https://lobid.org/",
"id": "00001002",
"name": "Gemeinsame Normdatei",
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"pattern": "[0-9X\\-]+",
"prefix": "gnd",
"sampleId": "117145750",
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}
},
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"aberowl": {
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"download_owl": "http://aber-owl.net/media/ontologies/GNO/27/gno.owl",
"homepage": "https://gnome.glyomics.org/",
"name": "Glycan Naming and Subsumption Ontology (GNOme)",
"prefix": "GNO"
},
"bioportal": {
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"name": "Nathan Edwards"
},
"description": "An ontology for glycans based on GlyTouCan, but organized by subsumption.",
"homepage": "https://github.com/glygen-glycan-data/GNOme",
"name": "Glycan Naming Ontology",
"prefix": "GNO",
"version": "V2.2.0"
},
"example": "10004892",
"example_extras": [
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],
"mappings": {
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"ols": "gno",
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},
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"contact.github": "edwardsnj",
"contact.label": "Nathan Edwards",
"contact.orcid": "0000-0001-5168-3196",
"deprecated": false,
"description": "GlyTouCan provides stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations). GNOme organizes these stable accessions for interative browsing, for text-based searching, and for automated reasoning with well-defined characterization levels.",
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"homepage": "https://gnome.glyomics.org/",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Glycan Naming and Subsumption Ontology (GNOme)",
"preferredPrefix": "GNO",
"prefix": "gno",
"publications": [
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],
"repository": "https://github.com/glygen-glycan-data/GNOme"
},
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"homepage": "https://gnome.glyomics.org/",
"name": "Glycan Naming Ontology",
"prefix": "gno",
"version": "2024-05-21",
"version.iri": "http://purl.obolibrary.org/obo/gno/2024-05-21/gno.owl"
},
"ontobee": {
"library": "Library",
"name": "Glycan Naming and Subsumption Ontology (GNOme)",
"prefix": "GNO"
},
"pattern": "^(\\d{8}|(\\w+\\d+\\w+))$",
"providers": [
{
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"description": "GNOme structure browser",
"homepage": "https://gnome.glyomics.org/StructureBrowser.html",
"name": "GNOme Structure Viewer",
"uri_format": "https://gnome.glyomics.org/StructureBrowser.html?focus=$1"
},
{
"code": "gno.composition",
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"homepage": "https://gnome.glyomics.org/CompositionBrowser.html",
"name": "GNOme Composition Browser",
"uri_format": "https://gnome.glyomics.org/CompositionBrowser.html?focus=$1"
}
],
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"title": "GNOme - Glycan Naming and Subsumption Ontology",
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}
],
"synonyms": [
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],
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},
"gnomad": {
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"github": "heidirehm",
"name": "Heidi L. Rehm",
"orcid": "0000-0002-6025-0015"
},
"contributor": {
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
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"homepage": "https://gnomad.broadinstitute.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "Genome Aggregation Database Consortium",
"name": "gnomAD",
"prefix": "nbdc02561",
"pubmeds": [
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],
"status": "Active",
"target_keywords": [
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"Genetic variation",
"Health/Disease"
]
},
"license": "CC0-1.0",
"mappings": {
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},
"name": "Genome Aggregation Database",
"publications": [
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"pmc": "PMC7334197",
"pubmed": "32461654",
"title": "The mutational constraint spectrum quantified from variation in 141,456 humans",
"year": 2020
},
{
"doi": "10.1038/s41586-020-2287-8",
"pmc": "PMC7334194",
"pubmed": "32461652",
"title": "A structural variation reference for medical and population genetics",
"year": 2020
}
],
"uri_format": "https://gnomad.broadinstitute.org/variant/$1"
},
"gnpis": {
"biocontext": {
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{
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}
],
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"name": "Gene Ontology",
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"license": "CC BY 4.0",
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}
],
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"twitter": "news4go"
},
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"description": "The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms.",
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"homepage": "http://geneontology.org/",
"name": "Gene Ontology",
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"version": "2024-06-17",
"version.iri": "http://purl.obolibrary.org/obo/go/releases/2024-06-17/extensions/go-plus.owl"
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"name": "Gene Ontology",
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"homepage": "http://www.geneontology.org ",
"name": "Gene Ontology Consortium",
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"prefixcommons": {
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],
"bioportal": "1070",
"description": "The Gene Ontology project provides an ontology of defined terms representing gene product properties. The ontology covers three domains: cellular component, molecular function, and biological process.",
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"homepage": "http://www.geneontology.org/",
"keywords": [
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"name": "The Gene Ontology",
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],
"uri_format": "http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:$1"
},
"providers": [
{
"code": "jax",
"description": "The JAX endpoint for exploring GO",
"homepage": "http://www.informatics.jax.org",
"name": "Jackson Laboratories",
"uri_format": "http://www.informatics.jax.org/vocab/gene_ontology/GO:$1"
},
{
"code": "nextprot",
"description": "The neXtProt endpoint for exploring GO",
"homepage": "https://www.nextprot.org/",
"name": "neXtProt GO Browser",
"uri_format": "https://www.nextprot.org/term/GO:$1"
},
{
"code": "miriam_obo_legacy",
"description": "An old URI style for MIRIAM + GO",
"homepage": "https://identifiers.org/",
"name": "MIRIAM OBO Legacy",
"uri_format": "http://identifiers.org/obo.go/GO:$1"
},
{
"code": "go_site",
"description": "A non-PURL link through the GO site",
"homepage": "http://www.geneontology.org",
"name": "GO Site Link",
"uri_format": "http://www.geneontology.org/GO:$1"
},
{
"code": "quickgo.legacy",
"description": "QuickGO (Gene Ontology browser)",
"homepage": "https://www.ebi.ac.uk/QuickGO/",
"name": "QuickGO (Legacy URL)",
"uri_format": "https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:$1"
},
{
"code": "quickgo",
"description": "Gene Ontology browser from the EBI",
"homepage": "https://www.ebi.ac.uk/QuickGO/",
"name": "QuickGO",
"uri_format": "https://www.ebi.ac.uk/QuickGO/term/GO:$1"
},
{
"code": "pantherdb",
"description": "GO Browser in PantherDB",
"homepage": "http://www.pantherdb.org/panther",
"name": "PatherDB",
"uri_format": "http://www.pantherdb.org/panther/category.do?categoryAcc=GO:$1"
}
],
"publications": [
{
"doi": "10.1093/nar/gkaa1113",
"pmc": "PMC7779012",
"pubmed": "33290552",
"title": "The Gene Ontology resource: enriching a GOld mine",
"year": 2021
},
{
"doi": "10.1093/nar/gky1055",
"pmc": "PMC6323945",
"pubmed": "30395331",
"title": "The Gene Ontology Resource: 20 years and still GOing strong",
"year": 2019
},
{
"doi": "10.1093/nar/gku1179",
"pmc": "PMC4383973",
"pubmed": "25428369",
"title": "Gene Ontology Consortium: going forward",
"year": 2014
},
{
"doi": "10.1186/1471-2164-14-513",
"pmc": "PMC3733925",
"pubmed": "23895341",
"title": "Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology",
"year": 2013
},
{
"doi": "10.1093/nar/gks1050",
"pmc": "PMC3531070",
"pubmed": "23161678",
"title": "Gene Ontology annotations and resources",
"year": 2012
},
{
"doi": "10.1093/nar/gkr1028",
"pmc": "PMC3245151",
"pubmed": "22102568",
"title": "The Gene Ontology: enhancements for 2011",
"year": 2011
},
{
"doi": "10.1093/nar/gkp1018",
"pmc": "PMC2808930",
"pubmed": "19920128",
"title": "The Gene Ontology in 2010: extensions and refinements",
"year": 2009
},
{
"doi": "10.1093/nar/gkh036",
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"pubmed": "14681407",
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},
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"pmc": "PMC3037419",
"pubmed": "10802651",
"title": "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium",
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}
],
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"synonyms": [
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"gocc",
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],
"togoid": {
"catalog": "nbdc00074",
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],
"keywords": [
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],
"name": "Gene ontology",
"pattern": "^GO[:_](?\\d{7})$",
"prefix": "Go",
"uri_format": "http://purl.obolibrary.org/obo/GO_$1"
},
"uniprot": {
"abbreviation": "GO",
"category": "Ontologies",
"homepage": "https://geneontology.org/",
"name": "Gene Ontology",
"prefix": "DB-0037",
"publications": [
{
"doi": "10.1093/nar/gky1055",
"pubmed": "30395331"
}
],
"uri_format": "https://www.ebi.ac.uk/QuickGO/term/$1"
},
"uri_format": "http://purl.obolibrary.org/obo/GO_$1",
"wikidata": {
"description": "identifier in the Gene Ontology",
"example": [
"GO:0005773",
"GO:0046872"
],
"homepage": "http://amigo.geneontology.org/",
"miriam": "GO",
"name": "Gene Ontology ID",
"pattern": "^GO:\\d{7}$",
"prefix": "P686",
"uri_format": "http://amigo.geneontology.org/amigo/term/$1"
}
},
"go.gpi": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "gpi",
"uri_format": "https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor_extras": [
{
"github": "sierra-moxon",
"name": "Sierra Moxon",
"orcid": "0000-0002-8719-7760"
}
],
"description": "This describes the metadata schema for the Gene Product Information (GPI) files in the Gene Ontology, i.e., the local unique identifiers in this identifier space refer to the columns in GPI files.",
"example": "db-object-id",
"homepage": "http://geneontology.org/docs/gene-product-information-gpi-format/#db-object-id",
"mappings": {
"biolink": "gpi"
},
"name": "Gene Product Information Schema",
"uri_format": "http://geneontology.org/docs/gene-product-information-gpi-format/#$1"
},
"go.model": {
"description": "GO-Causal Activity Models (GO-CAMs) use a defined βgrammarβ for linking multiple GO annotations into larger models of biological function (such as βpathwaysβ) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform.",
"example": "5fce9b7300001250",
"go": {
"homepage": "http://www.geneontology.org/gocam",
"name": "Gene Ontology Causal Activity Model Database",
"prefix": "gomodel",
"uri_format": "http://www.geneontology.org/gocam/$1"
},
"mappings": {
"go": "gomodel"
},
"name": "Gene Ontology Causal Assembly Model",
"uri_format": "http://noctua.geneontology.org/editor/graph/gomodel:$1"
},
"go.ref": {
"banana": "GO_REF",
"biocontext": {
"prefix": "GO_REF",
"uri_format": "http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:$1"
},
"go": {
"homepage": "http://geneontology.org/gorefs",
"name": "Gene Ontology Database references",
"prefix": "GO_REF"
},
"mappings": {
"biocontext": "GO_REF",
"go": "GO_REF",
"miriam": "go_ref",
"n2t": "go.ref"
},
"miriam": {
"deprecated": false,
"description": "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made.",
"homepage": "http://www.geneontology.org/cgi-bin/references.cgi",
"id": "00000450",
"name": "Gene Ontology Reference",
"namespaceEmbeddedInLui": true,
"pattern": "^GO_REF:\\d{7}$",
"prefix": "go_ref",
"sampleId": "0000041",
"uri_format": "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-$1.md"
},
"n2t": {
"description": "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made.",
"example": "GO_REF:0000041",
"homepage": "http://www.geneontology.org/cgi-bin/references.cgi",
"name": "Gene Ontology Reference at The Gene Ontology Consortium",
"namespaceEmbeddedInLui": false,
"pattern": "^GO_REF:\\d{7}$",
"prefix": "go.ref",
"uri_format": "http://www.geneontology.org/cgi-bin/references.cgi#$1"
},
"pattern": "^\\d{7}$",
"uri_format": "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md#goref$1"
},
"go.resource": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A database-specific registry supporting curation in the Gene Ontology",
"example": "CHEBI",
"homepage": "http://geneontology.org/",
"name": "Gene Ontology Registry",
"uri_format": "https://bioregistry.io/metaregistry/go/$1"
},
"go.rule": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "GO Rules are a way of documenting the set of filters and reports that should apply to GAF annotation data. Some rules are expressed as SPARQL on a triplestore, some are code in the GAF parsing software, ontobio.",
"example": "0000004",
"homepage": "https://github.com/geneontology/go-site/tree/master/metadata/rules",
"name": "Gene Ontology Rules",
"part_of": "go",
"pattern": "^\\d{7}$",
"preferred_prefix": "GORULE",
"uri_format": "https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-$1.md"
},
"goa": {
"biocontext": {
"prefix": "GOA"
},
"contact": {
"email": "r.huntley@ucl.ac.uk",
"github": "rachhuntley",
"name": "Rachael P. Huntley",
"orcid": "0000-0001-6718-3559"
},
"fairsharing": {
"abbreviation": "GOA",
"description": "The GO Annotation Database (GOA) provides Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. GOA files contain a mixture of manual annotation supplied by members of the Gene Onotology Consortium and computationally assigned GO terms describing gene products. Annotation type is clearly indicated by associated evidence codes and there are links to the source data.",
"homepage": "http://www.ebi.ac.uk/GOA",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "Gene Ontology Annotation Database",
"prefix": "FAIRsharing.7zffgc",
"publications": [
{
"doi": "10.1093/nar/gkn803",
"pubmed_id": 18957448,
"title": "The GOA database in 2009--an integrated Gene Ontology Annotation resource."
},
{
"doi": "10.1093/nar/gku1113",
"pubmed_id": 25378336,
"title": "The GOA database: gene Ontology annotation updates for 2015."
}
],
"subjects": [
"Life Science",
"Biology"
]
},
"integbio": {
"alt_name": "Gene Ontology Annotation Database",
"description": "GOA is a database of gene function and interaction information. The database contains manual and automated annotations of gene ontology. Users can download current and previous versions of the database including gene annotations, gene interactions, and ontology mapping files.",
"fairsharing": "biodbcore-000313",
"homepage": "https://www.ebi.ac.uk/GOA",
"information_keywords": [
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],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "GOA",
"prefix": "nbdc00468",
"pubmeds": [
"18957448",
"22123736",
"19744993"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
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"ncbi": "GOA",
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},
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"id": "00000196",
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"sampleId": "P12345",
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},
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"homepage": "https://www.ebi.ac.uk/GOA/",
"name": "GOA through QuickGO",
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"pattern": "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$",
"prefix": "goa",
"uri_format": "https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1"
},
"name": "Gene Ontology Annotation Database",
"ncbi": {
"example": "P01100",
"homepage": "http://www.ebi.ac.uk/GOA/",
"name": "Gene Ontology Annotation Database Identifier",
"prefix": "GOA"
},
"prefixcommons": {
"description": "The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups.",
"example": "go:0006915",
"homepage": "http://www.ebi.ac.uk/GOA",
"keywords": [
"gene",
"ontology",
"protein"
],
"name": "Gene Ontology Annotation",
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$",
"prefix": "goa",
"pubmed_ids": [
"18957448"
],
"synonyms": [
"goa-projects"
],
"uri_format": "http://www.ebi.ac.uk/QuickGO/GTerm?id=$1"
},
"provides": "uniprot",
"publications": [
{
"doi": "10.1093/nar/gku1113",
"pmc": "PMC4383930",
"pubmed": "25378336",
"title": "The GOA database: gene Ontology annotation updates for 2015",
"year": 2014
},
{
"doi": "10.1093/nar/gkn803",
"pmc": "PMC2686469",
"pubmed": "18957448",
"title": "The GOA database in 2009--an integrated Gene Ontology Annotation resource",
"year": 2008
}
]
},
"goche": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Represent chemical entities having particular CHEBI roles",
"download_owl": "https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl",
"example": "25512",
"homepage": "https://github.com/geneontology/go-ontology",
"name": "GO Chemicals",
"pattern": "^\\d+$",
"preferred_prefix": "GOCHE",
"rdf_uri_format": "http://purl.obolibrary.org/obo/GOCHE_$1",
"references": [
"https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638472847049400",
"https://github.com/geneontology/go-ontology/issues/19535"
],
"repository": "https://github.com/geneontology/go-ontology",
"synonyms": [
"go.chebi",
"go.chemical",
"go.chemicals"
],
"uri_format": "https://biopragmatics.github.io/providers/goche/$1"
},
"goeco": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported.",
"example": "IPI",
"homepage": "http://geneontology.org/docs/guide-go-evidence-codes/",
"name": "GO Evidence Code"
},
"gold": {
"contact": {
"email": "tbreddy@lbl.gov",
"github": "TBKReddy",
"name": "TBK Reddy",
"orcid": "0000-0002-0871-5567"
},
"fairsharing": {
"abbreviation": "JGI-GOLD",
"description": "Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. Information in GOLD is organized into levels to include Study, Organism or Biosample, Sequencing Project (SP), and Analysis Project (AP). All four levels, along with their complex list of metadata fields and controlled vocabulary (CV) terms, are connected to each other in a lucid framework to enhance scientific discovery. GOLD is a curated resource serving the research community and your input is critical to ensure high quality, accurate metadata in GOLD. ",
"homepage": "https://gold.jgi.doe.gov/",
"name": "Joint Genome Institute, Genomes OnLine Database",
"prefix": "FAIRsharing.5q1p14",
"publications": [
{
"doi": "11125068",
"pubmed_id": 11125068,
"title": "Genomes OnLine Database (GOLD): a monitor of genome projects world-wide."
},
{
"doi": "10.1093/nar/gkm884",
"pubmed_id": 17981842,
"title": "The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata."
},
{
"doi": "10.1093/bioinformatics/15.9.773",
"pubmed_id": 10498782,
"title": "Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide."
},
{
"doi": "10.1093/nar/gkp848",
"pubmed_id": 19914934,
"title": "The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata."
},
{
"doi": "10.1093/nar/gky977",
"pubmed_id": 30357420,
"title": "Genomes OnLine database (GOLD) v.7: updates and new features."
},
{
"doi": "10.1093/nar/gkaa983",
"pubmed_id": null,
"title": "Genomes OnLine Database (GOLD) v.8: overview and updates"
}
],
"subjects": [
"Metagenomics",
"Genomics",
"Phylogenetics",
"Metabolomics",
"Ontology and Terminology"
]
},
"integbio": {
"alt_name": "Genomes Online Database",
"description": "GOLD is a data management system that catalogs genome and metagenome sequencing projects with associated metadata from around the world. GOLD (v.6) provides information for 28,744 Studies, 272,234 Organisms, 21,910 Biosamples, 134,884 Sequencing Projects and 111,625 Analysis Projects. Advanced Search feature allow users to explore GOLD's different project levels above.",
"fairsharing": "biodbcore-000117",
"homepage": "https://gold.jgi.doe.gov/index",
"information_keywords": [
"Bibliography/Documents",
"Portal",
"Repository"
],
"maintainer": "DOE Joint Genome Institute",
"name": "GOLD",
"prefix": "nbdc00483",
"pubmeds": [
"27794040"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"mappings": {
"fairsharing": "FAIRsharing.5q1p14",
"integbio": "nbdc00483",
"miriam": "gold",
"prefixcommons": "gold",
"re3data": "r3d100010808"
},
"miriam": {
"deprecated": false,
"description": "The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.",
"homepage": "https://gold.jgi.doe.gov/",
"id": "00000733",
"name": "Genomes OnLine Database (GOLD)",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z][a-z][0-9]+$",
"prefix": "gold",
"sampleId": "Gs0000008",
"uri_format": "https://gold.jgi.doe.gov/resolver?id=$1"
},
"name": "Genomes Online Database",
"prefixcommons": {
"description": "GOLD: Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding complete and ongoing genome projects, as well as metagenomes and metadata, around the world.",
"example": "Gc01070",
"homepage": "http://www.genomesonline.org/",
"keywords": [
"genome"
],
"name": "Genomes Online Database",
"pattern": "^G[a-z]\\d+$",
"prefix": "gold",
"uri_format": "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkaa983",
"pmc": "PMC7778979",
"pubmed": "33152092",
"title": "Genomes OnLine Database (GOLD) v.8: overview and updates",
"year": 2021
},
{
"doi": "10.1093/nar/gky977",
"pmc": "PMC6323969",
"pubmed": "30357420",
"title": "Genomes OnLine database (GOLD) v.7: updates and new features",
"year": 2019
},
{
"doi": "10.1093/nar/gkp848",
"pmc": "PMC2808860",
"pubmed": "19914934",
"title": "The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata",
"year": 2009
},
{
"doi": "10.1093/nar/gkm884",
"pmc": "PMC2238992",
"pubmed": "17981842",
"title": "The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata",
"year": 2007
},
{
"doi": "10.1093/nar/29.1.126",
"pmc": "PMC29859",
"pubmed": "11125068",
"title": "Genomes OnLine Database (GOLD): a monitor of genome projects world-wide",
"year": 2001
},
{
"doi": "10.1093/bioinformatics/15.9.773",
"pubmed": "10498782",
"title": "Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide",
"year": 1999
}
],
"re3data": {
"description": "GOLD is currently the largest repository for genome project information world-wide. The accurate and efficient genome project tracking is a vital criterion for launching new genome sequencing projects, and for avoiding significant overlap between various sequencing efforts and centers.",
"homepage": "https://gold.jgi.doe.gov/index",
"name": "Genomes OnLine Database",
"prefix": "r3d100010808",
"synonyms": [
"GOLD"
],
"xrefs": {
"fairsharing": "FAIRsharing.5q1p14",
"nif": "0000-02918",
"omics": "06148",
"scr": "002817"
}
}
},
"gold.genome": {
"biocontext": {
"prefix": "GOLD.GENOME"
},
"mappings": {
"biocontext": "GOLD.GENOME",
"miriam": "gold.genome",
"n2t": "gold.genome"
},
"miriam": {
"deprecated": false,
"description": "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by βgoldβ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed βgoldβ namespace.\n\nThe GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes.",
"homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi",
"id": "00000401",
"name": "GOLD genome",
"namespaceEmbeddedInLui": false,
"pattern": "^(Gi|Gc)\\d+$",
"prefix": "gold.genome",
"sampleId": "Gi07796",
"uri_format": "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1"
},
"n2t": {
"description": "The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes.",
"example": "Gi07796",
"homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi",
"name": "GOLD genome at Department of Energy Joint Genome Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^[Gi|Gc]\\d+$",
"prefix": "gold.genome",
"uri_format": "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1"
}
},
"gold.meta": {
"biocontext": {
"prefix": "GOLD.META"
},
"has_canonical": "gold",
"mappings": {
"biocontext": "GOLD.META",
"miriam": "gold.meta",
"n2t": "gold.meta"
},
"miriam": {
"deprecated": false,
"description": "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by βgoldβ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed βgoldβ namespace. \n\nThe GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples.",
"homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi",
"id": "00000402",
"name": "GOLD metadata",
"namespaceEmbeddedInLui": false,
"pattern": "^Gm\\d+$",
"prefix": "gold.meta",
"sampleId": "Gm00047",
"uri_format": "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1"
},
"n2t": {
"description": "The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples.",
"example": "Gm00047",
"homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi",
"name": "GOLD metadata at Department of Energy Joint Genome Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^Gm\\d+$",
"prefix": "gold.meta",
"uri_format": "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1"
}
},
"goldbook": {
"bartoc": {
"description": "The Compendium is popularly referred to as the 'Gold Book', in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC 'Colour Books' on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books.\n\nTerminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC's Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry.\n\nSome minor editorial changes were made to the originally published definitions, to harmonise the presentation and to clarify their applicability, if this is limited to a particular sub-discipline. Verbal definitions of terms from Quantities, Units and Symbols in Physical Chemistry (the IUPAC Green Book, in which definitions are generally given as mathematical expressions) were developed specially for this Compendium by the Physical Chemistry Division of IUPAC. Definitions of a few physicochemical terms not mentioned in the Green Book were added at the same time (referred to here as Physical Chemistry Division, unpublished).\n\nThe first reference given at the end of each definition is to the page of Pure Appl. Chem. or other source where the original definition appears; other references given designate other places where compatible definitions of the same term or additional information may be found, in other IUPAC documents. The complete reference citations are given in the appended list of source documents. Highlighted terms within individual definitions link to other entries where additional information is available.",
"homepage": "http://goldbook.iupac.org/",
"name": "IUPAC Compendium of Chemical Terminology",
"prefix": "1884",
"wikidata_database": "Q902163"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Compendium is popularly referred to as the \"Gold Book\", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC \"Colour Books\" on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books.\n\nTerminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC's Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry.",
"example": "G02681",
"homepage": "https://goldbook.iupac.org",
"license": "CC BY 4.0-NC-ND",
"mappings": {
"bartoc": "1884",
"wikidata": "P4732"
},
"name": "IUPAC Gold Book Compendium of Chemical Terminology",
"uri_format": "https://goldbook.iupac.org/terms/view/$1",
"wikidata": {
"description": "identifier of definition in ''Compendium of Chemical Terminology'' (''IUPAC GoldBook'')",
"example": [
"A00204",
"A00212"
],
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"uri_format_rdf": "http://dx.doi.org/10.1351/goldbook.$1"
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},
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Search the world's most comprehensive index of full-text books.",
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"github_request_issue": 511,
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"wikidata": "P675"
},
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"example": [
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"7r14FzJdSuAC"
],
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"name": "Google Books ID",
"prefix": "P675",
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}
},
"google.patent": {
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"prefix": "GOOGLE.PATENT"
},
"cellosaurus": {
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},
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{
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"id": "00000537",
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"description": "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date.",
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"patent"
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"prefix": "GSID",
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},
"contributor": {
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.",
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"homepage": "https://scholar.google.com/",
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"biolink": "GSID"
},
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"gorel": {
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"prefix": "GOREL",
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},
"contributor": {
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.",
"download_owl": "ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl",
"example": "0002005",
"go": {
"description": "Additional relations pending addition into RO",
"name": "GO Extensions to OBO Relation Ontology Ontology",
"prefix": "GOREL"
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"mappings": {
"biolink": "GOREL",
"go": "GOREL"
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"name": "GO Relations",
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{
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}
],
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},
"gpcrdb": {
"biocontext": {
"prefix": "GPCRDB"
},
"fairsharing": {
"abbreviation": "GPCRdb",
"contact": {
"email": "david.gloriam@sund.ku.dk",
"name": "David Gloriam",
"orcid": "0000-0002-4299-7561"
},
"description": "The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). The GPCRDB contains data on sequences, ligand binding constants and mutations. In addition, many different types of computationally derived data are stored such as multiple sequence alignments and homology models.",
"homepage": "http://gpcrdb.org/",
"license": "Apache 2.0 License",
"name": "Information system for G protein-coupled receptors",
"prefix": "FAIRsharing.e4n3an",
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{
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"pubmed_id": 21045054,
"title": "GPCRDB: information system for G protein-coupled receptors."
},
{
"doi": "10.1093/nar/26.1.275",
"pubmed_id": 9399852,
"title": "GPCRDB: an information system for G protein-coupled receptors."
},
{
"doi": "10.1093/nar/gkg103",
"pubmed_id": 12520006,
"title": "GPCRDB information system for G protein-coupled receptors."
},
{
"doi": "10.1093/nar/gkt1255",
"pubmed_id": 24304901,
"title": "GPCRDB: an information system for G protein-coupled receptors."
},
{
"doi": "10.1093/nar/gkv1178",
"pubmed_id": 26582914,
"title": "GPCRdb: an information system for G protein-coupled receptors."
},
{
"doi": "10.1111/bph.13509",
"pubmed_id": 27155948,
"title": "GPCRdb: the G protein-coupled receptor database - an introduction."
},
{
"doi": "10.1093/nar/gkx1109",
"pubmed_id": 29155946,
"title": "GPCRdb in 2018: adding GPCR structure models and ligands."
}
],
"subjects": [
"Molecular biology",
"Life Science"
],
"twitter": "gpcrdb"
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"integbio": {
"description": "GPCRdb is a database of G-coupled protein receptor information. The database contains gene and protein sequence information as well as protein structure, binding site, and conservation data. Users can search by protein ID or keyword, browse by family, structure, model, or oligomers, or utilize several GPCR-specific tools.",
"fairsharing": "biodbcore-000292",
"homepage": "http://gpcrdb.org",
"information_keywords": [
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"3D structure"
],
"maintainer": "CMBI (Centre for Molecular and Biomolecular Informatics)",
"name": "GPCRdb",
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],
"status": "Active",
"target_keywords": [
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]
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"miriam": "gpcrdb",
"n2t": "gpcrdb",
"prefixcommons": "gpcrdb",
"uniprot": "DB-0038"
},
"miriam": {
"deprecated": false,
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"homepage": "http://www.gpcrdb.org/",
"id": "00000212",
"name": "GPCRDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "gpcrdb",
"sampleId": "RL3R1_HUMAN",
"uri_format": "http://www.gpcrdb.org/protein/$1/"
},
"n2t": {
"description": "The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models.",
"example": "RL3R1_HUMAN",
"homepage": "http://www.gpcrdb.org/",
"name": "GPCRDB at Radboud University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "gpcrdb",
"uri_format": "http://www.gpcrdb.org/protein/$1/"
},
"name": "G protein-coupled receptor database",
"prefixcommons": {
"description": "The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). The GPCRDB contains data on sequences, ligand binding constants and mutations. In addition, many different types of computationally derived data are stored such as multiple sequence alignments and homology models.",
"example": "RL3R1_HUMAN",
"homepage": "http://www.gpcr.org/7tm/",
"keywords": [
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"protein"
],
"name": "Information system for G protein-coupled receptors (GPCRs)",
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"prefix": "gpcrdb",
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],
"uri_format": "http://www.gpcr.org/7tm/proteins/$1"
},
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{
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"pubmed": "9399852",
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},
{
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"pmc": "PMC7778909",
"pubmed": "33270898",
"title": "GPCRdb in 2021: integrating GPCR sequence, structure and function",
"year": 2021
},
{
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"title": "GPCRdb in 2018: adding GPCR structure models and ligands",
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},
{
"doi": "10.1111/bph.13509",
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"pubmed": "27155948",
"title": "GPCRdb: the G protein-coupled receptor database - an introduction",
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},
{
"doi": "10.1093/nar/gkv1178",
"pmc": "PMC4702843",
"pubmed": "26582914",
"title": "GPCRdb: an information system for G protein-coupled receptors",
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},
{
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"pmc": "PMC3965068",
"pubmed": "24304901",
"title": "GPCRDB: an information system for G protein-coupled receptors",
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},
{
"doi": "10.1093/nar/gkq1009",
"pmc": "PMC3013641",
"pubmed": "21045054",
"title": "GPCRDB: information system for G protein-coupled receptors",
"year": 2010
},
{
"doi": "10.1093/nar/gkg103",
"pmc": "PMC165550",
"pubmed": "12520006",
"title": "GPCRDB information system for G protein-coupled receptors",
"year": 2003
},
{
"doi": "10.1093/nar/29.1.346",
"pmc": "PMC29816",
"pubmed": "11125133",
"title": "Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems",
"year": 2001
}
],
"uniprot": {
"abbreviation": "GPCRDB",
"category": "Protein family/group databases",
"homepage": "https://gpcrdb.org",
"name": "Information system for G protein-coupled receptors (GPCRs)",
"prefix": "DB-0038",
"publications": [
{
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"pubmed": "11125133"
}
],
"uri_format": "https://gpcrdb.org/protein/$1/"
},
"uri_format": "https://gpcrdb.org/protein/$1"
},
"gpcrnava": {
"mappings": {
"prefixcommons": "gnd"
},
"prefixcommons": {
"description": "The GPCR NaVa database describes sequence variants within the family of human G Protein-Coupled Receptors (GPCRs). GPCRs regulate many physiological functions and are the targets for most of today's medicines. The acronym NaVa stands for Natural Variant, which means any (non-artificial) variant that occurs in humans.",
"example": "1150",
"homepage": "http://nava.liacs.nl/",
"keywords": [
"protein",
"pathway"
],
"name": "GPCR Natural Variants database",
"pattern": "^\\d+$",
"prefix": "gnd",
"uri_format": "http://nava.liacs.nl/cgi-bin/nava.py?id=$1"
}
},
"gpmdb": {
"biocontext": {
"prefix": "GPMDB"
},
"contact": {
"email": "rbeavis@thegpm.org",
"github": "RonBeavis",
"name": "Ronald C. Beavis (Ron Beavis)",
"orcid": "0000-0001-5782-1000"
},
"fairsharing": {
"abbreviation": "gpmDB",
"description": "The Global Proteome Machine Database (gpmDB holds the minimum amount of information necessary for common bioinformatics-related tasks (such as sequence assignment validation) rather than being a complete record of a proteomics experiment. It was also created to aid in the process of validating peptide MS/MS spectra as well as protein coverage patterns. Most of the data is held in a set of XML files: the database serves as an index to those files, allowing for rapid lookups and reduced database storage requirements.",
"homepage": "https://www.thegpm.org/GPMDB/index.html",
"name": "The Global Proteome Machine Database",
"prefix": "FAIRsharing.fhcmwq",
"publications": [
{
"doi": "10.1021/pr049882h",
"pubmed_id": 15595733,
"title": "Open source system for analyzing, validating, and storing protein identification data."
}
],
"subjects": [
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"Proteomics"
],
"twitter": "GPMDB"
},
"mappings": {
"biocontext": "GPMDB",
"fairsharing": "FAIRsharing.fhcmwq",
"miriam": "gpmdb",
"n2t": "gpmdb"
},
"miriam": {
"deprecated": false,
"description": "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns.",
"homepage": "http://gpmdb.thegpm.org/",
"id": "00000649",
"name": "GPMDB",
"namespaceEmbeddedInLui": false,
"pattern": "^GPM\\d+$",
"prefix": "gpmdb",
"providers": [
{
"code": "omicsdi",
"description": "GPMDB through OmicsDI",
"homepage": "https://www.omicsdi.org/",
"name": "GPMDB through OmicsDI",
"uri_format": "https://www.omicsdi.org/dataset/gpmdb/$1"
}
],
"sampleId": "GPM32310002988",
"uri_format": "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1"
},
"n2t": {
"description": "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns.",
"example": "GPM32310002988",
"homepage": "http://gpmdb.thegpm.org/",
"name": "GPMDB",
"namespaceEmbeddedInLui": false,
"pattern": "^GPM\\d+$",
"prefix": "gpmdb",
"uri_format": "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1"
},
"name": "Global Proteome Machine Database",
"publications": [
{
"doi": "10.1021/pr049882h",
"pubmed": "15595733",
"title": "Open source system for analyzing, validating, and storing protein identification data",
"year": 2004
}
]
},
"graingenes.reference": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A database for Triticeae and Avena references.",
"example": "WGS-95-1333",
"homepage": "http://wheat.pw.usda.gov",
"name": "GrainGenes",
"uri_format": "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1"
},
"graingenes.symbol": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A database for Triticeae and Avena gene symbols.",
"example": "1-FEH+w3",
"homepage": "http://wheat.pw.usda.gov",
"name": "GrainGenes",
"uri_format": "http://wheat.pw.usda.gov/report?class=gene;name=$1"
},
"gramene.gene": {
"biocontext": {
"prefix": "GRAMENE.GENE"
},
"go": {
"homepage": "http://www.gramene.org/",
"name": "Gramene",
"prefix": "GR_GENE",
"synonyms": [
"GR_gene"
],
"uri_format": "http://www.gramene.org/db/genes/search_gene?acc=$1"
},
"mappings": {
"biocontext": "GRAMENE.GENE",
"go": "GR_GENE",
"miriam": "gramene.gene",
"n2t": "gramene.gene"
},
"miriam": {
"deprecated": false,
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene.",
"homepage": "http://www.gramene.org/",
"id": "00000182",
"name": "Gramene genes",
"namespaceEmbeddedInLui": false,
"pattern": "^GR\\:\\d+$",
"prefix": "gramene.gene",
"sampleId": "GR:0080039",
"uri_format": "http://www.gramene.org/db/genes/search_gene?acc=$1"
},
"n2t": {
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene.",
"example": "GR:0080039",
"homepage": "http://www.gramene.org/",
"name": "Gramene Genes at Cold Spring Harbor",
"namespaceEmbeddedInLui": false,
"pattern": "^GR\\:\\d+$",
"prefix": "gramene.gene",
"uri_format": "http://www.gramene.org/db/genes/search_gene?acc=$1"
},
"name": "Gramene Gene",
"synonyms": [
"GR_GENE"
]
},
"gramene.growthstage": {
"banana": "GRO",
"biocontext": {
"prefix": "GRAMENE.GROWTHSTAGE"
},
"bioportal": {
"contact": {
"email": "jaiswalp@oregonstate.edu",
"name": "Pankaj Jaiswal"
},
"description": "A structured controlled vocabulary for the anatomy of Gramineae. Please note that this ontology has now been superseded by the Plant Ontology.",
"homepage": "https://planteome.org/",
"name": "Cereal Plant Gross Anatomy Ontology",
"prefix": "GRO-CPGA",
"publication": "https://planteome.org/pub",
"version": "unknown"
},
"mappings": {
"biocontext": "GRAMENE.GROWTHSTAGE",
"bioportal": "GRO-CPGA",
"miriam": "gro",
"n2t": "gramene.growthstage",
"obofoundry": "gro",
"prefixcommons": "gramene.po"
},
"miriam": {
"deprecated": false,
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.",
"homepage": "http://www.gramene.org/",
"id": "00000508",
"name": "Gramene Growth Stage Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^GRO:\\d+$",
"prefix": "gro",
"sampleId": "0007133",
"uri_format": "http://www.gramene.org/db/ontology/search?id=GRO:$1"
},
"n2t": {
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.",
"example": "0007133",
"homepage": "http://www.gramene.org/",
"name": "Gramene Growth Stage Ontology at Cold Spring Harbor",
"namespaceEmbeddedInLui": true,
"pattern": "^GRO\\:\\d+$",
"prefix": "gramene.growthstage",
"uri_format": "http://www.gramene.org/db/ontology/search?id=GRO:$1"
},
"name": "Gramene Growth Stage Ontology",
"obofoundry": {
"contact": "po-discuss@plantontology.org",
"contact.label": "Plant Ontology Administrators",
"deprecated": true,
"domain": "anatomy and development",
"homepage": "http://www.gramene.org/plant_ontology/",
"name": "Cereal Plant Gross Anatomy",
"prefix": "gro"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"description": "A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part.",
"example": "GRO:0007143",
"homepage": "http://www.gramene.org/plant_ontology/",
"keywords": [
"obo",
"ontology",
"anatomy"
],
"name": "Plant Ontology",
"pattern": "^GRO:\\d+$",
"prefix": "gramene.po",
"uri_format": "http://www.gramene.org/db/ontology/search?id=$1"
},
"synonyms": [
"cpga",
"gro-cpga"
],
"uri_format": "http://www.gramene.org/db/ontology/search?id=GRO:$1"
},
"gramene.protein": {
"biocontext": {
"prefix": "GRAMENE.PROTEIN"
},
"go": {
"homepage": "http://www.gramene.org/",
"name": "Gramene",
"prefix": "GR_PROTEIN",
"synonyms": [
"GR_protein"
],
"uri_format": "http://www.gramene.org/db/protein/protein_search?acc=$1"
},
"mappings": {
"biocontext": "GRAMENE.PROTEIN",
"go": "GR_PROTEIN",
"miriam": "gramene.protein",
"n2t": "gramene.protein"
},
"miriam": {
"deprecated": false,
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene.",
"homepage": "http://www.gramene.org/",
"id": "00000181",
"name": "Gramene protein",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "gramene.protein",
"sampleId": "78073",
"uri_format": "http://www.gramene.org/db/protein/protein_search?protein_id=$1"
},
"n2t": {
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene.",
"example": "78073",
"homepage": "http://www.gramene.org/",
"name": "Gramene Protein at Cold Spring Harbor",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "gramene.protein",
"uri_format": "http://www.gramene.org/db/protein/protein_search?protein_id=$1"
},
"name": "Gramene protein",
"synonyms": [
"GR_PROTEIN"
]
},
"gramene.qtl": {
"biocontext": {
"prefix": "GRAMENE.QTL"
},
"go": {
"homepage": "http://www.gramene.org/",
"name": "Gramene",
"prefix": "GR_QTL",
"uri_format": "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1"
},
"mappings": {
"biocontext": "GRAMENE.QTL",
"go": "GR_QTL",
"miriam": "gramene.qtl",
"n2t": "gramene.qtl"
},
"miriam": {
"deprecated": false,
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene.",
"homepage": "http://www.gramene.org/",
"id": "00000184",
"name": "Gramene QTL",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "gramene.qtl",
"sampleId": "CQG5",
"uri_format": "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1"
},
"n2t": {
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene.",
"example": "CQG5",
"homepage": "http://www.gramene.org/",
"name": "Gramene Quantitative Trait Loci at Cold Spring Harbor",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "gramene.qtl",
"uri_format": "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1"
},
"name": "Gramene QTL",
"synonyms": [
"GR_QTL"
]
},
"gramene.reference": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Literature references in Gramene",
"example": "6200",
"homepage": "http://www.gramene.org",
"name": "Gramene Reference",
"pattern": "^\\d+$",
"synonyms": [
"gramene.ref"
],
"uri_format": "http://www.gramene.org/db/literature/pub_search?ref_id=$1"
},
"gramene.taxonomy": {
"banana": "GR_tax",
"banana_peel": ":",
"biocontext": {
"prefix": "GRAMENE.TAXONOMY"
},
"example": "013681",
"mappings": {
"biocontext": "GRAMENE.TAXONOMY",
"miriam": "gramene.taxonomy",
"n2t": "gramene.taxonomy"
},
"miriam": {
"deprecated": false,
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene.",
"homepage": "http://www.gramene.org/",
"id": "00000183",
"name": "Gramene Taxonomy",
"namespaceEmbeddedInLui": false,
"pattern": "^GR\\_tax\\:\\d+$",
"prefix": "gramene.taxonomy",
"sampleId": "GR_tax:013681",
"uri_format": "http://www.gramene.org/db/ontology/search?id=$1"
},
"n2t": {
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene.",
"example": "GR_tax:013681",
"homepage": "http://www.gramene.org/",
"name": "Gramene Taxonomy at Cold Spring Harbor",
"namespaceEmbeddedInLui": false,
"pattern": "^GR\\_tax\\:\\d+$",
"prefix": "gramene.taxonomy",
"uri_format": "http://www.gramene.org/db/ontology/search?id=$1"
},
"pattern": "^\\d+$",
"uri_format": "https://archive.gramene.org/db/ontology/search?id=GR_tax:$1"
},
"grassbase": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species.",
"example": "imp10873",
"github_request_issue": 218,
"homepage": "https://www.kew.org/data/grasses-syn/index.htm",
"mappings": {
"wikidata": "P1832"
},
"name": "GrassBase",
"pattern": "^(imp|gen)\\d{5}$",
"uri_format": "https://www.kew.org/data/grasses-db/www/$1",
"wikidata": {
"description": "identifier in GrassBase - The Online World Grass Flora",
"example": [
"gen00495",
"imp10873"
],
"homepage": "http://www.kew.org/data/grasses-syn/index.htm",
"name": "GrassBase ID",
"pattern": "^(imp|gen){1}\\d{5}$",
"prefix": "P1832",
"uri_format": "http://www.kew.org/data/grasses-db/www/$1"
}
},
"greengenes": {
"biocontext": {
"prefix": "GREENGENES"
},
"fairsharing": {
"abbreviation": "Greengenes",
"contact": {
"email": "GLAndersen@lbl.gov",
"name": "Gary L Andersen",
"orcid": "0000-0002-1618-9827"
},
"description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. Please note that this is a downloadable resource only, without an interactive web interface.",
"homepage": "http://greengenes.lbl.gov",
"name": "Greengenes",
"prefix": "FAIRsharing.bpxgb6",
"publications": [
{
"doi": "10.1128/AEM.03006-05",
"pubmed_id": 16820507,
"title": "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB."
}
],
"subjects": [
"Genetics",
"Life Science"
]
},
"integbio": {
"description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.",
"fairsharing": "FAIRsharing.bpxgb6",
"homepage": "http://greengenes.lbl.gov",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "LBNL (Lawrence Berkeley National Laboratory)",
"name": "Greengenes",
"prefix": "nbdc01824",
"pubmeds": [
"16820507"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"mappings": {
"biocontext": "GREENGENES",
"fairsharing": "FAIRsharing.bpxgb6",
"integbio": "nbdc01824",
"miriam": "greengenes",
"n2t": "greengenes",
"ncbi": "Greengenes",
"prefixcommons": "greengenes",
"re3data": "r3d100010549"
},
"miriam": {
"deprecated": false,
"description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.",
"homepage": "http://greengenes.lbl.gov/",
"id": "00000165",
"name": "GreenGenes",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "greengenes",
"sampleId": "100000",
"uri_format": "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1"
},
"n2t": {
"description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.",
"example": "100000",
"homepage": "http://greengenes.lbl.gov/",
"name": "GreenGenes at Lawrence Berkeley",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "greengenes",
"uri_format": "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1"
},
"ncbi": {
"example": "269185",
"homepage": "http://greengenes.lbl.gov/",
"name": "16S rRNA gene database",
"prefix": "Greengenes"
},
"prefixcommons": {
"description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.",
"example": "100000",
"homepage": "http://greengenes.lbl.gov",
"keywords": [
"RNA"
],
"name": "Greengenes:16S rRNA gene database",
"pattern": "^\\d+$",
"prefix": "greengenes",
"pubmed_ids": [
"16820507"
],
"uri_format": "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1"
},
"publications": [
{
"doi": "10.1128/aem.03006-05",
"pmc": "PMC1489311",
"pubmed": "16820507",
"title": "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB",
"year": 2006
}
],
"re3data": {
"description": "Greengenes is an Earth Sciences website that assists clinical and environmental microbiologists from around the globe in classifying microorganisms from their local environments. A 16S rRNA gene database addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.",
"homepage": "https://greengenes.secondgenome.com/",
"name": "Greengenes",
"prefix": "r3d100010549",
"synonyms": [
"The Greengenes Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.bpxgb6",
"miriam": "00000165",
"nif": "0000-02927",
"scr": "002830"
}
}
},
"grid": {
"biocontext": {
"prefix": "GRID"
},
"fairsharing": {
"abbreviation": "GRID",
"description": "Global Research Identifier Database (GRID) stores information on research-related organisations worldwide. GRID record contains a unique GRID ID, relevant metadata, and relationships between associated institutions.",
"homepage": "https://grid.ac/",
"license": "CC0-1.0",
"name": "Global Research Identifier Database",
"prefix": "FAIRsharing.0pUMYW",
"publications": [],
"subjects": [
"Data Management"
],
"twitter": "grid_ac"
},
"mappings": {
"biocontext": "GRID",
"fairsharing": "FAIRsharing.0pUMYW",
"miriam": "grid",
"n2t": "grid"
},
"miriam": {
"deprecated": false,
"description": "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally.",
"homepage": "https://www.grid.ac/",
"id": "00000593",
"name": "GRID",
"namespaceEmbeddedInLui": false,
"pattern": "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$",
"prefix": "grid",
"sampleId": "grid.225360.0",
"uri_format": "https://www.grid.ac/institutes/$1"
},
"n2t": {
"description": "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally.",
"example": "grid.225360.0",
"homepage": "https://www.grid.ac/",
"name": "GRID at Digital Science & Research Ltd.",
"namespaceEmbeddedInLui": false,
"pattern": "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$",
"prefix": "grid",
"uri_format": "https://www.grid.ac/institutes/$1"
},
"name": "Global Research Identifier Database"
},
"grin": {
"fairsharing": {
"abbreviation": "GRIN",
"description": "GRIN provides National Genetic Resources Program (NGRP) personnel and germplasm users continuous access to databases for the maintenance of passport, characterization, evaluation, inventory, and distribution data important for the effective management and utilization of national germplasm collections.",
"homepage": "https://www.ars-grin.gov/",
"name": "Germplasm Resources Information Network",
"prefix": "FAIRsharing.3axym7",
"publications": [],
"subjects": [
"Life Science"
]
},
"mappings": {
"fairsharing": "FAIRsharing.3axym7",
"prefixcommons": "grin"
},
"prefixcommons": {
"description": "GRIN provides National Genetic Resources Program (NGRP) personnel and germplasm users continuous access to databases for the maintenance of passport, characterization, evaluation, inventory, and distribution data important for the effective management and utilization of national germplasm collections.",
"example": "159787",
"homepage": "http://www.ars-grin.gov/",
"name": "Germplasm Resources Information Network",
"pattern": "^\\d+$",
"prefix": "grin",
"uri_format": "http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"grin.taxonomy": {
"biocontext": {
"prefix": "GRIN.TAXONOMY"
},
"go": {
"homepage": "https://www.ars-grin.gov/",
"name": "Germplasm Resources Information Network",
"prefix": "GRIN",
"synonyms": [
"grin"
],
"uri_format": "https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=$1"
},
"mappings": {
"biocontext": "GRIN.TAXONOMY",
"go": "GRIN",
"miriam": "grin.taxonomy",
"n2t": "grin.taxonomy",
"ncbi": "GRIN",
"wikidata": "P1421"
},
"miriam": {
"deprecated": false,
"description": "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact.",
"homepage": "http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en",
"id": "00000166",
"name": "GRIN Plant Taxonomy",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "grin.taxonomy",
"sampleId": "19333",
"uri_format": "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1"
},
"n2t": {
"description": "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact.",
"example": "19333",
"homepage": "http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en",
"name": "GRIN at Maryland",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "grin.taxonomy",
"uri_format": "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1"
},
"ncbi": {
"example": "1005973",
"homepage": "http://www.ars-grin.gov/",
"name": "Germplasm Resources Information Network",
"prefix": "GRIN"
},
"wikidata": {
"database": "Q19576476",
"description": "URL for a taxon in the GRIN website",
"example": [
"https://npgsweb.ars-grin.gov/gringlobal/taxonomydetail.aspx?id=42207",
"https://npgsweb.ars-grin.gov/gringlobal/taxonomyfamily.aspx?id=897",
"https://npgsweb.ars-grin.gov/gringlobal/taxonomygenus.aspx?id=10404"
],
"name": "GRIN URL",
"prefix": "P1421"
}
},
"gro": {
"aberowl": {
"description": "The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes.",
"download_owl": "http://aber-owl.net/media/ontologies/GRO/5/gro.owl",
"homepage": "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html",
"name": "Gene Regulation Ontology",
"prefix": "GRO",
"version": "0.5"
},
"bioportal": {
"contact": {
"email": "vlee@ebi.ac.uk",
"name": "Vivian Lee"
},
"description": "The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes.",
"homepage": "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html",
"name": "Gene Regulation Ontology",
"prefix": "GRO",
"version": "0.5"
},
"deprecated": true,
"example": "Lipid",
"mappings": {
"aberowl": "GRO",
"bioportal": "GRO"
},
"uri_format": "http://www.bootstrep.eu/ontology/GRO#$1"
},
"grsdb": {
"biocontext": {
"prefix": "GRSDB"
},
"mappings": {
"biocontext": "GRSDB",
"miriam": "grsdb",
"n2t": "grsdb",
"prefixcommons": "grsdb"
},
"miriam": {
"deprecated": false,
"description": "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.",
"homepage": "http://bioinformatics.ramapo.edu/GRSDB2/",
"id": "00000495",
"name": "GRSDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "grsdb",
"sampleId": "10142",
"uri_format": "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1"
},
"n2t": {
"description": "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.",
"example": "10142",
"homepage": "http://bioinformatics.ramapo.edu/GRSDB2/",
"name": "GRSDB v2 at Ramapo College of New Jersey",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "grsdb",
"uri_format": "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1"
},
"name": "G-Rich Sequences Database",
"prefixcommons": {
"description": "GRSDB2 is a second generation database of G-quadruplexes. Like its first version, GRSDB, it contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including that are alternatively processed (alternatively spliced or alternatively polyadenylated).",
"example": "3191",
"homepage": "http://bioinformatics.ramapo.edu/GRSDB2/",
"keywords": [
"DNA",
"RNA"
],
"name": "GRSDB",
"pattern": "^\\d+$",
"prefix": "grsdb",
"uri_format": "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1"
}
},
"gsfa": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The \"Codex General Standard for Food Additives\" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database.",
"example": "174",
"homepage": "http://www.fao.org/gsfaonline",
"name": "General Standard for Food Additives Online Database",
"pattern": "^\\d+$",
"synonyms": [
"FAO/WHO_standards"
],
"uri_format": "http://www.fao.org/gsfaonline/additives/details.html?id=$1"
},
"gsso": {
"aberowl": {
"description": "The Gender, Sex, and Sexual Orientation (GSSO) ontology has terms for annotating interdisciplinary information concerning gender, sex, and sexual orientation for primary usage in the biomedical and adjacent sciences.",
"download_owl": "http://aber-owl.net/media/ontologies/GSSO/73/gsso.owl",
"homepage": "https://gsso.research.cchmc.org/",
"name": "Gender, Sex, and Sexual Orientation (GSSO) ontology",
"prefix": "GSSO"
},
"bioportal": {
"contact": {
"email": "gsso.ontology@gmail.com",
"name": "Clair Kronk"
},
"description": "The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology.",
"homepage": "https://gsso.research.cchmc.org/",
"name": "Gender, Sex, and Sexual Orientation Ontology",
"prefix": "GSSO",
"publication": "https://doi.org/10.1093/jamia/ocaa061",
"version": "2.0.6"
},
"mappings": {
"aberowl": "GSSO",
"bioportal": "GSSO",
"miriam": "gsso",
"obofoundry": "gsso",
"ols": "gsso",
"ontobee": "GSSO"
},
"miriam": {
"deprecated": false,
"description": "The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology.",
"homepage": "https://bioportal.bioontology.org/",
"id": "00000712",
"name": "Gender, Sex, and Sexual Orientation (GSSO) Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^GSSO:\\d{6}$",
"prefix": "gsso",
"sampleId": "002368",
"uri_format": "http://purl.obolibrary.org/obo/GSSO_$1"
},
"name": "Gender, Sex, and Sexual Orientation Ontology",
"obofoundry": {
"appears_in": [
"ontoavida",
"scdo"
],
"contact": "kronkcj@mail.uc.edu",
"contact.github": "Superraptor",
"contact.label": "Clair Kronk",
"contact.orcid": "0000-0001-8397-8810",
"deprecated": false,
"description": "The Gender, Sex, and Sexual Orientation (GSSO) ontology has terms for annotating interdisciplinary information concerning gender, sex, and sexual orientation for primary usage in the biomedical and adjacent sciences.",
"domain": "organisms",
"download.json": "http://purl.obolibrary.org/obo/gsso.json",
"download.obo": "http://purl.obolibrary.org/obo/gsso.obo",
"download.owl": "http://purl.obolibrary.org/obo/gsso.owl",
"homepage": "https://gsso.research.cchmc.org/",
"license": "Apache 2.0 License",
"license.url": "http://www.apache.org/licenses/LICENSE-2.0",
"name": "Gender, Sex, and Sexual Orientation (GSSO) ontology",
"preferredPrefix": "GSSO",
"prefix": "gsso",
"repository": "https://github.com/Superraptor/GSSO"
},
"ols": {
"description": "GSSO is the Gender, Sex, and Sex Orientation ontology, including terms related to gender identity and expression, sexual and romantic identity and orientation, and sexual and reproductive behavior.",
"download_owl": "http://purl.obolibrary.org/obo/gsso.owl",
"homepage": "https://gsso.research.cchmc.org/",
"name": "GSSO - the Gender, Sex, and Sexual Orientation ontology",
"prefix": "gsso",
"version": "2.0.5",
"version.iri": "http://purl.obolibrary.org/obo/gsso/releases/2.0.5/gsso.owl"
},
"ontobee": {
"library": "Library",
"name": "Gender, Sex, and Sexual Orientation (GSSO) ontology",
"prefix": "GSSO"
},
"pattern": "^\\d{6}$",
"uri_format": "http://purl.obolibrary.org/obo/GSSO_$1"
},
"gtex": {
"biocontext": {
"prefix": "GTEX"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
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},
"bioportal": {
"contact": {
"email": "dwelter.ontologist@gmail.com",
"name": "Danielle Welter"
},
"description": "The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies. Please note that as of v2.0 (released July 2018), HANCESTRO (formerly ANCESTRO) has undergone some major changes including a revised namespace.",
"homepage": "https://github.com/EBISPOT/hancestro",
"name": "Human Ancestry Ontology",
"prefix": "HANCESTRO",
"publication": "https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1396-2",
"version": "2024-06-21"
},
"example": "0290",
"fairsharing": {
"abbreviation": "HANCESTRO",
"description": "The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies.",
"domains": [
"Genome-wide association study"
],
"homepage": "https://github.com/EBISPOT/hancestro",
"license": "CC-BY-4.0",
"name": "Human Ancestry Ontology",
"prefix": "FAIRsharing.rja8qp",
"publications": [
{
"doi": "10.1186/s13059-018-1396-2",
"pubmed": "29448949",
"title": "A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog",
"year": 2018
}
],
"repository": "https://github.com/EBISPOT/ancestro/issues",
"subjects": [
"Demographics",
"Human Genetics",
"Population Genetics"
]
},
"mappings": {
"aberowl": "HANCESTRO",
"biolink": "HANCESTRO",
"bioportal": "HANCESTRO",
"fairsharing": "FAIRsharing.rja8qp",
"obofoundry": "hancestro",
"ols": "hancestro",
"ontobee": "HANCESTRO"
},
"obofoundry": {
"contact": "dwelter.ontologist@gmail.com",
"contact.github": "daniwelter",
"contact.label": "Danielle Welter",
"contact.orcid": "0000-0003-1058-2668",
"deprecated": false,
"description": "The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies.",
"domain": "organisms",
"download.owl": "http://purl.obolibrary.org/obo/hancestro.owl",
"homepage": "https://ebispot.github.io/hancestro/",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Human Ancestry Ontology",
"preferredPrefix": "HANCESTRO",
"prefix": "hancestro",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/29448949",
"title": "A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog"
}
],
"repository": "https://github.com/EBISPOT/hancestro"
},
"ols": {
"description": "Human ancestry ontology for the NHGRI GWAS Catalog",
"download_owl": "http://purl.obolibrary.org/obo/hancestro.owl",
"homepage": "https://ebispot.github.io/hancestro/",
"name": "Human Ancestry Ontology",
"prefix": "hancestro",
"version": "2024-06-21",
"version.iri": "http://purl.obolibrary.org/obo/hancestro/releases/2024-06-21/hancestro.owl"
},
"ontobee": {
"library": "Library",
"name": "Human Ancestry Ontology",
"prefix": "HANCESTRO"
},
"owners": [
{
"name": "European Bioinformatics Institute",
"partnered": false,
"ror": "02catss52"
}
],
"pattern": "^\\d{4}$",
"providers": [
{
"code": "legacy",
"description": "Legacy URI",
"homepage": "http://www.ebi.ac.uk/ancestro",
"name": "Legacy",
"uri_format": "http://www.ebi.ac.uk/ancestro/ancestro_$1"
}
],
"publications": [
{
"doi": "10.1186/s13059-018-1396-2",
"pmc": "PMC5815218",
"pubmed": "29448949",
"title": "A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog",
"year": 2018
}
],
"repository": "https://github.com/EBISPOT/ancestro",
"uri_format": "http://purl.obolibrary.org/obo/HANCESTRO_$1"
},
"hao": {
"aberowl": {
"description": "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)",
"download_owl": "http://aber-owl.net/media/ontologies/HAO/28/hao.owl",
"homepage": "http://hymao.org",
"name": "Hymenoptera Anatomy Ontology",
"prefix": "HAO"
},
"biocontext": {
"prefix": "HAO"
},
"bioportal": {
"contact": {
"email": "diapriid@gmail.com",
"name": "HAO developers"
},
"description": "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, sawflies and ants)",
"homepage": "http://hymao.org",
"name": "Hymenoptera Anatomy Ontology",
"prefix": "HAO",
"version": "2023-06-01"
},
"example": "0000187",
"fairsharing": {
"abbreviation": "HAO",
"contact": {
"email": "andy_deans@ncsu.edu",
"name": "Andrew R Deans",
"orcid": "0000-0002-2119-4663"
},
"description": "The Hymenoptera Anatomy Ontology is a structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)",
"domains": [
"Image"
],
"homepage": "http://portal.hymao.org/projects/32/public/ontology/",
"name": "Hymenoptera Anatomy Ontology",
"prefix": "FAIRsharing.kj3m5n",
"publications": [
{
"doi": "10.1371/journal.pone.0015991",
"pubmed": "21209921",
"title": "A gross anatomy ontology for hymenoptera",
"year": 2011
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"mappings": {
"aberowl": "HAO",
"biocontext": "HAO",
"bioportal": "HAO",
"fairsharing": "FAIRsharing.kj3m5n",
"obofoundry": "hao",
"ols": "hao",
"ontobee": "HAO"
},
"obofoundry": {
"contact": "diapriid@gmail.com",
"contact.github": "mjy",
"contact.label": "Matt Yoder",
"contact.orcid": "0000-0002-5640-5491",
"deprecated": false,
"description": "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/hao.obo",
"download.owl": "http://purl.obolibrary.org/obo/hao.owl",
"homepage": "http://hymao.org",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Hymenoptera Anatomy Ontology",
"preferredPrefix": "HAO",
"prefix": "hao",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/21209921",
"title": "A gross anatomy ontology for hymenoptera"
}
],
"repository": "https://github.com/hymao/hao"
},
"ols": {
"description": "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)",
"download_owl": "http://purl.obolibrary.org/obo/hao.owl",
"homepage": "http://hymao.org",
"name": "Hymenoptera Anatomy Ontology",
"prefix": "hao",
"version": "2023-06-01",
"version.iri": "http://purl.obolibrary.org/obo/hao/2023-06-01/hao.owl"
},
"ontobee": {
"library": "Library",
"name": "Hymenoptera Anatomy Ontology",
"prefix": "HAO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1371/journal.pone.0015991",
"pmc": "PMC3012123",
"pubmed": "21209921",
"title": "A gross anatomy ontology for hymenoptera",
"year": 2010
}
],
"uri_format": "http://purl.obolibrary.org/obo/HAO_$1"
},
"hathitrust": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world.",
"example": "008893080",
"github_request_issue": 510,
"homepage": "https://www.hathitrust.org",
"name": "Hathi Trust Digital Library",
"pattern": "^\\d+$",
"uri_format": "https://catalog.hathitrust.org/Record/$1"
},
"hba": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A controlled vocabulary to support the study of transcription in the human brain",
"download_obo": "https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-hba.obo",
"example": "4005",
"example_extras": [
"265504410"
],
"homepage": "https://human.brain-map.org",
"name": "Human Brain Atlas",
"pattern": "^\\d+$",
"preferred_prefix": "HBA",
"uri_format": "https://biopragmatics.github.io/providers/hba/$1"
},
"hbvar": {
"mappings": {
"prefixcommons": "hbvar"
},
"prefixcommons": {
"description": "This is a relational database of information about hemoglobin variants and mutations that cause thalassemia.",
"example": "2526",
"homepage": "http://globin.cse.psu.edu/globin/hbvar",
"keywords": [
"protein"
],
"name": "A Database of Human Hemoglobin Variants and Thalassemias",
"pattern": "^\\d+$",
"prefix": "hbvar",
"uri_format": "http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"hc.din": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A Drug Identification Number (DIN) is a computer-generated eight digit number assigned by Health Canada to a drug product prior to being marketed in Canada. It uniquely identifies all drug products sold in a dosage form in Canada and is located on the label of prescription and over-the-counter drug products that have been evaluated and authorized for sale in Canada.",
"example": "02069237",
"hl7": {
"description": "A Drug Identification Number (DIN) is a computer-generated eight digit number assigned by Health Canada to a drug product prior to being marketed in Canada. It uniquely identifies all drug products sold in a dosage form in Canada and is located on the label of prescription and over-the-counter drug products that have been evaluated and authorized for sale in Canada.A DIN uniquely identifies the following product characteristics:manufacturer;product name;active ingredient(s);strength(s) of active ingredient(s);pharmaceutical form; androute of administration.Note: The number has a leading zeroMore information can be found here: https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/applications-submissions/guidance-documents/regulatory-requirements-drug-identification-numbers/document.html",
"homepage": "http://www.hc-sc.gc.ca/index-eng.php",
"name": "Health Canada Drug Id Number",
"organization": "Health Canada,Health Canada",
"preferred_prefix": "hc-DIN",
"prefix": "2.16.840.1.113883.5.1105",
"status": "Complete"
},
"homepage": "https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/fact-sheets/drug-identification-number.html",
"mappings": {
"hl7": "2.16.840.1.113883.5.1105"
},
"name": "Health Canada Drug Identification Number",
"pattern": "^\\d{8}$",
"references": [
"http://www.hc-sc.gc.ca/dhp-mps/prodpharma/databasdon/index-eng.php"
]
},
"hc.npn": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Licensed Natural Health Products Database contains information about natural health products that have been issued a product licence by Health Canada.",
"example": "18125",
"hl7": {
"description": "Natural Product Number (NPN) is an eight digit numerical code assigned to each natural health product approved to be marketed under the Natural Health Products Regulations. A Homeopathic Medicine Number (DIN-HM) is an eight digit numerical code assigned to each homeopathic medicine approved to be marketed under the Natural Health Products Regulations. More information can be found here: https://www.canada.ca/en/health-canada/services/drugs-health-products/natural-non-prescription/applications-submissions/product-licensing/licensed-natural-health-products-database.html",
"homepage": "http://www.hc-sc.gc.ca/index-eng.php",
"name": "Health Canada Natural Product Number",
"organization": "Health Canada,Health Canada",
"preferred_prefix": "hc-NPN",
"prefix": "2.16.840.1.113883.5.1107",
"status": "Complete"
},
"homepage": "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/search-rechercheReq.do?lang=eng",
"mappings": {
"hl7": "2.16.840.1.113883.5.1107"
},
"name": "Health Canada Natural Product Number",
"pattern": "^\\d+$",
"references": [
"https://www.canada.ca/en/health-canada/services/drugs-health-products/natural-non-prescription/applications-submissions/product-licensing/licensed-natural-health-products-database.html"
],
"uri_format": "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id=$1"
},
"hc.trial": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Health Canada, through its Clinical Trials Database, is providing to the public a listing of specific information relating to phase I, II and III clinical trials in patients. The database is managed by Health Canada and provides a source of information about Canadian clinical trials involving human pharmaceutical and biological drugs. [from website]",
"example": "239287",
"homepage": "https://health-products.canada.ca/ctdb-bdec",
"name": "Health Canada Clinical Trials Database",
"pattern": "^\\d+$",
"uri_format": "https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo=$1"
},
"hcao": {
"homepage": "https://www.humancellatlas.org",
"mappings": {
"ols": "hcao"
},
"no_own_terms": true,
"ols": {
"description": "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas.",
"download_owl": "https://raw.githubusercontent.com/ebi-ait/ontology/master/hcao.owl",
"name": "Human Cell Atlas Ontology",
"prefix": "hcao",
"version.iri": "http://ontology.data.humancellatlas.org/ontologies/hcao/releases/2023-05-16/hcao.owl"
}
},
"hco": {
"mappings": {
"miriam": "hco"
},
"miriam": {
"deprecated": false,
"description": "The Human Chromosome Ontology (HCO) provides simple and stable URIs for human reference genome versions to semantically identify human chromosomes.",
"homepage": "https://dbcls.rois.ac.jp/",
"id": "00001040",
"name": "Human Chromosome Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^.+$",
"prefix": "hco",
"sampleId": "MT",
"uri_format": "http://biohackathon.org/resource/hco#$1"
}
},
"hcpcs": {
"aberowl": {
"description": "Healthcare Common Procedure Coding System",
"homepage": "http://cms.hhs.gov",
"name": "Healthcare Common Procedure Coding System",
"prefix": "HCPCS",
"version": "2016AB"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "HCPCS",
"uri_format": "http://purl.bioontology.org/ontology/HCPCS/$1"
},
"bioportal": {
"contact": {
"email": "Cynthia.Hake@cms.hhs.gov",
"name": "Cynthia Hake"
},
"description": "Healthcare Common Procedure Coding System",
"homepage": "http://cms.hhs.gov",
"name": "Healthcare Common Procedure Coding System",
"prefix": "HCPCS",
"publication": "http://cms.hhs.gov",
"version": "2023AB"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers.",
"example": "G8944",
"fairsharing": {
"abbreviation": "HCPCS",
"description": "Each year, in the United States, health care insurers process over 5 billion claims for payment. For Medicare and other health insurance programs to ensure that these claims are processed in an orderly and consistent manner, standardized coding systems are essential. The HCPCS is divided into two principal subsystems, referred to as level I and level II of the HCPCS. Level I of the HCPCS is comprised of CPT (Current Procedural Terminology), a numeric coding system maintained by the American Medical Association (AMA). Level II of the HCPCS is a standardized coding system that is used primarily to identify products, supplies, and services not included in the CPT codes, such as ambulance services and durable medical equipment, prosthetics, orthotics, and supplies (DMEPOS) when used outside a physician's office.",
"homepage": "https://www.cms.gov/medicare/coding/medhcpcsgeninfo/index.html",
"name": "Healthcare Common Procedure Coding System",
"prefix": "FAIRsharing.x81wz8",
"subjects": [
"Business Administration",
"Biomedical Science"
]
},
"homepage": "https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo",
"mappings": {
"aberowl": "HCPCS",
"biolink": "HCPCS",
"bioportal": "HCPCS",
"fairsharing": "FAIRsharing.x81wz8"
},
"name": "Healthcare Common Procedure Coding System",
"uri_format": "http://purl.bioontology.org/ontology/HCPCS/$1"
},
"hcvdb": {
"biocontext": {
"prefix": "HCVDB"
},
"mappings": {
"biocontext": "HCVDB",
"miriam": "hcvdb",
"n2t": "hcvdb",
"prefixcommons": "hcv"
},
"miriam": {
"deprecated": false,
"description": "the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses.",
"homepage": "http://euhcvdb.ibcp.fr/euHCVdb/",
"id": "00000207",
"name": "HCVDB",
"namespaceEmbeddedInLui": false,
"pattern": "^M\\d{5}$",
"prefix": "hcvdb",
"sampleId": "M58335",
"uri_format": "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1"
},
"n2t": {
"description": "the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses.",
"example": "M58335",
"homepage": "http://euhcvdb.ibcp.fr/euHCVdb/",
"name": "HCVDB at CNRS",
"namespaceEmbeddedInLui": false,
"pattern": "^M\\d{5}$",
"prefix": "hcvdb",
"uri_format": "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1"
},
"name": "Hepatitis C Virus Database Project",
"prefixcommons": {
"description": "The HCV database group strives to present HCV-associated, hand-annotated genetic data in a userfriendly way, by providing access to the central database via web-accessible search interfaces and supplying a number of analysis tools.",
"example": "71867",
"homepage": "http://hcv.lanl.gov/",
"keywords": [
"gene"
],
"name": "Hepatitis C Virus (HCV) Database Project",
"pattern": "^\\d+$",
"prefix": "hcv",
"synonyms": [
"hcv_database"
],
"uri_format": "http://hcv.lanl.gov/components/sequence/HCV/asearch/query_one.comp?se_id=$1"
}
},
"hdl": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Welcome to the web site of the Handle.Net Registry (HNR), run by Corporation for National Research Initiatives (CNRI). CNRI is a Multi-Primary Administrator (MPA) of the Global Handle Registry (GHR), authorized by the DONA Foundation to allot prefixes to users of the Handle System. The DONA Foundation is a non-profit organization based in Geneva that has taken over responsibility for the evolution of CNRI's Digital Object (DO) Architecture including outreach around the world. One of the Foundation's responsibilities is to administer and maintain the overall operation of the GHR, a task that was previously performed by CNRI. (from website)",
"example": "2381/12775",
"example_extras": [
"391/00-0000-0000-0009-3C7E-F"
],
"fairsharing": {
"abbreviation": "hdl",
"description": "The Handle System is the Corporation for National Research Initiatives's proprietary registry assigning persistent identifiers, or handles, to information resources, and for resolving \"those handles into the information necessary to locate, access, and otherwise make use of the resources\". As with handles used elsewhere in computing, Handle System handles are opaque, and encode no information about the underlying resource, being bound only to metadata regarding the resource. Consequently, the handles are not rendered invalid by changes to the metadata.",
"domains": [
"Centrally registered identifier"
],
"homepage": "http://handle.net",
"name": "Handle",
"prefix": "FAIRsharing.0b7e54",
"subjects": [
"Subject Agnostic"
]
},
"homepage": "https://www.handle.net/",
"mappings": {
"fairsharing": "FAIRsharing.0b7e54"
},
"name": "Handle",
"pattern": "^\\d+/.+$",
"synonyms": [
"handle"
],
"uri_format": "http://hdl.handle.net/$1"
},
"hdr": {
"biocontext": {
"prefix": "HDR"
},
"mappings": {
"biocontext": "HDR",
"miriam": "hdr",
"n2t": "hdr",
"pathguide": "307",
"prefixcommons": "hdr"
},
"miriam": {
"deprecated": false,
"description": "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders.",
"homepage": "http://research.nhgri.nih.gov/apps/homeodomain/web/",
"id": "00000497",
"name": "Homeodomain Research",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "hdr",
"sampleId": "63",
"uri_format": "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1"
},
"n2t": {
"description": "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders.",
"example": "63",
"homepage": "http://research.nhgri.nih.gov/apps/homeodomain/web/",
"name": "Homeodomain Research at National Human Genome Research Institute (NIH)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "hdr",
"uri_format": "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1"
},
"pathguide": {
"abbreviation": "HDR",
"homepage": "http://research.nhgri.nih.gov/homeodomain/",
"name": "Homeodomain Resource Database",
"prefix": "307"
},
"prefixcommons": {
"description": "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic, and functional information on the homeodomain family. A description of each of the major sections of the database can be found below, and users can navigate through the site using the links found in the menu that appears on the left-hand side of every page within the site.",
"example": "5978",
"homepage": "http://research.nhgri.nih.gov/homeodomain/",
"keywords": [
"genome"
],
"name": "Homeodomain Resource Database",
"pattern": "^\\d+$",
"prefix": "hdr",
"synonyms": [
"homeodb"
],
"uri_format": "http://research.nhgri.nih.gov/homeodomain/?mode=view&view=proteins&id=$1"
}
},
"hemonc": {
"comment": "It is unclear if identifiers can be resolved on the website but a spreadsheet of the terminology is available via the NCI at https://evs.nci.nih.gov/ftp1/HemOnc/HemOnc_Terminology.xls",
"contributor": {
"email": "b.gyori@northeastern.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"description": "HemOnc.org is the largest freely available medical wiki of interventions, regimens, and general information relevant to the fields of hematology and oncology.",
"example": "15543",
"github_request_issue": 1149,
"homepage": "https://hemonc.org/",
"name": "HemOnc Terminology",
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1016/j.jbi.2019.103239",
"pmc": "PMC6697579",
"pubmed": "31238109",
"title": "HemOnc: A new standard vocabulary for chemotherapy regimen representation in the OMOP common data model",
"year": 2019
}
],
"reviewer": {
"github": "callahantiff",
"name": "Tiffany J. Callahan",
"orcid": "0000-0002-8169-9049"
}
},
"hepro": {
"contact": {
"email": "paul.fabry@usherbrooke.ca",
"github": "pfabry",
"name": "Paul Fabry",
"orcid": "0000-0002-3336-2476"
},
"contributor": {
"email": "paul.fabry@usherbrooke.ca",
"github": "pfabry",
"name": "Paul Fabry",
"orcid": "0000-0002-3336-2476"
},
"description": "HEPRO is an ontology of informational entities and processes related to health procedures and health activities.",
"download_json": "https://github.com/OpenLHS/HEPRO/raw/main/HEPRO.json",
"download_owl": "https://github.com/OpenLHS/HEPRO/raw/main/HEPRO.owl",
"example": "0000001",
"github_request_issue": 810,
"homepage": "https://openlhs.github.io/HEPRO/",
"license": "CC-BY-4.0",
"name": "Health Procedure Ontology",
"owners": [
{
"name": "UniversitΓ© de Sherbrooke",
"partnered": false,
"ror": "00kybxq39"
}
],
"pattern": "^\\d{7}$",
"preferred_prefix": "HEPRO",
"repository": "https://github.com/OpenLHS/HEPRO",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://purl.obolibrary.org/obo/HEPRO_$1"
},
"hesa": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An identifier for institutions in the United Kingdom, used in GRID and ROR.",
"example": "0154",
"homepage": "https://www.hesa.ac.uk",
"keywords": [
"bibliometrics",
"institution"
],
"name": "UK Higher Education Statistics Agency",
"pattern": "^\\d+$"
},
"hgmd": {
"biocontext": {
"prefix": "HGMD",
"uri_format": "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1"
},
"edam": {
"description": "Identifier of a HGMD database entry.",
"name": "HGMD",
"obsolete": false,
"prefix": "3265"
},
"integbio": {
"alt_name": "The Human Gene Mutation Database",
"description": "HGMD is a integrated database of germ-line mutations which are underlying or associated with human inherited disease in nuclear genes. This database contains all germ-line disease-causing mutations and disease-associated/functional polymorphisms reported in the literature. Furthermore, it includes the data about single base-pair substitutions in coding (e.g. missense and nonsense), regulatory and splicing-relevant regions of human nuclear genes, micro-deletions and micro-insertions, indels, repeat expansions, as well as gross gene lesions (deletions, insertions and duplications) and complex gene rearrangements. These data are provided in a readily accessible format to all interested parties, whether they are from an academic, clinical or commercial background.",
"homepage": "http://www.hgmd.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "Institute of Medical Genetics in Cardiff",
"name": "HGMD",
"prefix": "nbdc00097",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Health/Disease"
]
},
"mappings": {
"biocontext": "HGMD",
"edam": "3265",
"integbio": "nbdc00097",
"miriam": "hgmd",
"n2t": "hgmd"
},
"miriam": {
"deprecated": false,
"description": "The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases.",
"homepage": "http://www.hgmd.cf.ac.uk/ac/index.php",
"id": "00000392",
"name": "HGMD",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z_0-9]+$",
"prefix": "hgmd",
"sampleId": "CALM1",
"uri_format": "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1"
},
"n2t": {
"description": "The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases.",
"example": "CALM1",
"homepage": "http://www.hgmd.cf.ac.uk/ac/index.php",
"name": "HGMD at Cardiff University",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z_0-9]+$",
"prefix": "hgmd",
"uri_format": "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1"
},
"name": "Human Gene Mutation Database"
},
"hgnc": {
"aberowl": {
"description": "Human Genome Organisation (HUGO) Gene Nomenclature Committee at the European Bioinformatics Institute approves a gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database.",
"download_owl": "http://aber-owl.net/media/ontologies/HGNC/1/hgnc.owl",
"homepage": "http://www.genenames.org/",
"name": "HUGO Gene Nomenclature",
"prefix": "HGNC",
"version": "July2010"
},
"biocontext": {
"prefix": "HGNC",
"uri_format": "http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$1"
},
"bioportal": {
"contact": {
"email": "hgnc@genenames.org",
"name": "Elspeth Bruford"
},
"description": "Human Genome Organisation (HUGO) Gene Nomenclature Committee at the European Bioinformatics Institute approves a gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database.",
"homepage": "http://www.genenames.org/",
"name": "HUGO Gene Nomenclature",
"prefix": "HGNC",
"publication": "http://www.genenames.org/",
"version": "July2010"
},
"cellosaurus": {
"category": "Organism-specific databases",
"homepage": "https://www.genenames.org",
"name": "Human Gene Nomenclature Committee Database",
"prefix": "HGNC",
"uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$1"
},
"contact": {
"email": "elspeth@genenames.org",
"name": "Elspeth Bruford",
"orcid": "0000-0002-8380-5247"
},
"edam": {
"description": "Identifier for a gene approved by the HUGO Gene Nomenclature Committee.",
"name": "Gene ID (HGNC)",
"obsolete": false,
"prefix": "2298"
},
"example": "16793",
"fairsharing": {
"abbreviation": "HGNC",
"description": "The HGNC approves both a short-form abbreviation known as a gene symbol, and also a longer and more descriptive name. Each symbol is unique and the committee ensures that each gene is only given one approved gene symbol. This allows for clear and unambiguous reference to genes in scientific communications, and facilitates electronic data retrieval from databases and publications.",
"domains": [
"Gene name",
"Protein",
"Pseudogene",
"Non-coding RNA"
],
"homepage": "https://www.genenames.org/",
"name": "HGNC Gene Symbols, Gene Names and IDs",
"prefix": "FAIRsharing.amcv1e",
"publications": [
{
"doi": "10.1159/000131404",
"pubmed": "295268",
"title": "International system for human gene nomenclature (1979) ISGN (1979)",
"year": 1979
},
{
"doi": "10.1093/nar/gky930",
"pubmed": "30304474",
"title": "Genenames.org: the HGNC and VGNC resources in 2019",
"year": 2018
}
],
"subjects": [
"Life Science"
]
},
"go": {
"homepage": "http://www.genenames.org/",
"name": "HUGO Gene Nomenclature Committee",
"prefix": "HGNC",
"uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$1"
},
"hl7": {
"description": "HUGO Gene Nomenclature Committee (HGNC) is committee jointly funded by the US National Human Genome Research Institute and the Wellcome Trust (UK). It operates under the auspices of HUGO, with key policy advice from an International Advisory Committee, and is responsible for approving gene names and symbols. All approved symbols are stored in the HGNC database. Each symbol is unique and each gene is only given one approved gene symbol. More than 28,000 human gene symbols and names have been approved so far. The vast majority of these is for protein-coding genes, but also includes symbols for peudogenes, non-coding RNAs, phenotypes and genomic features. HGNC gene symbols can be used with the HL7 coded data type. For example, in the HL7 messages specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model Implementation Guide, HGNC gene symbols can be used to as the observation values for gene identifiers. For example, OBX|1|CWE|48018-6^Gene identifier^||BRCA1^HGNC|Versioning Information:The version of the HGNC database is reported using the last updated date and timestamp. The last updated date and timestamp is posted on the main HGNC Search screen in the format like \"Monday March 30 23:00:56 2009\".HGNC is updated daily.HGNC is a free database for the public.",
"homepage": "http://www.genenames.org/",
"name": "HUGO Gene Nomenclature",
"organization": "HUGO Gene Nomenclature Committee,HUGO Gene Nomenclature Committee",
"preferred_prefix": "hgnc",
"prefix": "2.16.840.1.113883.6.281",
"status": "Complete"
},
"homepage": "http://www.genenames.org",
"license": "CC0-1.0",
"mappings": {
"aberowl": "HGNC",
"biocontext": "HGNC",
"bioportal": "HGNC",
"cellosaurus": "HGNC",
"edam": "2298",
"fairsharing": "FAIRsharing.amcv1e",
"go": "HGNC",
"hl7": "2.16.840.1.113883.6.281",
"miriam": "hgnc",
"n2t": "hgnc",
"ncbi": "HGNC",
"prefixcommons": "hgnc",
"togoid": "Hgnc",
"uniprot": "DB-0042",
"wikidata": "P354"
},
"miriam": {
"deprecated": false,
"description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database.",
"homepage": "https://www.genenames.org",
"id": "00000080",
"name": "HGNC",
"namespaceEmbeddedInLui": false,
"pattern": "^((HGNC|hgnc):)?\\d{1,5}$",
"prefix": "hgnc",
"sampleId": "2674",
"uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1"
},
"n2t": {
"description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database.",
"example": "2674",
"homepage": "https://www.genenames.org",
"name": "HUGO Genome Nomenclature Committee",
"namespaceEmbeddedInLui": false,
"pattern": "^((HGNC|hgnc):)?\\d{1,5}$",
"prefix": "hgnc",
"uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1"
},
"name": "HUGO Gene Nomenclature Committee",
"ncbi": {
"example": "HGNC:2041",
"homepage": "http://www.genenames.org/cgi-bin/search",
"name": "Human Gene Nomenclature Database",
"prefix": "HGNC"
},
"pattern": "^\\d{1,5}$",
"prefixcommons": {
"bioportal": "1528",
"description": "The HGNC gives unique and meaningful names to every human gene. For each known human gene we approve a gene name and symbol (short-form abbreviation). All approved symbols are stored in the HGNC database.",
"example": "7",
"homepage": "http://www.genenames.org/",
"keywords": [
"classification",
"gene"
],
"name": "HUGO Gene Nomenclature Committee",
"pattern": "^\\d+$",
"prefix": "hgnc",
"synonyms": [
"hugo"
],
"uri_format": "http://www.genenames.org/data/hgnc_data.php?hgnc_id=$1"
},
"providers": [
{
"code": "indra",
"description": "A large scale database of biomedical statements.",
"homepage": "https://db.indra.bio",
"name": "INDRA Database",
"uri_format": "https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@HGNC"
},
{
"code": "gencc",
"description": "The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases. Curated gene-disease relationships are submitted by GenCC member organizations. The GenCC comprises organizations that currently provide online resources (e.g. ClinGen, DECIPHER, Genomics England PanelApp, OMIM, Orphanet, PanelApp Australia, TGMIβs G2P), as well as diagnostic laboratories that have committed to sharing their internal curated gene-level knowledge (e.g. Ambry, Illumina, Invitae, Myriad Womenβs Health, Mass General Brigham Laboratory for Molecular Medicine).",
"homepage": "https://thegencc.org",
"name": "The Gene Curation Coalition",
"uri_format": "https://search.thegencc.org/genes/HGNC:$1"
}
],
"publications": [
{
"doi": "10.1093/nar/gkaa980",
"pmc": "PMC7779007",
"pubmed": "33152070",
"title": "Genenames.org: the HGNC and VGNC resources in 2021",
"year": 2021
},
{
"doi": "10.1093/nar/gky930",
"pmc": "PMC6324057",
"pubmed": "30304474",
"title": "Genenames.org: the HGNC and VGNC resources in 2019",
"year": 2019
},
{
"doi": "10.1159/000131404",
"pubmed": "295268",
"title": "International system for human gene nomenclature (1979) ISGN (1979)",
"year": 1979
}
],
"togoid": {
"catalog": "nbdc01774",
"examples": [
"26199",
"38937",
"14027",
"21498",
"18185",
"1314",
"25960",
"2206",
"22224",
"19741"
],
"keywords": [
"Gene"
],
"name": "HGNC",
"pattern": "^(?:(?:HGNC|hgnc):)?(?\\d{1,5})$",
"prefix": "Hgnc",
"uri_format": "http://identifiers.org/hgnc/$1"
},
"uniprot": {
"abbreviation": "HGNC",
"category": "Organism-specific databases",
"homepage": "https://www.genenames.org/",
"name": "Human Gene Nomenclature Database",
"prefix": "DB-0042",
"publications": [
{
"doi": "10.1093/nar/gkaa980",
"pubmed": "33152070"
}
],
"uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1"
},
"wikidata": {
"description": "a unique ID provided by the HGNC for each gene with an approved symbol. HGNC IDs remain stable even if a name or symbol changes",
"example": [
"108",
"9957"
],
"homepage": "http://www.genenames.org/",
"miriam": "hgnc",
"name": "HGNC ID",
"pattern": "^[1-9]\\d{0,4}$",
"prefix": "P354",
"uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$1"
}
},
"hgnc.genefamily": {
"biocontext": {
"prefix": "HGNC.GENEFAMILY"
},
"example": "2029",
"has_canonical": "hgnc.genegroup",
"homepage": "http://www.genenames.org",
"mappings": {
"biocontext": "HGNC.GENEFAMILY",
"miriam": "hgnc.genefamily",
"n2t": "hgnc.genefamily"
},
"miriam": {
"deprecated": false,
"description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.",
"homepage": "https://www.genenames.org/",
"id": "00000573",
"name": "HGNC gene family",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "hgnc.genefamily",
"sampleId": "141",
"uri_format": "https://www.genenames.org/cgi-bin/genefamilies/set/$1"
},
"n2t": {
"description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.",
"example": "141",
"homepage": "https://www.genenames.org/",
"name": "HGNC gene family at HUGO Genome Nomenclature Committee",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "hgnc.genefamily",
"uri_format": "https://www.genenames.org/cgi-bin/genefamilies/set/$1"
},
"synonyms": [
"GFAM",
"HGNC_GROUP",
"hgnc.family"
]
},
"hgnc.genegroup": {
"mappings": {
"miriam": "hgnc.genegroup"
},
"miriam": {
"deprecated": false,
"description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.",
"homepage": "https://www.genenames.org",
"id": "00000709",
"name": "HGNC Gene Group",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "hgnc.genegroup",
"sampleId": "141",
"uri_format": "https://www.genenames.org/data/genegroup/#!/group/$1"
}
},
"hgnc.symbol": {
"biocontext": {
"prefix": "HGNC.SYMBOL"
},
"mappings": {
"biocontext": "HGNC.SYMBOL",
"miriam": "hgnc.symbol",
"n2t": "hgnc.symbol",
"togoid": "HgncSymbol",
"wikidata": "P353"
},
"miriam": {
"deprecated": false,
"description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol.",
"homepage": "https://www.genenames.org/",
"id": "00000362",
"name": "HGNC Symbol",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z-0-9_]+(\\@)?$",
"prefix": "hgnc.symbol",
"sampleId": "DAPK1",
"uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/symbol/$1"
},
"n2t": {
"description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol.",
"example": "DAPK1",
"homepage": "https://www.genenames.org/",
"name": "HGNC Symbol at HUGO Genome Nomenclature Committee",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z-0-9_]+(\\@)?$",
"prefix": "hgnc.symbol",
"uri_format": "https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1"
},
"providers": [
{
"code": "depmap",
"description": "DepMap summary of the given gene",
"homepage": "https://depmap.org",
"name": "DepMap Gene Summary",
"uri_format": "https://depmap.org/portal/gene/$1"
},
{
"code": "pathwaycommons",
"description": "Interactions between a given gene and other molecular entities",
"homepage": "https://www.pathwaycommons.org/",
"name": "Pathway Commons Gene Interations",
"uri_format": "https://apps.pathwaycommons.org/interactions?source=$1"
},
{
"code": "oncomx",
"description": "Mutation profiles for a gene",
"homepage": "https://oncomx.org",
"name": "OncoMX",
"uri_format": "https://oncomx.org/searchview/?gene=$1"
}
],
"togoid": {
"catalog": "nbdc01774",
"examples": [
"MBNL2",
"RGS20",
"LINC02011",
"IGHV1-14",
"SH3RF2",
"SPATA13",
"HNRNPCP10",
"LINC00334",
"TMEM241",
"RN7SL753P"
],
"keywords": [
"Gene"
],
"name": "HGNC gene symbol",
"pattern": "^(?[A-Z0-9_(orf)\\-]+\\@?)$",
"prefix": "HgncSymbol",
"uri_format": "http://identifiers.org/hgnc.symbol/$1"
},
"wikidata": {
"description": "the official gene symbol approved by the HGNC, which is typically a short form of the gene name",
"example": [
"ACHE",
"RELN"
],
"homepage": "http://www.genenames.org/",
"miriam": "hgnc.symbol",
"name": "HGNC gene symbol",
"pattern": "^[A-Z][0-9A-Za-z]{0,13}@?(-[0-9A-Z][0-9A-Za-z]{0,6})*$",
"prefix": "P353",
"uri_format": "https://www.genenames.org/tools/search/#!/all?query=$1"
}
},
"hgvs": {
"contact": {
"email": "reecehart@gmail.com",
"github": "reece",
"name": "Reece Hart",
"orcid": "0000-0003-3463-0775"
},
"contributor": {
"email": "miseming@sfu.ca",
"github": "miseminger",
"name": "Madeline Iseminger",
"orcid": "0000-0002-0548-891X"
},
"description": "The HGVS Nomenclature is an internationally-recognized standard for the description of DNA, RNA and protein sequence variants. It is used to convey variants in clinical reports and to share variants in publications and databases. The HGVS Nomenclature is administered by the [HGVS Variant Nomenclature Committee (HVNC)](https://hgvs-nomenclature.org/stable/hvnc/) under the auspices of the [Human Genome Organization (HUGO)](https://hugo-int.org/).",
"example": "NP_003997.1:p.Trp24Cys",
"example_extras": [
"NG_012337.3(NM_003002.4):c.274G>T",
"NG_012337.3(NM_003002.4):r.(274g>u)",
"NC_000011.10:g.112088970del",
"NC_000011.10(NM_001276503.2):c.169+998del",
"GRCh38(chr11):g.112088970del"
],
"github_request_issue": 1032,
"hl7": {
"description": "HGVS nomenclatures are the guidelines for mutation nomenclature made by the Human Genome Variation Society. HGVS nomenclature can be used with the HL7 coded data type (code data type that accepts expression data, or a coded expression data type). This coded data type should be able to distinguish expressions in HGVS nomenclature from coded concepts. For example, in the HL7 messages specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model, HGVS nomenclature can be used to as the observation values for DNA sequence variations. For example, OBX|1|CWE|48004-6^DNA Sequence Variation^LN||c.1129C>T^^HGVS|Versioning information:The HGVS nomenclature for the description of sequence variants was last modified Feb 20, 2008.The HGVS nomenclature for the description of protein sequence variants was last modified May 12, 2007. The HGVS nomenclature for the description of DNA sequence variants was last modified June 15, 2007The HGVS nomenclature for the description of RNA sequence variants was last modified May 12, 2007HGVS nomenclatures can be used freely by the public.",
"homepage": "http://www.hgvs.org/",
"organization": "HUGO Gene Nomenclature Committee,HUGO Gene Nomenclature Committee",
"preferred_prefix": "hgvs",
"prefix": "2.16.840.1.113883.6.282",
"status": "Complete"
},
"homepage": "https://hgvs-nomenclature.org/stable/background/simple/",
"mappings": {
"hl7": "2.16.840.1.113883.6.282",
"wikidata": "P3331"
},
"name": "Human Genome Variation Society Nomenclature",
"providers": [
{
"code": "mutalyzer",
"description": " The Mutalyzer tool suite is designed to be of help when working with HGVS sequence variant nomenclature descriptions.",
"homepage": "https://mutalyzer.nl",
"name": "LUMC Mutalyzer 3",
"uri_format": "https://mutalyzer.nl/api/description_to_model/$1"
}
],
"publications": [
{
"doi": "10.1002/humu.22981",
"pubmed": "26931183",
"title": "HGVS Recommendations for the Description of Sequence Variants: 2016 Update",
"year": 2016
},
{
"doi": "10.1093/bioinformatics/btu630",
"pmc": "PMC4287946",
"pubmed": "25273102",
"title": "A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature",
"year": 2014
}
],
"references": [
"https://github.com/biopragmatics/bioregistry/issues/460"
],
"repository": "https://github.com/HGVSnomenclature/hgvs-nomenclature",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"wikidata": {
"description": "Sequence Variant Nomenclature from the Human Genome Variation Society (HGVS)",
"homepage": "https://civic.genome.wustl.edu/#/home",
"name": "HGVS nomenclature",
"prefix": "P3331",
"uri_format": "http://reg.clinicalgenome.org/allele?hgvs=$1"
}
},
"hinv.locus": {
"biocontext": {
"prefix": "HINV.LOCUS"
},
"mappings": {
"biocontext": "HINV.LOCUS",
"miriam": "hinv.locus",
"n2t": "hinv.locus"
},
"miriam": {
"deprecated": false,
"description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view.",
"homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp",
"id": "00000167",
"name": "H-InvDb Locus",
"namespaceEmbeddedInLui": false,
"pattern": "^HIX\\d{7}(\\.\\d+)?$",
"prefix": "hinv.locus",
"sampleId": "HIX0004394",
"uri_format": "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1"
},
"n2t": {
"description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view.",
"example": "HIX0004394",
"homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp",
"name": "H-Invitational Locus View at BIRC",
"namespaceEmbeddedInLui": false,
"pattern": "^HIX\\d{7}(\\.\\d+)?$",
"prefix": "hinv.locus",
"uri_format": "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1"
}
},
"hinv.protein": {
"biocontext": {
"prefix": "HINV.PROTEIN"
},
"mappings": {
"biocontext": "HINV.PROTEIN",
"miriam": "hinv.protein",
"n2t": "hinv.protein"
},
"miriam": {
"deprecated": false,
"description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view.",
"homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp",
"id": "00000169",
"name": "H-InvDb Protein",
"namespaceEmbeddedInLui": false,
"pattern": "^HIP\\d{9}(\\.\\d+)?$",
"prefix": "hinv.protein",
"sampleId": "HIP000030660",
"uri_format": "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1"
},
"n2t": {
"description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view.",
"example": "HIP000030660",
"homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp",
"name": "H-Invitational Protein View at BIRC",
"namespaceEmbeddedInLui": false,
"pattern": "^HIP\\d{9}(\\.\\d+)?$",
"prefix": "hinv.protein",
"uri_format": "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1"
}
},
"hinv.transcript": {
"biocontext": {
"prefix": "HINV.TRANSCRIPT"
},
"mappings": {
"biocontext": "HINV.TRANSCRIPT",
"miriam": "hinv.transcript",
"n2t": "hinv.transcript"
},
"miriam": {
"deprecated": false,
"description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view.",
"homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp",
"id": "00000168",
"name": "H-InvDb Transcript",
"namespaceEmbeddedInLui": false,
"pattern": "^HIT\\d{9}(\\.\\d+)?$",
"prefix": "hinv.transcript",
"sampleId": "HIT000195363",
"uri_format": "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1"
},
"n2t": {
"description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view.",
"example": "HIT000195363",
"homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp",
"name": "H-Invitational Transcript View at BIRC",
"namespaceEmbeddedInLui": false,
"pattern": "^HIT\\d{9}(\\.\\d+)?$",
"prefix": "hinv.transcript",
"uri_format": "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1"
}
},
"hipsci": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://www.hipsci.org",
"name": "Human Induced Pluripotent Stem Cells Initiative",
"prefix": "HipSci",
"uri_format": "https://www.hipsci.org/lines/#/lines/$1"
},
"example": "HPSI0114i-bezi_1",
"mappings": {
"cellosaurus": "HipSci"
}
},
"hivreagentprogram": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.hivreagentprogram.org/",
"name": "NIH HIV Reagent Program",
"prefix": "HIVReagentProgram",
"uri_format": "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx"
},
"example": "ARP-1513",
"mappings": {
"cellosaurus": "HIVReagentProgram"
}
},
"hl7.v2codesystem": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR.",
"example": "0778",
"homepage": "https://terminology.hl7.org/codesystems-v2.html",
"name": "HL7 V2 Code Systems",
"pattern": "^\\d+$",
"uri_format": "http://terminology.hl7.org/CodeSystem/v2-$1"
},
"hl7.v3codesystem": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR.",
"example": "AcknowledgementCondition",
"homepage": "https://terminology.hl7.org/codesystems-v2.html",
"name": "HL7 V2 Code Systems",
"pattern": "^\\w+$",
"uri_format": "https://terminology.hl7.org/CodeSystem-v3-$1"
},
"hmdb": {
"biocontext": {
"prefix": "HMDB",
"uri_format": "http://www.hmdb.ca/metabolites/$1"
},
"cheminf": {
"description": "Database identifier used by Human Metabolome Database.",
"name": "HMDB",
"obsolete": false,
"prefix": "000408"
},
"contact": {
"email": "david.wishart@ualberta.ca",
"github": "DavidWishartLab",
"name": "David S. Wishart",
"orcid": "0000-0002-3207-2434"
},
"edam": {
"description": "Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB).",
"name": "Compound ID (HMDB)",
"obsolete": false,
"prefix": "2622"
},
"fairsharing": {
"abbreviation": "HMDB",
"description": "The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain or link three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. The database contains 220,945 metabolite entries including both water-soluble and lipid soluble metabolites. Additionally, 8,610 protein sequences (enzymes and transporters) are linked to these metabolite entries. Each MetaboCard entry contains 130 data fields with 2/3 of the information being devoted to chemical/clinical data and the other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases (KEGG, PubChem, MetaCyc, ChEBI, PDB, UniProt, and GenBank) and a variety of structure and pathway viewing applets. The HMDB database supports extensive text, sequence, chemical structure, MS and NMR spectral query searches. Four additional databases, DrugBank, T3DB, SMPDB and FooDB are also part of the HMDB suite of databases. \n",
"homepage": "https://hmdb.ca/",
"name": "The Human Metabolome Database",
"prefix": "FAIRsharing.sye5js",
"publications": [
{
"doi": "10.1093/nar/gks1065",
"pubmed_id": 23161693,
"title": "HMDB 3.0--The Human Metabolome Database in 2013"
},
{
"doi": "10.1093/nar/gkl923",
"pubmed_id": 17202168,
"title": "HMDB: the Human Metabolome Database."
},
{
"doi": "10.1093/nar/gkn810",
"pubmed_id": 17202168,
"title": "HMDB: a knowledgebase for the human metabolome"
},
{
"doi": "10.1093/nar/gkx1089",
"pubmed_id": 29140435,
"title": "HMDB 4.0: the human metabolome database for 2018"
},
{
"doi": "10.1093/nar/gkab1062",
"pubmed_id": 34986597,
"title": "HMDB 5.0: the Human Metabolome Database for 2022"
}
],
"subjects": [
"Molecular biology",
"Biochemistry",
"Bioinformatics",
"Proteomics",
"Life Science",
"Metabolomics",
"Phenomics",
"Omics"
],
"twitter": "WishartLab"
},
"integbio": {
"alt_name": "Human Metabolome Database",
"description": "HUMDB is a database of human metabolites. The database contains information on thousands of metabolites produced by and found in the human body as a result of metabolic processes. genes and proteins related to the metabolites are also affiliated with records, where appropriate. Data on metabolites and the associated genes and proteins are available for download.",
"fairsharing": "biodbcore-000552",
"homepage": "http://www.hmdb.ca/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Classification"
],
"maintainer": "University of Alberta",
"name": "HMDB",
"prefix": "nbdc00909",
"pubmeds": [
"18953024"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein",
"Health/Disease",
"Metabolite"
]
},
"mappings": {
"biocontext": "HMDB",
"cheminf": "000408",
"edam": "2622",
"fairsharing": "FAIRsharing.sye5js",
"integbio": "nbdc00909",
"miriam": "hmdb",
"n2t": "hmdb",
"pathguide": "244",
"prefixcommons": "hmdb",
"re3data": "r3d100011285",
"togoid": "Hmdb",
"wikidata": "P2057"
},
"miriam": {
"deprecated": false,
"description": "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.",
"homepage": "http://www.hmdb.ca/",
"id": "00000051",
"name": "HMDB",
"namespaceEmbeddedInLui": false,
"pattern": "^HMDB\\d+$",
"prefix": "hmdb",
"sampleId": "HMDB00001",
"uri_format": "http://www.hmdb.ca/metabolites/$1"
},
"n2t": {
"description": "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.",
"example": "HMDB00001",
"homepage": "http://www.hmdb.ca/",
"name": "The Human Metabolome Database",
"namespaceEmbeddedInLui": false,
"pattern": "^HMDB\\d+$",
"prefix": "hmdb",
"uri_format": "http://www.hmdb.ca/metabolites/$1"
},
"name": "Human Metabolome Database",
"pathguide": {
"abbreviation": "HMDB",
"homepage": "http://www.hmdb.ca/",
"name": "Human Metabolome Database",
"prefix": "244"
},
"prefixcommons": {
"description": "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.",
"example": "HMDB00001",
"homepage": "http://www.hmdb.ca",
"keywords": [
"chemical",
"human",
"metabolite"
],
"license": "http://www.hmdb.ca/about#cite",
"name": "The Human Metabolome Database",
"pattern": "^HMDB\\d{5}$",
"prefix": "hmdb",
"pubmed_ids": [
"17202168"
],
"uri_format": "http://www.hmdb.ca/metabolites/$1"
},
"publications": [
{
"doi": "10.1093/nar/gkab1062",
"pmc": "PMC8728138",
"pubmed": "34986597",
"title": "HMDB 5.0: the Human Metabolome Database for 2022",
"year": 2022
},
{
"doi": "10.1093/nar/gkx1089",
"pmc": "PMC5753273",
"pubmed": "29140435",
"title": "HMDB 4.0: the human metabolome database for 2018",
"year": 2018
},
{
"doi": "10.1093/nar/gks1065",
"pmc": "PMC3531200",
"pubmed": "23161693",
"title": "HMDB 3.0--The Human Metabolome Database in 2013",
"year": 2012
},
{
"doi": "10.1093/nar/gkl923",
"pmc": "PMC1899095",
"pubmed": "17202168",
"title": "HMDB: the Human Metabolome Database",
"year": 2007
}
],
"re3data": {
"description": "The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education.",
"homepage": "https://hmdb.ca/",
"name": "Human Metabolome Database",
"prefix": "r3d100011285",
"synonyms": [
"HMDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.sye5js",
"nlx": "152721",
"scr": "013647"
}
},
"synonyms": [
"HMDB"
],
"togoid": {
"catalog": "nbdc00909",
"examples": [
"HMDB0029433",
"HMDB0015609",
"HMDB0000042",
"HMDB0002360",
"HMDB0003345",
"HMDB0003550",
"HMDB0036769",
"HMDB0000935",
"HMDB0002755",
"HMDB0004369"
],
"keywords": [
"Compound"
],
"name": "HMDB",
"pattern": "^(?:hmdb:)?(?HMDB\\d+)$",
"prefix": "Hmdb",
"uri_format": "http://identifiers.org/hmdb/$1"
},
"wikidata": {
"description": "ID in Human Metabolome Database",
"example": [
"HMDB0002111",
"HMDB0034235"
],
"name": "Human Metabolome Database ID",
"pattern": "^HMDB\\d+$",
"prefix": "P2057",
"uri_format": "https://www.hmdb.ca/metabolites/$1"
}
},
"hms.lincs.antibody": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.",
"example": "80001",
"homepage": "https://lincs.hms.harvard.edu/db/antibodies/",
"name": "HMS Library of Integrated Network-based Cellular Signatures Antibodies",
"pattern": "^8\\d{4}$",
"uri_format": "https://lincs.hms.harvard.edu/db/antibodies/$1"
},
"hms.lincs.cell": {
"comment": "this is NOT the same as lincs.cell. On https://lincs.hms.harvard.edu/db/cells/?search=MCF-10A&extra_form_shown=&dataset_types=, you can see there's a mapping to the other resource.",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.",
"example": "50583",
"homepage": "https://lincs.hms.harvard.edu/db/cell/",
"name": "HMS LINCS Cell",
"pattern": "^5\\d{4}$",
"references": [
"https://github.com/identifiers-org/identifiers-org.github.io/issues/223"
],
"uri_format": "https://lincs.hms.harvard.edu/db/cells/$1"
},
"hms.lincs.compound": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.",
"example": "10001-101",
"example_extras": [
"11996-999"
],
"homepage": "https://lincs.hms.harvard.edu/db/sm/",
"name": "HMS LINCS Compound",
"pattern": "^1\\d{4}-\\d{3}$",
"synonyms": [
"HMS-LINCS",
"hmsl_id"
],
"uri_format": "https://lincs.hms.harvard.edu/db/sm/$1"
},
"hms.lincs.dataset": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "",
"example": "20003",
"homepage": "https://lincs.hms.harvard.edu/db/datasets/",
"name": "HMS Library of Integrated Network-based Cellular Signatures Datasets",
"pattern": "^2\\d{4}$",
"uri_format": "https://lincs.hms.harvard.edu/db/datasets/$1"
},
"hoelzel": {
"contact": {
"email": "info@hoelzel.de",
"name": "Carsten Linder",
"orcid": "0009-0009-3816-8777"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "HΓΆlzel is a life science reagent vendor based in Cologne, Germany. As a distributor, they offer products suitable for many kinds of research areas such as oncology, neuroscience, immunology, and more. Their portfolio consists of antibodies, recombinant proteins, inhibitors, ELISA-kits as well as other assays, arrays and kits. Their inhibitor portfolio can be easily accessed via the CAS-register catalog.",
"example": "40592-R001-100",
"homepage": "https://www.hoelzel-biotech.com",
"keywords": [
"antibodies",
"assays",
"biologics",
"elisa-kits",
"inhibitors",
"life sciences",
"proteins",
"vendor"
],
"logo": "https://www.hoelzel-biotech.com/skin/frontend/ultimo/custom/images/logo.png",
"name": "HΓΆlzel Diagnostika",
"synonyms": [
"hΓΆlzel"
],
"uri_format": "https://www.hoelzel-biotech.com/de/catalogsearch/result/?q=$1"
},
"hog": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc.",
"download_obo": "ftp://ftp.bgee.org/general/ontologies/HOG.obo",
"example": "0000255",
"homepage": "https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships",
"name": "Homologous Organ Groups",
"pattern": "^\\d{7}$",
"uri_format": "https://biopragmatics.github.io/providers/hog/$1"
},
"hogenom": {
"biocontext": {
"prefix": "HOGENOM"
},
"contact": {
"email": "perriere@biomserv.univ-lyon1.fr",
"name": "Guy Perrière",
"orcid": "0000-0002-6850-6265"
},
"fairsharing": {
"abbreviation": "HOGENOM",
"description": "HOGENOM is a phylogenomic database providing families of homologous genes and associated phylogenetic trees (and sequence alignments) for a wide set sequenced organisms.",
"homepage": "http://hogenom.univ-lyon1.fr/",
"name": "HOGENOM",
"prefix": "FAIRsharing.qe8tz8",
"publications": [
{
"doi": "10.1186/1471-2105-10-S6-S3",
"pubmed_id": 19534752,
"title": "Databases of homologous gene families for comparative genomics."
}
],
"subjects": [
"Phylogeny",
"Phylogenetics",
"Life Science"
]
},
"integbio": {
"description": "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.",
"fairsharing": "FAIRsharing.qe8tz8",
"homepage": "http://hogenom.univ-lyon1.fr/",
"information_keywords": [
"Classification",
"Sequence",
"Taxonomy"
],
"maintainer": "PBIL",
"name": "HOGENOM",
"prefix": "nbdc01858",
"pubmeds": [
"19534752"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"mappings": {
"biocontext": "HOGENOM",
"fairsharing": "FAIRsharing.qe8tz8",
"integbio": "nbdc01858",
"miriam": "hogenom",
"n2t": "hogenom",
"prefixcommons": "hogenom",
"uniprot": "DB-0044"
},
"miriam": {
"deprecated": false,
"description": "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.",
"homepage": "http://pbil.univ-lyon1.fr/databases/hogenom/",
"id": "00000213",
"name": "HOGENOM",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "hogenom",
"sampleId": "HBG284870",
"uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1"
},
"n2t": {
"description": "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.",
"example": "HBG284870",
"homepage": "http://pbil.univ-lyon1.fr/databases/hogenom/",
"name": "HOGENOM at CNRS",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "hogenom",
"uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1"
},
"name": "Database of Complete Genome Homologous Genes Families",
"prefixcommons": {
"description": "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.",
"example": "HBG284870",
"homepage": "http://pbil.univ-lyon1.fr/databases/hogenom.php",
"keywords": [
"classification",
"sequence"
],
"name": "The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms",
"pattern": "^\\w+$",
"prefix": "hogenom",
"pubmed_ids": [
"19534752"
],
"uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1"
},
"publications": [
{
"doi": "10.1186/1471-2105-10-s6-s3",
"pmc": "PMC2697650",
"pubmed": "19534752",
"title": "Databases of homologous gene families for comparative genomics",
"year": 2009
},
{
"doi": "10.1101/gr.10.3.379",
"pmc": "PMC311423",
"pubmed": "10720578",
"title": "HOBACGEN: database system for comparative genomics in bacteria",
"year": 2000
}
],
"uniprot": {
"abbreviation": "HOGENOM",
"category": "Phylogenomic databases",
"homepage": "http://hogenom.univ-lyon1.fr/",
"name": "The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms",
"prefix": "DB-0044",
"publications": [
{
"doi": "10.1186/1471-2105-10-s6-s3",
"pubmed": "19534752"
}
],
"uri_format": "http://hogenom.univ-lyon1.fr/query_sequence?seq=$1"
}
},
"hoip": {
"aberowl": {
"description": "Homeostasis imbalance process ontology (HoIP) is an ontology that systematizes a wide variety of terms involving homeostasis imbalance courses and processes. HoIP focuses on the course of COVID-19 infectious processes and cellular senescence.",
"download_owl": "http://aber-owl.net/media/ontologies/HOIP/65/hoip.owl",
"homepage": "https://github.com/yuki-yamagata/hoip",
"name": "Homeostasis imbalance process ontology",
"prefix": "HOIP",
"version": "2024/04/03"
},
"bioportal": {
"contact": {
"email": "yuki.yamagata@riken.jp",
"name": "Yuki Yamagata"
},
"description": "Homeostasis imbalance process ontology (HoIP) is an ontology that systematizes a wide variety of terms involving homeostasis imbalance courses and processes. HoIP focuses on the course of COVID-19 infectious processes and cellular senescence.",
"homepage": "https://github.com/yuki-yamagata/hoip",
"name": "Homeostasis imbalance process ontology",
"prefix": "HOIP",
"publication": "https://doi.org/10.1101/2023.03.09.531883",
"version": "2024/04/03"
},
"contact": {
"email": "yuki.yamagata@riken.jp",
"github": "yuki-yamagata",
"name": "Yuki Yamagata",
"orcid": "0000-0002-9673-1283"
},
"contributor": {
"email": "j.harry.caufield@gmail.com",
"github": "caufieldjh",
"name": "Harry Caufield",
"orcid": "0000-0001-5705-7831"
},
"description": "An ontology of processes triggered by homeostatic imbalance, with a focus on COVID-19 infectious processes.",
"download_owl": "https://github.com/yuki-yamagata/hoip/raw/master/hoip_0308.owl",
"example": "0040379",
"github_request_issue": 668,
"homepage": "https://knowledge.brc.riken.jp/bioresource/ontology/HOIP",
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "HOIP",
"bioportal": "HOIP"
},
"name": "Homeostasis imbalance process ontology",
"pattern": "^\\d{7}$",
"repository": "https://github.com/yuki-yamagata/hoip",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://purl.bioontology.org/ontology/HOIP/HOIP_$1"
},
"hom": {
"aberowl": {
"description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.",
"download_owl": "http://aber-owl.net/media/ontologies/HOM/7/hom.owl",
"homepage": "http://bioinfo.unil.ch",
"name": "Homology Ontology",
"prefix": "HOM"
},
"biocontext": {
"prefix": "HOM"
},
"bioportal": {
"contact": {
"email": "bgee@sib.swiss",
"name": "Bgee team"
},
"description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.",
"homepage": "https://bgee.org",
"name": "Ontology of Homology and Related Concepts in Biology",
"prefix": "HOM",
"publication": "http://dx.doi.org/10.1016/j.tig.2009.12.012",
"version": "releases/2015-01-07"
},
"example": "0000049",
"fairsharing": {
"abbreviation": "HOM",
"contact": {
"email": "julien.roux@unil.ch",
"name": "Julien Roux",
"orcid": "0000-0002-4192-5099"
},
"description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.",
"domains": [
"Molecular entity",
"Homologous",
"Life cycle stage"
],
"homepage": "http://bioportal.bioontology.org/ontologies/HOM/?p=summary",
"name": "HOMology",
"prefix": "FAIRsharing.efv7gw",
"publications": [
{
"doi": "10.1016/j.tig.2009.12.012",
"pubmed": "20116127",
"title": "An ontology to clarify homology-related concepts",
"year": 2010
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"mappings": {
"aberowl": "HOM",
"biocontext": "HOM",
"bioportal": "HOM",
"fairsharing": "FAIRsharing.efv7gw",
"obofoundry": "hom",
"ols": "hom",
"ontobee": "HOM"
},
"obofoundry": {
"contact": "bgee@sib.swiss",
"contact.github": "fbastian",
"contact.label": "Frederic Bastian",
"contact.orcid": "0000-0002-9415-5104",
"deprecated": false,
"description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.",
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/hom.owl",
"homepage": "https://github.com/BgeeDB/homology-ontology",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Homology Ontology",
"preferredPrefix": "HOM",
"prefix": "hom",
"publications": [
{
"id": "https://doi.org/10.1016/j.tig.2009.12.012",
"title": "An ontology to clarify homology-related concepts"
}
],
"repository": "https://github.com/BgeeDB/homology-ontology"
},
"ols": {
"description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.",
"download_owl": "http://purl.obolibrary.org/obo/hom.owl",
"homepage": "https://github.com/BgeeDB/homology-ontology",
"name": "Homology Ontology",
"prefix": "hom",
"version": "2015-01-07",
"version.iri": "http://purl.obolibrary.org/obo/hom/releases/2015-01-07/hom.owl"
},
"ontobee": {
"library": "Library",
"name": "Homology Ontology",
"prefix": "HOM"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1016/j.tig.2009.12.012",
"pubmed": "20116127",
"title": "An ontology to clarify homology-related concepts",
"year": 2010
}
],
"uri_format": "http://purl.obolibrary.org/obo/HOM_$1"
},
"homd.seq": {
"biocontext": {
"prefix": "HOMD.SEQ"
},
"contact": {
"email": "tchen@forsyth.org",
"github": "tsute",
"name": "Tsute Chen",
"orcid": "0000-0001-6689-317X"
},
"mappings": {
"biocontext": "HOMD.SEQ",
"miriam": "homd.seq",
"n2t": "homd.seq",
"prefixcommons": "homd.seq"
},
"miriam": {
"deprecated": false,
"description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.",
"homepage": "http://www.homd.org/index.php",
"id": "00000170",
"name": "HOMD Sequence Metainformation",
"namespaceEmbeddedInLui": false,
"pattern": "^SEQF\\d+$",
"prefix": "homd.seq",
"sampleId": "SEQF1003",
"uri_format": "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1"
},
"n2t": {
"description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.",
"example": "SEQF1003",
"homepage": "http://www.homd.org/index.php",
"name": "HOMD sequence metainformation at The Forsyth Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^SEQF\\d+$",
"prefix": "homd.seq",
"uri_format": "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1"
},
"prefixcommons": {
"description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.",
"example": "SEQF1003",
"keywords": [
"genome",
"microbial"
],
"name": "HOMD Sequence Metainformation",
"pattern": "^SEQF\\d+$",
"prefix": "homd.seq",
"pubmed_ids": [
"20624719"
],
"uri_format": "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1"
},
"publications": [
{
"doi": "10.1093/database/baq013",
"pmc": "PMC2911848",
"pubmed": "20624719",
"title": "The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information",
"year": 2010
}
]
},
"homd.taxon": {
"biocontext": {
"prefix": "HOMD.TAXON"
},
"contact": {
"email": "tchen@forsyth.org",
"github": "tsute",
"name": "Tsute Chen",
"orcid": "0000-0001-6689-317X"
},
"mappings": {
"biocontext": "HOMD.TAXON",
"miriam": "homd.taxon",
"n2t": "homd.taxon",
"ncbi": "HOMD",
"prefixcommons": "homd.taxon"
},
"miriam": {
"deprecated": false,
"description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.",
"homepage": "http://www.homd.org/index.php",
"id": "00000171",
"name": "HOMD Taxonomy",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "homd.taxon",
"sampleId": "811",
"uri_format": "http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$1&view=dynamic"
},
"n2t": {
"description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.",
"example": "811",
"homepage": "http://www.homd.org/index.php",
"name": "HOMD taxon information at The Forsyth Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "homd.taxon",
"uri_format": "http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$1&view=dynamic"
},
"ncbi": {
"example": "tax_078",
"homepage": "http://www.homd.org/",
"name": "Human Oral Microbiome Database",
"prefix": "HOMD"
},
"prefixcommons": {
"description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.",
"example": "811",
"keywords": [
"microbial",
"taxonomy"
],
"name": "HOMD Taxonomy",
"pattern": "^\\d+$",
"prefix": "homd.taxon",
"pubmed_ids": [
"20624719"
],
"uri_format": "http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$1&view=dynamic"
},
"publications": [
{
"doi": "10.1093/database/baq013",
"pmc": "PMC2911848",
"pubmed": "20624719",
"title": "The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information",
"year": 2010
}
],
"uri_format": "http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1"
},
"homologene": {
"biocontext": {
"prefix": "HOMOLOGENE",
"uri_format": "http://www.ncbi.nlm.nih.gov/homologene/$1"
},
"contact": {
"email": "sayers@ncbi.nlm.nih.gov",
"name": "Eric W. Sayers",
"orcid": "0000-0001-8394-3802"
},
"fairsharing": {
"abbreviation": "HomoloGene",
"description": "HomoloGene is an automated system for the detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. HomoloGene takes protein sequences from differing species and compares them to one another (using blastp) and matches are placed into groups, using a tree built from sequence similarity to guide the process, where closer related organisms are matched up first, and then further organisms are added as the tree is traversed toward the root. The protein alignments are mapped back to their corresponding DNA sequences, where distance metrics can be calculated (e.g. molecular distance, Ka/Ks ratio). Sequences are matched using synteny when applicable. Remaining sequences are matched up by using an algorithm for maximizing the score globally, rather than locally, in a bipartite matching. Cutoffs on bits per position and Ks values are set to prevent unlikely \"orthologs\" from being grouped together. These cutoffs are calculated based on the respective score distribution for the given groups of organisms. Paralogs are identified by finding sequences that are closer within species than other species.",
"homepage": "https://www.ncbi.nlm.nih.gov/homologene",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "NCBI HomoloGene Database",
"prefix": "FAIRsharing.mzc066",
"publications": [
{
"doi": "10.1093/nar/gkq1172",
"pubmed_id": 21097890,
"title": "Database resources of the National Center for Biotechnology Information."
}
],
"subjects": [
"Life Science"
]
},
"integbio": {
"description": "In Homologenes, users can find automatically constructed homologous gene sets from the full-length genome sequences of a wide range of eukaryotic species, as well as mRNA and protein sequences.",
"fairsharing": "biodbcore-000443",
"homepage": "http://www.ncbi.nlm.nih.gov/homologene",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "HomoloGene",
"prefix": "nbdc00101",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"mappings": {
"biocontext": "HOMOLOGENE",
"fairsharing": "FAIRsharing.mzc066",
"integbio": "nbdc00101",
"miriam": "homologene",
"n2t": "homologene",
"prefixcommons": "homologene",
"togoid": "Homologene",
"wikidata": "P593"
},
"miriam": {
"deprecated": false,
"description": "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.",
"homepage": "https://www.ncbi.nlm.nih.gov/homologene/",
"id": "00000275",
"name": "HomoloGene",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "homologene",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "Bio2RDF",
"homepage": "http://homologene.bio2rdf.org/fct",
"name": "Bio2RDF",
"uri_format": "http://homologene.bio2rdf.org/describe/?url=http://bio2rdf.org/homologene:$1"
}
],
"sampleId": "1000",
"uri_format": "https://www.ncbi.nlm.nih.gov/homologene/$1"
},
"n2t": {
"description": "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.",
"example": "1000",
"homepage": "https://www.ncbi.nlm.nih.gov/homologene/",
"name": "Homologene at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "homologene",
"uri_format": "https://www.ncbi.nlm.nih.gov/homologene/$1"
},
"name": "HomoloGene",
"prefixcommons": {
"description": "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.",
"example": "1000",
"homepage": "http://wwww.ncbi.nlm.nih.gov/homologene",
"keywords": [
"gene",
"genome"
],
"name": "NCBI Homologene",
"pattern": "^\\d+$",
"prefix": "homologene",
"pubmed_ids": [
"21097890"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/homologene/$1"
},
"publications": [
{
"doi": "10.1093/nar/gkq1172",
"pmc": "PMC3013733",
"pubmed": "21097890",
"title": "Database resources of the National Center for Biotechnology Information",
"year": 2010
}
],
"togoid": {
"catalog": "nbdc00101",
"examples": [
"117",
"17",
"6",
"142",
"55",
"132",
"61",
"109",
"137",
"134"
],
"keywords": [
"Ortholog"
],
"name": "HomoloGene",
"pattern": "^(?\\d+)$",
"prefix": "Homologene",
"uri_format": "http://identifiers.org/homologene/$1"
},
"wikidata": {
"description": "identifier in theΒ HomoloGene database",
"example": [
"193",
"68068",
"732"
],
"homepage": "http://www.ncbi.nlm.nih.gov/homologene",
"name": "HomoloGene ID",
"pattern": "^[1-9]\\d{0,5}$",
"prefix": "P593",
"uri_format": "https://www.ncbi.nlm.nih.gov/homologene?term=$1"
}
},
"horizon_discovery": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://horizondiscovery.com/",
"name": "Horizon Discovery cell line collection",
"prefix": "Horizon_Discovery",
"uri_format": "https://horizondiscovery.com/en/search?searchterm=$1"
},
"example": "HD+118-001",
"mappings": {
"cellosaurus": "Horizon_Discovery"
}
},
"hoso": {
"contact": {
"email": "paul.fabry@usherbrooke.ca",
"github": "pfabry",
"name": "Paul Fabry",
"orcid": "0000-0002-3336-2476"
},
"contributor": {
"email": "paul.fabry@usherbrooke.ca",
"github": "pfabry",
"name": "Paul Fabry",
"orcid": "0000-0002-3336-2476"
},
"description": "HOSO is an ontology of informational entities and processes related to healthcare organizations and services.",
"example": "0000001",
"github_request_issue": 813,
"homepage": "https://openlhs.github.io/HOSO/",
"license": "CC-BY-4.0",
"name": "Healthcare Organizations and Services Ontology",
"pattern": "^\\d{7}$",
"repository": "https://github.com/OpenLHS/HOSO",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"hovergen": {
"biocontext": {
"prefix": "HOVERGEN"
},
"fairsharing": {
"abbreviation": "HOVERGEN",
"contact": {
"email": "duret@biomserv.univ-lyon1.fr",
"name": "Laurent Duret",
"orcid": "0000-0003-2836-3463"
},
"description": "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.",
"homepage": "http://pbil.univ-lyon1.fr/databases/hovergen.html",
"name": "Homologous Vertebrate Genes Database",
"prefix": "FAIRsharing.dg1f0e",
"publications": [
{
"doi": "10.1093/bioinformatics/bti325",
"pubmed_id": 15713731,
"title": "Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases."
}
],
"subjects": [
"Life Science"
]
},
"homepage": "https://pbil.univ-lyon1.fr/databases/hovergen.php",
"integbio": {
"alt_name": "Homologous Vertebrate Genes Database",
"description": "HOVERGEN is a database of homologous vertebrate genes using the ACNUC sequence database. It contains all of vertebrate protein sequences from the UniProt Knowledgebase and all the corresponding nucleotide sequences in EMBL, and those information were structured in the ACNUC database.",
"fairsharing": "biodbcore-000501",
"homepage": "http://pbil.univ-lyon1.fr/databases/hovergen.php",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "Pole Bioinformatique Lyonnais",
"name": "HOVERGEN",
"prefix": "nbdc00284",
"pubmeds": [
"8036164",
"15713731"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"mappings": {
"biocontext": "HOVERGEN",
"fairsharing": "FAIRsharing.dg1f0e",
"integbio": "nbdc00284",
"miriam": "hovergen",
"n2t": "hovergen",
"prefixcommons": "hovergen"
},
"miriam": {
"deprecated": false,
"description": "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.",
"homepage": "http://pbil.univ-lyon1.fr/databases/hovergen.php",
"id": "00000074",
"name": "HOVERGEN",
"namespaceEmbeddedInLui": false,
"pattern": "^HBG\\d+$",
"prefix": "hovergen",
"sampleId": "HBG004341",
"uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN"
},
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"description": "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.",
"example": "HBG004341",
"homepage": "http://pbil.univ-lyon1.fr/databases/hovergen.php",
"name": "Hovergen",
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"prefix": "hovergen",
"uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN"
},
"name": "Homologous Vertebrate Genes Database",
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"description": "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.",
"example": "HBG004341",
"homepage": "http://pbil.univ-lyon1.fr/databases/hovergen.html",
"keywords": [
"gene",
"DNA",
"protein"
],
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"name": "HOVERGEN: Homologous Vertebrate Genes Database",
"pattern": "^HBG\\d+$",
"prefix": "hovergen",
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"15713731"
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{
"doi": "10.1093/bioinformatics/bti325",
"pubmed": "15713731",
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}
]
},
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"description": "Hypersensitivity Pneumonitis Ontology involves the domain of knowledge of 1. diseases caused by organic dusts exposure including hypersensitivity pneumonitis as well as 2. organic dusts.",
"download_owl": "http://aber-owl.net/media/ontologies/HP_O/1/hp_o.owl",
"homepage": "https://hypontology.herokuapp.com/",
"name": "Hypersensitivity pneumonitis ontology",
"prefix": "HP_O",
"version": "1.0"
},
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"homepage": "http://human-phenotype-ontology.github.io/",
"name": "Human Phenotype Ontology",
"prefix": "1937",
"wikidata_database": "Q17027854"
},
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"prefix": "HPO",
"uri_format": "http://human-phenotype-ontology.org/$1"
},
"bioportal": {
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"email": "marcinkgolec@gmail.com",
"name": "Marcin Golec"
},
"description": "Hypersensitivity Pneumonitis Ontology involves the domain of knowledge of 1. diseases caused by organic dusts exposure including hypersensitivity pneumonitis as well as 2. organic dusts.",
"homepage": "https://hypontology.herokuapp.com/",
"name": "Hypersensitivity pneumonitis ontology",
"prefix": "HP_O",
"version": "1.0"
},
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"download_obo": "http://purl.obolibrary.org/obo/hp.obo",
"example": "0011140",
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"abbreviation": "HP",
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"domains": [
"Phenotype",
"Disease"
],
"homepage": "https://hpo.jax.org/",
"license": "hpo",
"name": "Human Phenotype Ontology",
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},
{
"doi": "10.1093/nar/gkw1039",
"pubmed": "27899602",
"title": "The Human Phenotype Ontology in 2017",
"year": 2016
},
{
"doi": "10.1111/j.1399-0004.2010.01436.x",
"pubmed": "20412080",
"title": "The human phenotype ontology",
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},
{
"doi": "10.1093/nar/gky1105",
"pubmed": "30476213",
"title": "Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources",
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},
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"doi": "10.1016/j.ajhg.2008.09.017",
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"title": "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease",
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}
],
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"Genetics",
"Phenomics",
"Biomedical Science",
"Preclinical Studies"
],
"twitter": "hp_ontology"
},
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"name": "Human Phenotype Ontology",
"organization": "Lister Hill National Center for Biomedical Communications",
"preferred_prefix": "hpo",
"prefix": "2.16.840.1.113883.6.339",
"status": "Complete"
},
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"fairsharing": "FAIRsharing.kbtt7f",
"homepage": "https://hpo.jax.org",
"information_keywords": [
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"Ontology/Terminology/Nomenclature"
],
"maintainer": "The Jackson Laboratory",
"name": "HPO",
"prefix": "nbdc02559",
"pubmeds": [
"33264411"
],
"status": "Active",
"target_keywords": [
"Health/Disease",
"Genome/Gene"
]
},
"lov": {
"description": "An ontology to capture the staggering diversity of polymeric materials and their applications.",
"homepage": "http://w3id.org/emmo-hpo/hpo",
"keywords": [
"Industry"
],
"modified": "2024-04-12",
"name": "Hyperdimensional Polymer Ontology",
"prefix": "hpo",
"uri_prefix": "http://w3id.org/emmo-hpo/hpo#$1"
},
"mappings": {
"aberowl": "HP_O",
"bartoc": "1937",
"biocontext": "HPO",
"bioportal": "HP_O",
"fairsharing": "FAIRsharing.kbtt7f",
"hl7": "2.16.840.1.113883.6.339",
"integbio": "nbdc02559",
"lov": "hpo",
"miriam": "hp",
"n2t": "hp",
"obofoundry": "hp",
"ols": "hp",
"ontobee": "HP",
"wikidata": "P3841"
},
"mastodon": "hpo@masto.ai",
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"homepage": "http://human-phenotype-ontology.github.io/",
"id": "00000571",
"name": "Human Phenotype Ontology",
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"pattern": "^HP:\\d{7}$",
"prefix": "hp",
"sampleId": "0000118",
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},
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"name": "Human Phenotype Ontology at Institute for Medical Genetics and Human Genetics",
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},
"obofoundry": {
"appears_in": [
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],
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"license": "hpo",
"license.url": "https://hpo.jax.org/app/license",
"logo": "https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/logo/HPO-logo-black_small.png",
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"title": "The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data."
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"id": "https://www.ncbi.nlm.nih.gov/pubmed/30476213",
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"twitter": "hp_ontology"
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"ols": {
"description": "The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities and clinical features encountered in human disease.",
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"name": "Human Phenotype Ontology",
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"pubmed": "26119816",
"title": "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease",
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{
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"title": "The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data",
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{
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],
"homepage": "http://human-phenotype-ontology.github.io/about.html",
"name": "Human Phenotype Ontology ID",
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},
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"description": "The Human Protein Atlas (HPA) portal is a publicly available database with millions of high-resolution images showing the spatial distribution of proteins in a number of different wild-type tissues, cancer types and human cell lines. The goal of the HPA is to map all the human proteins in cells, tissues and organs using an integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. The HPA is composed of six parts: the Tissue Atlas, the Single Cell Type Atlas, the Pathology Atlas, the Blood Atlas, the Brain Atlas, and the Cell Atlas.",
"homepage": "https://www.proteinatlas.org/",
"license": "CC BY-SA 3.0",
"name": "The Human Protein Atlas",
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{
"doi": "10.15252/msb.20155865",
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"doi": "eaal3321",
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],
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],
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"keywords": [
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],
"name": "Human Protein Atlas",
"pattern": "^ENSG\\d{11}$",
"prefix": "hpa",
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"title": "A human protein atlas for normal and cancer tissues based on antibody proteomics",
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}
],
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"name": "The Human Protein Atlas",
"prefix": "r3d100010931",
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],
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}
},
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],
"uri_format": "https://www.proteinatlas.org/$1"
}
},
"hpath": {
"comment": "This ontology used to be available in OLS3, but is no longer available in OLS4.\n\nThe URI format string in this resource takes the form of an OBO PURL, but it is not itself registered with the OBO Foundry, and terms therefore redirect into http://ontologies.berkeleybop.org. This happens because the data is curated natively in the OBO Flat File Format from which CURIEs are automatically assumed to expand to OBO PURLs",
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},
"description": "An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species.\n\nThe original structure of the histopathology ontology was designed ab initio when the [INHAND](http://www.goreni.org/) manuscripts were not available. However, the ontology has been repetitively reviewed and updated to align with the subsequently published INHAND manuscripts. During this process cross references to INHAND lesion identifiers were added to the ontology. [from GitHub]",
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"example": "2000191",
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"name": "Histopathology Ontology",
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"references": [
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],
"repository": "https://github.com/Novartis/hpath",
"synonyms": [
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],
"uri_format": "http://purl.obolibrary.org/obo/MC_$1",
"uri_format_resolvable": false
},
"hpm.peptide": {
"biocontext": {
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},
"mappings": {
"biocontext": "HPM.PEPTIDE",
"miriam": "hpm.peptide",
"n2t": "hpm.peptide"
},
"miriam": {
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"homepage": "http://www.humanproteomemap.org/index.php",
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"example": "9606117",
"homepage": "http://www.humanproteomemap.org/index.php",
"name": "Human Proteome Map Peptide at Institute of Bioinformatics (Bangalore)",
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"pattern": "^\\d+$",
"prefix": "hpm.peptide",
"uri_format": "http://www.humanproteomemap.org/spectrum.php?pep_id=$1"
}
},
"hpm.protein": {
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"prefix": "HPM.PROTEIN"
},
"mappings": {
"biocontext": "HPM.PROTEIN",
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"ncbi": "HPM"
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"miriam": {
"deprecated": false,
"description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.",
"homepage": "http://www.humanproteomemap.org/index.php",
"id": "00000526",
"name": "Human Proteome Map Protein",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "hpm.protein",
"sampleId": "1968",
"uri_format": "http://www.humanproteomemap.org/protein.php?hpm_id=$1"
},
"n2t": {
"description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.",
"example": "1968",
"homepage": "http://www.humanproteomemap.org/index.php",
"name": "Human Proteome Map Protein at Institute of Bioinformatics (Bangalore)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "hpm.protein",
"uri_format": "http://www.humanproteomemap.org/protein.php?hpm_id=$1"
},
"ncbi": {
"example": "8106",
"homepage": "http://www.humanproteomemap.org/",
"name": "Human Proteome Map",
"prefix": "HPM"
}
},
"hprd": {
"biocontext": {
"prefix": "HPRD",
"uri_format": "http://www.hprd.org/protein/$1"
},
"fairsharing": {
"abbreviation": "HPRD",
"contact": {
"email": "pandey@jhmi.edu",
"name": "Akhilesh Pandey",
"orcid": "0000-0001-9943-6127"
},
"description": "The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.",
"homepage": "http://www.hprd.org/",
"name": "Human Protein Reference Database",
"prefix": "FAIRsharing.y2qws7",
"publications": [
{
"doi": "10.1093/nar/gkn892",
"pubmed_id": 18988627,
"title": "Human Protein Reference Database--2009 update."
}
],
"subjects": []
},
"integbio": {
"alt_name": "Human Protein Reference Database",
"description": "HPRD (Human Protein Reference Database) version 9 is a manually curated, fully GO compliant protein database.\nThe repository contains 30,047 protein entries, 41,327 protein-protein interactions and 93,710 posttranslational modifications. There are 112,158 occurrences of protein expression, 22,490 of subcellular positioning and 470 domains are identified. \nAll the information in HPRD, including features of proteins such as post-translational modifications, tissue expression, subcellular localization and protein-protein interactions, may be downloaded as XML and FLAT files. Permission is, however, necessary before this may be done.\nThe database can be browsed by selecting a protein, domain, motif, PTM or localization class of interest from a list that is provided. \nA Blast search option is available by entering a nucleotide or protein sequence.",
"fairsharing": "biodbcore-000395",
"homepage": "http://www.hprd.org",
"information_keywords": [
"Sequence"
],
"maintainer": "Institute of Bioinformatics",
"name": "HPRD",
"prefix": "nbdc00103",
"pubmeds": [
"18988627"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST",
"Protein",
"Health/Disease"
]
},
"mappings": {
"biocontext": "HPRD",
"fairsharing": "FAIRsharing.y2qws7",
"integbio": "nbdc00103",
"miriam": "hprd",
"n2t": "hprd",
"pathguide": "14",
"prefixcommons": "hprd",
"re3data": "r3d100010978"
},
"miriam": {
"deprecated": false,
"description": "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.",
"homepage": "http://www.hprd.org/",
"id": "00000377",
"name": "HPRD",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "hprd",
"sampleId": "00001",
"uri_format": "http://www.hprd.org/protein/$1"
},
"n2t": {
"description": "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.",
"example": "00001",
"homepage": "http://www.hprd.org/",
"name": "Human Protein Reference Database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "hprd",
"uri_format": "http://www.hprd.org/protein/$1"
},
"name": "Human Protein Reference Database",
"pathguide": {
"abbreviation": "HPRD",
"homepage": "http://www.hprd.org/",
"keywords": [
"PSI-MI"
],
"name": "Human Protein Reference Database",
"prefix": "14"
},
"prefixcommons": {
"description": "The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.",
"example": "00001",
"homepage": "http://www.hprd.org/",
"keywords": [
"protein",
"structure"
],
"name": "Human Protein Reference Database",
"pattern": "^\\d+$",
"prefix": "hprd",
"pubmed_ids": [
"18988627"
]
},
"publications": [
{
"doi": "10.1093/nar/gkn892",
"pmc": "PMC2686490",
"pubmed": "18988627",
"title": "Human Protein Reference Database--2009 update",
"year": 2008
}
],
"re3data": {
"description": "Human Protein Reference Database (HPRD) has been established by a team of biologists, bioinformaticists and software engineers. This is a joint project between the PandeyLab at Johns Hopkins University, and Institute of Bioinformatics, Bangalore. HPRD is a definitive repository of human proteins. This database should serve as a ready reckoner for researchers in their quest for drug discovery, identification of disease markers and promote biomedical research in general.\nHuman Proteinpedia (www.humanproteinpedia.org) is its associated data portal.",
"homepage": "http://www.hprd.org",
"name": "Human Protein Reference Database",
"prefix": "r3d100010978",
"synonyms": [
"HPRD"
],
"xrefs": {
"fairsharing": "FAIRsharing.y2qws7",
"nif": "0000-00137",
"omics": "02439",
"scr": "007027"
}
}
},
"hpscreg": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://hpscreg.eu",
"name": "Human Pluripotent Stem Cell Registry",
"prefix": "hPSCreg",
"uri_format": "https://hpscreg.eu/cell-line/$1"
},
"fairsharing": {
"abbreviation": "hPSCreg",
"contact": {
"email": "stefanie.seltmann@ibmt.fraunhofer.de",
"name": "Stefanie Seltmann",
"orcid": "0000-0002-8411-3226"
},
"description": "The human pluripotent stem cell registry (hPSCreg) is a public registry and data portal for human embryonic and induced pluripotent stem cell lines (hESC and hiPSC). The Registry provides comprehensive and standardized biological and legal information as well as tools to search and compare information from multiple hPSC sources and hence addresses a translational research need. To facilitate unambiguous identification over different resources, hPSCreg automatically creates a unique standardized name for each cell line registered. In addition to biological information, hPSCreg stores extensive data about ethical standards regarding cell sourcing and conditions for application and privacy protection. hPSCreg is the first global registry that holds both, manually validated scientific and ethical information on hPSC lines, and provides access by means of a user-friendly, mobile-ready web application.",
"homepage": "https://hpscreg.eu/",
"name": "Human Pluripotent Stem Cell Registry",
"prefix": "FAIRsharing.7C0aVE",
"publications": [
{
"doi": "S2213-6711(20)30235-6",
"pubmed_id": 32679065,
"title": "A Manually Curated Database on Clinical Studies Involving Cell Products Derived from Human Pluripotent Stem Cells."
},
{
"doi": "S1873-5061(20)30188-4",
"pubmed_id": 32707486,
"title": "Access to stem cell data and registration of pluripotent cell lines: The Human Pluripotent Stem Cell Registry (hPSCreg)."
},
{
"doi": "S1873-5061(19)30169-2",
"pubmed_id": 31450190,
"title": "A pathway for attesting ethical provenance of cell lines: Lessons from the European human pluripotent stem cell registry (hPSC(reg))."
},
{
"doi": "S2213-6711(17)30531-3",
"pubmed_id": 29320760,
"title": "A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells."
},
{
"doi": "10.1093/nar/gkv963",
"pubmed_id": 26400179,
"title": "hPSCreg--the human pluripotent stem cell registry."
}
],
"subjects": [
"Life Science",
"Biomedical Science"
]
},
"mappings": {
"cellosaurus": "hPSCreg",
"fairsharing": "FAIRsharing.7C0aVE",
"miriam": "hpscreg",
"n2t": "hpscreg",
"re3data": "r3d100012863"
},
"miriam": {
"deprecated": false,
"description": "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines).",
"homepage": "https://hpscreg.eu/",
"id": "00000674",
"name": "Human Pluripotent Stem Cell Registry",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$",
"prefix": "hpscreg",
"sampleId": "BCRTi001-A",
"uri_format": "https://hpscreg.eu/cell-line/$1"
},
"n2t": {
"description": "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines).",
"example": "BCRTi001-A",
"homepage": "https://hpscreg.eu/",
"name": "Human Pluripotent Stem Cell Registry",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$",
"prefix": "hpscreg",
"uri_format": "https://hpscreg.eu/cell-line/$1"
},
"publications": [
{
"doi": "10.1016/j.scr.2020.101887",
"pubmed": "32707486",
"title": "Access to stem cell data and registration of pluripotent cell lines: The Human Pluripotent Stem Cell Registry (hPSCreg)",
"year": 2020
},
{
"doi": "10.1016/j.stemcr.2020.06.014",
"pmc": "PMC7419703",
"pubmed": "32679065",
"title": "A Manually Curated Database on Clinical Studies Involving Cell Products Derived from Human Pluripotent Stem Cells",
"year": 2020
},
{
"doi": "10.1016/j.scr.2019.101539",
"pubmed": "31450190",
"title": "A pathway for attesting ethical provenance of cell lines: Lessons from the European human pluripotent stem cell registry (hPSC",
"year": 2019
},
{
"doi": "10.1016/j.stemcr.2017.12.002",
"pmc": "PMC5768986",
"pubmed": "29320760",
"title": "A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells",
"year": 2018
},
{
"doi": "10.1093/nar/gkv963",
"pmc": "PMC4702942",
"pubmed": "26400179",
"title": "hPSCreg--the human pluripotent stem cell registry",
"year": 2015
}
],
"re3data": {
"description": "The human pluripotent stem cell registry (hPSCreg) is a public registry and data portal for human embryonic and induced pluripotent stem cell lines (hESC and hiPSC). The Registry provides comprehensive and standardized biological and legal information as well as tools to search and compare information from multiple hPSC sources and hence addresses a translational research need. To facilitate unambiguous identification over different resources, hPSCreg automatically creates a unique standardized name (identifier) for each cell line registered. In addition to biological information, hPSCreg stores extensive data about ethical standards regarding cell sourcing and conditions for application and privacy protection. hPSCreg is the first global registry that holds both, manually validated scientific and ethical information on hPSC lines, and provides access by means of a user-friendly, mobile-ready web application.",
"homepage": "https://hpscreg.eu/",
"name": "hPSCreg",
"prefix": "r3d100012863",
"synonyms": [
"human Pluripotent Stem Cell registry"
],
"xrefs": {
"fairsharing": "FAIRsharing.7C0aVE",
"miriam": "00100898"
}
}
},
"hsapdv": {
"aberowl": {
"description": "Life cycle stages for Human",
"download_owl": "http://aber-owl.net/media/ontologies/HSAPDV/12/hsapdv.owl",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv",
"name": "Human Developmental Stages",
"prefix": "HSAPDV"
},
"biocontext": {
"prefix": "HSAPDV"
},
"biolink": {
"is_identifiers": false,
"is_obo": true,
"prefix": "HsapDv",
"uri_format": "http://purl.obolibrary.org/obo/HsapDv_$1"
},
"bioportal": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "Life cycle stages for Human. HsapDv was developed by the Bgee group with assistance from the core Uberon developers and the Human developmental anatomy ontology (EHDAA2) developers. Currently it includes both embryonic (Carnegie) stages and adult stages.",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv",
"name": "Human Developmental Stages Ontology",
"prefix": "HSAPDV"
},
"example": "0000194",
"fairsharing": {
"abbreviation": "HSAPDV",
"description": "Life cycle stages for Human. HsapDv was developed by the Bgee group with assistance from the core Uberon developers and the Human developmental anatomy ontology (EHDAA2) developers. Currently it includes both embryonic (Carnegie) stages and adult stages.",
"domains": [
"Life cycle stage"
],
"homepage": "https://obofoundry.org/ontology/hsapdv.html",
"license": "CC-BY-3.0",
"name": "Human Developmental Stages Ontology",
"prefix": "FAIRsharing.c6vhm3",
"repository": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv",
"subjects": [
"Anatomy",
"Developmental Biology"
]
},
"mappings": {
"aberowl": "HSAPDV",
"biocontext": "HSAPDV",
"biolink": "HsapDv",
"bioportal": "HSAPDV",
"fairsharing": "FAIRsharing.c6vhm3",
"obofoundry": "hsapdv",
"ols": "hsapdv",
"ontobee": "HsapDv"
},
"obofoundry": {
"appears_in": [
"scdo"
],
"contact": "frederic.bastian@unil.ch",
"contact.github": "fbastian",
"contact.label": "FrΓ©dΓ©ric Bastian",
"contact.orcid": "0000-0002-9415-5104",
"deprecated": false,
"description": "Life cycle stages for Human",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/hsapdv.obo",
"download.owl": "http://purl.obolibrary.org/obo/hsapdv.owl",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Human Developmental Stages",
"preferredPrefix": "HsapDv",
"prefix": "hsapdv",
"repository": "https://github.com/obophenotype/developmental-stage-ontologies"
},
"ols": {
"description": "Life cycle stages for Human",
"download_owl": "http://purl.obolibrary.org/obo/hsapdv.owl",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv",
"name": "Human Developmental Stages",
"prefix": "hsapdv"
},
"ontobee": {
"library": "Library",
"name": "Human Developmental Stages",
"prefix": "HsapDv"
},
"pattern": "^\\d{7}$",
"synonyms": [
"HsapDv"
],
"uri_format": "http://purl.obolibrary.org/obo/HsapDv_$1"
},
"hsdb": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas.",
"example": "5621",
"homepage": "https://pubchem.ncbi.nlm.nih.gov/source/hsdb",
"integbio": {
"alt_name": "Hazardous Substances Data Bank",
"description": "HSDB is a database of hazardous substances. The database contains information on toxic compounds gathered from primary, peer-reviewed literature. Users can search by compound, CAS, or symptom. Fact sheets and other support are also available.",
"homepage": "http://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?HSDB",
"information_keywords": [
"Bibliography/Documents",
"Chemical structure"
],
"maintainer": "NLM (National Library of Medicine)",
"name": "HSDB",
"prefix": "nbdc00930",
"pubmeds": [
"14728459",
"8545846"
],
"status": "Inactive",
"target_keywords": [
"Chemical compound"
]
},
"mappings": {
"integbio": "nbdc00930",
"wikidata": "P2062"
},
"name": "Hazardous Substances Data Bank",
"pattern": "^\\d+$",
"uri_format": "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1",
"wikidata": {
"description": "ID in Hazardous Substances Data Bank",
"example": [
"1112",
"8055"
],
"name": "HSDB ID",
"pattern": "^\\d+$",
"prefix": "P2062",
"uri_format": "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1"
}
},
"hso": {
"aberowl": {
"description": "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance.",
"download_owl": "http://aber-owl.net/media/ontologies/HSO/11/hso.owl",
"homepage": "https://w3id.org/hso",
"name": "Health Surveillance Ontology",
"prefix": "HSO"
},
"bioportal": {
"contact": {
"email": "fernanda.dorea@sva.se",
"name": "Fernanda DΓ³rea"
},
"description": "This is an ontology to support (one) health surveillance, focused on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc.",
"homepage": "http://datadrivensurveillance.org/ontology/",
"name": "Health Surveillance Ontology",
"prefix": "HSO",
"version": "3.1.1"
},
"example": "0000062",
"mappings": {
"aberowl": "HSO",
"bioportal": "HSO",
"obofoundry": "hso",
"ols": "hso",
"ontobee": "HSO"
},
"obofoundry": {
"contact": "fernanda.dorea@sva.se",
"contact.github": "nandadorea",
"contact.label": "Fernanda Dorea",
"contact.orcid": "0000-0001-8638-8525",
"depends_on": [
"bfo",
"ncbitaxon",
"obi",
"ro",
"uberon"
],
"deprecated": false,
"description": "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/hso.owl",
"homepage": "https://w3id.org/hso",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Health Surveillance Ontology",
"preferredPrefix": "HSO",
"prefix": "hso",
"repository": "https://github.com/SVA-SE/HSO"
},
"ols": {
"description": "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance.",
"download_owl": "http://purl.obolibrary.org/obo/hso.owl",
"homepage": "https://w3id.org/hso",
"name": "Health Surveillance Ontology",
"prefix": "hso",
"version": "2021-12-13",
"version.iri": "http://purl.obolibrary.org/obo/hso/2021-12-13/hso.owl"
},
"ontobee": {
"library": "Library",
"name": "Health Surveillance Ontology",
"prefix": "HSO"
},
"pattern": "^\\d{7}$",
"providers": [
{
"code": "hso.legacy",
"description": "An incorrect encoding of OBO purls",
"homepage": "http://purl.obolibrary.org/obo/hso",
"name": "HSO Hash",
"uri_format": "http://purl.obolibrary.org/obo/hso.owl#HSO_$1"
}
],
"uri_format": "http://purl.obolibrary.org/obo/HSO_$1"
},
"hssp": {
"biocontext": {
"prefix": "HSSP"
},
"contact": {
"email": "chris@sanderlab.org",
"name": "Chris Sander",
"orcid": "0000-0001-6059-6270"
},
"mappings": {
"biocontext": "HSSP",
"miriam": "hssp",
"n2t": "hssp",
"ncbi": "HSSP",
"prefixcommons": "hssp"
},
"miriam": {
"deprecated": false,
"description": "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.",
"homepage": "http://swift.cmbi.kun.nl/swift/hssp/",
"id": "00000215",
"name": "HSSP",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{4}$",
"prefix": "hssp",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "HSSP at CMBI",
"homepage": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/",
"name": "HSSP at CMBI",
"uri_format": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$1.hssp.bz2"
}
],
"sampleId": "102l",
"uri_format": "ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2"
},
"n2t": {
"description": "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.",
"example": "102l",
"homepage": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/",
"name": "HSSP at CMBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{4}$",
"prefix": "hssp",
"uri_format": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$1.hssp.bz2"
},
"ncbi": {
"example": "12GS",
"name": "Database of homology-derived secondary structure of proteins",
"prefix": "HSSP"
},
"prefixcommons": {
"description": "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.",
"example": "102l",
"homepage": "http://www.cmbi.kun.nl/gv/hssp/",
"keywords": [
"clustering",
"protein",
"sequence"
],
"name": "Homology-derived secondary structure of proteins database",
"pattern": "^\\w{4}$",
"prefix": "hssp",
"pubmed_ids": [
"7937066",
"8594579"
]
},
"publications": [
{
"doi": "10.1093/nar/24.1.201",
"pmc": "PMC145595",
"pubmed": "8594579",
"title": "The HSSP database of protein structure-sequence alignments",
"year": 1996
},
{
"pmc": "PMC308328",
"pubmed": "7937066",
"title": "The HSSP database of protein structure-sequence alignments",
"year": 1994
}
]
},
"htn": {
"aberowl": {
"description": "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines",
"download_owl": "http://aber-owl.net/media/ontologies/HTN/1/htn.owl",
"homepage": "https://github.com/aellenhicks/htn_owl",
"name": "Hypertension Ontology",
"prefix": "HTN"
},
"bioportal": {
"contact": {
"email": "aellenhicks@gmail.com",
"name": "Amanda Hicks"
},
"description": "The Hypertension Ontology is a realism-based reference ontology for semantically managing clinical data about hypertension. Definitions of hypertension and elevated blood pressure are highly sensitive to context. Thresholds may vary according to population, guidelines, or clinical context. Variations in the clinical interpretation of blood pressure pose challenges to using blood pressure data for cohort identification, semantic data integration across data sets, and semantically enriching clinical data for clinical decision support applications. The Hypertension Ontology provides a framework for connecting clinical data to context-sensitive definitions of elevated blood pressure and hypertension.",
"homepage": "https://github.com/aellenhicks/htn_owl",
"name": "Hypertension Ontology",
"prefix": "HTN"
},
"example": "00000014",
"mappings": {
"aberowl": "HTN",
"bioportal": "HTN",
"obofoundry": "htn",
"ols": "htn",
"ontobee": "HTN"
},
"obofoundry": {
"contact": "aellenhicks@gmail.com",
"contact.github": "aellenhicks",
"contact.label": "Amanda Hicks",
"contact.orcid": "0000-0002-1795-5570",
"deprecated": false,
"description": "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/htn.owl",
"homepage": "https://github.com/aellenhicks/htn_owl",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Hypertension Ontology",
"preferredPrefix": "HTN",
"prefix": "htn",
"repository": "https://github.com/aellenhicks/htn_owl"
},
"ols": {
"description": "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines",
"download_owl": "http://purl.obolibrary.org/obo/htn.owl",
"homepage": "https://github.com/aellenhicks/htn_owl",
"name": "Hypertension Ontology For Clinical Data",
"prefix": "htn"
},
"ontobee": {
"library": "Library",
"name": "Hypertension Ontology",
"prefix": "HTN"
},
"pattern": "^\\d{8}$",
"uri_format": "http://purl.obolibrary.org/obo/HTN_$1"
},
"huge": {
"biocontext": {
"prefix": "HUGE"
},
"contact": {
"email": "ohara@kazusa.or.jp",
"name": "Osamu Ohara",
"orcid": "0000-0002-3328-9571"
},
"fairsharing": {
"abbreviation": "HUGE",
"description": "HUGE is a database for human large proteins newly identified in the Kazusa cDNA project, the aim of which is to predict the primary structure of proteins from the sequences of human large cDNAs (>4 kb).",
"homepage": "http://www.kazusa.or.jp/huge/",
"name": "Human Unidentified Gene-Encoded large proteins database",
"prefix": "FAIRsharing.zx2ztd",
"publications": [
{
"doi": "10.1093/nar/gkh035",
"pubmed_id": 14681467,
"title": "HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE."
}
],
"subjects": [
"Computational Biology",
"Life Science"
]
},
"integbio": {
"alt_name": "A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project",
"description": "The HUGE database is published by the Kazusa DNA Research Institute based on the results of its Kazusa Human cDNA Project to sequence and analyze long (>4 kb) human cDNAs and establish methods to predict the primary structure of proteins with various biological activities. Information on the predicted primary structure of newly identified human proteins that may be involved in cellular structure/motility, gene expression and nucleic acid metabolism, cell signaling/communication, etc. is available.",
"fairsharing": "biodbcore-000407",
"homepage": "http://www.kazusa.or.jp/huge/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "HUGE",
"prefix": "nbdc00104",
"pubmeds": [
"9847221",
"10592264",
"11752282",
"14681467"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein"
]
},
"mappings": {
"biocontext": "HUGE",
"fairsharing": "FAIRsharing.zx2ztd",
"integbio": "nbdc00104",
"miriam": "huge",
"n2t": "huge",
"prefixcommons": "huge",
"uniprot": "DB-0049"
},
"miriam": {
"deprecated": false,
"description": "The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.",
"homepage": "http://www.kazusa.or.jp/huge/",
"id": "00000263",
"name": "HUGE",
"namespaceEmbeddedInLui": false,
"pattern": "^KIAA\\d{4}$",
"prefix": "huge",
"sampleId": "KIAA0001",
"uri_format": "http://www.kazusa.or.jp/huge/gfpage/$1/"
},
"n2t": {
"description": "The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.",
"example": "KIAA0001",
"homepage": "http://www.kazusa.or.jp/huge/",
"name": "HUGE at Kazusa DNA Research Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^KIAA\\d{4}$",
"prefix": "huge",
"uri_format": "http://www.kazusa.or.jp/huge/gfpage/$1/"
},
"name": "Human Unidentified Gene-Encoded",
"prefixcommons": {
"description": "HUGE is a database for human large proteins newly identified in the Kazusa cDNA project, the aim of which is to predict the primary structure of proteins from the sequences of human large cDNAs (>4 kb).",
"example": "KIAA0001",
"homepage": "http://www.kazusa.or.jp/huge/",
"keywords": [
"protein",
"DNA",
"structure"
],
"name": "Human Unidentified Gene-Encoded large proteins database",
"pattern": "^KIAA\\d{4}$",
"prefix": "huge",
"pubmed_ids": [
"14681467"
],
"uri_format": "http://www.kazusa.or.jp/huge/cgi/view_direct.cgi?id=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkh035",
"pmc": "PMC308769",
"pubmed": "14681467",
"title": "HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE",
"year": 2004
}
],
"uniprot": {
"abbreviation": "HUGE",
"category": "Organism-specific databases",
"homepage": "http://www.kazusa.or.jp/huge/",
"name": "Human Unidentified Gene-Encoded large proteins database",
"prefix": "DB-0049",
"publications": [
{
"doi": "10.1093/nar/gkh035",
"pubmed": "14681467"
}
],
"uri_format": "http://www.kazusa.or.jp/huge/gfpage/$1"
},
"uri_format": "https://www.kazusa.or.jp/huge/gfpage/$1"
},
"iao": {
"aberowl": {
"description": "An ontology of information entities.",
"download_owl": "http://aber-owl.net/media/ontologies/IAO/11/iao.owl",
"homepage": "https://github.com/information-artifact-ontology/IAO/",
"name": "Information Artifact Ontology",
"prefix": "IAO"
},
"biocontext": {
"prefix": "IAO"
},
"bioportal": {
"contact": {
"email": "alanruttenberg@gmail.com",
"name": "Alan Ruttenberg"
},
"description": "The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI consortium.
To import
Latest released version: http://purl.obolibrary.org/obo/iao.owl
Other versions
Developer (live) version: http://purl.obolibrary.org/obo/iao/dev/iao.owl
Ontology metadata properties and classes only: http://purl.obolibrary.org/obo/iao/dev/iao.owl
Dated versions
Please note: The ontology metrics displayed by BioPortal do not distinguish IAO-developed terms from terms imported from other ontologies.
Tracker: http://purl.obolibrary.org/obo/iao/tracker
Discussion group: http://groups.google.com/group/information-ontology",
"homepage": "http://purl.obolibrary.org/obo/iao",
"name": "Information Artifact Ontology",
"prefix": "IAO",
"publication": "http://purl.obolibrary.org/obo/iao/reports",
"version": "2022-11-07"
},
"download_obo": "http://purl.obolibrary.org/obo/iao.obo",
"fairsharing": {
"abbreviation": "IAO",
"contact": {
"email": "alanruttenberg@gmail.com",
"name": "Alan Ruttenberg",
"orcid": "0000-0002-1604-3078"
},
"description": "The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch.",
"domains": [
"Drug report",
"Experimental measurement",
"Data identity and mapping",
"Reagent",
"Assay",
"Protocol",
"Study design"
],
"homepage": "https://github.com/information-artifact-ontology/IAO/",
"license": "CC-BY-3.0",
"name": "Information Artifact Ontology",
"prefix": "FAIRsharing.gq1xtx",
"publications": [
{
"doi": "10.3233/978-1-61499-101-4-68",
"pubmed": "22874154",
"title": "An information artifact ontology perspective on data collections and associated representational artifacts",
"year": 2012
}
],
"repository": "https://github.com/information-artifact-ontology/IAO/wiki/Meeting_notes",
"subjects": [
"Knowledge and Information Systems",
"Data Management",
"Subject Agnostic",
"Biomedical Science"
]
},
"go": {
"description": "Ontology of information entities, including ontology metadata relations.",
"name": "Information Artifact Ontology",
"prefix": "IAO"
},
"mappings": {
"aberowl": "IAO",
"biocontext": "IAO",
"bioportal": "IAO",
"fairsharing": "FAIRsharing.gq1xtx",
"go": "IAO",
"miriam": "iao",
"n2t": "iao",
"obofoundry": "iao",
"ols": "iao",
"ontobee": "IAO"
},
"miriam": {
"deprecated": false,
"description": "An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch.",
"homepage": "http://www.ontobee.org/ontology/IAO",
"id": "00000603",
"name": "Information Artifact Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{7}$",
"prefix": "iao",
"sampleId": "0000030",
"uri_format": "http://purl.obolibrary.org/obo/IAO_$1"
},
"n2t": {
"description": "An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch.",
"example": "0000030",
"homepage": "http://www.ontobee.org/ontology/IAO",
"name": "IAO through Ontobee",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{7}$",
"prefix": "iao",
"uri_format": "http://purl.obolibrary.org/obo/IAO_$1"
},
"obofoundry": {
"appears_in": [
"agro",
"clyh",
"duo",
"ecocore",
"ecto",
"fovt",
"labo",
"maxo",
"mcro",
"pco",
"psdo",
"xpo"
],
"contact": "zhengj2007@gmail.com",
"contact.github": "zhengj2007",
"contact.label": "Jie Zheng",
"contact.orcid": "0000-0002-2999-0103",
"deprecated": false,
"description": "An ontology of information entities.",
"domain": "information",
"download.owl": "http://purl.obolibrary.org/obo/iao.owl",
"homepage": "https://github.com/information-artifact-ontology/IAO/",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"logo": "https://avatars0.githubusercontent.com/u/13591168?v=3&s=200",
"name": "Information Artifact Ontology",
"preferredPrefix": "IAO",
"prefix": "iao",
"repository": "https://github.com/information-artifact-ontology/IAO"
},
"ols": {
"description": "The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch.",
"download_owl": "http://purl.obolibrary.org/obo/iao.owl",
"homepage": "https://github.com/information-artifact-ontology/IAO/",
"name": "Information Artifact Ontology (IAO)",
"prefix": "iao",
"version": "2022-11-07",
"version.iri": "http://purl.obolibrary.org/obo/iao/2022-11-07/iao.owl"
},
"ontobee": {
"library": "Library",
"name": "Information Artifact Ontology",
"prefix": "IAO"
},
"providers": [
{
"code": "legacy",
"description": "A URI from the semanticweb.og",
"homepage": "http://www.semanticweb.org",
"name": "Legacy URI",
"uri_format": "http://www.semanticweb.org/ontologies/2011/9/Ontology1317751904226.owl#IAO_$1"
}
],
"publications": [
{
"doi": "10.3233/978-1-61499-101-4-68",
"pubmed": "22874154",
"title": "An information artifact ontology perspective on data collections and associated representational artifacts",
"year": 2012
}
],
"uri_format": "http://purl.obolibrary.org/obo/IAO_$1"
},
"icd10": {
"aberowl": {
"description": "International Statistical Classification of Diseases and Related Health Problems (ICD-10). 10th rev. Geneva",
"name": "International Classification of Diseases, Version 10",
"prefix": "ICD10",
"version": "2016AB"
},
"bartoc": {
"abbreviation": "ICD",
"description": "The International Classification of Diseases (ICD) is the standard diagnostic tool for epidemiology, health management and clinical purposes. This includes the analysis of the general health situation of population groups. It is used to monitor the incidence and prevalence of diseases and other health problems. It is used to classify diseases and other health problems recorded on many types of health and vital records including death certificates and health records. In addition to enabling the storage and retrieval of diagnostic information for clinical, epidemiological and quality purposes, these records also provide the basis for the compilation of national mortality and morbidity statistics by WHO Member States. It is used for reimbursement and resource allocation decision-making by countries. ICD-10 was endorsed by the Forty-third World Health Assembly in May 1990 and came into use in WHO Member States as from 1994. The 11th revision of the classification has already started and will continue until 2015.",
"homepage": "https://www.who.int/standards/classifications/classification-of-diseases",
"name": "International Statistical Classification of Diseases",
"prefix": "447",
"wikidata_database": "Q50018"
},
"biocontext": {
"prefix": "ICD"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "ICD10",
"uri_format": "https://icd.codes/icd9cm/$1"
},
"bioportal": {
"contact": {
"email": "info@who.int",
"name": "World Health Organization"
},
"description": "International Statistical Classification of Diseases and Related Health Problems (ICD-10). 10th rev. Geneva",
"name": "International Classification of Diseases, Version 10",
"prefix": "ICD10",
"version": "2023AB"
},
"contributor_extras": [
{
"github": "joeflack4",
"name": "Joe Flack",
"orcid": "0000-0002-2906-7319"
},
{
"email": "nicolas.matentzoglu@gmail.com",
"github": "matentzn",
"name": "Nicolas Matentzoglu",
"orcid": "0000-0002-7356-1779"
},
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"description": "The 10th revision of the International Classification of Diseases (ICD) issued by the World Health Organization (WHO). ICD is formally named 'The International Statistical Classification of Diseases and Related Health Problems'. It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases.\n\nNote that the WHO version of ICD-10 is distinct from the ICD-10-CM (Clinical Modification) issued by the U.S. National Center for Health Statistics for use in the United States.",
"edam": {
"description": "An identifier of a disease from the International Classification of Diseases (ICD) database.",
"name": "ICD",
"obsolete": false,
"prefix": "2611"
},
"example_decoys": [
"G00X",
"C34.90",
"C4A.8",
"C91.Z",
"C91.Z0"
],
"example_extras": [
"V20",
"G00",
"A01.1",
"XVIII",
"R25-R29",
"R25",
"R25.3"
],
"fairsharing": {
"abbreviation": "ICD-10",
"description": "The ICD is the international standard diagnostic classification for all general epidemiological, many health management purposes and clinical use. ICD-10 is the 10th revision of the International Statistical Classification of Diseases and Related Health Problems (ICD), a medical classification list by the World Health Organization (WHO). It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases.",
"domains": [
"Disease",
"Diagnosis"
],
"homepage": "http://www.who.int/classifications/icd/en/",
"license": "http://www.who.int/about/licensing/copyright_form/en",
"name": "International Classification of Diseases Version 10",
"prefix": "FAIRsharing.nj16g",
"subjects": [
"Health Science",
"Global Health",
"Biomedical Science",
"Epidemiology"
]
},
"hl7": {
"description": "International Classification of Diseases revision 10 (ICD 10)Note this does NOT have the CM changes, and is specifically for international use.This node is the ontological branch in the HL7 OID tree. The actual ICD10 code systems (the various national and international versions) are defined below this node.",
"homepage": "https://who.int",
"name": "ICD10",
"organization": "World Health Organization",
"preferred_prefix": "icd10",
"prefix": "2.16.840.1.113883.6.3",
"status": "Complete"
},
"homepage": "https://icd.who.int/browse10",
"license": "https://cdn.who.int/media/docs/default-source/publishing-policies/copyright/who-faq-licensing-icd-10.pdf",
"mappings": {
"aberowl": "ICD10",
"bartoc": "447",
"biocontext": "ICD",
"biolink": "ICD10",
"bioportal": "ICD10",
"edam": "2611",
"fairsharing": "FAIRsharing.nj16g",
"hl7": "2.16.840.1.113883.6.3",
"miriam": "icd",
"n2t": "icd",
"prefixcommons": "icd",
"wikidata": "P494"
},
"miriam": {
"deprecated": false,
"description": "The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes.",
"homepage": "http://www.who.int/classifications/icd/en/",
"id": "00000009",
"name": "ICD",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]\\d+(\\.[-\\d+])?$",
"prefix": "icd",
"sampleId": "C34",
"uri_format": "https://icd.who.int/browse10/2019/en#/$1"
},
"n2t": {
"description": "The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes.",
"example": "C34",
"homepage": "http://www.who.int/classifications/icd/en/",
"name": "International Statistical Classification of Diseases and Related Health Problems",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]\\d+(\\.[-\\d+])?$",
"prefix": "icd",
"uri_format": "http://apps.who.int/classifications/icd10/browse/2010/en#/$1"
},
"name": "International Classification of Diseases, 10th Revision",
"pattern": "^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\\.[0-9]))?))$",
"prefixcommons": {
"description": "The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes.",
"example": "C34",
"homepage": "http://www.who.int/classifications/icd/en/",
"keywords": [
"disease",
"taxonomy",
"classification"
],
"license": "http://www.who.int/about/copyright/en/index.html",
"name": "International Classification of Diseases",
"pattern": "^[A-Z]\\d+(\\.[-\\d+])?$",
"prefix": "icd",
"uri_format": "http://apps.who.int/classifications/icd10/browse/2010/en#/$1"
},
"providers": [
{
"code": "icdcodelookup",
"description": "This site is dedicated exclusively to helping you look up ICD-10 codes, quickly access the codes you use most, and become more comfortable with the new code set in general.",
"homepage": "https://icdcodelookup.com/icd-10/codes",
"name": "ICD Code Lookup",
"uri_format": "https://icdcodelookup.com/icd-10/codes/$1"
},
{
"code": "icd10_2015",
"description": "The 2015 revision of ICD-10",
"homepage": "https://icd.who.int/browse10/2015/en#",
"name": "ICD-10 Version 2015",
"uri_format": "https://icd.who.int/browse10/2015/en#/$1"
},
{
"code": "icd10_2010",
"description": "The 2010 revision of ICD-10",
"homepage": "https://icd.who.int/browse10/2010/en#",
"name": "ICD-10 Version 2010",
"uri_format": "https://icd.who.int/browse10/2010/en#/$1"
},
{
"code": "icd10_2008",
"description": "The 2008 revision of ICD-10",
"homepage": "https://icd.who.int/browse10/2008/en#",
"name": "ICD-10 Version 2008",
"uri_format": "https://icd.who.int/browse10/2008/en#/$1"
},
{
"code": "icd10_2014",
"description": "The 2014 revision of ICD-10",
"homepage": "https://icd.who.int/browse10/2014/en#",
"name": "ICD-10 Version 2014",
"uri_format": "https://icd.who.int/browse10/2014/en#/$1"
},
{
"code": "icd10_2016",
"description": "The 2016 revision of ICD-10",
"homepage": "https://icd.who.int/browse10/2016/en#",
"name": "ICD-10 Version 2016",
"uri_format": "https://icd.who.int/browse10/2016/en#/$1"
}
],
"synonyms": [
"ICD",
"ICD-10",
"ICD10",
"ICD10WHO"
],
"uri_format": "https://icd.who.int/browse10/2019/en#/$1",
"wikidata": {
"description": "identifier in theΒ ICD catalogue codes for diseases - Version 10",
"example": [
"J10",
"J11",
"R19.6"
],
"name": "ICD-10",
"pattern": "^[A-Z]\\d{2}(\\.\\d{1,2})?$",
"prefix": "P494",
"uri_format": "https://icd.who.int/browse10/2019/en#/$1"
}
},
"icd10cm": {
"aberowl": {
"description": "International Classification of Diseases, 10th Edition, Clinical Modification, 2011_01",
"homepage": "http://www.cms.hhs.gov/",
"name": "International Classification of Diseases, Version 10 - Clinical Modification",
"prefix": "ICD10CM",
"version": "2016AB"
},
"bioportal": {
"contact": {
"email": "pbrooks@hcfa.gov",
"name": "Patricia Brooks"
},
"description": "International Classification of Diseases, 10th Edition, Clinical Modification, 2011_01",
"homepage": "http://www.cms.hhs.gov/",
"name": "International Classification of Diseases, Version 10 - Clinical Modification",
"prefix": "ICD10CM",
"publication": "http://www.cms.hhs.gov/",
"version": "2023AB"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States issued by the National Center for Health Statistics (NCHS) and Centers for Medicare & Medicaid Services (CMS).",
"example": "F45.21",
"example_decoys": [
"C000",
"c00",
"C00-D499",
"C00-99",
"C34.90000"
],
"example_extras": [
"C00-D49",
"U49",
"C34",
"C34.90",
"C4A.8",
"C91.Z",
"C91.Z0",
"T37.0X1A"
],
"fairsharing": {
"abbreviation": "ICD-10-CM",
"description": "The International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) is a morbidity classification for classifying diagnoses and reason for visits in all American health care settings. The ICD-10-CM is based on the ICD-10, the statistical classification of disease published by the World Health Organization (WHO) which replaces ICD-9. ICD-10-CM replaced ICD-9-CM Volumes 1 and 2 from October 2015 onwards.",
"domains": [
"Electronic health record",
"Disease",
"Diagnosis",
"Morbidity"
],
"homepage": "https://www.cdc.gov/nchs/icd/icd10cm.htm",
"name": "International Classification of Diseases, Tenth Revision, Clinical Modification",
"prefix": "FAIRsharing.hpvbxb",
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"Health Science",
"Biomedical Science"
]
},
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"homepage": "http://www.cdc.gov/nchs/about/otheract/icd9/icd10cm.htm",
"name": "International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM)",
"organization": "National Center for Health Statistics/Centers for Disease Control and Prevention",
"preferred_prefix": "icd10CM",
"prefix": "2.16.840.1.113883.6.90",
"status": "Complete"
},
"homepage": "https://www.icd10data.com/ICD10CM",
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"wikidata": "P4229"
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"name": "International Classification of Diseases, 10th Revision, Clinical Modification",
"pattern": "^([A-Z][0-9][0-9AB]((-[A-Z][0-9][0-9AB])|(\\.[0-9A-KXZ]([0-9A-EXYZ]([0-9A-HX][0-59A-HJKMNP-S]?)?)?)?))$",
"providers": [
{
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}
],
"synonyms": [
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"description": "identifier in the ICD-10-CM (International Classification of Diseases, 10th Revision, Clinical Modification)",
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],
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}
},
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"version": "2016AB"
},
"bioportal": {
"contact": {
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"name": "Pat Brooks"
},
"description": "ICD-10-PCS, 2009",
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"name": "International Classification of Diseases, Version 10 - Procedure Coding System",
"prefix": "ICD10PCS",
"publication": "http://www.cms.hhs.gov",
"version": "2023AB"
},
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"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
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},
"description": "ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis.\n\nICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records.",
"example": "01N50ZZ",
"fairsharing": {
"abbreviation": "ICD-10-PCS",
"description": "The ICD-10 Procedure Coding System (ICD-10-PCS) is an international system of medical classification used for procedural coding. The ICD-10-PCS is a procedure classification published by the United States for classifying procedures performed in hospital inpatient health care settings. The ICD-10-PCS replaces the procedural coding portion (Volume 3) of ICD-9-CM.",
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"Hospital",
"Disease",
"Diagnosis",
"Classification",
"Morbidity"
],
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"Biomedical Science",
"Epidemiology"
]
},
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"description": "The International Classification of Diseases, 10th Revision, Procedure Coding System (ICD-10-PCS), describes the classification of inpatient procedures for statistical purposes and for the indexing of healthcare records by procedures. The ICD-10-PCS codes can be used as the value of the Act.cd attribute",
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"name": "International Classification of Diseases, 10th Revision, Procedure Coding System (ICD-10-PCS)",
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"prefix": "2.16.840.1.113883.6.4",
"status": "Complete"
},
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"wikidata": "P1690"
},
"name": "International Classification of Diseases, 10th Revision, Procedure Coding System",
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"description": "identifier in the ICD-10-PCS (Procedure Coding System, International Classification of Diseases, 10th revision)",
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"01N50ZZ",
"0SRD0JZ"
],
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"prefix": "P1690",
"uri_format": "https://www.findacode.com/code.php?set=ICD10PCS&c=$1"
}
},
"icd11": {
"comment": "The codes, such as RA00.0, need their own namespace.",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
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"orcid": "0000-0003-4423-4370"
},
"description": "Diagnostic tool for epidemiology, health management and clinical purposes, maintained by the World Health Organization (WHO). It provides a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease.",
"example": "402558626",
"fairsharing": {
"abbreviation": "ICD 11",
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"Morbidity"
],
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},
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"status": "Complete"
},
"homepage": "https://icd.who.int/",
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"fairsharing": "bsg-s001436/",
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],
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"Health/Disease"
]
},
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"name": "International Classification of Diseases, 11th Revision",
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],
"synonyms": [
"ICD-11"
],
"uri_format": "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1",
"wikidata": {
"description": "identifier in ICD terminology of diseases - Version 11 (foundation ID) (not Mortality and Morbidity Statistics ID)",
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"698285441",
"784669405"
],
"name": "ICD-11 (foundation)",
"pattern": "^[1-9]\\d*$",
"prefix": "P7807",
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},
"icd9": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "ICD9",
"uri_format": "http://translator.ncats.nih.gov/ICD9_$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics.",
"example": "277.9",
"hl7": {
"description": "International Classification of Diseases, Version 9 (ICD9)",
"homepage": "https://who.int",
"name": "International Classification of Diseases, Version 9",
"organization": "World Health Organization",
"preferred_prefix": "icd9",
"prefix": "2.16.840.1.113883.6.42",
"status": "Complete"
},
"homepage": "https://www.cdc.gov/nchs/icd/icd9.htm",
"mappings": {
"biolink": "ICD9",
"hl7": "2.16.840.1.113883.6.42",
"wikidata": "P493"
},
"name": "International Classification of Diseases, 9th Revision",
"synonyms": [
"ICD9",
"ICD9_2005",
"MTHICD9_2006"
],
"uri_format": "http://www.icd9data.com/getICD9Code.ashx?icd9=$1",
"wikidata": {
"database": "Q50018",
"description": "identifier in the ICD catalogue codes for diseases β Version 9",
"example": [
"487",
"995.81",
"E950",
"V15.01"
],
"name": "ICD-9 ID",
"pattern": "^(\\d\\d\\d|V\\d\\d|E[8-9]\\d\\d)(\\.\\d{1,2})?$",
"prefix": "P493",
"uri_format": "http://www.icd9data.com/getICD9Code.ashx?icd9=$1"
}
},
"icd9cm": {
"aberowl": {
"description": "The ICD is the international standard diagnostic classification for all general epidemiological, many health management purposes and clinical use.",
"homepage": "http://www.cms.hhs.gov/",
"name": "International Classification of Diseases, Version 9 - Clinical Modification",
"prefix": "ICD9CM",
"version": "2016AB"
},
"bioportal": {
"contact": {
"email": "pbrooks@hcfa.gov",
"name": "Patricia Brooks"
},
"description": "The ICD is the international standard diagnostic classification for all general epidemiological, many health management purposes and clinical use.",
"homepage": "http://www.cms.hhs.gov/",
"name": "International Classification of Diseases, Version 9 - Clinical Modification",
"prefix": "ICD9CM",
"version": "2023AB"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States.",
"example": "784",
"fairsharing": {
"abbreviation": "ICD-9-CM",
"description": "The ICD is the international standard diagnostic classification for all general epidemiological, many health management purposes and clinical use. The International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) is an adaption created by the U.S. National Center for Health Statistics (NCHS) and used in assigning diagnostic and procedure codes associated with inpatient, outpatient, and physician office utilization in the United States. The ICD-9-CM is based on the ICD-9 but provides for additional morbidity detail.",
"domains": [
"Disease",
"Diagnosis",
"Morbidity"
],
"homepage": "https://www.cdc.gov/nchs/icd/icd9cm.htm",
"name": "International Classification of Diseases, Ninth Revision, Clinical Modification",
"prefix": "FAIRsharing.10zsxb",
"subjects": [
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"Health Science",
"Biomedical Science",
"Epidemiology",
"Preclinical Studies"
]
},
"hl7": {
"description": "The International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM), Volumes I, II (diagnoses) and III (procedures) describes the classification of morbidity and mortality information for statistical purposes and for the indexing of healthcare records by diseases and procedures. The ICD-9-CM codes can be used as the value of the Act.cd attribute.Note that this has been retired in favor of an explicit split between the diagnosis codes and the procedures codes as per the Vocablary TC decision on Wednesday Q4, January 21, 2004. Replaced by 2.16.840.1.113883.6.103 and 2.16.840.1.113883.6.104 as voted by committee. -T. Klein",
"homepage": "http://www.cdc.gov/nchs/icd9.htm.",
"name": "National Center for Health Statistics",
"organization": "National Center for Health Statistics",
"preferred_prefix": "icd9cm",
"prefix": "2.16.840.1.113883.6.2",
"status": "Retired"
},
"homepage": "https://www.cdc.gov/nchs/icd/icd9cm.htm",
"mappings": {
"aberowl": "ICD9CM",
"bioportal": "ICD9CM",
"fairsharing": "FAIRsharing.10zsxb",
"hl7": "2.16.840.1.113883.6.2",
"wikidata": "P1692"
},
"name": "International Classification of Diseases, 9th Revision, Clinical Modification",
"pattern": "^([\\dA-Z]\\d{2}(\\.\\d{1,3}|))|(\\d{2}(\\.\\d{1,2}|))$",
"synonyms": [
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"ICD9CM",
"ICD9CM_2005",
"ICD9CM_2006",
"ICDCM_2005"
],
"uri_format": "http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1",
"wikidata": {
"database": "Q5737131",
"description": "identifier in theΒ ICD adaption assigning diagnostic and procedure codes",
"example": [
"135",
"42",
"503"
],
"name": "ICD-9-CM",
"pattern": "^([\\dA-Z]\\d{2}(\\.\\d{1,3}|))|(\\d{2}(\\.\\d{1,2}|))$",
"prefix": "P1692",
"uri_format": "http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1"
}
},
"icdc": {
"fairsharing": {
"abbreviation": "ICDC",
"contact": {
"email": "annika.jahnke-bornemann@uni-hamburg.de",
"name": "Annika Jahnke-Bornemann",
"orcid": "0000-0001-7815-151X"
},
"description": "The Integrated Climate Data Center (ICDC) allows easy access to climate relevant data from in-situ measurements and satellite remote sensing. These data are important to determine the status and the changes in the climate system. Some relevant re-analysis data are included, which are modeled on the basis of observational data.",
"homepage": "https://icdc.cen.uni-hamburg.de/en/icdc.html",
"name": "Integrated Climate Data Center",
"prefix": "FAIRsharing.d95034",
"publications": [],
"subjects": [
"Social Science",
"Meteorology",
"Earth Science",
"Atmospheric Science",
"Remote Sensing",
"Oceanography"
],
"twitter": "ICDC_Hamburg"
},
"mappings": {
"fairsharing": "FAIRsharing.d95034",
"miriam": "icdc",
"re3data": "r3d100010405"
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"miriam": {
"deprecated": false,
"description": "The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer.",
"homepage": "https://caninecommons.cancer.gov/#/",
"id": "00000812",
"name": "Integrated Canine Data Commons",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{6}$",
"prefix": "icdc",
"sampleId": "000009",
"uri_format": "https://caninecommons.cancer.gov/#/study/$1"
},
"re3data": {
"description": "The CliSAP-Integrated Climate Data Center (ICDC) allows easy access to climate relevant data from satellite remote sensing and in situ and other measurements in Earth System Sciences. These data are important to determine the status and the changes in the climate system. Additionally some relevant re-analysis data are included, which are modeled on the basis of observational data. ICDC cooperates with the \"Zentrum fΓΌr Nachhaltiges Forschungsdatenmanagement \"https://www.fdr.uni-hamburg.de/ to publish observational data with a doi.",
"homepage": "https://www.cen.uni-hamburg.de/en/icdc/data.html",
"name": "Integrated Climate Data Center",
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"ICDC"
],
"xrefs": {
"fairsharing": "FAIRsharing.d95034"
}
}
},
"icdo": {
"bartoc": {
"abbreviation": "ICD-O",
"description": "Used principally in tumour or cancer registries for coding the site (topography) and the histology (morphology) of neoplasms, usually obtained from a pathology report.\n\nA multi-axial classification of the site, morphology, behaviour, and grading of neoplasms. The topography axis uses the ICD-10 classification of malignant neoplasms (except those categories which relate to secondary neoplasms and to specified morphological types of tumours) for all types of tumours, thereby providing greater site detail for non-malignant tumours than is provided in ICD-10. In contrast to ICD-10, the ICD-O includes topography for sites of haematopoietic and reticuloendothelial tumours. The morphology axis provides five-digit codes ranging from M-8000/0 to M-9989/3. The first four digits indicate the specific histological term. The fifth digit after the slash (/) is the behaviour code, which indicates whether a tumour is malignant, benign, in situ, or uncertain (whether benign or malignant). A separate one-digit code is also provided for histologic grading (differentiation).",
"homepage": "http://www.who.int/classifications/icd/adaptations/oncology/",
"name": "International Classification of Diseases for Oncology",
"prefix": "445",
"wikidata_database": "Q1430635"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases",
"example": "9861/3",
"hl7": {
"description": "This branch node heads up the different versions of the International Classification of Diseases for Oncology, which must be identified as different coding systems under HL7 terminology rules.",
"homepage": "http://www.who.int/en/",
"name": "International Classification of Diseases for Oncology: ICD-O",
"organization": "World Health Organization (WHO)",
"preferred_prefix": "icd-o",
"prefix": "2.16.840.1.113883.6.43",
"status": "Complete"
},
"homepage": "https://www.who.int/classifications/icd/adaptations/oncology/en/",
"mappings": {
"bartoc": "445",
"hl7": "2.16.840.1.113883.6.43",
"prefixcommons": "icdo",
"wikidata": "P563"
},
"name": "International Classification of Diseases for Oncology",
"pattern": "^[8-9]\\d{3}(/[0-3])?$",
"prefixcommons": {
"bioportal": "1670",
"description": "Ontology of Oncology as based on CDC SEER's ICDO-3 Code classification",
"example": "M-8272/O",
"name": "International Classification of Diseases for Oncology",
"pattern": "^[A-Z0-9]+\\/[0-9]+$",
"prefix": "icdo",
"synonyms": [
"icdo3",
"icd-o"
]
},
"synonyms": [
"ICD-O",
"ICDO"
],
"uri_format": "http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1",
"wikidata": {
"description": "International Classification of Diseases for Oncology",
"example": [
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"M9860/3"
],
"name": "ICD-O",
"pattern": "^[8-9]\\d{3}(/[0-3])?$",
"prefix": "P563",
"uri_format": "http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1"
}
},
"iceberg.cime": {
"contact": {
"email": "hyou@sjtu.edu.cn",
"name": "Hong-Yu Ou",
"orcid": "0000-0001-9439-1660"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements.",
"example": "6",
"homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_CIME.php?type=alpha&alpha=100",
"keywords": [
"biology",
"genomics"
],
"name": "ICEberg cis-integrative and mobilizable element",
"part_of": "iceberg",
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1093/nar/gky1123",
"pmc": "PMC6323972",
"pubmed": "30407568",
"title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements",
"year": 2019
},
{
"doi": "10.1093/nar/gkr846",
"pmc": "PMC3244999",
"pubmed": "22009673",
"title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria",
"year": 2011
}
],
"uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php?cime_id=$1_CIME"
},
"iceberg.element": {
"biocontext": {
"prefix": "ICEBERG.ELEMENT"
},
"homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=alpha&alpha=100",
"mappings": {
"biocontext": "ICEBERG.ELEMENT",
"miriam": "iceberg.element",
"n2t": "iceberg.element"
},
"miriam": {
"deprecated": false,
"description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements.",
"homepage": "http://db-mml.sjtu.edu.cn/ICEberg/",
"id": "00000469",
"name": "ICEberg element",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "iceberg.element",
"sampleId": "100",
"uri_format": "http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1"
},
"n2t": {
"description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements.",
"example": "100",
"homepage": "http://db-mml.sjtu.edu.cn/ICEberg/",
"name": "ICEberg element at Shanghai Jiaotong University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "iceberg.element",
"uri_format": "http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1"
},
"name": "ICEberg integrative and conjugative element",
"part_of": "iceberg",
"publications": [
{
"doi": "10.1093/nar/gky1123",
"pmc": "PMC6323972",
"pubmed": "30407568",
"title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements",
"year": 2019
},
{
"doi": "10.1093/nar/gkr846",
"pmc": "PMC3244999",
"pubmed": "22009673",
"title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria",
"year": 2011
}
],
"synonyms": [
"iceberg.ice"
],
"uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=$1"
},
"iceberg.family": {
"biocontext": {
"prefix": "ICEBERG.FAMILY"
},
"contact": {
"email": "hyou@sjtu.edu.cn",
"name": "Hong-Yu Ou",
"orcid": "0000-0001-9439-1660"
},
"homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_fam.php",
"mappings": {
"biocontext": "ICEBERG.FAMILY",
"miriam": "iceberg.family",
"n2t": "iceberg.family"
},
"miriam": {
"deprecated": false,
"description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families.",
"homepage": "http://db-mml.sjtu.edu.cn/ICEberg/",
"id": "00000470",
"name": "ICEberg family",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "iceberg.family",
"sampleId": "1",
"uri_format": "http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$1"
},
"n2t": {
"description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families.",
"example": "1",
"homepage": "http://db-mml.sjtu.edu.cn/ICEberg/",
"name": "ICEberg family at Shanghai Jiaotong University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "iceberg.family",
"uri_format": "http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$1"
},
"part_of": "iceberg",
"publications": [
{
"doi": "10.1093/nar/gky1123",
"pmc": "PMC6323972",
"pubmed": "30407568",
"title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements",
"year": 2019
},
{
"doi": "10.1093/nar/gkr846",
"pmc": "PMC3244999",
"pubmed": "22009673",
"title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria",
"year": 2011
}
],
"uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id=$1"
},
"iceberg.ime": {
"contact": {
"email": "hyou@sjtu.edu.cn",
"name": "Hong-Yu Ou",
"orcid": "0000-0001-9439-1660"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements.",
"example": "1",
"homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_IME.php?type=alpha&alpha=100",
"keywords": [
"biology",
"genomics"
],
"name": "ICEberg integrative and mobilizable element",
"part_of": "iceberg",
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1093/nar/gky1123",
"pmc": "PMC6323972",
"pubmed": "30407568",
"title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements",
"year": 2019
},
{
"doi": "10.1093/nar/gkr846",
"pmc": "PMC3244999",
"pubmed": "22009673",
"title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria",
"year": 2011
}
],
"uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.php?ime_id=$1_IME"
},
"iceo": {
"aberowl": {
"description": "ICEO is an integrated biological ontology for the description of bacterial integrative and conjugative elements (ICEs).",
"download_owl": "http://aber-owl.net/media/ontologies/ICEO/22/iceo.owl",
"homepage": "https://github.com/ontoice/ICEO",
"name": "Integrative and Conjugative Element Ontology",
"prefix": "ICEO"
},
"bioportal": {
"homepage": "https://github.com/ontoice/ICEO",
"name": "Integrative and Conjugative Element Ontology",
"prefix": "ICEO",
"version": "2.1"
},
"example": "0000712_1",
"example_extras": [
"0000712"
],
"mappings": {
"aberowl": "ICEO",
"bioportal": "ICEO",
"obofoundry": "iceo",
"ols": "iceo",
"ontobee": "ICEO"
},
"obofoundry": {
"contact": "liumeng94@sjtu.edu.cn",
"contact.github": "Lemon-Liu",
"contact.label": "Meng LIU",
"contact.orcid": "0000-0003-3781-6962",
"deprecated": false,
"description": "ICEO is an integrated biological ontology for the description of bacterial integrative and conjugative elements (ICEs).",
"domain": "microbiology",
"download.owl": "http://purl.obolibrary.org/obo/iceo.owl",
"homepage": "https://github.com/ontoice/ICEO",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Integrative and Conjugative Element Ontology",
"preferredPrefix": "ICEO",
"prefix": "iceo",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/35058462",
"title": "ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements"
}
],
"repository": "https://github.com/ontoice/ICEO"
},
"ols": {
"description": "A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning.",
"download_owl": "http://purl.obolibrary.org/obo/iceo.owl",
"homepage": "https://github.com/ontoice/ICEO",
"name": "ICEO: Ontology of Integrative and Conjugative Elements",
"prefix": "iceo",
"version": "2.1"
},
"ontobee": {
"library": "Library",
"name": "Integrative and Conjugative Element Ontology",
"prefix": "ICEO"
},
"pattern": "^\\d{7}(_\\d)?$",
"publications": [
{
"doi": "10.1038/s41597-021-01112-5",
"pmc": "PMC8776819",
"pubmed": "35058462",
"title": "ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements",
"year": 2022
}
],
"uri_format": "http://purl.obolibrary.org/obo/ICEO_$1"
},
"icepo": {
"contact": {
"email": "pascale.gaudet@isb-sib.ch",
"github": "pgaudet",
"name": "Pascale Gaudet",
"orcid": "0000-0003-1813-6857"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. ",
"download_obo": "https://download.nextprot.org/pub/current_release/controlled_vocabularies/icepo.obo",
"example": "0000002",
"homepage": "https://download.nextprot.org/pub/current_release/controlled_vocabularies/",
"name": "Ion Channel Electrophysiology Ontology",
"pattern": "^\\d{7}$",
"publications": [
{
"pmc": "PMC4823818",
"title": "ICEPO: the ion channel electrophysiology ontology"
}
],
"twitter": "neXtProt_news",
"uri_format": "https://biopragmatics.github.io/providers/icepo/$1"
},
"icf": {
"aberowl": {
"description": "The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. These domains are classified from body, individual and societal perspectives by means of two lists: a list of body functions and structure, and a list of domains of activity and participation. Since an individual's functioning and disability occurs in a context, the ICF also includes a list of environmental factors.
Source: http://www.who.int/classifications/icf/en/",
"download_owl": "http://aber-owl.net/media/ontologies/ICF/3/icf.owl",
"homepage": "http://www.who.int/classifications/icf/en/",
"name": "International Classification of Functioning, Disability and Health",
"prefix": "ICF",
"version": "1.0.2"
},
"bioportal": {
"contact": {
"email": "info@who.int",
"name": "The World Health Organization"
},
"description": "The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. These domains are classified from body, individual and societal perspectives by means of two lists: a list of body functions and structure, and a list of domains of activity and participation. Since an individual's functioning and disability occurs in a context, the ICF also includes a list of environmental factors.
Source: http://www.who.int/classifications/icf/en/",
"homepage": "http://www.who.int/classifications/icf/en/",
"name": "International Classification of Functioning, Disability and Health",
"prefix": "ICF",
"version": "1.0.2"
},
"comment": "This might be possible to roll directly into ICD11",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. As the functioning and disability of an individual occurs in a context, ICF also includes a list of environmental factors. ICF is the WHO framework for measuring health and disability at both individual and population levels.",
"example": "326705068",
"fairsharing": {
"abbreviation": "ICF",
"description": "The International Classification of Functioning, Disability and Health (ICF) is a classification of health and health-related domains. As the functioning and disability of an individual occurs in a context, ICF also includes a list of environmental factors. ICF is the WHO framework for measuring health and disability at both individual and population levels. ICF was officially endorsed by all 191 WHO Member States in the Fifty-fourth World Health Assembly on 22 May 2001 (resolution WHA 54.21) as the international standard to describe and measure health and disability.",
"domains": [
"Electronic health record"
],
"homepage": "https://www.who.int/standards/classifications/international-classification-of-functioning-disability-and-health",
"license": "https://creativecommons.org/licenses/by-nc-sa/3.0/igo",
"name": "International Classification of Functioning, Disability and Health",
"prefix": "FAIRsharing.7rngj0",
"subjects": [
"Medicine",
"Health Science",
"Primary Health Care",
"Biomedical Science"
]
},
"hl7": {
"description": "ICF describes how people live with their health condition. ICF is a classification of health and health related domains that describe body functions and structures, activities and participation. The domains are classified from body, individual and societal perspectives. Since an individual's functioning and disability occurs in a context, ICF also includes a list of environmental factors. ICF is useful to understand and measure health outcomes. It can be used in clinical settings, health services or surveys at the individual or population level. Thus ICF complements ICD-10 , The International Statistical Classification of Diseases and Related Health Problems and therefore is looking beyond mortality and disease.",
"homepage": "http://www.who.int/classifications/icf/en/",
"name": "International Classification of Function",
"organization": "World Health Organisation",
"preferred_prefix": "icf",
"prefix": "2.16.840.1.113883.6.254",
"status": "Complete"
},
"homepage": "https://icd.who.int/dev11/l-icf/en",
"mappings": {
"aberowl": "ICF",
"bioportal": "ICF",
"fairsharing": "FAIRsharing.7rngj0",
"hl7": "2.16.840.1.113883.6.254"
},
"name": "International Classification of Functioning, Disability and Health",
"pattern": "^\\d+$",
"uri_format": "http://id.who.int/icd/entity/$1"
},
"iclc": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "http://www.iclc.it",
"name": "Interlab Cell Line Collection",
"prefix": "ICLC",
"uri_format": "http://www.iclc.it/details/det_list.php?line_id=$1"
},
"example": "ATL98012",
"mappings": {
"cellosaurus": "ICLC"
},
"pattern": "^\\w{3}\\d+$"
},
"icldb": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://entomology.ca.uky.edu/aginsectcellsdatabase",
"name": "Insect Cell Lines DataBase",
"prefix": "ICLDB",
"uri_format": "https://entomology.ca.uky.edu/content/$1"
},
"contact": {
"email": "surjeet.arya@uky.edu",
"name": "Surjeet Kumar Arya",
"orcid": "0000-0002-2212-4771"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "We have developed an online database describing the known cell lines from Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera that originated from crop pest insects. Cell line information has been primarily obtained from previous compilations of insect cell lines. (from homepage)",
"example": "64ba",
"homepage": "https://entomology.ca.uky.edu/aginsectcellsdatabase",
"mappings": {
"cellosaurus": "ICLDB"
},
"name": "Insect Cell Line Database",
"uri_format": "https://entomology.ca.uky.edu/content/$1"
},
"ico": {
"aberowl": {
"description": "An ontology of clinical informed consents",
"download_owl": "http://aber-owl.net/media/ontologies/ICO/16/ico.owl",
"homepage": "https://github.com/ICO-ontology/ICO",
"name": "Informed Consent Ontology",
"prefix": "ICO"
},
"biocontext": {
"prefix": "ICO"
},
"bioportal": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "Informed Consent Ontology (ICO) is a community-based ontology in the domain of informed consent. It is an OBO library ontology and developed by following the OBO Foundry principles.",
"homepage": "https://github.com/ICO-ontology/ICO",
"name": "Informed Consent Ontology",
"prefix": "ICO",
"publication": "http://ceur-ws.org/Vol-1327/icbo2014_paper_54.pdf",
"version": "1.0.187"
},
"example": "0000066",
"fairsharing": {
"abbreviation": "ICO",
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun He",
"orcid": "0000-0001-9189-9661"
},
"description": "Informed Consent Ontology (ICO) represents the documentations and processes involved in informed consent. ICO aims to support informed consent data integration and reasoning in the clinical research space. The core terms of ICO covers informed consent forms, the component inside the informed consent form, and various informed consent processes.",
"homepage": "https://github.com/ICO-ontology/ICO",
"name": "Informed Consent Ontology",
"prefix": "FAIRsharing.b9znd5",
"repository": "https://github.com/ICO-ontology/ICO/issues",
"subjects": [
"Medicine",
"Clinical Studies",
"Health Science",
"Biomedical Science"
]
},
"mappings": {
"aberowl": "ICO",
"biocontext": "ICO",
"bioportal": "ICO",
"fairsharing": "FAIRsharing.b9znd5",
"obofoundry": "ico",
"ols": "ico",
"ontobee": "ICO"
},
"obofoundry": {
"appears_in": [
"scdo"
],
"contact": "yongqunh@med.umich.edu",
"contact.github": "yongqunh",
"contact.label": "Yongqun Oliver He",
"contact.orcid": "0000-0001-9189-9661",
"deprecated": false,
"description": "An ontology of clinical informed consents",
"domain": "investigations",
"download.owl": "http://purl.obolibrary.org/obo/ico.owl",
"homepage": "https://github.com/ICO-ontology/ICO",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Informed Consent Ontology",
"preferredPrefix": "ICO",
"prefix": "ico",
"repository": "https://github.com/ICO-ontology/ICO"
},
"ols": {
"description": "The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field.",
"download_owl": "http://purl.obolibrary.org/obo/ico.owl",
"homepage": "https://github.com/ICO-ontology/ICO",
"name": "Informed Consent Ontology (ICO)",
"prefix": "ico",
"version": "1.0.187"
},
"ontobee": {
"library": "Library",
"name": "Informed Consent Ontology",
"prefix": "ICO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/ICO_$1"
},
"ideal": {
"biocontext": {
"prefix": "IDEAL"
},
"contact": {
"email": "sfukuchi@maebashi-it.ac.jp",
"github": "sfukuchi",
"name": "Satoshi Fukuchi",
"orcid": "0000-0002-5705-3061"
},
"fairsharing": {
"abbreviation": "IDEAL",
"description": "IDEAL (Intrinsically Disordered proteins with Extensive Annotations and Literature) is a collection of experimentally-verified intrinsically disordered proteins (IDPs) that cannot adopt stable globular structures under physiological conditions. IDEAL contains manually curated annotations on IDPs in locations, structures, and functional sites such as protein binding regions and post-translational modification sites together with references and structural domain assignments.",
"homepage": "http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/",
"license": "CC-BY-4.0",
"name": "Intrinsically Disordered proteins with Extensive Annotations and Literature",
"prefix": "FAIRsharing.h3y42f",
"publications": [
{
"doi": "10.1093/nar/gkt1010",
"pubmed_id": 24178034,
"title": "IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners."
}
],
"subjects": [
"Biology"
]
},
"homepage": "https://www.ideal-db.org",
"integbio": {
"alt_name": "Intrinsically Disordered proteins with Exten sive Annotations and Literatures",
"description": "This is a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references, and structural domain assignment. This database allows to browse by a list or search using keywords or BLAST. Data are downloadable with a XML file.",
"fairsharing": "biodbcore-000052",
"homepage": "https://www.ideal-db.org",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie",
"3D structure"
],
"maintainer": "IDEAL Development Team",
"name": "IDEAL",
"prefix": "nbdc01456",
"pubmeds": [
"22067451"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"mappings": {
"biocontext": "IDEAL",
"fairsharing": "FAIRsharing.h3y42f",
"integbio": "nbdc01456",
"miriam": "ideal",
"n2t": "ideal",
"pathguide": "701",
"uniprot": "DB-0251"
},
"miriam": {
"deprecated": false,
"description": "IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments.",
"homepage": "http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/",
"id": "00000398",
"name": "IDEAL",
"namespaceEmbeddedInLui": false,
"pattern": "^IID\\d+$",
"prefix": "ideal",
"sampleId": "IID00001",
"uri_format": "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1"
},
"n2t": {
"description": "IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments.",
"example": "IID00001",
"homepage": "http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/",
"name": "IDEAL at Maebashi Institute of Technology",
"namespaceEmbeddedInLui": false,
"pattern": "^IID\\d+$",
"prefix": "ideal",
"uri_format": "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/idealItem.php?id=$1"
},
"name": "Intrinsically Disordered proteins with Extensive Annotations and Literature",
"pathguide": {
"abbreviation": "IDEAL",
"homepage": "http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/",
"name": "Intrinsically Disordered proteins with Extensive Annotations and Literature",
"prefix": "701"
},
"publications": [
{
"doi": "10.1093/nar/gkt1010",
"pmc": "PMC3965115",
"pubmed": "24178034",
"title": "IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners",
"year": 2013
}
],
"uniprot": {
"abbreviation": "IDEAL",
"category": "Family and domain databases",
"homepage": "https://www.ideal-db.org/",
"name": "Intrinsically Disordered proteins with Extensive Annotations and Literature",
"prefix": "DB-0251",
"publications": [
{
"doi": "10.1093/nar/gkt1010",
"pubmed": "24178034"
}
],
"uri_format": "https://www.ideal-db.org/ideal.php?id=$1"
}
},
"ido": {
"aberowl": {
"download_owl": "http://aber-owl.net/media/ontologies/IDO/12/ido.owl",
"homepage": "http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology",
"name": "Infectious Disease Ontology",
"prefix": "IDO"
},
"biocontext": {
"prefix": "IDO"
},
"bioportal": {
"contact": {
"email": "johnbeverley2021@u.northwestern.edu",
"name": "John Beverley"
},
"description": "The IDO ontologies are designed as a set of interoperable ontologies that will together provide coverage of the infectious disease domain. At the core of the set is a general Infectious Disease Ontology (IDO-Core) of entities relevant to both biomedical and clinical aspects of most infectious diseases. Sub-domain specific extensions of IDO-Core complete the set providing ontology coverage of entities relevant to specific pathogens or diseases.
To import,
Latest version: http://purl.obolibrary.org/obo/ido.owl
This version (2010-12-02): http://purl.obolibrary.org/obo/ido/2010-12-02/ido.owl
Previous versions:
2010-05-26 http://purl.obolibrary.org/obo/ido/2010-05-26/ido.owl
2009-08-14 http://purl.obolibrary.org/obo/ido/2009-08-14/ido.owl
Latest release notes at http://infectiousdiseaseontology.org/page/Download
Please note: The ontology metrics displayed by BioPortal do not distinguish IDO-developed terms from terms imported from other ontologies.",
"homepage": "http://infectiousdiseaseontology.org",
"name": "Infectious Disease Ontology",
"prefix": "IDO",
"publication": "http://infectiousdiseaseontology.org/page/Publications",
"version": "8-3-20"
},
"contributor_extras": [
{
"email": "github@yohannparis.com",
"github": "YohannParis",
"name": "Yohann Paris",
"orcid": "0009-0006-6049-1392"
}
],
"fairsharing": {
"abbreviation": "IDO",
"contact": {
"email": "Lindsay.Cowell@utsouthwestern.edu",
"name": "Lindsay Cowell",
"orcid": "0000-0003-1617-8244"
},
"description": "The IDO ontologies are designed as a set of interoperable ontologies that will together provide coverage of the infectious disease domain. At the core of the set is a general Infectious Disease Ontology (IDO-Core) of entities relevant to both biomedical and clinical aspects of most infectious diseases. Sub-domain specific extensions of IDO-Core complete the set providing ontology coverage of entities relevant to specific pathogens or diseases. Please note that, while the ontology remains available at https://github.com/infectious-disease-ontology/infectious-disease-ontology, it has not been updated in 5 years and should be used with care. Further, the original homepages provided by the resource developers (http://infectiousdiseaseontology.org/ and https://www.bioontology.org//wiki/Index.php/Infectious_Disease_Ontology) are either unavailable or empty.",
"domains": [
"Disease process modeling",
"Disease",
"Classification"
],
"homepage": "https://github.com/infectious-disease-ontology/infectious-disease-ontology",
"license": "https://creativecommons.org/licenses/by/3.0/us",
"name": "Infectious Disease Ontology Core",
"prefix": "FAIRsharing.aae3v6",
"publications": [
{
"doi": "10.1186/s13326-021-00245-1",
"pubmed": "34275487",
"title": "The Infectious Disease Ontology in the age of COVID-19",
"year": 2021
}
],
"repository": "https://github.com/infectious-disease-ontology/infectious-disease-ontology",
"subjects": [
"Molecular Infection Biology",
"Biomedical Science",
"Preclinical Studies"
]
},
"mappings": {
"aberowl": "IDO",
"biocontext": "IDO",
"bioportal": "IDO",
"fairsharing": "FAIRsharing.aae3v6",
"miriam": "ido",
"n2t": "ido",
"obofoundry": "ido",
"ols": "ido",
"ontobee": "IDO"
},
"miriam": {
"deprecated": false,
"description": "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases.",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/ido",
"id": "00000677",
"name": "Infectious Disease Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "ido",
"sampleId": "0000504",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/ido/terms?obo_id=IDO:$1"
},
"n2t": {
"description": "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases.",
"example": "0000504",
"homepage": "https://www.ebi.ac.uk/ols/ontologies/ido",
"name": "IDO through OLS",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "ido",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1"
},
"obofoundry": {
"appears_in": [
"scdo"
],
"contact": "Lindsay.Cowell@utsouthwestern.edu",
"contact.github": "lgcowell",
"contact.label": "Lindsay Cowell",
"contact.orcid": "0000-0003-1617-8244",
"deprecated": false,
"description": "A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology that hosts terms of general relevance across the domain, while extension ontologies host terms to specific to a particular part of the domain.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/ido.owl",
"homepage": "http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology",
"license": "CC BY 3.0",
"license.url": "https://creativecommons.org/licenses/by/3.0/",
"name": "Infectious Disease Ontology",
"preferredPrefix": "IDO",
"prefix": "ido",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/34275487",
"title": "The Infectious Disease Ontology in the age of COVID-19"
}
],
"repository": "https://github.com/infectious-disease-ontology/infectious-disease-ontology"
},
"ols": {
"description": "A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology that hosts terms of general relevance across the domain, while extension ontologies host terms to specific to a particular part of the domain.",
"download_owl": "http://purl.obolibrary.org/obo/ido.owl",
"homepage": "http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology",
"name": "Infectious Disease Ontology",
"prefix": "ido",
"version": "2017-11-03",
"version.iri": "http://purl.obolibrary.org/obo/ido/2017-11-03/ido.owl"
},
"ontobee": {
"library": "Library",
"name": "Infectious Disease Ontology",
"prefix": "IDO"
},
"pattern": "^\\d{7}$",
"providers": [
{
"code": "obo.1",
"description": "This incorrect encoding was found inside IDO-COVID-19",
"homepage": "http://purl.obolibrary.org",
"name": "Nonstandard OBO PURL",
"uri_format": "http://purl.obolibrary.org/obo/ido.owl/IDO_$1"
}
],
"publications": [
{
"doi": "10.1186/s13326-021-00245-1",
"pmc": "PMC8286442",
"pubmed": "34275487",
"title": "The Infectious Disease Ontology in the age of COVID-19",
"year": 2021
}
],
"uri_format": "http://purl.obolibrary.org/obo/IDO_$1"
},
"idocovid19": {
"aberowl": {
"description": "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease.",
"download_owl": "http://aber-owl.net/media/ontologies/IDO-COVID-19/2/ido-covid-19.owl",
"homepage": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19",
"name": "The COVID-19 Infectious Disease Ontology",
"prefix": "IDO-COVID-19",
"version": "8-3-2020"
},
"bioportal": {
"contact": {
"email": "johnbeverley2021@u.northwestern.edu",
"name": "John Beverley"
},
"description": "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease.",
"homepage": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19",
"name": "The COVID-19 Infectious Disease Ontology",
"prefix": "IDO-COVID-19",
"version": "8-3-2020"
},
"contact": {
"email": "johnbeverley2021@u.northwestern.edu",
"github": "johnbeve",
"name": "John Beverly",
"orcid": "0000-0002-1118-1738"
},
"download_owl": "https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19",
"example": "0001191",
"mappings": {
"aberowl": "IDO-COVID-19",
"bioportal": "IDO-COVID-19",
"ols": "idocovid19"
},
"ols": {
"contact": "johnbeverley2021@u.northwestern.edu",
"description": "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease.",
"homepage": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19",
"name": "The COVID-19 Infectious Disease Ontology",
"prefix": "idocovid19",
"version": "2020-07-21",
"version.iri": "http://purl.obolibrary.org/obo/2020-21-07/ido-covid-19.owl"
},
"pattern": "^\\d{7}$",
"providers": [
{
"code": "obo1",
"description": "This variation uses incorrect usage of dashes instead of underscores",
"homepage": "http://purl.obolibrary.org",
"name": "Incorrect OBO PURL variation 1",
"uri_format": "http://purl.obolibrary.org/obo/IDO-COVID-19_$1"
}
],
"repository": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19",
"uri_format": "http://purl.obolibrary.org/obo/COVIDO_$1"
},
"idoden": {
"aberowl": {
"description": "An ontology for dengue fever.",
"download_owl": "http://aber-owl.net/media/ontologies/IDODEN/6/idoden.owl",
"homepage": "http://code.google.com/p/dengue-fever-ontology/",
"name": "Dengue Fever Ontology",
"prefix": "IDODEN",
"version": "0.15b"
},
"bioportal": {
"contact": {
"email": "elvira@imbb.forth.gr",
"name": "Elvira Mitraka"
},
"description": "An ontology for dengue fever.",
"homepage": "http://code.google.com/p/dengue-fever-ontology/",
"name": "Dengue Fever Ontology",
"prefix": "IDODEN",
"version": "0.15b"
},
"contact": {
"email": "elvira@imbb.forth.gr",
"name": "Elvira Mitraka",
"orcid": "0000-0003-0719-3485"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology for dengue fever.",
"example": "0003463",
"fairsharing": {
"abbreviation": "IDODEN",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://code.google.com/p/dengue-fever-ontology/",
"name": "Dengue Fever Ontology",
"prefix": "FAIRsharing.askzq4",
"subjects": [
"Medicine"
]
},
"homepage": "https://bioportal.bioontology.org/ontologies/IDODEN",
"mappings": {
"aberowl": "IDODEN",
"bioportal": "IDODEN",
"fairsharing": "FAIRsharing.askzq4"
},
"name": "Dengue Fever Ontology",
"pattern": "^\\d{7}$",
"references": [
"https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003479"
],
"uri_format": "http://purl.bioontology.org/ontology/IDODEN_$1"
},
"idog": {
"contact": {
"email": "baoym@big.ac.cn",
"name": "Yiming Bao",
"orcid": "0000-0002-9922-9723"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Provides the worldwide dog research community a variety of data services including access to genes, genomes, SNPs, breed/disease Traits, gene expression experiments, dog-guman homology, and literatur. In addition, iDog provides online tools for performing genomic data visualization and analyses.",
"example": "4",
"homepage": "https://ngdc.cncb.ac.cn/idog/",
"integbio": {
"description": "iDog is an integrated resource for domestic dog (Canis lupus familiaris) and wild canids. It includes information about Genes, Genomes, SNPs, Breed/Disease Traits, Gene Expressions, GO Function Annotations, Dog-Human Homolog Diseases and Literatures. In addition, it provides online tools for performing genomic data visualization and analyses.",
"homepage": "https://bigd.big.ac.cn/idog/",
"information_keywords": [
"Sequence",
"Expression",
"Phenotype",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences",
"name": "iDog",
"prefix": "nbdc02480",
"pubmeds": [
"30371881"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Organism",
"Health/Disease"
]
},
"license": "CC-BY-4.0",
"mappings": {
"integbio": "nbdc02480",
"re3data": "r3d100012176"
},
"name": "Integrated Resource for Domestic Dog",
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1093/nar/gky1041",
"pmc": "PMC6323916",
"pubmed": "30371881",
"title": "iDog: an integrated resource for domestic dogs and wild canids",
"year": 2019
}
],
"re3data": {
"description": "iDog, an integrated resource for domestic dog (Canis lupus familiaris) and wild canids, provides the worldwide dog research community a variety of data services. This includes Genes, Genomes, SNPs, Breed/Disease Traits, Gene Expressions, Single Cell, Dog-Human Homolog Diseases and Literatures. In addition, iDog provides Online tools for performing genomic data visualization and analyses.",
"homepage": "https://ngdc.cncb.ac.cn/idog/",
"name": "iDog",
"prefix": "r3d100012176",
"synonyms": [
"DoGSD",
"Dog Genome SNP Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.exc0vp"
}
},
"references": [
"https://github.com/biopragmatics/bioregistry/pull/725"
],
"uri_format": "https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=$1"
},
"idomal": {
"aberowl": {
"description": "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.",
"download_owl": "http://aber-owl.net/media/ontologies/IDOMAL/187/idomal.owl",
"homepage": "https://www.vectorbase.org/ontology-browser",
"name": "Malaria Ontology",
"prefix": "IDOMAL"
},
"biocontext": {
"prefix": "IDOMAL"
},
"bioportal": {
"contact": {
"email": "topalis@imbb.forth.gr",
"name": "Pantelis Topalis"
},
"description": "An application ontology for malaria extending the infectious disease ontology (IDO)",
"homepage": "http://anobase.vectorbase.org/idomal/IDOMAL.obo",
"name": "Malaria Ontology",
"prefix": "IDOMAL",
"publication": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2925367/?tool=pubmed",
"version": "1.3.9"
},
"download_obo": "http://purl.obolibrary.org/obo/idomal.obo",
"example": "0002350",
"example_extras": [
"50000015"
],
"fairsharing": {
"abbreviation": "IDOMAL",
"contact": {
"email": "topalis@imbb.forth.gr",
"name": "Pantelis Topalis",
"orcid": "0000-0002-1635-4810"
},
"description": "An application ontology for malaria extending the infectious disease ontology (IDO). With about half a billion cases, of which nearly one million fatal ones, malaria constitutes one of the major infectious diseases worldwide. A recently revived effort to eliminate the disease also focuses on IT resources for its efficient control, which prominently includes the control of the mosquito vectors that transmit the Plasmodium pathogens. As part of this effort, IDOMAL has been developed and it is continually being updated.",
"domains": [
"Malaria",
"Pathogen",
"Intervention design",
"Disease"
],
"homepage": "https://www.vectorbase.org/ontology-browser",
"license": "CC0-1.0",
"name": "Infection Disease Ontology Malaria",
"prefix": "FAIRsharing.2q8c28",
"publications": [
{
"doi": "10.1186/2041-1480-4-16",
"pubmed": "24034841",
"title": "IDOMAL: the malaria ontology revisited",
"year": 2013
},
{
"doi": "10.1186/1475-2875-9-230",
"pubmed": "20698959",
"title": "IDOMAL: an ontology for malaria",
"year": 2010
}
],
"subjects": [
"Molecular Infection Biology",
"Life Science",
"Biomedical Science"
],
"twitter": "VectorBase"
},
"mappings": {
"aberowl": "IDOMAL",
"biocontext": "IDOMAL",
"bioportal": "IDOMAL",
"fairsharing": "FAIRsharing.2q8c28",
"obofoundry": "idomal",
"ols": "idomal",
"ontobee": "IDOMAL"
},
"obofoundry": {
"appears_in": [
"scdo"
],
"contact": "topalis@imbb.forth.gr",
"contact.label": "Pantelis Topalis",
"deprecated": true,
"description": "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.",
"domain": "health",
"download.obo": "http://purl.obolibrary.org/obo/idomal.obo",
"download.owl": "http://purl.obolibrary.org/obo/idomal.owl",
"homepage": "https://www.vectorbase.org/ontology-browser",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Malaria Ontology",
"prefix": "idomal",
"repository": "https://github.com/VEuPathDB-ontology/IDOMAL"
},
"ols": {
"description": "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.",
"download_owl": "http://purl.obolibrary.org/obo/idomal.owl",
"homepage": "https://www.vectorbase.org/ontology-browser",
"name": "Malaria Ontology",
"prefix": "idomal",
"version": "2015-03-16",
"version.iri": "http://purl.obolibrary.org/obo/idomal/2015-03-16/idomal.owl"
},
"ontobee": {
"library": "Library",
"name": "Malaria Ontology",
"prefix": "IDOMAL"
},
"pattern": "^(5?)\\d{7}$",
"publications": [
{
"doi": "10.1186/2041-1480-4-16",
"pmc": "PMC3848731",
"pubmed": "24034841",
"title": "IDOMAL: the malaria ontology revisited",
"year": 2013
},
{
"doi": "10.1186/1475-2875-9-230",
"pmc": "PMC2925367",
"pubmed": "20698959",
"title": "IDOMAL: an ontology for malaria",
"year": 2010
}
]
},
"idoo": {
"mappings": {
"miriam": "idoo",
"n2t": "idoo"
},
"miriam": {
"deprecated": false,
"description": "Identifiers.org Ontology",
"homepage": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology",
"id": "00000683",
"name": "Identifiers.org Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9a-zA-Z]+$",
"prefix": "idoo",
"sampleId": "DataCollection",
"uri_format": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1"
},
"n2t": {
"description": "Identifiers.org Ontology",
"example": "DataCollection",
"homepage": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology",
"name": "Identifiers.org Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9a-zA-Z]+$",
"prefix": "idoo",
"uri_format": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1"
}
},
"idot": {
"biocontext": {
"prefix": "idot"
},
"homepage": "http://biomodels.net/vocab/idot.rdf",
"mappings": {
"biocontext": "idot",
"miriam": "idot",
"n2t": "idot"
},
"miriam": {
"deprecated": false,
"description": "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.",
"homepage": "https://identifiers.org/",
"id": "00000519",
"name": "Identifiers.org Terms",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z]+$",
"prefix": "idot",
"sampleId": "identifierPattern",
"uri_format": "https://biomodels.net/vocab/idot.rdf#$1"
},
"n2t": {
"description": "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.",
"example": "identifierPattern",
"homepage": "https://identifiers.org/",
"name": "IdoT via biomodels.net",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z]+$",
"prefix": "idot",
"uri_format": "https://biomodels.net/vocab/idot.rdf#$1"
},
"preferred_prefix": "idot",
"uri_format": "https://biomodels.net/vocab/idot.rdf#$1"
},
"idpo": {
"contact": {
"email": "f.quaglia@ibiom.cnr.it",
"github": "federicaquaglia",
"name": "Federica Quaglia",
"orcid": "0000-0002-0341-4888"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR.",
"example": "00056",
"homepage": "https://www.disprot.org/ontology",
"keywords": [
"protein structure",
"proteins",
"structural biochemistry",
"structural bioinformatics"
],
"name": "Intrinsically Disordered Proteins Ontology",
"pattern": "^\\d{5}$",
"uri_format": "https://www.disprot.org/idpo/IDPO:$1"
},
"idr": {
"fairsharing": {
"abbreviation": "IDR",
"contact": {
"email": "j.a.moore@dundee.ac.uk",
"name": "Josh Moore",
"orcid": "0000-0003-4028-811X"
},
"description": "IDR is a prototype platform for publishing, mining and integrating bioimaging data at scale, following the Euro-BioImaging/ELIXIR imaging strategy using the OMERO and Bio-Formats open source software built by the Open Microscopy Environment. Deployed on an OpenStack cloud running on the EMBL-EBIβs Embassy resource, it includes image data linked to independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super-resolution microscopy, and digital pathology.",
"homepage": "https://idr.openmicroscopy.org",
"name": "Image Data Resource",
"prefix": "FAIRsharing.6wf1zw",
"publications": [
{
"doi": "10.1038/nmeth.4326",
"pubmed_id": 28775673,
"title": "The Image Data Resource: A Bioimage Data Integration and Publication Platform."
}
],
"subjects": [
"Botany",
"Life Science",
"Biomedical Science"
],
"twitter": "openmicroscopy"
},
"mappings": {
"fairsharing": "FAIRsharing.6wf1zw",
"miriam": "idr",
"re3data": "r3d100012435"
},
"miriam": {
"deprecated": false,
"description": "Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created βreference image\" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools.",
"homepage": "https://idr.openmicroscopy.org",
"id": "00000743",
"name": "Image Data Resource",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]{4}$",
"prefix": "idr",
"sampleId": "0001",
"uri_format": "https://idr.openmicroscopy.org/search/?query=Name:idr$1"
},
"publications": [
{
"doi": "10.1038/nmeth.4326",
"pmc": "PMC5536224",
"pubmed": "28775673",
"title": "The Image Data Resource: A Bioimage Data Integration and Publication Platform",
"year": 2017
}
],
"re3data": {
"description": "The IDR makes datasets that have never previously been accessible publicly available, allowing the community to search, view, mine and even process and analyze large, complex, multidimensional life sciences image data. Sharing data promotes the validation of experimental methods and scientific conclusions, the comparison with new data obtained by the global scientific community, and enables data reuse by developers of new analysis and processing tools.",
"homepage": "https://idr.openmicroscopy.org/about/",
"name": "Image Data Resource",
"prefix": "r3d100012435",
"synonyms": [
"IDR"
],
"xrefs": {
"fairsharing": "FAIRsharing.6wf1zw",
"omics": "13850",
"scr": "017421"
}
}
},
"iedb": {
"contact": {
"email": "rvita@liai.org",
"github": "rvita",
"name": "Randi Vita",
"orcid": "0000-0001-8957-7612"
},
"fairsharing": {
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"prefix": "IMG.TAXON"
},
"contact": {
"email": "nckyrpides@lbl.gov",
"name": "Nikos C. Kyrpides",
"orcid": "0000-0002-6131-0462"
},
"mappings": {
"biocontext": "IMG.TAXON",
"miriam": "img.taxon",
"n2t": "img.taxon",
"prefixcommons": "img.taxon"
},
"miriam": {
"deprecated": false,
"description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information.",
"homepage": "http://img.jgi.doe.gov/",
"id": "00000175",
"name": "Integrated Microbial Genomes Taxon",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "img.taxon",
"sampleId": "648028003",
"uri_format": "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1"
},
"n2t": {
"description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information.",
"example": "648028003",
"homepage": "http://img.jgi.doe.gov/",
"name": "Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "img.taxon",
"uri_format": "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1"
},
"prefixcommons": {
"description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information.",
"example": "648028003",
"keywords": [
"genome",
"taxonomy"
],
"name": "Integrated Microbial Genomes Taxon",
"pattern": "^\\d+$",
"prefix": "img.taxon",
"pubmed_ids": [
"17933782"
],
"uri_format": "http://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&taxon_oid=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkm846",
"pmc": "PMC2238897",
"pubmed": "17933782",
"title": "The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions",
"year": 2007
}
]
},
"imgt.hla": {
"biocontext": {
"prefix": "IMGT.HLA"
},
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://www.ebi.ac.uk/ipd/imgt/hla/",
"name": "IPD-IMGT/HLA database",
"prefix": "IPD-IMGT/HLA",
"uri_format": "https://www.ebi.ac.uk/ipd/imgt/hla/cells/cell/?cellid=$1"
},
"edam": {
"description": "Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database.",
"name": "IMGT/HLA",
"obsolete": false,
"prefix": "2773"
},
"fairsharing": {
"abbreviation": "IPD-IMGT/HLA",
"contact": {
"email": "steven.marsh@ucl.ac.uk",
"name": "Steven G. E. Marsh",
"orcid": "0000-0003-2855-4120"
},
"description": "The IPD-IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (MHC) and includes the official sequences named by the WHO Nomenclature Committee For Factors of the HLA System. The IMGT/HLA Database was established to provide a locus-specific database (LSDB) for the allelic sequences of the genes in the HLA system, also known as the human MHC. The IMGT/HLA Database was first released in 1998 and subsequently incorporated as a module of IPD in 2012.",
"homepage": "https://www.ebi.ac.uk/ipd/imgt/hla/",
"license": "https://creativecommons.org/licenses/by-nd/4.0",
"name": "IPD-IMGT/HLA - Human Leukocyte Antigen Sequence Database",
"prefix": "FAIRsharing.e28v7g",
"publications": [
{
"doi": "10.1093/nar/gku1161",
"pubmed_id": 25414341,
"title": "The IPD and IMGT/HLA database: allele variant databases."
},
{
"doi": "10.1034/j.1399-0039.2000.550314.x",
"pubmed_id": 10777106,
"title": "IMGT/HLA database--a sequence database for the human major histocompatibility complex."
},
{
"doi": "10.1093/nar/29.1.210",
"pubmed_id": 11125094,
"title": "IMGT/HLA Database--a sequence database for the human major histocompatibility complex."
},
{
"doi": "10.1093/nar/gkn662",
"pubmed_id": 18838392,
"title": "The IMGT/HLA database."
},
{
"doi": "10.1007/978-1-60327-118-9_3",
"pubmed_id": 18449991,
"title": "The IMGT/HLA database."
},
{
"doi": "10.1002/humu.20406",
"pubmed_id": 16944494,
"title": "The IMGT/HLA and IPD databases."
},
{
"doi": "10.1093/nar/gkz950",
"pubmed_id": 31667505,
"title": "IPD-IMGT/HLA Database."
},
{
"doi": "10.1093/nar/gkg070",
"pubmed_id": 12520010,
"title": "IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex."
}
],
"subjects": [
"Immunogenetics",
"Immunology",
"Biomedical Science"
]
},
"go": {
"homepage": "http://www.ebi.ac.uk/imgt/hla",
"name": "IMGT/HLA human major histocompatibility complex sequence database",
"prefix": "IMGT_HLA"
},
"integbio": {
"description": "IMGT/HLA is a database that specializes in the human major histocompatibility complex and its sequences.\nThere are 8,949 allele sequences that are available, and of them, 6919 are HLA Class I Alleles, 1,875 are HLA Class II Alleles and 155 are other non-HLA Alleles.\nInformation about the source material, from which the sequences were obtained, is provided in detail.\nAuthors of publications regularly check their data against IMGT/HLA first to ascertain the official name of their sequence to avoid confusion due to multiple names for the same product.\nAn IMGT/HLA Alignment Tool is provided as well as protein and nucleotide Blast search options.",
"fairsharing": "biodbcore-000171",
"homepage": "http://www.ebi.ac.uk/imgt/hla/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Sequence"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "IPD-IMGT/HLA",
"prefix": "nbdc00106",
"pubmeds": [
"31667505",
"26826444",
"25048120"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle"
]
},
"mappings": {
"biocontext": "IMGT.HLA",
"cellosaurus": "IPD-IMGT/HLA",
"edam": "2773",
"fairsharing": "FAIRsharing.e28v7g",
"go": "IMGT_HLA",
"integbio": "nbdc00106",
"miriam": "imgt.hla",
"n2t": "imgt.hla",
"ncbi": "IMGT/HLA",
"prefixcommons": "imgthla",
"re3data": "r3d100010804"
},
"miriam": {
"deprecated": false,
"description": "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature.",
"homepage": "https://www.ebi.ac.uk/imgt/hla/allele.html",
"id": "00000331",
"name": "IMGT HLA",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9*:]+$",
"prefix": "imgt.hla",
"sampleId": "A*01:01:01:01",
"uri_format": "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1"
},
"n2t": {
"description": "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature.",
"example": "A*01:01:01:01",
"homepage": "https://www.ebi.ac.uk/imgt/hla/allele.html",
"name": "IMGT HLA at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9*:]+$",
"prefix": "imgt.hla",
"uri_format": "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1"
},
"ncbi": {
"example": "HLA00031",
"homepage": "http://www.ebi.ac.uk/imgt/hla/",
"name": "Immunogenetics database, human MHC",
"prefix": "IMGT/HLA"
},
"owners": [
{
"name": "European Bioinformatics Institute",
"partnered": false,
"ror": "02catss52"
}
],
"prefixcommons": {
"description": "The IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO Nomenclature Committee For Factors of the HLA System.",
"example": "A*01:01:01:01",
"homepage": "http://www.ebi.ac.uk/imgt/hla/",
"keywords": [
"DNA",
"RNA",
"protein"
],
"name": "IMGT/HLA",
"pattern": "^[A-Z0-9*:]+$",
"prefix": "imgthla",
"pubmed_ids": [
"16381979"
],
"uri_format": "http://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele.cgi?"
},
"publications": [
{
"doi": "10.1093/nar/gkz950",
"pmc": "PMC7145640",
"pubmed": "31667505",
"title": "IPD-IMGT/HLA Database",
"year": 2020
},
{
"doi": "10.1093/nar/gku1161",
"pmc": "PMC4383959",
"pubmed": "25414341",
"title": "The IPD and IMGT/HLA database: allele variant databases",
"year": 2014
},
{
"doi": "10.1093/nar/gkn662",
"pmc": "PMC2686596",
"pubmed": "18838392",
"title": "The IMGT/HLA database",
"year": 2008
},
{
"doi": "10.1007/978-1-60327-118-9_3",
"pubmed": "18449991",
"title": "The IMGT/HLA database",
"year": 2007
},
{
"doi": "10.1002/humu.20406",
"pubmed": "16944494",
"title": "The IMGT/HLA and IPD databases",
"year": 2006
},
{
"doi": "10.1093/nar/gkj088",
"pmc": "PMC1347451",
"pubmed": "16381979",
"title": "IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences",
"year": 2006
},
{
"doi": "10.1093/nar/gkg070",
"pmc": "PMC165517",
"pubmed": "12520010",
"title": "IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex",
"year": 2003
},
{
"doi": "10.1093/nar/29.1.210",
"pmc": "PMC29780",
"pubmed": "11125094",
"title": "IMGT/HLA Database--a sequence database for the human major histocompatibility complex",
"year": 2001
},
{
"doi": "10.1034/j.1399-0039.2000.550314.x",
"pubmed": "10777106",
"title": "IMGT/HLA database--a sequence database for the human major histocompatibility complex",
"year": 2000
}
],
"re3data": {
"description": "The IPD-IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (MHC) and includes the official sequences named by the WHO Nomenclature Committee For Factors of the HLA System. The IPD-IMGT/HLA Database is part of the international ImMunoGeneTics project (IMGT).\nThe database uses the 2010 naming convention for HLA alleles in all tools herein. To aid in the adoption of the new nomenclature, all search tools can be used with both the current and pre-2010 allele designations. The pre-2010 nomenclature designations are only used where older reports or outputs have been made available for download.",
"homepage": "https://www.ebi.ac.uk/ipd/imgt/hla/",
"name": "IMGT/HLA Database",
"prefix": "r3d100010804",
"synonyms": [
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"ImMunoGeneTics/HLA Database",
"International ImMunoGeneTics information system/Humane Leukozyten Antigene Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.e28v7g",
"nif": "0000-03014",
"scr": "002971"
}
},
"synonyms": [
"IPD-IMGT/HLA"
]
},
"imgt.ligm": {
"biocontext": {
"prefix": "IMGT.LIGM"
},
"contact": {
"email": "marie-paule.lefranc@umontpellier.fr",
"name": "Marie-Paule Lefranc",
"orcid": "0000-0003-0116-9353"
},
"go": {
"description": "Database of immunoglobulins and T cell receptors from human and other vertebrates, with translation for fully annotated sequences.",
"homepage": "http://www.imgt.org/",
"name": "ImMunoGeneTics database covering immunoglobulins and T-cell receptors",
"prefix": "IMGT_LIGM"
},
"mappings": {
"biocontext": "IMGT.LIGM",
"go": "IMGT_LIGM",
"miriam": "imgt.ligm",
"n2t": "imgt.ligm",
"ncbi": "IMGT/LIGM",
"prefixcommons": "imgt.ligm"
},
"miriam": {
"deprecated": false,
"description": "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates.",
"homepage": "http://www.imgt.org/",
"id": "00000287",
"name": "IMGT LIGM",
"namespaceEmbeddedInLui": false,
"pattern": "^M\\d+$",
"prefix": "imgt.ligm",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "IMGT LIGM through DKFZ (SRS)",
"homepage": "http://genius.embnet.dkfz-heidelberg.de/",
"name": "IMGT LIGM through DKFZ (SRS)",
"uri_format": "http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-id+4ktAl1fNMTA+-e+[IMGT:'$1']"
}
],
"sampleId": "M94112",
"uri_format": "http://www.imgt.org/ligmdb/view?id=$1"
},
"n2t": {
"description": "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates.",
"example": "M94112",
"homepage": "http://www.imgt.org/",
"name": "IMGT LIGM at CNRS",
"namespaceEmbeddedInLui": false,
"pattern": "^M\\d+$",
"prefix": "imgt.ligm",
"uri_format": "http://www.imgt.org/ligmdb/view?id=$1"
},
"ncbi": {
"example": "U03895",
"homepage": "http://www.imgt.org/IMGTinformation/LIGM.html",
"name": "Immunogenetics database, immunoglobulins and T-cell receptors",
"prefix": "IMGT/LIGM"
},
"prefixcommons": {
"description": "MGT/LIGM-DB is the IMGT comprehensive database of immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and other vertebrate species.",
"example": "A68511",
"homepage": "http://imgt.cines.fr/cgi-bin/IMGTlect.jv",
"keywords": [
"DNA"
],
"name": "IMGT/LIGM-DB",
"pattern": "^[A-Z]\\d+$",
"prefix": "imgt.ligm",
"pubmed_ids": [
"16381979"
],
"synonyms": [
"imgt_ligmdb"
]
},
"publications": [
{
"doi": "10.1093/nar/gkj088",
"pmc": "PMC1347451",
"pubmed": "16381979",
"title": "IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences",
"year": 2006
}
]
},
"imgt.primerdb": {
"mappings": {
"prefixcommons": "imgt.primerdb",
"re3data": "r3d100012535"
},
"prefixcommons": {
"description": "The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR).",
"example": "IPP900099",
"homepage": "http://imgt.org/IMGTPrimerDB/",
"keywords": [
"DNA"
],
"name": "IMGT/PRIMER-DB",
"pattern": "^IPP\\d+$",
"prefix": "imgt.primerdb",
"uri_format": "http://imgt.org/IMGTPrimerDB/Check_PrDB.pl?numacc0=$1&origin=view&source=PrList"
},
"re3data": {
"description": "The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR).",
"homepage": "https://www.imgt.org/IMGTPrimerDB/",
"name": "IMGT/PRIMER-DB",
"prefix": "r3d100012535",
"synonyms": [
"ImMunoGeneTics/PRIMER-DB",
"International ImMunoGeneTics information system/PRIMER-Database"
]
}
},
"imotdb": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"mappings": {
"pathguide": "207",
"prefixcommons": "imotdb"
},
"pathguide": {
"abbreviation": "iMOTdb",
"homepage": "http://caps.ncbs.res.in/imotdb/",
"name": "Interacting motifs in proteins database",
"prefix": "207"
},
"prefixcommons": {
"description": "The interacting motif database or iMOTdb , lists interacting motifs thatare identified for all structural entries in the PDB. The conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting the common motifs shared among all superfamily members.",
"example": "53784",
"homepage": "http://caps.ncbs.res.in/imotdb/",
"keywords": [
"interaction",
"protein"
],
"name": "Database of Spatially Interacting Motifs in Proteins",
"pattern": "^\\d+$",
"prefix": "imotdb",
"uri_format": "http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"imr": {
"biocontext": {
"prefix": "IMR"
},
"example": "0000001",
"mappings": {
"biocontext": "IMR",
"obofoundry": "imr",
"prefixcommons": "imr"
},
"obofoundry": {
"contact": "curator@inoh.org",
"contact.label": "INOH curators",
"deprecated": true,
"domain": "chemistry and biochemistry",
"homepage": "http://www.inoh.org",
"name": "Molecule role (INOH Protein name/family name ontology)",
"prefix": "imr"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1029",
"description": "MoleculeRole Ontology is an ontology for proteins/chemicals. It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data.",
"example": "IMR_0800118",
"homepage": "http://www.inoh.org",
"keywords": [
"ontology",
"protein",
"small molecule"
],
"name": "MoleculeRole Ontology (INOH Protein name/family name ontology)",
"pattern": "^IMR_\\d+$",
"prefix": "imr",
"synonyms": [
"molecule_role"
],
"uri_format": "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id=$1"
}
},
"imsr.apb": {
"description": "The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. [from RRID]",
"example": "7345",
"mappings": {
"rrid": "IMSR_APB"
},
"pattern": "^\\d+$",
"rrid": {
"abbreviation": "APB",
"homepage": "https://pb.apf.edu.au/phenbank/homePage.html",
"keywords": [
"allele",
"alteration",
"chromosome",
"database",
"embryo",
"gene",
"live mouse",
"murine",
"mutation",
"phenotype",
"sperm",
"strain",
"transgene",
"transgenic"
],
"name": "NHMRC Australian PhenomeBank",
"prefix": "IMSR_APB",
"scr": "006149"
},
"uri_format": "https://pb.apf.edu.au/phenbank/strain.html?id=$1"
},
"imsr_em": {
"contact": {
"email": "d.smedley@qmul.ac.uk",
"name": "Damian Smedley",
"orcid": "0000-0002-5836-9850"
},
"description": "Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.With more than 8400 mutant mouse strains and asmall but increasing number of rat mutant strains available, EMMA is the primary mouse repository in Europe and the third largest non-profit repository worldwide. [from RRID]",
"example": "11478",
"mappings": {
"rrid": "IMSR_EM"
},
"pattern": "^\\d+$",
"rrid": {
"abbreviation": "EMMA",
"homepage": "https://www.infrafrontier.eu/emma/",
"keywords": [
"",
"mouse",
"mutant mouse repository",
"mutant mouse strain",
"mutant strain"
],
"name": "European Mouse Mutant Archive",
"prefix": "IMSR_EM",
"pubmeds": [
"19783817",
"17709347"
],
"scr": "006136",
"twitter": "InfrafrontierEU"
},
"uri_format": "https://www.infrafrontier.eu/emma/strain-search/straindetails/?q=$1"
},
"imsr_tac": {
"description": "Supplier of mice for research purposes. [from RRID]",
"example": "1178",
"mappings": {
"rrid": "IMSR_TAC"
},
"rrid": {
"abbreviation": "TAC, TB",
"homepage": "https://www.taconic.com/",
"keywords": [
"gene",
"genetic engineering",
"knockout",
"mice",
"model",
"mouse",
"repository",
"research",
"strain",
"subject",
"supply",
"transgenic"
],
"name": "Taconic Biosciences",
"prefix": "IMSR_TAC",
"scr": "016410"
},
"uri_format": "https://scicrunch.org/resolver/RRID:IMSR_TAC_$1"
},
"inaturalist.observation": {
"contributor": {
"github": "oolonek",
"name": "Pierre-Marie Allard",
"orcid": "0000-0003-3389-2191"
},
"description": "The identifier for an observation in iNaturalist",
"example": "36010371",
"github_request_issue": 517,
"homepage": "https://www.inaturalist.org/observations",
"mappings": {
"wikidata": "P5683"
},
"name": "iNaturalist Observation",
"pattern": "^[1-9]\\d*$",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://www.inaturalist.org/observations/$1",
"wikidata": {
"description": "observation identifier in iNaturalist",
"name": "iNaturalist observation ID",
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"prefix": "P5683",
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"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
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"description": "Identifier for a place in iNaturalist",
"example": "7207",
"homepage": "https://www.inaturalist.org/places",
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},
"name": "iNaturalist Place",
"pattern": "^[1-9]\\d*$",
"uri_format": "https://www.inaturalist.org/places/$1",
"wikidata": {
"description": "identifier for a place in iNaturalist",
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"49955",
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"98521"
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"name": "iNaturalist place ID",
"pattern": "^[1-9]\\d*$",
"prefix": "P7471",
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}
},
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"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
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"description": "Identifier for a species in iNaturalist",
"example": "21723",
"homepage": "https://www.inaturalist.org/taxa",
"mappings": {
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},
"name": "iNaturalist Taxonomy",
"pattern": "^[1-9]\\d{0,6}$",
"uri_format": "https://www.inaturalist.org/taxa/$1",
"wikidata": {
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"9999"
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"name": "iNaturalist taxon ID",
"pattern": "^[1-9]\\d{0,6}$",
"prefix": "P3151",
"uri_format": "https://inaturalist.org/taxa/$1"
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"name": "Charles Tapley Hoyt",
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"description": "Identifier for a user in iNaturalist",
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"homepage": "https://www.inaturalist.org/users",
"keywords": [
"person"
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"name": "iNaturalist User",
"pattern": "^[1-9]\\d*$",
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"email": "jmg11@cam.ac.uk",
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"prefix": "FAIRsharing.ddk9t9",
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{
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"pubmed": "26081259",
"title": "Many InChIs and quite some feat",
"year": 2015
},
{
"doi": "10.1186/s13321-021-00517-z",
"title": "InChI version 1.06: now more than 99.99% reliable",
"year": 2021
}
],
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"Knowledge and Information Systems",
"Cheminformatics",
"Chemistry"
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"miriam": {
"deprecated": false,
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"name": "InChI through ChEBI",
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{
"code": "um",
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"sampleId": "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3",
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},
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"comment": "This nomenclature is available via email. Truly a disgrace.",
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},
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"homepage": "http://www.goreni.org/",
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},
"homepage": "https://www.goreni.org/gr3_nomenclature.php",
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"inn": {
"comment": "can not find a place to resolve to",
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"description": "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.",
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"Ψ£Ω
ΩΩΨͺΨ§Ω
ΩΩ",
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"EBI-9014072",
"EBI-1784742"
],
"keywords": [
"Interaction"
],
"name": "IntAct",
"pattern": "^(?EBI\\-[0-9]+)$",
"prefix": "Intact",
"uri_format": "http://identifiers.org/intact/$1"
},
"uniprot": {
"abbreviation": "IntAct",
"category": "Protein-protein interaction databases",
"homepage": "https://www.ebi.ac.uk/intact/",
"name": "Protein interaction database and analysis system",
"prefix": "DB-0051",
"publications": [
{
"doi": "10.1093/nar/gkt1115",
"pubmed": "24234451"
}
],
"uri_format": "https://www.ebi.ac.uk/intact/interactors/id:$1*"
}
},
"intact.molecule": {
"biocontext": {
"prefix": "INTACT.MOLECULE"
},
"mappings": {
"biocontext": "INTACT.MOLECULE",
"miriam": "intact.molecule",
"n2t": "intact.molecule"
},
"miriam": {
"deprecated": false,
"description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules.",
"homepage": "https://www.ebi.ac.uk/intact/",
"id": "00000427",
"name": "IntAct Molecule",
"namespaceEmbeddedInLui": false,
"pattern": "^EBI\\-[0-9]+$",
"prefix": "intact.molecule",
"sampleId": "EBI-366083",
"uri_format": "https://www.ebi.ac.uk/intact/molecule/$1"
},
"n2t": {
"description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules.",
"example": "EBI-366083",
"homepage": "https://www.ebi.ac.uk/intact/",
"name": "IntAct Molecule at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^EBI\\-[0-9]+$",
"prefix": "intact.molecule",
"uri_format": "https://www.ebi.ac.uk/intact/molecule/$1"
},
"uri_format": "https://www.ebi.ac.uk/intact/search?query=$1"
},
"integbio": {
"contact": {
"email": "kwsm@dbcls.rois.ac.jp",
"github": "skwsm",
"name": "Shuichi Kawashima",
"orcid": "0000-0001-7883-3756"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Integbio Database Catalog provides whereabouts information (URL), database description, biological species and other attributes (metadata) of Japanese and international life science databases to make it easier for users to find databases they need. This catalog has been developed as a part of the integration of life science databases promoted by four ministries in Japan: the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), The Ministry of Health, Labor, and Welfare (MHLW), the Ministry of Agriculture, Forestry, and Fisheries (MAFF), and the Ministry of Economy, Trade, and Industry of Japan (METI). (from https://integbio.jp/dbcatalog/en/about)",
"example": "nbdc01071",
"homepage": "https://integbio.jp/en/",
"license": "CC0-1.0",
"logo": "https://integbio.jp/templates/integbio/images/logo/logo.png",
"name": "Integbio",
"pattern": "^nbdc\\d+$",
"uri_format": "https://integbio.jp/dbcatalog/en/record/$1"
},
"interfil": {
"mappings": {
"prefixcommons": "interfil"
},
"prefixcommons": {
"description": "The Intermediate Filament Database functions as a continuously updated review of the intermediate filament field and it is hoped that users will contribute to the development and expansion of the database on a regular basis. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants.",
"example": "NM_006262",
"homepage": "http://www.interfil.org",
"keywords": [
"genome"
],
"name": "Human Intermediate Filament Database",
"pattern": "^N[A-Z]_\\d+$",
"prefix": "interfil",
"synonyms": [
"intermediate_filament_db"
],
"uri_format": "http://www.interfil.org/details.php?id=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"interlex": {
"contact": {
"email": "mmartone@ucsd.edu",
"github": "memartone",
"name": "Maryann Elizabeth Martone",
"orcid": "0000-0002-8406-3871"
},
"fairsharing": {
"abbreviation": "InterLex",
"description": "The InterLex terminology is a lexicon of biomedical terms built on the foundation of NeuroLex and contains all of the existing NeuroLex terms. The initial entries in NeuroLex were built from the NIFSTD ontologies and BIRNLex (Biomedical Informatics Research Network Project Lexicon). Final content review from NeuroLex is still ongoing.",
"domains": [
"Imaging",
"Brain"
],
"homepage": "https://scicrunch.org/scicrunch/interlex/dashboard",
"license": "CC-BY-3.0",
"name": "InterLex",
"prefix": "FAIRsharing.67sssf",
"publications": [
{
"doi": "10.3389/fninf.2013.00018",
"pubmed": "24009581",
"title": "NeuroLex.org: an online framework for neuroscience knowledge",
"year": 2013
}
],
"subjects": [
"Anatomy",
"Neurobiology",
"Biomedical Science"
]
},
"mappings": {
"fairsharing": "FAIRsharing.67sssf",
"miriam": "ilx",
"wikidata": "P696"
},
"miriam": {
"deprecated": false,
"description": "InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. ",
"homepage": "https://www.fdilab.org",
"id": "00000814",
"name": "InterLex",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "ilx",
"sampleId": "0101963",
"uri_format": "https://scicrunch.org/scicrunch/interlex/view/ilx_$1"
},
"name": "InterLex",
"publications": [
{
"doi": "10.3389/fninf.2013.00018",
"pmc": "PMC3757470",
"pubmed": "24009581",
"title": "NeuroLex.org: an online framework for neuroscience knowledge",
"year": 2013
}
],
"references": [
"https://github.com/AllenInstitute/nomenclature"
],
"synonyms": [
"ILX"
],
"wikidata": {
"description": "identifier in the Interlex database (used to be Neurolex)",
"example": [
"nlx_anat_090801",
"sao1103104164"
],
"homepage": "http://interlex.org",
"name": "Interlex ID",
"pattern": "^[0-9A-Za-z_]+$",
"prefix": "P696",
"uri_format": "http://uri.interlex.org/base/$1"
}
},
"interpro": {
"biocontext": {
"prefix": "IPR"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "interpro",
"uri_format": "https://www.ebi.ac.uk/interpro/entry/$1"
},
"deprecated": false,
"edam": {
"description": "Primary accession number of an InterPro entry.",
"name": "InterPro",
"obsolete": false,
"prefix": "1133"
},
"example": "IPR016380",
"fairsharing": {
"abbreviation": "InterPro",
"description": "InterPro is a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as signatures, provided by several different databases (referred to as member databases) that make up the InterPro consortium.",
"homepage": "https://www.ebi.ac.uk/interpro",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "Integrated resource of protein families, domains and functional sites",
"prefix": "FAIRsharing.pda11d",
"publications": [
{
"doi": "10.1093/nar/gky1100",
"pubmed_id": 30398656,
"title": "InterPro in 2019: improving coverage, classification and access to protein sequence annotations."
},
{
"doi": "10.1093/nar/gki106",
"pubmed_id": 15608177,
"title": "InterPro, progress and status in 2005."
}
],
"repository": "https://proteinswebteam.github.io/interpro-blog/",
"subjects": [
"Bioinformatics",
"Biology"
],
"twitter": "InterProDB"
},
"go": {
"homepage": "http://www.ebi.ac.uk/interpro/",
"name": "InterPro database of protein domains and motifs",
"prefix": "InterPro",
"synonyms": [
"INTERPRO",
"IPR"
],
"uri_format": "http://www.ebi.ac.uk/interpro/entry/$1"
},
"integbio": {
"alt_name": "Integrated documentation resource for protein families, domains and functional sites",
"description": "InterPro is a database that analyses proteins functionally and classifies them into families as well as predicts their domain and sites in the genome.\nThis repository harvests its content from a large number of related databases and consolidates its findings into a single searchable resource avoiding the occurrence of redundant entries.\nInterPro aims to update their content every 8 weeks.\nA keyword search is available and an option is provided where a protein sequence can be entered for analysis.",
"fairsharing": "biodbcore-000315",
"homepage": "http://www.ebi.ac.uk/interpro/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "InterPro",
"prefix": "nbdc00108",
"pubmeds": [
"22096229",
"22301074",
"15980438",
"21785143",
"18836194"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"mappings": {
"biocontext": "IPR",
"biolink": "interpro",
"edam": "1133",
"fairsharing": "FAIRsharing.pda11d",
"go": "InterPro",
"integbio": "nbdc00108",
"miriam": "interpro",
"n2t": "interpro",
"ncbi": "InterPro",
"obofoundry": "ipr",
"prefixcommons": "interpro",
"re3data": "r3d100010798",
"togoid": "Interpro",
"uniprot": "DB-0052",
"wikidata": "P2926"
},
"miriam": {
"deprecated": false,
"description": "InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.",
"homepage": "https://www.ebi.ac.uk/interpro/",
"id": "00000011",
"name": "InterPro",
"namespaceEmbeddedInLui": false,
"pattern": "^IPR\\d{6}$",
"prefix": "interpro",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "Bio2RDF",
"homepage": "http://interpro.bio2rdf.org/fct/",
"name": "Bio2RDF",
"uri_format": "http://interpro.bio2rdf.org/describe/?url=http://bio2rdf.org/interpro:$1"
}
],
"sampleId": "IPR000100",
"uri_format": "https://www.ebi.ac.uk/interpro/entry/$1"
},
"n2t": {
"description": "InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.",
"example": "IPR000100",
"homepage": "https://www.ebi.ac.uk/interpro/",
"name": "InterPro",
"namespaceEmbeddedInLui": false,
"pattern": "^IPR\\d{6}$",
"prefix": "interpro",
"uri_format": "https://www.ebi.ac.uk/interpro/entry/$1"
},
"name": "InterPro",
"ncbi": {
"example": "IPR002928",
"homepage": "http://www.ebi.ac.uk/interpro/",
"name": "InterPro protein sequence database",
"prefix": "InterPro"
},
"obofoundry": {
"contact": "interhelp@ebi.ac.uk",
"contact.label": "InterPro Help",
"deprecated": true,
"domain": "chemistry and biochemistry",
"homepage": "http://www.ebi.ac.uk/interpro/index.html",
"name": "Protein Domains",
"prefix": "ipr"
},
"preferred_prefix": "interpro",
"prefixcommons": {
"description": "InterPro is an integrated database of predictive protein \"signatures\" used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites.",
"example": "IPR000100",
"homepage": "http://www.ebi.ac.uk/interpro",
"keywords": [
"domain",
"protein"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Integrated resource of protein families, domains and functional sites",
"pattern": "^IPR\\d{6}$",
"prefix": "interpro",
"pubmed_ids": [
"15608177"
],
"synonyms": [
"ipr"
],
"uri_format": "http://www.ebi.ac.uk/interpro/IEntry?ac=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkac993",
"pmc": "PMC9825450",
"pubmed": "36350672",
"title": "InterPro in 2022",
"year": 2023
},
{
"doi": "10.1093/nar/gkaa977",
"pmc": "PMC7778928",
"pubmed": "33156333",
"title": "The InterPro protein families and domains database: 20 years on",
"year": 2021
},
{
"doi": "10.1093/nar/gky1100",
"pmc": "PMC6323941",
"pubmed": "30398656",
"title": "InterPro in 2019: improving coverage, classification and access to protein sequence annotations",
"year": 2019
},
{
"doi": "10.1093/nar/gki106",
"pmc": "PMC540060",
"pubmed": "15608177",
"title": "InterPro, progress and status in 2005",
"year": 2005
}
],
"rdf_uri_format": "http://purl.obolibrary.org/obo/IPR_$1",
"re3data": {
"description": "InterPro collects information about protein sequence analysis and classification, providing access to a database of predictive protein signatures used for the classification and automatic annotation of proteins and genomes. Sequences in InterPro are classified at superfamily, family, and subfamily. InterPro predicts the occurrence of functional domains, repeats, and important sites, and adds in-depth annotation such as GO terms to the protein signatures.",
"homepage": "https://www.ebi.ac.uk/interpro/",
"name": "InterPro",
"prefix": "r3d100010798",
"synonyms": [
"protein sequence analysis & classification"
],
"xrefs": {
"fairsharing": "FAIRsharing.pda11d",
"miriam": "00000011",
"nif": "0000-03035",
"omics": "01694",
"scr": "006695"
}
},
"synonyms": [
"IP",
"IPR",
"InterPro"
],
"togoid": {
"catalog": "nbdc00108",
"examples": [
"IPR038152",
"IPR040448",
"IPR036748",
"IPR034266",
"IPR005479",
"IPR036365",
"IPR000174",
"IPR001334",
"IPR000731",
"IPR001767"
],
"keywords": [
"Domain"
],
"name": "InterPro",
"pattern": "^(?IPR\\d{6})$",
"prefix": "Interpro",
"uri_format": "http://identifiers.org/interpro/$1"
},
"uniprot": {
"abbreviation": "InterPro",
"category": "Family and domain databases",
"homepage": "https://www.ebi.ac.uk/interpro/",
"name": "Integrated resource of protein families, domains and functional sites",
"prefix": "DB-0052",
"publications": [
{
"doi": "10.1093/nar/gkac993",
"pubmed": "36350672"
}
],
"uri_format": "https://www.ebi.ac.uk/interpro/entry/$1"
},
"uri_format": "https://www.ebi.ac.uk/interpro/entry/InterPro/$1",
"wikidata": {
"description": "InterPro unique identifier",
"example": [
"IPR000455",
"IPR001807",
"IPR039030"
],
"homepage": "https://www.ebi.ac.uk/interpro/",
"name": "InterPro ID",
"pattern": "^IPR\\d{6}$",
"prefix": "P2926",
"uri_format": "http://www.ebi.ac.uk/interpro/entry/$1"
}
},
"iobc": {
"aberowl": {
"description": "Interlinking Ontology for Biological Concepts (IOBC) contains approximately 80,000 biological concepts such as biological phenomena, diseases, molecular functions, gene products, chemicals, and medical cares, and approximately 20,000 related concepts such as earth science and environmental science. The concepts are structured by thirty-five relations such as has function, has role, has quality, and precedes. Each concept has both of English and Japanese labels. For further information including the developmental method, see papers in the PUBLICATIONS PAGE. The license for this ontology is specified in the Creative Commons Attribution-NonCommercial 4.0 International. If you use data from this ontology, please be sure attribute this ontology as follows: \"Interlinking Ontology for Biological Concepts Β© National Bioscience Database Center licensed under CC Attribution-NonCommercial 4.0 International\".",
"download_owl": "http://aber-owl.net/media/ontologies/IOBC/25/iobc.owl",
"homepage": "https://github.com/kushidat/IOBC",
"name": "Interlinking Ontology for Biological Concepts",
"prefix": "IOBC",
"version": "version 1.6.0"
},
"bioportal": {
"contact": {
"email": "kushida@biosciencedbc.jp",
"name": "Tatsuya Kushida"
},
"description": "Interlinking Ontology for Biological Concepts (IOBC) contains approximately 80,000 biological concepts such as biological phenomena, diseases, molecular functions, gene products, chemicals, and medical cares, and approximately 20,000 related concepts such as earth science and environmental science. The concepts are structured by thirty-five relations such as has function, has role, has quality, and precedes. Each concept has both of English and Japanese labels. For further information including the developmental method, see papers in the PUBLICATIONS PAGE. The license for this ontology is specified in the Creative Commons Attribution-NonCommercial 4.0 International. If you use data from this ontology, please be sure attribute this ontology as follows: \"Interlinking Ontology for Biological Concepts Β© National Bioscience Database Center licensed under CC Attribution-NonCommercial 4.0 International\".",
"homepage": "https://github.com/kushidat/IOBC",
"name": "Interlinking Ontology for Biological Concepts",
"prefix": "IOBC",
"publication": "http://purl.jp/bio/4/publications/iobc",
"version": "version 1.6.0"
},
"contact": {
"email": "kushida@biosciencedbc.jp",
"github": "kushidatatsuya",
"name": "Tatsuya Kushida",
"orcid": "0000-0002-0784-4113"
},
"example": "200906038218908385",
"example_extras": [
"AC21_cat",
"AC21",
"OWLClass_00000000000000000321"
],
"license": "CC-BY-NC-4.0",
"mappings": {
"aberowl": "IOBC",
"bioportal": "IOBC"
},
"publications": [
{
"doi": "10.1007/s00354-019-00074-y",
"title": "Interconnection of Biological Knowledge Using NikkajiRDF and Interlinking Ontology for Biological Concepts",
"year": 2019
}
],
"repository": "https://github.com/kushidat/IOBC",
"uri_format": "http://purl.jp/bio/4/id/$1"
},
"ipi": {
"biocontext": {
"prefix": "IPI"
},
"deprecated": true,
"integbio": {
"alt_name": "International Protein Index",
"homepage": "http://www.ebi.ac.uk/IPI/",
"information_keywords": [
"Sequence"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "IPI",
"prefix": "nbdc00911",
"pubmeds": [
"15221759"
],
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"mappings": {
"biocontext": "IPI",
"integbio": "nbdc00911",
"prefixcommons": "ipi"
},
"prefixcommons": {
"description": "IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI maintaisn a database of cross references between the primary data sources, it provides minimally redundant but complete sets of proteins for featured species, and it maintains stable and unique identifiers.",
"example": "IPI00000001",
"homepage": "http://www.ebi.ac.uk/IPI",
"keywords": [
"protein"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "International Protein Index",
"pattern": "^IPI\\d{8}$",
"prefix": "ipi",
"pubmed_ids": [
"15221759"
],
"uri_format": "http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$1&format=default"
},
"publications": [
{
"doi": "10.1002/pmic.200300721",
"pubmed": "15221759",
"title": "The International Protein Index: an integrated database for proteomics experiments",
"year": 2004
}
]
},
"irct": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Iranian Registry of Clinical Trials. This is a Primary Registry in the WHO Registry Network set up with the help from the Ministry of Health and Medical Education (MOHME) and hosted by Iran University of Medical Sciences (IUMS). (from homepage)\nNote that the website uses a different identifier then the one reported in this semantic space.",
"example": "IRCT20080904001199N7",
"homepage": "https://en.irct.ir/",
"name": "Iranian Registry of Clinical Trials",
"pattern": "^IRCT\\d+N\\d+$",
"references": [
"https://en.irct.ir/trial/65035"
]
},
"ird.segment": {
"biocontext": {
"prefix": "IRD.SEGMENT"
},
"contact": {
"email": "richard.scheuermann@nih.gov",
"github": "scheuerm",
"name": "Richard H. Scheuermann",
"orcid": "0000-0003-1355-892X"
},
"mappings": {
"biocontext": "IRD.SEGMENT",
"miriam": "ird.segment",
"n2t": "ird.segment",
"prefixcommons": "ird.segment"
},
"miriam": {
"deprecated": false,
"description": "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s).",
"homepage": "http://www.fludb.org/",
"id": "00000172",
"name": "IRD Segment Sequence",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$",
"prefix": "ird.segment",
"sampleId": "CY077097",
"uri_format": "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1"
},
"n2t": {
"description": "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s).",
"example": "CY077097",
"homepage": "http://www.fludb.org/",
"name": "IRD at BioHealthBase",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$",
"prefix": "ird.segment",
"uri_format": "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1"
},
"prefixcommons": {
"description": "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s).",
"example": "CY077097",
"keywords": [
"gene",
"protein"
],
"name": "IRD Segment Sequence",
"pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$",
"prefix": "ird.segment",
"pubmed_ids": [
"17965094"
],
"uri_format": "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkm905",
"pmc": "PMC2238987",
"pubmed": "17965094",
"title": "BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence",
"year": 2007
}
]
},
"irefweb": {
"biocontext": {
"prefix": "IREFWEB"
},
"contact": {
"email": "shoshana@sickkids.ca",
"name": "Shoshana J. Wodak",
"orcid": "0000-0002-0701-6545"
},
"fairsharing": {
"abbreviation": "iRefWeb",
"description": "iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID.",
"homepage": "http://wodaklab.org/iRefWeb/",
"name": "Interaction Reference Index Web Interface",
"prefix": "FAIRsharing.t31wcb",
"publications": [
{
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"wikidata": "P299"
},
"name": "ISO 3166-1 Country Code",
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},
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"description": "The primary purpose of ISO 15926 is to provide a foundation ontology to support the integration and sharing of data related to the lifecycle of a process plant in such a way that it is consistent, unambiguous, and minimizing the number of ways something could be expressed. Further purpose of ISO 15926-14 is to meet needs for OWL 2 ontologies that are based on ISO 15926-2, that enable efficient reasoning and that capture lifecycle information. A specific purpose is to demonstrate lifecycle modelling through a representation of the lifecycle model of ISO/IEC 81346-1. Another specific purpose is to exemplify how this standard can be used to develop industrial ontologies through various real-world use cases from industry. (from https://nfdi4cat.org/services/ontologie-sammlung/)",
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},
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{
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],
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},
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},
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},
"mappings": {
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"biolink": "issn",
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"miriam": "issn",
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},
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"homepage": "https://portal.issn.org",
"id": "00000301",
"name": "ISSN",
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{
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],
"sampleId": "0745-4570",
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"description": "The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books.",
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}
},
"istransbase": {
"contact": {
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"name": "Dongsheng Cao"
},
"contributor": {
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"github": "tanayshah2",
"name": "Tanay Shah",
"orcid": "0009-0001-1912-5132"
},
"description": "ISTransbase is a highly reliable and accessible database that focuses on inhibitors and substrates of drug transporters, offering a wealth of vital information encompassing experimental methods, transport parameters, and references.",
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"name": "ISTransbase",
"publications": [
{
"doi": "10.1093/database/baae053",
"pmc": "PMC11214160",
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"title": "ISTransbase: an online database for inhibitor and substrate of drug transporters",
"year": 2024
}
],
"reviewer": {
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"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"uri_format": "https://istransbase.scbdd.com/database/trans/$1"
},
"itis": {
"bartoc": {
"description": "ITIS is an easily accessible database with reliable information on species names and their hierarchical classification that is publicly accessible with unlimited free use. The database is reviewed periodically to ensure high quality with valid classifications, revisions, and additions of newly described species. The ITIS includes documented taxonomic information of flora and fauna from both aquatic and terrestrial habitats. For each scientific name, ITIS includes the authority, taxonomic rank, a unique taxonomic serial number, data source information, data quality indicators, and associated synonyms and vernacular names where available. Geographic coverage is worldwide, with an emphasis on North American taxa. The ITIS Web Services provide the ability to search and retrieve data from ITIS by providing access to the data behind the ITIS web site (http://www.itis.gov/web_service.html#). There is also web interface for viewing reports, and several options for text downloads. Each part of the basic WSDL web services is provided by a web service API, which defines the name, input to, and output from the service for a particular data request.",
"homepage": "https://www.itis.gov/",
"name": "Integrated Taxonomic Information System",
"prefix": "17791",
"wikidata_database": "Q82575"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world.",
"example": "589462",
"fairsharing": {
"abbreviation": "ITIS",
"contact": {
"email": "itiswebmaster@itis.gov",
"name": "Gerald Guala",
"orcid": "0000-0002-4972-3782"
},
"description": "The Integrated Taxonomic Information System (ITIS) provides taxonomic information on plants, animals, fungi, and microbes of North America and the world. The goal is to create an easily accessible database with reliable information on species names and their hierarchical classification. The database will be reviewed periodically to ensure high quality with valid classifications, revisions, and additions of newly described species. The ITIS includes documented taxonomic information of flora and fauna from both aquatic and terrestrial habitats.",
"homepage": "https://www.itis.gov/",
"name": "Integrated Taxonomic Information System",
"prefix": "FAIRsharing.t19hpa",
"publications": [],
"subjects": [
"Taxonomy",
"Biodiversity",
"Life Science"
]
},
"homepage": "https://www.itis.gov/",
"integbio": {
"description": "ITIS is a database of taxonomic nomenclature and information used in biodiversity and ecosystem preservation programs. The database contains information on species and serves as a respository for biodiversity information for US government programs. The database can be searched by taxon or hierarchically, and taxonomic data can be downloaded.",
"fairsharing": "biodbcore-000597",
"homepage": "http://www.itis.gov",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Bibliography/Documents",
"Taxonomy",
"Repository"
],
"maintainer": "Integrated Taxonomic Information System",
"name": "ITIS",
"prefix": "nbdc00916",
"status": "Active",
"target_keywords": [
"Organism"
]
},
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"fairsharing": "FAIRsharing.t19hpa",
"integbio": "nbdc00916",
"re3data": "r3d100011213",
"wikidata": "P815"
},
"name": "Integrated Taxonomic Information System",
"pattern": "^\\d+$",
"re3data": {
"description": "Here you will find authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world.",
"homepage": "https://www.itis.gov/",
"name": "ITIS",
"prefix": "r3d100011213",
"synonyms": [
"Integrated Taxonomic Information System"
]
},
"uri_format": "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1",
"wikidata": {
"description": "identifier for a taxon in the Integrated Taxonomic Information System",
"example": [
"160330",
"162003"
],
"homepage": "https://www.itis.gov",
"name": "ITIS TSN",
"pattern": "^[1-9]\\d{1,6}$",
"prefix": "P815",
"uri_format": "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1"
}
},
"itmctr": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The International Traditional Medicine Clinical Trial Registry (ITMCTR) is a non-profit online register of clinical trials being conducted in the field of traditional medicine. It isoperated by the China Academy of Chinese Medical Sciences and The China Center For Evidence Based Traditional Chinese Medicine. It is recognized as a Primary Registry of WHO, and contributes data to the WHO ICTRP. (from website)",
"example": "ITMCTR2023000002",
"homepage": "http://itmctr.ccebtcm.org.cn",
"logo": "http://itmctr.ccebtcm.org.cn/Content/images/ny_logo.png",
"name": "International Traditional Medicine Clinical Trial Registry",
"pattern": "^ITMCTR\\d+$"
},
"ito": {
"aberowl": {
"description": "The Intelligence Task Ontology and Knowledge Graph (ITO) provides a comprehensive, curated model of artificial intelligence tasks, benchmarks and benchmark results, including the biomedical domain. NOTE: The version uploaded to BioPortal has all instances and benchmark data removed because of performance issues with the BioPortal class browser. Please refer to https://github.com/OpenBioLink/ITO/ for downloading the full version of the ontology and dataset.",
"download_owl": "http://aber-owl.net/media/ontologies/ITO/17/ito.owl",
"homepage": "https://github.com/OpenBioLink/ITO/",
"name": "Intelligence Task Ontology",
"prefix": "ITO",
"version": "1.12 (PWC export dated 2022-07-30) - internal, just a minor fix"
},
"banana": "ITO",
"banana_peel": "_",
"bioportal": {
"description": "The Intelligence Task Ontology and Knowledge Graph (ITO) provides a comprehensive, curated model of artificial intelligence tasks, benchmarks and benchmark results, including the biomedical domain. NOTE: The version uploaded to BioPortal has all instances and benchmark data removed because of performance issues with the BioPortal class browser. Please refer to https://github.com/OpenBioLink/ITO/ for downloading the full version of the ontology and dataset.",
"homepage": "https://github.com/OpenBioLink/ITO/",
"name": "Intelligence Task Ontology",
"prefix": "ITO",
"version": "1.12 (PWC export dated 2022-07-30) - internal, just a minor fix"
},
"example": "01625",
"fairsharing": {
"abbreviation": "ITO",
"contact": {
"email": "matthias.samwald@meduniwien.ac.at",
"name": "Matthias Samwald",
"orcid": "0000-0002-4855-2571"
},
"description": "The Intelligence Task Ontology and Knowledge Graph (ITO) provides comprehensive, curated and interlinked data of artificial intelligence tasks, benchmarks, AI performance metrics, benchmark results and research papers. ITO ontology aims to support 1) Manual curation of AI task classification hierarchies and performance metrics, enabling more precise analyses; 2) Representing data as a graph, facilitating network-based query and analysis; 3) Allowing for easy integration and enrichment with external data, as well as simple extensibility for modeling related knowledge domains from other domains; 4) Allowing for automated deductive inference and automated knowledge base consistency checking; 5) Allowing for ongoing, collaborative expert curation of underlying ontological models. ITO aims to enable precise and network-based analyses of the global landscape of AI tasks and capabilities based on technologies that allow for easy integration and enrichment with external data, automated inference and continuous, collaborative expert curation of underlying ontological models. ",
"domains": [
"Natural language processing",
"Machine learning"
],
"homepage": "https://github.com/OpenBioLink/ITO",
"license": "CC-BY-4.0",
"name": "Intelligence Task Ontology and Knowledge Graph",
"prefix": "FAIRsharing.89e853",
"publications": [
{
"doi": "10.48550/arxiv.2110.01434",
"title": "A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks",
"year": 2021
},
{
"doi": "10.1038/s41597-022-01435-x",
"title": "A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks",
"year": 2022
},
{
"doi": "10.5281/zenodo.5561989",
"title": "Intelligence Task Ontology and Knowledge Graph (ITO)",
"year": 2022
}
],
"subjects": [
"Artificial Intelligence"
]
},
"homepage": "https://openbiolink.github.io/ITOExplorer/",
"mappings": {
"aberowl": "ITO",
"bioportal": "ITO",
"fairsharing": "FAIRsharing.89e853",
"miriam": "ito"
},
"miriam": {
"deprecated": false,
"description": "The Intelligence Task Ontology (ITO) provides a comprehensive map of machine intelligence tasks, as well as broader human intelligence or hybrid human/machine intelligence tasks.",
"homepage": "https://bioportal.bioontology.org/",
"id": "00000802",
"name": "Intelligence Task Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^.+$",
"prefix": "ito",
"sampleId": "ITO_01625",
"uri_format": "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:$1"
},
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1038/s41597-022-01435-x",
"pmc": "PMC9205953",
"pubmed": "35715466",
"title": "A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks",
"year": 2022
},
{
"doi": "10.5281/zenodo.5561989",
"title": "Intelligence Task Ontology and Knowledge Graph (ITO)",
"year": 2022
},
{
"doi": "10.48550/arxiv.2110.01434",
"title": "A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks",
"year": 2021
}
],
"repository": "https://github.com/OpenBioLink/ITO",
"uri_format": "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:ITO_$1"
},
"iuphar.family": {
"biocontext": {
"prefix": "IUPHAR.FAMILY"
},
"license": "CC-BY-SA-4.0",
"mappings": {
"biocontext": "IUPHAR.FAMILY",
"miriam": "iuphar.family",
"n2t": "iuphar.family",
"prefixcommons": "iuphar.family"
},
"miriam": {
"deprecated": false,
"description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits.",
"homepage": "http://www.guidetopharmacology.org/",
"id": "00000317",
"name": "IUPHAR family",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "iuphar.family",
"sampleId": "78",
"uri_format": "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1"
},
"n2t": {
"description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits.",
"example": "78",
"homepage": "http://www.guidetopharmacology.org/",
"name": "The IUPHAR/BPS Guide to PHARMACOLOGY",
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"pattern": "^\\d+$",
"prefix": "iuphar.family",
"uri_format": "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1"
},
"prefixcommons": {
"description": "IUPHAR G protein-coupled receptors database",
"example": "78",
"homepage": "http://www.iuphar-db.org/DATABASE/ReceptorFamiliesForward?type=GPCR",
"keywords": [
"protein"
],
"name": "G protein-coupled receptors database",
"pattern": "^\\d+$",
"prefix": "iuphar.family",
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"iuphar.gpcr"
],
"uri_format": "http://www.iuphar-db.org/DATABASE/FamilyIntroductionForward?familyId=$1"
},
"synonyms": [
"IUPHARfam"
]
},
"iuphar.ligand": {
"biocontext": {
"prefix": "IUPHAR.LIGAND"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "GTOPDB",
"uri_format": "https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1"
},
"license": "CC-BY-SA-4.0",
"mappings": {
"biocontext": "IUPHAR.LIGAND",
"biolink": "GTOPDB",
"miriam": "iuphar.ligand",
"n2t": "iuphar.ligand",
"togoid": "IupharLigand",
"wikidata": "P595"
},
"miriam": {
"deprecated": false,
"description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands.",
"homepage": "http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all",
"id": "00000457",
"name": "IUPHAR ligand",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "iuphar.ligand",
"sampleId": "1755",
"uri_format": "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1"
},
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"description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands.",
"example": "1755",
"homepage": "http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all",
"name": "IUPHAR ligand at University of Edinburgh",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "iuphar.ligand",
"uri_format": "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1"
},
"name": "Guide to Pharmacology Ligand",
"synonyms": [
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"IUPHAR_LIGAND_ID"
],
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"2355",
"2870",
"4047",
"50",
"5714",
"6382",
"7792",
"8339",
"965"
],
"keywords": [
"Compound"
],
"name": "IUPHAR ligand",
"pattern": "^(?\\d+)$",
"prefix": "IupharLigand",
"uri_format": "http://identifiers.org/iuphar.ligand/$1"
},
"wikidata": {
"description": "ligand identifier of the Guide to Pharmacology database",
"example": [
"1627",
"2286",
"5"
],
"homepage": "https://www.guidetopharmacology.org/",
"name": "Guide to Pharmacology Ligand ID",
"pattern": "^\\d{1,4}$",
"prefix": "P595",
"uri_format": "https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1"
}
},
"iuphar.receptor": {
"biocontext": {
"prefix": "IUPHAR.RECEPTOR"
},
"contact": {
"email": "simon.harding@igmm.ed.ac.uk",
"github": "simondharding",
"name": "Simon D Harding",
"orcid": "0000-0002-9262-8318"
},
"go": {
"homepage": "http://www.iuphar.org/",
"name": "International Union of Pharmacology",
"prefix": "IUPHAR_RECEPTOR",
"uri_format": "https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1"
},
"license": "CC-BY-SA-4.0",
"mappings": {
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"go": "IUPHAR_RECEPTOR",
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"wikidata": "P5458"
},
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"description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits.",
"homepage": "http://www.guidetopharmacology.org/targets.jsp",
"id": "00000281",
"name": "IUPHAR receptor",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "iuphar.receptor",
"sampleId": "101",
"uri_format": "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1"
},
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"description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits.",
"example": "101",
"homepage": "http://www.guidetopharmacology.org/targets.jsp",
"name": "IUPHAR Receptor at University of Edinburgh",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "iuphar.receptor",
"uri_format": "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1"
},
"name": "Guide to Pharmacology Target",
"publications": [
{
"doi": "10.1093/nar/gkab1010",
"pmc": "PMC8689838",
"pubmed": "34718737",
"title": "The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials",
"year": 2022
},
{
"doi": "10.1111/j.1476-5381.2012.02141.x",
"pmc": "PMC3575771",
"pubmed": "23003568",
"title": "GuideToPharmacology.org--an update",
"year": 2012
}
],
"synonyms": [
"IUPHAR_GPCR",
"IUPHARobj"
],
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"abbreviation": "GuidetoPHARMACOLOGY",
"category": "Chemistry databases",
"homepage": "https://www.guidetopharmacology.org",
"name": "IUPHAR/BPS Guide to PHARMACOLOGY",
"prefix": "DB-0182",
"publications": [
{
"doi": "10.1093/nar/gkab1010",
"pubmed": "34718737"
}
],
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},
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"description": "target identifier of the Guide to Pharmacology database",
"example": [
"1",
"214",
"620"
],
"homepage": "https://www.guidetopharmacology.org/GRAC/",
"name": "Guide to Pharmacology Target ID",
"pattern": "^[1-9]\\d{0,3}$",
"prefix": "P5458",
"uri_format": "https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1"
}
},
"ivdb": {
"mappings": {
"prefixcommons": "ivdb"
},
"prefixcommons": {
"description": "IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively.",
"example": "E13035",
"homepage": "http://influenza.psych.ac.cn/",
"keywords": [
"genome",
"DNA",
"gene"
],
"name": "Influenza Virus Database",
"pattern": "^[A-Z]+\\d+$",
"prefix": "ivdb",
"uri_format": "http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id=$1"
}
},
"jax": {
"biocontext": {
"prefix": "JAX",
"uri_format": "http://jaxmice.jax.org/strain/$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Information about the C57BL/6J. Includes genetic background and disease data.",
"example": "004435",
"fairsharing": {
"abbreviation": "JAX",
"description": "JAXΒ Mice are the industry standard for animal model research, using precise genome solutions to better understand human disease. Our rigorous Animal Health Programs and stringent genetic quality standards ensure the reproducibility and validity of your experimental data.",
"homepage": "http://jaxmice.jax.org/",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "JAX Mice Database",
"prefix": "FAIRsharing.5701h1",
"publications": [],
"subjects": [
"Life Science"
]
},
"homepage": "https://www.jax.org/strain",
"mappings": {
"biocontext": "JAX",
"fairsharing": "FAIRsharing.5701h1",
"rrid": "IMSR_JAX"
},
"name": "Jackson Laboratories Strain",
"pattern": "^\\d{6}$",
"rrid": {
"abbreviation": "JAX, JAX MS, JMS,IMSR_JAX",
"homepage": "https://www.jax.org/jax-mice-and-services",
"keywords": [
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"genetic engineering",
"knockout",
"mice",
"model",
"mouse",
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"subject",
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"prefix": "IMSR_JAX",
"scr": "016408",
"twitter": "jacksonlab"
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"description": "JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory.",
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"id": "00000337",
"name": "JAX Mice",
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"pattern": "^\\d+$",
"prefix": "jaxmice",
"sampleId": "005012",
"uri_format": "http://jaxmice.jax.org/strain/$1.html"
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"description": "JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory.",
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"homepage": "http://jaxmice.jax.org/",
"name": "JAX Mice at Jackson Laboratory",
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"pattern": "^\\d+$",
"prefix": "jaxmice",
"uri_format": "http://jaxmice.jax.org/strain/$1.html"
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},
"integbio": {
"description": "This site is a search tool of JCGGDB which is a database of glycan-related data in Japan. It allows to search glycan structures using the monosaccharide symbol defined by the Consortium for Functional Glycomics (CFG) in U.S.A.",
"homepage": "https://jcggdb.jp/idb/flash/GlycoEditor.jsp",
"information_keywords": [
"Image/Movie",
"Chemical structure"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
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"prefix": "nbdc01164",
"status": "Active",
"target_keywords": [
"Carbohydrate"
]
},
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"description": "JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc.",
"homepage": "http://jcggdb.jp/index_en.html",
"id": "00000479",
"name": "JCGGDB",
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"pattern": "^JCGG-STR\\d{6}$",
"prefix": "jcggdb",
"sampleId": "JCGG-STR008690",
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},
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"description": "JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc.",
"example": "JCGG-STR008690",
"homepage": "http://jcggdb.jp/index_en.html",
"name": "JCGGDB at Advanced Science Institute (Japan)",
"namespaceEmbeddedInLui": false,
"pattern": "^JCGG-STR\\d{6}$",
"prefix": "jcggdb",
"uri_format": "http://jcggdb.jp/idb/jcggdb/$1"
},
"name": "Japan Consortium for Glycobiology and Glycotechnology Database"
},
"jcm": {
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},
"fairsharing": {
"abbreviation": "JCM",
"description": "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2.",
"homepage": "http://www.jcm.riken.go.jp/",
"name": "Japan Collection of Microorganisms",
"prefix": "FAIRsharing.h2wrt2",
"publications": [],
"subjects": [
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]
},
"mappings": {
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"fairsharing": "FAIRsharing.h2wrt2",
"miriam": "jcm",
"n2t": "jcm",
"ncbi": "JCM",
"prefixcommons": "jcm"
},
"miriam": {
"deprecated": false,
"description": "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2.",
"homepage": "http://www.jcm.riken.go.jp/",
"id": "00000174",
"name": "Japan Collection of Microorganisms",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "jcm",
"sampleId": "17254",
"uri_format": "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1"
},
"n2t": {
"description": "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2.",
"example": "17254",
"homepage": "http://www.jcm.riken.go.jp/",
"name": "JCM at RIKEN BioResource Center",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "jcm",
"uri_format": "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1"
},
"ncbi": {
"example": "1339",
"homepage": "http://www.jcm.riken.go.jp/",
"name": "Japan Collection of Microorganisms",
"prefix": "JCM"
},
"prefixcommons": {
"description": "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2.",
"example": "17254",
"homepage": "http://www.jcm.riken.go.jp/",
"keywords": [
"microbial",
"taxonomy"
],
"name": "Japan Collection of Microorganisms",
"pattern": "^\\d+$",
"prefix": "jcm",
"uri_format": "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1"
}
},
"jcrb": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "http://cellbank.nibiohn.go.jp/english/",
"name": "Japanese Collection of Research Bioresources Cell Bank",
"prefix": "JCRB",
"uri_format": "http://cellbank.nibiohn.go.jp//~cellbank/en/search_res_det.cgi?RNO=$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"example": "JCRB1355",
"homepage": "https://cellbank.nibiohn.go.jp",
"mappings": {
"cellosaurus": "JCRB"
},
"name": "JRBC Cell Bank",
"pattern": "^JCRB\\d+$",
"uri_format": "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1"
},
"jcsd": {
"biocontext": {
"prefix": "JCSD"
},
"contributor_extras": [
{
"email": "b.gyori@northeastern.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
}
],
"mappings": {
"biocontext": "JCSD",
"miriam": "jcsd",
"n2t": "jcsd",
"prefixcommons": "jcsd"
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"miriam": {
"deprecated": false,
"description": "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST).",
"homepage": "http://jglobal.jst.go.jp/en/",
"id": "00000241",
"name": "Japan Chemical Substance Dictionary",
"namespaceEmbeddedInLui": false,
"pattern": "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$",
"prefix": "jcsd",
"sampleId": "J55.713G",
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},
"n2t": {
"description": "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST).",
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"homepage": "http://jglobal.jst.go.jp/en/",
"name": "Japan Chemical Substance Dictionary",
"namespaceEmbeddedInLui": false,
"pattern": "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$",
"prefix": "jcsd",
"uri_format": "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1"
},
"prefixcommons": {
"description": "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST).",
"example": "J55.713G",
"keywords": [
"chemical",
"structure"
],
"name": "Japan Chemical Substance Dictionary",
"pattern": "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$",
"prefix": "jcsd",
"uri_format": "http://nikkajiweb.jst.go.jp/nikkaji_web/pages/top_e.jsp?CONTENT=syosai&SN=$1"
}
},
"jgi.proposal": {
"contact": {
"email": "sewilson@lbl.gov",
"name": "Steven E. Wilson",
"orcid": "0000-0002-8489-208X"
},
"contributor": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"contributor_extras": [
{
"email": "aclum@lbl.gov",
"github": "aclum",
"name": "Alicia Clum",
"orcid": "0000-0002-5004-3362"
}
],
"description": "Identifiers for proposals/projects at the Joint Genome Institute",
"example": "502930",
"github_request_issue": 853,
"homepage": "https://genome.jgi.doe.gov/portal/",
"name": "Joint Genome Institute Proposals",
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1128/msystems.00804-20",
"pmc": "PMC8269246",
"pubmed": "34006627",
"title": "DOE JGI Metagenome Workflow",
"year": 2021
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue=$1"
},
"jrct": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "This system submits an implementation plan to the Minister of Health, Labor and Welfare for clinical research conducted at medical institutions, etc. based on the provisions of the 'Clinical Research Act' and the 'Act on Ensuring Safety of Regenerative Medicine, etc.' It is a system for performing notification procedures such as In addition, based on the clinical research practice standards stipulated in the same law, we disclose information that the World Health Organization (WHO) requires to be disclosed, information that ensures the transparency of the research process, and information that contributes to the selection of participation in clinical research by the public. (translated from website)",
"example": "jRCTs041220087",
"homepage": "https://jrct.niph.go.jp",
"name": "Japan Registry of Clinical Trials",
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"providers": [
{
"code": "",
"description": "",
"homepage": "",
"name": "",
"uri_format": "https://jrct.niph.go.jp/latest-detail/$1"
}
],
"uri_format": "https://jrct.niph.go.jp/en-latest-detail/$1"
},
"jstor": {
"biocontext": {
"prefix": "JSTOR"
},
"go": {
"homepage": "https://www.jstor.org/",
"name": "Digital archive of scholarly articles",
"prefix": "JSTOR",
"uri_format": "https://www.jstor.org/stable/$1"
},
"mappings": {
"biocontext": "JSTOR",
"go": "JSTOR",
"miriam": "jstor",
"n2t": "jstor"
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"miriam": {
"deprecated": false,
"description": "JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration.",
"homepage": "http://www.jstor.org/",
"id": "00000444",
"name": "JSTOR",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "jstor",
"sampleId": "3075966",
"uri_format": "http://www.jstor.org/stable/$1"
},
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"description": "JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration.",
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"homepage": "http://www.jstor.org/",
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"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "jstor",
"uri_format": "http://www.jstor.org/stable/$1"
}
},
"jws": {
"biocontext": {
"prefix": "JWS"
},
"contact": {
"email": "brettolivier@gmail.com",
"github": "bgoli",
"name": "Brett G. Olivier",
"orcid": "0000-0002-5293-5321"
},
"example": "achcar11",
"mappings": {
"biocontext": "JWS",
"miriam": "jws",
"n2t": "jws",
"prefixcommons": "jws"
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"miriam": {
"deprecated": false,
"description": "JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser.",
"homepage": "http://jjj.biochem.sun.ac.za/models/",
"id": "00000130",
"name": "JWS Online",
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"pattern": "^\\w+$",
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"providers": [
{
"code": "CURATOR_REVIEW",
"description": "JWS Online Model Repository at Manchester",
"homepage": "http://jjj.mib.ac.uk/index.html",
"name": "JWS Online Model Repository at Manchester",
"uri_format": "http://jjj.mib.ac.uk/models/$1"
},
{
"code": "CURATOR_REVIEW",
"description": "JWS Online Model Repository at Amsterdam",
"homepage": "http://jjj.bio.vu.nl/models/",
"name": "JWS Online Model Repository at Amsterdam",
"uri_format": "http://jjj.bio.vu.nl/models/$1/"
}
],
"sampleId": "curien",
"uri_format": "http://jjj.biochem.sun.ac.za/models/$1/"
},
"n2t": {
"description": "JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser.",
"example": "curien",
"homepage": "http://jjj.mib.ac.uk/index.html",
"name": "JWS Online Model Repository at Manchester",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "jws",
"uri_format": "http://jjj.mib.ac.uk/models/$1"
},
"prefixcommons": {
"description": "JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser.",
"example": "curien",
"homepage": "http://jjj.mib.ac.uk/index.html",
"keywords": [
"model",
"pathway"
],
"name": "JWS Online Model Repository",
"pattern": "^\\w+$",
"prefix": "jws",
"pubmed_ids": [
"15072998"
],
"uri_format": "http://jjj.mib.ac.uk/cgi-bin/processModelSelection.py?keytype=modelname&keyword=$1"
},
"publications": [
{
"doi": "10.1093/bioinformatics/bth200",
"pubmed": "15072998",
"title": "Web-based kinetic modelling using JWS Online",
"year": 2004
}
],
"uri_format": "https://jjj.bio.vu.nl/models/$1"
},
"kaggle": {
"mappings": {
"miriam": "kaggle",
"n2t": "kaggle",
"re3data": "r3d100012705"
},
"miriam": {
"deprecated": false,
"description": "Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions.",
"homepage": "https://kaggle.com",
"id": "00000682",
"name": "Kaggle",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9a-zA-Z\\-]+\\/[0-9a-zA-Z\\-]+$",
"prefix": "kaggle",
"sampleId": "nasa/kepler-exoplanet-search-results",
"uri_format": "https://www.kaggle.com/$1"
},
"n2t": {
"description": "Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions.",
"example": "nasa/kepler-exoplanet-search-results",
"homepage": "https://kaggle.com",
"name": "Kaggle",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9a-zA-Z\\-]+\\/[0-9a-zA-Z\\-]+$",
"prefix": "kaggle",
"uri_format": "https://www.kaggle.com/$1"
},
"re3data": {
"description": "Kaggle is a platform for predictive modelling and analytics competitions in which statisticians and data miners compete to produce the best models for predicting and describing the datasets uploaded by companies and users. This crowdsourcing approach relies on the fact that there are countless strategies that can be applied to any predictive modelling task and it is impossible to know beforehand which technique or analyst will be most effective.",
"homepage": "https://www.kaggle.com/datasets",
"name": "Kaggle",
"prefix": "r3d100012705",
"synonyms": [
"Your home for data science"
],
"xrefs": {
"fairsharing": "FAIRsharing.mjq9vj"
}
}
},
"kclb": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://cellbank.snu.ac.kr/eng/",
"name": "Korean Cell Line Bank",
"prefix": "KCLB",
"uri_format": "https://cellbank.snu.ac.kr/main/tmpl/sub_main.php?m_cd=6&m_id=0201&strQ=$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"example": "10020.2",
"homepage": "https://cellbank.snu.ac.kr/english",
"mappings": {
"cellosaurus": "KCLB"
},
"name": "Korean Cell Line Bank",
"uri_format": "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1"
},
"kcris": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Clinical Research Information Service (CRIS) is a non-profit online registration system for clinical trials (researches) to be conducted in Korea. It has been established at the Korea Disease Control and Prevention Agency (KDCA) with support from the Ministry of Health and Welfare (MOHW). It joined the WHO International Clinical Trials Registry Platform (ICTRP) as 11th member of Primary Registry. (from about page)\nNote that the web page that resolves this trial does not correspond to the semantic space",
"example": "KCT0008394",
"homepage": "https://cris.nih.go.kr",
"name": "Korean Clinical Research Information Service",
"pattern": "^KCT\\d+$",
"references": [
"https://cris.nih.go.kr/cris/search/detailSearchEn.do?seq=23973"
]
},
"kegg": {
"biocontext": {
"prefix": "KEGG"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "KEGG",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"cheminf": {
"description": "Database identifier used by KEGG.",
"name": "KEGG",
"obsolete": false,
"prefix": "000409"
},
"comment": "KEGG prefix has been split into several others",
"deprecated": true,
"go": {
"homepage": "http://www.genome.ad.jp/kegg/",
"name": "Kyoto Encyclopedia of Genes and Genomes",
"prefix": "KEGG"
},
"integbio": {
"alt_name": "Kyoto Encyclopedia of Genes and Genomes",
"description": "KEGG is an integrated database for interpretation of biological systems from genomic and molecular-level information. KEGG consists of 16 main databases categorized into systems information, genomic information and chemical information. This database features to map elementary datasets (genes, small molecules, etc) in each KEGG database to network datasets (pathway maps, hierarchical lists, etc). Users can perform keyword search against the entire KEGG database, as well as BLAST/FASTA search and SIMCOMP search.",
"fairsharing": "biodbcore-000663",
"homepage": "http://www.kegg.jp/kegg/",
"information_keywords": [
"Portal"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG",
"prefix": "nbdc00530",
"pubmeds": [
"9287494",
"16381885",
"14681412",
"24214961"
],
"status": "Active"
},
"mappings": {
"biocontext": "KEGG",
"biolink": "KEGG",
"cheminf": "000409",
"go": "KEGG",
"integbio": "nbdc00530",
"miriam": "kegg",
"n2t": "kegg",
"pathguide": "16",
"uniprot": "DB-0053"
},
"miriam": {
"deprecated": false,
"description": "Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.",
"homepage": "http://www.kegg.jp/",
"id": "00000578",
"name": "Kyoto Encyclopedia of Genes and Genomes",
"namespaceEmbeddedInLui": false,
"pattern": "^([CHDEGTMKR]\\d+)|(\\w+:[\\w\\d\\.-]*)|([a-z]{3,5})|(\\w{2,4}\\d{5})$",
"prefix": "kegg",
"sampleId": "hsa00190",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"n2t": {
"description": "Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.",
"example": "hsa00190",
"homepage": "http://www.kegg.jp/",
"name": "KEGG at Kyoto University Bioinformatics Center",
"namespaceEmbeddedInLui": false,
"pattern": "^([CHDEGTMKR]\\d+)|(\\w+:[\\w\\d\\.-]*)|([a-z]{3,5})|(\\w{2,4}\\d{5})$",
"prefix": "kegg",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"pathguide": {
"abbreviation": "KEGG",
"homepage": "http://www.genome.jp/kegg/",
"keywords": [
"BioPAX"
],
"name": "Kyoto Encyclopedia of Genes and Genomes",
"prefix": "16"
},
"publications": [
{
"doi": "10.1093/nar/gkw1092",
"pmc": "PMC5210567",
"pubmed": "27899662",
"title": "KEGG: new perspectives on genomes, pathways, diseases and drugs",
"year": 2016
}
],
"synonyms": [
"KEGG"
],
"uniprot": {
"abbreviation": "KEGG",
"category": "Genome annotation databases",
"homepage": "https://www.genome.jp/kegg/",
"name": "KEGG",
"prefix": "DB-0053",
"publications": [
{
"doi": "10.1093/nar/gkw1092",
"pubmed": "27899662"
}
],
"uri_format": "https://www.genome.jp/dbget-bin/www_bget?$1"
}
},
"kegg.brite": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "KEGG.BRITE",
"uri_format": "https://bioregistry.io/kegg.brite:$1"
},
"integbio": {
"alt_name": "Functional hierarchies and binary relationships of biological entities",
"description": "The KEGG BRITE database contains functional hierarchies and binary relationships of biological entities, and includes many types of relationships. KEGG BRITE maps large-scale molecular datasets in genomics, transcriptomics, proteomics, and metabolomics to BRITE functional hierarchies, and allows biological interpretation of higher-level systemic functions.",
"homepage": "http://www.genome.jp/kegg/brite.html",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Classification"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG BRITE",
"prefix": "nbdc00115",
"status": "Active"
},
"mappings": {
"biolink": "KEGG.BRITE",
"integbio": "nbdc00115",
"prefixcommons": "kegg.brite"
},
"part_of": "kegg",
"prefixcommons": {
"description": "KEGG BRITE is a collection of hierarchical classifications (see new hierarchies and last updates) representing our knowledge on various aspects of biological systems. In contrast to KEGG PATHWAY, which is limited to molecular interactions and reactions, KEGG BRITE incorporates many different types of relationships.",
"example": "ko00071",
"homepage": "http://www.genome.jp/kegg/brite.html",
"keywords": [
"pathway",
"classification",
"ontology"
],
"name": "KEGG BRITE",
"pattern": "^[ko/br]\\d+$",
"prefix": "kegg.brite",
"synonyms": [
"br",
"brite"
],
"uri_format": "http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br$1"
}
},
"kegg.compound": {
"biocontext": {
"prefix": "KEGG.COMPOUND"
},
"contact": {
"email": "kanehisa@kuicr.kyoto-u.ac.jp",
"name": "Minoru Kanehisa",
"orcid": "0000-0001-6123-540X"
},
"edam": {
"description": "Unique identifier of a chemical compound from the KEGG database.",
"name": "Compound ID (KEGG)",
"obsolete": false,
"prefix": "2605"
},
"integbio": {
"alt_name": "Metabolome informatics resource integrating genomics and chemistry",
"description": "KEGG COMPOUND is a database of biologically relevant compounds, including chemical structures and associated information for compounds in the KEGG database such as small molecules, biopolymers, and other related substances. The site also has a collection of links to other relevant KEGG resources such as GLYCAN.",
"homepage": "http://www.genome.jp/kegg/compound/",
"information_keywords": [
"Interaction/Pathway",
"Chemical structure"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG COMPOUND",
"prefix": "nbdc00814",
"pubmeds": [
"19327755",
"17921532",
"17400247",
"14505407",
"20460463"
],
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Protein",
"Chemical compound"
]
},
"mappings": {
"biocontext": "KEGG.COMPOUND",
"edam": "2605",
"integbio": "nbdc00814",
"miriam": "kegg.compound",
"n2t": "kegg.compound",
"prefixcommons": "kegg.compound",
"wikidata": "P665"
},
"miriam": {
"deprecated": false,
"description": "KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life.",
"homepage": "https://www.genome.jp/kegg/ligand.html",
"id": "00000013",
"name": "KEGG Compound",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d+$",
"prefix": "kegg.compound",
"sampleId": "C12345",
"uri_format": "https://www.kegg.jp/entry/$1"
},
"n2t": {
"description": "KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life.",
"example": "C12345",
"homepage": "https://www.genome.jp/kegg/ligand.html",
"name": "KEGG LIGAND Database",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d+$",
"prefix": "kegg.compound",
"uri_format": "https://www.kegg.jp/entry/$1"
},
"part_of": "kegg",
"prefixcommons": {
"description": "KEGG COMPOUND is a chemical structure database for metabolic compounds and other chemical substances that are relevant to biological systems.",
"example": "C12345",
"homepage": "http://www.genome.jp/kegg/compound/",
"keywords": [
"small molecule"
],
"name": "KEGG Compound",
"pattern": "^C\\d+$",
"prefix": "kegg.compound",
"pubmed_ids": [
"22700311"
],
"synonyms": [
"cpd",
"kegg.compounds"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?cpd:$1"
},
"publications": [
{
"doi": "10.1002/0471250953.bi0112s38",
"pubmed": "22700311",
"title": "Using the KEGG database resource",
"year": 2012
}
],
"synonyms": [
"KEGG COMPOUND",
"KEGG.COMPOUND"
],
"wikidata": {
"prefix": "P665"
}
},
"kegg.dgroup": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "KEGG.DGROUP",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": " KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. There are five types of drug groups.\n\n Chemical - grouped as identical chemical structures with minor variations of salts, hydration states, etc.\n Structure - grouped as similar chemical structures having the same skeleton, etc.\n Target - grouped by drug targets\n Class - drug classes often representing similar mechanisms of action\n Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters\n\nChemical groups are often used for identifying essentially the same active ingredients of drugs in different countries.",
"example": "DG00301",
"homepage": "http://www.genome.jp/kegg/reaction/",
"mappings": {
"biolink": "KEGG.DGROUP"
},
"name": "KEGG Drug Group",
"part_of": "kegg",
"pattern": "^DG\\d+$",
"references": [
"https://github.com/prefixcommons/prefixes/pull/4"
],
"synonyms": [
"KEGG_DGROUP",
"KEGG_DRUG_GROUP"
]
},
"kegg.disease": {
"biocontext": {
"prefix": "KEGG.DISEASE"
},
"integbio": {
"alt_name": "Diseases viewed as perturbed states of the molecular system",
"description": "KEGG DISEASE is a database of human diseases with information on perturbed molecular networks. Each disease entry contains a list of known disease genes, environmental factors (carcinogens, pathogens, etc), diagnostic markers and therapeutic drugs with reference information. This database provides maps of molecular networks associated with diseases through links to the KEGG PATHWAY database. Users can search human diseases by names, description, categories, pathways, and known causative genes.",
"homepage": "http://www.genome.jp/kegg/disease/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG DISEASE",
"prefix": "nbdc00813",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Drug"
]
},
"mappings": {
"biocontext": "KEGG.DISEASE",
"integbio": "nbdc00813",
"miriam": "kegg.disease",
"n2t": "kegg.disease",
"prefixcommons": "kegg.disease"
},
"miriam": {
"deprecated": false,
"description": "The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system.",
"homepage": "http://www.genome.jp/kegg/disease/",
"id": "00000475",
"name": "KEGG Disease",
"namespaceEmbeddedInLui": false,
"pattern": "^H\\d+$",
"prefix": "kegg.disease",
"sampleId": "H00076",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"n2t": {
"description": "The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system.",
"example": "H00076",
"homepage": "http://www.genome.jp/kegg/disease/",
"name": "KEGG Disease at Kyoto University Bioinformatics Center",
"namespaceEmbeddedInLui": false,
"pattern": "^H\\d+$",
"prefix": "kegg.disease",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"part_of": "kegg",
"prefixcommons": {
"description": "The KEGG DISEASE database is a new collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry is identified by the H number and contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs.",
"example": "H00047",
"homepage": "http://www.genome.jp/kegg/disease/",
"keywords": [
"classification"
],
"name": "KEGG Disease",
"pattern": "^H\\d+$",
"prefix": "kegg.disease",
"synonyms": [
"ds",
"kegg.diseases"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?ds:$1"
}
},
"kegg.drug": {
"biocontext": {
"prefix": "KEGG.DRUG"
},
"contact": {
"email": "kanehisa@kuicr.kyoto-u.ac.jp",
"name": "Minoru Kanehisa",
"orcid": "0000-0001-6123-540X"
},
"edam": {
"description": "Unique identifier of a drug from the KEGG Drug database.",
"name": "Drug ID (KEGG)",
"obsolete": false,
"prefix": "2609"
},
"integbio": {
"alt_name": "Drugs viewed as perturbants to the molecular system",
"description": "KEGG DRUG is a comprehensive database of drug information about all marketed drugs in Japan, as well as many prescription drugs in USA and Europe. KEGG DRUG is based on chemical structure or component, and each entry contains information about drug targets (pathways), metabolizing enzymes and other interacting molecules. This database also includes crude drugs and TCM (Tradictional Chinese Medicine). Users can check for drug-drug interaction, view structure maps representing the history of drug development and search drugs by generic names, trade names, and components.",
"homepage": "http://www.genome.jp/kegg/drug/",
"information_keywords": [
"Interaction/Pathway",
"Chemical structure"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG DRUG",
"prefix": "nbdc00812",
"status": "Active",
"target_keywords": [
"Drug"
]
},
"mappings": {
"biocontext": "KEGG.DRUG",
"edam": "2609",
"integbio": "nbdc00812",
"miriam": "kegg.drug",
"n2t": "kegg.drug",
"prefixcommons": "kegg.drug",
"wikidata": "P665"
},
"miriam": {
"deprecated": false,
"description": "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules.",
"homepage": "https://www.genome.jp/kegg/drug/",
"id": "00000025",
"name": "KEGG Drug",
"namespaceEmbeddedInLui": false,
"pattern": "^D\\d+$",
"prefix": "kegg.drug",
"sampleId": "D00123",
"uri_format": "https://www.kegg.jp/entry/$1"
},
"n2t": {
"description": "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules.",
"example": "D00123",
"homepage": "https://www.genome.jp/kegg/drug/",
"name": "KEGG DRUG Database",
"namespaceEmbeddedInLui": false,
"pattern": "^D\\d+$",
"prefix": "kegg.drug",
"uri_format": "https://www.kegg.jp/entry/$1"
},
"part_of": "kegg",
"prefixcommons": {
"description": "KEGG DRUG is a unified drug information resource that contains chemical structures and/or chemical components of all prescription and OTC drugs in Japan, most prescription drugs in the USA, and many prescription drugs in Europe.",
"example": "D00123",
"homepage": "http://www.genome.jp/kegg/drug/",
"keywords": [
"small molecule"
],
"name": "KEGG Drug",
"pattern": "^D\\d+$",
"prefix": "kegg.drug",
"pubmed_ids": [
"16381885"
],
"synonyms": [
"dr",
"kegg.drugs"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?dr:$1"
},
"publications": [
{
"doi": "10.1093/nar/gkj102",
"pmc": "PMC1347464",
"pubmed": "16381885",
"title": "From genomics to chemical genomics: new developments in KEGG",
"year": 2006
}
],
"synonyms": [
"KEGG DRUG",
"KEGG.DRUG"
],
"wikidata": {
"prefix": "P665"
}
},
"kegg.environ": {
"biocontext": {
"prefix": "KEGG.ENVIRON"
},
"deprecated": true,
"integbio": {
"description": "KEGG ENVIRON is a database of crude drugs, essential oils, and medicinal harbs, all of which are mostly natural products of plants. Each entry is associated with the chemical component, efficacy information, and source species information whenever applicable.",
"homepage": "http://www.genome.jp/kegg/drug/environ.html",
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG ENVIRON",
"prefix": "nbdc01059",
"status": "Closed",
"target_keywords": [
"Health/Disease",
"Chemical compound",
"Drug"
]
},
"mappings": {
"biocontext": "KEGG.ENVIRON",
"integbio": "nbdc01059",
"miriam": "kegg.environ",
"n2t": "kegg.environ"
},
"miriam": {
"deprecated": false,
"description": "KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable.",
"homepage": "http://www.genome.jp/kegg/drug/environ.html",
"id": "00000389",
"name": "KEGG Environ",
"namespaceEmbeddedInLui": false,
"pattern": "^(ev\\:)?E\\d+$",
"prefix": "kegg.environ",
"sampleId": "ev:E00032",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"n2t": {
"description": "KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable.",
"example": "ev:E00032",
"homepage": "http://www.genome.jp/kegg/drug/environ.html",
"name": "KEGG ENVIRON Database",
"namespaceEmbeddedInLui": false,
"pattern": "^(ev\\:)?E\\d+$",
"prefix": "kegg.environ",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"part_of": "kegg",
"synonyms": [
"KEGG.EDRUG"
]
},
"kegg.enzyme": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "KEGG.ENZYME",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"description": "KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links.",
"go": {
"homepage": "http://www.genome.jp/dbget-bin/www_bfind?enzyme",
"name": "KEGG Enzyme Database",
"prefix": "KEGG_ENZYME",
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?ec:$1"
},
"mappings": {
"biolink": "KEGG.ENZYME",
"go": "KEGG_ENZYME"
},
"name": "KEGG Enzyme",
"part_of": "kegg",
"provides": "eccode"
},
"kegg.genes": {
"biocontext": {
"prefix": "KEGG.GENES"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "KEGG.GENES",
"uri_format": "https://bioregistry.io/kegg.genes:bsu:$1"
},
"contact": {
"email": "kanehisa@kuicr.kyoto-u.ac.jp",
"name": "Minoru Kanehisa",
"orcid": "0000-0001-6123-540X"
},
"example": "bsu:BSU01340",
"mappings": {
"biocontext": "KEGG.GENES",
"biolink": "KEGG.GENES",
"miriam": "kegg.genes",
"n2t": "kegg.genes",
"prefixcommons": "kegg.gene",
"wikidata": "P665"
},
"miriam": {
"deprecated": false,
"description": "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources.",
"homepage": "http://www.genome.jp/kegg/genes.html",
"id": "00000070",
"name": "KEGG Genes",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+:[\\w\\d\\.-]*$",
"prefix": "kegg.genes",
"sampleId": "syn:ssr3451",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"n2t": {
"description": "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources.",
"example": "syn:ssr3451",
"homepage": "http://www.genome.jp/kegg/genes.html",
"name": "KEGG GENES Database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+:[\\w\\d\\.-]*$",
"prefix": "kegg.genes",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"part_of": "kegg",
"prefixcommons": {
"description": "KEGG GENES is a collection of gene catalogs for all complete genomes generated from publicly available resources, mostly NCBI RefSeq. They are subject to SSDB computation and KO assignment (gene annotation) by KOALA tool",
"example": "syn:ssr3451",
"homepage": "http://www.genome.jp/kegg/genes.html",
"keywords": [
"gene",
"DNA",
"protein"
],
"name": "KEGG Genes",
"pattern": "^\\w+:[\\w\\d\\.-]*$",
"prefix": "kegg.gene",
"pubmed_ids": [
"16381885"
],
"synonyms": [
"gene",
"kegg.genes"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?[?species]:$1"
},
"publications": [
{
"doi": "10.1093/nar/gkj102",
"pmc": "PMC1347464",
"pubmed": "16381885",
"title": "From genomics to chemical genomics: new developments in KEGG",
"year": 2006
}
],
"wikidata": {
"prefix": "P665"
}
},
"kegg.genome": {
"biocontext": {
"prefix": "KEGG.GENOME"
},
"contact": {
"email": "kanehisa@kuicr.kyoto-u.ac.jp",
"name": "Minoru Kanehisa",
"orcid": "0000-0001-6123-540X"
},
"example": "T06648",
"integbio": {
"alt_name": "Organisms and ecosystems with genome sequence information",
"description": "KEGG GENOME is a database of full genome sequence information for multiple species. The database is a collection of references to descriptive genome literature and has links to reaction pathways in each organism, comparative tools, and taxonomy based on KEGG information and provides KEGG pathway information and links to outside resources including primary literature.",
"homepage": "http://www.genome.jp/kegg/genome.html",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG GENOME",
"prefix": "nbdc00816",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"mappings": {
"biocontext": "KEGG.GENOME",
"integbio": "nbdc00816",
"miriam": "kegg.genome",
"n2t": "kegg.genome",
"prefixcommons": "kegg.genome",
"wikidata": "P665"
},
"miriam": {
"deprecated": false,
"description": "KEGG Genome is a collection of organisms whose genomes have been completely sequenced.",
"homepage": "http://www.genome.jp/kegg/catalog/org_list.html",
"id": "00000238",
"name": "KEGG Genome",
"namespaceEmbeddedInLui": false,
"pattern": "^(T0\\d+|\\w{3,5})$",
"prefix": "kegg.genome",
"sampleId": "eco",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"n2t": {
"description": "KEGG Genome is a collection of organisms whose genomes have been completely sequenced.",
"example": "eco",
"homepage": "http://www.genome.jp/kegg/catalog/org_list.html",
"name": "KEGG Genome Database",
"namespaceEmbeddedInLui": false,
"pattern": "^(T0\\d+|\\w{3,5})$",
"prefix": "kegg.genome",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"part_of": "kegg",
"prefixcommons": {
"description": "Complete organism genomes",
"example": "T00047",
"homepage": "http://www.genome.jp/kegg/catalog/org_list.html",
"name": "KEGG Genome",
"pattern": "^T\\d+$",
"prefix": "kegg.genome",
"pubmed_ids": [
"22080510"
],
"synonyms": [
"gn",
"kegg.genomes"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?gn:$1"
},
"publications": [
{
"doi": "10.1093/nar/gkr988",
"pmc": "PMC3245020",
"pubmed": "22080510",
"title": "KEGG for integration and interpretation of large-scale molecular data sets",
"year": 2011
}
],
"synonyms": [
"kegg_genome",
"kegg_genomes"
],
"wikidata": {
"prefix": "P665"
}
},
"kegg.glycan": {
"biocontext": {
"prefix": "KEGG.GLYCAN"
},
"contact": {
"email": "kanehisa@kuicr.kyoto-u.ac.jp",
"name": "Minoru Kanehisa",
"orcid": "0000-0001-6123-540X"
},
"edam": {
"description": "Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND).",
"name": "KEGG Glycan",
"obsolete": false,
"prefix": "2613"
},
"integbio": {
"alt_name": "Glycome informatics resource integrating genomics and chemistry",
"description": "KEGG GLYCAN is a database of glycan structures. The database contains structures of glycans involved in KEGG reactions and specifies several parameters of the glycans, as well as collecting links to other glycan-relevant databases. The database is searchable by KEGG G-index ID.",
"homepage": "http://www.genome.jp/kegg/glycan/",
"information_keywords": [
"Interaction/Pathway",
"Chemical structure"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG GLYCAN",
"prefix": "nbdc00533",
"pubmeds": [
"16014746",
"16362924",
"19327755",
"15215393",
"16159923",
"18546491"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein",
"Carbohydrate"
]
},
"mappings": {
"biocontext": "KEGG.GLYCAN",
"edam": "2613",
"integbio": "nbdc00533",
"miriam": "kegg.glycan",
"n2t": "kegg.glycan",
"prefixcommons": "kegg.glycan"
},
"miriam": {
"deprecated": false,
"description": "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways.",
"homepage": "https://www.genome.jp/kegg/glycan/",
"id": "00000026",
"name": "KEGG Glycan",
"namespaceEmbeddedInLui": false,
"pattern": "^G\\d+$",
"prefix": "kegg.glycan",
"sampleId": "G00123",
"uri_format": "https://www.kegg.jp/entry/$1"
},
"n2t": {
"description": "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways.",
"example": "G00123",
"homepage": "https://www.genome.jp/kegg/glycan/",
"name": "KEGG GLYCAN Database",
"namespaceEmbeddedInLui": false,
"pattern": "^G\\d+$",
"prefix": "kegg.glycan",
"uri_format": "https://www.kegg.jp/entry/$1"
},
"part_of": "kegg",
"prefixcommons": {
"description": "The KEGG GLYCAN structure database is a collection of experimentally determined glycan structures [1]. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways.",
"example": "G00123",
"homepage": "http://www.genome.jp/kegg/glycan/",
"keywords": [
"small molecule"
],
"name": "KEGG Glycan",
"pattern": "^G\\d+$",
"prefix": "kegg.glycan",
"pubmed_ids": [
"16014746"
],
"synonyms": [
"gl",
"kegg.glycans"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?gl:$1"
},
"publications": [
{
"doi": "10.1093/glycob/cwj010",
"pubmed": "16014746",
"title": "KEGG as a glycome informatics resource",
"year": 2005
}
]
},
"kegg.ligand": {
"comment": "This database has been discontinued by KEGG. It now lives inside the compound database",
"deprecated": true,
"go": {
"homepage": "http://www.genome.ad.jp/kegg/docs/upd_ligand.html",
"name": "KEGG LIGAND Database",
"prefix": "KEGG_LIGAND",
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?cpd:$1"
},
"mappings": {
"go": "KEGG_LIGAND"
},
"name": "KEGG LIGAND",
"part_of": "kegg"
},
"kegg.metagenome": {
"biocontext": {
"prefix": "KEGG.METAGENOME"
},
"contact": {
"email": "kanehisa@kuicr.kyoto-u.ac.jp",
"name": "Minoru Kanehisa",
"orcid": "0000-0001-6123-540X"
},
"mappings": {
"biocontext": "KEGG.METAGENOME",
"miriam": "kegg.metagenome",
"n2t": "kegg.metagenome",
"prefixcommons": "kegg.metagenome"
},
"miriam": {
"deprecated": false,
"description": "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species.",
"homepage": "http://www.genome.jp/kegg/catalog/org_list3.html",
"id": "00000239",
"name": "KEGG Metagenome",
"namespaceEmbeddedInLui": false,
"pattern": "^T3\\d+$",
"prefix": "kegg.metagenome",
"sampleId": "T30002",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"n2t": {
"description": "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species.",
"example": "T30002",
"homepage": "http://www.genome.jp/kegg/catalog/org_list3.html",
"name": "KEGG Metagenome Database",
"namespaceEmbeddedInLui": false,
"pattern": "^T3\\d+$",
"prefix": "kegg.metagenome",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"part_of": "kegg",
"prefixcommons": {
"description": "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species.",
"example": "T30002",
"keywords": [
"genome"
],
"name": "KEGG Metagenome",
"pattern": "^T3\\d+$",
"prefix": "kegg.metagenome",
"pubmed_ids": [
"22080510"
],
"synonyms": [
"kegg.metagenomes"
],
"uri_format": "http://www.genome.jp/kegg-bin/show_organism?org=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkr988",
"pmc": "PMC3245020",
"pubmed": "22080510",
"title": "KEGG for integration and interpretation of large-scale molecular data sets",
"year": 2011
}
]
},
"kegg.module": {
"biocontext": {
"prefix": "KEGG.MODULE"
},
"integbio": {
"description": "KEGG MODULE is a database of manually defined functional units called KEGG modules identified by M numbers, used for annotation and biological interpretation of sequenced genomes. It contains four types of KEGG modules;\n1) pathway modules - representing tight functional units in KEGG metabolic pathway maps\n2) structural complexes - often forming molecular machineries\n3) functional sets - for other types of essential sets, such as Aminoacyl-tRNA synthases, prokaryotes, etc.\n4) signature modules - as markers of phenotypes, such as EHEC pathogenicity signature, Shiga toxin, etc.",
"homepage": "http://www.genome.jp/kegg/module.html",
"information_keywords": [
"Phenotype",
"Interaction/Pathway"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG MODULE",
"prefix": "nbdc01428",
"pubmeds": [
"23384306"
],
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"mappings": {
"biocontext": "KEGG.MODULE",
"integbio": "nbdc01428",
"miriam": "kegg.module",
"n2t": "kegg.module"
},
"miriam": {
"deprecated": false,
"description": "KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules.",
"homepage": "http://www.kegg.jp/kegg/module.html",
"id": "00000474",
"name": "KEGG Module",
"namespaceEmbeddedInLui": false,
"pattern": "^([a-z]{3,5}_)?M\\d{5}$",
"prefix": "kegg.module",
"sampleId": "M00002",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"n2t": {
"description": "KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules.",
"example": "M00002",
"homepage": "http://www.kegg.jp/kegg/module.html",
"name": "KEGG Module at Kyoto University Bioinformatics Center",
"namespaceEmbeddedInLui": false,
"pattern": "^([a-z]{3,5}_)?M\\d{5}$",
"prefix": "kegg.module",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"part_of": "kegg"
},
"kegg.orthology": {
"biocontext": {
"prefix": "KEGG.ORTHOLOGY"
},
"mappings": {
"biocontext": "KEGG.ORTHOLOGY",
"miriam": "kegg.orthology",
"n2t": "kegg.orthology",
"prefixcommons": "kegg.orthology"
},
"miriam": {
"deprecated": false,
"description": "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms.",
"homepage": "http://www.genome.jp/kegg/ko.html",
"id": "00000116",
"name": "KEGG Orthology",
"namespaceEmbeddedInLui": false,
"pattern": "^K\\d+$",
"prefix": "kegg.orthology",
"sampleId": "K00001",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"n2t": {
"description": "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms.",
"example": "K00001",
"homepage": "http://www.genome.jp/kegg/ko.html",
"name": "KEGG Orthology Database",
"namespaceEmbeddedInLui": false,
"pattern": "^K\\d+$",
"prefix": "kegg.orthology",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"part_of": "kegg",
"prefixcommons": {
"description": "The KEGG reference pathway maps and BRITE functional hierarchies are represented in a general way to be applicable to all organisms. KEGG Orthology (KO) is the basis for this representation, consisting of manually defined ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes.",
"example": "K00001",
"homepage": "http://www.genome.jp/kegg/ko.html",
"keywords": [
"classification",
"pathway"
],
"name": "KEGG Orthology",
"pattern": "^K\\d+$",
"prefix": "kegg.orthology",
"synonyms": [
"ko"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?ko:$1"
}
},
"kegg.pathway": {
"biocontext": {
"prefix": "KEGG.PATHWAY"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "KEGG.PATHWAY",
"uri_format": "https://bioregistry.io/kegg.pathway:$1"
},
"contact": {
"email": "kanehisa@kuicr.kyoto-u.ac.jp",
"name": "Minoru Kanehisa",
"orcid": "0000-0001-6123-540X"
},
"edam": {
"description": "Identifier of a pathway from the KEGG pathway database.",
"name": "Pathway ID (KEGG)",
"obsolete": false,
"prefix": "2343"
},
"example": "rsk00410",
"go": {
"homepage": "http://www.genome.jp/kegg/pathway.html",
"name": "KEGG Pathways Database",
"prefix": "KEGG_PATHWAY",
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?path:$1"
},
"mappings": {
"biocontext": "KEGG.PATHWAY",
"biolink": "KEGG.PATHWAY",
"edam": "2343",
"go": "KEGG_PATHWAY",
"miriam": "kegg.pathway",
"n2t": "kegg.pathway",
"prefixcommons": "kegg.pathway",
"wikidata": "P665"
},
"miriam": {
"deprecated": false,
"description": "KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.",
"homepage": "https://www.genome.jp/kegg/pathway.html",
"id": "00000012",
"name": "KEGG Pathway",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{2,4}\\d{5}$",
"prefix": "kegg.pathway",
"sampleId": "hsa00620",
"uri_format": "https://www.kegg.jp/entry/$1"
},
"n2t": {
"description": "KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.",
"example": "hsa00620",
"homepage": "https://www.genome.jp/kegg/pathway.html",
"name": "KEGG PATHWAY Database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{2,4}\\d{5}$",
"prefix": "kegg.pathway",
"uri_format": "https://www.kegg.jp/entry/$1"
},
"part_of": "kegg",
"prefixcommons": {
"alt_uri_formats": [
"http://www.genome.jp/kegg-bin/show_pathway?#$1"
],
"description": "KEGG PATHWAY is a collection of manually drawn pathway maps (see new maps, change history, and last updates) representing our knowledge on the molecular interaction and reaction networks",
"example": "map00071",
"homepage": "http://www.genome.jp/kegg/pathway.html",
"keywords": [
"pathway"
],
"name": "KEGG Pathway",
"pattern": "^map\\d+$",
"prefix": "kegg.pathway",
"pubmed_ids": [
"22700311"
],
"synonyms": [
"path",
"kegg.pathways"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?map$1"
},
"publications": [
{
"doi": "10.1002/0471250953.bi0112s38",
"pubmed": "22700311",
"title": "Using the KEGG database resource",
"year": 2012
}
],
"synonyms": [
"KEGG-path",
"KEGG_PATHWAY"
],
"wikidata": {
"prefix": "P665"
}
},
"kegg.rclass": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "KEGG.RCLASS",
"uri_format": "https://www.genome.jp/dbget-bin/www_bget?rc:$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns.",
"example": "RC00001",
"homepage": "http://www.genome.jp/kegg/reaction/",
"integbio": {
"alt_name": "KEGG Reaction Class",
"description": "KEGG RCLASS is a database of enzymatic reactions as organized by the KEGG system and contains an expandable list of all reaction types organized hierarchically. A search function for reaction class is also available. Users can obtain the compounds and enzymes involved for each specified reaction pathway.",
"homepage": "http://www.genome.jp/kegg-bin/get_htext?br08204.keg",
"information_keywords": [
"Interaction/Pathway",
"Chemical structure"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG RCLASS",
"prefix": "nbdc00860",
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"mappings": {
"biolink": "KEGG.RCLASS",
"integbio": "nbdc00860"
},
"name": "KEGG Reaction Class",
"part_of": "kegg",
"pattern": "^RC\\d+$",
"references": [
"https://github.com/prefixcommons/prefixes/pull/2"
],
"synonyms": [
"KEGG_RCLASS",
"KEGG_REACTION_CLASS"
]
},
"kegg.reaction": {
"biocontext": {
"prefix": "KEGG.REACTION"
},
"contact": {
"email": "kanehisa@kuicr.kyoto-u.ac.jp",
"name": "Minoru Kanehisa",
"orcid": "0000-0001-6123-540X"
},
"edam": {
"description": "Identifier of a biological reaction from the KEGG reactions database.",
"name": "Reaction ID (KEGG)",
"obsolete": false,
"prefix": "2608"
},
"go": {
"homepage": "http://www.genome.jp/kegg/reaction/",
"name": "KEGG Reaction Database",
"prefix": "KEGG_REACTION",
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?rn:$1"
},
"integbio": {
"alt_name": "Knowledge base for predicting biodegradation and biosynthesis",
"description": "KEGG REACTION is a database of enzymatic reactions. The database contains all KEGG enzyme interactions and KEGG pathway metabolic reactions, including related pathways, and uses IUBMB nomenclature. Users can also find the reaction pathway of individual enzymes.",
"homepage": "http://www.genome.jp/kegg/reaction/",
"information_keywords": [
"Interaction/Pathway",
"Chemical structure",
"Classification"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG REACTION",
"prefix": "nbdc00818",
"pubmeds": [
"14505407",
"15600352",
"19477985",
"17516640",
"20435670"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"mappings": {
"biocontext": "KEGG.REACTION",
"edam": "2608",
"go": "KEGG_REACTION",
"integbio": "nbdc00818",
"miriam": "kegg.reaction",
"n2t": "kegg.reaction",
"prefixcommons": "kegg.reaction",
"wikidata": "P665"
},
"miriam": {
"deprecated": false,
"description": "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life.",
"homepage": "https://www.genome.jp/kegg/reaction/",
"id": "00000014",
"name": "KEGG Reaction",
"namespaceEmbeddedInLui": false,
"pattern": "^R\\d+$",
"prefix": "kegg.reaction",
"sampleId": "R00100",
"uri_format": "https://www.kegg.jp/entry/$1"
},
"n2t": {
"description": "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life.",
"example": "R00100",
"homepage": "https://www.genome.jp/kegg/reaction/",
"name": "KEGG Reaction Database",
"namespaceEmbeddedInLui": false,
"pattern": "^R\\d+$",
"prefix": "kegg.reaction",
"uri_format": "https://www.kegg.jp/entry/$1"
},
"name": "KEGG Reaction",
"part_of": "kegg",
"prefixcommons": {
"description": "KEGG REACTION contains all reactions taken from KEGG ENZYME and additional reactions taken from the metabolic pathway maps in KEGG PATHWAY.",
"example": "R00047",
"homepage": "http://www.genome.jp/kegg/reaction/",
"keywords": [
"enzyme",
"pathway"
],
"name": "KEGG Reaction",
"pattern": "^R\\d+$",
"prefix": "kegg.reaction",
"pubmed_ids": [
"22700311"
],
"synonyms": [
"rn",
"kegg.reactions"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?rn:$1"
},
"publications": [
{
"doi": "10.1002/0471250953.bi0112s38",
"pubmed": "22700311",
"title": "Using the KEGG database resource",
"year": 2012
}
],
"synonyms": [
"KEGG_REACTION"
],
"wikidata": {
"description": "identifier fromΒ databases dealing with genomes, enzymatic pathways, and biological chemicals",
"example": [
"D00018",
"D05961"
],
"homepage": "https://www.kegg.jp/",
"miriam": "kegg",
"name": "KEGG ID",
"pattern": "^[A-Z]\\d+$",
"prefix": "P665",
"uri_format": "https://www.kegg.jp/entry/$1",
"uri_format_rdf": "http://www.kegg.jp/entry/$1"
}
},
"kerafast": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.kerafast.com/",
"name": "Kerafast cell lines",
"prefix": "Kerafast",
"uri_format": "https://www.kerafast.com/Search?SearchTerm="$1""
},
"example": "EJH014",
"mappings": {
"cellosaurus": "Kerafast"
}
},
"kestrelo": {
"contact": {
"email": "lindsey.anderson@pnnl.gov",
"github": "lnanderson",
"name": "Lindsey N. Anderson",
"orcid": "0000-0002-8741-7823"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology for harmonizing and extending severeral existing resources in the vaccine and immunology domains",
"example": "0000001",
"homepage": "https://gitlab.pnnl.gov/kestrel/kestrel_ontology",
"name": "KESTREL Ontology",
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/kestrelo_$1"
},
"knapsack": {
"biocontext": {
"prefix": "KNAPSACK"
},
"integbio": {
"alt_name": "A Comprehensive Species-Metabolite Relationship Database",
"description": "This database provides information on how species and metabolites relate to each other.\nSearches can be done on the Web by entering the organism's name or that of the metabolite or its molecular weight or formula.\nThe site also offers the option to download the database and work offline.",
"homepage": "http://www.knapsackfamily.com/KNApSAcK/",
"information_keywords": [
"Bibliography/Documents",
"Chemical structure"
],
"maintainer": "Nara Institute of Science and Technology",
"name": "KNApSAcK",
"prefix": "nbdc00545",
"pubmeds": [
"22123792"
],
"status": "Active",
"target_keywords": [
"Metabolite",
"Chemical compound"
]
},
"mappings": {
"biocontext": "KNAPSACK",
"integbio": "nbdc00545",
"miriam": "knapsack",
"n2t": "knapsack",
"wikidata": "P2064"
},
"miriam": {
"deprecated": false,
"description": "KNApSAcK provides information on metabolites and the\ntaxonomic class with which they are associated.",
"homepage": "http://www.knapsackfamily.com/KNApSAcK/",
"id": "00000271",
"name": "KNApSAcK",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d{8}",
"prefix": "knapsack",
"sampleId": "C00000001",
"uri_format": "http://www.knapsackfamily.com/knapsack_core/information.php?word=$1"
},
"n2t": {
"description": "Knapsack provides information on metabolites and the taxonomic class with which they are associated.",
"example": "C00000001",
"homepage": "http://kanaya.aist-nara.ac.jp/KNApSAcK/",
"name": "KnapSack at Nara Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d{8}",
"prefix": "knapsack",
"uri_format": "http://kanaya.naist.jp/knapsack_jsp/information.jsp?word=$1"
},
"name": "KNApSAcK",
"wikidata": {
"description": "identifier in the KNApSAcK Core System",
"example": [
"C00000001",
"C00035015"
],
"name": "KNApSAcK ID",
"pattern": "^C\\d{8}$",
"prefix": "P2064",
"uri_format": "http://www.knapsackfamily.com/knapsack_core/information.php?sname=C_ID&word=$1"
}
},
"kupo": {
"appears_in": [
"cl"
],
"comment": "Website is down, now it redirects to something else that is not related",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"example": "0001009",
"homepage": "http://www.kupkb.org/",
"name": "Kidney and Urinary Pathway Ontology",
"pattern": "^\\d{7}$",
"references": [
"https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-2-S2-S7"
]
},
"kyinno": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.kyinno.com/",
"name": "KYinno cell lines",
"prefix": "KYinno",
"uri_format": "https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf"
},
"example": "KC-0979",
"mappings": {
"cellosaurus": "KYinno"
}
},
"labo": {
"aberowl": {
"description": "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents.",
"download_owl": "http://aber-owl.net/media/ontologies/LABO/3/labo.owl",
"homepage": "https://github.com/OpenLHS/LABO",
"name": "clinical LABoratory Ontology",
"prefix": "LABO"
},
"bioportal": {
"contact": {
"email": "paul.fabry@usherbrooke.ca",
"name": "Paul Fabry"
},
"description": "LABO is an ontology of informational entities describing laboratory tests prescriptions and reporting documents. LABO is a component of a core ontological model, along with the ontology of drug prescriptions PDRO, that aims to enable interoperability between various clinical data sources in the context of a Learning Health System.",
"homepage": "https://github.com/OpenLHS/LABO",
"name": "clinical LABoratory Ontology",
"prefix": "LABO"
},
"example": "0000124",
"mappings": {
"aberowl": "LABO",
"bioportal": "LABO",
"obofoundry": "labo",
"ols": "labo",
"ontobee": "LABO"
},
"obofoundry": {
"contact": "paul.fabry@usherbrooke.ca",
"contact.github": "pfabry",
"contact.label": "Paul Fabry",
"contact.orcid": "0000-0002-3336-2476",
"depends_on": [
"iao",
"obi",
"ogms",
"omiabis",
"omrse",
"opmi"
],
"deprecated": false,
"description": "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents.",
"domain": "information",
"download.owl": "http://purl.obolibrary.org/obo/labo.owl",
"homepage": "https://github.com/OpenLHS/LABO",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "clinical LABoratory Ontology",
"preferredPrefix": "LABO",
"prefix": "labo",
"publications": [
{
"id": "https://doi.org/10.5281/zenodo.6522019",
"title": "LABO: An Ontology for Laboratory Test Prescription and Reporting"
}
],
"repository": "https://github.com/OpenLHS/LABO"
},
"ols": {
"description": "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents.",
"download_owl": "http://purl.obolibrary.org/obo/labo.owl",
"homepage": "https://github.com/OpenLHS/LABO",
"name": "clinical LABoratory Ontology",
"prefix": "labo",
"version": "2021-06-08",
"version.iri": "http://purl.obolibrary.org/obo/labo/2021-06-08/labo.owl"
},
"ontobee": {
"library": "Library",
"name": "clinical LABoratory Ontology",
"prefix": "LABO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.5281/zenodo.6522019",
"title": "LABO: An ontology for laboratory test prescription and reporting",
"year": 2019
}
],
"uri_format": "http://purl.obolibrary.org/obo/LABO_$1"
},
"langual": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Langual stands for \"langua alimentaria\" or \"language of food\". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases",
"example": "B2067",
"github_request_issue": 507,
"homepage": "https://www.langual.org",
"name": "Langua aLimentaria Thesaurus",
"pattern": "^B\\d+$",
"uri_format": "https://www.langual.org/langual_thesaurus.asp?termid=$1"
},
"lbctr": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Lebanese Clinical Trials Registry is an online register of clinical trials being undertaken in Lebanon. It includes trials that target humans from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. (from homepage)",
"example": "LBCTR2023015204",
"homepage": "https://lbctr.moph.gov.lb/",
"name": "Lebanon Clinical Trials Registry",
"pattern": "^LBCTR\\d+$",
"references": [
"https://lbctr.moph.gov.lb/Trials/Details/5204"
]
},
"lbo": {
"aberowl": {
"description": "A vocabulary for buffalo, cattle, chicken, goat, horse, pig, and sheep breeds.",
"download_obo": "http://aber-owl.net/media/ontologies/LBO/9/lbo.obo",
"name": "Livestock Breed Ontology",
"prefix": "LBO",
"version": "2.2"
},
"agroportal": {
"contact": {
"email": "jreecy@iastate.edu",
"name": "Jim Reecy"
},
"description": "A vocabulary for buffalo, cattle, chicken, goat, horse, pig, and sheep breeds.",
"example_uri": "http://purl.obolibrary.org/obo/LBO_0000700",
"name": "Livestock Breed Ontology",
"prefix": "LBO",
"repository": "https://github.com/AnimalGenome/livestock-breed-ontology",
"version": "9.5"
},
"bioportal": {
"contact": {
"email": "jreecy@iastate.edu",
"name": "Jim Reecy"
},
"description": "A vocabulary for buffalo, cattle, chicken, goat, horse, pig, and sheep breeds.",
"homepage": "https://www.animalgenome.org/bioinfo/projects/lbo/",
"name": "Livestock Breed Ontology",
"prefix": "LBO",
"version": "9.5"
},
"contact": {
"email": "caripark@iastate.edu",
"github": "caripark",
"name": "Carissa Park",
"orcid": "0000-0002-2346-5201"
},
"download_obo": "https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.obo",
"download_owl": "https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.owl",
"example": "0000487",
"fairsharing": {
"abbreviation": "LBO",
"description": "The Livestock Breed Ontology (LBO) is a controlled vocabulary for the unambiguous description of breeds. Its utility include proper identification of inherited variation sources in genetics/genomic studies. ",
"homepage": "https://www.animalgenome.org/bioinfo/projects/lbo/",
"license": "CC BY-NC 4.0",
"name": "Livestock Breed Ontology",
"prefix": "FAIRsharing.309v57",
"repository": "https://github.com/AnimalGenome/livestock-breed-ontology",
"subjects": [
"Animal Breeding",
"Genomics",
"Genetics",
"Animal Husbandry"
]
},
"mappings": {
"aberowl": "LBO",
"agroportal": "LBO",
"bioportal": "LBO",
"fairsharing": "FAIRsharing.309v57",
"ols": "lbo"
},
"ols": {
"contact": "jreecy@iastate.edu",
"description": "A vocabulary for cattle, chicken, horse, pig, and sheep breeds.",
"download": "http://data.bioontology.org/ontologies/LBO/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb",
"homepage": "http://bioportal.bioontology.org/ontologies/LBO",
"name": "Livestock Breed Ontology",
"prefix": "lbo"
},
"pattern": "^\\d{7}$",
"rdf_uri_format": "http://purl.obolibrary.org/obo/LBO_$1",
"repository": "https://github.com/AnimalGenome/livestock-breed-ontology",
"uri_format": "https://bioportal.bioontology.org/ontologies/LBO/?p=classes&conceptid=http://purl.obolibrary.org/obo/LBO_$1"
},
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"abbreviation": "LCSH",
"description": "LCSH in this service includes all Library of Congress Subject Headings, free-floating subdivisions (topical and form), Genre/Form headings, Children's (AC) headings, and validation strings for which authority records have been created. The content includes a few name headings (personal and corporate), such as William Shakespeare, Jesus Christ, and Harvard University, and geographic headings that are added to LCSH as they are needed to establish subdivisions, provide a pattern for subdivision practice, or provide reference structure for other terms. This content is expanded beyond the print issue of LCSH (the 'red books') with inclusion of validation strings. *Validation strings: Some authority records are for headings that have been built by adding subdivisions. These records are the result of an ongoing project to programmatically create authority records for valid subject strings from subject heading strings found in bibliographic records. The authority records for these subject strings were created so the entire string could be machine-validated. The strings do not have broader, narrower, or related terms. Library of Congress Subject Headings (LCSH) has been actively maintained since 1898 to catalog materials held at the Library of Congress. By virtue of cooperative cataloging other libraries around the United States also use LCSH to provide subject access to their collections. In addition LCSH is used internationally, often in translation.",
"homepage": "http://id.loc.gov/authorities/subjects.html",
"license": "CC0-1.0",
"name": "Library of Congress Subject Headings",
"prefix": "454",
"wikidata_database": "Q1823134"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Library of Congress Subject Headings (LCSH) has been actively maintained since 1898 to catalog materials held at the Library of Congress. (from homepage)",
"example": "nb2018006591",
"fairsharing": {
"abbreviation": "LCSH",
"description": "The Library of Congress Subject Headings (LCSH) provides catalog headings for materials held at the Library of Congress. Libraries throughout the United States use LCSH to provide subject access to their collections. LCSH is also used internationally, often in translation. The LCSH online resource includes all Library of Congress Subject Headings, free-floating subdivisions (topical and form), Genre/Form headings, Children's (AC) headings, and validation strings for which authority records have been created.",
"homepage": "https://id.loc.gov/authorities/subjects.html",
"license": "https://www.loc.gov/legal",
"name": "Library of Congress Subject Headings",
"prefix": "FAIRsharing.d31795",
"subjects": [
"Subject Agnostic"
]
},
"homepage": "https://id.loc.gov/authorities",
"mappings": {
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"fairsharing": "FAIRsharing.d31795",
"wikidata": "P244"
},
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"synonyms": [
"lcnaf",
"lcnafid"
],
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"wikidata": {
"database": "Q17109002",
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"example": [
"n79022935",
"n81082970",
"n81092084",
"n84023326",
"sh2008005914",
"sh2020006558",
"sh85037527"
],
"homepage": "https://id.loc.gov",
"name": "Library of Congress authority ID",
"pattern": "^(gf|n|nb|nr|no|ns|sh|sj)([4-9][0-9]|00|20[0-2][0-9])[0-9]{6}$",
"prefix": "P244",
"short_name": [
"LCAuth",
"LOC authority ID"
],
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"uri_format_rdf": "http://id.loc.gov/authorities/names/$1"
}
},
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},
"name": "Leafsnap",
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"description": "identifier for a tree species of the United States and Canada on the Leafsnap electronic field guide",
"example": [
"Amelanchier laevis",
"Crataegus crus-galli"
],
"homepage": "http://leafsnap.com/",
"name": "Leafsnap ID",
"prefix": "P10538",
"uri_format": "http://leafsnap.com/species/$1/"
}
},
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"n2t": "lei"
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"homepage": "https://www.gleif.org/",
"id": "00000686",
"name": "Global LEI Index",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$",
"prefix": "lei",
"sampleId": "HWUPKR0MPOU8FGXBT394",
"uri_format": "https://www.gleif.org/lei/$1"
},
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"description": "Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland.",
"example": "HWUPKR0MPOU8FGXBT394",
"homepage": "https://www.gleif.org/",
"name": "Global LEI Index",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$",
"prefix": "lei",
"uri_format": "https://www.gleif.org/lei/$1"
}
},
"lepao": {
"aberowl": {
"description": "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. LEPAO is developed in part by BIOfid (The Specialised Information Service Biodiversity Research).",
"download_owl": "http://aber-owl.net/media/ontologies/LEPAO/2/lepao.owl",
"homepage": "https://github.com/insect-morphology/lepao",
"name": "Lepidoptera Anatomy Ontology",
"prefix": "LEPAO"
},
"bioportal": {
"contact": {
"email": "lagonzalezmo@unal.edu.co",
"name": "Luis A. Gonzalez-Montana"
},
"description": "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. LEPAO is developed in part by BIOfid (The Specialised Information Service Biodiversity Research).",
"homepage": "https://github.com/insect-morphology/lepao",
"name": "Lepidoptera Anatomy Ontology",
"prefix": "LEPAO",
"version": "2023-02-18"
},
"example": "0000005",
"mappings": {
"aberowl": "LEPAO",
"bioportal": "LEPAO",
"obofoundry": "lepao",
"ols": "lepao",
"ontobee": "LEPAO"
},
"obofoundry": {
"contact": "lagonzalezmo@unal.edu.co",
"contact.github": "luis-gonzalez-m",
"contact.label": "Luis A. Gonzalez-Montana",
"contact.orcid": "0000-0002-9136-9932",
"depends_on": [
"aism",
"bfo",
"bspo",
"caro",
"pato",
"ro",
"uberon"
],
"deprecated": false,
"description": "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. LEPAO is developed in part by BIOfid (The Specialised Information Service Biodiversity Research).",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/lepao.obo",
"download.owl": "http://purl.obolibrary.org/obo/lepao.owl",
"homepage": "https://github.com/insect-morphology/lepao",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Lepidoptera Anatomy Ontology",
"preferredPrefix": "LEPAO",
"prefix": "lepao",
"repository": "https://github.com/insect-morphology/lepao"
},
"ols": {
"description": "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research.",
"download_owl": "http://purl.obolibrary.org/obo/lepao.owl",
"homepage": "https://github.com/insect-morphology/lepao",
"name": "Lepidoptera Anatomy Ontology",
"prefix": "lepao",
"version": "2023-02-18",
"version.iri": "http://purl.obolibrary.org/obo/lepao/releases/2023-02-18/lepao.owl"
},
"ontobee": {
"library": "Library",
"name": "Lepidoptera Anatomy Ontology",
"prefix": "LEPAO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/LEPAO_$1"
},
"lgai.cede": {
"mappings": {
"miriam": "lgai.cede"
},
"miriam": {
"deprecated": false,
"description": "LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR).",
"homepage": "https://www.lgresearch.ai",
"id": "00000867",
"name": "LG Chemical Entity Detection Dataset (LGCEDe)",
"namespaceEmbeddedInLui": false,
"pattern": "^LGCEDe-S-\\d{9}$",
"prefix": "lgai.cede",
"sampleId": "LGCEDe-S-000002244",
"uri_format": "https://s3.us-east-2.amazonaws.com/lg.cede/$1"
}
},
"lgic": {
"biocontext": {
"prefix": "LGIC"
},
"comment": "Website is gone",
"deprecated": true,
"mappings": {
"biocontext": "LGIC",
"miriam": "lgic",
"n2t": "lgic",
"prefixcommons": "lgicdb"
},
"miriam": {
"deprecated": false,
"description": "The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available.",
"homepage": "https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php",
"id": "00000087",
"name": "Ligand-Gated Ion Channel database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "lgic",
"sampleId": "5HT3Arano",
"uri_format": "https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php"
},
"n2t": {
"description": "The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available.",
"example": "5HT3Arano",
"homepage": "https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php",
"name": "Ligand-Gated Ion Channel database at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "lgic",
"uri_format": "https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php"
},
"prefixcommons": {
"description": "The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available.",
"example": "5HT3Arano",
"homepage": "http://www.ebi.ac.uk/compneur-srv/LGICdb/",
"keywords": [
"gene",
"protein",
"sequence"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Ligand-Gated Ion Channel database",
"pattern": "^\\w+$",
"prefix": "lgicdb",
"pubmed_ids": [
"9847222"
],
"synonyms": [
"lgic"
],
"uri_format": "http://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php"
},
"publications": [
{
"doi": "10.1093/nar/27.1.340",
"pmc": "PMC148177",
"pubmed": "9847222",
"title": "The Ligand Gated Ion Channel Database",
"year": 1999
}
]
},
"licebase": {
"biocontext": {
"prefix": "LICEBASE"
},
"fairsharing": {
"abbreviation": "LiceBase",
"contact": {
"email": "Inge.Jonassen@uib.no",
"name": "Inge Jonassen",
"orcid": "0000-0003-4110-0748"
},
"description": "LiceBase is a database for sea lice genomics. LiceBase provides the genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, Blast functionality and access to related high-thoughput genomics data.",
"homepage": "https://licebase.org/",
"name": "LiceBase",
"prefix": "FAIRsharing.c7w81a",
"publications": [],
"subjects": [
"Life Science"
]
},
"integbio": {
"description": "LiceBase is a database for sea lice genomics. LiceBase provides the genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, Blast functionality and access to related high-thoughput genomics data.",
"fairsharing": "FAIRsharing.c7w81a",
"homepage": "https://licebase.org/",
"information_keywords": [
"Sequence",
"Image/Movie"
],
"maintainer": "Sea Lice Research Centre",
"name": "LiceBase",
"prefix": "nbdc02217",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"RNA",
"Organism"
]
},
"mappings": {
"biocontext": "LICEBASE",
"fairsharing": "FAIRsharing.c7w81a",
"integbio": "nbdc02217",
"miriam": "licebase",
"n2t": "licebase",
"re3data": "r3d100013547"
},
"miriam": {
"deprecated": false,
"description": "Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects.",
"homepage": "https://licebase.org",
"id": "00000628",
"name": "LiceBase",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9\\-\\/]+$",
"prefix": "licebase",
"sampleId": "EMLSAT00000003403",
"uri_format": "https://licebase.org/?q=$1"
},
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"description": "Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects.",
"example": "EMLSAT00000003403",
"homepage": "https://licebase.org",
"name": "LiceBase",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9\\-\\/]+$",
"prefix": "licebase",
"uri_format": "https://licebase.org/?q=$1"
},
"re3data": {
"description": "LiceBase is a database for sea lice genomics. LiceBase provides the genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, Blast functionality and access to related high-thoughput genomics data.",
"homepage": "https://licebase.org/",
"name": "LiceBase",
"prefix": "r3d100013547",
"xrefs": {
"fairsharing": "FAIRsharing.c7w81a"
}
}
},
"ligandbook": {
"mappings": {
"miriam": "ligandbook",
"n2t": "ligandbook"
},
"miriam": {
"deprecated": false,
"description": "Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community.",
"homepage": "https://ligandbook.org/",
"id": "00000681",
"name": "LigandBook",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "ligandbook",
"sampleId": "785",
"uri_format": "https://ligandbook.org/package/$1"
},
"n2t": {
"description": "Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community.",
"example": "785",
"homepage": "https://ligandbook.org/",
"name": "LigandBook",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "ligandbook",
"uri_format": "https://ligandbook.org/package/$1"
}
},
"ligandbox": {
"biocontext": {
"prefix": "LIGANDBOX"
},
"integbio": {
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"homepage": "http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en",
"information_keywords": [
"3D structure"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "LigandBox",
"prefix": "nbdc00551",
"pubmeds": [
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],
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"mappings": {
"biocontext": "LIGANDBOX",
"integbio": "nbdc00551",
"miriam": "ligandbox",
"n2t": "ligandbox"
},
"miriam": {
"deprecated": false,
"description": "LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds.",
"homepage": "http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en",
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"name": "LigandBox",
"namespaceEmbeddedInLui": false,
"pattern": "^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$",
"prefix": "ligandbox",
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},
"n2t": {
"description": "LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds.",
"example": "D00001",
"homepage": "http://ligandbox.protein.osaka-u.ac.jp/ligandbox//cgi-bin/index.cgi?LANG=en",
"name": "LigandBox at",
"namespaceEmbeddedInLui": false,
"pattern": "^D\\d{5}",
"prefix": "ligandbox",
"uri_format": "http://ligandbox.protein.osaka-u.ac.jp/ligandbox/cgi-bin/liginf.cgi?id=$1"
}
},
"ligandexpo": {
"biocontext": {
"prefix": "LIGANDEXPO"
},
"fairsharing": {
"abbreviation": "Ligand Expo",
"contact": {
"email": "jwest@rcsb.rutgers.edu",
"name": "John Westbrook",
"orcid": "0000-0002-6686-5475"
},
"description": "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry.",
"homepage": "http://ligand-depot.rutgers.edu/",
"name": "Ligand Expo",
"prefix": "FAIRsharing.2ma4gq",
"publications": [
{
"doi": "10.1093/bioinformatics/bth214",
"pubmed_id": 15059838,
"title": "Ligand Depot: a data warehouse for ligands bound to macromolecules."
}
],
"subjects": [
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]
},
"integbio": {
"description": "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry.",
"fairsharing": "FAIRsharing.2ma4gq",
"homepage": "http://ligand-depot.rutgers.edu/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"3D structure"
],
"maintainer": "Rutgers, The State University of New Jersey",
"name": "Ligand Expo",
"prefix": "nbdc01864",
"pubmeds": [
"15059838"
],
"status": "Active",
"target_keywords": [
"DNA",
"Protein",
"Chemical compound"
]
},
"mappings": {
"biocontext": "LIGANDEXPO",
"fairsharing": "FAIRsharing.2ma4gq",
"integbio": "nbdc01864",
"miriam": "ligandexpo",
"n2t": "ligandexpo",
"pathguide": "154",
"prefixcommons": "ligandexpo"
},
"miriam": {
"deprecated": false,
"description": "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.",
"homepage": "http://ligand-depot.rutgers.edu/index.html",
"id": "00000062",
"name": "Ligand Expo",
"namespaceEmbeddedInLui": false,
"pattern": "^(\\w){3}$",
"prefix": "ligandexpo",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "Ligand Expo at Rutgers",
"homepage": "http://ligand-expo.rcsb.org/",
"name": "Ligand Expo at Rutgers",
"uri_format": "http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid"
}
],
"sampleId": "ABC",
"uri_format": "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid"
},
"n2t": {
"description": "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.",
"example": "ABC",
"homepage": "http://ligand-expo.rcsb.org/",
"name": "Ligand Expo at Rutgers",
"namespaceEmbeddedInLui": false,
"pattern": "^(\\w){3}$",
"prefix": "ligandexpo",
"uri_format": "http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid"
},
"pathguide": {
"abbreviation": "Ligand Expo",
"homepage": "http://ligand-depot.rutgers.edu/",
"name": "Ligand Expo",
"prefix": "154"
},
"prefixcommons": {
"description": "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.",
"example": "ABC",
"homepage": "http://ligand-depot.rutgers.edu/",
"keywords": [
"interaction",
"structure",
"protein",
"chemical",
"nucleic acid"
],
"license": "http://ligand-depot.rutgers.edu/acknowledgements.html",
"name": "Ligand Expo",
"pattern": "^(\\w){3}$",
"prefix": "ligandexpo",
"pubmed_ids": [
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],
"uri_format": "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid"
},
"publications": [
{
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}
]
},
"ligea": {
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"category": "Polymorphism and mutation databases",
"homepage": "http://hpc-bioinformatics.cineca.it/fusion/main",
"name": "Cancer cell LInes GEne fusions portAl",
"prefix": "LiGeA",
"uri_format": "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1"
},
"comment": "This might just be a provider for CCLE",
"example": "CCLE_867",
"mappings": {
"cellosaurus": "LiGeA"
}
},
"limore": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://www.picb.ac.cn/limore/home",
"name": "Liver Cancer Model Repository",
"prefix": "LIMORE",
"uri_format": "https://www.picb.ac.cn/limore/cellLines/single?para=$1"
},
"example": "Li7",
"mappings": {
"cellosaurus": "LIMORE"
}
},
"lincs.cell": {
"biocontext": {
"prefix": "LINCS.CELL"
},
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "http://lincsportal.ccs.miami.edu/cells/",
"name": "LINCS Data Portal",
"prefix": "LINCS_LDP",
"uri_format": "http://lincsportal.ccs.miami.edu/cells/#/view/$1"
},
"mappings": {
"biocontext": "LINCS.CELL",
"cellosaurus": "LINCS_LDP",
"miriam": "lincs.cell",
"n2t": "lincs.cell"
},
"miriam": {
"deprecated": false,
"description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.",
"homepage": "http://lincsportal.ccs.miami.edu/cells/",
"id": "00000544",
"name": "LINCS Cell",
"namespaceEmbeddedInLui": false,
"pattern": "(^LCL-\\d+$)|(^LDC-\\d+$)|(^ES-\\d+$)|(^LSC-\\d+$)|(^LPC-\\d+$)",
"prefix": "lincs.cell",
"sampleId": "LCL-2085",
"uri_format": "http://lincsportal.ccs.miami.edu/cells/#/view/$1"
},
"n2t": {
"description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.",
"example": "LCL-2085",
"homepage": "http://lincsportal.ccs.miami.edu/cells/",
"name": "LINCS Portal",
"namespaceEmbeddedInLui": false,
"pattern": "(^LCL-\\d+$)|(^LDC-\\d+$)|(^ES-\\d+$)|(^LSC-\\d+$)|(^LPC-\\d+$)",
"prefix": "lincs.cell",
"uri_format": "http://lincsportal.ccs.miami.edu/cells/#/view/$1"
},
"pattern": "^(LCL|LDC|ES|LSC|LPC)-\\d+$",
"synonyms": [
"LINCS_LDP"
]
},
"lincs.data": {
"biocontext": {
"prefix": "LINCS.DATA"
},
"mappings": {
"biocontext": "LINCS.DATA",
"miriam": "lincs.data",
"n2t": "lincs.data"
},
"miriam": {
"deprecated": false,
"description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level).",
"homepage": "http://lincsportal.ccs.miami.edu/datasets/",
"id": "00000588",
"name": "LINCS Data",
"namespaceEmbeddedInLui": false,
"pattern": "^[EL]D[SG]-\\d+$",
"prefix": "lincs.data",
"providers": [
{
"code": "omicsdi",
"description": "Lincs through OmicsDI",
"homepage": "https://www.omicsdi.org/",
"name": "Lincs through OmicsDI",
"uri_format": "https://www.omicsdi.org/dataset/lincs/$1"
}
],
"sampleId": "LDS-1110",
"uri_format": "http://lincsportal.ccs.miami.edu/datasets/#/view/$1"
},
"n2t": {
"description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level).",
"example": "LDS-1110",
"homepage": "http://lincsportal.ccs.miami.edu/datasets/",
"name": "LINCS Data at University of Miami",
"namespaceEmbeddedInLui": false,
"pattern": "^[EL]D[SG]-\\d+$",
"prefix": "lincs.data",
"uri_format": "http://lincsportal.ccs.miami.edu/datasets/#/view/$1"
}
},
"lincs.protein": {
"biocontext": {
"prefix": "LINCS.PROTEIN"
},
"mappings": {
"biocontext": "LINCS.PROTEIN",
"miriam": "lincs.protein",
"n2t": "lincs.protein"
},
"miriam": {
"deprecated": false,
"description": "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins.",
"homepage": "http://lincs.hms.harvard.edu/db/proteins/",
"id": "00000545",
"name": "LINCS Protein",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "lincs.protein",
"sampleId": "200282",
"uri_format": "http://lincs.hms.harvard.edu/db/proteins/$1/"
},
"n2t": {
"description": "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins.",
"example": "200282",
"homepage": "http://lincs.hms.harvard.edu/db/proteins/",
"name": "LINCS Protein at Harvard Medical School",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "lincs.protein",
"uri_format": "http://lincs.hms.harvard.edu/db/proteins/$1/"
},
"uri_format": "https://lincs.hms.harvard.edu/db/proteins/$1"
},
"lincs.smallmolecule": {
"biocontext": {
"prefix": "LINCS.SMALLMOLECULE"
},
"mappings": {
"biocontext": "LINCS.SMALLMOLECULE",
"miriam": "lincs.smallmolecule",
"n2t": "lincs.smallmolecule"
},
"miriam": {
"deprecated": false,
"description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC).",
"homepage": "http://lincsportal.ccs.miami.edu/SmallMolecules/",
"id": "00000546",
"name": "LINCS Small Molecule",
"namespaceEmbeddedInLui": false,
"pattern": "^LSM-\\d+$",
"prefix": "lincs.smallmolecule",
"sampleId": "LSM-6306",
"uri_format": "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1"
},
"n2t": {
"description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC).",
"example": "LSM-6306",
"homepage": "http://lincsportal.ccs.miami.edu/SmallMolecules/",
"name": "LINCS Portal",
"namespaceEmbeddedInLui": false,
"pattern": "^LSM-\\d+$",
"prefix": "lincs.smallmolecule",
"uri_format": "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1"
},
"synonyms": [
"lincs"
]
},
"linguist": {
"homepage": "https://github.com/github/linguist",
"mappings": {
"miriam": "linguist"
},
"miriam": {
"deprecated": false,
"description": "Registry of programming languages for the Linguist program for detecting and highlighting programming languages.",
"homepage": "https://github.com/",
"id": "00000849",
"name": "Linguist",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-zA-Z0-9 +#'*]+$",
"prefix": "linguist",
"sampleId": "Python",
"uri_format": "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1"
},
"repository": "https://github.com/github/linguist"
},
"linkml": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "linkml",
"uri_format": "https://w3id.org/linkml/$1"
},
"comment": "Closes #508",
"contact": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks.",
"example": "SchemaDefinition",
"fairsharing": {
"abbreviation": "LinkML",
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"description": "LinkML is a flexible modeling language that allows you to author schemas in YAML that describe the structure of your data. Additionally, it is a framework for working with and validating data in a variety of formats (JSON, RDF, TSV), with generators for compiling LinkML schemas to other frameworks.",
"homepage": "https://linkml.io/linkml/schemas/",
"license": "https://creativecommons.org/licenses/by/1.0",
"name": "Linked (Open) Data Modeling Language",
"prefix": "FAIRsharing.cb7086",
"publications": [
{
"doi": "10.5281/zenodo.5598314",
"pubmed_id": null,
"title": "LinkML Model (v1.3.0rc7)"
}
],
"repository": "https://github.com/linkml/",
"subjects": [
"Data Integration",
"Ontology and Terminology"
],
"twitter": "linkml_data"
},
"github_request_issue": 512,
"homepage": "https://linkml.io/linkml-model/docs/SchemaDefinition/",
"mappings": {
"biolink": "linkml",
"fairsharing": "FAIRsharing.cb7086"
},
"name": "LinkML",
"preferred_prefix": "linkml",
"publications": [
{
"doi": "10.5281/zenodo.5598314",
"title": "linkml/linkml-model: v1.5.2",
"year": 2023
}
],
"uri_format": "https://w3id.org/linkml/$1"
},
"lipidbank": {
"biocontext": {
"prefix": "LIPIDBANK"
},
"contact": {
"email": "e-yasugi@umin.ac.jp",
"name": "Etsuko Yasugi",
"orcid": "0000-0003-1898-4426"
},
"edam": {
"description": "Identifier of an entry from the LipidBank database.",
"name": "LipidBank",
"obsolete": false,
"prefix": "2665"
},
"fairsharing": {
"abbreviation": "LipidBank",
"description": "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.",
"homepage": "http://lipidbank.jp/index.html",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "LipidBank",
"prefix": "FAIRsharing.bdn9br",
"publications": [
{
"doi": null,
"pubmed_id": 12058481,
"title": "[LIPIDBANK for Web, the newly developed lipid database]."
}
],
"subjects": [
"Life Science"
]
},
"integbio": {
"description": "Lipidbank is the official database of the Japanese Conference on the Biochemistry of Lipids (JCBL). Natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins can be freely searched. It also provides more than 6000 unique molecular structures (ChemDraw cdx format, MDL MOL format) with their lipid names (common name, IUPAC), spectral information (mass, UV, IR, NMR and others), and links to published information.",
"fairsharing": "biodbcore-000581",
"homepage": "http://lipidbank.jp/",
"information_keywords": [
"Image/Movie",
"Chemical structure"
],
"maintainer": "The Japanese Conference on the Biochemistry of Lipids",
"name": "LipidBank",
"prefix": "nbdc00126",
"pubmeds": [
"12058481"
],
"status": "Active",
"target_keywords": [
"Lipid"
]
},
"mappings": {
"biocontext": "LIPIDBANK",
"edam": "2665",
"fairsharing": "FAIRsharing.bdn9br",
"integbio": "nbdc00126",
"miriam": "lipidbank",
"n2t": "lipidbank",
"prefixcommons": "lipidbank"
},
"miriam": {
"deprecated": false,
"description": "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.",
"homepage": "http://lipidbank.jp/index.html",
"id": "00000115",
"name": "LipidBank",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+\\d+$",
"prefix": "lipidbank",
"sampleId": "BBA0001",
"uri_format": "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1"
},
"n2t": {
"description": "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.",
"example": "BBA0001",
"homepage": "http://lipidbank.jp/index.html",
"name": "LipidBank the Lipid database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+\\d+$",
"prefix": "lipidbank",
"uri_format": "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1"
},
"prefixcommons": {
"description": "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.",
"example": "BBA0001",
"homepage": "http://lipidbank.jp/index.html",
"keywords": [
"lipid",
"molecule",
"structure"
],
"name": "LipidBank",
"pattern": "^\\w+\\d+$",
"prefix": "lipidbank",
"pubmed_ids": [
"12058481"
],
"uri_format": "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1"
},
"publications": [
{
"pubmed": "12058481",
"title": "[LIPIDBANK for Web, the newly developed lipid database]",
"year": 2002
}
]
},
"lipidmaps": {
"biocontext": {
"prefix": "LIPIDMAPS"
},
"cheminf": {
"description": "Identifier used by the LipidMaps database, http://www.lipidmaps.org/.",
"name": "LipidMaps",
"obsolete": false,
"prefix": "000564"
},
"contact": {
"email": "edennis@ucsd.edu",
"name": "0000-0003-3738-3140",
"orcid": "0000-0003-3738-3140"
},
"edam": {
"description": "Identifier of an entry from the LIPID MAPS database.",
"name": "LIPID MAPS",
"obsolete": false,
"prefix": "2625"
},
"fairsharing": {
"abbreviation": "LIPID MAPS",
"description": "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.",
"homepage": "http://www.lipidmaps.org",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "LIPID MAPS",
"prefix": "FAIRsharing.cpneh8",
"publications": [
{
"doi": "10.1093/nar/gkl838",
"pubmed_id": 17098933,
"title": "LMSD: LIPID MAPS structure database."
},
{
"doi": "10.1093/nar/gkm324",
"pubmed_id": 17584797,
"title": "LIPID MAPS online tools for lipid research."
},
{
"doi": "10.1194/jlr.R800095-JLR200",
"pubmed_id": 19098281,
"title": "Update of the LIPID MAPS comprehensive classification system for lipids."
}
],
"subjects": [
"Endocrinology",
"Life Science",
"Biomedical Science",
"Systems Biology"
],
"twitter": "lipidmaps"
},
"mappings": {
"biocontext": "LIPIDMAPS",
"cheminf": "000564",
"edam": "2625",
"fairsharing": "FAIRsharing.cpneh8",
"miriam": "lipidmaps",
"n2t": "lipidmaps",
"pathguide": "503",
"prefixcommons": "lipidmaps",
"re3data": "r3d100012315",
"togoid": "Lipidmaps",
"wikidata": "P2063"
},
"miriam": {
"deprecated": false,
"description": "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.",
"homepage": "http://www.lipidmaps.org",
"id": "00000052",
"name": "LIPID MAPS",
"namespaceEmbeddedInLui": false,
"pattern": "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$",
"prefix": "lipidmaps",
"providers": [
{
"code": "scholia",
"description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.",
"homepage": "https://scholia.toolforge.org/",
"name": "Scholia",
"uri_format": "https://scholia.toolforge.org/lipidmaps/$1"
}
],
"sampleId": "LMPR0102010012",
"uri_format": "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1"
},
"n2t": {
"description": "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.",
"example": "LMPR0102010012",
"homepage": "http://www.lipidmaps.org",
"name": "Department of Bioengineering and the San Diego Supercomputer Center",
"namespaceEmbeddedInLui": false,
"pattern": "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$",
"prefix": "lipidmaps",
"uri_format": "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1"
},
"name": "LIPID MAPS",
"pathguide": {
"abbreviation": "LIPID MAPS",
"homepage": "http://www.lipidmaps.org/",
"name": "LIPID Metabolites and Pathways Strategy",
"prefix": "503"
},
"prefixcommons": {
"description": "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.",
"example": "LMPR0102010012",
"homepage": "http://www.lipidmaps.org",
"keywords": [
"lipid",
"structure",
"taxonomy"
],
"license": "http://www.lipidmaps.org/about/terms_of_use.html",
"name": "LIPID MAPS",
"pattern": "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$",
"prefix": "lipidmaps",
"pubmed_ids": [
"17098933",
"15722563"
],
"uri_format": "http://www.lipidmaps.org/data/get_lm_lipids_dbgif.php?LM_ID=$1"
},
"publications": [
{
"doi": "10.1194/jlr.r800095-jlr200",
"pmc": "PMC2674711",
"pubmed": "19098281",
"title": "Update of the LIPID MAPS comprehensive classification system for lipids",
"year": 2008
},
{
"doi": "10.1093/nar/gkm324",
"pmc": "PMC1933166",
"pubmed": "17584797",
"title": "LIPID MAPS online tools for lipid research",
"year": 2007
},
{
"doi": "10.1093/nar/gkl838",
"pmc": "PMC1669719",
"pubmed": "17098933",
"title": "LMSD: LIPID MAPS structure database",
"year": 2006
},
{
"doi": "10.1194/jlr.e400004-jlr200",
"pubmed": "15722563",
"title": "A comprehensive classification system for lipids",
"year": 2005
}
],
"re3data": {
"description": "Tthe Lipidomics Gateway - a free, comprehensive website for researchers interested in lipid biology, provided by the LIPID MAPS (Lipid Metabolites and Pathways Strategy) Consortium. The LIPID MAPS Lipidomics Gateway provides a rich collection of information and resources to help you stay abreast of the latest developments in this rapidly expanding field. LIPID Metabolites And Pathways Strategy (LIPID MAPSΒ) is a multi-institutional effort created in 2003 to identify and quantitate, using a systems biology approach and sophisticated mass spectrometers, all of the major β and many minor β lipid species in mammalian cells, as well as to quantitate the changes in these species in response to perturbation.\nThe ultimate goal of our research is to better understand lipid metabolism and the active role lipids play in diabetes, stroke, cancer, arthritis, Alzheimer's and other lipid-based diseases in order to facilitate development of more effective treatments.\nSince our inception, we have made great strides toward defining the \"lipidome\" (an inventory of the thousands of individual lipid molecular species) in the mouse macrophage. We have also worked to make lipid analysis easier and more accessible for the broader scientific community and to advance a robust research infrastructure for the international research community. We share new lipidomics findings and methods, hold annual meetings open to all interested investigators, and are exploring joint efforts to extend the use of these powerful new methods to new applications",
"homepage": "https://www.lipidmaps.org/",
"name": "LIPID MAPS",
"prefix": "r3d100012315",
"synonyms": [
"LIPID MAPS Lipidomics Gateway",
"LIPID Metabolites And Pathways Strategy"
],
"xrefs": {
"fairsharing": "FAIRsharing.cpneh8",
"nif": "0000-00368",
"omics": "02529",
"scr": "006579"
}
},
"synonyms": [
"LIPID MAPS",
"LIPID_MAPS_class",
"LIPID_MAPS_instance"
],
"togoid": {
"examples": [
"LMST01060010",
"LMFA01020229",
"LMFA03020019",
"LMGP01010915",
"LMSP03010080",
"LMFA07070005",
"LMFA06000216",
"LMGP01030144",
"LMFA01170119",
"LMGP02011194"
],
"keywords": [
"Lipid"
],
"name": "LIPID MAPS",
"pattern": "^(?LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?)$",
"prefix": "Lipidmaps",
"uri_format": "http://identifiers.org/lipidmaps/$1"
},
"wikidata": {
"description": "identifier used in the LIPID MAPS database for lipids",
"example": [
"LMFA07010511",
"LMPR0102010003"
],
"name": "LIPID MAPS ID",
"pattern": "^LM[A-Z][A-Z]\\d+([A-Z][A-Z]?\\d+)?$",
"prefix": "P2063",
"uri_format": "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessClassSearch&LMID=$1"
}
},
"lipro": {
"aberowl": {
"description": "Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied. The ontology describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define membership requirements for sub classes of lipid according to appropriate functional groups.",
"download_owl": "http://aber-owl.net/media/ontologies/LIPRO/4/lipro.owl",
"name": "Lipid Ontology",
"prefix": "LIPRO",
"version": "See Remote Site"
},
"biocontext": {
"prefix": "LIPRO"
},
"bioportal": {
"contact": {
"email": "bakerc@unb.ca",
"name": "Christipher Baker"
},
"description": "Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied. The ontology describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define membership requirements for sub classes of lipid according to appropriate functional groups.",
"name": "Lipid Ontology",
"prefix": "LIPRO",
"version": "See Remote Site"
},
"mappings": {
"aberowl": "LIPRO",
"biocontext": "LIPRO",
"bioportal": "LIPRO",
"obofoundry": "lipro"
},
"obofoundry": {
"contact": "bakerc@unb.ca",
"contact.label": "Christopher Baker",
"contact.orcid": "0000-0003-4004-6479",
"deprecated": true,
"description": "An ontology representation of the LIPIDMAPS nomenclature classification.",
"domain": "chemistry and biochemistry",
"name": "Lipid Ontology",
"prefix": "lipro"
}
},
"lncipedia": {
"contact": {
"email": "pieter.mestdagh@ugent.be",
"github": "OncoRNALab",
"name": "Pieter Mestdagh",
"orcid": "0000-0001-7821-9684"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A comprehensive compendium of human long non-coding RNAs",
"example": "SNHG3",
"fairsharing": {
"abbreviation": "LNCipedia",
"description": "LNCipedia is a database for human long non-coding RNA (lncRNA) transcripts and genes. In addition to basic transcript information and gene structure, several statistics are determined for each entry in the database, such as secondary structure information, protein coding potential and microRNA binding sites. Available literature on specific lncRNAs is linked, and users or authors can submit articles through a web interface. LNCipedia is publicly available and allows users to query and download lncRNA sequences and structures based on different search criteria.",
"homepage": "https://lncipedia.org/",
"name": "LNCipedia",
"prefix": "FAIRsharing.84c1a7",
"publications": [
{
"doi": "10.1093/nar/gku1060",
"pubmed_id": 25378313,
"title": "An update on LNCipedia: a database for annotated human lncRNA sequences."
},
{
"doi": "10.1093/nar/gkv295",
"pubmed_id": 25829178,
"title": "An update on LNCipedia: a database for annotated human lncRNA sequences."
},
{
"doi": "10.1093/nar/gks915",
"pubmed_id": 23042674,
"title": "LNCipedia: a database for annotated human lncRNA transcript sequences and structures."
}
],
"subjects": [
"Life Science"
]
},
"homepage": "https://lncipedia.org",
"mappings": {
"fairsharing": "FAIRsharing.84c1a7"
},
"name": "LNCipedia",
"publications": [
{
"doi": "10.1093/nar/gkv295",
"pmc": "PMC4417186",
"pubmed": "25829178",
"title": "An update on LNCipedia: a database for annotated human lncRNA sequences",
"year": 2015
},
{
"doi": "10.1093/nar/gku1060",
"pmc": "PMC4383901",
"pubmed": "25378313",
"title": "An update on LNCipedia: a database for annotated human lncRNA sequences",
"year": 2014
},
{
"doi": "10.1093/nar/gks915",
"pmc": "PMC3531107",
"pubmed": "23042674",
"title": "LNCipedia: a database for annotated human lncRNA transcript sequences and structures",
"year": 2012
}
]
},
"loggerhead": {
"biocontext": {
"prefix": "LOGGERHEAD"
},
"mappings": {
"biocontext": "LOGGERHEAD",
"obofoundry": "loggerhead"
},
"obofoundry": {
"contact": "peteremidford@yahoo.com",
"contact.label": "Peter Midford",
"contact.orcid": "0000-0001-6512-3296",
"deprecated": true,
"domain": "organisms",
"homepage": "http://www.mesquiteproject.org/ontology/Loggerhead/index.html",
"name": "Loggerhead nesting",
"prefix": "loggerhead"
}
},
"loinc": {
"aberowl": {
"description": "Logical Observation Identifier Names and Codes (LOINC)",
"homepage": "http://loinc.org/downloads",
"name": "Logical Observation Identifier Names and Codes",
"prefix": "LOINC",
"version": "2016AB"
},
"bartoc": {
"description": "LOINC was initiated in 1994 by Clem McDonald, an investigator at the Regenstrief Institute, which is an internationally respected non-profit medical research organization associated with Indiana University. Regenstrief organized the LOINC committee to develop a common terminology for laboratory and clinical observations because there was a growing trend to send clinical data electronically from laboratories and other data producers to hospitals, physician's offices, and payers who use the data for clinical care and management purposes.\n\nAt the time, and still today, most laboratories and clinical services use HL7 to send their results electronically from their reporting systems to their care systems. However, the tests in these messages are identified by means of their internal, idiosyncratic code values. As a result, receiving care system cannot fully \"understand\" and properly file the results they receive unless they either adopt the producer's test codes (which is impossible if they receive results from multiple sources), or invest in the work to map each result producer's code system to their internal code system.\n\nHere's the problem that LOINC solves: LOINC provides universal codes and names that provide the global lingua franca for identifying tests and observations.",
"homepage": "http://loinc.org/",
"name": "LOINC",
"prefix": "1897",
"wikidata_database": "Q502480"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "LOINC",
"uri_format": "http://loinc.org/rdf/$1"
},
"bioportal": {
"contact": {
"email": "loinc@regenstrief.org",
"name": "LOINC Support"
},
"description": "Logical Observation Identifier Names and Codes (LOINC)",
"homepage": "http://loinc.org/downloads",
"name": "Logical Observation Identifier Names and Codes",
"prefix": "LOINC",
"publication": "http://loinc.org/downloads",
"version": "2023AB"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The international standard for identifying health measurements, observations, and documents.",
"example": "LL379-9",
"fairsharing": {
"abbreviation": "LOINC",
"description": "LOINC is a common language (set of identifiers, names, and codes) for clinical and laboratory observations. LOINC is a catalog of measurements, including laboratory tests, clinical measures like vital signs and anthropomorphic measures, standardized survey instruments, and more. LOINC enables the exchange and aggregation of clinical results for care delivery, outcomes management, and research by providing a set of universal codes and structured names to unambiguously identify things you can measure or observe.",
"domains": [
"Genetic polymorphism",
"Assay",
"Phenotype",
"Diagnosis",
"Genetic disorder"
],
"homepage": "https://loinc.org/",
"license": "https://loinc.org/terms-of-use",
"name": "Logical Observation Identifier Names and Codes",
"prefix": "FAIRsharing.2mk2zb",
"publications": [
{
"doi": "10.1016/s1386-5056(98)00089-6",
"pubmed": "9749897",
"title": "Combining laboratory data sets from multiple institutions using the logical observation identifier names and codes (LOINC)",
"year": 1998
},
{
"doi": "10.1016/j.jbi.2012.01.005",
"pubmed": "22285984",
"title": "Enabling international adoption of LOINC through translation",
"year": 2012
},
{
"doi": "10.1093/jamia/ocu012",
"pubmed": "25656513",
"title": "Supporting interoperability of genetic data with LOINC",
"year": 2015
}
],
"subjects": [
"Life Science",
"Biomedical Science",
"Preclinical Studies"
],
"twitter": "LOINC"
},
"hl7": {
"description": "Logical Observation Identifiers Names and Codes (LOINC®) provides a set of universal codes and names for identifying laboratory and other clinical observations. One of the main goals of LOINC is to facilitate the exchange and pooling of results for clinical care, outcomes management, and research. LOINC was initiated by Regenstrief Institute research scientists who continue to develop it with the collaboration of the LOINC Committee. The LOINC table, LOINC codes, and LOINC panels and forms file are copyright © 1995-2010, Regenstrief Institute, Inc. and the LOINC Committee and available at no cost (http://loinc.org) under the license at http://loinc.org/terms-of-use.The laboratory portion of the LOINC database contains the usual clinical laboratory categories of chemistry, hematology, serology, microbiology (including parasitology and virology), toxicology; as well as categories for drugs and the cell counts, antibiotic susceptibilities, and more. The clinical portion of the LOINC database includes entries for vital signs, hemodynamics, intake/output, EKG, obstetric ultrasound, cardiac echo, radiology report titles, pulmonary ventilator management, document and section titles, patient assessment instruments (e.g. Glascow Coma Score, PHQ-9 depression scale, CMS-required patient assessment instruments), and other clinical observations.LOINC may be accessed at http://loinc.org",
"homepage": "http://www.regenstrief.org",
"name": "Logical Observation Identifier Names and Codes",
"organization": "Regenstrief Institute",
"preferred_prefix": "loinc",
"prefix": "2.16.840.1.113883.6.1",
"status": "Complete"
},
"homepage": "https://loinc.org/",
"license": "https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf",
"mappings": {
"aberowl": "LOINC",
"bartoc": "1897",
"biolink": "LOINC",
"bioportal": "LOINC",
"fairsharing": "FAIRsharing.2mk2zb",
"hl7": "2.16.840.1.113883.6.1",
"wikidata": "P4338"
},
"name": "Logical Observation Identifiers Names and Codes",
"pattern": "^(\\d|\\w)+-\\d$",
"publications": [
{
"doi": "10.1016/s1386-5056(98)00089-6",
"pubmed": "9749897",
"title": "Combining laboratory data sets from multiple institutions using the logical observation identifier names and codes (LOINC)",
"year": 1998
},
{
"doi": "10.1093/jamia/ocu012",
"pmc": "PMC5566197",
"pubmed": "25656513",
"title": "Supporting interoperability of genetic data with LOINC",
"year": 2015
},
{
"doi": "10.1016/j.jbi.2012.01.005",
"pmc": "PMC3376691",
"pubmed": "22285984",
"title": "Enabling international adoption of LOINC through translation",
"year": 2012
}
],
"synonyms": [
"LNC"
],
"uri_format": "https://loinc.org/$1",
"wikidata": {
"description": "identifier for medical observations, measurements, and documents in the Regenstrief Institute's Logical Observation Identifiers Names and Codes (LOINC), a database of internationalized medical terminology",
"example": [
"41995-2",
"69723-5"
],
"homepage": "https://loinc.org/",
"name": "LOINC ID",
"pattern": "^\\d+-\\d$",
"prefix": "P4338",
"uri_format": "https://loinc.org/$1",
"uri_format_rdf": "http://loinc.org/rdf/$1"
}
},
"lonza": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://knowledge.lonza.com",
"name": "Lonza Cell and Transfection Database",
"prefix": "Lonza",
"uri_format": "https://knowledge.lonza.com/cell?id=$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Contains information about cells and data sheets related to transfection.",
"example": "968",
"homepage": "https://knowledge.lonza.com",
"mappings": {
"cellosaurus": "Lonza"
},
"name": "Lonza",
"pattern": "^\\d+$",
"uri_format": "https://knowledge.lonza.com/cell?id=$1"
},
"loqate": {
"contact": {
"email": "maya.schuldiner@weizmann.ac.il",
"github": "Maya-Schuldiner-lab",
"name": "Maya Schuldiner",
"orcid": "0000-0001-9947-115X"
},
"mappings": {
"prefixcommons": "loqate"
},
"prefixcommons": {
"description": "The data presented here is a result of systematically tracking the localization and abundance of 5330 yeast proteins at single-cell resolution under three different stress conditions (DTT, H2O2 and nitrogen starvation) using the GFP-tagged yeast library",
"example": "1001",
"homepage": "http://www.weizmann.ac.il/molgen/loqate/",
"license": "http://www.weizmann.ac.il/molgen/loqate/downloads",
"name": "The localization and quantitation atlas of the yeast proteome",
"pattern": "^\\d+$",
"prefix": "loqate",
"pubmed_ids": [
"24150937"
],
"uri_format": "http://www.weizmann.ac.il/molgen/loqate/gene/view/$1"
},
"publications": [
{
"doi": "10.1093/nar/gkt933",
"pmc": "PMC3965041",
"pubmed": "24150937",
"title": "LoQAtE--Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast",
"year": 2013
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"lotus": {
"comment": "IDs are actually leading to the structural part of LOTUS only, which might change in the future. Will adapt the regexp in case.",
"contact": {
"email": "adriano.rutz@ik.me",
"github": "adafede",
"name": "Adriano Rutz",
"orcid": "0000-0003-0443-9902"
},
"contributor": {
"email": "adriano.rutz@ik.me",
"github": "adafede",
"name": "Adriano Rutz",
"orcid": "0000-0003-0443-9902"
},
"description": "LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produtsβs research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry.",
"example": "LTS0004651",
"github_request_issue": 222,
"homepage": "https://lotus.naturalproducts.net",
"keywords": [
"chemistry",
"drugs",
"metabolites"
],
"logo": "https://upload.wikimedia.org/wikipedia/commons/6/64/Lotus_initiative_logo.svg",
"name": "LOTUS Initiative for Open Natural Products Research",
"pattern": "^LTS\\d{7}$",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://lotus.naturalproducts.net/compound/lotus_id/$1",
"wikidata": {
"database": "Q104225190"
}
},
"lpt": {
"aberowl": {
"description": "The Livestock Product Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.",
"download_obo": "http://aber-owl.net/media/ontologies/LPT/3/lpt.obo",
"name": "Livestock Product Trait Ontology",
"prefix": "LPT",
"version": "1.4"
},
"agroportal": {
"contact": {
"email": "jreecy@iastate.edu",
"name": "Jim Reecy"
},
"description": "The Livestock Product Trait (LPT) Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.",
"example_uri": "http://purl.obolibrary.org/obo/LPT_0000156",
"homepage": "https://www.animalgenome.org/bioinfo/projects/lpt/",
"name": "Livestock Product Trait Ontology",
"prefix": "LPT",
"repository": "https://github.com/AnimalGenome/livestock-product-trait-ontology",
"version": "4.3"
},
"biocontext": {
"prefix": "LPT"
},
"bioportal": {
"contact": {
"email": "jreecy@iastate.edu",
"name": "Jim Reecy"
},
"description": "The Livestock Product Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.",
"homepage": "https://www.animalgenome.org/bioinfo/projects/lpt/",
"name": "Livestock Product Trait Ontology",
"prefix": "LPT",
"version": "4.3"
},
"contact": {
"email": "caripark@iastate.edu",
"github": "caripark",
"name": "Carissa Park",
"orcid": "0000-0002-2346-5201"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.",
"download_obo": "https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.obo",
"download_owl": "https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.owl",
"example": "0000156",
"fairsharing": {
"abbreviation": "LPT",
"description": "The Livestock Product Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.",
"domains": [
"Phenotype"
],
"homepage": "https://www.animalgenome.org/bioinfo/projects/lpt/",
"name": "Livestock Product Trait Ontology",
"prefix": "FAIRsharing.g78mbm",
"repository": "https://github.com/AnimalGenome/livestock-product-trait-ontology ",
"subjects": [
"Animal Husbandry"
]
},
"homepage": "https://github.com/AnimalGenome/livestock-product-trait-ontology",
"mappings": {
"aberowl": "LPT",
"agroportal": "LPT",
"biocontext": "LPT",
"bioportal": "LPT",
"fairsharing": "FAIRsharing.g78mbm"
},
"name": "Livestock Product Trait Ontology",
"pattern": "^\\d+$",
"repository": "https://github.com/AnimalGenome/livestock-product-trait-ontology",
"uri_format": "http://purl.obolibrary.org/obo/LPT_$1"
},
"lrg": {
"banana": "LRG",
"banana_peel": "_",
"biocontext": {
"prefix": "LRG"
},
"example": "1",
"hl7": {
"description": "In collaboration with NCBI, the European Bioinformatics Institute (EBI) is developing the Locus Reference Genomic Sequences (LRG) database, which is a database of reference sequences. LRG is a system for providing a genomic DNA sequence representation of a single gene that is idealized, has a permanent ID (with no versioning), and core content that never changes. LRG is not a nomenclature system. More than one LRG could be created for a region of interest, should that need arise. Additional annotations will be present that may change with time (each item carrying its own date stamp), so that the latest ancillary knowledge about a gene is directly available. In other words, an LRG sequence and its core annotation are not meant to represent current biology knowledge, but to provide a standard for reporting variation in a stable coordinate system. The combination of the LRG plus the updatable-annotation layer will be used to support the biological interpretation of variants.LRG identifiers can be used with the HL7 coded data type (code data type that accepts expression data, or a coded expression data type). This coded data type will be gene symbols can be used with the HL7 coded data type. For example, in the HL7 messages specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model, LRG identifiers can be used to as the observation values for Genomic Reference Sequence Identifier (LOINC code: 48013-7). LRG is a database that can be used freely by the public.",
"homepage": "http://ebi.ac.uk",
"name": "Locus Reference Genomic Sequences (LRG)",
"organization": "Wellcome Trust",
"preferred_prefix": "lrg",
"prefix": "2.16.840.1.113883.6.283",
"status": "Complete"
},
"integbio": {
"alt_name": "Locus Reference Genomic",
"description": "LRG is a database of stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. NCBI (RefSeq) and EMBL-EBI (Ensembl/GENCODE) are working together to rationalise differences in their gene sets. Records contain information about genomic, transcript and protein sequences, annotations, maps about the genome assembly, etc. This database allows users to search using LRG identifier, HGNC gene name, NCBI and Ensembl accession numbers (gene or transcript), gene synonym or LRG status (public or pending). Genome browsers on Ensembl, NCBI and UCSC are available.",
"homepage": "http://www.lrg-sequence.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)||NCBI (National Center for Biotechnology Information)",
"name": "LRG",
"prefix": "nbdc02566",
"pubmeds": [
"24285302"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Health/Disease"
]
},
"mappings": {
"biocontext": "LRG",
"hl7": "2.16.840.1.113883.6.283",
"integbio": "nbdc02566",
"miriam": "lrg",
"n2t": "lrg",
"togoid": "Lrg"
},
"miriam": {
"deprecated": false,
"description": "A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI.",
"homepage": "http://www.lrg-sequence.org/",
"id": "00000376",
"name": "Locus Reference Genomic",
"namespaceEmbeddedInLui": false,
"pattern": "^LRG_\\d+$",
"prefix": "lrg",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "Locus Reference Genomic through Ensembl",
"homepage": "http://www.ensembl.org/",
"name": "Locus Reference Genomic through Ensembl",
"uri_format": "http://www.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1"
},
{
"code": "CURATOR_REVIEW",
"description": "Locus Reference Genomic through Ensembl mirror (asia)",
"homepage": "http://asia.ensembl.org/",
"name": "Locus Reference Genomic through Ensembl mirror (asia)",
"uri_format": "http://asia.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1"
},
{
"code": "CURATOR_REVIEW",
"description": "Locus Reference Genomic through Ensembl mirror (US west)",
"homepage": "http://uswest.ensembl.org/",
"name": "Locus Reference Genomic through Ensembl mirror (US west)",
"uri_format": "http://uswest.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1"
},
{
"code": "CURATOR_REVIEW",
"description": "Locus Reference Genomic through Ensembl mirror (US east)",
"homepage": "http://useast.ensembl.org/",
"name": "Locus Reference Genomic through Ensembl mirror (US east)",
"uri_format": "http://useast.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1"
}
],
"sampleId": "LRG_1",
"uri_format": "http://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml"
},
"n2t": {
"description": "Locus Reference Genomic (LRG) provides identifiers to stable genomic DNA sequences for regions of the human genome, providing a recognized reference-sequence standard for reporting sequence variants. LRG is maintained by the NCBI and the European Bioinformatics Institute (EBI).",
"example": "LRG_1",
"homepage": "http://uswest.ensembl.org/",
"name": "Locus Reference Genomic through Ensembl mirror (US west)",
"namespaceEmbeddedInLui": false,
"pattern": "^LRG_\\d+$",
"prefix": "lrg",
"uri_format": "http://uswest.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1"
},
"pattern": "^\\d+$",
"togoid": {
"catalog": "nbdc02566",
"examples": [
"LRG_41",
"LRG_356",
"LRG_147",
"LRG_660",
"LRG_498",
"LRG_364",
"LRG_203",
"LRG_162",
"LRG_1271",
"LRG_884"
],
"keywords": [
"Gene"
],
"name": "LRG",
"pattern": "^(?LRG_\\d+)$",
"prefix": "Lrg",
"uri_format": "http://identifiers.org/lrg/$1"
}
},
"lspci": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)",
"example": "1",
"homepage": "https://labsyspharm.github.io/lspci/",
"keywords": [
"chemistry",
"drugs",
"metabolites"
],
"name": "Laboratory of Systems Pharmacology Compound",
"pattern": "^\\d+$",
"uri_format": "https://labsyspharm.github.io/lspci/$1"
},
"lter": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Ecological terms",
"example": "182",
"homepage": "https://vocab.lternet.edu/vocab/vocab/index.php",
"name": "Long Term Ecological Research Controlled Vocabulary",
"pattern": "^\\d+$",
"uri_format": "https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1"
},
"m4i": {
"bartoc": {
"abbreviation": "m4i",
"description": "The ontology Metadata4Ing is developed within the NFDI Consortium NFDI4Ing with the aim of providing a thorough framework for the semantic description of research data, with a particular focus on engineering sciences and neighbouring disciplines. This ontology allows a description of the whole data generation process (experiment, observation, simulation), embracing the object of investigation, all sample and data manipulation procedures, a summary of the data files and the informaton contained, and all personal and institutional roles. The subordinate classes and relations can be built according to the two principles of inheritance and modularity. \"Inheritance\" means that a subclass inherits all properties of its superordinate class, possibly adding some new ones. Modularity means that all expansions are independent of each other; this makes possible for instance to generate expanded ontologies for any possible combinations of method Γ object of research.\"",
"homepage": "https://w3id.org/nfdi4ing/metadata4ing",
"license": "CC-BY-4.0",
"name": "Metadata4Ing",
"prefix": "20402"
},
"contact": {
"email": "dorothea.iglezakis@ub.uni-stuttgart.de",
"github": "doigl",
"name": "Dorothea Iglezakis",
"orcid": "0000-0002-8524-0569"
},
"contributor": {
"email": "giacomo.lanza@ptb.de",
"github": "Zack-83",
"name": "Giacomo Lanza",
"orcid": "0000-0002-2239-3955"
},
"description": "The ontology Metadata4Ing is developed within the NFDI Consortium NFDI4Ing with the aim of providing a thorough framework for the semantic description of research data, with a particular focus on engineering sciences and neighbouring disciplines. This ontology allows a description of the whole data generation process (experiment, observation, simulation), embracing the object of investigation, all sample and data manipulation procedures, a summary of the data files and the information contained, and all personal and institutional roles. The subordinate classes and relations can be built according to the two principles of inheritance and modularity. \"Inheritance\" means that a subclass inherits all properties of its superordinate class, possibly adding some new ones. Modularity means that all expansions are independent of each other; this makes possible for instance to generate expanded ontologies for any possible combinations of method Γ object of research.",
"download_owl": "https://nfdi4ing.pages.rwth-aachen.de/metadata4ing/metadata4ing/ontology.xml",
"download_rdf": "https://nfdi4ing.pages.rwth-aachen.de/metadata4ing/metadata4ing/ontology.ttl",
"example": "Method",
"fairsharing": {
"abbreviation": "m4i",
"description": "The ontology Metadata4Ing is developed within the NFDI Consortium NFDI4Ing with the aim of providing a framework for the semantic description of research data, with a particular focus on engineering sciences and neighbouring disciplines. This ontology allows a thorough description of the whole data generation process (experiment, observation, simulation), embracing the object of investigation, all sample and data manipulation procedures, a summary of the data files and the information contained, and all personal and institutional roles. The subordinate classes and relations can be built according to the two principles of inheritance and modularity. \"Inheritance\" means that a subclass inherits all properties of its superordinate class, possibly adding some new ones. Modularity means that all expansions are independent of each other; this makes possible for instance to generate expanded ontologies for any possible combinations of method Γ object of research.",
"homepage": "http://metadata4ing.org",
"license": "CC-BY-4.0",
"name": "Metadata4Ing",
"prefix": "FAIRsharing.f8b3ec",
"subjects": [
"Engineering Science"
]
},
"github_request_issue": 970,
"homepage": "https://w3id.org/nfdi4ing/metadata4ing/",
"license": "CC-BY-4.0",
"lov": {
"description": "Metadata4Ing defines classes and properties or reuses such classes and properties from other ontologies to describe research processes and research data management in NFDI4Ing. \nNew concepts and properties are located in the namespace of Metadata4Ing.\nMetadata4Ing does not import complete ontologies for the sake of relevance, readability, understandability and usability by and for engineers.\nInstead, it tries to make re-use of existing identifiers for classes and properties by re-using all or a relevant subset of the axioms from the original ontology.\nThese statements have been extracted in different ways, e.g. by using ProtΓ©gΓ© tools importing an ontology and copying axioms of relevant items to Metadata4Ing or by download from data services or raw files of ontologies and manual copypasting.\nIn some cases there was a need to extend or modify the original set of statements about an entity, e.g. because labels and definitions were expressed with a different owl:AnnotationProperty than the rest of Metadata4Ing, or because a skos:preflabel or a skos:definition in any of the languages we would like to support was missing.\nAny editorial changes on elements from external ontologies are declared in Metadata4Ing by an annotation with skos:editorialNote at item-level.\nTo get the original set of statements we encourage to visit the original namespace of the respective item.\nMetadata4Ing reuses elements from the following ontologies:\n- BIBO = Bibliographic Ontology \n- BIRO = Bibliographic Reference Ontology \n- DCAT = Data Catalog \n- DCTERMS = Dublin Core Terms \n- FOAF = Friend of a Friend \n- OWL = Web Ontology Language \n- PROV = Provenance Namespace \n- QUDT = Quantities, Units, Dimensions and Types \n- RDF = Resource Description Framework \n- RDFS = RDF Schema \n- SCHEMA = schema.org \n- SKOS = Simple Knowledge Organization System \n- SSN = Semantic Sensor Network Ontology \n- VANN = Vocabulary for Annotating vocabulary descriptions \n- XSD = XML Schema Definition \n- EMMO = European Materials and Modelling Ontology \n- BFO = Basic Formal Ontology \n- RO = Relation Ontology \n- PIMS-II = PIMS Interoperability Infrastructure \n- D-SI = Digital System of Units",
"homepage": "https://nfdi4ing.pages.rwth-aachen.de/metadata4ing/metadata4ing/",
"keywords": [
"Academy",
"Metadata"
],
"modified": "2023-09-27",
"name": "Metadata4Ing: An ontology for describing the generation of research data within a scientific activity.",
"prefix": "m4i",
"uri_prefix": "http://w3id.org/nfdi4ing/metadata4ing#$1"
},
"mappings": {
"bartoc": "20402",
"fairsharing": "FAIRsharing.f8b3ec",
"lov": "m4i",
"wikidata": "Q111516803",
"zazuko": "m4i"
},
"mastodon": "nfdi4ing@nfdi.social",
"name": "Metadata4Ing",
"owners": [
{
"name": "Nationale Forschungsdateninfrastruktur",
"partnered": false,
"ror": "05qj6w324"
}
],
"pattern": "^\\w+$",
"repository": "https://git.rwth-aachen.de/nfdi4ing/metadata4ing/metadata4ing/",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://w3id.org/nfdi4ing/metadata4ing#$1",
"wikidata": {
"description": "ontology for the description of research data, with a particular focus on engineering sciences and neighbouring disciplines",
"name": "Metadata4Ing",
"prefix": "Q111516803"
},
"zazuko": {
"prefix": "m4i",
"uri_format": "http://w3id.org/nfdi4ing/metadata4ing#$1"
}
},
"ma": {
"aberowl": {
"description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus).",
"download_owl": "http://aber-owl.net/media/ontologies/MA/127/ma.owl",
"homepage": "https://github.com/obophenotype/mouse-anatomy-ontology",
"name": "Mouse adult gross anatomy",
"prefix": "MA"
},
"biocontext": {
"prefix": "MA"
},
"bioportal": {
"contact": {
"email": "Terry.Hayamizu@jax.org",
"name": "Terry Hayamizu"
},
"description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus).",
"homepage": "http://www.informatics.jax.org/searches/AMA_form.shtml",
"name": "Mouse Adult Gross Anatomy Ontology",
"prefix": "MA",
"version": "releases/2017-02-07"
},
"fairsharing": {
"abbreviation": "MA",
"description": "The Anatomy Ontology for the Adult Mouse is organized spatially and functionally, using \"is a\" and \"part of\" relationships to describe the anatomy of the postnatal mouse. Anatomical terms are arranged as a hierarchy from body region or organ system to tissue substructure. Modeling the anatomy hierarchically makes it possible to record expression results from assays with differing spatial resolution in a consistent and integrated manner. Organizing the anatomical terms as a Directed Acyclic Graph (DAG), i.e., in which a term can have more than one parent, allows presentation of the anatomy from multiple perspectives. In various locations, this ontology is also referred to as: 'Mouse Adult Gross Anatomy ontology', 'Adult Mouse Anatomy', 'Mouse Anatomy' or 'Mouse anatomical entity'. ",
"domains": [
"Organ",
"Tissue"
],
"homepage": "http://www.informatics.jax.org/vocab/gxd/ma_ontology/",
"license": "CC-BY-4.0",
"name": "Mouse Adult Gross Anatomy Ontology",
"prefix": "FAIRsharing.pdwqcr",
"publications": [
{
"doi": "10.1186/gb-2005-6-3-r29",
"pubmed": "15774030",
"title": "The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data",
"year": 2005
}
],
"repository": "https://github.com/obophenotype/mouse-anatomy-ontology",
"subjects": [
"Anatomy"
]
},
"go": {
"description": "Adult Mouse Anatomical Dictionary; part of Gene Expression Database",
"homepage": "http://www.informatics.jax.org/",
"name": "Adult Mouse Anatomical Dictionary",
"prefix": "MA",
"uri_format": "http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1"
},
"mappings": {
"aberowl": "MA",
"biocontext": "MA",
"bioportal": "MA",
"fairsharing": "FAIRsharing.pdwqcr",
"go": "MA",
"miriam": "ma",
"n2t": "ma",
"obofoundry": "ma",
"ols": "ma",
"ontobee": "MA",
"prefixcommons": "ma"
},
"miriam": {
"deprecated": false,
"description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)",
"homepage": "http://www.informatics.jax.org/",
"id": "00000445",
"name": "Mouse Adult Gross Anatomy",
"namespaceEmbeddedInLui": true,
"pattern": "^MA:\\d+$",
"prefix": "ma",
"sampleId": "0002502",
"uri_format": "http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1"
},
"n2t": {
"description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)",
"example": "0002502",
"homepage": "http://www.informatics.jax.org/",
"name": "Mouse Adult Gross Anatomy at The Jackson Laboratory",
"namespaceEmbeddedInLui": true,
"pattern": "^MA:\\d+$",
"prefix": "ma",
"uri_format": "http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1"
},
"obofoundry": {
"contact": "Terry.Hayamizu@jax.org",
"contact.github": "tfhayamizu",
"contact.label": "Terry Hayamizu",
"contact.orcid": "0000-0002-0956-8634",
"deprecated": false,
"description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus).",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/ma.obo",
"download.owl": "http://purl.obolibrary.org/obo/ma.owl",
"homepage": "https://github.com/obophenotype/mouse-anatomy-ontology",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Mouse adult gross anatomy",
"preferredPrefix": "MA",
"prefix": "ma",
"repository": "https://github.com/obophenotype/mouse-anatomy-ontology"
},
"ols": {
"description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus).",
"download_owl": "http://purl.obolibrary.org/obo/ma.owl",
"homepage": "https://github.com/obophenotype/mouse-anatomy-ontology",
"name": "Mouse adult gross anatomy",
"prefix": "ma",
"version": "2017-02-07",
"version.iri": "http://purl.obolibrary.org/obo/ma/releases/2017-02-07/ma.owl"
},
"ontobee": {
"library": "Library",
"name": "Mouse adult gross anatomy",
"prefix": "MA"
},
"pattern": "^\\d+$",
"prefixcommons": {
"alt_uri_formats": [
"http://purl.org/obo/owl/MA#$1"
],
"bioportal": "1000",
"description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus).",
"example": "MA:0000021",
"homepage": "http://www.informatics.jax.org/searches/AMA_form.shtml",
"keywords": [
"obo",
"anatomy",
"mouse"
],
"name": "Mouse adult gross anatomy",
"pattern": "^MA:\\d+$",
"prefix": "ma"
},
"publications": [
{
"doi": "10.1186/gb-2005-6-3-r29",
"pmc": "PMC1088948",
"pubmed": "15774030",
"title": "The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data",
"year": 2005
}
],
"uri_format": "http://purl.obolibrary.org/obo/MA_$1"
},
"macie": {
"biocontext": {
"prefix": "MACIE"
},
"contact": {
"email": "gemma.l.holliday@gmail.com",
"github": "GLHolliday79",
"name": "Gemma L. Holliday",
"orcid": "0000-0002-6731-6398"
},
"edam": {
"description": "Identifier of an enzyme reaction mechanism from the MACie database.",
"name": "Reaction ID (MACie)",
"obsolete": false,
"prefix": "2641"
},
"fairsharing": {
"abbreviation": "MACiE",
"description": "MACiE is an electronic database of well-characterised enzymatic reactions. MACiE is the result of more than three years' collaboration between the Mitchell and Murray-Rust groups in the Unilever Centre and Prof. Janet Thornton at the European Bioinformatics Institute. The database contains the reaction mechanisms for 100 individual enzymes; this includes the overall reactions and the multiple steps that constitute them.",
"homepage": "http://www.ebi.ac.uk/thornton-srv/databases/MACiE",
"name": "Mechanism, Annotation and Classification in Enzymes",
"prefix": "FAIRsharing.7xkx69",
"publications": [
{
"doi": "10.1093/bioinformatics/bti693",
"pubmed_id": 16188925,
"title": "MACiE: a database of enzyme reaction mechanisms."
},
{
"doi": "10.1093/nar/gkl774",
"pubmed_id": 17082206,
"title": "MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms."
}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"biocontext": "MACIE",
"edam": "2641",
"fairsharing": "FAIRsharing.7xkx69",
"miriam": "macie",
"n2t": "macie",
"prefixcommons": "macie"
},
"miriam": {
"deprecated": false,
"description": "MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved.",
"homepage": "https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html",
"id": "00000077",
"name": "MACiE",
"namespaceEmbeddedInLui": false,
"pattern": "^M\\d{4}$",
"prefix": "macie",
"sampleId": "M0001",
"uri_format": "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1"
},
"n2t": {
"description": "MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved.",
"example": "M0001",
"homepage": "https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html",
"name": "MACiE database of mechanisms, annotation and classification in enzymes",
"namespaceEmbeddedInLui": false,
"pattern": "^M\\d{4}$",
"prefix": "macie",
"uri_format": "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1"
},
"name": "Mechanism, Annotation and Classification in Enzymes",
"prefixcommons": {
"description": "MACiE is an electronic database of well-characterised enzymatic reactions. MACiE is the result of more than three years' collaboration between the Mitchell and Murray-Rust groups in the Unilever Centre and Prof. Janet Thornton at the European Bioinformatics Institute. The database contains the reaction mechanisms for 100 individual enzymes; this includes the overall reactions and the multiple steps that constitute them.",
"example": "M0001",
"homepage": "http://www.ebi.ac.uk/thornton-srv/databases/MACiE/",
"keywords": [
"enzyme",
"pathway"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "MACiE",
"pattern": "^M\\d{4}$",
"prefix": "macie",
"pubmed_ids": [
"17082206"
],
"uri_format": "http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/getPage.pl?id=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkl774",
"pmc": "PMC1634735",
"pubmed": "17082206",
"title": "MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms",
"year": 2006
},
{
"doi": "10.1093/bioinformatics/bti693",
"pmc": "PMC2748267",
"pubmed": "16188925",
"title": "MACiE: a database of enzyme reaction mechanisms",
"year": 2005
}
]
},
"maggot": {
"mappings": {
"miriam": "maggot"
},
"miriam": {
"deprecated": false,
"description": "Sharing descriptive Metadata is the first essential step towards Open Scientific Data. With this in mind, Maggot was specifically designed to annotate datasets by creating a metadata file to attach to the storage space. Indeed, it allows users to easily add descriptive metadata to datasets produced within a collective of people (research unit, platform, multi-partner project, etc.). This approach fits perfectly into a data management plan as it addresses the issues of data organization and documentation, data storage and frictionless metadata sharing within this same collective and beyond.",
"homepage": "https://eng-bfp.bordeaux-aquitaine.hub.inrae.fr/resources/metabolome-platform",
"id": "00001038",
"name": "Maggot",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9]+$",
"prefix": "maggot",
"sampleId": "frim1",
"uri_format": "https://pmb-bordeaux.fr/maggot/metadata/$1"
}
},
"maizegdb.locus": {
"biocontext": {
"prefix": "MAIZEGDB.LOCUS"
},
"contact": {
"email": "margaret.woodhouse@usda.gov",
"github": "margaretwoodhouse",
"name": "Margaret R. Woodhouse",
"orcid": "0000-0003-2164-8300"
},
"fairsharing": {
"abbreviation": "MaizeGDB",
"description": "MaizeGDB is the maize research community's central repository for genetics and genomics information.",
"homepage": "https://www.maizegdb.org",
"name": "Maize Genetics and Genomics Database",
"prefix": "FAIRsharing.aq280w",
"publications": [
{
"doi": "10.1155/2008/496957",
"pubmed_id": 18769488,
"title": "MaizeGDB: The maize model organism database for basic, translational, and applied research."
},
{
"doi": "10.1007/978-1-4939-3167-5_9",
"pubmed_id": 26519406,
"title": "MaizeGDB: The Maize Genetics and Genomics Database"
},
{
"doi": "10.1093/nar/gkv1007",
"pubmed_id": 26432828,
"title": "MaizeGDB update: new tools, data and interface for the maize model organism database"
},
{
"doi": "10.3389/fpls.2019.01050",
"pubmed_id": 31555312,
"title": "MaizeDIG: Maize Database of Images and Genomes."
},
{
"doi": "10.1093/nar/gky1046",
"pubmed_id": 30407532,
"title": "MaizeGDB 2018: the maize multi-genome genetics and genomics database"
}
],
"subjects": [
"Genomics",
"Genetics",
"Life Science"
]
},
"go": {
"homepage": "https://www.maizegdb.org/",
"name": "MaizeGDB",
"prefix": "MaizeGDB_Locus",
"uri_format": "https://www.maizegdb.org/gene_center/gene/$1"
},
"integbio": {
"alt_name": "Maize Genetics and Genomics Database",
"description": "MaizeGDB is a integrated database of the crop plant and model organism Zea mays. It contains maps, gene product information, loci and their various alleles, phenotypes (both naturally occurring and as a result of directed mutagenesis), stocks, sequences, molecular markers, references and contact information for maize researchers on worldwide. Moreover, users are able to obtain various community support service bulletin boards including the Editorial Board's list of high-impact papers, information about the Annual Maize genetics Conference and the Jobs board where employment opportunities are posted.",
"fairsharing": "biodbcore-000414",
"homepage": "http://www.maizegdb.org/",
"information_keywords": [
"Bioresource",
"Sequence",
"Expression",
"Interaction/Pathway",
"Image/Movie",
"Portal"
],
"maintainer": "MaizeGDB (Maize Genetics and Genomoics Database) Working Group",
"name": "MaizeGDB",
"prefix": "nbdc00129",
"pubmeds": [
"17202174",
"14681441",
"21565781"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"Protein",
"Organism"
]
},
"mappings": {
"biocontext": "MAIZEGDB.LOCUS",
"fairsharing": "FAIRsharing.aq280w",
"go": "MaizeGDB_Locus",
"integbio": "nbdc00129",
"miriam": "maizegdb.locus",
"n2t": "maizegdb.locus",
"ncbi": "MaizeGDB",
"prefixcommons": "maizegdb",
"re3data": "r3d100010795",
"uniprot": "DB-0058"
},
"miriam": {
"deprecated": false,
"description": "MaizeGDB is the maize research community's central repository for genetics and genomics information.",
"homepage": "http://www.maizegdb.org/",
"id": "00000177",
"name": "MaizeGDB Locus",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "maizegdb.locus",
"sampleId": "25011",
"uri_format": "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1"
},
"n2t": {
"description": "MaizeGDB is the maize research community's central repository for genetics and genomics information.",
"example": "25011",
"homepage": "http://www.maizegdb.org/",
"name": "MaizeGDB at Missouri",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "maizegdb.locus",
"uri_format": "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1"
},
"name": "MaizeGDB Locus",
"ncbi": {
"example": "635633",
"homepage": "http://www.maizegdb.org/",
"name": "Maize Genome Database unique identifiers",
"prefix": "MaizeGDB"
},
"prefixcommons": {
"description": "MaizeGDB is the maize research community's central repository for genetics and genomics information.",
"example": "25011",
"homepage": "http://www.maizegdb.org",
"keywords": [
"genome",
"DNA"
],
"name": "Maize Genetics and Genomics Database",
"pattern": "^\\d+$",
"prefix": "maizegdb",
"pubmed_ids": [
"18769488"
],
"synonyms": [
"maizegdb.locus",
"maizegdb_qtl"
],
"uri_format": "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1"
},
"publications": [
{
"doi": "10.3389/fpls.2019.01050",
"pmc": "PMC6724615",
"pubmed": "31555312",
"title": "MaizeDIG: Maize Database of Images and Genomes",
"year": 2019
},
{
"doi": "10.1093/nar/gky1046",
"pmc": "PMC6323944",
"pubmed": "30407532",
"title": "MaizeGDB 2018: the maize multi-genome genetics and genomics database",
"year": 2019
},
{
"doi": "10.1007/978-1-4939-3167-5_9",
"pubmed": "26519406",
"title": "MaizeGDB: The Maize Genetics and Genomics Database",
"year": 2016
},
{
"doi": "10.1093/nar/gkv1007",
"pmc": "PMC4702771",
"pubmed": "26432828",
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{
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{
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],
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"information_keywords": [
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"maintainer": "ICBMS (Institute for Molecular and Supramolecular Chemistry and Biochemistry, University of Lyon 1)",
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"prefix": "nbdc01222",
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"prefixcommons": {
"description": "MatrixDB is a database reporting mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. Full-length molecules, fragments and multimers present in the extracellular matrix are all included in the database.",
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"keywords": [
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"license": "http://dip.doe-mbi.ucla.edu/dip/termsofuse.html",
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"pattern": "^[A-Z]\\d+_[A-Z]\\d+$",
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"pubmed_ids": [
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"synonyms": [
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],
"re3data": {
"description": "MatrixDB is a freely available database focused on interactions established by extracellular proteins and polysaccharides.\nMatrixDB takes into account the multimetric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB includes interaction data extracted from the literature by manual curation in our lab, and offers access to relevant data involving extracellular proteins provided by our IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. MatrixDB is in charge of the curation of papers published in Matrix Biology since January 2009",
"homepage": "http://matrixdb.univ-lyon1.fr/",
"name": "MatrixDB",
"prefix": "r3d100010672",
"synonyms": [
"Extracellular Matrix interactions DataBase"
],
"xrefs": {
"issn": "2426-6949",
"nif": "0000-10226",
"omics": "01918",
"scr": "001727"
}
},
"uri_format": "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1"
},
"matrixdb.association": {
"biocontext": {
"prefix": "MATRIXDB.ASSOCIATION"
},
"mappings": {
"biocontext": "MATRIXDB.ASSOCIATION",
"miriam": "matrixdb.association",
"n2t": "matrixdb.association"
},
"miriam": {
"deprecated": false,
"description": "MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations.",
"homepage": "http://matrixdb.univ-lyon1.fr/",
"id": "00000068",
"name": "MatrixDB",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$",
"prefix": "matrixdb.association",
"sampleId": "P00747__P07355",
"uri_format": "http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association"
},
"n2t": {
"description": "MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations.",
"example": "P00747__P07355",
"homepage": "http://matrixdb.univ-lyon1.fr/",
"name": "MatrixDB Association",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$",
"prefix": "matrixdb.association",
"uri_format": "http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association"
},
"name": "MatrixDB Association"
},
"mavedb": {
"comment": "This is an interesting one as the full IDs as they appear on the page are of the form `urn:mavedb:00000011-a` suggesting this is the preferred URI expansion for identification purposes. However, mavedb hasn't been registered with IANA https://www.iana.org/assignments/urn-namespaces/urn-namespaces.xhtml",
"contact": {
"email": "alan.rubin@wehi.edu.au",
"github": "afrubin",
"name": "Alan Rubin",
"orcid": "0000-0003-1474-605X"
},
"contributor": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"description": "Some IDs may represent experiment sets, e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011 Others represent genomic regions (specifically deep mutational scans thereof) e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011-a",
"example": "00000011-a",
"example_extras": [
"00000011"
],
"github_request_issue": 1045,
"homepage": "https://www.mavedb.org",
"name": "Multiplexed Assays of Variant Effect Database",
"pattern": "^\\S+$",
"publications": [
{
"doi": "10.1186/s13059-019-1845-6",
"pmc": "PMC6827219",
"pubmed": "31679514",
"title": "MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect",
"year": 2019
}
],
"repository": "https://github.com/VariantEffect/mavedb-api",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://www.mavedb.org/#/experiments/urn:mavedb:$1"
},
"maxo": {
"aberowl": {
"description": "The Medical Action Ontology (MAxO) provides a broad view of medical actions and includes terms for medical procedures, interventions, therapies, treatments, and recommendations.",
"download_owl": "http://aber-owl.net/media/ontologies/MAXO/44/maxo.owl",
"homepage": "https://github.com/monarch-initiative/MAxO",
"name": "Medical Action Ontology",
"prefix": "MAXO"
},
"biolink": {
"is_identifiers": false,
"is_obo": true,
"prefix": "MAXO",
"uri_format": "http://purl.obolibrary.org/obo/MAXO_$1"
},
"bioportal": {
"contact": {
"email": "Leigh.Carmody@jax.org",
"name": "Leigh Carmody"
},
"description": "The Medical Action Ontology (MAxO) provides a structured vocabulary for medical procedures, interventions, therapies, and treatments for disease with an emphasis on rare disease (RD). It is often difficult to find relevant clinical literature about strategies to manage RD patients. Responding to this need, MAxO provides a vocabulary to annotate diseases and phenotypes with recommended treatments and interventions.",
"homepage": "https://github.com/monarch-initiative/MAxO",
"name": "Medical Action Ontology",
"prefix": "MAXO",
"version": "2024-07-29"
},
"example": "0000008",
"fairsharing": {
"abbreviation": "MAxO",
"contact": {
"email": "Leigh.Carmody@jax.org",
"name": "Leigh Carmody",
"orcid": "0000-0001-7941-2961"
},
"description": "The Medical Action Ontology (MAxO) is being developed to provide a structured vocabulary for medical procedures, interventions, therapies, and treatments for rare diseases.",
"domains": [
"Rare disease"
],
"homepage": "https://github.com/monarch-initiative/MAxO",
"license": "CC-BY-4.0",
"name": "Medical Action Ontology",
"prefix": "FAIRsharing.945c78",
"publications": [
{
"doi": "10.1101/2023.07.13.23292612",
"pubmed": "37503136",
"title": "The Medical Action Ontology: A Tool for Annotating and Analyzing Treatments and Clinical Management of Human Disease",
"year": 2023
}
],
"subjects": [
"Medicine"
]
},
"mappings": {
"aberowl": "MAXO",
"biolink": "MAXO",
"bioportal": "MAXO",
"fairsharing": "FAIRsharing.945c78",
"miriam": "maxo",
"obofoundry": "maxo",
"ols": "maxo",
"ontobee": "MAXO"
},
"miriam": {
"deprecated": false,
"description": "An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations.",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/maxo",
"id": "00001032",
"name": "Medical Action Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "\\d{7}",
"prefix": "maxo",
"sampleId": "0001073",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/maxo/terms?obo_id=MAXO:$1"
},
"obofoundry": {
"appears_in": [
"ecto"
],
"contact": "Leigh.Carmody@jax.org",
"contact.github": "LCCarmody",
"contact.label": "Leigh Carmody",
"contact.orcid": "0000-0001-7941-2961",
"depends_on": [
"chebi",
"foodon",
"go",
"hp",
"iao",
"nbo",
"obi",
"ro",
"uberon"
],
"deprecated": false,
"description": "The Medical Action Ontology (MAxO) provides a broad view of medical actions and includes terms for medical procedures, interventions, therapies, treatments, and recommendations.",
"domain": "health",
"download.json": "http://purl.obolibrary.org/obo/maxo.json",
"download.obo": "http://purl.obolibrary.org/obo/maxo.obo",
"download.owl": "http://purl.obolibrary.org/obo/maxo.owl",
"homepage": "https://github.com/monarch-initiative/MAxO",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"logo": "https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/maxo-logos/maxo_logo_black-banner.png",
"name": "Medical Action Ontology",
"preferredPrefix": "MAXO",
"prefix": "maxo",
"repository": "https://github.com/monarch-initiative/MAxO"
},
"ols": {
"description": "An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations.",
"download_owl": "http://purl.obolibrary.org/obo/maxo.owl",
"homepage": "https://github.com/monarch-initiative/MAxO",
"name": "Medical Action Ontology",
"prefix": "maxo",
"version": "2024-07-29",
"version.iri": "http://purl.obolibrary.org/obo/maxo/releases/2024-07-29/maxo.owl"
},
"ontobee": {
"library": "Library",
"name": "Medical Action Ontology",
"prefix": "MAXO"
},
"pattern": "^\\d{7}$",
"twitter": "MonarchInit",
"uri_format": "http://purl.obolibrary.org/obo/MAXO_$1"
},
"mba": {
"bioportal": {
"contact": {
"email": "chinhda@alleninstitute.org",
"name": "Allen Institute for Brain Science"
},
"description": "Allen Brain Atlas P56 Mouse Ontology",
"homepage": "http://www.brain-map.org",
"name": "Allen Brain Atlas (ABA) Adult Mouse Brain Ontology",
"prefix": "ABA-AMB",
"publication": "http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470054085.html",
"version": "1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A controlled vocabulary to support the study of transcription in the mouse brain",
"download_obo": "https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-mba.obo",
"example": "688",
"homepage": "https://mouse.brain-map.org",
"mappings": {
"bioportal": "ABA-AMB"
},
"name": "Mouse Brain Atlas",
"pattern": "^\\d+$",
"preferred_prefix": "MBA",
"uri_format": "https://biopragmatics.github.io/providers/mba/$1"
},
"mcc": {
"bioportal": {
"contact": {
"email": "usha@molecularconnections.com",
"name": "Usha Mahadevan"
},
"description": "Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive of machine-interpretable definitions of basic concepts in the domain and relations among them. The need for ontologies that provide a systematic arrangement of available data and allow cross talk across various related domains is gaining momentum. In this backdrop, we have developed a comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format.",
"homepage": "http://www.molecularconnections.com",
"name": "Cell Line Ontology [by Mahadevan]",
"prefix": "MCCL",
"version": "2"
},
"deprecated": true,
"example": "ThoracicArtery",
"mappings": {
"bioportal": "MCCL"
},
"name": "Cell Line Ontology [derivative]",
"uri_format": "http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#$1"
},
"mco": {
"aberowl": {
"description": "Microbial Conditions Ontology is an ontology...",
"download_owl": "http://aber-owl.net/media/ontologies/MCO/2/mco.owl",
"homepage": "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology",
"name": "Microbial Conditions Ontology",
"prefix": "MCO"
},
"bioportal": {
"contact": {
"email": "citlalli.mejiaalmonte@gmail.com",
"name": "Citlalli MejΓa-Almonte"
},
"description": "Microbial Conditions Ontology contains terms to describe growth conditions in microbiological experiments. The first version is based on gene regulation experiments in Escherichia coli K-12. It is being used in RegulonDB to link growth conditions to gene regulation data.",
"homepage": "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology",
"name": "Microbial Conditions Ontology",
"prefix": "MCO"
},
"example": "0000858",
"mappings": {
"aberowl": "MCO",
"bioportal": "MCO",
"obofoundry": "mco",
"ols": "mco",
"ontobee": "MCO"
},
"obofoundry": {
"contact": "citlalli.mejiaalmonte@gmail.com",
"contact.github": "citmejia",
"contact.label": "Citlalli MejΓa-Almonte",
"contact.orcid": "0000-0002-0142-5591",
"depends_on": [
"bfo",
"chebi",
"cl",
"clo",
"micro",
"ncbitaxon",
"ncit",
"obi",
"omit",
"omp",
"pato",
"peco",
"uberon",
"zeco"
],
"deprecated": false,
"description": "Microbial Conditions Ontology is an ontology...",
"domain": "investigations",
"download.obo": "http://purl.obolibrary.org/obo/mco.obo",
"download.owl": "http://purl.obolibrary.org/obo/mco.owl",
"homepage": "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Microbial Conditions Ontology",
"preferredPrefix": "MCO",
"prefix": "mco",
"repository": "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology"
},
"ols": {
"description": "Microbial Conditions Ontology is an ontology...",
"download_owl": "http://purl.obolibrary.org/obo/mco.owl",
"homepage": "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology",
"name": "Microbial Conditions Ontology",
"prefix": "mco",
"version": "2019-05-15",
"version.iri": "http://purl.obolibrary.org/obo/mco/releases/2019-05-15/mco.owl"
},
"ontobee": {
"library": "Library",
"name": "Microbial Conditions Ontology",
"prefix": "MCO"
},
"pattern": "^\\d+$",
"uri_format": "http://purl.obolibrary.org/obo/MCO_$1"
},
"mcro": {
"aberowl": {
"description": "An ontology representing the structure of model card reports - reports that describe basic characteristics of machine learning models for the public and consumers.",
"download_owl": "http://aber-owl.net/media/ontologies/MCRO/1/mcro.owl",
"homepage": "https://github.com/UTHealth-Ontology/MCRO",
"name": "Model Card Report Ontology",
"prefix": "MCRO"
},
"bioportal": {
"contact": {
"email": "muamith@utmb.edu",
"name": "Tuan Amith"
},
"description": "An ontology representing the structure of model card reports - reports that describe basic characteristics of machine learning models for the public and consumers.",
"homepage": "https://github.com/UTHealth-Ontology/MCRO",
"name": "Model Card Report Ontology",
"prefix": "MCRO",
"version": "2023-03-07"
},
"example": "0000001",
"mappings": {
"aberowl": "MCRO",
"bioportal": "MCRO",
"miriam": "mcro",
"obofoundry": "mcro",
"ontobee": "MCRO"
},
"miriam": {
"deprecated": false,
"description": "An ontology representing the model card structure, he aim of this work is to describe machine learning models to communicate information about specific details about the model (trade offs, intended users, licensing, etc.). ",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/mcro",
"id": "00001049",
"name": "Model Card Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^MCRO:\\d+$",
"prefix": "mcro",
"sampleId": "0000027",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/mcro/classes?obo_id=MCRO:$1"
},
"obofoundry": {
"contact": "muamith@utmb.edu",
"contact.github": "ProfTuan",
"contact.label": "Tuan Amith",
"contact.orcid": "0000-0003-4333-1857",
"depends_on": [
"iao",
"swo"
],
"deprecated": false,
"description": "An ontology representing the structure of model card reports - reports that describe basic characteristics of machine learning models for the public and consumers.",
"domain": "information technology",
"download.owl": "http://purl.obolibrary.org/obo/mcro.owl",
"homepage": "https://github.com/UTHealth-Ontology/MCRO",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Model Card Report Ontology",
"preferredPrefix": "MCRO",
"prefix": "mcro",
"publications": [
{
"id": "https://doi.org/10.1186/s12859-022-04797-6",
"title": "Toward a standard formal semantic representation of the model card report"
}
],
"repository": "https://github.com/UTHealth-Ontology/MCRO"
},
"ontobee": {
"library": "Library",
"name": "Model Card Report Ontology",
"prefix": "MCRO"
},
"pattern": "^\\d{7}$"
},
"mdm": {
"aberowl": {
"description": "The Mapping of Drug Names and MeSH 2022 (MDM) provides owl:sameAs relationships of similar concepts for Drug Names from the DrugBank vocabulary (released 2022-01-03 under version 5.1.9: https://go.drugbank.com/releases/latest#open-data) and the Medical Subject Headings (2022 version: http://id.nlm.nih.gov/mesh/). Two concepts are considered similar if they share the same concept name or a common synonym. Additional synonyms are generated using the Snowball stemming algorithm. The software implementation is available on github within the Maven project SNoKE in the module snoke.ontology: https://github.com/bernd-mueller/snoke/tree/master/snoke.ontology",
"download_owl": "http://aber-owl.net/media/ontologies/MDM/4/mdm.owl",
"homepage": "https://www.zbmed.de/",
"name": "Mapping of Drug Names and MeSH 2022",
"prefix": "MDM",
"version": "0.33"
},
"biocontext": {
"prefix": "MDM"
},
"bioportal": {
"contact": {
"email": "bernd.mueller@zbmed.de",
"name": "Bernd MΓΌller"
},
"description": "The Mapping of Drug Names and MeSH 2022 (MDM) provides owl:sameAs relationships as well as owl:equivalentClass of similar concepts for Drug Names from the DrugBank vocabulary (released 2022-01-03 under version 5.1.9: https://go.drugbank.com/releases/latest#open-data) and the Medical Subject Headings (2022 version: http://id.nlm.nih.gov/mesh/). Two concepts are considered similar if they share the same concept name or a common synonym. Additional synonyms are generated using the Snowball stemming algorithm. The software implementation is available on github within the Maven project SNoKE in the module snoke.ontology: https://github.com/bernd-mueller/snoke/tree/master/snoke.ontology",
"homepage": "https://www.zbmed.de/",
"name": "Mapping of Drug Names and MeSH 2022",
"prefix": "MDM",
"version": "0.330"
},
"contact": {
"email": "bernd.mueller@zbmed.de",
"name": "Bernd MΓΌller",
"orcid": "0000-0003-3062-8192"
},
"fairsharing": {
"abbreviation": "MDM",
"contact": {
"email": "dugas@uni-muenster.de",
"name": "Martin Dugas",
"orcid": "0000-0001-9740-0788"
},
"description": "MDM-Portal (Medical Data-Models) is a meta-data registry for creating, analysing, sharing and reusing medical forms, developed by the Institute of Medical Informatics, University of Muenster in Germany. see also http://www.ncbi.nlm.nih.gov/pubmed/26868052 Electronic forms for documentation of patient data are an integral part within the workflow of physicians. A huge amount of data is collected either through routine documentation forms (EHRs) for electronic health records or as case report forms (CRFs) for clinical trials. This raises major scientific challenges for health care, since different health information systems are not necessarily compatible with each other and thus information exchange of structured data is hampered. Software vendors provide a variety of individual documentation forms according to their standard contracts, which function as isolated applications. Furthermore, free availability of those forms is rarely the case. Currently less than 5 % of medical forms are freely accessible. Based on this lack of transparency harmonization of data models in health care is extremely cumbersome, thus work and know-how of completed clinical trials and routine documentation in hospitals are hard to be re-used. The MDM-Portal serves as an infrastructure for academic (non-commercial) medical research to contribute a solution to this problem. It already contains more than 6,000 system-independent forms (CDISC ODM Format, www.cdisc.org, Operational Data Model) with more than 470,000 data-elements. This enables researchers to view, discuss, download and export forms in most common technical formats such as PDF, CSV, Excel, SQL, SPSS, R, etc. A growing user community will lead to a growing database of medical forms. In this matter, we would like to encourage all medical researchers to register and add forms and discuss existing forms.",
"homepage": "https://medical-data-models.org",
"license": "CC BY-NC 4.0",
"name": "Medical Data Models",
"prefix": "FAIRsharing.wnk2eq",
"publications": [
{
"doi": "10.1093/database/bav121",
"pubmed_id": 26868052,
"title": "Portal of medical data models: information infrastructure for medical research and healthcare"
}
],
"subjects": [
"Medicine",
"Biomedical Science",
"Translational Medicine"
]
},
"mappings": {
"aberowl": "MDM",
"biocontext": "MDM",
"bioportal": "MDM",
"fairsharing": "FAIRsharing.wnk2eq",
"miriam": "mdm",
"n2t": "mdm",
"re3data": "r3d100013816"
},
"miriam": {
"deprecated": false,
"description": "The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems.",
"homepage": "https://medical-data-models.org/",
"id": "00000574",
"name": "MDM",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "mdm",
"sampleId": "4776",
"uri_format": "https://medical-data-models.org/forms/$1"
},
"n2t": {
"description": "The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems.",
"example": "4776",
"homepage": "https://medical-data-models.org/",
"name": "MDM at University of Muenster",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "mdm",
"uri_format": "https://medical-data-models.org/forms/$1"
},
"name": "Medical Data Models",
"publications": [
{
"doi": "10.1093/database/bav121",
"pmc": "PMC4750548",
"pubmed": "26868052",
"title": "Portal of medical data models: information infrastructure for medical research and healthcare",
"year": 2016
}
],
"re3data": {
"description": "MDM-Portal (Medical Data Models) is a meta-data registry for creating, analyzing, sharing and reusing medical forms. It serves as an infrastructure for academic (non-commercial) medical research to contribute a solution to this problem. It contains forms in the system-independent CDISC Operational Data Model (ODM) format with more than 500,000 data-elements. The Portal provides numerous core data sets, common data elements or data standards, code lists and value sets. This enables researchers to view, discuss, download and export forms in most common technical formats such as PDF, CSV, Excel, SQL, SPSS, R, etc.",
"homepage": "https://medical-data-models.org/",
"name": "Portal of Medical Data Models",
"prefix": "r3d100013816",
"synonyms": [
"MDM Portal"
],
"xrefs": {
"fairsharing": "FAIRsharing.wnk2eq"
}
}
},
"meddra": {
"aberowl": {
"description": "Medical Dictionary for Regulatory Activities Terminology (MedDRA)",
"homepage": "http://www.meddramsso.com/MSSOWeb/contact_us/index.htm",
"name": "Medical Dictionary for Regulatory Activities Terminology (MedDRA)",
"prefix": "MEDDRA",
"version": "2016AB"
},
"bartoc": {
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"homepage": "http://merops.sanger.ac.uk/",
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"prefix": "merops",
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{
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"pmc": "PMC148173",
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"title": "MEROPS: the peptidase database",
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{
"doi": "10.1042/bj2900205",
"pmc": "PMC1132403",
"pubmed": "8439290",
"title": "Evolutionary families of peptidases",
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},
{
"doi": "10.1093/nar/gkx1134",
"pmc": "PMC5753285",
"pubmed": "29145643",
"title": "The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database",
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{
"doi": "10.1093/nar/gkv1118",
"pmc": "PMC4702814",
"pubmed": "26527717",
"title": "Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors",
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},
{
"doi": "10.1016/j.biochi.2015.10.003",
"pmc": "PMC4756867",
"pubmed": "26455268",
"title": "Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation",
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},
{
"doi": "10.1093/nar/gkr987",
"pmc": "PMC3245014",
"pubmed": "22086950",
"title": "MEROPS: the database of proteolytic enzymes, their substrates and inhibitors",
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},
{
"doi": "10.1093/nar/gkm954",
"pmc": "PMC2238837",
"pubmed": "17991683",
"title": "MEROPS: the peptidase database",
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],
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{
"code": "mesh.ttl",
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{
"code": "mesh.n3",
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"mesh.2012": {
"biocontext": {
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"mappings": {
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
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"description": "Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump",
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"uri_format": "http://id.nlm.nih.gov/mesh/vocab#$1"
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"biocontext": {
"prefix": "METABOLIGHTS"
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"cellosaurus": {
"category": "Metabolomic databases",
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"prefix": "MetaboLights",
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"homepage": "https://www.ebi.ac.uk/metabolights/",
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"example": "MTBLS1",
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"name": "MetaboLights at EBI",
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"name": "MetaboLights Compound ID",
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"prefix": "MFO",
"version": "unknown"
},
"biocontext": {
"prefix": "MFO"
},
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"email": "Thorsten.Henrich@embl-heidelberg.de",
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"prefix": "MFO"
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"deprecated": true,
"description": "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.",
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"bioportal": "1027",
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"obo",
"anatomy",
"development",
"fish"
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"prefix": "mfo"
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"mfoem": {
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"prefix": "MFOEM"
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"biocontext": {
"prefix": "MFOEM"
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"contact": {
"email": "janna.hastings@gmail.com",
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"name": "Emotion Ontology",
"prefix": "MFOEM",
"publication": "https://github.com/jannahastings/emotion-ontology",
"version": "2022-07-19"
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"example": "000204",
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"email": "hastings@ebi.ac.uk",
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},
"description": "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings, designed to support interdisciplinary research by providing unified annotations. The ontology is a domain specialisation of the broader Mental Functioning Ontology.",
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"license": "Apache 2.0 License",
"name": "Emotion Ontology",
"prefix": "FAIRsharing.dx30m8",
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"subjects": [
"Biomedical Science"
]
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"bioportal": "MFOEM",
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"ols": "mfoem",
"ontobee": "MFOEM"
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"homepage": "https://github.com/jannahastings/emotion-ontology",
"name": "Emotion Ontology",
"prefix": "mfoem",
"version": "2022-07-19",
"version.iri": "http://purl.obolibrary.org/obo/MFOEM/2022-07-19/MFOEM.owl"
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"library": "Library",
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"prefix": "MFOEM"
},
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{
"doi": "10.1186/2041-1480-5-38",
"pmc": "PMC4417517",
"pubmed": "25937879",
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],
"uri_format": "http://purl.obolibrary.org/obo/MFOEM_$1"
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"mfomd": {
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"download_owl": "http://aber-owl.net/media/ontologies/MFOMD/3/mfomd.owl",
"homepage": "https://github.com/jannahastings/mental-functioning-ontology",
"name": "Mental Disease Ontology",
"prefix": "MFOMD"
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"biocontext": {
"prefix": "MFOMD"
},
"bioportal": {
"contact": {
"email": "janna.hastings@gmail.com",
"name": "Janna Hastings"
},
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"homepage": "https://github.com/jannahastings/mental-functioning-ontology",
"name": "MFO Mental Disease Ontology",
"prefix": "MFOMD",
"version": "2020-04-26"
},
"example": "0000046",
"fairsharing": {
"abbreviation": "MFOMD",
"description": "An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable.",
"domains": [
"Disease"
],
"homepage": "https://github.com/jannahastings/mental-functioning-ontology",
"name": "MFO Mental Disease Ontology",
"prefix": "FAIRsharing.q053vb",
"subjects": [
"Psychiatry"
]
},
"mappings": {
"aberowl": "MFOMD",
"biocontext": "MFOMD",
"bioportal": "MFOMD",
"fairsharing": "FAIRsharing.q053vb",
"obofoundry": "mfomd",
"ols": "mfomd",
"ontobee": "MFOMD"
},
"obofoundry": {
"contact": "janna.hastings@gmail.com",
"contact.github": "jannahastings",
"contact.label": "Janna Hastings",
"contact.orcid": "0000-0002-3469-4923",
"deprecated": false,
"description": "An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/mfomd.owl",
"homepage": "https://github.com/jannahastings/mental-functioning-ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Mental Disease Ontology",
"preferredPrefix": "MFOMD",
"prefix": "mfomd",
"repository": "https://github.com/jannahastings/mental-functioning-ontology"
},
"ols": {
"description": "The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF).",
"download_owl": "http://purl.obolibrary.org/obo/mfomd.owl",
"homepage": "https://github.com/jannahastings/mental-functioning-ontology",
"name": "Mental Disease Ontology",
"prefix": "mfomd",
"version": "2020-04-26",
"version.iri": "http://purl.obolibrary.org/obo/MFOMD/2020-04-26/MFOMD.owl"
},
"ontobee": {
"library": "Library",
"name": "Mental Disease Ontology",
"prefix": "MFOMD"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/MFOMD_$1"
},
"mge": {
"banana": "mge",
"biocontext": {
"prefix": "ACLAME"
},
"edam": {
"description": "An identifier of a mobile genetic element from the Aclame database.",
"name": "ACLAME",
"obsolete": false,
"prefix": "2631"
},
"fairsharing": {
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"description": "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.",
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"license": "http://opendatacommons.org/licenses/pddl/1.0",
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"prefix": "FAIRsharing.5tfcy8",
"publications": [
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"pubmed_id": 14681355,
"title": "ACLAME: a CLAssification of Mobile genetic Elements."
},
{
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"pubmed_id": 19933762,
"title": "ACLAME: a CLAssification of Mobile genetic Elements, update 2010."
}
],
"subjects": [
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},
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"description": "ACLAME Version 4 is a database of the mobile genetic elements (MGEs) as found in the genomes of all phages, plasmids and transposons known at present - 811 hosts in total.\nInformation on 122,154 proteins, discovered to be present in 2,326 MGEs, is provided.\nThe proteins were grouped in families as follows:\nThe prophages contained 6,822 clusters, the plasmids 18,228 groups, the viruses and prophages 16,057 groups and the viruses 11,503 clusters.\nThe database is in the process of developing a classification system of the functional modules of these MGEs at the protein level, gene level, and higher.\nKeyword and Blast search options are available.\nAn option is also offered whereby host-specific groups of MGEs can be viewed.",
"fairsharing": "biodbcore-000549",
"homepage": "http://aclame.ulb.ac.be/",
"information_keywords": [
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],
"maintainer": "Universite Libre de Bruxelles",
"name": "ACLAME",
"prefix": "nbdc00355",
"pubmeds": [
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"18238785",
"18234706",
"17614261",
"17482656",
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],
"status": "Inactive",
"target_keywords": [
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"DNA",
"Protein"
]
},
"mappings": {
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"fairsharing": "FAIRsharing.5tfcy8",
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"miriam": "mge",
"n2t": "mge",
"prefixcommons": "aclame"
},
"miriam": {
"deprecated": true,
"description": "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.",
"homepage": "http://aclame.ulb.ac.be/",
"id": "00000063",
"name": "Aclame",
"namespaceEmbeddedInLui": true,
"pattern": "^mge:\\d+$",
"prefix": "mge",
"sampleId": "2",
"uri_format": "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1"
},
"n2t": {
"description": "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.",
"example": "2",
"homepage": "http://aclame.ulb.ac.be/",
"name": "Aclame database of mobile genetic elements",
"namespaceEmbeddedInLui": true,
"pattern": "^mge:\\d+$",
"prefix": "mge",
"uri_format": "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1"
},
"pattern": "^\\d+$",
"prefixcommons": {
"description": "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.",
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"homepage": "http://aclame.ulb.ac.be",
"keywords": [
"genome",
"gene"
],
"miriam": "mge",
"name": "A CLAssification of Mobile genetic Elements",
"pattern": "^mge:\\d+$",
"prefix": "aclame",
"pubmed_ids": [
"14681355"
],
"uri_format": "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkp938",
"pmc": "PMC2808911",
"pubmed": "19933762",
"title": "ACLAME: a CLAssification of Mobile genetic Elements, update 2010",
"year": 2009
},
{
"doi": "10.1093/nar/gkh084",
"pmc": "PMC308818",
"pubmed": "14681355",
"title": "ACLAME: a CLAssification of Mobile genetic Elements",
"year": 2004
}
],
"synonyms": [
"aclame"
]
},
"mgi": {
"banana": "MGI",
"biocontext": {
"prefix": "MGI",
"uri_format": "http://www.informatics.jax.org/accession/MGI:$1"
},
"cellosaurus": {
"category": "Organism-specific databases",
"homepage": "http://www.informatics.jax.org",
"name": "Mouse Genome Database (MGD) from Mouse Genome Informatics",
"prefix": "MGI",
"uri_format": "http://www.informatics.jax.org/marker/$1"
},
"contact": {
"email": "joel.richardson@jax.org",
"github": "JoelRichardson",
"name": "Joel Richardson",
"orcid": "0000-0003-3342-5753"
},
"edam": {
"description": "Identifier of an object from the MGI database.",
"name": "MGI",
"obsolete": false,
"prefix": "3274"
},
"example": "6017782",
"fairsharing": {
"abbreviation": "MGI",
"description": "MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Data includes gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.",
"homepage": "http://www.informatics.jax.org/",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource",
"prefix": "FAIRsharing.fcwyhz",
"publications": [
{
"doi": "10.1093/nar/gkt1225",
"pubmed_id": 24285300,
"title": "The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse."
},
{
"doi": "10.1093/nar/gks1115",
"pubmed_id": 23175610,
"title": "The Mouse Genome Database: Genotypes, Phenotypes, and Models of Human Disease"
},
{
"doi": "10.1007/978-1-4939-6427-7_3",
"pubmed_id": 27933520,
"title": "Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research."
},
{
"doi": "10.1093/ilar/ilx013",
"pubmed_id": 28838066,
"title": "Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse."
},
{
"doi": "10.1093/nar/gkr974",
"pubmed_id": 22075990,
"title": "The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse"
},
{
"doi": "10.1093/nar/gkw1040",
"pubmed_id": 27899570,
"title": "Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse."
},
{
"doi": "10.1126/science.8091224",
"pubmed_id": 8091224,
"title": "A database for mouse development."
},
{
"doi": "10.1093/nar/gki113",
"pubmed_id": 15608240,
"title": "The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology."
},
{
"doi": "10.1093/nar/gky922",
"pubmed_id": 30335138,
"title": "The mouse Gene Expression Database (GXD): 2019 update."
},
{
"doi": "10.1093/nar/gky1056",
"pubmed_id": 30407599,
"title": "Mouse Genome Database (MGD) 2019."
}
],
"subjects": [
"Life Science",
"Ontology and Terminology"
],
"twitter": "mgi_mouse"
},
"go": {
"homepage": "http://www.informatics.jax.org/",
"name": "Mouse Genome Informatics",
"prefix": "MGI"
},
"integbio": {
"alt_name": "Medaka Genome Initiative",
"description": "MGI is a website of Medaka genome studies. The site has links to various projects, some of which are published papers and some of which can be searched and browsed further to obtain sequence and genome mapping information.",
"homepage": "http://park.itc.u-tokyo.ac.jp/K-medaka/MGI2/MGI.html",
"maintainer": "The University of Tokyo Graduate School of Frontier Sciences",
"name": "MGI",
"prefix": "nbdc00568",
"pubmeds": [
"15602912"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"license": "CC-BY-4.0",
"mappings": {
"biocontext": "MGI",
"cellosaurus": "MGI",
"edam": "3274",
"fairsharing": "FAIRsharing.fcwyhz",
"go": "MGI",
"integbio": "nbdc00568",
"miriam": "mgi",
"n2t": "mgi",
"ncbi": "MGI",
"prefixcommons": "mgi",
"re3data": "r3d100010266",
"rrid": "MGI",
"uniprot": "DB-0060",
"wikidata": "P671"
},
"miriam": {
"deprecated": false,
"description": "The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.",
"homepage": "http://www.informatics.jax.org/",
"id": "00000037",
"name": "Mouse Genome Database",
"namespaceEmbeddedInLui": true,
"pattern": "^MGI:\\d+$",
"prefix": "mgi",
"providers": [
{
"code": "agr",
"description": "MGI through the Alliance of Genome Resources",
"homepage": "https://www.alliancegenome.org",
"name": "MGI through the Alliance of Genome Resources",
"uri_format": "https://www.alliancegenome.org/gene/MGI:$1"
}
],
"sampleId": "2442292",
"uri_format": "http://www.informatics.jax.org/accession/MGI:$1"
},
"n2t": {
"description": "The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.",
"example": "2442292",
"homepage": "http://www.informatics.jax.org/",
"name": "Mouse Genome Informatics Database",
"namespaceEmbeddedInLui": true,
"pattern": "^MGI:\\d+$",
"prefix": "mgi",
"uri_format": "http://www.informatics.jax.org/accession/MGI:$1"
},
"name": "Mouse Genome Informatics",
"ncbi": {
"example": "MGI:1894891",
"homepage": "http://www.informatics.jax.org/",
"name": "Mouse Genome Informatics",
"prefix": "MGI"
},
"pattern": "^\\d+$",
"preferred_prefix": "MGI",
"prefixcommons": {
"description": "The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.",
"example": "95484",
"homepage": "http://www.informatics.jax.org/",
"keywords": [
"expression",
"phenotype",
"sequence"
],
"name": "Mouse genome database (MGD) from Mouse Genome Informatics (MGI)",
"pattern": "^\\d+$",
"prefix": "mgi",
"pubmed_ids": [
"15608240"
],
"synonyms": [
"mgd"
],
"uri_format": "http://www.informatics.jax.org/searches/accession_report.cgi?id=mgi:$1"
},
"providers": [
{
"code": "mgi.marker",
"description": "MGI Marker",
"homepage": "http://www.informatics.jax.org/marker",
"name": "MGI Marker",
"uri_format": "http://www.informatics.jax.org/marker/MGI:$1"
}
],
"publications": [
{
"doi": "10.1126/science.8091224",
"pubmed": "8091224",
"title": "A database for mouse development",
"year": 1994
},
{
"doi": "10.1093/nar/gky1056",
"pmc": "PMC6323923",
"pubmed": "30407599",
"title": "Mouse Genome Database (MGD) 2019",
"year": 2019
},
{
"doi": "10.1093/nar/gky922",
"pmc": "PMC6324054",
"pubmed": "30335138",
"title": "The mouse Gene Expression Database (GXD): 2019 update",
"year": 2019
},
{
"doi": "10.1093/ilar/ilx013",
"pmc": "PMC5886341",
"pubmed": "28838066",
"title": "Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse",
"year": 2017
},
{
"doi": "10.1007/978-1-4939-6427-7_3",
"pubmed": "27933520",
"title": "Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research",
"year": 2017
},
{
"doi": "10.1093/nar/gkw1040",
"pmc": "PMC5210536",
"pubmed": "27899570",
"title": "Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse",
"year": 2016
},
{
"doi": "10.1093/nar/gkt1225",
"pmc": "PMC3964950",
"pubmed": "24285300",
"title": "The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse",
"year": 2013
},
{
"doi": "10.1093/nar/gks1115",
"pmc": "PMC3531104",
"pubmed": "23175610",
"title": "The mouse genome database: genotypes, phenotypes, and models of human disease",
"year": 2012
},
{
"doi": "10.1093/nar/gkr974",
"pmc": "PMC3245042",
"pubmed": "22075990",
"title": "The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse",
"year": 2011
},
{
"doi": "10.1093/nar/gki113",
"pmc": "PMC540067",
"pubmed": "15608240",
"title": "The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology",
"year": 2005
}
],
"re3data": {
"description": "MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. The projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, MouseMine Project, MouseCyc Project at MGI",
"homepage": "https://www.informatics.jax.org/",
"name": "Mouse Genome Informatics",
"prefix": "r3d100010266",
"synonyms": [
"MGI"
],
"xrefs": {
"fairsharing": "FAIRsharing.fcwyhz",
"nif": "0000-00096",
"omics": "01656",
"scr": "006460"
}
},
"rrid": {
"homepage": "http://www.informatics.jax.org",
"keywords": [
"animal model",
"blast",
"data analysis service",
"function",
"gene",
"gene expression",
"genetics",
"genome",
"genotype",
"gold standard",
"human disease",
"human health",
"image",
"model",
"molecular neuroanatomy resource",
"orthology",
"pathology",
"pathway",
"phenotype",
"recombinase",
"single nucleotide polymorphism",
"strain",
"tumor"
],
"name": "Mouse Genome Informatics (MGI)",
"prefix": "MGI",
"pubmeds": [
"19274630",
"18428715"
],
"scr": "006460"
},
"synonyms": [
"MGD",
"MGI"
],
"uniprot": {
"abbreviation": "MGI",
"category": "Organism-specific databases",
"homepage": "https://www.informatics.jax.org/",
"name": "Mouse genome database (MGD) from Mouse Genome Informatics (MGI)",
"prefix": "DB-0060",
"publications": [
{
"doi": "10.1093/nar/gky1056",
"pubmed": "30407599"
}
],
"uri_format": "https://www.informatics.jax.org/marker/$1"
},
"wikidata": {
"description": "identifier for a gene in the Mouse Genome Informatics database",
"example": [
"MGI:2148705",
"MGI:95674",
"MGI:96922"
],
"homepage": "http://www.informatics.jax.org/",
"name": "Mouse Genome Informatics ID",
"pattern": "^MGI:\\d{1,7}$",
"prefix": "P671",
"uri_format": "http://www.informatics.jax.org/accession/$1"
}
},
"mgnify.analysis": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Analyses of microbiome data within MGnify",
"example": "MGYA00002270",
"homepage": "https://www.ebi.ac.uk/metagenomics/",
"name": "MGnify Analysis",
"pattern": "^MGYA\\d+$",
"uri_format": "https://www.ebi.ac.uk/metagenomics/analyses/$1"
},
"mgnify.proj": {
"mappings": {
"miriam": "mgnify.proj",
"n2t": "mgnify.proj"
},
"miriam": {
"deprecated": false,
"description": "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.",
"homepage": "https://www.ebi.ac.uk/metagenomics",
"id": "00000535",
"name": "MGnify Project",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]+[0-9]+$",
"prefix": "mgnify.proj",
"sampleId": "ERP004492",
"uri_format": "https://www.ebi.ac.uk/metagenomics/projects/$1"
},
"n2t": {
"description": "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.",
"example": "ERP004492",
"homepage": "https://www.ebi.ac.uk/metagenomics",
"name": "MGnify Project",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]+[0-9]+$",
"prefix": "mgnify.proj",
"uri_format": "https://www.ebi.ac.uk/metagenomics/projects/$1"
}
},
"mgnify.samp": {
"mappings": {
"miriam": "mgnify.samp",
"n2t": "mgnify.samp"
},
"miriam": {
"deprecated": false,
"description": "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.",
"homepage": "https://www.ebi.ac.uk/metagenomics",
"id": "00000510",
"name": "MGnify Sample",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]+[0-9]+$",
"prefix": "mgnify.samp",
"sampleId": "SRS086444",
"uri_format": "https://www.ebi.ac.uk/metagenomics/samples/$1"
},
"n2t": {
"description": "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.",
"example": "SRS086444",
"homepage": "https://www.ebi.ac.uk/metagenomics",
"name": "MGnify Sample",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]+[0-9]+$",
"prefix": "mgnify.samp",
"uri_format": "https://www.ebi.ac.uk/metagenomics/samples/$1"
}
},
"mi": {
"aberowl": {
"description": "A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions.",
"download_owl": "http://aber-owl.net/media/ontologies/MI/122/mi.owl",
"homepage": "https://github.com/HUPO-PSI/psi-mi-CV",
"name": "Molecular Interactions Controlled Vocabulary",
"prefix": "MI"
},
"biocontext": {
"prefix": "PSIMI"
},
"biolink": {
"is_identifiers": false,
"is_obo": true,
"prefix": "MI",
"uri_format": "http://purl.obolibrary.org/obo/MI_$1"
},
"bioportal": {
"contact": {
"email": "orchard@ebi.ac.uk",
"name": "Sandra Orchard"
},
"description": "A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Developed by the HUPO Proteomics Standards Initiative.",
"homepage": "https://github.com/HUPO-PSI/psi-mi-CV",
"name": "Molecular Interactions",
"prefix": "MI"
},
"example": "0058",
"fairsharing": {
"abbreviation": "PSI-MI CV",
"description": "A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Developed by the HUPO Proteomics Standards Initiative. The Molecular Interactions Working group page can be found at http://www.psidev.info/groups/molecular-interactions.",
"domains": [
"Protein interaction",
"Molecular interaction",
"Protein"
],
"homepage": "http://www.psidev.info/groups/molecular-interactions",
"license": "CC-BY-4.0",
"name": "PSI Molecular Interaction Controlled Vocabulary",
"prefix": "FAIRsharing.8qzmtr",
"repository": "https://github.com/HUPO-PSI/psi-mi-CV",
"subjects": [
"Life Science"
]
},
"go": {
"homepage": "http://www.psidev.info/",
"name": "Proteomic Standard Initiative for Molecular Interaction",
"prefix": "PSI-MI",
"synonyms": [
"MI"
]
},
"mappings": {
"aberowl": "MI",
"biocontext": "PSIMI",
"biolink": "MI",
"bioportal": "MI",
"fairsharing": "FAIRsharing.8qzmtr",
"go": "PSI-MI",
"miriam": "mi",
"n2t": "psimi",
"obofoundry": "mi",
"ols": "mi",
"ontobee": "MI",
"prefixcommons": "psi.mi"
},
"miriam": {
"deprecated": false,
"description": "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/mi",
"id": "00000109",
"name": "Molecular Interactions Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^MI:\\d{4}$",
"prefix": "mi",
"sampleId": "0308",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/mi/terms?obo_id=MI:$1"
},
"n2t": {
"description": "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.",
"example": "0308",
"homepage": "https://www.ebi.ac.uk/ols/ontologies/mi",
"name": "Molecular Interactions Ontology through OLS",
"namespaceEmbeddedInLui": true,
"pattern": "^MI:\\d{4}$",
"prefix": "psimi",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1"
},
"obofoundry": {
"contact": "luana.licata@gmail.com",
"contact.github": "luanalicata",
"contact.label": "Luana Licata",
"contact.orcid": "0000-0001-5084-9000",
"deprecated": false,
"description": "A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions.",
"domain": "investigations",
"download.obo": "http://purl.obolibrary.org/obo/mi.obo",
"download.owl": "http://purl.obolibrary.org/obo/mi.owl",
"homepage": "https://github.com/HUPO-PSI/psi-mi-CV",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Molecular Interactions Controlled Vocabulary",
"preferredPrefix": "MI",
"prefix": "mi",
"repository": "https://github.com/HUPO-PSI/psi-mi-CV"
},
"ols": {
"description": "A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions.",
"download_owl": "http://purl.obolibrary.org/obo/mi.owl",
"homepage": "https://github.com/HUPO-PSI/psi-mi-CV",
"name": "Molecular Interactions Controlled Vocabulary",
"prefix": "mi"
},
"ontobee": {
"library": "Library",
"name": "Molecular Interactions Controlled Vocabulary",
"prefix": "MI"
},
"pattern": "^\\d{4}$",
"prefixcommons": {
"alt_uri_formats": [
"http://purl.org/obo/owl/PSI-MI#$1"
],
"bioportal": "1040",
"description": "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.",
"example": "MI:0308",
"homepage": "http://psidev.sf.net",
"keywords": [
"obo",
"interaction",
"molecule"
],
"name": "Proteomic Standard Initiative for Molecular Interaction",
"pattern": "^MI:\\d{4}$",
"prefix": "psi.mi",
"pubmed_ids": [
"14755292"
],
"synonyms": [
"mi",
"obo.mi"
]
},
"publications": [
{
"doi": "10.1038/nbt926",
"pubmed": "14755292",
"title": "The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data",
"year": 2004
}
],
"synonyms": [
"PSI-MI"
],
"uri_format": "http://purl.obolibrary.org/obo/MI_$1"
},
"miaa": {
"comment": "same as MAT",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"name": "Minimal Information About Anatomy ontology",
"references": [
"https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/rols/inst/doc/rols.pdf"
]
},
"miapa": {
"aberowl": {
"description": "An application ontology to formalize annotation of phylogenetic data.",
"download_owl": "http://aber-owl.net/media/ontologies/MIAPA/2/miapa.owl",
"homepage": "http://www.evoio.org/wiki/MIAPA",
"name": "MIAPA Ontology",
"prefix": "MIAPA"
},
"biocontext": {
"prefix": "MIAPA"
},
"bioportal": {
"contact": {
"email": "hlapp@drycafe.net",
"name": "Hilmar Lapp"
},
"description": "An application ontology to formalize annotation of phylogenetic data according to the emerging Minimum Information About a Phylogenetic Analysis (MIAPA) metadata reporting standard.",
"homepage": "http://www.evoio.org/wiki/MIAPA",
"name": "MIAPA Ontology",
"prefix": "MIAPA"
},
"example": "0000010",
"fairsharing": {
"abbreviation": "MIAPA",
"description": "The MIAPA (minimum information about a phylogenetic analysis) checklist details the list of metadata necessary for researchers to evaluate or reuse a published phylogeny.",
"homepage": "http://www.evoio.org/wiki/MIAPA",
"name": "Minimal Information About a Phylogenetic Analysis",
"prefix": "FAIRsharing.ca48xs",
"publications": [
{
"doi": "10.1089/omi.2006.10.231",
"pubmed_id": 16901231,
"title": "Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)."
}
],
"repository": "https://github.com/miapa/miapa/blob/master/checklist/MIAPA-checklist.md",
"subjects": [
"Phylogeny",
"Phylogenetics",
"Life Science"
]
},
"mappings": {
"aberowl": "MIAPA",
"biocontext": "MIAPA",
"bioportal": "MIAPA",
"fairsharing": "FAIRsharing.ca48xs",
"obofoundry": "miapa",
"ols": "miapa",
"ontobee": "MIAPA"
},
"name": "Minimum Anformation About a Phylogenetic Analysis Ontology",
"obofoundry": {
"contact": "hilmar.lapp@duke.edu",
"contact.github": "hlapp",
"contact.label": "Hilmar Lapp",
"contact.orcid": "0000-0001-9107-0714",
"deprecated": false,
"description": "An application ontology to formalize annotation of phylogenetic data.",
"domain": "information",
"download.owl": "http://purl.obolibrary.org/obo/miapa.owl",
"homepage": "http://www.evoio.org/wiki/MIAPA",
"license": "CC0 1.0",
"license.url": "http://creativecommons.org/publicdomain/zero/1.0/",
"name": "MIAPA Ontology",
"preferredPrefix": "MIAPA",
"prefix": "miapa",
"publications": [
{
"id": "https://doi.org/10.1089/omi.2006.10.231",
"title": "Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)"
}
],
"repository": "https://github.com/evoinfo/miapa"
},
"ols": {
"description": "The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies.\n\nThis ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA.",
"download_owl": "http://purl.obolibrary.org/obo/miapa.owl",
"homepage": "http://www.evoio.org/wiki/MIAPA",
"name": "Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology",
"prefix": "miapa"
},
"ontobee": {
"library": "Library",
"name": "MIAPA Ontology",
"prefix": "MIAPA"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1089/omi.2006.10.231",
"pmc": "PMC3167193",
"pubmed": "16901231",
"title": "Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)",
"year": 2006
}
],
"uri_format": "http://purl.obolibrary.org/obo/MIAPA_$1"
},
"micro": {
"aberowl": {
"description": "An ontology of prokaryotic phenotypic and metabolic characters",
"download_owl": "http://aber-owl.net/media/ontologies/MICRO/3/micro.owl",
"homepage": "https://github.com/carrineblank/MicrO",
"name": "Ontology of Prokaryotic Phenotypic and Metabolic Characters",
"prefix": "MICRO"
},
"biocontext": {
"prefix": "MICRO"
},
"example": "0002999",
"fairsharing": {
"abbreviation": "MicrO",
"description": "MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The ontology was built to support the ongoing development of a natural language processing algorithm, MicroPIE (or, Microbial Phenomics Information Extractor). FAIRsharing curators have been unable to contact the project developers, and as such this record has been marked as Uncertain. Please contact us if you have any information on this resource.",
"domains": [
"Assay",
"Cell culture",
"Phenotype"
],
"homepage": "https://github.com/carrineblank/MicrO",
"license": "CC BY 2.0",
"name": "Ontology of Prokaryotic Phenotypic and Metabolic Characters",
"prefix": "FAIRsharing.brhpb0",
"publications": [
{
"doi": "10.1186/s13326-016-0060-6",
"pubmed": "27076900",
"title": "MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions",
"year": 2016
}
],
"repository": "https://github.com/carrineblank/MicrO/issues",
"subjects": [
"Bioinformatics",
"Microbiology"
]
},
"mappings": {
"aberowl": "MICRO",
"biocontext": "MICRO",
"fairsharing": "FAIRsharing.brhpb0",
"obofoundry": "micro",
"ols": "micro",
"ontobee": "MICRO"
},
"obofoundry": {
"appears_in": [
"mco"
],
"contact": "carrine.blank@umontana.edu",
"contact.github": "carrineblank",
"contact.label": "Carrine Blank",
"contact.orcid": "0000-0002-2100-6351",
"deprecated": true,
"description": "An ontology of prokaryotic phenotypic and metabolic characters",
"domain": "phenotype",
"download.owl": "http://purl.obolibrary.org/obo/micro.owl",
"homepage": "https://github.com/carrineblank/MicrO",
"license": "CC BY 2.0",
"license.url": "https://creativecommons.org/licenses/by/2.0/",
"name": "Ontology of Prokaryotic Phenotypic and Metabolic Characters",
"preferredPrefix": "MICRO",
"prefix": "micro",
"repository": "https://github.com/carrineblank/MicrO"
},
"ols": {
"description": "An ontology of prokaryotic phenotypic and metabolic characters",
"download_owl": "http://purl.obolibrary.org/obo/micro.owl",
"homepage": "https://github.com/carrineblank/MicrO",
"name": "Ontology of Prokaryotic Phenotypic and Metabolic Characters",
"prefix": "micro",
"version": "1.5.1"
},
"ontobee": {
"library": "Library",
"name": "Ontology of Prokaryotic Phenotypic and Metabolic Characters",
"prefix": "MICRO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1186/s13326-016-0060-6",
"pmc": "PMC4830071",
"pubmed": "27076900",
"title": "MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions",
"year": 2016
}
]
},
"microscope": {
"biocontext": {
"prefix": "MICROSCOPE"
},
"contact": {
"email": "cmedigue@genoscope.cns.fr",
"name": "MEDIGUE Claudine",
"orcid": "0000-0002-3905-1054"
},
"fairsharing": {
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},
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"doi": "10.1093/nar/gkr922",
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{
"doi": "10.1093/nar/gkv1100",
"pubmed_id": 26503249,
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"pubmed_ids": [
"22053087"
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{
"doi": "10.1093/nar/gkv1100",
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{
"doi": "10.1093/nar/gkr922",
"pmc": "PMC3245166",
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{
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]
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"biocontext": {
"prefix": "MINID"
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"fairsharing": {
"abbreviation": "minid",
"contact": {
"email": "foster@uchicago.edu",
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{
"doi": "10.1371/journal.pone.0294883",
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{
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"subjects": [
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"miriam": "minid.test"
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},
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"banana": "MINT",
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"prefix": "MINT"
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"description": "Unique identifier of an entry from the MINT database of protein-protein interactions.",
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"doi": "10.1093/nar/gkr930",
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],
"subjects": [
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"prefixcommons": "mint",
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"description": "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals.",
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{
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],
"sampleId": "MINT-10000",
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"n2t": {
"description": "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals.",
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"name": "MINT subset through IntAct",
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"name": "Molecular Interaction Database",
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"abbreviation": "MINT",
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"description": "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals.",
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"keywords": [
"protein",
"interaction"
],
"license": "http://dip.doe-mbi.ucla.edu/dip/termsofuse.html",
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"pattern": "^MINT\\-\\d{1,5}$",
"prefix": "mint",
"pubmed_ids": [
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"publications": [
{
"doi": "10.1093/nar/gkr930",
"pmc": "PMC3244991",
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},
{
"doi": "10.1093/nar/gkp983",
"pmc": "PMC2808973",
"pubmed": "19897547",
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{
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"pmc": "PMC1751541",
"pubmed": "17135203",
"title": "MINT: the Molecular INTeraction database",
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{
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"pubmed": "11911893",
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}
],
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"homepage": "https://mint.bio.uniroma2.it/",
"name": "Molecular INTeraction Database",
"prefix": "r3d100010414",
"synonyms": [
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],
"xrefs": {
"fairsharing": "FAIRsharing.2bdvmk",
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"omics": "02928",
"scr": "001523"
}
},
"uniprot": {
"abbreviation": "MINT",
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"homepage": "https://mint.bio.uniroma2.it/",
"name": "Molecular INTeraction database",
"prefix": "DB-0158",
"publications": [
{
"doi": "10.1093/nar/gkr930",
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}
],
"uri_format": "https://mint.bio.uniroma2.it/cgi-bin/protein.py?id=$1"
},
"uri_format": "https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-$1"
},
"mipmod": {
"biocontext": {
"prefix": "MIPMOD"
},
"contact": {
"email": "rsankar@iitk.ac.in",
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"prefix": "mipmod",
"sampleId": "HOSAPI0399",
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},
"n2t": {
"description": "MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures.",
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"homepage": "http://bioinfo.iitk.ac.in/MIPModDB",
"name": "MIPModDB at Indian Institute of Technology Kanpur",
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"pattern": "^\\w+$",
"prefix": "mipmod",
"uri_format": "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1"
},
"prefixcommons": {
"description": "MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures.",
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"homepage": "http://bioinfo.iitk.ac.in/MIPModDB",
"keywords": [
"protein",
"structure"
],
"name": "MIPModDB",
"pattern": "^\\w+$",
"prefix": "mipmod",
"pubmed_ids": [
"22080560"
],
"uri_format": "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkr914",
"pmc": "PMC3245135",
"pubmed": "22080560",
"title": "MIPModDB: a central resource for the superfamily of major intrinsic proteins",
"year": 2011
}
]
},
"mir": {
"banana": "MIR",
"biocontext": {
"prefix": "MIR"
},
"mappings": {
"biocontext": "MIR",
"miriam": "mir",
"n2t": "mir"
},
"miriam": {
"deprecated": false,
"description": "The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form βPREFIX:ACCESSIONβ or \"PROVIDER/PREFIX:ACCESSIONβ commonly used to specify bioinformatics and other data resources.",
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"pattern": "^MIR:\\d{8}$",
"prefix": "mir",
"sampleId": "00100037",
"uri_format": "https://resolver.api.identifiers.org/resolveMirId/MIR:$1"
},
"n2t": {
"description": "The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or \"PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources.",
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"homepage": "https://identifiers.org/registry",
"name": "Identifiers.org Registry through EBI",
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"pattern": "^MIR:\\d{8}$",
"prefix": "mir",
"uri_format": "https://identifiers.org/registry?query=\"MIR:$1\""
},
"pattern": "^\\d{8}$",
"uri_format": "https://registry.identifiers.org/registry?query=MIR:$1"
},
"mirbase": {
"biocontext": {
"prefix": "MIRBASE"
},
"biolink": {
"is_identifiers": true,
"is_obo": false,
"prefix": "mirbase",
"uri_format": "http://identifiers.org/mirbase$1"
},
"contact": {
"email": "sam.griffiths-jones@manchester.ac.uk",
"github": "samgriffithsjones",
"name": "Sam Griffiths-Jones",
"orcid": "0000-0001-6043-807X"
},
"edam": {
"description": "Identifier for a gene from the miRBase database.",
"name": "Gene ID (miRBase)",
"obsolete": false,
"prefix": "2642"
},
"example": "MI0026471",
"fairsharing": {
"abbreviation": "miRBase",
"description": "The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in miRBase represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation.",
"homepage": "http://www.mirbase.org/",
"name": "miRBase",
"prefix": "FAIRsharing.hmgte8",
"publications": [
{
"doi": "10.1093/nar/gkh023",
"pubmed_id": 14681370,
"title": "The microRNA Registry."
},
{
"doi": "10.1093/nar/gky1141",
"pubmed_id": 30423142,
"title": "miRBase: from microRNA sequences to function."
},
{
"doi": "10.1093/nar/gkt1181",
"pubmed_id": 24275495,
"title": "miRBase: annotating high confidence microRNAs using deep sequencing data."
},
{
"doi": "10.1093/nar/gkq1027",
"pubmed_id": 21037258,
"title": "miRBase: integrating microRNA annotation and deep-sequencing data."
},
{
"doi": "10.1093/nar/gkm952",
"pubmed_id": 17991681,
"title": "miRBase: tools for microRNA genomics."
},
{
"doi": "10.1093/nar/gkj112",
"pubmed_id": 16381832,
"title": "miRBase: microRNA sequences, targets and gene nomenclature."
}
],
"subjects": [
"Biology"
]
},
"homepage": "http://www.mirbase.org/",
"integbio": {
"alt_name": "microRNA database",
"description": "miRBase is a database for published microRNA sequences and annotations, which include mature miRNA sequences (indicated by miR), and hairpin structures predicted by sequences that are precursors for miRNA (indicated by mir). A variety of search methods can be used, including by keyword, genomic position, cluster, expression data, and user-provided sequences. Furthermore, these sequences and annotations can be downloaded.",
"fairsharing": "biodbcore-000569",
"homepage": "http://mirbase.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "Faculty of Life Sciences, The University of Manchester",
"name": "miRBase",
"prefix": "nbdc00136",
"status": "Active",
"target_keywords": [
"RNA"
]
},
"mappings": {
"biocontext": "MIRBASE",
"biolink": "mirbase",
"edam": "2642",
"fairsharing": "FAIRsharing.hmgte8",
"integbio": "nbdc00136",
"miriam": "mirbase",
"n2t": "mirbase",
"ncbi": "miRBase",
"pathguide": "210",
"prefixcommons": "mirbase",
"re3data": "r3d100010566",
"togoid": "Mirbase",
"wikidata": "P2870"
},
"miriam": {
"deprecated": false,
"description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR).",
"homepage": "http://www.mirbase.org/",
"id": "00000078",
"name": "miRBase Sequence",
"namespaceEmbeddedInLui": false,
"pattern": "MI\\d{7}",
"prefix": "mirbase",
"sampleId": "MI0000001",
"uri_format": "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1"
},
"n2t": {
"description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR).",
"example": "MI0000001",
"homepage": "http://www.mirbase.org/",
"name": "miRBase Sequence Database",
"namespaceEmbeddedInLui": false,
"pattern": "MI\\d{7}",
"prefix": "mirbase",
"uri_format": "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1"
},
"name": "miRBase pre-miRNA",
"ncbi": {
"example": "MI0000681",
"homepage": "http://www.mirbase.org/",
"name": "miRNA Database",
"prefix": "miRBase"
},
"pathguide": {
"abbreviation": "miRBase",
"homepage": "http://www.mirbase.org/index.shtml",
"name": "microRNA Database",
"prefix": "210"
},
"prefixcommons": {
"description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. The miRBase Registry continues to provide gene hunters with unique names for novel miRNA genes prior to publication of results. The miRBase Targets database is a new resource of predicted miRNA targets in animals",
"example": "MI0000001",
"homepage": "http://www.mirbase.org/",
"keywords": [
"RNA",
"gene"
],
"name": "miRBase Sequence Database",
"pattern": "^MI\\d{7}$",
"prefix": "mirbase",
"pubmed_ids": [
"14681370"
],
"uri_format": "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1"
},
"publications": [
{
"doi": "10.1093/nar/gky1141",
"pmc": "PMC6323917",
"pubmed": "30423142",
"title": "miRBase: from microRNA sequences to function",
"year": 2019
},
{
"doi": "10.1093/nar/gkt1181",
"pmc": "PMC3965103",
"pubmed": "24275495",
"title": "miRBase: annotating high confidence microRNAs using deep sequencing data",
"year": 2013
},
{
"doi": "10.1093/nar/gkq1027",
"pmc": "PMC3013655",
"pubmed": "21037258",
"title": "miRBase: integrating microRNA annotation and deep-sequencing data",
"year": 2010
},
{
"doi": "10.1093/nar/gkm952",
"pmc": "PMC2238936",
"pubmed": "17991681",
"title": "miRBase: tools for microRNA genomics",
"year": 2007
},
{
"doi": "10.1093/nar/gkj112",
"pmc": "PMC1347474",
"pubmed": "16381832",
"title": "miRBase: microRNA sequences, targets and gene nomenclature",
"year": 2006
},
{
"doi": "10.1093/nar/gkh023",
"pmc": "PMC308757",
"pubmed": "14681370",
"title": "The microRNA Registry",
"year": 2004
}
],
"re3data": {
"description": "The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download. The miRBase Registry provides miRNA gene hunters with unique names for novel miRNA genes prior to publication of results.",
"homepage": "https://www.mirbase.org/",
"name": "miRBase",
"prefix": "r3d100010566",
"xrefs": {
"fairsharing": "FAIRsharing.hmgte8",
"nif": "0000-03134",
"scr": "003152"
}
},
"togoid": {
"catalog": "nbdc00136",
"examples": [
"MI0003587",
"MI0000252",
"MI0000811",
"MI0014201",
"MI0003578",
"MI0000293",
"MI0006384",
"MI0006361",
"MI0000480",
"MI0006419"
],
"keywords": [
"Transcript"
],
"name": "miRBase",
"pattern": "^(?MI\\d{7})$",
"prefix": "Mirbase",
"uri_format": "http://identifiers.org/mirbase/$1"
},
"uri_format": "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1",
"wikidata": {
"description": "identifier for pre-miRNAs in miRBase, the reference database for microRNAs",
"example": [
"MI0000472",
"MI0016867",
"MI0024976"
],
"homepage": "http://www.mirbase.org/",
"name": "miRBase pre-miRNA ID",
"pattern": "^MI\\d{7}$",
"prefix": "P2870",
"uri_format": "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1"
}
},
"mirbase.family": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download.",
"example": "MIPF0000002",
"homepage": "http://www.mirbase.org/",
"name": "miRBase Families",
"synonyms": [
"MIRBASE_FAMILY"
],
"uri_format": "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1",
"wikidata": {
"database": "Q6826947"
}
},
"mirbase.mature": {
"biocontext": {
"prefix": "MIRBASE.MATURE"
},
"example": "MIMAT0046872",
"homepage": "http://www.mirbase.org/",
"mappings": {
"biocontext": "MIRBASE.MATURE",
"miriam": "mirbase.mature",
"n2t": "mirbase.mature",
"prefixcommons": "mirbase.mature",
"wikidata": "P2871"
},
"miriam": {
"deprecated": false,
"description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence.",
"homepage": "http://www.mirbase.org/",
"id": "00000235",
"name": "miRBase mature sequence",
"namespaceEmbeddedInLui": false,
"pattern": "MIMAT\\d{7}",
"prefix": "mirbase.mature",
"sampleId": "MIMAT0000001",
"uri_format": "http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1"
},
"n2t": {
"description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence.",
"example": "MIMAT0000001",
"homepage": "http://www.mirbase.org/",
"name": "miRBase",
"namespaceEmbeddedInLui": false,
"pattern": "MIMAT\\d{7}",
"prefix": "mirbase.mature",
"uri_format": "http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1"
},
"name": "miRBase mature miRNA",
"prefixcommons": {
"description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence.",
"example": "MIMAT0000001",
"keywords": [
"nucleotide",
"sequence"
],
"name": "miRBase mature sequence",
"pattern": "^MIMAT\\d{7}$",
"prefix": "mirbase.mature",
"uri_format": "http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1"
},
"synonyms": [
"MIRBASEM"
],
"uri_format": "http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1",
"wikidata": {
"description": "identifier for mature miRNAs in miRBase, the reference database for microRNAs",
"example": [
"MIMAT0000446",
"MIMAT0000682",
"MIMAT0003214"
],
"homepage": "http://www.mirbase.org/",
"name": "miRBase mature miRNA ID",
"pattern": "^MIMAT\\d{7}$",
"prefix": "P2871",
"uri_format": "http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1"
}
},
"mirex": {
"biocontext": {
"prefix": "MIREX"
},
"contact": {
"email": "wmk@amu.edu.pl",
"name": "Wojciech M. Karlowski",
"orcid": "0000-0002-8086-5404"
},
"fairsharing": {
"abbreviation": "mirEX",
"description": "mirEX2 is a comprehensive platform for comparative analysis of primary microRNA expression data. RTβqPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface.",
"homepage": "http://www.comgen.pl/mirex/",
"name": "mirEX",
"prefix": "FAIRsharing.q3b39v",
"publications": [
{
"doi": "10.1093/nar/gkr878",
"pubmed_id": 22013167,
"title": "mirEX: a platform for comparative exploration of plant pri-miRNA expression data."
},
{
"doi": "10.1186/s12870-015-0533-2",
"pubmed_id": 26141515,
"title": "mirEX 2.0 - an integrated environment for expression profiling of plant microRNAs."
}
],
"subjects": [
"Life Science"
]
},
"integbio": {
"description": "mirEX2 is a comprehensive platform for comparative analysis of primary microRNA expression data. RTβqPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface.",
"fairsharing": "FAIRsharing.q3b39v",
"homepage": "http://www.comgen.pl/mirex/",
"information_keywords": [
"Expression",
"Sequence",
"Localization"
],
"maintainer": "Wellcome Sanger Institute",
"name": "mirEX",
"prefix": "nbdc02064",
"pubmeds": [
"22013167",
"26141515"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"mappings": {
"biocontext": "MIREX",
"fairsharing": "FAIRsharing.q3b39v",
"integbio": "nbdc02064",
"miriam": "mirex",
"n2t": "mirex"
},
"miriam": {
"deprecated": false,
"description": "mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RTβqPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages.",
"homepage": "http://comgen.pl/mirex/?page=home",
"id": "00000329",
"name": "mirEX",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+(\\w+)?$",
"prefix": "mirex",
"sampleId": "165a",
"uri_format": "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes"
},
"n2t": {
"description": "mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages.",
"example": "165a",
"homepage": "http://comgen.pl/mirex/?page=home",
"name": "mirEX at Adam Mickiewicz University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+(\\w+)?$",
"prefix": "mirex",
"uri_format": "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes"
},
"publications": [
{
"doi": "10.1186/s12870-015-0533-2",
"pmc": "PMC4490709",
"pubmed": "26141515",
"title": "mirEX 2.0 - an integrated environment for expression profiling of plant microRNAs",
"year": 2015
},
{
"doi": "10.1093/nar/gkr878",
"pmc": "PMC3245179",
"pubmed": "22013167",
"title": "mirEX: a platform for comparative exploration of plant pri-miRNA expression data",
"year": 2011
}
]
},
"miriam": {
"edam": {
"description": "Unique identifier of a MIRIAM data resource.",
"name": "MIRIAM",
"obsolete": false,
"prefix": "1162"
},
"fairsharing": {
"abbreviation": "MIRIAM",
"contact": {
"email": "n.lenovere@gmail.com",
"name": "Nicolas Le Novère",
"orcid": "0000-0002-6309-7327"
},
"description": "The Minimal Information Required In the Annotation of Models (MIRIAM), initiated by the BioModels.net effort, is a set of guidelines for the consistent annotation and curation of computational models in biology. It is suitable for use with any structured format for computational models.",
"homepage": "http://co.mbine.org/standards/miriam",
"license": "CC BY-SA 4.0",
"name": "Minimal Information Required In the Annotation of Models",
"prefix": "FAIRsharing.ap169a",
"publications": [
{
"doi": "10.1186/1752-0509-1-58",
"pubmed_id": 18078503,
"title": "MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology."
},
{
"doi": "10.1093/nar/gkr1097",
"pubmed_id": 22140103,
"title": "Identifiers.org and MIRIAM Registry: community resources to provide persistent identification."
},
{
"doi": "10.1038/nbt1156",
"pubmed_id": 16333295,
"title": "Minimum information requested in the annotation of biochemical models (MIRIAM)."
}
],
"subjects": [
"Biochemistry",
"Life Science",
"Biomedical Science"
]
},
"mappings": {
"edam": "1162",
"fairsharing": "FAIRsharing.ap169a",
"miriam": "identifiers.namespace"
},
"miriam": {
"deprecated": false,
"description": "Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain.",
"homepage": "https://www.ebi.ac.uk",
"id": "00000859",
"name": "Identifiers.org namespace",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z_\\.]+$",
"prefix": "identifiers.namespace",
"sampleId": "pubmed",
"uri_format": "https://registry.identifiers.org/registry/$1"
},
"pattern": "^[0-9a-z_:\\.-]+$",
"publications": [
{
"doi": "10.1093/nar/gkr1097",
"pmc": "PMC3245029",
"pubmed": "22140103",
"title": "Identifiers.org and MIRIAM Registry: community resources to provide persistent identification",
"year": 2011
},
{
"doi": "10.1186/1752-0509-1-58",
"pmc": "PMC2259379",
"pubmed": "18078503",
"title": "MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology",
"year": 2007
},
{
"doi": "10.1038/nbt1156",
"pubmed": "16333295",
"title": "Minimum information requested in the annotation of biochemical models (MIRIAM)",
"year": 2005
}
],
"synonyms": [
"identifiers.namespace"
]
},
"miriam.collection": {
"banana": "MIR",
"biocontext": {
"prefix": "MIRIAM.COLLECTION"
},
"deprecated": true,
"example": "00000008",
"mappings": {
"biocontext": "MIRIAM.COLLECTION",
"miriam": "miriam.collection",
"n2t": "miriam.collection"
},
"miriam": {
"deprecated": true,
"description": "MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections.",
"id": "00000008",
"name": "MIRIAM Registry collection",
"namespaceEmbeddedInLui": false,
"pattern": "^MIR:000\\d{5}$",
"prefix": "miriam.collection",
"sampleId": "MIR:00000008"
},
"n2t": {
"description": "MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections.",
"example": "MIR:00000008",
"homepage": "https://www.ebi.ac.uk/miriam/",
"name": "MIRIAM Resources (data collection)",
"namespaceEmbeddedInLui": false,
"pattern": "^MIR:000\\d{5}$",
"prefix": "miriam.collection",
"uri_format": "https://www.ebi.ac.uk/miriam/main/$1"
},
"part_of": "miriam",
"pattern": "^000\\d{5}$"
},
"miriam.resource": {
"banana": "MIR",
"biocontext": {
"prefix": "MIRIAM.RESOURCE"
},
"deprecated": true,
"example": "00100005",
"mappings": {
"biocontext": "MIRIAM.RESOURCE",
"miriam": "miriam.resource",
"n2t": "miriam.resource",
"prefixcommons": "miriam.resource"
},
"miriam": {
"deprecated": false,
"description": "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases.",
"homepage": "https://www.ebi.ac.uk/miriam/",
"id": "00000188",
"name": "MIRIAM Registry resource",
"namespaceEmbeddedInLui": false,
"pattern": "^MIR:001\\d{5}$",
"prefix": "miriam.resource",
"sampleId": "MIR:00100005",
"uri_format": "https://www.ebi.ac.uk/miriam/main/resources/$1"
},
"n2t": {
"description": "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases.",
"example": "MIR:00100005",
"homepage": "https://www.ebi.ac.uk/miriam/",
"name": "MIRIAM Registry (resources)",
"namespaceEmbeddedInLui": false,
"pattern": "^MIR:001\\d{5}$",
"prefix": "miriam.resource",
"uri_format": "https://www.ebi.ac.uk/miriam/main/resources/$1"
},
"name": "MIRIAM Legacy Registry Identifier",
"part_of": "miriam",
"pattern": "^001\\d{5}$",
"prefixcommons": {
"description": "MIRIAM Resources is an online resource created to catalogue the data-types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding physical URLs, whether these are controlled vocabularies or databases.",
"example": "MIR:00100245",
"homepage": "http://www.ebi.ac.uk/miriam/",
"keywords": [
"registry"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "MIRIAM Resources",
"pattern": "^MIR:001\\d{5}$",
"prefix": "miriam.resource",
"pubmed_ids": [
"18078503"
],
"synonyms": [
"mir"
],
"uri_format": "http://www.ebi.ac.uk/miriam/main/resources/$1"
},
"publications": [
{
"doi": "10.1186/1752-0509-1-58",
"pmc": "PMC2259379",
"pubmed": "18078503",
"title": "MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology",
"year": 2007
}
]
},
"mirnao": {
"aberowl": {
"description": "An application ontology for microRNAs.",
"download_owl": "http://aber-owl.net/media/ontologies/MIRNAO/11/mirnao.owl",
"homepage": "https://code.google.com/p/mirna-ontology/",
"name": "microRNA Ontology",
"prefix": "MIRNAO",
"version": "1.7"
},
"biocontext": {
"prefix": "MIRNAO"
},
"bioportal": {
"contact": {
"email": "vdritsou@gmail.com",
"name": "Vicky Dritsou"
},
"description": "An application ontology for microRNAs.",
"homepage": "https://code.google.com/archive/p/mirna-ontology/",
"name": "MicroRNA Ontology",
"prefix": "MIRNAO",
"version": "1.7"
},
"contact": {
"email": "topalis@imbb.forth.gr",
"name": "Pantelis Topalis",
"orcid": "0000-0002-1635-4810"
},
"mappings": {
"aberowl": "MIRNAO",
"biocontext": "MIRNAO",
"bioportal": "MIRNAO",
"obofoundry": "mirnao",
"ontobee": "miRNAO"
},
"obofoundry": {
"contact": "topalis@imbb.forth.gr",
"contact.label": "Pantelis Topalis",
"deprecated": true,
"description": "An application ontology for use with miRNA databases.",
"domain": "chemistry and biochemistry",
"download.owl": "http://purl.obolibrary.org/obo/mirnao.owl",
"homepage": "http://code.google.com/p/mirna-ontology/",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "microRNA Ontology",
"prefix": "mirnao"
},
"ontobee": {
"library": "Library",
"name": "microRNA Ontology",
"prefix": "miRNAO"
}
},
"mirnest": {
"biocontext": {
"prefix": "MIRNEST"
},
"contact": {
"email": "miszcz@amu.edu.pl",
"name": "Michael SzczeΕniak",
"orcid": "0000-0002-6050-9525"
},
"fairsharing": {
"abbreviation": "miRNEST",
"description": "miRNEST is an integrative collection of animal, plant and virus microRNA data. miRNEST is being gradually developed to create an integrative resource of miRNA-associated data. The data comes from our computational predictions (new miRNAs, targets, mirtrons, miRNA gene structures) as well as from other databases and publications.",
"homepage": "http://mirnest.amu.edu.pl",
"name": "miRNEST",
"prefix": "FAIRsharing.5pfx4r",
"publications": [
{
"doi": "10.1093/nar/gkr1159",
"pubmed_id": 22135287,
"title": "miRNEST database: an integrative approach in microRNA search and annotation."
},
{
"doi": "10.1093/nar/gkt1156",
"pubmed_id": 24243848,
"title": "miRNEST 2.0: a database of plant and animal microRNAs."
}
],
"subjects": [
"Genomics",
"Life Science"
]
},
"integbio": {
"description": "miRNEST is an integrative collection of animal, plant and virus microRNA data. miRNEST is being gradually developed to create an integrative resource of miRNA-associated data. The data comes from our computational predictions (new miRNAs, targets, mirtrons, miRNA gene structures) as well as from other databases and publications.",
"fairsharing": "FAIRsharing.5pfx4r",
"homepage": "http://mirnest.amu.edu.pl",
"information_keywords": [
"Expression",
"Sequence",
"3D structure",
"Interaction/Pathway"
],
"maintainer": "Laboratory of Bioinformatics, Faculty of Biology, Adam Mickiewicz University",
"name": "miRNEST",
"prefix": "nbdc01703",
"pubmeds": [
"22135287",
"24243848"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"RNA"
]
},
"mappings": {
"biocontext": "MIRNEST",
"fairsharing": "FAIRsharing.5pfx4r",
"integbio": "nbdc01703",
"miriam": "mirnest",
"n2t": "mirnest",
"prefixcommons": "mirnest"
},
"miriam": {
"deprecated": false,
"description": "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species.",
"homepage": "http://rhesus.amu.edu.pl/mirnest/copy/",
"id": "00000246",
"name": "miRNEST",
"namespaceEmbeddedInLui": false,
"pattern": "^MNEST\\d+$",
"prefix": "mirnest",
"sampleId": "MNEST029358",
"uri_format": "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1"
},
"n2t": {
"description": "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species.",
"example": "MNEST029358",
"homepage": "http://rhesus.amu.edu.pl/mirnest/copy/",
"name": "miRNEST at Adam Mickiewicz University",
"namespaceEmbeddedInLui": false,
"pattern": "^MNEST\\d+$",
"prefix": "mirnest",
"uri_format": "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1"
},
"prefixcommons": {
"description": "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species.",
"example": "MNEST029358",
"homepage": "http://lemur.amu.edu.pl/share/php/mirnest/",
"keywords": [
"expression",
"prediction"
],
"name": "miRNEST",
"pattern": "^MNEST\\d+$",
"prefix": "mirnest",
"pubmed_ids": [
"22135287"
],
"uri_format": "http://lemur.amu.edu.pl/share/php/mirnest/search.php?search_term=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkt1156",
"pmc": "PMC3965105",
"pubmed": "24243848",
"title": "miRNEST 2.0: a database of plant and animal microRNAs",
"year": 2013
},
{
"doi": "10.1093/nar/gkr1159",
"pmc": "PMC3245016",
"pubmed": "22135287",
"title": "miRNEST database: an integrative approach in microRNA search and annotation",
"year": 2011
}
]
},
"miro": {
"aberowl": {
"description": "Application ontology for entities related to insecticide resistance in mosquitos",
"download_owl": "http://aber-owl.net/media/ontologies/MIRO/1/miro.owl",
"homepage": "http://anobase.vectorbase.org",
"name": "Mosquito insecticide resistance",
"prefix": "MIRO"
},
"biocontext": {
"prefix": "MIRO"
},
"bioportal": {
"contact": {
"email": "louis@imbb.forth.gr",
"name": "C. Louis"
},
"description": "Application ontology for entities related to insecticide resistance in mosquitos.",
"homepage": "http://www.anobase.org",
"name": "Mosquito Insecticide Resistance",
"prefix": "MIRO",
"version": "releases/2014-05-14"
},
"contact": {
"email": "louis@imbb.forth.gr",
"name": "Christos Louis",
"orcid": "0000-0003-2497-2210"
},
"download_obo": "http://purl.obolibrary.org/obo/miro.obo",
"example": "40000617",
"fairsharing": {
"abbreviation": "MIRO",
"description": "Monitoring of insect vector populations with respect to their susceptibility to one or more insecticides is a crucial element of the strategies used for the control of arthropod-borne diseases. This management task can nowadays be achieved more efficiently when assisted by IT (Information Technology) tools, ranging from modern integrated databases to GIS (Geographic Information System). MIRO is an application ontology that can be used for the purpose of controlling mosquitoes and, thus, the diseases that they transmit.",
"domains": [
"Insecticide resistance",
"Mutation",
"Phenotype"
],
"homepage": "https://www.vectorbase.org/ontology-browser",
"name": "Mosquito Insecticide Resistance Ontology",
"prefix": "FAIRsharing.sjf113",
"publications": [
{
"doi": "10.1371/journal.pntd.0000465",
"pubmed": "19547750",
"title": "MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide resistance in mosquito disease vectors",
"year": 2009
}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"aberowl": "MIRO",
"biocontext": "MIRO",
"bioportal": "MIRO",
"fairsharing": "FAIRsharing.sjf113",
"obofoundry": "miro",
"ols": "miro",
"ontobee": "MIRO"
},
"obofoundry": {
"contact": "louis@imbb.forth.gr",
"contact.label": "Christos (Kitsos) Louis",
"deprecated": true,
"description": "Application ontology for entities related to insecticide resistance in mosquitos",
"domain": "environment",
"download.obo": "http://purl.obolibrary.org/obo/miro.obo",
"download.owl": "http://purl.obolibrary.org/obo/miro.owl",
"homepage": "https://github.com/VEuPathDB-ontology/MIRO",
"name": "Mosquito insecticide resistance",
"prefix": "miro",
"repository": "https://github.com/VEuPathDB-ontology/MIRO"
},
"ols": {
"description": "Application ontology for entities related to insecticide resistance in mosquitos",
"download_owl": "http://purl.obolibrary.org/obo/miro.owl",
"name": "Mosquito insecticide resistance",
"prefix": "miro",
"version": "2014-05-14",
"version.iri": "http://purl.obolibrary.org/obo/miro/releases/2014-05-14/miro.owl"
},
"ontobee": {
"library": "Library",
"name": "Mosquito insecticide resistance",
"prefix": "MIRO"
},
"pattern": "^\\d{8}$",
"publications": [
{
"doi": "10.1371/journal.pntd.0000465",
"pmc": "PMC2694272",
"pubmed": "19547750",
"title": "MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide resistance in mosquito disease vectors",
"year": 2009
}
]
},
"mirtarbase": {
"biocontext": {
"prefix": "MIRTARBASE"
},
"contributor_extras": [
{
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"fairsharing": {
"abbreviation": "miRTarBase",
"contact": {
"email": "ken.sd.hsu@gmail.com",
"name": "Sheng-Da Hsu",
"orcid": "0000-0002-8214-1696"
},
"description": "As a database, miRTarBase has accumulated more than fifty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after data mining of the text systematically to filter research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. While containing the largest amount of validated MTIs, the miRTarBase provides the most updated collection by comparing with other similar, previously developed databases.",
"homepage": "http://miRTarBase.mbc.nctu.edu.tw",
"name": "miRTarBase",
"prefix": "FAIRsharing.f0bxfg",
"publications": [
{
"doi": "10.1093/nar/gkq1107",
"pubmed_id": 21071411,
"title": "miRTarBase: a database curates experimentally validated microRNA-target interactions."
}
],
"subjects": [
"Life Science"
]
},
"homepage": "https://mirtarbase.cuhk.edu.cn/",
"integbio": {
"description": "miRTarBase Version 3.5 is a database that contains information about miRNA-target interactions (MTIs) obtained by manual search of scientific literature with data on 4867 miRNA-target interactions, 726 miRNAs and 2789 target genes from 17 species. The database can be browsed or searched by keyword, as well as downloaded.",
"fairsharing": "biodbcore-000615",
"homepage": "http://mirtarbase.cuhk.edu.cn/php/index.php",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "Institute of Bioinformatics and Systems Biology, National Chiao Tung University",
"name": "miRTarBase",
"prefix": "nbdc01217",
"pubmeds": [
"21071411"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"mappings": {
"biocontext": "MIRTARBASE",
"fairsharing": "FAIRsharing.f0bxfg",
"integbio": "nbdc01217",
"miriam": "mirtarbase",
"n2t": "mirtarbase",
"pathguide": "715",
"wikidata": "P2646"
},
"miriam": {
"deprecated": false,
"description": "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments.",
"homepage": "http://mirtarbase.mbc.nctu.edu.tw/",
"id": "00000562",
"name": "miRTarBase",
"namespaceEmbeddedInLui": false,
"pattern": "^MIRT\\d{6}$",
"prefix": "mirtarbase",
"sampleId": "MIRT000002",
"uri_format": "http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1"
},
"n2t": {
"description": "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments.",
"example": "MIRT000002",
"homepage": "http://mirtarbase.mbc.nctu.edu.tw/",
"name": "miRTarBase at National Chiao Tung University",
"namespaceEmbeddedInLui": false,
"pattern": "^MIRT\\d{6}$",
"prefix": "mirtarbase",
"uri_format": "http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1"
},
"name": "mirTarBase",
"pathguide": {
"abbreviation": "miRTarBase",
"homepage": "http://mirtarbase.mbc.nctu.edu.tw/",
"name": "The Experimentally Validated microRNA-target Interactions Database",
"prefix": "715"
},
"publications": [
{
"doi": "10.1093/nar/gkq1107",
"pmc": "PMC3013699",
"pubmed": "21071411",
"title": "miRTarBase: a database curates experimentally validated microRNA-target interactions",
"year": 2010
},
{
"doi": "10.1093/nar/gkt1266",
"pmc": "PMC3965058",
"pubmed": "24304892",
"title": "miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions",
"year": 2014
},
{
"doi": "10.1093/nar/gkv1258",
"pmc": "PMC4702890",
"pubmed": "26590260",
"title": "miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database",
"year": 2016
},
{
"doi": "10.1093/nar/gkx1067",
"pmc": "PMC5753222 ",
"pubmed": "29126174",
"title": "miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions",
"year": 2018
},
{
"doi": "10.1093/nar/gkz896",
"pmc": "PMC7145596 ",
"pubmed": "31647101",
"title": "miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database",
"year": 2020
},
{
"doi": "10.1093/nar/gkab1079",
"pmc": "PMC8728135",
"pubmed": "34850920",
"title": "miRTarBase update 2022: an informative resource for experimentally validated miRNAβtarget interactions",
"year": 2022
}
],
"references": [
"https://github.com/biopragmatics/bioregistry/pull/940"
],
"uri_format": "https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid=$1",
"wikidata": {
"description": "identifier for the mirTarBase database, a database for microRNAs and their targets",
"example": [
"MIRT000312"
],
"homepage": "http://mirtarbase.mbc.nctu.edu.tw/php/download.php",
"name": "mirTarBase ID",
"pattern": "^MIRT\\d{6}$",
"prefix": "P2646",
"uri_format": "https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid=$1"
}
},
"mirte": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs",
"example": "miR-1",
"homepage": "http://www.russelllab.org/miRNAs/",
"name": "miRNA Target Prediction at EMBL"
},
"mixs": {
"aberowl": {
"description": "An RDF representation of the MIxS Family of Checklists",
"download_owl": "http://aber-owl.net/media/ontologies/MIXS/5/mixs.owl",
"name": "Minimal Information about any Sequence Ontology",
"prefix": "MIXS",
"version": "unknown"
},
"bioportal": {
"contact": {
"email": "rlwalls2008@gmail.com",
"name": "Ramona Walls"
},
"description": "An OWL representation of the Minimum Information for any (x) Standard (MIxS), managed by the Genomic Standards Consortium.",
"homepage": "https://github.com/GenomicsStandardsConsortium/mixs",
"name": "Minimal Information about any Sequence Ontology",
"prefix": "MIXS",
"version": "6.1.0"
},
"comment": "Some things to be decided before granting - [ ] should the prefix be mixs, gsc.mixs, MIxS, MIXS, ...? - [ ] MIxS terms are most commonly identified by a short computable stable label, e.g ph_regm. The GSC CIG team are creating numeric identifiers, e.g. MIXS:0001056 - Should we support both schemes? - If we do, should these be different prefixes? I would strongly recommend this. E.g. mixs.term:ph_regm, mixs:0001056. We can then have different regex patterns for both Additional notes: - The http://gensc.org/ns/mixs/ will likely changes to a w3id.org URI that will also serve as a semweb identifier - It currently redirects to the tdwg wiki but this is I assume temporary",
"contact": {
"email": "rlwalls2008@gmail.com",
"github": "ramonawalls",
"name": "Ramona Walls",
"orcid": "0000-0001-8815-0078"
},
"contributor": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"contributor_extras": [
{
"email": "chris@gigasciencejournal.com",
"github": "only1chunts",
"name": "Chris Hunter",
"orcid": "0000-0002-1335-0881"
},
{
"email": "lindsey.anderson@pnnl.gov",
"github": "lnanderson",
"name": "Lindsey N. Anderson",
"orcid": "0000-0002-8741-7823"
}
],
"description": "The GSC family of minimum information standards (checklists) β Minimum Information about any (x) Sequence (MIxS). MIxS identifiers are for terms describing an aspect of an environmental sample.",
"example": "0001056",
"fairsharing": {
"abbreviation": "MIxS",
"description": "The minimum information about any (x) sequence (MIxS) is an overarching framework of sequence metadata, that includes technology-specific checklists from the previous MIGS and MIMS standards, provides a way of introducing additional checklists such as MIMARKS, and also allows annotation of sample data using environmental packages.",
"homepage": "http://gensc.org/mixs/",
"name": "Minimum Information about any (x) Sequence",
"prefix": "FAIRsharing.9aa0zp",
"publications": [
{
"doi": "10.1038/nbt.1823",
"pubmed_id": 21552244,
"title": "Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications"
}
],
"subjects": []
},
"homepage": "https://www.gensc.org/pages/standards/all-terms.html",
"mappings": {
"aberowl": "MIXS",
"bioportal": "MIXS",
"fairsharing": "FAIRsharing.9aa0zp"
},
"name": "Minimal Information about any Sequence",
"pattern": "^\\d{7}$",
"providers": [
{
"code": "github",
"description": "MIxS LinkML schema",
"homepage": "https://genomicsstandardsconsortium.github.io/mixs",
"name": "MIxS LinkML schema",
"uri_format": "https://genomicsstandardsconsortium.github.io/mixs/$1"
}
],
"publications": [
{
"doi": "10.1038/nbt.1823",
"pmc": "PMC3367316",
"pubmed": "21552244",
"title": "Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications",
"year": 2011
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://w3id.org/mixs/$1"
},
"mlc": {
"mappings": {
"miriam": "mlc"
},
"miriam": {
"deprecated": false,
"description": "MLCommons Association artifacts, including benchmark results, datasets, and saved models.",
"homepage": "https://mlcommons.org/en/",
"id": "00000828",
"name": "MLCommons Association",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9a-zA-Z\\.\\-\\_]+$",
"prefix": "mlc",
"sampleId": "0.7-123",
"uri_format": "https://www.mlcommons.org/mlc-id/$1"
}
},
"mmdb": {
"biocontext": {
"prefix": "MMDB"
},
"contact": {
"email": "siqian.he@nih.gov",
"name": "Siqian He",
"orcid": "0000-0002-1707-4167"
},
"edam": {
"description": "An identifier of an entry from the MMDB database.",
"name": "MMDB",
"obsolete": false,
"prefix": "2667"
},
"mappings": {
"biocontext": "MMDB",
"edam": "2667",
"miriam": "mmdb",
"n2t": "mmdb",
"pathguide": "508",
"prefixcommons": "mmdb"
},
"miriam": {
"deprecated": false,
"description": "The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites.",
"homepage": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure",
"id": "00000121",
"name": "Molecular Modeling Database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{1,5}$",
"prefix": "mmdb",
"sampleId": "50885",
"uri_format": "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1"
},
"n2t": {
"description": "The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites.",
"example": "50885",
"homepage": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure",
"name": "MMDB at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{1,5}$",
"prefix": "mmdb",
"uri_format": "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1"
},
"pathguide": {
"abbreviation": "MMDB",
"homepage": "http://www.ncbi.nlm.nih.gov/Structure/MMDB/docs/mmdb_search.html",
"name": "Molecular Modeling Database",
"prefix": "508"
},
"prefixcommons": {
"description": "The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more.",
"example": "50885",
"homepage": "http://www.ncbi.nlm.nih.gov/Structure/",
"keywords": [
"structure",
"protein",
"DNA",
"small molecule",
"interaction"
],
"name": "Molecular Modeling Database",
"pattern": "^\\d{1,5}$",
"prefix": "mmdb",
"pubmed_ids": [
"17135201"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkl952",
"pmc": "PMC1751549",
"pubmed": "17135201",
"title": "MMDB: annotating protein sequences with Entrez's 3D-structure database",
"year": 2006
}
]
},
"mmmp.biomaps": {
"biocontext": {
"prefix": "MMMP:BIOMAPS"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "mmmp.biomaps",
"uri_format": "https://bioregistry.io/mmmp.biomaps:$1"
},
"mappings": {
"biocontext": "MMMP:BIOMAPS",
"biolink": "mmmp.biomaps",
"miriam": "mmmp:biomaps",
"n2t": "biomaps",
"prefixcommons": "mmmp"
},
"miriam": {
"deprecated": false,
"description": "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.",
"homepage": "http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp",
"id": "00000075",
"name": "Melanoma Molecular Map Project Biomaps",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "mmmp:biomaps",
"sampleId": "37",
"uri_format": "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1"
},
"n2t": {
"description": "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.",
"example": "37",
"homepage": "http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp",
"name": "main webpage",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "biomaps",
"uri_format": "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1"
},
"prefixcommons": {
"description": "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma",
"example": "37",
"homepage": "http://www.mmmp.org/MMMP/",
"keywords": [
"interaction",
"pathway",
"molecule"
],
"name": "Melanoma Molecular Map Project",
"pattern": "^\\d+$",
"prefix": "mmmp",
"synonyms": [
"biomaps"
],
"uri_format": "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1"
},
"synonyms": [
"mmmp:biomaps"
]
},
"mmo": {
"aberowl": {
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"twitter": "mmrc"
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},
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],
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},
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"status": "Active",
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"MONDO_0005344"
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"name": "Molecular Process Ontology",
"prefix": "MOP"
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"abbreviation": "MOP",
"description": "Instruments and/or voices, devices and other performers which make up a musical work.",
"homepage": "https://www.iflastandards.info/unimarc/terms/mop",
"license": "CC-BY-4.0",
"name": "UNIMARC: Medium of performance",
"prefix": "20466"
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"name": "Colin Batchelor"
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"example": "0000079",
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"abbreviation": "MOP",
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],
"homepage": "https://github.com/rsc-ontologies/rxno",
"license": "CC-BY-4.0",
"name": "Molecular Process Ontology",
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"subjects": [
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]
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},
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"contact.github": "batchelorc",
"contact.label": "Colin Batchelor",
"contact.orcid": "0000-0001-5985-7429",
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"description": "Processes at the molecular level",
"domain": "chemistry and biochemistry",
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"homepage": "https://github.com/rsc-ontologies/rxno",
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"contact": "chemistry-ontologies@googlegroups.com",
"description": "MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation.",
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"homepage": "https://github.com/rsc-ontologies/rxno",
"name": "MOP",
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"version": "2022-05-11",
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},
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"library": "Library",
"name": "Molecular Process Ontology",
"prefix": "MOP"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/MOP_$1"
},
"morpheus": {
"mappings": {
"miriam": "morpheus"
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"miriam": {
"deprecated": false,
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"prefix": "morpheus",
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"homepage": "https://github.com/DataONEorg/sem-prov-ontologies",
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"prefix": "MOSAIC",
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},
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"prefix": "MP"
},
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"prefix": "MP"
},
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"email": "pheno@jax.org",
"name": "JAX phenotype list"
},
"description": "Standard terms for annotating mammalian phenotypic data.",
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"name": "Mammalian Phenotype Ontology",
"prefix": "MP",
"version": "2024-07-02"
},
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"abbreviation": "MP",
"contact": {
"email": "susan.bello@jax.org",
"name": "Susan M. Bello",
"orcid": "0000-0003-4606-0597"
},
"description": "The observable morphological, physiological, behavioral and other characteristics of mammalian organisms that are manifested through development and lifespan.",
"domains": [
"Behavior",
"Phenotype"
],
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"pubmed": "15642099",
"title": "The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information",
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},
{
"doi": "10.1002/wsbm.44",
"pubmed": "20052305",
"title": "The mammalian phenotype ontology: enabling robust annotation and comparative analysis",
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},
{
"doi": "10.1007/s00335-012-9421-3",
"pubmed": "22961259",
"title": "The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data",
"year": 2012
},
{
"doi": "10.1186/s13326-015-0009-1",
"pubmed": "25825651",
"title": "Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens",
"year": 2015
}
],
"repository": "https://github.com/obophenotype/mammalian-phenotype-ontology",
"subjects": [
"Developmental Biology",
"Life Science",
"Physiology"
]
},
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"homepage": "https://bioportal.bioontology.org/ontologies/MP",
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"name": "Mammalian Phenotype Ontology",
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}
],
"sampleId": "0005452",
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},
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"description": "The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways.",
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"description": "Standard terms for annotating mammalian phenotypic data.",
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"license": "CC BY 4.0",
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"name": "Mammalian Phenotype Ontology",
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"title": "The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data"
}
],
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},
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"description": "The Mammalian Phenotype Ontology is being developed by Cynthia L. Smith, Susan M. Bello, Anna, Anagnostopoulos, Carroll W. Goldsmith and Janan T. Eppig, as part of the Mouse Genome Database (MGD) Project, Mouse Genome Informatics (MGI), The Jackson Laboratory, Bar Harbor, ME. This file contains pre-coordinated phenotype terms, definitions and synonyms that can be used to describe mammalian phenotypes. The ontology is represented as a directed acyclic graph (DAG). It organizes phenotype terms into major biological system headers such as nervous system and respiratory system. This ontology is currently under development. Weekly updates are available at the Mouse Genome Informatics (MGI) ftp site (ftp://ftp.informatics.jax.org/pub/reports/index.html#pheno) as well as the OBO Foundry site (http://obofoundry.org/). Japanese labels of MP were created by the MP Japanese Translation Project (https://github.com/dbcls/MP_Japanse). Questions, comments and suggestions are welcome, and should be directed to pheno@jax.org, Susan.Bello@jax.org or to GitHub tracker (https://github.com/mgijax/mammalian-phenotype-ontology/issues) MGD is funded by NIH/NHGRI grant HG000330.",
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"name": "The Mammalian Phenotype Ontology",
"prefix": "mp",
"version": "2024-07-02",
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},
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"name": "Mammalian Phenotype Ontology",
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},
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],
"bioportal": "1025",
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"homepage": "http://www.informatics.jax.org/searches/MP_form.shtml",
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"phenotype",
"mammalian"
],
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"prefix": "mp",
"uri_format": "http://www.informatics.jax.org/searches/Phat.cgi?id=$1"
},
"providers": [
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"homepage": "https://www.nextprot.org",
"name": "neXtProt MP Browser",
"uri_format": "https://www.nextprot.org/term/MP:$1"
}
],
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"pmc": "PMC4378007",
"pubmed": "25825651",
"title": "Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens",
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},
{
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"pmc": "PMC3463787",
"pubmed": "22961259",
"title": "The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data",
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},
{
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"title": "The mammalian phenotype ontology: enabling robust annotation and comparative analysis",
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},
{
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"pubmed": "15642099",
"title": "The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information",
"year": 2004
}
],
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"MP:0001716",
"MP:0001698",
"MP:0001092",
"MP:0000961",
"MP:0000245",
"MP:0000828",
"MP:0000826",
"MP:0005039",
"MP:0002840"
],
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],
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"uri_format": "http://identifiers.org/mp/MP:$1"
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},
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"homepage": "http://www.pathbase.net",
"name": "Mouse pathology ontology",
"prefix": "MPATH"
},
"biocontext": {
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},
"bioportal": {
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"name": "Mouse_pathology Administrators"
},
"description": "A structured controlled vocabulary of mutant and transgenic mouse pathological lesions and processes",
"homepage": "http://www.pathbase.net",
"name": "Mouse Pathology Ontology",
"prefix": "MPATH",
"version": "2020-05-19"
},
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"abbreviation": "MPATH",
"contact": {
"email": "pns12@cam.ac.uk",
"name": "Paul Schofield",
"orcid": "0000-0002-5111-7263"
},
"description": "Mouse PATHology (MPATH) ontology is a structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes. This resource was developed by the Pathology Consortium of Pathbase (www.pathbase.net).",
"domains": [
"Mutation",
"Histology",
"Phenotype",
"Disease",
"Genetic strain"
],
"homepage": "https://github.com/PaulNSchofield/mpath",
"name": "Mouse PATHology",
"prefix": "FAIRsharing.3wbgm0",
"publications": [
{
"doi": "10.1177/0300985810374845",
"pubmed": "20587689",
"title": "Pathbase and the MPATH ontology. Community resources for mouse histopathology",
"year": 2010
}
],
"subjects": [
"Anatomy",
"Biomedical Science"
]
},
"integbio": {
"alt_name": "Navigating a Potential Metabolic Pathway",
"description": "M-path DB is a database of metabolic pathways calculated sets of compounds from the PubChem and ChEBI databases. It contains putative metabolic pathways for a series of chemical species, and produces networks including some interesting pathways.",
"homepage": "http://bp.scitec.kobe-u.ac.jp/m-path/db/",
"information_keywords": [
"Interaction/Pathway",
"Chemical structure"
],
"maintainer": "Kobe University",
"name": "M-path",
"prefix": "nbdc01568",
"pubmeds": [
"25398612"
],
"status": "Inactive",
"target_keywords": [
"Metabolite"
]
},
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"biocontext": "MPATH",
"bioportal": "MPATH",
"fairsharing": "FAIRsharing.3wbgm0",
"integbio": "nbdc01568",
"obofoundry": "mpath",
"ols": "mpath",
"ontobee": "MPATH",
"prefixcommons": "mpath"
},
"obofoundry": {
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"contact.github": "PaulNSchofield",
"contact.label": "Paul Schofield",
"contact.orcid": "0000-0002-5111-7263",
"deprecated": false,
"description": "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/mpath.owl",
"homepage": "http://www.pathbase.net",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Mouse pathology ontology",
"preferredPrefix": "MPATH",
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"repository": "https://github.com/PaulNSchofield/mpath"
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"name": "Mouse pathology ontology",
"prefix": "mpath",
"version": "2020-05-19",
"version.iri": "http://purl.obolibrary.org/obo/mpath/2020-05-19/mpath.owl"
},
"ontobee": {
"library": "Not Specified/No",
"name": "Mouse pathology",
"prefix": "MPATH"
},
"pattern": "^\\d+$",
"prefixcommons": {
"bioportal": "1031",
"description": "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes",
"example": "MPATH_606",
"homepage": "http://www.pathbase.net",
"keywords": [
"obo",
"phenotype",
"mouse"
],
"name": "Mouse pathology",
"pattern": "^MPATH_\\d+$",
"prefix": "mpath"
},
"publications": [
{
"doi": "10.1177/0300985810374845",
"pmc": "PMC3038412",
"pubmed": "20587689",
"title": "Pathbase and the MPATH ontology. Community resources for mouse histopathology",
"year": 2010
}
],
"synonyms": [
"MPATH"
],
"uri_format": "http://purl.obolibrary.org/obo/MPATH_$1"
},
"mpid": {
"biocontext": {
"prefix": "MPID"
},
"contact": {
"email": "jgoll@emmes.com",
"name": "Johannes B. Goll",
"orcid": "0000-0002-9968-4080"
},
"fairsharing": {
"abbreviation": "MPIDB",
"description": "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts. This resource has been marked as Uncertain because its project home can no longer be found. Please get in touch if you have any information about this resource.",
"homepage": "http://www.jcvi.org/mpidb/about.php",
"name": "Microbial Protein Interaction Database",
"prefix": "FAIRsharing.eyjkws",
"publications": [
{
"doi": "10.1093/bioinformatics/btn285",
"pubmed_id": 18556668,
"title": "MPIDB: the microbial protein interaction database."
}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"biocontext": "MPID",
"fairsharing": "FAIRsharing.eyjkws",
"miriam": "mpid",
"n2t": "mpid",
"pathguide": "559",
"prefixcommons": "mpi"
},
"miriam": {
"deprecated": false,
"description": "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts.",
"homepage": "http://www.jcvi.org/mpidb/about.php",
"id": "00000124",
"name": "Microbial Protein Interaction Database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "mpid",
"providers": [
{
"code": "ebi",
"description": "Microbial Protein Interaction Database subset through IntAct",
"homepage": "https://www.ebi.ac.uk/intact/",
"name": "Microbial Protein Interaction Database subset through IntAct",
"uri_format": "https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$1"
}
],
"sampleId": "172",
"uri_format": "http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1"
},
"n2t": {
"description": "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts.",
"example": "172",
"homepage": "http://www.jcvi.org/mpidb/about.php",
"name": "Microbial Protein Interaction Database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "mpid",
"uri_format": "http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1"
},
"pathguide": {
"abbreviation": "MPID",
"homepage": "http://bioinformatics.cau.edu.cn/cgi-bin/zzd-cgi/ppi/mpid.pl",
"name": "Magnaporthe grisea Protein-protein Interaction Database",
"prefix": "559"
},
"prefixcommons": {
"description": "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts.",
"example": "172",
"homepage": "http://www.jcvi.org/mpidb/",
"keywords": [
"interaction",
"protein",
"small molecule"
],
"license": "http://www.jcvi.org/cms/legal/privacy-statement",
"name": "Microbial Protein Interaction Database",
"pattern": "^\\d+$",
"prefix": "mpi",
"pubmed_ids": [
"18556668"
],
"synonyms": [
"mpid",
"mpidb"
],
"uri_format": "http://www.jcvi.org/mpidb/interaction.php?pname=$1"
},
"publications": [
{
"doi": "10.1093/bioinformatics/btn285",
"pmc": "PMC2638870",
"pubmed": "18556668",
"title": "MPIDB: the microbial protein interaction database",
"year": 2008
}
],
"synonyms": [
"mpidb"
]
},
"mpio": {
"aberowl": {
"description": "An ontology of minimum information regarding potential drug-drug interaction information.",
"download_owl": "http://aber-owl.net/media/ontologies/MPIO/5/mpio.owl",
"homepage": "https://github.com/MPIO-Developers/MPIO",
"name": "Minimum PDDI Information Ontology",
"prefix": "MPIO"
},
"biocontext": {
"prefix": "MPIO"
},
"bioportal": {
"contact": {
"email": "mbrochhausen@uams.edu",
"name": "Mathias Brochhausen"
},
"description": "MPIO (Minimum PDDI Information Ontology) is an OWL representation of minimum information regarding potential drug-drug interaction information. It is based on and meant to be use in alignment with DIDEO or DINTO.",
"homepage": "https://github.com/MPIO-Developers/MPIO",
"name": "Minimum PDDI Information Ontology",
"prefix": "MPIO",
"version": "2023-10-17"
},
"example": "0000004",
"mappings": {
"aberowl": "MPIO",
"biocontext": "MPIO",
"bioportal": "MPIO",
"obofoundry": "mpio",
"ols": "mpio",
"ontobee": "MPIO"
},
"obofoundry": {
"contact": "mbrochhausen@uams.edu",
"contact.github": "mbrochhausen",
"contact.label": "Mathias Brochhausen",
"contact.orcid": "0000-0003-1834-3856",
"deprecated": false,
"description": "An ontology of minimum information regarding potential drug-drug interaction information.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/mpio.owl",
"homepage": "https://github.com/MPIO-Developers/MPIO",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Minimum PDDI Information Ontology",
"preferredPrefix": "MPIO",
"prefix": "mpio",
"repository": "https://github.com/MPIO-Developers/MPIO"
},
"ols": {
"description": "An ontology of minimum information regarding potential drug-drug interaction information.",
"download_owl": "http://purl.obolibrary.org/obo/mpio.owl",
"homepage": "https://github.com/MPIO-Developers/MPIO",
"name": "Minimum PDDI Information Ontology",
"prefix": "mpio",
"version": "2023-10-17",
"version.iri": "http://purl.obolibrary.org/obo/mpio/release/2023-10-17/mpio.owl"
},
"ontobee": {
"library": "Library",
"name": "Minimum PDDI Information Ontology",
"prefix": "MPIO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/MPIO_$1"
},
"mro": {
"aberowl": {
"description": "An ontology for Major Histocompatibility Complex (MHC) restriction in experiments",
"download_owl": "http://aber-owl.net/media/ontologies/MRO/58/mro.owl",
"homepage": "https://github.com/IEDB/MRO",
"name": "MHC Restriction Ontology",
"prefix": "MRO"
},
"biocontext": {
"prefix": "MRO"
},
"bioportal": {
"contact": {
"email": "sanju.tiwari.2007@gmail.com",
"name": "Sanju Tiwari"
},
"description": "It is an ontology for Military concepts",
"name": "Defen",
"prefix": "MRO"
},
"example": "0000634",
"fairsharing": {
"abbreviation": "MRO",
"description": "MHC molecules form a highly diverse family of proteins that play a key role in cellular immune recognition. No consistent nomenclature exists across different vertebrate species. To correctly represent MHC related data in The Immune Epitope Database (IEDB), we built upon a previously established MHC ontology (MaHCO) and created MRO to represent MHC molecules as they relate to immunological experiments. MRO models MHC protein chains from 16 species, deals with different approaches used to identify MHC, such as direct sequencing verses serotyping, relates engineered MHC molecules to naturally occurring ones, connects genetic loci, alleles, protein chains and multichain proteins, and establishes evidence codes for MHC restriction.",
"domains": [
"Major histocompatibility complex",
"Immune system"
],
"homepage": "https://github.com/IEDB/MRO",
"license": "CC-BY-3.0",
"name": "MHC Restriction Ontology",
"prefix": "FAIRsharing.k893xa",
"publications": [
{
"doi": "10.1186/s13326-016-0045-5",
"pubmed": "26759709",
"title": "An ontology for major histocompatibility restriction",
"year": 2016
}
],
"repository": "https://github.com/IEDB/MRO/issues",
"subjects": [
"Immunology"
]
},
"mappings": {
"aberowl": "MRO",
"biocontext": "MRO",
"bioportal": "MRO",
"fairsharing": "FAIRsharing.k893xa",
"obofoundry": "mro",
"ols": "mro",
"ontobee": "MRO"
},
"obofoundry": {
"contact": "bpeters@lji.org",
"contact.github": "bpeters42",
"contact.label": "Bjoern Peters",
"contact.orcid": "0000-0002-8457-6693",
"deprecated": false,
"description": "An ontology for Major Histocompatibility Complex (MHC) restriction in experiments",
"domain": "chemistry and biochemistry",
"download.owl": "http://purl.obolibrary.org/obo/mro.owl",
"homepage": "https://github.com/IEDB/MRO",
"license": "CC BY 3.0",
"license.url": "https://creativecommons.org/licenses/by/3.0/",
"name": "MHC Restriction Ontology",
"preferredPrefix": "MRO",
"prefix": "mro",
"repository": "https://github.com/IEDB/MRO"
},
"ols": {
"description": "The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions.",
"download_owl": "http://purl.obolibrary.org/obo/mro.owl",
"homepage": "https://github.com/IEDB/MRO",
"name": "MHC Restriction Ontology",
"prefix": "mro",
"version": "2024-08-02",
"version.iri": "http://purl.obolibrary.org/obo/mro/2024-08-02/mro.owl"
},
"ontobee": {
"library": "Library",
"name": "MHC Restriction Ontology",
"prefix": "MRO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1186/s13326-016-0045-5",
"pmc": "PMC4709943",
"pubmed": "26759709",
"title": "An ontology for major histocompatibility restriction",
"year": 2016
}
],
"uri_format": "http://purl.obolibrary.org/obo/MRO_$1"
},
"ms": {
"aberowl": {
"description": "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.",
"download_owl": "http://aber-owl.net/media/ontologies/MS/199/ms.owl",
"homepage": "http://www.psidev.info/groups/controlled-vocabularies",
"name": "Mass spectrometry ontology",
"prefix": "MS"
},
"biocontext": {
"prefix": "MS"
},
"bioportal": {
"contact": {
"email": "gerhard.mayer@rub.de",
"name": "Gerhard Mayer"
},
"description": "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry. Developed by the HUPO Proteomics Standards Initiative (PSI).",
"homepage": "http://www.psidev.info/groups/controlled-vocabularies",
"name": "Mass Spectrometry Ontology",
"prefix": "MS",
"publication": "http://database.oxfordjournals.org/content/2013/bat009.long",
"version": "4.1.169"
},
"example": "1000560",
"mappings": {
"aberowl": "MS",
"biocontext": "MS",
"bioportal": "MS",
"miriam": "ms",
"n2t": "ms",
"obofoundry": "ms",
"ols": "ms",
"ontobee": "MS"
},
"miriam": {
"deprecated": false,
"description": "The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance.",
"homepage": "https://bioportal.bioontology.org/ontologies/MS",
"id": "00000590",
"name": "Mass Spectrometry Controlled Vocabulary",
"namespaceEmbeddedInLui": true,
"pattern": "^MS:\\d{7}$",
"prefix": "ms",
"sampleId": "1000001",
"uri_format": "http://purl.bioontology.org/ontology/MS/MS:$1"
},
"n2t": {
"description": "The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance.",
"example": "1000001",
"homepage": "https://bioportal.bioontology.org/ontologies/MS",
"name": "Mass Spectrometry Controlled Vocabulary through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^MS:\\d{7}$",
"prefix": "ms",
"uri_format": "http://purl.bioontology.org/ontology/MS/MS:$1"
},
"obofoundry": {
"contact": "gerhard.mayer@rub.de",
"contact.github": "germa",
"contact.label": "Gerhard Mayer",
"contact.orcid": "0000-0002-1767-2343",
"depends_on": [
"pato",
"uo"
],
"deprecated": false,
"description": "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.",
"domain": "investigations",
"download.obo": "http://purl.obolibrary.org/obo/ms.obo",
"download.owl": "http://purl.obolibrary.org/obo/ms.owl",
"homepage": "http://www.psidev.info/groups/controlled-vocabularies",
"license": "CC BY 3.0",
"license.url": "https://creativecommons.org/licenses/by/3.0/",
"name": "Mass spectrometry ontology",
"preferredPrefix": "MS",
"prefix": "ms",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/23482073",
"title": "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary."
}
],
"repository": "https://github.com/HUPO-PSI/psi-ms-CV"
},
"ols": {
"contact": "psidev-ms-vocab@lists.sourceforge.net",
"description": "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.",
"download_owl": "http://purl.obolibrary.org/obo/ms.owl",
"homepage": "http://www.psidev.info/groups/controlled-vocabularies",
"name": "Mass spectrometry ontology",
"prefix": "ms",
"version": "4.1.168",
"version.iri": "http://purl.obolibrary.org/obo/ms/4.1.168/ms.owl"
},
"ontobee": {
"library": "Library",
"name": "Mass spectrometry ontology",
"prefix": "MS"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1093/database/bat009",
"pmc": "PMC3594986",
"pubmed": "23482073",
"title": "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary",
"year": 2013
}
],
"uri_format": "http://purl.obolibrary.org/obo/MS_$1"
},
"msigdb": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "MSigDB",
"uri_format": "https://www.gsea-msigdb.org/gsea/msigdb/$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can",
"example": "M1",
"homepage": "https://www.gsea-msigdb.org",
"integbio": {
"alt_name": "Molecular Signatures Database",
"description": "MSigDB is a collection of annotated gene sets for use with Enrichment Analysis (GSEA) software which is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. It contains 9 major collections of the gene sets;\nH: hallmark gene sets\nC1: positional gene sets\nC2: curated gene sets\nC3: regulatory target gene sets\nC4: computational gene sets\nC5: ontology gene sets\nC6: oncogenic signature gene sets\nC7: immunologic signature gene sets\nC8: cell type signature gene sets",
"homepage": "http://www.gsea-msigdb.org/gsea/msigdb/index.jsp",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Broad Institute of Harvard and MIT||UCSD (University of California San Diego)",
"name": "MSigDB",
"prefix": "nbdc02550",
"pubmeds": [
"16199517"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"mappings": {
"biolink": "MSigDB",
"integbio": "nbdc02550"
},
"name": "Molecular Signatures Database",
"pattern": "^M\\d+$",
"synonyms": [
"msig"
],
"uri_format": "https://biopragmatics.github.io/providers/msigdb/$1",
"wikidata": {
"paper": "Q34509167"
}
},
"msio": {
"example": "0000111",
"fairsharing": {
"abbreviation": "MSIO",
"contact": {
"email": "philippe.rocca-serra@oerc.ox.ac.uk",
"name": "Philippe Rocca-Serra",
"orcid": "0000-0001-9853-5668"
},
"description": "The Metabolomics Standards Initiative Ontology (MSIO) aims to support metabolomic experimental annotations for mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy techniques to identify, measure and quantify small molecules known as metabolites. MSIO covers metabolite profiling, targeted or untargeted, and tracer based applications. MSIO leverages other existing resource terms from other ontology collections such as CHEBI, DUO, NMRCV, OBI, and STATO.",
"domains": [
"Mass spectrum",
"Experimental measurement",
"Annotation",
"Nuclear Magnetic Resonance (NMR) spectroscopy",
"Omics data analysis"
],
"homepage": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO",
"license": "CC-BY-3.0",
"name": "Metabolomics Standards Initiative Ontology",
"prefix": "FAIRsharing.4c7f91",
"publications": [
{
"doi": "10.1007/s11306-007-0069-z",
"title": "Metabolomics standards initiative: ontology working group work in progress",
"year": 2007
}
],
"repository": "https://raw.githubusercontent.com/ISA-tools/MSIO/master/MSIO-edit.owl",
"subjects": [
"Metabolomics",
"Omics"
]
},
"keywords": [
"nmr"
],
"mappings": {
"fairsharing": "FAIRsharing.4c7f91",
"ols": "msio"
},
"name": "Metabolomics Standards Initiative Ontology",
"ols": {
"description": "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.",
"download_owl": "https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl",
"homepage": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO",
"name": "Metabolomics Standards Initiative Ontology (MSIO)",
"prefix": "msio",
"version": "1.0.1"
},
"pattern": "^\\d{7}$",
"repository": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO",
"uri_format": "http://purl.obolibrary.org/obo/MSIO_$1"
},
"mtbd": {
"mappings": {
"prefixcommons": "mtbd"
},
"prefixcommons": {
"description": "The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, and information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors.",
"example": "1374",
"homepage": "http://tumor.informatics.jax.org",
"keywords": [
"gene expression",
"DNA"
],
"name": "Mouse Tumor Biology Database",
"pattern": "^\\d+$",
"prefix": "mtbd",
"uri_format": "http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"multicellds": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.",
"example": "MCDS_S_0000000001",
"fairsharing": {
"abbreviation": "MultiCellDS",
"contact": {
"email": "samuel.friedman@cammlab.org",
"name": "Samuel Friedman",
"orcid": "0000-0001-8003-6860"
},
"description": "MultiCellDS (Multicellular data specification), an outgrowth of the earlier MultiCellXML project, aims to create a data standard for sharing multicellular experimental, simulation, and clinical data. Our ultimate goal is to foster a community that develops user-friendly tools that can read, write, and recombine data into better simulations and analyses for multicellular biology and predictive medicine. As part of this effort, we are developing MultiCellDB: a repository for a curated library of digital cell lines and peer-reviewed simulation and experimental data. A novel part of MultiCellDS is the digital cell line: a digital analogue of experimental cell lines that will help to collect biophysical cell line measurements coming from many research groups and make them readily accessible to an ecosystem of compatible computational models. You can learn more about digital cell lines and other core ideas on this page. We are currently preparing a draft of the upcoming MultiCellDS 1.0 specification. After a multiple rounds of comment and review by a multidisciplinary review panel and the general public, we target an October 2016 release of the data specification and software support tools.",
"homepage": "http://multicellds.org",
"name": "MultiCellular Data Standard",
"prefix": "FAIRsharing.pqzyd5",
"publications": [],
"subjects": [
"Life Science"
]
},
"homepage": "http://multicellds.org/MultiCellDB.php",
"mappings": {
"fairsharing": "FAIRsharing.pqzyd5"
},
"name": "MultiCellDS",
"uri_format": "http://multicellds.org/MultiCellDB/$1"
},
"multicellds.cell_line": {
"biocontext": {
"prefix": "MULTICELLDS.CELL_LINE"
},
"mappings": {
"biocontext": "MULTICELLDS.CELL_LINE",
"miriam": "multicellds.cell_line",
"n2t": "multicellds.cell_line"
},
"miriam": {
"deprecated": false,
"description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.",
"homepage": "http://multicellds.org/MultiCellDB.php",
"id": "00000584",
"name": "MultiCellDS Digital Cell Line",
"namespaceEmbeddedInLui": false,
"pattern": "^MCDS_L_[a-zA-Z0-9]{1,10}$",
"prefix": "multicellds.cell_line",
"sampleId": "MCDS_L_0000000001",
"uri_format": "http://multicellds.org/MultiCellDB/$1"
},
"n2t": {
"description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.",
"example": "MCDS_L_0000000001",
"homepage": "http://multicellds.org/MultiCellDB.php",
"name": "MultiCellDS Digital Cell Line at Keck School of Medicine",
"namespaceEmbeddedInLui": false,
"pattern": "^MCDS_L_[a-zA-Z0-9]{1,10}$",
"prefix": "multicellds.cell_line",
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},
"part_of": "multicellds"
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"biocontext": "MULTICELLDS.COLLECTION",
"miriam": "multicellds.collection",
"n2t": "multicellds.collection"
},
"miriam": {
"deprecated": false,
"description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections).",
"homepage": "http://multicellds.org/MultiCellDB.php",
"id": "00000582",
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"pattern": "^MCDS_C_[a-zA-Z0-9]{1,10}$",
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"description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections).",
"example": "MCDS_C_0000000001",
"homepage": "http://multicellds.org/MultiCellDB.php",
"name": "MultiCellDScollection at Keck School of Medicine",
"namespaceEmbeddedInLui": false,
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"prefix": "multicellds.collection",
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"miriam": "multicellds.snapshot",
"n2t": "multicellds.snapshot"
},
"miriam": {
"deprecated": false,
"description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data.",
"homepage": "http://multicellds.org/MultiCellDB.php",
"id": "00000583",
"name": "MultiCellDS Digital snapshot",
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},
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"description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data.",
"example": "MCDS_S_0000000001",
"homepage": "http://multicellds.org/MultiCellDB.php",
"name": "MultiCellDS snapshot at Keck School of Medicine",
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"prefix": "multicellds.snapshot",
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},
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"github": "lnanderson",
"name": "Lindsey Anderson",
"orcid": "0000-0002-8741-7823"
},
"description": "The CDC's National Center for Immunization and Respiratory Diseases ([NCIRD](https://www.cdc.gov/ncird/)) developed and maintains HL7 Table 0227, Manufacturers of Vaccines (MVX). It includes both active and inactive manufacturers of vaccines in the US. Inactive MVX codes allow transmission of historical immunization records. When [MVX code is paired with a CVX code](https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=tradename) (vaccine administered code), the specific trade named vaccine may be indicated.",
"example": "ASZ",
"github_request_issue": 986,
"hl7": {
"description": "CDC Vaccine Manufacturer CodesDO NOT USEThis OID was setup solely for use in the RRF research project in 1999. The correct OID for mvx is 2.16.840.1.113883.12.227",
"name": "MVX",
"preferred_prefix": "mvx",
"prefix": "2.16.840.1.113883.6.60",
"status": "Retired"
},
"homepage": "https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=mvx",
"mappings": {
"hl7": "2.16.840.1.113883.6.60"
},
"name": "Manufacturers of Vaccines",
"pattern": "^\\w+$",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.12.227&code=$1"
},
"mw.project": {
"biocontext": {
"prefix": "MW.PROJECT"
},
"mappings": {
"biocontext": "MW.PROJECT",
"miriam": "mw.project",
"n2t": "mw.project"
},
"miriam": {
"deprecated": false,
"description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).",
"homepage": "http://www.metabolomicsworkbench.org/",
"id": "00000647",
"name": "Metabolomics Workbench Project",
"namespaceEmbeddedInLui": false,
"pattern": "^PR[0-9]{6}$",
"prefix": "mw.project",
"sampleId": "PR000001",
"uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1"
},
"n2t": {
"description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).",
"example": "PR000001",
"homepage": "http://www.metabolomicsworkbench.org/",
"name": "Metabolomics Workbench Project",
"namespaceEmbeddedInLui": false,
"pattern": "^PR[0-9]{6}$",
"prefix": "mw.project",
"uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1"
}
},
"mw.study": {
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"mappings": {
"biocontext": "MW.STUDY",
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"miriam": {
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"description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).",
"homepage": "http://www.metabolomicsworkbench.org/",
"id": "00000646",
"name": "Metabolomics Workbench Study",
"namespaceEmbeddedInLui": false,
"pattern": "^ST[0-9]{6}$",
"prefix": "mw.study",
"providers": [
{
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"description": "Metabolomics Workbench Study through OmicsDI",
"homepage": "https://www.omicsdi.org/",
"name": "Metabolomics Workbench Study through OmicsDI",
"uri_format": "https://www.omicsdi.org/dataset/metabolomics_workbench/$1"
}
],
"sampleId": "ST000900",
"uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1"
},
"n2t": {
"description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).",
"example": "ST000900",
"homepage": "http://www.metabolomicsworkbench.org/",
"name": "Metabolomics Workbench Study",
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"pattern": "^ST[0-9]{6}$",
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"uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1"
}
},
"myco.lepra": {
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},
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"miriam": "myco.lepra",
"n2t": "myco.lepra",
"prefixcommons": "myco.lepra"
},
"miriam": {
"deprecated": false,
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.",
"homepage": "http://mycobrowser.epfl.ch/leprosy.html",
"id": "00000217",
"name": "MycoBrowser leprae",
"namespaceEmbeddedInLui": false,
"pattern": "^ML\\w+$",
"prefix": "myco.lepra",
"sampleId": "ML0224",
"uri_format": "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1"
},
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"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.",
"example": "ML0224",
"homepage": "http://mycobrowser.epfl.ch/leprosy.html",
"name": "MycoBrowser leprae at Global Health Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^ML\\w+$",
"prefix": "myco.lepra",
"uri_format": "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1"
},
"prefixcommons": {
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.",
"example": "ML0224",
"homepage": "http://mycobrowser.epfl.ch/leprosy.html",
"keywords": [
"genome",
"sequence"
],
"name": "MycoBrowser leprae",
"pattern": "^ML\\w+$",
"prefix": "myco.lepra",
"uri_format": "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1"
}
},
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"prefix": "MYCO.MARINUM"
},
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"biocontext": "MYCO.MARINUM",
"miriam": "myco.marinum",
"n2t": "myco.marinum",
"prefixcommons": "myco.marinum"
},
"miriam": {
"deprecated": false,
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information.",
"homepage": "http://mycobrowser.epfl.ch/marinolist.html",
"id": "00000218",
"name": "MycoBrowser marinum",
"namespaceEmbeddedInLui": false,
"pattern": "^MMAR\\_\\d+$",
"prefix": "myco.marinum",
"sampleId": "MMAR_2462",
"uri_format": "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1"
},
"n2t": {
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information.",
"example": "MMAR_2462",
"homepage": "http://mycobrowser.epfl.ch/marinolist.html",
"name": "MycoBrowser marinum at Global Health Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^MMAR\\_\\d+$",
"prefix": "myco.marinum",
"uri_format": "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1"
},
"prefixcommons": {
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information.",
"example": "MMAR_2462",
"homepage": "http://mycobrowser.epfl.ch/marinolist.html",
"keywords": [
"genome",
"sequence"
],
"name": "MycoBrowser marinum",
"pattern": "^MMAR\\_\\d+$",
"prefix": "myco.marinum",
"uri_format": "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1"
}
},
"myco.smeg": {
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"prefix": "MYCO.SMEG"
},
"mappings": {
"biocontext": "MYCO.SMEG",
"miriam": "myco.smeg",
"n2t": "myco.smeg",
"prefixcommons": "myco.smeg"
},
"miriam": {
"deprecated": false,
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.",
"homepage": "http://mycobrowser.epfl.ch/smegmalist.html",
"id": "00000219",
"name": "MycoBrowser smegmatis",
"namespaceEmbeddedInLui": false,
"pattern": "^MSMEG\\w+$",
"prefix": "myco.smeg",
"sampleId": "MSMEG_3769",
"uri_format": "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1"
},
"n2t": {
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.",
"example": "MSMEG_3769",
"homepage": "http://mycobrowser.epfl.ch/smegmalist.html",
"name": "MycoBrowser smegmatis at Global Health Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^MSMEG\\w+$",
"prefix": "myco.smeg",
"uri_format": "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1"
},
"prefixcommons": {
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.",
"example": "MSMEG_3769",
"homepage": "http://mycobrowser.epfl.ch/smegmalist.html",
"keywords": [
"genome",
"sequence"
],
"name": "MycoBrowser smegmatis",
"pattern": "^MSMEG\\w+$",
"prefix": "myco.smeg",
"uri_format": "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1"
}
},
"myco.tuber": {
"biocontext": {
"prefix": "MYCO.TUBER"
},
"contact": {
"email": "stewart.cole@epfl.ch",
"name": "Stewart Thomas Cole",
"orcid": "0000-0003-1400-5585"
},
"mappings": {
"biocontext": "MYCO.TUBER",
"miriam": "myco.tuber",
"n2t": "myco.tuber",
"ncbi": "TubercuList",
"prefixcommons": "tuberculist",
"uniprot": "DB-0106"
},
"miriam": {
"deprecated": false,
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information.",
"homepage": "http://tuberculist.epfl.ch/",
"id": "00000216",
"name": "MycoBrowser tuberculosis",
"namespaceEmbeddedInLui": false,
"pattern": "^Rv\\d{4}(A|B|c)?$",
"prefix": "myco.tuber",
"sampleId": "Rv1908c",
"uri_format": "http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1"
},
"n2t": {
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information.",
"example": "Rv1908c",
"homepage": "http://tuberculist.epfl.ch/",
"name": "MycoBrowser tuberculosis at Global Health Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^Rv\\d{4}(A|B|c)?$",
"prefix": "myco.tuber",
"uri_format": "http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1"
},
"ncbi": {
"example": "Rv3322c",
"homepage": "http://tuberculist.epfl.ch/",
"name": "TubercuList knowledge base",
"prefix": "TubercuList"
},
"prefixcommons": {
"description": "The TubercuList knowledge base integrates genome details, protein information, drug and transcriptome data, mutant and operon annotation, bibliography; structural views and comparative genomics, in a structured manner required for the rational development of new diagnostic, therapeutic and prophylactic measures against tuberculosis.",
"example": "Rv0115",
"homepage": "http://tuberculist.epfl.ch",
"keywords": [
"genome",
"protein",
"DNA"
],
"name": "Mycobacterium tuberculosis strain H37Rv genome database",
"pattern": "^Rv[0-9,a-z]+$",
"prefix": "tuberculist",
"uri_format": "http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1"
},
"publications": [
{
"doi": "10.1016/j.tube.2010.09.006",
"pubmed": "20980200",
"title": "The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes",
"year": 2010
}
],
"synonyms": [
"TubercuList"
],
"uniprot": {
"abbreviation": "TubercuList",
"category": "Organism-specific databases",
"homepage": "https://mycobrowser.epfl.ch/",
"name": "Mycobacterium tuberculosis strain H37Rv genome database",
"prefix": "DB-0106",
"publications": [
{
"doi": "10.1016/j.tube.2010.09.006",
"pubmed": "20980200"
}
],
"uri_format": "https://mycobrowser.epfl.ch/genes/$1"
}
},
"mycobank": {
"biocontext": {
"prefix": "MYCOBANK"
},
"contact": {
"email": "vrobert@unistra.fr",
"name": "Vincent Robert",
"orcid": "0000-0002-9370-4677"
},
"fairsharing": {
"abbreviation": "MycoBank",
"description": "MycoBank was created for the mycological community (as well as scientific community more generally) to document new mycological names, combinations and associated data (such as descriptions and illustrations). Pairwise sequence alignments and polyphasic identifications of fungi and yeasts against curated references databases are available. Nomenclatural experts will be available to check the validity, legitimacy and linguistic correctness of the proposed names in order to avoid nomenclatural error. Deposited names can remain confidential until after publication as required. Once public, the names are accessible through MycoBank, Index Fungorum, GBIF and other international biodiversity initiatives, where they will further be linked to other databases. MycoBank will (when applicable) provide onward links to other databases containing, for example, living cultures, DNA data, reference specimens and pleomorphic names linked to the same holomorph. Authors intending to publish nomenclatural novelties are encouraged to contribute.",
"homepage": "http://www.mycobank.org",
"name": "MycoBank",
"prefix": "FAIRsharing.v8se8r",
"publications": [
{
"doi": "10.5598/imafungus.2013.04.02.16",
"pubmed_id": 24563843,
"title": "MycoBank gearing up for new horizons."
}
],
"subjects": [
"Taxonomy",
"Biology"
]
},
"mappings": {
"biocontext": "MYCOBANK",
"fairsharing": "FAIRsharing.v8se8r",
"miriam": "mycobank",
"n2t": "mycobank",
"ncbi": "MycoBank",
"prefixcommons": "mycobank",
"re3data": "r3d100011222"
},
"miriam": {
"deprecated": false,
"description": "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.",
"homepage": "http://www.mycobank.org/",
"id": "00000178",
"name": "MycoBank",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "mycobank",
"sampleId": "349124",
"uri_format": "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1"
},
"n2t": {
"description": "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.",
"example": "349124",
"homepage": "http://www.mycobank.org/",
"name": "MycoBank at Fungal Biodiversity Centre",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "mycobank",
"uri_format": "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1"
},
"ncbi": {
"example": "8284",
"homepage": "http://www.mycobank.org",
"name": "Fungal Nomenclature and Species Bank",
"prefix": "MycoBank"
},
"prefixcommons": {
"description": "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.",
"example": "349124",
"homepage": "http://www.mycobank.org",
"keywords": [
"classification"
],
"name": "Fungal Nomenclature and Species Bank",
"pattern": "^\\d+$",
"prefix": "mycobank",
"uri_format": "http://www.mycobank.org/MycoTaxo.aspx?Link=T&Rec=$1"
},
"publications": [
{
"doi": "10.5598/imafungus.2013.04.02.16",
"pmc": "PMC3905949",
"pubmed": "24563843",
"title": "MycoBank gearing up for new horizons",
"year": 2013
}
],
"re3data": {
"description": "MycoBank is an on-line database aimed as a service to the mycological and scientific society by documenting mycological nomenclatural novelties (new names and combinations) and associated data, for example descriptions and illustrations. The nomenclatural novelties will each be allocated a unique MycoBank number that can be cited in the publication where the nomenclatural novelty is introduced. These numbers will also be used by the nomenclatural database Index Fungorum, with which MycoBank is associated.",
"homepage": "https://www.mycobank.org/",
"name": "MycoBank",
"prefix": "r3d100011222",
"synonyms": [
"Fungal databases, nomenclature and species banks"
],
"xrefs": {
"fairsharing": "FAIRsharing.v8se8r",
"nlx": "91803",
"scr": "004950"
}
}
},
"mzspec": {
"banana": "mzspec",
"biocontext": {
"prefix": "MZSPEC"
},
"contact": {
"email": "gerhard.mayer@rub.de",
"github": "germa",
"name": "Gerhard Mayer",
"orcid": "0000-0002-1767-2343"
},
"contributor_extras": [
{
"email": "lindsey.anderson@pnnl.gov",
"github": "lnanderson",
"name": "Lindsey N. Anderson",
"orcid": "0000-0002-8741-7823"
}
],
"fairsharing": {
"abbreviation": "USI",
"contact": {
"email": "edeutsch@systemsbiology.org",
"name": "Eric Deutsch",
"orcid": "0000-0001-8732-0928"
},
"description": "The Universal Spectrum Identifier (USI) is multi-part key identifier for identifying mass spectra contained in public data repositories, primarily focused on proteomics. The USI provides a standardized mechanism for encoding a virtual path to any single mass spectrum generated by a mass spectrometer contained/deposited to public proteomics dataset repositories for enabling greater transparency of spectral evidence. With more than 1 billion USI identifications from over 3 billion spectra already available through ProteomeXchange repositories, Universal Spectrum Identifier encodes the dataset, the MS Run, the scan number and the proposed peptidoform and charge of the ions responsible for the spectrum. The USI identifier is comprised of five key components (and an optional sixth component) in defining an abstract path to a specified spectrum. The USI core components include: 1) the prefix βmzspecβ to make clear that the following string is a USI and to aid in automated mapping of a USI string to a URL, 2) the subsequent dataset submission or dataset collection identifier assigned by the primary repository archive, 3) the mass spectrometry run name (or root name of the raw vendor format file) such as an mzML file (with or without the file extension), 4) a type flag (such as βscanβ, βindexβ or βnativeIdβ as defined in the current mzML specification) for indicating how to interpret the fifth component, 5) the index value (based on the flag type) within the specified MS run, and optionally 6) any relevant information for interpretation of the spectrum if available. ",
"domains": [
"Mass spectrum",
"Data retrieval",
"Data identity and mapping",
"Omics data analysis"
],
"homepage": "http://psidev.info/usi",
"license": "Apache 2.0 License",
"name": "HUPO-PSI Universal Spectrum Identifier",
"prefix": "FAIRsharing.b549b8",
"publications": [
{
"doi": "10.1038/s41592-021-01184-6",
"pubmed": "34183830",
"title": "Universal Spectrum Identifier for mass spectra",
"year": 2021
}
],
"repository": "https://github.com/HUPO-PSI/usi/tree/master/Specification",
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},
{
"code": "scholia",
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],
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"doi": "10.1093/nar/gkq1237",
"pmc": "PMC3013746",
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}
],
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"description": "The Gene database provides detailed information for known and predicted genes defined by nucleotide sequence or map position. Gene supplies gene-specific connections in the nexus of map, sequence, expression, structure, function, citation, and homology data. Unique identifiers are assigned to genes with defining sequences, genes with known map positions, and genes inferred from phenotypic information. These gene identifiers are used throughout NCBI's databases and tracked through updates of annotation. Gene includes genomes represented by NCBI Reference Sequences (or RefSeqs) and is integrated for indexing and query and retrieval from NCBI's Entrez and E-Utilities systems.",
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"synonyms": [
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"name": "Database of genes from NCBI RefSeq genomes",
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"description": "A GI number (for GenInfo Identifier, sometimes written in lower case, _gi_) is a simple series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Version number of the sequence record. Each time a sequence record is changed, it is assigned a new GI number.",
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},
"owners": [
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"ror": "02meqm098"
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],
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},
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"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "NCBI Protein",
"prefix": "nbdc00636",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"mappings": {
"biocontext": "NCBIProtein",
"go": "NCBI_NP",
"integbio": "nbdc00636",
"miriam": "ncbiprotein",
"n2t": "ncbiprotein",
"prefixcommons": "ncbi.protein",
"re3data": "r3d100010776"
},
"miriam": {
"deprecated": false,
"description": "The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.",
"homepage": "https://www.ncbi.nlm.nih.gov/protein",
"id": "00000344",
"name": "NCBI Protein",
"namespaceEmbeddedInLui": false,
"pattern": "^(\\w+\\d+(\\.\\d+)?)|(NP_\\d+)$",
"prefix": "ncbiprotein",
"sampleId": "CAA71118.1",
"uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1"
},
"n2t": {
"description": "The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.",
"example": "CAA71118.1",
"homepage": "https://www.ncbi.nlm.nih.gov/protein",
"name": "NCBI Protein at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^(\\w+\\d+(\\.\\d+)?)|(NP_\\d+)$",
"prefix": "ncbiprotein",
"uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1"
},
"owners": [
{
"name": "National Center for Biotechnology Information",
"partnered": false,
"ror": "02meqm098"
}
],
"preferred_prefix": "NCBIProtein",
"prefixcommons": {
"description": "The Entrez Protein search and retrieval system contains protein entries that have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.",
"example": "CAA71118.1",
"homepage": "http://www.ncbi.nlm.nih.gov/protein",
"keywords": [
"protein"
],
"name": "NCBI Protein",
"pattern": "^\\w+\\d+(\\.\\d+)?$",
"prefix": "ncbi.protein",
"synonyms": [
"protein",
"ncbi-proteinid"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/protein/$1"
},
"re3data": {
"description": "The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. Protein sequences are the fundamental determinants of biological structure and function.",
"homepage": "https://www.ncbi.nlm.nih.gov/protein",
"name": "NCBI Protein",
"prefix": "r3d100010776",
"xrefs": {
"nif": "0000-03178",
"scr": "003257"
}
}
},
"ncbitaxon": {
"aberowl": {
"description": "An ontology representation of the NCBI organismal taxonomy",
"download_owl": "http://aber-owl.net/media/ontologies/NCBITAXON/16/ncbitaxon.owl",
"homepage": "https://github.com/obophenotype/ncbitaxon",
"name": "NCBI organismal classification",
"prefix": "NCBITAXON"
},
"agroportal": {
"contact": {
"email": "info@ncbi.nlm.nih.gov",
"name": "NCBI information"
},
"description": "The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.",
"example_uri": "http://purl.bioontology.org/ontology/NCBITAXON/201174",
"homepage": "https://www.ncbi.nlm.nih.gov/",
"name": "National Center for Biotechnology Information (NCBI) Organismal Classification",
"prefix": "NCBITAXON",
"repository": "https://github.com/obophenotype/ncbitaxon",
"version": "2023ab"
},
"bartoc": {
"description": "The NCBI Taxonomy database is a curated set of names and classifications for all of the organisms that are represented in GenBank. When new sequences are submitted to GenBank, the submission is checked for new organism names, which are then classified and added to the Taxonomy database. As of April 2003, there were 176,890 total taxa represented.\n\nThere are two main tools for viewing the information in the Taxonomy database: the Taxonomy Browser, and Taxonomy Entrez. Both systems allow searching of the Taxonomy database for names, and both link to the relevant sequence data. However, the Taxonomy Browser provides a hierarchical view of the classification (the best display for most casual users interested in exploring our classification), whereas Entrez Taxonomy provides a uniform indexing, search, and retrieval engine with a common mechanism for linking between the Taxonomy and other relevant Entrez databases.\n\nOrganismal taxonomy is a powerful organizing principle in the study of biological systems. Inheritance, homology by common descent, and the conservation of sequence and structure in the determination of function are all central ideas in biology that are directly related to the evolutionary history of any group of organisms. Because of this, taxonomy plays an important cross-linking role in many of the NCBI tools and databases.\n\nThe NCBITaxon ontology is an automatic translation of the NCBI taxonomy (a taxonomic classification of living organisms and associated artifacts) database into obo/owl.",
"homepage": "http://www.ncbi.nlm.nih.gov/taxonomy",
"name": "National Center for Biotechnology Information Taxonomy",
"prefix": "509"
},
"biocontext": {
"prefix": "TAXONOMY"
},
"bioportal": {
"contact": {
"email": "info@ncbi.nlm.nih.gov",
"name": "NCBI information"
},
"description": "The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases.",
"homepage": "http://www.ncbi.nlm.nih.gov/taxonomy",
"name": "National Center for Biotechnology Information (NCBI) Organismal Classification",
"prefix": "NCBITAXON",
"version": "2023AB"
},
"cellosaurus": {
"category": "Taxonomy",
"homepage": "https://www.ncbi.nlm.nih.gov/taxonomy",
"name": "NCBI taxonomy database",
"prefix": "NCBI_TaxID",
"uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1&lvl=3"
},
"contact": {
"email": "schoch2@ncbi.nlm.nih.gov",
"name": "Conrad L Schoch",
"orcid": "0000-0003-1839-5322"
},
"download_obo": "http://purl.obolibrary.org/obo/ncbitaxon.obo",
"edam": {
"description": "A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database.",
"name": "NCBI taxonomy",
"obsolete": false,
"prefix": "1179"
},
"example": "2170610",
"fairsharing": {
"abbreviation": "NCBITAXON",
"description": "The NCBI Taxonomy is a database of taxonomic information. It does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts.",
"domains": [
"Taxonomic classification"
],
"homepage": "https://www.ncbi.nlm.nih.gov/taxonomy",
"license": "CC0-1.0",
"name": "NCBI Taxonomy",
"prefix": "FAIRsharing.fj07xj",
"publications": [
{
"doi": "10.1093/nar/gkx1094",
"pubmed": "29140468",
"title": "GenBank",
"year": 2017
},
{
"doi": "10.1093/nar/gkr1178",
"pubmed": "22139910",
"title": "The NCBI Taxonomy database",
"year": 2011
},
{
"doi": "10.1093/database/baaa062",
"pubmed": "32761142",
"title": "NCBI Taxonomy: a comprehensive update on curation, resources and tools",
"year": 2020
}
],
"repository": "https://github.com/obophenotype/ncbitaxon",
"subjects": [
"Taxonomy",
"Phylogenetics",
"Life Science"
]
},
"go": {
"homepage": "http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/",
"name": "NCBI Taxonomy",
"prefix": "NCBITaxon",
"synonyms": [
"taxon",
"ncbi_taxid"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=$1"
},
"hl7": {
"description": "NCBI Taxonomy. National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 2001. http://www.ncbi.nlm.nih.gov/Taxonomy/",
"name": "Taxonomy from NCBI",
"preferred_prefix": "NCBI",
"prefix": "2.16.840.1.113883.6.205",
"status": "Pending"
},
"mappings": {
"aberowl": "NCBITAXON",
"agroportal": "NCBITAXON",
"bartoc": "509",
"biocontext": "TAXONOMY",
"bioportal": "NCBITAXON",
"cellosaurus": "NCBI_TaxID",
"edam": "1179",
"fairsharing": "FAIRsharing.fj07xj",
"go": "NCBITaxon",
"hl7": "2.16.840.1.113883.6.205",
"miriam": "taxonomy",
"n2t": "taxonomy",
"ncbi": "taxon",
"obofoundry": "ncbitaxon",
"ols": "ncbitaxon",
"ontobee": "NCBITaxon",
"prefixcommons": "taxonomy",
"re3data": "r3d100010415",
"togoid": "Taxonomy",
"wikidata": "P685"
},
"miriam": {
"deprecated": false,
"description": "The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.",
"homepage": "https://www.ncbi.nlm.nih.gov/Taxonomy/",
"id": "00000006",
"name": "Taxonomy",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "taxonomy",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "Taxonomy through UniProt PURL",
"homepage": "https://www.uniprot.org/taxonomy/",
"name": "Taxonomy through UniProt PURL",
"uri_format": "https://purl.uniprot.org/taxonomy/$1"
},
{
"code": "ebi",
"description": "European Nucleotide Archive (ENA)",
"homepage": "https://www.ebi.ac.uk/ena/",
"name": "European Nucleotide Archive (ENA)",
"uri_format": "https://www.ebi.ac.uk/ena/data/view/Taxon:$1"
},
{
"code": "CURATOR_REVIEW",
"description": "Bio2RDF",
"homepage": "https://bio2rdf.org/",
"name": "Bio2RDF",
"uri_format": "https://bio2rdf.org/taxonomy:$1"
}
],
"sampleId": "9606",
"uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1"
},
"n2t": {
"description": "The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.",
"example": "9606",
"homepage": "https://www.ncbi.nlm.nih.gov/Taxonomy/",
"name": "NCBI Taxonomy",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "taxonomy",
"uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1"
},
"name": "NCBI Taxonomy",
"namespace_in_lui": false,
"ncbi": {
"example": "4932",
"homepage": "https://www.ncbi.nlm.nih.gov/taxonomy",
"name": "NCBI's taxonomic identifier",
"prefix": "taxon"
},
"obofoundry": {
"appears_in": [
"agro",
"chiro",
"cl",
"clo",
"ecto",
"envo",
"foodon",
"gallont",
"genepio",
"go",
"hso",
"mco",
"ons",
"pcl",
"pco",
"uberon",
"vbo"
],
"contact": "frederic.bastian@unil.ch",
"contact.github": "fbastian",
"contact.label": "Frederic Bastian",
"contact.orcid": "0000-0002-9415-5104",
"deprecated": false,
"description": "An ontology representation of the NCBI organismal taxonomy",
"domain": "organisms",
"download.json": "http://purl.obolibrary.org/obo/ncbitaxon.json",
"download.obo": "http://purl.obolibrary.org/obo/ncbitaxon.obo",
"download.owl": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
"homepage": "https://github.com/obophenotype/ncbitaxon",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "NCBI organismal classification",
"preferredPrefix": "NCBITaxon",
"prefix": "ncbitaxon",
"repository": "https://github.com/obophenotype/ncbitaxon"
},
"ols": {
"description": "An ontology representation of the NCBI organismal taxonomy",
"download_owl": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
"homepage": "https://github.com/obophenotype/ncbitaxon",
"name": "NCBI organismal classification",
"prefix": "ncbitaxon",
"version": "2024-07-03",
"version.iri": "http://purl.obolibrary.org/obo/ncbitaxon/2024-07-03/ncbitaxon.owl"
},
"ontobee": {
"library": "Library",
"name": "NCBI organismal classification",
"prefix": "NCBITaxon"
},
"owners": [
{
"name": "National Center for Biotechnology Information",
"partnered": false,
"ror": "02meqm098"
}
],
"pattern": "^\\d+$",
"prefixcommons": {
"alt_uri_formats": [
"http://purl.org/obo/owl/NCBITaxon#$1",
"http://purl.org/obo/owl/TAXON#$1",
"http://bioportal.bioontology.org/ontologies/1132?p=terms&conceptid=obo:NCBITaxon_#$1"
],
"bioportal": "1132",
"description": "The NCBI taxonomy database contains the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence.",
"example": "9606",
"homepage": "http://www.ncbi.nlm.nih.gov/taxonomy",
"keywords": [
"DNA",
"protein",
"structure",
"classification"
],
"license": "http://www.nlm.nih.gov/copyright.html",
"name": "NCBI Taxonomy",
"pattern": "^\\d+$",
"prefix": "taxonomy",
"synonyms": [
"taxid",
"taxon",
"ncbitaxon",
"ncbitaxonomy",
"newt",
"taxman",
"ncbi_taxid",
"ncbi_taxon_id"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=$1"
},
"providers": [
{
"code": "scholia",
"description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.",
"homepage": "https://scholia.toolforge.org/",
"name": "Scholia",
"uri_format": "https://scholia.toolforge.org/ncbi-taxon/$1"
}
],
"publications": [
{
"doi": "10.1093/database/baaa062",
"pmc": "PMC7408187",
"pubmed": "32761142",
"title": "NCBI Taxonomy: a comprehensive update on curation, resources and tools",
"year": 2020
},
{
"doi": "10.1093/nar/gkx1094",
"pmc": "PMC5753231",
"pubmed": "29140468",
"title": "GenBank",
"year": 2018
},
{
"doi": "10.1093/nar/gkr1178",
"pmc": "PMC3245000",
"pubmed": "22139910",
"title": "The NCBI Taxonomy database",
"year": 2011
}
],
"re3data": {
"description": "The NCBI Taxonomy database is a curated set of names and classifications for all of the organisms that are represented in GenBank. The EMBL and DDBJ databases, as well as GenBank, now use the NCBI Taxonomy as the standard classification for nucleotide sequences. Taxonomy Contains the names and phylogenetic lineages of more than 160,000 organisms that have molecular data in the NCBI databases. New taxa are added to the Taxonomy database as data are deposited for them. When new sequences are submitted to GenBank, the submission is checked for new organism names, which are then classified and added to the Taxonomy database.",
"homepage": "https://www.ncbi.nlm.nih.gov/taxonomy",
"name": "NCBI Taxonomy",
"prefix": "r3d100010415",
"synonyms": [
"Entrez Taxonomy"
],
"xrefs": {
"fairsharing": "FAIRsharing.fj07xj",
"nif": "0000-03179",
"scr": "003256"
}
},
"synonyms": [
"NCBI Taxonomy",
"NCBITaxon",
"NCBITaxonomyID",
"NCBI_Taxon_ID",
"NCBI_taxid",
"TAX",
"TaxonomyID",
"taxid",
"taxon",
"taxonomy",
"uniprot.taxonomy"
],
"togoid": {
"catalog": "nbdc00700",
"examples": [
"1171376",
"484906",
"1214242",
"1124991",
"1037911",
"1266844",
"243277",
"696747",
"263820",
"713604"
],
"keywords": [
"Organism"
],
"name": "Taxonomy",
"pattern": "^(?\\d+)$",
"prefix": "Taxonomy",
"uri_format": "http://identifiers.org/taxonomy/$1"
},
"uri_format": "http://purl.obolibrary.org/obo/NCBITaxon_$1",
"wikidata": {
"description": "identifier for a taxon in the Taxonomy Database by the National Center for Biotechnology Information",
"example": [
"9606",
"9986"
],
"homepage": "http://www.ncbi.nlm.nih.gov/taxonomy",
"name": "NCBI taxonomy ID",
"pattern": "^[1-9][0-9]{0,6}$",
"prefix": "P685",
"uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1",
"uri_format_rdf": "http://purl.uniprot.org/taxonomy/$1"
}
},
"nci.drug": {
"mappings": {
"wikidata": "P11623"
},
"wikidata": {
"description": "identifier of an entry in the NCI Drug Dictionary",
"example": [
"beta-carotene",
"edatrexate",
"hydroxychloroquine",
"l-carnitine-l-tartrate"
],
"homepage": "https://www.cancer.gov/publications/dictionaries/cancer-drug",
"name": "NCI Drug Dictionary ID",
"prefix": "P11623",
"uri_format": "https://www.cancer.gov/publications/dictionaries/cancer-drug/def/$1"
}
},
"ncim": {
"biocontext": {
"prefix": "NCIM"
},
"mappings": {
"biocontext": "NCIM",
"miriam": "ncim",
"n2t": "ncim"
},
"miriam": {
"deprecated": false,
"description": "NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical.",
"homepage": "http://ncim.nci.nih.gov/",
"id": "00000353",
"name": "NCIm",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d+$",
"prefix": "ncim",
"sampleId": "C0026339",
"uri_format": "http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1"
},
"n2t": {
"description": "NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical.",
"example": "C0026339",
"homepage": "http://ncim.nci.nih.gov/",
"name": "NCIm at National Cancer Institue",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d+$",
"prefix": "ncim",
"uri_format": "http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1"
},
"name": "NCI Metathesaurus",
"owners": [
{
"name": "National Cancer Institute",
"partnered": false,
"ror": "040gcmg81"
}
]
},
"ncit": {
"aberowl": {
"description": "NCI Thesaurus (NCIt)is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities. The NCIt OBO Edition aims to increase integration of the NCIt with OBO Library ontologies. NCIt OBO Edition releases should be considered experimental.",
"download_owl": "http://aber-owl.net/media/ontologies/NCIT/78/ncit.owl",
"homepage": "https://github.com/NCI-Thesaurus/thesaurus-obo-edition",
"name": "NCI Thesaurus OBO Edition",
"prefix": "NCIT"
},
"biocontext": {
"prefix": "NCIT"
},
"bioportal": {
"contact": {
"email": "ncithesaurus@mail.nih.gov",
"name": "NCI Thesaurus Mailbox"
},
"description": "Vocabulary for clinical care, translational and basic research, and public information and administrative activities.",
"homepage": "https://ncithesaurus.nci.nih.gov/ncitbrowser/",
"name": "National Cancer Institute Thesaurus",
"prefix": "NCIT",
"version": "24.01e"
},
"cellosaurus": {
"category": "Medical resources",
"homepage": "https://ncit.nci.nih.gov/ncitbrowser",
"name": "NCI thesaurus",
"prefix": "NCIt",
"uri_format": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=$1"
},
"download_obo": "http://purl.obolibrary.org/obo/ncit.obo",
"example": "C138986",
"fairsharing": {
"abbreviation": "NCIt",
"description": "NCI Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities. NCIt features: stable, unique codes for biomedical concepts; preferred terms, synonyms, research codes, external source codes, and other information; over 100,000 textual definitions; links to NCI Metathesaurus and other information sources; and over 400,000 cross-links between concepts, providing formal logic-based definition of many concepts. NCIt is a widely recognized standard for biomedical coding and reference, used by a broad variety of public and private partners both nationally and internationally including the Clinical Data Interchange Standards Consortium Terminology (CDISC), the U.S. Food and Drug Administration (FDA), the Federal Medication Terminologies (FMT), and the National Council for Prescription Drug Programs (NCPDP).",
"domains": [
"Cancer",
"Disease"
],
"homepage": "https://ncit.nci.nih.gov",
"license": "CC-BY-4.0",
"name": "NCI Thesaurus",
"prefix": "FAIRsharing.4cvwxa",
"publications": [
{
"doi": "10.3233/978-1-60750-949-3-33",
"pubmed": "15360769",
"title": "NCI Thesaurus: using science-based terminology to integrate cancer research results",
"year": 2004
}
],
"repository": "https://github.com/NCI-Thesaurus/thesaurus-obo-edition",
"subjects": [
"Biomedical Science",
"Translational Medicine",
"Preclinical Studies"
]
},
"hl7": {
"description": "NCI Thesaurus, 2004. Bethesda, MD: National Cancer Institute, National Institutes of Health, July 2004.This OID entry has been rejected upon review, as the object has already been registered by the NCI (owners).",
"name": "NCI Thesaurus",
"preferred_prefix": "NCI",
"prefix": "2.16.840.1.113883.6.206",
"status": "Rejected"
},
"integbio": {
"alt_name": "NCI Thesaurus",
"description": "NCI Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities. NCIt features: stable, unique codes for biomedical concepts; preferred terms, synonyms, research codes, external source codes, and other information; over 100,000 textual definitions; links to NCI Metathesaurus and other information sources; and over 400,000 cross-links between concepts, providing formal logic-based definition of many concepts. NCIt is a widely recognized standard for biomedical coding and reference, used by a broad variety of public and private partners both nationally and internationally including the Clinical Data Interchange Standards Consortium Terminology (CDISC), the U.S. Food and Drug Administration (FDA), the Federal Medication Terminologies (FMT), and the National Council for Prescription Drug Programs (NCPDP).",
"homepage": "https://ncithesaurus.nci.nih.gov/ncitbrowser/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "National Cancer Institute at Frederick",
"name": "NCIt",
"prefix": "nbdc02651",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"mappings": {
"aberowl": "NCIT",
"biocontext": "NCIT",
"bioportal": "NCIT",
"cellosaurus": "NCIt",
"fairsharing": "FAIRsharing.4cvwxa",
"hl7": "2.16.840.1.113883.6.206",
"integbio": "nbdc02651",
"miriam": "ncit",
"n2t": "ncit",
"obofoundry": "ncit",
"ols": "ncit",
"ontobee": "NCIT",
"prefixcommons": "ncit",
"wikidata": "P1748"
},
"miriam": {
"deprecated": false,
"description": "NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code.",
"homepage": "http://ncit.nci.nih.gov/",
"id": "00000139",
"name": "NCIt",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d+$",
"prefix": "ncit",
"sampleId": "C80519",
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},
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"name": "NCIt at National Cancer Institute",
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},
"name": "NCI Thesaurus",
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"mco",
"ontoavida",
"scdo"
],
"contact": "haendel@ohsu.edu",
"contact.github": "mellybelly",
"contact.label": "Melissa Haendel",
"contact.orcid": "0000-0001-9114-8737",
"deprecated": false,
"description": "NCI Thesaurus (NCIt)is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities. The NCIt OBO Edition aims to increase integration of the NCIt with OBO Library ontologies. NCIt OBO Edition releases should be considered experimental.",
"domain": "health",
"download.obo": "http://purl.obolibrary.org/obo/ncit.obo",
"download.owl": "http://purl.obolibrary.org/obo/ncit.owl",
"homepage": "https://github.com/NCI-Thesaurus/thesaurus-obo-edition",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "NCI Thesaurus OBO Edition",
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"repository": "https://github.com/NCI-Thesaurus/thesaurus-obo-edition"
},
"ols": {
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"homepage": "https://github.com/NCI-Thesaurus/thesaurus-obo-edition",
"name": "NCI Thesaurus OBO Edition",
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"version": "2024-05-07",
"version.iri": "http://purl.obolibrary.org/obo/ncit/releases/2024-05-07/ncit.owl"
},
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"prefix": "NCIT"
},
"owners": [
{
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"partnered": false,
"ror": "040gcmg81"
}
],
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"bioportal": "1032",
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"homepage": "https://cabig.nci.nih.gov/community/concepts/EVS/",
"keywords": [
"thesaurus"
],
"name": "NCI Thesaurus",
"pattern": "^C\\d+$",
"prefix": "ncit",
"pubmed_ids": [
"19789731"
],
"rdf_uri_format": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#$1",
"synonyms": [
"ncithesaurus",
"nci",
"nci2009_04d",
"nci_thesaurus_code"
],
"uri_format": "http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1"
},
"providers": [
{
"code": "evs",
"description": "Links to a no-longer existing OWL file",
"homepage": "https://ncit.nci.nih.gov/ncitbrowser/",
"name": "Legacy NCBI OWL",
"uri_format": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#$1"
}
],
"publications": [
{
"doi": "10.3233/ao-2008-0051",
"pmc": "PMC2753293",
"pubmed": "19789731",
"title": "Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages",
"year": 2008
},
{
"doi": "10.3233/978-1-60750-949-3-33",
"pubmed": "15360769",
"title": "NCI Thesaurus: using science-based terminology to integrate cancer research results",
"year": 2004
}
],
"synonyms": [
"NCI",
"NCI2004_11_17",
"NCIT",
"NCIT_Thesaurus",
"NCIThesaurus",
"NCITm",
"NCITt",
"NCI_Thesaurus",
"NCIt",
"NCit",
"ncithesaurus"
],
"uri_format": "http://purl.obolibrary.org/obo/NCIT_$1",
"wikidata": {
"description": "identifier in the United States National Cancer Institute Thesaurus, vocabulary for clinical care, translational and basic research, etc",
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"C12431",
"C75016"
],
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"name": "NCI Thesaurus ID",
"pattern": "^C\\d{3,7}$",
"prefix": "P1748",
"uri_format": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1",
"uri_format_rdf": "http://purl.obolibrary.org/obo/NCIT_$1"
}
},
"ncro": {
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"download_owl": "http://aber-owl.net/media/ontologies/NCRO/13/ncro.owl",
"homepage": "http://omnisearch.soc.southalabama.edu/OntologyFile.aspx",
"name": "Non-Coding RNA Ontology",
"prefix": "NCRO"
},
"biocontext": {
"prefix": "NCRO"
},
"bioportal": {
"contact": {
"email": "huang@southalabama.edu",
"name": "Jingshan Huang"
},
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"version": "Working version 06102015"
},
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"fairsharing": {
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"Non-coding RNA"
],
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"prefix": "FAIRsharing.vppyga",
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{
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}
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},
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},
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{
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}
],
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},
"ndc": {
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},
"hl7": {
"description": "National Drug Codes System (which includes both the National Drug Codes (NDC) and the National Health Related Item Codes (NHRIC)).",
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"name": "National Drug Codes System",
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"status": "Complete"
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"homepage": "http://www.accessdata.fda.gov/scripts/cder/ndc/",
"id": "00000431",
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],
"sampleId": "0002-1975-61",
"uri_format": "http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1"
},
"n2t": {
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},
"wikidata": {
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"example": [
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"0037-6824",
"50242-090"
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"homepage": "https://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html",
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"prefix": "P3640",
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}
},
"nddf": {
"aberowl": {
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"prefix": "NDDF",
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},
"biolink": {
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"is_obo": false,
"prefix": "NDDF",
"uri_format": "http://purl.bioontology.org/ontology/NDDF/$1"
},
"bioportal": {
"contact": {
"email": "cs@firstdatabank.com",
"name": "First DataBank Customer Support"
},
"description": "National Drug Data File Plus Source Vocabulary",
"name": "National Drug Data File",
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"version": "2023AB"
},
"contributor": {
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
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"example": "002678",
"fairsharing": {
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"description": "The National Drug Data File vocabulary supports clinical research and patient care. Please note that we have been unable to confirm the current status of NDDF and its relationship with FDB MedKnowledge. Until that time, the FAIRsharing team has marked this resource as having an Uncertain status. Please get in touch if you have any information.",
"domains": [
"Drug",
"Chemical entity"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1424",
"name": "National Drug Data File",
"prefix": "FAIRsharing.8qcbs0",
"subjects": [
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"Medicinal Chemistry"
]
},
"hl7": {
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"name": "National Drug Data File",
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"prefix": "2.16.840.1.113883.6.208",
"status": "Complete"
},
"homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDDF",
"license": "https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf",
"mappings": {
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"bioportal": "NDDF",
"fairsharing": "FAIRsharing.8qcbs0",
"hl7": "2.16.840.1.113883.6.208"
},
"name": "National Drug Data File",
"pattern": "^\\d{6}$",
"uri_format": "http://purl.bioontology.org/ontology/NDDF/$1"
},
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"github": "cthoyt",
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},
"description": "The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge.",
"example": "aa78a43f-9c4d-11eb-9e72-0ac135e8bacf",
"fairsharing": {
"abbreviation": "NDEx",
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"name": "Rudolf T. Pillich",
"orcid": "0000-0001-8682-0568"
},
"description": "NDEx is an online commons where scientists can upload, share, and publicly distribute biological networks and pathway models. The NDEx Project maintains a web-accessible public server, a documentation website, provides seamless connectivity to Cytoscape as well as programmatic access using a variety of languages including Python and Java and R. NDEx users can easily create accounts or sign in using their Google credentials thanks to the supported open authentication (OAUTH2) method and mint DOIs for their networks to use in publications or include in other resources for long term access.",
"homepage": "https://www.ndexbio.org",
"license": "https://www.home.ndexbio.org/disclaimer-license",
"name": "The Network Data Exchange",
"prefix": "FAIRsharing.8nq9t6",
"publications": [
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"pubmed_id": 28150243,
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},
{
"doi": "10.1016/j.cels.2015.10.001",
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},
{
"doi": "10.1158/0008-5472.CAN-17-0606",
"pubmed_id": 29092941,
"title": "NDEx 2.0: A Clearinghouse for Research on Cancer Pathways."
},
{
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"pubmed_id": null,
"title": "NDEx: Accessing Network Models and Streamlining Network Biology Workflows"
}
],
"repository": "https://github.com/ndexbio",
"subjects": [
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"Microbiology",
"Epidemiology"
],
"twitter": "NDExProject"
},
"homepage": "https://www.ndexbio.org",
"mappings": {
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"pmc": "PMC8544027",
"pubmed": "34570431",
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},
{
"doi": "10.1158/0008-5472.can-17-0606",
"pmc": "PMC5679399",
"pubmed": "29092941",
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},
{
"doi": "10.1007/978-1-4939-6783-4_13",
"pubmed": "28150243",
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},
{
"doi": "10.1016/j.cels.2015.10.001",
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"title": "NDEx, the Network Data Exchange",
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}
],
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"homepage": "https://home.ndexbio.org/index/",
"name": "Network Data Exchange",
"prefix": "r3d100012690",
"synonyms": [
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],
"xrefs": {
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}
},
"uri_format": "https://www.ndexbio.org/viewer/networks/$1"
},
"ndfrt": {
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"name": "National Drug File - Reference Terminology",
"prefix": "NDFRT",
"version": "2016AB"
},
"bioportal": {
"contact": {
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"name": "Michael J. Lincoln MD"
},
"description": "National Drug File - Reference Terminology Public Inferred Edition, 2008_03_11",
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"name": "National Drug File - Reference Terminology",
"prefix": "NDFRT",
"publication": "http://www.va.gov",
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"github": "cthoyt",
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},
"description": "NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction].",
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"description": "The National Drug File Reference Terminology contains a novel reference hierarchy to describe physiologic effects (PE) of drugs.",
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"Chemical entity"
],
"homepage": "http://bioportal.bioontology.org/ontologies/NDFRT",
"name": "National Drug File",
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}
],
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},
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"status": "Pending"
},
"homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDFRT",
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"prefixcommons": "ndfrt",
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},
"name": "National Drug File - Reference Terminology",
"ontobee": {
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"prefixcommons": {
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"name": "National Drug File",
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],
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"ndf-rt"
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],
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"uri_format_rdf": "http://purl.bioontology.org/ontology/NDFRT/$1"
}
},
"nembase": {
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"deprecated": true,
"mappings": {
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},
"prefixcommons": {
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"DNA"
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},
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"id": "00000744",
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"abbreviation": "neXtProt",
"category": "Organism-specific databases",
"homepage": "https://www.nextprot.org/",
"name": "neXtProt; the human protein knowledge platform",
"prefix": "DB-0161",
"publications": [
{
"doi": "10.1093/nar/gkz995",
"pubmed": "31724716"
}
],
"uri_format": "https://www.nextprot.org/entry/$1"
},
"wikidata": {
"database": "Q6983890"
}
},
"nextprot.family": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "NeXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data. \n(Developed by the SIB Swiss Institute of Bioinformatics)",
"example": "01406",
"homepage": "https://www.nextprot.org/",
"name": "neXtProt family",
"pattern": "^\\d+$",
"synonyms": [
"NXPFA"
],
"twitter": "neXtProt_news",
"uri_format": "https://www.nextprot.org/term/FA-$1"
},
"nfdi4chem.ontocape": {
"comment": "This ontology ecosystem is near unusable",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"description": "OntoCAPE is a large-scale ontology for the domain of Computer Aided Process Engineering (CAPE). Represented in a formal, machine-interpretable ontology language, OntoCAPE captures consensual knowledge of the process engineering domain in a generic way such that it can be reused and shared by groups of people and across software systems. On the basis of OntoCAPE, novel software support for various engineering activities can be developed; possible applications include the systematic management and retrieval of simulation models and design documents, electronic procurement of plant equipment, mathematical modeling, as well as the integration of design data from distributed sources.",
"homepage": "https://www.avt.rwth-aachen.de/cms/AVT/Forschung/Software/~ipts/OntoCape/",
"license": "GPL-2.0",
"name": "Ontology for computer aided process engineering"
},
"nfdi4chem.osmo": {
"comment": "locked behind a private GitLab instance",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"description": "OSMO is an ontologization and extension of MODA, a workflow metadata standard that constitutes a mandatory requirement within a number of European calls and projects in the context of materials modelling. OSMO was developed within the Horizon 2020 project VIMMP (Virtual Materials Marketplace) and is part of a larger effort in ontology engineering driven by the European Materials Modelling Council, with the European Materials and Modelling Ontology (EMMO) as its core. (from https://nfdi4cat.org/services/ontologie-sammlung/)",
"homepage": "https://zenodo.org/record/5237774#.YXq72hxCRGo",
"name": "Ontology for simulation, modelling, and optimization"
},
"ngbo": {
"aberowl": {
"description": "The Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.",
"download_owl": "http://aber-owl.net/media/ontologies/NGBO/2/ngbo.owl",
"homepage": "https://github.com/Dalalghamdi/NGBO",
"name": "Next Generation Biobanking Ontology",
"prefix": "NGBO"
},
"bioportal": {
"contact": {
"email": "dal.alghamdi92@gmail.com",
"name": "Dalia Alghamdi"
},
"description": "The Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.",
"homepage": "https://github.com/Dalalghamdi/NGBO",
"name": "Next Generation Biobanking Ontology",
"prefix": "NGBO",
"version": "2022-10-05"
},
"example": "6000122",
"mappings": {
"aberowl": "NGBO",
"bioportal": "NGBO",
"obofoundry": "ngbo",
"ols": "ngbo",
"ontobee": "NGBO"
},
"obofoundry": {
"contact": "dal.alghamdi92@gmail.com",
"contact.github": "dalalghamdi",
"contact.label": "Dalia Alghamdi",
"contact.orcid": "0000-0002-2801-0767",
"deprecated": false,
"description": "The Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.",
"domain": "investigations",
"download.owl": "http://purl.obolibrary.org/obo/ngbo.owl",
"homepage": "https://github.com/Dalalghamdi/NGBO",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Next Generation Biobanking Ontology",
"preferredPrefix": "NGBO",
"prefix": "ngbo",
"repository": "https://github.com/Dalalghamdi/NGBO"
},
"ols": {
"description": "Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.",
"download_owl": "http://purl.obolibrary.org/obo/ngbo.owl",
"homepage": "https://github.com/Dalalghamdi/NGBO",
"name": "Next generation biobanking ontology(NGBO).",
"prefix": "ngbo",
"version": "2022-10-05",
"version.iri": "http://purl.obolibrary.org/obo/ngbo/2022-10-05/ngbo.owl"
},
"ontobee": {
"library": "Library",
"name": "Next Generation Biobanking Ontology",
"prefix": "NGBO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/NGBO_$1"
},
"ngl": {
"biocontext": {
"prefix": "NGL"
},
"mappings": {
"biocontext": "NGL",
"miriam": "ngl",
"n2t": "ngl"
},
"miriam": {
"deprecated": false,
"description": "NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA.",
"homepage": "https://genelab-data.ndc.nasa.gov/genelab/",
"id": "00000618",
"name": "NASA GeneLab",
"namespaceEmbeddedInLui": false,
"pattern": "^GLDS-\\d+$",
"prefix": "ngl",
"sampleId": "GLDS-141",
"uri_format": "https://genelab-data.ndc.nasa.gov/genelab/accession/$1"
},
"n2t": {
"description": "NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA.",
"example": "GLDS-141",
"homepage": "https://genelab-data.ndc.nasa.gov/genelab/",
"name": "NASA GeneLab",
"namespaceEmbeddedInLui": false,
"pattern": "^GLDS-\\d+$",
"prefix": "ngl",
"uri_format": "https://genelab-data.ndc.nasa.gov/genelab/accession/$1"
}
},
"nhcdr": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://stemcells.nindsgenetics.org",
"name": "NINDS Human Cell and Data Repository",
"prefix": "NHCDR",
"uri_format": "https://stemcells.nindsgenetics.org?line=$1"
},
"example": "ND50028",
"mappings": {
"cellosaurus": "NHCDR"
}
},
"niaest": {
"biocontext": {
"prefix": "NIAEST"
},
"fairsharing": {
"abbreviation": "niaEST",
"contact": {
"email": "dawood@helix.nih.gov",
"name": "Dawood B. Dudekula",
"orcid": "0000-0002-4054-1827"
},
"description": "A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells was assembled. The cDNA libraries are freely distributed to the research community, providing a standard platform for expression studies using microarrays.",
"homepage": "http://lgsun.grc.nia.nih.gov/cDNA/cDNA.html",
"name": "NIA Mouse cDNA Project",
"prefix": "FAIRsharing.xwqg9h",
"publications": [
{
"doi": "10.1016/j.crvi.2003.09.008",
"pubmed_id": 14744099,
"title": "The NIA cDNA project in mouse stem cells and early embryos."
}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"biocontext": "NIAEST",
"fairsharing": "FAIRsharing.xwqg9h",
"miriam": "niaest",
"n2t": "niaest",
"ncbi": "niaEST",
"prefixcommons": "niaest"
},
"miriam": {
"deprecated": false,
"description": "A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones.",
"homepage": "http://lgsun.grc.nia.nih.gov/cDNA/",
"id": "00000305",
"name": "NIAEST",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w\\d{4}\\w\\d{2}(\\-[35])?$",
"prefix": "niaest",
"sampleId": "J0705A10",
"uri_format": "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1"
},
"n2t": {
"description": "A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones.",
"example": "J0705A10",
"homepage": "http://lgsun.grc.nia.nih.gov/cDNA/",
"name": "NIAEST at National Institute on Aging",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w\\d{4}\\w\\d{2}(\\-[35])?$",
"prefix": "niaest",
"uri_format": "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1"
},
"ncbi": {
"example": "L0304H12-3",
"homepage": "http://esbank.nia.nih.gov/",
"name": "NIA Mouse cDNA Project",
"prefix": "niaEST"
},
"prefixcommons": {
"description": "A searchable mouse cDNA library.",
"example": "J0705A10-3",
"homepage": "http://lgsun.grc.nia.nih.gov/cDNA/cDNA.html",
"keywords": [
"DNA"
],
"name": "NIA Mouse cDNA Project",
"pattern": "^[A-Z,0-9]+$",
"prefix": "niaest",
"uri_format": "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1"
},
"publications": [
{
"doi": "10.1016/j.crvi.2003.09.008",
"pubmed": "14744099",
"title": "The NIA cDNA project in mouse stem cells and early embryos",
"year": 2003
}
]
},
"niaid.chemdb": {
"homepage": "http://chemdb.niaid.nih.gov",
"mappings": {
"wikidata": "P2065"
},
"wikidata": {
"description": "ID in NIAID ChemDB",
"example": [
"059486",
"070944",
"112081"
],
"name": "NIAID ChemDB ID",
"prefix": "P2065",
"uri_format": "http://chemdb.niaid.nih.gov/CompoundDetails.aspx?AIDSNO=$1"
}
},
"nif.cell": {
"aberowl": {
"description": "Cell types from NIFSTD",
"download_owl": "http://aber-owl.net/media/ontologies/NIFCELL/15/nifcell.owl",
"homepage": "http://neuinfo.org/",
"name": "Neuroscience Information Framework (NIF) Cell Ontology",
"prefix": "NIFCELL",
"version": "v.1.10 - July 17, 2013"
},
"biocontext": {
"prefix": "NIF_CELL"
},
"bioportal": {
"contact": {
"email": "smtifahim@gmail.com",
"name": "Fahim Imam"
},
"description": "Cell types from NIFSTD",
"homepage": "http://neuinfo.org/",
"name": "Neuroscience Information Framework (NIF) Cell Ontology",
"prefix": "NIFCELL",
"version": "v.1.10 - July 17, 2013"
},
"contact": {
"email": "smtifahim@gmail.com",
"name": "Fahim Imam",
"orcid": "0000-0003-4752-543X"
},
"mappings": {
"aberowl": "NIFCELL",
"biocontext": "NIF_CELL",
"bioportal": "NIFCELL",
"obofoundry": "nif_cell"
},
"obofoundry": {
"contact": "smtifahim@gmail.com",
"contact.label": "Fahim Imam",
"contact.orcid": "0000-0003-4752-543X",
"deprecated": true,
"description": "Neuronal cell types",
"domain": "anatomy and development",
"homepage": "http://neuinfo.org/",
"name": "NIF Cell",
"prefix": "nif_cell"
},
"part_of": "nif"
},
"nif.dysfunction": {
"biocontext": {
"prefix": "NIF_DYSFUNCTION"
},
"contact": {
"email": "smtifahim@gmail.com",
"name": "Fahim Imam",
"orcid": "0000-0003-4752-543X"
},
"mappings": {
"biocontext": "NIF_DYSFUNCTION",
"obofoundry": "nif_dysfunction"
},
"obofoundry": {
"contact": "smtifahim@gmail.com",
"contact.label": "Fahim Imam",
"contact.orcid": "0000-0003-4752-543X",
"deprecated": true,
"domain": "health",
"homepage": "http://neuinfo.org/",
"name": "NIF Dysfunction",
"prefix": "nif_dysfunction"
},
"part_of": "nif"
},
"nif.ext": {
"contact": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"contributor": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"description": "NIFEXT covers IRIs that were \"external\" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed.",
"example": "7123",
"homepage": "https://github.com/SciCrunch/NIF-Ontology",
"license": "CC BY-4.0",
"name": "NIF Standard Ontology: External",
"part_of": "nif",
"pattern": "^\\d+$",
"repository": "https://github.com/SciCrunch/NIF-Ontology",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"synonyms": [
"NIFEXT"
],
"twitter": "SciCrunch",
"uri_format": "http://uri.neuinfo.org/nif/nifstd/nifext_$1"
},
"nif.grossanatomy": {
"biocontext": {
"prefix": "NIF_GROSSANATOMY"
},
"contact": {
"email": "smtifahim@gmail.com",
"name": "Fahim Imam",
"orcid": "0000-0003-4752-543X"
},
"mappings": {
"biocontext": "NIF_GROSSANATOMY",
"obofoundry": "nif_grossanatomy"
},
"obofoundry": {
"contact": "smtifahim@gmail.com",
"contact.label": "Fahim Imam",
"contact.orcid": "0000-0003-4752-543X",
"deprecated": true,
"domain": "anatomy and development",
"homepage": "http://neuinfo.org/",
"name": "NIF Gross Anatomy",
"prefix": "nif_grossanatomy"
},
"part_of": "nif"
},
"nif.std": {
"aberowl": {
"description": "NIF Standard ontology (NIFSTD) is a core component of Neuroscience Information Framework (NIF) project (http://neuinfo.org), a semantically enhanced portal for accessing and integrating neuroscience data, tools and information. NIFSTD includes a set of modular ontologies that provide a comprehensive collection of terminologies to describe neuroscience data and resources.",
"download_owl": "http://aber-owl.net/media/ontologies/NIFSTD/23/nifstd.owl",
"homepage": "http://ontology.neuinfo.org",
"name": "Neuroscience Information Framework (NIF) Standard Ontology",
"prefix": "NIFSTD",
"version": "3.0 - October 16, 2017"
},
"bioportal": {
"contact": {
"email": "tgbugs@gmail.com",
"name": "Tom Gillespie"
},
"description": "NIF Standard ontology (NIFSTD) is a core component of Neuroscience Information Framework (NIF) project (http://neuinfo.org), a semantically enhanced portal for accessing and integrating neuroscience data, tools and information. NIFSTD includes a set of modular ontologies that provide a comprehensive collection of terminologies to describe neuroscience data and resources.",
"homepage": "http://ontology.neuinfo.org",
"name": "Neuroscience Information Framework (NIF) Standard Ontology",
"prefix": "NIFSTD",
"publication": "http://neuinfo.org/about/publications.shtm",
"version": "3.1 - January 15, 2018"
},
"contact": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"contributor": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"description": "NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing.",
"example": "BAMSC981",
"fairsharing": {
"abbreviation": "NIFSTD",
"contact": {
"email": "tgbugs@gmail.com",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"description": "NIF Standard ontology (NIFSTD) is a core component of Neuroscience Information Framework (NIF) project (http://neuinfo.org), a semantically enhanced portal for accessing and integrating neuroscience data, tools and information. NIFSTD includes a set of modular ontologies that provide a comprehensive collection of terminologies to describe neuroscience data and resources.",
"homepage": "http://ontology.neuinfo.org",
"license": "CC-BY-4.0",
"name": "Neuroscience Information Framework Standard Ontology",
"prefix": "FAIRsharing.vgw1m6",
"publications": [
{
"doi": "10.1007/s12021-008-9032-z",
"pubmed": "18975148",
"title": "The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience",
"year": 2008
}
],
"subjects": [
"Neuroscience"
]
},
"homepage": "https://github.com/SciCrunch/NIF-Ontology",
"license": "CC BY-4.0",
"mappings": {
"aberowl": "NIFSTD",
"bioportal": "NIFSTD",
"fairsharing": "FAIRsharing.vgw1m6"
},
"name": "NIF Standard Ontology",
"part_of": "nif",
"pattern": "^BAMSC\\d+$",
"publications": [
{
"doi": "10.1007/s12021-008-9032-z",
"pmc": "PMC2743139",
"pubmed": "18975148",
"title": "The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience",
"year": 2008
}
],
"repository": "https://github.com/SciCrunch/NIF-Ontology",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"synonyms": [
"NIFSTD"
],
"twitter": "SciCrunch",
"uri_format": "http://uri.neuinfo.org/nif/nifstd/$1"
},
"nihhesc": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://grants.nih.gov/stem_cells/registry/current.htm",
"name": "NIH Human Embryonic Stem Cell Registry",
"prefix": "NIHhESC",
"uri_format": "https://grants.nih.gov/stem_cells/registry/current.htm?ID=$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The NIH registration number should be used on all NIH competing applications and annual progress reports to identify the stem cell line proposed for use. Identify the specific line(s) from the Registry using the NIH Registration Number (e.g., 0001), in the specified location in the application (from homepage)",
"example": "NIHhESC-10-0083",
"homepage": "https://grants.nih.gov/stem_cells/registry/current.htm",
"mappings": {
"cellosaurus": "NIHhESC"
},
"name": "NIH Human Embryonic Stem Cell Registry",
"uri_format": "https://grants.nih.gov/stem_cells/registry/current.htm?ID=$1"
},
"nihreporter.project": {
"contributor": {
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"description": "RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding.",
"example": "10343835",
"github_request_issue": 400,
"homepage": "https://reporter.nih.gov/",
"name": "NIH RePORTER",
"pattern": "^\\d+$",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://reporter.nih.gov/project-details/$1"
},
"nist": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species.",
"homepage": "https://webbook.nist.gov/chemistry/",
"name": "NIST Chemistry WebBook",
"no_own_terms": true,
"synonyms": [
"NIST",
"NIST Chemistry WebBook"
]
},
"nist.codata": {
"mappings": {
"wikidata": "P1645"
},
"wikidata": {
"description": "identifier for a physical constant",
"example": [
"c",
"h"
],
"homepage": "http://physics.nist.gov/cuu/Constants/index.html",
"name": "NIST/CODATA ID",
"prefix": "P1645",
"uri_format": "http://physics.nist.gov/cgi-bin/cuu/Value?$1"
}
},
"nkos": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "NKOS is devoted to the discussion of the functional and data model for enabling knowledge organization systems/services (KOS), such as classification systems, thesauri, gazetteers, and ontologies, as networked interactive information services to support the description and retrieval of diverse information resources through the Internet.\n\nKnowledge Organization Systems/Services (KOS) model the underlying semantic structure of a domain. Embodied as Web-based services, they can facilitate resource discovery and retrieval. They act as semantic road maps and make possible a common orientation by indexers and future users (whether human or machine). -- Douglas Tudhope, Traugott Koch (2004).",
"download_rdf": "https://nkos.dublincore.org/nkos.rdf",
"example": "alignedWith",
"homepage": "http://w3id.org/nkos",
"name": "Networked Knowledge Organization Systems/Services/Structures",
"uri_format": "http://w3id.org/nkos/$1"
},
"nlfff": {
"mappings": {
"miriam": "nlfff"
},
"miriam": {
"deprecated": false,
"description": "Nonlinear Force-Free Field Three-Dimensional Magnetic Fields Data of Solar Active Regions Database",
"homepage": "https://nlfff.dataset.deepsolar.space/en/",
"id": "00000988",
"name": "NLFFF Database",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "nlfff",
"sampleId": "345201101230312003",
"uri_format": "http://database.deepsolar.space:18080/dbs/nlfff/$1"
}
},
"nlm": {
"bartoc": {
"abbreviation": "NLM",
"description": "The NLM Classification covers the field of medicine and related sciences. The scheme is a system of classification intended to be used for the shelf arrangement of all library materials, regardless of format. Designed as a broad classification, it is suitable for both large and small library collections and may be adapted to handle specialized collections of any size. The NLM Classification is a system of mixed notation patterned after the Library of Congress (LC) Classification where alphabetical letters which denote broad subject categories are further subdivided by numbers. The NLM Classification utilizes schedules QS-QZ and W-WZ, permanently excluded from the LC Classification Schedules and is intended to be used with the LC schedules which supplement the NLM Classification for subjects bordering on medicine and for general reference materials. The LC schedules for Human Anatomy (QM), Microbiology (QR), and Medicine (R) are not used at all by the National Library of Medicine since they overlap the NLM Classification. The headings for the individual schedules are given in brief form (e.g., WE - Musculoskeletal System; WG - Cardiovascular System) and together they provide an outline of the subjects that constitute the NLM Classification. These headings are interpreted broadly and include the physiological system, the specialty or specialties connected with them, the regions of the body chiefly concerned and subordinate related fields. The Classification is hierarchical, and within each schedule, division by organ usually has priority. Each main schedule, as well as some sections within a schedule, begins with a group of form numbers ranging generally from 1-49 which are used to classify materials by publication type, e.g., dictionaries, atlases, laboratory manuals, etc. The main schedules QS-QZ, W-WY, and WZ (excluding WZ 220-270) are used to classify works published after 1913; the 19th century schedule is used for works published 1801-1913; and WZ 220-270 is used to provide century groupings for works published before 1801 and Americana. Geographic subdivision is provided for certain subjects in the NLM schedules by the application of Table G notations.",
"homepage": "http://www.nlm.nih.gov/class/",
"name": "National Library of Medicine Classification",
"pattern": "^[A-Z]+ [0-9]+(.[0-9](.[A-Z0-9]+)?)?$",
"prefix": "528",
"wikidata_database": "Q986957"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "NLMID",
"uri_format": "https://www.ncbi.nlm.nih.gov/nlmcatalog/?term=$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings.",
"example": "101775319",
"homepage": "https://www.ncbi.nlm.nih.gov/nlmcatalog",
"mappings": {
"bartoc": "528",
"biolink": "NLMID"
},
"name": "National Library of Medicine Catalog",
"pattern": "^\\d+$",
"uri_format": "https://www.ncbi.nlm.nih.gov/nlmcatalog/$1"
},
"nlx.anat": {
"contact": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "NLXANAT covers anatomy terms. Almost all terms are also in Uberon.",
"example": "090201",
"homepage": "https://scicrunch.org/scicrunch/interlex/dashboard",
"keywords": [
"anatomy"
],
"name": "NeuroLex Anatomy",
"part_of": "nif",
"pattern": "^\\d+$",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"twitter": "SciCrunch",
"uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1"
},
"nlx.br": {
"contact": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"contributor": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"description": "NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999).",
"example": "145",
"homepage": "https://github.com/SciCrunch/NIF-Ontology",
"keywords": [
"anatomy",
"brain regions",
"neuroscience"
],
"license": "CC BY-4.0",
"name": "NIF Standard Ontology: Brain Regions",
"part_of": "nif",
"pattern": "^\\d+$",
"repository": "https://github.com/SciCrunch/NIF-Ontology",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"synonyms": [
"NLXBR"
],
"twitter": "SciCrunch",
"uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_br_$1"
},
"nlx.cell": {
"contact": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"contributor": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"description": "NLXCELL conatins cell types with a focus on neuron types.",
"example": "091005",
"homepage": "https://github.com/SciCrunch/NIF-Ontology",
"keywords": [
"cell lines",
"cell types",
"cells",
"neuroscience"
],
"license": "CC BY-4.0",
"name": "NIF Standard Ontology: Cell Types",
"part_of": "nif",
"pattern": "^\\d+$",
"repository": "https://github.com/SciCrunch/NIF-Ontology",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"synonyms": [
"NLXCELL"
],
"twitter": "SciCrunch",
"uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1"
},
"nlx.chem": {
"contact": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"contributor": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"description": "NLXCHEM covers chemicals. Most classes are also in ChEBI.",
"example": "090801",
"homepage": "https://github.com/SciCrunch/NIF-Ontology",
"keywords": [
"chemistry"
],
"license": "CC BY-4.0",
"name": "NIF Standard Ontology: Chemical",
"part_of": "nif",
"pattern": "^\\d+$",
"repository": "https://github.com/SciCrunch/NIF-Ontology",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"synonyms": [
"NLXCHEM"
],
"twitter": "SciCrunch",
"uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1"
},
"nlx.dys": {
"appears_in": [
"mondo"
],
"contact": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc.",
"example": "20090602",
"homepage": "https://scicrunch.org/scicrunch/interlex/dashboard",
"keywords": [
"disease",
"disorders",
"phenotypes"
],
"name": "NeuroLex Dysfunction",
"part_of": "nif",
"pattern": "^\\d+$",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"twitter": "SciCrunch",
"uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1"
},
"nlx.func": {
"contact": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"contributor": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"description": "NLXFUNC covers terms for cognitive function.",
"example": "90801",
"homepage": "https://github.com/SciCrunch/NIF-Ontology",
"keywords": [
"neuroscience"
],
"license": "CC BY-4.0",
"name": "NIF Standard Ontology: Cognitive Function",
"part_of": "nif",
"pattern": "^\\d+$",
"repository": "https://github.com/SciCrunch/NIF-Ontology",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"synonyms": [
"NLXFUNC"
],
"twitter": "SciCrunch",
"uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_func_$1"
},
"nlx.inv": {
"contact": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"contributor": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"description": "NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis.",
"example": "90901",
"homepage": "https://github.com/SciCrunch/NIF-Ontology",
"keywords": [
"data analysis",
"funding agencies"
],
"license": "CC BY-4.0",
"name": "NIF Standard Ontology: Investigations",
"part_of": "nif",
"pattern": "^\\d+$",
"repository": "https://github.com/SciCrunch/NIF-Ontology",
"synonyms": [
"NLXINV"
],
"twitter": "SciCrunch",
"uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1"
},
"nlx.mol": {
"contact": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"contributor": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"description": "NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system.",
"example": "90806",
"homepage": "https://github.com/SciCrunch/NIF-Ontology",
"keywords": [
"biology",
"chemistry",
"neuroscience",
"proteins"
],
"license": "CC BY-4.0",
"name": "NIF Standard Ontology: Molecules",
"part_of": "nif",
"pattern": "^\\d+$",
"repository": "https://github.com/SciCrunch/NIF-Ontology",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"synonyms": [
"NLXMOL"
],
"twitter": "SciCrunch",
"uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1"
},
"nlx.oen": {
"contact": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"contributor": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"description": "NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results).",
"example": "0001000",
"homepage": "https://github.com/SciCrunch/NIF-Ontology",
"keywords": [
"neuroscience"
],
"license": "CC BY-4.0",
"name": "NIF Standard Ontology: OEN Terms in Neurolex",
"part_of": "nif",
"pattern": "^\\d+$",
"repository": "https://github.com/SciCrunch/NIF-Ontology",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"synonyms": [
"NLXOEN"
],
"twitter": "SciCrunch",
"uri_format": "http://uri.neuinfo.org/nif/nifstd/oen_$1"
},
"nlx.org": {
"contact": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"contributor": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"description": "NLXORG covers organisms.",
"example": "090701",
"homepage": "https://github.com/SciCrunch/NIF-Ontology",
"keywords": [
"taxonomy"
],
"license": "CC BY-4.0",
"name": "NIF Standard Ontology: Organisms",
"part_of": "nif",
"pattern": "^\\d+$",
"repository": "https://github.com/SciCrunch/NIF-Ontology",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"synonyms": [
"NLXORG"
],
"twitter": "SciCrunch",
"uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1"
},
"nlx.qual": {
"contact": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"contributor": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"description": "NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO).",
"example": "100810",
"homepage": "https://github.com/SciCrunch/NIF-Ontology",
"keywords": [
"dispositions",
"qualities"
],
"license": "CC BY-4.0",
"name": "NIF Standard Ontology: Qualities",
"part_of": "nif",
"pattern": "^\\d+$",
"repository": "https://github.com/SciCrunch/NIF-Ontology",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"synonyms": [
"NLXQUAL"
],
"twitter": "SciCrunch",
"uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1"
},
"nlx.res": {
"contact": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"contributor": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"description": "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites",
"example": "090924",
"homepage": "https://github.com/SciCrunch/NIF-Ontology",
"keywords": [
"software and information systems"
],
"license": "CC BY-4.0",
"name": "NIF Standard Ontology: Digital Resources",
"part_of": "nif",
"pattern": "^\\d+$",
"repository": "https://github.com/SciCrunch/NIF-Ontology",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"synonyms": [
"NLXRES"
],
"twitter": "SciCrunch",
"uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_res_$1"
},
"nlx.sub": {
"contact": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"contributor": {
"email": "tgbugs@gmail.com",
"github": "tgbugs",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"description": "NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO).",
"example": "090803",
"go": {
"homepage": "http://www.neurolex.org/wiki",
"name": "Neuroscience Information Framework standard ontology, subcellular hierarchy",
"prefix": "NIF_Subcellular",
"uri_format": "http://www.neurolex.org/wiki/$1"
},
"homepage": "https://github.com/SciCrunch/NIF-Ontology",
"keywords": [
"cellular components"
],
"license": "CC BY-4.0",
"mappings": {
"go": "NIF_Subcellular"
},
"name": "NIF Standard Ontology: Subcellular Entities",
"part_of": "nif",
"pattern": "^\\d+$",
"repository": "https://github.com/SciCrunch/NIF-Ontology",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"synonyms": [
"NLXSUB",
"nif_subcellular"
],
"twitter": "SciCrunch",
"uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1"
},
"nmdc": {
"contact": {
"email": "donny@polyneme.xyz",
"github": "dwinston",
"name": "Donny Winston",
"orcid": "0000-0002-8424-0604"
},
"contributor": {
"email": "donny@polyneme.xyz",
"github": "dwinston",
"name": "Donny Winston",
"orcid": "0000-0002-8424-0604"
},
"contributor_extras": [
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"description": "An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem.",
"example": "y3ax-8bq3-60",
"homepage": "https://microbiomedata.org/",
"keywords": [
"microbiome"
],
"mappings": {
"miriam": "nmdc"
},
"miriam": {
"deprecated": false,
"description": "The National Microbiome Data Collaborative (NMDC) is an initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem.",
"homepage": "http://www.lbl.gov/",
"id": "00000837",
"name": "National Microbiome Data Collaborative",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9._~\\-\\:]+$",
"prefix": "nmdc",
"sampleId": "6m4e-1vbv-03",
"uri_format": "https://w3id.org/nmdc/$1"
},
"name": "National Microbiome Data Collaborative",
"pattern": "^.{2,}$",
"providers": [
{
"code": "web",
"description": "Direct link",
"homepage": "https://drs.microbiomedata.org",
"name": "NMDC Web Page",
"uri_format": "https://drs.microbiomedata.org/objects/$1"
}
],
"rdf_uri_format": "https://w3id.org/nmdc/$1",
"references": [
"https://github.com/biopragmatics/bioregistry/pull/982"
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://w3id.org/nmdc/$1",
"wikidata": {
"database": "Q107698738"
}
},
"nmpdr": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"mappings": {
"ncbi": "NMPDR",
"prefixcommons": "nmpdr"
},
"ncbi": {
"example": "fig|306254.1.peg.183",
"homepage": "http://www.nmpdr.org",
"name": "National Microbial Pathogen Data Resource",
"prefix": "NMPDR"
},
"prefixcommons": {
"description": "The NMPDR provided curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma.",
"example": "fig|360108.3.peg.195",
"homepage": "http://www.nmpdr.org",
"keywords": [
"genome"
],
"name": "National Microbial Pathogen Data Resource",
"pattern": "^[A-Z,0-9]+$",
"prefix": "nmpdr",
"uri_format": "http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"nmr": {
"aberowl": {
"description": "This is the new msi-sanctioned nmr CV, created within the COSMOS EU project, to support the nmrML data standard for nuclear magnetic resonance data in metabolomics with meaningful raw data descriptors.",
"download_owl": "http://aber-owl.net/media/ontologies/NMR/12/nmr.owl",
"homepage": "http://nmrml.org/cv/",
"name": "NMR-Controlled Vocabulary",
"prefix": "NMR",
"version": "1.1.0"
},
"biocontext": {
"prefix": "NMR"
},
"bioportal": {
"contact": {
"email": "dschober@ipb-halle.de",
"name": "Daniel Schober"
},
"description": "This is the new msi-sanctioned nmr CV, created within the COSMOS EU project, to support the nmrML data standard for nuclear magnetic resonance data in metabolomics with meaningful raw data descriptors.",
"homepage": "http://nmrml.org/cv/",
"name": "NMR-Controlled Vocabulary",
"prefix": "NMR",
"version": "1.1.0"
},
"contact": {
"email": "schober@imbi.uni-freiburg.de",
"github": "DSchober",
"name": "Daniel Schober",
"orcid": "0000-0001-8014-6648"
},
"download_owl": "https://nmrml.org/cv/stable/nmrCV.owl",
"mappings": {
"aberowl": "NMR",
"biocontext": "NMR",
"bioportal": "NMR",
"miriam": "nmr",
"n2t": "nmr",
"obofoundry": "nmr",
"ols": "nmrcv",
"prefixcommons": "nmr"
},
"miriam": {
"deprecated": false,
"description": "nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi.",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/nmrcv",
"id": "00000639",
"name": "Nuclear Magnetic Resonance Controlled Vocabulary",
"namespaceEmbeddedInLui": true,
"pattern": "^NMR:\\d+$",
"prefix": "nmr",
"sampleId": "1000003",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/nmrcv/terms?short_form=NMR:$1"
},
"n2t": {
"description": "nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi.",
"example": "1000003",
"homepage": "https://www.ebi.ac.uk/ols/ontologies/nmrcv",
"name": "NMR through OLS",
"namespaceEmbeddedInLui": true,
"pattern": "^NMR:\\d+$",
"prefix": "nmr",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1"
},
"obofoundry": {
"contact": "schober@imbi.uni-freiburg.de",
"contact.label": "Schober Daniel",
"deprecated": true,
"description": "Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation.",
"domain": "investigations",
"download.owl": "http://purl.obolibrary.org/obo/nmr.owl",
"homepage": "http://msi-ontology.sourceforge.net/",
"name": "NMR-instrument specific component of metabolomics investigations",
"prefix": "nmr"
},
"ols": {
"description": "This artefact is an MSI-approved controlled vocabulary primarily developed under COSMOS EU and PhenoMeNal EU governance. The nmrCV is supporting the nmrML XML format with standardized terms. nmrML is a vendor agnostic open access NMR raw data standard. Its primaly role is analogous to the mzCV for the PSI-approved mzML XML format. It uses BFO2.0 as its Top level. This CV was derived from two predecessors (The NMR CV from the David Wishart Group, developed by Joseph Cruz) and the MSI nmr CV developed by Daniel Schober at the EBI. This simple taxonomy of terms (no DL semantics used) serves the nuclear magnetic resonance markup language (nmrML) with meaningful descriptors to amend the nmrML xml file with CV terms. Metabolomics scientists are encouraged to use this CV to annotrate their raw and experimental context data, i.e. within nmrML. The approach to have an exchange syntax mixed of an xsd and CV stems from the PSI mzML effort. The reason to branch out from an xsd into a CV is, that in areas where the terminology is likely to change faster than the nmrML xsd could be updated and aligned, an externally and decentrallised maintained CV can accompensate for such dynamics in a more flexible way. A second reason for this set-up is that semantic validity of CV terms used in an nmrML XML instance (allowed CV terms, position/relation to each other, cardinality) can be validated by rule-based proprietary validators: By means of cardinality specifications and XPath expressions defined in an XML mapping file (an instances of the CvMappingRules.xsd ), one can define what ontology terms are allowed in a specific location of the data model.",
"download_owl": "http://nmrml.org/cv/stable/nmrCV.owl",
"homepage": "http://nmrml.org/cv/",
"name": "nuclear magnetic resonance CV",
"prefix": "nmrcv",
"version": "1.1.0"
},
"pattern": "^\\d+$",
"prefixcommons": {
"bioportal": "1033",
"description": "Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation.",
"example": "NMR_400113",
"homepage": "http://msi-ontology.sourceforge.net/",
"keywords": [
"owl",
"nmr"
],
"name": "NMR-instrument specific component of metabolomics investigations",
"pattern": "^NMR_\\d+$",
"prefix": "nmr",
"rdf_uri_format": "http://msi-ontology.sourceforge.net/ontology/NMR.owl#$1",
"synonyms": [
"msi.nmr"
]
},
"synonyms": [
"nmrcv"
]
},
"nmrshiftdb2": {
"contributor_extras": [
{
"email": "b.gyori@northeastern.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
}
],
"fairsharing": {
"abbreviation": "nmrshiftdb2",
"contact": {
"email": "stefan.kuhn@dmu.ac.uk",
"name": "Stefan Kuhn",
"orcid": "0000-0002-5990-4157"
},
"description": "nmrshiftdb2 is an NMR database for organic structures and their nuclear magnetic resonance (NMR) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. It also features peer-reviewed submission of datasets by its users. The nmrshiftdb2 software is open source, the data is published under an open content license.",
"homepage": "https://nmrshiftdb.nmr.uni-koeln.de/",
"name": "nmrshiftdb2",
"prefix": "FAIRsharing.nYaZ1N",
"publications": [
{
"doi": "10.1021/ci0341363",
"pubmed_id": 14632418,
"title": "NMRShiftDB-constructing a free chemical information system with open-source components."
},
{
"doi": "10.1002/mrc.4263",
"pubmed_id": 25998807,
"title": "Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories."
},
{
"doi": "10.1016/j.phytochem.2004.08.027",
"pubmed_id": 15464159,
"title": "NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database."
}
],
"subjects": [
"Analytical Chemistry"
]
},
"mappings": {
"fairsharing": "FAIRsharing.nYaZ1N",
"miriam": "nmrshiftdb2",
"re3data": "r3d100010316",
"wikidata": "P9405"
},
"miriam": {
"deprecated": false,
"description": "NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties.",
"homepage": "https://nmrshiftdb.nmr.uni-koeln.de",
"id": "00000748",
"name": "NMR Shift Database",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "nmrshiftdb2",
"sampleId": "234",
"uri_format": "https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1"
},
"name": "NMRShiftDB structure",
"publications": [
{
"doi": "10.1002/mrc.4263",
"pubmed": "25998807",
"title": "Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories",
"year": 2015
},
{
"doi": "10.1016/j.phytochem.2004.08.027",
"pubmed": "15464159",
"title": "NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database",
"year": 2004
},
{
"doi": "10.1021/ci0341363",
"pubmed": "14632418",
"title": "NMRShiftDB-constructing a free chemical information system with open-source components",
"year": 2003
}
],
"re3data": {
"description": "nmrshiftdb is a NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. Last not least, it features peer-reviewed submission of datasets by its users. The nmrshiftdb2 software is open source, the data is published under an open content license. Please consult the documentation for more detailed information. nmrshiftdb2 is the continuation of the NMRShiftDB project with additional data and bugfixes and changes in the software.",
"homepage": "https://nmrshiftdb.nmr.uni-koeln.de/",
"name": "NMRshiftDB",
"prefix": "r3d100010316",
"xrefs": {
"fairsharing": "FAIRsharing.nYaZ1N",
"omics": "18926"
}
},
"synonyms": [
"NMRShiftDB"
],
"wikidata": {
"description": "structure identifiers in the NMRShiftDB",
"example": [
"20143612",
"20188613",
"20213347"
],
"homepage": "https://nmrshiftdb.nmr.uni-koeln.de/",
"name": "NMRShiftDB structure ID",
"pattern": "^\\d+$",
"prefix": "P9405",
"uri_format": "https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1"
}
},
"noaa": {
"contributor": {
"email": "meghan.balk@gmail.com",
"github": "megbalk",
"name": "Meghan Balk",
"orcid": "0000-0003-2699-3066"
},
"description": "Identifier for a species on the noaa fisheries website",
"example": "long-finned-pilot-whale",
"github_request_issue": 456,
"homepage": "https://www.fisheries.noaa.gov/species-directory",
"mappings": {
"wikidata": "P6049"
},
"name": "NOAA Fisheries Species Directory",
"pattern": "^[a-z]+(\\-[a-z]+)*$",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://www.fisheries.noaa.gov/species/$1",
"wikidata": {
"description": "identifier for a species on the NOAA Fisheries website",
"example": [
"alaska-snow-crab",
"blue-mussel",
"long-finned-pilot-whale"
],
"homepage": "https://www.fisheries.noaa.gov/species-directory",
"name": "NOAA Fisheries Species Directory ID",
"pattern": "^[a-z]+(\\-[a-z]+)*$",
"prefix": "P6049",
"uri_format": "https://www.fisheries.noaa.gov/species/$1"
}
},
"noaa.cameo": {
"description": "CAMEO Chemicals is a database of hazardous chemical datasheets that emergency responders and planners can use to get response recommendations and predict hazardsβsuch as explosions or toxic fumes.",
"mappings": {
"wikidata": "P11931"
},
"wikidata": {
"database": "http://www.wikidata.org/.well-known/genid/4a2681f823464601994d25a19df58aae",
"description": "chemical in the database supplied by National Oceanic and Atmospheric Administration",
"example": [
"19757",
"667",
"8754"
],
"homepage": "https://cameochemicals.noaa.gov",
"name": "CAMEO Chemicals ID",
"pattern": "^\\d*$",
"prefix": "P11931",
"uri_format": "https://cameochemicals.noaa.gov/chemical/$1"
}
},
"nomen": {
"aberowl": {
"description": "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature.",
"download_owl": "http://aber-owl.net/media/ontologies/NOMEN/9/nomen.owl",
"homepage": "https://github.com/SpeciesFileGroup/nomen",
"name": "NOMEN - A nomenclatural ontology for biological names",
"prefix": "NOMEN"
},
"bioportal": {
"contact": {
"email": "diapriid@gmail.com",
"name": "Matt Yoder"
},
"description": "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature.",
"homepage": "https://github.com/SpeciesFileGroup/nomen",
"name": "NOMEN - A nomenclatural ontology for biological names",
"prefix": "NOMEN"
},
"example": "0000295",
"mappings": {
"aberowl": "NOMEN",
"bioportal": "NOMEN",
"obofoundry": "nomen",
"ols": "nomen",
"ontobee": "NOMEN"
},
"name": "A nomenclatural ontology for biological names",
"obofoundry": {
"contact": "diapriid@gmail.com",
"contact.github": "mjy",
"contact.label": "Matt Yoder",
"contact.orcid": "0000-0002-5640-5491",
"deprecated": false,
"description": "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature.",
"domain": "information",
"download.owl": "http://purl.obolibrary.org/obo/nomen.owl",
"homepage": "https://github.com/SpeciesFileGroup/nomen",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "NOMEN - A nomenclatural ontology for biological names",
"preferredPrefix": "NOMEN",
"prefix": "nomen",
"repository": "https://github.com/SpeciesFileGroup/nomen"
},
"ols": {
"description": "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature.",
"download_owl": "http://purl.obolibrary.org/obo/nomen.owl",
"homepage": "https://github.com/SpeciesFileGroup/nomen",
"name": "NOMEN - A nomenclatural ontology for biological names",
"prefix": "nomen"
},
"ontobee": {
"library": "Library",
"name": "NOMEN - A nomenclatural ontology for biological names",
"prefix": "NOMEN"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/NOMEN_$1"
},
"noncodev3": {
"biocontext": {
"prefix": "NONCODEV3"
},
"contact": {
"email": "biozy@ict.ac.cn",
"name": "Yi Zhao",
"orcid": "0000-0001-6049-8347"
},
"mappings": {
"biocontext": "NONCODEV3",
"miriam": "noncodev3",
"n2t": "noncodev3",
"prefixcommons": "noncode"
},
"miriam": {
"deprecated": false,
"description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4.",
"homepage": "http://www.noncode.org/",
"id": "00000248",
"name": "NONCODE v3",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "noncodev3",
"sampleId": "377550",
"uri_format": "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1"
},
"n2t": {
"description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4.",
"example": "377550",
"homepage": "http://www.noncode.org/",
"name": "NONCODE at Chinese Academy of Sciences",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "noncodev3",
"uri_format": "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1"
},
"prefixcommons": {
"description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics.",
"example": "377550",
"homepage": "http://www.noncode.org/",
"keywords": [
"expression",
"nucleotide"
],
"name": "NONCODE",
"pattern": "^\\d+$",
"prefix": "noncode",
"pubmed_ids": [
"22135294"
],
"uri_format": "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkr1175",
"pmc": "PMC3245065",
"pubmed": "22135294",
"title": "NONCODE v3.0: integrative annotation of long noncoding RNAs",
"year": 2011
}
]
},
"noncodev4.gene": {
"biocontext": {
"prefix": "NONCODEV4.GENE"
},
"mappings": {
"biocontext": "NONCODEV4.GENE",
"miriam": "noncodev4.gene",
"n2t": "noncodev4.gene"
},
"miriam": {
"deprecated": false,
"description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions.",
"homepage": "http://www.bioinfo.org/NONCODEv4/",
"id": "00000480",
"name": "NONCODE v4 Gene",
"namespaceEmbeddedInLui": false,
"pattern": "^NONHSAG\\d{5}$",
"prefix": "noncodev4.gene",
"sampleId": "NONHSAG00001",
"uri_format": "http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1"
},
"n2t": {
"description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions.",
"example": "NONHSAG00001",
"homepage": "http://www.bioinfo.org/NONCODEv4/",
"name": "NONCODE v4 Gene at Chinese Academy of Sciences",
"namespaceEmbeddedInLui": false,
"pattern": "^NONHSAG\\d{5}$",
"prefix": "noncodev4.gene",
"uri_format": "http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1"
}
},
"noncodev4.rna": {
"biocontext": {
"prefix": "NONCODEV4.RNA"
},
"mappings": {
"biocontext": "NONCODEV4.RNA",
"miriam": "noncodev4.rna",
"n2t": "noncodev4.rna"
},
"miriam": {
"deprecated": false,
"description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts.",
"homepage": "http://www.bioinfo.org/NONCODEv4/",
"id": "00000481",
"name": "NONCODE v4 Transcript",
"namespaceEmbeddedInLui": false,
"pattern": "^NONHSAT\\d{6}$",
"prefix": "noncodev4.rna",
"sampleId": "NONHSAT000001",
"uri_format": "http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1"
},
"n2t": {
"description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts.",
"example": "NONHSAT000001",
"homepage": "http://www.bioinfo.org/NONCODEv4/",
"name": "NONCODE v4 Transcript at Chinese Academy of Sciences",
"namespaceEmbeddedInLui": false,
"pattern": "^NONHSAT\\d{6}$",
"prefix": "noncodev4.rna",
"uri_format": "http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1"
}
},
"norine": {
"biocontext": {
"prefix": "NORINE"
},
"contact": {
"email": "maude.pupin@univ-lille.fr",
"name": "Maude Pupin",
"orcid": "0000-0003-3197-0715"
},
"fairsharing": {
"abbreviation": "NORINE",
"description": "Norine is a platform that includes a database of nonribosomal peptides together with tools for their analysis.",
"homepage": "http://norine.univ-lille.fr/norine/",
"license": "CC BY-NC-SA 4.0",
"name": "Non-Ribosomal Peptides Database",
"prefix": "FAIRsharing.gf8yhy",
"publications": [
{
"doi": "10.1093/nar/gkm792",
"pubmed_id": 17913739,
"title": "NORINE: a database of nonribosomal peptides."
},
{
"doi": "10.1093/nar/gkz1000",
"pubmed_id": null,
"title": "Norine: update of the nonribosomal peptide resource"
}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"biocontext": "NORINE",
"fairsharing": "FAIRsharing.gf8yhy",
"miriam": "norine",
"n2t": "norine",
"prefixcommons": "norine"
},
"miriam": {
"deprecated": false,
"description": "Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings.",
"homepage": "http://bioinfo.lifl.fr/norine/",
"id": "00000498",
"name": "NORINE",
"namespaceEmbeddedInLui": false,
"pattern": "^NOR\\d+$",
"prefix": "norine",
"sampleId": "NOR00681",
"uri_format": "http://bioinfo.lifl.fr/norine/result.jsp?ID=$1"
},
"n2t": {
"description": "Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings.",
"example": "NOR00681",
"homepage": "http://bioinfo.lifl.fr/norine/",
"name": "NORINE at Computer Science Laboratory of Lille",
"namespaceEmbeddedInLui": false,
"pattern": "^NOR\\d+$",
"prefix": "norine",
"uri_format": "http://bioinfo.lifl.fr/norine/result.jsp?ID=$1"
},
"name": "Nonribosomal Peptides Database",
"prefixcommons": {
"description": "Norine is a platform that includes a database of nonribosomal peptides together with tools for their analysis. Norine currently contains more than 1000 peptides.",
"example": "NOR00681",
"homepage": "http://bioinfo.lifl.fr/norine/",
"keywords": [
"protein"
],
"name": "Non-Ribosomal Peptides Database",
"pattern": "^NOR\\d+$",
"prefix": "norine",
"uri_format": "http://bioinfo.lifl.fr/norine/result.jsp?ID=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkz1000",
"pmc": "PMC7145658",
"pubmed": "31691799",
"title": "Norine: update of the nonribosomal peptide resource",
"year": 2020
},
{
"doi": "10.1093/nar/gkm792",
"pmc": "PMC2238963",
"pubmed": "17913739",
"title": "NORINE: a database of nonribosomal peptides",
"year": 2007
}
]
},
"novus": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A vendor of antibodies and other biologics",
"example": "nb100-56351",
"homepage": "https://www.novusbio.com",
"name": "Novus Biologicals",
"uri_format": "https://www.novusbio.com/products/$1"
},
"npass": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data.\n",
"example": "NPC139585",
"homepage": "http://bidd.group/NPASS/",
"name": "Natural Product Activity and Species Source Database",
"pattern": "^NPC\\d+$"
},
"npm": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A repository of software packages written in Javascript, TypeScript, and related.",
"example": "@biopragmatics/curies",
"example_extras": [
"ansi-pad"
],
"homepage": "https://www.npmjs.com",
"name": "Node Package Manager",
"uri_format": "https://www.npmjs.com/package/$1"
},
"npo": {
"aberowl": {
"description": "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.",
"download_owl": "http://aber-owl.net/media/ontologies/NPO/31/npo.owl",
"homepage": "http://www.nano-ontology.org",
"name": "NanoParticle Ontology",
"prefix": "NPO",
"version": "2011-12-08 (yyyy-mm-dd)"
},
"bioportal": {
"contact": {
"email": "nathan.baker@pnl.gov",
"name": "Nathan Baker"
},
"description": "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.",
"homepage": "http://www.nano-ontology.org",
"name": "NanoParticle Ontology",
"prefix": "NPO",
"publication": "http://www.nano-ontology.org",
"version": "2011-12-08 (yyyy-mm-dd)"
},
"contact": {
"email": "nathan.baker@pnnl.gov",
"github": "sobolevnrm",
"name": "Nathan Baker",
"orcid": "0000-0002-5892-6506"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.",
"example": "1731",
"fairsharing": {
"abbreviation": "NPO",
"contact": {
"email": "nathan.baker@pnl.gov",
"name": "Nathan Baker",
"orcid": "0000-0002-5892-6506"
},
"description": "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.",
"domains": [
"Molecular entity",
"Nanoparticle",
"Structure"
],
"homepage": "http://www.nano-ontology.org",
"name": "NanoParticle Ontology",
"prefix": "FAIRsharing.vy0p71",
"publications": [
{
"doi": "10.1016/j.jbi.2010.03.001",
"pubmed": "20211274",
"title": "NanoParticle Ontology for cancer nanotechnology research",
"year": 2010
}
],
"subjects": [
"Life Science"
]
},
"homepage": "https://bioportal.bioontology.org/ontologies/NPO",
"mappings": {
"aberowl": "NPO",
"bioportal": "NPO",
"fairsharing": "FAIRsharing.vy0p71"
},
"name": "NanoParticle Ontology",
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1016/j.jbi.2010.03.001",
"pmc": "PMC3042056",
"pubmed": "20211274",
"title": "NanoParticle Ontology for cancer nanotechnology research",
"year": 2010
}
],
"repository": "https://github.com/sobolevnrm/npo",
"uri_format": "http://purl.bioontology.org/ontology/npo#NPO_$1"
},
"nrfc": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://mail.nbfgr.res.in/nrfc/",
"name": "National Repository of Fish Cell Line",
"prefix": "NRFC"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The NRFC was established at ICAR-National Bureau of Fish Genetic Resources, Lucknow in the form of a research project entitled βEstablishment of a National Repository at NBFGR, Lucknow for conservation and characterization of fish cell linesβ during 09 November, 2010 to 08 November, 2014 with the financial support from Department of Biotechnology, Govt. of India, New Delhi. NRFC aims to receive, authenticate, store and supply the fish cell lines to the researchers and academicians for Research & Development works and to serve as a National Referral Centre for fish cell lines in the country. NRFC also aims to provide need-based support for training and education to stakeholders. (from homepage)",
"example": "NRFC051",
"homepage": "https://mail.nbfgr.res.in/nrfc/index.php",
"mappings": {
"cellosaurus": "NRFC"
},
"name": "National Repository of Fish Cell Lines",
"pattern": "^NRFC\\d+$"
},
"nsc": {
"cheminf": {
"description": "Identifier used by the Cancer Chemotherapy National Service Center.",
"name": "National Service Center number",
"obsolete": false,
"prefix": "000565"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"example": "27223",
"homepage": "https://wiki.nci.nih.gov/display/NCIDTPdata/Chemical+Data",
"mappings": {
"cheminf": "000565"
},
"name": "USA National Service Center Number",
"pattern": "^\\d+$",
"references": [
"https://pubchem.ncbi.nlm.nih.gov/source/DTP/NCI"
],
"uri_format": "https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist=$1"
},
"nsf.award": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Information about research projects that NSF has funded since 1989 can be found by searching the Award Abstracts database. The information includes abstracts that describe the research, and names of principal investigators and their institutions. The database includes both completed and in-process research.",
"example": "1458400",
"homepage": "https://www.nsf.gov/awards/about.jsp",
"name": "National Science Foundation Award",
"pattern": "^\\d+$",
"uri_format": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=$1"
},
"nsrrc": {
"description": "Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research. [from RRID]",
"example": "0005",
"mappings": {
"rrid": "NSRRC"
},
"pattern": "^\\d+$",
"rrid": {
"homepage": "http://www.nsrrc.missouri.edu/",
"keywords": [
"biomaterial manufacture",
"breeding",
"consulting",
"cryopreservation",
"fetal fibroblast",
"fetus",
"fibroblast",
"genetically modified pig",
"genetics",
"genome",
"genotyping",
"health monitoring",
"live animal",
"phenotyping",
"pig",
"reproduction",
"tissue"
],
"name": "National Swine Resource and Research Center",
"prefix": "NSRRC",
"scr": "006855"
},
"uri_format": "https://nsrrc.missouri.edu/nsrrc$1info/"
},
"nucc.characteristic": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Provider Characteristics code set is for use with health care provider information for enrollment and credentialing transactions and their corresponding responses. It is intended to provide codified responses to questions presented to a health care provider applying to or registering with an entity and to report the outcome of such application or registration. It may also be used for responses to inquiries regarding provider participation or registration in a program or plan.",
"example": "2A",
"example_extras": [
"11",
"10"
],
"homepage": "https://nucc.org/index.php/code-sets-mainmenu-41/provider-characteristics-mainmenu-39",
"name": "National Uniform Claim Committee Characteristic",
"pattern": "^\\d(\\d|\\w)$"
},
"nucc.taxonomy": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Health Care Provider Taxonomy code set is an external, nonmedical data code set designed for use in an electronic environment, specifically within the ASC X12N Health Care transactions. This includes the transactions mandated under HIPAA.\n\nThe taxonomy code is a unique alphanumeric code, ten characters in length. The code set is structured into three distinct \"Levels\" including Provider Grouping, Classification, and Area of Specialization.\n\n - **Level I, Provider Grouping** A major grouping of service(s) or occupation(s) of health care providers. For example: Allopathic & Osteopathic Physicians, Dental Providers, Hospitals, etc.\n - **Level II, Classification** A more specific service or occupation related to the Provider Grouping. For example, the Classification for Allopathic & Osteopathic Physicians is based upon the General Specialty Certificates as issued by the appropriate national boards. The following boards will however, have their general certificates appear as Level III areas of specialization strictly due to display limitations of the code set for Boards that have multiple general certificates: Medical Genetics, Preventive Medicine, Psychiatry & Neurology, Radiology, Surgery, Otolaryngology, Pathology.\n - **Level III, Area of Specialization** A more specialized area of the Classification in which a provider chooses to practice or make services available. For example, the Area of Specialization for provider grouping Allopathic & Osteopathic Physicians is based upon the Subspecialty Certificates as issued by the appropriate national boards.",
"example": "207LH0002X",
"homepage": "https://taxonomy.nucc.org",
"name": "National Uniform Claim Committee Taxonomy",
"pattern": "^\\d{3}\\w(\\w|\\d_)\\d{4}X$",
"references": [
"https://www.nucc.org/images/stories/CSV/nucc_taxonomy_221.csv",
"https://www.nucc.org"
]
},
"nucleardb": {
"biocontext": {
"prefix": "NUCLEARBD"
},
"comment": "Note that the typo from MIRIAM has spread to several other sources",
"contact": {
"email": "vriend@cmbi.ru.nl",
"name": "Gert Vriend",
"orcid": "0000-0002-1067-7053"
},
"integbio": {
"alt_name": "information system for Nuclear Receptors",
"description": "NucleaRDB is a database of nuclear hormone receptors. The database contains gene and protein sequence, mutation, and ligand binding information. Users can search or browse receptors by family or structure. BLAST search and an alignment builidng tool are also available.",
"fairsharing": "biodbcore-000077",
"homepage": "http://www.receptors.org/nucleardb/",
"information_keywords": [
"Sequence"
],
"maintainer": "University of California, San Francisco, Centre for Molecular and Biomolecular Informatics",
"name": "NucleaRDB",
"prefix": "nbdc00599",
"pubmeds": [
"11125133"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"mappings": {
"biocontext": "NUCLEARBD",
"integbio": "nbdc00599",
"miriam": "nuclearbd",
"n2t": "nuclearbd",
"prefixcommons": "nucleardb"
},
"miriam": {
"deprecated": false,
"description": "NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs.",
"homepage": "http://www.receptors.org/nucleardb/",
"id": "00000356",
"name": "NucleaRDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+\\_\\w+$",
"prefix": "nuclearbd",
"sampleId": "prgr_human",
"uri_format": "http://www.receptors.org/nucleardb/proteins/$1"
},
"n2t": {
"description": "NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs.",
"example": "prgr_human",
"homepage": "http://www.receptors.org/nucleardb/",
"name": "NucleaRDB at Radboud University Nijmegen Medical Centre",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+\\_\\w+$",
"prefix": "nuclearbd",
"uri_format": "http://www.receptors.org/nucleardb/proteins/$1"
},
"prefixcommons": {
"description": "The NucleaRDB is a part of a project devoted to build Molecular Class-Specific Information Systems (MCSIS) to provide, disseminate and harvest heterogeneous data. The NucleaRDB was built using the software developed for the GPCRDB.",
"example": "prgr_human",
"homepage": "http://www.receptors.org/NR/",
"keywords": [
"classification"
],
"name": "NucleaRDB: An Information System for Nuclear Receptors",
"pattern": "^\\w+\\_\\w+$",
"prefix": "nucleardb",
"pubmed_ids": [
"22064856"
],
"uri_format": "http://www.receptors.org/NR/seq/DR/$1.html"
},
"publications": [
{
"doi": "10.1093/nar/gkr960",
"pmc": "PMC3245090",
"pubmed": "22064856",
"title": "NucleaRDB: information system for nuclear receptors",
"year": 2011
}
],
"synonyms": [
"nuclearbd"
]
},
"nucleotide": {
"has_canonical": "insdc",
"integbio": {
"description": "Nucleotide is a database of nucleic acid sequences. The database contains sequence entities from a variety of sources covering hundreds of organisms. The major resources GenBank and RefSeq repositories are both available through Nucleotide. Users can submit nucleotide sequences and data is available for download.",
"homepage": "http://www.ncbi.nlm.nih.gov/nuccore",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "Nucleotide",
"prefix": "nbdc00600",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation"
]
},
"mappings": {
"integbio": "nbdc00600",
"miriam": "nucleotide"
},
"miriam": {
"deprecated": false,
"description": "The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.",
"homepage": "https://www.ncbi.nlm.nih.gov/",
"id": "00000882",
"name": "Nucleotide",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-zA-Z0-9_\\.]+$",
"prefix": "nucleotide",
"sampleId": "880798137",
"uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1"
}
},
"nxr": {
"description": "National stock center for X. laevis and X. tropicalis and training center for advanced technologies (e.g. husbandry, cell biology, imaging, genetics, transgenesis, genomics). [from RRID]",
"example": "0024",
"mappings": {
"rrid": "NXR"
},
"pattern": "^\\d+$",
"rrid": {
"homepage": "http://www.mbl.edu/xenopus/",
"keywords": [
"Xenopus",
"laevis",
"tropicalis"
],
"name": "National Xenopus Resource",
"prefix": "NXR",
"scr": "013731"
},
"uri_format": "https://scicrunch.org/resolver/RRID:NXR_$1"
},
"nztcs": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor_extras": [
{
"email": "sumirp77@gmail.com",
"github": "SumirHPandit",
"name": "Sumir Pandit",
"orcid": "0000-0002-1216-4761"
}
],
"keywords": [
"taxon",
"taxonomy"
],
"license": "CC-BY-4.0",
"mappings": {
"wikidata": "P9889"
},
"name": "New Zealand Threat Classification System",
"references": [
"https://github.com/biopragmatics/bioregistry/pull/1083"
],
"wikidata": {
"description": "identifier for species classified under the New Zealand Threat Classification System",
"example": [
"11061",
"11974",
"13104",
"26916",
"3004"
],
"homepage": "https://nztcs.org.nz/",
"name": "NZTCS ID",
"pattern": "^[1-9]\\d{3,7}$",
"prefix": "P9889",
"uri_format": "https://nztcs.org.nz/nztcs-species/$1"
}
},
"oa": {
"aberowl": {
"description": "The Web Annotation Data Model specification describes a structured model and format to enable annotations to be shared and reused across different hardware and software platforms. Annotations are typically used to convey information about a resource or associations between resources. Simple examples include a comment or tag on a single web page or image, or a blog post about a news article.",
"download_owl": "http://aber-owl.net/media/ontologies/OA/4/oa.owl",
"homepage": "https://www.w3.org/TR/annotation-model/",
"name": "Web Annotation Ontology",
"prefix": "OA",
"version": "2016-11-12T21:28:11Z"
},
"biocontext": {
"prefix": "oa",
"uri_format": "http://www.w3.org/ns/oa#$1"
},
"bioportal": {
"description": "The Web Annotation Data Model specification describes a structured model and format to enable annotations to be shared and reused across different hardware and software platforms. Annotations are typically used to convey information about a resource or associations between resources. Simple examples include a comment or tag on a single web page or image, or a blog post about a news article.",
"homepage": "https://www.w3.org/TR/annotation-model/",
"name": "Web Annotation Ontology",
"prefix": "OA",
"version": "2016-11-12T21:28:11Z"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture.",
"example": "sourceDateStart",
"homepage": "http://www.w3.org/ns/oa",
"lov": {
"description": "The Open Annotation Core Data Model specifies an interoperable framework for creating associations between related resources, annotations, using a methodology that conforms to the Architecture of the World Wide Web. This ontology is a non-normative OWL formalization of the textual OA specification at http://www.openannotation.org/spec/core/20130208/index.html",
"homepage": "http://www.w3.org/ns/oa#",
"keywords": [
"Quality"
],
"modified": "2016-11-12",
"name": "Open Annotation Data Model",
"prefix": "oa",
"uri_prefix": "http://www.w3.org/ns/oa#$1"
},
"mappings": {
"aberowl": "OA",
"biocontext": "oa",
"bioportal": "OA",
"lov": "oa",
"zazuko": "oa"
},
"name": "Web Annotation Ontology",
"preferred_prefix": "oa",
"uri_format": "http://www.w3.org/ns/oa#$1",
"zazuko": {
"prefix": "oa",
"uri_format": "http://www.w3.org/ns/oa#$1"
}
},
"oae": {
"aberowl": {
"description": "A biomedical ontology in the domain of adverse events",
"download_owl": "http://aber-owl.net/media/ontologies/OAE/178/oae.owl",
"homepage": "https://github.com/OAE-ontology/OAE/",
"name": "Ontology of Adverse Events",
"prefix": "OAE"
},
"biocontext": {
"prefix": "OAE"
},
"bioportal": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun \"Oliver\" He"
},
"description": "The Ontology of Adverse Events (OAE) is a community-based biomedical ontology in the domain of adverse events. OAE is developed to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. Its development follows the OBO Foundry principles.",
"homepage": "http://www.oae-ontology.org/",
"name": "Ontology of Adverse Events",
"prefix": "OAE",
"publication": "http://www.ncbi.nlm.nih.gov/pubmed/25093068",
"version": "1.2.47"
},
"example": "0002959",
"fairsharing": {
"abbreviation": "OAE",
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun \"Oliver\" He",
"orcid": "0000-0001-9189-9661"
},
"description": "The Ontology of Adverse Events (OAE) is a community-driven ontology that is developed to standardize and integrate data on biomedical adverse events (e.g., vaccine and drug adverse events) and support computer-assisted reasoning. As a result of a medical intervention, events may occur which lie outside the intended consequences of the intervention. Some of these events are adverse events, in the sense that they are pathological bodily processes. For many such adverse events it is unclear whether they are causal consequences of the medical intervention which preceded them, since adverse events may also occur due to other reasons (for example a natural viral infection). OAE was created to represent the whole process from initial medical intervention to subsequent outcomes.",
"domains": [
"Drug",
"Adverse Reaction",
"Vaccine"
],
"homepage": "https://github.com/oae-ontology",
"license": "CC-BY-3.0",
"name": "Ontology of Adverse Events",
"prefix": "FAIRsharing.tw4q8x",
"publications": [
{
"doi": "10.1186/2041-1480-5-29",
"pubmed": "25093068",
"title": "OAE: The Ontology of Adverse Events",
"year": 2014
}
],
"subjects": [
"Biomedical Science"
]
},
"mappings": {
"aberowl": "OAE",
"biocontext": "OAE",
"bioportal": "OAE",
"fairsharing": "FAIRsharing.tw4q8x",
"obofoundry": "oae",
"ols": "oae",
"ontobee": "OAE"
},
"obofoundry": {
"contact": "yongqunh@med.umich.edu",
"contact.github": "yongqunh",
"contact.label": "Yongqunh He",
"contact.orcid": "0000-0001-9189-9661",
"deprecated": false,
"description": "A biomedical ontology in the domain of adverse events",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/oae.owl",
"homepage": "https://github.com/OAE-ontology/OAE/",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Ontology of Adverse Events",
"preferredPrefix": "OAE",
"prefix": "oae",
"repository": "https://github.com/OAE-ontology/OAE"
},
"ols": {
"description": "The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc.",
"download_owl": "http://purl.obolibrary.org/obo/oae.owl",
"homepage": "https://github.com/OAE-ontology/OAE/",
"name": "OAE: Ontology of Adverse Events",
"prefix": "oae",
"version": "1.2.47"
},
"ontobee": {
"library": "Library",
"name": "Ontology of Adverse Events",
"prefix": "OAE"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1186/2041-1480-5-29",
"pmc": "PMC4120740",
"pubmed": "25093068",
"title": "OAE: The Ontology of Adverse Events",
"year": 2014
}
],
"uri_format": "http://purl.obolibrary.org/obo/OAE_$1"
},
"oarcs": {
"aberowl": {
"description": "OArCS is an ontology describing the Arthropod ciruclatory system.",
"download_owl": "http://aber-owl.net/media/ontologies/OARCS/3/oarcs.owl",
"homepage": "https://github.com/aszool/oarcs",
"name": "Ontology of Arthropod Circulatory Systems",
"prefix": "OARCS"
},
"biocontext": {
"prefix": "OARCS"
},
"bioportal": {
"contact": {
"email": "mjyoder@illinois.edu",
"name": "Matt Yoder"
},
"description": "OArCS is an ontology describing the Arthropod ciruclatory system.",
"homepage": "https://github.com/aszool/oarcs",
"name": "Ontology of Arthropod Circulatory Systems",
"prefix": "OARCS",
"version": "2019-04-18"
},
"example": "0000029",
"fairsharing": {
"abbreviation": "OArCS",
"description": "OArCS is a structural model for the description of anatomical features (morphemes) using ontologies. Its domain is the Arthropod ciruclatory system. This ontology has not been updated recently, and therefore has been marked as uncertain. Please get in touch with us if you have any information.",
"homepage": "https://github.com/aszool/oarcs",
"name": "Ontology of Arthropod Circulatory Systems",
"prefix": "FAIRsharing.yqn857",
"publications": [
{
"doi": "10.1093/sysbio/syw108",
"title": "The first organ-based free ontology for arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its integration into a novel formalization scheme for morphological descriptions",
"year": 2017
}
],
"subjects": [
"Anatomy",
"Angiology"
]
},
"mappings": {
"aberowl": "OARCS",
"biocontext": "OARCS",
"bioportal": "OARCS",
"fairsharing": "FAIRsharing.yqn857",
"obofoundry": "oarcs",
"ols": "oarcs",
"ontobee": "OARCS"
},
"obofoundry": {
"contact": "mjyoder@illinois.edu",
"contact.github": "mjy",
"contact.label": "Matt Yoder",
"contact.orcid": "0000-0002-5640-5491",
"deprecated": false,
"description": "OArCS is an ontology describing the Arthropod ciruclatory system.",
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/oarcs.owl",
"homepage": "https://github.com/aszool/oarcs",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Ontology of Arthropod Circulatory Systems",
"preferredPrefix": "OARCS",
"prefix": "oarcs",
"repository": "https://github.com/aszool/oarcs"
},
"ols": {
"description": "OArCS is an ontology describing the Arthropod ciruclatory system.",
"download_owl": "http://purl.obolibrary.org/obo/oarcs.owl",
"homepage": "https://github.com/aszool/oarcs",
"name": "Ontology of Arthropod Circulatory Systems",
"prefix": "oarcs",
"version": "2019-04-18",
"version.iri": "http://purl.obolibrary.org/obo/hao/2019-04-18/hao.owl"
},
"ontobee": {
"library": "Library",
"name": "Ontology of Arthropod Circulatory Systems",
"prefix": "OARCS"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1093/sysbio/syw108",
"pubmed": "28123116",
"title": "The First Organ-Based Ontology for Arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its Integration into a Novel Formalization Scheme for Morphological Descriptions",
"year": 2017
}
],
"uri_format": "http://purl.obolibrary.org/obo/OARCS_$1"
},
"oba": {
"aberowl": {
"description": "A collection of biological attributes (traits) covering all kingdoms of life.",
"download_owl": "http://aber-owl.net/media/ontologies/OBA/21/oba.owl",
"homepage": "https://github.com/obophenotype/bio-attribute-ontology",
"name": "Ontology of Biological Attributes",
"prefix": "OBA"
},
"agroportal": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "The Ontology of Biological Attributes (OBA) is a formalised, species-independent collection of interoperable phenotypic trait categories that is intended to fulfil a data integration role. OBA is a standardised representational framework for observable attributes that are characteristics of biological entities, organisms, or parts of organisms. It is collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO., A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO.",
"example_uri": "http://purl.obolibrary.org/obo/OBA_0000005",
"homepage": "https://github.com/obophenotype/bio-attribute-ontology",
"license": "CC0-1.0",
"name": "Ontology of Biological Attributes",
"prefix": "OBA",
"publication": "https://doi.org/10.1007/s00335-023-09992-1",
"repository": "https://github.com/obophenotype/bio-attribute-ontology",
"version": "2024-06-27"
},
"biocontext": {
"prefix": "OBA"
},
"bioportal": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO.",
"homepage": "https://github.com/obophenotype/bio-attribute-ontology",
"name": "Ontology of Biological Attributes",
"prefix": "OBA",
"version": "2024-06-27"
},
"download_json": "http://purl.obolibrary.org/obo/oba.json",
"example": "0000001",
"example_extras": [
"VT0003769"
],
"fairsharing": {
"abbreviation": "OBA",
"description": "A collection of biological attributes / traits covering all kingdoms of life. It is interoperable with a number of other community ontologies.",
"homepage": "https://github.com/obophenotype/bio-attribute-ontology",
"license": "CC0-1.0",
"name": "Ontology of Biological Attributes",
"prefix": "FAIRsharing.mp0rwf",
"subjects": [
"Biology"
]
},
"mappings": {
"aberowl": "OBA",
"agroportal": "OBA",
"biocontext": "OBA",
"bioportal": "OBA",
"fairsharing": "FAIRsharing.mp0rwf",
"obofoundry": "oba",
"ols": "oba",
"ontobee": "OBA"
},
"obofoundry": {
"appears_in": [
"fovt"
],
"contact": "cjmungall@lbl.gov",
"contact.github": "cmungall",
"contact.label": "Chris Mungall",
"contact.orcid": "0000-0002-6601-2165",
"deprecated": false,
"description": "A collection of biological attributes (traits) covering all kingdoms of life.",
"domain": "phenotype",
"download.obo": "http://purl.obolibrary.org/obo/oba.obo",
"download.owl": "http://purl.obolibrary.org/obo/oba.owl",
"homepage": "https://github.com/obophenotype/bio-attribute-ontology",
"license": "CC0 1.0",
"license.url": "http://creativecommons.org/publicdomain/zero/1.0/",
"name": "Ontology of Biological Attributes",
"preferredPrefix": "OBA",
"prefix": "oba",
"publications": [
{
"id": "https://doi.org/10.1007/s00335-023-09992-1",
"title": "The Ontology of Biological Attributes (OBA) - computational traits for the life sciences"
}
],
"repository": "https://github.com/obophenotype/bio-attribute-ontology"
},
"ols": {
"description": "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO.",
"download_owl": "http://purl.obolibrary.org/obo/oba.owl",
"homepage": "https://github.com/obophenotype/bio-attribute-ontology",
"name": "Ontology of Biological Attributes (OBA)",
"prefix": "oba",
"version": "2024-06-27",
"version.iri": "http://purl.obolibrary.org/obo/oba/releases/2024-06-27/oba.owl"
},
"ontobee": {
"library": "Library",
"name": "Ontology of Biological Attributes",
"prefix": "OBA"
},
"pattern": "^(VT)?\\d{7}$",
"publications": [
{
"doi": "10.1007/s00335-023-09992-1",
"pubmed": "37076585",
"title": "The Ontology of Biological Attributes (OBA)-computational traits for the life sciences",
"year": 2023
},
{
"doi": "10.1101/2023.01.26.525742",
"pmc": "PMC9900877",
"pubmed": "36747660",
"title": "The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences",
"year": 2023
}
],
"uri_format": "http://purl.obolibrary.org/obo/OBA_$1"
},
"oban": {
"biocontext": {
"prefix": "OBAN",
"uri_format": "http://purl.org/oban/$1"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "OBAN",
"uri_format": "http://purl.org/oban/$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "It is an ontology model used to describe associations between biomedical entities in triple format based on W3C specification. OBAN is a generic association representation model that loosely couples a subject and object (e.g. disease and its associated phenotypes supported by the source of evidence for that association) via a construction of class OBAN:association. [from GitHub]",
"download_owl": "https://raw.githubusercontent.com/EBISPOT/OBAN/master/ontology/oban_core.owl",
"download_rdf": "https://raw.githubusercontent.com/EBISPOT/OBAN/master/ontology/oban_core.ttl",
"example": "provenance",
"homepage": "https://github.com/EBISPOT/OBAN",
"mappings": {
"biocontext": "OBAN",
"biolink": "OBAN"
},
"name": "Open Biomedical Annotations",
"pattern": "^\\w+$",
"repository": "https://github.com/EBISPOT/OBAN",
"uri_format": "http://purl.org/oban/$1"
},
"obcs": {
"aberowl": {
"description": "A biomedical ontology in the domain of biological and clinical statistics.",
"download_owl": "http://aber-owl.net/media/ontologies/OBCS/16/obcs.owl",
"homepage": "https://github.com/obcs/obcs",
"name": "Ontology of Biological and Clinical Statistics",
"prefix": "OBCS"
},
"biocontext": {
"prefix": "OBCS"
},
"bioportal": {
"contact": {
"email": "jiezheng@upenn.edu",
"name": "Jie Zheng"
},
"description": "The Ontology of Biological and Clinical Statistics (OBCS) is a biomedical ontology in the domain of biological and clinical statistics. OBCS is primarily targeted for statistical representation in the fields in biological, biomedical, and clinical domains. OBCS uses the Basic Formal Ontology (BFO) as the upper level ontology. OBCS imports all biostatistics related terms in the Ontology for Biomedical Investigations (OBI) including all logical axioms.",
"homepage": "https://github.com/obcs/obcs",
"name": "Ontology of Biological and Clinical Statistics",
"prefix": "OBCS",
"publication": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5024438/",
"version": "2023-12-08"
},
"example": "0000121",
"fairsharing": {
"abbreviation": "OBCS",
"description": "The Ontology of Biological and Clinical Statistics (OBCS) is a biomedical ontology in the domain of biological and clinical statistics. OBCS is primarily targeted for statistical representation in the fields in biological, biomedical, and clinical domains. OBCS uses the Basic Formal Ontology (BFO) as the upper level ontology. OBCS imports all biostatistics related terms in the Ontology for Biomedical Investigations (OBI) including all logical axioms.",
"domains": [
"Vaccine"
],
"homepage": "https://github.com/obcs/obcs",
"license": "CC-BY-3.0",
"name": "Ontology of Biological and Clinical Statistics",
"prefix": "FAIRsharing.5p12xh",
"publications": [
{
"doi": "10.1186/s13326-016-0100-2",
"pubmed": "27627881",
"title": "The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis",
"year": 2016
}
],
"repository": "https://github.com/obcs/obcs/issues",
"subjects": [
"Medicine",
"Statistics",
"Biomedical Science",
"Biology",
"Medical Informatics"
]
},
"mappings": {
"aberowl": "OBCS",
"biocontext": "OBCS",
"bioportal": "OBCS",
"fairsharing": "FAIRsharing.5p12xh",
"miriam": "obcs",
"obofoundry": "obcs",
"ols": "obcs",
"ontobee": "OBCS"
},
"miriam": {
"deprecated": false,
"description": "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI)",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/obcs",
"id": "00001053",
"name": " Ontology of Biological and Clinical Statistics",
"namespaceEmbeddedInLui": true,
"pattern": "^OBCS:\\d+$",
"prefix": "obcs",
"sampleId": "0000086",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/obcs/classes?obo_id=OBCS:$1"
},
"obofoundry": {
"contact": "jiezhen@med.umich.edu",
"contact.github": "zhengj2007",
"contact.label": "Jie Zheng",
"contact.orcid": "0000-0002-2999-0103",
"deprecated": false,
"description": "A biomedical ontology in the domain of biological and clinical statistics.",
"domain": "information technology",
"download.owl": "http://purl.obolibrary.org/obo/obcs.owl",
"homepage": "https://github.com/obcs/obcs",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Ontology of Biological and Clinical Statistics",
"preferredPrefix": "OBCS",
"prefix": "obcs",
"repository": "https://github.com/obcs/obcs"
},
"ols": {
"description": "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012.",
"download_owl": "http://purl.obolibrary.org/obo/obcs.owl",
"homepage": "https://github.com/obcs/obcs",
"name": "OBCS: Ontology of Biological and Clinical Statistics",
"prefix": "obcs",
"version": "2023-12-08",
"version.iri": "http://purl.obolibrary.org/obo/obcs/2023-12-08/obcs.owl"
},
"ontobee": {
"library": "Library",
"name": "Ontology of Biological and Clinical Statistics",
"prefix": "OBCS"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1186/s13326-016-0100-2",
"pmc": "PMC5024438",
"pubmed": "27627881",
"title": "The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis",
"year": 2016
}
],
"uri_format": "http://purl.obolibrary.org/obo/OBCS_$1"
},
"obi": {
"aberowl": {
"description": "An integrated ontology for the description of life-science and clinical investigations",
"download_owl": "http://aber-owl.net/media/ontologies/OBI/54/obi.owl",
"homepage": "http://obi-ontology.org",
"name": "Ontology for Biomedical Investigations",
"prefix": "OBI"
},
"banana": "OBI",
"banana_peel": ":",
"biocontext": {
"prefix": "OBI"
},
"bioportal": {
"contact": {
"email": "bpeters@liai.org",
"name": "Bjoern Peters"
},
"description": "OBI is an ontology of investigations, the protocols and instrumentation used, the material used, the data generated and the types of analysis performed on it.
To import,
Latest version: http://purl.obolibrary.org/obo/obi.owl
Latest release notes at http://purl.obolibrary.org/obo/obi/release-notes.html
Note: BFO 2.0 pre-Graz release (not official release version) was used in this release.",
"homepage": "http://purl.obolibrary.org/obo/obi",
"name": "Ontology for Biomedical Investigations",
"prefix": "OBI",
"publication": "http://purl.obolibrary.org/obo/obi/Technical_Reports",
"version": "2024-06-10"
},
"download_obo": "https://github.com/obi-ontology/obi/raw/master/views/obi.obo",
"example": "0400109",
"fairsharing": {
"abbreviation": "OBI",
"contact": {
"email": "bpeters@lji.org",
"name": "Bjoern Peters",
"orcid": "0000-0002-8457-6693"
},
"description": "The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI fosters clear communication about scientific investigations by defining more than 2500 terms for assays, devices, objectives, and more.",
"domains": [
"Reagent",
"Report",
"Assay",
"Protocol",
"Device",
"Data transformation",
"Study design"
],
"homepage": "http://obi-ontology.org/",
"license": "CC-BY-3.0",
"name": "Ontology for Biomedical Investigations",
"prefix": "FAIRsharing.284e1z",
"publications": [
{
"doi": "10.1186/2041-1480-4-s1-s6",
"pubmed": "23734660",
"title": "Query enhancement through the practical application of ontology: the IEDB and OBI",
"year": 2013
},
{
"doi": "10.4056/sigs.1994602",
"pubmed": "22180825",
"title": "Minimum Information about a Genotyping Experiment (MIGEN)",
"year": 2011
},
{
"doi": "10.1093/database/bau132",
"pubmed": "25632945",
"title": "Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach",
"year": 2015
},
{
"doi": "10.1371/journal.pone.0154556",
"pubmed": "27128319",
"title": "The Ontology for Biomedical Investigations",
"year": 2016
},
{
"doi": "10.1186/2041-1480-1-s1-s7",
"pubmed": "20626927",
"title": "Modeling biomedical experimental processes with OBI",
"year": 2010
}
],
"repository": "https://github.com/obi-ontology/obi",
"subjects": [
"Functional Genomics",
"Life Science",
"Biomedical Science"
]
},
"go": {
"homepage": "http://obi-ontology.org/",
"name": "Ontology for Biomedical Investigations",
"prefix": "OBI"
},
"mappings": {
"aberowl": "OBI",
"biocontext": "OBI",
"bioportal": "OBI",
"fairsharing": "FAIRsharing.284e1z",
"go": "OBI",
"miriam": "obi",
"n2t": "obi",
"obofoundry": "obi",
"ols": "obi",
"ontobee": "OBI",
"prefixcommons": "obi"
},
"miriam": {
"deprecated": false,
"description": "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).",
"homepage": "http://www.ontobee.org/",
"id": "00000127",
"name": "Ontology for Biomedical Investigations",
"namespaceEmbeddedInLui": false,
"pattern": "(^OBI:\\d{7}$)|(^OBI_\\d{7}$)",
"prefix": "obi",
"sampleId": "OBI_0000070",
"uri_format": "http://purl.obolibrary.org/obo/$1"
},
"n2t": {
"description": "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).",
"example": "OBI_0000070",
"homepage": "http://www.ontobee.org/",
"name": "OBI through Ontobee",
"namespaceEmbeddedInLui": false,
"pattern": "(^OBI:\\d{7}$)|(^OBI_\\d{7}$)",
"prefix": "obi",
"uri_format": "http://purl.obolibrary.org/obo/$1"
},
"namespace_in_lui": true,
"obofoundry": {
"appears_in": [
"agro",
"foodon",
"gallont",
"hso",
"labo",
"maxo",
"mco",
"one",
"ons",
"proco",
"rbo",
"scdo"
],
"contact": "bpeters@lji.org",
"contact.github": "bpeters42",
"contact.label": "Bjoern Peters",
"contact.orcid": "0000-0002-8457-6693",
"deprecated": false,
"description": "An integrated ontology for the description of life-science and clinical investigations",
"domain": "investigations",
"download.obo": "http://purl.obolibrary.org/obo/obi.obo",
"download.owl": "http://purl.obolibrary.org/obo/obi.owl",
"homepage": "http://obi-ontology.org",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"logo": "https://svn.code.sf.net/p/obi/code/trunk/web/htdocs/images/obi-lotext.png",
"name": "Ontology for Biomedical Investigations",
"preferredPrefix": "OBI",
"prefix": "obi",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/27128319",
"title": "The Ontology for Biomedical Investigations"
}
],
"repository": "https://github.com/obi-ontology/obi"
},
"ols": {
"description": "An ontology for representing biomedical investigations, including study designs, the collection and preparation of the targets of investigation, assays, instrumentation and reagents used, as well as the data generated and the types of analysis performed on the data to reach conclusions, and their documentation.",
"download_owl": "http://purl.obolibrary.org/obo/obi.owl",
"homepage": "http://obi-ontology.org",
"name": "Ontology for Biomedical Investigations",
"prefix": "obi",
"version": "2024-06-10",
"version.iri": "http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl"
},
"ontobee": {
"library": "Foundry",
"name": "Ontology for Biomedical Investigations",
"prefix": "OBI"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"alt_uri_formats": [
"http://purl.org/obo/owl/OBI#$1"
],
"bioportal": "1123",
"description": "The Ontology for Biomedical Investigations (OBI) an ontology of investigations, the protocols and instrumentation used, the material used, the data generated and the types of analysis performed on it.",
"example": "OBI_0000011",
"homepage": "http://purl.obolibrary.org/obo/obi",
"keywords": [
"ontology"
],
"license": "CC-BY-3.0",
"name": "Ontology for Biomedical Investigations",
"pattern": "^OBI_\\d{7}$",
"prefix": "obi",
"synonyms": [
"obo.obi"
]
},
"publications": [
{
"doi": "10.1371/journal.pone.0154556",
"pmc": "PMC4851331",
"pubmed": "27128319",
"title": "The Ontology for Biomedical Investigations",
"year": 2016
},
{
"doi": "10.1093/database/bau132",
"pmc": "PMC4309925",
"pubmed": "25632945",
"title": "Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach",
"year": 2015
},
{
"doi": "10.1186/2041-1480-4-s1-s6",
"pmc": "PMC3633001",
"pubmed": "23734660",
"title": "Query enhancement through the practical application of ontology: the IEDB and OBI",
"year": 2013
},
{
"doi": "10.4056/sigs.1994602",
"pmc": "PMC3235517",
"pubmed": "22180825",
"title": "Minimum Information about a Genotyping Experiment (MIGEN)",
"year": 2011
},
{
"doi": "10.1186/2041-1480-1-s1-s7",
"pmc": "PMC2903726",
"pubmed": "20626927",
"title": "Modeling biomedical experimental processes with OBI",
"year": 2010
}
],
"uri_format": "http://purl.obolibrary.org/obo/OBI_$1"
},
"obib": {
"aberowl": {
"description": "An ontology built for annotation and modeling of biobank repository and biobanking administration",
"download_owl": "http://aber-owl.net/media/ontologies/OBIB/15/obib.owl",
"homepage": "https://github.com/biobanking/biobanking",
"name": "Ontology for Biobanking",
"prefix": "OBIB"
},
"biocontext": {
"prefix": "OBIB"
},
"bioportal": {
"contact": {
"email": "jiezheng@upenn.edu",
"name": "Jie Zheng"
},
"description": "The ontology for Biobanking (OBIB) is an ontology built for annotation and modeling of biobank repository and biobanking administration. It is developed based on subset of Ontology for Biomedical Investigations (OBI) using Basic Formal Ontology (BFO) as top ontology and following OBO Foundry principles. The first version of the ontology is merged of two existing biobank related ontologies, OMIABIS and biobank ontology.",
"homepage": "https://github.com/biobanking/biobanking/wiki",
"name": "Ontology for Biobanking",
"prefix": "OBIB",
"version": "2023-04-05"
},
"example": "0000389",
"fairsharing": {
"abbreviation": "OBIB",
"description": "The ontology for Biobanking (OBIB) is an ontology built for annotation and modeling of biobank repository and biobanking administration. It is developed based on subset of Ontology for Biomedical Investigations (OBI) using Basic Formal Ontology (BFO) as top ontology and following OBO Foundry principles. The first version of the ontology is merged of two existing biobank related ontologies, OMIABIS and biobank ontology.",
"domains": [
"Biobank"
],
"homepage": "https://github.com/biobanking/biobanking/wiki",
"license": "CC-BY-4.0",
"name": "Ontology for Biobanking",
"prefix": "FAIRsharing.bxc508",
"publications": [
{
"doi": "10.1186/s13326-016-0068-y",
"title": "OBIB-a novel ontology for biobanking",
"year": 2016
}
],
"subjects": [
"Health Science"
]
},
"mappings": {
"aberowl": "OBIB",
"biocontext": "OBIB",
"bioportal": "OBIB",
"fairsharing": "FAIRsharing.bxc508",
"obofoundry": "obib",
"ols": "obib",
"ontobee": "OBIB"
},
"obofoundry": {
"contact": "jmwhorton@uams.edu",
"contact.github": "jmwhorton",
"contact.label": "Justin Whorton",
"contact.orcid": "0009-0003-4268-6207",
"deprecated": false,
"description": "An ontology built for annotation and modeling of biobank repository and biobanking administration",
"domain": "investigations",
"download.owl": "http://purl.obolibrary.org/obo/obib.owl",
"homepage": "https://github.com/biobanking/biobanking",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Ontology for Biobanking",
"preferredPrefix": "OBIB",
"prefix": "obib",
"repository": "https://github.com/biobanking/biobanking"
},
"ols": {
"description": "The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology.",
"download_owl": "http://purl.obolibrary.org/obo/obib.owl",
"homepage": "https://github.com/biobanking/biobanking",
"name": "Ontology for BIoBanking (OBIB)",
"prefix": "obib",
"version": "2023-04-05",
"version.iri": "http://purl.obolibrary.org/obo/obib/2023-04-05/obib.owl"
},
"ontobee": {
"library": "Library",
"name": "Ontology for Biobanking",
"prefix": "OBIB"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1186/s13326-016-0068-y",
"pmc": "PMC4855778",
"pubmed": "27148435",
"title": "OBIB-a novel ontology for biobanking",
"year": 2016
}
],
"uri_format": "http://purl.obolibrary.org/obo/OBIB_$1"
},
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{
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"pmc": "PMC2814061",
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"title": "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration",
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}
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"abbreviation": "OBO Format",
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},
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"prefix": "20430"
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},
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"id": "00000693",
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"prefix": "occ",
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"name": "OpenCitations Corpus",
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"prefix": "occ",
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"occo": {
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"description": "An ontology representing occupations. It is designed to facilitate harmonization of existing occupation standards, such as the US Bureau of Labor Statistics Standard Occupational Classification (US SOC), the International Standard Classification of Occupations (ISCO), the UK National Statistics Standard Occupational Classification (UK SOC), and the European Skills, Competences, Qualifications and Occupations (ESCO) of the European Union.",
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"prefix": "OCCO"
},
"bioportal": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun (Oliver) He"
},
"description": "This Occupaton Ontology (OccO) is an ontology in the domain of human occupations. Current OccO version is developed based on the US Bureau of Labor Statistics Standard Occupation Classification (SOC) and the related O*Net System. The OccO development follows the principles of the Open Biological and Biomedical (OBO) Foundry.",
"homepage": "https://hegroup.org/",
"name": "Occupation Ontology",
"prefix": "OCCO",
"version": "2023-08-20"
},
"example": "00000001",
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"aberowl": "OCCO",
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},
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"contact.label": "Jie Zheng",
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"description": "An ontology representing occupations. It is designed to facilitate harmonization of existing occupation standards, such as the US Bureau of Labor Statistics Standard Occupational Classification (US SOC), the International Standard Classification of Occupations (ISCO), the UK National Statistics Standard Occupational Classification (UK SOC), and the European Skills, Competences, Qualifications and Occupations (ESCO) of the European Union.",
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"ontobee": {
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"oci": {
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"id": "00000660",
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"prefix": "oci",
"sampleId": "01027931310-01022252312",
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},
"n2t": {
"description": "Each OCI (Open Citation Identifier) has a simple structure: oci:number-number, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/ for additional information. OCIs for citations stored within the OpenCitations Corpus are constructed by combining the OpenCitations Corpus local identifiers for the citing and cited bibliographic resources, separating them with a dash. For example, oci:2544384-7295288 is a valid OCI for the citation between two papers stored within the OpenCitations Corpus. OCIs can also be created for bibliographic resources described in an external bibliographic database, if they are similarly identified there by identifiers having a unique numerical part. For example, the OCI for the citation that exists between Wikidata resources Q27931310 and Q22252312 is oci:01027931310–01022252312. OCIs can also be created for bibliographic resources described in external bibliographic database such as Crossref or DataCite where they are identified by alphanumeric Digital Object Identifiers (DOIs), rather than purely numerical strings.",
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"name": "OpenCitations",
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"pattern": "^[0-9]+-[0-9]+$",
"prefix": "oci",
"uri_format": "https://w3id.org/oc/oci/$1"
},
"name": "Open Citation Identifier"
},
"ocid": {
"banana": "ocid",
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"miriam": "ocid"
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"miriam": {
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"homepage": "https://ontochem.com/",
"id": "00000738",
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},
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},
"oclc": {
"biocontext": {
"prefix": "OCLC"
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"mappings": {
"biocontext": "OCLC",
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"n2t": "oclc"
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"homepage": "https://www.oclc.org/en/about.html",
"id": "00000669",
"name": "Online Computer Library Center (OCLC) WorldCat",
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"pattern": "^[0-9]+$",
"prefix": "oclc",
"sampleId": "634515043",
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"n2t": {
"description": "The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information.",
"example": "634515043",
"homepage": "https://www.oclc.org/en/about.html",
"name": "Online Computer Library Center (OCLC) WorldCat",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"prefix": "oclc",
"uri_format": "https://www.worldcat.org/oclc/$1"
},
"name": "Online Computer Library Center WorldCat"
},
"odam": {
"mappings": {
"miriam": "odam"
},
"miriam": {
"deprecated": false,
"description": "Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed.",
"homepage": "https://metabolome.cgfb.u-bordeaux.fr/",
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"name": "Open Data for Access and Mining",
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"pattern": "^[A-Za-z0-9]+$",
"prefix": "odam",
"sampleId": "frim1",
"uri_format": "http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1"
}
},
"odamexplorer": {
"mappings": {
"miriam": "odam.explorer"
},
"miriam": {
"deprecated": false,
"description": "ODAM (Open Data for Access and Mining) is an Experimental data table management software (EDTMS) to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines.\n\nODAM allows datasets to be explored and then extracted in whole or in part as needed.\n\nFor more information/explanation, see ODAM User's Guide : https://inrae.github.io/ODAM/",
"homepage": "https://eng-bfp.bordeaux-aquitaine.hub.inrae.fr/",
"id": "00001076",
"name": "ODAM Data explorer",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z][A-Za-z0-9]+$",
"prefix": "odam.explorer",
"sampleId": "frim1",
"uri_format": "https://pmb-bordeaux.fr/dataexplorer/?ds=$1"
}
},
"odc.sci": {
"fairsharing": {
"abbreviation": "ODC-SCI",
"contact": {
"email": "jgrethe@ucsd.edu",
"name": "Jeffrey Grethe",
"orcid": "0000-0001-5212-7052"
},
"description": "The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data. There are several challenges for scientific reproducibility and bench-to-bedside translation. For example, only research and data that are published actually get disseminated, a phenomenon known as publication bias. Published research reflects to only a small fraction of all data collected, and data that do not lead to publication are largely ignored, hidden away in filing cabinets and hard drives. This results in an abundance of inaccessible scientific data known as βdark dataβ. Even when research is disseminated, it is usually in the form of summary reports of aggregated data (e.g. averages across individual subjects) such as scientific articles. The fact that the individual subject-level data are inaccessible further contributes to dark data. The spinal cord injury (SCI) community created the ODC-SCI to mitigate dark data in SCI research. The ODC-SCI also aims to increase transparency with individual-level data, enhance collaboration, facilitate advanced analytics, and conform to increasing mandates by funders and publishers to make data accessible. Members of the ODC-SCI have access to a private digital lab space managed by the PI or multi-PIs for dataset storage and sharing. The PIs can share their labsβ datasets with the registered members of the ODC-SCI community and make their datasets public and citable. The ODC-SCI implements stewardship principles that scientific data be made FAIR (Findable, Accessible, Interoperable and Reusable) and has been widely adopted by the international SCI research community.",
"homepage": "https://odc-sci.org",
"license": "CC-BY-4.0",
"name": "Open Data Commons for Spinal Cord Injury",
"prefix": "FAIRsharing.M6Ruz3",
"publications": [
{
"doi": "10.1038/ncomms9581",
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"title": "Topological data analysis for discovery in preclinical spinal cord injury and traumatic brain injury."
},
{
"doi": "10.1007/s12975-011-0121-1",
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"title": "Syndromics: a bioinformatics approach for neurotrauma research."
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{
"doi": "10.1089/neu.2014.3399",
"pubmed_id": 25077610,
"title": "Development of a database for translational spinal cord injury research."
},
{
"doi": "10.1371/journal.pone.0059712",
"pubmed_id": 23544088,
"title": "Derivation of multivariate syndromic outcome metrics for consistent testing across multiple models of cervical spinal cord injury in rats."
},
{
"doi": "10.1089/neu.2019.6674",
"pubmed_id": 31608767,
"title": "FAIR SCI Ahead: The Evolution of the Open Data Commons for Pre-Clinical Spinal Cord Injury Research."
},
{
"doi": "S0014-4886(17)30137-1",
"pubmed_id": 28576567,
"title": "Developing a data sharing community for spinal cord injury research."
},
{
"doi": "10.1038/nn.3838",
"pubmed_id": 25349910,
"title": "Big data from small data: data-sharing in the 'long tail' of neuroscience."
}
],
"subjects": [
"Neurobiology",
"Neurology",
"Biomedical Science",
"Neuroscience"
]
},
"mappings": {
"fairsharing": "FAIRsharing.M6Ruz3",
"miriam": "odc.sci",
"re3data": "r3d100014071"
},
"miriam": {
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"description": "The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data.",
"homepage": "https://odc-sci.org",
"id": "00000804",
"name": "Open Data Commons for Spinal Cord Injury",
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"doi": "10.1089/neu.2019.6674",
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"pubmed": "31608767",
"title": "FAIR SCI Ahead: The Evolution of the Open Data Commons for Pre-Clinical Spinal Cord Injury Research",
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},
{
"doi": "10.1016/j.expneurol.2017.05.012",
"pmc": "PMC6448396",
"pubmed": "28576567",
"title": "Developing a data sharing community for spinal cord injury research",
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},
{
"doi": "10.1038/ncomms9581",
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"pubmed": "26466022",
"title": "Topological data analysis for discovery in preclinical spinal cord injury and traumatic brain injury",
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},
{
"doi": "10.1038/nn.3838",
"pmc": "PMC4728080",
"pubmed": "25349910",
"title": "Big data from small data: data-sharing in the 'long tail' of neuroscience",
"year": 2014
},
{
"doi": "10.1089/neu.2014.3399",
"pmc": "PMC4186058",
"pubmed": "25077610",
"title": "Development of a database for translational spinal cord injury research",
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},
{
"doi": "10.1371/journal.pone.0059712",
"pmc": "PMC3609747",
"pubmed": "23544088",
"title": "Derivation of multivariate syndromic outcome metrics for consistent testing across multiple models of cervical spinal cord injury in rats",
"year": 2013
},
{
"doi": "10.1007/s12975-011-0121-1",
"pmc": "PMC3236294",
"pubmed": "22207883",
"title": "Syndromics: a bioinformatics approach for neurotrauma research",
"year": 2011
}
],
"re3data": {
"description": "A community platform to Share Data, Publish Data with a DOI, and get Citations. Advancing Spinal Cord Injury research through sharing of data from basic and clinical research.",
"homepage": "https://odc-sci.org/",
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"prefix": "r3d100014071",
"synonyms": [
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],
"xrefs": {
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}
},
"odc.tbi": {
"mappings": {
"miriam": "odc.tbi"
},
"miriam": {
"deprecated": false,
"description": "The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data.",
"homepage": "https://odc-tbi.org",
"id": "00000816",
"name": "Open Data Commons for Traumatic Brain Injury",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]*$",
"prefix": "odc.tbi",
"sampleId": "408",
"uri_format": "https://odc-tbi.org/data/$1"
}
},
"odor": {
"biocontext": {
"prefix": "ODOR"
},
"mappings": {
"biocontext": "ODOR",
"miriam": "odor",
"n2t": "odor"
},
"miriam": {
"deprecated": false,
"description": "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors",
"homepage": "http://senselab.med.yale.edu/OdorDB",
"id": "00000500",
"name": "Odor Molecules DataBase",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "odor",
"sampleId": "74",
"uri_format": "http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5"
},
"n2t": {
"description": "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors",
"example": "74",
"homepage": "http://senselab.med.yale.edu/OdorDB",
"name": "Odor Molecules DataBase at Yale University School of Medicine",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "odor",
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}
},
"odrl": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The ODRL Vocabulary and Expression defines a set of concepts and terms (the vocabulary) and encoding mechanism (the expression) for permissions and obligations statements describing digital content usage based on the ODRL Information Model.",
"download_rdf": "https://www.w3.org/ns/odrl/2/ODRL22.rdf",
"example": "assetConcepts",
"homepage": "http://www.w3.org/ns/odrl/2",
"lov": {
"description": "The Open Digital Rights Language (ODRL) provides flexible and interoperable mechanisms to support transparent and innovative use of digital content in publishing, distribution, and consumption of of digital media across all sectors and communities. The ODRL Policy model is broad enough to support traditional rights expressions for commercial transaction, open access expressions for publicly distributed content, and privacy expressions for social media.",
"homepage": "https://www.w3.org/TR/odrl-vocab/",
"keywords": [
"Metadata"
],
"modified": "2017-09-16",
"name": "The Open Digital Rights Language (ODRL) Ontology",
"prefix": "odrl",
"uri_prefix": "http://www.w3.org/ns/odrl/2/$1"
},
"mappings": {
"lov": "odrl"
},
"name": "Open Digital Rights Language Ontology",
"uri_format": "http://www.w3.org/ns/odrl/2/$1"
},
"oecd.template": {
"comment": "The identifiers have two numbers separated by a dot. The first one corresponds to the template number which can be found on the homepage. The second number referes to the row within the corresponding spreadsheet.",
"contributor": {
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"description": "The Organisation for Economic Co-operation and Development (OECD) Harmonised Templates (OHTs) are standard data formats for reporting information used for the risk assessment of chemicals, mainly studies done on chemicals to determine their properties or effects on human health and the environment, but also for storing data on use and exposure.",
"example": "74.186",
"github_request_issue": 997,
"homepage": "https://www.oecd.org/ehs/templates/",
"name": "OECD Harmonised Templates",
"pattern": "^\\d+\\.\\d+$",
"references": [
"https://github.com/biopragmatics/bioregistry/issues/991"
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"ogg": {
"aberowl": {
"description": "A formal ontology of genes and genomes of biological organisms.",
"download_owl": "http://aber-owl.net/media/ontologies/OGG/4/ogg.owl",
"homepage": "https://bitbucket.org/hegroup/ogg",
"name": "The Ontology of Genes and Genomes",
"prefix": "OGG"
},
"biocontext": {
"prefix": "OGG"
},
"bioportal": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets.",
"homepage": "https://bitbucket.org/hegroup/ogg",
"name": "Ontology of Genes and Genomes",
"prefix": "OGG",
"version": "Vision Release: 1.0.59"
},
"example": "3000887619",
"fairsharing": {
"abbreviation": "OGG",
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun He",
"orcid": "0000-0001-9189-9661"
},
"description": "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms. Each gene in OGG has over 10 annotation items, includes gene-associated Gene Ontology (GO) and PubMed article information. OGG has represented genes in human, two viruses, and four bacteria. Additionally, 7 OGG subsets are developed to represent genes and genomes of 7 model systems including mouse, fruit fly, zebrafish, yeast, A. thaliana, C. elegans, and P. falciparum.",
"domains": [
"Gene name",
"Gene",
"Genome"
],
"homepage": "https://bitbucket.org/hegroup/ogg",
"license": "CC-BY-3.0",
"name": "Ontology of Genes and Genomes",
"prefix": "FAIRsharing.zmx7nn",
"subjects": [
"Life Science",
"Biology"
]
},
"mappings": {
"aberowl": "OGG",
"biocontext": "OGG",
"bioportal": "OGG",
"fairsharing": "FAIRsharing.zmx7nn",
"obofoundry": "ogg",
"ols": "ogg",
"ontobee": "OGG"
},
"obofoundry": {
"contact": "yongqunh@med.umich.edu",
"contact.github": "yongqunh",
"contact.label": "Yongqun Oliver He",
"contact.orcid": "0000-0001-9189-9661",
"deprecated": false,
"description": "A formal ontology of genes and genomes of biological organisms.",
"domain": "biological systems",
"download.owl": "http://purl.obolibrary.org/obo/ogg.owl",
"homepage": "https://bitbucket.org/hegroup/ogg",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "The Ontology of Genes and Genomes",
"preferredPrefix": "OGG",
"prefix": "ogg",
"repository": "https://bitbucket.org/hegroup/ogg"
},
"ols": {
"description": "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets.",
"download_owl": "http://purl.obolibrary.org/obo/ogg.owl",
"homepage": "https://bitbucket.org/hegroup/ogg",
"name": "OGG: Ontology of Genes and Genomes",
"prefix": "ogg",
"version": "1.0.59"
},
"ontobee": {
"library": "Library",
"name": "The Ontology of Genes and Genomes",
"prefix": "OGG"
},
"pattern": "^\\d+$",
"uri_format": "http://purl.obolibrary.org/obo/OGG_$1"
},
"ogi": {
"aberowl": {
"description": "Using BFO as its framwork, OGI formalized the genomic element by defining an upper class 'genetic interval'. The definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.",
"download_owl": "http://aber-owl.net/media/ontologies/OGI/18/ogi.owl",
"homepage": "https://code.google.com/p/ontology-for-genetic-interval/",
"name": "Ontology for genetic interval",
"prefix": "OGI",
"version": "2.0"
},
"biocontext": {
"prefix": "OGI"
},
"bioportal": {
"contact": {
"email": "linikujp@gmail.com",
"name": "Yu Lin"
},
"description": "Using BFO as its framwork, OGI formalized the genomic element by defining an upper class 'genetic interval'. The definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.",
"homepage": "https://code.google.com/p/ontology-for-genetic-interval/",
"name": "Ontology for Genetic Interval",
"prefix": "OGI",
"version": "2.0"
},
"deprecated": true,
"example": "0000019",
"homepage": "https://code.google.com/archive/p/ontology-for-genetic-interval/",
"mappings": {
"aberowl": "OGI",
"biocontext": "OGI",
"bioportal": "OGI",
"obofoundry": "ogi",
"ols": "ogi",
"ontobee": "OGI"
},
"obofoundry": {
"contact": "linikujp@gmail.com",
"contact.github": "linikujp",
"contact.label": "Asiyah Yu Lin",
"contact.orcid": "0000-0002-5379-5359",
"deprecated": true,
"description": "An ontology that formalizes the genomic element by defining an upper class genetic interval",
"domain": "chemistry and biochemistry",
"download.owl": "http://purl.obolibrary.org/obo/ogi.owl",
"homepage": "https://code.google.com/p/ontology-for-genetic-interval/",
"name": "Ontology for genetic interval",
"prefix": "ogi"
},
"ols": {
"description": "OGI formalized the genomic element by defining an upper class 'genetic interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) βGenome, Gene, Interval and Ontologyβ Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\nYu Lin, Hiroshi Tarui, Peter Simons (2009) βFrom Ontology for Genetic Interval(OGI) to Sequence Assembly β Ontology apply to next generation sequencingβ Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons (2010) βDNA sequence from below: A Nominalist Approachβ Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n",
"download": "http://purl.obolibrary.org/obo/ogi.owl",
"homepage": "https://code.google.com/p/ontology-for-genetic-interval/",
"name": "Ontology for genetic interval",
"prefix": "ogi",
"version": "2.0"
},
"ontobee": {
"library": "Library",
"name": "Ontology for genetic interval",
"prefix": "OGI"
},
"pattern": "^\\d{7}$",
"synonyms": [
"OGI.owl"
]
},
"ogms": {
"aberowl": {
"description": "An ontology for representing treatment of disease and diagnosis and on carcinomas and other pathological entities",
"download_owl": "http://aber-owl.net/media/ontologies/OGMS/19/ogms.owl",
"homepage": "https://github.com/OGMS/ogms",
"name": "Ontology for General Medical Science",
"prefix": "OGMS"
},
"bartoc": {
"description": "BFO grows out of a philosophical orientation which overlaps with that of DOLCE and SUMO. Unlike these, however, it is narrowly focused on the task of providing a genuine upper ontology which can be used in support of domain ontologies developed for scientific research, as for example in biomedicine within the framework of the OBO Foundry. Thus BFO does not contain physical, chemical, biological or other terms which would properly fall within the special sciences domains.\n\nThe BFO project was initiated in 2002. The theory behind BFO was developed initially by Barry Smith and Pierre Grenon and presented in a series of publications listed here. Since then important contributions to BFO have been made by many people, including: Werner Ceusters, Chris Mungall, Fabian Neuhaus, Holger Stenzhorn, Alan Ruttenberg, Mathias Brochausen, Bjoern Peters, Kerry Trentelman, and by more than hundred other members of the BFO Discussion Group. Its development has been carried out under the auspices of the project Forms of Life sponsored by the Volkswagen Foundation.",
"homepage": "http://www.ifomis.org/bfo/",
"prefix": "216",
"wikidata_database": "Q4866972"
},
"biocontext": {
"prefix": "OGMS"
},
"bioportal": {
"contact": {
"email": "rscheuermann@jcvi.org",
"name": "Richard Scheuermann"
},
"description": "The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. See http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf",
"homepage": "https://github.com/OGMS/ogms",
"name": "Ontology for General Medical Science",
"prefix": "OGMS",
"publication": "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf",
"version": "2021-08-19"
},
"download_obo": "http://purl.obolibrary.org/obo/ogms.obo",
"example": "0000031",
"fairsharing": {
"abbreviation": "OGMS",
"contact": {
"email": "rscheuermann@jcvi.org",
"name": "Richard Scheuermann",
"orcid": "0000-0003-1355-892X"
},
"description": "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies.",
"domains": [
"Cancer",
"Disease phenotype",
"Disease",
"Diagnosis"
],
"homepage": "https://github.com/OGMS/ogms",
"name": "Ontology for General Medical Science",
"prefix": "FAIRsharing.rvz0m9",
"publications": [
{
"doi": "10.1186/2041-1480-4-42",
"pubmed": "24314207",
"title": "The neurological disease ontology",
"year": 2013
}
],
"repository": "https://github.com/OGMS/ogms/issues",
"subjects": [
"Medicine",
"Biomedical Science"
]
},
"mappings": {
"aberowl": "OGMS",
"bartoc": "216",
"biocontext": "OGMS",
"bioportal": "OGMS",
"fairsharing": "FAIRsharing.rvz0m9",
"obofoundry": "ogms",
"ols": "ogms",
"ontobee": "OGMS"
},
"obofoundry": {
"appears_in": [
"labo",
"scdo"
],
"contact": "baeverma@jcvi.org",
"contact.github": "BAevermann",
"contact.label": "Brian Aevermann",
"contact.orcid": "0000-0003-1346-1327",
"deprecated": false,
"description": "An ontology for representing treatment of disease and diagnosis and on carcinomas and other pathological entities",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/ogms.owl",
"homepage": "https://github.com/OGMS/ogms",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"logo": "https://avatars2.githubusercontent.com/u/12973154?s=200&v=4",
"name": "Ontology for General Medical Science",
"preferredPrefix": "OGMS",
"prefix": "ogms",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/21347182",
"preferred": true,
"title": "Toward an ontological treatment of disease and diagnosis"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/25991121",
"title": "Biomarkers in the Ontology for General Medical Science"
}
],
"repository": "https://github.com/OGMS/ogms"
},
"ols": {
"description": "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats.\n\nOGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.",
"download_owl": "http://purl.obolibrary.org/obo/ogms.owl",
"homepage": "https://github.com/OGMS/ogms",
"name": "Ontology for General Medical Science",
"prefix": "ogms",
"version": "2021-08-19",
"version.iri": "http://purl.obolibrary.org/obo/ogms/2021-08-19/ogms.owl"
},
"ontobee": {
"library": "Library",
"name": "Ontology for General Medical Science",
"prefix": "OGMS"
},
"pattern": "^\\d{7}$",
"publications": [
{
"pubmed": "25991121",
"title": "Biomarkers in the ontology for general medical science",
"year": 2015
},
{
"doi": "10.1186/2041-1480-4-42",
"pmc": "PMC4028878",
"pubmed": "24314207",
"title": "The neurological disease ontology",
"year": 2013
},
{
"pmc": "PMC3041577",
"pubmed": "21347182",
"title": "Toward an ontological treatment of disease and diagnosis",
"year": 2009
}
],
"synonyms": [
"ogms/OMRE"
],
"uri_format": "http://purl.obolibrary.org/obo/OGMS_$1",
"wikidata": {
"database": "Q4866972"
}
},
"ogsf": {
"aberowl": {
"description": "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.",
"download_owl": "http://aber-owl.net/media/ontologies/OGSF/11/ogsf.owl",
"homepage": "none",
"name": "Ontology of Genetic Susceptibility Factor",
"prefix": "OGSF"
},
"biocontext": {
"prefix": "OGSF"
},
"bioportal": {
"contact": {
"email": "linikujp@gmail.com",
"name": "Asiyah Yu Lin"
},
"description": "Ontology for Genetic Susceptibility Factor (OGSF) is an application ontology to model/represent the notion of genetic susceptibility to a specific disease or an adverse event or a pathological biological process. It is developed using BFO2.0's framwork. The ontology is under the domain of genetic epidemiology.",
"homepage": "https://code.google.com/p/ogsf/",
"name": "Ontology for Genetic Susceptibility Factor",
"prefix": "OGSF",
"version": "2.0"
},
"example": "0000025",
"fairsharing": {
"abbreviation": "OGSF",
"contact": {
"email": "linikujp@gmail.com",
"name": "Asiyah Yu Lin",
"orcid": "0000-0003-2620-0345"
},
"description": "Ontology for Genetic Susceptibility Factor (OGSF) is an application ontology to model/represent the notion of genetic susceptibility to a specific disease or an adverse event or a pathological biological process. It is developed using BFO 2.0's framework. The ontology is under the domain of genetic epidemiology. OGSF is built from a combination of three ontologies: the Ontology of Geographical Region (OGR), the Ontology of Glucose Metabolism (OGMD), and the Ontology of Genetic Disease Investigations (OGDI). ",
"domains": [
"Adverse Reaction",
"Disease",
"Genetic disorder"
],
"homepage": "https://github.com/linikujp/OGSF",
"name": "Ontology for Genetic Susceptibility Factor",
"prefix": "FAIRsharing.egv2cz",
"publications": [
{
"doi": "10.1186/2041-1480-5-19",
"pubmed": "24963371",
"title": "The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events",
"year": 2014
},
{
"pubmed": "20847592",
"title": "Ontology driven modeling for the knowledge of genetic susceptibility to disease",
"year": 2009
}
],
"subjects": [
"Genetics",
"Biomedical Science",
"Epidemiology"
]
},
"mappings": {
"aberowl": "OGSF",
"biocontext": "OGSF",
"bioportal": "OGSF",
"fairsharing": "FAIRsharing.egv2cz",
"obofoundry": "ogsf",
"ols": "ogsf",
"ontobee": "OGSF"
},
"obofoundry": {
"contact": "linikujp@gmail.com",
"contact.github": "linikujp",
"contact.label": "Asiyah Yu Lin",
"contact.orcid": "0000-0002-5379-5359",
"deprecated": true,
"description": "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.",
"domain": "investigations",
"download.owl": "http://purl.obolibrary.org/obo/ogsf.owl",
"homepage": "https://github.com/linikujp/OGSF",
"license": "CC BY 3.0",
"license.url": "https://creativecommons.org/licenses/by/3.0/",
"name": "Ontology of Genetic Susceptibility Factor",
"preferredPrefix": "OGSF",
"prefix": "ogsf",
"repository": "https://github.com/linikujp/OGSF"
},
"ols": {
"description": "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.",
"download_owl": "http://purl.obolibrary.org/obo/ogsf.owl",
"homepage": "https://github.com/linikujp/OGSF",
"name": "Ontology of Genetic Susceptibility Factor",
"prefix": "ogsf",
"version": "2.0"
},
"ontobee": {
"library": "Library",
"name": "Ontology of Genetic Susceptibility Factor",
"prefix": "OGSF"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1186/2041-1480-5-19",
"pmc": "PMC4068904",
"pubmed": "24963371",
"title": "The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events",
"year": 2014
},
{
"pubmed": "20847592",
"title": "Ontology driven modeling for the knowledge of genetic susceptibility to disease",
"year": 2009
}
],
"uri_format": "http://purl.obolibrary.org/obo/OGSF_$1"
},
"ohd": {
"aberowl": {
"description": "The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies.",
"download_owl": "http://aber-owl.net/media/ontologies/OHD/8/ohd.owl",
"homepage": "https://purl.obolibrary.org/obo/ohd/home",
"name": "Oral Health and Disease Ontology",
"prefix": "OHD"
},
"biocontext": {
"prefix": "OHD"
},
"bioportal": {
"contact": {
"email": "wdduncan@gmail.com",
"name": "Bill Duncan"
},
"description": "The Oral Health and Disease Ontology is intended as a BFO and OBO Foundry compliant ontology for the oral health domain. It is currently used to represent the content of dental practice health records and is intended to be further developed for use in translation medicine. It demonstrates a principled split between billing codes as information entities and what the codes are about, such as dental procedures, materials, and patients. OHD is structured using BFO uses terms from OGMS, OBI, IAO and FMA. In addition it uses terms from CARO, OMRSE, NCBITaxon, and a subset of terms from the Current Dental Terminology (CDT) OHD is in early development and subject to change without notice.",
"homepage": "https://github.com/oral-health-and-disease-ontologies/ohd-ontology",
"name": "The Oral Health and Disease Ontology",
"prefix": "OHD",
"version": "2024-06-21"
},
"example": "0000006",
"fairsharing": {
"abbreviation": "OHD",
"description": "The Oral Health and Disease Ontology is intended as a BFO and OBO Foundry compliant ontology for the oral health domain. It is currently used to represent the content of dental practice health records and is intended to be further developed for use in translation medicine. It demonstrates a principled split between billing codes as information entities and what the codes are about, such as dental procedures, materials, and patients. OHD is structured using BFO uses terms from OGMS, OBI, IAO and FMA. In addition it uses terms from CARO, OMRSE, NCBITaxon, and a subset of terms from the Current Dental Terminology (CDT) OHD is in early development and subject to change without notice.",
"homepage": "https://github.com/oral-health-and-disease-ontologies/ohd-ontology",
"name": "The Oral Health and Disease Ontology",
"prefix": "FAIRsharing.bg7bb6",
"subjects": [
"Medicine",
"Dentistry",
"Oral Surgery"
]
},
"mappings": {
"aberowl": "OHD",
"biocontext": "OHD",
"bioportal": "OHD",
"fairsharing": "FAIRsharing.bg7bb6",
"obofoundry": "ohd",
"ols": "ohd",
"ontobee": "OHD"
},
"obofoundry": {
"contact": "wdduncan@gmail.com",
"contact.github": "wdduncan",
"contact.label": "Bill Duncan",
"contact.orcid": "0000-0001-9625-1899",
"deprecated": false,
"description": "The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/ohd.owl",
"homepage": "https://purl.obolibrary.org/obo/ohd/home",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Oral Health and Disease Ontology",
"preferredPrefix": "OHD",
"prefix": "ohd",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/32819435",
"title": "Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology"
}
],
"repository": "https://github.com/oral-health-and-disease-ontologies/ohd-ontology"
},
"ols": {
"description": "The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies.",
"download_owl": "http://purl.obolibrary.org/obo/ohd.owl",
"homepage": "https://purl.obolibrary.org/obo/ohd/home",
"name": "Oral Health and Disease Ontology",
"prefix": "ohd",
"version": "2024-06-21",
"version.iri": "http://purl.obolibrary.org/obo/ohd/releases/2024-06-21/ohd.owl"
},
"ontobee": {
"library": "Library",
"name": "Oral Health and Disease Ontology",
"prefix": "OHD"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1186/s13326-020-00222-0",
"pmc": "PMC7439527",
"pubmed": "32819435",
"title": "Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology",
"year": 2020
}
],
"uri_format": "http://purl.obolibrary.org/obo/OHD_$1"
},
"ohmi": {
"aberowl": {
"description": "The Ontology of Host-Microbiome Interactions aims to ontologically represent and standardize various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions.",
"download_owl": "http://aber-owl.net/media/ontologies/OHMI/16/ohmi.owl",
"homepage": "https://github.com/ohmi-ontology/ohmi",
"name": "Ontology of Host-Microbiome Interactions",
"prefix": "OHMI"
},
"biocontext": {
"prefix": "OHMI"
},
"bioportal": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.",
"homepage": "https://github.com/ohmi-ontology/ohmi",
"name": "Ontology of Host-Microbe Interactions",
"prefix": "OHMI",
"version": "2019-09-17"
},
"example": "0000460",
"fairsharing": {
"abbreviation": "OHMI",
"description": "OHMI is aimed to ontologically represent various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions.",
"domains": [
"Host",
"Microbiome"
],
"homepage": "https://github.com/ohmi-ontology/ohmi",
"name": "Ontology of Host-Microbe Interactions",
"prefix": "FAIRsharing.cz9cnp",
"subjects": [
"Life Science"
]
},
"mappings": {
"aberowl": "OHMI",
"biocontext": "OHMI",
"bioportal": "OHMI",
"fairsharing": "FAIRsharing.cz9cnp",
"obofoundry": "ohmi",
"ols": "ohmi",
"ontobee": "OHMI"
},
"obofoundry": {
"contact": "yongqunh@med.umich.edu",
"contact.github": "yongqunh",
"contact.label": "Yongqun Oliver He",
"contact.orcid": "0000-0001-9189-9661",
"deprecated": false,
"description": "The Ontology of Host-Microbiome Interactions aims to ontologically represent and standardize various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions.",
"domain": "organisms",
"download.owl": "http://purl.obolibrary.org/obo/ohmi.owl",
"homepage": "https://github.com/ohmi-ontology/ohmi",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Ontology of Host-Microbiome Interactions",
"preferredPrefix": "OHMI",
"prefix": "ohmi",
"repository": "https://github.com/ohmi-ontology/ohmi"
},
"ols": {
"description": "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.",
"download_owl": "http://purl.obolibrary.org/obo/ohmi.owl",
"homepage": "https://github.com/ohmi-ontology/ohmi",
"name": "OHMI: Ontology of Host-Microbiome Interactions",
"prefix": "ohmi",
"version": "2019-09-17",
"version.iri": "http://purl.obolibrary.org/obo/ohmi/2019-09-17/ohmi.owl"
},
"ontobee": {
"library": "Library",
"name": "Ontology of Host-Microbiome Interactions",
"prefix": "OHMI"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/OHMI_$1"
},
"ohpi": {
"aberowl": {
"description": "OHPI is a community-driven ontology of host-pathogen interactions (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs in the Victors database become less virulence inside a host organism or host cells. It is developed to represent manually curated HPI knowledge available in the PHIDIAS resource.",
"download_owl": "http://aber-owl.net/media/ontologies/OHPI/12/ohpi.owl",
"homepage": "https://github.com/OHPI/ohpi",
"name": "Ontology of Host Pathogen Interactions",
"prefix": "OHPI"
},
"bioportal": {
"contact": {
"email": "edong@umich.edu",
"name": "Edison Ong"
},
"description": "The Ontology of Host-Pathogen Interactions (OHPI) is a biomedical ontology of the host-pathogen interactions. Its development follows the OBO Foundry Principles.",
"homepage": "https://github.com/OHPI/ohpi/",
"name": "Ontology of Host-Pathogen Interactions",
"prefix": "OHPI",
"publication": "https://www.ncbi.nlm.nih.gov/pubmed/30365026",
"version": "1.0.26"
},
"example": "9001411",
"fairsharing": {
"abbreviation": "OHPI",
"contact": {
"email": "edong@umich.edu",
"name": "Edison Ong",
"orcid": "0000-0002-5159-414X"
},
"description": "OHPI is a community-driven ontology of host-pathogen interactions (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs in the Victors database become less virulence inside a host organism or host cells. It is also developed to represent manually curated HPI knowledge available in the PHIDIAS resource.",
"domains": [
"Pathogen",
"Host",
"Infection"
],
"homepage": "https://github.com/OHPI/ohpi",
"license": "CC-BY-4.0",
"name": "Ontology of Host-Pathogen Interactions",
"prefix": "FAIRsharing.vxpUJ6",
"publications": [
{
"doi": "10.1093/nar/gky999",
"pubmed": "30365026",
"title": "Victors: a web-based knowledge base of virulence factors in human and animal pathogens",
"year": 2018
}
],
"repository": "https://github.com/OHPI/ohpi/issues",
"subjects": [
"Bioinformatics",
"Biomedical Science"
]
},
"mappings": {
"aberowl": "OHPI",
"bioportal": "OHPI",
"fairsharing": "FAIRsharing.vxpUJ6",
"obofoundry": "ohpi",
"ols": "ohpi",
"ontobee": "OHPI"
},
"obofoundry": {
"contact": "edong@umich.edu",
"contact.github": "e4ong1031",
"contact.label": "Edison Ong",
"contact.orcid": "0000-0002-5159-414X",
"deprecated": false,
"description": "OHPI is a community-driven ontology of host-pathogen interactions (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs in the Victors database become less virulence inside a host organism or host cells. It is developed to represent manually curated HPI knowledge available in the PHIDIAS resource.",
"domain": "biological systems",
"download.owl": "http://purl.obolibrary.org/obo/ohpi.owl",
"homepage": "https://github.com/OHPI/ohpi",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Ontology of Host Pathogen Interactions",
"preferredPrefix": "OHPI",
"prefix": "ohpi",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/30365026",
"title": "Victors: a web-based knowledge base of virulence factors in human and animal pathogens"
}
],
"repository": "https://github.com/OHPI/ohpi"
},
"ols": {
"description": "OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration).",
"download_owl": "http://purl.obolibrary.org/obo/ohpi.owl",
"homepage": "https://github.com/OHPI/ohpi",
"name": "OHPI: Ontology of Host-Pathogen Interactions",
"prefix": "ohpi",
"version": "2019-09-30",
"version.iri": "http://purl.obolibrary.org/obo/ohpi/releases/2019-09-30"
},
"ontobee": {
"library": "Library",
"name": "Ontology of Host Pathogen Interactions",
"prefix": "OHPI"
},
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1093/nar/gky999",
"pmc": "PMC6324020",
"pubmed": "30365026",
"title": "Victors: a web-based knowledge base of virulence factors in human and animal pathogens",
"year": 2019
}
],
"uri_format": "http://purl.obolibrary.org/obo/OHPI_$1"
},
"oid": {
"contributor_extras": [
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"example_extras": [
"2",
"2.16",
"2.16.840.1",
"2.16.840.1.113883",
"2.16.840.1.113883.6",
"2.16.840.1.113883.6.88"
],
"mappings": {
"miriam": "oid",
"n2t": "oid"
},
"miriam": {
"deprecated": false,
"description": "OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes.",
"homepage": "http://www.oid-info.com/introduction.htm",
"id": "00000673",
"name": "OID Repository",
"namespaceEmbeddedInLui": false,
"pattern": "^[\\d.]+$",
"prefix": "oid",
"sampleId": "2.16.840",
"uri_format": "http://www.oid-info.com/cgi-bin/display?oid=$1&submit=Display&action=display"
},
"n2t": {
"description": "OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes.",
"example": "2.16.840",
"homepage": "http://www.oid-info.com/introduction.htm",
"name": "OID Repository",
"namespaceEmbeddedInLui": false,
"pattern": "^[\\d.]+$",
"prefix": "oid",
"uri_format": "http://www.oid-info.com/cgi-bin/display?oid=$1&submit=Display&action=display"
},
"name": "ISO Object Identifier",
"providers": [
{
"code": "orange",
"description": "Mirror of OID site from Orange",
"homepage": "https://oid-rep.orange-labs.fr",
"name": "Mirror of OID site from Orange",
"uri_format": "https://oid-rep.orange-labs.fr/get/$1"
},
{
"code": "oid_www",
"description": "OID w/ WWW",
"homepage": "http://www.oid-info.com",
"name": "OID w/ WWW",
"uri_format": "http://www.oid-info.com/get/$1"
}
],
"references": [
"https://en.wikipedia.org/wiki/Object_identifier"
],
"uri_format": "http://oid-info.com/get/$1"
},
"olatdv": {
"aberowl": {
"description": "Life cycle stages for Medaka",
"download_owl": "http://aber-owl.net/media/ontologies/OLATDV/9/olatdv.owl",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv",
"name": "Medaka Developmental Stages",
"prefix": "OLATDV"
},
"biocontext": {
"prefix": "OLATDV"
},
"bioportal": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "Life cycle stages for Medaka. OlatDv is based on the original medaka stage ontology MFO by Thorsten Henrich. Currently it includes only pre-adult stages.",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv",
"name": "Medaka Developmental Stages",
"prefix": "OLATDV"
},
"example": "0000210",
"fairsharing": {
"abbreviation": "OlatDv",
"description": "Life cycle stages for Medaka. OlatDv is based on the original medaka stage ontology MFO by Thorsten Henrich. Currently it includes only pre-adult stages.",
"domains": [
"Life cycle stage"
],
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv",
"license": "CC-BY-3.0",
"name": "Medaka Stage Ontology",
"prefix": "FAIRsharing.c86z66",
"repository": "https://github.com/obophenotype/developmental-stage-ontologies/issues",
"subjects": [
"Aquaculture",
"Developmental Biology",
"Life Science"
]
},
"mappings": {
"aberowl": "OLATDV",
"biocontext": "OLATDV",
"bioportal": "OLATDV",
"fairsharing": "FAIRsharing.c86z66",
"obofoundry": "olatdv",
"ols": "olatdv",
"ontobee": "OlatDv"
},
"obofoundry": {
"contact": "frederic.bastian@unil.ch",
"contact.github": "fbastian",
"contact.label": "FrΓ©dΓ©ric Bastian",
"contact.orcid": "0000-0002-9415-5104",
"deprecated": true,
"description": "Life cycle stages for Medaka",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/olatdv.obo",
"download.owl": "http://purl.obolibrary.org/obo/olatdv.owl",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Medaka Developmental Stages",
"preferredPrefix": "OlatDv",
"prefix": "olatdv",
"repository": "https://github.com/obophenotype/developmental-stage-ontologies"
},
"ols": {
"description": "Life cycle stages for Medaka",
"download_owl": "http://purl.obolibrary.org/obo/olatdv.owl",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv",
"name": "Medaka Developmental Stages",
"prefix": "olatdv"
},
"ontobee": {
"library": "Library",
"name": "Medaka Developmental Stages",
"prefix": "OlatDv"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/OlatDv_$1"
},
"om": {
"aberowl": {
"description": "The Ontology of units of Measure (OM) 2.0 models concepts and relations important to scientific research. It has a strong focus on units, quantities, measurements, and dimensions. OM is modelled in OWL 2 - Web Ontology Language. The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units metre and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant or the quantity vaselife. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology and Typography.",
"download_owl": "http://aber-owl.net/media/ontologies/OM/31/om.owl",
"homepage": "https://github.com/HajoRijgersberg/OM",
"name": "Ontology of units of Measure",
"prefix": "OM",
"version": "2.0.57"
},
"agroportal": {
"contact": {
"email": "hajo.rijgersberg@wur.nl",
"name": "Hajo Rijgersberg"
},
"description": "The Ontology of units of Measure (OM) 2.0 models concepts and relations important to scientific research. It has a strong focus on units, quantities, measurements, and dimensions.",
"example_uri": "http://www.wurvoc.org/vocabularies/om-1.8/Molar_energy",
"homepage": "http://www.ontology-of-units-of-measure.org/",
"license": "CC-BY-4.0",
"name": "Ontology of units of Measure",
"prefix": "OM",
"repository": "https://github.com/HajoRijgersberg/OM",
"version": "2.0.57"
},
"bioportal": {
"contact": {
"email": "hajo.rijgersberg@wur.nl",
"name": "Hajo Rijgersberg"
},
"description": "The Ontology of units of Measure (OM) 2.0 models concepts and relations important to scientific research. It has a strong focus on units, quantities, measurements, and dimensions. OM is modelled in OWL 2 - Web Ontology Language. The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units metre and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant or the quantity vaselife. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology and Typography.",
"homepage": "https://github.com/HajoRijgersberg/OM",
"name": "Ontology of units of Measure",
"prefix": "OM",
"publication": "https://github.com/HajoRijgersberg/OM/blob/master/README.md#papers-on-om",
"version": "2.0.57"
},
"example": "Dimension",
"mappings": {
"aberowl": "OM",
"agroportal": "OM",
"bioportal": "OM",
"ols": "om"
},
"name": "Ontology of units of Measure",
"ols": {
"contact": "hajo.rijgersberg@wur.nl",
"description": "The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units meter and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant: km/s/Mpc, or the quantity vaselife. OM defines the complete set of concepts in the domain as distinguished in the textual standards. As a result the ontology can answer a wider range of competency questions than the existing approaches do. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology; Typography; Shipping; Food engineering; Post-harvest; technology; Dynamics of texture and taste; Packaging",
"download_rdf": "https://raw.githubusercontent.com/HajoRijgersberg/OM/master/om-2.0.rdf",
"homepage": "https://github.com/HajoRijgersberg/OM",
"name": "Ontology of units of Measure (OM)",
"prefix": "om",
"version": "2.0.57"
},
"repository": "https://github.com/HajoRijgersberg/OM",
"uri_format": "http://www.ontology-of-units-of-measure.org/resource/om-2/$1"
},
"oma.grp": {
"biocontext": {
"prefix": "OMA.GRP"
},
"mappings": {
"biocontext": "OMA.GRP",
"miriam": "oma.grp",
"n2t": "oma.grp"
},
"miriam": {
"deprecated": false,
"description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs.",
"homepage": "https://omabrowser.org/cgi-bin/gateway.pl",
"id": "00000343",
"name": "OMA Group",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]+$",
"prefix": "oma.grp",
"sampleId": "LCSCCPN",
"uri_format": "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1"
},
"n2t": {
"description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs.",
"example": "LCSCCPN",
"homepage": "https://omabrowser.org/cgi-bin/gateway.pl",
"name": "OMA Group through OMA browser at ETH Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]+$",
"prefix": "oma.grp",
"uri_format": "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1"
}
},
"oma.hog": {
"banana": "HOG",
"example": "0459895",
"mappings": {
"miriam": "oma.hog"
},
"miriam": {
"deprecated": false,
"description": "Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. ",
"homepage": "https://omabrowser.org",
"id": "00000785",
"name": "OMA HOGs",
"namespaceEmbeddedInLui": true,
"pattern": "^HOG:[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$",
"prefix": "oma.hog",
"sampleId": "0459895",
"uri_format": "https://omabrowser.org/oma/hog/resolve/HOG:$1/"
},
"pattern": "^[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$",
"uri_format": "https://omabrowser.org/oma/hog/HOG:$1"
},
"oma.protein": {
"biocontext": {
"prefix": "OMA.PROTEIN"
},
"mappings": {
"biocontext": "OMA.PROTEIN",
"miriam": "oma.protein",
"n2t": "oma.protein",
"togoid": "OmaProtein"
},
"miriam": {
"deprecated": false,
"description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records.",
"homepage": "https://omabrowser.org/cgi-bin/gateway.pl",
"id": "00000342",
"name": "OMA Protein",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]{5}\\d+$",
"prefix": "oma.protein",
"sampleId": "HUMAN16963",
"uri_format": "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1"
},
"n2t": {
"description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records.",
"example": "HUMAN16963",
"homepage": "https://omabrowser.org/cgi-bin/gateway.pl",
"name": "OMA Protein through OMA browser at ETH Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]{5}\\d+$",
"prefix": "oma.protein",
"uri_format": "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1"
},
"togoid": {
"catalog": "nbdc02221",
"examples": [
"ACIB400217",
"ACIB400465",
"HUMAN00333",
"HUMAN01170",
"HUMAN00470",
"HUMAN03367",
"ACIB400486",
"HUMAN01061",
"HUMAN02190",
"HUMAN02112"
],
"keywords": [
"Protein"
],
"name": "OMA protein",
"pattern": "^(?[A-Z]{3}[A-Z0-9]{2}[0-9]{5,6})$",
"prefix": "OmaProtein",
"uri_format": "http://identifiers.org/oma.protein/$1"
}
},
"omia": {
"biocontext": {
"prefix": "OMIA"
},
"contact": {
"email": "imke.tammen@sydney.edu.au",
"github": "ImkeTammen",
"name": "Imke Tammen",
"orcid": "0000-0002-5520-6597"
},
"contributor_extras": [
{
"email": "imke.tammen@sydney.edu.au",
"github": "ImkeTammen",
"name": "Imke Tammen",
"orcid": "0000-0002-5520-6597"
}
],
"deprecated": false,
"description": "Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources). The 'omia' prefix is used for phenes, either across species (omia:001000) or in a specific species (omia:001000-9615)",
"example": "001000",
"example_extras": [
"001000-9615"
],
"homepage": "https://omia.org",
"integbio": {
"alt_name": "Online Mendelian Inheritance in Animals",
"description": "OMIA is a database of inherited disorders, other (single-locus) traits, and genes in animals which is not include human, mouse and rat because of presence of their own resources. The records contain basical textual information, references, and links to OMIM, PubMed, and gene. The content on the site is manually curated.",
"fairsharing": "biodbcore-000579",
"homepage": "https://omia.org/home/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "University of Sydney",
"name": "OMIA",
"prefix": "nbdc00153",
"pubmeds": [
"12520001",
"33156546"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"keywords": [
"disorders",
"model organism database",
"traits"
],
"mappings": {
"biocontext": "OMIA",
"integbio": "nbdc00153",
"miriam": "omia",
"n2t": "omia",
"prefixcommons": "omia"
},
"miriam": {
"deprecated": false,
"description": "Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse).",
"homepage": "https://www.omia.org/home/",
"id": "00000142",
"name": "OMIA",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "omia",
"sampleId": "1000",
"uri_format": "https://www.omia.org/OMIA$1"
},
"n2t": {
"description": "Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse).",
"example": "1000",
"homepage": "http://omia.angis.org.au/",
"name": "OMIA at University of Sydney",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "omia",
"uri_format": "http://omia.angis.org.au/$1/"
},
"name": "Online Mendelian Inheritance in Animals",
"pattern": "^\\d{6}(-\\d+)?$",
"prefixcommons": {
"description": "Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse).",
"example": "1000",
"homepage": "http://omia.angis.org.au/",
"keywords": [
"gene",
"classification"
],
"name": "Online Mendelian Inheritance in Animals",
"pattern": "^\\d+$",
"prefix": "omia",
"uri_format": "http://omia.angis.org.au/retrieve.shtml?pid=$1"
},
"uri_format": "https://omia.org/phene/omia:$1"
},
"omiabis": {
"aberowl": {
"description": "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)",
"download_owl": "http://aber-owl.net/media/ontologies/OMIABIS/2/omiabis.owl",
"homepage": "https://github.com/OMIABIS/omiabis-dev",
"name": "Ontologized MIABIS",
"prefix": "OMIABIS"
},
"biocontext": {
"prefix": "OMIABIS"
},
"bioportal": {
"name": "Ontologized MIABIS",
"prefix": "OMIABIS"
},
"example": "0001079",
"mappings": {
"aberowl": "OMIABIS",
"biocontext": "OMIABIS",
"bioportal": "OMIABIS",
"obofoundry": "omiabis",
"ols": "omiabis",
"ontobee": "OMIABIS"
},
"obofoundry": {
"appears_in": [
"labo"
],
"contact": "mbrochhausen@gmail.com",
"contact.label": "Mathias Brochhausen",
"contact.orcid": "0000-0003-1834-3856",
"deprecated": true,
"description": "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/omiabis.owl",
"homepage": "https://github.com/OMIABIS/omiabis-dev",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Ontologized MIABIS",
"prefix": "omiabis",
"repository": "https://github.com/OMIABIS/omiabis-dev"
},
"ols": {
"description": "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)",
"homepage": "https://github.com/OMIABIS/omiabis-dev",
"name": "Ontologized MIABIS",
"prefix": "omiabis",
"version": "2014-05-28"
},
"ontobee": {
"library": "Library",
"name": "Ontologized MIABIS",
"prefix": "OMIABIS"
},
"pattern": "^\\d{7}$"
},
"omid": {
"mappings": {
"miriam": "omid"
},
"miriam": {
"deprecated": false,
"description": "Every entity in OpenCitations Meta (https://opencitations.net/meta) is assigned persistent internal identifier called OpenCitations Meta Identifier (OMID). The OMID has structure [[entity_type_abbreviation]]/[[supplier_prefix]][[sequential_number]]. For example, the first journal article ever processed has OMID br/0601 (the full URI is https://w3id.org/oc/meta/br/0601), where br is the abbreviation of bibliographic resource, and 060 corresponds to the supplier prefix, helpful in recognising at a glance the index it belongs to (i.e., OpenCitations Meta). Finally, 1 indicates that this is the index's first bibliographic resource ever minted.",
"homepage": "http://opencitations.net/",
"id": "00001004",
"name": "OpenCitations Meta Identifier",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z][a-z]/06[1-9]*0[1-9][0-9]*$",
"prefix": "omid",
"sampleId": "br/0601",
"uri_format": "https://w3id.org/oc/meta/$1"
}
},
"omim": {
"aberowl": {
"description": "Online Mendelian Inheritance in Man, OMIM (TM). McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine",
"homepage": "http://www.ncbi.nlm.nih.gov/omim/",
"name": "Online Mendelian Inheritance in Man",
"prefix": "OMIM",
"version": "2016AB"
},
"biocontext": {
"prefix": "OMIM"
},
"bioportal": {
"contact": {
"email": "custserv@nlm.nih.gov",
"name": "NLM Customer Service"
},
"description": "Online Mendelian Inheritance in Man, OMIM (TM). McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine",
"homepage": "http://www.ncbi.nlm.nih.gov/omim/",
"name": "Online Mendelian Inheritance in Man",
"prefix": "OMIM",
"publication": "http://www.ncbi.nlm.nih.gov/omim/",
"version": "2023AB"
},
"contact": {
"email": "ahamosh@jhmi.edu",
"github": "ahamosh",
"name": "Ada Hamosh",
"orcid": "0000-0002-1780-5230"
},
"edam": {
"description": "Identifier of an entry from the OMIM database.",
"name": "OMIM",
"obsolete": false,
"prefix": "1153"
},
"fairsharing": {
"abbreviation": "OMIM Ontology",
"description": "OMIM is a comprehensive, authoritative compendium of human genes and genetic phenotypes as well as the relationship between them, that is freely available and updated daily. The OMIM ontology contains terms used within the OMIM database.",
"domains": [
"Disease process modeling",
"Phenotype",
"Disease",
"Genetic disorder",
"Genotype"
],
"homepage": "http://omim.org/",
"name": "Online Mendelian Inheritance in Man Ontology",
"prefix": "FAIRsharing.b084yh",
"publications": [
{
"doi": "10.1093/nar/gku1205",
"pubmed": "25428349",
"title": "OMIM.org: Online Mendelian Inheritance in Man (OMIM(R)), an online catalog of human genes and genetic disorders",
"year": 2014
}
],
"subjects": [
"Biomedical Science"
]
},
"go": {
"homepage": "https://omim.org/",
"name": "Mendelian Inheritance in Man",
"prefix": "OMIM",
"synonyms": [
"MIM"
],
"uri_format": "https://omim.org/entry/$1"
},
"hl7": {
"description": "Online Mendelian Inheritance in Man (OMIM). Baltimore (MD): Johns Hopkins University, Center for Biotechnology Information, 1994.",
"name": "Online Mendelian Inheritance in Man 1993",
"preferred_prefix": "MIM",
"prefix": "2.16.840.1.113883.6.174",
"status": "Pending"
},
"integbio": {
"alt_name": "Online Mendelian Inheritance in Man",
"description": "OMIM is a database of human disease and genetic information and the online representation of Mendelian Inheritance in Man, a project initiated in the 1960s. The database summarizes heritable traits and provides information on both the trait and experimentally determined genetic causes. The database is manually curated by experts and can be searched by OMIM ID, gene, disease, or phenotype.",
"fairsharing": "biodbcore-000761",
"homepage": "http://www.ncbi.nlm.nih.gov/omim",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "OMIM",
"prefix": "nbdc00154",
"pubmeds": [
"18842627"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"license": "https://www.omim.org/help/agreement",
"mappings": {
"aberowl": "OMIM",
"biocontext": "OMIM",
"bioportal": "OMIM",
"edam": "1153",
"fairsharing": "FAIRsharing.b084yh",
"go": "OMIM",
"hl7": "2.16.840.1.113883.6.174",
"integbio": "nbdc00154",
"miriam": "mim",
"n2t": "mim",
"ncbi": "MIM",
"prefixcommons": "omim",
"uniprot": "DB-0062",
"wikidata": "P492"
},
"miriam": {
"deprecated": false,
"description": "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.",
"homepage": "https://omim.org/",
"id": "00000016",
"name": "OMIM",
"namespaceEmbeddedInLui": false,
"pattern": "^[*#+%^]?\\d{6}$",
"prefix": "mim",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "OMIM mirror at John Hopkins",
"homepage": "http://mirror.omim.org/",
"name": "OMIM mirror at John Hopkins",
"uri_format": "http://mirror.omim.org/entry/$1"
}
],
"sampleId": "603903",
"uri_format": "https://omim.org/entry/$1"
},
"n2t": {
"description": "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.",
"example": "603903",
"homepage": "https://omim.org/",
"name": "OMIM at John Hopkins",
"namespaceEmbeddedInLui": false,
"pattern": "^[*#+%^]?\\d{6}$",
"prefix": "mim",
"uri_format": "https://omim.org/entry/$1"
},
"name": "Online Mendelian Inheritance in Man",
"ncbi": {
"example": "123456",
"homepage": "https://www.ncbi.nlm.nih.gov/omim",
"name": "Mendelian Inheritance in Man numbers",
"prefix": "MIM"
},
"pattern": "^\\d+$",
"prefixcommons": {
"alt_uri_formats": [
"http://europe.omim.org/entry/#$1",
"http://us-east.omim.org/entry/#$1",
"http://omim.org/entry/#$1"
],
"description": "OMIM is a comprehensive, authoritative, and timely compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype.",
"example": "603903",
"homepage": "http://www.ncbi.nlm.nih.gov/omim/",
"keywords": [
"gene",
"gene expression"
],
"license": "http://www.nlm.nih.gov/copyright.html",
"name": "Online Mendelian Inheritance in Man",
"pattern": "^[*#+%^]?\\d{6}$",
"prefix": "omim",
"pubmed_ids": [
"15608251"
],
"synonyms": [
"mim"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/omim/$1"
},
"providers": [
{
"code": "legacy",
"description": "This is the actual endpoint for OMIM entries",
"homepage": "https://www.omim.org",
"name": "OMIM",
"uri_format": "https://www.omim.org/entry/$1"
},
{
"code": "miriam_legacy",
"description": "Legacy URLs for identifiers.org",
"homepage": "http://identifiers.org",
"name": "MIRIAM Legacy",
"uri_format": "http://identifiers.org/omim/$1"
},
{
"code": "ncbi.omim",
"description": "An NCBI endpoint for OMIM entries",
"homepage": "http://www.ncbi.nlm.nih.gov/omim",
"name": "NCBI",
"uri_format": "http://www.ncbi.nlm.nih.gov/omim/$1"
},
{
"code": "purl",
"description": "An extra purl that was registred, but probably won't be used.",
"homepage": "https://www.omim.org",
"name": "OMIM PURL (not in use)",
"uri_format": "https://purl.org/mim/MIM:$1"
},
{
"code": "purl2",
"description": "An extra purl that was registred, but probably won't be used.",
"homepage": "https://www.omim.org",
"name": "OMIM PURL (not in use)",
"uri_format": "https://omim.org/OMIM:$1"
}
],
"publications": [
{
"doi": "10.1093/nar/gku1205",
"pmc": "PMC4383985",
"pubmed": "25428349",
"title": "OMIM.org: Online Mendelian Inheritance in Man (OMIMΒ), an online catalog of human genes and genetic disorders",
"year": 2014
},
{
"doi": "10.1093/nar/gki033",
"pmc": "PMC539987",
"pubmed": "15608251",
"title": "Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders",
"year": 2005
}
],
"references": [
"https://github.com/biopragmatics/bioregistry/issues/497"
],
"synonyms": [
"OMIM",
"mim"
],
"uniprot": {
"abbreviation": "MIM",
"category": "Organism-specific databases",
"homepage": "https://www.omim.org/",
"name": "Online Mendelian Inheritance in Man (OMIM)",
"prefix": "DB-0062",
"publications": [
{
"doi": "10.1093/nar/gky1151",
"pubmed": "30445645"
}
],
"uri_format": "https://www.omim.org/entry/$1"
},
"uri_format": "https://omim.org/MIM:$1",
"wikidata": {
"database": "Q7187",
"description": "Online \"Mendelian Inheritance in Man\" catalogue codes for diseases, genes, or phenotypes",
"example": [
"143100",
"614371"
],
"name": "OMIM ID",
"pattern": "^\\d{6}$",
"prefix": "P492",
"uri_format": "https://omim.org/OMIM:$1"
}
},
"omim.ps": {
"banana": "PS",
"banana_peel": "",
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "OMIM.PS",
"uri_format": "https://www.omim.org/phenotypicSeries/$1"
},
"contact": {
"email": "ahamosh@jhmi.edu",
"github": "ahamosh",
"name": "Ada Hamosh",
"orcid": "0000-0002-1780-5230"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor_extras": [
{
"github": "sierra-moxon",
"name": "Sierra Moxon",
"orcid": "0000-0002-8719-7760"
}
],
"description": "A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.",
"example": "214100",
"homepage": "https://www.omim.org/phenotypicSeriesTitles/all",
"license": "https://www.omim.org/help/agreement",
"mappings": {
"biolink": "OMIM.PS"
},
"name": "OMIM Phenotypic Series",
"part_of": "omim",
"pattern": "^\\d+$",
"providers": [
{
"code": "legacy",
"description": "This is the actual endpoint for OMIM phenotypic series entries",
"homepage": "https://www.omim.org",
"name": "OMIM",
"uri_format": "https://omim.org/phenotypicSeries/PS$1"
}
],
"synonyms": [
"MIMPS",
"OMIMPS",
"PS",
"mim.ps"
],
"uri_format": "https://omim.org/MIM:PS$1"
},
"omit": {
"aberowl": {
"description": "Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain",
"download_owl": "http://aber-owl.net/media/ontologies/OMIT/41/omit.owl",
"homepage": "http://omit.cis.usouthal.edu/",
"name": "Ontology for MIRNA Target",
"prefix": "OMIT"
},
"biocontext": {
"prefix": "OMIT"
},
"bioportal": {
"contact": {
"email": "huang@southalabama.edu",
"name": "Jingshan Huang"
},
"description": "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). OMIT has reused and extended a set of well-established concepts from existing bio-ontologies, e.g., Gene Ontology, Sequence Ontology, Protein Ontology, NCBI Organism Taxonomy, Human Disease Ontology, Foundational Model of Anatomy, and so forth.",
"homepage": "http://omnisearch.soc.southalabama.edu/",
"name": "Ontology for MicroRNA Target",
"prefix": "OMIT",
"version": "OBO 4.0-12122013-2338"
},
"download_obo": "https://raw.githubusercontent.com/OmniSearch/omit/master/src/ontology/omit.obo",
"example": "0000069",
"fairsharing": {
"abbreviation": "OMIT",
"description": "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). Please note that, although the ontology is available at the stated GitHub repository, it has not been updated in a number of years and you may wish to carefully review the ontology before use.",
"domains": [
"Annotation",
"Computational biological predictions",
"Gene prediction",
"Molecular entity",
"Cell",
"Regulation of gene expression",
"Molecular interaction",
"Protein",
"Micro RNA",
"Gene"
],
"homepage": "https://github.com/OmniSearch/omit",
"license": "CC-BY-3.0",
"name": "Ontology for MicroRNA Target",
"prefix": "FAIRsharing.mf91p5",
"publications": [
{
"doi": "10.1371/journal.pone.0100855",
"pubmed": "25025130",
"title": "OMIT: dynamic, semi-automated ontology development for the microRNA domain",
"year": 2014
},
{
"doi": "10.1007/s11095-011-0573-8",
"pubmed": "21879385",
"title": "OMIT: a domain-specific knowledge base for microRNA target prediction",
"year": 2011
},
{
"doi": "10.1186/s13326-016-0064-2",
"pubmed": "27175225",
"title": "OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data",
"year": 2016
}
],
"repository": "https://github.com/OmniSearch/omit",
"subjects": [
"Life Science",
"Biology"
]
},
"mappings": {
"aberowl": "OMIT",
"biocontext": "OMIT",
"bioportal": "OMIT",
"fairsharing": "FAIRsharing.mf91p5",
"miriam": "omit",
"n2t": "omit",
"obofoundry": "omit",
"ols": "omit",
"ontobee": "OMIT"
},
"miriam": {
"deprecated": false,
"description": "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes).",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/omit/",
"id": "00000605",
"name": "OMIT",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{7}$",
"prefix": "omit",
"sampleId": "0005506",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/omit/terms?short_form=OMIT_$1"
},
"n2t": {
"description": "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes).",
"example": "0005506",
"homepage": "https://www.ebi.ac.uk/ols/ontologies/omit/",
"name": "Ontology for miRNA Target (OMIT) through OLS",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{7}$",
"prefix": "omit",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$1"
},
"name": "Ontology for MicroRNA Target",
"obofoundry": {
"appears_in": [
"mco"
],
"contact": "huang@southalabama.edu",
"contact.github": "Huang-OMIT",
"contact.label": "Jingshan Huang",
"contact.orcid": "0000-0003-2408-2883",
"deprecated": false,
"description": "Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain",
"domain": "chemistry and biochemistry",
"download.owl": "http://purl.obolibrary.org/obo/omit.owl",
"homepage": "http://omit.cis.usouthal.edu/",
"license": "CC BY 3.0",
"license.url": "https://creativecommons.org/licenses/by/3.0/",
"name": "Ontology for MIRNA Target",
"preferredPrefix": "OMIT",
"prefix": "omit",
"repository": "https://github.com/OmniSearch/omit"
},
"ols": {
"description": "Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain",
"download_owl": "http://purl.obolibrary.org/obo/omit.owl",
"homepage": "http://omit.cis.usouthal.edu/",
"name": "Ontology for MIRNA Target",
"prefix": "omit",
"version": "dev",
"version.iri": "http://purl.obolibrary.org/obo/omit/dev/omit.owl"
},
"ontobee": {
"library": "Library",
"name": "Ontology for MIRNA Target",
"prefix": "OMIT"
},
"publications": [
{
"doi": "10.1186/s13326-016-0064-2",
"pmc": "PMC4863347",
"pubmed": "27175225",
"title": "OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data",
"year": 2016
},
{
"doi": "10.1371/journal.pone.0100855",
"pmc": "PMC4099014",
"pubmed": "25025130",
"title": "OMIT: dynamic, semi-automated ontology development for the microRNA domain",
"year": 2014
},
{
"doi": "10.1007/s11095-011-0573-8",
"pubmed": "21879385",
"title": "OMIT: a domain-specific knowledge base for microRNA target prediction",
"year": 2011
}
],
"synonyms": [
"OMIT"
],
"uri_format": "http://purl.obolibrary.org/obo/OMIT_$1",
"wikidata": {
"database": "Q55118529"
}
},
"omo": {
"aberowl": {
"description": "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO).",
"download_owl": "http://aber-owl.net/media/ontologies/OMO/10/omo.owl",
"homepage": "https://github.com/information-artifact-ontology/ontology-metadata",
"name": "OBO Metadata Ontology",
"prefix": "OMO"
},
"bioportal": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "The OBO Metadata Ontology (OMO) specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO) before.",
"homepage": "https://github.com/information-artifact-ontology/ontology-metadata",
"name": "OBO Metadata Ontology",
"prefix": "OMO"
},
"example": "0003003",
"mappings": {
"aberowl": "OMO",
"bioportal": "OMO",
"obofoundry": "omo",
"ols": "omo",
"ontobee": "OMO"
},
"obofoundry": {
"appears_in": [
"pcl",
"uberon"
],
"contact": "cjmungall@lbl.gov",
"contact.github": "cmungall",
"contact.label": "Chris Mungall",
"contact.orcid": "0000-0002-6601-2165",
"deprecated": false,
"description": "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO).",
"domain": "information",
"download.owl": "http://purl.obolibrary.org/obo/omo.owl",
"homepage": "https://github.com/information-artifact-ontology/ontology-metadata",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "OBO Metadata Ontology",
"preferredPrefix": "OMO",
"prefix": "omo",
"repository": "https://github.com/information-artifact-ontology/ontology-metadata"
},
"ols": {
"description": "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO).",
"download_owl": "http://purl.obolibrary.org/obo/omo.owl",
"homepage": "https://github.com/information-artifact-ontology/ontology-metadata",
"name": "OBO Metadata Ontology",
"prefix": "omo",
"version": "2023-11-02",
"version.iri": "http://purl.obolibrary.org/obo/omo/releases/2023-11-02/omo.owl"
},
"ontobee": {
"library": "Library",
"name": "OBO Metadata Ontology",
"prefix": "OMO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/OMO_$1"
},
"omon": {
"contributor": {
"email": "oga.t@northeastern.edu",
"github": "tomo-oga",
"name": "Tomohiro Oga",
"orcid": "0009-0001-6787-3995"
},
"description": "The new national clinical trials registry of the Netherlands",
"example": "53367",
"homepage": "https://onderzoekmetmensen.nl/en",
"logo": "https://onderzoekmetmensen.nl/themes/custom/trialregister/logo.svg",
"name": "Overview of Medical Research in the Netherlands",
"pattern": "^\\d{5}$",
"reviewer": {
"email": "b.gyori@northeastern.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"uri_format": "https://onderzoekmetmensen.nl/en/trial/$1"
},
"omop": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor_extras": [
{
"email": "nicolas.matentzoglu@gmail.com",
"github": "matentzn",
"name": "Nicolas Matentzoglu",
"orcid": "0000-0002-7356-1779"
}
],
"description": "The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format.",
"example": "1",
"homepage": "https://www.ohdsi.org/data-standardization/the-common-data-model/",
"name": "Observational Medical Outcomes Partnership",
"pattern": "^\\d+$",
"providers": [
{
"code": "ohdsi.api",
"description": "Programmatic access to OMOP terms",
"homepage": "http://api.ohdsi.org",
"name": "OHDSI API",
"uri_format": "http://api.ohdsi.org/WebAPI/vocabulary/concept/$1"
},
{
"code": "ohdsi.data",
"description": " https://faircookbook.elixir-europe.org/content/recipes/applied-examples/ehden-ohdsi.html suggests https://data.ohdsi.org/concept/ as another uri expansion but it does not resolve.",
"homepage": "https://data.ohdsi.org/concept",
"name": "OHDSI Data Endpoint",
"uri_format": "https://data.ohdsi.org/concept/$1"
}
],
"references": [
"https://github.com/callahantiff/OMOP2OBO",
"https://github.com/biopragmatics/bioregistry/issues/599",
"https://github.com/biopragmatics/bioregistry/pull/600"
],
"synonyms": [
"OMOP"
],
"uri_format": "https://athena.ohdsi.org/search-terms/terms/$1"
},
"omp": {
"aberowl": {
"description": "An ontology of phenotypes covering microbes",
"download_owl": "http://aber-owl.net/media/ontologies/OMP/59/omp.owl",
"homepage": "http://microbialphenotypes.org",
"name": "Ontology of Microbial Phenotypes",
"prefix": "OMP"
},
"biocontext": {
"prefix": "OMP"
},
"bioportal": {
"contact": {
"email": "d-siegele@tamu.edu",
"name": "Deborah A. Siegele"
},
"description": "OMP is a formal ontology of phenotypes observed in all microbes: bacteria, archaea, protists, fungi, and viruses. OMP is being developed to be compatible with other microbial phenotype ontologies, such as the Fission Yeast Phenotype Ontology (FYPO) and the Ascomycete Phenotype Ontology (APO), and aims to standardize the capture of phenotypic information to allow improved cross-species data mining and analysis.",
"homepage": "microbialphenotypes.org",
"name": "Ontology of Microbial Phenotypes",
"prefix": "OMP",
"publication": "https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-014-0294-3",
"version": "releases/2019-06-07"
},
"example": "0005067",
"fairsharing": {
"abbreviation": "OMP",
"description": "The Ontology of Microbial Phenotypes (OMP) is a community ontology for annotating microbial phenotypes, including bacteria, archaea, protists, fungi, and viruses. It has been created to help with standardized capture of essential phenotypic information. OMP is designed to be compatible with other microbial phenotype ontologies, such as the Fission Yeast Phenotype Ontology (FYPO) and the Ascomycete Phenotype Ontology (APO), and aims to standardize the capture of phenotypic information to allow improved cross-species data mining and analysis.",
"domains": [
"Phenotype"
],
"homepage": "https://microbialphenotypes.org",
"license": "CC-BY-3.0",
"name": "Ontology of Microbial Phenotypes",
"prefix": "FAIRsharing.cc3f2x",
"publications": [
{
"doi": "10.1186/s12866-014-0294-3",
"pubmed": "25433798",
"title": "An ontology for microbial phenotypes",
"year": 2014
}
],
"repository": "https://github.com/microbialphenotypes/OMP-ontology",
"subjects": [
"Data Mining",
"Microbiology",
"Biology"
]
},
"mappings": {
"aberowl": "OMP",
"biocontext": "OMP",
"bioportal": "OMP",
"fairsharing": "FAIRsharing.cc3f2x",
"obofoundry": "omp",
"ols": "omp",
"ontobee": "OMP"
},
"obofoundry": {
"appears_in": [
"mco"
],
"contact": "jimhu@tamu.edu",
"contact.github": "jimhu-tamu",
"contact.label": "James C. Hu",
"contact.orcid": "0000-0001-9016-2684",
"deprecated": false,
"description": "An ontology of phenotypes covering microbes",
"domain": "phenotype",
"download.obo": "http://purl.obolibrary.org/obo/omp.obo",
"download.owl": "http://purl.obolibrary.org/obo/omp.owl",
"homepage": "http://microbialphenotypes.org",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Ontology of Microbial Phenotypes",
"preferredPrefix": "OMP",
"prefix": "omp",
"publications": [
{
"id": "https://doi.org/10.1186/s12866-014-0294-3",
"title": "An ontology for microbial phenotypes"
}
],
"repository": "https://github.com/microbialphenotypes/OMP-ontology"
},
"ols": {
"description": "An ontology of phenotypes covering microbes",
"download_owl": "http://purl.obolibrary.org/obo/omp.owl",
"homepage": "http://microbialphenotypes.org",
"name": "Ontology of Microbial Phenotypes",
"prefix": "omp",
"version": "2024-03-25",
"version.iri": "http://purl.obolibrary.org/obo/omp/releases/2024-03-25/omp.owl"
},
"ontobee": {
"library": "Library",
"name": "Ontology of Microbial Phenotypes",
"prefix": "OMP"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1186/s12866-014-0294-3",
"pmc": "PMC4287307",
"pubmed": "25433798",
"title": "An ontology for microbial phenotypes",
"year": 2014
}
],
"uri_format": "http://purl.obolibrary.org/obo/OMP_$1",
"wikidata": {
"database": "Q81661753"
}
},
"omrse": {
"aberowl": {
"description": "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations.",
"download_owl": "http://aber-owl.net/media/ontologies/OMRSE/58/omrse.owl",
"homepage": "https://github.com/mcwdsi/OMRSE/wiki/OMRSE-Overview",
"name": "Ontology for Modeling and Representation of Social Entities",
"prefix": "OMRSE"
},
"biocontext": {
"prefix": "OMRSE"
},
"bioportal": {
"contact": {
"email": "hoganwr@gmail.com",
"name": "Bill Hogan"
},
"description": "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations.",
"homepage": "https://github.com/mcwdsi/OMRSE",
"name": "Ontology for Modeling and Representation of Social Entities",
"prefix": "OMRSE",
"publication": "https://github.com/mcwdsi/OMRSE#list-of-publications",
"version": "2024-03-22"
},
"download_json": "http://purl.obolibrary.org/obo/omrse.json",
"download_obo": "https://github.com/ufbmi/OMRSE/raw/master/omrse-full.obo",
"example": "00000022",
"fairsharing": {
"abbreviation": "OMRSE",
"contact": {
"email": "hoganwr@gmail.com",
"name": "William Hogan",
"orcid": "0000-0002-9881-1017"
},
"description": "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations. For more information on the social entities represented in OMRSE, please visit our wiki page or list of publications. OMRSE is designed to be a mid-level ontology that bridges the gap between BFO, which it reuses for its top-level hierarchy, and more specific domain or application ontologies. For this reason, we are always open to working with ontology developers who want to build interoperability between their projects and OMRSE.",
"domains": [
"Patient care",
"Hospital"
],
"homepage": "https://github.com/mcwdsi/OMRSE",
"license": "CC-BY-4.0",
"name": "Ontology for Modeling and Representation of Social Entities",
"prefix": "FAIRsharing.z0p37e",
"publications": [
{
"doi": "10.1186/s13326-016-0087-8",
"pubmed": "27406187",
"title": "The ontology of medically related social entities: recent developments",
"year": 2016
}
],
"repository": "https://github.com/mcwdsi/OMRSE/issues",
"subjects": [
"Demographics",
"Social Science",
"Health Science",
"Biomedical Science"
]
},
"mappings": {
"aberowl": "OMRSE",
"biocontext": "OMRSE",
"bioportal": "OMRSE",
"fairsharing": "FAIRsharing.z0p37e",
"obofoundry": "omrse",
"ols": "omrse",
"ontobee": "OMRSE"
},
"obofoundry": {
"appears_in": [
"labo"
],
"contact": "hoganwr@gmail.com",
"contact.github": "hoganwr",
"contact.label": "Bill Hogan",
"contact.orcid": "0000-0002-9881-1017",
"deprecated": false,
"description": "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/omrse.owl",
"homepage": "https://github.com/mcwdsi/OMRSE/wiki/OMRSE-Overview",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Ontology for Modeling and Representation of Social Entities",
"preferredPrefix": "OMRSE",
"prefix": "omrse",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/27406187",
"title": "The ontology of medically related social entities: recent developments"
}
],
"repository": "https://github.com/mcwdsi/OMRSE"
},
"ols": {
"description": "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations.",
"download_owl": "http://purl.obolibrary.org/obo/omrse.owl",
"homepage": "https://github.com/mcwdsi/OMRSE/wiki/OMRSE-Overview",
"name": "Ontology for Modeling and Representation of Social Entities",
"prefix": "omrse",
"version": "2024-03-22",
"version.iri": "http://purl.obolibrary.org/obo/omrse/releases/2024-03-22/omrse.owl"
},
"ontobee": {
"library": "Library",
"name": "Ontology for Modeling and Representation of Social Entities",
"prefix": "OMRSE"
},
"pattern": "^\\d{8}$",
"publications": [
{
"doi": "10.1186/s13326-016-0087-8",
"pmc": "PMC4942889",
"pubmed": "27406187",
"title": "The ontology of medically related social entities: recent developments",
"year": 2016
}
],
"uri_format": "http://purl.obolibrary.org/obo/OMRSE_$1"
},
"omx.dataset": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "OncoMX is a knowledgebase for exploring cancer biomarkers in the context of related cancer and healthy data. This resource is for datasets within OncoMX.",
"example": "000059",
"homepage": "https://data.oncomx.org",
"name": "OncoMX Dataset",
"pattern": "^\\d+$",
"uri_format": "https://data.oncomx.org/OMX_$1"
},
"oncotree": {
"appears_in": [
"efo"
],
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research.",
"example": "BLL",
"homepage": "http://oncotree.mskcc.org",
"keywords": [
"cancer",
"clinical decision support systems",
"oncology"
],
"name": "OncoTree",
"uri_format": "http://oncotree.mskcc.org/api/tumorTypes/search/code/$1"
},
"one": {
"aberowl": {
"description": "An ontology to standardize research output of nutritional epidemiologic studies.",
"download_owl": "http://aber-owl.net/media/ontologies/ONE/9/one.owl",
"homepage": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies",
"name": "Ontology for Nutritional Epidemiology",
"prefix": "ONE"
},
"bioportal": {
"contact": {
"email": "Chen.Yang@UGent.be",
"name": "Chen Yang"
},
"description": "Nutritional epidemiology is a specific research area. The generic ontologies for food science, nutrition science or medical science failed to cover the specific characteristics of nutritional epidemiologic studies. As a result, we developed the ontology for nutritional epidemiology (ONE) in order to describe nutritional epidemiologic studies accurately.",
"homepage": "https://github.com/cyang0128/Nutritional-epidemiological-ontologies",
"name": "Ontology for Nutritional Epidemiology",
"prefix": "ONE",
"publication": "https://www.mdpi.com/2072-6643/11/6/1300",
"version": "V2.2"
},
"example": "0001021",
"fairsharing": {
"abbreviation": "ONE",
"contact": {
"email": "carl.lachat@ugent.be",
"name": "Carl Lachat",
"orcid": "0000-0002-1389-8855"
},
"description": "The ontology for nutritional epidemiology (ONE) describes nutritional epidemiologic studies, and was created to improve on how generic ontologies for food science, nutrition science or medical science covered the specific characteristics of nutritional epidemiologic studies.",
"domains": [
"Diet"
],
"homepage": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies",
"license": "CC-BY-4.0",
"name": "Ontology for Nutritional epidemiology",
"prefix": "FAIRsharing.USxx0K",
"publications": [
{
"pubmed": "31181762",
"title": "An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content",
"year": 2019
}
],
"repository": "https://github.com/cyang0128/Nutritional-Epidemiologic-ontologies",
"subjects": [
"Nutritional Science",
"Metabolomics",
"Epidemiology"
]
},
"mappings": {
"aberowl": "ONE",
"bioportal": "ONE",
"fairsharing": "FAIRsharing.USxx0K",
"obofoundry": "one",
"ols": "one",
"ontobee": "ONE"
},
"obofoundry": {
"contact": "chenyangnutrition@gmail.com",
"contact.github": "cyang0128",
"contact.label": "Chen Yang",
"contact.orcid": "0000-0001-9202-5309",
"depends_on": [
"foodon",
"obi",
"ons"
],
"deprecated": false,
"description": "An ontology to standardize research output of nutritional epidemiologic studies.",
"domain": "diet, metabolomics, and nutrition",
"download.owl": "http://purl.obolibrary.org/obo/one.owl",
"homepage": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Ontology for Nutritional Epidemiology",
"preferredPrefix": "ONE",
"prefix": "one",
"repository": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies"
},
"ols": {
"description": "An ontology to standardize research output of nutritional epidemiologic studies.",
"download_owl": "http://purl.obolibrary.org/obo/one.owl",
"homepage": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies",
"name": "Ontology for Nutritional Epidemiology",
"prefix": "one"
},
"ontobee": {
"library": "Library",
"name": "Ontology for Nutritional Epidemiology",
"prefix": "ONE"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.3390/nu11061300",
"pmc": "PMC6628051",
"pubmed": "31181762",
"title": "An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content",
"year": 2019
}
],
"uri_format": "http://purl.obolibrary.org/obo/ONE_$1"
},
"ons": {
"aberowl": {
"description": "An ontology for description of concepts in the nutritional studies domain.",
"download_owl": "http://aber-owl.net/media/ontologies/ONS/28/ons.owl",
"homepage": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies",
"name": "Ontology for Nutritional Studies",
"prefix": "ONS"
},
"agroportal": {
"contact": {
"email": "francesco.vitali.bio@gmail.com",
"name": "Francesco Vitali"
},
"description": "ONS was developed under the ENPADASI European project, to assist the standardized description of (human) nutritional studies. As such, it includes and covers classes and relations that are commonly encountered while conducting, storing, harmonizing, integrating, describing and querying for nutritional studies. ONS main objective and long-term goal, is to represent a comprehensive resource for the description of concepts in the broader human nutrition domain, representing a solid and extensible formal ontology framework, where integration of new information can be easily achieved by the addition of extra modules.",
"example_uri": "http://purl.obolibrary.org/obo/ONS_0000083",
"name": "Ontology for Nutritional Studies",
"prefix": "ONS",
"version": "Relese version 1.0"
},
"bioportal": {
"contact": {
"email": "francesco.vitali@ibba.cnr.it",
"name": "Francesco Vitali"
},
"description": "Ontology For Nutritional Studies (ONS) is the first systematic effort to provide a formal ontology framework for the description of nutritional studies.",
"homepage": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies",
"name": "Ontology for Nutritional Studies",
"prefix": "ONS",
"publication": "https://doi.org/10.1186/s12263-018-0601-y",
"version": "2024-07-03"
},
"example": "0000060",
"fairsharing": {
"abbreviation": "ONS",
"description": "Ontology For Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies. It is the first systematic effort to provide a formal ontology framework for the description of nutritional studies.",
"homepage": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies",
"license": "CC-BY-4.0",
"name": "Ontology for Nutritional Studies",
"prefix": "FAIRsharing.rfec93",
"repository": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies/issues",
"subjects": [
"Nutritional Science",
"Biomedical Science"
]
},
"mappings": {
"aberowl": "ONS",
"agroportal": "ONS",
"bioportal": "ONS",
"fairsharing": "FAIRsharing.rfec93",
"obofoundry": "ons",
"ols": "ons",
"ontobee": "ONS"
},
"obofoundry": {
"appears_in": [
"one"
],
"contact": "francesco.vitali@ibba.cnr.it",
"contact.github": "FrancescoVit",
"contact.label": "Francesco Vitali",
"contact.orcid": "0000-0001-9125-4337",
"depends_on": [
"bfo",
"chebi",
"envo",
"foodon",
"ncbitaxon",
"obi",
"ro",
"uberon"
],
"deprecated": false,
"description": "An ontology for description of concepts in the nutritional studies domain.",
"domain": "diet, metabolomics, and nutrition",
"download.owl": "http://purl.obolibrary.org/obo/ons.owl",
"homepage": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Ontology for Nutritional Studies",
"preferredPrefix": "ONS",
"prefix": "ons",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/29736190",
"title": "ONS: an ontology for a standardized description of interventions and observational studies in nutrition"
}
],
"repository": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies"
},
"ols": {
"description": "An ontology for description of concepts in the nutritional studies domain.",
"download_owl": "http://purl.obolibrary.org/obo/ons.owl",
"homepage": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies",
"name": "Ontology for Nutritional Studies",
"prefix": "ons",
"version": "2024-07-03",
"version.iri": "https://raw.githubusercontent.com/enpadasi/Ontology-for-Nutritional-Studies/releases/download/v2024-07-03/ons.owl"
},
"ontobee": {
"library": "Library",
"name": "Ontology for Nutritional Studies",
"prefix": "ONS"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1186/s12263-018-0601-y",
"pmc": "PMC5928560",
"pubmed": "29736190",
"title": "ONS: an ontology for a standardized description of interventions and observational studies in nutrition",
"year": 2018
}
],
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},
"ontie": {
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"email": "bpeters@lji.org",
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"name": "Bjoern Peters",
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},
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
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},
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"example": "0000001",
"fairsharing": {
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"domains": [
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"Major histocompatibility complex"
],
"homepage": "http://ontology.iedb.org",
"name": "Ontology of Immune Epitopes",
"prefix": "FAIRsharing.kx2md1",
"subjects": [
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"Life Science"
]
},
"homepage": "https://ontology.iedb.org/",
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},
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},
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"name": "OntoAvida: ontology for Avida digital evolution platform",
"prefix": "ONTOAVIDA"
},
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"name": "OntoAvida: ontology for Avida digital evolution platform",
"prefix": "ONTOAVIDA"
},
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"bioportal": "ONTOAVIDA",
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"ols": "ontoavida",
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"license": "CC BY 4.0",
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"name": "OntoAvida: ontology for Avida digital evolution platform",
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"homepage": "https://gitlab.com/fortunalab/ontoavida",
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"prefix": "ontoavida",
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"homepage": "ontoneo.com",
"name": "Obstetric and Neonatal Ontology",
"prefix": "ONTONEO"
},
"biocontext": {
"prefix": "ONTONEO"
},
"bioportal": {
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"name": "Fernanda Farinelli"
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"name": "Obstetric and Neonatal Ontology",
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"version": "2021-04-29"
},
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"abbreviation": "ONTONEO",
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}
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},
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}
],
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},
"oostt": {
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},
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},
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"prefix": "OOSTT",
"version": "release version - 2024-01-25"
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"name": "Ontology of Organizational Structures of Trauma centers and Trauma systems",
"prefix": "FAIRsharing.b4sa0w",
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"subjects": [
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},
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},
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"download.owl": "http://purl.obolibrary.org/obo/oostt.owl",
"homepage": "https://github.com/OOSTT/OOSTT",
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"license.url": "http://creativecommons.org/licenses/by/4.0/",
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},
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"version": "2024-01-25",
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},
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"name": "Ontology of Organizational Structures of Trauma centers and Trauma systems",
"prefix": "OOSTT"
},
"pattern": "^\\d{8}$",
"uri_format": "http://purl.obolibrary.org/obo/OOSTT_$1"
},
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"download_owl": "http://aber-owl.net/media/ontologies/OPB/13/opb.owl",
"homepage": "https://sites.google.com/site/semanticsofbiologicalprocesses/projects/the-ontology-of-physics-for-biology-opb",
"name": "Ontology of Physics for Biology",
"prefix": "OPB",
"version": "1.05"
},
"banana": "OPB",
"banana_peel": "_",
"biocontext": {
"prefix": "OPB"
},
"bioportal": {
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},
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"homepage": "https://sites.google.com/site/semanticsofbiologicalprocesses/projects/the-ontology-of-physics-for-biology-opb",
"name": "Ontology of Physics for Biology",
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"version": "1.2"
},
"contact": {
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"name": "Maxwell L. Neal",
"orcid": "0000-0002-2390-6572"
},
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"github": "bgyori",
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"orcid": "0000-0001-9439-5346"
}
],
"example": "00573",
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"description": "The Ontology of Physics for Biology is a reference of classical physics as applied to the dynamics of biological systems. This resource provides a reference ontology of physical properties (e.g., pressure, chemical concentration) and principles (e.g., Ohmβs law, Fickeβs law) by which the physical meaning of biosimulation models may be annotated.",
"domains": [
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"Concentration",
"Kinetic model"
],
"homepage": "https://sites.google.com/site/semanticsofbiologicalprocesses/projects/the-ontology-of-physics-for-biology-opb",
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"year": 2012
},
{
"doi": "10.1186/2041-1480-4-41",
"pubmed": "24295137",
"title": "Ontology of physics for biology: representing physical dependencies as a basis for biological processes",
"year": 2013
}
],
"subjects": [
"Life Science",
"Physics"
]
},
"mappings": {
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"biocontext": "OPB",
"bioportal": "OPB",
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"miriam": "opb",
"n2t": "opb",
"prefixcommons": "opb"
},
"miriam": {
"deprecated": false,
"description": "The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.",
"homepage": "http://bioportal.bioontology.org/ontologies/OPB",
"id": "00000129",
"name": "Ontology of Physics for Biology",
"namespaceEmbeddedInLui": false,
"pattern": "^OPB_\\d+$",
"prefix": "opb",
"sampleId": "OPB_00573",
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},
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"example": "OPB_00573",
"homepage": "http://bioportal.bioontology.org/ontologies/OPB",
"name": "Ontology of Physics for Biology through Bioportal",
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"pattern": "^OPB_\\d+$",
"prefix": "opb",
"uri_format": "http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23$1"
},
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"description": "The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.",
"example": "OPB_00573",
"homepage": "https://sites.google.com/site/semanticsofbiologicalprocesses/projects/the-ontology-of-physics-for-biology-opb",
"keywords": [
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"structure"
],
"name": "Ontology of Physics for Biology",
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"prefix": "opb",
"rdf_uri_format": "http://bhi.washington.edu/OPB#$1",
"synonyms": [
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]
},
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"pmc": "PMC3904761",
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},
{
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"pubmed": "22216106",
"title": "Physical properties of biological entities: an introduction to the ontology of physics for biology",
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}
],
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},
"openalex": {
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"github": "hpiwowar",
"name": "Heather Piwowar",
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},
"contributor": {
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},
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"example": "W2741809807",
"github_request_issue": 280,
"homepage": "https://openalex.org/",
"keywords": [
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"wikidata"
],
"name": "OpenAlex",
"pattern": "^[WAICV]\\d{2,}$",
"reviewer": {
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://openalex.org/$1"
},
"openwemi": {
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"github": "kcoyle",
"name": "Karen Coyle",
"orcid": "0000-0002-1085-7089"
},
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "openWEMI is a minimally constrained vocabulary for describing created resources using the concepts of Work, Expression, Manifestation, Item.",
"example": "Endeavor",
"homepage": "https://dcmi.github.io/openwemi/",
"license": "CC0-1.0",
"name": "openWEMI Vocabulary",
"pattern": "^\\w+$",
"references": [
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"http://archive.ifla.org/VII/s13/frbr/frbr_2008.pdf"
],
"repository": "https://github.com/dcmi/openwemi",
"uri_format": "https://dcmi.github.io/openwemi/ns#$1"
},
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"homepage": "https://github.com/OPL-ontology/OPL",
"name": "Ontology for Parasite LifeCycle",
"prefix": "OPL"
},
"biocontext": {
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},
"bioportal": {
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"name": "Priti Parikh"
},
"description": "The Ontology for Parasite LifeCycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.",
"homepage": "http://knoesis.wright.edu/trykipedia/parasitelifecycle",
"name": "Ontology for Parasite LifeCycle",
"prefix": "OPL",
"publication": "http://knoesis.wright.edu/trykipedia/parasitelifecycle",
"version": "2023-08-28"
},
"example": "0000319",
"fairsharing": {
"abbreviation": "OPL",
"description": "OPL models the life cycle stage details of T.cruzi and two related kinetoplastids, Trypanosoma brucei and Leishmania major. In addition, the ontology also models necessary contextual details such as host information, vector information, strain and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.",
"domains": [
"Parasite",
"Host",
"Life cycle",
"Life cycle stage"
],
"homepage": "https://bioportal.bioontology.org/ontologies/OPL",
"name": "Ontology for Parasite LifeCycle",
"prefix": "FAIRsharing.ez2nhb",
"publications": [
{
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"pubmed": "22621763",
"title": "The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms",
"year": 2012
}
],
"repository": "https://github.com/OPL-ontology/OPL",
"subjects": [
"Anatomy",
"Developmental Biology",
"Life Science"
]
},
"mappings": {
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"biocontext": "OPL",
"bioportal": "OPL",
"fairsharing": "FAIRsharing.ez2nhb",
"miriam": "opl",
"obofoundry": "opl",
"ols": "opl",
"ontobee": "OPL"
},
"miriam": {
"deprecated": false,
"description": "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc.",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/opl",
"id": "00001047",
"name": "Ontology for Parasite Lifecycle",
"namespaceEmbeddedInLui": true,
"pattern": "^OPL:\\d+$",
"prefix": "opl",
"sampleId": "0000134",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/opl/classes?obo_id=OPL:$1"
},
"obofoundry": {
"contact": "zhengj2007@gmail.com",
"contact.github": "zhengj2007",
"contact.label": "Jie Zheng",
"contact.orcid": "0000-0002-2999-0103",
"deprecated": false,
"description": "A reference ontology for parasite life cycle stages.",
"domain": "organisms",
"download.owl": "http://purl.obolibrary.org/obo/opl.owl",
"homepage": "https://github.com/OPL-ontology/OPL",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Ontology for Parasite LifeCycle",
"preferredPrefix": "OPL",
"prefix": "opl",
"repository": "https://github.com/OPL-ontology/OPL"
},
"ols": {
"description": "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.",
"download_owl": "http://purl.obolibrary.org/obo/opl.owl",
"homepage": "https://github.com/OPL-ontology/OPL",
"name": "Ontology for Parasite Lifecycle",
"prefix": "opl",
"version": "2023-08-28",
"version.iri": "http://purl.obolibrary.org/obo/opl/2023-08-28/opl.owl"
},
"ontobee": {
"library": "Library",
"name": "Ontology for Parasite LifeCycle",
"prefix": "OPL"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1186/2041-1480-3-5",
"pmc": "PMC3488002",
"pubmed": "22621763",
"title": "The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms",
"year": 2012
}
],
"uri_format": "http://purl.obolibrary.org/obo/OPL_$1"
},
"opm": {
"biocontext": {
"prefix": "OPM"
},
"fairsharing": {
"abbreviation": "OPM",
"description": "The Open Provenance Model (OPM) is a model of provenance that is designed to meet the following requirements: (1) To allow provenance information to be exchanged between systems, by means of a compatibility layer based on a shared provenance model. (2) To allow developers to build and share tools that operate on such a provenance model. (3) To define provenance in a precise, technology-agnostic manner. (4) To support a digital representation of provenance for any 'thing', whether produced by computer systems or not. (5) To allow multiple levels of description to coexist. (6) To define a core set of rules that identify the valid inferences that can be made on provenance representation.",
"homepage": "https://doi.org/10.1016/j.future.2010.07.005",
"name": "Open Provenance Model",
"prefix": "FAIRsharing.7c683b",
"publications": [],
"subjects": [
"Data Management",
"Computer Science"
]
},
"mappings": {
"biocontext": "OPM",
"fairsharing": "FAIRsharing.7c683b",
"miriam": "opm",
"n2t": "opm"
},
"miriam": {
"deprecated": false,
"description": "The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization.",
"homepage": "http://opm.phar.umich.edu/",
"id": "00000333",
"name": "OPM",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9][A-Za-z0-9]{3}$",
"prefix": "opm",
"sampleId": "1h68",
"uri_format": "http://opm.phar.umich.edu/protein.php?pdbid=$1"
},
"n2t": {
"description": "The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization.",
"example": "1h68",
"homepage": "http://opm.phar.umich.edu/",
"name": "OPM at University of Michigan",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9][A-Za-z0-9]{3}$",
"prefix": "opm",
"uri_format": "http://opm.phar.umich.edu/protein.php?pdbid=$1"
},
"name": "Orientations of Proteins in Membranes Database"
},
"opmi": {
"aberowl": {
"description": "The Ontology of Precision Medicine and Investigation (OPMI) aims to ontologically represent and standardize various entities and relations associated with precision medicine and related investigations at different conditions.",
"download_owl": "http://aber-owl.net/media/ontologies/OPMI/29/opmi.owl",
"homepage": "https://github.com/OPMI/opmi",
"name": "Ontology of Precision Medicine and Investigation",
"prefix": "OPMI"
},
"bioportal": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "The Ontology of Precision Medicine and Investigation (OPMI) is an application ontology to support precision medicine and its related investigations. OPMI is community-driven and developed by following the OBO Foundry ontology development principles. OPMI reuses, aligns, and integrates related terms from existing OBO ontologies.",
"homepage": "https://github.com/OPMI/opmi",
"name": "Ontology of Precision Medicine and Investigation",
"prefix": "OPMI",
"version": "Vision Release: 1.0.166"
},
"example": "0000101",
"fairsharing": {
"abbreviation": "OPMI",
"contact": {
"email": "yongqunh@umich.edu",
"name": "Yongqun He",
"orcid": "0000-0001-9189-9661"
},
"description": "The Ontology of Precision Medicine and Investigation (OPMI) ontology is an application ontology to support precision medicine and related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles. OPMI reuses, aligns, and integrates related terms from existing ontologies in the OBO ontology library. OPMI aims to represent and standardize the entities associated with precision medicine, including all the data/metadata types, investigation processes, and analysis in various aspects of clinical, pathological, and molecular studies to be conducted in KPMP. The Kidney Tissue Atlas Ontology (KTAO) is a more kidney-specific complementary addition to OMPI precision medicine-related terms that can be used in parallel. ",
"domains": [
"Disease"
],
"homepage": "https://github.com/OPMI/opmi",
"license": "CC-BY-4.0",
"name": "Ontology of Precision Medicine and Investigation",
"prefix": "FAIRsharing.d2d84f",
"subjects": [
"Clinical Studies",
"Omics"
]
},
"mappings": {
"aberowl": "OPMI",
"bioportal": "OPMI",
"fairsharing": "FAIRsharing.d2d84f",
"obofoundry": "opmi",
"ols": "opmi",
"ontobee": "OPMI"
},
"obofoundry": {
"appears_in": [
"labo",
"scdo"
],
"contact": "yongqunh@med.umich.edu",
"contact.github": "yongqunh",
"contact.label": "Yongqun Oliver He",
"contact.orcid": "0000-0001-9189-9661",
"deprecated": false,
"description": "The Ontology of Precision Medicine and Investigation (OPMI) aims to ontologically represent and standardize various entities and relations associated with precision medicine and related investigations at different conditions.",
"domain": "investigations",
"download.owl": "http://purl.obolibrary.org/obo/opmi.owl",
"homepage": "https://github.com/OPMI/opmi",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Ontology of Precision Medicine and Investigation",
"preferredPrefix": "OPMI",
"prefix": "opmi",
"repository": "https://github.com/OPMI/opmi"
},
"ols": {
"description": "OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles.",
"download_owl": "http://purl.obolibrary.org/obo/opmi.owl",
"homepage": "https://github.com/OPMI/opmi",
"name": "OPMI: Ontology of Precision Medicine and Investigation",
"prefix": "opmi",
"version": "1.0.166"
},
"ontobee": {
"library": "Library",
"name": "Ontology of Precision Medicine and Investigation",
"prefix": "OPMI"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/OPMI_$1"
},
"orcid": {
"bartoc": {
"description": "ORCID provides a persistent digital identifier that distinguishes you from every other researcher and, through integration in key research workflows such as manuscript and grant submission, supports automated linkages between you and your professional activities ensuring that your work is recognized.",
"homepage": "http://orcid.org/",
"license": "CC0-1.0",
"name": "ORCID",
"prefix": "2021",
"wikidata_database": "Q51044"
},
"biocontext": {
"prefix": "ORCID"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "ORCID",
"uri_format": "https://orcid.org/$1"
},
"contact": {
"email": "w.simpson@orcid.org",
"github": "wjrsimpson",
"name": "Will Simpson",
"orcid": "0000-0003-4654-1403"
},
"example": "0000-0003-4423-4370",
"fairsharing": {
"abbreviation": "ORCID",
"description": "ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. The ORCID Registry is a repository of unique researcher identifiers which allows researchers to manage a record of their research activities. In addition, there are APIs that support system-to-system communication and authentication. ORCID makes its code available under an open source license, and will post an annual public data file under a CC0 waiver for free download.",
"homepage": "http://orcid.org/",
"license": "http://orcid.org/node/43",
"name": "Open Researcher and Contributor ID Registry",
"prefix": "FAIRsharing.nx58jg",
"publications": [
{
"doi": "10.23640/07243.16687207.v1",
"pubmed_id": null,
"title": "From Vision to Value: ORCID's 2022β2025 Strategic Plan"
},
{
"doi": "10.23640/07243.12009255.v3",
"pubmed_id": null,
"title": "ORCID's 2025 Vision"
}
],
"repository": "https://github.com/ORCID",
"subjects": [
"Subject Agnostic"
],
"twitter": "ORCID_Org"
},
"go": {
"description": "ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers.",
"homepage": "https://orcid.org/",
"name": "Open Researcher and Contributor",
"prefix": "orcid",
"uri_format": "https://orcid.org/$1"
},
"keywords": [
"person"
],
"mappings": {
"bartoc": "2021",
"biocontext": "ORCID",
"biolink": "ORCID",
"fairsharing": "FAIRsharing.nx58jg",
"go": "orcid",
"miriam": "orcid",
"n2t": "orcid",
"wikidata": "P496"
},
"mastodon": "ORCID_Org@scicomm.xyz",
"miriam": {
"deprecated": false,
"description": "ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities.",
"homepage": "https://orcid.org",
"id": "00000382",
"name": "ORCID",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$",
"prefix": "orcid",
"sampleId": "0000-0002-5355-2576",
"uri_format": "https://orcid.org/$1"
},
"n2t": {
"description": "ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities.",
"example": "0000-0002-5355-2576",
"homepage": "https://orcid.org",
"name": "ORCID at Bethesda",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$",
"prefix": "orcid",
"uri_format": "https://orcid.org/$1"
},
"name": "Open Researcher and Contributor",
"providers": [
{
"code": "scholia",
"description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.",
"homepage": "https://scholia.toolforge.org/",
"name": "Scholia",
"uri_format": "https://scholia.toolforge.org/orcid/$1"
}
],
"publications": [
{
"doi": "10.23640/07243.16687207.v1",
"title": "From Vision to Value: ORCID's 2022β2025 Strategic Plan",
"year": 2021
},
{
"doi": "10.23640/07243.12009255.v3",
"title": "ORCID's 2025 Vision",
"year": 2020
}
],
"synonyms": [
"ORCID",
"ORCiD"
],
"wikidata": {
"description": "identifier for a person",
"example": [
"0000-0001-8994-2210",
"0000-0002-1003-5675",
"0000-0002-1825-0097"
],
"homepage": "https://orcid.org/",
"miriam": "orcid",
"name": "ORCID iD",
"pattern": "^\\d{4}-\\d{4}-\\d{4}-\\d{3}[\\dX]$",
"prefix": "P496",
"uri_format": "https://orcid.org/$1",
"uri_format_rdf": "https://orcid.org/$1"
}
},
"ordb": {
"biocontext": {
"prefix": "ORDB"
},
"fairsharing": {
"abbreviation": "ORDB",
"description": "ORDB began as a database of vertebrate OR genes and proteins and continues to support sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family.",
"homepage": "http://senselab.med.yale.edu/OrDB/",
"license": "https://senselab.med.yale.edu/OrDB",
"name": "Olfactory Receptor Database",
"prefix": "FAIRsharing.6375zh",
"publications": [
{
"doi": "10.1093/nar/30.1.354",
"pubmed_id": 11752336,
"title": "Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences."
},
{
"doi": "10.1093/database/baw132",
"pubmed_id": 27694208,
"title": "ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions."
},
{
"doi": "10.1093/nar/28.1.341",
"pubmed_id": 10592268,
"title": "Olfactory receptor database: a sensory chemoreceptor resource."
}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"biocontext": "ORDB",
"fairsharing": "FAIRsharing.6375zh",
"miriam": "ordb",
"n2t": "ordb",
"pathguide": "65",
"prefixcommons": "ordb"
},
"miriam": {
"deprecated": false,
"description": "The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs).",
"homepage": "http://senselab.med.yale.edu/OrDB/",
"id": "00000499",
"name": "Olfactory Receptor Database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "ordb",
"sampleId": "8497",
"uri_format": "http://senselab.med.yale.edu/ORDB/Data/$1"
},
"n2t": {
"description": "The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs).",
"example": "8497",
"homepage": "http://senselab.med.yale.edu/OrDB/",
"name": "Olfactory Receptor Database at Yale University School of Medicine",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "ordb",
"uri_format": "http://senselab.med.yale.edu/ORDB/Data/$1"
},
"pathguide": {
"abbreviation": "ORDB",
"homepage": "http://senselab.med.yale.edu/OrDB/",
"name": "Olfactory Receptor Database",
"prefix": "65"
},
"prefixcommons": {
"description": "ORDB began as a database of vertebrate OR genes and proteins and continues to support sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family.",
"example": "14673",
"homepage": "http://senselab.med.yale.edu/senselab/ordb/",
"keywords": [
"gene",
"protein"
],
"name": "Olfactory Receptor Database",
"pattern": "^\\d+$",
"prefix": "ordb",
"synonyms": [
"ord"
],
"uri_format": "http://senselab.med.yale.edu/ordb/eavdata.asp?o=$1"
},
"publications": [
{
"doi": "10.1093/database/baw132",
"pmc": "PMC5045865",
"pubmed": "27694208",
"title": "ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions",
"year": 2016
},
{
"doi": "10.1093/nar/30.1.354",
"pmc": "PMC99065",
"pubmed": "11752336",
"title": "Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences",
"year": 2002
},
{
"doi": "10.1093/nar/28.1.341",
"pmc": "PMC102443",
"pubmed": "10592268",
"title": "Olfactory receptor database: a sensory chemoreceptor resource",
"year": 2000
}
]
},
"oridb.sacch": {
"biocontext": {
"prefix": "ORIDB.SACCH"
},
"mappings": {
"biocontext": "ORIDB.SACCH",
"miriam": "oridb.sacch",
"n2t": "oridb.sacch"
},
"miriam": {
"deprecated": false,
"description": "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae.",
"homepage": "http://cerevisiae.oridb.org/index.php",
"id": "00000369",
"name": "OriDB Saccharomyces",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "oridb.sacch",
"sampleId": "1",
"uri_format": "http://cerevisiae.oridb.org/details.php?id=$1"
},
"n2t": {
"description": "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae.",
"example": "1",
"homepage": "http://cerevisiae.oridb.org/index.php",
"name": "OriDB Saccharomyces at University of Nottingham",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "oridb.sacch",
"uri_format": "http://cerevisiae.oridb.org/details.php?id=$1"
}
},
"oridb.schizo": {
"biocontext": {
"prefix": "ORIDB.SCHIZO"
},
"mappings": {
"biocontext": "ORIDB.SCHIZO",
"miriam": "oridb.schizo",
"n2t": "oridb.schizo"
},
"miriam": {
"deprecated": false,
"description": "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe.",
"homepage": "http://pombe.oridb.org/index.php",
"id": "00000368",
"name": "OriDB Schizosaccharomyces",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "oridb.schizo",
"sampleId": "1",
"uri_format": "http://pombe.oridb.org/details.php?id=$1"
},
"n2t": {
"description": "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe.",
"example": "1",
"homepage": "http://pombe.oridb.org/index.php",
"name": "OriDB Schizosaccharomyces at University of Nottingham",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "oridb.schizo",
"uri_format": "http://pombe.oridb.org/details.php?id=$1"
}
},
"ornaseq": {
"aberowl": {
"description": "An application ontology designed to annotate next-generation sequencing experiments performed on RNA.",
"download_owl": "http://aber-owl.net/media/ontologies/ORNASEQ/2/ornaseq.owl",
"homepage": "http://kim.bio.upenn.edu/software/ornaseq.shtml",
"name": "Ontology of RNA Sequencing",
"prefix": "ORNASEQ"
},
"bioportal": {
"contact": {
"email": "safisher@upenn.edu",
"name": "Stephen Fisher"
},
"description": "This is an application ontology used to annotate next-generation sequencing experiments performed on RNA (RNAseq). It uses terms from BFO, CHEBI, CL, GENEPIO, GO, IAO, NCBITaxon, NCIT, OBI, OBIws, OGMS, OMIABIS, SO, TAXRANK, and UBERON as well as EFO.",
"homepage": "http://kim.bio.upenn.edu/software/ornaseq.shtml",
"name": "Ontology of RNA Sequencing",
"prefix": "ORNASEQ"
},
"download_obo": "http://purl.obolibrary.org/obo/ornaseq.obo",
"example": "0000010",
"mappings": {
"aberowl": "ORNASEQ",
"bioportal": "ORNASEQ",
"obofoundry": "ornaseq",
"ols": "ornaseq",
"ontobee": "ORNASEQ"
},
"obofoundry": {
"contact": "safisher@upenn.edu",
"contact.github": "safisher",
"contact.label": "Stephen Fisher",
"contact.orcid": "0000-0001-8034-7685",
"deprecated": false,
"description": "An application ontology designed to annotate next-generation sequencing experiments performed on RNA.",
"domain": "investigations",
"download.owl": "http://purl.obolibrary.org/obo/ornaseq.owl",
"homepage": "http://kim.bio.upenn.edu/software/ornaseq.shtml",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Ontology of RNA Sequencing",
"preferredPrefix": "ORNASEQ",
"prefix": "ornaseq",
"repository": "https://github.com/safisher/ornaseq"
},
"ols": {
"description": "An application ontology designed to annotate next-generation sequencing experiments performed on RNA.",
"download_owl": "http://purl.obolibrary.org/obo/ornaseq.owl",
"homepage": "http://kim.bio.upenn.edu/software/ornaseq.shtml",
"name": "Ontology for RNA sequencing (ORNASEQ)",
"prefix": "ornaseq",
"version": "2019-07-08",
"version.iri": "http://purl.obolibrary.org/obo/ornaseq/2019-07-08/ornaseq.owl"
},
"ontobee": {
"library": "Library",
"name": "Ontology of RNA Sequencing",
"prefix": "ORNASEQ"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/ORNASEQ_$1"
},
"orphanet": {
"biocontext": {
"prefix": "Orphanet",
"uri_format": "http://www.orpha.net/ORDO/Orphanet_$1"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "orphanet",
"uri_format": "http://www.orpha.net/ORDO/Orphanet_$1"
},
"contact": {
"email": "bliemsl@xs4all.nl",
"name": "Spencer L. Liem",
"orcid": "0000-0002-1575-9365"
},
"download_owl": "http://www.orphadata.org/data/ORDO/ordo_orphanet.owl",
"fairsharing": {
"abbreviation": "Orphanet",
"description": "Orphanet is the reference resource for information on rare diseases and orphan drugs for all publics. Its aim is to contribute to the improvement of the diagnosis, care and treatment of patients with rare diseases. Orphanet maintains the Orphanet nomenclature, essential for interoperability, and the Orphanet Rare Disease Ontology (ORDO).",
"homepage": "http://www.orpha.net/consor/cgi-bin/index.php?lng=EN",
"license": "CC-BY-4.0",
"name": "Orphanet",
"prefix": "FAIRsharing.6bd5k6",
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{
"doi": null,
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"title": "[Orphanet and the Dutch Steering Committee Orphan Drugs. A European and Dutch databank of information on rare diseases]."
}
],
"subjects": [
"Life Science",
"Ontology and Terminology"
],
"twitter": "orphanet"
},
"integbio": {
"description": "Orphanet is a portal site for rare diseases and orphan drugs. It provides inventory of rare diseases and classification, inventory of orphan drugs, clinical trials, etc.",
"fairsharing": "biodbcore-000497",
"homepage": "http://www.orpha.net/consor/cgi-bin/Disease_Search_List.php?lng=EN",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Orphanet",
"name": "Orphanet",
"prefix": "nbdc01422",
"pubmeds": [
"12655825"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
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"biolink": "orphanet",
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},
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"homepage": "http://www.orpha.net/consor/",
"id": "00000220",
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"pattern": "^\\d+$",
"prefix": "orphanet",
"providers": [
{
"code": "CURATOR_REVIEW",
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"homepage": "http://orphanet.bio2rdf.org/fct",
"name": "Bio2RDF",
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"sampleId": "85163",
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"description": "Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases.",
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"name": "Orphanet at Inserm",
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"pattern": "^\\d+$",
"prefix": "orphanet",
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"description": "Orphanet is a database of information on rare diseases and orphan drugs for all publics. Its aim is to contribute to the improvement of the diagnosis, care and treatment of patients with rare diseases.",
"example": "85163",
"homepage": "http://www.orpha.net/consor/cgi-bin/home.php?Lng=GB",
"keywords": [
"disease",
"drug",
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],
"license": "CC BY-ND 3.0",
"name": "Orphanet; a database dedicated to information on rare diseases and orphan drugs",
"pattern": "^\\d+$",
"prefix": "orphanet",
"pubmed_ids": [
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},
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{
"pubmed": "19058507",
"title": "[Orphanet and the Dutch Steering Committee Orphan Drugs. A European and Dutch databank of information on rare diseases]",
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}
],
"synonyms": [
"ORPHA"
],
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"abbreviation": "Orphanet",
"category": "Organism-specific databases",
"homepage": "https://www.orpha.net/consor/cgi-bin/index.php",
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"prefix": "DB-0068",
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"wikidata": {
"database": "Q929833",
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"example": [
"723",
"82038"
],
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"name": "Orphanet ID",
"pattern": "^[1-9]\\d{0,5}$",
"prefix": "P1550",
"uri_format": "https://www.orpha.net/en/disease/detail/$1"
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},
"banana": "Orphanet",
"banana_peel": "_",
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"prefix": "ORPHANET.ORDO"
},
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"is_obo": false,
"prefix": "ORPHA",
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},
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"name": "Orphanet Rare Disease Ontology",
"prefix": "ORDO",
"version": "4.5"
},
"cellosaurus": {
"category": "Medical resources",
"homepage": "https://www.ebi.ac.uk/ols/ontologies/ordo",
"name": "Orphanet Rare Disease Ontology",
"prefix": "ORDO",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/ordo/terms?iri=http://www.orpha.net/ORDO/$1"
},
"download_owl": "http://www.orphadata.org/data/ORDO/ordo_orphanet.owl",
"example": "C023",
"example_extras": [
"478"
],
"fairsharing": {
"abbreviation": "ORDO",
"contact": {
"email": "ordo.orphanet@inserm.fr",
"name": "Ana Rath",
"orcid": "0000-0003-4308-6337"
},
"description": "Orphanet Rare Diseases Ontology (ORDO) provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.",
"domains": [
"Rare disease",
"Phenotype",
"Disease",
"Diagnosis",
"Gene"
],
"homepage": "http://www.orphadata.org/cgi-bin/inc/ordo_orphanet.inc.php",
"license": "CC-BY-4.0",
"name": "Orphanet Rare Diseases Ontology",
"prefix": "FAIRsharing.pbbnwa",
"publications": [
{
"pubmed": "22874158",
"title": "Rare diseases knowledge management: the contribution of proximity measurements in OntoOrpha and OMIM",
"year": 2012
}
],
"subjects": [
"Health Science",
"Biomedical Science"
]
},
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "ordo",
"biocontext": "ORPHANET.ORDO",
"biolink": "ORPHA",
"bioportal": "ORDO",
"cellosaurus": "ORDO",
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"miriam": "orphanet.ordo",
"n2t": "orphanet.ordo",
"ols": "ordo"
},
"miriam": {
"deprecated": false,
"description": "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.\r\nIt integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).",
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"name": "Orphanet Rare Disease Ontology",
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},
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"description": "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).",
"example": "Orphanet_C023",
"homepage": "https://www.ebi.ac.uk/ols/ontologies/ordo",
"name": "ORDO via OLS",
"namespaceEmbeddedInLui": false,
"pattern": "^Orphanet(_|:)C?\\d+$",
"prefix": "orphanet.ordo",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/ordo/terms?short_form=$1"
},
"ols": {
"description": "The Orphanet Rare Disease ontology (ORDO) is jointly developed by Orphanet and the EBI to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It derived from the Orphanet database (www.orpha.net ) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA),databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10).",
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{
"pubmed": "22874158",
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}
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"ordo"
],
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"orth": {
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"description": "Orthology Ontology",
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"homepage": "https://github.com/qfo/OrthologyOntology",
"name": "Orthology Ontology",
"prefix": "ORTH",
"version": "2015-11-27"
},
"bioportal": {
"contact": {
"email": "jfernand@um.es",
"name": "Jesualdo TomΓ‘s FernΓ‘ndez-Breis"
},
"description": "Orthology Ontology",
"homepage": "https://github.com/qfo/OrthologyOntology",
"name": "Orthology Ontology",
"prefix": "ORTH",
"publication": "http://www.jbiomedsem.com/content/7/1/34",
"version": "2.0"
},
"contact": {
"email": "jfernand@um.es",
"github": "jesualdotomasfernandezbreis",
"name": "Jesualdo TomΓ‘s FernΓ‘ndez-Breis",
"orcid": "0000-0002-7558-2880"
},
"download_owl": "https://github.com/qfo/OrthologyOntology/raw/master/orthOntology_RC_v2_A.owl",
"example": "HomologyRelation",
"fairsharing": {
"abbreviation": "ORTH",
"description": "ORTH ontology is designed to describe sequence homology data such as gene region, gene and protein-centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures in a single terminology.",
"domains": [
"Protein",
"Sequence",
"Gene",
"Homologous",
"Orthologous",
"Paralogous"
],
"homepage": "https://github.com/qfo/OrthologyOntology",
"license": "CC-BY-4.0",
"name": "Orthology Ontology",
"prefix": "FAIRsharing.4877h0",
"publications": [
{
"doi": "10.1186/s13326-016-0077-x",
"title": "The Orthology Ontology: development and applications",
"year": 2016
}
],
"subjects": [
"Comparative Genomics"
]
},
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"mappings": {
"aberowl": "ORTH",
"bioportal": "ORTH",
"fairsharing": "FAIRsharing.4877h0",
"ols": "orth"
},
"ols": {
"description": "The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way.",
"homepage": "http://purl.org/net/orth",
"name": "Orthology Ontology",
"prefix": "orth",
"version": "2.0",
"version.iri": "http://purl.org/net/orth/2.0"
},
"publications": [
{
"doi": "10.1186/s13326-016-0077-x",
"pmc": "PMC4893294",
"pubmed": "27259657",
"title": "The Orthology Ontology: development and applications",
"year": 2016
}
],
"repository": "https://github.com/qfo/OrthologyOntology",
"uri_format": "http://purl.org/net/orth#$1"
},
"orthodb": {
"biocontext": {
"prefix": "ORTHODB"
},
"contact": {
"email": "evgeny.zdobnov@unige.ch",
"name": "Evgeny M Zdobnov",
"orcid": "0000-0002-5178-1498"
},
"fairsharing": {
"abbreviation": "OrthoDB",
"description": "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny.",
"homepage": "http://www.orthodb.org/v9/",
"license": "CC-BY-4.0",
"name": "Database of Orthologous Groups",
"prefix": "FAIRsharing.x989d5",
"publications": [
{
"doi": "10.1093/nar/gku1220",
"pubmed_id": 25428351,
"title": "OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software."
},
{
"doi": "10.1093/nar/gkq930",
"pubmed_id": 20972218,
"title": "OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011."
}
],
"subjects": [
"Life Science"
]
},
"homepage": "https://www.orthodb.org",
"mappings": {
"biocontext": "ORTHODB",
"fairsharing": "FAIRsharing.x989d5",
"miriam": "orthodb",
"n2t": "orthodb",
"prefixcommons": "orthodb",
"uniprot": "DB-0143"
},
"miriam": {
"deprecated": false,
"description": "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups",
"homepage": "http://cegg.unige.ch/orthodb4",
"id": "00000221",
"name": "OrthoDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "orthodb",
"sampleId": "Q9P0K8",
"uri_format": "http://cegg.unige.ch/orthodb/results?searchtext=$1"
},
"n2t": {
"description": "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups",
"example": "Q9P0K8",
"homepage": "http://cegg.unige.ch/orthodb4",
"name": "OrthoDB at Swiss Institute of Bioinformatics",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "orthodb",
"uri_format": "http://cegg.unige.ch/orthodb/results?searchtext=$1"
},
"prefixcommons": {
"description": "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny.",
"example": "EOG9VMFMQ",
"homepage": "http://cegg.unige.ch/orthodb/browse",
"keywords": [
"eukaryotic",
"protein",
"DNA"
],
"name": "Database of Orthologous Groups",
"pattern": "^EOG[A-Z,0-9]+$",
"prefix": "orthodb",
"pubmed_ids": [
"20972218"
],
"uri_format": "http://cegg.unige.ch/orthodb3/results?searchtext=$1"
},
"provides": "uniprot",
"publications": [
{
"doi": "10.1093/nar/gky1053",
"pmc": "PMC6323947",
"pubmed": "30395283",
"title": "OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs",
"year": 2019
},
{
"doi": "10.1093/nar/gku1220",
"pmc": "PMC4383991",
"pubmed": "25428351",
"title": "OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software",
"year": 2014
},
{
"doi": "10.1093/nar/gkq930",
"pmc": "PMC3013786",
"pubmed": "20972218",
"title": "OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011",
"year": 2010
}
],
"uniprot": {
"abbreviation": "OrthoDB",
"category": "Phylogenomic databases",
"homepage": "https://www.orthodb.org",
"name": "Database of Orthologous Groups",
"prefix": "DB-0143",
"publications": [
{
"doi": "10.1093/nar/gky1053",
"pubmed": "30395283"
}
],
"uri_format": "https://www.orthodb.org/?gene=$1"
}
},
"oryzabase.gene": {
"biocontext": {
"prefix": "ORYZABASE.GENE"
},
"mappings": {
"biocontext": "ORYZABASE.GENE",
"miriam": "oryzabase.gene",
"n2t": "oryzabase.gene"
},
"miriam": {
"deprecated": false,
"description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information.",
"homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/",
"id": "00000482",
"name": "Oryzabase Gene",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "oryzabase.gene",
"sampleId": "117",
"uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1"
},
"n2t": {
"description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information.",
"example": "117",
"homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/",
"name": "Oryzabase v4 Gene at National Institute of Genetics (Japan)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "oryzabase.gene",
"uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1"
}
},
"oryzabase.mutant": {
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"miriam": "oryzabase.mutant",
"n2t": "oryzabase.mutant"
},
"miriam": {
"deprecated": false,
"description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information.",
"homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/",
"id": "00000483",
"name": "Oryzabase Mutant",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "oryzabase.mutant",
"sampleId": "21393",
"uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1"
},
"n2t": {
"description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information.",
"example": "21393",
"homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/",
"name": "Oryzabase v4 Mutant at National Institute of Genetics (Japan)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "oryzabase.mutant",
"uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1"
}
},
"oryzabase.reference": {
"mappings": {
"miriam": "oryzabase.reference",
"n2t": "oryzabase.reference"
},
"miriam": {
"deprecated": false,
"description": "The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan.",
"homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/",
"id": "00000689",
"name": "Oryzabase",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "oryzabase.reference",
"sampleId": "42840",
"uri_format": "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1"
},
"n2t": {
"description": "The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan.",
"example": "42840",
"homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/",
"name": "Oryzabase",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "oryzabase.reference",
"uri_format": "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1"
},
"name": "Oryzabase Reference"
},
"oryzabase.stage": {
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"prefix": "ORYZABASE.STAGE"
},
"mappings": {
"biocontext": "ORYZABASE.STAGE",
"miriam": "oryzabase.stage",
"n2t": "oryzabase.stage"
},
"miriam": {
"deprecated": false,
"description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information.",
"homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/",
"id": "00000485",
"name": "Oryzabase Stage",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "oryzabase.stage",
"sampleId": "34",
"uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1"
},
"n2t": {
"description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information.",
"example": "34",
"homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/",
"name": "Oryzabase v4 Stage at National Institute of Genetics (Japan)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "oryzabase.stage",
"uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1"
}
},
"oryzabase.strain": {
"biocontext": {
"prefix": "ORYZABASE.STRAIN"
},
"mappings": {
"biocontext": "ORYZABASE.STRAIN",
"miriam": "oryzabase.strain",
"n2t": "oryzabase.strain"
},
"miriam": {
"deprecated": false,
"description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information.",
"homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/",
"id": "00000484",
"name": "Oryzabase Strain",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "oryzabase.strain",
"sampleId": "1",
"uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1"
},
"n2t": {
"description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information.",
"example": "1",
"homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/",
"name": "Oryzabase v4 Strain at National Institute of Genetics (Japan)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "oryzabase.strain",
"uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1"
}
},
"oslc": {
"contact": {
"email": "jamsden@us.ibm.com",
"name": "Jim Amsden"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains.",
"example": "Property",
"homepage": "http://open-services.net/ns/core",
"lov": {
"description": "The Open Services for Lifecycle Collaboration (OSLC) initiative is creating a family of web services specifications for products, services and other tools that support all phases of the software and product lifecycle. This OSLC Core Specification sets out the common features that every OSLC Service can be expected to support",
"homepage": "http://open-services.net/bin/view/Main/OslcCoreSpecification",
"keywords": [
"PLM"
],
"modified": "2014-05-23",
"name": "OSLC Core Vocabulary",
"prefix": "oslc",
"uri_prefix": "http://open-services.net/ns/core#$1"
},
"mappings": {
"lov": "oslc"
},
"name": "OASIS Open Services for Lifecycle Collaboration Core Vocabulary",
"preferred_prefix": "oslc",
"uri_format": "http://open-services.net/ns/core#$1"
},
"osti.article": {
"comment": "Corresponding GitHub linked to software registrations is located at https://github.com/doecode. All related contact information can be found here https://www.osti.gov/contact",
"contributor": {
"email": "Lindsey.Anderson@pnnl.gov",
"github": "lnanderson",
"name": "Lindsey Anderson",
"orcid": "0000-0002-8741-7823"
},
"description": "The U.S. Department of Energy (DOE) Office of Scientific and Technical Information (OSTI) is the main metadata archive for permanent storage of registered [DOE DOI products](https://www.osti.gov/pids/doi-services/doe-data-id-service) (datasets, code, articles, patents, multimedia, etc.). When a DOI is minted a unique OSTI identifier for each record [{osti_id}](https://www.osti.gov/api/v1/docs#endpoints-singlerecord) is provided as the suffix in the DOI schema ([{site-specific-prefix}/{user-supplied-doi-infix}/{osti_id}](https://www.osti.gov/pids/doi-services)) and can be alternatively used as the main product identifier endpoint when [searching OSTI.GOV](https://www.osti.gov/search-tools) registry archive (see example below). OSTI.GOV is the primary registry and search tool for all Department of Energy (DOE) funded science, technology, and engineering research and development (R&D) results and the organizational hub for information about the DOE Office of Scientific and Technical Information (OSTI. **Data Product Type Example:** - https://www.osti.gov/biblio/1668761 - https://www.osti.gov/search/semantic:1668761 - https://www.osti.gov/dataexplorer/biblio/dataset/1668761 - https://www.osti.gov/api/v1/records/1668761 - https://doi.org/10.11578/1668761 **Other Core Product Registry Examples:** - Journal Articles: https://www.osti.gov/pages/biblio - Datasets: https://www.osti.gov/dataexplorer/biblio/dataset/ - Software: https://www.osti.gov/doecode/biblio/ - Patents: https://www.osti.gov/doepatents/biblio/ - Multimedia: https://www.osti.gov/sciencecinema/biblio/",
"example": "1668761",
"github_request_issue": 1050,
"homepage": "https://www.osti.gov/",
"keywords": [
"article",
"articles",
"publication",
"publications"
],
"license": "https://www.osti.gov/disclaim",
"mappings": {
"wikidata": "P3894"
},
"name": "Office of Scientific and Technical Information (OSTI)",
"pattern": "^\\d+$",
"references": [
"https://www.energy.gov/doe-public-access-plan"
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://www.osti.gov/biblio/$1",
"wikidata": {
"description": "identifier of a scientific article at Office of Scientific and Technical Information",
"example": [
"1121958",
"1271300",
"6071133"
],
"name": "OSTI article ID",
"pattern": "^\\d+$",
"prefix": "P3894",
"uri_format": "https://www.osti.gov/biblio/$1"
}
},
"otl": {
"biocontext": {
"prefix": "OTL"
},
"contact": {
"email": "guiderdoni@cirad.fr",
"name": "Emmanuel Guiderdoni",
"orcid": "0000-0003-2760-2864"
},
"fairsharing": {
"abbreviation": "OTL",
"description": "Oryza Tag Line consists in a searchable database developed under the Oracle management system integrating phenotypic data resulting from the evaluation of the Genoplante rice insertion line library.",
"homepage": "http://oryzatagline.cirad.fr/",
"name": "Oryza Tag Line",
"prefix": "FAIRsharing.61c2x6",
"publications": [
{
"doi": "17947330",
"pubmed_id": 17947330,
"title": "Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library."
}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"biocontext": "OTL",
"fairsharing": "FAIRsharing.61c2x6",
"miriam": "otl",
"n2t": "otl",
"prefixcommons": "otl"
},
"miriam": {
"deprecated": false,
"description": "Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information.",
"homepage": "http://oryzatagline.cirad.fr/",
"id": "00000486",
"name": "Oryza Tag Line",
"namespaceEmbeddedInLui": false,
"pattern": "^A[A-Z]+\\d+$",
"prefix": "otl",
"sampleId": "AADB12",
"uri_format": "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1"
},
"n2t": {
"description": "Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information.",
"example": "AADB12",
"homepage": "http://oryzatagline.cirad.fr/",
"name": "Oryza Tag Line at CIRAD-INRA-SUPAGRO-UMI",
"namespaceEmbeddedInLui": false,
"pattern": "^A[A-Z]+\\d+$",
"prefix": "otl",
"uri_format": "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1"
},
"prefixcommons": {
"description": "Oryza Tag Line consists in a searchable database developed under the Oracle management system integrating phenotypic data resulting from the evaluation of the GΓ©noplante rice insertion line library.",
"example": "AGFC04",
"homepage": "http://urgi.versailles.inra.fr/OryzaTagLine/",
"keywords": [
"DNA"
],
"name": "Oryza Tag Line: An integrated database for the functional analysis of the rice genome",
"pattern": "^A[A-Z]+\\d+$",
"prefix": "otl",
"uri_format": "http://urgi.versailles.inra.fr/OryzaTagLine/cgi-bin/general_mutant.pl?line=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkm762",
"pmc": "PMC2238859",
"pubmed": "17947330",
"title": "Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library",
"year": 2007
}
]
},
"otol": {
"contributor": {
"email": "meghan.balk@gmail.com",
"github": "megbalk",
"name": "Meghan Balk",
"orcid": "0000-0003-2699-3066"
},
"description": "Identifier for an entity in open tree of life",
"example": "3905431",
"github_request_issue": 470,
"homepage": "https://tree.opentreeoflife.org",
"mappings": {
"wikidata": "P9157"
},
"name": "Open Tree of Life",
"pattern": "^[1-9]\\d*$",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://tree.opentreeoflife.org/taxonomy/browse?id=$1",
"wikidata": {
"database": "Q22661281",
"description": "identifier for an entity in Open Tree of Life, a comprehensive, dynamic and digitally-available tree of life by synthesizing published phylogenetic trees along with taxonomic data",
"example": [
"259588",
"309263",
"3905431"
],
"homepage": "https://tree.opentreeoflife.org/opentree",
"name": "Open Tree of Life ID",
"pattern": "^[1-9]\\d*$",
"prefix": "P9157",
"uri_format": "https://tree.opentreeoflife.org/taxonomy/browse?id=$1"
}
},
"ovae": {
"aberowl": {
"description": "A biomedical ontology in the domain of vaccine adverse events.",
"download_owl": "http://aber-owl.net/media/ontologies/OVAE/11/ovae.owl",
"homepage": "http://www.violinet.org/ovae/",
"name": "Ontology of Vaccine Adverse Events",
"prefix": "OVAE"
},
"biocontext": {
"prefix": "OVAE"
},
"bioportal": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "The Ontology of Vaccine Adverse Events (OVAE) is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the Ontology of Adverse Events (OAE) and the Vaccine Ontology (VO). OVAE is aimed to represent and analyze various vaccine-specific adverse events.",
"homepage": "http://www.violinet.org/ovae",
"name": "Ontology of Vaccine Adverse Events",
"prefix": "OVAE",
"version": "Vision Release: 1.0.34"
},
"example": "0000609",
"fairsharing": {
"abbreviation": "OVAE",
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqunh He",
"orcid": "0000-0001-9189-9661"
},
"description": "The Ontology of Vaccine Adverse Events (OVAE) is a biomedical ontology in the area of vaccine adverse events. While they are extremely useful in decreasing infection prevalence in human populations, vaccines may also induce some unintended adverse events. As vaccine usage increases, the risk of adverse events proportionally increases. To protect public health, it is necessary to represent, study, and analyze various vaccine adverse events (VAES). Two existing ontologies are closely related to the VAE studies. The Ontology of Adverse Events (OAE) is a community-based biomedical ontology in the area of adverse events. The Vaccine Ontology (VO) represents various vaccines, vaccine components, and vaccinations. Both OAE and VO are OBO Foundry candidate ontologies and are developed by following the OBO Foundry principles. To better represent various VAEs and support vaccine safety study, we developed the Ontology of Vaccine Adverse Events (OVAE) as an extension of the biomedical ontologies OAE and VO.",
"domains": [
"Adverse Reaction",
"Vaccine"
],
"homepage": "https://github.com/OVAE-Ontology/ovae",
"license": "Apache 2.0 License",
"name": "Ontology of Vaccine Adverse Events",
"prefix": "FAIRsharing.w4x6n4",
"publications": [
{
"doi": "10.1186/2041-1480-4-40",
"pubmed": "24279920",
"title": "The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines",
"year": 2013
}
],
"subjects": [
"Biomedical Science"
]
},
"mappings": {
"aberowl": "OVAE",
"biocontext": "OVAE",
"bioportal": "OVAE",
"fairsharing": "FAIRsharing.w4x6n4",
"obofoundry": "ovae",
"ols": "ovae",
"ontobee": "OVAE"
},
"obofoundry": {
"contact": "yongqunh@med.umich.edu",
"contact.github": "yongqunh",
"contact.label": "Yongqunh He",
"contact.orcid": "0000-0001-9189-9661",
"deprecated": false,
"description": "A biomedical ontology in the domain of vaccine adverse events.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/ovae.owl",
"homepage": "http://www.violinet.org/ovae/",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Ontology of Vaccine Adverse Events",
"preferredPrefix": "OVAE",
"prefix": "ovae",
"repository": "https://github.com/OVAE-Ontology/ovae"
},
"ols": {
"description": "OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE).",
"download_owl": "http://purl.obolibrary.org/obo/ovae.owl",
"homepage": "http://www.violinet.org/ovae/",
"name": "OVAE: Ontology of Vaccine Adverse Events",
"prefix": "ovae",
"version": "1.0.34"
},
"ontobee": {
"library": "Library",
"name": "Ontology of Vaccine Adverse Events",
"prefix": "OVAE"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1186/2041-1480-4-40",
"pmc": "PMC4177204",
"pubmed": "24279920",
"title": "The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines",
"year": 2013
}
],
"uri_format": "http://purl.obolibrary.org/obo/OVAE_$1"
},
"owl": {
"biocontext": {
"prefix": "owl",
"uri_format": "http://www.w3.org/2002/07/owl#$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. ",
"download_owl": "https://triplydb.com/w3c/owl/download.trig.gz",
"example": "Ontology",
"fairsharing": {
"abbreviation": "OWL",
"contact": {
"email": "rmrich5@gmail.com",
"name": "Rafael Richards",
"orcid": "0000-0001-5699-0515"
},
"description": "The Web Ontology Language (OWL) is a family of knowledge representation languages or ontology languages for authoring ontologies or knowledge bases. The languages are characterized by formal semantics and RDF/XML-based serializations for the Semantic Web. OWL is endorsed by the World Wide Web Consortium (W3C) and has attracted academic, medical and commercial interest. The OWL 2 Web Ontology Language, informally OWL 2, is an ontology language for the Semantic Web with formally defined meaning. OWL 2 ontologies provide classes, properties, individuals, and data values and are stored as Semantic Web documents. OWL 2 ontologies can be used along with information written in RDF, and OWL 2 ontologies themselves are primarily exchanged as RDF documents.",
"homepage": "http://www.w3.org/TR/owl-overview/",
"name": "Web Ontology Language",
"prefix": "FAIRsharing.atygwy",
"publications": [],
"subjects": [
"Informatics",
"Computer Science",
"Subject Agnostic",
"Ontology and Terminology"
]
},
"homepage": "https://www.w3.org/TR/owl-features/",
"integbio": {
"description": "OWL Version 31.1 is a database comprised of the results of a comparative study of 4 sources of sequence information.\nThese sources are SWISS-PROT, PIR, GenBank and NRL-3D.\nRedundancies of sequences have been avoided at all cost, even by eliminating sequences that display trivial differences from other sequences that are already present.\nOWL is therefore a comparatively small repository, simplifying the process of similarity checks.\nThis version of the repository contains 279,796 entries and 89,624,288 residues.\nThe database can be searched by means of entering an accession number, a database code, a sequence or by making use of the provided keyword search option.",
"homepage": "http://www.bioinf.manchester.ac.uk/dbbrowser/OWL/index.php",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Manchester Bioinformatics Education and Research",
"name": "OWL",
"prefix": "nbdc00307",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"lov": {
"description": "This ontology partially describes the built-in classes and properties that together form the basis of the RDF/XML syntax of OWL 2.",
"homepage": "http://www.w3.org/TR/owl2-rdf-based-semantics/",
"keywords": [
"W3C Rec"
],
"modified": "2009-11-15",
"name": "The OWL 2 Schema vocabulary",
"prefix": "owl",
"uri_prefix": "http://www.w3.org/2002/07/owl#$1"
},
"mappings": {
"biocontext": "owl",
"fairsharing": "FAIRsharing.atygwy",
"integbio": "nbdc00307",
"lov": "owl",
"ols": "owl",
"zazuko": "owl"
},
"name": "Web Ontology Language",
"ols": {
"name": "The OWL 2 Schema vocabulary (OWL 2)",
"prefix": "owl",
"version": "$Date: 2009/11/15 10:54:12 $",
"version.iri": "http://www.w3.org/2002/07/owl"
},
"preferred_prefix": "owl",
"uri_format": "http://www.w3.org/2002/07/owl#$1",
"zazuko": {
"prefix": "owl",
"uri_format": "http://www.w3.org/2002/07/owl#$1"
}
},
"owlstar": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "os",
"uri_format": "https://github.com/cmungall/owlstar/blob/master/owlstar.ttl$1"
},
"contact": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "This proposed vocabulary allows edges in Property Graphs (e.g Neo4j, RDF*) to be augmented with edge properties that specify ontological semantics, including (but not limited) to OWL-DL interpretations. [from GitHub]",
"download_rdf": "https://github.com/linkml/owlstar/raw/master/owlstar.ttl",
"example": "AllSomeInterpretation",
"homepage": "https://linkml.io/owlstar/",
"license": "CC0-1.0",
"mappings": {
"biolink": "os"
},
"name": "Ontological Interpretations for Web Property Graphs",
"pattern": "^\\w+$",
"repository": "https://github.com/linkml/owlstar",
"uri_format": "http://w3id.org/owlstar/$1"
},
"p3db.protein": {
"biocontext": {
"prefix": "P3DB.PROTEIN"
},
"mappings": {
"biocontext": "P3DB.PROTEIN",
"miriam": "p3db.protein",
"n2t": "p3db.protein",
"prefixcommons": "p3db"
},
"miriam": {
"deprecated": false,
"description": "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites.",
"homepage": "http://www.p3db.org/",
"id": "00000501",
"name": "P3DB Protein",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "p3db.protein",
"sampleId": "70",
"uri_format": "http://www.p3db.org/protein.php?id=$1&ref=0"
},
"n2t": {
"description": "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites.",
"example": "70",
"homepage": "http://www.p3db.org/",
"name": "P3DB Protein at University of Missouri",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "p3db.protein",
"uri_format": "http://www.p3db.org/protein.php?id=$1&ref=0"
},
"prefixcommons": {
"description": "P3DB was established with an overall objective to provide a resource of protein phosphorylation data from multiple plants. P3DB uses MySQL database to store phosphorylation data.",
"example": "6401",
"homepage": "http://www.p3db.org",
"keywords": [
"protein",
"small molecule"
],
"name": "Plant Protein Phosphorylation Database",
"pattern": "^\\d+$",
"prefix": "p3db",
"uri_format": "http://digbio.missouri.edu/p3db/data/protein.php?id=$1"
}
},
"p3db.site": {
"biocontext": {
"prefix": "P3DB.SITE"
},
"mappings": {
"biocontext": "P3DB.SITE",
"miriam": "p3db.site",
"n2t": "p3db.site"
},
"miriam": {
"deprecated": false,
"description": "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins.",
"homepage": "http://www.p3db.org/",
"id": "00000502",
"name": "P3DB Site",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "p3db.site",
"sampleId": "65",
"uri_format": "http://www.p3db.org/phosphosite.php?id=$1&ref=0"
},
"n2t": {
"description": "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins.",
"example": "65",
"homepage": "http://www.p3db.org/",
"name": "P3DB Site at University of Missouri",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "p3db.site",
"uri_format": "http://www.p3db.org/phosphosite.php?id=$1&ref=0"
}
},
"packagist": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
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{
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{
"doi": "10.1021/pr5006636",
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"title": "Panorama: a targeted proteomics knowledge base."
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{
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{
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"Proteomics",
"Drug Metabolism",
"Human Genetics",
"Molecular Microbiology",
"Metabolomics",
"Transcriptomics",
"Cell Biology",
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"maintainer": "Memorial Sloan-Kettering Cancer Center, the University of Toronto",
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"gene"
],
"name": "Pathguide: The Pathway Resource List",
"pattern": "^\\d+$",
"prefix": "pathguide",
"uri_format": "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"pathoplant": {
"mappings": {
"pathguide": "333",
"prefixcommons": "pathoplant"
},
"pathguide": {
"abbreviation": "PathoPlant",
"homepage": "http://www.pathoplant.de/",
"name": "PathoPlant",
"prefix": "333"
},
"prefixcommons": {
"description": "PathoPlantΒ is a database on plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. PathoPlantΒ also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon pathogen infection or elicitor treatment.",
"example": "MO000027",
"homepage": "http://www.pathoplant.de",
"keywords": [
"interaction",
"pathway",
"small molecule",
"gene expression",
"protein"
],
"name": "PathoPlantΒ",
"pattern": "^MO\\d+$",
"prefix": "pathoplant",
"uri_format": "http://www.pathoplant.de/detail.php?accNo=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"pathwaycommons": {
"biocontext": {
"prefix": "PATHWAYCOMMONS"
},
"contact": {
"email": "chris@sanderlab.org",
"github": "sanderlab",
"name": "Chris Sander",
"orcid": "0000-0001-6059-6270"
},
"mappings": {
"biocontext": "PATHWAYCOMMONS",
"miriam": "pathwaycommons",
"n2t": "pathwaycommons",
"prefixcommons": "pathwaycommons",
"re3data": "r3d100012731",
"uniprot": "DB-0253"
},
"miriam": {
"deprecated": false,
"description": "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.",
"homepage": "http://www.pathwaycommons.org/pc/",
"id": "00000073",
"name": "Pathway Commons",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "pathwaycommons",
"sampleId": "485991",
"uri_format": "http://www.pathwaycommons.org/pc/record2.do?id=$1"
},
"n2t": {
"description": "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.",
"example": "485991",
"homepage": "http://www.pathwaycommons.org/pc/",
"name": "Pathway Commons",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "pathwaycommons",
"uri_format": "http://www.pathwaycommons.org/pc/record2.do?id=$1"
},
"prefixcommons": {
"description": "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases",
"example": "485991",
"homepage": "http://www.pathwaycommons.org/pc/",
"keywords": [
"pathway"
],
"license": "http://www.pathwaycommons.org/pc/about.do",
"name": "Pathway Commons",
"pattern": "^\\d+$",
"prefix": "pathwaycommons",
"synonyms": [
"cpath"
],
"uri_format": "http://www.pathwaycommons.org/pc/record2.do?id=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkq1039",
"pmc": "PMC3013659",
"pubmed": "21071392",
"title": "Pathway Commons, a web resource for biological pathway data",
"year": 2010
}
],
"re3data": {
"description": "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. The data is freely available under the license terms of each contributing database.",
"homepage": "https://www.pathwaycommons.org/",
"name": "Pathway Commons",
"prefix": "r3d100012731",
"xrefs": {
"fairsharing": "FAIRsharing.5y3gdd",
"nif": "0000-20884",
"omics": "02761",
"scr": "002103"
}
},
"uniprot": {
"abbreviation": "PathwayCommons",
"category": "Enzyme and pathway databases",
"homepage": "https://www.pathwaycommons.org",
"name": "Pathway Commons web resource for biological pathway data",
"prefix": "DB-0253",
"publications": [
{
"doi": "10.1093/nar/gkz946/5606621",
"pubmed": "31647099"
}
],
"uri_format": "https://apps.pathwaycommons.org/search?q=$1"
}
},
"pato": {
"aberowl": {
"description": "An ontology of phenotypic qualities (properties, attributes or characteristics)",
"download_owl": "http://aber-owl.net/media/ontologies/PATO/196/pato.owl",
"homepage": "https://github.com/pato-ontology/pato/",
"name": "Phenotype And Trait Ontology",
"prefix": "PATO"
},
"agroportal": {
"contact": {
"email": "g.gkoutos@gmail.com",
"name": "George Gkoutos"
},
"description": "An ontology of phenotypic qualities (properties, attributes or characteristics). This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested.",
"example_uri": "http://purl.obolibrary.org/obo/PATO_0001464",
"homepage": "https://github.com/pato-ontology",
"license": "CC-BY-3.0",
"name": "Phenotype And Trait Ontology",
"prefix": "PATO",
"repository": "https://github.com/pato-ontology/pato/",
"version": "2024-03-28"
},
"biocontext": {
"prefix": "PATO"
},
"bioportal": {
"contact": {
"email": "g.gkoutos@gmail.com",
"name": "George Gkoutos"
},
"description": "Phenotypic qualities (properties). This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested.",
"homepage": "https://github.com/pato-ontology/pato/",
"name": "Phenotypic Quality Ontology",
"prefix": "PATO",
"version": "2024-03-28"
},
"fairsharing": {
"abbreviation": "PATO",
"contact": {
"email": "g.gkoutos@gmail.com",
"name": "George Gkoutos",
"orcid": "0000-0002-2061-091X"
},
"description": "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily phenotype annotation. This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes.",
"domains": [
"Phenotype"
],
"homepage": "https://github.com/pato-ontology/pato/",
"license": "CC-BY-3.0",
"name": "Phenotypic QualiTy Ontology",
"prefix": "FAIRsharing.ezwdhz",
"publications": [
{
"doi": "10.1186/gb-2004-6-1-r8",
"pubmed": "15642100",
"title": "Using ontologies to describe mouse phenotypes",
"year": 2005
},
{
"doi": "10.1186/gb-2010-11-1-r2",
"pubmed": "20064205",
"title": "Integrating phenotype ontologies across multiple species",
"year": 2010
}
],
"repository": "https://github.com/pato-ontology/pato/blob/master/CHANGES.md",
"subjects": [
"Biodiversity",
"Biology"
]
},
"go": {
"homepage": "http://www.obofoundry.org/ontology/pato.html",
"name": "Phenotypic quality ontology",
"prefix": "PATO"
},
"mappings": {
"aberowl": "PATO",
"agroportal": "PATO",
"biocontext": "PATO",
"bioportal": "PATO",
"fairsharing": "FAIRsharing.ezwdhz",
"go": "PATO",
"miriam": "pato",
"n2t": "pato",
"obofoundry": "pato",
"ols": "pato",
"ontobee": "PATO",
"prefixcommons": "pato"
},
"miriam": {
"deprecated": false,
"description": "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.",
"homepage": "http://bioportal.bioontology.org/ontologies/PATO",
"id": "00000112",
"name": "PATO",
"namespaceEmbeddedInLui": true,
"pattern": "^PATO:\\d{7}$",
"prefix": "pato",
"sampleId": "0001998",
"uri_format": "http://purl.bioontology.org/ontology/PATO/PATO:$1"
},
"n2t": {
"description": "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.",
"example": "0001998",
"homepage": "http://bioportal.bioontology.org/ontologies/PATO",
"name": "PATO through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^PATO:\\d{7}$",
"prefix": "pato",
"uri_format": "http://purl.bioontology.org/ontology/PATO/PATO:$1"
},
"obofoundry": {
"appears_in": [
"agro",
"aism",
"cdno",
"cl",
"colao",
"ecocore",
"ecto",
"fovt",
"gallont",
"lepao",
"mco",
"ms",
"pcl",
"pco",
"phipo",
"planp",
"proco",
"rbo",
"uberon",
"xpo",
"zp"
],
"contact": "g.gkoutos@gmail.com",
"contact.github": "gkoutos",
"contact.label": "George Gkoutos",
"contact.orcid": "0000-0002-2061-091X",
"deprecated": false,
"description": "An ontology of phenotypic qualities (properties, attributes or characteristics)",
"domain": "phenotype",
"download.json": "http://purl.obolibrary.org/obo/pato.json",
"download.obo": "http://purl.obolibrary.org/obo/pato.obo",
"download.owl": "http://purl.obolibrary.org/obo/pato.owl",
"homepage": "https://github.com/pato-ontology/pato/",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Phenotype And Trait Ontology",
"preferredPrefix": "PATO",
"prefix": "pato",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/28387809",
"title": "The anatomy of phenotype ontologies: principles, properties and applications"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/15642100",
"title": "Using ontologies to describe mouse phenotypes"
}
],
"repository": "https://github.com/pato-ontology/pato"
},
"ols": {
"description": "An ontology of phenotypic qualities (properties, attributes or characteristics).",
"download_owl": "http://purl.obolibrary.org/obo/pato.owl",
"homepage": "https://github.com/pato-ontology/pato/",
"name": "PATO - the Phenotype And Trait Ontology",
"prefix": "pato",
"version": "2024-03-28",
"version.iri": "http://purl.obolibrary.org/obo/pato/releases/2024-03-28/pato.owl"
},
"ontobee": {
"library": "Foundry",
"name": "Phenotype And Trait Ontology",
"prefix": "PATO"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"alt_uri_formats": [
"http://purl.org/obo/owl/PATO#$1"
],
"bioportal": "1107",
"description": "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.",
"example": "PATO:0001998",
"homepage": "http://obofoundry.org/wiki/index.php/PATO:Main_Page",
"keywords": [
"obo",
"ontology",
"quality",
"phenotype"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "PATO",
"pattern": "^PATO:\\d{7}$",
"prefix": "pato",
"synonyms": [
"obo.pato"
]
},
"providers": [
{
"code": "purl",
"description": "Legacy PURLs found in OAE",
"homepage": "http://purl.org/obo/owl/",
"name": "Legacy PURL",
"uri_format": "http://purl.org/obo/owl/PATO#PATO_$1"
}
],
"publications": [
{
"doi": "10.1093/bib/bbx035",
"pmc": "PMC6169674",
"pubmed": "28387809",
"title": "The anatomy of phenotype ontologies: principles, properties and applications",
"year": 2018
},
{
"doi": "10.1186/gb-2010-11-1-r2",
"pmc": "PMC2847714",
"pubmed": "20064205",
"title": "Integrating phenotype ontologies across multiple species",
"year": 2010
},
{
"doi": "10.1186/gb-2004-6-1-r8",
"pmc": "PMC549069",
"pubmed": "15642100",
"title": "Using ontologies to describe mouse phenotypes",
"year": 2004
}
],
"uri_format": "http://purl.obolibrary.org/obo/PATO_$1"
},
"pav": {
"aberowl": {
"description": "PAV is a lightweight ontology for tracking Provenance, Authoring and Versioning. PAV specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources. This ontology describes the defined PAV properties and their usage. Note that PAV does not define any explicit classes or domain/ranges, as every property is meant to be used directly on the described online resource.",
"download_owl": "http://aber-owl.net/media/ontologies/PAV/3/pav.owl",
"homepage": "https://github.com/pav-ontology/pav/",
"name": "PAV Provenance, Authoring and Versioning",
"prefix": "PAV",
"version": "2.3.1"
},
"biocontext": {
"prefix": "pav",
"uri_format": "http://purl.org/pav/$1"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "pav",
"uri_format": "http://purl.org/pav/$1"
},
"bioportal": {
"contact": {
"email": "stian@soiland-reyes.com",
"name": "Stian Soiland-Reyes"
},
"description": "PAV is a lightweight ontology for tracking Provenance, Authoring and Versioning. PAV specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources. This ontology describes the defined PAV properties and their usage. Note that PAV does not define any explicit classes or domain/ranges, as every property is meant to be used directly on the described online resource.",
"homepage": "https://github.com/pav-ontology/pav/",
"name": "PAV Provenance, Authoring and Versioning",
"prefix": "PAV",
"publication": "https://github.com/pav-ontology/pav/wiki/Publications",
"version": "2.3.1"
},
"contributor": {
"email": "nicolas.matentzoglu@gmail.com",
"github": "matentzn",
"name": "Nicolas Matentzoglu",
"orcid": "0000-0002-7356-1779"
},
"contributor_extras": [
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"description": "PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources.",
"example": "authoredBy",
"fairsharing": {
"abbreviation": "PAV",
"contact": {
"email": "stian@soiland-reyes.com",
"name": "Stian Soiland-Reyes",
"orcid": "0000-0001-9842-9718"
},
"description": "PAV is a lightweight ontology for tracking Provenance, Authoring and Versioning. PAV specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources. This ontology describes the defined PAV properties and their usage. Note that PAV does not define any explicit classes or domain/ranges, as every property is meant to be used directly on the described online resource.",
"domains": [
"Citation",
"Resource metadata"
],
"homepage": "https://github.com/pav-ontology/pav/",
"license": "Apache 2.0 License",
"name": "Provenance, Authoring and Versioning Ontology",
"prefix": "FAIRsharing.nbfwwv",
"publications": [
{
"doi": "10.1186/2041-1480-4-37",
"pubmed": "24267948",
"title": "PAV ontology: provenance, authoring and versioning",
"year": 2013
}
],
"repository": "http://pav-ontology.github.io/pav/",
"subjects": [
"Data Management",
"Subject Agnostic"
]
},
"github_request_issue": 186,
"homepage": "https://pav-ontology.github.io/pav/",
"lov": {
"description": "PAV is a lightweight ontology for tracking Provenance, Authoring and Versioning. PAV specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources.",
"homepage": "http://pav-ontology.github.io/pav/",
"keywords": [
"Quality"
],
"modified": "2014-08-28",
"name": "Provenance, Authoring and Versioning",
"prefix": "pav",
"uri_prefix": "http://purl.org/pav/$1"
},
"mappings": {
"aberowl": "PAV",
"biocontext": "pav",
"biolink": "pav",
"bioportal": "PAV",
"fairsharing": "FAIRsharing.nbfwwv",
"lov": "pav"
},
"name": "Provenance, Authoring, and Versioning Vocabulary",
"pattern": "^[a-z][a-zA-Z]+$",
"preferred_prefix": "pav",
"publications": [
{
"doi": "10.1186/2041-1480-4-37",
"pmc": "PMC4177195",
"pubmed": "24267948",
"title": "PAV ontology: provenance, authoring and versioning",
"year": 2013
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://purl.org/pav/$1"
},
"paxdb.organism": {
"biocontext": {
"prefix": "PAXDB.ORGANISM"
},
"mappings": {
"biocontext": "PAXDB.ORGANISM",
"miriam": "paxdb.organism",
"n2t": "paxdb.organism"
},
"miriam": {
"deprecated": false,
"description": "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species.",
"homepage": "http://pax-db.org/",
"id": "00000488",
"name": "PaxDb Organism",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "paxdb.organism",
"sampleId": "9606",
"uri_format": "http://pax-db.org/#!species/$1"
},
"n2t": {
"description": "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species.",
"example": "9606",
"homepage": "http://pax-db.org/",
"name": "PaxDb v3 at University of Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "paxdb.organism",
"uri_format": "http://pax-db.org/#!species/$1"
}
},
"paxdb.protein": {
"biocontext": {
"prefix": "PAXDB.PROTEIN"
},
"mappings": {
"biocontext": "PAXDB.PROTEIN",
"miriam": "paxdb.protein",
"n2t": "paxdb.protein"
},
"miriam": {
"deprecated": false,
"description": "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels.",
"homepage": "http://pax-db.org/",
"id": "00000489",
"name": "PaxDb Protein",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "paxdb.protein",
"sampleId": "977869",
"uri_format": "http://pax-db.org/#!protein/$1"
},
"n2t": {
"description": "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels.",
"example": "977869",
"homepage": "http://pax-db.org/",
"name": "PaxDb v3 at University of Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "paxdb.protein",
"uri_format": "http://pax-db.org/#!protein/$1"
}
},
"pazar": {
"biocontext": {
"prefix": "PAZAR"
},
"fairsharing": {
"abbreviation": "PAZAR",
"contact": {
"email": "wyeth@cmmt.ubc.ca",
"name": "Wyeth W. Wasserman",
"orcid": "0000-0001-6098-6412"
},
"description": "PAZAR is a software framework for the construction and maintenance of regulatory sequence data annotations; a framework which allows multiple boutique databases to function independently within a larger system (or information mall). The goal of PAZAR is to be the public repository for regulatory data.",
"homepage": "http://www.pazar.info/",
"name": "PAZAR",
"prefix": "FAIRsharing.33yggg",
"publications": [
{
"doi": "10.1093/nar/gkn783",
"pubmed_id": 18971253,
"title": "The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences."
},
{
"doi": "10.1186/gb-2007-8-10-r207",
"pubmed_id": 17916232,
"title": "PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation."
}
],
"subjects": [
"Life Science"
]
},
"integbio": {
"alt_name": "A Public Database of Transcription Factor and Regulatory Sequence Annotation",
"description": "PAZAR is a database of regulatory sequence information, including information about transcription factors. The database contains information collected from dozens of published studies of gene regulatory information. Users can search by transcription factor, target gene, or regulatory sequence of interest as well as browse by gene or study.",
"fairsharing": "biodbcore-000499",
"homepage": "http://www.pazar.info",
"information_keywords": [
"Sequence"
],
"maintainer": "Centre for Molecular Medicine and Therapeutic",
"name": "PAZAR",
"prefix": "nbdc00611",
"pubmeds": [
"17916232",
"18971253"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"mappings": {
"biocontext": "PAZAR",
"fairsharing": "FAIRsharing.33yggg",
"integbio": "nbdc00611",
"miriam": "pazar",
"n2t": "pazar",
"pathguide": "521",
"prefixcommons": "pazar"
},
"miriam": {
"deprecated": false,
"description": "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors.",
"homepage": "http://www.pazar.info/",
"id": "00000306",
"name": "Pazar Transcription Factor",
"namespaceEmbeddedInLui": false,
"pattern": "^TF\\w+$",
"prefix": "pazar",
"sampleId": "TF0001053",
"uri_format": "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1"
},
"n2t": {
"description": "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors.",
"example": "TF0001053",
"homepage": "http://www.pazar.info/",
"name": "Pazar Transcription Factor at University of British Columbia",
"namespaceEmbeddedInLui": false,
"pattern": "^TF\\w+$",
"prefix": "pazar",
"uri_format": "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1"
},
"pathguide": {
"abbreviation": "PAZAR",
"homepage": "http://www.pazar.info/",
"name": "A Public Database of Transcription Factor and Regulatory Sequence Annotation",
"prefix": "521"
},
"prefixcommons": {
"description": "PAZAR is a software framework for the construction and maintenance of regulatory sequence data annotations; a framework which allows multiple boutique databases to function independently within a larger system (or information mall). The goal of PAZAR is to be the public repository for regulatory data.",
"example": "TF0000448",
"homepage": "http://www.pazar.info/",
"keywords": [
"regulation",
"DNA",
"RNA"
],
"name": "PAZAR",
"pattern": "^TF\\d+$",
"prefix": "pazar",
"uri_format": "http://www.pazar.info/cgi-bin/tf_search.cgi?searchtab=tfs&ID_list=PAZAR_TF&geneID=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkn783",
"pmc": "PMC2686574",
"pubmed": "18971253",
"title": "The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences",
"year": 2008
},
{
"doi": "10.1186/gb-2007-8-10-r207",
"pmc": "PMC2246282",
"pubmed": "17916232",
"title": "PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation",
"year": 2007
}
]
},
"pba": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A controlled vocabulary to support the study of transcription in the primate brain",
"download_obo": "https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-pba.obo",
"example": "128011350",
"homepage": "https://www.blueprintnhpatlas.org/",
"name": "Primate Brain Atlas",
"pattern": "^\\d+$",
"preferred_prefix": "PBA",
"uri_format": "https://biopragmatics.github.io/providers/pba/$1"
},
"pcl": {
"aberowl": {
"description": "Cell types that are provisionally defined by experimental techniques such as single cell or single nucleus transcriptomics rather than a straightforward & coherent set of properties.",
"download_owl": "http://aber-owl.net/media/ontologies/PCL/25/pcl.owl",
"homepage": "https://github.com/obophenotype/provisional_cell_ontology",
"name": "Provisional Cell Ontology",
"prefix": "PCL"
},
"bioportal": {
"contact": {
"email": "davidos@ebi.ac.uk",
"name": "David Osumi-Sutherland"
},
"description": "Cell types that are provisionally defined by experimental techniques such as single cell or single nucleus transcriptomics rather than a straightforward & coherent set of properties.",
"homepage": "https://github.com/obophenotype/provisional_cell_ontology",
"name": "Provisional Cell Ontology",
"prefix": "PCL",
"publication": "https://doi.org/10.1101/2021.10.10.463703",
"version": "2024-07-11"
},
"example": "0011124",
"fairsharing": {
"abbreviation": "PCL",
"contact": {
"email": "davidos@ebi.ac.uk",
"name": "David Osumi-Sutherland",
"orcid": "0000-0002-7073-9172"
},
"description": "PCL is an ontology created to record claims of potential new cell types derived from single cell data analysis, where there is no additional evidence that supports the addition of corresponding classically defined cell type to the Cell Ontology (CL). PCL hence provides a place for terms that might not be ready for CL.",
"domains": [
"Annotation",
"Cell"
],
"homepage": "https://github.com/obophenotype/provisional_cell_ontology",
"license": "CC-BY-4.0",
"name": "Provisional Cell Ontology",
"prefix": "FAIRsharing.bfcfd0",
"publications": [
{
"doi": "10.1101/2021.10.10.463703",
"title": "Brain Data Standards Ontology: A data-driven ontology of transcriptomically defined cell types in the primary motor cortex",
"year": 2021
}
],
"repository": "https://github.com/obophenotype/provisional_cell_ontology/issues",
"subjects": [
"Anatomy",
"Life Science",
"Cell Biology"
]
},
"mappings": {
"aberowl": "PCL",
"bioportal": "PCL",
"fairsharing": "FAIRsharing.bfcfd0",
"obofoundry": "pcl",
"ols": "pcl",
"ontobee": "PCL"
},
"obofoundry": {
"contact": "davidos@ebi.ac.uk",
"contact.github": "dosumis",
"contact.label": "David Osumi-Sutherland",
"contact.orcid": "0000-0002-7073-9172",
"depends_on": [
"bfo",
"chebi",
"cl",
"go",
"nbo",
"ncbitaxon",
"omo",
"pato",
"pr",
"ro",
"so",
"uberon"
],
"deprecated": false,
"description": "Cell types that are provisionally defined by experimental techniques such as single cell or single nucleus transcriptomics rather than a straightforward & coherent set of properties.",
"domain": "phenotype",
"download.json": "http://purl.obolibrary.org/obo/pcl.json",
"download.obo": "http://purl.obolibrary.org/obo/pcl.obo",
"download.owl": "http://purl.obolibrary.org/obo/pcl.owl",
"homepage": "https://github.com/obophenotype/provisional_cell_ontology",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Provisional Cell Ontology",
"preferredPrefix": "PCL",
"prefix": "pcl",
"repository": "https://github.com/obophenotype/provisional_cell_ontology"
},
"ols": {
"description": "Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties.",
"download_owl": "http://purl.obolibrary.org/obo/pcl.owl",
"homepage": "https://github.com/obophenotype/provisional_cell_ontology",
"name": "Provisional Cell Ontology",
"prefix": "pcl",
"version": "2024-07-11",
"version.iri": "http://purl.obolibrary.org/obo/pcl/releases/2024-07-11/pcl.owl"
},
"ontobee": {
"library": "Library",
"name": "Provisional Cell Ontology",
"prefix": "PCL"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1101/2021.10.10.463703",
"title": "Brain Data Standards - A method for building data-driven cell-type ontologies",
"year": 2021
}
],
"uri_format": "http://purl.obolibrary.org/obo/PCL_$1"
},
"pco": {
"aberowl": {
"description": "An ontology about groups of interacting organisms such as populations and communities",
"download_owl": "http://aber-owl.net/media/ontologies/PCO/18/pco.owl",
"homepage": "https://github.com/PopulationAndCommunityOntology/pco",
"name": "Population and Community Ontology",
"prefix": "PCO"
},
"agroportal": {
"contact": {
"email": "rwalls2008@gmail.com",
"name": "Ramona Walls"
},
"description": "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology.",
"example_uri": "http://purl.obolibrary.org/obo/PCO_0000061",
"homepage": "https://github.com/PopulationAndCommunityOntology/pco",
"license": "CC0-1.0",
"name": "Population and Community Ontology",
"prefix": "PCO",
"repository": "https://github.com/PopulationAndCommunityOntology/pco",
"version": "2013-10-03"
},
"biocontext": {
"prefix": "PCO"
},
"bioportal": {
"contact": {
"email": "rlwalls2008@gmail.com",
"name": "Ramona Walls"
},
"description": "The Population and Community Ontology (PCO) models material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. The PCO is complient with the Basic Formal Ontology (BFO) and is designed to be compatible with other OBO Foundry ontologies.",
"homepage": "https://github.com/PopulationAndCommunityOntology/pco",
"name": "Population and Community Ontology",
"prefix": "PCO",
"version": "2013-10-03"
},
"download_obo": "http://purl.obolibrary.org/obo/pco.obo",
"ecoportal": {
"contact": {
"email": "rlwalls2008@gmail.com",
"name": "Ramona Walls"
},
"description": "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology.",
"homepage": "https://github.com/PopulationAndCommunityOntology/pco",
"name": "Population and Community Ontology",
"prefix": "PCO",
"publication": "https://github.com/PopulationAndCommunityOntology/pco",
"version": "2021-05-03"
},
"example": "0000021",
"fairsharing": {
"abbreviation": "PCO",
"contact": {
"email": "rlwalls2008@gmail.com",
"name": "Ramona Walls",
"orcid": "0000-0001-8815-0078"
},
"description": "Population and Community Ontology (PCO) is an ontology standard for describing the collective and interacting species of any taxa such as humans or plants. PCO has useful application in community health care, plant pathology, behavioral studies, sociology, and ecology. The PCO is compliant with the Basic Formal Ontology (BFO) and is designed to be compatible with other OBO Foundry ontologies.",
"domains": [
"Evolution"
],
"homepage": "https://github.com/PopulationAndCommunityOntology/pco",
"license": "CC0-1.0",
"name": "Population and Community Ontology",
"prefix": "FAIRsharing.vq28qp",
"repository": "https://github.com/PopulationAndCommunityOntology/pco/issues",
"subjects": [
"Ecology",
"Biodiversity",
"Community Care",
"Social and Behavioural Science",
"Population Genetics"
]
},
"mappings": {
"aberowl": "PCO",
"agroportal": "PCO",
"biocontext": "PCO",
"bioportal": "PCO",
"ecoportal": "PCO",
"fairsharing": "FAIRsharing.vq28qp",
"obofoundry": "pco",
"ols": "pco",
"ontobee": "PCO"
},
"obofoundry": {
"appears_in": [
"ecocore",
"envo"
],
"contact": "rlwalls2008@gmail.com",
"contact.github": "ramonawalls",
"contact.label": "Ramona Walls",
"contact.orcid": "0000-0001-8815-0078",
"depends_on": [
"bfo",
"caro",
"envo",
"go",
"iao",
"ncbitaxon",
"pato",
"ro"
],
"deprecated": false,
"description": "An ontology about groups of interacting organisms such as populations and communities",
"domain": "environment",
"download.owl": "http://purl.obolibrary.org/obo/pco.owl",
"homepage": "https://github.com/PopulationAndCommunityOntology/pco",
"license": "CC0 1.0",
"license.url": "http://creativecommons.org/publicdomain/zero/1.0/",
"name": "Population and Community Ontology",
"preferredPrefix": "PCO",
"prefix": "pco",
"repository": "https://github.com/PopulationAndCommunityOntology/pco"
},
"ols": {
"description": "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology.",
"download_owl": "http://purl.obolibrary.org/obo/pco.owl",
"homepage": "https://github.com/PopulationAndCommunityOntology/pco",
"name": "Population and Community Ontology",
"prefix": "pco",
"version": "2021-05-03",
"version.iri": "http://purl.obolibrary.org/obo/pco/releases/2021-05-03/pco.owl"
},
"ontobee": {
"library": "Library",
"name": "Population and Community Ontology",
"prefix": "PCO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/PCO_$1"
},
"pd_st": {
"biocontext": {
"prefix": "PD_ST"
},
"mappings": {
"biocontext": "PD_ST",
"obofoundry": "pd_st"
},
"obofoundry": {
"contact": "henrich@embl.de",
"contact.github": "ThorstenHen",
"contact.label": "Thorsten Henrich",
"contact.orcid": "0000-0002-1548-3290",
"deprecated": true,
"domain": "anatomy and development",
"homepage": "http://4dx.embl.de/platy",
"name": "Platynereis stage ontology",
"prefix": "pd_st"
}
},
"pdb": {
"biocontext": {
"prefix": "PDB",
"uri_format": "http://www.ebi.ac.uk/pdbsum/$1"
},
"edam": {
"description": "An identifier of an entry from the PDB database.",
"name": "PDB",
"obsolete": false,
"prefix": "1127"
},
"fairsharing": {
"abbreviation": "PDBj",
"contact": {
"email": "harukin@protein.osaka-u.ac.jp",
"name": "Haruki Nakamura",
"orcid": "0000-0001-6690-5863"
},
"description": "PDBj (Protein Data Bank Japan) maintains the single global PDB/BMRB/EMDB archives of macromolecular structures and provide integrated tools, under the Joint Usage and Research activities of the Institute for Protein Research. Supports browsing in multiple languages such as Japanese, Chinese, and Korean; SeSAW identifies functionally or evolutionarily conserved motifs by locating and annotating sequence and structural similarities, tools for bioinformaticians, and more.",
"homepage": "http://www.pdbj.org/",
"license": "CC0-1.0",
"name": "Protein Data Bank Japan",
"prefix": "FAIRsharing.rs2815",
"publications": [
{
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{
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"title": "[Development of PDBj: Advanced database for protein structures]."
},
{
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"pubmed_id": 20798081,
"title": "PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan."
},
{
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"pubmed_id": 21796434,
"title": "Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr."
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{
"doi": "10.1093/nar/gkw962",
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"title": "Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures."
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{
"doi": "10.1002/pro.4211",
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"title": "Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data"
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],
"subjects": [
"Bioinformatics",
"Structural Biology",
"Proteomics",
"Virology",
"Epidemiology"
],
"twitter": "PDBj_en"
},
"go": {
"homepage": "https://www.rcsb.org/pdb/",
"name": "Protein Data Bank",
"prefix": "PDB",
"uri_format": "https://www.rcsb.org/structure/$1"
},
"integbio": {
"alt_name": "Protein Data Bank Europe",
"description": "PDBe is a database of protein structures. The database is the European resource for the Protein Databank and contains molecular structure coordinates and visualizations of thousands of proteins. Users can search for entries, browse by several curated categories, submit structures, and download coordinate data.",
"fairsharing": "biodbcore-000322",
"homepage": "http://www.ebi.ac.uk/pdbe/",
"information_keywords": [
"Image/Movie",
"3D structure",
"Repository"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "PDBe",
"prefix": "nbdc00613",
"pubmeds": [
"22110033"
],
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Protein"
]
},
"mappings": {
"biocontext": "PDB",
"edam": "1127",
"fairsharing": "FAIRsharing.rs2815",
"go": "PDB",
"integbio": "nbdc00613",
"miriam": "pdb",
"n2t": "pdb",
"ncbi": "PDB",
"pathguide": "398",
"prefixcommons": "pdbj",
"re3data": "r3d100010910",
"togoid": "Pdb",
"uniprot": "DB-0172",
"wikidata": "P638"
},
"miriam": {
"deprecated": false,
"description": "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.",
"homepage": "https://www.wwpdb.org/",
"id": "00000020",
"name": "Protein Data Bank",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9][A-Za-z0-9]{3}$",
"prefix": "pdb",
"providers": [
{
"code": "ebi",
"description": "Protein Databank through PDBsum",
"homepage": "https://www.ebi.ac.uk/pdbsum/",
"name": "Protein Databank through PDBsum",
"uri_format": "https://www.ebi.ac.uk/pdbsum/$1"
},
{
"code": "rcsb",
"description": "RCSB PDB",
"homepage": "https://www.rcsb.org/",
"name": "RCSB PDB",
"uri_format": "https://www.rcsb.org/structure/$1"
},
{
"code": "pdbj",
"description": "Protein Data Bank Japan (PDBj)",
"homepage": "http://www.pdbj.org/",
"name": "Protein Data Bank Japan (PDBj)",
"uri_format": "https://pdbj.org/mine/summary/$1"
},
{
"code": "pdbe",
"description": "Protein Databank in Europe (PDBe)",
"homepage": "http://www.pdbe.org/",
"name": "Protein Databank in Europe (PDBe)",
"uri_format": "https://www.ebi.ac.uk/pdbe/entry/pdb/$1"
},
{
"code": "CURATOR_REVIEW",
"description": "Proteopedia",
"homepage": "http://www.proteopedia.org/",
"name": "Proteopedia",
"uri_format": "http://proteopedia.org/wiki/index.php/$1"
}
],
"sampleId": "2gc4",
"uri_format": "https://www.wwpdb.org/pdb?id=$1"
},
"n2t": {
"description": "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.",
"example": "2gc4",
"homepage": "https://www.pdb.org/",
"name": "RCSB PDB",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9][A-Za-z0-9]{3}$",
"prefix": "pdb",
"uri_format": "https://www.rcsb.org/pdb/explore/explore.do?structureId=$1"
},
"name": "PDB Structure",
"ncbi": {
"example": "12GS",
"homepage": "http://www.rcsb.org/pdb/",
"name": "Biological macromolecule three dimensional structure database",
"prefix": "PDB"
},
"pathguide": {
"abbreviation": "RCSB PDB",
"homepage": "http://www.rcsb.org/pdb/home/home.do",
"name": "The Research Collaboratory for Structural Bioinformatics Protein Data Bank",
"prefix": "398"
},
"prefixcommons": {
"description": "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.",
"example": "2OM1",
"homepage": "http://www.pdbj.org/",
"keywords": [
"protein",
"structure"
],
"name": "Protein Data Bank Japan",
"pattern": "^\\d+[A-Z]+$",
"prefix": "pdbj",
"uri_format": "http://service.pdbj.org/mine/Detail?PDBID=$1&PAGEID=Summary"
},
"publications": [
{
"doi": "10.1002/pro.4211",
"pmc": "PMC8740847",
"pubmed": "34664328",
"title": "Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data",
"year": 2021
},
{
"doi": "10.1002/pro.3273",
"pmc": "PMC5734392",
"pubmed": "28815765",
"title": "New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)",
"year": 2017
},
{
"doi": "10.1093/nar/gkw962",
"pmc": "PMC5210648",
"pubmed": "27789697",
"title": "Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures",
"year": 2016
},
{
"doi": "10.1093/nar/gkr811",
"pmc": "PMC3245181",
"pubmed": "21976737",
"title": "Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format",
"year": 2011
},
{
"doi": "10.1007/s10822-011-9460-y",
"pubmed": "21796434",
"title": "Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr",
"year": 2011
},
{
"doi": "10.1093/database/baq021",
"pmc": "PMC2997606",
"pubmed": "20798081",
"title": "PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan",
"year": 2010
},
{
"pubmed": "12099029",
"title": "[Development of PDBj: Advanced database for protein structures]",
"year": 2002
}
],
"re3data": {
"description": "PDBj (Protein Data Bank Japan) provides a centralized PDB archive of macromolecular structures, integrated tools for data retrieval, visualization, and functional characterization. PDBj is supported by JST-NBDC and Osaka University.",
"homepage": "https://pdbj.org/",
"name": "PDBj",
"prefix": "r3d100010910",
"synonyms": [
"Protein Data Bank Japan"
],
"xrefs": {
"fairsharing": "FAIRsharing.rs2815",
"nlx": "151484",
"scr": "008912"
}
},
"synonyms": [
"RCSB_PDB",
"pdbe",
"pdbj",
"wwpdb"
],
"togoid": {
"catalog": "nbdc00156",
"examples": [
"3PFQ",
"2OUY",
"6EBX",
"5GHP",
"6ETH",
"1Y28",
"6FB2",
"5JO3",
"2JQZ",
"5L5P"
],
"keywords": [
"Structure"
],
"name": "PDB",
"pattern": "^(?[0-9][A-Za-z0-9]{3})$",
"prefix": "Pdb",
"uri_format": "http://rdf.wwpdb.org/pdb/$1"
},
"uniprot": {
"abbreviation": "PDBj",
"category": "3D structure databases",
"homepage": "https://pdbj.org/",
"name": "Protein Data Bank Japan",
"prefix": "DB-0172",
"publications": [
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"doi": "10.1002/pro.4211",
"pubmed": "34664328"
}
],
"uri_format": "https://pdbj.org/mine/summary/$1"
},
"wikidata": {
"description": "identifier for 3D structural data as per the PDB (Protein Data Bank) database",
"example": [
"1XU7",
"4P38",
"4ZHD"
],
"homepage": "https://www.rcsb.org/",
"miriam": "pdb",
"name": "PDB structure ID",
"pattern": "^[0-9][0-9A-Za-z]{3}$",
"prefix": "P638",
"uri_format": "https://www.rcsb.org/structure/$1",
"uri_format_rdf": "https://rdf.wwpdb.org/pdb/$1"
}
},
"pdb-ccd": {
"biocontext": {
"prefix": "PDB-CCD"
},
"comment": "might be same as pdb.ligand, not sure though",
"contact": {
"email": "berman@rcsb.rutgers.edu",
"name": "Helen Berman",
"orcid": "0000-0002-3337-0660"
},
"contributor_extras": [
{
"email": "bmeldal@ebi.ac.uk",
"github": "bmeldal-eg",
"name": "Birgit Meldal",
"orcid": "0000-0003-4062-6158"
}
],
"example_extras": [
"A",
"PI"
],
"has_canonical": "pdb.ligand",
"mappings": {
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"keywords": [
"chemical",
"classification"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Chemical Component Dictionary",
"pattern": "^\\w{3}$",
"prefix": "ccd",
"pubmed_ids": [
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{
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"title": "Announcing the worldwide Protein Data Bank",
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}
],
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"pdbechem"
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"A6M",
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"Compound"
],
"name": "PDB CCD",
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},
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},
"pdb.ligand": {
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"prefix": "PDB.LIGAND"
},
"mappings": {
"biocontext": "PDB.LIGAND",
"miriam": "pdb.ligand",
"n2t": "pdb.ligand",
"pathguide": "169",
"prefixcommons": "pdbligand",
"wikidata": "P3636"
},
"miriam": {
"deprecated": false,
"description": "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands.",
"homepage": "http://www.pdb.org/",
"id": "00000490",
"name": "Protein Data Bank Ligand",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9]+$",
"prefix": "pdb.ligand",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "PDB Ligand at Protein Databank in Europe (PDBe)",
"homepage": "https://www.pdbe.org/",
"name": "PDB Ligand at Protein Databank in Europe (PDBe)",
"uri_format": "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1"
}
],
"sampleId": "TRQ",
"uri_format": "http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$1"
},
"n2t": {
"description": "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands.",
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"homepage": "http://www.pdb.org/",
"name": "PDB Ligand at RCSB",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9]+$",
"prefix": "pdb.ligand",
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},
"name": "PDB ligand",
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"abbreviation": "PDB-Ligand",
"homepage": "http://www.idrtech.com/PDB-Ligand/",
"name": "PDB-Ligand",
"prefix": "169"
},
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"description": "PDB-Ligand is a three dimensional structure database of small molecular ligands that are bound to larger biolomocules deposited in the Protein Data Bank (PDB).",
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"homepage": "http://www.idrtech.com/PDB-Ligand/",
"keywords": [
"small molecule",
"protein",
"interaction",
"structure"
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"prefix": "pdbligand"
},
"synonyms": [
"PDB_CHEM_ID"
],
"wikidata": {
"description": "identifier for small molecules and ligands in the Protein Data Bank (PDB)",
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"010",
"032",
"601"
],
"homepage": "http://www.wwpdb.org/",
"miriam": "pdb.ligand",
"name": "PDB ligand ID",
"pattern": "^[A-Z0-9]{1,3}|PRD_[0-9]+$",
"prefix": "P3636",
"uri_format": "https://www.rcsb.org/ligand/$1"
}
},
"pdbsum": {
"fairsharing": {
"abbreviation": "PDBsum",
"contact": {
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"name": "Roman Laskowski",
"orcid": "0000-0001-5528-0087"
},
"description": "PDBsum provides an overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.",
"homepage": "http://www.ebi.ac.uk/pdbsum",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "PDBsum; at-a-glance overview of macromolecular structures",
"prefix": "FAIRsharing.7vjq5t",
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"pubmed_id": 24153109,
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{
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"pubmed_id": 28875543,
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},
{
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"title": "PDBsum new things."
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],
"subjects": [
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},
"integbio": {
"description": "PDBsum is a database that contains the annotated 3-dimensional structures of all the proteins in the Protein Data Bank (PDB).\nThe diagrams indicate the protein chains, ligands, DNA and the metal ions present in the protein structures and also how these molecules interact with each other.\nThis database contains 92,037 ProteinDataBase entries.\nPDB code, text and sequence search options are available.\nData files can also be downloaded from the site.",
"fairsharing": "biodbcore-000323",
"homepage": "http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/",
"information_keywords": [
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"3D structure"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "PDBsum",
"prefix": "nbdc00308",
"pubmeds": [
"18996896",
"15608193",
"11125097",
"9433130",
"17384425"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"mappings": {
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"integbio": "nbdc00308",
"pathguide": "461",
"prefixcommons": "pdbsum",
"uniprot": "DB-0119"
},
"pathguide": {
"abbreviation": "PDBsum",
"homepage": "http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=index.html",
"name": "PDBsum: pictorial database of 3D structures in the Protein Data Bank",
"prefix": "461"
},
"prefixcommons": {
"description": "PDBsum provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.",
"example": "1kfv",
"homepage": "http://www.ebi.ac.uk/pdbsum",
"keywords": [
"protein",
"structure",
"interaction"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "PDBsum; at-a-glance overview of macromolecular structures",
"pattern": "^[A-Z,0-9]+$",
"prefix": "pdbsum",
"uri_format": "http://www.ebi.ac.uk/pdbsum/$1"
},
"provides": "pdb",
"publications": [
{
"doi": "10.1002/pro.3289",
"pmc": "PMC5734310",
"pubmed": "28875543",
"title": "PDBsum: Structural summaries of PDB entries",
"year": 2017
},
{
"doi": "10.1093/nar/gkt940",
"pmc": "PMC3965036",
"pubmed": "24153109",
"title": "PDBsum additions",
"year": 2013
},
{
"doi": "10.1093/nar/gkn860",
"pmc": "PMC2686501",
"pubmed": "18996896",
"title": "PDBsum new things",
"year": 2008
}
],
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uniprot": {
"abbreviation": "PDBsum",
"category": "3D structure databases",
"homepage": "https://www.ebi.ac.uk/pdbsum/",
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"prefix": "DB-0119",
"publications": [
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"doi": "10.1002/pro.3289",
"pubmed": "28875543"
}
],
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}
},
"pdc.study": {
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"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"description": "The National Cancer Institute's Proteomic Data Commons (PDC) makes cancer-related proteomic datasets easily accessible to the public.",
"example": "PDC000351",
"github_request_issue": 430,
"homepage": "https://pdc.cancer.gov/pdc",
"name": "Proteomic Data Commons",
"pattern": "^PDC\\d+$",
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
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},
"uri_format": "https://pdc.cancer.gov/pdc/study/$1"
},
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"homepage": "https://github.com/OpenLHS/PDRO",
"name": "The Prescription of Drugs Ontology",
"prefix": "PDRO"
},
"biocontext": {
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"prefix": "PDRO"
},
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"domains": [
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],
"homepage": "https://github.com/OpenLHS/PDRO",
"license": "CC-BY-4.0",
"name": "The Prescription of Drugs Ontology",
"prefix": "FAIRsharing.9te3ev",
"subjects": [
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"ols": "pdro",
"ontobee": "PDRO"
},
"obofoundry": {
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"contact.label": "Paul Fabry",
"contact.orcid": "0000-0002-3336-2476",
"deprecated": false,
"description": "An ontology to describe entities related to prescription of drugs",
"domain": "information",
"download.owl": "http://purl.obolibrary.org/obo/pdro.owl",
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"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "The Prescription of Drugs Ontology",
"preferredPrefix": "PDRO",
"prefix": "pdro",
"publications": [
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}
],
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},
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"homepage": "https://github.com/OpenLHS/PDRO",
"name": "The Prescription of Drugs Ontology",
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"version": "2021-06-08",
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},
"ontobee": {
"library": "Library",
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},
"pattern": "^\\d{7}$",
"providers": [
{
"code": "pdro.legacy",
"description": "An incorrect encoding of OBO purls",
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"name": "PDRO Hash",
"uri_format": "http://purl.obolibrary.org/obo/PDRO/PDRO.owl#PDRO_$1"
}
],
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"pmc": "PMC8619589",
"pubmed": "34831777",
"title": "The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its Parts",
"year": 2021
}
],
"uri_format": "http://purl.obolibrary.org/obo/PDRO_$1"
},
"pdumdv": {
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"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv",
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"prefix": "PDUMDV"
},
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},
"bioportal": {
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},
"description": "Life cycle stages for Platynereis dumerilii.",
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"description": "Life cycle stages for Platynereis dumerilii. The status of this resource is \"in development\", confirmed via developer remarks within the GitHub project stating that the ontology is not ready.",
"domains": [
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],
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/tree/master/src/pdumdv",
"name": "Platynereis Developmental Stages",
"prefix": "FAIRsharing.493qns",
"repository": "https://github.com/obophenotype/developmental-stage-ontologies/wiki",
"subjects": [
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"Life Science"
]
},
"mappings": {
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"biocontext": "PDUMDV",
"bioportal": "PDUMDV",
"fairsharing": "FAIRsharing.493qns",
"obofoundry": "pdumdv",
"ols": "pdumdv",
"ontobee": "PdumDv"
},
"obofoundry": {
"contact": "frederic.bastian@unil.ch",
"contact.github": "fbastian",
"contact.label": "FrΓ©dΓ©ric Bastian",
"contact.orcid": "0000-0002-9415-5104",
"deprecated": true,
"description": "Life cycle stages for Platynereis dumerilii",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/pdumdv.obo",
"download.owl": "http://purl.obolibrary.org/obo/pdumdv.owl",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Platynereis Developmental Stages",
"preferredPrefix": "PdumDv",
"prefix": "pdumdv",
"repository": "https://github.com/obophenotype/developmental-stage-ontologies"
},
"ols": {
"description": "Life cycle stages for Platynereis dumerilii",
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"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv",
"name": "Platynereis Developmental Stages",
"prefix": "pdumdv"
},
"ontobee": {
"library": "Library",
"name": "Platynereis Developmental Stages",
"prefix": "PdumDv"
},
"pattern": "^\\d{7}$",
"synonyms": [
"PdumDv"
],
"uri_format": "http://purl.obolibrary.org/obo/PdumDv_$1"
},
"peco": {
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"download_owl": "http://aber-owl.net/media/ontologies/PECO/30/peco.owl",
"homepage": "http://planteome.org/",
"name": "Plant Experimental Conditions Ontology",
"prefix": "PECO"
},
"agroportal": {
"contact": {
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"name": "Pankaj Jaiswal"
},
"description": "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.",
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"license": "CC-BY-4.0",
"name": "Plant Experimental Conditions Ontology",
"prefix": "PECO",
"repository": "https://github.com/Planteome/plant-experimental-conditions-ontology",
"version": "July 2023"
},
"biocontext": {
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},
"bioportal": {
"contact": {
"email": "jaiswalp@science.oregonstate.edu",
"name": "Pankaj Jaiswal"
},
"description": "The Plant Experimental Conditions Ontology describes the treatments, growing conditions, and/or study types used in plant biology experiments. The subjects of the studies may also include in vitro plant structures (PO:0000004). A plant treatment is the most specific,and may be a component of a plant growing condition, and the plant study type. The broadest classes are the plant study types where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own and it may also involve instances of biotic and abiotic treatments and different growing conditions.",
"homepage": "http://browser.planteome.org/amigo/term/EO:0007359",
"name": "Plant Experimental Conditions Ontology",
"prefix": "PECO",
"publication": "http://planteome.org/pub",
"version": "releases/2023-11-10"
},
"download_obo": "https://raw.githubusercontent.com/Planteome/plant-experimental-conditions-ontology/master/peco.obo",
"example": "0007114",
"fairsharing": {
"abbreviation": "PECO",
"description": "PECO is a structured, controlled vocabulary for the representation of plant experimental conditions. It describes the treatments, growing conditions, and/or study types used in various types of plant biology experiments.",
"domains": [
"Experimental measurement",
"Study design",
"Experimentally determined"
],
"homepage": "https://github.com/Planteome/plant-experimental-conditions-ontology",
"license": "CC-BY-4.0",
"name": "Plant Experimental Condition Ontology",
"prefix": "FAIRsharing.6yNXYK",
"publications": [
{
"doi": "10.1093/nar/gkx1152",
"pubmed": "29186578",
"title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics",
"year": 2017
}
],
"repository": "https://github.com/Planteome/plant-experimental-conditions-ontology/issues",
"subjects": [
"Botany"
],
"user_defined_tags": [
"Experimental condition"
]
},
"mappings": {
"aberowl": "PECO",
"agroportal": "PECO",
"biocontext": "PECO",
"bioportal": "PECO",
"fairsharing": "FAIRsharing.6yNXYK",
"obofoundry": "peco",
"ols": "peco",
"ontobee": "PECO"
},
"obofoundry": {
"appears_in": [
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"mco"
],
"contact": "jaiswalp@science.oregonstate.edu",
"contact.github": "jaiswalp",
"contact.label": "Pankaj Jaiswal",
"contact.orcid": "0000-0002-1005-8383",
"deprecated": false,
"description": "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.",
"domain": "investigations",
"download.obo": "http://purl.obolibrary.org/obo/peco.obo",
"download.owl": "http://purl.obolibrary.org/obo/peco.owl",
"homepage": "http://planteome.org/",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"logo": "http://planteome.org/sites/default/files/garland_logo.PNG",
"name": "Plant Experimental Conditions Ontology",
"preferredPrefix": "PECO",
"prefix": "peco",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/29186578",
"title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics."
}
],
"repository": "https://github.com/Planteome/plant-experimental-conditions-ontology"
},
"ols": {
"description": "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.",
"download_owl": "http://purl.obolibrary.org/obo/peco.owl",
"homepage": "http://planteome.org/",
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{
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"description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.",
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"name": "PharmGKB Drug at Stanford",
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"prefix": "pharmgkb.drug",
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"description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.",
"example": "PA448710",
"keywords": [
"drug",
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],
"name": "PharmGKB Drug",
"pattern": "^PA\\d+$",
"prefix": "pharmgkb.drug",
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"11908751",
"22103613"
],
"uri_format": "http://www.pharmgkb.org/drug/$1"
},
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{
"doi": "10.2217/bmm.11.94",
"pmc": "PMC3339046",
"pubmed": "22103613",
"title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource",
"year": 2011
},
{
"doi": "10.1038/sj.tpj.6500035",
"pubmed": "11908751",
"title": "Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base",
"year": 2001
}
],
"wikidata": {
"prefix": "P7001"
}
},
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"biocontext": {
"prefix": "PHARMGKB.GENE"
},
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"is_identifiers": false,
"is_obo": false,
"prefix": "PHARMGKB.GENE",
"uri_format": "https://www.pharmgkb.org/gene/$1"
},
"bioportal": {
"name": "PharmGKB Ontology",
"prefix": "PHARMGKB"
},
"contact": {
"email": "teri.klein@stanford.edu",
"github": "TeriKlein",
"name": "Teri E Klein",
"orcid": "0000-0001-5527-6475"
},
"go": {
"homepage": "https://www.pharmgkb.org",
"name": "Pharmacogenetics and Pharmacogenomics Knowledge Base",
"prefix": "PharmGKB",
"uri_format": "https://www.pharmgkb.org/do/serve?objId=$1"
},
"mappings": {
"biocontext": "PHARMGKB.GENE",
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"go": "PharmGKB",
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"n2t": "pharmgkb.gene",
"prefixcommons": "pharmgkb.gene",
"uniprot": "DB-0074",
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"id": "00000245",
"name": "PharmGKB Gene",
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"pattern": "^PA\\w+$",
"prefix": "pharmgkb.gene",
"sampleId": "PA131",
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"description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.",
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"pattern": "^PA\\w+$",
"prefix": "pharmgkb.gene",
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"name": "PharmGKB Gene",
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"description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.",
"example": "PA131",
"keywords": [
"gene",
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],
"name": "PharmGKB Gene",
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"prefix": "pharmgkb.gene",
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"22103613"
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{
"doi": "10.2217/bmm.11.94",
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"pubmed": "22103613",
"title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource",
"year": 2011
},
{
"doi": "10.1385/1-59259-957-5:179",
"pubmed": "16100408",
"title": "PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base",
"year": 2005
}
],
"uniprot": {
"abbreviation": "PharmGKB",
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{
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],
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},
"wikidata": {
"prefix": "P7001"
}
},
"pharmgkb.pathways": {
"biocontext": {
"prefix": "PHARMGKB.PATHWAYS"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "PHARMGKB.PATHWAYS",
"uri_format": "https://www.pharmgkb.org/pathway/$1"
},
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"email": "teri.klein@stanford.edu",
"github": "TeriKlein",
"name": "Teri E Klein",
"orcid": "0000-0001-5527-6475"
},
"edam": {
"description": "Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).",
"name": "Pathway ID (PharmGKB)",
"obsolete": false,
"prefix": "2650"
},
"mappings": {
"biocontext": "PHARMGKB.PATHWAYS",
"biolink": "PHARMGKB.PATHWAYS",
"edam": "2650",
"miriam": "pharmgkb.pathways",
"n2t": "pharmgkb.pathways",
"prefixcommons": "pharmgkb.pathways",
"wikidata": "P7001"
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"miriam": {
"deprecated": false,
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"id": "00000089",
"name": "PharmGKB Pathways",
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"pattern": "^PA\\d+$",
"prefix": "pharmgkb.pathways",
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"pattern": "^PA\\d+$",
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"name": "PharmGKB",
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"description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies.",
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"prefix": "pharmgkb.pathways",
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{
"doi": "10.2217/bmm.11.94",
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{
"doi": "10.1038/sj.tpj.6500035",
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}
],
"wikidata": {
"description": "unique identifier for an entity in the PharmGKB knowledgebase",
"example": [
"PA134955224",
"PA356",
"PA443560",
"PA451581",
"PA451906"
],
"homepage": "https://www.pharmgkb.org/",
"name": "PharmGKB ID",
"pattern": "^PA[1-9]\\d*$",
"prefix": "P7001",
"uri_format": "https://www.pharmgkb.org/accession/$1"
}
},
"pharmvar": {
"contact": {
"email": "agaedigk@cmh.edu",
"name": "Andrea Gaedigk",
"orcid": "0000-0001-6968-1893"
},
"mappings": {
"prefixcommons": "pharmvar"
},
"name": "Pharmacogene Variation Consortium",
"prefixcommons": {
"description": "The Pharmacogene Variation (PharmVar) Consortium is the new home for PGx gene nomenclature serving as a centralized βNext-Generationβ Pharmacogene Variation data repository. The major focus of PharmVar is to catalogue allelic variation of genes impacting drug metabolism, disposition and response and provide a unifying designation system (nomenclature) for the global pharmacogenetic/genomic community. Efforts are synchronized between PharmVar, the Pharmacogenomic KnowledgeBase, and the Clinical Pharmacogenetic Implementation Consortium.",
"example": "CYP2A6",
"homepage": "https://www.pharmvar.org",
"keywords": [
"variant",
"gene",
"pharmacogenomics"
],
"name": "PharmVar",
"pattern": "^[A-z0-9]+$",
"prefix": "pharmvar",
"pubmed_ids": [
"29134625"
],
"synonyms": [
"pharmvar.gene"
],
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},
"provides": "hgnc.symbol",
"publications": [
{
"doi": "10.1002/cpt.910",
"pmc": "PMC5836850",
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"title": "The Pharmacogene Variation (PharmVar) Consortium: Incorporation of the Human Cytochrome P450 (CYP) Allele Nomenclature Database",
"year": 2017
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"phenolexplorer": {
"biocontext": {
"prefix": "PHENOLEXPLORER"
},
"mappings": {
"biocontext": "PHENOLEXPLORER",
"miriam": "phenolexplorer",
"n2t": "phenolexplorer",
"re3data": "r3d100012197"
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"miriam": {
"deprecated": false,
"description": "Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis.",
"homepage": "http://www.phenol-explorer.eu/foods/",
"id": "00000268",
"name": "Phenol-Explorer",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "phenolexplorer",
"sampleId": "75",
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},
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"description": "Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis.",
"example": "75",
"homepage": "http://www.phenol-explorer.eu/foods/",
"name": "Phenol-Explorer Database on Phenol content of foods",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "phenolexplorer",
"uri_format": "http://phenol-explorer.eu/foods/$1"
},
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"description": "Phenol-Explorer is the first comprehensive database on polyphenol content in foods",
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"name": "Phenol-Explorer",
"prefix": "r3d100012197",
"synonyms": [
"Database on Polyphenol Content in Foods"
],
"xrefs": {
"nif": "0000-32996",
"scr": "008647"
}
}
},
"phenx": {
"aberowl": {
"description": "Standard measures related to complex diseases, phenotypic traits and environmental exposures",
"download_owl": "http://aber-owl.net/media/ontologies/PHENX/16/phenx.owl",
"name": "PhenX Phenotypic Terms",
"prefix": "PHENX",
"version": "1.2"
},
"bioportal": {
"contact": {
"email": "yingqin@rti.org",
"name": "PhenX Admin"
},
"description": "Standard measures related to complex diseases, phenotypic traits and environmental exposures",
"name": "PhenX Phenotypic Terms",
"prefix": "PHENX",
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},
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"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants.",
"example": "130502",
"fairsharing": {
"abbreviation": "PhenX",
"description": "Standard measures related to complex diseases, phenotypic traits and environmental exposures.",
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"Phenotype",
"Disease",
"Exposure"
],
"homepage": "https://www.phenx.org/",
"name": "PhenX Phenotypic Terms",
"prefix": "FAIRsharing.y5jcwa",
"publications": [
{
"doi": "10.1097/mol.0b013e3283377395",
"pubmed": "20154612",
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"year": 2010
},
{
"doi": "10.1093/aje/kwr193",
"pubmed": "21749974",
"title": "The PhenX Toolkit: get the most from your measures",
"year": 2011
},
{
"doi": "10.1038/gim.2016.199",
"pubmed": "28079902",
"title": "PhenX measures for phenotyping rare genetic conditions",
"year": 2017
}
],
"subjects": [
"Environmental Science",
"Life Science",
"Biomedical Science"
]
},
"github_request_issue": 503,
"homepage": "https://www.phenxtoolkit.org/",
"integbio": {
"description": "The PhenX (consensus measures for Phenotypes and eXposures) Toolkit is a web-based catalog of recommended, standard measures of phenotypes and environmental exposures for use in biomedical research. The PhenX Toolkit offers well-established, broadly validated measures of phenotypes and exposures relevant to investigators in human genomics, epidemiology, and biomedical research. The measures in the Toolkit are selected by Working Groups of domain experts using a consensus process. The Toolkit provides detailed protocols, information about the measures, and tools to help investigators incorporate PhenX measures into their studies.",
"fairsharing": "FAIRsharing.2wa7v7",
"homepage": "https://www.phenxtoolkit.org",
"information_keywords": [
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],
"maintainer": "Pat West",
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"prefix": "nbdc02244",
"pubmeds": [
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"22954959"
],
"status": "Active",
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]
},
"mappings": {
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"name": "PhenX Toolkit",
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{
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},
{
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"pmc": "PMC3141081",
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},
{
"doi": "10.1097/mol.0b013e3283377395",
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}
],
"synonyms": [
"phenxtoolkit"
],
"uri_format": "https://www.phenxtoolkit.org/protocols/view/$1"
},
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"download_owl": "http://aber-owl.net/media/ontologies/PHIPO/38/phipo.owl",
"homepage": "https://github.com/PHI-base/phipo",
"name": "Pathogen Host Interaction Phenotype Ontology",
"prefix": "PHIPO"
},
"bioportal": {
"contact": {
"email": "alayne.cuzick@rothamsted.ac.uk",
"name": "Alayne Cuzick"
},
"description": "PHIPO is a formal ontology of species-neutral phenotypes observed in pathogen-host interactions. PHIPO is being developed to support the comprehensive and detailed representation of phenotypes in PHI-base, the multi-species Pathogen-Host Interactions database available online at http://www.phi-base.org. PHIPO is pre-composed and logically defined.",
"homepage": "https://github.com/PHI-base/phipo",
"name": "Pathogen Host Interaction Phenotype Ontology",
"prefix": "PHIPO",
"version": "2024-04-04"
},
"example": "0000001",
"mappings": {
"aberowl": "PHIPO",
"bioportal": "PHIPO",
"obofoundry": "phipo",
"ols": "phipo",
"ontobee": "PHIPO"
},
"obofoundry": {
"contact": "alayne.cuzick@rothamsted.ac.uk",
"contact.github": "CuzickA",
"contact.label": "Alayne Cuzick",
"contact.orcid": "0000-0001-8941-3984",
"depends_on": [
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],
"deprecated": false,
"description": "PHIPO is a formal ontology of species-neutral phenotypes observed in pathogen-host interactions.",
"domain": "phenotype",
"download.obo": "http://purl.obolibrary.org/obo/phipo.obo",
"download.owl": "http://purl.obolibrary.org/obo/phipo.owl",
"homepage": "https://github.com/PHI-base/phipo",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Pathogen Host Interaction Phenotype Ontology",
"preferredPrefix": "PHIPO",
"prefix": "phipo",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/34788826",
"title": "PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions"
}
],
"repository": "https://github.com/PHI-base/phipo"
},
"ols": {
"description": "Ontology of species-neutral phenotypes observed in pathogen-host interactions.",
"download_owl": "http://purl.obolibrary.org/obo/phipo.owl",
"homepage": "https://github.com/PHI-base/phipo",
"name": "Pathogen Host Interactions Phenotype Ontology",
"prefix": "phipo",
"version": "2024-04-04",
"version.iri": "http://purl.obolibrary.org/obo/phipo/releases/2024-04-04/phipo.owl"
},
"ontobee": {
"library": "Library",
"name": "Pathogen Host Interaction Phenotype Ontology",
"prefix": "PHIPO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1093/nar/gkab1037",
"pmc": "PMC8728202",
"pubmed": "34788826",
"title": "PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions",
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}
],
"uri_format": "http://purl.obolibrary.org/obo/PHIPO_$1"
},
"phosphopoint.kinase": {
"biocontext": {
"prefix": "PHOSPHOPOINT.KINASE"
},
"mappings": {
"biocontext": "PHOSPHOPOINT.KINASE",
"miriam": "phosphopoint.kinase",
"n2t": "phosphopoint.kinase"
},
"miriam": {
"deprecated": false,
"description": "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information.",
"homepage": "http://kinase.bioinformatics.tw/",
"id": "00000385",
"name": "PhosphoPoint Kinase",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "phosphopoint.kinase",
"sampleId": "AURKA",
"uri_format": "http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1"
},
"n2t": {
"description": "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information.",
"example": "AURKA",
"homepage": "http://kinase.bioinformatics.tw/",
"name": "PhosphoPoint Kinase at National Taiwan University",
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"pattern": "^\\w+$",
"prefix": "phosphopoint.kinase",
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}
},
"phosphopoint.protein": {
"biocontext": {
"prefix": "PHOSPHOPOINT.PROTEIN"
},
"mappings": {
"biocontext": "PHOSPHOPOINT.PROTEIN",
"miriam": "phosphopoint.protein",
"n2t": "phosphopoint.protein"
},
"miriam": {
"deprecated": false,
"description": "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information.",
"homepage": "http://kinase.bioinformatics.tw/",
"id": "00000386",
"name": "PhosphoPoint Phosphoprotein",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "phosphopoint.protein",
"sampleId": "AURKA",
"uri_format": "http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0"
},
"n2t": {
"description": "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information.",
"example": "AURKA",
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"name": "PhosphoPoint Phosphoprotein at National Taiwan University",
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"pattern": "^\\w+$",
"prefix": "phosphopoint.protein",
"uri_format": "http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0"
}
},
"phosphosite.curation": {
"contributor": {
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"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"description": "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to curation records that collect information extracted from specific publications.",
"example": "34665743",
"homepage": "https://www.phosphosite.org",
"name": "PhosphoSite Curation",
"pattern": "^\\d+$",
"uri_format": "https://www.phosphosite.org/curatedInfoAction.action?record=$1"
},
"phosphosite.protein": {
"biocontext": {
"prefix": "PHOSPHOSITE.PROTEIN"
},
"mappings": {
"biocontext": "PHOSPHOSITE.PROTEIN",
"miriam": "phosphosite.protein",
"n2t": "phosphosite.protein"
},
"miriam": {
"deprecated": false,
"description": "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database.",
"homepage": "http://www.phosphosite.org/homeAction.do",
"id": "00000105",
"name": "PhosphoSite Protein",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{5}$",
"prefix": "phosphosite.protein",
"sampleId": "12300",
"uri_format": "http://www.phosphosite.org/proteinAction.do?id=$1"
},
"n2t": {
"description": "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database.",
"example": "12300",
"homepage": "http://www.phosphosite.org/homeAction.do",
"name": "PhosphoSite",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{5}$",
"prefix": "phosphosite.protein",
"uri_format": "http://www.phosphosite.org/proteinAction.do?id=$1"
}
},
"phosphosite.residue": {
"biocontext": {
"prefix": "PHOSPHOSITE.RESIDUE"
},
"mappings": {
"biocontext": "PHOSPHOSITE.RESIDUE",
"miriam": "phosphosite.residue",
"n2t": "phosphosite.residue"
},
"miriam": {
"deprecated": false,
"description": "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence.",
"homepage": "http://www.phosphosite.org/homeAction.do",
"id": "00000125",
"name": "PhosphoSite Residue",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "phosphosite.residue",
"sampleId": "2842",
"uri_format": "http://www.phosphosite.org/siteAction.do?id=$1"
},
"n2t": {
"description": "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence.",
"example": "2842",
"homepage": "http://www.phosphosite.org/homeAction.do",
"name": "PhosphoSite Residue",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "phosphosite.residue",
"uri_format": "http://www.phosphosite.org/siteAction.do?id=$1"
}
},
"phosphosite.sitegroup": {
"comment": "Potentially could use a URI format like https://www.phosphosite.org/siteGroupAction.action?protOrg=1156&id=$1, but it's not obvious what the protOrg does.",
"contributor": {
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"description": "Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur.",
"example": "447860",
"homepage": "https://www.phosphosite.org",
"keywords": [
"biochemistry",
"grouping",
"post-translational modification"
],
"name": "PhosphoSite Site Group",
"pattern": "^\\d+$",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"phrr": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Philippine Health Research Registry (PHRR), managed by the Philippine Council for Health Research and Development, is a tool for good governance to promote transparency and accountability in health research. PHRR is a publicly accessible database on newly approved health researches. It includes clinical trials and non-clinical studies conducted in the Philippines. The registry is compliant with the World Health Organization (WHO) standard for clinical trials registry. [from website]",
"example": "4195",
"homepage": "https://registry.healthresearch.ph",
"name": "Philippine Health Research Registry",
"uri_format": "https://registry.healthresearch.ph/index.php/registry?view=research&layout=details&cid=$1"
},
"phylomedb": {
"biocontext": {
"prefix": "PHYLOMEDB"
},
"contact": {
"email": "toni.gabaldon@crg.eu",
"github": "tgabaldon",
"name": "Toni GabaldΓ³n",
"orcid": "0000-0003-0019-1735"
},
"fairsharing": {
"abbreviation": "PhylomeDB",
"description": "PhylomeDB is a unique knowledge base providing public access to minable and browsable catalogues of pre-computed, genome-wide collections of annotated sequences, alignments and phylogenies (i.e. phylomes) of homologous genes, as well as to their corresponding phylogeny-based orthology and paralogy relationships. In addition, PhylomeDB trees and alignments can be downloaded for further processing to detect and date gene duplication events, infer past events of inter-species hybridization and horizontal gene transfer, as well as to uncover footprints of selection, introgression, gene conversion, or other relevant evolutionary processes in the genes and organisms of interests. The v5 release also represents a significant core data expansion, with the database providing access to 534 phylomes, comprising over 8 million trees, and homology relationships for genes in over 6000 species. This makes PhylomeDB the largest and most comprehensive public repository of gene phylogenies ",
"homepage": "http://phylomedb.org",
"license": "CC BY-NC-SA 2.0",
"name": "PhylomeDB",
"prefix": "FAIRsharing.7hxxc4",
"publications": [
{
"doi": "10.1093/nar/gkm899",
"pubmed_id": 17962297,
"title": "PhylomeDB: a database for genome-wide collections of gene phylogenies."
},
{
"doi": "10.1093/nar/gkq1109",
"pubmed_id": 21075798,
"title": "PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions."
},
{
"doi": "10.1093/nar/gkt1177",
"pubmed_id": 24275491,
"title": "PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome."
},
{
"doi": "10.1093/nar/gkab966",
"pubmed_id": 34718760,
"title": "PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies."
}
],
"subjects": [
"Taxonomy",
"Phylogeny",
"Phylogenetics",
"Phylogenomics",
"Life Science"
],
"twitter": "phylomedb"
},
"integbio": {
"description": "PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes). Researchers are able to use this resource to visualise the history of genes with the available phylogentic trees and multiple sequence alignments.",
"fairsharing": "FAIRsharing.7hxxc4",
"homepage": "http://phylomedb.org",
"information_keywords": [
"Classification",
"Sequence"
],
"maintainer": "CRG (Comparative Genomics Group)",
"name": "PhylomeDB",
"prefix": "nbdc01764",
"pubmeds": [
"17962297",
"21075798",
"24275491"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"mappings": {
"biocontext": "PHYLOMEDB",
"fairsharing": "FAIRsharing.7hxxc4",
"integbio": "nbdc01764",
"miriam": "phylomedb",
"n2t": "phylomedb",
"prefixcommons": "phylomedb",
"uniprot": "DB-0144"
},
"miriam": {
"deprecated": false,
"description": "PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins.",
"homepage": "http://phylomedb.org/",
"id": "00000223",
"name": "PhylomeDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "phylomedb",
"sampleId": "Phy000CLXM_RAT",
"uri_format": "http://phylomedb.org/?seqid=$1"
},
"n2t": {
"description": "PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins.",
"example": "Phy000CLXM_RAT",
"homepage": "http://phylomedb.org/",
"name": "PhylomeDB at Centro de Investigación Príncipe Felipe",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "phylomedb",
"uri_format": "http://phylomedb.org/?seqid=$1"
},
"prefixcommons": {
"description": "PhylomeDB is a public database for complete collections of gene phylogenies (phylomes). It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments.",
"example": "Phy000CLXM_RAT",
"homepage": "http://phylomedb.bioinfo.cipf.es",
"keywords": [
"genome",
"protein",
"taxonomy"
],
"name": "Database for complete collections of gene phylogenies",
"pattern": "^\\w+$",
"prefix": "phylomedb",
"pubmed_ids": [
"17962297"
],
"uri_format": "http://phylomedb.org/?seqid=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkab966",
"pmc": "PMC8728271",
"pubmed": "34718760",
"title": "PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies",
"year": 2022
},
{
"doi": "10.1093/nar/gkt1177",
"pmc": "PMC3964985",
"pubmed": "24275491",
"title": "PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome",
"year": 2013
},
{
"doi": "10.1093/nar/gkq1109",
"pmc": "PMC3013701",
"pubmed": "21075798",
"title": "PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions",
"year": 2010
},
{
"doi": "10.1093/nar/gkm899",
"pmc": "PMC2238872",
"pubmed": "17962297",
"title": "PhylomeDB: a database for genome-wide collections of gene phylogenies",
"year": 2007
}
],
"uniprot": {
"abbreviation": "PhylomeDB",
"category": "Phylogenomic databases",
"homepage": "http://phylomedb.org/",
"name": "Database for complete collections of gene phylogenies",
"prefix": "DB-0144",
"publications": [
{
"doi": "10.1093/nar/gkab966",
"pubmed": "34718760"
}
],
"uri_format": "http://phylomedb.org/search_phylome/?seqid=$1"
}
},
"phytozome.locus": {
"biocontext": {
"prefix": "PHYTOZOME.LOCUS"
},
"mappings": {
"biocontext": "PHYTOZOME.LOCUS",
"miriam": "phytozome.locus",
"n2t": "phytozome.locus",
"ncbi": "Phytozome"
},
"miriam": {
"deprecated": false,
"description": "Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information.",
"homepage": "http://www.phytozome.net/",
"id": "00000432",
"name": "Phytozome Locus",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9]+$",
"prefix": "phytozome.locus",
"sampleId": "Glyma0021s00410",
"uri_format": "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1"
},
"n2t": {
"description": "Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information.",
"example": "Glyma0021s00410",
"homepage": "http://www.phytozome.net/",
"name": "Phytozome Locus at Joint Genome Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9]+$",
"prefix": "phytozome.locus",
"uri_format": "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1"
},
"ncbi": {
"example": "Glyma0021s00410",
"homepage": "http://phytozome.jgi.doe.gov/pz/portal.html",
"name": "Plant Genome Network",
"prefix": "Phytozome"
},
"synonyms": [
"JGI Phytozome"
]
},
"pibase": {
"mappings": {
"pathguide": "183",
"prefixcommons": "pibase"
},
"name": "Database of structurally defined protein interfaces",
"pathguide": {
"abbreviation": "PIBASE",
"homepage": "http://modbase.compbio.ucsf.edu/pibase/introduction.html",
"name": "PIBASE",
"prefix": "183"
},
"prefixcommons": {
"description": "PIBASE is a collection of all protein structural interfaces extracted from the Protein Data Bank and PQS structure databases. Both chain-chain and domain-domain (SCOP and CATH definitions) interfaces are detected.",
"example": "21692",
"homepage": "http://salilab.org/pibase",
"keywords": [
"protein",
"structure"
],
"name": "PIBASE: a database of structurally defined protein interfaces",
"pattern": "^\\d+$",
"prefix": "pibase",
"uri_format": "http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"pictar": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"example": "hsa-let-7a",
"homepage": "https://pictar.mdc-berlin.de/",
"name": "PicTar",
"synonyms": [
"pictar-vert"
]
},
"pid.pathway": {
"biocontext": {
"prefix": "PID.PATHWAY"
},
"contact": {
"email": "schaefec@mail.nih.gov",
"name": "Carl F. Schaefer",
"orcid": "0000-0002-5941-3390"
},
"edam": {
"description": "Identifier of a pathway from the NCI-Nature pathway database.",
"name": "Pathway ID (NCI-Nature)",
"obsolete": false,
"prefix": "2344"
},
"example": "eff796f3-6195-11e5-8ac5-06603eb7f303",
"fairsharing": {
"abbreviation": "PID",
"description": "The Pathway Interaction Database is a highly-structured, curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways.",
"homepage": "http://pid.nci.nih.gov/",
"name": "Pathway Interaction Database",
"prefix": "FAIRsharing.ncgh1j",
"publications": [
{
"doi": "10.1093/nar/gkn653",
"pubmed_id": 18832364,
"title": "PID: the Pathway Interaction Database."
}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"biocontext": "PID.PATHWAY",
"edam": "2344",
"fairsharing": "FAIRsharing.ncgh1j",
"miriam": "pid.pathway",
"n2t": "pid.pathway",
"pathguide": "119",
"prefixcommons": "pid"
},
"miriam": {
"deprecated": false,
"description": "The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information.",
"homepage": "http://pid.nci.nih.gov/",
"id": "00000133",
"name": "NCI Pathway Interaction Database: Pathway",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "pid.pathway",
"sampleId": "pi3kcipathway",
"uri_format": "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1"
},
"n2t": {
"description": "The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information.",
"example": "pi3kcipathway",
"homepage": "http://pid.nci.nih.gov/",
"name": "NCI Pathway Interaction Database (Pathway)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "pid.pathway",
"uri_format": "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1"
},
"pathguide": {
"abbreviation": "PID",
"homepage": "http://pid.nci.nih.gov/",
"keywords": [
"BioPAX"
],
"name": "NCI-Nature Pathway Interaction Database",
"prefix": "119"
},
"pattern": "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$",
"prefixcommons": {
"description": "The Pathway Interaction Database is a highly-structured, curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways",
"example": "p38alphabetadownstreampathway",
"homepage": "http://pid.nci.nih.gov/",
"keywords": [
"pathway",
"small molecule",
"gene",
"protein"
],
"license": "http://www.cancer.gov/global/web/policies/allpages#5",
"name": "Pathway Interaction Database",
"pattern": "^\\w+$",
"prefix": "pid",
"pubmed_ids": [
"18832364"
],
"synonyms": [
"pid.pathway"
],
"uri_format": "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkn653",
"pmc": "PMC2686461",
"pubmed": "18832364",
"title": "PID: the Pathway Interaction Database",
"year": 2008
}
],
"synonyms": [
"pid"
]
},
"pigqtldb": {
"biocontext": {
"prefix": "PIGQTLDB"
},
"mappings": {
"biocontext": "PIGQTLDB",
"miriam": "pigqtldb",
"n2t": "pigqtldb",
"prefixcommons": "pigqtldb"
},
"miriam": {
"deprecated": false,
"description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs.",
"homepage": "https://www.animalgenome.org/QTLdb",
"id": "00000506",
"name": "Animal Genome Pig QTL",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "pigqtldb",
"sampleId": "14",
"uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"
},
"n2t": {
"description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs.",
"example": "14",
"homepage": "http://www.animalgenome.org/cgi-bin/QTLdb/SS/index",
"name": "Animal QTL Pig at Iowa State University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "pigqtldb",
"uri_format": "http://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=$1"
},
"part_of": "qtldb",
"prefixcommons": {
"description": "This Pig Quantitative Trait Locus (QTL) database (Pig QTLdb) has gathered all pig QTL data published during the past 10+ years. The database and its peripheral tools make it possible to compare, confirm and locate on pig chromosomes the most feasible location for genes responsible for quantitative trait important to pig production.",
"example": "66",
"homepage": "http://www.animalgenome.org/cgi-bin/QTLdb/SS/index",
"keywords": [
"DNA",
"genome"
],
"name": "Pig Quantitative Trait Locus database",
"pattern": "^\\d+$",
"prefix": "pigqtldb",
"uri_format": "http://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=$1"
}
},
"pina": {
"biocontext": {
"prefix": "PINA"
},
"fairsharing": {
"abbreviation": "PINA",
"contact": {
"email": "wujm@bjmu.edu.cn",
"name": "Jianmin Wu",
"orcid": "0000-0002-8876-128X"
},
"description": "Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization, and management. It integrates protein-protein interaction (PPI) data from public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. In particular, it provides a variety of built-in tools to filter and analyze the networks for gaining biological and functional insights into the network.",
"homepage": "http://omics.bjcancer.org/pina/",
"name": "Protein Interaction Network Analysis platform",
"prefix": "FAIRsharing.7q4gsz",
"publications": [
{
"doi": "10.1038/nmeth.1282",
"pubmed_id": 19079255,
"title": "Integrated network analysis platform for protein-protein interactions."
},
{
"doi": "10.1093/nar/gkr967",
"pubmed_id": 22067443,
"title": "PINA v2.0: mining interactome modules."
},
{
"doi": "10.1093/nar/gkaa1075",
"pubmed_id": null,
"title": "PINA 3.0: mining cancer interactome"
}
],
"subjects": [
"Life Science",
"Data Visualization"
]
},
"mappings": {
"biocontext": "PINA",
"fairsharing": "FAIRsharing.7q4gsz",
"miriam": "pina",
"n2t": "pina",
"pathguide": "348"
},
"miriam": {
"deprecated": false,
"description": "Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms.",
"homepage": "http://cbg.garvan.unsw.edu.au/pina/",
"id": "00000359",
"name": "PINA",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$",
"prefix": "pina",
"sampleId": "Q13485",
"uri_format": "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?ac=$1&showExtend=null"
},
"n2t": {
"description": "Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms.",
"example": "Q13485",
"homepage": "http://cbg.garvan.unsw.edu.au/pina/",
"name": "Protein Interaction Network Analysis (PINA) at Garvan Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$",
"prefix": "pina",
"uri_format": "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?ac=$1&showExtend=null"
},
"name": "Protein Interaction Network Analysis",
"pathguide": {
"abbreviation": "PINA",
"homepage": "http://omics.bjcancer.org/pina/",
"name": "Protein Interaction Network Analysis",
"prefix": "348"
},
"provides": "uniprot",
"publications": [
{
"doi": "10.1093/nar/gkaa1075",
"pmc": "PMC7779002",
"pubmed": "33231689",
"title": "PINA 3.0: mining cancer interactome",
"year": 2021
},
{
"doi": "10.1093/nar/gkr967",
"pmc": "PMC3244997",
"pubmed": "22067443",
"title": "PINA v2.0: mining interactome modules",
"year": 2011
},
{
"doi": "10.1038/nmeth.1282",
"pubmed": "19079255",
"title": "Integrated network analysis platform for protein-protein interactions",
"year": 2008
}
],
"uri_format": "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1"
},
"piroplasma": {
"biocontext": {
"prefix": "PIROPLASMA"
},
"mappings": {
"biocontext": "PIROPLASMA",
"miriam": "piroplasma",
"n2t": "piroplasma"
},
"miriam": {
"deprecated": false,
"description": "PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"homepage": "http://piroplasmadb.org/",
"id": "00000351",
"name": "PiroplasmaDB",
"namespaceEmbeddedInLui": false,
"pattern": "^TA\\d+$",
"prefix": "piroplasma",
"sampleId": "TA14985",
"uri_format": "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"
},
"n2t": {
"description": "PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"example": "TA14985",
"homepage": "http://piroplasmadb.org/",
"name": "PiroplasmaBD at EuPathDB",
"namespaceEmbeddedInLui": false,
"pattern": "^TA\\d+$",
"prefix": "piroplasma",
"uri_format": "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"
}
},
"pirsf": {
"biocontext": {
"prefix": "PIRSF"
},
"contact": {
"email": "wuc@udel.edu",
"name": "Cathy H. Wu",
"orcid": "0000-0001-6379-8601"
},
"edam": {
"description": "Unique identifier of an entry from the PIRSF database.",
"name": "PIRSF",
"obsolete": false,
"prefix": "1136"
},
"fairsharing": {
"abbreviation": "PIRSF",
"description": "The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.",
"homepage": "https://proteininformationresource.org/pirwww/dbinfo/pirsf.shtml",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "PIR SuperFamily",
"prefix": "FAIRsharing.vssch2",
"publications": [
{
"doi": "10.1093/nar/gkh097",
"pubmed_id": 14681371,
"title": "PIRSF: family classification system at the Protein Information Resource."
}
],
"subjects": [
"Proteomics",
"Life Science"
]
},
"go": {
"homepage": "http://pir.georgetown.edu/pirsf/",
"name": "PIR Superfamily Classification System",
"prefix": "PIRSF",
"uri_format": "http://pir.georgetown.edu/cgi-bin/ipcSF?id=$1"
},
"mappings": {
"biocontext": "PIRSF",
"edam": "1136",
"fairsharing": "FAIRsharing.vssch2",
"go": "PIRSF",
"miriam": "pirsf",
"n2t": "pirsf",
"prefixcommons": "pirsf",
"uniprot": "DB-0079"
},
"miriam": {
"deprecated": false,
"description": "The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.",
"homepage": "https://pir.georgetown.edu/",
"id": "00000017",
"name": "PIRSF",
"namespaceEmbeddedInLui": false,
"pattern": "^PIRSF\\d{6}$",
"prefix": "pirsf",
"sampleId": "PIRSF000100",
"uri_format": "https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1"
},
"n2t": {
"description": "The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.",
"example": "PIRSF000100",
"homepage": "https://pir.georgetown.edu/",
"name": "PIRSF",
"namespaceEmbeddedInLui": false,
"pattern": "^PIRSF\\d{6}$",
"prefix": "pirsf",
"uri_format": "https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1"
},
"prefixcommons": {
"description": "The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.",
"example": "PIRSF000100",
"homepage": "http://pir.georgetown.edu/pirsf/",
"keywords": [
"protein",
"structure"
],
"name": "PIRSF; a whole-protein classification database",
"pattern": "^PIRSF\\d{6}$",
"prefix": "pirsf",
"pubmed_ids": [
"14681371"
],
"uri_format": "http://pir.georgetown.edu/cgi-bin/ipcSF?id=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkh097",
"pmc": "PMC308831",
"pubmed": "14681371",
"title": "PIRSF: family classification system at the Protein Information Resource",
"year": 2004
}
],
"uniprot": {
"abbreviation": "PIRSF",
"category": "Family and domain databases",
"homepage": "https://proteininformationresource.org/pirwww/dbinfo/pirsf.shtml",
"name": "PIRSF; a whole-protein classification database",
"prefix": "DB-0079",
"publications": [
{
"doi": "10.1093/nar/gkh097",
"pubmed": "14681371"
}
],
"uri_format": "https://proteininformationresource.org/cgi-bin/ipcSF?id=$1"
}
},
"pkdb": {
"fairsharing": {
"abbreviation": "PK-DB",
"contact": {
"email": "konigmatt@googlemail.com",
"name": "Matthias KΓΆnig",
"orcid": "0000-0003-1725-179X"
},
"description": "PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration.",
"homepage": "https://pk-db.com",
"name": "Pharmacokinetics Database",
"prefix": "FAIRsharing.AYegqK",
"publications": [
{
"doi": "10.1093/nar/gkaa990",
"pubmed_id": 33151297,
"title": "PK-DB: pharmacokinetics database for individualized and stratified computational modeling"
}
],
"repository": "https://github.com/matthiaskoenig/pkdb/issues",
"subjects": [
"Clinical Veterinary Medicine",
"Clinical Studies",
"Personalized Medicine",
"Pharmacology",
"Life Science",
"Pharmacogenomics",
"Preclinical Studies"
]
},
"mappings": {
"fairsharing": "FAIRsharing.AYegqK",
"miriam": "pkdb"
},
"miriam": {
"deprecated": false,
"description": "PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. ",
"homepage": "https://www.hu-berlin.de/?set_language=en&cl=en",
"id": "00000708",
"name": "PK-DB",
"namespaceEmbeddedInLui": false,
"pattern": "^PKDB[0-9]{5}$",
"prefix": "pkdb",
"sampleId": "PKDB00198",
"uri_format": "https://pk-db.com/data/$1"
},
"publications": [
{
"doi": "10.1093/nar/gkaa990",
"pmc": "PMC7779054",
"pubmed": "33151297",
"title": "PK-DB: pharmacokinetics database for individualized and stratified computational modeling",
"year": 2021
}
]
},
"plana": {
"aberowl": {
"description": "PLANA, the planarian anatomy ontology, encompasses the anatomy and life cycle stages for both __Schmidtea mediterranea__ biotypes.",
"download_owl": "http://aber-owl.net/media/ontologies/PLANA/28/plana.owl",
"homepage": "https://github.com/obophenotype/planaria-ontology",
"name": "planaria-ontology",
"prefix": "PLANA"
},
"biocontext": {
"prefix": "PLANA"
},
"bioportal": {
"contact": {
"email": "smr@stowers.org",
"name": "Sofia Robb"
},
"description": "Anatomy ontology for planaria and terms specific to the developmental stages of the planarian Schmidtea mediterranea.",
"homepage": "https://github.com/obophenotype/planaria-ontology",
"name": "Planarian Anatomy and Developmental Stage Ontolgoy",
"prefix": "PLANA",
"version": "2023-03-13"
},
"example": "0000001",
"fairsharing": {
"abbreviation": "PLANA",
"description": "Anatomy ontology for planaria and terms specific to the developmental stages of the planarian Schmidtea mediterranea. As the regenerative flatworm Schmidtea mediterranea gains popularity as a developmental research organism the need for standard nomenclature and a centralized repository of anatomical terms has become increasingly apparent. Utilization of a controlled vocabulary creates opportunities to catalogue genes and expression data for computational searches across research groups and cross-species comparisons, all while establishing a framework for integration of new terms. We created a Planarian Anatomy Ontology containing 327 terms and definitions for cellular organelles, cell types, tissues, organ systems, anatomical entities, life cycle stages and developmental processes described in the literature. Where possible, extant terms and definitions from Uberon and other open source anatomy ontologies were imported into the ontology to strengthen cross-species queries.",
"domains": [
"Organelle",
"Organ",
"Tissue"
],
"homepage": "https://planosphere.stowers.org/anatomyontology",
"license": "CC-BY-3.0",
"name": "Planarian Anatomy and Developmental Stage Ontology",
"prefix": "FAIRsharing.g1qrqs",
"repository": "https://github.com/obophenotype/planaria-ontology",
"subjects": [
"Anatomy",
"Developmental Biology",
"Life Science"
]
},
"mappings": {
"aberowl": "PLANA",
"biocontext": "PLANA",
"bioportal": "PLANA",
"fairsharing": "FAIRsharing.g1qrqs",
"obofoundry": "plana",
"ols": "plana",
"ontobee": "PLANA"
},
"name": "Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology",
"obofoundry": {
"appears_in": [
"planp"
],
"contact": "smr@stowers.org",
"contact.github": "srobb1",
"contact.label": "Sofia Robb",
"contact.orcid": "0000-0002-3528-5267",
"depends_on": [
"ro",
"uberon"
],
"deprecated": false,
"description": "PLANA, the planarian anatomy ontology, encompasses the anatomy and life cycle stages for both __Schmidtea mediterranea__ biotypes.",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/plana.obo",
"download.owl": "http://purl.obolibrary.org/obo/plana.owl",
"homepage": "https://github.com/obophenotype/planaria-ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "planaria-ontology",
"preferredPrefix": "PLANA",
"prefix": "plana",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/34318308",
"title": "Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms"
}
],
"repository": "https://github.com/obophenotype/planaria-ontology"
},
"ols": {
"description": "PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea.",
"download_owl": "http://purl.obolibrary.org/obo/plana.owl",
"homepage": "https://github.com/obophenotype/planaria-ontology",
"name": "Planarian Anatomy Ontology (PLANA)",
"prefix": "plana",
"version": "2023-03-13",
"version.iri": "http://purl.obolibrary.org/obo/plana/releases/2023-03-13"
},
"ontobee": {
"library": "Library",
"name": "planaria-ontology",
"prefix": "PLANA"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1242/dev.196097",
"pmc": "PMC8353266",
"pubmed": "34318308",
"title": "Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms",
"year": 2021
}
],
"uri_format": "http://purl.obolibrary.org/obo/PLANA_$1"
},
"planp": {
"aberowl": {
"description": "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea.",
"download_owl": "http://aber-owl.net/media/ontologies/PLANP/6/planp.owl",
"homepage": "https://github.com/obophenotype/planarian-phenotype-ontology",
"name": "Planarian Phenotype Ontology",
"prefix": "PLANP"
},
"bioportal": {
"contact": {
"email": "smr@stowers.org",
"name": "Sofia Robb"
},
"description": "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea. Many of the phenotypes were seen durning RNAi experiments.",
"homepage": "https://github.com/obophenotype/planarian-phenotype-ontology",
"name": "Planarian Phenotype Ontology",
"prefix": "PLANP"
},
"example": "0000001",
"mappings": {
"aberowl": "PLANP",
"bioportal": "PLANP",
"obofoundry": "planp",
"ols": "planp",
"ontobee": "PLANP"
},
"obofoundry": {
"contact": "smr@stowers.org",
"contact.github": "srobb1",
"contact.label": "Sofia Robb",
"contact.orcid": "0000-0002-3528-5267",
"depends_on": [
"go",
"pato",
"plana",
"ro"
],
"deprecated": false,
"description": "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea.",
"domain": "phenotype",
"download.obo": "http://purl.obolibrary.org/obo/planp.obo",
"download.owl": "http://purl.obolibrary.org/obo/planp.owl",
"homepage": "https://github.com/obophenotype/planarian-phenotype-ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Planarian Phenotype Ontology",
"preferredPrefix": "PLANP",
"prefix": "planp",
"repository": "https://github.com/obophenotype/planarian-phenotype-ontology"
},
"ols": {
"description": "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea.",
"download_owl": "http://purl.obolibrary.org/obo/planp.owl",
"homepage": "https://github.com/obophenotype/planarian-phenotype-ontology",
"name": "Planarian Phenotype Ontology (PLANP)",
"prefix": "planp",
"version": "2020-03-28",
"version.iri": "http://purl.obolibrary.org/obo/planp/releases/2020-03-28/planp.owl"
},
"ontobee": {
"library": "Library",
"name": "Planarian Phenotype Ontology",
"prefix": "PLANP"
},
"pattern": "^\\d+$",
"uri_format": "http://purl.obolibrary.org/obo/PLANP_$1"
},
"planttfdb": {
"biocontext": {
"prefix": "PLANTTFDB"
},
"contact": {
"email": "gaog@mail.cbi.pku.edu.cn",
"github": "gao-ge",
"name": "Ge Gao",
"orcid": "0000-0001-6470-8815"
},
"fairsharing": {
"abbreviation": "PlantTFDB",
"description": "Plant Transcription Factor Database (PlantTFDB) provides a comprehensive, high-quality resource of plant transcription factors (TFs), regulatory elements and interactions between them. In the latest version, It contains 320 370 TFs, classified into 58 families, from 165 species. Abundant functional and evolutionary annotations (e.g., GO, functional description, binding motifs, cis-element, regulation, references, orthologous groups and phylogenetic tree, etc.) are provided for identified TFs. In addition, multiple online tools are set up for TF identification, regulation prediction and functional enrichment analyses.",
"homepage": "http://planttfdb.cbi.pku.edu.cn",
"name": "Plant Transcription Factor Database",
"prefix": "FAIRsharing.ex3fqk",
"publications": [
{
"doi": "10.1093/molbev/msv058",
"pubmed_id": 25750178,
"title": "An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors"
},
{
"doi": "10.1093/nar/gkt1016",
"pubmed_id": 24174544,
"title": "PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors"
},
{
"doi": "10.1093/nar/gkw982",
"pubmed_id": null,
"title": "PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants"
}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"biocontext": "PLANTTFDB",
"fairsharing": "FAIRsharing.ex3fqk",
"miriam": "planttfdb",
"n2t": "planttfdb",
"pathguide": "497",
"prefixcommons": "planttfdb",
"re3data": "r3d100011301"
},
"miriam": {
"deprecated": false,
"description": "The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors.",
"homepage": "http://planttfdb.cbi.pku.edu.cn",
"id": "00000579",
"name": "Plant Transcription Factor Database",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\\._\\-#]*)$",
"prefix": "planttfdb",
"sampleId": "Ath_AT1G01030.1",
"uri_format": "http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1"
},
"n2t": {
"description": "The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors.",
"example": "Ath_AT1G01030.1",
"homepage": "http://planttfdb.cbi.pku.edu.cn",
"name": "PlantTFDB at Peking University",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\\._\\-#]*)$",
"prefix": "planttfdb",
"uri_format": "http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1"
},
"pathguide": {
"abbreviation": "PlantTFDB",
"homepage": "http://planttfdb.cbi.pku.edu.cn/",
"name": "Plant Transcription Factor Database",
"prefix": "497"
},
"prefixcommons": {
"description": "Plant Transcription Factor Database collected 40976 transcription factors from 39 species, and they are classified into 58 families.",
"example": "Ath005712",
"homepage": "http://planttfdb.cbi.pku.edu.cn",
"keywords": [
"regulation",
"DNA",
"RNA",
"small molecule",
"protein",
"gene"
],
"name": "Plant Transcription Factor Database",
"pattern": "^[a-z]+\\d+$",
"prefix": "planttfdb",
"uri_format": "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=[?species_name]&did=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkw982",
"pmc": "PMC5210657",
"pubmed": "27924042",
"title": "PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants",
"year": 2016
},
{
"doi": "10.1093/molbev/msv058",
"pmc": "PMC4476157",
"pubmed": "25750178",
"title": "An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors",
"year": 2015
},
{
"doi": "10.1093/nar/gkt1016",
"pmc": "PMC3965000",
"pubmed": "24174544",
"title": "PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors",
"year": 2013
}
],
"re3data": {
"description": "Species included in PlantTFDB 4.0 covers the main lineages of green plants. Therefore, PlantTFDB provides genomic TF repertoires across Viridiplantae. To provide comprehensive information for the TF family, a brief introduction and key references are presented for each family. Comprehensive annotations are made for each identified TF, including functional domains, 3D structures, gene ontology (GO), plant ontology (PO), expression information, expert-curated functional description, regulation information, interaction, conserved elements, references, and annotations in various databases such as UniProt, RefSeq, TransFac, STRING, and VISTA.\nBy inferring orthologous groups and constructing phylogenetic trees, evolutionary relationships among identified TFs were inferred. In addition, PlantTFDB has a simple and user-friendly interface to allow users to query based on combined conditions or make sequence similarity search using BLAST.\nThe new version PlantTFDB 5.0 has been incorporated into PlantRegMap http://plantregmap.gao-lab.org/.",
"homepage": "http://planttfdb.gao-lab.org/",
"name": "Plant Transcription Factor Database",
"prefix": "r3d100011301",
"synonyms": [
"PlantTFDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.ex3fqk",
"nif": "0000-03311",
"omics": "00560",
"scr": "003362"
}
}
},
"plasmodb": {
"biocontext": {
"prefix": "PLASMODB"
},
"contact": {
"email": "oharb@upenn.edu",
"github": "ramobrah",
"name": "Omar S. Harb",
"orcid": "0000-0003-4446-6200"
},
"fairsharing": {
"abbreviation": "PlasmoDB",
"description": "PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.",
"homepage": "https://plasmodb.org",
"name": "PlasmoDB",
"prefix": "FAIRsharing.g4n8sw",
"publications": [
{
"doi": "10.1093/nar/gkn814",
"pubmed_id": 18957442,
"title": "PlasmoDB: a functional genomic database for malaria parasites."
}
],
"subjects": [
"Genomics",
"Infectious Disease Medicine"
],
"twitter": "VEuPathDB"
},
"go": {
"homepage": "https://plasmodb.org",
"name": "PlasmoDB",
"prefix": "PlasmoDB",
"uri_format": "https://plasmodb.org/plasmo/app/record/gene/$1"
},
"integbio": {
"description": "PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.",
"fairsharing": "FAIRsharing.g4n8sw",
"homepage": "http://PlasmoDB.org",
"information_keywords": [
"Sequence",
"Expression",
"Ontology/Terminology/Nomenclature"
],
"name": "PlasmoDB",
"prefix": "nbdc01783",
"pubmeds": [
"18957442"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Organism",
"cDNA/EST"
]
},
"mappings": {
"biocontext": "PLASMODB",
"fairsharing": "FAIRsharing.g4n8sw",
"go": "PlasmoDB",
"integbio": "nbdc01783",
"miriam": "plasmodb",
"n2t": "plasmodb",
"ncbi": "ApiDB_PlasmoDB",
"pathguide": "514",
"prefixcommons": "plasmodb",
"re3data": "r3d100011569"
},
"miriam": {
"deprecated": false,
"description": "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"homepage": "http://plasmodb.org/plasmo/",
"id": "00000150",
"name": "PlasmoDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "plasmodb",
"sampleId": "PF11_0344",
"uri_format": "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"
},
"n2t": {
"description": "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"example": "PF11_0344",
"homepage": "http://plasmodb.org/plasmo/",
"name": "PlasmoDB at EuPathDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "plasmodb",
"uri_format": "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"
},
"ncbi": {
"example": "PF11_0344",
"homepage": "http://www.plasmodb.org/plasmo/home.jsp",
"name": "Plasmodium Genome Resources",
"prefix": "ApiDB_PlasmoDB"
},
"pathguide": {
"abbreviation": "PlasmoDB",
"homepage": "http://plasmodb.org/plasmo/",
"name": "Plasmodium Genomics Resource",
"prefix": "514"
},
"prefixcommons": {
"description": "PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.",
"example": "PFA0765c",
"homepage": "http://PlasmoDB.org",
"keywords": [
"genome"
],
"name": "PlasmoDB",
"pattern": "^PF[A-Z,0-9]+$",
"prefix": "plasmodb",
"pubmed_ids": [
"18957442"
],
"uri_format": "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1&project_id=PlasmoDB"
},
"publications": [
{
"doi": "10.1093/nar/gkn814",
"pmc": "PMC2686598",
"pubmed": "18957442",
"title": "PlasmoDB: a functional genomic database for malaria parasites",
"year": 2008
}
],
"re3data": {
"description": "PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.",
"homepage": "https://plasmodb.org/plasmo/app/",
"name": "PlasmoDB",
"prefix": "r3d100011569",
"synonyms": [
"Plasmodium Genomics Resource"
],
"xrefs": {
"fairsharing": "FAIRsharing.g4n8sw",
"miriam": "00000150",
"nif": "0000-03314",
"omics": "02765",
"scr": "013331"
}
},
"synonyms": [
"ApiDB_PlasmoDB"
]
},
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"biocontext": {
"prefix": "PLO"
},
"mappings": {
"biocontext": "PLO",
"obofoundry": "plo"
},
"name": "Plasmodium Life Cycle",
"obofoundry": {
"contact": "mb4@sanger.ac.uk",
"contact.label": "Matt Berriman",
"deprecated": true,
"domain": "anatomy and development",
"homepage": "http://www.sanger.ac.uk/Users/mb4/PLO/",
"name": "Plasmodium life cycle",
"prefix": "plo"
}
},
"pmap.cutdb": {
"biocontext": {
"prefix": "PMAP.CUTDB"
},
"contact": {
"email": "adam@burnham.org",
"name": "Adam Godzik",
"orcid": "0000-0002-2425-852X"
},
"mappings": {
"biocontext": "PMAP.CUTDB",
"miriam": "pmap.cutdb",
"n2t": "pmap.cutdb",
"prefixcommons": "pmap.cutdb"
},
"miriam": {
"deprecated": false,
"description": "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites).",
"homepage": "http://cutdb.burnham.org",
"id": "00000225",
"name": "CutDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "pmap.cutdb",
"sampleId": "25782",
"uri_format": "http://cutdb.burnham.org/relation/show/$1"
},
"n2t": {
"description": "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites).",
"example": "25782",
"homepage": "http://cutdb.burnham.org",
"name": "CutDB at The Burnham Institute for Medical Research",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "pmap.cutdb",
"uri_format": "http://cutdb.burnham.org/relation/show/$1"
},
"prefixcommons": {
"description": "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites).",
"example": "pmap.21243",
"homepage": "http://www.proteolysis.org/",
"keywords": [
"pathway",
"protein",
"enzyme"
],
"name": "CutDB - Proteolytic event database",
"pattern": "^pmap.\\d+$",
"prefix": "pmap.cutdb",
"pubmed_ids": [
"17142225"
],
"uri_format": "http://www.proteolysis.org/proteases/m_summarypg/$1"
},
"publications": [
{
"doi": "10.1093/nar/gkl813",
"pmc": "PMC1669773",
"pubmed": "17142225",
"title": "CutDB: a proteolytic event database",
"year": 2006
}
]
},
"pmap.substratedb": {
"biocontext": {
"prefix": "PMAP.SUBSTRATEDB"
},
"contact": {
"email": "eroshkin@burnham.org",
"name": "Alexey M. Eroshkin",
"orcid": "0000-0003-2023-4608"
},
"mappings": {
"biocontext": "PMAP.SUBSTRATEDB",
"miriam": "pmap.substratedb",
"n2t": "pmap.substratedb",
"prefixcommons": "pmap.substratedb"
},
"miriam": {
"deprecated": false,
"description": "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates.",
"homepage": "http://substrate.burnham.org/",
"id": "00000224",
"name": "SubstrateDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "pmap.substratedb",
"sampleId": "1915",
"uri_format": "http://substrate.burnham.org/protein/annotation/$1/html"
},
"n2t": {
"description": "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates.",
"example": "1915",
"homepage": "http://substrate.burnham.org/",
"name": "SubstrateDB at The Burnham Institute for Medical Research",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "pmap.substratedb",
"uri_format": "http://substrate.burnham.org/protein/annotation/$1/html"
},
"prefixcommons": {
"description": "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates.",
"example": "1915",
"keywords": [
"domain",
"protein",
"reaction"
],
"name": "SubstrateDB - Protease substrates",
"pattern": "^\\w+$",
"prefix": "pmap.substratedb",
"pubmed_ids": [
"18842634"
],
"uri_format": "http://substrate.burnham.org/protein/annotation/$1/html"
},
"publications": [
{
"doi": "10.1093/nar/gkn683",
"pmc": "PMC2686432",
"pubmed": "18842634",
"title": "PMAP: databases for analyzing proteolytic events and pathways",
"year": 2008
}
]
},
"pmc": {
"biocontext": {
"prefix": "PMCID",
"uri_format": "http://www.ncbi.nlm.nih.gov/pmc/$1"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "PMC",
"uri_format": "http://europepmc.org/articles/PMC$1"
},
"comment": "Note that the Europe PMC instance redirects canonical local unique identifiers from https://europepmc.org/articles/PMC3084216 to https://europepmc.org/article/PMC/3084216. However, this is an implementation detail and does not reflect the official format of a PMC identifier, which indeed does include `PMC` at the beginning of the local unique identifier",
"contact": {
"email": "beck@ncbi.nlm.nih.gov",
"github": "jeffbeckncbi",
"name": "Jeff Beck",
"orcid": "0000-0002-1798-9797"
},
"example_extras": [
"PMC7418728",
"PMC7418728.1",
"PMC7418728.2"
],
"fairsharing": {
"abbreviation": "PMC ID",
"description": "Identifier schema for PubMed Central, a U.S. National Institutes of Health's National Library of Medicine (NIH/NLM) free full-text archive of biomedical and life sciences journal literature.",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmc",
"name": "PubMed Central Identifier",
"prefix": "FAIRsharing.2b4316",
"subjects": [
"Knowledge and Information Systems"
]
},
"go": {
"homepage": "https://www.ncbi.nlm.nih.gov/pmc/",
"name": "Pubmed Central",
"prefix": "PMCID",
"synonyms": [
"PMC"
],
"uri_format": "https://www.ncbi.nlm.nih.gov/pmc/articles/$1"
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"mappings": {
"biocontext": "PMCID",
"biolink": "PMC",
"fairsharing": "FAIRsharing.2b4316",
"go": "PMCID",
"miriam": "pmc",
"n2t": "pmc",
"prefixcommons": "pmc",
"wikidata": "P932"
},
"miriam": {
"deprecated": false,
"description": "PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature.",
"homepage": "http://europepmc.org/",
"id": "00000147",
"name": "PMC International",
"namespaceEmbeddedInLui": false,
"pattern": "PMC\\d+",
"prefix": "pmc",
"sampleId": "PMC3084216",
"uri_format": "http://europepmc.org/articles/$1"
},
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"description": "PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature.",
"example": "PMC3084216",
"homepage": "http://europepmc.org/",
"name": "Europe PMC",
"namespaceEmbeddedInLui": false,
"pattern": "PMC\\d+",
"prefix": "pmc",
"uri_format": "http://europepmc.org/articles/$1"
},
"name": "PubMed Central",
"pattern": "^PMC\\d+(\\.\\d+)?$",
"prefixcommons": {
"description": "PubMed Central (PMC) is the U.S. National Institutes of Health (NIH) digital archive of biomedical and life sciences journal literature.",
"example": "PMC3084216",
"homepage": "http://www.pubmedcentral.nih.gov/",
"keywords": [
"bibliography"
],
"name": "Pubmed Central",
"pattern": "^PMC\\d+$",
"prefix": "pmc",
"synonyms": [
"pmcid"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/pmc/articles/$1/?tool=pmcentrez"
},
"providers": [
{
"code": "ncbi.pmc",
"description": "PubMed Central",
"homepage": "https://www.ncbi.nlm.nih.gov/pmc/",
"name": "PubMed Central",
"uri_format": "https://www.ncbi.nlm.nih.gov/pmc/articles/$1"
}
],
"publications": [
{
"doi": "10.1093/nar/gkr1184",
"pmc": "PMC3245031",
"pubmed": "22140104",
"title": "Database resources of the National Center for Biotechnology Information",
"year": 2011
},
{
"doi": "10.1093/nar/gkq1172",
"pmc": "PMC3013733",
"pubmed": "21097890",
"title": "Database resources of the National Center for Biotechnology Information",
"year": 2010
}
],
"references": [
"https://github.com/biopragmatics/bioregistry/issues/965"
],
"synonyms": [
"PMC",
"PMCID"
],
"wikidata": {
"database": "Q11801904",
"description": "identifier for a scientific work issued by PubMed Central (without \"PMC\" prefix)",
"example": [
"1201091",
"3682911"
],
"homepage": "https://www.ncbi.nlm.nih.gov/pmc/",
"name": "PMC publication ID",
"pattern": "^[1-9]\\d+$",
"prefix": "P932",
"uri_format": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC$1"
}
},
"pmdb": {
"biocontext": {
"prefix": "PMDB"
},
"fairsharing": {
"abbreviation": "PMDB",
"description": "The Protein Model DataBase (PMDB) is a database that stores three dimensional protein models obtained by structure prediction techniques.",
"homepage": "http://srv00.recas.ba.infn.it/PMDB/main.php",
"name": "Protein Model Database",
"prefix": "FAIRsharing.wkaakq",
"publications": [
{
"doi": "10.1093/nar/gkj105",
"pubmed_id": 16381873,
"title": "The PMDB Protein Model Database."
}
],
"subjects": [
"Structural Biology"
]
},
"mappings": {
"biocontext": "PMDB",
"fairsharing": "FAIRsharing.wkaakq",
"miriam": "pmdb",
"n2t": "pmdb",
"prefixcommons": "pmdb"
},
"miriam": {
"deprecated": false,
"description": "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques.",
"homepage": "https://bioinformatics.cineca.it/PMDB/",
"id": "00000190",
"name": "Protein Model Database",
"namespaceEmbeddedInLui": false,
"pattern": "^PM\\d{7}",
"prefix": "pmdb",
"sampleId": "PM0012345",
"uri_format": "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1"
},
"n2t": {
"description": "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques.",
"example": "PM0012345",
"homepage": "https://bioinformatics.cineca.it/PMDB/",
"name": "Protein Model Database at University of Rome",
"namespaceEmbeddedInLui": false,
"pattern": "^PM\\d{7}",
"prefix": "pmdb",
"uri_format": "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1"
},
"prefixcommons": {
"description": "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques.",
"example": "PM0012345",
"homepage": "http://www.caspur.it/PMDB/",
"keywords": [
"protein",
"structure"
],
"name": "Protein Model Database",
"pattern": "^PM\\d{7}$",
"prefix": "pmdb",
"uri_format": "http://mi.caspur.it/PMDB/user/search.php?idsearch=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkj105",
"pmc": "PMC1347467",
"pubmed": "16381873",
"title": "The PMDB Protein Model Database",
"year": 2006
}
]
},
"pmp": {
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"prefix": "PMP"
},
"contact": {
"email": "torsten.schwede@unibas.ch",
"name": "Torsten Schwede",
"orcid": "0000-0003-2715-335X"
},
"mappings": {
"biocontext": "PMP",
"miriam": "pmp",
"n2t": "pmp",
"pathguide": "438",
"prefixcommons": "pmp"
},
"miriam": {
"deprecated": false,
"description": "The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers.",
"id": "00000227",
"name": "PMP",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$",
"prefix": "pmp",
"sampleId": "Q0VCA6"
},
"n2t": {
"description": "The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers.",
"example": "Q0VCA6",
"homepage": "http://www.proteinmodelportal.org/",
"name": "PMP at University of Basel",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$",
"prefix": "pmp",
"uri_format": "http://www.proteinmodelportal.org/query/uniprot/$1"
},
"name": "Protein Model Portal",
"pathguide": {
"abbreviation": "PMP",
"homepage": "http://www.proteinmodelportal.org/",
"name": "The Protein Model Portal",
"prefix": "438"
},
"prefixcommons": {
"description": "The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models.",
"example": "Q0VCA6",
"homepage": "http://www.proteinmodelportal.org/",
"keywords": [
"prediction",
"protein",
"structure"
],
"name": "Protein Model Portal",
"pattern": "^\\d+$",
"prefix": "pmp",
"pubmed_ids": [
"19037750"
],
"synonyms": [
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],
"uri_format": "http://www.proteinmodelportal.org/query/uniprot/$1"
},
"provides": "uniprot",
"publications": [
{
"doi": "10.1007/s10969-008-9048-5",
"pmc": "PMC2704613",
"pubmed": "19037750",
"title": "The Protein Model Portal",
"year": 2008
}
]
},
"pmr": {
"aberowl": {
"description": "Knowledge representation related to computer-based decision support in rehabilitation; concepts and relationships in the rehabilitation domain, integrating clinical practice, the ICD (specifically its 11th revision), the clinical investigator record ontology, the ICF and SNOMED CT.",
"download_owl": "http://aber-owl.net/media/ontologies/PMR/4/pmr.owl",
"homepage": "https://sites.google.com/site/laiasubirats",
"name": "Physical Medicine and Rehabilitation",
"prefix": "PMR",
"version": "1.6"
},
"bioportal": {
"contact": {
"email": "laia.subirats@gmail.com",
"name": "Laia Subirats"
},
"description": "Knowledge representation related to computer-based decision support in rehabilitation; concepts and relationships in the rehabilitation domain, integrating clinical practice, the ICD (specifically its 11th revision), the clinical investigator record ontology, the ICF and SNOMED CT.",
"homepage": "https://sites.google.com/site/laiasubirats",
"name": "Physical Medicine and Rehabilitation",
"prefix": "PMR",
"publication": "https://sites.google.com/site/laiasubirats/publications",
"version": "1.6"
},
"contact": {
"email": "laia.subirats@gmail.com",
"name": "Laia Subirats",
"orcid": "0000-0001-8646-5463"
},
"fairsharing": {
"abbreviation": "PMR",
"description": "The Physiome Model Repository (PMR) is the main online repository for the IUPS Physiome Project, providing version and access controlled repositories, called workspaces, for users to store their data. PMR also provides a mechanism to create persistent access to specific revisions of a workspace, termed exposures. Exposure plugins are available for specific types of data (e.g., CellML or FieldML documents) which enable customizable views of the data when browsing the repository via a web browser, or an application accessing the repositoryβs content via web services.",
"homepage": "https://models.physiomeproject.org",
"name": "Physiome Model Repository",
"prefix": "FAIRsharing.bcjrnq",
"publications": [
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"pubmed_id": 21216774,
"title": "The Physiome Model Repository 2."
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{
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"pubmed_id": 18658182,
"title": "The CellML Model Repository."
},
{
"doi": "10.1098/rsta.2008.0310",
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"title": "CellML metadata standards, associated tools and repositories."
},
{
"doi": "10.1186/1471-2105-12-22",
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"title": "Revision history aware repositories of computational models of biological systems."
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{
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"title": "Toward a curated CellML model repository."
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{
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],
"subjects": [
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"Life Science",
"Physiology",
"Biomedical Science",
"Systems Biology"
],
"twitter": "physiomeproject"
},
"mappings": {
"aberowl": "PMR",
"bioportal": "PMR",
"fairsharing": "FAIRsharing.bcjrnq",
"miriam": "pmr"
},
"miriam": {
"deprecated": false,
"description": "Resource for the community to store, retrieve, search, reference, and reuse CellML models.",
"homepage": "https://www.auckland.ac.nz/en.html",
"id": "00000845",
"name": "Physiome Model Repository",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z0-9]{32,32}$",
"prefix": "pmr",
"sampleId": "ebf69ca24298b28b2361e7d43eb52d6c",
"uri_format": "https://models.physiomeproject.org/exposure/$1"
},
"publications": [
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"pmc": "PMC4759754",
"pubmed": "27051515",
"title": "The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable",
"year": 2016
},
{
"doi": "10.1186/1471-2105-12-22",
"pmc": "PMC3033326",
"pubmed": "21235804",
"title": "Revision history aware repositories of computational models of biological systems",
"year": 2011
},
{
"doi": "10.1093/bioinformatics/btq723",
"pubmed": "21216774",
"title": "The Physiome Model Repository 2",
"year": 2011
},
{
"doi": "10.1098/rsta.2008.0310",
"pmc": "PMC3268215",
"pubmed": "19380315",
"title": "CellML metadata standards, associated tools and repositories",
"year": 2009
},
{
"doi": "10.1093/bioinformatics/btn390",
"pubmed": "18658182",
"title": "The CellML Model Repository",
"year": 2008
},
{
"doi": "10.1109/iembs.2006.260202",
"pubmed": "17947072",
"title": "Toward a curated CellML model repository",
"year": 2006
}
]
},
"pmr.workspace": {
"mappings": {
"miriam": "pmr.workspace"
},
"miriam": {
"deprecated": false,
"description": "Workspace (Git repository) for modeling projects managed by the Physiome Model Repository",
"homepage": "https://www.auckland.ac.nz/en.html",
"id": "00000948",
"name": "Physiome Model Repository workspace",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-zA-Z0-9_\\-]+(/.*?)?$",
"prefix": "pmr.workspace",
"sampleId": "modularmassactionprimer",
"uri_format": "https://models.physiomeproject.org/workspace/$1"
}
},
"po": {
"aberowl": {
"description": "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.",
"download_owl": "http://aber-owl.net/media/ontologies/PO/27/po.owl",
"homepage": "http://browser.planteome.org/amigo",
"name": "Plant Ontology",
"prefix": "PO"
},
"agroportal": {
"contact": {
"email": "cooperl@science.oregonstate.edu",
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}
],
"subjects": [
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},
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"name": "Protein Ontology",
"prefix": "PR",
"synonyms": [
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]
},
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"homepage": "https://proconsortium.org/pro.shtml",
"information_keywords": [
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],
"maintainer": "University of Delaware||Georgetown University Medical Center",
"name": "PRO",
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"status": "Active",
"target_keywords": [
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},
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"title": "The representation of protein complexes in the Protein Ontology (PRO)",
"year": 2011
},
{
"doi": "10.1093/nar/gkq907",
"pmc": "PMC3013777",
"pubmed": "20935045",
"title": "The Protein Ontology: a structured representation of protein forms and complexes",
"year": 2010
},
{
"doi": "10.1186/1471-2105-8-s9-s1",
"pmc": "PMC2217659",
"pubmed": "18047702",
"title": "Framework for a protein ontology",
"year": 2007
}
],
"references": [
"https://github.com/biopragmatics/bioregistry/issues/959"
],
"synonyms": [
"PR",
"PRO"
],
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"category": "Miscellaneous databases",
"homepage": "https://proconsortium.org/",
"name": "Protein Ontology",
"prefix": "DB-0181",
"publications": [
{
"doi": "10.1093/nar/gkt1173",
"pubmed": "24270789"
}
],
"uri_format": "https://proconsortium.org/app/entry/$1"
},
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"PR:000023661",
"PR:000049515"
],
"homepage": "https://pir.georgetown.edu/pro/pro.shtml",
"name": "PRotein Ontology ID",
"pattern": "^PR:\\d*$",
"prefix": "P4926",
"uri_format": "https://proconsortium.org/app/entry/$1/"
}
},
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A registry of life science prefxes",
"example": "ChEBI",
"homepage": "https://prefixcommons.org",
"name": "Prefix Commons",
"uri_format": "https://bioregistry.io/metaregistry/prefixcommons/$1"
},
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"name": "PRIDE Controlled Vocabulary",
"prefix": "PRIDE"
},
"biocontext": {
"prefix": "PRIDE"
},
"contact": {
"email": "yperez@ebi.ac.uk",
"github": "ypriverol",
"name": "Yasset Perez-Riverol",
"orcid": "0000-0001-6579-6941"
},
"example": "0000006",
"fairsharing": {
"abbreviation": "PRIDE",
"description": "The PRIDE PRoteomics IDEntifications (PRIDE) Archive database is a centralized, standards compliant, public data repository for mass spectrometry proteomics data, including protein and peptide identifications and the corresponding expression values, post-translational modifications and supporting mass spectra evidence (both as raw data and peak list files). PRIDE is a core member in the ProteomeXchange (PX) consortium, which provides a standardised way for submitting mass spectrometry based proteomics data to public-domain repositories. ",
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"license": "http://opendatacommons.org/licenses/pddl/1.0",
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"prefix": "FAIRsharing.e1byny",
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"pubmed_id": 25047258,
"title": "How to submit MS proteomics data to ProteomeXchange via the PRIDE database."
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{
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"pubmed_id": 16041671,
"title": "PRIDE: the proteomics identifications database."
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{
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"pubmed_id": 26527722,
"title": "2016 update of the PRIDE database and its related tools."
},
{
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"pubmed_id": 18428683,
"title": "Using the Proteomics Identifications Database (PRIDE)."
},
{
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"pubmed_id": 16381953,
"title": "PRIDE: a public repository of protein and peptide identifications for the proteomics community."
},
{
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"pubmed_id": 23203882,
"title": "The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013."
},
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},
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"pubmed_id": 30395289,
"title": "The PRIDE database and related tools and resources in 2019: improving support for quantification data."
},
{
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"pubmed_id": null,
"title": "The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences"
}
],
"subjects": [
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],
"twitter": "pride_ebi"
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"integbio": {
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"homepage": "http://mrg.psc.riken.go.jp/PRIDE/index.html",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "PRIDE",
"prefix": "nbdc00630",
"status": "Inactive",
"target_keywords": [
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},
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"n2t": "pride",
"ols": "pride",
"prefixcommons": "pride",
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"uniprot": "DB-0130"
},
"miriam": {
"deprecated": true,
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"homepage": "https://www.ebi.ac.uk/pride/",
"id": "00000065",
"name": "PRIDE",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "pride",
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"uri_format": "https://www.ebi.ac.uk/pride/archive/assays/$1"
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"prefix": "pride",
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"download_owl": "https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/pride_cv.owl",
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"year": 2022
},
{
"doi": "10.1093/nar/gky1106",
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"pubmed": "30395289",
"title": "The PRIDE database and related tools and resources in 2019: improving support for quantification data",
"year": 2019
},
{
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"pmc": "PMC4702828",
"pubmed": "26527722",
"title": "2016 update of the PRIDE database and its related tools",
"year": 2015
},
{
"doi": "10.1002/pmic.201400120",
"pubmed": "25047258",
"title": "How to submit MS proteomics data to ProteomeXchange via the PRIDE database",
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},
{
"doi": "10.1038/nbt.2839",
"pmc": "PMC3986813",
"pubmed": "24727771",
"title": "ProteomeXchange provides globally coordinated proteomics data submission and dissemination",
"year": 2014
},
{
"doi": "10.1093/nar/gks1262",
"pmc": "PMC3531176",
"pubmed": "23203882",
"title": "The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013",
"year": 2012
},
{
"doi": "10.1002/0471250953.bi1308s21",
"pubmed": "18428683",
"title": "Using the Proteomics Identifications Database (PRIDE)",
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},
{
"doi": "10.1093/nar/gkm1021",
"pmc": "PMC2238846",
"pubmed": "18033805",
"title": "PRIDE: new developments and new datasets",
"year": 2007
},
{
"doi": "10.1093/nar/gkj138",
"pmc": "PMC1347500",
"pubmed": "16381953",
"title": "PRIDE: a public repository of protein and peptide identifications for the proteomics community",
"year": 2006
},
{
"doi": "10.1002/pmic.200401303",
"pubmed": "16041671",
"title": "PRIDE: the proteomics identifications database",
"year": 2005
}
],
"re3data": {
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"homepage": "https://www.ebi.ac.uk/pride/",
"name": "PRoteomics IDEntifications Database",
"prefix": "r3d100010137",
"synonyms": [
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"xrefs": {
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"scr": "003411"
}
},
"repository": "https://github.com/PRIDE-Utilities/pride-ontology",
"uniprot": {
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"category": "Proteomic databases",
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"prefix": "DB-0130",
"publications": [
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"uri_format": "https://www.ebi.ac.uk/pride/searchSummary.do?queryTypeSelected=identification%20accession%20number&identificationAccessionNumber=$1"
},
"uri_format": "http://purl.obolibrary.org/obo/PRIDE_$1"
},
"pride.project": {
"biocontext": {
"prefix": "PRIDE.PROJECT"
},
"cellosaurus": {
"category": "Proteomic databases",
"homepage": "https://www.ebi.ac.uk/pride/archive/",
"name": "PRoteomics IDEntifications archive",
"prefix": "PRIDE",
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"mappings": {
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"id": "00000515",
"name": "PRIDE Project",
"namespaceEmbeddedInLui": false,
"pattern": "^P(X|R)D\\d{6}$",
"prefix": "pride.project",
"providers": [
{
"code": "omicsdi",
"description": "PRIDE Project through OmicsDI",
"homepage": "https://www.omicsdi.org/",
"name": "PRIDE Project through OmicsDI",
"uri_format": "https://www.omicsdi.org/dataset/pride/$1"
}
],
"sampleId": "PXD000440",
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"name": "PRIDE Project at EBI",
"namespaceEmbeddedInLui": false,
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"prefix": "pride.project",
"uri_format": "https://www.ebi.ac.uk/pride/archive/projects/$1"
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},
"prints": {
"biocontext": {
"prefix": "PRINTS"
},
"contact": {
"email": "teresa.k.attwood@manchester.ac.uk",
"name": "Teresa K. Attwood",
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},
"fairsharing": {
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"description": "PRINTS is a collection of groups of conserved protein motifs, called fingerprints, used to define a protein family. A fingerprint is a group of conserved motifs used to characterize a protein family. Usually, the motifs do not overlap, though they may be contiguous in 3D space. Fingerprints can encode protein folds and functionalities more flexibly than single motifs. Please note that the last release of this database on the PRINTS website was in 2007.",
"homepage": "http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/PRINTS.html",
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},
{
"doi": "10.1093/nar/gkg030",
"pubmed_id": 12520033,
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},
{
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"pubmed_id": 22508994,
"title": "The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012."
}
],
"subjects": [
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"Biology"
]
},
"go": {
"homepage": "http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/",
"name": "PRINTS compendium of protein fingerprints",
"prefix": "PRINTS",
"uri_format": "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=$1"
},
"integbio": {
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"fairsharing": "biodbcore-000568",
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},
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},
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"homepage": "http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/",
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},
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"description": "PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours.",
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},
"prefixcommons": {
"description": "SPRINT provides search access to the data bank of protein family fingerprints (PRINTS).",
"example": "PR00001",
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"domain",
"protein"
],
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"pubmed_ids": [
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],
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},
"providers": [
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"uri_format": "http://130.88.97.239/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=$1"
}
],
"publications": [
{
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"pmc": "PMC3326521",
"pubmed": "22508994",
"title": "The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012",
"year": 2012
},
{
"doi": "10.1093/nar/gkg030",
"pmc": "PMC165477",
"pubmed": "12520033",
"title": "PRINTS and its automatic supplement, prePRINTS",
"year": 2003
},
{
"doi": "10.1093/bioinformatics/15.10.799",
"pubmed": "10705433",
"title": "FingerPRINTScan: intelligent searching of the PRINTS motif database",
"year": 1999
},
{
"doi": "10.1093/nar/28.1.225",
"pmc": "PMC102408",
"pubmed": "10592232",
"title": "PRINTS-S: the database formerly known as PRINTS",
"year": 2000
}
],
"synonyms": [
"sprint"
],
"uniprot": {
"abbreviation": "PRINTS",
"category": "Family and domain databases",
"homepage": "http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/",
"name": "Protein Motif fingerprint database; a protein domain database",
"prefix": "DB-0082",
"publications": [
{
"doi": "10.1093/database/bas019",
"pubmed": "22508994"
}
],
"uri_format": "https://www.ebi.ac.uk/interpro/entry/prints/$1"
}
},
"probesanddrugs": {
"contact": {
"email": "ctibor.skuta@img.cas.cz",
"name": "Ctibor Ε kuta",
"orcid": "0000-0001-5325-4934"
},
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
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},
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},
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],
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}
},
"probonto": {
"banana": "PROB",
"banana_peel": "_",
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},
"contact": {
"email": "pierre.grenon@ifomis.uni-saarland.de",
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},
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],
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"name": "Ontology and Knowledge Base of Probability Distributions",
"prefix": "FAIRsharing.8zqzm9",
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{
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"pubmed_id": 27153608,
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],
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"subjects": [
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"Mathematics",
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},
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"homepage": "https://www.ebi.ac.uk/ols4/ontologies/probonto",
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"prefix": "probonto",
"sampleId": "PROB_c0000005",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/probonto/terms?short_form=$1"
},
"n2t": {
"description": "ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities.",
"example": "PROB_c0000005",
"homepage": "https://www.ebi.ac.uk/ols/ontologies/probonto",
"name": "ProbOnto through OLS",
"namespaceEmbeddedInLui": false,
"pattern": "^PROB_c\\d+$",
"prefix": "probonto",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=$1"
},
"ols": {
"contact": "probonto.dev@gmail.com",
"description": "ProbOnto, is an ontology-based knowledge base of probability distributions, featuring more than eighty uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulas.",
"download_rdf": "file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/probonto.ttl",
"homepage": "http://probonto.org",
"name": "Probability Distribution Ontology",
"prefix": "probonto",
"version": "2.5.0"
},
"pattern": "^(c|k)\\d{7}$",
"publications": [
{
"doi": "10.1093/bioinformatics/btw170",
"pmc": "PMC5013898",
"pubmed": "27153608",
"title": "ProbOnto: ontology and knowledge base of probability distributions",
"year": 2016
}
],
"repository": "https://github.com/probonto/ontology",
"uri_format": "http://www.probonto.org/ontology#PROB_$1"
},
"proco": {
"aberowl": {
"description": "PROCO covers process chemistry, the chemical field concerned with scaling up laboratory syntheses to commercially viable processes.",
"download_owl": "http://aber-owl.net/media/ontologies/PROCO/1/proco.owl",
"homepage": "https://github.com/proco-ontology/PROCO",
"name": "Process Chemistry Ontology",
"prefix": "PROCO"
},
"bioportal": {
"contact": {
"email": "wes_schafer@merck.com",
"name": "Wes Schafer"
},
"description": "PROCO covers process chemistry, the chemical field concerned with scaling up laboratory syntheses to commercially viable processes.",
"homepage": "https://github.com/proco-ontology/PROCO",
"name": "Process Chemistry Ontology",
"prefix": "PROCO",
"version": "PROCO release 20220414"
},
"example": "0000001",
"mappings": {
"aberowl": "PROCO",
"bioportal": "PROCO",
"obofoundry": "proco",
"ols": "proco",
"ontobee": "PROCO"
},
"obofoundry": {
"contact": "wes_schafer@merck.com",
"contact.github": "schaferw",
"contact.label": "Wes Schafer",
"contact.orcid": "0000-0002-8786-1756",
"depends_on": [
"chebi",
"cheminf",
"obi",
"pato",
"ro",
"sbo"
],
"deprecated": false,
"description": "PROCO covers process chemistry, the chemical field concerned with scaling up laboratory syntheses to commercially viable processes.",
"domain": "chemistry and biochemistry",
"download.owl": "http://purl.obolibrary.org/obo/proco.owl",
"homepage": "https://github.com/proco-ontology/PROCO",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Process Chemistry Ontology",
"preferredPrefix": "PROCO",
"prefix": "proco",
"repository": "https://github.com/proco-ontology/PROCO"
},
"ols": {
"description": "PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry.",
"download_owl": "http://purl.obolibrary.org/obo/proco.owl",
"homepage": "https://github.com/proco-ontology/PROCO",
"name": "PROCO: PROcess Chemistry Ontology",
"prefix": "proco",
"version": "2022-04-11",
"version.iri": "http://purl.obolibrary.org/obo/proco/releases/2022-04-11/proco.owl"
},
"ontobee": {
"library": "Library",
"name": "Process Chemistry Ontology",
"prefix": "PROCO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/PROCO_$1"
},
"prodom": {
"biocontext": {
"prefix": "PRODOM"
},
"contact": {
"email": "Daniel.Kahn@toulouse.inra.fr",
"name": "Daniel Kahn",
"orcid": "0000-0003-1644-0169"
},
"fairsharing": {
"abbreviation": "ProDom",
"description": "ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.",
"homepage": "http://prodom.prabi.fr/",
"name": "ProDom",
"prefix": "FAIRsharing.a8z6gz",
"publications": [
{
"doi": "10.1093/nar/gki034",
"pubmed_id": 15608179,
"title": "The ProDom database of protein domain families: more emphasis on 3D"
},
{
"doi": "10.1093/bib/3.3.246",
"pubmed_id": 12230033,
"title": "ProDom: automated clustering of homologous domains."
}
],
"subjects": [
"Life Science"
]
},
"integbio": {
"description": "ProDom is an extensive database providing information on protein domain families.\nIt was created automatically by performing a global comparison of all the protein sequences that could be found.\nThe database can be searched by means of accession number, SWISS-PROT/TrEMBL identifier, or keywords.\nThe site also provides access to related databases namely InterPro, PROSITE, PFAM and PDB.\nThe ProDom domains may also be viewed on 3D structures created by the graphical interface.",
"fairsharing": "biodbcore-000375",
"homepage": "http://prodom.prabi.fr/prodom/current/html/home.php",
"information_keywords": [
"Classification"
],
"maintainer": "Rhone-Alpes Bioinformatics Center",
"name": "ProDom",
"prefix": "nbdc00174",
"pubmeds": [
"9009835",
"9399865",
"9847197",
"10592243",
"12230033",
"15608179"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"mappings": {
"biocontext": "PRODOM",
"fairsharing": "FAIRsharing.a8z6gz",
"integbio": "nbdc00174",
"miriam": "prodom",
"n2t": "prodom",
"prefixcommons": "prodom"
},
"miriam": {
"deprecated": false,
"description": "ProDom is a database of protein domain families generated from the global comparison of all available protein sequences.",
"homepage": "http://prodom.prabi.fr/prodom/current/html/home.php",
"id": "00000117",
"name": "ProDom",
"namespaceEmbeddedInLui": false,
"pattern": "^PD\\d+$",
"prefix": "prodom",
"sampleId": "PD10000",
"uri_format": "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1"
},
"n2t": {
"description": "ProDom is a database of protein domain families generated from the global comparison of all available protein sequences.",
"example": "PD10000",
"homepage": "http://prodom.prabi.fr/prodom/current/html/home.php",
"name": "ProDom Protein Domain Database",
"namespaceEmbeddedInLui": false,
"pattern": "^PD\\d+$",
"prefix": "prodom",
"uri_format": "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1"
},
"prefixcommons": {
"description": "ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database",
"example": "PD10000",
"homepage": "http://prodom.prabi.fr/",
"keywords": [
"protein",
"classification"
],
"name": "ProDom; a protein domain database",
"pattern": "^PD\\d+$",
"prefix": "prodom",
"pubmed_ids": [
"15608179"
],
"uri_format": "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1"
},
"publications": [
{
"doi": "10.1093/nar/gki034",
"pmc": "PMC539988",
"pubmed": "15608179",
"title": "The ProDom database of protein domain families: more emphasis on 3D",
"year": 2005
},
{
"doi": "10.1093/bib/3.3.246",
"pubmed": "12230033",
"title": "ProDom: automated clustering of homologous domains",
"year": 2002
}
]
},
"proglyc": {
"biocontext": {
"prefix": "PROGLYC"
},
"mappings": {
"biocontext": "PROGLYC",
"miriam": "proglyc",
"n2t": "proglyc"
},
"miriam": {
"deprecated": false,
"description": "ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information.",
"homepage": "http://www.proglycprot.org/",
"id": "00000354",
"name": "ProGlycProt",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]C\\d{1,3}$",
"prefix": "proglyc",
"sampleId": "AC119",
"uri_format": "http://www.proglycprot.org/detail.aspx?ProId=$1"
},
"n2t": {
"description": "ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information.",
"example": "AC119",
"homepage": "http://www.proglycprot.org/",
"name": "ProGlycProt at IMT",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]C\\d{1,3}$",
"prefix": "proglyc",
"uri_format": "http://www.proglycprot.org/detail.aspx?ProId=$1"
}
},
"propreo": {
"aberowl": {
"description": "A comprehensive proteomics data and process provenance ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/PROPREO/2/propreo.owl",
"homepage": "http://knoesis.wright.edu/research/semsci/application_domain/sem_life_sci/glycomics/resources/ontologies/propreo/",
"name": "Proteomics Data and Process Provenance Ontology",
"prefix": "PROPREO",
"version": "1.1"
},
"biocontext": {
"prefix": "PROPREO"
},
"bioportal": {
"contact": {
"email": "satyasahoo@ieee.org",
"name": "Satya S. Sahoo"
},
"description": "A comprehensive proteomics data and process provenance ontology.",
"homepage": "http://knoesis.wright.edu/research/semsci/application_domain/sem_life_sci/glycomics/resources/ontologies/propreo/",
"name": "Proteomics Data and Process Provenance Ontology",
"prefix": "PROPREO",
"publication": "http://knoesis.wright.edu/research/semsci/application_domain/sem_life_sci/glycomics/resources/ontologies/propreo/",
"version": "1.1"
},
"contact": {
"email": "satyasahoo@ieee.org",
"name": "Satya S. Sahoo",
"orcid": "0000-0001-9190-4256"
},
"mappings": {
"aberowl": "PROPREO",
"biocontext": "PROPREO",
"bioportal": "PROPREO",
"obofoundry": "propreo",
"prefixcommons": "propreo"
},
"obofoundry": {
"contact": "satya30@uga.edu",
"contact.label": "Satya S. Sahoo",
"deprecated": true,
"domain": "chemistry and biochemistry",
"homepage": "http://lsdis.cs.uga.edu/projects/glycomics/propreo/",
"name": "Proteomics data and process provenance",
"prefix": "propreo"
},
"prefixcommons": {
"bioportal": "1039",
"description": "A comprehensive proteomics data and process provenance ontology.",
"example": "protein",
"homepage": "http://knoesis.wright.edu/research/semsci/application_domain/sem_life_sci/glycomics/resources/ontologies/propreo/",
"keywords": [
"owl",
"proteomics"
],
"name": "Proteomics data and process provenance",
"pattern": "^\\w+$",
"prefix": "propreo",
"rdf_uri_format": "http://lsdis.cs.uga.edu/projects/glycomics/propreo#$1"
}
},
"prosite": {
"biocontext": {
"prefix": "PROSITE"
},
"contact": {
"email": "Ioannis.Xenarios@unil.ch",
"name": "Ioannis Xenarios",
"orcid": "0000-0002-3413-6841"
},
"fairsharing": {
"abbreviation": "PROSITE",
"description": "PROSITE is a database of protein families and domains. PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.",
"homepage": "https://prosite.expasy.org/",
"name": "PROSITE",
"prefix": "FAIRsharing.vwc6bd",
"publications": [
{
"doi": "10.1093/nar/gkj063",
"pubmed_id": 16381852,
"title": "The PROSITE database."
},
{
"doi": "10.1093/bioinformatics/btt129",
"pubmed_id": 23505298,
"title": "pfsearchV3: a code acceleration and heuristic to search PROSITE profiles."
},
{
"doi": "10.1093/nar/gks1067",
"pubmed_id": 23161676,
"title": "New and continuing developments at PROSITE."
}
],
"subjects": [
"Biology"
]
},
"go": {
"homepage": "https://prosite.expasy.org/",
"name": "Prosite database of protein families and domains",
"prefix": "Prosite",
"uri_format": "https://prosite.expasy.org/$1"
},
"integbio": {
"alt_name": "Database of protein domains, families and functional sites",
"description": "ExPASy PROSITE is a database of protein domains, protein families and their functional sites.\nThis repository also provides profiles and associated patterns, which can be used to identify the above.\nThis version (20.91) was made available on 4 March 2013.\nIt contains 1,661 documentation entries, 1,053 profiles and 1,308 patterns.\nThe database can be searched by entering a document number, a ProRule description, a taxonomic series or by calling up a page, whereupon the proteins are listed according to the number of positive UniProtKB hits, from most to least.\nThe option is also provided to have a sequence scanned against PROSITE patterns and profiles.\nIn the Advanced search option that is available, additional criteria may be added when a scan request is entered to specify the results more accurately.",
"fairsharing": "biodbcore-000527",
"homepage": "http://prosite.expasy.org/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "PROSITE",
"prefix": "nbdc00241",
"pubmeds": [
"12230035",
"19858104",
"12230035",
"16845026",
"16091411"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"mappings": {
"biocontext": "PROSITE",
"fairsharing": "FAIRsharing.vwc6bd",
"go": "Prosite",
"integbio": "nbdc00241",
"miriam": "prosite",
"n2t": "prosite",
"prefixcommons": "prosite",
"togoid": "Prosite",
"uniprot": "DB-0084",
"wikidata": "P4355"
},
"miriam": {
"deprecated": false,
"description": "PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.",
"homepage": "https://www.expasy.org/prosite/",
"id": "00000032",
"name": "PROSITE",
"namespaceEmbeddedInLui": false,
"pattern": "^PS\\d{5}$",
"prefix": "prosite",
"sampleId": "PS00001",
"uri_format": "https://prosite.expasy.org/$1"
},
"n2t": {
"description": "PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.",
"example": "PS00001",
"homepage": "https://www.expasy.org/prosite/",
"name": "ExPASy PROSITE",
"namespaceEmbeddedInLui": false,
"pattern": "^PS\\d{5}$",
"prefix": "prosite",
"uri_format": "https://prosite.expasy.org/$1"
},
"name": "PROSITE",
"prefixcommons": {
"description": "PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them",
"example": "PS00001",
"homepage": "http://www.expasy.org/prosite",
"keywords": [
"protein",
"structure"
],
"license": "http://www.isb-sib.ch/disclaimer.html",
"name": "PROSITE; a protein domain and family database",
"pattern": "^PS\\d{5}$",
"prefix": "prosite",
"pubmed_ids": [
"16381852"
],
"synonyms": [
"prositedoc"
],
"uri_format": "http://www.expasy.org/cgi-bin/nicesite.pl?$1"
},
"publications": [
{
"doi": "10.1093/bioinformatics/btt129",
"pmc": "PMC3634184",
"pubmed": "23505298",
"title": "pfsearchV3: a code acceleration and heuristic to search PROSITE profiles",
"year": 2013
},
{
"doi": "10.1093/nar/gks1067",
"pmc": "PMC3531220",
"pubmed": "23161676",
"title": "New and continuing developments at PROSITE",
"year": 2012
},
{
"doi": "10.1093/nar/gkj063",
"pmc": "PMC1347426",
"pubmed": "16381852",
"title": "The PROSITE database",
"year": 2006
}
],
"togoid": {
"catalog": "nbdc00241",
"examples": [
"PS01177",
"PS00516",
"PS01065",
"PS00418",
"PS01085",
"PS01086",
"PS01293",
"PS00355",
"PS01253",
"PS00992"
],
"keywords": [
"Domain"
],
"name": "PROSITE",
"pattern": "^(?PS\\d{5})$",
"prefix": "Prosite",
"uri_format": "http://identifiers.org/prosite/$1"
},
"uniprot": {
"abbreviation": "PROSITE",
"category": "Family and domain databases",
"homepage": "https://prosite.expasy.org/",
"name": "PROSITE; a protein domain and family database",
"prefix": "DB-0084",
"publications": [
{
"doi": "10.1093/nar/gks1067",
"pubmed": "23161676"
}
],
"uri_format": "https://prosite.expasy.org/doc/$1"
},
"wikidata": {
"description": "identifier for a protein family, domain or functional site, in the PROSITE database",
"example": [
"PDOC00263",
"PDOC00550",
"PDOC51055"
],
"name": "PROSITE documentation ID",
"pattern": "^PDOC\\d{5}$",
"prefix": "P4355",
"uri_format": "https://prosite.expasy.org/$1"
}
},
"protclustdb": {
"biocontext": {
"prefix": "PROTCLUSTDB"
},
"contact": {
"email": "klimke@ncbi.nlm.nih.gov",
"name": "William Klimke"
},
"fairsharing": {
"abbreviation": "ProtClustDB",
"description": "ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.",
"homepage": "https://www.ncbi.nlm.nih.gov/proteinclusters",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "NCBI Protein Clusters Database",
"prefix": "FAIRsharing.da493y",
"publications": [
{
"doi": "10.1093/nar/gkn734",
"pubmed_id": 18940865,
"title": "The National Center for Biotechnology Information's Protein Clusters Database."
}
],
"subjects": [
"Genomics",
"Genetics",
"Life Science"
]
},
"mappings": {
"biocontext": "PROTCLUSTDB",
"fairsharing": "FAIRsharing.da493y",
"miriam": "protclustdb",
"n2t": "protclustdb",
"prefixcommons": "protclustdb"
},
"miriam": {
"deprecated": false,
"description": "ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.",
"homepage": "https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters",
"id": "00000226",
"name": "ProtClustDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "protclustdb",
"sampleId": "O80725",
"uri_format": "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1"
},
"n2t": {
"description": "ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.",
"example": "O80725",
"homepage": "https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters",
"name": "ProtClustDB at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "protclustdb",
"uri_format": "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1"
},
"prefixcommons": {
"description": "ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.",
"example": "2728498",
"homepage": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=proteinclusters",
"keywords": [
"protein",
"structure"
],
"name": "ProtClustDB",
"pattern": "^\\d+$",
"prefix": "protclustdb",
"pubmed_ids": [
"18940865"
],
"synonyms": [
"protein_clusters"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=ShowDetailView&TermToSearch=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkn734",
"pmc": "PMC2686591",
"pubmed": "18940865",
"title": "The National Center for Biotechnology Information's Protein Clusters Database",
"year": 2008
}
]
},
"protcom": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"mappings": {
"pathguide": "242",
"prefixcommons": "protcom"
},
"pathguide": {
"abbreviation": "PROTCOM",
"homepage": "http://www.ces.clemson.edu/compbio/protcom",
"name": "Database of Protein Complexes",
"prefix": "242"
},
"prefixcommons": {
"description": "This database is a collection of protein-protein homo- and hetero-complexes as well as domain-domain structures. This issue of the database contains 17.024 entries (as of October 2007) of which 1350 are two-chain protein hetero-complexes, 7773 homodimers and 1589 are one-chain proteins parsed into two domains (domain structures).",
"example": "12e8LH",
"homepage": "http://www.ces.clemson.edu/compbio/protcom",
"keywords": [
"protein",
"structure"
],
"name": "Database of protein-protein complexes",
"pattern": "^[A-Z,0-9]+$",
"prefix": "protcom",
"uri_format": "http://www.ces.clemson.edu/compbio/protcom/print_file.cgi?pdbid=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"proteomicsdb.peptide": {
"biocontext": {
"prefix": "PROTEOMICSDB.PEPTIDE"
},
"comment": "The fact that this has .peptide as a subspace is a bit of a misnomer. Its original registration with MIRIAM uses a subview over the protein to point to peptides, but the identifiers in this semantic space seem to be about proteins.",
"mappings": {
"biocontext": "PROTEOMICSDB.PEPTIDE",
"miriam": "proteomicsdb.peptide",
"n2t": "proteomicsdb.peptide"
},
"miriam": {
"deprecated": false,
"description": "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein.",
"homepage": "https://www.proteomicsdb.org/#peptideSearch",
"id": "00000525",
"name": "ProteomicsDB Peptide",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "proteomicsdb.peptide",
"sampleId": "53504",
"uri_format": "https://www.proteomicsdb.org/#human/proteinDetails/$1/peptides/"
},
"n2t": {
"description": "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein.",
"example": "53504",
"homepage": "https://www.proteomicsdb.org/#peptideSearch",
"name": "Proteomics DB Peptide at Center for Integrated Protein Science",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "proteomicsdb.peptide",
"uri_format": "https://www.proteomicsdb.org/#human/proteinDetails/$1/peptides/"
},
"uri_format": "https://www.proteomicsdb.org/#human/proteinDetails/$1"
},
"proteomicsdb.protein": {
"biocontext": {
"prefix": "PROTEOMICSDB.PROTEIN"
},
"mappings": {
"biocontext": "PROTEOMICSDB.PROTEIN",
"miriam": "proteomicsdb.protein",
"n2t": "proteomicsdb.protein"
},
"miriam": {
"deprecated": false,
"description": "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins.",
"homepage": "https://www.proteomicsdb.org/#human",
"id": "00000524",
"name": "ProteomicsDB Protein",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "proteomicsdb.protein",
"sampleId": "53504",
"uri_format": "https://www.proteomicsdb.org/#human/proteinDetails/$1/summary"
},
"n2t": {
"description": "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins.",
"example": "53504",
"homepage": "https://www.proteomicsdb.org/#human",
"name": "Proteomics DB Protein at Center for Integrated Protein Science",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "proteomicsdb.protein",
"uri_format": "https://www.proteomicsdb.org/#human/proteinDetails/$1/summary"
}
},
"protonet.cluster": {
"biocontext": {
"prefix": "PROTONET.CLUSTER"
},
"contact": {
"email": "michall@cc.huji.ac.il",
"github": "LinialLab",
"name": "Michal Linial",
"orcid": "0000-0002-9357-4526"
},
"mappings": {
"biocontext": "PROTONET.CLUSTER",
"miriam": "protonet.cluster",
"n2t": "protonet.cluster",
"prefixcommons": "protonet.cluster"
},
"miriam": {
"deprecated": false,
"description": "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information.",
"homepage": "http://www.protonet.cs.huji.ac.il/",
"id": "00000229",
"name": "ProtoNet Cluster",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "protonet.cluster",
"sampleId": "4349895",
"uri_format": "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1"
},
"n2t": {
"description": "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information.",
"example": "4349895",
"homepage": "http://www.protonet.cs.huji.ac.il/",
"name": "ProtoNet at Hebrew University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "protonet.cluster",
"uri_format": "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1"
},
"prefixcommons": {
"description": "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information.",
"example": "4349895",
"keywords": [
"classification",
"clustering",
"protein"
],
"name": "ProtoNet Cluster",
"pattern": "^\\d+$",
"prefix": "protonet.cluster",
"pubmed_ids": [
"16672244"
],
"uri_format": "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1"
},
"publications": [
{
"doi": "10.1110/ps.062185706",
"pmc": "PMC2242553",
"pubmed": "16672244",
"title": "Functional annotation prediction: all for one and one for all",
"year": 2006
}
]
},
"protonet.proteincard": {
"biocontext": {
"prefix": "PROTONET.PROTEINCARD"
},
"contact": {
"email": "michall@cc.huji.ac.il",
"github": "LinialLab",
"name": "Michal Linial",
"orcid": "0000-0002-9357-4526"
},
"mappings": {
"biocontext": "PROTONET.PROTEINCARD",
"miriam": "protonet.proteincard",
"n2t": "protonet.proteincard",
"prefixcommons": "protonet.proteincard"
},
"miriam": {
"deprecated": false,
"description": "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information.",
"homepage": "http://www.protonet.cs.huji.ac.il/",
"id": "00000228",
"name": "ProtoNet ProteinCard",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "protonet.proteincard",
"sampleId": "16941567",
"uri_format": "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1"
},
"n2t": {
"description": "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information.",
"example": "16941567",
"homepage": "http://www.protonet.cs.huji.ac.il/",
"name": "ProtoNet at Hebrew University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "protonet.proteincard",
"uri_format": "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1"
},
"prefixcommons": {
"description": "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information.",
"example": "16941567",
"keywords": [
"protein"
],
"name": "ProtoNet ProteinCard",
"pattern": "^\\d+$",
"prefix": "protonet.proteincard",
"pubmed_ids": [
"16672244"
],
"uri_format": "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1"
},
"publications": [
{
"doi": "10.1110/ps.062185706",
"pmc": "PMC2242553",
"pubmed": "16672244",
"title": "Functional annotation prediction: all for one and one for all",
"year": 2006
}
]
},
"prov": {
"aberowl": {
"description": "PROV is a superset of PROV (the Provenance Ontology). The relationship between these two ontologies is described at http://www.w3.org/ns/prov",
"download_owl": "http://aber-owl.net/media/ontologies/PROV/1/prov.owl",
"homepage": "http://www.w3.org/TR/prov-o/",
"name": "Superset of Provenance Ontology",
"prefix": "PROV",
"version": "Recommendation version 2013-04-30"
},
"biocontext": {
"prefix": "prov",
"uri_format": "http://www.w3.org/ns/prov#$1"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "prov",
"uri_format": "http://www.w3.org/ns/prov#$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web.",
"example": "Activity",
"homepage": "https://www.w3.org/ns/prov",
"lov": {
"description": "The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web.",
"homepage": "http://www.w3.org/TR/prov-o/",
"keywords": [
"W3C Rec"
],
"modified": "2015-01-11",
"name": "W3C PROVenance Interchange",
"prefix": "prov",
"uri_prefix": "http://www.w3.org/ns/prov#$1"
},
"mappings": {
"aberowl": "PROV",
"biocontext": "prov",
"biolink": "prov",
"lov": "prov",
"ols": "prov",
"zazuko": "prov"
},
"name": "PROV Namespace",
"ols": {
"homepage": "https://www.w3.org/TR/prov-o/",
"name": "Provenance Ontology (PROV-O)",
"prefix": "prov"
},
"preferred_prefix": "prov",
"uri_format": "http://www.w3.org/ns/prov#$1",
"zazuko": {
"prefix": "prov",
"uri_format": "http://www.w3.org/ns/prov#$1"
}
},
"pscdb": {
"biocontext": {
"prefix": "PSCDB"
},
"contact": {
"email": "mota@i.nagoya-u.ac.jp",
"name": "Motonori Ota",
"orcid": "0000-0001-9090-668X"
},
"fairsharing": {
"abbreviation": "PSCDB",
"description": "The Protein Structural Change DataBase (PSCDB) presents the structural changes found in proteins, represented by pairs of ligand-free and ligand-bound structures of identical proteins, and links these changes to ligand-binding.",
"homepage": "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/",
"name": "Protein Structure Change Database",
"prefix": "FAIRsharing.3d4jx0",
"publications": [
{
"doi": "10.1016/j.jmb.2011.02.058",
"pubmed_id": 21376729,
"title": "Classification and annotation of the relationship between protein structural change and ligand binding."
},
{
"doi": "10.1093/nar/gkr966",
"pubmed_id": 22080505,
"title": "PSCDB: a database for protein structural change upon ligand binding."
}
],
"subjects": [
"Life Science"
]
},
"integbio": {
"alt_name": "Protein Structural Change DataBase",
"description": "The PSCDB contains information on the relationship between protein structural changes and ligand binding. Structural changes are classified into seven distinct classes based on the location of the ligand binding site and the mechanism underlying the structural change.",
"homepage": "https://www.ideal-db.org/pscdb/",
"information_keywords": [
"3D structure",
"Interaction/Pathway"
],
"maintainer": "Nagoya University, Graduate School of Information Science",
"name": "PSCDB",
"prefix": "nbdc01636",
"pubmeds": [
"22080505",
"21376729"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"mappings": {
"biocontext": "PSCDB",
"fairsharing": "FAIRsharing.3d4jx0",
"integbio": "nbdc01636",
"miriam": "pscdb",
"n2t": "pscdb"
},
"miriam": {
"deprecated": false,
"description": "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion.",
"homepage": "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html",
"id": "00000370",
"name": "PSCDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "pscdb",
"sampleId": "051",
"uri_format": "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html"
},
"n2t": {
"description": "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion.",
"example": "051",
"homepage": "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html",
"name": "PSCDB at Nagoya University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "pscdb",
"uri_format": "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html"
},
"name": "Protein Structural Change Database",
"publications": [
{
"doi": "10.1093/nar/gkr966",
"pmc": "PMC3245091",
"pubmed": "22080505",
"title": "PSCDB: a database for protein structural change upon ligand binding",
"year": 2011
},
{
"doi": "10.1016/j.jmb.2011.02.058",
"pubmed": "21376729",
"title": "Classification and annotation of the relationship between protein structural change and ligand binding",
"year": 2011
}
]
},
"psdo": {
"aberowl": {
"description": "Ontology to reproducibly study visualizations of clinical performance",
"download_owl": "http://aber-owl.net/media/ontologies/PSDO/2/psdo.owl",
"homepage": "https://github.com/Display-Lab/psdo",
"name": "Performance Summary Display Ontology",
"prefix": "PSDO"
},
"bioportal": {
"contact": {
"email": "zachll@umich.edu",
"name": "Zach Landis-Lewis"
},
"description": "The Performance Summary Display Ontology (PSDO) is a lightweight application ontology used to reproducibly study visualizations of clinical performance and their associated outcomes in healthcare quality improvement settings. PSDO extends boundaries of visual representation artifacts by the IAO in the domain of distributed representations. PSDO describes dimensional representations of relational information displays that can be used to study the influence of feedback interventions on clinical practice.",
"homepage": "https://github.com/Display-Lab/psdo",
"name": "Performance Summary Display Ontology",
"prefix": "PSDO",
"publication": "https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf",
"version": "1.0.1"
},
"example": "0000055",
"mappings": {
"aberowl": "PSDO",
"bioportal": "PSDO",
"obofoundry": "psdo",
"ols": "psdo",
"ontobee": "PSDO"
},
"obofoundry": {
"contact": "zachll@umich.edu",
"contact.github": "zachll",
"contact.label": "Zach Landis-Lewis",
"contact.orcid": "0000-0002-9117-9338",
"depends_on": [
"bfo",
"iao",
"ro",
"stato"
],
"deprecated": false,
"description": "Ontology to reproducibly study visualizations of clinical performance",
"domain": "information",
"download.owl": "http://purl.obolibrary.org/obo/psdo.owl",
"homepage": "https://github.com/Display-Lab/psdo",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Performance Summary Display Ontology",
"preferredPrefix": "PSDO",
"prefix": "psdo",
"repository": "https://github.com/Display-Lab/psdo"
},
"ols": {
"description": "Performance Summary Display Ontology (PSDO) is an application ontology about motivating information in performance summaries and the visual and textual entities that are used to communicate about performance. Motivating information includes performance comparisons and changes that motivate improvement or sustainment, such as improvement towards a goal, loss of high performer status, or the presence of a performance gap. Visual and textual entities include charts, tables, and graphs that display performance information. PSDO's domain focus is healthcare organizations that use clinical quality dashboards and feedback interventions for healthcare professionals and teams. Performance information is commonly about the quality of care and health outcomes that have been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is supported by the NIH, National Library of Medicine (1K01LM012528-01, 1R01LM013894-01).\n\nLandis-Lewis Z, Stansbury C, RincΓ³n J, Gross C. Performance Summary Display Ontology: Feedback intervention content, delivery, and interpreted information. International Conference on Biomedical Ontology 2022 (ICBO 2022). https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf",
"download_owl": "http://purl.obolibrary.org/obo/psdo.owl",
"homepage": "https://github.com/Display-Lab/psdo",
"name": "Performance Summary Display Ontology",
"prefix": "psdo",
"version": "1.0.1",
"version.iri": "http://purl.obolibrary.org/obo/2022-02-23/psdo.owl"
},
"ontobee": {
"library": "Library",
"name": "Performance Summary Display Ontology",
"prefix": "PSDO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/PSDO_$1"
},
"pseudogene": {
"bioportal": {
"contact": {
"email": "yhl3@gersteinlab.org",
"name": "Gerstein Lab"
},
"name": "Pseudogene",
"prefix": "pseudo",
"version": "0.1"
},
"contact": {
"email": "mark@gersteinlab.org",
"name": "Mark Gerstein",
"orcid": "0000-0002-9746-3719"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase.",
"example": "PGOHUM00000289843",
"homepage": "http://www.pseudogene.org",
"integbio": {
"description": "Pseudogene.org is a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase. It contains annotations, nucleotide sequences, amino acid sequence, individual sequence alignment about Eukaryote and Prokaryote pseudogenes and pseudomotifs.\nPseudogenes are analyzed using sequence alignment programs (such as FASTA or BLAST) to detect matching regions in the nucleotide sequence.",
"homepage": "http://www.pseudogene.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "Yale University",
"name": "Pseudogene.org",
"prefix": "nbdc00178",
"pubmeds": [
"17099229"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"mappings": {
"bioportal": "pseudo",
"integbio": "nbdc00178",
"prefixcommons": "pseudogene"
},
"name": "PseudoGene",
"prefixcommons": {
"description": "Pseudogene is a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase.",
"example": "4",
"homepage": "http://www.pseudogene.org/",
"keywords": [
"gene"
],
"name": "PseudoGene",
"pattern": "^\\d+$",
"prefix": "pseudogene",
"uri_format": "http://tables.pseudogene.org/[?species_name]/$1"
},
"synonyms": [
"pseudogene.org"
],
"wikidata": {
"database": "Q7254809"
}
},
"pseudomonas": {
"biocontext": {
"prefix": "PSEUDOMONAS"
},
"mappings": {
"biocontext": "PSEUDOMONAS",
"miriam": "pseudomonas",
"n2t": "pseudomonas"
},
"miriam": {
"deprecated": false,
"description": "The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.",
"homepage": "http://www.pseudomonas.com/",
"id": "00000180",
"name": "Pseudomonas Genome Database",
"namespaceEmbeddedInLui": false,
"pattern": "^P\\w+$",
"prefix": "pseudomonas",
"sampleId": "PSEEN0001",
"uri_format": "http://www.pseudomonas.com/feature/show/?locus_tag=$1"
},
"n2t": {
"description": "The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.",
"example": "PSEEN0001",
"homepage": "http://www.pseudomonas.com/",
"name": "Pseudomonas Genome Database at Simon Fraser University",
"namespaceEmbeddedInLui": false,
"pattern": "^P\\w+$",
"prefix": "pseudomonas",
"uri_format": "http://www.pseudomonas.com/feature/show/?locus_tag=$1"
}
},
"psipar": {
"banana": "PAR",
"biocontext": {
"prefix": "PSIPAR"
},
"comment": "This resource is no longer loaded on XML and the sourceforge link from the HUPO website to the psi-par.obo artifact is dead.",
"deprecated": true,
"example": "0116",
"homepage": "https://www.psidev.info/psi-par",
"mappings": {
"biocontext": "PSIPAR",
"miriam": "psipar",
"n2t": "psipar"
},
"miriam": {
"deprecated": false,
"description": "Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms.",
"homepage": "https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR",
"id": "00000533",
"name": "Protein Affinity Reagents",
"namespaceEmbeddedInLui": false,
"pattern": "^PAR:\\d+$",
"prefix": "psipar",
"sampleId": "PAR:0116",
"uri_format": "https://www.ebi.ac.uk/ontology-lookup/?termId=$1"
},
"n2t": {
"description": "Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms.",
"example": "PAR:0116",
"homepage": "https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR",
"name": "Protein Affinity Reagents through OLS",
"namespaceEmbeddedInLui": false,
"pattern": "^PAR:\\d+$",
"prefix": "psipar",
"uri_format": "https://www.ebi.ac.uk/ontology-lookup/?termId=$1"
},
"pattern": "^\\d+$",
"uri_format": "https://www.ebi.ac.uk/ontology-lookup/?termId=PAR:$1"
},
"pso": {
"aberowl": {
"description": "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter.",
"download_owl": "http://aber-owl.net/media/ontologies/PSO/5/pso.owl",
"homepage": "https://github.com/Planteome/plant-stress-ontology",
"name": "Plant Stress Ontology",
"prefix": "PSO"
},
"agroportal": {
"contact": {
"email": "cooperl@oregonstate.edu",
"name": "Laurel Cooper"
},
"description": "The Plant Stress Ontology (PSO) describes biotic and abiotic stresses that a plant may encounter. An ontology containing biotic and abiotic plant stresses. Part of the Planteome suite of reference ontologies.",
"example_uri": "http://purl.obolibrary.org/obo/PSO_0000013",
"homepage": "https://planteome.org/",
"license": "CC-BY-4.0",
"name": "Plant Stress Ontology",
"prefix": "PSO",
"repository": "https://github.com/Planteome/plant-stress-ontology",
"version": "2023-11-14"
},
"bioportal": {
"contact": {
"email": "schrader@th-brandenburg.de",
"name": "Thomas Schrader"
},
"description": "It is the ontology embedding PRIME (Prospective Risk Analysis in Medical Environments) in related issues of patient safety research and activities. It classifies terms and express relations between them. The ontology building in an ongoing process. Any comments are welcome.",
"name": "PatientSafetyOntology",
"prefix": "PSO",
"version": "008:2017-08-04: Einarbeitung der ZustΓ€nde"
},
"example": "0000013",
"fairsharing": {
"abbreviation": "PSO",
"description": "It is the ontology embedding PRIME (Prospective Risk Analysis in Medical Environments) in related issues of patient safety research and activities. It classifies terms and express relations between them. The ontology building in an ongoing process. Any comments are welcome.",
"domains": [
"Monitoring",
"Hospital"
],
"homepage": "http://bioportal.bioontology.org/ontologies/PSO",
"name": "PatientSafetyOntology",
"prefix": "FAIRsharing.dyj433",
"subjects": [
"Occupational Medicine",
"Medical Informatics"
]
},
"mappings": {
"aberowl": "PSO",
"agroportal": "PSO",
"bioportal": "PSO",
"fairsharing": "FAIRsharing.dyj433",
"obofoundry": "pso",
"ols": "pso",
"ontobee": "PSO"
},
"obofoundry": {
"contact": "cooperl@oregonstate.edu",
"contact.github": "cooperl09",
"contact.label": "Laurel Cooper",
"contact.orcid": "0000-0002-6379-8932",
"depends_on": [
"ro"
],
"deprecated": false,
"description": "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter.",
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"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Database of researchers to track publications, citation metrics, peer reviews, and journal editing work.",
"example": "1981638",
"homepage": "https://publons.com/researcher",
"mappings": {
"biolink": "ResearchID"
},
"name": "Publons Researcher",
"pattern": "^\\d+$",
"uri_format": "https://publons.com/researcher/$1"
},
"pubmed": {
"biocontext": {
"prefix": "PUBMED"
},
"cellosaurus": {
"category": "Reference resources",
"homepage": "https://www.ncbi.nlm.nih.gov/pubmed",
"name": "PubMed",
"prefix": "PubMed",
"uri_format": "https://www.ncbi.nlm.nih.gov/pubmed/$1"
},
"cheminf": {
"description": [],
"name": "PubChem Identifier",
"obsolete": false,
"prefix": "000302"
},
"contact": {
"email": "beck@ncbi.nlm.nih.gov",
"github": "jeffbeckncbi",
"name": "Jeff Beck",
"orcid": "0000-0002-1798-9797"
},
"edam": {
"description": "PubMed unique identifier of an article.",
"name": "PubMed",
"obsolete": false,
"prefix": "1187"
},
"fairsharing": {
"abbreviation": "PMID",
"description": "The PubMed Unique Identifier (PMID) is a 1- to 8-digit accession number with no leading zeros for managing and disseminating records at the PubMed repository. The PMID is a unique reference number for PubMed citations and is a distinctly different number from the PMCID and is used only for PubMed records. PMIDs are not reused after records are deleted. Prior to the 2004 version of PubMed (available December 3, 2003), many records contained a MEDLINE Unique Identifier in addition to the PMID. NLM no longer displays the MEDLINE Unique Identifier. The PMID has become the unique identifier for the MEDLINE record.",
"domains": [
"Citation",
"Bibliography",
"Publication"
],
"homepage": "https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmid",
"name": "PubMed Unique Identifier",
"prefix": "FAIRsharing.2b9b61",
"subjects": [
"Biomedical Science"
]
},
"go": {
"homepage": "https://www.ncbi.nlm.nih.gov/pubmed",
"name": "PubMed",
"prefix": "PMID",
"synonyms": [
"PUBMED"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/pubmed/$1"
},
"integbio": {
"description": "This database contains bibliographic information from journal articles in the field of life science as well as MEDLINE (title, authors, journal name, abstracts). Links are provided for articles with free access to the full article.",
"fairsharing": "biodbcore-000456",
"homepage": "http://www.ncbi.nlm.nih.gov/pubmed",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "PubMed",
"prefix": "nbdc00179",
"status": "Active"
},
"mappings": {
"biocontext": "PUBMED",
"cellosaurus": "PubMed",
"cheminf": "000302",
"edam": "1187",
"fairsharing": "FAIRsharing.2b9b61",
"go": "PMID",
"integbio": "nbdc00179",
"miriam": "pubmed",
"n2t": "pubmed",
"prefixcommons": "pubmed",
"togoid": "Pubmed",
"wikidata": "P698"
},
"miriam": {
"deprecated": false,
"description": "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.",
"homepage": "https://www.ncbi.nlm.nih.gov/PubMed/",
"id": "00000015",
"name": "PubMed",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "pubmed",
"providers": [
{
"code": "hubmed",
"description": "HubMed",
"homepage": "http://www.hubmed.org/",
"name": "HubMed",
"uri_format": "http://www.hubmed.org/display.cgi?uids=$1"
},
{
"code": "epmc",
"description": "Europe PMC",
"homepage": "http://europepmc.org/",
"name": "Europe PMC",
"uri_format": "http://europepmc.org/abstract/MED/$1"
},
{
"code": "CURATOR_REVIEW",
"description": "PubMed through Linkedlife data",
"homepage": "http://linkedlifedata.com/",
"name": "PubMed through Linkedlife data",
"uri_format": "http://linkedlifedata.com/resource/pubmed/id/$1"
},
{
"code": "scholia",
"description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.",
"homepage": "https://scholia.toolforge.org/",
"name": "Scholia",
"uri_format": "https://scholia.toolforge.org/pubmed/$1"
}
],
"sampleId": "16333295",
"uri_format": "https://www.ncbi.nlm.nih.gov/pubmed/$1"
},
"n2t": {
"description": "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.",
"example": "16333295",
"homepage": "https://www.ncbi.nlm.nih.gov/PubMed/",
"name": "NCBI PubMed",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "pubmed",
"uri_format": "https://www.ncbi.nlm.nih.gov/pubmed/$1"
},
"name": "PubMed",
"prefixcommons": {
"alt_uri_formats": [
"http://europepmc.org/abstract/MED/#$1",
"http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-view+MedlineFull+[medline-PMID:#]$1",
"http://www.hubmed.org/display.cgi?uids=#$1"
],
"description": "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.",
"example": "23735196",
"homepage": "http://www.ncbi.nlm.nih.gov/pubmed/",
"keywords": [
"bibliography"
],
"name": "PubMed",
"pattern": "^\\d+$",
"prefix": "pubmed",
"pubmed_ids": [
"16381840"
],
"synonyms": [
"pmid",
"medline"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/pubmed/$1"
},
"providers": [
{
"code": "uniprot.citation",
"description": "UniProt mints PURLs for citations identifiers",
"homepage": "https://uniprot.org/",
"name": "UniProt",
"uri_format": "http://purl.uniprot.org/citations/$1"
},
{
"code": "uniprot.pubmed",
"description": "UniProt mints PURLs for PubMed identifiers",
"homepage": "https://uniprot.org/",
"name": "UniProt",
"uri_format": "http://purl.uniprot.org/pubmed/$1"
},
{
"code": "pubmed.new",
"description": "New-style link for pubmed",
"homepage": "https://pubmed.ncbi.nlm.nih.gov",
"name": "PubMed (new)",
"uri_format": "https://pubmed.ncbi.nlm.nih.gov/$1"
}
],
"publications": [
{
"doi": "10.1093/nar/gkj158",
"pmc": "PMC1347520",
"pubmed": "16381840",
"title": "Database resources of the National Center for Biotechnology Information",
"year": 2006
}
],
"synonyms": [
"MEDLINE",
"PMID",
"PubMed",
"pmid"
],
"togoid": {
"catalog": "nbdc00179",
"examples": [
"19281226",
"19879151",
"20858243",
"10773016",
"16527252",
"28499733",
"10397770",
"15149666",
"23861362",
"10577920"
],
"keywords": [
"Literature"
],
"name": "PubMed",
"pattern": "^(?:pmid:|PMID:)?(?\\d+)$",
"prefix": "Pubmed",
"uri_format": "http://rdf.ncbi.nlm.nih.gov/pubmed/$1"
},
"wikidata": {
"database": "Q2082879",
"description": "identifierΒ for journal articles/abstracts in PubMed",
"example": [
"17246615",
"32768924",
"4388",
"823"
],
"homepage": "https://pubmed.ncbi.nlm.nih.gov",
"name": "PubMed publication ID",
"pattern": "^([1-3]\\d{7}|[1-9]\\d{0,6})$",
"prefix": "P698",
"uri_format": "https://pubmed.ncbi.nlm.nih.gov/$1",
"uri_format_rdf": "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/$1"
}
},
"puro": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology for the characterisation of the roles of agents β people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians.",
"example": "RoleInTime",
"fairsharing": {
"abbreviation": "PRO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Publishing Roles Ontology (PRO) is an ontology for the characterisation of the roles of agents β people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/pro",
"license": "CC-BY-4.0",
"name": "Publishing Roles Ontology",
"prefix": "FAIRsharing.3e88d6",
"publications": [
{
"doi": "10.1145/2362499.2362502",
"title": "Scholarly publishing and Linked Data: describing roles, statuses, temporal and contextual extents",
"year": 2012
}
],
"repository": "https://github.com/sparontologies/pro",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"homepage": "http://www.sparontologies.net/ontologies/pro",
"mappings": {
"fairsharing": "FAIRsharing.3e88d6"
},
"name": "Publishing Roles Ontology",
"preferred_prefix": "PuRO",
"publications": [
{
"doi": "10.1145/2362499.2362502",
"title": "Scholarly publishing and linked data",
"year": 2012
}
],
"repository": "https://github.com/sparontologies/pro",
"uri_format": "http://purl.org/spar/pro/$1"
},
"pw": {
"aberowl": {
"description": "A controlled vocabulary for annotating gene products to pathways.",
"download_owl": "http://aber-owl.net/media/ontologies/PW/87/pw.owl",
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
"name": "Pathway ontology",
"prefix": "PW"
},
"biocontext": {
"prefix": "PW"
},
"bioportal": {
"contact": {
"email": "gthayman@mcw.edu",
"name": "G. Thomas Hayman"
},
"description": "The goal of the Pathway Ontology is to cover all types of biological pathways, including altered and disease pathways, and to capture the relationships between them within the hierarchical structure of a Directed Acyclic Graph (DAG). The five nodes of the ontology are: classic metabolic, regulatory, signaling, drug and disease pathways. An extensive survey of the review literature along with searches of existing pathway databases have been used to choose terms and their position within the tree. The ontology is continually expanding along with the development of Pathway and Disease Portals at RGD. Mapping of pathways in other databases to terms in PW as synonyms further increased the content of the ontology. It also provided the means to bring in annotations made by these databases and link to their sites via automatic pipelines built at RGD. The ontology allows for the standardized annotation of rat as well as human and mouse genes to pathway terms. It also serves as a vehicle to connect between genes and ontology reports, between reports and interactive pathway diagrams, between pathways that directly connect to one another within a diagram or between pathways that in some fashion are globally related in pathway suites and suite networks. Metabolic, regulatory or signaling pathway terms have associated terms for the altered version of the pathway and the level at which the alteration(s) may occur. Proteins with mutations known to affect a particular pathway can be annotated to the normal and altered version(s) of the pathway and to a disease pathway, if known. Both the provision of terms for the altered versions of pathways and the representation of disease pathway diagrams as a collection of altered pathways are unique to the PW ontology and RGD's pathway data. The Pathway ontology is distributed under the terms of the Creative Commons Attribution license version 3.0 Unported (CC BY 3.0), see http://creativecommons.org/licenses/by/3.0 for details.",
"homepage": "https://rgd.mcw.edu/rgdweb/ontology/search.html",
"name": "Pathway Ontology",
"prefix": "PW",
"publication": "http://rgd.mcw.edu/wg/home/pathway2/molecular-pathways/#pwrpubs",
"version": "7.85"
},
"download_obo": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo",
"example": "0000423",
"fairsharing": {
"abbreviation": "PW",
"contact": {
"email": "vpetri@mcw.edu",
"name": "Victoria Petri",
"orcid": "0000-0002-5540-8498"
},
"description": "The goal of the Pathway Ontology is to cover all types of biological pathways, including altered and disease pathways, and to capture the relationships between them within the hierarchical structure of a Directed Acyclic Graph (DAG). The five nodes of the ontology are: classic metabolic, regulatory, signaling, drug and disease pathways. An extensive survey of the review literature along with searches of existing pathway databases have been used to choose terms and their position within the tree. The ontology is continually expanding along with the development of Pathway and Disease Portals at RGD.",
"domains": [
"Mathematical model",
"Network model",
"Molecular entity",
"Drug",
"Signaling",
"Biological regulation",
"Enzymatic reaction",
"Disease",
"Pathway model"
],
"homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=PW:0000001",
"license": "CC-BY-4.0",
"name": "Pathway Ontology",
"prefix": "FAIRsharing.f73xhd",
"publications": [
{
"doi": "10.1186/2041-1480-5-7",
"pubmed": "24499703",
"title": "The pathway ontology - updates and applications",
"year": 2014
},
{
"doi": "10.1186/s40246-014-0017-8",
"pubmed": "25265995",
"title": "Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease",
"year": 2014
}
],
"subjects": [
"Drug Metabolism",
"Life Science"
]
},
"mappings": {
"aberowl": "PW",
"biocontext": "PW",
"bioportal": "PW",
"fairsharing": "FAIRsharing.f73xhd",
"miriam": "pw",
"n2t": "pw",
"obofoundry": "pw",
"ols": "pw",
"ontobee": "PW",
"prefixcommons": "pw",
"wikidata": "P7333"
},
"miriam": {
"deprecated": false,
"description": "The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions.",
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
"id": "00000242",
"name": "Pathway Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^PW:\\d{7}$",
"prefix": "pw",
"sampleId": "0000208",
"uri_format": "http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:$1"
},
"n2t": {
"description": "The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions.",
"example": "0000208",
"homepage": "http://bioportal.bioontology.org/ontologies/PW",
"name": "Pathway Ontology through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^PW:\\d{7}$",
"prefix": "pw",
"uri_format": "http://purl.bioontology.org/ontology/PW/PW:$1"
},
"obofoundry": {
"contact": "gthayman@mcw.edu",
"contact.github": "gthayman",
"contact.label": "G. Thomas Hayman",
"contact.orcid": "0000-0002-9553-7227",
"deprecated": false,
"description": "A controlled vocabulary for annotating gene products to pathways.",
"domain": "biological systems",
"download.obo": "http://purl.obolibrary.org/obo/pw.obo",
"download.owl": "http://purl.obolibrary.org/obo/pw.owl",
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"logo": "http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif",
"name": "Pathway ontology",
"preferredPrefix": "PW",
"prefix": "pw",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/21478484",
"title": "The Rat Genome Database pathway portal."
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/24499703",
"title": "The pathway ontology - updates and applications."
}
],
"repository": "https://github.com/rat-genome-database/PW-Pathway-Ontology"
},
"ols": {
"description": "A controlled vocabulary for annotating gene products to pathways.",
"download_owl": "http://purl.obolibrary.org/obo/pw.owl",
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
"name": "Pathway ontology",
"prefix": "pw",
"version": "7.85",
"version.iri": "http://purl.obolibrary.org/obo/pw/7.85/pw.owl"
},
"ontobee": {
"library": "Library",
"name": "Pathway ontology",
"prefix": "PW"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1035",
"description": "The goal of the Pathway Ontology is to capture the various kinds of biological networks, the relationships between them and the alterations or malfunctioning of such networks within a hierarchical structure. The five nodes are: classic metabolic pathways, regulatory pathways, signaling pathways, drug pathways and disease pathways for complex human conditions.",
"example": "PW_0000002",
"homepage": "ftp://rgd.mcw.edu/pub/data_release/ontology_obo_files/",
"keywords": [
"obo",
"pathway",
"human"
],
"name": "Pathway ontology",
"pattern": "^PW_\\d{7}$",
"prefix": "pw",
"pubmed_ids": [
"21478484"
],
"synonyms": [
"obo.pw"
],
"uri_format": "http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=$1"
},
"providers": [
{
"code": "miriam_obo_legacy",
"description": "An old URI style for MIRIAM",
"homepage": "https://identifiers.org/",
"name": "MIRIAM OBO Legacy",
"uri_format": "http://identifiers.org/obo.pw/PW:$1"
}
],
"publications": [
{
"doi": "10.1186/s40246-014-0017-8",
"pmc": "PMC4191248",
"pubmed": "25265995",
"title": "Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease",
"year": 2014
},
{
"doi": "10.1186/2041-1480-5-7",
"pmc": "PMC3922094",
"pubmed": "24499703",
"title": "The pathway ontology - updates and applications",
"year": 2014
},
{
"doi": "10.1093/database/bar010",
"pmc": "PMC3072770",
"pubmed": "21478484",
"title": "The Rat Genome Database pathway portal",
"year": 2011
}
],
"twitter": "ratgenome",
"uri_format": "http://purl.obolibrary.org/obo/PW_$1",
"wikidata": {
"database": "Q28864280",
"description": "identifier in the Pathway Ontology database",
"example": [
"PW:0000003",
"PW:0000125",
"PW:0000624"
],
"homepage": "http://bioportal.bioontology.org/ontologies/PW",
"name": "Pathway Ontology ID",
"pattern": "^PW:([0-9]{7})$",
"prefix": "P7333",
"uri_format": "https://purl.bioontology.org/ontology/PW/$1"
}
},
"pwo": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity.",
"example": "Workflow",
"fairsharing": {
"abbreviation": "PWO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Publishing Workflow Ontology (PWO) is a simple ontology for describing the steps in the workflow associated with the publication of a document or other publication entity.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/pwo",
"license": "CC-BY-4.0",
"name": " Publishing Workflow Ontology ",
"prefix": "FAIRsharing.c4e46c",
"publications": [
{
"doi": "10.3233/sw-160230",
"title": "The Publishing Workflow Ontology (PWO)",
"year": 2014
}
],
"repository": "https://github.com/sparontologies/pwo",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"homepage": "http://www.sparontologies.net/ontologies/pwo",
"lov": {
"description": "An ontology for describing the workflow associated with the publication of a document.",
"homepage": "http://purl.org/spar/pwo",
"keywords": [
"SPAR"
],
"modified": "2015-06-18",
"name": "The Publishing Workflow Ontology",
"prefix": "pwo",
"uri_prefix": "http://purl.org/spar/pwo/$1"
},
"mappings": {
"fairsharing": "FAIRsharing.c4e46c",
"lov": "pwo"
},
"name": "Publishing Workflow Ontology",
"preferred_prefix": "PWO",
"publications": [
{
"doi": "10.3233/sw-160230",
"title": "The Publishing Workflow Ontology (PWO)",
"year": 2017
}
],
"repository": "https://github.com/sparontologies/pwo",
"uri_format": "http://purl.org/spar/pwo/$1"
},
"px": {
"biocontext": {
"prefix": "PX"
},
"mappings": {
"biocontext": "PX",
"miriam": "px",
"n2t": "px"
},
"miriam": {
"deprecated": false,
"description": "The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination.",
"homepage": "http://www.proteomexchange.org/",
"id": "00000513",
"name": "ProteomeXchange",
"namespaceEmbeddedInLui": false,
"pattern": "^(R)?PXD\\d{6}$",
"prefix": "px",
"sampleId": "PXD000500",
"uri_format": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1"
},
"n2t": {
"description": "The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination.",
"example": "PXD000500",
"homepage": "http://www.proteomexchange.org/",
"name": "ProteomeXchange at Seattle",
"namespaceEmbeddedInLui": false,
"pattern": "^(R)?PXD\\d{6}$",
"prefix": "px",
"uri_format": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1"
}
},
"pypi": {
"mappings": {
"miriam": "pypi"
},
"miriam": {
"deprecated": false,
"description": "The Python Package Index (PyPI) is a repository for Python packages.",
"homepage": "https://www.python.org/psf/",
"id": "00000863",
"name": "PyPI",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-zA-Z_][a-zA-Z0-9\\-_]+$",
"prefix": "pypi",
"sampleId": "numpy",
"uri_format": "https://pypi.org/project/$1/"
},
"uri_format": "https://pypi.org/project/$1"
},
"qb": {
"contact": {
"email": "richard@cyganiak.de",
"github": "cygri",
"name": "Richard Cyganiak",
"orcid": "0000-0001-9950-5209"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF. It is based on the core information model from SDMX (and thus also DDI).",
"download_rdf": "http://purl.org/linked-data/cube#",
"example": "Observation",
"homepage": "https://www.w3.org/TR/vocab-data-cube",
"lov": {
"description": "This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF.",
"homepage": "http://www.w3.org/TR/vocab-data-cube/",
"keywords": [
"Methods",
"W3C Rec"
],
"modified": "2014-07-31",
"name": "The data cube vocabulary",
"prefix": "qb",
"uri_prefix": "http://purl.org/linked-data/cube#$1"
},
"mappings": {
"lov": "qb",
"zazuko": "qb"
},
"name": "The data cube vocabulary",
"pattern": "^\\w+$",
"preferred_prefix": "qb",
"repository": "UKGovLD/publishing-statistical-data",
"uri_format": "http://purl.org/linked-data/cube#$1",
"zazuko": {
"prefix": "qb",
"uri_format": "http://purl.org/linked-data/cube#$1"
}
},
"qtldb": {
"mappings": {
"miriam": "qtldb"
},
"miriam": {
"deprecated": false,
"description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent.",
"homepage": "https://www.animalgenome.org/QTLdb",
"id": "00000798",
"name": "Animal Genome QTL",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "qtldb",
"sampleId": "4685",
"uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"
}
},
"qudt": {
"aberowl": {
"description": "The QUDT, or 'Quantity, Unit, Dimension and Type' collection of ontologies define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems. The goal of the QUDT ontology is to provide a unified model of, measurable quantities, units for measuring different kinds of quantities, the numerical values of quantities in different units of measure and the data structures and data types used to store and manipulate these objects in software. This OWL schema is a foundation for a basic treatment of units.",
"download_owl": "http://aber-owl.net/media/ontologies/QUDT/4/qudt.owl",
"homepage": "http://qudt.org/",
"name": "Quantities, Units, Dimensions, and Types Ontology",
"prefix": "QUDT",
"version": "$Id: OSG_qudt-(v1.1).ttl 4989 2011-06-01 21:56:40Z RalphHodgson $"
},
"bartoc": {
"abbreviation": "QUDT",
"description": "QUDT is more than a set of vocabularies representing the various quantity and unit standards:\n\nMain QUDT Ontology\nQUDT Datatype Ontology\nQUDT Units Vocabulary\nQUDT QuantityKinds Vocabulary\nQUDT DimensionVectors Vocabulary\nQUDT Physical Constants Vocabulary\nQUDT Systems of Units Vocabulary",
"homepage": "http://qudt.org/",
"name": "Quantities, Units, Dimensions and Types",
"prefix": "18206"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "qud",
"uri_format": "http://qudt.org/1.1/schema/qudt#$1"
},
"bioportal": {
"description": "The QUDT, or 'Quantity, Unit, Dimension and Type' collection of ontologies define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems. The goal of the QUDT ontology is to provide a unified model of, measurable quantities, units for measuring different kinds of quantities, the numerical values of quantities in different units of measure and the data structures and data types used to store and manipulate these objects in software. This OWL schema is a foundation for a basic treatment of units.",
"homepage": "http://qudt.org/",
"name": "Quantities, Units, Dimensions, and Types Ontology",
"prefix": "QUDT"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types.",
"download_rdf": "http://qudt.org/schema/qudt/",
"example": "baseDimensionEnumeration",
"fairsharing": {
"abbreviation": "QUDT",
"description": "The QUDT, or 'Quantity, Unit, Dimension and Type' collection of ontologies define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems. QUDT provides a unified model of measurable quantities, units for measuring different kinds of quantities, the numerical values of quantities in different units of measure and the data structures and data types used to store and manipulate these objects in software. This OWL schema is a foundation for a basic treatment of units. Originally developed by TopQuadrant for the NASA Exploration Initiatives Ontology Models (NExIOM) project, they now form the basis of the NASA QUDT Handbook. QUDT aims to improve interoperability of data and the specification of information structures through industry standards for Units of Measure, Quantity Kinds, Dimensions and Data Types.",
"domains": [
"Experimental measurement",
"Unit"
],
"homepage": "http://qudt.org/",
"license": "CC-BY-4.0",
"name": "Quantities, Units, Dimensions and Types",
"prefix": "FAIRsharing.d3pqw7",
"repository": "https://github.com/qudt/qudt-public-repo/blob/master/docs/2020-04-28%20Intro%20to%20QUDT.pdf",
"subjects": [
"Astrophysics and Astronomy"
]
},
"homepage": "https://qudt.org",
"lov": {
"description": "The QUDT, or 'Quantity, Unit, Dimension and Type' collection of ontologies define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems.",
"homepage": "http://qudt.org",
"keywords": [
"Methods"
],
"modified": "2020-04-20",
"name": "Quantities, Units, Dimensions and Types",
"prefix": "qudt",
"uri_prefix": "http://qudt.org/schema/qudt/$1"
},
"mappings": {
"aberowl": "QUDT",
"bartoc": "18206",
"biolink": "qud",
"bioportal": "QUDT",
"fairsharing": "FAIRsharing.d3pqw7",
"lov": "qudt",
"zazuko": "qudt"
},
"name": "Quantities, Units, Dimensions, and Types Ontology",
"preferred_prefix": "qudt",
"providers": [
{
"code": "v11",
"description": "Version 1.1 provider",
"homepage": "http://qudt.org",
"name": "Version 1.1",
"uri_format": "http://qudt.org/1.1/schema/qudt#$1"
}
],
"repository": "https://github.com/qudt/qudt-public-repo",
"uri_format": "http://qudt.org/schema/qudt#$1",
"zazuko": {
"prefix": "qudt",
"uri_format": "http://qudt.org/schema/qudt/$1"
}
},
"radiomics": {
"bioportal": {
"contact": {
"email": "alberto.traverso@maastro.nl",
"name": "Alberto Traverso"
},
"description": "The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual",
"name": "Radiomics Ontology",
"prefix": "RO",
"version": "2.1"
},
"contact": {
"email": "alberto.traverso@maastro.nl",
"name": "Alberto Traverso",
"orcid": "0000-0001-6183-4429"
},
"description": "The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual. [bioportal]",
"example": "LK99",
"homepage": "http://www.radiomics.org/RO",
"mappings": {
"bioportal": "RO"
},
"uri_format": "http://www.radiomics.org/RO/$1"
},
"radlex": {
"aberowl": {
"description": "RadLex is a controlled terminology for radiology-a single unified source of radiology terms for radiology practice, education, and research. For license information see : http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/RadLex_License_Agreement_and_Terms_of_Use_V2_Final.pdf Converted to use OWL format submissions",
"download_owl": "http://aber-owl.net/media/ontologies/RADLEX/37/radlex.owl",
"homepage": "http://www.rsna.org/RadLex.aspx",
"name": "Radiology Lexicon",
"prefix": "RADLEX",
"version": "3.14"
},
"bioportal": {
"contact": {
"email": "radlex-feedback@lists.rsna.org",
"name": "Radiological Society of North America"
},
"description": "RadLex OWL, as downloaded from BioPortal, includes a set of puns in order to facilitate browsing and display. The base RadLex ontology, without puns, is available at http://radlex.org/",
"homepage": "https://www.rsna.org/practice-tools/data-tools-and-standards/radlex-radiology-lexicon",
"name": "Radiology Lexicon",
"prefix": "RADLEX",
"version": "4.1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A comprehensive set of radiology terms for use in radiology reporting, decision support, data mining, data registries, education and research.\n\nRadLex provides the foundation for vital data resources used in radiology:\n\n- The LOINC/RSNA Radiology Playbook\n- RadElement Common Data Elements\n-RadReport Radiology Reporting Templates\n\nThe development of RadLex has been supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the cancer Biomedical Informatics Grid (caBIG) project.",
"example": "RID1",
"fairsharing": {
"abbreviation": "RadLex",
"description": "RadLex is a comprehensive lexiconβa unified language of radiology termsβfor standardized indexing and retrieval of radiology information resources. With more than 68,000 terms, RadLex satisfies the needs of software developers, system vendors and radiology users by adopting the best features of existing terminology systems while producing new terms to fill critical gaps. RadLex also provides a comprehensive and technology-friendly replacement for the ACR Index for Radiological Diagnoses. It unifies and supplements other lexicons and standards, such as SNOMED-CT and DICOM. RadLex development has received support from both the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the cancer Biomedical Informatics Grid (caBIG) project.",
"domains": [
"Medical imaging",
"Diagnosis"
],
"homepage": "https://www.rsna.org/en/practice-tools/data-tools-and-standards/radlex-radiology-lexicon",
"name": "Radiology Lexicon",
"prefix": "FAIRsharing.shm2f2",
"publications": [
{
"doi": "10.2214/ajr.174.5.1741463",
"pubmed": "10789815",
"title": "Radiology lexicon",
"year": 2000
},
{
"doi": "10.1016/j.jvir.2008.10.022",
"pubmed": "19081735",
"title": "The IR RadLex project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology",
"year": 2008
},
{
"doi": "10.1016/j.jvir.2009.04.031",
"pubmed": "19560008",
"title": "The IR Radlex Project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology",
"year": 2009
}
],
"subjects": [
"Anatomy",
"Radiology",
"Clinical Studies",
"Biomedical Science",
"Medical Informatics"
]
},
"hl7": {
"description": "RadLex terminology comprises coded terms used in the acquisition and management of diagnostic images and related data, and in the representation of imaging-related findings and results. RadLex terms would be used in both Orders and Observations, appearing in HL7 V2 OBX segments and in HL7 V3 Acts describing both imaging procedures and the observations derived therefrom. RadLex codes will also be used in HL7 CDA documents, as they will be in related DICOM Structured Reporting (SR) objects used in imaging applications.",
"homepage": "http://www.radlex.org",
"name": "RadLex",
"organization": "Radiological Society of North America",
"preferred_prefix": "radLex",
"prefix": "2.16.840.1.113883.6.256",
"status": "Complete"
},
"homepage": "https://radlex.org",
"license": "http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/RadLex_License_Agreement_and_Terms_of_Use_V2_Final.pdf",
"mappings": {
"aberowl": "RADLEX",
"bioportal": "RADLEX",
"fairsharing": "FAIRsharing.shm2f2",
"hl7": "2.16.840.1.113883.6.256"
},
"name": "RSNA Informatics RadLex",
"pattern": "^RID\\d+$",
"publications": [
{
"doi": "10.1016/j.jvir.2009.04.031",
"pubmed": "19560008",
"title": "The IR Radlex Project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology",
"year": 2009
},
{
"doi": "10.1016/j.jvir.2008.10.022",
"pubmed": "19081735",
"title": "The IR RadLex project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology",
"year": 2008
},
{
"doi": "10.2214/ajr.174.5.1741463",
"pubmed": "10789815",
"title": "Radiology lexicon",
"year": 2000
}
],
"uri_format": "https://radlex.org/RID/$1",
"version": "4.1"
},
"rapdb.locus": {
"mappings": {
"miriam": "rapdb.locus"
},
"miriam": {
"deprecated": false,
"description": "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB.",
"homepage": "https://rapdb.dna.affrc.go.jp/",
"id": "00000702",
"name": "RAP-DB Locus",
"namespaceEmbeddedInLui": false,
"pattern": "^Os\\S+g\\d{7}$",
"prefix": "rapdb.locus",
"sampleId": "Os01g0883800",
"uri_format": "https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$1"
},
"synonyms": [
"irgsp"
]
},
"rapdb.transcript": {
"go": {
"homepage": "https://rapdb.dna.affrc.go.jp",
"name": "Rice annotation Project database",
"prefix": "RAP-DB",
"uri_format": "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1"
},
"mappings": {
"go": "RAP-DB",
"miriam": "rapdb.transcript",
"ncbi": "RAP-DB",
"prefixcommons": "rapdb"
},
"miriam": {
"deprecated": false,
"description": "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB.",
"homepage": "https://rapdb.dna.affrc.go.jp/",
"id": "00000762",
"name": "RAP-DB Transcript",
"namespaceEmbeddedInLui": false,
"pattern": "^Os\\S+t\\d{7}-\\d{2}$",
"prefix": "rapdb.transcript",
"sampleId": "Os01t0883800-02",
"uri_format": "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1"
},
"ncbi": {
"example": "Os01g1234567",
"homepage": "http://rapdb.dna.affrc.go.jp/",
"name": "Rice Annotation Project Database",
"prefix": "RAP-DB"
},
"prefixcommons": {
"description": "The Rice Annotation Project (RAP) was conceptualized upon the completion of the rice genome sequencing in 2004 with the aim of providing the scientific community with an accurate and timely annotation of the rice genome sequence.",
"example": "Os01g0102600",
"homepage": "http://rapdb.dna.affrc.go.jp/",
"keywords": [
"genome",
"DNA"
],
"name": "The Rice Annotation Project Database",
"pattern": "^[A-Z,0-9]+$",
"prefix": "rapdb",
"uri_format": "http://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/build5?name=[$1"
}
},
"ratmap": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"mappings": {
"ncbi": "RATMAP",
"prefixcommons": "ratmap"
},
"ncbi": {
"example": "5",
"name": "Rat Genome Database",
"prefix": "RATMAP"
},
"prefixcommons": {
"description": "The Rat Genome Database RatMap is focused on presenting rat genes, DNA-markers, QTL:s etc that is localized to chromosome. The database is dedicated to rat gene nomenclature and should be consulted for queries in such matters",
"example": "ENSRNOG00000008380",
"homepage": "http://ratmap.org",
"keywords": [
"genome",
"gene",
"DNA"
],
"name": "RatMap, the rat genome database",
"pattern": "^[A-Z]+\\d+$",
"prefix": "ratmap",
"uri_format": "http://ratmap.org/Showgene.php?gene_stable_id=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"rbk": {
"biocontext": {
"prefix": "RBK"
},
"contact": {
"email": "oxburl@mmc.org",
"name": "Leif Oxburgh",
"orcid": "0000-0002-2825-7663"
},
"fairsharing": {
"abbreviation": "RBK",
"description": "This site contains data generated by (Re)Building a Kidney (RBK), an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function. RBK's goal is to coordinate and support studies that will result in the ability to generate or repair nephrons that can function within the kidney. This resource includes data from both the RBK project and the GenitoUrinary Development Molecular Anatomy Project (GUDMAP). Data submission is restricted to members of the Consortium only.",
"homepage": "https://rebuildingakidney.org",
"name": "(Re)Building a Kidney",
"prefix": "FAIRsharing.78d3ad",
"publications": [
{
"doi": "10.1681/ASN.2016101077",
"pubmed_id": 28096308,
"title": "(Re)Building a Kidney."
}
],
"repository": "https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Create-citable-datasets",
"subjects": [
"Molecular biology",
"Genomics",
"Developmental Biology",
"Cell Biology"
]
},
"mappings": {
"biocontext": "RBK",
"fairsharing": "FAIRsharing.78d3ad",
"miriam": "rbk",
"n2t": "rbk"
},
"miriam": {
"deprecated": false,
"description": "(Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function.",
"homepage": "https://www.rebuildingakidney.org/",
"id": "00000659",
"name": "Rebuilding a Kidney",
"namespaceEmbeddedInLui": false,
"pattern": "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$",
"prefix": "rbk",
"sampleId": "Q-2958",
"uri_format": "https://www.rebuildingakidney.org/id/$1"
},
"n2t": {
"description": "(Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function.",
"example": "Q-2958",
"homepage": "https://www.rebuildingakidney.org/",
"name": "Rebuilding a Kidney",
"namespaceEmbeddedInLui": false,
"pattern": "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$",
"prefix": "rbk",
"uri_format": "https://www.rebuildingakidney.org/id/$1"
},
"publications": [
{
"doi": "10.1681/asn.2016101077",
"pmc": "PMC5407737",
"pubmed": "28096308",
"title": "(Re)Building a Kidney",
"year": 2017
}
]
},
"rbo": {
"aberowl": {
"description": "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.",
"download_owl": "http://aber-owl.net/media/ontologies/RBO/28/rbo.owl",
"homepage": "https://github.com/Radiobiology-Informatics-Consortium/RBO",
"name": "Radiation Biology Ontology",
"prefix": "RBO"
},
"bioportal": {
"contact": {
"email": "kristen.m.peach@nasa.gov",
"name": "Kristen Peach"
},
"description": "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.",
"homepage": "https://github.com/Radiobiology-Informatics-Consortium/RBO/tree/master/src/ontology",
"name": "Radiation Biology Ontology",
"prefix": "RBO",
"publication": "https://doi.org/10.1080/09553002.2023.2173823",
"version": "2024-05-31"
},
"example": "00000105",
"example_extras": [
"010007"
],
"mappings": {
"aberowl": "RBO",
"bioportal": "RBO",
"obofoundry": "rbo",
"ols": "rbo",
"ontobee": "RBO"
},
"obofoundry": {
"contact": "daniel.c.berrios@nasa.gov",
"contact.github": "DanBerrios",
"contact.label": "Daniel C. Berrios",
"contact.orcid": "0000-0003-4312-9552",
"depends_on": [
"bfo",
"chmo",
"envo",
"obi",
"pato",
"ro",
"uo"
],
"deprecated": false,
"description": "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.",
"domain": "environment",
"download.json": "http://purl.obolibrary.org/obo/rbo.json",
"download.obo": "http://purl.obolibrary.org/obo/rbo.obo",
"download.owl": "http://purl.obolibrary.org/obo/rbo.owl",
"homepage": "https://github.com/Radiobiology-Informatics-Consortium/RBO",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Radiation Biology Ontology",
"preferredPrefix": "RBO",
"prefix": "rbo",
"repository": "https://github.com/Radiobiology-Informatics-Consortium/RBO"
},
"ols": {
"description": "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.",
"download_owl": "http://purl.obolibrary.org/obo/rbo.owl",
"homepage": "https://github.com/Radiobiology-Informatics-Consortium/RBO",
"name": "Radiation Biology Ontology",
"prefix": "rbo",
"version": "2024-05-31",
"version.iri": "http://purl.obolibrary.org/obo/rbo/releases/2024-05-31/rbo.owl"
},
"ontobee": {
"library": "Library",
"name": "Radiation Biology Ontology",
"prefix": "RBO"
},
"pattern": "^\\d{6,8}$",
"uri_format": "http://purl.obolibrary.org/obo/RBO_$1"
},
"rcb": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://cell.brc.riken.jp/en/rcb",
"name": "RIKEN Bioresource Center Cell Bank",
"prefix": "RCB",
"uri_format": "http://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1&lang=En"
},
"contact": {
"email": "atsushi.yoshiki@riken.jp",
"name": "Atsushi Yoshiki",
"orcid": "0000-0002-9450-5151"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center.",
"example": "RCB0002",
"homepage": "https://cell.brc.riken.jp/en/rcb",
"mappings": {
"cellosaurus": "RCB",
"rrid": "IMSR_RBRC"
},
"name": "RIKEN Bioresource Center Cell Bank",
"pattern": "^RCB\\d+$",
"rrid": {
"abbreviation": "BRC, RIKEN BRC",
"homepage": "http://www.brc.riken.jp/inf/en",
"keywords": [
"FASEB list",
"animal",
"bioresource",
"cell",
"cell line",
"cultured cell",
"cultured cell line",
"dna",
"embryo",
"experimental animal",
"experimental plant",
"gene",
"genetic material",
"organ",
"plant",
"recombinant host",
"seed",
"sperm",
"tissue",
"virus"
],
"name": "RIKEN BioResource Center",
"prefix": "IMSR_RBRC",
"pubmeds": [
"19448331",
"34532769"
],
"scr": "003250"
},
"uri_format": "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1"
},
"rdf": {
"biocontext": {
"prefix": "rdf",
"uri_format": "http://www.w3.org/1999/02/22-rdf-syntax-ns#$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts",
"example": "type",
"fairsharing": {
"abbreviation": "RDF",
"contact": {
"email": "rmrich5@gmail.com",
"name": "Rafael Richards",
"orcid": "0000-0001-5699-0515"
},
"description": "The Resource Description Framework (RDF) is a framework for representing information in the Web. This document defines an abstract syntax (a data model) which serves to link all RDF-based languages and specifications. The abstract syntax has two key data structures: RDF graphs are sets of subject-predicate-object triples, where the elements may be IRIs, blank nodes, or datatyped literals. They are used to express descriptions of resources. RDF datasets are used to organize collections of RDF graphs, and comprise a default graph and zero or more named graphs. RDF 1.1 Concepts and Abstract Syntax also introduces key concepts and terminology, and discusses datatyping and the handling of fragment identifiers in IRIs within RDF graphs.",
"homepage": "http://www.w3.org/TR/2014/REC-rdf11-concepts-20140225/",
"name": "Resource Description Framework",
"prefix": "FAIRsharing.p77ph9",
"publications": [],
"subjects": [
"Computer Science",
"Subject Agnostic"
]
},
"homepage": "http://www.w3.org/1999/02/22-rdf-syntax-ns",
"lov": {
"description": "This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts.",
"homepage": "http://www.w3.org/TR/rdf11-concepts/",
"keywords": [
"W3C Rec"
],
"modified": "2019-12-16",
"name": "The RDF Concepts Vocabulary",
"prefix": "rdf",
"uri_prefix": "http://www.w3.org/1999/02/22-rdf-syntax-ns#$1"
},
"mappings": {
"biocontext": "rdf",
"fairsharing": "FAIRsharing.p77ph9",
"lov": "rdf",
"zazuko": "rdf"
},
"name": "Resource Description Framework",
"preferred_prefix": "rdf",
"uri_format": "http://www.w3.org/1999/02/22-rdf-syntax-ns#$1",
"zazuko": {
"prefix": "rdf",
"uri_format": "http://www.w3.org/1999/02/22-rdf-syntax-ns#$1"
}
},
"rdfa": {
"contact": {
"email": "ivan@w3.org",
"github": "iherman",
"name": "Ivan Herman",
"orcid": "0000-0003-0782-2704"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "RDFa Core is a specification for attributes to express structured data in any markup language. The embedded data already available in the markup language (e.g., HTML) can often be reused by the RDFa markup, so that publishers don't need to repeat significant data in the document content. (from https://www.w3.org/TR/rdfa-core/)",
"download_rdf": "http://www.w3.org/ns/rdfa.ttl",
"example": "PrefixOrTermMapping",
"homepage": "http://www.w3.org/ns/rdfa",
"lov": {
"description": "This document describes the RDFa Vocabulary for Term and Prefix Assignment. The Vocabulary is used to modify RDFa 1.1 processing behavior",
"homepage": "http://www.w3.org/ns/rdfa#",
"keywords": [
"RDF"
],
"modified": "2013-03-11",
"name": "RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting",
"prefix": "rdfa",
"uri_prefix": "http://www.w3.org/ns/rdfa#$1"
},
"mappings": {
"lov": "rdfa",
"zazuko": "rdfa"
},
"name": "RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting",
"uri_format": "http://www.w3.org/ns/rdfa#$1",
"zazuko": {
"prefix": "rdfa",
"uri_format": "http://www.w3.org/ns/rdfa#$1"
}
},
"rdfs": {
"aberowl": {
"description": "RDF Schema provides a data-modelling vocabulary for RDF data",
"download_owl": "http://aber-owl.net/media/ontologies/RDFS/3/rdfs.owl",
"name": "The RDF Schema vocabulary",
"prefix": "RDFS",
"version": "1.1"
},
"biocontext": {
"prefix": "rdfs",
"uri_format": "http://www.w3.org/2000/01/rdf-schema#$1"
},
"bioportal": {
"contact": {
"email": "danbri@w3.org",
"name": "Dan Brickley"
},
"description": "RDF Schema provides a data-modelling vocabulary for RDF data",
"name": "The RDF Schema vocabulary",
"prefix": "RDFS",
"version": "1.1"
},
"contact": {
"email": "danbri@w3.org",
"name": "Dan Brickley",
"orcid": "0000-0002-6450-7041"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary.",
"download_owl": "https://triplydb.com/w3c/rdfs/download.trig.gz",
"example": "label",
"fairsharing": {
"abbreviation": "RDFS",
"description": "RDF Schema (RDFS) is the RDF vocabulary description language. RDFS defines classes and properties that may be used to describe classes, properties and other resources.",
"homepage": "https://www.w3.org/TR/rdf-schema/",
"name": "Resource Description Framework Schema",
"prefix": "FAIRsharing.v9n3gk",
"publications": [],
"subjects": [
"Bioinformatics",
"Life Science",
"Ontology and Terminology",
"Linguistics"
]
},
"homepage": "https://www.w3.org/TR/rdf-schema/",
"lov": {
"description": "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary.",
"homepage": "http://www.w3.org/TR/rdf-schema/",
"keywords": [
"W3C Rec"
],
"modified": "2014-02-25",
"name": "The RDF Schema vocabulary",
"prefix": "rdfs",
"uri_prefix": "http://www.w3.org/2000/01/rdf-schema#$1"
},
"mappings": {
"aberowl": "RDFS",
"biocontext": "rdfs",
"bioportal": "RDFS",
"fairsharing": "FAIRsharing.v9n3gk",
"lov": "rdfs",
"ols": "rdfs",
"zazuko": "rdfs"
},
"name": "RDF Schema",
"ols": {
"name": "The RDF Schema vocabulary (RDFS)",
"prefix": "rdfs"
},
"preferred_prefix": "rdfs",
"uri_format": "http://www.w3.org/2000/01/rdf-schema#$1",
"zazuko": {
"prefix": "rdfs",
"uri_format": "http://www.w3.org/2000/01/rdf-schema#$1"
}
},
"rdo": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms.",
"download_obo": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.obo",
"download_owl": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.owl",
"example": "9002859",
"homepage": "https://ratmine.mcw.edu/ontology/disease/",
"name": "RGD Disease Ontology",
"pattern": "^\\d{7}$",
"uri_format": "http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1"
},
"re3data": {
"bartoc": {
"description": "The re3data.org schema is a list of metadata properties describing a research data repository regarding its general scope, content and infrastructure as well as its compliance with technical, metadata and quality standards. The schema includes required metadata properties and optional properties providing additional information. The schema is designed to recommend a standard for describing a research data repository; provide the basis for interoperability between research data repositories and re3data.org; be one of the first steps towards the goal of a certificate for research data repositories.",
"homepage": "http://www.re3data.org/schema/",
"license": "CC-BY-3.0",
"name": "Schema for the description of research data repositories",
"prefix": "822"
},
"mappings": {
"bartoc": "822",
"miriam": "re3data"
},
"miriam": {
"deprecated": false,
"description": "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines.",
"homepage": "https://datacite.org",
"id": "00000861",
"name": "re3data",
"namespaceEmbeddedInLui": false,
"pattern": "^r3d\\d{9,9}$",
"prefix": "re3data",
"sampleId": "r3d100010772",
"uri_format": "https://www.re3data.org/repository/$1"
}
},
"reactome": {
"biocontext": {
"prefix": "REACTOME"
},
"cheminf": {
"description": "Database identifier used by Reactome.",
"name": "Reactome",
"obsolete": false,
"prefix": "000411"
},
"contact": {
"email": "deustp01@med.nyu.edu",
"github": "deustp01",
"name": "Peter D'Eustachio",
"orcid": "0000-0002-5494-626X"
},
"contributor_extras": [
{
"email": "smoxon@lbl.gov",
"github": "sierra-moxon",
"name": "Sierra Moxon",
"orcid": "0000-0002-8719-7760"
}
],
"edam": {
"description": "Identifier of an entry from the Reactome database.",
"name": "Pathway ID (reactome)",
"obsolete": false,
"prefix": "1155"
},
"example": "R-BTA-418592",
"go": {
"homepage": "https://www.reactome.org/",
"name": "Reactome - a curated knowledgebase of biological pathways",
"prefix": "Reactome",
"synonyms": [
"REACTOME",
"REAC"
],
"uri_format": "https://www.reactome.org/content/detail/$1"
},
"integbio": {
"description": "REACTOME is a database of human pathways for basic research, genome analysis, pathway modeling, systems biology and education. It contains manually curated and peer-reviewed pathway data which are annotated by expert biologists, in collaboration with Reactome editorial staff and cross-referenced to many bioinformatics databases. This database provides an intuitive website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. The curated human pathway data are available to infer orthologous events in 20 non-human species including mouse, rat, chicken, worm, fly, yeast, plant and bacteria. Using species comparison tool, users are able to compare predicted pathways with those of human to find reactions and pathways common to a selected species and human.",
"fairsharing": "biodbcore-000329",
"homepage": "https://reactome.org",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Reactome team",
"name": "REACTOME",
"prefix": "nbdc00185",
"pubmeds": [
"15608231",
"29145629"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"mappings": {
"biocontext": "REACTOME",
"cheminf": "000411",
"edam": "1155",
"go": "Reactome",
"integbio": "nbdc00185",
"miriam": "reactome",
"n2t": "reactome",
"pathguide": "103",
"prefixcommons": "reactome",
"re3data": "r3d100010861",
"togoid": "ReactomePathway",
"wikidata": "P3937"
},
"miriam": {
"deprecated": false,
"description": "The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.",
"homepage": "https://www.reactome.org/",
"id": "00000018",
"name": "Reactome",
"namespaceEmbeddedInLui": false,
"pattern": "(^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$)|(^REACT_\\d+(\\.\\d+)?$)",
"prefix": "reactome",
"sampleId": "R-HSA-201451",
"uri_format": "https://reactome.org/content/detail/$1"
},
"n2t": {
"description": "The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.",
"example": "R-HSA-201451",
"homepage": "https://www.reactome.org/",
"name": "Reactome, a curated knowledgebase of biological pathways",
"namespaceEmbeddedInLui": false,
"pattern": "(^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$)|(^REACT_\\d+(\\.\\d+)?$)",
"prefix": "reactome",
"uri_format": "https://reactome.org/content/detail/$1"
},
"name": "Reactome",
"pathguide": {
"abbreviation": "Reactome",
"homepage": "http://www.reactome.org",
"keywords": [
"BioPAX",
"PSI-MI",
"SBML"
],
"name": "Reactome KnowledgeBase",
"prefix": "103"
},
"pattern": "^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$",
"prefixcommons": {
"description": "The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.",
"example": "REACT_1590",
"homepage": "http://www.reactome.org",
"keywords": [
"human",
"pathway",
"reaction"
],
"name": "Reactome - a curated knowledgebase of biological pathways",
"pattern": "^REACT_\\d+(\\.\\d+)?$",
"prefix": "reactome",
"pubmed_ids": [
"15608231"
],
"synonyms": [
"identifier.reactome"
],
"uri_format": "http://www.reactome.org/cgi-bin/eventbrowser_st_id?FROM_REACTOME=1&ST_ID=$1"
},
"providers": [
{
"code": "pathwaycommons",
"description": "Pathway diagram drawn with Cytoscape",
"homepage": "https://www.pathwaycommons.org",
"name": "Pathway Commons",
"uri_format": "https://apps.pathwaycommons.org/pathways?uri=http%3A%2F%2Fidentifiers.org%2Freactome%2F$1"
},
{
"code": "browser",
"description": "An interactive view over pathways.",
"homepage": "https://reactome.org/PathwayBrowser/",
"name": "Reactome Pathway Browser",
"uri_format": "https://reactome.org/PathwayBrowser/#/$1"
}
],
"publications": [
{
"doi": "10.1093/nar/gki072",
"pmc": "PMC540026",
"pubmed": "15608231",
"title": "Reactome: a knowledgebase of biological pathways",
"year": 2005
}
],
"re3data": {
"description": "Reactome is a manually curated, peer-reviewed pathway database, annotated by expert biologists and cross-referenced to bioinformatics databases. Its aim is to share information in the visual representations of biological pathways in a computationally accessible format. Pathway annotations are authored by expert biologists, in collaboration with Reactome editorial staff and cross-referenced to many bioinformatics databases. These include NCBI Gene, Ensembl and UniProt databases, the UCSC and HapMap Genome Browsers, the KEGG Compound and ChEBI small molecule databases, PubMed, and Gene Ontology.",
"homepage": "https://reactome.org/",
"name": "Reactome",
"prefix": "r3d100010861",
"synonyms": [
"a curated pathway database"
],
"xrefs": {
"fairsharing": "FAIRsharing.tf6kj8",
"miriam": "00000018",
"nif": "0000-03390",
"omics": "02771",
"scr": "003485"
}
},
"references": [
"https://github.com/biopragmatics/bioregistry/pull/1086"
],
"synonyms": [
"RE",
"REACT",
"reactome.pathway"
],
"togoid": {
"catalog": "nbdc00185",
"examples": [
"R-HSA-165159",
"R-DRE-1630316",
"R-SCE-9634635",
"R-DRE-140834",
"R-HSA-2142753",
"R-BTA-383280",
"R-MMU-5218900",
"R-RNO-5654219",
"R-MMU-8875791",
"R-MMU-9648025"
],
"keywords": [
"Pathway"
],
"name": "Reactome pathway",
"pattern": "^(?R-[A-Z]{3}-\\d+)(?:\\.\\d+)?$",
"prefix": "ReactomePathway",
"uri_format": "http://identifiers.org/reactome/$1"
},
"wikidata": {
"description": "Identifier used in Reactome to uniquely identify a biological pathway",
"example": [
"R-HSA-191273",
"R-HSA-6807047",
"R-HSA-71403"
],
"homepage": "http://www.reactome.org/",
"name": "Reactome ID",
"prefix": "P3937",
"uri_format": "https://reactome.org/content/detail/$1"
}
},
"reaxys": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier.",
"edam": {
"description": "Beilstein registry number of a chemical compound.",
"name": "Chemical registry number (Beilstein)",
"obsolete": false,
"prefix": "1003"
},
"example": "1257009",
"homepage": "https://www.reaxys.com",
"mappings": {
"edam": "1003",
"wikidata": "P1579"
},
"name": "Reaxys",
"pattern": "^\\d+$",
"synonyms": [
"Beilstein",
"Reaxys"
],
"wikidata": {
"description": "identifier for chemical substance in Reaxys",
"example": [
"2018",
"635680",
"93704"
],
"name": "Reaxys registry number",
"pattern": "^\\d+$",
"prefix": "P1579"
}
},
"rebase": {
"biocontext": {
"prefix": "REBASE"
},
"contact": {
"email": "roberts@neb.com",
"name": "Richard John Roberts",
"orcid": "0000-0002-4348-0169"
},
"edam": {
"description": "Identifier of an enzyme from the REBASE enzymes database.",
"name": "REBASE enzyme number",
"obsolete": false,
"prefix": "2325"
},
"fairsharing": {
"abbreviation": "REBASE",
"description": "A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data.",
"homepage": "http://rebase.neb.com",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "Restriction enzymes and methylases database",
"prefix": "FAIRsharing.9sb9qh",
"publications": [
{
"doi": "10.1093/nar/gku1046",
"pubmed_id": 25378308,
"title": "REBASE-a database for DNA restriction and modification: enzymes, genes and genomes."
},
{
"doi": "10.1093/nar/gkp874",
"pubmed_id": 19846593,
"title": "REBASE--a database for DNA restriction and modification: enzymes, genes and genomes."
}
],
"subjects": [
"Life Science"
]
},
"go": {
"homepage": "http://rebase.neb.com/rebase/rebase.html",
"name": "REBASE restriction enzyme database",
"prefix": "REBASE",
"uri_format": "http://rebase.neb.com/rebase/enz/$1.html"
},
"integbio": {
"alt_name": "The Restriction Enzyme Database",
"description": "REBASE is a database of restriction enzymes. The database contains entries by publication authors, and the database can be searched by identifiers such as name and number. Tools for digests and comparison of sequences are provided.",
"fairsharing": "biodbcore-000475",
"homepage": "http://rebase.neb.com/rebase/rebase.html",
"information_keywords": [
"Bioresource",
"Sequence",
"Repository"
],
"maintainer": "New England Biolabs Inc.",
"name": "REBASE",
"prefix": "nbdc00648",
"pubmeds": [
"19846593"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"mappings": {
"biocontext": "REBASE",
"edam": "2325",
"fairsharing": "FAIRsharing.9sb9qh",
"go": "REBASE",
"integbio": "nbdc00648",
"miriam": "rebase",
"n2t": "rebase",
"pathguide": "72",
"prefixcommons": "rebase",
"re3data": "r3d100012171",
"uniprot": "DB-0089",
"wikidata": "P4866"
},
"miriam": {
"deprecated": false,
"description": "REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.",
"homepage": "http://rebase.neb.com/rebase/",
"id": "00000230",
"name": "REBASE",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "rebase",
"sampleId": "101",
"uri_format": "http://rebase.neb.com/rebase/enz/$1.html"
},
"n2t": {
"description": "REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.",
"example": "101",
"homepage": "http://rebase.neb.com/rebase/",
"name": "REBASE at New England Biolabs",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "rebase",
"uri_format": "http://rebase.neb.com/rebase/enz/$1.html"
},
"pathguide": {
"abbreviation": "REBASE",
"homepage": "http://rebase.neb.com/rebase/rebase.html",
"name": "Restriction Enzyme Database",
"prefix": "72"
},
"prefixcommons": {
"description": "A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data.",
"example": "101",
"homepage": "http://rebase.neb.com",
"keywords": [
"enzyme",
"protein",
"structure",
"small molecule",
"genome",
"DNA",
"RNA"
],
"name": "Restriction enzymes and methylases database",
"pattern": "^\\d+$",
"prefix": "rebase",
"pubmed_ids": [
"19846593"
],
"uri_format": "http://rebase.neb.com/rebase/enz/$1.html"
},
"publications": [
{
"doi": "10.1093/nar/gku1046",
"pmc": "PMC4383893",
"pubmed": "25378308",
"title": "REBASE--a database for DNA restriction and modification: enzymes, genes and genomes",
"year": 2014
},
{
"doi": "10.1093/nar/gkp874",
"pmc": "PMC2808884",
"pubmed": "19846593",
"title": "REBASE--a database for DNA restriction and modification: enzymes, genes and genomes",
"year": 2009
}
],
"re3data": {
"description": "The Restriction Enzyme Database is a collection of information about restriction enzymes, methylases, the microorganisms from which they have been isolated, recognition sequences, cleavage sites, methylation specificity, the commercial availability of the enzymes, and references - both published and unpublished observations (dating back to 1952). REBASE is updated daily and is constantly expanding.",
"homepage": "http://rebase.neb.com/rebase/rebase.html",
"name": "REBASE",
"prefix": "r3d100012171",
"synonyms": [
"The Restriction Enzyme Database"
],
"xrefs": {
"nif": "0000-03391",
"scr": "007886"
}
},
"uniprot": {
"abbreviation": "REBASE",
"category": "Protein family/group databases",
"homepage": "http://rebase.neb.com/rebase/rebase.html",
"name": "Restriction enzymes and methylases database",
"prefix": "DB-0089",
"publications": [
{
"doi": "10.1093/nar/gku1046",
"pubmed": "25378308"
}
],
"uri_format": "http://rebase.neb.com/rebase/enz/$1.html"
},
"wikidata": {
"description": "ID in REBASE (Restriction Enzyme Database)",
"example": [
"1",
"6974",
"993"
],
"name": "REBASE Enzyme Number",
"pattern": "^[1-9]\\d*$",
"prefix": "P4866",
"uri_format": "http://rebase.neb.com/cgi-bin/reb_get.pl?enzname=$1"
}
},
"rebec": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Presents the new fast tracks for clinical research and observational studies on INDIGENOUS PEOPLE AND TRADITIONAL COMMUNITIES and on NEGLECTED TROPICAL DISEASES (NTDs). Fast-track can reduce the normal approval period for clinical trials to less than 48 hours, if the documentation, information and any mandatory changes requested are provided by the registrant.",
"example": "RBR-6qvdftm",
"homepage": "https://ensaiosclinicos.gov.br",
"name": "Brazilian Registry of Clinical Trials",
"pattern": "^RBR-\\w+$",
"uri_format": "https://ensaiosclinicos.gov.br/rg/$1"
},
"receptome.family": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database.",
"example": "5.1",
"homepage": "http://www.receptome.org",
"mappings": {
"prefixcommons": "hpmr"
},
"name": "Human Plasma Membrane Receptome Families",
"prefixcommons": {
"description": "Plasma membrane protein sequences, literature, and expression database",
"example": "14",
"homepage": "http://www.receptome.org/HPMR/",
"keywords": [
"protein"
],
"name": "Human Plasma Membrane Receptome",
"pattern": "^\\d+$",
"prefix": "hpmr",
"uri_format": "http://www.receptome.org/HPMR/Families/Frameset_family.asp?FamId=$1"
},
"uri_format": "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1"
},
"redfly": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"mappings": {
"pathguide": "265",
"prefixcommons": "redfly"
},
"pathguide": {
"abbreviation": "REDfly",
"homepage": "http://redfly.ccr.buffalo.edu/",
"name": "Regulatory Element Database for Drosophila",
"prefix": "265"
},
"prefixcommons": {
"description": "REDflyis a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs).",
"example": "8",
"homepage": "http://redfly.ccr.buffalo.edu",
"keywords": [
"regulation"
],
"name": "Regulatory Elements Database for Drosophila",
"pattern": "^\\d+$",
"prefix": "redfly",
"uri_format": "http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"refseq": {
"biocontext": {
"prefix": "RefSeq",
"uri_format": "http://www.ncbi.nlm.nih.gov/refseq/?term=$1"
},
"contact": {
"email": "pruitt@ncbi.nlm.nih.gov",
"name": "Kim Dixon Pruitt",
"orcid": "0000-0001-7950-1374"
},
"contributor_extras": [
{
"github": "slobentanzer",
"name": "Sebastian Lobentanzer",
"orcid": "0000-0003-3399-6695"
}
],
"edam": {
"description": "Accession number of a RefSeq database entry.",
"name": "RefSeq",
"obsolete": false,
"prefix": "1098"
},
"example_extras": [
"WP_029104145.1"
],
"fairsharing": {
"abbreviation": "RefSeq",
"description": "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.",
"homepage": "http://www.ncbi.nlm.nih.gov/RefSeq/",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "Reference Sequence Database",
"prefix": "FAIRsharing.4jg0qw",
"publications": [
{
"doi": "10.1093/nar/gkl842",
"pubmed_id": 17130148,
"title": "NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins."
}
],
"subjects": [
"Genetics",
"Computational Biology",
"Life Science"
]
},
"go": {
"homepage": "http://www.ncbi.nlm.nih.gov/RefSeq/",
"name": "RefSeq",
"prefix": "RefSeq"
},
"has_canonical": "ncbiprotein",
"hl7": {
"description": "The Reference Sequence (RefSeq) is one of the NCBI projects, the RefSeq collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. ReqSeq is accessible via BLAST, Entrez, and the NCBI FTP site. Information is also available in Entrez Genomes and Entrez Gene, and for some genomes additional information is available in the Map Viewer. RefSeq entries can be used with the HL7 coded data type. For example, in the HL7 messages specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model, RefSeq entries can be used to as the observation values for genomic reference sequence identifiers (LOINC #: 48013-7). More information may be found at: http://www.ncbi.nlm.nih.gov/RefSeqVersioning informaiton:The latest release of RefSeq was released on May 13, 2009 with the release number of 35.RefSeq generates new releases roughly every two months. The dates of the three previous releases were:Release 34, March 12, 2009Release 33, January 20, 2009Release 32, November 17, 2008RefSeq is a free database for the public.",
"homepage": "http://www.ncbi.nlm.nih.gov",
"organization": "National Center for Biotechnology Information,National Center for Biotechnology Information",
"preferred_prefix": "refSeq",
"prefix": "2.16.840.1.113883.6.280",
"status": "Complete"
},
"integbio": {
"alt_name": "Reference Sequence",
"description": "RefSeq is a database of standard reference genomic, transcript, and protein sequences. The database contains consensus sequence data for over 20,000 organisms and over 27 million proteins and is designed to provide a common basis for experimental studies that can be searched using accession ID, keyword, or BLAST. Bulk data is available for FTP download.",
"fairsharing": "biodbcore-000457",
"homepage": "https://www.ncbi.nlm.nih.gov/refseq/",
"information_keywords": [
"Sequence"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "RefSeq",
"prefix": "nbdc00187",
"pubmeds": [
"22121212",
"18927115",
"10592200"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"RNA",
"Protein",
"Cell/Organelle"
]
},
"mappings": {
"biocontext": "RefSeq",
"edam": "1098",
"fairsharing": "FAIRsharing.4jg0qw",
"go": "RefSeq",
"hl7": "2.16.840.1.113883.6.280",
"integbio": "nbdc00187",
"miriam": "refseq",
"n2t": "refseq",
"prefixcommons": "refseq",
"re3data": "r3d100010285",
"uniprot": "DB-0117"
},
"miriam": {
"deprecated": false,
"description": "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.",
"homepage": "https://www.ncbi.nlm.nih.gov/projects/RefSeq/",
"id": "00000039",
"name": "RefSeq",
"namespaceEmbeddedInLui": false,
"pattern": "^(((WP|AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\\d+)|(NZ\\_[A-Z]{2,4}\\d+))(\\.\\d+)?$",
"prefix": "refseq",
"sampleId": "NP_012345",
"uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1"
},
"n2t": {
"description": "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.",
"example": "NP_012345",
"homepage": "https://www.ncbi.nlm.nih.gov/projects/RefSeq/",
"name": "The NCBI Reference Sequence database",
"namespaceEmbeddedInLui": false,
"pattern": "^((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\\d+|(NZ\\_[A-Z]{4}\\d+))(\\.\\d+)?$",
"prefix": "refseq",
"uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1"
},
"name": "Reference Sequence Collection",
"pattern": "^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\\d+)|(NZ_[A-Z]{2,4}\\d+))(\\.\\d+)?$",
"prefixcommons": {
"description": "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.",
"example": "NP_012345",
"homepage": "http://www.ncbi.nlm.nih.gov/RefSeq/",
"keywords": [
"protein",
"DNA",
"RNA"
],
"name": "Reference Sequence Database",
"pattern": "^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\\d+(\\.\\d+)?$",
"prefix": "refseq",
"pubmed_ids": [
"17130148"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/nuccore/$1"
},
"publications": [
{
"doi": "10.1093/nar/gkv1189",
"pmc": "PMC4702849",
"pubmed": "26553804",
"title": "Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation",
"year": 2015
},
{
"doi": "10.1093/nar/gkl842",
"pmc": "PMC1716718",
"pubmed": "17130148",
"title": "NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins",
"year": 2006
}
],
"re3data": {
"description": "The Reference Sequence (RefSeq) collection provides a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. RefSeq sequences form a foundation for medical, functional, and diversity studies. They provide a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis (especially RefSeqGene records), expression studies, and comparative analyses.",
"homepage": "https://www.ncbi.nlm.nih.gov/refseq/",
"name": "NCBI Reference Sequence Database",
"prefix": "r3d100010285",
"synonyms": [
"RefSeq"
],
"xrefs": {
"fairsharing": "FAIRsharing.4jg0qw",
"nif": "0000-03397",
"omics": "01659",
"scr": "003496"
}
},
"references": [
"https://github.com/biopragmatics/bioregistry/issues/545"
],
"synonyms": [
"REFSEQ_PROT"
],
"uniprot": {
"abbreviation": "RefSeq",
"category": "Sequence databases",
"homepage": "https://www.ncbi.nlm.nih.gov/refseq/",
"name": "NCBI Reference Sequences",
"prefix": "DB-0117",
"publications": [
{
"doi": "10.1093/nar/gkv1189",
"pubmed": "26553804"
}
],
"uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1"
}
},
"reo": {
"comment": "From James O.: It was an ontology for \"reagents\" developed by @Matthew Brush. Since OBI was interested in reagents, Matt developed it in coordination with OBI and had plans to submit it to OBO. I believe that REO was once included in Ontobee, and OBI even started using some REO terms. But REO was never submitted to OBO. I believe it was abandoned.",
"contact": {
"email": "matt@tislab.org",
"github": "mbrush",
"name": "Matthew Brush",
"orcid": "0000-0002-1048-5019"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied βchemicallyβ in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs.",
"download_owl": "https://github.com/tis-lab/reagent-ontology/raw/master/reo/ontology_files/reo_pre-merged_or_reasoned_files/reo_reasoned_9-6-12.owl",
"example": "0000079",
"homepage": "https://github.com/tis-lab/reagent-ontology",
"mappings": {
"ontobee": "REO"
},
"name": "Reagent Ontology",
"ontobee": {
"library": "Not Specified/No",
"name": "Reagent Ontology",
"prefix": "REO"
},
"pattern": "^\\d{7}$",
"references": [
"https://github.com/obi-ontology/obi/issues/1015",
"https://code.google.com/archive/p/reagent-ontology/",
"https://github.com/obi-ontology/obi/issues/1135"
],
"repository": "https://github.com/tis-lab/reagent-ontology",
"uri_format": "http://purl.obolibrary.org/obo/REO_$11"
},
"repeatsdb.protein": {
"mappings": {
"miriam": "repeatsdb.protein"
},
"miriam": {
"deprecated": false,
"description": "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database.",
"homepage": "https://repeatsdb.org/",
"id": "00000792",
"name": "RepeatsDB Protein",
"namespaceEmbeddedInLui": false,
"pattern": "^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$",
"prefix": "repeatsdb.protein",
"sampleId": "P29894",
"uri_format": "https://repeatsdb.org/protein/$1"
},
"provides": "uniprot"
},
"repeatsdb.structure": {
"mappings": {
"miriam": "repeatsdb.structure"
},
"miriam": {
"deprecated": false,
"description": "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database.",
"homepage": "https://repeatsdb.org/",
"id": "00000764",
"name": "RepeatsDB Structure",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$",
"prefix": "repeatsdb.structure",
"sampleId": "2gc4E",
"uri_format": "https://repeatsdb.org/structure/$1"
}
},
"repec": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Peruvian Clinical Trials Registry - REPEC is a non-profit online information system developed in 2007 by INS. It is a publicly accessible prospective registry aimed at providing information about clinical trials underway in Peru. REPEC also includes Registries for Trial Sites, Institutional Research Ethics Committees, Sponsors and Contract Research Organizations. REPEC contains records of clinical trials since 1995. Since December 14, 2012, the Peruvian National Institute of Health, by means of the General Office for Research and Technological Transfer (OGITT), has started a process to improve REPEC and to join the WHO International Clinical Trials Registry Platform (ICTRP) and to be acknowledged as a Primary Registry. More information about primary registries is available in ICRTP at http://apps.who.int/trialsearch/. (from website)",
"example": "046-19",
"homepage": "https://ensayosclinicos-repec.ins.gob.pe/en/",
"logo": "https://ensayosclinicos-repec.ins.gob.pe/images/plantilla/img_logo_principal_repec_en.png",
"name": "Peruvian Clinical Trial Registry",
"pattern": "^\\d+-\\d+(-[A-Z])?$",
"uri_format": "https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC=$1"
},
"reproduceme": {
"aberowl": {
"description": "The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials and settings required for its reproducibility.",
"download_owl": "http://aber-owl.net/media/ontologies/REPRODUCE-ME/7/reproduce-me.owl",
"homepage": "https://w3id.org/reproduceme/research",
"name": "REPRODUCE-ME",
"prefix": "REPRODUCE-ME",
"version": "1.1"
},
"bioportal": {
"contact": {
"email": "sheeba.samuel@uni-jena.de",
"name": "Sheeba Samuel"
},
"description": "The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials and settings required for its reproducibility.",
"homepage": "https://w3id.org/reproduceme/research",
"name": "REPRODUCE-ME",
"prefix": "REPRODUCE-ME",
"publication": "https://w3id.org/reproduceme/research",
"version": "1.1"
},
"contact": {
"email": "sheeba.samuel@uni-jena.de",
"name": "Sheeba Samuel",
"orcid": "0000-0002-7981-8504"
},
"example": "MicrobeamManipulation",
"mappings": {
"aberowl": "REPRODUCE-ME",
"bioportal": "REPRODUCE-ME",
"ols": "reproduceme"
},
"ols": {
"contact": "sheeba.samuel@uni-jena.de",
"description": "The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility.",
"homepage": "https://w3id.org/reproduceme/research",
"name": "REPRODUCE-ME Ontology",
"prefix": "reproduceme",
"version": "1.1"
},
"uri_format": "https://w3id.org/reproduceme#$1"
},
"resid": {
"biocontext": {
"prefix": "RESID"
},
"edam": {
"description": "Identifier of a protein modification catalogued in the RESID database.",
"name": "RESID",
"obsolete": false,
"prefix": "2619"
},
"go": {
"homepage": "https://proteininformationresource.org/resid/resid.shtml",
"name": "RESID Database of Protein Modifications",
"prefix": "RESID",
"uri_format": "https://proteininformationresource.org/cgi-bin/resid?id=$1"
},
"homepage": "https://proteininformationresource.org/resid/",
"mappings": {
"biocontext": "RESID",
"edam": "2619",
"go": "RESID",
"miriam": "resid",
"n2t": "resid",
"obofoundry": "resid",
"prefixcommons": "resid"
},
"miriam": {
"deprecated": false,
"description": "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.",
"homepage": "http://pir0.georgetown.edu/resid/",
"id": "00000046",
"name": "RESID",
"namespaceEmbeddedInLui": false,
"pattern": "^AA\\d{4}$",
"prefix": "resid",
"sampleId": "AA0001",
"uri_format": "http://pir0.georgetown.edu/cgi-bin/resid?id=$1"
},
"n2t": {
"description": "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.",
"example": "AA0001",
"homepage": "http://pir0.georgetown.edu/resid/",
"name": "RESID at Georgetown University",
"namespaceEmbeddedInLui": false,
"pattern": "^AA\\d{4}$",
"prefix": "resid",
"uri_format": "http://pir0.georgetown.edu/cgi-bin/resid?id=$1"
},
"obofoundry": {
"contact": "john.garavelli@ebi.ac.uk",
"contact.label": "John Garavelli",
"contact.orcid": "0000-0002-4131-735X",
"deprecated": true,
"description": "For the description of covalent bonds in proteins.",
"domain": "chemistry and biochemistry",
"homepage": "http://www.ebi.ac.uk/RESID/",
"name": "Protein covalent bond",
"prefix": "resid"
},
"prefixcommons": {
"description": "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.",
"example": "AA0001",
"homepage": "http://www.ebi.ac.uk/RESID/",
"keywords": [
"protein",
"small molecule",
"structure"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "RESID Database of Protein Modifications",
"pattern": "^AA\\d{4}$",
"prefix": "resid",
"pubmed_ids": [
"15174124"
],
"uri_format": "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$1']"
},
"publications": [
{
"doi": "10.1002/pmic.200300764",
"pubmed": "15174124",
"title": "Annotation of post-translational modifications in the Swiss-Prot knowledge base",
"year": 2004
}
],
"uri_format": "https://proteininformationresource.org/cgi-bin/resid?id=$1"
},
"reto": {
"aberowl": {
"description": "An application ontology for the domain of gene transcription regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI and orthological properties from RO and SIO.",
"download_obo": "http://aber-owl.net/media/ontologies/RETO/7/reto.obo",
"homepage": "http://www.semantic-systems-biology.org/apo/",
"name": "Regulation of Transcription Ontology",
"prefix": "RETO",
"version": "2015"
},
"bioportal": {
"contact": {
"email": "vladimir.n.mironov@gmail.com",
"name": "Vladimir Mironov"
},
"description": "An application ontology for the domain of gene transcription regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI and orthological properties from RO and SIO.",
"homepage": "http://www.semantic-systems-biology.org/apo/",
"name": "Regulation of Transcription Ontology",
"prefix": "RETO",
"publication": "http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0386-y",
"version": "2015"
},
"download_obo": "https://www.bio.ntnu.no/ontology/ReTO/reto.obo",
"download_owl": "https://www.bio.ntnu.no/ontology/ReTO/reto.owl",
"fairsharing": {
"abbreviation": "ReTO",
"description": "An application ontology for the domain of gene transcription regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI and orthological properties from RO and SIO.",
"domains": [
"Regulation of gene expression",
"Transcript"
],
"homepage": "https://bioportal.bioontology.org/ontologies/RETO",
"name": "Regulation of Transcription Ontolology",
"prefix": "FAIRsharing.4qyf0f",
"subjects": [
"Life Science",
"Transcriptomics"
]
},
"mappings": {
"aberowl": "RETO",
"bioportal": "RETO",
"fairsharing": "FAIRsharing.4qyf0f",
"ols": "reto"
},
"no_own_terms": true,
"ols": {
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{
"doi": "10.1093/database/bat015",
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{
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{
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"title": "The Rat Genome Database, update 2007--easing the path from disease to data and back again",
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"description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.",
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"name": "RiceNetDB",
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"pattern": "^LOC\\_Os\\d{1,2}g\\d{5}\\.\\d$",
"prefix": "ricenetdb.gene",
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}
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"homepage": "http://bis.zju.edu.cn/ricenetdb",
"id": "00000668",
"name": "RiceNetDB miRNA",
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"pattern": "^osa-miR\\d{3,5}[a-z]{0,1}$",
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"sampleId": "osa-miR446",
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"description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.",
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"name": "RiceNetDB miRNA",
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"id": "00000665",
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"sampleId": "LOC_Os01g49190",
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"homepage": "http://bis.zju.edu.cn/ricenetdb",
"id": "00000667",
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"pattern": "^OSR\\d{4}$",
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"name": "RiceNetDB Reaction",
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},
"rism": {
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"miriam": {
"deprecated": false,
"description": "RISM Online is a new service that will publish the bibliographic and authority data from the catalogue of the RΓ©pertoire International des Sources Musicales project.",
"homepage": "https://rism.digital/",
"id": "00000911",
"name": "RISM Online",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z]+/[0-9]+$",
"prefix": "rism",
"sampleId": "people/11035",
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"mappings": {
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"description": "RNA STRAND contains known RNA secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known RNA secondary structures, and to provide the scientific community with simple yet powerful ways of analysing, searching and updating the proposed database.",
"example": "CRW_00469",
"homepage": "http://www.rnasoft.ca/sstrand",
"keywords": [
"RNA",
"structure"
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"name": "RNA SSTRAND",
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"prefix": "rna_sstrand",
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},
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"prefix": "RNACENTRAL"
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"contact": {
"email": "bsweeney@ebi.ac.uk",
"github": "blakesweeney",
"name": "Blake A Sweeney",
"orcid": "0000-0002-6497-2883"
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"edam": {
"description": "Identifier of an entry from the RNA central database of annotated human miRNAs.",
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"obsolete": false,
"prefix": "3856"
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"name": "RNAcentral",
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{
"doi": "10.1093/nar/gkw1008",
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],
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"subjects": [
"Bioinformatics",
"Biology"
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"twitter": "RNAcentral"
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"name": "RNAcentral",
"prefix": "RNAcentral",
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"information_keywords": [
"Sequence",
"Bibliography/Documents"
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"maintainer": "Institute for Molecular Bioscience, The University of Queensland",
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"21112873"
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"RNA"
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"ncbi": "RNAcentral",
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"pattern": "^URS[0-9A-F]{10}(\\_\\d+)?$",
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"description": "RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases.",
"example": "URS0000759CF4",
"homepage": "https://rnacentral.org/",
"name": "RNAcentral through EMBL-EBI",
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"pattern": "^URS[0-9A-F]{10}(\\_\\d+)?$",
"prefix": "rnacentral",
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"name": "Noncoding RNA Sequence Database",
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},
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{
"doi": "10.1093/nar/gky1034",
"pmc": "PMC6324050",
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"year": 2019
},
{
"doi": "10.1093/nar/gkw1008",
"pmc": "PMC5210518",
"pubmed": "27794554",
"title": "RNAcentral: a comprehensive database of non-coding RNA sequences",
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}
],
"synonyms": [
"LNCRNADB"
],
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"URS0000413C32_559292",
"URS000080E36F_9606"
],
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"name": "RNACentral ID",
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}
},
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"contact": {
"email": "ygyingli@ncsu.edu",
"name": "Yaroslava G Yingling",
"orcid": "0000-0002-8557-9992"
},
"example": "8668",
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"abbreviation": "RNAJunction",
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"name": "RNAJunction",
"prefix": "FAIRsharing.zzgvrv",
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{
"doi": "10.1093/nar/gkm842",
"pubmed_id": 17947325,
"title": "RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign."
}
],
"subjects": [
"Structural Biology"
]
},
"mappings": {
"fairsharing": "FAIRsharing.zzgvrv",
"prefixcommons": "rnajunction"
},
"name": "Database of RNA Junctions and Kissing loop Structures",
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"description": "Within this database you will to able to find more than 12,000 extracted three-dimensional junction and kissing loop structures as well as detailed annotations for each.",
"example": "10387",
"homepage": "http://rnajunction.abcc.ncifcrf.gov",
"keywords": [
"structure",
"RNA"
],
"name": "RNAJunction: A Database of RNA Junction and Kissing loop Structure",
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"prefix": "rnajunction",
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{
"doi": "10.1093/nar/gkm842",
"pmc": "PMC2238914",
"pubmed": "17947325",
"title": "RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign",
"year": 2007
}
],
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://rnajunction.ncifcrf.gov/JunctionPage.php?jid=$1"
},
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"contact": {
"email": "Maciej.Antczak@cs.put.poznan.pl",
"github": "mantczak",
"name": "Maciej Antczak",
"orcid": "0000-0002-5320-2023"
},
"contributor": {
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"description": "Rnaloops stores the information about n-way junctions (where nβ₯3) found in experimentally determined rna 3d structures deposited in the protein data bank.",
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"homepage": "https://rnaloops.cs.put.poznan.pl",
"keywords": [
"rna",
"structural bioinformatcs"
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"name": "RNAloops",
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"email": "cthoyt@gmail.com",
"github": "cthoyt",
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},
"description": "A comprehensive listing of post-transcriptionally modified nucleosides from RNA -",
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"homepage": "http://rna.rega.kuleuven.be/rnamods/",
"keywords": [
"post-transcriptional modification",
"rna",
"structural bioinformatcs"
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"name": "The RNA Modification Database",
"pattern": "^\\d{3}$",
"uri_format": "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1"
},
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"prefix": "RNAMODS"
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"go": {
"homepage": "https://mods.rna.albany.edu/",
"name": "RNA Modification Database",
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"RNAMDB"
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"description": "The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA.",
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"name": "RNA Modification Database at University of Utah",
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"pattern": "^\\d{3}$",
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"description": "The RNA modification database provides a comprehensive listing of posttranscriptionally modified nucleosides from RNA and is maintained as an updated version of the initial printed report.",
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"RNA",
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},
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},
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{
"doi": "10.3233/ao-2011-0082",
"title": "The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data",
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}
],
"subjects": [
"Biochemistry",
"Life Science"
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},
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"prefixcommons": "rnao"
},
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"deprecated": true,
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"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
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"description": "Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures.",
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{
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]
},
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"description": "The RNA Virus Database is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments and contains translated genome sequences for all species.",
"example": "164750",
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"genome"
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"name": "RNA Virus Database",
"pattern": "^\\d+$",
"prefix": "rvd",
"uri_format": "http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id=$1"
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},
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"name": "Relation Ontology",
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},
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"name": "Chris Mungall"
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"homepage": "https://github.com/oborel/obo-relations/",
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"name": "Relations Ontology",
"prefix": "RO",
"repository": "http://purl.obolibrary.org/obo/ro.owl",
"version": "2024-04-24"
},
"banana_peel": "_",
"biocontext": {
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"biolink": {
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"is_obo": true,
"prefix": "RO",
"uri_format": "http://purl.obolibrary.org/obo/RO_$1"
},
"bioportal": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "A collection of relations intended primarily for standardization across ontologies in the OBO Foundry and wider OBO library. It incorporates ROCore upper-level relations such as part of as well as biology-specific relationship types such as develops from.",
"homepage": "https://github.com/oborel/obo-relations/",
"name": "Relations Ontology",
"prefix": "OBOREL",
"version": "2024-04-24"
},
"example": "0002533",
"example_extras": [
"HOM0000022"
],
"fairsharing": {
"abbreviation": "RO",
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"description": "RO is a collection of relations intended primarily for standardization across ontologies in the OBO Foundry and wider OBO library. It incorporates ROCore upper-level relations such as part of as well as biology-specific relationship types such as develops from. The predecessor of RO was OBO_REL. Many of the relations in OBO_REL have been ceded to BFO.",
"homepage": "https://github.com/oborel/obo-relations/",
"license": "CC0-1.0",
"name": "OBO Relations Ontology",
"prefix": "FAIRsharing.9w8ea0",
"repository": "https://github.com/oborel/obo-relations/wiki/ROAndBFO",
"subjects": [
"Life Science"
],
"user_defined_tags": [
"Relations"
]
},
"go": {
"description": "A collection of relations used across OBO ontologies",
"name": "OBO Relation Ontology Ontology",
"prefix": "RO"
},
"mappings": {
"aberowl": "RO",
"agroportal": "RO",
"biocontext": "RO",
"biolink": "RO",
"bioportal": "OBOREL",
"fairsharing": "FAIRsharing.9w8ea0",
"go": "RO",
"miriam": "ro",
"n2t": "ro",
"obofoundry": "ro",
"ols": "ro",
"ontobee": "RO",
"prefixcommons": "ro",
"wikidata": "P3590"
},
"miriam": {
"deprecated": false,
"description": "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies.",
"homepage": "http://obofoundry.org/ontology/ro.html",
"id": "00000120",
"name": "Relation Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^RO_\\d{7}$",
"prefix": "ro",
"sampleId": "RO_0002533",
"uri_format": "http://purl.obolibrary.org/obo/$1"
},
"n2t": {
"description": "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies.",
"example": "RO_0002533",
"homepage": "http://obofoundry.org/ontology/ro.html",
"name": "OBO Relation Ontology through OntoBee",
"namespaceEmbeddedInLui": false,
"pattern": "^RO_\\d{7}$",
"prefix": "ro",
"uri_format": "http://purl.obolibrary.org/obo/$1"
},
"name": "Relation Ontology",
"namespace_in_lui": true,
"obofoundry": {
"appears_in": [
"agro",
"aism",
"cdno",
"cl",
"clao",
"clyh",
"colao",
"cteno",
"ecao",
"ecocore",
"ecto",
"envo",
"foodon",
"fovt",
"gallont",
"genepio",
"go",
"hso",
"lepao",
"maxo",
"ons",
"ontoavida",
"pcl",
"pco",
"plana",
"planp",
"poro",
"proco",
"psdo",
"pso",
"rbo",
"uberon",
"xpo",
"zp",
"upa"
],
"contact": "cjmungall@lbl.gov",
"contact.github": "cmungall",
"contact.label": "Chris Mungall",
"contact.orcid": "0000-0002-6601-2165",
"deprecated": false,
"description": "Relationship types shared across multiple ontologies",
"domain": "upper",
"download.json": "http://purl.obolibrary.org/obo/ro.json",
"download.obo": "http://purl.obolibrary.org/obo/ro.obo",
"download.owl": "http://purl.obolibrary.org/obo/ro.owl",
"homepage": "https://oborel.github.io/",
"license": "CC0 1.0",
"license.url": "http://creativecommons.org/publicdomain/zero/1.0/",
"name": "Relation Ontology",
"preferredPrefix": "RO",
"prefix": "ro",
"repository": "https://github.com/oborel/obo-relations"
},
"ols": {
"description": "Relationship types shared across multiple ontologies",
"download_owl": "http://purl.obolibrary.org/obo/ro.owl",
"homepage": "https://oborel.github.io/",
"name": "Relation Ontology",
"prefix": "ro",
"version": "2024-04-24",
"version.iri": "http://purl.obolibrary.org/obo/ro/releases/2024-04-24/ro.owl"
},
"ontobee": {
"library": "Library",
"name": "Relation Ontology",
"prefix": "RO"
},
"pattern": "^(HOM)?\\d{7}$",
"prefixcommons": {
"alt_uri_formats": [
"http://purl.org/obo/owl/RO_REL#$1",
"http://purl.org/obo/owlapi/relationship#$1"
],
"bioportal": "1042",
"description": "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies.",
"example": "part_of",
"homepage": "http://www.obofoundry.org/ro",
"keywords": [
"obo",
"relations"
],
"license": "CC-BY-3.0",
"name": "Relation Ontology",
"pattern": "^\\w+$",
"prefix": "ro",
"pubmed_ids": [
"15892874"
],
"synonyms": [
"obo_rel",
"obo.ro",
"ro_proposed_relation"
]
},
"publications": [
{
"doi": "10.1186/2041-1480-5-41",
"pmc": "PMC4177597",
"pubmed": "25276335",
"title": "Structuring research methods and data with the research object model: genomics workflows as a case study",
"year": 2014
},
{
"doi": "10.1186/gb-2005-6-5-r46",
"pmc": "PMC1175958",
"pubmed": "15892874",
"title": "Relations in biomedical ontologies",
"year": 2005
}
],
"synonyms": [
"RO_proposed_relation",
"obo_rel",
"oborel"
],
"uri_format": "http://purl.obolibrary.org/obo/RO_$1",
"wikidata": {
"description": "ID in the Relations Ontology",
"homepage": "https://github.com/oborel/obo-relations/",
"name": "Relations Ontology ID",
"pattern": "^(RO|BFO)_[0-9]{7}$",
"prefix": "P3590"
}
},
"roleo": {
"aberowl": {
"description": "The Role Ontology (RoleO) is a ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles.",
"download_owl": "http://aber-owl.net/media/ontologies/ROLEO/1/roleo.owl",
"homepage": "http://sourceforge.net/projects/roleo",
"name": "Role Ontology",
"prefix": "ROLEO",
"version": "Vision Release; 1.0.11"
},
"banana": "RoleO",
"banana_peel": "_",
"bioportal": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "The Role Ontology (RoleO) is an ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO development follows the OBO Foundry principles. RoleO has represented all the occupations defined in the Standard Occupational Classification (SOC) System from the USA Bureau of Labor Statistics.",
"homepage": "https://github.com/roleontology/roleo",
"name": "Role Ontology",
"prefix": "ROLEO",
"version": "Vision Release: 1.0.16"
},
"comment": "This resource doesn't exist on the web anymore",
"contact": {
"email": "yongqunh@med.umich.edu",
"github": "yongqunh",
"name": "Yongqun Oliver He",
"orcid": "0000-0001-9189-9661"
},
"deprecated": true,
"example": "0000002",
"mappings": {
"aberowl": "ROLEO",
"bioportal": "ROLEO",
"prefixcommons": "roleo"
},
"pattern": "^\\d{7}$",
"preferred_prefix": "RoleO",
"prefixcommons": {
"bioportal": "1538",
"description": "The Role Ontology (RoleO) is a ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles.",
"example": "RoleO_0000002",
"homepage": "http://sourceforge.net/projects/roleo",
"keywords": [
"obo"
],
"name": "Role Ontology",
"pattern": "^RoleO_\\d{7}$",
"prefix": "roleo"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "http://purl.obolibrary.org/obo/RoleO_$1"
},
"ror": {
"bartoc": {
"abbreviation": "ROR",
"description": "ROR is a global, community-led registry of open persistent identifiers for research organizations",
"homepage": "https://ror.org/",
"license": "CC-BY-4.0",
"name": "Research Organization Registry",
"prefix": "20474",
"wikidata_database": "Q110235640"
},
"contact": {
"email": "maria.gould@ucop.edu",
"github": "mariagould",
"name": "Maria Gould",
"orcid": "0000-0002-2916-3423"
},
"download_owl": "https://w3id.org/rorio/rorio.owl",
"fairsharing": {
"abbreviation": "ROR",
"contact": {
"email": "info@ror.org",
"name": "Maria Gould",
"orcid": "0000-0002-2916-3423"
},
"description": "ROR is a community-led project to develop an open, sustainable, usable, and unique identifier for every research organization in the world. Implementation of ROR IDs in scholarly infrastructure and metadata will enable more efficient discovery and tracking of research outputs across institutions and funding bodies.",
"homepage": "https://ror.org",
"license": "CC0-1.0",
"name": "Research Organization Registry",
"prefix": "FAIRsharing.1jKfji",
"publications": [],
"repository": "https://github.com/ror-community",
"subjects": [
"Data Management"
],
"twitter": "ResearchOrgs"
},
"mappings": {
"bartoc": "20474",
"fairsharing": "FAIRsharing.1jKfji",
"miriam": "ror",
"n2t": "ror"
},
"mastodon": "ResearchOrgs@mastodon.social",
"miriam": {
"deprecated": false,
"description": "ROR (Research Organization Registry) is a global, community-led registry\nof open persistent identifiers for research organizations. ROR is jointly\noperated by California Digital Library, Crossref, and Datacite.",
"homepage": "https://ror.org",
"id": "00000961",
"name": "ROR",
"namespaceEmbeddedInLui": false,
"pattern": "^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$",
"prefix": "ror",
"sampleId": "03yrm5c26",
"uri_format": "https://ror.org/$1"
},
"n2t": {
"example": "03yrm5c26",
"homepage": "http://ror.org",
"name": "Research Organization Registry",
"namespaceEmbeddedInLui": false,
"prefix": "ror",
"uri_format": "https://ror.org/$1"
},
"name": "Research Organization Registry"
},
"rouge": {
"biocontext": {
"prefix": "ROUGE"
},
"contact": {
"email": "ohara@kazusa.or.jp",
"name": "Osamu Ohara",
"orcid": "0000-0002-3328-9571"
},
"fairsharing": {
"abbreviation": "ROUGE",
"description": "The ROUGE protein database is a sister database of HUGE protein database which has accumulated the results of comprehensive sequence analysis of human long cDNAs (KIAA cDNAs). The ROUGE protein database has been created to publicize the information obtained from mouse homologues of the KIAA cDNAs (mKIAA cDNAs).",
"homepage": "http://www.kazusa.or.jp/rouge/",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "ROdent Unidentified Gene-Encoded large proteins",
"prefix": "FAIRsharing.vdbagq",
"publications": [
{
"doi": "10.1093/nar/gkh035",
"pubmed_id": 14681467,
"title": "HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE."
}
],
"subjects": [
"Life Science"
]
},
"integbio": {
"alt_name": "A Database of Rodent Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Mouse cDNA Project",
"description": "ROUGE is a database of long rodent cDNA clones designed to compliment the HUGE database of long human cDNA clones. The database contains sequence information for mouse clones from the mKIAA sequencing project, which can be browsed or searched. ROUGE was conducted as part of the CREATE program.",
"fairsharing": "biodbcore-000408",
"homepage": "http://www.kazusa.or.jp/rouge/index.html",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "ROUGE",
"prefix": "nbdc00672",
"pubmeds": [
"15368895",
"15449545",
"15188409",
"14621295",
"12693553",
"12465718"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"RNA",
"Protein"
]
},
"mappings": {
"biocontext": "ROUGE",
"fairsharing": "FAIRsharing.vdbagq",
"integbio": "nbdc00672",
"miriam": "rouge",
"n2t": "rouge",
"prefixcommons": "rouge",
"uniprot": "DB-0092"
},
"miriam": {
"deprecated": false,
"description": "The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.",
"homepage": "http://www.kazusa.or.jp/rouge/",
"id": "00000293",
"name": "Rouge",
"namespaceEmbeddedInLui": false,
"pattern": "^m\\w+$",
"prefix": "rouge",
"sampleId": "mKIAA4200",
"uri_format": "http://www.kazusa.or.jp/rouge/gfpage/$1/"
},
"n2t": {
"description": "The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.",
"example": "mKIAA4200",
"homepage": "http://www.kazusa.or.jp/rouge/",
"name": "Rouge at Kazusa DNA Research Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^m\\w+$",
"prefix": "rouge",
"uri_format": "http://www.kazusa.or.jp/rouge/gfpage/$1/"
},
"name": "Rodent Unidentified Gene-Encoded Large Proteins",
"prefixcommons": {
"description": "The ROUGE protein database is a sister database of HUGE protein database which has accumulated the results of comprehensive sequence analysis of human long cDNAs (KIAA cDNAs). The ROUGE protein database has been created to publicize the information obtained from mouse homologues of the KIAA cDNAs (mKIAA cDNAs).",
"example": "mKIAA0701",
"homepage": "http://www.kazusa.or.jp/rouge/",
"keywords": [
"protein",
"DNA"
],
"name": "A Database of Rodent Unidentified Gene-Encoded Large Proteins Analyzed",
"pattern": "^mKIAA\\d+$",
"prefix": "rouge",
"uri_format": "http://www.kazusa.or.jp/rouge/gfpage/$1/"
},
"publications": [
{
"doi": "10.1093/nar/gkh035",
"pmc": "PMC308769",
"pubmed": "14681467",
"title": "HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE",
"year": 2004
}
],
"uniprot": {
"abbreviation": "Rouge",
"category": "Organism-specific databases",
"homepage": "http://www.kazusa.or.jp/rouge/",
"name": "Rodent Unidentified Gene-Encoded large proteins database",
"prefix": "DB-0092",
"publications": [
{
"doi": "10.1093/nar/gkh035",
"pubmed": "14681467"
}
],
"uri_format": "http://www.kazusa.or.jp/rouge/gfpage/$1"
},
"uri_format": "https://www.kazusa.or.jp/rouge/gfpage/$1"
},
"rpcec": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Cuban Public Registry of Clinical Trials (RPCEC) is a website with a database of clinical trials, with national coverage. It was established in 2007 under the leadership of the National Coordinating Center of Clinical Trials (CENCEC) and with INFOMED collaboration. (from homepage)",
"example": "RPCEC00000423",
"homepage": "https://rpcec.sld.cu/en/home",
"name": "Cuban Registry of Clinical Trials",
"pattern": "^RPCEC\\d+$",
"uri_format": "https://rpcec.sld.cu/en/trials/$1"
},
"rrid": {
"banana": "RRID",
"biocontext": {
"prefix": "RRID"
},
"contact": {
"email": "bandrow@gmail.com",
"github": "bandrow",
"name": "Anita Bandrowski",
"orcid": "0000-0002-5497-0243"
},
"contributor_extras": [
{
"email": "bandrow@gmail.com",
"github": "bandrow",
"name": "Anita Bandrowski",
"orcid": "0000-0002-5497-0243"
}
],
"fairsharing": {
"abbreviation": "RRID",
"description": "Research Resource Identifiers (#RRID) are ID numbers assigned to help researchers cite key resources (antibodies, model organisms and software projects) in the biomedical literature to improve transparency of research methods. \n\n\n\n",
"domains": [
"Citation",
"Resource metadata",
"Annotation",
"Data retrieval",
"Centrally registered identifier"
],
"homepage": "https://www.rrids.org/",
"name": "Research Resource Identifier",
"prefix": "FAIRsharing.ATwSZG",
"publications": [
{
"doi": "10.12688/f1000research.6555.2",
"pubmed": "26594330",
"title": "The Resource Identification Initiative: A cultural shift in publishing",
"year": 2015
},
{
"doi": "10.1016/j.neuron.2016.04.030",
"pubmed": "27151636",
"title": "RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods",
"year": 2016
},
{
"doi": "10.1002/cne.23913",
"pubmed": "26599696",
"title": "The Resource Identification Initiative: A Cultural Shift in Publishing",
"year": 2015
},
{
"doi": "10.7717/peerj.148",
"pubmed": "24032093",
"title": "On the reproducibility of science: unique identification of research resources in the biomedical literature",
"year": 2013
},
{
"doi": "10.1038/nmeth.3995",
"pubmed": "27595404",
"title": "A proposal for validation of antibodies",
"year": 2016
}
],
"subjects": [
"Knowledge and Information Systems",
"Chemistry",
"Life Science"
]
},
"homepage": "https://rrid.site",
"mappings": {
"biocontext": "RRID",
"fairsharing": "FAIRsharing.ATwSZG",
"miriam": "rrid",
"n2t": "rrid"
},
"miriam": {
"deprecated": false,
"description": "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\r\nThe initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch.",
"homepage": "https://scicrunch.org/resolver",
"id": "00000558",
"name": "RRID",
"namespaceEmbeddedInLui": true,
"pattern": "^RRID:[a-zA-Z]+.+$",
"prefix": "rrid",
"sampleId": "AB_262044",
"uri_format": "https://scicrunch.org/resolver/RRID:$1"
},
"n2t": {
"description": "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools. The initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch.",
"example": "AB_262044",
"homepage": "https://scicrunch.org/resolver",
"name": "RRID at SciCrunch",
"namespaceEmbeddedInLui": true,
"pattern": "^RRID:[A-Z_a-z-0-9]+$",
"prefix": "rrid",
"uri_format": "https://scicrunch.org/resolver/RRID:$1"
},
"name": "Research Resource Identification",
"pattern": "^[a-zA-Z]+.+$",
"publications": [
{
"doi": "10.1093/nar/gkac927",
"pmc": "PMC9825422",
"pubmed": "36370112",
"title": "The Antibody Registry: ten years of registering antibodies",
"year": 2023
},
{
"doi": "10.1093/gigascience/giac058",
"pmc": "PMC9197678",
"pubmed": "35701373",
"title": "A decade of GigaScience: What can be learned from half a million RRIDs in the scientific literature?",
"year": 2022
},
{
"doi": "10.1371/journal.pcbi.1008967",
"pmc": "PMC8189493",
"pubmed": "34043624",
"title": "Antibody Watch: Text mining antibody specificity from the literature",
"year": 2021
},
{
"doi": "10.1002/cnr2.1150",
"pmc": "PMC7941525",
"pubmed": "32721132",
"title": "Improving transparency and scientific rigor in academic publishing",
"year": 2018
},
{
"doi": "10.7554/elife.41676",
"pmc": "PMC6351100",
"pubmed": "30693867",
"title": "Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines",
"year": 2019
},
{
"doi": "10.1038/nmeth.3995",
"pmc": "PMC10335836",
"pubmed": "27595404",
"title": "A proposal for validation of antibodies",
"year": 2016
},
{
"doi": "10.1016/j.neuron.2016.04.030",
"pmc": "PMC5854161",
"pubmed": "27151636",
"title": "RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods",
"year": 2016
},
{
"doi": "10.1002/cne.23913",
"pmc": "PMC4684178",
"pubmed": "26599696",
"title": "The Resource Identification Initiative: A Cultural Shift in Publishing",
"year": 2016
},
{
"doi": "10.12688/f1000research.6555.2",
"pmc": "PMC4648211",
"pubmed": "26594330",
"title": "The Resource Identification Initiative: A cultural shift in publishing",
"year": 2015
},
{
"doi": "10.7717/peerj.148",
"pmc": "PMC3771067",
"pubmed": "24032093",
"title": "On the reproducibility of science: unique identification of research resources in the biomedical literature",
"year": 2013
}
]
},
"rrrc": {
"description": "Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models. [from RRID]",
"example": "961",
"mappings": {
"rrid": "RRRC"
},
"pattern": "^\\d+$",
"rrid": {
"abbreviation": "NRRRC, RRRC, NCRR RRRC",
"homepage": "http://www.rrrc.us/",
"keywords": [
"animal",
"biomedical",
"catalog",
"cell line",
"cryopreserved",
"database",
"disease",
"drug",
"embryo",
"embryonic stem cell",
"gamete",
"genome",
"genotyping",
"germplasma",
"human",
"hybrid",
"inbred",
"infectious",
"molecular",
"mutant",
"nuclear",
"ovarian",
"pathogen",
"protocol",
"rat",
"rat model",
"reagent",
"research",
"stem cell",
"strain",
"tissue"
],
"name": "Rat Resource and Research Center",
"prefix": "RRRC",
"scr": "002044"
},
"uri_format": "https://www.rrrc.us/Strain/?x=$1"
},
"rs": {
"aberowl": {
"description": "Ontology of rat strains",
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"homepage": "http://rgd.mcw.edu/rgdweb/search/strains.html",
"name": "Rat Strain Ontology",
"prefix": "RS"
},
"biocontext": {
"prefix": "RS"
},
"bioportal": {
"contact": {
"email": "akwitek@mcw.edu",
"name": "Anne Kwitek"
},
"description": "This ontology defines the hierarchical display of the different rat strains as derived from the parental strains",
"homepage": "http://rgd.mcw.edu/rgdweb/search/strains.html",
"name": "Rat Strain Ontology",
"prefix": "RS",
"publication": "http://www.ncbi.nlm.nih.gov/pubmed/23603846",
"version": "6.229"
},
"download_obo": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.obo",
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"example": "0001807",
"fairsharing": {
"abbreviation": "RS",
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"domains": [
"Mutation",
"Genetic strain"
],
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457",
"name": "Rat Strain Ontology",
"prefix": "FAIRsharing.vajn3f",
"publications": [
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"pubmed": "23603846",
"title": "PhenoMiner: quantitative phenotype curation at the rat genome database",
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},
{
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}
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"subjects": [
"Life Science"
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"prefixcommons": "rs"
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"contact.github": "shurjenw",
"contact.label": "Shur-Jen Wang",
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"domain": "organisms",
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"homepage": "http://rgd.mcw.edu/rgdweb/search/strains.html",
"license": "CC BY 4.0",
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"logo": "http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif",
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"preferredPrefix": "RS",
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{
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"title": "Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD."
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],
"repository": "https://github.com/rat-genome-database/RS-Rat-Strain-Ontology"
},
"ols": {
"description": "Ontology of rat strains",
"download_owl": "http://purl.obolibrary.org/obo/rs.owl",
"homepage": "http://rgd.mcw.edu/rgdweb/search/strains.html",
"name": "Rat Strain Ontology",
"prefix": "rs",
"version": "6.229",
"version.iri": "http://purl.obolibrary.org/obo/rs/6.229/rs.owl"
},
"ontobee": {
"library": "Library",
"name": "Rat Strain Ontology",
"prefix": "RS"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1150",
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"keywords": [
"obo"
],
"name": "Rat Strain Ontology",
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"prefix": "rs"
},
"publications": [
{
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"pmc": "PMC4177145",
"pubmed": "24267899",
"title": "Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD",
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{
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"title": "PhenoMiner: quantitative phenotype curation at the rat genome database",
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],
"twitter": "ratgenome",
"uri_format": "http://purl.obolibrary.org/obo/RS_$1"
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"description": "Identifier used by the RTECS database (http://www.cdc.gov/niosh/rtecs/).",
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"obsolete": false,
"prefix": "000566"
},
"contact": {
"email": "vep1@cdc.gov",
"name": "Vernon Putz-Anderson",
"orcid": "0000-0002-3588-3259"
},
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "RTECS is a compendium of data extracted from the open scientific literature. The data are recorded in the format developed by the RTECS staff and arranged in alphabetical order by prime chemical name. Six types of toxicity data are included in the file: (1) primary irritation; (2) mutagenic effects; (3) reproductive effects; (4) tumorigenic effects; (5) acute toxicity; and (6) other multiple dose toxicity. Specific numeric toxicity values such as LD50, LC50, TDLo, and TCLo are noted as well as species studied and route of administration used. For each citation, the bibliographic source is listed thereby enabling the user to access the actual studies cited. No attempt has been made to evaluate the studies cited in RTECS. The user has the responsibility of making such assessments.",
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"homepage": "https://www.cdc.gov/niosh/rtecs/",
"mappings": {
"cheminf": "000566"
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"name": "Registry of Toxic Effects of Chemical Substances",
"pattern": "^AB\\d+$",
"proprietary": true,
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{
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"year": 1999
}
],
"references": [
"https://www.cdc.gov/niosh/docs/97-119/pdfs/97-119.pdf",
"https://www.cdc.gov/niosh/npg/npgdrtec.html"
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},
"rubygems": {
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"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
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"example": "bel",
"homepage": "https://rubygems.org",
"name": "RubyGems",
"uri_format": "https://rubygems.org/gems/$1"
},
"runbiosimulations": {
"mappings": {
"miriam": "runbiosimulations"
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"miriam": {
"deprecated": false,
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"homepage": "https://icahn.mssm.edu/",
"id": "00000897",
"name": "runBioSimulations",
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"pattern": "[0-9a-z]{24,24}",
"prefix": "runbiosimulations",
"sampleId": "5fde96bdc5f1aa9ff0cce18a",
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},
"rxno": {
"aberowl": {
"description": "Connects organic name reactions to their roles in an organic synthesis and to processes in MOP",
"download_owl": "http://aber-owl.net/media/ontologies/RXNO/40/rxno.owl",
"homepage": "https://github.com/rsc-ontologies/rxno",
"name": "Name Reaction Ontology",
"prefix": "RXNO"
},
"biocontext": {
"prefix": "RXNO"
},
"bioportal": {
"contact": {
"email": "batchelorc@rsc.org",
"name": "Colin Batchelor"
},
"description": "RXNO, the name reaction ontology, connects organic name reactions such as the Diels-Alder cyclization and the Cannizzaro reaction to their roles in an organic synthesis.",
"homepage": "https://code.google.com/p/rxno/",
"name": "Name Reaction Ontology",
"prefix": "RXNO",
"version": "releases/2021-12-16"
},
"download_obo": "https://github.com/rsc-ontologies/rxno/raw/master/rxno.obo",
"example": "0000253",
"fairsharing": {
"abbreviation": "RXNO",
"description": "The Name Reaction Ontology (RXNO) connects organic name reactions such as the Diels-Alder cyclization and the Cannizzaro reaction to their roles in organic synthesis.",
"domains": [
"Reaction data"
],
"homepage": "https://github.com/rsc-ontologies/rxno/",
"license": "CC-BY-4.0",
"name": "Name Reaction Ontology",
"prefix": "FAIRsharing.w4tncg",
"subjects": [
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},
"mappings": {
"aberowl": "RXNO",
"biocontext": "RXNO",
"bioportal": "RXNO",
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"obofoundry": "rxno",
"ols": "rxno",
"ontobee": "RXNO",
"wikidata": "P2106"
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"contact.github": "batchelorc",
"contact.label": "Colin Batchelor",
"contact.orcid": "0000-0001-5985-7429",
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"description": "Connects organic name reactions to their roles in an organic synthesis and to processes in MOP",
"domain": "chemistry and biochemistry",
"download.owl": "http://purl.obolibrary.org/obo/rxno.owl",
"homepage": "https://github.com/rsc-ontologies/rxno",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Name Reaction Ontology",
"preferredPrefix": "RXNO",
"prefix": "rxno",
"repository": "https://github.com/rsc-ontologies/rxno"
},
"ols": {
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"description": "RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the DielsβAlder cyclization.",
"download_owl": "http://purl.obolibrary.org/obo/rxno.owl",
"homepage": "https://github.com/rsc-ontologies/rxno",
"name": "RXNO",
"prefix": "rxno",
"version": "2021-12-16",
"version.iri": "http://purl.obolibrary.org/obo/rxno/releases/2021-12-16/rxno.owl"
},
"ontobee": {
"library": "Library",
"name": "Name Reaction Ontology",
"prefix": "RXNO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/RXNO_$1",
"wikidata": {
"description": "RSC ontology for organic reactions",
"example": [
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"RXNO:0000135",
"RXNO:0000233"
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"homepage": "https://github.com/rsc-ontologies/rxno",
"name": "RXNO Ontology",
"prefix": "P2106",
"uri_format": "http://www.rsc.org/publishing/journals/prospect/ontology.asp?id=$1"
}
},
"rxnorm": {
"aberowl": {
"description": "RxNorm Vocabulary",
"name": "RxNORM",
"prefix": "RXNORM",
"version": "2016AB"
},
"biocontext": {
"prefix": "RXCUI",
"uri_format": "http://purl.bioontology.org/ontology/RXNORM/$1"
},
"biolink": {
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"is_obo": false,
"prefix": "RXNORM",
"uri_format": "http://purl.bioontology.org/ontology/RXNORM/$1"
},
"bioportal": {
"contact": {
"email": "custserv@nlm.nih.gov",
"name": "NLM Customer Service"
},
"description": "RxNorm Vocabulary",
"name": "RxNORM",
"prefix": "RXNORM",
"version": "2023AB"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary.",
"example": "221058",
"fairsharing": {
"abbreviation": "RxNORM",
"description": "RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, MediSpan, Gold Standard Drug Database, and Multum. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary. RxNorm now includes the National Drug File - Reference Terminology (NDF-RT) from the Veterans Health Administration. NDF-RT is a terminology used to code clinical drug properties, including mechanism of action, physiologic effect, and therapeutic category.",
"domains": [
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"Drug"
],
"homepage": "https://www.nlm.nih.gov/research/umls/rxnorm/",
"name": "RxNORM",
"prefix": "FAIRsharing.36pf8q",
"publications": [
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"title": "RxTerms - a drug interface terminology derived from RxNorm",
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{
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},
{
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"title": "RxNorm: prescription for electronic drug information exchange",
"year": 2005
}
],
"subjects": [
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"Preclinical Studies"
]
},
"hl7": {
"description": "RxNorm provides standard names for clinical drugs (active ingredient + strength + dose form) and for dose forms as administered to a patient. It provides links from clinical drugs, both branded and generic, to their active ingredients, drug components (active ingredient + strength), and related brand names. NDCs (National Drug Codes) for specific drug products (where there are often many NDC codes for a single product) are linked to that product in RxNorm. RxNorm links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, MediSpan, and Multum. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary.RxNorm is one of a suite of designated standards for use in U.S. Federal Government systems for the electronic exchange of clinical health information.",
"homepage": "http://www.nlm.nih.gov/",
"name": "RxNorm",
"organization": "National Library of Medicine",
"preferred_prefix": "rxNorm",
"prefix": "2.16.840.1.113883.6.88",
"status": "Complete"
},
"homepage": "https://www.nlm.nih.gov/research/umls/rxnorm/",
"license": "https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf",
"mappings": {
"aberowl": "RXNORM",
"biocontext": "RXCUI",
"biolink": "RXNORM",
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"wikidata": "P3345"
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"name": "RxNorm",
"pattern": "^[0-9]{1,7}$",
"providers": [
{
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"name": "BioPortal",
"uri_format": "http://purl.bioontology.org/ontology/RXNORM/$1"
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],
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"title": "Normalized names for clinical drugs: RxNorm at 6 years",
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},
{
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"pubmed": "18998891",
"title": "RxTerms - a drug interface terminology derived from RxNorm",
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},
{
"doi": "10.1109/mitp.2005.122",
"title": "RxNorm: prescription for electronic drug information exchange",
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"synonyms": [
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}
},
"s_mart_db": {
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"description": "S/MARt DB is a database of cellular scaffolds and matrix data. The database contains scaffold, matrix, and nuclear matrix information from species ranging from yeast to humans. genes with experimentally identified interactions with scaffold and matrix components are available in tabular or searchable formats.",
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"information_keywords": [
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],
"maintainer": "Gesellschaft fur Biotechnologische Forschung",
"name": "S/MARt DB",
"prefix": "nbdc00674",
"pubmeds": [
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],
"status": "Active",
"target_keywords": [
"DNA",
"Protein"
]
},
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"prefixcommons": "s_mart_db"
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"pathguide": {
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"homepage": "http://smartdb.bioinf.med.uni-goettingen.de/",
"name": "The S/MAR transaction DataBase",
"prefix": "47"
},
"prefixcommons": {
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"example": "SM0000020",
"homepage": "http://smartdb.bioinf.med.uni-goettingen.de/",
"keywords": [
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],
"name": "The S/MAR transaction DataBase",
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"prefix": "s_mart_db",
"synonyms": [
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],
"uri_format": "http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi?$1"
},
"reviewer": {
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"github": "cthoyt",
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"homepage": "http://sabiork.h-its.org/",
"id": "00000688",
"name": "SABIO-RK Compound",
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"pattern": "^\\d+$",
"prefix": "sabiork.compound",
"sampleId": "75",
"uri_format": "http://sabiork.h-its.org/newSearch?q=$1"
},
"n2t": {
"description": "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information.",
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"name": "SABIO-RK Compound",
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"prefix": "sabiork.compound",
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}
},
"sabiork.ec": {
"biocontext": {
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},
"contact": {
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"name": "Ulrike Wittig",
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},
"mappings": {
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"description": "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data.",
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"description": "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data.",
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"name": "SABIO-RK Reaction Kinetics Database - Enzyme Classification (EC)",
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"name": "SABIO-RK EC Record",
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},
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"description": "The SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.",
"homepage": "http://sabio.villa-bosch.de/",
"name": "SABIO Reaction Kinetics",
"prefix": "SABIO-RK",
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"prefixcommons": "sabiork.kinetic"
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"miriam": {
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"description": "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information.",
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},
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"description": "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information.",
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"classification",
"enzyme",
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],
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"17822389"
],
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"sabiok",
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},
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{
"pubmed": "17822389",
"title": "Storing and annotating of kinetic data",
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}
]
},
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"email": "ulrike.wittig@h-its.org",
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},
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"description": "Identifier of a biological reaction from the SABIO-RK reactions database.",
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},
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"license": "http://opendatacommons.org/licenses/pddl/1.0",
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{
"doi": "10.1093/nar/gkr1046",
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],
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"Biochemistry",
"Life Science"
]
},
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"BioPAX",
"SBML"
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"description": "The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information.",
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],
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],
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},
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{
"doi": "10.1093/nar/gkr1046",
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}
],
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}
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},
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
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},
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{
"doi": "10.1002/cfg.434",
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}
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},
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],
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
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},
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"download_owl": "http://aber-owl.net/media/ontologies/SALMON/2/salmon.owl",
"homepage": "https://github.com/DataONEorg/sem-prov-ontologies/",
"name": "Salmon Ontology",
"prefix": "SALMON",
"version": "0.3.1"
},
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"contact": {
"email": "jones@nceas.ucsb.edu",
"name": "Matthew Jones"
},
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"homepage": "https://github.com/DataONEorg/sem-prov-ontologies/",
"name": "Salmon Ontology",
"prefix": "SALMON",
"version": "0.3.2"
},
"contact": {
"email": "brycemecum@gmail.com",
"github": "amoeba",
"name": "Bryce Mecum",
"orcid": "0000-0002-0381-3766"
},
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"bioportal": "SALMON"
},
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},
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"homepage": "http://ccdb.ucsd.edu/SAO",
"name": "Subcellular Anatomy Ontology",
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"version": "Version 1.2"
},
"biocontext": {
"prefix": "SAO"
},
"bioportal": {
"contact": {
"email": "mmartone@ucsd.edu",
"name": "Maryann Martone"
},
"description": "SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules.",
"name": "Subcellular Anatomy Ontology",
"prefix": "SAO",
"version": "Version 1.2"
},
"example": "5277619",
"mappings": {
"aberowl": "SAO",
"biocontext": "SAO",
"bioportal": "SAO",
"obofoundry": "sao",
"prefixcommons": "sao"
},
"name": "Subcellular Anatomy Ontology",
"obofoundry": {
"contact": "slarson@ncmir.ucsd.edu",
"contact.label": "Stephen Larson",
"deprecated": true,
"domain": "anatomy and development",
"homepage": "http://ccdb.ucsd.edu/CCDBWebSite/sao.html",
"name": "Subcellular anatomy ontology",
"prefix": "sao"
},
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"prefixcommons": {
"bioportal": "1068",
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"homepage": "http://ccdb.ucsd.edu/SAO",
"keywords": [
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"biochemistry"
],
"name": "Subcellular Anatomy Ontology (SAO)",
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"prefix": "sao",
"rdf_uri_format": "http://ccdb.ucsd.edu/SAO/1.2#$1",
"synonyms": [
"sao:"
]
},
"references": [
"http://www.ontobee.org/ontology/SAO"
],
"uri_format": "http://uri.neuinfo.org/nif/nifstd/sao$1"
},
"sasap": {
"aberowl": {
"description": "An ontology which represents information about the State of Alaska's Salmon and People (SASAP) project, as well as knowledge about salmon, features of their habitats, salmon stakeholders, and related entities.",
"download_owl": "http://aber-owl.net/media/ontologies/SASAP/2/sasap.owl",
"homepage": "https://github.com/DataONEorg/sem-prov-ontologies",
"name": "The State of Alaska's Salmon and People Ontology",
"prefix": "SASAP",
"version": "0.1.1"
},
"bioportal": {
"contact": {
"email": "mecum@nceas.ucsb.edu",
"name": "Bryce Mecum"
},
"description": "An ontology which represents information about the State of Alaska's Salmon and People (SASAP) project, as well as knowledge about salmon, features of their habitats, salmon stakeholders, and related entities.",
"homepage": "https://github.com/DataONEorg/sem-prov-ontologies",
"name": "The State of Alaska's Salmon and People Ontology",
"prefix": "SASAP",
"version": "0.3.1"
},
"contact": {
"email": "brycemecum@gmail.com",
"github": "amoeba",
"name": "Bryce Mecum",
"orcid": "0000-0002-0381-3766"
},
"example": "00000101",
"mappings": {
"aberowl": "SASAP",
"bioportal": "SASAP"
},
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"uri_format": "https://purl.dataone.org/odo/SASAP_$1"
},
"sasbdb": {
"biocontext": {
"prefix": "SASBDB"
},
"fairsharing": {
"abbreviation": "SASBDB",
"contact": {
"email": "a.kikhney@embl-hamburg.de",
"name": "Al Kikhney",
"orcid": "0000-0003-1321-3956"
},
"description": "Curated repository for small angle scattering data and models. SASBDB contains X-ray (SAXS) and neutron (SANS) scattering data from biological macromolecules in solution.",
"homepage": "https://www.sasbdb.org/",
"name": "Small angle scattering biological data bank",
"prefix": "FAIRsharing.i1F3Hb",
"publications": [
{
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"pubmed_id": 25352555,
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}
],
"subjects": [
"Molecular biology",
"Life Science"
]
},
"mappings": {
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"fairsharing": "FAIRsharing.i1F3Hb",
"miriam": "sasbdb",
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"re3data": "r3d100012273",
"uniprot": "DB-0258"
},
"miriam": {
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"description": "Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data.",
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"id": "00000572",
"name": "SASBDB",
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"prefix": "sasbdb",
"sampleId": "SASDAX8",
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},
"n2t": {
"description": "Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data.",
"example": "SASDAX8",
"homepage": "http://www.sasbdb.org/",
"name": "SASBDB at European Molecular Biology Laboratory",
"namespaceEmbeddedInLui": false,
"pattern": "^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$",
"prefix": "sasbdb",
"uri_format": "http://www.sasbdb.org/data/$1"
},
"name": "Small Angle Scattering Biological Data Bank",
"publications": [
{
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"pmc": "PMC6933840",
"pubmed": "31576635",
"title": "SASBDB: Towards an automatically curated and validated repository for biological scattering data",
"year": 2019
},
{
"doi": "10.1093/nar/gku1047",
"pmc": "PMC4383894",
"pubmed": "25352555",
"title": "SASBDB, a repository for biological small-angle scattering data",
"year": 2014
}
],
"re3data": {
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"name": "SASBDB",
"prefix": "r3d100012273",
"synonyms": [
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],
"xrefs": {
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}
},
"uniprot": {
"abbreviation": "SASBDB",
"category": "3D structure databases",
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"name": "Small Angle Scattering Biological Data Bank",
"prefix": "DB-0258",
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{
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"pubmed": "31576635"
}
],
"uri_format": "https://www.sasbdb.org/uniprot/$1/"
}
},
"sbo": {
"aberowl": {
"description": "Terms commonly used in Systems Biology, and in particular in computational modeling.",
"download_owl": "http://aber-owl.net/media/ontologies/SBO/816/sbo.owl",
"homepage": "http://www.ebi.ac.uk/sbo/",
"name": "Systems Biology Ontology",
"prefix": "SBO"
},
"biocontext": {
"prefix": "SBO"
},
"bioportal": {
"contact": {
"email": "sheriff@ebi.ac.uk",
"name": "Rahuman Sheriff"
},
"description": "The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. The ontology consists of six orthogonal vocabularies defining: the roles of reaction participants (eg. \"substrate\"), quantitative parameters (eg. \"Michaelis constant\"), a precise classification of mathematical expressions that describe the system (eg. \"mass action rate law\"), the modeling framework used (eg. \"logical framework\"), and a branch each to describe entity (eg. \"macromolecule\") and interaction (eg. \"process\") types, and a branch to define the different types of metadata that may be present within a model. SBO terms can be used to introduce a layer of semantic information into the standard description of a model, or to annotate the results of biochemical experiments in order to facilitate their efficient reuse. SBO is an Open Biomedical Ontologies (OBO) candidate ontology, and is free for use. More information about SBO can be found from the project FAQ, at http://www.ebi.ac.uk/sbo/ SBO is a project of the BioModels.net effort and is developed through community collaboration.",
"homepage": "https://github.com/EBI-BioModels/SBO",
"name": "Systems Biology Ontology",
"prefix": "SBO",
"version": "28:08:2021 03:13"
},
"download_obo": "http://purl.obolibrary.org/obo/sbo.obo",
"example": "0000485",
"fairsharing": {
"abbreviation": "SBO",
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"domains": [
"Mathematical model",
"Modeling and simulation",
"Molecular interaction",
"Pathway model"
],
"homepage": "http://www.ebi.ac.uk/sbo/",
"name": "Systems Biology Ontology",
"prefix": "FAIRsharing.s19src",
"publications": [
{
"doi": "10.1038/msb.2011.77",
"pubmed": "22027554",
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}
],
"subjects": [
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],
"twitter": "biomodels"
},
"mappings": {
"aberowl": "SBO",
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"miriam": "sbo",
"n2t": "sbo",
"obofoundry": "sbo",
"ols": "sbo",
"ontobee": "SBO",
"prefixcommons": "sbo"
},
"miriam": {
"deprecated": false,
"description": "The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort.",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/sbo",
"id": "00000024",
"name": "Systems Biology Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^SBO:\\d{7}$",
"prefix": "sbo",
"sampleId": "0000262",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/sbo/terms?obo_id=SBO:$1"
},
"n2t": {
"description": "The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort.",
"example": "0000262",
"homepage": "https://www.ebi.ac.uk/sbo/",
"name": "SBO",
"namespaceEmbeddedInLui": true,
"pattern": "^SBO:\\d{7}$",
"prefix": "sbo",
"uri_format": "https://www.ebi.ac.uk/sbo/main/SBO:$1"
},
"obofoundry": {
"appears_in": [
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"scdo"
],
"contact": "sheriff@ebi.ac.uk",
"contact.github": "rsmsheriff",
"contact.label": "Rahuman Sheriff",
"contact.orcid": "0000-0003-0705-9809",
"deprecated": false,
"description": "Terms commonly used in Systems Biology, and in particular in computational modeling.",
"domain": "chemistry and biochemistry",
"download.owl": "http://purl.obolibrary.org/obo/sbo.owl",
"homepage": "http://www.ebi.ac.uk/sbo/",
"license": "Artistic License 2.0",
"license.url": "http://opensource.org/licenses/Artistic-2.0",
"name": "Systems Biology Ontology",
"preferredPrefix": "SBO",
"prefix": "sbo",
"repository": "https://github.com/EBI-BioModels/SBO"
},
"ols": {
"description": "Terms commonly used in Systems Biology, and in particular in computational modeling.",
"download_owl": "http://purl.obolibrary.org/obo/sbo.owl",
"homepage": "http://www.ebi.ac.uk/sbo/",
"name": "Systems Biology Ontology",
"prefix": "sbo",
"version": "2021-08-28"
},
"ontobee": {
"library": "Library",
"name": "Systems Biology Ontology",
"prefix": "SBO"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"alt_uri_formats": [
"http://purl.org/obo/owl/SBO#$1"
],
"bioportal": "1046",
"description": "The Systems Biology Ontology is a set of controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modelling.",
"example": "SBO:0000262",
"homepage": "http://www.ebi.ac.uk/sbo/",
"keywords": [
"obo",
"systems biology"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Systems Biology Ontology",
"pattern": "^SBO:\\d{7}$",
"prefix": "sbo",
"pubmed_ids": [
"17118155"
],
"synonyms": [
"biomodels.sbo",
"Systems_Biology_Ontology"
],
"uri_format": "http://www.ebi.ac.uk/sbo/main/$1"
},
"providers": [
{
"code": "biomodels",
"description": "Provider for SBO at BioModels",
"homepage": "http://biomodels.net",
"name": "BioModels",
"uri_format": "http://biomodels.net/SBO/SBO_$1"
}
],
"publications": [
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"pmc": "PMC3261705",
"pubmed": "22027554",
"title": "Controlled vocabularies and semantics in systems biology",
"year": 2011
},
{
"doi": "10.1186/1471-2202-7-s1-s11",
"pmc": "PMC1775041",
"pubmed": "17118155",
"title": "Model storage, exchange and integration",
"year": 2006
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"name": "Scopus EID",
"pattern": "^2-s2\\.0-\\d+$",
"prefix": "P1154",
"uri_format": "http://www.scopus.com/record/display.url?origin=inward&eid=$1"
}
},
"scoro": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator).",
"example": "IntellectualContribution",
"fairsharing": {
"abbreviation": "SCoRO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Scholarly Contributions and Roles Ontology (SCoRO) is an ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator)",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/scoro",
"license": "CC-BY-4.0",
"name": "Scholarly Contributions and Roles Ontology ",
"prefix": "FAIRsharing.c86b48",
"publications": [
{
"doi": "10.3233/sw-150177",
"title": "The Document Components Ontology (DoCO)",
"year": 2016
}
],
"repository": "https://github.com/sparontologies/deo",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"homepage": "http://www.sparontologies.net/ontologies/scoro",
"lov": {
"description": "SCoRO, the Scholarly Contributions and Roles Ontology, is an ontology for use by authors and publishers for describing the contributions that may be made and the roles that may be held by a person with respect to a journal article or other publication, and by research administrators and others for describing contributions and roles with respect to other aspects of scholarly research.",
"homepage": "https://sparontologies.github.io/scoro/current/scoro.html",
"keywords": [
"Academy"
],
"modified": "2017-09-04",
"name": "Scholarly Contributions and Roles Ontology",
"prefix": "scoro",
"uri_prefix": "http://purl.org/spar/scoro/$1"
},
"mappings": {
"fairsharing": "FAIRsharing.c86b48",
"lov": "scoro"
},
"name": "Scholarly Contributions and Roles Ontology",
"preferred_prefix": "SCoRO",
"publications": [
{
"doi": "10.3233/sw-150177",
"title": "TheΒ DocumentΒ ComponentsΒ OntologyΒ (DoCO)",
"year": 2016
}
],
"repository": "https://github.com/sparontologies/scoro",
"uri_format": "http://purl.org/spar/scoro/$1"
},
"scpd": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"mappings": {
"pathguide": "130",
"prefixcommons": "scpd"
},
"pathguide": {
"abbreviation": "SCPD",
"homepage": "http://rulai.cshl.edu/SCPD/",
"name": "The Promoter Database of Saccharomyces cerevisiae",
"prefix": "130"
},
"prefixcommons": {
"description": "Database containing promotor sequences found in Saccharomyces cerevisiae.",
"example": "CDC2",
"homepage": "http://rulai.cshl.edu/SCPD/",
"keywords": [
"DNA",
"RNA"
],
"name": "Saccharomyces cerevisiae promoter database",
"pattern": "^[A-Z.0-9]+$",
"prefix": "scpd",
"uri_format": "http://rulai.cshl.edu/cgi-bin/SCPD/getgene2?$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"scr": {
"contact": {
"email": "abandrowski@ncmir.ucsd.edu",
"name": "Anita Bandrowski",
"orcid": "0000-0002-5497-0243"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources.",
"example": "022586",
"fairsharing": {
"abbreviation": "SciCrunch",
"description": "The SciCrunch Data Dashboard is a data sharing and display platform that pulls information from primary data repositories. Anyone can create a custom portal where they can select searchable subsets of hundreds of data sources, brand their web pages and create their community. SciCrunch will push data updates automatically to all portals on a weekly basis. SciCrunch resource registry is the new name of the NIF registry. ",
"homepage": "https://scicrunch.org/browse/datadashboard",
"name": "SciCrunch Data Dashboard",
"prefix": "FAIRsharing.kj4pvk",
"publications": [
{
"doi": "10.1002/cne.23913",
"pubmed_id": 26599696,
"title": "The Resource Identification Initiative: A Cultural Shift in Publishing."
}
],
"subjects": [
"Neurobiology",
"Life Science"
]
},
"github_request_issue": 421,
"homepage": "https://scicrunch.org/browse/resourcedashboard",
"integbio": {
"description": "SciCrunch resource registry is the new name of the NIF registry. SciCrunch is a data sharing and display platform. Anyone can create a custom portal where they can select searchable subsets of hundreds of data sources, brand their web pages and create their community. SciCrunch will push data updates automatically to all portals on a weekly basis.",
"fairsharing": "FAIRsharing.kj4pvk",
"homepage": "https://scicrunch.org",
"information_keywords": [
"Portal",
"Repository"
],
"name": "SciCrunch",
"prefix": "nbdc01937",
"pubmeds": [
"26599696"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"Health/Disease"
]
},
"mappings": {
"fairsharing": "FAIRsharing.kj4pvk",
"integbio": "nbdc01937",
"rrid": "SCR"
},
"name": "SciCrunch Registry",
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1002/cne.23913",
"pmc": "PMC4684178",
"pubmed": "26599696",
"title": "The Resource Identification Initiative: A Cultural Shift in Publishing",
"year": 2016
}
],
"rrid": {
"homepage": "https://scicrunch.org/scicrunch/about/sources/nlx_144509-1",
"keywords": [
"interactive portal",
"nih initiative",
"rrid"
],
"name": "SciCrunch Registry",
"prefix": "SCR",
"pubmeds": [
"22434839"
],
"scr": "005400"
},
"synonyms": [
"scicrunch"
],
"uri_format": "http://scicrunch.org/resolver/SCR_$1"
},
"scretf": {
"biocontext": {
"prefix": "SCRETF"
},
"mappings": {
"biocontext": "SCRETF",
"miriam": "scretf",
"n2t": "scretf"
},
"miriam": {
"deprecated": false,
"description": "ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor.",
"homepage": "http://stormo.wustl.edu/ScerTF/",
"id": "00000244",
"name": "ScerTF",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "scretf",
"sampleId": "RSC3",
"uri_format": "http://stormo.wustl.edu/ScerTF/details/$1/"
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"n2t": {
"description": "ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor.",
"example": "RSC3",
"homepage": "http://stormo.wustl.edu/ScerTF/",
"name": "ScerTF at Washington University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "scretf",
"uri_format": "http://stormo.wustl.edu/ScerTF/details/$1/"
},
"uri_format": "http://stormo.wustl.edu/ScerTF/details/$1"
},
"sdap": {
"mappings": {
"prefixcommons": "sdap"
},
"prefixcommons": {
"description": "SDAP is a Web server that integrates a database of allergenic proteins with various bioinformatics tools for performing structural studies related to allergens and characterization of their epitopes.",
"example": "610",
"homepage": "http://fermi.utmb.edu/SDAP",
"keywords": [
"protein",
"structure"
],
"name": "Structural Database of Allergenic Proteins",
"pattern": "^\\d+$",
"prefix": "sdap",
"uri_format": "http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"sdbs": {
"biocontext": {
"prefix": "SDBS"
},
"integbio": {
"alt_name": "Spectral Database for Organic Compounds",
"description": "The SDBS database consists of of sensory characteristics of vision, hearing, and touch measured by National Institute of Advanced Industrial Science and Technology. To allow searches for conditions such as age and types of disability, target people with disabilities and/or older people, totaling more than 3,000, were subjected to measurement. Their characteristics data were adopted as Japanese Industrial Standards (JISs) \"Guidelines for older persons and persons with disabilities\".",
"homepage": "http://sdbs.db.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi",
"information_keywords": [
"Chemical structure"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "SDBS",
"prefix": "nbdc01520",
"status": "Inactive",
"target_keywords": [
"Chemical compound"
]
},
"mappings": {
"biocontext": "SDBS",
"integbio": "nbdc01520",
"miriam": "sdbs",
"n2t": "sdbs"
},
"miriam": {
"deprecated": false,
"description": "The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra.",
"homepage": "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi",
"id": "00000319",
"name": "Spectral Database for Organic Compounds",
"namespaceEmbeddedInLui": false,
"pattern": "\\d+$",
"prefix": "sdbs",
"sampleId": "4544",
"uri_format": "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1"
},
"n2t": {
"description": "The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra.",
"example": "4544",
"homepage": "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi",
"name": "SDBS at AIST",
"namespaceEmbeddedInLui": false,
"pattern": "\\d+$",
"prefix": "sdbs",
"uri_format": "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1"
}
},
"sdgio": {
"agroportal": {
"contact": {
"email": "pier.buttigieg@awi.de",
"name": "Pier Luigi Buttigieg (ORCID: orcid.org/0000-0002-4366-3088)"
},
"description": "The SDGIO aims to provide a semantic bridge between 1) the Sustainable Development Goals, their targets, and indicators and 2) the large array of entities they refer to. It will import classes from numerous exisitng ontologies and map to vocabularies such as GEMET to promote interoperability. New classes will be minted and defined where no external class exists.",
"example_uri": "http://purl.unep.org/sdg/SDGIO_00010073",
"homepage": "https://github.com/SDG-InterfaceOntology/sdgio",
"name": "Sustainable Development Goals Interface Ontology",
"prefix": "SDGIO",
"publication": "http://ceur-ws.org/Vol-1747/IT201_ICBO2016.pdf",
"repository": "https://github.com/SDG-InterfaceOntology",
"version": "2018-05-11"
},
"download_owl": "https://github.com/SDG-InterfaceOntology/sdgio/raw/master/sdgio.owl",
"example": "00020134",
"fairsharing": {
"abbreviation": "SDGIO",
"contact": {
"email": "pier.buttigieg@awi.de",
"name": "Pier Luigi Buttigieg",
"orcid": "0000-0002-4366-3088"
},
"description": "The Sustainable Development Goals Interface Ontology (SDGIO) aims to provide a semantic bridge between 1) the Sustainable Development Goals, their targets, and indicators and 2) the large array of entities they refer to. SDGIO will reuse existing ontologies where appropriate.",
"domains": [
"Sustainability"
],
"homepage": "https://github.com/SDG-InterfaceOntology/sdgio",
"name": "Sustainable Development Goals Interface Ontology",
"prefix": "FAIRsharing.d5ff6e",
"publications": [
{
"doi": "10.1186/s13326-016-0097-6",
"pubmed": "27664130",
"title": "The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation",
"year": 2016
}
],
"repository": "https://github.com/SDG-InterfaceOntology/sdgio/wiki",
"subjects": [
"Environmental Science"
]
},
"mappings": {
"agroportal": "SDGIO",
"fairsharing": "FAIRsharing.d5ff6e",
"ols": "sdgio",
"ontobee": "SDGIO"
},
"ols": {
"description": "An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators.",
"download_owl": "http://purl.unep.org/sdg/sdgio.owl",
"homepage": "https://github.com/SDG-InterfaceOntology/sdgio",
"name": "Sustainable Development Goals Interface Ontology",
"prefix": "sdgio",
"version.iri": "http://purl.unep.org/sdg/releases/2018-08-10/sdgio.owl"
},
"ontobee": {
"library": "Not Specified/No",
"name": "Sustainable Development Goals Interface Ontology",
"prefix": "SDGIO"
},
"pattern": "^\\d{8}$",
"publications": [
{
"doi": "10.1186/s13326-016-0097-6",
"pmc": "PMC5035502",
"pubmed": "27664130",
"title": "The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation",
"year": 2016
}
],
"references": [
"https://github.com/SDG-InterfaceOntology/sdgio/issues/233"
],
"repository": "https://github.com/SDG-InterfaceOntology/sdgio",
"uri_format": "http://purl.unep.org/sdg/SDGIO_$1"
},
"sdis": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Selventa legacy disease namespace used with the Biological Expression Language",
"example": "D0001",
"homepage": "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-diseases.txt",
"keywords": [
"bel",
"diseases",
"selventa"
],
"license": "Apache-2.0",
"name": "Selventa Diseases",
"pattern": "^D\\d{4}$",
"uri_format": "https://biopragmatics.github.io/providers/sdis/$1"
},
"sedml.format": {
"mappings": {
"miriam": "sedml.format"
},
"miriam": {
"deprecated": false,
"description": "Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).",
"homepage": "http://sed-ml.org/",
"id": "00000841",
"name": "SED-ML data format",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z]+(\\..*?)?$",
"prefix": "sedml.format",
"sampleId": "csv",
"uri_format": "https://sed-ml.org/urns.html#format:$1"
}
},
"sedml.language": {
"mappings": {
"miriam": "sedml.language"
},
"miriam": {
"deprecated": false,
"description": "Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).",
"homepage": "http://sed-ml.org/",
"id": "00000843",
"name": "SED-ML model format",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z]+(\\..*?)?$",
"prefix": "sedml.language",
"sampleId": "sbml.level-3.version-2",
"uri_format": "https://sed-ml.org/urns.html#language:$1"
}
},
"seed": {
"biocontext": {
"prefix": "SEED"
},
"fairsharing": {
"abbreviation": "SEED",
"description": "The Standard for the Exchange of Earthquake Data (SEED) is a data format intended primarily for the archival and exchange of seismological time series data and related metadata. The format is maintained by the International Federation of Digital Seismograph Networks (FDSN). Originally designed in the late 1980s, the format has been enhanced and refined a number of times and remains in widespread use.",
"homepage": "http://www.fdsn.org/pdf/SEEDManual_V2.4.pdf",
"name": "Standard for the Exchange of Earthquake Data",
"prefix": "FAIRsharing.68b03f",
"publications": [],
"subjects": [
"Earth Science"
]
},
"go": {
"description": "Project to annotate the first 1000 sequenced genomes, develop detailed metabolic reconstructions, and construct the corresponding stoichiometric matrices",
"homepage": "http://www.theseed.org",
"name": "The SEED;",
"prefix": "SEED",
"uri_format": "http://www.theseed.org/linkin.cgi?id=$1"
},
"mappings": {
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"fairsharing": "FAIRsharing.68b03f",
"go": "SEED",
"miriam": "seed",
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},
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"id": "00000552",
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"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "seed",
"sampleId": "Biotin_biosynthesis"
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"name": "SEED Subsystem at Argonne National Laboratory",
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"pattern": "^\\w+$",
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},
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"example": "fig|83331.1.peg.1",
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"name": "The SEED Database",
"prefix": "SEED"
}
},
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},
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"description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.",
"homepage": "http://modelseed.org/",
"id": "00000553",
"name": "SEED Compound",
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"prefix": "seed.compound",
"sampleId": "cpd15380",
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"description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.",
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"name": "SEED Compound at Argonne National Laboratory",
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},
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"prefix": "SEED.REACTION",
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},
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"homepage": "http://modelseed.org/biochem/reactions/",
"id": "00000692",
"name": "SEED Reactions",
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"pattern": "^rxn\\d+$",
"prefix": "seed.reaction",
"sampleId": "rxn00001",
"uri_format": "http://modelseed.org/biochem/reactions/$1"
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"description": "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions.",
"example": "rxn00001",
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"name": "SEED Reactions",
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"pattern": "^rxn\\d+$",
"prefix": "seed.reaction",
"uri_format": "http://modelseed.org/biochem/reactions/$1"
}
},
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"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A vocabulary about species to support the environmental research community in Arizona and New Mexico",
"example": "762",
"github_request_issue": 653,
"homepage": "https://swbiodiversity.org/seinet/index.php",
"mappings": {
"wikidata": "P6209"
},
"name": "Southwestern Environmental Information Network",
"pattern": "^\\d+$",
"reviewer": {
"github": "callahantiff",
"name": "Tiffany J. Callahan",
"orcid": "0000-0002-8169-9049"
},
"uri_format": "https://swbiodiversity.org/seinet/taxa/index.php?taxon=$1",
"wikidata": {
"description": "identifier for a species on the SEINet website",
"example": [
"1522",
"3314",
"762"
],
"homepage": "http://swbiodiversity.org/seinet/index.php",
"name": "SEINet ID",
"pattern": "^[1-9]\\d*$",
"prefix": "P6209",
"uri_format": "http://swbiodiversity.org/seinet/taxa/index.php?taxon=$1"
}
},
"semapv": {
"bartoc": {
"abbreviation": "semapv",
"description": "The Semantic Mapping Vocabulary provides and defines terms used for creating and maintaining semantic mappings, in particular mapping metadata.",
"homepage": "https://mapping-commons.github.io/semantic-mapping-vocabulary/",
"license": "CC0-1.0",
"name": "Semantic Mapping Vocabulary",
"prefix": "20428"
},
"contact": {
"email": "nicolas.matentzoglu@gmail.com",
"github": "matentzn",
"name": "Nicolas Matentzoglu",
"orcid": "0000-0002-7356-1779"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Semantic Mapping Vocabulary provides and defines terms used for creating and maintaining semantic mappings, in particular mapping metadata.",
"download_owl": "https://raw.githubusercontent.com/mapping-commons/semantic-mapping-vocabulary/main/semapv.owl",
"example": "LexicalMatching",
"homepage": "https://mapping-commons.github.io/semantic-mapping-vocabulary/",
"license": "CC0-1.0",
"mappings": {
"bartoc": "20428"
},
"name": "Semantic Mapping Vocabulary",
"owners": [
{
"name": "Semanticly",
"partnered": true,
"wikidata": "Q115518213"
}
],
"references": [
"https://github.com/biopragmatics/bioregistry/pull/714"
],
"uri_format": "https://w3id.org/semapv/vocab/$1"
},
"semion": {
"example": "22132778",
"mappings": {
"wikidata": "P7671"
},
"wikidata": {
"description": "identifier of an author or reviewer, in Semion",
"example": [
"1085144",
"17963667",
"2975999"
],
"homepage": "https://www.semion.io",
"name": "Semion author ID",
"pattern": "^\\d+$",
"prefix": "P7671",
"uri_format": "https://www.semion.io/Author/$1"
}
},
"senso": {
"aberowl": {
"description": "The SENSO ontology is designed to provide classification terms for labeling sensitive data for data archival and sharing.",
"download_owl": "http://aber-owl.net/media/ontologies/SENSO/1/senso.owl",
"homepage": "https://github.com/DataONEorg/sem-prov-ontologies",
"name": "Sensitive Data Ontology",
"prefix": "SENSO",
"version": "Version 0.1.0"
},
"bioportal": {
"contact": {
"email": "mecum@nceas.ucsb.edu",
"name": "Bryce Mecum"
},
"description": "The SENSO ontology is designed to provide classification terms for labeling sensitive data for data archival and sharing.",
"homepage": "https://github.com/DataONEorg/sem-prov-ontologies",
"name": "Sensitive Data Ontology",
"prefix": "SENSO",
"version": "Version 0.1.0"
},
"contact": {
"email": "brycemecum@gmail.com",
"github": "amoeba",
"name": "Bryce Mecum",
"orcid": "0000-0002-0381-3766"
},
"download_rdf": "https://ontologies.dataone.org/SENSO.ttl",
"example": "00000003",
"mappings": {
"aberowl": "SENSO",
"bioportal": "SENSO"
},
"pattern": "^\\d+$",
"uri_format": "http://purl.dataone.org/odo/SENSO_$1"
},
"seo": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "SEO is a reference ontology for modelling data about scientific events such as conferences, symposioums and workshops.",
"download_rdf": "https://raw.githubusercontent.com/saidfathalla/SEOontology/master/SEO.ttl",
"example": "Symposium",
"homepage": "https://w3id.org/seo",
"lov": {
"description": "The vocabulary allows for the description of data about scientific events such as conferences, symposiums and workshops.",
"homepage": "https://saidfathalla.github.io/SEOontology/Documentation/SEO.html",
"keywords": [
"Academy",
"Events"
],
"modified": "2019-04-10",
"name": "The Scientific Events Ontology",
"prefix": "seo",
"uri_prefix": "https://w3id.org/seo#$1"
},
"mappings": {
"lov": "seo"
},
"name": "Scientific Event Ontology",
"uri_format": "https://w3id.org/seo#$1"
},
"sep": {
"aberowl": {
"description": "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments, such as, and including, gel electrophoresis, column chromatography, capillary electrophoresis, centrifugation and so on. Developed jointly by the HUPO Proteomics Standards Initiative and The Metabolomics Standards Initiative.",
"download_obo": "http://aber-owl.net/media/ontologies/SEP/4/sep.obo",
"homepage": "http://psidev.info/index.php?q=node/312",
"name": "Sample Processing and Separation Techniques Ontology",
"prefix": "SEP",
"version": "1.070708"
},
"biocontext": {
"prefix": "SEP"
},
"bioportal": {
"contact": {
"email": "psidev-gps-dev@lists.sourceforge.net",
"name": "SEP developers"
},
"description": "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments, such as, and including, gel electrophoresis, column chromatography, capillary electrophoresis, centrifugation and so on. Developed jointly by the HUPO Proteomics Standards Initiative and The Metabolomics Standards Initiative.",
"homepage": "http://psidev.info/index.php?q=node/312",
"name": "Sample Processing and Separation Techniques Ontology",
"prefix": "SEP",
"version": "1.070708"
},
"download_obo": "https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo",
"example": "00073",
"homepage": "https://psidev.info/sepcv",
"mappings": {
"aberowl": "SEP",
"biocontext": "SEP",
"bioportal": "SEP",
"obofoundry": "sep",
"ontobee": "SEP",
"prefixcommons": "sep"
},
"obofoundry": {
"contact": "psidev-gps-dev@lists.sourceforge.net",
"contact.label": "SEP developers via the PSI and MSI mailing lists",
"deprecated": true,
"description": "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments.",
"domain": "investigations",
"download.owl": "http://purl.obolibrary.org/obo/sep.owl",
"homepage": "http://psidev.info/index.php?q=node/312",
"name": "Sample processing and separation techniques",
"prefix": "sep"
},
"ontobee": {
"library": "Library",
"name": "Sample processing and separation techniques",
"prefix": "SEP"
},
"pattern": "^\\d{5,6}$",
"prefixcommons": {
"bioportal": "1044",
"description": "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments, such as, and including, gel electrophoresis, column chromatography, capillary electrophoresis, centrifugation and so on. Developed jointly by the HUPO Proteomics Standards Initiative and The Metabolomics Standards Initiative.",
"example": "sep_00005",
"homepage": "http://psidev.info/index.php?q=node/312",
"keywords": [
"obo",
"protein"
],
"name": "Sample processing and separation techniques",
"pattern": "^sep_\\d+$",
"prefix": "sep"
}
},
"sepio": {
"aberowl": {
"description": "An ontology for representing the provenance of scientific claims and the evidence that supports them.",
"download_owl": "http://aber-owl.net/media/ontologies/SEPIO/4/sepio.owl",
"homepage": "https://github.com/monarch-initiative/SEPIO-ontology",
"name": "Scientific Evidence and Provenance Information Ontology",
"prefix": "SEPIO"
},
"biocontext": {
"prefix": "SEPIO"
},
"bioportal": {
"contact": {
"email": "mhb120@gmail.com",
"name": "Matthew Brush"
},
"description": "The Scientific Evidence and Provenance Information Ontology (SEPIO) was developed to support description of evidence and provenance information for scientific claims. The core model represents the relationships between claims, their evidence lines, the information items that comprise these lines of evidence, and the methods, tools, and agents involved in the creation of these entities. Use cases driving SEPIO development include integration of scientific claims and their associated evidence/provenance metadata, and support for the discovery, analysis, and evaluation of claims based on this metadata.",
"homepage": "https://github.com/monarch-initiative/SEPIO-ontology",
"name": "Scientific Evidence and Provenance Information Ontology",
"prefix": "SEPIO",
"version": "2023-06-13"
},
"example": "0000048",
"mappings": {
"aberowl": "SEPIO",
"biocontext": "SEPIO",
"bioportal": "SEPIO",
"obofoundry": "sepio",
"ols": "sepio",
"ontobee": "SEPIO"
},
"obofoundry": {
"contact": "mhb120@gmail.com",
"contact.github": "mbrush",
"contact.label": "Matthew Brush",
"contact.orcid": "0000-0002-1048-5019",
"deprecated": false,
"description": "An ontology for representing the provenance of scientific claims and the evidence that supports them.",
"domain": "investigations",
"download.owl": "http://purl.obolibrary.org/obo/sepio.owl",
"homepage": "https://github.com/monarch-initiative/SEPIO-ontology",
"license": "CC BY 3.0",
"license.url": "https://creativecommons.org/licenses/by/3.0/",
"logo": "https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/SEPIO-LOGOS/sepio_logo_black-banner.png",
"name": "Scientific Evidence and Provenance Information Ontology",
"preferredPrefix": "SEPIO",
"prefix": "sepio",
"repository": "https://github.com/monarch-initiative/SEPIO-ontology"
},
"ols": {
"description": "An ontology for representing the provenance of scientific claims and the evidence that supports them.",
"download_owl": "http://purl.obolibrary.org/obo/sepio.owl",
"homepage": "https://github.com/monarch-initiative/SEPIO-ontology",
"name": "Ontology for Scientific Evidence and Provenance Information",
"prefix": "sepio",
"version": "2023-06-13",
"version.iri": "http://purl.obolibrary.org/obo/sepio/releases/2023-06-13/sepio.owl"
},
"ontobee": {
"library": "Library",
"name": "Scientific Evidence and Provenance Information Ontology",
"prefix": "SEPIO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/SEPIO_$1"
},
"sfam": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Selventa legacy protein family namespace used with the Biological Expression Language",
"example": "F0001",
"homepage": "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-protein-families.txt",
"keywords": [
"bel",
"protein families",
"selventa"
],
"license": "Apache-2.0",
"name": "Selventa Families",
"pattern": "^F\\d{4}$",
"uri_format": "https://biopragmatics.github.io/providers/sfam/$1"
},
"sgd": {
"biocontext": {
"prefix": "SGD",
"uri_format": "https://www.yeastgenome.org/locus/$1"
},
"contact": {
"email": "cherry@genome.stanford.edu",
"name": "J. Michael Cherry",
"orcid": "0000-0001-9163-5180"
},
"edam": {
"description": "Identifier of an entry from the Saccharomyces genome database (SGD).",
"name": "SGD",
"obsolete": false,
"prefix": "2632"
},
"example": "S000002493",
"fairsharing": {
"abbreviation": "SGD",
"description": "The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms.",
"homepage": "http://www.yeastgenome.org/",
"license": "https://www.stanford.edu/site/terms",
"name": "Saccharomyces Genome Database",
"prefix": "FAIRsharing.pzvw40",
"publications": [
{
"doi": "10.1093/database/bau075",
"pubmed_id": 25052702,
"title": "Standardized description of scientific evidence using the Evidence Ontology (ECO)."
},
{
"doi": "10.1093/database/bat054",
"pubmed_id": 23842463,
"title": "A guide to best practices for Gene Ontology (GO) manual annotation."
},
{
"doi": "10.1093/database/bas001",
"pubmed_id": 22434836,
"title": "CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations."
},
{
"doi": "10.1093/nar/gkr1029",
"pubmed_id": 22110037,
"title": "Saccharomyces Genome Database: the genomics resource of budding yeast."
},
{
"doi": "10.1002/9780470089941.et1104s01",
"pubmed_id": null,
"title": "Using Model Organism Databases (MODs)."
},
{
"doi": "10.1093/database/bap001",
"pubmed_id": 20157474,
"title": "New mutant phenotype data curation system in the Saccharomyces Genome Database."
},
{
"doi": "10.1093/nar/gkl931",
"pubmed_id": 17142221,
"title": "Expanded protein information at SGD: new pages and proteome browser."
},
{
"doi": "10.1002/yea.1400",
"pubmed_id": 17001629,
"title": "Saccharomyces cerevisiae S288C genome annotation: a working hypothesis."
},
{
"doi": "10.1093/nar/gkj117",
"pubmed_id": 16381907,
"title": "Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome."
},
{
"doi": "10.1093/bib/5.1.9",
"pubmed_id": 15153302,
"title": "Saccharomyces genome database: underlying principles and organisation."
},
{
"doi": "10.1093/nar/gkt1158",
"pubmed_id": 24265222,
"title": "Saccharomyces Genome Database provides new regulation data."
},
{
"doi": "10.1534/g3.113.008995",
"pubmed_id": 24374639,
"title": "The reference genome sequence of Saccharomyces cerevisiae: then and now."
},
{
"doi": "10.1093/database/bat012",
"pubmed_id": 23487186,
"title": "The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database."
},
{
"doi": "10.1093/database/bat004",
"pubmed_id": 23396302,
"title": "The YeastGenome app: the Saccharomyces Genome Database at your fingertips."
},
{
"doi": "10.1093/database/bar062",
"pubmed_id": 22434830,
"title": "YeastMine - An integrated data warehouse for S. cerevisiae data as a multi-purpose tool-kit."
},
{
"doi": "10.1093/database/bar057",
"pubmed_id": 22434826,
"title": "Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report."
},
{
"doi": "10.1093/database/bar004",
"pubmed_id": 21411447,
"title": "Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study."
},
{
"doi": "10.1093/nar/gkp917",
"pubmed_id": 19906697,
"title": "Saccharomyces Genome Database provides mutant phenotype data."
},
{
"doi": "10.1016/j.tim.2009.04.005",
"pubmed_id": 19577472,
"title": "Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns."
},
{
"doi": "10.1093/nar/gkm909",
"pubmed_id": 17982175,
"title": "Gene Ontology annotations at SGD: new data sources and annotation methods."
},
{
"doi": "10.1093/nar/gki023",
"pubmed_id": 15608219,
"title": "Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD)."
},
{
"doi": "10.1093/nar/gkh033",
"pubmed_id": 14681421,
"title": "Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms."
},
{
"doi": "10.1093/database/baw020",
"pubmed_id": 26989152,
"title": "From one to many: expanding the Saccharomyces cerevisiae reference genome panel."
},
{
"doi": "10.1093/nar/gkg054",
"pubmed_id": 12519985,
"title": "Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins."
},
{
"doi": "10.1016/s0076-6879(02)50972-1",
"pubmed_id": 12073322,
"title": "Saccharomyces Genome Database"
},
{
"doi": "10.1101/pdb.top083840",
"pubmed_id": 26631132,
"title": "The Saccharomyces Genome Database: A Tool for Discovery."
},
{
"doi": "10.1093/nar/30.1.69",
"pubmed_id": 11752257,
"title": "Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)."
},
{
"doi": "10.1093/nar/gkv1250",
"pubmed_id": 26578556,
"title": "The Saccharomyces Genome Database Variant Viewer."
},
{
"doi": "10.1101/pdb.prot088922",
"pubmed_id": 26631126,
"title": "The Saccharomyces Genome Database: Exploring Genome Features and Their Annotations."
},
{
"doi": null,
"pubmed_id": 9169866,
"title": "Genetic and physical maps of Saccharomyces cerevisiae."
},
{
"doi": "10.1002/(SICI)1097-0061(199812)14:16<1453::AID-YEA348>3.0.CO;2-G",
"pubmed_id": 9885151,
"title": "Expanding yeast knowledge online."
},
{
"doi": "10.1101/pdb.prot088898",
"pubmed_id": 26631123,
"title": "The Saccharomyces Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes."
},
{
"doi": "10.1002/dvg.22862",
"pubmed_id": 25997651,
"title": "Biocuration at the Saccharomyces Genome Database."
},
{
"doi": "10.1371/journal.pone.0120671",
"pubmed_id": 25781462,
"title": "AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae."
},
{
"doi": "10.1093/nar/gku975",
"pubmed_id": 25313161,
"title": "The complex portal - an encyclopaedia of macromolecular complexes."
},
{
"doi": "10.1101/pdb.prot088914",
"pubmed_id": 26631125,
"title": "The Saccharomyces Genome Database: Gene Product Annotation of Function, Process, and Component."
},
{
"doi": "10.1101/pdb.prot088906",
"pubmed_id": 26631124,
"title": "The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining."
},
{
"doi": "10.1093/nar/29.1.80",
"pubmed_id": 11125055,
"title": "Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data."
},
{
"doi": "10.1093/nar/26.1.73",
"pubmed_id": 9399804,
"title": "SGD: Saccharomyces Genome Database."
},
{
"doi": "10.1093/nar/27.1.74",
"pubmed_id": 9847146,
"title": "Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure."
},
{
"doi": "10.1126/science.282.5396.2022",
"pubmed_id": 9851918,
"title": "Comparison of the complete protein sets of worm and yeast: orthology and divergence."
},
{
"doi": "10.1126/science.277.5330.1259",
"pubmed_id": 9297238,
"title": "Yeast as a model organism."
},
{
"doi": "10.1093/nar/28.1.77",
"pubmed_id": 10592186,
"title": "Integrating functional genomic information into the Saccharomyces genome database."
},
{
"doi": "10.1073/pnas.94.11.5506",
"pubmed_id": 9159100,
"title": "Molecular linguistics: extracting information from gene and protein sequences."
},
{
"doi": null,
"pubmed_id": 7660459,
"title": "Genetic nomenclature guide. Saccharomyces cerevisiae."
}
],
"subjects": [
"Epigenetics",
"Proteomics",
"Life Science",
"Transcriptomics"
],
"twitter": "yeastgenome"
},
"go": {
"homepage": "http://www.yeastgenome.org/",
"name": "Saccharomyces Genome Database",
"prefix": "SGD",
"synonyms": [
"SGDID"
],
"uri_format": "https://www.yeastgenome.org/search?q=$1&is_quick=true"
},
"integbio": {
"alt_name": "Saccharomyces Genome Database",
"description": "This is an integrated database for budding yeast Saccharomyces cerevisiae. It contains search and analysis tools based on genes, sequences, and functions, as well as information related to citations, and the community. The information is updated and maintained by curators. It enables users to find functional relationships to sequences and gene products of fungi and higher organisms can also be verified. The SGD also maintains all gene names for budding yeast through the gene Name Registry.",
"fairsharing": "biodbcore-000100",
"homepage": "http://www.yeastgenome.org/",
"information_keywords": [
"Bioresource",
"Ontology/Terminology/Nomenclature",
"Sequence",
"Expression",
"Interaction/Pathway",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Stanford University",
"name": "SGD",
"prefix": "nbdc00202",
"pubmeds": [
"9399804",
"22110037"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein",
"Organism"
]
},
"license": "CC-BY-4.0",
"mappings": {
"biocontext": "SGD",
"edam": "2632",
"fairsharing": "FAIRsharing.pzvw40",
"go": "SGD",
"integbio": "nbdc00202",
"miriam": "sgd",
"n2t": "sgd",
"ncbi": "SGD",
"prefixcommons": "sgd",
"re3data": "r3d100010419",
"togoid": "Sgd",
"uniprot": "DB-0095",
"wikidata": "P3406"
},
"miriam": {
"deprecated": false,
"description": "The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae.",
"homepage": "https://www.yeastgenome.org/",
"id": "00000023",
"name": "SGD",
"namespaceEmbeddedInLui": false,
"pattern": "^((S\\d+$)|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?))$",
"prefix": "sgd",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "Bio2RDF",
"homepage": "http://sgd.bio2rdf.org/fct",
"name": "Bio2RDF",
"uri_format": "http://sgd.bio2rdf.org/describe/?url=http://bio2rdf.org/sgd:$1"
},
{
"code": "agr",
"description": "SGD through the Alliance of Genome Resources",
"homepage": "https://www.alliancegenome.org",
"name": "SGD through the Alliance of Genome Resources",
"uri_format": "https://www.alliancegenome.org/gene/SGD:$1"
}
],
"sampleId": "S000003909",
"uri_format": "https://www.yeastgenome.org/locus/$1"
},
"n2t": {
"description": "The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae.",
"example": "S000003909",
"homepage": "https://www.yeastgenome.org/",
"name": "SGD",
"namespaceEmbeddedInLui": false,
"pattern": "^((S\\d+$)|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?))$",
"prefix": "sgd",
"uri_format": "https://www.yeastgenome.org/locus/$1"
},
"name": "Saccharomyces Genome Database",
"ncbi": {
"example": "L0000470",
"homepage": "http://www.yeastgenome.org/",
"name": "Saccharomyces Genome Database",
"prefix": "SGD"
},
"prefixcommons": {
"description": "The Saccharomyces Genome Database (SGD) collects and organizes information about the molecular biology and genetics of the yeast Saccharomyces cerevisiae. SGD contains a variety of biological information and tools with which to search and analyze it.",
"example": "S000006169",
"homepage": "http://www.yeastgenome.org/",
"keywords": [
"eukaryotic",
"genome",
"nucleotide"
],
"name": "Saccharomyces Genome Database",
"pattern": "^S\\d+$",
"prefix": "sgd",
"pubmed_ids": [
"14681421"
],
"uri_format": "http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=$1"
},
"publications": [
{
"doi": "10.1002/(sici)1097-0061(199812)14:16<1453::aid-yea348>3.0.co;2-g",
"pmc": "PMC3037831",
"pubmed": "9885151",
"title": "Expanding yeast knowledge online",
"year": 1998
},
{
"doi": "10.1126/science.282.5396.2022",
"pmc": "PMC3057080",
"pubmed": "9851918",
"title": "Comparison of the complete protein sets of worm and yeast: orthology and divergence",
"year": 1998
},
{
"doi": "10.1093/nar/27.1.74",
"pmc": "PMC148101",
"pubmed": "9847146",
"title": "Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure",
"year": 1999
},
{
"doi": "10.1093/nar/26.1.73",
"pmc": "PMC147204",
"pubmed": "9399804",
"title": "SGD: Saccharomyces Genome Database",
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"example": "13",
"github_request_issue": 607,
"homepage": "https://www.sharkipedia.org/",
"name": "Sharkipedia Trait",
"part_of": "sharkipedia",
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1038/s41597-022-01655-1",
"pmc": "PMC9464254",
"pubmed": "36088355",
"title": "Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series",
"year": 2022
}
],
"repository": "https://github.com/sharkipedia/sharkipedia",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://www.sharkipedia.org/traits/$1",
"wikidata": {
"database": "Q113989515"
}
},
"sharkipedia.trend": {
"contact": {
"email": "creeas@gmail.com",
"github": "creeas",
"name": "Christopher Mull",
"orcid": "0000-0003-1710-8256"
},
"contributor": {
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"description": "Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone.",
"example": "3447",
"github_request_issue": 607,
"homepage": "https://www.sharkipedia.org/",
"name": "Sharkipedia Trend",
"part_of": "sharkipedia",
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1038/s41597-022-01655-1",
"pmc": "PMC9464254",
"pubmed": "36088355",
"title": "Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series",
"year": 2022
}
],
"repository": "https://github.com/sharkipedia/sharkipedia",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://www.sharkipedia.org/trends/$1",
"wikidata": {
"database": "Q113989515"
}
},
"sheepqtldb": {
"biocontext": {
"prefix": "SHEEPQTLDB"
},
"mappings": {
"biocontext": "SHEEPQTLDB",
"miriam": "sheepqtldb",
"n2t": "sheepqtldb",
"prefixcommons": "sheepqtldb"
},
"miriam": {
"deprecated": false,
"description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs.",
"homepage": "https://www.animalgenome.org/QTLdb",
"id": "00000507",
"name": "Animal Genome Sheep QTL",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "sheepqtldb",
"sampleId": "19803",
"uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"
},
"n2t": {
"description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs.",
"example": "19803",
"homepage": "http://www.animalgenome.org/cgi-bin/QTLdb/OA/index",
"name": "Animal QTL Sheep at Iowa State University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "sheepqtldb",
"uri_format": "http://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=$1"
},
"part_of": "qtldb",
"prefixcommons": {
"description": "This Sheep Quantitative Trait Locus (QTL) database (Sheep QTLdb) has gathered all sheep QTL data published during the past 10+ years. The database and its peripheral tools make it possible to compare, confirm and locate on sheep chromosomes the most feasible location for genes responsible for quantitative trait important to sheep production.",
"example": "66",
"homepage": "http://www.animalgenome.org/cgi-bin/QTLdb/OA/index",
"keywords": [
"DNA",
"genome"
],
"name": "Sheep Quantitative Trait Locus database",
"pattern": "^\\d+$",
"prefix": "sheepqtldb",
"uri_format": "http://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=$1"
}
},
"shex": {
"contact": {
"email": "gregg@greggkellogg.net",
"github": "gkellogg",
"name": "Gregg Kellogg"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Shape Expressions (ShEx) language describes RDF nodes and graph structures. A node constraint describes an RDF node (IRI, blank node or literal) and a shape describes the triples involving nodes in an RDF graph. These descriptions identify predicates and their associated cardinalities and datatypes. ShEx shapes can be used to communicate data structures associated with some process or interface, generate or validate data, or drive user interfaces.",
"download_rdf": "https://www.w3.org/ns/shex.ttl",
"example": "TripleExpression",
"homepage": "http://www.w3.org/ns/shex#",
"keywords": [
"metadata",
"rdf",
"semantic web"
],
"mappings": {
"zazuko": "shex"
},
"name": "Shape Expression Vocabulary",
"pattern": "^\\w+$",
"preferred_prefix": "shex",
"repository": "https://github.com/shexspec/shexspec.github.io",
"uri_format": "http://www.w3.org/ns/shex#$1",
"zazuko": {
"prefix": "shex",
"uri_format": "http://www.w3.org/ns/shex#$1"
}
},
"shibase": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"mappings": {
"prefixcommons": "shibase"
},
"prefixcommons": {
"description": "The database focuses on the comparative genomics of Shigella and provides a way to summarize large volumes of genomic and comparison data in a visually intuitive format.",
"example": "SDY2614",
"homepage": "http://www.mgc.ac.cn/ShiBASE/",
"keywords": [
"genome"
],
"name": "ShiBASE",
"pattern": "^[A-Z]+\\d+$",
"prefix": "shibase",
"uri_format": "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"sibo": {
"aberowl": {
"description": "Social Behavior in insects",
"download_owl": "http://aber-owl.net/media/ontologies/SIBO/2/sibo.owl",
"homepage": "https://github.com/obophenotype/sibo",
"name": "Social Insect Behavior Ontology",
"prefix": "SIBO"
},
"biocontext": {
"prefix": "SIBO"
},
"bioportal": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "Social behavior in insects.",
"homepage": "https://github.com/obophenotype/sibo",
"name": "Social Insect Behavior Ontology",
"prefix": "SIBO"
},
"example": "0000509",
"fairsharing": {
"abbreviation": "SIBO",
"description": "The Social Inset Behavior Ontology mostly contains terms related to Chemical, Anatomy, Behavior, Species. The most developed use cases are for Pogonomyrmex harvester ant foraging and apis mellifera honeybee colony defense.\n",
"homepage": "https://github.com/obophenotype/sibo",
"license": "CC-BY-3.0",
"name": "Social Inset Behavior Ontology",
"prefix": "FAIRsharing.q09hck",
"subjects": [
"Biology"
]
},
"mappings": {
"aberowl": "SIBO",
"biocontext": "SIBO",
"bioportal": "SIBO",
"fairsharing": "FAIRsharing.q09hck",
"obofoundry": "sibo",
"ols": "sibo",
"ontobee": "SIBO"
},
"obofoundry": {
"contact": "cjmungall@lbl.gov",
"contact.label": "Chris Mungall",
"contact.orcid": "0000-0002-6601-2165",
"deprecated": true,
"description": "Social Behavior in insects",
"domain": "biological systems",
"download.obo": "http://purl.obolibrary.org/obo/sibo.obo",
"download.owl": "http://purl.obolibrary.org/obo/sibo.owl",
"homepage": "https://github.com/obophenotype/sibo",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Social Insect Behavior Ontology",
"preferredPrefix": "SIBO",
"prefix": "sibo",
"repository": "https://github.com/obophenotype/sibo"
},
"ols": {
"description": "Social Behavior in insects",
"download_owl": "http://purl.obolibrary.org/obo/sibo.owl",
"homepage": "https://github.com/obophenotype/sibo",
"name": "Social Insect Behavior Ontology",
"prefix": "sibo",
"version": "2015-06-15",
"version.iri": "http://purl.obolibrary.org/obo/sibo/releases/2015-06-15/sibo.owl"
},
"ontobee": {
"library": "Library",
"name": "Social Insect Behavior Ontology",
"prefix": "SIBO"
},
"pattern": "^\\d{7}$"
},
"sider.drug": {
"biocontext": {
"prefix": "SIDER.DRUG"
},
"mappings": {
"biocontext": "SIDER.DRUG",
"miriam": "sider.drug",
"n2t": "sider.drug"
},
"miriam": {
"deprecated": false,
"description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER.",
"homepage": "http://sideeffects.embl.de/",
"id": "00000435",
"name": "SIDER Drug",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "sider.drug",
"sampleId": "2244",
"uri_format": "http://sideeffects.embl.de/drugs/$1/"
},
"n2t": {
"description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER.",
"example": "2244",
"homepage": "http://sideeffects.embl.de/",
"name": "SIDER Drug v2 at EMBL (Heidelberg)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "sider.drug",
"uri_format": "http://sideeffects.embl.de/drugs/$1/"
},
"uri_format": "http://sideeffects.embl.de/drugs/$1"
},
"sider.effect": {
"biocontext": {
"prefix": "SIDER.EFFECT"
},
"mappings": {
"biocontext": "SIDER.EFFECT",
"miriam": "sider.effect",
"n2t": "sider.effect"
},
"miriam": {
"deprecated": false,
"description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER.",
"homepage": "http://sideeffects.embl.de/",
"id": "00000436",
"name": "SIDER Side Effect",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d+$",
"prefix": "sider.effect",
"sampleId": "C0017565",
"uri_format": "http://sideeffects.embl.de/se/$1/"
},
"n2t": {
"description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER.",
"example": "C0017565",
"homepage": "http://sideeffects.embl.de/",
"name": "SIDER Side Effect v2 at EMBL (Heidelberg)",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d+$",
"prefix": "sider.effect",
"uri_format": "http://sideeffects.embl.de/se/$1/"
},
"provides": "umls",
"uri_format": "http://sideeffects.embl.de/se/$1"
},
"sigmaaldrich": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Sigma Aldrich is a life sciences supply vendor.",
"example": "HPA000698",
"github_request_issue": 216,
"homepage": "https://www.sigmaaldrich.com",
"keywords": [
"biology",
"chemistry",
"life sciences",
"vendor"
],
"mappings": {
"pathguide": "236"
},
"name": "Sigma Aldrich",
"pathguide": {
"abbreviation": "SIGMA-ALDRICH",
"homepage": "http://www.sigmaaldrich.com/Area_of_Interest/Life_Science/Cell_Signaling/Scientific_Resources/Pathway_Slides___Charts.html",
"name": "Cell Signalling Pathway Slides & Charts",
"prefix": "236"
},
"uri_format": "https://www.sigmaaldrich.com/US/en/product/sigma/$1"
},
"signaling-gateway": {
"biocontext": {
"prefix": "SIGNALING-GATEWAY"
},
"contact": {
"email": "kenan@ucsd.edu",
"name": "Kenan Azam",
"orcid": "0000-0001-7016-8624"
},
"mappings": {
"biocontext": "SIGNALING-GATEWAY",
"miriam": "signaling-gateway",
"n2t": "signaling-gateway",
"pathguide": "87",
"prefixcommons": "signaling-gateway"
},
"miriam": {
"deprecated": false,
"description": "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.",
"homepage": "http://www.signaling-gateway.org/molecule",
"id": "00000045",
"name": "Signaling Gateway",
"namespaceEmbeddedInLui": false,
"pattern": "A\\d{6}$",
"prefix": "signaling-gateway",
"sampleId": "A001094",
"uri_format": "http://www.signaling-gateway.org/molecule/query?afcsid=$1"
},
"n2t": {
"description": "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.",
"example": "A001094",
"homepage": "http://www.signaling-gateway.org/molecule",
"name": "Signaling Gateway Molecule Pages",
"namespaceEmbeddedInLui": false,
"pattern": "A\\d{6}$",
"prefix": "signaling-gateway",
"uri_format": "http://www.signaling-gateway.org/molecule/query?afcsid=$1"
},
"pathguide": {
"abbreviation": "Signaling Gateway",
"homepage": "http://www.signaling-gateway.org/molecule/",
"keywords": [
"BioPAX",
"SBML"
],
"name": "UCSD-Nature Signaling Gateway Molecule Pages",
"prefix": "87"
},
"prefixcommons": {
"description": "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.",
"example": "A001094",
"homepage": "http://www.signaling-gateway.org/molecule/",
"keywords": [
"pathway",
"protein",
"small molecule"
],
"license": "http://www.signaling-gateway.org/copyright/afcs.html",
"name": "The Signaling Gateway",
"pattern": "^A\\d{6}$",
"prefix": "signaling-gateway",
"pubmed_ids": [
"17965093",
"12478304",
"21505029"
],
"synonyms": [
"afcs",
"sgmp"
],
"uri_format": "http://www.signaling-gateway.org/molecule/query?afcsid=$1"
},
"publications": [
{
"doi": "10.1093/bioinformatics/btr190",
"pmc": "PMC3106186",
"pubmed": "21505029",
"title": "Signaling gateway molecule pages--a data model perspective",
"year": 2011
},
{
"doi": "10.1093/nar/gkm907",
"pmc": "PMC2238911",
"pubmed": "17965093",
"title": "The Molecule Pages database",
"year": 2007
},
{
"doi": "10.1038/nature01307",
"pubmed": "12478304",
"title": "The Molecule Pages database",
"year": 2002
}
]
},
"signor": {
"example": "SIGNOR-C41",
"fairsharing": {
"abbreviation": "SIGNOR",
"contact": {
"email": "gianni.cesareni@torvergata.it",
"name": "Gianni Cesareni",
"orcid": "0000-0002-9528-6018"
},
"description": "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The entire network can be freely downloaded and used to support logic modeling or to interpret high content datasets. Each relationship is linked to the literature reporting the experimental evidence. In addition each node is annotated with the chemical inhibitors that modulate its activity. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms.",
"homepage": "https://signor.uniroma2.it/user_guide.php",
"name": "SIGnaling Network Open Resource",
"prefix": "FAIRsharing.ss78t4",
"publications": [
{
"doi": "10.1093/nar/gkv1048",
"pubmed_id": 26467481,
"title": "SIGNOR: a database of causal relationships between biological entities."
}
],
"subjects": [
"Biology"
]
},
"license": "CC-BY-NC-4.0",
"mappings": {
"fairsharing": "FAIRsharing.ss78t4",
"miriam": "signor",
"pathguide": "599",
"uniprot": "DB-0206"
},
"miriam": {
"deprecated": false,
"description": "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature.",
"homepage": "https://signor.uniroma2.it/",
"id": "00000808",
"name": "SIGNOR",
"namespaceEmbeddedInLui": false,
"pattern": "^SIGNOR\\-[A-Z]+\\d+$",
"prefix": "signor",
"sampleId": "SIGNOR-C2",
"uri_format": "https://signor.uniroma2.it/relation_result.php?id=$1"
},
"name": "Signaling Network Open Resource",
"pathguide": {
"abbreviation": "SIGNOR",
"homepage": "http://signor.uniroma2.it/",
"keywords": [
"SBML"
],
"name": "The SIGnaling Network Open Resource",
"prefix": "599"
},
"publications": [
{
"doi": "10.1093/nar/gkv1048",
"pmc": "PMC4702784",
"pubmed": "26467481",
"title": "SIGNOR: a database of causal relationships between biological entities",
"year": 2015
},
{
"doi": "10.1093/nar/gkac883",
"pmc": "PMC9825604",
"pubmed": "36243968",
"title": "SIGNOR 3.0, the SIGnaling network open resource 3.0: 2022 update",
"year": 2022
}
],
"synonyms": [
"SIGNOR"
],
"uniprot": {
"abbreviation": "SIGNOR",
"category": "Enzyme and pathway databases",
"homepage": "https://signor.uniroma2.it/",
"name": "SIGNOR Signaling Network Open Resource",
"prefix": "DB-0206",
"publications": [
{
"doi": "10.1093/nar/gkac883",
"pubmed": "36243968"
}
],
"uri_format": "https://signor.uniroma2.it/relation_result.php?id=$1"
}
},
"signor.relation": {
"comment": "Currently, you can put a SIGNOR relation ID into the main page search box and it will resolve, but there is not currently a way to resolve them via a URL pattern",
"contributor": {
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"description": "Identifiers for relationships between proteins and complexes, along with their type and provenance",
"example": "SIGNOR-252737",
"homepage": "https://signor.uniroma2.it",
"keywords": [
"protein-protein interactions"
],
"name": "SIGNOR Relation",
"part_of": "signor",
"pattern": "^SIGNOR-\\d+$",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"sio": {
"aberowl": {
"description": "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. It provides vocabulary for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.",
"download_owl": "http://aber-owl.net/media/ontologies/SIO/94/sio.owl",
"homepage": "http://sio.semanticscience.org",
"name": "Semanticscience Integrated Ontology",
"prefix": "SIO",
"version": "1.59"
},
"agroportal": {
"contact": {
"email": "michel.dumontier@gmail.com",
"name": "Michel Dumontier"
},
"description": "The semanticscience integrated ontology (SIO) provides a simple, integrated ontology (types, relations) for objects, processes and their attributes. This project provides foundational support for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects. website: http://semanticscience.org email: sio-ontology@googlegroups.com mailing list: http://groups.google.com/group/sio-ontology , processes and their attributes. This project provides foundational support for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.",
"example_uri": "http://semanticscience.org/resource/SIO_000837",
"homepage": "http://sio.semanticscience.org/",
"license": "CC-BY-4.0",
"name": "Semanticscience Integrated Ontology",
"prefix": "SIO",
"publication": "http://www.jbiomedsem.com/content/5/1/14",
"repository": "https://github.com/micheldumontier/semanticscience",
"version": "1.59"
},
"banana": "SIO",
"banana_peel": "_",
"biocontext": {
"prefix": "SIO",
"uri_format": "http://semanticscience.org/resource/SIO_$1"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "SIO",
"uri_format": "http://semanticscience.org/resource/SIO_$1"
},
"bioportal": {
"contact": {
"email": "michel.dumontier@gmail.com",
"name": "Michel Dumontier"
},
"description": "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. It provides vocabulary for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.",
"homepage": "http://sio.semanticscience.org",
"name": "Semanticscience Integrated Ontology",
"prefix": "SIO",
"publication": "http://sio.semanticscience.org",
"version": "1.59"
},
"contact": {
"email": "michel.dumontier@gmail.com",
"github": "micheldumontier",
"name": "Michel Dumontier",
"orcid": "0000-0003-4727-9435"
},
"example": "000912",
"fairsharing": {
"abbreviation": "SIO",
"contact": {
"email": "michel.dumontier@gmail.com",
"name": "Michel Dumontier",
"orcid": "0000-0003-4727-9435"
},
"description": "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. It provides vocabulary for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.",
"domains": [
"Knowledge representation"
],
"homepage": "https://github.com/MaastrichtU-IDS/semanticscience",
"license": "CC-BY-4.0",
"name": "Semanticscience Integrated Ontology",
"prefix": "FAIRsharing.dpkb5f",
"publications": [
{
"doi": "10.1186/2041-1480-5-14",
"pubmed": "24602174",
"title": "The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery",
"year": 2014
}
],
"repository": "https://github.com/MaastrichtU-IDS/semanticscience/issues",
"subjects": [
"Natural Science",
"Subject Agnostic"
]
},
"lov": {
"description": "The semanticscience integrated ontology (SIO) provides a simple, integrated ontology (types, relations) for objects, processes and their attributes. This project provides foundational support for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.",
"homepage": "http://semanticscience.org",
"keywords": [
"Biology"
],
"modified": "2016-09-27",
"name": "Semanticscience Integrated Ontology",
"prefix": "sio",
"uri_prefix": "http://semanticscience.org/resource/$1"
},
"mappings": {
"aberowl": "SIO",
"agroportal": "SIO",
"biocontext": "SIO",
"biolink": "SIO",
"bioportal": "SIO",
"fairsharing": "FAIRsharing.dpkb5f",
"lov": "sio",
"miriam": "sio",
"ols": "sio",
"ontobee": "SIO"
},
"miriam": {
"deprecated": false,
"description": "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities.",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/sio",
"id": "00000851",
"name": "Semanticscience Integrated Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^SIO_\\d{6,6}$",
"prefix": "sio",
"sampleId": "SIO_000276",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/sio/terms?short_form=$1"
},
"ols": {
"contact": "sio-ontology@googlegroups.com",
"description": "The Semanticscience Integrated Ontology (SIO) provides a simple, integrated ontology of types and relations for rich description of objects, processes and their attributes.",
"download_owl": "https://raw.githubusercontent.com/micheldumontier/semanticscience/master/ontology/sio/release/sio-release.owl",
"homepage": "https://github.com/micheldumontier/semanticscience",
"name": "Semanticscience Integrated Ontology",
"prefix": "sio",
"version": "1.59",
"version.iri": "http://semanticscience.org/ontology/sio/v1.59/sio-release.owl"
},
"ontobee": {
"library": "Not Specified/No",
"name": "Semanticscience Integrated Ontology",
"prefix": "SIO"
},
"pattern": "^\\d{6}$",
"publications": [
{
"doi": "10.1186/2041-1480-5-14",
"pmc": "PMC4015691",
"pubmed": "24602174",
"title": "The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery",
"year": 2014
}
],
"repository": "https://github.com/micheldumontier/semanticscience"
},
"siren": {
"agroportal": {
"contact": {
"email": "patrice.buche@inrae.fr",
"name": "Buche"
},
"description": "This ontology contains a OWL representation of SIREN food terms using Langual thesaurus. SIREN is the Scientific Information and Retrieval Exchange Network of the US Food and Drug administration.",
"example_uri": "http://purl.obolibrary.org/obo/FOODON_03306963",
"name": "SIREN",
"prefix": "SIREN"
},
"comment": "appears in FOODON, there is no website other than the spreadsheet referenced below on langual's site",
"contact": {
"email": "patrice.buche@inrae.fr",
"name": "Patrice Buche",
"orcid": "0000-0002-9134-5404"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A modern method of records management and an automated cross-referenced subject index for accurate and comprehensive information retrieval developed by the US FDA's Bureau of Foods",
"example": "F11903",
"homepage": "https://www.langual.org/langual_indexed_datasets.asp",
"mappings": {
"agroportal": "SIREN"
},
"name": "Scientific Information Retrieval and Exchange Network",
"pattern": "^F\\d+$",
"publications": [
{
"doi": "10.1093/jaoac/65.5.1268",
"title": "SIREN: Data Base Approach to Scientific Information Handling in the Bureau of Foods, Food and Drug Administration",
"year": 1982
}
],
"references": [
"https://github.com/FoodOntology/foodon/issues/267",
"https://www.langual.org/download/IndexedDatasets/FDA/SIREN%20(updated).TXT"
],
"synonyms": [
"SUBSET_SIREN"
]
},
"sisu": {
"biocontext": {
"prefix": "SISU"
},
"fairsharing": {
"abbreviation": "SISu",
"contact": {
"email": "hannele.laivuori@helsinki.fi",
"name": "Hannele Laivuori",
"orcid": "0000-0003-3212-7826"
},
"description": "The Sequencing Initiative Suomi (SISu) search engine offers a way to search for data on sequence variants in the Finnish population. It provides valuable summary data for researchers and clinicians as well as other researchers with an interest in genetics in Finland. With SISu, you can examine the attributes and appearance of different variants in Finnish cohorts and see their aggregate distribution in Finland visualized on a map. The SISu project is an international collaboration between multiple research groups aiming to build tools for genomic medicine.",
"homepage": "http://www.sisuproject.fi/",
"name": "Sequencing Initiative Suomi",
"prefix": "FAIRsharing.t1a232",
"publications": [
{
"doi": "10.1371/journal.pone.0128524",
"pubmed_id": 26030606,
"title": "Targeted resequencing of the pericentromere of chromosome 2 linked to constitutional delay of growth and puberty."
},
{
"doi": "10.1371/journal.pgen.1004494",
"pubmed_id": 25078778,
"title": "Distribution and medical impact of loss-of-function variants in the Finnish founder population."
}
],
"subjects": [
"Medicine",
"Genomics",
"Biomedical Science",
"Epidemiology",
"Preclinical Studies"
]
},
"mappings": {
"biocontext": "SISU",
"fairsharing": "FAIRsharing.t1a232",
"miriam": "sisu",
"n2t": "sisu"
},
"miriam": {
"deprecated": false,
"description": "The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies.",
"homepage": "http://www.sisuproject.fi/",
"id": "00000624",
"name": "SISu",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+:[0-9]+$",
"prefix": "sisu",
"sampleId": "17:41223048",
"uri_format": "http://search.sisuproject.fi/#/variant/$1"
},
"n2t": {
"description": "The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies.",
"example": "17:41223048",
"homepage": "http://www.sisuproject.fi/",
"name": "SISu",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+:[0-9]+$",
"prefix": "sisu",
"uri_format": "http://search.sisuproject.fi/#/variant/$1"
},
"name": "Sequencing Initiative Suomi",
"publications": [
{
"doi": "10.1371/journal.pone.0128524",
"pmc": "PMC4452275",
"pubmed": "26030606",
"title": "Targeted resequencing of the pericentromere of chromosome 2 linked to constitutional delay of growth and puberty",
"year": 2015
},
{
"doi": "10.1371/journal.pgen.1004494",
"pmc": "PMC4117444",
"pubmed": "25078778",
"title": "Distribution and medical impact of loss-of-function variants in the Finnish founder population",
"year": 2014
}
]
},
"sitex": {
"biocontext": {
"prefix": "SITEX"
},
"contact": {
"email": "imedvedeva@celgene.com",
"github": "imedvedeva-celgene",
"name": "Irina Medvedeva",
"orcid": "0000-0003-2802-8198"
},
"fairsharing": {
"abbreviation": "SitEx",
"description": "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.",
"homepage": "http://www-bionet.sscc.ru/sitex/",
"name": "SitEx database of eukaryotic protein functional sites",
"prefix": "FAIRsharing.5mr9c5",
"publications": [
{
"doi": "10.1093/nar/gkr1187",
"pubmed_id": 22139920,
"title": "SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes."
}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"biocontext": "SITEX",
"fairsharing": "FAIRsharing.5mr9c5",
"miriam": "sitex",
"n2t": "sitex",
"prefixcommons": "sitex"
},
"miriam": {
"deprecated": false,
"description": "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.",
"homepage": "http://www-bionet.sscc.ru/sitex/",
"id": "00000252",
"name": "SitEx",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "sitex",
"sampleId": "1000",
"uri_format": "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1"
},
"n2t": {
"description": "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.",
"example": "1000",
"homepage": "http://www-bionet.sscc.ru/sitex/",
"name": "SitEx at Novosibirsk State University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "sitex",
"uri_format": "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1"
},
"prefixcommons": {
"description": "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.",
"example": "1000",
"homepage": "http://www-bionet.sscc.ru/sitex/",
"keywords": [
"domain",
"eukaryotic",
"sequence",
"structure"
],
"name": "SitEx database of eukaryotic protein functional sites",
"pattern": "^\\d+$",
"prefix": "sitex",
"pubmed_ids": [
"22139920"
],
"uri_format": "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkr1187",
"pmc": "PMC3245165",
"pubmed": "22139920",
"title": "SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes",
"year": 2011
}
]
},
"skip": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://www.skip.stemcellinformatics.org/en/",
"name": "Stemcell Knowledge and Information Portal",
"prefix": "SKIP",
"uri_format": "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine.",
"example": "SKIP001214",
"homepage": "https://skip.stemcellinformatics.org/en/",
"mappings": {
"cellosaurus": "SKIP"
},
"name": "Stemcell Knowledge and Information Portal",
"pattern": "^SKIP\\d+$",
"uri_format": "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1"
},
"skm": {
"mappings": {
"miriam": "skm"
},
"miriam": {
"deprecated": false,
"description": "Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors. ",
"homepage": "http://www.nib.si/eng/",
"id": "00000968",
"name": "Stress Knowledge Map",
"namespaceEmbeddedInLui": false,
"pattern": "^rx[0-9]{5}$",
"prefix": "skm",
"sampleId": "rx00408",
"uri_format": "https://skm.nib.si/api/pss/reactions?reaction_id=$1&return_field=summary"
}
},
"skos": {
"aberowl": {
"description": "This file is imported by vivo-core-1.5.owl. It contains terms relating to concepts from the http://www.w3.org/2004/02/skos/core# namespace of the SKOS (Simple Knowledge Organization System) ontology that are included in the vivo ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/skos/1/skos.owl",
"homepage": "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology",
"name": "SKOS (concepts)",
"prefix": "skos",
"version": "1.5"
},
"biocontext": {
"prefix": "skos",
"uri_format": "http://www.w3.org/2004/02/skos/core#$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web",
"example": "prefLabel",
"fairsharing": {
"abbreviation": "SKOS",
"contact": {
"email": "alistair.miles@linacre.ox.ac.uk",
"name": "Alistair Miles",
"orcid": "0000-0001-9018-4680"
},
"description": "Simple Knowledge Organization System (SKOS) is a common data model for sharing and linking knowledge organization systems via the Web. Many knowledge organization systems, such as thesauri, taxonomies, classification schemes and subject heading systems, share a similar structure, and are used in similar applications. SKOS captures much of this similarity and makes it explicit, to enable data and technology sharing across diverse applications. The SKOS data model provides a standard, low-cost migration path for porting existing knowledge organization systems to the Semantic Web. SKOS also provides a lightweight, intuitive language for developing and sharing new knowledge organization systems. It may be used on its own, or in combination with formal knowledge representation languages such as the Web Ontology language (OWL). The main objective of SKOS is to enable easy sharing and linking of controlled structured vocabularies for semantic web.",
"homepage": "http://www.w3.org/TR/skos-reference",
"name": "Simple Knowledge Organization System",
"prefix": "FAIRsharing.48e326",
"publications": [],
"subjects": [
"Subject Agnostic"
]
},
"homepage": "https://www.w3.org/2004/02/skos/",
"lov": {
"description": "The Simple Knowledge Organization System (SKOS) is a common data model for sharing and linking knowledge organization systems via the Semantic Web.",
"homepage": "http://www.w3.org/2009/08/skos-reference/skos.html",
"keywords": [
"W3C Rec"
],
"modified": "2009-08-18",
"name": "Simple Knowledge Organization System",
"prefix": "skos",
"uri_prefix": "http://www.w3.org/2004/02/skos/core#$1"
},
"mappings": {
"aberowl": "skos",
"biocontext": "skos",
"fairsharing": "FAIRsharing.48e326",
"lov": "skos",
"ols": "skos",
"zazuko": "skos"
},
"name": "Simple Knowledge Organization System",
"ols": {
"download_rdf": "http://www.w3.org/TR/skos-reference/skos.rdf",
"prefix": "skos"
},
"preferred_prefix": "skos",
"uri_format": "http://www.w3.org/2004/02/skos/core#$1",
"zazuko": {
"prefix": "skos",
"uri_format": "http://www.w3.org/2004/02/skos/core#$1"
}
},
"skosxl": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Simple Knowledge Organization System (SKOS) is a common data model for sharing and linking knowledge organization systems via the Semantic Web. SKOS-XL defines an extension for the Simple Knowledge Organization System, providing additional support for describing and linking lexical entities.This document provides a brief description of the SKOS-XL vocabulary.",
"example": "literalForm",
"homepage": "http://www.w3.org/2008/05/skos-xl#",
"keywords": [
"data model",
"metadata",
"semantic web",
"skos"
],
"lov": {
"description": "SKOS-XL defines an extension for the Simple Knowledge Organization System, providing additional support for describing and linking lexical entities.",
"homepage": "http://www.w3.org/TR/skos-reference/skos-xl.html",
"keywords": [
"W3C Rec"
],
"modified": "2009-08-18",
"name": "SKOS eXtension for Labels",
"prefix": "skosxl",
"uri_prefix": "http://www.w3.org/2008/05/skos-xl#$1"
},
"mappings": {
"lov": "skosxl",
"zazuko": "skosxl"
},
"name": "Simple Knowledge Organization System eXtension for Labels",
"preferred_prefix": "skosxl",
"uri_format": "http://www.w3.org/2008/05/skos-xl#$1",
"zazuko": {
"prefix": "skosxl",
"uri_format": "http://www.w3.org/2008/05/skos-xl#$1"
}
},
"slctr": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Sri Lanka Clinical Trials Registry (SLCTR) is a Registry for clinical trials involving human subjects, conducted in Sri Lanka or overseas. The SLCTR is a Primary Registry linked to the Registry Network of the International Clinical Trials Registry Platform of the WHO (WHO-ICTRP). It is a not-for-profit Registry, with free and open access to researchers, clinicians, and the general public. (from homepage)",
"example": "SLCTR/2023/010",
"homepage": "https://slctr.lk/",
"logo": "https://slctr.lk/images/logo.png",
"name": "Sri Lanka Clinical Trials Registry",
"pattern": "^SLCTR/\\d{4}/\\d+$",
"references": [
"https://slctr.lk/trials/slctr-2023-010"
]
},
"slkbase": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://sumlineknowledgebase.com/",
"name": "SUM Breast Cancer Cell Line Knowledge Base",
"prefix": "SLKBase",
"uri_format": "https://sumlineknowledgebase.com/?page_id=$1"
},
"example": "3618",
"mappings": {
"cellosaurus": "SLKBase"
},
"pattern": "^\\d+$"
},
"slm": {
"banana": "SLM",
"biocontext": {
"prefix": "SWISSLIPID"
},
"example": "000000341",
"fairsharing": {
"abbreviation": "SwissLipids",
"contact": {
"email": "swisslipids@isb-sib.ch",
"name": "Alan Bridge",
"orcid": "0000-0003-2148-9135"
},
"description": "SwissLipids is an expert-curated resource that provides a framework for the integration of lipid and lipidomic data with biological knowledge and models. SwissLipids is updated daily.",
"homepage": "http://www.swisslipids.org/#/",
"license": "https://creativecommons.org/licenses/by-nc-nd/4.0",
"name": "SwissLipids",
"prefix": "FAIRsharing.pxr7x2",
"publications": [
{
"doi": "10.1093/bioinformatics/btv285",
"pubmed_id": 25943471,
"title": "The SwissLipids knowledgebase for lipid biology."
}
],
"subjects": [
"Life Science",
"Metabolomics"
]
},
"integbio": {
"description": "SwissLipids is an expert-curated resource that provides a framework for the integration of lipid and lipidomic data with biological knowledge and models. SwissLipids is updated daily.",
"fairsharing": "FAIRsharing.pxr7x2",
"homepage": "http://www.swisslipids.org/#/",
"information_keywords": [
"Chemical structure",
"Interaction/Pathway"
],
"maintainer": "Swiss-Prot group, SIB Swiss Institute of Bioinformatics||Vital-IT group, SIB Swiss Institute of Bioinformatics",
"name": "SwissLipids",
"prefix": "nbdc02026",
"pubmeds": [
"25943471"
],
"status": "Active",
"target_keywords": [
"Protein",
"Lipid"
]
},
"mappings": {
"biocontext": "SWISSLIPID",
"fairsharing": "FAIRsharing.pxr7x2",
"integbio": "nbdc02026",
"miriam": "slm",
"n2t": "swisslipid",
"ols": "slm",
"pathguide": "687",
"re3data": "r3d100012603",
"togoid": "Swisslipids",
"uniprot": "DB-0197",
"wikidata": "P8691"
},
"miriam": {
"deprecated": false,
"description": "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions.",
"homepage": "http://www.swisslipids.org/#/",
"id": "00000550",
"name": "SwissLipids",
"namespaceEmbeddedInLui": true,
"pattern": "^SLM:\\d+$",
"prefix": "slm",
"sampleId": "000048885",
"uri_format": "http://www.swisslipids.org/#/entity/SLM:$1/"
},
"n2t": {
"description": "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions.",
"example": "000048885",
"homepage": "http://www.swisslipids.org/#/",
"name": "SwissLipids at Swiss Institute of Bioinformatics",
"namespaceEmbeddedInLui": true,
"pattern": "^SLM:\\d+$",
"prefix": "swisslipid",
"uri_format": "http://www.swisslipids.org/#/entity/SLM:$1/"
},
"name": "SwissLipid",
"ols": {
"description": "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions.",
"download_rdf": "file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/swisslipids.ttl",
"name": "SwissLipids",
"prefix": "slm"
},
"pathguide": {
"abbreviation": "SwissLipids",
"homepage": "http://www.swisslipids.org/#/",
"name": "A Knowledge Resource for Lipids and their Biology",
"prefix": "687"
},
"pattern": "^\\d+$",
"preferred_prefix": "SLM",
"publications": [
{
"doi": "10.1093/bioinformatics/btv285",
"pmc": "PMC4547616",
"pubmed": "25943471",
"title": "The SwissLipids knowledgebase for lipid biology",
"year": 2015
}
],
"re3data": {
"description": "SwissLipids is an expert curated resource that provides a framework for the integration of lipid and lipidomic data with biological knowledge and models.",
"homepage": "https://www.swisslipids.org/#/",
"name": "SwissLipids",
"prefix": "r3d100012603",
"synonyms": [
"A knowledge resource for lipids and their biology",
"Swiss+Lipids"
],
"xrefs": {
"fairsharing": "FAIRsharing.pxr7x2",
"miriam": "00100727",
"omics": "08652"
}
},
"synonyms": [
"swisslipid",
"swisslipids"
],
"togoid": {
"catalog": "nbdc02026",
"examples": [
"SLM:000000002",
"SLM:000000003",
"SLM:000000006",
"SLM:000000007",
"SLM:000000035",
"SLM:000000042",
"SLM:000000043",
"SLM:000000044",
"SLM:000000047",
"SLM:000000048"
],
"keywords": [
"Lipid"
],
"name": "SwissLipids",
"pattern": "^SLM[:_](?\\d+)$",
"prefix": "Swisslipids",
"uri_format": "http://identifiers.org/slm/SLM:$1"
},
"uniprot": {
"abbreviation": "SwissLipids",
"category": "Chemistry databases",
"homepage": "https://www.swisslipids.org",
"name": "SwissLipids knowledge resource for lipid biology",
"prefix": "DB-0197",
"publications": [
{
"doi": "10.1093/bioinformatics/btv285",
"pubmed": "25943471"
}
],
"uri_format": "https://www.swisslipids.org/#/entity/$1/"
},
"uri_format": "https://www.swisslipids.org/#/entity/SLM:$1",
"wikidata": {
"description": "identifier for lipids used by the SwissLipids database",
"example": [
"SLM:000000274",
"SLM:000000510"
],
"homepage": "https://www.swisslipids.org/#/",
"name": "SwissLipids ID",
"prefix": "P8691",
"uri_format": "https://www.swisslipids.org/#/entity/$1/"
}
},
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"download_owl": "http://aber-owl.net/media/ontologies/SLSO/3/slso.owl",
"homepage": "https://github.com/nasa/LSDAO",
"name": "Space Life Sciences Ontology",
"prefix": "SLSO"
},
"bioportal": {
"contact": {
"email": "daniel.c.berrios@nasa.gov",
"name": "Dan Berrios"
},
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"homepage": "https://github.com/nasa/LSDAO/tree/master/src/ontology",
"name": "Space Life Sciences Ontology",
"prefix": "SLSO",
"version": "2024-05-17"
},
"example": "0000000",
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"aberowl": "SLSO",
"bioportal": "SLSO",
"obofoundry": "slso",
"ontobee": "SLSO"
},
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"contact.github": "DanBerrios",
"contact.label": "Dan Berrios",
"contact.orcid": "0000-0003-4312-9552",
"deprecated": false,
"description": "The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive and other systems that contain space life science research data.",
"domain": "investigations",
"download.json": "http://purl.obolibrary.org/obo/slso.json",
"download.obo": "http://purl.obolibrary.org/obo/slso.obo",
"download.owl": "http://purl.obolibrary.org/obo/slso.owl",
"homepage": "https://github.com/nasa/LSDAO",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Space Life Sciences Ontology",
"preferredPrefix": "SLSO",
"prefix": "slso",
"repository": "https://github.com/nasa/LSDAO"
},
"ontobee": {
"library": "Library",
"name": "Space Life Sciences Ontology",
"prefix": "SLSO"
}
},
"smart": {
"biocontext": {
"prefix": "SMART"
},
"contact": {
"email": "chris.ponting@ed.ac.uk",
"name": "Chris P. Ponting",
"orcid": "0000-0003-0202-7816"
},
"fairsharing": {
"abbreviation": "SMART",
"description": "SMART (Simple Modular Architecture Research Tool) is a web resource providing simple identification and extensive annotation of protein domains and the exploration of protein domain architectures. It allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. More than 500 domain families found in signalling, extracellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. Each domain found in a non-redundant protein database as well as search parameters and taxonomic information are stored in a relational database system. User interfaces to this database allow searches for proteins containing specific combinations of domains in defined taxa.",
"homepage": "http://smart.embl.de",
"license": "CC BY-SA 3.0",
"name": "Simple Modular Architecture Research Tool",
"prefix": "FAIRsharing.hsbpq3",
"publications": [
{
"doi": "10.1093/nar/gkr931",
"pubmed_id": 22053084,
"title": "SMART 7: recent updates to the protein domain annotation resource."
},
{
"doi": "10.1016/S0959-440X(99)80055-4",
"pubmed_id": 10361098,
"title": "Protein families in multicellular organisms."
},
{
"doi": "10.1093/nar/gkn808",
"pubmed_id": 18978020,
"title": "SMART 6: recent updates and new developments."
},
{
"doi": "10.1093/nar/gkj079",
"pubmed_id": 16381859,
"title": "SMART 5: domains in the context of genomes and networks."
},
{
"doi": "10.1093/nar/gkh088",
"pubmed_id": 14681379,
"title": "SMART 4.0: towards genomic data integration."
},
{
"doi": "10.1093/nar/28.1.231",
"pubmed_id": 10592234,
"title": "SMART: a web-based tool for the study of genetically mobile domains."
},
{
"doi": "10.1093/nar/27.1.229",
"pubmed_id": 9847187,
"title": "SMART: identification and annotation of domains from signalling and extracellular protein sequences."
},
{
"doi": "10.1093/nar/30.1.242",
"pubmed_id": 11752305,
"title": "Recent improvements to the SMART domain-based sequence annotation resource."
},
{
"doi": "10.1093/nar/gkx922",
"pubmed_id": 29040681,
"title": "20 years of the SMART protein domain annotation resource."
},
{
"doi": "10.1093/nar/gku949",
"pubmed_id": 25300481,
"title": "SMART: recent updates, new developments and status in 2015."
}
],
"subjects": [
"Life Science"
]
},
"go": {
"homepage": "http://smart.embl-heidelberg.de/",
"name": "Simple Modular Architecture Research Tool",
"prefix": "SMART",
"uri_format": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=$1"
},
"integbio": {
"alt_name": "Simple Modular Architecture Research Tool",
"description": "SMART is a database of protein domains found in several different protein classes. The database contains classification information for domains and the proteins they can be found in. Users can search by sequence or domain information. The database can also be requested for local installation.",
"fairsharing": "FAIRsharing.hsbpq3",
"homepage": "http://smart.embl-heidelberg.de",
"information_keywords": [
"3D structure",
"Chemical structure",
"Classification"
],
"maintainer": "EMBL (European Molecular Biology Laboratory)",
"name": "SMART",
"prefix": "nbdc00682",
"pubmeds": [
"22053084",
"18978020",
"16381859",
"9600884"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"mappings": {
"biocontext": "SMART",
"fairsharing": "FAIRsharing.hsbpq3",
"go": "SMART",
"integbio": "nbdc00682",
"miriam": "smart",
"n2t": "smart",
"prefixcommons": "smart",
"togoid": "Smart",
"uniprot": "DB-0097"
},
"miriam": {
"deprecated": false,
"description": "The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures.",
"homepage": "http://smart.embl-heidelberg.de/",
"id": "00000118",
"name": "SMART",
"namespaceEmbeddedInLui": false,
"pattern": "^SM\\d{5}$",
"prefix": "smart",
"sampleId": "SM00015",
"uri_format": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1"
},
"n2t": {
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"example": "SM00015",
"homepage": "http://smart.embl-heidelberg.de/",
"name": "SMART (Simple Modular Architecture Research Tool)",
"namespaceEmbeddedInLui": false,
"pattern": "^SM\\d{5}$",
"prefix": "smart",
"uri_format": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1"
},
"prefixcommons": {
"description": "The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures.",
"example": "SM00015",
"homepage": "http://smart.embl.de/",
"keywords": [
"domain",
"protein",
"structure"
],
"license": "CC BY-SA 3.0",
"name": "Simple Modular Architecture Research Tool; a protein domain database",
"pattern": "^SM\\d{5}$",
"prefix": "smart",
"pubmed_ids": [
"9847187"
],
"uri_format": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1"
},
"publications": [
{
"doi": "10.1093/nar/27.1.229",
"pmc": "PMC148142",
"pubmed": "9847187",
"title": "SMART: identification and annotation of domains from signalling and extracellular protein sequences",
"year": 1999
},
{
"doi": "10.1093/nar/gkx922",
"pmc": "PMC5753352",
"pubmed": "29040681",
"title": "20 years of the SMART protein domain annotation resource",
"year": 2018
},
{
"doi": "10.1093/nar/gku949",
"pmc": "PMC4384020",
"pubmed": "25300481",
"title": "SMART: recent updates, new developments and status in 2015",
"year": 2014
},
{
"doi": "10.1093/nar/gkr931",
"pmc": "PMC3245027",
"pubmed": "22053084",
"title": "SMART 7: recent updates to the protein domain annotation resource",
"year": 2011
},
{
"doi": "10.1093/nar/gkn808",
"pmc": "PMC2686533",
"pubmed": "18978020",
"title": "SMART 6: recent updates and new developments",
"year": 2008
},
{
"doi": "10.1093/nar/gkj079",
"pmc": "PMC1347442",
"pubmed": "16381859",
"title": "SMART 5: domains in the context of genomes and networks",
"year": 2006
},
{
"doi": "10.1093/nar/gkh088",
"pmc": "PMC308822",
"pubmed": "14681379",
"title": "SMART 4.0: towards genomic data integration",
"year": 2004
},
{
"doi": "10.1093/nar/30.1.242",
"pmc": "PMC99073",
"pubmed": "11752305",
"title": "Recent improvements to the SMART domain-based sequence annotation resource",
"year": 2002
},
{
"doi": "10.1093/nar/28.1.231",
"pmc": "PMC102444",
"pubmed": "10592234",
"title": "SMART: a web-based tool for the study of genetically mobile domains",
"year": 2000
},
{
"doi": "10.1016/s0959-440x(99)80055-4",
"pubmed": "10361098",
"title": "Protein families in multicellular organisms",
"year": 1999
}
],
"togoid": {
"catalog": "nbdc00682",
"examples": [
"SM00130",
"SM00239",
"SM00043",
"SM00091",
"SM00104",
"SM01001",
"SM00135",
"SM00281",
"SM00996",
"SM00015"
],
"keywords": [
"Domain"
],
"name": "SMART",
"pattern": "^(?SM\\d{5})$",
"prefix": "Smart",
"uri_format": "http://identifiers.org/smart/$1"
},
"uniprot": {
"abbreviation": "SMART",
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"homepage": "https://smart.embl.de/",
"name": "Simple Modular Architecture Research Tool; a protein domain database",
"prefix": "DB-0097",
"publications": [
{
"doi": "10.1093/nar/gkx922",
"pubmed": "29040681"
}
],
"uri_format": "https://smart.embl.de/smart/do_annotation.pl?DOMAIN=$1"
}
},
"smid": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C. elegans and other nematodes. SMIDs aim to make life easier for describing biogenic small molecules in metabolomic and genomic applications. ",
"example": "137",
"homepage": "https://smid-db.org/",
"name": "C. elegans Small Molecule Identifier Database",
"pattern": "^\\d+$",
"synonyms": [
"SMID-DB"
],
"uri_format": "https://smid-db.org/smid/$1"
},
"smiles": {
"contact": {
"email": "tim.vandermeersch@gmail.com",
"github": "timvdm",
"name": "Tim Vandermeersch"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor_extras": [
{
"github": "NishaSharma14",
"name": "Nisha Sharma",
"orcid": "0009-0006-4755-1039"
}
],
"description": "Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions.",
"example": "CC2(C)C\\1CCC(C)/C=C/12",
"fairsharing": {
"abbreviation": "SMILES",
"description": "This format is an open specification version of the SMILES language, a typographical line notation for specifying chemical structure. It is hosted under the banner of the Blue Obelisk project, with the intent to solicit contributions and comments from the entire computational chemistry community.",
"homepage": "http://opensmiles.org/opensmiles.html",
"name": "Simplified Molecular Input Line Entry Specification Format",
"prefix": "FAIRsharing.qv4b3c",
"publications": [
{
"doi": "10.1021/ci00062a008",
"pubmed_id": null,
"title": "SMILES. 2. Algorithm for generation of unique SMILES notation"
},
{
"doi": "10.1186/1758-2946-4-24",
"pubmed_id": 23031664,
"title": "mol2chemfig, a tool for rendering chemical structures from molfile or SMILES format to LATE X code."
},
{
"doi": "10.1021/ci00057a005",
"pubmed_id": null,
"title": "SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules"
},
{
"doi": "10.1021/ci00067a005",
"pubmed_id": null,
"title": "SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules"
}
],
"repository": "https://github.com/timvdm/OpenSMILES/blob/master/discussion_summary.txt",
"subjects": [
"Chemistry",
"Life Science"
]
},
"homepage": "https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html",
"mappings": {
"fairsharing": "FAIRsharing.qv4b3c",
"wikidata": "P233"
},
"name": "Simplified molecular-input line-entry system",
"providers": [
{
"code": "cms.descriptor",
"description": "Returns descriptors calculated from the molecule with RDKit",
"homepage": "https://api.naturalproducts.net/latest/docs#/chem/get_descriptors_chem_descriptors_get",
"name": "RDKit Descriptor via the Cheminformatics Microservice",
"uri_format": "https://api.naturalproducts.net/latest/chem/descriptors?smiles=$1"
},
{
"code": "cms.depict2d",
"description": "Generates a 2D depiction of a molecule using CDK or RDKit with the given parameters.",
"homepage": "https://api.naturalproducts.net/latest/docs#/depict/Depict2D_molecule_depict_2D_get",
"name": "Depict 2D via the Cheminformatics Microservice",
"uri_format": "https://api.naturalproducts.net/latest/depict/2D?smiles=$1"
},
{
"code": "cms.depict3d",
"description": "Generate 3D depictions of molecules using OpenBabel or RDKit.",
"homepage": "https://api.naturalproducts.net/latest/docs#/depict/Depict3D_Molecule_depict_3D_get",
"name": "Depict 3D via the Cheminformatics Microservice",
"uri_format": "https://api.naturalproducts.net/latest/depict/3D?smiles=$1"
},
{
"code": "cms.coordinates2d",
"description": "Generates 2D Coordinates using the CDK Structure diagram generator/RDKit/Open Babel and returns the mol block.",
"homepage": "https://api.naturalproducts.net/latest/docs#/convert/Create2D_Coordinates_convert_mol2D_get",
"name": "Generate 2D coordinates via the Cheminformatics Microservice",
"uri_format": "https://api.naturalproducts.net/latest/convert/mol2D?smiles=$1"
},
{
"code": "cms.coordinates3d",
"description": "Generates a random 3D conformer from SMILES using the specified molecule toolkit.",
"homepage": "https://api.naturalproducts.net/latest/docs#/convert/Create3D_Coordinates_convert_mol3D_get",
"name": "Generate 3D conformer via the Cheminformatics Microservice",
"uri_format": "https://api.naturalproducts.net/latest/convert/mol3D?smiles=$1"
},
{
"code": "cms.canonicalize",
"description": "Canonicalizes a given SMILES string according to the allowed toolkits.",
"homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_Canonicalise_convert_canonicalsmiles_get",
"name": "Canonicalizes a SMILES via the Cheminformatics Microservice",
"uri_format": "https://api.naturalproducts.net/latest/convert/canonicalsmiles?smiles=$1"
},
{
"code": "cms.cxsmiles",
"description": "Convert SMILES to CXSMILES. For more informations.",
"homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_CXSMILES_convert_cxsmiles_get",
"name": "Convert SMILES to CXSMILES via the Cheminformatics Microservice",
"uri_format": "https://api.naturalproducts.net/latest/convert/cxsmiles?smiles=$1"
},
{
"code": "cms.inchi",
"description": "Convert SMILES to InChI.",
"homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_InChI_convert_inchi_get",
"name": "Convert SMILES to InChI via the Cheminformatics Microservice",
"uri_format": "https://api.naturalproducts.net/latest/convert/inchi?smiles=$1"
},
{
"code": "cms.inchikey",
"description": "Convert SMILES to InChIKey.",
"homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_InChIKey_convert_inchikey_get",
"name": "Convert SMILES to InChIKey via the Cheminformatics Microservice",
"uri_format": "https://api.naturalproducts.net/latest/convert/inchikey?smiles=$1"
},
{
"code": "cms.iupac",
"description": "Generates IUPAC name for given SMILES using [STOUT](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00512-4) package.",
"homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_IUPACname_convert_iupac_get",
"name": "Generate IUPAC name from SMILES via the Cheminformatics Microservice",
"uri_format": "https://api.naturalproducts.net/latest/convert/iupac?smiles=$1"
},
{
"code": "cms.selfies",
"description": "Generates SELFIES string for a given SMILES string.",
"homepage": "https://api.naturalproducts.net/latest/docs#/convert/encode_SELFIES_convert_selfies_get",
"name": "Generates SELFIES for a SMILES via the Cheminformatics Microservice",
"uri_format": "https://api.naturalproducts.net/latest/convert/selfies?smiles=$1"
},
{
"code": "cms.convert",
"description": "Convert SMILES to various molecular formats using different toolkits.",
"homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_convert_to_Formats_convert_formats_get",
"name": "Convert SMILES to various molecular formats via the Cheminformatics Microservice",
"uri_format": "https://api.naturalproducts.net/latest/convert/formats?smiles=$1"
}
],
"publications": [
{
"doi": "10.1186/1758-2946-4-24",
"pmc": "PMC3551648",
"pubmed": "23031664",
"title": "mol2chemfig, a tool for rendering chemical structures from molfile or SMILES format to LATE X code",
"year": 2012
},
{
"doi": "10.1021/ci00067a005",
"title": "SMILES. 3. DEPICT. Graphical depiction of chemical structures",
"year": 1990
},
{
"doi": "10.1021/ci00062a008",
"title": "SMILES. 2. Algorithm for generation of unique SMILES notation",
"year": 1989
},
{
"doi": "10.1021/ci00057a005",
"title": "SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules",
"year": 1988
}
],
"references": [
"https://github.com/biopragmatics/bioregistry/issues/931"
],
"wikidata": {
"database": "Q466769",
"description": "Simplified Molecular Input Line Entry Specification (canonical format)",
"example": [
"CC2(C)C\\1CCC(C)/C=C/12",
"CCO",
"[Au]"
],
"name": "canonical SMILES",
"pattern": "^[A-Za-z0-9+\\-\\*=#$:().>/\\\\\\[\\]%]+$",
"prefix": "P233",
"uri_format": "https://www.simolecule.com/cdkdepict/depict/bow/svg?smi=$1&zoom=2.0&annotate=cip"
}
},
"smpdb": {
"biocontext": {
"prefix": "SMPDB",
"uri_format": "http://smpdb.ca/view/$1"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "PathWhiz",
"uri_format": "http://smpdb.ca/pathways/#$1"
},
"contact": {
"email": "david.wishart@ualberta.ca",
"github": "DavidWishartLab",
"name": "David S. Wishart",
"orcid": "0000-0002-3207-2434"
},
"edam": {
"description": "Identifier of a pathway from the Small Molecule Pathway Database (SMPDB).",
"name": "Pathway ID (SMPDB)",
"obsolete": false,
"prefix": "2659"
},
"example": "SMP0000219",
"fairsharing": {
"abbreviation": "SMPDB",
"description": "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.",
"homepage": "http://www.smpdb.ca/",
"name": "Small Molecule Pathway Database",
"prefix": "FAIRsharing.y1zyaq",
"publications": [
{
"doi": "doi:10.1093/nar/gkp1002",
"pubmed_id": 19948758,
"title": "SMPDB: The Small Molecule Pathway Database."
},
{
"doi": "10.1093/nar/gkt1067",
"pubmed_id": 24203708,
"title": "SMPDB 2.0: big improvements to the Small Molecule Pathway Database."
}
],
"subjects": [
"Life Science"
],
"twitter": "WishartLab"
},
"integbio": {
"alt_name": "Small Molecule Pathway Database",
"description": "SMPDB is a database of the biological pathways of small molecules. The database contains pathway information on hundreds of small molecules, many unique to SMPDB. Users can browse pathways by category, search the database, or use structure, sequence, and small molecule tools to explore pathways.",
"fairsharing": "biodbcore-000352",
"homepage": "http://www.smpdb.ca/",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "University of Alberta",
"name": "SMPDB",
"prefix": "nbdc00908",
"pubmeds": [
"19948758"
],
"status": "Active",
"target_keywords": [
"Protein",
"Metabolite"
]
},
"mappings": {
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"biolink": "PathWhiz",
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"fairsharing": "FAIRsharing.y1zyaq",
"integbio": "nbdc00908",
"miriam": "smpdb",
"n2t": "smpdb",
"pathguide": "311",
"prefixcommons": "smpdb"
},
"miriam": {
"deprecated": false,
"description": "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.",
"homepage": "https://smpdb.ca/",
"id": "00000104",
"name": "Small Molecule Pathway Database",
"namespaceEmbeddedInLui": false,
"pattern": "^SMP\\d+$",
"prefix": "smpdb",
"sampleId": "SMP00001",
"uri_format": "http://smpdb.ca/view/$1"
},
"n2t": {
"description": "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.",
"example": "SMP00001",
"homepage": "http://www.smpdb.ca/pathways",
"name": "Small Molecule Pathway Database",
"namespaceEmbeddedInLui": false,
"pattern": "^SMP\\d+$",
"prefix": "smpdb",
"uri_format": "http://smpdb.ca/view/$1"
},
"name": "Small Molecule Pathway Database",
"pathguide": {
"abbreviation": "SMPDB",
"homepage": "http://www.smpdb.ca/",
"keywords": [
"BioPAX",
"SBML"
],
"name": "Small Molecule Pathway Database",
"prefix": "311"
},
"pattern": "^SMP\\d+$",
"prefixcommons": {
"description": "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.",
"example": "SMP00001",
"homepage": "http://www.smpdb.ca/",
"keywords": [
"chemical",
"human",
"metabolite",
"pathway"
],
"license": "http://www.smpdb.ca/about#cite",
"name": "Small Molecule Pathway Database",
"pattern": "^SMP\\d{5}$",
"prefix": "smpdb",
"uri_format": "http://pathman.smpdb.ca/pathways/$1/pathway"
},
"publications": [
{
"doi": "10.1093/nar/gkt1067",
"pmc": "PMC3965088",
"pubmed": "24203708",
"title": "SMPDB 2.0: big improvements to the Small Molecule Pathway Database",
"year": 2013
},
{
"doi": "10.1093/nar/gkp1002",
"pmc": "PMC2808928",
"pubmed": "19948758",
"title": "SMPDB: The Small Molecule Pathway Database",
"year": 2009
}
],
"synonyms": [
"SMP"
],
"uri_format": "https://smpdb.ca/view/$1"
},
"snap": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality.",
"example": "Quality",
"homepage": "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf",
"mappings": {
"pathguide": "494",
"prefixcommons": "snap"
},
"name": "Snapshot",
"pathguide": {
"abbreviation": "Snap",
"homepage": "http://snap.genomics.org.cn/",
"name": "a Single Nucleotide Polymorphism Annotation Platform",
"prefix": "494"
},
"prefixcommons": {
"description": "Snap is a sequence analysis tool providing a simple but detailed analysis of human genes and their variations. For each gene, a gene-gene relationship network can be generated based on protein-protein interaction data, metabolic pathway connections and extended through phylogenetic relations.",
"example": "ENSG00000187634",
"homepage": "http://snap.humgen.au.dk",
"keywords": [
"gene",
"protein",
"interaction",
"pathway"
],
"name": "SNAP: a SNP Annotation Platform",
"pattern": "^ENSG\\d+$",
"prefix": "snap",
"uri_format": "http://snap.humgen.au.dk/views/geneview.cgi?gene=$1"
},
"uri_format": "http://www.ifomis.org/bfo/1.1/snap#$1"
},
"snctp": {
"comment": "it appears they cede information into WHO",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The SNCTP (Swiss National Clinical Trials Portal) is the portal where clinical trials in Switzerland are published. It contains data from two sources: from BASEC, the national platform for submitting applications for research projects to ethics committees, and from the ICTRP (the WHO International Clinical Trials Registry Platform), which covers the 17 primary registries worldwide. The ICTRP clinical trials shown on the SNCTP are limited to those conducted in Switzerland; there is also an option to display trials conducted in one of Switzerland's neighbouring countries. [from homepage]",
"example": "SNCTP000005580",
"homepage": "https://kofam.ch/en/snctp-portal",
"name": "Swiss National Clinical Trials Portal"
},
"snomedct": {
"aberowl": {
"description": "SNOMED Clinical Terms",
"homepage": "http://www.snomed.org",
"name": "SNOMED CT",
"prefix": "SNOMEDCT",
"version": "2016AB"
},
"biocontext": {
"prefix": "SNOMEDCT"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "SNOMEDCT",
"uri_format": "http://snomed.info/id/$1"
},
"bioportal": {
"contact": {
"email": "custserv@nlm.nih.gov",
"name": "NLM Customer Service"
},
"description": "SNOMED Clinical Terms",
"homepage": "http://www.snomed.org",
"name": "SNOMED CT",
"prefix": "SNOMEDCT",
"publication": "http://www.snomed.org",
"version": "2023AB"
},
"contributor_extras": [
{
"email": "nicolas.matentzoglu@gmail.com",
"github": "matentzn",
"name": "Nicolas Matentzoglu",
"orcid": "0000-0002-7356-1779"
}
],
"fairsharing": {
"abbreviation": "SNOMEDCT",
"description": "The Systematized Nomenclature of Medicine Clinical Terms is a reference terminology that can be used to cross-map standardized healthcare languages across healthcare disciplines.",
"homepage": "http://www.snomed.org/snomed-ct/five-step-briefing",
"name": "Systematized Nomenclature of Medicine-Clinical Terms",
"prefix": "FAIRsharing.d88s6e",
"publications": [
{
"doi": "10.1097/00024665-200609000-00011",
"pubmed": "16980782",
"title": "Standardized nursing language in the systematized nomenclature of medicine clinical terms: A cross-mapping validation method",
"year": 2006
}
],
"subjects": [
"Medicine",
"Health Science",
"Biomedical Science",
"Preclinical Studies"
]
},
"hl7": {
"description": "SNOMED CT is a concept-based, scientifically validated terminology that provides a unique and permanent concept identifier that can be included in multiple HL7 data types including CD and CE. The concepts are managed to avoid \"semantic drift\" so the meaning remains constant. If the concept is found to be ambiguous or the meaning changes, the concept is inactivated but still retained and the identifier is never reused. SNOMED CT's concepts are interrelated hierarchically and using description logic. SNOMED CT concepts have a unique \"fully-specified name\", a preferred term, and, optionally, synonyms. The description languages include English and Spanish. ",
"homepage": "http://www.ihtsdo.org",
"name": "SNOMED Clinical Terms",
"organization": "International Health Terminology Standards Development Organisation ",
"preferred_prefix": "snomed-CT",
"prefix": "2.16.840.1.113883.6.96",
"status": "Complete"
},
"license": "https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf",
"mappings": {
"aberowl": "SNOMEDCT",
"biocontext": "SNOMEDCT",
"biolink": "SNOMEDCT",
"bioportal": "SNOMEDCT",
"fairsharing": "FAIRsharing.d88s6e",
"hl7": "2.16.840.1.113883.6.96",
"miriam": "snomedct",
"n2t": "snomedct",
"ols": "snomed",
"prefixcommons": "snomedct",
"wikidata": "P5806"
},
"miriam": {
"deprecated": false,
"description": "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc.",
"homepage": "http://www.snomedbrowser.com/",
"id": "00000269",
"name": "SNOMED CT",
"namespaceEmbeddedInLui": false,
"pattern": "^(\\w+)?\\d+$",
"prefix": "snomedct",
"sampleId": "284196006",
"uri_format": "http://www.snomedbrowser.com/Codes/Details/$1"
},
"n2t": {
"description": "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc.",
"example": "284196006",
"homepage": "http://www.snomedbrowser.com/",
"name": "SNOMED-CT at The National Pathology Exchange",
"namespaceEmbeddedInLui": false,
"pattern": "^(\\w+)?\\d+$",
"prefix": "snomedct",
"uri_format": "http://www.snomedbrowser.com/Codes/Details/$1"
},
"ols": {
"description": "SNOMED CT or SNOMED Clinical Terms is a systematically organized computer processable collection of medical terms providing codes, terms, synonyms and definitions used in clinical documentation and reporting.",
"download_owl": "file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/snomed-inferred.owl",
"name": "SNOMED CT (International Edition)",
"prefix": "snomed",
"version": "2020-01-31",
"version.iri": "http://snomed.info/sct/900000000000207008/version/20200131"
},
"prefixcommons": {
"bioportal": "1353",
"description": "SNOMED Clinical Terms",
"example": "284196006",
"homepage": "http://ihtsdo.org",
"name": "Systematized Nomenclature of Medicine - Clinical Terms",
"pattern": "^(\\w+)?\\d+$",
"prefix": "snomedct",
"synonyms": [
"snomed",
"snomedct_2010_1_31",
"snomedct_2013_01_31"
]
},
"publications": [
{
"doi": "10.1097/00024665-200609000-00011",
"pubmed": "16980782",
"title": "Standardized nursing language in the systematized nomenclature of medicine clinical terms: A cross-mapping validation method",
"year": 2006
}
],
"synonyms": [
"SCTID",
"SCTID_2010_1_31",
"SNOMECT",
"SNOMED",
"SNOMEDCT",
"SNOMEDCTCT",
"SNOMEDCTCT_2018_03_01",
"SNOMEDCTCT_2019_03_01",
"SNOMEDCT_2005_07_31",
"SNOMEDCT_2010_1_31",
"SNOMEDCT_2020_03_01",
"SNOMEDCT_US",
"SNOMEDCT_US_2015_03_01",
"SNOMEDCT_US_2016_03_01",
"SNOMEDCT_US_2018_03_01",
"SNOMEDCT_US_2018_09_01",
"SNOMEDCT_US_2019_03_01",
"SNOMEDCT_US_2019_09_01",
"SNOMEDCT_US_2020_03_01",
"SNOMEDCT_US_2020_09_01",
"SNOMEDCT_US_2021_03_01",
"SNOMEDCT_US_2021_07_31",
"SNOMEDCT_US_2021_09_01",
"SNOMEDCT_US_2022_07_31",
"SNOMEDCT_US_2022_09_01",
"SNOMEDCT_US_2022_12_31",
"SNOMEDCT_US_2023_02_28",
"SNOMEDCT_US_2023_03_01",
"SNOMEDCT_US_2023_09_01",
"SNOMEDCT_US_2023_10_01",
"SNOMEDCT_US_2023_11_01",
"SNOMED_CT",
"SNOMED_CT_US_2018_03_01",
"SNOWMEDCT",
"SNOWMEDCT_US",
"SNOWMEDCT_US_2018_03_01"
],
"uri_format": "http://snomed.info/id/$1",
"wikidata": {
"description": "identifier in the SNOMED CT catalogue codes for diseases, symptoms and procedures",
"example": [
"267718000",
"464035001",
"64859006"
],
"homepage": "http://snomed.info/",
"name": "SNOMED CT ID",
"pattern": "^[0-9]*$",
"prefix": "P5806",
"uri_format": "http://snomed.info/id/$1",
"uri_format_rdf": "http://snomed.info/id/$1"
}
},
"snornabase": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A comprehensive database of\n\nhuman H/ACA and C/D box snoRNAs.",
"example": "SR0000178",
"homepage": "https://www-snorna.biotoul.fr/",
"integbio": {
"description": "SnoRNABase is an extensive database of human small nucleolar RNAs (snoRNAs) constructed with the invaluable assistance of Laboratoire de Biologie Mol?culaire Eucaryote (LBME) and Jean-Pierre Bachellerie in particular. \nThis repository provides the sequences of both snoRNA classes, namely C/D box snoRNAs and H/ACA box snoRNAs.\nIn version 2 of the database each class contains information on a set of four proteins.\nIn the updated version 3 of the database different sequences are used and the nucleotides are numbered differently.\nKeyword search and Blast search options are available.",
"homepage": "http://www-snorna.biotoul.fr/",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "Laboratoire de Biologie Moleculaire des Eucaryotes",
"name": "snoRNABase",
"prefix": "nbdc00323",
"pubmeds": [
"16381836"
],
"status": "Active",
"target_keywords": [
"RNA"
]
},
"mappings": {
"integbio": "nbdc00323",
"prefixcommons": "snornalbmedb"
},
"name": "snoRNABase",
"prefixcommons": {
"description": "This is a database of human C/D box and H/ACA modification guide RNAs",
"example": "HBII-240",
"homepage": "http://www-snorna.biotoul.fr/",
"keywords": [
"RNA"
],
"name": "snoRNA-LBME-db",
"pattern": "^[A-Z,0-9]+$",
"prefix": "snornalbmedb",
"synonyms": [
"snornabase"
],
"uri_format": "http://www-snorna.biotoul.fr/plus.php?id=$1"
},
"wikidata": {
"paper": "Q24675417"
}
},
"snp2tfbs": {
"mappings": {
"miriam": "snp2tfbs"
},
"miriam": {
"deprecated": false,
"description": "SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome.",
"homepage": "https://ccg.epfl.ch/snp2tfbs/",
"id": "00000766",
"name": "SNP2TFBS",
"namespaceEmbeddedInLui": false,
"pattern": "^rs[0-9]+$",
"prefix": "snp2tfbs",
"sampleId": "rs11603840",
"uri_format": "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1"
},
"name": "SNP to Transcription Factor Binding Sites",
"provides": "dbsnp"
},
"snp500cancer": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"mappings": {
"prefixcommons": "snp500cancer"
},
"prefixcommons": {
"description": "The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer.",
"example": "TP53-47",
"homepage": "http://snp500cancer.nci.nih.gov",
"keywords": [
"DNA"
],
"name": "SNP500Cancer",
"pattern": "^TP\\d+-\\d+$",
"prefix": "snp500cancer",
"uri_format": "http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"so": {
"aberowl": {
"description": "A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases.",
"download_owl": "http://aber-owl.net/media/ontologies/SO/289/so.owl",
"homepage": "http://www.sequenceontology.org/",
"name": "Sequence types and features ontology",
"prefix": "SO"
},
"agroportal": {
"contact": {
"email": "barry.moore@genetics.utah.edu",
"name": "Barry Moore (Software Developer)"
},
"description": "A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases.",
"example_uri": "http://purl.obolibrary.org/obo/SO_0001673",
"homepage": "http://www.sequenceontology.org/",
"name": "Sequence Types and Features Ontology",
"prefix": "SO",
"publication": "http://www.sequenceontology.org/?page_id=296",
"repository": "https://github.com/The-Sequence-Ontology/SO-Ontologies"
},
"biocontext": {
"prefix": "SO"
},
"bioportal": {
"contact": {
"email": "song-devel@lists.sourceforge.net",
"name": "SO Administrators"
},
"description": "SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/",
"homepage": "http://www.sequenceontology.org",
"name": "Sequence Types and Features Ontology",
"prefix": "SO",
"version": "unknown"
},
"download_obo": "https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/master/Ontology_Files/so.obo",
"example": "0001157",
"fairsharing": {
"abbreviation": "SO",
"contact": {
"email": "keilbeck@fruitfly.org",
"name": "Karen Eilbeck",
"orcid": "0000-0002-0831-6427"
},
"description": "SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. The Sequence Ontology is a set of terms and relationships used to describe the features and attributes of biological sequence. SO includes different kinds of features which can be located on the sequence.",
"domains": [
"Sequence annotation",
"Deoxyribonucleic acid",
"Ribonucleic acid",
"Sequence",
"Sequence feature",
"Gene",
"Genome"
],
"homepage": "http://www.sequenceontology.org/",
"license": "CC-BY-4.0",
"name": "Sequence Ontology",
"prefix": "FAIRsharing.6bc7h9",
"publications": [
{
"doi": "10.1186/gb-2010-11-8-r88",
"pubmed": "20796305",
"title": "A standard variation file format for human genome sequences",
"year": 2010
},
{
"doi": "10.1186/gb-2005-6-5-r44",
"pubmed": "15892872",
"title": "The Sequence Ontology: a tool for the unification of genome annotations",
"year": 2005
},
{
"doi": "10.1016/j.jbi.2010.03.002",
"pubmed": "20226267",
"title": "Evolution of the Sequence Ontology terms and relationships",
"year": 2010
}
],
"repository": "https://github.com/The-Sequence-Ontology/SO-Ontologies",
"subjects": [
"Bioinformatics",
"Life Science",
"Biology"
]
},
"go": {
"homepage": "http://www.sequenceontology.org/",
"name": "Sequence Ontology",
"prefix": "SO"
},
"mappings": {
"aberowl": "SO",
"agroportal": "SO",
"biocontext": "SO",
"bioportal": "SO",
"fairsharing": "FAIRsharing.6bc7h9",
"go": "SO",
"miriam": "so",
"n2t": "so",
"obofoundry": "so",
"ols": "so",
"ontobee": "SO",
"prefixcommons": "so"
},
"miriam": {
"deprecated": false,
"description": "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data.",
"homepage": "http://www.sequenceontology.org/",
"id": "00000081",
"name": "Sequence Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^SO:\\d{7}$",
"prefix": "so",
"sampleId": "0000704",
"uri_format": "http://www.sequenceontology.org/miso/current_release/term/SO:$1"
},
"n2t": {
"description": "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data.",
"example": "0000704",
"homepage": "http://bioportal.bioontology.org/ontologies/SO",
"name": "Sequence Ontology through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^SO:\\d{7}$",
"prefix": "so",
"uri_format": "http://purl.bioontology.org/ontology/SO/SO:$1"
},
"obofoundry": {
"appears_in": [
"pcl"
],
"contact": "keilbeck@genetics.utah.edu",
"contact.github": "keilbeck",
"contact.label": "Karen Eilbeck",
"contact.orcid": "0000-0002-0831-6427",
"deprecated": false,
"description": "A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases.",
"domain": "chemistry and biochemistry",
"download.obo": "http://purl.obolibrary.org/obo/so.obo",
"download.owl": "http://purl.obolibrary.org/obo/so.owl",
"homepage": "http://www.sequenceontology.org/",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"logo": "https://obofoundry.org/images/so_logo.png",
"name": "Sequence types and features ontology",
"preferredPrefix": "SO",
"prefix": "so",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/15892872",
"title": "The Sequence Ontology: a tool for the unification of genome annotations."
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/20226267",
"title": "Evolution of the Sequence Ontology terms and relationships."
}
],
"repository": "https://github.com/The-Sequence-Ontology/SO-Ontologies"
},
"ols": {
"description": "A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases.",
"download_owl": "http://purl.obolibrary.org/obo/so.owl",
"homepage": "http://www.sequenceontology.org/",
"name": "Sequence types and features ontology",
"prefix": "so",
"version": "2024-06-05",
"version.iri": "http://purl.obolibrary.org/obo/so/2024-06-05/so.owl"
},
"ontobee": {
"library": "Library",
"name": "Sequence types and features ontology",
"prefix": "SO"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"alt_uri_formats": [
"http://purl.org/obo/owl/SO#$1"
],
"bioportal": "1109",
"description": "The Sequence Ontology is a set of terms and relationships used to describe the features and attributes of biological sequence. SO includes different kinds of features which can be located on the sequence.",
"example": "SO:0000704",
"homepage": "http://www.sequenceontology.org/",
"keywords": [
"obo",
"ontology",
"DNA",
"RNA",
"structure"
],
"license": "http://www.sequenceontology.org/about/citing.html",
"name": "Sequence Ontology",
"pattern": "^SO:\\d{7}$",
"prefix": "so",
"pubmed_ids": [
"15892872"
],
"synonyms": [
"obo.so"
],
"uri_format": "http://www.sequenceontology.org/miso/current_release/term/$1"
},
"publications": [
{
"doi": "10.1186/gb-2010-11-8-r88",
"pmc": "PMC2945790",
"pubmed": "20796305",
"title": "A standard variation file format for human genome sequences",
"year": 2010
},
{
"doi": "10.1016/j.jbi.2010.03.002",
"pmc": "PMC3052763",
"pubmed": "20226267",
"title": "Evolution of the Sequence Ontology terms and relationships",
"year": 2010
},
{
"doi": "10.1186/gb-2005-6-5-r44",
"pmc": "PMC1175956",
"pubmed": "15892872",
"title": "The Sequence Ontology: a tool for the unification of genome annotations",
"year": 2005
}
],
"uri_format": "http://purl.obolibrary.org/obo/SO_$1"
},
"sopharm": {
"aberowl": {
"description": "SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. SO-Pharm articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables to represent pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables to represent patient and more largely panel included in trials, and populations. SO-Pharm enables the representation of measured items on this patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains.",
"download_owl": "http://aber-owl.net/media/ontologies/SOPHARM/18/sopharm.owl",
"homepage": "https://members.loria.fr/ACoulet/files/sopharm2.0_description.php",
"name": "Suggested Ontology for Pharmacogenomics",
"prefix": "SOPHARM",
"version": "The new release (March 02, 2017) 2.2 includes concept and properties labels in French.\nImports have been abandoned in favor of simple references to distant URI"
},
"biocontext": {
"prefix": "SOPHARM"
},
"bioportal": {
"contact": {
"email": "adrien.coulet@loria.fr",
"name": "Adrien Coulet"
},
"description": "SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. SO-Pharm articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables to represent pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables to represent patient and more largely panel included in trials, and populations. SO-Pharm enables the representation of measured items on this patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains.",
"homepage": "https://members.loria.fr/ACoulet/files/sopharm2.0_description.php",
"name": "Suggested Ontology for Pharmacogenomics",
"prefix": "SOPHARM",
"publication": "http://hal.inria.fr/inria-00089824/en/",
"version": "Version: SO-Pharm 2.2\nRelease: 02 Mar 2017"
},
"contact": {
"email": "adrien.coulet@loria.fr",
"name": "Adrien Coulet",
"orcid": "0000-0002-1466-062X"
},
"mappings": {
"aberowl": "SOPHARM",
"biocontext": "SOPHARM",
"bioportal": "SOPHARM",
"obofoundry": "sopharm"
},
"obofoundry": {
"contact": "Adrien.Coulet@loria.fr",
"contact.label": "Adrien Coulet",
"deprecated": true,
"domain": "chemistry and biochemistry",
"homepage": "http://www.loria.fr/~coulet/sopharm2.0_description.php",
"name": "Suggested Ontology for Pharmacogenomics",
"prefix": "sopharm"
}
},
"soybase": {
"biocontext": {
"prefix": "SOYBASE"
},
"fairsharing": {
"abbreviation": "SoyBase",
"contact": {
"email": "Jacqueline.Campbell@usda.gov",
"name": "Jacqueline Campbell",
"orcid": "0000-0003-2787-3955"
},
"description": "SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. The quantitative trait loci (QTL) represent more than 18 years of QTL mapping of more than 90 unique traits. SoyBase also contains the well-annotated 'Williams 82' genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. SoyBase is the repository for controlled vocabularies for soybean growth, development and trait terms, which are also linked to the more general plant ontologies.",
"homepage": "https://soybase.org/",
"name": "SoyBase",
"prefix": "FAIRsharing.z4agsr",
"publications": [
{
"doi": "10.1093/nar/gkp798",
"pubmed_id": 20008513,
"title": "SoyBase, the USDA-ARS soybean genetics and genomics database."
}
],
"subjects": [
"Plant Breeding",
"Agriculture",
"Life Science",
"Comparative Genomics"
],
"twitter": "SoyBaseDatabase"
},
"integbio": {
"description": "SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. The quantitative trait loci (QTL) represent more than 18 years of QTL mapping of more than 90 unique traits. SoyBase also contains the well-annotated 'Williams 82' genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. SoyBase is the repository for controlled vocabularies for soybean growth, development and trait terms, which are also linked to the more general plant ontologies.",
"fairsharing": "FAIRsharing.z4agsr",
"homepage": "https://soybase.org",
"information_keywords": [
"Phenotype",
"Ontology/Terminology/Nomenclature",
"Expression",
"Image/Movie",
"Interaction/Pathway",
"Sequence",
"Method"
],
"maintainer": "Iowa State University",
"name": "SoyBase",
"prefix": "nbdc01817",
"pubmeds": [
"20008513"
],
"status": "Active",
"target_keywords": [
"Organism",
"Genome/Gene",
"Genetic variation",
"DNA",
"Protein"
]
},
"mappings": {
"biocontext": "SOYBASE",
"fairsharing": "FAIRsharing.z4agsr",
"integbio": "nbdc01817",
"miriam": "soybase",
"n2t": "soybase",
"ncbi": "SoyBase",
"pathguide": "44",
"prefixcommons": "soy",
"re3data": "r3d100010846"
},
"miriam": {
"deprecated": false,
"description": "SoyBase is a repository for curated genetics, genomics and related data resources for soybean.",
"homepage": "http://soybase.org/",
"id": "00000291",
"name": "SoyBase",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\-)?\\w+(\\-)?\\w+$",
"prefix": "soybase",
"sampleId": "BARC-013845-01256",
"uri_format": "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1"
},
"n2t": {
"description": "SoyBase is a repository for curated genetics, genomics and related data resources for soybean.",
"example": "BARC-013845-01256",
"homepage": "http://soybase.org/",
"name": "SoyBase at Iowa State University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\-)?\\w+(\\-)?\\w+$",
"prefix": "soybase",
"uri_format": "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1"
},
"name": "SoyBase",
"ncbi": {
"example": "Satt005",
"homepage": "http://soybase.org",
"name": "Glycine max Genome Database",
"prefix": "SoyBase"
},
"pathguide": {
"abbreviation": "SoyBase",
"homepage": "http://soybase.org/",
"name": "USDA-ARS Soybean Genetics and Genome Database",
"prefix": "44"
},
"prefixcommons": {
"bioportal": "3028",
"description": "Growth, trait and development ontology for soybean",
"example": "SOY_0001650",
"homepage": "http://soybase.org",
"keywords": [
"obo",
"development",
"phenotype",
"spider"
],
"name": "SoyOntology",
"pattern": "^SOY_\\d{7}$",
"prefix": "soy"
},
"publications": [
{
"doi": "10.1093/nar/gkp798",
"pmc": "PMC2808871",
"pubmed": "20008513",
"title": "SoyBase, the USDA-ARS soybean genetics and genomics database",
"year": 2009
}
],
"re3data": {
"description": "SoyBase is a professionally curated repository for genetics, genomics and related data resources for soybean. It contains current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. SoyBase includes annotated \"Williams 82\" genomic sequence and associated data mining tools. The repository maintains controlled vocabularies for soybean growth, development, and traits that are linked to more general plant ontologies.",
"homepage": "https://soybase.org/",
"name": "SoyBase",
"prefix": "r3d100010846",
"synonyms": [
"SoyBase and the Soybean Breeder's Toolbox"
],
"xrefs": {
"fairsharing": "FAIRsharing.z4agsr",
"miriam": "00000291",
"nif": "0000-03483",
"omics": "02778",
"scr": "005096"
}
}
},
"span": {
"comment": "see also snap. This ontology only exists in description in the paper and does not have an associated web resource",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality.",
"homepage": "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf",
"keywords": [
"ontology",
"upper-level ontology"
],
"name": "Span"
},
"spbase": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"integbio": {
"alt_name": "Strongylocentrotus purpuratus database",
"description": "SpBase is a database of the sea urchin genome. In addition to a genome browser, the database contains several types of sequence and gene expression information as well as links to external resources. Bulk data is available for download.",
"homepage": "http://www.spbase.org/SpBase/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "California Institute of Technology",
"name": "SpBase",
"prefix": "nbdc00686",
"pubmeds": [
"19010966"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"mappings": {
"integbio": "nbdc00686",
"prefixcommons": "spbase"
},
"prefixcommons": {
"description": "SpBase, is designed to present the results of the genome sequencing project for the purple sea urchin. THe sequences and annotations emerging from this effort are organized in a database that provides the research community access to those data not normally presented through NCBI and other large databases.",
"example": "SPU_000001",
"homepage": "http://spbase.org",
"keywords": [
"genome",
"DNA",
"RNA"
],
"name": "SpBase",
"pattern": "^SPU_\\d+$",
"prefix": "spbase",
"uri_format": "http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"spd": {
"aberowl": {
"description": "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).",
"download_owl": "http://aber-owl.net/media/ontologies/SPD/26/spd.owl",
"homepage": "http://research.amnh.org/atol/files/",
"name": "Spider Ontology",
"prefix": "SPD"
},
"biocontext": {
"prefix": "SPD"
},
"bioportal": {
"contact": {
"email": "michalik@uni-greifswald.de",
"name": "Peter Michalik"
},
"description": "An ontology for spider anatomy.",
"name": "Spider Anatomy Ontology",
"prefix": "SPD",
"version": "1.1"
},
"download_obo": "http://purl.obolibrary.org/obo/spd.obo",
"example": "0000001",
"fairsharing": {
"abbreviation": "SPD",
"contact": {
"email": "ramirez@macn.gov.ar",
"name": "Martin Ramirez",
"orcid": "0000-0002-0358-0130"
},
"description": "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).",
"domains": [
"Behavior"
],
"homepage": "https://github.com/obophenotype/spider-ontology",
"license": "CC-BY-3.0",
"name": "Spider Anatomy Ontology",
"prefix": "FAIRsharing.yecp83",
"publications": [
{
"doi": "10.3390/d11100202",
"title": "The Spider Anatomy Ontology (SPD)βA Versatile Tool to Link Anatomy with Cross-Disciplinary Data",
"year": 2019
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"mappings": {
"aberowl": "SPD",
"biocontext": "SPD",
"bioportal": "SPD",
"fairsharing": "FAIRsharing.yecp83",
"obofoundry": "spd",
"ols": "spd",
"ontobee": "SPD",
"prefixcommons": "spdo",
"wikidata": "P4537"
},
"obofoundry": {
"contact": "ramirez@macn.gov.ar",
"contact.github": "martinjramirez",
"contact.label": "Martin Ramirez",
"contact.orcid": "0000-0002-0358-0130",
"deprecated": false,
"description": "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).",
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/spd.owl",
"homepage": "http://research.amnh.org/atol/files/",
"license": "CC BY 3.0",
"license.url": "https://creativecommons.org/licenses/by/3.0/",
"name": "Spider Ontology",
"preferredPrefix": "SPD",
"prefix": "spd",
"publications": [
{
"id": "https://doi.org/10.3390/d11100202",
"title": "The Spider Anatomy Ontology (SPD)βA Versatile Tool to Link Anatomy with Cross-Disciplinary Data"
}
],
"repository": "https://github.com/obophenotype/spider-ontology"
},
"ols": {
"description": "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).",
"download_owl": "http://purl.obolibrary.org/obo/spd.owl",
"homepage": "http://research.amnh.org/atol/files/",
"name": "Spider Ontology",
"prefix": "spd"
},
"ontobee": {
"library": "Library",
"name": "Spider Ontology",
"prefix": "SPD"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1091",
"description": "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).",
"example": "SPD_0000464",
"homepage": "http://research.amnh.org/atol/files/",
"keywords": [
"obo",
"anatomy",
"spider"
],
"name": "Spider Ontology",
"pattern": "^SPD_\\d{7}$",
"prefix": "spdo"
},
"publications": [
{
"doi": "10.3390/d11100202",
"title": "The Spider Anatomy Ontology (SPD)βA Versatile Tool to Link Anatomy with Cross-Disciplinary Data",
"year": 2019
}
],
"uri_format": "http://purl.obolibrary.org/obo/SPD_$1",
"wikidata": {
"description": "identifier for the Spider Ontology which provides a controlled vocabulary for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow)",
"example": [
"0000200",
"0000623"
],
"miriam": "SPD",
"name": "Spider Ontology ID",
"pattern": "^[0-9]{7}$",
"prefix": "P4537",
"uri_format": "http://purl.obolibrary.org/obo/SPD_$1",
"uri_format_rdf": "http://purl.obolibrary.org/obo/SPD_$1"
}
},
"spdx": {
"homepage": "https://spdx.org/licenses",
"mappings": {
"miriam": "spdx",
"n2t": "spdx"
},
"miriam": {
"deprecated": false,
"description": "The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception.",
"homepage": "https://spdx.org",
"id": "00000687",
"name": "SPDX License List",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9A-Za-z\\-.]+$",
"prefix": "spdx",
"sampleId": "CC-BY-1.0",
"uri_format": "https://spdx.org/licenses/$1"
},
"n2t": {
"description": "The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception.",
"example": "CC-BY-1.0",
"homepage": "https://spdx.org",
"name": "SPDX License List",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9A-Za-z\\-.]+$",
"prefix": "spdx",
"uri_format": "https://spdx.org/licenses/$1"
},
"name": "Software Package Data Exchange License"
},
"sphn": {
"contact": {
"email": "Sabine.Oesterle@sib.swiss",
"name": "Sabine Oesterle",
"orcid": "0000-0003-3248-7899"
},
"contributor": {
"email": "deepak.unni3@gmail.com",
"github": "deepakunni3",
"name": "Deepak Unni",
"orcid": "0000-0002-3583-7340"
},
"description": "The Swiss Personalized Health Network is a national infrastructure initiative with the aim to develop, implement, and validate coordinated data infrastructures in order to make health-relevant data interoperable and shareable for research in Switzerland. The sphn RDF schema builds the foundation for all data exchanges within the sphn by integrating semantic information defined in the [sphn dataset](https://sphn.ch/document/sphn-dataset/).",
"download_owl": "https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology/-/raw/master/rdf_schema/sphn_rdf_schema.owl",
"download_rdf": "https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology/-/raw/master/rdf_schema/sphn_rdf_schema.ttl",
"example": "Allergy",
"github_request_issue": 535,
"homepage": "https://www.sphn.ch",
"license": "CC-BY-4.0",
"name": "Swiss Personalized Health Network Schema",
"pattern": "^\\S+$",
"repository": "https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://biomedit.ch/rdf/sphn-ontology/sphn#$1"
},
"spike.map": {
"biocontext": {
"prefix": "SPIKE.MAP"
},
"contact": {
"email": "Yossih@tauex.tau.ac.il",
"name": "Yosef Shiloh",
"orcid": "0000-0002-1538-6060"
},
"mappings": {
"biocontext": "SPIKE.MAP",
"miriam": "spike.map",
"n2t": "spike.map",
"prefixcommons": "spike"
},
"miriam": {
"deprecated": false,
"description": "SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps.",
"homepage": "http://www.cs.tau.ac.il/~spike/",
"id": "00000321",
"name": "SPIKE Map",
"namespaceEmbeddedInLui": false,
"pattern": "^spike\\d{5}$",
"prefix": "spike.map",
"sampleId": "spike00001",
"uri_format": "http://www.cs.tau.ac.il/~spike/maps/$1.html"
},
"n2t": {
"description": "SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps.",
"example": "spike00001",
"homepage": "http://www.cs.tau.ac.il/~spike/",
"name": "SPIKE database at Tel Aviv University",
"namespaceEmbeddedInLui": false,
"pattern": "^spike\\d{5}$",
"prefix": "spike.map",
"uri_format": "http://www.cs.tau.ac.il/~spike/maps/$1.html"
},
"prefixcommons": {
"description": "SPIKE (Signaling Pathway Integrated Knowledge Engine) is an interactive software environment that graphically displays biological signaling networks, allows dynamic layout and navigation through these networks, and enables the superposition of DNA microarray and other functional genomics data on interaction maps.",
"example": "spike00001",
"homepage": "http://www.cs.tau.ac.il/~spike/",
"keywords": [
"pathway",
"DNA",
"gene expression"
],
"name": "Signaling Pathway Integrated Knowledge Engine",
"pattern": "^spike\\d{5}$",
"prefix": "spike",
"pubmed_ids": [
"18289391",
"21097778"
],
"synonyms": [
"spike.map"
]
},
"publications": [
{
"doi": "10.1093/nar/gkq1167",
"pmc": "PMC3014840",
"pubmed": "21097778",
"title": "SPIKE: a database of highly curated human signaling pathways",
"year": 2010
},
{
"doi": "10.1186/1471-2105-9-110",
"pmc": "PMC2263022",
"pubmed": "18289391",
"title": "SPIKE--a database, visualization and analysis tool of cellular signaling pathways",
"year": 2008
}
]
},
"splash": {
"biocontext": {
"prefix": "SPLASH"
},
"mappings": {
"biocontext": "SPLASH",
"miriam": "splash",
"n2t": "splash"
},
"miriam": {
"deprecated": false,
"description": "The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance.",
"homepage": "http://mona.fiehnlab.ucdavis.edu/",
"id": "00000566",
"name": "SPLASH",
"namespaceEmbeddedInLui": false,
"pattern": "^splash\\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$",
"prefix": "splash",
"sampleId": "splash10-0zq2000000-77302b0326a418630a84",
"uri_format": "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1"
},
"n2t": {
"description": "The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance.",
"example": "splash10-0zq2000000-77302b0326a418630a84",
"homepage": "http://mona.fiehnlab.ucdavis.edu/",
"name": "Mass Bank of North America (MoNA)",
"namespaceEmbeddedInLui": false,
"pattern": "^splash\\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$",
"prefix": "splash",
"uri_format": "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1"
},
"name": "Spectra Hash Code"
},
"splicenest": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"mappings": {
"prefixcommons": "splicenest"
},
"prefixcommons": {
"description": "SpliceNest [1] is a web based graphical tool to explore gene structure, including alternative splicing, based on a mapping on the EST consensus sequences (contigs) from GeneNest [2] to the complete human genome.",
"example": "Hs635",
"homepage": "http://splicenest.molgen.mpg.de/",
"keywords": [
"gene",
"DNA",
"genome"
],
"name": "SpliceNest",
"pattern": "^[a-z]+\\d+$",
"prefix": "splicenest",
"uri_format": "http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
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"homepage": "https://w3id.org/sssom",
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},
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"stitch": {
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"fairsharing": {
"abbreviation": "STITCH",
"description": "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.",
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"name": "Search Tool for Interactions of Chemicals",
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"name": "Chemical-Protein Interaction Networks",
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},
"prefixcommons": {
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"homepage": "http://stitch.embl.de",
"keywords": [
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"protein",
"small molecule"
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"name": "STITCH: Chemical-Protein Interactions",
"pattern": "^\\w{14}$",
"prefix": "stitch",
"pubmed_ids": [
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},
"publications": [
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},
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},
{
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},
{
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}
],
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"homepage": "http://stitch.embl.de/",
"name": "STITCH",
"prefix": "r3d100012165",
"synonyms": [
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],
"xrefs": {
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"nif": "0000-03499",
"scr": "007947"
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}
},
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The pre-IND tracking number for submissions to the FDA",
"example": "125768",
"homepage": "https://www.fda.gov/media/128698/download",
"name": "FDA Submission Tracking Number"
},
"storedb": {
"banana": "STOREDB",
"biocontext": {
"prefix": "STOREDB"
},
"example": "STUDY1040",
"fairsharing": {
"abbreviation": "STOREDB",
"contact": {
"email": "PNS12@cam.ac.uk",
"name": "Dr Paul Schofield",
"orcid": "0000-0002-5111-7263"
},
"description": "STOREDB provides infrastructure for sharing data and resources in radiation biology and epidemiology. It is a platform for the archiving and sharing of primary data and outputs of all kinds, including epidemiological and experimental data, from research on the effects of radiation. It also provides a directory of bioresources and databases containing information and materials that investigators are willing to share. STORE supports the creation of a radiation research commons.",
"homepage": "https://www.storedb.org",
"license": "https://creativecommons.org",
"name": "STOREDB",
"prefix": "FAIRsharing.6h8d2r",
"publications": [],
"subjects": [
"Ecology",
"Life Science",
"Biomedical Science",
"Epidemiology",
"Preclinical Studies"
]
},
"integbio": {
"description": "STOREDB provides infrastructure for sharing data and resources in radiation biology and epidemiology. It is a platform for the archiving and sharing of primary data and outputs of all kinds, including epidemiological and experimental data, from research on the effects of radiation. It also provides a directory of bioresources and databases containing information and materials that investigators are willing to share. STORE supports the creation of a radiation research commons.",
"fairsharing": "FAIRsharing.6h8d2r",
"homepage": "https://www.storedb.org",
"information_keywords": [
"Expression",
"Method",
"Bibliography/Documents",
"Repository"
],
"maintainer": "CONCERT-European Joint Programme for the Integration of Radiation Protection Research",
"name": "STOREDB",
"prefix": "nbdc02191",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease",
"Organism"
]
},
"mappings": {
"biocontext": "STOREDB",
"fairsharing": "FAIRsharing.6h8d2r",
"integbio": "nbdc02191",
"miriam": "storedb",
"n2t": "storedb",
"re3data": "r3d100011049"
},
"miriam": {
"deprecated": false,
"description": "STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons.",
"homepage": "https://www.storedb.org/",
"id": "00000577",
"name": "STOREDB",
"namespaceEmbeddedInLui": false,
"pattern": "^STOREDB:(STUDY|FILE|DATASET)\\d+$",
"prefix": "storedb",
"sampleId": "STOREDB:STUDY1040",
"uri_format": "https://www.storedb.org/?$1"
},
"n2t": {
"description": "STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons.",
"example": "STOREDB:STUDY1040",
"homepage": "https://www.storedb.org/",
"name": "STOREDB at University of Cambridge",
"namespaceEmbeddedInLui": false,
"pattern": "^STOREDB:(STUDY|FILE|DATASET)\\d+$",
"prefix": "storedb",
"uri_format": "https://www.storedb.org/?$1"
},
"name": "Store DB",
"namespace_in_lui": true,
"pattern": "^(STUDY|FILE|DATASET)\\d+$",
"re3data": {
"description": "STOREDB is a platform for the archiving and sharing of primary data and outputs of all kinds, including epidemiological and experimental data, from research on the effects of radiation. It also provides a directory of bioresources and databases containing information and materials that investigators are willing to share. STORE supports the creation of a radiation research commons.",
"homepage": "https://www.storedb.org/store_v3/",
"name": "STOREDB",
"prefix": "r3d100011049",
"synonyms": [
"STORE",
"Sustaining access to Tissues and data frOm Radiobiological Experiments"
],
"xrefs": {
"fairsharing": "FAIRsharing.6h8d2r",
"miriam": "00000577",
"scr": "023207"
}
},
"uri_format": "https://www.storedb.org/?$1"
},
"storedb.dataset": {
"comment": "Unfortunately, the resolver itself doesn't work since datasets are actually hierarchically assigned within studies.",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"description": "Datasets inside StoreDB",
"example": "1251",
"homepage": "https://www.storedb.org/",
"name": "STOREDB at University of Cambridge",
"part_of": "storedb",
"pattern": "^\\d+$",
"uri_format": "https://www.storedb.org/?STOREDB:DATASET$1"
},
"storedb.file": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "File inside StoreDB",
"example": "12929",
"homepage": "https://www.storedb.org/",
"name": "STOREDB at University of Cambridge",
"part_of": "storedb",
"pattern": "^\\d+$",
"uri_format": "https://www.storedb.org/store_v3/download.jsp?fileId=$1"
},
"storedb.study": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Study inside StoreDB",
"example": "1174",
"homepage": "https://www.storedb.org/",
"name": "STOREDB at University of Cambridge",
"part_of": "storedb",
"pattern": "^\\d+$",
"providers": [
{
"code": "doi",
"description": "DOIs for studies",
"homepage": "https://www.storedb.org/",
"name": "StoreDB DOI",
"uri_format": "http://dx.doi.org/doi:10.20348/STOREDB/$1"
}
],
"uri_format": "https://www.storedb.org/store_v3/study.jsp?studyId=$1"
},
"string": {
"biocontext": {
"prefix": "STRING"
},
"edam": {
"description": "Unique identifier of an entry from the STRING database of protein-protein interactions.",
"name": "STRING",
"obsolete": false,
"prefix": "2302"
},
"fairsharing": {
"abbreviation": "STRING",
"contact": {
"email": "bork@embl.de",
"name": "Peer Bork",
"orcid": "0000-0002-2627-833X"
},
"description": "STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations.",
"homepage": "https://string-db.org/",
"license": "CC-BY-4.0",
"name": "STRING",
"prefix": "FAIRsharing.9b7wvk",
"publications": [
{
"doi": "10.1093/bioinformatics/btv696",
"pubmed_id": 26614125,
"title": "SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles."
},
{
"doi": "10.1093/nar/gks1094",
"pubmed_id": 23203871,
"title": "STRING v9.1: protein-protein interaction networks, with increased coverage and integration."
},
{
"doi": "10.1093/nar/gku1003",
"pubmed_id": 25352553,
"title": "STRING v10: protein-protein interaction networks, integrated over the tree of life."
},
{
"doi": "10.1093/nar/gky1131",
"pubmed_id": 30476243,
"title": "STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets."
},
{
"doi": "10.1093/nar/gkw937",
"pubmed_id": 27924014,
"title": "The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible."
},
{
"doi": "10.1093/nar/gkn760",
"pubmed_id": 18940858,
"title": "STRING 8--a global view on proteins and their functional interactions in 630 organisms."
}
],
"subjects": [
"Life Science",
"Biology"
]
},
"integbio": {
"alt_name": "Search Tool for the Retrieval of Interacting Genes/Proteins",
"description": "STRING is a database of known and predicted protein interactions, including both physical and functional interactions. It contains data which derived from four sources: genomic context, high-throughput experiments, coexpression and previous knowledge. This database quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable. It performs iterative searches and visualizes the results in their genomic context. Many data including protein sequences, protein network, interaction types for protein links, orthologous groups or full database dumps (license required) are downloadable.",
"fairsharing": "biodbcore-000340",
"homepage": "http://string-db.org/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Classification"
],
"maintainer": "STRING Consortium",
"name": "STRING",
"prefix": "nbdc00690",
"pubmeds": [
"18940858",
"17098935",
"15608232",
"12519996",
"10982861"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"mappings": {
"biocontext": "STRING",
"edam": "2302",
"fairsharing": "FAIRsharing.9b7wvk",
"integbio": "nbdc00690",
"miriam": "string",
"n2t": "string",
"pathguide": "93",
"prefixcommons": "string",
"re3data": "r3d100010604",
"uniprot": "DB-0141"
},
"miriam": {
"deprecated": false,
"description": "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions.\r\nThe interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.",
"homepage": "http://string.embl.de/",
"id": "00000265",
"name": "STRING",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$",
"prefix": "string",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "STRING Mirror at Heidelberg",
"homepage": "http://string-db.org/",
"name": "STRING Mirror at Heidelberg",
"uri_format": "http://string-db.org/interactions/$1"
}
],
"sampleId": "P53350",
"uri_format": "http://string.embl.de/interactions/$1"
},
"n2t": {
"description": "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.",
"example": "P53350",
"homepage": "http://string-db.org/",
"name": "STRING Mirror at Heidelberg",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$",
"prefix": "string",
"uri_format": "http://string-db.org/interactions/$1"
},
"name": "Search Tool for Retrieval of Interacting Genes/Proteins",
"pathguide": {
"abbreviation": "STRING",
"homepage": "http://string-db.org",
"name": "Search Tool for the Retrieval of Interacting Genes/Proteins",
"prefix": "93"
},
"prefixcommons": {
"description": "STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations",
"example": "P53350",
"homepage": "http://string-db.org",
"keywords": [
"protein",
"interaction"
],
"name": "STRING: functional protein association networks",
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$",
"prefix": "string",
"pubmed_ids": [
"18940858"
]
},
"provides": "uniprot",
"publications": [
{
"doi": "10.1093/nar/gky1131",
"pmc": "PMC6323986",
"pubmed": "30476243",
"title": "STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets",
"year": 2019
},
{
"doi": "10.1093/nar/gkw937",
"pmc": "PMC5210637",
"pubmed": "27924014",
"title": "The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible",
"year": 2016
},
{
"doi": "10.1093/bioinformatics/btv696",
"pmc": "PMC4896368",
"pubmed": "26614125",
"title": "SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles",
"year": 2015
},
{
"doi": "10.1093/nar/gku1003",
"pmc": "PMC4383874",
"pubmed": "25352553",
"title": "STRING v10: protein-protein interaction networks, integrated over the tree of life",
"year": 2014
},
{
"doi": "10.1093/nar/gks1094",
"pmc": "PMC3531103",
"pubmed": "23203871",
"title": "STRING v9.1: protein-protein interaction networks, with increased coverage and integration",
"year": 2012
},
{
"doi": "10.1093/nar/gkn760",
"pmc": "PMC2686466",
"pubmed": "18940858",
"title": "STRING 8--a global view on proteins and their functional interactions in 630 organisms",
"year": 2008
}
],
"re3data": {
"description": "STRING is a database of known and predicted protein interactions.\nThe interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:\n- Genomic Context\n- High-throughput Experiments\n- (Conserved) Coexpression\n- Previous Knowledge\nSTRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.",
"homepage": "https://string-db.org/",
"name": "STRING",
"prefix": "r3d100010604",
"synonyms": [
"Known and Predicted Protein-Protein Interactions"
],
"xrefs": {
"fairsharing": "FAIRsharing.9b7wvk",
"miriam": "00000265",
"nif": "0000-03503",
"omics": "29032",
"scr": "005223"
}
},
"uniprot": {
"abbreviation": "STRING",
"category": "Protein-protein interaction databases",
"homepage": "https://string-db.org/",
"name": "STRING",
"prefix": "DB-0141",
"publications": [
{
"doi": "10.1093/nar/gky1131",
"pubmed": "30476243"
}
],
"uri_format": "https://string-db.org/network/$1"
}
},
"sty": {
"aberowl": {
"description": "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types. This section of the documentation provides an overview of the Semantic Network, and describes the files of the Semantic Network. Sample records illustrate structure and content of these files. The Semantic Network is distributed as one of the UMLS Knowledge Sources and as an open source resource available on the Semantic Network Web site, subject to these terms and conditions.",
"homepage": "https://semanticnetwork.nlm.nih.gov/",
"name": "Semantic Types Ontology",
"prefix": "STY",
"version": "2016AB"
},
"agroportal": {
"contact": {
"email": "olivier@nlm.nih.gov",
"name": "Olivier Bodenreider"
},
"description": "The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types. This section of the documentation provides an overview of the Semantic Network, and describes the files of the Semantic Network. Sample records illustrate structure and content of these files.",
"example_uri": "http://purl.bioontology.org/ontology/STY/T057",
"homepage": "https://lhncbc.nlm.nih.gov/semanticnetwork/",
"license": "CC0-1.0",
"name": "UMLS Semantic Network",
"prefix": "STY",
"version": "12 (2022AA)"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "UMLSSG",
"uri_format": "https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt$1"
},
"bioportal": {
"contact": {
"email": "support@bioontology.org",
"name": "bioportal"
},
"description": "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types. This section of the documentation provides an overview of the Semantic Network, and describes the files of the Semantic Network. Sample records illustrate structure and content of these files. The Semantic Network is distributed as one of the UMLS Knowledge Sources and as an open source resource available on the Semantic Network Web site, subject to these terms and conditions.",
"homepage": "https://semanticnetwork.nlm.nih.gov/",
"name": "Semantic Types Ontology",
"prefix": "STY",
"version": "2023AB"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"contributor_extras": [
{
"email": "tiago.lubiana.alves@usp.br",
"github": "lubianat",
"name": "Tiago Lubiana",
"orcid": "0000-0003-2473-2313"
}
],
"description": "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types.",
"ecoportal": {
"contact": {
"email": "gs_bouazzoun@esi.dz",
"name": "Syphax Bouazzouni"
},
"description": "The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types. This section of the documentation provides an overview of the Semantic Network, and describes the files of the Semantic Network. Sample records illustrate structure and content of these files.",
"example_uri": "http://purl.bioontology.org/ontology/STY/T057",
"name": "STY",
"prefix": "STY"
},
"example": "T039",
"homepage": "https://lhncbc.nlm.nih.gov/semanticnetwork/",
"mappings": {
"aberowl": "STY",
"agroportal": "STY",
"biolink": "UMLSSG",
"bioportal": "STY",
"ecoportal": "STY",
"wikidata": "P11955"
},
"name": "UMLS Semantic Types Ontology",
"pattern": "^T\\d{3}$",
"providers": [
{
"code": "bioportal.purl",
"description": "BioPortal PURL",
"homepage": "http://purl.bioontology.org/ontology/STY",
"name": "BioPortal PURL",
"uri_format": "http://purl.bioontology.org/ontology/STY/$1"
}
],
"synonyms": [
"UMLSSG",
"umls.st",
"umls.sty"
],
"uri_format": "https://uts.nlm.nih.gov/uts/umls/semantic-network/$1",
"wikidata": {
"description": "identifier for a concept in the Semantic Network vocabulary of the Unified Medical Language System",
"example": [
"T005",
"T015"
],
"homepage": "https://uts.nlm.nih.gov/uts/umls/semantic-network/root",
"name": "UMLS Semantic Network ID",
"prefix": "P11955",
"uri_format": "https://uts.nlm.nih.gov/uts/umls/semantic-network/$1"
}
},
"subtilist": {
"biocontext": {
"prefix": "SUBTILIST"
},
"contact": {
"email": "antoine.danchin@normalesup.org",
"name": "Antoine Danchin",
"orcid": "0000-0002-6350-5001"
},
"fairsharing": {
"abbreviation": "SubtiList",
"description": "Its purpose is to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments",
"homepage": "http://genolist.pasteur.fr/SubtiList/",
"name": "Bacillus subtilis strain 168 genome",
"prefix": "FAIRsharing.40j2vd",
"publications": [
{
"doi": "10.1093/nar/30.1.62",
"pubmed_id": 11752255,
"title": "SubtiList: the reference database for the Bacillus subtilis genome."
}
],
"subjects": []
},
"mappings": {
"biocontext": "SUBTILIST",
"fairsharing": "FAIRsharing.40j2vd",
"miriam": "subtilist",
"n2t": "subtilist",
"ncbi": "SubtiList",
"prefixcommons": "subtilist"
},
"miriam": {
"deprecated": false,
"description": "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\r\nSubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments.",
"homepage": "http://genolist.pasteur.fr/SubtiList/",
"id": "00000433",
"name": "SubtiList",
"namespaceEmbeddedInLui": false,
"pattern": "^BG\\d+$",
"prefix": "subtilist",
"sampleId": "BG11523",
"uri_format": "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1"
},
"n2t": {
"description": "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments.",
"example": "BG11523",
"homepage": "http://genolist.pasteur.fr/SubtiList/",
"name": "SubtiList at Pasteur Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^BG\\d+$",
"prefix": "subtilist",
"uri_format": "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1"
},
"ncbi": {
"example": "BG10001",
"homepage": "http://genolist.pasteur.fr/SubtiList/",
"name": "Bacillus subtilis genome sequencing project",
"prefix": "SubtiList"
},
"prefixcommons": {
"description": "Its purpose is to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments",
"example": "BG11523",
"homepage": "http://genolist.pasteur.fr/SubtiList/",
"keywords": [
"genome",
"DNA",
"protein"
],
"name": "Bacillus subtilis strain 168 genome database",
"pattern": "^BG\\d+$",
"prefix": "subtilist"
},
"publications": [
{
"doi": "10.1093/nar/30.1.62",
"pmc": "PMC99059",
"pubmed": "11752255",
"title": "SubtiList: the reference database for the Bacillus subtilis genome",
"year": 2002
}
]
},
"subtiwiki": {
"biocontext": {
"prefix": "SUBTIWIKI"
},
"contact": {
"email": "jstuelk@gwdg.de",
"name": "JΓΆrg StΓΌlke",
"orcid": "0000-0001-5881-5390"
},
"fairsharing": {
"abbreviation": "SubtiWiki",
"description": "Collaborative resource for the Bacillus community.",
"homepage": "http://subtiwiki.uni-goettingen.de",
"name": "SubtiWiki",
"prefix": "FAIRsharing.2ck3st",
"publications": [
{
"doi": "10.1093/database/bap012",
"pubmed_id": 20157485,
"title": "A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki."
},
{
"doi": "10.1099/mic.0.035790-0",
"pubmed_id": 19959575,
"title": "Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis."
},
{
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},
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},
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},
"fairsharing": {
"abbreviation": "SWISS-MODEL",
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"description": "The SWISS-MODEL Repository is a database of annotated 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for protein sequences of selected model organisms.",
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"license": "CC BY-SA 4.0",
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"description": "The Software Ontology (SWO) describes software used in research, primarily Bioinformatics. The SWO covers areas such as the software type, licence, manufacturer of the software, the input and output data types and the uses (i.e. objectives) to which the software can be put.",
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}
],
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},
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"download.owl": "http://purl.obolibrary.org/obo/t4fs.owl",
"homepage": "https://github.com/terms4fairskills/FAIRterminology",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "terms4FAIRskills",
"preferredPrefix": "T4FS",
"prefix": "t4fs",
"publications": [
{
"id": "https://doi.org/10.5281/zenodo.4705219",
"title": "EOSC Co-creation funded project 074: Delivery of a proof of concept for terms4FAIRskills: Technical report"
}
],
"repository": "https://github.com/terms4fairskills/FAIRterminology"
},
"ols": {
"description": "A terminology for the skills necessary to make data FAIR and to keep it FAIR.",
"download_owl": "http://purl.obolibrary.org/obo/t4fs.owl",
"homepage": "https://github.com/terms4fairskills/FAIRterminology",
"name": "terms4FAIRskills",
"prefix": "t4fs",
"version": "2023-03-02",
"version.iri": "http://purl.obolibrary.org/obo/t4fs/releases/2023-03-02/t4fs.owl"
},
"ontobee": {
"library": "Library",
"name": "terms4FAIRskills",
"prefix": "T4FS"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.5281/zenodo.4772741",
"title": "EOSC Co-creation funded project 074: Delivery of a proof of concept for terms4FAIRskills: Technical report",
"year": 2021
},
{
"doi": "10.5281/zenodo.4705219",
"title": "EOSC Co-creation funded project 074: Delivery of a proof of concept for terms4FAIRskills: Technical report",
"year": 2021
}
],
"repository": "https://github.com/terms4fairskills/FAIRterminology",
"uri_format": "http://purl.obolibrary.org/obo/T4FS_$1"
},
"tads": {
"aberowl": {
"description": "The anatomy of the Tick, Families: Ixodidae, Argassidae",
"download_owl": "http://aber-owl.net/media/ontologies/TADS/18/tads.owl",
"homepage": "https://www.vectorbase.org/ontology-browser",
"name": "Tick Anatomy Ontology",
"prefix": "TADS"
},
"biocontext": {
"prefix": "TADS"
},
"bioportal": {
"contact": {
"email": "dsonensh@odu.edu",
"name": "Daniel Sonenshine"
},
"description": "The anatomy of the Tick, Families: Ixodidae, Argassidae",
"homepage": "http://www.anobase.org",
"name": "Tick Gross Anatomy Ontology",
"prefix": "TADS",
"version": "1.21"
},
"download_obo": "http://purl.obolibrary.org/obo/tads.obo",
"example": "0000547",
"fairsharing": {
"abbreviation": "TADS",
"contact": {
"email": "dsonensh@odu.edu",
"name": "Daniel Sonenshine",
"orcid": "0000-0001-9370-918X"
},
"description": "This ontology covers all the terms relevant for the gross anatomy of the tick (family Ixodida).",
"homepage": "https://www.vectorbase.org/ontology-types/tick-anatomy",
"name": "Tick Gross Anatomy",
"prefix": "FAIRsharing.8wm364",
"publications": [
{
"doi": "10.1111/j.1365-2583.2008.00781.x",
"pubmed": "18237287",
"title": "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase",
"year": 2008
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"mappings": {
"aberowl": "TADS",
"biocontext": "TADS",
"bioportal": "TADS",
"fairsharing": "FAIRsharing.8wm364",
"obofoundry": "tads",
"ols": "tads",
"ontobee": "TADS"
},
"obofoundry": {
"contact": "dsonensh@odu.edu",
"contact.label": "Daniel Sonenshine",
"deprecated": true,
"description": "The anatomy of the Tick, Families: Ixodidae, Argassidae",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/tads.obo",
"download.owl": "http://purl.obolibrary.org/obo/tads.owl",
"homepage": "https://www.vectorbase.org/ontology-browser",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Tick Anatomy Ontology",
"prefix": "tads",
"repository": "https://github.com/VEuPathDB-ontology/TADS"
},
"ols": {
"description": "The anatomy of the Tick, Families: Ixodidae, Argassidae",
"download_owl": "http://purl.obolibrary.org/obo/tads.owl",
"homepage": "https://www.vectorbase.org/ontology-browser",
"name": "Tick Anatomy Ontology",
"prefix": "tads",
"version": "2015-08-20",
"version.iri": "http://purl.obolibrary.org/obo/tads/2015-08-20/tads.owl"
},
"ontobee": {
"library": "Library",
"name": "Tick Anatomy Ontology",
"prefix": "TADS"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1111/j.1365-2583.2008.00781.x",
"pubmed": "18237287",
"title": "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase",
"year": 2008
}
]
},
"tahe": {
"biocontext": {
"prefix": "TAHE"
},
"mappings": {
"biocontext": "TAHE",
"obofoundry": "tahe"
},
"obofoundry": {
"contact": "pierre.sprumont@unifr.ch",
"contact.label": "Pierre Sprumont",
"deprecated": true,
"domain": "anatomy and development",
"name": "Terminology of Anatomy of Human Embryology",
"prefix": "tahe"
}
},
"tahh": {
"biocontext": {
"prefix": "TAHH"
},
"mappings": {
"biocontext": "TAHH",
"obofoundry": "tahh"
},
"obofoundry": {
"contact": "pierre.sprumont@unifr.ch",
"contact.label": "Pierre Sprumont",
"deprecated": true,
"domain": "health",
"name": "Terminology of Anatomy of Human Histology",
"prefix": "tahh"
}
},
"tair.gene": {
"banana": "Gene",
"banana_peel": ":",
"biocontext": {
"prefix": "TAIR.GENE"
},
"contact": {
"email": "aisling.doyle9@gmail.com",
"name": "Aisling Doyle",
"orcid": "0000-0003-3871-858X"
},
"example": "2200934",
"mappings": {
"biocontext": "TAIR.GENE",
"miriam": "tair.gene",
"n2t": "tair.gene",
"prefixcommons": "tair.gene"
},
"miriam": {
"deprecated": false,
"description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus.",
"homepage": "http://arabidopsis.org/index.jsp",
"id": "00000049",
"name": "TAIR Gene",
"namespaceEmbeddedInLui": false,
"pattern": "^Gene:\\d{7}$",
"prefix": "tair.gene",
"sampleId": "Gene:2200934"
},
"n2t": {
"description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus.",
"example": "Gene:2200934",
"homepage": "http://arabidopsis.org/index.jsp",
"name": "The Arabidopsis Information Resource (TAIR) Gene",
"namespaceEmbeddedInLui": false,
"pattern": "^Gene:\\d{7}$",
"prefix": "tair.gene"
},
"part_of": "tair",
"pattern": "^\\d{7}$",
"prefixcommons": {
"description": "The reference gene model for a given locus",
"example": "Gene:2200934",
"keywords": [
"gene"
],
"name": "TAIR-Gene",
"pattern": "^Gene:\\d{7}$",
"prefix": "tair.gene",
"pubmed_ids": [
"12444417"
]
},
"publications": [
{
"doi": "10.1007/s10142-002-0077-z",
"pubmed": "12444417",
"title": "TAIR: a resource for integrated Arabidopsis data",
"year": 2002
}
],
"uri_format": "http://arabidopsis.org/servlets/TairObject?accession=Gene:$1"
},
"tair.locus": {
"biocontext": {
"prefix": "TAIR.LOCUS"
},
"contact": {
"email": "aisling.doyle9@gmail.com",
"name": "Aisling Doyle",
"orcid": "0000-0003-3871-858X"
},
"contributor_extras": [
{
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
}
],
"go": {
"homepage": "http://www.arabidopsis.org/",
"name": "The Arabidopsis Information Resource",
"prefix": "TAIR"
},
"mappings": {
"biocontext": "TAIR.LOCUS",
"go": "TAIR",
"miriam": "tair.locus",
"n2t": "tair.locus",
"ncbi": "TAIR",
"prefixcommons": "tair.locus"
},
"miriam": {
"deprecated": false,
"description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS.",
"homepage": "http://arabidopsis.org/index.jsp",
"id": "00000050",
"name": "TAIR Locus",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{7}$",
"prefix": "tair.locus",
"sampleId": "2200950",
"uri_format": "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1"
},
"n2t": {
"description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS.",
"example": "2200950",
"homepage": "http://arabidopsis.org/index.jsp",
"name": "The Arabidopsis Information Resource (TAIR) Locus",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{7}$",
"prefix": "tair.locus",
"uri_format": "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1"
},
"ncbi": {
"example": "AT1F51370",
"homepage": "http://www.arabidopsis.org/servlets/Search?type=gene&action=new_search",
"name": "Arabidopsis IR",
"prefix": "TAIR"
},
"pattern": "^\\d+$",
"prefixcommons": {
"description": "The locus name",
"example": "AT1G01030",
"keywords": [
"genome"
],
"name": "TAIR-Locus",
"pattern": "^AT[1-5]G\\d{5}$",
"prefix": "tair.locus",
"pubmed_ids": [
"12444417"
],
"uri_format": "http://arabidopsis.org/servlets/TairObject?type=locus&name=$1"
},
"providers": [
{
"code": "thalemine",
"description": "Data mining on aradopsis",
"homepage": "https://bar.utoronto.ca/thalemine",
"name": "ThaleMine",
"uri_format": "https://bar.utoronto.ca/thalemine/portal.do?externalids=$1"
}
],
"publications": [
{
"doi": "10.1007/s10142-002-0077-z",
"pubmed": "12444417",
"title": "TAIR: a resource for integrated Arabidopsis data",
"year": 2002
}
]
},
"tair.protein": {
"banana": "AASequence",
"banana_peel": ":",
"biocontext": {
"prefix": "TAIR.PROTEIN"
},
"contact": {
"email": "aisling.doyle9@gmail.com",
"name": "Aisling Doyle",
"orcid": "0000-0003-3871-858X"
},
"example": "1009107926",
"mappings": {
"biocontext": "TAIR.PROTEIN",
"miriam": "tair.protein",
"n2t": "tair.protein",
"prefixcommons": "tair.protein"
},
"miriam": {
"deprecated": false,
"description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept",
"homepage": "http://arabidopsis.org/index.jsp",
"id": "00000048",
"name": "TAIR Protein",
"namespaceEmbeddedInLui": false,
"pattern": "^AASequence:\\d{10}$",
"prefix": "tair.protein",
"sampleId": "AASequence:1009107926"
},
"n2t": {
"description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept",
"example": "AASequence:1009107926",
"homepage": "http://arabidopsis.org/index.jsp",
"name": "The Arabidopsis Information Resource (TAIR) Protein",
"namespaceEmbeddedInLui": false,
"pattern": "^AASequence:\\d{10}$",
"prefix": "tair.protein"
},
"pattern": "^\\d{10}$",
"prefixcommons": {
"description": "The protein entry",
"example": "AASequence:1009107926",
"keywords": [
"protein"
],
"name": "TAIR-Protein",
"pattern": "^AASequence:\\d{10}$",
"prefix": "tair.protein",
"pubmed_ids": [
"12444417"
]
},
"publications": [
{
"doi": "10.1007/s10142-002-0077-z",
"pubmed": "12444417",
"title": "TAIR: a resource for integrated Arabidopsis data",
"year": 2002
}
],
"uri_format": "http://arabidopsis.org/servlets/TairObject?accession=AASequence:$1"
},
"tao": {
"aberowl": {
"description": "TAO is a multispecies anatomy ontology for teleost fishes. Originally seeded from ZFA, but intended to cover terms relevant to other taxa.",
"download_obo": "http://aber-owl.net/media/ontologies/TAO/135/tao.obo",
"homepage": "https://www.nescent.org/phenoscape/Main_Page",
"name": "Teleost Anatomy Ontology",
"prefix": "TAO",
"version": "2012-08-10"
},
"biocontext": {
"prefix": "TAO"
},
"bioportal": {
"contact": {
"email": "wasila.dahdul@usd.edu",
"name": "Wasila Dahdul"
},
"description": "TAO is a multispecies anatomy ontology for teleost fishes. Originally seeded from ZFA, but intended to cover terms relevant to other taxa.",
"homepage": "https://www.nescent.org/phenoscape/Main_Page",
"name": "Teleost Anatomy Ontology",
"prefix": "TAO",
"publication": "http://dx.doi.org/10.1093/sysbio/syq013",
"version": "2012-08-10"
},
"example": "0000086",
"mappings": {
"aberowl": "TAO",
"biocontext": "TAO",
"bioportal": "TAO",
"obofoundry": "tao",
"ols": "tao",
"prefixcommons": "tao"
},
"name": "Teleost Anatomy Ontology",
"obofoundry": {
"contact": "wasila.dahdul@usd.edu",
"contact.label": "Wasila Dahdul",
"contact.orcid": "0000-0003-3162-7490",
"deprecated": true,
"description": "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa",
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/tao.owl",
"homepage": "http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology",
"license": "CC0 1.0",
"license.url": "http://creativecommons.org/publicdomain/zero/1.0/",
"name": "Teleost Anatomy Ontology",
"prefix": "tao",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/20547776",
"title": "The teleost anatomy ontology: anatomical representation for the genomics age"
}
]
},
"ols": {
"description": "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa",
"homepage": "http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology",
"name": "Teleost Anatomy Ontology",
"prefix": "tao",
"version": "2012-08-10",
"version.iri": "http://purl.obolibrary.org/obo/tao/2012-08-10/tao.owl"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1110",
"description": "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa",
"example": "TAO_0000297",
"homepage": "https://www.nescent.org/phenoscape/Main_Page",
"keywords": [
"obo",
"classification",
"anatomy"
],
"name": "Teleost Anatomy Ontology",
"pattern": "^TAO_\\d{7}$",
"prefix": "tao",
"synonyms": [
"teleost_anatomy"
]
},
"publications": [
{
"doi": "10.1093/sysbio/syq013",
"pmc": "PMC2885267",
"pubmed": "20547776",
"title": "The teleost anatomy ontology: anatomical representation for the genomics age",
"year": 2010
}
],
"synonyms": [
"TAO_RETIRED"
]
},
"tarbase": {
"biocontext": {
"prefix": "TARBASE"
},
"fairsharing": {
"abbreviation": "TarBase",
"description": "DIANA-TarBase is a reference database that indexes experimentally-supported microRNA (miRNA) targets. It integrates information on cell-type specific miRNAβgene regulation and includes miRNA-binding locations. The target data provided by DIANA-TarBase is supported by information on methodologies, cell types/tissues and experimental conditions.",
"homepage": "http://www.microrna.gr/tarbase",
"name": "TarBase",
"prefix": "FAIRsharing.a0k4cd",
"publications": [
{
"doi": "10.1093/nar/gkx1141",
"pubmed_id": 29156006,
"title": "DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions."
},
{
"doi": "10.1093/nar/gkn809",
"pubmed_id": 18957447,
"title": "The database of experimentally supported targets: a functional update of TarBase."
},
{
"doi": "10.1261/rna.2239606",
"pubmed_id": 16373484,
"title": "TarBase: A comprehensive database of experimentally supported animal microRNA targets."
},
{
"doi": "10.1093/nar/gku1215",
"pubmed_id": 25416803,
"title": "DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions."
}
],
"subjects": [
"Life Science",
"Biomedical Science"
]
},
"integbio": {
"description": "DIANA-TarBase was initially released in 2006 and it was the first database aiming to catalogue published experimentally validated miRNA:gene interactions. DIANA-TarBase (v7.0), provides hundreds of thousands of high quality manually curated experimentally validated miRNA:gene interactions, enhanced with detailed meta-data.",
"fairsharing": "FAIRsharing.a0k4cd",
"homepage": "http://www.microrna.gr/tarbase",
"information_keywords": [
"Bibliography/Documents",
"Method",
"Interaction/Pathway"
],
"maintainer": "IBI (Institute for Biomedical Informatics, University of Pennsylvania)||Diana Lab Group||BSRC (Biomedical Sciences Research Center Alexander Fleming)",
"name": "TarBase",
"prefix": "nbdc02102",
"pubmeds": [
"18957447",
"16373484",
"25416803"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"mappings": {
"biocontext": "TARBASE",
"fairsharing": "FAIRsharing.a0k4cd",
"integbio": "nbdc02102",
"miriam": "tarbase",
"n2t": "tarbase",
"pathguide": "283"
},
"miriam": {
"deprecated": false,
"description": "TarBase stores microRNA (miRNA) information for miRNAβgene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used.",
"homepage": "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index",
"id": "00000340",
"name": "TarBase",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z]{3}\\-(mir|let|lin)\\-\\w+(\\-\\w+\\-\\w+)?",
"prefix": "tarbase",
"sampleId": "hsa-let-7a-2-3p",
"uri_format": "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1"
},
"n2t": {
"description": "TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used.",
"example": "hsa-let-7a-2-3p",
"homepage": "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index",
"name": "TarBase v7 at University of Thessaly",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z]{3}\\-(mir|let|lin)\\-\\w+(\\-\\w+\\-\\w+)?",
"prefix": "tarbase",
"uri_format": "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1"
},
"pathguide": {
"abbreviation": "TarBase",
"homepage": "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index",
"name": "TarBase",
"prefix": "283"
},
"publications": [
{
"doi": "10.1093/nar/gkx1141",
"pmc": "PMC5753203",
"pubmed": "29156006",
"title": "DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions",
"year": 2018
},
{
"doi": "10.1093/nar/gku1215",
"pmc": "PMC4383989",
"pubmed": "25416803",
"title": "DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions",
"year": 2014
},
{
"doi": "10.1093/nar/gkn809",
"pmc": "PMC2686456",
"pubmed": "18957447",
"title": "The database of experimentally supported targets: a functional update of TarBase",
"year": 2008
},
{
"doi": "10.1261/rna.2239606",
"pmc": "PMC1370898",
"pubmed": "16373484",
"title": "TarBase: A comprehensive database of experimentally supported animal microRNA targets",
"year": 2005
}
]
},
"taxrank": {
"aberowl": {
"description": "A vocabulary of taxonomic ranks (species, family, phylum, etc)",
"download_owl": "http://aber-owl.net/media/ontologies/TAXRANK/10/taxrank.owl",
"homepage": "https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary",
"name": "Taxonomic rank vocabulary",
"prefix": "TAXRANK"
},
"agroportal": {
"contact": {
"email": "peter.midford@gmail.com",
"name": "Peter Midford"
},
"description": "A vocabulary of taxonomic ranks developed as part of Phenoscape's Vertebrate Taxonomy Ontology. It provides terms for taxonomic ranks drawn from both the NCBI taxonomy database and from a rank vocabulary developed for the TDWG biodiversity information standards group. Cross references to appearances of each term in each source are provided. Consistent with its intended use as a vocabulary of labels, there is no relation specifying an ordering of the rank terms.",
"name": "Taxonomic Rank Ontology",
"prefix": "TAXRANK"
},
"biocontext": {
"prefix": "TAXRANK"
},
"bioportal": {
"contact": {
"email": "peteremidford@yahoo.com",
"name": "Peter Midford"
},
"description": "A vocabulary of taxonomic ranks intended to replace the sets of rank terms found in the Teleost Taxonomy Ontology, the OBO translation of the NCBI taxonomy and similar OBO taxonomy ontologies. It provides terms for taxonomic ranks drawn from both the NCBI taxonomy database and from a rank vocabulary developed for the TDWG biodiversity information standards group. Cross references to appearances of each term in each source are provided. Consistent with its intended use as a vocabulary of labels, there is no relation specifying an ordering of the rank terms.",
"homepage": "https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary",
"name": "Taxonomic Rank Vocabulary",
"prefix": "TAXRANK",
"version": "unknown"
},
"example": "0000001",
"fairsharing": {
"abbreviation": "TAXRANK",
"contact": {
"email": "peteremidford@yahoo.com",
"name": "Peter E. Midford",
"orcid": "0000-0001-6512-3296"
},
"description": "This is a vocabulary of taxonomic ranks intended to replace the sets of rank terms found in the Teleost Taxonomy Ontology, the OBO translation of the NCBI taxonomy and similar OBO taxonomy ontologies. It provides terms for taxonomic ranks drawn from both the NCBI taxonomy database and from a rank vocabulary developed for the TDWG biodiversity information standards group. Each term contains cross reference links to the resources that use the terms. Consistent with its intended use as a vocabulary, there is no relation specifying an ordering of the rank terms. Likewise, all terms are directly descended from the term 'taxonomic rank' (TAXRANK:0000000).",
"domains": [
"Taxonomic classification"
],
"homepage": "https://wiki.phenoscape.org/wiki/Ontologies#Taxonomic_Rank_Vocabulary_.28TAXRANK.29",
"license": "CC0-1.0",
"name": "Taxonomic Rank Vocabulary",
"prefix": "FAIRsharing.p1sejz",
"repository": "https://github.com/phenoscape/taxrank",
"subjects": [
"Taxonomy",
"Life Science"
]
},
"mappings": {
"aberowl": "TAXRANK",
"agroportal": "TAXRANK",
"biocontext": "TAXRANK",
"bioportal": "TAXRANK",
"fairsharing": "FAIRsharing.p1sejz",
"obofoundry": "taxrank",
"ols": "taxrank",
"ontobee": "TAXRANK",
"prefixcommons": "taxrank"
},
"obofoundry": {
"contact": "balhoff@renci.org",
"contact.github": "balhoff",
"contact.label": "Jim Balhoff",
"contact.orcid": "0000-0002-8688-6599",
"deprecated": false,
"description": "A vocabulary of taxonomic ranks (species, family, phylum, etc)",
"domain": "organisms",
"download.obo": "http://purl.obolibrary.org/obo/taxrank.obo",
"download.owl": "http://purl.obolibrary.org/obo/taxrank.owl",
"homepage": "https://github.com/phenoscape/taxrank",
"license": "CC0 1.0",
"license.url": "http://creativecommons.org/publicdomain/zero/1.0/",
"name": "Taxonomic rank vocabulary",
"preferredPrefix": "TAXRANK",
"prefix": "taxrank",
"publications": [
{
"id": "https://doi.org/10.1186/2041-1480-4-34",
"title": "The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes"
}
],
"repository": "https://github.com/phenoscape/taxrank"
},
"ols": {
"description": "A vocabulary of taxonomic ranks (species, family, phylum, etc)",
"download_owl": "http://purl.obolibrary.org/obo/taxrank.owl",
"homepage": "https://github.com/phenoscape/taxrank",
"name": "Taxonomic rank vocabulary",
"prefix": "taxrank",
"version": "2016-04-15",
"version.iri": "http://purl.obolibrary.org/obo/taxrank/releases/2016-04-15/taxrank.owl"
},
"ontobee": {
"library": "Library",
"name": "Taxonomic rank vocabulary",
"prefix": "TAXRANK"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1419",
"description": "Taxonomic ranks drawn from both the NCBI taxonomy database and from a rank vocabulary developed for the TDWG biodiversity information standards group.",
"example": "TAXRANK:0000001",
"homepage": "https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary",
"keywords": [
"obo"
],
"name": "Taxonomic rank vocabulary",
"pattern": "^TAXRANK:\\d+$",
"prefix": "taxrank",
"synonyms": [
"taxonomic_rank"
]
},
"publications": [
{
"doi": "10.1186/2041-1480-4-34",
"pmc": "PMC4177199",
"pubmed": "24267744",
"title": "The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes",
"year": 2013
}
],
"uri_format": "http://purl.obolibrary.org/obo/TAXRANK_$1"
},
"tcb": {
"cellosaurus": {
"category": "Cell line collections",
"homepage": "https://www.pirbright.ac.uk/tick-cell-lines-views-page",
"name": "Tick Cell Biobank",
"prefix": "TCB",
"uri_format": "https://www.pirbright.ac.uk/node/$1"
},
"example": "2966",
"mappings": {
"cellosaurus": "TCB"
},
"pattern": "^\\d+$"
},
"tccd": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"mappings": {
"prefixcommons": "tccd"
},
"prefixcommons": {
"description": "Cell Cycle Database is a collection of genes and proteins involved in human and yeast cell cycle",
"example": "TP53",
"homepage": "http://www.itb.cnr.it/cellcycle",
"keywords": [
"gene",
"protein",
"pathway"
],
"name": "The Cell Cycle DB",
"pattern": "^[A-Z,0-9]+$",
"prefix": "tccd",
"uri_format": "http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"tcdb": {
"biocontext": {
"prefix": "TCDB"
},
"edam": {
"description": "Identifier of a membrane transport proteins from the transport classification database (TCDB).",
"name": "TC",
"obsolete": false,
"prefix": "2756"
},
"fairsharing": {
"abbreviation": "TCDB",
"contact": {
"email": "msaier@ucsd.edu",
"name": "Milton H. Saier, Jr.",
"orcid": "0000-0001-5530-0017"
},
"description": "This freely accessible database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information for organisms of all types. As of August 1, 2021, TCDB consists of 22,132 proteins classified in 17,390 transport systems with 1,604 tabulated 3D structures, 21,174 reference citations describing 1,708 transporter families, of which 25% are members of 94 recognized superfamilies. Overall, this is an increase of over 50% since the last published update of the database in 2016. The most recent update of the database contents and features include (1) adoption of a chemical ontology for substrates of transporters, (2) inclusion of new superfamilies, (3) a domain-based characterization of transporter families (tcDoms) for the identification of new members as well as functional and evolutionary relationships between families, (4) development of novel software to facilitate curation and use of the database, (5) addition of new subclasses of transport systems including 11 novel types of channels and 3 types of group translocators, and (6) the inclusion of many man-made (artificial) transmembrane pores/channels and carriers.",
"homepage": "https://tcdb.org/",
"license": "CC BY-SA 3.0",
"name": "Transporter Classification Database",
"prefix": "FAIRsharing.p3bzqb",
"publications": [
{
"doi": "10.1093/nar/gkt1097",
"pubmed_id": 24225317,
"title": "The transporter classification database"
},
{
"doi": "10.1093/nar/gkaa1004",
"pubmed_id": 33170213,
"title": "The Transporter Classification Database (TCDB): 2021 update"
},
{
"doi": "10.1093/nar/gkj001",
"pubmed_id": 16381841,
"title": "TCDB: the Transporter Classification Database for membrane transport protein analyses and information."
},
{
"doi": "10.1093/nar/gkn862",
"pubmed_id": 19022853,
"title": "The Transporter Classification Database: recent advances."
},
{
"doi": "10.1093/nar/gkv1103",
"pubmed_id": 26546518,
"title": "The Transporter Classification Database (TCDB): recent advances"
}
],
"subjects": [
"Knowledge and Information Systems",
"Phylogenetics",
"Computational Biology",
"Life Science",
"Cell Biology"
]
},
"go": {
"homepage": "http://www.tcdb.org/",
"name": "Transport Protein Database",
"prefix": "TC",
"uri_format": "http://www.tcdb.org/tcdb/index.php?tc=$1"
},
"homepage": "https://www.tcdb.org",
"mappings": {
"biocontext": "TCDB",
"edam": "2756",
"fairsharing": "FAIRsharing.p3bzqb",
"go": "TC",
"miriam": "tcdb",
"n2t": "tcdb",
"pathguide": "104",
"prefixcommons": "tcdb",
"uniprot": "DB-0135",
"wikidata": "P7260"
},
"miriam": {
"deprecated": false,
"description": "The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally.",
"homepage": "http://www.tcdb.org/",
"id": "00000040",
"name": "Transport Classification Database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+(\\.[A-Z])?(\\.\\d+)?(\\.\\d+)?(\\.\\d+)?$",
"prefix": "tcdb",
"sampleId": "5.A.1.1.1",
"uri_format": "http://www.tcdb.org/search/result.php?tc=$1"
},
"n2t": {
"description": "The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally.",
"example": "5.A.1.1.1",
"homepage": "http://www.tcdb.org/",
"name": "TCDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+(\\.[A-Z])?(\\.\\d+)?(\\.\\d+)?(\\.\\d+)?$",
"prefix": "tcdb",
"uri_format": "http://www.tcdb.org/search/result.php?tc=$1"
},
"name": "Transporter Classification Database",
"pathguide": {
"abbreviation": "TCDB",
"homepage": "http://www.tcdb.org/",
"name": "Transporter Classification Database",
"prefix": "104"
},
"prefixcommons": {
"description": "TCDB is a curated database of factual information from over 10,000 published references; it contains about 5,600 unique protein sequences that are classified into over 600 transporter families based on the TC-system.",
"example": "5.A.1.1.1",
"homepage": "http://www.tcdb.org/",
"keywords": [
"protein",
"structure"
],
"name": "Transport Classification Database",
"pattern": "^\\d+\\.[A-Z]\\.\\d+\\.\\d+\\.\\d+$",
"prefix": "tcdb",
"pubmed_ids": [
"16381841"
],
"synonyms": [
"tc"
],
"uri_format": "http://www.tcdb.org/search/result.php?tc=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkaa1004",
"pmc": "PMC7778945",
"pubmed": "33170213",
"title": "The Transporter Classification Database (TCDB): 2021 update",
"year": 2021
},
{
"doi": "10.1093/nar/gkv1103",
"pmc": "PMC4702804",
"pubmed": "26546518",
"title": "The Transporter Classification Database (TCDB): recent advances",
"year": 2015
},
{
"doi": "10.1093/nar/gkt1097",
"pmc": "PMC3964967",
"pubmed": "24225317",
"title": "The transporter classification database",
"year": 2013
},
{
"doi": "10.1093/nar/gkn862",
"pmc": "PMC2686586",
"pubmed": "19022853",
"title": "The Transporter Classification Database: recent advances",
"year": 2008
},
{
"doi": "10.1093/nar/gkj001",
"pmc": "PMC1334385",
"pubmed": "16381841",
"title": "TCDB: the Transporter Classification Database for membrane transport protein analyses and information",
"year": 2006
}
],
"synonyms": [
"TC"
],
"uniprot": {
"abbreviation": "TCDB",
"category": "Protein family/group databases",
"homepage": "https://www.tcdb.org/",
"name": "Transport Classification Database",
"prefix": "DB-0135",
"publications": [
{
"doi": "10.1093/nar/gkaa1004",
"pubmed": "33170213"
}
],
"uri_format": "https://www.tcdb.org/search/result.php?tc=$1"
},
"wikidata": {
"description": "classifies transport proteins similar to how EC classifies enzymes",
"example": [
"1.A.1",
"2.A.1.1.28",
"3.A.3"
],
"homepage": "https://www.tcdb.org",
"name": "Transporter Classification Database ID",
"pattern": "^\\d|(\\d\\.[A-Z](\\.(\\d{1,3}){0,3}))$",
"prefix": "P7260",
"uri_format": "http://www.tcdb.org/search/result.php?tc=$1"
}
},
"tctr": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The TCTR was estabished in 2009 and has been operated by Clinical Research Collaboration Network (CRCN), an organization under the Medical Research Foundation, which is a non-profit organization, and financially supported by Thailand Center of Excellence for Life Sciences (TCELS). CRCN has been retitled the Medical Research Network (MedResNet) since June 15, 2012. (from homepage)",
"example": "TCTR20230429001",
"homepage": "https://www.thaiclinicaltrials.org",
"name": "Thai Clinical Trials Registry",
"pattern": "^TCTR\\d+$",
"uri_format": "https://www.thaiclinicaltrials.org/show/$1"
},
"te": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Terminologia Embryologica (TE) is a standardized list of words used in the description of human embryologic and fetal structures. It was produced by the Federative International Committee on Anatomical Terminology on behalf of the International Federation of Associations of Anatomists and posted on the Internet since 2010. [wikipedia]",
"example": "E5.11.2.0.0.0.4",
"homepage": "https://ifaa.unifr.ch/",
"mappings": {
"wikidata": "P1693"
},
"name": "Terminologia Embryologica",
"references": [
"https://en.wikipedia.org/wiki/Terminologia_Embryologica"
],
"wikidata": {
"description": "standardized list of words used in the description of human embryologic and fetal structures",
"name": "Terminologia Embryologica",
"prefix": "P1693"
}
},
"tfclass": {
"contact": {
"email": "edgar.wingender@edgar-wingender.de",
"name": "Edgar Wingender",
"orcid": "0000-0002-7729-8453"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here..",
"example": "2.1.1",
"fairsharing": {
"abbreviation": "TFClass",
"description": "TFClass is a resource that classifies eukaryotic transcription factors (TFs) according to their DNA-binding domains. Combining information from different resources, manually checking the retrieved mammalian TF sequences and applying extensive phylogenetic analyses, >39,000 TFs from up to 41 mammalian species were assigned to the Superclasses, Classes, Families and Subfamilies of TFClass. TFClass provides corresponding sequence collections in FASTA format; sequence logos and phylogenetic trees at different classification levels; predicted TF binding sites for human, mouse, dog and cow genomes; and links to several external databases.",
"domains": [
"Expression data",
"Transcription factor binding site prediction",
"Binding",
"Transcription factor",
"Binding site"
],
"homepage": "http://tfclass.bioinf.med.uni-goettingen.de/index.jsf",
"name": "Transcription Factor Class",
"prefix": "FAIRsharing.XykycZ",
"publications": [
{
"doi": "10.1093/nar/gkx987",
"pubmed": "29087517",
"title": "TFClass: expanding the classification of human transcription factors to their mammalian orthologs",
"year": 2017
}
],
"subjects": [
"Bioinformatics",
"Phylogenetics",
"Transcriptomics"
]
},
"go": {
"homepage": "http://tfclass.bioinf.med.uni-goettingen.de/",
"name": "TFClass is a resource for the classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains",
"prefix": "TFClass",
"synonyms": [
"TFCLASS_FAMILY",
"tfclass"
],
"uri_format": "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1"
},
"homepage": "http://tfclass.bioinf.med.uni-goettingen.de",
"mappings": {
"fairsharing": "FAIRsharing.XykycZ",
"go": "TFClass",
"pathguide": "666"
},
"name": "Classification of Transcription Factors in Mammalia",
"pathguide": {
"abbreviation": "TFClass",
"homepage": "http://tfclass.bioinf.med.uni-goettingen.de/tfclass",
"name": "Classification of Human Transcription Factors and Mouse Orthologs",
"prefix": "666"
},
"publications": [
{
"doi": "10.1093/nar/gkx987",
"pmc": "PMC5753292",
"pubmed": "29087517",
"title": "TFClass: expanding the classification of human transcription factors to their mammalian orthologs",
"year": 2018
}
],
"uri_format": "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1"
},
"tgd": {
"biocontext": {
"prefix": "TGD"
},
"go": {
"homepage": "http://www.ciliate.org/",
"name": "Tetrahymena Genome Database",
"prefix": "TGD"
},
"mappings": {
"biocontext": "TGD",
"go": "TGD",
"miriam": "tgd",
"n2t": "tgd",
"prefixcommons": "tgd"
},
"miriam": {
"deprecated": false,
"description": "The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature.",
"homepage": "http://ciliate.org/index.php/",
"id": "00000313",
"name": "Tetrahymena Genome Database",
"namespaceEmbeddedInLui": false,
"pattern": "^TTHERM\\_\\d+$",
"prefix": "tgd",
"sampleId": "TTHERM_00648910",
"uri_format": "http://ciliate.org/index.php/feature/details/$1"
},
"n2t": {
"description": "The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature.",
"example": "TTHERM_00648910",
"homepage": "http://ciliate.org/index.php/",
"name": "TGD at Stanford University",
"namespaceEmbeddedInLui": false,
"pattern": "^TTHERM\\_\\d+$",
"prefix": "tgd",
"uri_format": "http://ciliate.org/index.php/feature/details/$1"
},
"prefixcommons": {
"description": "Pages with links to phage information are also available, including a T4 genetic map reference figure, RB69, RB49, and Aeh1 Map figures, electron micrographs, annotation tables, sequence files, and links to NCBI T4 and Integrated Genomics RB69 annotation sites are available.",
"example": "RB51",
"homepage": "http://phage.bioc.tulane.edu",
"keywords": [
"genome"
],
"name": "T4-like genome database",
"pattern": "^[A-Z,0-9]+$",
"prefix": "tgd",
"uri_format": "http://phage.bioc.tulane.edu/cgi-bin/gbrowse/$1?name=$1"
}
},
"tgma": {
"aberowl": {
"description": "A structured controlled vocabulary of the anatomy of mosquitoes.",
"download_owl": "http://aber-owl.net/media/ontologies/TGMA/18/tgma.owl",
"homepage": "https://www.vectorbase.org/ontology-browser",
"name": "Mosquito gross anatomy ontology",
"prefix": "TGMA"
},
"biocontext": {
"prefix": "TGMA"
},
"bioportal": {
"contact": {
"email": "louis@imbb.forth.gr",
"name": "C. Louis"
},
"description": "A structured controlled vocabulary of the anatomy of mosquitoes.",
"homepage": "http://www.anobase.org",
"name": "Mosquito Gross Anatomy Ontology",
"prefix": "TGMA",
"version": "releases/2013-06-03"
},
"contact": {
"email": "topalis@imbb.forth.gr",
"name": "Pantelis Topalis",
"orcid": "0000-0002-1635-4810"
},
"download_obo": "http://purl.obolibrary.org/obo/tgma.obo",
"example": "0000984",
"fairsharing": {
"abbreviation": "TGMA",
"description": "A structured controlled vocabulary of the anatomy of mosquitoes.",
"homepage": "https://www.vectorbase.org/ontology-browser",
"name": "Mosquito gross anatomy",
"prefix": "FAIRsharing.dqnfkg",
"publications": [
{
"doi": "10.1111/j.1365-2583.2008.00781.x",
"pubmed": "18237287",
"title": "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase",
"year": 2008
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"mappings": {
"aberowl": "TGMA",
"biocontext": "TGMA",
"bioportal": "TGMA",
"fairsharing": "FAIRsharing.dqnfkg",
"obofoundry": "tgma",
"ols": "tgma",
"ontobee": "TGMA",
"prefixcommons": "tgma"
},
"obofoundry": {
"contact": "topalis@imbb.forth.gr",
"contact.label": "Pantelis Topalis",
"deprecated": true,
"description": "A structured controlled vocabulary of the anatomy of mosquitoes.",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/tgma.obo",
"download.owl": "http://purl.obolibrary.org/obo/tgma.owl",
"homepage": "https://www.vectorbase.org/ontology-browser",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Mosquito gross anatomy ontology",
"prefix": "tgma",
"repository": "https://github.com/VEuPathDB-ontology/TGMA"
},
"ols": {
"description": "A structured controlled vocabulary of the anatomy of mosquitoes.",
"download_owl": "http://purl.obolibrary.org/obo/tgma.owl",
"homepage": "https://www.vectorbase.org/ontology-browser",
"name": "Mosquito gross anatomy ontology",
"prefix": "tgma",
"version": "2013-06-03",
"version.iri": "http://purl.obolibrary.org/obo/tgma/releases/2013-06-03/tgma.owl"
},
"ontobee": {
"library": "Library",
"name": "Mosquito gross anatomy ontology",
"prefix": "TGMA"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1030",
"description": "A structured controlled vocabulary of the anatomy of mosquitoes.",
"example": "TGMA_0001525",
"homepage": "http://www.anobase.org",
"keywords": [
"obo",
"anatomy",
"mosquito"
],
"name": "Mosquito gross anatomy",
"pattern": "^TGMA_\\d{7}$",
"prefix": "tgma"
},
"publications": [
{
"doi": "10.1111/j.1365-2583.2008.00781.x",
"pubmed": "18237287",
"title": "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase",
"year": 2008
}
]
},
"tgn": {
"bartoc": {
"abbreviation": "TGN",
"description": "TGN is a structured vocabulary currently containing around 1,106,000 names and other information about places. Names for a place may include names in the vernacular language, English, other languages, historical names, names and in natural order and inverted order. Among these names, one is flagged as the preferred name. TGN is a thesaurus, compliant with ISO and NISO standards for thesaurus construction; it contains hierarchical, equivalence, and associative relationships. Note that TGN is not a GIS (Geographic Information System). While many records in TGN include coordinates, these coordinates are approximate and are intended for reference only. The focus of each TGN record is a place. There are around 912,000 places in the TGN. In the database, each place record (also called a subject) is identified by a unique numeric ID. Linked to the record for the place are names, the place's parent or position in the hierarchy, other relationships, geographic coordinates, notes, sources for the data, and place types, which are terms describing the role of the place (e.g., inhabited place and state capital). The temporal coverage of the TGN ranges from prehistory to the present and the scope is global. The TGN is a hierarchical database; its trees branch from a root called Top of the TGN hierarchies (Subject_ID: 1000000). Currently there are two TGN facets, World and Extraterrestrial Places. Under the facet World, places are arranged in hierarchies generally representing the current political and physical world, although some historical nations and empires are also included. There may be multiple broader contexts, making the TGN polyhierarchical. The primary users of the Getty vocabularies include museums, art libraries, archives, visual resource collection catalogers, bibliographic projects concerned with art, researchers in art and art history, and the information specialists who are dealing with the needs of these users. In addition, a significant number of users of the Getty vocabularies are students or members of the general public.",
"homepage": "http://www.getty.edu/research/tools/vocabularies/tgn/",
"license": "http://www.opendatacommons.org/licenses/by/1.0",
"name": "Getty Thesaurus of Geographic Names",
"prefix": "109",
"wikidata_database": "Q1520117"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"example": "1023371",
"homepage": "https://www.getty.edu/research/tools/vocabularies/tgn/",
"mappings": {
"bartoc": "109"
},
"name": "Getty Thesaurus of Geographic Names",
"pattern": "^\\d+$",
"references": [
"https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200"
],
"uri_format": "http://vocab.getty.edu/page/tgn/$1"
},
"th": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]",
"example": "H3.03.00.0.00007",
"homepage": "https://ifaa.unifr.ch/",
"keywords": [
"biology",
"cytology",
"histology",
"life sciences"
],
"name": "Terminologia Histologica",
"references": [
"https://en.wikipedia.org/wiki/Terminologia_Histologica"
]
},
"thermofisher": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "ThermoFisher is a life sciences supply vendor.",
"example": "OSR00185W",
"homepage": "https://www.thermofisher.com",
"keywords": [
"biology",
"chemistry",
"life sciences",
"vendor"
],
"name": "Thermo Fisher Scientific",
"pattern": "^\\w+$",
"uri_format": "https://www.thermofisher.com/antibody/product/$1"
},
"tigrfam": {
"biocontext": {
"prefix": "TIGRFAM"
},
"contributor_extras": [
{
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
}
],
"edam": {
"description": "Accession number of an entry (family) from the TIGRFam database.",
"name": "TIGRFam",
"obsolete": false,
"prefix": "1141"
},
"mappings": {
"biocontext": "TIGRFAM",
"edam": "1141",
"miriam": "tigrfam",
"n2t": "tigrfam",
"ncbi": "TIGRFAM",
"prefixcommons": "tigrfams"
},
"miriam": {
"deprecated": false,
"description": "TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins.",
"homepage": "http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi",
"id": "00000315",
"name": "TIGRFAMS",
"namespaceEmbeddedInLui": false,
"pattern": "^TIGR\\d+$",
"prefix": "tigrfam",
"sampleId": "TIGR00010",
"uri_format": "http://www.jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=$1"
},
"n2t": {
"description": "TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins.",
"example": "TIGR00010",
"homepage": "http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi",
"name": "TIGRFAM at JCVI",
"namespaceEmbeddedInLui": false,
"pattern": "^TIGR\\d+$",
"prefix": "tigrfam",
"uri_format": "http://www.jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=$1"
},
"ncbi": {
"example": "TIGR00094",
"homepage": "http://www.tigr.org/TIGRFAMs/index.shtml",
"name": "TIGR protein families",
"prefix": "TIGRFAM"
},
"prefixcommons": {
"description": "TIGRFAMs are protein families based on Hidden Markov Models or HMMs. This collection is used to see the curated seed alignmet for each TIGRFam, the full alignment of all family members and the cutoff scores for inclusion in each of the TIGRFAMs.",
"example": "TIGR00254",
"homepage": "http://www.jcvi.org/cms/research/projects/tigrfams/",
"keywords": [
"protein"
],
"name": "TIGRFAMs HMM collection at the J. Craig Venter Institute",
"pattern": "^TIGR\\d+$",
"prefix": "tigrfams",
"synonyms": [
"jcvi.tigrfams"
],
"uri_format": "http://cmr.jcvi.org/cgi-bin/CMR/HmmReport.cgi?hmm_acc=$1"
},
"references": [
"https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/license_and_availability.txt",
"https://github.com/biopragmatics/bioregistry/issues/366"
],
"uri_format": "https://www.ncbi.nlm.nih.gov/cdd?term=$1"
},
"time": {
"aberowl": {
"description": "OWL-Time is an OWL-2 DL ontology of temporal concepts, for describing the temporal properties of resources in the world or described in Web pages. The ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. Time positions and durations may be expressed using either the conventional (Gregorian) calendar and clock, or using another temporal reference system such as Unix-time, geologic time, or different calendars.",
"download_owl": "http://aber-owl.net/media/ontologies/TIME/2/time.owl",
"homepage": "https://www.w3.org/TR/owl-time/",
"name": "OWL-Time",
"prefix": "TIME",
"version": "2017"
},
"bioportal": {
"contact": {
"email": "chris.little@metoffice.gov.uk",
"name": "Chris Little"
},
"description": "OWL-Time is an OWL-2 DL ontology of temporal concepts, for describing the temporal properties of resources in the world or described in Web pages. The ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. Time positions and durations may be expressed using either the conventional (Gregorian) calendar and clock, or using another temporal reference system such as Unix-time, geologic time, or different calendars.",
"homepage": "https://www.w3.org/TR/owl-time/",
"name": "OWL-Time",
"prefix": "TIME",
"version": "2017"
},
"contact": {
"email": "dr.shorthair@pm.me",
"github": "dr-shorthair",
"name": "Simon Cox",
"orcid": "0000-0002-3884-3420"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Owl-time is an owl-2 dl ontology of temporal concepts, for describing the temporal properties of resources in the world or described in web pages. the ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. time positions and durations may be expressed using either the conventional (gregorian) calendar and clock, or using another temporal reference system such as unix-time, geologic time, or different calendars.",
"example": "DateTimeDescription",
"fairsharing": {
"abbreviation": "TIME",
"contact": {
"email": "simon.cox@csiro.au",
"name": "Simon Cox, Chris Little",
"orcid": "0000-0002-3884-3420"
},
"description": "OWL-Time is an OWL-2 DL ontology of temporal concepts, for describing the temporal properties of resources in the world or described in Web pages. The ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. Time positions and durations may be expressed using either the conventional (Gregorian) calendar and clock, or using another temporal reference system such as Unix-time, geologic time, or different calendars.",
"domains": [
"Resource metadata",
"Data model"
],
"homepage": "https://www.w3.org/TR/owl-time/",
"license": "CC-BY-4.0",
"name": "OWL-Time",
"prefix": "FAIRsharing.hw3bh2",
"subjects": [
"Subject Agnostic"
],
"user_defined_tags": [
"Data coordination",
"Metadata standardization"
]
},
"github_request_issue": 505,
"homepage": "https://www.w3.org/TR/owl-time/",
"lov": {
"description": "This vocabulary defines temporal entities such as time intervals, their properties and relationships.",
"homepage": "http://www.w3.org/TR/owl-time",
"keywords": [
"Time"
],
"modified": "2017-04-06",
"name": "Time Ontology",
"prefix": "time",
"uri_prefix": "http://www.w3.org/2006/time#$1"
},
"mappings": {
"aberowl": "TIME",
"bioportal": "TIME",
"fairsharing": "FAIRsharing.hw3bh2",
"lov": "time",
"zazuko": "time"
},
"name": "Time Ontology in OWL",
"repository": "https://github.com/w3c/sdw/",
"uri_format": "http://www.w3.org/2006/time#$1",
"zazuko": {
"prefix": "time",
"uri_format": "http://www.w3.org/2006/time#$1"
}
},
"tkg": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "http://www2.idac.tohoku.ac.jp/dep/ccr/",
"name": "Tohoku University cell line catalog",
"prefix": "TKG",
"uri_format": "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvo10%n/$1.html"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells.",
"example": "0221",
"homepage": "http://www2.idac.tohoku.ac.jp/dep/ccr/",
"mappings": {
"cellosaurus": "TKG"
},
"name": "Tohoku University cell line catalog",
"pattern": "^\\d+$",
"uri_format": "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html"
},
"tngb": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "http://biobanknetwork.telethon.it/",
"name": "Telethon Network of Genetic Biobanks",
"prefix": "TNGB",
"uri_format": "http://biobanknetwork.telethon.it/Sample/View?sampleId=$1"
},
"example": "67035",
"mappings": {
"cellosaurus": "TNGB"
},
"pattern": "^\\d+$"
},
"to": {
"aberowl": {
"description": "A controlled vocabulary to describe phenotypic traits in plants.",
"download_owl": "http://aber-owl.net/media/ontologies/TO/11/to.owl",
"homepage": "http://browser.planteome.org/amigo",
"name": "Plant Trait Ontology",
"prefix": "TO"
},
"agroportal": {
"contact": {
"email": "cooperl@science.oregonstate.edu",
"name": "Laurel Cooper"
},
"description": "An ontology that describes phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant.",
"example_uri": "http://purl.obolibrary.org/obo/TO_0000064",
"homepage": "https://planteome.org/",
"license": "CC-BY-4.0",
"name": "Plant Trait Ontology",
"prefix": "TO",
"publication": "https://planteome.org/references",
"repository": "https://github.com/Planteome/plant-trait-ontology",
"version": "July 2023"
},
"biocontext": {
"prefix": "TO"
},
"bioportal": {
"contact": {
"email": "jaiswalp@oregonstate.edu",
"name": "Pankaj Jaiswal"
},
"description": "A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part.",
"homepage": "http://www.planteome.org",
"name": "Plant Trait Ontology",
"prefix": "PTO",
"version": "July 2023"
},
"example": "0000630",
"fairsharing": {
"abbreviation": "TO",
"contact": {
"email": "cooperl@science.oregonstate.edu",
"name": "Laurel Cooper",
"orcid": "0000-0002-6379-8932"
},
"description": "A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part. The TO is part of the Planteome Project.",
"domains": [
"Phenotype",
"Structure",
"Life cycle"
],
"homepage": "http://browser.planteome.org/amigo/term/TO:0000387#display-lineage-tab",
"license": "CC-BY-4.0",
"name": "Plant Trait Ontology",
"prefix": "FAIRsharing.w69t6r",
"publications": [
{
"doi": "10.1093/nar/gkx1152",
"pubmed": "29186578",
"title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics",
"year": 2017
}
],
"repository": "https://github.com/Planteome/plant-trait-ontology",
"subjects": [
"Botany"
]
},
"mappings": {
"aberowl": "TO",
"agroportal": "TO",
"biocontext": "TO",
"bioportal": "PTO",
"fairsharing": "FAIRsharing.w69t6r",
"obofoundry": "to",
"ols": "to",
"ontobee": "TO",
"prefixcommons": "pto"
},
"obofoundry": {
"appears_in": [
"agro"
],
"contact": "jaiswalp@science.oregonstate.edu",
"contact.github": "jaiswalp",
"contact.label": "Pankaj Jaiswal",
"contact.orcid": "0000-0002-1005-8383",
"deprecated": false,
"description": "A controlled vocabulary to describe phenotypic traits in plants.",
"domain": "phenotype",
"download.obo": "http://purl.obolibrary.org/obo/to.obo",
"download.owl": "http://purl.obolibrary.org/obo/to.owl",
"homepage": "http://browser.planteome.org/amigo",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"logo": "http://planteome.org/sites/default/files/garland_logo.PNG",
"name": "Plant Trait Ontology",
"preferredPrefix": "TO",
"prefix": "to",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/29186578",
"title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics."
}
],
"repository": "https://github.com/Planteome/plant-trait-ontology"
},
"ols": {
"description": "A controlled vocabulary to describe phenotypic traits in plants.",
"download_owl": "http://purl.obolibrary.org/obo/to.owl",
"homepage": "http://browser.planteome.org/amigo",
"name": "Plant Trait Ontology",
"prefix": "to",
"version": "2023-07-17",
"version.iri": "http://purl.obolibrary.org/obo/to/releases/2023-07-17/to.owl"
},
"ontobee": {
"library": "Library",
"name": "Plant Trait Ontology",
"prefix": "TO"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1037",
"description": "A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part.",
"example": "TO_0000017",
"homepage": "http://www.gramene.org/plant_ontology/",
"keywords": [
"obo",
"plant",
"trait"
],
"name": "Plant Trait Ontology",
"pattern": "^TO_\\d{7}$",
"prefix": "pto",
"synonyms": [
"to",
"gramene.po"
]
},
"publications": [
{
"doi": "10.1093/nar/gkx1152",
"pmc": "PMC5753347",
"pubmed": "29186578",
"title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics",
"year": 2018
}
],
"uri_format": "http://purl.obolibrary.org/obo/TO_$1"
},
"togoid": {
"contact": {
"email": "ktym@dbcls.jp",
"github": "ktym",
"name": "Toshiaki Katayama",
"orcid": "0000-0003-2391-0384"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "TogoID is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. TogoID supports datasets from various biological categories such as gene, protein, chemical compound, pathway, disease, etc. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations. (from https://togoid.dbcls.jp/)",
"download_rdf": "https://raw.githubusercontent.com/togoid/togoid-config/main/ontology/togoid-ontology.ttl",
"example": "AffyProbeset",
"homepage": "https://togoid.dbcls.jp/ontology",
"name": "TogoID Ontology",
"publications": [
{
"doi": "10.1093/bioinformatics/btac491",
"pmc": "PMC9438948",
"pubmed": "35801937",
"title": "TogoID: an exploratory ID converter to bridge biological datasets",
"year": 2022
}
],
"rdf_uri_format": "https://togoid.dbcls.jp/ontology#$1",
"repository": "https://github.com/dbcls/togoid/togoid-config",
"uri_format": "https://togoid.dbcls.jp/#$1"
},
"togovar": {
"integbio": {
"alt_name": "Integrated database of Japanese genomic variation",
"description": "TogoVar (NBDC's integrated database of Japanese genomic variation) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them. TogoVar provides variant frequencies in the Japanese population that have been aggregated across research projects. Two available datasets, JGA-NGS and JGA-SNP, are obtained by aggregating individual genomic data that have been registered in the NBDC Human Database / Japanese Genotype-phenotype Archive (JGA). In addition, TogoVar integrates information related to genotypes or phenotypes that has been compiled independently in a variety of different databases and provides information for interpreting variants in a one-stop, easy-to-understand manner.\nUsers can learn how to use it by a movie: https://togotv.dbcls.jp/en/20181012.html",
"fairsharing": "biodbcore-001182/",
"homepage": "https://togovar.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)||DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "TogoVar",
"prefix": "nbdc02359",
"pubmeds": [],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"mappings": {
"integbio": "nbdc02359",
"miriam": "togovar",
"togoid": "Togovar"
},
"miriam": {
"deprecated": false,
"description": "TogoVar (A comprehensive Japanese genetic variation database) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them.",
"homepage": "https://grch38.togovar.org/",
"id": "00001006",
"name": "TogoVar",
"namespaceEmbeddedInLui": false,
"pattern": "^tgv[0-9]+$",
"prefix": "togovar",
"sampleId": "tgv139393198",
"uri_format": "https://grch38.togovar.org/variant/$1"
},
"togoid": {
"catalog": "nbdc02359",
"examples": [
"tgv100005930",
"tgv100000890",
"tgv16331",
"tgv10000341",
"tgv21330879",
"tgv15847",
"tgv1354996",
"tgv100002132",
"tgv16568524",
"tgv62035164"
],
"keywords": [
"Variant"
],
"name": "TogoVar variant",
"pattern": "^(?tgv\\d+)$",
"prefix": "Togovar",
"uri_format": "http://identifiers.org/togovar/$1"
}
},
"tokue": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "http://cell-lines.toku-e.com",
"name": "TOKU-E Cell-culture Database",
"prefix": "TOKU-E",
"uri_format": "http://cell-lines.toku-e.com/Cell-Lines_$1.html"
},
"deprecated": true,
"mappings": {
"cellosaurus": "TOKU-E"
}
},
"tol": {
"bartoc": {
"description": "The Tree of Life Web Project is a collection of information about biodiversity compiled collaboratively by hundreds of expert and amateur contributors. Its goal is to contain a page with pictures, text, and other information for every species and for each group of organisms, living or extinct. Connections between Tree of Life web pages follow phylogenetic branching patterns between groups of organisms, so visitors can browse the hierarchy of life and learn about phylogeny and evolution as well as the characteristics of individual groups.",
"homepage": "http://tolweb.org/tree/phylogeny.html",
"prefix": "400",
"wikidata_database": "Q2300489"
},
"biocontext": {
"prefix": "TOL"
},
"contributor_extras": [
{
"email": "meghan.balk@gmail.com",
"github": "megbalk",
"name": "Meghan Balk",
"orcid": "0000-0003-2699-3066"
}
],
"mappings": {
"bartoc": "400",
"biocontext": "TOL",
"miriam": "tol",
"n2t": "tol",
"wikidata": "P5221"
},
"miriam": {
"deprecated": false,
"description": "The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). \r\n\r\nEach page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things.",
"homepage": "http://tolweb.org/tree/",
"id": "00000405",
"name": "Tree of Life",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "tol",
"sampleId": "98034",
"uri_format": "http://tolweb.org/$1"
},
"n2t": {
"description": "The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). Each page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things.",
"example": "98034",
"homepage": "http://tolweb.org/tree/",
"name": "Tree of Life Web",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "tol",
"uri_format": "http://tolweb.org/$1"
},
"name": "Tree of Life Web Project",
"synonyms": [
"tol.webproj"
],
"wikidata": {
"description": "identifier in the Tree of Life Web Project",
"example": [
"16952",
"5838"
],
"homepage": "http://tolweb.org/tree/",
"name": "Tree of Life Web Project ID",
"pattern": "^[1-9]\\d*$",
"prefix": "P5221",
"uri_format": "http://tolweb.org/$1"
}
},
"topdb": {
"biocontext": {
"prefix": "TOPDB"
},
"edam": {
"description": "Unique identifier for a membrane protein from the TopDB database.",
"name": "Protein ID (TopDB)",
"obsolete": false,
"prefix": "2789"
},
"mappings": {
"biocontext": "TOPDB",
"edam": "2789",
"miriam": "topdb",
"n2t": "topdb",
"prefixcommons": "topdb"
},
"miriam": {
"deprecated": false,
"description": "The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases.",
"homepage": "http://topdb.enzim.hu/",
"id": "00000503",
"name": "TOPDB",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]+$",
"prefix": "topdb",
"sampleId": "AP00378",
"uri_format": "http://topdb.enzim.hu/?m=show&id=$1"
},
"n2t": {
"description": "The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases.",
"example": "AP00378",
"homepage": "http://topdb.enzim.hu/",
"name": "TOPDB at Hungarian Academy of Sciences",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]+$",
"prefix": "topdb",
"uri_format": "http://topdb.enzim.hu/?m=show&id=$1"
},
"name": "Topology Data Bank of Transmembrane Proteins",
"prefixcommons": {
"description": "The Topology Data Bank of Transmembrane Proteins (TOPDB) is currently the most complete and comprehensive collection of transmembrane protein datasets containing experimentally derived topology information.",
"example": "AB00979",
"homepage": "http://topdb.enzim.hu",
"keywords": [
"protein"
],
"name": "The Topology Databank",
"pattern": "^[A-Z]+\\d+$",
"prefix": "topdb",
"uri_format": "http://topdb.enzim.hu/?m=show&id=$1"
}
},
"topfind": {
"biocontext": {
"prefix": "TOPFIND"
},
"contact": {
"email": "chris.overall@ubc.ca",
"name": "Christopher M. Overall",
"orcid": "0000-0001-5844-2731"
},
"fairsharing": {
"abbreviation": "TopFIND",
"description": "The Termini-Oriented Protein Function INferred Database (TopFIND) is an integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing state of proteins and functional implications thereof derived from research literature, contributions by the scientific community and biological databases.",
"homepage": "https://topfind.clip.msl.ubc.ca/",
"license": "CC BY-ND 3.0",
"name": "Termini-Oriented Protein Function INferred Database",
"prefix": "FAIRsharing.rkpmhn",
"publications": [
{
"doi": "10.1093/nar/gku1012",
"pubmed_id": 25332401,
"title": "Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events."
},
{
"doi": "10.1038/nmeth.1669",
"pubmed_id": 21822272,
"title": "TopFIND, a knowledgebase linking protein termini with function."
},
{
"doi": "10.1093/nar/gkr1025",
"pubmed_id": 22102574,
"title": "TopFIND 2.0βlinking protein termini with proteolytic processing and modifications altering protein function"
}
],
"subjects": [
"Life Science"
]
},
"homepage": "https://topfind.clip.msl.ubc.ca",
"mappings": {
"biocontext": "TOPFIND",
"fairsharing": "FAIRsharing.rkpmhn",
"miriam": "topfind",
"n2t": "topfind",
"re3data": "r3d100012721"
},
"miriam": {
"deprecated": false,
"description": "TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.",
"homepage": "http://clipserve.clip.ubc.ca/topfind",
"id": "00000255",
"name": "TopFind",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$",
"prefix": "topfind",
"sampleId": "Q9UKQ2",
"uri_format": "http://clipserve.clip.ubc.ca/topfind/proteins/$1"
},
"n2t": {
"description": "TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.",
"example": "Q9UKQ2",
"homepage": "http://clipserve.clip.ubc.ca/topfind",
"name": "TopFind at University of British Columbia",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$",
"prefix": "topfind",
"uri_format": "http://clipserve.clip.ubc.ca/topfind/proteins/$1"
},
"provides": "uniprot",
"publications": [
{
"doi": "10.1093/nar/gku1012",
"pmc": "PMC4383881",
"pubmed": "25332401",
"title": "Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events",
"year": 2014
},
{
"doi": "10.1093/nar/gkr1025",
"pmc": "PMC3244998",
"pubmed": "22102574",
"title": "TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function",
"year": 2011
},
{
"doi": "10.1038/nmeth.1669",
"pubmed": "21822272",
"title": "TopFIND, a knowledgebase linking protein termini with function",
"year": 2011
}
],
"re3data": {
"description": "TopFIND is a protein-centric database for the annotation of protein termini currently in its third version. Non-canonical protein termini can be the result of multiple different biological processes, including pre-translational processes such as alternative splicing and alternative translation initiation or post-translational protein processing by proteases that cleave proteases as part of protein maturation or as a regulatory modification. Accordingly, protein termini evidence in TopFIND is inferred from other databases such as ENSEMBL transcripts, TISdb for alternative translation initiation, MEROPS for protein cleavage by proteases, and UniProt for canonical and protein isoform start sites.",
"homepage": "https://topfind.clip.msl.ubc.ca/",
"name": "TopFIND",
"prefix": "r3d100012721",
"synonyms": [
"The public knowledgebase for protein termini and protease processing"
],
"xrefs": {
"fairsharing": "FAIRsharing.rkpmhn",
"nlx": "151607",
"omics": "10578",
"scr": "008918"
}
}
},
"toxoplasma": {
"biocontext": {
"prefix": "TOXOPLASMA"
},
"mappings": {
"biocontext": "TOXOPLASMA",
"miriam": "toxoplasma",
"n2t": "toxoplasma"
},
"miriam": {
"deprecated": false,
"description": "ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"homepage": "http://toxodb.org/toxo/",
"id": "00000153",
"name": "ToxoDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "toxoplasma",
"sampleId": "TGME49_053730",
"uri_format": "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"
},
"n2t": {
"description": "ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"example": "TGME49_053730",
"homepage": "http://toxodb.org/toxo/",
"name": "ToxoDB at EuPathDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "toxoplasma",
"uri_format": "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"
}
},
"trans": {
"aberowl": {
"description": "An ontology representing the disease transmission process during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host.",
"download_owl": "http://aber-owl.net/media/ontologies/TRANS/5/trans.owl",
"homepage": "https://github.com/DiseaseOntology/PathogenTransmissionOntology",
"name": "Pathogen Transmission Ontology",
"prefix": "TRANS"
},
"biocontext": {
"prefix": "TRANS"
},
"bioportal": {
"contact": {
"email": "philip.shields@live.vu.edu.au",
"name": "Philip Shields"
},
"description": "This is an ontology of a transitional care nurse's process domain",
"name": "Nurse Transitional",
"prefix": "TRANS"
},
"example": "0000024",
"fairsharing": {
"abbreviation": "TRANS",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/TRANS",
"name": "Nurse Transitional",
"prefix": "FAIRsharing.nygmp7",
"subjects": [
"Health Science"
]
},
"mappings": {
"aberowl": "TRANS",
"biocontext": "TRANS",
"bioportal": "TRANS",
"fairsharing": "FAIRsharing.nygmp7",
"obofoundry": "trans",
"ols": "trans",
"ontobee": "TRANS",
"prefixcommons": "pt"
},
"obofoundry": {
"contact": "lynn.schriml@gmail.com",
"contact.github": "lschriml",
"contact.label": "Lynn Schriml",
"contact.orcid": "0000-0001-8910-9851",
"deprecated": false,
"description": "An ontology representing the disease transmission process during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host.",
"domain": "health",
"download.obo": "http://purl.obolibrary.org/obo/trans.obo",
"download.owl": "http://purl.obolibrary.org/obo/trans.owl",
"homepage": "https://github.com/DiseaseOntology/PathogenTransmissionOntology",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Pathogen Transmission Ontology",
"preferredPrefix": "TRANS",
"prefix": "trans",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/19850722",
"title": "GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/34755882",
"title": "The Human Disease Ontology 2022 update"
}
],
"repository": "https://github.com/DiseaseOntology/PathogenTransmissionOntology"
},
"ols": {
"description": "The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.",
"download_owl": "http://purl.obolibrary.org/obo/trans.owl",
"homepage": "https://github.com/DiseaseOntology/PathogenTransmissionOntology",
"name": "Pathogen Transmission Ontology",
"prefix": "trans",
"version": "2022-10-10",
"version.iri": "http://purl.obolibrary.org/obo/trans/releases/2022-10-10/trans.owl"
},
"ontobee": {
"library": "Library",
"name": "Pathogen Transmission Ontology",
"prefix": "TRANS"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1094",
"description": "This vocabulary describes a process that is the means of how a pathogen is transmitted from one host, reservoir, or source to another host. This transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.",
"example": "TRANS_0000001",
"homepage": "http://diseaseontology.sourceforge.net/",
"keywords": [
"obo",
"pathogen"
],
"name": "Pathogen transmission",
"pattern": "^TRANS_\\d{7}$",
"prefix": "pt",
"synonyms": [
"trans"
]
},
"publications": [
{
"doi": "10.1093/nar/gkab1063",
"pmc": "PMC8728220",
"pubmed": "34755882",
"title": "The Human Disease Ontology 2022 update",
"year": 2022
},
{
"doi": "10.1093/nar/gkp832",
"pmc": "PMC2808878",
"pubmed": "19850722",
"title": "GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database",
"year": 2009
}
],
"uri_format": "http://purl.obolibrary.org/obo/TRANS_$1"
},
"transportdb": {
"mappings": {
"pathguide": "105",
"prefixcommons": "transportdb"
},
"pathguide": {
"abbreviation": "TransportDB",
"homepage": "http://www.membranetransport.org/transportDB2/index.html",
"name": "TransportDB",
"prefix": "105"
},
"prefixcommons": {
"description": "TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available.",
"example": "MMP0523",
"homepage": "http://www.membranetransport.org",
"keywords": [
"protein"
],
"name": "TransportDB",
"pattern": "^MMP\\d+$",
"prefix": "transportdb",
"uri_format": "http://www.membranetransport.org/protein.php?pOID=mmar1&pSynonym=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"transyt": {
"mappings": {
"miriam": "transyt"
},
"miriam": {
"deprecated": false,
"description": "The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes.",
"homepage": "https://www.bio.di.uminho.pt/",
"id": "00000736",
"name": "TranSyT",
"namespaceEmbeddedInLui": false,
"pattern": "T[A-Z]\\d{7}",
"prefix": "transyt",
"sampleId": "TR0000001",
"uri_format": "https://transyt.bio.di.uminho.pt/reactions/$1"
},
"name": "Transport Systems Tracker"
},
"tred": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"mappings": {
"pathguide": "167",
"prefixcommons": "tred"
},
"pathguide": {
"abbreviation": "TRED",
"homepage": "https://cb.utdallas.edu/cgi-bin/TRED/tred.cgi?process=home",
"name": "Transcriptional Regulatory Element Database",
"prefix": "167"
},
"prefixcommons": {
"description": "Transcriptional Regulatory Element Database (TRED) has been built in response to increasing needs of an integrated repository for both cis- and trans- regulatory elements in mammals, and the lack of such resources at present.",
"example": "21552",
"homepage": "http://rulai.cshl.edu/TRED",
"keywords": [
"DNA",
"regulation"
],
"name": "Transcriptional Regulatory Element Database",
"pattern": "^\\d+$",
"prefix": "tred",
"uri_format": "http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid=$1"
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"treebase": {
"biocontext": {
"prefix": "TREEBASE"
},
"contact": {
"email": "rutgeraldo@gmail.com",
"github": "rvosa",
"name": "Rutger Vos",
"orcid": "0000-0001-9254-7318"
},
"fairsharing": {
"abbreviation": "TreeBase",
"description": "TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. TreeBASE is temporarily offline except to provide access to editors/curators, as security updates are required before re-publishing the site.",
"homepage": "https://www.treebase.org",
"name": "TreeBase",
"prefix": "FAIRsharing.zcn4w4",
"publications": [
{
"doi": "10.1186/1471-2148-9-93",
"pubmed_id": 19426482,
"title": "Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment."
}
],
"repository": "https://github.com/TreeBASE/treebase/issues",
"subjects": [
"Phylogenetics",
"Phylogenomics"
],
"twitter": "treebase"
},
"integbio": {
"description": "TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa.",
"fairsharing": "FAIRsharing.zcn4w4",
"homepage": "http://www.treebase.org/",
"information_keywords": [
"Taxonomy",
"Sequence"
],
"maintainer": "Naturalis Biodiversity Center",
"name": "TreeBase",
"prefix": "nbdc01882",
"pubmeds": [
"19426482"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"mappings": {
"biocontext": "TREEBASE",
"fairsharing": "FAIRsharing.zcn4w4",
"integbio": "nbdc01882",
"miriam": "treebase",
"n2t": "treebase",
"prefixcommons": "treebase",
"re3data": "r3d100010170"
},
"miriam": {
"deprecated": false,
"description": "TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc.",
"homepage": "http://treebase.org/",
"id": "00000312",
"name": "TreeBASE",
"namespaceEmbeddedInLui": false,
"pattern": "^TB[1,2]?:[A-Z][a-z]?\\d+$",
"prefix": "treebase",
"sampleId": "TB2:S1000",
"uri_format": "http://purl.org/phylo/treebase/phylows/study/$1?format=html"
},
"n2t": {
"description": "TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc.",
"example": "TB2:S1000",
"homepage": "http://treebase.org/",
"name": "TreeBASE (hosted at National Evolutionary Synthesis Center)",
"namespaceEmbeddedInLui": false,
"pattern": "^TB[1,2]?:[A-Z][a-z]?\\d+$",
"prefix": "treebase",
"uri_format": "http://purl.org/phylo/treebase/phylows/study/$1?format=html"
},
"prefixcommons": {
"description": "TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa.",
"example": "1245",
"homepage": "http://www.treebase.org/",
"keywords": [
"classification"
],
"name": "TreeBase",
"pattern": "^\\d+$",
"prefix": "treebase",
"uri_format": "http://www.treebase.org/treebase-web/search/study/summary.html?id=$1"
},
"publications": [
{
"doi": "10.1186/1471-2148-9-93",
"pmc": "PMC2685121",
"pubmed": "19426482",
"title": "Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment",
"year": 2009
}
],
"re3data": {
"description": "TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but are only available to the authors, publication editors, or reviewers using a special access code.",
"homepage": "https://www.treebase.org/treebase-web/home.html",
"name": "TreeBASE",
"prefix": "r3d100010170",
"synonyms": [
"a database of phylogenetic knowledge"
],
"xrefs": {
"fairsharing": "FAIRsharing.zcn4w4",
"nif": "0000-03587",
"scr": "005688"
}
}
},
"treefam": {
"biocontext": {
"prefix": "TREEFAM"
},
"contact": {
"email": "Fab.Schreiber@gmail.com",
"github": "fabsta",
"name": "Fabian Schreiber",
"orcid": "0000-0001-9150-5706"
},
"integbio": {
"description": "TreeFam is a database of phylogenetic trees inferred from animal genomes. It provides the following information about the TreeFam gene family:\n1) Summary page\nTextual background information on the TreeFam gene family\n2) Trees\nReconciled gene tree \n3) Alignment\nAn alignment of all homologous sequences in the TreeFam family\n4) Sequences\nInformation about sequences in the TreeFam family, including e-values, Pfam domains, sequence description, and the species name\n5) Species\nInteractive tree graphic displaying species distribution for the full alignment.",
"homepage": "http://www.treefam.org",
"information_keywords": [
"Sequence",
"Taxonomy",
"Classification"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "TreeFam",
"prefix": "nbdc01596",
"pubmeds": [
"16381935",
"18056084"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"mappings": {
"biocontext": "TREEFAM",
"integbio": "nbdc01596",
"miriam": "treefam",
"n2t": "treefam",
"prefixcommons": "treefam",
"uniprot": "DB-0185"
},
"miriam": {
"deprecated": false,
"description": "TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments.",
"homepage": "http://www.treefam.org/",
"id": "00000395",
"name": "TreeFam",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{1,2}\\d+$",
"prefix": "treefam",
"sampleId": "TF101014",
"uri_format": "http://www.treefam.org/family/$1"
},
"n2t": {
"description": "TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments.",
"example": "TF101014",
"homepage": "http://www.treefam.org/",
"name": "TreeFam database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{1,2}\\d+$",
"prefix": "treefam",
"uri_format": "http://www.treefam.org/family/$1"
},
"prefixcommons": {
"description": "TreeFam (Tree families database) is a database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families.",
"example": "TF101142",
"homepage": "http://www.treefam.org",
"keywords": [
"gene",
"classification"
],
"name": "TreeFam",
"pattern": "^TF\\d+$",
"prefix": "treefam",
"uri_format": "http://www.treefam.org/cgi-bin/TFinfo.pl?ac=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkt1055",
"pmc": "PMC3965059",
"pubmed": "24194607",
"title": "TreeFam v9: a new website, more species and orthology-on-the-fly",
"year": 2013
}
],
"uniprot": {
"abbreviation": "TreeFam",
"category": "Phylogenomic databases",
"homepage": "http://www.treefam.org",
"name": "TreeFam database of animal gene trees",
"prefix": "DB-0185",
"publications": [
{
"doi": "10.1093/nar/gkt1055",
"pubmed": "24194607"
}
],
"uri_format": "http://www.treefam.org/family/$1"
}
},
"tricdb": {
"mappings": {
"miriam": "tricdb"
},
"miriam": {
"deprecated": false,
"description": "TriΒ©DB is a newly developed integrated platform functioning as a knowledge base and reporting system for cancer precision medicine. This platform harmonizes and mines cancer-related data from various aspects, presenting them on a centralized platform with enhanced accessibility, rich annotations, and robust analysis capabilities. The development of TriΒ©DB is aimed at meeting the needs of a broad range of researchers, thereby propelling both foundational and translational research in cancer precision medicine.",
"homepage": "http://www.biomeddb.org/",
"id": "00001036",
"name": "tricdb",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$",
"prefix": "tricdb",
"sampleId": "1eec8393-e598-41ed-9d8b-6d5b0db94470",
"uri_format": "http://biomeddb.org/Disease/Details?DISEASEID=$1"
}
},
"trichdb": {
"biocontext": {
"prefix": "TRICHDB"
},
"fairsharing": {
"abbreviation": "TrichDB",
"contact": {
"email": "oharb@pcbi.upenn.edu",
"name": "Omar Harb",
"orcid": "0000-0003-4446-6200"
},
"description": "TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"homepage": "http://trichdb.org/trichdb/",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "TrichDB",
"prefix": "FAIRsharing.pv0ezt",
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{
"doi": "10.1093/nar/gkn631",
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],
"subjects": [
"Genomics"
],
"twitter": "eupathdb"
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"description": "TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"fairsharing": "FAIRsharing.pv0ezt",
"homepage": "http://trichdb.org/trichdb/",
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"maintainer": "CBIL (Computational Biology and Informatics Laboratory, University of Pennsylvania)||Center for Tropical & Emerging Global Diseases, University of Georgia",
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"Genome/Gene",
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"example": "TVAG_386080",
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"name": "TrichDB at EuPathDB",
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"pattern": "^\\w+$",
"prefix": "trichdb",
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{
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],
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"description": "TrichDB integrated genomic resources for the eukaryotic protist pathogens Trichomonas vaginalis.",
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"name": "TrichDB",
"prefix": "r3d100012461",
"synonyms": [
"Trichomonas vaginalis Sequence Database"
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}
},
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"biocontext": {
"prefix": "TRITRYPDB"
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"fairsharing": {
"abbreviation": "TriTrypDB",
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"email": "oharb@pcbi.upenn.edu",
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},
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"homepage": "http://tritrypdb.org/tritrypdb/",
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"prefix": "FAIRsharing.fs1z27",
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{
"doi": "10.1093/nar/gkp851",
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"Comparative Genomics"
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"twitter": "VEuPathDB"
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"go": {
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"name": "TriTrypDB",
"prefix": "TriTrypDB",
"uri_format": "https://tritrypdb.org/tritrypdb/app/record/gene/$1"
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"fairsharing": "FAIRsharing.fs1z27",
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"Expression",
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"maintainer": "CBIL (Computational Biology and Informatics Laboratory, University of Pennsylvania)||Center for Tropical & Emerging Global Diseases, University of Georgia||Wellcome Sanger Institute",
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"Organism",
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},
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"description": "TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
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"homepage": "http://tritrypdb.org/tritrypdb/",
"name": "TriTrypDB at EuPathDB",
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"pattern": "^\\w+(\\.)?\\w+(\\.)?\\w+",
"prefix": "tritrypdb",
"uri_format": "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"
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{
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}
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"description": "TriTrypDB is an integrated genomic and functional genomic database for pathogens of the family Trypanosomatidae, including organisms in both Leishmania and Trypanosoma genera. TriTrypDB and its continued development are possible through the collaborative efforts between EuPathDB, GeneDB and colleagues at the Seattle Biomedical Research Institute (SBRI).",
"homepage": "https://tritrypdb.org/tritrypdb/app",
"name": "TriTrypDB",
"prefix": "r3d100011479",
"synonyms": [
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"nlx": "152064",
"omics": "03144",
"scr": "007043"
}
}
},
"trnadbce": {
"comment": "requires authentication to access",
"integbio": {
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"homepage": "http://trna.ie.niigata-u.ac.jp",
"information_keywords": [
"Sequence"
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"maintainer": "Niigata University Faculty of Engineering Department of Information Engineering",
"name": "tRNADB-CE",
"prefix": "nbdc00720",
"pubmeds": [
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"RNA"
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"example": "265912",
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"RNA",
"gene",
"genome",
"DNA"
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"name": "tRNA Gene Database",
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"prefix": "trnadbce",
"uri_format": "http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID=$1"
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"proprietary": true,
"reviewer": {
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"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
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},
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"description": "Centralized repository and distribution site for variety of Tetrahymena strains and species. Maintains diverse array of wild type, mutant, and genetically engineered strains of T. thermophila, the most commonly used laboratory species, and variety of other species derived from both laboratory maintained stocks and wild isolates. All stocks are stored in liquid nitrogen to maintain genetic integrity and prevent senescence. In addition to providing worldwide access to strains currently in collection, TSC continually upgrades collection by accepting deposition of newly developed laboratory strains and well characterized wild isolates collected from clearly defined natural sites. [from RRID]",
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"rrid": "TSC"
},
"pattern": "^SD\\d+$",
"rrid": {
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"cell",
"cellular",
"culture",
"eukaryota",
"genetics",
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"name": "Tetrahymena Stock Center",
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"scr": "008362"
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"uri_format": "https://tetrahymena.vet.cornell.edu/display.php?stockid=$1"
},
"ttd.drug": {
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"edam": {
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"obsolete": false,
"prefix": "2653"
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"description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.",
"homepage": "http://bidd.nus.edu.sg/group/ttd/ttd.asp",
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"name": "TTD Drug",
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"pattern": "^DAP\\d+$",
"prefix": "ttd.drug",
"sampleId": "DAP000773",
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"description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.",
"example": "DAP000773",
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"name": "Therapeutic Target Database Drug",
"namespaceEmbeddedInLui": false,
"pattern": "^DAP\\d+$",
"prefix": "ttd.drug",
"uri_format": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1"
}
},
"ttd.target": {
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},
"edam": {
"description": "Identifier of a target protein from the Therapeutic Target Database (TTD).",
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"obsolete": false,
"prefix": "2654"
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"mappings": {
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"homepage": "http://bidd.nus.edu.sg/group/ttd/ttd.asp",
"id": "00000093",
"name": "TTD Target",
"namespaceEmbeddedInLui": false,
"pattern": "^TTDS\\d+$",
"prefix": "ttd.target",
"sampleId": "TTDS00056",
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"description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.",
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"name": "Therapeutic Target Database Target",
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"pattern": "^TTDS\\d+$",
"prefix": "ttd.target",
"uri_format": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1"
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},
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"homepage": "https://www.nescent.org/phenoscape/Main_Page",
"name": "Teleost taxonomy ontology",
"prefix": "TTO"
},
"biocontext": {
"prefix": "TTO"
},
"bioportal": {
"contact": {
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"name": "Peter Midford"
},
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"homepage": "http://obofoundry.org/ontology/tto.html",
"name": "Teleost Taxonomy Ontology",
"prefix": "TTO",
"version": "unknown"
},
"example": "1058367",
"fairsharing": {
"abbreviation": "TTO",
"contact": {
"email": "pmabee@usd.edu",
"name": "Paula Mabee",
"orcid": "0000-0002-8455-3213"
},
"description": "This is an ontology of taxonomic terms (names of taxonomic groups) used in the systematics of fish, including non-teleost groups such as Chondrichthys (sharks and rays), Sarcopterygii (lungfish and coelacanths), lampreys, and hagfish.",
"domains": [
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],
"homepage": "https://wiki.phenoscape.org/wiki/Ontologies#Teleost_Taxonomy_Ontology_.28TTO.29",
"license": "CC0-1.0",
"name": "Teleost Taxonomy Ontology",
"prefix": "FAIRsharing.1rj558",
"subjects": [
"Life Science"
]
},
"mappings": {
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"biocontext": "TTO",
"bioportal": "TTO",
"fairsharing": "FAIRsharing.1rj558",
"obofoundry": "tto",
"ols": "tto",
"ontobee": "TTO",
"prefixcommons": "tto"
},
"obofoundry": {
"contact": "balhoff@renci.org",
"contact.github": "balhoff",
"contact.label": "Jim Balhoff",
"contact.orcid": "0000-0002-8688-6599",
"deprecated": false,
"description": "An ontology covering the taxonomy of teleosts (bony fish)",
"domain": "organisms",
"download.obo": "http://purl.obolibrary.org/obo/tto.obo",
"download.owl": "http://purl.obolibrary.org/obo/tto.owl",
"homepage": "https://github.com/phenoscape/teleost-taxonomy-ontology",
"license": "CC0 1.0",
"license.url": "http://creativecommons.org/publicdomain/zero/1.0/",
"name": "Teleost taxonomy ontology",
"preferredPrefix": "TTO",
"prefix": "tto",
"publications": [
{
"id": "https://doi.org/10.1038/npre.2010.4629.1",
"title": "The Teleost Taxonomy Ontology"
}
],
"repository": "https://github.com/phenoscape/teleost-taxonomy-ontology"
},
"ols": {
"description": "An ontology covering the taxonomy of teleosts (bony fish)",
"download_owl": "http://purl.obolibrary.org/obo/tto.owl",
"homepage": "https://github.com/phenoscape/teleost-taxonomy-ontology",
"name": "Teleost taxonomy ontology",
"prefix": "tto"
},
"ontobee": {
"library": "Library",
"name": "Teleost taxonomy ontology",
"prefix": "TTO"
},
"pattern": "^\\d+$",
"prefixcommons": {
"bioportal": "1081",
"description": "The Teleost taxonomy ontology is being used to facilitate annotation of phenotypes, particularly for taxa that are not covered by NCBI because no submissions of molecular data have been made.",
"example": "TTO_2",
"homepage": "https://www.nescent.org/phenoscape/Main_Page",
"keywords": [
"obo",
"phenotype",
"fish"
],
"name": "Teleost taxonomy Ontology",
"pattern": "^TTO_\\d$",
"prefix": "tto",
"synonyms": [
"teleost_taxonomy"
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},
"publications": [
{
"doi": "10.1038/npre.2010.4629.1",
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}
],
"uri_format": "http://purl.obolibrary.org/obo/TTO_$1",
"wikidata": {
"database": "Q81661821"
}
},
"txpo": {
"aberowl": {
"description": "TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.",
"download_owl": "http://aber-owl.net/media/ontologies/TXPO/28/txpo.owl",
"homepage": "https://toxpilot.nibiohn.go.jp/",
"name": "Toxic Process Ontology",
"prefix": "TXPO"
},
"bioportal": {
"contact": {
"email": "yuki.yamagata@riken.jp",
"name": "Yuki Yamagata"
},
"description": "TOXic Process Ontology (TXPO) includes entities related to toxic mechanisms (toxic courses) and processes, mainly focusing on hepatotoxicity. Application system TOXPILOT: https://toxpilot.nibiohn.go.jp",
"homepage": "https://toxpilot.nibiohn.go.jp",
"name": "Toxic Process Ontology",
"prefix": "TXPO",
"publication": "https://pubmed.ncbi.nlm.nih.gov/32883995/",
"version": "2022/12/07"
},
"example": "0002066",
"mappings": {
"aberowl": "TXPO",
"bioportal": "TXPO",
"obofoundry": "txpo",
"ols": "txpo",
"ontobee": "TXPO"
},
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"contact": "yuki.yamagata@riken.jp",
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"contact.orcid": "0000-0002-9673-1283",
"deprecated": false,
"description": "TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.",
"domain": "chemistry and biochemistry",
"download.owl": "http://purl.obolibrary.org/obo/txpo.owl",
"homepage": "https://toxpilot.nibiohn.go.jp/",
"license": "CC BY 3.0",
"license.url": "https://creativecommons.org/licenses/by/3.0/",
"name": "Toxic Process Ontology",
"preferredPrefix": "TXPO",
"prefix": "txpo",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/32883995",
"title": "Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management"
}
],
"repository": "https://github.com/txpo-ontology/TXPO"
},
"ols": {
"description": "Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.\n\nThe TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms.\n\nIn applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp",
"download_owl": "http://purl.obolibrary.org/obo/txpo.owl",
"homepage": "https://toxpilot.nibiohn.go.jp/",
"name": "TOXic Process Ontology (TXPO)",
"prefix": "txpo",
"version": "2022-12-07",
"version.iri": "http://purl.obolibrary.org/obo/txpo/releases/2022-12-07/txpo.owl"
},
"ontobee": {
"library": "Library",
"name": "Toxic Process Ontology",
"prefix": "TXPO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1038/s41598-020-71370-7",
"pmc": "PMC7471325",
"pubmed": "32883995",
"title": "Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management",
"year": 2020
}
],
"uri_format": "http://purl.obolibrary.org/obo/TXPO_$1"
},
"uberon": {
"aberowl": {
"description": "An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies",
"download_owl": "http://aber-owl.net/media/ontologies/UBERON/302/uberon.owl",
"homepage": "http://uberon.org",
"name": "Uberon multi-species anatomy ontology",
"prefix": "UBERON"
},
"biocontext": {
"prefix": "UBERON"
},
"bioportal": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.",
"homepage": "http://uberon.org",
"name": "Uber Anatomy Ontology",
"prefix": "UBERON",
"publication": "http://genomebiology.com/content/13/1/R5",
"version": "2023-07-25"
},
"cellosaurus": {
"category": "Anatomy/cell type resources",
"homepage": "https://uberon.github.io/",
"name": "Uber-anatomy ontology",
"prefix": "UBERON",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http://purl.obolibrary.org/obo/$1"
},
"download_json": "http://purl.obolibrary.org/obo/uberon.json",
"download_obo": "http://purl.obolibrary.org/obo/uberon/basic.obo",
"example": "2005080",
"fairsharing": {
"abbreviation": "UBERON",
"description": "Uberon is an integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies. It represents a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.",
"homepage": "http://uberon.org/",
"license": "CC-BY-3.0",
"name": "UBER anatomy ONtology",
"prefix": "FAIRsharing.4c0b6b",
"publications": [
{
"doi": "10.1186/2041-1480-5-21",
"pubmed": "25009735",
"title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon",
"year": 2014
},
{
"doi": "10.1186/gb-2012-13-1-r5",
"pubmed": "22293552",
"title": "Uberon, an integrative multi-species anatomy ontology",
"year": 2012
}
],
"repository": "https://github.com/obophenotype/uberon/wiki/Manual",
"subjects": [
"Anatomy",
"Taxonomy",
"Developmental Biology",
"Life Science"
],
"twitter": "uberanat"
},
"go": {
"description": "A multi-species anatomy ontology",
"homepage": "http://uberon.org",
"name": "Uber-anatomy ontology",
"prefix": "UBERON"
},
"mappings": {
"aberowl": "UBERON",
"biocontext": "UBERON",
"bioportal": "UBERON",
"cellosaurus": "UBERON",
"fairsharing": "FAIRsharing.4c0b6b",
"go": "UBERON",
"miriam": "uberon",
"n2t": "uberon",
"obofoundry": "uberon",
"ols": "uberon",
"ontobee": "UBERON",
"togoid": "Uberon",
"wikidata": "P1554"
},
"miriam": {
"deprecated": false,
"description": "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/uberon",
"id": "00000446",
"name": "UBERON",
"namespaceEmbeddedInLui": true,
"pattern": "^UBERON:\\d+$",
"prefix": "uberon",
"sampleId": "0008203",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/uberon/terms?obo_id=UBERON:$1"
},
"n2t": {
"description": "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.",
"example": "0008203",
"homepage": "http://bioportal.bioontology.org/ontologies/UBERON",
"name": "UBERON through bioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^UBERON\\:\\d+$",
"prefix": "uberon",
"uri_format": "http://purl.bioontology.org/ontology/UBERON/UBERON:$1"
},
"name": "Uber Anatomy Ontology",
"obofoundry": {
"appears_in": [
"aism",
"amphx",
"chiro",
"cl",
"clo",
"clyh",
"colao",
"cteno",
"ecao",
"ecocore",
"ecto",
"envo",
"foodon",
"fovt",
"genepio",
"go",
"hso",
"lepao",
"maxo",
"mco",
"ons",
"pcl",
"plana",
"poro",
"zp",
"mfmo"
],
"contact": "cjmungall@lbl.gov",
"contact.github": "cmungall",
"contact.label": "Chris Mungall",
"contact.orcid": "0000-0002-6601-2165",
"depends_on": [
"bfo",
"bspo",
"chebi",
"cl",
"envo",
"go",
"nbo",
"ncbitaxon",
"omo",
"pato",
"pr",
"ro"
],
"deprecated": false,
"description": "An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies",
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/uberon.owl",
"homepage": "http://uberon.org",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"logo": "https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/uberon-logos/uberon_logo_black-banner.png",
"name": "Uberon multi-species anatomy ontology",
"preferredPrefix": "UBERON",
"prefix": "uberon",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/22293552",
"title": "Uberon, an integrative multi-species anatomy ontology"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/25009735",
"title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon"
}
],
"repository": "https://github.com/obophenotype/uberon",
"twitter": "uberanat"
},
"ols": {
"description": "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.",
"download_owl": "http://purl.obolibrary.org/obo/uberon.owl",
"homepage": "http://uberon.org",
"name": "Uber-anatomy ontology",
"prefix": "uberon",
"version": "2024-08-07",
"version.iri": "http://purl.obolibrary.org/obo/uberon/releases/2024-08-07/uberon.owl"
},
"ontobee": {
"library": "Library",
"name": "Uberon multi-species anatomy ontology",
"prefix": "UBERON"
},
"pattern": "^\\d+$",
"providers": [
{
"code": "cellxgene",
"description": "Explore single cell data through the CZ CELLxGENE portal",
"homepage": "https://onto.cellxgene-labs.prod.si.czi.technology",
"name": "CELLxGENE",
"uri_format": "https://onto.cellxgene-labs.prod.si.czi.technology/a/ontology/UBERON/UBERON:$1"
},
{
"code": "cellguide",
"description": "CellGuide is a comprehensive resource for knowledge about cell types.",
"homepage": "https://cellxgene.cziscience.com/cellguide",
"name": "Cell Guide",
"uri_format": "https://cellxgene.cziscience.com/cellguide/tissues/UBERON_$1"
}
],
"publications": [
{
"doi": "10.1186/2041-1480-5-21",
"pmc": "PMC4089931",
"pubmed": "25009735",
"title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon",
"year": 2014
},
{
"doi": "10.1186/gb-2012-13-1-r5",
"pmc": "PMC3334586",
"pubmed": "22293552",
"title": "Uberon, an integrative multi-species anatomy ontology",
"year": 2012
}
],
"synonyms": [
"UBERON",
"Uber-anatomy ontology",
"Uberon"
],
"togoid": {
"examples": [
"UBERON:0002115",
"UBERON:0001004",
"UBERON:0000007",
"UBERON:0001044",
"UBERON:0001825",
"UBERON:0001361",
"UBERON:0002186",
"UBERON:0000945",
"UBERON:0036068",
"UBERON:0001017"
],
"keywords": [
"Anatomy"
],
"name": "UBERON",
"pattern": "^UBERON[:_](?\\d{7})$",
"prefix": "Uberon",
"uri_format": "http://purl.obolibrary.org/obo/UBERON_$1"
},
"uri_format": "http://purl.obolibrary.org/obo/UBERON_$1",
"wikidata": {
"description": "identifier from UBERON ontology (without prefix)",
"example": [
"0000033",
"0000057"
],
"homepage": "http://uberon.github.io",
"miriam": "UBERON",
"name": "UBERON ID",
"pattern": "^\\d{7}$",
"prefix": "P1554",
"uri_format": "http://purl.obolibrary.org/obo/UBERON_$1",
"uri_format_rdf": "http://purl.obolibrary.org/obo/UBERON_$1"
}
},
"ubio.namebank": {
"biocontext": {
"prefix": "UBIO.NAMEBANK"
},
"mappings": {
"biocontext": "UBIO.NAMEBANK",
"miriam": "ubio.namebank",
"n2t": "ubio.namebank"
},
"miriam": {
"deprecated": false,
"description": "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context.",
"homepage": "http://www.ubio.org",
"id": "00000338",
"name": "uBio NameBank",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "ubio.namebank",
"sampleId": "2555646",
"uri_format": "http://www.ubio.org/browser/details.php?namebankID=$1"
},
"n2t": {
"description": "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context.",
"example": "2555646",
"homepage": "http://www.ubio.org",
"name": "uBio NameBank at The Marine Biological Laboratory",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "ubio.namebank",
"uri_format": "http://www.ubio.org/browser/details.php?namebankID=$1"
}
},
"ubprop": {
"comment": "All of these are typedefs in uberon now",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"name": "Uberon Property",
"synonyms": [
"UBPROP",
"UBREL"
]
},
"ucas": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An identifier for institutions in the United Kingdom, used in GRID and ROR.",
"example": "N21",
"homepage": "https://www.ucas.com",
"keywords": [
"bibliometrics",
"institution"
],
"name": "UK Universities and Colleges Admissions Service",
"pattern": "^\\w\\d+$"
},
"ucsc": {
"biocontext": {
"prefix": "UCSC",
"uri_format": "ftp://hgdownload.cse.ucsc.edu/goldenPath/$1"
},
"contact": {
"email": "max@soe.ucsc.edu",
"github": "maximilianh",
"name": "Maximilian Haeussler",
"orcid": "0000-0001-8721-8253"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations.",
"example": "uc001rvw.5",
"homepage": "https://genome.ucsc.edu/",
"mappings": {
"biocontext": "UCSC",
"uniprot": "DB-0139",
"wikidata": "P2576"
},
"name": "UCSC Genome Browser",
"publications": [
{
"doi": "10.1093/nar/gky1095",
"pmc": "PMC6323953",
"pubmed": "30407534",
"title": "The UCSC Genome Browser database: 2019 update",
"year": 2019
}
],
"uniprot": {
"abbreviation": "UCSC",
"category": "Genome annotation databases",
"homepage": "https://genome.ucsc.edu/",
"name": "UCSC genome browser",
"prefix": "DB-0139",
"publications": [
{
"doi": "10.1093/nar/gky1095",
"pubmed": "30407534"
}
],
"uri_format": "https://genome.ucsc.edu/cgi-bin/hgLinkIn?resource=uniprot&id=$1"
},
"wikidata": {
"description": "identifier of a UCSC's release of a genome",
"example": [
"Chr 19: 34.85 β 34.89 Mb",
"hg38",
"uc002xza.4"
],
"homepage": "https://genome.ucsc.edu",
"name": "UCSC Genome Browser assembly ID",
"prefix": "P2576",
"uri_format": "https://genome.ucsc.edu/cgi-bin/hgTracks?db=$1"
}
},
"ucum": {
"bartoc": {
"abbreviation": "UCUM",
"description": "The Unified Code for Units of Measure is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business. The purpose is to facilitate unambiguous electronic communication of quantities together with their units. The focus is on electronic communication, as opposed to communication between humans. A typical application of The Unified Code for Units of Measure are electronic data interchange (EDI) protocols, but there is nothing that prevents it from being used in other types of machine communication. How does it relate?\n\nThe Unified Code for Units of Measure is inspired by and heavily based on ISO 2955-1983, ANSI X3.50-1986, and HL7's extensions called ISO+. The respective ISO and ANSI standards are both entitled Representation of [...] units in systems with limited character sets where ISO 2955 refers to SI and other units provided by ISO 1000-1981, while ANSI X3.50 extends ISO 2955 to include U.S. customary units. Because these standards carry the restriction of limited character sets in their names they seem to be of less value today where graphical user interface and laser printers are in wide-spread use, which is why the european standard ENV 12435 in its clause 7.3 declares ISO 2955 obsolete.\n\nENV 12435 is dedicated exclusively to the communication of measurements between humans in display and print, and does not provide codes that can be used in communication between systems. It does not even provide a specification that would allow communication of units from one system to the screen or printer of another system. The issue about displaying units in the common style defined by the 9th ConfΓ©rence GΓ©nΓ©rale des Poids et Mesures (CGPM) in 1947 is not just the character set. Although The Unicode Standard and its predecessor ISO/IEC 10646 is the richest character set ever it is still not enough to specify the presentation of units because there are important typographical details such as superscripts, subscripts, roman and italics.\"\n\nSeveral URI namespaces and encoding methods have been proposed to map UCUM codes to URIs.",
"homepage": "http://unitsofmeasure.org/",
"name": "Unified Code for Units of Measure",
"prefix": "1895",
"wikidata_database": "Q2494286"
},
"contact": {
"email": "dr.shorthair@pm.me",
"github": "dr-shorthair",
"name": "Simon Cox",
"orcid": "0000-0002-3884-3420"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Unified Code for Units of Measure (UCUM) is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business.",
"example": "aBq",
"example_extras": [
"/A/s3/cg3/T3",
"/g",
"/m3",
"%",
"Cel.d-1",
"dL/g",
"dlm",
"dlx",
"Em.s-2",
"g.cm-3",
"K2",
"kW/h",
"m/s",
"m.s-2",
"m/s/d",
"mmol.mL-1",
"mol.L-1",
"mol.um",
"ng-1",
"pA",
"ug.mL-1",
"umol.L-1",
"us",
"Wb"
],
"fairsharing": {
"abbreviation": "UCUM",
"description": "The Unified Code for Units of Measure is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business. The purpose is to facilitate unambiguous electronic communication of quantities together with their units. The focus is on electronic communication, as opposed to communication between humans. A typical application of The Unified Code for Units of Measure are electronic data interchange (EDI) protocols, but there is nothing that prevents it from being used in other types of machine communication.",
"domains": [
"Data identity and mapping",
"Unit",
"Measurement"
],
"homepage": "https://ucum.org/trac",
"name": "The Unified Code for Units of Measure",
"prefix": "FAIRsharing.27w8k0",
"publications": [
{
"doi": "10.1136/jamia.1999.0060151",
"pubmed": "10094068",
"title": "Units of measure in clinical information systems",
"year": 1999
}
],
"subjects": [
"Subject Agnostic"
]
},
"hl7": {
"description": "Unified Code for Units of Measure. The Unified Code for Units of Measure is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business. The purpose is to facilitate unambiguous electronic communication of quantities together with their units. The focus is on electronic communication, as opposed to communication between humans. A typical application of The Unified Code for Units of Measure are electronic data interchange (EDI) protocols, but there is nothing that prevents it from being used in other types of machine communication.http://unitsofmeasure.org/",
"homepage": "http://www.regenstrief.org",
"name": "Unified Code for Units of Measure",
"organization": "Regenstrief Institute",
"preferred_prefix": "ucum",
"prefix": "2.16.840.1.113883.6.8",
"status": "Complete"
},
"homepage": "https://ucum.org",
"lov": {
"description": "The instances of this ontology have been automatically\n generated from the UCUM (The Unified Code for Units of Measure).\n See http://aurora.rg.iupui.edu/UCUM/ for more details\n on UCUM. The members of the MyMobileWeb consortium\n explicitly acknowledge the copyright of the data from\n the UCUM ontology.",
"homepage": "http://purl.oclc.org/NET/muo/ucum/",
"keywords": [
"General & Upper"
],
"modified": "2008-01-01",
"name": "Units of measurement ontology",
"prefix": "ucum",
"uri_prefix": "http://purl.oclc.org/NET/muo/ucum/$1"
},
"mappings": {
"bartoc": "1895",
"fairsharing": "FAIRsharing.27w8k0",
"hl7": "2.16.840.1.113883.6.8",
"lov": "ucum"
},
"name": "Unified Code for Units of Measure",
"publications": [
{
"doi": "10.1136/jamia.1999.0060151",
"pmc": "PMC61354",
"pubmed": "10094068",
"title": "Units of measure in clinical information systems",
"year": 1999
}
],
"references": [
"https://units-of-measurement.org/"
],
"repository": "https://github.com/ucum-org/ucum",
"uri_format": "https://units-of-measurement.org/$1"
},
"ukprn": {
"comment": "Added because of appearance in ROR",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "identifier for an educational organization issued by the UK Register of Learning Providers",
"example": "10007835",
"homepage": "https://www.ukrlp.co.uk",
"mappings": {
"wikidata": "P4971"
},
"name": "UK Provider Reference Number",
"pattern": "^[1-9]\\d*$",
"synonyms": [
"ukprns"
],
"uri_format": "https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails?x=&pn_p_id=$1&pv_status=VERIFIED&pv_vis_code=L",
"wikidata": {
"description": "identifier for an educational organization issued by the UK Register of Learning Providers",
"example": [
"10007835",
"10008408"
],
"homepage": "https://www.ukrlp.co.uk/",
"name": "UK Provider Reference Number",
"pattern": "^[1-9][0-9]{7}$",
"prefix": "P4971",
"uri_format": "https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails?x=&pn_p_id=$1&pv_status=VERIFIED&pv_vis_code=L"
}
},
"umbbd.compound": {
"biocontext": {
"prefix": "UMBBD.COMPOUND"
},
"mappings": {
"biocontext": "UMBBD.COMPOUND",
"miriam": "umbbd.compound",
"n2t": "umbbd.compound",
"wikidata": "P8121"
},
"miriam": {
"deprecated": false,
"description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information.",
"homepage": "http://umbbd.ethz.ch/",
"id": "00000276",
"name": "UM-BBD Compound",
"namespaceEmbeddedInLui": false,
"pattern": "^c\\d+$",
"prefix": "umbbd.compound",
"sampleId": "c0001",
"uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1"
},
"n2t": {
"description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information.",
"example": "c0001",
"homepage": "http://umbbd.ethz.ch/",
"name": "Biocatalysis/Biodegradation Database Mirror (Compound) at ETH Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^c\\d+$",
"prefix": "umbbd.compound",
"uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1"
},
"name": "UM-BBD compound",
"part_of": "umbbd",
"synonyms": [
"UM-BBD_compID"
],
"uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1",
"wikidata": {
"description": "ID for chemical compound in The University of Minnesota Biocatalysis/Biodegradation Database",
"example": [
"c0001",
"c0002",
"c0003"
],
"homepage": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=allcomps",
"name": "UM-BBD compound ID",
"prefix": "P8121",
"uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1"
}
},
"umbbd.enzyme": {
"biocontext": {
"prefix": "UMBBD.ENZYME"
},
"go": {
"homepage": "http://eawag-bbd.ethz.ch/",
"name": "EAWAG Biocatalysis/Biodegradation Database",
"prefix": "UM-BBD_enzymeID",
"uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1"
},
"mappings": {
"biocontext": "UMBBD.ENZYME",
"go": "UM-BBD_enzymeID",
"miriam": "umbbd.enzyme",
"n2t": "umbbd.enzyme"
},
"miriam": {
"deprecated": false,
"description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information.",
"homepage": "http://umbbd.ethz.ch/",
"id": "00000326",
"name": "UM-BBD Enzyme",
"namespaceEmbeddedInLui": false,
"pattern": "^e\\d+$",
"prefix": "umbbd.enzyme",
"sampleId": "e0333",
"uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1"
},
"n2t": {
"description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information.",
"example": "e0333",
"homepage": "http://umbbd.ethz.ch/",
"name": "Biocatalysis/Biodegradation Database Mirror (Enzyme) at ETH Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^e\\d+$",
"prefix": "umbbd.enzyme",
"uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1"
},
"part_of": "umbbd",
"synonyms": [
"UM-BBD_enzymeID"
],
"uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1"
},
"umbbd.pathway": {
"biocontext": {
"prefix": "UMBBD.PATHWAY"
},
"go": {
"homepage": "http://eawag-bbd.ethz.ch/",
"name": "EAWAG Biocatalysis/Biodegradation Database",
"prefix": "UM-BBD_pathwayID",
"uri_format": "http://eawag-bbd.ethz.ch/$1/$1_map.html"
},
"mappings": {
"biocontext": "UMBBD.PATHWAY",
"go": "UM-BBD_pathwayID",
"miriam": "umbbd.pathway",
"n2t": "umbbd.pathway"
},
"miriam": {
"deprecated": false,
"description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information.",
"homepage": "http://umbbd.ethz.ch/",
"id": "00000327",
"name": "UM-BBD Pathway",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "umbbd.pathway",
"sampleId": "ala",
"uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1"
},
"n2t": {
"description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information.",
"example": "ala",
"homepage": "http://umbbd.ethz.ch/",
"name": "Biocatalysis/Biodegradation Database Mirror (Pathway) at ETH Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "umbbd.pathway",
"uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1"
},
"part_of": "umbbd",
"providers": [
{
"code": "eawag",
"description": "Graphical depiction of pathway",
"homepage": "http://eawag-bbd.ethz.ch",
"name": "Pathway map diagram",
"uri_format": "http://eawag-bbd.ethz.ch/$1/$1_map.html"
}
],
"synonyms": [
"UM-BBD_pathwayID"
],
"uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1"
},
"umbbd.reaction": {
"biocontext": {
"prefix": "UMBBD.REACTION"
},
"go": {
"homepage": "http://eawag-bbd.ethz.ch/",
"name": "EAWAG Biocatalysis/Biodegradation Database",
"prefix": "UM-BBD_reactionID",
"uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1"
},
"mappings": {
"biocontext": "UMBBD.REACTION",
"go": "UM-BBD_reactionID",
"miriam": "umbbd.reaction",
"n2t": "umbbd.reaction"
},
"miriam": {
"deprecated": false,
"description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information.",
"homepage": "http://umbbd.ethz.ch/",
"id": "00000325",
"name": "UM-BBD Reaction",
"namespaceEmbeddedInLui": false,
"pattern": "^r\\d+$",
"prefix": "umbbd.reaction",
"sampleId": "r0001",
"uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1"
},
"n2t": {
"description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information.",
"example": "r0001",
"homepage": "http://umbbd.ethz.ch/",
"name": "Biocatalysis/Biodegradation Database Mirror (Reaction) at ETH Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^r\\d+$",
"prefix": "umbbd.reaction",
"uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1"
},
"part_of": "umbbd",
"synonyms": [
"UM-BBD_reactionID"
],
"uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1",
"wikidata": {
"database": "Q24188985"
}
},
"umbbd.rule": {
"biocontext": {
"prefix": "UMBBD.RULE"
},
"go": {
"homepage": "http://eawag-bbd.ethz.ch/",
"name": "EAWAG Biocatalysis/Biodegradation Database",
"prefix": "UM-BBD_ruleID",
"uri_format": "http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=$1"
},
"mappings": {
"biocontext": "UMBBD.RULE",
"go": "UM-BBD_ruleID",
"miriam": "umbbd.rule",
"n2t": "umbbd.rule"
},
"miriam": {
"deprecated": false,
"description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules.",
"homepage": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules",
"id": "00000328",
"name": "UM-BBD Biotransformation Rule",
"namespaceEmbeddedInLui": false,
"pattern": "^bt\\d+$",
"prefix": "umbbd.rule",
"sampleId": "bt0001",
"uri_format": "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1"
},
"n2t": {
"description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules.",
"example": "bt0001",
"homepage": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules",
"name": "Biocatalysis/Biodegradation Database Mirror (Biotransformation Rule) at ETH Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^bt\\d+$",
"prefix": "umbbd.rule",
"uri_format": "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1"
},
"part_of": "umbbd",
"synonyms": [
"UM-BBD_ruleID"
]
},
"uminctr": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An additional Japanese clinical trial registry",
"example": "UMIN000049383",
"homepage": "https://www.umin.ac.jp/ctr/index.htm",
"integbio": {
"alt_name": "UMIN Clinical Trials Registry",
"description": "UMIN-CTR is a registration database for clinical trials. Each entry contains title of the study, condition, objectives, assessment, study design, intervention, public contact, etc. It requires a UMIN ID and password in order to register clinical trials, but not to browse and search data.",
"homepage": "http://www.umin.ac.jp/ctr/index.htm",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "UMIN (University Hospital Medical Information Network Center)",
"name": "UMIN-CTR",
"prefix": "nbdc01470",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"mappings": {
"integbio": "nbdc01470"
},
"name": "University hospital Medical Information Network Clinical Trial Registry",
"pattern": "^UMIN\\d+$|^C\\d+$",
"references": [
"https://center6.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000056224"
]
},
"umls": {
"bartoc": {
"abbreviation": "UMLS",
"description": "The Unified Medical Language System (UMLS) is a compendium of many controlled vocabularies in the biomedical sciences.",
"homepage": "https://www.nlm.nih.gov/research/umls/index.html",
"name": "Unified Medical Language System",
"prefix": "20052",
"wikidata_database": "Q455338"
},
"biocontext": {
"prefix": "UMLS",
"uri_format": "http://linkedlifedata.com/resource/umls/id/$1"
},
"edam": {
"description": "An identifier of a concept from the UMLS vocabulary.",
"name": "UMLS concept",
"obsolete": false,
"prefix": "1181"
},
"example": "C2584994",
"hl7": {
"description": "UMLS codes as CUIs making up the values in a coding system. More information may be found at http://www.nlm.nih.gov/research/umls/",
"homepage": "http://www.nlm.nih.gov",
"name": "Unified Medical Language System",
"organization": "National Library of Medicine",
"preferred_prefix": "umls",
"prefix": "2.16.840.1.113883.6.86",
"status": "Complete"
},
"homepage": "https://www.nlm.nih.gov/research/umls",
"license": "https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/license_agreement.html",
"logo": "https://uts.nlm.nih.gov/uts/assets/images/umls_tree_sm.jpg",
"mappings": {
"bartoc": "20052",
"biocontext": "UMLS",
"edam": "1181",
"hl7": "2.16.840.1.113883.6.86",
"miriam": "umls",
"n2t": "umls",
"wikidata": "P2892"
},
"miriam": {
"deprecated": false,
"description": "The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank.",
"homepage": "http://linkedlifedata.com/",
"id": "00000559",
"name": "UMLS",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d+$",
"prefix": "umls",
"sampleId": "C0021390",
"uri_format": "http://linkedlifedata.com/resource/umls/id/$1"
},
"n2t": {
"description": "The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank.",
"example": "C0021390",
"homepage": "http://linkedlifedata.com/",
"name": "Unified Medical Language System at LinkedLifeData",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d+$",
"prefix": "umls",
"uri_format": "http://linkedlifedata.com/resource/umls/id/$1"
},
"name": "Unified Medical Language System Concept Unique Identifier",
"synonyms": [
"UMLS",
"UMLS CUI",
"UMLS_CUI",
"umls.cui"
],
"uri_format": "https://uts.nlm.nih.gov/uts/umls/concept/$1",
"wikidata": {
"database": "Q455338",
"description": "NLM Unified Medical Language System (UMLS) controlled biomedical vocabulary unique identifier",
"example": [
"C0011551",
"C0037379",
"C1274928"
],
"homepage": "https://www.nlm.nih.gov/research/umls/rxnorm/",
"miriam": "umls",
"name": "UMLS CUI",
"pattern": "^C\\w\\d{6}$",
"prefix": "P2892",
"uri_format": "https://ncim-stage.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20Metathesaurus&code=$1"
}
},
"umls.aui": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An identifier for an atom; the smallest unit of naming in a source, viz, a specific string with specific code values and identifiers from a specific source. As such, they can be thought of as representing a single meaning with a source Atoms are the units of terminology that come from sources and form the building blocks of the concepts in the Metathesaurus.",
"example": "A0118748",
"homepage": "https://www.nlm.nih.gov/research/umls",
"name": "Unified Medical Language System Atomic Unique Identifier",
"pattern": "^A\\d+$",
"synonyms": [
"UMLS_ICD9CM_2005_AUI"
]
},
"unichem": {
"mappings": {
"wikidata": "P11089"
},
"name": "UniChem compound",
"wikidata": {
"description": "identifier of a compound in the UniChem database",
"example": [
"161671",
"289153",
"39562"
],
"homepage": "https://chembl.gitbook.io/unichem/downloads",
"name": "UniChem compound ID",
"pattern": "^\\d+$",
"prefix": "P11089",
"uri_format": "https://www.ebi.ac.uk/unichem/compoundsources?type=uci&compound=$1"
}
},
"unigene": {
"biocontext": {
"prefix": "UNIGENE"
},
"deprecated": true,
"fairsharing": {
"abbreviation": "UniGene",
"description": "Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.",
"homepage": "http://www.ncbi.nlm.nih.gov/unigene",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "UniGene gene-oriented nucleotide sequence clusters",
"prefix": "FAIRsharing.ge1c3p",
"publications": [
{
"doi": "10.1093/nar/gkg033",
"pubmed_id": 12519941,
"title": "Database resources of the National Center for Biotechnology."
}
],
"subjects": [
"Life Science"
]
},
"integbio": {
"description": "This database contains sets of transcriptional sequences obtained from the same locus. It includes information such as the homology between transcripts and the reference protein, expression pattern, cDNA clones, and genomic position.",
"fairsharing": "biodbcore-000459",
"homepage": "http://www.ncbi.nlm.nih.gov/unigene",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "UniGene",
"prefix": "nbdc00220",
"pubmeds": [
"8849440",
"7670480"
],
"status": "Closed",
"target_keywords": [
"cDNA/EST",
"Protein"
]
},
"mappings": {
"biocontext": "UNIGENE",
"fairsharing": "FAIRsharing.ge1c3p",
"integbio": "nbdc00220",
"miriam": "unigene",
"n2t": "unigene",
"prefixcommons": "unigene",
"re3data": "r3d100010774"
},
"miriam": {
"deprecated": true,
"description": "A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.",
"homepage": "http://www.ncbi.nlm.nih.gov/unigene",
"id": "00000346",
"name": "UniGene",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "unigene",
"sampleId": "4900",
"uri_format": "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1"
},
"n2t": {
"description": "A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.",
"example": "4900",
"homepage": "http://www.ncbi.nlm.nih.gov/unigene",
"name": "UniGene at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "unigene",
"uri_format": "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1"
},
"prefixcommons": {
"description": "Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.",
"example": "4900",
"homepage": "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene",
"keywords": [
"DNA",
"gene",
"gene expression",
"protein"
],
"name": "UniGene gene-oriented nucleotide sequence clusters",
"pattern": "^\\d+$",
"prefix": "unigene",
"uri_format": "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkg033",
"pmc": "PMC165480",
"pubmed": "12519941",
"title": "Database resources of the National Center for Biotechnology",
"year": 2003
}
],
"re3data": {
"description": "<<>>!!!>>>. Although the web pages are no longer available, you will still be able to download the final UniGene builds as static content from the FTP site https://ftp.ncbi.nlm.nih.gov/repository/UniGene/. You will also be able to match UniGene cluster numbers to Gene records by searching Gene with UniGene cluster numbers. For best results, restrict to the βUniGene Cluster Numberβ field rather than all fields in Gene. For example, a search with Mm.2108[UniGene Cluster Number] finds the mouse transthyretin Gene record (Ttr). You can use the advanced search page https://www.ncbi.nlm.nih.gov/gene/advanced to help construct these searches. Keep in mind that the Gene record contains selected Reference Sequences and GenBank mRNA sequences rather than the larger set of expressed sequences in the UniGene cluster.",
"homepage": "https://www.ncbi.nlm.nih.gov/unigene",
"name": "UniGene",
"prefix": "r3d100010774",
"xrefs": {
"nlx": "41571",
"scr": "004405"
}
}
},
"unii": {
"biocontext": {
"prefix": "UNII",
"uri_format": "http://fdasis.nlm.nih.gov/srs/unii/$1"
},
"cheminf": {
"description": "Identifier used by the USA Food and Drug Administration.",
"name": "Unique Ingredient Identifier",
"obsolete": false,
"prefix": "000563"
},
"mappings": {
"biocontext": "UNII",
"cheminf": "000563",
"miriam": "unii",
"n2t": "unii",
"wikidata": "P652"
},
"miriam": {
"deprecated": false,
"description": "The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substanceβs molecular structure and/or descriptive information.",
"homepage": "https://precision.fda.gov/uniisearch",
"id": "00000531",
"name": "UNII",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]+$",
"prefix": "unii",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "UNII at U.S. Food and Drug Administration",
"homepage": "http://fdasis.nlm.nih.gov/srs/",
"name": "UNII at U.S. Food and Drug Administration",
"uri_format": "http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=$1"
}
],
"sampleId": "3G6A5W338E",
"uri_format": "https://precision.fda.gov/uniisearch/srs/unii/$1"
},
"n2t": {
"description": "The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information.",
"example": "3G6A5W338E",
"homepage": "http://fdasis.nlm.nih.gov/srs/",
"name": "UNII at U.S. Food and Drug Administration",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]+$",
"prefix": "unii",
"uri_format": "http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=$1"
},
"name": "Unique Ingredient Identifier",
"wikidata": {
"description": "identifier issued by the FDA / Unique Ingredient Identifier",
"example": [
"3XMK78S47O",
"97C5T2UQ7J",
"YKH834O4BH"
],
"homepage": "http://fdasis.nlm.nih.gov/srs",
"miriam": "unii",
"name": "UNII",
"pattern": "^[0-9A-Za-z]{10}$",
"prefix": "P652",
"uri_format": "https://gsrs.ncats.nih.gov/ginas/app/beta/substances/$1"
}
},
"unimod": {
"biocontext": {
"prefix": "UNIMOD"
},
"contact": {
"email": "jcottrell@matrixscience.com",
"name": "John Cottrell",
"orcid": "0000-0003-3843-0818"
},
"edam": {
"description": "Identifier of a protein modification catalogued in the Unimod database.",
"name": "Unimod",
"obsolete": false,
"prefix": "3757"
},
"fairsharing": {
"abbreviation": "Unimod",
"description": "Unimod is a community-supported, comprehensive database of protein modifications for mass spectrometry applications. The aim is to provide accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide).",
"homepage": "http://www.unimod.org",
"name": "Unimod",
"prefix": "FAIRsharing.zZHCUQ",
"publications": [
{
"doi": "10.1002/pmic.200300744",
"pubmed_id": 15174123,
"title": "Unimod: Protein modifications for mass spectrometry."
}
],
"subjects": [
"Bioinformatics"
]
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"download_owl": "https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/unimod.owl",
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}
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},
{
"code": "iptmnet",
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"name": "iPTMnet",
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},
{
"code": "indra",
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"name": "INDRA Database",
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},
{
"code": "scholia",
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"name": "Scholia",
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},
{
"code": "oma",
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"uri_format": "http://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p2=orthologs&p1=$1"
},
{
"code": "drugbank",
"description": "DrugBank PolyPeptide.",
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"name": "DrugBank Polypeptide",
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}
],
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{
"doi": "10.1093/nar/gkj161",
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}
],
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"scr": "004426"
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"A0A1V4U2Y9",
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"O43423",
"D4IJI4",
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"D3TBR4",
"D4ILS5"
],
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},
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"keywords": [
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],
"modified": "2012-10-03",
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},
"mappings": {
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"description": "The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary.",
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"name": "UniProt Diseases",
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"description": "The post-translational modifications used in the UniProt knowledgebase (Swiss-Prot and TrEMBL). The definition of the post-translational modifications usage as well as other information is provided in the following format",
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},
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"deprecated": true,
"homepage": "http://pkuxxj.pku.edu.cn/UNPD/",
"name": "Universal Natural Products Database",
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{
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},
{
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"pmc": "PMC3636197",
"pubmed": "23638153",
"title": "Use of natural products as chemical library for drug discovery and network pharmacology",
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}
],
"references": [
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},
"uo": {
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"homepage": "https://github.com/bio-ontology-research-group/unit-ontology",
"name": "Units of measurement ontology",
"prefix": "UO"
},
"agroportal": {
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"name": "George Gkoutos"
},
"description": "Units Ontology (UO) is an ontology currently being used in many scientific resources for the standardized description of units of measurements. Metrical units for use in conjunction with PATO",
"example_uri": "http://purl.obolibrary.org/obo/UO_0000294",
"homepage": "https://github.com/bio-ontology-research-group/unit-ontology",
"license": "CC-BY-3.0",
"name": "Units of Measurement Ontology",
"prefix": "UO",
"publication": "https://doi.org/10.1093/database/bas033",
"repository": "https://github.com/bio-ontology-research-group/unit-ontology",
"version": "2023-05-25"
},
"biocontext": {
"prefix": "UO"
},
"bioportal": {
"contact": {
"email": "g.gkoutos@gmail.com",
"name": "George Gkoutos"
},
"description": "Metrical units for use in conjunction with PATO",
"homepage": "https://github.com/bio-ontology-research-group/unit-ontology",
"name": "Units of Measurement Ontology",
"prefix": "UO",
"version": "2023-05-25"
},
"fairsharing": {
"abbreviation": "UO",
"contact": {
"email": "geg18@aber.ac.uk",
"name": "George Gkoutos",
"orcid": "0000-0002-2061-091X"
},
"description": "The Units Ontology (UO) models metrical units for use in conjunction with PATO. Units are basic scientific tools that render meaning to numerical data. Their standardization and formalization caters for the report, exchange, process, reproducibility and integration of quantitative measurements. The Units Ontology is an ontology currently being used for the standardized description of units of measurements.",
"domains": [
"Unit",
"Measurement"
],
"homepage": "https://github.com/bio-ontology-research-group/unit-ontology",
"license": "CC-BY-3.0",
"name": "Units Ontology",
"prefix": "FAIRsharing.mjnypw",
"publications": [
{
"doi": "10.1093/database/bas033",
"pubmed": "23060432",
"title": "The Units Ontology: a tool for integrating units of measurement in science",
"year": 2012
}
],
"repository": "https://github.com/bio-ontology-research-group/unit-ontology/issues",
"subjects": [
"Mathematics",
"Life Science"
]
},
"mappings": {
"aberowl": "UO",
"agroportal": "UO",
"biocontext": "UO",
"bioportal": "UO",
"fairsharing": "FAIRsharing.mjnypw",
"miriam": "uo",
"n2t": "uo",
"obofoundry": "uo",
"ols": "uo",
"ontobee": "UO",
"prefixcommons": "uo"
},
"miriam": {
"deprecated": false,
"description": "Ontology of standardized units",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/uo",
"id": "00000136",
"name": "Unit Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^UO:\\d{7}?",
"prefix": "uo",
"sampleId": "0000080",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/uo/terms?obo_id=UO:$1"
},
"n2t": {
"description": "Ontology of standardized units",
"example": "0000080",
"homepage": "http://bioportal.bioontology.org/ontologies/UO",
"name": "Unit Ontology through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^UO:\\d{7}?",
"prefix": "uo",
"uri_format": "http://purl.bioontology.org/ontology/UO/UO:$1"
},
"obofoundry": {
"appears_in": [
"agro",
"ms",
"rbo",
"scdo"
],
"contact": "g.gkoutos@gmail.com",
"contact.github": "gkoutos",
"contact.label": "George Gkoutos",
"contact.orcid": "0000-0002-2061-091X",
"deprecated": false,
"description": "Metrical units for use in conjunction with PATO",
"domain": "phenotype",
"download.obo": "http://purl.obolibrary.org/obo/uo.obo",
"download.owl": "http://purl.obolibrary.org/obo/uo.owl",
"homepage": "https://github.com/bio-ontology-research-group/unit-ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Units of measurement ontology",
"preferredPrefix": "UO",
"prefix": "uo",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/23060432",
"title": "The Units Ontology: a tool for integrating units of measurement in science"
}
],
"repository": "https://github.com/bio-ontology-research-group/unit-ontology"
},
"ols": {
"description": "Metrical units for use in conjunction with PATO",
"download_owl": "http://purl.obolibrary.org/obo/uo.owl",
"homepage": "https://github.com/bio-ontology-research-group/unit-ontology",
"name": "Units of measurement ontology",
"prefix": "uo",
"version": "2023-05-25",
"version.iri": "http://purl.obolibrary.org/obo/uo/releases/2023-05-25/uo.owl"
},
"ontobee": {
"library": "Library",
"name": "Units of measurement ontology",
"prefix": "UO"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"alt_uri_formats": [
"http://purl.org/obo/owl/UO#$1",
"http://mimi.case.edu/ontologies/2009/1/UnitsOntology#$1"
],
"bioportal": "1112",
"description": "Ontology of standardized units in conjunction with PATO",
"example": "UO:0000080",
"homepage": "http://code.google.com/p/unit-ontology/",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"name": "Unit Ontology",
"pattern": "^UO:\\d{7}?$",
"prefix": "uo",
"synonyms": [
"obo.unit",
"unit"
]
},
"publications": [
{
"doi": "10.1093/database/bas033",
"pmc": "PMC3468815",
"pubmed": "23060432",
"title": "The Units Ontology: a tool for integrating units of measurement in science",
"year": 2012
}
],
"uri_format": "http://purl.obolibrary.org/obo/UO_$1"
},
"upa": {
"aberowl": {
"description": "A manually curated resource for the representation and annotation of metabolic pathways",
"download_owl": "http://aber-owl.net/media/ontologies/UPA/2/upa.owl",
"homepage": "https://github.com/geneontology/unipathway",
"name": "Unipathway",
"prefix": "UPA"
},
"biocontext": {
"prefix": "UNIPATHWAY"
},
"bioportal": {
"contact": {
"email": "Anne.Morgat@sib.swiss",
"name": "Anne Morgat"
},
"description": "UniPathway (http://www.unipathway.org) is a fully manually curated resource for the representation and annotation of metabolic pathways. UniPathway provides explicit representations of enzyme-catalyzed and spontaneous chemical reactions, as well as a hierarchical representation of metabolic pathways. This hierarchy uses linear subpathways as the basic building block for the assembly of larger and more complex pathways, including species-specific pathway variants. All of the pathway data in UniPathway has been extensively cross-linked to existing pathway resources such as KEGG and MetaCyc, as well as sequence resources such as the UniProt KnowledgeBase (UniProtKB), for which UniPathway provides a controlled vocabulary for pathway annotation. We introduce here the basic concepts underlying the UniPathway resource, with the aim of allowing users to fully exploit the information provided by UniPathway.",
"homepage": "https://github.com/geneontology/unipathway",
"name": "Unipathway",
"prefix": "UPA",
"publication": "https://www.ncbi.nlm.nih.gov/pubmed/22102589",
"version": "UniPathway Release 2015_03"
},
"deprecated": true,
"download_obo": "https://raw.githubusercontent.com/geneontology/unipathway/master/upa.obo",
"edam": {
"description": "Identifier of a biological pathway from the Unipathway database.",
"name": "Pathway ID (Unipathway)",
"obsolete": false,
"prefix": "2645"
},
"example": "UCR00513",
"go": {
"description": "UniPathway is a a metabolic door to UniProtKB/Swiss-Prot, a curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase.",
"homepage": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway",
"name": "UniPathway",
"prefix": "UniPathway",
"uri_format": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1"
},
"mappings": {
"aberowl": "UPA",
"biocontext": "UNIPATHWAY",
"bioportal": "UPA",
"edam": "2645",
"go": "UniPathway",
"obofoundry": "upa",
"ols": "upa",
"ontobee": "UPA",
"pathguide": "414",
"prefixcommons": "unipathway"
},
"obofoundry": {
"contact": "Anne.Morgat@sib.swiss",
"contact.github": "amorgat",
"contact.label": "Anne Morgat",
"contact.orcid": "0000-0002-1216-2969",
"depends_on": [
"ro"
],
"deprecated": true,
"description": "A manually curated resource for the representation and annotation of metabolic pathways",
"domain": "biological systems",
"download.obo": "http://purl.obolibrary.org/obo/upa.obo",
"download.owl": "http://purl.obolibrary.org/obo/upa.owl",
"homepage": "https://github.com/geneontology/unipathway",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Unipathway",
"prefix": "upa",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/22102589",
"title": "UniPathway: a resource for the exploration and annotation of metabolic pathways"
}
],
"repository": "https://github.com/geneontology/unipathway"
},
"ols": {
"description": "A manually curated resource for the representation and annotation of metabolic pathways",
"download_owl": "http://purl.obolibrary.org/obo/upa.owl",
"homepage": "https://github.com/geneontology/unipathway",
"name": "Unipathway",
"prefix": "upa",
"version": "2024-03-06",
"version.iri": "http://purl.obolibrary.org/obo/upa/releases/2024-03-06/upa.owl"
},
"ontobee": {
"library": "Library",
"name": "Unipathway",
"prefix": "UPA"
},
"pathguide": {
"abbreviation": "UniPathway",
"homepage": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway",
"name": "UniPathway: a resource for the exploration of metabolic pathways",
"prefix": "414"
},
"pattern": "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\\d{5}$",
"prefixcommons": {
"description": "UniPathway is a manually curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase. It provides a structured controlled vocabulary to describe the role of a protein in a metabolic pathway.",
"example": "UPA00206",
"homepage": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway",
"keywords": [
"pathway"
],
"name": "UniPathway, a metabolic door to UniProtKB/Swiss-Prot",
"pattern": "^UPA\\d{5}$",
"prefix": "unipathway",
"uri_format": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkr1023",
"pmc": "PMC3245108",
"pubmed": "22102589",
"title": "UniPathway: a resource for the exploration and annotation of metabolic pathways",
"year": 2011
}
],
"synonyms": [
"UPa",
"unipathway",
"unipathway.pathway"
],
"wikidata": {
"database": "Q85719315"
}
},
"upheno": {
"aberowl": {
"description": "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/UPHENO/5/upheno.owl",
"homepage": "https://github.com/obophenotype/upheno",
"name": "Unified phenotype ontology (uPheno)",
"prefix": "UPHENO"
},
"biocontext": {
"prefix": "UPHENO"
},
"bioportal": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "Combined phenotype ontology",
"name": "Combined Phenotype Ontology",
"prefix": "UPHENO"
},
"fairsharing": {
"abbreviation": "UPHENO",
"description": "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology. Version 2 is the active release of the ontology, while version 1 should be considered deprecated. ",
"domains": [
"Phenotype"
],
"homepage": "https://github.com/obophenotype/upheno",
"license": "CC0-1.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBa01CIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--3f5258d2bcf30a7e127b5a9fe209b27e25e88883/up.png?disposition=inline",
"name": "Unified phenotype ontology",
"prefix": "FAIRsharing.r41qhx",
"subjects": [
"Evolutionary Biology",
"Phenomics"
]
},
"mappings": {
"aberowl": "UPHENO",
"biocontext": "UPHENO",
"bioportal": "UPHENO",
"fairsharing": "FAIRsharing.r41qhx",
"obofoundry": "upheno",
"ols": "upheno",
"ontobee": "UPHENO"
},
"name": "Unified Phenotype Ontology",
"no_own_terms": true,
"obofoundry": {
"contact": "vasilevs@ohsu.edu",
"contact.github": "nicolevasilevsky",
"contact.label": "Nicole Vasilevsky",
"contact.orcid": "0000-0001-5208-3432",
"deprecated": false,
"description": "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.",
"domain": "phenotype",
"download.owl": "http://purl.obolibrary.org/obo/upheno.owl",
"homepage": "https://github.com/obophenotype/upheno",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Unified phenotype ontology (uPheno)",
"preferredPrefix": "UPHENO",
"prefix": "upheno",
"publications": [
{
"id": "https://zenodo.org/record/2382757",
"title": "Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species"
},
{
"id": "https://zenodo.org/record/3352149",
"title": "Phenotype Ontologies Traversing All The Organisms (POTATO) workshop: 2nd edition"
}
],
"repository": "https://github.com/obophenotype/upheno"
},
"ols": {
"description": "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.",
"download": "http://purl.obolibrary.org/obo/upheno.owl",
"homepage": "https://github.com/obophenotype/upheno",
"name": "Unified phenotype ontology (uPheno)",
"prefix": "upheno",
"version": "2017-10-31"
},
"ontobee": {
"library": "Library",
"name": "Unified phenotype ontology (uPheno)",
"prefix": "UPHENO"
}
},
"uspto": {
"biocontext": {
"prefix": "USPTO"
},
"comment": "Information about the regular expression was derived from examples at https://patft.uspto.gov/netahtml/PTO/srchnum.htm. TODO, make the regular expression work for '100000000'",
"contributor_extras": [
{
"github": "dhimmel",
"name": "Daniel Himmelstein",
"orcid": "0000-0002-3012-7446"
}
],
"example_extras": [
"10,000,000",
"6923014",
"0000001",
"D000152",
"PP07514",
"RE12345",
"T855019",
"H001234",
"AI00007",
"X000001",
"RX00001"
],
"mappings": {
"biocontext": "USPTO",
"miriam": "uspto",
"n2t": "uspto"
},
"miriam": {
"deprecated": false,
"description": "The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement.",
"homepage": "http://patft.uspto.gov/netahtml/PTO/index.html",
"id": "00000538",
"name": "USPTO",
"namespaceEmbeddedInLui": false,
"pattern": "^(D|PP|R|T|H|X|AI)?\\d+$",
"prefix": "uspto",
"sampleId": "4145692",
"uri_format": "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1"
},
"n2t": {
"description": "The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement.",
"example": "4145692",
"homepage": "http://patft.uspto.gov/netahtml/PTO/index.html",
"name": "USPTO patents at USPTO",
"namespaceEmbeddedInLui": false,
"pattern": "^(D|PP|R|T|H|X|AI)?\\d+$",
"prefix": "uspto",
"uri_format": "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1"
},
"name": "United States Patent and Trademark Office",
"pattern": "^(\\d{1,2},?\\d{3},?\\d{3}|(PP|RE|AI|RX)\\d{2},?\\d{3}|(D|T|H|X)\\d{3},?\\d{3})$",
"references": [
"https://github.com/biopragmatics/bioregistry/issues/253"
]
},
"utrdb": {
"integbio": {
"description": "UTRdb is a database of untranslated region sequences and other information related to the regulation of genes by way of 5' and 3' UTRs. The database contains sequence information for hundreds of thousands of genes in dozens of species, and a second, more comprehensive resource specifically dedicated to human UTRs. Tools for analyzing UTRs and bulk data downloads are available.",
"homepage": "http://utrdb.ba.itb.cnr.it/",
"information_keywords": [
"Sequence"
],
"maintainer": "Institute for Biomedical Technologies",
"name": "UTRdb",
"prefix": "nbdc00730",
"pubmeds": [
"19880380",
"15608165",
"11752330",
"11897027",
"11591473",
"10592223"
],
"status": "Active",
"target_keywords": [
"RNA"
]
},
"mappings": {
"integbio": "nbdc00730",
"miriam": "utrdb"
},
"miriam": {
"deprecated": false,
"description": "A curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs. In the current update, the UTR entries are organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets. ",
"homepage": "https://utrdb.cloud.ba.infn.it/utrdb/index_107.html",
"id": "00000993",
"name": "UTRdb",
"namespaceEmbeddedInLui": false,
"pattern": "([3-5][A-Z])\\w+[^A-Z][0-9]",
"prefix": "utrdb",
"sampleId": "5UTR_107_ENST00000517291.2",
"uri_format": "https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e=$1"
}
},
"vac": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Vaccine Adjuvant Compendium (VAC) was established in 2020 by the NIAID Division of Allergy, Immunology, and Transplantation to foster collaborations between NIAID-supported adjuvant researchers and the broader scientific community. The VAC displays adjuvant characteristics or metadata defined through NIAID-supported adjuvant studies to help vaccine developers identify suitable adjuvants for various vaccine indications, including immune-mediated and infectious diseases. In addition, the VAC welcomes the inclusion of adjuvant metadata generated by other research programs.",
"example": "15",
"homepage": "https://vac.niaid.nih.gov",
"keywords": [
"biology",
"immunology",
"vaccines"
],
"name": "Vaccine Adjuvant Compendium",
"pattern": "^\\d+$",
"uri_format": "https://vac.niaid.nih.gov/view?id=$1"
},
"validatordb": {
"biocontext": {
"prefix": "VALIDATORDB"
},
"example": "2h6o",
"fairsharing": {
"abbreviation": "ValidatorDB",
"contact": {
"email": "david.sehnal@gmail.com",
"name": "David Sehnal",
"orcid": "0000-0002-0682-3089"
},
"description": "ValidatorDB is a collection of validation results for the entire Protein Data Bank. Annotation (3-letter code) of HET residues larger than 6 heavy atoms is inspected, i.e. if the residue has the same topology and stereochemistry as the model ligand or residue stored in the wwCCD. Validation reports for the entire database can be inspected as well as for the arbitrary set of PDB entries or PDB annotations (3-letter residue code). Results are available in graphical form via Web UI and can be downloaded in the form of CSV files for further inspection.",
"homepage": "http://webchem.ncbr.muni.cz/Platform/ValidatorDB",
"name": "ValidatorDB",
"prefix": "FAIRsharing.c9psgb",
"publications": [
{
"doi": "10.1093/nar/gku1118",
"pubmed_id": 25392418,
"title": "ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank."
}
],
"subjects": [
"Life Science"
]
},
"integbio": {
"description": "ValidatorDB is a collection of validation results for the entire Protein Data Bank. Annotation (3-letter code) of HET residues larger than 6 heavy atoms is inspected, i.e. if the residue has the same topology and stereochemistry as the model ligand or residue stored in the wwCCD. Validation reports for the entire database can be inspected as well as for the arbitrary set of PDB entries or PDB annotations (3-letter residue code). Results are available in graphical form via Web UI and can be downloaded in the form of CSV files for further inspection.",
"fairsharing": "FAIRsharing.c9psgb",
"homepage": "http://webchem.ncbr.muni.cz/Platform/ValidatorDB",
"information_keywords": [
"3D structure"
],
"maintainer": "Central European Institute of Technology",
"name": "ValidatorDB",
"prefix": "nbdc02174",
"pubmeds": [
"25392418"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"mappings": {
"biocontext": "VALIDATORDB",
"fairsharing": "FAIRsharing.c9psgb",
"integbio": "nbdc02174",
"miriam": "validatordb",
"n2t": "validatordb"
},
"miriam": {
"deprecated": false,
"description": "Database of validation results for ligands and non-standard residues in the Protein Data Bank.",
"homepage": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/",
"id": "00000633",
"name": "ValidatorDB",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9\\/]+$",
"prefix": "validatordb",
"sampleId": "ByStructure/2h6o",
"uri_format": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/$1"
},
"n2t": {
"description": "Database of validation results for ligands and non-standard residues in the Protein Data Bank.",
"example": "ByStructure/2h6o",
"homepage": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/",
"name": "ValidatorDB",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9\\/]+$",
"prefix": "validatordb",
"uri_format": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/$1"
},
"provides": "pdb",
"publications": [
{
"doi": "10.1093/nar/gku1118",
"pmc": "PMC4383933",
"pubmed": "25392418",
"title": "ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank",
"year": 2014
}
],
"uri_format": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1"
},
"vandf": {
"aberowl": {
"description": "NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes.",
"homepage": "http://www.pbm.va.gov/NationalFormulary.aspx",
"name": "Veterans Health Administration National Drug File",
"prefix": "VANDF",
"version": "2016AB"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "VANDF",
"uri_format": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/$1"
},
"bioportal": {
"contact": {
"email": "michael.lincoln@med.va.gov",
"name": "Michael Lincoln"
},
"description": "NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes.",
"homepage": "http://www.pbm.va.gov/NationalFormulary.aspx",
"name": "Veterans Health Administration National Drug File",
"prefix": "VANDF",
"version": "2023AB"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes. ",
"example": "4019477",
"fairsharing": {
"abbreviation": "VANDF",
"description": "Veterans Health Administration National Drug File is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies.",
"domains": [
"Drug",
"Drug interaction"
],
"homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/",
"name": "Veterans Health Administration National Drug File",
"prefix": "FAIRsharing.xn3pb3",
"publications": [
{
"pubmed": "12463886",
"title": "A semantic normal form for clinical drugs in the UMLS: early experiences with the VANDF",
"year": 2002
}
],
"subjects": [
"Pharmacology",
"Biomedical Science"
]
},
"hl7": {
"description": "U.S. Department of Veterns Affairs, Veterans Health Administration National Drug File. Department of Veterans Affairs, Washington, DC. URL: http://www.vapbm.org/PBM/natform.htm",
"name": "National Drug File",
"preferred_prefix": "VANDF",
"prefix": "2.16.840.1.113883.6.229",
"status": "Pending"
},
"homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF",
"mappings": {
"aberowl": "VANDF",
"biolink": "VANDF",
"bioportal": "VANDF",
"fairsharing": "FAIRsharing.xn3pb3",
"hl7": "2.16.840.1.113883.6.229"
},
"name": "Veterans Administration National Drug File",
"pattern": "^\\d+$",
"publications": [
{
"pmc": "PMC2244318",
"pubmed": "12463886",
"title": "A semantic normal form for clinical drugs in the UMLS: early experiences with the VANDF",
"year": 2002
}
],
"uri_format": "http://purl.bioontology.org/ontology/VANDF/$1"
},
"vann": {
"contact": {
"email": "nospam@iandavis.com",
"github": "iand",
"name": "Ian Davis"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "This document describes a vocabulary for annotating descriptions of vocabularies with examples and usage notes.",
"example": "usageNote",
"homepage": "https://vocab.org/vann/",
"lov": {
"description": "A vocabulary for annotating descriptions of vocabularies with examples and usage notes.",
"homepage": "http://purl.org/vocab/vann/",
"keywords": [
"Metadata"
],
"modified": "2010-06-07",
"name": "VANN: A vocabulary for annotating vocabulary descriptions",
"prefix": "vann",
"uri_prefix": "http://purl.org/vocab/vann/$1"
},
"mappings": {
"lov": "vann",
"zazuko": "vann"
},
"name": "A vocabulary for annotating vocabulary descriptions",
"preferred_prefix": "vann",
"uri_format": "https://vocab.org/vann/#$1",
"zazuko": {
"prefix": "vann",
"uri_format": "http://purl.org/vocab/vann/$1"
}
},
"vario": {
"aberowl": {
"description": "Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations.",
"download_owl": "http://aber-owl.net/media/ontologies/VARIO/19/vario.owl",
"homepage": "http://variationontology.org",
"name": "Variation Ontology",
"prefix": "VARIO"
},
"agroportal": {
"contact": {
"email": "mauno.vihinen@med.lu.se",
"name": "Mauno Vihinen"
},
"description": "Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations. VariO allows unambiguous description of variation effects as well as computerized analyses over databases utilizing the ontology for annotation. VariO is a position specific ontology that can be used to describe effects of variations on DNA, RNA and/or protein level, whatever is appropriate.",
"example_uri": "http://purl.obolibrary.org/obo/VariO_0117",
"homepage": "http://variationontology.org/",
"name": "Variation Ontology",
"prefix": "VARIO",
"publication": "http://genome.cshlp.org/content/early/2013/10/25/gr.157495.113.abstract",
"version": "2017-02-06"
},
"banana": "VariO",
"biocontext": {
"prefix": "VARIO"
},
"bioportal": {
"contact": {
"email": "mauno.vihinen@med.lu.se",
"name": "Mauno Vihinen"
},
"description": "Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations. Ontology is unreachable as of 2024, but continues to be available on BioPortal as a retired ontology.",
"homepage": "http://variationontology.org",
"name": "Variation Ontology",
"prefix": "VARIO",
"publication": "https://obofoundry.org/ontology/vario",
"version": "2018-11-09"
},
"contact": {
"email": "mauno.vihinen@med.lu.se",
"github": "maunov",
"name": "Mauno Vihinen",
"orcid": "0000-0002-9614-7976"
},
"example": "0376",
"fairsharing": {
"abbreviation": "VariO",
"description": "Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations. VariO allows unambiguous description of variation effects as well as computerized analyses over databases utilizing the ontology for annotation. VariO is a position specific ontology that can be used to describe effects of variations on DNA, RNA and/or proteins.",
"domains": [
"DNA structural variation",
"Deoxyribonucleic acid",
"Ribonucleic acid",
"Protein",
"Sequence variant"
],
"homepage": "http://variationontology.org",
"name": "Variation Ontology",
"prefix": "FAIRsharing.65xkbs",
"publications": [
{
"doi": "10.1101/gr.157495.113",
"pubmed": "24162187",
"title": "Variation Ontology for annotation of variation effects and mechanisms",
"year": 2013
},
{
"doi": "10.1007/s00439-015-1529-6",
"pubmed": "25616435",
"title": "Types and effects of protein variations",
"year": 2015
},
{
"doi": "10.1186/2041-1480-5-9",
"pubmed": "24533660",
"title": "Variation ontology: annotator guide",
"year": 2014
},
{
"doi": "10.1002/humu.22954",
"pubmed": "26773573",
"title": "VariOtator, a Software Tool for Variation Annotation with the Variation Ontology",
"year": 2016
},
{
"doi": "10.1186/s12864-018-5262-0",
"pubmed": "30591019",
"title": "Systematics for types and effects of DNA variations",
"year": 2018
}
],
"subjects": [
"Genetics"
]
},
"mappings": {
"aberowl": "VARIO",
"agroportal": "VARIO",
"biocontext": "VARIO",
"bioportal": "VARIO",
"fairsharing": "FAIRsharing.65xkbs",
"miriam": "vario",
"n2t": "vario",
"obofoundry": "vario",
"ols": "vario",
"ontobee": "VariO"
},
"miriam": {
"deprecated": false,
"description": "The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level.",
"homepage": "http://bioportal.bioontology.org/ontologies/VARIO",
"id": "00000406",
"name": "VariO",
"namespaceEmbeddedInLui": true,
"pattern": "^VariO:\\d+$",
"prefix": "vario",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "VariO at Lund University",
"homepage": "http://www.variationontology.org/",
"name": "VariO at Lund University",
"uri_format": "http://www.ontobee.org/search?ontology=VariO&keywords=VariO_$1&submit=Search+terms"
}
],
"sampleId": "0294",
"uri_format": "https://purl.bioontology.org/ontology/VARIO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVariO_$1"
},
"n2t": {
"description": "The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level.",
"example": "0294",
"homepage": "http://bioportal.bioontology.org/ontologies/VARIO",
"name": "VariO through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^VariO:\\d+$",
"prefix": "vario",
"uri_format": "http://purl.bioontology.org/ontology/VARIO/VariO:$1"
},
"name": "Variation Ontology",
"obofoundry": {
"contact": "mauno.vihinen@med.lu.se",
"contact.github": "maunov",
"contact.label": "Mauno Vihinen",
"contact.orcid": "0000-0002-9614-7976",
"deprecated": true,
"description": "Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations.",
"domain": "biological systems",
"download.obo": "http://purl.obolibrary.org/obo/vario.obo",
"download.owl": "http://purl.obolibrary.org/obo/vario.owl",
"homepage": "http://variationontology.org",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Variation Ontology",
"preferredPrefix": "VariO",
"prefix": "vario",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/24162187",
"title": "Variation Ontology for annotation of variation effects and mechanisms"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/24533660",
"title": "Variation ontology: annotator guide"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/25616435",
"title": "Types and effects of protein variations"
}
]
},
"ols": {
"description": "Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations.",
"download": "http://purl.obolibrary.org/obo/vario.owl",
"homepage": "http://variationontology.org",
"name": "Variation Ontology",
"prefix": "vario",
"version": "2018-11-09",
"version.iri": "http://purl.obolibrary.org/obo/vario/2018-11-09/vario.owl"
},
"ontobee": {
"library": "Library",
"name": "Variation Ontology",
"prefix": "VariO"
},
"pattern": "^\\d+$",
"preferred_prefix": "VariO",
"publications": [
{
"doi": "10.1186/s12864-018-5262-0",
"pmc": "PMC6309100",
"pubmed": "30591019",
"title": "Systematics for types and effects of DNA variations",
"year": 2018
},
{
"doi": "10.1002/humu.22954",
"pubmed": "26773573",
"title": "VariOtator, a Software Tool for Variation Annotation with the Variation Ontology",
"year": 2016
},
{
"doi": "10.1007/s00439-015-1529-6",
"pubmed": "25616435",
"title": "Types and effects of protein variations",
"year": 2015
},
{
"doi": "10.1186/2041-1480-5-9",
"pmc": "PMC3931275",
"pubmed": "24533660",
"title": "Variation ontology: annotator guide",
"year": 2014
},
{
"doi": "10.1101/gr.157495.113",
"pmc": "PMC3912426",
"pubmed": "24162187",
"title": "Variation Ontology for annotation of variation effects and mechanisms",
"year": 2013
}
]
},
"vbase2": {
"biocontext": {
"prefix": "VBASE2"
},
"fairsharing": {
"abbreviation": "VBASE2",
"contact": {
"email": "wmueller@gbf.de",
"name": "Werner MΓΌller",
"orcid": "0000-0002-1297-9725"
},
"description": "VBASE2 is an integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank.",
"homepage": "http://www.vbase2.org",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "VBASE2",
"prefix": "FAIRsharing.qvxhb1",
"publications": [
{
"doi": "10.1093/nar/gki088",
"pubmed_id": 15608286,
"title": "VBASE2, an integrative V gene database."
}
],
"subjects": [
"Life Science"
]
},
"integbio": {
"description": "VBASE2 is an integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank.",
"fairsharing": "FAIRsharing.qvxhb1",
"homepage": "http://www.vbase2.org",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Cologne",
"name": "VBASE2",
"prefix": "nbdc01897",
"pubmeds": [
"15608286"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Protein"
]
},
"mappings": {
"biocontext": "VBASE2",
"fairsharing": "FAIRsharing.qvxhb1",
"integbio": "nbdc01897",
"miriam": "vbase2",
"n2t": "vbase2",
"ncbi": "VBASE2",
"prefixcommons": "vbase2"
},
"miriam": {
"deprecated": false,
"description": "The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes.",
"homepage": "http://www.vbase2.org/vbase2.php",
"id": "00000320",
"name": "Vbase2",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "vbase2",
"sampleId": "humIGHV025",
"uri_format": "http://www.vbase2.org/vgene.php?id=$1"
},
"n2t": {
"description": "The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes.",
"example": "humIGHV025",
"homepage": "http://www.vbase2.org/vbase2.php",
"name": "Vbase2 at German Research Centre for Biotechnology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "vbase2",
"uri_format": "http://www.vbase2.org/vgene.php?id=$1"
},
"ncbi": {
"example": "humIGKV165",
"homepage": "http://www.vbase2.org/",
"name": "Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse",
"prefix": "VBASE2"
},
"prefixcommons": {
"description": "VBASE2 is an integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank.",
"example": "humIGHV025",
"homepage": "http://www.vbase2.org",
"keywords": [
"gene"
],
"name": "VBASE2",
"pattern": "^\\w+$",
"prefix": "vbase2",
"pubmed_ids": [
"15608286"
],
"uri_format": "http://www.vbase2.org/vgene.php?id=$1"
},
"publications": [
{
"doi": "10.1093/nar/gki088",
"pmc": "PMC540042",
"pubmed": "15608286",
"title": "VBASE2, an integrative V gene database",
"year": 2005
}
]
},
"vbo": {
"aberowl": {
"description": "Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.",
"download_owl": "http://aber-owl.net/media/ontologies/VBO/9/vbo.owl",
"homepage": "https://github.com/monarch-initiative/vertebrate-breed-ontology",
"name": "Vertebrate Breed Ontology",
"prefix": "VBO"
},
"bioportal": {
"contact": {
"email": "Sabrina@tislab.org",
"name": "Sabrina Toro"
},
"description": "Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.",
"homepage": "https://github.com/monarch-initiative/vertebrate-breed-ontology",
"name": "Vertebrate Breed Ontology",
"prefix": "VBO",
"version": "2024-05-22"
},
"example": "0000038",
"mappings": {
"aberowl": "VBO",
"bioportal": "VBO",
"obofoundry": "vbo",
"ols": "vbo",
"ontobee": "VBO"
},
"obofoundry": {
"contact": "Sabrina@tislab.org",
"contact.github": "sabrinatoro",
"contact.label": "Sabrina Toro",
"contact.orcid": "0000-0002-4142-7153",
"depends_on": [
"ncbitaxon"
],
"deprecated": false,
"description": "Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.",
"domain": "organisms",
"download.json": "http://purl.obolibrary.org/obo/vbo.json",
"download.obo": "http://purl.obolibrary.org/obo/vbo.obo",
"download.owl": "http://purl.obolibrary.org/obo/vbo.owl",
"homepage": "https://github.com/monarch-initiative/vertebrate-breed-ontology",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Vertebrate Breed Ontology",
"preferredPrefix": "VBO",
"prefix": "vbo",
"repository": "https://github.com/monarch-initiative/vertebrate-breed-ontology"
},
"ols": {
"description": "Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.",
"download_owl": "http://purl.obolibrary.org/obo/vbo.owl",
"homepage": "https://github.com/monarch-initiative/vertebrate-breed-ontology",
"name": "Vertebrate Breed Ontology",
"prefix": "vbo",
"version": "2024-05-22",
"version.iri": "http://purl.obolibrary.org/obo/vbo/releases/2024-05-22/vbo.owl"
},
"ontobee": {
"library": "Library",
"name": "Vertebrate Breed Ontology",
"prefix": "VBO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/VBO_$1"
},
"vbrc": {
"biocontext": {
"prefix": "VBRC"
},
"mappings": {
"biocontext": "VBRC",
"miriam": "vbrc",
"n2t": "vbrc",
"prefixcommons": "vbrc"
},
"miriam": {
"deprecated": false,
"description": "The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis.",
"homepage": "http://vbrc.org/",
"id": "00000448",
"name": "VBRC",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "vbrc",
"sampleId": "35742",
"uri_format": "http://vbrc.org/gene_detail.asp?gene_id=$1"
},
"n2t": {
"description": "The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis.",
"example": "35742",
"homepage": "http://vbrc.org/",
"name": "VBRC at University of Alabama",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "vbrc",
"uri_format": "http://vbrc.org/gene_detail.asp?gene_id=$1"
},
"name": "Viral Bioinformatics Resource Center",
"prefixcommons": {
"description": "The VBRC is one of eight NIH/NIAID-funded Bioinformatics Resource Centers nationwide providing a comprehensive web-based battery of informational and analytical tools and resources.",
"example": "VP0033331",
"homepage": "http://vbrc.org",
"name": "Viral Bioinformatics Resource Center",
"pattern": "^VP\\d+$",
"prefix": "vbrc"
}
},
"vcell": {
"mappings": {
"miriam": "vcell"
},
"miriam": {
"deprecated": false,
"description": "Models developed with the Virtual Cell (VCell) software prorgam.",
"homepage": "https://health.uconn.edu/",
"id": "00000893",
"name": "VCell Published Models",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{5,}$",
"prefix": "vcell",
"sampleId": "201022999",
"uri_format": "https://vcell.org/biomodel-$1"
}
},
"vdrc": {
"description": "Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID. [from RRID]",
"example": "100291",
"mappings": {
"rrid": "VDRC"
},
"pattern": "^\\d+$",
"rrid": {
"homepage": "http://stockcenter.vdrc.at/control/main",
"keywords": [
"biomaterial supply resource",
"drosophila",
"fly lines"
],
"name": "Vienna Drosophila Resource Center",
"prefix": "VDRC",
"scr": "013805"
},
"uri_format": "https://shop.vbc.ac.at/vdrc_store/$1.html"
},
"vectorbase": {
"biocontext": {
"prefix": "VECTORBASE"
},
"contact": {
"email": "d.e.starns@liv.ac.uk",
"github": "obsidian83",
"name": "David Starns",
"orcid": "0000-0001-6583-9067"
},
"fairsharing": {
"abbreviation": "VectorBase",
"description": "VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes (as well as a number of non-vector genomes for comparative analysis) providing an integrated resource for the research community. VectorBase contains genome information for organisms such as Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever. Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes.",
"homepage": "https://vectorbase.org/vectorbase/app",
"name": "VectorBase",
"prefix": "FAIRsharing.3etvdn",
"publications": [
{
"doi": "10.1093/nar/gkn857",
"pubmed_id": 19028744,
"title": "VectorBase: a data resource for invertebrate vector genomics."
},
{
"doi": "10.1093/nar/gku1117",
"pubmed_id": 25510499,
"title": "VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases."
}
],
"subjects": [
"Functional Genomics",
"Population Dynamics",
"Genomics",
"Comparative Genomics",
"Population Genetics"
],
"twitter": "VectorBase"
},
"integbio": {
"description": "VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes (as well as a number of non-vector genomes for comparative analysis) providing an integrated resource for the research community. VectorBase contains genome information for organisms such as Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever. Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes.",
"fairsharing": "FAIRsharing.3etvdn",
"homepage": "https://vectorbase.org/vectorbase/app",
"information_keywords": [
"Sequence",
"Expression",
"Localization",
"Environment"
],
"maintainer": "United States Department of Health and Human Services||VectorBase",
"name": "VectorBase",
"prefix": "nbdc01909",
"pubmeds": [
"19028744"
],
"status": "Active",
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"Genome/Gene",
"Protein",
"Organism"
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},
"mappings": {
"biocontext": "VECTORBASE",
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"ncbi": "VectorBase",
"prefixcommons": "vectorbase",
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"miriam": {
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"namespaceEmbeddedInLui": false,
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"name": "Vectorbase at EMBL-EBI",
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"ncbi": {
"example": "ENSANGG00000007825",
"homepage": "http://www.vectorbase.org/index.php",
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"prefix": "VectorBase"
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"example": "ISCW007415",
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"gene",
"genome",
"protein"
],
"name": "Invertebrate Vectors of Human Pathogens",
"pattern": "^\\D{4}\\d{6}(\\-\\D{2})?$",
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"uri_format": "http://www.vectorbase.org/[?species_name]/Gene/Summary?db=core;g=$1"
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"providers": [
{
"code": "vectorbase.alt1",
"description": "An alternate provider based on the search functionality",
"homepage": "https://www.vectorbase.org",
"name": "Vectorbase Alt. 1",
"uri_format": "https://www.vectorbase.org/search/site/$1?&site=\"Genome\""
},
{
"code": "vectorbase.alt2",
"description": "An alternate provider based on the app structure",
"homepage": "https://www.vectorbase.org",
"name": "Vectorbase Alt. 2",
"uri_format": "https://vectorbase.org/vectorbase/app/record/gene/$1"
}
],
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{
"doi": "10.1093/nar/gku1117",
"pmc": "PMC4383932",
"pubmed": "25510499",
"title": "VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases",
"year": 2014
},
{
"doi": "10.1093/nar/gkn857",
"pmc": "PMC2686483",
"pubmed": "19028744",
"title": "VectorBase: a data resource for invertebrate vector genomics",
"year": 2008
}
],
"re3data": {
"description": "VectorBase provides data on arthropod vectors of human pathogens. Sequence data, gene expression data, images, population data, and insecticide resistance data for arthropod vectors are available for download. VectorBase also offers genome browser, gene expression and microarray repository, and BLAST searches for all VectorBase genomes. VectorBase Genomes include Aedes aegypti, Anopheles gambiae, Culex quinquefasciatus, Ixodes scapularis, Pediculus humanus, Rhodnius prolixus. VectorBase is one the Bioinformatics Resource Centers (BRC) projects which is funded by National Institute of Allergy and Infectious Diseases (NAID).",
"homepage": "https://vectorbase.org/vectorbase/app",
"name": "VectorBase",
"prefix": "r3d100010880",
"synonyms": [
"Bioinformatics Resource for Invertebrate Vectors of Human Pathogens"
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"nif": "0000-03624",
"omics": "03146"
}
}
},
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"email": "cthoyt@gmail.com",
"github": "cthoyt",
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"orcid": "0000-0003-4423-4370"
},
"description": "A repository for high-quality gene models produced by the manual annotation of vertebrate genomes.",
"example": "OTTHUMG00000169812",
"fairsharing": {
"abbreviation": "VEGA",
"contact": {
"email": "jla1@sanger.ac.uk",
"name": "Jennifer L Harrow",
"orcid": "0000-0003-0338-3070"
},
"description": "The Vertebrate Genome Annotation (VEGA) database is a central repository for high quality manual annotation of vertebrate finished genome sequence.",
"homepage": "https://vega.archive.ensembl.org/index.html",
"name": "The Vertebrate Genome Annotation Database",
"prefix": "FAIRsharing.mr293q",
"publications": [
{
"doi": "10.1093/nar/gkm987",
"pubmed_id": 18003653,
"title": "The vertebrate genome annotation (Vega) database."
},
{
"doi": "10.1093/nar/gkt1241",
"pubmed_id": 24316575,
"title": "The Vertebrate Genome Annotation browser 10 years on."
}
],
"subjects": [
"Life Science"
]
},
"homepage": "https://vega.archive.ensembl.org/index.html",
"mappings": {
"fairsharing": "FAIRsharing.mr293q",
"prefixcommons": "vega",
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"name": "Vertebrate Genome Annotation Database",
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"description": "The Vertebrate Genome Annotation (VEGA) database is a central repository for high quality manual annotation of vertebrate finished genome sequence.",
"example": "OTTHUMG00000017411",
"homepage": "http://vega.sanger.ac.uk/",
"keywords": [
"genome"
],
"name": "The Vertebrate Genome Annotation Database",
"pattern": "^[A-Z]+\\d+$",
"prefix": "vega",
"uri_format": "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkt1241",
"pmc": "PMC3964964",
"pubmed": "24316575",
"title": "The Vertebrate Genome Annotation browser 10 years on",
"year": 2013
},
{
"doi": "10.1093/nar/gkm987",
"pmc": "PMC2238886",
"pubmed": "18003653",
"title": "The vertebrate genome annotation (Vega) database",
"year": 2007
}
],
"re3data": {
"description": "A repository for high-quality gene models produced by the manual annotation of vertebrate genomes. The final update of Vega, version 68, was released in February 2017 and is now archived at vega.archive.ensembl.org. We plan to maintain this resource until Feb 2020.",
"homepage": "http://vega.archive.ensembl.org/index.html",
"name": "Vega",
"prefix": "r3d100012575",
"synonyms": [
"Vertebrate Genome Annotation database"
],
"xrefs": {
"fairsharing": "FAIRsharing.mr293q",
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}
},
"synonyms": [
"VEGA"
]
},
"vegbank": {
"mappings": {
"miriam": "vegbank",
"re3data": "r3d100010153"
},
"miriam": {
"deprecated": false,
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"homepage": "http://vegbank.org/",
"id": "00000723",
"name": "VegBank",
"namespaceEmbeddedInLui": false,
"pattern": "^VB\\.[A-Za-z][A-Za-z]\\..*$",
"prefix": "vegbank",
"sampleId": "VB.Ob.3736.GRSM125",
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},
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"description": "VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain the actual plot records, vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. VegBank receives its data from the VegBank community of users.",
"homepage": "http://vegbank.org/vegbank/index.jsp",
"name": "VegBank",
"prefix": "r3d100010153",
"synonyms": [
"The Vegetation Plot Archive Project"
]
}
},
"venom": {
"appears_in": [
"vbo"
],
"contact": {
"email": "DBrodbelt@RVC.AC.UK",
"name": "David Brodbelt",
"orcid": "0000-0001-5628-4194"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Veterinary Nomenclature (VeNom) is a standard set of clinical veterinary terms for use in referral veterinary hospital electronic patient records and first opinion veterinary practice management systems.",
"example": "12969",
"homepage": "https://venomcoding.org/",
"name": "Veterinary Nomenclature",
"pattern": "^\\d+$",
"preferred_prefix": "VeNom",
"proprietary": true,
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},
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"email": "r.court@ed.ac.uk",
"name": "Robert Court",
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},
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"license": "CC BY-SA 4.0",
"name": "Virtual Fly Brain",
"prefix": "FAIRsharing.nzaz6z",
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{
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{
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{
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}
],
"subjects": [
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"Life Science"
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},
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"name": "Virtual Fly Brain",
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"pattern": "^[0-9a-zA-Z]{8}$",
"prefix": "vfb",
"sampleId": "00000001",
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"description": "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster.",
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"homepage": "https://VirtualFlyBrain.org",
"name": "Virtual Fly Brain",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9a-zA-Z]{8}$",
"prefix": "vfb",
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},
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{
"doi": "10.1186/1471-2105-13-122",
"pmc": "PMC3412715",
"pubmed": "22676296",
"title": "Web tools for large-scale 3D biological images and atlases",
"year": 2012
},
{
"doi": "10.1093/bioinformatics/bts113",
"pubmed": "22402613",
"title": "A strategy for building neuroanatomy ontologies",
"year": 2012
},
{
"doi": "10.1093/bioinformatics/btr677",
"pubmed": "22180411",
"title": "The Virtual Fly Brain browser and query interface",
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}
],
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"description": "Virtual Fly Brain (VFB) - an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster CNS.",
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"name": "Virtual Fly Brain",
"prefix": "r3d100011373",
"synonyms": [
"VFB",
"VFB Drosophila melanogaster fly brain atlas"
],
"xrefs": {
"fairsharing": "FAIRsharing.nzaz6z",
"nlx": "143644",
"scr": "004229"
}
}
},
"vfdb.gene": {
"biocontext": {
"prefix": "VFDB.GENE"
},
"mappings": {
"biocontext": "VFDB.GENE",
"miriam": "vfdb.gene",
"n2t": "vfdb.gene"
},
"miriam": {
"deprecated": false,
"description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes.",
"homepage": "http://www.mgc.ac.cn/VFs/",
"id": "00000472",
"name": "VFDB Gene",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "vfdb.gene",
"sampleId": "VFG2154",
"uri_format": "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1"
},
"n2t": {
"description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes.",
"example": "VFG2154",
"homepage": "http://www.mgc.ac.cn/VFs/",
"name": "VFDB Gene at Institute of Pathogen Biology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "vfdb.gene",
"uri_format": "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1"
}
},
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"biocontext": {
"prefix": "VFDB.GENUS"
},
"mappings": {
"biocontext": "VFDB.GENUS",
"miriam": "vfdb.genus",
"n2t": "vfdb.genus"
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"miriam": {
"deprecated": false,
"description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus.",
"homepage": "http://www.mgc.ac.cn/VFs/",
"id": "00000471",
"name": "VFDB Genus",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "vfdb.genus",
"sampleId": "Chlamydia",
"uri_format": "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1"
},
"n2t": {
"description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus.",
"example": "Chlamydia",
"homepage": "http://www.mgc.ac.cn/VFs/",
"name": "VFDB Genus at Institute of Pathogen Biology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "vfdb.genus",
"uri_format": "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1"
}
},
"vgnc": {
"cellosaurus": {
"category": "Organism-specific databases",
"homepage": "https://vertebrate.genenames.org/",
"name": "Vertebrate Gene Nomenclature Committee Database",
"prefix": "VGNC",
"uri_format": "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/VGNC:$1"
},
"contact": {
"email": "stweedie@ebi.ac.uk",
"name": "Susan Tweedie",
"orcid": "0000-0003-1818-8243"
},
"example": "3792",
"fairsharing": {
"abbreviation": "VGNC",
"description": "The VGNC approves both a short-form abbreviation known as a gene symbol, and also a longer and more descriptive name. Each symbol is unique and the committee ensures that each gene is only given one approved gene symbol. This allows for clear and unambiguous reference to genes in scientific communications, and facilitates electronic data retrieval from databases and publications.",
"homepage": "https://vertebrate.genenames.org/download/statistics-and-files/",
"name": "VGNC Gene Symbols, Gene Names and IDs",
"prefix": "FAIRsharing.5NhJFK",
"subjects": [
"Life Science"
]
},
"integbio": {
"alt_name": "Vertebrate Gene Nomenclature Committee",
"description": "The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in selected vertebrate species that lack a nomenclature authority; currently these are chimpanzee, macaque, dog, cat, cattle, pig and horse. The VGNC also coordinates with the existing vertebrate nomenclature committees, MGNC (mouse), RGNC (rat), CGNC (chicken), XNC (Xenopus frog) and ZNC (zebrafish), to ensure genes are named in line with their human homologs.",
"fairsharing": "FAIRsharing.eBP3tb",
"homepage": "https://vertebrate.genenames.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Vertebrate Gene Nomenclature Committee",
"name": "VGNC",
"prefix": "nbdc02624",
"pubmeds": [
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],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"mappings": {
"cellosaurus": "VGNC",
"fairsharing": "FAIRsharing.5NhJFK",
"integbio": "nbdc02624",
"miriam": "vgnc",
"ncbi": "VGNC",
"togoid": "Vgnc",
"uniprot": "DB-0226"
},
"miriam": {
"deprecated": false,
"description": "The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee.",
"homepage": "https://vertebrate.genenames.org",
"id": "00000765",
"name": "VGNC",
"namespaceEmbeddedInLui": false,
"pattern": "^((VGNC|vgnc):)?\\d{1,9}$",
"prefix": "vgnc",
"sampleId": "VGNC:3792",
"uri_format": "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1"
},
"ncbi": {
"example": "VGNC:4927",
"homepage": "http://vertebrate.genenames.org/data/gene-symbol-report/#!/",
"name": "Vertebrate Gene Nomenclature Committee",
"prefix": "VGNC"
},
"pattern": "^\\d{1,9}$",
"publications": [
{
"doi": "10.1093/nar/gkaa980",
"pmc": "PMC7779007",
"pubmed": "33152070",
"title": "Genenames.org: the HGNC and VGNC resources in 2021",
"year": 2021
}
],
"togoid": {
"catalog": "nbdc02624",
"examples": [
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"49608",
"85188",
"76040",
"72808",
"73601",
"9436",
"78821",
"74596",
"5304"
],
"keywords": [
"Gene"
],
"name": "VGNC",
"pattern": "^((VGNC|vgnc):)?(?\\d{1,9})$",
"prefix": "Vgnc",
"uri_format": "http://identifiers.org/vgnc/$1"
},
"uniprot": {
"abbreviation": "VGNC",
"category": "Organism-specific databases",
"homepage": "https://vertebrate.genenames.org/",
"name": "Vertebrate Gene Nomenclature Database",
"prefix": "DB-0226",
"publications": [
{
"doi": "10.1093/nar/gkaa980",
"pubmed": "33152070"
}
],
"uri_format": "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1"
}
},
"vhog": {
"aberowl": {
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"download_obo": "http://aber-owl.net/media/ontologies/VHOG/12/vhog.obo",
"homepage": "http://bgee.unil.ch",
"name": "Vertebrate Homologous Organ Group Ontology",
"prefix": "VHOG",
"version": "unknown"
},
"biocontext": {
"prefix": "VHOG"
},
"bioportal": {
"contact": {
"email": "bgee@isb-sib.ch",
"name": "Bgee team"
},
"description": "vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 \"historical homology\". Each mapping has been manually reviewed, and we provide confidence codes and references when available.",
"homepage": "http://bgee.unil.ch",
"name": "Vertebrate Homologous Organ Group Ontology",
"prefix": "VHOG",
"publication": "http://www.unil.ch/dee/page31219_en.html",
"version": "unknown"
},
"download_obo": "ftp://ftp.bgee.org/general/ontologies/vHOG.obo",
"example": "0000411",
"mappings": {
"aberowl": "VHOG",
"biocontext": "VHOG",
"bioportal": "VHOG",
"obofoundry": "vhog",
"prefixcommons": "vhog"
},
"name": "Vertebrate Homologous Organ Group Ontology",
"obofoundry": {
"deprecated": true,
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/vhog.owl",
"logo": "http://bgee.org/img/logo/bgee13_logo.png",
"name": "Vertebrate Homologous Ontology Group Ontology",
"prefix": "vhog"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1574",
"description": "vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 \"historical homology\". Each mapping has been manually reviewed, and we provide confidence codes and references when available.",
"example": "VHOG_0000555",
"homepage": "http://bgee.unil.ch",
"keywords": [
"obo",
"anatomy",
"development"
],
"name": "vertebrate Homologous Organ Groups",
"pattern": "^VHOG_\\d{7}$",
"prefix": "vhog"
},
"synonyms": [
"VHOG_RETIRED"
]
},
"viaf": {
"bartoc": {
"abbreviation": "VIAF",
"description": "The Virtual International Authority File (VIAF) is an international service designed to provide convenient access to the world's major name authority files. Its creators envision the VIAF as a building block for the Semantic Web to enable switching of the displayed form of names for persons to the preferred language and script of the Web user. VIAF began as a joint project with the Library of Congress (LC), the Deutsche Nationalbibliothek (DNB), the Bibliothèque nationale de France (BNF) and OCLC. It has, over the past decade, become a cooperative effort involving an expanding number of other national libraries and other agencies. (...)\n\nVIAF helps to make library authority files less expensive to maintain and more generally useful to the library domain and beyond. To achieve this, VIAF matches and links the authority files of national libraries and groups all authority records for a given entity into a merged 'super' authority record that brings together the different names for that entity. By linking disparate names for the same person or organization, VIAF provides a convenient means for a wider community of libraries and other agencies to repurpose bibliographic data produced by libraries serving different language communities.",
"homepage": "http://viaf.org/",
"license": "http://www.opendatacommons.org/licenses/by/1.0",
"name": "Virtual International Authority File",
"pattern": "^[1-9]\\d(\\d{0,7}|\\d{17,20})]$",
"prefix": "2053",
"wikidata_database": "Q54919"
},
"fairsharing": {
"abbreviation": "VIAF",
"description": "The VIAFΒ (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web.",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://viaf.org/",
"name": "Virtual International Authority File",
"prefix": "FAIRsharing.a15ac6",
"subjects": [
"Knowledge and Information Systems"
]
},
"mappings": {
"bartoc": "2053",
"fairsharing": "FAIRsharing.a15ac6",
"miriam": "viaf",
"n2t": "viaf"
},
"miriam": {
"deprecated": false,
"description": "The VIAFΒ (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web.",
"homepage": "http://viaf.org",
"id": "00000685",
"name": "Virtual International Authority File",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "viaf",
"sampleId": "75121530",
"uri_format": "http://viaf.org/viaf/$1"
},
"n2t": {
"description": "The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web.",
"example": "75121530",
"homepage": "http://viaf.org",
"name": "Virtual International Authority File",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "viaf",
"uri_format": "http://viaf.org/viaf/$1"
},
"providers": [
{
"code": "viaf.https",
"description": "A duplicate endpoint over HTTPS",
"first_party": true,
"homepage": "http://viaf.org",
"name": "VIAF (https)",
"uri_format": "https://viaf.org/$1"
},
{
"code": "scholia",
"description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.",
"homepage": "https://scholia.toolforge.org/",
"name": "Scholia",
"uri_format": "https://scholia.toolforge.org/viaf/$1"
}
]
},
"vido": {
"aberowl": {
"description": "The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc.",
"download_owl": "http://aber-owl.net/media/ontologies/VIDO/3/vido.owl",
"homepage": "https://github.com/infectious-disease-ontology-extensions/ido-virus",
"name": "Virus Infectious Disease Ontology",
"prefix": "VIDO",
"version": "10-27-2022"
},
"bioportal": {
"contact": {
"email": "johnbeve@buffalo.edu",
"name": "John Beverley"
},
"description": "The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc.",
"homepage": "https://github.com/infectious-disease-ontology-extensions/ido-virus",
"name": "Virus Infectious Disease Ontology",
"prefix": "VIDO",
"publication": "https://osf.io/5bx8c",
"version": "10-27-2022"
},
"contact": {
"email": "johnbeverley2021@u.northwestern.edu",
"github": "johnbeve",
"name": "John Beverly",
"orcid": "0000-0002-1118-1738"
},
"download_owl": "https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-virus/master/ontology/vido.owl",
"example": "0001114",
"homepage": "https://github.com/infectious-disease-ontology-extensions/ido-virus",
"mappings": {
"aberowl": "VIDO",
"bioportal": "VIDO",
"ols": "vido",
"ontobee": "VIDO"
},
"ols": {
"contact": "johnbeverley2021@u.northwestern.edu",
"description": "The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc.",
"download": "https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-virus/master/ontology/vido.owl",
"homepage": "https://github.com/infectious-disease-ontology-extensions/ido-virus",
"name": "The Virus Infectious Disease Ontology",
"prefix": "vido",
"version": "2020-08-25",
"version.iri": "http://purl.obolibrary.org/obo/2020-25-08/vido.owl"
},
"ontobee": {
"library": "Not Specified/No",
"name": "Virus Infectious Disease Ontology",
"prefix": "VIDO"
},
"pattern": "^\\d{7}$",
"providers": [
{
"code": "obo.1",
"description": "This incorrect encoding was found inside IDO-COVID-19",
"homepage": "http://purl.obolibrary.org",
"name": "Nonstandard OBO PURL",
"uri_format": "http://purl.obolibrary.org/VIDO_$1"
}
],
"repository": "https://github.com/infectious-disease-ontology-extensions/ido-virus",
"uri_format": "http://purl.obolibrary.org/obo/VIDO_$1"
},
"violinnet": {
"appears_in": [
"oae"
],
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"description": "Defunct vaccine information source from the He Lab",
"example": "4140",
"mappings": {
"wikidata": "P1925"
},
"name": "ViolinNet",
"pattern": "^\\d+$",
"synonyms": [
"violinID",
"violinId"
],
"uri_format": "http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=$1",
"wikidata": {
"description": "identifier in the VIOLIN database for vaccines and related subjects",
"example": [
"597",
"740"
],
"name": "VIOLIN ID",
"prefix": "P1925",
"uri_format": "http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=$1"
}
},
"viperdb": {
"integbio": {
"description": "VIPERdb is a database of viral capsid structures. The database contains structural x-ray crystallographic and cryo-EM data on the structures of 350 icosahedral viruses. Structures are interactive and available for download, and can be searched by PDB ID or virus name.",
"homepage": "http://viperdb.scripps.edu/",
"information_keywords": [
"Sequence",
"Image/Movie",
"3D structure"
],
"maintainer": "The Scripps Research Institute",
"name": "VIPERdb",
"prefix": "nbdc00835",
"pubmeds": [
"18981051"
],
"status": "Inactive",
"target_keywords": [
"RNA",
"Protein"
]
},
"mappings": {
"integbio": "nbdc00835",
"prefixcommons": "viperdb",
"re3data": "r3d100012362"
},
"prefixcommons": {
"description": "VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration.",
"example": "2c6s",
"homepage": "http://viperdb.scripps.edu/",
"keywords": [
"structure",
"small molecule"
],
"name": "VIPERdb",
"pattern": "^[A-Z,0-9]+$",
"prefix": "viperdb",
"uri_format": "http://viperdb.scripps.edu/info_page.php?VDB=$1"
},
"provides": "pdb",
"re3data": {
"description": "VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools.",
"homepage": "https://viperdb.org/",
"name": "VIPERdb",
"prefix": "r3d100012362",
"synonyms": [
"Virus Particle Explorer database"
],
"xrefs": {
"fairsharing": "FAIRsharing.45e0f5",
"nif": "0000-03630",
"scr": "007970"
}
},
"uri_format": "https://viperdb.org/Info_Page.php?VDB=$1"
},
"vipr": {
"biocontext": {
"prefix": "VIPR"
},
"fairsharing": {
"abbreviation": "ViPR",
"contact": {
"email": "rscheuermann@jcvi.org",
"name": "Richard Scheuermann",
"orcid": "0000-0003-1355-892X"
},
"description": "The Virus Pathogen Database and Analysis Resource (ViPR) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR captures various types of information, including sequence records, gene and protein annotations, 3D protein structures, immune epitope locations, clinical and surveillance metadata and novel data derived from comparative genomics analysis. The database is available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens and other viruses.",
"homepage": "http://www.viprbrc.org",
"name": "Virus Pathogen Database and Analysis Resource",
"prefix": "FAIRsharing.2qx8n8",
"publications": [
{
"doi": "10.1093/nar/gkr859",
"pubmed_id": 22006842,
"title": "ViPR: an open bioinformatics database and analysis resource for virology research."
},
{
"doi": "10.3390/v4113209",
"pubmed_id": null,
"title": "Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community"
},
{
"doi": "10.1016/b978-0-12-801238-3.95728-3",
"pubmed_id": null,
"title": "Virus Databases β"
},
{
"doi": "10.1016/b978-0-12-809633-8.20995-3",
"pubmed_id": null,
"title": "Database and Analytical Resources for Viral Research Community"
}
],
"repository": "https://github.com/VirusBRC",
"subjects": [
"Genomics",
"Proteomics",
"Virology",
"Life Science",
"Biomedical Science",
"Epidemiology"
]
},
"keywords": [
"immunology"
],
"mappings": {
"biocontext": "VIPR",
"fairsharing": "FAIRsharing.2qx8n8",
"miriam": "vipr",
"n2t": "vipr",
"ncbi": "ViPR",
"re3data": "r3d100011931"
},
"miriam": {
"deprecated": false,
"description": "The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information.",
"homepage": "http://www.viprbrc.org/brc/home.do?decorator=vipr",
"id": "00000407",
"name": "ViPR Strain",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z 0-9]+$",
"prefix": "vipr",
"sampleId": "BeAn 70563",
"uri_format": "http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena"
},
"n2t": {
"description": "The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information.",
"example": "BeAn 70563",
"homepage": "http://www.viprbrc.org/brc/home.do?decorator=vipr",
"name": "ViPR Strain at J. Craig Venter Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z 0-9]+$",
"prefix": "vipr",
"uri_format": "http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena"
},
"ncbi": {
"example": "HRV-A34_p1058_sR263_2008",
"homepage": "http://www.viprbrc.org/brc/home.do?decorator=vipr",
"name": "Virus Pathogen Resource",
"prefix": "ViPR"
},
"publications": [
{
"doi": "10.3390/v4113209",
"pmc": "PMC3509690",
"pubmed": "23202522",
"title": "Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community",
"year": 2012
},
{
"doi": "10.1093/nar/gkr859",
"pmc": "PMC3245011",
"pubmed": "22006842",
"title": "ViPR: an open bioinformatics database and analysis resource for virology research",
"year": 2011
},
{
"doi": "10.1016/b978-0-12-809633-8.20995-3",
"pmc": "PMC7173540",
"title": "Database and Analytical Resources for Viral Research Community",
"year": 2021
},
{
"doi": "10.1016/b978-0-12-801238-3.95728-3",
"pmc": "PMC7157461",
"title": "Virus Databases β",
"year": 2017
}
],
"re3data": {
"description": "<<>>!!!>>>\nMigration of the data, tools, and services from IRD and ViPR to BV-BRC is complete! We are now in the sunsetting phase of the transition. Starting on October 31, 2022, launching the IRD or ViPR home pages will redirect you to the new BV-BRC home page. The current plan is to completely shut down IRD and ViPR by the end of this calendar year. Although it will still be possible to use those sites until shutdown, we strongly encourage you to start using BV-BRC now.",
"homepage": "https://www.viprbrc.org/brc/home.spg?decorator=vipr",
"name": "Virus Pathogen Resource",
"prefix": "r3d100011931",
"synonyms": [
"ViPR"
],
"xrefs": {
"fairsharing": "FAIRsharing.2qx8n8",
"miriam": "00000407",
"nif": "0000-25312",
"scr": "012983"
}
}
},
"viralzone": {
"biocontext": {
"prefix": "VIRALZONE"
},
"fairsharing": {
"abbreviation": "ViralZone",
"contact": {
"email": "Philippe.Lemercier@sib.swiss",
"name": "Philippe Le Mercier",
"orcid": "0000-0001-8528-090X"
},
"description": "ViralZone is a web resource for viral genes and families, providing detailed molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot viral protein entries.",
"homepage": "http://viralzone.expasy.org/",
"license": "CC BY-NC 4.0",
"name": "ViralZone",
"prefix": "FAIRsharing.tppk10",
"publications": [
{
"doi": "10.1093/nar/gks1220",
"pubmed_id": 23193299,
"title": "ViralZone: recent updates to the virus knowledge resource."
},
{
"doi": "10.1093/nar/gkq901",
"pubmed_id": 20947564,
"title": "ViralZone: a knowledge resource to understand virus diversity."
}
],
"subjects": [
"Molecular biology",
"Virology",
"Life Science",
"Epidemiology"
]
},
"go": {
"homepage": "http://viralzone.expasy.org/",
"name": "ViralZone",
"prefix": "VZ",
"uri_format": "http://viralzone.expasy.org/all_by_protein/$1.html"
},
"integbio": {
"description": "ViralZone is a web resource for viral genes and families, providing detailed molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot viral protein entries.",
"fairsharing": "FAIRsharing.tppk10",
"homepage": "http://viralzone.expasy.org/",
"information_keywords": [
"Sequence",
"Expression",
"Taxonomy"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "ViralZone",
"prefix": "nbdc02226",
"pubmeds": [
"20947564",
"23193299"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Health/Disease"
]
},
"mappings": {
"biocontext": "VIRALZONE",
"fairsharing": "FAIRsharing.tppk10",
"go": "VZ",
"integbio": "nbdc02226",
"miriam": "viralzone",
"n2t": "viralzone",
"prefixcommons": "vz",
"re3data": "r3d100013314"
},
"miriam": {
"deprecated": false,
"description": "ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.",
"homepage": "http://www.expasy.org/viralzone/",
"id": "00000449",
"name": "ViralZone",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "viralzone",
"sampleId": "992",
"uri_format": "http://viralzone.expasy.org/all_by_protein/$1.html"
},
"n2t": {
"description": "ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.",
"example": "992",
"homepage": "http://www.expasy.org/viralzone/",
"name": "ViralZone at SIB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "viralzone",
"uri_format": "http://viralzone.expasy.org/all_by_protein/$1.html"
},
"prefixcommons": {
"description": "ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures",
"example": "886",
"homepage": "http://viralzone.expasy.org/",
"keywords": [
"virus"
],
"name": "ViralZone",
"pattern": "^\\d+$",
"prefix": "vz",
"uri_format": "http://viralzone.expasy.org/all_by_protein/$1.html"
},
"providers": [
{
"code": "viralzone.alt1",
"description": "Alternate view",
"homepage": "http://viralzone.expasy.org",
"name": "Viralzone Alt 1.",
"uri_format": "http://viralzone.expasy.org/all_by_protein/$1"
}
],
"publications": [
{
"doi": "10.1093/nar/gks1220",
"pmc": "PMC3531065",
"pubmed": "23193299",
"title": "ViralZone: recent updates to the virus knowledge resource",
"year": 2012
},
{
"doi": "10.1093/nar/gkq901",
"pmc": "PMC3013774",
"pubmed": "20947564",
"title": "ViralZone: a knowledge resource to understand virus diversity",
"year": 2010
}
],
"re3data": {
"description": "ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries.",
"homepage": "https://viralzone.expasy.org/",
"name": "ViralZone",
"prefix": "r3d100013314",
"xrefs": {
"fairsharing": "FAIRsharing.tppk10",
"nlx": "144372",
"scr": "006563"
}
},
"synonyms": [
"vz"
],
"uri_format": "https://viralzone.expasy.org/$1",
"wikidata": {
"database": "Q15674507"
}
},
"virgen": {
"mappings": {
"prefixcommons": "virgen"
},
"prefixcommons": {
"description": "VirGen a comprehensive viral genome resource, which organizes the βsequence spaceβ of viral genomes in a structured fashion. It has been developed with an objective to serve as an annotated and curated database for complete viral genome sequences.",
"example": "AY321118",
"homepage": "http://bioinfo.ernet.in/virgen/virgen.html",
"keywords": [
"genome"
],
"name": "VirGen",
"pattern": "^A[A-Z]\\d+$",
"prefix": "virgen"
}
},
"virmirdb": {
"mappings": {
"prefixcommons": "virmirdb"
},
"prefixcommons": {
"description": "A database containing predicted viral miRNA candidate hairpins.",
"example": "11002",
"homepage": "http://alk.ibms.sinica.edu.tw",
"keywords": [
"RNA",
"structure"
],
"name": "Vir-Mir db",
"pattern": "^\\d+$",
"prefix": "virmirdb",
"uri_format": "http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id=$1"
},
"provides": "ncbitaxon",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"viroligo": {
"mappings": {
"prefixcommons": "viroligo"
},
"prefixcommons": {
"description": "The VirOligo database (1) is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place.",
"example": "BM0456",
"homepage": "http://viroligo.okstate.edu",
"keywords": [
"small molecule"
],
"name": "VirOligo",
"pattern": "^[A-Z]+\\d+$",
"prefix": "viroligo",
"uri_format": "http://viroligo.okstate.edu/main.php?vid=$1"
}
},
"virsirna": {
"biocontext": {
"prefix": "VIRSIRNA"
},
"mappings": {
"biocontext": "VIRSIRNA",
"miriam": "virsirna",
"n2t": "virsirna"
},
"miriam": {
"deprecated": false,
"description": "The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region.",
"homepage": "http://crdd.osdd.net/servers/virsirnadb",
"id": "00000249",
"name": "VIRsiRNA",
"namespaceEmbeddedInLui": false,
"pattern": "^virsi\\d+$",
"prefix": "virsirna",
"sampleId": "virsi1909",
"uri_format": "http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1"
},
"n2t": {
"description": "The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region.",
"example": "virsi1909",
"homepage": "http://crdd.osdd.net/servers/virsirnadb",
"name": "VIRsiRNA at Institute of Microbial Technology",
"namespaceEmbeddedInLui": false,
"pattern": "^virsi\\d+$",
"prefix": "virsirna",
"uri_format": "http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1"
}
},
"virushostdb": {
"contact": {
"email": "ogata@kuicr.kyoto-u.ac.jp",
"name": "Hiroyuki Ogata",
"orcid": "0000-0001-6594-377X"
},
"integbio": {
"description": "Virus-Host DB is a database about the relationships between viruses and their hosts. It provides information of the relationships represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts. This database covers viruses with complete genomes stored in 1) NCBI/RefSeq and 2) GenBank whose accession numbers are listed in EBI Genomes. The host information is collected from RefSeq, GenBank (in free text format), UniProt, ViralZone, and manually curated with additional information obtained from literatures.",
"homepage": "http://www.genome.jp/virushostdb",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "Virus-Host DB",
"prefix": "nbdc02395",
"pubmeds": [
"26938550"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
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"integbio": "nbdc02395",
"prefixcommons": "virushostdb"
},
"prefixcommons": {
"description": "Virus-Host DB organizes data about the relationships between viruses and their hosts, represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts. Virus-Host DB covers viruses with complete genomes stored in 1) NCBI/RefSeq and 2) GenBank whose accession numbers are listed in EBI Genomes. The host information is collected from RefSeq, GenBank (in free text format), UniProt, ViralZone, and manually curated with additional information obtained by literature surveys.",
"example": "438782",
"homepage": "https://www.genome.jp/virushostdb/",
"keywords": [
"virus"
],
"license": "CC BY-NC-SA 4.0",
"name": "Virus-HostDB",
"pattern": "^\\d+$",
"prefix": "virushostdb",
"pubmed_ids": [
"26938550"
],
"synonyms": [
"virus-hostdb"
],
"uri_format": "https://www.genome.jp/virushostdb/$1"
},
"provides": "ncbitaxon",
"publications": [
{
"doi": "10.3390/v8030066",
"pmc": "PMC4810256",
"pubmed": "26938550",
"title": "Linking Virus Genomes with Host Taxonomy",
"year": 2016
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"vita": {
"mappings": {
"prefixcommons": "vita"
},
"name": "Virus' miRNA target",
"prefixcommons": {
"description": "ViTa is a database which collects virus data from miRBase and ICTV, VirGne, VBRC.., etc, including known miRNAs on virus and supporting predicted host miRNA targets by miRanda and TargetScan. ViTa also rovide effective annotations, including human miRNA expression, virus infected tissues, annotation of virus and comparisons.",
"example": "AB016785",
"homepage": "http://vita.mbc.nctu.edu.tw/",
"keywords": [
"RNA",
"structure",
"gene expression"
],
"name": "ViTa: virus' miRNA target",
"pattern": "^[A-Z]+\\d+$",
"prefix": "vita",
"uri_format": "http://vita.mbc.nctu.edu.tw/search.php?acc=$1"
}
},
"vmc": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "VMC",
"uri_format": "https://github.com/ga4gh/vr-spec/$1"
},
"deprecated": true,
"mappings": {
"biolink": "VMC"
},
"name": "Variation Modelling Collaboration",
"references": [
"https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.67hbe76b6a4z",
"https://github.com/ga4gh/vr-spec"
]
},
"vmhgene": {
"mappings": {
"miriam": "vmhgene"
},
"miriam": {
"deprecated": false,
"description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.",
"homepage": "https://www.vmh.life/",
"id": "00000774",
"name": "VMH Gene",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+\\.[0-9]+",
"prefix": "vmhgene",
"sampleId": "8639.1",
"uri_format": "https://www.vmh.life/#gene/$1"
}
},
"vmhmetabolite": {
"biocontext": {
"prefix": "VMHMETABOLITE"
},
"mappings": {
"biocontext": "VMHMETABOLITE",
"miriam": "vmhmetabolite",
"n2t": "vmhmetabolite"
},
"miriam": {
"deprecated": false,
"description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.",
"homepage": "https://www.vmh.life/",
"id": "00000636",
"name": "VMH metabolite",
"namespaceEmbeddedInLui": false,
"pattern": "[a-zA-Z0-9_\\(\\_\\)\\[\\]]+",
"prefix": "vmhmetabolite",
"sampleId": "h2o",
"uri_format": "https://www.vmh.life/#metabolite/$1"
},
"n2t": {
"description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.",
"example": "h2o",
"homepage": "http://vmh.uni.lu",
"name": "VMH metabolite",
"namespaceEmbeddedInLui": false,
"pattern": "[a-zA-Z0-9_\\(\\_\\)\\[\\]]+",
"prefix": "vmhmetabolite",
"uri_format": "http://vmh.uni.lu/#metabolite/$1"
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},
"vmhreaction": {
"biocontext": {
"prefix": "VMHREACTION"
},
"mappings": {
"biocontext": "VMHREACTION",
"miriam": "vmhreaction",
"n2t": "vmhreaction"
},
"miriam": {
"deprecated": false,
"description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.",
"homepage": "https://www.vmh.life/",
"id": "00000640",
"name": "VMH reaction",
"namespaceEmbeddedInLui": false,
"pattern": "[a-zA-Z0-9_\\(\\_\\)\\[\\]]+",
"prefix": "vmhreaction",
"sampleId": "HEX1",
"uri_format": "https://www.vmh.life/#reaction/$1"
},
"n2t": {
"description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.",
"example": "HEX1",
"homepage": "https://vmh.uni.lu",
"name": "VMH reaction",
"namespaceEmbeddedInLui": false,
"pattern": "[a-zA-Z0-9_\\(\\_\\)\\[\\]]+",
"prefix": "vmhreaction",
"uri_format": "https://vmh.uni.lu/#reaction/$1"
}
},
"vo": {
"aberowl": {
"description": "VO is a biomedical ontology in the domain of vaccine and vaccination.",
"download_owl": "http://aber-owl.net/media/ontologies/VO/302/vo.owl",
"homepage": "https://violinet.org/vaccineontology",
"name": "Vaccine Ontology",
"prefix": "VO"
},
"biocontext": {
"prefix": "VO"
},
"bioportal": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqunh He"
},
"description": "A biomedical ontology in the vaccine domain",
"homepage": "https://github.com/vaccineontology/VO",
"name": "Vaccine Ontology",
"prefix": "VO",
"version": "2024-07-13"
},
"example": "0000093",
"fairsharing": {
"abbreviation": "VO",
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqunh He",
"orcid": "0000-0001-9189-9661"
},
"description": "The Vaccine Ontology (VO) was created as part of an international community-based effort to represent vaccine knowledge and to support automated reasoning. VO describes the detailed classification and definitions of vaccine components and vaccine administration processes. To ensure consistent representation of vaccine knowledge and to support automated reasoning, a community-based effort to develop the Vaccine Ontology (VO) has been initiated. This international collaborative VO development effort has been joined by many institutes and disciplines around the world. The Vaccine Ontology is also being used in a variety of applications by many user groups in academia and industry.",
"domains": [
"Biological process",
"Pathogen",
"Vaccine",
"Vaccination"
],
"homepage": "https://github.com/vaccineontology/VO",
"license": "CC-BY-3.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaUFDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--0d3898a5618b34c0bc948bb0d101e906f212f05f/vo_banner.png?disposition=inline",
"name": "The Vaccine Ontology",
"prefix": "FAIRsharing.zwtww5",
"publications": [
{
"doi": "10.1186/1745-7580-6-s1-s5",
"pubmed": "20875156",
"title": "Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN",
"year": 2010
},
{
"doi": "10.1186/2041-1480-3-17",
"pubmed": "23256535",
"title": "Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses",
"year": 2012
},
{
"doi": "10.2174/1381612826666201125112131",
"pubmed": "33238868",
"title": "Ontology-based Precision Vaccinology for Deep Mechanism Understanding and Precision Vaccine Development",
"year": 2020
}
],
"repository": "https://github.com/vaccineontology",
"subjects": [
"Pathobiochemistry",
"Biomedical Science"
]
},
"keywords": [
"immunology"
],
"mappings": {
"aberowl": "VO",
"biocontext": "VO",
"bioportal": "VO",
"fairsharing": "FAIRsharing.zwtww5",
"obofoundry": "vo",
"ols": "vo",
"ontobee": "VO",
"prefixcommons": "vo",
"wikidata": "P1928"
},
"obofoundry": {
"appears_in": [
"scdo"
],
"contact": "yongqunh@med.umich.edu",
"contact.github": "yongqunh",
"contact.label": "Yongqunh He",
"contact.orcid": "0000-0001-9189-9661",
"deprecated": false,
"description": "VO is a biomedical ontology in the domain of vaccine and vaccination.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/vo.owl",
"homepage": "https://violinet.org/vaccineontology",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Vaccine Ontology",
"preferredPrefix": "VO",
"prefix": "vo",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/23256535",
"title": "Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/21624163",
"title": "Mining of vaccine-associated IFN-Ξ³ gene interaction networks using the Vaccine Ontology"
}
],
"repository": "https://github.com/vaccineontology/VO"
},
"ols": {
"description": "The Vaccine Ontology (VO) is a community-based biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine types and annotations, integrate various vaccine data, and support computer-assisted reasoning. The VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities.",
"download_owl": "http://purl.obolibrary.org/obo/vo.owl",
"homepage": "https://violinet.org/vaccineontology",
"name": "Vaccine Ontology",
"prefix": "vo",
"version": "2024-07-13",
"version.iri": "http://purl.obolibrary.org/obo/vo/releases/2024-07-13/vo.owl"
},
"ontobee": {
"library": "Library",
"name": "Vaccine Ontology",
"prefix": "VO"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1172",
"description": "A biomedical ontology in the vaccine domain",
"example": "VO_0000811",
"homepage": "http://www.violinet.org/vaccineontology",
"keywords": [
"obo",
"ontology",
"small molecule",
"vaccine"
],
"name": "Vaccine ontology",
"pattern": "^VO_\\d{7}$",
"prefix": "vo"
},
"publications": [
{
"doi": "10.2174/1381612826666201125112131",
"pubmed": "33238868",
"title": "Ontology-based Precision Vaccinology for Deep Mechanism Understanding and Precision Vaccine Development",
"year": 2021
},
{
"doi": "10.1186/2041-1480-3-17",
"pmc": "PMC3639077",
"pubmed": "23256535",
"title": "Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses",
"year": 2012
},
{
"doi": "10.1186/2041-1480-2-s2-s8",
"pmc": "PMC3102897",
"pubmed": "21624163",
"title": "Mining of vaccine-associated IFN-Ξ³ gene interaction networks using the Vaccine Ontology",
"year": 2011
},
{
"doi": "10.1186/1745-7580-6-s1-s5",
"pmc": "PMC2946783",
"pubmed": "20875156",
"title": "Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN",
"year": 2010
}
],
"uri_format": "http://purl.obolibrary.org/obo/VO_$1",
"wikidata": {
"description": "identifier in the Vaccine Ontology database",
"example": [
"VO_0000455",
"VO_0000867",
"VO_0011559"
],
"name": "Vaccine Ontology ID",
"pattern": "^VO_[0-9]{7}$",
"prefix": "P1928"
}
},
"voc4cat": {
"comment": "The most current version of a concept can be accessed so * https://w3id.org/nfdi4cat/voc4cat_0000123 other/older versions from releases like so * https://w3id.org/nfdi4cat/voc4cat/v2023-08-17/voc4cat_0000123. This is pretty unique and isn't tracked by the Bioregistry currently.",
"contact": {
"email": "nikolaos.moustakas@catalysis.de",
"github": "nmoust",
"name": "Nikolaos Moustakas",
"orcid": "0000-0002-6242-2167"
},
"contributor": {
"email": "David.Linke@catalysis.de",
"github": "dalito",
"name": "David Linke",
"orcid": "0000-0002-5898-1820"
},
"description": "Voc4Cat is a [SKOS](https://www.w3.org/TR/2009/REC-skos-reference-20090818/) vocabulary for the catalysis disciplines. The vocabulary was created in the [NFDI4Cat](http://www.nfdi4cat.org/) initiative. The first collection of terms was published in June 2023 with a focus on photo catalysis. Our goal is to continuously extend the vocabulary to other areas of catalysis and related disciplines like chemical engineering or materials science.",
"example": "0000123",
"github_request_issue": 957,
"homepage": "https://nfdi4cat.github.io/voc4cat/",
"license": "CC0-1.0",
"name": "A vocabulary for the catalysis disciplines",
"pattern": "^\\d{7,}$",
"repository": "https://github.com/nfdi4cat/voc4cat",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uri_format": "https://w3id.org/nfdi4cat/voc4cat_$1"
},
"void": {
"biocontext": {
"prefix": "void",
"uri_format": "http://rdfs.org/ns/void#$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary.",
"example": "feature",
"homepage": "http://vocab.deri.ie/void",
"lov": {
"description": "The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets.",
"homepage": "http://www.w3.org/TR/void/",
"keywords": [
"Metadata"
],
"modified": "2011-03-06",
"name": "Vocabulary of Interlinked Datasets",
"prefix": "void",
"uri_prefix": "http://rdfs.org/ns/void#$1"
},
"mappings": {
"biocontext": "void",
"lov": "void",
"zazuko": "void"
},
"name": "Vocabulary of Interlinked Datasets",
"preferred_prefix": "void",
"uri_format": "http://rdfs.org/ns/void#$1",
"zazuko": {
"prefix": "void",
"uri_format": "http://rdfs.org/ns/void#$1"
}
},
"vsao": {
"aberowl": {
"description": "VSAO is an anatomy ontology covering the vertebrate skeletal system. VSAO integrates terms for skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system.",
"download_obo": "http://aber-owl.net/media/ontologies/VSAO/20/vsao.obo",
"homepage": "http://phenoscape.org/wiki/Main_Page",
"name": "Vertebrate Skeletal Anatomy Ontology",
"prefix": "VSAO",
"version": "2012-11-06"
},
"biocontext": {
"prefix": "VSAO"
},
"bioportal": {
"contact": {
"email": "wasila.dahdul@usd.edu",
"name": "Wasila Dahdul"
},
"description": "VSAO is an anatomy ontology covering the vertebrate skeletal system. VSAO integrates terms for skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system.",
"homepage": "http://phenoscape.org/wiki/Main_Page",
"name": "Vertebrate Skeletal Anatomy Ontology",
"prefix": "VSAO",
"publication": "http://dx.plos.org/10.1371/journal.pone.0051070",
"version": "2012-11-06"
},
"example": "0000183",
"mappings": {
"aberowl": "VSAO",
"biocontext": "VSAO",
"bioportal": "VSAO",
"obofoundry": "vsao",
"ols": "vsao",
"prefixcommons": "vao"
},
"name": "Vertebrate Skeletal Anatomy Ontology",
"obofoundry": {
"contact": "wasila.dahdul@usd.edu",
"contact.label": "Wasila Dahdul",
"contact.orcid": "0000-0003-3162-7490",
"deprecated": true,
"description": "Vertebrate skeletal anatomy ontology.",
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/vsao.owl",
"homepage": "https://www.nescent.org/phenoscape/Main_Page",
"name": "Vertebrate Skeletal Anatomy Ontology-",
"prefix": "vsao"
},
"ols": {
"description": "Vertebrate skeletal anatomy ontology.",
"homepage": "https://www.nescent.org/phenoscape/Main_Page",
"name": "Vertebrate Skeletal Anatomy Ontology-",
"prefix": "vsao",
"version": "2012-11-06",
"version.iri": "http://purl.obolibrary.org/obo/vsao/2012-11-06/vsao.owl"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1555",
"description": "Vertebrate anatomy ontology. Currently covers the skeletal system",
"example": "VSAO_0000183",
"homepage": "https://www.nescent.org/phenoscape/Main_Page",
"keywords": [
"obo",
"anatomy",
"vertebrate"
],
"name": "Vertebrate Anatomy Ontology",
"pattern": "^VSA_\\d{7}$",
"prefix": "vao",
"synonyms": [
"vsao"
]
},
"synonyms": [
"VSAO_RETIRED"
]
},
"vsdb": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source.",
"example": "1868",
"homepage": "https://sitem.herts.ac.uk/aeru/vsdb",
"name": "Veterinary Substances DataBase",
"pattern": "^\\d+$",
"uri_format": "https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm"
},
"vsmo": {
"contact": {
"email": "lars.eisen@colostate.edu",
"name": "Lars Eisen",
"orcid": "0000-0002-0094-3186"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems.",
"download_json": "https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.json",
"download_obo": "https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.obo",
"download_owl": "https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.owl",
"example": "0000000",
"homepage": "https://code.google.com/archive/p/vector-surveillance-and-management-ontology/",
"license": "New BSD License",
"name": "Ontology for vector surveillance and management",
"publications": [
{
"doi": "10.1603/me12169",
"pmc": "PMC3695545",
"pubmed": "23427646",
"title": "Ontology for vector surveillance and management",
"year": 2013
}
],
"uri_format": "http://purl.obolibrary.org/obo/VSMO_$1"
},
"vso": {
"aberowl": {
"description": "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.",
"download_owl": "http://aber-owl.net/media/ontologies/VSO/1/vso.owl",
"homepage": "http://code.google.com/p/vital-sign-ontology/",
"name": "Vital Sign Ontology",
"prefix": "VSO",
"version": "2012-04-25"
},
"bioportal": {
"contact": {
"email": "albertgoldfain@gmail.com",
"name": "Albert Goldfain"
},
"description": "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.",
"homepage": "http://code.google.com/p/vital-sign-ontology/",
"name": "Vital Sign Ontology",
"prefix": "VSO",
"publication": "http://ontology.buffalo.edu/smith/articles/Vital_Sign_Ontology.pdf",
"version": "2012-04-25"
},
"description": "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. ",
"example": "0000041",
"fairsharing": {
"abbreviation": "VSO",
"description": "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.",
"domains": [
"Experimental measurement",
"Blood"
],
"homepage": "https://code.google.com/p/vital-sign-ontology/",
"name": "Vital Sign Ontology",
"prefix": "FAIRsharing.jjb2p2",
"subjects": [
"Health Science",
"Biomedical Science"
]
},
"homepage": "https://bioportal.bioontology.org/ontologies/VSO",
"mappings": {
"aberowl": "VSO",
"bioportal": "VSO",
"fairsharing": "FAIRsharing.jjb2p2",
"prefixcommons": "vso",
"zazuko": "vso"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "3124",
"description": "The Vital Sign Ontology (VSO) covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.",
"example": "VSO_0000015",
"homepage": "http://code.google.com/p/vital-sign-ontology/",
"keywords": [
"owl",
"health"
],
"name": "Vital Sign Ontology",
"pattern": "^VSO_\\d{7}$",
"prefix": "vso"
},
"uri_format": "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1",
"zazuko": {
"prefix": "vso",
"uri_format": "http://purl.org/vso/ns#$1"
}
},
"vt": {
"aberowl": {
"description": "An ontology of traits covering vertebrates",
"download_owl": "http://aber-owl.net/media/ontologies/VT/109/vt.owl",
"homepage": "https://github.com/AnimalGenome/vertebrate-trait-ontology",
"name": "Vertebrate trait ontology",
"prefix": "VT"
},
"agroportal": {
"contact": {
"email": "jreecy@iastate.edu",
"name": "Jim Reecy"
},
"description": "The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.",
"example_uri": "http://purl.obolibrary.org/obo/VT_1000047",
"homepage": "https://www.animalgenome.org/bioinfo/projects/vt/",
"license": "CC-BY-4.0",
"name": "Vertebrate Trait Ontology",
"prefix": "VT",
"repository": "https://github.com/AnimalGenome/vertebrate-trait-ontology",
"version": "2024-07-22"
},
"biocontext": {
"prefix": "VT"
},
"bioportal": {
"contact": {
"email": "jreecy@iastate.edu",
"name": "Jim Reecy"
},
"description": "The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.",
"homepage": "https://www.animalgenome.org/bioinfo/projects/vt/",
"name": "Vertebrate Trait Ontology",
"prefix": "VT",
"publication": "https://www.animalgenome.org/bioinfo/projects/vt/",
"version": "releases/2024-07-22"
},
"download_obo": "https://github.com/AnimalGenome/vertebrate-trait-ontology/raw/master/current_release/vt.obo",
"example": "0000685",
"fairsharing": {
"abbreviation": "VT",
"description": "The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.",
"domains": [
"Phenotype",
"Morphology"
],
"homepage": "https://github.com/AnimalGenome/vertebrate-trait-ontology",
"license": "CC-BY-4.0",
"name": "Vertebrate Trait Ontology",
"prefix": "FAIRsharing.10gr18",
"publications": [
{
"doi": "10.1186/2041-1480-4-13",
"pubmed": "23937709",
"title": "The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species",
"year": 2013
}
],
"repository": "https://github.com/AnimalGenome/vertebrate-trait-ontology/issues",
"subjects": [
"Animal Physiology",
"Developmental Biology",
"Physiology",
"Biology"
]
},
"mappings": {
"aberowl": "VT",
"agroportal": "VT",
"biocontext": "VT",
"bioportal": "VT",
"fairsharing": "FAIRsharing.10gr18",
"obofoundry": "vt",
"ols": "vt",
"ontobee": "VT",
"prefixcommons": "vt"
},
"obofoundry": {
"appears_in": [
"scdo"
],
"contact": "caripark@iastate.edu",
"contact.github": "caripark",
"contact.label": "Carissa Park",
"contact.orcid": "0000-0002-2346-5201",
"deprecated": false,
"description": "An ontology of traits covering vertebrates",
"domain": "phenotype",
"download.owl": "http://purl.obolibrary.org/obo/vt.owl",
"homepage": "https://github.com/AnimalGenome/vertebrate-trait-ontology",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Vertebrate trait ontology",
"preferredPrefix": "VT",
"prefix": "vt",
"repository": "https://github.com/AnimalGenome/vertebrate-trait-ontology"
},
"ols": {
"description": "The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.",
"download_owl": "http://purl.obolibrary.org/obo/vt.owl",
"homepage": "https://github.com/AnimalGenome/vertebrate-trait-ontology",
"name": "The Vertebrate Trait Ontology",
"prefix": "vt",
"version": "2024-07-22",
"version.iri": "http://purl.obolibrary.org/obo/vt/releases/2024-07-22/vt.owl"
},
"ontobee": {
"library": "Library",
"name": "Vertebrate trait ontology",
"prefix": "VT"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1659",
"description": "The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.",
"example": "VT_0015074",
"keywords": [
"obo",
"vertebrate",
"trait"
],
"name": "Vertebrate Trait Ontology",
"pattern": "^VT_\\d{7}$",
"prefix": "vt"
},
"publications": [
{
"doi": "10.1186/2041-1480-4-13",
"pmc": "PMC3851175",
"pubmed": "23937709",
"title": "The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species",
"year": 2013
}
],
"uri_format": "http://purl.obolibrary.org/obo/VT_$1"
},
"vto": {
"aberowl": {
"description": "Comprehensive hierarchy of extinct and extant vertebrate taxa.",
"download_owl": "http://aber-owl.net/media/ontologies/VTO/15/vto.owl",
"homepage": "https://github.com/phenoscape/vertebrate-taxonomy-ontology",
"name": "Vertebrate Taxonomy Ontology",
"prefix": "VTO"
},
"biocontext": {
"prefix": "VTO"
},
"bioportal": {
"contact": {
"email": "balhoff@renci.org",
"name": "James Balhoff"
},
"description": "The Vertebrate Taxonomy Ontology includes both extinct and extant vertebrates, aiming to provide one comprehensive hierarchy. The hierarchy backbone for extant taxa is based on the NCBI taxonomy. Since the NCBI taxonomy only includes species associated with archived genetic data, to complement this, we also incorporate taxonomic information across the vertebrates from the Paleobiology Database (PaleoDB). The Teleost Taxonomy Ontology (TTO) and AmphibiaWeb (AWeb) are incorporated to provide a more authoritative hierarchy and a richer set of names for specific taxonomic groups.",
"homepage": "http://code.google.com/p/vertebrate-taxonomy-ontology/",
"name": "Vertebrate Taxonomy Ontology",
"prefix": "VTO",
"version": "unknown"
},
"example": "9008500",
"fairsharing": {
"abbreviation": "VTO",
"description": "The Vertebrate Taxonomy Ontology includes both extinct and extant vertebrates, aiming to provide one comprehensive hierarchy. The hierarchy backbone for extant taxa is based on the NCBI taxonomy. Since the NCBI taxonomy only includes species associated with archived genetic data, to complement this, we also incorporate taxonomic information across the vertebrates from the Paleobiology Database (PaleoDB). The Teleost Taxonomy Ontology (TTO) and AmphibiaWeb (AWeb) are incorporated to provide a more authoritative hierarchy and a richer set of names for specific taxonomic groups.",
"domains": [
"Bone"
],
"homepage": "https://gitlab.com/phenoscape/vto",
"name": "Vertebrate Taxonomy Ontology",
"prefix": "FAIRsharing.akmeb9",
"subjects": [
"Taxonomy"
]
},
"mappings": {
"aberowl": "VTO",
"biocontext": "VTO",
"bioportal": "VTO",
"fairsharing": "FAIRsharing.akmeb9",
"obofoundry": "vto",
"ols": "vto",
"ontobee": "VTO"
},
"obofoundry": {
"contact": "balhoff@renci.org",
"contact.github": "balhoff",
"contact.label": "Jim Balhoff",
"contact.orcid": "0000-0002-8688-6599",
"deprecated": false,
"description": "Comprehensive hierarchy of extinct and extant vertebrate taxa.",
"domain": "organisms",
"download.obo": "http://purl.obolibrary.org/obo/vto.obo",
"download.owl": "http://purl.obolibrary.org/obo/vto.owl",
"homepage": "https://github.com/phenoscape/vertebrate-taxonomy-ontology",
"license": "CC0 1.0",
"license.url": "http://creativecommons.org/publicdomain/zero/1.0/",
"name": "Vertebrate Taxonomy Ontology",
"preferredPrefix": "VTO",
"prefix": "vto",
"publications": [
{
"id": "https://doi.org/10.1186/2041-1480-4-34",
"title": "The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes"
}
],
"repository": "https://github.com/phenoscape/vertebrate-taxonomy-ontology"
},
"ols": {
"description": "Comprehensive hierarchy of extinct and extant vertebrate taxa.",
"download_owl": "http://purl.obolibrary.org/obo/vto.owl",
"homepage": "https://github.com/phenoscape/vertebrate-taxonomy-ontology",
"name": "Vertebrate Taxonomy Ontology",
"prefix": "vto",
"version": "2020-11-13",
"version.iri": "http://purl.obolibrary.org/obo/vto/2020-11-13/vto.owl"
},
"ontobee": {
"library": "Library",
"name": "Vertebrate Taxonomy Ontology",
"prefix": "VTO"
},
"pattern": "^\\d{7}$",
"publications": [
{
"doi": "10.1186/2041-1480-4-34",
"pmc": "PMC4177199",
"pubmed": "24267744",
"title": "The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes",
"year": 2013
}
],
"uri_format": "http://purl.obolibrary.org/obo/VTO_$1"
},
"vuid": {
"comment": "The example corresponds to acetaminophen",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Veterans Health Administration is Americaβs largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year.",
"example": "4007166",
"homepage": "https://www.va.gov/health",
"name": "Veterans Health Administration (VHA) unique identifier",
"pattern": "^\\d+$",
"references": [
"https://academic.oup.com/jamia/article/17/4/432/866953"
]
},
"wb.rnai": {
"biocontext": {
"prefix": "WB.RNAI"
},
"mappings": {
"biocontext": "WB.RNAI",
"miriam": "wb.rnai",
"n2t": "wb.rnai"
},
"miriam": {
"deprecated": false,
"description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes.",
"homepage": "https://www.wormbase.org/",
"id": "00000466",
"name": "WormBase RNAi",
"namespaceEmbeddedInLui": false,
"pattern": "^WBRNAi\\d{8}$",
"prefix": "wb.rnai",
"sampleId": "WBRNAi00086878",
"uri_format": "https://www.wormbase.org/species/c_elegans/rnai/$1"
},
"n2t": {
"description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes.",
"example": "WBRNAi00086878",
"homepage": "https://www.wormbase.org/",
"name": "WormBase RNAi",
"namespaceEmbeddedInLui": false,
"pattern": "^WBRNAi\\d{8}$",
"prefix": "wb.rnai",
"uri_format": "https://www.wormbase.org/species/c_elegans/rnai/$1"
}
},
"wbbt": {
"aberowl": {
"description": "A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.",
"download_owl": "http://aber-owl.net/media/ontologies/WBBT/28/wbbt.owl",
"homepage": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology",
"name": "C. elegans Gross Anatomy Ontology",
"prefix": "WBBT"
},
"biocontext": {
"prefix": "WBbt"
},
"biolink": {
"is_identifiers": false,
"is_obo": true,
"prefix": "WBbt",
"uri_format": "http://purl.obolibrary.org/obo/WBbt_$1"
},
"bioportal": {
"contact": {
"email": "raymond@caltech.edu",
"name": "Raymond Lee"
},
"description": "A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.",
"homepage": "http://www.wormbase.org/",
"name": "C. elegans Gross Anatomy Vocabulary",
"prefix": "WB-BT",
"version": "releases/2024-07-01"
},
"example": "0001290",
"fairsharing": {
"abbreviation": "WB-BT",
"contact": {
"email": "raymond@caltech.edu",
"name": "Raymond Lee",
"orcid": "0000-0002-8151-7479"
},
"description": "A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.",
"domains": [
"Cell"
],
"homepage": "https://www.wormbase.org/tools/ontology_browser",
"name": "C. elegans gross anatomy",
"prefix": "FAIRsharing.phk7dd",
"publications": [
{
"doi": "10.1002/cfg.248",
"pubmed": "18629098",
"title": "Building a cell and anatomy ontology of Caenorhabditis elegans",
"year": 2008
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"go": {
"homepage": "http://www.wormbase.org/",
"name": "C. elegans gross anatomy",
"prefix": "WBbt"
},
"mappings": {
"aberowl": "WBBT",
"biocontext": "WBbt",
"biolink": "WBbt",
"bioportal": "WB-BT",
"fairsharing": "FAIRsharing.phk7dd",
"go": "WBbt",
"obofoundry": "wbbt",
"ols": "wbbt",
"ontobee": "WBbt",
"prefixcommons": "wbbt"
},
"obofoundry": {
"contact": "raymond@caltech.edu",
"contact.github": "raymond91125",
"contact.label": "Raymond Lee",
"contact.orcid": "0000-0002-8151-7479",
"deprecated": false,
"description": "A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/wbbt.obo",
"download.owl": "http://purl.obolibrary.org/obo/wbbt.owl",
"homepage": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "C. elegans Gross Anatomy Ontology",
"preferredPrefix": "WBbt",
"prefix": "wbbt",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/18629098",
"title": "Building a cell and anatomy ontology of Caenorhabditis elegans"
}
],
"repository": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology"
},
"ols": {
"description": "Ontology about the gross anatomy of the C. elegans",
"download_owl": "http://purl.obolibrary.org/obo/wbbt.owl",
"homepage": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology",
"name": "C. elegans Gross Anatomy Ontology",
"prefix": "wbbt",
"version": "2024-07-01",
"version.iri": "http://purl.obolibrary.org/obo/wbbt/releases/2024-07-01/wbbt.owl"
},
"ontobee": {
"library": "Library",
"name": "C. elegans Gross Anatomy Ontology",
"prefix": "WBbt"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1048",
"description": "A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.",
"example": "WBbt_0005733",
"homepage": "http://www.wormbase.org/",
"keywords": [
"obo",
"anatomy",
"worm"
],
"name": "C. elegans gross anatomy",
"pattern": "^WBbt_\\d{7}$",
"prefix": "wbbt",
"synonyms": [
"worm_anatomy"
],
"uri_format": "http://wormbase.org/db/ontology/anatomy?name=$1"
},
"publications": [
{
"doi": "10.1002/cfg.248",
"pmc": "PMC2447384",
"pubmed": "18629098",
"title": "Building a cell and anatomy ontology of Caenorhabditis elegans",
"year": 2003
}
],
"synonyms": [
"WBbt"
],
"uri_format": "http://purl.obolibrary.org/obo/WBbt_$1"
},
"wbls": {
"aberowl": {
"description": "A structured controlled vocabulary of the development of Caenorhabditis elegans.",
"download_owl": "http://aber-owl.net/media/ontologies/WBLS/33/wbls.owl",
"homepage": "https://github.com/obophenotype/c-elegans-development-ontology",
"name": "C. elegans development ontology",
"prefix": "WBLS"
},
"biocontext": {
"prefix": "WBLS"
},
"biolink": {
"is_identifiers": false,
"is_obo": true,
"prefix": "WBls",
"uri_format": "http://purl.obolibrary.org/obo/WBls_$1"
},
"bioportal": {
"contact": {
"email": "wchen@its.caltech.edu",
"name": "Worm_development Administrators"
},
"description": "A structured controlled vocabulary of the development of Caenorhabditis elegans.",
"homepage": "http://www.wormbase.org/",
"name": "C. elegans Development Vocabulary",
"prefix": "WB-LS",
"version": "unknown"
},
"example": "0000690",
"fairsharing": {
"abbreviation": "WBLS",
"description": "A structured controlled vocabulary of the development of Caenorhabditis elegans. This resource is also referred to as the Life Stage ontology on the wormbase database.",
"domains": [
"Life cycle",
"Life cycle stage"
],
"homepage": "https://www.wormbase.org/tools/ontology_browser",
"name": "C. elegans development",
"prefix": "FAIRsharing.sm90nh",
"repository": "https://github.com/obophenotype/c-elegans-development-ontology",
"subjects": [
"Developmental Biology",
"Life Science"
]
},
"go": {
"homepage": "http://www.wormbase.org/",
"name": "C. elegans development",
"prefix": "WBls",
"uri_format": "http://www.wormbase.org/get?name=$1"
},
"mappings": {
"aberowl": "WBLS",
"biocontext": "WBLS",
"biolink": "WBls",
"bioportal": "WB-LS",
"fairsharing": "FAIRsharing.sm90nh",
"go": "WBls",
"obofoundry": "wbls",
"ols": "wbls",
"ontobee": "WBls",
"prefixcommons": "wbls"
},
"obofoundry": {
"contact": "cgrove@caltech.edu",
"contact.github": "chris-grove",
"contact.label": "Chris Grove",
"contact.orcid": "0000-0001-9076-6015",
"deprecated": false,
"description": "A structured controlled vocabulary of the development of Caenorhabditis elegans.",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/wbls.obo",
"download.owl": "http://purl.obolibrary.org/obo/wbls.owl",
"homepage": "https://github.com/obophenotype/c-elegans-development-ontology",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "C. elegans development ontology",
"preferredPrefix": "WBls",
"prefix": "wbls",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/31642470",
"title": "WormBase: a modern Model Organism Information Resource"
}
],
"repository": "https://github.com/obophenotype/c-elegans-development-ontology"
},
"ols": {
"description": "Ontology about the development and life stages of the C. elegans",
"download_owl": "http://purl.obolibrary.org/obo/wbls.owl",
"homepage": "https://github.com/obophenotype/c-elegans-development-ontology",
"name": "C. elegans Development Ontology",
"prefix": "wbls",
"version": "2024-04-09",
"version.iri": "http://purl.obolibrary.org/obo/wbls/releases/2024-04-09/wbls.owl"
},
"ontobee": {
"library": "Library",
"name": "C. elegans development ontology",
"prefix": "WBls"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1049",
"description": "A structured controlled vocabulary of the development of Caenorhabditis elegans.",
"example": "WBls_0000003",
"homepage": "http://www.wormbase.org/",
"keywords": [
"obo",
"development",
"worm"
],
"name": "C. elegans development",
"pattern": "^WBIs_\\d{7}$",
"prefix": "wbls",
"synonyms": [
"worm_development"
]
},
"publications": [
{
"doi": "10.1093/nar/gkz920",
"pmc": "PMC7145598",
"pubmed": "31642470",
"title": "WormBase: a modern Model Organism Information Resource",
"year": 2020
}
],
"synonyms": [
"WBls"
],
"uri_format": "http://purl.obolibrary.org/obo/WBls_$1"
},
"wbphenotype": {
"aberowl": {
"description": "A structured controlled vocabulary of Caenorhabditis elegans phenotypes",
"download_owl": "http://aber-owl.net/media/ontologies/WBPHENOTYPE/80/wbphenotype.owl",
"homepage": "https://github.com/obophenotype/c-elegans-phenotype-ontology",
"name": "C. elegans phenotype",
"prefix": "WBPHENOTYPE"
},
"biocontext": {
"prefix": "WBPhenotype"
},
"bioportal": {
"contact": {
"email": "garys@caltech.edu",
"name": "Gary Schindelman"
},
"description": "A structured controlled vocabulary of Caenorhabditis elegans phenotypes",
"homepage": "http://www.wormbase.org/",
"name": "C. elegans Phenotype Vocabulary",
"prefix": "WB-PHENOTYPE",
"version": "releases/2024-06-05"
},
"example": "0000983",
"fairsharing": {
"abbreviation": "WB-PHENOTYPE",
"contact": {
"email": "garys@caltech.edu",
"name": "Gary Schindelman",
"orcid": "0000-0001-7883-4388"
},
"description": "A structured controlled vocabulary of Caenorhabditis elegans phenotypes .",
"domains": [
"Phenotype"
],
"homepage": "https://wormbase.org/tools/ontology_browser#o_browser",
"name": "C. elegans phenotype",
"prefix": "FAIRsharing.agvc7y",
"publications": [
{
"doi": "10.1186/1471-2105-12-32",
"pubmed": "21261995",
"title": "Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community",
"year": 2011
}
],
"repository": "https://github.com/obophenotype/c-elegans-phenotype-ontology",
"subjects": [
"Anatomy",
"Life Science"
]
},
"go": {
"homepage": "http://www.wormbase.org/",
"name": "WormBase phenotype ontology",
"prefix": "WBPhenotype",
"uri_format": "http://www.wormbase.org/get?name=$1"
},
"mappings": {
"aberowl": "WBPHENOTYPE",
"biocontext": "WBPhenotype",
"bioportal": "WB-PHENOTYPE",
"fairsharing": "FAIRsharing.agvc7y",
"go": "WBPhenotype",
"obofoundry": "wbphenotype",
"ols": "wbphenotype",
"ontobee": "WBPhenotype",
"prefixcommons": "wbphenotype"
},
"obofoundry": {
"contact": "cgrove@caltech.edu",
"contact.github": "chris-grove",
"contact.label": "Chris Grove",
"contact.orcid": "0000-0001-9076-6015",
"deprecated": false,
"description": "A structured controlled vocabulary of Caenorhabditis elegans phenotypes",
"domain": "phenotype",
"download.obo": "http://purl.obolibrary.org/obo/wbphenotype.obo",
"download.owl": "http://purl.obolibrary.org/obo/wbphenotype.owl",
"homepage": "https://github.com/obophenotype/c-elegans-phenotype-ontology",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "C. elegans phenotype",
"preferredPrefix": "WBPhenotype",
"prefix": "wbphenotype",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/21261995",
"title": "Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community."
}
],
"repository": "https://github.com/obophenotype/c-elegans-phenotype-ontology"
},
"ols": {
"description": "Ontology about C. elegans and other nematode phenotypes",
"download_owl": "http://purl.obolibrary.org/obo/wbphenotype.owl",
"homepage": "https://github.com/obophenotype/c-elegans-phenotype-ontology",
"name": "C elegans Phenotype Ontology",
"prefix": "wbphenotype",
"version": "2024-06-05",
"version.iri": "http://purl.obolibrary.org/obo/wbphenotype/releases/2024-06-05/wbphenotype.owl"
},
"ontobee": {
"library": "Library",
"name": "C. elegans phenotype",
"prefix": "WBPhenotype"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1067",
"description": "A structured controlled vocabulary of Caenorhabditis elegans phenotypes",
"example": "WBPhenotype_0000517",
"homepage": "http://www.wormbase.org/",
"keywords": [
"obo",
"phenotype",
"worm"
],
"name": "C. elegans phenotype",
"pattern": "^WBPhenotype_\\d{7}$",
"prefix": "wbphenotype",
"synonyms": [
"worm_phenotype"
]
},
"publications": [
{
"doi": "10.1186/1471-2105-12-32",
"pmc": "PMC3039574",
"pubmed": "21261995",
"title": "Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community",
"year": 2011
}
],
"synonyms": [
"WBPhenotype"
],
"uri_format": "http://purl.obolibrary.org/obo/WBPhenotype_$1"
},
"webelements": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Browser for the periodic table of the elements",
"example": "chromium",
"homepage": "https://www.webelements.com/",
"keywords": [
"chemistry"
],
"name": "Web Elements",
"pattern": "^\\w+$",
"uri_format": "https://www.webelements.com/$1"
},
"wgs84": {
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "wgs",
"uri_format": "http://www.w3.org/2003/01/geo/wgs84_pos$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum",
"example": "latitude",
"homepage": "https://www.w3.org/2003/01/geo/wgs84_pos",
"lov": {
"description": "A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum.",
"homepage": "http://www.w3.org/2003/01/geo/",
"keywords": [
"Geography"
],
"modified": "2009-04-20",
"name": "WGS84 Geo Positioning",
"prefix": "geo",
"uri_prefix": "http://www.w3.org/2003/01/geo/wgs84_pos#$1"
},
"mappings": {
"biolink": "wgs",
"lov": "geo"
},
"name": "WGS84 Geo Positioning",
"uri_format": "http://www.w3.org/2003/01/geo/wgs84_pos#$1"
},
"wicell": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.wicell.org",
"name": "WiCell Research Institute Cell Collection",
"prefix": "WiCell",
"uri_format": "https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true"
},
"example": "ai10e-kctd13b",
"mappings": {
"cellosaurus": "WiCell"
}
},
"wikidata": {
"bartoc": {
"abbreviation": "WD",
"description": "Wikidata is a free linked database that can be read and edited by both humans and machines. Wikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wikisource, and others. Wikidata also provides support to many other sites and services beyond just Wikimedia projects! The content of Wikidata is available under a free license, exported using standard formats, and can be interlinked to other open data sets on the linked data web.",
"homepage": "https://www.wikidata.org/wiki/Wikidata:Main_Page",
"license": "CC0-1.0",
"name": "Wikidata",
"pattern": "^Q[0-9]+$",
"prefix": "1940",
"wikidata_database": "Q2013"
},
"biocontext": {
"prefix": "WIKIDATA"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "WIKIDATA",
"uri_format": "https://www.wikidata.org/entity/$1"
},
"cellosaurus": {
"category": "Encyclopedic resources",
"homepage": "https://www.wikidata.org/wiki/Wikidata:Main_Page",
"name": "Wikidata",
"prefix": "Wikidata",
"uri_format": "https://www.wikidata.org/wiki/$1"
},
"contact": {
"email": "vrandecic@gmail.com",
"github": "vrandezo",
"name": "Denny VrandeΔiΔ",
"orcid": "0000-0002-9593-2294"
},
"example": "Q47475003",
"fairsharing": {
"abbreviation": "Wikidata",
"description": "Free knowledge database project hosted by Wikimedia and edited by volunteers.",
"homepage": "http://wikidata.org/",
"license": "CC0-1.0",
"name": "Wikidata",
"prefix": "FAIRsharing.6s749p",
"publications": [
{
"doi": "10.1145/2187980.2188242",
"pubmed_id": null,
"title": "Wikidata: a new platform for collaborative data collection"
}
],
"subjects": [
"Genomics",
"Proteomics",
"Chemistry",
"Metabolomics",
"Subject Agnostic"
],
"twitter": "wikidata"
},
"license": "CC0-1.0",
"mappings": {
"bartoc": "1940",
"biocontext": "WIKIDATA",
"biolink": "WIKIDATA",
"cellosaurus": "Wikidata",
"cheminf": "000567",
"fairsharing": "FAIRsharing.6s749p",
"miriam": "wikidata",
"n2t": "wikidata"
},
"miriam": {
"deprecated": false,
"description": "Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic.",
"homepage": "https://www.wikidata.org/",
"id": "00000549",
"name": "Wikidata",
"namespaceEmbeddedInLui": false,
"pattern": "^(Q|P)\\d+$",
"prefix": "wikidata",
"sampleId": "Q2207226",
"uri_format": "http://www.wikidata.org/entity/$1"
},
"n2t": {
"description": "Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic.",
"example": "Q2207226",
"homepage": "https://www.wikidata.org/",
"name": "Wikidata at Wikimedia Foundation",
"namespaceEmbeddedInLui": false,
"pattern": "^Q\\d+$",
"prefix": "wikidata",
"uri_format": "https://www.wikidata.org/wiki/$1"
},
"providers": [
{
"code": "scholia",
"description": "Scholia can generally resolve many Wikidata entries in the biomedical and bibliometric domains",
"homepage": "https://scholia.toolforge.org",
"name": "Scholia",
"uri_format": "https://scholia.toolforge.org/$1"
}
],
"publications": [
{
"doi": "10.1145/2187980.2188242",
"title": "Wikidata",
"year": 2012
}
],
"synonyms": [
"WD_Entity",
"wd"
]
},
"wikidata.property": {
"biocontext": {
"prefix": "WD_Prop",
"uri_format": "https://www.wikidata.org/wiki/Property:$1"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "WIKIDATA_PROPERTY",
"uri_format": "https://www.wikidata.org/prop/$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Wikidata is a free and open knowledge base that can be read and edited by both humans and machines.\nWikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. ",
"example": "P4355",
"homepage": "https://www.wikidata.org",
"license": "CC0-1.0",
"mappings": {
"biocontext": "WD_Prop",
"biolink": "WIKIDATA_PROPERTY"
},
"name": "Wikidata Property",
"part_of": "wikidata",
"pattern": "^P\\d+$",
"providers": [
{
"code": "scholia",
"description": "Scholia can generally resolve many Wikidata entries in the biomedical and bibliometric domains",
"homepage": "https://scholia.toolforge.org",
"name": "Scholia",
"uri_format": "https://scholia.toolforge.org/$1"
}
]
},
"wikigenes": {
"biocontext": {
"prefix": "WIKIGENES"
},
"mappings": {
"biocontext": "WIKIGENES",
"miriam": "wikigenes",
"n2t": "wikigenes"
},
"miriam": {
"deprecated": false,
"description": "WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process.",
"homepage": "http://www.wikigenes.org/",
"id": "00000437",
"name": "WikiGenes",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "wikigenes",
"sampleId": "3771877",
"uri_format": "http://www.wikigenes.org/e/gene/e/$1.html"
},
"n2t": {
"description": "WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process.",
"example": "3771877",
"homepage": "http://www.wikigenes.org/",
"name": "WikiGenes at Massachusetts Institute of Technology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "wikigenes",
"uri_format": "http://www.wikigenes.org/e/gene/e/$1.html"
},
"provides": "ncbigene"
},
"wikipathways": {
"biocontext": {
"prefix": "WIKIPATHWAYS"
},
"contact": {
"email": "egon.willighagen@gmail.com",
"github": "egonw",
"name": "Egon Willighagen",
"orcid": "0000-0001-7542-0286"
},
"contributor_extras": [
{
"email": "egon.willighagen@gmail.com",
"github": "egonw",
"name": "Egon Willighagen",
"orcid": "0000-0001-7542-0286"
}
],
"description": "WikiPathways is a database of biological pathways maintained by and for the scientific community.",
"edam": {
"description": "Identifier of a pathway from the WikiPathways pathway database.",
"name": "Pathway ID (WikiPathways)",
"obsolete": false,
"prefix": "3952"
},
"example": "WP732",
"fairsharing": {
"abbreviation": "WIKIPATHWAYS",
"description": "WikiPathways simplifies the contribution and maintenance of biological pathway information. It is an open and collaborative platform that curates pathways, complementing existing databases like KEGG, Reactome, and Pathway Commons. The web-based format makes it easy for anyone to participate, from students to experts. The community takes on peer review, editorial curation, and maintenance tasks.",
"domains": [
"Reaction data",
"Protein interaction",
"Signaling",
"Biological regulation",
"Molecular interaction",
"Genetic interaction",
"Drug interaction",
"Pathway model"
],
"homepage": "http://www.wikipathways.org/",
"name": "WikiPathways",
"prefix": "FAIRsharing.g7b4rj",
"subjects": [
"Virology",
"Epidemiology"
]
},
"integbio": {
"description": "WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community.",
"fairsharing": "FAIRsharing.1x53qk",
"homepage": "http://wikipathways.org",
"information_keywords": [
"Image/Movie",
"Interaction/Pathway"
],
"maintainer": "Universiteit Maastricht||Gladstone Institutes",
"name": "WikiPathways",
"prefix": "nbdc02116",
"pubmeds": [
"18651794",
"19649250",
"26481357",
"22096230"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"license": "CC0-1.0",
"logo": "https://www.wikipathways.org/assets/img/wikipathways-logo-horizontal.svg",
"mappings": {
"biocontext": "WIKIPATHWAYS",
"edam": "3952",
"fairsharing": "FAIRsharing.g7b4rj",
"integbio": "nbdc02116",
"miriam": "wikipathways",
"n2t": "wikipathways",
"pathguide": "237",
"prefixcommons": "wikipathways",
"re3data": "r3d100013316",
"togoid": "Wikipathways",
"wikidata": "P2410"
},
"mastodon": "wikipathways@fosstodon.org",
"miriam": {
"deprecated": false,
"description": "WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki-like style.",
"homepage": "http://www.wikipathways.org/",
"id": "00000076",
"name": "WikiPathways",
"namespaceEmbeddedInLui": false,
"pattern": "WP\\d{1,5}(\\_r\\d+)?$",
"prefix": "wikipathways",
"providers": [
{
"code": "scholia",
"description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.\n",
"homepage": "https://scholia.toolforge.org/",
"name": "Scholia",
"uri_format": "https://scholia.toolforge.org/wikipathways/$1"
}
],
"sampleId": "WP100",
"uri_format": "http://www.wikipathways.org/instance/$1"
},
"n2t": {
"description": "WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style. All content is under the Creative Commons Attribution 3.0 Unported license.",
"example": "WP100",
"homepage": "http://www.wikipathways.org/",
"name": "Wikipathways",
"namespaceEmbeddedInLui": false,
"pattern": "WP\\d{1,5}(\\_r\\d+)?$",
"prefix": "wikipathways",
"uri_format": "http://www.wikipathways.org/instance/$1"
},
"name": "WikiPathways",
"pathguide": {
"abbreviation": "WikiPathways",
"homepage": "http://wikipathways.org/index.php/WikiPathways",
"keywords": [
"BioPAX"
],
"name": "WikiPathways",
"prefix": "237"
},
"prefixcommons": {
"description": "WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style.",
"example": "WP100",
"homepage": "http://wikipathways.org/",
"keywords": [
"pathway"
],
"license": "CC0-1.0",
"name": "WikiPathways",
"pattern": "^P\\d{1,5}(\\_r\\d+)?$",
"prefix": "wikipathways",
"pubmed_ids": [
"18651794"
],
"uri_format": "http://www.wikipathways.org/index.php/Pathway:$1"
},
"publications": [
{
"doi": "10.1093/nar/gkad960",
"pmc": "PMC10767877",
"pubmed": "37941138",
"title": "WikiPathways 2024: next generation pathway database",
"year": 2024
},
{
"doi": "10.1093/nar/gkaa1024",
"pmc": "PMC7779061",
"pubmed": "33211851",
"title": "WikiPathways: connecting communities",
"year": 2021
},
{
"doi": "10.1093/nar/gkx1064",
"pmc": "PMC5753270",
"pubmed": "29136241",
"title": "WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research",
"year": 2018
},
{
"doi": "10.1093/nar/gkv1024",
"pmc": "PMC4702772",
"pubmed": "26481357",
"title": "WikiPathways: capturing the full diversity of pathway knowledge",
"year": 2015
},
{
"doi": "10.1093/nar/gkr1074",
"pmc": "PMC3245032",
"pubmed": "22096230",
"title": "WikiPathways: building research communities on biological pathways",
"year": 2011
},
{
"doi": "10.1371/journal.pbio.0060184",
"pmc": "PMC2475545",
"pubmed": "18651794",
"title": "WikiPathways: pathway editing for the people",
"year": 2008
}
],
"re3data": {
"description": "WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. Building on the same MediaWiki software that powers Wikipedia, we added a custom graphical pathway editing tool and integrated databases covering major gene, protein, and small-molecule systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.",
"homepage": "https://www.wikipathways.org/",
"name": "WikiPathways",
"prefix": "r3d100013316",
"xrefs": {
"fairsharing": "FAIRsharing.1x53qk",
"nif": "0000-20925",
"scr": "002134"
}
},
"togoid": {
"catalog": "nbdc02116",
"examples": [
"WP1531",
"WP4312",
"WP4877",
"WP5020",
"WP4400",
"WP4474",
"WP4183",
"WP3650",
"WP4545",
"WP4462"
],
"keywords": [
"Pathway"
],
"name": "WikiPathways",
"pattern": "^(?WP\\d{1,5})(?:\\_r\\d+)?$",
"prefix": "Wikipathways",
"uri_format": "http://identifiers.org/wikipathways/$1"
},
"twitter": "WikiPathways",
"wikidata": {
"description": "describes in which biological pathways a biological entity occurs",
"example": [
"WP2253",
"WP2533",
"WP4921"
],
"homepage": "http://www.wikipathways.org",
"miriam": "wikipathways",
"name": "WikiPathways ID",
"pattern": "^WP\\d{1,4}$",
"prefix": "P2410",
"uri_format": "https://new.wikipathways.org/pathways/$1",
"uri_format_rdf": "http://identifiers.org/wikipathways/$1"
}
},
"wikipathways.vocab": {
"aberowl": {
"description": "The WP ontology for WikiPathways.",
"download_owl": "http://aber-owl.net/media/ontologies/WIKIPATHWAYS/225/wikipathways.owl",
"homepage": "http://www.wikipathways.org/",
"name": "WikiPathways",
"prefix": "WIKIPATHWAYS"
},
"bioportal": {
"contact": {
"email": "egon.willighagen@gmail.com",
"name": "Egon Willighagen"
},
"description": "The WP ontology for WikiPathways.",
"homepage": "https://www.wikipathways.org/",
"name": "WikiPathways",
"prefix": "WIKIPATHWAYS",
"publication": "https://scholia.toolforge.org/topic/Q7999828"
},
"contact": {
"email": "egon.willighagen@gmail.com",
"github": "egonw",
"name": "Egon Willighagen",
"orcid": "0000-0001-7542-0286"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "An ontology supporting data modeling in WikiPathways",
"example": "DataNode",
"homepage": "http://www.wikipathways.org",
"mappings": {
"aberowl": "WIKIPATHWAYS",
"bioportal": "WIKIPATHWAYS"
},
"mastodon": "wikipathways@fosstodon.org",
"name": "WikiPathways Ontology",
"references": [
"https://github.com/biopragmatics/bioregistry/issues/818"
],
"uri_format": "https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/?p=classes&conceptid=http%3A%2F%2Fvocabularies.wikipathways.org%2Fwp%23$1"
},
"wikipedia.en": {
"biocontext": {
"prefix": "WIKIPEDIA.EN"
},
"contributor_extras": [
{
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
}
],
"example_extras": [
"Pharyngeal_pouch_(embryology)"
],
"go": {
"homepage": "http://en.wikipedia.org/",
"name": "Wikipedia",
"prefix": "Wikipedia",
"uri_format": "http://en.wikipedia.org/wiki/$1"
},
"mappings": {
"biocontext": "WIKIPEDIA.EN",
"go": "Wikipedia",
"miriam": "wikipedia.en",
"n2t": "wikipedia.en",
"prefixcommons": "wikipedia"
},
"miriam": {
"deprecated": false,
"description": "Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay.",
"homepage": "http://en.wikipedia.org/wiki/Main_Page",
"id": "00000384",
"name": "Wikipedia (En)",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z-0-9_]+$",
"prefix": "wikipedia.en",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "Wikipedia structured content through DBpedia",
"homepage": "http://wiki.dbpedia.org/",
"name": "Wikipedia structured content through DBpedia",
"uri_format": "http://dbpedia.org/page/$1"
}
],
"sampleId": "SM_UB-81",
"uri_format": "http://en.wikipedia.org/wiki/$1"
},
"n2t": {
"description": "Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay.",
"example": "SM_UB-81",
"homepage": "http://wiki.dbpedia.org/",
"name": "Wikipedia structured content through DBpedia",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z-0-9_]+$",
"prefix": "wikipedia.en",
"uri_format": "http://dbpedia.org/page/$1"
},
"name": "Wikipedia",
"pattern": "^\\S+$",
"prefixcommons": {
"description": "Encyclopedia of Everything.",
"example": "SM_UB-81",
"homepage": "http://en.wikipedia.org/",
"name": "Wikipedia",
"pattern": "^[A-Za-z0-9_]+$",
"prefix": "wikipedia",
"synonyms": [
"wikipedia.en"
],
"uri_format": "http://en.wikipedia.org/wiki/$1"
},
"providers": [
{
"code": "volupedia",
"description": "A mix of wikipedia and 3d",
"homepage": "http://en.volupedia.org",
"name": "Volupedia",
"uri_format": "http://en.volupedia.org/wiki/$1"
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],
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"https://github.com/biopragmatics/bioregistry/issues/794"
],
"synonyms": [
"wikipedia"
]
},
"worfdb": {
"biocontext": {
"prefix": "WORFDB"
},
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"alt_name": "Worm ORFeome Database",
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"Sequence"
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"maintainer": "Harvard Medical School",
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"15489327",
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"cDNA/EST"
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},
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"deprecated": false,
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"id": "00000288",
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"pattern": "^\\w+(\\.\\d+)?",
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"sampleId": "T01B6.1",
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"description": "WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends).",
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"pattern": "^\\w+(\\.\\d+)?",
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"ncbi": {
"example": "pos-1",
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"prefix": "WorfDB"
},
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"description": "In total, approximately 12,500 C. elegans ORFs are now available as Gateway Entry clones for various reverse proteomics (ORFeome v3.1). This work illustrates why the cloning of a complete C. elegans ORFeome, and likely the ORFeomes of other multicellular organisms, needs to be an iterative process that requires multiple rounds of experimental validation together with gradually improving gene predictions.",
"example": "R10E9.1",
"homepage": "http://worfdb.dfci.harvard.edu/",
"keywords": [
"DNA"
],
"name": "The C.elegans ORFeome cloning project",
"pattern": "^[A-Z,0-9]+$",
"prefix": "worfdb",
"uri_format": "http://worfdb.dfci.harvard.edu/searchallwormorfs.pl?sid=$1"
}
},
"world2dpage": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"mappings": {
"prefixcommons": "world2dpage",
"uniprot": "DB-0121"
},
"prefixcommons": {
"description": "A public repository, standards compliant, for proteomics image data published in the literature. This repository currently contains data from 16 published articles, putting together 22 reference maps for 15 species, totalizing nearly 4'400 identified spots.",
"example": "0020",
"homepage": "http://world-2dpage.expasy.org/repository/",
"keywords": [
"protein",
"structure",
"2d-page"
],
"name": "The World-2DPAGE database",
"pattern": "^\\d+$",
"prefix": "world2dpage",
"uri_format": "http://world-2dpage.expasy.org/repository/database=$1"
},
"publications": [
{
"doi": "10.1016/j.jprot.2008.02.005",
"pubmed": "18617148",
"title": "The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server",
"year": 2008
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"uniprot": {
"abbreviation": "World-2DPAGE",
"category": "2D gel databases",
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"name": "The World-2DPAGE database",
"prefix": "DB-0121",
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{
"doi": "10.1016/j.jprot.2008.02.005",
"pubmed": "18617148"
}
],
"uri_format": "https://world-2dpage.expasy.org/repository/$1"
}
},
"worldavatar.compchem": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Linked-data framework for connecting species in chemical kinetic reaction mechanisms with quantum calculations. A mechanism can be constructed from thermodynamic, reaction rate, and transport data that has been obtained either experimentally, computationally, or by a combination of both. In order to implement this approach, two existing ontologies, namely OntoKin, for representing chemical kinetic reaction mechanisms, and OntoCompChem, for representing quantum chemistry calculations, are extended. (from https://nfdi4cat.org/services/ontologie-sammlung/)",
"download_owl": "http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl",
"homepage": "https://como.ceb.cam.ac.uk/preprints/223/",
"name": "Computational Chemistry Ontology",
"no_own_terms": true
},
"worldavatar.kin": {
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "Represents chemical kinetic reaction mechanisms.",
"download_owl": "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl",
"example": "ElementNumber",
"homepage": "http://www.theworldavatar.com/ontokin/",
"name": "Ontology for Chemical Kinetic Reaction Mechanisms",
"uri_format": "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#$1"
},
"wormbase": {
"biocontext": {
"prefix": "WormBase",
"uri_format": "https://www.wormbase.org/get?name=$1"
},
"biolink": {
"is_identifiers": false,
"is_obo": false,
"prefix": "WBVocab",
"uri_format": "http://bio2rdf.org/wormbase_vocabulary$1"
},
"contact": {
"email": "todd@wormbase.org",
"github": "tharris",
"name": "Todd W Harris",
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{
"email": "cjmungall@lbl.gov",
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"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
}
],
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"description": "Gene identifier used by WormBase database.",
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"prefix": "1805"
},
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"name": "WormBase",
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{
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{
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"title": "The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species."
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{
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"title": "nGASP--the nematode genome annotation assessment project."
},
{
"doi": "10.1093/nar/gkz920",
"pubmed_id": 31642470,
"title": "WormBase: a modern Model Organism Information Resource."
},
{
"doi": "10.1093/nar/gkx998",
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"title": "WormBase 2017: molting into a new stage."
}
],
"subjects": [
"Anatomy",
"Life Science"
],
"twitter": "wormbase"
},
"go": {
"homepage": "http://www.wormbase.org/",
"name": "WormBase database of nematode biology",
"prefix": "WB_REF",
"uri_format": "http://www.wormbase.org/get?name=$1"
},
"integbio": {
"description": "WormBase is a database of information on nematodes and other worms. The database contains extensive information on a number of species including genome sequences, genes, gene expression, proteins, and phenotypes. Users can search by keyword, BLAST, or BLAT, and create user accounts to save searches and other useful information.",
"fairsharing": "biodbcore-000156",
"homepage": "http://www.wormbase.org",
"information_keywords": [
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"Ontology/Terminology/Nomenclature",
"Sequence",
"Expression",
"Image/Movie",
"Bibliography/Documents",
"Repository"
],
"maintainer": "Ontario Institute For Cancer Research",
"name": "WormBase",
"prefix": "nbdc00740",
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],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"Protein",
"Organism",
"Health/Disease"
]
},
"license": "CC0-1.0",
"mappings": {
"biocontext": "WormBase",
"biolink": "WBVocab",
"edam": "1805",
"fairsharing": "FAIRsharing.zx1td8",
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"integbio": "nbdc00740",
"miriam": "wb",
"n2t": "wb",
"ncbi": "WormBase",
"pathguide": "426",
"prefixcommons": "wormbase",
"re3data": "r3d100010424",
"rrid": "WB-STRAIN:WBStrain",
"uniprot": "DB-0110",
"wikidata": "P3860"
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"homepage": "https://www.wormbase.org/",
"id": "00000027",
"name": "WormBase",
"namespaceEmbeddedInLui": false,
"pattern": "^WB[A-Z][a-z]+\\d+$",
"prefix": "wb",
"providers": [
{
"code": "agr",
"description": "WormBase through the Alliance of Genome Resources",
"homepage": "https://www.alliancegenome.org",
"name": "WormBase through the Alliance of Genome Resources",
"uri_format": "https://www.alliancegenome.org/gene/WB:$1"
}
],
"sampleId": "WBGene00000001",
"uri_format": "https://www.wormbase.org/get?name=$1"
},
"n2t": {
"description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities.",
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"name": "WormBase",
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"pattern": "^WB[A-Z][a-z]+\\d+$",
"prefix": "wb",
"uri_format": "https://www.wormbase.org/get?name=$1"
},
"name": "WormBase",
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"example": "R13H7",
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"prefix": "WormBase"
},
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"abbreviation": "WormBase",
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"name": "Worm Base",
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},
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"homepage": "http://www.wormbase.org/",
"keywords": [
"genome",
"gene",
"anatomy"
],
"license": "http://wiki.wormbase.org/index.php/WormBaseWiki:Copyrights",
"name": "WormBase",
"pattern": "^WBGene\\d{8}$",
"prefix": "wormbase",
"pubmed_ids": [
"11125056"
],
"synonyms": [
"wb"
]
},
"providers": [
{
"code": "wormbase.c_elegans",
"description": "Pages describing C. Elegans genes.",
"homepage": "http://www.wormbase.org",
"name": "WormBase C. Elegans Gene Portal",
"uri_format": "http://www.wormbase.org/species/c_elegans/gene/$1"
}
],
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"year": 2020
},
{
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"pubmed": "29069413",
"title": "WormBase 2017: molting into a new stage",
"year": 2018
},
{
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"pubmed": "21595960",
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},
{
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"pubmed": "21071413",
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},
{
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"title": "Localizing triplet periodicity in DNA and cDNA sequences",
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},
{
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"pubmed": "19921742",
"title": "Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology",
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},
{
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"pubmed": "19920128",
"title": "The Gene Ontology in 2010: extensions and refinements",
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},
{
"doi": "10.1093/nar/gkp952",
"pmc": "PMC2808986",
"pubmed": "19910365",
"title": "WormBase: a comprehensive resource for nematode research",
"year": 2009
},
{
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"pmc": "PMC2719631",
"pubmed": "19622167",
"title": "Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation",
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},
{
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},
{
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"pmc": "PMC2651883",
"pubmed": "19099578",
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},
{
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"pmc": "PMC29781",
"pubmed": "11125056",
"title": "WormBase: network access to the genome and biology of Caenorhabditis elegans",
"year": 2001
}
],
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"description": "Launched in 2000, WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and some related nematodes. In addition to their curation work, all sites have ongoing programs in bioinformatics research to develop the next generations of WormBase structure, content and accessibility",
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"name": "WormBase",
"prefix": "r3d100010424",
"synonyms": [
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],
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"nif": "0000-00053",
"omics": "01664",
"scr": "003098"
}
},
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"homepage": "http://www.wormbase.org",
"keywords": [
"FASEB list",
"blast",
"c elegans",
"catalog",
"database",
"gene expression",
"gene function",
"gene mapping",
"gene prediction",
"geneotype",
"genomic sequence",
"genomics",
"ortholog",
"orthology assignment",
"phenotype",
"roundworm",
"transposon family",
"wormmart"
],
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"WB_REF",
"wb",
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"abbreviation": "WormBase",
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"name": "WormBase",
"prefix": "DB-0110",
"publications": [
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"pubmed": "31642470"
}
],
"uri_format": "https://wormbase.org/db/seq/protein?name=$1;class=CDS"
},
"wikidata": {
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"WBGene00000875",
"WBGene00000898",
"WBGene00000973"
],
"homepage": "http://www.wormbase.org",
"miriam": "wb",
"name": "Wormbase Gene ID",
"prefix": "P3860",
"uri_format": "http://www.wormbase.org/db/gene/gene?name=$1;class=Gene"
}
},
"wormpep": {
"biocontext": {
"prefix": "WORMPEP"
},
"mappings": {
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"miriam": "wormpep",
"n2t": "wormpep",
"prefixcommons": "wormpep"
},
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"description": "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project.",
"homepage": "https://www.wormbase.org/db/seq/protein",
"id": "00000031",
"name": "Wormpep",
"namespaceEmbeddedInLui": false,
"pattern": "^CE\\d{5}$",
"prefix": "wormpep",
"sampleId": "CE28239",
"uri_format": "https://www.wormbase.org/db/seq/protein?name=$1"
},
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"description": "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project.",
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"homepage": "https://www.wormbase.org/db/seq/protein",
"name": "Wormpep (Master)",
"namespaceEmbeddedInLui": false,
"pattern": "^CE\\d{5}$",
"prefix": "wormpep",
"uri_format": "https://www.wormbase.org/db/seq/protein?name=WP:$1"
},
"prefixcommons": {
"description": "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project.",
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"homepage": "http://www.wormbase.org/db/seq/protein",
"keywords": [
"protein",
"structure"
],
"name": "Caenorhabditis elegans genome sequencing project protein database",
"pattern": "^CE\\d{5}$",
"prefix": "wormpep",
"uri_format": "http://www.wormbase.org/db/seq/protein?name=$1"
}
},
"worms": {
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"homepage": "http://www.marinespecies.org/",
"license": "CC-BY-3.0",
"name": "World Register of Marine Species",
"prefix": "720",
"wikidata_database": "Q604063"
},
"biocontext": {
"prefix": "WORMS"
},
"contributor_extras": [
{
"email": "meghan.balk@gmail.com",
"github": "megbalk",
"name": "Meghan Balk",
"orcid": "0000-0003-2699-3066"
}
],
"fairsharing": {
"abbreviation": "WoRMS",
"contact": {
"email": "leen.vandepitte@vliz.be",
"name": "Leen Vandepitte",
"orcid": "0000-0002-8160-7941"
},
"description": "The aim of a World Register of Marine Species (WoRMS) is to provide an authoritative and comprehensive list of names of marine organisms, including information on synonymy. While highest priority goes to valid names, other names in use are included so that this register can serve as a guide to interpret taxonomic literature.",
"homepage": "http://www.marinespecies.org",
"license": "CC-BY-4.0",
"name": "World Register of Marine Species",
"prefix": "FAIRsharing.7g1bzj",
"publications": [
{
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"license": "CC-BY-3.0",
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"Genomics",
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"twitter": "Xenbase"
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"go": {
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"prefix": "xenbase",
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},
{
"doi": "10.1016/j.ydbio.2016.03.030",
"pmc": "PMC5045824",
"pubmed": "27039265",
"title": "Xenopus genomic data and browser resources",
"year": 2016
},
{
"doi": "10.1093/database/bau108",
"pmc": "PMC4224262",
"pubmed": "25380782",
"title": "The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud",
"year": 2014
},
{
"doi": "10.1093/nar/gku956",
"pmc": "PMC4384024",
"pubmed": "25313157",
"title": "Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes",
"year": 2014
},
{
"doi": "10.1186/2041-1480-4-31",
"pmc": "PMC3816597",
"pubmed": "24139024",
"title": "Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase",
"year": 2013
},
{
"doi": "10.1093/nar/gkp953",
"pmc": "PMC2808955",
"pubmed": "19884130",
"title": "Xenbase: gene expression and improved integration",
"year": 2009
}
],
"re3data": {
"description": "Xenbase's mission is to provide the international research community with a comprehensive, integrated and easy to use web based resource that gives access the diverse and rich genomic, expression and functional data available from Xenopus research. Xenbase also provides a critical data sharing infrastructure for many other NIH-funded projects, and is a focal point for the Xenopus community. In addition to our primary goal of supporting Xenopus researchers, Xenbase enhances the availability and visibility of Xenopus data to the broader biomedical research community.",
"homepage": "https://www.xenbase.org/xenbase/",
"name": "Xenbase",
"prefix": "r3d100011331",
"synonyms": [
"Xenopus Genomics Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.jrv6wj",
"miriam": "00000186",
"nif": "0000-01286",
"scr": "003280"
}
},
"synonyms": [
"Xenbase"
],
"uniprot": {
"abbreviation": "Xenbase",
"category": "Organism-specific databases",
"homepage": "https://www.xenbase.org/",
"name": "Xenopus laevis and tropicalis biology and genomics resource",
"prefix": "DB-0129",
"publications": [
{
"doi": "10.1093/nar/gkx936",
"pubmed": "29059324"
}
],
"uri_format": "https://www.xenbase.org/gene/showgene.do?method=display&geneId=$1"
},
"uri_format": "https://www.xenbase.org/entry/$1"
},
"ximbio": {
"cellosaurus": {
"category": "Cell line collections (Providers)",
"homepage": "https://ximbio.com",
"name": "Ximbio reagents online portal",
"prefix": "Ximbio",
"uri_format": "https://ximbio.com/reagent/$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"example": "151022",
"homepage": "https://ximbio.com",
"mappings": {
"cellosaurus": "Ximbio"
},
"name": "Ximbio",
"pattern": "^\\d+$",
"uri_format": "https://ximbio.com/reagent/$1"
},
"xl": {
"aberowl": {
"name": "Cross-linker reagents ontology",
"prefix": "XL"
},
"biocontext": {
"prefix": "XL"
},
"deprecated": true,
"mappings": {
"aberowl": "XL",
"biocontext": "XL",
"ols": "xl",
"ontobee": "XL"
},
"ols": {
"contact": "psidev-ms-vocab@lists.sourceforge.net",
"description": "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.",
"download": "http://purl.obolibrary.org/obo/xl.owl",
"homepage": "http://www.psidev.info/groups/controlled-vocabularies",
"name": "Cross-linker reagents ontology",
"prefix": "xl"
},
"ontobee": {
"library": "Library",
"name": "Cross-linker reagents ontology",
"prefix": "XL"
}
},
"xlmod": {
"aberowl": {
"description": "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.",
"download_owl": "http://aber-owl.net/media/ontologies/XLMOD/2/xlmod.owl",
"homepage": "http://www.psidev.info/groups/controlled-vocabularies",
"name": "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary",
"prefix": "XLMOD"
},
"bioportal": {
"contact": {
"email": "gerhard.mayer@rub.de",
"name": "Gerhard Mayer"
},
"description": "XLMOD is an ontology for cross-linking mass spectrometry reagents and GC-MS derivatization reagents.",
"homepage": "https://github.com/HUPO-PSI/mzIdentML/tree/master/cv",
"name": "mass spectrometry cross-linking and derivatization reagents",
"prefix": "XLMOD",
"version": "release/2019-10-28"
},
"contact": {
"email": "gerhard.mayer@rub.de",
"github": "germa",
"name": "Gerhard Mayer",
"orcid": "0000-0002-1767-2343"
},
"example": "00050",
"fairsharing": {
"abbreviation": "XLMOD",
"contact": {
"email": "lutz.fischer@tu-berlin.de",
"name": "Lutz Fischer",
"orcid": "0000-0003-4978-0864"
},
"description": "The XLMOD ontology is a structured, controlled vocabulary for cross-linking reagents and cross-linker related post-translational modifications used in cross-linking mass spectrometry experiments and derivatization reagents for GC-MS. Developed by the HUPO Proteomics Standards Initiative (PSI).",
"domains": [
"Mass spectrum",
"Experimental measurement",
"Mass spectrometry assay"
],
"homepage": "https://github.com/HUPO-PSI/xlmod-CV",
"license": "CC-BY-3.0",
"name": "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary",
"prefix": "FAIRsharing.6ccbe6",
"repository": "https://github.com/HUPO-PSI/xlmod-CV",
"subjects": [
"Chemical Biology",
"Metabolomics",
"Omics"
]
},
"mappings": {
"aberowl": "XLMOD",
"bioportal": "XLMOD",
"fairsharing": "FAIRsharing.6ccbe6",
"obofoundry": "xlmod",
"ols": "xlmod",
"ontobee": "XLMOD"
},
"obofoundry": {
"contact": "lutz.fischer@tu-berlin.de",
"contact.github": "lutzfischer",
"contact.label": "Lutz Fischer",
"contact.orcid": "0000-0003-4978-0864",
"deprecated": false,
"description": "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.",
"domain": "chemistry and biochemistry",
"download.obo": "http://purl.obolibrary.org/obo/xlmod.obo",
"download.owl": "http://purl.obolibrary.org/obo/xlmod.owl",
"homepage": "http://www.psidev.info/groups/controlled-vocabularies",
"license": "CC BY 3.0",
"license.url": "https://creativecommons.org/licenses/by/3.0/",
"name": "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary",
"preferredPrefix": "XLMOD",
"prefix": "xlmod",
"repository": "https://github.com/HUPO-PSI/xlmod-CV"
},
"ols": {
"contact": "psidev-ms-vocab@lists.sourceforge.net",
"description": "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.",
"download_owl": "http://purl.obolibrary.org/obo/xlmod.owl",
"homepage": "http://www.psidev.info/groups/controlled-vocabularies",
"name": "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary",
"prefix": "xlmod",
"version": "2019-10-28",
"version.iri": "http://purl.obolibrary.org/obo/xlmod/release/2019-10-28/xlmod.owl"
},
"ontobee": {
"library": "Library",
"name": "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary",
"prefix": "XLMOD"
},
"pattern": "^\\d{5}$",
"uri_format": "http://purl.obolibrary.org/obo/XLMOD_$1"
},
"xmetdb": {
"banana": "XMETDB",
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"description": "Metabolites in the Xenobiotics Metabolism Database.",
"example": "171",
"homepage": "https://xmetdb.org",
"name": "Xenobiotics Metabolism Database",
"pattern": "^\\d+$",
"uri_format": "http://www.xmetdb.org/xmetdb/protocol/$1"
},
"xml": {
"biocontext": {
"prefix": "xml",
"uri_format": "http://www.w3.org/XML/1998/namespace$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Extensible Markup Language (XML) is a subset of SGML that is completely described in this document. Its goal is to enable generic SGML to be served, received, and processed on the Web in the way that is now possible with HTML. XML has been designed for ease of implementation and for interoperability with both SGML and HTML.",
"example": "lang",
"fairsharing": {
"abbreviation": "XML",
"description": "The Extensible Markup Language (XML) describes a class of data objects called XML documents and partially describes the behavior of computer programs which process them. XML is an application profile or restricted form of SGML, the Standard Generalized Markup Language [ISO 8879]. By construction, XML documents are conforming SGML documents. XML documents are made up of storage units called entities, which contain either parsed or unparsed data. Parsed data is made up of characters, some of which form character data, and some of which form markup. Markup encodes a description of the document's storage layout and logical structure. XML provides a mechanism to impose constraints on the storage layout and logical structure.",
"homepage": "https://www.w3.org/TR/xml/",
"name": "Extensible Markup Language",
"prefix": "FAIRsharing.b5cc91",
"publications": [],
"subjects": [
"Subject Agnostic"
]
},
"homepage": "https://www.w3.org/TR/xml/",
"mappings": {
"biocontext": "xml",
"fairsharing": "FAIRsharing.b5cc91"
},
"name": "Extensible Markup Language",
"uri_format": "http://www.w3.org/XML/1998/namespace#$1"
},
"xpo": {
"aberowl": {
"description": "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis.",
"download_owl": "http://aber-owl.net/media/ontologies/XPO/16/xpo.owl",
"homepage": "https://github.com/obophenotype/xenopus-phenotype-ontology",
"name": "Xenopus Phenotype Ontology",
"prefix": "XPO"
},
"biolink": {
"is_identifiers": false,
"is_obo": true,
"prefix": "XPO",
"uri_format": "http://purl.obolibrary.org/obo/XPO_$1"
},
"bioportal": {
"contact": {
"email": "esegerd3@gmail.com",
"name": "Erik Segerdell"
},
"description": "An ontology of anatomical, cellular, and gene function phenotypes in Xenopus, the African clawed frogs. The Xenopus Phenotype Ontology represents and standardizes anatomical, cellular, and gene function phenotypes in Xenopus, the African clawed frogs. The XPO is being designed primarily to support phenotype curation in Xenbase, the model organism database for Xenopus, and to facilitate mappings between frog phenotypes and human disease.",
"homepage": "https://github.com/obophenotype/xenopus-phenotype-ontology",
"name": "Xenopus Phenotype Ontology",
"prefix": "XPO",
"version": "2024-04-18"
},
"example": "0100002",
"mappings": {
"aberowl": "XPO",
"biolink": "XPO",
"bioportal": "XPO",
"obofoundry": "xpo",
"ols": "xpo",
"ontobee": "XPO"
},
"obofoundry": {
"contact": "Erik.Segerdell@cchmc.org",
"contact.github": "seger",
"contact.label": "Erik Segerdell",
"contact.orcid": "0000-0002-9611-1279",
"depends_on": [
"bfo",
"chebi",
"cl",
"go",
"iao",
"pato",
"ro",
"xao"
],
"deprecated": false,
"description": "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis.",
"domain": "phenotype",
"download.obo": "http://purl.obolibrary.org/obo/xpo.obo",
"download.owl": "http://purl.obolibrary.org/obo/xpo.owl",
"homepage": "https://github.com/obophenotype/xenopus-phenotype-ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Xenopus Phenotype Ontology",
"preferredPrefix": "XPO",
"prefix": "xpo",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/35317743",
"title": "The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development."
}
],
"repository": "https://github.com/obophenotype/xenopus-phenotype-ontology"
},
"ols": {
"description": "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis.",
"download_owl": "http://purl.obolibrary.org/obo/xpo.owl",
"homepage": "https://github.com/obophenotype/xenopus-phenotype-ontology",
"name": "Xenopus Phenotype Ontology",
"prefix": "xpo",
"version": "2024-04-18",
"version.iri": "http://purl.obolibrary.org/obo/xpo/releases/2024-04-18/xpo.owl"
},
"ontobee": {
"library": "Library",
"name": "Xenopus Phenotype Ontology",
"prefix": "XPO"
},
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1186/s12859-022-04636-8",
"pmc": "PMC8939077",
"pubmed": "35317743",
"title": "The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development",
"year": 2022
}
],
"uri_format": "http://purl.obolibrary.org/obo/XPO_$1"
},
"xsd": {
"biocontext": {
"prefix": "xsd",
"uri_format": "http://www.w3.org/2001/XMLSchema#$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language.",
"example": "decimal",
"homepage": "http://www.w3.org/2001/XMLSchema",
"lov": {
"description": "The XML Schema representation",
"homepage": "http://www.w3.org/2001/XMLSchema",
"keywords": [
"W3C Rec"
],
"name": "XML Schema",
"prefix": "xsd",
"uri_prefix": "http://www.w3.org/2001/XMLSchema#$1"
},
"mappings": {
"biocontext": "xsd",
"lov": "xsd",
"zazuko": "xsd"
},
"name": "XML Schema Definition",
"preferred_prefix": "xsd",
"uri_format": "http://www.w3.org/2001/XMLSchema#$1",
"zazuko": {
"prefix": "xsd",
"uri_format": "http://www.w3.org/2001/XMLSchema#$1"
}
},
"xuo": {
"appears_in": [
"hsapdv"
],
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
"name": "XUO"
},
"ydpm": {
"biocontext": {
"prefix": "YDPM"
},
"mappings": {
"biocontext": "YDPM",
"miriam": "ydpm",
"n2t": "ydpm",
"prefixcommons": "ydpm"
},
"miriam": {
"deprecated": false,
"description": "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition.",
"homepage": "http://www-deletion.stanford.edu/YDPM/",
"id": "00000465",
"name": "YDPM",
"namespaceEmbeddedInLui": false,
"pattern": "^Y[A-Z]{2}\\d+[CW]$",
"prefix": "ydpm",
"sampleId": "YAL001C",
"uri_format": "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1"
},
"n2t": {
"description": "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition.",
"example": "YAL001C",
"homepage": "http://www-deletion.stanford.edu/YDPM/",
"name": "YDPM at Stanford University School of Medicine",
"namespaceEmbeddedInLui": false,
"pattern": "^Y[A-Z]{2}\\d+[CW]$",
"prefix": "ydpm",
"uri_format": "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1"
},
"name": "Yeast Deletion and the Mitochondrial Proteomics Project",
"prefixcommons": {
"description": "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The database is hyperlinked with other public databases. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell",
"example": "YBL031W",
"homepage": "http://www-deletion.stanford.edu/YDPM/YDPM_index.html",
"keywords": [
"protein"
],
"name": "Yeast Deletion Project and Proteomics of Mitochondria Database",
"pattern": "^[A-Z,0-9]+$",
"prefix": "ydpm"
}
},
"yeastintron": {
"biocontext": {
"prefix": "YEASTINTRON"
},
"mappings": {
"biocontext": "YEASTINTRON",
"miriam": "yeastintron",
"n2t": "yeastintron"
},
"miriam": {
"deprecated": false,
"description": "The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460].",
"homepage": "http://intron.ucsc.edu/yeast4.3/",
"id": "00000521",
"name": "Yeast Intron Database v4.3",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]+$",
"prefix": "yeastintron",
"sampleId": "SNR17A",
"uri_format": "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1"
},
"n2t": {
"description": "The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460].",
"example": "SNR17A",
"homepage": "http://intron.ucsc.edu/yeast4.3/",
"name": "Yeast Intron Database version 4.3 at Baskin School of Engineering",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]+$",
"prefix": "yeastintron",
"uri_format": "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1"
}
},
"yeastract": {
"contact": {
"email": "isacorreia@tecnico.ulisboa.pt",
"name": "Isabel SΓ‘-Correia",
"orcid": "0000-0003-2208-5183"
},
"fairsharing": {
"abbreviation": "YEASTRACT",
"description": "YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references.",
"homepage": "http://www.yeastract.com",
"name": "Yeast Searching for Transcriptional Regulators and Consensus Tracking",
"prefix": "FAIRsharing.mphj4z",
"publications": [
{
"doi": "10.1093/nar/gkt1015",
"pubmed_id": 24170807,
"title": "The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae."
},
{
"doi": "10.1093/nar/gkj013",
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{
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{
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}
],
"subjects": [
"Life Science"
]
},
"mappings": {
"fairsharing": "FAIRsharing.mphj4z",
"pathguide": "205",
"prefixcommons": "yeastract"
},
"pathguide": {
"abbreviation": "YEASTRACT",
"homepage": "http://www.yeastract.com/",
"name": "YEAst Search for Transcriptional Regulators And Consensus Tracking",
"prefix": "205"
},
"prefixcommons": {
"description": "YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references.",
"example": "YBR125c",
"homepage": "http://www.yeastract.com",
"keywords": [
"regulation",
"DNA",
"small molecule",
"gene"
],
"name": "Yeast Searching for Transcriptional Regulators and Consensus Tracking",
"pattern": "^[A-Z,0-9]+$",
"prefix": "yeastract",
"uri_format": "http://www.yeastract.com/view.php?existing=locus&orfname=$1"
},
"publications": [
{
"doi": "10.1093/nar/gkt1015",
"pmc": "PMC3965121",
"pubmed": "24170807",
"title": "The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae",
"year": 2013
},
{
"doi": "10.1093/nar/gkq964",
"pmc": "PMC3013800",
"pubmed": "20972212",
"title": "YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface",
"year": 2010
},
{
"doi": "10.1093/nar/gkm976",
"pmc": "PMC2238916",
"pubmed": "18032429",
"title": "YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae",
"year": 2007
},
{
"doi": "10.1093/nar/gkj013",
"pmc": "PMC1347376",
"pubmed": "16381908",
"title": "The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae",
"year": 2006
}
],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"yetfasco": {
"biocontext": {
"prefix": "YETFASCO"
},
"mappings": {
"biocontext": "YETFASCO",
"miriam": "yetfasco",
"n2t": "yetfasco"
},
"miriam": {
"deprecated": false,
"description": "The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats.",
"homepage": "http://yetfasco.ccbr.utoronto.ca/",
"id": "00000339",
"name": "YeTFasCo",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+\\_\\d+(\\.\\d+)?$",
"prefix": "yetfasco",
"sampleId": "YOR172W_571.0",
"uri_format": "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1"
},
"n2t": {
"description": "The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats.",
"example": "YOR172W_571.0",
"homepage": "http://yetfasco.ccbr.utoronto.ca/",
"name": "YeTFasCo at University of Toronto",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+\\_\\d+(\\.\\d+)?$",
"prefix": "yetfasco",
"uri_format": "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1"
}
},
"ygob": {
"comment": "This resource doesn't exist on the web anymore",
"deprecated": true,
"mappings": {
"prefixcommons": "ygob"
},
"prefixcommons": {
"description": "YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes.",
"example": "ADH1",
"homepage": "http://wolfe.gen.tcd.ie/ygob",
"keywords": [
"gene",
"genome"
],
"name": "Yeast Genome Order Browser",
"pattern": "^[A-Z,0-9]+$",
"prefix": "ygob",
"uri_format": "http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene=$1"
},
"provides": "hgnc.symbol",
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
},
"yid": {
"biocontext": {
"prefix": "YID"
},
"mappings": {
"biocontext": "YID",
"miriam": "yid",
"n2t": "yid"
},
"miriam": {
"deprecated": false,
"description": "The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521].",
"homepage": "http://compbio.soe.ucsc.edu/yeast_introns.html",
"id": "00000460",
"name": "Yeast Intron Database v3",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]+$",
"prefix": "yid",
"sampleId": "SNR17A",
"uri_format": "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1"
},
"n2t": {
"description": "The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521].",
"example": "SNR17A",
"homepage": "http://compbio.soe.ucsc.edu/yeast_introns.html",
"name": "Yeast Intron Database version 3 at Baskin School of Engineering",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]+$",
"prefix": "yid",
"uri_format": "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1"
}
},
"ymdb": {
"contact": {
"email": "david.wishart@ualberta.ca",
"github": "DavidWishartLab",
"name": "David S. Wishart",
"orcid": "0000-0002-3207-2434"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Bakerβs yeast and Brewerβs yeast).",
"example": "YMDB00001",
"fairsharing": {
"abbreviation": "YMDB",
"description": "The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Bakerβs yeast and Brewerβs yeast). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions and other electronic databases.",
"homepage": "http://www.ymdb.ca",
"name": "The Yeast Metabolome Database",
"prefix": "FAIRsharing.tawpg2",
"publications": [
{
"doi": "10.1093/nar/gkr916",
"pubmed_id": 22064855,
"title": "YMDB: the Yeast Metabolome Database."
}
],
"subjects": [
"Life Science",
"Metabolomics"
],
"twitter": "WishartLab"
},
"homepage": "http://www.ymdb.ca",
"mappings": {
"fairsharing": "FAIRsharing.tawpg2",
"pathguide": "388",
"re3data": "r3d100012733"
},
"name": "Yeast Metabolome Database",
"pathguide": {
"abbreviation": "YMDB",
"homepage": "http://www.ymdb.ca/",
"name": "The Yeast Metabolome Database",
"prefix": "388"
},
"pattern": "^YMDB\\d+$",
"publications": [
{
"doi": "10.1093/nar/gkr916",
"pmc": "PMC3245085",
"pubmed": "22064855",
"title": "YMDB: the Yeast Metabolome Database",
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}
],
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"description": "The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Bakerβs yeast and Brewerβs yeast). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions and other electronic databases.",
"homepage": "https://www.ymdb.ca/",
"name": "The Yeast Metabolome Database",
"prefix": "r3d100012733",
"synonyms": [
"YMDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.tawpg2",
"scr": "005890"
}
},
"uri_format": "http://www.ymdb.ca/compounds/$1"
},
"ypo": {
"biocontext": {
"prefix": "YPO"
},
"mappings": {
"biocontext": "YPO",
"obofoundry": "ypo"
},
"name": "Yeast Phenotype Ontology",
"obofoundry": {
"contact": "cherry@genome.stanford.edu",
"contact.label": "Mike Cherry",
"contact.orcid": "0000-0001-9163-5180",
"deprecated": true,
"domain": "phenotype",
"homepage": "http://www.yeastgenome.org/",
"name": "Yeast phenotypes",
"prefix": "ypo"
},
"uri_format": "http://purl.obolibrary.org/obo/YPO_$1"
},
"yrcpdr": {
"biocontext": {
"prefix": "YRCPDR"
},
"fairsharing": {
"abbreviation": "YRC PDR",
"contact": {
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"name": "Michael Riffle",
"orcid": "0000-0003-1633-8607"
},
"description": "The National Center for Research Resources' Yeast Resource Center is located at the University of Washington in Seattle, Washington. The mission of the center is to facilitate the identification and characterization of protein complexes in the yeast Saccharomyces cerevisiae.",
"homepage": "http://www.yeastrc.org/pdr/",
"name": "Yeast Resource Center Public Data Repository",
"prefix": "FAIRsharing.karvzj",
"publications": [],
"subjects": [
"Computational Biology",
"Life Science"
]
},
"mappings": {
"biocontext": "YRCPDR",
"fairsharing": "FAIRsharing.karvzj",
"miriam": "yrcpdr",
"n2t": "yrcpdr",
"prefixcommons": "yrc",
"re3data": "r3d100010975"
},
"miriam": {
"deprecated": false,
"description": "The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions.",
"homepage": "http://www.yeastrc.org/pdr/",
"id": "00000459",
"name": "YRC PDR",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "yrcpdr",
"sampleId": "2673500",
"uri_format": "http://yeastrc.org/pdr/viewProtein.do?id=$1"
},
"n2t": {
"description": "The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions.",
"example": "2673500",
"homepage": "http://www.yeastrc.org/pdr/",
"name": "YRC PDR at University of Washington",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "yrcpdr",
"uri_format": "http://yeastrc.org/pdr/viewProtein.do?id=$1"
},
"prefixcommons": {
"description": "The National Center for Research Resources' Yeast Resource Center is located at the University of Washington in Seattle, Washington. The mission of the center is to facilitate the identification and characterization of protein complexes in the yeast Saccharomyces cerevisiae.",
"example": "846763",
"homepage": "http://www.yeastrc.org/pdr/",
"keywords": [
"protein"
],
"name": "Yeast Resource Center Public Data Repository",
"pattern": "^\\d+$",
"prefix": "yrc",
"uri_format": "http://www.yeastrc.org/pdr/viewProtein.do?id=$1"
},
"re3data": {
"description": "The Yeast Resource Center provides access to data about mass spectrometry, yeast two-hybrid arrays, deconvolution florescence microscopy, protein structure prediction and computational biology. These services are provided to further the goal of a complete understanding of the chemical interactions required for the maintenance and faithful reproduction of a living cell. The observation that the fundamental biological processes of yeast are conserved among all eukaryotes ensures that this knowledge will shape and advance our understanding of living systems.",
"homepage": "http://depts.washington.edu/yeastrc/",
"name": "Yeast Resource Center",
"prefix": "r3d100010975",
"synonyms": [
"Yeast Resource Center Public Data Repository"
],
"xrefs": {
"fairsharing": "FAIRsharing.karvzj",
"nif": "0000-03650",
"scr": "007942"
}
}
},
"zazuko": {
"contact": {
"email": "ktk@netlabs.org",
"github": "ktk",
"name": "Adrian Gschwend",
"orcid": "0000-0002-2079-9636"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "This service fills a gap between services like prefix.cc and LOV or looking up the original vocabulary specification. Not all vocabularies (or schema or ontology, whatever you want to call them) provide an HTML view. If you resolve some of the common prefixes all you get back is some RDF serialization which is not ideal. (from )",
"example": "frbr",
"homepage": "https://prefix.zazuko.com/",
"license": "MIT",
"name": "Zazuko Prefix Server",
"uri_format": "https://prefix.zazuko.com/prefix/$1:"
},
"zea": {
"aberowl": {
"download_obo": "http://aber-owl.net/media/ontologies/ZEA/2/zea.obo",
"homepage": "http://www.maizemap.org/",
"name": "Maize Gross Anatomy Ontology",
"prefix": "ZEA",
"version": "1.2"
},
"biocontext": {
"prefix": "ZEA"
},
"bioportal": {
"contact": {
"email": "Leszek@missouri.edu",
"name": "Leszek Vincent"
},
"homepage": "http://www.maizemap.org/",
"name": "Maize Gross Anatomy Ontology",
"prefix": "ZEA",
"version": "1.2"
},
"example": "0015177",
"mappings": {
"aberowl": "ZEA",
"biocontext": "ZEA",
"bioportal": "ZEA",
"obofoundry": "zea",
"prefixcommons": "zea"
},
"obofoundry": {
"contact": "Leszek@missouri.edu",
"contact.label": "Leszek Vincent",
"contact.orcid": "0000-0002-9316-2919",
"deprecated": true,
"domain": "anatomy and development",
"homepage": "http://www.maizemap.org/",
"name": "Maize gross anatomy",
"prefix": "zea"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1050",
"description": "Maize gross anatomy",
"example": "ZEA_0015177",
"homepage": "http://www.maizemap.org/",
"keywords": [
"obo",
"anatomy",
"maize"
],
"name": "Maize gross anatomy",
"pattern": "^ZEA_\\d{7}$",
"prefix": "zea"
}
},
"zeco": {
"aberowl": {
"description": "Experimental conditions applied to zebrafish, developed to facilitate experiment condition annotation at ZFIN",
"download_owl": "http://aber-owl.net/media/ontologies/ZECO/10/zeco.owl",
"homepage": "https://github.com/ybradford/zebrafish-experimental-conditions-ontology",
"name": "Zebrafish Experimental Conditions Ontology",
"prefix": "ZECO"
},
"biocontext": {
"prefix": "ZECO"
},
"bioportal": {
"contact": {
"email": "ybradford@zfin.org",
"name": "Yvonne Bradford"
},
"description": "This ontology is designed to represent the experimental conditions applied to zebrafish and has been developed to facilitate experiment condition annotation at ZFIN.",
"homepage": "https://github.com/ybradford/zebrafish-experimental-conditions-ontology",
"name": "Zebrafish Experimental Conditions Ontology",
"prefix": "ZECO",
"version": "2022-02-14"
},
"example": "0000171",
"fairsharing": {
"abbreviation": "ZECO",
"description": "This ontology is designed to represent the experimental conditions applied to zebrafish and has been developed to facilitate experiment condition annotation at ZFIN.",
"domains": [
"Expression data",
"Bibliography",
"Model organism",
"Disease process modeling",
"Mutation",
"Phenotype",
"Gene",
"Allele",
"Genome"
],
"homepage": "https://github.com/ybradford/zebrafish-experimental-conditions-ontology",
"name": "Zebrafish Experimental Conditions Ontology",
"prefix": "FAIRsharing.np2wfz",
"subjects": [
"Genomics",
"Animal Physiology",
"Genetics",
"Developmental Biology"
]
},
"mappings": {
"aberowl": "ZECO",
"biocontext": "ZECO",
"bioportal": "ZECO",
"fairsharing": "FAIRsharing.np2wfz",
"obofoundry": "zeco",
"ols": "zeco",
"ontobee": "ZECO"
},
"obofoundry": {
"appears_in": [
"mco"
],
"contact": "ybradford@zfin.org",
"contact.github": "ybradford",
"contact.label": "Yvonne Bradford",
"contact.orcid": "0000-0002-9900-7880",
"deprecated": false,
"description": "Experimental conditions applied to zebrafish, developed to facilitate experiment condition annotation at ZFIN",
"domain": "environment",
"download.json": "http://purl.obolibrary.org/obo/zeco.json",
"download.obo": "http://purl.obolibrary.org/obo/zeco.obo",
"download.owl": "http://purl.obolibrary.org/obo/zeco.owl",
"homepage": "https://github.com/ybradford/zebrafish-experimental-conditions-ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Zebrafish Experimental Conditions Ontology",
"preferredPrefix": "ZECO",
"prefix": "zeco",
"repository": "https://github.com/ybradford/zebrafish-experimental-conditions-ontology"
},
"ols": {
"description": "Ontology of Zebrafish Experimental Conditions",
"download_owl": "http://purl.obolibrary.org/obo/zeco.owl",
"homepage": "https://github.com/ybradford/zebrafish-experimental-conditions-ontology",
"name": "Zebrafish Experimental Conditions Ontology",
"prefix": "zeco",
"version": "2022-02-14",
"version.iri": "http://purl.obolibrary.org/obo/zeco/releases/2022-02-14/zeco.owl"
},
"ontobee": {
"library": "Library",
"name": "Zebrafish Experimental Conditions Ontology",
"prefix": "ZECO"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/ZECO_$1"
},
"zenodo.record": {
"contributor": {
"email": "benjamin_gyori@hms.harvard.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"description": "Zenodo is an open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts.",
"example": "4390079",
"fairsharing": {
"abbreviation": "Zenodo",
"contact": {
"email": "lars.holm.nielsen@cern.ch",
"name": "Lars Holm Nielsen",
"orcid": "0000-0001-8135-3489"
},
"description": "Zenodo is a generalist research data repository built and developed by OpenAIRE and CERN. It was developed to aid Open Science and is built on open source code. Zenodo helps researchers receive credit by making the research results citable and through OpenAIRE integrates them into existing reporting lines to funding agencies like the European Commission. Citation information is also passed to DataCite and onto the scholarly aggregators. Content is available publicly under any one of 400 open licences (from opendefinition.org and spdx.org). Restricted and Closed content is also supported. Free for researchers below 50 GB/dataset. Content is both online on disk and offline on tape as part of a long-term preservation policy. Zenodo supports managed access (with an access request workflow) as well as embargoing generally and during peer review. The base infrastructure of Zenodo is provided by CERN, a non-profit IGO. Projects are funded through grants.",
"homepage": "https://www.zenodo.org",
"license": "http://about.zenodo.org/policies",
"name": "Zenodo",
"prefix": "FAIRsharing.wy4egf",
"publications": [],
"subjects": [
"Data Management",
"Subject Agnostic"
],
"twitter": "zenodo_org"
},
"github_request_issue": 454,
"homepage": "https://zenodo.org",
"integbio": {
"description": "Generalist research data repository built and developed by OpenAIRE and CERN, to ensure that everyone can join in Open Science.",
"fairsharing": "FAIRsharing.wy4egf",
"homepage": "https://www.zenodo.org",
"information_keywords": [
"Bibliography/Documents",
"Repository"
],
"maintainer": "CERN (European Organisation for Nuclear Research)",
"name": "Zenodo",
"prefix": "nbdc02187",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"mappings": {
"fairsharing": "FAIRsharing.wy4egf",
"integbio": "nbdc02187",
"re3data": "r3d100010468",
"wikidata": "P4901"
},
"name": "Zenodo",
"pattern": "^\\d+$",
"re3data": {
"description": "ZENODO builds and operates a simple and innovative service that enables researchers, scientists, EU projects and institutions to share and showcase multidisciplinary research results (data and publications) that are not part of the existing institutional or subject-based repositories of the research communities.\nZENODO enables researchers, scientists, EU projects and institutions to:\neasily share the long tail of small research results in a wide variety of formats including text, spreadsheets, audio, video, and images across all fields of science.\ndisplay their research results and get credited by making the research results citable and integrate them into existing reporting lines to funding agencies like the European Commission.\neasily access and reuse shared research results.",
"homepage": "https://zenodo.org/",
"name": "Zenodo",
"prefix": "r3d100010468",
"xrefs": {
"fairsharing": "FAIRsharing.wy4egf",
"nlx": "158614",
"scr": "004129"
}
},
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"synonyms": [
"zenodo"
],
"uri_format": "https://zenodo.org/record/$1",
"wikidata": {
"description": "ID of a work in Zenodo repository",
"example": [
"1038611",
"1481308"
],
"name": "Zenodo ID",
"pattern": "^[1-9]\\d+$",
"prefix": "P4901",
"uri_format": "https://zenodo.org/record/$1"
}
},
"zfa": {
"aberowl": {
"description": "A structured controlled vocabulary of the anatomy and development of the Zebrafish",
"download_owl": "http://aber-owl.net/media/ontologies/ZFA/87/zfa.owl",
"homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources",
"name": "Zebrafish anatomy and development ontology",
"prefix": "ZFA"
},
"biocontext": {
"prefix": "ZFA"
},
"bioportal": {
"contact": {
"email": "zfinadmin@zfin.org",
"name": "ZFIN administrators"
},
"description": "A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio).",
"homepage": "http://zfin.org/zf_info/anatomy/dict/sum.html",
"name": "Zebrafish Anatomy and Development Ontology",
"prefix": "ZFA",
"publication": "http://www.jbiomedsem.com/content/5/1/12",
"version": "releases/2022-12-09"
},
"download_json": "http://purl.obolibrary.org/obo/zfa.json",
"example": "0005926",
"fairsharing": {
"abbreviation": "ZFA",
"description": "A structured controlled vocabulary of the anatomy and development of the Zebrafish. If you work on the project responsible for \"Zebrafish anatomy and development\" then please consider helping us by claiming this record and updating it appropriately.",
"domains": [
"Morphology",
"Structure",
"Life cycle",
"Life cycle stage"
],
"homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources",
"name": "Zebrafish anatomy and development",
"prefix": "FAIRsharing.s3r6sk",
"publications": [
{
"doi": "10.1186/2041-1480-5-12",
"pubmed": "24568621",
"title": "The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio",
"year": 2014
}
],
"subjects": [
"Anatomy",
"Developmental Biology",
"Life Science"
]
},
"mappings": {
"aberowl": "ZFA",
"biocontext": "ZFA",
"bioportal": "ZFA",
"fairsharing": "FAIRsharing.s3r6sk",
"obofoundry": "zfa",
"ols": "zfa",
"ontobee": "ZFA",
"prefixcommons": "zfa"
},
"obofoundry": {
"appears_in": [
"zp"
],
"contact": "van_slyke@zfin.org",
"contact.github": "cerivs",
"contact.label": "Ceri Van Slyke",
"contact.orcid": "0000-0002-2244-7917",
"deprecated": false,
"description": "A structured controlled vocabulary of the anatomy and development of the Zebrafish",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/zfa.obo",
"download.owl": "http://purl.obolibrary.org/obo/zfa.owl",
"homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Zebrafish anatomy and development ontology",
"preferredPrefix": "ZFA",
"prefix": "zfa",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/24568621",
"title": "The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio."
}
],
"repository": "https://github.com/cerivs/zebrafish-anatomical-ontology"
},
"ols": {
"description": "ZFA description.",
"download_owl": "http://purl.obolibrary.org/obo/zfa.owl",
"homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources",
"name": "Zebrafish Anatomy Ontology (ZFA)",
"prefix": "zfa",
"version": "2022-12-09",
"version.iri": "http://purl.obolibrary.org/obo/zfa/releases/2022-12-09/zfa.owl"
},
"ontobee": {
"library": "Foundry",
"name": "Zebrafish anatomy and development ontology",
"prefix": "ZFA"
},
"pattern": "^\\d{7}$",
"prefixcommons": {
"bioportal": "1051",
"description": "A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio).",
"example": "ZFS_0000011",
"homepage": "http://zfin.org/zf_info/anatomy/dict/sum.html",
"keywords": [
"obo",
"anatomy",
"zebrafish"
],
"name": "Zebrafish anatomy and development Ontology",
"pattern": "^ZFS_\\d{7}$",
"prefix": "zfa"
},
"publications": [
{
"doi": "10.1186/2041-1480-5-12",
"pmc": "PMC3944782",
"pubmed": "24568621",
"title": "The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio",
"year": 2014
}
],
"synonyms": [
"ZFA_RETIRED"
],
"uri_format": "http://purl.obolibrary.org/obo/ZFA_$1"
},
"zfin": {
"biocontext": {
"prefix": "ZFIN",
"uri_format": "http://zfin.org/$1"
},
"fairsharing": {
"abbreviation": "ZFIN",
"contact": {
"email": "dhowe@zfin.org",
"name": "Doug Howe",
"orcid": "0000-0001-5831-7439"
},
"description": "The Zebrafish Information Network, ZFIN, serves as the primary community database resource for the laboratory use of zebrafish. We develop and support integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases.",
"homepage": "https://zfin.org/",
"name": "The Zebrafish Information Network",
"prefix": "FAIRsharing.ybxnhg",
"publications": [
{
"doi": "10.1093/nar/gkj086",
"pubmed_id": 16381936,
"title": "The Zebrafish Information Network: the zebrafish model organism database."
},
{
"doi": "10.1093/nar/gkq1077",
"pubmed_id": 21036866,
"title": "ZFIN: enhancements and updates to the Zebrafish Model Organism Database."
},
{
"doi": "10.1093/nar/gkg027",
"pubmed_id": 12519991,
"title": "The Zebrafish Information Network (ZFIN): the zebrafish model organism database."
},
{
"doi": "10.1016/s0168-9525(99)01741-2",
"pubmed_id": 10354586,
"title": "Zebrafish in the Net."
},
{
"doi": "10.1002/0471250953.bi0118s31.",
"pubmed_id": 20836073,
"title": "Exploring zebrafish genomic, functional and phenotypic data using ZFIN."
},
{
"doi": "10.1016/B978-0-12-374814-0.00017-3",
"pubmed_id": 21924170,
"title": "Data extraction, transformation, and dissemination through ZFIN."
},
{
"doi": "10.1093/nar/gky1090",
"pubmed_id": 30407545,
"title": "The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources."
},
{
"doi": "10.1093/nar/gks938",
"pubmed_id": 23074187,
"title": "ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics."
},
{
"doi": "10.1093/nar/gkm956",
"pubmed_id": 17991680,
"title": "The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes."
}
],
"subjects": [
"Genomics",
"Animal Physiology",
"Genetics",
"Developmental Biology"
],
"twitter": "zfinmod"
},
"go": {
"homepage": "http://zfin.org/",
"name": "Zebrafish Information Network",
"prefix": "ZFIN"
},
"integbio": {
"alt_name": "The Zebrafish Model Organism Database",
"description": "ZFIN is a central repository and web-based resource for zebrafish genetics and development. This database contains manually curated data for zebrafish genes, phenotypes, genotypes, gene expression, antibodies, anatomical structures and publications from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. The database also contains a wide-ranging collection of web-based search forms and tools facilitates access to integrated views of these data promoting analysis and scientific discovery. ZFIN works closely with ZIRC to connect their genetic data with available probes and fish lines.",
"fairsharing": "biodbcore-000575",
"homepage": "http://zfin.org/",
"information_keywords": [
"Bioresource",
"Ontology/Terminology/Nomenclature",
"Sequence",
"Expression",
"Bibliography/Documents",
"Repository"
],
"maintainer": "University of Oregon/Zebrafish Information Network",
"name": "ZFIN",
"prefix": "nbdc00746",
"pubmeds": [
"21036866",
"17991680",
"11125057",
"10354586",
"9891346",
"9441953"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"Protein",
"Organism"
]
},
"mappings": {
"biocontext": "ZFIN",
"fairsharing": "FAIRsharing.ybxnhg",
"go": "ZFIN",
"integbio": "nbdc00746",
"miriam": "zfin",
"n2t": "zfin",
"ncbi": "ZFIN",
"prefixcommons": "zfin",
"re3data": "r3d100010421",
"rrid": "ZIRC",
"uniprot": "DB-0113",
"wikidata": "P3870"
},
"miriam": {
"deprecated": false,
"description": "ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN.",
"homepage": "http://zfin.org",
"id": "00000079",
"name": "ZFIN Bioentity",
"namespaceEmbeddedInLui": false,
"pattern": "^ZDB\\-\\w+\\-\\d+\\-\\d+$",
"prefix": "zfin",
"providers": [
{
"code": "agr",
"description": "ZFIN through the Alliance of Genome Resources",
"homepage": "https://www.alliancegenome.org",
"name": "ZFIN through the Alliance of Genome Resources",
"uri_format": "https://test.alliancegenome.org/gene/ZFIN:$1"
}
],
"sampleId": "ZDB-GENE-041118-11",
"uri_format": "http://zfin.org/$1"
},
"n2t": {
"description": "ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN.",
"example": "ZDB-GENE-041118-11",
"homepage": "http://zfin.org",
"name": "ZFIN at University of Oregon",
"namespaceEmbeddedInLui": false,
"pattern": "^ZDB\\-\\w+\\-\\d+\\-\\d+$",
"prefix": "zfin",
"uri_format": "http://zfin.org/$1"
},
"name": "Zebrafish Information Network Gene",
"ncbi": {
"example": "ZDB-GENE-011205-17",
"homepage": "http://zfin.org",
"name": "Zebrafish Information Network",
"prefix": "ZFIN"
},
"prefixcommons": {
"description": "ZFIN serves as the zebrafish model organism database.",
"example": "ZDB-GENE-041118-11",
"homepage": "http://zfin.org/",
"keywords": [
"zebrafish",
"gene",
"genome"
],
"name": "Zebrafish Information Network genome database",
"pattern": "^ZDB\\-GENE\\-\\d+\\-\\d+$",
"prefix": "zfin",
"pubmed_ids": [
"17991680"
],
"uri_format": "http://zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID=$1"
},
"publications": [
{
"doi": "10.1093/nar/gky1090",
"pmc": "PMC6323962",
"pubmed": "30407545",
"title": "The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources",
"year": 2019
},
{
"doi": "10.1093/nar/gks938",
"pubmed": "23074187",
"title": "ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics"
},
{
"doi": "10.1016/b978-0-12-374814-0.00017-3",
"pubmed": "21924170",
"title": "Data extraction, transformation, and dissemination through ZFIN"
},
{
"doi": "10.1093/nar/gkq1077",
"pubmed": "21036866",
"title": "ZFIN: enhancements and updates to the Zebrafish Model Organism Database"
},
{
"doi": "10.1002/0471250953.bi0118s31.",
"pubmed": "20836073",
"title": "Exploring zebrafish genomic, functional and phenotypic data using ZFIN"
},
{
"doi": "10.1093/nar/gkm956",
"pmc": "PMC2238839",
"pubmed": "17991680",
"title": "The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes",
"year": 2007
},
{
"doi": "10.1093/nar/gkj086",
"pubmed": "16381936",
"title": "The Zebrafish Information Network: the zebrafish model organism database"
},
{
"doi": "10.1093/nar/gkg027",
"pubmed": "12519991",
"title": "The Zebrafish Information Network (ZFIN): the zebrafish model organism database"
},
{
"doi": "10.1016/s0168-9525(99)01741-2",
"pubmed": "10354586",
"title": "Zebrafish in the Net"
}
],
"re3data": {
"description": "ZFIN serves as the zebrafish model organism database. The long term goals for ZFIN are a) to be the community database resource for the laboratory use of zebrafish, b) to develop and support integrated zebrafish genetic, genomic and developmental information, c) to maintain the definitive reference data sets of zebrafish research information, d) to link this information extensively to corresponding data in other model organism and human databases, e) to facilitate the use of zebrafish as a model for human biology and f) to serve the needs of the research community.\nZIRC is the Zebrafish International Resource Center, an independent NIH-funded facility providing a wide range of zebrafish lines, probes and health services. ZFIN works closely with ZIRC to connect our genetic data with available probes and fish lines.",
"homepage": "https://zfin.org/",
"name": "The Zebrafish Information Network",
"prefix": "r3d100010421",
"synonyms": [
"The zebrafish model organism database (formerly)",
"ZFIN"
],
"xrefs": {
"fairsharing": "FAIRsharing.ybxnhg",
"nif": "0000-21427",
"omics": "01666",
"scr": "002560"
}
},
"rrid": {
"homepage": "http://zebrafish.org",
"keywords": [
"adult",
"antibody",
"cdna",
"embryo",
"expressed sequence tag",
"fish",
"pathology",
"research",
"zebrafish line"
],
"name": "Zebrafish International Resource Center",
"prefix": "ZIRC",
"scr": "005065",
"twitter": "ZFINmod"
},
"synonyms": [
"ZFIN"
],
"uniprot": {
"abbreviation": "ZFIN",
"category": "Organism-specific databases",
"homepage": "https://zfin.org/",
"name": "Zebrafish Information Network genome database",
"prefix": "DB-0113",
"publications": [
{
"doi": "10.1093/nar/gky1090",
"pubmed": "30407545"
}
],
"uri_format": "https://zfin.org/$1"
},
"wikidata": {
"description": "identifier for a genetic element in the Zebrafish Model Organism Database",
"example": [
"ZDB-GENE-030131-1564",
"ZDB-GENE-080416-2",
"ZDB-GENE-980526-388"
],
"homepage": "http://zfin.org",
"name": "ZFIN Gene ID",
"prefix": "P3870",
"uri_format": "https://zfin.org/$1"
}
},
"zfs": {
"aberowl": {
"description": "Developmental stages of the Zebrafish",
"download_owl": "http://aber-owl.net/media/ontologies/ZFS/9/zfs.owl",
"homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources",
"name": "Zebrafish developmental stages ontology",
"prefix": "ZFS"
},
"biocontext": {
"prefix": "ZFS"
},
"bioportal": {
"contact": {
"email": "zfinadmin@zfin.org",
"name": "ZFIN administrators"
},
"description": "An ontology of developmental stages of the Zebrafish (Danio rerio). Note that ZFA includes the leaf nodes of this ontology.",
"name": "Zebrafish Developmental Stages",
"prefix": "ZFS"
},
"example": "0000050",
"fairsharing": {
"abbreviation": "ZFS",
"description": "An ontology of developmental stages of the Zebrafish (Danio rerio). Note that ZFA includes the leaf nodes of this ontology.",
"domains": [
"Aging",
"Life cycle"
],
"homepage": "http://bioportal.bioontology.org/ontologies/ZFS",
"name": "Zebrafish Developmental Stages",
"prefix": "FAIRsharing.bc8ayj",
"subjects": [
"Anatomy",
"Zoology",
"Marine Biology",
"Developmental Biology"
]
},
"mappings": {
"aberowl": "ZFS",
"biocontext": "ZFS",
"bioportal": "ZFS",
"fairsharing": "FAIRsharing.bc8ayj",
"obofoundry": "zfs",
"ols": "zfs",
"ontobee": "ZFS"
},
"obofoundry": {
"contact": "van_slyke@zfin.org",
"contact.github": "cerivs",
"contact.label": "Ceri Van Slyke",
"contact.orcid": "0000-0002-2244-7917",
"deprecated": false,
"description": "Developmental stages of the Zebrafish",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/zfs.obo",
"download.owl": "http://purl.obolibrary.org/obo/zfs.owl",
"homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Zebrafish developmental stages ontology",
"preferredPrefix": "ZFS",
"prefix": "zfs",
"repository": "https://github.com/cerivs/zebrafish-anatomical-ontology"
},
"ols": {
"description": "Developmental stages of the Zebrafish",
"download_owl": "http://purl.obolibrary.org/obo/zfs.owl",
"homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources",
"name": "Zebrafish developmental stages ontology",
"prefix": "zfs",
"version": "2020-03-10",
"version.iri": "http://purl.obolibrary.org/obo/zfs/releases/2020-03-10/zfs.owl"
},
"ontobee": {
"library": "Library",
"name": "Zebrafish developmental stages ontology",
"prefix": "ZFS"
},
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/ZFS_$1"
},
"zinc": {
"biocontext": {
"prefix": "ZINC"
},
"mappings": {
"biocontext": "ZINC",
"miriam": "zinc",
"n2t": "zinc",
"re3data": "r3d100010372",
"wikidata": "P2084"
},
"miriam": {
"deprecated": false,
"description": "ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number.",
"homepage": "http://zinc15.docking.org/",
"id": "00000529",
"name": "ZINC",
"namespaceEmbeddedInLui": false,
"pattern": "^(ZINC)?\\d+$",
"prefix": "zinc",
"sampleId": "ZINC1084",
"uri_format": "http://zinc15.docking.org/substances/$1"
},
"n2t": {
"description": "ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number.",
"example": "ZINC1084",
"homepage": "http://zinc15.docking.org/",
"name": "ZINC at University of California (San Francisco)",
"namespaceEmbeddedInLui": false,
"pattern": "^(ZINC)?\\d+$",
"prefix": "zinc",
"uri_format": "http://zinc15.docking.org/substances/$1"
},
"name": "ZINC is not Commercial",
"re3data": {
"description": "The ZINC Database contains commercially available compounds for structure based virtual screening. It currently has compounds that can simply be purchased. It is provided in ready-to-dock, 3D formats with molecules represented in biologically relevant forms. It is available in subsets for general screening as well as target-, chemotype- and vendor-focused subsets. ZINC is free for everyone to use and download at the website zinc.docking.org.",
"homepage": "https://cartblanche22.docking.org/",
"name": "ZINC",
"prefix": "r3d100010372",
"synonyms": [
"CartBlanche"
],
"xrefs": {
"nif": "0000-31930",
"scr": "008596"
}
},
"wikidata": {
"description": "identifier for a chemical compound in the ZINC database",
"example": [
"13476531",
"1562396",
"6032158"
],
"homepage": "http://zinc.docking.org/",
"name": "ZINC ID",
"pattern": "^\\d{5,10}$",
"prefix": "P2084",
"uri_format": "http://zinc.docking.org/substances/ZINC$1"
}
},
"zp": {
"aberowl": {
"description": "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.",
"download_owl": "http://aber-owl.net/media/ontologies/ZP/10/zp.owl",
"homepage": "https://github.com/obophenotype/zebrafish-phenotype-ontology",
"name": "Zebrafish Phenotype Ontology",
"prefix": "ZP"
},
"biocontext": {
"prefix": "ZP"
},
"bioportal": {
"contact": {
"email": "ybradford@zfin.org",
"name": "Yvonne Bradford"
},
"description": "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.",
"homepage": "https://github.com/obophenotype/zebrafish-phenotype-ontology",
"name": "Zebrafish Phenotype Ontology",
"prefix": "ZP",
"version": "2024-04-18"
},
"example": "0019030",
"mappings": {
"aberowl": "ZP",
"biocontext": "ZP",
"bioportal": "ZP",
"obofoundry": "zp",
"ols": "zp",
"ontobee": "ZP"
},
"obofoundry": {
"contact": "ybradford@zfin.org",
"contact.github": "ybradford",
"contact.label": "Yvonne Bradford",
"contact.orcid": "0000-0002-9900-7880",
"depends_on": [
"bfo",
"bspo",
"go",
"pato",
"ro",
"uberon",
"zfa"
],
"deprecated": false,
"description": "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.",
"domain": "phenotype",
"download.obo": "http://purl.obolibrary.org/obo/zp.obo",
"download.owl": "http://purl.obolibrary.org/obo/zp.owl",
"homepage": "https://github.com/obophenotype/zebrafish-phenotype-ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Zebrafish Phenotype Ontology",
"preferredPrefix": "ZP",
"prefix": "zp",
"repository": "https://github.com/obophenotype/zebrafish-phenotype-ontology"
},
"ols": {
"description": "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.",
"download_owl": "http://purl.obolibrary.org/obo/zp.owl",
"homepage": "https://github.com/obophenotype/zebrafish-phenotype-ontology",
"name": "Zebrafish Phenotype Ontology (ZP)",
"prefix": "zp",
"version": "2024-04-18",
"version.iri": "http://purl.obolibrary.org/obo/zp/releases/2024-04-18/zp.owl"
},
"ontobee": {
"library": "Library",
"name": "Zebrafish Phenotype Ontology",
"prefix": "ZP"
},
"pattern": "^\\d+$",
"uri_format": "http://purl.obolibrary.org/obo/ZP_$1"
}
} ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723255146.0
bioregistry-0.11.12/src/bioregistry/data/collections.json 0000644 0001751 0000177 00000033737 14655544552 023132 0 ustar 00runner docker {
"collections": [
{
"authors": [
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"description": "These resources were listed in [Sharing biological data: why, when, and how](https://doi.org/10.1002/1873-3468.14067), which prompted further novel curation of the Bioregistry which included the addition of GenBank, Panorama Public, EMPIAR, and SSBD. It also prompted the curation of mappings to FAIRSharing when possible.",
"identifier": "0000001",
"name": "Resources mentioned in \"Sharing biological data: why, when, and how\"",
"resources": [
"biostudies",
"bmrb",
"cellimage",
"ega.dataset",
"ega.study",
"emdb",
"empiar",
"genbank",
"geo",
"idr",
"insdc.sra",
"massive",
"panorama",
"pdb",
"peptideatlas.dataset",
"pride",
"ssbd.dataset",
"ssbd.project"
]
},
{
"authors": [
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"context": "semweb",
"description": "Resources used in the semantic web, drawing from lists in [BioContext](https://github.com/prefixcommons/biocontext/blob/master/registry/semweb_context.yaml) and [LinkML](https://github.com/linkml/prefixmaps/blob/main/src/prefixmaps/data/linked_data.curated.yaml) as well as W3C recommendations.",
"identifier": "0000002",
"name": "Semantic Web Context",
"resources": [
"ac",
"bibo",
"dc",
"dcat",
"dcterms",
"dctypes",
"doap",
"faldo",
"foaf",
"idot",
"oa",
"oboinowl",
"oslc",
"owl",
"pav",
"prov",
"qb",
"qudt",
"rdf",
"rdfs",
"schema",
"sh",
"shex",
"skos",
"skosxl",
"swrl",
"vann",
"void",
"xsd"
]
},
{
"authors": [
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"description": "The data sources used in xrefs in the ChEBI ontology. More information in the \"Data Sources\" section of [this document](https://docs.google.com/document/d/13_FqP_8qkDdw5RFv5qMYo7xRyfY4xUiuVtLn845A6Io/edit#heading=h.dkfn7xf53tpx).",
"identifier": "0000003",
"name": "ChEBI Data Sources",
"resources": [
"chebi",
"chemidplus",
"come",
"drugbank",
"ecmdb",
"eurofir",
"google.patent",
"hmdb",
"kegg.compound",
"kegg.drug",
"kegg.glycan",
"knapsack",
"lincs.smallmolecule",
"lipidmaps",
"metacyc.compound",
"molbase.sheffield",
"pdb",
"pdb-ccd",
"pesticides",
"resid",
"smid",
"umbbd.compound",
"webelements",
"ymdb"
]
},
{
"authors": [
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"description": "This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions.",
"identifier": "0000004",
"name": "International Classifications of Diseases",
"resources": [
"icd10",
"icd10cm",
"icd10pcs",
"icd11",
"icd9",
"icd9cm",
"icdo"
]
},
{
"authors": [
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"description": "This collection contains various brain atlases from the Allen Institute.",
"identifier": "0000005",
"name": "Allen Institute Ontologies",
"resources": [
"dhba",
"dmba",
"hba",
"mba",
"pba"
]
},
{
"authors": [
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"context": "spar",
"description": "The [Semantic Publishing and Referencing (SPAR) Ontologies](http://www.sparontologies.net/ontologies) are a suite of orthogonal and complementary OWL 2 ontologies that enable all aspects of the publishing process to be described in machine-readable metadata statements, encoded using RDF.",
"identifier": "0000006",
"name": "SPAR Ontologies",
"resources": [
"bido",
"biro",
"c4o",
"cito",
"datacite",
"deo",
"doco",
"fabio",
"frapo",
"pso",
"puro",
"pwo",
"scoro"
]
},
{
"authors": [
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"description": "Prefixes useful in annotating documentation provenance.",
"identifier": "0000007",
"name": "Publication Provenance Prefixes",
"resources": [
"arxiv",
"doi",
"pmc",
"pubmed"
]
},
{
"authors": [
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"description": "Prefixes exported for the epidemiology domain knowledge graph in the ASKEM project.",
"identifier": "0000008",
"name": "ASKEM Epidemiology Prefixes",
"resources": [
"bfo",
"caro",
"doi",
"doid",
"dso",
"hp",
"ido",
"oae",
"oboinowl",
"ovae",
"owl",
"pmc",
"pubmed",
"rdfs",
"ro",
"symp",
"trans",
"vo"
]
},
{
"authors": [
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"description": "Prefixes mentioned on the _external_ list on the FHIR [Code Systems](https://hl7.org/fhir/terminologies-systems.html) page. This list is mostly complete. Notably, some entries that have not been curated:\n\n- HGVS (see discussion at [#460](https://github.com/biopragmatics/bioregistry/issues/460))\n- [NUBC](http://www.nubc.org) (National Uniform Billing Committee) - could not find information about the terminology or its entries\n- [ICPC](http://www.ph3c.org/) (International Classification of Primary Care) _same_\n- [GTIN](https://www.gs1.org/standards/id-keys/gtin) (Global Trade Item Number) _same_\n- [MDC](https://www.iso.org/standard/37890.html) (Medical Device Codes) since that appears to be part of a larger ISO standard vocabulary that needs further investigation",
"identifier": "0000009",
"name": "FHIR External Terminologies",
"resources": [
"atcc",
"clinicaltrials",
"clinvar",
"cosmic",
"cpt",
"cvx",
"dbsnp",
"dicom",
"dsm5",
"ensembl",
"hc.din",
"hc.npn",
"hgnc",
"hl7.v2codesystem",
"hl7.v3codesystem",
"icd10",
"icd9",
"icf",
"ietf.language",
"imgt.hla",
"iso.3166",
"loinc",
"lrg",
"ncit",
"ndc",
"ndfrt",
"nucc.taxonomy",
"omim",
"pharmgkb.gene",
"pubmed",
"radlex",
"refseq",
"rxnorm",
"snomedct",
"so",
"ucum",
"unii"
]
},
{
"authors": [
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"description": "The [Global Biodata Coalition](https://globalbiodata.org) released a [curated list](https://globalbiodata.org/scientific-activities/global-core-biodata-resources/) of 37 life sciences databases in December 2022 that they consider as having significant importance (see criteria [here](https://doi.org/10.5281/zenodo.5845116)). While it's not a primary goal of the Bioregistry to cover life science databases (other resources like Wikidata and [FAIRsharing](https://fairsharing.org) already do an excellent job of this), many notable databases induce one or more semantic spaces that are relevant for curation and prefix assignment in the Bioregistry. Therefore, a large number of the resources in this list correspond 1-to-1 with prefixes in the Bioregistry, a small number (e.g., Orphanet, CIViC, PharmGKB) correspond to multiple prefixes, some have a complicated relationship with many-to-1 relationships to prefixes (DNA Data Bank of Japan, European Nucleotide Archive), and some constitute databases that simply reuse other key vocabularies (e.g., STRING reuses UniProt, GWAS Catalog reuses dbSNP and EFO). Among the databases that don't induce semantic spaces or have simple relationships to prefixes are:\n\n- [Clinical Genome Resource](https://www.clinicalgenome.org/) (uses HGNC, MONDO, PharmGKB, etc.)\n- [DNA Data Bank of Japan](https://www.ddbj.nig.ac.jp/) (uses INSDC)\n- [GENCODE](https://www.gencodegenes.org/) (uses GenBank)\n- [GWAS Catalog](https://www.ebi.ac.uk/gwas/) (uses dbSNP, EFO, etc)\n- [STRING](https://string-db.org/) (uses UniProt)",
"identifier": "0000010",
"name": "Global Biodata Coalition - Global Core Biodata Resources",
"resources": [
"agrkb",
"bacdive",
"brenda",
"brenda.ligand",
"brenda.ligandgroup",
"bto",
"chebi",
"chembl",
"civic.aid",
"civic.did",
"civic.eid",
"civic.gid",
"civic.sid",
"civic.tid",
"civic.vid",
"ecocyc",
"ena.embl",
"ensembl",
"eupath",
"flybase",
"gbif",
"gnomad",
"go",
"hgnc",
"interpro",
"mgi",
"orphanet",
"orphanet.ordo",
"panther.family",
"panther.node",
"panther.pathway",
"panther.pthcmp",
"pdb",
"pharmgkb.disease",
"pharmgkb.drug",
"pharmgkb.gene",
"pharmgkb.pathways",
"pmc",
"pombase",
"px",
"reactome",
"rgd",
"rhea",
"sgd",
"ucsc",
"uniprot",
"wormbase",
"zfin"
]
},
{
"authors": [
{
"email": "hendrik.borgelt@tu-dortmund.de",
"github": "HendrikBorgelt",
"name": " Hendrik Borgelt",
"orcid": "0000-0001-5886-7860"
},
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"description": "A collection of ontologies relevant for chemistry.\n\nThe NFDI program deploys a [custom instance](https://terminology.tib.eu/ts/ontologies?collection=NFDI4CAT&and=false&page=1) of the Ontology Lookup Service (OLS) that provides the ontologies in this list.\n\nA further analysis of the metadata landscape of the ontologies in this list can be found [here](https://github.com/nfdi4cat/Ontology-Overview-of-NFDI4Cat).\n\nOntoCompChem and OntoKin appear on the NFDI4Cat list but have not yet been registered in the Bioregistry because the resources are missing/incomplete such that they do not meet minimum Bioregistry metadata standards. These might be added in the future if additional metadata can be found.",
"identifier": "0000011",
"name": "NDFI4Cat Collection",
"references": [
"https://nfdi4cat.org/services/ontologie-sammlung/",
"https://terminology.tib.eu/ts/ontologies?collection=NFDI4CAT&and=false&page=1",
"https://github.com/nfdi4cat/Ontology-Overview-of-NFDI4Cat"
],
"resources": [
"afo",
"bfo",
"cao",
"chebi",
"cheminf",
"chmo",
"dolce",
"emmo",
"emmo.cif",
"iso15926",
"nfdi4chem.ontocape",
"nfdi4chem.osmo",
"rex",
"rxno",
"sbo",
"voc4cat"
]
},
{
"authors": [
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"description": "A collection of clinical trial registries appearing in the World Health Organization's [International Clinical Trials Registry Platform (ICTRP)](https://trialsearch.who.int/)",
"identifier": "0000012",
"name": "Clinical Trial Registries",
"resources": [
"anzctr",
"chictr",
"clinicaltrials",
"ctis",
"ctri",
"drks",
"euclinicaltrials",
"hc.trial",
"irct",
"isrctn",
"itmctr",
"jrct",
"kcris",
"lbctr",
"pactr",
"phrr",
"rebec",
"repec",
"rpcec",
"slctr",
"snctp",
"tctr",
"uminctr"
]
},
{
"authors": [
{
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
}
],
"description": "These resources represent software repositories",
"identifier": "0000013",
"name": "Software Package Repositories",
"resources": [
"cran",
"crates",
"npm",
"packagist",
"pypi",
"rubygems"
]
}
]
} ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723255146.0
bioregistry-0.11.12/src/bioregistry/data/contexts.json 0000644 0001751 0000177 00000002550 14655544552 022450 0 ustar 00runner docker {
"obo": {
"blacklist": [
"icd9"
],
"custom_prefix_map": {
"PMID": "https://www.ncbi.nlm.nih.gov/pubmed/"
},
"description": "The OBO Context exists for the following reasons:\n\n- Reconciling \"database cross-references\" used by OBO ontologies and centralising their validation.\n- Standardising and validating SSSOM mappings provided in the context of OBO ontologies.\n- Providing an incentive for the documentation of non-standard prefixes for OBO ontologies.",
"include_synonyms": false,
"maintainers": [
{
"github": "matentzn",
"name": "Nico Matentzoglu",
"orcid": "0000-0002-7356-1779"
},
{
"email": "anitac@ebi.ac.uk",
"github": "anitacaron",
"name": "Anita Caron",
"orcid": "0000-0002-6523-4866"
}
],
"name": "Open Biomedical Ontologies Context",
"prefix_priority": [
"obofoundry.preferred",
"preferred",
"obofoundry",
"default"
],
"prefix_remapping": {
"ensembl": "ENSEMBL",
"icd10": "ICD10WHO",
"mesh": "MESH",
"omim.ps": "OMIMPS",
"orphanet.ordo": "Orphanet",
"pubmed": "PMID",
"snomedct": "SCTID",
"umls": "UMLS"
},
"uri_prefix_priority": [
"obofoundry",
"rdf",
"default",
"biocontext",
"miriam",
"ols"
]
}
} ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723255146.0
bioregistry-0.11.12/src/bioregistry/data/metaregistry.json 0000644 0001751 0000177 00000165531 14655544552 023331 0 ustar 00runner docker {
"metaregistry": [
{
"availability": {
"alternate_providers": "missing",
"contact": "missing",
"description": "required",
"example": "present",
"homepage": "required",
"license": "missing",
"name": "required",
"pattern": "missing",
"provider": "present",
"search": true,
"synonyms": "missing",
"version": "present"
},
"bibtex": "Hoehndorf2015",
"contact": {
"email": "ali.syed@kaust.edu.sa",
"github": "aliraza995",
"name": "Ali Syed",
"orcid": "0000-0002-5103-9058"
},
"description": "AberOWL is a framework for ontology-based access to biological data. It consists of a repository of bio-ontologies, a set of webservices which provide access to OWL(-EL) reasoning over the ontologies, and several frontends which utilise the ontology repository and reasoning services to provide access to specific biological datasets.",
"download": "http://aber-owl.net/api/ontology/?format=json",
"example": "CHEBI",
"governance": {
"accepts_external_contributions": false,
"curates": false,
"curation": "import",
"imports": true,
"public_version_controlled_data": false,
"review_team": "n/a",
"scope": "bio-ontologies",
"status": "active"
},
"homepage": "http://aber-owl.net",
"license": "See https://github.com/biopragmatics/bioregistry/issues/339",
"logo_url": "http://aber-owl.net/static/images/logo-owl-small.33629e604a66.png",
"name": "AberOWL",
"prefix": "aberowl",
"provider_uri_format": "http://aber-owl.net/ontology/$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"resolver_type": "lookup",
"resolver_uri_format": "http://aber-owl.net/ontology/$1/#/Browse/",
"search_uri_format": "http://aber-owl.net/#/$1/Ontologies"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "present",
"description": "required",
"example": "present",
"homepage": "required",
"license": "present",
"name": "required",
"pattern": "missing",
"provider": "required",
"search": true,
"synonyms": "missing",
"version": "present"
},
"bibtex": "Jonquet2018",
"contact": {
"email": "clement.jonquet@inrae.fr",
"github": "jonquet",
"name": "Clement Jonquet",
"orcid": "0000-0002-2404-1582"
},
"description": "A vocabulary and ontology repository for agronomy and related domains.",
"example": "ENVO",
"governance": {
"accepts_external_contributions": true,
"curates": true,
"curation": "opaque-review",
"imports": false,
"issue_tracker": "https://github.com/agroportal/project-management/issues",
"public_version_controlled_data": false,
"review_team": "private",
"scope": "agro-ontologies",
"status": "active"
},
"homepage": "http://agroportal.lirmm.fr",
"license": "See https://github.com/biopragmatics/bioregistry/issues/336",
"logo_url": "https://avatars.githubusercontent.com/u/16088111",
"name": "AgroPortal",
"prefix": "agroportal",
"provider_uri_format": "http://agroportal.lirmm.fr/ontologies/$1",
"qualities": {
"automatable_download": true,
"bulk_data": false,
"no_authentication": false,
"structured_data": true
},
"resolver_type": "lookup"
},
{
"availability": {
"alternate_providers": "present",
"contact": "present",
"description": "present",
"example": "missing",
"homepage": "present",
"license": "present",
"name": "required",
"pattern": "present",
"provider": "missing",
"search": true,
"synonyms": "missing",
"version": "missing"
},
"bioregistry_prefix": "bartoc",
"contact": {
"email": "andreas.ledl1@fhnw.ch",
"github": "nichtich",
"name": "Andreas Ledl",
"orcid": "0000-0002-0629-0446"
},
"description": "The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries.\\nThe main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOCβs search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO).",
"download": "https://bartoc.org/data/dumps/latest.ndjson",
"example": "181",
"governance": {
"accepts_external_contributions": true,
"code_repository": "https://github.com/gbv/bartoc.org",
"curates": true,
"curation": "opaque-review",
"imports": false,
"issue_tracker": "https://github.com/gbv/bartoc.org/issues",
"public_version_controlled_data": false,
"review_team": "public",
"scope": "general",
"status": "active"
},
"homepage": "https://bartoc.org/",
"license": "PDDL 1.0",
"logo_url": "https://bartoc.org/img/bartoc-logo.svg",
"name": "Basic Register of Thesauri, Ontologies & Classifications",
"prefix": "bartoc",
"provider_uri_format": "https://bartoc.org/en/node/$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"short_name": "BARTOC"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "missing",
"description": "missing",
"example": "missing",
"homepage": "missing",
"license": "missing",
"name": "missing",
"pattern": "missing",
"provider": "present",
"search": false,
"synonyms": "missing",
"version": "missing"
},
"bibtex": "biocontext",
"contact": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"description": "BioContext contains modular JSON-LD contexts for bioinformatics data.",
"download": "https://raw.githubusercontent.com/prefixcommons/biocontext/master/registry/commons_context.jsonld",
"example": "CHEBI",
"governance": {
"accepts_external_contributions": true,
"code_repository": "https://github.com/prefixcommons/biocontext",
"curates": true,
"curation": "open-review",
"data_repository": "https://github.com/prefixcommons/biocontext",
"imports": false,
"issue_tracker": "https://github.com/prefixcommons/biocontext/issues",
"public_version_controlled_data": true,
"review_team": "inferrable",
"scope": "internal",
"status": "active"
},
"homepage": "https://github.com/prefixcommons/biocontext",
"license": "missing",
"name": "BioContext",
"prefix": "biocontext",
"provider_uri_format": "https://bioregistry.io/metaregistry/biocontext/$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
}
},
{
"availability": {
"alternate_providers": "missing",
"contact": "missing",
"description": "missing",
"example": "missing",
"homepage": "missing",
"license": "present",
"name": "required",
"pattern": "missing",
"provider": "required",
"search": false,
"synonyms": "missing",
"version": "missing"
},
"bibtex": "Unni2022",
"bioregistry_prefix": "biolink",
"contact": {
"email": "deepak.unni3@lbl.gov",
"github": "deepakunni3",
"name": "Deepak Unni",
"orcid": "0000-0002-3583-7340"
},
"description": "A modeling paradigm-specific registry of prefixes and their URL expansions",
"download": "https://raw.githubusercontent.com/biolink/biolink-model/master/biolink-model.yaml",
"example": "doi",
"governance": {
"accepts_external_contributions": true,
"code_repository": "https://github.com/biolink/biolink-model",
"curates": true,
"curation": "open-review",
"data_repository": "https://github.com/biolink/biolink-model",
"imports": false,
"issue_tracker": "https://github.com/biolink/biolink-model/issues",
"public_version_controlled_data": true,
"review_team": "inferrable",
"scope": "internal",
"status": "active"
},
"homepage": "https://github.com/biolink/biolink-model",
"license": "Apache 2.0",
"logo_url": "https://avatars.githubusercontent.com/u/25489141",
"name": "Biolink Model Registry",
"prefix": "biolink",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"short_name": "Biolink"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "present",
"description": "required",
"example": "present",
"homepage": "required",
"license": "missing",
"name": "required",
"pattern": "missing",
"provider": "required",
"search": true,
"synonyms": "missing",
"version": "required"
},
"bibtex": "Whetzel2011",
"bioregistry_prefix": "bioportal",
"contact": {
"email": "jgraybeal@stanford.edu",
"github": "graybeal",
"name": "John Graybeal",
"orcid": "0000-0001-6875-5360"
},
"description": "The BioPortal is a less stringent registry of biomedical ontologies than the OBO Foundry",
"example": "CHEBI",
"governance": {
"accepts_external_contributions": true,
"curates": true,
"curation": "opaque-review",
"imports": false,
"issue_tracker": "https://github.com/ncbo/bioportal-project/issues",
"public_version_controlled_data": false,
"review_team": "private",
"scope": "bio-ontologies",
"status": "active"
},
"homepage": "https://bioportal.bioontology.org/",
"license": "See https://github.com/biopragmatics/bioregistry/issues/337",
"logo_url": "https://ontoportal.org/images/alliance_member_logos/bioportal.png",
"name": "BioPortal Prefixes",
"prefix": "bioportal",
"provider_uri_format": "https://bioportal.bioontology.org/ontologies/$1",
"qualities": {
"automatable_download": true,
"bulk_data": false,
"no_authentication": false,
"structured_data": true
},
"resolver_type": "lookup",
"short_name": "BioPortal"
},
{
"availability": {
"alternate_providers": "present",
"contact": "present",
"description": "required",
"example": "required",
"homepage": "required",
"license": "present",
"name": "required",
"pattern": "present",
"provider": "present",
"search": true,
"synonyms": "present",
"version": "present"
},
"bibtex": "Hoyt2022",
"bioregistry_prefix": "bioregistry",
"contact": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database.",
"download": "https://bioregistry.io/api/registry/",
"example": "chebi",
"governance": {
"accepts_external_contributions": true,
"code_repository": "https://github.com/biopragmatics/bioregistry",
"curates": true,
"curation": "open-review",
"data_repository": "https://github.com/biopragmatics/bioregistry",
"imports": true,
"issue_tracker": "https://github.com/biopragmatics/bioregistry/issues",
"public_version_controlled_data": true,
"review_team": "public",
"scope": "life sciences",
"status": "active"
},
"homepage": "https://bioregistry.io",
"license": "CC0",
"logo_url": "https://bioregistry.io/static/logo.svg",
"name": "Bioregistry",
"prefix": "bioregistry",
"provider_uri_format": "https://bioregistry.io/registry/$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"resolver_type": "resolver",
"resolver_uri_format": "https://bioregistry.io/$1:$2"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "missing",
"description": "missing",
"example": "missing",
"homepage": "required",
"license": "missing",
"name": "required",
"pattern": "missing",
"provider": "required",
"search": false,
"synonyms": "missing",
"version": "missing"
},
"bibtex": "Bairoch2018",
"bioregistry_prefix": "cellosaurus.resource",
"contact": {
"email": "Amos.Bairoch@sib.swiss",
"github": "AmosBairoch",
"name": "Amos Bairoch",
"orcid": "0000-0003-2826-6444"
},
"description": "The set of prefixes used in the Cellosaurus resource",
"example": "4DN",
"governance": {
"accepts_external_contributions": false,
"curates": true,
"curation": "private",
"imports": false,
"public_version_controlled_data": false,
"review_team": "n/a",
"scope": "internal",
"status": "active"
},
"homepage": "https://web.expasy.org/cellosaurus/",
"license": "CC BY 4.0",
"logo_url": "https://www.cellosaurus.org/images/cellosaurus/cellosaurus.png",
"name": "Cellosaurus Registry",
"prefix": "cellosaurus",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"short_name": "Cellosaurus"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "missing",
"description": "missing",
"example": "missing",
"homepage": "missing",
"license": "missing",
"name": "required",
"pattern": "missing",
"provider": "missing",
"search": false,
"synonyms": "missing",
"version": "missing"
},
"bibtex": "Hastings2011",
"bioregistry_prefix": "cheminf",
"contact": {
"email": "egon.willighagen@gmail.com",
"github": "egonw",
"name": "Egon Willighagen",
"orcid": "0000-0001-7542-0286"
},
"description": "Contains entries for various database identifiers",
"example": "000140",
"governance": {
"accepts_external_contributions": true,
"code_repository": "https://github.com/semanticchemistry/semanticchemistry",
"curates": true,
"curation": "open-review",
"data_repository": "https://github.com/semanticchemistry/semanticchemistry",
"imports": false,
"issue_tracker": "https://github.com/semanticchemistry/semanticchemistry/issues",
"public_version_controlled_data": true,
"review_team": "inferrable",
"scope": "chemistry",
"status": "unresponsive"
},
"homepage": "https://github.com/semanticchemistry/semanticchemistry",
"license": "CC BY 3.0",
"name": "Chemical Information Ontology",
"prefix": "cheminf",
"provider_uri_format": "https://semanticscience.org/resource/CHEMINF_$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"resolver_type": "lookup",
"short_name": "CHEMINF"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "missing",
"description": "missing",
"example": "present",
"homepage": "required",
"license": "missing",
"name": "required",
"pattern": "missing",
"provider": "required",
"search": true,
"synonyms": "missing",
"version": "missing"
},
"bibtex": "Arnaud2020",
"contact": {
"email": "e.arnaud@cgiar.org",
"github": "elizabetharnaud",
"name": "Elizabeth Arnaud",
"orcid": "0000-0002-6020-5919"
},
"description": "The Crop Ontology (CO) current objective is to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms",
"download": "https://cropontology.org/metadata",
"example": "CO_325",
"governance": {
"accepts_external_contributions": true,
"curates": true,
"curation": "opaque-review",
"imports": false,
"issue_tracker": "https://github.com/EBISPOT/OLS/issues",
"public_version_controlled_data": false,
"review_team": "public",
"scope": "agro-ontologies",
"status": "active"
},
"homepage": "https://www.cropontology.org",
"license": "CC BY 4.0",
"logo_url": "https://cropontology.org/cropontology_static/crop_ontology_logo_2.png",
"name": "Crop Ontology Curation Tool",
"prefix": "cropoct",
"provider_uri_format": "https://cropontology.org/ontology/$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"resolver_type": "lookup",
"resolver_uri_format": "https://cropontology.org/term/$1:$2",
"short_name": "CropOCT"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "present",
"description": "required",
"example": "present",
"homepage": "present",
"license": "present",
"name": "required",
"pattern": "missing",
"provider": "present",
"search": true,
"synonyms": "missing",
"version": "present"
},
"bibtex": "Kechagioglou2021",
"contact": {
"email": "xeni.kechagioglou@lifewatch.eu",
"github": "xeniacs",
"name": "Xeni Kechagioglou",
"orcid": "0000-0003-4494-839X"
},
"description": "The LifeWatch ERIC repository of semantic resources for the ecological domain.",
"example": "AGROVOC",
"governance": {
"accepts_external_contributions": true,
"curates": true,
"curation": "opaque-review",
"imports": false,
"public_version_controlled_data": false,
"review_team": "private",
"scope": "eco-ontologies",
"status": "active"
},
"homepage": "http://ecoportal.lifewatch.eu",
"license": "See https://github.com/biopragmatics/bioregistry/issues/338",
"logo_url": "https://metadatacatalogue.lifewatch.eu/srv/api/records/95a44a9c-6f70-454f-9d3e-5e9d5684bb51/attachments/EcoPortal%20Positivo2.png",
"name": "EcoPortal",
"prefix": "ecoportal",
"provider_uri_format": "http://ecoportal.lifewatch.eu/ontologies/$1",
"qualities": {
"automatable_download": true,
"bulk_data": false,
"no_authentication": false,
"structured_data": true
},
"resolver_type": "lookup"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "missing",
"description": "missing",
"example": "missing",
"homepage": "missing",
"license": "missing",
"name": "required",
"pattern": "missing",
"provider": "missing",
"search": true,
"synonyms": "missing",
"version": "missing"
},
"bibtex": "Ison2013",
"bioregistry_prefix": "edam.data",
"contact": {
"email": "matus.kalas@uib.no",
"github": "matuskalas",
"name": "MatΓΊΕ‘ KalaΕ‘",
"orcid": "0000-0002-1509-4981"
},
"description": "EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within computational biology, bioinformatics, and bioimage informatics. EDAM includes types of data and data identifiers, data formats, operations, and topics related to data analysis in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use.",
"download": "http://edamontology.org/EDAM.owl",
"example": "1004",
"governance": {
"accepts_external_contributions": true,
"code_repository": "https://github.com/edamontology/edamontology",
"curates": true,
"curation": "community",
"data_repository": "https://github.com/edamontology/edamontology",
"imports": false,
"issue_tracker": "https://github.com/edamontology/edamontology/issues",
"public_version_controlled_data": true,
"review_team": "inferrable",
"scope": "Life Sciences",
"status": "active"
},
"homepage": " http://edamontology.org",
"license": "CC BY-SA 4.0",
"logo_url": "https://avatars.githubusercontent.com/u/7922809",
"name": "EDAM Ontology",
"prefix": "edam",
"provider_uri_format": "http://edamontology.org/data_$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"short_name": "EDAM"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "required",
"description": "required",
"example": "missing",
"homepage": "required",
"license": "missing",
"name": "required",
"pattern": "missing",
"provider": "missing",
"search": true,
"synonyms": "missing",
"version": "missing"
},
"bibtex": "Sansone2019",
"bioregistry_prefix": "fairsharing",
"contact": {
"email": "allyson.lister@oerc.ox.ac.uk",
"github": "allysonlister",
"name": "Allyson Lister",
"orcid": "0000-0002-7702-4495"
},
"description": "A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies.",
"example": "FAIRsharing.62qk8w",
"governance": {
"accepts_external_contributions": true,
"curates": true,
"curation": "opaque-review",
"imports": false,
"public_version_controlled_data": false,
"review_team": "private",
"scope": "life sciences",
"status": "active"
},
"homepage": "https://fairsharing.org/",
"license": "CC BY-SA 4.0",
"logo_url": "https://api.fairsharing.org/img/fairsharing-attribution.svg",
"name": "FAIRSharing",
"prefix": "fairsharing",
"provider_uri_format": "https://fairsharing.org/$1",
"qualities": {
"automatable_download": true,
"bulk_data": false,
"no_authentication": false,
"structured_data": true
}
},
{
"availability": {
"alternate_providers": "present",
"contact": "missing",
"description": "present",
"example": "present",
"homepage": "present",
"license": "missing",
"name": "required",
"pattern": "present",
"provider": "present",
"search": false,
"synonyms": "missing",
"version": "missing"
},
"bibtex": "TheGeneOntologyConsortium2019",
"bioregistry_prefix": "go.resource",
"contact": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"description": "A database-specific registry supporting curation in the Gene Ontology",
"download": "https://raw.githubusercontent.com/geneontology/go-site/master/metadata/db-xrefs.yaml",
"example": "CHEBI",
"governance": {
"accepts_external_contributions": true,
"code_repository": "https://github.com/geneontology/go-site",
"curates": true,
"curation": "open-review",
"data_repository": "https://github.com/geneontology/go-site",
"imports": false,
"issue_tracker": "https://github.com/geneontology/go-site/issues",
"public_version_controlled_data": true,
"review_team": "inferrable",
"scope": "internal",
"status": "inactive"
},
"homepage": "http://geneontology.org/",
"license": "CC BY 4.0",
"logo_url": "http://geneontology.org/assets/go-logo.large.png",
"name": "Gene Ontology Registry",
"prefix": "go",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"short_name": "GO"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "present",
"description": "present",
"example": "missing",
"homepage": "present",
"license": "missing",
"name": "required",
"pattern": "missing",
"provider": "missing",
"search": false,
"synonyms": "missing",
"version": "missing"
},
"bibtex": "Bender2013",
"bioregistry_prefix": "oid",
"contact": {
"email": "hq@HL7.org",
"name": "HL7 Support"
},
"description": "HL7 External Code Systems are stored within the greater OID system",
"example": "2.16.840.1.113883.6.88",
"governance": {
"accepts_external_contributions": true,
"curates": true,
"curation": "opaque-review",
"imports": false,
"public_version_controlled_data": false,
"review_team": "n/a",
"scope": "general",
"status": "active"
},
"homepage": "http://www.oid-info.com/get/2.16.840.1.113883.6",
"license": "See https://github.com/biopragmatics/bioregistry/issues/586",
"logo_url": "https://comjoodoc.de/wp-content/uploads/2019/03/blog_comjoodoc_hl7fhir-1200x800.png",
"name": "HL7 External Code Systems",
"prefix": "hl7",
"provider_uri_format": "http://oid-info.com/get/$1",
"qualities": {
"automatable_download": false,
"bulk_data": false,
"no_authentication": true,
"structured_data": true
},
"short_name": "HL7"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "missing",
"description": "required",
"example": "missing",
"homepage": "present",
"license": "missing",
"name": "required",
"pattern": "missing",
"provider": "missing",
"search": false,
"synonyms": "missing",
"version": "missing"
},
"bioregistry_prefix": "integbio",
"contact": {
"email": "kwsm@dbcls.rois.ac.jp",
"github": "skwsm",
"name": "Shuichi Kawashima",
"orcid": "0000-0001-7883-3756"
},
"description": "Integbio Database Catalog provides whereabouts information (URL), database description, biological species and other attributes (metadata) of Japanese and international life science databases to make it easier for users to find databases they need. This catalog has been developed as a part of the integration of life science databases promoted by four ministries in Japan: the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), The Ministry of Health, Labor, and Welfare (MHLW), the Ministry of Agriculture, Forestry, and Fisheries (MAFF), and the Ministry of Economy, Trade, and Industry of Japan (METI). (from https://integbio.jp/dbcatalog/en/about)",
"download": "https://integbio.jp/dbcatalog/files/zip/en_integbio_dbcatalog_cc0_20240112_utf8.csv.zip",
"example": "nbdc01071",
"governance": {
"accepts_external_contributions": false,
"curates": false,
"curation": "import",
"imports": true,
"public_version_controlled_data": false,
"review_team": "n/a",
"scope": "bio-ontologies",
"status": "active"
},
"homepage": "https://integbio.jp/en/",
"license": "CC0",
"logo_url": "https://integbio.jp/templates/integbio/images/logo/logo.png",
"name": "Integbio",
"prefix": "integbio",
"provider_uri_format": "https://integbio.jp/dbcatalog/en/record/$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"search_uri_format": "https://integbio.jp/dbcatalog/dbsearch-en?cck=database_catalog&order_en=1&dbcat_search_all_en=$1&tag2_en=&tag3_en=&inst_country_en=&inst_country_others_en=&dbarchive_en=&togotv_en=&data_downloadable_en=&biosharing_en=&record_creation_en=&status_en=&dbcat_ministry=&taxonomy=&lang=en&search=database_catalog_search_en&task=search"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "missing",
"description": "present",
"example": "missing",
"homepage": "present",
"license": "missing",
"name": "required",
"pattern": "missing",
"provider": "present",
"search": true,
"synonyms": "missing",
"version": "missing"
},
"contact": {
"email": "py.vandenbussche@gmail.com",
"github": "pyvandenbussche",
"name": "Pierre-Yves Vandenbussche",
"orcid": "0000-0003-0591-6109"
},
"description": "A vocabulary in LOV gathers definitions of a set of classes and properties (together simply called terms of the vocabulary), useful to describe specific types of things, or things in a given domain or industry, or things at large but for a specific usage. Terms of vocabularies also provide the links in linked data, in the above case between a Person and a City. The definitions of terms provided by the vocabularies bring clear semantics to descriptions and links, thanks to the formal language they use (some dialect of RDF such as RDFS or OWL). In short, vocabularies provide the semantic glue enabling Data to become meaningful Data. [from https://lov.linkeddata.es/dataset/lov/about]",
"download": "https://lov.linkeddata.es/lov.n3.gz",
"example": "m4i",
"governance": {
"accepts_external_contributions": true,
"code_repository": "https://github.com/pyvandenbussche/lov",
"curates": true,
"curation": "import",
"imports": true,
"issue_tracker": "https://github.com/pyvandenbussche/lov/issues",
"public_version_controlled_data": false,
"review_team": "n/a",
"scope": "semantic web",
"status": "active"
},
"homepage": "https://lov.linkeddata.es",
"license": "CC BY 4.0",
"logo_url": "https://lov.linkeddata.es/img/icon-LOV.png",
"name": "Linked Open Vocabularies",
"prefix": "lov",
"provider_uri_format": "https://lov.linkeddata.es/dataset/lov/vocabs/$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"search_uri_format": "https://lov.linkeddata.es/dataset/lov/vocabs?q=$1",
"short_name": "LOV"
},
{
"availability": {
"alternate_providers": "present",
"contact": "missing",
"description": "required",
"example": "required",
"homepage": "required",
"license": "missing",
"name": "required",
"pattern": "required",
"provider": "required",
"search": true,
"synonyms": "missing",
"version": "missing"
},
"bibtex": "Juty2012",
"bioregistry_prefix": "miriam",
"contact": {
"email": "hhe@ebi.ac.uk",
"github": "hHermjakob",
"name": "Henning Hermjakob",
"orcid": "0000-0001-8479-0262"
},
"description": "The Identifiers.org Resolution Service provides consistent access to life science data using Compact Identifiers. Compact Identifiers consist of an assigned unique prefix and a local provider designated accession number (prefix:accession).",
"download": "https://registry.api.identifiers.org/resolutionApi/getResolverDataset",
"example": "chebi",
"governance": {
"accepts_external_contributions": true,
"code_repository": "https://github.com/identifiers-org/cloud-satellite-web-spa",
"curates": true,
"curation": "opaque-review",
"imports": false,
"issue_tracker": "https://github.com/identifiers-org/identifiers-org.github.io/issues",
"public_version_controlled_data": false,
"review_team": "private",
"scope": "life sciences",
"status": "unresponsive"
},
"homepage": "https://identifiers.org",
"license": "CC BY 4.0",
"logo_url": "https://identifiers.org/identifiers_logo.f6737b08.png",
"name": "Identifiers.org",
"prefix": "miriam",
"provider_uri_format": "https://registry.identifiers.org/registry/$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"resolver_type": "resolver",
"resolver_uri_format": "https://identifiers.org/$1:$2"
},
{
"availability": {
"alternate_providers": "present",
"contact": "missing",
"description": "required",
"example": "required",
"homepage": "required",
"license": "missing",
"name": "required",
"pattern": "required",
"provider": "required",
"search": false,
"synonyms": "present",
"version": "missing"
},
"bibtex": "Wimalaratne2018",
"bioregistry_prefix": "n2t",
"contact": {
"email": "jak@ucop.edu",
"github": "jkunze",
"name": "John Kunze",
"orcid": "0000-0001-7604-8041"
},
"description": "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org",
"download": "https://n2t.net/e/n2t_full_prefixes.yaml",
"example": "chebi",
"governance": {
"accepts_external_contributions": false,
"curates": false,
"curation": "import",
"imports": true,
"public_version_controlled_data": false,
"review_team": "n/a",
"scope": "life sciences",
"status": "active"
},
"homepage": "https://n2t.net",
"license": "CC0",
"logo_url": "https://n2t.net/e/images/n2t_net_logo.png",
"name": "Name-to-Thing",
"prefix": "n2t",
"provider_uri_format": "https://n2t.net/$1:",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"resolver_type": "resolver",
"resolver_uri_format": "https://n2t.net/$1:$2",
"short_name": "N2T"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "missing",
"description": "missing",
"example": "required",
"homepage": "required",
"license": "missing",
"name": "required",
"pattern": "missing",
"provider": "missing",
"search": false,
"synonyms": "missing",
"version": "missing"
},
"bibtex": "Clark2016",
"bioregistry_prefix": "ncbi.resource",
"contact": {
"email": "gb-admin@ncbi.nlm.nih.gov",
"name": "GenBank Support"
},
"description": "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources",
"example": "ECOCYC",
"governance": {
"accepts_external_contributions": false,
"curates": true,
"curation": "private",
"imports": false,
"public_version_controlled_data": false,
"review_team": "n/a",
"scope": "internal",
"status": "inactive"
},
"homepage": "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/",
"license": "See https://github.com/biopragmatics/bioregistry/issues/342",
"logo_url": "https://upload.wikimedia.org/wikipedia/commons/0/07/US-NLM-NCBI-Logo.svg",
"name": "National Center for Biotechnology Information Registry",
"prefix": "ncbi",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": false
},
"short_name": "NCBI"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "required",
"description": "required",
"example": "missing",
"homepage": "required",
"license": "required",
"name": "required",
"pattern": "missing",
"provider": "missing",
"search": true,
"synonyms": "missing",
"version": "missing"
},
"bibtex": "Jackson2021",
"contact": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"description": "The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate.",
"download": "http://www.obofoundry.org/registry/ontologies.yml",
"example": "CHEBI",
"governance": {
"accepts_external_contributions": true,
"code_repository": "https://github.com/OBOFoundry/OBOFoundry.github.io",
"curates": true,
"curation": "open-review",
"data_repository": "https://github.com/OBOFoundry/OBOFoundry.github.io",
"imports": false,
"issue_tracker": "https://github.com/OBOFoundry/OBOFoundry.github.io/issues",
"public_version_controlled_data": true,
"review_team": "public",
"scope": "bio-ontologies",
"status": "active"
},
"homepage": "http://www.obofoundry.org/",
"license": "CC0",
"logo_url": "https://obofoundry.org/images/foundrylogo.png",
"name": "OBO Foundry",
"prefix": "obofoundry",
"provider_uri_format": "https://www.obofoundry.org/ontology/$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"resolver_type": "resolver",
"resolver_uri_format": "http://purl.obolibrary.org/obo/$1_$2"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "present",
"description": "required",
"example": "present",
"homepage": "present",
"license": "required",
"name": "required",
"pattern": "missing",
"provider": "present",
"search": true,
"synonyms": "missing",
"version": "present"
},
"bibtex": "Cote2006a",
"contact": {
"email": "henriette007@ebi.ac.uk",
"github": "henrietteharmse",
"name": "Henriette Harmse",
"orcid": "0000-0001-7251-9504"
},
"description": "The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. ",
"example": "chebi",
"governance": {
"accepts_external_contributions": true,
"code_repository": "https://github.com/EBISPOT/ols4",
"comments": "Accepts suggestions through the OLS issue tracker at https://github.com/EBISPOT/ols4/issues",
"curates": false,
"curation": "import",
"data_repository": "https://github.com/EBISPOT/OLS",
"imports": true,
"issue_tracker": "https://github.com/EBISPOT/ols4/issues/",
"public_version_controlled_data": true,
"review_team": "inferrable",
"scope": "bio-ontologies",
"status": "active"
},
"homepage": "https://www.ebi.ac.uk/ols4",
"license": "See https://github.com/biopragmatics/bioregistry/issues/340",
"logo_url": "https://www.ebi.ac.uk/ols4/logo.png",
"name": "Ontology Lookup Service",
"prefix": "ols",
"provider_uri_format": "https://www.ebi.ac.uk/ols4/ontologies/$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"resolver_type": "lookup",
"short_name": "OLS"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "required",
"description": "required",
"example": "present",
"homepage": "required",
"license": "missing",
"name": "required",
"pattern": "missing",
"provider": "present",
"search": false,
"synonyms": "missing",
"version": "missing"
},
"bibtex": "Ong2017",
"contact": {
"email": "yongqunh@med.umich.edu",
"github": "yongqunh",
"name": "Yongqun Oliver He",
"orcid": "0000-0001-9189-9661"
},
"description": "Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis.",
"example": "AGRO",
"governance": {
"accepts_external_contributions": true,
"curates": false,
"curation": "import",
"imports": true,
"issue_tracker": "https://github.com/OntoZoo/ontobee/issues",
"public_version_controlled_data": false,
"review_team": "n/a",
"scope": "bio-ontologies",
"status": "active"
},
"homepage": "http://www.ontobee.org/",
"license": "See https://github.com/biopragmatics/bioregistry/issues/341",
"logo_url": "https://ontobee.org/public/images/logo.gif",
"name": "OntoBee",
"prefix": "ontobee",
"provider_uri_format": "http://www.ontobee.org/ontology/$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": false
},
"resolver_type": "lookup",
"resolver_uri_format": "http://www.ontobee.org/ontology/$1?iri=http://purl.obolibrary.org/obo/$1_$2"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "missing",
"description": "present",
"example": "missing",
"homepage": "required",
"license": "missing",
"name": "required",
"pattern": "missing",
"provider": "missing",
"search": true,
"synonyms": "missing",
"version": "missing"
},
"bioregistry_prefix": "pathguide",
"contact": {
"email": "gary.bader@utoronto.ca",
"github": "gbader",
"name": "Gary Bader",
"orcid": "0000-0003-0185-8861"
},
"description": "Pathguide contains information about 702 biological pathway related resources and molecular interaction related resources. Click on a link to go to the resource home page or 'Details' for a description page. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated. (from homepage)",
"example": "235",
"governance": {
"accepts_external_contributions": true,
"curates": true,
"curation": "opaque-review",
"imports": false,
"public_version_controlled_data": false,
"review_team": "n/a",
"scope": "bio-ontologies",
"status": "active"
},
"homepage": "http://pathguide.org",
"license": "Unknown",
"logo_url": "http://pathguide.org/images/logo.gif",
"name": "Pathguide",
"prefix": "pathguide",
"provider_uri_format": "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=$1",
"qualities": {
"automatable_download": false,
"bulk_data": false,
"no_authentication": true,
"structured_data": false
}
},
{
"availability": {
"alternate_providers": "present",
"contact": "missing",
"description": "missing",
"example": "missing",
"homepage": "missing",
"license": "missing",
"name": "missing",
"pattern": "missing",
"provider": "required",
"search": false,
"synonyms": "missing",
"version": "missing"
},
"contact": {
"email": "richard@cyganiak.de",
"github": "cygri",
"name": "Richard Cyganiak",
"orcid": "0000-0001-9950-5209"
},
"description": "A web-developer centric archive of prefixes and URI prefixes",
"download": "https://prefix.cc/context.jsonld",
"example": "foaf",
"governance": {
"accepts_external_contributions": true,
"code_repository": "https://github.com/cygri/prefix.cc/",
"curates": true,
"curation": "community",
"imports": false,
"issue_tracker": "https://github.com/cygri/prefix.cc/issues",
"public_version_controlled_data": false,
"review_team": "democratic",
"scope": "general",
"status": "active"
},
"homepage": "https://prefix.cc/",
"license": "CC0",
"name": "Prefix.cc",
"prefix": "prefixcc",
"provider_uri_format": "https://prefix.cc/$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
}
},
{
"availability": {
"alternate_providers": "present",
"contact": "missing",
"description": "present",
"example": "present",
"homepage": "present",
"license": "missing",
"name": "required",
"pattern": "present",
"provider": "present",
"search": true,
"synonyms": "present",
"version": "missing"
},
"bibtex": "prefixcommons",
"bioregistry_prefix": "prefixcommons",
"contact": {
"email": "michel.dumontier@gmail.com",
"github": "micheldumontier",
"name": "Michel Dumontier",
"orcid": "0000-0003-4727-9435"
},
"description": "A registry of commonly used prefixes in the life sciences and linked data. The source data for this registry is a spreadsheet on Google called the Life Science Registry. This registry was previously known as Prefix Commons and was available at https://prefixcommons.org.",
"download": "http://tinyurl.com/lsregistry",
"example": "doi",
"governance": {
"accepts_external_contributions": true,
"curates": true,
"curation": "community",
"imports": false,
"public_version_controlled_data": false,
"review_team": "public",
"scope": "life sciences",
"status": "active"
},
"homepage": "https://registry.bio2kg.org",
"license": "CC0",
"logo_url": "https://avatars.githubusercontent.com/u/15466415",
"name": "Prefix Commons",
"prefix": "prefixcommons",
"provider_uri_format": "https://registry.bio2kg.org/resource/$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
}
},
{
"availability": {
"alternate_providers": "missing",
"contact": "present",
"description": "required",
"example": "missing",
"homepage": "required",
"license": "present",
"name": "required",
"pattern": "missing",
"provider": "missing",
"search": true,
"synonyms": "missing",
"version": "missing"
},
"bibtex": "Pampel2013",
"bioregistry_prefix": "re3data",
"contact": {
"email": "mwitt@purdue.edu",
"github": "mwittin",
"name": "Michael Witt",
"orcid": "0000-0003-4221-7956"
},
"description": "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines.",
"example": "r3d100014165",
"governance": {
"accepts_external_contributions": true,
"curates": true,
"curation": "opaque-review",
"imports": false,
"public_version_controlled_data": false,
"review_team": "private",
"scope": "general",
"status": "active"
},
"homepage": "https://www.re3data.org",
"license": "CC0",
"logo_url": "https://www.re3data.org/bundles/kitlibraryre3dataapp/img/re3datalogo_black.png",
"name": "Registry of Research Data Repositories",
"prefix": "re3data",
"provider_uri_format": "https://www.re3data.org/repository/$1",
"qualities": {
"automatable_download": true,
"bulk_data": false,
"no_authentication": true,
"structured_data": false
},
"short_name": "re3data"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "present",
"description": "missing",
"example": "missing",
"homepage": "required",
"license": "present",
"name": "required",
"pattern": "missing",
"provider": "missing",
"search": true,
"synonyms": "present",
"version": "missing"
},
"bibtex": "",
"bioregistry_prefix": "rrid",
"contact": {
"email": "bandrow@gmail.com",
"github": "bandrow",
"name": "Anita Bandrowski",
"orcid": "0000-0002-5497-0243"
},
"description": "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools",
"download": "https://docs.google.com/spreadsheets/d/1BEPZXZsENhK7592AR83xUwbPbR2J-GVQ/edit?usp=sharing&ouid=107737386203376389514&rtpof=true&sd=true",
"example": "AB",
"governance": {
"accepts_external_contributions": true,
"curates": true,
"curation": "opaque-review",
"imports": false,
"public_version_controlled_data": false,
"review_team": "private",
"scope": "life sciences",
"status": "active"
},
"homepage": "https://rrid.site",
"license": "CC BY 4.0",
"logo_url": "https://scicrunch.org/upload/community-logo/rin-resources_69984.png",
"name": "Research Resource Identifiers",
"prefix": "rrid",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"resolver_type": "lookup",
"resolver_uri_format": "https://scicrunch.org/resolver/RRID:$1_$2",
"short_name": "RRID"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "missing",
"description": "missing",
"example": "required",
"homepage": "required",
"license": "missing",
"name": "required",
"pattern": "required",
"provider": "required",
"search": false,
"synonyms": "missing",
"version": "missing"
},
"bioregistry_prefix": "togoid",
"contact": {
"email": "ktym@dbcls.jp",
"github": "ktym",
"name": "Toshiaki Katayama",
"orcid": "0000-0003-2391-0384"
},
"description": "TogoID is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. TogoID supports datasets from various biological categories such as gene, protein, chemical compound, pathway, disease, etc. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations. (from https://togoid.dbcls.jp/)",
"download": "https://raw.githubusercontent.com/togoid/togoid-config/main/ontology/togoid-ontology.ttl",
"example": "AffyProbeset",
"governance": {
"accepts_external_contributions": true,
"code_repository": "https://github.com/togoid/togoid-config",
"curates": false,
"curation": "import",
"data_repository": "https://github.com/togoid/togoid-config",
"imports": true,
"issue_tracker": "https://github.com/togoid/togoid-config/issues",
"public_version_controlled_data": true,
"review_team": "inferrable",
"scope": "bio-ontologies",
"status": "active"
},
"homepage": "https://togoid.dbcls.jp/",
"license": "CC BY 4.0",
"name": "TogoID",
"prefix": "togoid",
"provider_uri_format": "https://togoid.dbcls.jp/#$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
}
},
{
"availability": {
"alternate_providers": "missing",
"contact": "missing",
"description": "missing",
"example": "missing",
"homepage": "required",
"license": "missing",
"name": "required",
"pattern": "missing",
"provider": "required",
"search": true,
"synonyms": "missing",
"version": "missing"
},
"bibtex": "Bateman2021",
"bioregistry_prefix": "uniprot.resource",
"contact": {
"email": "agb@ebi.ac.uk",
"github": "bateman-research",
"name": "Alex Bateman",
"orcid": "0000-0002-6982-4660"
},
"description": "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources.",
"download": "https://www.uniprot.org/database/?format=rdf",
"example": "DB-0174",
"governance": {
"accepts_external_contributions": false,
"curates": true,
"curation": "private",
"imports": false,
"public_version_controlled_data": false,
"review_team": "n/a",
"scope": "internal",
"status": "active"
},
"homepage": "https://www.uniprot.org/database/",
"license": "CC BY 4.0",
"logo_url": "https://www.uniprot.org/uniprot-logo.img.0df091.svg",
"name": "UniProt Cross-ref database",
"prefix": "uniprot",
"provider_uri_format": "https://www.uniprot.org/database/$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"short_name": "UniProt"
},
{
"availability": {
"alternate_providers": "present",
"contact": "present",
"description": "required",
"example": "present",
"homepage": "present",
"license": "present",
"name": "required",
"pattern": "present",
"provider": "present",
"search": true,
"synonyms": "missing",
"version": "present"
},
"bibtex": "Waagmeester2020",
"bioregistry_prefix": "wikidata",
"contact": {
"email": "info@wikidata.org",
"name": "WikiData Support"
},
"description": "An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries.",
"example": "P683",
"governance": {
"accepts_external_contributions": true,
"curates": true,
"curation": "open-review",
"imports": false,
"public_version_controlled_data": false,
"review_team": "inferrable",
"scope": "general",
"status": "active"
},
"homepage": "https://www.wikidata.org",
"license": "CC0",
"logo_url": "https://upload.wikimedia.org/wikipedia/commons/6/66/Wikidata-logo-en.svg",
"name": "Wikidata Property",
"prefix": "wikidata",
"provider_uri_format": "http://www.wikidata.org/entity/$1",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"short_name": "Wikidata"
},
{
"availability": {
"alternate_providers": "missing",
"contact": "missing",
"description": "missing",
"example": "missing",
"homepage": "missing",
"license": "missing",
"name": "missing",
"pattern": "missing",
"provider": "present",
"search": true,
"synonyms": "missing",
"version": "missing"
},
"bioregistry_prefix": "zazuko",
"contact": {
"email": "ktk@netlabs.org",
"github": "ktk",
"name": "Adrian Gschwend",
"orcid": "0000-0002-2079-9636"
},
"description": "This service fills a gap between services like prefix.cc and LOV or looking up the original vocabulary specification. Not all vocabularies (or schema or ontology, whatever you want to call them) provide an HTML view. If you resolve some of the common prefixes all you get back is some RDF serialization which is not ideal. (from )",
"download": "https://prefix.zazuko.com/api/v1/prefixes",
"example": "frbr",
"governance": {
"accepts_external_contributions": true,
"code_repository": "https://github.com/zazuko/prefix-server",
"curates": true,
"curation": "open-review",
"data_repository": "https://github.com/zazuko/rdf-vocabularies",
"imports": true,
"issue_tracker": "https://github.com/zazuko/rdf-vocabularies/issues",
"public_version_controlled_data": true,
"review_team": "inferrable",
"scope": "semantic web",
"status": "active"
},
"homepage": "https://prefix.zazuko.com/",
"license": "MIT",
"logo_url": "https://prefix.zazuko.com/_nuxt/img/zazuko-logo.2dc686c.svg",
"name": "Zazuko Prefix Server",
"prefix": "zazuko",
"provider_uri_format": "https://prefix.zazuko.com/prefix/$1:",
"qualities": {
"automatable_download": true,
"bulk_data": true,
"no_authentication": true,
"structured_data": true
},
"resolver_type": "lookup",
"resolver_uri_format": "https://prefix.zazuko.com/$1:$2",
"short_name": "Zazuko"
}
]
} ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723255146.0
bioregistry-0.11.12/src/bioregistry/data/mismatch.json 0000644 0001751 0000177 00000006423 14655544552 022411 0 ustar 00runner docker {
"abcd": {
"fairsharing": "FAIRsharing.kr3215"
},
"abs": {
"aberowl": "ABS"
},
"ac": {
"bioportal": "AC",
"fairsharing": "FAIRsharing.md3e78",
"lov": "ac"
},
"aeo": {
"agroportal": "AEO"
},
"afo": {
"agroportal": "AFO"
},
"agricola": {
"lov": "agr"
},
"ark": {
"bartoc": "20297"
},
"atc": {
"agroportal": "ATC",
"hl7": "2.16.840.1.113883.6.77"
},
"bcgo": {
"fairsharing": "FAIRsharing.2hzttx"
},
"bto": {
"lov": "bto"
},
"cco": {
"lov": "cco"
},
"citexplore": {
"aberowl": "CTX",
"bioportal": "CTX"
},
"cl": {
"lov": "cl"
},
"cmo": {
"lov": "cmo"
},
"cp": {
"fairsharing": "FAIRsharing.wP3t2L"
},
"cro": {
"lov": "cro"
},
"csp": {
"lov": "csp"
},
"cst": {
"aberowl": "CST",
"bioportal": "CST",
"hl7": "2.16.840.1.113883.6.62"
},
"cto": {
"lov": "cto"
},
"dicom": {
"lov": "dicom"
},
"dpo": {
"lov": "dpo"
},
"dpv": {
"zazuko": "dpv"
},
"dso": {
"lov": "dso"
},
"eo": {
"bioportal": "EO"
},
"eol": {
"fairsharing": "FAIRsharing.3J6NYn"
},
"epio": {
"fairsharing": "FAIRsharing.p6412v"
},
"epo": {
"aberowl": "EPO",
"bioportal": "EPO"
},
"epso": {
"fairsharing": "FAIRsharing.p6412v"
},
"gc": {
"lov": "gc"
},
"geo": {
"aberowl": "GEO",
"biocontext": "GEO",
"bioportal": "GEO",
"fairsharing": "FAIRsharing.27rndz",
"lov": "geo",
"obofoundry": "geo",
"ols": "geo",
"ontobee": "GEO",
"zazuko": "geo"
},
"geonames": {
"fairsharing": "FAIRsharing.56a0Uj"
},
"gnd": {
"prefixcommons": "gnd"
},
"gold": {
"lov": "gold"
},
"gro": {
"biocontext": "GRO",
"miriam": "gro",
"obofoundry": "gro"
},
"hpath": {
"fairsharing": "FAIRsharing.kj336a"
},
"icdo": {
"aberowl": "ICDO",
"bioportal": "ICDO",
"ontobee": "ICDO"
},
"ma": {
"zazuko": "ma"
},
"mo": {
"lov": "mo"
},
"mod": {
"bartoc": "20333",
"lov": "mod"
},
"ncbitaxon": {
"lov": "taxon",
"prefixcommons": "uniprot.taxonomy"
},
"nemo": {
"aberowl": "NEMO",
"bioportal": "NEMO",
"fairsharing": "FAIRsharing.n66krd"
},
"ngl": {
"bartoc": "20302"
},
"oae": {
"lov": "oae"
},
"om": {
"lov": "om"
},
"omim": {
"bioportal": "MIM",
"fairsharing": "FAIRsharing.azq2t6"
},
"omim.ps": {
"miriam": "ps"
},
"opm": {
"lov": "opm"
},
"otl": {
"lov": "otl"
},
"peco": {
"lov": "peco"
},
"plo": {
"lov": "plo"
},
"po": {
"lov": "po"
},
"ppo": {
"lov": "ppo"
},
"pr": {
"lov": "pro"
},
"pso": {
"lov": "pso"
},
"rdo": {
"aberowl": "RDO",
"bioportal": "RDO"
},
"reactome": {
"lov": "react"
},
"ro": {
"bioportal": "OBOREL",
"fairsharing": "FAIRsharing.cp0ybc",
"lov": "ro"
},
"sao": {
"bartoc": "1756",
"lov": "sao"
},
"string": {
"zazuko": "string"
},
"sty": {
"biolink": "UMLSSG"
},
"tao": {
"lov": "tao"
},
"te": {
"lov": "te"
},
"uniprot.ptm": {
"prefixcommons": "ptmswitchboard"
},
"vso": {
"lov": "vso"
},
"wikipathways": {
"aberowl": "wikipathways",
"bioportal": "wikipathways"
}
} ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9459667
bioregistry-0.11.12/src/bioregistry/export/ 0000755 0001751 0000177 00000000000 14655546227 020315 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/export/__init__.py 0000644 0001751 0000177 00000000074 14655542206 022420 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Exports for the Bioregistry."""
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/export/__main__.py 0000644 0001751 0000177 00000000171 14655542206 022377 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Export the Bioregistry."""
from .cli import export
if __name__ == "__main__":
export()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/export/cli.py 0000644 0001751 0000177 00000001327 14655542206 021432 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Export the Bioregistry."""
import click
@click.command()
@click.pass_context
def export(ctx: click.Context):
"""Export the Bioregistry."""
from .prefix_maps import generate_contexts
from .rdf_export import export_rdf
from .sssom_export import export_sssom
from .tables_export import export_tables
from .tsv_export import export_tsv
from .warnings_export import export_warnings
from .yaml_export import export_yaml
ctx.invoke(export_warnings)
ctx.invoke(export_rdf)
ctx.invoke(export_tsv)
ctx.invoke(export_yaml)
ctx.invoke(export_sssom)
ctx.invoke(export_tables)
ctx.invoke(generate_contexts)
if __name__ == "__main__":
export()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/export/prefix_maps.py 0000644 0001751 0000177 00000004727 14655542206 023207 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Export extended prefix maps (EPMs), JSON-LD contexts, and SHACL RDF documents.
.. seealso:: https://github.com/biopragmatics/bioregistry/pull/972
"""
import json
import click
import curies
from bioregistry.constants import (
CONTEXT_BIOREGISTRY_PATH,
EXPORT_CONTEXTS,
SHACL_TURTLE_PATH,
)
from bioregistry.resource_manager import manager
REVERSE_PREFIX_MAP_PATH = EXPORT_CONTEXTS.joinpath("bioregistry.rpm.json")
EXTENDED_PREFIX_MAP_PATH = EXPORT_CONTEXTS.joinpath("bioregistry.epm.json")
@click.command()
def generate_contexts():
"""Generate various context files."""
reverse_prefix_map = manager.get_reverse_prefix_map(include_prefixes=True, strict=False)
REVERSE_PREFIX_MAP_PATH.write_text(json.dumps(reverse_prefix_map, indent=4, sort_keys=True))
_context_prefix_maps()
_collection_prefix_maps()
converter = manager.get_converter(include_prefixes=True)
curies.write_jsonld_context(converter, CONTEXT_BIOREGISTRY_PATH)
curies.write_shacl(converter, SHACL_TURTLE_PATH)
curies.write_extended_prefix_map(converter, EXTENDED_PREFIX_MAP_PATH)
def _collection_prefix_maps():
converter = manager.get_converter()
for collection in manager.collections.values():
name = collection.context
if name is None:
continue
path_stub = EXPORT_CONTEXTS.joinpath(name)
subconverter = converter.get_subconverter(collection.resources)
curies.write_jsonld_context(subconverter, path_stub.with_suffix(".context.jsonld"))
curies.write_shacl(subconverter, path_stub.with_suffix(".context.ttl"))
def _context_prefix_maps():
for key in manager.contexts:
converter = manager.get_converter_from_context(key)
stub = EXPORT_CONTEXTS.joinpath(key)
curies.write_jsonld_context(converter, stub.with_suffix(".context.jsonld"))
curies.write_shacl(converter, stub.with_suffix(".context.ttl"))
curies.write_extended_prefix_map(converter, stub.with_suffix(".epm.json"))
if key == "obo": # Special case, maybe put this in data model
synonyms_stub = EXPORT_CONTEXTS.joinpath(f"{key}_synonyms")
curies.write_jsonld_context(
converter, synonyms_stub.with_suffix(".context.jsonld"), include_synonyms=True
)
curies.write_shacl(
converter, synonyms_stub.with_suffix(".context.ttl"), include_synonyms=True
)
if __name__ == "__main__":
generate_contexts()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/export/prefixcc.py 0000644 0001751 0000177 00000003270 14655542206 022465 0 ustar 00runner docker """Update Prefix.cc to reflect the content of the Bioregistry.
.. seealso:: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1038
"""
import random
import click
import requests
import bioregistry
def create(curie_prefix: str, uri_prefix: str) -> requests.Response:
"""Send a CURIE prefix/URI prefix to the Prefix.cc "create" endpoint."""
return requests.post(
f"https://prefix.cc/{curie_prefix}",
data={"create": uri_prefix},
)
def main():
"""Add an OBO Foundry prefix to Prefix.cc."""
prefix_cc_map = requests.get("https://prefix.cc/context").json()["@context"]
records = []
for record in bioregistry.resources():
if not record.get_obofoundry_prefix():
continue
uri_prefix = record.get_uri_prefix()
if not uri_prefix:
continue
if uri_prefix == prefix_cc_map.get(record.prefix):
# No need to re-create something that's already
# both available and correct wrt Bioregistry/OBO
continue
records.append(record)
if not records:
click.echo("No records left to submit to Prefix.cc, good job!")
return
click.echo(f"{len(records):,} records remain to submit to Prefix.cc")
# shuffle records to make sure that if there's an error, it doesn't
# lock the update permanently
random.shuffle(records)
# Pick only the first record, since we can only make one update per day
record = records[0]
uri_prefix = record.get_uri_prefix()
click.echo(f"Attempting to create a record for {record.prefix} {uri_prefix}")
res = create(record.prefix, uri_prefix)
click.echo(res.text)
if __name__ == "__main__":
main()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/export/rdf_export.py 0000644 0001751 0000177 00000021235 14655542206 023037 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Export the Bioregistry to RDF."""
import logging
from typing import Any, Callable, List, Optional, Tuple, Union, cast
import click
import rdflib
from rdflib import (
DCAT,
DCTERMS,
DOAP,
FOAF,
RDF,
RDFS,
SKOS,
XSD,
Literal,
Namespace,
URIRef,
)
from rdflib.term import _is_valid_uri
import bioregistry
from bioregistry import Manager
from bioregistry.constants import (
RDF_JSONLD_PATH,
RDF_NT_PATH,
RDF_TURTLE_PATH,
SCHEMA_JSONLD_PATH,
SCHEMA_NT_PATH,
SCHEMA_TURTLE_PATH,
)
from bioregistry.schema.constants import (
ROR,
WIKIDATA,
_add_schema,
_graph,
bioregistry_metaresource,
bioregistry_resource,
bioregistry_schema,
get_schema_rdf,
)
from bioregistry.schema.struct import Collection, Registry, Resource
logger = logging.getLogger(__name__)
NAMESPACES = {
_ns: Namespace(_uri) for _ns, _uri in bioregistry.manager.get_internal_prefix_map().items()
}
NAMESPACE_WARNINGS = set()
@click.command()
def export_rdf():
"""Export RDF."""
from bioregistry import manager
schema_rdf = get_schema_rdf()
schema_rdf.serialize(SCHEMA_TURTLE_PATH.as_posix(), format="turtle")
schema_rdf.serialize(SCHEMA_NT_PATH.as_posix(), format="nt", encoding="utf-8")
schema_rdf.serialize(
SCHEMA_JSONLD_PATH.as_posix(),
format="json-ld",
context={
"@language": "en",
**dict(schema_rdf.namespaces()),
},
sort_keys=True,
ensure_ascii=False,
)
graph = get_full_rdf(manager=manager) + schema_rdf
graph.serialize(RDF_TURTLE_PATH.as_posix(), format="turtle")
graph.serialize(RDF_NT_PATH.as_posix(), format="nt", encoding="utf-8")
# Currently getting an issue with not being able to shorten URIs
# graph.serialize(os.path.join(DOCS_DATA, "bioregistry.xml"), format="xml")
context = {
"@language": "en",
**dict(graph.namespaces()),
}
graph.serialize(
RDF_JSONLD_PATH.as_posix(),
format="json-ld",
context=context,
sort_keys=True,
ensure_ascii=False,
)
def get_full_rdf(manager: Manager) -> rdflib.Graph:
"""Get a combine RDF graph representing the Bioregistry using :mod:`rdflib`."""
graph = _graph(manager=manager)
_add_schema(graph)
for registry in manager.metaregistry.values():
registry.add_triples(graph)
for collection in manager.collections.values():
collection.add_triples(graph)
for resource in manager.registry.values():
uri_prefix = resource.get_uri_prefix()
if uri_prefix:
graph.bind(resource.prefix, uri_prefix)
_add_resource(graph=graph, manager=manager, resource=resource)
return graph
def collection_to_rdf_str(
collection: Collection,
manager: Manager,
fmt: Optional[str] = None,
) -> str:
"""Get a collection as an RDF string."""
graph = _graph(manager=manager)
collection.add_triples(graph)
return graph.serialize(format=fmt or "turtle")
def metaresource_to_rdf_str(
registry: Registry,
manager: Manager,
fmt: Optional[str] = None,
) -> str:
"""Get a collection as an RDF string."""
graph = _graph(manager=manager)
registry.add_triples(graph)
return graph.serialize(format=fmt or "turtle")
def resource_to_rdf_str(
resource: Resource,
manager: Manager,
fmt: Optional[str] = None,
) -> str:
"""Get a collection as an RDF string."""
graph = _graph(manager=manager)
_add_resource(resource, manager=manager, graph=graph)
return graph.serialize(format=fmt or "turtle")
def _get_resource_functions() -> List[Tuple[Union[str, URIRef], Callable[[Resource], Any], URIRef]]:
return [
("0000008", Resource.get_pattern, XSD.string),
("0000006", Resource.get_uri_format, XSD.string),
("0000024", Resource.get_uri_prefix, XSD.string),
("0000005", Resource.get_example, XSD.string),
("0000012", Resource.is_deprecated, XSD.boolean),
(DCTERMS.description, Resource.get_description, XSD.string),
]
def _get_resource_function_2() -> List[Tuple[Union[str, URIRef], Callable[[Resource], Any]]]:
return [
("0000027", Resource.get_example_iri),
(FOAF.homepage, Resource.get_homepage),
(DOAP.GitRepository, Resource.get_repository),
]
def _add_resource(resource: Resource, *, manager: Manager, graph: rdflib.Graph): # noqa:C901
node = cast(URIRef, bioregistry_resource[resource.prefix])
graph.add((node, RDF.type, bioregistry_schema["0000001"]))
graph.add((node, RDFS.label, Literal(resource.get_name())))
graph.add((node, bioregistry_schema["0000029"], Literal(resource.prefix)))
graph.add((node, DCTERMS.isPartOf, bioregistry_metaresource["bioregistry"]))
graph.add((bioregistry_metaresource["bioregistry"], DCTERMS.hasPart, node))
for synonym in resource.get_synonyms():
graph.add((node, bioregistry_schema["0000023"], Literal(synonym)))
for keyword in resource.get_keywords():
graph.add((node, DCAT.keyword, Literal(keyword)))
for predicate, func, datatype in _get_resource_functions():
value = func(resource)
if value is None:
continue
if not isinstance(predicate, URIRef):
predicate = bioregistry_schema[predicate]
graph.add((node, predicate, Literal(value, datatype=datatype)))
for predicate, func in _get_resource_function_2():
value = func(resource)
if value is None or not _is_valid_uri(value):
continue
if not isinstance(predicate, URIRef):
predicate = bioregistry_schema[predicate]
graph.add((node, predicate, URIRef(value)))
download = (
resource.get_download_owl()
or resource.get_download_obo()
or resource.get_download_obograph()
)
if download:
graph.add((node, bioregistry_schema["0000010"], URIRef(download)))
# Ontological relationships
for depends_on in manager.get_depends_on(resource.prefix) or []:
graph.add((node, bioregistry_schema["0000017"], bioregistry_resource[depends_on]))
for appears_in in manager.get_appears_in(resource.prefix) or []:
graph.add((node, bioregistry_schema["0000018"], bioregistry_resource[appears_in]))
for owner in resource.owners or []:
if owner.ror:
obj = ROR[owner.ror]
elif owner.wikidata:
obj = WIKIDATA[owner.wikidata]
else:
continue
graph.add((node, bioregistry_schema["0000026"], obj))
part_of = manager.get_part_of(resource.prefix)
if part_of:
graph.add((node, DCTERMS.isPartOf, bioregistry_resource[part_of]))
graph.add((bioregistry_resource[part_of], DCTERMS.hasPart, node))
provides = manager.get_provides_for(resource.prefix)
if provides:
graph.add((node, bioregistry_schema["0000011"], bioregistry_resource[provides]))
if resource.has_canonical:
graph.add(
(node, bioregistry_schema["0000016"], bioregistry_resource[resource.has_canonical])
)
contact = resource.get_contact()
if contact is not None:
contact_node = contact.add_triples(graph)
graph.add((node, bioregistry_schema["0000019"], contact_node))
if resource.reviewer is not None and resource.reviewer.orcid:
reviewer_node = resource.reviewer.add_triples(graph)
graph.add((node, bioregistry_schema["0000021"], reviewer_node))
if resource.contributor is not None and resource.contributor.orcid:
contributor_node = resource.contributor.add_triples(graph)
graph.add((contributor_node, DCTERMS.contributor, node))
mappings = resource.get_mappings()
for metaprefix, metaidentifier in (mappings or {}).items():
metaresource = manager.metaregistry[metaprefix]
if metaprefix not in NAMESPACES and metaresource.bioregistry_prefix in NAMESPACES:
metaprefix = metaresource.bioregistry_prefix
if metaprefix not in NAMESPACES:
if metaprefix not in NAMESPACE_WARNINGS:
logger.warning(f"can not find prefix-uri pair for {metaprefix}")
NAMESPACE_WARNINGS.add(metaprefix)
continue
graph.add((node, SKOS.exactMatch, NAMESPACES[metaprefix][metaidentifier]))
graph.add(
(
NAMESPACES[metaprefix][metaidentifier],
DCTERMS.isPartOf,
bioregistry_metaresource[metaresource.prefix],
)
)
graph.add(
(
bioregistry_metaresource[metaresource.prefix],
DCTERMS.hasPart,
NAMESPACES[metaprefix][metaidentifier],
)
)
if __name__ == "__main__":
export_rdf()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/export/schema_export.py 0000644 0001751 0000177 00000000741 14655542206 023523 0 ustar 00runner docker """Export the schema diagram."""
import click
from networkx.drawing.nx_agraph import to_agraph
from bioregistry.constants import SCHEMA_PDF_PATH, SCHEMA_SVG_PATH
from bioregistry.schema.constants import get_schema_nx
@click.command()
def schema_export():
"""Export the schema diagram."""
agraph = to_agraph(get_schema_nx())
agraph.layout(prog="dot")
agraph.draw(SCHEMA_SVG_PATH)
agraph.draw(SCHEMA_PDF_PATH)
if __name__ == "__main__":
schema_export()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/export/sssom_export.py 0000644 0001751 0000177 00000006552 14655542206 023435 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Export the Bioregistry to SSSOM."""
import csv
import logging
from collections import namedtuple
import click
import yaml
import bioregistry
from bioregistry import manager
from bioregistry.constants import SSSOM_METADATA_PATH, SSSOM_PATH
from bioregistry.utils import curie_to_str
__all__ = [
"export_sssom",
]
logger = logging.getLogger(__name__)
Row = namedtuple("Row", "subject_id predicate_id object_id match_type")
CURIE_MAP = manager.get_internal_prefix_map()
METADATA = {
"license": "https://creativecommons.org/publicdomain/zero/1.0/",
"mapping_provider": "https://github.com/biopragmatics/bioregistry",
"mapping_set_group": "bioregistry",
"mapping_set_id": "bioregistry",
"mapping_set_title": "Bioregistry",
"curie_map": CURIE_MAP,
}
@click.command()
def export_sssom():
"""Export the meta-registry as SSSOM."""
rows = []
for prefix, resource in bioregistry.read_registry().items():
mappings = resource.get_mappings()
for metaprefix, metaidentifier in mappings.items():
if metaprefix not in CURIE_MAP:
continue
rows.append(
_make_row("bioregistry", prefix, "skos", "exactMatch", metaprefix, metaidentifier)
)
for appears_in in bioregistry.get_appears_in(prefix) or []:
rows.append(
_make_row(
"bioregistry",
prefix,
"bioregistry.schema",
"0000018",
"bioregistry",
appears_in,
)
)
for depends_on in bioregistry.get_depends_on(prefix) or []:
rows.append(
_make_row(
"bioregistry",
prefix,
"bioregistry.schema",
"0000017",
"bioregistry",
depends_on,
)
)
if resource.part_of and bioregistry.normalize_prefix(resource.part_of):
rows.append(
_make_row("bioregistry", prefix, "bfo", "0000050", "bioregistry", resource.part_of)
)
if resource.provides:
rows.append(
_make_row(
"bioregistry",
prefix,
"bioregistry.schema",
"0000011",
"bioregistry",
resource.provides,
)
)
if resource.has_canonical:
rows.append(
_make_row(
"bioregistry",
prefix,
"bioregistry.schema",
"0000016",
"bioregistry",
resource.has_canonical,
)
)
with SSSOM_PATH.open("w") as file:
writer = csv.writer(file, delimiter="\t")
writer.writerow(Row._fields)
writer.writerows(rows)
with SSSOM_METADATA_PATH.open("w") as file:
yaml.safe_dump(METADATA, file)
def _make_row(mp1: str, mi1: str, rp: str, ri: str, mp2: str, mi2: str) -> Row:
return Row(
subject_id=curie_to_str(mp1, mi1),
predicate_id=curie_to_str(rp, ri),
object_id=curie_to_str(mp2, mi2),
match_type="sssom:HumanCurated",
)
if __name__ == "__main__":
export_sssom()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/export/tables_export.py 0000644 0001751 0000177 00000021442 14655542206 023536 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Make tables exports."""
from textwrap import dedent
import click
import pandas as pd
import bioregistry
from bioregistry.constants import (
TABLES_GOVERNANCE_LATEX_PATH,
TABLES_GOVERNANCE_TSV_PATH,
TABLES_METADATA_LATEX_PATH,
TABLES_METADATA_TSV_PATH,
TABLES_SUMMARY_LATEX_PATH,
)
from bioregistry.summary import BioregistrySummary
__all__ = [
"export_tables",
]
# YES = "β"
YES = "Y"
# MAYBE = "β"
MAYBE = "o"
NO = ""
#: This is Table S2 in the paper
GOVERNANCE_COLUMNS = [
"Registry",
"Scope",
"Status",
"Imports External Prefixes",
"Curates Novel Prefixes",
"Accepts External Contributions",
"Public Version Control",
"Public Issue Tracker",
"Has Public Review Team",
]
def _render_bool(x: bool, true_value: str = YES, false_value: str = NO) -> str:
return true_value if x else false_value
def _replace_na(s: str) -> str:
if s.lower() == "n/a":
return ""
return s
def _short_name_bibtex(registry) -> str:
name = registry.get_short_name()
return f"{name}~\\cite{{{registry.bibtex}}}" if registry.bibtex else name
schema_status_map = {
True: YES,
False: NO,
"required": YES,
"required*": f"{YES}*",
"present": MAYBE,
"present*": f"{MAYBE}*",
"missing": NO,
}
def _sort_key(registry):
if registry.prefix == "bioregistry":
return 0, registry.prefix
return 1, registry.prefix
def _get_governance_df() -> pd.DataFrame:
rows = []
keep_metaprefixes = set(bioregistry.count_mappings())
for registry in sorted(bioregistry.read_metaregistry().values(), key=_sort_key):
if registry.prefix not in keep_metaprefixes:
continue
rows.append(
(
_short_name_bibtex(registry),
registry.governance.scope.title(),
registry.governance.status.title(),
_render_bool(registry.governance.imports),
_render_bool(registry.governance.curates),
_render_bool(registry.governance.accepts_external_contributions),
_render_bool(registry.governance.public_version_controlled_data),
_render_bool(registry.governance.issue_tracker is not None),
registry.governance.review_team_icon,
)
)
return pd.DataFrame(rows, columns=GOVERNANCE_COLUMNS)
#: This is Table 2 in the paper
DATA_MODEL_CAPABILITIES = [
("", "Registry"),
("Metadata Model", "Name"),
("Metadata Model", "Homepage"),
("Metadata Model", "Desc."),
("Metadata Model", "Example ID"),
("Metadata Model", "ID Pattern"),
("Metadata Model", "Provider"),
("Metadata Model", "Alt. Providers"),
("Metadata Model", "Alt. Prefixes"),
("Metadata Model", "License"),
("Metadata Model", "Version"),
("Metadata Model", "Contact"),
("Capabilities and Qualities", "Structured Data"),
("Capabilities and Qualities", "Bulk Data"),
("Capabilities and Qualities", "No Auth. for Data"),
("Capabilities and Qualities", "Permissive License"),
("Capabilities and Qualities", "Prefix Search"),
("Capabilities and Qualities", "Prefix Provider"),
("Capabilities and Qualities", "Resolve CURIEs"),
("Capabilities and Qualities", "Lookup CURIEs"),
]
def _get_metadata_df() -> pd.DataFrame:
rows = []
keep_metaprefixes = set(bioregistry.count_mappings())
for registry in sorted(bioregistry.read_metaregistry().values(), key=_sort_key):
if registry.prefix not in keep_metaprefixes:
continue
rows.append(
(
_short_name_bibtex(registry),
*(
schema_status_map[t]
for t in (
# Data Model
registry.availability.name,
registry.availability.homepage,
registry.availability.description,
registry.availability.example,
registry.availability.pattern,
registry.availability.provider,
registry.availability.alternate_providers,
registry.availability.synonyms,
registry.availability.license,
registry.availability.version,
registry.availability.contact,
# Qualities and Capabilities
registry.qualities.structured_data,
registry.qualities.bulk_data,
registry.qualities.no_authentication,
registry.has_permissive_license,
registry.availability.search,
registry.is_prefix_provider,
registry.is_resolver,
registry.is_lookup,
)
),
)
)
return pd.DataFrame(rows, columns=pd.MultiIndex.from_tuples(DATA_MODEL_CAPABILITIES))
@click.command()
def export_tables():
"""Export tables.
1. TODO: Export data model comparison, see also https://bioregistry.io/related#data-models
2. Export governance comparison, see also https://bioregistry.io/related#governance
"""
governance_df = _get_governance_df()
governance_df.to_csv(TABLES_GOVERNANCE_TSV_PATH, sep="\t", index=False)
TABLES_GOVERNANCE_LATEX_PATH.write_text(
governance_df.to_latex(
index=False,
bold_rows=True,
label="tab:registry-comparison-governance",
escape=False,
caption=dedent(
"""\
A survey of registries' governance and maintenance models. The scope column describes the
kinds of prefixes contained within the registry. The status column is active if the registry
is currently being maintained and is responsive to public external feedback, unresponsive if
the registry is currently being maintained but is not responsive to public external feedback,
and inactive otherwise. The imports external prefixes column denotes if the registry reuses
and harmonizes content from external registries. The curates novel prefixes column denotes
whether novel curation of prefixes and their associated metadata is done for the registry.
The accepts external contributions column denotes whether the registry has both the governance
model and technical infrastructure for accepting external contributions in the form of the
suggestion of new prefixes, improvement to metadata associated with existing prefixes, etc.
The uses public version control column denotes whether the data underlying the registry and/or
its associated code are stored in a publicly accessible version-controlled system (e.g., git
via GitHub). The has public review team column denotes whether there is a publicly accessible
list of the reviewers. Asterisks in this column denote that rather than an explicit list, the
reviewers can be inferred through the registry's version control system.
"""
)
.strip()
.replace("\n", " "),
),
encoding="utf-8",
)
metadata_df = _get_metadata_df()
metadata_df.to_csv(TABLES_METADATA_TSV_PATH, sep="\t", index=False)
metadata_caption = dedent(
f"""\
An overview on registries covering biomedical ontologies, controlled vocabularies, and databases.
A {YES} means the field is required. A {MAYBE} means it is part of the schema, but not required or incomplete
on some entries. A blank cell means that it is not part of the metadata schema. The FAIR column denotes that a
structured dump of the data is easily findable, accessible, and in a structured format in bulk. For
lookup services, some fields (i.e., Example ID, Default Provider, Alternate Providers) are omitted
because inclusion would be redundant. The search column means there is a URL into which a search
query can be formatted to show a list of results. The provider column means there is a URL into
which a prefix can be formatted to show a dedicated page for its metadata.
"""
)
# TODO move remark about non-english language registries in the OntoPortal Alliance
TABLES_METADATA_LATEX_PATH.write_text(
metadata_df.to_latex(
index=False,
bold_rows=True,
escape=False,
label="tab:registry-comparison-governance",
caption=metadata_caption.strip().replace("\n", " "),
),
encoding="utf-8",
)
s = BioregistrySummary.make()
TABLES_SUMMARY_LATEX_PATH.write_text(s.get_table_latex())
if __name__ == "__main__":
export_tables()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/export/tsv_export.py 0000644 0001751 0000177 00000007711 14655542206 023103 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Export components of the bioregistry to TSV."""
import csv
import click
from ..constants import (
COLLECTIONS_TSV_PATH,
METAREGISTRY_TSV_PATH,
REGISTRY_TSV_PATH,
URI_FORMAT_KEY,
)
from ..schema_utils import read_collections, read_metaregistry, read_registry
from ..uri_format import get_uri_format
@click.command()
def export_tsv():
"""Export TSV."""
with COLLECTIONS_TSV_PATH.open("w") as file:
writer = csv.writer(file, delimiter="\t")
writer.writerow(COLLECTIONS_HEADER)
writer.writerows(get_collections_rows())
with METAREGISTRY_TSV_PATH.open("w") as file:
writer = csv.writer(file, delimiter="\t")
writer.writerow(METAREGISTRY_HEADER)
writer.writerows(get_metaregistry_rows())
with REGISTRY_TSV_PATH.open("w") as file:
writer = csv.writer(file, delimiter="\t")
writer.writerow(REGISTRY_HEADER)
writer.writerows(get_registry_rows())
COLLECTIONS_HEADER = [
"identifier",
"name",
"description",
"resources",
"author_names",
"author_orcids",
]
METAREGISTRY_HEADER = [
"metaprefix",
"name",
"homepage",
"description",
"download",
"example",
"contact.name",
"contact.email",
"contact.github",
"provider_uri_format",
"resolver_uri_format",
"resolver_type",
]
METAPREFIXES = [
k
for k in sorted(read_metaregistry())
if k not in {"bioregistry", "biolink", "ncbi", "fairsharing", "go"}
]
REGISTRY_HEADER = [
"identifier",
"name",
"homepage",
"description",
"pattern",
"example",
"email",
URI_FORMAT_KEY,
"download.owl",
"download.obo",
"synonyms",
"deprecated",
*METAPREFIXES,
"part_of",
"provides",
"has_canonical",
# 'type',
]
def get_collections_rows():
"""Get a dataframe of all collections."""
rows = []
for identifier, collection in read_collections().items():
rows.append(
(
identifier,
collection.name,
collection.description,
"|".join(collection.resources),
"|".join(author.name for author in collection.authors),
"|".join(author.orcid for author in collection.authors),
)
)
return rows
def get_metaregistry_rows():
"""Get a dataframe of all metaresources."""
rows = []
for metaprefix, data in read_metaregistry().items():
rows.append(
(
metaprefix,
data.name,
data.homepage,
data.description,
data.download,
data.example,
data.contact.name,
data.contact.email,
data.contact.github,
data.provider_uri_format,
data.resolver_uri_format,
data.resolver_type,
)
)
return rows
def get_registry_rows():
"""Get a dataframe of all resources."""
rows = []
for prefix, data in read_registry().items():
mappings = data.get_mappings()
rows.append(
(
prefix,
data.get_name(),
data.get_homepage(),
data.get_description(),
data.get_pattern(),
data.get_example(),
data.get_contact_email(),
get_uri_format(prefix),
data.download_owl,
data.download_obo,
"|".join(sorted(data.get_synonyms())),
data.is_deprecated(),
*[mappings.get(metaprefix) for metaprefix in METAPREFIXES],
# '|'.join(data.get('appears_in', [])),
data.part_of,
data.provides,
data.has_canonical,
# data.get('type'),
# TODO could add more, especially mappings
)
)
return rows
if __name__ == "__main__":
export_tsv()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/export/warnings_export.py 0000644 0001751 0000177 00000011271 14655542206 024113 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Generate the warnings file.
This lists any sorts of things that should be fixed upstream, but are instead manually curated in the Bioregistry.
"""
import os
from typing import Callable
import click
import yaml
from tqdm import tqdm
import bioregistry
from bioregistry.constants import DOCS_DATA, EXTERNAL
from bioregistry.resolve import get_external
__all__ = [
"export_warnings",
]
CURATIONS_PATH = DOCS_DATA.joinpath("curation.yml")
ENTRIES = sorted(
(prefix, resource.dict(exclude_none=True))
for prefix, resource in bioregistry.read_registry().items()
)
def _g(predicate: Callable[[str], bool]):
return [
{
"prefix": prefix,
"name": bioregistry.get_name(prefix),
"homepage": bioregistry.get_homepage(prefix),
}
for prefix in sorted(bioregistry.read_registry())
if predicate(prefix)
]
def get_unparsable_uris():
"""Get a list of IRIs that can be constructed, but not parsed."""
rows = []
for prefix in tqdm(bioregistry.read_registry(), desc="Checking URIs"):
example = bioregistry.get_example(prefix)
if example is None:
continue
uri = bioregistry.get_iri(prefix, example, use_bioregistry_io=False)
if uri is None:
continue
k, v = bioregistry.parse_iri(uri)
if k is None:
rows.append((prefix, example, uri, k, v))
return rows
@click.command()
def export_warnings():
"""Make warnings list."""
# unparsable = get_unparsable_uris()
missing_wikidata_database = _g(
lambda prefix: get_external(prefix, "wikidata").get("database") is None
and not bioregistry.has_no_terms(prefix)
)
missing_pattern = _g(
lambda prefix: bioregistry.get_pattern(prefix) is None
and not bioregistry.has_no_terms(prefix)
)
missing_format_url = _g(
lambda prefix: bioregistry.get_uri_format(prefix) is None
and not bioregistry.has_no_terms(prefix)
)
missing_example = _g(
lambda prefix: bioregistry.get_example(prefix) is None
and not bioregistry.has_no_terms(prefix)
and bioregistry.get_provides_for(prefix) is None
)
prefix_xrefs = [
{
"metaprefix": metaprefix,
"name": registry.get_short_name(),
}
for metaprefix, registry in sorted(bioregistry.read_metaregistry().items())
if EXTERNAL.joinpath(metaprefix, "curation.tsv").is_file()
]
with CURATIONS_PATH.open("w") as file:
yaml.safe_dump(
{
"wikidata": missing_wikidata_database,
"pattern": missing_pattern,
"formatter": missing_format_url,
"example": missing_example,
"prefix_xrefs": prefix_xrefs,
# "unparsable": unparsable,
},
file,
)
miriam_pattern_wrong = [
dict(
prefix=prefix,
name=bioregistry.get_name(prefix),
homepage=bioregistry.get_homepage(prefix),
correct=entry["pattern"],
miriam=entry["miriam"]["pattern"],
)
for prefix, entry in ENTRIES
if "miriam" in entry
and "pattern" in entry
and entry["pattern"] != entry["miriam"]["pattern"]
]
miriam_embedding_rewrites = [
dict(
prefix=prefix,
name=bioregistry.get_name(prefix),
homepage=bioregistry.get_homepage(prefix),
pattern=bioregistry.get_pattern(prefix),
correct=entry["namespace.embedded"],
miriam=entry["miriam"]["namespaceEmbeddedInLui"],
)
for prefix, entry in ENTRIES
if "namespace.embedded" in entry
]
# When are namespace rewrites required?
miriam_prefix_rewrites = [
dict(
prefix=prefix,
name=bioregistry.get_name(prefix),
homepage=bioregistry.get_homepage(prefix),
pattern=bioregistry.get_pattern(prefix),
correct=entry["namespace.rewrite"],
)
for prefix, entry in ENTRIES
if "namespace.rewrite" in entry
]
with open(os.path.join(DOCS_DATA, "warnings.yml"), "w") as file:
yaml.safe_dump(
{
"wrong_patterns": miriam_pattern_wrong,
"embedding_rewrites": miriam_embedding_rewrites,
"prefix_rewrites": miriam_prefix_rewrites,
"license_conflict": [
dict(prefix=prefix, obo=obo, ols=ols)
for prefix, _override, obo, ols in bioregistry.get_license_conflicts()
],
},
file,
)
if __name__ == "__main__":
export_warnings()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/export/yaml_export.py 0000644 0001751 0000177 00000002455 14655542206 023231 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Export components of the bioregistry to YAML."""
import json
import click
import yaml
from ..constants import (
COLLECTIONS_YAML_PATH,
METAREGISTRY_YAML_PATH,
REGISTRY_JSON_PATH,
REGISTRY_YAML_PATH,
)
from ..resource_manager import manager
from ..schema import sanitize_mapping
from ..schema_utils import read_collections, read_metaregistry
from ..utils import get_hexdigests
@click.command()
def export_yaml():
"""Export the registry as YAML."""
pre_digests = get_hexdigests()
registry = manager.rasterize()
metaregistry = sanitize_mapping(read_metaregistry())
collections = sanitize_mapping(read_collections())
with REGISTRY_YAML_PATH.open("w") as file:
yaml.safe_dump(stream=file, data=registry, allow_unicode=True)
with REGISTRY_JSON_PATH.open("w") as file:
json.dump(registry, file, indent=2, sort_keys=True, ensure_ascii=False)
with METAREGISTRY_YAML_PATH.open("w") as file:
yaml.safe_dump(stream=file, data=metaregistry, allow_unicode=True)
with COLLECTIONS_YAML_PATH.open("w") as file:
yaml.safe_dump(stream=file, data=collections, allow_unicode=True)
if pre_digests != get_hexdigests():
click.echo("::set-output name=BR_UPDATED::true")
if __name__ == "__main__":
export_yaml()
././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9499667
bioregistry-0.11.12/src/bioregistry/external/ 0000755 0001751 0000177 00000000000 14655546227 020616 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/__init__.py 0000644 0001751 0000177 00000005476 14655542206 022734 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Acquisition, processing, and alignment of external registries."""
from typing import Callable, List, Tuple
from .aberowl import get_aberowl
from .bartoc import get_bartoc
from .biocontext import get_biocontext
from .biolink import get_biolink
from .bioportal import get_agroportal, get_bioportal, get_ecoportal
from .cellosaurus import get_cellosaurus
from .cheminf import get_cheminf
from .cropoct import get_cropoct
from .edam import get_edam
from .fairsharing import get_fairsharing
from .go import get_go
from .hl7 import get_hl7
from .integbio import get_integbio
from .lov import get_lov
from .miriam import get_miriam
from .n2t import get_n2t
from .ncbi import get_ncbi
from .obofoundry import get_obofoundry
from .ols import get_ols
from .ontobee import get_ontobee
from .pathguide import get_pathguide
from .prefixcommons import get_prefixcommons
from .re3data import get_re3data
from .rrid import get_rrid
from .togoid import get_togoid
from .uniprot import get_uniprot
from .wikidata import get_wikidata
from .zazuko import get_zazuko
__all__ = [
"GETTERS",
# Getter functions
"get_biocontext",
"get_biolink",
"get_bioportal",
"get_cellosaurus",
"get_cheminf",
"get_fairsharing",
"get_go",
"get_miriam",
"get_n2t",
"get_ncbi",
"get_obofoundry",
"get_ols",
"get_ontobee",
"get_prefixcommons",
"get_uniprot",
"get_wikidata",
"get_edam",
"get_re3data",
"get_hl7",
"get_bartoc",
"get_integbio",
"get_lov",
"get_pathguide",
"get_togoid",
"get_zazuko",
"get_rrid",
]
GETTERS: List[Tuple[str, str, Callable]] = [
("obofoundry", "OBO", get_obofoundry),
("ols", "OLS", get_ols),
("miriam", "MIRIAM", get_miriam),
("wikidata", "Wikidata", get_wikidata),
("n2t", "N2T", get_n2t),
("go", "GO", get_go),
("bioportal", "BioPortal", get_bioportal),
("prefixcommons", "Prefix Commons", get_prefixcommons),
("biocontext", "BioContext", get_biocontext),
("biolink", "Biolink", get_biolink),
("ncbi", "NCBI", get_ncbi),
("uniprot", "UniProt", get_uniprot),
("cellosaurus", "Cellosaurus", get_cellosaurus),
("ontobee", "OntoBee", get_ontobee),
("cheminf", "CHEMINF", get_cheminf),
("fairsharing", "FAIRsharing", get_fairsharing),
("agroportal", "AgroPortal", get_agroportal),
("ecoportal", "EcoPortal", get_ecoportal),
("aberowl", "AberOWL", get_aberowl),
("cropoct", "CropOCT", get_cropoct),
("edam", "EDAM", get_edam),
("re3data", "re3data", get_re3data),
("hl7", "HL7", get_hl7),
("bartoc", "BARTOC", get_bartoc),
("integbio", "Integbio", get_integbio),
("lov", "LOV", get_lov),
("pathguide", "Pathguide", get_pathguide),
("togoid", "TogoID", get_togoid),
("zazuko", "Zazuko", get_zazuko),
("rrid", "RRID", get_rrid),
]
././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9499667
bioregistry-0.11.12/src/bioregistry/external/aberowl/ 0000755 0001751 0000177 00000000000 14655546227 022251 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/aberowl/__init__.py 0000644 0001751 0000177 00000004443 14655542206 024360 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download the AberOWL registry."""
import json
from pathlib import Path
import yaml
from pystow.utils import download
from bioregistry.constants import RAW_DIRECTORY
from bioregistry.external.alignment_utils import Aligner
__all__ = [
"get_aberowl",
"AberOWLAligner",
]
DIRECTORY = Path(__file__).parent.resolve()
RAW_PATH = RAW_DIRECTORY / "aberowl.json"
PROCESSED_PATH = DIRECTORY / "processed.json"
ABEROWL_URL = "http://aber-owl.net/api/ontology/?drf_fromat=json&format=json"
def get_aberowl(force_download: bool = False):
"""Get the AberOWL registry."""
if PROCESSED_PATH.exists() and not force_download:
with PROCESSED_PATH.open() as file:
return json.load(file)
download(url=ABEROWL_URL, path=RAW_PATH, force=True)
with RAW_PATH.open() as file:
entries = yaml.full_load(file)
rv = {entry["acronym"]: _process(entry) for entry in entries}
with PROCESSED_PATH.open("w") as file:
json.dump(rv, file, indent=2, sort_keys=True)
return rv
def _process(entry):
rv = {
"prefix": entry["acronym"],
"name": entry["name"],
}
submission = entry.get("submission", {})
if submission:
rv["homepage"] = submission.get("home_page")
description = submission.get("description")
if description:
description = (
description.strip().replace("\r\n", " ").replace("\n", " ").replace(" ", " ")
)
rv["description"] = description
version = submission.get("version")
if version:
rv["version"] = version.strip()
download_url_suffix = submission.get("download_url")
if not download_url_suffix:
pass
elif download_url_suffix.endswith(".owl"):
rv["download_owl"] = f"http://aber-owl.net/{download_url_suffix}"
elif download_url_suffix.endswith(".obo"):
rv["download_obo"] = f"http://aber-owl.net/{download_url_suffix}"
else:
pass # what's going on here?
return {k: v for k, v in rv.items() if k and v}
class AberOWLAligner(Aligner):
"""Aligner for AberOWL."""
key = "aberowl"
getter = get_aberowl
curation_header = ["name", "homepage", "description"]
if __name__ == "__main__":
AberOWLAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723255144.0
bioregistry-0.11.12/src/bioregistry/external/aberowl/processed.json 0000644 0001751 0000177 00002500751 14655544550 025142 0 ustar 00runner docker {
"ABA-AMB": {
"description": "Allen Brain Atlas P56 Mouse Ontology",
"download_owl": "http://aber-owl.net/media/ontologies/ABA-AMB/1/aba-amb.owl",
"homepage": "http://www.brain-map.org",
"name": "Allen Brain Atlas (ABA) Adult Mouse Brain Ontology",
"prefix": "ABA-AMB",
"version": "1"
},
"ABBS": {
"name": "abbssm",
"prefix": "ABBS"
},
"ABD": {
"description": "Our disease ontology provides information on infectious diseases, disease synonyms, transmission pathways, disease agents, affected populations and disease properties. Diseases have been grouped into syndromic disease categories, such that programmers can look through relevant categories, as well as at specific diseases. Organisms, linked to both agents and populations, are structured hierarchically, to provide multiple levels of organism resolution. In addition, both disease transmission and relevant disease properties are available to search. Disease properties include tags like 'notifiable diseases' and 'economic importance' to flag particular disease characteristics that may be of interest, but are not captured elsewhere.",
"download_owl": "http://aber-owl.net/media/ontologies/ABD/4/abd.owl",
"homepage": "http://brd.bsvgateway.org/disease",
"name": "Anthology of Biosurveillance Diseases",
"prefix": "ABD"
},
"ABS": {
"name": "Biosurveillance Diseases",
"prefix": "ABS"
},
"ACESO": {
"description": "An ontology to help describe data about Adverse Childhood Experiences.",
"download_owl": "http://aber-owl.net/media/ontologies/ACESO/3/aceso.owl",
"name": "Adverse Childhood Experiences Ontology",
"prefix": "ACESO",
"version": "1.1"
},
"ACGT-MO": {
"description": "The intention of the ACGT Master Ontology (MO) is to represent the domain of cancer research and management in a computationally tractable manner.",
"download_owl": "http://aber-owl.net/media/ontologies/ACGT-MO/2/acgt-mo.owl",
"homepage": "http://www.ifomis.org/acgt",
"name": "Cancer Research and Management ACGT Master Ontology",
"prefix": "ACGT-MO",
"version": "1.1"
},
"ACVD_ONTOLOGY": {
"description": "The ontology describes the related aspects of atherosclerotic cerebrovascular disease, and provides a clear set of cross-lingual concepts and terms with an explicit hierarchical structure, helping scientific researchers to quickly retrieve relevant medical literature, assisting data scientists to efficiently identify relevant contents in electronic health records, and providing a clear domain framework for academic reference. The current ontology included 10 top-level classes, respectively clinical manifestation, comorbidity, complication, diagnosis, model of atherosclerotic cerebrovascular disease, pathogenesis, prevention, rehabilitation, risk factor, and treatment. Totally, there are 1715 concepts in the 11-level ontology, covering 4588 Chinese terms, 6617 English terms, and 972 definitions.",
"download_owl": "http://aber-owl.net/media/ontologies/ACVD_ONTOLOGY/2/acvd_ontology.owl",
"name": "Atherosclerotic Cerebrovascular Disease Ontology",
"prefix": "ACVD_ONTOLOGY",
"version": "1.0"
},
"AD-DROP": {
"description": "Alzheimer Disease Relevance Ontology by Process (AD-DROP) aimed at classifying Disease Relevant Process according to their specificity, frequency and pathogenic intensity properties toward AD",
"download_owl": "http://aber-owl.net/media/ontologies/AD-DROP/1/ad-drop.owl",
"name": "Alzheimer Disease Relevance Ontology by Process",
"prefix": "AD-DROP",
"version": "alpha"
},
"ADALAB": {
"description": "AdaLab ontology",
"download_owl": "http://aber-owl.net/media/ontologies/ADALAB/10/adalab.owl",
"name": "AdaLab ontology",
"prefix": "ADALAB",
"version": "0.9.2"
},
"ADALAB-META": {
"description": "AdaLab meta ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/ADALAB-META/12/adalab-meta.owl",
"name": "AdaLab-meta ontology",
"prefix": "ADALAB-META",
"version": "0.9.2"
},
"ADAR": {
"description": "The autism DSM-ADI-R (ADAR) ontology extends an ontology by Tu et al. with additional SWRL rules to infer phenotypes from ADI-R items. It includes OWL class definitions representing DSM IV diagnostic criteria for autistic disorder and ASD criteria for Autism Spectrum Disorder OWL Reasoners can thus infer autism-related phenotypes from ADI-R questionnaire results Tu SW, Tennakoon L, Connor MO, Das A. Using an Integrated Ontology and Information Model for Querying and Reasoning about Phenotypes\u202f: The Case of Autism. AMIA Annu Symp Proc 2008;727\u201331",
"download_owl": "http://aber-owl.net/media/ontologies/ADAR/1/adar.owl",
"name": "Autism DSM-ADI-R ontology",
"prefix": "ADAR",
"version": "1.1"
},
"ADCAD": {
"description": "Ontology to support disciplinary annotation of datasets housed at the Arctic Data Center (https://arcticdata.io)",
"download_owl": "http://aber-owl.net/media/ontologies/ADCAD/1/adcad.owl",
"homepage": "https://github.com/NCEAS/adc-disciplines",
"name": "Arctic Data Center Academic Disciplines Ontology",
"prefix": "ADCAD",
"version": "Version 1.0.0"
},
"ADHER_INTCARE_EN": {
"description": "This ontology includes concepts in English related to adherence to therapeutic plans in the context of integrated care. Includes maps with Snomed CT, bibliographic references and definitions from the Dictionary of the Royal Academy of Medicine of Spain. Ontology developed with the support of the project StandICT.eu. The equivalent ontology in Spanish is ADHER_INTCARE_SP.",
"download_owl": "http://aber-owl.net/media/ontologies/ADHER_INTCARE_EN/1/adher_intcare_en.owl",
"name": "Adherence and Integrated Care",
"prefix": "ADHER_INTCARE_EN",
"version": "English 051319"
},
"ADHER_INTCARE_SP": {
"description": "This ontology includes concepts in Spanish related to adherence to therapeutic plans in the context of integrated care. Includes maps with Snomed CT, bibliographic references and definitions from the Dictionary of the Royal Academy of Medicine of Spain. Ontology developed with the support of the project StandICT.eu.",
"download_owl": "http://aber-owl.net/media/ontologies/ADHER_INTCARE_SP/6/adher_intcare_sp.owl",
"name": "Adherence and Integrated Care in Spanish",
"prefix": "ADHER_INTCARE_SP",
"version": "Spanish 052319"
},
"ADMF": {
"name": "alzhaimer dessiese main factors",
"prefix": "ADMF"
},
"ADMIN": {
"description": "This is an ontology showing a nurse administrator's process domain",
"download_owl": "http://aber-owl.net/media/ontologies/ADMIN/1/admin.owl",
"name": "Nurse Administrator",
"prefix": "ADMIN"
},
"ADMO": {
"description": "Alzheimer\u2019s disease (AD) pathophysiology is still imperfectly understood and current paradigms have not led to curative outcome. Omics technologies offer great promises for improving our understanding and generating new hypotheses. However, integration and interpretation of such data pose major challenges, calling for adequate knowledge models. AlzPathway is a disease map that gives a detailed and broad account of AD pathophysiology. However, AlzPathway lacks formalism, which can lead to ambiguity and misinterpretation. Ontologies are an adequate framework to overcome this limitation, through their axiomatic definitions and logical reasoning prop-erties. We introduce the AD Map Ontology (ADMO), an ontological upper model based on systems biology terms. We then propose to convert AlzPathway into an ontology and to integrate it into ADMO.",
"download_owl": "http://aber-owl.net/media/ontologies/ADMO/4/admo.owl",
"name": "Alzheimer Disease Map Ontology",
"prefix": "ADMO",
"version": "beta"
},
"ADO": {
"description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining.",
"download_owl": "http://aber-owl.net/media/ontologies/ADO/8/ado.owl",
"homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO",
"name": "Alzheimer's Disease Ontology",
"prefix": "ADO"
},
"ADW": {
"description": "An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.",
"download_owl": "http://aber-owl.net/media/ontologies/ADW/2/adw.owl",
"homepage": "http://www.animaldiversity.org",
"name": "Animal Natural History and Life History Ontology",
"prefix": "ADW",
"version": "10/11/04"
},
"AEO": {
"description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology",
"download_owl": "http://aber-owl.net/media/ontologies/AEO/8/aeo.owl",
"homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology/",
"name": "Anatomical Entity Ontology",
"prefix": "AEO"
},
"AERO": {
"description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events.",
"download_owl": "http://aber-owl.net/media/ontologies/AERO/45/aero.owl",
"homepage": "http://purl.obolibrary.org/obo/aero",
"name": "Adverse Event Reporting Ontology",
"prefix": "AERO",
"version": "unknown"
},
"AFO": {
"description": "Allotrope Merged Ontology Suite
The AFO is an ontology suite that provides a standard vocabulary and semantic model for the representation of laboratory analytical processes. The AFO suite is aligned at the upper layer to the Basic Formal Ontology (BFO). The core domains modeled include: Equipment, Material, Process, and Results.
This version of Allotrope Foundation Ontology (AFO) has been prepared specifically for publication on the NCBO platform.
license: http://purl.allotrope.org/voc/creative-commons-attribution-license
rights: http://purl.allotrope.org/voc/copyright
Please get the latest version of AFO from http://purl.allotrope.org
",
"download_owl": "http://aber-owl.net/media/ontologies/AFO/38/afo.owl",
"homepage": "http://purl.allotrope.org",
"name": "Allotrope Merged Ontology Suite",
"prefix": "AFO",
"version": "REC/2024/06"
},
"AFPO": {
"description": "AfPO is a tool which enables to annotate the African individuals, and brings together knowledge accumulated about existing populations with their genetic fingerprint in a standardized format.",
"download_owl": "http://aber-owl.net/media/ontologies/AFPO/1/afpo.owl",
"homepage": "https://github.com/h3abionet/afpo",
"name": "African Population Ontology",
"prefix": "AFPO"
},
"AGENSAKONGONLINE": {
"name": "Keris99-Agen-Sakong-Online-Capsa-Susun-Bandar-Poker-Judi-Domino99-BandarQ-AduQ",
"prefix": "AGENSAKONGONLINE"
},
"AGRO": {
"description": "Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments",
"download_owl": "http://aber-owl.net/media/ontologies/AGRO/7/agro.owl",
"homepage": "https://github.com/AgriculturalSemantics/agro",
"name": "Agronomy Ontology",
"prefix": "AGRO"
},
"AGROCYMAC": {
"description": "Agrocymac es una ontolog\u00eda creada para estructurar informaci\u00f3n sobre el control y monitoreo de plagas, malezas y enfermedades que afectan espec\u00edficamente a los cultivos de Arroz, Caf\u00e9 y Cacao.",
"download_owl": "http://aber-owl.net/media/ontologies/AGROCYMAC/2/agrocymac.owl",
"name": "Control y Monitoreo de afecciones en los cultivos",
"prefix": "AGROCYMAC"
},
"AGROMOP": {
"description": "Ontologia con informaci\u00f3n relevante al cuidado del cacao de manera org\u00e1nica contra plagas y enfermedades.",
"download_owl": "http://aber-owl.net/media/ontologies/AGROMOP/1/agromop.owl",
"name": "Control de Cacao",
"prefix": "AGROMOP",
"version": "1.1"
},
"AHOL": {
"description": "AHOL (Animal Health Ontology for Livestock) is an ontology of characteristics defining health issues of livestock in their environment (EOL) linked to their phenotypes (ATOL). AHOL aims to: - provide a reference ontology of health traits of farm animals for the international scientific and educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the AHOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production",
"download_owl": "http://aber-owl.net/media/ontologies/AHOL/1/ahol.owl",
"homepage": "http://147.99.156.182/ontologies/visualisation/ontologie/",
"name": "Animal Health Ontology for Livestock",
"prefix": "AHOL",
"version": "1.0"
},
"AHSO": {
"description": "(Work in progress - please contact ahso@datadrivensurveillance.org before using this ontology) This is an ontology for health surveillance, assuming that surveillance data is recorded at three main levels: SAMPLE data - data about specific collected samples; OBSERVATIONS, which can aggregate several samples; and OBSERVATIONAL CONTEXT, which is the context in which the observations were made (for instance clinical observation, surveillance sampling, etc). HEALTH EVENT is the occurrence in the real World to be modeled. This occurrence is an abstract concept, as it generally cannot be determined what are its boundaries in time, space, or population units. We assume that several OBSERVATIONS are derived from each health event, and recorded in the same or different databases - for instance clinical journal, laboratory database, abattoir. At the same time or not. AHSO attempts to model these time specific observations. The ontology is focused on the modeling of the animal and health information connected to a single observation, made at a specific point on time. All the information recorded is relative to that specific point in time. For instance, an animal belongs to a herd, which belongs to an owner, AT THE TIME OF THE OBSERVATION. We do not attempt to model how that animal changed herds on time. Similarly, we do not model clinical progression. It is up to those using the data to create definitions of when two observations should be connected to the same event.",
"download_owl": "http://aber-owl.net/media/ontologies/AHSO/1/ahso.owl",
"homepage": "http://datadrivensurveillance.org/ahso",
"name": "Animal Health Surveillance Ontology",
"prefix": "AHSO",
"version": "0.1.0"
},
"AI-RHEUM": {
"description": "AI/RHEUM is used for the diagnosis of rheumatologic diseases. AI/RHEUM contains findings, such as clinical signs, symptoms, laboratory test results, radiologic observations, tissue biopsy results, and intermediate diagnosis hypotheses. Findings and hypotheses, which include definitions, are used to reach diagnostic conclusions with definite, probable, or possible certainty. AI/RHEUM is used by clinicians and informatics researchers.",
"name": "Artificial Intelligence Rheumatology Consultant System Ontology",
"prefix": "AI-RHEUM",
"version": "2016AB"
},
"AIDSCLIN": {
"description": "This new ontology will cover the knowledge on AIDS and the relevant clinic activities, which imports the HIV ontology at the site https://bioportal.bioontology.org/ontologies/HIVO004 as its main or basic concept system. The new ontology is named AIDSClinic001.owl",
"download_owl": "http://aber-owl.net/media/ontologies/AIDSCLIN/4/aidsclin.owl",
"homepage": "http://bhf.miforum.net/english/index_english.htm",
"name": "AIDSClinicOntology",
"prefix": "AIDSCLIN",
"version": "001"
},
"AIDSONT": {
"description": "This ontology will cover the knowledge on AIDS and the relevant clinic activities, which imports the HIV ontology at the site https://bioportal.bioontology.org/ontologies/HIVO004 as its main or basic concept system.",
"download_owl": "http://aber-owl.net/media/ontologies/AIDSONT/1/aidsont.owl",
"name": "AIDSOntology",
"prefix": "AIDSONT",
"version": "001"
},
"AIO": {
"description": "This ontology models classes and relationships describing deep learning networks, their component layers and activation functions, as well as potential biases.",
"download_owl": "http://aber-owl.net/media/ontologies/AIO/17/aio.owl",
"homepage": "https://github.com/berkeleybop/artificial-intelligence-ontology",
"name": "Artificial Intelligence Ontology",
"prefix": "AIO",
"version": "2024-08-02"
},
"AION": {
"description": "This ontology models classes and relationships describing Ensemble Learning, their classes, and subclasses.",
"download_owl": "http://aber-owl.net/media/ontologies/AION/1/aion.owl",
"homepage": "https://bioportal.bioontology.org/ontologies/AION",
"name": "AI Ontology (AION)",
"prefix": "AION",
"version": "2023-09-08"
},
"AIPBC": {
"download_owl": "http://aber-owl.net/media/ontologies/AIPBC/1/aipbc.owl",
"name": "Aromatase_Inhibitor_Pathway_Breast_Cell_Pharmacodynamics",
"prefix": "AIPBC",
"version": "1.1"
},
"AIRBUS": {
"description": "A simple vocabulary for Airbus Aircraft",
"name": "Airbus",
"prefix": "AIRBUS",
"version": "1.0.4"
},
"AISM": {
"description": "The AISM contains terms used in insect biodiversity research for describing structures of the exoskeleton and the skeletomuscular system. It aims to serve as the basic backbone of generalized terms to be expanded with order-specific terminology.",
"download_owl": "http://aber-owl.net/media/ontologies/AISM/19/aism.owl",
"homepage": "https://github.com/insect-morphology/aism",
"name": "Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)",
"prefix": "AISM"
},
"AJAY": {
"name": "ajaykumar",
"prefix": "AJAY"
},
"ALLERGIDOC": {
"name": "Allergy Ontology",
"prefix": "ALLERGIDOC"
},
"ALLERGYDETECTOR": {
"description": "Allergy Detection Ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/ALLERGYDETECTOR/1/allergydetector.owl",
"name": "Allergy Detector II",
"prefix": "ALLERGYDETECTOR",
"version": "0.0.1"
},
"AMINO-ACID": {
"description": "An ontology of amino acids and their properties. Inferred version.",
"download_owl": "http://aber-owl.net/media/ontologies/AMINO-ACID/2/amino-acid.owl",
"homepage": "http://www.co-ode.org/ontologies/amino-acid/2009/02/16/",
"name": "Amino Acid Ontology",
"prefix": "AMINO-ACID",
"version": "classified"
},
"AMPHX": {
"description": "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).",
"download_owl": "http://aber-owl.net/media/ontologies/AMPHX/4/amphx.owl",
"homepage": "https://github.com/EBISPOT/amphx_ontology",
"name": "The Amphioxus Development and Anatomy Ontology",
"prefix": "AMPHX"
},
"ANC": {
"name": "ANC",
"prefix": "ANC"
},
"ANCESTRO": {
"description": "The Ancestry Ontology (Ancestro) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies",
"download_owl": "http://aber-owl.net/media/ontologies/ANCESTRO/2/ancestro.owl",
"homepage": "https://github.com/daniwelter/ancestro",
"name": "Ancestry Ontology",
"prefix": "ANCESTRO",
"version": "1.0"
},
"AO": {
"description": "Asthma ontology",
"download_owl": "http://aber-owl.net/media/ontologies/AO/2/ao.owl",
"homepage": "www.clininf.eu",
"name": "Asthma Ontology",
"prefix": "AO",
"version": "1.3"
},
"APACOMPUTER": {
"description": "APA Computer Cluster",
"download_owl": "http://aber-owl.net/media/ontologies/APACOMPUTER/1/apacomputer.owl",
"name": "Computer Cluster",
"prefix": "APACOMPUTER"
},
"APADISORDERS": {
"description": "APA Disorders cluster, owls loaded from urls.",
"download_owl": "http://aber-owl.net/media/ontologies/APADISORDERS/1/apadisorders.owl",
"name": "Disorders cluster",
"prefix": "APADISORDERS"
},
"APAEDUCLUSTER": {
"description": "APA Educational Cluster, URI based ontology load",
"download_owl": "http://aber-owl.net/media/ontologies/APAEDUCLUSTER/1/apaeducluster.owl",
"name": "Educational Cluster",
"prefix": "APAEDUCLUSTER"
},
"APANEUROCLUSTER": {
"description": "APA Neuropsychology and Neurology Cluster",
"download_owl": "http://aber-owl.net/media/ontologies/APANEUROCLUSTER/1/apaneurocluster.owl",
"name": "APA Neuro Cluster",
"prefix": "APANEUROCLUSTER"
},
"APAOCUEMPLOY": {
"description": "APA Occupational and Employment Cluster",
"download_owl": "http://aber-owl.net/media/ontologies/APAOCUEMPLOY/1/apaocuemploy.owl",
"name": "APA Occupational and Employment cluster",
"prefix": "APAOCUEMPLOY"
},
"APAONTO": {
"description": "APA thesaurus . Flat ontology file",
"download_owl": "http://aber-owl.net/media/ontologies/APAONTO/4/apaonto.owl",
"name": "Psychology Ontology",
"prefix": "APAONTO",
"version": "4"
},
"APASTATISTICAL": {
"description": "APA Statistical Cluster",
"download_owl": "http://aber-owl.net/media/ontologies/APASTATISTICAL/1/apastatistical.owl",
"name": "APA Statistical Cluster",
"prefix": "APASTATISTICAL"
},
"APATANDT": {
"description": "APA Tests and Testing Cluster",
"download_owl": "http://aber-owl.net/media/ontologies/APATANDT/1/apatandt.owl",
"name": "APA Tests and Testing cluster",
"prefix": "APATANDT"
},
"APATREATMENT": {
"description": "APA Treatment Cluster",
"download_owl": "http://aber-owl.net/media/ontologies/APATREATMENT/1/apatreatment.owl",
"name": "APA Treatment Cluster",
"prefix": "APATREATMENT"
},
"APO": {
"description": "A structured controlled vocabulary for the phenotypes of Ascomycete fungi",
"download_owl": "http://aber-owl.net/media/ontologies/APO/57/apo.owl",
"homepage": "http://www.yeastgenome.org/",
"name": "Ascomycete phenotype ontology",
"prefix": "APO"
},
"APOLLO-SV": {
"description": "Apollo-SV, developed as an OWL specification, defines the terms and relations necessary for interoperation between epidemic simulators and public health application software that interface with these simulators.",
"download_owl": "http://aber-owl.net/media/ontologies/APOLLO-SV/21/apollo-sv.owl",
"homepage": "https://github.com/ApolloDev/apollo-sv",
"name": "Apollo Structured Vocabulary",
"prefix": "APOLLO-SV",
"version": "v4.0.1"
},
"APOLLO_SV": {
"description": "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.",
"download_owl": "http://aber-owl.net/media/ontologies/APOLLO_SV/24/apollo_sv.owl",
"homepage": "https://github.com/ApolloDev/apollo-sv",
"name": "Apollo Structured Vocabulary",
"prefix": "APOLLO_SV"
},
"APRO": {
"description": "APRO\uff08Ancient Poet Resource Ontology\uff09\u662f\u4e00\u4e2a\u65e8\u5728\u7cfb\u7edf\u6027\u5730\u7ec4\u7ec7\u548c\u63cf\u8ff0\u4e0e\u4e2d\u56fd\u53e4\u4ee3\u8bd7\u4eba\u53ca\u5176\u4f5c\u54c1\u76f8\u5173\u4fe1\u606f\u7684\u672c\u4f53\u3002\u672c\u4f53\u8986\u76d6\u4e86\u53e4\u4ee3\u8bd7\u4eba\u7684\u751f\u5e73\u3001\u4f5c\u54c1\u3001\u5386\u53f2\u80cc\u666f\u548c\u76f8\u5173\u4e8b\u4ef6\uff0c\u4ee5\u53ca\u4e0e\u5176\u4f5c\u54c1\u76f8\u5173\u7684\u60c5\u611f\u548c\u98ce\u683c\u7279\u5f81\u3002\u901a\u8fc7\u96c6\u6210\u5386\u53f2\u3001\u6587\u5b66\u548c\u6587\u5316\u7814\u7a76\u7684\u5143\u7d20\uff0cAPRO\u63d0\u4f9b\u4e86\u4e00\u4e2a\u4e30\u5bcc\u7684\u6846\u67b6\uff0c\u7528\u4e8e\u5206\u6790\u548c\u63a2\u7d22\u4e2d\u56fd\u53e4\u4ee3\u8bd7\u6b4c\u7684\u4e30\u5bcc\u6027\u548c\u590d\u6742\u6027\u3002 \u4e3b\u8981\u7279\u70b9\u548c\u7ec4\u4ef6\u5305\u62ec\uff1a \u4eba\u7269\u7c7b\uff1a\u5305\u542b\u53e4\u4ee3\u8bd7\u4eba\u7684\u57fa\u672c\u4fe1\u606f\uff0c\u5982\u59d3\u540d\u3001\u5b57\u3001\u53f7\u3001\u51fa\u751f\u548c\u901d\u4e16\u65e5\u671f\uff0c\u4ee5\u53ca\u4ed6\u4eec\u7684\u4e3b\u8981\u6210\u5c31\u548c\u751f\u5e73\u4e8b\u4ef6\u3002 \u4f5c\u54c1\u7c7b\uff1a\u8be6\u7ec6\u63cf\u8ff0\u4e86\u8bd7\u4eba\u7684\u4e3b\u8981\u4f5c\u54c1\uff0c\u5305\u62ec\u4f5c\u54c1\u540d\u79f0\u3001\u521b\u4f5c\u65f6\u95f4\u3001\u4f53\u88c1\u3001\u4e3b\u9898\u548c\u98ce\u683c\u3002 \u4e8b\u4ef6\u7c7b\uff1a\u8bb0\u5f55\u4e86\u4e0e\u8bd7\u4eba\u548c\u5176\u4f5c\u54c1\u76f8\u5173\u7684\u91cd\u8981\u5386\u53f2\u4e8b\u4ef6\u3002 \u60c5\u611f\u7c7b\uff1a\u6db5\u76d6\u4e86\u4f5c\u54c1\u4e2d\u8868\u8fbe\u7684\u60c5\u611f\u503e\u5411\u548c\u98ce\u683c\u7279\u5f81\u3002 \u8d44\u6e90\u7c7b\uff1a\u6d89\u53ca\u4e0e\u8bd7\u4eba\u53ca\u5176\u4f5c\u54c1\u76f8\u5173\u7684\u5404\u7c7b\u8d44\u6e90\uff0c\u5982\u6587\u732e\u3001\u7814\u7a76\u6587\u7ae0\u548c\u6559\u80b2\u6750\u6599\u3002 \u65f6\u95f4\u548c\u5730\u70b9\u7c7b\uff1a\u8be6\u7ec6\u8bf4\u660e\u4e86\u8bd7\u4eba\u6d3b\u52a8\u7684\u65f6\u95f4\u548c\u5730\u70b9\uff0c\u4ee5\u53ca\u4f5c\u54c1\u7684\u521b\u4f5c\u80cc\u666f\u3002 APRO\u672c\u4f53\u9002\u7528\u4e8e\u6587\u5b66\u7814\u7a76\u8005\u3001\u5386\u53f2\u5b66\u5bb6\u3001\u6559\u80b2\u5de5\u4f5c\u8005\u4ee5\u53ca\u5bf9\u4e2d\u56fd\u53e4\u4ee3\u8bd7\u6b4c\u611f\u5174\u8da3\u7684\u4eba\u58eb\uff0c\u7528\u4e8e\u6559\u5b66\u3001\u5b66\u672f\u7814\u7a76\u548c\u6587\u5316\u4f20\u627f\u3002\u672c\u4f53\u7684\u8bbe\u8ba1\u5145\u5206\u8003\u8651\u4e86\u6613\u7528\u6027\u548c\u6269\u5c55\u6027\uff0c\u652f\u6301\u8de8\u9886\u57df\u7684\u67e5\u8be2\u548c\u5206\u6790\u3002 APRO (Ancient Poet Resource Ontology) is an ontology designed to systematically organize and describe information related to ancient Chinese poets and their works. The ontology encompasses the life, works, historical context, and related events of ancient poets, as well as emotional and stylistic characteristics associated with their works. Integrating elements of historical, literary, and cultural studies, APRO provides a rich framework for analyzing and exploring the richness and complexity of ancient Chinese poetry. Key features and components include: Person Class: Contains basic information about ancient poets, such as their names, courtesy names, art names, birth and death dates, major achievements, and life events. Work Class: Details the main works of the poets, including the name of the work, time of creation, genre, theme, and style. Event Class: Records significant historical events related to the poets and their works. Emotion Class: Covers the emotional tendencies and stylistic features expressed in the works. Resource Class: Pertains to various resources associated with the poets and their works, such as literature, research papers, and educational materials. Time and Place Class: Specifies the times and places of the poets' activities, as well as the background of the creation of their works. The APRO ontology is suitable for literary researchers, historians, educators, and anyone interested in ancient Chinese poetry, for use in teaching, academic research, and cultural heritage preservation. The design of the ontology takes into account ease of use and extensibility, supporting cross-disciplinary queries and analysis.",
"download_owl": "http://aber-owl.net/media/ontologies/APRO/1/apro.owl",
"name": "Ancient Poet Resource Ontology",
"prefix": "APRO"
},
"ARCRC": {
"name": "Arctic Report Card",
"prefix": "ARCRC"
},
"ARO": {
"description": "Antibiotic resistance genes and mutations",
"download_owl": "http://aber-owl.net/media/ontologies/ARO/29/aro.owl",
"homepage": "https://github.com/arpcard/aro",
"name": "Antibiotic Resistance Ontology",
"prefix": "ARO"
},
"ASDPTO": {
"description": "Autism Spectrum Disorder Phenotype Ontology encapsulates the Autism Spectrum Disorder behavioral phenotype, informed by the standard ASD assessment instruments and the currently known characteristics of this disorder. http://www.ncbi.nlm.nih.gov/pubmed/24163114",
"download_owl": "http://aber-owl.net/media/ontologies/ASDPTO/1/asdpto.owl",
"name": "Autism Spectrum Disorder Phenotype Ontology",
"prefix": "ASDPTO",
"version": "1"
},
"ASPECT": {
"description": "This is a taxonomy (i.e. controlled vocabulary) of variables, parameters, and constants used in the wind energy community.",
"homepage": "http://purl.org/aspect",
"name": "ASPECT: wind energy vAriableS, ParametErs and ConsTants",
"prefix": "ASPECT",
"version": "0.1.0"
},
"ASSAYNODE": {
"description": "An ontology providing controlled vocabularies for Sequence Analysis and sequencing instrument model.",
"download_owl": "http://aber-owl.net/media/ontologies/ASSAYNODE/2/assaynode.owl",
"name": "Assaynode",
"prefix": "ASSAYNODE",
"version": "1.0"
},
"ASSSE": {
"name": "11",
"prefix": "ASSSE"
},
"ATC": {
"description": "The Anatomical Therapeutic Chemical (ATC) Classification System is used for the classification of active ingredients of drugs according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. It is controlled by the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC), and was first published in 1976.",
"name": "Anatomical Therapeutic Chemical Classification",
"prefix": "ATC",
"version": "2016AB"
},
"ATMO": {
"description": "African Traditional Medicine Ontology (ATMO) describes the actors' function (healer, fetishist or soothsayer); the different types of proposed process treatment, the symptom's roles and the disease consideration.",
"download_obo": "http://aber-owl.net/media/ontologies/ATMO/3/atmo.obo",
"homepage": "http://www.eurecom.fr/~atemezin/",
"name": "African Traditional Medicine Ontology",
"prefix": "ATMO",
"version": "1.101"
},
"ATO": {
"description": "A taxonomy of Amphibia",
"download_obo": "http://aber-owl.net/media/ontologies/ATO/2/ato.obo",
"homepage": "http://www.amphibanat.org",
"name": "Amphibian Taxonomy Ontology",
"prefix": "ATO",
"version": "See Remote Site"
},
"ATOL": {
"description": "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientific and educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production",
"download_owl": "http://aber-owl.net/media/ontologies/ATOL/1/atol.owl",
"homepage": "www.atol-ontology.com",
"name": "Animal Trait Ontology for Livestock",
"prefix": "ATOL"
},
"ATOM": {
"description": "An ontology model for anatomical atlases.",
"download_owl": "http://aber-owl.net/media/ontologies/ATOM/1/atom.owl",
"homepage": "https://github.com/SciCrunch/NIF-Ontology",
"name": "Atlas Ontology Model",
"prefix": "ATOM",
"version": "2023-04-27"
},
"AUDITORYH": {
"description": "A hierarchy of functional regions related to auditory system.",
"download_owl": "http://aber-owl.net/media/ontologies/AUDITORYH/1/auditoryh.owl",
"name": "NeuroMorpho.Org auditory functional regions",
"prefix": "AUDITORYH",
"version": "0.6"
},
"AURA": {
"description": "KB_Bio_101 is the ontology of the AURA + Inquire project @ SRI International, Menlo Park. This work is owned by Vulcan Inc. and is licensed for use under the Creative Commons Attribution-NonCommerical-ShareAlike 3.0 license (http://creativecommons.org/licenses/by-nc-sa/3.0/). Vulcan Inc., June 2013",
"download_owl": "http://aber-owl.net/media/ontologies/AURA/1/aura.owl",
"homepage": "http://www.ai.sri.com/people/chaudhri",
"name": "KB_Bio_101",
"prefix": "AURA",
"version": "1.0"
},
"BANDARQ": {
"name": "CapsaBandarQ.com Capsa Online, Agen Bandar Q, Domino 99, Qiu Qiu Online, BandarQ",
"prefix": "BANDARQ"
},
"BAO": {
"description": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 1000 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc.). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation.",
"download_owl": "http://aber-owl.net/media/ontologies/BAO/32/bao.owl",
"homepage": "http://www.bioassayontology.org/",
"name": "BioAssay Ontology",
"prefix": "BAO",
"version": "2.3.3"
},
"BAO-GPCR": {
"description": "The G protein-coupled receptors (GPCRs) ontology (http://www.bioassayontology.org/bao_gpcr) describes pharmacology, biochemistry and physiology of these important and therapeutically promising class of academic and pharmaceutical research targets. Incorporation and comparison of various small molecule screening data sets, such as those deposited in PubChem, ChEMBL, KEGG, PDSP, and/or IUPHAR databases, requires a formalized electronic organization system. In order to bridge the gap between the overflow of HTS data and the bottleneck of integrated analysis tools, herein, we provide the first comprehensive GPCR ontology. The development and utility of GPCR ontology was based on previously developed BioAssay Ontology (BAO). The GPCR ontology contains information about biochemical, pharmacological, and functional properties of individual GPCRs as well as GPCR-selective ligands inclusive of their HTS screening results and other records. This provides the first all-inclusive GPCR ontology with all available data to model the relationship between the GPCR binding sites and their physiologic and pharmacologic role in physiology via small molecule chemical structures. We developed this system using emerging semantic technologies, by leveraging existing and descriptive domain level ontologies.",
"download_owl": "http://aber-owl.net/media/ontologies/BAO-GPCR/23/bao-gpcr.owl",
"homepage": "http://www.bioassayontology.org/",
"name": "G Protein-Coupled Receptor BioAssays Ontology",
"prefix": "BAO-GPCR",
"version": "1.1"
},
"BCGO": {
"description": "An application ontology built for beta cell genomics studies.",
"download_owl": "http://aber-owl.net/media/ontologies/BCGO/3/bcgo.owl",
"homepage": "https://github.com/obi-bcgo/bcgo",
"name": "Beta Cell Genomics Ontology",
"prefix": "BCGO"
},
"BCI-O": {
"description": "The BCI ontology specifies a foundational metadata model set for real-world multimodal Brain-Computer Interaction (BCI) data capture activities. Its structure depicts a conceptual framework that BCI applications can extend and use in their implementations, to define core concepts that capture a relevant and interoperable metadata vocabulary. This ontology is aligned to the Semantic Sensor Network Ontology (SSN): a domain-independent and end-to-end model for sensor/actuator applications. Hence, its structure has been normalized to assist its use in conjunction with other ontologies or linked data resources to specify any particular definitions (such as units of measurement, time and time series, and location and mobility), that specialized applications in the BCI domain might need. Its spec provides general alignment data modeling guidelines for core concepts, to help BCI applications in their design.",
"download_owl": "http://aber-owl.net/media/ontologies/BCI-O/6/bci-o.owl",
"homepage": "http://lov.okfn.org/dataset/lov/vocabs/bci",
"name": "Brain-Computer Interaction (BCI) Ontology",
"prefix": "BCI-O",
"version": "0.9.6"
},
"BCLION": {
"description": "The Breast Cancer Lifestyle Ontology (BCLION) captures various factors related to lifestyle choices and behaviors that may influence the risk of developing breast cancer. It provides a structured representation of these factors in a hierarchical manner, allowing for a comprehensive understanding of the different aspects of breast cancer lifestyle.",
"download_owl": "http://aber-owl.net/media/ontologies/BCLION/1/bclion.owl",
"name": "Breast Cancer Lifestyle Ontology",
"prefix": "BCLION",
"version": "1.0"
},
"BCO": {
"description": "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.",
"download_owl": "http://aber-owl.net/media/ontologies/BCO/12/bco.owl",
"homepage": "https://github.com/tucotuco/bco",
"name": "Biological Collections Ontology",
"prefix": "BCO"
},
"BCON": {
"description": "The Breast Cancer Ontology (BCON) aims to capture the diverse aspects of breast cancer, including its molecular biology, pathology, epidemiology, clinical data, and lifestyle factors. By representing this knowledge in a standardized and machine-readable format, the ontology enables researchers, clinicians, and other stakeholders to access, share, and analyze breast cancer-related information more effectively. It serves as a valuable resource for organizing existing knowledge, discovering new insights, and supporting decision-making processes in the field of breast cancer research and healthcare.",
"download_owl": "http://aber-owl.net/media/ontologies/BCON/2/bcon.owl",
"name": "Breast Cancer Ontology",
"prefix": "BCON",
"version": "1.0"
},
"BCS7": {
"name": "Breast Cancer Staging - 7th Edition",
"prefix": "BCS7"
},
"BCS8": {
"name": "Breast Cancer Staging - 8th Edition",
"prefix": "BCS8"
},
"BCSR-ONTO": {
"description": "BCSR-Onto represents knowledge about risk assessment and recommendations by diverse guidelines for breast cancer screening both for women at high and average risk of developing breast cancer.",
"download_owl": "http://aber-owl.net/media/ontologies/BCSR-ONTO/3/bcsr-onto.owl",
"name": "Breast cancer screening recommendation ontology",
"prefix": "BCSR-ONTO",
"version": "2.1"
},
"BCTEO": {
"description": "Ontology that describes the field of Tissue Engineering for what concerns bone and cartilage tissues.",
"download_obo": "http://aber-owl.net/media/ontologies/BCTEO/4/bcteo.obo",
"name": "Bone and Cartilage Tissue Engineering Ontology",
"prefix": "BCTEO",
"version": "releases/2013-08"
},
"BCTT": {
"description": "BCT Taxonomy v0.4",
"download_owl": "http://aber-owl.net/media/ontologies/BCTT/6/bctt.owl",
"homepage": "http://www.ucl.ac.uk/behaviour-change-techniques",
"name": "Behaviour Change Technique Taxonomy",
"prefix": "BCTT",
"version": "0.4"
},
"BDO": {
"description": "The Bone Dysplasia ontology provides a comprehensive and formal representation of the different domain concepts involved in documenting the full complexity of the skeletal dysplasia domain. It captures and combines the genetic features that discriminate the bone dysplasias with the multitude of phenotypic characteristics manifested by patients and required to be taken into account in order to support the diagnosis process.",
"download_owl": "http://aber-owl.net/media/ontologies/BDO/9/bdo.owl",
"name": "Bone Dysplasia Ontology",
"prefix": "BDO",
"version": "1.5"
},
"BE": {
"name": "Bioentities",
"prefix": "BE"
},
"BERKAH": {
"name": "berkah",
"prefix": "BERKAH"
},
"BERO": {
"description": "Biological and Environmental Research Ontology (BERO) is an application ontology developed by the combination of many ontologies (base or subsets) namely : ChEBI, ECOCORE, EDAM, ENVO, GO, MeSH, MOP, NCBITaxon, NCIT, OBI, OMO, PATO, PO and TO.",
"download_owl": "http://aber-owl.net/media/ontologies/BERO/3/bero.owl",
"homepage": "https://github.com/berkeleybop/bero",
"name": "Biological and Environmental Research Ontology",
"prefix": "BERO",
"version": "2022-12-23"
},
"BFLC": {
"description": "An experimental extension to BIBFRAME 2.0 primarily for use by the Library of Congress, but with additions also applicable for other users",
"download_owl": "http://aber-owl.net/media/ontologies/BFLC/3/bflc.owl",
"homepage": "http://id.loc.gov/ontologies/bflc.html",
"name": "LC BIBFRAME 2.0 Vocabulary Extension",
"prefix": "BFLC",
"version": "1.2.0"
},
"BFO": {
"description": "The upper level ontology upon which OBO Foundry ontologies are built.",
"download_owl": "http://aber-owl.net/media/ontologies/BFO/5/bfo.owl",
"homepage": "http://ifomis.org/bfo/",
"name": "Basic Formal Ontology",
"prefix": "BFO"
},
"BHF": {
"description": "The ontology covers the knowledge on AIDS and the relevant clinical activities, which imports the HIV ontology as its concepts of main frame.",
"download_owl": "http://aber-owl.net/media/ontologies/BHF/1/bhf.owl",
"homepage": "http://bhf.miforum.net/english/index_english.htm",
"name": "Han Fei Bao",
"prefix": "BHF",
"version": "001"
},
"BHN": {
"description": "L'activit\u00e9 innovante de biologie et d'anatomo-pathologie r\u00e9alis\u00e9e notamment dans les Centres Hospitalo-Universitaires est habituellement appel\u00e9e \"activit\u00e9 hors nomenclature\" (BHN pour la biologie hors nomenclature et PHN pour l'anatomo-pathologie hors nomenclature). Ce caract\u00e8re \"hors nomenclature\" signifie que l'assurance maladie n'a pas encore int\u00e9gr\u00e9 ces actes dans la Nomenclature des Actes de Biologie M\u00e9dicale (NABM) ou la Nomenclature G\u00e9n\u00e9rale des Actes Professionnels (NGAP).",
"download_owl": "http://aber-owl.net/media/ontologies/BHN/1/bhn.owl",
"homepage": "http://www.chu-montpellier.fr/publication/inter_pub/R300/rubrique.jsp",
"name": "Biologie Hors Nomenclature",
"prefix": "BHN",
"version": "3.2"
},
"BHO": {
"description": "An application ontology devoted to the standardized recording of phenotypic data related to hemorrhagic disorders.",
"download_owl": "http://aber-owl.net/media/ontologies/BHO/3/bho.owl",
"homepage": "http://www.rockefeller.edu/ccts/bioinformatics.php",
"name": "Bleeding History Phenotype Ontology",
"prefix": "BHO",
"version": "0.4"
},
"BIBFRAME": {
"description": "Initiated by the Library of Congress, BIBFRAME provides a foundation for the future of bibliographic description, both on the web, and in the broader networked world. In addition to being a replacement for MARC, BIBFRAME serves as a general model for expressing and connecting bibliographic data. A major focus of the initiative will be to determine a transition path for the MARC 21 formats while preserving a robust data exchange that has supported resource sharing and cataloging cost savings in recent decades.",
"download_owl": "http://aber-owl.net/media/ontologies/BIBFRAME/3/bibframe.owl",
"homepage": "https://www.loc.gov/bibframe/",
"name": "BIBFRAME 2.0",
"prefix": "BIBFRAME",
"version": "2017-05-04T14:49:12.796-04:00"
},
"BIBLIOTEK-O": {
"description": "An ontology recommendation for modeling bibliographic metadata",
"download_owl": "http://aber-owl.net/media/ontologies/BIBLIOTEK-O/3/bibliotek-o.owl",
"homepage": "http://bibliotek-o.org/",
"name": "The Biblioteko Ontology",
"prefix": "BIBLIOTEK-O",
"version": "Version 1.1.0"
},
"BIFO": {
"description": "BIFO is intended to provide a biofilm ontology capable of understanding fundamental terminologies the relations between common biofilm terminologies following the guidelines of the Basic Formal Ontology (BFO).",
"download_owl": "http://aber-owl.net/media/ontologies/BIFO/1/bifo.owl",
"homepage": "https://github.com/biofilmDB/ontology ",
"name": "Biofilm Ontology",
"prefix": "BIFO"
},
"BILELTEST": {
"name": "Bileltest",
"prefix": "BILELTEST"
},
"BIM": {
"description": "Biomedical images published within the scientific literature play a central role in reporting and facilitating life science discoveries. Existing ontologies and vocabularies describing biomedical images, particularly sequence images, do not provide sufficient semantic representation for image annotations generated automatically and/or semi-automatically. We present an open ontology for the annotation of biomedical images (BIM) scripted in OWL/RDF. The BIM ontology provides semantic vocabularies to describe the manually curated image annotations as well as annotations generated by online bioinformatics services using content extracted from images by the Semantic Enrichment of Biomedical Images (SEBI) system. The BIM ontology is represented in three parts; (i) image vocabularies - which holds vocabularies for the annotation of an image and/or region of interests (ROI) inside an image, as well as vocabularies to represent the pre and post processing states of an image, (ii) text entities - covers annotations from the text that are associated with an image (e.g. image captions) and provides semantic representation for NLP algorithm outputs, (iii) a provenance model - that contributes towards the maintenance of annotation versioning. To illustrate the BIM ontology\u2019s utility, we provide three annotation cases generated by BIM in conjunction with the SEBI image annotation engine.",
"download_owl": "http://aber-owl.net/media/ontologies/BIM/6/bim.owl",
"homepage": "https://sites.google.com/site/bimontology/",
"name": "Biomedical Image Ontology",
"prefix": "BIM",
"version": "1.3"
},
"BIN": {
"description": "This ontology was created as a part of V\u00edt\u011bzslav Vacek's masters thesis and is describing the terminology used within the Body in Numbers (BiN) project that is currently underway (as of 2019-05-01) at the University of West Bohemia, Czech Republic and focuses on the terminology used during the data collection process.",
"download_owl": "http://aber-owl.net/media/ontologies/BIN/2/bin.owl",
"name": "Body in Numbers project terminology",
"prefix": "BIN",
"version": "1.1"
},
"BIOBIPON": {
"description": "bioBiPON (a sub-ontology of BiPON) aims at organizing the systemic description of biological information",
"download_owl": "http://aber-owl.net/media/ontologies/BIOBIPON/2/biobipon.owl",
"name": "Biological part of Bacterial interlocked Process ONtology",
"prefix": "BIOBIPON"
},
"BIODIVTHES": {
"description": "This bilingual thesaurus organizes the key concepts of biodiversity sciences, in their basic and applied ecological components. It uses polyhierarchy and includes 818 reciprocal associative relationships. The 1654 French and English descriptors (designating 827 concepts) are enriched with a large number of synonyms (1860) and hidden variants (7020) in both languages. Concepts are grouped into 82 collections, by semantic categories, thematic fields and EBV classes (Essential Biodiversity Variables). Definitions are given with their sources. This resource is aligned with the international thesauri AGROVOC, GEMET (GEneral Multilingual Environmental Thesaurus) and EnvThes (Environmental Thesaurus), as well as with the ontology ENVO (Environment Ontology).",
"homepage": "https://www.loterre.fr/skosmos/BLH/en/",
"name": "Biodiversity Thesaurus",
"prefix": "BIODIVTHES",
"version": "2.1"
},
"BIOLINK": {
"description": "A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations",
"download_owl": "http://aber-owl.net/media/ontologies/BIOLINK/62/biolink.owl",
"homepage": "https://biolink.github.io/biolink-model/",
"name": "Biolink Model",
"prefix": "BIOLINK",
"version": "2.2.13"
},
"BIOMO": {
"description": "The BIOMO ontology maps the HDF5 based BIOM format (http://biom-format.org/) to OWL, offering a method to convert a BIOM file to RDF and therefore publish it as Linked Data",
"download_owl": "http://aber-owl.net/media/ontologies/BIOMO/1/biomo.owl",
"homepage": "http://github.com/mikel-egana-aranguren/biom-ld",
"name": "Biological Observation Matrix Ontology",
"prefix": "BIOMO",
"version": "0.0.1"
},
"BIOMODELS": {
"description": "OWL Representation of the models in the BioModels repository.",
"download_owl": "http://aber-owl.net/media/ontologies/BIOMODELS/3/biomodels.owl",
"homepage": "https://code.google.com/p/sbmlharvester/",
"name": "BioModels Ontology",
"prefix": "BIOMODELS",
"version": "21"
},
"BIPOM": {
"description": "BiPOm is an ontology based on systemic representation of metabolic processes. BiPOm is an ontological model carrying the main biological processes and molecular roles/functions at a high level of genericity where the usual annotated resources are treated as instances. BiPOm, 1) contains biological knowledge as instances and 2) uses automatic reasoning through Semantic Web Rule Language (SWRL) in order to automatically infer, formalize and refine properties of molecules.",
"download_owl": "http://aber-owl.net/media/ontologies/BIPOM/3/bipom.owl",
"name": "Biological interlocked Process Ontology for metabolism",
"prefix": "BIPOM",
"version": "Core"
},
"BIPOM-CC-INF": {
"description": "BiPOm instantiated with metabolic reactions and post-translational modifications for the Calvin cycle followed by SWRL rules based reasoning.",
"download_owl": "http://aber-owl.net/media/ontologies/BIPOM-CC-INF/3/bipom-cc-inf.owl",
"name": "BiPOm inferences for Calvin cycle",
"prefix": "BIPOM-CC-INF",
"version": "alpha"
},
"BIPOM-CC-INST": {
"description": "BiPOm instantiated with metabolic reactions and post-translational modifications for the Calvin cycle.",
"download_owl": "http://aber-owl.net/media/ontologies/BIPOM-CC-INST/3/bipom-cc-inst.owl",
"name": "BiPOm Calvin cycle instantiation",
"prefix": "BIPOM-CC-INST",
"version": "alpha"
},
"BIPOM-ECMET-INF": {
"description": "BiPOm instantiated with metabolic reactions and post-translational modifications for the metabolism of Escherichia coli.",
"download_owl": "http://aber-owl.net/media/ontologies/BIPOM-ECMET-INF/2/bipom-ecmet-inf.owl",
"name": "BiPOm E-Coli metabolism instantiation",
"prefix": "BIPOM-ECMET-INF",
"version": "alpha"
},
"BIPOM-ECMET-INFF": {
"description": "BiPOm instantiated with metabolic reactions and post-translational modifications for the metabolism of Escherichia coli followed by SWRL rules based reasoning.",
"download_owl": "http://aber-owl.net/media/ontologies/BIPOM-ECMET-INFF/2/bipom-ecmet-inff.owl",
"name": "BiPOm inferences for E-Coli metabolism",
"prefix": "BIPOM-ECMET-INFF",
"version": "alpha"
},
"BIPON": {
"description": "BiPON is an ontology permitting a multi-scale systemic representation of bacterial cellular processes and the coupling to their mathematical models. BiPON is further composed of two sub- ontologies, bioBiPON and modelBiPON. bioBiPON aims at organizing the systemic description of biological information while modelBiPON aims at describing the mathematical models (including parameters) associated to each biological process.",
"download_owl": "http://aber-owl.net/media/ontologies/BIPON/3/bipon.owl",
"name": "Bacterial interlocked Process ONtology",
"prefix": "BIPON",
"version": "2017-11-08-bis"
},
"BIRNLEX": {
"description": "The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design.",
"download_owl": "http://aber-owl.net/media/ontologies/BIRNLEX/1/birnlex.owl",
"homepage": "http://xwiki.nbirn.net:8080/xwiki/bin/view/%20BIRN-OTF-Public/Home",
"name": "Biomedical Informatics Research Network Project Lexicon",
"prefix": "BIRNLEX",
"version": "1.3.1"
},
"BIRTHDAYH": {
"description": "A hierarchy of neuron types based on its birthdate.",
"download_owl": "http://aber-owl.net/media/ontologies/BIRTHDAYH/4/birthdayh.owl",
"name": "NeuroMorpho.Org cell types birthdate",
"prefix": "BIRTHDAYH",
"version": "2.0"
},
"BIRTHONTO": {
"description": "US Birth ontology is a formal representation of the concepts, properties, and relationships that are relevant to the domain of US birth data Competency questions are: 1. What is the total number of live births in the United States for a given year? 2. What is the distribution of birth weight for babies born to mothers of different ages? 3. What is the prevalence of preterm births among babies born to mothers who smoke during pregnancy? 4. What is the relationship between maternal age and the likelihood of having a multiple birth? 5. What is the difference in birth outcomes between mothers who receive prenatal care and those who do not? 6. What is the trend in the rate of low birth weight babies over time? 7. What is the impact of socioeconomic status on birth outcomes, such as birth weight and gestational age? 8. What is the relationship between the mother's race and ethnicity and the likelihood of having a preterm birth? 9. What are the common risk factors for adverse birth outcomes, and how do they interact with each other? US Birth ontology can be used to facilitate data integration, analysis, and sharing across different data sources and systems. It can help to ensure that data is consistent, interoperable, and reusable, and can facilitate data discovery and reuse. The ontology can be used by researchers, healthcare professionals, and policymakers to ask and answer questions about birth outcomes, risk factors, and trends in the US birth data.",
"download_owl": "http://aber-owl.net/media/ontologies/BIRTHONTO/1/birthonto.owl",
"homepage": "https://koolgax99.github.io/abhilash-US-birth-onto/index-en.html",
"name": "BirthOnto: Birth Data Analysis",
"prefix": "BIRTHONTO",
"version": "1.1"
},
"BKO": {
"description": "The BricKs Ontology (BKO) provides Systems Biology Graphical Notation representations of recurring concepts in molecular networks. These representations, called bricks, are associated in the ontology with terms describing the concepts. Part of these terms are borrowed from the Gene Ontology and the Systems Biology Ontology. The bricks can be used for both the template-based construction of molecular networks maps as well as for their annotation.",
"download_owl": "http://aber-owl.net/media/ontologies/BKO/1/bko.owl",
"homepage": "http://sbgnbricks.org",
"name": "Bricks ontology",
"prefix": "BKO",
"version": "13:07:2018 10:45"
},
"BLM": {
"description": "A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations",
"download_owl": "http://aber-owl.net/media/ontologies/BLM/79/blm.owl",
"homepage": "https://biolink.github.io/biolink-model/",
"name": "BioLink Model",
"prefix": "BLM",
"version": "1.0.0"
},
"BMHO": {
"description": "Esta ontologia foi desenvolvida para auxiliar na gest\u00e3o da rede de aten\u00e7\u00e3o em sa\u00fade mental no contexto do Brasil, a fim de proporcionar uma estrutura sem\u00e2ntica que pode ser utilizada para cria\u00e7\u00e3o de ferramentas computacionais inteligentes, permitindo a integra\u00e7\u00e3o e interoperabilidade de bases de dados independentes e possibilitando a gera\u00e7\u00e3o de indicadores relevantes para a sa\u00fade mental, visando melhorar a tomada de decis\u00e3o e o planejamento p\u00fablico, aumentando a efici\u00eancia e efic\u00e1cia dos servi\u00e7os prestados \u00e0 comunidade.",
"download_owl": "http://aber-owl.net/media/ontologies/BMHO/7/bmho.owl",
"homepage": "https://saudeconectada.org/",
"name": "Brazilian Mental Health Ontology",
"prefix": "BMHO",
"version": "1"
},
"BMO": {
"download_owl": "http://aber-owl.net/media/ontologies/BMO/1/bmo.owl",
"name": "Biomarker Ontology",
"prefix": "BMO",
"version": "0.1"
},
"BMONT": {
"description": "The Biomarker Ontology (BMO) is a comprehensive knowledge representation involving a variety of fields of medical and biological aspects. BMO is built in line with Basic Formal Ontology (BFO) and Open Biological and Biomedical Ontology (OBO) principles. Entities and definitions are added by reviewing the biomarker ontology (created by Fraunhofer SCAI 10 years ago and used for the validation of the companion biomarker for a anticancer drug), as well as collected from scientific publications and books from different fields capturing various diseases.",
"download_owl": "http://aber-owl.net/media/ontologies/BMONT/1/bmont.owl",
"name": "The Biomarker Ontology",
"prefix": "BMONT",
"version": "Version Release: 0.5.4"
},
"BMPO": {
"description": "The Bombyx Mori Phenotype Ontology (BMPO) defines all phenotypes of Bombyx Mori.",
"download_owl": "http://aber-owl.net/media/ontologies/BMPO/9/bmpo.owl",
"name": "Bombyx Mori Phenotype Ontology",
"prefix": "BMPO",
"version": "3.3"
},
"BMS-LM": {
"description": "Biomedical research data reuse and sharing is essential for fostering research progress. To this aim, data producers need to master data management and reporting through standard and rich metadata, as encouraged by open data initiatives such as the FAIR (Findable, Accessible, Interoperable, Reusable) guidelines. This helps data re-users to understand and reuse the shared data with confidence. Therefore, dedicated frameworks are required. The provenance reporting throughout a biomedical study lifecycle has been proposed as a way to increase confidence in data while reusing it. The Biomedical Study - Lifecycle Management (BMS-LM) data model has implemented provenance and lifecycle traceability for several multimodal-imaging techniques but this is not enough for data understanding while reusing it. Actually, in the large scope of biomedical research, a multitude of metadata sources, also called Knowledge Organization Systems (KOSs), are available for data annotation. In addition, data producers uses local terminologies or KOSs, containing vernacular terms for data reporting. The result is a set of heterogeneous KOSs (local and published) with different formats and levels of granularity. To manage the inherent heterogeneity, semantic interoperability is encouraged by the Research Data Management (RDM) community. Ontologies, and more specifically top ontologies such as BFO and DOLCE, make explicit the metadata semantics and enhance semantic interoperability. Based on the BMS-LM data model and the BFO top ontology, the BioMedical Study - Lifecycle Management (BMS-LM) core ontology is proposed together with an associated framework for semantic interoperability between heterogeneous KOSs. It is made of four ontological levels: top/core/domain/local and aims to build bridges between local and published KOSs. In this paper, the conversion of the BMS-LM data model to a core ontology is detailed. The implementation of its semantic interoperability in a specific domain context is explained and illustrated with examples from small animal preclinical research.",
"download_owl": "http://aber-owl.net/media/ontologies/BMS-LM/1/bms-lm.owl",
"name": "BioMedical Study Lifecycle Management",
"prefix": "BMS-LM",
"version": "Version 1.1"
},
"BMT": {
"description": "An ontology of biological and biomedical topics, created from merging the EDAM Topics sub-ontology with auxiliary topics that are out of scope of EDAM.",
"download_owl": "http://aber-owl.net/media/ontologies/BMT/1/bmt.owl",
"name": "Biomedical Topics",
"prefix": "BMT",
"version": "1.4"
},
"BMTO": {
"description": "An ontology of biological and biomedical topics, created from merging the EDAM Topics sub-ontology with auxiliary topics that are out of scope of EDAM.",
"download_owl": "http://aber-owl.net/media/ontologies/BMTO/5/bmto.owl",
"name": "Biomedical Topics Ontology",
"prefix": "BMTO",
"version": "1.4"
},
"BNO": {
"description": "The Bionutrition Ontology relates concepts and terminologies used for human nutrition in a clinical and biomedical setting.",
"download_owl": "http://aber-owl.net/media/ontologies/BNO/2/bno.owl",
"name": "Bionutrition Ontology",
"prefix": "BNO",
"version": "0.2"
},
"BODA": {
"name": "Botryllus schlosseri Anatomy and Development Ontology",
"prefix": "BODA"
},
"BOF": {
"description": "An ontology of biodiversity of INPA",
"download_owl": "http://aber-owl.net/media/ontologies/BOF/2/bof.owl",
"name": "Biodiversity Ontology",
"prefix": "BOF",
"version": "1.2"
},
"BP": {
"description": "The BioPAX ontology (www.biopax.org) is a standard language for formally representing biological pathways. BioPAX Level 3 supports the representation of metabolic pathways, signal transduction pathways, protein-protein interaction networks, gene regulatory networks and genetic interactions.",
"download_owl": "http://aber-owl.net/media/ontologies/BP/1/bp.owl",
"homepage": "www.biopax.org",
"name": "BioPAX Ontology of Biological Pathways",
"prefix": "BP",
"version": "Level3 v1.0"
},
"BP-METADATA": {
"description": "This ontology represents the structure that BioPortal uses to represent all of its metadata (ontology details, mappings, notes, reviews, views)",
"download_owl": "http://aber-owl.net/media/ontologies/BP-METADATA/6/bp-metadata.owl",
"homepage": "http://www.bioontology.org/wiki/index.php/BioPortal_Metadata",
"name": "BioPortal Metadata Ontology",
"prefix": "BP-METADATA",
"version": "0.9.5"
},
"BPFORMS": {
"name": "Ontology of chemically concrete, composable DNA, RNA, and protein residue and crosslinks",
"prefix": "BPFORMS"
},
"BPM": {
"name": "Bus Pariwisata Medan",
"prefix": "BPM"
},
"BPT": {
"description": "Biological Pathway Taxonomy (BPT) - hierarchical taxonomy of cellular and molecular mechanisms, metabolic reactions, and diseases that can be shown as signaling pathways. BPT was created manually based on the Elsevier Pathway Collection available for public usage. \uf0e0\uf0e0\uf0e0 There are 3 types of entities in BPT \u2013 pathway, group, and folder of pathways and groups. \uf0e0\uf0e0\uf0e0 Group is the list of genes and proteins associated with biological function and diseases. \uf0e0\uf0e0\uf0e0 Pathway is an interactive model of molecular interactions in human and mammalian cells described in the literature. Each model was reconstructed based on facts published in peer-reviewed journals, with manually quality control. \uf0e0\uf0e0\uf0e0 BPT pathway entity includes several properties such as link to the model in Pathway Studio software which allows reading supported sentences from published articles and additional information about members. \uf0e0\uf0e0\uf0e0 The link can be found among synonymes. List of members for each model can be provided by request. Property \u201cnetwork\u201d describes maps without logical causal relationships between members to distinguish them from actual models of molecular mechanisms (\u201csignaling\u201d). \uf0e0\uf0e0\uf0e0 The index folder contains all pathways and groups sorted alphabetically.",
"download_obo": "http://aber-owl.net/media/ontologies/BPT/2/bpt.obo",
"name": "Biological Pathway Taxonomy",
"prefix": "BPT",
"version": "BPT.properties.2022"
},
"BRAIN-COF": {
"description": "BRAIN-COF is an ontology for representing neuroanatomical concepts aligned with the Desikan\u2013Killiany\u2013Tourville (DKT) brain atlas. Using hierarchical relationships, our ontology explicitly encodes a priori neuroanatomical relationships amongst brain regions. Brain-COF implements computationally efficient calculation of volumetric deviation indicative of disease pathology.",
"download_owl": "http://aber-owl.net/media/ontologies/BRAIN-COF/2/brain-cof.owl",
"homepage": "https://explaination.net/",
"name": "Computational Ontology Framework for Brain Profiles",
"prefix": "BRAIN-COF",
"version": "3"
},
"BRCT": {
"description": "The BRCT stands for Brain Region and Cell Type terminology, which was built with the purpose of organizing the knowledge domain of brain anatomy with a top-down granularity, from gross regions to cell types. This resource has been created for use in the IMI-funded AETIONOMY project (www.aetionomy.org).",
"download_owl": "http://aber-owl.net/media/ontologies/BRCT/1/brct.owl",
"name": "Brain Region & Cell Type terminology",
"prefix": "BRCT",
"version": "3.0"
},
"BRIDG": {
"description": "The Biomedical Research Integrated Domain Group (BRIDG) Model is a collaborative effort engaging stakeholders from the Clinical Data Interchange Standards Consortium (CDISC), the HL7 Regulated Clinical Research Information Management Technical Committee (RCRIM TC), the National Cancer Institute (NCI) and its Cancer Biomedical Informatics Grid (caBIG\u00ae), and the US Food and Drug Administration (FDA). The BRIDG model is an instance of a Domain Analysis Model (DAM). The goal of the BRIDG Model is to produce a shared view of the dynamic and static semantics for the domain of protocol-driven research and its associated regulatory artifacts. This domain of interest is further defined as: Protocol-driven research and its associated regulatory artifacts: i.e. the data, organization, resources, rules, and processes involved in the formal assessment of the utility, impact, or other pharmacological, physiological, or psychological effects of a drug, procedure, process, or device on a human, animal, or other subject or substance plus all associated regulatory artifacts required for or derived from this effort, including data specifically associated with post-marketing adverse event reporting. This OWL version of the BRIDG model is create by the National Cancer Institute (NCI). Source repository: https://ncisvn.nci.nih.gov/WebSVN/listing.php?repname=bridg-model&path=%2Ftrunk%2FModel+-+OWL%2F&",
"download_owl": "http://aber-owl.net/media/ontologies/BRIDG/1/bridg.owl",
"homepage": "http://www.bridgmodel.org/",
"name": "Biomedical Research Integrated Domain Group Model",
"prefix": "BRIDG",
"version": "3.2"
},
"BRO": {
"description": "A controlled terminology of resources, which is used to improve the sensitivity and specificity of web searches.",
"download_owl": "http://aber-owl.net/media/ontologies/BRO/14/bro.owl",
"homepage": "http://www.ncbcs.org/biositemaps/",
"name": "Biomedical Resource Ontology",
"prefix": "BRO",
"version": "3.2.1"
},
"BRO-Activity": {
"description": "This view represents a subset of the BRO containing all the Activity classes that are relevant in the biomedical domain.",
"download_owl": "http://aber-owl.net/media/ontologies/BRO-Activity/2/bro-activity.owl",
"homepage": "http://www.biositemaps.org/",
"name": "Biomedical Resource Ontology - Activity View",
"prefix": "BRO-Activity",
"version": "3.1"
},
"BRO-AreaOfResearch": {
"description": "This view represents a subset of the BRO containing all the Area of Research classes that are relevant in the biomedical domain.",
"download_owl": "http://aber-owl.net/media/ontologies/BRO-AreaOfResearch/2/bro-areaofresearch.owl",
"homepage": "http://www.biositemaps.org/",
"name": "Biomedical Resource Ontology - Area of Research View",
"prefix": "BRO-AreaOfResearch",
"version": "3.1"
},
"BRO-Chinese": {
"description": "This view contains the entire BRO with the addition of three DataType properties, i.e., preferredName, shortName and synonym; then for all the classes and properties, Simplified Chinese (and some English) annotations were inserted into the ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/BRO-Chinese/1/bro-chinese.owl",
"name": "Biomedical Resource Ontology with Simplified Chinese annotations.",
"prefix": "BRO-Chinese",
"version": "2.5"
},
"BRO-Resource": {
"description": "This view represents a subset of the BRO containing all the Resource types that are relevant for the biomedical domain. This view also includes the Deprecated Resource types.",
"download_owl": "http://aber-owl.net/media/ontologies/BRO-Resource/3/bro-resource.owl",
"homepage": "http://www.biositemaps.org/",
"name": "BRO Resource View",
"prefix": "BRO-Resource",
"version": "3.1"
},
"BRODMANNH": {
"description": "A hierarchy of Neocortex Brodmann areas.",
"download_owl": "http://aber-owl.net/media/ontologies/BRODMANNH/4/brodmannh.owl",
"name": "NeuroMorpho.Org Brodmann areas",
"prefix": "BRODMANNH",
"version": "2.0"
},
"BRO_ACRONYM": {
"description": "Uploading ontology for the first time",
"download_owl": "http://aber-owl.net/media/ontologies/BRO_ACRONYM/1/bro_acronym.owl",
"name": "Bro_Name",
"prefix": "BRO_ACRONYM",
"version": "3.1"
},
"BRSO": {
"description": "Biological Resource Schema Ontology",
"download_owl": "http://aber-owl.net/media/ontologies/BRSO/1/brso.owl",
"homepage": "https://github.com/dbcls/brso",
"name": "Biological Resource Schema Ontology",
"prefix": "BRSO",
"version": "0.02"
},
"BSAO": {
"description": "The first ontology describing the anatomy and the development of Botryllus schlosseri. Working group : Lucia Manni, Fabio Gasparini, Kohji Hotta, Katherine J. Ishizuka J, Lorenzo Ricci, Stefano Tiozzo, Ayelet Voskoboynik, Delphine Dauga",
"download_obo": "http://aber-owl.net/media/ontologies/BSAO/1/bsao.obo",
"name": "Botryllus schlosseri anatomy and development ontology",
"prefix": "BSAO",
"version": "Version 1"
},
"BSPO": {
"description": "An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces",
"download_owl": "http://aber-owl.net/media/ontologies/BSPO/31/bspo.owl",
"homepage": "https://github.com/obophenotype/biological-spatial-ontology",
"name": "Biological Spatial Ontology",
"prefix": "BSPO"
},
"BT": {
"description": "A top-domain ontology that provides definitions for the foundational entities of biomedicine as a basic vocabulary to unambiguously describe facts in this domain.",
"download_owl": "http://aber-owl.net/media/ontologies/BT/12/bt.owl",
"homepage": "http://purl.org/biotop",
"name": "BioTop Ontology",
"prefix": "BT",
"version": "Last modification\nApr 24, 2012 by Stefan Schulz"
},
"BT-ONTOLOGY": {
"description": "BrainTeaser Ontology (BTO) whose purpose is to jointly model both Amyotrophic Lateral Sclerosis (ALS) and Multiple Sclerosis (MS). The BTO serves multiple purposes: - to provide a unified and comprehensive conceptual view about ALS and MS, which are typically dealt with separately, allowing us to coherently integrate the data coming from the different medical partners in the project; - to seamlessly represent both retrospective data and prospective data, produced during the lifetime of BRAINTEASER - to allow for sharing and re-using the BRAINTEASER datasets according to Open Science and FAIR principles. For more details, visit the BTO documentation page: https://brainteaser.dei.unipd.it/ontology/",
"download_owl": "http://aber-owl.net/media/ontologies/BT-ONTOLOGY/3/bt-ontology.owl",
"homepage": "https://brainteaser.dei.unipd.it/ontology/",
"name": "BrainTeaser Ontology (BTO)",
"prefix": "BT-ONTOLOGY",
"version": "2.0"
},
"BTO": {
"description": "A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.",
"download_owl": "http://aber-owl.net/media/ontologies/BTO/39/bto.owl",
"homepage": "http://www.brenda-enzymes.org",
"name": "BRENDA tissue / enzyme source",
"prefix": "BTO"
},
"BTO-BFO": {
"name": "Brinell Test Ontology-BFO",
"prefix": "BTO-BFO"
},
"BTO-EMMO": {
"description": "Brinell Test Ontology (BTO) has developed for representing the Brinell testing process, testing equipment requirements, test pieces charactristics, and related testing parameters and their measurement procedure according to DIN EN ISO 6506-1 standard. Versions info: V2 developed using BFO+CCO top-level ontologies. V3 developed using EMMO+CHAMEO top-level ontologies. V4 developed using PROVO+PMDco top-level ontologies. V5 developed using BFO+IOF top-level ontologies.",
"download_owl": "http://aber-owl.net/media/ontologies/BTO-EMMO/3/bto-emmo.owl",
"homepage": "https://gitlab.com/kupferdigital/process-graphs/brinell-hardness-test/",
"name": "Brinell Test Ontology-EMMO",
"prefix": "BTO-EMMO",
"version": "3.0.4 (EMMO, CHAMEO, MT)"
},
"BTO-PROVO": {
"name": "Brinell Test Ontology-PROVO",
"prefix": "BTO-PROVO"
},
"BTO_ONTOLOGY": {
"description": "The purpose of this work is to develop an ontology-based framework for developing an information retrieval system to cater to specific queries of users. For creating such an ontology, information was obtained from a wide range of information sources involved with brain tumour study and research. The information thus obtained was compiled and analysed to provide a standard, reliable and relevant information base to aid our proposed system. Facet-based methodology has been used for ontology formalization for quite some time. Ontology formalization involves different steps such as identification of the terminology, analysis, synthesis, standardization and ordering. A vast majority of the ontologies being developed nowadays lack flexibility. This becomes a formidable constraint when it comes to interoperability. We found that a facet-based method provides a distinct guideline for the development of a robust and flexible model concerning the domain of brain tumours. Our attempt has been to bridge library and information science and computer science, which itself involved an experimental approach. It was discovered that a faceted approach is really enduring, as it helps in the achievement of properties like navigation, exploration and faceted browsing. Computer-based brain tumour ontology supports the work of researchers towards gathering information on brain tumour research and allows users across the world to intelligently access new scientific information quickly and efficiently.",
"download_owl": "http://aber-owl.net/media/ontologies/BTO_ONTOLOGY/1/bto_ontology.owl",
"homepage": "https://github.com/subhashishhh/BTO-Ontology/blob/master/BrainTumour_ontology.owl",
"name": "Brain Tumour Ontology",
"prefix": "BTO_ONTOLOGY",
"version": "1"
},
"BTSE": {
"name": "Bussines Travel Singapore And Euro",
"prefix": "BTSE"
},
"BiositemapIM": {
"description": "This view represents a subset of the BRO containing the classes that define the biositemap information model (IM).",
"download_owl": "http://aber-owl.net/media/ontologies/BiositemapIM/2/biositemapim.owl",
"homepage": "http://www.biositemaps.org/",
"name": "Biositemap Information Model",
"prefix": "BiositemapIM",
"version": "3.1"
},
"CABRO": {
"description": "a web ontology for the semantic representation of the computer assisted brain trauma rehabilitation domain. This is a novel and emerging domain, since it employs the use of robotic devices, adaptation software and machine learning to facilitate interactive, adaptive and personalized rehabilitation care, patient monitoring and assisted living.",
"download_owl": "http://aber-owl.net/media/ontologies/CABRO/1/cabro.owl",
"name": "Computer Assisted Brain Injury Rehabilitation Ontology",
"prefix": "CABRO",
"version": "0.5"
},
"CANCO": {
"description": "The Cancer Chemoprevention Ontology constitutes a vocabulary that is able to describe and semantically interconnect the different paradigms of the cancer chemoprevention domain.",
"download_owl": "http://aber-owl.net/media/ontologies/CANCO/3/canco.owl",
"name": "Cancer Chemoprevention Ontology",
"prefix": "CANCO",
"version": "0.3"
},
"CANONT": {
"description": "Providing an upper-level ontology for cancer.",
"download_obo": "http://aber-owl.net/media/ontologies/CANONT/1/canont.obo",
"name": "Upper-Level Cancer Ontology ",
"prefix": "CANONT",
"version": "unknown"
},
"CAO": {
"description": "CAO ontology is designed for supporting the COG enrichment study by using Fisher's exact test",
"download_owl": "http://aber-owl.net/media/ontologies/CAO/3/cao.owl",
"homepage": "http://cao.sourceforge.net/",
"name": "Clusters of Orthologous Groups (COG) Analysis Ontology",
"prefix": "CAO",
"version": "1.4"
},
"CARELEX": {
"description": "Contains controlled vocabulary terms from National Cancer Institute used to classify clinical trial electronic content (documents, images, etc). A Content model contains content classification categories (classes) and metadata properties (data properties). Data properties should be assigned to each Content Type. This model has been published as part of the new OASIS eTMF Standard, a draft specification available at: http://oasis-open.org/committees/etmf. CareLex is a non-profit organization formed to promote eClinical application and content interoperability for the life sciences and healthcare industries. For more info go to www.CareLex.Org",
"download_owl": "http://aber-owl.net/media/ontologies/CARELEX/43/carelex.owl",
"homepage": "http://www.carelex.org",
"name": "Content Archive Resource Exchange Lexicon",
"prefix": "CARELEX",
"version": "1.02"
},
"CARO": {
"description": "An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species",
"download_owl": "http://aber-owl.net/media/ontologies/CARO/17/caro.owl",
"homepage": "https://github.com/obophenotype/caro/",
"name": "Common Anatomy Reference Ontology",
"prefix": "CARO"
},
"CAROLIO": {
"description": "We present CaroliO, an ontology for Caroli's disease and syndrome, aimed at enhancing the diagnosis and treatment of these rare liver conditions. Our work addresses the pressing need for structured knowledge resources in the field of rare diseases, which often present significant diagnostic and treatment challenges due to limited information. We developed our ontology in two versions: CaroliO VB, which is the Basic ontology; and CaroliO VA, the Applied Version, which includes more complex axioms i.e. closure axioms and axioms that indicate combinations of scenarios among symptoms, signs, treatments, and outcomes. The Basic Version follows the underlying Open World Assumption and is suitable for ontologists and future researches, while the Applied Version includes more complex axioms to better reflect real world decision making in diagnosis and choosing treatments for Caroli\u2019s disease and syndrome based on our current knowledge.",
"download_owl": "http://aber-owl.net/media/ontologies/CAROLIO/1/carolio.owl",
"homepage": "https://github.com/TootooniLab/CaroliO",
"name": "Caroli's Disease and Syndrome Ontology",
"prefix": "CAROLIO",
"version": "2.2"
},
"CARRE": {
"description": "Clinical risk factors, evidence and observables",
"download_owl": "http://aber-owl.net/media/ontologies/CARRE/3/carre.owl",
"homepage": "http://www.carre-project.eu",
"name": "CARRE Risk Factor ontology",
"prefix": "CARRE",
"version": "0.2"
},
"CASE-BASE-ONTO": {
"description": "The case-base ontology was developed for a CBR system to diagnose gastric dystemperament in the Persian medicine.",
"download_owl": "http://aber-owl.net/media/ontologies/CASE-BASE-ONTO/1/case-base-onto.owl",
"name": "Case-base ontology for gastric dystemperament in Persian medicine",
"prefix": "CASE-BASE-ONTO",
"version": "1.0"
},
"CBLAYERH": {
"description": "A hierarchy of layers in the Cerebellum of Gnathostomes.",
"download_owl": "http://aber-owl.net/media/ontologies/CBLAYERH/2/cblayerh.owl",
"name": "NeuroMorpho.Org Cerebellum layers",
"prefix": "CBLAYERH",
"version": "2.0"
},
"CBO": {
"description": "The Cell Behavior Ontology (CBO) describes multi-cell computational models. In particular to describe both the existential behaviors of cells (spatiality, growth, movement, adhesion, death, ...) and computational models of those behaviors.",
"download_owl": "http://aber-owl.net/media/ontologies/CBO/22/cbo.owl",
"homepage": "http://cbo.biocomplexity.indiana.edu/cbo/",
"name": "Cell Behavior Ontology",
"prefix": "CBO",
"version": "Version 1.1.0 added classes for OMERO-Tiff files similar to those for VTK files \nVersion 1.0.0 is the initial release of the Cell Behavior Ontology (CBO). \nVersion 1.0.1 added Journal citation for the Cell Behavior Ontology (CBO). \nVersion 1.0.2 corrected a few annotations that had \"snap:process\" that should be \"span:process\".\nVersion 1.0.3 corrected/changed class \"SpacialExclusive\" to \"SpatialExclusive\" and property \"has_Quality\" to \"has_quality\"."
},
"CC": {
"description": "Client category",
"name": "CC",
"prefix": "CC",
"version": "1"
},
"CCCNO": {
"description": "This is nursing diagnosis ontology of Clinical Care Classification",
"download_owl": "http://aber-owl.net/media/ontologies/CCCNO/1/cccno.owl",
"name": "CCC Nursing Ontology",
"prefix": "CCCNO"
},
"CCF": {
"description": "The Common Coordinate Framework (CCF) Ontology is an application ontology built to support the development of the Human Reference Atlas (HRA). It unifies vocabulary for HRA construction and usage\u2014making it possible to ingest external data sources; supporting uniform tissue sample registration that includes the spatial positioning and semantic annotations within 3D reference organs; and supporting user-formulated cross-domain queries over tissue donor properties, anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology consists of three major ontologies. The Biological Structure Ontology records anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships between them. The ASCT+B tables are authored by human experts using templated Google Sheets. The biomarkers, cell types, and anatomical structures are mapped to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible. All relationships between anatomical structures and from cell types to anatomical structures are valid Uberon and CL relationships. The Spatial Ontology defines the shape, size, location, and rotation of experimental tissue and data major anatomical structures in the 3D Reference Object Library. The Specimen Ontology captures the sex, age, and other information on donors that provided tissue data used in the construction of the HRA.",
"download_owl": "http://aber-owl.net/media/ontologies/CCF/16/ccf.owl",
"homepage": "https://lod.humanatlas.io/vocab/ccf/latest",
"name": "Human Reference Atlas Common Coordinate Framework Ontology",
"prefix": "CCF",
"version": "3.0.0"
},
"CCFO": {
"description": "This ontology is designed to cover the portions of reality relevant to assessing patient frailty. While we believe it to be relevant to frailty in general, during its development we were specifically focused on decisions relating to cardiac care. We gathered terms using existent instruments, physician interviews, and automated chart reviews. The hierarchical structure was taken from SNOMED-CT. We could not simply use SNOMED-CT because it is too exhaustive to be useful. We add entities where necessary to remain true to our data.",
"download_owl": "http://aber-owl.net/media/ontologies/CCFO/2/ccfo.owl",
"name": "Cardiac-centered Frailty Ontology",
"prefix": "CCFO",
"version": "1.1"
},
"CCLAYERH": {
"description": "A hierarchy of Neocortex layers dimension.",
"download_owl": "http://aber-owl.net/media/ontologies/CCLAYERH/4/cclayerh.owl",
"name": "NeuroMorpho.Org Cortical layers",
"prefix": "CCLAYERH",
"version": "2.0"
},
"CCO": {
"description": "An application ontology integrating knowledge about the eukaryotic cell cycle.",
"download_owl": "http://aber-owl.net/media/ontologies/CCO/9/cco.owl",
"homepage": "http://www.semantic-systems-biology.org/apo/",
"name": "Cell Cycle Ontology",
"prefix": "CCO",
"version": "2015"
},
"CCON": {
"description": "The ontology of Cerrado wood plant dynamics was created in order to represent the set of concepts about the dynamics, that is, changes over time of the wood vegetation structure, of Cerrado. Ccon describes the main parameters used to measure the changes, such as mortality rate and recruitment rate.",
"download_owl": "http://aber-owl.net/media/ontologies/CCON/8/ccon.owl",
"name": "Cerrado concepts and plant community dynamics",
"prefix": "CCON",
"version": "0.9.3"
},
"CCONT": {
"description": "CCONT is an ontology for the formal representation of cell lines and their correspnding culture conditions.",
"download_owl": "http://aber-owl.net/media/ontologies/CCONT/3/ccont.owl",
"name": "Cell Culture Ontology",
"prefix": "CCONT",
"version": "1.1"
},
"CCTOO": {
"description": "The Cancer Care: Treatment Outcomes Ontology (CCTOO) catalogues various clinical endpoints used in evaluating outcomes of cancer treatment. In addition to a vocabulary list, CCTOO also curates the dependencies between individual concepts, in form of production rules, for translating clinical findings recorded in the electronic medical records (EMR) into literature-based concepts. An earlier version of this ontology was presented as a scientific abstract alongside the American Society of Clinical Oncology annual meeting 2017, Chicago, USA (J Clin Oncol 2017; 35 suppl; abstr e18137).",
"download_obo": "http://aber-owl.net/media/ontologies/CCTOO/2/cctoo.obo",
"name": "Cancer Care: Treatment Outcome Ontology",
"prefix": "CCTOO",
"version": "releases/2018-05-11"
},
"CDAO": {
"description": "a formalization of concepts and relations relevant to evolutionary comparative analysis",
"download_owl": "http://aber-owl.net/media/ontologies/CDAO/11/cdao.owl",
"homepage": "https://github.com/evoinfo/cdao",
"name": "Comparative Data Analysis Ontology",
"prefix": "CDAO"
},
"CDMONTO": {
"description": "The Common Diabetes Medications Ontology (CDMOnto) is an ontology-based decision support system that has been developed with the objective of providing appropriate treatment suggestions for diabetic patients. The CDMOnto Ontology serves as a foundation for shared semantics, domain-specific, standard, and interoperable knowledge pertinent to common diabetes medications. It encompasses the knowledge of diabetes medications and offers a unified terminology that can be disseminated and processed by medical professionals, pharmacists, and diabetic patients.",
"download_owl": "http://aber-owl.net/media/ontologies/CDMONTO/1/cdmonto.owl",
"name": "Common Diabetes Medications Ontology",
"prefix": "CDMONTO",
"version": "2"
},
"CDNO": {
"description": "CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet.",
"download_owl": "http://aber-owl.net/media/ontologies/CDNO/15/cdno.owl",
"homepage": "https://cdno.info/",
"name": "Compositional Dietary Nutrition Ontology",
"prefix": "CDNO"
},
"CDO": {
"description": "Note: The abbreviation of Chinese Diabetes Mellitus Ontology was changed to CDMO. CDMO is an OWL 2 ontology designed to cover the diabetes mellitus knowledge represented in Chinese language. The ontology is based on BFO and OGMS. In addition, the top hierarchical structure was adapted from SNOMED-CT, and strive for mapping with other medical ontologies in English, such as SNOMED-CT, HPO, DOID, DRON.",
"download_owl": "http://aber-owl.net/media/ontologies/CDO/6/cdo.owl",
"name": "Chinese Diabetes Mellitus Ontology",
"prefix": "CDO",
"version": "3.0"
},
"CDOH": {
"description": "Commercial factors including the production, distribution, and marketing of goods and services, may exert a substantial influence on health outcomes. This ontology covers concepts and relationships relevant to non-clinical factors resulting from commercial determinants of health(CDoH).",
"download_owl": "http://aber-owl.net/media/ontologies/CDOH/1/cdoh.owl",
"name": "Commercial determinant of Health Ontology",
"prefix": "CDOH",
"version": "v1"
},
"CDPEO": {
"description": "This ontology is used to recommend personalized education materials to chronic disease patients. The constructed ontology mainly consists of two levels. Level 1 includes 5 terms: demographic, disease, vital sign, lifestyle and medication, which describe the characteristics contained in the patient data, as well as the topics of education materials. Leve 2 contains the detailed elements for each Level 1 class. The patient profile class is used to generate the instance of patient data, using object properties to connect to the specific characteristic class. The patient data will be mapped to a vector space generated from the Level 2 classes. SWRL rules are added to implement the semantic logic of mapping from patient original data to the ontology vector space. The pulblication of the ontology is in preperation.",
"download_owl": "http://aber-owl.net/media/ontologies/CDPEO/1/cdpeo.owl",
"name": "Chronic Disease Patient Education Ontology",
"prefix": "CDPEO",
"version": "1.0.0"
},
"CEDARPC": {
"description": "CEDAR Provisional Classes",
"download_owl": "http://aber-owl.net/media/ontologies/CEDARPC/1/cedarpc.owl",
"homepage": "http://metadatacenter.org/",
"name": "CEDAR Provisional Classes",
"prefix": "CEDARPC"
},
"CEDARVS": {
"description": "Value Sets used by the CEDAR project",
"download_owl": "http://aber-owl.net/media/ontologies/CEDARVS/4/cedarvs.owl",
"homepage": "http://cedar.stanford.edu",
"name": "CEDAR Value Sets",
"prefix": "CEDARVS",
"version": "0.2.2"
},
"CEI-10": {
"description": "Es la Ontologia del Hospital Garrahan de Pediatria",
"download_owl": "http://aber-owl.net/media/ontologies/CEI-10/8/cei-10.owl",
"name": "CEI-10_Garrahan (test)",
"prefix": "CEI-10",
"version": "0"
},
"CEI10": {
"description": "Base de Datos test",
"download_owl": "http://aber-owl.net/media/ontologies/CEI10/7/cei10.owl",
"name": "CEI10_Garrahan",
"prefix": "CEI10"
},
"CEI_10": {
"description": "En edicion por el Hospital de pediatria Garrahan",
"download_owl": "http://aber-owl.net/media/ontologies/CEI_10/16/cei_10.owl",
"name": "Codificacion De Enfermedades Pediatricas (En Edici\u00f3n)",
"prefix": "CEI_10",
"version": "1"
},
"CELEGANH": {
"description": "A hierarchy of C. elegans cell and anatomy & Organs.",
"download_owl": "http://aber-owl.net/media/ontologies/CELEGANH/2/celeganh.owl",
"name": "NeuroMorpho.Org C. elegans regions",
"prefix": "CELEGANH",
"version": "2.0"
},
"CEPATHAMIL": {
"name": "caracepathaml",
"prefix": "CEPATHAMIL"
},
"CEPH": {
"description": "An anatomical and developmental ontology for cephalopods",
"download_owl": "http://aber-owl.net/media/ontologies/CEPH/2/ceph.owl",
"homepage": "https://github.com/obophenotype/cephalopod-ontology",
"name": "Cephalopod Ontology",
"prefix": "CEPH"
},
"CGBOARD": {
"name": "Cg Board 10th Time Table 2019",
"prefix": "CGBOARD"
},
"CHARITYAUER": {
"name": "How Sun Shade Sails Can Enhance Your Outdoor Lifestyle",
"prefix": "CHARITYAUER"
},
"CHD": {
"description": "An ontology that describes the Congenital Heart Defects data.",
"download_owl": "http://aber-owl.net/media/ontologies/CHD/5/chd.owl",
"homepage": "http://homes.esat.kuleuven.be/~bioiuser/chdwiki",
"name": "Congenital Heart Defects Ontology",
"prefix": "CHD",
"version": "1.1"
},
"CHEAR": {
"description": "Children's health and wellbeing are influenced by interactions between environmental and genetic factors. NIEHS is establishing an infrastructure, the Children's Health Exposure Analysis Resource (CHEAR), to provide the extramural research community access to laboratory and data analyses that add or expand the inclusion of environmental exposures in children's health research. The goal of CHEAR is to provide tools so researchers can assess the full range of environmental exposures which may affect children's health. We anticipate that CHEAR will be used by children's health researchers conducting epidemiological or clinical studies that currently have limited consideration of environmental exposures, or those who have collected exposure data but seek more extensive analyses.",
"download_owl": "http://aber-owl.net/media/ontologies/CHEAR/5/chear.owl",
"name": "Children's Health Exposure Analysis Resource",
"prefix": "CHEAR",
"version": "1.1"
},
"CHEBI": {
"description": "A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds.",
"download_owl": "http://aber-owl.net/media/ontologies/CHEBI/196/chebi.owl",
"homepage": "http://www.ebi.ac.uk/chebi",
"name": "Chemical Entities of Biological Interest",
"prefix": "CHEBI"
},
"CHEMBIO": {
"description": "Ontology for Systems Chemical Biology and Chemogenomics",
"download_owl": "http://aber-owl.net/media/ontologies/CHEMBIO/9/chembio.owl",
"homepage": "http://chem2bio2rdf.org/owl",
"name": "Systems Chemical Biology and Chemogenomics Ontology ",
"prefix": "CHEMBIO",
"version": "unknown"
},
"CHEMINF": {
"description": "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.",
"download_owl": "http://aber-owl.net/media/ontologies/CHEMINF/49/cheminf.owl",
"homepage": "https://github.com/semanticchemistry/semanticchemistry",
"name": "Chemical Information Ontology",
"prefix": "CHEMINF"
},
"CHEMROF": {
"description": "CHEMROF is an ontological framework for Chemical Entities Mixtures Reactions Ontological Framework. This OWL ontology is an automated Translation of the source LinkML schema, https://w3id.org/chemrof",
"download_owl": "http://aber-owl.net/media/ontologies/CHEMROF/4/chemrof.owl",
"homepage": "https://w3id.org/chemrof",
"name": "CHEMROF",
"prefix": "CHEMROF"
},
"CHIRO": {
"description": "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.",
"download_owl": "http://aber-owl.net/media/ontologies/CHIRO/1/chiro.owl",
"homepage": "https://github.com/obophenotype/chiro",
"name": "CHEBI Integrated Role Ontology",
"prefix": "CHIRO"
},
"CHMO": {
"description": "CHMO, the chemical methods ontology, describes methods used to",
"download_owl": "http://aber-owl.net/media/ontologies/CHMO/32/chmo.owl",
"homepage": "https://github.com/rsc-ontologies/rsc-cmo",
"name": "Chemical Methods Ontology",
"prefix": "CHMO"
},
"CHO": {
"description": "ChemoOnto, an ontology to qualify the course of chemotherapies",
"download_owl": "http://aber-owl.net/media/ontologies/CHO/1/cho.owl",
"homepage": "https://team.inria.fr/heka/team-members/rogier/",
"name": "ChemoOnto",
"prefix": "CHO",
"version": "Version: 1.0.1\nDate: Dec 12, 2024\nAuthor: Alice Rogier, Inria Paris, CRC (Inserm, Univ. Paris-Cit\u00e9)\nLicence: MIT License"
},
"CHRO": {
"description": "Functional and biochemical description of covalent histone modifiers and chromatin remodeler proteins.",
"download_owl": "http://aber-owl.net/media/ontologies/CHRO/2/chro.owl",
"name": "Chromatin Regulator Ontology",
"prefix": "CHRO"
},
"CIDO": {
"description": "The Coronavirus Infectious Disease Ontology (CIDO) aims to ontologically represent and standardize various aspects of coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment.",
"download_owl": "http://aber-owl.net/media/ontologies/CIDO/35/cido.owl",
"homepage": "https://github.com/cido-ontology/cido",
"name": "Coronavirus Infectious Disease Ontology",
"prefix": "CIDO"
},
"CIDOC-CRM": {
"description": "The CIDOC Conceptual Reference Model (CRM) provides definitions and a formal structure for describing the implicit and explicit concepts and relationships used in cultural heritage documentation. The CIDOC CRM is intended to promote a shared understanding of cultural heritage information by providing a common and extensible semantic framework that any cultural heritage information can be mapped to. It is intended to be a common language for domain experts and implementers to formulate requirements for information systems and to serve as a guide for good practice of conceptual modelling. In this way, it can provide the \"semantic glue\" needed to mediate between different sources of cultural heritage information, such as that published by museums, libraries and archives.",
"download_owl": "http://aber-owl.net/media/ontologies/CIDOC-CRM/2/cidoc-crm.owl",
"homepage": "http://www.cidoc-crm.org/",
"name": "CIDOC Conceptual Reference Model",
"prefix": "CIDOC-CRM",
"version": "v6.2"
},
"CIE-10": {
"name": "CIE-10",
"prefix": "CIE-10"
},
"CIINTEADO": {
"description": "The first ontology describing the anatomy and the development of Ciona intestinalis, based on the Hotta developmental table.",
"download_obo": "http://aber-owl.net/media/ontologies/CIINTEADO/2/ciinteado.obo",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Ciona intestinalis Anatomy and Development Ontology",
"prefix": "CIINTEADO",
"version": "Version 1"
},
"CIO": {
"description": "An ontology to capture confidence information about annotations.",
"download_owl": "http://aber-owl.net/media/ontologies/CIO/2/cio.owl",
"homepage": "https://github.com/BgeeDB/confidence-information-ontology",
"name": "Confidence Information Ontology",
"prefix": "CIO"
},
"CIPTO_JUNAEDY": {
"name": "Cipto Junaedy",
"prefix": "CIPTO_JUNAEDY"
},
"CIRCUITH": {
"description": "A hierarchy of neuron types classified according to their circuit role.",
"download_owl": "http://aber-owl.net/media/ontologies/CIRCUITH/3/circuith.owl",
"name": "NeuroMorpho.Org Cell type Circuitry",
"prefix": "CIRCUITH",
"version": "2.0"
},
"CIROBUADO": {
"name": "Ciona robusta Anatomy and Development Ontology",
"prefix": "CIROBUADO"
},
"CISAVIADO": {
"description": "The first ontology describing the anatomy and the development of Ciona savignyi, based on the Hotta developmental table.",
"download_obo": "http://aber-owl.net/media/ontologies/CISAVIADO/2/cisaviado.obo",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Ciona savignyi Anatomy and Development Ontology ",
"prefix": "CISAVIADO"
},
"CKDO": {
"description": "The Chronic Kidney Disease Ontology was developed to assist routine data studies and case identification of CKD in primary care.",
"download_owl": "http://aber-owl.net/media/ontologies/CKDO/1/ckdo.owl",
"homepage": "clininf.eu",
"name": "Chronic Kidney Disease Ontology",
"prefix": "CKDO",
"version": "v0.1"
},
"CL": {
"description": "The Cell Ontology is a structured controlled vocabulary for cell types in animals.",
"download_owl": "http://aber-owl.net/media/ontologies/CL/107/cl.owl",
"homepage": "https://obophenotype.github.io/cell-ontology/",
"name": "Cell Ontology",
"prefix": "CL"
},
"CL-SIMPLE": {
"description": "Cell Ontology treated as a simple existential graph of the terms defined in an ontology",
"download_owl": "http://aber-owl.net/media/ontologies/CL-SIMPLE/14/cl-simple.owl",
"homepage": "https://cell-ontology.github.io/",
"name": "Cell Ontology Simple",
"prefix": "CL-SIMPLE",
"version": "2024-07-10"
},
"CLAO": {
"description": "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).",
"download_owl": "http://aber-owl.net/media/ontologies/CLAO/2/clao.owl",
"homepage": "https://github.com/luis-gonzalez-m/Collembola",
"name": "Collembola Anatomy Ontology",
"prefix": "CLAO"
},
"CLO": {
"description": "An ontology to standardize and integrate cell line information and to support computer-assisted reasoning.",
"download_owl": "http://aber-owl.net/media/ontologies/CLO/7/clo.owl",
"homepage": "https://github.com/CLO-Ontology/CLO",
"name": "Cell Line Ontology",
"prefix": "CLO"
},
"CLYH": {
"description": "The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle.",
"download_owl": "http://aber-owl.net/media/ontologies/CLYH/3/clyh.owl",
"homepage": "https://github.com/EBISPOT/clyh_ontology",
"name": "Clytia hemisphaerica Development and Anatomy Ontology",
"prefix": "CLYH"
},
"CMDO": {
"description": "The Clinical MetaData Ontology is designed to be used to classify Common Data Elements (CDEs) from different studies and clinical documents. CDEs can be efficiently searched, shared and reused by using our ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/CMDO/10/cmdo.owl",
"homepage": "http://www.snubi.org/software/cmo/",
"name": "Clinical MetaData Ontology",
"prefix": "CMDO",
"version": "1.1.4"
},
"CMECS": {
"description": "The Coastal and Marine Ecological Classification Standard (CMECS, FGDC-STD-018-2012) is collection of defined terms (\"units\") used to describe and classify marine ecological data. It is a national scheme for classifying and integrating observational data collected in coastal, marine, and lacustrine environments in U.S. waters. CMECS was published by the U.S. Federal Geographic Data Committee (FGDC) in 2012.",
"download_owl": "http://aber-owl.net/media/ontologies/CMECS/2/cmecs.owl",
"homepage": "https://github.com/NCEI-NOAAGov/cmecs",
"name": "Coastal and Marine Ecological Classification Standard Catalog",
"prefix": "CMECS",
"version": "1.1.0"
},
"CMF": {
"name": "CranioMaxilloFacial ontology",
"prefix": "CMF"
},
"CMO": {
"description": "Morphological and physiological measurement records generated from clinical and model organism research and health programs.",
"download_owl": "http://aber-owl.net/media/ontologies/CMO/127/cmo.owl",
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
"name": "Clinical measurement ontology",
"prefix": "CMO"
},
"CMOBET": {
"name": "agenbola",
"prefix": "CMOBET"
},
"CMPO": {
"description": "The Cellular Microscopy Phenotype Ontology (CMPO) is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is an application ontology developed in OWL that contains precomposed phenotypes descriptions that are defined using the Gene Ontology (GO) and the Phenotype Trait Ontology (PATO).",
"download_owl": "http://aber-owl.net/media/ontologies/CMPO/14/cmpo.owl",
"homepage": "https://github.com/EBISPOT/CMPO",
"name": "Cellular microscopy phenotype ontology",
"prefix": "CMPO",
"version": "1.3"
},
"CMR-QA": {
"description": "CMR-QA ontology aims at defining the semantics of free-text quality assessment annotations associated to Cardiac Magnetic Resonance (CMR) Imaging.",
"download_owl": "http://aber-owl.net/media/ontologies/CMR-QA/1/cmr-qa.owl",
"homepage": "https://github.com/ernestojimenezruiz/CMR-QA-Semantic-Layer/",
"name": "Cardiovascular Magnetic Resonance Quality Assessment Ontology",
"prefix": "CMR-QA",
"version": "0.4.5"
},
"CN": {
"description": "Computer networks ontology",
"download_owl": "http://aber-owl.net/media/ontologies/CN/1/cn.owl",
"name": "computer network",
"prefix": "CN"
},
"CNO": {
"description": "CNO is a controlled vocabulary of terms used in Computational Neurosciences to describe models of the nervous system. This first release of CNO is an alpha version and should be further aligned with other ontologies accessible on Bioportal and should be made compliant with the OBO foundry recommendations. This work is licensed under the Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. If you have any comments, questions or suggestions, please contact Yann Le Franc at ylefranc(at)gmail.com.",
"download_owl": "http://aber-owl.net/media/ontologies/CNO/8/cno.owl",
"name": "Computational Neuroscience Ontology",
"prefix": "CNO",
"version": "version 0.5"
},
"CNO_ACRONYM": {
"description": "test",
"download_owl": "http://aber-owl.net/media/ontologies/CNO_ACRONYM/1/cno_acronym.owl",
"name": "CNO_NAME",
"prefix": "CNO_ACRONYM",
"version": "version 0.5"
},
"CO-WHEAT": {
"description": "This ontology defines traits of the International Wheat Information System (IWIS) database and wheat descriptor.",
"download_obo": "http://aber-owl.net/media/ontologies/CO-WHEAT/1/co-wheat.obo",
"homepage": "http://cropontology.org/",
"name": "Wheat Trait Ontology ",
"prefix": "CO-WHEAT",
"version": "08.11.2010"
},
"COB": {
"description": "COB brings together key terms from a wide range of OBO projects to improve interoperability.",
"download_owl": "http://aber-owl.net/media/ontologies/COB/11/cob.owl",
"homepage": "https://obofoundry.org/COB/",
"name": "Core Ontology for Biology and Biomedicine",
"prefix": "COB"
},
"CODO": {
"description": "The initial version, CODO ontology v1.0 to v1.3, encompasses pivotal features such as classes like patients, clinical findings, symptoms, and properties like relationships between patients, travel history, and test results. It facilitates tracking specific pandemic cases, detailing how patients may have been infected, and identifying potential contacts at risk due to their connection with the infected individual. CODO also enables monitoring of clinical tests, travel history, available resources, and actual needs like ICU beds and invasive ventilators. With capabilities for advanced analytics, contact tracing, trend studies, and growth projections based on daily COVID-19 data, CODO supports the organization and representation of COVID-19 data on a daily basis. It allows semantic querying and data retrieval and aids in behavior analysis of the disease and transmission routes. In contrast, Version 1.4, also known as CODO_COVIDRO 1.4 or COVID-19 Drug and Risk Ontology (COViDRO), presents a formal model specifically designed to tackle the multifaceted challenges associated with COVID-19 treatment, risk factors, and drug interactions. The knowledge embedded in the COViDRO model is extracted from diverse medical literature and treatment guidelines provided by reputable organizations such as the World Health Organization (WHO), the National Institutes of Health (NIH), the Food and Drug Administration (FDA), and the Centers for Disease Control and Prevention (CDC). The model incorporates information on therapeutics, adverse effects, and drug interactions from authoritative medical literature, making a significant contribution to patient care, research, and public health strategies. COViDRO, or COVID-19 Drug and Risk Ontology 1.4, seamlessly integrates into knowledge graph information systems or recommender systems. It assists healthcare professionals in suggesting appropriate treatments by considering a comprehensive set of factors, abbreviated as \"PRADiCT\" (Patient Risk factors, Adverse effects, Drug interaction, Clinical findings, and Treatment procedure). These factors encompass patient risk level, risk factors (such as underlying health conditions, age, immunocompromised state, and occupation), drug interactions, drug adverse effects, clinical findings (including diagnosis, signs, symptoms, and status), and treatment procedures. By offering a standardized framework for organizing and integrating data from diverse sources like clinical trials, medical literature, and real-world patient data, COViDRO enhances informed decision-making, thereby elevating the quality of patient care. It stands as a patient-centric solution, facilitating COVID-19 treatment options and personalized care based on individual patient characteristics. CODO V1.5 extends the previous CODO V1.4 with the focus on COVID-19 Virus Genomics for representation of genomic sequence data. VGO model comprises 261 classes, 55 object properties, and 14 data properties. Designed to streamline the use and dissemination of COVID-19 genomic sequence data, VGO serves as a robust resource for researchers and healthcare professionals. It incorporates data from the Global Initiative on Sharing All Influenza Data (GISAID), which facilitates efficient querying and visualization of genomic data, thereby improving both accessibility and usability. VGO includes a variety of classes that represent COVID-19-related data such as variants, mutations, amino acids, genes, proteins, genome sequencing, samples, hosts, sampling strategies, and assembly methods. Furthermore, VGO supports automated reasoning, enhancing its functionality for in-depth analysis and interpretation. By integrating GISAID data into the VGO knowledge graph, the model not only enriches its conceptual representation but also optimizes the querying and visualization processes, making genomic data more accessible and usable for the scientific and medical communities.",
"download_owl": "http://aber-owl.net/media/ontologies/CODO/6/codo.owl",
"homepage": "https://github.com/biswanathdutta/CODO",
"name": "CODO: an Ontology for collection and analysis of COviD-19 data",
"prefix": "CODO",
"version": "1.5"
},
"COGAT": {
"description": "The Cognitive Atlas is a collaborative knowledge building project that aims to develop an ontology that characterizes the state of current thought in cognitive science. It defines a set of mental concepts along with a set of mental tasks, and the measurement relations between those classes.",
"download_owl": "http://aber-owl.net/media/ontologies/COGAT/7/cogat.owl",
"homepage": "http://www.cognitiveatlas.org",
"name": "Cognitive Atlas Ontology",
"prefix": "COGAT",
"version": "0.3.1"
},
"COGPO": {
"description": "This ontology is used to describe the experimental conditions within cognitive/behavioral experiments, primarily in humans.",
"download_owl": "http://aber-owl.net/media/ontologies/COGPO/1/cogpo.owl",
"homepage": "http://www.cogpo.org",
"name": "Cognitive Paradigm Ontology",
"prefix": "COGPO",
"version": "1"
},
"COHSI2STUDY": {
"description": "These ontologies are created under the CoHSI2 Study.",
"name": "cohsi2study",
"prefix": "COHSI2STUDY",
"version": "0.2.8"
},
"COHSI2TERMSWEEKX": {
"description": "Vocabularies are created to descibe week X report for CoHSI2 study",
"name": "cohsi2termsweekx",
"prefix": "COHSI2TERMSWEEKX"
},
"COID": {
"description": "A domain ontology for inflammatory diseases, with ICD-10 used as a foundation. Ontology is expanded to include medical therapies, anatomy, and symptoms. With the addition of synonyms and lay terms derived from embedding models.",
"download_owl": "http://aber-owl.net/media/ontologies/COID/1/coid.owl",
"homepage": "https://github.com/sap218/coid",
"name": "Combined Ontology for Inflammatory Diseases",
"prefix": "COID",
"version": "1.0.0"
},
"COKPME": {
"description": "The ontology will be used by analysts for finding the relative and precautionary measures that can be put in action for controlling the spread. Also, it should be able to handle the competence question like: \uf0d8 Which properties of the patient should be considered for modeling \uf0d8 Which properties of patient changes \uf0d8 Which properties of patient confirm COVID positive \uf0d8 Do the symptom of the patient change over time *** \uf0d8 Do the treatment provided depends on the category of patient \uf0d8 Do other comorbid conditions derive any interestingness **** \uf0d8 Which symptom is high in a particular district? (Or) Does the geographical location influence the patient category These keep change over an iterative process of ontology development",
"download_owl": "http://aber-owl.net/media/ontologies/COKPME/1/cokpme.owl",
"name": "COKPME - COVID19 Ontology for analyzing the Karnataka Private Medical Establishments Data ",
"prefix": "COKPME",
"version": "1.0"
},
"COLAO": {
"description": "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. It has been built using the Ontology Develoment Kit, with the Ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM) as a backbone.",
"download_owl": "http://aber-owl.net/media/ontologies/COLAO/10/colao.owl",
"homepage": "https://github.com/insect-morphology/colao",
"name": "Coleoptera Anatomy Ontology (COLAO)",
"prefix": "COLAO"
},
"COLL": {
"description": "An anatomical ontology for Collembola (Arthropoda: Hexapoda). This ontology is developed for morphological descriptions in Collembola and is part of doctoral research \"Taxonomical revision of neotropical species belongs to genus Lepidocyrtus (Entombryidae: Lepidocyrtinae)",
"download_owl": "http://aber-owl.net/media/ontologies/COLL/7/coll.owl",
"name": "Collembola Anatomy Ontology",
"prefix": "COLL",
"version": "2020-25-02"
},
"COMET": {
"description": "A collection of common metadata elements and terms for constructing LinkML Schemas and Data Models",
"download_owl": "http://aber-owl.net/media/ontologies/COMET/3/comet.owl",
"homepage": "https://github.com/linkml/linkml-common",
"name": "LinkML Common Metadata Elements and Terms",
"prefix": "COMET"
},
"COMODI": {
"description": "An ontology to characterise differences in versions of computational models in biology",
"download_owl": "http://aber-owl.net/media/ontologies/COMODI/6/comodi.owl",
"homepage": "http://comodi.sems.uni-rostock.de",
"name": "COMODI",
"prefix": "COMODI"
},
"CONDOR": {
"description": "The CONDOR is a comprehensive framework designed to encapsulate the multifaceted aspects of liver cancer patient care. It encompasses essential elements ranging from patient profiles to disease classifications and treatment options. This ontology aims to streamline the process of liver cancer analysis and treatment, enabling more personalized and effective patient care strategies.",
"download_owl": "http://aber-owl.net/media/ontologies/CONDOR/1/condor.owl",
"homepage": "https://www.ki.uni-stuttgart.de/departments/ac/research/projects/ATLAS/",
"name": "Liver Cancer Ontology Diagnosis Treatment",
"prefix": "CONDOR",
"version": "0.1"
},
"CONTSONTO": {
"description": "The Ontology of Continuity of care (ContSOnto) is an emerging research area consisting of the extension of a healthcare ontology to inform the continuity of care domain. This field is positioned at the confluence of health informatics, nursing informatics, process modelling, and artificial intelligence. This research relating to ContSOnto is underpinned by health informatics standard ISO 13940 Systems of Concepts for Continuity of Care ContSOnto focuses on how information flows from different information systems across and between services for clinical applications and health care professionals to use. Figure 14.2 provides an illustration (see https://contsys.org/pages/Guest%20blog/FormalOntology)of how the different classes and relationships in the standard are represented. Subject of care refers to the individual service user and health care actors can be human or non-human, for example, a health care professional or an organisation.",
"download_owl": "http://aber-owl.net/media/ontologies/CONTSONTO/5/contsonto.owl",
"homepage": "http://purl.org/net/for-coc",
"name": "Continuity of care",
"prefix": "CONTSONTO",
"version": "1.5"
},
"COP": {
"description": "COP is a core ontology, which can be used to specify phenotype algorithms as ontologies (Phenotype Algorithm Specification Ontology, PASO).",
"download_owl": "http://aber-owl.net/media/ontologies/COP/1/cop.owl",
"homepage": "https://github.com/Onto-Med/COP/tree/v0.2.0",
"name": "Core Ontology of Phenotypes",
"prefix": "COP",
"version": "v0.2.0"
},
"COPDO": {
"description": "The COPD Ontology is a biomedical ontology used for modelling concepts associated to chronic obstructive pulmonary disease in routine clinical databases.",
"download_owl": "http://aber-owl.net/media/ontologies/COPDO/1/copdo.owl",
"homepage": "clininf.eu",
"name": "COPD Ontology",
"prefix": "COPDO",
"version": "1"
},
"COSTART": {
"description": "Coding Symbols for Thesaurus of Adverse Reaction Terms (COSTART). 5th ed. Rockville (MD). COSTART is used for coding, filing, and retrieving post-marketing adverse drug and biologic experience reports. COSTART is organized in body system and pathophysiology hierarchies, as well as a separate fetal/neonatal category of less than 20 terms. COSTART has been superseded by the Medical Dictionary for Regulatory Activities (MedDRA) Terminology. For more information about MedDRA in the Metathesaurus, see the MedDRA source synopsis. COSTART was last updated in the Metathesaurus in 1999.",
"homepage": "http://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/CST/",
"name": "Coding Symbols for a Thesaurus of Adverse Reaction Terms",
"prefix": "COSTART",
"version": "2016AB"
},
"COVID-19": {
"description": "The COVID-19 ontology covers the role of molecular and cellular entities in virus-host-interactions, in the virus life cycle, as well as a wide spectrum of medical and epidemiological concepts linked to COVID-19.",
"download_owl": "http://aber-owl.net/media/ontologies/COVID-19/3/covid-19.owl",
"name": "COVID-19 Ontology",
"prefix": "COVID-19",
"version": "Version Release: 1.0.0"
},
"COVID-19-ONT-PM": {
"description": "This ontology focuses on the aspects of the scientific findings in the COVID-19 fields in order to help the efforts against the outbreak of the pandemic. It is expected, through the ontology, to understand the medical conditions and make medical decisions in more integrated or systematic ways, by the engineerized or calculatable methods, rahter than the experience-based ways, usually used in the Traditional Information-Pieces-Accumulation Medicine(TIPAM). The researches of the ontology involve the exploratory works of the Pattern Medicine(PM) and so called the Generalized Biomedical Dynamics(GBMD) , especially concentrating to the relations between the molecular and clinic levels. Please pay attention to the background researches or the pilot project related to this ontolgy, and the introduction and publications, as well. The relative artcle under going is at stie: https://blog.51.ca/u-345129/2020/11/13/the-preliminary-researches-on-the-data-dynamics-of-covid-19/",
"download_owl": "http://aber-owl.net/media/ontologies/COVID-19-ONT-PM/9/covid-19-ont-pm.owl",
"homepage": "https://blog.51.ca/u-345129/2020/11/13/the-preliminary-researches-on-the-data-dynamics-of-covid-19/",
"name": "COVID-19OntologyInPatternMedicine",
"prefix": "COVID-19-ONT-PM",
"version": "007"
},
"COVID19": {
"description": "The COVID-19 Surveillance Ontology is an application ontology used to support SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) surveillance in primary care. The ontology facilitates monitoring of COVID-19 cases and related respiratory conditions using data from multiple brands of computerised medical record systems.",
"download_owl": "http://aber-owl.net/media/ontologies/COVID19/3/covid19.owl",
"homepage": "https://orchid.phc.ox.ac.uk/index.php/cov-19/",
"name": "COVID-19 Surveillance Ontology",
"prefix": "COVID19",
"version": "V1.0"
},
"COVID19-IBO": {
"description": "Covid19 Impact on Banking Ontology (Covid19-IBO) provides semantic information about the impact of the Covid-19 on the banking sector of India",
"download_owl": "http://aber-owl.net/media/ontologies/COVID19-IBO/6/covid19-ibo.owl",
"name": "Covid19 Impact on Banking Ontology",
"prefix": "COVID19-IBO",
"version": "1.5"
},
"COVIDCRFRAPID": {
"description": "This is a semantic data model for the WHO's COVID-19 case record form RAPID version from April 8 2020. It aims at providing semantic references to the questions and answers of the form. Changes in the version 1.1.4: - Corrected: Urea_(BUN) to remove the \"()\", which may cause resolution and validation issues; Changes in the version 1.1.3: - Corrected: Chloroquine/hydroxychloroquine to remove the \"/\", which may cause resolution issues; Changes in version 1.1.2: - Corrected: Cough with haemoptysis because the IRI was mispelled; - Corrected: CPAP/NIV Mask to remove the \"/\", which may cause resolution issues; - Added: missing \"part of\" property for section 1g. - Added: \"has other measurement unit label\" property for the laboratory results that may use a different unit than specified in the CRF; - Added: missing \"has value\" for the Which coronavirus question; - Added: missing possibility to enter the name of a specific antibiotic in section 3c of the CRF; - Added: missing question on testing the presence of other pathogenic of public health interest from section 3a of the CRF. Changes in version 1.1.1: - Added: Facility Name to identify the care facility in which the case is reported from. Changes in version 1.1.0: - This version covers the modifications introduced by the WHO COVID-19 Rapid CRF from April 8, 2020. The model maintains backward compatibility with the WHO COVID-19 Rapid CRF from March 23, 2020.",
"download_owl": "http://aber-owl.net/media/ontologies/COVIDCRFRAPID/12/covidcrfrapid.owl",
"homepage": "http://purl.org/vodan/whocovid19crfsemdatamodel/",
"name": "WHO COVID-19 Rapid Version CRF semantic data model",
"prefix": "COVIDCRFRAPID",
"version": "1.1.4"
},
"CPRO": {
"description": "A uniform core set of data elements (whose formal semantics are captured in OWL) for use in a Computer-Based Patient Record (CPR)",
"download_owl": "http://aber-owl.net/media/ontologies/CPRO/3/cpro.owl",
"homepage": "https://code.google.com/p/cpr-ontology/",
"name": "Computer-Based Patient Record Ontology",
"prefix": "CPRO",
"version": "Last modification: July 31th, 2011 Chimezie Ogbuji"
},
"CPT": {
"description": "Current Procedural Terminology",
"homepage": "http://www.ama-assn.org/ama/pub/category/3113.html",
"name": "Current Procedural Terminology",
"prefix": "CPT",
"version": "2016AB"
},
"CPT-mod": {
"description": "Modifiers denote that a certain procedure/service has been altered by a particular circumstance, but not changed in its definition, therefore the same code is used and a modifier is added to denote what has been altered.",
"download_owl": "http://aber-owl.net/media/ontologies/CPT-mod/1/cpt-mod.owl",
"name": "CPT modifiers",
"prefix": "CPT-mod",
"version": "unknown"
},
"CPTAC": {
"description": "a basic ontology which describes the proteomics pipeline infrastructure for CPTAC project",
"download_owl": "http://aber-owl.net/media/ontologies/CPTAC/3/cptac.owl",
"name": "CPTAC Proteomics Pipeline Infrastructure Ontology",
"prefix": "CPTAC",
"version": "alpha 1.1"
},
"CRC-ONTO": {
"description": "This ontology is an comprehensive approach, including various aspects associated with CRC disease. We developed this ontology as an assistive solution for enhancing the semantic interoperability among various Health Information Systems (HISs) in Iran using the CRC data elements.",
"download_owl": "http://aber-owl.net/media/ontologies/CRC-ONTO/1/crc-onto.owl",
"name": "Colorectal cancer ontology",
"prefix": "CRC-ONTO",
"version": "1.00"
},
"CRENO": {
"description": "This work undertakes the possibility of using the Web Ontology Language (OWL2) to describe concepts related to \"culture\", \"race\", \"ethnicity\", and \"nationality\" - concepts that are sometimes misunderstood/misused due to lack of standardization and biases. The project also attempts to link data relating to these broad concepts to health data, like cancer rates, and shed light on understanding health disparities that impact certain communities. This work is early in development and preliminary.",
"download_owl": "http://aber-owl.net/media/ontologies/CRENO/2/creno.owl",
"homepage": "https://github.com/UTHealth-Ontology/CRENO",
"name": "Culture, Race, Ethnicity and Nationality Ontology",
"prefix": "CRENO",
"version": "0.6"
},
"CRISP": {
"description": "Computer Retrieval of Information on Scientific Projects (CRISP)",
"name": "Computer Retrieval of Information on Scientific Projects Thesaurus",
"prefix": "CRISP",
"version": "2016AB"
},
"CRO": {
"description": "A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability.",
"download_owl": "http://aber-owl.net/media/ontologies/CRO/5/cro.owl",
"homepage": "https://github.com/data2health/contributor-role-ontology",
"name": "Contributor Role Ontology",
"prefix": "CRO"
},
"CRYOEM": {
"description": "Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles",
"download_owl": "http://aber-owl.net/media/ontologies/CRYOEM/4/cryoem.owl",
"homepage": "http://scipion.i2pc.es/ontology/cryoem",
"name": "Cryo Electron Microscopy",
"prefix": "CRYOEM",
"version": "2021-03-09"
},
"CS": {
"name": "Coping Strategies for Adverse Drug Events Ontology",
"prefix": "CS"
},
"CSEO": {
"description": "The CSEO has potential to become a widely used standard within the academic and industrial community. Mainly because of the emerging need of systems toxicology to controlled vocabularies and also the lack of suitable ontologies for this domain, the CSEO prepares the ground for integrative systems-based research in the exposure science.",
"download_owl": "http://aber-owl.net/media/ontologies/CSEO/2/cseo.owl",
"homepage": "https://publicwiki-01.fraunhofer.de/CSEO-Wiki/index.php/Main_Page",
"name": "Cigarette Smoke Exposure Ontology",
"prefix": "CSEO",
"version": "1.0"
},
"CSO": {
"description": "Ontology to describe general clinical studies.",
"download_owl": "http://aber-owl.net/media/ontologies/CSO/1/cso.owl",
"name": "Clinical Study Ontology",
"prefix": "CSO"
},
"CSSO": {
"description": "An ontology for describing clinical signs and symptoms.",
"download_owl": "http://aber-owl.net/media/ontologies/CSSO/6/csso.owl",
"homepage": "http://mdb.bio.titech.ac.jp/csso",
"name": "Clinical Signs and Symptoms Ontology",
"prefix": "CSSO",
"version": "Version 0.6"
},
"CST": {
"name": "Cancer Staging Terms",
"prefix": "CST"
},
"CSTD": {
"name": "Clinical smell and taste disorders",
"prefix": "CSTD"
},
"CTCAE": {
"description": "A coding system for reporting adverse events that occur in the course of cancer therapy. It was derived from the Common Toxicity Criteria (CTC) v2.0 and is maintained by the Cancer Therapy Evaluation Program (CTEP) at the National Cancer Institution (NCI).",
"download_owl": "http://aber-owl.net/media/ontologies/CTCAE/2/ctcae.owl",
"name": "Common Terminology Criteria for Adverse Events",
"prefix": "CTCAE",
"version": "4.03"
},
"CTENO": {
"description": "An anatomical and developmental ontology for ctenophores (Comb Jellies)",
"download_owl": "http://aber-owl.net/media/ontologies/CTENO/2/cteno.owl",
"homepage": "https://github.com/obophenotype/ctenophore-ontology",
"name": "Ctenophore Ontology",
"prefix": "CTENO"
},
"CTGO": {
"description": "The Clinical Trials Gov Ontology (CTGO) is based on the AACT database schema for Aggregate Analysis of ClinicalTrials.gov. AACT contains information about clinical studies that have been registered at ClinicalTrials.gov. AACT includes all of the protocol and results data elements for studies publicly available at ClinicalTrials.gov.",
"download_owl": "http://aber-owl.net/media/ontologies/CTGO/1/ctgo.owl",
"homepage": "http://mraas.ai/ontologies/ctgo.ttl",
"name": "Clinical Trials Gov Ontology",
"prefix": "CTGO",
"version": "1.0"
},
"CTO": {
"description": "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials.",
"download_owl": "http://aber-owl.net/media/ontologies/CTO/5/cto.owl",
"homepage": "https://github.com/ClinicalTrialOntology/CTO/",
"name": "CTO: Core Ontology of Clinical Trials",
"prefix": "CTO"
},
"CTO-NDD": {
"description": "The CTO-NDD stands for Clinical Trial Ontology-Neurodegenerative Diseases, which was built with the purpose of organizing the knowledge domain of clinical trials in neurodegeneration field. This resource has been created for use in the IMI-funded AETIONOMY project (www.aetionomy.org).",
"download_owl": "http://aber-owl.net/media/ontologies/CTO-NDD/1/cto-ndd.owl",
"name": "Clinical Trials Ontology - Neurodegenerative Diseases",
"prefix": "CTO-NDD",
"version": "0.6"
},
"CTONT": {
"download_owl": "http://aber-owl.net/media/ontologies/CTONT/1/ctont.owl",
"name": "Epoch Clinical Trial Ontology",
"prefix": "CTONT",
"version": "\n \n | \n Version\n | \n \n 0.97\n | \n
\n \n | \n Date\n | \n \n 3/2/2007
\n | \n
\n
\n
"
},
"CTP": {
"name": "Current Procedural Terminology",
"prefix": "CTP"
},
"CTU_BEREADY_GEM": {
"description": "Ontology used for project 1694, BEReady (be ready for future pandemics)",
"homepage": "http://www.ctu.unibe.ch",
"name": "CTU Bern BEReady Gemeinden",
"prefix": "CTU_BEREADY_GEM",
"version": "gem_onto_1level_v0_01"
},
"CTX": {
"description": "The ontology represents CTX phenotypes, genetic variants, and bidirectional relationships between them though a patient model. The CTX ontology was build reusing the Human Phenotype Ontology (HPO) and the Snomed ct ontologies. A set of temporal clinical manifestations are semantically annotated with a domain phenotype ontology and registered with a time-stamped value.",
"download_owl": "http://aber-owl.net/media/ontologies/CTX/2/ctx.owl",
"homepage": "http://www.usc.es/keam/~mariataboada/",
"name": "Cerebrotendinous Xanthomatosis Ontology",
"prefix": "CTX",
"version": "vtemp2"
},
"CU-VO": {
"description": "An ontology of venoms and venom-related compounds, designed to facilitate the discovery of novel venom-derived therapeutics.",
"download_owl": "http://aber-owl.net/media/ontologies/CU-VO/1/cu-vo.owl",
"name": "Venom Ontology",
"prefix": "CU-VO",
"version": "1.0"
},
"CVAO": {
"description": "Stroke ontology",
"download_owl": "http://aber-owl.net/media/ontologies/CVAO/2/cvao.owl",
"name": "STO",
"prefix": "CVAO",
"version": "STO_V1.1"
},
"CVDO": {
"description": "An ontology to describe entities related to cardiovascular diseases",
"download_owl": "http://aber-owl.net/media/ontologies/CVDO/6/cvdo.owl",
"homepage": "https://github.com/OpenLHS/CVDO",
"name": "Cardiovascular Disease Ontology",
"prefix": "CVDO"
},
"CWD": {
"description": "Consumer Wearable Devices (CWD) enable passive, low-burden, longitudinal collection of data relevant to health behaviors, human performance, and biometrics. Such data are increasingly used to tailor clinical and public health interventions and as outcome measures in clinical trials. The uptake of CWD in research applications warrants an examination of the data collected from these products. This ontology was developed based on a review of publicly available documentation and data sets from three CWD vendors and is open for researchers to modify + extend as new features become available.",
"download_owl": "http://aber-owl.net/media/ontologies/CWD/1/cwd.owl",
"name": "Consumer Wearable Device",
"prefix": "CWD"
},
"CYTO": {
"description": "It is flat ontology showing cytokine synonyms. It has been produced by merging cytokine branches, using SOMA (Synonym Ontology Mapping Approach) method, of 10 Bioportal ontologies.",
"download_owl": "http://aber-owl.net/media/ontologies/CYTO/27/cyto.owl",
"name": "CYTOKINE",
"prefix": "CYTO",
"version": "Cytokines"
},
"D1245": {
"name": "Data Center",
"prefix": "D1245"
},
"DATACITE": {
"description": "The DataCite Ontology (DataCite) is an ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF.",
"download_owl": "http://aber-owl.net/media/ontologies/DATACITE/2/datacite.owl",
"homepage": "http://www.sparontologies.net/ontologies/datacite",
"name": "SPAR DataCite Ontology",
"prefix": "DATACITE",
"version": "1.2"
},
"DATACITE-VOCAB": {
"description": "Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is Datacite Controlled Vocabulary. This controlled vocabulary is produced based on description of Datacite Schema V4.4. The work of creating this controlled vocabulary is part of FAIRware project which if funded by RoRi. sheet2rdf is used to build Datacite Controlled Vocabulary, while PURL, is used to persist and resolve identifiers via BioPortal for the vocabulary terms.",
"homepage": "https://github.com/metadatacenter/datacite-controlled-vocabulary",
"name": "DATACITE V4.4",
"prefix": "DATACITE-VOCAB",
"version": "0.1.0"
},
"DATASET": {
"description": "You can choose what Dataset you want",
"download_owl": "http://aber-owl.net/media/ontologies/DATASET/1/dataset.owl",
"name": "dataset",
"prefix": "DATASET",
"version": "1.0.0"
},
"DC": {
"description": "The Dublin Core Schema is a small set of vocabulary terms that can be used to describe several kinds of resources. Dublin Core Metadata may be used for multiple purposes, from simple resource description, to combining metadata vocabularies of different metadata standards, to providing interoperability for metadata vocabularies in the Linked Data cloud and Semantic Web implementations.",
"download_owl": "http://aber-owl.net/media/ontologies/DC/3/dc.owl",
"homepage": "http://dublincore.org",
"name": "Dublin Core",
"prefix": "DC"
},
"DCAT": {
"description": "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web.",
"download_owl": "http://aber-owl.net/media/ontologies/DCAT/2/dcat.owl",
"homepage": "https://www.w3.org/TR/vocab-dcat/",
"name": "Data Catalog Vocabulary",
"prefix": "DCAT"
},
"DCAT-FDC": {
"description": "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web. This document defines the schema and provides examples for its use. DCAT enables a publisher to describe datasets and data services in a catalog using a standard model and vocabulary that facilitates the consumption and aggregation of metadata from multiple catalogs. This can increase the discoverability of datasets and data services. It also makes it possible to have a decentralized approach to publishing data catalogs and makes federated search for datasets across catalogs in multiple sites possible using the same query mechanism and structure. Aggregated DCAT metadata can serve as a manifest file as part of the digital preservation process. The namespace for DCAT terms is http://www.w3.org/ns/dcat# The suggested prefix for the DCAT namespace is dcat",
"download_owl": "http://aber-owl.net/media/ontologies/DCAT-FDC/1/dcat-fdc.owl",
"homepage": "https://www.w3.org/TR/vocab-dcat-3/",
"name": "Data Catalog Vocabulary (DCAT)",
"prefix": "DCAT-FDC",
"version": "Questa \u00e8 una copia aggiornata del vocabolario DCAT v2.0 disponibile in https://www.w3.org/ns/dcat.ttl"
},
"DCAT3": {
"description": "DCAT",
"download_owl": "http://aber-owl.net/media/ontologies/DCAT3/1/dcat3.owl",
"name": "DCAT3",
"prefix": "DCAT3",
"version": "3"
},
"DCCDFV": {
"description": "The Collection Description Accrual Policy Vocabulary provides a set of terms that can be used as values of the dcterms:accrualPolicy property in descriptions of collections.",
"homepage": "http://dublincore.org/groups/collections/accrual-policy/",
"name": "Dublin Core Collection Description Frequency Vocabulary",
"prefix": "DCCDFV"
},
"DCM": {
"description": "DICOM Controlled Terminology (PS3.16 2017d Annex D)",
"download_owl": "http://aber-owl.net/media/ontologies/DCM/12/dcm.owl",
"homepage": "http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html",
"name": "DICOM Controlled Terminology",
"prefix": "DCM",
"version": "2017d_20170924"
},
"DCMITYPE": {
"description": "The DCMI Type Vocabulary provides a general, cross-domain list of approved terms that may be used as values for the Resource Type element to identify the genre of a resource",
"download_owl": "http://aber-owl.net/media/ontologies/DCMITYPE/4/dcmitype.owl",
"homepage": "http://dublincore.org/documents/dcmi-type-vocabulary",
"name": "DCMI Type Vocabulary",
"prefix": "DCMITYPE"
},
"DCO": {
"description": "Dispedia Core Ontology is a schema for information brokering and knowledge management in the complex field of rare diseases. On the one hand, the Dispedia schema uses semantic technologies to describe patients affected by rare diseases, and on the other hand, to record expertise concerning these particular diseases in machine-processable form. In addition to the differentiated attribution of facts to the individual need for information, Dispedia enables information brokering which adjusts to the type of recipient, its character as well as its personal attitude. The schema was initially geared to an exemplified disease, Amyotrophe Lateralsclerose (ALS).",
"download_owl": "http://aber-owl.net/media/ontologies/DCO/34/dco.owl",
"homepage": "www.dispedia.de",
"name": "Dispedia Core Ontology",
"prefix": "DCO",
"version": "0.7.0.0002"
},
"DCO-DEBUGIT": {
"description": "The Debugit Core Ontology (dco) covers the complete conceptual space of the domain of interest in the DebugIT project. It focuses on the management of antibiotics resistance within hospitals and infectious diseases to cover the clinical monitoring use cases. The ontology shall provide a semantic reference as logically defined classes in a formal and computer understandable format. It is supposed to formally represent all basic kinds of entities in the domain of interest, together with their invariant and context-independent properties. The ontology is therefore distinct from the representation of clinical knowledge as targeted by the DebugIT WP 4. Instead, it has a supportive semantic glue Function as it provides standardized and formally described meaning identifiers across the whole project, hence serving the Interoperability platform as well.",
"download_owl": "http://aber-owl.net/media/ontologies/DCO-DEBUGIT/1/dco-debugit.owl",
"homepage": "http://www.debugit.eu/index.php",
"name": "DebugIT Core Ontology",
"prefix": "DCO-DEBUGIT",
"version": "1.1"
},
"DCT": {
"description": "Specification of all metadata terms maintained by the Dublin Core Metadata Initiative. Included are the fifteen terms of the Dublin Core Metadata Element Set",
"download_owl": "http://aber-owl.net/media/ontologies/DCT/1/dct.owl",
"name": "DC Terms",
"prefix": "DCT"
},
"DCTERMS": {
"description": "DCMI properties in the /terms/ namespace",
"homepage": "http://dublincore.org/documents/dcmi-terms/",
"name": "DCMI Metadata Terms: properties in /terms/ namespace",
"prefix": "DCTERMS"
},
"DDANAT": {
"description": "A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum",
"download_owl": "http://aber-owl.net/media/ontologies/DDANAT/134/ddanat.owl",
"homepage": "http://dictybase.org/",
"name": "Dictyostelium discoideum anatomy",
"prefix": "DDANAT"
},
"DDI": {
"description": "The goal of DDI project is to develop an ontology for the description of drug discovery investigations. DDI aims to follow to the OBO (Open Biomedical Ontologies) Foundry principles, uses relations laid down in the OBO Relation Ontology, and be compliant with Ontology for biomedical investigations (OBI).",
"download_owl": "http://aber-owl.net/media/ontologies/DDI/2/ddi.owl",
"homepage": "http://purl.org/ddi/home",
"name": "Ontology for Drug Discovery Investigations",
"prefix": "DDI",
"version": "$Revision$"
},
"DDIEM": {
"description": "DDIEM Ontology for the Drug Database for Inborn Errors of Metabolism. The DDIEM database is a database of therapeutic strategies and treatments for inborn errors of metabolism. These strategies are classified by mechanism and outcome using the DDIEM Ontology. The DDIEM database also includes descriptions of the phenotypes addressed by the treatment, together with drugs and procedures applied.",
"download_owl": "http://aber-owl.net/media/ontologies/DDIEM/4/ddiem.owl",
"homepage": "http://ddiem.phenomebrowser.net/",
"name": "Drug Database for Inborn Errors of Metabolism (DDIEM) Ontology",
"prefix": "DDIEM",
"version": "1.2"
},
"DDIO": {
"description": "Drug Drug Interaction Ontology",
"download_owl": "http://aber-owl.net/media/ontologies/DDIO/1/ddio.owl",
"name": "Drug Drug Interaction Ontology",
"prefix": "DDIO",
"version": "1"
},
"DDO": {
"description": "An ontology for diagnosis of diabetes containing the diabetes related complications, symptoms, drugs, lab tests, etc.",
"download_owl": "http://aber-owl.net/media/ontologies/DDO/3/ddo.owl",
"name": "Diabetes Mellitus Diagnosis Ontology",
"prefix": "DDO",
"version": "2015-11-20"
},
"DDPHENO": {
"description": "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum.",
"download_owl": "http://aber-owl.net/media/ontologies/DDPHENO/165/ddpheno.owl",
"homepage": "http://dictybase.org/",
"name": "Dictyostelium discoideum phenotype ontology",
"prefix": "DDPHENO"
},
"DDSS": {
"name": "Health_ontology",
"prefix": "DDSS"
},
"DEB": {
"description": "An ontology developed to facilitate information curation in the area of medical devices, experimental scaffolds and biomaterials. The ontology was designed to complement existing medical vocabularies, with emphasis on material processing, structures and features associated with biomaterials and experimental scaffolds. It is used as part of an automated text mining pipeline which populates the database of Experimental Biomaterials and their Biological Effect (DEBBIE). DEBBIE is an EU Horizon 2020 funded project. For more information visit https://projectdebbie.github.io/",
"download_owl": "http://aber-owl.net/media/ontologies/DEB/7/deb.owl",
"homepage": "https://projectdebbie.github.io/",
"name": "Devices, Experimental scaffolds and Biomaterials Ontology",
"prefix": "DEB",
"version": "4.0"
},
"DECIDE": {
"description": "Ontology is developed for decision support tools for different animal species as a part of DECIDE project (https://decideproject.eu).",
"download_owl": "http://aber-owl.net/media/ontologies/DECIDE/1/decide.owl",
"homepage": "https://github.com/decide-project-eu",
"name": "DECIDE ONTOLOGY",
"prefix": "DECIDE"
},
"DELME1": {
"description": "Test Ontology, Delete on sight",
"download_owl": "http://aber-owl.net/media/ontologies/DELME1/1/delme1.owl",
"name": "deleteme1",
"prefix": "DELME1"
},
"DERMLEX": {
"description": "Version 1.0 of the American Academy of Dermatology's DermLex: The Dermatology Lexicon, a standardized terminology of dermatologic diagnoses, therapies, procedures, and laboratory tests.",
"download_owl": "http://aber-owl.net/media/ontologies/DERMLEX/4/dermlex.owl",
"homepage": "http://www.aad.org/research/lexicon/",
"name": "Dermatology Lexicon",
"prefix": "DERMLEX",
"version": "1"
},
"DERMO": {
"description": "Ontology of human dermatologic disease",
"download_obo": "http://aber-owl.net/media/ontologies/DERMO/10/dermo.obo",
"name": "Human Dermatological Disease Ontology",
"prefix": "DERMO",
"version": "1.19"
},
"DFO": {
"description": "The Databank Family Ontology describes groups of data banks with similar record prompts and originators.",
"download_owl": "http://aber-owl.net/media/ontologies/DFO/1/dfo.owl",
"homepage": "https://w3id.org/dfo",
"name": "Databank Family Ontology",
"prefix": "DFO",
"version": "0.1"
},
"DIAB": {
"description": "Diabetes ontology",
"download_owl": "http://aber-owl.net/media/ontologies/DIAB/73/diab.owl",
"name": "BioMedBridges Diabetes Ontology",
"prefix": "DIAB",
"version": "2.0"
},
"DIAGONT": {
"description": "We built a computational diagnostic ontology containing 91 elements, including classes and sub-classes, which are required to conduct SR-MA (Systematic Review - Meta Analysis) for diagnostic studies, that will assist in standardized reporting of diagnostic articles. We also report high percentage of agreement among five observers as a result of the inter-observer agreement that we conducted among them to tag 13 articles using the diagnostic ontology. Moreover, we extend our existing repository CERR-N (Center of Excellence in Research Reporting in Neurosurgery) to include diagnostic studies.",
"download_owl": "http://aber-owl.net/media/ontologies/DIAGONT/1/diagont.owl",
"name": "Diagnostic Ontology",
"prefix": "DIAGONT",
"version": "2.0"
},
"DIDEO": {
"description": "The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology",
"download_owl": "http://aber-owl.net/media/ontologies/DIDEO/54/dideo.owl",
"homepage": "https://github.com/DIDEO/DIDEO",
"name": "Drug-drug Interaction and Drug-drug Interaction Evidence Ontology",
"prefix": "DIDEO"
},
"DIKB": {
"description": "An evidence taxonomy for pharmacologic studies that, when combined with a set of inclusion criteria, enable drug experts to specify what their confidence in a drug mechanism assertion would be if it were supported by a specific set of evidence. Boyce R, Collins C, Horn J, Kalet I. Computing with evidence Part I: A drug-mechanism evidence taxonomy oriented toward confidence assignment. J Biomed Inform. 2009 Dec;42(6):979-89. Epub 2009 May 10. PubMed PMID: 19435613; PubMed Central PMCID: PMC2783801.",
"download_owl": "http://aber-owl.net/media/ontologies/DIKB/5/dikb.owl",
"homepage": "http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/front-page.html",
"name": "Drug Interaction Knowledge Base Ontology",
"prefix": "DIKB",
"version": "Version 1.6"
},
"DILIo": {
"description": "A SNOMED subset of terms related to histological and clinical descriptions of Drug Induced Liver Injury (DILI). See Wang et al., \"A Unifying Ontology to Integrate Histological and Clinical Observations for Drug-Induce Liver Injury\" The American Journal of Pathology, 182:4,1180-1187 (2013). This view contains both of the DILIo major branches; SNOMED:Body Structure and SNOMED:Clinical finding Some of the class names have been changed to correspond to the preferred names in SNOMED of 7/31/2011. In DILIo publication -> in this file; Disorder of liver -> Disease of liver; Finding of general form of body -> General form of body - finding; Finding of size of liver -> size of liver - finding; Subacute necrosis of liver -> subacute hepatic necrosis",
"download_owl": "http://aber-owl.net/media/ontologies/DILIo/1/dilio.owl",
"name": "Drug-Induce Liver Injury (combined)",
"prefix": "DILIo",
"version": "1.0.0"
},
"DILON": {
"description": "DILON was created to represent dietary lifestyle data. Concepts were pulled from Korean dietary assessment scales and English assessment scales. Concepts are labeled in English and Korean translations are also provided.",
"download_owl": "http://aber-owl.net/media/ontologies/DILON/2/dilon.owl",
"name": "Dietary lifestyle ontology",
"prefix": "DILON",
"version": "2"
},
"DINTO": {
"description": "DINTO is an OWL ontology that systematically organizes all drug-drug interaction (DDI) related information. Drug-drug interactions (DDIs) form a significant risk group for adverse effects associated with pharmaceutical treatment. These interactions are often reported in the literature, however, they are sparsely represented in machine-readable resources, such as online databases, thesauri or ontologies. DINTO is an ontology that describes and categorizes DDIs and all the possible mechanisms that can lead to them (including both pharmacodynamic and pharmacokinetic DDI mechanisms).",
"download_owl": "http://aber-owl.net/media/ontologies/DINTO/5/dinto.owl",
"homepage": "http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto",
"name": "The Drug-Drug Interactions Ontology",
"prefix": "DINTO",
"version": "1.3"
},
"DISDRIV": {
"description": "Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. Built in collaboration with EnvO, ExO, ECTO and ChEBI.",
"download_owl": "http://aber-owl.net/media/ontologies/DISDRIV/2/disdriv.owl",
"homepage": "http://www.disease-ontology.org",
"name": "Disease Drivers Ontology",
"prefix": "DISDRIV"
},
"DLO": {
"description": "Taxonomy of Deep Learning networks and layers. TODO: partonomy",
"download_owl": "http://aber-owl.net/media/ontologies/DLO/2/dlo.owl",
"homepage": "https://github.com/turbomam/deep-learning-ontology",
"name": "Deep Learning Ontology",
"prefix": "DLO",
"version": "2021-07-27"
},
"DLORO": {
"description": "Dependency Layered Ontology for Radiation Oncology",
"download_owl": "http://aber-owl.net/media/ontologies/DLORO/1/dloro.owl",
"homepage": "https://ont2bn.radonc.washington.edu/IROK/",
"name": "Dependency Layered Ontology for Radiation Oncology",
"prefix": "DLORO"
},
"DMDSONT": {
"description": "Diabetes Mellitus Diagnosis and Support Ontology (DMDSOnt) is created using OWL 2.0 according to the directions given in the IDF\u2019s guidelines (2022). As required and directed in the IDF\u2019s guidelines, DMDSOnt contains concepts and relations about the signs and symptoms observed in DM, active lifestyle expected from patients, genetic conditions of patients, physical activities to be followed, laboratory tests, other factors/criteria in the diagnosis of DM, and supportive treatment recommendations for the proper management of DM risk. IDF:\tAmerican Diabetes Association Professional Practice Committee. (2022). 2.Classification and diagnosis of diabetes: standards of medical care in diabetes\u20142022. Diabetes Care, 45, (Supplement_1), S17-S38, DOI: /10.2337/dc22-S002, http://diabetesjournals.org/care/article-pdf/45/Supplement_1/S17/637547/dc22s002.pdf.",
"download_owl": "http://aber-owl.net/media/ontologies/DMDSONT/1/dmdsont.owl",
"name": "Diabetes Mellitus Diagnosis and Support Ontology ",
"prefix": "DMDSONT",
"version": "ver 1.0"
},
"DMTO": {
"description": "DMTO is an OWL 2 ontology for creating customized treatment plans for diabetic patients. The ontology is based on BFO and OGMS. In addition, it extends the DDO ontology by adding the treatment classes and axioms to the existing diagnosis part.",
"download_owl": "http://aber-owl.net/media/ontologies/DMTO/5/dmto.owl",
"name": "Diabetes Mellitus Treatment Ontology",
"prefix": "DMTO",
"version": "2015-11-20"
},
"DOCCC": {
"description": "Diagnosis Ontology of Clinical Care Classification (CCC)",
"download_owl": "http://aber-owl.net/media/ontologies/DOCCC/3/doccc.owl",
"name": "Diagnosis Ontology of Clinical Care Classification",
"prefix": "DOCCC",
"version": "20131004"
},
"DOID": {
"description": "An ontology for describing the classification of human diseases organized by etiology.",
"download_owl": "http://aber-owl.net/media/ontologies/DOID/684/doid.owl",
"homepage": "http://www.disease-ontology.org",
"name": "Human Disease Ontology",
"prefix": "DOID"
},
"DOIDSH": {
"download_owl": "http://aber-owl.net/media/ontologies/DOIDSH/3/doidsh.owl",
"name": "Diseases Ontology - Shrinked version",
"prefix": "DOIDSH",
"version": "0.3"
},
"DOREMUS-KEYS": {
"description": "The sum of relations, melodic and harmonic, existing between the tones of a scale or musical system.",
"name": "Doremus List of Keys",
"prefix": "DOREMUS-KEYS"
},
"DOVES": {
"description": "The Digital medicine Outcomes Value Set (DOVeS) ontology aims to provide users with a set of ontologically structured healthcare outcomes (clinical, operational, economic, technical, and others) tailored to digital medicine and digital therapeutic applications.",
"download_owl": "http://aber-owl.net/media/ontologies/DOVES/2/doves.owl",
"name": "Digital medicine Outcomes Value Set (DOVeS) Ontology",
"prefix": "DOVES",
"version": "releases/2023-03-01"
},
"DPCO": {
"description": "The Diabetes Pharmacology Ontology contains the classes needed to describe antihyperglycemic therapies, pharmacotherapy factors, and diagnostic factors.",
"download_owl": "http://aber-owl.net/media/ontologies/DPCO/2/dpco.owl",
"homepage": "https://tetherless-world.github.io/diabetes-pharmacology-ontology/",
"name": "Diabetes Pharmacology Ontology",
"prefix": "DPCO",
"version": "1.0"
},
"DPO": {
"description": "An ontology of commonly encountered and/or high level Drosophila phenotypes.",
"download_owl": "http://aber-owl.net/media/ontologies/DPO/33/dpo.owl",
"homepage": "http://purl.obolibrary.org/obo/fbcv",
"name": "Drosophila Phenotype Ontology",
"prefix": "DPO"
},
"DRANPTO": {
"description": "DRANPTO is developed for representing the domain knowledge specific to non-pharmacological intervention for agitation in dementia, particularly for the long-term care setting.",
"download_owl": "http://aber-owl.net/media/ontologies/DRANPTO/1/dranpto.owl",
"name": "Dementia-Related Agitation Non-Pharmacological Treatment Ontology",
"prefix": "DRANPTO",
"version": "Version 1.0"
},
"DREAMDNPTO": {
"description": "DREAMDNPTO represents the domain knowledge specific to the non-pharmacological treatment of emotional and mood disturbances (e.g., depression and anxiety in dementia) in people with dementia living in the long-term care setting.",
"download_owl": "http://aber-owl.net/media/ontologies/DREAMDNPTO/1/dreamdnpto.owl",
"name": "Dementia-Related Emotional And Mood Disturbance Non-Pharmacological Treatment Ontology",
"prefix": "DREAMDNPTO",
"version": "v1.0"
},
"DRMO": {
"name": "Dental Restorative Material Ontology",
"prefix": "DRMO"
},
"DRON": {
"description": "An ontology to support comparative effectiveness researchers studying claims data.",
"download_owl": "http://aber-owl.net/media/ontologies/DRON/25/dron.owl",
"homepage": "https://github.com/ufbmi/dron",
"name": "The Drug Ontology",
"prefix": "DRON"
},
"DRPSNPTO": {
"description": "The DRPSNPTO ontology represents the domain knowledge specific to non-pharmacological treatment of psychotic symptoms in dementia in the long-term care setting.",
"download_owl": "http://aber-owl.net/media/ontologies/DRPSNPTO/1/drpsnpto.owl",
"name": "Dementia-Related Psychotic Symptoms Non-Pharmacological Treatment Ontology",
"prefix": "DRPSNPTO",
"version": "v1.0"
},
"DS": {
"name": "Data Science",
"prefix": "DS"
},
"DSEO": {
"description": "Simple ISA hierarchical taxonomy denoting subfields of study in data science for use in educational applications.",
"download_owl": "http://aber-owl.net/media/ontologies/DSEO/2/dseo.owl",
"homepage": "http://bigdatau.org/about_erudite",
"name": "Data Science Education Ontology",
"prefix": "DSEO",
"version": "1.0"
},
"DSIP": {
"name": "Pharmacy mock data",
"prefix": "DSIP"
},
"DSIP1V": {
"description": "This is vocabularies for the DSIP Group 1 FieldLabs",
"name": "DSIP1_vocabulary",
"prefix": "DSIP1V"
},
"DSIP2324_DEMO": {
"description": "This is an ontology made for the purposes of demonstrating the process of vocabulary creation for the Data Science in Practice course. Update V0.2: Fixed Leiden University coupling to DBpedia",
"name": "DSIP2324_Demonstration",
"prefix": "DSIP2324_DEMO",
"version": "0.2"
},
"DSIP7": {
"description": "The Human Trafficking Vocabulary is an essential resource for researchers and analysts working with raw interview data gathered from refugees affected by human trafficking. It offers a standardized framework for categorizing and understanding various aspects of human trafficking incidents. The vocabulary includes terms for describing the nationality and location of human traffickers, the number of times traffickers are mentioned by independent sources, the type of observation obtained (first-hand or second-hand), and more. This vocabulary was created as part of Data Science in Practice Fieldlab-7, with guidance from Kai Smiths. It is continuously updated to reflect new insights and developments in the field of human trafficking research.",
"download_owl": "http://aber-owl.net/media/ontologies/DSIP7/1/dsip7.owl",
"name": "DSIP_FieldLab_7",
"prefix": "DSIP7"
},
"DSIP8": {
"description": "refugee datapod updated ontology after feedback",
"name": "DSIP8REFUGEE",
"prefix": "DSIP8"
},
"DSIPF7": {
"description": "The Human Trafficking Vocabulary is an essential resource for researchers and analysts working with raw interview data gathered from refugees affected by human trafficking. It offers a standardized framework for categorizing and understanding various aspects of human trafficking incidents. The vocabulary includes terms for describing the nationality and location of human traffickers, the number of times traffickers are mentioned by independent sources, the type of observation obtained (first-hand or second-hand), and more. This vocabulary was created as part of Data Science in Practice Fieldlab-7, with guidance from Kai Smiths. It is continuously updated to reflect new insights and developments in the field of human trafficking research.",
"download_owl": "http://aber-owl.net/media/ontologies/DSIPF7/3/dsipf7.owl",
"name": "DSIP FiledLab7 ",
"prefix": "DSIPF7"
},
"DSIPFL7": {
"description": "The Human Trafficking Vocabulary is an essential resource for researchers and analysts working with raw interview data gathered from refugees affected by human trafficking. It offers a standardized framework for categorizing and understanding various aspects of human trafficking incidents. The vocabulary includes terms for describing the nationality and location of human traffickers, the number of times traffickers are mentioned by independent sources, the type of observation obtained (first-hand or second-hand), and more. This vocabulary was created as part of Data Science in Practice Fieldlab-7, with guidance from Kai Smiths. It is continuously updated to reflect new insights and developments in the field of human trafficking research.",
"name": "DSIP_Fieldlab_7",
"prefix": "DSIPFL7",
"version": "latest"
},
"DSIP_FL_7": {
"description": "The Human Trafficking Vocabulary is an essential resource for researchers and analysts working with raw interview data gathered from refugees affected by human trafficking. It offers a standardized framework for categorizing and understanding various aspects of human trafficking incidents. The vocabulary includes terms for describing the nationality and location of human traffickers, the number of times traffickers are mentioned by independent sources, the type of observation obtained (first-hand or second-hand), and more. This vocabulary was created as part of Data Science in Practice Fieldlab-7, with guidance from Kai Smiths. It is continuously updated to reflect new insights and developments in the field of human trafficking research.",
"download_owl": "http://aber-owl.net/media/ontologies/DSIP_FL_7/1/dsip_fl_7.owl",
"name": "DSIP_FL_7",
"prefix": "DSIP_FL_7",
"version": "v1"
},
"DTO": {
"description": "Drug Target Ontology (DTO) is being developed at the University of Miami in the research group of Stephan Sch\u00fcrer. DTO is supported by grant U54CA189205 (Illuminating the Druggable Genome Knowledge Management Center, Tudor Oprea, PI) awarded by the NCI through the NIH Common Fund. It is a component of the Illuminating the Druggable Genome (IDG) project (https://commonfund.nih.gov/idg). The DTO project develops a novel semantic framework to formalize knowledge about drug targets with a focus on the current IDG protein families. The DTO is developed as a reference for drug targets with the longer-term goal to create a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The first version of the DTO consists of asserted class hierarchies of the four IDG protein families, GPCRs, kinases, ion channels, and nuclear hormone receptors. Protein classes are linked to tissue and disease via different levels of confidence. DTO also contains drug target development level classifications developed in the IDG project (http://targetcentral.ws/), and functional and qualitative annotations and classifications for kinase proteins, GPCR ligands and ion channels. DTO is modeled in OWL2-DL to enable further classification by inference reasoning and SPARQL queries. DTO is implemented following a modularization approach. DTO is used as the organizational framework for drug targets in the IDG PHAROS User Interface Portal (https://pharos.nih.gov) and also the Tin-X Target Importance and Novelty Explorer (http://newdrugtargets.org).",
"download_owl": "http://aber-owl.net/media/ontologies/DTO/4/dto.owl",
"homepage": "http://drugtargetontology.org/",
"name": "Drug Target Ontology",
"prefix": "DTO",
"version": "1.1"
},
"DUO": {
"description": "DUO is an ontology which represent data use conditions.",
"download_owl": "http://aber-owl.net/media/ontologies/DUO/9/duo.owl",
"homepage": "https://github.com/EBISPOT/DUO",
"name": "Data Use Ontology",
"prefix": "DUO"
},
"E-PPO": {
"description": "The Enhanced Personal Profile Ontology (e-PPO) provides personal profile of personnel that are required for software requirement engineering task selection. Properties of the ontology includes static and dynamic features. Name, gender, date of birth, etc. are static in nature and may not change. Other static properties such as educational qualification and skills acquired can be updated while others including area of specialization and profession are dynamic and can be changed. Also, areas of specializations cannot be out of the scope of one\u2019s profession, although one personnel can have multiple profession and skills, more than one profession can share things in common such as the same professional qualification may be required.",
"download_owl": "http://aber-owl.net/media/ontologies/E-PPO/1/e-ppo.owl",
"name": "Enhanced Personal Profile Ontology",
"prefix": "E-PPO"
},
"EBP": {
"description": "Clinical practice guidelines, behaviour change theories, and associated behaviour change strategies for the management of hypertension.",
"download_owl": "http://aber-owl.net/media/ontologies/EBP/2/ebp.owl",
"name": "EmpowerBP",
"prefix": "EBP",
"version": "2.5"
},
"ECAO": {
"description": "An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586).",
"download_owl": "http://aber-owl.net/media/ontologies/ECAO/3/ecao.owl",
"homepage": "https://github.com/echinoderm-ontology/ecao_ontology",
"name": "The Echinoderm Anatomy and Development Ontology",
"prefix": "ECAO"
},
"ECDO": {
"description": "This is an ontology for elderly dementia care in the Netherlands.",
"name": "Elderly Care Dementia Ontology",
"prefix": "ECDO"
},
"ECG": {
"description": "The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms.",
"download_owl": "http://aber-owl.net/media/ontologies/ECG/12/ecg.owl",
"homepage": "http://www.cvrgrid.org",
"name": "Electrocardiography Ontology",
"prefix": "ECG",
"version": "1"
},
"ECGF": {
"description": "This is a subset of the ECG Ontology, focused on two classification systems used extensively in heart diseases research.",
"download_owl": "http://aber-owl.net/media/ontologies/ECGF/1/ecgf.owl",
"homepage": "http://www.cvrgrid.org",
"name": "ECG Findings",
"prefix": "ECGF",
"version": "1"
},
"ECGT": {
"description": "This is a listing of all the terms within the ECG Ontology, to make it easier to search for a term to annotate an ECG",
"download_owl": "http://aber-owl.net/media/ontologies/ECGT/5/ecgt.owl",
"name": "ECG Terms",
"prefix": "ECGT",
"version": "1"
},
"ECM4M-MD-VOCABS": {
"description": "Collection of EarthCube M4M vocabularies for sample metadata definitions.",
"homepage": "https://github.com/go-fair-us/EarthCubeM4M",
"name": "EarthCube M4M Metadata Vocabulary",
"prefix": "ECM4M-MD-VOCABS",
"version": "0.1.2"
},
"ECO": {
"description": "An ontology for experimental and other evidence statements.",
"download_owl": "http://aber-owl.net/media/ontologies/ECO/113/eco.owl",
"homepage": "https://www.evidenceontology.org",
"name": "Evidence and Conclusion Ontology",
"prefix": "ECO"
},
"ECOCORE": {
"description": "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.",
"download_owl": "http://aber-owl.net/media/ontologies/ECOCORE/8/ecocore.owl",
"homepage": "https://github.com/EcologicalSemantics/ecocore",
"name": "An ontology of core ecological entities",
"prefix": "ECOCORE"
},
"ECOSIM": {
"description": "An ontology of variables for earth system simulation, derived from the ecosim framework.",
"download_owl": "http://aber-owl.net/media/ontologies/ECOSIM/1/ecosim.owl",
"homepage": "https://github.com/cmungall/ecosim-ontology",
"name": "ecosim ontology",
"prefix": "ECOSIM"
},
"ECP": {
"description": "Our focus in this work is to define in a formal way (ontology-based) and platform independent representative metadata and relationships of care plans. This approach has as goal to work as an umbrella over all these systems and provides some advantages regarding the management, the organization and the searching of formal care plans.",
"download_owl": "http://aber-owl.net/media/ontologies/ECP/2/ecp.owl",
"homepage": "http://iris.med.duth.gr/research/ecp/ontology",
"name": "Electronic Care Plan",
"prefix": "ECP",
"version": "0.6"
},
"ECSO": {
"description": "DataONE ontology of Carbon Flux measurements for MsTMIP and LTER Use Cases",
"download_owl": "http://aber-owl.net/media/ontologies/ECSO/51/ecso.owl",
"name": "The Ecosystem Ontology",
"prefix": "ECSO",
"version": "0.9.1"
},
"ECTO": {
"description": "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology).",
"download_owl": "http://aber-owl.net/media/ontologies/ECTO/12/ecto.owl",
"homepage": "https://github.com/EnvironmentOntology/environmental-exposure-ontology",
"name": "Environmental conditions, treatments and exposures ontology",
"prefix": "ECTO"
},
"EDAM": {
"description": "EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within bioinformatics and computational biology, including types of data and data identifiers, data formats, operations and topics. EDAM is a simply-structured ontology - essentially a set of concepts with preferred terms and synonyms, definitions, and some additional information - organised into a simple and intuitive hierarchy for convenient use by information curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries.",
"download_owl": "http://aber-owl.net/media/ontologies/EDAM/36/edam.owl",
"homepage": "http://edamontology.org",
"name": "EDAM bioinformatics operations, types of data, data formats, identifiers, and topics",
"prefix": "EDAM",
"version": "1.19"
},
"EDAM-BIOIMAGING": {
"description": "Bioimage informatics operations, types of data, data formats, and bioimaging topics EDAM-bioimaging is an extension to the EDAM ontology (edamontology.org) for bioimage analysis, bioimage informatics, and bioimaging, developed in collaboration with partners from NEUBIAS Cost Action CA15124 (neubias.org) and EuroBioImaging PP2.",
"download_owl": "http://aber-owl.net/media/ontologies/EDAM-BIOIMAGING/2/edam-bioimaging.owl",
"homepage": "http://webprotege.stanford.edu/#projects/2ce704bf-83ed-4d2e-985f-84c4841fac71/edit/Classes",
"name": "EDAM Bioimaging Ontology",
"prefix": "EDAM-BIOIMAGING",
"version": "alpha02"
},
"EDAM2": {
"download_owl": "http://aber-owl.net/media/ontologies/EDAM2/1/edam2.owl",
"name": "EDAM2",
"prefix": "EDAM2",
"version": "1"
},
"EDAMT": {
"description": "An ontology of bioinformatics, biological and biomedical topics (EDAM Topics)",
"download_owl": "http://aber-owl.net/media/ontologies/EDAMT/1/edamt.owl",
"homepage": "edamontology.org",
"name": "EDAM Topics Subset",
"prefix": "EDAMT",
"version": "1.4"
},
"EDDA": {
"description": "The EDDA Study Designs Taxonomy (v2.0) was developed by the Evidence in Documents, Discovery, and Analytics (EDDA) Group: Tanja Bekhuis (Principal Scientist); Eugene Tseytlin (Systems Developer); Ashleigh Faith (Taxonomist); Faina Linkov (Epidemiologist). The EDDA Group is a division of TCB Research & Indexing LLC. This work was made possible, in part, by the US National Library of Medicine, National Institutes of Health, grant no. R00LM010943. Foundational research is described in Bekhuis T, Demner Fushman D, Crowley RS. Comparative effectiveness research designs: an analysis of terms and coverage in Medical Subject Headings (MeSH) and Emtree. Journal of the Medical Library Association (JMLA). 2013 April;101(2):92-100. PMC3634392. Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries. A PDF of this taxonomy is available in ResearchGate DOI: 10.13140/RG.2.1.3769.2406/1. The EDDA Study Designs Taxonomy by Tanja Bekhuis and Eugene Tseytlin is licensed under a Creative Commons Attribution\u2013NonCommercial\u2013ShareAlike 4.0 International License (CC BY-NC-SA 4.0). For information about this license, see https://creativecommons.org/licenses/by-nc-sa/4.0/.",
"download_owl": "http://aber-owl.net/media/ontologies/EDDA/11/edda.owl",
"name": "EDDA Study Designs Taxonomy",
"prefix": "EDDA",
"version": "2.0"
},
"EDDA_PT": {
"description": "The EDDA Publication Types Taxonomy (v1.0) was developed by Tanja Bekhuis (Principal Scientist) and Eugene Tseytlin (Systems Developer) of the Evidence in Documents, Discovery, and Analytics (EDDA) Group. The EDDA Group is a division of TCB Research & Indexing LLC. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCIT, Emtree, and dictionaries. The EDDA Publication Types Taxonomy by Tanja Bekhuis and Eugene Tseytlin is licensed under a Creative Commons Attribution\u2013NonCommercial\u2013ShareAlike 4.0 International License (CC BY-NC-SA 4.0). For information about this license, see https://creativecommons.org/licenses/by-nc-sa/4.0/.",
"download_owl": "http://aber-owl.net/media/ontologies/EDDA_PT/1/edda_pt.owl",
"name": "EDDA Publication Types Taxonomy",
"prefix": "EDDA_PT",
"version": "1.0"
},
"EDEM-CONNECTONTO": {
"description": "The EDEM-CONNECTONTO has been created to incorporate domain knowledge about the various types of agitation observed in people with dementia (PwD), as well as the dyadic relationship existing between PwD and their informal caregivers. Furthermore, it offers a structured framework for non-pharmacological interventions, enabling caregivers to effectively manage and mitigate the bidirectional effects of agitation in PwD.",
"download_owl": "http://aber-owl.net/media/ontologies/EDEM-CONNECTONTO/1/edem-connectonto.owl",
"name": "eDEM-Connect: Ontology of Dementia-related Agitation and Relationship between Informal Caregivers and Persons with Dementia",
"prefix": "EDEM-CONNECTONTO",
"version": "Version 1.0"
},
"EDU": {
"name": "Jobs",
"prefix": "EDU"
},
"EFO": {
"description": "The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental variables in multiple resources at the EBI and Open Targets. The ontology has been developed to increase the richness of the annotations that are currently made in resources and to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology pulls together classes from reference ontologies such as disease, cell line, cell type and anatomy and adds axiomatisation as necessary to connect areas such as disease to phenotype. Contact EFO users list for information: efo-users@lists.sourceforge.net",
"download_owl": "http://aber-owl.net/media/ontologies/EFO/168/efo.owl",
"homepage": "http://www.ebi.ac.uk/efo",
"name": "Experimental Factor Ontology",
"prefix": "EFO",
"version": "2.89"
},
"EGO": {
"description": "The Epigenome Ontology (EGO) a biomedical ontology for integrative epigenome knowledge representation and data analysis.",
"download_owl": "http://aber-owl.net/media/ontologies/EGO/1/ego.owl",
"homepage": "https://github.com/EGO-ontology",
"name": "Epigenome Ontology",
"prefix": "EGO",
"version": "Arbor version; 1.0.1"
},
"EHDA": {
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once.",
"download_obo": "http://aber-owl.net/media/ontologies/EHDA/6/ehda.obo",
"homepage": "http://genex.hgu.mrc.ac.uk/",
"name": "Human Developmental Anatomy Ontology, timed version",
"prefix": "EHDA",
"version": "unknown"
},
"EHDAA": {
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release.",
"download_obo": "http://aber-owl.net/media/ontologies/EHDAA/6/ehdaa.obo",
"homepage": "http://genex.hgu.mrc.ac.uk/",
"name": "Human Developmental Anatomy Ontology, abstract version 1",
"prefix": "EHDAA",
"version": "unknown"
},
"EHDAA2": {
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the developing human.",
"download_owl": "http://aber-owl.net/media/ontologies/EHDAA2/33/ehdaa2.owl",
"homepage": "http://genex.hgu.mrc.ac.uk/",
"name": "Human developmental anatomy, abstract",
"prefix": "EHDAA2"
},
"ELD": {
"description": "This is the list of Ethiopian Diseases approved by MOH Ethiopia",
"name": "EthiopianListOfDiseases",
"prefix": "ELD",
"version": "4"
},
"ELECTRICA": {
"description": "An ontology to help describe data for ELEctronic tool for Clinicians, Trainers and Researchers In Child Abuse",
"download_owl": "http://aber-owl.net/media/ontologies/ELECTRICA/5/electrica.owl",
"homepage": "https://github.com/fatibaba/electrica",
"name": "Ontology for ELEctronic tool for Clinicians, Trainers and Researchers In Child Abuse",
"prefix": "ELECTRICA",
"version": "2024-07-06"
},
"ELIG": {
"description": "We derived a set of 1,437 eligibility features that were organized into a feature hierarchy using 80 breast cancer trials.",
"download_owl": "http://aber-owl.net/media/ontologies/ELIG/1/elig.owl",
"name": "Eligibility Feature Hierarchy",
"prefix": "ELIG",
"version": "v. 1.0"
},
"ELTER_CL": {
"description": "eLTER Controlled Lists are used in different environmental projects related to the eLTER community.",
"name": "eLTER Controlled Lists",
"prefix": "ELTER_CL",
"version": "1.1.1"
},
"EMAPA": {
"description": "An ontology for mouse anatomy covering embryonic development and postnatal stages.",
"download_owl": "http://aber-owl.net/media/ontologies/EMAPA/24/emapa.owl",
"homepage": "http://www.informatics.jax.org/expression.shtml",
"name": "Mouse Developmental Anatomy Ontology",
"prefix": "EMAPA"
},
"EMIF-AD": {
"description": "Ontology developed as part of European Medical Information Framework' s (EMIF) Alzheimer\u2019s disease (AD) project.",
"download_owl": "http://aber-owl.net/media/ontologies/EMIF-AD/3/emif-ad.owl",
"homepage": "http://www.emif.eu/emif-ad-2/",
"name": "EMIF-AD ontology",
"prefix": "EMIF-AD",
"version": "0.0.2"
},
"EMO": {
"description": "This ontology describes the components of an enzyme and its reaction mechanism including the roles that the components play in the reaction mechanism.",
"download_owl": "http://aber-owl.net/media/ontologies/EMO/1/emo.owl",
"name": "Enzyme Mechanism Ontology",
"prefix": "EMO"
},
"ENDOCRINEH": {
"description": "A hierarchy of regions in endocrine system.",
"download_owl": "http://aber-owl.net/media/ontologies/ENDOCRINEH/2/endocrineh.owl",
"name": "NeuroMorpho.Org endocrine system",
"prefix": "ENDOCRINEH",
"version": "0.6"
},
"ENEM-EC": {
"description": "This ontology map the education objects and the places where they appear. Their content is based in the brazilian exam Exame Nacional do Ensino M\u00e9dio (ENEM).",
"download_owl": "http://aber-owl.net/media/ontologies/ENEM-EC/1/enem-ec.owl",
"name": "ENEM Educational Contexts",
"prefix": "ENEM-EC",
"version": "0.1"
},
"ENM": {
"download_owl": "http://aber-owl.net/media/ontologies/ENM/17/enm.owl",
"name": "eNanoMapper",
"prefix": "ENM",
"version": "6.0"
},
"ENMT": {
"description": "The eNanoMapper ontology covers the full scope of terminology needed to support research into nanomaterial safety. It builds on multiple pre-existing external ontologies such as the NanoParticle Ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/ENMT/1/enmt.owl",
"homepage": "http://enanomapper.net/",
"name": "eNanoMapper",
"prefix": "ENMT",
"version": "6.0"
},
"ENTITY": {
"description": "Entity Membership",
"download_owl": "http://aber-owl.net/media/ontologies/ENTITY/1/entity.owl",
"name": "ISO-15926-2_2003_entityMembership",
"prefix": "ENTITY",
"version": "Created 2008-07-14. Version 1.0."
},
"ENTITYCANDIDATES": {
"description": "ISO entity candidates for oil and gas",
"download_owl": "http://aber-owl.net/media/ontologies/ENTITYCANDIDATES/1/entitycandidates.owl",
"name": "ISO-15926-2_2003_entityMembershipCandidates",
"prefix": "ENTITYCANDIDATES",
"version": "Created 2008-07-14. Version 1.0."
},
"ENVO": {
"description": "An ontology of environmental systems, components, and processes.",
"download_owl": "http://aber-owl.net/media/ontologies/ENVO/60/envo.owl",
"homepage": "http://environmentontology.org/",
"name": "Environment Ontology",
"prefix": "ENVO"
},
"ENVS_VARIABLES": {
"description": "Quantitative and qualitative variables describing environmental state",
"homepage": "https://github.com/m4m-dk/workshop-2-vocabulary",
"name": "ENVS variables",
"prefix": "ENVS_VARIABLES",
"version": "0.1.1"
},
"ENVTHES": {
"description": "EnvThes",
"name": "Thesaurus for long-term ecological research, monitoring, experiments",
"prefix": "ENVTHES",
"version": "5.0.5"
},
"EO": {
"description": "The Ethnicity Ontology (EO) has been developed by extending the Basic Formal Ontology 2 standard in order to have a common reference for ethnicity concepts for semantic integration of datasets. It attempts to utilise iterated proxy markers for ethnicity such language spoken and interpreter requirements in order to support health care research studies.",
"download_owl": "http://aber-owl.net/media/ontologies/EO/1/eo.owl",
"homepage": "www.ClinInf.eu",
"name": "Ethnicity Ontoloy",
"prefix": "EO",
"version": "1.0"
},
"EO1": {
"description": "Ontology with some information about patient's origin and disabilities",
"name": "Example Ontology",
"prefix": "EO1"
},
"EOL": {
"description": "L'ontologie EOL d\u00e9crit les conditions d'environnement des \u00e9levages d'animaux domestiques. Elle d\u00e9crit plus particuli\u00e8rement les modalit\u00e9s de l'alimentation, de l'environnement, de la structure des \u00e9levages et des syst\u00e8mes d'\u00e9levage",
"download_owl": "http://aber-owl.net/media/ontologies/EOL/1/eol.owl",
"name": "Environment Ontology for Livestock",
"prefix": "EOL"
},
"EP": {
"description": "The Cardiac Electrophysiology Ontology contains terms describing single-channel electrophysiological experiments and data obtained using voltage-clamp, current clamp and fluorescence imaging techniques applied at the cell level and multi-channel fluorescence imaging techniques applied at the cell, tissue and whole heart levels.",
"download_owl": "http://aber-owl.net/media/ontologies/EP/2/ep.owl",
"homepage": "http://www.cvrgrid.org",
"name": "Cardiac Electrophysiology Ontology",
"prefix": "EP",
"version": "1"
},
"EPIE": {
"description": "Biological entities associated with changes in the regulation of gene activity without alteration of genetic structure. Development of this terminology was funded by the National Institute of Child Health and Human Development in support of the Placental Atlas Tool (PAT) with final verification by the PAT External Scientific Panel. This terminology was developed through a combination of resources including existing biomedical ontology resources, such as the Gene Ontology and the National Cancer Institute Thesaurus, web-based content, and epigenetic literature.",
"download_owl": "http://aber-owl.net/media/ontologies/EPIE/4/epie.owl",
"name": "Epigenetic Entity",
"prefix": "EPIE",
"version": "1.3"
},
"EPILONT": {
"description": "Ontology about the epilepsy domain and epileptic seizures. Based on the diagnosis proposed by the International League Against Epilepsy (ILAE).",
"download_owl": "http://aber-owl.net/media/ontologies/EPILONT/2/epilont.owl",
"homepage": "www.epilepsiae.eu",
"name": "Epilepsy Ontology",
"prefix": "EPILONT",
"version": "V1"
},
"EPIO": {
"description": "A application driven Epilepsy Ontology with official terms from the ILAE.",
"download_owl": "http://aber-owl.net/media/ontologies/EPIO/3/epio.owl",
"homepage": "https://github.com/SCAI-BIO/EpilepsyOntology",
"name": "Epilepsy Ontology",
"prefix": "EPIO"
},
"EPIP": {
"description": "Biological processes associated with changes in the regulation of gene activity without alteration of genetic structure. Development of this terminology was funded by the National Institute of Child Health and Human Development in support of the Placental Atlas Tool (PAT) with final verification by the PAT External Scientific Panel. This terminology was developed through a combination of resources including existing biomedical ontology resources, such as the Gene Ontology and the National Cancer Institute Thesaurus, web-based content, and epigenetic literature.",
"download_owl": "http://aber-owl.net/media/ontologies/EPIP/4/epip.owl",
"name": "Epigenetic Process",
"prefix": "EPIP",
"version": "1.3"
},
"EPISEM": {
"description": "An ontology designed to capture the semiology of epilepsy including ictal, post-ictal, inter-ictal, and aura signs. For the branches entitled \"disease\", \"etiologic factor\", \"epidemiologic factor\"--see ESSO ontology on this website for origin of terms.",
"download_owl": "http://aber-owl.net/media/ontologies/EPISEM/8/episem.owl",
"name": "Epilepsy Semiology",
"prefix": "EPISEM",
"version": "5.0"
},
"EPO": {
"description": "The early pregnancy ontology contains the concepts to describe ectopic pregnancy ultrasound images, organized into several subsumption hierarchies for types of ectopic pregnancies and the signs, anatomical structures and technical elements of imaging associated with ectopic pregnancy. Version 1.1 was used for ultrasound image annotations (Dhombres et al. Developing a knowledge base to support the annotation of ultrasound images of ectopic pregnancy. J Biomed Semantics, 2017)",
"download_owl": "http://aber-owl.net/media/ontologies/EPO/1/epo.owl",
"name": "Early Pregnancy Ontology",
"prefix": "EPO",
"version": "1.1"
},
"EPSO": {
"description": "A application driven Epilepsy Ontology sith official terms from the ILAE.",
"download_owl": "http://aber-owl.net/media/ontologies/EPSO/3/epso.owl",
"name": "Epilepsy Ontology",
"prefix": "EPSO"
},
"ERO": {
"description": "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.",
"download_owl": "http://aber-owl.net/media/ontologies/ERO/15/ero.owl",
"homepage": "https://open.med.harvard.edu/wiki/display/eaglei/Ontology",
"name": "eagle-i resource ontology",
"prefix": "ERO"
},
"ESFO": {
"description": "The ESFO provides a new paradigm for organizing enzyme sequence, structure, and function information, whereby specific elements of enzyme sequence and structure are mapped to specific conserved aspects of function, thus facilitating the functional annotation of uncharacterized enzymes. The ESFO helps prevent misannotation by emphasizing annotation of enzymes only at the level of functional granularity warranted by available information.",
"download_owl": "http://aber-owl.net/media/ontologies/ESFO/1/esfo.owl",
"homepage": "http://sfld.rbvi.ucsf.edu/",
"name": "Enzyme Structure Function Ontology",
"prefix": "ESFO",
"version": "1"
},
"ESO": {
"name": "Emergency Ontology",
"prefix": "ESO"
},
"ESO_C": {
"description": "Semiology of Epilepsy",
"download_owl": "http://aber-owl.net/media/ontologies/ESO_C/1/eso_c.owl",
"name": "Epilepsy Semiology Ontology",
"prefix": "ESO_C",
"version": "1.0"
},
"ESSO": {
"description": "This ontology contains epilepsy syndromes, seizure types, and data elements associated with them.",
"download_owl": "http://aber-owl.net/media/ontologies/ESSO/5/esso.owl",
"name": "Epilepsy Syndrome Seizure Ontology",
"prefix": "ESSO",
"version": "1.03"
},
"ETANC": {
"description": "Ethiopian Antenatal care (ANC) register vocabulary",
"name": "ETHIOPIANC",
"prefix": "ETANC",
"version": "0.2"
},
"ETHANC": {
"description": "Antenatal care registry for Ethiopia",
"name": "ETHANC",
"prefix": "ETHANC",
"version": "14"
},
"ETHIOPIADISEASES": {
"name": "EthiopiaDiseasesList",
"prefix": "ETHIOPIADISEASES"
},
"ETHOPD": {
"description": "This is an Ethiopian Out Patient Department register vocabulary",
"name": "Ethiopian OPD",
"prefix": "ETHOPD",
"version": "0.3"
},
"ETH_ANC": {
"name": "ETH_ANC",
"prefix": "ETH_ANC"
},
"EUPATH": {
"description": "An ontology is developed to support Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org).",
"download_owl": "http://aber-owl.net/media/ontologies/EUPATH/20/eupath.owl",
"homepage": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology",
"name": "VEuPathDB ontology",
"prefix": "EUPATH"
},
"EVI": {
"description": "The Evidence Graph ontology extends core concepts from the W3C Provenance Ontology PROV-O and Bioschemas' Profiles to describe evidence for correctness of findings in biomedical publications. The semantic data model in EVI is expressed using OWL2 Web Ontology Language.",
"download_owl": "http://aber-owl.net/media/ontologies/EVI/7/evi.owl",
"homepage": "https://evidencegraph.github.io/EVI/",
"name": "Evidence Graph Ontology",
"prefix": "EVI",
"version": "1.1"
},
"EXACT": {
"description": "EXACT aims to explicitly define the semantics of experimental protocols in order to ensure their reproducibility, and to support computer applications that assist biologists in the preparation, maintenance, submission and sharing of experimental protocols.",
"download_owl": "http://aber-owl.net/media/ontologies/EXACT/2/exact.owl",
"homepage": "https://github.com/larisa-soldatova/EXACT",
"name": "An ontology for experimental actions",
"prefix": "EXACT",
"version": "2"
},
"EXMO": {
"description": "A core reference ontology built upon BFO about exercise medicine. This ontology contains the related terms for healthy people, people with chronic conditions and people living with diability to exercise.",
"download_owl": "http://aber-owl.net/media/ontologies/EXMO/3/exmo.owl",
"homepage": "https://github.com/DarkKnight0-0/exmo",
"name": "Exercise Medicine Ontology",
"prefix": "EXMO",
"version": "1.1"
},
"EXO": {
"description": "Vocabularies for describing exposure data to inform understanding of environmental health.",
"download_owl": "http://aber-owl.net/media/ontologies/EXO/15/exo.owl",
"homepage": "https://github.com/CTDbase/exposure-ontology",
"name": "Exposure ontology",
"prefix": "EXO"
},
"EXON": {
"description": "Experiment focused in the compatibility with proteg'e software to create and upload ontologies on Bioportal",
"download_owl": "http://aber-owl.net/media/ontologies/EXON/1/exon.owl",
"name": "Experimental Ontology",
"prefix": "EXON"
},
"EXTRACT": {
"description": "Controlled vocabularies such as taxonomies allow an accurate and controlled approach in describing datasets. One of such controlled vocabulary is Wind Energy Taxonomy of External Conditions. This taxonomy is the result of EERA JP WIND IRPWind Open Data initiative that took place in 2017 in which wind energy experts generated the first version of the taxonomy as an input for defining and structuring wind energy metadata.",
"homepage": "https://github.com/DTUWindEnergy/EXTRACT-taxonomy",
"name": "EXTeRnAl Conditions Taxonomy (EXTRACT)",
"prefix": "EXTRACT",
"version": "v0.1.0"
},
"FALDO": {
"description": "FALDO is the Feature Annotation Location Description Ontology. It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources. The aim of this ontology is to describe the position of a sequence region or a feature. It does not aim to describe features or regions itself, but instead depends on resources such as the Sequence Ontology or the UniProt core ontolgy.",
"download_owl": "http://aber-owl.net/media/ontologies/FALDO/1/faldo.owl",
"homepage": "http://biohackathon.org/resource/faldo",
"name": "Feature Annotation Location Description Ontology ",
"prefix": "FALDO",
"version": "Created at the Biohackathon 2012 and 2013"
},
"FALL": {
"description": "fall detection scenario",
"download_owl": "http://aber-owl.net/media/ontologies/FALL/1/fall.owl",
"name": "MyOntoServiceFull_FallDetection",
"prefix": "FALL",
"version": "1"
},
"FALLS": {
"description": "This ontology is about a falls prevention intervention record.",
"download_owl": "http://aber-owl.net/media/ontologies/FALLS/1/falls.owl",
"name": "falls prevention ",
"prefix": "FALLS",
"version": "0.1"
},
"FAO": {
"description": "A structured controlled vocabulary for the anatomy of fungi.",
"download_owl": "http://aber-owl.net/media/ontologies/FAO/28/fao.owl",
"homepage": "https://github.com/obophenotype/fungal-anatomy-ontology/",
"name": "Fungal gross anatomy",
"prefix": "FAO"
},
"FAST-CHRONO": {
"description": "FAST is an enumerative, faceted subject heading schema derived from the Library of Congress Subject Headings (LCSH). The purpose of adapting the LCSH with a simplified syntax to create FAST is to retain the very rich vocabulary of LCSH while making the schema easier to understand, control, apply, and use. This facet includes chronological terms derived from LCSH.",
"name": "FAST (Faceted Access of Subject Terminology) Chronological Facet",
"prefix": "FAST-CHRONO"
},
"FAST-EVENT": {
"description": "FAST is an enumerative, faceted subject heading schema derived from the Library of Congress Subject Headings (LCSH). The purpose of adapting the LCSH with a simplified syntax to create FAST is to retain the very rich vocabulary of LCSH while making the schema easier to understand, control, apply, and use. The schema maintains upward compatibility with LCSH, and any valid set of LC subject headings can be converted to FAST headings. This is the Event facet.",
"download_owl": "http://aber-owl.net/media/ontologies/FAST-EVENT/1/fast-event.owl",
"homepage": "http://www.oclc.org/research/themes/data-science/fast/download.html",
"name": "FAST (Faceted Application of Subject Terminology) Event",
"prefix": "FAST-EVENT"
},
"FAST-EVENT-SKOS": {
"description": "This is a test of submitting FAST-EVENT with Format dropdown set to SKOS (instead of OWL)",
"name": "FAST (Faceted Application of Subject Terminology) Event Facet",
"prefix": "FAST-EVENT-SKOS"
},
"FAST-FORMGENRE": {
"description": "FAST is an enumerative, faceted subject heading schema derived from the Library of Congress Subject Headings (LCSH). The purpose of adapting the LCSH with a simplified syntax to create FAST is to retain the very rich vocabulary of LCSH while making the schema easier to understand, control, apply, and use.",
"name": "FAST (Faceted Application of Subject Terminology) FormGenre facet",
"prefix": "FAST-FORMGENRE"
},
"FAST-GENREFORM": {
"description": "FAST is an enumerative, faceted subject heading schema derived from the Library of Congress Subject Headings (LCSH).",
"download_owl": "http://aber-owl.net/media/ontologies/FAST-GENREFORM/1/fast-genreform.owl",
"homepage": "http://www.oclc.org/research/themes/data-science/fast/download.html",
"name": "FAST (Faceted Access of Subject Terminology) GenreForm",
"prefix": "FAST-GENREFORM"
},
"FAST-TITLE": {
"description": "FAST (Faceted Application of Subject Terminology) is an enumerative, faceted subject heading schema derived from the Library of Congress Subject Headings (LCSH). The purpose of adapting the LCSH with a simplified syntax to create FAST is to retain the very rich vocabulary of LCSH while making the schema easier to understand, control, apply, and use.",
"homepage": "http://www.oclc.org/research/themes/data-science/fast/download.html",
"name": "FAST (Faceted Application of Subject Terminology) Title Facet",
"prefix": "FAST-TITLE"
},
"FAST-TOPICAL": {
"description": "AST is an enumerative, faceted subject heading schema derived from the Library of Congress Subject Headings (LCSH). The purpose of adapting the LCSH with a simplified syntax to create FAST is to retain the very rich vocabulary of LCSH while making the schema easier to understand, control, apply, and use.",
"name": "FAST (Faceted Application of Subject Terminology) Topical Facet",
"prefix": "FAST-TOPICAL"
},
"FASTO": {
"description": "FHIR And SSN based Type 1 diabetes Ontology (FASTO) is an OWL 2 ontology for real time management of insulin for diabetes patients especially type 1 diabetics. The ontology is based on BFO as the top-level ontology, SSN sensor ontology, and HL7 FHIR standard. This ontology can support the development of mobile health applications. It supports the interoperability between clinical decision support systems on a cloud environment, distributed electronic health records, mobile devices, and wireless body area networks.",
"download_owl": "http://aber-owl.net/media/ontologies/FASTO/2/fasto.owl",
"name": "HL7 FHIR and SSN ontology based Type 1 Diabetes Mellitus Ontology",
"prefix": "FASTO",
"version": "2015-11-20"
},
"FB-BT": {
"description": "A structured controlled vocabulary of the anatomy of Drosophila melanogaster.",
"download_obo": "http://aber-owl.net/media/ontologies/FB-BT/40/fb-bt.obo",
"homepage": "http://sourceforge.net/p/fbbtdv/wiki/Home/",
"name": "Drosophila Gross Anatomy Ontology",
"prefix": "FB-BT",
"version": "2017-09-06"
},
"FB-CV": {
"description": "A structured controlled vocabulary used for various aspects of annotation by FlyBase.
This ontology is maintained by FlyBase for various aspects of annotation not covered, or not yet covered, by other OBO ontologies. If and when community ontologies are available for the domains here covered FlyBase will use them. This ontology includes the Drosophila phenotype ontology (DPO), provided here together with FBcv for legacy purposes.",
"download_owl": "http://aber-owl.net/media/ontologies/FB-CV/21/fb-cv.owl",
"homepage": "http://sourceforge.net/p/fbcv/wiki/Home/",
"name": "FlyBase Controlled Vocabulary",
"prefix": "FB-CV",
"version": "2014-09-23"
},
"FB-DV": {
"description": "A structured controlled vocabulary of the development of Drosophila melanogaster.",
"download_obo": "http://aber-owl.net/media/ontologies/FB-DV/19/fb-dv.obo",
"homepage": "http://sourceforge.net/p/fbbtdv/wiki/Home/",
"name": "Drosophila Development Ontology",
"prefix": "FB-DV",
"version": "2016-10-14"
},
"FB-SP": {
"description": "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.",
"download_obo": "http://aber-owl.net/media/ontologies/FB-SP/7/fb-sp.obo",
"homepage": "http://www.flybase.org/",
"name": "Fly Taxonomy",
"prefix": "FB-SP",
"version": "unknown"
},
"FBBI": {
"description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.",
"download_owl": "http://aber-owl.net/media/ontologies/FBBI/7/fbbi.owl",
"homepage": "http://cellimagelibrary.org/",
"name": "Biological Imaging Methods Ontology",
"prefix": "FBBI"
},
"FBBT": {
"description": "An ontology representing the gross anatomy of Drosophila melanogaster.",
"download_owl": "http://aber-owl.net/media/ontologies/FBBT/41/fbbt.owl",
"homepage": "http://purl.obolibrary.org/obo/fbbt",
"name": "Drosophila gross anatomy",
"prefix": "FBBT"
},
"FBCV": {
"description": "A structured controlled vocabulary used for various aspects of annotation by FlyBase.",
"download_owl": "http://aber-owl.net/media/ontologies/FBCV/34/fbcv.owl",
"homepage": "http://purl.obolibrary.org/obo/fbcv",
"name": "FlyBase Controlled Vocabulary",
"prefix": "FBCV"
},
"FBDV": {
"description": "A structured controlled vocabulary of the development of Drosophila melanogaster.",
"download_owl": "http://aber-owl.net/media/ontologies/FBDV/37/fbdv.owl",
"homepage": "http://purl.obolibrary.org/obo/fbdv",
"name": "Drosophila development",
"prefix": "FBDV"
},
"FBbi": {
"description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.",
"download_obo": "http://aber-owl.net/media/ontologies/FBbi/14/fbbi.obo",
"homepage": "http://cellimagelibrary.org/",
"name": "Biological Imaging Methods Ontology",
"prefix": "FBbi",
"version": "unknown"
},
"FCC1": {
"description": "Fernald Community Cohort meta data",
"download_owl": "http://aber-owl.net/media/ontologies/FCC1/1/fcc1.owl",
"homepage": "http://www.semanticweb.org/diwaleva/ontologies/2019/9/fcc-ontology",
"name": "Fernald Community Cohort N",
"prefix": "FCC1",
"version": "1.0"
},
"FDC-GDMT": {
"description": "Controlled terms and semantic properties used in the FAIR Data Collective's Generic Dataset Metadata Template.",
"homepage": "https://github.com/fair-data-collective/generic-dataset-metadata-template",
"name": "Ontology for Generic Dataset Metadata Template",
"prefix": "FDC-GDMT",
"version": "v0.3.7"
},
"FDSAJFAHSJK": {
"description": "dasf",
"download_owl": "http://aber-owl.net/media/ontologies/FDSAJFAHSJK/1/fdsajfahsjk.owl",
"name": "OWL_XML_Tool5",
"prefix": "FDSAJFAHSJK"
},
"FDT-O": {
"description": "The FAIR Data Train Ontology provides the definitions of concepts and relations used in the FAIR Data Train environment.",
"download_owl": "http://aber-owl.net/media/ontologies/FDT-O/9/fdt-o.owl",
"name": "FAIR Data Train Ontology",
"prefix": "FDT-O",
"version": "- Refactored FHIR API and FHIR Train as sub-classes of REST API and REST Train, respectively."
},
"FENICS": {
"description": "The Functional Epilepsy Nomenclature for Ion Channels (FENICS) is allowing the consistent evaluation of electrophysiology experiments on Ion Channels in the context of neurological disorders, in particular epilepsy.",
"download_owl": "http://aber-owl.net/media/ontologies/FENICS/9/fenics.owl",
"name": "Functional Electrophysiology Nomenclature for Ion Channels",
"prefix": "FENICS",
"version": "0.0.5"
},
"FG": {
"description": "The FAIR Genomes semantic metadata schema to power reuse of NGS data in research and healthcare.",
"download_owl": "http://aber-owl.net/media/ontologies/FG/4/fg.owl",
"homepage": "https://w3id.org/fair-genomes",
"name": "FAIR Genomes",
"prefix": "FG",
"version": "1.2-Minor"
},
"FGNHNS": {
"description": "Ontology of food groups of the National Health and Nutrition Examination Survey issued by the Ministry of Health, Labour and Welfare. Foods are divided into major, medium, and minor categories, and the English and Japanese names of foods belonging to the minor categories are noted.",
"download_owl": "http://aber-owl.net/media/ontologies/FGNHNS/18/fgnhns.owl",
"name": "FoodGroupNHNS",
"prefix": "FGNHNS",
"version": "0.169"
},
"FHHO": {
"description": "The FHHO facilitates representing the family health histories of persons related by biological and/or social family relationships (e.g. step, adoptive) who share genetic, behavioral, and/or environmental risk factors for disease. SWRL rules are included to compute 3 generations of biological relationships based on parentage and family history findings based on personal health findings.",
"download_owl": "http://aber-owl.net/media/ontologies/FHHO/1/fhho.owl",
"homepage": "http://healthsystems.engr.wisc.edu/Alumni/JanePeace.html",
"name": "Family Health History Ontology",
"prefix": "FHHO",
"version": "1"
},
"FIDEO": {
"description": "Food-Drug interactions automatically extracted from scientific literature",
"download_owl": "http://aber-owl.net/media/ontologies/FIDEO/9/fideo.owl",
"homepage": "https://gitub.u-bordeaux.fr/erias/fideo",
"name": "Food Interactions with Drugs Evidence Ontology",
"prefix": "FIDEO"
},
"FIRE": {
"description": "The ontology of Fire was created in order to represent the set of concepts about the fire occurring in natural vegetation, its characteristics, causes and effects, with focus on Cerrado vegetation domain. The fire plays a determinant role on the structure and composition of Cerrado physiognomies.",
"download_owl": "http://aber-owl.net/media/ontologies/FIRE/7/fire.owl",
"name": "Fire Ontology",
"prefix": "FIRE",
"version": "0.8"
},
"FISH ANAT": {
"download_obo": "http://aber-owl.net/media/ontologies/FISH ANAT/1/fish anat.obo",
"homepage": "http://purl.obolibrary.org/obo/zfa.obo",
"name": "zebrafish anatomy",
"prefix": "FISH ANAT",
"version": "1"
},
"FISH-AST": {
"description": "Terminology used for recording the techniques, recovery methods and materials associated with archaeological sciences. Maintained by Historic England on behalf of the FISH Terminology Working Group.",
"homepage": "http://heritagedata.org/live/schemes/560.html",
"name": "FISH Archaeological Sciences Thesaurus",
"prefix": "FISH-AST"
},
"FISHO": {
"description": "This Fish Ontology is an ontology created as how the author views the fish structure following the book \"The Diversity of Fishes: Biology, Evolution and Ecology\" as the main reference, which covers one part of view on ichthyology, with an emphasis on diversity and adaptation. This ontology is created with the mindset of categorizing fish automatically based on the attributes and terms mined from the fish specimen. Most of the basic organization from this ontology follows Nelson's research due to its synthetic and broad approach, while recognizing that Nelson's conclusions are one of many alternative interpretations of the literature, which is mostly agreed by our main references, and many fish and fisheries researchers. Most of the classification used in this ontology is in no means completed and just following the recent classification provided by the books For now our work focused more on two group of fish which is early jawless fish, and advanced jawed fishes. The classification from both of this group are structured following the reference.",
"download_owl": "http://aber-owl.net/media/ontologies/FISHO/1/fisho.owl",
"homepage": "https://mohdnajib1985.github.io/FOWebPage/",
"name": "Fish Ontology",
"prefix": "FISHO",
"version": "Version 1.0.3 (Possible addition)-Considering to add more fish study related terms in the ontology such as fish immune sytem, and Fish Locomotion and Feeding Behavior.-Also focused on completing other classification of fish, and adding more relationships between the classes.Version 1.0.2-Added a lot of annotations and metadata for fish terms, and added several more subclasses for the ontology. Version 1.0.1-Change the structure and the hierarchy of a lot of classes to follow the main references. Several classes are deleted and marked as \"deprecated\" or \"In Review\" in case they might be useful later.Version 1.0.0-The first version of the fish ontology is created."
},
"FIT_BIT": {
"description": "This contains vocabulary information for Fitbit data for a single source user from the online API",
"name": "Fitbit Vocabularies ",
"prefix": "FIT_BIT"
},
"FIX": {
"description": "An ontology of physico-chemical methods and properties.",
"download_owl": "http://aber-owl.net/media/ontologies/FIX/119/fix.owl",
"name": "Physico-chemical methods and properties",
"prefix": "FIX"
},
"FLDLB3": {
"description": "This is the final ontology of fieldlab 3 check 3",
"homepage": "https://github.com/Rens-byte/Fieldlab3-2/tree/main",
"name": "FIELDLAB3_2023_2",
"prefix": "FLDLB3",
"version": "3"
},
"FLOPO": {
"description": "Traits and phenotypes of flowering plants occurring in digitized Floras",
"download_owl": "http://aber-owl.net/media/ontologies/FLOPO/10/flopo.owl",
"homepage": "https://github.com/flora-phenotype-ontology/flopoontology",
"name": "Flora Phenotype Ontology",
"prefix": "FLOPO"
},
"FLU": {
"description": "Starting in the fall of 2007, a collaborative group of influenza researchers have established an influenza ontology. The influenza ontology is an application ontology. Consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS)",
"download_owl": "http://aber-owl.net/media/ontologies/FLU/27/flu.owl",
"homepage": "http://purl.obolibrary.org/obo/flu/",
"name": "Influenza Ontology",
"prefix": "FLU",
"version": "0.9.0"
},
"FLYGLYCODB": {
"description": "Ontology to describe glycogenes of Drosophila. Includes mutants, activity, references and links to FlyBase and UniProt.",
"download_owl": "http://aber-owl.net/media/ontologies/FLYGLYCODB/2/flyglycodb.owl",
"homepage": "http://fly.glycoinfo.org",
"name": "FlyGlycoDB",
"prefix": "FLYGLYCODB",
"version": "1.0.0"
},
"FMA": {
"description": "This is currently a slimmed down version of FMA",
"download_owl": "http://aber-owl.net/media/ontologies/FMA/139/fma.owl",
"homepage": "http://si.washington.edu/projects/fma",
"name": "Foundational Model of Anatomy Ontology (subset)",
"prefix": "FMA"
},
"FMA-SUBSET": {
"description": "Obo format translation of the FMA, omitting all relationships other than is_a, part_of and has_part. Future versions of fma_obo will include more relationships",
"download_obo": "http://aber-owl.net/media/ontologies/FMA-SUBSET/1/fma-subset.obo",
"name": "Foundational Model of Anatomy (subset)",
"prefix": "FMA-SUBSET",
"version": "2"
},
"FMPM": {
"description": "Food matrix ontology for predictive microbiology.",
"download_owl": "http://aber-owl.net/media/ontologies/FMPM/5/fmpm.owl",
"name": "Food Matrix for Predictive Microbiology",
"prefix": "FMPM",
"version": "0.9.2"
},
"FNS-H": {
"description": "Application ontology for the FNS-Cloud project ontology PURL: https://purl.org/fns-h",
"download_owl": "http://aber-owl.net/media/ontologies/FNS-H/2/fns-h.owl",
"homepage": "https://github.com/panovp/FNS-Harmony",
"name": "FNS-Harmony",
"prefix": "FNS-H",
"version": "1.3"
},
"FO": {
"description": "Fern Ontology (FO) is a controlled and structured vocabulary of fern specific anatomy and lifecycle.",
"download_owl": "http://aber-owl.net/media/ontologies/FO/6/fo.owl",
"name": "Fern Ontology",
"prefix": "FO",
"version": "0.05"
},
"FOAF": {
"description": "Friend of a Friend Vocabulary",
"download_owl": "http://aber-owl.net/media/ontologies/FOAF/1/foaf.owl",
"name": "Friend of a Friend Vocabulary",
"prefix": "FOAF",
"version": "0.99"
},
"FOBI": {
"description": "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data",
"download_owl": "http://aber-owl.net/media/ontologies/FOBI/7/fobi.owl",
"homepage": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology",
"name": "Food-Biomarker Ontology",
"prefix": "FOBI"
},
"FOO": {
"description": "The Forest Observatory Ontology (FOO) ( is an ontology for describing wildlife data generated by sensors. FOO's scope evolves around the Internet of Things (IoT) and wildlife habitats. To illustrate our datasets of interest, we modelled the concept to represent \"sensors observing animals and land\". These sensors generate observations. For example, the animal GPS collar tracks an elephant and records its geo-location observations for different and equally spaced time intervals and temperature every specified time interval. We adopted classes and properties from SOSA and BBC wildlife ontologies to model the domain coverage.",
"download_owl": "http://aber-owl.net/media/ontologies/FOO/21/foo.owl",
"homepage": "ontology.forest-observatory.org",
"name": "Forest Observatory Ontology",
"prefix": "FOO",
"version": "BBC Wildlife Ontology Reused 26 June 2024"
},
"FOODON": {
"description": "A broadly scoped ontology representing entities which bear a \u201cfood role\u201d. It encompasses materials in natural ecosystems and agriculture that are consumed by humans and domesticated animals. This includes any generic (unbranded) raw or processed food material found in processing plants, markets, stores or food distribution points. FoodOn also imports nutritional component and dietary pattern terms from other OBO Foundry ontologies to support interoperability in diet and nutrition research",
"download_owl": "http://aber-owl.net/media/ontologies/FOODON/86/foodon.owl",
"homepage": "https://foodon.org/",
"name": "Food Ontology",
"prefix": "FOODON"
},
"FOOD_ONT": {
"description": "We built food ontology primarily to support comparative effectiveness researchers studying food components or ingredients data. Food Ontology Knowledgebase (FOKB) is developed in English and Turkish that contains details of food ingredients such as their codes (e-codex or codex numbers) and also side effects of them such as allergy. Initially, the first stage of the research project was funded in 2013 by TUBITAK (The Scientific and Technological Research Council of Turkey- http://www.tubitak.gov.tr/en) \u2013 1512 Progressive Entrepreneurship Support Program (Project No: 2120357, \u201cSemantic-based Personal Safe Food Consumption System for Allergic Individuals via Smart Devices\u201d) by the Semantica Trd. Ltd. Co (http://www.semantica.com.tr/en). The initial proposal of the first stage project is presented in Hindawi Publishing Corporation http://www.hindawi.com- The Scientific World Journal with the title \u201cFoodWiki: Ontology-driven Mobile Safe Food Consumption System\u201d. After that, another project as an extension of the first stage project was funded again by TUBITAK toward the end of 2014. It is titled \u201cArtificial Intelligence-based Mobile System for Conscious Food Consumption through Ontology\u201d and recorded with the project number 3140417 in cooperation with Semantica Internet and Software Services Trd. Ltd. Co. and Ac\u0131badem Hospitals Group[1] in consultation with Asst. Prof. Dr. Duygu \u00c7elik. Copyrights of the Food Ontology Knowledgebase (FOKB) and FoodWiki system are reserved by Semantica Trd. Ltd. Co and Ac\u0131badem Hospitals Group (http://www.acibademinternational.com/)",
"download_owl": "http://aber-owl.net/media/ontologies/FOOD_ONT/2/food_ont.owl",
"name": "FOOD_ONTOLOGY_OWL",
"prefix": "FOOD_ONT",
"version": "v1.0"
},
"FOOD_ONTOLOGY": {
"description": "We built food ontology primarily to support comparative effectiveness researchers studying food components or ingredients data. Food Ontology Knowledgebase (FOKB) is developed in English and Turkish that contains details of food ingredients such as their codes (e-codex or codex numbers) and also side effects of them such as allergy. Initially, the first stage of the research project was funded in 2013 by TUBITAK (The Scientific and Technological Research Council of Turkey- http://www.tubitak.gov.tr/en) \u2013 1512 Progressive Entrepreneurship Support Program (Project No: 2120357, \u201cSemantic-based Personal Safe Food Consumption System for Allergic Individuals via Smart Devices\u201d) by the Semantica Trd. Ltd. Co (http://www.semantica.com.tr/en). The initial proposal of the first stage project is presented in Hindawi Publishing Corporation http://www.hindawi.com- The Scientific World Journal with the title \u201cFoodWiki: Ontology-driven Mobile Safe Food Consumption System\u201d. After that, another project as an extension of the first stage project was funded again by TUBITAK toward the end of 2014. It is titled \u201cArtificial Intelligence-based Mobile System for Conscious Food Consumption through Ontology\u201d and recorded with the project number 3140417 in cooperation with Semantica Internet and Software Services Trd. Ltd. Co. and Ac\u0131badem Hospitals Group in consultation with Asst. Prof. Dr. Duygu \u00c7elik. Copyrights of the Food Ontology Knowledgebase (FOKB) and FoodWiki system are reserved by Semantica Trd. Ltd. Co and Ac\u0131badem Hospitals Group (http://www.acibademinternational.com/).",
"download_owl": "http://aber-owl.net/media/ontologies/FOOD_ONTOLOGY/1/food_ontology.owl",
"name": "Food Ontology",
"prefix": "FOOD_ONTOLOGY",
"version": "v1.0"
},
"FOUR-M_VOCABS": {
"description": "Vocabulary for the 4M nursing framework",
"name": "AGE-FRIENDLY 4M VOCABULARY",
"prefix": "FOUR-M_VOCABS",
"version": "1"
},
"FOVT": {
"description": "FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA).",
"download_owl": "http://aber-owl.net/media/ontologies/FOVT/7/fovt.owl",
"homepage": "https://github.com/futres/fovt",
"name": "FuTRES Ontology of Vertebrate Traits",
"prefix": "FOVT"
},
"FPLX": {
"name": "FamPlex",
"prefix": "FPLX"
},
"FRAPO": {
"name": "Funding, Research Administration and Projects Ontology",
"prefix": "FRAPO"
},
"FRMO": {
"description": "We have developed an ontology representing major fall risk management entities to support approaches to text mining, data descriptions and linkage in the context of fall risk management. This ontology contains concepts related to fall risk factors, fall risk interventions, and fall consequences.",
"download_owl": "http://aber-owl.net/media/ontologies/FRMO/18/frmo.owl",
"name": "Fall Risk Management Ontology ",
"prefix": "FRMO",
"version": "09.10"
},
"FTC": {
"description": "The Functional Therapeutic Chemical Classification System (FTC) defines over 20'000 mechanisms and modes of action for approuved drugs. The resource abstracts away from the traditional chemical structure-based approach and focuses solely on the mode of action of drugs. The classification sorts therapeutic agents based on their function in the human body.",
"download_owl": "http://aber-owl.net/media/ontologies/FTC/1/ftc.owl",
"homepage": "https://www.ebi.ac.uk/chembl/ftc",
"name": "Functional Therapeutic Chemical Classification System",
"prefix": "FTC",
"version": "1"
},
"FUNCTIONALH": {
"description": "A hierarchy of neuron types based on functional role.",
"download_owl": "http://aber-owl.net/media/ontologies/FUNCTIONALH/3/functionalh.owl",
"name": "NeuroMorpho.Org cell types function",
"prefix": "FUNCTIONALH",
"version": "2.0"
},
"FYPO": {
"description": "FYPO is a formal ontology of phenotypes observed in fission yeast.",
"download_owl": "http://aber-owl.net/media/ontologies/FYPO/464/fypo.owl",
"homepage": "https://github.com/pombase/fypo",
"name": "Fission Yeast Phenotype Ontology",
"prefix": "FYPO"
},
"FaBiO": {
"description": "This file is imported by the vivo-core-public-1.5.owl file. It contains terms relating to documents from the http://purl.org/spar/fabio/ namespace that are included in the VIVO ontology. FaBiO is a FRBR-aligned Bibliographic Ontology that is part of the Semantic Publishing and Referencing (SPAR) suite of ontologies.",
"download_owl": "http://aber-owl.net/media/ontologies/FaBiO/1/fabio.owl",
"homepage": "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology",
"name": "FaBiO (bibliographic)",
"prefix": "FaBiO",
"version": "1.5"
},
"G-O": {
"description": "The Ontology defines the Geriatrics system with classes. It also has object properties and data properties which are used to create a Decision support system for the elderly.",
"download_owl": "http://aber-owl.net/media/ontologies/G-O/1/g-o.owl",
"homepage": "http://healthcareelderly.me/GeriatricsWebApp/web/ontoBrowser.html",
"name": "Geriatrics Ontology",
"prefix": "G-O",
"version": "1.0"
},
"G-PROV": {
"description": "The ontology provides the vocabulary for enabling provenance in clinical decision support systems.",
"download_owl": "http://aber-owl.net/media/ontologies/G-PROV/1/g-prov.owl",
"homepage": "https://tetherless-world.github.io/GProv/",
"name": "Guideline Provenance",
"prefix": "G-PROV",
"version": "1"
},
"G4-DSIP": {
"description": "Group 4 Data Science in Practice",
"name": "Group 4-Data Science in Practice",
"prefix": "G4-DSIP",
"version": "1.0.0"
},
"GALEN": {
"description": "A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.",
"download_owl": "http://aber-owl.net/media/ontologies/GALEN/1/galen.owl",
"homepage": "http://www.co-ode.org/galen/",
"name": "Galen Ontology",
"prefix": "GALEN",
"version": "1.1"
},
"GALLONT": {
"description": "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls.",
"download_owl": "http://aber-owl.net/media/ontologies/GALLONT/5/gallont.owl",
"homepage": "https://adeans.github.io/gallont/",
"name": "Plant Gall Ontology",
"prefix": "GALLONT"
},
"GAMUTS": {
"description": "In radiology, a \"gamut\" is the set of conditions that can cause a specified imaging finding. The Radiology Gamuts Ontology (RGO) links more than 16,000 diseases and imaging findings. The causal relation (may_cause; inverse, may_be_caused_by) connects findings and possible causes. This work is made available under provisions of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) license.",
"download_owl": "http://aber-owl.net/media/ontologies/GAMUTS/25/gamuts.owl",
"homepage": "https://www.gamuts.net/",
"name": "Radiology Gamuts Ontology",
"prefix": "GAMUTS",
"version": "2.0"
},
"GANGLIONH": {
"description": "A hierarchy of Ganglion cell types based on Retinal function.",
"download_owl": "http://aber-owl.net/media/ontologies/GANGLIONH/2/ganglionh.owl",
"name": "NeuroMorpho.Org Ganglion cell type",
"prefix": "GANGLIONH",
"version": "2.0"
},
"GAZ": {
"description": "Gazetteer",
"download_obo": "http://aber-owl.net/media/ontologies/GAZ/14/gaz.obo",
"homepage": "http://gensc.org/gc_wiki/index.php/GAZ_Project",
"name": "Gazetteer",
"prefix": "GAZ",
"version": "$Revision: 1.512 $"
},
"GB": {
"description": "GlycanBind is an ontology for representing glycan and pathogen binding interaction data in RDF. Many of the terms are based on the data originally contained in the SugarBind database.",
"download_owl": "http://aber-owl.net/media/ontologies/GB/3/gb.owl",
"name": "GlycanBind",
"prefix": "GB",
"version": "1.1.1"
},
"GBM": {
"description": "Ontology of Glioblastoma",
"download_owl": "http://aber-owl.net/media/ontologies/GBM/1/gbm.owl",
"name": "Glioblastoma",
"prefix": "GBM"
},
"GBOL": {
"description": "Genome Biology Ontology Language (GBOL)",
"download_owl": "http://aber-owl.net/media/ontologies/GBOL/1/gbol.owl",
"homepage": "http://gbol.life",
"name": "GBOL",
"prefix": "GBOL",
"version": "1"
},
"GCBO": {
"description": "An initial version of the Global Code Book Ontology",
"download_owl": "http://aber-owl.net/media/ontologies/GCBO/3/gcbo.owl",
"name": "Global Code Book Ontology",
"prefix": "GCBO",
"version": "2024-05-01"
},
"GCO": {
"description": "The Genome Component Ontology is intended to define the abstract division of the total genetic information of an organism by its physical separation into different components, thereby providing a high level reference point to which more specific descriptions of the characteristics of these components can be linked.",
"download_owl": "http://aber-owl.net/media/ontologies/GCO/3/gco.owl",
"name": "Genome Component Ontology",
"prefix": "GCO",
"version": "0.2"
},
"GDCO": {
"description": "The Data Collection Ontology (DCO) is an ontology designed for data collection providing classes and relations on top of the Basic Formal Ontology (BFO) to facilitate data collection processes, subjects, and data anaylsis through the use of classifiers. DCO is based on the notion of reasoning to validate incoming data through their definitions based on classifiers.",
"download_owl": "http://aber-owl.net/media/ontologies/GDCO/1/gdco.owl",
"name": "Data Collection Ontology",
"prefix": "GDCO",
"version": "1.0"
},
"GDMT": {
"description": "An initial version of the Generic Dataset Metadata Template vocabulary",
"homepage": "https://github.com/bmir-radx/gdmt",
"name": "Generic Dataset Metadata Template Vocabulary",
"prefix": "GDMT",
"version": "1.0.0-alpha"
},
"GDPR": {
"download_owl": "http://aber-owl.net/media/ontologies/GDPR/1/gdpr.owl",
"name": "Data Protection",
"prefix": "GDPR",
"version": "1"
},
"GECCO": {
"name": "COVID-19 Common Datamodel",
"prefix": "GECCO"
},
"GECKO": {
"description": "An ontology to represent genomics cohort attributes",
"download_owl": "http://aber-owl.net/media/ontologies/GECKO/10/gecko.owl",
"homepage": "https://github.com/IHCC-cohorts/GECKO",
"name": "Genomics Cohorts Knowledge Ontology",
"prefix": "GECKO"
},
"GENDER": {
"description": "This vocabulary makes up the different gender identities - Female, Male and Other.",
"name": "Gender Identity",
"prefix": "GENDER"
},
"GENE-CDS": {
"description": "The Genomic CDS ontology aims to unify several functionalities in a single resource, being: * A knowledge base for clinical pharmacogenomics/pharmacogenetics that can be used for question-answering (e.g., which SNPs are associated with this drug?) * A rule base for clinical decision support (e.g., inferring that a patient with a specific set of SNPs requires a lowered dose of warfarin and generating a CDS message that can be viewed by clinicians) * A tool for checking data consistency (e.g., highlighting which allele definitions in PharmGKB are overlapping, or which clinical decision support rules are matching the same group of patients)",
"download_owl": "http://aber-owl.net/media/ontologies/GENE-CDS/1/gene-cds.owl",
"homepage": "http://samwald.info",
"name": "Genomic Clinical Decision Support Ontology",
"prefix": "GENE-CDS",
"version": "0.8.0"
},
"GENEPIO": {
"description": "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.",
"download_owl": "http://aber-owl.net/media/ontologies/GENEPIO/24/genepio.owl",
"homepage": "http://genepio.org/",
"name": "Genomic Epidemiology Ontology",
"prefix": "GENEPIO"
},
"GENEVIEVE": {
"name": "Charlotte",
"prefix": "GENEVIEVE"
},
"GENO": {
"description": "An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases.",
"download_owl": "http://aber-owl.net/media/ontologies/GENO/28/geno.owl",
"homepage": "https://github.com/monarch-initiative/GENO-ontology/",
"name": "Genotype Ontology",
"prefix": "GENO"
},
"GEO": {
"description": "An ontology of geographical entities",
"download_owl": "http://aber-owl.net/media/ontologies/GEO/5/geo.owl",
"homepage": "https://github.com/ufbmi/geographical-entity-ontology/wiki",
"name": "Geographical Entity Ontology",
"prefix": "GEO"
},
"GEOSPARQL": {
"description": "The OGC GeoSPARQL standard supports representing and querying geospatial data on the Semantic Web. GeoSPARQL defines a vocabulary for representing geospatial data in RDF, and it defines an extension to the SPARQL query language for processing geospatial data. In addition, GeoSPARQL is designed to accommodate systems based on qualitative spatial reasoning and systems based on quantitative spatial computations.",
"download_owl": "http://aber-owl.net/media/ontologies/GEOSPARQL/1/geosparql.owl",
"name": "GeoSPARQL",
"prefix": "GEOSPARQL",
"version": "OGC GeoSPARQL 1.0"
},
"GEOSPECIES": {
"description": "This ontology was designed to help integrate species concepts with species occurrences, gene sequences, images, references and geographical information. See also Taxonconcept.org",
"download_owl": "http://aber-owl.net/media/ontologies/GEOSPECIES/1/geospecies.owl",
"homepage": "http://lod.geospecies.org/",
"name": "GeoSpecies Ontology",
"prefix": "GEOSPECIES",
"version": "2009-05-04"
},
"GEPECO": {
"name": "Gerry Peter Coen Ontology",
"prefix": "GEPECO"
},
"GEPECOONT": {
"name": "Gerard Peter Coen Ontology",
"prefix": "GEPECOONT"
},
"GEXO": {
"description": "An application ontology for the domain of gene expression. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, and orthology relations using ontological properties from RO and ISO.",
"download_owl": "http://aber-owl.net/media/ontologies/GEXO/2/gexo.owl",
"homepage": "http://www.semantic-systems-biology.org/apo",
"name": "Gene Expression Ontology",
"prefix": "GEXO",
"version": "2015"
},
"GFF-M4M": {
"description": "Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is M4M Vocabulary. This controlled vocabulary is produced in Metadata 4 Machine (M4M) Workshop. sheet2rdf is used to build and serve M4M Vocabulary, while PURL is used to persist identifiers for the vocabulary: http://purl.org/m4m/",
"homepage": "https://github.com/gofair-foundation/m4m-vocabulary",
"name": "GO FAIR M4M",
"prefix": "GFF-M4M",
"version": "0.0.5"
},
"GFFO": {
"description": "An ontology to represent genome feature annotations in gff3 format.",
"download_owl": "http://aber-owl.net/media/ontologies/GFFO/1/gffo.owl",
"homepage": "https://github.com/mpievolbio-scicomp/GenomeFeatureFormatOntology",
"name": "Genetic Feature Format Ontology",
"prefix": "GFFO",
"version": "0.0.1"
},
"GFO": {
"description": "The General Formal Ontology (GFO) is a top-level ontology integrating objects and processes.",
"download_owl": "http://aber-owl.net/media/ontologies/GFO/1/gfo.owl",
"homepage": "http://www.onto-med.de/ontologies/gfo/",
"name": "General Formal Ontology",
"prefix": "GFO",
"version": "Version 1.0 ($Revision: 1.13 $)"
},
"GFO-BIO": {
"description": "GFO-Bio is a biological core ontology built on the General Formal Ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/GFO-BIO/1/gfo-bio.owl",
"homepage": "http://www.onto-med.de/ontologies/gfo-bio/",
"name": "General Formal Ontology for Biology",
"prefix": "GFO-BIO",
"version": "1.1"
},
"GFVO": {
"description": "The Genomic Feature and Variation Ontology (GFVO) is modeled to represent genomic data using the Resource Description Format (RDF) or Linked Data using JSON (JSON-LD). It is captures the contents of data files that adhere to the Generic Feature Format Version 3 (GFF3, http://www.sequenceontology.org/resources/gff3.html), the General Transfer Format (GTF, http://mblab.wustl.edu/GTF22.html), the Genome Variation Format Version 1 (GVF, http://www.sequenceontology.org/resources/gvf.html), and the Variant Call Format (VCF, http://vcftools.sourceforge.net/specs.html), as well as the FASTA format (http://en.wikipedia.org/wiki/FASTA_format). The creation of the ontology was inspired by previous work of Robert Hoehndorf on RDF2OWL (http://code.google.com/p/rdf2owl). NOTE: GFVO in BioPortal is a simplified version without ontology imports and having class/property equivalences removed. The full ontology is available at: http://www.biointerchange.org/gfvo",
"download_owl": "http://aber-owl.net/media/ontologies/GFVO/20/gfvo.owl",
"homepage": "https://www.codamono.com/biointerchange/",
"name": "Genomic Feature and Variation Ontology",
"prefix": "GFVO",
"version": "1.0.6"
},
"GLOMA_ONTOLOGY": {
"description": "\u4e00\u4e2a\u4e2d\u6587\u8111\u80f6\u8d28\u7624\u9884\u540e\u672c\u4f53",
"download_owl": "http://aber-owl.net/media/ontologies/GLOMA_ONTOLOGY/2/gloma_ontology.owl",
"name": "lanxin huang",
"prefix": "GLOMA_ONTOLOGY",
"version": "1.0"
},
"GLYCO": {
"description": "The GlycO ontology provides an up-to-date knowledge base of experimentally verified glycan structures. Glycan (oligosaccharide or polysaccharide) structures are represented as trees of monosaccharide residues. Linkage to proteins and lipids is supported as well. Insertion of a new glycan is controlled by curation process that includes matching the new glycan against a canonical glyco-tree (a highly branched representation for a family of glycans).",
"download_owl": "http://aber-owl.net/media/ontologies/GLYCO/1/glyco.owl",
"homepage": "http://glycomics.ccrc.uga.edu/core4/informatics-ontologies.html",
"name": "Glycomics Ontology",
"prefix": "GLYCO",
"version": "4.6.0.0"
},
"GLYCOCOO": {
"description": "GlycoConjugate Ontology (GlycoCoO) as a standard semantic framework to describe and represent glycoconjugate data in RDF.",
"download_owl": "http://aber-owl.net/media/ontologies/GLYCOCOO/2/glycocoo.owl",
"homepage": "https://github.com/glycoinfo/GlycoCoO",
"name": "GlycoConjugate Ontology",
"prefix": "GLYCOCOO",
"version": "1.1.3"
},
"GLYCORDF": {
"description": "Ontology for Glycomcis data.",
"download_owl": "http://aber-owl.net/media/ontologies/GLYCORDF/14/glycordf.owl",
"homepage": "https://github.com/ReneRanzinger/GlycoRDF",
"name": "GlycoRDF",
"prefix": "GLYCORDF",
"version": "1.00"
},
"GML": {
"description": "The Geography Markup Language (GML) is an RDF encoding for the transport and storage of geographic information, including both the geometry and properties of geographic features. Vocabulary terms are declared using OWL language to support RDF applications.",
"download_owl": "http://aber-owl.net/media/ontologies/GML/1/gml.owl",
"name": "Ontology for Geography Markup Language (GML3.0)",
"prefix": "GML",
"version": "version 1.0"
},
"GMM": {
"description": "GoMapMan is an open web-accessible resource for gene functional annotations in the plant sciences. It was developed to facilitate improvement, consolidation and visualization of gene annotations across several plant species.",
"download_obo": "http://aber-owl.net/media/ontologies/GMM/25/gmm.obo",
"homepage": "http://www.gomapman.org/",
"name": "GoMapMan",
"prefix": "GMM",
"version": "1.2"
},
"GMO": {
"description": "A structured controlled vocabulary for describing ingredients that constitute microbial growth media used in biological research centers.",
"download_owl": "http://aber-owl.net/media/ontologies/GMO/6/gmo.owl",
"name": "Growth Medium Ontology",
"prefix": "GMO",
"version": "0.16 Beta"
},
"GNO": {
"description": "GlyTouCan provides stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations). GNOme organizes these stable accessions for interative browsing, for text-based searching, and for automated reasoning with well-defined characterization levels.",
"download_owl": "http://aber-owl.net/media/ontologies/GNO/27/gno.owl",
"homepage": "https://gnome.glyomics.org/",
"name": "Glycan Naming and Subsumption Ontology (GNOme)",
"prefix": "GNO"
},
"GO": {
"description": "An ontology for describing the function of genes and gene products",
"download_owl": "http://aber-owl.net/media/ontologies/GO/1789/go.owl",
"homepage": "http://geneontology.org/",
"name": "Gene Ontology",
"prefix": "GO"
},
"GO-EXT": {
"description": "Gene Ontology Extension",
"download_obo": "http://aber-owl.net/media/ontologies/GO-EXT/2/go-ext.obo",
"homepage": "http://www.geneontology.org",
"name": "Gene Ontology Extension",
"prefix": "GO-EXT",
"version": "2"
},
"GO-PLUS": {
"download_owl": "http://aber-owl.net/media/ontologies/GO-PLUS/467/go-plus.owl",
"homepage": "http://geneontology.org",
"name": "go-plus",
"prefix": "GO-PLUS"
},
"GOLDTERMS": {
"description": "A rendering of the JGI GOLD ecosystem classification (https://gold.jgi.doe.gov/ecosystem_classification)",
"download_owl": "http://aber-owl.net/media/ontologies/GOLDTERMS/3/goldterms.owl",
"homepage": "https://github.com/cmungall/gold-ontology",
"name": "GOLD Ecosystem Classification",
"prefix": "GOLDTERMS"
},
"GPML": {
"description": "GPML is the file format used to store pathway content at WikiPathways. GPML is short for Graphical Pathway Markup Language, and it is a custom XML format compatible with pathway visualization and analysis tools such as Cytoscape and PathVisio. Get it as RDFa in HTML: http://vocabularies.wikipathways.org/gpml Or get it translated to RDF/XML from either of these URLs: http://getschema.org/rdfaliteextractor?url=http%3A%2F%2Fvocabularies.wikipathways.org%2Fgpml&out=rdf or http://rdf-translator.appspot.com/convert/rdfa/xml/http%3A%2F%2Fvocabularies.wikipathways.org%2Fgpml",
"download_owl": "http://aber-owl.net/media/ontologies/GPML/331/gpml.owl",
"name": "Graphical Pathway Markup Language",
"prefix": "GPML",
"version": "2013a"
},
"GRO": {
"description": "The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes.",
"download_owl": "http://aber-owl.net/media/ontologies/GRO/5/gro.owl",
"homepage": "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html",
"name": "Gene Regulation Ontology",
"prefix": "GRO",
"version": "0.5"
},
"GSSO": {
"description": "The Gender, Sex, and Sexual Orientation (GSSO) ontology has terms for annotating interdisciplinary information concerning gender, sex, and sexual orientation for primary usage in the biomedical and adjacent sciences.",
"download_owl": "http://aber-owl.net/media/ontologies/GSSO/73/gsso.owl",
"homepage": "https://gsso.research.cchmc.org/",
"name": "Gender, Sex, and Sexual Orientation (GSSO) ontology",
"prefix": "GSSO"
},
"GTO": {
"description": "The ontology integrated multiple well-known genetic testing resources, to provide scientific evidence accordingly",
"download_owl": "http://aber-owl.net/media/ontologies/GTO/1/gto.owl",
"homepage": "http://qianzhu-lab.umbc.edu/",
"name": "Genetic Test",
"prefix": "GTO"
},
"GVO": {
"description": "The Genome Variation Ontology (GVO) is an ontology for the systematic description of various genomic variations, including complex structural variations in genomes.",
"download_owl": "http://aber-owl.net/media/ontologies/GVO/3/gvo.owl",
"homepage": "http://genome-variation.org/resource/gvo",
"name": "Genome Variation Ontology",
"prefix": "GVO",
"version": "2022-09-09"
},
"GVP": {
"description": "The AAT, TGN, ULAN, and CONA contain structured terminology for art and other material culture, archival materials, visual surrogates, and bibliographic materials. Compliant with international standards, they provide authoritative information for catalogers and researchers, and can be used to enhance access to databases and Web sites. The Getty Vocabularies are produced by the Getty Vocabulary Program (GVP) and grow through contributions.",
"download_owl": "http://aber-owl.net/media/ontologies/GVP/5/gvp.owl",
"name": "Getty Vocabulary Program ontology",
"prefix": "GVP"
},
"GWAS_EFO_SKOS": {
"description": "This is an experimental view that uses the Simple Knowledge Organisation System (SKOS) to represent a view over EFO terms. These EFO terms are a subset of terms that are being used to annotate data for the Genome Wide Association Studies (GWAS) curators.",
"download_owl": "http://aber-owl.net/media/ontologies/GWAS_EFO_SKOS/1/gwas_efo_skos.owl",
"name": "GWAS view",
"prefix": "GWAS_EFO_SKOS",
"version": "unknown"
},
"GYRISULCIH": {
"description": "A hierarchy of Neocortex gyri and sulci in Primates.",
"download_owl": "http://aber-owl.net/media/ontologies/GYRISULCIH/3/gyrisulcih.owl",
"name": "NeuroMorpho.Org Cortical Gyri & Sulci",
"prefix": "GYRISULCIH",
"version": "2.0"
},
"H1_NMOABA_1_0": {
"description": "Light version of the Allen Brain Atlas ontology that is customized for the NeuroMorpho.Org brain regions. The ontology includes NeuroMorpho.Org rodent data instantiated for direct matching classes.",
"download_owl": "http://aber-owl.net/media/ontologies/H1_NMOABA_1_0/1/h1_nmoaba_1_0.owl",
"homepage": "www.neuromorpho.org",
"name": "NeuroMorpho.Org Allen Brain Atlas ontology v.1.0",
"prefix": "H1_NMOABA_1_0",
"version": "1"
},
"H1_NMOABA_2_0": {
"description": "Light version of the Allen Brain Atlas ontology that is customized for the NeuroMorpho.Org brain regions. This ontology instantiates 90% of rodent brain regions from NeuroMorpho.Org v5.2.",
"download_owl": "http://aber-owl.net/media/ontologies/H1_NMOABA_2_0/1/h1_nmoaba_2_0.owl",
"homepage": "www.neuromorpho.org",
"name": "NeuroMorpho.Org Allen Brain Atlas ontology v.2.0",
"prefix": "H1_NMOABA_2_0",
"version": "2"
},
"H1_NMOABA_4_0": {
"description": "Light version of the Allen Brain Atlas ontology that is customized for the NeuroMorpho.Org brain regions. This ontology instantiates 90% of rodent brain regions from NeuroMorpho.Org v5.2.",
"download_owl": "http://aber-owl.net/media/ontologies/H1_NMOABA_4_0/1/h1_nmoaba_4_0.owl",
"homepage": "www.neuromorpho.org",
"name": "NeuroMorpho.Org Allen Brain Atlas ontology v.4.0",
"prefix": "H1_NMOABA_4_0",
"version": "4"
},
"H1_NMOABA_4_1": {
"description": "Light version of the Allen Brain Atlas ontology that is customized for the NeuroMorpho.Org brain regions. This ontology instantiates 90% of rodent brain regions from NeuroMorpho.Org v5.2.",
"download_owl": "http://aber-owl.net/media/ontologies/H1_NMOABA_4_1/1/h1_nmoaba_4_1.owl",
"homepage": "www.neuromorpho.org",
"name": "NeuroMorpho.Org Allen Brain Atlas ontology v.4.1",
"prefix": "H1_NMOABA_4_1",
"version": "4.1"
},
"H2_HIPClassicRegions": {
"description": "A classical regional partition hierarchy of cornu ammonis of rodent hippocampus.",
"download_owl": "http://aber-owl.net/media/ontologies/H2_HIPClassicRegions/2/h2_hipclassicregions.owl",
"homepage": "www.neuromorpho.org",
"name": "NeuroMorpho.Org hippocampal regions",
"prefix": "H2_HIPClassicRegions",
"version": "2"
},
"H3_HIPSeptotemporalAxis": {
"description": "longitudinal partitioning of rodent hippocampus",
"download_owl": "http://aber-owl.net/media/ontologies/H3_HIPSeptotemporalAxis/2/h3_hipseptotemporalaxis.owl",
"homepage": "www.neuromorpho.org",
"name": "NeuroMorpho.Org longitudinal hippocampal regions",
"prefix": "H3_HIPSeptotemporalAxis",
"version": "2"
},
"HAAURAADO": {
"description": "The first ontology describing the anatomy and the development of Halocynthia aurantium.",
"download_obo": "http://aber-owl.net/media/ontologies/HAAURAADO/2/haauraado.obo",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Halocynthia aurantium Anatomy and Development Ontology",
"prefix": "HAAURAADO"
},
"HAKMSVU": {
"description": "OntologyForSvu",
"download_owl": "http://aber-owl.net/media/ontologies/HAKMSVU/2/hakmsvu.owl",
"homepage": "http://SemanticWeb.org/Hakm",
"name": "Hakm",
"prefix": "HAKMSVU",
"version": "Latest"
},
"HALLIE": {
"name": "Hallie Richardson",
"prefix": "HALLIE"
},
"HAMIDEHSGH": {
"description": "Inherited retinal dystrophy (IRD) as one of the rare ocular diseases encompasses different types of hereditary retinal degenerations appearing by involvement of the different layers of the posterior ocular segment. In respect of the importance of the classification systems regarding the recorded history of biologic and natural sciences, there is no classification regarding the IRD diagnoses. Therefore, we aimed to present a novel classification in this regard.",
"download_owl": "http://aber-owl.net/media/ontologies/HAMIDEHSGH/1/hamidehsgh.owl",
"name": "Inherited Retinal Dystrophy",
"prefix": "HAMIDEHSGH"
},
"HANCESTRO": {
"description": "The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies.",
"download_owl": "http://aber-owl.net/media/ontologies/HANCESTRO/17/hancestro.owl",
"homepage": "https://ebispot.github.io/hancestro/",
"name": "Human Ancestry Ontology",
"prefix": "HANCESTRO"
},
"HAO": {
"description": "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)",
"download_owl": "http://aber-owl.net/media/ontologies/HAO/28/hao.owl",
"homepage": "http://hymao.org",
"name": "Hymenoptera Anatomy Ontology",
"prefix": "HAO"
},
"HAROREADO": {
"description": "The first ontology describing the anatomy and the development of Halocynthia roretzi.",
"download_obo": "http://aber-owl.net/media/ontologies/HAROREADO/2/haroreado.obo",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Halocynthia roretzi Anatomy and Development Ontology",
"prefix": "HAROREADO"
},
"HASCO": {
"description": "The Human-Aware Science Ontology (HAScO) integrates a collection of well-established science-related ontologies, and aims to address issues related to data annotation for large data ecosystem, where data can come from diverse data sources including sensors, lab results, and questionnaires. The HAScO has been used to annotate data collections to facilitate data exploration and analysis for numerous scientific projects. Data files produced by scientific studies are processed to identify and annotate the objects (a gene, for instance) with the appropriate ontological terms.",
"download_owl": "http://aber-owl.net/media/ontologies/HASCO/3/hasco.owl",
"homepage": "http://www.hadatac.org/hasco-ontology/",
"name": "Human-Aware Science Ontology",
"prefix": "HASCO",
"version": "0.9"
},
"HASSET": {
"description": "The Humanities And Social Science Electronic Thesaurus (HASSET) is the leading British English thesaurus for the social sciences. HASSET has been compiled at the UK Data Archive for over thirty years. It was developed initially as an information retrieval tool to access data deposited in the UK Data Archive. Its scope has now expanded to cover the collections held by the UK Data Service. Copyright University of Essex. All rights reserved. You may view the thesaurus online. Prior to downloading and/or using the full version of HASSET, SKOS-HASSET or any related product, a licence agreement must be completed between the user and the University of Essex.",
"homepage": "https://hasset.ukdataservice.ac.uk/",
"name": "Humanities And Social Science Electronic Thesaurus",
"prefix": "HASSET",
"version": "2.00"
},
"HCDR": {
"description": "This ontology utilizes the European Typology of Homelessness and Housing Exclusion (ETHOS), a respected conceptual framework used to define degrees of housing insecurity and homelessness internationally, to conceptualize, define, and link homelessness in SNOMED, Read CTV3, and Read 2 codes to clinical data extraction. The ontology uses the ETHOS as a general framework, leading to endpoints represented by codes from across the three databases. This is useful for researchers and medical professionals seeking to understand how homelessness is represented in clinical data, how homelessness is defined internationally, and what types of services are available for homeless individuals.",
"download_owl": "http://aber-owl.net/media/ontologies/HCDR/1/hcdr.owl",
"name": "Homelessness and Clinical Data Recording",
"prefix": "HCDR",
"version": "1"
},
"HCIOTO": {
"description": "A sensor based health care ontology",
"download_owl": "http://aber-owl.net/media/ontologies/HCIOTO/1/hcioto.owl",
"name": "HealthCareOntology",
"prefix": "HCIOTO"
},
"HCODONONT": {
"description": "This ontology contains the information of the frequency of usage and the relative frequency of usage of Human Gene Codons, to be used to the operations by The Project Of HIV Ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/HCODONONT/4/hcodonont.owl",
"homepage": "http://blog.51.ca/u-345129/",
"name": "HGeneCodonOntology",
"prefix": "HCODONONT",
"version": "2"
},
"HCOT": {
"description": "It is a sensor based health care ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/HCOT/1/hcot.owl",
"name": "HealthCare Ontology",
"prefix": "HCOT"
},
"HCPCS": {
"description": "Healthcare Common Procedure Coding System",
"homepage": "http://cms.hhs.gov",
"name": "Healthcare Common Procedure Coding System",
"prefix": "HCPCS",
"version": "2016AB"
},
"HCPCS-mod": {
"description": "Modifiers denote that a certain procedure/service has been altered by a particular circumstance, but not changed in its definition, therefore the same code is used and a modifier is added to denote what has been altered.",
"download_owl": "http://aber-owl.net/media/ontologies/HCPCS-mod/1/hcpcs-mod.owl",
"name": "HCPCS modifiers",
"prefix": "HCPCS-mod",
"version": "unknown"
},
"HDMPONTO": {
"description": "A Hierarchical Data Mining Process Ontology, by combined OntoKDD and DMWF.",
"download_owl": "http://aber-owl.net/media/ontologies/HDMPONTO/1/hdmponto.owl",
"name": "HierarchicalDMProcessOnto",
"prefix": "HDMPONTO"
},
"HECON": {
"description": "Health Condition Evolution Ontology (HECON), is a formal model representation of the evolution of medical events over time.",
"download_owl": "http://aber-owl.net/media/ontologies/HECON/1/hecon.owl",
"homepage": "http://kmi.open.ac.uk/conrad/HECON",
"name": "HECON: Health Condition Evolution Ontology",
"prefix": "HECON",
"version": "0.1"
},
"HED": {
"description": "HED (Hierarchical Event Descriptors) is a standardized vocabulary for describing what happens during experiments and a framework for mapping these terms and other metadata onto the experimental timeline to enable analysis. HED is a subtag system organized by the top-level categories: Event, Agent, Action, Item, Property, and Relation. Users create HED annotations as comma-separated, parenthesized lists of terms. See https://www.hed-resource.org for documentation, tutorials and other resources. Recently we have created an ontology representation of the HED vocabulary (HED schema) to provide a better mechanism for linking the HED terms to terms from other ontologies and to provide better provenance information. The HED tags as well as auxiliary information such as types of units and types of values are represented as classes. The HED schema attributes are represented either as DataProperty or ObjectProperty depending on their range. Some additional attributes that are not inherited are represented as AnnotationProperty. HED is the standard used for event annotation in BIDS (Brain Imaging Data Structure) a standard for storing neuroimaging repository and is used by datasets on several repositories such as openNeuro and Nemar.",
"download_owl": "http://aber-owl.net/media/ontologies/HED/1/hed.owl",
"homepage": "www.hedtags.org",
"name": "Hierarchical Event Descriptors",
"prefix": "HED",
"version": "releases/2024-06-10"
},
"HEIO": {
"description": "The purpose of this ontology is to develop a model for regional healthcare system interoperability and information exchange quantification (measured by the electronic health information exchange (eHIE) indicator). The eHIE is hypothesized as a leading measure of regional healthcare system integration. A publication associated with this ontology is currently under review.",
"download_owl": "http://aber-owl.net/media/ontologies/HEIO/17/heio.owl",
"name": "Regional Healthcare System Interoperability and Information Exchange Measurement Ontology",
"prefix": "HEIO",
"version": "Version 1.15"
},
"HELIFIT": {
"description": "This an ontology for healthcare.",
"download_owl": "http://aber-owl.net/media/ontologies/HELIFIT/1/helifit.owl",
"name": "HeLiFit-Ontology",
"prefix": "HELIFIT"
},
"HENECON": {
"description": "HeNeCOn (Head and Neck Cancer Ontology) is the first ontology specifically focused on the Head and Neck Cancer (HNC) domain. It provides a clinically reliable data model for HNC processes during all phases of the disease: prognosis, treatment, and follow-up. The ontology is established based on an annotated dataset to provide formal reference descriptions, contains 170 clinical variables organized into a taxonomy, and is expanded and mapped to formalize and integrate multiple databases into the HeNeCOn ontology. The outcomes of this iterative process were reviewed and validated by clinicians and statisticians. HeNeCOn, with roughly 500 classes, is a very specific ontology which includes a taxonomy with a hierarchical structure, semantic definitions of 283 medical terms and detailed relations between them, which makes it a reference data model.",
"download_owl": "http://aber-owl.net/media/ontologies/HENECON/1/henecon.owl",
"name": "Head and Neck Cancer Ontology",
"prefix": "HENECON",
"version": "1.0"
},
"HENEGEO": {
"description": "HeNeGeO (Head and Neck Cancer - Clinical and Gene Ontology) presents a data model that encompasses both clinical and genomic aspects of Head and Neck Cancer (HNC) across every stage of the disease, covering prognosis, treatment and follow-up. This ontology builds upon the foundation laid by HENECON (Head and Neck Cancer Ontology) and has been significantly expanded with a focus on information pertaining to cancer recurrence, alongside a comprehensive list of genes that offer valuable insights throughout the entire head and neck cancer progression. To enhance clarity, novel medical terms have been thoughtfully annotated with their respective semantic meanings. This comprehensive update includes the incorporation of 29,770 genes, featuring essential details such as NCBI GeneID (EntrezID), gene symbol, gene name, gene alias, and the HGNC ID. The development of this ontology underwent rigorous review and validation by experts in both clinical and genomic domains.",
"download_owl": "http://aber-owl.net/media/ontologies/HENEGEO/1/henegeo.owl",
"name": "Head and Neck Cancer - Clinical and Gene Ontology",
"prefix": "HENEGEO",
"version": "1.0"
},
"HFO": {
"description": "Heart failure ontology is an attempt to define heart-failure-relevant information including the causes and risk factors, signs and symptoms, diagnostic tests and results, and treatment.",
"download_owl": "http://aber-owl.net/media/ontologies/HFO/1/hfo.owl",
"name": "Heart Failure Ontology",
"prefix": "HFO",
"version": "version 1.0"
},
"HGNC": {
"description": "Human Genome Organisation (HUGO) Gene Nomenclature Committee at the European Bioinformatics Institute approves a gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database.",
"download_owl": "http://aber-owl.net/media/ontologies/HGNC/1/hgnc.owl",
"homepage": "http://www.genenames.org/",
"name": "HUGO Gene Nomenclature",
"prefix": "HGNC",
"version": "July2010"
},
"HGNC-NR": {
"description": "HUGO Gene Nomenclature Committee Ontology with recurring uploads",
"download_owl": "http://aber-owl.net/media/ontologies/HGNC-NR/8/hgnc-nr.owl",
"name": "HGNC New Releases Ontology",
"prefix": "HGNC-NR",
"version": "2023-09-18"
},
"HHEAR": {
"description": "The Human Health Exposure Analysis Resource (HHEAR) measures exposures that cover the breadth of the \u201cexposome,\u201d which encompasses all environmental exposures including chemical, physical, and biological stressors, as well as lifestyle and social environments, from conception through adulthood.",
"download_owl": "http://aber-owl.net/media/ontologies/HHEAR/8/hhear.owl",
"homepage": "https://hhearprogram.org",
"name": "Human Health Exposure Analysis Resource",
"prefix": "HHEAR",
"version": "1.5"
},
"HHEARP": {
"description": "An ontology of properties used to annotate the studies included in the Human Health Exposure Analysis Resource (HHEAR) knowledge graph; visit https://hheardatacenter.mssm.edu for more information regarding HHEAR.",
"download_owl": "http://aber-owl.net/media/ontologies/HHEARP/3/hhearp.owl",
"name": "HHEAR Properties",
"prefix": "HHEARP",
"version": "0.0.3"
},
"HHEARVS": {
"name": "HHEAR Value Sets",
"prefix": "HHEARVS"
},
"HHS": {
"name": "CIDOnto",
"prefix": "HHS"
},
"HINO": {
"description": "The Human Interaction Network Ontology (HINO) is an INO extension for the domain of human interaction networks. It has currently incoporated Reactome reactions and pathways. Like INO, HINO aligns with BFO. HINO is developed by following the OBO Foundry principles.",
"download_owl": "http://aber-owl.net/media/ontologies/HINO/6/hino.owl",
"homepage": "http://www.ino-ontology.org/",
"name": "Human Interaction Network Ontology",
"prefix": "HINO",
"version": "Vision Release: 1.0.69"
},
"HIO": {
"description": "The Hearing Impairment Ontology (HIO) is a common controlled hearing impairment (HI) vocabulary, which is expected to enhance collaborative research. This ontology is currently the most comprehensive and standardized human- and machine-readable resource that unambiguously defines HI concepts and terminology for researchers, patients and clinicians in order to help process, reuse and re-apply existing HI knowledge in biomedical research and health-care systems. In the context of big data analytics, this ontology may facilitate a retrospective data harmonization and contribute to mapping HI datasets to functional knowledge to enable the subsequent HI research translation into clinical applications and policy guidelines. The HIO will allow researchers, clinicians and patients to readily access standardized HI-related knowledge in a single location and promote HI data integration, interoperability and sharing, including epidemiological, socio-environmental, biomedical, genetic and phenotypic datasets.",
"download_owl": "http://aber-owl.net/media/ontologies/HIO/3/hio.owl",
"name": "Hearing Impairment Ontology",
"prefix": "HIO",
"version": "1"
},
"HIPLAYERH": {
"description": "A hierarchy of layers in the Hippocampus.",
"download_owl": "http://aber-owl.net/media/ontologies/HIPLAYERH/2/hiplayerh.owl",
"name": "NeuroMorpho.Org Hippocampus layers",
"prefix": "HIPLAYERH",
"version": "2.0"
},
"HIV": {
"description": "The HIV ontology encompasses all knowledge about HIV",
"download_obo": "http://aber-owl.net/media/ontologies/HIV/12/hiv.obo",
"homepage": "bio-toolkit.com",
"name": "HIV ontology",
"prefix": "HIV",
"version": "2.7"
},
"HIVCRS": {
"description": "The Ontology to express the ternary relations of HIV1",
"download_owl": "http://aber-owl.net/media/ontologies/HIVCRS/1/hivcrs.owl",
"homepage": "http://blog.51.ca/u-345129/",
"name": "HIVCompoundRels",
"prefix": "HIVCRS",
"version": "1"
},
"HIVGENETICS": {
"name": "HIVGenetics",
"prefix": "HIVGENETICS"
},
"HIVHPVFGS": {
"description": "Vocabulary for testing and vaccination records for HIV, HPV, and FGS in Uganda.",
"name": "HIV, HPV, FGS vocabulary",
"prefix": "HIVHPVFGS"
},
"HIVHPVSCHISTOSOM": {
"description": "This is the ontology containing the controlled terms and semantic properties used in the HIV, HPV and Schistosomiasis dataset obtained from the MOH Uganda",
"name": "HIVHPVSchistosomiasis",
"prefix": "HIVHPVSCHISTOSOM",
"version": "1.1"
},
"HIVHPVSTOM": {
"name": "HIVHPVStom",
"prefix": "HIVHPVSTOM"
},
"HIVMT": {
"description": "This is an ontology about the mutations Of HIV1 and the relations between them and the clinical practices. And it has imported the main ontology: https://bioportal.bioontology.org/ontologies/HIVO004.",
"download_owl": "http://aber-owl.net/media/ontologies/HIVMT/6/hivmt.owl",
"homepage": "https://blog.51.ca/u-345129/",
"name": "HIVMutation",
"prefix": "HIVMT",
"version": "01"
},
"HIVO004": {
"description": "A Project Of Biomedical Ontology for Systems Biomedicine The Project includes so far a main ontology (HIVOnt0**.owl) which is imported by two sub ontologies AIDSClinic0**.owl and HumanGeneCodon0**.owl. The goals of the Project of HIV Ontology(PHIVO) for Knowledge Integrations include 1. Providing AIDS clinics and HIV virology and the future biomedicines, including the Systems Biomedicine(SBM), the Precision Biomedicine(PBM) and the Knowledge-Integrated Biomedicine(KIMB), with the knowledge resources expressed in the way of ontology, which is able to be operated on engineering ground. 2. Carrying out the methodology researches for the goals above.",
"download_owl": "http://aber-owl.net/media/ontologies/HIVO004/16/hivo004.owl",
"homepage": "http://blog.51.ca/u-345129/",
"name": "HIVOntologymain.owl",
"prefix": "HIVO004",
"version": "016"
},
"HL7": {
"description": "This version is the first update to Normative RIM, Release 3. It is based on changes approved in Harmonization in November 2010. This release of the RIM is bound to HL7 Abstract Data Types Release 2.",
"homepage": "http://www.hl7.org",
"name": "Health Level Seven Reference Implementation Model, Version 3",
"prefix": "HL7",
"version": "2016AB"
},
"HMADO": {
"name": "Human Microbiome Associated Disease Ontology ",
"prefix": "HMADO"
},
"HMIS033B": {
"name": "HMIS 033",
"prefix": "HMIS033B"
},
"HMISLAB0115": {
"description": "Assignment for group 5 of DSIP",
"name": "HMIS LAB 011 5",
"prefix": "HMISLAB0115"
},
"HMSG": {
"name": "Hack Mudah Slot Games",
"prefix": "HMSG"
},
"HNS": {
"description": "The purpose of this research is to develop an ontology with subsequent testing and evaluation, for identifying utility and value. The domain that has been chosen is human nervous system (HNS) disorders. It is hypothesized here that an ontology-based patient records management system is more effective in meeting and addressing complex information needs of health-care personnel. Therefore, this study has been based on the premise that developing an ontology and using it as a component of the search interface in hospital records management systems will lead to more efficient and effective management of health-care. It is proposed here to develop an ontology of the domain of HNS disorders using a standard vocabulary such as MeSH or SNOMED CT. The principal classes of an ontology include facet analysis for arranging concepts based on their common characteristics to build mutually exclusive classes. We combine faceted theory with description logic, which helps us to better query and retrieve data by implementing an ontological model. Prot\u00e9g\u00e9 5.2.0 was used as ontology editor. The use of ontologies for domain modelling will be of acute help to doctors for searching patient records. In this paper we show how the faceted approach helps us to build a flexible model and retrieve better information. We use the medical domain as a case study to show examples and implementation.",
"download_owl": "http://aber-owl.net/media/ontologies/HNS/1/hns.owl",
"homepage": "https://github.com/subhashishhh/HNS-Ontology/blob/master/HNS_ontology.owl",
"name": "HNS_Ontolgoy",
"prefix": "HNS",
"version": "4.0"
},
"HO": {
"description": "A Histological Ontology of the Human Cardiovascular System v. 1.1",
"download_owl": "http://aber-owl.net/media/ontologies/HO/78/ho.owl",
"name": "Histological Ontology",
"prefix": "HO",
"version": "1.1"
},
"HOIP": {
"description": "Homeostasis imbalance process ontology (HoIP) is an ontology that systematizes a wide variety of terms involving homeostasis imbalance courses and processes. HoIP focuses on the course of COVID-19 infectious processes and cellular senescence.",
"download_owl": "http://aber-owl.net/media/ontologies/HOIP/65/hoip.owl",
"homepage": "https://github.com/yuki-yamagata/hoip",
"name": "Homeostasis imbalance process ontology",
"prefix": "HOIP",
"version": "2024/04/03"
},
"HOM": {
"description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.",
"download_owl": "http://aber-owl.net/media/ontologies/HOM/7/hom.owl",
"homepage": "http://bioinfo.unil.ch",
"name": "Homology Ontology",
"prefix": "HOM"
},
"HOM-ICD9": {
"description": "This is the ICD9 ontology with a different hierarchical view, but based on the same nomenclature and code structure. Useful for researchers that look for a disease by ICD9 code.",
"download_owl": "http://aber-owl.net/media/ontologies/HOM-ICD9/4/hom-icd9.owl",
"name": "ICD9 for Health Ontology Mapper",
"prefix": "HOM-ICD9",
"version": "2"
},
"HOM-UCSF_UCareDispostion": {
"description": "All Disposition/Discharge Codes and Values listed in the UCSF- UCare patient source data",
"download_owl": "http://aber-owl.net/media/ontologies/HOM-UCSF_UCareDispostion/1/hom-ucsf_ucaredispostion.owl",
"name": "Health Ontology Mapper - UCSF_UCareDischargeDisposition",
"prefix": "HOM-UCSF_UCareDispostion",
"version": "1.1"
},
"HOME": {
"description": "An ontology to record the physical, emotional and psychological effects resulting from differences in treatment that citizens receive based on their identity when entering healthcare institutions. We present the first version of such a Health Ontology for Minority Equity (HOME)",
"download_owl": "http://aber-owl.net/media/ontologies/HOME/1/home.owl",
"name": "Health Ontology for Minority Equity",
"prefix": "HOME",
"version": "1"
},
"HOOM": {
"description": "Orphanet provides phenotypic annotations of the rare diseases in the Orphanet nomenclature using the Human Phenotype Ontology (HPO). HOOM is a module that qualifies the annotation between a clinical entity and phenotypic abnormalities according to a frequency and by integrating the notion of diagnostic criterion. In ORDO a clinical entity is either a group of rare disorders, a rare disorder or a subtype of disorder. The phenomes branch of ORDO has been refactored as a logical import of HPO, and the HPO-ORDO phenotype disease-annotations have been provided in a series of triples in OBAN format in which associations, frequency and provenance are modeled. HOOM is provided as an OWL (Ontologies Web Languages) file, using OBAN, the Orphanet Rare Disease Ontology (ORDO), and HPO ontological models. HOOM provides extra possibilities for researchers, pharmaceutical companies and others wishing to co-analyse rare and common disease phenotype associations, or re-use the integrated ontologies in genomic variants repositories or match-making tools.",
"download_owl": "http://aber-owl.net/media/ontologies/HOOM/10/hoom.owl",
"homepage": "https://www.orphadata.com",
"name": "HPO - ORDO Ontological Module",
"prefix": "HOOM",
"version": "2.2"
},
"HORD": {
"description": "This ontology describes the bio-psico-social state of a person of rare diseses in a holistic way. It considers several contents such as disease, psychological, social, environmental state of the person.",
"download_owl": "http://aber-owl.net/media/ontologies/HORD/1/hord.owl",
"homepage": "https://sites.google.com/site/laiasubirats",
"name": "Holistic Ontology of Rare Diseases",
"prefix": "HORD",
"version": "1.0"
},
"HP": {
"description": "A structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease.",
"download_owl": "http://aber-owl.net/media/ontologies/HP/613/hp.owl",
"homepage": "http://www.human-phenotype-ontology.org/",
"name": "Human Phenotype Ontology",
"prefix": "HP"
},
"HPIO": {
"description": "Ontology for host pathogen interactions in farmed animals",
"download_owl": "http://aber-owl.net/media/ontologies/HPIO/2/hpio.owl",
"name": "Host Pathogen Interactions Ontology",
"prefix": "HPIO",
"version": "1"
},
"HPO": {
"description": "The Hypertension Ontology, developed using the Protege tool, serves as a comprehensive knowledge framework for representing and organizing information related to hypertensive disorders. This ontology is designed to capture various aspects of hypertension, including its types, causes, and associated risks, with the aim of providing valuable insights for healthcare professionals, researchers, and policymakers. Leveraging the power of Protege, the ontology employs the OWL (Web Ontology Language) format to define classes, properties, and relationships, ensuring semantic clarity and interoperability. The taxonomy within the ontology encompasses a wide range of hypertensive conditions, allowing for detailed classification and representation. The ontology facilitates queries and exploration of hypertensive data through the use of the DL Query module in Protege, offering a practical tool for evaluating its usefulness. To enhance accessibility, the ontology is made available for download, enabling seamless integration into existing healthcare information systems. Its development involved a rigorous review of scientific literature and consideration of established methodologies, ensuring its alignment with best practices in ontology engineering. This Hypertension Ontology aims to contribute to the advancement of hypertension research, clinical practice, and healthcare decision-making.",
"download_owl": "http://aber-owl.net/media/ontologies/HPO/1/hpo.owl",
"name": "Hypertension-Ontology",
"prefix": "HPO"
},
"HPV": {
"name": "HPV Cancer Dictionary",
"prefix": "HPV"
},
"HP_O": {
"description": "Hypersensitivity Pneumonitis Ontology involves the domain of knowledge of 1. diseases caused by organic dusts exposure including hypersensitivity pneumonitis as well as 2. organic dusts.",
"download_owl": "http://aber-owl.net/media/ontologies/HP_O/1/hp_o.owl",
"homepage": "https://hypontology.herokuapp.com/",
"name": "Hypersensitivity pneumonitis ontology",
"prefix": "HP_O",
"version": "1.0"
},
"HRA": {
"description": "The Human Reference Atlas (HRA) is a comprehensive, high-resolution, three-dimensional atlas of all the cells in the healthy human body. The Human Reference Atlas provides standard terminologies and data structures for describing specimens, biological structures, and spatial positions linked to existing ontologies.",
"download_owl": "http://aber-owl.net/media/ontologies/HRA/1/hra.owl",
"name": "Human Reference Atlas",
"prefix": "HRA",
"version": "2.1.0"
},
"HRAVS": {
"description": "A collection of curated and standardized values used by the HuBMAP (Human BioMolecular Atlas Program) and SenNet (Cellular Senescence Network) metadata records to ensure uniformity in the description of samples and single-cell data produced by the consortium.",
"name": "HuBMAP Research Attributes Value Set",
"prefix": "HRAVS",
"version": "2.5.9"
},
"HRDO": {
"description": "This resource was designed during a PhD in medical informatics (funded by INSERM, 2010-2012). Its components are (i) a core ontology consistent with a metamodel (disorders and groups of disorders, genes, clinical signs and their relations) and (ii) an instantiation of this metamodel with Orphanet Data (available on http://orphadata.org). Research experiments demonstrated (i) efficient classifications generation based on SPARQL Construct, (ii) perspectives in semantic audit of a knowledge base, (iii) semantic comparison with OMIM (www.omim.org) using proximity measurements and (iv) opened perspectives in knowledge sharing (LORD, http://lord.bndmr.fr). Current production services of Orphanet developed ORDO, released in 2014, an ontology synchronized with their production database. This ontology is now available on Bioportal.",
"download_owl": "http://aber-owl.net/media/ontologies/HRDO/2/hrdo.owl",
"name": "Disease core ontology applied to Rare Diseases",
"prefix": "HRDO",
"version": "V2"
},
"HSAPDV": {
"description": "Life cycle stages for Human",
"download_owl": "http://aber-owl.net/media/ontologies/HSAPDV/12/hsapdv.owl",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv",
"name": "Human Developmental Stages",
"prefix": "HSAPDV"
},
"HSCLO38": {
"name": "Homo sapiens Chromosomal Location Ontology for GRCh38",
"prefix": "HSCLO38"
},
"HSDB_OCRe": {
"description": "This view contains HSDB extensions of OCRe. It contains additional defined classes in OCRe_ext (which imports OCRe) and annotations (in HSDB_OCRe) needed for the automatic generation of HSDB XSD.",
"download_owl": "http://aber-owl.net/media/ontologies/HSDB_OCRe/3/hsdb_ocre.owl",
"name": "HSDB OCRe view",
"prefix": "HSDB_OCRe",
"version": "$Revision$"
},
"HSO": {
"description": "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance.",
"download_owl": "http://aber-owl.net/media/ontologies/HSO/11/hso.owl",
"homepage": "https://w3id.org/hso",
"name": "Health Surveillance Ontology",
"prefix": "HSO"
},
"HSPO": {
"description": "The HSPO is an ontology that aims to represent and link together information about an individual from multiple domains. This work is motivated by the need to better understand the drivers of health outcomes that may arise from other domains including, but not limited to, the social determinants of health (e.g. ethnicity, transportation, education). This ontology can also describe a group of individuals that share similar characteristics (i.e. a cohort). Through this ontology we attempt to define a number of social contexts or social domains which can be useful to organise information coming from different terminologies such as ICD and SNOMED. Git Repository, Documentation and License details: https://github.com/IBM/hspo-ontology Apache License 2.0",
"download_owl": "http://aber-owl.net/media/ontologies/HSPO/3/hspo.owl",
"homepage": "https://github.com/IBM/hspo-ontology",
"name": "Health and Social Person-centric Ontology",
"prefix": "HSPO",
"version": "0.1.0"
},
"HTN": {
"description": "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines",
"download_owl": "http://aber-owl.net/media/ontologies/HTN/1/htn.owl",
"homepage": "https://github.com/aellenhicks/htn_owl",
"name": "Hypertension Ontology",
"prefix": "HTN"
},
"HTO": {
"description": "This is just a test ontology. Called the Horridge Test Ontology (HTO)",
"download_owl": "http://aber-owl.net/media/ontologies/HTO/1/hto.owl",
"name": "Horridge Test Ontology",
"prefix": "HTO",
"version": "0.0.1"
},
"HUGO": {
"description": "Human Genome Organisation (HUGO) Gene Nomenclature Committee at the European Bioinformatics Institute approves a gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database.",
"download_owl": "http://aber-owl.net/media/ontologies/HUGO/3/hugo.owl",
"homepage": "http://www.genenames.org/",
"name": "Human Genome Organization Gene Symbols",
"prefix": "HUGO",
"version": "July2010"
},
"HUPSON": {
"description": "Large biomedical simulation initiatives, such as the Virtual Physiological Human (VPH), are substantially dependent on controlled vocabularies to facilitate the exchange of information, of data and of models. Hindering these initiatives is a lack of a comprehensive ontology that covers the essential concepts of the simulation domain. We propose a first version of a newly constructed ontology, HuPSON, as a basis for shared semantics and interoperability of simulations, of models, of algorithms and of other resources in this domain. The ontology is based on the Basic Formal Ontology, and adheres to the MIREOT principles.",
"download_owl": "http://aber-owl.net/media/ontologies/HUPSON/1/hupson.owl",
"homepage": "http://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads.html",
"name": "Human Physiology Simulation Ontology",
"prefix": "HUPSON",
"version": "1.1.1"
},
"HUSAT": {
"name": "HuBMAP Samples Added Terms",
"prefix": "HUSAT"
},
"HYDROMAX": {
"name": "hydroxtreme7",
"prefix": "HYDROMAX"
},
"I-ADOPT": {
"description": "The I-ADOPT Framework is an ontology designed to facilitate interoperability between existing variable description models (including ontologies, taxonomy, and structured controlled vocabularies). One of the challenges in representing semantic descriptions of variables is getting people to agree about what they mean when describing the components that define the variables. The I-ADOPT ontology addresses this by providing core components and their relations that can be applied to define machine-interpretable variable descriptions that re-use FAIR vocabulary terms. This first version of the ontology has been developed by a core group of terminology experts and users from the Research Data Alliance (RDA) InteroperAble Descriptions of Observable Property Terminology (I-ADOPT) Working Group.",
"download_owl": "http://aber-owl.net/media/ontologies/I-ADOPT/5/i-adopt.owl",
"homepage": "https://www.rd-alliance.org/group/interoperable-descriptions-observable-property-terminology-wg-i-adopt-wg/wiki/i-adopt-0",
"name": "I-ADOPT Framework Ontology",
"prefix": "I-ADOPT",
"version": "1.0.3"
},
"I2SV": {
"description": "Terms used to describe research concepts, methods and processes for addressing complex societal and environmental problems, especially investigations involving integration across different disciplinary and stakeholder perspectives, as well as implementation of findings into policy and practice change. The terms were originally developed for the Integration and Implementation Insights blog (http://i2Insights.org).",
"homepage": "https://i2insights.org/index/integration-and-implementation-sciences-vocabulary/",
"name": "Integration and Implementation Sciences Vocabulary",
"prefix": "I2SV",
"version": "1.0.0"
},
"IAML-MOP": {
"description": "Instruments and/or voices, devices and other performers which make up a musical work.",
"name": "IAML Medium of Performance Vocabulary",
"prefix": "IAML-MOP"
},
"IAO": {
"description": "An ontology of information entities.",
"download_owl": "http://aber-owl.net/media/ontologies/IAO/11/iao.owl",
"homepage": "https://github.com/information-artifact-ontology/IAO/",
"name": "Information Artifact Ontology",
"prefix": "IAO"
},
"IBD": {
"description": "Indian Biodiversity Ontology contains the semantic information about the domain of Indian Biodiversity",
"download_owl": "http://aber-owl.net/media/ontologies/IBD/1/ibd.owl",
"name": "Indian Biodiversity Ontology",
"prefix": "IBD",
"version": "1.1"
},
"IBIO": {
"description": "Conceptualization of knowledge of Indian Biodiversity domain.",
"download_owl": "http://aber-owl.net/media/ontologies/IBIO/1/ibio.owl",
"name": "IndianBiodiversity",
"prefix": "IBIO"
},
"IBO": {
"name": "Imaging Biomarker Ontology",
"prefix": "IBO"
},
"ICD-O-3": {
"description": "Ontology used for oncology research derived from the European Cancer Information System (ECIS)",
"download_owl": "http://aber-owl.net/media/ontologies/ICD-O-3/5/icd-o-3.owl",
"homepage": "https://data.jrc.ec.europa.eu/dataset/88ff4ec5-1832-403e-abe1-64928592568f",
"name": "International Classification of Diseases for Oncology, 3rd edition",
"prefix": "ICD-O-3",
"version": "OCD-O Revision 3.2 (complete)"
},
"ICD-O-3-M": {
"description": "ICD-O-3-M International Classification of Diseases for Oncology, Morphology version: ICD-O-3.1 (2011)",
"download_owl": "http://aber-owl.net/media/ontologies/ICD-O-3-M/3/icd-o-3-m.owl",
"name": "ICD-O-3-M International Classification of Diseases for Oncology Morphology",
"prefix": "ICD-O-3-M",
"version": "1.0.0"
},
"ICD-O-3-T": {
"description": "International Classification of Diseases for Oncology - Topography",
"download_owl": "http://aber-owl.net/media/ontologies/ICD-O-3-T/2/icd-o-3-t.owl",
"name": "ICD-O-3-T International Classification of Diseases for Oncology Topography",
"prefix": "ICD-O-3-T",
"version": "1.0.0"
},
"ICD-O-3_MORPH": {
"description": "International Classification of Diseases for Oncology, 3rd revision, morphology",
"download_owl": "http://aber-owl.net/media/ontologies/ICD-O-3_MORPH/1/icd-o-3_morph.owl",
"name": "ICD-O-3 Morphology",
"prefix": "ICD-O-3_MORPH",
"version": "3.1"
},
"ICD10": {
"description": "International Statistical Classification of Diseases and Related Health Problems (ICD-10). 10th rev. Geneva",
"name": "International Classification of Diseases, Version 10",
"prefix": "ICD10",
"version": "2016AB"
},
"ICD10CM": {
"description": "International Classification of Diseases, 10th Edition, Clinical Modification, 2011_01",
"homepage": "http://www.cms.hhs.gov/",
"name": "International Classification of Diseases, Version 10 - Clinical Modification",
"prefix": "ICD10CM",
"version": "2016AB"
},
"ICD10PCS": {
"description": "ICD-10-PCS, 2009",
"homepage": "http://www.cms.hhs.gov",
"name": "International Classification of Diseases, Version 10 - Procedure Coding System",
"prefix": "ICD10PCS",
"version": "2016AB"
},
"ICD11-BODYSYSTEM": {
"description": "This is a set of body-system terms used in the ICD 11 revision",
"download_owl": "http://aber-owl.net/media/ontologies/ICD11-BODYSYSTEM/1/icd11-bodysystem.owl",
"name": "Body System Terms from ICD11",
"prefix": "ICD11-BODYSYSTEM",
"version": "1"
},
"ICD9CM": {
"description": "The ICD is the international standard diagnostic classification for all general epidemiological, many health management purposes and clinical use.",
"homepage": "http://www.cms.hhs.gov/",
"name": "International Classification of Diseases, Version 9 - Clinical Modification",
"prefix": "ICD9CM",
"version": "2016AB"
},
"ICD9CM-PROC": {
"description": "This view contains only the PROCEDURES sub-tree of the ICD9CM ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/ICD9CM-PROC/1/icd9cm-proc.owl",
"name": "ICD9CM Procedures",
"prefix": "ICD9CM-PROC",
"version": "1"
},
"ICDO": {
"description": "A biomedical ontology for logical representation of the terms and relations related to the International Classification of Diseases (ICD)",
"download_owl": "http://aber-owl.net/media/ontologies/ICDO/13/icdo.owl",
"homepage": "https://github.com/icdo/ICDO",
"name": "International Classification of Diseases Ontology",
"prefix": "ICDO",
"version": "1.0.83"
},
"ICECI": {
"description": "The International Classification of External Causes of Injury (ICECI) is a system of classifications to enable systematic description of how injuries occur. It is designed especially to assist injury prevention. The ICECI was originally designed for use in settings in which information is recorded in a way that allows statistical reporting--for example, injury surveillance based on collection of information about cases attending a sample of hospital emergency departments. It has also been found useful for other purposes. For example, it has been used as a reference classification during revision of another classification, to record risk-factor exposure of children in a cohort study, as the basis for special-purpose classifications and in a growing number of other ways.",
"download_owl": "http://aber-owl.net/media/ontologies/ICECI/6/iceci.owl",
"name": "International Classification of External Causes of Injuries",
"prefix": "ICECI",
"version": "Original Source: 1.2; OWL version 1.02"
},
"ICEO": {
"description": "ICEO is an integrated biological ontology for the description of bacterial integrative and conjugative elements (ICEs).",
"download_owl": "http://aber-owl.net/media/ontologies/ICEO/22/iceo.owl",
"homepage": "https://github.com/ontoice/ICEO",
"name": "Integrative and Conjugative Element Ontology",
"prefix": "ICEO"
},
"ICF": {
"description": "The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. These domains are classified from body, individual and societal perspectives by means of two lists: a list of body functions and structure, and a list of domains of activity and participation. Since an individual's functioning and disability occurs in a context, the ICF also includes a list of environmental factors.
Source: http://www.who.int/classifications/icf/en/",
"download_owl": "http://aber-owl.net/media/ontologies/ICF/3/icf.owl",
"homepage": "http://www.who.int/classifications/icf/en/",
"name": "International Classification of Functioning, Disability and Health",
"prefix": "ICF",
"version": "1.0.2"
},
"ICF-NOCM": {
"description": "This is a version of ICF OWL ontology that has the WHO-FIC \"content model\" entities stripped out. Definitions and labels were moved from content model individuals to entity annotations.",
"download_owl": "http://aber-owl.net/media/ontologies/ICF-NOCM/1/icf-nocm.owl",
"name": "ICF without content model",
"prefix": "ICF-NOCM",
"version": "1.0.2"
},
"ICF-NoCodeLabel": {
"description": "This view contains ICF 1.01 ontology with rdfs:label values that do not contain the codes",
"download_owl": "http://aber-owl.net/media/ontologies/ICF-NoCodeLabel/1/icf-nocodelabel.owl",
"name": "ICF with label-without-code",
"prefix": "ICF-NoCodeLabel",
"version": "unknown"
},
"ICF-d1": {
"description": "The \"ACTIVITIES AND PARTICIPATION CHAPTER 1: LEARNING AND APPLYING KNOWLEDGE\" (d1) sub-tree of the \"International Classification of Functioning, Disability and Health (ICF)\" ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/ICF-d1/1/icf-d1.owl",
"name": "ICF-d1. LEARNING AND APPLYING KNOWLEDGE",
"prefix": "ICF-d1",
"version": "1"
},
"ICF-d2": {
"description": "The \"ACTIVITIES AND PARTICIPATION CHAPTER 2: GENERAL TASKS AND DEMANDS\" (d2) sub-tree of the \"International Classification of Functioning, Disability and Health (ICF)\" ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/ICF-d2/1/icf-d2.owl",
"name": "ICF-d2. GENERAL TASKS AND DEMANDS",
"prefix": "ICF-d2",
"version": "1"
},
"ICF-d3": {
"description": "The \"ACTIVITIES AND PARTICIPATION CHAPTER 3: COMMUNICATION\" (d3) sub-tree of the \"International Classification of Functioning, Disability and Health (ICF)\" ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/ICF-d3/1/icf-d3.owl",
"name": "ICF-d3. COMMUNICATION",
"prefix": "ICF-d3",
"version": "1"
},
"ICF-d4": {
"description": "The \"ACTIVITIES AND PARTICIPATION CHAPTER 4: MOBILITY\" (d4) sub-tree of the \"International Classification of Functioning, Disability and Health (ICF)\" ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/ICF-d4/1/icf-d4.owl",
"name": "ICF-d4. MOBILITY",
"prefix": "ICF-d4",
"version": "1"
},
"ICF-d5": {
"description": "The \"ACTIVITIES AND PARTICIPATION CHAPTER 5: SELF-CARE\" (d5) sub-tree of the \"International Classification of Functioning, Disability and Health (ICF)\" ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/ICF-d5/1/icf-d5.owl",
"name": "ICF-d5. SELF-CARE",
"prefix": "ICF-d5",
"version": "1"
},
"ICF-d6": {
"description": "The \"ACTIVITIES AND PARTICIPATION CHAPTER 6: DOMESTIC LIFE\" (d6) sub-tree of the \"International Classification of Functioning, Disability and Health (ICF)\" ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/ICF-d6/1/icf-d6.owl",
"name": "ICF-d6. DOMESTIC LIFE",
"prefix": "ICF-d6",
"version": "1"
},
"ICF-d7": {
"description": "The \"ACTIVITIES AND PARTICIPATION CHAPTER 7: INTERPERSONAL INTERACTIONS AND RELATIONSHIPS\" (d7) sub-tree of the \"International Classification of Functioning, Disability and Health (ICF)\" ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/ICF-d7/1/icf-d7.owl",
"name": "ICF-d7. INTERPERSONAL INTERACTIONS AND RELATIONSHIPS",
"prefix": "ICF-d7",
"version": "1"
},
"ICF-d8": {
"description": "The \"ACTIVITIES AND PARTICIPATION CHAPTER 8: MAJOR LIFE AREAS\" (d8) sub-tree of the \"International Classification of Functioning, Disability and Health (ICF)\" ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/ICF-d8/1/icf-d8.owl",
"name": "ICF-d8. MAJOR LIFE AREAS",
"prefix": "ICF-d8",
"version": "1"
},
"ICF-d810-d839": {
"description": "The \"ACTIVITIES AND PARTICIPATION CHAPTER 8: MAJOR LIFE AREAS -> Education\" (d810-d839) sub-tree of the \"International Classification of Functioning, Disability and Health (ICF)\" ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/ICF-d810-d839/1/icf-d810-d839.owl",
"name": "ICF-d810-d839. Education",
"prefix": "ICF-d810-d839",
"version": "1"
},
"ICF-d840-d859": {
"description": "The \"ACTIVITIES AND PARTICIPATION CHAPTER 8: MAJOR LIFE AREAS -> Work and employment\" (d840-d859) sub-tree of the \"International Classification of Functioning, Disability and Health (ICF)\" ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/ICF-d840-d859/1/icf-d840-d859.owl",
"name": "ICF-d840-d859. Work and employment",
"prefix": "ICF-d840-d859",
"version": "1"
},
"ICF-d860-d879": {
"description": "The \"ACTIVITIES AND PARTICIPATION CHAPTER 8: MAJOR LIFE AREAS -> Economic life\" (d860-d879) sub-tree of the \"International Classification of Functioning, Disability and Health (ICF)\" ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/ICF-d860-d879/1/icf-d860-d879.owl",
"name": "ICF-d860-d879. Economic life",
"prefix": "ICF-d860-d879",
"version": "1"
},
"ICF-d9": {
"description": "The \"ACTIVITIES AND PARTICIPATION CHAPTER 9: COMMUNITY, SOCIAL AND CIVIC LIFE\" (d9) sub-tree of the \"International Classification of Functioning, Disability and Health (ICF)\" ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/ICF-d9/1/icf-d9.owl",
"name": "ICF-d9. COMMUNITY, SOCIAL AND CIVIC LIFE",
"prefix": "ICF-d9",
"version": "1"
},
"ICHOM-PROMS-PCB": {
"description": "The ICHOM Set of Patient-Centered Outcome Measures for Pregnancy And Childbirth is the result of hard work by a group of leading physicians, measurement experts and patients. It is a recommendation of the outcomes that matter most to persons experiencing Pregnancy And Childbirth.",
"name": "ICHOM Set Pregnancy and Childbirth",
"prefix": "ICHOM-PROMS-PCB"
},
"ICNP": {
"description": "International Classification for Nursing Practice",
"download_owl": "http://aber-owl.net/media/ontologies/ICNP/4/icnp.owl",
"homepage": "http://www.icn.ch/what-we-do/international-classification-for-nursing-practice-icnpr/",
"name": "International Classification for Nursing Practice",
"prefix": "ICNP",
"version": "2015"
},
"ICO": {
"description": "An ontology of clinical informed consents",
"download_owl": "http://aber-owl.net/media/ontologies/ICO/16/ico.owl",
"homepage": "https://github.com/ICO-ontology/ICO",
"name": "Informed Consent Ontology",
"prefix": "ICO"
},
"ICPC": {
"description": "The International Classification of Primary Care (ICPC). Denmark: World Organisation of Family Doctors, 1993.",
"name": "International Classification of Primary Care",
"prefix": "ICPC",
"version": "2016AB"
},
"ICPC2P": {
"description": "ICPC-2 PLUS",
"homepage": "http://www.fmrc.org.au/",
"name": "International Classification of Primary Care - 2 PLUS",
"prefix": "ICPC2P",
"version": "2016AB"
},
"ICPCFRE": {
"description": "ICPC, French Translation",
"name": "ICPC, French Translation",
"prefix": "ICPCFRE",
"version": "2016AB"
},
"ICPS": {
"description": "Ontology network about Patient Safety Incident. This work has been carried out by the Ontological Engineering Group, using sources from the University of Saint Etienne and the Australian Patient Safety Foundation, and supported by the World Health Organisation under the International Classification for Patient Safety programme.",
"download_owl": "http://aber-owl.net/media/ontologies/ICPS/7/icps.owl",
"homepage": "http://www.oeg-upm.net/",
"name": "International Classification for Patient Safety",
"prefix": "ICPS",
"version": "2.0"
},
"ICW": {
"description": "The International Classification of Wellness (ICW) is Wellness taxonomy. ICW provides a scheme for classifying Wellness events (activities) in which persons (users) can participate. ICW furthers the goals of preventative medicine and population health by supporting goal setting, quantifying user engagement in wellness activities, and correlating user engagement in wellness activities with health outcomes.",
"download_owl": "http://aber-owl.net/media/ontologies/ICW/4/icw.owl",
"name": "International Classification of Wellness",
"prefix": "ICW",
"version": "1.2"
},
"ID-AMR": {
"description": "Collections of terms for the ZonMW ID&AMR programme. These terms are based on vocabularies provided for describing project and data content metadata. This submission was created using sheet2rdf GitHub workflow.",
"homepage": "https://github.com/fair-data-collective/zonmw-id-amr-vocabulary",
"name": "Infectious Diseases and Antimicrobial Resistance",
"prefix": "ID-AMR",
"version": "1.2.1"
},
"IDCLOUDSEO": {
"name": "Idcloudseo",
"prefix": "IDCLOUDSEO"
},
"IDEM": {
"description": "Controlled vocabularies such as taxonomies allow an accurate and controlled approach in describing datasets. One of such controlled vocabulary is Wind Energy Taxonomy of Models. This taxonomy is the result of EERA JP WIND IRPWind Open Data initiative that took place in 2017 in which wind energy experts generated the first version of the taxonomy as an input for defining and structuring wind energy metadata. The report of this work is available at Zenodo: https://www.zenodo.org/record/1199489#.XSD6haeQ3RY In 2018, the taxonomy of topics was improved during the internal project of DTU Wind Energy titled 'FAIR Digitalization': https://www.zenodo.org/record/1493874#.XSD7TaeQ3RY In 2021, the taxonomy was converted into FAIR machine-actionable controlled vocabulary using sheet2rdf. The controlled vocabulary is served to humans and machines using an instace of OntoStack hosted by DTU Wind Energy. sheet2rdf and OntoStack are developed by FAIR Data Collective. Additionally, in 2021, the persistent URL purl.org/idem has been registered for the taxonomy. This allows us to: If there is a needed to move the taxonomy to another domain (currently under data.windenergy.dtu.dk) URLs will be still resolvable and unchanged Use short URls as PIDs for the taxonomy terms and properties.",
"homepage": "https://github.com/DTUWindEnergy/IDEM-taxonomy",
"name": "IDEM: wInD Energy Models Taxonomy",
"prefix": "IDEM",
"version": "v0.1.0"
},
"IDG_GL": {
"description": "List of genes studied under the IDG project",
"download_owl": "http://aber-owl.net/media/ontologies/IDG_GL/5/idg_gl.owl",
"name": "IDG gene list",
"prefix": "IDG_GL",
"version": "1.0"
},
"IDO": {
"download_owl": "http://aber-owl.net/media/ontologies/IDO/12/ido.owl",
"homepage": "http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology",
"name": "Infectious Disease Ontology",
"prefix": "IDO"
},
"IDO-COVID-19": {
"description": "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease.",
"download_owl": "http://aber-owl.net/media/ontologies/IDO-COVID-19/2/ido-covid-19.owl",
"homepage": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19",
"name": "The COVID-19 Infectious Disease Ontology",
"prefix": "IDO-COVID-19",
"version": "8-3-2020"
},
"IDOBRU": {
"description": "Brucellosis Ontology is a biomedical ontology in the domain of zoonotic disease brucellosis that is caused by Brucella, a facultative intracellular baterium.",
"download_owl": "http://aber-owl.net/media/ontologies/IDOBRU/61/idobru.owl",
"homepage": "http://www.phidias.us/bbp/idobru/index.php",
"name": "Brucellosis Ontology",
"prefix": "IDOBRU",
"version": "Arbor version; 1.2.92"
},
"IDODEN": {
"description": "An ontology for dengue fever.",
"download_owl": "http://aber-owl.net/media/ontologies/IDODEN/6/idoden.owl",
"homepage": "http://code.google.com/p/dengue-fever-ontology/",
"name": "Dengue Fever Ontology",
"prefix": "IDODEN",
"version": "0.15b"
},
"IDOMAL": {
"description": "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.",
"download_owl": "http://aber-owl.net/media/ontologies/IDOMAL/187/idomal.owl",
"homepage": "https://www.vectorbase.org/ontology-browser",
"name": "Malaria Ontology",
"prefix": "IDOMAL"
},
"IDQA": {
"description": "Image and Data Quality Assessment for scientific data management",
"download_obo": "http://aber-owl.net/media/ontologies/IDQA/8/idqa.obo",
"homepage": "http://idqa.wordpress.com",
"name": "Image and Data Quality Assessment Ontology",
"prefix": "IDQA",
"version": "v50"
},
"IFAR": {
"description": "An application ontology devoted to the standardized recording of data related to Fanconi Anemia (FA). This ontology was created using an OWL file provided by Dr. Ada Hamish (and Francois Schiettecatte) at the Centers for Mendelian Genetics, with their permission. Their original ontology can be found at: http://phenodb.net/help/features. Modifications were made using HPO, OMIM, NCI, and SNOMED. Novel classes pertaining to FA were added and defined as appropriate.",
"download_owl": "http://aber-owl.net/media/ontologies/IFAR/5/ifar.owl",
"homepage": "http://lab.rockefeller.edu/smogorzewska/ifar/",
"name": "Fanconi Anemia Ontology",
"prefix": "IFAR",
"version": "3"
},
"IGTO": {
"description": "The ontology introduced a novel integrative genetic testing resource called Genetic Testing Ontology (GTO). More specifically,GTO integrated multiple well-known genetic testing resources, including Genetic Testing Registry (GTR), ClinVar, and Human Phenotype Ontology (HPO) in Web Ontology Language (OWL). A meta-ontology has been designed to capture semantics and associations based on the nature of the selected data via Prot\u00e9g\u00e9. The GTO was built on top of the meta-ontology subsequently by populating specific genetic testing data. In addition, literature data from Semantic MEDLINE (SM) has been extracted and integrated in the GTO to provide scientific evidence accordingly.",
"download_owl": "http://aber-owl.net/media/ontologies/IGTO/2/igto.owl",
"homepage": "http://qianzhu-lab.umbc.edu/",
"name": "Scientific Evidence Based Genetic Testing Ontology",
"prefix": "IGTO"
},
"ILLNESSINJURY": {
"description": "This list of Illness and Injury (Morbidity and Mortality) classifications is an abbreviated version of the World Health Organization's (WHO) Startup Mortality List (ICD-10-SMoL). ICD-10-SMoL is the WHO's application of ICD-10 for low-resource settings initial cause of death collection. ICD-10-SMoL was chosen because it is a simplified version of the ICD-10. ICD (International Classification of Diseases) \"is the foundation for the identification of health trends and statistics globally, and the international standard for reporting diseases and health conditions. It is the diagnostic classification standard for all clinical and research purposes. ICD defines the universe of diseases, disorders, injuries and other related health conditions\" [http://www.who.int/classifications/icd/en/]. Version 1.0 of this ontology was compiled for the Canadian Writing Research Collaboratory (CWRC) ontology project and reflects the need to have causes of death and health issues organized in a way to allow for analysis of cultural data. A simplified list was deemed sufficient since the domain under study (cultural documents) will not have detailed medical information with regards to cause of death or health issues. But instead of accepting a list of general usage terms for causes of death or health issues that appear in some sources (e.g. Wikipedia, Wikidatak, etc.), a standardized, medical classification was selected so that it could be of use for future analysis regarding questions involving the intersection of health and culture. ICD-10-SMoL was chosen since it was the latest version of this list (June, 2018). A stable version of ICD-11 was to be available in June 2018 but there was no ICD-11-SMoL available at this time. To obtain the ICD10-SMoL: http://www.who.int/healthinfo/civil_registration/ICD_10_SMoL.pdf?ua=1",
"download_owl": "http://aber-owl.net/media/ontologies/ILLNESSINJURY/1/illnessinjury.owl",
"name": "Illness and Injury",
"prefix": "ILLNESSINJURY",
"version": "1.0"
},
"IMGT-ONTOLOGY": {
"description": "IMGT-ONTOLOGY is the first ontology for immunogenetics and immunoinformatics. It provides a semantic specification of the terms to be used in immunogenetics and immunoinformatics and manages the related knowledge, thus allowing the standardization for immunogenetics data from genome, proteome, genetics, two-dimensional (2D) and three-dimensional (3D) structures. IMGT-ONTOLOGY manages the knowledge through diverse facets relying on seven axioms, \"IDENTIFICATION\", \"CLASSIFICATION\", \"DESCRIPTION\", \"NUMEROTATION\", \"LOCALIZATION\", \"ORIENTATION\" and \"OBTENTION\". These axioms postulate that any object, any process and any relation can be identified, classified, described, numbered, localized and orientated, and the way it is obtained can be characterized. The axioms constitute the Formal IMGT-ONTOLOGY, also designated as IMGT-Kaleidoscope. As the same axioms can be used to generate concepts for multi-scale level approaches, the Formal IMGT-ONTOLOGY represents a paradigm for system biology ontologies, which need to identify, to classify, to describe, to number, to localize and to orientate objects, processes and relations at the molecule, cell, tissue, organ, organism or population levels. IMGT\u00ae, the international ImMunoGeneTics information system\u00ae, has been built on IMGT-ONTOLOGY. The version 1.0.2 of IMGT-ONTOLOGY includes the concepts of IDENTIFICATION and the concepts of CLASSIFICATION.",
"download_owl": "http://aber-owl.net/media/ontologies/IMGT-ONTOLOGY/4/imgt-ontology.owl",
"homepage": "http://www.imgt.org/",
"name": "Immunogenetics Ontology",
"prefix": "IMGT-ONTOLOGY",
"version": "1.0.2"
},
"IMMDIS": {
"description": "The Immune Disorder Ontology was generated as part of the Bioinformatics Integration Support Contract (BISC) funded by the Division of Allergy, Immunology and Transplantation (DAIT) within NIAID. The ontology is based on the National Library of Medicine (NLM) Medical Subject Headings; National Cancer Institute Thesaurus; International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM); ICD-10; and other open source public databases.
Lineage(s)
A class may be related to its superclass through a true is_a relationship (e.g., Polymyositis is a Dermatomyositis, which is an Autoimmune_Disease, which is an Immune_Disorder). Based on description logic, a class inherits all the Relationships (Object Properties) and Datatype Properties (if any) assigned to its superclass. In a few occasions, a class may have more than one superclass and belongs to more than one lineage.
Annotations
Specific information may be available about a class, including Preferred_Name, DEFINITION, Synonym, etc. The following provides more detail on annotation information presented:
DEFINITION: A human-readable definition is provided for each class in the ontology and the displayed format is Owner|Definition (Source).
FULL_SYN: Synonym of a class in the ontology with type (PT: preferred term, SY: synonym) and source of this synonym indicated. Synonym|Type of Synonym|Source of Synonym is the format displayed.
ICD-10_Code: Code of International Classification of Diseases and Related Health Problems, 10th revision. ICD-10 is a detailed description of known diseases and injuries. It is published by the World Health Organization (WHO) and is used worldwide for mortality statistics.
ICD-9_Code: Code of International Classification of Diseases and Related Health Problems, 9th revision.
Class Name: Class_Name is used as a unique identifier by Protege-OWL, the environment where this ontology is being developed and therefore has to be OWL-compliant. Class_Name is composed of a string only made of digits, letters, underscores, and hyphens. A Class_Name cannot start with a digit.
Preferred_Name: A human-friendly and commonly used name in plain English.
Synonym: Synonym of a class in plain English, including those in plural form or British spelling. In contrast to FULL_SYN, no type nor source of synonym is indicated. Synonym is human-friendly and not OWL-compliant. A class may have multiple synonyms.
UMLS_CUI: Concept Unique Identifier in Unified Medical Language System that is produced and distributed by NLM. There are three UMLS Knowledge Sources: the Metathesaurus, the Semantic Network, and SPECIALIST Lexicon. The purpose of UMLS is to facilitate the development of computer systems that behave as if they \"understand\" the meaning of the language of biomedicine and health.
Relationships (Object Properties)
Relationships are properties by which one class is related to another class in the ontology. For example, \"Population_Group\" (a class) has_susceptibility_to_disease (a relationship) \"Immune_Disorder\" (a class). This box may be empty if no relationship has been used for modeling.
Datatype Properties
Datatype Properties are properties by which a class is related to a datatype. This box may be empty if no datatype property has been used for modeling.",
"download_obo": "http://aber-owl.net/media/ontologies/IMMDIS/1/immdis.obo",
"name": "Immune Disorder Ontology",
"prefix": "IMMDIS",
"version": "unknown"
},
"IMOBO": {
"description": "Intelligent Medicine oriented Biobank Ontology (IMOBO) is an ontology developed to facilitate the annotation and modeling of biobank repositories, metadata, and biobanking administration, supporting the paradigm shift towards AI in medicine. IMOBO focuses on AI modeling in both clinical applications and healthcare, with a specific emphasis on engaging clinical doctors and patients in data collection. Its goal is to structure knowledge for the future patient-centered medical paradigm. As measurement technologies and medical artificial intelligence continue to evolve, IMOBO will continually enhance its content and structure.",
"download_owl": "http://aber-owl.net/media/ontologies/IMOBO/1/imobo.owl",
"name": "Intelligent Medicine oriented Biobank Ontology",
"prefix": "IMOBO",
"version": "0.1"
},
"INBANCIDO": {
"name": "Assessment of Indian Economy During Covid-19 ",
"prefix": "INBANCIDO"
},
"INBIO": {
"description": "The Invasion Biology Ontology (INBIO) contains terms and concepts relevant in the field of invasion biology, which is a research area dealing with the translocation, establishment, spread, impact and management of species outside of their native ranges, where they are called non-native or alien species. This first version of the ontology covers terms and concepts needed to describe twelve major invasion hypotheses building the hierarchical hypothesis network (see also Jeschke JM, Heger T (Eds) (2018) Invasion Biology: Hypotheses and Evidence. CABI, Wallingford, UK).",
"download_owl": "http://aber-owl.net/media/ontologies/INBIO/2/inbio.owl",
"name": "Invasion Biology Ontology",
"prefix": "INBIO",
"version": "1.1"
},
"INBIODIV": {
"description": "InBiodiv-O: An Ontology for Indian Biodiversity Knowledge Management",
"download_owl": "http://aber-owl.net/media/ontologies/INBIODIV/1/inbiodiv.owl",
"name": "An Ontology for Indian Biodiversity Knowledge Management",
"prefix": "INBIODIV",
"version": "1.1"
},
"INCENTIVE": {
"description": "DEMO vocabulary only! Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is INCENTIVE Controlled Vocabulary. This controlled vocabulary is a result of Metadata 4 Machine (M4M) Workshop 18 and 22 (M4M.18 and M4M.22) provided to the INCENTIVE community. sheet2rdf and OntoStack are used to build and serve INCENTIVE Controlled Vocabulary, while PURL is used to persist identifiers for the vocabulary terms.",
"homepage": "https://raw.githubusercontent.com/gofair-foundation/vocabs_archive/main/M4M22.ttl",
"name": "INCENTIVE Community Controlled Vocabulary",
"prefix": "INCENTIVE",
"version": "0.1.3"
},
"INCENTIVE-VARS": {
"description": "Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is INCENTIVE Variables. This controlled vocabulary is a result of Metadata 4 Machine (M4M) Workshop 18 (M4M.18) provided to the INCENTIVE community (https://zenodo.org/communities/incentive/about/). sheet2rdf and OntoStack, developed by FAIR Data Collective, are used to build and serve INCENTIVE Variable, while PURL is used to persist identifiers for the vocabulary terms and properties: http://purl.org/incentive/variables/",
"homepage": "https://github.com/fair-data-collective/M4M18-vocabulary",
"name": "INCENTIVE Variables",
"prefix": "INCENTIVE-VARS",
"version": "0.1.0"
},
"INFECTION_TRANS": {
"description": "The Infection Transmission Ontology is developed in order to make transmission data reusable and interoperable. The ontology captures every step of analysing data from the transmission process, especially for quantification of trans- mission parameters. It is applicable to animal and human (hospital) data from both experimental and observational stud- ies. The lack of a common terminology in the infection transmission experiments leads to repetition of costly experiments. By developing a domain ontology we can reuse and combine the transmission data, which leads to the improvement of an estimation of transmission parameters and prediction of outcomes of yet unobserved situations.",
"download_owl": "http://aber-owl.net/media/ontologies/INFECTION_TRANS/2/infection_trans.owl",
"homepage": "https://raw.githubusercontent.com/UtrechtUniversity/summer-fair/master/src/create_ontology/map_ontology/infection_trans.owl#",
"name": "Infection Transmission Ontology",
"prefix": "INFECTION_TRANS",
"version": "1.0.2"
},
"INFRA-EN": {
"name": "Infrastructure",
"prefix": "INFRA-EN"
},
"INFRARISK": {
"description": "The InfraRisk Ontology: Enabling Semantic Interoperability for Critical Infrastructures at Risk from Natural Hazards. This InfraRisk ontology may be used for representing relevant information about natural hazard events and their impact on infrastructure components. Earthquakes, landslides, and other natural hazard events have severe negative socio-economic impacts.",
"download_owl": "http://aber-owl.net/media/ontologies/INFRARISK/1/infrarisk.owl",
"homepage": "https://www.infrarisk-fp7.eu",
"name": "InfraRisk Ontology",
"prefix": "INFRARISK",
"version": "1.0"
},
"INJURYTYPES": {
"description": "This class is associated with the different injury types.",
"name": "Injury Types",
"prefix": "INJURYTYPES"
},
"INM-NPI": {
"description": "Interventionnelle Non M\u00e9dicamenteuse, Non-Pharmacological Interventions",
"download_owl": "http://aber-owl.net/media/ontologies/INM-NPI/3/inm-npi.owl",
"homepage": "http://www.cepsplatform.eu",
"name": "Interventionnelle Non M\u00e9dicamenteuse (INM)",
"prefix": "INM-NPI",
"version": "2.0"
},
"INO": {
"description": "An ontology of interactions and interaction networks",
"download_owl": "http://aber-owl.net/media/ontologies/INO/32/ino.owl",
"homepage": "https://github.com/INO-ontology/ino",
"name": "Interaction Network Ontology",
"prefix": "INO"
},
"INSECTH": {
"description": "NeuroMorpho.Org insect brain regions ontology is compiled to create data annotation standard for depositing insect data. Currently at v6.2, NeuroMorpho.Org hosts over 17k neuronal reconstructions mostly from the fly. The insect ontology follows the standard nomenclature of the insect brain (Ito et al., 2013) and the virtualfly.org.",
"download_owl": "http://aber-owl.net/media/ontologies/INSECTH/4/insecth.owl",
"name": "insectH",
"prefix": "INSECTH",
"version": "0.1"
},
"INSNAME": {
"description": "This is the list of facilities participating in FAIRification of data.",
"name": "VODANAINSNAMES",
"prefix": "INSNAME",
"version": "5"
},
"INTO": {
"description": "Creating the largest comprehensive knowledge base of terrorism and related activities, people and agencies involved, and extremist movements; and providing a platform to the society, the government, and the military personnel in order to combat the evolving threat of the global menace of terrorism.",
"download_owl": "http://aber-owl.net/media/ontologies/INTO/1/into.owl",
"name": "Indian Terrorism Ontology",
"prefix": "INTO",
"version": "1.1"
},
"INTVEETYPE": {
"description": "This class refers to the different types of Interviewees.",
"name": "Interviewee Type",
"prefix": "INTVEETYPE"
},
"INTVMODE": {
"description": "This class refers to the different modes of Interview",
"name": "Interview Mode",
"prefix": "INTVMODE"
},
"INVERSEROLES": {
"description": "ISO inverse roles ontology for oil and gas",
"download_owl": "http://aber-owl.net/media/ontologies/INVERSEROLES/1/inverseroles.owl",
"name": "ISO-15926-2_2003_inverseRoles",
"prefix": "INVERSEROLES",
"version": "Generated 2008-09-03T19:12:44.687+02:00"
},
"IOBC": {
"description": "Interlinking Ontology for Biological Concepts (IOBC) contains approximately 80,000 biological concepts such as biological phenomena, diseases, molecular functions, gene products, chemicals, and medical cares, and approximately 20,000 related concepts such as earth science and environmental science. The concepts are structured by thirty-five relations such as has function, has role, has quality, and precedes. Each concept has both of English and Japanese labels. For further information including the developmental method, see papers in the PUBLICATIONS PAGE. The license for this ontology is specified in the Creative Commons Attribution-NonCommercial 4.0 International. If you use data from this ontology, please be sure attribute this ontology as follows: \"Interlinking Ontology for Biological Concepts \u00a9 National Bioscience Database Center licensed under CC Attribution-NonCommercial 4.0 International\".",
"download_owl": "http://aber-owl.net/media/ontologies/IOBC/25/iobc.owl",
"homepage": "https://github.com/kushidat/IOBC",
"name": "Interlinking Ontology for Biological Concepts",
"prefix": "IOBC",
"version": "version 1.6.0"
},
"IPD": {
"description": "IPD-Onto divides product injury into five unified classes (host, vector, agent, environment, and consequences) and constructs the accident process through the object properties (lead to, touch, accident, etc.)IPD-Onto is used to realise the transformation and reorganisation from product injury to injury information, to reproduce the process of accident occurrence, and realise human-computer interactions to meet the needs of data query.",
"download_owl": "http://aber-owl.net/media/ontologies/IPD/2/ipd.owl",
"name": "injury process description ontology",
"prefix": "IPD",
"version": "1.0"
},
"IRD": {
"description": "Inherited retinal dystrophy (IRD) as one of the rare ocular diseases encompasses different types of hereditary retinal degenerations appearing by involvement of the different layers of the posterior ocular segment. In respect of the importance of the classification systems regarding the recorded history of biologic and natural sciences, there is no classification regarding the IRD diagnoses. Therefore, a novel classification for this type of hereditary ocular disease was developed and presented.",
"download_owl": "http://aber-owl.net/media/ontologies/IRD/1/ird.owl",
"name": "Inherited Retinal Dystrophies",
"prefix": "IRD"
},
"IRD1": {
"description": "Inherited retinal dystrophy (IRD) as one of the rare ocular diseases encompasses different types of hereditary retinal degenerations appearing by involvement of the different layers of the posterior ocular segment. In respect of the importance of the classification systems regarding the recorded history of biologic and natural sciences, there is no classification regarding the IRD diagnoses. Therefore, a novel classification for this type of hereditary ocular disease was developed and presented.",
"download_owl": "http://aber-owl.net/media/ontologies/IRD1/1/ird1.owl",
"name": "Inherited retinal disorders",
"prefix": "IRD1",
"version": "1"
},
"IRD2": {
"description": "Inherited retinal dystrophy (IRD) as one of the rare ocular diseases encompasses different types of hereditary retinal degenerations appearing by involvement of the different layers of the posterior ocular segment. In respect of the importance of the classification systems regarding the recorded history of biologic and natural sciences, there is no classification regarding the IRD diagnoses. Therefore, a novel classification for this type of hereditary ocular disease was developed and presented.",
"download_owl": "http://aber-owl.net/media/ontologies/IRD2/1/ird2.owl",
"name": "Inherited retinal disorders 2",
"prefix": "IRD2",
"version": "2"
},
"IRD3": {
"description": "nherited retinal dystrophy (IRD) as one of the rare ocular diseases encompasses different types of hereditary retinal degenerations appearing by involvement of the different layers of the posterior ocular segment. In respect of the importance of the classification systems regarding the recorded history of biologic and natural sciences, there is no classification regarding the IRD diagnoses. Therefore, a novel classification for this type of hereditary ocular disease was developed and presented.",
"download_owl": "http://aber-owl.net/media/ontologies/IRD3/1/ird3.owl",
"name": "Inherited retinal dystrophy",
"prefix": "IRD3",
"version": "3"
},
"IRDG": {
"description": "Ontology used to describe the data system in harmonized surveillance system of malaria between french Guiana and Brazil. Developed by the IRD and the Fiocruz.",
"download_owl": "http://aber-owl.net/media/ontologies/IRDG/1/irdg.owl",
"name": "Data harmonization ontology for cross border malaria surveillance ",
"prefix": "IRDG"
},
"ISO-15926-2_2003": {
"description": "This ontology describes gas and oil field process level descriptions",
"download_owl": "http://aber-owl.net/media/ontologies/ISO-15926-2_2003/1/iso-15926-2_2003.owl",
"name": "ISO-15926-2_2003_oil",
"prefix": "ISO-15926-2_2003",
"version": "Generated 2008-02-21T17:29:19.558+01:00"
},
"ISO-ANNOTATIONS": {
"description": "Oil and Gas Annotations",
"download_owl": "http://aber-owl.net/media/ontologies/ISO-ANNOTATIONS/1/iso-annotations.owl",
"name": "ISO-15926-2_2003_annotations",
"prefix": "ISO-ANNOTATIONS"
},
"ISO-FOOD": {
"description": "To link and harmonize different knowledge repositories with respect to isotopic data, we propose an ISO-FOOD ontology as a domain ontology for describing isotopic data within Food Science. The ISO-FOOD ontology consists of metadata and provenance data that needs to be stored together with data elements in order to describe isotopic measurements with all necessary information required for future analysis. The new domain has been linked with existing ontologies, such as Units of Measurements Ontology, Food, Nutrient and the Bibliographic Ontology. So linked ontology consists of several superclasses, and for each of these the relevant subclasses, object properties and data properties are defined. To show how such an ontology can be used in practice, it was populated with 20 isotopic measurements of Slovenian food samples. Describing data in this way offers a powerful technique for organizing and sharing stable isotope data across Food Science.",
"download_owl": "http://aber-owl.net/media/ontologies/ISO-FOOD/1/iso-food.owl",
"homepage": "http://cs.ijs.si/repository/ISO-FOOD/ISO-FOOD_Ontology.zip",
"name": "A formal representation of the knowledge within the domain of Isotopes for Food Science",
"prefix": "ISO-FOOD"
},
"ISO19108TO": {
"description": "ISO 19108 Temporal Objects",
"download_owl": "http://aber-owl.net/media/ontologies/ISO19108TO/2/iso19108to.owl",
"name": "ISO 19108 Temporal Objects",
"prefix": "ISO19108TO",
"version": "2006-10-15"
},
"ISO19110": {
"description": "ISO 19110:2005 Methodology for feature cataloguing",
"download_owl": "http://aber-owl.net/media/ontologies/ISO19110/1/iso19110.owl",
"name": "ISO 19110 Methodology for Feature Cataloguing",
"prefix": "ISO19110",
"version": "2005-02-15"
},
"ISO19115": {
"description": "ISO19115:2003",
"download_owl": "http://aber-owl.net/media/ontologies/ISO19115/2/iso19115.owl",
"name": "ISO 19115",
"prefix": "ISO19115",
"version": "2014"
},
"ISO19115CC": {
"description": "ISO 19115 Common Classes",
"download_owl": "http://aber-owl.net/media/ontologies/ISO19115CC/2/iso19115cc.owl",
"name": "ISO 19115 Common Classes",
"prefix": "ISO19115CC",
"version": "2014"
},
"ISO19115CI": {
"description": "Citation and responsible part ontology",
"download_owl": "http://aber-owl.net/media/ontologies/ISO19115CI/3/iso19115ci.owl",
"name": "ISO 19115 Citation Information",
"prefix": "ISO19115CI",
"version": "2014"
},
"ISO19115CON": {
"name": "ISO 19115 Constraints Information",
"prefix": "ISO19115CON"
},
"ISO19115DI": {
"description": "ISO 19115 Distribution Information",
"download_owl": "http://aber-owl.net/media/ontologies/ISO19115DI/2/iso19115di.owl",
"name": "ISO 19115 Distribution Information",
"prefix": "ISO19115DI",
"version": "2014"
},
"ISO19115DTC": {
"description": "ISO 19115 Date Type Codes",
"download_owl": "http://aber-owl.net/media/ontologies/ISO19115DTC/1/iso19115dtc.owl",
"name": "ISO 19115 Date Type Code",
"prefix": "ISO19115DTC",
"version": "2.0"
},
"ISO19115EX": {
"description": "ISO 19115 Extent Information",
"download_owl": "http://aber-owl.net/media/ontologies/ISO19115EX/28/iso19115ex.owl",
"name": "ISO 19115 Extent Information",
"prefix": "ISO19115EX",
"version": "2014"
},
"ISO19115ID": {
"description": "ISO 19115-1:2014 Identification Information Section for describing Geospatial Datasets",
"download_owl": "http://aber-owl.net/media/ontologies/ISO19115ID/2/iso19115id.owl",
"name": "ISO 19115 Identification Information",
"prefix": "ISO19115ID",
"version": "2006-07-01"
},
"ISO19115MI": {
"description": "ISO 19115 Metadata Information section",
"download_owl": "http://aber-owl.net/media/ontologies/ISO19115MI/136/iso19115mi.owl",
"name": "ISO 19115 Metadata Information",
"prefix": "ISO19115MI",
"version": "2014"
},
"ISO19115PR": {
"name": "ISO 19115 Codelists",
"prefix": "ISO19115PR"
},
"ISO19115ROLES": {
"description": "Role Codes for use in ISO 19115-1:2014 metadata",
"name": "ISO 19115 Role Codes",
"prefix": "ISO19115ROLES",
"version": "2.0"
},
"ISO19115SRS": {
"description": "ISO 19115 Spatial reference systems",
"download_owl": "http://aber-owl.net/media/ontologies/ISO19115SRS/3/iso19115srs.owl",
"name": "ISO 19115 Reference Systems",
"prefix": "ISO19115SRS",
"version": "2014"
},
"ISO19115TCC": {
"description": "ISO 19115 Topic Category Codes",
"download_owl": "http://aber-owl.net/media/ontologies/ISO19115TCC/10/iso19115tcc.owl",
"name": "ISO 19115 Topic Categories",
"prefix": "ISO19115TCC",
"version": "Created with TopBraid Composer"
},
"ISO639-1": {
"description": "Language codes from ISO 639-1, as expressed in https://www.w3schools.com/tags/ref_language_codes.asp and converted to SKOS using http://labs.sparna.fr/skos-play/convert.",
"name": "ISO 639-1: Codes for the Representation of Names of Languages - Part 1: Two-letter codes for languages",
"prefix": "ISO639-1",
"version": "1.0.0"
},
"ISO639-2": {
"description": "ISO 639-2 is part of the ISO 639 language code family, which provides also a two-character code set (ISO 639-1) for the representation of names of languages. ISO 639-2 contains codes for all languages contained in ISO 639-1 and several hundred additional languages. The ISO 639-2 (Bibliographic) codes were devised for use in bibliographic metadata, e.g., for libraries, information services, and publishers, and ISO 639-2 (Terminology) targets terminology, lexicography, and linguistic applications. The lists are the same except for 20 languages that have different Bibliographic and Terminology codes. The list contains over 500 discrete codes.",
"download_owl": "http://aber-owl.net/media/ontologies/ISO639-2/3/iso639-2.owl",
"homepage": "http://id.loc.gov/vocabulary/iso639-2.html",
"name": "ISO 639-2: Codes for the Representation of Names of Languages",
"prefix": "ISO639-2"
},
"ISPO": {
"description": "ISPO delivers an integrated controlled vocabulary for symptom phenotypes, with both clinical and biomedical literature synonyms in Chinese and English languages, it would enhance the semantic interoperability among heterogeneous medical data sources and clinical decision support systems. Furthermore, symptom ontology would propose a standard vocabulary for teasing the symptom-gene associations and thus become a vital requirement for symptom science and TCM biological discovery.",
"download_owl": "http://aber-owl.net/media/ontologies/ISPO/1/ispo.owl",
"homepage": "http://www.tcmkg.com/",
"name": "Integrated Ontology for Symptom Phenotype Terminologies",
"prefix": "ISPO",
"version": "2023V1"
},
"ISSVA": {
"description": "The International Society for the Study of Vascular Anomalies (ISSVA) is a multidisciplinary international society of physicians, scientists, and health care providers united by an interest in vascular anomalies. The Society aims to promote the highest standards of care for patients with vascular anomalies by advancing clinical and scientific knowledge concerning causes, diagnosis and treatment, and by education of physicians, health care providers, patients and the community. The Society encourages the free flow of information between its members and interested groups, through workshop meetings and teaching programs, and by the dissemination of a classification scheme and pertinent scientific data. The updated classification was approved at the May, 2018 General Assembly in Amsterdam, the Netherlands and can be found at https://www.issva.org/classification. What is the ISSVA Ontology? The ISSVA ontology has been created to represent a sharable semantic data model of the ISSVA classification. This ontological representation of the ISSVA classification is machine-readable and facilitates interoperability between systems that capture data about vascular anomalies. It is structured hierarchically and contains all concepts of the ISSVA classification and the relationships between them. The ontology is available in the Web Ontology Language (OWL) format, and can be browsed and downloaded online: https://bioportal.bioontology.org/ontologies/ISSVA How to Use the ISSVA Ontology? The ISSVA ontology does not substitute the ISSVA classification, instead, it should be used as an additional component to facilitate interoperability. Every concept in the ISSVA ontology has a unique code that should be attached to the corresponding data element. In the context of databases, the ISSVA ontology codes could be added as an extra column to the existing data. Mappings to Other Ontologies? The ISSVA ontology contains machine-readable mappings to equivalent concepts in other ontologies, namely: the Orphanet Rare Disease Ontology (ORDO), SNOMED Clinical Terms (SNOMED CT), National Cancer Institute thesaurus (NCIT), and the Human Phenotype Ontology (HPO). This means that data annotated with codes from the ISSVA ontology are interoperable with data annotated with the aforementioned ontologies, without any extra effort, as long as there exists a mapping between the concepts. Issue Reporting Please contact ISSVA at info@issva.org in case you have any issues and/or feature requests for the ISSVA ontology. The ontology can then be updated accordingly.",
"download_owl": "http://aber-owl.net/media/ontologies/ISSVA/5/issva.owl",
"homepage": "https://www.issva.org",
"name": "International Society for the Study of Vascular Anomalies (ISSVA) Ontology",
"prefix": "ISSVA",
"version": "1.1.3"
},
"ITEMAS": {
"description": "The defined ontology is focused on addressing medical innovation technology in public healthcare institutions. This ontology is currently only in Spanish language. It has been developed the Platform for Innovation Medical and Health Technology (ITEMAS) a network composed by 67 Spanish healthcare organizations (including hospitals, healthcare centers, Ministry of Health, Social Services and Equality and more than 100 organizations focused on medical technology innovation. The ITEMAS Platform has been by Carlos III National Health Institute (PT13/0006/0036), both co-funded by FEDER from European Regional Development Funds (European Union).",
"download_owl": "http://aber-owl.net/media/ontologies/ITEMAS/1/itemas.owl",
"homepage": "www.itemas.org",
"name": "Medical Technology Innovation in healthcare centers",
"prefix": "ITEMAS",
"version": "1.1."
},
"ITO": {
"description": "The Intelligence Task Ontology and Knowledge Graph (ITO) provides a comprehensive, curated model of artificial intelligence tasks, benchmarks and benchmark results, including the biomedical domain. NOTE: The version uploaded to BioPortal has all instances and benchmark data removed because of performance issues with the BioPortal class browser. Please refer to https://github.com/OpenBioLink/ITO/ for downloading the full version of the ontology and dataset.",
"download_owl": "http://aber-owl.net/media/ontologies/ITO/17/ito.owl",
"homepage": "https://github.com/OpenBioLink/ITO/",
"name": "Intelligence Task Ontology",
"prefix": "ITO",
"version": "1.12 (PWC export dated 2022-07-30) - internal, just a minor fix"
},
"IXNO": {
"description": "The Interaction ontology (IxnO) was developed to enable curation of chemical-gene and chemical-protein interactions for the Comparative Toxicogenomics Database (CTD). CTD is a freely available resource that aims to promote understanding and novel hypothesis development about the effects of the environment on human health.",
"download_obo": "http://aber-owl.net/media/ontologies/IXNO/2/ixno.obo",
"homepage": "http://ctd.mdibl.org",
"name": "Interaction Ontology",
"prefix": "IXNO",
"version": "1"
},
"InterNano": {
"description": "The InterNano Taxonomy is a unique, custom-built terminology to describe the nanomanufacturing enterprise. This project is supported by the National Science Foundation CMMI-1025020",
"download_owl": "http://aber-owl.net/media/ontologies/InterNano/138/internano.owl",
"homepage": "http://internano.org",
"name": "InterNano Nanomanufacturing Taxonomy",
"prefix": "InterNano",
"version": "1.4"
},
"JERM": {
"description": "The JERM ontology is an application ontology that describes the relationships between the data, models and other research assets that can be shared through the FAIRDOM platform, for sharing Systems and Synthetic Biology experiments. JERM 2 includes a new model for describing Biosamples, developed during the ELIXIR-lead Biosamples club",
"download_owl": "http://aber-owl.net/media/ontologies/JERM/15/jerm.owl",
"homepage": "https://fair-dom.org/",
"name": "Just Enough Results Model Ontology",
"prefix": "JERM",
"version": "2"
},
"KENYAANC": {
"description": "Ontology on kenyan ANC terms.",
"download_owl": "http://aber-owl.net/media/ontologies/KENYAANC/1/kenyaanc.owl",
"name": "kenyaancfile",
"prefix": "KENYAANC",
"version": "1"
},
"KERIS99SAKONG": {
"name": "keris99-agen-sakong-online-capsa-susun-bandarpoker-judi-domino99-bandarq-aduq",
"prefix": "KERIS99SAKONG"
},
"KETO": {
"name": "Kerala Tourism Ontology",
"prefix": "KETO"
},
"KGCL": {
"description": "Knowledge Graph Change Language ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/KGCL/6/kgcl.owl",
"homepage": "https://github.com/INCATools/kgcl",
"name": "Knowledge Graph Change Language",
"prefix": "KGCL",
"version": "0.1.0"
},
"KIOSASLIQQ": {
"name": "belalang",
"prefix": "KIOSASLIQQ"
},
"KISAO": {
"description": "A classification of algorithms for simulating biology and their outputs",
"download_owl": "http://aber-owl.net/media/ontologies/KISAO/36/kisao.owl",
"homepage": "http://co.mbine.org/standards/kisao",
"name": "Kinetic Simulation Algorithm Ontology",
"prefix": "KISAO"
},
"KONTES": {
"name": "kontes seo",
"prefix": "KONTES"
},
"KORO": {
"description": "An ontology to define the parts of a Knowledge Object and their relations built using the Basic Formal Ontology and Information Artifact Ontology",
"download_owl": "http://aber-owl.net/media/ontologies/KORO/2/koro.owl",
"name": "Knowledge Object Reference Ontology",
"prefix": "KORO",
"version": "1.1"
},
"KTAO": {
"description": "The Kidney Tissue Atlas Ontology (KTAO) is an ontology that integrates kidney-related cell types, cell states, locations, gene markers, disease, etc., and their relations. KTAO is developed to support the NIH-NIDDK-funed Kidney Precision Medicine Project (KPMP).",
"download_owl": "http://aber-owl.net/media/ontologies/KTAO/20/ktao.owl",
"homepage": "https://github.com/KPMP/KTAO",
"name": "Kidney Tissue Atlas Ontology",
"prefix": "KTAO",
"version": "Vision Release: 1.0.121"
},
"LABO": {
"description": "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents.",
"download_owl": "http://aber-owl.net/media/ontologies/LABO/3/labo.owl",
"homepage": "https://github.com/OpenLHS/LABO",
"name": "clinical LABoratory Ontology",
"prefix": "LABO"
},
"LAND-SURFACE": {
"description": "Machine-readable representation of the classifiers described in chapter 7 Land Surface, by R.C. McDonald, R.F. Isbell and J.G. Speight, in Australian soil and land survey field handbook (3rd edn). Land surface is concerned mainly with surface phenomena affecting land use and soil development that have traditionally been noted at the point of soil observation.",
"name": "Land Surface classifiers",
"prefix": "LAND-SURFACE",
"version": "3rd Edition"
},
"LANDFORM": {
"description": "Machine-readable representation of the classifiers described in chapter 5 Landform, by J.G. Speight, in Australian soil and land survey field handbook (3rd edn). In this technique for describing landforms, the whole land surface is viewed as a mosaic of tiles of odd shapes and sizes. The scheme is intended to produce a record of observations rather than inferences. The data was converted from the print representation to this linked-data form by Linda Gregory assisted by Simon J D Cox.",
"name": "Landform classifiers",
"prefix": "LANDFORM",
"version": "3rd edition"
},
"LATESTGOVTJOBS": {
"name": "Latest Govt Jobs",
"prefix": "LATESTGOVTJOBS"
},
"LBO": {
"description": "A vocabulary for buffalo, cattle, chicken, goat, horse, pig, and sheep breeds.",
"download_obo": "http://aber-owl.net/media/ontologies/LBO/9/lbo.obo",
"name": "Livestock Breed Ontology",
"prefix": "LBO",
"version": "2.2"
},
"LC-CARRIERS": {
"description": "Carriers Scheme is derived from a controlled list of values representing the format of the storage medium and its media type, which is principally used in RDA cataloging.",
"homepage": "http://id.loc.gov/vocabulary/carriers.html",
"name": "Library of Congress Carriers Scheme",
"prefix": "LC-CARRIERS"
},
"LC-CONTENT": {
"homepage": "http://id.loc.gov/vocabulary/contentTypes.html",
"name": "Library of Congress Content Types Scheme",
"prefix": "LC-CONTENT"
},
"LC-MEDIA": {
"description": "Media Types Scheme is derived from a controlled list of values reflecting the general type of intermediation device required to view, play, run, etc., the content of a resource, which is principally used in RDA cataloging.",
"homepage": "http://id.loc.gov/vocabulary/mediaTypes.html",
"name": "Library of Congress Media Types Scheme",
"prefix": "LC-MEDIA"
},
"LC-SUBJSCHEMES": {
"description": "ubject Schemes contains a list of subject schemes and assigns a URI to each scheme. The purpose of these properties is to permit users to associate controlled subjects with the appropriate subject schemes. These schemes are general subject heading and thesauri, such as the Library of Congress Subject Headings, along with a number of focused subject term lists like Medical Subject Headings or Getty Thesaurus of Geographic Names.",
"homepage": "http://id.loc.gov/vocabulary/subjectSchemes.html",
"name": "Library of Congress Subject Schemes",
"prefix": "LC-SUBJSCHEMES"
},
"LCDGT": {
"description": "The Library of Congress Demographic Group Terms (LCDGT) is designed to describe the characteristics of the intended audiences of resources, and also the creators of, and contributors to, those resources.",
"homepage": "http://id.loc.gov/authorities/demographicTerms.html",
"name": "Library of Congress Demographic Group Terms",
"prefix": "LCDGT"
},
"LCGFT": {
"description": "The Library of Congress Genre/Form Terms for Library and Archival Materials (LCGFT) is a thesaurus that describes what a work is versus what it is about. For instance, the subject heading Horror films, with appropriate subdivisions, would be assigned to a book about horror films. A cataloger assigning headings to the movie The Texas Chainsaw Massacre would also use Horror films, but it would be a genre/form term since the movie is a horror film, not a movie about horror films. The thesaurus combines both genres and forms. Form is defined as a characteristic of works with a particular format and/or purpose. A \"short\" is a particular form, for example, as is \"animation.\" Genre refers to categories of works that are characterized by similar plots, themes, settings, situations, and characters. Examples of genres are westerns and thrillers. In the term Horror films\"horror\" is the genre and \"films\" is the form.",
"homepage": "http://id.loc.gov/authorities/genreForms.html",
"name": "Library of Congress Genre/Form Thesaurus for Library and Archival Materials",
"prefix": "LCGFT",
"version": "2017-09-05"
},
"LCGFT_SKOS": {
"description": "The Library of Congress Genre/Form Terms for Library and Archival Materials (LCGFT) is a thesaurus that describes what a work is versus what it is about.",
"name": "Library of Congress Genre/Form Terms (SKOS)",
"prefix": "LCGFT_SKOS",
"version": "using output of skosify"
},
"LCMPT": {
"description": "Vocabulary that provides terminology to describe the instruments, voices, etc., used in the performance of musical works.",
"homepage": "http://id.loc.gov/authorities/performanceMediums.html",
"name": "Library of Congress Medium of Performance Thesaurus for Music",
"prefix": "LCMPT",
"version": "31 Aug 2017"
},
"LDA": {
"description": "We present the short review of language terms used in the domain of autism and populate them into ontology available for consultation and sharing. The language terms were obtained via text mining and automatic retrieval of terms from the corpus of PubMed abstracts.",
"download_owl": "http://aber-owl.net/media/ontologies/LDA/1/lda.owl",
"name": "Ontology of Language Disorder in Autism",
"prefix": "LDA",
"version": "12-15-2008"
},
"LDBASE": {
"description": "LDbase is an NIH-funded behavioral research data repository. The LDbase taxonomy includes project descriptors for projects in the fields of educational and developmental sciences. Developed as a collaboration between researchers and librarians, this first-of-its-kind project-oriented data repository contains decades of knowledge and includes data on individuals across the full range of abilities. The LDbase ontology is used to describe research projects in the developmental sciences.",
"homepage": "LDbase.org",
"name": "LDbase",
"prefix": "LDBASE",
"version": "0.0.1"
},
"LEGALAPA": {
"description": "this is a test with the legal cluster of apa ontology",
"download_owl": "http://aber-owl.net/media/ontologies/LEGALAPA/1/legalapa.owl",
"name": "legalapa",
"prefix": "LEGALAPA",
"version": "01"
},
"LEGALAPATEST2": {
"description": "Legal cluster for APA ontology",
"download_owl": "http://aber-owl.net/media/ontologies/LEGALAPATEST2/1/legalapatest2.owl",
"name": "apalegal",
"prefix": "LEGALAPATEST2",
"version": "1"
},
"LEPAO": {
"description": "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. LEPAO is developed in part by BIOfid (The Specialised Information Service Biodiversity Research).",
"download_owl": "http://aber-owl.net/media/ontologies/LEPAO/2/lepao.owl",
"homepage": "https://github.com/insect-morphology/lepao",
"name": "Lepidoptera Anatomy Ontology",
"prefix": "LEPAO"
},
"LHO": {
"description": "The Live Stock Health Ontology (LHO) is an extension of the DECIDE ontology. LHO follows OBO Foundry guidelines and contains information related to the health and well-being of livestock animal species such as cattle. Furthermore, it represents the explicit structured and standardized framework for specific domain knowledge and data integration of livestock species. During the development process, knowledge can be retrieved from domain experts, and after the retrieving process, the first prototype is designed for reasoning and planning of data related to cattle. Moreover, LHO contains information regarding farms Identifications, their samples, geolocation, breed, diagnostic tests, Pathogen identifications, and Pathogen results for specific bacteria such as Histophilus somni (HS), Mannheimia haemolytica (MH), Pasteurella multocida (PM), Bovine coronavirus (BCV) bacterial mycoplasma and aerobic culture results for the respiratory track in cattle. This information is represented in the form of concepts of classes, subclasses, and their relationship in the form of object and data properties.",
"download_owl": "http://aber-owl.net/media/ontologies/LHO/1/lho.owl",
"name": "LivestockHealthOntology",
"prefix": "LHO",
"version": "1.0.0"
},
"LICO": {
"description": "Liver Case Ontology (LiCO) is a case-centric ontology for liver patient cases called lico (Liver Case Ontology) that integrates several ontologies and lexicons developed for sub-disciplines of medicine such as RadLex (Radiology Lexicon), SNOMED CT (Systematized Nomenclature of Medicine, Clinical Terms), LOINC (The Logical Observation Identifier Names and Codes). It is an extension of ONLIRA (Ontology of the Liver for Radiology) that represents the liver and lesions from a radiological perspective.",
"download_owl": "http://aber-owl.net/media/ontologies/LICO/2/lico.owl",
"name": "Liver Case Ontology (LiCO)",
"prefix": "LICO",
"version": "changes\n* Segments and Regions are modelling as Classes in order to identify which patient (liver) they belong to.\n* Redundant restrictions are removed"
},
"LIFO": {
"description": "The Life Ontology (LifO) is an ontology of the life of organism. LifO represents the life processes of organisms and related entities and relations. LifO is a general purpose ontology that covers the common features associated with different organisms such as unicellular prokaryotes (e.g., E. coli) and multicellular organisms (e.g., human).",
"download_owl": "http://aber-owl.net/media/ontologies/LIFO/1/lifo.owl",
"homepage": "https://github.com/lifeontology/lifo",
"name": "Life Ontology",
"prefix": "LIFO",
"version": "Vision Release: 1.0.17"
},
"LINKALTERNATIF": {
"name": "santikumala",
"prefix": "LINKALTERNATIF"
},
"LINK_ALTERNATIF": {
"name": "santi kumala",
"prefix": "LINK_ALTERNATIF"
},
"LION": {
"description": "Lipid ontology (LION) associates >50,000 lipid species to biophysical, chemical, and cell biological features.",
"download_obo": "http://aber-owl.net/media/ontologies/LION/1/lion.obo",
"homepage": "www.lipidontology.com",
"name": "LipidOntology",
"prefix": "LION",
"version": "1.1"
},
"LIPRO": {
"description": "Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied. The ontology describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define membership requirements for sub classes of lipid according to appropriate functional groups.",
"download_owl": "http://aber-owl.net/media/ontologies/LIPRO/4/lipro.owl",
"name": "Lipid Ontology",
"prefix": "LIPRO",
"version": "See Remote Site"
},
"LOINC": {
"description": "Logical Observation Identifier Names and Codes (LOINC)",
"homepage": "http://loinc.org/downloads",
"name": "Logical Observation Identifier Names and Codes",
"prefix": "LOINC",
"version": "2016AB"
},
"LONGCOVID": {
"description": "Long Covid phenotype ontology",
"download_owl": "http://aber-owl.net/media/ontologies/LONGCOVID/2/longcovid.owl",
"name": "Long Covid Phenotype Ontology",
"prefix": "LONGCOVID",
"version": "20211006"
},
"LPT": {
"description": "The Livestock Product Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.",
"download_obo": "http://aber-owl.net/media/ontologies/LPT/3/lpt.obo",
"name": "Livestock Product Trait Ontology",
"prefix": "LPT",
"version": "1.4"
},
"LSHO": {
"description": "Ontology is the formal and explicit description of a data model within an application domain in which relationships occur between individuals, making it easy to reuse and knowledge sharing. LSHO contains the information related to the health and well-being of livestock animal species such as cattle. Furthermore, it represents the explicit structured and standardized framework for specific domain knowledge and data integration of livestock species. During the development process, knowledge can be retrieved from domain experts, and after the retrieving process, the first prototype is designed for reasoning and planning of data related to cattle. Moreover, LSHO contains information regarding farms Identifications, their samples, geolocation, breed, diagnostic tests, Pathogen identifications, and Pathogen results for specific bacteria such as Histophilus somni (HS), Mannheimia haemolytica (MH), Pasteurella multocida (PM), Bovine coronavirus (BCV) bacterial mycoplasma and aerobic culture results for the respiratory track . This information is represented in the form of concepts of classes, subclasses, and their relationship in the form of object and data properties.",
"download_owl": "http://aber-owl.net/media/ontologies/LSHO/1/lsho.owl",
"name": "LiveStockHealthOntologyCattleUseCase ",
"prefix": "LSHO",
"version": "1.0.0"
},
"LUNGMAP-HUMAN": {
"description": "Anatomic Ontology for Human Lung Maturation (LungMAP Human Anatomy (LMHA) Developed by Susan E Wert, Gail H. Deutsch, Helen Pan, and the NHLBI Molecular Atlas of Lung Development Program Consortium Ontology Subcommittee",
"download_owl": "http://aber-owl.net/media/ontologies/LUNGMAP-HUMAN/6/lungmap-human.owl",
"homepage": "https://www.lungmap.net/breath-ontology-browser/",
"name": "Anatomic Ontology for Human Lung Maturation",
"prefix": "LUNGMAP-HUMAN",
"version": "1.4"
},
"LUNGMAP-HUMAN1": {
"description": "Submission of LUNGMAP-HUMAN ontology by JBG",
"download_owl": "http://aber-owl.net/media/ontologies/LUNGMAP-HUMAN1/1/lungmap-human1.owl",
"name": "human lung development ontology",
"prefix": "LUNGMAP-HUMAN1"
},
"LUNGMAP-MOUSE": {
"description": "Anatomic ontology for Mouse Lung Maturation (LungMAP Mouse Anatomy (LMMA) Developed by Susan E Wert, Gail H. Deutsch, Helen Pan, and the NHLBI Molecular Atlas of Lung Development Program Consortium Ontology Subcommittee",
"download_owl": "http://aber-owl.net/media/ontologies/LUNGMAP-MOUSE/4/lungmap-mouse.owl",
"homepage": "https://lungmap.net/breath-ontology-browser/",
"name": "Anatomic Ontology for Mouse Lung Maturation",
"prefix": "LUNGMAP-MOUSE",
"version": "1.2"
},
"LUNGMAP_H_CELL": {
"description": "Cell Ontology for Human Lung Maturation (LungMAP Human Anatomy (LMHA)) Developed by Susan E Wert, Gail H. Deutsch, Helen Pan, and the NHLBI Molecular Atlas of Lung Development Program Consortium Ontology Subcommittee",
"download_owl": "http://aber-owl.net/media/ontologies/LUNGMAP_H_CELL/6/lungmap_h_cell.owl",
"homepage": "https://www.lungmap.net/breath-ontology-browser/",
"name": "Cell Ontology for Human Lung Maturation",
"prefix": "LUNGMAP_H_CELL",
"version": "3.2"
},
"LUNGMAP_M_CELL": {
"description": "Cell Ontology for Mouse Lung Maturation (LungMAP Mouse Anatomy (LMMA)) Developed by Susan E Wert, Gail H. Deutsch, Helen Pan, and the NHLBI Molecular Atlas of Lung Development Program Consortium Ontology Subcommittee",
"download_owl": "http://aber-owl.net/media/ontologies/LUNGMAP_M_CELL/5/lungmap_m_cell.owl",
"homepage": "https://www.lungmap.net/breath-ontology-browser/",
"name": "Cell Ontology for Mouse Lung Maturation",
"prefix": "LUNGMAP_M_CELL",
"version": "3.2"
},
"M4M-20-SUBJECTS": {
"description": "Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is Psychology Subjects. This controlled vocabulary is produced in Metadata 4 Machine (M4M) Workshop 20 (M4M.20 FAIRware Psychology), which one of deliverables of FAIRware project which if funded by RoRi. sheet2rdf is used to build and serve Psychology Subjects, while PURL is used to persist identifiers for the vocabulary, which resolve on BioPortal (Stanford's ontology service): http://purl.org/m4m20/subjects/",
"homepage": "https://github.com/fair-data-collective/M4M-20-FAIRware-Psychology-Subjects",
"name": "M4M.20 FAIRWare Subjects",
"prefix": "M4M-20-SUBJECTS",
"version": "0.1.3"
},
"M4M-20-VARIABLES": {
"description": "DEMO vocabulary only! Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is Psychology Variables. This controlled vocabulary is produced in Metadata 4 Machine (M4M) Workshop 20 (M4M.20 FAIRware Psychology), which is one of deliverables of FAIRware project funded by RoRi. sheet2rdf is used to build and serve Psychology Variables, while PURL is used to persist identifiers for the vocabulary, which resolve on BioPortal (Stanford's ontology service):",
"homepage": "https://raw.githubusercontent.com/gofair-foundation/vocabs_archive/main/M4M20_variables.ttl",
"name": "M4M.20 FAIRWare Variables",
"prefix": "M4M-20-VARIABLES",
"version": "0.1.3"
},
"M4M-21-SUBJECTS": {
"description": "Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is Neuroscience Subjects. This controlled vocabulary is produced in Metadata 4 Machine (M4M) Workshop 21 (M4M.21 FAIRware Neuroscience), which is one of deliverables of FAIRware project funded by RoRi. sheet2rdf is used to build and serve Neuroscience Subjects, while PURL is used to persist identifiers for the vocabulary, which resolve on BioPortal (Stanford's ontology service): http://purl.org/m4m21/subjects/",
"homepage": "https://github.com/fair-data-collective/M4M-21-FAIRware-Neuroscience-Subjects",
"name": "M4M.21 FAIRWare Subjects",
"prefix": "M4M-21-SUBJECTS",
"version": "0.1.2"
},
"M4M-21-VARIABLES": {
"description": "Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is Neuroscience Variables. This controlled vocabulary is produced in Metadata 4 Machine (M4M) Workshop 21 (M4M.21 FAIRware Neuroscience), which is one of deliverables of FAIRware project funded by RoRi. sheet2rdf is used to build and serve Neuroscience Variables, while PURL is used to persist identifiers for the vocabulary, which resolve on BioPortal (Stanford's ontology service): http://purl.org/m4m21/variables/",
"homepage": "https://github.com/fair-data-collective/M4M-21-FAIRware-Neuroscience-Variables",
"name": "M4M.21 FAIRWare Variables",
"prefix": "M4M-21-VARIABLES",
"version": "0.1.2"
},
"M4M-CHAR": {
"description": "M4M Charlotseville Vocabulary",
"name": "M4M-CHAR",
"prefix": "M4M-CHAR",
"version": "0.0.1"
},
"M4M19-SUBS": {
"description": "Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is NICEST-2 Subjects. This controlled vocabulary is a result of Metadata 4 Machine (M4M) Workshop 19 (M4M.19 funded by EOSC-Nordic ) provided to the NICEST-2 project. sheet2rdf and OntoStack, developed by FAIR Data Collective, are used to build and serve NICEST-2 Subjects, while PURL will be used to persist identifiers for the vocabulary terms and properties: http://purl.org/m4m19/subjects/",
"homepage": "https://github.com/fair-data-collective/M4M19-subjects-vocabulary",
"name": "M4M19 Subjects",
"prefix": "M4M19-SUBS",
"version": "0.1.0"
},
"M4M19-VARS": {
"description": "Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is NICEST-2 Variables. This controlled vocabulary is a result of Metadata 4 Machine (M4M) Workshop 19 (M4M.19 funded by EOSC-Nordic ) provided to the NICEST-2 project. sheet2rdf and OntoStack, developed by FAIR Data Collective, are used to build and serve NICEST-2 Subjects, while PURL will be used to persist identifiers for the vocabulary terms and properties: http://purl.org/m4m19/variables/",
"homepage": "https://github.com/fair-data-collective/M4M19-variables-vocabulary",
"name": "M4M19 Variables",
"prefix": "M4M19-VARS",
"version": "0.2.0"
},
"MA": {
"description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus).",
"download_owl": "http://aber-owl.net/media/ontologies/MA/127/ma.owl",
"homepage": "https://github.com/obophenotype/mouse-anatomy-ontology",
"name": "Mouse adult gross anatomy",
"prefix": "MA"
},
"MAAS Ontology": {
"name": "Multi Agent Autonomous Systems Ontology",
"prefix": "MAAS Ontology"
},
"MACROALGAETRAITS": {
"description": "The Macroalgae Traits Thesaurus contains several concepts on demographic and functional traits. It has been developed and published by LifeWatch Italy, the Italian node of the e-science European infrastructure for biodiversity and ecosystem research (LifeWatch ERIC). It reflects the agreement of a scientific expert community to fix semantic properties (e.g. label, definition) of approximately 100 traits.",
"homepage": "http://thesauri.lifewatchitaly.eu/Macroalgae/index.php",
"name": "Macroalgae Traits Thesaurus",
"prefix": "MACROALGAETRAITS"
},
"MADS-RDF": {
"description": "MADS-RDF is a knowledge organization system (KOS) designed for use with controlled values for names (personal, corporate, geographic, etc.), thesauri, taxonomies, subject heading systems, and other controlled value lists. It is closely related to SKOS, the Simple Knowledge Organization System and a widely supported and adopted RDF vocabulary. MADS/RDF has been fully mapped to SKOS. It is presented as an OWL ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/MADS-RDF/1/mads-rdf.owl",
"homepage": "http://www.loc.gov/standards/mads/rdf/",
"name": "Metadata Authority Description Schema in RDF",
"prefix": "MADS-RDF",
"version": "1.0"
},
"MAMO": {
"description": "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.",
"download_owl": "http://aber-owl.net/media/ontologies/MAMO/17/mamo.owl",
"homepage": "http://sourceforge.net/p/mamo-ontology/wiki/Home/",
"name": "Mathematical modeling ontology",
"prefix": "MAMO"
},
"MAMO-SCR-ONTO": {
"description": "The Mammography Screening Ontology (MAMO-SCR-Onto) is designed to provide mammography application recommendations for the early detection of breast cancer in patients at average risk of the disease.",
"download_owl": "http://aber-owl.net/media/ontologies/MAMO-SCR-ONTO/1/mamo-scr-onto.owl",
"name": "Mammography Screening Ontology",
"prefix": "MAMO-SCR-ONTO",
"version": "1.0"
},
"MAMOVIEW": {
"description": "View for MAMO : Mathematical Ontology",
"download_owl": "http://aber-owl.net/media/ontologies/MAMOVIEW/1/mamoview.owl",
"name": "Math Ontolofy View",
"prefix": "MAMOVIEW",
"version": "2015-10-17"
},
"MARC-LANGUAGES": {
"description": "MARC List for Languages provides three-character lowercase alphabetic strings that serve as the identifiers of languages and language groups. The codes are usually based on the first three letters of the English form or, in some cases, vernacular form of the corresponding language name. The codes are varied where necessary to resolve conflicts and are not intended to be abbreviations of a language name. When the name of a language is changed in the list, the original code is generally retained. The codes in this list are equivalent to those of ISO 639-2 (Bibliographic) codes and some codes from ISO 639-5, although the language name labels may differ. They are linked to the equivalent codes in ISO 639-2 and ISO 639-5 and the corresponding two-character codes in ISO 639-1.",
"homepage": "http://id.loc.gov/vocabulary/languages.html",
"name": "MARC List for Languages",
"prefix": "MARC-LANGUAGES"
},
"MARC-RELATORS": {
"description": "Relator terms and their associated codes designate the relationship between a name and a bibliographic resource. The relator codes are three-character lowercase alphabetic strings that serve as identifiers. Either the term or the code may be used as controlled values.",
"name": "MARC Code List for Relators",
"prefix": "MARC-RELATORS"
},
"MARKETING": {
"name": "Willy Mike",
"prefix": "MARKETING"
},
"MAT": {
"description": "Minimal set of terms for anatomy",
"download_obo": "http://aber-owl.net/media/ontologies/MAT/3/mat.obo",
"name": "Minimal Anatomical Terminology",
"prefix": "MAT",
"version": "1.1"
},
"MATERIALSMINE": {
"name": "MaterialsMine Ontology",
"prefix": "MATERIALSMINE"
},
"MATR": {
"description": "List of material Objects from SWEET ontology",
"download_owl": "http://aber-owl.net/media/ontologies/MATR/1/matr.owl",
"name": "Material",
"prefix": "MATR",
"version": "2.3"
},
"MATRCOMPOUND": {
"description": "Material Compound details from SWEET ontology",
"download_owl": "http://aber-owl.net/media/ontologies/MATRCOMPOUND/1/matrcompound.owl",
"name": "Material Compound",
"prefix": "MATRCOMPOUND",
"version": "2.3"
},
"MATRELEMENT": {
"description": "Material Element part of SWEET ontology",
"download_owl": "http://aber-owl.net/media/ontologies/MATRELEMENT/1/matrelement.owl",
"name": "Material Element",
"prefix": "MATRELEMENT",
"version": "2.3"
},
"MATRROCK": {
"description": "RocK material",
"download_owl": "http://aber-owl.net/media/ontologies/MATRROCK/1/matrrock.owl",
"name": "Material Rock",
"prefix": "MATRROCK",
"version": "2.3"
},
"MATRROCKIGNEOUS": {
"description": "matrRockIgneous",
"download_owl": "http://aber-owl.net/media/ontologies/MATRROCKIGNEOUS/2/matrrockigneous.owl",
"name": "Material Rock Igneouus",
"prefix": "MATRROCKIGNEOUS",
"version": "2.3"
},
"MAT_TEST_CASE2": {
"description": "Testing",
"download_owl": "http://aber-owl.net/media/ontologies/MAT_TEST_CASE2/1/mat_test_case2.owl",
"name": "Maternity_Test_Case2",
"prefix": "MAT_TEST_CASE2"
},
"MAXO": {
"description": "The Medical Action Ontology (MAxO) provides a broad view of medical actions and includes terms for medical procedures, interventions, therapies, treatments, and recommendations.",
"download_owl": "http://aber-owl.net/media/ontologies/MAXO/44/maxo.owl",
"homepage": "https://github.com/monarch-initiative/MAxO",
"name": "Medical Action Ontology",
"prefix": "MAXO"
},
"MCBCC": {
"description": "Contains a comprehensive list of cell lines derived from breast tissue, both normal and pathological. The ontology in built in OWL with cross relation to classes- genetic variation, pathological condition, genes, chemicals and drugs. The relations built enable semantic query across different classes",
"download_owl": "http://aber-owl.net/media/ontologies/MCBCC/2/mcbcc.owl",
"homepage": "www.molecularconnections.com",
"name": "Breast Tissue Cell Lines Ontology",
"prefix": "MCBCC",
"version": "2"
},
"MCCL": {
"description": "Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive of machine-interpretable definitions of basic concepts in the domain and relations among them. The need for ontologies that provide a systematic arrangement of available data and allow cross talk across various related domains is gaining momentum. In this backdrop, we have developed a comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format.",
"download_owl": "http://aber-owl.net/media/ontologies/MCCL/2/mccl.owl",
"homepage": "http://www.molecularconnections.com",
"name": "Cell Line Ontology [by Mahadevan]",
"prefix": "MCCL",
"version": "2"
},
"MCCV": {
"description": "Structured controlled vocabulary for describing meta information of microbial calture collection maintained in biological research centers",
"download_owl": "http://aber-owl.net/media/ontologies/MCCV/10/mccv.owl",
"name": "Microbial Culture Collection Vocabulary",
"prefix": "MCCV",
"version": "Version 0.96 beta"
},
"MCHVODANATERMS": {
"description": "Ontology containing the controlled terms and semantic properties used in the Maternal Child Health Care generic template used within different facilities in VODANA",
"name": "MCHVODANATERMS",
"prefix": "MCHVODANATERMS",
"version": "3.0"
},
"MCO": {
"description": "Microbial Conditions Ontology is an ontology...",
"download_owl": "http://aber-owl.net/media/ontologies/MCO/2/mco.owl",
"homepage": "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology",
"name": "Microbial Conditions Ontology",
"prefix": "MCO"
},
"MCRO": {
"description": "An ontology representing the structure of model card reports - reports that describe basic characteristics of machine learning models for the public and consumers.",
"download_owl": "http://aber-owl.net/media/ontologies/MCRO/1/mcro.owl",
"homepage": "https://github.com/UTHealth-Ontology/MCRO",
"name": "Model Card Report Ontology",
"prefix": "MCRO"
},
"MDDB": {
"description": "Master Drug Data Base, 2009_08_05",
"homepage": "http://www.medispan.com",
"name": "Master Drug Data Base Clinical Drugs",
"prefix": "MDDB",
"version": "2016AB"
},
"MDIM": {
"description": "The Mapping of Drug Names, ICD-11 and MeSH 2021 (MDIM) provides owl:sameAs relationships of similar concepts for Drug Names from the DrugBank vocabulary (https://go.drugbank.com/releases/latest#open-data), the International Classification of Diseases Version 11 (https://icd.who.int/) and the Medical Subject Headings (http://id.nlm.nih.gov/mesh/). Two concepts are considered similar if they share the same concept name or the same synonym. Additional synonyms for each of the concepts are generated using the Snowball stemming algorithm. The software implementation is available on github within the Maven project snoke in the module snoke.ontology: https://github.com/bernd-mueller/snoke/tree/master/snoke.ontology",
"download_owl": "http://aber-owl.net/media/ontologies/MDIM/2/mdim.owl",
"homepage": "https://www.zbmed.de/",
"name": "Mapping of Drug Names, ICD-11 and MeSH 2021",
"prefix": "MDIM",
"version": "0.2"
},
"MDM": {
"description": "The Mapping of Drug Names and MeSH 2022 (MDM) provides owl:sameAs relationships of similar concepts for Drug Names from the DrugBank vocabulary (released 2022-01-03 under version 5.1.9: https://go.drugbank.com/releases/latest#open-data) and the Medical Subject Headings (2022 version: http://id.nlm.nih.gov/mesh/). Two concepts are considered similar if they share the same concept name or a common synonym. Additional synonyms are generated using the Snowball stemming algorithm. The software implementation is available on github within the Maven project SNoKE in the module snoke.ontology: https://github.com/bernd-mueller/snoke/tree/master/snoke.ontology",
"download_owl": "http://aber-owl.net/media/ontologies/MDM/4/mdm.owl",
"homepage": "https://www.zbmed.de/",
"name": "Mapping of Drug Names and MeSH 2022",
"prefix": "MDM",
"version": "0.33"
},
"MDRFRE": {
"description": "Medical Dictionary for Regulatory Activities Terminology (MedDRA), French Edition",
"homepage": "http://www.meddramsso.com",
"name": "MedDRA French",
"prefix": "MDRFRE",
"version": "2016AB"
},
"MDRGER": {
"description": "This is the German translation of the Medical Dictionary for Regulatory Activities (MedDRA).",
"homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MDR/index.html",
"name": "MedDRA German",
"prefix": "MDRGER",
"version": "2023AB"
},
"MECHANOH": {
"description": "A hierarchy of regions involved in mechanoreception system.",
"download_owl": "http://aber-owl.net/media/ontologies/MECHANOH/2/mechanoh.owl",
"name": "NeuroMorpho.Org mechanoreception system",
"prefix": "MECHANOH",
"version": "0.6"
},
"MEDDRA": {
"description": "Medical Dictionary for Regulatory Activities Terminology (MedDRA)",
"homepage": "http://www.meddramsso.com/MSSOWeb/contact_us/index.htm",
"name": "Medical Dictionary for Regulatory Activities Terminology (MedDRA)",
"prefix": "MEDDRA",
"version": "2016AB"
},
"MEDEON": {
"description": "This is a demo version of the patient safety ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/MEDEON/1/medeon.owl",
"name": "Medical Error Ontology",
"prefix": "MEDEON"
},
"MEDLINEPLUS": {
"description": "MedlinePlus Health Topics;National Library of Medicine;June 14, 2008;Bethesda, MD",
"homepage": "http://www.nlm.nih.gov/medlineplus/xmldescription.html",
"name": "MedlinePlus Health Topics",
"prefix": "MEDLINEPLUS",
"version": "2016AB"
},
"MEDO": {
"description": "A representation of experimental design for high-throughput mouse analysis pipelines.",
"download_owl": "http://aber-owl.net/media/ontologies/MEDO/1/medo.owl",
"name": "Mouse Experimental Design Ontology",
"prefix": "MEDO",
"version": "1.0"
},
"MEDRT": {
"description": "MED-RT is a replacement and successor to NDF-RT. Both terminologies are formal ontological representations of medication terminology, pharmacologic classifications, and asserted authoritative relationships between them. Description MED-RT includes native pharmacologic classification concepts (e.g. mechanisms of action (MoA), physiologic effects (PE), Established Pharmacologic Class (EPC)) and all relationships asserted between concepts in any namespace. MED-RT incorporates the following terminologies: RxNorm for prescribable medications, active ingredients, and relationships between them MeSH for indexing chemical structure and therapeutics using its concept hierarchies SNOMED CT International to aid in mapping between FDA pharmacologic classes and its product and substance hierarchies MED-RT will maintain the pharmacologic classification relationships from NDF-RT. It also maintains the National Committee on Vital and Health Statistics (NCVHS) standards for describing medication pharmacologic classification: MoA and PE hierarchy concepts. The concepts are components of the Federal Medication Terminologies (FMT) interagency collaboration.",
"name": "MED-RT",
"prefix": "MEDRT",
"version": "2018AB"
},
"MEGO": {
"description": "MeGO is a Gene Ontology under construction dedicated to the functions of mobile genetic elements. The terms defined in MeGO are used to annotate phage and plasmid protein families in ACLAME.",
"download_obo": "http://aber-owl.net/media/ontologies/MEGO/2/mego.obo",
"homepage": "http://aclame.ulb.ac.be",
"name": "Mobile Genetic Element Ontology",
"prefix": "MEGO",
"version": "2_1"
},
"MELLO-D": {
"description": "MEdical LifeLog Ontology for the people with Disability",
"download_owl": "http://aber-owl.net/media/ontologies/MELLO-D/5/mello-d.owl",
"name": "MEdical LifeLog Ontology for people with Disability",
"prefix": "MELLO-D",
"version": "1.4"
},
"MELO": {
"description": "Ontology of melanoma disease, composed of terms of disease, drug, symptoms, molecular abnormality\uff0canatomical structure, diagnosis, treatment and relationships between them.",
"download_owl": "http://aber-owl.net/media/ontologies/MELO/2/melo.owl",
"name": "Melanoma Ontology",
"prefix": "MELO",
"version": "1.0"
},
"MEO": {
"description": "An Ontology for organismal habitats (especially focused on microbes)",
"download_owl": "http://aber-owl.net/media/ontologies/MEO/9/meo.owl",
"homepage": "http://microbedb.jp",
"name": "Metagenome and Microbes Environmental Ontology",
"prefix": "MEO",
"version": "0.9"
},
"MEPO": {
"description": "The Mapping of Epilepsy Ontologies (MEPO) provides owl:sameAs relationships of similar concepts for the ontologies EpSO, ESSO, EPILONT, EPISEM, and FENICS. Two concepts are considered similar if they share the same concept name or the same synonym. Additional synonyms for each of the concepts are generated using the Snowball stemming algorithm. The software implementation is available on github within the Maven project snoke in the module snoke.ontology: https://github.com/bernd-mueller/snoke/tree/master/snoke.ontology",
"download_owl": "http://aber-owl.net/media/ontologies/MEPO/6/mepo.owl",
"homepage": "https://www.zbmed.de/",
"name": "Mapping of Epilepsy Ontologies",
"prefix": "MEPO",
"version": "0.6"
},
"MERA": {
"description": "The educational resource ontology is designed in order to provide structure to resources aggregated by the educational resource aggregator. The aim of the educational resource aggregator is to harvest educational resources from 3rd party repositories, present these to the medical expert for annotation and rating, and output the results of the annotation (together with resource metadata) to the CARRE public RDF repository. The main parts of this aggregator are: the Resource Retriever, the Resource Rating, the Resource Metadata Processing, and the User Application. The educational metadata involve the Resource Metadata processing module.This module is a combination of 3 services that collect data per article, making multiple SPARQL requests to enrich the data and finally store it as a unique identified resource into the local datastore. Then data is transformed into RDF triples in order to be inserted to CARRE educational repository. The ontology is developed using the Prot\u00e9g\u00e9 v5.0 , a free, open-source ontology editor from the Stanford University. The ontology is available on CARRE rdf repository among the other ontologies. CARRE url : http://carre.kmi.open.ac.uk/ontology/educational.owl",
"download_owl": "http://aber-owl.net/media/ontologies/MERA/1/mera.owl",
"homepage": "https://edu.carre-project.eu",
"name": "Medical Educational Resource Aggregator",
"prefix": "MERA",
"version": "0.0.1"
},
"MESH": {
"description": "Medical Subject Headings (MeSH);National Library of Medicine; 2011",
"homepage": "http://www.nlm.nih.gov/mesh/meshhome.html",
"name": "Medical Subject Headings",
"prefix": "MESH",
"version": "2016AB"
},
"METABUS": {
"description": "The metaBUS hierarchical taxonomy of ~5,000 constructs studied in applied psychology, organizational behavior, and human resource management.",
"download_owl": "http://aber-owl.net/media/ontologies/METABUS/18/metabus.owl",
"homepage": "http://www.metabus.org",
"name": "metaBUS controlled vocabulary for organizational and applied psychology research",
"prefix": "METABUS",
"version": "0.2.4"
},
"MF": {
"description": "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning.",
"download_owl": "http://aber-owl.net/media/ontologies/MF/28/mf.owl",
"homepage": "https://github.com/jannahastings/mental-functioning-ontology",
"name": "Mental Functioning Ontology",
"prefix": "MF"
},
"MFMO": {
"description": "The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors.",
"download_owl": "http://aber-owl.net/media/ontologies/MFMO/2/mfmo.owl",
"homepage": "http://feedexp.org",
"name": "Mammalian Feeding Muscle Ontology",
"prefix": "MFMO"
},
"MFO": {
"description": "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.",
"download_obo": "http://aber-owl.net/media/ontologies/MFO/14/mfo.obo",
"name": "Medaka Fish Anatomy and Development Ontology",
"prefix": "MFO",
"version": "unknown"
},
"MFOEM": {
"description": "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings.",
"download_owl": "http://aber-owl.net/media/ontologies/MFOEM/39/mfoem.owl",
"homepage": "https://github.com/jannahastings/emotion-ontology",
"name": "Emotion Ontology",
"prefix": "MFOEM"
},
"MFOMD": {
"description": "An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable",
"download_owl": "http://aber-owl.net/media/ontologies/MFOMD/3/mfomd.owl",
"homepage": "https://github.com/jannahastings/mental-functioning-ontology",
"name": "Mental Disease Ontology",
"prefix": "MFOMD"
},
"MGBD": {
"description": "MGB Drug List",
"download_owl": "http://aber-owl.net/media/ontologies/MGBD/7/mgbd.owl",
"name": "MGB Drug List",
"prefix": "MGBD",
"version": "0.6"
},
"MHC": {
"description": "The MaHCO contains terms necessary for describing and categorizing concepts related to MHC, in general, and for a number of model species, and also for humans.",
"download_owl": "http://aber-owl.net/media/ontologies/MHC/4/mhc.owl",
"homepage": "http://purl.org/stemnet/",
"name": "Major Histocompatibility Complex Ontology",
"prefix": "MHC",
"version": "1.0.1"
},
"MHCRO": {
"description": "The MHC Restriction Ontology (MRO) is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions.",
"download_owl": "http://aber-owl.net/media/ontologies/MHCRO/1/mhcro.owl",
"homepage": "https://github.com/IEDB/MRO",
"name": "MHC Restriction Ontology",
"prefix": "MHCRO",
"version": "2016-12-15"
},
"MHMO": {
"description": "This ontology can assist in the management of mental healthcare networks. It allows the integration and semantic interoperability between independent health databases, promotes the ability to infer knowledge in this domain, enables the generation of relevant indicators for mental health to improve decision-making, and increases mental health management and planning efficiency and effectiveness. The MHMO is developed by the Laboratory of Health Intelligence - Ribeirao Preto Medical School, University of Sao Paulo, Brazil.",
"download_owl": "http://aber-owl.net/media/ontologies/MHMO/9/mhmo.owl",
"homepage": "http://mental-ontology.com/",
"name": "Mental Health Management Ontology",
"prefix": "MHMO",
"version": "3.2"
},
"MI": {
"description": "A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions.",
"download_owl": "http://aber-owl.net/media/ontologies/MI/122/mi.owl",
"homepage": "https://github.com/HUPO-PSI/psi-mi-CV",
"name": "Molecular Interactions Controlled Vocabulary",
"prefix": "MI"
},
"MIAPA": {
"description": "An application ontology to formalize annotation of phylogenetic data.",
"download_owl": "http://aber-owl.net/media/ontologies/MIAPA/2/miapa.owl",
"homepage": "http://www.evoio.org/wiki/MIAPA",
"name": "MIAPA Ontology",
"prefix": "MIAPA"
},
"MICRO": {
"description": "An ontology of prokaryotic phenotypic and metabolic characters",
"download_owl": "http://aber-owl.net/media/ontologies/MICRO/3/micro.owl",
"homepage": "https://github.com/carrineblank/MicrO",
"name": "Ontology of Prokaryotic Phenotypic and Metabolic Characters",
"prefix": "MICRO"
},
"MIDO": {
"description": "MIDO is an OWL 2 ontology for creating a standardized format for modeling data in medical imaging tasks such as Disease Classification/ Diagnosis as well as Disease localization/segmentation",
"download_owl": "http://aber-owl.net/media/ontologies/MIDO/1/mido.owl",
"name": "Medical Imaging and Diagnostic Ontology",
"prefix": "MIDO",
"version": "2015-11-20"
},
"MIM": {
"description": "The Molecular Interaction Map (MIM) notation seeks to provide a standardized method to draw diagrams for bioregulatory networks with features similar to technical diagrams in other fields. This vocabulary uses the term hierarchy from the Formal MIM Notation Specification. Where possible, Systems Biology Ontology (SBO) and Biological Pathway Exchange (BioPAX) terms and IRIs are used. If no SBO or BioPAX term is available, a new term and IRI are created. This is currently only a partial implementation. Many elements still need to be added to cover the full the specification.",
"download_owl": "http://aber-owl.net/media/ontologies/MIM/3/mim.owl",
"homepage": "http://discover.nci.nih.gov/mim/",
"name": "Molecular Interaction Map",
"prefix": "MIM",
"version": "10:30:2014 16:04"
},
"MINERAL": {
"description": "Material Mineral",
"download_owl": "http://aber-owl.net/media/ontologies/MINERAL/1/mineral.owl",
"name": "Material Mineral",
"prefix": "MINERAL",
"version": "2.3"
},
"MINI-FAST-1": {
"description": "Test of SKOS vocab to see if skos/core#Concept is required",
"name": "mini fast test",
"prefix": "MINI-FAST-1"
},
"MIO": {
"description": "The myocardial infarction ontology (MIO) is a disease-specific ontology that characterizes the knowledge field of myocardial infarction.",
"download_owl": "http://aber-owl.net/media/ontologies/MIO/3/mio.owl",
"name": "Myocardial Infarction Ontology",
"prefix": "MIO",
"version": "V1.0.0"
},
"MIRNAO": {
"description": "An application ontology for microRNAs.",
"download_owl": "http://aber-owl.net/media/ontologies/MIRNAO/11/mirnao.owl",
"homepage": "https://code.google.com/p/mirna-ontology/",
"name": "microRNA Ontology",
"prefix": "MIRNAO",
"version": "1.7"
},
"MIRO": {
"description": "Application ontology for entities related to insecticide resistance in mosquitos",
"download_owl": "http://aber-owl.net/media/ontologies/MIRO/1/miro.owl",
"homepage": "http://anobase.vectorbase.org",
"name": "Mosquito insecticide resistance",
"prefix": "MIRO"
},
"MISINFO": {
"name": "COVID-19 misinformation",
"prefix": "MISINFO"
},
"MIXS": {
"description": "An RDF representation of the MIxS Family of Checklists",
"download_owl": "http://aber-owl.net/media/ontologies/MIXS/5/mixs.owl",
"name": "Minimal Information about any Sequence Ontology",
"prefix": "MIXS",
"version": "unknown"
},
"MIXSCV": {
"description": "Controlled vocabularies for the MIxS family of metadata checklists. See http://gensc.org/gc_wiki/index.php/MIxS for details on the MIxS checklists.",
"download_obo": "http://aber-owl.net/media/ontologies/MIXSCV/2/mixscv.obo",
"name": "Minimal Information about any Sequence (MIxS) Controlled Vocabularies",
"prefix": "MIXSCV",
"version": "1"
},
"MIZZOU_CCO": {
"description": "Care Coordination ontology",
"download_owl": "http://aber-owl.net/media/ontologies/MIZZOU_CCO/8/mizzou_cco.owl",
"name": "Care Coordination Ontology",
"prefix": "MIZZOU_CCO",
"version": "1"
},
"MKN_10_TEST": {
"description": "MKN--like the ICD10",
"download_owl": "http://aber-owl.net/media/ontologies/MKN_10_TEST/2/mkn_10_test.owl",
"name": "MKN_10_test",
"prefix": "MKN_10_TEST",
"version": "1"
},
"MLTX": {
"description": "The machine learning methodology taxonomy mapping project is focused on gathering the terminology focused on machine learning and mapping the controlled and users' natural language to form a mapping file across these terminologies. This work was originally associated with dissertation research.",
"download_owl": "http://aber-owl.net/media/ontologies/MLTX/1/mltx.owl",
"name": "Machine Learning Methodology Taxonomy Mapping",
"prefix": "MLTX",
"version": "1"
},
"MMO": {
"description": "A representation of the variety of methods used to make clinical and phenotype measurements.",
"download_owl": "http://aber-owl.net/media/ontologies/MMO/88/mmo.owl",
"homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000",
"name": "Measurement method ontology",
"prefix": "MMO"
},
"MMUSDV": {
"description": "Life cycle stages for Mus Musculus",
"download_owl": "http://aber-owl.net/media/ontologies/MMUSDV/10/mmusdv.owl",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv",
"name": "Mouse Developmental Stages",
"prefix": "MMUSDV"
},
"MNR": {
"description": "Natural Resource",
"download_owl": "http://aber-owl.net/media/ontologies/MNR/1/mnr.owl",
"name": "Material Natural Resource ",
"prefix": "MNR",
"version": "2.3"
},
"MNV": {
"description": "migrants ontologies",
"name": "VODANA Migrants",
"prefix": "MNV",
"version": "1.0"
},
"MO": {
"description": "Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1.",
"download_owl": "http://aber-owl.net/media/ontologies/MO/1/mo.owl",
"homepage": "http://mged.sourceforge.net/ontologies/MGEDontology.php",
"name": "Microarray and Gene Expression Data Ontology",
"prefix": "MO",
"version": "1.3.1.1"
},
"MOBLAYERH": {
"description": "A hierarchy of layers in the Main Olfactory Bulb of mammals.",
"download_owl": "http://aber-owl.net/media/ontologies/MOBLAYERH/2/moblayerh.owl",
"name": "NeuroMorpho.Org Main Olfactory Bulb layers",
"prefix": "MOBLAYERH",
"version": "2.0"
},
"MOC": {
"description": "Organic Compound",
"download_owl": "http://aber-owl.net/media/ontologies/MOC/1/moc.owl",
"name": "Material Organic Compound",
"prefix": "MOC",
"version": "2.3"
},
"MOD": {
"description": "PSI-MOD is an ontology consisting of terms that describe protein chemical modifications",
"download_owl": "http://aber-owl.net/media/ontologies/MOD/122/mod.owl",
"homepage": "http://www.psidev.info/MOD",
"name": "Protein modification",
"prefix": "MOD"
},
"MODSCI": {
"description": "ModSci is a reference ontology for modelling different types of modern sciences and related entities, such as scientific discoveries, renowned scientists, instruments, phenomena ... etc.",
"download_owl": "http://aber-owl.net/media/ontologies/MODSCI/3/modsci.owl",
"homepage": "https://saidfathalla.github.io/Science-knowledge-graph-ontologies/doc/ModSci_doc/index-en.html",
"name": "Modern Science Ontology",
"prefix": "MODSCI",
"version": "1.0"
},
"MOMCARE": {
"description": "MomCare Vocabulary",
"name": "MomCareVocabulary",
"prefix": "MOMCARE",
"version": "1.1"
},
"MONDO": {
"description": "A global community effort to harmonize multiple disease resources to yield a coherent merged ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/MONDO/91/mondo.owl",
"homepage": "https://monarch-initiative.github.io/mondo",
"name": "Mondo Disease Ontology",
"prefix": "MONDO"
},
"MONO": {
"description": "Monogenean Ontology",
"download_owl": "http://aber-owl.net/media/ontologies/MONO/2/mono.owl",
"name": "Monogenean Ontology",
"prefix": "MONO"
},
"MOOCCIADO": {
"description": "The first ontology describing the anatomy and the development of Molgula occidentalis.",
"download_obo": "http://aber-owl.net/media/ontologies/MOOCCIADO/2/moocciado.obo",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Molgula occidentalis Anatomy and Development Ontology",
"prefix": "MOOCCIADO"
},
"MOOCCUADO": {
"description": "The first ontology describing the anatomy and the development of Molgula occulta.",
"download_obo": "http://aber-owl.net/media/ontologies/MOOCCUADO/2/mooccuado.obo",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Molgula occulta Anatomy and Development Ontology",
"prefix": "MOOCCUADO"
},
"MOOCULADO": {
"description": "The first ontology describing the anatomy and the development of Molgula oculata.",
"download_obo": "http://aber-owl.net/media/ontologies/MOOCULADO/2/mooculado.obo",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Molgula oculata Anatomy and Development Ontology",
"prefix": "MOOCULADO"
},
"MOP": {
"description": "Processes at the molecular level",
"download_owl": "http://aber-owl.net/media/ontologies/MOP/8/mop.owl",
"homepage": "https://github.com/rsc-ontologies/rxno",
"name": "Molecular Process Ontology",
"prefix": "MOP"
},
"MOSAIC": {
"description": "Ontology to support Semantic Annotation of MOSAiC datasets housed in the Arctic Data Center (https://arcticdata.io).",
"download_owl": "http://aber-owl.net/media/ontologies/MOSAIC/4/mosaic.owl",
"homepage": "https://github.com/DataONEorg/sem-prov-ontologies",
"name": "The MOSAiC Ontology",
"prefix": "MOSAIC",
"version": "Version 1.0.1"
},
"MOVIE": {
"name": "Nonton Gratis Movie Online",
"prefix": "MOVIE"
},
"MP": {
"description": "Standard terms for annotating mammalian phenotypic data.",
"download_owl": "http://aber-owl.net/media/ontologies/MP/115/mp.owl",
"homepage": "https://www.informatics.jax.org/vocab/mp_ontology/",
"name": "Mammalian Phenotype Ontology",
"prefix": "MP"
},
"MPATH": {
"description": "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes",
"download_owl": "http://aber-owl.net/media/ontologies/MPATH/173/mpath.owl",
"homepage": "http://www.pathbase.net",
"name": "Mouse pathology ontology",
"prefix": "MPATH"
},
"MPIO": {
"description": "An ontology of minimum information regarding potential drug-drug interaction information.",
"download_owl": "http://aber-owl.net/media/ontologies/MPIO/5/mpio.owl",
"homepage": "https://github.com/MPIO-Developers/MPIO",
"name": "Minimum PDDI Information Ontology",
"prefix": "MPIO"
},
"MPO": {
"description": "An ontology for describing microbial phenotypes",
"download_owl": "http://aber-owl.net/media/ontologies/MPO/7/mpo.owl",
"name": "Microbial Phenotype Ontology",
"prefix": "MPO",
"version": "Version 0.5 alpha"
},
"MRO": {
"description": "An ontology for Major Histocompatibility Complex (MHC) restriction in experiments",
"download_owl": "http://aber-owl.net/media/ontologies/MRO/58/mro.owl",
"homepage": "https://github.com/IEDB/MRO",
"name": "MHC Restriction Ontology",
"prefix": "MRO"
},
"MS": {
"description": "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.",
"download_owl": "http://aber-owl.net/media/ontologies/MS/199/ms.owl",
"homepage": "http://www.psidev.info/groups/controlled-vocabularies",
"name": "Mass spectrometry ontology",
"prefix": "MS"
},
"MSHFRE": {
"description": "Thesaurus Biomedical Francais/Anglais (French translation of the Medical Subject Headings)",
"homepage": "http://www.inserm.fr",
"name": "Thesaurus Biomedical Francais/Anglais [French translation of MeSH]",
"prefix": "MSHFRE",
"version": "2016AB"
},
"MSO": {
"description": "Multiple sclerosis ontology integrated with Basic formal ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/MSO/2/mso.owl",
"homepage": "http://www.scai.fraunhofer.de/de/geschaeftsfelder/bioinformatik/downloads.html",
"name": "Multiple sclerosis ontology",
"prefix": "MSO"
},
"MSR": {
"description": "This is an ontology that represents a variety of entities and classifications that share the knowledge of the recommendations provided by the guideline from the American Cancer Society on Breast Cancer Screening for Women at Average Risk. This ontology was developed as part of an ontology course on UdelaR Univeristy. Mentored by Regina Motz and Edelweis Rohrer",
"download_owl": "http://aber-owl.net/media/ontologies/MSR/1/msr.owl",
"name": "Mammography screening recommendation",
"prefix": "MSR",
"version": "0.0.1"
},
"MSTDE": {
"description": "Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy. Bethesda, MD: National Library of Medicine, 2001.",
"name": "Minimal Standard Terminology of Digestive Endoscopy",
"prefix": "MSTDE",
"version": "2016AB"
},
"MSTDE-FRE": {
"description": "Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy, French Translation, 2001",
"name": "Minimal Standard Terminology of Digestive Endoscopy, French",
"prefix": "MSTDE-FRE",
"version": "2016AB"
},
"MSV": {
"description": "An ontology for metagenome sample metadata. This ontology mainly defines predicates.",
"download_owl": "http://aber-owl.net/media/ontologies/MSV/2/msv.owl",
"homepage": "http://microbedb.jp",
"name": "Metagenome Sample Vocabulary",
"prefix": "MSV",
"version": "0.2"
},
"MTO": {
"name": "MyTestOntology",
"prefix": "MTO"
},
"MVAONT": {
"description": "MVAont is about the description of Indian Mosquito Vectors and their Associations with Biocontrol Agents",
"download_owl": "http://aber-owl.net/media/ontologies/MVAONT/2/mvaont.owl",
"name": "Mosquito Vector Association Ontology with Biocontrol Agents",
"prefix": "MVAONT",
"version": "Version2"
},
"MWLA": {
"description": "This ontology designed and developed in order to represent the detected intentions from the Web Lifestyle Data Aggregator. In particular, it seeks to represent what is involved in the gathering of data from the web and social lifestyle of user on the Internet. We decided, therefore, to develop the ontology using the Prot\u00e9g\u00e9 v5.0, a free, open-source ontology editor from the Stanford University. The outcome of Prot\u00e9g\u00e9 is available on the following URL: http://carre.kmi.open.ac.uk/ontology/lifestyle.owl The presented ontology is generic and can support different type of providers (e.g. web searches, Facebook, Twitter etc.). Additionally, the predefined intentions are also generic supporting the majority of intentions in the Web. In the context of CARRE, we utilize, as a first attempt, the web searches as provider and we only upload the relevant intentions (health and travel) to CARRE in the private RDF repository. A user (representing an individual person whose data is being represented using the terms of this ontology) has connections. A connection represents that a Web Lifestyle Data Aggregator of a particular personal computer of user provides intentions for particulars providers. A connection is therefore associated with a UUID (Universal Unique Identifier) that represents an installation of the aggregator. A provider can be the web searches, Facebook or Twitter. A measurement is associated with a provider and a connection in order to declare the connection (i.e. the Web Lifestyle Data Aggregator of a particular personal computer) from which a measurement came. Every measurement must have a date at which the detected intention was taken, a weight which defines the importance of an intention and of course the detected intention that is only relevant to CARRE.",
"download_owl": "http://aber-owl.net/media/ontologies/MWLA/1/mwla.owl",
"homepage": "https://www.carre-project.eu/innovation/web-lifestyle-data-aggregator/",
"name": "Medical Web Lifestyle Aggregator",
"prefix": "MWLA",
"version": "0.0.1"
},
"MWS22": {
"description": "This ontology is about svu university",
"download_owl": "http://aber-owl.net/media/ontologies/MWS22/1/mws22.owl",
"name": "Svu ontology",
"prefix": "MWS22"
},
"MYFACILITYNAME": {
"description": "This is the first vocabulary",
"name": "MY FACILITY NAME",
"prefix": "MYFACILITYNAME",
"version": "5"
},
"MY_SYRIANCINEMA": {
"description": "I have an anthology that describes Syrian cinema It contains the film's class, the actor's class, the director's class, the producer's class, and other classes Each class has the necessary properties There are several relationships between classes The project is a practical assignment in the Semantic Web course for a graduate student in the Master of Web Science program",
"download_owl": "http://aber-owl.net/media/ontologies/MY_SYRIANCINEMA/1/my_syriancinema.owl",
"homepage": "https://www.facebook.com/share/Lahi4gL4qiX647wW/?mibextid=qi2Omg",
"name": "MWS-WSM Syrian Cinema Ontology",
"prefix": "MY_SYRIANCINEMA",
"version": "4.3"
},
"ModSci": {
"description": "Modern Science Ontology (ModSci), for modeling relationships between modern science branches and related entities, such as scientific discoveries, phenomena, renowned scientists, instruments, etc. ModSci is an upper ontology that provides a unifying framework for the various domain ontologies that make up the Science Knowledge Graph Ontology Suite. The Systematic Approach for Building Ontologies (SABiO) has been followed in the development of ModSci. ModSci is a poly-hierarchical ontology that can be utilized in semantic web applications. ModSci powers two projects for semantically representing scholarly information: Open Research Knowledge Graph (for the categorization of research papers) and OpenResearch.org (for the categorization of the information about scientific events, research projects, scientific papers, publishers, and journals).",
"download_owl": "http://aber-owl.net/media/ontologies/ModSci/2/modsci.owl",
"homepage": "https://saidfathalla.github.io/Science-knowledge-graph-ontologies/doc/ModSci_doc/index-en.html",
"name": "Modern Science Ontology",
"prefix": "ModSci",
"version": "1.1"
},
"N-CDOH": {
"name": "Non Clinical Determinants of Health",
"prefix": "N-CDOH"
},
"NAMBOBI": {
"description": "OUT PATIENT REGISTER FOR UGANDA",
"download_owl": "http://aber-owl.net/media/ontologies/NAMBOBI/1/nambobi.owl",
"name": "NAMBOBI'S ONTOLOGY",
"prefix": "NAMBOBI"
},
"NAMKHOA": {
"name": "phong kham nam khoa",
"prefix": "NAMKHOA"
},
"NANDO": {
"description": "Creating a comprehensive hierarchical controlled vocabulary for intractable and rare disease (i.e., nanbyo) representation in Japan.",
"download_owl": "http://aber-owl.net/media/ontologies/NANDO/15/nando.owl",
"homepage": "https://nanbyodata.jp",
"name": "Nanbyo Disease Ontology",
"prefix": "NANDO",
"version": "2023-11-28"
},
"NATPRO": {
"description": "An ontology for describing biological activities of natural products.",
"download_owl": "http://aber-owl.net/media/ontologies/NATPRO/1/natpro.owl",
"name": "Natural Products Ontology",
"prefix": "NATPRO",
"version": "unknown"
},
"NBO": {
"description": "An ontology of human and animal behaviours and behavioural phenotypes",
"download_owl": "http://aber-owl.net/media/ontologies/NBO/38/nbo.owl",
"homepage": "https://github.com/obo-behavior/behavior-ontology/",
"name": "Neuro Behavior Ontology",
"prefix": "NBO"
},
"NCBITAXON": {
"description": "An ontology representation of the NCBI organismal taxonomy",
"download_owl": "http://aber-owl.net/media/ontologies/NCBITAXON/16/ncbitaxon.owl",
"homepage": "https://github.com/obophenotype/ncbitaxon",
"name": "NCBI organismal classification",
"prefix": "NCBITAXON"
},
"NCBITAXONSH": {
"download_owl": "http://aber-owl.net/media/ontologies/NCBITAXONSH/3/ncbitaxonsh.owl",
"name": "NCBI Taxonomy Ontology - Shrinked version",
"prefix": "NCBITAXONSH",
"version": "0.3"
},
"NCBI_NMOsp_1_0_0": {
"description": "A lighter version of the NCBI taxonomy that is customized for the NeuroMorpho.Org species.",
"download_obo": "http://aber-owl.net/media/ontologies/NCBI_NMOsp_1_0_0/1/ncbi_nmosp_1_0_0.obo",
"name": "NeuroMorpho.Org Species Ontology v.1.0.0",
"prefix": "NCBI_NMOsp_1_0_0",
"version": "1"
},
"NCBI_NMOsp_1_2_2": {
"description": "A lighter version of the NCBI taxonomy that is customized for the NeuroMorpho.Org species. The ontology also include NIFSTD, Rat strain and Jax mice terms that are arranged in a single parent hierarchical tree.",
"download_obo": "http://aber-owl.net/media/ontologies/NCBI_NMOsp_1_2_2/1/ncbi_nmosp_1_2_2.obo",
"name": "NeuroMorpho.Org Species Ontology v.1.2.2",
"prefix": "NCBI_NMOsp_1_2_2",
"version": "1.2.2"
},
"NCCNEHR": {
"description": "The NCCN EHR Oncology Advisory Group was formed to address the high variance in oncology history documentation within EHR systems. Specifically, there is a lack of standardization in the names of oncology history categories across institutions. Moreover, no synonym list or mapping currently exists between the varied category names. Furthermore, oncology history documentation is often inconsistent, incomplete, and not updated appropriately. The NCCN EHR Oncology Advisory Group has established best practices and is working with EHR vendors to implement and enhance tools for documentation of oncology history. This ontology is a result of the work of the group, and provides users with a list of oncology history categories and synonyms. It is our sincere hope that this work can form the basis of improving standardization and interoperability of oncology history documentation within EHR systems.",
"download_owl": "http://aber-owl.net/media/ontologies/NCCNEHR/1/nccnehr.owl",
"homepage": "https://www.nccn.org/",
"name": "NCCN EHR Oncology Categories",
"prefix": "NCCNEHR",
"version": "1.0.0"
},
"NCCO": {
"description": "Nursing Care Coordination Ontology contains activities that nurses use while coordinating care among patients.",
"download_owl": "http://aber-owl.net/media/ontologies/NCCO/1/ncco.owl",
"name": "Nursing Care Coordination Ontology",
"prefix": "NCCO",
"version": "1.0"
},
"NCI": {
"description": "human anatomy",
"download_owl": "http://aber-owl.net/media/ontologies/NCI/1/nci.owl",
"name": "human anatomy",
"prefix": "NCI"
},
"NCIT": {
"description": "NCI Thesaurus (NCIt)is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities. The NCIt OBO Edition aims to increase integration of the NCIt with OBO Library ontologies. NCIt OBO Edition releases should be considered experimental.",
"download_owl": "http://aber-owl.net/media/ontologies/NCIT/78/ncit.owl",
"homepage": "https://github.com/NCI-Thesaurus/thesaurus-obo-edition",
"name": "NCI Thesaurus OBO Edition",
"prefix": "NCIT"
},
"NCIT_NEOPLASM": {
"description": "The NCIt Neoplasm provides a core reference set of NCIt neoplasm classification concepts that is designed to facilitate consistent coding, analysis, and data sharing across a broad range of NCI and related resources.",
"download_owl": "http://aber-owl.net/media/ontologies/NCIT_NEOPLASM/1/ncit_neoplasm.owl",
"name": "Neoplasm",
"prefix": "NCIT_NEOPLASM",
"version": "16.05e"
},
"NCIt-Activity": {
"description": "Activity subtree of NCIt.",
"download_owl": "http://aber-owl.net/media/ontologies/NCIt-Activity/1/ncit-activity.owl",
"name": "Activity-View",
"prefix": "NCIt-Activity",
"version": "09.0"
},
"NCOD": {
"description": "National Disease classification of Ethiopia",
"name": "NCoD",
"prefix": "NCOD",
"version": "0.1.1"
},
"NCRO": {
"description": "An ontology for non-coding RNA, both of biological origin, and engineered.",
"download_owl": "http://aber-owl.net/media/ontologies/NCRO/13/ncro.owl",
"homepage": "http://omnisearch.soc.southalabama.edu/OntologyFile.aspx",
"name": "Non-Coding RNA Ontology",
"prefix": "NCRO"
},
"NDDF": {
"description": "National Drug Data File Plus Source Vocabulary",
"name": "National Drug Data File",
"prefix": "NDDF",
"version": "2016AB"
},
"NDDO": {
"description": "Neurodegenerative Disease Data Ontology (NDDO) is an ontology for describing data on neurodegenerative disease patients.",
"download_owl": "http://aber-owl.net/media/ontologies/NDDO/10/nddo.owl",
"homepage": "http://www.ontodm.com/doku.php?id=nddo",
"name": "Neurodegenerative Disease Data Ontology",
"prefix": "NDDO",
"version": "0.2"
},
"NDF-RT": {
"description": "Logically inferred version in OWL of the National Drug File \u2013 Reference Terminology (NDF-RT). NDF-RT is the terminology used by FDA and the FedMed collaboration to code these essential pharmacologic properties of medications: Mechanism of Action, Physiologic Effect, Structural Class.",
"download_owl": "http://aber-owl.net/media/ontologies/NDF-RT/1/ndf-rt.owl",
"name": "National Drug File \u2013 Reference Terminology",
"prefix": "NDF-RT",
"version": "NDF-RT2 [Public Edition]"
},
"NDFRT": {
"description": "National Drug File - Reference Terminology Public Inferred Edition, 2008_03_11",
"homepage": "http://www.va.gov",
"name": "National Drug File - Reference Terminology",
"prefix": "NDFRT",
"version": "2016AB"
},
"NEGO": {
"description": "It represents standards for nutritional epidemiological studies in ontology format. In the strict sense, it is not an ontology. Its hierarchy follows structure of each standard, not OWL rules.",
"download_owl": "http://aber-owl.net/media/ontologies/NEGO/1/nego.owl",
"homepage": "https://github.com/cyang0128/Nutritional-epidemiological-ontologies",
"name": "Nutritional Epidemiological STandard",
"prefix": "NEGO",
"version": "V1.0"
},
"NEIC-ONTO": {
"description": "Terms used to describe different aspects of NeIC activities",
"name": "Unoffical NeIC Organisation Vocabulary",
"prefix": "NEIC-ONTO",
"version": "0.2.2"
},
"NEICBEER": {
"description": "This vocabulary is used to create a machine actionable dataset of beer and beer consumption",
"name": "The NeIC PaRI beer vocabulary",
"prefix": "NEICBEER",
"version": "0.1.0"
},
"NEIO": {
"description": "The Neural Electronic Interface Ontology represents the types of devices used to interface with the central nervous system to enhance (or augment) stimuli from a subject's external environment, the conditions under which these devices should be employed, the assessment of a subject's sensory ability, and the metrics for evaluating the performance.",
"download_owl": "http://aber-owl.net/media/ontologies/NEIO/3/neio.owl",
"homepage": "https://github.com/uflcod/neural-electronic-interface-ontology/",
"name": "Neural Electronic Interface Ontology",
"prefix": "NEIO",
"version": "2024-06-25"
},
"NEMO": {
"description": "Neural ElectroMagnetic Ontology (NEMO) describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters). Working (unstable), Release (stable), and Old (archival) versions of NEMO can be found on sourceforge: http://sourceforge.net/projects/nemoontologies/.",
"download_owl": "http://aber-owl.net/media/ontologies/NEMO/24/nemo.owl",
"homepage": "http://nemo.nic.uoregon.edu",
"name": "Neural ElectroMagnetic Ontology",
"prefix": "NEMO",
"version": "v3.10"
},
"NEO": {
"description": "An ontology to capture findings from the neurological examination. The ontology is based on concepts from UMLS Metathesaurus and SNOMED CT. Only abnormal findings are included. The purpose of the ontology is to act as a limited vocabulary for coding the neurological examination for big data projects or machine learning. Hier DB, Brint SU. A Neuro-ontology for the neurological examination. BMC Med Inform Decis Mak. 2020;20(1):47. Published 2020 Mar 4. doi:10.1186/s12911-020-1066-7",
"download_owl": "http://aber-owl.net/media/ontologies/NEO/90/neo.owl",
"homepage": "https://doi.org/10.1186/s12911-020-1066-7",
"name": "Neurologic Examination Ontology",
"prefix": "NEO",
"version": "49.0"
},
"NEOMARK3": {
"description": "Ontology that describes the medical information necessary for early detection of the oral cancer reoccurrence extracted from the NeoMark Project.",
"download_owl": "http://aber-owl.net/media/ontologies/NEOMARK3/2/neomark3.owl",
"homepage": "http://www.neomark.eu/portal/",
"name": "Neomark Oral Cancer Ontology, version 3",
"prefix": "NEOMARK3",
"version": "3.1"
},
"NEOMARK4": {
"description": "Ontology that describes the medical information necessary for early detection of the oral cancer reoccurrence extracted from the NeoMark Project.",
"download_owl": "http://aber-owl.net/media/ontologies/NEOMARK4/1/neomark4.owl",
"homepage": "http://www.neomark.eu",
"name": "Neomark Oral Cancer Ontology, version 4",
"prefix": "NEOMARK4",
"version": "4.1"
},
"NERO": {
"description": "Named Entity Recognition Ontology (NERO) developed specifically for describing textual entities in biomedical texts, which accounts for diverse levels of ambiguity, bridging the scientific sublanguages of molecular biology, genetics, biochemistry, and medicine. The annotation of natural science texts is more challenging than in other domains. Biomedical language is replete with ambiguity distinct from that observed in news articles or informal text online. In biomedical texts, alternative meanings are not always clearly separated. For example, in some biomedical contexts, the words for a named entity may refer to a gene or a protein with nearly equal probability; for example, \u201ca mutant hemoglobin \u03b1_2\u201d can refer to either a gene or a protein. If the author meant gene-or-protein A, and we force an annotator to choose either interpretation gene A or protein A, the resulting annotation is of limited utility because the choice between gene and protein is random if the meanings are equally likely based on context. NERO attempts to minimize unwarranted, arbitrary annotative semantic label assignments for textual entities. NERO defines ambiguous concepts, such as GeneOrProtein, which subsumes both Gene and Protein using the following axiom: EquivalentTo: \u2018Gene\u2019 or \u2018Protein.\u2019 There are no biological entities that are either a gene or a protein, but there are lexical entities that can correspond to either or both of these entities.",
"download_owl": "http://aber-owl.net/media/ontologies/NERO/1/nero.owl",
"name": "Named Entity Recognition Ontology ",
"prefix": "NERO",
"version": "The main developer of NERO is Prof. Robert Stevens, the University of Manchester"
},
"NEST": {
"description": "It represents standards for nutritional epidemiological studies in ontology format. In the strict sense, it is not an ontology. Its hierarchy follows structure of each standard, not OWL rules.",
"download_owl": "http://aber-owl.net/media/ontologies/NEST/5/nest.owl",
"homepage": "https://github.com/cyang0128/Nutritional-epidemiological-ontologies",
"name": "Nutritional Epidemiological STandards",
"prefix": "NEST",
"version": "V1.2"
},
"NETFLIX": {
"description": "Learning how to biuld ontologies during UHC 2023 Summer Institute",
"download_owl": "http://aber-owl.net/media/ontologies/NETFLIX/1/netflix.owl",
"name": "Netflix Class Ontology ",
"prefix": "NETFLIX"
},
"NEUDIGS": {
"description": "Neuroscience Domain Insight Graphs provide a framework for expressing linked open data about",
"download_owl": "http://aber-owl.net/media/ontologies/NEUDIGS/1/neudigs.owl",
"homepage": "http://dig.isi.edu",
"name": "Neuroscience Domain Insight Graph",
"prefix": "NEUDIGS",
"version": "0.0.1"
},
"NEUMORE": {
"description": "Neural Functional Motor Recovery Ontology",
"download_owl": "http://aber-owl.net/media/ontologies/NEUMORE/1/neumore.owl",
"homepage": "http://cis.usouthal.edu/~huang/",
"name": "Neural Motor Recovery Ontology",
"prefix": "NEUMORE",
"version": "0.1"
},
"NEUROBRG": {
"description": "NeuroBridge ontology is being developed as part of the NeuroBridge project to implement FAIR principles for neuroimaging and neurophysiology data using computable provenance metadata. The NeuroBridge ontology extends the W3C PROV ontology and the ProvCaRe ontology with terms from the SchizConnect and Data Bridge ontology aligned and merged into the original class structure of the ProvCaRe ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/NEUROBRG/2/neurobrg.owl",
"homepage": "https://portal.neurobridges.org/",
"name": "NeuroBridge Ontology",
"prefix": "NEUROBRG",
"version": "1.0 (Release 2023)"
},
"NEUROTRANSH": {
"description": "A hierarchy of neuron types based on Neurotransmitter.",
"download_owl": "http://aber-owl.net/media/ontologies/NEUROTRANSH/4/neurotransh.owl",
"name": "NeuroMorpho.Org NT cell types",
"prefix": "NEUROTRANSH",
"version": "2.0"
},
"NEWS": {
"name": "NEWS ARTICLES",
"prefix": "NEWS"
},
"NGBO": {
"description": "The Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.",
"download_owl": "http://aber-owl.net/media/ontologies/NGBO/2/ngbo.owl",
"homepage": "https://github.com/Dalalghamdi/NGBO",
"name": "Next Generation Biobanking Ontology",
"prefix": "NGBO"
},
"NGSONTO": {
"description": "The NGSOnto ontology aims at capturing the workflow of all the processes involved in a Next Generation Sequencing, in order to ensure the reproducibility of the entire process, through the use of a controled and specific vocabulary.",
"download_owl": "http://aber-owl.net/media/ontologies/NGSONTO/32/ngsonto.owl",
"name": "NGS ontology",
"prefix": "NGSONTO",
"version": "1.2"
},
"NIAID-GSC-BRC": {
"description": "It is a subset of OBI containing all terms representing NIAID GSCID and BRC Core Metadata.",
"download_owl": "http://aber-owl.net/media/ontologies/NIAID-GSC-BRC/3/niaid-gsc-brc.owl",
"name": "NIAID GSC and BRC View",
"prefix": "NIAID-GSC-BRC",
"version": "2015-04-13"
},
"NIDHIAGARWAL": {
"name": "nidhiagarwal",
"prefix": "NIDHIAGARWAL"
},
"NIDM-RESULTS": {
"description": "NIDM-Results is a data model that enable sharing neuroimaging results using a common descriptive standard across neuroimaging software. NIDM-Results focuses on mass-univariate studies and is mostly targeted at fMRI but is also suitable for anatomical MRI (with Voxel-Based Morphometry), and Positron Emission Tomography (PET). NIDM-Results packs provide a lightweight solution to share maps generated by neuroimaging studies along with their metadata. Export to NIDM-Results is natively implemented in SPM, NeuroVault and CBRAIN and a Python library is ready for integration in FSL. NeuroVault additionally can import NIDM-Results packs.",
"download_owl": "http://aber-owl.net/media/ontologies/NIDM-RESULTS/2/nidm-results.owl",
"homepage": "http://nidm.nidash.org/specs/nidm-results.html",
"name": "NIDM-Results",
"prefix": "NIDM-RESULTS",
"version": "Recommendation version 2013-04-30"
},
"NIF-RTH": {
"description": "This is a view of NIFSTD (version 2.82) containing the Resource Type Hierarchy.",
"download_owl": "http://aber-owl.net/media/ontologies/NIF-RTH/2/nif-rth.owl",
"name": "NIF - Resource Type Hieracrchy (view)",
"prefix": "NIF-RTH",
"version": "unknown"
},
"NIFCELL": {
"description": "Cell types from NIFSTD",
"download_owl": "http://aber-owl.net/media/ontologies/NIFCELL/15/nifcell.owl",
"homepage": "http://neuinfo.org/",
"name": "Neuroscience Information Framework (NIF) Cell Ontology",
"prefix": "NIFCELL",
"version": "v.1.10 - July 17, 2013"
},
"NIFDYS": {
"description": "This ontology contains the former BIRNLex-Disease, version 1.3.2. -- The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. It is built using the organizational framework provided by the foundational Basic Formal Ontology (BFO). It uses an abstract biomedical layer on top of that - OBO-UBO which has been constructed as a proposal to the OBO Foundry. This is meant to support creating a sharable view of core biomedical objects such as biomaterial_entity, and organismal_entity that all biomedical ontologies are likely to need and want to use with the same intended meaning. The BIRNLex biomaterial entities have already been factored to separately maintained ontology - BIRNLexBiomaterialEntity.owl which this BIRNLex-Main.owl file imports. The Ontology of Biomedical Investigation (OBI) is also imported and forms the foundation for the formal description of all experiment-related artifacts. The BIRNLex will serve as the basis for construction of a formal ontology for the multiscale investigation of neurological disease.",
"download_owl": "http://aber-owl.net/media/ontologies/NIFDYS/15/nifdys.owl",
"homepage": "http://neuinfo.org/",
"name": "Neuroscience Information Framework (NIF) Dysfunction Ontlogy",
"prefix": "NIFDYS",
"version": "1.5 (December, 2012)"
},
"NIFSTD": {
"description": "NIF Standard ontology (NIFSTD) is a core component of Neuroscience Information Framework (NIF) project (http://neuinfo.org), a semantically enhanced portal for accessing and integrating neuroscience data, tools and information. NIFSTD includes a set of modular ontologies that provide a comprehensive collection of terminologies to describe neuroscience data and resources.",
"download_owl": "http://aber-owl.net/media/ontologies/NIFSTD/23/nifstd.owl",
"homepage": "http://ontology.neuinfo.org",
"name": "Neuroscience Information Framework (NIF) Standard Ontology",
"prefix": "NIFSTD",
"version": "3.0 - October 16, 2017"
},
"NIFSUBCELL": {
"description": "http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl",
"download_owl": "http://aber-owl.net/media/ontologies/NIFSUBCELL/1/nifsubcell.owl",
"name": "Neuroscience Information Framework (NIF) Subcellular Ontology",
"prefix": "NIFSUBCELL",
"version": "1.3 (May 2012)"
},
"NIGO": {
"description": "The Neural-Immune Gene Ontology (NIGO) is a subset of GO directed for neurological and immunological systems. NIGO was created by clipping those GO terms that are not associated to any gene in human, rat and mouse, and by clipping terms not found to be relevant to the neural and/or immune domains.",
"download_obo": "http://aber-owl.net/media/ontologies/NIGO/2/nigo.obo",
"name": "Neural-Immune Gene Ontology",
"prefix": "NIGO",
"version": "v1"
},
"NIHSS": {
"description": "Domain ontology for National Institutes of Health Stroke Scale (NIHSS). Scores range from 0-42. Patients are given more points for greater deficiencies. A score of 0 indicates that the test is normal.",
"download_owl": "http://aber-owl.net/media/ontologies/NIHSS/11/nihss.owl",
"name": "National Institutes of Health Stroke Scale Ontology",
"prefix": "NIHSS",
"version": "2016/09"
},
"NIO": {
"description": "An integrative ontology of the four main domains of neuropsychological diseases, brain areas, cognitive functions and neuropsychological tests",
"download_owl": "http://aber-owl.net/media/ontologies/NIO/2/nio.owl",
"name": "Neuropsychological Integrative Ontology",
"prefix": "NIO",
"version": "1.1.1"
},
"NIST_GEL": {
"description": "Genome editing technology is a fast-growing and rapidly advancing global bioscience field with applications in many biotechnology sectors. Genome editing is used to modify the nucleic acids of a genetic code, which can be composed of DNA or RNA, in a site-specific manner. Modifications can include insertion, deletion or alteration of nucleic acids. The technology operates by biochemical principles generally applicable to every kind of cell. Examples of genome editing technology applications with global significance include human cell-based therapeutics, agriculture, microbial based therapeutics, synthetic biology and biomanufacturing. While genome editing technology is being actively utilized, there is a need for international standardization in terms and definitions for this field, so as to enhance interpretation and communication of concepts, data and results. This document has been developed to provide a unified standard set of terms and definitions that serve the needs of biotechnology stakeholders and act as a reference for genome editing technology.",
"download_owl": "http://aber-owl.net/media/ontologies/NIST_GEL/7/nist_gel.owl",
"homepage": "https://www.nist.gov/programs-projects/nist-genome-editing-lexicon",
"name": "NIST Genome Editing Lexicon",
"prefix": "NIST_GEL",
"version": "2.1"
},
"NLMVS": {
"description": "NIH NLM Value Set as a SKOS terminology",
"homepage": "https://github.com/ncbo/NLMVS2RDF",
"name": "NIH NLM Value Sets",
"prefix": "NLMVS",
"version": "1.0"
},
"NLN": {
"description": "The NLighten ontology is an ontology designed to model clinical research/trials educational resourcses. It includes a model of educational resources and a taxonomy of clinical research competencies. The educational resource model reuses many schema.org concepts, the taxonomy is based on a variety of domain competency frameworks, and the ontology is designed to work with the eagle-i software platform.",
"download_owl": "http://aber-owl.net/media/ontologies/NLN/1/nln.owl",
"homepage": "https://github.com/NLightenGroup/nlighten-ontology",
"name": "NLighten Ontology",
"prefix": "NLN",
"version": "2018-02-28"
},
"NMDCO": {
"description": "The NMDC Ontology (NMDCO) is used by the National Microbiome Data Collaborative (NMDC, https://microbiomedata.org) to annotate multi-omic microbiome metadata. It merges a number of ontologies relevant to the NMDC (such as the plant and environment ontologies) into a single ontology. The ontology can be download from Github at https://github.com/microbiomedata/nmdc-ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/NMDCO/8/nmdco.owl",
"homepage": "https://github.com/microbiomedata/nmdc-ontology",
"name": "NMDC Ontology",
"prefix": "NMDCO",
"version": "2024-03-15"
},
"NMOBR": {
"description": "The species, brain regions and cell types are integrated into a single ontology for enabling OntoSearch functionality to mine the latest v7.0 release of NeuroMorpho.Org.",
"download_owl": "http://aber-owl.net/media/ontologies/NMOBR/32/nmobr.owl",
"name": "NeuroMorpho.Org brain region ontologies",
"prefix": "NMOBR",
"version": "2.0"
},
"NMOBR_1": {
"description": "The complete hierarchy of species, brain regions, cell types, and experimental conditions representing the neuronal reconstructions shared on NeuroMorpho.Org.",
"download_owl": "http://aber-owl.net/media/ontologies/NMOBR_1/18/nmobr_1.owl",
"name": "NeuroMorpho.Org Complete Metadata Ontology",
"prefix": "NMOBR_1",
"version": "2.1"
},
"NMOBR_2": {
"description": "NeuroMorpho.Org v7.0 Ontologies for human readability.",
"download_owl": "http://aber-owl.net/media/ontologies/NMOBR_2/6/nmobr_2.owl",
"name": "NeuroMorpho.Org Hierarchies for browsing",
"prefix": "NMOBR_2",
"version": "2.2"
},
"NMOCT": {
"description": "A hierarchy of several neuron description dimensions including circuit type, morphology, neurotransmitter, and functional properties.",
"download_owl": "http://aber-owl.net/media/ontologies/NMOCT/5/nmoct.owl",
"name": "NeuroMorpho.Org cell type ontologies",
"prefix": "NMOCT",
"version": "2.0"
},
"NMOSP": {
"description": "The species ontology of NeuroMorpho.Org was updated (OntoSearch v1.3) to map the new species and strains added in NeuroMorpho.Org v6.3 release.",
"download_owl": "http://aber-owl.net/media/ontologies/NMOSP/18/nmosp.owl",
"homepage": "NeuroMorpho.Org",
"name": "NeuroMorpho.Org species ontology",
"prefix": "NMOSP",
"version": "1.3"
},
"NMR": {
"description": "This is the new msi-sanctioned nmr CV, created within the COSMOS EU project, to support the nmrML data standard for nuclear magnetic resonance data in metabolomics with meaningful raw data descriptors.",
"download_owl": "http://aber-owl.net/media/ontologies/NMR/12/nmr.owl",
"homepage": "http://nmrml.org/cv/",
"name": "NMR-Controlled Vocabulary",
"prefix": "NMR",
"version": "1.1.0"
},
"NND_CD": {
"description": "This view represents a subset of the Human Disease Ontology (DOID) containing all the clinical diagnoses that are relevant for the most common neurodegenerative and psychiatric disorders in the Netherlands Brain Bank.",
"download_owl": "http://aber-owl.net/media/ontologies/NND_CD/2/nnd_cd.owl",
"name": "NND_Clinical_Diagnosis",
"prefix": "NND_CD",
"version": "2023-03-31"
},
"NND_CH": {
"description": "Netherlands Neurogenetics Database Clinical History ontology. This ontology describes clinical signs, symptoms and findings from the most common neurodegenerative and psychiatric disorders in the Netherlands Brain Bank and can be used for cross-disorder brain research. These attributes encompass 19 groupings, including \u2018Disturbances in mood and behavior\u2019, \u2018Extrapyramidal signs\u2019, \u2018Cognitive and memory impairment\u2019 in 5 broad domains: Psychiatric, Cognitive, Motor, Sensory/autonomic, and General.",
"download_obo": "http://aber-owl.net/media/ontologies/NND_CH/2/nnd_ch.obo",
"name": "NND_Clinical_history",
"prefix": "NND_CH",
"version": "1"
},
"NND_ND": {
"description": "Netherlands Neurogenetics Database Neuropathological Diagnosis ontology. This ontology describes the most common neurodegenerative and psychiatric disorders in the Netherlands Brain Bank and can be used for cross-disorder brain research.",
"download_owl": "http://aber-owl.net/media/ontologies/NND_ND/2/nnd_nd.owl",
"name": "NND_Neuropathological_Diagnosis",
"prefix": "NND_ND",
"version": "2023-03-31"
},
"NOMEN": {
"description": "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature.",
"download_owl": "http://aber-owl.net/media/ontologies/NOMEN/9/nomen.owl",
"homepage": "https://github.com/SpeciesFileGroup/nomen",
"name": "NOMEN - A nomenclatural ontology for biological names",
"prefix": "NOMEN"
},
"NONRCTO": {
"description": "We built an ontology to help the systematic review and meta-analysis process of non randomized clinical trials.",
"download_owl": "http://aber-owl.net/media/ontologies/NONRCTO/1/nonrcto.owl",
"name": "Non-Randomized Controlled Trials Ontology",
"prefix": "NONRCTO",
"version": "2.0"
},
"NORREG": {
"description": "Norway has 52 national quality registers with over 5000 different variables, which each has their own value set. This is a mapping between similar variables and to other ontologies.",
"download_owl": "http://aber-owl.net/media/ontologies/NORREG/1/norreg.owl",
"homepage": "https://docs.google.com/spreadsheets/d/1w2NatnnDfacYqrs24HDxQuEBM_xmGxL8-DilqAHVFDM/edit#gid=1014457671",
"name": "Norwegian national quality registries- Variabelbibliotek for medisinske kvalitetsregistre ",
"prefix": "NORREG"
},
"NPHO": {
"description": "first draft",
"download_owl": "http://aber-owl.net/media/ontologies/NPHO/1/npho.owl",
"name": "Nightshade Phenotype Ontology",
"prefix": "NPHO"
},
"NPI": {
"description": "Terminologies of Non-Pharmacological Interventions",
"download_owl": "http://aber-owl.net/media/ontologies/NPI/4/npi.owl",
"homepage": "http://www.cepsplatform.eu",
"name": "Non-Pharmacological Interventions (NPIs)",
"prefix": "NPI",
"version": "Version 2.0"
},
"NPO": {
"description": "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.",
"download_owl": "http://aber-owl.net/media/ontologies/NPO/31/npo.owl",
"homepage": "http://www.nano-ontology.org",
"name": "NanoParticle Ontology",
"prefix": "NPO",
"version": "2011-12-08 (yyyy-mm-dd)"
},
"NPOKB": {
"description": "An ontology of neuron types based on the phenotypic dimensions of cells that can be measure experimentally.",
"download_owl": "http://aber-owl.net/media/ontologies/NPOKB/15/npokb.owl",
"homepage": "https://github.com/SciCrunch/NIF-Ontology",
"name": "Neuron Phenotype Ontology",
"prefix": "NPOKB",
"version": "2024-08-01"
},
"NRO": {
"description": "The neural reprogramming ontology encompasses the domain of neural regenerative cell reprogramming knowledge. As research progresses, researchers and specialists in the field of reprogramming could continue to expand the bounds of this foundation, so adding to its depth.",
"download_owl": "http://aber-owl.net/media/ontologies/NRO/1/nro.owl",
"name": "NeuralReprogrammingOntology",
"prefix": "NRO",
"version": "1.0.0"
},
"NTDO": {
"description": "The Neglected Tropical Disease Ontology (NTDO) aims at representing classes and relations to a specific set of diseases which persist in exactly the physical, psychosocial and economic situation of the poorest, most marginalized populations of the developing world, the Neglected Tropical Diseases (NTD). The current focus of NTDO is related to the transmission of vector-borne diseases and how they are related to the death. NTDO is based on BioTop (main classes and relations) and GFO (Time Representation) and represented in Description Logics (DL). NTDO includes information about the proper disease, its causative agent (when available), dispositions, and the geographic location the disease happens. In addition, NTDO includes a generic attempt to identify the process which leads a person to death, due to NTDs or other diseases. NTDO was built with a rich set of axioms and the intended usage is related to Health Surveillance of NTD-related morbidity and mortality cases.",
"download_owl": "http://aber-owl.net/media/ontologies/NTDO/1/ntdo.owl",
"homepage": "http://www.cin.ufpe.br/~ntdo",
"name": "Neglected Tropical Disease Ontology",
"prefix": "NTDO",
"version": "Rev. 368"
},
"NXDX": {
"description": "A test for ontology submission",
"download_owl": "http://aber-owl.net/media/ontologies/NXDX/1/nxdx.owl",
"name": "Test NXDX",
"prefix": "NXDX",
"version": "2021/8/10"
},
"NeuroFMA": {
"description": "A view of FMA for neuroanatomy",
"download_owl": "http://aber-owl.net/media/ontologies/NeuroFMA/1/neurofma.owl",
"name": "NeuroFMA",
"prefix": "NeuroFMA",
"version": "1"
},
"O-REXTECH": {
"description": "second draft, M4M workshop, testing SKOS-Play and workflows. Add top concepts and more hierarchy.",
"name": "OSIRIS-REx Analytical Technique",
"prefix": "O-REXTECH",
"version": "0.0.2"
},
"OA": {
"description": "The Web Annotation Data Model specification describes a structured model and format to enable annotations to be shared and reused across different hardware and software platforms. Annotations are typically used to convey information about a resource or associations between resources. Simple examples include a comment or tag on a single web page or image, or a blog post about a news article.",
"download_owl": "http://aber-owl.net/media/ontologies/OA/4/oa.owl",
"homepage": "https://www.w3.org/TR/annotation-model/",
"name": "Web Annotation Ontology",
"prefix": "OA",
"version": "2016-11-12T21:28:11Z"
},
"OAE": {
"description": "A biomedical ontology in the domain of adverse events",
"download_owl": "http://aber-owl.net/media/ontologies/OAE/178/oae.owl",
"homepage": "https://github.com/OAE-ontology/OAE/",
"name": "Ontology of Adverse Events",
"prefix": "OAE"
},
"OARCS": {
"description": "OArCS is an ontology describing the Arthropod ciruclatory system.",
"download_owl": "http://aber-owl.net/media/ontologies/OARCS/3/oarcs.owl",
"homepage": "https://github.com/aszool/oarcs",
"name": "Ontology of Arthropod Circulatory Systems",
"prefix": "OARCS"
},
"OBA": {
"description": "A collection of biological attributes (traits) covering all kingdoms of life.",
"download_owl": "http://aber-owl.net/media/ontologies/OBA/21/oba.owl",
"homepage": "https://github.com/obophenotype/bio-attribute-ontology",
"name": "Ontology of Biological Attributes",
"prefix": "OBA"
},
"OBCS": {
"description": "A biomedical ontology in the domain of biological and clinical statistics.",
"download_owl": "http://aber-owl.net/media/ontologies/OBCS/16/obcs.owl",
"homepage": "https://github.com/obcs/obcs",
"name": "Ontology of Biological and Clinical Statistics",
"prefix": "OBCS"
},
"OBI": {
"description": "An integrated ontology for the description of life-science and clinical investigations",
"download_owl": "http://aber-owl.net/media/ontologies/OBI/54/obi.owl",
"homepage": "http://obi-ontology.org",
"name": "Ontology for Biomedical Investigations",
"prefix": "OBI"
},
"OBIB": {
"description": "An ontology built for annotation and modeling of biobank repository and biobanking administration",
"download_owl": "http://aber-owl.net/media/ontologies/OBIB/15/obib.owl",
"homepage": "https://github.com/biobanking/biobanking",
"name": "Ontology for Biobanking",
"prefix": "OBIB"
},
"OBIWS": {
"description": "The Bioinformatics Web Services ontology (OBIws) is an ontology that extends the Ontology for Biomedical Investigations (OBI) to build an Ontology that supports consistent annotation of Bioinformatics Web services.",
"download_owl": "http://aber-owl.net/media/ontologies/OBIWS/2/obiws.owl",
"homepage": "http://code.google.com/p/obi-webservice/",
"name": "Bioinformatics Web Service Ontology",
"prefix": "OBIWS",
"version": "Release v1.1"
},
"OBI_BCGO": {
"description": "Beta Cell Genomics Ontology (BCGO) is an application ontology built for the Beta Cell Genomics database (http://genomics.betacell.org/gbco/) aiming to support database annotation, complicated semantic queries, and automated cell type classification. The ontology is developed using Basic Formal Ontology (BFO) as upper ontology, Ontology for Biomedical Investigations (OBI) as ontology framework and integrated subsets of multiple OBO Foundry (candidate) ontologies. Current the BCGO contains 2383 classes including terms referencing to 24 various OBO Foundry ontologies including CL, CLO, UBERON, GO, PRO, UO, etc.",
"download_owl": "http://aber-owl.net/media/ontologies/OBI_BCGO/14/obi_bcgo.owl",
"homepage": "https://github.com/obi-bcgo/bcgo",
"name": "Beta Cell Genomics Ontology",
"prefix": "OBI_BCGO",
"version": "2015-07-08"
},
"OBI_IEDB_view": {
"description": "OBI view for IMMUNE EPITOPE DATABASE (IEDB) community. The OBI terms used by IEDB were tagged by inSubSet annotation with the value \"IEDB\". The IEDB friendly labels were provided as IEDB alternative term.",
"download_owl": "http://aber-owl.net/media/ontologies/OBI_IEDB_view/1/obi_iedb_view.owl",
"name": "IEDB View",
"prefix": "OBI_IEDB_view",
"version": "2011-12-13"
},
"OBI_IEE": {
"description": "Inner Ear Electrophysiology (IEE) is an application ontology created to describe electrophysiology and biophysical data collections of the anatomical entities and cells (e.g., outer hair cells) of the inner ear. The ontology is developed with The Ontology for Biomedical Investigations (OBI) and integrated subsets of multiple OBO ontologies, especially, PATO, FMA, CHEBI, and OBA.",
"download_owl": "http://aber-owl.net/media/ontologies/OBI_IEE/1/obi_iee.owl",
"name": "The Ontology for Biomedical Investigation based Inner Ear Electrophysiology ",
"prefix": "OBI_IEE",
"version": "2018-05-23"
},
"OBOE": {
"description": "The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations. The main concepts in OBOE include: - Observation: an event in which one or more measurements are taken - Measurement: the measured value of a property for a specific object or phenomenon (e.g., 3.2) - Entity: an object or phenomenon on which measurements are made (e.g., Quercus rubrum) - Characteristic: the property being measured (e.g., VolumetricDensity) - Standard: units and controlled vocabularies for interpreting measured values (e.g., g/cm^3) - Protocol: the procedures followed to obtain measurements (e.g., DensityProtocol2014) OBOE can characterize the context of an observation (e.g., space and time), as well as dependencies such as nested experimental observations. It includes an extensive set of unit definitions (e.g., grams of carbon per liter of seawater), and can facilitate automatic unit conversions (e.g., pounds to kilograms). OBOE can be easily extended to create Entities and Characteristics for specific research domains, making it both broadly applicable and highly customizable. OBOE is being used to improve data interpretation, facilitate reuse, and create precise and effective systems for data search and discovery.",
"download_owl": "http://aber-owl.net/media/ontologies/OBOE/4/oboe.owl",
"homepage": "https://github.com/NCEAS/oboe",
"name": "The Extensible Observation Ontology",
"prefix": "OBOE",
"version": "Version 1.2"
},
"OBOE-SBC": {
"description": "Extensible Observation Ontology for the Santa Barbara Coastal Long Term Ecological Research project (SBC-LTER). OBOE SBC extends core concepts defined in the OBOE suite that are particular to the Santa Barbara Coastal Long Term Ecological Research project's data collection activities. These include specific measurement protocols, sites, etc. This is mean as a case study ontology for the Semtools project.",
"download_owl": "http://aber-owl.net/media/ontologies/OBOE-SBC/1/oboe-sbc.owl",
"homepage": "https://semtools.ecoinformatics.org/",
"name": "Santa Barbara Coastal Observation Ontology",
"prefix": "OBOE-SBC",
"version": "Version 1.0"
},
"OBOREL": {
"description": "A collection of relations intended primarily for standardization across ontologies in the OBO Foundry and wider OBO library. It incorporates ROCore upper-level relations such as part of as well as biology-specific relationship types such as develops from.",
"download_owl": "http://aber-owl.net/media/ontologies/OBOREL/10/oborel.owl",
"homepage": "https://github.com/oborel/obo-relations/",
"name": "Relations Ontology",
"prefix": "OBOREL"
},
"OBS": {
"description": "Application ontology for covariate selection support.",
"download_owl": "http://aber-owl.net/media/ontologies/OBS/5/obs.owl",
"name": "OntoBioStat",
"prefix": "OBS"
},
"OCCO": {
"description": "An ontology representing occupations. It is designed to facilitate harmonization of existing occupation standards, such as the US Bureau of Labor Statistics Standard Occupational Classification (US SOC), the International Standard Classification of Occupations (ISCO), the UK National Statistics Standard Occupational Classification (UK SOC), and the European Skills, Competences, Qualifications and Occupations (ESCO) of the European Union.",
"download_owl": "http://aber-owl.net/media/ontologies/OCCO/8/occo.owl",
"homepage": "https://github.com/Occupation-Ontology/OccO",
"name": "Occupation Ontology",
"prefix": "OCCO"
},
"OCD": {
"description": "The Obsessive Compulsive Disorder Ontology (OCD) is a domain-specific ontology for representing the knowledge of OCD.",
"download_owl": "http://aber-owl.net/media/ontologies/OCD/8/ocd.owl",
"name": "OCD ontology",
"prefix": "OCD"
},
"OCD-O-3_TOPO": {
"description": "International Classification of Diseases for Oncology, 3rd Revision, Topography",
"download_owl": "http://aber-owl.net/media/ontologies/OCD-O-3_TOPO/1/ocd-o-3_topo.owl",
"name": "ICD-O-3 Topography",
"prefix": "OCD-O-3_TOPO",
"version": "3.1"
},
"OCDM": {
"description": "The Ontology of Craniofacial Development and Malformation (OCDM) is a mechanism for representing knowledge about craniofacial development and malformation, and for using that knowledge to facilitate integrating craniofacial data obtained via multiple techniques from multiple labs and at multiple levels of granularity. The OCDM is a project of the NIDCR-sponsored FaceBase Consortium, whose goal is to promote and enable research into the genetic and epigenetic causes of specific craniofacial abnormalities through the provision of publicly accessible, integrated craniofacial data.",
"download_owl": "http://aber-owl.net/media/ontologies/OCDM/4/ocdm.owl",
"homepage": "https://www.facebase.org/ocdm/",
"name": "Ontology of Craniofacial Development and Malformation",
"prefix": "OCDM",
"version": "1.8"
},
"OCE": {
"description": "The Ontology of Chemical Elements (OCE) is a community-based ontology in the domain of chemical elements. OCE systematically represents and annotates the known 118 chemical elements and their charactistics and relations with other entities. OCE imports the basic chemical element information from ChEBI and adds more classes, annotations, and axioms. OCE specifically focuses on adding all the related information from the Periodic Table of Chemical Elements.",
"download_owl": "http://aber-owl.net/media/ontologies/OCE/2/oce.owl",
"homepage": "https://github.com/ontologyofchemicalelements/OCE",
"name": "Ontology of Chemical Elements",
"prefix": "OCE",
"version": "Vision Release: 1.0.29"
},
"OCHV": {
"description": "A SKOS-encoded implementation of the \"Open Access, Collaborative Consumer Health Vocabulary Initiative\" by the University of Utah (consumerhealthvocab.org and layhealthinformatics.com)",
"download_owl": "http://aber-owl.net/media/ontologies/OCHV/1/ochv.owl",
"name": "Ontology of Consumer Health Vocabulary",
"prefix": "OCHV",
"version": "1"
},
"OCIMIDO": {
"description": "Application ontology for Ocular Immune-mediated Inflammatory Diseases, built from domain experts in ophthalmology, clinical guidelines, and enhanced with patient-preferred terms.",
"download_owl": "http://aber-owl.net/media/ontologies/OCIMIDO/2/ocimido.owl",
"homepage": "https://github.com/sap218/ocimido",
"name": "Ocular Immune-Mediated Inflammatory Diseases Ontology",
"prefix": "OCIMIDO",
"version": "1.2"
},
"OCMR": {
"description": "OCMR is a biomedical ontology that represents anti-rheumatism traditional Chinese medicines and related information.",
"download_owl": "http://aber-owl.net/media/ontologies/OCMR/3/ocmr.owl",
"homepage": "https://github.com/biomedontology/ocmr",
"name": "Ontology of Chinese Medicine for Rheumatism",
"prefix": "OCMR",
"version": "Vision Release; 1.0.11"
},
"OCO": {
"description": "Open healthCare Ontology (OpenCare) is an integrated metadata vocabulary expressed as an ontological data model, to facilitate the effective reasoning of patient-specific electronic health record (EHR) data. The OpenCare model identifies the concepts and semantic types in the EHR data with the aim of enabling the representation of clinical data in a way that is accessible and usable by researchers and healthcare facility users. The development of OpenCare and its components is formalized using the Ontology Web Language (OWL). This framework aims to enhance the accessibility and user-friendliness of EHR clinical data.",
"download_owl": "http://aber-owl.net/media/ontologies/OCO/2/oco.owl",
"homepage": "https://w3id.org/opencare",
"name": "OpenCareOntology ",
"prefix": "OCO",
"version": "1.1"
},
"OCRE": {
"description": "OCRe is an ontology designed to support systematic description of, and interoperable queries on, human studies and study elements.",
"download_owl": "http://aber-owl.net/media/ontologies/OCRE/23/ocre.owl",
"homepage": "http://rctbank.ucsf.edu/home/ocre",
"name": "Ontology of Clinical Research",
"prefix": "OCRE",
"version": "Revision 315"
},
"OCVDAE": {
"description": "OCVDAE is a biomedical ontology of cardiovascular disease drug-associated adverse events",
"download_owl": "http://aber-owl.net/media/ontologies/OCVDAE/2/ocvdae.owl",
"name": "Ontology of Cardiovascular Drug Adverse Events",
"prefix": "OCVDAE",
"version": "Vision Release; 1.0.4"
},
"ODAE": {
"description": "The Ontology of Drug Adverse Events (ODAE) is a biomedical ontology in the area of drug adverse events, developed by following OBO Foundry principles (e.g., openness, collaboration).",
"download_owl": "http://aber-owl.net/media/ontologies/ODAE/1/odae.owl",
"homepage": "https://github.com/ODAE-ontology/ODAE",
"name": "Ontology of Drug Adverse Events",
"prefix": "ODAE",
"version": "Vision Release: 1.0.08"
},
"ODHT": {
"description": "An ontology of digital health technologies (DHTs) with a specific focus on DHT use in clinical trials.",
"download_owl": "http://aber-owl.net/media/ontologies/ODHT/2/odht.owl",
"name": "Digital Health Technologies",
"prefix": "ODHT",
"version": "0.2"
},
"ODNAE": {
"description": "ODNAE is an extension of OAE with a focus on drug-associated neuropathy adverse events.",
"download_owl": "http://aber-owl.net/media/ontologies/ODNAE/3/odnae.owl",
"homepage": "https://github.com/odnae/odnae",
"name": "Ontology of Drug Neuropathy Adverse Events",
"prefix": "ODNAE",
"version": "Vision Release; 1.0.13"
},
"OF": {
"description": "This is an ontology with SWRL rules of nutrition for diabetic patient. We can import the value of Blood Sugar and Weight by .xls and use that like instance for generate the rules with rule engine Jess.",
"download_owl": "http://aber-owl.net/media/ontologies/OF/1/of.owl",
"name": "OntoFood",
"prefix": "OF",
"version": "1.0"
},
"OFSMR": {
"description": "Food-matrix ontology for Open Food Safety Model Repository",
"download_owl": "http://aber-owl.net/media/ontologies/OFSMR/19/ofsmr.owl",
"homepage": "https://sites.google.com/site/openfsmr/open-fsmr-detailfilter",
"name": "Open Predictive Microbiology Ontology",
"prefix": "OFSMR",
"version": "0.4"
},
"OGDI": {
"description": "It is the ontology used to model the scientific investigation, especially Genome-Wide Association Study (GWAS), to find out genetic susceptibility factor to disease, such as Diabetes. It models the genetic varaints, polymorphisms, statistical measurement, populations and other elements that are essential to determine a genetic susceptibility factor in GWAS study. It must be used with other two ontologies, in the case of Diabetes, :Ontology of Geographical Region (OGR) and Ontology of Glucose Metabolism Disorder (OGMD) .",
"download_owl": "http://aber-owl.net/media/ontologies/OGDI/3/ogdi.owl",
"name": "Ontology for Genetic Disease Investigations",
"prefix": "OGDI",
"version": "1.0"
},
"OGG": {
"description": "A formal ontology of genes and genomes of biological organisms.",
"download_owl": "http://aber-owl.net/media/ontologies/OGG/4/ogg.owl",
"homepage": "https://bitbucket.org/hegroup/ogg",
"name": "The Ontology of Genes and Genomes",
"prefix": "OGG"
},
"OGG-MM": {
"description": "OGG-Mm is the OGG Mus musculus (mouse) subset. The OGG (Ontology of Genes and Genomes) is a formal ontology of genes and genomes of biological organisms. OGG is developed by following OBO Foundry principles and aligning with the BFO top ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/OGG-MM/2/ogg-mm.owl",
"homepage": "https://bitbucket.org/hegroup/ogg-mouse",
"name": "Ontology of Genes and Genomes - Mouse",
"prefix": "OGG-MM",
"version": "Vision Release: 1.0.63"
},
"OGI": {
"description": "Using BFO as its framwork, OGI formalized the genomic element by defining an upper class 'genetic interval'. The definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.",
"download_owl": "http://aber-owl.net/media/ontologies/OGI/18/ogi.owl",
"homepage": "https://code.google.com/p/ontology-for-genetic-interval/",
"name": "Ontology for genetic interval",
"prefix": "OGI",
"version": "2.0"
},
"OGMD": {
"description": "Including the disease names. phenotypes and their classifications involved in Glucose Metabolism Disorder, Diabetes. (OBO and OWL format are available in sourceforge.) OWL file is downloadable as the different view here.",
"download_obo": "http://aber-owl.net/media/ontologies/OGMD/33/ogmd.obo",
"homepage": "http://sourceforge.net/projects/ogmd/",
"name": "Ontology of Glucose Metabolism Disorder",
"prefix": "OGMD",
"version": "1"
},
"OGMD_OWL": {
"description": "OWL file of the ontology",
"download_owl": "http://aber-owl.net/media/ontologies/OGMD_OWL/1/ogmd_owl.owl",
"homepage": "https://sourceforge.net/projects/ogmd/",
"name": "Ontology of Glucose Metabolism Disorder OWL View",
"prefix": "OGMD_OWL",
"version": "3.0"
},
"OGMS": {
"description": "An ontology for representing treatment of disease and diagnosis and on carcinomas and other pathological entities",
"download_owl": "http://aber-owl.net/media/ontologies/OGMS/19/ogms.owl",
"homepage": "https://github.com/OGMS/ogms",
"name": "Ontology for General Medical Science",
"prefix": "OGMS"
},
"OGR": {
"description": "This OWL ontology classified the geograhical regions related vocabularies extracted from UMLS. It used with other ontologies to represent the genetic susceptibility factors of diabetes.",
"download_owl": "http://aber-owl.net/media/ontologies/OGR/2/ogr.owl",
"name": "Ontology of Geographical Region",
"prefix": "OGR",
"version": "1.1"
},
"OGROUP": {
"description": "Ontology to help prossessing the information from orthologous groups in order to infer new functional annotations. The ontology integrates definitions from diverse ontologies.",
"download_owl": "http://aber-owl.net/media/ontologies/OGROUP/1/ogroup.owl",
"name": "Orthologous Group Ontology",
"prefix": "OGROUP",
"version": "1.0"
},
"OGSF": {
"description": "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.",
"download_owl": "http://aber-owl.net/media/ontologies/OGSF/11/ogsf.owl",
"homepage": "none",
"name": "Ontology of Genetic Susceptibility Factor",
"prefix": "OGSF"
},
"OHD": {
"description": "The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies.",
"download_owl": "http://aber-owl.net/media/ontologies/OHD/8/ohd.owl",
"homepage": "https://purl.obolibrary.org/obo/ohd/home",
"name": "Oral Health and Disease Ontology",
"prefix": "OHD"
},
"OHMI": {
"description": "The Ontology of Host-Microbiome Interactions aims to ontologically represent and standardize various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions.",
"download_owl": "http://aber-owl.net/media/ontologies/OHMI/16/ohmi.owl",
"homepage": "https://github.com/ohmi-ontology/ohmi",
"name": "Ontology of Host-Microbiome Interactions",
"prefix": "OHMI"
},
"OHPI": {
"description": "OHPI is a community-driven ontology of host-pathogen interactions (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs in the Victors database become less virulence inside a host organism or host cells. It is developed to represent manually curated HPI knowledge available in the PHIDIAS resource.",
"download_owl": "http://aber-owl.net/media/ontologies/OHPI/12/ohpi.owl",
"homepage": "https://github.com/OHPI/ohpi",
"name": "Ontology of Host Pathogen Interactions",
"prefix": "OHPI"
},
"OLAM": {
"description": "The OLAM is community-based biomedical ontology in the field of laboratory animal medicine, with the aim to ontologically represent entities and the relations among the entities related to laboratory animal medicine.",
"download_owl": "http://aber-owl.net/media/ontologies/OLAM/7/olam.owl",
"homepage": "https://github.com/olam-ontology/OLAM",
"name": "Ontology of Laboratory Animal Medicine",
"prefix": "OLAM",
"version": "Vision Release: 1.0.20"
},
"OLATDV": {
"description": "Life cycle stages for Medaka",
"download_owl": "http://aber-owl.net/media/ontologies/OLATDV/9/olatdv.owl",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv",
"name": "Medaka Developmental Stages",
"prefix": "OLATDV"
},
"OLIVES": {
"description": "The Ontology for Vaccine Effectiveness Studies (OLIVES)",
"download_owl": "http://aber-owl.net/media/ontologies/OLIVES/1/olives.owl",
"name": "Ontology for Influenza Vaccine Effectiveness Studies",
"prefix": "OLIVES",
"version": "Inital work-in-progress"
},
"OM": {
"description": "The Ontology of units of Measure (OM) 2.0 models concepts and relations important to scientific research. It has a strong focus on units, quantities, measurements, and dimensions. OM is modelled in OWL 2 - Web Ontology Language. The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units metre and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant or the quantity vaselife. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology and Typography.",
"download_owl": "http://aber-owl.net/media/ontologies/OM/31/om.owl",
"homepage": "https://github.com/HajoRijgersberg/OM",
"name": "Ontology of units of Measure",
"prefix": "OM",
"version": "2.0.57"
},
"OMDO": {
"description": "The OligoMetastatic Disease Ontology(OMDO) is a disease-specific ontology that characterizes the knowledge field of oligometastatic disease/oligometastatic cancer.",
"download_owl": "http://aber-owl.net/media/ontologies/OMDO/1/omdo.owl",
"name": "OligoMetastatic Disease Ontology",
"prefix": "OMDO"
},
"OMIABIS": {
"description": "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)",
"download_owl": "http://aber-owl.net/media/ontologies/OMIABIS/2/omiabis.owl",
"homepage": "https://github.com/OMIABIS/omiabis-dev",
"name": "Ontologized MIABIS",
"prefix": "OMIABIS"
},
"OMIM": {
"description": "Online Mendelian Inheritance in Man, OMIM (TM). McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine",
"homepage": "http://www.ncbi.nlm.nih.gov/omim/",
"name": "Online Mendelian Inheritance in Man",
"prefix": "OMIM",
"version": "2016AB"
},
"OMIT": {
"description": "Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain",
"download_owl": "http://aber-owl.net/media/ontologies/OMIT/41/omit.owl",
"homepage": "http://omit.cis.usouthal.edu/",
"name": "Ontology for MIRNA Target",
"prefix": "OMIT"
},
"OMO": {
"description": "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO).",
"download_owl": "http://aber-owl.net/media/ontologies/OMO/10/omo.owl",
"homepage": "https://github.com/information-artifact-ontology/ontology-metadata",
"name": "OBO Metadata Ontology",
"prefix": "OMO"
},
"OMP": {
"description": "An ontology of phenotypes covering microbes",
"download_owl": "http://aber-owl.net/media/ontologies/OMP/59/omp.owl",
"homepage": "http://microbialphenotypes.org",
"name": "Ontology of Microbial Phenotypes",
"prefix": "OMP"
},
"OMRSE": {
"description": "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations.",
"download_owl": "http://aber-owl.net/media/ontologies/OMRSE/58/omrse.owl",
"homepage": "https://github.com/mcwdsi/OMRSE/wiki/OMRSE-Overview",
"name": "Ontology for Modeling and Representation of Social Entities",
"prefix": "OMRSE"
},
"OMV": {
"description": "A standard for ontology metadata; a vocabulary of terms and definitions describing ontologies which specifies reusability-enhancing ontology features for human and machine processing purposes.",
"download_owl": "http://aber-owl.net/media/ontologies/OMV/1/omv.owl",
"homepage": "http://omv2.sourceforge.net/index.html",
"name": "Ontology Metadata Vocabulary",
"prefix": "OMV",
"version": "2.4.1"
},
"ONE": {
"description": "An ontology to standardize research output of nutritional epidemiologic studies.",
"download_owl": "http://aber-owl.net/media/ontologies/ONE/9/one.owl",
"homepage": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies",
"name": "Ontology for Nutritional Epidemiology",
"prefix": "ONE"
},
"ONL-DP": {
"description": "This ontology is a module of the OntoNeuroLOG ontology, developed in the context of the NeuroLOG project, a french project supported by ANR (ANR-06-TLOG-024 grant) aiming at integrating distributed heterogeous resources in neuroimaging. If covers the domain of Datasets and the processing of datasets. It includes a detailed taxonomy of datasets in the area of neuroimaging (and especially MR imaging) as well as a taxonomy of medical image processing.",
"download_owl": "http://aber-owl.net/media/ontologies/ONL-DP/1/onl-dp.owl",
"homepage": "http://neurolog.unice.fr/ontoneurolog/v3.0/Documentation_OntoNeuroLOGv3.pdf",
"name": "Dataset processing",
"prefix": "ONL-DP",
"version": "V1"
},
"ONL-MR-DA": {
"description": "This ontology is a module of the OntoNeuroLOG ontology, developed in the context of the NeuroLOG project, a french project supported by ANR (ANR-06-TLOG-024 grant) aiming at integrating distributed heterogeneous resources in neuroimaging. If covers the domain of Magnetic Resonance Imaging (MRI) dataset acquisition, i.e. MRI protocols, and MRI sequence parameters. In particular, it includes a multi-axial classification of MR sequences.",
"download_owl": "http://aber-owl.net/media/ontologies/ONL-MR-DA/1/onl-mr-da.owl",
"homepage": "http://neurolog.unice.fr/ontoneurolog/v3.0/Documentation_OntoNeuroLOGv3.pdf",
"name": "Magnetic Resonance Dataset Acquisition Ontology",
"prefix": "ONL-MR-DA",
"version": "V1"
},
"ONL-MSA": {
"description": "This ontology is a module of the OntoNeuroLOG ontology, developed in the context of the NeuroLOG project, a french project supported by ANR (ANR-06-TLOG-024 grant) aiming at integrating distributed heterogeous resources in neuroimaging. This MSA ontology module covers the field of mental state assessments, i.e. instruments, instrument variables, assessments, and resulting scores. It includes a generic domain core ontology, that provides a general model of such entities and a general taxonomy of behavioural, neurosychological and neuroclinical instruments, that can be easily extended to model any particular kind of instrument. It also includes such extensions for 8 relatively standard instruments, namely: (1) the Beck-depression-inventory-(BDI-II), (2) the Expanded-Disability-Status-Scale, (3) the Controlled-oral-word-association-test, (4) the Free-and-Cued-Selective-Reminding-Test-with-Immediate-Recall-16-item-version-(The-Gr\u00f6ber-and-Buschke-test), (5) the Mini-Mental-State, (6) the Stroop-color-and-word-test, (7) the Trail-making-test-(TMT), (8) the Wechsler-Adult-Intelligence-Scale-third-edition, (9) the Clinical-Dementia-Rating-scale, (10) the Category-verbal-fluency, (11) the Rey-Osterrieth-Complex-Figure-Test-(CFT).",
"download_owl": "http://aber-owl.net/media/ontologies/ONL-MSA/1/onl-msa.owl",
"homepage": "http://neurolog.unice.fr/ontoneurolog/v3.0/Documentation_OntoNeuroLOGv3.pdf",
"name": "Mental State Assessment",
"prefix": "ONL-MSA",
"version": "v1"
},
"ONL-TASKS": {
"description": "This ontology is an extension of the OntoNeuroLOG ontology, developed in the context of a project supported by Russian Foundation for Basic Research (19-29-01017 grant). The ontology organizes tests that are used for assessing cognitive reserves with the focus on keywords that can be employed in mining of PubMed publications.",
"download_owl": "http://aber-owl.net/media/ontologies/ONL-TASKS/1/onl-tasks.owl",
"name": "Cognitive Reserves Assessment Tasks",
"prefix": "ONL-TASKS"
},
"ONLIRA": {
"description": "ONLIRA (Ontology of the Liver for Radiology) focuses on a semantic specification of imaging observations of CT scans for the liver. ONLIRA extends RadLex with semantic relationships that describe and relate the concepts. Thus, automated processing tasks, such as identifying similar patients, are supported.",
"download_owl": "http://aber-owl.net/media/ontologies/ONLIRA/4/onlira.owl",
"homepage": "http://vavlab.ee.boun.edu.tr/pages.php?p=research/CARERA/carera.html",
"name": "Ontology of Liver for Radiology",
"prefix": "ONLIRA",
"version": "changes\n* Segments and Regions are modelling as Classes in order to identify which patient (liver) they belong to.\n* Redundant restrictions are removed"
},
"ONS": {
"description": "An ontology for description of concepts in the nutritional studies domain.",
"download_owl": "http://aber-owl.net/media/ontologies/ONS/28/ons.owl",
"homepage": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies",
"name": "Ontology for Nutritional Studies",
"prefix": "ONS"
},
"ONSTR": {
"description": "Ontology for Newborn Screening Follow-up and Translational Research (ONSTR) is an application ontology covering the domain of newborn screening, follow-up and translational research pertaining to patients diagnosed with inheritable and congenital diseases mainly identified through newborn dried blood spot screening. ONSTR is a central component of the project Newborn Screening Follow-up Data Integration Collaborative (NBSDC). ONSTR uses the Basic Formal Ontology v2 (BFO2, v2012-07-20) as top-level ontology and extends the classes imported from OBO Foundry ontologies and candidate ontologies. For latest release notes please see: http://onstr.googlecode.com/svn/tags/currentRelease/2013-05-02/ NBSDC project page: https://nbsdc.org (under construction).",
"download_owl": "http://aber-owl.net/media/ontologies/ONSTR/5/onstr.owl",
"homepage": "http://code.google.com/p/onstr/",
"name": "Ontology for Newborn Screening Follow-up and Translational Research",
"prefix": "ONSTR",
"version": "0.4"
},
"ONTOAD": {
"description": "OntoAD is a bilingual (English-French) domain ontology for modeling knowledge about Alzheimer's Disease and Related Syndromes.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTOAD/2/ontoad.owl",
"name": "Bilingual Ontology of Alzheimer's Disease and Related Diseases",
"prefix": "ONTOAD",
"version": "1.0"
},
"ONTOAVIDA": {
"description": "OntoAvida develops an integrated vocabulary for the description of the most widely-used computational approach for studying evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment).",
"download_owl": "http://aber-owl.net/media/ontologies/ONTOAVIDA/3/ontoavida.owl",
"homepage": "https://gitlab.com/fortunalab/ontoavida",
"name": "OntoAvida: ontology for Avida digital evolution platform",
"prefix": "ONTOAVIDA"
},
"ONTODM-ALGORITHM": {
"description": "OntoDM-algorithms is an ontology for data mining and machine learning entities.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTODM-ALGORITHM/2/ontodm-algorithm.owl",
"name": "OntoDM-core/algorithms",
"prefix": "ONTODM-ALGORITHM",
"version": "0.1"
},
"ONTODM-CORE": {
"description": "OntoDM is a generic ontology for the domain of data mining. The ontology includes the information processing processes that occur in the domain of data mining, participants in the processes and their specifications. OntoDM is highly transferable and extendable due to its adherence to accepted standards, and compliance with existing ontology resources. The generality in scope allows wide number of applications of the ontology, such as semantic annotation of data mining scenarios, ontology based support for QSARs, etc.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTODM-CORE/8/ontodm-core.owl",
"homepage": "www.ontodm.com",
"name": "Ontology of Core Data Mining Entities",
"prefix": "ONTODM-CORE",
"version": "1.0R"
},
"ONTODM-KDD": {
"description": "OntoDM-KDD is an ontology for representing data mining investigations. Its goal is to allow the representation of knowledge discovery processes and be general enough to represent the data mining investigations. The ontology is based on the CRISP-DM process methodology.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTODM-KDD/1/ontodm-kdd.owl",
"homepage": "www.ontodm.com",
"name": "Ontology of Data Mining Investigations",
"prefix": "ONTODM-KDD",
"version": "0.1"
},
"ONTODRC": {
"name": "ONTODRC",
"prefix": "ONTODRC"
},
"ONTODT": {
"description": "This ontology contains entities such as: datatype, datatype generator, datatype qualiy and others giving the possibility to represent arbitrary complex datatypes. This is an important fact for a general data mining ontology that wants to represent and query over modelling algorithms for mining structured data. The ontology was first developed under the OntoDM (Ontology of Data Mining is available at http://kt.ijs.si/panovp/OntoDM) ontology, but for generality and reuse purpose it was decided to export it as a separate ontology. Additionaly, the OntoDT ontology is based on and ISO/IEC 11404 (http://www.iso.org/iso/catalogue_detail.htm?csnumber=39479) standard and can be reused used independently by any domain ontology that requires representation and reasoning about general purpose datatypes.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTODT/8/ontodt.owl",
"homepage": "http://www.ontodt.com",
"name": "Ontology of Datatypes",
"prefix": "ONTODT",
"version": "1.0"
},
"ONTOKBCF": {
"description": "OntoKBCF is an ontological knowledge base model for cystic fibrosis. There are molecular genetic information (i.e. gene mutations) and health information included in OntoKBCF. The purposes of OntoKBCF include management of molecular genetic information and health information and embedding OntoKBCF into EHR settings.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTOKBCF/3/ontokbcf.owl",
"name": "Ontological Knowledge Base Model for Cystic Fibrosis",
"prefix": "ONTOKBCF",
"version": "1301"
},
"ONTOLOCO": {
"description": "The OntoLoco provides a standardized vocabulary of the stroke domain for effective communication and knowledge-sharing across virtual-reality-based locomotion rehabilitation programs.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTOLOCO/1/ontoloco.owl",
"name": "Virtual Reality Ontology for Locomotion Rehabilitation Training of Stroke Injuries",
"prefix": "ONTOLOCO",
"version": "V 1.1"
},
"ONTOLURGENCES": {
"description": "Emergency care ontology build during LERUDI project. http://www.ncbi.nlm.nih.gov/pubmed/25160343 (v4.0)",
"download_owl": "http://aber-owl.net/media/ontologies/ONTOLURGENCES/1/ontolurgences.owl",
"name": "Emergency care ontology",
"prefix": "ONTOLURGENCES",
"version": "3.0.4"
},
"ONTOMA": {
"description": "Common concepts for communication between traditional medicine and western medicine. (In French)",
"download_owl": "http://aber-owl.net/media/ontologies/ONTOMA/1/ontoma.owl",
"homepage": "www.lavima.org",
"name": "Ontology of Alternative Medicine, French",
"prefix": "ONTOMA",
"version": "Version 1.1\nDate: 11-2011"
},
"ONTONEO": {
"description": "The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTONEO/12/ontoneo.owl",
"homepage": "ontoneo.com",
"name": "Obstetric and Neonatal Ontology",
"prefix": "ONTONEO"
},
"ONTONEO-CORE": {
"description": "Collect the basic information required to work with Obstetric and Neonatal care.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTONEO-CORE/1/ontoneo-core.owl",
"homepage": "ontoneo.wordpress.com",
"name": "OntONeo-core",
"prefix": "ONTONEO-CORE",
"version": "Version 1.0"
},
"ONTONEO-DOC": {
"description": "Focus on the documents used along the Obstetric and Neonatal care such EHRs and consent form.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTONEO-DOC/1/ontoneo-doc.owl",
"homepage": "ontoneo.wordpress.com",
"name": "OntONeo-documents",
"prefix": "ONTONEO-DOC",
"version": "Version 1.0"
},
"ONTOPARON": {
"description": "Ontology of ALS (amyotrophic lateral sclerosis), social module + coordination module + medical module developped by neurologists (ICM) and knowledge engineers (LIMICS). This version (11/15/2018) is upload with inferred axioms but without equivalent classe axioms. It serves in this version in a Gate pipeline for a semantic annotation task. This version (03/20/2019) is upload with object properties, inferred axioms and equivalent classes axioms. This version (11/10/2020) is uploaded with small corrections.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTOPARON/9/ontoparon.owl",
"name": "Ontology of Amyotrophic Lateral Sclerosis, all modules",
"prefix": "ONTOPARON",
"version": "1.1"
},
"ONTOPARON_SOCIAL": {
"name": "Ontology of amyotrophic lateral sclerosis, social module",
"prefix": "ONTOPARON_SOCIAL"
},
"ONTOPBM": {
"description": "OntoPBM is an ontology of core entities for process-based modeling of dynamical systems.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTOPBM/13/ontopbm.owl",
"name": "Ontology for Process-Based Modeling of Dynamical Systems (OntoPBM)",
"prefix": "ONTOPBM",
"version": "0.1"
},
"ONTOPNEUMO": {
"description": "Ontology of pneumology (french version). The ONTOPNEUMO ontology was developped by Audrey Baneyx, under the direction of Jean Charlet about knowledge engineering expertise and by Fran\u00e7ois-Xavier Blanc in collaboration with Bruno Housset about medical expertise. The OWL compliant ONTOPNEUMO ontology is available under Creative Commons license \u201cAttribution-Non-Commercial-No Derivative Works 2.0 UK\u201d. Details of this license are accessible at : http://creativecommons.org/licenses/ by-nc-nd/2.0/uk/.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTOPNEUMO/1/ontopneumo.owl",
"name": "Ontology of Pneumology",
"prefix": "ONTOPNEUMO",
"version": "0.1"
},
"ONTOPPS": {
"description": "A patient safety ontology",
"download_owl": "http://aber-owl.net/media/ontologies/ONTOPPS/1/ontopps.owl",
"name": "Ontopps",
"prefix": "ONTOPPS",
"version": "1"
},
"ONTOPSYCHIA": {
"description": "Ontology of social and environmental determinants for psychiatry",
"download_owl": "http://aber-owl.net/media/ontologies/ONTOPSYCHIA/1/ontopsychia.owl",
"name": "OntoPsychia, social module",
"prefix": "ONTOPSYCHIA",
"version": "1.0"
},
"ONTOREPLICOV": {
"description": "OntoRepliCov is an ontology designed to describe the different stages of the SARS-CoV-2 replication process.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTOREPLICOV/1/ontoreplicov.owl",
"name": "OntoRepliCov",
"prefix": "ONTOREPLICOV",
"version": "0"
},
"ONTOSIM": {
"description": "[pt] A Ontologia do SIM foi desenvolvida no contexto do projeto DIASUS. Ela buscou resgatar a estrutura presente na ficha de preenchimento da Declara\u00e7\u00e3o de \u00d3bito - DO, do Sistema de Informa\u00e7\u00e3o de Mortalidade - SIM, do Sistema \u00danico de Sa\u00fade, do Brasil. [en] The SIM Ontology was developed in the context of DIASUS project. This ontology intent to rescue the data structure presented in Death Certificate form, from Information System on Mortality - SIM, from Brazilian Public Health System - SUS.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTOSIM/2/ontosim.owl",
"name": "The Ontology of Information System on Mortality",
"prefix": "ONTOSIM",
"version": "1.0.0"
},
"ONTOSINASC": {
"description": "[pt-br] A Ontologia do SINASC foi desenvolvida no contexto do projeto DIASUS. Ela buscou resgatar a estrutura presente na ficha de preenchimento da Declara\u00e7\u00e3o de Nascido Vivo - DN, do Sistema de Informa\u00e7\u00e3o de Nascidos Vivos - SINASC, do Sistema \u00danico de Sa\u00fade, do Brasil. [en] The SINASC Ontology was developed in the context of DIASUS project. This ontology intent to rescue the data structure presented in Live Birth Certificate form, from Information System on Live Births - SINASC, from Brazilian Public Health System - SUS.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTOSINASC/1/ontosinasc.owl",
"name": "Ontology of Information System on Live Births",
"prefix": "ONTOSINASC",
"version": "1.0.0"
},
"ONTOTOX": {
"description": "OntoTox is an ontology designed to represent chemotherapy toxicities extracted from various data in Clinical Data Warehouses. OntoTox can integrate toxicities and grading information extracted from heterogeneous sources. Examples of OntoTox instantiations can be found in GitHub : https://github.com/TeamHeka/OntoTox",
"download_owl": "http://aber-owl.net/media/ontologies/ONTOTOX/1/ontotox.owl",
"homepage": "https://github.com/TeamHeka/OntoTox",
"name": "Chemotherapy Toxicities Ontology",
"prefix": "ONTOTOX",
"version": "1.0"
},
"ONTOTOXNUC": {
"description": "Ontology of nuclear toxicity developed during ToxNuc project <>.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTOTOXNUC/2/ontotoxnuc.owl",
"name": "Ontology of Nuclear Toxicity",
"prefix": "ONTOTOXNUC",
"version": "1.0"
},
"ONTRISCAL": {
"description": "This ontology organizes concepts and properties of risk stratification in mental health. Stratification aims to determine the patient's risk level by scoring signs and symptoms. Psychotherapeutic treatments aim to minimize patient risk by producing qualitative data reported in therapeutic sessions. Thus, the ONTRISCAL is applied in projects that organize the knowledge about quali-quanti data produced by risk stratification and mental health treatments. Quali-quanti data, semantically annotated by ONTRISCAL, can be ingested into knowledge graphs. Domain specialists can use knowledge graphs to navigate the ONTRISCAL concepts, analyze psychotherapeutic treatments, and control risks in mental health. This is a non-profit and open-source project.",
"download_owl": "http://aber-owl.net/media/ontologies/ONTRISCAL/1/ontriscal.owl",
"name": "Ontology of Risk Stratification in Mental Health",
"prefix": "ONTRISCAL",
"version": "1.0"
},
"OOEVV": {
"description": "The ontology of experimental variables and values provides a lightweight representation of (a) the variables used to measure experimental properties and (b) the measurement scales that form the complex data types supporting that data. Many different variables measure the same thing, here we use a lightweight representation driven by a small number of classes and a large number of variables to focus only on providing a vocabulary of variables that may be extended for consolidation to standardized variables for specific things and functions to map between values from different measurements scales. We use the base ontology description to provide a very lightweight representation of the basic elements of an experimental design and we use views to instantiate it for specific domains.",
"download_owl": "http://aber-owl.net/media/ontologies/OOEVV/4/ooevv.owl",
"homepage": "http://bmkeg.isi.edu",
"name": "Ontology of Experimental Variables and Values",
"prefix": "OOEVV",
"version": "0.0.4"
},
"OOSTT": {
"description": "An ontology built for representating the organizational components of trauma centers and trauma systems.",
"download_owl": "http://aber-owl.net/media/ontologies/OOSTT/12/oostt.owl",
"homepage": "https://github.com/OOSTT/OOSTT",
"name": "Ontology of Organizational Structures of Trauma centers and Trauma systems",
"prefix": "OOSTT"
},
"OPB": {
"description": "The OPB is a reference ontology of classical physics and thermodynamics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.",
"download_owl": "http://aber-owl.net/media/ontologies/OPB/13/opb.owl",
"homepage": "https://sites.google.com/site/semanticsofbiologicalprocesses/projects/the-ontology-of-physics-for-biology-opb",
"name": "Ontology of Physics for Biology",
"prefix": "OPB",
"version": "1.05"
},
"OPD-NAMBOBI": {
"name": "SELECTED OTHER PRIORITY DISEASES UNDER IDSR (INTEGRATED DISEASE SURVEILLANCE AND RESPONSES)",
"prefix": "OPD-NAMBOBI"
},
"OPDE": {
"description": "This is an OPD Registry Form in Ethiopia.",
"name": "OPD-Ethiopia",
"prefix": "OPDE"
},
"OPDRE": {
"name": "OPD Regitry Ethiopia",
"prefix": "OPDRE"
},
"OPDRONT": {
"description": "Vocabulary creation for OPD Register: MINISTRY OF HEALTH AND CHILD CARE",
"name": "OPD Register Ontology",
"prefix": "OPDRONT",
"version": "0.0.1"
},
"OPDT": {
"description": "opd test for group 2",
"name": "opd_test",
"prefix": "OPDT"
},
"OPDZIMBABWE": {
"description": "OPD Terms that are used in Zimbabwe.",
"name": "OPDZimbabwe",
"prefix": "OPDZIMBABWE",
"version": "1.1"
},
"OPE": {
"description": "The Ontology of Physical Exercises (OPE) provides a reference for describing an exercise in terms of functional movements, engaged musculoskeletal system parts, related equipment or monitoring devices, intended health outcomes, as well as target ailments for which the exercise might be employed as a treatment or preventative measure.",
"download_owl": "http://aber-owl.net/media/ontologies/OPE/6/ope.owl",
"name": "Ontology of Physical Exercises",
"prefix": "OPE",
"version": "0.0.1"
},
"OPL": {
"description": "A reference ontology for parasite life cycle stages.",
"download_owl": "http://aber-owl.net/media/ontologies/OPL/12/opl.owl",
"homepage": "https://github.com/OPL-ontology/OPL",
"name": "Ontology for Parasite LifeCycle",
"prefix": "OPL"
},
"OPMI": {
"description": "The Ontology of Precision Medicine and Investigation (OPMI) aims to ontologically represent and standardize various entities and relations associated with precision medicine and related investigations at different conditions.",
"download_owl": "http://aber-owl.net/media/ontologies/OPMI/29/opmi.owl",
"homepage": "https://github.com/OPMI/opmi",
"name": "Ontology of Precision Medicine and Investigation",
"prefix": "OPMI"
},
"OPP": {
"name": "Obat Pembesar Penis",
"prefix": "OPP"
},
"OPTIMAL": {
"description": "OPTImAL is a reusable formal model of factors affecting CVD patient adherence to physical activity and exercise. The basis for this model relies on the analysis of data/evidence published in the scientific literature and enables identification of adherence based on the patient profile. In the model, the patient profile is seen from the perspective of 60 multidimensional aspects (320 factors). Each factor is associated with defined adherence to a particular patient activity behavior.",
"download_owl": "http://aber-owl.net/media/ontologies/OPTIMAL/1/optimal.owl",
"name": "OPTImAL: An ontology for patient adherence modeling in physical activity domain",
"prefix": "OPTIMAL",
"version": "1"
},
"OPTION": {
"description": "OPTION:OPTImization Algorithm Benchmarking ONtology",
"download_owl": "http://aber-owl.net/media/ontologies/OPTION/1/option.owl",
"name": "OPTImization Algorithm Benchmarking ONtology",
"prefix": "OPTION",
"version": "1.0.0"
},
"OPTION-ONTOLOGY": {
"description": "OPTImization Algorithm Benchmarking ONtology",
"download_owl": "http://aber-owl.net/media/ontologies/OPTION-ONTOLOGY/3/option-ontology.owl",
"name": "Optimization Algorithm Benchmarking Ontology",
"prefix": "OPTION-ONTOLOGY",
"version": "1.0.0"
},
"ORCS": {
"description": "The Ontology for Representing CDM Semantics (ORCS) is an application ontology that was developed to represent the semantics underlying the National Patient-Centered Outcomes Research Network's (PCORnet) Common Data Model (CDM).",
"download_owl": "http://aber-owl.net/media/ontologies/ORCS/1/orcs.owl",
"homepage": "https://github.com/ufbmi/ORCS",
"name": "Ontology for Representing CDM Semantics",
"prefix": "ORCS",
"version": "2021-11-13"
},
"ORDO": {
"description": "The Orphanet Rare Disease ontology (ORDO) is jointly developed by Orphanet and the EBI to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It derived from the Orphanet database (www.orpha.net ) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, SNOMED CT, UMLS, MedDRA),databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10). The ontology will be maintained by Orphanet and further populated with new data. Orphanet classifications can be browsed in the OLS view. The Orphanet Rare Disease Ontology is updated monthly and follows the OBO guidelines on deprecation of terms. It constitutes the official ontology of rare diseases produced and maintained by Orphanet (INSERM, US14).",
"download_owl": "http://aber-owl.net/media/ontologies/ORDO/11/ordo.owl",
"homepage": "http://www.orpha.net",
"name": "Orphanet Rare Disease Ontology",
"prefix": "ORDO",
"version": "2.4"
},
"ORDO_CS": {
"description": "This ontology is the czech version of ORDO with definition, labels and synonyms in czech.",
"download_owl": "http://aber-owl.net/media/ontologies/ORDO_CS/5/ordo_cs.owl",
"homepage": "https://www.orphadata.com/ordo/",
"name": "ORDO Czech",
"prefix": "ORDO_CS",
"version": "4.5"
},
"ORDO_DE": {
"description": "This ontology is the german version of ORDO with definition, labels and synonyms in german.",
"download_owl": "http://aber-owl.net/media/ontologies/ORDO_DE/15/ordo_de.owl",
"homepage": "https://www.orphadata.com/ordo/",
"name": "ORDO GERMAN",
"prefix": "ORDO_DE",
"version": "4.5"
},
"ORDO_ES": {
"description": "This ontology is the spanish version of ORDO with definition, labels and synonyms in spanish.",
"download_owl": "http://aber-owl.net/media/ontologies/ORDO_ES/13/ordo_es.owl",
"homepage": "https://www.orphadata.com/ordo/",
"name": "ORDO SPANISH",
"prefix": "ORDO_ES",
"version": "4.5"
},
"ORDO_FR": {
"description": "This ontology is the french version of ORDO with definition, labels and synonyms in french. Cette ontologie est la version fran\u00e7aise d'ORDO avec les d\u00e9finitions, labels et synonymes en fran\u00e7ais.",
"download_owl": "http://aber-owl.net/media/ontologies/ORDO_FR/14/ordo_fr.owl",
"homepage": "https://www.orphadata.com/ordo/",
"name": "ORDO FRENCH",
"prefix": "ORDO_FR",
"version": "4.5"
},
"ORDO_IT": {
"description": "This ontology is the italian version of ORDO with definition, labels and synonyms in italian.",
"download_owl": "http://aber-owl.net/media/ontologies/ORDO_IT/10/ordo_it.owl",
"homepage": "https://www.orphadata.com/ordo/",
"name": "ORDO ITALIAN",
"prefix": "ORDO_IT",
"version": "4.5"
},
"ORDO_NL": {
"description": "This ontology is the dutch version of ORDO with definition, labels and synonyms in dutch.",
"download_owl": "http://aber-owl.net/media/ontologies/ORDO_NL/16/ordo_nl.owl",
"homepage": "https://www.orphadata.com/ordo/",
"name": "ORDO DUTCH",
"prefix": "ORDO_NL",
"version": "4.5"
},
"ORDO_OBO": {
"description": "This is the OBO version of the Orphanet Rare Disease ontology (ORDO) which is jointly developed by Orphanet and the EBI to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It derived from the Orphanet database (www.orpha.net ) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, SNOMED CT, UMLS, MedDRA),databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10).",
"download_obo": "http://aber-owl.net/media/ontologies/ORDO_OBO/1/ordo_obo.obo",
"homepage": "http://www.orpha.net",
"name": "Orphanet Rare Diseases Ontology in OBO",
"prefix": "ORDO_OBO",
"version": "1.0"
},
"ORDO_PL": {
"description": "This ontology is the polish version of ORDO with definition, labels and synonyms in polish.",
"download_owl": "http://aber-owl.net/media/ontologies/ORDO_PL/10/ordo_pl.owl",
"homepage": "https://www.orphadata.com/ordo/",
"name": "ORDO POLISH",
"prefix": "ORDO_PL",
"version": "4.5"
},
"ORDO_PT": {
"description": "This ontology is the portuguese version of ORDO with definition, labels and synonyms in portuguese.",
"download_owl": "http://aber-owl.net/media/ontologies/ORDO_PT/6/ordo_pt.owl",
"homepage": "https://www.orphadata.com/ordo/",
"name": "ORDO Portuguese",
"prefix": "ORDO_PT",
"version": "4.5"
},
"OREX-SAM": {
"description": "Sample types from JSC-SAMIS Interface Control Document. Edited by S.M. Richard. These sample types are limited to those expected from the OSIRIS-REx sample return, this is not an exhaustive sample type categorization.",
"name": "OSIRIS-REx sample type",
"prefix": "OREX-SAM",
"version": "0.2.0"
},
"OREX-WG": {
"description": "Workgroups organized to analyzed samples returned by OSIRIS-REx mission from asteroid Bennu. Mostly for reference in other metadata records.",
"name": "OSIRIS-REx sample analysis workgroups",
"prefix": "OREX-WG",
"version": "0.1.0"
},
"ORNASEQ": {
"description": "An application ontology designed to annotate next-generation sequencing experiments performed on RNA.",
"download_owl": "http://aber-owl.net/media/ontologies/ORNASEQ/2/ornaseq.owl",
"homepage": "http://kim.bio.upenn.edu/software/ornaseq.shtml",
"name": "Ontology of RNA Sequencing",
"prefix": "ORNASEQ"
},
"ORON": {
"description": "Currently, ontology for representing observational study manuscript is still missing. This ontology is developed as a representation ontology based on STROBE-nut reporting guideline. 1) Manuscript items are developed as classes; 2) STROBE-nut recommendations are developed as datatype properties.",
"download_owl": "http://aber-owl.net/media/ontologies/ORON/2/oron.owl",
"homepage": "https://github.com/cyang0128/Nutritional-epidemiological-ontologies",
"name": "Ontology for Reporting of Observational studies in Nutrition",
"prefix": "ORON",
"version": "V1.0"
},
"ORTH": {
"description": "Orthology Ontology",
"download_owl": "http://aber-owl.net/media/ontologies/ORTH/4/orth.owl",
"homepage": "https://github.com/qfo/OrthologyOntology",
"name": "Orthology Ontology",
"prefix": "ORTH",
"version": "2015-11-27"
},
"OSM": {
"description": "Esta ontologia foi desenvolvida para auxiliar na gest\u00e3o da Rede de Aten\u00e7\u00e3o Psicossocial no contexto brasileiro, a fim de possibilitar a cria\u00e7\u00e3o de ferramentas computacionais inteligentes, permitindo a integra\u00e7\u00e3o e interoperabilidade entre bases de dados independentes e possibilitando a gera\u00e7\u00e3o de indicadores para a sa\u00fade mental, visando melhorar a tomada de decis\u00e3o, o planejamento e a efici\u00eancia e efic\u00e1cia dos servi\u00e7os prestados \u00e0 comunidade.",
"download_owl": "http://aber-owl.net/media/ontologies/OSM/1/osm.owl",
"homepage": "https://saudeconectada.org/",
"name": "Ontologia de Sa\u00fade Mental",
"prefix": "OSM",
"version": "1"
},
"OVAE": {
"description": "A biomedical ontology in the domain of vaccine adverse events.",
"download_owl": "http://aber-owl.net/media/ontologies/OVAE/11/ovae.owl",
"homepage": "http://www.violinet.org/ovae/",
"name": "Ontology of Vaccine Adverse Events",
"prefix": "OVAE"
},
"OntoVIP": {
"description": "The OntoVIP ontology was developed in the context of the Virtual Imaging Platform project (VIP), a french project supported by ANR (ANR-09-COSI-03 grant) aiming at sharing medical image simulation resources. This ontology describes the content of the models used in medical image simulation. This ontology can be used to annotate such models in order to highlight the different entities that are present in the 3D scene to be imaged, i.e. anatomical structures, pathological structures, foreign bodies, contrast agents etc. The model allows also to associate to these entities information about their physical qualities, which are used in the medical image simulation process (to mimick physical phenomena involved in CT, MR, US and PET imaging). This ontology partly relies on the OntoNeuroLOG ontology (ONL-DP ONL-MR-DA), as well as PATO, RadLex, FMA and ChEBI.",
"download_owl": "http://aber-owl.net/media/ontologies/OntoVIP/1/ontovip.owl",
"homepage": "http://vip.creatis.insa-lyon.fr/ontovip/v1.0/Documentation_OntoVIPv1.pdf",
"name": "Medical image simulation",
"prefix": "OntoVIP",
"version": "v1"
},
"PACO": {
"description": "Physical Activity Concept Ontology (PACO) contains various concepts that are required to describe one's physical activity.",
"download_owl": "http://aber-owl.net/media/ontologies/PACO/2/paco.owl",
"name": "Physical Activity Ontology",
"prefix": "PACO",
"version": "0.2"
},
"PAE": {
"description": "REPLACED BY: Plant Ontology (PO). A controlled vocabulary of plant morphological and anatomical structures representing organs, tissues, cell types, and their biological relationships based on spatial and developmental organization. Note that this has been subsumed into the PO. This file is created by filtering plant_ontology_assert.obo to contain only terms from the plant anatomical entity branch of the PO. For more information, please see: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/",
"download_obo": "http://aber-owl.net/media/ontologies/PAE/13/pae.obo",
"homepage": "http://www.plantontology.org",
"name": "Plant Anatomy",
"prefix": "PAE",
"version": "Release #20"
},
"PAINO": {
"name": "Pain Ontology",
"prefix": "PAINO"
},
"PANDA": {
"description": "Probabilistic Knowledge Assembly (PANDA) Ontology has been developed in the context of the DARPA's Big Mechanism research program. It provides a semantic interface for capturing information on molecular interactions extracted from scientific texts.",
"download_owl": "http://aber-owl.net/media/ontologies/PANDA/2/panda.owl",
"name": "Probabilistic Knowledge Assembly Ontology",
"prefix": "PANDA",
"version": "0.9"
},
"PANET": {
"description": "The PaNET ontology provides a taxonomy and thesaurus of photon and neutron (PaN) experimental techniques, based mainly on accelerator-based light sources and neutron facilities. The primary use of the ontology is to enhance the FAIRness of PaN data catalogues services. The ontology defines specific techniques in terms of more general technique classes and provides synonyms and references.",
"download_owl": "http://aber-owl.net/media/ontologies/PANET/25/panet.owl",
"name": "PaN Experimental technique",
"prefix": "PANET",
"version": "1.0.0-3-g6a0b629-dirty"
},
"PARTUMDO": {
"description": "This ontology is for use in extracting postpartum depression condition codes, and also comorbidities and diseases often mistaken for postpartum depression. The ontology describes not only the codes but also the relationships between these various diseases/risk factors for use in automatically extracting relevant patient populations from Electronic Health Records",
"download_owl": "http://aber-owl.net/media/ontologies/PARTUMDO/1/partumdo.owl",
"name": "postpartum depression ontology",
"prefix": "PARTUMDO"
},
"PATAXO": {
"name": "Technical Taxonomies for Patents",
"prefix": "PATAXO"
},
"PATCT": {
"description": "Cell types associated with placental structure and function. This Cell Type ontology builds on the Cell Ontology (CL) as well as the BRENDA Tissue and Enzyme Source Ontology (BTO) and was further developed by PAT External Scientific Panel Members and contributions from other subject matter experts.",
"download_owl": "http://aber-owl.net/media/ontologies/PATCT/1/patct.owl",
"name": "Placental Cell Type",
"prefix": "PATCT",
"version": "1.0"
},
"PATEL": {
"description": "Covid19 Impact on Banking Ontology (Covid19-IBO) provides semantic information about the impact of the Covid-19 on the banking sector of India",
"download_owl": "http://aber-owl.net/media/ontologies/PATEL/1/patel.owl",
"name": "Archana Patel",
"prefix": "PATEL",
"version": "1"
},
"PATGV": {
"description": "Includes variations of DNA sequence, chromosomal structure and copy number, as well as RNA and translational variation. The Genetic Variation ontology expands on work done for Variation Ontology (VariO) and Sequence Types and Features Ontology (SO) which can be found on NCBO. This ontology was further developed by PAT External Scientific Panel Members and contributions from other subject matter experts.",
"download_owl": "http://aber-owl.net/media/ontologies/PATGV/1/patgv.owl",
"name": "Placental Genetic Variance",
"prefix": "PATGV",
"version": "1.0"
},
"PATHLEX": {
"description": "PathLex, a comprehensive lexicon\u2014a unified language of anatomic pathology terms\u2014for standardized indexing and retrieval of anatomic pathology information resources.",
"download_owl": "http://aber-owl.net/media/ontologies/PATHLEX/5/pathlex.owl",
"name": "Anatomic Pathology Lexicon",
"prefix": "PATHLEX",
"version": "1.2"
},
"PATIENTPERSONAL": {
"name": "Patient ontology",
"prefix": "PATIENTPERSONAL"
},
"PATIT": {
"description": "Experimental methods and observation types used in placental research. The PAT Investigative Techniques ontology builds on work done for a handful of existing ontologies, including the Ontology for Biomedical Investigations (OBI) and NCI Thesaurus (NCIT), and was further developed by PAT External Scientific Panel Members and contributions from other subject matter experts.",
"download_owl": "http://aber-owl.net/media/ontologies/PATIT/1/patit.owl",
"name": "Placental Investigative Technique",
"prefix": "PATIT",
"version": "1.0"
},
"PATMHC": {
"description": "Physical and psychological disorders in the mother that occur during pregnancy, childbirth, and the postpartum period. These include both pre-existing and gestational maternal health conditions that may result in adverse pregnancy outcomes. The Maternal Conditions Ontology builds on the work done for a handful of existing ontologies, including the Human Phenotype Ontology (HPO) and NCI Thesaurus (NCIT), and was further developed by PAT External Scientific Panel Members and contributions from other subject matter experts.",
"download_owl": "http://aber-owl.net/media/ontologies/PATMHC/1/patmhc.owl",
"name": "Placental Maternal Health Conditions",
"prefix": "PATMHC",
"version": "1.0"
},
"PATO": {
"description": "An ontology of phenotypic qualities (properties, attributes or characteristics)",
"download_owl": "http://aber-owl.net/media/ontologies/PATO/196/pato.owl",
"homepage": "https://github.com/pato-ontology/pato/",
"name": "Phenotype And Trait Ontology",
"prefix": "PATO"
},
"PAV": {
"description": "PAV is a lightweight ontology for tracking Provenance, Authoring and Versioning. PAV specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources. This ontology describes the defined PAV properties and their usage. Note that PAV does not define any explicit classes or domain/ranges, as every property is meant to be used directly on the described online resource.",
"download_owl": "http://aber-owl.net/media/ontologies/PAV/3/pav.owl",
"homepage": "https://github.com/pav-ontology/pav/",
"name": "PAV Provenance, Authoring and Versioning",
"prefix": "PAV",
"version": "2.3.1"
},
"PAYMENTMODE": {
"description": "This class refers to the different payment methods.",
"name": "Payment Mode",
"prefix": "PAYMENTMODE"
},
"PAYOR": {
"description": "This class refers to the entity that made the payment on behalf of the interviewee.",
"name": "Payor",
"prefix": "PAYOR"
},
"PBO": {
"description": "The need of standardizing the language used within a community has been recognized as one of the major components to enable a better integration of data as well as their further analysis. The plant breeding community makes use of a very specialized language, which has been evolving according to the new technologies and needs of their final users (e.g. farmers). That community is distributed all over the world. Therefore, a translation of the most common used terms has always been a key asset to accomplish their objectives as well as the ones of their collaborators. Here, we present the Plant Breeding Ontology (PBO), a resource for the plant breeding community which captures 80 core terms in 5 different languages: English (main language), Spanish, French, Dutch, German, and Japanese, as well as their definitions, synonyms, derived terms and samples of their usage. It also contains more than 2000 related terms. PBO has been built partially manually and semi-automatically. It is still under development.",
"download_owl": "http://aber-owl.net/media/ontologies/PBO/5/pbo.owl",
"name": "Plant Breeding Ontology",
"prefix": "PBO"
},
"PCALION": {
"description": "PCLiON:Prostate Cancer Lifestyle Ontology",
"download_owl": "http://aber-owl.net/media/ontologies/PCALION/6/pcalion.owl",
"homepage": "http://pcaontology.net/PCaLifeStyleDefault.aspx",
"name": "Prostate Cancer Lifestyle Ontology",
"prefix": "PCALION",
"version": "3.0"
},
"PCAO": {
"description": "Here, we introduce the Prostate cancer ontology (PCaO) as a comprehensive semantic framework covering the whole breadth of the PCa\u2019s knowledge domain. This ontology with a subclass-based taxonomic hierarchy not only covers the broad spectrum of major biomedical concepts from molecular to clinical features of the disease, but also the different views on disease features held by molecular biologists, clinicians and drug developers. PCaO organized under three biological viewpoints, i.e., epidemiology, diagnosis, and treatment.",
"download_owl": "http://aber-owl.net/media/ontologies/PCAO/2/pcao.owl",
"homepage": "http://pcaontology.net",
"name": "Prostate Cancer Ontology",
"prefix": "PCAO",
"version": "2.0"
},
"PCL": {
"description": "Cell types that are provisionally defined by experimental techniques such as single cell or single nucleus transcriptomics rather than a straightforward & coherent set of properties.",
"download_owl": "http://aber-owl.net/media/ontologies/PCL/25/pcl.owl",
"homepage": "https://github.com/obophenotype/provisional_cell_ontology",
"name": "Provisional Cell Ontology",
"prefix": "PCL"
},
"PCMO": {
"description": "Pediatric Consultation and Monitoring Ontology consists of 10 main classes, 10 sub-classes, 39 properties (object-type and sub-object-type properties, data type), numerous OWL individuals and almost 90 SWRL rules (medical cases based on ARTI based diseases for pediatric patients). Almost all the rules of the knowledge base consider: -Body temperature -Currently observed number of the local, major, and minor symptoms -Medications used and time of use in recent period (has drug and has drug time properties) -Presence of medical cold treatment applied in recent period \u21d2 only one of medical case will be inferencing result. Project Funding: \u201cThis research project was funded in 2014 by the National Science Foundation- The Scientific and Technological Research Council of Turkey (TUBITAK) under 1501 type funding program with the \u20183140417\u2019 grant number. The titled \u201cMobile Pediatric Consultation and Monitoring System\u201d project was successfully completed by the end of 2015. The project was completed by collaboration of the Ac\u0131badem Hospitals Group, Istanbul Aydin University and Semantica Internet and Software Services Trd. Ltd. Company in Turkey\u201d.",
"download_owl": "http://aber-owl.net/media/ontologies/PCMO/4/pcmo.owl",
"homepage": "http://cmpe.emu.edu.tr/duygu/",
"name": "Pediatric Consultation and Monitoring Ontology ",
"prefix": "PCMO",
"version": "v.4.0"
},
"PCO": {
"description": "An ontology about groups of interacting organisms such as populations and communities",
"download_owl": "http://aber-owl.net/media/ontologies/PCO/18/pco.owl",
"homepage": "https://github.com/PopulationAndCommunityOntology/pco",
"name": "Population and Community Ontology",
"prefix": "PCO"
},
"PCPCKB": {
"description": "Still",
"download_owl": "http://aber-owl.net/media/ontologies/PCPCKB/2/pcpckb.owl",
"homepage": "https://github.com",
"name": "PC Parts Compatibility Knowledge Base",
"prefix": "PCPCKB",
"version": "1.1"
},
"PDO": {
"description": "An ontology for describing both human infectious diseases caused by microbes and the diseases that is related to microbial infection.",
"download_owl": "http://aber-owl.net/media/ontologies/PDO/6/pdo.owl",
"homepage": "http://mdb.bio.titech.ac.jp/pdo",
"name": "Pathogenic Disease Ontology",
"prefix": "PDO",
"version": "Version 0.7"
},
"PDON": {
"description": "Here, we introduce the Parkinson\u2019s disease ontology (PDO) as a comprehensive semantic framework covering the whole breadth of the Parkinson\u2019s knowledge domain. This ontology with a subclass-based taxonomic hierarchy not only covers the broad spectrum of major biomedical concepts from molecular to clinical features of the disease, but also the different views on disease features held by molecular biologists, clinicians and drug developers. This resource has been created for use in the IMI-funded AETIONOMY project (www.aetionomy.org).",
"download_owl": "http://aber-owl.net/media/ontologies/PDON/1/pdon.owl",
"name": "Parkinson's Disease Ontology",
"prefix": "PDON",
"version": "1.0"
},
"PDO_CAS": {
"description": "Plant Diversity Ontology (PDO) is the outcome of the construction tasks of domain ontology of science in the project of Scientific & Technological Knowledge Organization Systems (STKOS). The structure of PDO centers on species, including micro level of molecular, cell and tissue, medium level of plant organs, species and population, and macro level of ecosystem. The classes of PDO also capture the habitat, environmental conditions and expand the general characteristics of plants, completing the instances richness for plant species, geographical, classification and morphology. Furthermore, PDO builds the relationships among species, region, morphology, plant organs, developmental stage, revealing the list of species in an area, the morphology and life form of plants, and development process of species. In sum, PDO shows a growth process or development stage of a species and its structure characteristics in particular space and time scale, realizing the description of species diversity, ecosystem diversity and genetic diversity. At present, PDO has been applied to the platform of Go to Selected Open Access Journals (GoOA) developed by National Science Library of Chinese Academy of Sciences, supporting concept retrieval and concept extension for GoOA.",
"download_owl": "http://aber-owl.net/media/ontologies/PDO_CAS/1/pdo_cas.owl",
"homepage": "http://gooa.las.ac.cn/external/index.jsp",
"name": "Plant Diversity Ontology",
"prefix": "PDO_CAS"
},
"PDQ": {
"description": "Physician Data Query (PDQ) Terminology is part of NCI's comprehensive cancer information database, which contains expert summaries on a wide range of cancer topics, a listing of some 30,000 cancer clinical trials from around the world, a directory of genetics services professionals, the NCI Dictionary of Cancer Terms, and the NCI Drug Dictionary.",
"name": "Physician Data Query",
"prefix": "PDQ",
"version": "2016AB"
},
"PDRO": {
"description": "An ontology to describe entities related to prescription of drugs",
"download_owl": "http://aber-owl.net/media/ontologies/PDRO/8/pdro.owl",
"homepage": "https://github.com/OpenLHS/PDRO",
"name": "The Prescription of Drugs Ontology",
"prefix": "PDRO"
},
"PDUMDV": {
"description": "Life cycle stages for Platynereis dumerilii",
"download_owl": "http://aber-owl.net/media/ontologies/PDUMDV/10/pdumdv.owl",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv",
"name": "Platynereis Developmental Stages",
"prefix": "PDUMDV"
},
"PE": {
"description": "A controlled vocabulary of PE-relevant information. Currently, only treatment information is available.",
"download_owl": "http://aber-owl.net/media/ontologies/PE/1/pe.owl",
"name": "Pulmonary Embolism Ontology",
"prefix": "PE",
"version": "version 1.0"
},
"PE-O": {
"description": "The PEO incorporates a wide range of key concepts and terms of PE from clinical and biomedical research in structuring the knowledge base that is specific to PE.",
"download_owl": "http://aber-owl.net/media/ontologies/PE-O/3/pe-o.owl",
"name": "Pre-eclampsia Ontology",
"prefix": "PE-O",
"version": "1.1.2"
},
"PEAO": {
"description": "The Plant domain has been the subject of several attempts to structure and formally define terms and corresponding relations, such as their anatomical features, developmental stages, and the application of particular experimental procedures to a biological problem. However, a focus on experimental assays in order to describe the whole experimental procedure, to the best of our knowledge, has only been attempted in the context of a very general description based on classical views of the scientific method. In this study, we focus on the development and proposal of an ontology dedicated to the description of these experimental procedures, regardless of the scientific questions that prompted the assays. This ontology includes entities from three distinct realms (biological, physical and data), which include both experimental products, their relations and the protocols describing their manipulation. The final outcome is a useful and comprehensive ontology in the plant domain, to be used as a log book by experimentalists, providing a formal relation between entities.",
"download_owl": "http://aber-owl.net/media/ontologies/PEAO/1/peao.owl",
"homepage": "https://bitbucket.org/PlantExpAssay/ontology",
"name": "Plant Experimental Assay Ontology",
"prefix": "PEAO"
},
"PECO": {
"description": "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.",
"download_owl": "http://aber-owl.net/media/ontologies/PECO/30/peco.owl",
"homepage": "http://planteome.org/",
"name": "Plant Experimental Conditions Ontology",
"prefix": "PECO"
},
"PEDTERM": {
"description": "Terms associated with pediatrics, representing information related to child health and development from pre-birth through 21 years of age; contributed by the National Institute of Child Health and Human Development.",
"download_owl": "http://aber-owl.net/media/ontologies/PEDTERM/5/pedterm.owl",
"name": "Pediatric Terminology",
"prefix": "PEDTERM",
"version": "Version 2.0"
},
"PEO": {
"description": "The Parasite Experiment Ontology (PEO) models provenance metadata associated with experiment protocols used in parasite research. The PEO extends the upper-level Provenir ontology (http://knoesis.wright.edu/provenir/provenir.owl) to represent parasite domain-specific provenance terms. The PEO (v 1.0) includes Proteome, Microarray, Gene Knockout, and Strain Creation experiment terms along with other terms that are used in pathway.",
"download_owl": "http://aber-owl.net/media/ontologies/PEO/5/peo.owl",
"homepage": "http://wiki.knoesis.org/index.php/Parasite_Experiment_ontology",
"name": "Parasite Experiment Ontology",
"prefix": "PEO",
"version": "1"
},
"PESONT": {
"description": "Preposition-enabled Spatial Ontology (PeSONT) is a model that describes health service with related concepts, sub-concepts, attributes, and relations among concepts. Inferences of new knowledge are possible using queries. PeSONT classifies linguistic place terms using (Bennett and Agarwal, 2007) and uses prepositions of English language for location identification. Its implementation is to further the application of the PeNLP parser on human related problems by classifying place-like terms in natural language and for extracting geolocations.",
"download_owl": "http://aber-owl.net/media/ontologies/PESONT/2/pesont.owl",
"name": "Preposition_enabled Spatial Ontology",
"prefix": "PESONT"
},
"PGHD-BP": {
"description": "Ontology containing terms describing the ancillary information surrounding the collection of Blood Pressure data and the communication via Interactive Voice Response in the context of the VODAN-Africa project.",
"homepage": "https://github.com/RenVit318/pghd",
"name": "PGHD Auxillary - BP",
"prefix": "PGHD-BP",
"version": "1.1"
},
"PGHD-COM": {
"description": "Vocabulary describing the method with which a specific metadata instance was sent to CEDAR",
"name": "DATA COMMUNICATION",
"prefix": "PGHD-COM"
},
"PGHD-COMM": {
"description": "Ontology containing terms describing the ancillary information surrounding the collection of Blood Pressure data and the communication via Interactive Voice Response in the context of the VODAN-Africa project.",
"homepage": "https://github.com/abdullahikawu/PGHD/",
"name": "PGHD COMMUNICATION",
"prefix": "PGHD-COMM",
"version": "1.2"
},
"PGHD_CONNECT": {
"description": "Overarching ontology containg terms to describe the various types of Patient Generated Health Data that are generated on a specific patients. Meant for implementation in the VODAN-Africa project.",
"homepage": "https://github.com/RenVit318/pghd",
"name": "PGHD_CONNECT",
"prefix": "PGHD_CONNECT",
"version": "1.0"
},
"PGXO": {
"description": "PGxO: a lite Pharmacogenomic Ontology. This ontology aims at providing a small set of concepts and roles that may type elements of pharmacogenomic relationships. Its concepts has been mapped to other existing ontologies. Mappings are not included in this version for lisibility purposes. Mapping are available on demand.",
"download_owl": "http://aber-owl.net/media/ontologies/PGXO/2/pgxo.owl",
"homepage": "https://members.loria.fr/ACoulet/",
"name": "PGxO",
"prefix": "PGXO",
"version": "0.2"
},
"PHAGE": {
"description": "This ontology represents the seven steps of phylogenetic analyses. Each root concept step is composed from a set of resource annotations (to represent the data-flow) and programs (to represent the control flow). Object properties serve to represent relations to annotate data (e.g. has_RetrievedInDatabase, has_ModeledBy, etc.) and reorder the sequence of programs (e.g. has_InputOutput).This ontology has been collected in a semi-automated way from well-known databases such as NCBI, GeneOntology, UniProtKB and Felsenstein\u2019s Web site through Web crawling and mapping techniques.",
"download_owl": "http://aber-owl.net/media/ontologies/PHAGE/5/phage.owl",
"name": "Phylogenetics Ontology",
"prefix": "PHAGE",
"version": "5.0"
},
"PHARE": {
"description": "The PHArmacogenomic RElationships Ontology (or PHARE) proposes concepts and roles to represent relationships of pharmacogenomics interest.",
"download_owl": "http://aber-owl.net/media/ontologies/PHARE/2/phare.owl",
"homepage": "http://bioportal.bioontology.org/ontologies/45138",
"name": "Pharmacogenomic Relationships Ontology",
"prefix": "PHARE",
"version": "Developed by the Helix Group, Department of Genetics, Stanford University, \nand by the Orpailleur Group, LORIA - INRIA Nancy."
},
"PHENX": {
"description": "Standard measures related to complex diseases, phenotypic traits and environmental exposures",
"download_owl": "http://aber-owl.net/media/ontologies/PHENX/16/phenx.owl",
"name": "PhenX Phenotypic Terms",
"prefix": "PHENX",
"version": "1.2"
},
"PHFUMIADO": {
"description": "The first ontology describing the anatomy and the development of Phallusia fumigata.",
"download_obo": "http://aber-owl.net/media/ontologies/PHFUMIADO/2/phfumiado.obo",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Phallusia fumigata Anatomy and Development Ontology",
"prefix": "PHFUMIADO"
},
"PHIPO": {
"description": "PHIPO is a formal ontology of species-neutral phenotypes observed in pathogen-host interactions.",
"download_owl": "http://aber-owl.net/media/ontologies/PHIPO/38/phipo.owl",
"homepage": "https://github.com/PHI-base/phipo",
"name": "Pathogen Host Interaction Phenotype Ontology",
"prefix": "PHIPO"
},
"PHMAMMADO": {
"description": "The first ontology describing the anatomy and the development of Phallusia mammillata.",
"download_obo": "http://aber-owl.net/media/ontologies/PHMAMMADO/2/phmammado.obo",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Phallusia mammillata Anatomy and Development Ontology",
"prefix": "PHMAMMADO"
},
"PHYLO": {
"description": "This phylogenetic ontology represent phylogenetic analyses tasks.",
"download_owl": "http://aber-owl.net/media/ontologies/PHYLO/4/phylo.owl",
"name": "Phylontology_v1.0",
"prefix": "PHYLO",
"version": "1.0"
},
"PHYLONT": {
"description": "Ontology for Phylogenetic Analysis",
"download_owl": "http://aber-owl.net/media/ontologies/PHYLONT/7/phylont.owl",
"name": "Phylogenetic Ontology",
"prefix": "PHYLONT",
"version": "ver8"
},
"PIERO": {
"description": "Enzyme Reaction Ontology for annotating Partial Information of chemical transformation",
"download_owl": "http://aber-owl.net/media/ontologies/PIERO/10/piero.owl",
"homepage": "http://reactionontology.org",
"name": "Enzyme Reaction Ontology for annotating Partial Information of chemical transformation",
"prefix": "PIERO"
},
"PINO": {
"description": "An ontology about pregnancy information needs across all stages of pregnancy",
"download_owl": "http://aber-owl.net/media/ontologies/PINO/2/pino.owl",
"homepage": "https://github.com/henryhezhe2003/Pregnancy_Infomation_Needs_Ontology",
"name": "Pregnancy Information Needs Ontology",
"prefix": "PINO",
"version": "1.1"
},
"PLANA": {
"description": "PLANA, the planarian anatomy ontology, encompasses the anatomy and life cycle stages for both __Schmidtea mediterranea__ biotypes.",
"download_owl": "http://aber-owl.net/media/ontologies/PLANA/28/plana.owl",
"homepage": "https://github.com/obophenotype/planaria-ontology",
"name": "planaria-ontology",
"prefix": "PLANA"
},
"PLANP": {
"description": "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea.",
"download_owl": "http://aber-owl.net/media/ontologies/PLANP/6/planp.owl",
"homepage": "https://github.com/obophenotype/planarian-phenotype-ontology",
"name": "Planarian Phenotype Ontology",
"prefix": "PLANP"
},
"PLANTSO": {
"description": "This ontology describes biotic and abiotic stresses that a plant may encounter.",
"download_owl": "http://aber-owl.net/media/ontologies/PLANTSO/3/plantso.owl",
"homepage": "https://github.com/Planteome/plant-stress-ontology",
"name": "Plant Stress Ontology",
"prefix": "PLANTSO",
"version": "2023-11-14"
},
"PLIO": {
"description": "The protein--ligand interaction ontology (PLIO) was developed around three main concepts, namely target, ligand and interaction, and was enriched by adding synonyms, useful annotations and references.",
"download_owl": "http://aber-owl.net/media/ontologies/PLIO/1/plio.owl",
"name": "Protein-ligand interaction ontology",
"prefix": "PLIO",
"version": "1.0"
},
"PLOSTHES": {
"description": "The PLOS Thesaurus includes over 10,000 Subject Area terms covering the wide range of research topics included the PLOS journals. It was initially built for PLOS in 2012 by Access Innovations (http://www.accessinn.com/). The entire corpus of PLOS articles was analysed to ensure that the thesaurus covers relevant research domains comprehensively. Updates are released several times a year.",
"homepage": "https://github.com/PLOS/plos-thesaurus",
"name": "PLOS Thesaurus",
"prefix": "PLOSTHES",
"version": "plosthes.2017-1"
},
"PMA": {
"description": "The Portfolio Management Application (PMA) is a system for tracking grants and producing reports - Users can access grant data through a query interface and a variety of pre-defined forms and reports",
"download_owl": "http://aber-owl.net/media/ontologies/PMA/4/pma.owl",
"name": "Portfolio Management Application",
"prefix": "PMA",
"version": "0.9.1"
},
"PMAPP-PMO": {
"description": "The Precision Medicine Ontology (PMO) has been developed as a standardized ontology for human precision medicine with consistent, reusable and sustainable descriptions of human disease terms, genomic molecular, phenotype characteristics and related medical vocabulary disease concepts through collaborative efforts of researchers at Institute of Medical Information, Chinese Academy of Medical Sciences. The Precision Medicine Ontology focuses on the development of a high level patients-centric ontology for the academic research, thus, it systematically integrates biomedicine vocabularies from GO, NCBI Gene, DrugBank, HPO, MeSH, SNOMED CT, etc. This work is supported by the National Key Research and Development Program of China (Precision Medicine Knowledge Base, Grant No. 2016YFC0901901).",
"download_owl": "http://aber-owl.net/media/ontologies/PMAPP-PMO/1/pmapp-pmo.owl",
"homepage": "http://www.phoc.org.cn/pmo/",
"name": "PMO Precision Medicine Ontology",
"prefix": "PMAPP-PMO",
"version": "4.0"
},
"PMD": {
"description": "PMD is an ontology that represents classification and related information of Persian medicine diseases. Persian medicine also known as Iranian traditional medicine is one of famous and most ancient forms of traditional medicines. This ontology is based on the top-level ontology GFO (General Formal Ontology)",
"download_owl": "http://aber-owl.net/media/ontologies/PMD/1/pmd.owl",
"name": "Persian Medicine Diseases Ontology",
"prefix": "PMD",
"version": "1.0"
},
"PMDO": {
"description": "The Parkinson Movement Disorder Ontology (PMDO) uses a systematic analysis of movement disorder instruments, extensive review of literature led by movement disorder specialists, and the AMP PD knowledge portal with an iterative ontology engineering process. The current version of PMDO is focused on parkinsonian disorders with classes representing three broad categories of: (1) neurological findings, (2) treatment plans, and (3) instruments used to evaluate various traits of PD. Release notes (v1.0): This version models the MDS Clinical Diagnostic Criteria for Parkinson\u2019s Disease (2015), including: 1. Essential criteria (1) 2. Supportive criteria (4) 3. Absolute exclusion criteria (9) 4. Red flags (10)",
"download_owl": "http://aber-owl.net/media/ontologies/PMDO/4/pmdo.owl",
"homepage": "https://bmhinformatics.case.edu/",
"name": "Parkinson and Movement Disorder Ontology",
"prefix": "PMDO",
"version": "1.1"
},
"PMO": {
"description": "An extension to the Library of Congress BIBFRAME ontology for performed music.",
"download_owl": "http://aber-owl.net/media/ontologies/PMO/11/pmo.owl",
"name": "Performed Music Ontology",
"prefix": "PMO",
"version": "1.0"
},
"PMO-IMICAMS": {
"description": "The Precision Medicine Ontology (PMO) has been developed as a standardized ontology for human precision medicine with consistent, reusable and sustainable descriptions of human disease terms, genomic molecular, phenotype characteristics and related medical vocabulary disease concepts through collaborative efforts of researchers at Institute of Medical Information, Chinese Academy of Medical Sciences. The Precision Medicine Ontology focuses on the development of a high level patients-centric ontology for the academic research, thus, it systematically integrates biomedicine vocabularies from GO, NCBI Gene, DrugBank, HPO, MeSH, SNOMED CT, etc. This work is supported by the National Key Research and Development Program of China (Precision Medicine Knowledge Base, Grant No. 2016YFC0901901).",
"download_owl": "http://aber-owl.net/media/ontologies/PMO-IMICAMS/1/pmo-imicams.owl",
"homepage": "http://www.phoc.org.cn/pmo/",
"name": "PMO: Precision Medicine Ontology",
"prefix": "PMO-IMICAMS",
"version": "4.0"
},
"PMO-SPEED": {
"description": "Vocabulary for playing speeds of audio carriers, e.g., audio discs, audio cassettes, piano/organ rolls, primarily for use with the Performed Music Ontology, or other similar music ontologies.",
"homepage": "https://github.com/LD4P/PerformedMusicOntology/tree/master/Vocabularies",
"name": "PMO Playing Speed Vocabulary",
"prefix": "PMO-SPEED",
"version": "1.0"
},
"PMR": {
"description": "Knowledge representation related to computer-based decision support in rehabilitation; concepts and relationships in the rehabilitation domain, integrating clinical practice, the ICD (specifically its 11th revision), the clinical investigator record ontology, the ICF and SNOMED CT.",
"download_owl": "http://aber-owl.net/media/ontologies/PMR/4/pmr.owl",
"homepage": "https://sites.google.com/site/laiasubirats",
"name": "Physical Medicine and Rehabilitation",
"prefix": "PMR",
"version": "1.6"
},
"PNADO": {
"description": "Pneumonia Diagnosis Ontology (PNADO) provides the necessary knowledge to diagnose infective pneumonia. It covers symptoms and clinical signs, clinical history, pathogens, laboratory tests and results, imaging, differential diagnosis, complications and pneumonia types.",
"download_owl": "http://aber-owl.net/media/ontologies/PNADO/1/pnado.owl",
"name": "Pneumonia Diagnosis Ontology",
"prefix": "PNADO",
"version": "Version 1.0, 2021/02/01"
},
"PO": {
"description": "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.",
"download_owl": "http://aber-owl.net/media/ontologies/PO/27/po.owl",
"homepage": "http://browser.planteome.org/amigo",
"name": "Plant Ontology",
"prefix": "PO"
},
"PORO": {
"description": "An ontology covering the anatomy of the taxon Porifera (sponges)",
"download_owl": "http://aber-owl.net/media/ontologies/PORO/10/poro.owl",
"homepage": "https://github.com/obophenotype/porifera-ontology",
"name": "Porifera Ontology",
"prefix": "PORO"
},
"POSITIONALH": {
"description": "A hierarchy of bilateral positions commonly attached to all brain regions in bilateral species.",
"download_owl": "http://aber-owl.net/media/ontologies/POSITIONALH/2/positionalh.owl",
"name": "NeuroMorpho.Org bilateral positions",
"prefix": "POSITIONALH",
"version": "2.0"
},
"PP": {
"description": "To answer the need for a workflow representing a sequence of data transformations, a high-level process ontology was defined, denoted Pipeline Patterns (PP) ontology. Every concept is generically a Data (class from EDAM), which can be further specified as an Entry (P:00002) or an Exit (P:00009). All Entries can be subjected to an Operation (class from EDAM) producing an Intermediate (P:00010). An Intermediate has a TemporalEntity associated to represent its time of creation. Some Entries are specifically of the type Exit, meaning that they will represent concepts that exit the current category and be passed to the next one on the workflow. Additionally, in order to permit the treatment of a set of objects as a single entity, this high-level ontology considers the concept of List (P:00004) and more specifically an Aggregate (P:00005), containing a set of Data or Entry, respectively. The concept Intermediate is an Entry, allowing for the successive application of an operation to an Element. This is particularly useful in the case of the application of sequential set of operations.",
"download_owl": "http://aber-owl.net/media/ontologies/PP/1/pp.owl",
"homepage": "https://bitbucket.org/PlantExpAssay/ontology",
"name": "Pipeline Patterns Ontology",
"prefix": "PP",
"version": "1.0"
},
"PPIO": {
"description": "A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Developed by the HUPO Proteomics Standards Initiative.",
"download_obo": "http://aber-owl.net/media/ontologies/PPIO/23/ppio.obo",
"homepage": "http://psidev.sf.net",
"name": "Protein-Protein Interaction Ontology",
"prefix": "PPIO",
"version": "3.79.0"
},
"PPLC": {
"name": "Placental Pathology Lesion Classification",
"prefix": "PPLC"
},
"PPO": {
"description": "An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales.",
"download_owl": "http://aber-owl.net/media/ontologies/PPO/9/ppo.owl",
"homepage": "https://github.com/PlantPhenoOntology/PPO",
"name": "Plant Phenology Ontology",
"prefix": "PPO"
},
"PR": {
"description": "An ontological representation of protein-related entities",
"download_owl": "http://aber-owl.net/media/ontologies/PR/84/pr.owl",
"homepage": "http://proconsortium.org",
"name": "PRotein Ontology (PRO)",
"prefix": "PR"
},
"PRANAYTC": {
"name": "pranaytc",
"prefix": "PRANAYTC"
},
"PRE-CLINICAL": {
"name": "taimoor Ontology",
"prefix": "PRE-CLINICAL"
},
"PREGONTO": {
"description": "The pregnancy ontology is a biomedical ontology used for identifying pregnancies in routine health databases. The ontology was primarily developed for conducting surveillance of vaccine uptake in pregnant women in the UK.",
"download_owl": "http://aber-owl.net/media/ontologies/PREGONTO/1/pregonto.owl",
"name": "Pregnancy Ontology",
"prefix": "PREGONTO"
},
"PREMEDONTO": {
"description": "Precision MedicinePreMedOnto is an application ontology built for the precision medicine domain on top of gold standard biomedical ontologies. The ontology learning process involves mining the PubMed repository to extract domain specific texts, abstracts and vocabulary as sources of data. The information gathered is clustered and outlined to determine main modules. It reuses terms and concepts from NCIT, MESH and IOBC to construct the ontology hierarchy.",
"download_owl": "http://aber-owl.net/media/ontologies/PREMEDONTO/1/premedonto.owl",
"name": "Precision Medicine Ontology",
"prefix": "PREMEDONTO"
},
"PREO": {
"description": "The Presence Ontology is a systematic vocabulary of terms with defined relationships that models the encounters taking place every day among providers, patients, and family members or friends in environments such as hospitals and clinics. The Presence Ontology provides a conceptual model for the human experience in medicine. This is a preliminary approach, but further use of methods we have developed here may aid in providing clarity and consensus to topics in healthcare. The ontology is also a model for interdisciplinary collaboration, as it was developed in conjunction with experts from bioinformatics, medicine, anthropology, business, and communication sciences through multiple iterative stages.",
"download_owl": "http://aber-owl.net/media/ontologies/PREO/1/preo.owl",
"homepage": "http://med.stanford.edu/presence/about.html",
"name": "Presence Ontology",
"prefix": "PREO",
"version": "1.0.0"
},
"PRIDE": {
"name": "PRIDE Controlled Vocabulary",
"prefix": "PRIDE"
},
"PROCCHEMICAL": {
"description": "Chemical process",
"download_owl": "http://aber-owl.net/media/ontologies/PROCCHEMICAL/1/procchemical.owl",
"name": "Chemical Process",
"prefix": "PROCCHEMICAL",
"version": "2.3"
},
"PROCO": {
"description": "PROCO covers process chemistry, the chemical field concerned with scaling up laboratory syntheses to commercially viable processes.",
"download_owl": "http://aber-owl.net/media/ontologies/PROCO/1/proco.owl",
"homepage": "https://github.com/proco-ontology/PROCO",
"name": "Process Chemistry Ontology",
"prefix": "PROCO"
},
"PROJ": {
"description": "The PROJECT ontology is a profile of PROV-O which is designed to enable publication of information describing projects, including research projects. It is not designed to support project management, though sub-activities are included. As far as possible PROJECT is intended to be domain-neutral, and it is expected that domains and applications will specialize or extend this ontology for more specific purposes. The ontology gives terms to support the representation of: project planning, funding, goals project stakeholders and relationships project activities and timeline Primary documentation is at http://linked.data.gov.au/def/project",
"download_owl": "http://aber-owl.net/media/ontologies/PROJ/2/proj.owl",
"homepage": "http://linked.data.gov.au/def/project",
"name": "Project ontology",
"prefix": "PROJ",
"version": "2020"
},
"PROPREO": {
"description": "A comprehensive proteomics data and process provenance ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/PROPREO/2/propreo.owl",
"homepage": "http://knoesis.wright.edu/research/semsci/application_domain/sem_life_sci/glycomics/resources/ontologies/propreo/",
"name": "Proteomics Data and Process Provenance Ontology",
"prefix": "PROPREO",
"version": "1.1"
},
"PROV": {
"description": "PROV is a superset of PROV (the Provenance Ontology). The relationship between these two ontologies is described at http://www.w3.org/ns/prov",
"download_owl": "http://aber-owl.net/media/ontologies/PROV/1/prov.owl",
"homepage": "http://www.w3.org/TR/prov-o/",
"name": "Superset of Provenance Ontology",
"prefix": "PROV",
"version": "Recommendation version 2013-04-30"
},
"PROVO": {
"description": "The PROV Ontology (PROV-O) expresses the PROV Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes, properties, and restrictions that can be used to represent and interchange provenance information generated in different systems and under different contexts. It can also be specialized to create new classes and properties to model provenance information for different applications and domains.",
"download_owl": "http://aber-owl.net/media/ontologies/PROVO/124/provo.owl",
"homepage": "http://www.w3.org/TR/prov-o/",
"name": "Provenance Ontology",
"prefix": "PROVO",
"version": "Recommendation version 2013-04-30"
},
"PSDO": {
"description": "Ontology to reproducibly study visualizations of clinical performance",
"download_owl": "http://aber-owl.net/media/ontologies/PSDO/2/psdo.owl",
"homepage": "https://github.com/Display-Lab/psdo",
"name": "Performance Summary Display Ontology",
"prefix": "PSDO"
},
"PSDS": {
"description": "REPLACED BY: Plant Ontology (PO). A controlled vocabulary of growth and developmental stages in various plants. Note that this has been subsumed into the Plant Ontology (PO). This file is created by filtering plant_ontology_assert.obo to contain only terms from the plant structure development stage branch of the PO. For more information, please see: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/",
"download_obo": "http://aber-owl.net/media/ontologies/PSDS/6/psds.obo",
"homepage": "http://www.plantontology.org",
"name": "Plant Structure Development Stage",
"prefix": "PSDS",
"version": "Release #20"
},
"PSIMOD": {
"description": "PSI-MOD is an ontology consisting of terms that describe protein chemical modifications, logically linked by an is_a relationship in such a way as to form a direct acyclic graph (DAG). The PSI-MOD ontology has more than 45 top-level nodes, and provides alternative hierarchical paths for classifying protein modifications either by the molecular structure of the modification, or by the amino acid residue that is modified.",
"download_obo": "http://aber-owl.net/media/ontologies/PSIMOD/4/psimod.obo",
"homepage": "http://www.psidev.info/MOD",
"name": "Protein Modification Ontology",
"prefix": "PSIMOD",
"version": "1.013.0"
},
"PSO": {
"description": "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter.",
"download_owl": "http://aber-owl.net/media/ontologies/PSO/5/pso.owl",
"homepage": "https://github.com/Planteome/plant-stress-ontology",
"name": "Plant Stress Ontology",
"prefix": "PSO"
},
"PSO_2": {
"description": "This is a revised version of the Patient Safety Ontology",
"download_owl": "http://aber-owl.net/media/ontologies/PSO_2/3/pso_2.owl",
"name": "PatientSafetyOntologyRevisted",
"prefix": "PSO_2",
"version": "005"
},
"PSY-LKSR": {
"download_owl": "http://aber-owl.net/media/ontologies/PSY-LKSR/1/psy-lksr.owl",
"name": "Psych Phenotypes Test Ontology (LKSR)",
"prefix": "PSY-LKSR",
"version": "0.0.1"
},
"PTO": {
"description": "A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part.",
"download_owl": "http://aber-owl.net/media/ontologies/PTO/427/pto.owl",
"homepage": "http://www.planteome.org",
"name": "Plant Trait Ontology",
"prefix": "PTO",
"version": "September 2016"
},
"PTRANS": {
"description": "This vocabulary describes a process that is the means of how a pathogen is transmitted from one host, reservoir, or source to another host. This transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.",
"download_obo": "http://aber-owl.net/media/ontologies/PTRANS/14/ptrans.obo",
"homepage": "http://diseaseontology.sourceforge.net/",
"name": "Pathogen Transmission Ontology",
"prefix": "PTRANS",
"version": "unknown"
},
"PTS": {
"description": "Pathwas terminology systems integrates biological Events and various Pathway types.",
"download_owl": "http://aber-owl.net/media/ontologies/PTS/1/pts.owl",
"name": "Pathway Terminology System",
"prefix": "PTS",
"version": "1.0"
},
"PVONTO": {
"description": "A pharmacovigilance ontology to connect known facts on drugs, disease, ADEs, and their molecular mechanisms.",
"download_owl": "http://aber-owl.net/media/ontologies/PVONTO/1/pvonto.owl",
"homepage": "http://people.eecs.ku.edu/~jhuan/",
"name": "Pharmacovigilance Ontology",
"prefix": "PVONTO",
"version": "0.1"
},
"PW": {
"description": "A controlled vocabulary for annotating gene products to pathways.",
"download_owl": "http://aber-owl.net/media/ontologies/PW/87/pw.owl",
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
"name": "Pathway ontology",
"prefix": "PW"
},
"PXO": {
"description": "The Proteasix Ontology (PxO) is a new application ontology that supports the Proteasix tool (http://www.proteasix.org/). Proteasix is an open-source peptide-centric tool that can be used to predict automatically and in a large-scale fashion in silico the proteases involved in the generation of proteolytic cleavage fragments (peptides).",
"download_owl": "http://aber-owl.net/media/ontologies/PXO/10/pxo.owl",
"name": "Proteasix Ontology",
"prefix": "PXO",
"version": "2.0"
},
"PYRAMIDAL1H": {
"description": "A hierarchy of Pyramidal cell microcolumnar connectivity within the cortex.",
"download_owl": "http://aber-owl.net/media/ontologies/PYRAMIDAL1H/2/pyramidal1h.owl",
"name": "NeuroMorpho.Org Pyramidal cell microconnectivity",
"prefix": "PYRAMIDAL1H",
"version": "2.0"
},
"PYRAMIDAL2H": {
"description": "A hierarchy of Pyramidal cell gross connectivity projecting to different cortico-cortical or cortico-subcortical regions.",
"download_owl": "http://aber-owl.net/media/ontologies/PYRAMIDAL2H/2/pyramidal2h.owl",
"name": "NeuroMorpho.Org Pyramidal cell gross connectivity",
"prefix": "PYRAMIDAL2H",
"version": "2.0"
},
"PYRAMIDAL3H": {
"description": "A hierarchy of Pyramidal cell types based on their dendritic shape.",
"download_owl": "http://aber-owl.net/media/ontologies/PYRAMIDAL3H/2/pyramidal3h.owl",
"name": "NeuroMorpho.Org Pyramidal cell dendritic shape ",
"prefix": "PYRAMIDAL3H",
"version": "2.0"
},
"PYRAMIDALH": {
"description": "A hierarchy of Pyramidal cell types projecting to achieve specific systems connectivity such as cortico-thalamic, cortico-spinal, cortico-cortical projections.",
"download_owl": "http://aber-owl.net/media/ontologies/PYRAMIDALH/3/pyramidalh.owl",
"name": "NeuroMorpho.Org Pyramidal cell systems connectivity",
"prefix": "PYRAMIDALH",
"version": "2.0"
},
"Pheno-e": {
"download_owl": "http://aber-owl.net/media/ontologies/Pheno-e/7/pheno-e.owl",
"name": "Pheno-e Ontology",
"prefix": "Pheno-e",
"version": "0.0.6"
},
"PhenomeNET": {
"description": "An integrated phenotype ontology, combining phenotypes from human, mouse, fish.",
"download_owl": "http://aber-owl.net/media/ontologies/PhenomeNET/1/phenomenet.owl",
"name": "PhenomeNET Ontology",
"prefix": "PhenomeNET",
"version": "1.1"
},
"PhenomeNETSH": {
"download_owl": "http://aber-owl.net/media/ontologies/PhenomeNETSH/8/phenomenetsh.owl",
"name": "PhenomeNET Ontology - Shrinked version",
"prefix": "PhenomeNETSH",
"version": "2020"
},
"Python acronym": {
"name": "Python name",
"prefix": "Python acronym"
},
"QIBO": {
"description": "An ontology that describes various concepts in quantitative imaging biomarkers.",
"download_owl": "http://aber-owl.net/media/ontologies/QIBO/2/qibo.owl",
"name": "Quantitative Imaging Biomarker Ontology",
"prefix": "QIBO",
"version": "unknown"
},
"QUDT": {
"description": "The QUDT, or 'Quantity, Unit, Dimension and Type' collection of ontologies define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems. The goal of the QUDT ontology is to provide a unified model of, measurable quantities, units for measuring different kinds of quantities, the numerical values of quantities in different units of measure and the data structures and data types used to store and manipulate these objects in software. This OWL schema is a foundation for a basic treatment of units.",
"download_owl": "http://aber-owl.net/media/ontologies/QUDT/4/qudt.owl",
"homepage": "http://qudt.org/",
"name": "Quantities, Units, Dimensions, and Types Ontology",
"prefix": "QUDT",
"version": "$Id: OSG_qudt-(v1.1).ttl 4989 2011-06-01 21:56:40Z RalphHodgson $"
},
"QUDT2": {
"description": "The QUDT, or \"Quantity, Unit, Dimension and Type\" schema defines the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems. The goal of the QUDT ontology is to provide a unified model of, measurable quantities, units for measuring different kinds of quantities, the numerical values of quantities in different units of measure and the data structures and data types used to store and manipulate these objects in software. Except for unit prefixes, all units are specified in separate vocabularies.",
"download_owl": "http://aber-owl.net/media/ontologies/QUDT2/1/qudt2.owl",
"homepage": "http://qudt.org/doc/2016/DOC_SCHEMA-QUDT-v2.0.html",
"name": "Quantities, Units, Dimensions and Types (QUDT) Schema - Version 2.0",
"prefix": "QUDT2",
"version": "2.0"
},
"QUDT2-1": {
"name": "Quantities, Units, Dimensions and Types (QUDT Version 2.1)",
"prefix": "QUDT2-1"
},
"RADLEX": {
"description": "RadLex is a controlled terminology for radiology-a single unified source of radiology terms for radiology practice, education, and research. For license information see : http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/RadLex_License_Agreement_and_Terms_of_Use_V2_Final.pdf Converted to use OWL format submissions",
"download_owl": "http://aber-owl.net/media/ontologies/RADLEX/37/radlex.owl",
"homepage": "http://www.rsna.org/RadLex.aspx",
"name": "Radiology Lexicon",
"prefix": "RADLEX",
"version": "3.14"
},
"RADXTT-MVREASONS": {
"description": "These concepts define the different reasons values might be missing from the RADx data record. The concepts have been approved by the RADx Executive Committee to fill in fields that do not have a value in them. The concepts in this vocabulary were developed by the RADx Missing Values Tiger Team. The protocols for managing these concepts in the RADx Data Hub environment are still being developed and will be improved and described as part of the RADx program.",
"homepage": "https://github.com/bmir-radx/radx-missing-value-reasons",
"name": "RADx Tiger Team Missing Value Reasons",
"prefix": "RADXTT-MVREASONS",
"version": "0.1.2"
},
"RAFIRAJOGUJA": {
"name": "Sewa Bus Jogja",
"prefix": "RAFIRAJOGUJA"
},
"RAO": {
"description": "A controlled vocabulary of RA-relevant information. Currently, only treatment information is available.",
"download_owl": "http://aber-owl.net/media/ontologies/RAO/1/rao.owl",
"name": "Rheumatoid Arthritis ontology",
"prefix": "RAO",
"version": "Version 1.0"
},
"RB": {
"description": "The RegenBase ontology describes biological entities and processes studied in spinal cord injury (SCI) research.",
"download_owl": "http://aber-owl.net/media/ontologies/RB/5/rb.owl",
"homepage": "http://regenbase.org",
"name": "RegenBase ontology",
"prefix": "RB",
"version": "1.0"
},
"RBMS": {
"description": "These thesauri provide standardized vocabulary for retrieving special collections materials by form, genre, or by various physical characteristics that are typically of interest to researchers and special collections librarians, and for relating materials to individuals or corporate bodies.",
"homepage": "http://rbms.info/vocabularies/",
"name": "RBMS Controlled Vocabularies",
"prefix": "RBMS",
"version": "1.0"
},
"RBO": {
"description": "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.",
"download_owl": "http://aber-owl.net/media/ontologies/RBO/28/rbo.owl",
"homepage": "https://github.com/Radiobiology-Informatics-Consortium/RBO",
"name": "Radiation Biology Ontology",
"prefix": "RBO"
},
"RBO-LKK": {
"download_owl": "http://aber-owl.net/media/ontologies/RBO-LKK/3/rbo-lkk.owl",
"name": "RBO",
"prefix": "RBO-LKK",
"version": "0.0.test3"
},
"RCD": {
"description": "Clinical Terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre",
"name": "Read Codes, Clinical Terms Version 3 (CTV3) ",
"prefix": "RCD",
"version": "2016AB"
},
"RCTONT": {
"description": "We developed and evaluated an ontology specifically for Randomized Controlled Trials in order to facilitate the production of systematic reviews and metaanalysis.",
"download_owl": "http://aber-owl.net/media/ontologies/RCTONT/1/rctont.owl",
"name": "Randomized Controlled Trials Ontology",
"prefix": "RCTONT",
"version": "2.0"
},
"RCTV2": {
"description": "NHS UK Read Codes Version 2",
"download_owl": "http://aber-owl.net/media/ontologies/RCTV2/1/rctv2.owl",
"name": "Read Clinical Terminology Version 2",
"prefix": "RCTV2",
"version": "2015"
},
"RDA-CONTENT": {
"description": "A categorization reflecting the fundamental form of communication in which the content is expressed and the human sense through which it is intended to be perceived. Required data for RDA (Resource Description and Access)",
"download_owl": "http://aber-owl.net/media/ontologies/RDA-CONTENT/1/rda-content.owl",
"homepage": "http://www.rdaregistry.info/termList/RDAContentType/",
"name": "RDA Content type",
"prefix": "RDA-CONTENT"
},
"RDA-ISSUANCE": {
"description": "RDA vocabulary for mode of issuance of a resource (single unit, multipart monograph, etc.)",
"download_owl": "http://aber-owl.net/media/ontologies/RDA-ISSUANCE/2/rda-issuance.owl",
"homepage": "https://www.rdaregistry.info/termList/ModeIssue/",
"name": "RDA Mode of Issuance",
"prefix": "RDA-ISSUANCE",
"version": "1.0"
},
"RDAU": {
"description": "The Unconstrained properties element set consists of properties representing the attributes and relationships of all of the RDA entities. Each property in the element set has semantics which are independent of the FRBR model and has no specified domain or range. The Unconstrained properties are intended for use in applications that do not require the FRBR semantics.",
"download_owl": "http://aber-owl.net/media/ontologies/RDAU/1/rdau.owl",
"homepage": "http://www.rdaregistry.info/Elements/u/",
"name": "RDA unconstrained properties",
"prefix": "RDAU"
},
"RDFS": {
"description": "RDF Schema provides a data-modelling vocabulary for RDF data",
"download_owl": "http://aber-owl.net/media/ontologies/RDFS/3/rdfs.owl",
"name": "The RDF Schema vocabulary",
"prefix": "RDFS",
"version": "1.1"
},
"RDL": {
"description": "RDL",
"download_owl": "http://aber-owl.net/media/ontologies/RDL/1/rdl.owl",
"name": "RDL",
"prefix": "RDL",
"version": "Generated 2013-03-28T19:01:04.897+01:00"
},
"RDO": {
"description": "Facilitating Biodiversity information",
"download_owl": "http://aber-owl.net/media/ontologies/RDO/1/rdo.owl",
"name": "Reusable Biodiversity Ontology",
"prefix": "RDO",
"version": "1.1"
},
"REGN_BRO": {
"description": "A controlled terminology of resources, which is used to improve the sensitivity and specificity of web searches.",
"download_owl": "http://aber-owl.net/media/ontologies/REGN_BRO/1/regn_bro.owl",
"name": "REGN_BRO",
"prefix": "REGN_BRO",
"version": "1.1"
},
"REGN_GO": {
"description": "Provides structured controlled vocabularies for the annotation of gene products with respect to their molecular function, cellular component, and biological role. The Gene Ontology consists of three Vocabularies.",
"download_owl": "http://aber-owl.net/media/ontologies/REGN_GO/1/regn_go.owl",
"name": "REGN_GO",
"prefix": "REGN_GO",
"version": "2023-01-01"
},
"RELO": {
"description": "A collection of relations intended primarily for standardization across ontologies in the OBO Foundry and wider OBO library. It incorporates ROCore upper-level relations such as part of as well as biology-specific relationship types such as develops from.",
"download_owl": "http://aber-owl.net/media/ontologies/RELO/2/relo.owl",
"homepage": "https://github.com/oborel/obo-relations/",
"name": "Relations Ontology",
"prefix": "RELO"
},
"RENTALBUSJOGJA20": {
"name": "Rental Bus Jogja",
"prefix": "RENTALBUSJOGJA20"
},
"RENTALBUSJOGJA51": {
"name": "Rental Bus Jogja 2",
"prefix": "RENTALBUSJOGJA51"
},
"REPO": {
"description": "Ontology for livestock reproductive traits and phenotypes",
"download_owl": "http://aber-owl.net/media/ontologies/REPO/3/repo.owl",
"name": "Reproductive Trait and Phenotype Ontology",
"prefix": "REPO",
"version": "1.1"
},
"REPOS": {
"name": "repository",
"prefix": "REPOS"
},
"REPRODUCE-ME": {
"description": "The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials and settings required for its reproducibility.",
"download_owl": "http://aber-owl.net/media/ontologies/REPRODUCE-ME/7/reproduce-me.owl",
"homepage": "https://w3id.org/reproduceme/research",
"name": "REPRODUCE-ME",
"prefix": "REPRODUCE-ME",
"version": "1.1"
},
"REST_MANAG": {
"name": "Restaurant Management",
"prefix": "REST_MANAG"
},
"RETO": {
"description": "An application ontology for the domain of gene transcription regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI and orthological properties from RO and SIO.",
"download_obo": "http://aber-owl.net/media/ontologies/RETO/7/reto.obo",
"homepage": "http://www.semantic-systems-biology.org/apo/",
"name": "Regulation of Transcription Ontology",
"prefix": "RETO",
"version": "2015"
},
"REX": {
"description": "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time.",
"download_owl": "http://aber-owl.net/media/ontologies/REX/1/rex.owl",
"name": "Physico-chemical process",
"prefix": "REX"
},
"REXO": {
"description": "An application ontology for the domain of gene expression regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, and orthology relations using ontological properties from RO and ISO.",
"download_owl": "http://aber-owl.net/media/ontologies/REXO/6/rexo.owl",
"homepage": "http://www.semantic-systems-biology.org/apo",
"name": "Regulation of Gene Expression Ontolology",
"prefix": "REXO",
"version": "2015"
},
"RGD": {
"name": "RRB Group D",
"prefix": "RGD"
},
"RH-MESH": {
"description": "Medical Subjects Headings Thesaurus 2014, Modified version. This is an OWL representation of MeSH so that it can be integrated with other ontologies represented in OWL. It contains all terms that are in MeSH and in the MeSH concept tree, including the pharmacological actions (represented as subclass relations). Concepts in the MeSH concept tree are merged with MeSH term ids. --------------------------
Note that, while this ontology is composed of MeSH terms, it does not correspond directly to UMLS MeSH. In particular, a single term in UMLS MeSH often results in multiple classes in this ontology. For example, in MeSH there is a single term with the label \"Heart\". The internal code (unique identifier) for this term is A07.541. In this ontology there are two entirely different terms, both of which have the label \"Heart\". The codes for these terms are A07.541 and D006321.",
"download_owl": "http://aber-owl.net/media/ontologies/RH-MESH/3/rh-mesh.owl",
"homepage": "https://code.google.com/p/pharmgkb-owl/",
"name": "Robert Hoehndorf Version of MeSH",
"prefix": "RH-MESH",
"version": "2014"
},
"RIVERSTATE": {
"name": "elections",
"prefix": "RIVERSTATE"
},
"RNAO": {
"description": "The central aim of the RNA Ontology Consortium (ROC) is to develop an ontology to capture all aspects of RNA - from primary sequence to alignments, secondary and tertiary structure from base pairing and base stacking to sophisticated motifs.",
"download_obo": "http://aber-owl.net/media/ontologies/RNAO/4/rnao.obo",
"homepage": "https://github.com/BGSU-RNA/rnao",
"name": "RNA ontology",
"prefix": "RNAO",
"version": "r113"
},
"RNPRIO": {
"description": "Ontology for Inventories of Clinical Data Research Networks, Patient-Powered Research Networks, and Patient Registries",
"download_owl": "http://aber-owl.net/media/ontologies/RNPRIO/1/rnprio.owl",
"name": "Research Network and Patient Registry Inventory Ontology",
"prefix": "RNPRIO",
"version": "1"
},
"RNRMU": {
"description": "The terms of RNRMU",
"download_owl": "http://aber-owl.net/media/ontologies/RNRMU/1/rnrmu.owl",
"name": "RNRMU",
"prefix": "RNRMU",
"version": "0.1"
},
"RO": {
"description": "Relationship types shared across multiple ontologies",
"download_owl": "http://aber-owl.net/media/ontologies/RO/30/ro.owl",
"homepage": "https://oborel.github.io/",
"name": "Relation Ontology",
"prefix": "RO"
},
"ROCKNROLLTEST": {
"description": "This Vocabulary describes some few terms of high level geologic concept hierarchy. This vocabulary is not complete and half randomly made up, but based on the USGS North American Geological Map Data Model. It is a test before the M4M workshop.",
"name": "ROCK-N-ROLL-TEST",
"prefix": "ROCKNROLLTEST"
},
"ROLEO": {
"description": "The Role Ontology (RoleO) is a ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles.",
"download_owl": "http://aber-owl.net/media/ontologies/ROLEO/1/roleo.owl",
"homepage": "http://sourceforge.net/projects/roleo",
"name": "Role Ontology",
"prefix": "ROLEO",
"version": "Vision Release; 1.0.11"
},
"ROO": {
"description": "The Radiation Oncology Ontology aims to cover the radiation oncology domain with a strong focus on re-using existing ontologies.",
"download_owl": "http://aber-owl.net/media/ontologies/ROO/3/roo.owl",
"homepage": "http://www.cancerdata.org/roo",
"name": "Radiation Oncology Ontology",
"prefix": "ROO",
"version": "0.3"
},
"ROS": {
"description": "This ontology describes commonly contoured (anatomical and treatment planning) structures for radiation treatment planning. 22000 structures labels (created over a 16 years period in our radiation department) were extracted, classified and categorized to produce this ontology. Lymph nodes delineation international guidelines are provided. This ontology was created to ease and standardize the integration of radiation oncology data into clinical datawarehouses for multicentric studies. The high granularity of this ontology will allow precise dosimetric evaluations.",
"download_owl": "http://aber-owl.net/media/ontologies/ROS/6/ros.owl",
"homepage": "http://www.twitter.com/jebibault",
"name": "Radiation Oncology Structures Ontology",
"prefix": "ROS",
"version": "1.2.2"
},
"ROXY": {
"name": "Roxy",
"prefix": "ROXY"
},
"RPO": {
"description": "RAPID phenotype ontology presents controlled vocabulary of ontology class structures and entities of observed phenotypic terms for primary immunodeficiency diseases (PIDs) that facilitate global sharing and free exchange of PID data with users\u2019 communities",
"download_owl": "http://aber-owl.net/media/ontologies/RPO/2/rpo.owl",
"homepage": "http://rapid.rcai.riken.jp/ontology/v1.0/phenomer.php",
"name": "Resource of Asian Primary Immunodeficiency Diseases (RAPID) Phenotype Ontology",
"prefix": "RPO",
"version": "Version 1.0"
},
"RS": {
"description": "Ontology of rat strains",
"download_owl": "http://aber-owl.net/media/ontologies/RS/171/rs.owl",
"homepage": "http://rgd.mcw.edu/rgdweb/search/strains.html",
"name": "Rat Strain Ontology",
"prefix": "RS"
},
"RSA": {
"description": "An ontology for sequence annotations and how to preserve them with reference sequences.",
"download_owl": "http://aber-owl.net/media/ontologies/RSA/5/rsa.owl",
"name": "Reference Sequence Annotation",
"prefix": "RSA",
"version": "0.6"
},
"RVO": {
"description": "RVO, Research Variable Ontology, proposes a schema that can be use to record empirical data analytics research and can be use as a knowledge-base to support knowledge exploration phase of a new analytics research to learn and get recommendation. RVO is designed around the research variables, which form the basis of the hypothesis that analysts test through building a model.",
"download_owl": "http://aber-owl.net/media/ontologies/RVO/2/rvo.owl",
"homepage": "http://w3id.org/rv-ontology/info",
"name": "Research Variable Ontology",
"prefix": "RVO",
"version": "1.0"
},
"RXNO": {
"description": "Connects organic name reactions to their roles in an organic synthesis and to processes in MOP",
"download_owl": "http://aber-owl.net/media/ontologies/RXNO/40/rxno.owl",
"homepage": "https://github.com/rsc-ontologies/rxno",
"name": "Name Reaction Ontology",
"prefix": "RXNO"
},
"RXNORM": {
"description": "RxNorm Vocabulary",
"name": "RxNORM",
"prefix": "RXNORM",
"version": "2016AB"
},
"RadLex_OWL": {
"description": "An OWL representation of the RadLex ontology, following the transformation described at http://www.bioontology.org/wiki/index.php/FMAInOwl",
"download_owl": "http://aber-owl.net/media/ontologies/RadLex_OWL/1/radlex_owl.owl",
"name": "RadLex in OWL",
"prefix": "RadLex_OWL",
"version": "1"
},
"SALMON": {
"description": "An ontology representing knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. This ontology is considered to be in the early stages of development, though it is based upon considerable previous work. Contributions of all kinds are welcome and encouraged, including alignments, updates to existing terms, and new terms.",
"download_owl": "http://aber-owl.net/media/ontologies/SALMON/2/salmon.owl",
"homepage": "https://github.com/DataONEorg/sem-prov-ontologies/",
"name": "Salmon Ontology",
"prefix": "SALMON",
"version": "0.3.1"
},
"SANJAY": {
"name": "Sanjay",
"prefix": "SANJAY"
},
"SANTIKUMALA": {
"name": "santihui",
"prefix": "SANTIKUMALA"
},
"SAO": {
"description": "SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules.",
"download_owl": "http://aber-owl.net/media/ontologies/SAO/2/sao.owl",
"homepage": "http://ccdb.ucsd.edu/SAO",
"name": "Subcellular Anatomy Ontology",
"prefix": "SAO",
"version": "Version 1.2"
},
"SARSMUTONTO": {
"description": "The SARSMutOnto ontology provides a list of all SARS-CoV-2 Pango lineages while maintaining their hierarchy (lineage/sublineage) describing in detail all lineage mutations",
"download_owl": "http://aber-owl.net/media/ontologies/SARSMUTONTO/7/sarsmutonto.owl",
"homepage": "https://github.com/jbakkas/SARSMutOnto",
"name": "Ontology for SARS-CoV-2 lineages and mutations",
"prefix": "SARSMUTONTO",
"version": "1.1"
},
"SASAP": {
"description": "An ontology which represents information about the State of Alaska's Salmon and People (SASAP) project, as well as knowledge about salmon, features of their habitats, salmon stakeholders, and related entities.",
"download_owl": "http://aber-owl.net/media/ontologies/SASAP/2/sasap.owl",
"homepage": "https://github.com/DataONEorg/sem-prov-ontologies",
"name": "The State of Alaska's Salmon and People Ontology",
"prefix": "SASAP",
"version": "0.1.1"
},
"SATO": {
"description": "Designing effective theory-driven digital behaviour change interventions (DBCI) is a challenging task. To ease the design process, and assist with knowledge sharing and evaluation of the DBCI, we propose the SATO (IDEASexpAnded wiTh BCIO) design workflow based on the IDEAS (Integrate, Design, Assess, and Share) framework and aligned with the Behaviour Change Intervention Ontology (BCIO). BCIO is a structural representation of the knowledge in behaviour change domain supporting evaluation of behaviour change interventions (BCIs) but it is not straightforward to utilise it during DBCI design. IDEAS (Integrate, Design, Assess, and Share) framework guides multi-disciplinary teams through the mobile health (mHealth) application development life-cycle but it is not aligned with BCIO entities. SATO couples BCIO entities with workflow steps and extends IDEAS Integrate stage with consideration of customisation and personalisation. The SATO ontology provides the extensions of BCIO along with examples of a BCI Scenario of Fatigue Reduction.",
"download_owl": "http://aber-owl.net/media/ontologies/SATO/2/sato.owl",
"name": "SATO (IDEAS expAnded wiTh BCIO): workflow for designers of patient-centered mobile health behaviour change intervention applications",
"prefix": "SATO",
"version": "v2"
},
"SBO": {
"description": "Terms commonly used in Systems Biology, and in particular in computational modeling.",
"download_owl": "http://aber-owl.net/media/ontologies/SBO/816/sbo.owl",
"homepage": "http://www.ebi.ac.uk/sbo/",
"name": "Systems Biology Ontology",
"prefix": "SBO"
},
"SBOL": {
"description": "Synthetic Biology Open Language Visual (SBOLv) is an ontology to represent standardized graphical notation for synthetic biology.",
"download_obo": "http://aber-owl.net/media/ontologies/SBOL/2/sbol.obo",
"homepage": "www.sbolstandard.org/visual",
"name": "Synthetic Biology Open Language Visual Ontology",
"prefix": "SBOL",
"version": "unknown"
},
"SCDO": {
"description": "An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease.",
"download_owl": "http://aber-owl.net/media/ontologies/SCDO/18/scdo.owl",
"homepage": "https://scdontology.h3abionet.org/",
"name": "Sickle Cell Disease Ontology",
"prefix": "SCDO"
},
"SCHEMA": {
"description": "A collection of schemas that webmasters can use to markup HTML pages in ways recognized by major search providers, and that can also be used for structured data interoperability (e.g. in JSON).",
"download_owl": "http://aber-owl.net/media/ontologies/SCHEMA/2/schema.owl",
"homepage": "http://schema.org/",
"name": "Schema.org core and all extension vocabularies",
"prefix": "SCHEMA",
"version": "3.2"
},
"SCHEMAORG": {
"description": "A collection of schemas that webmasters can use to markup HTML pages in ways recognized by major search providers, and that can also be used for structured data interoperability (e.g. in JSON).",
"download_owl": "http://aber-owl.net/media/ontologies/SCHEMAORG/2/schemaorg.owl",
"homepage": "https://schema.org/",
"name": "Schema.org core and all extension vocabularies",
"prefix": "SCHEMAORG",
"version": "3.4"
},
"SCIO": {
"description": "Representation of pre-clinical studies in the domain of spinal cord injury therapies",
"download_owl": "http://aber-owl.net/media/ontologies/SCIO/2/scio.owl",
"homepage": "http://www.psink.de",
"name": "Spinal Cord Injury Ontology",
"prefix": "SCIO",
"version": "1"
},
"SCO": {
"description": "The Study Cohort Ontology (SCO) is developed to model overall structure and patterns of cohort variables and control/intervention groups defined within the structured population descriptions (commonly referred to as Table1's or Cohort Summary Tables)of observational case studies and clinical trials. We maintain only domain agnostic and commonly occuring subject variables and interventions in SCO, and we have a suite of ontologies (Diseases, Medications, LabResults etc) to encode Diabetes related terminology. We have adopted a bottom-up approach to modeling and we have revised the structure of SCO upon investigation of a few research studies (11 to be precise) from the Pharmacological Interventions (Chapter 8) and Cardiovascular Complications (Chapter 9) of the American Diabetes Association (ADA)\u2019s Standards of Medical Care 2018 CPG. We enable deep drive visualizations driven off queries to knowledge graphs modeled on SCO, to help assist physician visualize the similarity of a patient to a study group, at a quick glance. We welcome contributions and suggestions to extend SCO to represent cohort descriptions of publications targeted to other diseases, and we plan to release set of tools to make this process seamless.",
"download_owl": "http://aber-owl.net/media/ontologies/SCO/5/sco.owl",
"homepage": "https://tetherless-world.github.io/study-cohort-ontology/",
"name": "Study Cohort Ontology",
"prefix": "SCO",
"version": "1.1.0"
},
"SCTO": {
"description": "The Systematized Nomenclature of Medicine Clinical Term Upper-Level Ontology (SCTO) attempts to create a basic OWL 2 ontology for SNOMED CT terminology. The ontology is built based on the Ontology of General Medical Science (OGMS). This ontology implements the SNOMED CT concept model by adding the appropriate axioms to its top-level concepts. The resulting ontology can prevent redundancies and inconsistencies in this large terminology. Moreover, the terminology maintenance can become more accurate. Finally, SNOMED CT can be used in a healthcare environment to create more complex post-coordinated expressions and constraints in a more accurate manner.",
"download_owl": "http://aber-owl.net/media/ontologies/SCTO/14/scto.owl",
"name": "SNOMED CT Standard Ontology Based on the Ontology for General Medical Science",
"prefix": "SCTO",
"version": "21-11-2017"
},
"SCTSPA": {
"description": "SNOMED Terminos Clinicos (SNOMED CT), Edicion en Espanol, Distribucion Internacional, Octubre de 2008, 2009_04_30",
"name": "SNOMED Terminos Clinicos",
"prefix": "SCTSPA",
"version": "2016AB"
},
"SD3": {
"description": "The taxonomy will facilitate quality assurance in scenario delivery, permit standardized descriptors of simulation delivery deviations, and enable researchers to quantify the impact that scenario delivery and documentation deviations have upon participant performance. Though created specifically for high-fidelity mannequin-based simulation, the taxonomy can be applied to other simulation modalities.",
"download_owl": "http://aber-owl.net/media/ontologies/SD3/1/sd3.owl",
"name": "Simulation Delivery and Documentation Deviations",
"prefix": "SD3",
"version": "1.0"
},
"SDO": {
"description": "An application ontology for the domain of Sleep Medicine.",
"download_owl": "http://aber-owl.net/media/ontologies/SDO/4/sdo.owl",
"homepage": "https://mimi.case.edu/concepts",
"name": "Sleep Domain Ontology",
"prefix": "SDO",
"version": "Last modification: Feb. 11, 2013 Sivaram Arabandi"
},
"SDOHO": {
"name": "social determinants of health ontology-TaoLab",
"prefix": "SDOHO"
},
"SDPV": {
"description": "an ontology for syndrome differentiation and treatment of Psoriasis Vulgaris in Traditional Chinese Medicine",
"download_owl": "http://aber-owl.net/media/ontologies/SDPV/1/sdpv.owl",
"name": "Syndrome Differentiation of Psoriasis Vulgaris in Traditional Chinese Medicine",
"prefix": "SDPV",
"version": "Version 1.0"
},
"SEDI": {
"description": "An ontology for DICOM as used in the SeDI project.",
"download_owl": "http://aber-owl.net/media/ontologies/SEDI/6/sedi.owl",
"homepage": "http://semantic-dicom.org",
"name": "Semantic DICOM Ontology",
"prefix": "SEDI",
"version": "0.6 alpha"
},
"SENSO": {
"description": "The SENSO ontology is designed to provide classification terms for labeling sensitive data for data archival and sharing.",
"download_owl": "http://aber-owl.net/media/ontologies/SENSO/1/senso.owl",
"homepage": "https://github.com/DataONEorg/sem-prov-ontologies",
"name": "Sensitive Data Ontology",
"prefix": "SENSO",
"version": "Version 0.1.0"
},
"SEP": {
"description": "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments, such as, and including, gel electrophoresis, column chromatography, capillary electrophoresis, centrifugation and so on. Developed jointly by the HUPO Proteomics Standards Initiative and The Metabolomics Standards Initiative.",
"download_obo": "http://aber-owl.net/media/ontologies/SEP/4/sep.obo",
"homepage": "http://psidev.info/index.php?q=node/312",
"name": "Sample Processing and Separation Techniques Ontology",
"prefix": "SEP",
"version": "1.070708"
},
"SEPIO": {
"description": "An ontology for representing the provenance of scientific claims and the evidence that supports them.",
"download_owl": "http://aber-owl.net/media/ontologies/SEPIO/4/sepio.owl",
"homepage": "https://github.com/monarch-initiative/SEPIO-ontology",
"name": "Scientific Evidence and Provenance Information Ontology",
"prefix": "SEPIO"
},
"SEPON": {
"name": "Sepsis Ontology",
"prefix": "SEPON"
},
"SEQ": {
"name": "Sequence Ontology",
"prefix": "SEQ"
},
"SERVICE": {
"name": "Rafter Loft Conversions Ltd",
"prefix": "SERVICE"
},
"SEWABUSJOGJA06": {
"name": "Sewa Bus Jogja Terbaik",
"prefix": "SEWABUSJOGJA06"
},
"SEWABUSJOGJA24": {
"name": "Sewa Bus Jogja 6",
"prefix": "SEWABUSJOGJA24"
},
"SEWABUSJOGJA47": {
"name": "Sewa Bus Jogja 3",
"prefix": "SEWABUSJOGJA47"
},
"SEWABUSJOGJA68": {
"name": "Sewa Bus Jogja",
"prefix": "SEWABUSJOGJA68"
},
"SEWABUSJOGJA76": {
"name": "Sewa Bus Jogja 2",
"prefix": "SEWABUSJOGJA76"
},
"SEWABUSJOGJA89": {
"name": "Sewa Bus Jogja Murah",
"prefix": "SEWABUSJOGJA89"
},
"SEWAELFJOGJA20": {
"name": "Sewa Elf Jogja",
"prefix": "SEWAELFJOGJA20"
},
"SEWAELFJOGJA31": {
"name": "Sewa Elf Jogja 7",
"prefix": "SEWAELFJOGJA31"
},
"SEWAELFJOGJA53": {
"name": "Sewa Elf Jogja 6",
"prefix": "SEWAELFJOGJA53"
},
"SEWAELFJOGJA91": {
"name": "Sewa Elf Jogja 2",
"prefix": "SEWAELFJOGJA91"
},
"SEWAHIACEJOGJA12": {
"name": "Sewa Hiace Jogja",
"prefix": "SEWAHIACEJOGJA12"
},
"SEWAHIACEJOGJA24": {
"name": "Sewa Hiace Jogja Terbaik",
"prefix": "SEWAHIACEJOGJA24"
},
"SEWAHIACEJOGJA32": {
"name": "Sewa Hiace Jogja Murah",
"prefix": "SEWAHIACEJOGJA32"
},
"SEWAHIACEJOGJA41": {
"name": "Sewa Hiace Jogja 5",
"prefix": "SEWAHIACEJOGJA41"
},
"SEWAHIACEJOGJA53": {
"name": "Sewa Hiace Jogja 3",
"prefix": "SEWAHIACEJOGJA53"
},
"SEWAHIACEJOGJA55": {
"name": "Sewa Hiace Jogja 6",
"prefix": "SEWAHIACEJOGJA55"
},
"SEWAMOBILJOGJA09": {
"name": "Sewa Mobil Jogja Terbaik",
"prefix": "SEWAMOBILJOGJA09"
},
"SEWAMOBILJOGJA44": {
"name": "Sewa Mobil Jogja",
"prefix": "SEWAMOBILJOGJA44"
},
"SHERIF": {
"name": "Sherif",
"prefix": "SHERIF"
},
"SHR": {
"description": "The goal of SHR project is to develop an ontology for the description of student health records. Student health records are created for entering college students in order to provide better health services will be formed. This file contains various sections such as history of disease, family history of disease, public examinations and ... .",
"download_owl": "http://aber-owl.net/media/ontologies/SHR/3/shr.owl",
"homepage": "http://www.shojaee.com/shr/",
"name": "Student Health Record Ontology",
"prefix": "SHR",
"version": "1.1"
},
"SIBO": {
"description": "Social Behavior in insects",
"download_owl": "http://aber-owl.net/media/ontologies/SIBO/2/sibo.owl",
"homepage": "https://github.com/obophenotype/sibo",
"name": "Social Insect Behavior Ontology",
"prefix": "SIBO"
},
"SIMM": {
"description": "MAATrica is a novel metric for assessing the coherence of methodologies in research papers within the fields of medicinal and nutraceutical chemistry. MAATrica employs user-controlled and customizable ontologies (in silico, in vitro and in vivo), enabling personalized analysis of research papers in the fields of medicinal and nutraceutical chemistry.",
"download_obo": "http://aber-owl.net/media/ontologies/SIMM/1/simm.obo",
"name": "In Silico Methodologies Ontology for MAATrica metric",
"prefix": "SIMM"
},
"SIMON": {
"name": "Simple Measurement Ontology",
"prefix": "SIMON"
},
"SIO": {
"description": "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. It provides vocabulary for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.",
"download_owl": "http://aber-owl.net/media/ontologies/SIO/94/sio.owl",
"homepage": "http://sio.semanticscience.org",
"name": "Semanticscience Integrated Ontology",
"prefix": "SIO",
"version": "1.59"
},
"SITBAC": {
"description": "Context-based healthcare access-control policies",
"download_owl": "http://aber-owl.net/media/ontologies/SITBAC/3/sitbac.owl",
"homepage": "http://mis.hevra.haifa.ac.il/~morpeleg/",
"name": "Situation-Based Access Control Ontology",
"prefix": "SITBAC",
"version": "1.3"
},
"SITUSJUALRUMAH": {
"name": "Jual Rumah",
"prefix": "SITUSJUALRUMAH"
},
"SK": {
"description": "An abstraction based approach.",
"download_owl": "http://aber-owl.net/media/ontologies/SK/1/sk.owl",
"name": "Digital Forensic",
"prefix": "SK"
},
"SLSO": {
"description": "The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive and other systems that contain space life science research data.",
"download_owl": "http://aber-owl.net/media/ontologies/SLSO/3/slso.owl",
"homepage": "https://github.com/nasa/LSDAO",
"name": "Space Life Sciences Ontology",
"prefix": "SLSO"
},
"SMARTLHSONTOV1": {
"description": "SMARTLHSONTO is an ontology for Learning Health System Framework covering the 15 top pillars (Benefits, Community, Consumer, Culture, Data, Governance, Leadership, ModelofCare, Organisation, Policies, Standards, Strategies, Technology, WorkForce, WorkForceSkillsets) , their subclasses and inter-relationship between the pillars and subclasses.",
"download_owl": "http://aber-owl.net/media/ontologies/SMARTLHSONTOV1/1/smartlhsontov1.owl",
"homepage": "https://bioportal.bioontology.org/ontologies/SMARTLHSONTO",
"name": "SMARTLHSONTO",
"prefix": "SMARTLHSONTOV1",
"version": "1.0"
},
"SMASH": {
"description": "The SMASH (Semantic Mining of Activity, Social, and Health data) system ontology describes concepts used in describing the semantic features of healthcare data and social networks. The SMASH system primarily addresses the research topic of sustained weight loss with continued intervention with frequent social contacts.",
"download_owl": "http://aber-owl.net/media/ontologies/SMASH/6/smash.owl",
"name": "SMASH Ontology",
"prefix": "SMASH"
},
"SMASHBIOMARKER": {
"description": "The SMASH (Semantic Mining of Activity, Social, and Health data) system ontology describes concepts used in describing the semantic features of healthcare data and social networks. The SMASH system primarily addresses the research topic of sustained weight loss with continued intervention with frequent social contacts. Biomedical measures for users in SMASH ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/SMASHBIOMARKER/4/smashbiomarker.owl",
"name": "SMASH ontology, Biomarker Ontology",
"prefix": "SMASHBIOMARKER"
},
"SMASHPHYSICAL": {
"description": "The SMASH (Semantic Mining of Activity, Social, and Health data) system ontology describes concepts used in describing the semantic features of healthcare data and social networks. The SMASH system primarily addresses the research topic of sustained weight loss with continued intervention with frequent social contacts. Physical activities for users in SMASH ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/SMASHPHYSICAL/4/smashphysical.owl",
"name": "SMASH ontology, Physical Activity Ontology",
"prefix": "SMASHPHYSICAL"
},
"SMASHSOCIAL": {
"description": "The SMASH (Semantic Mining of Activity, Social, and Health data) system ontology describes concepts used in describing the semantic features of healthcare data and social networks. The SMASH system primarily addresses the research topic of sustained weight loss with continued intervention with frequent social contacts. Social activities for users in the SMASH ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/SMASHSOCIAL/4/smashsocial.owl",
"name": "SMASH ontology, Social Activity Ontology",
"prefix": "SMASHSOCIAL"
},
"SMD_NPLSM": {
"description": "subset of snomed-ct regarding neoplasm and hamartoma",
"download_owl": "http://aber-owl.net/media/ontologies/SMD_NPLSM/1/smd_nplsm.owl",
"name": "Neoplasm_hamartoma",
"prefix": "SMD_NPLSM",
"version": "unknown"
},
"SMD_NPLSM_BRST": {
"description": "This a subset of Neoplasm_hamartoma view, based on Snomed clinical practice's used terms (Fondazione S.Maugeri anatomic pathology dep.). This subset is not to be meant exhaustive, it has been created in order to built a proper ontology for our project, ONCO-i2b2, through the NCBO Ontology Tools.",
"download_owl": "http://aber-owl.net/media/ontologies/SMD_NPLSM_BRST/1/smd_nplsm_brst.owl",
"name": "Neoplasm_breast_cancer",
"prefix": "SMD_NPLSM_BRST",
"version": "unknown"
},
"SMO": {
"description": "Syrian Movies Ontology, For Education.",
"download_owl": "http://aber-owl.net/media/ontologies/SMO/1/smo.owl",
"name": "Syrian Movies Ontology",
"prefix": "SMO"
},
"SNMD_BC": {
"description": "This a subset of snomed-ct regarding neoplasm and hamartoma, based on Snomed clinical practice's used terms (Fondazione S.Maugeri anatomic pathology dep.). This subset is not to be meant exhaustive, it has been created in order to built a proper ontology for our project, ONCO-i2b2, through the NCBO Ontology Tools.",
"download_owl": "http://aber-owl.net/media/ontologies/SNMD_BC/1/snmd_bc.owl",
"name": "Snomed neoplasm, breast cancer",
"prefix": "SNMD_BC",
"version": "unknown"
},
"SNMD_BDY": {
"description": "The Body Structure subtree in SNOMED-CT. It has been created in order to built a proper ontology for our project, ONCO-i2b2, through the NCBO Ontology Tools.",
"download_owl": "http://aber-owl.net/media/ontologies/SNMD_BDY/2/snmd_bdy.owl",
"name": "Snomed, Body Structure",
"prefix": "SNMD_BDY",
"version": "unknown"
},
"SNMI": {
"description": "Cote, Roger A., editor. Systematized Nomenclature of Human and Veterinary Medicine: SNOMED International. Northfield (IL): College of American Pathologists; Schaumburg (IL): American Veterinary Medical Association, Version 3.5, 1998.",
"name": "Systematized Nomenclature of Medicine, International Version",
"prefix": "SNMI",
"version": "2016AB"
},
"SNOMED-Ethnic-Group": {
"description": "Ethnic Group From SNOMED CT",
"download_owl": "http://aber-owl.net/media/ontologies/SNOMED-Ethnic-Group/2/snomed-ethnic-group.owl",
"name": "SNOMED Ethnic Group",
"prefix": "SNOMED-Ethnic-Group",
"version": "1"
},
"SNOMEDCT": {
"description": "SNOMED Clinical Terms",
"homepage": "http://www.snomed.org",
"name": "SNOMED CT",
"prefix": "SNOMEDCT",
"version": "2016AB"
},
"SNOMEDCT-MAS": {
"description": "The Morphologically Abnormal Structure subtree of SNOMED CT",
"download_owl": "http://aber-owl.net/media/ontologies/SNOMEDCT-MAS/1/snomedct-mas.owl",
"name": "SNOMED Morphologically Abnormal Structure",
"prefix": "SNOMEDCT-MAS",
"version": "1"
},
"SNOMEDCTSPA": {
"name": "SNOMED CT SPA",
"prefix": "SNOMEDCTSPA"
},
"SNOMED_ANATOMY": {
"description": "The Anatomy class subtree in SNOMED-CT based on SNOMED CT 2009.07.31",
"download_owl": "http://aber-owl.net/media/ontologies/SNOMED_ANATOMY/1/snomed_anatomy.owl",
"name": "SNOMED Anatomy",
"prefix": "SNOMED_ANATOMY",
"version": "1.2"
},
"SNOMED_CF": {
"description": "Extract from SNOMED",
"download_owl": "http://aber-owl.net/media/ontologies/SNOMED_CF/1/snomed_cf.owl",
"name": "SNOMED Clinical Finding",
"prefix": "SNOMED_CF"
},
"SNOMED_ORG": {
"description": "The Organism subtree in SNOMED-CT based on SNOMED-CT v. 2009.01.31",
"download_owl": "http://aber-owl.net/media/ontologies/SNOMED_ORG/1/snomed_org.owl",
"name": "SNOMED Organism",
"prefix": "SNOMED_ORG",
"version": "1.1"
},
"SNOMED_TEST": {
"description": "The Test Findings subtree in SNOMED-CT based on SNOMED-CT v. 2009.01.31",
"download_owl": "http://aber-owl.net/media/ontologies/SNOMED_TEST/1/snomed_test.owl",
"name": "SNOMED Test Findings",
"prefix": "SNOMED_TEST",
"version": "1.1"
},
"SNPO": {
"description": "SNP-Ontology is a domain ontology that provides a formal representation (OWL-DL) of genomic variations. Despite its name, SNP-Ontology, is not limited to the representation of SNPs but it encompasses genomic variations in a broader meaning. SNP-Ontology is general enough to enable the representation of variations observed in genome of various species. Latest versions of SNP-Ontology include the representation of haplotype and of CNV. The unambiguous representation of genomic variations provided by SNP-Ontology enables to integrate heterogeneous data related to genomic variations. To achieve this goal SNP-Ontology enables (1) to represent one variation in accordance with various ways that exist for describing it, (2) to represent the equivalence between two distinct descriptions of one variation, and (3) to represent correspondence between a genomic variation and its outcome at the transcriptome and proteome levels.",
"download_owl": "http://aber-owl.net/media/ontologies/SNPO/4/snpo.owl",
"homepage": "https://members.loria.fr/ACoulet/files/snpontology1.6_description.html",
"name": "Single-Nucleotide Polymorphism (SNP) Ontology",
"prefix": "SNPO",
"version": "version: full 1.6\nrelease: 14/03/2017"
},
"SO": {
"description": "A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases.",
"download_owl": "http://aber-owl.net/media/ontologies/SO/289/so.owl",
"homepage": "http://www.sequenceontology.org/",
"name": "Sequence types and features ontology",
"prefix": "SO"
},
"SOCPRES": {
"description": "The social prescribing ontology specifies concepts associated to social prescribing practices and the well being of social prescribing recipients. The ontology will be primary used to harmonise data related social prescribing processes across various parts of the health system.",
"download_owl": "http://aber-owl.net/media/ontologies/SOCPRES/1/socpres.owl",
"name": "Social Prescribing Ontology",
"prefix": "SOCPRES"
},
"SOHO": {
"description": "SOHO has terminologies covering societal factors, such as where a person was born, grew up, works, lives, etc., along with socio-economic and community factors that affect an individual\u2019s health.",
"download_owl": "http://aber-owl.net/media/ontologies/SOHO/4/soho.owl",
"name": "Social Determinants of Health Ontology",
"prefix": "SOHO",
"version": "3"
},
"SOIL-PROF": {
"name": "Soil Profile classifiers",
"prefix": "SOIL-PROF"
},
"SOPHARM": {
"description": "SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. SO-Pharm articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables to represent pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables to represent patient and more largely panel included in trials, and populations. SO-Pharm enables the representation of measured items on this patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains.",
"download_owl": "http://aber-owl.net/media/ontologies/SOPHARM/18/sopharm.owl",
"homepage": "https://members.loria.fr/ACoulet/files/sopharm2.0_description.php",
"name": "Suggested Ontology for Pharmacogenomics",
"prefix": "SOPHARM",
"version": "The new release (March 02, 2017) 2.2 includes concept and properties labels in French.\nImports have been abandoned in favor of simple references to distant URI"
},
"SOS": {
"description": "Um teste",
"download_owl": "http://aber-owl.net/media/ontologies/SOS/1/sos.owl",
"name": "emerg\u00eancia",
"prefix": "SOS"
},
"SOY": {
"description": "Growth, trait and development ontology for soybean",
"download_obo": "http://aber-owl.net/media/ontologies/SOY/2/soy.obo",
"homepage": "soybase.org",
"name": "Soy Ontology",
"prefix": "SOY",
"version": "unknown"
},
"SP": {
"description": "The SeMAntic RepresenTation for Protocols, SMART Protocols, provides a structured OWL vocabulary of experimental protocols. SMART Protocols ontology includes two modules, SP-document and SP-workflow. SP-document, aims to provide a structured vocabulary of concepts to represent information necessary and sufficient for reporting an experimental protocol. SP-Workflow represents: i) the executable elements of a protocol, protocol instructions; ii) the experimental actions and material entities that participates in instructions (sample/specimen, organisms, reagents, instruments); and iii) the order of execution of the instructions.",
"download_owl": "http://aber-owl.net/media/ontologies/SP/6/sp.owl",
"homepage": "https://smartprotocols.github.io/",
"name": "SMART Protocols",
"prefix": "SP",
"version": "4.0"
},
"SPD": {
"description": "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).",
"download_owl": "http://aber-owl.net/media/ontologies/SPD/26/spd.owl",
"homepage": "http://research.amnh.org/atol/files/",
"name": "Spider Ontology",
"prefix": "SPD"
},
"SPINALH": {
"description": "A hierarchy of Spinal Cord regions in Bilateral species.",
"download_owl": "http://aber-owl.net/media/ontologies/SPINALH/3/spinalh.owl",
"name": "NeuroMorpho.Org spinal cord regions ",
"prefix": "SPINALH",
"version": "2.0"
},
"SPO": {
"download_owl": "http://aber-owl.net/media/ontologies/SPO/1/spo.owl",
"homepage": "www.lboro.ac.uk",
"name": "Skin Physiology Ontology",
"prefix": "SPO",
"version": "2"
},
"SPRUCHE": {
"name": "All Germany ontology",
"prefix": "SPRUCHE"
},
"SPTO": {
"description": "Solanaceae crop phenotypes and traits, developed in collaboration with the research community, especially for breeder traits of agronomic importance.",
"download_obo": "http://aber-owl.net/media/ontologies/SPTO/5/spto.obo",
"homepage": "solgenomics.net",
"name": "Solanaceae Phenotype Ontology",
"prefix": "SPTO",
"version": "unknown"
},
"SP_ONTOLOGY": {
"description": "The ontology developed for the SmartPITeS project contains decision rules established in clinical practice on which a software developed for clinical decision support for the pharmacological prescription and de-prescription of complex chronic patients is based. Specifically patients with atrial fibrillation under treatment with anticoagulants.",
"download_owl": "http://aber-owl.net/media/ontologies/SP_ONTOLOGY/1/sp_ontology.owl",
"name": "SmartPITeS Proyect Ontology for Complex Chronic Patients",
"prefix": "SP_ONTOLOGY"
},
"SSE": {
"description": "Memorial Sloan-Kettering Cancer Center Surgical Secondary Events Ontology (Adverse Events)",
"download_owl": "http://aber-owl.net/media/ontologies/SSE/2/sse.owl",
"homepage": "http://www.mskcc.org/sse",
"name": "Surgical Secondary Events",
"prefix": "SSE",
"version": "1.1"
},
"SSN": {
"description": "This ontology describes sensors, actuators and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.",
"download_owl": "http://aber-owl.net/media/ontologies/SSN/2/ssn.owl",
"homepage": "https://www.w3.org/TR/vocab-ssn/",
"name": "Semantic Sensor Network Ontology",
"prefix": "SSN",
"version": "New modular version of the SSN ontology. \n\nThis ontology was originally developed in 2009-2011 by the W3C Semantic Sensor Networks Incubator Group (SSN-XG). For more information on the group's activities see: http://www.w3.org/2005/Incubator/ssn/. The ontology was revised and modularized in 2015-2017 by the W3C/OGC Spatial Data on the Web Working Group, see: https://www.w3.org/2015/spatial/wiki/Semantic_Sensor_Network_Ontology. \n\nIn particular, (a) the scope is extended to include actuation and sampling; (b) the core concepts and properties are factored out into the SOSA ontology. The SSN ontology imports SOSA and adds formal axiomatization consistent with the text definitions in SOSA, and adds classes and properties to accommodate the scope of the original SSN ontology."
},
"SSO": {
"description": "The SSO encodes agreement among experts about how Emergency Department (ED) chief complaints are grouped into syndromes of public health importance (consensus definitions).",
"download_owl": "http://aber-owl.net/media/ontologies/SSO/1/sso.owl",
"name": "Syndromic Surveillance Ontology",
"prefix": "SSO",
"version": "1"
},
"STATO": {
"description": "STATO is a general-purpose STATistics Ontology. Its aim is to provide coverage for processes such as statistical tests, their conditions of application, and information needed or resulting from statistical methods, such as probability distributions, variables, spread and variation metrics. STATO also covers aspects of experimental design and description of plots and graphical representations commonly used to provide visual cues of data distribution or layout and to assist review of the results.",
"download_owl": "http://aber-owl.net/media/ontologies/STATO/14/stato.owl",
"homepage": "http://stato-ontology.org/",
"name": "The Statistical Methods Ontology",
"prefix": "STATO"
},
"STMSO": {
"description": "STMSO is the first comprehensive semantic representation of symptomatic treatment of MS and provides a major step toward the development of intelligent Clinical Decision Support System (CDSS) for MS symptomatic treatment.",
"download_owl": "http://aber-owl.net/media/ontologies/STMSO/1/stmso.owl",
"name": "symptomatic treatment of multiple sclerosis ontology",
"prefix": "STMSO"
},
"STO": {
"description": "Stroke ontology covers the knowledge domain of stroke based on expert views and translational continuum of stroke research. The Stroke Ontology (STO) presented here, is the first draft and we hope that the scientific community can contribute to the enrichment of this draft. The ontology can be used a reference for a variety of bioinformatics applications such as annotation of terms, harmonization of experimental data, text-mining, and modeling disease mechanism.",
"download_owl": "http://aber-owl.net/media/ontologies/STO/3/sto.owl",
"name": "Stroke Ontology",
"prefix": "STO",
"version": "2017-11-01"
},
"STO-DRAFT": {
"description": "The Stroke Ontology (STO) covers the knowledge domain of stroke based on expert views and translational continuum of stroke research.",
"download_owl": "http://aber-owl.net/media/ontologies/STO-DRAFT/1/sto-draft.owl",
"name": "The Stroke Ontology",
"prefix": "STO-DRAFT",
"version": "2017-11-01"
},
"STUFF": {
"description": "a core ontology of types of macroscopic stuff (types of masses/matter)",
"download_owl": "http://aber-owl.net/media/ontologies/STUFF/3/stuff.owl",
"homepage": "http://www.meteck.org/stuff.html",
"name": "Stuff Ontology",
"prefix": "STUFF",
"version": "1.5"
},
"STY": {
"description": "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types. This section of the documentation provides an overview of the Semantic Network, and describes the files of the Semantic Network. Sample records illustrate structure and content of these files. The Semantic Network is distributed as one of the UMLS Knowledge Sources and as an open source resource available on the Semantic Network Web site, subject to these terms and conditions.",
"homepage": "https://semanticnetwork.nlm.nih.gov/",
"name": "Semantic Types Ontology",
"prefix": "STY",
"version": "2016AB"
},
"SUGARBIND": {
"description": "Ontology for representing glycan and pathogen binding interaction data in RDF. Many of the terms are based on the data originally contained in the SugarBind database.",
"download_owl": "http://aber-owl.net/media/ontologies/SUGARBIND/1/sugarbind.owl",
"name": "SugarBind",
"prefix": "SUGARBIND",
"version": "1.0.0"
},
"SURGICAL": {
"description": "This is an ontology of a surgical nurse's process domain",
"download_owl": "http://aber-owl.net/media/ontologies/SURGICAL/1/surgical.owl",
"name": "Nurse Surgical",
"prefix": "SURGICAL"
},
"SVU_MWS_WSM": {
"description": "Syrian Cinema Othology this othology releted to Protege project which is a practical assignment in the Semantic Web course for a graduate student in the Master of Web Science program with Dr.Bassel Al Khatib This ontology conten seven class Each class has the necessary data properties and several object properties which represent relationship between classes",
"download_owl": "http://aber-owl.net/media/ontologies/SVU_MWS_WSM/1/svu_mws_wsm.owl",
"homepage": "rahaf_246783@svuonline.org",
"name": "Syrian Cinema Ontology",
"prefix": "SVU_MWS_WSM",
"version": "1.0"
},
"SVU_MWS_WSM_F23": {
"description": "This ontology releted to Protege project which is a practical assignment in the Semantic Web course for a graduate student in the Master of Web Science program with Dr.Bassel Al Khatib This ontology contens seven class Each class has the necessary data properties and several object properties which represent relationship between classes",
"download_owl": "http://aber-owl.net/media/ontologies/SVU_MWS_WSM_F23/1/svu_mws_wsm_f23.owl",
"homepage": "rahaf_246783@svuonline.org",
"name": "MWS-WSM-F23 Syrian Cinema Ontology",
"prefix": "SVU_MWS_WSM_F23",
"version": "1.0"
},
"SWEET": {
"description": "The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research). Originally developed by NASA Jet Propulsion Labs under Rob Raskin, SWEET is now officially under the governance of the ESIP foundation.",
"download_owl": "http://aber-owl.net/media/ontologies/SWEET/2/sweet.owl",
"homepage": "https://github.com/ESIPFed/sweet/blob/master/README.md",
"name": "Semantic Web for Earth and Environment Technology Ontology",
"prefix": "SWEET",
"version": "3.1.0"
},
"SWO": {
"description": "The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community.",
"download_owl": "http://aber-owl.net/media/ontologies/SWO/32/swo.owl",
"homepage": "https://github.com/allysonlister/swo",
"name": "Software ontology",
"prefix": "SWO"
},
"SYMP": {
"description": "An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease.",
"download_owl": "http://aber-owl.net/media/ontologies/SYMP/42/symp.owl",
"homepage": "http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page",
"name": "Symptom Ontology",
"prefix": "SYMP"
},
"SYN": {
"description": "The controlled vocabulary used for various entity properties in the Synapse platform.",
"download_owl": "http://aber-owl.net/media/ontologies/SYN/3/syn.owl",
"name": "Sage Bionetworks Synapse Ontology",
"prefix": "SYN",
"version": ".3"
},
"SYRIAN-CINEMA": {
"description": "Syrian Cenima antology by Mouaz Al-Shahmeh - 216212",
"download_owl": "http://aber-owl.net/media/ontologies/SYRIAN-CINEMA/3/syrian-cinema.owl",
"name": "Syrian Cinema",
"prefix": "SYRIAN-CINEMA",
"version": "1.0.0"
},
"SciRes": {
"description": "This file is imported by vivo-core-public-1.5.owl. It contains terms related to scientific research resources that are included in the vivo ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/SciRes/1/scires.owl",
"homepage": "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology",
"name": "Scientific Research Resources",
"prefix": "SciRes",
"version": "1.5"
},
"Spitali": {
"description": "se di",
"download_owl": "http://aber-owl.net/media/ontologies/Spitali/1/spitali.owl",
"homepage": "Desktop",
"name": "Dallendyshe",
"prefix": "Spitali",
"version": "se di"
},
"T123": {
"name": "Test123",
"prefix": "T123",
"version": "0.1.0"
},
"T4FS": {
"description": "A terminology for the skills necessary to make data FAIR and to keep it FAIR.",
"download_owl": "http://aber-owl.net/media/ontologies/T4FS/3/t4fs.owl",
"homepage": "https://github.com/terms4fairskills/FAIRterminology",
"name": "terms4FAIRskills",
"prefix": "T4FS"
},
"TADS": {
"description": "The anatomy of the Tick, Families: Ixodidae, Argassidae",
"download_owl": "http://aber-owl.net/media/ontologies/TADS/18/tads.owl",
"homepage": "https://www.vectorbase.org/ontology-browser",
"name": "Tick Anatomy Ontology",
"prefix": "TADS"
},
"TAO": {
"description": "TAO is a multispecies anatomy ontology for teleost fishes. Originally seeded from ZFA, but intended to cover terms relevant to other taxa.",
"download_obo": "http://aber-owl.net/media/ontologies/TAO/135/tao.obo",
"homepage": "https://www.nescent.org/phenoscape/Main_Page",
"name": "Teleost Anatomy Ontology",
"prefix": "TAO",
"version": "2012-08-10"
},
"TAXRANK": {
"description": "A vocabulary of taxonomic ranks (species, family, phylum, etc)",
"download_owl": "http://aber-owl.net/media/ontologies/TAXRANK/10/taxrank.owl",
"homepage": "https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary",
"name": "Taxonomic rank vocabulary",
"prefix": "TAXRANK"
},
"TCDO": {
"description": "More than 400 popular TCD decoction pieces (TCD-DP) were selected from authoritative textbooks, standards and terminologies, as well as their crudes, Chinese medicinal material (CMM). The TCD-DP entities are categorized in 23 upper level terms by their clinical effects. Their properties like nature, flavor, toxicity and meridian entries are also defined formally by logical relations. CMM\u2019s species is mapped to the NCBITaxon taxonomy ontology, which establishes a link between traditional medicine and modern biomedical science. TCDO contains over 1,500 terms, including terms drawn from existing ontologies and more than 1,000 TCD-specific terms, labeled in both Chinese and English.",
"download_owl": "http://aber-owl.net/media/ontologies/TCDO/3/tcdo.owl",
"homepage": "https://github.com/TCMOntology/TCDO",
"name": "Traditional Chinese Drug Ontology",
"prefix": "TCDO",
"version": "0.05"
},
"TCO": {
"description": "Thyroid cancer ontology (TCO) contains 578 concepts organized under 6 biological viewpoints, i.e., Anatomy and Histoembryology, Basic Information of Patient, Cellular or Molecular Interactions, Clinical Aspects, Etiology, Pathology",
"download_owl": "http://aber-owl.net/media/ontologies/TCO/2/tco.owl",
"name": "Thyroid Cancer Ontology",
"prefix": "TCO",
"version": "1.0"
},
"TDT": {
"name": "Tour Danau Toba",
"prefix": "TDT"
},
"TDWGSPEC": {
"description": "Biodiversity Information Standards (TDWG) is an international not-for-profit group that develops standards and protocols for sharing biodiversity data. They have a detailed collection of vocabularies and ontologies for studies of biological organisms.",
"download_owl": "http://aber-owl.net/media/ontologies/TDWGSPEC/1/tdwgspec.owl",
"name": "TDWG Specimen LSID Ontology",
"prefix": "TDWGSPEC",
"version": "0.3"
},
"TEDDY": {
"description": "The TErminology for the Description of DYnamics (TEDDY) project aims to provide an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.",
"download_owl": "http://aber-owl.net/media/ontologies/TEDDY/11/teddy.owl",
"homepage": "http://teddyontology.sourceforge.net/",
"name": "Terminology for the Description of Dynamics",
"prefix": "TEDDY",
"version": "rel-2014-04-24 (inferred)"
},
"TEMPO": {
"description": "TempO is a lightweight ontology for describing temporal validity and efficacy according to a tritemporal data model.",
"download_owl": "http://aber-owl.net/media/ontologies/TEMPO/3/tempo.owl",
"homepage": "https://github.com/hroptatyr/tempo/",
"name": "TempO",
"prefix": "TEMPO",
"version": "0.1"
},
"TEO": {
"description": "The Time Event Ontology (TEO) is an ontology for representing events, time, and their relationships.",
"download_owl": "http://aber-owl.net/media/ontologies/TEO/4/teo.owl",
"name": "Time Event Ontology",
"prefix": "TEO",
"version": "1.0.8"
},
"TEPHRAM4MEXAMPLE": {
"description": "Test of a Tephra controlled vocabulary for Station to be used for a M4M workshop.",
"name": "Tephra M4M Example",
"prefix": "TEPHRAM4MEXAMPLE",
"version": "0.1.1"
},
"TERRADCAT_AP": {
"description": "Terra DCAT AP is the Broad Data Sciences Platform's application profile. It is an RDF vocabulary which extends the W3C's Data Catalog Vocabulary (https://www.w3.org/TR/vocab-dcat/)",
"download_owl": "http://aber-owl.net/media/ontologies/TERRADCAT_AP/2/terradcat_ap.owl",
"homepage": "https://github.com/DataBiosphere/terra-interoperability-model",
"name": "Terra DCAT Application Profile",
"prefix": "TERRADCAT_AP",
"version": "alpha"
},
"TEST-M4M20-PAV": {
"description": "Test",
"name": "test-m4m20-subjects-pav",
"prefix": "TEST-M4M20-PAV",
"version": "0.1.0"
},
"TEST1234": {
"name": "test123",
"prefix": "TEST1234"
},
"TESTEX": {
"description": "first ontology creation format",
"download_owl": "http://aber-owl.net/media/ontologies/TESTEX/1/testex.owl",
"name": "test1",
"prefix": "TESTEX",
"version": "0.0.1"
},
"TESTING_BOSCO": {
"description": "Testing upload",
"download_owl": "http://aber-owl.net/media/ontologies/TESTING_BOSCO/12/testing_bosco.owl",
"name": "Test_bosco",
"prefix": "TESTING_BOSCO",
"version": "0.9.2"
},
"TESTUDEM2222": {
"name": "TestUdeM2222",
"prefix": "TESTUDEM2222"
},
"TEST_A": {
"description": "This is an example ontology created by owlready2 python library",
"download_owl": "http://aber-owl.net/media/ontologies/TEST_A/1/test_a.owl",
"name": "TEST_A",
"prefix": "TEST_A"
},
"TEST_CBI": {
"description": "Testing CBI ontology",
"download_owl": "http://aber-owl.net/media/ontologies/TEST_CBI/1/test_cbi.owl",
"name": "test_cbi",
"prefix": "TEST_CBI"
},
"TEST_IDKWHATIMDO": {
"name": "Tanya ",
"prefix": "TEST_IDKWHATIMDO"
},
"TGMA": {
"description": "A structured controlled vocabulary of the anatomy of mosquitoes.",
"download_owl": "http://aber-owl.net/media/ontologies/TGMA/18/tgma.owl",
"homepage": "https://www.vectorbase.org/ontology-browser",
"name": "Mosquito gross anatomy ontology",
"prefix": "TGMA"
},
"THREE-ST": {
"description": "This ontology contains classes, sub-classes, and relationships that map onto the 3-Step Theory of suicide (3ST). The classes represent the four factors that make up the central tenets of the theory: 1) psychological pain, 2) hopelessness, 3) connectedness, and 4) capacity for suicide. The instances of each subclass are terms that were found in VA clinical notes and indicate presence or absence of the associated 3ST factor. The terms are intended to be used in an NLP pipeline to extract 3ST information from clinical progress notes. Psychological pain, hopelessness, and capacity for suicide are major risk factors for suicide, whereas connectedness is a protective factor. In brief, the theory holds that suicide only occurs if pain and hopelessness outweigh connectedness and only then if the capacity for suicide is present.",
"download_owl": "http://aber-owl.net/media/ontologies/THREE-ST/4/three-st.owl",
"name": "3-Step Theory of suicide",
"prefix": "THREE-ST",
"version": "1.0.1"
},
"THREELPH": {
"description": "A hierarchy of three layers that are most commonly referred to in subcortical regions.",
"download_owl": "http://aber-owl.net/media/ontologies/THREELPH/2/threelph.owl",
"name": "NeuroMorpho.Org three layers in subcortical regions",
"prefix": "THREELPH",
"version": "2.0"
},
"TIM": {
"description": "The Terra Interoperability Model captures a common set of concepts and relationships for biomedical research intended to facilitate and encourage data sharing and reuse. Its purpose is to enable researchers to find highly connected biomedical data in a federated search space and support interoperability among datasets.",
"download_owl": "http://aber-owl.net/media/ontologies/TIM/1/tim.owl",
"homepage": "https://github.com/DataBiosphere/terra-interoperability-model",
"name": "Terra Interoperability Model",
"prefix": "TIM",
"version": "Created with TopBraid Composer"
},
"TIME": {
"description": "OWL-Time is an OWL-2 DL ontology of temporal concepts, for describing the temporal properties of resources in the world or described in Web pages. The ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. Time positions and durations may be expressed using either the conventional (Gregorian) calendar and clock, or using another temporal reference system such as Unix-time, geologic time, or different calendars.",
"download_owl": "http://aber-owl.net/media/ontologies/TIME/2/time.owl",
"homepage": "https://www.w3.org/TR/owl-time/",
"name": "OWL-Time",
"prefix": "TIME",
"version": "2017"
},
"TIMEBANK": {
"description": "The Timebank Ontology is used to describe Timebank systems for Peer-to-Peer Service Exchange. A Timebank allows user to store virtual money, often called a Time Dollar, into a bank account. This virtual currency can be earned by helping fellow Timebank users and spent by requesting help from others. The main goal of the ontology is to facilitate the matching between helpers and requesters of help.",
"download_owl": "http://aber-owl.net/media/ontologies/TIMEBANK/2/timebank.owl",
"homepage": "https://w3id.org/timebank",
"name": "Timebank Ontology",
"prefix": "TIMEBANK",
"version": "0.3"
},
"TM-CONST": {
"description": "The value set for the Constitution property of the International Classification of Traditional Medicine (ICTM).",
"download_owl": "http://aber-owl.net/media/ontologies/TM-CONST/1/tm-const.owl",
"homepage": "https://sites.google.com/site/whoictm/home",
"name": "Traditional Medicine Constitution Value Set",
"prefix": "TM-CONST",
"version": "1"
},
"TM-MER": {
"description": "The meridian value set used in the International Classification of Traditional Medicine.",
"download_owl": "http://aber-owl.net/media/ontologies/TM-MER/1/tm-mer.owl",
"homepage": "https://sites.google.com/site/whoictm/home",
"name": "Traditional Medicine Meridian Value Sets",
"prefix": "TM-MER",
"version": "1"
},
"TM-OTHER-FACTORS": {
"description": "The value set for the Other Factors property of the International Classification of Traditional Medicine (ICTM).",
"download_owl": "http://aber-owl.net/media/ontologies/TM-OTHER-FACTORS/1/tm-other-factors.owl",
"homepage": "https://sites.google.com/site/whoictm/home",
"name": "Traditional Medicine Other Factors Value Set",
"prefix": "TM-OTHER-FACTORS",
"version": "1"
},
"TM-SIGNS-AND-SYMPTS": {
"description": "The value set for the Signs and Symptoms property of the International Classification of Traditional Medicine (ICTM).",
"download_owl": "http://aber-owl.net/media/ontologies/TM-SIGNS-AND-SYMPTS/1/tm-signs-and-sympts.owl",
"homepage": "https://sites.google.com/site/whoictm/home",
"name": "Traditional Medicine Signs and Symptoms Value Set",
"prefix": "TM-SIGNS-AND-SYMPTS",
"version": "1"
},
"TMA": {
"description": "Tissue microarrays (TMA) are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential. The Resource Description Framework (RDF) provides a flexible method to represent knowledge in triples, which take the form Subject-Predicate-Object. All data resources are described using Uniform Resource Identifiers (URI), which are global in scope. We present an OWL (Web Ontology Language) schema that expands upon the TMA data exchange specification to address this issue and assist in data sharing and integration.",
"download_owl": "http://aber-owl.net/media/ontologies/TMA/1/tma.owl",
"name": "Tissue Microarray Ontology",
"prefix": "TMA",
"version": "1.0.0"
},
"TMD": {
"name": "Tam Minh Duogn Pharmacy",
"prefix": "TMD"
},
"TML": {
"description": "a set of metadata to record transformative machine learning experiments with LINCS dataset",
"download_owl": "http://aber-owl.net/media/ontologies/TML/1/tml.owl",
"name": "trasformative machine learning metadata",
"prefix": "TML",
"version": "0.1"
},
"TMO": {
"description": "This project focuses on the development of a high level patient-centric ontology for the pharmaceutical industry. The ontology should enable silos in discovery research, hypothesis management, experimental studies, compounds, formulation, drug development, market size, competitive data, population data, etc. to be brought together. This would enable scientists to answer new questions, and to answer existing scientific questions more quickly. This will help pharmaceutical companies to model patient-centric information, which is essential for the tailoring of drugs, and for early detection of compounds that may have sub-optimal safety profiles. The ontology should link to existing publicly available domain ontologies.",
"download_owl": "http://aber-owl.net/media/ontologies/TMO/13/tmo.owl",
"homepage": "http://esw.w3.org/HCLSIG/PharmaOntology",
"name": "Translational Medicine Ontology",
"prefix": "TMO",
"version": "1.0.2"
},
"TO": {
"description": "A controlled vocabulary to describe phenotypic traits in plants.",
"download_owl": "http://aber-owl.net/media/ontologies/TO/11/to.owl",
"homepage": "http://browser.planteome.org/amigo",
"name": "Plant Trait Ontology",
"prefix": "TO"
},
"TOCWWE": {
"description": "Ontology of epilepsy treatment, particularly for childbearing-age women with epilepsy.",
"download_owl": "http://aber-owl.net/media/ontologies/TOCWWE/1/tocwwe.owl",
"name": "Treatment of Childbearing-age Women with Epilepsy ",
"prefix": "TOCWWE",
"version": "20210819"
},
"TODZ": {
"name": "Test Ontology",
"prefix": "TODZ"
},
"TOK": {
"description": "An Ontology describing Resources having different formats. This Ontology can be used to annotate and describe Terminological, Ontological Knowledge resources.",
"download_owl": "http://aber-owl.net/media/ontologies/TOK/3/tok.owl",
"homepage": "http://cui.unige.ch/~ghoula/",
"name": "Terminological and Ontological Knowledge Resources Ontology",
"prefix": "TOK",
"version": "0.2.1"
},
"TOP-MENELAS": {
"description": "The two main goals MENELAS contributes to are to (i) Provide better account of and better access to medical information through natural languages in order to help physicians in their daily practice, and to (ii) Enhance European cooperation by multilingual access to standardised medical nomenclatures. The major achievements of MENELAS are the realisation of its two functional systems: (i) The Document Indexing System encodes free text PDSs into both an internal representation (a set of Conceptual Graphs) and international nomenclature codes (ICD-9-CM). Instances of the Document Indexing System have been realised for French, English and Dutch ; (ii) The Consultation System allows users to access the information contained in PDSs previously indexed by the Document Indexing System. The test domain for the project was coronary diseases. The existing prototype shows promising results for information retrieval from natural language PDSs and for automatically encoding PDSs into an existing classification such as ICD-9-CM. A set of components, tools, knowledge bases and methods has also been produced by the project. These include language-independent ontology and models for the domain of coronary diseases; conceptual description of the relevant ICD-9-CM codes. This ontology includes a top-ontology, a top-domain ontology and a domain ontology (Coronay diseases surgery). The menelas-top ontology here is the part of the whole ontology without any reference to medical domain.",
"download_owl": "http://aber-owl.net/media/ontologies/TOP-MENELAS/4/top-menelas.owl",
"name": "Menelas Project Top-Level Ontology",
"prefix": "TOP-MENELAS",
"version": "1.1"
},
"TP4": {
"description": "relation familiales",
"download_owl": "http://aber-owl.net/media/ontologies/TP4/1/tp4.owl",
"name": "Oualid",
"prefix": "TP4"
},
"TP_REL_FAM": {
"description": "TP4 concernant les relations familiales",
"download_owl": "http://aber-owl.net/media/ontologies/TP_REL_FAM/2/tp_rel_fam.owl",
"name": "Relation familiales",
"prefix": "TP_REL_FAM"
},
"TRAK": {
"description": "TRAK (Taxonomy for RehAbilitation of Knee conditions) is an ontology that formally models information relevant for the rehabilitation of knee conditions. TRAK provides the framework that can be used to collect coded data in sufficient detail to support epidemiologic studies so that the most effective treatment components can be identified, new interventions developed and the quality of future randomized control trials improved to incorporate a control intervention that is well defined and reflects clinical practice.",
"download_obo": "http://aber-owl.net/media/ontologies/TRAK/5/trak.obo",
"homepage": "http://www.cs.cf.ac.uk/trak",
"name": "Taxonomy for Rehabilitation of Knee Conditions",
"prefix": "TRAK",
"version": "unknown"
},
"TRANS": {
"description": "An ontology representing the disease transmission process during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host.",
"download_owl": "http://aber-owl.net/media/ontologies/TRANS/5/trans.owl",
"homepage": "https://github.com/DiseaseOntology/PathogenTransmissionOntology",
"name": "Pathogen Transmission Ontology",
"prefix": "TRANS"
},
"TRIAGE": {
"description": "An ontology showing the process domain of a triage nurse.",
"download_owl": "http://aber-owl.net/media/ontologies/TRIAGE/2/triage.owl",
"name": "Nurse triage",
"prefix": "TRIAGE"
},
"TRIKMENANGJUDI": {
"name": "trik menang judi online",
"prefix": "TRIKMENANGJUDI"
},
"TRON": {
"description": "TrOn is an ontology about the anatomical structures of the red flour beetle Tribolium castaneum in the developmental stages larva, pupa and adult.",
"download_obo": "http://aber-owl.net/media/ontologies/TRON/2/tron.obo",
"homepage": "http://ibeetle-base.uni-goettingen.de/ontology/overview.jsf",
"name": "Tribolium Ontology",
"prefix": "TRON",
"version": "unknown"
},
"TST-VODAN": {
"description": "migrants ontologies",
"name": "VODANA Migrants News Vocabulary",
"prefix": "TST-VODAN",
"version": "2.0"
},
"TST7": {
"description": "Final skos",
"homepage": "https://cedar.metadatacenter.org/templates/edit/https://repo.metadatacenter.org/templates/1bcab355-0b9f-4449-9f12-99c3552df353?folderId=https:%2F%2Frepo.metadatacenter.org%2Ffolders%2Fe4bd3d33-b817-4357-aed7-812b84200c88",
"name": "FIELDLAB3_2023",
"prefix": "TST7"
},
"TT476": {
"name": "Tony Tran",
"prefix": "TT476"
},
"TTO": {
"description": "An ontology covering the taxonomy of teleosts (bony fish)",
"download_owl": "http://aber-owl.net/media/ontologies/TTO/44/tto.owl",
"homepage": "https://www.nescent.org/phenoscape/Main_Page",
"name": "Teleost taxonomy ontology",
"prefix": "TTO"
},
"TUNIGO-SLIM": {
"name": "Tunicate GO Slim",
"prefix": "TUNIGO-SLIM"
},
"TWCP": {
"description": "..",
"download_owl": "http://aber-owl.net/media/ontologies/TWCP/1/twcp.owl",
"name": "Top Women Chess Players",
"prefix": "TWCP",
"version": "1.0"
},
"TXPO": {
"description": "TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.",
"download_owl": "http://aber-owl.net/media/ontologies/TXPO/28/txpo.owl",
"homepage": "https://toxpilot.nibiohn.go.jp/",
"name": "Toxic Process Ontology",
"prefix": "TXPO"
},
"TYPON": {
"description": "TyPon provides a comprehensive description of the existing microbial typing methods for the identification of bacterial Isolates and their classification. Such a description constitutes an universal format for the exchange of information on the microbial typing field, providing a vehicle for the integration of the numerous disparate online databases. In its current version, TyPon describes most used microbial typing methods but it is, and always will be, a work in progress given the constant advances in the microbial typing field.",
"download_owl": "http://aber-owl.net/media/ontologies/TYPON/11/typon.owl",
"homepage": "http://www.phyloviz.net/typon/",
"name": "Microbial Typing Ontology",
"prefix": "TYPON",
"version": "20140929"
},
"TYSON": {
"name": "ZTWOEM",
"prefix": "TYSON"
},
"Test Ontology for Non-bio": {
"description": "Test ontology",
"download_owl": "http://aber-owl.net/media/ontologies/Test Ontology for Non-bio/1/test ontology for non-bio.owl",
"name": "Sudalai Mari",
"prefix": "Test Ontology for Non-bio",
"version": "v1"
},
"Test Ontology for Non-bio 2": {
"download_owl": "http://aber-owl.net/media/ontologies/Test Ontology for Non-bio 2/1/test ontology for non-bio 2.owl",
"name": "MyProject",
"prefix": "Test Ontology for Non-bio 2",
"version": "v1"
},
"Test Ontology for Non-biological": {
"description": "Test",
"download_owl": "http://aber-owl.net/media/ontologies/Test Ontology for Non-biological/1/test ontology for non-biological.owl",
"name": "Sudalai Mari Test",
"prefix": "Test Ontology for Non-biological",
"version": "V1"
},
"UBERON": {
"description": "An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies",
"download_owl": "http://aber-owl.net/media/ontologies/UBERON/302/uberon.owl",
"homepage": "http://uberon.org",
"name": "Uberon multi-species anatomy ontology",
"prefix": "UBERON"
},
"UGANDAFACILITIES": {
"description": "This is the list of health facilities registered under VODANA Project.",
"name": "UGANDAFACILITIES",
"prefix": "UGANDAFACILITIES",
"version": "1"
},
"UGANDA_DISEASES": {
"description": "This is the seventh version of the Uganda diseases",
"name": "Uganda_diseases",
"prefix": "UGANDA_DISEASES",
"version": "7"
},
"UHC-METADATA": {
"description": "Draft of onotlogy for UHC meta hub",
"download_owl": "http://aber-owl.net/media/ontologies/UHC-METADATA/1/uhc-metadata.owl",
"name": "UHC Metadata",
"prefix": "UHC-METADATA",
"version": "v0.0.1"
},
"UK": {
"description": "it is just for show some details about the UK",
"download_owl": "http://aber-owl.net/media/ontologies/UK/1/uk.owl",
"name": "uk geography",
"prefix": "UK",
"version": "1"
},
"UMMS": {
"description": "This is an in-progress ontology for the numerous use cases of UMMS Enterprise Data & Analytics dept",
"download_owl": "http://aber-owl.net/media/ontologies/UMMS/3/umms.owl",
"name": "FirstOntologyForUMMS",
"prefix": "UMMS",
"version": "0.3"
},
"UNITSONT": {
"description": "A small ontology for the units of measurement developed during the development of the Sleep Domain Ontology (SDO). It supports the use of SDO within the PhysioMIMI application.",
"download_owl": "http://aber-owl.net/media/ontologies/UNITSONT/1/unitsont.owl",
"homepage": "https://mimi.case.edu/concepts",
"name": "Units Ontology",
"prefix": "UNITSONT",
"version": "1.0"
},
"UO": {
"description": "Metrical units for use in conjunction with PATO",
"download_owl": "http://aber-owl.net/media/ontologies/UO/61/uo.owl",
"homepage": "https://github.com/bio-ontology-research-group/unit-ontology",
"name": "Units of measurement ontology",
"prefix": "UO"
},
"UP": {
"name": "UP Board Exam Date Sheet 2019",
"prefix": "UP"
},
"UPA": {
"description": "A manually curated resource for the representation and annotation of metabolic pathways",
"download_owl": "http://aber-owl.net/media/ontologies/UPA/2/upa.owl",
"homepage": "https://github.com/geneontology/unipathway",
"name": "Unipathway",
"prefix": "UPA"
},
"UPHENO": {
"description": "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/UPHENO/5/upheno.owl",
"homepage": "https://github.com/obophenotype/upheno",
"name": "Unified phenotype ontology (uPheno)",
"prefix": "UPHENO"
},
"URLO": {
"name": "Uniform Resource Locator Ontology",
"prefix": "URLO"
},
"VANDF": {
"description": "NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes.",
"homepage": "http://www.pbm.va.gov/NationalFormulary.aspx",
"name": "Veterans Health Administration National Drug File",
"prefix": "VANDF",
"version": "2016AB"
},
"VARIO": {
"description": "Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations.",
"download_owl": "http://aber-owl.net/media/ontologies/VARIO/19/vario.owl",
"homepage": "http://variationontology.org",
"name": "Variation Ontology",
"prefix": "VARIO"
},
"VBO": {
"description": "Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.",
"download_owl": "http://aber-owl.net/media/ontologies/VBO/9/vbo.owl",
"homepage": "https://github.com/monarch-initiative/vertebrate-breed-ontology",
"name": "Vertebrate Breed Ontology",
"prefix": "VBO"
},
"VCSR": {
"description": "This is a tacit knowledge ontology. The ontology contains entities, individuals and properties in the domain of Victorian (Australia) Health's Covid surge workforce during the Covid outbreak 2020-2022. This ontology aims to be: 1) An historical resource for future planning. 2) A formal taxonomy of terms. 3) Corporate memory. The ontology represents many Public Health Officer's (PHO's) perspective of the domain. The author and people who inputted terms to the ontology were PHOs during this period. The ontology is PHOs lived experience of a multitude of ever-changing moving parts during the pandemic. The ontology was constructed in Prot\u00e9g\u00e9 5.2.0 and is best downloaded and viewed on that platform.",
"download_owl": "http://aber-owl.net/media/ontologies/VCSR/6/vcsr.owl",
"homepage": "www.ontohealth.com.au",
"name": "Victorian Australia, Covid surge response",
"prefix": "VCSR",
"version": "Version 1.91"
},
"VDOT": {
"description": "VDOT is a middle-layer ontology for the health care domain with special emphasis on viral infections and transplantation medicine.",
"download_owl": "http://aber-owl.net/media/ontologies/VDOT/35/vdot.owl",
"name": "Viral Disease Ontology Trunk",
"prefix": "VDOT",
"version": "Initial Version\nrelease date 28/02/2017"
},
"VEO": {
"description": "Visual Emotion Ontology (VEO) is an ontology that links visualizations with specific emotions from the Ortony, Clore, and Collins' description of human emotions.",
"download_owl": "http://aber-owl.net/media/ontologies/VEO/1/veo.owl",
"name": "Visualized Emotion Ontology",
"prefix": "VEO",
"version": "0.5"
},
"VFB_DRIVERS": {
"description": "An ontology of Drosophila melanogaster drivers and expression patterns.",
"download_owl": "http://aber-owl.net/media/ontologies/VFB_DRIVERS/130/vfb_drivers.owl",
"name": "vfb_drivers",
"prefix": "VFB_DRIVERS",
"version": "2024-08-05"
},
"VHO": {
"description": "Ontology of terms used for annotating data in Virtual Fly Brain, including anatomical templates.",
"download_owl": "http://aber-owl.net/media/ontologies/VHO/1/vho.owl",
"name": "VFB Helper Ontology",
"prefix": "VHO"
},
"VHOG": {
"description": "vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 \"historical homology\". Each mapping has been manually reviewed, and we provide confidence codes and references when available.",
"download_obo": "http://aber-owl.net/media/ontologies/VHOG/12/vhog.obo",
"homepage": "http://bgee.unil.ch",
"name": "Vertebrate Homologous Organ Group Ontology",
"prefix": "VHOG",
"version": "unknown"
},
"VICO": {
"description": "The Vaccination Informed Consent Ontology (VICO) is a community-driven ontology in the domain of vaccination/immunization informed consent.",
"download_owl": "http://aber-owl.net/media/ontologies/VICO/10/vico.owl",
"homepage": "https://github.com/VICO-ontology",
"name": "Vaccination Informed Consent Ontology",
"prefix": "VICO",
"version": "Arbor version; 1.0.52"
},
"VIDO": {
"description": "The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc.",
"download_owl": "http://aber-owl.net/media/ontologies/VIDO/3/vido.owl",
"homepage": "https://github.com/infectious-disease-ontology-extensions/ido-virus",
"name": "Virus Infectious Disease Ontology",
"prefix": "VIDO",
"version": "10-27-2022"
},
"VIMM": {
"description": "MAATrica is a novel metric for assessing the coherence of methodologies in research papers within the fields of medicinal and nutraceutical chemistry. MAATrica employs user-controlled and customizable ontologies (in silico, in vitro and in vivo), enabling personalized analysis of research papers in the fields of medicinal and nutraceutical chemistry. Here we present the in vitro ontology we developed for the scope.",
"download_obo": "http://aber-owl.net/media/ontologies/VIMM/1/vimm.obo",
"name": "In Vitro Methodologies Ontology for MAATrica metric",
"prefix": "VIMM"
},
"VIO": {
"description": "VIO is an VO-extended ontology with the aim to standardize the metadata types in various vaccine investigation studies.",
"download_owl": "http://aber-owl.net/media/ontologies/VIO/1/vio.owl",
"homepage": "https://github.com/vaccineontology/VIO",
"name": "Vaccine Investigation Ontology",
"prefix": "VIO",
"version": "Vision Release: 1.0.01"
},
"VIVO": {
"description": "The VIVO ontology represents researchers in the context of their experience, outputs, interests, accomplishments, and associated institutions.",
"download_owl": "http://aber-owl.net/media/ontologies/VIVO/2/vivo.owl",
"homepage": "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology",
"name": "VIVO Ontology for Researcher Discovery",
"prefix": "VIVO",
"version": "version 1.1"
},
"VIVO-ISF": {
"description": "The Integrated Semantic Framework ontology modules for VIVO (the VIVO-ISF ontology) provide a set of types (classes) and relationships (properties) to represent researchers and the full context in which they work.",
"download_owl": "http://aber-owl.net/media/ontologies/VIVO-ISF/1/vivo-isf.owl",
"homepage": "vivoweb.org",
"name": "VIVO-Integrated Semantic Framework",
"prefix": "VIVO-ISF",
"version": "1.6"
},
"VO": {
"description": "VO is a biomedical ontology in the domain of vaccine and vaccination.",
"download_owl": "http://aber-owl.net/media/ontologies/VO/302/vo.owl",
"homepage": "https://violinet.org/vaccineontology",
"name": "Vaccine Ontology",
"prefix": "VO"
},
"VODANA-GENERAL": {
"description": "VODANA's General list of terms that are used within Outpatient Department Registration and Antenatal Care Templates.",
"name": "VODANATERMS",
"prefix": "VODANA-GENERAL",
"version": "8"
},
"VODANA-METRICS": {
"description": "These are specific metrics of VODANA project",
"name": "SPECIFICMETRICS",
"prefix": "VODANA-METRICS",
"version": "5"
},
"VODANA-MI": {
"description": "Migrants Interviews Ontologies",
"name": "VODANA-MIGRANTS-INTERVIEWS",
"prefix": "VODANA-MI",
"version": "2.0"
},
"VODANA-MIGRANTS": {
"description": "migrants ontologies",
"name": "VODANA MIGRANTS VOCABULARY",
"prefix": "VODANA-MIGRANTS",
"version": "1"
},
"VODANA-MNV": {
"description": "These are vocabularies created for migrant data",
"name": "VODANA-MIGRANTS-NEWS-VOCABULARY",
"prefix": "VODANA-MNV",
"version": "5.0"
},
"VODANA-MPA": {
"description": "migrants Press Articles ontologies",
"name": "VODANA-MIGRANTS-PRESS ARTICLES",
"prefix": "VODANA-MPA",
"version": "2"
},
"VODANA-TERMS": {
"description": "This is the HEIGHT/LENGTH FOR AGE Z-SCORE term.",
"name": "HEIGHT/LENGTH FOR AGE Z-SCORE",
"prefix": "VODANA-TERMS",
"version": "1"
},
"VODANA-UG": {
"name": "VODANA-Uganda",
"prefix": "VODANA-UG"
},
"VODANA-UG-OPD": {
"description": "This is an ontology on the data collected using an Out Patient Register within at the hospitals and facilities in Uganda.",
"download_owl": "http://aber-owl.net/media/ontologies/VODANA-UG-OPD/1/vodana-ug-opd.owl",
"name": "VODANA-UGANDA-OPD",
"prefix": "VODANA-UG-OPD"
},
"VODANACOVID": {
"description": "Ontology containing the controlled terms and semantic properties used in the COVID-19 generic template used within different facilities in VODANA",
"name": "VODANA-COVIDTERMS",
"prefix": "VODANACOVID",
"version": "3.0"
},
"VODANADISEASES": {
"description": "Vodana disease terms based on WHO's ICD-11 standards intended for coding health information for FAIR implementation countries in Africa",
"name": "VODANADiseases",
"prefix": "VODANADISEASES",
"version": "2.0.1"
},
"VODANAKENYA": {
"description": "Ontology containing the controlled terms and semantic properties used in the Ontology for Out-patient Claim Form NHIS",
"name": "VODANA KENYA",
"prefix": "VODANAKENYA",
"version": "0.1.1"
},
"VODANAMFLCODE": {
"description": "This is the list of VODANA health facilities with VODANA MFL Code.",
"name": "VODANAFACILITIESLIST",
"prefix": "VODANAMFLCODE",
"version": "4.0"
},
"VODANANIGERIA": {
"description": "This ontology contains controlled terms and properties of the out patient register claim report used to collect out patient information within different facilities in Nigeria.",
"name": "VODANANIGERIA",
"prefix": "VODANANIGERIA",
"version": "2.0"
},
"VODANAUGANDA": {
"description": "This is an ontology comprising of controlled vocabulary terms and properties about the data collected using the Out Patient Register 002 in different health facilities in Uganda.",
"name": "VODANAUGANDA",
"prefix": "VODANAUGANDA",
"version": "2.0"
},
"VODANA_UG": {
"description": "This is an ontology comprising of terms and controlled vocabulary about the data collected using the Out Patient Register 002 and other registars in different facilities in Uganda.",
"download_owl": "http://aber-owl.net/media/ontologies/VODANA_UG/1/vodana_ug.owl",
"name": "VODANA_UG",
"prefix": "VODANA_UG",
"version": "1.0"
},
"VODANETHIOPIA_OR": {
"name": "ETHIOPIA_OUTPATIENT",
"prefix": "VODANETHIOPIA_OR"
},
"VODAN_ANC": {
"description": "This is a general comment that will be ignored. The converter will detect automatically the line containing the column titles below, so you can have a header as long as you want.",
"homepage": "https://vodan-totafrica.info/ANC",
"name": "VODAN ANC Vocabulary ",
"prefix": "VODAN_ANC",
"version": "VI"
},
"VPS": {
"name": "vps windows",
"prefix": "VPS"
},
"VRD": {
"description": "This is test",
"download_owl": "http://aber-owl.net/media/ontologies/VRD/1/vrd.owl",
"name": "Vaccineresearchdata",
"prefix": "VRD",
"version": "2.0"
},
"VSAO": {
"description": "VSAO is an anatomy ontology covering the vertebrate skeletal system. VSAO integrates terms for skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system.",
"download_obo": "http://aber-owl.net/media/ontologies/VSAO/20/vsao.obo",
"homepage": "http://phenoscape.org/wiki/Main_Page",
"name": "Vertebrate Skeletal Anatomy Ontology",
"prefix": "VSAO",
"version": "2012-11-06"
},
"VSO": {
"description": "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.",
"download_owl": "http://aber-owl.net/media/ontologies/VSO/1/vso.owl",
"homepage": "http://code.google.com/p/vital-sign-ontology/",
"name": "Vital Sign Ontology",
"prefix": "VSO",
"version": "2012-04-25"
},
"VT": {
"description": "An ontology of traits covering vertebrates",
"download_owl": "http://aber-owl.net/media/ontologies/VT/109/vt.owl",
"homepage": "https://github.com/AnimalGenome/vertebrate-trait-ontology",
"name": "Vertebrate trait ontology",
"prefix": "VT"
},
"VTO": {
"description": "Comprehensive hierarchy of extinct and extant vertebrate taxa.",
"download_owl": "http://aber-owl.net/media/ontologies/VTO/15/vto.owl",
"homepage": "https://github.com/phenoscape/vertebrate-taxonomy-ontology",
"name": "Vertebrate Taxonomy Ontology",
"prefix": "VTO"
},
"VVMM": {
"description": "MAATrica is a novel metric for assessing the coherence of methodologies in research papers within the fields of medicinal and nutraceutical chemistry. MAATrica employs user-controlled and customizable ontologies (in silico, in vitro and in vivo), enabling personalized analysis of research papers in the fields of medicinal and nutraceutical chemistry. Here we present the in vivo ontology we developed for the scope.",
"download_obo": "http://aber-owl.net/media/ontologies/VVMM/1/vvmm.obo",
"name": "In Vivo Methodologies Ontology for MAATrica metric",
"prefix": "VVMM"
},
"WB-BT": {
"description": "A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.",
"download_obo": "http://aber-owl.net/media/ontologies/WB-BT/116/wb-bt.obo",
"homepage": "http://www.wormbase.org/",
"name": "C. elegans Gross Anatomy Vocabulary",
"prefix": "WB-BT",
"version": "2016-06-01"
},
"WB-LS": {
"description": "A structured controlled vocabulary of the development of Caenorhabditis elegans.",
"download_obo": "http://aber-owl.net/media/ontologies/WB-LS/49/wb-ls.obo",
"homepage": "http://www.wormbase.org/",
"name": "C. elegans Development Vocabulary",
"prefix": "WB-LS",
"version": "unknown"
},
"WB-PHENOTYPE": {
"description": "A structured controlled vocabulary of Caenorhabditis elegans phenotypes",
"download_obo": "http://aber-owl.net/media/ontologies/WB-PHENOTYPE/267/wb-phenotype.obo",
"homepage": "http://www.wormbase.org/",
"name": "C. elegans Phenotype Vocabulary",
"prefix": "WB-PHENOTYPE",
"version": "releases/2017-11-22"
},
"WBBT": {
"description": "A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.",
"download_owl": "http://aber-owl.net/media/ontologies/WBBT/28/wbbt.owl",
"homepage": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology",
"name": "C. elegans Gross Anatomy Ontology",
"prefix": "WBBT"
},
"WBLS": {
"description": "A structured controlled vocabulary of the development of Caenorhabditis elegans.",
"download_owl": "http://aber-owl.net/media/ontologies/WBLS/33/wbls.owl",
"homepage": "https://github.com/obophenotype/c-elegans-development-ontology",
"name": "C. elegans development ontology",
"prefix": "WBLS"
},
"WBPHENOTYPE": {
"description": "A structured controlled vocabulary of Caenorhabditis elegans phenotypes",
"download_owl": "http://aber-owl.net/media/ontologies/WBPHENOTYPE/80/wbphenotype.owl",
"homepage": "https://github.com/obophenotype/c-elegans-phenotype-ontology",
"name": "C. elegans phenotype",
"prefix": "WBPHENOTYPE"
},
"WC": {
"description": "Ontology for whole-cell (WC) modeling See https://wholecell.org for more information about WC modeling",
"download_obo": "http://aber-owl.net/media/ontologies/WC/13/wc.obo",
"homepage": "https://github.com/karrlab/wc_onto",
"name": "Whole-cell modeling ontology",
"prefix": "WC",
"version": "0.0.1"
},
"WCM": {
"description": "Ontology for whole-cell (WC) modeling See https://wholecell.org for more information about WC modeling",
"download_obo": "http://aber-owl.net/media/ontologies/WCM/4/wcm.obo",
"name": "Whole-cell modeling ontology",
"prefix": "WCM",
"version": "0.0.1"
},
"WEAR": {
"description": "Controlled vocabularies such as taxonomies allow an accurate and controlled approach in describing datasets. One of such controlled vocabulary is Wind Energy Taxonomy of Activities. This taxonomy is the result of EERA JP WIND IRPWind Open Data initiative that took place in 2017 in which wind energy experts generated the first version of the taxonomy as an input for defining and structuring wind energy metadata. The report of this work is available at Zenodo: https://www.zenodo.org/record/1199489#.XSD6haeQ3RY In 2018, the taxonomy of topics was improved during the internal project of DTU Wind Energy titled 'FAIR Digitalization': https://www.zenodo.org/record/1493874#.XSD7TaeQ3RY In 2021, the taxonomy was converted into FAIR machine-actionable controlled vocabulary using sheet2rdf. The controlled vocabulary is served to humans and machines using an instace of OntoStack hosted by DTU Wind Energy. sheet2rdf and OntoStack are developed by FAIR Data Collective. Additionally, in 2021, the persistent URL purl.org/wear has been registered for the taxonomy. This allows us to: If there is a needed to move the taxonomy to another domain (currently under data.windenergy.dtu.dk) URLs will be still resolvable and unchanged Use short URls as PIDs for the taxonomy terms and properties.",
"homepage": "https://github.com/DTUWindEnergy/WEAR-taxonomy",
"name": "WEAR: Wind Energy mAteRials Taxonomy",
"prefix": "WEAR",
"version": "v0.1.0"
},
"WEAVE": {
"description": "Controlled vocabularies such as taxonomies allow an accurate and controlled approach in describing datasets. One of such controlled vocabulary is Wind Energy Taxonomy of Activities. This taxonomy is the result of EERA JP WIND IRPWind Open Data initiative that took place in 2017 in which wind energy experts generated the first version of the taxonomy as an input for defining and structuring wind energy metadata. The report of this work is available at Zenodo: https://www.zenodo.org/record/1199489#.XSD6haeQ3RY In 2018, the taxonomy of topics was improved during the internal project of DTU Wind Energy titled 'FAIR Digitalization': https://www.zenodo.org/record/1493874#.XSD7TaeQ3RY In 2021, the taxonomy was converted into FAIR machine-actionable controlled vocabulary using sheet2rdf. The controlled vocabulary is served to humans and machines using an instace of OntoStack hosted by DTU Wind Energy. sheet2rdf and OntoStack are developed by FAIR Data Collective. Additionally, in 2021, the persistent URL purl.org/weave has been registered for the taxonomy. This allows us to: If there is a needed to move the taxonomy to another domain (currently under data.windenergy.dtu.dk) URLs will be still resolvable and unchanged Use short URls as PIDs for the taxonomy terms and properties such as: purl.org/weave/Measurements",
"homepage": "https://github.com/DTUWindEnergy/WEAVE-taxonomy#weave-wind-energy-activities",
"name": "WEAVE: Wind Energy ActiVitiEs",
"prefix": "WEAVE",
"version": "v0.1.0"
},
"WEDDING": {
"name": "Naadia",
"prefix": "WEDDING"
},
"WETAXTOPICS": {
"description": "Controlled vocabularies such as taxonomies allow an accurate and controlled approach in describing datasets. One of such controlled vocabulary is Wind Energy Taxonomy of Topics. This taxonomy is the result of EERA JP WIND IRPWind Open Data initiative that took place in 2017 in which wind energy experts generated the first version of the taxonomy as an input for defining and structuring wind energy metadata. The report of this work is available at Zenodo: https://www.zenodo.org/record/1199489#.XSD6haeQ3RY In 2018, the taxonomy of topics was improved during the internal project of DTU Wind Energy titled 'FAIR Digitalization': https://www.zenodo.org/record/1493874#.XSD7TaeQ3RY In 2020, the definition of taxonomy terms were added and the taxonomy was converted into FAIR machine-actionable controlled vocabulary using sheet2rdf. The controlled vocabulary is served to humans and machines using an instace of OntoStack hosted by DTU Wind Energy.",
"homepage": "http://purl.org/neat/",
"name": "NEAT: wiNd Energy tAxonomy of Topics",
"prefix": "WETAXTOPICS",
"version": "v0.1.1"
},
"WHEAT": {
"name": "walgreens wheat ridge co",
"prefix": "WHEAT"
},
"WHO-ART": {
"description": "WHO Adverse Reaction Terminology, 1997",
"homepage": "http://www.who.int/",
"name": "World Health Organization (WHO) Adverse Reaction Terminology",
"prefix": "WHO-ART",
"version": "2016AB"
},
"WHOFRE": {
"description": "WHOART, French Translation",
"homepage": "http://www.who.int/",
"name": "WHOART, French Translation",
"prefix": "WHOFRE",
"version": "2016AB"
},
"WIKIPATHWAYS": {
"description": "The WP ontology for WikiPathways.",
"download_owl": "http://aber-owl.net/media/ontologies/WIKIPATHWAYS/225/wikipathways.owl",
"homepage": "http://www.wikipathways.org/",
"name": "WikiPathways",
"prefix": "WIKIPATHWAYS"
},
"WISATAJOGJA29": {
"name": "Paket Wisata Jogja 6",
"prefix": "WISATAJOGJA29"
},
"WISATAJOGJA52": {
"name": "Paket Wisata Jogja 5",
"prefix": "WISATAJOGJA52"
},
"WISATA_JOGJA23": {
"name": "Paket Wisata Jogja Murah",
"prefix": "WISATA_JOGJA23"
},
"WISATA_JOGJA78": {
"name": "Paket Wisata Jogja",
"prefix": "WISATA_JOGJA78"
},
"WSIO": {
"description": "Web Service Interaction Ontology (WSIO) enables automated interaction with more complex Web services that are typical for example within life sciences. WSIO is however independent of the application domain and relevant for both SOAP and REST Web services, and for batch execution engines in general. If the interaction scenario with a Web service is nontrivial (and incorporates session handling), annotation with WSIO concepts will enable automatic generation of client programs, scripts, or interactive applications with a graphical user interface. WSIO also enables automation of different ways of data transfer and data un-/compression or en-/decoding. We strongly discourage providers from developing complex interaction and data-transfer/compression scenarios, however when needed, WSIO may enable smooth automated interaction with them. Future versions will support more interaction scenarios. WSIO aims to serve also as a means to standardise the complex interaction scenarios primarily within both SOAP and REST Web services, and secondarily to apply also to batch execution infrastructure in general.",
"download_obo": "http://aber-owl.net/media/ontologies/WSIO/4/wsio.obo",
"homepage": "http://wsio.org",
"name": "Web-Service Interaction Ontology",
"prefix": "WSIO",
"version": "beta2"
},
"WWECA": {
"description": "This is an ontology for the management of women of child-bearing age with epilepsy.",
"download_owl": "http://aber-owl.net/media/ontologies/WWECA/4/wweca.owl",
"name": "Women with Epilepsy of Child-bearing Age Ontology",
"prefix": "WWECA",
"version": "3.0"
},
"XAO": {
"description": "XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis.",
"download_owl": "http://aber-owl.net/media/ontologies/XAO/33/xao.owl",
"homepage": "http://www.xenbase.org/anatomy/xao.do?method=display",
"name": "Xenopus Anatomy Ontology",
"prefix": "XAO"
},
"XCO": {
"description": "Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.",
"download_owl": "http://aber-owl.net/media/ontologies/XCO/114/xco.owl",
"homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000",
"name": "Experimental condition ontology",
"prefix": "XCO"
},
"XEO": {
"description": "XeO has been created to help plant scientists in documenting and sharing metadata describing the abiotic environment.",
"download_obo": "http://aber-owl.net/media/ontologies/XEO/4/xeo.obo",
"homepage": "http://xeo.codeplex.com/",
"name": "XEML Environment Ontology",
"prefix": "XEO",
"version": "1.6"
},
"XL": {
"name": "Cross-linker reagents ontology",
"prefix": "XL"
},
"XLMOD": {
"description": "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.",
"download_owl": "http://aber-owl.net/media/ontologies/XLMOD/2/xlmod.owl",
"homepage": "http://www.psidev.info/groups/controlled-vocabularies",
"name": "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary",
"prefix": "XLMOD"
},
"XPO": {
"description": "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis.",
"download_owl": "http://aber-owl.net/media/ontologies/XPO/16/xpo.owl",
"homepage": "https://github.com/obophenotype/xenopus-phenotype-ontology",
"name": "Xenopus Phenotype Ontology",
"prefix": "XPO"
},
"XREF-FUNDER-REG": {
"description": "The Funder Registry provides a common taxonomy of international funding body names that funding data participants should use to normalize funder names and IDs for deposit with Crossref. The list can be used to present authors with a pre-populated \"Funder Name\" option at the time of submission, and can also be used to match funder names extracted from papers. The list is available to download as an RDF file, and is freely available under a CC0 license waiver. This information was obtained from a GitLab repository created by Bryan Vickery (see Homepage). The first version downloaded was 1.34.",
"homepage": "https://gitlab.com/crossref/open_funder_registry",
"name": "CrossRef Funder Registry",
"prefix": "XREF-FUNDER-REG"
},
"ZAHRAHADDAD": {
"name": "\u0627\u0631\u062a\u0628\u0627\u0637\u0627\u062a",
"prefix": "ZAHRAHADDAD"
},
"ZEA": {
"download_obo": "http://aber-owl.net/media/ontologies/ZEA/2/zea.obo",
"homepage": "http://www.maizemap.org/",
"name": "Maize Gross Anatomy Ontology",
"prefix": "ZEA",
"version": "1.2"
},
"ZECO": {
"description": "Experimental conditions applied to zebrafish, developed to facilitate experiment condition annotation at ZFIN",
"download_owl": "http://aber-owl.net/media/ontologies/ZECO/10/zeco.owl",
"homepage": "https://github.com/ybradford/zebrafish-experimental-conditions-ontology",
"name": "Zebrafish Experimental Conditions Ontology",
"prefix": "ZECO"
},
"ZFA": {
"description": "A structured controlled vocabulary of the anatomy and development of the Zebrafish",
"download_owl": "http://aber-owl.net/media/ontologies/ZFA/87/zfa.owl",
"homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources",
"name": "Zebrafish anatomy and development ontology",
"prefix": "ZFA"
},
"ZFS": {
"description": "Developmental stages of the Zebrafish",
"download_owl": "http://aber-owl.net/media/ontologies/ZFS/9/zfs.owl",
"homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources",
"name": "Zebrafish developmental stages ontology",
"prefix": "ZFS"
},
"ZONMW-ADMIN-MD": {
"description": "Collections of terms for the ZonMW COVID Training project. These terms are based on vocabularies provided for describing project-level metadata. This submission was created using SKOS Play from an Excel spreadsheet.",
"homepage": "https://github.com/fair-data-collective/zonmw-project-admin/tree/main/ontology",
"name": "ZonMW Administrative Metadata Vocabulary",
"prefix": "ZONMW-ADMIN-MD",
"version": "1.2.0a"
},
"ZONMW-CONTENT": {
"description": "Collections of terms for the ZonMW COVID19 programme. These terms are based on vocabularies provided for describing project and data content metadata. This submission was created using sheet2rdf GitHub workflow.",
"homepage": "https://github.com/fair-data-collective/zonmw-covid19-vocabulary",
"name": "ZonMW COVID-19",
"prefix": "ZONMW-CONTENT",
"version": "2.4.0"
},
"ZONMW-GENERIC": {
"description": "General-purpose terms for the ZonMw",
"homepage": "https://raw.githubusercontent.com/fair-data-collective/zonmw-generic-vocabulary/",
"name": "ZonMw Generic Terms",
"prefix": "ZONMW-GENERIC",
"version": "1.5.0"
},
"ZP": {
"description": "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.",
"download_owl": "http://aber-owl.net/media/ontologies/ZP/10/zp.owl",
"homepage": "https://github.com/obophenotype/zebrafish-phenotype-ontology",
"name": "Zebrafish Phenotype Ontology",
"prefix": "ZP"
},
"a": {
"name": "z",
"prefix": "a"
},
"alperk": {
"name": "Alper K.",
"prefix": "alperk"
},
"arp": {
"download_owl": "http://aber-owl.net/media/ontologies/arp/1/arp.owl",
"homepage": "http://www.arpenteur.org/",
"name": "Arpenteur",
"prefix": "arp",
"version": "09-12-2019"
},
"bibliographic": {
"description": "This file is imported by vivo-core-public-1.5.owl This file contains selected terms from the bibliographic ontology (see http://bibliontology.com/) which relate to information resources.",
"download_owl": "http://aber-owl.net/media/ontologies/bibliographic/1/bibliographic.owl",
"homepage": "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology",
"name": "Bibliographic",
"prefix": "bibliographic",
"version": "1.5"
},
"bioscience": {
"name": "123",
"prefix": "bioscience"
},
"building": {
"download_owl": "http://aber-owl.net/media/ontologies/building/1/building.owl",
"name": "Building and Sub Elements",
"prefix": "building",
"version": "1.0"
},
"cd": {
"name": "ashuu",
"prefix": "cd"
},
"citation": {
"description": "This file is imported by vivo-core-public-1.5.owl This file contains terms that relate to citation counts from the Citation Counting and Context Characterization ontology of the Semantic Publishing and Referencing ontology suite (http://sempublishing.svn.sourceforge.net/viewvc/sempublishing/SPAR/index.html)",
"download_owl": "http://aber-owl.net/media/ontologies/citation/1/citation.owl",
"homepage": "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology",
"name": "Citation Counting",
"prefix": "citation",
"version": "1.5"
},
"cmt": {
"description": "OAEI Conference 2019",
"download_owl": "http://aber-owl.net/media/ontologies/cmt/1/cmt.owl",
"homepage": "https://gite.lirmm.fr/opendata/yampp-online/raw/4606498a7c3aa8f3704898a4cc3f513c7a79ba2f/cmt.owl",
"name": "cmt",
"prefix": "cmt",
"version": "1.0"
},
"cyber": {
"description": "teste",
"download_owl": "http://aber-owl.net/media/ontologies/cyber/1/cyber.owl",
"name": "stix",
"prefix": "cyber",
"version": "1"
},
"dcelements": {
"description": "This file is imported by vivo-core-public-1.5.owl. It contains selected terms from the \thttp://purl.org/dc/elements/1.1/ namespace that are included in the vivo core ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/dcelements/1/dcelements.owl",
"homepage": "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology",
"name": "dcelements",
"prefix": "dcelements",
"version": "1.5"
},
"dcterms": {
"description": "This file is imported by vivo-core-public-1.5.owl. It contains terms from the http://purl.org/dc/terms/ namespace that are included in the vivo ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/dcterms/1/dcterms.owl",
"homepage": "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology",
"name": "dcterms",
"prefix": "dcterms",
"version": "1.5"
},
"dlgkj": {
"name": "fdkgj",
"prefix": "dlgkj"
},
"envo_153": {
"description": "envo_153",
"download_obo": "http://aber-owl.net/media/ontologies/envo_153/1/envo_153.obo",
"name": "envo_153",
"prefix": "envo_153",
"version": "1.53"
},
"event": {
"description": "This file is imported by vivo-core-public-1.5.owl. This file contains terms from the http://purl.org/NET/c4dm/event.owl# namespace that are included in the vivo ontology",
"download_owl": "http://aber-owl.net/media/ontologies/event/1/event.owl",
"homepage": "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#shortDef",
"name": "Event",
"prefix": "event",
"version": "1.5"
},
"foaf": {
"description": "This file is imported by vivo-core-public-1.5.owl. It contains terms relating to people, groups and organizations from the http://xmlns.com/foaf/0.1/ namespace that are included in the vivo ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/foaf/1/foaf.owl",
"homepage": "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology",
"name": "FOAF (people, organizations, groups)",
"prefix": "foaf",
"version": "1.5"
},
"geopolitical": {
"description": "This file is imported by vivo-core-public-1.5.owl This is the geopolitical ontology from the Food and Agriculture Organization of the United Nations",
"download_owl": "http://aber-owl.net/media/ontologies/geopolitical/1/geopolitical.owl",
"homepage": "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology",
"name": "Geopolitical",
"prefix": "geopolitical",
"version": "version 1.1"
},
"goslim_candida": {
"description": "Developed by Candida Genome Database ().",
"download_obo": "http://aber-owl.net/media/ontologies/goslim_candida/1/goslim_candida.obo",
"name": "Candida albicans slim",
"prefix": "goslim_candida",
"version": "1.6 (CVS revision)"
},
"goslim_goa": {
"description": "Developed by N. Mulder, M. Pruess",
"download_obo": "http://aber-owl.net/media/ontologies/goslim_goa/1/goslim_goa.obo",
"name": "GOA and whole proteome analysis",
"prefix": "goslim_goa",
"version": "1.761 (CVS version)"
},
"goslim_pir": {
"description": "Developed by Darren Natale of PIR",
"download_obo": "http://aber-owl.net/media/ontologies/goslim_pir/1/goslim_pir.obo",
"name": "Protein Information Resource slim",
"prefix": "goslim_pir",
"version": "1.6 (CVS version)"
},
"goslim_plant": {
"description": "Developed by The Arabidopsis Information Resource (http://www.arabidopsis.org/).",
"download_obo": "http://aber-owl.net/media/ontologies/goslim_plant/1/goslim_plant.obo",
"name": "Plant slim",
"prefix": "goslim_plant",
"version": "1.738 (CVS version)"
},
"goslim_pombe": {
"description": "Developed by Val Wood.",
"download_obo": "http://aber-owl.net/media/ontologies/goslim_pombe/1/goslim_pombe.obo",
"name": "Schizosaccharomyces pombe slim",
"prefix": "goslim_pombe",
"version": "1.6 (CVS version)"
},
"goslim_yeast": {
"description": "Developed by Saccharomyces Genome Database",
"download_obo": "http://aber-owl.net/media/ontologies/goslim_yeast/1/goslim_yeast.obo",
"name": "Yeast slim",
"prefix": "goslim_yeast",
"version": "1.729 (CVS version)"
},
"gr": {
"download_owl": "http://aber-owl.net/media/ontologies/gr/1/gr.owl",
"name": "gr_ontology",
"prefix": "gr",
"version": "juhiygh"
},
"hi": {
"name": "pizza",
"prefix": "hi"
},
"iceci-activity": {
"description": "ICECI ACTIVITY WHEN INJURED(C.5)",
"download_owl": "http://aber-owl.net/media/ontologies/iceci-activity/2/iceci-activity.owl",
"name": "iceci-activity",
"prefix": "iceci-activity",
"version": "1.02"
},
"iceci-countermeasures": {
"description": "ICECI PERSONAL COUNTERMEASURES(S.3) and ENVIRONMENTAL COUNTERMEASURES(S.4)",
"download_owl": "http://aber-owl.net/media/ontologies/iceci-countermeasures/2/iceci-countermeasures.owl",
"name": "iceci-countermeasures",
"prefix": "iceci-countermeasures",
"version": "1.02"
},
"iceci-descriptor_for_intent": {
"description": "ICECI Descriptors for Intent V.1 - V.7",
"download_owl": "http://aber-owl.net/media/ontologies/iceci-descriptor_for_intent/3/iceci-descriptor_for_intent.owl",
"name": "iceci-descriptor_for_intent",
"prefix": "iceci-descriptor_for_intent",
"version": "1.02"
},
"iceci-details_for_activity": {
"description": "ICICI Details for activity O1-O2 and S1-S2",
"download_owl": "http://aber-owl.net/media/ontologies/iceci-details_for_activity/3/iceci-details_for_activity.owl",
"name": "iceci-details_for_activity",
"prefix": "iceci-details_for_activity",
"version": "1.02"
},
"iceci-details_for_mechanism": {
"description": "ICECI Details for Mechanism T1 - T4",
"download_owl": "http://aber-owl.net/media/ontologies/iceci-details_for_mechanism/2/iceci-details_for_mechanism.owl",
"name": "iceci-details_for_mechanism",
"prefix": "iceci-details_for_mechanism",
"version": "1.02"
},
"iceci-details_for_place_of_occurrence": {
"description": "ICECI Details for place of occurrence P1-P7",
"download_owl": "http://aber-owl.net/media/ontologies/iceci-details_for_place_of_occurrence/2/iceci-details_for_place_of_occurrence.owl",
"name": "iceci-details_for_place_of_occurrence",
"prefix": "iceci-details_for_place_of_occurrence",
"version": "1.02"
},
"iceci-instrument_object_substance": {
"description": "ICECI Object/substance producing injury C3",
"download_owl": "http://aber-owl.net/media/ontologies/iceci-instrument_object_substance/2/iceci-instrument_object_substance.owl",
"name": "iceci-instrument_object_substance",
"prefix": "iceci-instrument_object_substance",
"version": "1.02"
},
"iceci-intent": {
"description": "ICECI Intent C1",
"download_owl": "http://aber-owl.net/media/ontologies/iceci-intent/2/iceci-intent.owl",
"name": "iceci-intent",
"prefix": "iceci-intent",
"version": "1.02"
},
"iceci-mechanism": {
"description": "ICECI Mechanism of injury-full version C2",
"download_owl": "http://aber-owl.net/media/ontologies/iceci-mechanism/2/iceci-mechanism.owl",
"name": "iceci-mechanism",
"prefix": "iceci-mechanism",
"version": "1.02"
},
"iceci-place_of_occurrence": {
"description": "ICECI Place of occurrence C4",
"download_owl": "http://aber-owl.net/media/ontologies/iceci-place_of_occurrence/2/iceci-place_of_occurrence.owl",
"name": "iceci-place_of_occurrence",
"prefix": "iceci-place_of_occurrence",
"version": "1.02"
},
"iceci-substance_use": {
"description": "ICECI Substance use\t C6 and C7",
"download_owl": "http://aber-owl.net/media/ontologies/iceci-substance_use/2/iceci-substance_use.owl",
"name": "iceci-substance_use",
"prefix": "iceci-substance_use",
"version": "1.02"
},
"mph(A)": {
"name": "ISRA GHORI",
"prefix": "mph(A)"
},
"obi-device": {
"description": "Subset of OBI that contains the term obi:device and all children terms.",
"download_owl": "http://aber-owl.net/media/ontologies/obi-device/1/obi-device.owl",
"name": "OBI Device branch",
"prefix": "obi-device",
"version": "1"
},
"obi-fged": {
"description": "Subset of OBI terms of interest to the Functional Genomics Data (FGED) Society",
"download_owl": "http://aber-owl.net/media/ontologies/obi-fged/11/obi-fged.owl",
"name": "FGED View",
"prefix": "obi-fged",
"version": "2013-10-25"
},
"ooevv-tractTrace": {
"description": "This serves as an instantiation of the OoEVV ontology design pattern for variables derived from models of neuroanatomical tract-tracing experiments described in detail in Russ et al. 2011 (http://www.biomedcentral.com/1471-2105/12/351). This serves as a well-developed example system for development of the KEfED formulation.",
"download_owl": "http://aber-owl.net/media/ontologies/ooevv-tractTrace/1/ooevv-tracttrace.owl",
"homepage": "http://bmkeg.isi.edu",
"name": "OoEVV tract tracing experiments ",
"prefix": "ooevv-tractTrace",
"version": "unknown"
},
"ooevv-vaccine": {
"description": "This serves as an instantiation of the OoEVV ontology design pattern for variables derived from vaccine protection studies that have been previously indexed in the Los Alamos National Laboratories (LANL) HIV Vaccine Trials Database. This is a comprehensive index of research outcomes derived from vaccine studies in nonhuman primates and provides an excellent index of papers for examination with our approach.",
"download_owl": "http://aber-owl.net/media/ontologies/ooevv-vaccine/1/ooevv-vaccine.owl",
"homepage": "http://bmkeg.isi.edu",
"name": "OoEVV vaccine protection experiments ",
"prefix": "ooevv-vaccine",
"version": "0.0.4"
},
"ordo": {
"download_owl": "http://aber-owl.net/media/ontologies/ordo/1/ordo.owl",
"homepage": "https://www.ebi.ac.uk/ols/ontologies/ordo",
"name": "Orphanet Rare Disease Ontology",
"prefix": "ordo",
"version": "2.7"
},
"provenance": {
"description": "This file is imported by vivo-core-public-1.5.owl. It contains terms related to people for the purpose of accumulating information about persons who are not fully identified.",
"download_owl": "http://aber-owl.net/media/ontologies/provenance/1/provenance.owl",
"homepage": "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology",
"name": "Provenance",
"prefix": "provenance",
"version": "1.5"
},
"pseudo": {
"download_obo": "http://aber-owl.net/media/ontologies/pseudo/1/pseudo.obo",
"name": "Pseudogene",
"prefix": "pseudo",
"version": "0.1"
},
"rare_deneme": {
"download_owl": "http://aber-owl.net/media/ontologies/rare_deneme/1/rare_deneme.owl",
"name": "Alper K.",
"prefix": "rare_deneme",
"version": "1.0"
},
"skos": {
"description": "This file is imported by vivo-core-1.5.owl. It contains terms relating to concepts from the http://www.w3.org/2004/02/skos/core# namespace of the SKOS (Simple Knowledge Organization System) ontology that are included in the vivo ontology.",
"download_owl": "http://aber-owl.net/media/ontologies/skos/1/skos.owl",
"homepage": "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology",
"name": "SKOS (concepts)",
"prefix": "skos",
"version": "1.5"
},
"suicideo": {
"description": "ontology for suicidology",
"download_owl": "http://aber-owl.net/media/ontologies/suicideo/1/suicideo.owl",
"name": "suicideonto",
"prefix": "suicideo",
"version": "2"
},
"svuOnt": {
"download_owl": "http://aber-owl.net/media/ontologies/svuOnt/1/svuont.owl",
"name": "svuOntology",
"prefix": "svuOnt",
"version": "3"
},
"tfernandes": {
"name": "Thiago",
"prefix": "tfernandes"
},
"usecase": {
"download_owl": "http://aber-owl.net/media/ontologies/usecase/2/usecase.owl",
"name": "usecase",
"prefix": "usecase",
"version": "Version2"
},
"vfdsad": {
"name": "sdf",
"prefix": "vfdsad"
},
"zinnane": {
"name": "fatima",
"prefix": "zinnane"
}
} ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/align.py 0000644 0001751 0000177 00000004034 14655542206 022254 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Workflows for aligning external registries."""
from class_resolver import ClassResolver
from .aberowl import AberOWLAligner
from .alignment_utils import Aligner
from .bartoc import BartocAligner
from .biocontext import BioContextAligner
from .biolink import BiolinkAligner
from .bioportal.bioportal import (
AgroPortalAligner,
BioPortalAligner,
EcoPortalAligner,
OntoPortalAligner,
)
from .cellosaurus import CellosaurusAligner
from .cheminf import ChemInfAligner
from .cropoct import CropOCTAligner
from .edam import EDAMAligner
from .fairsharing import FairsharingAligner
from .go import GoAligner
from .hl7 import HL7Aligner
from .integbio import IntegbioAligner
from .lov import LOVAligner
from .miriam import MiriamAligner
from .n2t import N2TAligner
from .ncbi import NcbiAligner
from .obofoundry import OBOFoundryAligner
from .ols import OLSAligner
from .ontobee import OntobeeAligner
from .pathguide import PathguideAligner
from .prefixcommons import PrefixCommonsAligner
from .re3data import Re3dataAligner
from .rrid import RRIDAligner
from .togoid import TogoIDAligner
from .uniprot import UniProtAligner
from .wikidata import WikidataAligner
from .zazuko import ZazukoAligner
__all__ = [
# Abstract
"Aligner",
"aligner_resolver",
# Concrete
"AberOWLAligner",
"BartocAligner",
"BioContextAligner",
"BiolinkAligner",
"BioPortalAligner",
"CropOCTAligner",
"EcoPortalAligner",
"AgroPortalAligner",
"CellosaurusAligner",
"ChemInfAligner",
"FairsharingAligner",
"GoAligner",
"MiriamAligner",
"N2TAligner",
"NcbiAligner",
"OBOFoundryAligner",
"OLSAligner",
"OntobeeAligner",
"PrefixCommonsAligner",
"UniProtAligner",
"WikidataAligner",
"EDAMAligner",
"Re3dataAligner",
"HL7Aligner",
"ZazukoAligner",
"LOVAligner",
"IntegbioAligner",
"PathguideAligner",
"RRIDAligner",
"TogoIDAligner",
]
aligner_resolver = ClassResolver.from_subclasses(
base=Aligner,
skip={OntoPortalAligner},
)
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/alignment_utils.py 0000644 0001751 0000177 00000025056 14655542206 024367 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Utilities for registry alignment."""
import csv
from typing import Any, Callable, ClassVar, Dict, Iterable, Mapping, Optional, Sequence
import click
from tabulate import tabulate
from ..constants import METADATA_CURATION_DIRECTORY
from ..resource_manager import Manager
from ..schema import Resource
from ..schema_utils import is_mismatch
from ..utils import norm
__all__ = [
"Aligner",
]
class Aligner:
"""A class for aligning new registries."""
#: The key for the external registry
key: ClassVar[str]
#: Header to put on the curation table, corresponding to ``get_curation_row()``
curation_header: ClassVar[Sequence[str]]
#: The function that gets the external registry as a dictionary from the string identifier to
#: the entries (could be anything, but a dictionary is probably best)
getter: ClassVar[Callable[..., Mapping[str, Any]]]
#: Keyword arguments to pass to the getter function on call
getter_kwargs: ClassVar[Optional[Mapping[str, Any]]] = None
#: Should new entries be included automatically? Only set this true for aligners of
#: very high confidence (e.g., OBO Foundry but not BioPortal)
include_new: ClassVar[bool] = False
#: Set this if there's another part of the data besides the ID that should be matched
alt_key_match: ClassVar[Optional[str]] = None
alt_keys_match: ClassVar[Optional[str]] = None
#: Set to true if you don't want to align to deprecated resources
skip_deprecated: ClassVar[bool] = False
subkey: ClassVar[str] = "prefix"
normalize_invmap: ClassVar[bool] = False
def __init__(self, force_download: Optional[bool] = None):
"""Instantiate the aligner."""
if not hasattr(self.__class__, "key"):
raise TypeError
if not hasattr(self.__class__, "curation_header"):
raise TypeError
self.manager = Manager()
if self.key not in self.manager.metaregistry:
raise TypeError(f"invalid metaprefix for aligner: {self.key}")
kwargs = dict(self.getter_kwargs or {})
kwargs.setdefault("force_download", True)
if force_download is not None:
kwargs["force_download"] = force_download
self.external_registry = self.__class__.getter(**kwargs)
self.skip_external = self.get_skip()
# Get all of the pre-curated mappings from the Bioregistry
self.external_id_to_bioregistry_id = self.manager.get_registry_invmap(
self.key,
normalize=self.normalize_invmap,
)
# Run lexical alignment
self._align()
@property
def internal_registry(self) -> Dict[str, Resource]:
"""Get the internal registry."""
return self.manager.registry
def get_skip(self) -> Mapping[str, str]:
"""Get the mapping prefixes that should be skipped to their reasons (strings)."""
return {}
def _align(self):
"""Align the external registry."""
for external_id, external_entry in sorted(self.external_registry.items()):
if external_id in self.skip_external:
continue
bioregistry_id = self.external_id_to_bioregistry_id.get(external_id)
# There's already a mapping for this external ID to a bioregistry
# entry. Just add all of the latest metadata and move on
if bioregistry_id is not None:
self._align_action(bioregistry_id, external_id, external_entry)
continue
# try to lookup with lexical match
if not self.alt_key_match:
bioregistry_id = self.manager.normalize_prefix(external_id)
else:
alt_match = external_entry.get(self.alt_key_match)
if alt_match:
bioregistry_id = self.manager.normalize_prefix(alt_match)
if bioregistry_id is None and self.alt_keys_match:
for alt_match in external_entry.get(self.alt_keys_match, []):
bioregistry_id = self.manager.normalize_prefix(alt_match)
if bioregistry_id:
break
# A lexical match was possible
if bioregistry_id is not None:
# check this external ID for curated mismatches, and move
# on if one has already been curated
if is_mismatch(bioregistry_id, self.key, external_id):
continue
if self.skip_deprecated and self.manager.is_deprecated(bioregistry_id):
continue
self._align_action(bioregistry_id, external_id, external_entry)
continue
# add the identifier from an external resource if it's been marked as high quality
elif self.include_new:
bioregistry_id = norm(external_id)
if is_mismatch(bioregistry_id, self.key, external_id):
continue
self.internal_registry[bioregistry_id] = Resource(prefix=bioregistry_id)
self._align_action(bioregistry_id, external_id, external_entry)
continue
def _align_action(
self, bioregistry_id: str, external_id: str, external_entry: Dict[str, Any]
) -> None:
if self.internal_registry[bioregistry_id].mappings is None:
self.internal_registry[bioregistry_id].mappings = {}
self.internal_registry[bioregistry_id].mappings[self.key] = external_id # type:ignore
_entry = self.prepare_external(external_id, external_entry)
_entry[self.subkey] = external_id
self.internal_registry[bioregistry_id][self.key] = _entry
self.external_id_to_bioregistry_id[external_id] = bioregistry_id
def prepare_external(self, external_id: str, external_entry: Dict[str, Any]) -> Dict[str, Any]:
"""Prepare a dictionary to be added to the bioregistry for each external registry entry.
The default implementation returns `external_entry` unchanged.
If you need more than that, override this method.
:param external_id: The external registry identifier
:param external_entry: The external registry data
:return: The dictionary to be added to the bioregistry for the aligned entry
"""
return external_entry
def write_registry(self) -> None:
"""Write the internal registry."""
self.manager.write_registry()
@classmethod
def align(
cls,
dry: bool = False,
show: bool = False,
force_download: Optional[bool] = None,
) -> None:
"""Align and output the curation sheet.
:param dry: If true, don't write changes to the registry
:param show: If true, print a curation table
:param force_download: Force re-download of the data
"""
instance = cls(force_download=force_download)
if not dry:
instance.write_registry()
if show:
instance.print_curation_table()
instance.write_curation_table()
@classmethod
def cli(cls):
"""Construct a CLI for the aligner."""
@click.command()
@click.option("--dry", is_flag=True, help="if set, don't write changes to the registry")
@click.option("--show", is_flag=True, help="if set, print a curation table")
@click.option(
"--no-force", is_flag=True, help="if set, do not force re-downloading the data"
)
def _main(dry: bool, show: bool, no_force: bool):
cls.align(dry=dry, show=show, force_download=not no_force)
_main()
def get_curation_row(self, external_id, external_entry) -> Sequence[str]:
"""Get a sequence of items that will be ech row in the curation table.
:param external_id: The external registry identifier
:param external_entry: The external registry data
:return: A sequence of cells to add to the curation table.
:raises TypeError: If an invalid value is encountered
The default implementation of this function iterates over all of the keys
in the class variable :data:`curation_header` and looks inside each record
for those in order.
.. note:: You don't need to pass the external ID. this will automatically be the first element.
""" # noqa:DAR202
rv = []
for k in self.curation_header:
value = external_entry.get(k)
if value is None:
rv.append("")
elif isinstance(value, str):
rv.append(value.strip().replace("\n", " ").replace(" ", " "))
elif isinstance(value, bool):
rv.append("true" if value else "false")
elif isinstance(value, (list, tuple, set)):
rv.append("|".join(sorted(v.strip() for v in value)))
else:
raise TypeError(f"unexpected type in curation header: {value}")
return rv
def _iter_curation_rows(self) -> Iterable[Sequence[str]]:
for external_id, external_entry in sorted(
self.external_registry.items(), key=lambda s: (s[0].casefold(), s[0])
):
if external_id in self.skip_external:
continue
bioregistry_id = self.external_id_to_bioregistry_id.get(external_id)
if bioregistry_id is None:
yield (
external_id,
*self.get_curation_row(external_id, external_entry),
)
def write_curation_table(self) -> None:
"""Write the curation table to a TSV."""
path = METADATA_CURATION_DIRECTORY.joinpath(self.key).with_suffix(".tsv")
rows = list(self._iter_curation_rows())
if not rows:
if path.is_file():
path.unlink()
return
path.parent.mkdir(exist_ok=True, parents=True)
with path.open("w") as file:
writer = csv.writer(file, delimiter="\t", quoting=csv.QUOTE_MINIMAL)
writer.writerow((self.subkey, *self.curation_header))
writer.writerows(rows)
def get_curation_table(self, **kwargs) -> Optional[str]:
"""Get the curation table as a string, built by :mod:`tabulate`."""
kwargs.setdefault("tablefmt", "rst")
headers = (self.subkey, *self.curation_header)
rows = list(self._iter_curation_rows())
if not rows:
return None
return tabulate(
rows,
headers=headers,
**kwargs,
)
def print_curation_table(self, **kwargs) -> None:
"""Print the curation table."""
s = self.get_curation_table(**kwargs)
if s:
print(s) # noqa:T201
././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9499667
bioregistry-0.11.12/src/bioregistry/external/bartoc/ 0000755 0001751 0000177 00000000000 14655546227 022070 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/bartoc/__init__.py 0000644 0001751 0000177 00000006002 14655542206 024170 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download the BARTOC registry."""
import json
from pathlib import Path
from typing import Any, Mapping
import requests
from tqdm import tqdm
from bioregistry.constants import URI_FORMAT_KEY
from bioregistry.license_standardizer import standardize_license
from ..alignment_utils import Aligner
__all__ = [
"get_bartoc",
"BartocAligner",
]
HERE = Path(__file__).parent.resolve()
PROCESSED_PATH = HERE / "processed.json"
URL = "https://bartoc.org/data/dumps/latest.ndjson"
def get_bartoc(force_download: bool = True) -> Mapping[str, Mapping[str, Any]]:
"""Get the BARTOC registry.
:param force_download: If true, forces download. If false and the file
is already cached, reuses it.
:returns: The BARTOC registry
.. seealso:: https://bartoc.org/
"""
if PROCESSED_PATH.is_file() and not force_download:
return json.loads(PROCESSED_PATH.read_text())
rv = {}
for line in requests.get(URL).iter_lines():
record = json.loads(line)
record = _process_bartoc_record(record)
rv[record["prefix"]] = record
PROCESSED_PATH.write_text(json.dumps(rv, indent=2, ensure_ascii=False, sort_keys=True))
return rv
def _process_bartoc_record(record):
prefix = record["uri"][len("http://bartoc.org/en/node/") :]
rv = {
"prefix": prefix,
"description": record.get("definition", {}).get("en", [""])[0].strip('"').strip(),
"homepage": record.get("url", "").strip(),
"name": record.get("prefLabel", {}).get("en", "").strip(),
}
pattern = record.get("notationPattern")
if pattern:
rv["pattern"] = "^" + pattern.strip().lstrip("^").rstrip("$") + "$"
for identifier in record.get("identifier", []):
if identifier.startswith("http://www.wikidata.org/entity/"):
rv["wikidata_database"] = identifier[len("http://www.wikidata.org/entity/") :]
abbreviations = record.get("notation")
if abbreviations:
if len(abbreviations) > 1:
tqdm.write(f"[bartoc:{prefix}] got multiple abbr.: {abbreviations}")
abbreviation = abbreviations[0].strip()
if " " in abbreviation:
tqdm.write(f"[bartoc:{prefix}] space in abbr.: {abbreviation}")
rv["abbreviation"] = abbreviation
for license_dict in record.get("license", []):
license_key = standardize_license(license_dict["uri"].strip())
if license_key:
rv["license"] = license_key
uri_pattern = record.get("uriPattern")
if uri_pattern and "(" in uri_pattern and ")" in uri_pattern:
left_pos = uri_pattern.find("(")
right_pos = uri_pattern.find(")")
rv[URI_FORMAT_KEY] = uri_pattern[:left_pos] + "$1" + uri_pattern[1 + right_pos :]
return {k: v for k, v in rv.items() if k and v}
class BartocAligner(Aligner):
"""Aligner for BARTOC."""
key = "bartoc"
getter = get_bartoc
alt_key_match = "abbreviation"
curation_header = ["name", "homepage", "description"]
if __name__ == "__main__":
BartocAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254802.0
bioregistry-0.11.12/src/bioregistry/external/bartoc/processed.json 0000644 0001751 0000177 00010467773 14655544022 024772 0 ustar 00runner docker {
"10": {
"description": "The APAIS thesaurus lists the subject terms used to index articles for APAIS: Australian Public Affairs Information Service, a subject guide to literature in the social sciences and humanities. The APAIS thesaurus was introduced in 1978 when APAIS became available as an online database and was first published by the National Library of Australia in 1980 to facilitate online searching. While still primarily used as an indexing tool, the APAIS thesaurus is an essential aid for efficient online searching of the APAIS and Australian Public Affairs - Full Text databases. Besides serving the APAIS clients the published Thesaurus has been adopted in a number of wider projects that require a structured list of Australian subject terms, such as the recommendation for its use for subject indexing when using the Australian Government Locator Service metadata standard.",
"homepage": "http://www.nla.gov.au/apais/thesaurus/",
"name": "Australian Public Affairs Information Service Thesaurus",
"prefix": "10"
},
"100": {
"description": "The IEEE Thesaurus is a controlled vocabulary of over 9,000 descriptive engineering, technical, and scientific terms as well as IEEE-specific society terms. The thesaurus represents terminology and vocabulary usage drawn from IEEE transactions and journal articles, conference papers, and standards. The vocabulary uses American-based spellings with cross references to British variant spellings. The scope and structure of the IEEE Thesaurus reflect the engineering and scientific disciplines that comprise the societies, councils, and communities of IEEE in addition to the technologies IEEE serves. The IEEE Thesaurus contains controlled vocabulary referred to as descriptors or preferred terms*. These descriptors are considered the preferred terms for index usage. Thesaurus construction is based on the ANSI/NISO Z39.19-2005 standard, Guidelines for the Construction, Format, and Management of Monolingual Controlled Vocabularies. Each descriptor included in the thesaurus represents a single concept or unit of thought. The scope of the descriptors is based on the material as presented in IEEE periodical articles, conference papers, standards, and/or IEEE organizational material. The IEEE Thesaurus is a tool to improve and enhance the indexing and retrieval of articles and other material from IEEE periodicals, conferences, standards, and other publications that are made available on IEEE Xplore. It provides a common and consistent language for authors, researchers and online discovery.",
"homepage": "http://www.ieee.org/publications_standards/publications/services/thesaurus_access_page.html",
"license": "CC BY-NC-ND 3.0",
"name": "The Institute of Electrical and Electronics Engineers Thesaurus",
"prefix": "100"
},
"1000": {
"description": "Classification by subject headings, without the proper and constant reevaluations and updates made by experts from each field of study, tends to become a pile of words with little efficacy for the collection, storage and retrieval of documents. In the case of larger libraries, able to update their headline lists, this classification is valid, the library of a research institute with well-designed study programs should support its researchers with indexes based on specific thesauri.\n\nΒ In this sense, the thesaurus for gender studies and women presented below represents the appropriate instrument not only for a more precise indexing of collections on gender and women of any library, but also to facilitate access to information on the feminine condition , Or to expedite bibliographical surveys and possible mapping of gender studies.",
"homepage": "http://www.fcc.org.br/conteudosespeciais/tesauro/arquivos/TPEDGESM.pdf",
"name": "Thesaurus for Gender Studies and Women",
"prefix": "1000"
},
"1001": {
"description": "This controlled thesaurus of keyterms in homeopathy is for use when indexing literature on homeopathy and also when searching databases which have been indexed according to this list of terms. This thesaurus can be used in conjunction with the Amed Thesaurus from the British Library and the MeSH Medical Subject Headings from the National Library of Medicine, USA (used for Medline). It was developed as an addition to the Amed thesaurus to give greater depth of indexing for homeopathy, as there are only a few terms on homeopathy available in Amed. Terms in English have been translated into French, German and Italian to produce this multilingual edition of the thesaurus. However, the main language for this thesaurus remains English.",
"homepage": "http://homeopathyeurope.org/thesaurus/",
"name": "European Committee for Homeopathy Homeopathic Thesaurus",
"prefix": "1001"
},
"1002": {
"description": "Thesaurus of the Geographical Literature Database GEODOK.",
"homepage": "http://www.geodok.uni-erlangen.de/",
"name": "GEODOK Thesaurus",
"prefix": "1002"
},
"1003": {
"description": "CAPs indicate Xwi7xwa subject headings. (LC) are Library of Congress subject headings. (other) are non-Xwi7xwa and non-Library of Congress subject headings.",
"homepage": "https://xwi7xwa.library.ubc.ca/files/2011/09/bcfn.pdf",
"name": "British Columbia First Nations Subject Headings",
"prefix": "1003"
},
"1004": {
"homepage": "http://thesaurusbuilder.com/Downloads/",
"prefix": "1004"
},
"1005": {
"description": "Eurovoc is a multilingual thesaurus. As a thesaurus, it can be used to classify documents according to subject and, more specifically, to organise or classify the document database of the European Union and thus make consulting the database an easier task. Given that Eurovoc is a multilingual thesaurus (it has been translated into all the official languages of the European Union), it allows any user wishing to find a specific document to perform a search in their own language, even if the document is written in another. Furthermore, and considering that equivalences established between the various languages are stable and fixed, Eurovoc can also be considered a multilingual dictionary, thus helping considerably with translations generally as well as terminology standardisation. With the translation of Eurovoc, Basque has now placed itself at the same level as the official languages of the European Union.",
"homepage": "http://www.bizkaia.net/kultura/eurovoc/index.asp",
"name": "European Union multilingual Thesaurus",
"prefix": "1005"
},
"1006": {
"description": "The Eurovoc thesaurus is a multilingual, multidisciplinary prepared by the Parliament and the Office for Official Publications of the European Communities (OPOCE) that covers all areas of activity of the European Union and allows indexed documents that manage institutions Europe in order to facilitate their consultation. (...) in Spain, the thesaurus Eurovoc has been translated into Basque by the Provincial Council of Biscay, and Catalan, by the Parliament of Catalonia. If While the original purpose of the treatment was Eurovoc documentation generated by the Community institutions, the thesaurus is also a tool for multidisciplinary broad enough to cover the different national perspectives, with a very strong accent in all that concerns at parliamentary level. that is why, apart from European institutions such as the Parliament or the Office for Official Publications of the European Union, is also the instrument of falling ripciΓ³ used by many national parliaments, regional and regional government and some from across the European Union. The international nature of the institution makes obviously Eurovoc thesaurus is multidisciplinary and multilingual, and you try and actually, it aconsegueix- a framework generic description theme in almost all areas, in one way or on the other, are common to any political institution in all its aspects (economic, social, agricultural, audiovisual, etc.).\n\nHowever, the same instrument thematic description can hardly meet the expectations of all international institutions to make use of. There are several factors (social, political, linguistic, geographical, etc.) that make the needs of each institution are different descriptive. Therefore, indexing language should be primarily serving the institution uses so it can meet the specific needs of information retrieval in the same administration and in general for all users.\n\nThe Parliament of Catalonia, when the thesaurus Eurovoc translated into Catalan, chose to make its own development, with new descriptors and non-descriptors felt that there should be a needs index the institution and the new associative relations or explanatory notes seemed appropriate.\n\nThus, since 2000, the thesaurus Eurovoc own development with the Parliament of Catalonia is the instrument description that is used to index all parliamentary initiatives, which facilitates you can very easily see the entire parliamentary activity that has taken place in the Catalan parliament.",
"homepage": "http://www.parlament.cat/web/documentacio/recursos-documentals/tesaurus/index.html",
"name": "The thesaurus of the Parliament of Catalonia",
"prefix": "1006"
},
"1007": {
"description": "The Glossary is a collection of the EHEA multilingual Catalan, Spanish, English and French keywords on the European Higher Education explained extensively from the documentation generated by this new reality. The aim of this material is to facilitate the understanding of European higher education and to be a useful resource for the writing and translation of educational documents generated within this framework.",
"homepage": "http://www.upc.edu/slt/glosEEES/menu.php",
"name": "Glossary of the European Higher Education",
"prefix": "1007"
},
"1008": {
"description": "This work is a collection of about a thousand words, the result of two centuries of accumulated scientific development. (...) The minimum information that each glossary term is: input and speech.\n\nMoreover, there are terms that have additional information, such as: - Definition. - equivalences in English, Spanish, French and German. - synonyms. - Notes. - Related Terms.",
"homepage": "http://cit.iec.cat/obresx.asp",
"license": "CC BY-NC-ND 3.0",
"name": "A table of geologic time",
"prefix": "1008"
},
"1009": {
"description": "The BBC ontology is used to describe BBC concepts in the store. For example, the BBC divisions (products) publishing linked data and interfacing with the triplestore, the platforms for which we produce content and the web documents that publish or are relevant to the BBC's content.",
"homepage": "https://www.bbc.co.uk/ontologies/bbc",
"name": "BBC Ontology",
"prefix": "1009"
},
"101": {
"description": "A hierarchically ordered controlled thesaurus, containing more than 20,000 subject terms. 3 Parts.\" Used in the database 'International Index to Film Periodicals'.",
"homepage": "http://www.vocabularyserver.com/fiaf/",
"name": "International Index to Film Periodicals Subject Headings",
"prefix": "101"
},
"1010": {
"description": "The Business News Ontology describes the concepts that occur in BBC business news.",
"homepage": "https://www.bbc.co.uk/ontologies/business",
"name": "Business News Ontology",
"prefix": "1010"
},
"1011": {
"description": "An ontology to represent the content management systems and their interaction with the triplestore. For instance, how should an entity in the triplestore, e.g., the URI for Manchester United, be linked to an external CMS that provides more information about Manchester United, e.g., sports statistics, or how should a creative work URI in the triplestore refer to the CMS it was created. The CMS ontology provides the Linked Data Platform customers with pointers to additional information about a thing in other systems.",
"homepage": "http://www.bbc.co.uk/ontologies/cms",
"name": "CMS Ontology",
"prefix": "1011"
},
"1012": {
"description": "The generic BBC ontology for people, places,events, organisations, themes which represent things that make sense across the BBC. This model is meant to be generic enough, and allow clients (domain experts) link their own concepts e.g., athletes or politicians using rdfs:sublClassOf the particular concept.",
"homepage": "http://www.bbc.co.uk/ontologies/coreconcepts",
"name": "Core Concepts Ontology",
"prefix": "1012"
},
"1013": {
"description": "This is the model we use to express the minimum metadata necessary to express a piece of creative content in the platform. The creative work ontology is continuously evolving based on our clients' requirements. There is a core class in this model, which is the CreativeWork class and properties that support information the LDP clients need to build their products such as title, thumbnail, URL e.t.c.",
"homepage": "http://www.bbc.co.uk/ontologies/creativework",
"name": "Creative Work Ontology",
"prefix": "1013"
},
"1014": {
"description": "This ontology aims to provide data model and vocabularies for describing the national curricula within the UK.",
"homepage": "http://www.bbc.co.uk/ontologies/curriculum",
"name": "Curriculum Ontology",
"prefix": "1014"
},
"1015": {
"description": "A simple vocabulary for describing recipes, ingredients, menus and diets.",
"homepage": "http://data.lirmm.fr/ontologies/food",
"license": "CC-BY-3.0",
"name": "Food Ontology",
"prefix": "1015"
},
"1016": {
"description": "An ontology which describes a model for politics, specifically in terms of local government and elections. This is an evolving spec, originally designed to cope with UK (England and Northern Ireland) Local, and European Elections in May 2014.",
"homepage": "http://www.bbc.co.uk/ontologies/politics",
"name": "Politics Ontology",
"prefix": "1016"
},
"1017": {
"description": "A vocabulary for programme data. It defines concepts such as brands, series, episodes, broadcasts, etc.",
"homepage": "http://purl.org/ontology/po/",
"name": "Programmes ontology",
"prefix": "1017"
},
"1018": {
"description": "The provenance ontology supports data management and auditing tasks. It is used to define the different types of named graphs we used in the store (quad store) and enables their association with metadata that allow us to manage, validate and expose data to our services.",
"homepage": "http://www.bbc.co.uk/ontologies/provenance",
"name": "Provenance Ontology",
"prefix": "1018"
},
"1019": {
"description": "The News Storyline Ontology is a generic model for describing and organising the stories news organisations tell. The ontology is intended to be flexible to support any given news or media publisher's approach to handling news stories. At the heart of the ontology, is the concept of Storyline. As a nuance of the English language the word 'story' has multiple meanings. In news organisations, a story can be an individual piece of content, such as an article or news report. It can also be the editorial view on events occurring in the world.",
"homepage": "http://www.bbc.co.uk/ontologies/storyline",
"license": "CC BY-SA 3.0",
"name": "Storyline Ontology",
"prefix": "1019"
},
"102": {
"description": "The 3 thesauri in free consultation on this site are the result of several years of work and have been specially created to meet the specific needs of the museums members of the AICIM Network, which evolve every day thanks to the additions and suggestions of the museums. Goals are to standardize the vocabulary used in the inventory records and to facilitate the search of objects in the AICIM database.",
"homepage": "http://aicim.be/main/fr/thesaurus.php",
"name": "The Thesaurus Network Computerized access to the Collections of Museums Institutions",
"prefix": "102"
},
"1020": {
"description": "A simple vocabulary for describing biological species and related taxa. The vocabulary defines terms for describing the names and ranking of taxa, as well as providing support for describing their habitats, conservation status, and behavioural characteristics, etc.",
"homepage": "http://www.bbc.co.uk/ontologies/wo",
"name": "Wildlife Ontology",
"prefix": "1020"
},
"1021": {
"description": "Thousands of cell lines have been artificially developed and used for different applications. Information about cell lines is typically stored in public repositories and indexed catalogues. Most cell lines are commercially available. Some cell lines are only transferred between academic laboratories. Information about cell lines has not been well standardized and machine-readable to date. Integration of data from multiple sources is a challenge, confounded by lack of consistent naming conventions, contamination of cell lines, and provision of the same cell lines by multiple commercial sources but with different biological attributes. The Cell Line Ontology (CLO) is a community-based effort to represent all cell lines in a starndard ontology approach.",
"homepage": "http://www.clo-ontology.org/",
"name": "Cell Line Ontology",
"prefix": "1021"
},
"1023": {
"description": "The \"Thesaurus Technology and Management (TEMA) offers (...) the most comprehensive structured collection of the current technical vocabulary for production and technology-oriented management\". (...) He is continually maintained by WTI and further developed into an ontology 'technology' in a joint project with the Technical Information Library of Hannover (TIB).",
"homepage": "http://wtiweb.wti-frankfurt.de/cgi-bin/ip_monitor.pl?APPL=tu-graz&SYSTEM=tecfinder&WEICHE2=auswahl",
"name": "Thesaurus engineering and management",
"prefix": "1023"
},
"1024": {
"description": "CCO basically contains genes, proteins, interactions (comprising genes or proteins that participate in them), processes from the cell cycle subtree of GO, molecular functions (GO), taxa, and ontological constructs (like an upper level ontology and relationships) to stick everything together. The knowledge represented in the system is expected to grow in quantity (integrating more data and different resources) and quality (organizing everything with Ontology Design Patterns and new relationships).",
"homepage": "http://www.cellcycleontology.org/",
"name": "Cell Cycle Ontology",
"prefix": "1024"
},
"1025": {
"description": "Plant Ontology project is a major international bioinformatics effort on standardizing the nomenclature, definitions, synonyms and relations of various terms/keywords/vocabularies that describe anatomical entities as well as the growth and developmental stages of plants. This collaborative project involves team members and projects with expertise on plant functional and comparative genomics, genetics, systematics, anatomy, developmental biology, computational biology, ontology development, etc. By developing the standardized vocabularies and their integration in the annotation of various data sets such as the annotation of plant part and its developmental stage that was used for analyzing the transcriptome, proteome, metabolome, phenotype and gene-gene interaction data sets. The successful integration facilitates users to perform queries on one or more data sets within a database or even between multiple remote database resources.",
"homepage": "http://plantontology.org/",
"name": "Plant Ontology",
"prefix": "1025",
"wikidata_database": "Q7201529"
},
"1026": {
"description": "With over 350,000 in print, the Clinician's Thesaurus is an indispensable practitioner resource and course text. It presents thousands of standard words, phrases, clinical tips, and interview questions to help practitioners conduct thorough assessments, accurately describe nearly any clinical situation, and shape clinical observations into effective reports. Finding exactly the right terminology can save hours of paperwork time and improve the quality of documentation. Structured to follow the sequence of a mental health evaluation, the book includes report formats, treatment planning pointers, all DSM-IV-TR and ICD-9-CM diagnostic codes, and much more β all in a large-size format with convenient lay-flat binding.",
"homepage": "http://www.guilford.com/books/Clinicians-Thesaurus/Edward-Zuckerman/9781606238745",
"name": "Clinician's Thesaurus",
"prefix": "1026"
},
"1027": {
"description": "The Healthcare Common Procedure Coding System (HCPCS, often pronounced by its acronym as \"hick picks\") is a set of health care procedure codes based on the American Medical Association's Current Procedural Terminology (CPT).",
"homepage": "http://cms.hhs.gov",
"name": "Healthcare Common Procedure Coding System",
"prefix": "1027",
"wikidata_database": "Q5691200"
},
"1028": {
"description": "The Evidence Ontology (ECO) describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about things (such as scientific conclusions, gene annotations, or other statements of fact) that result from scientific research. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as βa type of information that is used to support an assertion,β and assertion method is defined as βa means by which a statement is made about an entity.β Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology.",
"homepage": "http://code.google.com/p/evidenceontology/",
"name": "Evidence Codes Ontology",
"prefix": "1028"
},
"1029": {
"description": "The anatomy of the Tick, Families: Ixodidae, Argassidae",
"homepage": "http://anobase.vectorbase.org/",
"name": "Tick Gross Anatomy Ontology",
"prefix": "1029"
},
"103": {
"description": "7053 terms, 8052 relationships between terms, 881 terms not preferred.",
"homepage": "https://ilamdocs.org/documento/3079/",
"name": "List of Museological Art Terms of the Acceder Collective Catalog",
"prefix": "103"
},
"1030": {
"abbreviation": "ICC",
"description": "(...) ICC (.) is based on the premises that whenever information is to be generated or to be presented (in code form) at least two items are necessary one which plays the part of a subject and the other one that of the predicate of a sentence, with both these items being framed into a third one. The first basic division is by the categorial concepts denoting general entities and general aspects/determinations of being, framed into an evolutionary pattern of levels creating the 81 subject groups of ICC. Each of these subject groups is structured by a socalled systematifier, applying a recurring series of facets.",
"prefix": "1030",
"wikidata_database": "Q20827699"
},
"1031": {
"abbreviation": "KAB",
"description": "The classification for general libraries (KAB) is a library classification developed by the Zentralinstitut fΓΌr Bibliothekswesen (GDR) and is still being used today (in an revised version) in most municipal libraries of the new federal states, according to the General System for Public Libraries (ASB ), As the east-German counterpart, it is the most widely distributed system in public libraries in Germany.",
"homepage": "https://asb-kab-online.de/",
"name": "Classification for general libraries",
"pattern": "^[A-Z]( [0-9]+(.?[0-9])?)?$",
"prefix": "1031",
"wikidata_database": "Q1744613"
},
"1032": {
"description": "The\" Zangemeister signatures \"go back to Heidelberg's chief librarian, Karl Zangemeister, who headed the University Library from 1873 to 1902. He divided the entire collection into systematic specialist groups. The old stock of the library is still set up according to this system.",
"homepage": "http://nbn-resolving.de/urn:nbn:de:bsz:16-diglit-21531",
"license": "CC BY-SA 3.0",
"name": "System of the Real-Catalog of the University Library of Heidelberg",
"prefix": "1032"
},
"1033": {
"description": "The so - called\" garter catalog \"for dissertations, programs and brochures covered literature up to the year 1935, into 44 systematic groups, within which the titles were arranged in alphabetical order. It comprises a total of 1,200 volumes with approximately 586,000 titles. The odd-looking name was given to the catalog according to its original form, with the titles on paper strips between cardboard being held together by a strong webbing (therefore 'garter').",
"homepage": "http://www.ub.uni-heidelberg.de/wir/geschichte/Strumpfbandkatalog.pdf",
"name": "Systematic overview of the catalog of dissertations, programs and brochures",
"prefix": "1033"
},
"1034": {
"description": "In 1975, the Systematic Catalog of the University Library of Berlin (...) was aborted, as it did not allow a materialization of the material to meet the requirements of teaching and research. It was decided to develop the new Systematic Catalog on the basis of the Soviet Bibliographical, bibliographical, bibliographical, bibliographical, bibliographical, bibliographical, bibliographical, bibliographic, bibliographical, bibliographic, bibliographical, bibliographic, bibliographic, bibliographical, .) The notation form of the general key has been completely redesignated as a pure numeric notation enclosed in single quotation marks. On the other hand, the notation form of the geographic key, a numeric or numeric notation in parentheses, Of course using the letters of the Latin alphabet. It should be noted here that the alphabet notation of the main series of the librarian-bibliographic classification has been replaced by two-digit numbers, which are deduced from the following digits by a plus sign. Since some 'arrangement overviews' in the librarian-bibliographic classification contain annexes, which partly correspond to groups of the general key, the relevant key groups are used instead of these attachments.",
"homepage": "http://edoc.hu-berlin.de/series/schriftenreihe-ub/30/PDF/30.pdf",
"name": "The new systematic catalog of the University Library of Berlin",
"prefix": "1034"
},
"1035": {
"description": "Since the first edition in 1923, the Sears List has served the unique needs of small and medium-sized libraries, suggesting headings appropriate for use in their catalogs and providing patterns and instructions for adding new headings as they are required. The successive editors of the List have faced the need to accommodate change while maintaining a sound continuity. The new and revised headings in each edition reflect developments in the material catalogued and in the use of the English language, aiming always to make library collections as easily available as possible to library users.",
"homepage": "http://support.epnet.com/uploads/kb/sears_19th_edition.pdf",
"name": "Sears List of Subject Headings",
"prefix": "1035"
},
"1036": {
"description": "RVM has been a world leader in controlled French vocabularies for more than 70 years, serving French-language and bilingual libraries in Quebec and elsewhere in Canada. It offers 4 thesauruses with MARC 21- and SKOS-coded data.",
"homepage": "https://rvmweb.bibl.ulaval.ca/accueil",
"name": "Directory of Materials",
"prefix": "1036",
"wikidata_database": "Q3456268"
},
"1037": {
"name": "Systematic and alphabetical keyword register of the catalog group",
"prefix": "1037"
},
"1038": {
"description": "The goal behind this project is the development of an extensive Arabic thesaurus that would encompass all fields of knowledge β something that most libraries and information centers in the Arab world lack β to serve as the basic instrument of subjective analysis of information retrieval devices, and to keep abreast with developments taking place in information technology. In mid 1993, an agreement for developing an extensive trilingual (Arabic β English β French) Arab thesaurus was concluded between AHS Foundation, the Dubai Municipality, and Jumβah Al-Majid Center for Culture and Heritage in Dubai, UAE. By mid 1995, the first paperback edition of the thesaurus was issued, containing some 48,000 terms. The electronic version was issued in mid 2001 on CD, and it contained some 50,000 terms. This version is marked by a set of technical specifications that were specifically added to suit the purposes of this issue of the thesaurus as well as to make search and retrieval easier for persons doing the indexing and cataloging.",
"homepage": "http://maknaz.org/",
"name": "Expanded Thesaurus",
"prefix": "1038"
},
"1039": {
"description": "Subject cataloging, in principle, is the same in all types of libraries. Variations and adaptions are developed as these principles are applied to special collections or general collections for limited or specific patrons. This list of subject headings is intended for use wherever material for use by children from the elementary through the junior high school level is brought together in the public or school library. Children's interests are universal but their vocabulary is still growing along with their learning processes so subject headings which anticipate their approach to a wide variety of material and which employ terminology with which they are familiar are needed to facilitate their use of the library catalog. However, the language and approach of the children must be captured without completely losing touch with standard cataloging practice so that the mastery of the children's catalog will be a step on the road to the understanding and use of the adult catalog in future years.\n\nIn compiling this list in accordance with these principles our personal experiences in school and public libraries were an important factor, but personal opinions have been substantiated by considerable study and research including a master's thesis by Eloise Rue, 'Preferences of Elementary Children for Subject Heading Form'; scrutiny of outstanding courses of study for grades one through nine issued\n\nsince 1944 and an examination of standard tools in use; the results of a questionnaire to school library supervisors, children's departments in public libraries, curriculum specialists, children's catalogers and library school faculties. These formed the basis for original decisions. When the preliminary draft had been completed, consultants throughout the United States and Canada were called upon to examine and comment on it. The present list incorporates many of their suggestions and comments.",
"homepage": "http://hdl.handle.net/2027/mdp.39015030782539",
"name": "Subject headings for children's materials",
"prefix": "1039"
},
"104": {
"description": "12799 terms. Applied in the 'MMSH Phonotheque' database.",
"homepage": "http://phonotheque.mmsh.univ-aix.fr/ListRecord.htm",
"name": "Mediterranean House of Human Sciences Phonotheque Thesaurus",
"prefix": "104"
},
"1040": {
"description": "The UNISDR Terminology aims to promote a common understanding and usage of disaster risk reduction concepts and to assist the disaster risk reduction efforts of authorities, practitioners and the public. The previous version 'Terminology: Basic terms of disaster risk reduction' was published in 'Living with risk: a global review of disaster risk reduction initiatives' in 2004. The following year, the Hyogo Framework for Action 2005-2015 requested the UNISDR secretariat to 'update and widely disseminate international standard terminology related to disaster risk reduction, at least in all official United Nations languages, for use in programme and institutions development, operations, research, training curricula and public information programmes'.",
"homepage": "http://www.unisdr.org/we/inform/terminology",
"name": "United Nations Office for Disaster Risk Reduction Terminology",
"prefix": "1040"
},
"1041": {
"description": "The Proposed international standard nomenclature for fields of science and technology was proposed in 1973 and 1974 by the Division of Science Policy and Statistics for Science and Technology of UNESCO and adopted by the Scientific Advisory Committee. This is a classification system widely used in knowledge management of research projects and dissertations. Categories are divided into three hierarchical levels: Fields: Refering to general sections. Encoded with two digits and comprises several disciplines. Disciplines: Provide an overview of specialty groups in Science and Technology. Encoded with four digits. Despite being different from each other disciplines with cross references, or within the same field, are considered to have common characteristics. Subdisciplines: Entries are the more specific elements of the nomenclature and represent the activities that take place within a discipline. Encoded with six digits. In turn, must correspond to individual specialties in science and technology.",
"license": "CC BY-NC-SA 3.0",
"name": "Proposed International Standard Nomenclature for Fields of Science and Technology",
"prefix": "1041"
},
"1042": {
"abbreviation": "FOS",
"description": "Statistical units in the PNP sector are classified into the six major fields of science and technology suggested in UNESCOβs 'Recommendation Concerning the International Standardisation of Statistics on Science and Technology' (1978). (...) While the major fields of science and technology are clearly defined, the level of disaggregation within each component field is left to each country. (...) The criterion for classification is the major field of science in which most of the R&D activity is undertaken. When a major private NPI has significant R&D activity in more than one field of science, an attempt may be made to split the statistical unit into smaller units and classify them to relevant major fields of science.\" (2002) \"The existing FOS classification does not fully reflect changes in the science and technology area, especially with regard to emerging technology fields such as ICT, biotechnology and nanotechnology. This, as well as the need to obtain better coverage of the data based on the FOS, the most appropriate classification for R&D in the public sector, motivated the NESTI Group to review the classification.\" (2007)",
"name": "Field of Science and Technology Classification",
"pattern": "^[1-6](\\.([1-9]|1[0-9]))?$",
"prefix": "1042"
},
"1043": {
"abbreviation": "thema",
"description": "Thema is intended for use by all parts of the book trade: unlike other book trade subject classifications, it aims to be globally applicable. And in contrast to various library classifications that are used internationally, it is tailored for commercial use within the trade. It is a flexible standard that allows each market to retain its unique cultural voice while still presenting a unified subject hierarchy that rationalises book classification. The goals of Thema are to reduce the duplication of effort required by the many distinct national subject schemes, and to eliminate the need for scheme-to-scheme mapping that inevitably degrades the accuracy of classification, by providing a single scheme for international use. It can be used alongside existing national schemes like BIC, BISAC, WGS or CLIL, and has the potential to eventually replace them (though this is not an immediate goal).",
"homepage": "http://www.editeur.org/151/thema/en/welcome-to-thema/",
"name": "Thema subject classification scheme",
"prefix": "1043"
},
"1044": {
"description": "Note this scheme was originally published as a draft and called e4libraries Subject Category Headings. This scheme was revised by a panel of experts and the new UKSLC scheme is the result of this process. The UKSLC is based on the BIC standard subject categories used in bookshops and by online retailers. The scheme is designed for the public library sector to provide library-oriented category headings applicable across the full range of adult non-fiction, fiction and children's/young adult stock. Many library authorities have adopted categorisation schemes for fiction and non-fiction over the past forty years. The majority of them apply these categories solely at item level to determine shelf display, though a minority also use them to provide a searchable option within the main title-level catalogue record. However, most of these schemes are unique to the authority concerned and rely heavily for their operation on costly and time-consuming staff intervention. Adoption of a scheme of BIC-based standard subject/genre categories, made available to libraries in addition to existing Dewey classifications, offers the opportunity to reduce cost and streamline workflows by automating the categorisation process, and to support further improvements in stock selection, management, discovery and display. (...) At the same time it offers authorities a degree of flexibility in determining item-level shelfmarks, the categories used to organise and display stock in individual locations, allowing them to customise the scheme to meet their specific needs and to integrate it with existing schemes they have already developed. It is very much hoped that UK libraries and their suppliers will adopt UKSLC.",
"homepage": "http://www.bic.org.uk/51/UK-Standard-Library-Categories/",
"name": "UK Standard Library Categories",
"prefix": "1044"
},
"1045": {
"description": "These codes are for marketing purposes only. They do not replace the BIC Subject Categories. Data collection agencies like BML and Nielsen BookScan can use these new codes to provide a breakdown of the different categories of children's books sales through the retail trade, to enable you to measure how different parts of your list are doing relative to each other and the size of your market share.",
"homepage": "http://www.bic.org.uk/8/Children%27s-Books-Marketing-Classifications/",
"name": "Children's Books Marketing Classifications",
"prefix": "1045"
},
"1046": {
"description": "The product group system was developed by the bar retailers and has been used in the book trade since 1997. It has been strongly oriented towards logistical needs\n\nThe use of the data is decisively changed: The product group system serves as the basis for all statistics on the economic development of individual segments in the book trade. This required a revision of the entire structure of the system. (...) The core of the changes is a change of perspective and the new goal connected with the WGS. The focus is not on more logistics aspects, but on marketing aspects. The goal is to present the market situation of the industry as transparently as possible via the system.",
"homepage": "http://www.boersenverein.de/sixcms/media.php/976/wgs2012.pdf",
"name": "Product group system",
"prefix": "1046"
},
"1047": {
"description": "System for Information on Grey Literature in Europe, is your open access to 700.000 bibliographical references of grey literature (paper) produced in Europe and allows you to export records and locate the documents.",
"homepage": "http://www.opengrey.eu/subjects/",
"license": "CC BY-NC-ND 3.0",
"name": "System for Information on Grey Literature in Europe Classification",
"prefix": "1047"
},
"1048": {
"description": "The Hornbostel-Sachs system is a classification system for musical instruments, published in 1914 by Erich Moritz von Hornbostel and Curt Sachs in the Zeitschrift fur Ethnologie under the title Systematik der Musikinstrumente Classification of musical instruments (...) The Hornbostel-Sachs system has a hierarchical structure, each category corresponds to a number, with a number being added in each detail step, so that the number of digits increases with increasing concretization Of the number, while further characters (-,:,], +) allow the notation of special meanings.",
"homepage": "http://www.oberlin.edu/faculty/rknight/Organology/H-S-1914-German.pdf",
"license": "CC0-1.0",
"name": "Hornbostel-Sachs-systematics",
"prefix": "1048",
"wikidata_database": "Q496327"
},
"1049": {
"description": "The need for a scheme/system to classify state documents has become increasingly apparent as more and more emphasis has been placed on libraries to acquire and service this important body of material. Because of the diversity in library organizational patterns, documents librarians could probably never agree on one system for classifying state documents. However, those libraries which maintain a separate collection of state documents and also a separate federal documents collection classified by the Superintendent of Documents Classification scheme will be interested in the classification scheme for State of Illinois documents used by the Documents Section, Library, University of Illinois at Chicago Circle. By applying similar principles, this scheme is easily adaptable for publications of other states. Although the scheme is now presented in nearly as complete a form as possible, it is still subject to any changes made necessary by Illinois government organizational changes.",
"homepage": "http://hdl.handle.net/2142/3824",
"license": "https://www.w3.org/Consortium/Legal/2015/doc-license",
"name": "Classification Scheme for Illinois State Publications",
"prefix": "1049"
},
"105": {
"description": "The thesaurus has been developed specifically for our collection. The Powerhouse collection covers a wide variety of subject areas and many different types of objects are included. There are approximately 8,600 terms. But we do not claim to have a comprehensive list of all objects and we are actively seeking contributions to broaden the appeal of the thesaurus. We have recently added a number of new terms at the request of the National Museum of Australia, and we continue to work with them in developing the thesaurus. We are hopeful that with contributions from other institutions we can create an Australian standard for object name terminology. This object name thesaurus provides a standard terminology for naming objects. It does not claim to provide the correct name for an object. It merely provides a name for use in museum cataloguing systems to enable accurate retrieval of information about objects. The hierarchical structure of the thesaurus assists in searching. By organising object names, the relationships between objects can be made explicit. Object names are organised according to their hierarchical, associative or equivalence relationships. The object name thesaurus allows for more than one broader term for each object name. Any term is permitted to have multiple broader terms, for example 'Bubble pipes' has the broader terms of 'Pipes' and 'Toys'. There is no single hierarchy in which an object name is located, enabling it to by found by searchers approaching with different concepts in mind. All terms within the thesaurus are plural. This standard was determined when the thesaurus was first published. The thesaurus attempts to place object names within an Australian context; we therefore commonly use the Macquarie Dictionary as a general guideline when deciding on the preferred or non-preferred spelling for a term. The purpose of the Powerhouse Museum Object Name Thesaurus is to provide object name terms within an Australian context, for indexing museum collections. It also provides a controlled vocabulary that facilitates easier searching of collection databases for specific object types. A secondary purpose of a thesaurus can be to aid in the general understanding of a subject area. A thesaurus can provide a 'semantic map' by showing the inter-relationship between objects and help to provide definitions of terms. This is particularly true for the Powerhouse Museum Object Name Thesaurus which can provide a greater understanding of an object and the relationships between different types of objects.",
"homepage": "http://www.powerhousemuseum.com/pdf/publications/phm-thesaurus-sept09.pdf",
"name": "Powerhouse Museum Object Names Thesaurus",
"prefix": "105"
},
"1050": {
"abbreviation": "SKJ",
"description": "The systematic classification of children's and youth libraries is based on age grades and on formal criteria, whereby children's and youth literature is structured in the same way as the ASB groups.",
"homepage": "https://www.oebib.de/medien/katalog-aufstellung/aufstellung/",
"name": "Systematics for children's and youth libraries",
"pattern": "^[1-7]+(.[1-3])?$",
"prefix": "1050"
},
"1051": {
"abbreviation": "SSD",
"description": "The classfication of the city library Duisburg (SSD) is a classification for the content development of public libraries and was developed specifically for the needs of the Stadtbibliothek Duisburg in line with the ASB. It was first published in 1966 and has since been revised several times; The versions published in 1980 and 1987 bear the name 'classification of the literary literature and the fine literature'. The SSD is widely used in many public libraries and school libraries in Germany and Austria.",
"homepage": "https://www2.duisburg.de/stadtbib/medien/bindata/SSD_CD-ROM.pdf",
"name": "Classfication of the city library Duisburg",
"pattern": "^[A-Z]+( ([0-9]+)?)?$",
"prefix": "1051",
"wikidata_database": "Q2376983"
},
"1052": {
"description": "The sound carrier systematics are practice-oriented according to content (musical genres and forms) as well as formal (occupation) criteria.",
"name": "Sound carrier systematics",
"prefix": "1052"
},
"1053": {
"description": "The Andalusian Historical Heritage Thesaurus (TPHA) is the first integrating experience of all disciplines related to Historical Heritage in a single documentary language.\n\nΒ From the beginning, we opted for an innovative concept of Historical Heritage that understands the patrimonial property in relation to the context in which it is developed and from a polyvalent interpretation of it. In this sense, it is an ambitious and novel instrument that allows the possibility of approaching heritage from different perspectives and allows the description of the same object from different disciplinary perspectives.\n\nΒ In 1995, the Andalusian Institute of Historical Heritage from its Documentation Center, opted for the development of a documentary language capable of facilitating the processing and retrieval of information, as well as the integration of the different heritage databases that make up the System Of Historical Andalusian Heritage Information (SIPHA), resulting in the end of 1998 the publication of the Andalusian Historical Heritage Thesaurus.\n\nThe Andalusian Historical Heritage Thesaurus has the vocation to be useful to all those institutions and researchers related to the knowledge and systematization of historical heritage information, not only at the regional level but also at the national level, constituting an instrument capable of adapting to the needs Raised from the different patrimonial areas.\n\nWith the same purpose and objectives, we present the Internet version of the TPHA, which allows the consultation of the Thesaurus through its hierarchical and alphabetical structure, making it accessible to all types of users.\n\nFrom here, we invite its use and enrichment, since we are convinced that the application of the same documentary language in the systematization of the information of the Historical Heritage will have a positive impact on the knowledge and management of the same.",
"homepage": "http://www.iaph.es/tesauro/init.htm",
"name": "Andalusian Historical Heritage Thesaurus",
"prefix": "1053"
},
"1054": {
"description": "The SFI Group System is the most widely-used classification system for maritime and offshore industries worldwide. The SFI Group System ties together all vessel management functions, such as operations, purchasing, accounting, maintenance, quality, etc. The SFI Code is an international classification standard providing a highly functional division of technical and financial information.",
"homepage": "http://www.dtic.mil/cgi-bin/GetTRDoc?AD=ADA446592",
"name": "SFI Coding and Classification System for Ship Information",
"prefix": "1054",
"wikidata_database": "Q7389960"
},
"1055": {
"description": "At the same time, the National Library, the National Archives and the Greater Montréal Public Library, the Bibliothèque et Archives nationales du Québec (BAnQ) gathers, preserves and disseminates the Quebec and Québec documentary heritage.",
"homepage": "http://s7d9.scene7.com/is/content/SAQ/plan-classification-fr",
"name": "Document Classification Scheme",
"prefix": "1055"
},
"1056": {
"homepage": "http://www.podcastmcq.org/fr/documents/complexe/plan_classification.pdf",
"prefix": "1056"
},
"1057": {
"homepage": "https://www.banq.qc.ca/a_propos_banq/acces_a_linfo/plan_de_classification/",
"prefix": "1057"
},
"1058": {
"description": "Hydro-QuΓ©bec's classification classification plan is a hierarchical and logical structure made up of headings in which the company's activities are presented and which allows the classification, classification and identification of documents produced or received by the company, Company, whatever the medium. Each heading contains a code, a title and a description.",
"homepage": "http://www.hydroquebec.com/publications/fr/loi-sur-acces/plan-classification-documents.html",
"name": "Hydro-QuΓ©bec Document Classification Scheme",
"prefix": "1058"
},
"1059": {
"description": "The classification plan is a structure consisting of ratings and headings describing all the processes and activities of the DGEQ, which are used to classify all documents and files and to contribute to their identification. Reference and research, this plan helps to know our activities for which documents and files have been produced and received, thus facilitating the exercise of the right of access to information.",
"homepage": "http://www.electionsquebec.qc.ca/documents/pdf/plan-de-classification.pdf",
"name": "Classification Plan",
"prefix": "1059"
},
"106": {
"description": "The structure is designed to accommodate additional terms. It is hierarchically structured using the 'kind of' rule, eg public telephone kiosk is a kind of telephone kiosk, but you can also find terms by a search function and an A-Z index. Importantly, this thesaurus has a wiki facility so you can add additional scope notes and non-preferred terms straightaway. Connected Earth's Telecommunciations Object Thesaurus gives a common language for telecommunciations heritage objects.",
"homepage": "http://www.connected-earth.com/Thecollection/Thesaurus/",
"name": "Telecommunications Object Thesaurus",
"prefix": "106"
},
"1060": {
"description": "The file plan provides all the tasks of a community from. In addition to its core tasks are the one hand, the management tasks, on the other hand support and cross-cutting issues (...). The file plan is the basis for the control and structured storage of all necessary documents. In the digital business management The file system also provides the basis for a management and information system to store access rights and metadata such as retention periods or locations, enabling efficient and at least partially automated management of documents throughout the life cycle.",
"homepage": "http://www.staatsarchiv.zh.ch/internet/justiz_inneres/sta/de/gemeinden/musteraktenplaene.html",
"name": "Model files for evangelical-reformed political communities",
"prefix": "1060"
},
"1061": {
"homepage": "http://www.staatsarchiv.zh.ch/internet/justiz_inneres/sta/de/gemeinden/musteraktenplaene.html",
"prefix": "1061"
},
"1062": {
"description": "The file plan provides all the tasks of a community from. In addition to its core tasks are the one hand, the management tasks, on the other hand support and cross-cutting issues (...). The file plan is the basis for the control and structured storage of all necessary documents. In the digital business management The file system also provides the basis for a management and information system to store access rights and metadata such as retention periods or locations, enabling efficient and at least partially automated management of documents throughout the life cycle.",
"homepage": "http://www.staatsarchiv.zh.ch/internet/justiz_inneres/sta/de/gemeinden/musteraktenplaene.html",
"name": "Model files plan for evangelical-reformed church communities",
"prefix": "1062"
},
"1063": {
"homepage": "http://www.staatsarchiv.zh.ch/internet/justiz_inneres/sta/de/gemeinden/musteraktenplaene.html",
"prefix": "1063"
},
"1064": {
"description": "The PK FCS is based on the functions and activities of peacekeeping operations. It has three main purposes: to organize records created or received in the course of peacekeeping operations; to find and access records; to support the implementation of records management policies by linking PK FCS categories to those in the Peacekeeping Operations Retention Schedule (PORS). (...) The PK FCS\n\n is divided into 28 functional categories.",
"homepage": "https://archives.un.org/sites/archives.un.org/files/files/Policy_Guideline/File%20Classification/FCS_Guidance_withAnnexes.pdf",
"name": "Peacekeeping File Classification Scheme",
"prefix": "1064"
},
"1065": {
"description": "Every unit shall use the RCRP to organize, sort, destroy or permanently retain records produced or received during the course of their activities. Your main responsibility as a staff member is to apply the Records Management Program to documents whether they are on hard copy or electronic format. The retention periods included in the RCRP have been established in coordination with the concerned units, it has also been reviewed by OGC before being approved by BibliothΓ¨que et Archives nationales du QuΓ©bec (BAnQ). Therefore, the RCRP has a legal value and every unit must apply the retention rules stated in the RCRP.\"\n\n\"The Records Classification and Retention Plan (RCRP) is the official guideline that sets up the filing system for all the records created, used and held by every employee of the University, it comprises also the retention period attached to each of these records and states their final disposition. RCRP is now the tool where youβll be able to find all the information you need for managing your records. RCRP comprises 9 series divided in sub-series. These broad categories are subdivided into more precise activities and thatβs where youβll find the retention period and the final disposition of the records.",
"homepage": "http://archives.concordia.ca/rcrp",
"name": "Records Classification and Retention Plan",
"prefix": "1065"
},
"1066": {
"description": "The harmonized accounting model MCH2 provides the basis for the presentation of the financial statements of the cantons and municipalities and was developed from MCH1 by the Study Group for Cantonal Finances (FkF) at the request of the Conference of In accordance with the International Public Sector Accounting Standards (IPSAS) and in co-ordination with the new Federal Accounting Model, the FkF has developed the 20 recommendations of the MCH2. (CDF) was adopted by the Conference of Cantonal Finance Directors (CDF) in January 2008. The latter also advises the cantons and municipalities to implement these recommendations as soon as possible, Over the next 10 years. \"\n\nΒ \"The Expert Group Reform of Financial Statistics made a policy decision to organize the future functional classification based on the structure in place so far. At the same time, the new classification must be compatible with the International Classification, the Classification of Functions of Government (COFOG). The present nomenclature is based on the results of the consultation procedure organized by the FkF, the municipal finance supervisory authorities, CORSTAT, the Federal Statistical Office, the Federal Office for Social Insurance, Federal Finance Administration, in particular to the RPT Project Directorate. In addition, further discussions were held with the main users of the data.",
"homepage": "http://www.srs-cspcp.ch/srscspcp.nsf/vwBaseDocuments/PCSRS01",
"name": "Chart of Accounts and Functional Classification",
"prefix": "1066"
},
"1067": {
"description": "Agreed terminology is essential for communication, shared research and joint action, especially at the international level. This is why a glossary of hydrology is so important β to stimulate further progress in water sciences and to facilitate the translation of technical and scientific publications that may be of interest to a wider audience but are available only in one language.",
"name": "International Glossary of Hydrology",
"prefix": "1067"
},
"1068": {
"homepage": "http://www.wmo.int/pages/prog/lsp/meteoterm_wmo_en.html",
"prefix": "1068"
},
"1069": {
"homepage": "http://www.ciriec.ulg.ac.be/fr/telechargements/thesaurusep.pdf",
"name": "Public Company Thesaurus",
"prefix": "1069"
},
"107": {
"description": "996 terms, 110 relationships between terms, 240 equivalent terms.",
"homepage": "http://www.vocabularyserver.com/cadiz/",
"name": "Thesaurus of Audiovisual Documentation",
"prefix": "107"
},
"1070": {
"description": "CIRAC is a center of research and expertise on the German economy and society and Franco-German relations.",
"homepage": "http://www.cirac.u-cergy.fr/documents_autres/thesaurus.pdf",
"name": "Thesaurus Bibliothèque du Cirac",
"prefix": "1070"
},
"1071": {
"description": "This nomenclature is important since it allows the viewer to search for data via a thematic entry, and is required for sharing with all GeoBretagne partners who are invited to use this nomenclature for the internal classification of their data. Has been structured according to 2 levels, so as to have large branches allowing synthetic counting. An appropriate search in the tools implementing the thesaurus makes it possible to put all the cards / data corresponding to a level 1 back. Thesaurus in cataloging tools is highly recommended.",
"homepage": "http://kartenn.region-bretagne.fr/wiki/doku.php",
"license": "CC BY-NC-SA 3.0",
"name": "Thematic Nomenclature GeoBretagne",
"prefix": "1071"
},
"1072": {
"homepage": "http://www.d-p-h.info/IMG/pdf/thesaurus_dph_fr.pdf",
"prefix": "1072"
},
"1073": {
"description": "The classification of the soil has the objective of systematically classifying soils due to their diverse profile and location characteristics, making it possible to identify, compare, distinguish and assess subsoil soils.The classification has its importance mainly within the soil customer himself, Since pedological research and experiments should always be carried out on well-defined and classified soils, so that results can be compared. The classification of soil is also important in many interdisciplinary researches as well as in teaching.",
"homepage": "http://www.soil.ch/cms/home/",
"name": "Classification of soils in Switzerland",
"prefix": "1073"
},
"1074": {
"description": "This work is basically derived from the one made in an international project produced by the Ministry for Cultural and Environmental Heritage, by the Central Institute for Catalog and Documentation, the Cd-rom\" Thesaurus Multilingual Of the Ecclesiastical Kit \"(ICCD, Rome 1999) and by the Ministry of Culture et de la Communication the volume\" Thesaurus Objets religieux du culte catholique - Religious Objects of Catholic Faith - ecclesiastical Kit of Catholic Cult \"(Γ©ditions du Patrimoine, Paris 1999).\n\nThe research was subsequently updated and integrated thanks to the contribution of the Catholic University of Lisbon and the results of the collaboration produced by Italy a CD-ROM (ICCD, Roma 2004) in four languages ββ(Italian, French, English and Portuguese ) And by Portugal, by the Universidade CatΓ³lica Portuguesa - FundaΓ§ao from Casa de BraganΓ§a, a volume in Portuguese \"Thesaurus - Vocabulary of Objectos do Culto CatΓ³lico - Catholic ecclesiastical bodywork - Objets religieux du culte catholique - Religious Objects of Catholic Faith \"(Vila ViΓ§osa, 2004), with the translation of terms in other languages. In 2009, the Spanish section was added thanks to the participation of the Universidad Nacional Nacional de Autonoma de Mexico - Instituto de Investigaciones EstΓ©ticas.\n\nN.B. For the Italian, Portuguese and Spanish sections this version integrates the previous one of 2005; The terms for which there is no linguistic level or the perfect alignment between the other languages ββ(English, French and Spanish) have not yet been identified automatically postpone the upper end of the same category.\n\nThe project was realized by the institutional subjects and the technical references listed in the credits.\n\nCoordination of the Thesaurus evolution on www site with this product was done by Sandra Vasco Rocca (ICCD).",
"homepage": "http://www.culturaitalia.it/opencms/viewItem.jsp",
"license": "https://www.w3.org/Consortium/Legal/2015/doc-license",
"name": "Thesaurus of Religious Objects of the Catholic faith",
"prefix": "1074"
},
"1075": {
"description": "The purpose of this thesaurus, is to present the special standardized terminology used for the storage of, and search for, information in the APTIG file. This second edition consists of this standardized terminology and illustrates the rules formulated for its use. The thesaurus should control the terminology and enable any inconsistencies to be resolved when indexers or searchers translate from the language of each document, or search request, into the conceptual system language presented here.",
"homepage": "http://nepis.epa.gov/Exe/ZyPURL.cgi?Dockey=2000WVQP.TXT",
"name": "Standard Air Pollution Classification Network: a Thesaurus of Terms",
"prefix": "1075"
},
"1076": {
"description": "Federal and international agencies, private sector organizations, and academics use terms and definitions differently in their microbial risk assessments. This Thesaurus is a compendium of risk assessment terms found in frameworks, methodologies, and assessments. It provides insight into how various entities use specific microbial risk assessment terms in their activities and helps those responsible for such assessments both conduct and communicate about them more effectively.",
"homepage": "http://water.epa.gov/scitech/swguidance/standards/criteria/health/microbial/thesaurus_index.cfm",
"name": "Thesaurus of Terms Used in Microbial Risk Assessment",
"prefix": "1076"
},
"1077": {
"description": "The Coastal and Marine Ecological Classification Standard (CMECS) is a catalog of terms that provides a means for classifying ecological units using a simple, standard format and common terminology (CMECS uses the term 'unit' to refer to any defined entity in the standard at any level of the hierarchy; 'units' include seagrass bed, sand, lagoon, and water mass). CMECS offers a way to organize and interpret data about the marine environment, and it provides a common platform for inter-relating data. It builds upon approaches from published national, regional, and local habitat classification procedures, and it offers an umbrella under which a national coastal and marine ecological classification can grow and evolve.",
"homepage": "http://coast.noaa.gov/digitalcoast/publications/cmecs",
"name": "Coastal and Marine Ecological Classification Standard",
"prefix": "1077"
},
"1078": {
"description": "The classification codes and descriptions are broad subject headings that are specific to various databases. (...) Each code is prefaced by another two-character code that indicates in which database or equivalent printed abstracts journal, the record originally appeared.",
"homepage": "http://proquest.libguides.com/ld.php?content_id=3028189",
"name": "ASFA and Oceanic Abstracts Classification Codes",
"prefix": "1078"
},
"1079": {
"description": "The University of Glasgow Historical Thesaurus of English was initiated by the late Professor Michael Samuels in 1965, and the first full version of the Thesaurus was completed in 2008 under the direction of Professor Christian Kay. It contains almost 800,000 words from Old English to the present day arranged into detailed hierarchies within broad conceptual categories such as Thought or Music. It is primarily based on the second edition of the Oxford English Dictionary and its Supplements, with additional materials from A Thesaurus of Old English, and was published in print as the Historical Thesaurus of the OED by Oxford University Press in October 2009.\"\n\nThe \"online version enables users to pinpoint the range of meanings of a word throughout its history, their synonyms, and their relationship to words of more general or more specific meaning. In addition to providing hitherto unavailable information for linguists, historians of language, authors, students of English, and textual scholars, the Historical Thesaurus is a rich and unparalleled resource for investigating social and cultural history, showing the development of concepts through the words that refer to them.",
"homepage": "http://historicalthesaurus.arts.gla.ac.uk/",
"name": "Historical Thesaurus of English",
"prefix": "1079",
"wikidata_database": "Q5773986"
},
"1080": {
"description": "The thesaurus was originally compiled by J P Jenkins of the Rock Mechanics Information Service in 1976-1977. Since then it has been used and developed primarily for internal use. With the public availability of the Geomechanics Abstracts data base (GMA) on the Pergamon-InfoLine on-line system, the thesaurus is being published as an aid to users of GMA. The thesaurus derives in style principally from the Thesaurus of Engineering and Scientific Terms. Other publications consulted include CSIR Rock Mechanics Thesaurus, ASCE Soil Mechanics Thesaurus, US Army Engineer Waterways Experiment Station Microthesaurus of Soil Mechanics Terms, Geodex Soil Mechanics Thesaurus, Canada Mines Branch Mining Thesaurus, and Geosystems' Geosaurus. (...) The thesaurus is a structured list of \"controlled\" terms (or keywords) used to index the material contained in the Geomechanics Abstracts data base. This data base contains bibliographic references to publications pertaining to the fields of rock and soil mechanics.",
"homepage": "http://samples.sainsburysebooks.co.uk/9781483137636_sample_761188.pdf",
"name": "Thesaurus of Rock and Soil Mechanics Terms",
"prefix": "1080"
},
"1081": {
"description": "The Dana System of Mineralogy was first published in 1837 by James Dwight Dana, a leading geologist of his time; it is in its eighth edition (1997 ed.). The Dana classification, assigns a four-part number to a mineral species. First is its class, based on important compositional groups; next, the type gives the ratio of cations to anions in the mineral; finally, the last two numbers group minerals by structural similarity with a given type or class.",
"name": "Dana Classification",
"prefix": "1081",
"wikidata_database": "Q934210"
},
"1082": {
"description": "The Unified Soil Classification System (USCS) is a soil classification system used in engineering and geology to describe the texture and grain size of a soil. The classification system can be applied to most unconsolidated materials, and is represented by a two-letter symbol.",
"name": "Unified Soil Classification System",
"prefix": "1082",
"wikidata_database": "Q905795"
},
"1083": {
"description": "The E&P Thesaurus is a collection of words and phrases that are descriptive of the concepts and equipment pertaining to petroleum exploration, development and production, exclusive of geographic areas and named geologic terms, which are included in the Geographic Thesaurus and its supplement. Further, the E&P Thesaurus is a controlled vocabulary for this subject area, in which the various concepts have been linked by means of generic or hierarchical relationships. These relationships may be truly generic or may be associations by use, or even convenience. Synonyms are handled as follows: all terms of like meaning are directed to one term for use as the index term for that particular concept. This selection usually follows popular usage and the patterns set by existing terms in the Thesaurus. The chosen term is called a 'valid' index term; the other like terms are called 'invalid' and are not used for indexing.\n\nThe E&P Thesaurus terms are interrelated on the concept-oriented (faceted) principle, and all descriptors are narrower terms of one of ten facet headings.",
"homepage": "https://www.pa.utulsa.edu/products/tulsadatabase/thesaurus",
"name": "Petroleum AbstractsΒ Exploration and Production Thesaurus",
"prefix": "1083"
},
"1084": {
"description": "Over the past twenty years, Rapra Technology Limited has developed a computer database for use by the rubber and plastics industries, together with the necessary thesaurus. Prior to this development, a suitable system of classification by subject was essential for the provision of efficient information and library services by Rapra. A Classification Code was developed which, although it has required numerous revisions over the years in order to keep pace with changes in industry and advancing technology, is still in use today, despite the recent development of computerised systems. The Classification Code presently in use, details of which are given in this chapter, plays an essential part in the process of information transfer carried out at Rapra on behalf of the rubber and plastics industries.",
"homepage": "https://www.polymerlibrary.com/ClassificationCode.pdf",
"name": "RAPRA Classification Code",
"prefix": "1084"
},
"1085": {
"homepage": "http://www.ub.bildarchiv-dkg.uni-frankfurt.de/Bildprojekt/formular/arrayformular.php",
"name": "Thesaurus of the Bildarchiv of the German colonial society in the university library in Frankfurt am Main",
"prefix": "1085"
},
"1086": {
"abbreviation": "FULD",
"description": "The subject system, which divides the knowledge areas into main groups and subgroups and is expressed by a combination of letters and numbers (notation), allows you to search professional-thematically in the search portal. Select a subject and follow the thematic subdivision. You can then display the literature listed under the found system in the search portal.",
"homepage": "http://www.ulb.hhu.de/nc/recherchieren/fachsystematiken-und-fachinformationen/fachsystematik.html",
"name": "Subject area system of the University and State Library DΓΌsseldorf",
"pattern": "^[a-z]{4}[0-9]+([+]| ff)?$",
"prefix": "1086"
},
"1087": {
"description": "The thesaurus provides a standardised language for describing foods, specifically for classifying food products for information retrieval. (...) As constructed, LanguaLβ’ is a multilingual thesaural system using facetted classification. Each food is described by a set of standard, controlled terms chosen from facets characteristic of the nutritional and/or hygienic quality of a food, as for example the biological origin, the methods of cooking and conservation, and technological treatments.",
"homepage": "http://www.danfood.info/Publications.asp",
"name": "LanguaLβ’ Thesaurus",
"prefix": "1087"
},
"1088": {
"description": "Much time and effort is wasted both within and between industry, commerce, government and professional and academic institutions when ambiguities arise as a result of the inability to differentiate adequately between such terms as βstatement coverageβ and βdecision coverageβ, βtest suiteβ, βtest specificationβ and βtest planβ, and similar terms which form an interface between various sectors of society. Moreover, the professional or technical use of these terms is often at variance, with differentmeanings attributed to them.\n\n In compiling this glossary, the working group has sought the views and comments of a broad spectrum of opinion in industry, commerce and government bodies and organizations, with the aim of producing an international testing standard that would gain wide acceptance. Total agreement will rarely, if ever, be achieved in compiling a document of this nature. Contributions to this glossary have been received from testing communities from all over the world.",
"homepage": "http://www.istqb.org/downloads/glossary.html",
"name": "Standard Glossary of Terms used in Software Testing",
"prefix": "1088"
},
"1089": {
"description": "The T-SITA proposes a non-exhaustive, semantically structured, list of traits and ecological preferences. Terms are organized into a conceptual hierarchical tree with their fathers and sons ('Browse hierarchy' tab). Each term is conceptually included into its father term. For instance, the 'Reproduction type' trait term was included in the father term 'Physiology'. It means that the concept linked to the 'Reproduction type' term is included into the concept linked to the 'Physiology' term. 'Reproduction type' has two son terms: 'Asexual reproduction' and 'Sexual reproduction'. It means that the concepts linked to the 'Asexual reproduction' and 'Sexual reproduction' terms are included into the concept linked to the 'Reproduction type' term.\n\nEach term is typified by a unit. Traits and ecological preferences terms are identified by having either a numerical unit or being 'categorical'. Quantitative traits/ecological preferences are informed by numerical values and have therefore a numerical unit. For instance, the unit of the 'body length' trait term is mm. Otherwise, qualitative traits/ecological preferences are informed by textual data. To be usable, they need to be categorized into attributes, e.g. by fuzzy coding procedures (Chevenet et al. 1994). As a consequence, their unit is specified as being 'categorical'. For instance, the unit of the 'habitat' preference term is 'categorical'. 'Habitat' is categorized into several attributes, such as 'Agricultural area' or 'Wetland' terms. Such attributes appear as son terms of the habitat preference in the thesaurus hierarchy. Attributes are identified in the thesaurus by having a unit specified as being an attribute. For instance, the unit of 'Wetland' term is 'attribute'. In addition, a categorical trait or ecological preference can have multi-levels sons. For instance, the habitat preference is the father of 'Agricultural area' which is itself the father of 'Arable land', 'Fallow' and 'Perennial crop'. It was done to take into account the heterogeneous accuracy of the textual literature informing the categorical traits or preferences.",
"homepage": "http://t-sita.cesab.org/",
"name": "Thesaurus for Soil Invertebrate Trait-based Approaches",
"prefix": "1089"
},
"109": {
"abbreviation": "TGN",
"description": "TGN is a structured vocabulary currently containing around 1,106,000 names and other information about places. Names for a place may include names in the vernacular language, English, other languages, historical names, names and in natural order and inverted order. Among these names, one is flagged as the preferred name. TGN is a thesaurus, compliant with ISO and NISO standards for thesaurus construction; it contains hierarchical, equivalence, and associative relationships. Note that TGN is not a GIS (Geographic Information System). While many records in TGN include coordinates, these coordinates are approximate and are intended for reference only. The focus of each TGN record is a place. There are around 912,000 places in the TGN. In the database, each place record (also called a subject) is identified by a unique numeric ID. Linked to the record for the place are names, the place's parent or position in the hierarchy, other relationships, geographic coordinates, notes, sources for the data, and place types, which are terms describing the role of the place (e.g., inhabited place and state capital). The temporal coverage of the TGN ranges from prehistory to the present and the scope is global. The TGN is a hierarchical database; its trees branch from a root called Top of the TGN hierarchies (Subject_ID: 1000000). Currently there are two TGN facets, World and Extraterrestrial Places. Under the facet World, places are arranged in hierarchies generally representing the current political and physical world, although some historical nations and empires are also included. There may be multiple broader contexts, making the TGN polyhierarchical. The primary users of the Getty vocabularies include museums, art libraries, archives, visual resource collection catalogers, bibliographic projects concerned with art, researchers in art and art history, and the information specialists who are dealing with the needs of these users. In addition, a significant number of users of the Getty vocabularies are students or members of the general public.",
"homepage": "http://www.getty.edu/research/tools/vocabularies/tgn/",
"license": "http://www.opendatacommons.org/licenses/by/1.0",
"name": "Getty Thesaurus of Geographic Names",
"prefix": "109",
"wikidata_database": "Q1520117"
},
"1090": {
"description": "This Thesaurus is a collection of terms and concepts that survey the broad discourse on sustainability. Most definitions of sustainability, and the various disciplinary attempts to put it into practice, are not well suited in and of themselves for the actual achievement of sustainability. These definitions are descriptive of a future state of sustainability but lack a prescriptive process that presents how the transition from the present state of unsustainability to a future sustainability process may occur. The first section of this Thesaurus presents various attempts at defining sustainability. These abstract definitions have provided just enough information to inspire many different and often times conflicting attempts of reducing the level of unsustainability, which are categorized in the second section of this Thesaurus. Recently, social constructivists have entered the fray and have deemed sustainability 'an essentially contested concept', because of the many diverse approaches to the subject. The third section of this Thesaurus explores this debate and offers a way out of the unworkable conundrum in which social constructivist analysis places sustainability. Finally, the fourth section presents a definition of sustainability that describes an operational process through which sustainability may be achieved in practice. The information in this Thesaurus is no way exhaustive, but it largely represents the major issues and approaches of the sustainability debate. This document seeks to clarify the language surrounding sustainability, place current approaches in what the authors interpret as their proper contexts, and present a process that integrates scientific disciplines and local stakeholder participation into an ongoing balance-seeking process well suited to the achievement of sustainable city-regions. The Thesaurus is organized so that by reading the chapter headings as a first pass the reader will get a sense of the more detailed content within.",
"homepage": "https://ens.as.uky.edu/thesaurus-sustainability",
"name": "Thesaurus of Sustainability",
"prefix": "1090"
},
"1091": {
"description": "The EMCS is a detailed and comprehensive structure for analysis, facilitating the comparison of companies across two levels; sector and subsector, and across national boundaries. The system defines environmental market companies and allocates each to the subsector whose definition most closely describes the nature of its business. There are currently seven Sectors and 29 Subsectors.",
"homepage": "http://www.ftse.com/products/downloads/FTSE_Environmental_Markets_Classification_System.pdf",
"name": "FTSE Environmental Markets Classification System",
"prefix": "1091"
},
"1092": {
"description": "The Classification covers the field of medicine and its related sciences. With it are used the various schedules of the Library of Congress Classification in order to provide an orderly arrangement for subjects bordering on medicine and for non-medical reference books. The LC schedules are used extensively; for example, social questions relating to the blind and the deaf are classified in HV (Social Sciences). When classification according to the LC schedules is indicated, only the class letters have been furnished in the present index. Specific numbers for LC classes have been omitted on the theory that each library will determine for itself the amount of specificity it desires in its use of the LC Classification tables. At AML, specific subdivisions of more general classes are used only when it appears that the number of titles to be classified will justify their use.",
"homepage": "https://archive.org/details/101589080.nlm.nih.gov",
"name": "Army Medical Library Classification Medicine",
"prefix": "1092"
},
"1093": {
"description": "The Medical and Health Related Sciences Thesaurus is the list of indexing terms developed and maintained as an integral component of CRISP (Computer Retrieval of Information on Scientific Projects), a comprehensive system furnishing scientific data on all research projects supported by the Public Health Services. CRISP is operated by the Research Documentation Section, Statistics and Analysis Branch, Division of Research Grants. The Thesaurus also comprises the vocabulary base for subject headings appearing in the annual Research Awards Index, a product of CRISP also produced by the Section. Documents used as source material for information entering the Thesaurus, CRISP and the Index represent current research projects for FY 1981 covering many widely diversified areas of medicine, dentistry, mental health, and allied public health fields. In order to maintain a vocabulary of terms which is both timely and representative of these changing and expanding research areas, constant revisions are being made. These revisions are reflected in updated editions of the Thesaurus published annually, As in the past, it is hoped that this revised edition will further aid the efforts of research analysts, information specialists, librarians and other individuals who have the responsibility for scientific communication systems.",
"homepage": "http://catalog.hathitrust.org/Record/002507962",
"name": "Medical and Health Related Sciences Thesaurus",
"prefix": "1093"
},
"1094": {
"abbreviation": "ΓFOS",
"description": "The Austrian Systematics of the Sciences 2012 (ΓFOS 2012) is the version of the revised International Classification of Fields of Science and Technology (FOS), adapted to the Austrian situation, whose application is binding in international comparison, and particularly within the European statistical system ΓFOS 2012 consists of 6 main groups: natural sciences (1), technical sciences (2), human medicine, health sciences (3), agricultural sciences, veterinary medicine (4), social sciences (5) and the humanities (6) 3-digit groups In order to be able to deal more closely with the national situation in the new Austrian system of scientific branches, these 3-positioners were provided with further subgroups (4-positioners), taking into account the explanations of the international classification Groups, currently no , The 3-positioner has the same designation as the subgroup (4-positioner, e.g. Mathematics: 101 and 1010 respectively).",
"homepage": "https://data.statistik.gv.at/web/meta.jsp?dataset=OGDEXT_KLASSDB_OEFOS2012_1",
"name": "Austrian system of the scientific branches",
"prefix": "1094"
},
"1095": {
"description": "When any substantial volume of data has to be recorded, a coherent system of classifying and coding the data is essential, particularly where electronic or mechanical means of retrieval or analysis are to be used. The Application of the International Classification of Diseases to Dentistry and Stomatology (ICD-DA) is intended to provide a practical and convenient basis for the classification and coding of data by all those working in the field of oral and dental disorders. It is derived directly from the Tenth Revision of the International Classification of Diseases (ICD-10), and is concerned with all diseases and conditions that occur in, have manifestations in, or are associated with the oral cavity and adjacent structures. For the purposes of ICD-DA, most of the classifications provided by ICD-10\n\nhave been subdivided and expanded; however, data from ICD-DA can be reassembled into ICD categories by simple addition. It is strongly recommended that ICD-DA be used with ICD-10 available for reference.",
"homepage": "http://extranet.who.int/iris/restricted/bitstream/10665/40919/1/9241544678_eng.pdf",
"name": "Application of the International Classification of Diseases to Dentistry and Stomatology",
"prefix": "1095"
},
"1096": {
"description": "Ovid Nursing Subject Thesaurus is a proprietary Controlled Vocabulary and associated Nursing Lexicon which βspeaks nurseβ to meet the specific needs of nursing professionals of all types and is designed to enhance retrieval of relevant documents for nursing professionals and students. (...) ONST takes the familiar terminology of Medical Subject Headings (MeSH) as a starting point. While the thesaurus is MeSH-compatible, many inverted MeSH headings, (e.g. Education, Continuing) have been flipped to direct order (e.g., Continuing Education). This order maps more closely to natural-language forms, thereby making the selection of terms more intuitive for the end-user. (...) The ONST uses the 'flat format' of thesauri, in which all synonyms and relationships are displayed within an alphabetical array of descriptors. Users can easily see broader, narrower, related and βused forβ references in a single view, without having to link to other thesaurus displays. The relationship indicators are spelled out, not abbreviated, minimizing the need to consult Help files. This format is the most commonly used thesaurus display format, and is found in the Thesaurus of ERIC Descriptors, and the Thesaurus of Psychological Index Terms. (...) Unlike MeSH, ONST does not include subheadings. This simple structure is easy for the enduser to understand and use. Descriptors can be simply combined at the searching stage, without the need to check complex instructions on subheadings. Work is continuing on ONST, and more terms, definitions, and relationships will be added on an ongoing basis.",
"homepage": "http://ovidsupport.custhelp.com/app/answers/detail/a_id/3590/~/ovid-nursing-subject-thesaurus",
"name": "Ovid Nursing Subject Thesaurus",
"prefix": "1096"
},
"1097": {
"description": "The SRS Research Information System Thesaurus was empirically derived from the language of reports of research supported by the Social and Rehabilitation Service, Department of Health, Education, and Welfare. The subject domain common to SRS researchers came to be described during the course of the thesaurus-Βbuilding project as 'the individualized effects of societal dysfunctions and the attempts made to understand and correct them.' To clarify the meaning of societal dysfunctions, they must be seen in perspective with normal societal functions; therefore, the domain of this thesaurus is the total social system, but with emphasis on social dysfunctions. The purpose of this thesaurus is to control the language used to index and retrieve documents of interest to SRS and the personnel it serves. At present the indexing so controlled is the SRS Research Information System Index. Searchers using that document need to be guided by the thesaurus. SRS hopes, however, that the effort expended to study the SRS language and to set it forth, showing interrelationships among terms, will be of use also to those interested in such things as social science language per se, the scope of activities of SRS, and the categories of clients served.",
"homepage": "http://catalog.hathitrust.org/Record/000008746",
"name": "SRS Research Information System Thesaurus",
"prefix": "1097"
},
"1098": {
"description": "The classification system's purpose is to control the nuances of expression relevant to indexing and retrieving information, technology, and literature of interest to rehabilitation personnel and others concerned with program evaluation. The classification system includes: (1) a hierarchic outline consisting of 323 terms, which provides a systematic set of constructs for describing all the elements (environment, goals, resources, methodology, results, and utilization) that relate to the input, process, and output of program evaluation in the rehabilitation service system; and (2) an alphabetic thesaurus which includes all of the terms contained in the hierarchic outline as well as terms that refer a user to an accepted system term. Both the hierarchic outline and alphabetic thesaurus were developed in a manner that complements the existing Rehabilitation Service Administration's Research Information System Thesaurus.",
"homepage": "http://eric.ed.gov/?id=ED117471",
"name": "Classification System for Rehabilitation Program Evaluation Technology and Literature",
"prefix": "1098"
},
"1099": {
"description": "The thesaurus delineates the standard terminology used to index and retrieve instructional materials for exceptional children in the Special Education Instructional Materials Center/Regional Media Centers Network. The thesaurus is presented in three formats: an alphabetical listing (word by word rather than letter by letter), a rotated index, and a listing by category. The alphabetical listing of descriptors provides definitions for all terms, and scope notes which indicate the scope or boundaries of the descriptor for selected terms. Numerous cross references are provided. In the rotated index format, all key words excluding prepositions and articles from single and multiword format, each descriptor has been placed in one or more of 19 categorical groupings.",
"homepage": "http://eric.ed.gov/?id=ED101492",
"name": "Instructional Materials Thesaurus for Special Education",
"prefix": "1099"
},
"11": {
"abbreviation": "CSH",
"description": "CSH on the Web offers free, up-to-date access to over 6000 subject authority records in the English language, providing in-depth coverage of Canadian topics, including those recently in the news. Canadian Subject Headings (CSH) is a list of subject headings to access and express the subject content of documents on Canada and Canadian topics.",
"homepage": "https://www.bac-lac.gc.ca/eng/services/canadian-subject-headings/Pages/canadian-subject-headings.aspx",
"name": "Canadian Subject Headings",
"prefix": "11",
"wikidata_database": "Q5030602"
},
"110": {
"description": "While developing terminology for application to the moving image holdings of archives and libraries, the Moving Image Genre-Form Guide follows the traditional methods of film and television scholarship as closely as possible. The vast and steadily growing literature of genre studies has been relied upon: hundreds of books and many more articles authored on genre theory, as well as analyzing specific genres. In addition, the many genre and content lists that archives have developed over the years were examined, along with such other indexing tools as the retrospective indices to the writing on film, the terms in each volume in the American Film Institute Catalog series, and commercial guides to videos. Nonetheless, with the broad range of types of moving image works, there is no single, ready resource to appropriate for a guide to such terms in their archival application. Utilizing this range of previous work, a committee within the Motion Picture/Broadcasting/Recorded Sound Division has compiled a comprehensive, practical guide to moving image genre and form terminology ever created, covering some 150 terms, all fully defined and exemplified. However, in addition to fulfilling the needs of archivists and librarians, a guide to genre-form terms must also satisfy such other interested groups as moving image scholars and filmmakers. In order to be widely comprehensible to researchers, a guide should offer terms and definitions conforming to general classification practice. Since searches of online databases will be increasingly conducted over the internet, instead of with the assistance of reference librarians, the Moving Image Genre-Form Guide aims to promote the likelihood of outside researchers finding the desired bibliographic records through use of the basic terms in the field. With each term, we have provided a definition, describing conventions of story construction, character types, and setting, and, as necessary, additional definitional notes that indicate related or overlapping genres, and other considerations when applying the term. For nearly every genre and form, a variety of examples from different periods and nations are given. The examples are meant to be both typical of the genre as well as to indicate its breath, themes, and significant sub-types. The very comprehensiveness that is the hallmark of the Moving Image Genre-Form Guide will give it additional value beyond those involved in cataloging and inventorying moving image works. The issues encountered in developing such a guide encompass many of the same problems that academia tackles in classes and research. Just as the Moving Image Genre- Form Guide has followed the literature of genre studies, this guide may also be able to make a contribution to such scholarship. Since the archival perspective frequently extends beyond some of the more abstract, theoretical discourse and the possibilities traditionally recognized for critical generic analysis, scholars may benefit from a project that necessarily applies to all forms and periods, with a greater emphasis on marginal genres. The Moving Image Genre-Form Guide may be of value in pinpointing categories that are worthy of further study but have been previously neglected or overlooked, as genres that have not received critical recognition become evident in the cataloging of archival holdings. There are entire undertheorized areas that must be incorporated, such as genres specific to television, from Home shopping to Public access. To facilitate recognition from researchers, we have included categories for some little-known genres that represent significant, unavoidable generic groups of archival holdings. Thus the Moving Image Genre-Form Guide can achieve a positive and exciting exchange between the academic and archival communities, in addition to its practical value as an indexing tool to scholars searching the archives.",
"homepage": "http://www.loc.gov/rr/mopic/miggen.html",
"name": "The Moving Image Genre-Form Guide",
"prefix": "110"
},
"1100": {
"description": "ANASTASIA is a documentary network specializing in psycho-social sciences, health promotion, nursing, office and business management, sustainable development, psychomotricity, agronomy, hotel management, poverty , In matters related to immigration, North-South relations, pedagogy.",
"homepage": "http://anastasia.province.namur.be/ListRecord.htm?list=table&%3Btable=5",
"prefix": "1100"
},
"1101": {
"description": "The library is a major player in the acquisition and sharing of knowledge. It provides organizational, technological and educational support to clients through a documentary watch on new health, through the acquisition of periodicals, books and Purchase of databases to meet the needs.",
"homepage": "http://catalogue.cssslaval.qc.ca/ListRecord.htm",
"name": "Thesaurus Library of the Center for Health and Social Services of Laval",
"prefix": "1101"
},
"1102": {
"description": "The research activities of the Laboratory of Solid Physics cover a broader field than its title would suggest, and we are interested in condensed matter in all its diversity, even if we like to group our activities According to three main axes, involving a roughly equivalent number of researchers: New electronic states of matter, Physical phenomena with reduced dimensions, Soft matter and physical-biological interface.\n\nIn the first axis, there are both experimental and theoretical studies relating to the properties of correlated fermions (superconduction, magnetism, metal-insulating transition, etc.)\n\nIn the second category, activities falling within the broad sense of 'nanosciences'. They are discussed here from the point of view of fundamental properties, when the dimensions of an object become as small as certain characteristic distances (coherence length, mean free path, ...).\n\nFinally, the third axis extends the concept of \"soft matter\" to biological systems. Themes range from complex systems to living tissues, from liquid crystals to foams, to polymers or granular systems. These physical studies at the interface touch physico-chemistry and biology.",
"homepage": "https://kentika.lps.u-psud.fr/ListThesau.htm",
"name": "Thesaurus Laboratory of Solid Physics",
"prefix": "1102"
},
"1103": {
"description": "ONIRIS is an institution of higher education and research of the Ministry of Food of Agriculture and Fisheries. Anchored in its territory and open to the European space, it has a very wide range of topics including Animal health and public health, clinical, biomedical and health biotechnology, food science and process engineering. The aim of ONIRIS is to be an actor in the fields of animal and human health, Actively contributing to the concept of 'one medicine, one health' and food. To these two main themes, there is also a contribution to a cross-cutting theme concerning environment and sustainable development.",
"homepage": "http://kentika.oniris-nantes.fr/ListRecord.htm",
"name": "Thesaurus Oniris Chantrerie",
"prefix": "1103"
},
"1104": {
"description": "ONIRIS is an institution of higher education and research of the Ministry of Food of Agriculture and Fisheries. Anchored in its territory and open to the European space, it has a very wide range of topics including Animal health and public health, clinical, biomedical and health biotechnology, food science and process engineering. The aim of ONIRIS is to be an actor in the fields of animal and human health, Actively contributing to the concept of 'one medicine, one health' and food. To these two main themes, there is also a contribution to a cross-cutting theme concerning environment and sustainable development.",
"homepage": "http://kentika.oniris-nantes.fr:8002/ListRecord.htm",
"name": "Thesaurus Oniris Géraudière",
"prefix": "1104"
},
"1105": {
"description": "The specificity of the curriculum given at the Bosio Pavilion is to provide its students with a versatile training in Art & Scenography and to give them the tools they need to translate their personal research into the spaces of the stage as well as those of the exhibition .",
"homepage": "http://www.pavillonbosio-bibliotheque.com/ListThesau.htm",
"name": "Thesaurus Pavillon Bosio - Higher School of Plastic Arts",
"prefix": "1105"
},
"1106": {
"description": "Since it exercises the authority of the Overseas State in the Overseas Departments, its powers are those exercised by the Ministry of the Interior in metropolitan France. New Caledonia and the other territorial collectivities, it exercises the authority of the State in compliance with the statutes and the organization of these territories ... Through the financing of social housing, (...) Coordination of the action of the Ministries which intervene overseas in specific fields (for example: education, culture, youth and sports, etc.) or to work to promote the integration of young people in the Overseas Departments. To its economic and social development (eg industry, agriculture, employment, etc.).",
"homepage": "https://documentation.outre-mer.gouv.fr/ListThesau.htm",
"name": "Thesaurus Overseas",
"prefix": "1106"
},
"1107": {
"description": "The National Veterinary School of Alfort is a public and administrative institution of higher education and research under the supervision of the Ministry of Agriculture, Food and Forestry and maintains strong ties with the University of Paris -Est, ANSES, INRA, INSERM.",
"homepage": "http://bibliotheque.vet-alfort.fr/ListThesau.htm",
"name": "Thesaurus National Alpine Veterinary School",
"prefix": "1107"
},
"1108": {
"description": "The Integrated Center for Information Management (CIGI) is a unique documentation center specializing in physical disability accessible from a distance. Its extensive collection includes nearly 4,500 documents and 200 periodicals.",
"homepage": "http://www.cigi.irdpq.qc.ca/ListRecord.htm",
"name": "Thesaurus Integrated Center for Information Management",
"prefix": "1108"
},
"1109": {
"description": "The Alpha Collective has been organizing literacy courses for adults, men and women for the past 40 years, from the age of 18. More than 600 people a year, over 40 nationalities, attend the evening or evening classes, Saint-Gilles, Forest and Molenbeek. the Collectif Alpha also part of the literacy network associations 'Read and Write', participates in training literacy trainers and manages a specialized documentation center.",
"homepage": "http://www.cdoc-alpha.be/ListThesau.htm",
"name": "Thesaurus Collective Alpha",
"prefix": "1109"
},
"111": {
"description": "Applied in the online catalog 'PasseparCirque' of the 'Cirquotheque'. This library contains various documents on circus arts and siblings.",
"homepage": "http://www.passeparcirque.com/pmb/opac_css/index.php?lvl=index",
"name": "Thesaurus Circus",
"prefix": "111"
},
"1110": {
"description": "The development of the NCHEM taxonomy came about because of a need for standardized and comprehensive structures for cataloging and organizing information on the multitude of instructional programs and activities presently functioning in the various levels and sectors of education. Although considerable effort has gone into the development of the NCHEMS postsecondary education\n\nsubject matter taxonomy, the final result is not entirely satisfactory. This is due in part to inadequacies in the foundations upon which the proposed taxonomy has been based (that is, two existing taxonomies, both of which have internal inconsistencies) and in part to the restriction of the taxonomy to a four-digit coding structure. This proposed taxonomy has not attempted to resolve these issues but does seek to lay out issues and alternatives for consideration by others who may be concerned with the development of subject matter taxonomies.",
"homepage": "http://eric.ed.gov/?id=ED125382",
"name": "A Proposed Taxonomy of Postsecondary Education Subject Matter Areas",
"prefix": "1110"
},
"1111": {
"description": "The Thesaurus lists the authority name, nicknames (including military and civilian titles), use for names, related planet (usually homeworld), political alliance/related alliance, and related characters for each Principal Character. Nicknames will appear only under the main entry, and will not have a separate entry traced to the main entry. The Thesaurus is limited to Principal Characters only, as the many minor or supporting characters frequently lacked enough descriptive information to be included in the Thesaurus categories. Occasionally a Principal Character will appear in the Other Character category for a particular novel, but are included in the Thesaurus in their capacity as Principal Characters.",
"homepage": "http://files.eric.ed.gov/fulltext/ED413911.pdf",
"name": "Star Wars Thesaurus",
"prefix": "1111"
},
"1112": {
"description": "This controlled vocabulary comprising approximately 1,030 terms commonly used in the field of international development communication was created by the Clearinghouse on Development Communication of the Academy for Educational Development to analyze and index documents. This standard list of terms, designed to provide subject access to information in this area, was constructed by extracting key concepts from relevant documents. The initial list was revised after testing for precision and recall, and reviews by clearinghouse personnel and other subject experts. Arranged in alphabetical order with cross references, the controlled vocabulary has several features. Terms accepted for indexing and searching are printed in upper case letters and are called descriptors; synonyms appear in lower case letters and are not valid descriptors. Symbols appearing under descriptors are used to direct the searcher to a preferred term, clarify meaning, and indicate relationships of terms. Some proper names of countries and international organizations appear in the thesaurus as identifiers, and 'pubtypes' identify types of documents. It is recommended that the most specific terms available to fit the specificity of the document be assigned, and that the real content of the document be indexed. Procedures for updating the thesaurus and thesauri consulted are included.",
"homepage": "http://eric.ed.gov/?id=ED208834",
"name": "Thesaurus of Development Communication",
"prefix": "1112"
},
"1113": {
"description": "A research project undertook to develop a system whereby information could be exchanged about exemplary secondary school programs within California. A survey was sent to 375 randomly selected districts throughout the State requesting information about model programs dealing with any of the following: curriculum, staffing patterns, office organization, gifted programs, slow learner programs, programs for the emotionally disturbed, individualized learning, advisory committees, career and vocational education, the use of department chairmen, or other innovative programs. The returned data were organized into a taxonomy of educational programs in order to facilitate easy retrieval. The six major categories of 1) alternative education, 2) career-vocational education, 3) curriculum, 4) instructional techniques, 5) management, and 6) special education were developed; subcategories were constructed for each of the foregoing and programs arranged alphabetically in each class. Each of the more than 800 citations in the taxonomy supplies information on the program's title, a description of its features, the district's name, location and chief characteristics, and the person to contact for additional details.",
"homepage": "http://eric.ed.gov/?id=ED089710",
"name": "Taxonomy of Exemplary Secondary School Programs in the State of California",
"prefix": "1113"
},
"1114": {
"description": "This is a hierarchical decimal classification of information related to various types of carcinogenesis (Chemical, viral, hormonal, radiation), cancer demography, and selected descriptive and 'in vitro' aspects of cancer pathology. It is a working draft of categories taken from an extensive classification of many fields of biomedical information. Because the classification identifies very small areas of cancer information, it can be used for precise matching of cancer researchers with useful documents or data in information systems, and for detailed analysis of large cancer research programs.",
"homepage": "http://eric.ed.gov/?id=ED070467",
"name": "Cancer Etiology and Selected Aspects of Cancer Pathology: A Decimal Classification",
"prefix": "1114"
},
"1115": {
"description": "This is a hierarchical decimal classification of information related to cancer biochemistry, to host-tumor interactions (including cancer immunology), and to occurrence of cancer in special types of animals and plants. It is a working draft of categories taken from an extensive classification of many fields of biomedical information. Because the classification identifies very small areas of cancer information, it can be used for precise matching of cancer researchers with useful documents or data in information systems, and for detailed analysis of large cancer research programs.",
"homepage": "http://eric.ed.gov/?id=ED070468",
"name": "Cancer Biochemistry and Host-Tumor Interactions: A Decimal Classification",
"prefix": "1115"
},
"1116": {
"description": "The classification may be used (1) to identify cancer research efforts supported by NCI in selected areas of research (at any general or specific level desired), (2) to store information related to cancer research and retrieve this information on request, and (3) to match interests of cancer research scientists against information in published articles so that scientists can receive copies of articles specifically related to their research (Selective Dissemination). The outline of major categories for cancer research information is as follows: 51.1 Selected general topics related to cancer research, 51.2 Clinical aspects of diagnosis and treatment, 51.3 Pre-clinical aspects of diagnosis and treatment, 51.4 Cancer epidemiology, etiology, carcinogeneses, 51.5 Cancer pathology, related physiology, cytology, and tissue culture studies, 51.6 Biochemistry of tumors and tumorbearing hosts, 51.7 Host-tumor interactions, and 51.8 Cancer in specific types of host.",
"homepage": "http://eric.ed.gov/?id=ED025270",
"name": "Hierarchical Decimal Classification of Information Related to Cancer Research",
"prefix": "1116"
},
"1117": {
"description": "Almost all disciplines make extensive use of the resources provided by slide libraries and picture collections. Growing demands for pictorial material have stimulated a concern for making slide and picture collections more useful and more usable by better physical arrangement and more thorough indexing. The system provides a classification scheme for the organization of general collections of slides and pictures with a broad subject coverage as opposed to the more typical slide classification system which deals with a single subject field. A suggested method of automatic indexing is included. This document will be useful to builders of general collections, and is published as a tool for libraries and other collectors of slides and pictures who have had no ready-made system of classification available.",
"homepage": "http://eric.ed.gov/?id=ED048879",
"name": "Slide Classification System for the Organization and Automatic Indexing of Interdisciplinary Collections of Slides and Pictures",
"prefix": "1117"
},
"1118": {
"description": "The introductory section of the paper expresses its purpose: to devise a classification scheme for career education resource material, which will be used to develop the USOE Office of Career Education Resource Library and will be disseminated to interested State departments of education and local school districts to assist them in classifying their own career education resource materials. The second section of the paper describes the classification of career education resource material, revised after critiquing by 50 randomly selected career education practitioners. The third section describes the classification scheme, defines the nine cataloging terms used, and lists the 40 key descriptors utilized in the filing system. The classification headings are discussed to eliminate confusion of terms. The fourth section describes the use of the key descriptors and card catalog for the purpose of searching and retrieving needed material, and the storage problem is discussed. Section five explains how the index card is designed for conversion to computer card, and the main advantages of a computer system of retrieval are discussed. Brief descriptions of discipline and content areas, of special groups, and of types of materials are appended, as well as a sample index card.",
"homepage": "http://eric.ed.gov/?id=ED110829",
"name": "Classification Scheme for Career Education Resource Materials",
"prefix": "1118"
},
"1119": {
"description": "The development of a new scheme for classifying the more than 7,000 documents on reading in the ERIC/CRIER data collection is described. An original scheme, developed in the early days of the clearinghouse, provided a means for listing documents in any of 45 broad subject categories in the field of reading and for identification by grade level. The system was found to be inadequate in that it did not permit sufficient precision for effective retrieval. The newly developed classification scheme proposes 27 classes into which documents can be divided. Each of these uses a numerical schedule which includes subclasses and provides means of adding more as needed. Further classification by grade level, source of material, type of material, and date of publication is also provided through a faceting technique. To facilitate use of the classification scheme, an index was developed which alphabetically lists terms included in the scheme. Testing of the scheme by ERIC/CRIER personnel was carried out on a 200-document sample, and comparisons were made of their notations. Overall agreement of better than a designated standard of 60 percent was determined for 77 percent of the documents, with higher agreement noted in individual parts of the notation. Illustrations of aspects of the scheme are included.",
"homepage": "http://eric.ed.gov/",
"name": "The Development of a Classification Scheme for Reading Research and Reading Resources",
"prefix": "1119"
},
"112": {
"description": "The thesaurus of the designation develops in a methodical form the 1135 terms useful for the designation of architectural works and the 2529 useful for the designation of the movable works The organization proper to the thesaurus thus makes it possible to situate each term in a hierarchy whose entries Are categorized according to functional categories related to religious, funeral, industrial, etc. It also includes all necessary references, summary definitions, use notes, etc. The American and English equivalents used in the The Art and Architecture Thesaurus and the Royal Commission on the Historical Monuments of England, as well as the Italian translation of the descriptors by the Istituto Centrale per il Catalogo e la Documentazione, pave the way for an international consultation Of data, facilitated by the development of electronic communication networks. These terms allow the indexing of ensembles, buildings and aedicules, analyzed in the French heritage database, the MΓ©rimΓ©e national database. As to the terms of the designation of movable works, they allow the indexing of architectural elements, stained-glass windows, furniture, objects, musical instruments, sicnetific instruments, industrial machines and boats analyzed in the database on French heritage, National Palissy.",
"license": "CC BY-SA 3.0",
"name": "Thesaurus for the Designation of Architectural and Structural Works",
"prefix": "112",
"wikidata_database": "Q3527385"
},
"1120": {
"description": "The Authority's classification plan is a hierarchical and logical structure composed of groupings and sub-groupings based on the processes and activities of the organization.",
"homepage": "http://www.lautorite.qc.ca/fr/plan-classification-doc-admin-corpo.html",
"license": "CC-BY-3.0",
"name": "Classification plan of the AutoritΓ© des MarchΓ©s Financiers",
"prefix": "1120"
},
"1121": {
"description": "This Thesaurus pulls together all the knowledge acquired in the development of ET until now, to update the existing inventory of the terms in this field and to make up a complete list (as complete as it is virtually possible) of the current terms describing all the areas of ET, to single out separate areas of ET and to structure it as a special field, to differentiate between separate phenomena and specify the meaning of the existing terms, and also to give the educators, researchers, students, developers of educational software and educational administrators the tool for understanding and using ET. (...)\n\nThis Thesaurus can be used by researchers in the areas of Educational Technology and education in general, by technology-practicing teachers and faculty, by the students of Schools and Colleges of Education, by designers and developers of educational software and courseware, and editors of relevant books and journals. Thesaurus can serve regulatory, standardizing goals (for professional to correctly use the terms), educational goals (teaching students and educators at large the field of ET and its terminology), and research (to define the structure and contents of the ET field and its units).",
"homepage": "http://eric.ed.gov/?id=ED445666",
"name": "Thesaurus of Educational Technology Terms and Their Collocations",
"prefix": "1121"
},
"1122": {
"description": "Presented in this thesaurus are keywords and cross references for the indexing and retrieval of outdoor recreation literature. It was compiled to facilitate the development of a common language for outdoor recreation planning, programming, research, and resource management. Terms selected are pertinent to both the natural and physical resources, their value, management, development, and user requirements. The format consists of six sections: (1) alphabetical list of terms with notes showing broader term (BT), narrower term (NT), scope note (SN), preferred term (USE), and UF meaning used for or instead of another term or concept; (2) straight alphabetical listing of terms; (3) display of terms alphabetically within 26 subject categories; (4) grouped array of terms rotated within each of the 26 groups; (5) a rotated array of all terms; and (6) a classified arrangement of terms based on the major categories: (a) Outdoor Recreation Resources and Facilities, (b) Administration, (c) Recreation Activities, Equipment, and Users, (d) Economic Aspects, and (e) Supporting Information. An explanation of sample listings is given together with suggestions for using the thesaurus.",
"homepage": "http://eric.ed.gov/",
"name": "Thesaurus of Outdoor Recreation Terms",
"prefix": "1122"
},
"1123": {
"description": "This list of program types and keywords (with codes) was prepared for program officers at the National Endowment for the Humanities, the National Institute of Education, and the National Science Foundation to use when preparing program announcements and requests for proposals. Staff persons responsible for screening such documents at colleges and universities may then use the codes to identify which of the faculty at their institutions should be notified. Twenty-four program types are listed for coding funding announcements or solicitations to indicate the type of activity which may be supported. A Keywords Categorical List includes geographic terms which may either be the subject of research or a project location. The remaining keywords are divided into nine broad categories representing major classifications: (1) agriculture/food sciences/food; (2) arts/humanities/cultural activities; (3) behavioral/social sciences; (4) education; (5) engineering; (6) health and safety; (7) law; (8) management/commerce; and (9) science and technology/mathematics/computer science. An \"other\" category includes fire/flammability studies, military science/military history/peace/amnesty, recreation and leisure studies, and university/industry cooperative activities.",
"homepage": "http://eric.ed.gov/",
"name": "Keyword Thesaurus. A List of Terms and Codes to Identify Areas of Interest for Research and Other Types of Sponsored Programs",
"prefix": "1123"
},
"1124": {
"description": "The thesaurus contains approximately 4,000 terms used in indexing material for the National Center on Child Abuse and Neglect. It is explained that the descriptor compilation was first developed in 1975 from existing thesauri and dictionaries. Descriptors are arranged in alphabetic, permuted and group displays, and listings include references to broader, narrower and related terms.",
"homepage": "http://hdl.handle.net/2027/umn.31951p009635332",
"name": "Child Abuse and Neglect Thesaurus",
"prefix": "1124"
},
"1125": {
"description": "This thesaurus was designed for users of the Adult and Continuing Education Research Collection in Syracuse University (New York), which contains the archives of organizations and individuals central to the development of adult education as a field of study and practice. The thesaurus serves the historical and archival adult education materials of a specific place and is collection specific: the work represents the archive it serves. The thesaurus consists of three displays: conceptual, alphabetic, and rotated. The conceptual and rotated displays show only preferred terms (usable), whereas the alphabetic display consists of preferred and nonpreferred terms. The conceptual display indicates relationships among terms as they occur in the archive. The alphabetic display comprises the preferred terms, entry terms, scope notes, hierarchical relationships, and those of equivalence and of association. The rotated display indexes each word of both single and multiword preferred terms in alphabetical sequence.",
"homepage": "http://eric.ed.gov/",
"name": "Kellogg Adult Education Thesaurus",
"prefix": "1125"
},
"1126": {
"description": "Der Thesaurus umfasst einen systematischen und einen alphabetischen Teil. Der systematische Teil ist das 'HerzstΓΌck' dieses Dokuments. Er enthΓ€lt die wesentlichen Informationen, die fΓΌr den Benutzer bedeutungsvoll sind, sofern er nicht selbst Dokumentationsarbeit leistet. Bei der Verschlagwortung der VerΓΆffentlichungen, die in die Dokumentation aufgenommen werden, ist der alphabetische Teil notwendig, damit man sich schnell darΓΌber informieren kann, welche Begriffe fΓΌr die Einordnung bestimmter Aussagen zur VerfΓΌgung stehen. Der systematische Teil erlaubt es, sich eingehend und ΓΌbersichtlich ΓΌber das System zu orientieren, nach dem die Einordnung der Dokumente vor sich geht. Er ist in acht Kategorien eingeteilt.",
"homepage": "http://eric.ed.gov/",
"prefix": "1126"
},
"1127": {
"description": "This is a thesaurus of terms used in evaluation. It is not restricted in scope to educational or program evaluation. It refers to product and personnel and proposal evaluation as well as to quality control and the grading of work samples. The text contains practical suggestions and procedures, comments and criticisms, as well as definitions and distinctions. The criteria for inclusion of an entry were that at least a few participants in workshops or classes requested it; a short account was possible; the account was found useful; or the author thought it should be included for the edification or amusement of professionals and/or amateurs. Only key references are provided. The scholar may find more references in the few that are given as that was a criterion for selection.",
"homepage": "http://eric.ed.gov/",
"name": "Evaluation Thesaurus",
"prefix": "1127"
},
"1128": {
"description": "This thesaurus is designed to provide the vocational education community and its relevant audiences with a comprehensive, organized listing of outcome questions and hypotheses. The first of two sections includes a discussion of the importance as well as problems of attempting to develop a classification system for categorizing vocational outcomes. It also explains how the outcome questions are classified and how the reader can locate outcome questions of interest. The second section contains 252 outcome questions categorized into three areas: (1) outcome questions having the individual as the affected entity, (2) outcome questions having social entities or society-in-general as affected entities, and (3) outcome questions having special needs sub-populations as affected entities. Outcome questions are further categorized according to educational level, and those that are economically or occupationally related and those non-economically related. Also included is an index of specific topics which identifies related outcome questions.",
"homepage": "http://eric.ed.gov/",
"name": "Vocational Education Outcomes: A Thesaurus of Outcome Questions",
"prefix": "1128"
},
"1129": {
"description": "This taxonomy provides a structure for identifying human factors for the purpose of scientific research and system test and evaluation. The information contained in this document is provided as guidance, not mandated as direction. This taxonomy can be considered during the planning, conduct, and analysis of human factors. The objectives of this taxonomy are to: (1) identify an extensive list of human factors, (2) promote commonality in nomenclature and units of measurement, and (3) enable the development and use of a common human-factors taxonomy for data collection and data processing. The purpose of this Guide is to aid the reader in identifying human factors. The reader is assumed to have a basic knowledge of experimental design, statistics, and human performance. This Guide may also be used for task analysis. The purpose of analyzing performance of selected tasks, subtasks, and task elements contained in the task inventory by addressing the lowest taxonomic level specified by the procuring activity is to describe task performance in terms of human performance time and accuracy. The product of the analytic effort is intended for use in support of equipment design, testing and evaluation, training requirements identification, manning and workload assessment, development of training and maintenance manuals, and other documentation and reporting.",
"homepage": "http://tg.hfes.org/astg/Human%20Factors%20Taxonomy.docx",
"name": "Human-Factors Taxonomy",
"prefix": "1129"
},
"113": {
"homepage": "http://www.culture.gouv.fr/culture/inventai/telechar/thesau_objets.pdf",
"name": "Thesaurus of Household Objects",
"prefix": "113"
},
"1130": {
"description": "A classification scheme is given for materials related to occupational and educational opportunities collected by the Rutgers College Placement Office Library. The scheme assigns a four digit number to each item. The first digit designates which of the library's general areas the material covers: general, occupational, educational, or one of the special areas to be designated in the future. The second and third digits broadly and then more specifically define the educational areas dealt with or assumed as the background for the occupation covered. The fourth digit indicates geographic location. The classes are listed and defined, provisions for expansion are indicated, and class numbers are given for 74 occupations.",
"homepage": "http://eric.ed.gov/?id=ED130676",
"name": "A Classification System and Manual for Placement Office Libraries",
"prefix": "1130"
},
"1131": {
"description": "Shelf classification of the ZBSport",
"homepage": "http://www.dshs-koeln.de/zentralbibliothek/recherche-kataloge/aufstellungssystematik/",
"name": "Shelf classification of the Central Library of Sports Sciences",
"prefix": "1131"
},
"1132": {
"description": "Microthesaurus Tesqual is a controlled vocabulary with a structure based on hierarchical, associative and equivalence relationships. It is aimed at scientists, researchers, education professionals, students and the general users who use a 'key' vocabulary to conceptualize and define the content of specific documents. The final aim is to help experts store and recover these documents coming from a particular information system.",
"homepage": "http://cdn.intechopen.com/pdfs-wm/11618.pdf",
"name": "Tesqual",
"prefix": "1132"
},
"1133": {
"description": "The Maritime Knowledge Centre (MKC) provides collections, information resources and services to support the IMO Secretariat, Member States, representatives and delegates. Its specialized collections comprise the archives of official documents and IMO Publications. The MKC also collects resources covering maritime affairs, shipping and other subjects relevant to the work of the Organization.",
"homepage": "http://www.imo.org/KnowledgeCentre/Search%20the%20Online%20Catalogue%20SeaLibrary/Documents/Thesaurus.pdf",
"name": "IMO Thesaurus",
"prefix": "1133"
},
"1134": {
"description": "The Pro Senectute Library is Switzerland's largest media and information center on the topics of age, aging and generational relationships. It is open to the public and is supported by the Swiss Social Insurance Office.",
"homepage": "http://www.bibliothek.pro-senectute.ch/uploads/media/150122_Schlagwortliste_01.pdf",
"name": "Keyword list of the Pro Senectute library",
"prefix": "1134"
},
"1135": {
"description": "We keep our Subject Headings simple and limited to fewer than 100, so we can index law review articles quickly and get the Current Index to Legal Periodicals (CILP) into your hands as soon as possible.",
"name": "Current Index to Legal Periodicals Subject Headings",
"prefix": "1135"
},
"1136": {
"description": "The good old ViBI can still be used for a transitional period for orientation about the stock (works created until March 2010). The order of the works on the basis of the old classification is, however, obsolete, since the new library contains the Regensburg classclass (. ..).",
"homepage": "http://is.uni-sb.de/vibi/klassif.html",
"name": "Classification Scheme of the Institute Library Information Science",
"prefix": "1136"
},
"1137": {
"description": "1) The following subject categories were not included in the keyword list: Keywords (example: Kisch, Egon Erwin), Geographical / Ethnographical Keywords (example: Germany; (Example: SaarbrΓΌcken / University), title words (example: the computerization of the company / Nora, Simon), that is, in this keyword list there are only keywords.\n\n2.) The keywords were taken into account: rules according to the keyword catalog (RSWK). After that, keywords must also be recorded according to the new spelling. Pre-Combined Keywords * start in the first word with a large initial letter as they present the heading character. Application of the new German spelling in terms of German and foreign language components. Application of professional reference books, generalcyclopedia, Duden dictionary. English terms, which are naturalized in German, are subject to German spelling. For the sake of form, these were written in small letters (except the initial letter in the first word), since a selection according to naturalized and not naturalized terms is too time-consuming. Foreign language composites, which were not to be found in the dictionary, spelling of the German language, not in specialist reference books and not in generalcyclopedia, the hyphenation rules of the corresponding language were applied. For example: information retrieval but: information retrieval system\n\n3.) In order to avoid confusion, ambiguous keywords (homonyms) were provided with corresponding additions. Example: Java Β«Programming languageΒ»\n\n4.) In order to improve the depth of information, many abbreviations were also provided with corresponding additions. For example, ASP Active Server Pages",
"homepage": "https://saar.infowiss.net/vibi/schlagw/",
"name": "List index of the institute library information science",
"prefix": "1137"
},
"1138": {
"description": "The National Clearinghouse on Aging Thesaurus provides a retrieval vocabulary for the document collection currently housed at the Administration on Aging. It also provides, through its structure, a means for adding new terms and new word relationships as new material is acquired.",
"homepage": "http://hdl.handle.net/2027/uiug.30112048976390",
"name": "National Clearinghouse on Aging Thesaurus",
"prefix": "1138"
},
"1139": {
"description": "The List itself is not exhaustive, nor is it meant to be. For the subjects represented all practically useful 'see' (x) references and 'see also' (sa) references have been added but not all of them need to be used. However, it seems desirable to make them available particularly for the cataloger whose experience has been somewhat limited. A few international law, comparative law and foreign law subjects have been included because they seem to be needed regardless of the size of the collection. (...) In addition a limited number of non-legal subjects are included not only because of the fairly broad scope of the collection at the Northwestern University Law School but because to an increasing extent legal collections are including materials in related areas. Among such additional headings are the following: Biology, Eugenics, Heredity, Logic, Mathematics, Physics, Thought and thinking, etc.",
"homepage": "http://hdl.handle.net/2027/mdp.39015033887996",
"name": "List of Subject Headings for Small to Medium Sized Law Libraries",
"prefix": "1139"
},
"114": {
"abbreviation": "TGM",
"description": "The thesaurus includes more than 7,000 subject terms and 650 genre/format terms to index types of photographs, prints, design drawings, ephemera, and other pictures. In 2007, the subject and genre/format vocabularies, previously maintained separately, were merged into a single list and migrated to new software, MultiTes. The Thesaurus for Graphic Materials is a tool for indexing visual materials by subject and by genre/format.",
"homepage": "http://www.loc.gov/pictures/collection/tgm/",
"name": "Thesaurus for Graphic Materials",
"prefix": "114"
},
"1140": {
"description": "The Moys Classification Scheme is a system of library classification for legal materials. It was designed by Betty Moys and first published in 1968. It is used primarily in law libraries in many common law jurisdictions such as Canada, Australia, New Zealand, and the United Kingdom.",
"homepage": "http://www.library.uow.edu.au/eresources/UOW026516.html",
"name": "Moys Classification Scheme",
"prefix": "1140",
"wikidata_database": "Q17125789"
},
"1141": {
"description": "The documents of the collection of our library are not indexed, but are classified by means of the legal classification of French-speaking Switzerland. This one, compound of a combination of letters and of figures, aims at describing the intellectual contents of the document. It is possible to make a research by classification in the Explore tool.",
"name": "Legal Classification of French-Speaking Switzerland",
"prefix": "1141"
},
"1142": {
"homepage": "http://www.unige.ch/lettres/alman/index.php/download_file/view/215/244/",
"name": "Classification Modern literature",
"prefix": "1142"
},
"1143": {
"homepage": "http://www.unige.ch/lettres/alman/index.php/download_file/view/40/244/",
"name": "Classification Literature Middle Ages",
"prefix": "1143"
},
"1144": {
"homepage": "http://www.unige.ch/lettres/alman/index.php/download_file/view/370/244/",
"name": "Linguistic Classification",
"prefix": "1144"
},
"1145": {
"description": "Classification reference works and dictionaries and bibliographies",
"homepage": "http://www.unige.ch/lettres/alman/index.php/download_file/view/108/244/",
"name": "Classification reference works / dictionaries / bibliographies.",
"prefix": "1145"
},
"1146": {
"homepage": "http://www.unige.ch/lettres/alman/index.php/download_file/view/68/244/",
"prefix": "1146"
},
"1147": {
"description": "NILS INsource is a Web-based regulatory research tool designed exclusively for insurance compliance professionals. By leveraging INsourceβs insurance terminology indexing, line-of-business searching, and compliance topic and subtopic categories, compliance professionals can obtain focused, accurate content in significantly less time-vastly enhancing your firmβs compliance efforts. More than 10,000 insurance professionals and departments in all 50 states, the District of Columbia, Puerto Rico, and the U.S. Virgin Islands rely on NILS INsource as a definitive primary content resource.",
"homepage": "https://insource.nils.com/includes/thesaurus/Thesaurus-A.htm",
"name": "NILS INsource Insurance Thesaurus",
"prefix": "1147"
},
"1148": {
"description": "The T.M.C. Asser Instituut is a foundation (registered on 17 February 1994 with the Chamber of Commerce Haaglanden, The Netherlands, under file number 41158427) with the purpose of performing and maintaining scientific research and education in the areas of international and European law. It is a non-profit organisation, primarily funded by the Dutch Ministry for Education, Culture and Science and administered through the University of Amsterdam.\n\nLocated in the βinternational zoneβ of The Hague β the City of Justice, Peace and Security, the Institute is a unique clustering of knowledge and experience in scholarly research, education and training, knowledge management and dissemination, publishing and academic community organising.\n\nThe Instituteβs international community of scholars is engaged in research, postgraduate training and dissemination of knowledge in furtherance of the purposes and principles of international law. This inter-university Institute cooperates closely with and supports the Dutch universitiesβ activities in the relevant disciplines and is in turn vastly networked to universities and institutions, governments and NGOs on a global level.",
"homepage": "http://www.asser.nl/upload/pil-webroot/documents/cms_pil_2_1_classification.pdf",
"name": "T.M.C. Asser Instituut Classification Scheme",
"prefix": "1148"
},
"1149": {
"description": "To achieve the implementation of land-use planning and land management cooperation among experts from the disciplines involved and integration of the respective results are required in order to identify and evaluate all biophysical, socio-economic and legal attributes of the land. The glossary aims to contribute to the development of a common technical language in land resources planning and management. The terms, methods and concepts used by the different sectors involved should be understood by all partners in an identical way, independent from their backgrounds and professional experiences.",
"homepage": "http://www.iapad.org/wp-content/uploads/2015/07/landglossary.pdf",
"name": "Terminology for Integrated Resources Planning and Management",
"prefix": "1149"
},
"115": {
"description": "The thesaurus comprises two parts. The first arranges the descriptors by subject fields in an introductory general scheme. The second part of the thesaurus contains an alphabetical list of descriptors. The thesaurus is a documentation language devised for the purpose of analysing works, articles, reports and other documents referring to the problems of mass communication according to the particular medium to which they refer: books, the press, records, films, radio or television. While its main purpose is to characterize the information in a sufficiently precise manner to allow post-storage retrieval of the documents containing it, it has the secondary purpose of enabling queries to be expressed in a form which will match the information available. In addition, by providing a valid basis for the exchange of data between documentation systems, it will allow national or international networks to operate in a fully satisfactory consistent manner. In the social sciences and the humanities there are still relatively few fields in which a documentation language has been tried out in a systematic manner. A thesaurus on communication can reasonably be expected to make a contribution to scientific communication, and it would be a pity if full use were not made of the facilities it provides in this regard to both research workers and practicians, in a sector which social changes have brought particularly to the fore.",
"homepage": "http://unesdoc.unesco.org/images/0001/000150/015031MB.pdf",
"name": "Thesaurus Mass Communication",
"prefix": "115"
},
"1150": {
"description": "This is the first comprehensive classification of the field of Landscape Architecture. It attempts to show in detail both the subjects making up the field, as far as possible in their logical relations and as regarded from various points of view, and also the relation of the field itself to tangent fields. The profession of Landscape Architecture is now so well established, with a background of accomplishment, and public familiarity with the subject and with its literature is now so general, that a classification can be produced with the reasonable certainty that its main divisions will remain permanently useful, and that future developments of the subject can find logical places within the present outline, with changes, if at all, only in some of the minor headings. This classification has been worked out primarily for use with the extensive collections of the Harvard School of Landscape Architecture Library, and has proved increasingly satisfactory through eight years of development and adaptation.",
"homepage": "http://libsysdigi.library.illinois.edu/oca/Books2008-06/landscapearchite00hubb/",
"name": "Landscape Architecture Classification",
"prefix": "1150"
},
"1151": {
"description": "This list of subject headings is used at the Morris Swett Library. It has been compiled by past and present librarians as well as library staffs. Some subject headings have been taken directly from Library of Congress headings. They have been added to and adjusted to meet artillery needs. This product represents a consensus of agreement between artillery specialists and librarians as to the best terminology to use.",
"homepage": "http://www.dtic.mil/cgi-bin/GetTRDoc",
"name": "Subject Headings of the Morris Swett Library",
"prefix": "1151"
},
"1152": {
"description": "This annotated bibliography is focused on contextual theology in Aotearoa New Zealand. It is an amended and updated version of an earlier 2002 article: Contextual theology in Aotearoa New Zealand. Asian Christian theologies: a research guide to authors, movements, sources. J. C. England, J. Kuttianimattathil, J. M. Prior et al. Maryknoll, New York, ISPCK/Claretian Publishers/Orbis Books. 1: 541-598.",
"homepage": "http://hdl.handle.net/2292/447",
"name": "Theology in Aotearoa New Zealand: An Annotated Bibliography under Subject Headings",
"prefix": "1152"
},
"1153": {
"description": "This thesaurus is a presentation of terms to be used for the indexing and retrieval of documents dealing with the subject area of Low Intensity Conflict (LIC). A wide range of documents and reports relevant to LIC were selected, catalogued and indexed from open literature as part of a feasibility study on an Information Analysis Centre (IAC). The Thesaurus of Engineering and Scientific Terms (TEST) was used initially for indexing terms but it became apparent that the subject matter required a broader range of terms in areas not covered comprehensively by TEST. Catalogers added terms as needed and gradually a 'working vocabulary' of something less than one thousand descriptors emerged. This original word list was edited following the rules and conventions adopted for the construction of TEST. Undesirable terms were removed, new ones were added and all hierarchical relationships and cross-references were entered and checked. The present thesaurus contains 950 descriptors and 225 USE references in the Thesaurus of Terms. A more detailed discussion of the process of construction of the LIC Thesaurus (LICT) is available in a separate report. LICT borrows heavily from TEST in format, rules and conventions followed and in many of the descriptors listed. The instructions and explanations about the use of LICT have been patterned after those in TEST.",
"name": "Low Intensity Conflict Thesaurus",
"prefix": "1153"
},
"1154": {
"description": "The DTNSRDC Library Subject Thesaurus, which exists both as a printed document and as an on-line computer file, supports the indexing and retrieval functions of the library's automated storage and retrieval system. The hierarchical structure of the vocabulary permits generic retrieval. For example, a search on NAVAL VESSELS will retrieve documents that had been indexed under all naval ship types. Several 'switching' relationships provide an automatic cross-referencing capability.",
"homepage": "http://www.dtic.mil/cgi-bin/GetTRDoc",
"name": "DTNSRDC Library Subject Thesaurus",
"prefix": "1154"
},
"1155": {
"description": "The PCA Cement and Concrete Thesaurus, a list of accepted terminology for all aspects of cement and concrete, can now be accessed online. The Thesaurus was first compiled by PCA staff in the 1960s, and revised in 1982. With the introduction of computerized library software in the early 1990s, it became possible to reexamine and update the Thesaurus more efficiently, allowing the addition of hundreds of new terms and other changes as new materials have been cataloged. A thesaurus has a very practical purpose. It ensures that authors of research reports, database compilers, and others use consistent terminology when documenting or indexing the material, so that end users can retrieve needed information more efficiently. (...) The PCA Concrete and Cement Thesaurus, a searchable .pdf, is (and always will be) a 'work in progress', due to the continuous introduction of new materials and technologies.",
"homepage": "http://www.cement.org/for-concrete-books-learning/library/pca-cement-and-concrete-thesaurus",
"name": "PCA Cement and Concrete Thesaurus",
"prefix": "1155"
},
"1156": {
"description": "In the fall of 1965, two large projects were set in motion to develop contemporary thesauri in the fields of engineering and science. One was originated by Engineers Joint Council to revise the first edition of its Thesaurus of Engineering Terms (1964); the other, by the Department of Defense, under the sponsorship of the Office of Naval Research and known as Project LEX, which had as its mission the development of the first Department of Defense technical thesaurus. The large number of related and overlapping interests of these two separate projects soon motivated a merging of the efforts. The need for commonality in information systems and in reduction of communication barriers was also a driving force, as was the economic advantage of pooling resources, especially available technical personnel. Preparation and presentation agreements were readily reached and a joint working arrangement made for the two projects to join forces in one operation. Hence, this single work, Thesaurus of Engineering and Scientific Terms, which is also available on magnetic tape, is a thesaurus for both Engineers Joint Council and the Department of Defense.",
"homepage": "http://www.dtic.mil/cgi-bin/GetTRDoc",
"name": "Thesaurus of Engineering and Scientific Terms",
"prefix": "1156"
},
"1157": {
"description": "Biological inspiration for engineering design has occurred through a variety of techniques such as database searches, keyword and antonym searches, knowledge of biology, observations of nature and other 'aha' moments. This research aims to alleviate the knowledge gap problem by providing a link between engineering and biology with a thesaurus. The biologically connotative terms that comprise the thesaurus were collected utilizing an organized verb-noun search; collocated words were extracted from texts based on a functional search word. This thesaurus should enable the engineering and biology communities to better collaborate, create and discover.",
"homepage": "https://dspace.lib.cranfield.ac.uk/bitstream/handle/1826/3719/An_Engineering-to-Biology_Thesaurus_To_Promote_Better_Collaboration_Creativity_and_Discovery-2009.pdf;jsessionid=760331A8860BE6FFEBBF58B013EE7836?sequence=4",
"name": "Engineering-to-Biology Thesaurus",
"prefix": "1157"
},
"1158": {
"description": "DEFTEST now contains 24000 entry terms with 155000 cross references. Approximately 1000 new terms have been added. The meaning or usage of terms and their hierarchies is represented by cross references. The hierarchical display assists in the choice of the most appropriate level of specificity for indexing and retrieval. (...) DEFTEST is not Intended as a comprehensive coverage of the fields of science and technology, but of Defence related topics in those fields, as represented inthe database.",
"name": "Defence Technological and Scientific Thesaurus",
"prefix": "1158"
},
"1159": {
"description": "Categories covered in this hierarchy: Manpower; Recruitment, Selection/Classification/Assignment; Education and Training; Human Resources Management; Organizations; Human Factors Engineering; Information Processing/Cognition; Human Performance; Data Management; Program Management; Defense/Welfare; Personnel; Skills; Task/System Analysis; Quantification/Analysis Techniques; Safety/Environmental Factors; Systems/Equipment; and Media/Documents.",
"homepage": "http://www.worldcat.org/wcpa/oclc/227940825",
"name": "MATRIS Indexing and Retrieval Thesaurus",
"prefix": "1159"
},
"116": {
"description": "Containing 1480 entries from Accordeon to Zvegljica. All terms and hierarchical relationships come from the Library of Congress Subject Headings, 24th edition (2001).",
"homepage": "http://alteriseculo.com/instruments/",
"name": "Thesaurus of Musical Instruments",
"prefix": "116"
},
"1160": {
"description": "This edition, with 3,123 descriptors, includes new terms established since the last publication, in November, 1965. Further, it is presented in the format developed by Project LEX for the Thesaurus of Engineering and Scientific Terms, issued recently by the Department of Defense. The purpose of this thesaurus is to provide a definitive, working vocabulary for the field of civil aviation; its terms or descriptors serve as reference standards for the indexing and retrieval of information. The thesaurus is designed to permit effective specific descriptions of documents on input and answerable search queries on output.",
"homepage": "http://www.dtic.mil/cgi-bin/GetTRDoc",
"name": "Thesaurus of FAA Descriptors",
"prefix": "1160"
},
"1161": {
"description": "Among the features of this third edition of the thesaurus are: (1) Listing of new or not previously listed pharmaceuticals from the above countries. (2) Listing of new uses for previously identified pharmaceuticals. It should be noted that pharmaceutical usages as indicated in this thesaurus are those indicated in the literature of the countries involved, and do not necessarily coincide with US usage of the same compound. (3) Listing of country of origin of both new and previously identified pharmaceuticals whenever possible. The country of origin of the article in which the compound was mentioned is not presumed to be the country in which the compound is marketed under that name. Therefore, many compounds do not have a country of origin listed. (4) Listing of synonymous names for both new and previously identified pharmaceuticals. In accomplishing this objective two methods have been utilized. In some instances the literature specifically states that two compounds are synonymous. In addition, compounds synonymous to the same compound are considered synonymous to each other. Compounds with the same name but with different chemical formulas are listed as separate pharmaceuticals. (5) Identification of 'drugs of choice' in the USSR.",
"homepage": "http://www.dtic.mil/cgi-bin/GetTRDoc",
"name": "Thesaurus for Pharmacological Literature of the U.S.S.R., East European Communist Countries, and People's Republic of China",
"prefix": "1161"
},
"1162": {
"homepage": "http://digital.fides.org.pl/Content/4/tlowg.pdf",
"name": "Keyword dictionary of theology",
"prefix": "1162"
},
"1163": {
"description": "This forest terminology largely follows that contained in the British Commonwealth Forest Terminology, or the Forest Terminology of the Society of American Foresters. Where these references have not been in agreement, the definition more suitable to the condition in Ontario has been used. Certain terms in this glossary either are not found in, or are not in agreement with, these texts. Such terms are marked with an asterisk.",
"name": "Glossary of Forest Terminology",
"prefix": "1163"
},
"1164": {
"description": "The terms and their definitions were collected from publications and by utilising the Internet. Forestry experts were also consulted to provide their input in the case of some of the compiled terms. The terms were taken directly from the identified sources. For some terms more than one source are mentioned. This means that the same definition was found within several literature sources without necessarily indicating the most likely original source of that definition. The listing of several sources referring to the same definition was thought to emphasise that a particular definition is more commonly used in scientific literature.",
"homepage": "http://www.efi.int/files/attachments/publications/ir_06.pdf",
"name": "Compilation of Forestry Terms and Definitions",
"prefix": "1164"
},
"1165": {
"homepage": "https://www.ncforestry.org/teachers/glossary-of-forestry-terms/",
"name": "Glossary of Forestry Terms",
"prefix": "1165"
},
"1166": {
"homepage": "http://www.maced.org/foi/generalforestryglossary.htm",
"name": "Glossary of Common Forestry Terminology",
"prefix": "1166"
},
"1167": {
"description": "We prepared this reference bulletin primarily for forest landowners. We hope it will help owners, foresters, and loggers communicate effectively. Poor communication often results in undesirable management practices. We included forestry terms commonly used in Washington.",
"homepage": "http://extension.oregonstate.edu/deschutes/sites/default/files/terminology_for_forest_owners_-eb1353.pdf",
"name": "Terminology for Forest Landowners",
"prefix": "1167"
},
"1168": {
"description": "You are a member of an important group. Together, the private, nonindustrial timberland owners control most of our state's timber resources. You and other timberland owners hold the key to the future of Mississippi's forest economy. As you begin or continue to manage your timber, you will come in contact with foresters who may use terms with which you are unfamiliar. This publication is meant to help you better understand special terms and abbreviations commonly used in forestry. Hopefully, this publication will help you make decisions about the productive management of your timber.",
"homepage": "http://extension.msstate.edu/publications/publications/forestry-terms-for-mississippi-landowners",
"name": "Forestry Terms for Mississippi Landowners",
"prefix": "1168"
},
"1169": {
"description": "Greater economic value will result in an increased number of intrusions into forestlands. Those intrusions may take many forms, including trespassing on land and timber, boundary-line disputes, land-title problems, timber-cutting disagreements, contract interpretation problems, and increased litigation. As a forest landowner, you must be aware of the legal aspects of forest management and ownership. This expertise will allow you to better safeguard land and timber. This publication contains selected legal terms and concepts important to forest landowners. A careful study of the information provided will help you deal with the increasing number of possible legal problems associated with land and timber ownership.",
"homepage": "http://msucares.com/pubs/publications/p1762.pdf",
"name": "Legal Terms and Concepts for Forest Landowners",
"prefix": "1169"
},
"117": {
"description": "These thesauri provide standardized vocabulary for retrieving special collections materials by form, genre, or by various physical characteristics that are typically of interest to researchers and special collections librarians, and for relating materials to individuals or corporate bodies.",
"homepage": "http://www.rbms.info/committees/bibliographic_standards/controlled_vocabularies/",
"name": "Controlled Vocabularies for Use in Rare Book and Special Collections Cataloging",
"prefix": "117"
},
"1170": {
"description": "This glossary was first published in June 1986 by the Engineering Division of the FAA Technical Center, under the title \"Glossaryof Fiber Optic Terms\" (Division Report CT-110-86-15). It has now been revised and expanded, and is made available for wider distribution. It is intended to be an introductory reference for those with a technical background (engineers, scientists, and technicians) who have an interest in optical communication, but are not familiar with some of the more common terms used in this field. For a more rigorous and complete treatment of the subject matter, the reader is directed to appropriate references.",
"homepage": "http://www.dtic.mil/cgi-bin/GetTRDoc",
"name": "Glossary of Optical Communication Terms",
"prefix": "1170"
},
"1171": {
"description": "It is not unusual for students to forget important concepts learned in an earlier course. This set of definitions is intended to stir memories of those wonderful times when you were learning statistics and econometrics. It is not intended to replace a statistics course but to provide you with a handy guide to the definition of some important terms in the statistical tools used by economists.",
"homepage": "http://cnx.org/contents/1423f1f2-3633-48cd-8376-78e812087f6a@3/Statistical_terminology",
"license": "CC-BY-3.0",
"name": "Statistical Terminology",
"prefix": "1171"
},
"1172": {
"description": "Terminology for string players.",
"homepage": "http://cnx.org/contents/931bf098-bdd4-4054-a55b-ce1da3eb213f@8/Common_Violin_Terminology",
"name": "Common Violin Terminology",
"prefix": "1172"
},
"1173": {
"description": "Find the definitions and examples you're looking for.",
"homepage": "http://www.poetryfoundation.org/learning/glossary-terms",
"name": "Glossary of Poetic Terms",
"prefix": "1173"
},
"1174": {
"description": "This book defines and discusses terms, critical theories, and points of view that are commonly used to classify, analyze, interpret, and write the history of works of literature. The individual entries, together with the guides to further reading included in most of them, are oriented especially toward undergraduate students of English, American, and other literatures. Over the decades, however, they have proved to be a useful work of reference also for advanced students, as well as for the general reader with literary interests.",
"homepage": "http://www.ohio.edu/people/hartleyg/ref../abrams_mh.pdf",
"name": "Glossary of Literary Terms",
"prefix": "1174"
},
"1175": {
"description": "This is a glossary of terms used in the morphological, syntactic, and pragmatic analysis of text.",
"homepage": "http://www-01.sil.org/linguistics/glossaryoflinguisticterms/",
"name": "Glossary of Linguistic Terms",
"prefix": "1175"
},
"1176": {
"description": "The AIRS Linked Open Vocabulary is a way to describe human services information and referral (I&R) concepts. AIRS is the Alliance of Information and Referral Services (airs.org), which possesses over 1,000 member agencies primarily in the United States and Canada. The AIRS LOV is based on the AIRS XML Schema, available at: https://airs-xml.googlecode.com/hg/tags/3.1/airs.xsd",
"homepage": "https://github.com/airsalliance/lov",
"name": "The Alliance of Information and Referral Services Linked Open Vocabulary",
"prefix": "1176"
},
"1177": {
"description": "The search of Thesaurus in BAMS 2.0 consists of a simple yet powerful form, which allows users to search by strings included in the thesaurus' terms, abbreviations, references and definitions.",
"homepage": "http://brancusi1.usc.edu/thesaurus/list/",
"name": "Brain Architecture Management System Thesaurus",
"prefix": "1177"
},
"1178": {
"description": "The aim of the Glossary is to provide a list of emergency management terms and definitions. Terms included are those likely to be encountered by emergency management workers. The types of organisations that would find the Glossary of value include: local governments; State and Commonwealth government departments; professional groups; processing, storage and transport industries; other large private sector organisations; hospitals, educational institutions, etc; and community organisations. (...) Confusion in emergency management often arises from a misunderstanding over words\n\nbecause emergency management is at the nexus of many fields. There is also an increasing proliferation and duplication of terms and definitions, as the emergency management field itself is still evolving and adapting itself to new and changing contexts. The Glossary provides information on the range of terms and definitions encountered in emergency management, and may, in the future, lead to a consensus on terms and definitions. This Glossary does not present new or different definitions of terms, but draws together definitions from many existing sources. It also suggests a set of core terms (...).",
"homepage": "https://www.em.gov.au/Documents/Manual03-AEMGlossary.PDF",
"name": "Australian Emergency Management Glossary",
"prefix": "1178"
},
"1179": {
"description": "The recovery of information has been and continues to be a key issue in information science since its emergence as a scientific field to date.With the advances of science and technology and the era of the information society, the Internet and the vertiginous proliferation of information, Thesauri are essential tools in the search and access to information.The consistency, precision and relevance of the information are basic qualities in this process and depend mainly on thesauri.\n\nAmong the few thesauri of information science in the world, we highlight that of the United States, today's Association for Information Science and Technology - ASIS & T, formerly American Society for Information Science and Technology, ASIS & T Thesaurus of Information Science, Technology and Librarianship, in Third Edition, 2005, edited by Alice Redmond-Neal and Marjorie MK Hlava.\n\nThe Brazilian Thesaurus of Information Science has a wide application not only for indexers, but also researchers, professors and information professionals in general. It is a fundamental instrument for the consistency of terminology and vocabulary of a given field of knowledge.\n\nIbict owed this work to those who deal with issues of documentary language, since the initiative to build a thesaurus in information science, 1989, was not published, was restricted to internal use and did not continue.\n\nA work of this magnitude requires knowledge of the area, experience and arduous theoretical and conceptual effort of many years of dedication. It was left to Lena Vania Ribeiro Pinheiro, a researcher and teacher at Ibict, to meet this challenge, with the collaboration of Helena Dodd Ferrez, principal author of the thesaurus for museum collections.\n\nIn the elaboration of the thesaurus, the authors had the collaboration of researchers and teachers, as well as information science technicians, with whom they maintained productive dialogues, which contributed a lot to the making of this instrument. Also important were the sources they resorted to, like other thesauri and dictionaries, all identified in this publication.\n\nWith great pride, Ibict launches this thesaurus, encompassing some 1,800 terms, most with an English and Spanish version, complemented by definitions, in the expectation that the Brazilian Thesaurus of Information Science will play a central role in the information retrieval in Brazil And in Portuguese-speaking countries.",
"homepage": "http://www.ibict.br/publicacoes-e-institucionais/tesauro-brasileiro-de-ciencia-da-informacao-1/tesauro-brasileiro-de-ciencia-da-informacao/resolveuid/1c60ede36f47aee60c48957ef6db7510",
"name": "Brazilian Thesaurus of Information Science",
"prefix": "1179"
},
"118": {
"abbreviation": "ULAN",
"description": "The ULAN is a structured vocabulary currently containing around 293,000 names and other information about artists. Names in ULAN may include given names, pseudonyms, variant spellings, names in multiple languages, and names that have changed over time (e.g., married names). Among these names, one is flagged as the preferred name. Although it is displayed as a list, ULAN is structured as a thesaurus, compliant with ISO and NISO standards for thesaurus construction; it contains hierarchical, equivalence, and associative relationships. The focus of each ULAN record is an artist. Currently there are around 120,000 artists in the ULAN. In the database, each artist record (also called a subject in this manual) is identified by a unique numeric ID. Linked to each artist record are names, related artists, sources for the data, and notes. The temporal coverage of the ULAN ranges from Antiquity to the present and the scope is global. Although originally intended only for use by Getty projects, the broader art information community outside the Getty expressed a need to use ULAN for cataloging and retrieval. The Getty thus distributed ULAN for broader use according to the tenets previously established for the construction and maintenance of the AAT: Its scope includes names needed to catalog and retrieve information about the visual arts and architecture; it is based on terminology that is current, warranted for use by authoritative literary sources, and validated by use in the scholarly art and architectural history community; and it is compiled and edited in response to the needs of the user community. Originally constructed as a simple alphabetized \"union list\" of clustered artist names and biographies, in order to make it consistent with the AAT and TGN, in the late 1990s ULAN was brought into compliance with national and international standards for thesaurus construction. Its scope was broadened to include corporate bodies such as architectural firms and repositories of art, which may have hierarchical levels.",
"homepage": "http://www.getty.edu/research/tools/vocabularies/ulan/",
"license": "http://www.opendatacommons.org/licenses/by/1.0",
"name": "The Union List of Artist Names",
"prefix": "118",
"wikidata_database": "Q2494649"
},
"1180": {
"description": "A guide for locating valid subject headings used in indexing Bills Legislative Session. (...) Valid subject headings appear in all CAPITAL letters. Terms appearing in lower case are not valid subject headings and simply refer you to the valid heading.",
"homepage": "http://www.njleg.state.nj.us/bills/thes2000.asp",
"name": "New Jersey State Legislature Thesaurus",
"prefix": "1180"
},
"1181": {
"description": "The original thesaurus consisted of an OVERVIEW (only upper terms, = at the same time position of the library, file system), an INDEX (Alphaliste of all slogans) and a SYSTEMATIK (overview with all subdivisions, synonyms, related terms) .\n\nFor reasons of space, only the main terms, ie the OVERVIEW, are presented here (with their own index); The systematic part contains the actual key words under 'main'. The whole thing was integrated into a full-text database in the form of different word lists (index, synonyms) and also served as a storage and library system.",
"homepage": "http://www.physiologus.de/thes/thes-frm.htm",
"name": "Thesaurus craft",
"prefix": "1181"
},
"1182": {
"description": "Leeds University Library has a unique classification scheme.",
"homepage": "https://library.leeds.ac.uk/downloads/download/156/classification_scheme",
"name": "Leeds University Library Classification Scheme",
"prefix": "1182"
},
"1183": {
"description": "Library Classification Scheme for marine microbiology of the Max Planck Institute.",
"homepage": "http://magnum.mpi-bremen.de/biblio/deutsch/dyn/systematik/hauptgr.shtml",
"name": "Max Planck Institute for Marine Microbiology Library Classification Scheme",
"prefix": "1183"
},
"1184": {
"description": "Xwi7xwa Library uses a modified version of the Brian Deer classification system, developed by Kahnawake librarian Brian Deer for the National Indian Brotherhood (now the Assembly of First Nations) in the 1970s. Xwi7xwa Library employs a modified version of the classification scheme in order to better reflect the library's unique collection and clientele.",
"name": "Brian Deer Classification Scheme",
"prefix": "1184"
},
"1185": {
"description": "The National Statistical Institute has prepared a complete and coherent classification of legal entities by legal form. The aim is to ensure more uniformity of the information contained in administrative data bases and to promote, within the National Statistical System, a Common language between the central and local authorities.\n\nThe classification is divided into two sections: the first refers to the legal forms governed by private law, the second to the forms governed by public law, for a total of 16 divisions and 62 classes.\n\nEach legal form - an individual entrepreneur, a freelance professional, a company of persons or capital, association, foundation, state administration, public body, local authority, etc. - is classified with a four-digit code, where the first digit identifies the section, the second the division and the last two the class. When the division does not articulate into classes, the last two digits are zeros.\n\nThe legal sources considered for the classification are the Constitution of the Republic, the Civil Code and the special legislation. In addition, in order to capture certain phenomena not attributable to typical legal forms, reference has been made to case law.\n\nThis classification is updated with the regulations in force on 31 December 2004. It will be revised over time in the event of regulatory changes.",
"homepage": "http://en.istat.it/strumenti/definizioni/unita_legali/classformegiuridiche.pdf",
"license": "CC-BY-3.0",
"name": "Classification of Legal Forms of Legal Units",
"prefix": "1185"
},
"1186": {
"description": "The business classification is a requirement of capacity and solvency must certify businesses in procedures for the award of certain typical administrative contracts (Article 65 of TRLCSP).\n\nThe fourth transitional provision of TRLCSP amended by Article 43 of Law 14/2013 of 27 September, supporting entrepreneurs and their internationalization concerning the determination of cases where it is required the classification of companies states that paragraph 1 of article 65, as determined by the contracts for the celebration of which is required prior classification enter into force in accordance with the provisions of the regulations implementing this law which are defined groups, subgroups and categories that classify these agreements and continues in force until then, paragraph 1 of article 25 of the revised Act contractres of government.\n\nHowever, the classification is not required in works contracts estimated value of less than β¬ 500,000 or contracts for services estimated value of less than 200,000 euros.\n\nThey do not require business classification, so typical concession contracts for public works, public service management, supply, collaboration between the public sector and the private sector and certain categories of services (*). In these contracts, whatever your budget tender must necessarily require proof of economic solvency and technical bidders according to one, several or all means provided for in articles 74 to 79 in the TRLCSP depending on the typical contract in question.\n\nIn works contracts estimated value of less than 500,000 euros and services estimated value of less than β¬ 200,000 can not be established as a prerequisite to apply for the classification of companies. These tenders must be determined in the Administrative clauses the economic, financial and technical entrepreneurs by one, several or all means to the provisions of Articles 74 and 79 of TRLCSP included this information in the ad tender.\n\nRequire business classification as a mandatory condition for participation in tenders for contracts for works and services when the estimated value is less established in the 4th DT. TRLCSP -modifying by Article 43 of Law 14/2013 of 27 September-, is to prevent the participation of companies not classified contracts, according to the current regulations do not require this capability requirement.\n\nImposing a requirement (for example, business classification) that prevents the participation of companies in public tenders when the legal requirement does not require this directly affects the principle of concurrent business activity is not subject to the Administration Act and therefore, we can say that root vitiate the validity of the contract award.",
"homepage": "http://economia.gencat.cat/ca/70_ambits_actuacio/contractacio_publica/junta_consultiva_de_contractacio_administrativa/classificacio_empresarial/",
"name": "business Rating",
"prefix": "1186"
},
"1187": {
"description": "The Friedensauer Bibliothek-Systematik combines large parts of the system for libraries (SfB - http://www.sfb-online.de) with specially created system groups for archeology, children's books (KiBΓΌ), theology (theol) and Hochschulschriften (HSS) ,This, on the one hand, makes it possible to provide a suitable picture of the Library of the Theological University of Friedensau. On the other hand special attention is needed at certain points: - The 'religion' area is only valid from Rel 001 to Rel 205, except Rel 125-129. The \"Theology\" section covers the rest of the topic. - The following system groups of the SfB are named differently in the FBS: o The Department of Mathematics (SfB: Ma, FBS: Math) o The Department of Law (SfB: R; FBS: Law) o The Theater (SfB: Th; FBS: Theat ) - For selected systems with 'AZ notation' (eg Med 830), an overview with the breakdown of the internally selected abbreviations for the respective system locations can be found at the end of this document. - Compared to the official version of the SfB, changes have also been made to selected systems. Affected system locations and references can be found in the red font. In this case, links are also kept in red letters.",
"homepage": "http://www.thh-friedensau.de/downloads/13560/",
"name": "Friedensauer library system",
"prefix": "1187"
},
"1188": {
"description": "By the end of July 2010, the publicly available institute library was structured according to the following system.",
"homepage": "http://www1.iwe.unisg.ch/org/iwe/web.nsf/wwwPubService/D4AD40C59E7BF8D6C12569ED00638C22",
"name": "Institute of Economic Ethics",
"prefix": "1188"
},
"1189": {
"description": "A PDF file about the library systematics of the Freie Theologische Hochschule Giessen",
"homepage": "http://www.fthgiessen.de/fileadmin/fth2013/bilder/Gebaeude/Bibliothek/Systematik_FTH.pdf",
"name": "Library system Theological Theological College GieΓen",
"prefix": "1189"
},
"119": {
"description": "Discover the circus arts through our illustrated vocabulary grouped under a tree of subjects. It is a real gold mine of information: definitions, photographs, historical notes, synonyms and bibliographic references. This non-exhaustive vocabulary, developed for information purposes by the Library with the support of its documentary resources, is an excellent tool for starting or deepening your documentary research on the circus arts.",
"homepage": "http://www.bibliotheque.enc.qc.ca/Record.htm?record=19117188146919353609",
"name": "Vocabulary of Circus",
"prefix": "119"
},
"1190": {
"description": "Shelf Classification of the Library of Topography of Terror Foundation.",
"homepage": "http://www.topographie.de/bibliothek/systematik/",
"name": "Shelf Classification of the Library of Topography of Terror Foundation",
"prefix": "1190"
},
"1191": {
"description": "It wasn't until the 70s that the stock was categorised and stored systematically. Through collaboration with the provincial library, a system of numerical and colour-coded classification was developed.",
"homepage": "http://www.neuegalerie-archiv.at/biblio/system.html",
"name": "Categorization Scheme of Neue Galerie Graz",
"prefix": "1191"
},
"1192": {
"description": "Library structure of the German Protestant Institute of Archaeology.",
"homepage": "http://deiahl.de/tl_files/deiahl/ueber%20das%20dei/Bibliothekssystematik.pdf",
"name": "German Protestant Institute of Ancient World Studies of the Holy Land Jerusalem Library Systematics",
"prefix": "1192"
},
"1193": {
"description": "The classification system of the Library of the Hamburg Institute for Social Research is a general system that determines the on-site location of our holdings. In keeping with the Instituteβs profile, the classification systemβs main subject areas are history, politics, and the social sciences. The classification system was revised in early 2009 (...).",
"homepage": "http://www.his-online.de/bibliothek/literaturrecherche/systematik/",
"name": "Classification System of the Library of the Hamburg Institute for Social Research",
"prefix": "1193"
},
"1194": {
"homepage": "https://www.tuwien.at/ar/soziologie",
"name": "Library systematics of the Department of Sociology at the Vienna University of Technology",
"prefix": "1194"
},
"1195": {
"description": "Classification System of the University of Navarra Library",
"homepage": "http://www.unav.edu/web/biblioteca/conocenos/clasificacion",
"name": "University of Navarra Library Classification System",
"prefix": "1195"
},
"1196": {
"description": "El sistema de clasificaciΓ³n temΓ‘tica de los libros, de diseΓ±o propio, desarrolla las Γ‘reas y subΓ‘reas de la sociologΓa jurΓdica permitiendo localizar las secciones de interΓ©s para cada investigador, unido a las facilidades del acceso directo a los fondos.",
"homepage": "http://www.iisj.net/es/system/files/2016-mural%20completo%20-%202%20p%C3%A1gina_0.pdf",
"name": "ClasificaciΓ³n TemΓ‘tica - Biblioteca Instituto Internacional de SociologΓa JurΓdica",
"prefix": "1196"
},
"1197": {
"description": "In the development of the RESI-2 prototype system within the framework of the research project 'Information System on Reactor Safety RESI', a first approach has emerged for a structured index in the problem area 'Atomic Approval Approval Procedure' The computer-assisted system RESI-2, developed by the Institute for Reactor Development of the Gesellschaft fΓΌr Kernforschung mbR, Karlsruhe, works with the GOLEM program from Siemens, which contains an alphabetical thesaurus for both the so-called bound descriptors (aspects) such as Also for free descriptors The structuring into sub-and superspecies as well as the introduction of synonym links requires a separate work process And overlapping between the administrative and technical vocabulary in the field of reactor safety and the nuclear licensing procedures. The creation of the directory was inter alia. Because there was no other suitable thes\n\naurus available in the problem area.",
"homepage": "http://bibliothek.fzk.de/zb/kfk-berichte/KFK1902.pdf",
"name": "RESI-Thesaurus for the information system for reactor safety",
"prefix": "1197"
},
"1198": {
"description": "This guide to subject headings for church or synagogue libraries begins by providing guidelines for the subject cataloging process. These guidelines are presented under seven headings: (1) Selecting the Subject Heading (by names of persons, religious congregations and orders, sects and denominations, places, holidays, and new subjects); (2) Specific Entry; (3) Subdivisions; (4) Cross References; (5) Subject Entry Cards; (6) Classification Numbers; and (7) Subject Authority File. Practical examples are provided which correspond to each of these headings. The subject heading list, which makes up the major part of the publication, includes classification numbers for each term that would most likely be found in a church or synagogue library. Suggestions for additional headings may be found in both the guidelines and in works listed in the bibliography. A list of some of the subject headings most used in collections of non-fiction children's books is also provided.",
"homepage": "https://eric.ed.gov/?id=ED327215",
"name": "Subject Headings for Church or Synagogue Libraries",
"prefix": "1198"
},
"1199": {
"description": "ThESS - Thesaurus of Economics and Social Sciences of the Library Mario Rostoni is a controlled vocabulary constructed by drawing the terms mainly but not just from business-legal and business documents. ThESS is born and grows in relation to library acquisitions and the necessity to express the contents of the books to favor searches by subject.\n\nIt is used in the following functions: Cataloging Acquired Library Material: Thesaurus terms are assigned to each bibliographic record as keywords and combined by catalogers in cohesive subject strings to express the subject of the book. Document Retrieval: Thesaurus terms enable those who seek to retrieve documents, either by combining them with a search mask or by scrolling through the lists. Terminology-Conceptual Analysis in Research Processes: The relationship between the terms of the thesaurus allows to enrich the terminological heritage of a field or a research topic, guiding other words related to meaning used in the library catalog or any other tool . This thesaurus usage is widely presented in the Information Literacy courses of the Laurea and Master's Degree courses at the LIUC University. ThESS is born with a priority reference to the needs of the study and research community formed by the students, researchers and faculty of the Faculty of Business Economics, Management Engineering and Law of the Carlo Cattaneo - LIUC University. It can also be useful to librarians, catalogers, information specialists who manage and bibliographic and documentary collections of the same disciplinary areas. ThESS is a multidisciplinary thesaurus, one-hierarchical, organized based on categories of about 7000 terms. Includes proper names. It is compiled in accordance with ISO 2788 (1986) and BS 8723-1/2 (2005) standards.",
"homepage": "http://www.biblio.liuc.it/pagineita.asp?codice=210",
"name": "Thesaurus of economics and social sciences",
"prefix": "1199"
},
"12": {
"homepage": "http://vocabularyserver.com/acl/",
"name": "Adult Community Learning Thesaurus",
"prefix": "12"
},
"120": {
"description": "All of the subject terms in the catalogue have been organized by common themes and groups in a Zine Thesaurus. In the thesaurus there is an entry for each 'preferred' subject term in bold with similar or related terms listed below it. The subject terms in the Zine Thesaurus were selected by volunteer cataloguers at the Anchor Archive. The Zine Thesaurus is a good place to look up subject terms because you can see all similar and related terms together and get ideas for words to use when searching or cataloguing. Browsing the thesaurus will give you an idea of the many subjects covered by zines at the Anchor Archive Zine Library.",
"homepage": "https://anchorarchive.org/index.php/subject-thesaurus",
"name": "ZINE Thesaurus of Subject Terms",
"prefix": "120"
},
"1200": {
"homepage": "http://documentation.aviation-civile.gouv.fr/ListRecord.htm",
"name": "Civil Aviation Technical Service Thesaurus",
"prefix": "1200"
},
"1201": {
"description": "Search by term allows to search by keywords in different thesauri.",
"homepage": "http://bibliotheque.catholique78.fr/",
"name": "Diocesan Library of Versailles Thesaurus",
"prefix": "1201"
},
"1202": {
"description": "All of us are frequently confronted with the problem of identifying musical instruments and their components correctly, whether in the process of defining a part that has been damaged or restored, or trying to transmit our knowledge to school children, students or our academic colleagues. Occasionally this task is a distinct challenge due to the lack of a standardized terminology in the field of organology.\n\nRecognizing this fact, the Brasswind Terminology Working Group, which consists of four brass scholars at this point (Stewart Carter, Arnold Myers, Bradley Strauchen and myself), tries to develop a coherent terminology for brasswind instruments and their components in English. Our approach differs from hierarchical systems, such as the Hornbostel-Sachs classification - which is a 'downward' system - in its 'upward' orientation. We derive our terminology from the detailed inspection and delineation of an instrument in its musical, social, historical and technological contexts, rather than its classification according to general characteristics.\n\nThe primary goal of the Brasswind Terminology Working Group is the standardization of brasswind terminology to create a commonly accepted, precise language, which eventually can be used by anyone concerned with this instrument type (organologists, musicologists, museum curators, instrument makers and others who have need to refer to these instruments).\n\nWe hope that this project will stimulate the development of similar working groups for other types of instruments, and in languages other than English. A long-term goal is to create a generally accepted terminology for the field of organology that applies to instruments and their parts in a clear and consistent manner.",
"homepage": "http://www.homepages.ed.ac.uk/am/itt/ittb.html",
"name": "CIMCIM Terminology",
"prefix": "1202"
},
"1203": {
"description": "To classify maps, atlases, and globes most advantageously in a collection extensively used by geographers, historians, economists, technicians or other specialists and students, it is believed that the categories to be considered, in order of importance, are: (1) Area, (2) Subject, and (3) Date, with (4) Author, frequently necessary. When these four categories are insufficient to differentiate between maps in the collection, a fifth, Title, may be used. A sixth, Physical form, must be taken into account in filing globes, relief maps, maps mounted on rigid board or equipped with sticks or rods. The area-subject classification of maps corresponds to the classification of books by subject. The addition of date and, when necessary, author (or publisher), usually completes the differentiation of each map from every other map. Thus classified, a map has a single specific filing position relative to all the other maps; the flexible classification permits unlimited intercalation of new maps in their logical positions, regardless of the chance order of accession into the collection. It is believed that the notation which has been adopted, in which area is represented by numbers, and subject is represented by letters, gains merit from this obvious separation. The classification system needs at the outset to provide the framework for inclusion of every likely map subject, though it need not give an absolute location for the less common subjects. This forms a contrast with the subject heading list, which is infinitely expansive by nature.",
"homepage": "http://hdl.handle.net/2027/mdp.39015020109107",
"name": "Boggs and Lewis Classification of Maps and Atlases",
"prefix": "1203"
},
"1204": {
"description": "Library System of the Hans-Bredow-Institut for Media Research at the University of Hamburg",
"homepage": "http://www.hans-bredow-institut.de/de/bibliothekssystematik/bibliothekssystematik",
"name": "Library System of the Hans-Bredow-Institut",
"prefix": "1204"
},
"1205": {
"description": "The library's holdings are systematically organized, ie organized according to subject areas. The underlying, very differentiated classification system is a special strength of the library, because the content structure of the library through its systematic setup guarantees a clear overview and allows a targeted access. Classification scheme is available in different languages.",
"homepage": "http://dli.institute/wp/bibliothek/systematik-der-bibliothek/",
"name": "Shelf Classification of the Library of Deutsches Liturgisches Institut",
"prefix": "1205"
},
"1206": {
"description": "Library System of the Helmholtz Center for Ocean Research",
"homepage": "http://www.geomar.de/zentrum/einrichtungen/bibliothek/systematik/",
"name": "GEOMAR Helmholtz Center for Ocean Research Kiel Library System",
"prefix": "1206"
},
"1207": {
"homepage": "http://bibliothek.geomar.de/keywords/list",
"name": "GEOMAR Helmholtz Centre for Ocean Research Kiel Subject Headings",
"prefix": "1207"
},
"1208": {
"description": "Im Zeitraum vom 1960 bis 1980 wurde eine speziell auf die Erwerbungspolitik der JFKI-Bibliothek zugeschnittene hauseigene Systematik entwickelt. Diese liegt leider nicht in digitalisierter Form vor, sondern kann nur in gedruckter Form (blaue BΓ€nde im untersten Fach des Neuerwerbungsregals im Bibliotheksflur) eingesehen werden.",
"homepage": "http://www.jfki.fu-berlin.de/library/holdings/classifications/index.html",
"name": "John-F.-Kennedy-Institut fΓΌr Nordamerikastudien Bibliothekssystematik",
"prefix": "1208"
},
"1209": {
"description": "The new entries after 1979 are cataloged according to 23 groups.",
"homepage": "http://www.theaterforschung.de/institution.php4?ID=86",
"prefix": "1209"
},
"121": {
"description": "Keywords are always nouns:.. Either yksittΓ€istermejΓ€, word associations, or compound words Key words are either singular or plural unit are abstract concepts and activities described by the words plural are usually tangible, quantifiable concepts of the words for terms can be singular and the plural different meaning.. whereby the two forms appear in the dictionary (grammar - grammars). preparing thesaurus have been observed in Finnish thesaurus preparation and maintenance instructions (SFS 5471) Tesaurusmuodosaa indicating the subject headings hierarchical and semantic relation to It can also be found references on the same topic to broader and narrower, as well as parallel terms... indexterms relationship indicated by the following abbreviations:. = USE reference to the thermal control word thing, the term substituted BT = LT = a broader term, a narrower term = ST, RT = apposition, Coordinate equivalence ratio indicated by the abbreviations USE and KT (co rvattu term). USE-approved abbreviation of the controls to use the selected key words, rather than control, the term may be used as a word thing. USE-reference eliminates synonyms, and combined with close meanings of terms. The hierarchical relationship indicated by the abbreviations LT (broader term) and ST (narrower term). Association is indicated by the abbreviation RT (in apposition, Coordinate). RT-ratio controls the vocabulary of users will find other keywords related to a particular issue. Means the case, the association relationship between the concepts, which is looser than a hierarchical relationship. Such relationships could be countless. Vocabulary words associated with some thing explanations. They are immediately after the thing without the word abbreviation code. The Explanatory Memorandum provides for example. instructions not included in the dictionary of keywords use (the so-called. unrestricted crawling word groups).",
"homepage": "http://kaino.kotus.fi/www/verkkojulkaisut/asiasanasto.html",
"name": "Linguistics Thesaurus",
"prefix": "121"
},
"1210": {
"description": "Each book is numbered using the JGSGB's own Library Classification Code. Books are shelved in sequence using this code. e.g. 110 Jhse. The comments field in the catalogue is used to show the Library Classification Code. The first part of each book's code number is determined from the following list. Author or other code is then appended.",
"homepage": "http://www.librarything.com/profile/jgsgblib",
"name": "JGSGB Library Classification Code",
"prefix": "1210"
},
"1211": {
"homepage": "http://www.uibk.ac.at/europarecht/bibliotheken/downloads/bib_systematik_ererweitert.pdf",
"name": "Library system of the Geographisches Institut der Ruhr-UniversitΓ€t Bochum",
"prefix": "1211"
},
"1212": {
"description": "The stock of the DHBW Mannheim library is arranged according to an in-house classification scheme.",
"homepage": "http://www.bib.dhbw-mannheim.de/infos-zur-bibliothek/systematik/",
"name": "Library of the DHBW Mannheim system",
"prefix": "1212"
},
"1213": {
"description": "This preliminary overview (as of 2011) unites about 41,000 titles that have been registered so far in short abstracts, organized into a thematic order (classification scheme). It is constantly being revised and serves only for a rough orientation about the library collection!",
"homepage": "http://www.bibliothek-oechslin.ch/bibliothek/systematik",
"name": "Werner Oechslin Library Foundation systematics",
"prefix": "1213"
},
"1214": {
"homepage": "https://www.wi.uni-muenster.de/sites/wi/files/seitenstruktur/das-institut/bibliothek/bibliothekssystematik.pdf",
"name": "Institute of Business Information Systems",
"prefix": "1214"
},
"1215": {
"homepage": "https://www.slm.uni-hamburg.de/astub/service/bibliothek/systematik.html",
"prefix": "1215"
},
"1216": {
"homepage": "https://www.unibe.ch/unibe/portal/content/e809/e962/e963/e6331/e6370/e6371/e34475/pane34477/e106496/4_7_1Systematikchrkath_141985752035_ger.pdf",
"name": "Library Christian Catholic Theology Systematics",
"prefix": "1216"
},
"1217": {
"homepage": "https://www.unibe.ch/unibe/portal/content/e809/e962/e963/e6331/e6370/e6372/e34511/pane34513/e106505/4_7_2SystematikevangTheologie_141985685466_ger.pdf",
"name": "Library Evangelical Theology systematics",
"prefix": "1217"
},
"1218": {
"description": "Library systematics of the musicology seminar.",
"homepage": "http://www.muwi.uni-freiburg.de/bibliothek/Bibliothekssystematik.pdf",
"name": "Musicology Seminar Library Systematics",
"prefix": "1218"
},
"1219": {
"description": "Shelf classification of the Department library of Scandinavian Studies",
"homepage": "http://www.ub.ruhr-uni-bochum.de/imperia/md/content/systematik_skand.pdf",
"name": "Faculty of Philology, Department Library of Scandinavian Studies Shelf classification",
"prefix": "1219"
},
"122": {
"description": "935 terms.",
"homepage": "http://vocabularyserver.com/linguistic/",
"name": "Linguistics Thesaurus",
"prefix": "122"
},
"1220": {
"description": "Shelf classification of the Department of Classical Philology",
"homepage": "http://www.ub.ruhr-uni-bochum.de/imperia/md/content/fachbib/philologie/systematik_klassphil.pdf",
"name": "Faculty of Philology, Department Library Classical Philology Shelf Classification",
"prefix": "1220"
},
"1221": {
"description": "Shelf classification of the department library for comparative studies",
"homepage": "http://www.ub.ruhr-uni-bochum.de/imperia/md/content/systematik_komp.pdf",
"name": "Faculty of Philology, Faculty Library of Comparative Studies",
"prefix": "1221"
},
"1222": {
"description": "Systematics: Linguistics, Description of Slavic Individual Languages, Linguistics / Semiotics / Literary Theory, Literary History, Authors / Reginal studies.",
"homepage": "http://www.ub.ruhr-uni-bochum.de/imperia/md/content/fachbib/philologie/systematik-slavistik.pdf",
"name": "Faculty of Philology, department library Slavic Shelf classification",
"prefix": "1222"
},
"1223": {
"description": "Shelf classification of the department library for linguistic research",
"homepage": "http://www.ub.ruhr-uni-bochum.de/imperia/md/content/systematik_sprachl.pdf",
"name": "Faculty of Philology, Department library of Linguistics Shelf classification",
"prefix": "1223"
},
"1224": {
"description": "Shelf classification of the Department of Romance Studies",
"homepage": "http://www.ub.ruhr-uni-bochum.de/imperia/md/content/systematik_rom.pdf",
"name": "Faculty of Philology, Department library for Romance Shelf classification",
"prefix": "1224"
},
"1225": {
"description": "The media science publications are assigned to the upper groups of film, television and media science.",
"homepage": "http://www.ub.ruhr-uni-bochum.de/imperia/md/content/fachbib/philologie/systematik_medien.pdf",
"name": "Faculty of Philology, Department Library Media Studies Shelf classification",
"prefix": "1225"
},
"1226": {
"description": "Shelf classification of the Department library of Theater Studies",
"homepage": "http://www.ub.ruhr-uni-bochum.de/imperia/md/content/fachbib/philologie/systematik_theater.pdf",
"name": "Faculty of Philology, Department library for Theater science Shelf classification",
"prefix": "1226"
},
"1227": {
"description": "The linguistic literature is gathered under the signature group Sp on the 3rd floor. The other institute libraries of the Faculty of Philology also have a large linguistic literature. Many linguistic specialist books are relevant to individual philologies.",
"homepage": "http://www.ub.ruhr-uni-bochum.de/imperia/md/content/syslin.pdf",
"name": "Faculty of Philology, Department of German Studies German Studies Linguistics",
"prefix": "1227"
},
"1228": {
"description": "Shelf classification of the Department of German Studies library of the Faculty of Philology for Dutch Studies",
"homepage": "http://www.ub.ruhr-uni-bochum.de/imperia/md/content/sysnied.pdf",
"name": "Faculty of Philology, Department of German Studies, Shelf Classification of Dutch studies",
"prefix": "1228"
},
"1229": {
"description": "Shelf classification of the Department of German Studies library of the Faculty of Philology for Folklore",
"homepage": "http://www.ub.ruhr-uni-bochum.de/imperia/md/content/sysvolk.pdf",
"name": "Faculty of Philology, Department of German Studies library, Shelf classification Folklore",
"prefix": "1229"
},
"123": {
"description": "153 terms.",
"homepage": "http://ihlc.udea.edu.co/delc/",
"name": "Electronic Dictionary of Colombian Literature",
"prefix": "123"
},
"1230": {
"description": "Installation system for the field of media studies",
"homepage": "http://www.ub.ruhr-uni-bochum.de/imperia/md/content/sysmed.pdf",
"name": "Faculty of Philology, Department of German Studies, media studies",
"prefix": "1230"
},
"1231": {
"description": "Installation system for the field of Medieval Latin",
"homepage": "http://www.ub.ruhr-uni-bochum.de/imperia/md/content/sysmitte.pdf",
"name": "Faculty of Philology, Department of German Studies Medieval Latin",
"prefix": "1231"
},
"1232": {
"description": "Nomenclature for Museum Cataloging is a structured and controlled list of object terms organized in a classification system to provide a basis for indexing and cataloging collections of human-made objects. Nomenclature is used in the creation and management of object records in human history collections within museums and other organizations, and it focuses on objects relevant to North American history and culture. Nomenclature is the most extensively used museum classification and controlled vocabulary for historical and ethnological collections in North America.",
"homepage": "http://www.nomenclature.info/",
"license": "CC-BY-4.0",
"name": "Nomenclature for Museum Cataloging",
"pattern": "^[1-9][0-9]+$",
"prefix": "1232",
"wikidata_database": "Q64351785"
},
"1233": {
"description": "The Department of Finance Controlled Subject Vocabulary (gcfin) is based on the organizational chart of the Department of Finance. It is a combined functional and subject vocabulary that reflects the policy development activities of the department and requires regular updating to reflect changes in the organizational structure.\n\nThe Vocabulary is used to catalogue web pages on the Finance Canada Website and is applied in an instance of the dc.subject Dublin Core metadata element. Another instance of dc.subject is populated using the Government of Canada Core Subject Thesaurus (gccore) and does not currently appear in the metadata of the site. The gcfin values are not searchable and but may be used for future search and navigation features on the Finance Website. (...)\n\nThe Vocabulary is presented in taxonomy and alphabetical form. The Vocabulary is registered with Library and Archives Canada.",
"homepage": "http://www.fin.gc.ca/admin/gcfin-eng.asp",
"prefix": "1233"
},
"1234": {
"description": "This list includes many of the terms commonly used in anti-racism and equity discourse today. They are gleaned from a variety of sources (...). Many of the terms have been in the public domain so long that the source of the original definition is no longer known as they have come into common parlance. The terminology in this field is constantly evolving, so the list remains a work in progress. Should any discrepancies arise during a training session or discussion, it is best to take a moment to determine the current understanding and why people may be more comfortable adding further definitions to the list in the present context.",
"homepage": "http://www.crrf-fcrr.ca/en/resources/glossary-a-terms-en-gb-1",
"name": "Canadian Race Relations Foundation Glossary of Terms",
"prefix": "1234"
},
"1235": {
"description": "If you wish to be positive that you find everything there is in WAVES about a particular species, or that is in a certain series, or that is by a particular corporate body, you may use the Thesaurus Search option on the left menu. These three fields use what is known as a controlled vocabulary. For example, some authors may have used the term Atlantic cod, others may have used northern cod, or simply cod in the title or abstract of an item.",
"homepage": "http://waves-vagues.dfo-mpo.gc.ca/waves-vagues/thesaurus/thesaurus",
"name": "WAVES Thesaurus",
"prefix": "1235"
},
"1236": {
"description": "The Global Medical Device Nomenclature (GMDN) is a system of internationally agreed generic descriptors used to identify all medical device products. Such products include those used in the diagnosis, prevention, monitoring, treatment or alleviation of disease or injury in humans.\n\nThe main purpose of the GMDN is to provide health authorities and regulators, health care providers, medical device manufacturers and suppliers, conformity assessment bodies and others with a single generic naming system that will support patient safety.\n\nThe GMDN is used for: Data exchange between manufacturers, regulators and healthcare authorities; Exchange of post-market vigilance information; Supporting inventory control in hospitals; Purchasing and supply chain management.\n\nMedical device experts from around the world (manufacturers, healthcare authorities and regulators) compiled the GMDN, based on the international standard ISO 15225. The work was mandated by the European Commission in order to provide the necessary tool to carry out the implementation of the Medical Devices Directive, including the European databank for medical devices, Eudamed.\n\nThe GMDN meets the need to identify medical devices at the global level, as identified by the Global Harmonization Task Force (GHTF) and is now used by over 50 national medical device regulators. The GMDN is managed by the GMDN Agency, a non-profit organization, which reports to its Board of Trustees, that represents medical device regulators and industry.\n\nThe GMDN Agency updates the GMDN utilizing member change requests, to add a new device terms to the GMDN. The decisions are made by an international expert team on how the new term is to be described, according to ISO 15225. The GMDN is available in English and 24 other languages.\n\nThe GMDN Agency releases new and updated GMDN terms on a daily basis, on their interactive website, the GMDN Database. Information in the form of a 5 digit numeric GMDN Code is cross-referenced to a precisely defined descriptive Preferred Term, with which all specific devices have substantially similar generic features.",
"homepage": "https://www.gmdnagency.org/",
"name": "Global Medical Device Nomenclature",
"prefix": "1236",
"wikidata_database": "Q5570492"
},
"1237": {
"description": "In the late 1990s, the International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH) developed MedDRA, a rich and highly specific standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. ICHβs powerful tool, MedDRA is available to all for use in the registration, documentation and safety monitoring of medical products both before and after a product has been authorised for sale. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. Today, its growing use worldwide by regulatory authorities, pharmaceutical companies, clinical research organisations and health care professionals allows better global protection of patient health.",
"homepage": "http://www.meddra.org/",
"name": "MedDRA",
"prefix": "1237",
"wikidata_database": "Q1539689"
},
"1238": {
"description": "In-house classification scheme.",
"homepage": "http://www.ub.uni-mainz.de/files/2013/11/Systematik-Politikwissenschaft1.pdf",
"name": "Library Systematics Political Science",
"prefix": "1238"
},
"1239": {
"homepage": "http://www.ruhr-uni-bochum.de/bib-geogr/SYSTEMATIK-BIB.pdf",
"name": "Library of the Geographical Institute",
"prefix": "1239"
},
"124": {
"description": "The purpose of this project was to examine the issues involved in thesaurus construction and to undertake the creation of thesaurus of Harry Potter novels. The thesaurus covers various aspects of Harry Potter universe as depicted in four novels (Harry Potter and the Sorcererβs Stone, Harry Potter and the Chamber of Secrets, Harry Potter and the Prisoner of Azkaban, and Harry Potter and the Goblet of Fire) and two βtextbooksβ (Quidditch Through the Ages and Fantastic Beasts and Where to Find Them) by J.K. Rowling. The thesaurus is intended as a resource for both controlling the vocabulary, and to serve as a gateway to Harry Potter world. The final product is Web based. It consists of two parts: a thesaurus and a name authority file. The thesaurus has hierarchical and alphabetical displays.",
"homepage": "http://www.angelfire.com/ks2/stasa/hpt/first.htm",
"name": "Harry Potter Thesaurus",
"prefix": "124"
},
"1240": {
"description": "Classification scheme of the library of the University of Veterinary Medicine Vienna.",
"homepage": "http://www.vetmeduni.ac.at/de/universitaetsbibliothek/virtuelle-bibliothek/suchmaschinen/systematik-suche/systematikgruppen/",
"name": "Classification System of the University Library Vetmed",
"prefix": "1240"
},
"1241": {
"description": "All media from the Zentralbibliothek of the Hanover University of Applied Sciences are freely accessible and systematically arranged according to subject areas. When you click on the system sites, you will be shown in the online catalogs all the media that are part of this department.",
"homepage": "http://www.hs-hannover.de/bibl/literatursuche/systematiken/systematik-zentralbibliothek/",
"name": "Classifications of the Central Library",
"prefix": "1241"
},
"1242": {
"description": "The holdings of an archive are basically formed according to their origin and their place of origin. This serves to prove the documents in their former business context and allows the user to retroactively establish a historical classification. This procedure of archiving of archives is called the 'principle of provenance'. Furthermore, each archive stock for the purpose of acquiring the usage is assigned its own systematic / classification, which is based on the file plan of the former management.",
"homepage": "http://www.werne.de/index.php?id=429",
"prefix": "1242"
},
"1243": {
"homepage": "http://studienzentrum-rotenburg.bibliotheca-open.de/%c3%9cberuns/Bibliothekssystematik.aspx",
"name": "Classification Scheme of the Library of the Center of Finance and Justice Rotenburg a.d. Fulda",
"prefix": "1243"
},
"1244": {
"description": "Here you will find the systematics for the music writing (books), for the music (notes) and for the phonograms (we also use for videos and DVDs) as well as a register to the phonogram system as a pdf file (...) You can also browse the OPAC within the 'extended search' to see the works you are looking for.",
"homepage": "http://www.muho-mannheim.de/bibliothek/systematik.htm",
"name": "State College of Music and Performing Arts Mannheim Bibliothekssystematik",
"prefix": "1244"
},
"1245": {
"description": "The IfZ system provides you with structured access to the collection areas of the library in chronological and thematic groups. You can start literary research with the notation of the IfZ system in the search field 'IfZ-Systematik'.",
"homepage": "http://bastion.ifz-muenchen.de/bibliothek/systematik_typo.html",
"name": "Institute of Contemporary History Library Classification System",
"prefix": "1245"
},
"1246": {
"description": "Systematics of the library of the Gellert Museum",
"homepage": "http://www.gellert-museum.de/index1024.php",
"name": "Systematics of the Gellert library",
"prefix": "1246"
},
"1247": {
"description": "A system provides information on the layout of the outdoor area of the Lesesaal.",
"homepage": "http://www.sfu.ac.at/data/Kernbibliothek_2014_11_10.pdf",
"name": "Sigmund Freud Private University of Vienna Library Systems",
"prefix": "1247"
},
"1248": {
"homepage": "http://www.ash-berlin.eu/studienangebot/bibliothek/bibliotheksnutzung/bibliothek-a-z/bestand-und-aufstellung/",
"name": "Alice Salomon University of Applied Sciences Berlin Library Classification Scheme",
"prefix": "1248"
},
"1249": {
"homepage": "http://www.ifm.uni-mannheim.de/unter/Bib/Bibliothekssystematik.pdf",
"name": "Institut fΓΌr Mittelstandsforschung Library Classification Scheme",
"prefix": "1249"
},
"125": {
"description": "Kirjallisuudentutkimuksen thing vocabulary been prepared according to Finnish language thesauri preparation and maintenance instructions (SFS 5471) and the principles of the general Finnish thesaurus, which are here the main points in brief: Keywords are always nouns; either yksittΓ€istermejΓ€, word associations, or compound words (for example, genre, literary language, ambiguity in point.) . keywords are plural or singular. plural are usually concrete, representing quantifiable concepts keywords (eg. poems, writers, artists). the unit of agent words, abstract concepts and describing the operation of the words (eg. poetry, literature, writing, translation). The terms may be the singular and the plural, a different meaning to both forms may be present in the glossary, for example, novel (type literature) - novels (concrete works), the author (writer abstract concept, profession) - authors (for individual representatives of the profession ), Cinema (art form) - movies (works of art). The glossary includes relationships between terms, ie references to broader, narrower and parallel terms. In addition, it has a control terms that guide the user to the selected key words accepted in place of the replaced term. Some of the terms associated with the explanations. the content of the text aims to describe the most accurate possible search words, but in order to facilitate information retrieval is often used also subject generally descriptive term. Kirjallisuudentutkimuksen thesaurus is a tool for indexing and information retrieval according to the topic, which will help asiasanoittajia and knowledge to use the same terminology. SKS's library to use the vocabulary dossiers asiasanoittamiseen in the following databases: Helka - joint database of the University of Helsinki libraries, Linda - University Libraries, Arto - a reference database of domestic articles",
"homepage": "http://dbgw.finlit.fi/asiasanastot/asiasanahaku.php",
"name": "Literature study case glossary",
"prefix": "125"
},
"1250": {
"description": "The aim of the institution is to provide doctoral students and WU staff who are involved in applied empirical research with competent advice on the use of statistical concepts and methods. Above all, the offer of the consulting service is aimed at enabling the scientists to carry out their empirical studies and the data evaluation on a high scientific level correctly and independently.",
"homepage": "http://statmath.wu.ac.at/library/libaryclassification.html",
"name": "Library systematics of the Institute of Statistics and Mathematics",
"prefix": "1250"
},
"1251": {
"description": "The Mediothek is named after the historian Joseph Wulf (1912-1974), who failed in the sixties with the attempt to set up a documentary center in the villa for the investigation of the national socialism.",
"homepage": "http://www.ghwk-bibliothekskatalog.de/vufind/",
"name": "Joseph Wulf Mediothek Systematics",
"prefix": "1251"
},
"1252": {
"description": "The inventory of the library is covered by a uniform system, and an overview of the inventory (space plan) is available.",
"homepage": "http://www.adic-germany.de//Material/Bibliothekssystematik.pdf",
"name": "Arbitration Documentation and Information Center Library Systematics",
"prefix": "1252"
},
"1253": {
"description": "Shelf classification of the department of \"Historische Fachinformatik und Dokumentation\" at the University of Graz.",
"homepage": "http://hfi.uni-graz.at/bibliothek/systematik/",
"name": "Department of \"Historische Fachinformatik und Dokumentation\" Library Classification Scheme",
"prefix": "1253"
},
"1254": {
"description": "In the course of the integration into the faculty library, all books are given a new signature according to the Regensburger classification.",
"homepage": "http://www.wisotech.rwth-aachen.de/?page_id=60",
"name": "Economic, social and technological history Descriptors / Keywords of the library system",
"prefix": "1254"
},
"1255": {
"description": "Classification scheme of the study centre \"house Birkach\" of the evangelic state church of WΓΌrttemberg.",
"homepage": "http://www.hausbirkach.de/downloads/images/Bibliothekssystematik_Birkach.pdf",
"name": "Classification scheme of the Birkach house",
"prefix": "1255"
},
"1256": {
"description": "This International Standard is intended to facilitate international communication in the field of information and documentation. It presents terms and definitions of selected concepts relevant to the field and identifies relations between the entries. It contains around 2.000 definitions and a bibliography of 353 titles including other ISO standards.",
"homepage": "https://www.iso.org/standard/59743.html",
"name": "ISO 5127 Information and Documentation Vocabulary",
"prefix": "1256"
},
"1257": {
"description": "This part of ISO 4791 lists the names of items of laboratory apparatus, made essentially from glass, porcelain or vitreous silica, together with items of equipment, made from other materials, which are commonly used in association with such apparatus. A vocabulary of technical terms, with their definitions and applicable to the manufacture, adjustment and use of such laboratory apparatus, will be issued as Part 2. The purpose of the vocabulary is to provide an aid to translators and readers of scientific literature. Because of the need to translate older documents, certain items of equipment now regarded as obsolete have been included.",
"homepage": "https://www.iso.org/standard/10770.html",
"name": "ISO 4791-1:1985 Laboratory Apparatus Vocabulary",
"prefix": "1257"
},
"1258": {
"description": "This International Standard defines the terms used in the heat treatment of ferrous products. The vocabulary is divided into a main part (clause 3) and a complementary section (clause 4). The main part gives an alphabetical list of the terms with their definitions and, where appropriate, comments. A definition of a foreign term for which the language in question has no equivalent is given at the end of the main part. The complementary section comprises the definitions of terms necessary to understand the main part. The comments are given in note form in order to differentiate them from the definitions.\n\nAny term defined in the main part of this International Standard and used elsewhere in a definition or a comment is printed in bolder type than the main text.",
"homepage": "https://www.iso.org/standard/10878.html",
"name": "ISO 4885:1996 Ferrous Products - Heat Treatments Vocabulary",
"prefix": "1258"
},
"1259": {
"description": "Office machines give rise to numerous international commercial exchanges which often become difficult, either because of the great variety of terms used in various fields or languages to express the same concept, or because of the absence of, or the imprecision of, useful concepts. To avoid misunderstandings due to this situation and to facilitate such exchanges, it is advisable to select terms to be used in various languages or in various countries to express the same concept and to establish definitions providing satisfactory equivalents for the various terms in different languages. The work of the ISO Sub-Committee charged with the study of the Vocabulary was based on various international documents issued by Sub-Committees of ISO Technical Committee 95 and on national drafts or standards. ISO 5138 consists of several sections published separately, each section dealing with a category of office machines. The numbering of these sections, beginning with 01, depends on the chronological order of their development. A basic classification of machines has been introduced at the beginning of each section, before the vocabulary proper.",
"prefix": "1259"
},
"126": {
"description": "194 terms, 1928 relations between terms.",
"homepage": "http://www.ufrgs.br/thesinfantojuv",
"name": "Children and Youth Literature",
"prefix": "126"
},
"1260": {
"description": "Micrographics gives rise to numerous international exchanges of both an intellectual and a material nature. These exchanges often become difficult, either because of the great variety of terms used in various fields or languages to express the same concept, or because of the absence or imprecision of the definitions of useful concepts. To avoid misunderstandings and to facilitate such exchanges it is essential to clarify the concepts, to select terms to be used in various languages or in various countries to express the same concept, and to establish definitions providing satisfactory equivalents for the various terms in different languages.",
"name": "ISO 6196 Micrographics Vocabulary",
"prefix": "1260"
},
"1261": {
"description": "Establishes a vocabulary with terms and definitions relating to fuel injection pumps for compression-ignition engines. Alphabetical indexes in English, French, and Russian are also included.",
"name": "ISO 787 Fuel Injection Equipment Vocabulary",
"prefix": "1261"
},
"1262": {
"description": "This International Standard establishes the vocabulary for the various terms in use relative to the most important components of derrick rigs on ships. It lays down terms and definitions used in connection with derrick rigs, and adds terms for winches in accordance with ISO 3828. Where more than one term is given for a concept, the first term is the preferred one and others, although used within the marine industry, are non-preferred. Deprecated terms are also so indicated. A multilingual vocabulary is given in annex A, arranged numerically in the order of the reference numbers;",
"homepage": "http://www.iso.org/iso/home/store/catalogue_tc/catalogue_detail.htm?csnumber=15231",
"name": "ISO 8147:1995 Shipbuilding and Marine Structures - Derrick Rigs and Component Parts Vocabulary",
"prefix": "1262"
},
"1263": {
"homepage": "http://www.technoseum.de/fileadmin/media/pdf/pdf_Sammlungen/Register.pdf",
"name": "TECHNOSEUM Keyword register for library systematics",
"prefix": "1263"
},
"1264": {
"homepage": "http://www.berliner-geschichtswerkstatt.de/tl_files/bgw/archiv/bgw-bibliothek-systematik.pdf",
"name": "Systematics archive and library of the Berliner Geschichtswerkstatt e.V.",
"prefix": "1264"
},
"1265": {
"description": "Shelf Classification Cultural Anthropology of the Textile of the Emil-Figge Library.",
"homepage": "https://www.ub.uni-dortmund.de/Fachinformation/Kunst/bmg_systematik_textil.html",
"name": "Shelf Classification Cultural anthropology of the textile",
"prefix": "1265"
},
"1266": {
"description": "Classification scheme of the Herzog Anton Ulrich museum in Brunswick",
"homepage": "http://www.3landesmuseen.de/fileadmin/user_upload/HAUM/bilder/layoutbilder/ueber_uns/bibliothek/Systematik_pdf_doc.pdf",
"name": "Classification scheme of the Herzog Anton Ulrich museum",
"prefix": "1266"
},
"1267": {
"homepage": "http://www.moderne-kunst.org/archiv/bestand.html",
"name": "Institute for Modern Art Nuremberg Archive / Library Classification Scheme",
"prefix": "1267"
},
"1268": {
"description": "This is the Library's 'three-figure' classification scheme which is used to determine the subject stem of the classmarks of the great majority of monographs on the open shelves. (It is also used in a simplified form in combination with various prefixes for special types of material: R, the reference collection in the Reading Room; S, 'select' books on closed access; P, L, T, Q, primary, secondary, select and dead periodicals, respectively; Z, mutilated books. Some other open access collections, such as music and reference collections in specialised reading rooms, have their own schemes.) This edition represents current practice and interpretation; inspection of the shelves will reveal classes superseded by more detailed subdivision or abandoned entirely, while policy on some of the less specific categories or on new areas of study will be found to have evolved over time. In recent years it has rarely been possible to reclassify in accordance with such changes and developments.",
"homepage": "http://www.lib.cam.ac.uk/class/",
"name": "Cambridge University Library Classification Scheme",
"prefix": "1268"
},
"1269": {
"description": "Because the library BASIS mainly includes Swiss law, it has its own system.",
"homepage": "http://www.ius.uzh.ch/library/collection/basis.html",
"name": "Study Library BASIC system",
"prefix": "1269"
},
"127": {
"description": "The systematic thesaurus of the Opac is a hierarchical collection of categorization covers, which are used to assign the entries in the database to corresponding subject areas, time sections or geographic locations.You can search all categories by full-text search or alphabetical tabs, or in the tree view of the systematic thesaurus The thesaurus divides the titles according to: Geographical assignment, time allocation, thematic assignment.",
"homepage": "http://opac.regesta-imperii.de/lang_de/thesaurus.php",
"name": "Regus of the Empire Thesaurus",
"prefix": "127"
},
"1270": {
"description": "Classification scheme of the Institute of Law of the University of Zurich.",
"homepage": "http://www.ius.uzh.ch/de/library/collection/system.html",
"name": "Classification scheme of the Institute of Law",
"prefix": "1270"
},
"1271": {
"description": "The Library of the American Planning Association (APA) developed the American Planning Association Library Classification Scheme. It was created to meet the needs of APAβs researchers and members; the scheme focuses specifically on planning and provides a level of practical detail not found in other published systems. In the APA Library, the scheme is used in conjunction with the Library of Congress Classification Scheme. A planning agency or library may choose to use the scheme independently or in conjunction with more broadly based schemes such as Library of Congress or Dewey Decimal.",
"homepage": "https://planning-org-uploaded-media.s3.amazonaws.com/legacy_resources/library/pdf/classificationscheme.pdf",
"name": "American Planning Association Library Classification Scheme",
"prefix": "1271"
},
"1272": {
"homepage": "http://www.fhnw.ch/campus-olten/bibliothek/bibliothekssystematik_ovr_20140618.pdf",
"name": "FHNW Olten Classification Scheme",
"prefix": "1272"
},
"1273": {
"description": "The Schiller system is a locally developed system for classifying foreign, comparative, pre-literate, ancient, medieval, and religious law materials. A call number in the Schiller classification system is comprised of an abbreviation to designate a legal system, followed by a number indicating the specific subject area within the system.",
"homepage": "http://web.law.columbia.edu/sites/default/files/microsites/library/files/Schiller_for_web_20130606.pdf",
"name": "Schiller Classification System",
"prefix": "1273"
},
"1274": {
"description": "The Library has separate sections either for jurisdictions or for certain legal systems or legal topics. Within each section, materials are shelved according to the (.) general scheme (.).",
"homepage": "http://www.bodleian.ox.ac.uk/law/finding/collections/catalogues/classification",
"name": "Bodleian Law Library Classification",
"prefix": "1274"
},
"1275": {
"description": "This proposed new classification scheme is based on two main elements: hierarchism and binary theory. Hence, it is called Universal Binary Classification (UBC). Some advantages of this classification are highlighted including subject heading development, construction of a thesaurus, and all terms with meaningful features arranged in tabular form that can help researchers, through a semantic process, to find what they need. This classification scheme is fully consistent with the classification of knowledge. The classification of knowledge is also based on hierarchism and binary principle.",
"homepage": "http://hdl.handle.net/10760/11392",
"name": "Universal Binary Classification",
"prefix": "1275"
},
"1276": {
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1139227",
"name": "Classification for Asian and African studies",
"prefix": "1276"
},
"1277": {
"homepage": "http://libraryguides.helsinki.fi/c.php",
"name": "Classification of the antiquarian research",
"prefix": "1277"
},
"1278": {
"description": "Kaisa House Shelf Ratings: EU Information Center",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1139237",
"name": "Classification for European Documentation Centre",
"prefix": "1278"
},
"1279": {
"description": "A classification for philosophy of the Helsinki University Library.",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1139238",
"name": "Classification for philosophy",
"prefix": "1279"
},
"128": {
"description": "1079 terms, 998 relationships between terms, 92 equivalent terms.",
"homepage": "http://doteine.uc3m.es/tesauros/lengua/index.php",
"name": "Thesaurus of Language and Literature",
"prefix": "128"
},
"1280": {
"description": "Kaisa House Shelf Ratings: History of Finland, Scandinavia and the Baltic States",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1145485",
"name": "Classification for history of Finland, Scandinavia and Baltic countries",
"prefix": "1280"
},
"1281": {
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1145486",
"prefix": "1281"
},
"1282": {
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1145487",
"name": "Archeology shelf classification",
"prefix": "1282"
},
"1283": {
"description": "A classification for folkloristics of the Helsinki University Library.",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1145488",
"name": "Classification for folkloristics",
"prefix": "1283"
},
"1284": {
"description": "Kaisa-Haus Shelf Classification: Ethnology",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1145489",
"name": "National Shelf Classification",
"prefix": "1284"
},
"1285": {
"description": "Kaisa House Shelf Ratings: North American Research",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1145490",
"name": "North America Research Shelf Rating",
"prefix": "1285"
},
"1286": {
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1145491",
"name": "Shelf rating of research in Russia and Eastern Europe",
"prefix": "1286"
},
"1287": {
"description": "Kaisa-Haus Shelf Classification: Fiction",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1139240",
"name": "Fiction classification of fiction",
"prefix": "1287"
},
"1288": {
"description": "Shelf ratings of Kaisa House: Finnish language",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1162850",
"name": "Classification for Finnish",
"prefix": "1288"
},
"1289": {
"description": "Shelf ratings of Kaisa House: Finnish-Ugrian languages",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1162851",
"name": "Classification for Finno-Ugrian Studies",
"prefix": "1289"
},
"129": {
"description": "It contains some 5,200 English descriptors (or preferred terms). An additional 6,900 non-preferred terms guide the user to preferred terms. Developed as an indexing and retrieval tool for the ASC library collection, the African Studies Thesaurus reflects the characteristics and main thematic areas of the collection. Specific Africa-related descriptors include the names of countries and regions, ethnic groups, African languages, African polities and political parties in Africa. It is used for indexing and retrieving material in the library collection and is directly linked to the catalogue.",
"homepage": "http://thesaurus.ascleiden.nl/",
"name": "African Studies Thesaurus",
"prefix": "129"
},
"1290": {
"description": "Kaisa House Shelf Ratings: English Language",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1162852",
"name": "Classification for English",
"prefix": "1290"
},
"1291": {
"description": "A classification for Germanic languages",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1162853",
"name": "Classification for Germanic languages",
"prefix": "1291"
},
"1292": {
"description": "Kaisa House Shelf Ratings: Nordic Languages",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1162854",
"name": "Classification of Nordic languages",
"prefix": "1292"
},
"1293": {
"description": "-",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1162855",
"name": "Romance Language Classification",
"prefix": "1293"
},
"1294": {
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1162856",
"name": "Classification for Slavonic and Baltic languages",
"prefix": "1294"
},
"1295": {
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1162857",
"prefix": "1295"
},
"1296": {
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1225501",
"name": "Law School Shelf Rating",
"prefix": "1296"
},
"1297": {
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1239403",
"name": "Shelf Rating of Literary Research, Aesthetics, Theater Science, Film and Television Research",
"prefix": "1297"
},
"1298": {
"description": "Music Anthropology shelf classification",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1239404",
"name": "Classification for musicology",
"prefix": "1298"
},
"1299": {
"homepage": "http://libraryguides.helsinki.fi/c.php",
"name": "Shelf rating of art history",
"prefix": "1299"
},
"13": {
"description": "1883 terms, 2729 relations between terms, 493 non-preferred terms. Generic terms used by the CSPS Library.",
"homepage": "http://www.vocabularyserver.com/csps/",
"name": "Canada School of Public Service Controlled Vocabulary",
"prefix": "13"
},
"130": {
"description": "The AFS Ethnographic Thesaurus (version 2.2) is a vocabulary that can be used to improve access to information about folklore, ethnomusicology, ethnology, and related fields. The American Folklore Society developed the Thesaurus in cooperation with the American Folklife Center of the Library of Congress and supported by a generous grant from the Scholarly Communications Program of the Andrew W. Mellon Foundation.",
"homepage": "http://id.loc.gov/vocabulary/ethnographicTerms.html",
"name": "American Folklore Society Ethnographic Thesaurus",
"prefix": "130"
},
"1300": {
"description": "Kaisa House Shelf Ratings: Biblical and Judaism",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1281064",
"name": "Classification for biblical and Jewish studies",
"prefix": "1300"
},
"1301": {
"description": "The Helka catalogue includes collections of Helsinki University Library, National Library, Institute for the Languages of Finland, National Board of Antiquities Library, Finnish Literature Society, Library of the Labour Movement and Baltia-kirjasto.",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1281065",
"name": "\"Practical Theology Shelf Rating \"",
"prefix": "1301"
},
"1302": {
"abbreviation": "Coct",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1281066",
"name": "Classification of the Orthodox Church and theology",
"prefix": "1302"
},
"1303": {
"description": "The Helka catalogue includes collections of Helsinki University Library, National Library, Institute for the Languages of Finland, National Board of Antiquities Library, Finnish Literature Society, Library of the Labour Movement and Baltia-kirjasto.",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1281067",
"name": "Practical Theology Shelf Rating",
"prefix": "1303"
},
"1304": {
"homepage": "http://libraryguides.helsinki.fi/c.php",
"name": "Luther study shelf rating",
"prefix": "1304"
},
"1305": {
"description": "Kaisa House Shelf Ratings: Systematic Theology",
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1281070",
"name": "Classification for systematic theology",
"prefix": "1305"
},
"1306": {
"homepage": "http://libraryguides.helsinki.fi/c.php?g=172710&p=1634777",
"name": "Classification for social sciences",
"prefix": "1306"
},
"1307": {
"description": "Classification of the Department of English and American Studies at the University of Vienna.",
"homepage": "http://bibliothek.univie.ac.at/fb-anglistik/classification_2.html",
"name": "English and American Studies Library Classification",
"prefix": "1307"
},
"1308": {
"homepage": "http://www.sirkusinfo.fi/fi/luokitus-ja-hyllypaikat",
"prefix": "1308"
},
"1309": {
"description": "This Archives Classification Schedule is an outline of the holdings of the University Archives. Record groups are the major administrative divisions of the overall collection. Record series within these record groups are the discrete, distinct collections.",
"homepage": "https://www.library.uni.edu/collections/special-collections/university-archives/classification-schedule",
"name": "University Archives Classification Schedule",
"prefix": "1309"
},
"131": {
"description": "This thesaurus is based upon the Art & Architecture Thesaurus (AAT) produced by The Getty Research Institute and follows as closely as possible its theoretical model for the organization of concepts (categories). Where the AAT differs in its description of an object or concept found in the AMNH collection, the AMNH term is inserted into the appropriate position in the existing AAT hierarchy. It was designed to demonstrate the capabilities of a thesaurus in searching across the AMNH anthropological collections and to generate feedback from researchers and the public. It currently contains around 1,000 categories and 10,000 terms linked to these categories. Currently, the seven 'top level' terms and the vast majority of the 'mid level' terms (categories) come directly from the AAT while all of the 'bottom level' terms and a few of the 'mid level' terms are derived from AMNH keywords. The goal of this thesaurus is to allow users to browse through a hierarchical structure to locate individual objects and to see broader, narrower, and related terms rather than having to perform a tradition search on individual terms. The terms are used to retrieve objects in the collections database.",
"homepage": "http://anthro.amnh.org/thesaurus",
"name": "American Museum of Natural History/Division of Anthropology/Collections Thesaurus",
"prefix": "131"
},
"1310": {
"description": "Our mission includes the prevention of landslides and coastal erosion, sustainable and effective soil works, know-how and methods to remediate contaminated sites and climate adaptation. We contribute towards achieving the national environmental objectives. The environmental objectives that affect our operations are above all A good built environment and A toxic-free environment.",
"homepage": "http://www.ipu-berlin.de/bibliothek/literatur/systematik.html",
"name": "International Psychoanalytic University classification scheme",
"prefix": "1310"
},
"1311": {
"description": "The Roy classification is unique to the Law Library of the UniversitΓ© de MontrΓ©al, and our documentation is entirely classified according to an alphabetical system that divides it into two main areas: general collections and specialized collections.",
"homepage": "http://www.bib.umontreal.ca/DR/a-propos/classification-detaillee.htm",
"name": "Classification Roy",
"prefix": "1311"
},
"1312": {
"description": "BAnQ has a collection of more than 100,000 sound recordings, and the collection's classification system makes it easy to find a record and make great discoveries.\" The Iris catalog offers helpful help features for more detailed research. Classification system is divided into seven main categories.",
"homepage": "https://www.banq.qc.ca/collections/collection_universelle/musique_films/classification_enregistrements_films/index.html?language_id=3#sonores",
"name": "Classification system for sound recordings",
"prefix": "1312"
},
"1313": {
"description": "Fiction films are grouped into eight major cinematographic genres to help you choose from the collection. The films are sorted in alphabetical order according to each genre.",
"homepage": "https://www.banq.qc.ca/collections/collection_universelle/musique_films/classification_enregistrements_films/index.html?language_id=3#films",
"name": "Film Classification Plan",
"prefix": "1313"
},
"1314": {
"description": "Library system of the German Historical Institute Warsaw.",
"name": "German Historical Institute Warsaw Library System",
"prefix": "1314"
},
"1315": {
"description": "The Gay Museum * was founded in 1985 and today is one of the largest and most important institutions for archiving, researching and communicating the history and culture of the LGBT * with its highly acclaimed exhibitions, archive collections, numerous research papers and more than thirty-five - mostly volunteer employees - I * Q communities. Changing exhibitions and events deal in a variety of ways with lesbian, gay, trans * identical, bisexual and queer life stories, themes and concepts in history, art and culture.",
"homepage": "http://www.schwulesmuseum.de/bibliothek/systematik/",
"prefix": "1315"
},
"1316": {
"description": "The literature in our library is organized in a systematic manner. The subject group index provides detailed information on the contents of the individual signature groups and thus helps in the search for content.",
"homepage": "http://www.wiwi.uni-tuebingen.de/fachbereich/einrichtungen-und-service/bibliothek/recherche/systematik.html",
"name": "Systematics of the subject library economics",
"prefix": "1316"
},
"1317": {
"homepage": "http://www.muwi.uni-freiburg.de/bibliothek/Bibliothekssystematik.pdf/at_download/file",
"prefix": "1317"
},
"1318": {
"description": "Bibliothekssystematik fΓΌr Kognitions- und Neurowissenschaften des Max Planck Institutes.",
"name": "Max-Planck-Institut (MPI) fΓΌr Kognitions- und Neurowissenschaften Bibliothekssystematik",
"prefix": "1318"
},
"1319": {
"description": "You can also click directly in the OPAC through the systematics and display the titles by selecting the corresponding systematic group in the search field (eg A-Gb) in the advanced search in the scrolling menu 'System group' and then right on the tab click.",
"homepage": "http://www.mh-trossingen.de/hochschule/institutionen/bibliothek/systematik.html",
"name": "Library of the State College of Music Trossingen Systematics",
"prefix": "1319"
},
"132": {
"description": "Welcome to the Indigenous and Northern Affairs Canada Subject Thesaurus (IST), which was developed to make retrieval of Indigenous and Northern Affairs Canada (INAC) information more efficient. A subject thesaurus is a list of subject keywords that can be used to index or classify documents that are about a particular topic. These subject keywords can then be used by search engines to provide relevant results pertaining to a particular subject. The IST includes relationships between keywords and phrases such as broader terms, narrower terms, preferred terms, non-preferred terms or related terms. The purpose of these relationships is to help indexers/classifiers to find the best subject keywords to describe the \"aboutness\" of documents. Also, these relationships can help searchers by providing preferred and related subject terms to use in a search.\n\nThe IST is a bilingual thesaurus of subject terms describing the work of INAC. It includes more than 2800 terms in English and more that 2900 terms in French, including almost 1300 preferred terms in each language. The IST conforms to internationally accepted standards and conventions for thesaurus construction (i.e. Guidelines for the construction, format and management of monolingual controlled vocabularies (ANSI/NISO Z39.19-2005), Guidelines for the establishment and development of monolingual thesauri (ISO 2788-1986) and the Guidelines for the establishment and development of multilingual thesauri (ISO 5964-1985)).",
"homepage": "http://www.aadnc-aandc.gc.ca/eng/1484594838764/1484594869729",
"name": "Indigenous and Northern Affairs Canada Subject Thesaurus",
"prefix": "132"
},
"1320": {
"homepage": "http://www.ph-gmuend.de/fileadmin/redakteure/ph-hauptseite/redakteure/daten/download/einrichtungen/bibliothek/Aufstellungssystematik_komplett_Jan_18.pdf",
"name": "University of Applied Sciences SchwΓ€bisch GmΓΌnd Installation system of the university library",
"prefix": "1320"
},
"1321": {
"description": "Classification scheme of the house of the history of women in Bonn",
"homepage": "http://www.hdfg.de/bibliothek.php#Bibliothekssystematik",
"name": "Classification scheme of the house of the history of women",
"prefix": "1321"
},
"1322": {
"description": "Classification of the Iglf-Bibliothek",
"homepage": "http://www.csgkoeln.de/Texte/website/bibliothek/systematik.htm",
"name": "Classification of the Iglf-Bibliothek",
"prefix": "1322"
},
"1323": {
"abbreviation": "GOK",
"description": "You get systematic access to the GΓΆttinger UniversitΓ€tskatalog (GUK) through the GΓΆttinger Online-Klassifikation (GOK). That is a universal classification system, which attempts to order the entire spectrum of sciences into a hierarchic system. Most of the important additions after 1993 have been made accessible in this system.",
"homepage": "http://www.sub.uni-goettingen.de/goettinger-online-klassifikation/",
"name": "GΓΆttingen online classification",
"pattern": "^[A-Z]+ ([0-9]{3}|XXX)$",
"prefix": "1323"
},
"1324": {
"abbreviation": "SEB",
"description": "The media collections of Protestant libraries are developed with the aid of the system for Protestant libraries (SEB). According to this system, the media is placed on the shelf and is shown in the systematic catalog.",
"homepage": "https://www.xn--bchereiservice-gsb.de/fileadmin/redakteur/B%C3%BCcherei_Service/Dokumente/Buechereipraxis/Feb_2022/BP-Praxishilfe_Systematik_f%C3%BCr_Evangelische_B%C3%BCchereien_und_Index_Februar_2022.pdf",
"name": "Systematics for Protestant libraries",
"pattern": "^([A-Z1-2]([a-z\\.]([1-2 ]([0-9]+)?)?)?)?$",
"prefix": "1324"
},
"1325": {
"abbreviation": "SKB",
"description": "The presentation of the material from the various fields of knowledge, also as a report, an experience sign, a guidebook or a reference book, are organized according to the 'Specialist System for Catholic Public Libraries' (SKB-E) and the enlarged version (SKB-E) Non-book media for children are classified according to the 'Systematics for Children's Books' The systematic catalog opens up the material stock in libraries according to content (systematics) and provides information on the question whether media is available on a specific topic or subject area, For example, which media are to be found in the library on the subject of the \"family\" or \"child education\" The classification of the subject media into the shelves is determined by the systematics, the 'Sachbuch-Systematik for Catholic public libraries' Library in two differently finely divided editions: The basic edition (p KB) is used in Catholic public libraries with small non-fiction books. The extended version (SKB-E) is used in libraries with a more specialized subject book. The notations of both variants of the system are given in the review magazines of the Catholic library work, the 'bookprofiles' and the 'media profiles', for each revised title. A 'Stich- und Schlagwortregister' was published on the Sachbuch system. On the one hand, it helps in the librarianship in the consultation of readers. It also makes it easier to classify newly acquired books and other media into the relevant subject groups. The register provides, for example, information on the question of where books and media are classified as 'age'. Through the use of appropriate library software the classification of the newly acquired titles into the subject groups and the information service in the library are made much easier. The programs developed for the Catholic Library work contain the entire system and the terms from the 'Stich- und Schlagwortregister'.",
"homepage": "http://www.eopac.net/AGX000921/accesslist/notation/",
"name": "Nonfiction classification of Catholic public libraries",
"pattern": "^[A-Z]+( [0-9]+(.[0-9]+)?)?$",
"prefix": "1325"
},
"1326": {
"description": "The collection contains books, journals, pamphlets, etc. about Schleswig in all 5 languages and dialects of Danish, German, Frisian, Sudan, Jutland and Plateau. The topics include history, art, language and dialect research, social relations, nature and the environment & Much more. Also fiction and children's books from the Schleswig-Holstein region are richly represented in the collection. As a matter of fact, the Schleswig Collection contains a large book-historical collection, some of which originate from the 16th century.",
"homepage": "https://www.dcbib.dk/sites/sydslesvig.ddbcms.dk/files/files/page/signaturer_og_klassifikation.pdf",
"name": "The Schleswig Collection Signatures & Classification",
"prefix": "1326"
},
"1327": {
"description": "The Pontifical Gregorian University Library has developed her own system to classify books and periodicals. The Book Classification System is composed of: 910 general subject areas indicated by a number included from number 1 to number 910; many sub-subject areas indicated by the number of related subject area (1 - 910) and by one or more alphabet letter.",
"homepage": "http://www.unigre.it/Newbiblio/specifico/classificazione_it.php",
"name": "Library Classification System of the Gregorian Pontifical University",
"prefix": "1327"
},
"1328": {
"description": "Fiction narratives are sorted according to a genre rating specifically designed by the Aosta cataloging center. Sixteen are the expected genres, expressed through Arabic numerals and preceded by RN.",
"homepage": "http://biblio.regione.vda.it/biblioteche-sbv/Aosta-Biblioteca-regionale/ragazzi/generi-narrativa-ragazzi",
"name": "Classification of Youth Literature Genres",
"prefix": "1328"
},
"1329": {
"description": "TESEO is a classification system used in the most important databases of the Senate, the Chamber and some regions. It consists of 3668 descriptors (2001, edition 3.1), organized in a system Hierarchical relationships, affinity and preference.The classification terms are, with obvious updates, those used for Senate parliamentary acts since 1848. The logical structure according to which the terms are ordered is that of the Universal Decimal Classification (CDU ): It is a tesauro not specialized in a particular branch, but, as is the case of parliamentary matter, extended to the whole social, juridical and scientific reality.",
"homepage": "http://www.senato.it/ric/sddl/raffinaricerca.do",
"name": "TEsauro Sealed for Organization of Parliamentary Documents",
"prefix": "1329"
},
"133": {
"description": "The EURISLAM bibliographic database for researchers and teachers lists all publications on the current situation in the wider Europe of Islam as a religion (beliefs, religious practices, religious sensibilities) and Muslims as (Muslim immigration, community institutions, public regulation). The database takes into account journal articles, works or contributions to collective works, reports of studies or surveys, and theses.",
"homepage": "http://www.misha.fr/sites_bdd.htm",
"name": "EURISLAM Thesaurus",
"prefix": "133"
},
"1330": {
"homepage": "http://dati.senato.it/21",
"prefix": "1330"
},
"1331": {
"homepage": "http://dati.camera.it/ocd/",
"name": "Ontologia Camera dei Deputati",
"prefix": "1331"
},
"1332": {
"description": "In order to facilitate this process, the books are arranged according to a so - called system of positioning, which is reflected in the signatures The individual signature groups in this sense refer to the main contents or types of literature listed in the (.) Overview.",
"homepage": "http://www.zikg.eu/bibliothek/pdf/systematik-der-buchaufstellung/view",
"name": "Central Institute of Art History",
"prefix": "1332"
},
"1333": {
"homepage": "http://library.au.dk/fagsider/slettede-fagsider/teologireligionsvidenskabarabisk-semitisk/klassifikationssystem/",
"name": "Classification system for The Faculty of Theology",
"prefix": "1333"
},
"1334": {
"description": "1351 terms, 458 relations between terms, 240 non-preferred terms.",
"name": "Agricultural Communications Thesaurus",
"prefix": "1334"
},
"1335": {
"description": "The schedules that form the Marianist Library Classification were developed because the classification scheme most commonly used in Marianist libraries, 'Marianist Classification 1960; For Archives and Documentary Libraries' developed by Father William Ferree, SM, became impossible to implement successfully. Years of work and consultation with experts in Marianist history and spirituality as well as input from Mr. Thompson A. Yee, Acting Chief of the Cataloging and Policy Support Office at the Library of Congress, have resulted in this new approach to classifying materials by and about the Marianists. The organizational basis for the schedules comes from the classes developed and defined by Brother Lawrence Scrivani, SM, in his 'Classification Scheme for Marianist Documents Libraries'. In their application, the present schedules gather and organize Marianist works by topic or subject and are designed to follow Library of Congress cataloging practices and procedures.",
"homepage": "http://www.nacms.org/library/marianist-library-classification#.VT34jGOEM83",
"name": "Marianist Library Classification",
"prefix": "1335"
},
"1336": {
"homepage": "http://www.oats.inaf.it/index.php/it/2014-09-12-11-41-37/servizi-oats/biblioteca/193-osservatorio/servizi-oats/biblioteca/315-biblioteca-sistema-di-classificazione.html",
"name": "Astronomical Observatory of Trieste Library Classification system",
"prefix": "1336"
},
"1337": {
"description": "The Library of Biblical Exegesis has a comprehensive classification system that applies to all sub-areas. (...) Library of Church History has four independent classification systems. (...) There are three systems in the Library of Systematic Theology, one for dogmatics, ethics and Religious philosophy. Practical theology and ecumenical theology each have their own system.",
"homepage": "http://teol.ku.dk/bibliotek/klassifikation/",
"name": "The Faculty of Theology Faculty Library Classification Schemes",
"prefix": "1337"
},
"1338": {
"description": "Classiification sheme of the Zentralbibliothek of the Roman-Germanic Central Museum.",
"homepage": "http://web.rgzm.de/fileadmin/Gruppen/Bibliothek/Bibliothekssystematik.pdf",
"name": "Classifications of the Zentralbibliothek of the Roman-Germanic Central Museum",
"prefix": "1338"
},
"1339": {
"abbreviation": "HTWG",
"description": "Classification scheme for the Hochschule Konstanz University of Applied Sciences (HTWG).",
"homepage": "https://www.htwg-konstanz.de/hochschule/einrichtungen/bibliothek/nutzung-ausleihe/buchaufstellung-und-grundriss/",
"license": "CC0-1.0",
"name": "Hochschule Konstanz University of Applied Sciences (HTWG) classification scheme",
"pattern": "^[A-Z][A-Z]?[A-Z]?[0-9]*$",
"prefix": "1339"
},
"134": {
"description": "GeoEthno is a geographical thesaurus designed for the geographic indexing of documents in the field of anthropology and is a documentary tool for establishing a standardized list of keywords that can be used for indexing and / Questioning the bibliographic database of the Eric-de-Dampierre library (the 'catalog') and more broadly in the other libraries of the 'Ethnology Network'.",
"homepage": "http://www.mae.u-paris10.fr/dbtw-wpd/bed/index-lesc.html",
"name": "Geographic Thesaurus for Ethnology",
"prefix": "134"
},
"1340": {
"description": "The books on our shelves are arranged according to Sachthemen, and our library system allows you to see where in the house you can find works on a certain topic.",
"homepage": "https://stadtarchiv-bielefeld.de/Best%C3%A4nde/Bibliothek/LgB-Systematik",
"name": "Classification of the Country library",
"prefix": "1340"
},
"1341": {
"description": "In addition to the library systematic for all subject groups, we also offer the search for a Bielefeld system in the online catalog, especially for the literature on Bielefeld, which serves to further improve the factual relevance of these publications, and also has the advantage of being quickly comprehensible. According to this system, however, only the Bielefeld literature has been fully documented since the acquisition year 2008. The retrospective expansion is being worked on.",
"homepage": "https://www.stadtarchiv-bielefeld.de/Best%C3%A4nde/Landesgeschichtliche-Bibliothek/Systematik",
"name": "Bielefeld systematics",
"prefix": "1341"
},
"1342": {
"description": "The inventory of the University Library of Cottbus, which is freely accessible to our users, is arranged in a systematic order, and the system underlying this list is divided into several hierarchical levels, within which the different groups are represented by a notation consisting of numbers and partial numbers Numbers and letters.",
"homepage": "http://www.tu-cottbus.de/einrichtungen/ikmz/servicebereiche/bibliothek/benutzung-und-service/bestandsaufstellung/systematik/hauptgruppen.html",
"name": "Brandenburg University of Technology (BTU) Cottbus-Senftenberg Systematics of the University Library",
"prefix": "1342"
},
"1343": {
"description": "The system serves the content development of the media and can also help to limit the amount of hits.",
"homepage": "http://www.buechereien.wien.at/media/file/334_WS_B_11_2009.pdf",
"name": "Viennese system for public libraries",
"prefix": "1343"
},
"1344": {
"description": "forestal shelf classification of the university for forestry in rottenburg",
"homepage": "https://www.hs-rottenburg.net/die-hochschule/einrichtungen-der-hfr/bibliothek/wissenschaftliches-arbeiten/forstliche-aufstellungssystematik-kurzfassung/",
"name": "University for forestry in rottenburg (HFR)",
"prefix": "1344"
},
"1345": {
"description": "SK2 (Systematic Catalog 2nd Edition) is used for books in the University Library Collections acquired since 1995.",
"homepage": "http://www.kb.dk/da/klassifikation/index.html",
"name": "The Royal Library Systematic Catalog 2nd Edition.",
"prefix": "1345"
},
"1346": {
"description": "SK1 (Systematic Catalog 1st Edition) is used for books in the University Library Collections acquired 1980 - 1995.",
"homepage": "http://www.kb.dk/da/klassifikation/index.html",
"name": "The Royal Library Systematic Catalog 1.th.",
"prefix": "1346"
},
"1347": {
"description": "In 2013, the Royal Library has made a pragmatic assurance that the Nordic Journal of Criminal Law and its replacement of the Nordic Journal of Criminal Science from the period 1912-2012 has been made available on the internet. In addition, Nell Rasmussen, Vagn Greve and Lene Kielgast : Bibliography of Nordic Criminal journals and yearbooks 1878-1982, Jurist and Economic Union Publishers, Copenhagen 1984, and Lene Kielgast: Author Register for Bibliography of Nordic Criminal Magazines and Yearbooks 1878-1982, Criminal Institute's Stencil Series, No. 32, Copenhagen 1985, what Which makes it considerably easier to find the relevant ones in the journals. However, it has left a gap in the registers for the years 1983-2012: this hole is searched through this register. This registry uses essentially the same systematics and criteria as the earlier.",
"homepage": "http://www.kb.dk/e-mat/dod/130020753073.pdf",
"name": "Systematic Register to the Nordic Journal of Criminal Science 1983-2012",
"prefix": "1347"
},
"1348": {
"description": "To facilitate the user access to the document and to use the information contained therein, a classification plan for 19 topics, based on the same tabular storage on the shelf after a quota system.",
"homepage": "http://www.ipleiria.pt/sdoc/centro-de-documentacao-europeia/#classificacao",
"name": "European Documentation Center Classification Plan",
"prefix": "1348"
},
"1349": {
"homepage": "http://www.rug.nl/bibliotheek/services/bibgmw/collection/classification",
"name": "University Groningen University Classification Scheme",
"prefix": "1349"
},
"135": {
"description": "It is derived from the waka, iwi and hapΕ« names in He Puna Kupu MΔori and TΔpuhi and has been reviewed by Te Taura Whiri (MΔori Language Commission). This list has been developed for the wider library and archives communities and will be used by the National Library of New Zealand to enhance its service to MΔori library users. However it should not be seen as authoritative beyond its intended purpose for use in libraries and archives.",
"homepage": "http://iwihapu.natlib.govt.nz/iwi-hapu/",
"name": "Iwi-HapΕ« Names List",
"prefix": "135"
},
"1350": {
"description": "The hospital system classification system (SKS) consists of several thousand codes that are used to provide structured information to different information systems. The codes span a very wide range and to find just that code that accurately reflects a given event or condition is not Always a trivial task. Therefore, we have made some online tools - they are far from perfect, but hopefully help. All tools are based on an online database that contains only SKS and SHAK codes. The database is updated continuously , And the data content of the tools is thus always updated.",
"homepage": "http://www.medinfo.dk/sks/brows.php",
"name": "Hospital System Classification System",
"prefix": "1350"
},
"1351": {
"description": "The Classification of Surgical Procedures (NCSP) is based on the traditions of the surgical profession in the Nordic countries and reflects surgical practice in these countries in 1994. It constitutes the first common Nordic classification of surgical procedures. In producing this classification attention has been paid to generally accepted requirements for surgical procedure components as seen in concurrent classification development. In addition the classification is designed to give reasonable scope for expansion to meet anticipated future advances in the field of surgical procedures. With these updates the NCSP is expected to do good service as a regional classification for some years.",
"homepage": "http://www.nordclass.se/ncsp_e.htm",
"name": "NOMESCO Classification of Surgical Procedures",
"prefix": "1351"
},
"1352": {
"description": "Management Classification (...) is a new classification developed for use in property management. Management Classification replaces SfB Building Panel, which for a number of years has been the usual standard for classification of building components in the Danish construction sector. Management Classification has been prepared by the National Fund in cooperation With the management's classification society, as with its SfB Building Panel, it is possible to keep track of its building components. So, it is actually a little easier, partly because building parts in terrain and building parts in buildings are now clearly separated. It will also be easier to keep Controls the characteristics of the building components because the classification includes a systematic description of property data. The main innovation of the Management Classification, however, is that it includes the overall systematics required when moving from the traditional document-based situation where the same information often finds S in several places and in several variants and into a modern digital web-based world where the individual information is only available and updated in one place and from which it is accessible to everyone.",
"name": "Management Classification",
"prefix": "1352"
},
"1353": {
"description": "Consists of three relational, reliable, and valid components designed to be used together: Problem Classification Scheme (client assessment); Intervention Scheme (care plans and services); Problem Rating Scale for Outcomes (client change/evaluation). Is a research-based, comprehensive, standardized taxonomy or classification that exists in the public domain. It is designed to enhance practice, documentation, and information management. It is intended for use across the continuum of care for individuals, families, and communities who represent all ages, geographic locations, medical diagnoses, socio-economic ranges, spiritual beliefs, ethnicity, and cultural values. Has terms that are arranged in a hierarchy (i.e. from general to specific), and are intended to be easily understood by health care professionals and the general public. It provides a structure to document client needs and strengths, describe multidisciplinary practitioner interventions, and measure client outcomes in a simple and user-friendly, yet comprehensive, manner. Enables collection, aggregation, and analysis of clinical data. It supports quality improvement, critical thinking, and communication. It fosters research involving best practices/evidence-based practice. It links clinical data to demographic, financial, administrative, and staffing data. It is a middle range theory that supports other established health care theories. Examples include Donabedianβs structure, process, and outcome approach and the Neuman Systems Model. (...) Current users are nurses, physical therapists, occupational therapists, speech and language pathologists, social workers/counselors, physicians, registered dieticians, recreational therapists, chaplains, pharmacists, community health workers, chiropractors, and other health care providers. Users also include nursing educators, researchers, and students enrolled in associate degree to doctoral programs, and educators and students from other health-related disciplines. Current users and their sites now include the continuum of care: home care, public health, and school health practice settings, nurse-managed center staff, hospital-based and managed care case managers, educators and students, occupational health nurses, faith community staff, acute care and rehabilitation hospital/long-term care staff, researchers, members of various disciplines, and computer software vendors. The majority of Omaha System users are located in the United States.",
"homepage": "http://omahasystem.org/",
"name": "Omaha System",
"prefix": "1353",
"wikidata_database": "Q17072524"
},
"1354": {
"description": "The library of Tecnun has a system of classification of works of its own.The signature of each work is alphanumeric being formed by one or several letters and by a number, which indicate:\n\n The matter (A Mechanics, B Computer science, etc.)\n\n The sub-material (indicated in letters and numbers: A Tribology 001)\n\n The order number within each section",
"homepage": "http://www4.tecnun.es/servicios/biblioteca/informacion-general/sistema-de-clasificacion.html",
"name": "Classification Scheme of the Tecnun Library",
"prefix": "1354"
},
"1355": {
"description": "The Classification Plan is proposed as a tool for ordering, organizing and finding the documents generated or received by the University in the fulfillment of its duties, competencies and activities. The Proteos Protocol System uses the classification plan to open processes The activities were distributed in large classes and subdivided into categories, according to the characteristics of each area of activity, Reflect the activities of USP (teaching, research and extension).",
"homepage": "http://www.usp.br/arquivogeral/?page_id=90",
"name": "General Archive of the University of SΓ£o Paulo Classification Plan",
"prefix": "1355"
},
"1356": {
"homepage": "http://www.ufrgs.br/saaufrgs/Manuais/planocassificacao.pdf",
"name": "Document Classification Plan of the Federal University of Rio Grande do Sul",
"prefix": "1356"
},
"1357": {
"description": "The lawyers' office of the library is a resource center specializing in the acquisition, technical processing and dissemination of legal information, with the primary objective to meet the information requirements of lawyer and legal trainee.",
"homepage": "http://www.oa.pt/cd/Conteudos/Artigos/detalhe_artigo.aspx?sidc=58102&idsc=58658&ida=40331",
"name": "Library of the Order of Lawyers Classification plan of the documentation",
"prefix": "1357"
},
"1358": {
"description": "The classification code is a working tool used to classify any document produced or received by the Superior Labor Court (TST), and, where applicable, it will also be adopted by the Superior Council of Labor Justice (CSJT) and by the The classification by subjects is used to group the documents under the same theme, as a way of accelerating the recovery and facilitating the activities related to the evaluation, selection, elimination In the classification code, subjects are given numerical codes, which reflect the functional hierarchy of the organ, defined through classes, subclasses, groups and subgroups, always starting from the general to the particular. In the preparation of this code, the decimal classification model. That is, the system consists of a numeric code , Divided into ten classes, these are subdivided into ten subclasses and so on.",
"homepage": "http://www.csjt.jus.br/c/document_library/get_file?uuid=fba76fff-2c20-4c99-ad09-1fe2433c43e1&groupId=955023",
"name": "Classification Plan and Temporary Table of Administrative and Judicial Documents of the Superior Labor Court",
"prefix": "1358"
},
"1359": {
"description": "Classification scheme of the medical school of the University Hospital Magdeburg.",
"homepage": "https://www.mzb.ovgu.de/Literatursuche/Systematik.html",
"name": "Classification of the medical central library",
"prefix": "1359"
},
"136": {
"description": "This is a controlled vocabulary of education-related subjects and terms linked to the Hebrew index.",
"homepage": "http://www.jewish-education-sources.co.il/",
"name": "Treasures of Jewish Education Thesaurus",
"prefix": "136"
},
"1360": {
"homepage": "http://www.uni-muenster.de/imperia/md/content/staedtegeschichte/pdf-dateien/wissenschaftsservice/bibliothek/bibliothekssystematik.pdf",
"name": "Institute of Comparative City History Library Systematics",
"prefix": "1360"
},
"1361": {
"description": "Library system of the Museum of Film and Television.",
"name": "German Kinemathek - Museum for Film and Television library system",
"prefix": "1361"
},
"1362": {
"description": "Library classification from the year 1783.",
"homepage": "http://nbn-resolving.de/urn:nbn:de:bsz:16-diglit-70735",
"license": "CC BY-SA 3.0",
"name": "Codices Salemitani X,44a library system",
"prefix": "1362"
},
"1363": {
"description": "There are already in the field many rival schemes of classification for libraries. The present publication is not intended to add one to the number, but rather to offer a way of escape for those who shrink from the intricacies and difficulties of the elaborate systems, and to substitute for painstaking analytical classification a simple arrangement which it is believed is better adapted to be practically useful in a library, while doing away with most of the work involved in carrying out one of these schemes.",
"homepage": "https://archive.org/details/libraryclassifi00flet",
"name": "Library Classification",
"prefix": "1363"
},
"1364": {
"description": "The IAC library has its own book classification system.",
"homepage": "http://www.iac.es/adjuntos/biblioteca/sistema-biblio-iac.pdf",
"name": "IAC Library Book Classification System",
"prefix": "1364"
},
"1365": {
"description": "In this course, the initial assumptions of the project were maintained, namely: a) Creation of a single tool with classification and evaluation concerns; b) Construction of an instrument that promotes transversality and semantic interoperability; ) Application of the classification plan to the documentation at the stage of its creation or reception.\n\nΒ Is not an instrument of retroactive application, nor does it intend to reorganize the documentation already produced; (D) Use of the instrument to classify documentation on paper or other media. Applies to electronic file management systems (SEGA) as well as to electronic information systems in the support or business areas (SIE); (...) It presents the complete attributes of each class: classification code, class title, description, application notes and exclusion notes. The presentation is preceded by the conceptual map that was the basis of the identification, ordering and coding of the 3rd levels, as well as a small explanatory text about the concept map and the coding rules.",
"homepage": "http://arquivos.dglab.gov.pt/wp-content/uploads/sites/16/2014/02/PC_AL_2014_01_311.pdf",
"name": "Archival Information Classification Plan for Local Administration",
"prefix": "1365"
},
"1366": {
"description": "The SMA - 6 Resolution of 8-2-2007, published in the Official Gazette of February 10, 2007, approved the Classification Plan and the Timetable of Documents of the Activities - End of the State Secretariat of the Environment The Document Classification Plan and the Temporary Document Table are the basic instruments of Document Management and are the result of a process of analysis that allows the identification of the values ββof the documents for the purposes of defining their custody and destination deadlines. In the Temporary Table of SMA Activity-End Documents were identified: (1) a function that is the Management of State Environmental Policy, 6 (six) subfunctions corresponding to the large areas of operation of the SMA, 18 activities developed by the various organs With these instruments, SMA will reduce to the essential the documents accumulated in its archives, without prejudice to the safeguard of the acts Administrative, constitutive and extinguishing rights, information indispensable to the decision-making process and the preservation of institutional memory. In 2003, SMA began to manage documents related to Environmental Activities, observing the current norms and directives of the central body of SAESP, the State Archives, since then the SMA has been carrying out actions aimed at implementing a document management system Compatible with the new organizational paradigms and in accordance with the current legislation, covering its activities end, in a pioneering attitude, since adopted before such providence became mandatory. The Technical Group, established by the Resolution No. CC-33 of April 8, 2004, of the Civil House to carry out the planning and strategy for the implementation of the Single Protocol, For the adaptation of the requirements of the application of the System, as well as the elaboration of a strategic plan for its implementation, depends on an exhaustive knowledge of the documentary production generated and accumulated by the organs of the state administration, reason why it selected some organs to participate in the pilot project , Among which is the SMA. The elaboration of the Classification Plan and the Temporary Table of Documents counted on the involvement and collaboration of technicians from the different areas of the SMA. The joint action of these professionals was of fundamental importance for the accomplishment of the work. With the application of the Tables of Temporality of Documents we are performing the elimination of documents, a procedure that is part of the management of documents and aims at the rationalization of space, reduction of documentary mass, rationalization of production and document flow, agility in the recovery of Documents and information, administrative efficiency and preservation of memory.",
"homepage": "http://www.ambiente.sp.gov.br/a-secretaria/quem-somos/plano-de-classificacao/",
"name": "Secretariat of the Environment Classification Plan",
"prefix": "1366"
},
"1367": {
"homepage": "http://cedo.ina.pt/docbweb/thres.asp",
"name": "INA Web Thesaurus",
"prefix": "1367"
},
"1368": {
"description": "In creating TUT we relied extensively on existing finding aids to generate terms and tested the thesaurus against a broad range of record series, thus ensuring that the vocabulary would have literary warrant. We wanted a system that was easy to learn and use and that did not impose a too-limited context on the descriptors. The most difficult and important task was arriving at an organizational scheme that is not tied to the organizational structure of this university. The university's structure and delegation of tasks is in a constant state of flux. A system based on the status quo would not necessarily work in ten years or even for records ten years old. The thesaurus that we created will describe the activities and functions of the university regardless of who performed them. We also have no desire to duplicate the physical arrangement which makes possible easy retrieval of records by office of origin. What resulted from our efforts is a four-part subject thesaurus that describes the people, functions, and activities of the university. The first section, Hierarchy of university Terms (HUT), is for functions and activities. The second, Administrative and academic departments, Schools, and Centers (ASC) is for names of these organizational units. The third, GEOgraphic locations (GEO) is for names of buildings and campus locations. (Although these two are of only local value we have included them to show how we handled the problem of specific names and titles that are necessary for description, especially to modify university activities and to limit searches. They also provide a pattern for creating similar lists for other institutions.) The fourth part, FORM, is a list of record types or forms that is used primarily as a device to narrow searches. (A search for information about a student government event can prevent retrieval of posters, for example.)",
"homepage": "http://hdl.handle.net/2027/mdp.39015048537719",
"license": "CC BY-NC-SA 3.0",
"name": "Thesaurus of University Terms",
"prefix": "1368"
},
"1369": {
"description": "Is not an instrument of retroactive application, nor does it intend to reorganize the documentation already produced; (D) Use of the instrument to classify documentation on paper or other media. Applies to electronic file management systems (SEGA) as well as to electronic information systems in the support or business areas (SIE); (...) It presents the complete attributes of each class: classification code, class title, description, application notes and exclusion notes. The presentation is preceded by the conceptual map that was the basis of the identification, ordering and coding of the 3rd levels, as well as a small explanatory text about the concept map and the coding rules.",
"homepage": "http://www.modernizacao.mpf.mp.br/formularios/consulta-publica-da-proposta-de-plano-de-classificacao-de-documentos/PLANO_CLASSIFICACAO_MPF.pdf",
"name": "Document Classification Plan",
"prefix": "1369"
},
"137": {
"description": "Asia glossary contains key terminology folklore studies, cultural anthropology, ethnomusicology, comparative religion (especially the people of faith study) and ethnology in. The glossary provides 1566 actual key words, as well as 376 Finnish and 288 English-language control term, which guides the approved thing word use. Key words can apply for an alphabetical listing by browsing or by keyword search . Cultural research thesaurus is a tool for indexing and the subject according to the information retrieval, which will help asiasanoittajia and knowledge to use the same terminology SKS's library to use the vocabulary dossiers asiasanoittamisessa the following databases:. Helka - joint database of the University of Helsinki libraries, Linda - University libraries, Arto - a reference database of domestic articles",
"homepage": "http://dbgw.finlit.fi/asiasanastot/asiasanahaku.php",
"name": "Cultural Research Thesaurus",
"prefix": "137"
},
"1370": {
"description": "The Thesaurus is divided into three major sections: the Schedule of Descriptors, the Scope Note Index, and the charts of Generic Relationships. The Schedule of Descriptors comprises (1) an alphabetical list of Descriptor Fields covering the ASTIA (AD) collection in terms of subject matter disciplines; (2) the Descriptor Fields divided into distinct Descriptor Groups indicating the extent of each Descriptor Field; and (3) an alphabetical-numerical list of these Descriptor Groups, displaying the individual Descriptors within each group.",
"homepage": "http://hdl.handle.net/2027/mdp.39015023455044",
"name": "Thesaurus of ASTIA Descriptors",
"prefix": "1370"
},
"1371": {
"description": "The Energy Data Base: Subject Thesaurus contains the standard vocabulary of indexing terms (descriptors) developed and structured by the technical staff of the Office of Science and Technical Information as part of its subject indexing activities for the building and maintenance of energy information data bases for the Department of Energy. This structured vocabulary reflects the scope of DOE's research, development, and technological programs and encompasses terminology derived not only from the basic sciences but also from the areas of energy resources, conservation, safety, environmental impact, and regulation. The terminology of this thesaurus controls the subject searching of the Energy Data Base (EDB) available on the DOE on-line retrieval systems. The terminology is also used for the subject control of other OSTI data bases available only on DOE/RECON. Descriptors are added to the thesaurus on the basis of need, i.e., when a document contains a concept for which there is no adequate term or terms in the thesaurus. (...) There are over 25,000 entries.",
"homepage": "http://hdl.handle.net/2027/umn.31951d015646597",
"name": "Energy Data Base Subject Thesaurus",
"prefix": "1371"
},
"1372": {
"description": "The International Energy Agency: Subject Thesaurus contains the standard vocabulary of indexing terms (descriptors) developed and structured to build and maintain energy information databases. Involved in this cooperative task are (1) the technical staff of the U.S. DOE Office of Scientific and Technical Information (OSTI) in cooperation with the member countries of the International Energy Agency`s Energy Technology Data Exchange (ETDE) and (2) the International Atomic Energy Agency`s International Nuclear Information System (INIS) staff representing the more than 100 countries and organizations that record and index information for the international nuclear information community. ETDE member countries are also members of INIS. Nuclear information prepared for INIS by ETDE member countries is included in the ETDE Energy Database, which contains the online equivalent of the printed INIS Atomindex. Indexing terminology is therefore cooperatively standardized for use in both information systems. This structured vocabulary reflects the scope of international energy research, development, and technological programs. The terminology of this thesaurus aids in subject searching on commercial systems, such as 'Energy Science & Technology' by DIALOG Information Services, 'Energy' by STN International and the 'ETDE Energy Database' by SilverPlatter. It is also the thesaurus for the Integrated Technical Information System (ITIS) online databases of the US Department of Energy. Descriptors are added to the thesaurus as needed (i.e., when a document contains a concept for which there is no adequate term or terms in the thesaurus). More than 27,000 appear in this document, which replaces the U.S. DOE publication Energy Data Base: Subject Thesaurus.",
"homepage": "http://dx.doi.org/10.2172/10104004",
"name": "International Energy Subject Thesaurus",
"prefix": "1372"
},
"1373": {
"description": "This thesaurus of terminology associated with the geopressured geothermal energy field has been developed as a part of the Geopressured Geothermal Information System data base.",
"homepage": "http://dx.doi.org/10.2172/6355146",
"name": "Geopressured Geothermal Bibliography",
"prefix": "1373"
},
"1374": {
"description": "The Thesaurus used for the NYIT Energy Information Center is presented. The center is a comprehensive information service covering every aspect of energy conservation and related technology, including conservation programs and practices, alternative energy systems, energy legislation, and public policy development in the United States and abroad. The Thesaurus includes all subject headings found in the Vertical File as well as other cross referenced terms likely to come to mind when seeking information on a specific energy area.",
"homepage": "http://dx.doi.org/10.2172/6719876",
"name": "Thesaurus of Descriptors for the Vertical File System",
"prefix": "1374"
},
"1375": {
"description": "The Environmental/Chemical Thesaurus approaches scientific language control problems from a multidisciplinary view. The Environmental/Biomedical Terminology Index (EBTI) was used as a base for the present thesaurus. The Environmental/Chemical Thesaurus, funded by the Environmental Protection Agency, used as its source of new terms those major terms found in 13 Environmental Protection Agency data bases. The scope of this thesaurus includes not only environmental and biomedical sciences, but also the physical sciences with emphasis placed on chemistry. Specific chemical compounds are not included; only classes of chemicals are given. To adhere to this level of classification, drugs and pesticides are identified by class rather than by specific chemical name. An attempt was also made to expand the areas of sociology and economics. Terminology dealing with law, demography, and geography was expanded. Proper names of languages and races were excluded. Geographic terms were expanded to include proper names for oceans, continents, major lakes, rivers, and islands. Political divisions were added to allow for proper names of countries and states. With such a broad scope, terminology for specific sciences does not provide for indexing to the lowest levels in plant, animal, or chemical classifications.",
"homepage": "http://dx.doi.org/10.2172/6643293",
"name": "Environmental/Chemical thesaurus",
"prefix": "1375"
},
"1376": {
"description": "The iDAI.Gazetteer is a webservice that connects place names with coordinates and works in two directions. Inside, it serves as a standard datavocabular for all DAI's location-specific information and information systems. To the outside he should connect these with the global Gazetteer systems.",
"homepage": "http://gazetteer.dainst.org/app/",
"license": "CC-BY-3.0",
"name": "iDAI.gazetteer Thesaurus",
"prefix": "1376"
},
"1377": {
"description": "The document classification code is a working tool used to classify any document produced or received by an organ in the exercise of its functions and activities. Subject classification is used for the purpose of grouping the documents under The same theme, as a way to expedite its recovery and to facilitate the archival tasks related to the evaluation, selection, elimination, transfer, recollection and access to these documents, since the archival work is carried out based on the content of the document, which The classification defines, therefore, the physical organization of the archived documents, constituting a basic reference for its recovery. In the classification code, the functions, activities, species and Document types generally referred to as subjects, are hierarchically According to the functions and activities performed by the body. In other words, the sums are given numeric codes, which reflect the functional hierarchy of the organ, defined through classes, subclasses, groups and subgroups, always starting from the general to the particular. For this instrument the model of decimal classification code was adopted. As the name implies, the decimal system of classification by subjects constitutes a numerical code divided in ten classes and these in turn in ten subclasses and so on.",
"homepage": "http://www.dirad.fiocruz.br/upload/uploads/CodClass2007.pdf",
"name": "Code of Classification of Archive Documents of the Oswaldo Cruz Foundation",
"prefix": "1377"
},
"1378": {
"description": "In the historical department the philosophical primary and secondary literatures are placed, arranged chronologically according to the birth years of the philosophers, beginning with -800 (Zarathustra), the year of birth being a primary part of the site signature And the year of publication of the present title, or the year of publication of the first edition. (...) In the systematic section, all works are subdivided from the historical section for formal reasons, eg bibliographies, lexicons, , But also introductions, philosophical histories, or works from other areas of knowledge. The signatures of this section begin with a code letter.",
"homepage": "http://www.ruhr-uni-bochum.de/philosophy/bib_system.html.de",
"name": "Teaching unit Philosophy Library system",
"prefix": "1378"
},
"1379": {
"description": "Systematics of the library of the University of Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysArubi.pdf",
"name": "Systematics ARUBI",
"prefix": "1379"
},
"138": {
"description": "The following reference lists represent NMAI controlled terminologies in their respective hierarchies. Use these reference lists if you are in doubt about what terms are used or how they should be entered for searches. If you cannot quickly locate a term you may use your browser's 'Find' ('Ctrl' + 'F') option combination to see if a term is listed. When you click on a term in a Reference List, a search is automatically performed across all applicable collections categories. Peoples/Cultures Thesaurus Reference List: Includes the six highest levels of cultural terms used in this website. More specific terms may appear on item detail pages. Materials/Media Reference List: Includes all object materials and media used in this website. Techniques Reference List: Includes all object techniques used in this website. Object Types Reference List: Includes all standard object types and names used in this website. These terms are referred to in the site as 'Type of Item', 'Type of Object', or 'Object Name'.",
"homepage": "http://www.nmai.si.edu/searchcollections/help/reference.aspx",
"name": "National Museum of the American Indian Reference Lists (Thesauri)",
"prefix": "138"
},
"1380": {
"description": "Systematics for Biology at the University of Kaiserslautern",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysBio.pdf",
"name": "Systematics Biology",
"prefix": "1380"
},
"1381": {
"description": "Systematics for Bibliology and Librarianship at the University of Kaiserslautern",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysBuch.pdf",
"name": "Systematics Bibliology and Librarianship",
"prefix": "1381"
},
"1382": {
"description": "Systematics for Chemistry at the University of Kaiserslautern",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysChe.pdf",
"name": "Systematics Chemistry",
"prefix": "1382"
},
"1383": {
"description": "Classification sheme of the Electrical Engineering and Information Technology of the Department of Electrical Engineering and Information Technology, University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysEit.pdf",
"name": "Classifications of Electrical Engineering and Computer Engineering",
"prefix": "1383"
},
"1384": {
"description": "Systematics for Pedagogy of the University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysPaed.pdf",
"name": "Systematics Pedagogy",
"prefix": "1384"
},
"1385": {
"description": "Systematics for the subject of History of the University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysGes.pdf",
"name": "Systematics History",
"prefix": "1385"
},
"1386": {
"description": "Systematics for Computer Science of the University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysInf.pdf",
"name": "Systematics Computer Science",
"prefix": "1386"
},
"1387": {
"description": "Systematics for the Arts and Media of the University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysMedien.pdf",
"name": "Systematics Art / Media",
"prefix": "1387"
},
"1388": {
"description": "Systematics for Mechanical Engineering and Process Engineering at the University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysMas.pdf",
"name": "Mechanical Engineering / Process Engineering",
"prefix": "1388"
},
"1389": {
"description": "Systematics of Mathematics, University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysMat.pdf",
"name": "Systematics Mathmatics",
"prefix": "1389"
},
"139": {
"description": "The ASHA Thesaurus is a controlled vocabulary used to organize information in the fields of audiology and speech-language pathology.",
"homepage": "http://www.asha.org/thesaurus/",
"name": "American Speech-Language-Hearing Association Thesaurus",
"prefix": "139"
},
"1390": {
"description": "Systematics of Mathematics, University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysMat_2.pdf",
"name": "Location-free systematics Mathematics",
"prefix": "1390"
},
"1391": {
"description": "Systematics for Music of the University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysMusik.pdf",
"name": "Systematics Music",
"prefix": "1391"
},
"1392": {
"description": "Systematics for Philosophy of the University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysPhil.pdf",
"name": "Systematic Philosophy",
"prefix": "1392"
},
"1393": {
"description": "Systematics for Physics of the University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysPhy.pdf",
"name": "Systematic Physics",
"prefix": "1393"
},
"1394": {
"description": "System for policy of the University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysPol.pdf",
"name": "Systematic Politics",
"prefix": "1394"
},
"1395": {
"description": "Systematics for Psychology of the University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysPsy.pdf",
"name": "Systematic Psychology",
"prefix": "1395"
},
"1396": {
"description": "Systematics for the subject area Law of the University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysRecht.pdf",
"name": "Systematic Law",
"prefix": "1396"
},
"1397": {
"description": "Systematics for Sociology of the University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysSoz.pdf",
"name": "Systematics Sociology",
"prefix": "1397"
},
"1398": {
"description": "Systematics Sport of the University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysSpo.pdf",
"name": "Systematics Sport",
"prefix": "1398"
},
"1399": {
"description": "Systematics of the language and literature sciences of the University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysLit.pdf",
"name": "Systematics Linguistics and literary sciences",
"prefix": "1399"
},
"14": {
"abbreviation": "ELSST",
"description": "The European Language Social Science Thesaurus (ELSST) is a broad-based, multilingual thesaurus for the social sciences. It is owned and published by the Consortium of European Social Science Data Archives (CESSDA) and its national Service Providers. The thesaurus consists of over 3,300 concepts and covers the core social science disciplines: politics, sociology, economics, education, law, crime, demography, health, employment, information and communication technology, and environmental science.\nELSST is used for data discovery within CESSDA and facilitates access to data resources across Europe, independent of domain, resource, language or vocabulary.\nELSST is currently available in 16 languages: Danish, Dutch, Czech, English, Finnish, French, German, Greek, Hungarian, Icelandic, Lithuanian, Norwegian, Romanian, Slovenian, Spanish, and Swedish.\nELSST employs the usual range of terms and thesaural relationships: preferred terms and non-preferred terms (entry terms); the hierarchical relationships (broader concepts (BTs) and narrower concepts (NTs)); and the associative relationship/related concepts (RTs). Definitions are used to define the intended meaning and usage of the preferred term within the domain of the thesaurus. Its main aim is to facilitate access to data resources across Europe, independent of domain, resource, language and vocabulary. ELSST is used to aid retrieval in the multinational CESSDA data portal.",
"homepage": "https://elsst.cessda.eu/",
"license": "CC BY-SA 4.0",
"name": "European Language Social Science Thesaurus",
"prefix": "14"
},
"140": {
"description": "A thesaurus developed by our thesaurus staff is used to standardize the terms used in the bibliography. Terms come from the literature itself. To reflect the changing needs and interests of the scholarly community, the thesaurus undergoes constant revision. At present over 45,000 terms and 327,000 names are controlled.",
"name": "Modern Language Association Thesaurus",
"prefix": "140"
},
"1400": {
"description": "Systematics for the Department of Religion of the University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysRel.pdf",
"name": "Systematic Religion",
"prefix": "1400"
},
"1401": {
"description": "Systematics for Economics of the University Library Kaiserslautern.",
"homepage": "http://www.ub.uni-kl.de/fileadmin/ub/pdf/Systematiken/SysWir.pdf",
"name": "Systematics Economics",
"prefix": "1401"
},
"1402": {
"description": "The Clinical Care Classification (CCC) System (...) provides a standardized framework and a unique coding structure for assessing, documenting, and classifying patient care by nurses and other clinical professionals in any health care setting. The CCC system consists of two interrelated terminologies: CCC of Nursing Diagnoses consists of 176 (60 major & 116 subcategories). CCC of Nursing Interventions/Actions consists of 804 Concepts (201 Core Interventions [77 major & 124 subcategories)]. The two terminologies are both classified by 21 Care Components that represent the Functional, Health Behavioral, Physiological, and Psychological Patterns of Patient Care. (...) The coding structure for the two terminologies is based on the ICD-10 (International Statistical Classification of Diseases and Health-Related Problems, 1990) consisting of five alphanumeric characters for information exchange among health care terminologies promoting interoperability. They are used to track and measure patient/client care holistically over time, across settings, population groups, and geographic locations. (...) The CCC System is recognized as the terminology of choice for documenting the essence of patient care in the electronic health record (EHR) systems. It meets all the features of a concept-oriented terminology and has been formally accepted by the various standards organizations. (...) The CCC System is being used to document nursing care in the electronic health record (EHR) computer-based patient record (CPR) and Personal Health Record (PHR) Systems. It serves as a language for nursing and other health care providers such as physical, occupational, and speech therapists, medical social workers, etc.",
"homepage": "http://www.sabacare.com/",
"name": "Clinical Care Classification System",
"prefix": "1402",
"wikidata_database": "Q5133752"
},
"1403": {
"description": "The parliamentary documentation supports you (.) With the thesaurus 'PARTHES', which contains a fixed vocabulary of slogans which are assigned to the documents, but also synonyms are fully recorded in the thesaurus and refer to the keyword 'Used for the synonym' radicalism ', you can search for both terms in such a case, since the referral ensures that you can also find with' radicalism 'all the documents found with' extremism ' The terms contained in 'PARTHES' accurately represent the parliamentary work.To determine whether your search word is included in the thesaurus, you can call the thesaurus function via the corresponding button next to selected search fields.",
"homepage": "https://opac.bundestag.de/aDISWeb/app?service=direct/0/Home/%24DirectLink&sp=SOPAC",
"name": "Thesaurus for Parliamentary Materials",
"prefix": "1403"
},
"1404": {
"description": "This OWL file defines a class for each indicator defined in the ISO 37120 standard. Names for each indicator are provided. Text definitions are provided only for Economy, Education and Energy indicators, due to copyright restrictions imposed by ISO. This file is meant to provide a single URI for each indicator. An ontology for representing an indicator's supporting data plus meta information such as provenance, validity and trust can be found in: http://ontology.eil.utoronto.ca/GCI/Foundation/GCI-Foundation.owl Documentation of the ontology can be found in: http://eil.utoronto.ca/smartcities/papers/GCI-Foundation-Ontology.pdf.",
"homepage": "http://ontology.eil.utoronto.ca/ISO37120.owl",
"name": "ISO 37120 indicator URIs",
"prefix": "1404"
},
"1405": {
"description": "Contains the foundation ontologies required to represent ISO 37120 city indicators, including Placenames, Time, Measurement, Provenance, Statistics, Validity and Trust. See: Fox, M.S., (2013), 'A Foundation Ontology for Global City Indicators', Global City Institute Working Paper, Vol. 1, No.4, pp. 1-45. Global Cities Institute, University of Toronto. Latest Version: http://eil.utoronto.ca/smartcities/papers/GCI-Foundation-Ontology.pdf Designed to represent the ISO 37120 Sustainable development of communities β Indicators for city services and quality of life.",
"homepage": "http://ontology.eil.utoronto.ca/GCI/Foundation/GCI-Foundation.owl",
"name": "Global City Indicator Foundation Ontology",
"prefix": "1405"
},
"1406": {
"description": "This ontology generalizes the concepts that appear in 311 open data files published by several cities (Toronto, New York, Chicago, Vancouver) across North America. It provides a generis representation of 311 data that other cities can map their data onto and be used as a means of achieving interoperability.\n\nNalchigar, S, and Fox, M.S., (2014), 'An Ontology for Open 311 Data\", Proceedings of the AAAI Workshop on Semantic Cities: Beyond Opend Data to Models, Standards and Reasoning', Association for the Advancement of Artificial Intelligence. http://eil.utoronto.ca/smartcities/papers/nalchigar-AAAI14.pdf",
"name": "Open 311 Ontology",
"prefix": "1406"
},
"1407": {
"description": "This ontology provides basic classes and more detailed properties for representating international street addresses, phone numbers and emails. Rather than using existing ontologies, such as vcard, it was decided to create a new one as the vcard and foaf ignore the details of international addresses, phone numbers, etc. The important part of the ontology are the object and data properties used to describe addresses primarily and phone numbers.",
"name": "International Contact Ontology",
"prefix": "1407"
},
"1408": {
"description": "Based on: Fox, M.S., Barbuceanu, M., Gruninger, M., and Lin, J., (1998), 'An Organisation Ontology for Enterprise Modeling', In Simulating Organizations: Computational Models of Institutions and Groups, M. Prietula, K. Carley & L. Gasser (Eds), Menlo Park CA: AAAI/MIT Press, pp. 131-152. http://www.eil.utoronto.ca/enterprise-modelling/papers/org-prietula-23aug97.pdf",
"name": "TOVE Organization Ontology",
"prefix": "1408"
},
"1409": {
"abbreviation": "GACS",
"description": "GACS explored the possibility of creating a global repository of concepts and terminology in the area of agriculture. This first beta is the result of the first experimental attempt, and it went very well! We now have a pool of concepts based on a mapping between AGROVOC, the CAB Thesaurus and the NAL Thesaurus. An analysis of the the coverage of GACS beta with respect to AGROVOC showed that it could already be used to index AGRIS, with no significant loss of indexing concepts.",
"homepage": "http://browser.agrisemantics.org/gacs/en/",
"name": "Global Agricultural Concept Scheme",
"prefix": "1409"
},
"141": {
"description": "Hierarchy and preferential relations: management of linguistic equivalents The descriptors are arranged on the same hierarchical level in each large lexical field.To limit their number, it is decided to keep a certain number of non-descriptors (which refer to descriptors They could have been used as generic terms, but it is unfortunately not possible to manage several levels of specificity in an alphabetical index. A descriptor can belong to several lexical fields, followed by a mention of belonging to one (or more) other lexical field, the descriptors close to the semantic level (in the same Lexical field or from one lexical field to another) will be followed by association relations. T from guides, anthologies, dictionaries of works and themes, reading files for pupils or teachers; We find them partly in the lists of the youth sector of the BCP du Doubs, the youth section of the Jean-Jacques Rousseau multimedia library in ChambΓ©ry, the high schools in Grenoble, the Schools Catalog Information Service under the Australian National Cataloging Agency for Schools, The Bibliography of Canadian Children's Fiction and the thesauri developed by Mr. Michel Bernard.\n\nIndex fiction in CDIs and libraries for youth, to transgress forms, genres and supports.",
"homepage": "http://dompnier.nicolas.free.fr/Fiction/thesaurus/2003.pdf",
"name": "Thesaurus for Fiction",
"prefix": "141"
},
"1410": {
"description": "RASUQAM is an encyclopaedic thesaurus developed since 1994 by the Library Service of the UniversitΓ© du QuΓ©bec Γ MontrΓ©al and is used for the indexing of its collections.RASUQAM has about 47,000 descriptors , Including common names, organization names, titles, geographical names, chronological terms, form descriptors, and some uncontrolled descriptors.",
"homepage": "http://catalogue.uqam.ca/rasuqam",
"name": "Directory of UQAM Authorities-Subject",
"prefix": "1410",
"wikidata_database": "Q3419990"
},
"1411": {
"description": "Recognized as the authoritative reference to the terminology of information science, technology, and librarianship, the updated and expanded third edition of the ASIST Thesaurus is an essential resource for indexers, researchers, scholars, students, and practitioners in the field. An optional CD-ROM includes the complete contents of the print thesaurus along with Data Harmony's Thesaurus Master software. In addition to powerful search and display features, the CD-ROM allows users to add, change, and delete terms, and to learn the fundamentals of thesaurus construction while exploring the professional vocabulary of library and information science and technology.",
"name": "ASIS&T Thesaurus of Information Science, Technology, and Librarianship",
"prefix": "1411"
},
"1412": {
"description": "The Education, Skills and Children's Services Thesaurus is the controlled vocabulary developed and maintained by the UK Department for Children, Schools and Families. It was developed in the 1980s and has been continuously updated to reflect new topics and new Departmental responsibilities.",
"homepage": "http://public.lexaurus.net/culturegrid/browse",
"name": "Education, Skills and Children's Services Thesaurus",
"prefix": "1412"
},
"1413": {
"abbreviation": "CERL",
"description": "The CERL Thesaurus File is a unique facility developed to address the particularly European issue that place name and personal names in Europe varied from country to country in the period of hand press printing (1450 - c. 1830). As such, it is an essential research tool for scholars and researchers of the period. The CERL Thesaurus file contains forms of imprint places, imprint names, personal names and corporate names as found in material printed before the middle of the nineteenth century - including variant spellings, forms in Latin and other languages, and fictitious names. Authority files contributed by CERL member libraries and other libraries/projects concentrating on the history of the book are brought together and made searchable in one single system (...). The CERL Thesaurus merges standard and authority forms of names that are used in present day library catalogues without imposing CERLβs own authoritative form of name. Instead, standard and variant forms are listed alphabetically with a clear indication of the institutions that use a particular standard form.",
"homepage": "https://thesaurus.cerl.org/cgi-bin/search.pl",
"license": "CC-BY-3.0",
"name": "CERL Thesaurus",
"pattern": "^[a-z]{3}[0-9]{8}$",
"prefix": "1413"
},
"1414": {
"description": "Terms used at all hierarchical levels in the ICAN global thesaurus for coastal erosion. Terms used to populate drop-down lists in discovery portals.",
"homepage": "http://vocab.nerc.ac.uk/collection/A01/current/",
"name": "International Coastal Atlas Network Coastal Erosion Global Thesaurus",
"prefix": "1414"
},
"1415": {
"description": "Terms used at all hierarchical levels in the Oregon Coastal Atlas for coastal erosion layers, datasets and discovery.",
"homepage": "http://vocab.nerc.ac.uk/collection/A02/current/",
"name": "Oregon Coastal Atlas Coastal Erosion Thesaurus Markup Terms",
"prefix": "1415"
},
"1416": {
"description": "Terms used at all hierarchical levels in the Oregon Coastal Atlas for categorisation and discovery, but not for layer or dataset markup.",
"homepage": "http://vocab.nerc.ac.uk/collection/A03/current/",
"name": "Oregon Coastal Atlas Coastal Erosion Thesaurus Discovery Terms",
"prefix": "1416"
},
"1417": {
"description": "A collection of terms used by the Irish Marine Data Atlas in association with the topic of coastal erosion.",
"homepage": "http://vocab.nerc.ac.uk/collection/A04/current/",
"prefix": "1417"
},
"1418": {
"description": "Terms used to classify the type of reference material used by laboratories in the verification of analytical techniques in terms of consistency, accuracy and precision.",
"homepage": "http://vocab.nerc.ac.uk/collection/B03/current/",
"name": "BODC Annotated Reference Material Classifiers",
"prefix": "1418"
},
"1419": {
"description": "The 'old' system for the field of media science in the library of the University of Konstanz was no longer up to the requirements of the rapidly developing subject, the list was too coarse, a differentiated research was not possible, we wanted to thank our scientists and the large number of researchers The library of the University of Constance under the leadership of Ralph Hafner (specialist for media science) in cooperation with the university The media in Stuttgart (Prof. B. HΓΌtter and Prof. Dr. R. Stang) and the Department of Media Studies at the University of Konstanz (Prof. Dr. B. Ochnser) developed a new system of media science in project seminars with dedicated students from the two universities Summer 2009 is the Ie new systematics in practice, the new area of ββmedia science is built up of reworked and new titles, and thanks to the work of Fr. Dr. D. Harrer, A. Walker and the Machining Stewards.",
"homepage": "https://konsys.uni-konstanz.de/home/browse#238491",
"name": "Systematics Media studies, Performing Arts, Theater, Dance, Artistics, Film, Broadcasting, Radio, Television",
"prefix": "1419"
},
"142": {
"description": "Pathways contains the terms we use to describe the items in the AIATSIS Collections. Including, a thesaurus for subjects relating to Australian Aboriginal and Torres Strait Islander studies, language groups and people, and place names.\n\nThe Subject Thesaurus contains the AIATSIS Library's in-house, faceted subject headings. It reflects AIATSIS' exclusive interest in Aboriginal and Torres Strait Islander studies. Where possible, the choice of headings tries to reflect Indigenous perspectives.\n\nThe Language and Peoples Thesaurus contains headings for languages and peoples within Australia. The headings include the language code (eg. (N156)) and a grid reference to the 1:250,000 map grid series (eg. Mutumui language (Y63.1) (Qld SD55-09)).\n\nThe Place Thesaurus contains headings for place names within Australia, using the Indigenous place name first, wherever possible. The headings include the grid reference to the 1:250,000 map grid series (eg. Lake Hindmarsh (NW Vic SJ54-03)).",
"homepage": "http://www1.aiatsis.gov.au/",
"name": "Australian Institute of Aboriginal and Torres Straight Islander Studies Thesauri",
"prefix": "142"
},
"1420": {
"description": "Systematics for Philosophy of the University Library of Constance.",
"name": "Systematic Philosophy",
"prefix": "1420"
},
"1421": {
"description": "Classification sheme of the German Language and Literature Science of the University Library of Constance.",
"homepage": "http://www.ub.uni-konstanz.de/fi/germanistik/bibliotheksbenutzung/",
"name": "Classifications of the German Language and Literature Science",
"prefix": "1421"
},
"1422": {
"description": "A systematic for general linguistics at the University of Konstanz",
"name": "Systematics General Linguistics",
"prefix": "1422"
},
"1423": {
"description": "Systematic book setting up of ancient science, classical philology of the communication, information, media center (KIM) of the University of Konstanz.",
"homepage": "https://www.kim.uni-konstanz.de/beratung-und-kurse/fachspezifische-informationen/fachinformation-klassische-philologie-altertumswissenschaft/",
"name": "Systematic book setting up of the Ancient Classical Studies, Classical Philology",
"prefix": "1423"
},
"1424": {
"description": "Systematics for Archeology at the University of Konstanz",
"homepage": "http://www.ub.uni-konstanz.de/de/fi/archaeologie/bibliotheksbenutzung/",
"name": "Systematics Archaeology",
"prefix": "1424"
},
"1425": {
"description": "A system of the Unibibliothek Konstanz for the educational sciences",
"homepage": "http://www.ub.uni-konstanz.de/fileadmin/Dateien/Fachreferenten/Jochum/ERZ-Systematische_Buchaufstellung.pdf",
"name": "Overview of the subject classification system of Educational sciences",
"prefix": "1425"
},
"1426": {
"description": "A german shelf mark about kid-books. \"kid\" is the abbreviation for \"cybernetics informations data-handling\".",
"homepage": "http://www.ub.uni-konstanz.de/fi/informatik-informationswissenschaften/bibliotheksbenutzung/kid-signaturen/",
"name": "kid-shelf-mark",
"prefix": "1426"
},
"1427": {
"description": "Systematic book setting up of the law of the communication, information, media center (KIM) of the University of Konstanz.",
"homepage": "https://www.kim.uni-konstanz.de/beratung-und-kurse/fachspezifische-informationen/fachinformation-rechtswissenschaft-jura/",
"name": "Systematic book setting up of the law",
"prefix": "1427"
},
"1428": {
"description": "The signature of the mat books is composed of the basic signature and the individual signature, the basic signature is separated from the individual signature in the OPAC by '/', and on the signature sticker in the book by a horizontal line (...) The unambiguous identification of a book becomes By means of the individual signature.It is formed by the initial letter of the title followed by two digits.Then the volumes are followed by '-' in multi-volume works, if there are several editions of the book, the edition is indicated in parentheses.",
"homepage": "http://www.ub.uni-konstanz.de/fi/mathematik/bibliotheksbenutzung/fachgruppen-mathematik/",
"name": "Shelf Classification Mathmatics",
"prefix": "1428"
},
"1429": {
"description": "Systematic book setting up of music of the communication, information, media center (KIM) of the University of Konstanz.",
"homepage": "https://www.kim.uni-konstanz.de/beratung-und-kurse/fachspezifische-informationen/fachinformation-musik/",
"name": "Systematic book setting up of music",
"prefix": "1429"
},
"143": {
"description": "The list of over 1,000 headings and their associated references is appropriate for use at a public library level. The purpose is to provide a structured path to subjects that Maori customers can relate to and use to find material in libraries. It is not intended to be used as a dictionary. It has been developed so that cataloguers and descriptive archivists have a reliable and comprehensive resource to use when describing material either in or about Maori. It will be used by the National Library of New Zealand to enhance its service to Maori library users. However it should not be seen as authoritative beyond its intended purpose for use in libraries and archives.",
"homepage": "http://mshupoko.natlib.govt.nz/mshupoko/",
"license": "CC BY-NC-ND 3.0",
"name": "Maori Subject Headings",
"prefix": "143"
},
"1430": {
"description": "The signature of the phy books is composed of the signature and individual signature, the basic signature is separated from the individual signature in the OPAC by '/', on the signature sticker in the book by a horizontal line (...) The unambiguous identification of a book is achieved by means of the individual signature, which is formed by the author 's initial letter followed by two digits, and in the case of multi - volume works, the band is followed by' - ' The circulation is indicated in brackets.",
"homepage": "https://www.kim.uni-konstanz.de/beratung-und-kurse/fachspezifische-informationen/fachinformation-physik/",
"name": "Systematic Table of Physics",
"prefix": "1430"
},
"1431": {
"description": "Systematic book setting up of sociology of the communication, information, media center (KIM) of the University of Konstanz.",
"homepage": "https://www.kim.uni-konstanz.de/beratung-und-kurse/fachspezifische-informationen/fachinformation-soziologie-und-ethnologie/",
"name": "Systematic book setting up of sociology",
"prefix": "1431"
},
"1432": {
"description": "Systematics of the Ethnology of the University Library of Constance.",
"homepage": "http://www.ub.uni-konstanz.de/fileadmin/Dateien/Fachreferenten/Heeg/systemstellen_atp.pdf",
"prefix": "1432"
},
"1433": {
"description": "Systematic book setting up of sports science of the communication, information, media center (KIM) of the University of Konstanz.",
"homepage": "https://www.kim.uni-konstanz.de/beratung-und-kurse/fachspezifische-informationen/fachinformation-sport/",
"name": "Systematic book setting up of sports science",
"prefix": "1433"
},
"1434": {
"description": "A systematics of the University Library of Constance for the Literary Studies",
"homepage": "http://www.ub.uni-konstanz.de/fileadmin/Dateien/Fachreferenten/Jochum/lit/lit-systematik.pdf",
"name": "Overview of the subject area of general literary studies",
"prefix": "1434"
},
"1435": {
"description": "Systematic book setting up of English studies/American studies of the communication, information, media center (KIM) of the University of Konstanz.",
"homepage": "https://www.kim.uni-konstanz.de/beratung-und-kurse/fachspezifische-informationen/fachinformation-amerikanistik-anglistik/",
"name": "Systematic book setting up of the English studies/American studies",
"prefix": "1435"
},
"1436": {
"description": "Systematic book setting up of Near Eastern studies of the communication, information, media center (KIM) of the University of Konstanz.",
"homepage": "https://www.kim.uni-konstanz.de/beratung-und-kurse/fachspezifische-informationen/fachinformation-orientalistik-sonstige-sprachen-und-literaturen/",
"name": "Systematic book setting up of Near Eastern studies",
"prefix": "1436"
},
"1437": {
"description": "Systematic book setting up of other Languages ββand Literatures of the communication, information, media center (KIM) of the University of Konstanz.",
"homepage": "https://www.kim.uni-konstanz.de/beratung-und-kurse/fachspezifische-informationen/fachinformation-orientalistik-sonstige-sprachen-und-literaturen/",
"name": "Systematic book setting up of other Languages ββand Literatures",
"prefix": "1437"
},
"1438": {
"description": "Since its inception as a university of applied sciences, excellence in teaching and study, internationality and interdisciplinary cooperation have existed for the University of Konstanz in 1966. This visionary idea of founding can be traced back into architecture: the short distances of the campus university create a communication- Which naturally brings together scientific disciplines and fosters a culture of creative exchange.",
"homepage": "http://www.ub.uni-konstanz.de/de/fi/romanistik/bibliotheksbenutzung/buchaufstellung-romanisitk/",
"name": "Book collection system Romanistik",
"prefix": "1438"
},
"1439": {
"homepage": "http://www.ub.uni-konstanz.de/de/fi/slavistik/bibliotheksbenutzung/buchaufstellung-slavistik/",
"prefix": "1439"
},
"144": {
"description": "The information it contains is not definitive and is subject to editorial review and discussion by the scientific community. The collaboration of the users is expected.",
"homepage": "http://www.tesauroregional.cl/trp/publico/buscar.htm",
"name": "Regional Asset Thesaurus",
"prefix": "144"
},
"1440": {
"description": "Systematic book setting up of theology of the communication, information, media center (KIM) of the University of Konstanz.",
"homepage": "https://www.kim.uni-konstanz.de/beratung-und-kurse/fachspezifische-informationen/fachinformation-theologie/",
"name": "Systematic book setting up of Theology",
"prefix": "1440"
},
"1441": {
"description": "Systematic book setting up of economic sciences of the communication, information, media center (KIM) of the University of Konstanz.",
"homepage": "https://www.kim.uni-konstanz.de/beratung-und-kurse/fachspezifische-informationen/fachinformation-wirtschaft/",
"name": "Systematic book setting up of Economic Sciences",
"prefix": "1441"
},
"1442": {
"description": "Systematic book setting up of Stastical Source Material\n\n of the communication, information, media center (KIM) of the University of Konstanz.",
"name": "Systematic book setting up of Stastical Source Material",
"prefix": "1442"
},
"1443": {
"abbreviation": "KonSys",
"description": "The Konstanzer Systematik (KonSys) is a classification scheme for academic libraries, developed at the Library of the University of Konstanz in 1966 for the newly founded University as an in-house classification scheme for its own extensive holdings on the open shelves. Since that time the classification of the University Library of Konstanz was maintained and developed further by the subject specialsists of the Library.",
"homepage": "https://konsys.uni-konstanz.de/",
"license": "CC0-1.0",
"name": "Konstanz library classification",
"pattern": "^[a-z]+ [0-9]+( - )?(:[a-z0-9]+)?( [-] )?|.[0-9]+(:[a-z]+)?( [-] )?$",
"prefix": "1443"
},
"1444": {
"description": "The SOC was designed to allow the various academic and administrative units of the UniversitΓ© de MontrΓ©al to classify, index and classify their active documents and files in a consistent and systematic manner.",
"homepage": "http://www.archiv.umontreal.ca/service/classification/Class_structure.html",
"name": "Official Classification System",
"prefix": "1444"
},
"1445": {
"description": "The subject catalog offers you the media available in the central library according to subject areas and sorted by topic, within the subject areas, so it is well suited for a specific subject-specific, thematic search entry.In each subject area, you will find formally defined sections such as magazines and bibliographies The subjects of the subject follow in a factual sequence in an increasingly subtropical subdivision, similar to a textbook of the respective subject, the subject of which can be divided into the subject matter of each subject, the psychology, for example, psy, which is combined with a three - digit number (...) Not all areas of knowledge are identified by their own subject system, and smaller subjects are often grouped together with neighboring ones, for example, archiving and genealogy form sections in Ges (Gsb 225-253 and gsb 260-275, respectively), cartography is a section in geography (ggr 710-978).",
"homepage": "http://www.ub.uni-kiel.de/fach/systematik",
"name": "Subject catalog of the Central Library Kiel for thematic search",
"prefix": "1445"
},
"1446": {
"description": "Systematic division of subjects from the Staatliche Bibliothek Passau.",
"homepage": "http://www.ub.uni-passau.de/fileadmin/dokumente/download/Homepage/benutzung/Systematik_SBPassau.pdf",
"name": "Systematic compartments of the State Library Passau",
"prefix": "1446"
},
"1447": {
"description": "The old prints (up to the year 1800) of the University Library of EichstΓ€tt-Ingolstadt and the libraries which it administers are, for the most part, not developed and arranged according to the 'Regensburg System' Of the Central Library of the Bavarian Capuchin (AltΓΆtting) until the year of the year 1800 are developed with the help of the group system of the former state library of Eichstatt.",
"homepage": "http://www.ku-eichstaett.de/Bibliothek/allgemein/standorte/handschriftenabteilung/altdrucke/",
"name": "Group system of the former state library EichstΓ€tt",
"prefix": "1447"
},
"1448": {
"description": "The system opens up the number of publications on Marburg and the Marburg-Biedenkopf district in the University Library from 1970 onwards.",
"homepage": "http://www.uni-marburg.de/bis/ueber_uns/ub/sondsam/hassiaca/marsys/",
"name": "Systematics for collection focus Marburgensia",
"prefix": "1448"
},
"1449": {
"description": "The holdings of the two theological faculties are arranged according to their own system.",
"homepage": "http://www.ub.uni-mainz.de/fakultaeten-systematik/",
"name": "Catholic theology",
"prefix": "1449"
},
"1450": {
"description": "The holdings of the two theological faculties are arranged according to their own system.",
"homepage": "http://www.ub.uni-mainz.de/fakultaeten-systematik/",
"name": "Evangelische Theologie - Shelf Classification",
"prefix": "1450"
},
"1451": {
"description": "The media are arranged according to an in-house system (...).",
"homepage": "http://www.ub.uni-mainz.de/files/2015/04/Systematik.pdf",
"name": "Systematics of the Library of Film Science / Media Dramaturgy",
"prefix": "1451"
},
"1452": {
"description": "Shelf Classification for the subject of Foreign European Languages and Literatures",
"homepage": "http://www.ub.uni-mainz.de/gedruckte-bestaende-aussereuropaeische-sprachen-und-literaturen/",
"name": "Shelf Classification for the subject of Foreign European Languages and Literatures",
"prefix": "1452"
},
"1453": {
"description": "The sports science media are organized according to an in-house sports system (...). The individual areas understand themselves in their relation to sport as 'sports pedagogy', 'sports psychology', etc.",
"homepage": "http://www.ub.uni-mainz.de/files/2013/11/Sportsystematik1.pdf",
"name": "Sports systematics",
"prefix": "1453"
},
"1454": {
"description": "Classification sheme of the drama science of the Johannes Gutenberg Universityl.",
"homepage": "http://www.ub.uni-mainz.de/theaterwissenschaft/",
"name": "Classifications of drama science",
"prefix": "1454"
},
"1455": {
"description": "The literature is written according to a very fine-art in-house system (...).",
"homepage": "http://www.ub.uni-mainz.de/kunstgeschichte/",
"name": "Systematics of the Library of the Institute of Art History",
"prefix": "1455"
},
"1456": {
"description": "Systematics for university didactics of the University Library of Mainz.",
"homepage": "http://www.ub.uni-mainz.de/files/2013/11/Systematik_Hochschuldidaktik.pdf",
"name": "Systematics for university didactics",
"prefix": "1456"
},
"1457": {
"description": "With the number 01 ... - 07 ... the geographical classification (...) is called 'Thematic System bodies' in paragraphs 11 ... - 93 ... to 'Regional points system'.",
"homepage": "http://www.ub.uni-mainz.de/files/2013/11/Systematik-Geographie1.pdf",
"name": "Systematics Geography",
"prefix": "1457"
},
"1458": {
"description": "The systematics of the geoscientific system (...) consist of a combination of uppercase letters (which denote the individual basic disciplines general, geology, mineralogy, paleontology, geophysics, geography, geography, archeology, biology, mathematics, physics and chemistry) and digits.",
"homepage": "http://www.ub.uni-mainz.de/files/2013/11/Systematik-Geowissenschaften.pdf",
"name": "Systematics Geosciences",
"prefix": "1458"
},
"1459": {
"description": "The media are arranged according to an in-house systematic.",
"homepage": "http://www.ub.uni-mainz.de/files/2013/11/Systematik-Publizistik.pdf",
"name": "Systematics Journalism",
"prefix": "1459"
},
"146": {
"description": "'Gregorius' is a database of an international bibliography on the history of canon law.",
"homepage": "http://www.misha.fr/sites_bdd.htm",
"name": "Gregorius Thesaurus",
"prefix": "146"
},
"1460": {
"description": "The media are set up according to an in-house system (...), which has been valid since 1995.",
"homepage": "http://www.ub.uni-mainz.de/files/2013/11/Systematik-Soziologie.pdf",
"name": "Systematics Sociology",
"prefix": "1460"
},
"1461": {
"description": "Systematics of Mainz University Library of Anthropology.",
"name": "Systematics Ethnology",
"prefix": "1461"
},
"1462": {
"description": "Systematics of African Studies at the University Library Mainz.",
"homepage": "http://www.ub.uni-mainz.de/files/2014/04/Systematik_Afrikanistik.pdf",
"name": "Systematics African Studies",
"prefix": "1462"
},
"1463": {
"description": "Systematics for African literatures of the Jahn-Bibliothek Mainz.",
"homepage": "http://www.ub.uni-mainz.de/files/2015/02/Systematik_JahnBibliothek.pdf",
"name": "Systematics Jahn Library for African Literatures",
"prefix": "1463"
},
"1464": {
"description": "(...) until 30.09.1994.\"\n\nSystematics of sociology according to Hradil / SchwΓ€gler of the University Library of Mainz.",
"homepage": "http://www.ub.uni-mainz.de/files/2013/11/Soziologie_Systematik_Hradil_Schwaegler.pdf",
"name": "Systematics Sociology Hradil / SchwΓ€gler",
"prefix": "1464"
},
"1465": {
"description": "(...) to 30.09.94.\"\n\nSystematics of sociology according to Landwehrmann / Nedelmann of the University Library of Mainz.",
"homepage": "http://www.ub.uni-mainz.de/files/2013/11/Soziologie_Systematik_Landwehrmann_Nedelmann.pdf",
"prefix": "1465"
},
"1466": {
"description": "Systematics for General and Comparative Literary Studies at the University of Mainz",
"homepage": "http://www.ub.uni-mainz.de/allgemeine-und-vergleichende-literaturwissenschaft-avl/",
"name": "Systematics of General and Comparative Literary Studies",
"prefix": "1466"
},
"1467": {
"homepage": "http://www.ub.uni-mainz.de/allgemeine-und-vergleichende-sprachwissenschaft-avs/",
"prefix": "1467"
},
"1468": {
"description": "Systematics for Ancient History at the University of Mainz",
"homepage": "http://www.ub.uni-mainz.de/alte-geschichte/",
"name": "Systematics of Ancient History",
"prefix": "1468"
},
"1469": {
"description": "Systematics for Book science at the University of Mainz",
"homepage": "http://www.ub.uni-mainz.de/buchwissenschaft/",
"name": "Systematic of book science",
"prefix": "1469"
},
"147": {
"description": "The Brucellosis Ontology (IDOBRU), a biomedical ontology in the brucellosis domain, is an extension ontology of the core Infectious Disease Ontology (IDO-core) and follows OBO Foundry principles. Currently IDOBRU contains 1503 ontology terms, which includes 739 Brucella-specific terms, 414 IDO-core terms, and 350 terms imported from 10 existing ontologies. IDOBRU is the first reported bacterial infectious disease ontology developed to represent different disease aspects in a formal logical format. It serves as a brucellosis knowledgebase and supports brucellosis data integration and automated reasoning.",
"homepage": "http://www.phidias.us/bbp/idobru/",
"name": "Brucellosis Ontology",
"prefix": "147"
},
"1470": {
"description": "Systematics for Byzantine Studies at the University of Mainz",
"homepage": "http://www.ub.uni-mainz.de/byzantinistik/",
"name": "Systematics of Byzantine Studies",
"prefix": "1470"
},
"1471": {
"description": "Systematics for German Studies at the University of Mainz",
"homepage": "http://www.ub.uni-mainz.de/germanistik/",
"name": "Systematics of German Studies",
"prefix": "1471"
},
"1472": {
"description": "Systematics for English / American Studies at the University of Mainz",
"homepage": "http://www.ub.uni-mainz.de/anglistik-amerikanistik/",
"name": "Systematics of English / American Studies",
"prefix": "1472"
},
"1473": {
"description": "Classification scheme of the Classical Archeology of the Johannes Gutenberg University.",
"homepage": "http://www.ub.uni-mainz.de/klassische-archaeologie/",
"name": "Classification of the Classical Archeology",
"prefix": "1473"
},
"1474": {
"description": "Classification scheme of the classical philology of the Johannes Gutenberg University.",
"homepage": "http://www.ub.uni-mainz.de/klassische-philologie/",
"name": "Classification of the Classical Philology",
"prefix": "1474"
},
"1475": {
"description": "Classification scheme of the neo-tradition of the Johannes Gutenberg University.",
"homepage": "http://www.ub.uni-mainz.de/klassische-philologie/",
"name": "Systematics of neo-tradition",
"prefix": "1475"
},
"1476": {
"description": "Classification scheme of the cultural anthropology / folklore of the Johannes Gutenberg University.",
"homepage": "http://www.ub.uni-mainz.de/kulturanthropologie-volkskunde/",
"name": "Classification of the Cultural anthropology / folklore",
"prefix": "1476"
},
"1477": {
"description": "Classification scheme of the Middle and Modern History of the Johannes Gutenberg University.",
"homepage": "http://www.ub.uni-mainz.de/mittlere-und-neuere-geschichte/",
"name": "Systematics of the Middle and Modern History",
"prefix": "1477"
},
"1478": {
"description": "Classification scheme of the East European History of the Johannes Gutenberg University.",
"homepage": "http://www.ub.uni-mainz.de/osteuropaeische-geschichte/",
"name": "Classifications of the Eastern European history",
"prefix": "1478"
},
"1479": {
"description": "Classification scheme of philosophy of the Johannes Gutenberg University.",
"homepage": "http://www.ub.uni-mainz.de/philosophie/",
"name": "Systematics of philosophy",
"prefix": "1479"
},
"148": {
"description": "The NIFSTD ontology is composed of a collection of OWL modules covering distinct domains of bio-medical reality. We are using a semantic wiki to expose the content of the NIFSTD vocabularies to the community for comment and development. We are experimenting with Wiki's abilities for collaborative editing and commenting on the NIFSTD. Each class in NIFSTD has been turned into a Wiki page, using technologies developed as part of the Semantic Media Wiki project.",
"homepage": "https://confluence.crbs.ucsd.edu/display/NIF/Download+NIF+Ontologies",
"name": "NIFSTD Ontology",
"prefix": "148"
},
"1481": {
"description": "Classification sheme of the slavistics of the Johannes Gutenberg University.",
"homepage": "http://www.ub.uni-mainz.de/slavistik/",
"name": "Systematics of the Slavistics",
"prefix": "1481"
},
"1482": {
"description": "Shelf Classification of Anthropology of the University Library Mainz.",
"homepage": "http://www.ub.uni-mainz.de/files/2014/03/SYSANTHROP.pdf",
"name": "Shelf Classification Anthropology",
"prefix": "1482"
},
"1483": {
"description": "Shelf Classification of Botany of the University Library Mainz.",
"homepage": "http://www.ub.uni-mainz.de/files/2014/03/SYSBOT.pdf",
"name": "Shelf Classification Botany",
"prefix": "1483"
},
"1484": {
"description": "This is the classification system for Zoology at the University Library of Trier.",
"homepage": "http://www.ub.uni-mainz.de/files/2014/03/SYSZOO.pdf",
"name": "Shelf Classification Zoology",
"prefix": "1484"
},
"1485": {
"homepage": "http://www.dnl-online.de/aDISWeb/app",
"name": "Documentation Nature and Landscape - online Thesaurus",
"prefix": "1485"
},
"1486": {
"description": "The university library has a unique stock of more than 2,100 final theses, which have been submitted to the EVHN and its predecessors since 1980. (...) Searching for the work of certain faculties is possible through the search with the system.",
"homepage": "https://www.evhn.de/hochschule/bibliothek/literatursuche/abschlussarbeiten",
"name": "Protestant University of Applied Sciences Nuremberg",
"prefix": "1486"
},
"1487": {
"description": "Systematics of the Testothek of the Evangelische Hochschule NΓΌrnberg - (EVHN) - University of Applied Sciences.",
"homepage": "https://www.evhn.de/hochschule/bibliothek/literatursuche/testothek",
"name": "Evangelical University of Nuremberg systematics of the Testothek",
"prefix": "1487"
},
"1488": {
"description": "Classification scheme of the design stock of the University of the Arts Berlin.",
"homepage": "https://www.udk-berlin.de/fileadmin/2_dezentral/Universitaetsbibliothek/Universitaetsbibliothek/PDF/Design-Systematik.pdf",
"name": "Classifications of design",
"prefix": "1488"
},
"1489": {
"description": "Classification scheme of the of the university library University of the Arts Berlin.",
"homepage": "https://www.udk-berlin.de/fileadmin/2_dezentral/Universitaetsbibliothek/Universitaetsbibliothek/PDF/EW-Systematik.pdf",
"name": "Classifications of education",
"prefix": "1489"
},
"149": {
"description": "Over a decade's, diligent research was devoted to a professional search for an existing thesaurus β to facilitate the classification, and processing, of all essential information on Roman Catholicism. Personal visits were made to Catholic Universities; many librarians and scholars were interviewed; extensive correspondence was exchanged with religious orders; specialized institutes were contacted; all applicable library science, and data-processing literature was analyzed. Two consistent responses emerged from the preponderance of respondents. First, 'There is no existing, broad-scope, professional-quality, Catholic-information, classification system!' Second, 'We sure need a practical, classification system to: promptly and efficiently process the overwhelming flood of incoming information; facilitate its entrance into the electronic era!' The reasons for the research and gradual development of the Thesaurus are discussed under five sub-headings: Information-processing, Broadness of application, Clarification of Catholic communication, Holiness-nurturing, Research-enhancement.",
"homepage": "http://www.therealpresence.org/Thesaurus/intro.htm",
"name": "Pocket Catholic Thesaurus",
"prefix": "149"
},
"1490": {
"description": "The set-up system for the subject areas of the UdK (visual communication with film and photography, corporate and economic communication, electronic business), summarized here under the term 'communication', is based on that in many German libraries ) Was used for the use of the Regensburg classification system RVK (...), but this system was reduced and, if necessary, simplified or modified for use at the UdK A * marked in the following list indicate the specifications for the previously mentioned place, which are no longer used for new books.",
"homepage": "https://www.udk-berlin.de/fileadmin/2_dezentral/Universitaetsbibliothek/Universitaetsbibliothek/PDF/Komm-Systematik.pdf",
"name": "Systematics Communication",
"prefix": "1490"
},
"1491": {
"description": "The system of visual art and architecture gives the objective order for the establishment of the freely accessible (= 'freehand') literature stock in the reading room. (...) In the search for literature, it should be noted that in the case of different aspects for the Classification in general the following order of priority applies: 1. the person (artist or architect) 2. the concept (eg art theory, motif, type of building) 3. the historical concept (epoch or style) 4. only in art: the (Including new media) 5. the region (countries, places).",
"name": "Systematics Art / Architecture",
"prefix": "1491"
},
"1492": {
"description": "Systematics for Music and Theater at the University Library of the University of the Arts, Berlin.",
"name": "Systematics Music / Theatre",
"prefix": "1492"
},
"1493": {
"description": "The grades of the library (...) have not been included in the system!",
"homepage": "http://www.udk-berlin.de/sites/universitaetsbibliothek/content/e286/e305/index_ger.html",
"name": "Systematic Notes",
"prefix": "1493"
},
"1494": {
"description": "A structured list of various film genres",
"name": "Film genres",
"prefix": "1494"
},
"1495": {
"description": "While doing research on how to represent real world camera and lenses the real meanings behind the 'focus-related' terms we use in the film industry. This post is more of a journal of the terms Iβve had to re-learn.\" in Maya I have had to do a lot more research into optics and",
"homepage": "http://www.cinematographydb.com/2015/04/cinema-optics-terminology/",
"name": "Cinema Optics Terminology",
"prefix": "1495"
},
"1496": {
"description": "The following is a dictionary for terminology used in the study of human and animal vision. It includes terms from the areas of biological and machine vision, visual psychophysics, visual neuroscience and other related fields.",
"homepage": "http://www.liden.cc/Visionary/",
"name": "Visionary",
"prefix": "1496"
},
"1497": {
"description": "Terms discussed here include people, places, agencies, technology, jargon and clichΓ©s used in the aftermath of the attack on the United States. The glossary is organized by topics: terrorism, war, geopolitics, religion, homeland security, disaster recovery and miscellaneous. In some cases, the glossary notes alternative spellings of Arabic and other non-English words. Others may have alternative spellings not noted here. Highlighted links will open in a new window, taking you to sites offering more information on selected topics.",
"homepage": "http://www.newslab.org/resources/terrorgloss.htm",
"name": "Buzz Words and Catch Phrases",
"prefix": "1497"
},
"1498": {
"description": "While many of us are aware of basic banking terms, there is a plethora of confusing technical terminology associated with banking and finance. This Buzzle article presents to you a glossary of banking terms and definitions that might help resolve your doubts.",
"homepage": "http://www.buzzle.com/articles/banking-terms-glossary-of-banking-terms-and-definitions.html",
"name": "Glossary of Banking Terms and Definitions",
"prefix": "1498"
},
"1499": {
"description": "Politics is awash with terms and phrases that are beloved of commentators and politicians alike. Here is a guide to some of the key terms.",
"homepage": "http://www.bbc.com/news/election-2015-32613441",
"name": "Glossary of Election Terms",
"prefix": "1499"
},
"15": {
"abbreviation": "EuroVoc",
"description": "EuroVoc is a multilingual, multidisciplinary thesaurus covering the activities of the EU, the European Parliament in particular. It contains terms in 23 EU languages (Bulgarian, Croatian, Czech, Danish, Dutch, English, Estonian, Finnish, French, German, Greek, Hungarian, Italian, Latvian, Lithuanian, Maltese, Polish, Portuguese, Romanian, Slovak, Slovenian, Spanish and Swedish), plus in three languages of countries which are candidates for EU accession: ΠΌΠ°ΠΊΠ΅Π΄ΠΎΠ½ΡΠΊΠΈ (mk), shqip (sq) and cΡΠΏΡΠΊΠΈ (sr).\n\nIt is a multi-disciplinary thesaurus covering fields which are sufficiently wide-ranging to encompass both Community and national points of view, with a certain emphasis on parliamentary activities. EuroVoc is a controlled set of vocabulary which can be used outside the EU institutions, particularly by parliaments.\n\nThe aim of the thesaurus is to provide the information management and dissemination services with a coherent indexing tool for the effective management of their documentary resources and to enable users to carry out documentary searches using controlled vocabulary.",
"homepage": "https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/eurovoc",
"license": "CC0-1.0",
"name": "Multilingual Thesaurus of the European Union",
"prefix": "15",
"wikidata_database": "Q1370467"
},
"150": {
"description": "The VOCABULARY CONTROLLED (VC) consists of a standardized list of topics and identifiers. It is composed of about 1,500 terms on different aspects of education, which have been compiled over the 27 years of IRESIE development. Work for the classification and indexing of articles and documents that enter the IRESIE databases and the Index of Educational Documents (IDOCED).\n\nA large percentage of these words were taken from the UNESCO-OEI Education Thesaurus in its different editions and from the ERIC (Educational Resources Information Center) thesaurus. Sometimes, some words adapted to the terminology used in Mexico. There are also terms that have been introduced by IRESIE documentalists in accordance with the new subdisciplines and the evolution of concepts in the field of education.",
"homepage": "http://de.scribd.com/doc/140532482/IRESIE-Vocabulario-Controlado",
"name": "Index of Higher Education Journals and Educational Research Controlled Vocabulary",
"prefix": "150"
},
"1500": {
"description": "Glossary of Library & Information Science is a glossary of terms and acronyms of librarianship, library science, information science, information technology, and knowledge organization & management. Consider the glossary as a free Online Dictionary of Library and Information Science. The entries of the glossary are given an encyclopedic treatment, they are far more exhaustive than a typical glossary or dictionary entry which in many cases are equivalent to an article in an Encyclopedia of Library of Information Science. The glossary will include everything from traditional library terms to a vocabulary of modern avenues in information science and technology. Glossary entries will include anything and everything required for an advanced study and reference on the Library and Information Science (LIS) topics, including biographies of famous librarians. Glossary of Library and Information Science is expected to become an essential part of every libraryβs and librarianβs reference collection and will also be helpful to librarians, LIS i-School Master of Library and Information Science (MLIS) & Ph.D. students, scholars, researchers, and IT professionals. (...) Glossary of Library & Information Science aims to support the purpose of Librarianship Studies & Information Technology blog, which is: To provide leadership for the development, promotion, and improvement of library and information services and the profession of librarianship in order to enhance learning and ensure access to information for all.",
"homepage": "https://www.librarianshipstudies.com/2015/04/glossary-of-library-information-science.html",
"license": "CC BY-NC-SA 3.0",
"name": "Glossary of Library & Information Science",
"prefix": "1500"
},
"1501": {
"description": "A General Chemistry Glossary by Genereal Chemistry Online",
"homepage": "http://antoine.frostburg.edu/chem/senese/101/glossary.shtml",
"name": "General Chemistry Glossary",
"prefix": "1501"
},
"1502": {
"description": "Prior to the internet, wireless and high speed communications, 'fax' and 'vcr' were the buzzwords of the day. Now terms and acronyms enter our vocabulary on a monthly (if not daily) basis. Here is a short list of terms and acronyms that are essential lingo in today's telecom and techno world.",
"homepage": "http://www.vividfuture.org/content/glossary",
"name": "Telecom Terms and Acronyms",
"prefix": "1502"
},
"1503": {
"homepage": "http://www.socialsecurity.gov/agency/glossary/",
"name": "Glossary of Social Security Terms",
"prefix": "1503"
},
"1504": {
"homepage": "http://termcoord.eu/termania/topical-terminology-projects/glossary-ebola-related-terms/",
"prefix": "1504"
},
"1505": {
"description": "This glossary has been compiled by DG TRADβs Terminology Coordination Unit to help Members, their assistants and EP staff find explanations of terms commonly used in Parliament. It contains 120 terms in English, French and German, with explanations in English. The main sources were the EUβs terminology database (IATE), Parliamentβs Rules of Procedure (July 2014), the Europarl website, the Treaty on the Functioning of the European Union and other official documents and institutional resources.",
"homepage": "http://www.termcoord.eu/wp-content/uploads/2014/11/23094-BROCHURE-A5-EN.pdf",
"name": "Terminology for Parliamentary Work",
"prefix": "1505"
},
"1506": {
"homepage": "http://www.parliament.uk/site-information/glossary/",
"name": "Glossary of Key Parliamentary Terms and their Definition",
"prefix": "1506"
},
"1507": {
"description": "The Masonic Classification herewith presented is the result of some twenty-two years of practical experience in the largest masonic library in the world β the Library of the Supreme Council, 33rd Degree at Washington. This Library, in addition to its thousands of items on Freemasonry and related societies, contains also thousands upon thousands of general works in all branches of literature. These latter works are classified according to the well-known Dewey Decimal System, but this system provides no classification of freemasonry, assigning one class only to the subject, which class is practically incapable of subdivision. The scheme which I have devised and which is in successful practical operation, provides for nearly four hundred classes and sub-classes.\n\nPractically all masonic libraries contain much general literature, but as they specialize on freemasonry, it becomes necessary to provide some system which will allow of their classification independently of the general library. Many libraries use the Dewey Decimal System, and I have devised the present scheme to prevent confusion, not only in the classification, but also in the catalogue card number, the book label number, the shelf guide number, and in various other ways, the letter \"M\" (Masonry) arbitrarily prefixed to the digits, always indicating the card, the book, its label, and the shelf-guide, as of masonic import.\n\nThe entire range of masonic literature is divided into ten great classes, somewhat similar to Dewey's ten great classes of general literature. These ten classes are subdivided again and again to suit the requirements of the literature on a given subject. For example, if we have a general history of freemasonry, it goes in class M10. If it is a history of Freemasonry in Europe, it goes in class M17.940, the M17, indicating that it is a geographical division of masonic history, and the 940, indicating that it is a history of Freemasonry in Europe, the 940 being Dewey's notation for Europe. Again, take the class M20, which is Customs and Paraphernalia. Any general work on the subject would go in this class, but if the library possessed literature on the Obituary Rites of freemasonry, it would go in class M20.01; if it had works on Paraphernalia, they would go in class M21; Jewels and Medals would go in M22, and so on.",
"name": "Classification of the Literature of Freemasonry and Related Societies",
"prefix": "1507"
},
"1508": {
"description": "Glossary of the National Institute on Aging about Clinical Research Terms.",
"homepage": "https://www.nia.nih.gov/research/dgcg/clinical-research-study-investigators-toolbox/nia-glossary-clinical-research-terms",
"name": "NIA Glossary of Clinical Research Terms",
"prefix": "1508"
},
"1509": {
"description": "Weather forecasts and warnings have to compress a lot of information into standardised, brief messages. Forecast and warning weather terms represent the more detailed definitions provided here. Forecasts and warnings have to accommodate variations across the time range, and often large areas, that they apply to. It is important to understand the use of duration and distribution terms, especially for elements like showers and thunderstorms, when considering the impact for a specific location or time.",
"homepage": "http://www.bom.gov.au/info/wwords/",
"license": "CC-BY-3.0",
"name": "Weather Words",
"prefix": "1509"
},
"151": {
"description": "You can search for the hierarchical thesaurus of BiBIL. If you want to search for entries that have been indexed with a certain keyword, select the keyword (it will be blue) and press the search button.",
"homepage": "https://bibil.unil.ch/bibil/public/indexThesaurusSearch.action",
"name": "Thesaurus Bibliography Computerized Bibliography of Lausanne",
"prefix": "151"
},
"1510": {
"description": "Traditional roofing has a vocabulary of unfamiliar technical terms for materials and techniques. (...) This short publication explains the terms used in stone roofing and illustrates many of them.",
"homepage": "http://www.englishstone.org.uk/documents/Stone%20slate%20glossary.pdf",
"name": "Glossary of Stone Slate Roofing",
"prefix": "1510"
},
"1511": {
"description": "A glossary about plumbing.",
"homepage": "http://www.wpjheating.co.uk/the-complete-plumbing-glossary/",
"name": "The Complete Plumbing Glossary",
"prefix": "1511"
},
"1512": {
"description": "Glossary about the Pamplona's City Walls by the Ayuntamiento de Pamplona.",
"homepage": "http://www.murallasdepamplona.com/glosario/",
"license": "https://www.w3.org/Consortium/Legal/2015/doc-license",
"name": "Walls of Pamplona Glossary",
"prefix": "1512"
},
"1513": {
"description": "When you first arrive at university in your first year things can seem a little overwhelming. Here is a definitive guide to things that you may hear whilst you are studying at university and what they mean!",
"homepage": "http://www.grb.uk.com/higher-education-glossary",
"name": "Higher Education Glossary",
"prefix": "1513"
},
"1514": {
"description": "Electropedia (also known as the 'IEV Online') is the world's most comprehensive online electrical and electronic terminology database containing more than 20 000 terms and definitions in English and French organized by subject area, with equivalent terms in various other languages (...). (...) Electropedia is produced by the IEC, the worldβs leading organization that prepares and publishes International Standards for all electrical, electronic and related technologies β collectively known as 'electrotechnology'. Electropedia contains all the terms and definitions in the International Electrotechnical Vocabulary or IEV which is published also as a set of publications in the IEC 60050 series that can be ordered separately from the IEC webstore.",
"homepage": "http://www.electropedia.org/",
"name": "Electropedia: The World's Online Electrotechnical Vocabulary",
"prefix": "1514",
"wikidata_database": "Q1667710"
},
"1515": {
"description": "The IEC Glossary is a compilation of electrotechnical terminology in English and French extracted from the \"Terms and Definitions\" clause of IEC publications (those issued since 2002). In some cases terms and definitions have also been collected from earlier publications (e.g. from TC 37, 77, 86 and CISPR). The database contains currently some 40,000 items drawn from 1,800 publications, with new ones being added on a continuous basis. (...) The Glossary complements and in many cases draws from the International Electrotechnical Vocabulary (IEV) published by TC 1 (Terminology). The IEV is the authoritative source for 'standardized IEC terminology' organized into some 80 subject areas. The Glossary is of a more limited nature. Its definitions relate to the source standard from which they are extracted. A term can therefore have different meanings, depending on the context in which it is used. The Glossary should be considered as an informative document as the terms and definitions have been separated from the context in which they are applied.",
"homepage": "http://std.iec.ch/glossary",
"name": "International Electrotechnical Commission Glossary",
"prefix": "1515"
},
"1516": {
"description": "Some terms used in discussing nanotechnology and other anticipated technologies",
"homepage": "http://www.foresight.org/UTF/Unbound_LBW/Glossary.html",
"name": "Nanotechnology Glossary",
"prefix": "1516"
},
"1517": {
"description": "This vocabulary is part of a collection of thematic vocabularies published by the General Delegation for the French Language and the Languages ββof France, under the French Language Enrichment Device. The various vocabularies contain the terms and expressions recommended by the General Commission on Terminology and Neology, which it publishes regularly in the Official Journal of the French Republic, pursuant to the decree of 3 July 1996 on the enrichment of the French language. Proposed by various specialized committees of terminology and neology and subject to an approval procedure involving the General Committee, the French Academy and the Minister concerned. Their publication in the Official Journal renders their use compulsory, instead of foreign equivalents, for Services (Article 11 of the Decree of 3 July T 1996) The terminology lists published in the Official Journal cover many technical fields in high-tech sectors such as information and communication (internet, computers, telecommunications), sciences (biology, chemistry, nuclear engineering, space science and technology ), Industry (automobile, oil), agriculture, culture, defense, law, economics and finance, education, environment, international relations, medicine, sports , Transport, in fact all the areas of competence of the various ministries. The publication of these terms and definitions is intended to enrich the French language by facilitating the understanding of concepts that are sometimes poorly known to the public and recommending their use, including outside professional circles, Express in French.",
"homepage": "http://www.culturecommunication.gouv.fr/content/download/103335/1217334/version/2/file/Vocabulaire_2014_relations-int.pdf",
"name": "International Relations Vocabulary",
"prefix": "1517"
},
"1518": {
"description": "This vocabulary is part of a collection of thematic vocabularies published by the General Delegation for the French Language and the Languages ββof France, under the French Language Enrichment Device. The various vocabularies contain the terms and expressions recommended by the General Commission on Terminology and Neology, which it publishes regularly in the Official Journal of the French Republic, pursuant to the decree of 3 July 1996 on the enrichment of the French language. Proposed by various specialized committees of terminology and neology and subject to an approval procedure involving the General Committee, the French Academy and the Minister concerned. Their publication in the Official Journal renders their use compulsory, instead of foreign equivalents, for Services (Article 11 of the Decree of 3 July T 1996) The terminology lists published in the Official Journal cover many technical fields in high-tech sectors such as information and communication (internet, computers, telecommunications), sciences (biology, chemistry, nuclear engineering, space science and technology ), Industry (automobile, oil), agriculture, culture, defense, law, economics and finance, education, environment, international relations, medicine, sports , Transport, in fact all the areas of competence of the different ministries. The publication of these terms and definitions is intended to enrich the French language by facilitating the understanding of concepts that are sometimes poorly known to the public and recommending their use, including outside professional circles, Express in French.",
"homepage": "http://www.culturecommunication.gouv.fr/content/download/93743/841993/version/4/file/voca-en-ligne_2014_droit_def.pdf",
"name": "Vocabulary of Law",
"prefix": "1518"
},
"1519": {
"description": "This vocabulary is part of a collection of thematic vocabularies published by the General Delegation for the French Language and the Languages ββof France, under the French Language Enrichment Device. The various vocabularies contain the terms and expressions recommended by the General Commission on Terminology and Neology, which it publishes regularly in the Official Journal of the French Republic, pursuant to the decree of 3 July 1996 on the enrichment of the French language. Proposed by various specialized committees of terminology and neology and subject to an approval procedure involving the General Committee, the French Academy and the Minister concerned. Their publication in the Official Journal renders their use compulsory, instead of foreign equivalents, for Services (Article 11 of the Decree of 3 July T 1996) The terminology lists published in the Official Journal cover many technical fields in high-tech sectors such as information and communication (internet, computers, telecommunications), sciences (biology, chemistry, nuclear engineering, space science and technology ), Industry (automobile, oil), agriculture, culture, defense, law, economics and finance, education, environment, international relations, medicine, sports , Transport, in fact all the areas of competence of the various ministries. The publication of these terms and definitions is intended to enrich the French language by facilitating the understanding of concepts that are sometimes poorly known to the public and recommending their use, including outside professional circles, Express in French.",
"homepage": "http://www.culturecommunication.gouv.fr/content/download/93742/841989/version/4/file/voca_en_ligne_2013_spatial_def.pdf",
"name": "Vocabulary of Space Science and Technology",
"prefix": "1519"
},
"152": {
"description": "The Water Quality Library Database is indexed using controlled vocabulary from the WQPB Library Thesaurus. This thesaurus was developed to create a standardized vocabulary for water concepts that may be phrased in a variety of ways in the literature, it should be used as a guide to searching keywords in the library. The terms are arranged according to lead terms, together with both broader and narrower hierarchical relationship terms and related terms. USE references are noted to satisfy desirable standardization requirements.",
"name": "Water Quality Planning Bureau Library Thesaurus",
"prefix": "152"
},
"1520": {
"description": "This vocabulary is part of a collection of thematic vocabularies published by the General Delegation for the French Language and the Languages ββof France, under the French Language Enrichment Device. The various vocabularies contain the terms and expressions recommended by the General Commission on Terminology and Neology, which it publishes regularly in the Official Journal of the French Republic, pursuant to the decree of 3 July 1996 on the enrichment of the French language. Proposed by various specialized committees of terminology and neology and subject to an approval procedure involving the General Committee, the French Academy and the Minister concerned. Their publication in the Official Journal renders their use compulsory, instead of foreign equivalents, for Services (Article 11 of the Decree of 3 July T 1996) The terminology lists published in the Official Journal cover many technical fields in high-tech sectors such as information and communication (internet, computers, telecommunications), sciences (biology, chemistry, nuclear engineering, space science and technology ), Industry (automobile, oil), agriculture, culture, defense, law, economics and finance, education, environment, international relations, medicine, sports , Transport, in fact all the areas of competence of the various ministries. The publication of these terms and definitions is intended to enrich the French language by facilitating the understanding of concepts that are sometimes poorly known to the public and recommending their use, including outside professional circles, Express in French.",
"homepage": "http://www.culturecommunication.gouv.fr/content/download/93741/841985/version/4/file/voca_en_ligne_2013_sante_def.pdf",
"name": "Vocabulary of Health",
"prefix": "1520"
},
"1521": {
"description": "This vocabulary is part of a collection of thematic vocabularies published by the General Delegation for the French Language and the Languages ββof France, under the French Language Enrichment Device. The various vocabularies contain the terms and expressions recommended by the General Commission on Terminology and Neology, which it publishes regularly in the Official Journal of the French Republic, pursuant to the decree of 3 July 1996 on the enrichment of the French language. Proposed by various specialized committees of terminology and neology and subject to an approval procedure involving the General Committee, the French Academy and the Minister concerned. Their publication in the Official Journal renders their use compulsory, instead of foreign equivalents, for Services (Article 11 of the Decree of 3 July T 1996) The terminology lists published in the Official Journal cover many technical fields in high-tech sectors such as information and communication (internet, computers, telecommunications), sciences (biology, chemistry, nuclear engineering, space science and technology ), Industry (automobile, oil), agriculture, culture, defense, law, economics and finance, education, environment, international relations, medicine, sports , Transport, in fact all the areas of competence of the various ministries. The publication of these terms and definitions is intended to enrich the French language by facilitating the understanding of concepts that are sometimes poorly known to the public and recommending their use, including outside professional circles, Express in French.",
"homepage": "http://www.culturecommunication.gouv.fr/content/download/93740/841981/version/5/file/voca_en_ligne_2013_education_def.pdf",
"name": "Vocabulary of Education and Research",
"prefix": "1521"
},
"1522": {
"description": "This vocabulary is part of a collection of thematic vocabularies published by the General Delegation for the French Language and the Languages ββof France, under the French Language Enrichment Device. The various vocabularies contain the terms and expressions recommended by the General Commission on Terminology and Neology, which it publishes regularly in the Official Journal of the French Republic, pursuant to the decree of 3 July 1996 on the enrichment of the French language. Proposed by various specialized committees of terminology and neology and subject to an approval procedure involving the General Committee, the French Academy and the Minister concerned. Their publication in the Official Journal renders their use compulsory, instead of foreign equivalents, for Services (Article 11 of the Decree of 3 July T 1996) The terminology lists published in the Official Journal cover many technical fields in high-tech sectors such as information and communication (internet, computers, telecommunications), sciences (biology, chemistry, nuclear engineering, space science and technology ), Industry (automobile, oil), agriculture, culture, defense, law, economics and finance, education, environment, international relations, medicine, sports , Transport, in fact all the areas of competence of the various ministries. The publication of these terms and definitions is intended to enrich the French language by facilitating the understanding of concepts that are sometimes poorly known to the public and recommending their use, including outside professional circles, Express in French.",
"homepage": "http://www.culturecommunication.gouv.fr/content/download/93736/841965/version/3/file/voca_2012_economie_finances_def.pdf",
"name": "Vocabulary of Economics and Finance",
"prefix": "1522"
},
"1523": {
"description": "This vocabulary is part of a collection of thematic vocabularies published by the General Delegation for the French Language and the Languages ββof France, under the French Language Enrichment Device. The various vocabularies contain the terms and expressions recommended by the General Commission on Terminology and Neology, which it publishes regularly in the Official Journal of the French Republic, pursuant to the decree of 3 July 1996 on the enrichment of the French language. Proposed by various specialized committees of terminology and neology and subject to an approval procedure involving the General Committee, the French Academy and the Minister concerned. Their publication in the Official Journal renders their use compulsory, instead of foreign equivalents, for Services (Article 11 of the Decree of 3 July T 1996) The terminology lists published in the Official Journal cover many technical fields in high-tech sectors such as information and communication (internet, computers, telecommunications), sciences (biology, chemistry, nuclear engineering, space science and technology ), Industry (automobile, oil), agriculture, culture, defense, law, economics and finance, education, environment, international relations, medicine, sports , Transport, in fact all the areas of competence of the various ministries. The publication of these terms and definitions is intended to enrich the French language by facilitating the understanding of concepts that are sometimes poorly known to the public and recommending their use, including outside professional circles, Express in French.",
"homepage": "http://www.culturecommunication.gouv.fr/content/download/93735/841961/version/3/file/voca_2011_sports_def.pdf",
"name": "Vocabulary of Sports",
"prefix": "1523"
},
"1524": {
"description": "This vocabulary is part of a collection of thematic vocabularies published by the General Delegation for the French Language and the Languages ββof France, under the French Language Enrichment Device. The various vocabularies contain the terms and expressions recommended by the General Commission on Terminology and Neology, which it publishes regularly in the Official Journal of the French Republic, pursuant to the decree of 3 July 1996 on the enrichment of the French language. Proposed by various specialized committees of terminology and neology and subject to an approval procedure involving the General Committee, the French Academy and the Minister concerned. Their publication in the Official Journal renders their use compulsory, instead of foreign equivalents, for Services (Article 11 of the Decree of 3 July T 1996) The terminology lists published in the Official Journal cover many technical fields in high-tech sectors such as information and communication (internet, computers, telecommunications), sciences (biology, chemistry, nuclear engineering, space science and technology ), Industry (automobile, oil), agriculture, culture, defense, law, economics and finance, education, environment, international relations, medicine, sports , Transport, in fact all the areas of competence of the various ministries. The publication of these terms and definitions is intended to enrich the French language by facilitating the understanding of concepts that are sometimes poorly known to the public and recommending their use, including outside professional circles, Express in French.",
"homepage": "http://www.culturecommunication.gouv.fr/content/download/93734/841957/version/3/file/voca_2010_audiovisuel%20et%20de%20la%20communication_def.pdf",
"name": "Audiovisual and Communication Vocabulary",
"prefix": "1524"
},
"1525": {
"description": "This vocabulary is part of a collection of thematic vocabularies published by the General Delegation for the French Language and the Languages ββof France, under the French Language Enrichment Device. The various vocabularies contain the terms and expressions recommended by the General Commission on Terminology and Neology, which it publishes regularly in the Official Journal of the French Republic, pursuant to the decree of 3 July 1996 on the enrichment of the French language. Proposed by various specialized committees of terminology and neology and subject to an approval procedure involving the General Committee, the French Academy and the Minister concerned. Their publication in the Official Journal renders their use compulsory, instead of foreign equivalents, for Services (Article 11 of the Decree of 3 July T 1996) The terminology lists published in the Official Journal cover many technical fields in high-tech sectors such as information and communication (internet, computers, telecommunications), sciences (biology, chemistry, nuclear engineering, space science and technology ), Industry (automobile, oil), agriculture, culture, defense, law, economics and finance, education, environment, international relations, medicine, sports , Transport, in fact all the areas of competence of the different ministries. The publication of these terms and definitions is intended to enrich the French language by facilitating the understanding of concepts that are sometimes poorly known to the public and recommending their use, including outside professional circles, Express in French.",
"homepage": "http://www.culturecommunication.gouv.fr/content/download/93733/841953/version/3/file/voca_2009_information_com_tic_def.pdf",
"name": "Vocabulary of Information and Communication Technologies (ICT)",
"prefix": "1525"
},
"1526": {
"description": "This vocabulary is part of a collection of thematic vocabularies published by the General Delegation for the French Language and the Languages ββof France, under the French Language Enrichment Device. The various vocabularies contain the terms and expressions recommended by the General Commission on Terminology and Neology, which it publishes regularly in the Official Journal of the French Republic, pursuant to the decree of 3 July 1996 on the enrichment of the French language. Proposed by various specialized committees of terminology and neology and subject to an approval procedure involving the General Committee, the French Academy and the Minister concerned. Their publication in the Official Journal renders their use compulsory, instead of foreign equivalents, for Services (Article 11 of the Decree of 3 July T 1996) The terminology lists published in the Official Journal cover many technical fields in high-tech sectors such as information and communication (internet, computers, telecommunications), sciences (biology, chemistry, nuclear engineering, space science and technology ), Industry (automobile, oil), agriculture, culture, defense, law, economics and finance, education, environment, international relations, medicine, sports , Transport, in fact all the areas of competence of the various ministries. The publication of these terms and definitions is intended to enrich the French language by facilitating the understanding of concepts that are sometimes poorly known to the public and recommending their use, including outside professional circles, Express in French.",
"homepage": "http://www.culturecommunication.gouv.fr/content/download/93732/841949/version/4/file/voca_2008_mots_autos_def.pdf",
"name": "Vocabulary of the Automobile",
"prefix": "1526"
},
"1527": {
"description": "The fascicles of this collection include the lists of terms, expressions and definitions published in the Official Journal of the French Republic by the General Commission for Terminology and Neology, in application of the Decree of 3 July 1996 on the enrichment of the French language The terms proposed by the specialized committees for terminology and neology are subject to an approval procedure involving the General Committee on Terminology and Neology, the French Academy and the Minister concerned. (Article 11 of the Decree of 3 July 1996) The terminology lists published in the Official Journal cover a wide range of technical fields in Information and communication (internet, informatics), (Chemistry, nuclear engineering, space science and technology), industry (automotive, petroleum), economy and finance, health, agriculture, defense, transport, culture , In fact all the areas of competence of the various ministries.",
"homepage": "http://www.culturecommunication.gouv.fr/content/download/93731/841945/version/3/file/voca_2007_petrole_gaz_def.pdf",
"name": "Vocabulary of Oil and Gas",
"prefix": "1527"
},
"1528": {
"description": "The fascicles of this collection include the lists of terms, expressions and definitions published in the Official Journal of the French Republic by the General Commission for Terminology and Neology, in application of the Decree of 3 July 1996 on the enrichment of the French language The terms proposed by the specialized committees for terminology and neology are subject to an approval procedure involving the General Committee on Terminology and Neology, the French Academy and the Minister concerned. (Article 11 of the Decree of 3 July 1996) The terminology lists published in the Official Journal cover a wide range of technical fields in Information and communication (internet, informatics), (Chemistry, nuclear engineering, space science and technology), industry (automotive, petroleum), economy and finance, health, agriculture, defense, transport, culture , In fact all the areas of competence of the various ministries.",
"homepage": "http://www.culturecommunication.gouv.fr/content/download/93730/841941/version/3/file/voca_2007_equipement_transports_tourisme_def.pdf",
"name": "Vocabulary of Equipment, Transport and Tourism",
"prefix": "1528"
},
"1529": {
"homepage": "http://www.culturecommunication.gouv.fr/content/download/93728/841933/version/3/file/voca_2007_chimie_materiaux_def.pdf",
"name": "Vocabulary of Chemistry and Materials",
"prefix": "1529"
},
"153": {
"description": "The Thesaurus Ethics in the Life Sciences is a multilingual and controlled indexing and research tool that covers all areas of bioethics. With the help of the thesaurus, it is possible to present and contribute to current developments in the heterogeneous and multidisciplinary field of bioethics. The various functionalities of the thesaurus are geared primarily to the needs of the two most important target groups: researching users - both professionals and non-professionals - as well as librarian and documentary specialists who index bioethics literature and documents.",
"homepage": "http://www.drze.de/thesaurus",
"name": "Thesaurus Ethics in the life sciences",
"prefix": "153"
},
"1530": {
"homepage": "http://www.culturecommunication.gouv.fr/content/download/93727/841929/version/3/file/voca_2006_nucleaire_def.pdf",
"name": "Vocabulary of Nuclear Engineering",
"prefix": "1530"
},
"1531": {
"description": "The fascicles of this collection include the lists of terms, expressions and definitions published in the Official Journal of the French Republic by the General Commission for Terminology and Neology, in application of the Decree of 3 July 1996 on the enrichment of the French language The terms proposed by the specialized committees for terminology and neology are subject to an approval procedure involving the General Committee on Terminology and Neology, the French Academy and the Minister concerned. (...) The terms, expressions and definitions contained in this specification are to be understood as references to the term \" Drawn up by the Specialized Committee on Terminology and Defense Neology (Chairman: Mr Michel Brem) This publication is for the use of professionals, teachers and students, translators and anyone wishing to publish in French. It is a limited set of terms and definitions in the field of defense, which are not usually found in or found in general dictionaries, but with a different meaning from those in Area. This set is likely to be completed as scientific and technical progress evolves. The publication of these terms and definitions is the means of enriching the French language by facilitating the understanding of concepts that are often poorly understood by the public and by expanding the use of them outside the professional circle by any speaker who is anxious to express himself or herself French.",
"homepage": "http://www.culturecommunication.gouv.fr/content/download/93726/841925/version/3/file/voca_2006_defense_def.pdf",
"name": "Vocabulary of the Defense",
"prefix": "1531"
},
"1532": {
"description": "Terms for art media, design, and photography.",
"homepage": "http://babel-linguistics.com/wp-content/uploads/2013/08/Glossary-Art.pdf",
"prefix": "1532"
},
"1533": {
"homepage": "http://babel-linguistics.com/wp-content/uploads/2013/08/Glossary-Legal1.pdf",
"name": "Glossary of Legal Terms",
"prefix": "1533"
},
"1534": {
"homepage": "http://babel-linguistics.com/wp-content/uploads/2013/08/Glossary-Linguistics.pdf",
"prefix": "1534"
},
"1535": {
"description": "Provides a thorough understanding of todayβs tools and resources used by translators and interpreters, as well as technical details of their work.",
"homepage": "http://babel-linguistics.com/wp-content/uploads/2013/08/Glossary-Translation.pdf",
"name": "Glossary of Translation & Interpreting Terms & Definitions",
"prefix": "1535"
},
"1536": {
"homepage": "http://babel-linguistics.com/wp-content/uploads/2013/08/Glossary-Psychology.pdf",
"name": "Glossary of Psychology and Therapy Terms",
"prefix": "1536"
},
"1537": {
"description": "The UIS Glossary includes statistical terms related to education, science, technology and innovation, culture, and communication & information. Some of the entries contain translations in one or more of the following languages: Arabic, English, French and Spanish. Other entries provide more detailed information, such as definitions, calculation formulas for indicators and sources. Indicators are marked with an asterisk (*). This is a dynamic tool, which is regularly updated by the UIS.",
"homepage": "http://www.uis.unesco.org/Pages/Glossary.aspx",
"name": "UNESCO Institute for Statistics Glossary",
"prefix": "1537"
},
"1538": {
"description": "This dictionary contains more than two thousand terms with the names and the definition and the equivalents in Spanish and English, concerning the theory, fieldwork and laboratory construction and performance, covering areas as diverse as the numismatic the musivΓ ria, dating techniques or methods of excavation. This is the online version of the Dictionary of archeology, work produced by LluΓs Garcia Petit, Josep Miret and Teacher, Maria Teresa MirΓ³ Alaix and Genis and RibΓ© Monge 2002, with the advice and terminological editing TERMCAT and sponsored by ArqueoCat, ArqueociΓ¨ncia Cultural Services, penthouses and Codex Archeology and Heritage. the original data may have been updated or supplemented later by TERMCAT.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/18",
"license": "CC BY-ND 3.0",
"name": "Dictionary of Archeology",
"prefix": "1538"
},
"1539": {
"description": "This dictionary compiled by Jaume SalvΓ i Lara, with the advice and review TERMCAT 1294 includes Catalan terms related to the following areas: painting and drawing, sculpture, architecture and urbanism, decorative arts , engraving and ceramics. We have the names and the definition in Catalan and Spanish and English equivalents. This is a revised and expanded version of the dictionary published in 2002. Specifically, we have added two more -Center terms and equivalents in English.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/147",
"license": "CC BY-ND 3.0",
"name": "Dictionary of arts: architecture, sculpture and painting",
"prefix": "1539"
},
"154": {
"description": "The flood of data and factual knowledge in biology and medicine requires principled approaches to their proper analysis and management. A cornerstone in this effort constitutes the precise and complete description of the fundamental entities within this domain in terms of formal ontologies.\n\nHowever, biomedical ontology development often still do not adhere to basic design principles: For example, even very low-level domain terms often lack precise and unambiguous (logical) definitions. This impedes the move towards semantic standardization that is needed for their intended knowledge management task. Rather, it leads to inconsistencies, fragmentation and overlap both within and inbetween different ontologies.\n\nIn light of this we introduce BioTop, a top-domain ontology that provides definitions for the foundational entities of biomedicine as a basic vocabulary to unambiguously describe facts in this domain. BioTop can furthermore serve as top-level model for creating new ontologies for more specific domains or as aid for aligning or improving existing ones.\n\nBioTop is founded upon formal design principles (as propagated by the OBO Foundry initiative) and implemented in OWL-DL, the standard ontology language on the Semantic Web. BioTop makes use of the whole range of constructors of OWL-DL. The use of OWL-DL makes it possible to apply description logics reasoners for maintaining consistency by continuous classficiation during development and to automatically infer its hierarchical structure. To this end, we try to fully define as much classes as possible (in terms of necessary and sufficient conditions).",
"homepage": "http://purl.org/biotop/biotop.owl",
"name": "BioTop",
"prefix": "154"
},
"1540": {
"description": "This dictionary includes hundreds of terms commonly used in the field, with the names in Catalan and definition, part of speech and some additional notes. The terms have been reviewed by experts of the League of Young Children Tarragona. the contents of the leaflet Dictionary come from the world casteller: basic terminology, that made TERMCAT 2001 in collaboration with the City of Terrace, the Consortium for Language Normalization and the Coordinator Gang castles of Catalonia. the terminology of this leaflet has been completed with other sources, among which especially casteller dictionary developed by Xavier Brotons and reviewed by TERMCAT (Barcelona Provincial Council, 2001).",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/2",
"license": "CC BY-ND 3.0",
"name": "Dictionary casteller",
"prefix": "1540"
},
"1541": {
"description": "This dictionary contains about three hundred terms related specialties circus acrobatics, aerial and acrobatics. Each term includes Catalan terms, definitions, equivalents in Spanish, French, English and, in some cases, Italian and German and, if necessary, additional notes. the work makes available to users with a selection of terms Dictionary circus TERMCAT produced with the support of Ministry of Culture of the Generalitat of Catalonia and collaboration Association of Circus Professionals of Catalonia. TERMCAT wanted to advance the spread of partial data to facilitate public consultation information, which is considered as sufficiently advanced with the intention of completing it go progressively content updates after the incorporation of the terms of other subject areas dictionary. with the publication online will want to reinforce the main work of this term inolΓ²gic consensus: the circus terminology accessible to all sectors that are users. We encourage you therefore to use it, spreading it among the community involved and send us any suggestions for improvement or upgrade.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/165",
"license": "CC BY-ND 3.0",
"name": "Circus Dictionary",
"prefix": "1541"
},
"1542": {
"description": "Development cooperation is an increasingly important global activity in the world, which encourages collaborative work of a variety of actors at all levels. The humanitarian actors can be individuals or organizations (governmental or not government) local, regional or universal. for this reason, TERMCAT considered necessary the elaboration of a terminology compilation containing the basic terminology of the field. this dictionary contains about a hundred terms. Each term includes names in Catalan, a definition equivalents in Spanish, French and English and, if necessary, additional notes. the work has been prepared by TERMCAT and has taken advice from the Catalan Agency for Development Cooperation and the Directorate General for Development Cooperation, and with the support of the Government of Andorra. This dictionary aims to be a practical reference tool for t othom involved in development cooperation. We encourage you therefore to use it, spreading it among the community involved and send us any suggestions for improvement or upgrade.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/190",
"license": "CC BY-ND 3.0",
"name": "Dictionary for development cooperation",
"prefix": "1542"
},
"1543": {
"description": "This dictionary includes about two thousand and defines terms from the world of education and its facets: general pedagogy, social pedagogy, educational research, educational organization and management, Counseling, teaching, special education and educational technology . Each item also contains the name of Catalan, the equivalents in Spanish, French and English definition, and often one or more explanatory notes. This is the online version of the Dictionary of education, and prepared by TERMCAT the Department of Education of the Generalitat of Catalonia with the support of the Government of Andorra and the collaboration of the Catalan Society of Education at the Institute of Catalan Studies.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/132",
"license": "CC BY-ND 3.0",
"name": "Dictionary of Education",
"prefix": "1543"
},
"1544": {
"description": "This vocabulary Brief prepared by Marta, includes nearly 200 terms relating to the LGBT sphere, ie, the group of lesbian, gay, bisexual and transgender. This is basic terminology related to sexual orientation, sexual and gender identity and LGBT relationship with society (activism, rights and family, leisure, etc.). the vocabulary comes from a final master author and has been reviewed by TERMCAT specifically Dolors Montes terminology. it is an open work is expected to be expanded with new terms and new topics branches. the cards contain the name Catalan terminology concept with the corresponding definition, subject area, the equivalent Spanish, French and English, the lexical category of each form in different languages and sometimes explanatory notes.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/164",
"name": "LGBT terminology vocabulary",
"prefix": "1544"
},
"1545": {
"description": "Dictionary of the world's languages is a systematic collection of information about 1264 languages structured as a dictionary file. You will find the name of the languages Catalan, Arabic, Welsh, German, English, Spanish, Basque, French , Galician Guarani, Italian, Japanese, Dutch, Occitan, Portuguese, Russian, Swahili, Berber and Chinese, and the language itself in question. it also includes information on personal language, where they speak, their situation sociolinguistic vitality, some historical aspects, etc. the data contained in this dictionary are from a project LinguamΓ³n-House of Languages was held in collaboration with the Study Group on Endangered Languages of the UB, the Ciemen and Catalan Encyclopedia.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/130/",
"license": "CC BY-ND 3.0",
"name": "Dictionary of World Languages",
"prefix": "1545"
},
"1546": {
"description": "This dictionary includes terms referring to twenty ingredients and dishes of the cuisine of the Middle East and North Africa, which have recently become part of the gastronomic scene of Catalonia. Catalan All forms have been standardized by the Council supervisor TERMCAT, with the collaboration of experts in Arabic and taking into account the principles of transcription and adaptation established by the Institute of Catalan Studies. As for equivalents in other languages, collected most documented forms without going to assess their suitability in any case.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/32/",
"license": "CC BY-ND 3.0",
"name": "Middle Eastern cuisine",
"prefix": "1546"
},
"1547": {
"description": "This dictionary includes twenty terms refer to ingredients and dishes of the cuisine of Japan, which have become part recently in the dining scene of Catalonia. Most Catalan forms have been standardized by the Supervisory Council TERMCAT with in collaboration with experts in Japanese and have followed romanji Hepburn transcription system, which is the most widespread internationally. Exceptionally, according to the treatment given to other reference sources and dissemination experienced by the terms, in some cases we opted for slightly different ways. as for equivalents in other languages, collected most of the documented forms without going to assess their suitability in any case.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/33",
"license": "CC BY-ND 3.0",
"name": "Japanese cuisine",
"prefix": "1547"
},
"1548": {
"description": "This dictionary includes more than a hundred terms related to games and toys, along with the names and equivalents in Spanish, French and English from the multilingual Glossary of Industry, published by TERMCAT 2010.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/4",
"license": "CC BY-ND 3.0",
"name": "Dictionary of toys and games",
"prefix": "1548"
},
"1549": {
"description": "The online dictionary la carte dishes makes available user names 7765 Catalan dishes and drinks with corresponding equivalents in Spanish, French, Italian, English and German. The information in this repertoire comes from the base application data Plats a la carte tool developed and managed by the Directorate General for Language Policy of the Generalitat of Catalonia in collaboration with TERMCAT and confegida from names of dishes and drinks suggested by users implementation, in order to provide the catering sector preparing menus in Catalan.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/116",
"license": "CC BY-ND 3.0",
"name": "A la carte",
"prefix": "1549"
},
"155": {
"description": "643 terms, 3676 relationships between terms, 12 non-preferred terms. This listing is not intended to be a thesaurus, however it is intended for use in indexing library material.\n\nIt presents the relations between philosophers, schools, currents, epochs and philosophical stages. The death of St. Augustine is adopted as a criterion of division between Ancient and Medieval Philosophy. Words written in parentheses are not considered descriptors, they only contribute to the ordering of terms.",
"homepage": "http://ffyl.uncuyo.edu.ar/catalogos",
"name": "Controlled Vocabulary of Philosophy",
"prefix": "155"
},
"1550": {
"description": "This dictionary contains about three hundred terms related procedures culinary and actions that occur when carrying out the names and the definition in Catalan and equivalents in Spanish, French and English. This is the version online procedures culinary dictionary, published by TERMCAT 2005 and prepared by Julius Blanco GonzΓ‘lez, Aznar and Luis Francisco PapiΓ³ Ignasi Miquel Vila, advised TERMCAT terminology. the original data may have been updated or supplemented later by TERMCAT.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/20",
"license": "CC BY-ND 3.0",
"name": "Dictionary of culinary procedures",
"prefix": "1550"
},
"1551": {
"description": "Dictionary of Religions 1604 spreads Catalan denominations corresponding to 1,427 different items. Each term is assigned to one or more religious traditions in Catalonia with more presence (Baha'i, Buddhism, Catholicism, Orthodox Christianity, Hinduism, Islam , Jainism, Judaism, Protestantism, Sikhism and Zoroastrianism), apart from other groups who have similar tools (free churches, new religions, indigenous religions, religions of China and Japan). Some terms have been assigned to cross-cutting areas such as science and religion secular terms. Part of the material comes from the vocabulary of this dictionary of religions to the media, which was published on paper in 2004 and now is almost can not be found. for this reason, s' has driven the development of this online edition that allows access to information is difficult to obtain by other means. it includes more than three hundred new posts A significant number of amendments and additions, and a general reorganization of the information offered to make it more easily accessible consultation screen. This dictionary has been possible thanks to the initiative of the Directorate General for Religious Affairs to re-gather the four agencies that ten years ago were involved in this project: the UNESCO Association for Interreligious Dialogue (AUDIR) TERMCAT, Obra Social la Caixa and the same Directorate General for Religious Affairs.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/193",
"license": "CC BY-ND 3.0",
"name": "Dictionary of Religions",
"prefix": "1551"
},
"1552": {
"description": "The Glossary of flavors in the world is a collection of terms 47 terms worked because of the different editions (2012, 2013 and 2014) of the sample flavors of the world. Flavors of the world is a gastronomic which aims to products food and culinary creations of the different cultures that live in the neighborhood Fondo de Santa Coloma de Gramenet. the ultimate goals of the exhibition is to promote local business, social cohesion and the promotion of Catalan as a common language. Tastes of the world is an initiative of the Association of Merchants and Professionals Trade Fund, with the collaboration of CNL the Ivy, the City of Santa Coloma de Gramenet and the University of Barcelona. this glossary will find much food ( vegetables, fruits, beverages, breads) and culinary (appetizers, dishes of meat or fish sauces, sweets and desserts) worldwide: products and preparations of Chinese, Japanese, Korean, Indian, Armenian, Turkish, throughout the Middle East, the Middle East, North Africa, West Africa or Central and South America. More than a fifth of terms including the glossary terms are standardized flavors of the world, that is approved by the Supervisory Council TERMCAT, the body responsible for the standardization of terminology Catalan. It especially product names vegetables: banana male tropical cucumber, Chinese cabbage, lettuce, asparagus, melted, etc. Each card contains the name in Catalan (some of which are simply proposals) equivalents in Spanish, French and English definition and subject area, but not systematically. That is why this collection conceived as a project open, ongoing work, because we have to be completed, both in terms of the information that it contains terms and, where appropriate, to incorporate new terms future editions of the show.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/201",
"license": "CC BY-ND 3.0",
"name": "Glossary of flavors of the world",
"prefix": "1552"
},
"1553": {
"description": "This dictionary includes terms with almost three hundred names and Catalan definition and the equivalents in Spanish, French and English, from the Dictionary of traffic and reviewed by experts in the field.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/25",
"license": "CC BY-ND 3.0",
"name": "Dictionary Road Safety",
"prefix": "1553"
},
"1554": {
"description": "This dictionary is the online version of the Dictionary of social services, a joint project between the Department of Social Welfare and Family of the Generalitat of Catalonia and Terminology Center TERMCAT systematised in this field terminology in Catalan. The work contains almost nine hundred terms related to social services and aims to be a practical reference tool for all those working in the world of social services for professionals in other fields who act in a coordinated manner. Each term includes Catalan name, Spanish equivalents (some records also contain equivalents in English and French), defining, and often also explanatory notes.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/118",
"license": "CC BY-ND 3.0",
"name": "Dictionary of social services",
"prefix": "1554"
},
"1555": {
"description": "In the light of forestry research in a changing world, the forestry world needs a clear and comprehensible language and a forum to study and reconsider the correct meaning of forestry terms. With the participation of an increasing number of non-foresters in the decision-making process in forestry, the need for a clear and well defined forest terminology exists worldwide. In order to ensure the continued updating and revision of the terminology basic stock and inclusion of new forestry terms, international cooperation is of extreme importance. In February 1995, IUFRO started a pilot project on forest terminology called SilvaVoc.\n\nSilvaVoc objectives are: to provide bibliographical and consultation services about forest terminologies and terminological activities; to contribute to the harmonization and integration of existing and future terminological data; to make compiled and improved data available in electronic form through computer networks; to produce special glossaries for specific target groups in an appropriate medium of publication. These activities will both benefit to and from co-operation with Working Party 6.03.02 'Trends in forest terminology'.",
"homepage": "http://www.iufro.org/science/special/silvavoc/silvaterm/query-silvaterm-database/",
"name": "SilvaVoc Terminology",
"prefix": "1555"
},
"1556": {
"description": "The dictionary contains 3622 terms of anatomy directly related to the human anatomy. Each term includes the equivalent names in Catalan and Spanish and English, and the names corresponding to the Anatomical Terminology (TA, formerly Nomina Anatomica) nomenclature standardized international scientific specific to this field of knowledge. this is the online version of the Dictionary of anatomy developed in 1993 by TERMCAT Barcelona Foundation and with the support of the Ministry of Culture of the Generalitat of Catalonia and GΓΆtzens advice of Victor, professor of the Faculty of Medicine of the University of Barcelona. This corresponds to an online edition updated and expanded second edition, which was developed with support from the Department of Health of the Generalitat of Catalonia and advice Josep Reig, professor of the Faculty of Medicine at the Autonomous University of Barcelona. the DICC- Onar wants to be a practical reference tool for all professionals who use medical terminology in both academic areas, such as areas of disclosure. We invite you to use it and spread it and to send us any suggestions for improvement or upgrade.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/182",
"license": "CC BY-ND 3.0",
"name": "Dictionary of Anatomy",
"prefix": "1556"
},
"1557": {
"description": "The health sciences terminology presented in a single product from thirteen dictionaries terminology related to medical science and pharmacology, TERMCAT made by or with the advice and published in the collection Online dictionaries. Specifically, this product contains information on the following dictionaries: Dictionary of anatomy, homeopathy Dictionary, Dictionary of immunology; Dictionary of nursing; Dictionary of ophthalmology, otorhinolaryngology Dictionary, Dictionary of physiotherapy; Dictionary of neuroscience, psychiatry dictionary; dictionary clinical research, drug dictionary Sinology, chronic terminology, vocabulary aids. in preparing each of these dictionaries, as is explained in the credits of corresponding works, individual artists have participated, equipment TERMCAT and specialists, and has had, in each case, with the help of an ex tight network of experts from different areas of health sciences, the Department of Health of the Generalitat of Catalonia and various institutions in the medical and pharmaceutical sector. Terminology of Health Sciences offers a unified way, consultation fourteen thousand six hundred terminological files include the name in Catalan, equivalents in other languages, definition (except the chips from the Dictionary of Anatomy), and where appropriate, notes that provide additional information. With the desire to provide a consistent set of terms and to facilitate the matching of each file with its original dictionary, we decided to replace specific information about the subject area they belong chips (consulted on trees field and chips from the respective original works) for the indication of origin of dictionaries each terminological files.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/198",
"name": "Terminology health sciences",
"prefix": "1557"
},
"1558": {
"description": "This dictionary contains 80 terms in the field of health and prevention of chronicity, the result of joint work and consensus among professionals terminology formalized program of prevention and chronicity care at the Department of Health and TERMCAT has had the collaboration of institutions and organizations of the sectors involved. Each article contains the names in Catalan, Spanish and English equivalents, and definition.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/160",
"license": "CC BY-ND 3.0",
"name": "Terminology chronicity",
"prefix": "1558"
},
"1559": {
"description": "Encyclopedic Dictionary of Medicine (DEMCAT). Version online job offers available to users data ongoing project work DEMCAT, which aims at developing a new medicine in Catalan Dictionary . This version offered to the public consultation initially contains about 70,000 terms Catalans definition equivalents in Spanish, French and English (possibly in German and Italian and, in cases relevant scientific nomenclature) and also also notes. it corresponds to an evolved version of the second edition of the online encyclopedic dictionary of medicine, which is currently consulting on the website of T's Institute of Catalan Studies. the contents of the encyclopedic dictionary of medicine (DEMCAT): working version will be progressively reviewing and completing periodic updates based on the phases of the project. to facilitate users to weigh the information provided in each tab has established a simple marking system, which identifies files that are no longer made any intervention:\n\n - Identifies where the chips have been minor changes\n\n - Identifies tokens of the terms that are being reviewed systematically terminology\n\n - Identifies tokens validated by the Directorate Editorial DEMCAT\n\n This marking is visible on each tab, and allows access through thematic see the selection of appropriate terms.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/183",
"license": "CC BY-ND 3.0",
"name": "Encyclopedic dictionary of medicine",
"prefix": "1559"
},
"156": {
"description": "BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. It is an open and collaborative effort by the community of researchers, software developers, and institutions.",
"homepage": "http://www.biopax.org/",
"name": "BioPAX",
"prefix": "156",
"wikidata_database": "Q4914639"
},
"1560": {
"description": "This dictionary contains more than three thousand terms that designate the most widely used drugs with names in Catalan and equivalents in Spanish, French and English, in addition to the registered number CAS and their mechanisms of action and therapeutic actions the most common, which can also be accessed via the Access theme. the nomenclature is updated annually to incorporate new international nonproprietary names of drugs approved that are available separately in the section new additions. in addition, includes a review and update of the Rules practices for the Catalan version of the international nonproprietary names (INN) for pharmaceutical substances, which is based in the Catalan version of the drugs that are coming into this work, with new criteria graphic adaptation and some indications on ways and phrasal stress. This is the version and n Online Lexicon of drugs that have made the College of Pharmacists of Barcelona and TERMCAT and edited the College in April 2008 sponsored by Obra Social Caixa Sabadell.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/12",
"license": "CC BY-ND 3.0",
"name": "Lexicon of drugs",
"prefix": "1560"
},
"1561": {
"description": "The dictionary includes 1,800 specific terms physiotherapy in the field of physiotherapy classified into ten areas: general concepts, anatomy, physiology, semiology, pathology examination and diagnosis, therapy and prevention; conceptual and methodological trends, body positions and units of measure. This dictionary expands and updates the content of physiotherapy glossary, prepared by Eva Cardona and Jordi Esquirol 2009 and published by the Publications Service of the Autonomous University of Barcelona. This online edition has been the advice TERMCAT terminology and a new principal with respect to the first edition also includes new input equivalent in English. It also includes equivalent terms in Spanish for which the paper edition only picked the name Catalan . another notable difference compared to the glossary is subject classification terms. Each tab ter minolΓ²gica name contains the main Catalan and Catalan denominations considered synonymous, if any; equivalents in Spanish and English; some latinism; Symbols in the case of units of measurement; definition and, where appropriate, explanatory notes. It also includes the subject area or subject areas in which the term is classified.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/196",
"name": "Dictionary of Physiotherapy",
"prefix": "1561"
},
"1562": {
"description": "This dictionary includes more than two thousand words belonging primarily in the areas of biogeography, the science of soil, climate, geomorphology and hydrology. Each article terminology also contains the name Catalan, equivalences in Spanish, French and English definition and often explanatory notes. in addition, you will find a dozen boxes containing more than a thousand Catalan terms. This is the online version of the Dictionary of physical geography, made in TERMCAT by 2003 with support from the Department of Environment Government of Catalonia and the Cartographic Institute of Catalonia and the collaboration of specialists from the University of Barcelona and the University of Valencia.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/124",
"license": "CC BY-ND 3.0",
"name": "Dictionary of Physical Geography",
"prefix": "1562"
},
"1563": {
"description": "This dictionary is the online version of the Dictionary of homeopathy, developed by Xavier CabrΓ© and PlayΓ advised TERMCAT terminology, in collaboration with the Medical Association of Homeopathic Academy of Barcelona and Barcelona Heel-sponsored Phinter. the dictionary, published by TERMCAT 2004, contains 400 terms in Catalan, which have accompanied the speech, the equivalents in Spanish, French and English definition and, most cases explanatory notes. in addition, it also indicated the relationship between the terms or synonyms.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/115",
"license": "CC BY-ND 3.0",
"name": "Dictionary homeopathy",
"prefix": "1563"
},
"1564": {
"description": "The dictionary contains more than 1,300 immunology terms directly related to this field of knowledge. Each term includes equivalents names in Catalan and in Spanish, English and French, with corresponding definitions and, eventually, with explanatory notes. In If drugs are also given the registered number CAS. Besides, the work offers consulting three blocks terminology specific groups of proteins relevant to human immunology: cytokines, chemokines and the groups of differentiation (CD ). This is the online version of the Dictionary of immunology that made TERMCAT in 2005 with the collaboration of the Catalan Society for Immunology (subsidiary of the Academy of Medical Sciences and Health Catalonia and the Balearic Islands) and the support of the Department of Health of the Generalitat of Catalonia. This corresponds to an online edition updated and expanded second edition, which was drawn at the advice of two specialists from the Catalan Society for Immunology, Odette ViΓ±as (Hospital Clinic of Barcelona) and Mariona Mestre (University Hospital of Bellvitge), supported by the Department of Health of the Government Catalonia. The dictionary aims to be a practical reference tool for all professionals who use the terms of immunology, both in academic areas, such as areas of disclosure. We invite you to use it and spread it and to send us any suggestions for improvement or upgrade.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/189",
"license": "CC BY-ND 3.0",
"name": "Dictionary of Immunology",
"prefix": "1564"
},
"1565": {
"description": "This dictionary includes nearly a thousand terms used in nursing, considered the most important from a point of view, with the names and Catalan definition and the equivalents in Spanish, French and English and often contextual notes. This is the online version of the dictionary nursing work developed by TERMCAT with support from the Department of Health of the Generalitat of Catalonia and the Government of Andorra, in collaboration with the Council graduates of Colleges of Nursing of Catalonia and the NORCAI College of Nursing Barcelona, jointly published by LID and TERMCAT.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/34",
"license": "CC BY-ND 3.0",
"name": "Dictionary of Nursing",
"prefix": "1565"
},
"1566": {
"description": "This work, Names of marine mammals is a descriptive dictionary compiled by Jordi Lleonart with terminology TERMCAT advice and support of the Biological Sciences Section of the Institute of Catalan Studies. It contains more than 350 names Catalan marine mammals in correspondence with about 150 scientific names, presented in sheets terminology related taxa zoos, which are sources of documentation. Each card includes the Catalan terms with equivalents in Spanish, English, French, scientific name with reference authoring and code 3-alpha FAO ASFIS basically documented, the list of species of interest to FAO fishery statistics. Since it is a descriptive dictionary, you should read the foreword and the introduction of this work to see what you can find and what value you assign names to each collecting tokens.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/159",
"license": "CC BY-ND 3.0",
"name": "Names of marine mammals",
"prefix": "1566"
},
"1567": {
"description": "This dictionary contains about two thousand terms used in neuroscience along with definition, explanatory notes and equivalents in Spanish and English. The book is organized according to a thematic structure in which there is room neuroanatomy, the neurohistologia, cellular neurobiology, developmental neurobiology, neurochemistry, neuropharmacology the, cellular and systems neurophysiology, behavioral neurobiology, neurology, psychiatry and neuropsychology, computational neuroscience and related disciplines with neuroscience. This is the online version of the dictionary neuroscience, neuroscience expert initiative Antoni Valero-Cabre and prepared by a team of medical specialists from various universities coordinated by professors at the Autonomous University of Barcelona Josep Reig and Xavier Navarro, in collaboration with TERMCAT, which was responsible for coordinating the proje ct and management of terminology work. The Vives Network has overseen the project, which has been supported by the Department of Health of the Generalitat of Catalonia and is sponsored by the Social Work CatalunyaCaixa.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/140",
"license": "CC BY-ND 3.0",
"name": "Dictionary of Neuroscience",
"prefix": "1567"
},
"1568": {
"description": "This work, online dictionary names of plants. FitonΓnimia Corpus Catalan is a descriptive dictionary, compiled in the framework of Catalan names of plants by a team of specialists led by Joan VallΓ¨s Xirau and formed by Joan Veny, Josep Vigo, M. Angels Bonet Julia Antonia M. and Joan Carles Villalonga, in collaboration with TERMCAT. the development of this project and the publication of results could be realized thanks to the support of many people and institutions who have believed and have contributed in various ways (see credits). in addition to the direct participation of the Laboratory of Botany, Faculty of Pharmacy, University of Barcelona, ββhas enjoyed a subsidy of Obra Social la Caixa, which has been managed by the Catalan Institute of Natural History, a subsidiary of the scientific society Institute of Catalan Studies. And during the editing process of the work have been sum also at the financial support and collaboration of the University of Barcelona and the Government of Andorra. The online dictionary of plant names. Corpus fitonΓmia Catalan presents the outcome of research conducted on fitonΓmica dataset collected over the years on the project. Consulting offers over 35,000 Catalan names and scientific names of 8400, the weighted organized and structured terminological cards in 5800. It also includes additional texts that complement fitonΓmiques data to facilitate the interpretation and presentation of texts and introduction accompanying the paper edition of this work. Since it is a descriptive dictionary, you should read the presentation and introduction (see also documents and background information) to see what you can find and what value you assign names to each of which includes the chips. The information collected in this work has been the subject of a careful selection, the result of a painstaking reflection and multidisciplinary explained in the aforementioned documents.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/191",
"license": "CC BY-ND 3.0",
"name": "Names of plants",
"prefix": "1568"
},
"1569": {
"description": "This dictionary includes 1,200 terms in the field of ophthalmology, corresponding to the six thematic areas: anatomy, physiology, examination, semiotics, pathology and therapy. In presenting and defining names in Catalan and Spanish equivalents English and, where appropriate, international anatomical terms. This is the online version of the Dictionary of ophthalmology, made in 2011 by TERMCAT with the support of the Government of Catalonia and the collaboration of specialists from the University Barcelona and the Catalan Society of Ophthalmology.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/121",
"license": "CC BY-ND 3.0",
"name": "Dictionary of Ophthalmology",
"prefix": "1569"
},
"157": {
"description": "This documentary tool is used by most documentation centers in the continuing education / continuing education sector.",
"homepage": "http://lllearning.free-h.net/A-GRAF/documents/biblio/thesaurus_af.htm",
"name": "Association of Self-Study Research Group Thesaurus",
"prefix": "157"
},
"1570": {
"description": "This dictionary includes nearly a thousand names and terms with the Catalan definition and the equivalents in Spanish, French, English and German. Mental health is now one of the priority areas of health care. In addition to new approaches in treatment of mental illness in the understanding of mental processes, mental disorders are described emerging of great social impact, such as Alzheimer-type dementia or behavioral disorders food. This is the online version of the dictionary psychiatry, prepared by TERMCAT work supported by the Department of Health and the help of a team of specialists from the Catalan Society of Psychiatry and Mental Health, jointly published by Elsevier and TERMCAT Doyma-sponsored by Almirall.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/21",
"license": "CC BY-ND 3.0",
"name": "Dictionary of Psychiatry",
"prefix": "1570"
},
"1571": {
"description": "This dictionary includes over 1,100 terms in the field of otolaryngology, corresponding to five themes: Otology, Rhinology, faringologia, laringΓ³logo and related disciplines. In presenting and defining names in Catalan, Spanish and English equivalents and if applicable, international anatomical terms. This is the online version of the Dictionary of otolaryngology, developed in 2001 by TERMCAT with the support of the Government of Catalonia and the collaboration of specialists Pere AbellΓ³, and Miquel Quer Josep Maria Fabra, the Autonomous University of Barcelona (Hospital de Sant Pau) and the Catalan Society of Otolaryngology. This corresponds to an online edition updated and expanded second edition, which was produced with the support Department of Health of the Generalitat of Catalonia and the advice Montserrat Bonet, of the University of Barcelona.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/148",
"license": "CC BY-ND 3.0",
"name": "Dictionary of otolaryngology",
"prefix": "1571"
},
"1572": {
"description": "This dictionary contains more than seven hundred words belonging to the field of clinical trials that have the drug as a core, especially those related to the methodology and biostatistics, pharmacology, bioethics, and epidemiology public health, research and scientific publishing and legal regulation and quality control. Complete a brief selection of the work terms that designate the main actors involved in the various phases of a clinical trial. Each term includes names Catalan and equivalents in English and Spanish, in addition to a definition and, if necessary, additional notes. This is the online version of the dictionary of clinical medicine, developed jointly by the Esteve Foundation and TERMCAT, with the support of the Department of Health of the Generalitat of Catalonia. with the online publication of the work aims to strengthen the main aim of this work terminol gic consensus: the terminology of clinical research of medicines accessible to all sectors that are users (doctors, pharmacists, documentary, epidemiologists, students, journalists, translators and editors of specialized texts, etc.). We encourage you therefore to use it, spreading it among the community involved and send us any suggestions for improvement or upgrade.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/157",
"license": "CC BY-ND 3.0",
"name": "Dictionary of clinical drugs",
"prefix": "1572"
},
"1573": {
"description": "This dictionary contains more than 400 terms relating to HIV and AIDS that are commonly used in the healthcare setting. You can find terms related to the biological characteristics of HIV, epidemiological and clinical aspects of infection HIV and AIDS and the treatment of the disease. Each term has equivalents in seven denominations Romance languages ββ(Catalan, Spanish -variants Europe and Mexico, French, Galician, Italian, Portuguese and European -variants of Brasil- and Romanian) with corresponding indicators speech and also in English. (...) the vocabulary has been prepared within the framework of the Network Panlatin Terminology (really), created on the initiative of the Union America, which aims to promote the development of the Romance languages. the project has been coordinated by the TERMCAT, which has facilitated the naming game in Catalan, Spanish, French and ang les, from the terminology of AIDS, which was developed in 2005 in collaboration with the Department of Health. You can find more information about this dictionary in loans, the introduction of tree and field references. Also, included are three annexes containing terminology: a table of antiretroviral drugs table of AIDS defining illnesses and a table protein of HIV-1 and HIV-2.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/134",
"license": "CC BY-ND 3.0",
"name": "Multilingual Vocabulary of AIDS",
"prefix": "1573"
},
"1574": {
"description": "Dictionary of Sinology Online makes available to users over 1,100 terms specific to this discipline, especially terms related to breast anatomy and physiology, diagnostic techniques, pathology and treatment of breast cancer. each term includes the equivalent names in Catalan and in Spanish, English, French and Italian and, where applicable, the names of the Anatomical Terminology (TA) with corresponding definitions and, eventually, with explanatory notes. the work has been prepared jointly by Pere Culell, Adelaida Fandos and Maribel Nieto, medical professionals linked to the College of Sinology Section of the medical Association of Barcelona, ββwith the advice of TERMCAT. the Department of Health of the Government of Catalonia are supported. With the publication online will want to reinforce the main work of this terminological consensus that terminology is accessible Sinology all sectors that are users. Then encourage them to use it, spreading it among the community involved and send us any suggestions for improvement or upgrade.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/117",
"license": "CC BY-ND 3.0",
"name": "Dictionary of Sinology",
"prefix": "1574"
},
"1575": {
"description": "The DataCite Metadata Schema is a list of core metadata properties chosen for the accurate and consistent identification of a resource for citation and retrieval purposes, along with recommended use instructions. The resource that is being identified can be of any kind, but it is typically a dataset. We use the term 'dataset' in its broadest sense. We mean it to include not only numerical data, but any other research data outputs.",
"homepage": "https://schema.datacite.org/",
"name": "DataCite Metadata Schema",
"prefix": "1575"
},
"1576": {
"description": "CERIF is: A concept about research entities and their relationships β Specification (Conceptual Level); A description of research entities and their relationships β Model (Logical Level); A formalization of research entities and their relationships β Database Scripts (Physical Level). (...) The data model (data-centric) allows for a (metadata) representation of research entities, their activities / interconnections (research) and their output (results) as well as high flexibility with formal (semantic) relationships, enables quality maintenance, archiving, access and interchange of research information and supports knowledge transfer to decision makers, for research evaluation, research managers, strategists, researchers, editors and the general public.\n\nA CRIS can be implemented using a subset or superset of the full CERIF model for projects, people, organisations, publications, patents, products, services and facilities (equipment in particular) with role-based, temporally-bound relationships. The advantages of CERIF are: its neutral architecture; the data model can be implemented [relational, object-oriented, information retrieval (including WWW)]; the process model can be implemented [DBMS and query (centralised or distributed), HTML web / harvesting / IR-query, advanced knowledge-based technology].\n\nBut interoperation requires a structured schema. Today CERIF is used as a model for implementation of a standalone CRIS (but interoperation ready), as a model to define the wrapper around a legacy non-CERIF CRIS to allow homogeneous access to heterogeneous systems and as a definition of a data exchange format to create a common data warehouse from several CRIS.",
"homepage": "https://eurocris.org/services/main-features-cerif",
"license": "CC-BY-3.0",
"name": "CERIF",
"prefix": "1576"
},
"1577": {
"description": "This dictionary defines and brings together nearly six thousand Catalan terms with the equivalents in Spanish, French and English, pertaining to the thematic areas of pathology and histopathology, pathogens and disease, clinical animal production , reproduction and printing techniques, identification systems, bromatology, veterinary inspection and pets, among others. This is the online version of the dictionary veterinary and livestock, and Encyclopedia edited by TERMCAT Catalan in 2002 and prepared under the direction and coordination of scientific Iscle Selga with terminology TERMCAT coordination and participation of the Department of Health and Social Security and the Ministry of Agriculture, Livestock and Fisheries of the Government of Catalonia; Veterinary Schools Council of Catalonia, the Catalan Agricultural Foundation, the Association of Agricultural Engineers of Catalonia and the Association of Agricultural Engineers and Agricultural Experts of Catalonia. This edition allows first consultation subject of the data dictionary and incorporates amendments specific with respect to the paper version, the result of maintenance work to date of the data conducted by TERMCAT, and also includes the terminology in paper version was compiled without defining tables in appendices devoted to ethnology and morphology of animals.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/163",
"license": "CC BY-ND 3.0",
"name": "Dictionary of veterinary medicine and livestock",
"prefix": "1577"
},
"1578": {
"description": "This dictionary offers more than three hundred Catalan terms coming from the βEuropean Communitiesβ section in the Eurovoc multilingual thesaurus, with the equivalents in Spanish, French and English. Terms refer to European Union and public service institutions, Community law, European construction and Community finances, which have been revised by a team of specialists from the EU Department in the Catalan Government.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/27",
"license": "CC BY-ND 3.0",
"name": "Lexicon of the European Communities",
"prefix": "1578"
},
"1579": {
"description": "This dictionary contains 1,130 terms with the definition and explanatory notes in Catalan, Spanish and equivalents subject area, which can be accessed through the option Access theme. This is the online version of the Dictionary of Administrative Law TERMCAT which was co-authored and published by the Department of Justice. the work is part of the collection together with the Legal Terms Vocabulary penitentiary and criminal law and civil law dictionary.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/169",
"license": "CC BY-ND 3.0",
"name": "Administrative Law Dictionary",
"prefix": "1579"
},
"158": {
"description": "A key enabling technology for Biositemaps is the Biomedical Resource Ontology (BRO) which is a controlled terminology for the 'resource_type' and which is used to improve the sensitivity and specificity of web searches. This is under development by a number of NIH-funded researchers who have a combined interest in classification of biomedical resources.",
"homepage": "http://purl.bioontology.org/ontology/BRO",
"name": "Biomedical Resource Ontology",
"prefix": "158"
},
"1580": {
"description": "This dictionary contains 1160 words corresponding to the five major traditional areas of civil law: general civil law, civil law of obligations and contracts, real rights, family law and inheritance law. Each article contains the names in Catalan equivalents Spanish definitions and often explanatory notes. There is a dictionary of Catalan civil law, but also includes the Catalan civil law, the concepts of civil law applicable to Catalonia. it is the online version of the dictionary civil, prepared by TERMCAT and the Justice Department of the Generalitat of Catalonia, published in 2005. the original data can be updated and subsequently completed.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/150",
"license": "CC BY-ND 3.0",
"name": "Dictionary of civil law",
"prefix": "1580"
},
"1581": {
"description": "This vocabulary contains 2,705 terms related to four thematic groups: criminal law, criminal procedural law, penal law and military criminal law. Each article displays the names in Catalan, Spanish equivalent, subject area -which can be accessed through Access the tool temΓ tic- and often explanatory notes. This is the online version of the vocabulary of criminal law and penal TERMCAT prepared by the Justice Department and the Government of Catalonia, published on paper in 2000. in this time, some of the original data have been updated or completed. the work is the first title of the collection Legal Terms, which are also part of the Dictionary of civil law and administrative law dictionary, all available line.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/172",
"license": "CC BY-ND 3.0",
"name": "Vocabulary criminal and prison law",
"prefix": "1581"
},
"1582": {
"description": "The terminology includes 129 basic elections terms related to the process and electoral systems. Each term includes Catalan terms, definitions, equivalents in Spanish, French and English and, if necessary, additional notes. The work has been made by TERMCAT collaboration with the Ministry of Home Affairs and Institutional Relations of the Generalitat of Catalonia. He has also participated in the project by the Department of Spanish Language Directorate-General for Translation of the European Commission, which has provided documentary information. This Dictionary aims to be a practical tool of reference for all professionals using the terminology elections, either in areas theoretical or academic, whether in areas of outreach. We encourage you therefore to use it, spread it between group involved and send us any suggestions for improvement or upgrade.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/179",
"license": "CC BY-ND 3.0",
"name": "Terminology Basic elections",
"prefix": "1582"
},
"1583": {
"description": "This dictionary includes more than two hundred words, with the names and Catalan definition and the equivalents in Spanish, French, English and Portuguese. These are the terms most commonly used in both the organization and the development of fairs and congresses. This is the online version of the trade fairs and congresses terminology, dictionary developed by TERMCAT 2003 in collaboration with the Department of Employment, Industry, Trade and Tourism and highly experienced professionals in the field.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/31",
"license": "CC BY-NC-ND 3.0",
"name": "Terminology trade fairs and congresses",
"prefix": "1583"
},
"1584": {
"description": "This vocabulary includes the Catalan denominations of more than a thousand products, most of which can be found in a department store with its equivalents in Spanish, French, Portuguese and English. To facilitate your search, you can check classified sections, such as supermarkets. also contained in these five languages more than three hundred fifty expressions that can occur regularly in conversations between buyer and seller, also arranged thematically. this is the version line of the second edition, expanded and updated, the basic vocabulary of stores, a joint project between the Government of Andorra and Terminology Center TERMCAT we hope to facilitate multilingual communication to our businesses, particularly drives are the use of Catalan.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/129",
"license": "CC BY-ND 3.0",
"name": "Basic vocabulary of stores",
"prefix": "1584"
},
"1585": {
"description": "This dictionary gathers about six hundred terms with the Catalan definition and equivalents in Spanish, French and English, related to financial markets and corresponding to seven thematic fields: organization, structure and functioning, people and entities, assets, transactions, hiring process and assets and issuers analysis.\n\nIt is the online version for the Diccionari dels mercats financers, a joint project carried out by the Catalan Government Economy and Finance Department and TERMCAT that systematizes for the first time the financial terminology in Catalan.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/23",
"license": "CC BY-ND 3.0",
"name": "Dictionary of financial markets",
"prefix": "1585"
},
"1586": {
"description": "This dictionary contains about six hundred terms specific processes such as excellent the relations between unions and collective enterprises, working conditions, collective agreements, management of human resources and the particularities of the labor market. Apart and the definition of the names in Catalan, the dictionary provides the equivalents in Spanish, French and English. This is the online version of the Dictionary of collective bargaining, developed jointly by TERMCAT and the Department of Labor of the Government of Catalonia 2000.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/5",
"license": "CC BY-ND 3.0",
"name": "Dictionary of collective bargaining",
"prefix": "1586"
},
"1587": {
"description": "This dictionary includes about three hundred words, which are most commonly used in the note and presents the names and the definition in Catalan and Spanish equivalents. In addition to more typical of the world of notary also include terms from other areas of law closely linked to the daily work of the notary, such as civil law, mortgage law or commercial law. This is the online version of notarial terminology, made the 2004 TERMCAT and the Association of notaries of the Balearic Islands and Catalonia, with the support of the Language Policy Service of the Government of Andorra and the schools mentioned above.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/17",
"license": "CC BY-ND 3.0",
"name": "Notary Terminology",
"prefix": "1587"
},
"1588": {
"description": "More and more institutions plan their future in a strategic way, analyzing and organizing its objectives and tasks necessary to achieve them, taking into account the internal and external factors that may have no effect. This Dictionary contains basic terms used in this planning methodology. for each term and definition denominations present in Catalan equivalents in Spanish, French and English and, in some cases, linguistic or conceptual clarification. the vocabulary is been reviewed by many industry experts and neologisms Catalan language raises questions such as SWOT matrix, goal, mission or vision, have been studied by the Supervisory Council TERMCAT.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/35",
"license": "CC BY-ND 3.0",
"name": "Vocabulary of strategic planning",
"prefix": "1588"
},
"1589": {
"description": "This dictionary includes the basic terms for the declaration of income and assets. It is about 122 names with terms and definition in Catalan and Spanish equivalents, reviewed by specialists from the Association of Administrative Managers of Catalonia \".",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/6",
"license": "CC BY-ND 3.0",
"name": "Dictionary of income",
"prefix": "1589"
},
"159": {
"description": "The Australian Thesaurus of Education Descriptors (ATED) is the definitive reference on Australian terminology in the area of education. It reflects terminology used to describe research and practice in Australian education. ATED is used to index the Australian Education Index, Education Research Theses and the ACER library catalogue and can also be used to consult these databases. The Thesaurus can be used to index documents, whether in print or electronic and also to index web sites. It can also be used to organise reading lists and bibliographies.",
"homepage": "http://cunningham.acer.edu.au/multites2007/index.html",
"name": "Australian Thesaurus of Education Descriptors",
"prefix": "159"
},
"1590": {
"description": "The social responsibility of companies, organizations and public authorities is increasingly important in today's society. For this reason, TERMCAT considered necessary the elaboration of a terminology compilation containing the basic terminology of this field. the vocabulary includes a total of 36 terms. Each term and definition includes the names in Catalan equivalents in Spanish, French, English and German, and in some cases, conceptual clarifications or notes as an example. for the preparation of this vocabulary has received the support of Josep Maria Canyelles, specialist in social responsibility.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/175",
"license": "CC BY-ND 3.0",
"name": "Vocabulary of social responsibility",
"prefix": "1590"
},
"1591": {
"description": "This dictionary contains about four hundred fifty terms used in athletics with the names and Catalan definition and the equivalents in Spanish, French and English. The terminology collection under tree field Dictionary refers mainly to the space race, the methods and tests each type of equipment required, athletes, judges and organization. to create this dictionary must match the Dictionary athletics TERMCAT published in 1992 for the Olympic Games in Barcelona. in order to ensure currently, however, there has been a complete review of names, definitions and equivalents in accordance with general Dictionary sports that TERMCAT is about to publish.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/19",
"license": "CC BY-ND 3.0",
"name": "Dictionary athletics",
"prefix": "1591"
},
"1592": {
"description": "This dictionary contains over two hundred terms related to the world of motoring, with the names and Catalan definition and the equivalents in Spanish, French and English, mostly from the General Dictionary of Sport, published by TERMCAT 2010 and reviewed by specialists of the Catalan Federation of Motor Racing Circuit and Catalonia. Additionally have reproduced thirty terms of dictionary terms leaflet Formula 1.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/162",
"license": "CC BY-ND 3.0",
"name": "Dictionary of Motoring",
"prefix": "1592"
},
"1593": {
"description": "This dictionary includes the basic terms used in cricket, a sport very popular in Anglo-Saxon countries, which gradually took root in Catalonia. The vocabulary, which contains the names and the definition in Catalan equivalents in Spanish and English, has been carried out with the collaboration of the Sports Federation Union of Catalonia and the Consortium for Language Normalization and has been reviewed by specialists of the Union of Catalan Sport Cricket Clubs. there are a number of Catalan neologisms such as track innings and stuck out TERMCAT the Supervisory Board ratified as an alternative to the original anglicisms.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/138",
"license": "CC BY-ND 3.0",
"name": "Basic vocabulary of cricket",
"prefix": "1593"
},
"1594": {
"description": "This dictionary includes hundreds of terms specific to the game of chess with the names and Catalan definition and the equivalents in Spanish, French, English and German. All the information coming from the General Dictionary of the sport and have been reviewed by specialists of the Catalan Federation of Chess.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/16",
"license": "CC BY-ND 3.0",
"name": "Chess Terminology",
"prefix": "1594"
},
"1595": {
"description": "This dictionary includes nearly five hundred names and terms with the Catalan definition and the equivalents in Spanish, French and English, from the General Dictionary of Sport, published by TERMCAT 2010, and reviewed by experts Catalan Fencing Federation. These terms have their origin in the Dictionary fencing published on the occasion of the Barcelona Olympics in 1992.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/26",
"license": "CC BY-ND 3.0",
"name": "Dictionary fencing",
"prefix": "1595"
},
"1596": {
"description": "This dictionary is the online versiono f the Diccionari general de lβesport ('General Dictionary of Sport'), a work created by TERMCAT, in cooperation with the Catalan Union of Sports Federations and several Balearic and Valencian federations, and supported by the Catalan, Andorran and Balearic governements.\n\nThe Diccionari general de lβesport, which gathers 11,000 terms belonging to 80 different sports, aims to be a useful tool to a wide range of users: sportspeople, coaches, referees, enthusiasts, journalists or translators, interested in learning the Catalan designation for a term, its equivalent designations in Spanish, French or English, the exact meaning of a term or, for example, what is the most common terminology of a particular sport.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/114",
"license": "CC BY-ND 3.0",
"name": "General Dictionary of Sport",
"prefix": "1596"
},
"1597": {
"description": "This dictionary includes over seven hundred terms used in water sports, corresponding to the current five sports competitions: swimming, synchronized swimming, diving, water polo and open water swimming. At present the names and the definition and Catalan equivalents in Spanish, French and English. it is a dictionary that holds the base and the specificity of swimming Dictionary 1991, published on the occasion of the Olympic Games of Barcelona, with updates general Dictionary of the sport in 2010 and the addition of swimming in open water.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/155",
"license": "CC BY-ND 3.0",
"name": "Dictionary of watersports",
"prefix": "1597"
},
"1598": {
"description": "This dictionary includes terms with seventy names and Catalan definition and the equivalents in Spanish, French and English, from the General Dictionary of Sport, published by TERMCAT 2010. To facilitate understanding both the full each sport as the same sport, have been included in this terminology sporting activities (eg kite surfing) and, simultaneously, the basic object with which they made (the kite and surfboard traction kite for kite surfing or even dog mushing nordic in the case).",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/28",
"license": "CC BY-ND 3.0",
"name": "Terminology Adventure sport",
"prefix": "1598"
},
"1599": {
"description": "This dictionary contains about one thousand three hundred with names and terms in Catalan definition and the equivalents in Spanish, French and English, from the General Dictionary of the sport.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/29",
"name": "Terminology winter sports",
"prefix": "1599"
},
"16": {
"abbreviation": "GEMET",
"description": "The basic idea for the development of GEMET was to use the best of the presently available excellent multilingual thesauri, in order to save time, energy and funds. GEMET was conceived as a 'general' thesaurus, aimed to define a common general language, a core of general terminology for the environment. Specific thesauri and descriptor systems (e.g. on Nature Conservation, on Wastes, on Energy, etc.) have been excluded from the first step of development of the thesaurus and have been taken into account only for their structure and upper level terminology. The merging has been performed both on conceptual and formal basis. Coinciding concepts in the different thesauri have been identified and scored. Like in other multilingual thesauri, e. g. Infoterra EnVoc, a neutral alphanumerical notation allows the identification of a concept independently on the user's language.\n\nThe links with the original thesauri are ensured by the respective identifiers or code notations. Following the identification of the coinciding concepts, a selection was made by the experts of the National Focal Points of the organisations involved. The resulting 6.562 terms have been arranged in a classification scheme made of 3 super-groups, 30 groups plus 5 accessory, instrumental groups. Each descriptor has been arranged in a hierarchical structure headed by a Top Term. The level of poly-hierarchy, i.e. the allocation of a descriptor to more than one group, has been kept to a minimum. Further, to allow a thematic retrieval of terms thematically related but scattered in different groups, a set of 40 themes have been agreed upon with the EEA and each descriptor has been assigned to as many themes as necessary. Thus, the user can access the thesaurus through the group- hierarchical list, through the thematic list or through the alphabetical list. As a complement to the hierarchical 'vertical' relations, an exhaustive series of strong 'horizontal' relations between terms (RT, Related Terms) have been introduced. A progressive Line Number has been assigned to each descriptor of the systematic list, in order to help the user of the lists to identify the descriptor in the different lists. The Line Number is merely a neutral identifier for the present version. The GEMET size, formerly figured at about 200000 descriptors, rose to more than 5.000 in the course of merging, due to the limited overlapping between the different thesauri, to constraints of the selection work carried out by the parental organisations and to a few new additions, mainly from CDS indexing work. The present version 2001* of GEMET is the result of a close collaboration between CNR and UBA under contract and supervision of the ETC/CDS. It presents 5.298 descriptors, including 109 Top Terms, and 1.264 synonyms in English. The 5.524 terms belonging to the parental thesauri and not included in GEMET, constitute an accessory alphabetical list of free terms. GEMET has been developed as an indexing, retrieval and control tool for the European Topic Centre on Catalogue of Data Sources (ETC/CDS) and the European Environment Agency (EEA), Copenhagen.",
"homepage": "http://www.eionet.europa.eu/gemet/",
"license": "CC-BY-3.0",
"name": "General Multilingual Environmental Thesaurus",
"prefix": "16",
"wikidata_database": "Q1485161"
},
"160": {
"description": "161 terms, 14 relations between terms, 4 equivalent terms.",
"homepage": "http://vocabularyserver.com/mercosur/uruguay/",
"name": "Educational Terminology Bank",
"prefix": "160"
},
"1600": {
"description": "This dictionary includes nearly a thousand of terms from the fields of sailing, surfing, water skiing, motorboat, rowing and canoeing with names and Catalan definition and the equivalents in Spanish, French English. This dictionary is an updated and expanded second edition of which was published in 2005. the terms of the Dictionary of sports come from the general Dictionary of sport, published by TERMCAT 2010. These terms that have their origin in the 1992 Olympic dictionaries (Dictionary of sailing, rowing and dictionary dictionary canoeing), appropriately updated and reviewed by specialists lexical respective federations for other sports.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/10",
"license": "CC BY-ND 3.0",
"name": "Dictionary of Water Sports",
"prefix": "1600"
},
"1601": {
"description": "This dictionary includes more than seven thousand names with terms and definitions in Catalan and equivalents in Spanish, French and English, from the General Dictionary of Sport, published by TERMCAT 2010. It contains the following sports terminology : athletics, badminton, basketball, baseball, boxing, cycling, fencing, football, gymnastics, weightlifting, handball, equestrian, field hockey, judo, wrestling, swimming, synchronized swimming, modern pentathlon, canoeing, rowing, diving, taekwondo, tennis , table tennis, archery, Olympic shooting, sailing, volleyball and water polo. These are terms that have their origin in the 1992 Olympic dictionaries, appropriately updated and reviewed by specialists lexical respective federations.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/30",
"license": "CC BY-ND 3.0",
"name": "Dictionary of Olympic sports",
"prefix": "1601"
},
"1602": {
"description": "This dictionary contains about four hundred terms related to the world of football, with the names and Catalan definition and the equivalents in Spanish, French, Italian, English and German, from the General Dictionary of Sport, published by TERMCAT 2010 and reviewed by specialists of the Catalan football Federation. We especially thank Claudio Critelli completion of Italian equivalents. the collection updates the dictionary edited by TERMCAT football with the Olympic Games in Barcelona.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/3",
"license": "CC BY-ND 3.0",
"name": "Football Dictionary",
"prefix": "1602"
},
"1603": {
"description": "This dictionary includes terms with two hundred names and Catalan definition and the equivalents in Spanish, French and English, from the General Dictionary of sport and reviewed by specialists of the Catalan Championship and Tour of Catalonia \".",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/7",
"license": "CC BY-ND 3.0",
"name": "Dictionary of motorcycling",
"prefix": "1603"
},
"1604": {
"description": "This dictionary contains hundreds of names and terms with the Catalan definition and the equivalents in Spanish, French and English, from the General Dictionary of Sport, published by TERMCAT 2010, and reviewed by specialists Catalan Federation of Winter Sports.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/8",
"license": "CC BY-ND 3.0",
"name": "Dictionary of figure skating",
"prefix": "1604"
},
"1605": {
"description": "This dictionary includes more than two hundred names and terms with the Catalan definition and the equivalents in Spanish, French and English, from the General Dictionary of Sport, published by TERMCAT 2010. These terms that have their origin in the dictionary published in 1995 by TERMCAT rugby within the collection of dictionaries Olympics, now revised, updated and expanded specialists federations Catalan and Andorran rugby and Northern Catalonia.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/24",
"license": "CC BY-ND 3.0",
"name": "Dictionary of rugby",
"prefix": "1605"
},
"1606": {
"description": "This dictionary includes nearly one hundred fifty with the names and terms in Catalan definition and the equivalents in Spanish, French and English. The terms come from the dictionary of the snow, published by TERMCAT 2001, where available terms other winter sports in nivology, geomorphology, sports medicine, and rescue facilities and equipment.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/14",
"license": "CC BY-ND 3.0",
"name": "Terminology Snowboarding",
"prefix": "1606"
},
"1607": {
"description": "This lexicon contains about four hundred terms that designate food additives authorized in Spain in accordance with current regulations. Each term includes the equivalent names in Catalan and Spanish, French and English, in addition to the number identification and functional common classes, which can also be accessed via the Access theme. it should be noted that systematized the names of additives in Catalan, Spanish and French names corresponding compounds chemical expression of the second forming a prepositional phrase introduced by the preposition instead of resorting to adjectives (eg sodium acetate instead of sodium acetate, sodium acetate, sodium acetate instead; acetate sodium, rather than sodique acetate).",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/135",
"license": "CC BY-ND 3.0",
"name": "Lexicon of food additives",
"prefix": "1607"
},
"1608": {
"description": "This dictionary includes the basic terms used in the field of e-government, and also the most common concepts related to the improvement and simplification of administrative processes. It includes 164 terminological files containing names in Catalan, Spanish, French English, Catalan definitions, explanatory notes and some indication of the subject area. the terms correspond to the six following thematic areas: technology infrastructure, processing electronics, security, administrative, quality and strategic planning and analysis, process improvement and simplification . the work has been prepared by TERMCAT, which has taken over the terminology work, and the Department of Governance and Institutional Relations of the Generalitat of Catalonia, which has offered specialized collaboration.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/170",
"license": "CC BY-ND 3.0",
"name": "EGovernment basic terminology and processes",
"prefix": "1608"
},
"1609": {
"description": "What is it? Diccionaris cartogrΓ fics (βCartographic dictionariesβ) is a compilation of four dictionaries edited by the Cartographic and Geological Institute of Catalonia with the advice of TERMCAT, printed by EnciclopΓ¨dia Catalana. The titles and authors of the four dictionaries are:\n\n- RABELLA i VIVES, Josep M.; PANAREDA i CLOPΓS, Josep M.; RAMAZZINI i GOBBO, Graziana. Diccionari terminolΓ²gic de cartografia.\n\n- FRA PALEO, Urbano. Diccionari terminolΓ²gic de fotogrametria.\n\n- NUNES, Joan. Diccionari terminolΓ²gic de sistemes d'informaciΓ³ geogrΓ fica.\n\n- PONS FERNΓNDEZ, Xavier; ARCALΓS PLANAS, Anna. Diccionari terminolΓ²gic de teledetecciΓ³.\n\nDiccionaris cartogrΓ fics, therefore, provide in a unified query more than eight thousand eight hundred terms related to cartography, with equivalents and definitions, and often with notes that provide new information.\n\nIs the origin of the terms indicated? With the aim of respecting the area, the characteristics and the authorship of each product, the origin of each term is indicated by means of the bibliographic citation.\n\nWhat actions have been done? The publication in a single online dictionary has only involved formal modifications in the data. Basically, in addition to marking the origin of each term, the representation of notes has been unified, and the encyclopaedic definitions have been divided, so there is a paragraph starting with the definition itself and additional information is offered in different parts according to their meaning.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/197",
"license": "CC BY-ND 3.0",
"name": "cartographic Dictionaries",
"prefix": "1609"
},
"161": {
"description": "The Bioinformatics Web Services ontology (OBIws) is an ontology that extends the Ontology for Biomedical Investigations (OBI) to build an Ontology that supports consistent annotation of Bioinformatics Web services. We also consider reuse of terms available from the EMBRACE Data And Methods (EDAM) ontology. We follow a systematic methodology for enriching OBI with terms to support Web service Annotation. This process involves the design of ontology analysis diagrams for Web services and their subsequent analysis to discover terms that need to be added to the ontology. Current OBIws ontology is focusing on sequence analysis web services. With developed patterns of modeling web services, OBIws can be extended easily to support annotations of different kind web services.",
"homepage": "http://code.google.com/p/obi-webservice/",
"name": "Bioinformatics Web Services Ontology",
"prefix": "161"
},
"1610": {
"description": "This dictionary contains almost three hundred names and terms with the Catalan definition and the equivalents in Spanish, French and English. These are terms commonly used in this new variant of the trade, which already ranks among remarkable our habits of consumption. This is the online version of the e-commerce terminology, dictionary TERMCAT made in 2005 in collaboration with the Government of Andorra and specialists from academia, business and Administration.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/15",
"license": "CC BY-ND 3.0",
"name": "Terminology Ecommerce",
"prefix": "1610"
},
"1611": {
"description": "This dictionary contains fifty terms related to mobile devices, especially smartphones and tablets, as defined in Catalan and equivalents in Spanish, French and English. Some listings also include explanatory notes and illustrations. both the glossary as user touch gestures have been published on the occasion of the mobile World Congress 2014 (MWC) in order to spread widely alternatives Catalan terms used among users of mobile devices in companies and the media echo of developments in this technology consumer. as strong character of neologisms terminology, this dictionary is a product that remains open for continuous updating of the content. the work TERMCAT been developed by collaboration with other agencies of the Government of Catalonia: the telecommunications s and Information Technology, the Department of Public Service Broadcasting and the Ministry of the Presidency and the Directorate General of Telecommunications and Information Society of the Department of Enterprise and Employment.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/171",
"license": "CC BY-ND 3.0",
"name": "Basic terminology of mobile devices",
"prefix": "1611"
},
"1612": {
"description": "Dictionary of physics, developed jointly by the Polytechnic University of Catalonia, Catalan Encyclopaedia and TERMCAT, brings together more than three thousand and defines terms used in physics. It is part of the collection of scientific and technical dictionaries Science and Technology. the dictionary has had the collaboration of the Foundation La Pedrera Catalonia and the Foundation Torrens-Ibern. the physics in its purpose of describing the world, from the smallest particles known to the whole cosmos is considered a broad range of science, much terminology. This dictionary, however, is conceived as a collection of basic terminology, aiming to offer a practical reference tool. Includes terms of the following areas: mechanics, thermodynamics, electromagnetism, optics, relativity, quantum physics, particle physics, nuclear physics, atomic physics and condensed matter physics. Rounding out the selec tion naming a blog devoted to the physics of the Earth and space and one dedicated to the medical physics. For each of these branches, the reader will find terms related to theories, equations and phenomena, and laws and models that explain, among the most important experiments and measurement units used or more of historical interest. The starting point of the nomenclature of the dictionary was the database of Catalan Encyclopedia and must be added the terms required to understand some of the concepts have been defined and eliminated more general. Each article contains the following information: the name Catalan considered the main lexical category; Catalan names synonymous, if necessary, also with the lexical category and indicating the type of remission (synonyms, abbreviations and synonyms complementary); equivalent in Spanish; French equivalents; equivalent in English; symbols, if applicable; subject area or subject areas in which the term is classified; definition, and, when deemed necessary for more information, a note or more.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/149",
"license": "CC BY-ND 3.0",
"name": "Dictionary of Physics",
"prefix": "1612"
},
"1613": {
"description": "This dictionary includes nearly 1,400 terms carpentry, corresponding to seven subject areas: equipment, utensils, tools and instruments, machinery and auxiliary equipment, structural and machine tools, materials, structures, techniques and processes, trades and installations . at present the names and the definition in Catalan equivalents in Spanish, French and English and, where appropriate, notes and illustrations that provide additional information about the name or concept defined. This is the online version of the dictionary carpentry, prepared by Peter and Pitu Basart PujolΓ s with terminology TERMCAT advice and collaboration of experts in the field, and published in 2005 by TERMCAT sponsored by Bauhaus.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/188",
"license": "CC BY-ND 3.0",
"name": "Carpentry dictionary",
"prefix": "1613"
},
"1614": {
"description": "This dictionary includes sixty terms standardized by the Supervisory Council TERMCAT corresponding to wood currently used in Europe but from countries outside Europe, mainly in Africa, Asia and America. Each term contains the names and the definition Catalan and equivalents in Spanish, French, English and German. most equivalents taken from the UNE-EN 13556, which is also the official Spanish version of the European standard 13556, June 2003. explicit definitions the place of origin of the wood, the species of which is drawn (often more than one species) and other important features (weight, hardness, color heartwood, sapwood color , etc.). for more information about these botanical species coming from the woods Cercaterm.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/11",
"license": "CC BY-ND 3.0",
"name": "Exotic woods terminology",
"prefix": "1614"
},
"1615": {
"description": "This dictionary contains 1302 terms in the field of gemology, especially those related species gemmolΓ²giques, physical properties and characteristics of crystalline gems, inclusions and sizes. Also includes materials obtained in laboratory treatments used to improve the color and appearance of the gems, carving processes, machines and tools necessary to do it and end products that result, and measuring devices and accessories used in various analytical techniques. Each article contains the names in Catalan, equivalents in Spanish, French, Italian, English and German, and definition. This is the online version of the dictionary gemology, published by TERMCAT and Editions University of Barcelona in 1999, prepared under the direction and coordination of scientific Joaquim M. NoguΓ©s, with terminology coordination TERMCAT. This edition or can first consult thematic data dictionary and incorporates specific amendments with respect to the paper version, the result of the maintenance of updated data carried out by TERMCAT.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/168",
"license": "CC BY-ND 3.0",
"name": "Gemology dictionary",
"prefix": "1615"
},
"1616": {
"description": "This lexicon contains more than thirteen thousand Catalan terms with equivalents in Spanish, French and English, concerning the most representative industrial sectors in Catalonia. This dictionary is the online version of the Lexicon multilingual industry, the work developed by TERMCAT with support of the Department of Innovation, Universities and Enterprise of the Generalitat of Catalonia. Both institutions hope that this release will facilitate the consultation of information and constantly updated. this will encourage everyone to make us your comments to improve the work.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/22",
"license": "CC BY-ND 3.0",
"prefix": "1616"
},
"1617": {
"description": "This dictionary defines and brings together nearly two hundred terms relating to the publishing industry relating to areas such as editing, printing, marketing and advertising. Each article contains the name and definition in Catalan. Most come terms Pan-Latin Vocabulary of dissemination and distribution of books, multilingual work made within the network Panlatin Terminology (really) under the coordination of the Office québécois de la langue française, and which has participated TERMCAT terms Catalan terminology. the vocabulary complete with equivalents in Spanish, English, French, Italian, Portuguese, Galician and Romanian can be downloaded free in pDF format.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/143",
"license": "CC BY-ND 3.0",
"name": "Book Terminology",
"prefix": "1617"
},
"1618": {
"description": "In the field of digital marketing and social media are all learning and there is a big stage to explore creative. Everything moves fast, the pace is steady and there is no option to choose between being there or not. If possible faces the challenge is that users do not join us. the digital marketing strategies are here to stay, and it is necessary to know the basics to understand what rules work. for this reason, TERMCAT considered necessary the elaboration of a terminology compilation containing the basic terminology of the field. the corpus, and in many cases also the denominations have agreed through the proposals and comments of users on social networks . in terms neological cases, a group of experts reached consensus on a work session the best alternatives Catalan were then evaluated by the Supervisory Board. the terminology includes more than one hundred terms. Each term and definition includes the names in Catalan equivalents in Spanish, English and French, and in some cases, conceptual clarifications or notes as an example.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/185",
"license": "CC BY-ND 3.0",
"name": "Terminology Digital Marketing",
"prefix": "1618"
},
"1619": {
"description": "The international vocabulary of metrology reflects the terminology of the Catalan translation of the International Vocabulary of Metrology. Fundamental concepts and associated terms and generals, 3rd ed. (VIM3). The work was translated by the Catalan Association of Clinical Laboratory Sciences with advice TERMCAT terminology, and published in 2012. this vocabulary contains 144 Catalan terms of this specific field of knowledge with the definitions corresponding equivalents in Spanish, French and Portuguese, and the reference code that identifies each section VIM3 terms. in some cases, offer conceptual clarifications or notes as an example.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/192",
"name": "International Vocabulary of Metrology",
"prefix": "1619"
},
"1620": {
"description": "To assist in decision making linguistic and terminology during the creation or translation of computer products in Catalan, we present a set of chips that collect terminology and phraseology common in this industry. You will find: More 2,450 terminology records relating to areas of interest to the field of location: office, graphic and electronic publishing, e-commerce, mobile telephony, Internet, video games, information society ... over 3650 examples of which include chips 'phraseological units in Catalan and English, commonly used in the creation and translation of computer. in this case, the phrase Catalan is a proposal among various possible wordings appropriate.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/123",
"license": "CC BY-ND 3.0",
"name": "Terminology and phraseology of computer products",
"prefix": "1620"
},
"1621": {
"description": "This online dictionary Occitan dictionary contains version information society. New technologies and the Internet. 2nd ed., Published by TERMCAT 2003. The work includes more than two thousand names and terms to the definition in Occitan and equivalents in Catalan, Spanish, French and English. the content has been written by Occitan Claudi Balaguer and validated by the Occitan Language group, a group created to support the Language Policy Secretariat in implementing the statutory mandate ordering the Occitan language is official in Catalonia. the project was carried out under TERMCAT methodological advice and the support of the Secretariat of Linguistic Policy of the Generalitat of Catalonia.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/38",
"license": "CC BY-ND 3.0",
"name": "Information society. Novelas technologies and Internet",
"prefix": "1621"
},
"1622": {
"description": "This dictionary contains about three hundred names and terms with Catalan definition and the equivalents in Spanish, French, English and German. The work is the result of a collaboration between industry experts and terminologists . (...) the video game industry is now a mass phenomenon. the first gaming machines, which appeared in the eighties, has given way to a market that is gradually becoming one of the most important audiovisual sectors. the development of computing and new technologies, along with the widespread use of the Internet and the preponderance of new leisure habits, have been largely responsible. in the Catalan-speaking territories is a dynamic profession game development studios and an intense interaction among the large group of players, but often it uses the language that uses English in their own solutions cases where alternatives can be used Catalan. With the aim of making available to the group of producers and users of gaming solutions necessary terminology in Catalan, we present terminology videogame result of a collaboration between terminology and industry experts.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/9",
"license": "CC BY-ND 3.0",
"name": "Video Game Terminology",
"prefix": "1622"
},
"1623": {
"homepage": "http://www.meteorites.ucla.edu/glossary/",
"name": "Glossary of Cosmochemistry",
"prefix": "1623"
},
"1624": {
"description": "This dictionary contains more than two hundred specific terms in this field in eleven different languages. The terms and definitions contained the names of seven of the eight European languages not state who participated in the project (Aromanian, Catalan, Corsican, Galician , Ladin, Occitan and Sardinian). in addition, you can see the corresponding equivalent in the four languages most widely in the international sector (Spanish, French, English and German). TERMCAT has coordinated the preparation of this lexicon, which involved representatives of various linguistic groups that make up the project Linmiter which, driven by the Latin Union, aims to encourage the development of lexicographical and terminological Latin languages in the context of cooperation Panlatin.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/36",
"license": "CC BY-ND 3.0",
"name": "Lexicon of tourist transport",
"prefix": "1624"
},
"1625": {
"description": "This vocabulary contains 114 terms related to different social networks, especially Facebook and Twitter. Each term has the equivalent names in six Romance languages ββ(Catalan, Spanish -variants Europe and Mexico, French, Galician, Italian and Portuguese -variants Europe and Brazil), with corresponding indicators speech and also in English. the definitions are in Catalan and, in some cases, also in Spanish. It has been elaborated within the framework of the Network Panlatin Terminology (really), which aims to promote the development of the Romance languages. the project coordination was conducted TERMCAT, which has facilitated the naming game in Catalan, Spanish and English and definitions from basic terminology of social networking, which was developed in 2012 in collaboration with the Directorate General of Public Service Broadcasting and the Ministry of Presidency the Government of Catalonia. Of all the terminology that generates this field, the terms currently included are drawn mainly from the use and style guide on social networks of the Generalitat of Catalonia, which sets common guidelines the presence of the Government homogeneous social networks. However, this dictionary is a product that remains open for continuous updating of content.",
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/156",
"license": "CC BY-ND 3.0",
"name": "Pan-Latin vocabulary of social networks",
"prefix": "1625"
},
"1626": {
"description": "Treasures terminology: Archeology, Ethnography, Decorative art, numismatics, fine arts, science and technology, documents, RAMEAU",
"homepage": "http://tezaur.cimec.ro/IndexVizualizare.aspx",
"prefix": "1626"
},
"1627": {
"description": "Treasures terminology: Archeology, Ethnography, Decorative art, numismatics, fine arts, science and technology, documents, RAMEAU",
"homepage": "http://tezaur.cimec.ro/IndexVizualizare.aspx",
"name": "Decorative Art Treasures terminology",
"prefix": "1627"
},
"1628": {
"homepage": "http://tezaur.cimec.ro/IndexVizualizare.aspx",
"prefix": "1628"
},
"1629": {
"description": "Treasures terminology: Archeology, Ethnography, Decorative art, numismatics, fine arts, science and technology, documents, RAMEAU",
"homepage": "http://tezaur.cimec.ro/IndexVizualizare.aspx",
"name": "Treasures terminology Documents",
"prefix": "1629"
},
"163": {
"description": "EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. The applications of EDAM are within organising tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web.",
"homepage": "http://www.edamontology.org/",
"name": "EMBRACE Data and Methods",
"prefix": "163"
},
"1630": {
"description": "Treasures terminology: Archeology, Ethnography, Decorative art, numismatics, fine arts, science and technology, documents, RAMEAU",
"homepage": "http://tezaur.cimec.ro/IndexVizualizare.aspx",
"name": "Treasures terminology Ethnography",
"prefix": "1630"
},
"1631": {
"description": "Treasures terminology: Archeology, Ethnography, Decorative art, numismatics, fine arts, science and technology, documents, RAMEAU",
"homepage": "http://tezaur.cimec.ro/IndexVizualizare.aspx",
"name": "Numismatic Treasures terminology",
"prefix": "1631"
},
"1632": {
"homepage": "http://tezaur.cimec.ro/IndexVizualizare.aspx",
"prefix": "1632"
},
"1633": {
"description": "Content:\n\nA - the culture corner\n\n00 - preparation for competition and professional examinations\n\n10 - frame of publication\n\n20 - public action\n\n30 - questions international and european\n\n40 - questions economic and social\n\n50 - questions budget, financial and accounting\n\n60 - questions administrative and juristic\n\n70 - function public\n\n80 - management\n\n90 - professional tools",
"homepage": "http://docplayer.fr/6752984-Systeme-de-classification-du-centre-de-ressources-documentaires-de-l-institut-regional-d-administration-de-lyon.html",
"name": "Classification Scheme of the Documentary Resources Center of the Regional Institute of Administration of Lyon",
"prefix": "1633"
},
"1634": {
"description": "Launched in 1997, Uniclass, the classification for the construction industry, is the UK implementation of BS ISO 12006-2, providing a structured approach to classifying the building information by organising information based upon common characteristics. The recent developments and wide-adoption of BIM to manage information across the project timeline, has meant the need for a unified approach to classification, ensuring that information is universally structured regardless of the author. This lead to a review of Uniclass and the development of Uniclass2.\"\n\n\"A classification system is an essential tool for organising information. Without an agreed, comprehensive system for organising construction information it will be impossible to ensure interoperability between different information systems, design tools, and facilities management tools, with data entered once and re-used several times through the process. A construction classification system must include buildings, infrastructure and integrated project and office management. It must be able to map project information from the initial concept through brief, detailed design, construction, handover and facility operation and maintenance. To fully adopt the BIM process it is important to organise such information systematically and consistently. Uniclass 2 has been developed to produce a classification system for structuring information that is freely available for all participants throughout the life cycle of a project and beyond, which is endorsed by all construction and property bodies and professional institutions. It is dynamic, available online in various formats and managed by a team of experts who will monitor requests, update and control versioning.",
"license": "https://www.w3.org/Consortium/Legal/2015/doc-license",
"name": "Uniclass",
"prefix": "1634",
"wikidata_database": "Q7884732"
},
"1635": {
"description": "The 'Subject Areas' panel on each article page displays a set of terms selected for that article based on its content. The Subject Areas belong to a thesaurus of over 10,000 terms initially built for us over the course of 2012 by Access Innovations, taking into account the controlled vocabulary of classification terms that had been in use in PLOS Editorial Manager. The entire corpus of PLOS articles was analysed to ensure that the thesaurus covers the research domain comprehensively.\n\nSpecific terms are associated with articles by Machine Aided Indexing (MAI) which identifies text strings in the articles and matches them to Subject Area terms from the thesaurus. The output ranks the matches in order of frequency of hits within the text of the article and the top eight terms are selected for display. Whereas previously the eight terms were presented in alphabetical order, we are introducing weightings to the Subject Area panel, such that the order of Subject Areas will reflect the frequency of hits in the MAI process. This new presentation will be introduced progressively, beginning with the main Article tab.\n\nThe MAI process uses a Rulebase to guide Subject Area selection. Whereas identifying a phrase such as 'Retinitis pigmentosa' is relatively straightforward for software, the issue is more complex for a word such as 'Sodium' where the relevant Subject Area might be 'Voltage-gated sodium channels', any of several sodium compounds or even just 'Sodium' the element. The rule for terms such as 'Sodium' are therefore compound and include conditional statements to disambiguate these different contexts. While the vast majority of terms are effectively indexed there remain ambiguities for some terms and part of our work is to continue to identify these cases and modify the Rulebase accordingly.\n\nThe Subject Area terms are related to each other with a system of broader/narrower term relationships. The thesaurus structure is a polyhierarchy, so for example the Subject Area 'White blood cells' has two broader terms 'Blood cells' and 'Immune cells'. At its deepest the hierarchy is ten tiers deep, with all terms tracking back to one or more of the top tier Subject Areas, such as 'Biology and life sciences' or 'Social sciences'.\n\nThe Subject Area terms can be used to filter PLOS content via the Subject-specific option in Advanced Search. The MAI Rulebase accommodates synonyms, so a Subject-specific Search for 'Highly active antiretroviral therapy' will retrieve articles based on MAI matches to 'HAART' (a known synonym) as well as 'Highly active antiretroviral therapy' in one step. Additionally, because we select the most frequently MAI-indexed Subject Areas for each article the Search returns articles where the Subject Area in question ranks highly enough to be included in the top eight MAI-retrieved terms, so is of relatively high significance, whereas a query term in an βAll fieldsβ search will return every article that contains even a single match to the query term.\n\nThe hierarchical nature of the thesaurus also enhances article retrieval in Search. Not only does Search retrieve all articles specifically indexed by MAI with the query Subject Area term in question, but it also retrieves all articles specifically indexed with any Subject Area term that sits deeper into the hierarchy than the query Subject Area term, but on the same broader/narrower term path. Thus, in the 'White blood cells' example, queries for either 'Blood cells' or 'Immune cells' will return all articles indexed with 'White blood cells'.\n\nThe Subject Area terms on all article pages are hyperlinked and following the link returns a listing of all articles to which that Subject Area term applies. Subject Area terms can also be used as the basis for Saved Searches, RSS feeds and PLOS ONE customized Journal Alerts.\n\nThe content of the PLOS thesaurus and the Rulebase that governs the application of Subject Areas to the articles is constantly under review. We incorporate analysis of the Subject Area panel 'feedback' clicks into this review process, and are always happy to receive specific input on Subject Area terms and their application by email. We update the thesaurus behind the PLOS sites several times each year.",
"license": "CC0-1.0",
"name": "PLOS Subject Area Thesaurus",
"prefix": "1635"
},
"1636": {
"description": "In this system, the two main tasks of a modern political-social education are contained: (1) the mediation and reflection of political and social knowledge for the purpose of the individual judgment and opinion formation with regard to upcoming social problems and problems; The promotion and support of competences, motives and emotional dispositions for competent and socially responsible commitment and action to deal with or solve these tasks and problems. The systematic approach follows a trend - setting trend which has been empirically observable for several years in political education Outside-school youth and adult education in general - in addition to the mediation and processing of information and knowledge the development of skills, motivation and social-moral dispositions gain in importance.",
"homepage": "http://www.die-bonn.de/esprid/dokumente/doc-2003/koerber03_01.pdf",
"name": "Checklist Political Education",
"prefix": "1636"
},
"1637": {
"description": "The Combined Nomenclature is the goods classification used within the EU for the purposes of foreign trade statistics. It is also used by Directorate General 'Taxation and Customs Union' of the European Commission for customs duty purposes. The classification is maintained by Eurostat for the statistical aspects and by Taxation and Customs Union DG for the tariff aspects. The classification is based on the Harmonized System (HS) which it sub-divides where necessary for purposes of external trade, agricultural regulation and customs duties. The CN was introduced in 1988 together with the HS. Subheadings in the CN are identified by means of an eight-digit numerical code. The very considerable number of subdivisions within the CN were introduced with the EU's specific customs and foreign trade statistics requirements in mind. The CN is revised annually and, as a Council Regulation, is binding on the Member States. It appears in all EU official languages (except Irish).",
"homepage": "http://ec.europa.eu/eurostat/ramon/nomenclatures/index.cfm",
"name": "Combined Nomenclature",
"prefix": "1637",
"wikidata_database": "Q1427897"
},
"1638": {
"description": "CDCβs Thesaurus is structured around preferred concepts, sourced whenever possible from standard vocabularies, with their associated properties (metadata) in a polyhierarchical framework. The preferred concept bacillus anthracis, for example, has defined associations to the concept Anthrax (the disease caused by the target organism) and to the concept Anthrax vaccines (the prevention for the disease). This organism term is 'treed' in the polyhierarchy as both a soilborne bacillus organism and as a biological agent. The parent concept Anthrax has child concepts Cutaneous anthrax, Gastrointestinal anthrax, and Pulmonary anthrax. Thus the utilization of this cluster of concepts on a website or within an application enables a rich retrieval of all anthrax-related information. (...) The Controlled Health Thesaurus is a public health view of pertinent concepts from the National Library of Medicineβs Metathesaurus. Additional concepts needed to cover the public health domain are being added and will be advanced to NLM. CDC Research revealed that the National Library of Medicineβs Medical Subject Headings (MeSH) provided the broadest coverage of concepts for public health. Additional concepts from other UMLS vocabularies, such as the Computerized Retrieval of Information on Scientific Projects (CRISP), Alcohol and Other Drug Thesaurus (AOD), and Library of Congress Subject Headings will be utilized as needed. CDC is leveraging the expertise of its subject matter experts and its public health partners to add additional public health concepts. Requirements for Thesaurus structuring and metadata selection came from the ANSI/NISO Z39.19 Guidelines for the Construction, Format, and Management of Monolingual Thesauri. The standard deals with aspects of term selection and the means for establishing and displaying relationships between terms.",
"homepage": "http://www.cdc.gov/phin/library/archive_2005/CHT_Download_05-04-05.zip",
"name": "Controlled Health Thesaurus",
"prefix": "1638"
},
"1639": {
"description": "Power Thesaurus is a fast, convenient and comprehensive online thesaurus. It's crowdsourced, meaning it has been built by a community of writers for writers. The vast collection of terms in Power Thesaurus is original and is based upon editorial work of our team and review of visitors' suggestions for many years. Users enjoy easy-to-follow look & feel, yet with powerful assisting tools. Visitors rate suggested words with handy voting, helping other writers to find the best term. Power Thesaurus is a constantly growing and improving synonym finder with the collective power of its visitors and editorial team!",
"homepage": "https://www.powerthesaurus.org/",
"name": "Power Thesaurus",
"prefix": "1639"
},
"164": {
"description": "The British Education Index continues to serve its original, 50-year old, purpose as an independent subject and author index to the contents of significant education journals published in the UK. Within limitiations imposed by its self-financing status, the BEI also seeks to identify information from an increasingly diverse research environment, particularly addressing texts on the Internet and events, as detailed below. All BEI services are created and maintained by staff whose costs are met by income from royalties and from occasional contracted work, and who use custom-built but potentially widely exploitable information management tools to do their work. The British Education Thesaurus vocabulary was used for subject indexing, for example, allowing for the eventual closer connection between Education-line and the BEI database. (The British Education Thesaurus was first produced by the BEI in 1988 to provide a means to facilitate consistent subject indexing of literature by the Index.)",
"homepage": "http://www.leeds.ac.uk/bei/COLN/COLN_default.html",
"name": "British Education Thesaurus",
"prefix": "164"
},
"1640": {
"description": "The central archive classification scheme was developed to control the content, form, and function of questions from surveys of empirical social research, which is why the naming of the categories is based on the variational language of survey research And the retrieval of study descriptions in the data stock catalog (.) 36 main classes (collection categories), each with several categories and subcategories, index (alphabetical register) with about 1000 entries.",
"homepage": "https://dbk.gesis.org/dbksearch/Kategorien.htm",
"name": "Central Archive classification scheme",
"prefix": "1640"
},
"1641": {
"description": "Indexing and retrieval of the methodological approach of literature and research projects. (40) Descriptors, 100 synonyms.",
"name": "Method list for the databases SOFIS and SOLIS",
"prefix": "1641"
},
"1642": {
"description": "Classification of and Basis of Topics for Literature, Links Collection as well as the 'News' (Scientific News, Event Calendar, Call for Papers, Job Market, CEWS News) in the CEWS-Portal.",
"homepage": "http://www.gesis.org/fileadmin/upload/dienstleistung/tools_standards/CEWS-Kategorien.pdf",
"name": "CEWS categories \"Women in science and research\"",
"prefix": "1642"
},
"1643": {
"description": "The Language of Bindings Thesaurus (LoB) includes terms which can be used to describe historical binding structures. The thesaurus can be used as a lookup resource through this website and also as a software service where the terms can be retrieved directly through your own application. LoB is a young project and community contribution will ensure that it will be improved. (...) The thesaurus is structured based on the Simple Knowledge Organisation System (SKOS). Some of the main principle of that system are: We define concepts (not words) to avoid common problems such as when different communities use different words for the same idea. Each concept can have a number of labels (language words) which refer to the concept, with one of them being a recommended label (preferred label) and the rest being the alternative labels. Concepts are organised from the more general ones, the broader concepts, to the more specific ones, the narrower (broader / narrower relationship). A narrower term should always describe a concept which is included in the parent concept. For example, adzes is a narrower concept of tools and equipment because all adzes are tools. (...) LoB concepts are described in the so-called scope notes, which aim to give both a brief definition of each concept as well as a broader indication of what the concept is about, together with some historical information where this is known and relevant. (...) Where possible we have matched our concepts with concepts from the Getty AAT. Our intention is to submit LoB concepts to the AAT where corresponding terms do not exist. (...) The thesaurus is meant to be used as part of a documentation system. We recognise the value of the CIDOC-CRM in the documentation of cultural heritage. For this reason we have chosen our top concepts to match CIDOC-CRM entities so that their narrower concept hierarchies can be used as E55 Type for these entities in a documentation system. However, using a CRM compatible documentation system is not required.",
"homepage": "http://www.ligatus.org.uk/lob/",
"name": "Language of Bindings Thesaurus",
"prefix": "1643"
},
"1644": {
"abbreviation": "CRM",
"description": "The CIDOC Conceptual Reference Model (CRM) provides definitions and a formal structure for describing the implicit and explicit concepts and relationships used in cultural heritage documentation. The CIDOC CRM is intended to promote a shared understanding of cultural heritage information by providing a common and extensible semantic framework that any cultural heritage information can be mapped to. It is intended to be a common language for domain experts and implementers to formulate requirements for information systems and to serve as a guide for good practice of conceptual modelling. In this way, it can provide the 'semantic glue' needed to mediate between different sources of cultural heritage information, such as that published by museums, libraries and archives.",
"homepage": "http://www.cidoc-crm.org/cidoc-crm/",
"name": "CIDOC Conceptual Reference Model",
"pattern": "^[A-Z]{1,2}[0-9]+i?(_[A-Za-z_]+)?$",
"prefix": "1644",
"wikidata_database": "Q624005"
},
"1645": {
"description": "This presentation of Old English vocabulary is conceptually arranged, and is therefore entitled A Thesaurus of Old English (TOE). The vocabulary of Anglo-Saxon England is presented within ordered categories. Ideally, the reader should approach the materials of the TOE by subject rather than through the alphabetic index of the printed edition. Roget-owners have long been accustomed to begin with a word and, by trying a few locations listed in the index, find the vocabulary group wanted. Moreover, for inclusiveness they trade detailed information. Should a word's precise meaning be wanted, a dictionary is needed. Most conceptually-organized thesauri tend therefore to be used by native speakers of a language, who know the meanings of the words scanned. Less assured speakers may turn to those alphabetically-organized thesauri where they will find more help with meaning but far fewer words. In the TOE any small group of items listed together as sharing a component of meaning resembles the strings of words that make up the entries of an alphabetically-organized thesaurus, but they are embedded within an inclusive conceptual scheme. The provision of brief indications of meaning at all levels of this scheme looks back behind Roget, to the way in which Wilkins supplies notions and words, where word-senses follow on from ideas explained. Thus, this thesaurus incorporates information about word meaning and could be described as an inside-out dictionary, with meanings first and then words.",
"homepage": "http://oldenglishthesaurus.arts.gla.ac.uk/",
"name": "Thesaurus of Old English",
"prefix": "1645"
},
"1646": {
"description": "Classification System for Knowledge Organization Literature was devised by Ingetraut Dahlberg and is currently used by the editors of the Knowledge Organization Literature bulletins at ISKO.",
"name": "Classification System for Knowledge Organization Literature",
"prefix": "1646"
},
"1647": {
"homepage": "http://www.frauenmediaturm.de/frauenmediaturm/publikationen/feministischer-thesaurus/",
"prefix": "1647"
},
"1648": {
"description": "With this project idea thesaurA - the name represents the feminist transformation of the male term 'thesaurus' and accentuated by the capitalization of the feminine ending the Austrian-specific approach - a concept was adopted which had already been implemented several times internationally: already in the 70s The American Thesaurus 'On Equal Terms' had been published, the first German-language thesaurus was published in 1994 by the Cologne 'FrauenMediaTurm'.\n\nLanguage and language behavior in a society are, as is well known, characterized by power structures and governance processes. This also means that linguistic norms represent linguistic actions. The use of language in our society is based on male values ββand at the same time discriminates against women in several ways: he is sexist. Since keyword catalogs and thesauri are basically based on compilations of predominantly natural language terms, the conventional spelling of conventional Austrian documentation facilities is sexist.\n\nBut also in other respects an anachronistic and useless hostile state is to be established. Within the last twenty years, in the context of the New Women's Movement and the influence of feminist criticism, social awareness about gender relations has been at least a reflection process. This has also resulted in different intensity reactions in science and in daily politics. The constantly growing amount of women-oriented literature, however, is opposed to a catchword which is not suitable for exhaustively evaluating feminist / woman-specific documentation material.\n\nThis deficit is to be countered by proposing suggestions and providing assistance in the implementation of three sociolinguistic principles. The linguistic visualization of women is to be enforced by eliminating the universally argued male language form. Thus, if the content of a document refers to women and men, a codification must be carried out, which makes both sexes visible. Here, however, a gender specification is meant not only with regard to person names such as \"asylum seekers\" or \"asylum seekers\" or \"female youngsters\" or \"male youngsters\", but also as a feminine innovation in the case of composites such as \"workers' Workers 'movement' and 'Christianity'. (...)\n\nThe first Austrian women's thesaurus as a reference book for orientation in the field of women's and gender studies contains 467 pages and consists of a manual, the main part with about 3000 terms, a permutation register and an index of the subjects according to subject group systematics; As additional documentary tools, four special lists - professional groups, form keywords, geographics and time-lapse words - are attached.\n\nThe target groups of thesaurA include the content developers in both institutionalized documentation institutions and libraries, as well as in smaller specialized women's libraries, archives and documentation centers. However, the vocabulary should also be available to the users of these institutions in order to assist in the effective search for information.",
"homepage": "http://www.frida.at/thesaura.htm",
"name": "thesaurA",
"prefix": "1648"
},
"1649": {
"name": "Canadian Feminist Thesaurus",
"prefix": "1649"
},
"165": {
"description": "In the development of this thesaurus, a total of 262 terms have been included, of which 167 are descriptors and 95 are descriptors, and 31 relations of association and 135 relations of hierarchy are presented.",
"homepage": "http://www.um.es/isgat/navegacion.php",
"name": "Computer Network Thesaurus",
"prefix": "165"
},
"1650": {
"name": "Female Language",
"prefix": "1650"
},
"1651": {
"name": "Thesaurus on Women in Development",
"prefix": "1651"
},
"1652": {
"name": "On Equal Terms: A Thesaurus for Nonsexist Indexing and Cataloging",
"prefix": "1652"
},
"1653": {
"description": "Thesaurus Pedagogy, published by the Documentation Center Pedagogy (DOPAED). Edited by the documentation of the Pedagogical Center, Berlin.",
"name": "Thesaurus pedagogy",
"prefix": "1653"
},
"1654": {
"name": "DOMA Thesaurus Mechanical Engineering",
"prefix": "1654"
},
"1655": {
"description": "A Vocabulary Listing for use in Indexing, Storage and Retrieval of Technical Information in Metallurgy",
"name": "Thesaurus of Metallurgical Terms",
"prefix": "1655"
},
"1656": {
"description": "The system presented here applies to the old stocks of the library (...).",
"homepage": "http://www.wisotech.rwth-aachen.de/?page_id=60",
"name": "Descriptors / Keywords of the library system",
"prefix": "1656"
},
"1657": {
"description": "The Library-Bibliographical Classification (LBC), which is the National Classification System of the Russian Federation, is considered as one of the largest universal classification systems according to the opinion of International Society of Knowledge Organization (ISKO). The LBC is the newest classification system applied in the world today. It appeared in 1960-s, whereas Melwil Deweyβs Decimal Classification (DDC) was submitted in 1876, the Universal Decimal Classification (UDC) β in 1895β1905, the Library of Congress Classification (LCC) β in 1912, S. R. Ranganathanβs Colon Classification (CC) β in 1936. By its semantic power the LBC can be compared with the UDC. The LBC belongs to the combinative systems (as well as the UDC); its capability cannot be measured in the quantity of main schedules divisions because the quantity of combinations with divisions of auxiliary classification tables is immeasurable. The systemβs newness indicates its science-based structure and the accordance between its content and the contemporary level of science development and social practice. The LBC is a permanently developing system. The LBC has a broad range of options available β for scientific, public (termed 'mass' in the USSR before 1991), regional libraries as well as full, medium or abridged schedules β presented now both in books and in machine-readable (electronic) form. None of existing classification system could have survived that sort of severe social upheaval which had fallen to the lot of the LBC. Created in the USSR, it fully reflected the ideology of Soviet society. Only few years needed to accomplish the task of deideologization of its content entirely and to ensure the process of modernization, in fact, the updating of all the structure and contents. As a result, there came a schedules different from the Soviet LBC for its structure and content. In 2001, the commencing issue of the Medium LBC schedules appeared (the publishing is still proceeding: 6 of 9-10 issues have already been published). It is hard for libraries to have time to master each new issue of the schedules: the changes are so significant that it can even be necessary to start new ranges of catalogs, to restructure the book collections completely. The LBC is the National classification system of the Russian Federation. It adequately covers history, philosophy, economics, and geography of Russia, art and culture of its peoples, doing that as completely as no foreign classification could do. The LBC is now used in 95% of libraries in our country.",
"homepage": "http://lod.rsl.ru/",
"name": "Library-Bibliographical Classification",
"prefix": "1657",
"wikidata_database": "Q856579"
},
"1658": {
"description": "The Bank of Finnish Terminology in Arts and Sciences is a multidisciplinary project which aims to gather a permanent terminological database for all fields of research in Finland. The project has created a Semantic MediaWiki platform, which offers a collaborative environment. The semantic MediaWiki platform is an open collaborative website. This means that anyone can freely use it and also participate in the discussion about terms. The data available for all users includes the following details: The term and its synonyms in Finnish; Definition(s); The concept's place in the concept system and concept diagrams; Information about the termβs morphological structure; Ostensive definitions (e.g. pictures); Contexts (e.g. links to abstracts of articles); Term equivalents in other languages (and information about the translatability of terms when necessary).\n\nThe working method is a type of limited crowd-sourcing. The terminology will be gathered among expert groups in different fields of research. The project is being carried out in three pilot projects: botany, jurisprudence, and linguistics. In the course of the pilot projects, the operations models for the teamwork of expert groups will be developed in order to take into account varying practices and terminological demands in different subfields of research. The published view of each terminological entry will be defined by the relevant expert group and customized to fit the special needs of each field of research.\n\nThe core of the terminological work is done by expert teams from various fields of the arts and science. The members of each expert team have access to a wide range of wiki editing resources and can add information into every slot of the database in their field of expertise. They will also label the definition of a term as βcheckedβ when they think that it meets the standards of the field. It is also possible to include existing terminologies in the bank β of course with the permission of those who own the copyright.",
"homepage": "http://tieteentermipankki.fi/wiki/Termipankki:Etusivu",
"license": "CC-BY-3.0",
"name": "The national term bank of science",
"prefix": "1658",
"wikidata_database": "Q20916948"
},
"1659": {
"description": "A listing of computer game platforms. Work in progress.",
"homepage": "http://gamemetadata.org/uri/platform",
"name": "GAMECIP - Computer Game Platforms",
"prefix": "1659"
},
"166": {
"description": "The Semantic Network Service (SNS) of the Federal Environment Agency provides support for all questions concerning environmental terms including the common place names. (...) SNS contains a bi-lingual (German/English) semantic network which consists of three components:\n\n- the Environmental Thesaurus UMTHESΒ with more than 50,000 inter-networked terms. (Descriptors and Non-Descriptors).\n\n- the Geo-Thesaurus-Environment (GTU) with more than 25,000 geographic names and the spatial intersections of all these places.\n\n- an Environmental Chronology containing more than 600 contemporary and historical events that affected the environment.\n\nThe Federal Environment Agency provides this service to encourage the practice of a common domain language in the German Environmental Informatics, and to make this terminology accessible by the public.",
"homepage": "https://sns.uba.de",
"license": "CC BY-NC-ND 3.0",
"name": "Semantic Network Service",
"prefix": "166"
},
"1660": {
"description": "The following classification scheme covers the following areas: general, secondary disciplines, economics, economics and industry, business economics, sociology, political science and political sociology But there are different and equivalent possibilities of the location, especially in the case of interdisciplinary and equally worked questions: these are then referred to as references or pragmatic all aspects of the subject are grouped together in individual subject groups: cf., for example, subject groups 010 019, 123, 340, 385 or 721.",
"homepage": "http://www.ub.unibas.ch/fileadmin/redaktion/wwz/pdf/VERZ_rh_klassifikation_UB_Wirtschaft_20131001_bdu_do.pdf",
"name": "UniversitΓ€tsbibliothek Business Classification Freehand Area (RH Signatures)",
"prefix": "1660"
},
"1661": {
"description": "The PSYNDEX terms are the controlled vocabulary of the PSYNDEX database, which is based on the\" Thesaurus of Psychological Index Terms \"(Copyright American Psychological Association, all rights reserved), whose entire word stock has been translated into German Has been updated and now contains 5973 main terms of the psychological specialist language in German and English, with a total of 4188 references. In the new edition, 360 main concepts and 334 references have been added.",
"homepage": "http://www.zpid.de/index.php",
"name": "PSYNDEX Terms",
"prefix": "1661"
},
"1662": {
"description": "Welcome to the Biggest Technical Theatre Glossary on the Web, now in its 18th year! OVER 1900 TERMS NOW LISTED, AND MORE ADDED REGULARLY! NEW: MOBILE SEARCH Go to http://m.theatrecrafts.com.",
"homepage": "http://www.theatrecrafts.com/glossaryofterms",
"name": "Glossary of Technical Theatre Terms",
"prefix": "1662"
},
"1663": {
"description": "A term generally used to describe art that is not representational or based on external reality or nature.",
"homepage": "http://www.moma.org/learn/moma_learning/glossary",
"name": "Glossary of Art Terms",
"prefix": "1663"
},
"1664": {
"description": "Relationships between entities of different types and relationships between entities of the same type",
"homepage": "https://github.com/dcmi/repository/blob/master/mediawiki_wiki/NKOS_Vocabularies.md#KOS_Relation_Vocabulary",
"name": "KOS Relation-Type Vocabulary",
"prefix": "1664"
},
"1665": {
"abbreviation": "nkostype",
"description": "The NKOS KOS Types vocabulary have been developed as Dublin Core Application Profile by the Networked Knowledge Organization Systems (NKOS) group based on an overview of KOS types by Marcia Zeng.",
"homepage": "https://nkos.dublincore.org/nkos-type.html",
"name": "KOS Types Vocabulary",
"prefix": "1665"
},
"1666": {
"description": "This subject-based controlled vocabulary is used to tag content and improve information and service searches by staff and the public. Examples of City of Toronto services that tag content with subject terms include 311, Council and Committee meetings and agendas and Open Data.",
"homepage": "http://opendata.toronto.ca/clerk/controlled.vocabulary/subject_thesaurus.xml",
"name": "City of Toronto (Canada) Subject Thesaurus",
"prefix": "1666"
},
"1667": {
"description": "The classification of cancer by anatomic disease extent, i.e. stage, is the major determinant of appropriate treatment and prognosis. Stage is an increasingly important component of cancer surveillance and cancer control and an endpoint for the evaluation of the population-based screening and early detection efforts. The UICC has published the UICC TNM classification of malignant tumours for over 50 years. The UICC TNM classification is the internationally accepted standard for cancer staging. The UICC TNM Classification is an anatomically based system that records the primary and regional nodal extent of the tumor and the absence or presence of metastases. (...) The UICC TNM staging system is the common language in which oncology health professionals can communicate on the cancer extent for individual patients as a basis for decision making on treatment management and individual prognosis but can also be used, to inform and evaluate treatment guidelines, national cancer planning and research. (...) The TNM classification is a unified standard and is a prerequisite for ensuring the quality of care in all resource-settings. It goes beyond clinician practice and constitutes vital information for policy-makers developing or implementing cancer control and prevention plans and it is therefore important to include the TNM classification as part of cancer registration.",
"homepage": "http://www.uicc.org/resources/tnm",
"license": "CC BY-NC-SA 3.0",
"name": "TNM Classification of Malignant Tumors",
"prefix": "1667",
"wikidata_database": "Q668115"
},
"1668": {
"description": "The authority list 'Actions' brings together descriptors designating stocks, intervention methods or procedures. These descriptors are not by themselves indexing terms but must be associated with one or more of the thesaurus descriptors",
"homepage": "http://data.culture.fr/thesaurus/resource/ark:/67717/T2",
"license": "CC BY-SA 3.0",
"name": "List of Authority Actions for the Indexing of Local Archives",
"prefix": "1668"
},
"1669": {
"description": "The Historical Context list contains descriptors for historical events or periods. These descriptors are not by themselves indexing terms, but must be associated with one or more descriptors of the subject thesaurus, if The documentary context requires it.",
"homepage": "http://data.culture.fr/thesaurus/resource/ark:/67717/T4",
"name": "Authority List Historical Context for the Indexing of Local Archives",
"prefix": "1669"
},
"167": {
"description": "The Canadian Literacy Thesaurus/ThΓ©saurus canadien d' alphabΓ©tisation was first published in 1992 by the Canadian Literacy Thesaurus Coalition. A second edition, published in 1996, brought the total number of terms to 1890 in English and 1950 in French. A revised, on-line version of the Thesaurus, launched early 2008, has brought the total number of terms to 2097 in English and 2201 in French. The online version of the Canadian Literacy Thesaurus replaces the print version. The Thesaurus can be used to index documents, whether they are print, audiovisual, or electronic. It can also be used to organize reading lists and bibliographies. People can consult the Thesaurus when searching in existing databases such as library catalogues. Finally, the Thesaurus will be helpful to people who wish to familiarize themselves with terminology or emerging concepts in the Canadian literacy field.",
"homepage": "http://thesaurusalpha.org/",
"name": "Canadian Literacy Thesaurus",
"prefix": "167"
},
"1670": {
"description": "The 'Documentary typology' authority list includes terms that refer to easily identifiable categories of documents (eg chrono, register, plan) or more precise terms, but refer to documents that are generally paid and stored in series (example: These descriptors are not by themselves indexing terms but must be associated with one or more descriptors of the subject thesaurus, if the documentary context so requires.",
"homepage": "http://data.culture.fr/thesaurus/resource/ark:/67717/T3",
"name": "Authority List Typology Documentary for the Indexing of Local Archives",
"prefix": "1670"
},
"1671": {
"description": "The purpose of this vocabulary is to provide a standardized list of terms for describing the variety of photographic techniques that archival holdings can contain. It is structured into five main parts corresponding to the steps of identifying a photograph: the polarity of The image (negative or positive) which constitutes the first level of indexing; the type of medium, which constitutes a second level of indexing (to be used whenever it is not possible to identify the method The type of process, which corresponds to a third level of indexation (the identification of the type of process can make it easier to identify fragile, precious or even rare documents, including the conservation or The mode of representation (to be used in second level in substitution of the nature of the support, and to supplement possibly pa) R the process by which it was created); The mode of reproduction.",
"homepage": "http://data.culture.fr/thesaurus/resource/ark:/67717/2012b973-ddb2-4540-a775-9157c3c1d7fd",
"license": "CC BY-SA 3.0",
"name": "Vocabulary for Photographic Techniques",
"prefix": "1671"
},
"1672": {
"description": "The FOSTER portal is an e-learning platform that brings together the best training resources for those who need to know more about Open Science, or who need to develop strategies and skills for implementing Open Science practices in their daily workflows. Here you will find a growing collection of training materials to meet the needs of many different users, from early-career researchers, to data managers, librarians, funders, and graduate schools.\" Click on \"View the taxonomy tree\".",
"homepage": "https://www.fosteropenscience.eu/foster-taxonomy/open-science",
"name": "Open Science Taxonomy",
"prefix": "1672"
},
"1673": {
"description": "The EMN Glossary improves comparability by enabling a common understanding and use of terms and definitions relating to asylum and migration. The Glossary draws on a variety of sources, but primarily on the legislation of the EU asylum and immigration acquis, and makes terms available in the majority of Member State languages.",
"homepage": "http://ec.europa.eu/dgs/home-affairs/what-we-do/networks/european_migration_network/glossary/index_a_en.htm",
"name": "European Migration Network Glossary & Thesaurus",
"prefix": "1673"
},
"1674": {
"description": "The GeoNames geographical database is available for download free of charge under a creative commons attribution license. It contains over 10 million geographical names and consists of over 9 million unique features whereof 2.8 million populated places and 5.5 million alternate names. All features are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes. (...) The data is accessible free of charge through a number of webservices and a daily database export. GeoNames is already serving up to over 150 million web service requests per day.\n\nGeoNames is integrating geographical data such as names of places in various languages, elevation, population and others from various sources. All lat/long coordinates are in WGS84 (World Geodetic System 1984). Users may manually edit, correct and add new names using a user friendly wiki interface. GeoNames has Ambassadors in many countries who assist with their help and expertise.",
"homepage": "http://www.geonames.org/",
"license": "CC-BY-3.0",
"name": "GeoNames",
"prefix": "1674",
"wikidata_database": "Q830106"
},
"1675": {
"description": "The Resource Type vocabulary defines concepts to identify the genre of a resource. Such resources, like publications, research data, audio and video objects, are typically deposited in institutional and thematic repositories or published in ejournals. This vocabulary supports a hierarchical model that relates narrower and broader concepts. Multilingual labels regard regional distinctions in language and term. Concepts of this vocabulary are mapped with terms and concepts of similar vocabularies and dictionaries. The Resource Type vocabulary builds on and extends the controlled list of publication types defined in info:eu-repo/semantics. Backward compatibility is ensured by a suggested mapping. The Resource Type vocabulary is part of the COAR Controlled Vocabularies.",
"homepage": "https://www.coar-repositories.org/activities/repository-interoperability/ig-controlled-vocabularies-for-repository-assets/coar-vocabularies/deliverables/",
"license": "CC-BY-3.0",
"name": "Resource Type Vocabulary",
"prefix": "1675"
},
"1676": {
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/176",
"name": "Thesaurus for research terms",
"prefix": "1676"
},
"1677": {
"description": "See \"IOE Thesaurus Terminology Rules\" (http://eprints.ioe.ac.uk/18585/7/IOE%20Thesaurus%20Terminology%20Rules%20v1.docx).",
"homepage": "http://eprints.ioe.ac.uk/18585/",
"license": "CC-BY-3.0",
"name": "Institute of Education Thesaurus",
"prefix": "1677"
},
"1678": {
"description": "Languages are classified (...) into 243 families and 189 isolates, i.e., one-member families. This classification is the best guess by the Glottolog editors and the classification principles are described (...). Users should be aware that for many groups of languages, there is little available historical-comparative research, so the classifications are subject to change as scholarship and interest in those languages increase.",
"homepage": "http://glottolog.org/glottolog/family",
"license": "CC BY-SA 3.0",
"name": "Glottolog Classification",
"prefix": "1678",
"wikidata_database": "Q17165062"
},
"1679": {
"description": "TRBC classifies the primary business activity of over 72,000 listed companies from 130 countries into a five level hierarchy. Dedicated, local language speaking analysts utilize company filings, Reuters news and Thomson Reuters corporate actions services in order to assign and maintain a company's activity. TRBC helps you identify, monitor and analyze companies and industries across global markets and is the ideal tool for benchmarking, peer comparison and navigation. TRBC is the basis for Thomson Reuters sector indices, and is also available for investors and managers looking to build custom sector and thematic indices.",
"homepage": "http://thomsonreuters.com/en/products-services/financial/market-indices/business-classification.html",
"name": "Thomson Reuters Business Classification",
"prefix": "1679",
"wikidata_database": "Q7795893"
},
"168": {
"description": "In order to make sure products are properly and consistently classified, the Global Product Classification is used in the GDSN The GPC provides a common language for all partners involved in the master data exchange to group products in the same way, Improves the integrity and quality of the master data in the GDS network, and reduces language barriers, as the GPC is available in multiple languages, and enables evaluations across different product groups.",
"homepage": "http://www.gs1.ch/gs1-system/das-gs1-system/gdsn/gpc",
"name": "Global Product Classification",
"prefix": "168",
"wikidata_database": "Q731100"
},
"1680": {
"description": "Product classification is simply a logical, unambiguous classification (taxonomy) of products in different product classes (categories), designed so that anyone within the sector can communicate about those products without misunderstandings. The ETIM model gives a listing of the most important technical characteristics of each product class to describe and find the products. Each class has several synonyms, thereby finding the right product is much easier for everyone! (...) Uniform product classification in itself is not a final product as it is. The product classification is also not a software application, product database, product generator or search engine. Those are applications that use the article classification as a basis. The product classification offers the structure for standardised product data that you can exchange in a uniform way via the communication standards and which can be used in numerous applications. (...) With the gradual growth of acceptance of product classification, it is remarkable how trading companies hesitate to participate out of fear of price comparison. They are afraid that the transparency of product information makes it easier to compare product prices. This does contain a grain of truth. On the other hand, this is already possible with current technology and the product price is of course only one of the many selection criteria for a customer. Aspects such as quality, delivery reliability, logistical performance and supplier expertise also play an important role for a customer. A supplier that is capable of providing product information electronically has the preference, because it saves the parties a lot of time and therefore also money.",
"homepage": "http://prod.etim-international.com/class",
"name": "ETIM Classification",
"prefix": "1680",
"wikidata_database": "Q1276102"
},
"1681": {
"description": "DBK was the first bid for a coherent classification system for construction in Denmark and was developed in the period 2003-2006. DBK is a common system for classification of building and building information - developed for the Digital Building. DBK replaces the old SfB system And different industry-oriented or home-based systems. DBK is subsequently replaced by CCS. Classification is necessary to keep track of the many different types of information that is part of a construction project or in connection with building operations. The DBK classification system establishes a basic information structure, a coherent systematics And a common conceptual device that ensures precise communication. At the same time, it identifies any piece of information uniquely, making it easy to retrieve and recognize. It is a crucial prerequisite for digitizing the construction processes - and at the same time provides the basis for developing requirements specifications for development Off i T tools for construction. DBK establishes frameworks to classify all parts of the construction throughout its life cycle - from program to disposal. The system thus classifies not only building parts, buildings and rooms, but also actors, processes, documents, experience and building knowledge information, etc. DBK is also considerably more complex than, for example, SfB, as DBK considers a building component from different aspects or angles. For this reason, DBK operates with a product aspect (what the object consists of), a form aspect (how it looks), a functional aspect (how it is used) and a placement aspect (how it is built).",
"homepage": "https://bips.dk/v%C3%A6rkt%C3%B8jsemne/dbk-klassifikation#0",
"name": "DBK-Classification",
"prefix": "1681"
},
"1682": {
"description": "DK5 is the common setup and classification system for the Danish public and school libraries. The system consists of a systematic overview of subject areas and an alphabetical and a systematic register, respectively. (...) DK5 is an aspect-oriented classification system. The 100 main groups are Subdivided according to the decimal principle. The primary division in the decimal class division takes place according to disciplines and subjects. The structure is in principle hierarchical in both notation and group relations. The aim is that DK5's systematics reflect as much as possible the knowledge universe that is expressed in the current Danish Publicity The objective of timeliness implies that audits can be made in the system and system terminology on an ongoing basis. It must be kept up to date in accordance with professional / social development. However, in a controlled system, there will always be some reversal in the audit work. General level: DK5's specificity Developed to correspond to the need for comminution by the national bibliographic registration of physical materials that are set up according to the system. In other words, the development of the general level of DK5 relates to its function as a setup system.",
"homepage": "http://www.dbc.dk/nationale-opgaver/dk5",
"name": "DK5 Decimal Classification",
"prefix": "1682",
"wikidata_database": "Q12306866"
},
"1683": {
"description": "PeriodO is a gazetteer of scholarly definitions of historical, art-historical, and archaeological periods. It eases the task of linking among datasets that define periods differently. It also helps scholars and students see where period definitions overlap or diverge.",
"homepage": "http://perio.do/",
"name": "PeriodO",
"prefix": "1683"
},
"1684": {
"description": "The Dutch Institute for Sound and Vision has teamed up with some other Dutch organizations operating audiovisual cultural heritage developed the Common Thesaurus for Audiovisual Archives (GTAA). The GTAA is used to efficiently characterize the content of audiovisual material from the archive with labels originated from a controlled and structured list of terms, a thesaurus. the thesaurus will be placed at Sound and mainly used in the manual description process, but also more and more automatic annotation techniques. using linked data principles dressings can also between the private collection, and other sources of data. Each time the GTAA can act as a scaffold and connection means.",
"homepage": "http://gtaa.beeldengeluid.nl/",
"license": "ODBL",
"name": "Common Thesaurus of Audiovisual Archives",
"prefix": "1684",
"wikidata_database": "Q19366588"
},
"1685": {
"description": "Descriptor and Thematic classification: the descriptors are accessible by the index (search screen) and by the thematic classification, which, based on the Dewey Classification, allows to know all the descriptors coming from a specific domain used In Mandragore, some descriptors that can be covered by several domains and gives access to the full description of the descriptor which sometimes contains additional information.",
"homepage": "http://mandragore.bnf.fr/",
"name": "Mandragore Thematic descriptor and classification",
"prefix": "1685"
},
"1686": {
"description": "The TOP-Thesaurus defines standards for a functional approach to plant diversity by stabilizing the terminology for concepts widely used in ecology and evolution. TOP provides names, definitions, formal units and synonyms for more than 700 plant features: plant traits, environmental preferences and spatial distribution. TOP can be searched via: FACETED SEARCH, filtering the available information by grouping terms into facets; HIERARCHY SEARCH, providing a tree that progressively unfolds; INDEX, a complete alphabetical list of all concepts defined in TOP. Regular updates of the TOP-Thesaurus are planned based on community involvement.",
"homepage": "http://top-thesaurus.org/",
"name": "TOP-Thesaurus",
"prefix": "1686"
},
"1688": {
"description": "The growing availability of data on the Web provided by Web 2.0 applications and, more recently through Linked Data, brought the computational pattern expressed as ETL to reemerge in a scenario with additional complexity, where the number of data sources and the data heterogeneity that needs to be supported by ETL drastically increases. In this scenario, issues with data quality and trustworthiness may strongly impact the data utility for end-users. The barriers involved in building an ETL infrastructure under the complexity and scale of the available Web-based data supply scenario, demands the deο¬nition of strategies which can provide data quality warranties and also minimize the effort associated with data management.\n\nIn this context, provenance, the representation of artifacts, processes and agents behind a piece of information, becomes a fundamental element of the data infrastructure. Provenance have a large spectrum of applications including documentation & reproducibility and data quality assessment & trustworthiness and consistency-checking & semantic reconciliation. However, in an environment where data is produced and consumed by different systems, the representation of provenance should be made interoperable across systems.\n\nStandardization eο¬orts towards the convergence into a common provenance model generated the Open Provenance Model (OPM). OPM provides a basic description of provenance which allows interoperability on the level of workο¬ow structure. The deο¬nition of this common provenance ground allows systems with different provenance representations to share at least a workο¬ow-level semantics (the causal dependencies between artifacts, processes and the intervention of agents). OPM, however, is not intended to be a complete provenance model, but demands the complementary use of additional provenance models in order to enable uses of provenance which requires higher level of semantic interoperability.\n\nCogs is an ETL Provenance Vocabulary which extends the workflow semantics provided by OPM and Prov-O, allowing the description of ETL processes and objects. The Cogs vocabulary can be used to describe data transformations in general, outside the scope of ETL tools and practices. The core objective of the vocabulary is to improve the level of semantic interoperability of data transformation provenance descriptors, building upon the OPM and Prov-O standardization efforts.",
"homepage": "http://vocab.deri.ie/cogs",
"name": "COGS",
"prefix": "1688"
},
"1689": {
"description": "orca, the Ontology of Reasoning, Certainty and Attribution, is an ontology for characterizing the certainty of information, how it is known, and its source.",
"homepage": "http://vocab.deri.ie/orca",
"name": "orca",
"prefix": "1689"
},
"169": {
"description": "If you want to search for documents on a particular topic but you have not found it by browsing the thesaurus, try to find it via the search by terms. Simply enter the term or search terms and the search is then performed only on the thesaurus. More than 38,000 terms",
"homepage": "http://www.cocof-cbdp.irisnet.be/opac_css/index.php",
"name": "Brussels Center for Educational Documentation Thesaurus",
"prefix": "169"
},
"1690": {
"description": "There are many situations where it would be useful to be able to publish multi-dimensional data, such as statistics, on the web in such a way that it can be linked to related data sets and concepts. The Data Cube vocabulary provides a means to do this using the W3C RDF (Resource Description Framework) standard. The model underpinning the Data Cube vocabulary is compatible with the cube model that underlies SDMX (Statistical Data and Metadata eXchange), an ISO standard for exchanging and sharing statistical data and metadata among organizations. The Data Cube vocabulary is a core foundation which supports extension vocabularies to enable publication of other aspects of statistical data flows or other multi-dimensional data sets.",
"homepage": "http://www.w3.org/TR/vocab-data-cube/",
"name": "Data Cube Vocabulary",
"prefix": "1690"
},
"1691": {
"description": "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web.",
"homepage": "http://www.w3.org/ns/dcat",
"name": "Data Catalog Vocabulary",
"prefix": "1691",
"wikidata_database": "Q16892890"
},
"1692": {
"description": "The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID.",
"homepage": "https://www.w3.org/TR/void/",
"name": "Vocabulary of Interlinked Datasets",
"prefix": "1692",
"wikidata_database": "Q7939443"
},
"1693": {
"description": "SLUA (Semantically Linked Users and Actions) ontology aims to model users and tasks in crowdsourcing systems in terms of the human factors such as actions, capabilities, and rewards.",
"homepage": "http://vocab.deri.ie/slua",
"name": "Semantically Linked Users and Actions",
"prefix": "1693"
},
"1694": {
"description": "A controlled vocabulary for instruments that can be used to populate Marine Community Profile metadata. The vocabulary will be used by the faceted search facility in the AODN/IMOS Portal 1-2-3.",
"homepage": "https://vocabs.ands.org.au/aodn-instrument-vocabulary",
"name": "AODN Instrument Vocabulary",
"prefix": "1694"
},
"1695": {
"description": "Controlled vocabulary of Norwegian terms with Universal Decimal Classification numbers; library metadata from the Norwegian University of Science and Technology.",
"homepage": "http://datahub.io/dataset/tekord",
"license": "CC0-1.0",
"name": "Tekord",
"prefix": "1695",
"wikidata_database": "Q24254677"
},
"1696": {
"description": "Realfagstermer is a multilingual, controlled vocabulary of pre-coordinated subject headings which mainly covers the physical sciences, mathematics and computer science. It is maintained by the University of Oslo Science Library in collaboration with the University of Bergen Science Library, and covers mainly the physical sciences, mathematics and computer science. As of January 2015, the vocabulary consists of approximately 15 000 single concept headings, and about 16 000 compound headings (\"subject strings\"), published as open data for everyone to use freely.",
"license": "CC0-1.0",
"name": "Science subject terms",
"prefix": "1696",
"wikidata_database": "Q22927024"
},
"1697": {
"description": "The Climate Tagger is backed by the expansive Climate Compatible Development Thesaurus, a vast catalogue of specialized terminology, including mapped links to synonyms and related terms, in five languages and across a range of sectors relevant for climate compatible development. REEEP began compiling the Climate Compatible Development Thesaurus (or Climate Thesaurus) in 2011 (...). The Climate Thesaurus is regularly updated and expanded to additional areas and languages, and can be targeted to incorporate specific sectors on an as-needed basis. Updates to the Climate Thesaurus are automatically integrated into systems using Climate Tagger.",
"name": "REEEP Climate Smart Thesaurus",
"prefix": "1697"
},
"1698": {
"description": "The importance of e-business and electronic data has never been as important as today, regardless of whether it is a marketplace on the Internet, an eProcurement system, a shop or catalog creation software - every participant at PVH uses electronic data almost every day, (...) The consequences of this lack of standardization: Just about every data delivery has to be controlled manually and adapted to almost everyone And the classification standard proficl @ ss, which has been developed in 2003 and has since then been regularly updated, makes this unevenness and the associated handling problems in the PVH ultimately a thing of the past, because all relevant information, eg technical product data, pictures, short - and Langtexte to de N individual products, can be transferred without a layout and imported into the database by the data receiver (customer, dealer, Internet marketplace).",
"homepage": "http://www.proficlass.de/front_content.php?idcat=6",
"name": "Classification proficl @ ss",
"prefix": "1698"
},
"1699": {
"description": "The purpose of this classification is to organize media of all kinds, which is of interest to the topic of\" digital library \", but the scope of application is not restricted to virtual or digital libraries, but conventional libraries can also use this classification without problems. ) The classification is intended to fully meet the needs of specialized libraries, and has been designed to be linked to already established universal classifications, in order to subdivide the topic of 'digital library'.\n\nThe compatibility with the Dewey Decimal Classification was emphasized (...). Therefore: it is hierarchical, reflects this hierarchy in the notation and has a purely numeric notation.",
"homepage": "http://fkdigbib.de/",
"name": "Classification Digital Library",
"prefix": "1699",
"wikidata_database": "Q26903363"
},
"17": {
"description": "The Government of Canada Core Subject Thesaurus is a bilingual thesaurus consisting of terminology which represents all the fields treated in information resources of the Government of Canada. It contains 4,801 terms in English and 4,868 in French, including 2,180 preferred terms in each language. All fields of knowledge are represented in the thesaurus, to varying degrees. Because of the great variety of subjects covered by the thesaurus, its terminology is rather general. By design, it does not include specialized terminology used in specific and limited disciplines.\n\nThe tool is primarily intended for content managers, librarians, indexers and metadata developers in federal departments and agencies who must select controlled subject terms to index Government of Canada Web resources. In the Treasury Board Standard on Metadata, the Government of Canada Core Subject Thesaurus is identified as the preferred source of controlled vocabulary for that purpose. Using the CST will help to reduce the duplication of effort in creating a variety of controlled vocabularies in the Government of Canada, as well as increase the interoperability of government web sites.",
"homepage": "http://www.thesaurus.gc.ca/recherche-search/thes-eng.html",
"name": "Government of Canada Core Subject Thesaurus",
"prefix": "17"
},
"170": {
"description": "Surface Water Classifications are designations applied to surface water bodies, such as streams, rivers and lakes, which define the best uses to be protected within these waters (for example swimming, fishing, drinking water supply) and carry with them an associated set of water quality standards to protect those uses. Surface water classifications are one tool that state and federal agencies use to manage and protect all streams, rivers, lakes, and other surface waters in North Carolina. Classifications and their associated protection rules may be designed to protect water quality, fish and wildlife, or other special characteristics. Each classification has associated standards that are used to determine if the designated uses are being protected.",
"homepage": "http://deq.nc.gov/about/divisions/water-resources/planning/classification-standards/classifications",
"name": "Surface Water Classifications",
"prefix": "170"
},
"1700": {
"description": "Index terms are a key part of AGU's strategy for categorizing and electronic distribution of journal articles, books, meeting abstracts, and e-mail alerts. They are used in database searches, in subject indices, and in identifying articles for inclusion in AGU Personal Choice journals.",
"name": "AGU Index Terms",
"prefix": "1700"
},
"1701": {
"description": "This controlled vocabulary covers parameter terms and their descriptions. It can be used for marking up Marine Community Profile metadata and a classified version of the terms is used to control faceted searching in the AODN/IMOS portal.",
"homepage": "https://vocabs.ands.org.au/aodn-discovery-parameter-vocabulary",
"name": "AODN Discovery Parameter Vocabulary",
"prefix": "1701"
},
"1702": {
"description": "Metis is a flexible, intuitive and child-friendly system of library categorization. It uses whole language, visual cues, and logic that reflects children's own experiences. It puts the child in the center of his or her own search. Our decision to create Metis is a result of our progressive approach to education and the library. The system isn't a cut-down version of adult thinking. Kids feel empowered to navigate the library because it is organized in a way that they understand. Metis increases the success rate of finding books, which fosters self-reliance and produces joyous discovery. We have named the system in honor of the crafty Titan who is the mother of Athena and the eternal source of good advice for Zeus.",
"homepage": "http://metisinnovations.com/",
"name": "Metis Classification",
"prefix": "1702",
"wikidata_database": "Q17154345"
},
"1703": {
"description": "The Cairo Gazetteer is a tool for the identification and indexing of documentary collections relating to Cairo's monuments, which raise difficulties of treatment because of the many variants resulting from the transliteration into Latin characters of Arabic toponyms. The form of a concordance table which lists the orthographic variants of the names of the monuments, this trilingual reference frame (French, Arabic, English), in SKOS format, identifies, describes and locates the 600 classified buildings in Cairo.",
"homepage": "http://cairogazetteer.fr/invisu/page/ark:/67717/b8b2b220-4f23-4d81-95d0-dbce50dde2c6",
"license": "CC-BY-3.0",
"prefix": "1703"
},
"1704": {
"description": "The Strokesaurus is a thesaurus from the National Stroke Foundation.",
"homepage": "https://enableme.org.au/strokesaurus",
"name": "Strokesaurus",
"prefix": "1704"
},
"1705": {
"description": "The ISPE Glossary of Pharmaceutical and Biotechnology Terminology is the result of many years of gathering material from sources such as scientific journals, industrial magazines, professional organizations, the world wide web, industry seminars, company guides, vendor and manufacturer information, national and international codes, and diverse individuals. This compilation of abbreviations, acronyms, and terminology is a reference for engineers, designers, technicians, owners, contractors, and others in the pharmaceutical and biopharmaceutical industries. It includes terms used in water treatment, welding, metallurgy, medicine, biology, chemistry, computer technology, manufacturing processes, HVAC, etc.",
"homepage": "http://www.ispe.org/glossary",
"name": "ISPE Glossary of Pharmaceutical and Biotechnology Terminology",
"prefix": "1705"
},
"1706": {
"description": "Glossary about the topic Open Data by Open Knowledge International.",
"homepage": "http://opendatahandbook.org/glossary/",
"license": "CC-BY-3.0",
"name": "Open Data Handbook Glossary",
"prefix": "1706"
},
"1707": {
"abbreviation": "ULBB",
"description": "βThe entire Romance Studies Collection of the Bonn USL is indexed according to a special classification system (more than 250,000 titles).",
"license": "CC0-1.0",
"name": "Classification for Romance Studies of the Bonn University and State Library",
"prefix": "1707"
},
"1708": {
"abbreviation": "FBUP",
"description": "The 'Fachsystematik BΓΌcher' of the University Library of Paderborn (UB) serves as a layout for the creation of the book inventory in the freehand areas of the UB. Since it is possible to search in the catalog for individual 'system sites' of the Fachsystematik, it offers one of several possibilities of the Factual research on the stock of printed books in the UB.\n\nThe subject system is based on the 'Gesamt-Hochschul-Bibliotheks-Systematik' (GHBS), which (...) was further developed by the libraries together with the Hochschulbibliothekszentrum in KΓΆln (hbz). This cooperative further development was carried out on the basis of a majority decision of the o.g. Libraries in October 2004. In essence, this decision was based on the fact that the systematics of the individual libraries had evolved significantly over time, despite the commitment to the co-operative part of the care, and that a common approach to the revision required in some areas was not appropriate. Since autumn 2004, the UB Paderborn has continually been adapting its 'Fachsystematik BΓΌcher' to the development of science in general and the teaching and research foci of the University of Paderborn in particular. It has, inter alia, Two fundamental aspects: on the one hand, in the case of adaptations, it is necessary to maintain the character of specialist systematics as a \"pragmatic universal regulation\" which takes into account all scientific disciplines. On the other hand, changes have to be critically examined under cost-benefit aspects in each individual case, as they are usually associated with very personnel-intensive workflows.\n\nIn total there are 35 individual systems. Each individual system has a number assigned to it in ascending line from 01 to 04, 07, etc. to 94, which also represents the layout scheme when the journals are drawn up. The compartment numbers or the notation from three to four uppercase letters of the individual system locations are part of the signature system of the UB. The subject system is an enumerative system. The notation range is from AAA to ZZZZ (three- or four-letter code). This framework has not been fully exploited so that there are limited and limited quotation quotas within and between individual systems.\n\nIf the individual systems are compared with one another, subject systems such as 'other philologies' and 'other fields of technology' are excluded, since they do not concern a single subject by name. Rather, they are a summary of several disciplines. The subject system 'Authors' Humanities' also stands out from the other individual subject systems; It is not primarily organized according to factual criteria, but first of all arranged in a very coherent chronology (antiquity, medieval and modern times), and on the second level of organization alphabetically according to the names of authors from the field of humanities.\n\nIn addition to the system locations, the subject system also contains references (as 'See-Referral' or 'See-Referral'); It can be referred to points within the same subject system as well as to other individual systematics. In the case of the latter, the abbreviated name of this subject system is also indicated for quick orientation. The abbreviated name usually consists of the three initial letters of the subject systematics and can be seen from the table of contents.",
"homepage": "https://data.ub.uni-paderborn.de/fachsystematik/",
"name": "Subject Taxonomy Books University Library Paderborn",
"prefix": "1708"
},
"1709": {
"description": "The first section is an alphabetical arrangement of keyword terms. In this section the first 6 digits represent the code number, and the next 2 digits indicate the category in the hierarchical section of the Thesaurus. Digits are followed on the same line by corresponding keywords. The first word is the coded keyword term or concept, followed by a slash //, which separates the coded work from its next hierarchical level. (One, two, or three level hierarchical arrangement.)\n\nThe second section is the hierarchical arrangement of the coded terms. It is divided into 10 categories. Each category has up to 3 levels of keyword terms or concepts, each level intended from the preceding level and preceded by a code number.",
"homepage": "http://hdl.handle.net/2027/umn.31951002847366c",
"name": "Animal Disease Thesaurus",
"prefix": "1709"
},
"171": {
"description": "The fund is mainly focused on the pedagogy of adults with low knowledge.",
"homepage": "http://www.illettrisme.org/ressources-documentaires/au-centre-de-documentation/thesaurus",
"license": "CC BY-NC-SA 3.0",
"name": "Center Ressources Illettrisme Provence-Alpes-CΓ΄te d'Azur Thesaurus",
"prefix": "171"
},
"1710": {
"description": "An AODN controlled vocabulary describing organisation categories for classifying organisational entities.",
"homepage": "https://vocabs.ands.org.au/aodn-organisation-category-vocabulary",
"name": "AODN Organisation Category Vocabulary",
"prefix": "1710"
},
"1711": {
"description": "Folklorists also use motif to refer to the recognizable and consistently repeated story elements (e.g., common characters, objects, actions, and events) that are used in the traditional plot structures, or tale types, of many stories and folktales. These motifs, which Dr. Margaret Read Macdonald calls 'each small part of a tale,' (.) were indexed in 1932 by Stith Thompson and published as the Motif-lndex of Folk-Literature. (.) Thompson built upon the research of Antti Aarne (and the tale type index he created) when he compiled, classified, and numbered the traditional motifs of the mostly European folktale types in Aarneβs index and then cross referenced those motifs with Aarneβs tale types (Dundes). (.) Folklorist Alan Dundes explains that Stith Thompsonβs 'six-volume Motif-Index of Folk-Literature and the Aarne-Thompson tale type index constitute two of the most valuable tools in the professional folklorist's arsenal of aids for analysis'.",
"homepage": "https://sites.ualberta.ca/~urban/Projects/English/Motif_Index.htm",
"name": "Motif-Index of Folk-Literature",
"prefix": "1711",
"wikidata_database": "Q19062048"
},
"1712": {
"description": "In 'The Types of International Folktales', the 'ATU Catalogue' edited by Hans-JΓΆrg Uther (2004), ATU numbers replace AT numbers. And ATU (from the surname initials of Aarne, Thompson, and Uther) allows 'the type numbers that have been in use for nearly one hundred years [to] remain unchanged,' says Uther. To allow that and to accomplish that are two different things, though, for at least one Norwegian folktale that is well over a hundred years, is missing completely in the new ATU system. Its old AT number (211*) has disappeared.\n\nAnother side to the revision is that the overall content of various types of tales has been changed, in both small ways and more comprehensively. And such changes mean that old 'AT umbrellas' (numbers) for the types of tales, do not serve as well as before as classification devices in every case, for example in many Norwegian folktales I have checked and commented on in Norwegian. (.) However, the new ATU-types are now the classification devices in force.",
"name": "ATU Types of Folktales",
"prefix": "1712",
"wikidata_database": "Q301545"
},
"172": {
"description": "OCIS provides a flexible, comprehensive classification system for all optical author input and user retrieval needs. OCIS has a two-level hierarchical structure containing 36 main headers and approximately 1100 subcategories. OSA authors, presenters, and reviewers use OCIS to classify and index journal articles, meeting abstracts and presentations, and areas of research interest and expertise.",
"homepage": "http://www.opticsinfobase.org/submit/ocis/",
"name": "Optics Classification and Indexing Scheme",
"prefix": "172",
"wikidata_database": "Q7098917"
},
"173": {
"description": "DISCO, the European Dictionary of Skills and Competences, is an online thesaurus that currently covers more than 90,000 skills and competence terms and approximately 8,000 example phrases. Available in ten European languages, DISCO is one of the largest collections of its kind in the education and labour market. The DISCO Thesaurus offers a multilingual and peer-reviewed terminology for the classification, description and translation of skills and competences. It is compatible with European tools such as Europass, ESCO, EQF, and ECVET, and supports the international comparability of skills and competences in applications such as personal CVs and e-portfolios, job advertisements and matching, and qualification and learning outcome descriptions.",
"homepage": "http://disco-tools.eu/disco2_portal/",
"prefix": "173"
},
"174": {
"description": "This service provides ca. 300,000 precise definitions for types of product or services that extend the schema.org and GoodRelations standards for e-commerce markup. You can use this ontology to describe any object for which a matching entry in the English Wikipedia exists. Thanks to the many links between the multiple language editions of Wikipedia, you can search for the best class in your favorite language, e.g. in the German or Italian Wikipedia, and then click on the English translation on the left-hand side to get to the matching page in the English Wikipedia.",
"homepage": "http://www.productontology.org/",
"name": "Product Types Ontology",
"prefix": "174"
},
"1743": {
"description": "Roget's Thesaurus is composed of six primary classes. (...) Each class is composed of multiple divisions and then sections. This may be conceptualized as a tree containing over a thousand branches for individual 'meaning clusters' or semantically linked words. Although these words are not strictly synonyms, they can be viewed as colours or connotations of a meaning or as a spectrum of a concept. One of the most general words is chosen to typify the spectrum as its headword, which labels the whole group.\n\nRoget's schema of classes and their subdivisions is based on the philosophical work of Leibniz (...), itself following a long tradition of epistemological work starting with Aristotle. Some of Aristotle's Categories are included in Roget's first class 'abstract relations'.",
"name": "Roget's Thesaurus",
"prefix": "1743",
"wikidata_database": "Q1636316"
},
"1748": {
"name": "NEBIS Subject Index",
"prefix": "1748"
},
"175": {
"description": "The Saffir-Simpson Hurricane Wind Scale is a 1 to 5 rating based on a hurricane's sustained wind speed. This scale estimates potential property damage. Hurricanes reaching Category 3 and higher are considered major hurricanes because of their potential for significant loss of life and damage. Category 1 and 2 storms are still dangerous, however, and require preventative measures. In the western North Pacific, the term 'super typhoon' is used for tropical cyclones with sustained winds exceeding 150 mph.",
"homepage": "http://www.nhc.noaa.gov/aboutsshws.php",
"name": "Saffir-Simpson Hurricane Wind Scale",
"prefix": "175",
"wikidata_database": "Q205801"
},
"1750": {
"description": "The Gazetteer provides an exhaustive Place Name Index to Great Britain, containing over 50,000 entries. It lists the historic county and the main administrative areas in which each place lies. It forms a valuable resource for those working in the media, tourism, heritage, publishing or education. It is also of great value for local and family historians.",
"name": "Gazetteer of British Place Names",
"prefix": "1750"
},
"1751": {
"description": "The SSC is based solely on surface based observations at an individual station. Four-times daily observations of temperature, dew point, wind, pressure, and cloud cover are incorporated into the model. It does not take upper-level conditions into account, and does not concern itself with the origin of the air above a station, though there are obvious correlations. Hence, the SSC is most properly called a weather type classification and not an air mass classification system.\n\n Within the SSC scheme, weather-type characteristics change from station to station and day to day. Thus, a Moist Tropical weather type is hotter and more humid in the southeastern US, nearer its source region, than in the northeastern US, after it has modified somewhat. Similarly, MT is warmer at all locations in July than in January. (...)\n\n On this website, SSC 'calendars' are available for nearly 400 stations across the US, Canada, and parts of Europe. The European calendars are limited to 1974-2000, but the US and Canadian calendars generally cover a station's total period of record. A total of over 8,000,000 days have been classified across all of these stations. The SSC is also being continually updated - you can see yesterday's (preliminary) classifications and today's and tomorrow's forecast classifications as well. The 'official' SSC calendar for a year will be added to this site within a couple of months of the calendar year's end.",
"homepage": "http://sheridan.geog.kent.edu/ssc.html",
"name": "Spatial Synoptic Classification",
"prefix": "1751",
"wikidata_database": "Q7574047"
},
"1754": {
"description": "The EMA (European Medicines Agency) provides information on the linguistic aspects of the product information for a medicine, which includes the summary of product characteristics, labelling and package leaflet. It explains the content that should be included in these documents, as well as standard headings and the most commonly used standard statements and terms in all official European Union languages plus Icelandic and Norwegian, and defines the format and layout for the product information.\n\nThe European Medicines Agency has developed these templates and glossaries to provide applicants with practical advice on how to draw up the product information. The glossaries were created by manually processing these documents.",
"homepage": "http://www.ema.europa.eu/docs/en_GB/document_library/Regulatory_and_procedural_guideline/2009/10/WC500004445.pdf",
"name": "EMA Templates β Names of EU-EEA countries",
"prefix": "1754"
},
"1756": {
"abbreviation": "SAO",
"description": "Swedish subject headings (SAO) is a controlled subject headings system containing 38 000 terms from all disciplines. The system has been around since 2000 and is used by most university libraries and many LIBRIS libraries. In Swedish subject headings, you can find subject headings to search library catalogs and other databases, and to index the literature and other materials.",
"homepage": "http://www.kb.se/katalogisering/Svenska-amnesord/",
"name": "Swedish Subject Headings",
"prefix": "1756",
"wikidata_database": "Q24262283"
},
"1757": {
"description": "The SMGloM is a structured terminology for mathematics. It combines lexical information about the 'Words of Mathematics' (in multiple languages) with semantic information about their dependencies. Multiple services can be derived from this terminology, e.g. a classical glossary and a math dictionary.",
"homepage": "https://mathhub.info/mh/glossary",
"name": "SMGloM",
"prefix": "1757"
},
"1758": {
"description": "The Aquo-lex provides a\" default language \"that aims to prevent speech confusion between people and / or information systems. Errors that occur in data exchange often arise because of differences in meaning. Aquo-lex, the\" water dictionary \", contains approximately 7500 definitions for terms. The use of terms from Aquo lex and the corresponding definitions lead to better data exchange.\n\nThe Aquo lex can be used in the following ways:\n\nΒ Β Β Β 1. When compiling a report, use the terms as included in Aquo lex so that the reader of your report can find out what the term is.\n\nΒ Β Β Β 2. When designing an information system, use the user interface and database terms that match the definitions in Aquo lex.\n\nΒ Β Β Β 3. In addition, you can also search for the definition of a domain value in Aquo lex (for example, you can check which individual parameters a sum parameter is built up).\n\nYou can consult the Aquo lex using the Aquo LOC tool (Aquo Lex and Object Catalog). In Aquo LOC, you can easily find terms and place them in their context, because the relationships between the terms are also displayed. For example, if you are looking for the term bridge, you will see in the Aquo OC next to the bridge definition that the bridge is a work of art and distinguishes between a fixed and a movable bridge. In addition, Aquo LOC offers the possibility to directly refer to the data.",
"homepage": "http://www.aquolex.nl/",
"name": "Aquo-lex",
"prefix": "1758"
},
"1759": {
"name": "International Thesaurus of Gay and Lesbian Index Terms",
"prefix": "1759"
},
"176": {
"description": "The A-Z of terms is the controlled vocabulary developed and maintained by the Department for Education. It was first developed in the 1980s and has been continually updated to reflect new topics and departmental responsibilities. It groups terms together so that when you search you can see the term that you are looking for in the context of other terms in the vocabulary - this helps you to browse for information. Terms are listed with all their relationships, plus a scope note (to help define a term and explain how it should be used) where necessary. This controlled vocabulary is used to tag content added to this website, so that when you look for terms through the A-Z of terms, you will also find the relevant content that has been assigned to those categories.",
"homepage": "http://webarchive.nationalarchives.gov.uk/20130123124929/http://www.education.gov.uk/vocabularies/educationtermsandtags",
"name": "Education terms",
"prefix": "176"
},
"1760": {
"description": "The language of standard indexing and classification systems-terms used in most journals, libraries, filing systems, and databases-does not offer vocabulary consistently or sufficiently detailed and up-to-date to retrieve the wealth of resources available. Existing classifications frequently overlook emerging topics of special concern to women. As a result, important information is lumped under 'women' or is inaccessible. Prefixes and suffixes attached to terminology ostensibly gender neutral reflect implicitly male norms and define women in terms of their relationships to men (labels like \"nontraditional employment\" or \"unwed mothers\"). Worse, by juxtaposition, indexing systems condition our response to important topics. Grouping lesbian issues and prostitution in categories of sexuality, for example, skews complex social, political, and personal concerns. --This text refers to an out of print or unavailable edition of this title.",
"name": "A Women's Thesaurus",
"prefix": "1760"
},
"1761": {
"description": "This is an International Thesaurus of Lesbian, Gay, Bisexual and Transgender Index Terms that is currently used by https://www.digitaltransgenderarchive.net.\n\nThis vocabulary was originally a project of the International Homo/Lesbian Informatiecentre & Archives and compiled by Jack van der Wel (with support of Ellen Greenblatt) in 2013. That offline document has been transcrabed into the Linked Data provider under development here.",
"homepage": "http://homosaurus.org/",
"prefix": "1761",
"wikidata_database": "Q26936735"
},
"1763": {
"description": "CONTENT\n\nALPHABETICAL LIST OF TERMS\n\nabbreviations meaning\n\nList of genres of audiovisual material\n\nHierarchical view of the special book form\n\nRegister of preferred terms",
"homepage": "https://www.kb.nl/sites/default/files/docs/genrethesaurus-hoofddeel.pdf",
"name": "Genre Thesaurus for the opening of store collections of children's books",
"prefix": "1763"
},
"1764": {
"name": "Glossary feminine terminology",
"prefix": "1764"
},
"1765": {
"description": "As learning progresses it becomes more complex. SOLO, which stands for the Structure of the Observed Learning Outcome, is a means of classifying learning outcomes in terms of their complexity, enabling us to assess studentsβ work in terms of its quality not of how many bits of this and of that they got right. At first we pick up only one or few aspects of the task (unistructural), then several aspects but they are unrelated (multistructural), then we learn how to integrate them into a whole (relational), and finally, we are able to generalised that whole to as yet untaught applications (extended abstract). The diagram lists verbs typical of each such level.\n\nSOLO can be used not only in assessment, but in designing the curriculum in terms of the learning outcomes intended, which is helpful in implementing constructive alignment. SOLO can also explain why those who use low complexity arguments in political or marital disputes usually win β in the short term. But in politics thatβs all you need.",
"homepage": "http://www.johnbiggs.com.au/academic/solo-taxonomy/",
"prefix": "1765"
},
"17656": {
"description": "This glossary was born of the need to expand the repertoires terminographic about contemporary art that included the galician as a working language. Today, art is to acquire a big push in India, mainly thanks to the activity of new museums, galleries and exhibition halls that show the work of younger artists or innovative on the international scene. however, translators and professionals working with texts on contemporary art are an empty terminogrΓ‘fico when seeking upgraded features that help them to the translation of texts and to include the concepts modern, possibly adapted to the new regulations galician 2003.",
"homepage": "http://sli.webs.uvigo.es/arquivos/Glosario_da_Arte_en_gl_es.pdf",
"name": "Glossary of Contemporary Art",
"prefix": "17656"
},
"1766": {
"description": "Bloom's taxonomy is a way of distinguishing the fundamental questions within the education system. It is named after Benjamin Bloom, who chaired the committee of educators that devised the taxonomy. He also edited the first volume of the standard text, Taxonomy of Educational Objectives: The Classification of Educational Goals. (...) Although named after Bloom, the publication of Taxonomy of Educational Objectives followed a series of conferences from 1949 to 1953, which were designed to improve communication between educators on the design of curricula and examinations. (...)\n\nThe first volume of the taxonomy, Handbook I: Cognitive (Bloom et al. 1956) was published in 1956. \"Handbook II: Affective\" (Krathwohl, Bloom & Masia 1965)Simpson (1966), Harrow (1972) and Dave (1975). (...) A revised version of the taxonomy for the cognitive domain was created in 2000. (...) Bloomβs taxonomy serves as the backbone of many teaching philosophies, in particular those that lean more towards skills rather than content. (...) These educators would view content as a vessel for teaching skills. The emphasis on higher-order thinking inherent in such philosophies is based on the top levels of the taxonomy including analysis, evaluation, synthesis and creation. Bloomβs taxonomy can be used as a teaching tool to help balance assessment and evaluative questions in class, assignments and texts to ensure all orders of thinking are exercised in studentβs learning.",
"license": "CC BY-NC 3.0",
"name": "Bloom's Taxonomy",
"prefix": "1766",
"wikidata_database": "Q1774565"
},
"17662": {
"description": "Glossary of Financial Terms by Klosterman, Kane & Company, LLP - Certified Public Accountants",
"homepage": "http://www.rk-cpa.com/glossary.php",
"name": "Financial Terms Glossary",
"prefix": "17662"
},
"1767": {
"description": "The CDISC Glossary (...) defines terms commonly used in clinical research (including acronyms, abbreviations, and initials). The Glossary serves the community of clinical researchers by selecting and defining terms pertaining to clinical research, particularly eClinical investigations, sponsored by the pharmaceutical industry or a federal agency. Note this CDISC Glossary is NOT comprehensive for all words bearing on human health, medicine, or laboratory methods.\n\nThe Glossary includes references and links to other glossaries such as regulatory dictionaries and to health-related controlled terminologies known to be useful in conducting clinical research, including the CDISC Terminology Project. Glossary terms are organized alphabetically, by first word, according to the opinion of the Glossary Project Team concerning most common usage in clinical research. Thus 'source document verification' would appear under 'source', not 'verification'. The Glossary follows the practice of preceding certain terms with the letter 'e' to denote that they pertain to electronic or Web implementation.",
"homepage": "http://www.cdisc.org/cdisc-glossary",
"name": "CDISC Clinical Research Glossary",
"prefix": "1767"
},
"17678": {
"description": "Formerly titled A Glossary of House-Building and Site-Development Terms, this invaluable reference text has been used for three decades by people in the housing industry and by university and college students enrolled in construction-related education programs. Completely revised, this comprehensive, up-to-date glossary incorporates more than 300 new definitions to reflect current construction terminology.",
"name": "Glossary of Housing Terms",
"prefix": "17678"
},
"1768": {
"description": "Bureau Metadata Encoding Scheme used for web page 'Subject'.",
"homepage": "http://www.bom.gov.au/meta/word_lists/bom_subject_thesaurus.shtml",
"license": "CC-BY-3.0",
"name": "Bureau of Meteorology Subject Thesaurus",
"prefix": "1768"
},
"17682": {
"description": "Glossary about Vision-Related Terminology by VisionAware.\n\n\"VisionAware helps adults who are losing their sight continue to live full and independent lives by providing timely information, step-by-step daily living techniques, a directory of national and local services, and a supportive online community.",
"homepage": "http://www.visionaware.org/info/your-eye-condition/glossary-of-vision-related-terminology/12",
"name": "Glossary of Vision-Related Terminology",
"prefix": "17682"
},
"17688": {
"homepage": "http://www.armstrong.com/commceilingsna/acoustic-performance-glossary.html",
"name": "Acoustical Performance Terms",
"prefix": "17688"
},
"17689": {
"description": "A furniture glossary by Furniture Row",
"homepage": "http://www.furniturerow.com/fr/furniture-glossary/",
"name": "Furniture GlossaryΒ",
"prefix": "17689"
},
"1769": {
"description": "The terms and definitions found in this glossary relate to the science of meteorology.",
"homepage": "http://www.bom.gov.au/lam/glossary/",
"license": "CC-BY-3.0",
"name": "Bureau of Meteorology Glossary",
"prefix": "1769"
},
"17693": {
"homepage": "http://www.brown.edu/Departments/Joukowsky_Institute/courses/greekpast/4033.html",
"name": "Glossary of Key Terms",
"prefix": "17693"
},
"177": {
"description": "The environmental classification serves the content development of objects (literature, R & D projects / legislation, ...) in the interdisciplinary thematic area 'Environment', which makes it possible to assign them to specific environmental topics, thus facilitating an accurate yet comprehensive (re- ) This classification is usually presented as a meta-information in directories about the storage location of the objects (eg databases, library catalogs) For clarification, the classification can be imagined as a group of 14 columns that symbolize the environmental areas (Eg, LU11, WA54), which in principle are the same in all areas of the environment (columns). The columns are subdivided into seven slices (layers) into groups of 10 (from 10 to 70) Significance (Exceptions are the environmental areas UR = 'environmental law' and UA = 'general and over Environmental issues'). In particular, this consistently uniform slicing is intended to facilitate the assertion of environmental classification and thus its application. The actual classification takes place at the level of these discs (= environmental classes).",
"homepage": "http://elise.bafg.de/servlet/is/1768/Klassifikationend83b.html?command=downloadContent&filename=Klassifikationen.htm",
"name": "Environmental Classification",
"prefix": "177"
},
"1770": {
"description": "The BGS Geoscience Thesaurus contains approximately 6000 descriptor terms for concepts in the geoscience and related subjects. Some entries have scope notes to further explain the term. The original source of the data was the Australian Mineral Foundation thesaurus of geoscience; some terms have been added or updated to suit BGS needs and the content will continue to be updated as required. The thesaurus includes synonyms to descriptor terms, hierarchical relationships, symmetric (see also) relationships and lapsed (deprecated) term replacements.",
"homepage": "http://www.bgs.ac.uk/discoverymetadata/13603129.html",
"name": "BGS Geoscience Thesaurus",
"prefix": "1770"
},
"17703": {
"description": "Verbal conjugation or verbal inflection is the set of forms of a verb according to the categories of person, number, time, aspect, mode, voice, etc. (although not all languages in the world include all these categories, The French verbs are classified in three conjugations (in French: conjugaisons), but they also exist in the French verb conjugations, Many irregular verbs (almost all located in the 3rd group), of which avoir, Γͺtre and faire are the most used.",
"homepage": "http://glosarios.servidor-alicante.com/conjugacion-verbal-francesa_fr-es",
"name": "Glossary of French verbal conjugation",
"prefix": "17703"
},
"17704": {
"description": "The glossary with the automotive terms by the editorial team of Motori.it.",
"homepage": "http://www.motori.it/glossario/",
"name": "Glossary of the car",
"prefix": "17704"
},
"17705": {
"description": "This dictionary has been intentionally limited in scope to military subject matter and directly related fields. It has been compiled primarily for use by American military personnel with at least a fair knowledge of German.",
"homepage": "http://www.talpo.it/files/-tm-30-506-20-may-1944-german-military-dictionary-german-english-english-german.pdf",
"prefix": "17705"
},
"17706": {
"description": "Il glossario Γ¨ stato ricavato mediante fusione di diverse fonti, le cui rispettive voci rimangono riconoscibili mediante i colori associati:\n\nUTi dictionary - UTi Worldwide Inc. (ex UNION TRANSPORT) http://www.utrac.com/dictionary/a.htm\n\nLIBRO VERDE SULLA POLITICA DI SPETTRO RADIO nel contesto delle politiche della ComunitΓ europea: telecomunicazioni, radioemissioni, trasporti e R&S\n\nGlossary of Terms - Philadelphia Ports &international trade - resource library http://ppc.org/pahouse/glossary.html\n\nGlossario dei termini doganali (Ministero delle Finanze) http://www.finanze.it/dogane/italiano/xglossario.htm\n\nINCOTERMS - A set of international rules for the uniform interpretation of common contract clauses in international trad.\n\nMARITIME project - Definitions and abbreviations (AP 218, Ship Structures)\n\nVTMIS Glossary of Terms compiled in the Concerted Action VTMIS or in related R&D actions.",
"homepage": "http://docplayer.net/32642561-Glossario-di-tecnica-informatica-documentazione-e-contrattualistica-per-i-trasporti-in-particolare-marittimi.html",
"name": "Glossario di Tecnica, Informatica, Documentazione e Contrattualistica per i Trasporti in Particolare Marittimi",
"prefix": "17706"
},
"17709": {
"homepage": "http://www.dea.univr.it/documenti/OccorrenzaIns/matdid/matdid982559.pdf",
"name": "Supply Chain Management Terms and Glossary",
"prefix": "17709"
},
"1771": {
"description": "The USP Controlled Vocabulary is a list of subjects used for the indexing of information resources in the Bibliographic Database of USP - DEDALUS. The Vocabulary covers the areas of knowledge inherent to the teaching, research and extension activities of the University of SΓ£o Paulo. The USP Controlled Vocabulary can be used by the information units to index their collections through a query in that interface (Website); However, it will not be available for export to systems outside of USP. We would like to inform you that SIBi / USP will no longer be publishing the vocabulary in CD-ROM format from 2003 onwards.",
"homepage": "http://143.107.154.62/Vocab/Sibix652.dll",
"name": "SIBi / USP Controlled Vocabulary",
"prefix": "1771"
},
"17710": {
"description": "Throughout the 11th and 12th centuries there was a growing spirit of religious fervour in Europe. Groups of pilgrims embarked upon journeys to holy sites and the Crusades were organized to set the Holy Land free from the Muslims. At the same time, more and more devotees renounced the mundane world to retire into religious communities called monasteries. Soon monks gained great influence on all aspects of contemporary society. Besides devoting themselves to a strict devotional life, they also cultivated a knowledge of both intellectual and manual work that highly contributed to the social prosperity.",
"homepage": "https://aleelatan.files.wordpress.com/2010/10/04-romanesque.pdf",
"name": "Romanesque Art",
"prefix": "17710"
},
"17712": {
"description": "A glossary suitable for the first several years of instruction, with emphasis on the vocabulary of easy literary texts, early royal inscriptions, and uncomplicated economic and administrative documents.",
"homepage": "http://gizidda.altervista.org/ebooks/Daniel-Foxvog-SumerianGlossary.pdf",
"name": "Elementary Sumerian Glossary",
"prefix": "17712"
},
"17715": {
"description": "The Glossary presented in this part of the website has been compiled by AFEMSβs Technical Committee on the base of its practical experience and intends to provide an operative support to the Member of the Association dealing with the proper definition of technical words in the most common EU languages.\n\nIt is not a comprehensive instrument, because it doesnβt cover the full range of terms used in our industry and the termβs definitions could be subject in the time to further change and refinement. The Glossary doesnβt intend to provide any legal definition of the terms included.",
"homepage": "http://www.afems.org/glossary.html",
"name": "AFEMS Glossary",
"prefix": "17715"
},
"17718": {
"description": "Banca Generali is a leading banking group in the management of savings, one of the largest offering of investment solutions on the market and assistance in client financial planning. Conscious of the need to implement diversified approaches for each customer, the group Banca Generali has structured two different distribution networks: Banca Generali and Banca Generali Private Banking.",
"homepage": "https://www.bancagenerali.it/site/home/help/glossario.html",
"name": "Glossary of the General Bank",
"prefix": "17718"
},
"1772": {
"description": "The Legal Thesaurus of the Supreme Court of the Nation is a valuable linguistic resource dedicated to simplifying the work of documentalists in the use of specialized language during their work of thematic classification, which entails facilitating the retrieval of information in form Pertinent and useful.This way, it provides support to the users of the information, in the definition of the criteria for their search or consultation through the computer systems available, with which it is intended to reduce the impact it produces The legal thesaurus that I am pleased to place at the disposal of the legal community, the centers that manage documentary collections or provide information services. Consultation, and of course society in general, is nourished by a controlled, structural vocabulary Hierarchically and systematically through the analysis of legal terms, mainly. It unambiguously represents the contents of the different types of documents that are part of the collections of the Supreme Court, without this being an obstacle to be constituted as a useful tool for those who work in the treatment and indexation of the Information, due to the methodology followed for its integration; As well as help for all interested in knowing the legal language from a different perspective; Since, starting from a basic scheme of the main subjects that analyze the subjects of the Law, the figures are ordered conceptually. Its elaboration was in charge of the Center of Documentation and Analysis, Archives and Compilation of Laws; And for the validation of the descriptors and concepts included in this third edition, the Institute of Legal Research of the National Autonomous University of Mexico recently collaborated.",
"name": "Legal Thesaurus of the Supreme Court of Justice of the Nation. Controlled and Structured Vocabulary",
"prefix": "1772"
},
"17720": {
"description": "Isfol's multimedia glossary is an instrument for accompanying portal consultation. It is characterized as an open work: it is constantly updated and receives contributions from scholars and experts through telematic participation.",
"homepage": "http://archivio.isfol.it/Glossario/",
"name": "ISFOL Multimedial Glossary",
"prefix": "17720"
},
"17721": {
"description": "The Guide to Costa Rica Real Estate. The majority of these definitions, with the exception of those specifically aimed at the Costa Rican market, were taken from Barronβs Dictionary of Real Estate Terms.",
"homepage": "http://guidetocostaricarealestate.com/christopher-howards-guide-to-real-estate-in-costa-rica/christopher-howards-guide-to-real-estate-in-costa-rica/chapter-18-reference-section/glossary-of-real-estate-terms-in-english-with-a-spanish-equivalent",
"name": "Glossary of Real Estate Terms in English with a Spanish Equivalent",
"prefix": "17721"
},
"17722": {
"description": "Online glossary of linguistics terminology | Greek-English & English-Greek",
"homepage": "http://users.uoi.gr/gjxydo/lexicon/glossary.html",
"name": "Online Glossary of Linguistic Terminology",
"prefix": "17722"
},
"17723": {
"description": "The Information Technology TermBase INFORTERM is trilingual and includes the Greek terms produced by the Group ELOT/TE48/OE1 Β«Information Technology TerminologyΒ» and equivalent English terms and French terms, based on International Standards (ISO/IEC 2382 series) of the International Organization for Standardization (ISO) and the International Electrotechnical Commission (IEC).",
"homepage": "http://inforterm.cs.aueb.gr/english/search.php",
"name": "Information Technology TermBase INFORTERM",
"prefix": "17723"
},
"17724": {
"description": "The Centre for the Standardization of Welsh Terminology has been active in Wales since 1993, producing numerous terminology dictionaries in that time, both in printed form and in innovative digital formats. This Terminology Portal is a free, convenient, national resource which provides a one-stop shop for your terminology needs, allowing you to search through most of those terminology dictionaries on the web.\n\nDetails of the dictionaries which have been included in the Terminology Portal are available here. New terminology dictionaries currently being developed by the Centre for the Standardization of Welsh Terminology will be added as the become available.",
"homepage": "http://termau.cymru/",
"name": "Welsh National Terminology Portal",
"prefix": "17724"
},
"17725": {
"description": "Sierterm is an R&D Project funded by the Universidad Europea de Madrid for a year with the aim of creating a terminological trilingual glossary (terminology records) for translators working in the fields of Intelligent Systems and Renewable Energies. More specifically, Sierterm concentrates on: β’ Compiling documents for term identification and extraction. β’ Uploading these terms into a collaborative platform that allows for public access and collaboration.",
"homepage": "http://www.sierterm.es/",
"name": "Sierterm",
"prefix": "17725"
},
"17726": {
"description": "The DAMT is a unique multilingual dictionary grouping the concepts of globalization, economics and social issues pertaining to the field of Industrial Relations. This Dictionary was started in 2004 under Jeanne Dancetteβs direction, professor at the Department of Linguistics and Translation, UniversitΓ© de MontrΓ©al. The aim is to provide better understanding of the concepts of globalization, economics and labour. This is why a typical entry contains a definition, a context and a descriptive summary of the concept referred to, as well as a list of associated terms. Thus, you can read them as mini encyclopaedic articles giving basic information about past and present realities. The definitions offered are general and consensual. The information presented results from our own synthesis of authorized texts written by experts in the field. The articles are written in English, French and Spanish. However, they are not translations; they differ according to the information found in each language, sometimes complementing each other. The DAMT is also a thesaurus. Its aim is to provide terminology in three different languages. The Dictionary features a system of semantic relations between termsβan innovative approach conceived to help unveil the nuances between concepts. Translators, students and researchers will find it useful.",
"homepage": "http://damt-dico.rhcloud.com/",
"name": "DAMT",
"prefix": "17726"
},
"17727": {
"description": "NATOTerm contains non-classified military terminology, as well as non-military terminology relevant to NATO. NATOTerm is available in both NATO official languages, i.e. English and French, and is maintained by the NATO Terminology Office, which is part of the NATO Standardization Office. This database is the result of a data migration from the former NATO Terminology Management System (NTMS), which is expected to be completed by the end of 2015. The NATO Terminology Office, which administers the database, has concentrated on the terminology that is 'NATO Agreed' first. This migration is still ongoing. The user is therefore invited to consult the 'Latest updates' section for further details. The next step will be to add the terminology from NATO glossaries that is not yet NATO Agreed.",
"homepage": "https://nso.nato.int/natoterm/content/nato/pages/home.html?lg=en",
"license": "CC-BY-3.0",
"name": "NATOTerm",
"prefix": "17727"
},
"17728": {
"description": "This covers all lexica and sections of vocabulary drawn up by UZEI, Basque Centre for Terminology and Lexicography. It currently holds more than 100,000 terminological records, with the equivalent terms in Spanish, French, English and Latin (in taxonomy). Terms are constantly updated according to the rules of Euskaltzaindia (Royal Academy of the Basque Language) and the proposals for terminology normalization (technical committees and Terminology Commission).",
"homepage": "http://www.euskara.euskadi.net/r59-euskalte/eu/q91EusTermWar/kontsultaJSP/q91aAction.do",
"name": "Euskalterm",
"prefix": "17728",
"wikidata_database": "Q12257615"
},
"17729": {
"description": "WIPOβs multilingual terminology portal gives access to scientific and technical terms derived from patent documents. It helps promote accurate and consistent use of terms across different languages, and makes it easier to search and share scientific and technical knowledge.",
"homepage": "http://www.wipo.int/reference/en/wipopearl",
"license": "CC-BY-3.0",
"name": "WIPO Pearl",
"prefix": "17729"
},
"1773": {
"description": "Terms included in this glossary are the kind that typically come up in data science discussions and job postings. Most are from the worlds of statistics, machine learning, and software development.",
"homepage": "http://www.datascienceglossary.org/",
"name": "Data Science Glossary",
"prefix": "1773"
},
"17730": {
"description": "TERMDAT is an extensive multilingual specialist dictionary, and is a versatile aid for communication, text composition and translation. TERMDAT contains the terminology of Swiss law, public administration and the public sector in Switzerlandβs four national languages β German, French, Italian and Romansh β and in English. It can be accessed free of charge online. (...) TERMDAT contains terms from a wide range of specialist fields, including law, public administration, agriculture, culture, economics, energy, environment, finance, industry, IT, medicine, the military, politics, science, technology, telecommunications, trade and transport. It contains a comprehensive collection of terms from Swiss federal law. (...) The entries in TERMDAT not only explain legal and administrative terminology, in most cases the equivalent term is also given in the other national languages, and sometimes in English. So if someone is required to translate a specialist term into another language, thanks to TERMDAT they can be sure of using the right one. Besides terms and their definitions and explanatory notes (e.g. how a word is to be used), TERMDAT contains further useful information such as official designations and abbreviations of Swiss and international authorities, institutions and organisations, and the titles and abbreviations of all federal legislation.",
"homepage": "https://www.bk.admin.ch/bk/en/home/dokumentation/languages/termdat.html",
"name": "TERMDAT",
"prefix": "17730"
},
"17731": {
"description": "TERMPOST is the Universal Postal Union's official terminology database created from the manual Vocabulaire polyglotte, available on paper from 1952 to 2003. It contains data in 8 languages: Arabic, Chinese, English, French, German, Portuguese, Russian and Spanish. Definitions are currently provided in English and French only. TERMPOST contains a selection of postal terms and expressions drawn from the UPU Acts and publications. It also includes everyday vocabulary used within the postal sector.",
"homepage": "http://www.upu.int/en/resources/termpost-terminology-database/",
"name": "TERMPOST",
"prefix": "17731"
},
"17732": {
"description": "The TERM PORTAL has been created to store, manage and update concepts, terms and definitions related to the various fields of FAOβs activity. The idea is to offer a single search window for all glossaries, in one or several languages, as a mechanism to enhance the exchange of information and facilitate communication.",
"homepage": "http://www.fao.org/faoterm/",
"name": "FAO TERM PORTAL",
"prefix": "17732"
},
"17733": {
"description": "Humanterm is an R&D Project funded by the Universidad Europea de Madrid for a year with the aim of creating a terminological multilingual glossary for translators working in the humanitarian field. More specifically, Humanterm concentrates in: β’ Compiling documents for term identification and extraction β’ Uploading these terms into a collaborative platform that allows for public access and collaboration.",
"homepage": "http://www.humantermuem.es/",
"name": "Humanterm",
"prefix": "17733"
},
"17734": {
"description": "TERMIUM PlusΒ, one of the largest terminology and linguistic data banks in the world, gives you access to millions of terms in English, French, Spanish and Portuguese. You can find terms, abbreviations, definitions and usage examples in a wide range of specialized fields. The data bank is an essential tool for understanding an acronym, checking an official title, finding an equivalent in another language, and much more.",
"homepage": "http://www.btb.termiumplus.gc.ca/",
"name": "TERMIUM PlusΒ",
"prefix": "17734",
"wikidata_database": "Q3518487"
},
"17735": {
"description": "Latvian terminology about IT",
"homepage": "http://termini.letonika.lv/",
"name": "terminology porta",
"prefix": "17735"
},
"17736": {
"description": "TEPA is a term bank compiled and maintained by the Finnish Terminology Centre TSK (Sanastokeskus TSK). It contains special language terms and their definitions which are displayed as multilingual terminological entries. TSK's own publications form the core of TEPA, but it also contains other special field vocabularies compiled by specialists. TEPA is implemented with Kielikone Ltd's MOTΒ dictionary software.\n\nTEPA vocabularies have been arranged into groups according to their source. The vocabulary groups are listed in the top left corner. The option All is selected by default, and it includes the whole term bank. You can also limit your search to specific vocabulary groups by selecting them from the list. TEPA consists of the Finnish Terminology Centre's own vocabularies (TSK's vocabularies), vocabularies of the Swedish Centre for Terminology (Terminologicentrum TNC) (TNC's vocabularies), vocabularies compiled at the Swedish Language Department of the Institute for the Languages of Finland (Kotus vocabularies) and Other vocabularies.\n\nThe Finnish Terminology Centre TSK maintains TEPA as free-of-charge with the financing provided by the Finnish Ministry of Education and Culture. The term bank renewal work was financed by a project subsidy granted by the Ministry of Education and Culture in 2006β2007.",
"homepage": "http://www.tsk.fi/tepa/",
"prefix": "17736"
},
"17737": {
"description": "IΒ·ATE is an interactive multilingual glossary on culinary terms that allows to share common knowledge, discover and preserve related concepts widespread across Europe. (...) IΒ·ATE works on the basis of the relationship between the concept and its designations in the European multilingual environment. The glossary presents a culinary term and its equivalents in the countries in which the concept exists. Every term is linked to a map displaying a geographical area that indicates how gastronomy can go beyond national borders. This leads to an historical reflexion linked to a cultural and common traditional heritage. The aim is also to propose an active glossary so that the user can submit a suggestion by a specific form to add a designation and a definition with picture.",
"homepage": "http://termcoord.eu/i-ate/",
"name": "Iβ’ATE",
"prefix": "17737"
},
"17738": {
"description": "The English-Spanish/Spanish-English equivalent translations of scientific and management terms (jargon) commonly used in the field of natural resource management are presented. The glossary is useful in improving communications and fostering understanding between Spanish- and English-speaking persons.",
"homepage": "http://www.fs.fed.us/rm/pubs_rm/rm_gtr152.pdf",
"name": "An English-Spanish Glossary of Terminology used in Forestry, Range, Wildlife, Fishery, Soils, and Botany",
"prefix": "17738"
},
"1774": {
"description": "The State of Minnesota Thesaurus is a comprehensive, cross-indexed set of subjects intended for search assistance. It is based on current vocabularies, including the: Legislative Indexing Vocabulary; Minnesota GIS Community. The thesaurus allows like communities to use a common vocabulary when describing and detailing Web resources.",
"homepage": "http://mn.gov/xml/Thesaurus",
"name": "State of Minnesota Thesaurus",
"prefix": "1774"
},
"17740": {
"description": "A planet is a celestial body in orbit around a star or stellar remnants, that has sufficient mass for self-gravity and is nearly spherical in shape. A planet must not share its orbital region with other bodies of significant size (except for its own satellites), and must be below the threshold for thermonuclear fusion of\n\ndeuterium. If a celestial body meets those requirements, it is considered a planet; at that point, the planet is further classified by its atmosphere and surface conditions into one of twenty-two categories.",
"homepage": "http://sttff.net/planetaryclass.html",
"name": "Star Trek Planetary Classification",
"prefix": "17740",
"wikidata_database": "Q923148"
},
"17741": {
"description": "A nebula is an interstellar cloud of dust, gas, and plasma, where star formation usually occurs. In the year 2400, the Federation introduced a new system to classify nebulae. The new system first assigns the nebula a letter designation based upon its general composition. If the nebula has any unusual quirks, it is assigned an additional number designation. For example, a Class F2 Nebula is a Dark Nebula that contains disruptive electromagnetic radiation.",
"homepage": "http://sttff.net/ast/AST_nebulaclassification.html",
"name": "Star Trek Nebula Classification",
"prefix": "17741"
},
"17742": {
"description": "Sector Classification for the Star Trek Universe.",
"homepage": "http://sttff.net/sectorclass.html",
"name": "Star Trek Sector Classification",
"prefix": "17742"
},
"17743": {
"description": "A sector is a volume of space approximately 20 cubic light years. In Federation space, a typical sector contains between six and ten star systems.",
"homepage": "http://sttff.net/ast/sector.html",
"name": "Star Trek Sector List",
"prefix": "17743"
},
"17744": {
"description": "Stars can generally be classified by their color. A purple star is always Class O, a yellow star is always Class G. However, there can be vast differences within each class. Most Class M stars are tiny and don't emit much light... however, many K- and G-type stars can evolve into red giants. That makes them Class M, but they are NOTHING like the tiny stars that make up the vast majority of Class M stars. Since most stars spend most of their lives on the Main Sequence, the descriptions on this page can be applied to the majority of stars. The oddballs and outsiders don't necessarily fit the exact parameters here (and will be discussed elsewhere), but even the oddballs conform to the interstellar color scheme, so even a blue oddball is class B.",
"homepage": "http://sttff.net/ast/spectralclassification.html",
"name": "Star Trek Spectral Classification",
"prefix": "17744"
},
"17745": {
"description": "The Yosemite Decimal System (YDS) is a three-part system used for rating the difficulty of walks, hikes, and climbs. It is primarily used by mountaineers in the United States and Canada. The Class 5 portion of the Class scale is primarily a rock climbing classification system, while the Classes 1-3 are used mainly in hiking and trail running. Originally the system was a single-part classification system. In recent years, Grade and Protection categories were added to the system. The new categories do not apply to every climb and usage varies widely. The grades are subjective, reflecting the first ascenscionist's opinion of the climb's difficulty. There are also systematic regional differences in grading within the United States.",
"name": "Yosemite Decimal System",
"prefix": "17745",
"wikidata_database": "Q8055930"
},
"17746": {
"description": "ECTS is a credit system designed to make it easier for students to move between different countries. Since they are based on the learning achievements and workload of a course, a student can transfer their ECTS credits from one university to another so they are added up to contribute to an individual's degree programme or training. ECTS helps to make learning more student-centred. It is a central tool in the Bologna Process, which aims to make national systems more compatible. ECTS also helps with the planning, delivery and evaluation of study programmes, and makes them more transparent.",
"homepage": "http://ec.europa.eu/education/ects/users-guide/glossary_en.htm#ectsTop",
"name": "European Credit Transfer and Accumulation System Glossary",
"prefix": "17746"
},
"17747": {
"homepage": "http://labclup.letras.up.pt/repentino/docs/docs.html",
"name": "classification system of Repentino",
"prefix": "17747"
},
"17748": {
"description": "NUR stands for Dutch-language Uniform Classification. It is a three-digit code that reflects the subject of a book.",
"homepage": "http://www.boek.nl/nur",
"name": "Dutch-speaking Uniform Classification",
"prefix": "17748",
"wikidata_database": "Q1961315"
},
"17749": {
"description": "Kleuter ZIZO is a thematic classification system for toddler and toddler books (target group 0-6 years). You can use the system both for fiction and non-fiction. Only poems, fairy tales and reading stories were included in this classification system. Libraries are often presented with age-crossing. Therefore, the choice for choosing these genres is not for the thematic classification system. The classification system has clear color icons and a standard label.",
"homepage": "http://www.cultuurconnect.be/diensten/plaatsingssystemen-en-etiketten/zizo-plaatsingssystemen",
"name": "Kleuter ZIZO",
"prefix": "17749",
"wikidata_database": "Q2022490"
},
"1775": {
"description": "Controlled vocabulary specialized in architecture, art, design and urbanism. (...) 2750 Terms, 758 Relationships between terms, 351 Equivalent terms.",
"homepage": "http://vocabularyserver.com/vitruvio/",
"name": "Vitruvio",
"prefix": "1775"
},
"17750": {
"description": "ZIZO Youth is a thematic classification system for informative materials with target audience 6+. The classification system has clear color and standard labels.",
"homepage": "http://www.cultuurconnect.be/diensten/plaatsingssystemen-en-etiketten/zizo-plaatsingssystemen",
"name": "ZIZO Youth",
"prefix": "17750",
"wikidata_database": "Q2022490"
},
"17751": {
"description": "ZIZO adults is a thematic classification scheme that allows you to organize the adult non-fiction collection of a public library. ZIZO tries to bring the user to the desired subject, staged and intuitively. The various aspects of a subject are brought together as much as possible so that the The user gets an overview of the information sources that can answer his question. The rating system has clear color and standard labels.",
"homepage": "http://www.cultuurconnect.be/diensten/plaatsingssystemen-en-etiketten/zizo-plaatsingssystemen",
"name": "ZIZO Adults",
"prefix": "17751",
"wikidata_database": "Q2022490"
},
"17752": {
"description": "A small part of the library's holdings are organized according to the (...) earlier system of the central library, which is an older, only weakly used media unit, which is therefore moved into our closed magazine the central library is for our classification work today no longer relevant additions are classified rather since mid-2012, according to the Regensburg classification (RVK) and -. as the majority of the reclassified to RVK stocks our university library - freely accessible even after this system of order \".",
"homepage": "http://www.hs-lu.de/service/bibliothek/informationen-zur-bibliothek/bibliothekssystematik/fruehere-systematik-zentralbibliothek.html#c2833",
"name": "Classifications of the Central Library of the University of Ludwigshafen on the Rhine",
"prefix": "17752"
},
"17753": {
"description": "A small part of the library's social and health care system is organized according to the previous system of the sub-library, Department IV, Social and Health Care, which is older, only weakly used and therefore outsourced to our closed magazine. (...) This former system of the specialized library of social and health care is no longer relevant for our classification work. New entries are classified according to the Regensburger Systematik (RVK) since mid-2012 and - like the majority of the collections of our university library, Also freely accessible according to this system.",
"homepage": "http://www.hs-lu.de/service/bibliothek/informationen-zur-bibliothek/bibliothekssystematik/fuehere-systematik-teilbibliothek-fb-iv.html#c9449",
"name": "Classifications of the Partial Library Social and Health Care",
"prefix": "17753"
},
"17754": {
"description": "When the Documents Section of the North Carolina State Library was organized between 1957-1960, this classification scheme was devised by the documents librarian, Sangster Parrott, for the Library's large collection of North Carolina public documents. Documents are arranged by state government agency and then by function. The scheme is partially adapted from the U.S. Superintendent of Documents Classification System which is used for Federal documents collections. The current edition shows agency name changes in general, but should not be relied upon as a complete history of a name due to the complex agency reorganizations, mergers, and dissolutions that have occurred since 1960.",
"homepage": "http://statelibrary.ncdcr.gov/ghl/services/statepubsclassification.html",
"name": "State Publications Classification",
"prefix": "17754"
},
"17755": {
"description": "Since 2013, a bilingual thesaurus (dt./en.) For the fields of computer science, business and transport has been established at the library of TH Wildau, with the aim of providing students with an overview of their subject area and related fields Thesaurus as a research aid in Wilbert's library search machine.",
"name": "Thesaurus for the areas of computer science, business and transport",
"prefix": "17755"
},
"17756": {
"homepage": "http://www.bodleian.ox.ac.uk/__data/assets/pdf_file/0004/192568/Classification-guide.pdf",
"name": "Bodleian Old Theology Library Scheme",
"prefix": "17756"
},
"17757": {
"description": "We also receive and distribute state government publications as mandated by ORC 149.11. Access to available documents, periodicals and items available in our digital collection are included below. For more information on how these documents are classified, consult our classification scheme index.",
"homepage": "https://library.ohio.gov/collections/government-documents/classification-scheme/",
"name": "State Library of Ohio Classification Scheme",
"prefix": "17757"
},
"17758": {
"description": "The British Catalogue of Music Classification (BCM Classification) is a faceted classification that was commissioned from E. J. Coates by the Council of the British National Bibliography to organize the content of the British Catalogue of Music. The published schedule (1960) was considerably expanded by Patrick Mills of the British Library up until its use was abandoned in 1998. Entries in the catalogue were organized by BCM classmark from the catalogue's inception in 1957 until 1982. From that year the British Catalogue of Music (which from 1974 onward was published by The British Library) was organized instead by Dewey Decimal Classification number, though BCM classmarks continued to be added to entries up to the 1998 annual cumulation.",
"homepage": "http://cms.slwa.wa.gov.au/find/guides/music/general_information/british_catalogue_of_music_classification_scheme",
"name": "British Catalogue of Music Classification",
"prefix": "17758",
"wikidata_database": "Q4835206"
},
"17759": {
"description": "The dictionary is shared infrastructure meant to serve as a key component of the national and international interoperability strategies of research organizations. It represents the integrated outputs (and ongoing maintenance) of an international network of subject matter experts from stakeholder organizations. The dictionary is intended as a canonical collection of common terms and their descriptors as well as basic structural groupings to facilitate controlled information exchanges between stakeholders. Please search for specific terms or use the menu to alphabetically browse all standard Terms, Objects, Attributes or Lists. If you do not find a term or structure you are looking for please join the Casrai initiative to help add new contents to this shared resource.",
"homepage": "http://dictionary.casrai.org/",
"license": "CC-BY-3.0",
"name": "CASRAI Dictionar",
"prefix": "17759"
},
"1776": {
"homepage": "https://www.governodigital.gov.br/eixos-de-atuacao/governo/interoperabilidade/vocabulario-controlado-do-governo-eletronico-vcge",
"license": "CC BY-SA 3.0",
"name": "Electronic Government Controlled Vocabulary",
"prefix": "1776"
},
"17760": {
"description": "PRGPG agreed that in the long term classification harmonisation across the whole higher education and research sector would be desirable and that the Research Councils should aim to achieve alignment over a period of a few years and would not adopt JACS at this stage, although JACS could be used for external reporting. With the exception of MRC (which has signed up to a UK-wide classification system for health research, the Health Research Classification System, HRCS, the hierarchical structure of which MRC considers cannot be accommodated within the RCUK structure) the Research Councils will initially seek to harmonise the classifications across the Councils. Two Classification workshops were organised, as a result of which the RCs have delivered to UK SBS enough defined structure and content to create the required three-level research classification and reviewer matching structure. The information which will be used to populate the top two levels of the structure are 90% accurate as agreed (apart from possible typos and stylistic considerations). There are, however, some duplications (some of which are intentional and some unintentional) that should ideally be reviewed. The third level of the hierarchy (Keys), required by EPSRC and BBSRC for reviewer matching are 90% compliant with the requirements of UK SBS. Unfortunately, the third level hierarchy (Keys) will not provide a reviewer matching functionality for EPSRC that is fit for purpose without further review. While the structure of the hierarchy is very unlikely to change over time, agreed changes will, inevitably, need to be made to data fields in the future and in the short term to Keys, to make them fit for purpose for reviewer matching. Attention will now be given to how this will be handled, given that PRGPG is not a standing group.",
"homepage": "http://www.rcuk.ac.uk/research/efficiency/researchadmin/harmonisation/",
"name": "RCUK Subject Classification",
"prefix": "17760"
},
"17761": {
"description": "A high-level classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. (...) The classification includes, but is not limited to, traditional authorship roles. That is, these roles are not intended to define what constitutes authorship. Rather, the roles are intended to apply to all those who contribute to research that results in scholarly published works, and it is recommended that all tagged contributors be listed, whether they are formally listed as authors or named in acknowledgements. An individual contributor may be assigned multiple roles, and a given role may be assigned to multiple contributors. When there are multiple people serving in the same role, a degree of contribution may optionally be specified as βleadβ, βequalβ, or βsupportingβ. It is recommended that corresponding authors assume responsibility for role assignment, and that all contributors be given the opportunity to review and confirm assigned roles.",
"license": "CC BY-ND 3.0",
"name": "Contributor Roles Taxonomy",
"prefix": "17761",
"wikidata_database": "Q25851719"
},
"17762": {
"description": "This database contains the AzDoc Classification Scheme, used to classify state documents for the state of Arizona. The classification scheme was developed by the Arizona State University Library. Like the Superintendent of Documents classification system (SuDocs), it arranges materials by issuing agency rather than by subject.",
"homepage": "http://apps.azlibrary.gov/azdocs/",
"name": "Arizona Governmental Publications Agency Names and Classification Codes",
"prefix": "17762"
},
"17763": {
"description": "Types of content licences.",
"homepage": "http://dictionary.casrai.org/Licence_Types",
"license": "CC-BY-3.0",
"name": "Licence Types",
"prefix": "17763"
},
"17764": {
"description": "This term of insurance and financial terms contains more than 1500 terms and has been motivated by the love we have for our work as an expert, but because we are not linguists or lexicographers, we make it clear that it should not be considered complete and therefore You should also refer to other official printed dictionaries.",
"homepage": "http://www.pragmatognomones.gr/lexicon/lexicongr.shtm",
"name": "Greek-English Dictionary of Insurance and Financial terms",
"prefix": "17764"
},
"17765": {
"description": "Glossary of the European Central Bank",
"homepage": "https://www.ecb.europa.eu/home/glossary/",
"name": "European Central Bank Glossary",
"prefix": "17765"
},
"17766": {
"homepage": "https://www.scribd.com/document/3139827/English-Greek-dictionary-of-statistics",
"name": "English-Greek Dictionary of Statistics",
"prefix": "17766"
},
"17767": {
"description": "The Language Centre opened in 1980 as an independent university-wide service. It moved to its present well-equipped home at 12 Woodstock Road, near Somerville College, in 1992. For over thirty years, we have supported members of the University and Colleges who need foreign languages for study and research, for academic exchange, and for personal and professional development, through excellent library resources and a mixture of paid and free courses. In August 2015 the Language Centre was moved to sit alongside the Oxford Learning Institute in the Academic Administration Division.",
"homepage": "http://www.lang.ox.ac.uk/links/languages.html",
"name": "Languages in the Library",
"prefix": "17767"
},
"17768": {
"description": "The Language Centre supports the teaching and learning of languages throughout the University. It does so flexibly in accordance with the needs of its users; it uses IT to underpin its operations and its activities are informed by relevant research in second language acquisition and educational technology.",
"homepage": "http://www.langcen.cam.ac.uk/lc/resources/",
"name": "John Trim Centre Resources",
"prefix": "17768"
},
"17769": {
"description": "A Glossary of Meteorological Terms with Definitions",
"homepage": "http://www.hnms.gr/hnms/greek/meteorology/full_story_html?dr_url=/docs/lexikon/lexicon&dr_page_number=1",
"name": "Glossary of Meteorological Terms",
"prefix": "17769"
},
"1777": {
"description": "Anvisa publishes (...) the Controlled Vocabulary of Pharmaceutical Forms, Pathways of Administration and Packaging of Medicines.\" The publication will be available on the Agency's website, under the link 'Medicamentos.' The booklet contains the standardization of nomenclatures and concepts related to Pharmaceutical forms, administration routes and packaging of medicinal products to be used as a primary reference, especially in the registration and post-registration of medicines.Another important aspect is the abbreviations of technical characteristics, widely used in official publications. The concepts and nomenclatures should also be used in the package inserts and labels, in the information systems, in the certification of Good Manufacturing Practices and in other activities that require standardized information.The lack of standardization hinders the correct classification Two doctors Common understanding.",
"homepage": "http://portal.anvisa.gov.br/wps/wcm/connect/ed15f600474590b59944dd3fbc4c6735/vocabulario_controlado_medicamentos_.pdf?MOD=AJPERES",
"name": "Controlled Vocabulary of Pharmaceutical Forms, Pathways of Administration and Packaging of Medications",
"prefix": "1777"
},
"17770": {
"homepage": "http://www.iatronet.gr/iatriko-lexiko/",
"name": "Medical Dictionary - Medical Encyclopedia",
"prefix": "17770"
},
"17771": {
"description": "Dictionary of football terms (Greek, English, French)",
"homepage": "http://www.fa3.gr/nomothesia_2/nomoth_athl/KANONISMOI/soccer/Lexiko_oron.htm",
"name": "Football Terms Glossary",
"prefix": "17771"
},
"17772": {
"description": "This terminology list contains over 150,000 terms useful to translators working with IMF material. It provides English terms with their equivalents in a number of languages. This list includes words, phrases, and institutional titles commonly encountered in IMF documents in areas such as money and banking, public finance, balance of payments, and economic growth. A number of entries include a usage field within square brackets, denoting the origin of the termβe.g., [OECD]βor a contextβe.g., [trade]; others contain a cross reference to related records. Acronyms are also included.",
"name": "International Monetary Fund Terminology",
"prefix": "17772"
},
"17773": {
"homepage": "http://www.lawnet.gr/lexiko.html",
"name": "Law Dictionary",
"prefix": "17773"
},
"17774": {
"homepage": "http://www.hope.ac.uk/media/liverpoolhope/contentassets/documents/library/collections/media",
"name": "Centre for the Study of African and Asian Christianity Classification",
"prefix": "17774"
},
"17775": {
"description": "The MIMO (Musical Instrument Museums Online) project has created a single access point to digital content and information on the collections of musical instruments held in a consortium of European museums. (...) The MIMO project has also involved the revision of the Hornbostel Sachs classification of musical instruments, with the main aim of classifying instruments such those in the new Electrophones class 5, invented since the publication of the original scheme of 1914 by Erich M. von Hornbostel and Curt Sachs. A number of scholars have at various times revised or extended the scheme. The MIMO consortiumβs version is closely based on the revised version (classes 1-4) by Jeremy Montagu to whom the consortium owes a debt of gratitude for generously sharing with us with us all resources associated with it; (...). This version of classification has been incorporated within the databases of a number of the museums in the MIMO project.",
"homepage": "http://network.icom.museum/fileadmin/user_upload/minisites/cimcim/documents/H-S_20classification_20final_20version_20_282013_29_20without_20editorial_20markings-2.pdf",
"name": "Classification of Musical Instruments",
"prefix": "17775",
"wikidata_database": "Q26836418"
},
"17776": {
"description": "The London Library has a unique and rather unorthodox classification scheme. Described as 'unusual but serviceable' by Alan Bell (Librarian of the London Library from 1993 to 2001), its application and maintenance are both a joy and a challenge. The scheme was devised by Sir Charles Theodore Hagberg Wright (1862-1940), Librarian of the London Library from 1893 until his death. (...): it was created on the principle of literary warrant, that is, it was designed around the books the Library held at the time. Like the scheme devised for the Library of Congress it was made to fit a particular collection with no thought of it ever being adopted by another library. LCC has since been adopted by many libraries, the London Library classification hasnβt had a comparable impact but it was adopted by the House of Commons Library where it continued to be used until 2000.",
"homepage": "http://londonlibrary.co.uk/ll-collections/books",
"name": "London Library Classification Scheme",
"prefix": "17776"
},
"17777": {
"description": "We have developed a new Eating and Drinking Ability Classification System (EDACS) for people with cerebral palsy. EDACS describes five distinct levels of ability using the key features of safety and efficiency (...). Our new Eating and Drinking Ability Classification System (EDACS) offers an alternative to subjective terms such as mild and moderate and severe which have no agreed definition. We developed EDACS by consulting with people with cerebral palsy, parents and experts around the world. EDACS has been tested to see how easy and reliable it is when used by speech and language therapists and parents.",
"homepage": "http://www.sussexcommunity.nhs.uk/get-involved/research/chailey-research/eating-drinking-classification.htm",
"name": "Eating and Drinking Ability Classification System for Individuals with Cerebral Palsy",
"prefix": "17777"
},
"17778": {
"description": "A wide range of models of PR and communication evaluation exist using a wide range of terms including inputs, outputs, outtakes, outflows, outgrowths, effects, results, and impact. An even wider range of metrics and methods for evaluation are proposed for each stage. The field is confusing for many practitioners. This page presents a taxonomy of evaluation tailored to strategic public communication β a taxonomy being a mapping of a field to produce a categorisation of concepts and terms β in short, to show where things go and where they fit in relation to each other. (...) A taxonomy is not the same as a model, as a taxonomy attempts to list ALL the main concepts, terms, metrics, methods, etc. in a field, while a model is an illustration of a specific program or activity to be applied in practice. However, models should be based on the concepts and methods identified as legitimate in the field and apply them appropriately. An important benefit of a taxonomy is that it puts concepts, metrics, methods, etc. in their right place β e.g., it avoids output metrics being confused with outcome metrics.",
"homepage": "http://amecorg.com/amecframework/home/supporting-material/taxonomy/#taxonomy-table",
"prefix": "17778"
},
"17779": {
"description": "The nominal type of unique ID used for an organization.",
"homepage": "http://dictionary.casrai.org/Org_ID_Types",
"license": "CC-BY-3.0",
"name": "Organization ID Types",
"prefix": "17779"
},
"1778": {
"description": "XML format of the standard file as used for the normalization of the artist names in prometheus. The file contains only the artists, of whom different names of their names are known.",
"homepage": "http://prometheus-bildarchiv.de/tools/pknd",
"name": "Prometheus artistNamensanetzungsFile",
"prefix": "1778"
},
"17780": {
"description": "Cooking Terms Glossary pubished by GreekMasa.",
"homepage": "http://www.greekmasa.gr/index.php?option=com_glossary&func=display&letter=All&Itemid=93&catid=89&page=1",
"name": "Cooking Terms Glossary",
"prefix": "17780"
},
"17781": {
"description": "Basic terms used in the field of wastewater treatment.",
"name": "Wastewater terminology",
"prefix": "17781"
},
"17783": {
"description": "Thesaurus of the library of the Friedrich Ebert Foundation",
"homepage": "http://library.fes.de/tematres/vocab/",
"name": "Thesaurus of the library of the Friedrich Ebert Foundation",
"prefix": "17783"
},
"17784": {
"abbreviation": "DARE",
"description": "The Digital Atlas of the Roman Empire (DARE) is a gazetteer of ancient places of the Roman Empire, based on the Barrington Atlas of the Greek and Roman World among other sources. The atlas is available via API and download as raw data and visual map.",
"homepage": "http://dare.ht.lu.se/",
"license": "CC BY-SA 3.0",
"name": "Digital Atlas of the Roman Empire",
"prefix": "17784",
"wikidata_database": "Q24575107"
},
"17785": {
"description": "This website is devoted to terms and their definitions used in applied ontology. Since ontology is an interdisciplinary field, it is especially important to have a guide for how specific terms are used since their meaning may vary across disciplines.",
"name": "IAOA Ontology Terminology",
"prefix": "17785"
},
"17786": {
"description": "Thesaurus used for monument preservation and related disciplines.",
"homepage": "http://xtree-public.digicult-verbund.de/vocnet/?uriVocItem=http%3A//lvr.vocnet.org/wnk/&startNode=wk000249&lang=de&d=n",
"name": "Wordnet culture",
"prefix": "17786"
},
"17788": {
"description": "Register of geographic names in Germany",
"name": "Geographic Names",
"prefix": "17788"
},
"1779": {
"description": "PIM is an alphabetic word system (as opposed to a numerical hierarchical system such as SISO) that consists of two levels: categories (\" subject areas \") and keywords below.\n\nΒ There are 27 fixed categories (visible by icons). These subject areas are grouped into ten clusters (colors) of related subject areas. The clusters can be directional for the visitor and for the collection of collections in the library. (For example, the categories \"Hobbies\" and \"Sports and Games\" are both orange; Libraries can choose to draw them in close proximity).\n\nΒ The PIM keywords in principle correspond to the first keyword granted by Media Aanbod to the media based on the NBD Biblion Trefwoordenthesaurus. When publicly-friendly media presentation on the shelf demands, another or broader keyword will be assigned. If the PIM keyword is too long for the label, it breaks down in a \"logical\" location, so that two nouns occur. (For example: Organization Development becomes: Organization Development) The same keyword can occur in different categories. The category format and a specific assigned keyword determine the location on the shelf of a unique medium in a library collection.",
"homepage": "http://www.nbdbiblion.nl/product/pim",
"name": "Presentation system Informative Media",
"prefix": "1779"
},
"17790": {
"abbreviation": "PESI",
"description": "PESI provides standardised and authoritative taxonomic information by integrating and securing Europeβs taxonomically authoritative species name registers and nomenclators (name databases) and associated exper(tise) networks that underpin the management of biodiversity in Europe.\n\nPESI defines and coordinates strategies to enhance the quality and reliability of European biodiversity information by integrating the infrastructural components of four major community networks on taxonomic indexing into a joint work programme. This will result in functional knowledge networks of taxonomic experts and regional focal points, which will collaborate on the establishment of standardised and authoritative taxonomic (meta-) data.\n\nPESI will coordinate the integration and synchronisation of the European taxonomic information systems into a joint e-infrastructure and the set up of a common user-interface disseminating the pan-European checklists and associated user-services results.\n\nThe organisation of national and regional focal point networks as projected not only assures the efficient access to local expertise, but is also important for the synergistic promotion of taxonomic standards throughout Europe, for instance to liaison with national governmental bodies on the implementation of European biodiversity legislations.\n\nPESI will provide a robust infrastructure to support the nomenclatural needs of European users and stakeholders. PESI will specifically address the issues of: pooling resources, standardisation, sustainability, accessibility and international cooperation.",
"homepage": "http://www.eu-nomen.eu/portal/",
"name": "Pan-European Species directories Infrastructure",
"prefix": "17790",
"wikidata_database": "Q25100264"
},
"17791": {
"description": "ITIS is an easily accessible database with reliable information on species names and their hierarchical classification that is publicly accessible with unlimited free use. The database is reviewed periodically to ensure high quality with valid classifications, revisions, and additions of newly described species. The ITIS includes documented taxonomic information of flora and fauna from both aquatic and terrestrial habitats. For each scientific name, ITIS includes the authority, taxonomic rank, a unique taxonomic serial number, data source information, data quality indicators, and associated synonyms and vernacular names where available. Geographic coverage is worldwide, with an emphasis on North American taxa. The ITIS Web Services provide the ability to search and retrieve data from ITIS by providing access to the data behind the ITIS web site (http://www.itis.gov/web_service.html#). There is also web interface for viewing reports, and several options for text downloads. Each part of the basic WSDL web services is provided by a web service API, which defines the name, input to, and output from the service for a particular data request.",
"homepage": "https://www.itis.gov/",
"name": "Integrated Taxonomic Information System",
"prefix": "17791",
"wikidata_database": "Q82575"
},
"17792": {
"description": "Prokaryotic Nomenclature up-to-date' is a compilation of all names of Bacteria and Archaea which have been validly published according to the Bacteriological Code since 1. Jan. 1980, and nomenclatural changes which have been validly published since. It will be updated with the publication of each new issue of the Int. J. Syst. Evol. Microbiol. (IJSEM).\n\n 'Prokaryotic Nomenclature up-to-date' is based on the work of N. Weiss and M. Kracht and is maintained by Dorothea Gleim who may be consulted on technical aspects (database resp. online access).",
"homepage": "https://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date.html",
"name": "Prokaryotic Nomenclature Up-to-Date",
"prefix": "17792"
},
"17793": {
"description": "ISO 3166 is the International Standard for country codes and codes for their subdivisions. The purpose of ISO 3166 is to define internationally recognised codes of letters and/or numbers that we can use when we refer to countries and subdivisions. However, it does not define the names of countries β this information comes from United Nations sources (Terminology Bulletin Country Names and the Country and Region Codes for Statistical Use maintained by the United Nations Statistics Divisions).",
"homepage": "https://www.iso.org/obp/ui/",
"name": "ISO 3166 Country Codes",
"prefix": "17793",
"wikidata_database": "Q106487"
},
"17794": {
"description": "Glossary of Anesthesia Terms published by Evangelia Papapostolou.",
"homepage": "http://anesthesia.gr/temp/wp-content/uploads/2016/09/Anazoogonisi2015_web.pdf",
"name": "Glossary of Anesthesia Terms",
"prefix": "17794"
},
"17795": {
"description": "English Greek chemical terms glossary published by chem.gr.",
"homepage": "http://www.chem.gr/%CE%B1%CE%B3%CE%B3%CE%BB%CE%BF%CE%B5%CE%BB%CE%BB%CE%B7%CE%BD%CE%B9%CE%BA%CF%8C-%CE%BB%CE%B5%CE%BE%CE%B9%CE%BA%CF%8C/",
"name": "English Greek chemical terms glossary",
"prefix": "17795"
},
"17796": {
"description": "Law Glossary published by Express Publishing.",
"homepage": "https://www.expresspublishing.co.uk/assets/pdf/epnegr/law_glossary.pdf",
"name": "Law Glossary",
"prefix": "17796"
},
"17797": {
"description": "Most of the chemical terms that have been collected come from foreign words, mainly Latin, many of which have Greek origin or similar word of common origin. It does not attempt to interpret or describe the term, with some exceptions. Also by way of exception, in some cases the historical context on which the creation of the word was based is developed. The words that are said to belong to broader fields, such as mineralogy, biochemistry, pharmacology and some commercial products.\n\nThere are no words of obvious Greek origin (eg lithium, choline), but there are some terms derived from relatively unknown or otherwise ancient Greek (eg cobalt, theobromine). Wherever possible, the reasoning of the empirical name is justified, since it is not obvious, even for some common word terms (eg rule, codon).",
"homepage": "http://195.134.76.37/scinews/Reports/Rep_Etymol_lexicon.htm",
"name": "ETHNOLOGICAL DOCUMENT OF CHEMICAL TERMS",
"prefix": "17797"
},
"17798": {
"description": "Classification of typical object genres found in German university collections.",
"homepage": "https://portal.wissenschaftliche-sammlungen.de/ConceptScheme/33",
"name": "object genres of university collections in Germany",
"prefix": "17798"
},
"17799": {
"description": "The Biological Collections Ontology (BCO) is an application ontology developed as part of the Biocode Commons project, within the OBO Foundry framework. The goal of the BCO is to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. The BCO covers distinctions between individuals, organisms, voucher specimens, lots, samples, the relations between these entities, and the processes governing the creation and use of 'samples'. Also within scope are properties including collector, location, time, storage environment, containers, institution, and collection identifiers.",
"homepage": "https://github.com/BiodiversityOntologies/bco",
"name": "Biological Collections Ontology",
"prefix": "17799"
},
"178": {
"description": "The revised and corrected 2001 edition of the thesaurus has 3,889 terms, ie 1,855 descriptors and 2,034 non-descriptors (synonyms and quasi-synonyms), followed by a qualifier to clarify the meaning of the descriptor. : CompΓ©tition (Psychologie) This is an integral part of the descriptor and must therefore be used with it when indexing or researching The purpose of this thesaurus is to assist the personnel of the documentation centers and the libraries of the milieu To organize their collection and to index their documentation. It can also be used as a research tool for online research.",
"homepage": "http://www.cdc.qc.ca/multites_fr.htm",
"name": "Education Thesaurus",
"prefix": "178"
},
"1780": {
"description": "The NBD | Biblion Trefwoordenthesaurus is an automated subject termination system for collections in public libraries, based on the terms assigned to NBD | Biblion's bibliographic products. In this thesaurus, all NBD | Biblion approved release terms for all media types are included . This has the advantage that the term of the term is consistent, that is, users are not confronted with different terms for the same understanding. By networking, libraries can consult each other's catalogs and exchange bibliographic data. Central cataloging, such as the Common Automated Cataloging System (GGC) of OCLC plays an important role in this. Libraries with a regional support function, for example, make use of terms from the NBD | Biblion Trefwoordenthesaurus for the subject termination of their title descriptions in the GGC. They regularly make proposals for n Old terms. NBD | Biblion takes care of the tuning and management of the thesaurus as the central public library catalog of public libraries. The thesaurus terminals may also be available for inclusion in (part) thesauri that can be used for the subject termination in specific (bibliographic) products.\n\nThis is possible by applying so-called type indicators that indicate which file or product will be assigned the termination terms.",
"homepage": "http://www.nbdbiblion.nl/product/abonnement-trefwoordenthesaurus",
"name": "Keyword Thesaurus",
"prefix": "1780"
},
"17800": {
"description": "Phenotypic qualities (properties). This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested.",
"homepage": "http://purl.bioontology.org/ontology/PATO",
"name": "Phenotypic Quality Ontology",
"prefix": "17800"
},
"17802": {
"description": "The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations. (...) OBOE can characterize the context of an observation (e.g., space and time), as well as dependencies such as nested experimental observations. It includes an extensive set of unit definitions (e.g., grams of carbon per liter of seawater), and can facilitate automatic unit conversions (e.g., pounds to kilograms). OBOE can be easily extended to create Entities and Characteristics for specific research domains, making it both broadly applicable and highly customizable. OBOE is being used to improve data interpretation, facilitate reuse, and create precise and effective systems for data search and discovery.",
"homepage": "https://github.com/NCEAS/oboe/",
"license": "CC-BY-3.0",
"name": "Extensible Observation Ontology",
"prefix": "17802"
},
"17803": {
"description": "The EUNIS habitat classification is a comprehensive pan-European system to facilitate the harmonised description and collection of data across Europe through the use of criteria for habitat identification. It is hierarchical and covers all types of habitat types from natural to artificial, from terrestrial to freshwater and marine.",
"homepage": "http://eunis.eea.europa.eu/habitats.jsp",
"license": "CC-BY-3.0",
"name": "EUNIS Habitat Classification",
"prefix": "17803"
},
"17804": {
"description": "The Coastal and Marine Ecological Classification Standard (CMECS) provides a national framework for organizing information about coasts and oceans and their living systems. It provides a structure for developing and synthesizing data so that ecosystems can be identified, characterized, and mapped in a standard way across regional and national boundaries. CMECS also supports status and trend monitoring activities, policy development, restoration planning, and fisheries management. The standard complements existing wetland and upland classification systems.\n\nThe six components of the classification standard represent the different aspects of the seascape (water column, geoform, substrate, biotic communities, biogeographic setting, and aquatic setting), starting with the broadest systems (marine, estuarine, and lacustrine) and narrowing to the most detailed physical and biological elements associated with a specific habitat type (biotic community).\n\nCMECS is periodically updated to reflect the best science and the needs of the coastal management communities. The framework of a dynamic standard process has been developed to receive input from researchers and users of the standard and to accomplish modifications to the classification system.",
"homepage": "https://www.cmecscatalog.org/",
"name": "Coastal and Marine Ecological Classification Standard",
"prefix": "17804"
},
"17805": {
"description": "The CoRIS glossary contains terms concerned with ecology, biogeography, evolution, taxonomy, morphology, physiology, cell and molecular biology, genetics, mapping, development, fisheries, oceanography, geosciences, conservation programs, remote-sensing, physics, chemistry, and data and information management.",
"homepage": "http://www.coris.noaa.gov/glossary/",
"name": "CoRIS Glossary",
"prefix": "17805"
},
"17806": {
"description": "The modern stellar spectral classification scheme (also known as the Harvard Spectral Classification Scheme) was created by Annie Jump Cannon through her examination of spectra from 1918 to 1924. Originally, the scheme used capital letters running alphabetically, but was later reordered to reflect the surface temperatures of stars. In order of decreasing temperature, these types were O, B, A, F, G, K and M. Three additional categories also in the scheme: R, N, and S types, were later realized to represent stars with peculiar heavy-metal abundances. Other types (Q for novae, W for Wolf-Rayet stars, etc) are not encountered frequently. According to astronomical myth, Henry Norris Russell suggested the following mnemonic to assist students in remembering the scheme: Oh Be A Fine Girl, Kiss Me!",
"homepage": "http://www.star.ucl.ac.uk/~pac/spectral_classification.html",
"name": "Harvard Spectral Classification Scheme",
"prefix": "17806"
},
"17807": {
"description": "Iβve broken the horror genre down into 10 sub-genres and 3 additional non-sub-genre classifications. Each page includes a full breakdown of the category with descriptions for each classification. Additionally, each classification includes a list of films that exemplify that particular corner of the horror genre. This is an ongoing project, so individual pages and lists will open as I complete them.",
"homepage": "https://openivorytower.org/taxonomy/",
"name": "Taxonomy of Horror Sub-Genres",
"prefix": "17807"
},
"1781": {
"description": "Principles of Epidemiology in Public Health Practice, Third Edition. An Introduction to Applied Epidemiology and Biostatistics",
"homepage": "http://www.cdc.gov/ophss/csels/dsepd/ss1978/glossary.html",
"name": "Principles of Epidemiology in Public Health Practice Glossary",
"prefix": "1781"
},
"17813": {
"homepage": "http://www.irit.fr/recherches/MELODI/ontologies/SAN",
"name": "SAN (Semantic Actuator Network)",
"prefix": "17813"
},
"17814": {
"homepage": "http://purl.org/acco/ns",
"name": "Accomodation Ontology",
"prefix": "17814"
},
"17815": {
"homepage": "http://www.w3.org/ns/auth/acl",
"name": "Basic Access Control ontology",
"prefix": "17815"
},
"17816": {
"homepage": "http://www.rkbexplorer.com/ontologies/acm",
"name": "ACM Classification Ontology",
"prefix": "17816"
},
"17817": {
"homepage": "http://privatealpha.com/ontology/certification/1",
"name": "Agent Certification Ontology",
"prefix": "17817"
},
"17818": {
"homepage": "http://www.w3.org/ns/adms",
"name": "Asset Description Metadata Schema",
"prefix": "17818"
},
"17819": {
"homepage": "http://purl.org/ontology/af/",
"name": "Audio Features Ontology",
"prefix": "17819"
},
"1782": {
"description": "This is a national vocabulary identifying accessibility of learning content. An access profile specifies functionality and experiences supported by learning content.",
"homepage": "http://vocabulary.curriculum.edu.au/access.html",
"name": "Australian Access Profile",
"prefix": "1782"
},
"17820": {
"homepage": "http://www.agls.gov.au/agls/terms",
"name": "AGLS Metadata Terms",
"prefix": "17820"
},
"17821": {
"homepage": "http://d-nb.info/standards/elementset/agrelon.owl",
"name": "Agent Relationship Ontology",
"prefix": "17821"
},
"17822": {
"homepage": "http://purl.org/vocab/aiiso/schema",
"name": "Academic Institution Internal Structure Ontology",
"prefix": "17822"
},
"17823": {
"homepage": "https://raw.githubusercontent.com/airs-linked-data/lov/latest/src/airs_vocabulary.ttl",
"name": "Alliance of Information and Referral Services (AIRS) Vocabulary",
"prefix": "17823"
},
"17824": {
"homepage": "http://www.aktors.org/ontology/portal",
"name": "AKT Reference Ontology",
"prefix": "17824"
},
"17825": {
"homepage": "http://www.aktors.org/ontology/support",
"name": "AKT Support Ontology",
"prefix": "17825"
},
"17826": {
"homepage": "http://securitytoolbox.appspot.com/securityAlgorithms",
"name": "Algorithms Ontology",
"prefix": "17826"
},
"17827": {
"homepage": "http://open-services.net/ns/asset",
"name": "OSLC Asset Management Vocabulary",
"prefix": "17827"
},
"17828": {
"homepage": "http://purl.org/ontology/ao/core",
"name": "Association Ontology",
"prefix": "17828"
},
"17829": {
"homepage": "http://rdf.muninn-project.org/ontologies/appearances",
"name": "Appearances Ontology Specification",
"prefix": "17829"
},
"1783": {
"description": "Three years ago, with the help of some dedicated library volunteers, I decided I was 'Done with Dewey' - we built our own classification system from the ground up based on how my students and staff search for books. I call it the Monarch Method. The best comparison is that it makes looking for books in my library similar to buying a book online through Amazon.ο»Ώ",
"homepage": "http://www.monarchmethod.com/",
"license": "CC BY-NC 3.0",
"name": "Monarch Method",
"prefix": "1783"
},
"17830": {
"homepage": "http://purl.org/linked-data/api/vocab",
"name": "Linked Data API Vocabulary",
"prefix": "17830"
},
"17831": {
"homepage": "http://semweb.mmlab.be/ns/apps4X",
"name": "The vocabulary for Co-creation Events based on Open Data",
"prefix": "17831"
},
"17832": {
"homepage": "http://purl.org/archival/vocab/arch",
"name": "Archival collections ontology",
"prefix": "17832"
},
"17833": {
"homepage": "http://bblfish.net/work/atom-owl/2006-06-06/",
"name": "Atom Syndication Ontology",
"prefix": "17833"
},
"17834": {
"homepage": "http://purl.oclc.org/NET/ssnx/meteo/aws",
"name": "Ontology for Meteorological sensors",
"prefix": "17834"
},
"17835": {
"description": "The Basic Registration of Addresses and Buildings (BAG) is part of the government system of basic registrations. The BAG Vocabulary is the associated ontology published as Linked Data.",
"homepage": "https://bag.basisregistraties.overheid.nl/def/bag",
"name": "Basic registrations addresses and buildings vocabulary (BAG)",
"prefix": "17835",
"wikidata_database": "Q2274762"
},
"17836": {
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19103/2005/basic",
"name": "OWL representation of ISO 19103 (Basic types package)",
"prefix": "17836"
},
"1784": {
"description": "As screenwriters venture deeper and deeper into the waters of movie studio development offices, agencies, and management companies β after years of trying to break through and finally seeing some attention - itβs imperative that they are prepared for the meetings, the conversations, the emails, and more important, the terminology.\n\nDevelopment and acquisition talk can be another language to some. Below we will cover some of the most common terms that screenwriters may come across. Terms that are most commonly utilized in development phases of Hollywood. While youβve likely heard them before, itβs important to understand the meaning, the usage, and what it means for your own script and writing in question.",
"homepage": "https://screencraft.org/2015/09/25/the-screenwriters-ultimate-guide-to-hollywood-meeting-terminology/",
"name": "Screenwriter's Ultimate Guide to Hollywood Meeting Terminology",
"prefix": "1784"
},
"17840": {
"homepage": "https://w3id.org/BCI-ontology",
"name": "Brain Computing Interface (BCI) Ontology",
"prefix": "17840"
},
"17841": {
"homepage": "http://contextus.net/ontology/ontomedia/ext/common/being",
"name": "OntoMedia Being Representation",
"prefix": "17841"
},
"17842": {
"homepage": "http://rdfs.co/bevon/",
"name": "BEVON: Beverage Ontology",
"prefix": "17842"
},
"17844": {
"homepage": "http://purl.org/ontology/bibo/",
"name": "The Bibliographic Ontology",
"prefix": "17844"
},
"17845": {
"homepage": "http://purl.org/net/nknouf/ns/bibtex",
"name": "BibTeX ontology",
"prefix": "17845"
},
"17846": {
"homepage": "http://purl.org/vocab/bio/0.1/",
"name": "BIO: A vocabulary for biographical information",
"prefix": "17846"
},
"17847": {
"homepage": "http://purl.org/NET/biol/ns",
"name": "Biological Taxonomy Vocabulary 0.2 (Core)",
"prefix": "17847"
},
"17849": {
"homepage": "http://purl.org/spar/biro",
"name": "The Bibliographic Reference Ontology",
"prefix": "17849"
},
"17850": {
"abbreviation": "blt",
"description": "British Library Terms is a small vocabulary complementing existing bibliographic schemas.",
"homepage": "http://www.bl.uk/schemas/bibliographic/blterms",
"name": "British Library Terms RDF schema",
"prefix": "17850"
},
"17851": {
"homepage": "http://purl.org/NET/biol/botany",
"name": "Biological Taxonomy Vocabulary 0.2 (Botany)",
"prefix": "17851"
},
"17852": {
"homepage": "http://vocab.deri.ie/br",
"name": "Brainstorm Ontology",
"prefix": "17852"
},
"17853": {
"homepage": "http://vocab.deri.ie/c4n",
"name": "Call for Anything vocabulary",
"prefix": "17853"
},
"17854": {
"homepage": "http://purl.org/spar/c4o",
"name": "C4O, the Citation Counting and Context Characterization Ontology",
"prefix": "17854"
},
"17855": {
"homepage": "http://www.w3.org/2002/12/cal/ical",
"name": "Internet Calendaring and Scheduling Core Object Specification",
"prefix": "17855"
},
"17856": {
"homepage": "http://purl.org/net/cartCoord",
"name": "cartCoordOnt",
"prefix": "17856"
},
"17857": {
"description": "The Comic Book Ontology is a metadata vocabulary for describing comic books and comic book collections. It is a work in progress and part of a larger research project exploring the organization and description of data about comic books.",
"homepage": "http://comicmeta.org/cbo/",
"license": "CC-BY-3.0",
"name": "Comic Book Ontology",
"prefix": "17857"
},
"17858": {
"homepage": "http://creativecommons.org/ns",
"name": "Creative Commons Rights Expression Language",
"prefix": "17858"
},
"17859": {
"homepage": "http://purl.org/ontology/cco/core",
"name": "Cognitive Characteristics Ontology",
"prefix": "17859"
},
"1786": {
"description": "The ANDS Vocabularies for vocabulary schema (lists of terms or permissible data values) are a source for metadata values recorded in the ANDS Vocabulary Portal.",
"homepage": "https://vocabs.ands.org.au/viewById/13",
"license": "CC-BY-3.0",
"name": "Vocabularies for Vocabulary Schema",
"prefix": "1786"
},
"17860": {
"homepage": "http://purl.org/twc/ontology/cdm.owl",
"name": "Conceptual Depth and Momentum",
"prefix": "17860"
},
"17861": {
"homepage": "http://purl.org/cld/cdtype/",
"name": "The Collection Description Type Namespace",
"prefix": "17861"
},
"17862": {
"homepage": "http://www.ebusiness-unibw.org/ontologies/consumerelectronics/v1",
"name": "Consumer Electronics Ontology",
"prefix": "17862"
},
"17864": {
"homepage": "http://www.w3.org/ns/auth/cert",
"name": "The Cert Ontology",
"prefix": "17864"
},
"17865": {
"homepage": "http://purl.oclc.org/NET/ssnx/cf/cf-feature",
"name": "Climate and Forecast (CF) features",
"prefix": "17865"
},
"17866": {
"homepage": "http://purl.oclc.org/NET/ssnx/cf/cf-property",
"name": "Climate and Forecast (CF) standard names parameter vocabulary",
"prefix": "17866"
},
"17867": {
"homepage": "http://linkeddata.finki.ukim.mk/lod/ontology/cfrl",
"name": "Corporate Financial Reports and Loans Ontology",
"prefix": "17867"
},
"17868": {
"homepage": "http://reference.data.gov.uk/def/central-government",
"name": "Central Government Ontology",
"prefix": "17868"
},
"17869": {
"homepage": "http://purl.org/ontology/chord/",
"name": "The OMRAS2 Chord Ontology",
"prefix": "17869"
},
"1787": {
"description": "Online Coins of the Roman Empire (OCRE), a joint project of the American Numismatic Society and the Institute for the Study of the Ancient World at New York University (...). The project will ultimately record every published type of Roman Imperial Coinage from Augustus in 31 BC, until the death of Zeno in AD 491.",
"homepage": "http://numismatics.org/ocre/",
"license": "ODBL",
"prefix": "1787",
"wikidata_database": "Q24577239"
},
"17871": {
"homepage": "http://www.essepuntato.it/2013/03/cito-functions",
"name": "Functions of Citations",
"prefix": "17871"
},
"17872": {
"homepage": "http://advene.org/ns/cinelab/ld",
"name": "Cinelab ontology",
"prefix": "17872"
},
"17873": {
"homepage": "http://purl.org/cld/terms/",
"name": "The Collection Description Terms",
"prefix": "17873"
},
"17874": {
"homepage": "http://purl.org/twc/ontologies/cmo.owl",
"name": "Conceptual Model Ontology",
"prefix": "17874"
},
"17875": {
"homepage": "http://www.w3.org/2011/content",
"name": "Representing Content in RDF",
"prefix": "17875"
},
"17876": {
"homepage": "http://purl.org/ontology/co/core",
"name": "Counter Ontology",
"prefix": "17876"
},
"17878": {
"homepage": "http://purl.org/configurationontology",
"name": "'Configuration as Linked Data' ontology",
"prefix": "17878"
},
"17879": {
"homepage": "http://purl.org/co",
"name": "Collections Ontology",
"prefix": "17879"
},
"1788": {
"abbreviation": "CRRO",
"description": "Coinage of the Roman Republic Online (CRRO) harnesses Linked Open Data to provide links across digital projects in Roman numismatics and beyond. At its launch CRRO provides access to six online collections containing over 20,000 specimens of Republican coinage.\n\nThe description of coin types provided here is based on Michael Crawford's 1974 publication Roman Republican Coinage (RRC), which is still the primary typology used for the identification of Roman Republican coin types. Since its publication in 1974 there have been significant revisions to the dating of the series following the discovery of new hoards, but no attempt has been made to reflect these or make any other amendments to the published typology at this stage. The descriptions for these coins are based on the typology set out in RRC, but have been modified to meet the standards of the British Museumβs collection management system by Eleanor Ghey and Ian Leins. These were previously published in Ghey and Leins 2010, which forms an update to the 1910 catalogue of the collection by Grueber. Additional types not in the British Museumβs collection were added to this database by Richard Witschonke of the ANS.",
"homepage": "http://numismatics.org/crro/",
"license": "ODBL",
"name": "Coinage of the Roman Republic Online",
"prefix": "1788",
"wikidata_database": "Q24577251"
},
"17880": {
"homepage": "http://vocab.resc.info/communication",
"name": "Vocabulary related to incident communication",
"prefix": "17880"
},
"17881": {
"homepage": "http://www.w3.org/2000/10/swap/pim/contact",
"name": "Contact",
"prefix": "17881"
},
"17882": {
"homepage": "http://purl.org/twc/vocab/conversion/",
"name": "Conversion Ontology",
"prefix": "17882"
},
"17883": {
"homepage": "http://purl.org/coo/ns",
"name": "Car Options Ontology",
"prefix": "17883"
},
"17884": {
"homepage": "http://www.ontologydesignpatterns.org/schemas/cpannotationschema.owl",
"name": "Content Pattern Annotations",
"prefix": "17884"
},
"17885": {
"homepage": "http://rhizomik.net/ontologies/copyrightonto.owl",
"name": "Copyright Ontology",
"prefix": "17885"
},
"17886": {
"homepage": "http://courseware.rkbexplorer.com/ontologies/courseware",
"name": "ReSIST Courseware Ontology",
"prefix": "17886"
},
"17887": {
"homepage": "http://purl.org/vocab/changeset/schema",
"name": "Changeset",
"prefix": "17887"
},
"17888": {
"homepage": "http://vocab.deri.ie/csp",
"name": "Constraint Satisfaction Problems Vocabulary",
"prefix": "17888"
},
"17889": {
"homepage": "http://www.w3.org/ns/csvw",
"name": "CSV on the Web Vocabulary",
"prefix": "17889"
},
"1789": {
"description": "A key success factor, while performing incident response, is to share a common understanding of the security incident. A common definition can be achieved by a shared vocabulary as described below.",
"homepage": "https://www.circl.lu/pub/taxonomy/",
"name": "CIRCL Taxonomy",
"prefix": "1789"
},
"17890": {
"homepage": "http://www.tele.pw.edu.pl/~sims-onto/ConnectivityType.owl",
"name": "Connectivity types",
"prefix": "17890"
},
"17891": {
"homepage": "http://commontag.org/ns",
"name": "Common Tag Vocabulary",
"prefix": "17891"
},
"17892": {
"homepage": "http://purl.org/ctic/infraestructuras/organizacion",
"prefix": "17892"
},
"17893": {
"homepage": "http://www.demcare.eu/ontologies/contextdescriptor.owl",
"name": "Context Descriptor Pattern",
"prefix": "17893"
},
"17894": {
"homepage": "http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1",
"name": "D2RQ - Language Specification",
"prefix": "17894"
},
"17895": {
"homepage": "http://vocab.deri.ie/dady",
"name": "Dataset Dynamics (dady) vocabulary",
"prefix": "17895"
},
"17896": {
"homepage": "http://purl.org/ontology/daia",
"name": "Document Availability Information Ontology",
"prefix": "17896"
},
"17897": {
"homepage": "http://purl.org/eis/vocab/daq",
"name": "Dataset Quality Vocabulary",
"prefix": "17897"
},
"17898": {
"description": "DBpedia Data ID is an ontology with the goal of describing LOD datasets via RDF files in a uniform way. Established vocabularies like DCAT, VoID, Prov-O and SPARQL Service Description are used for maximum compatibility.",
"homepage": "http://wiki.dbpedia.org/projects/dbpedia-dataid",
"name": "DataID",
"prefix": "17898"
},
"17899": {
"homepage": "http://contextus.net/ontology/ontomedia/misc/date",
"name": "OntoMedia Date Part Representation",
"prefix": "17899"
},
"179": {
"description": "UMTHESΒ includes 13,500 descriptors and 40,000 linked German-language synonyms with 35,000 English translations / equivalents and around 11,000 definitions. The environmental thesaurus (UMTHESΒ) presents concepts for the big theme of 'Environment (environmental use / environmental pollution / environmental protection)' (More general / more specific terms, among others), and collects the various words, including English translations, on which computer programs automatically support effective information search beyond language boundaries.",
"homepage": "http://sns.uba.de/umthes/",
"name": "Environmental thesaurus",
"prefix": "179"
},
"1790": {
"description": "The field of children's literature recognizes its specificity within literary studies and, at the same time, establishes relationships with other fields such as cultural studies, studies on childhood, editorial production and the study of illustration and Design as fields of study and professional practice. \" 843 Terms, 274 Relationship between terms, 76 Equivalent terms.",
"homepage": "http://www.bnm.me.gov.ar/vocabularios/lij/",
"name": "Terminological Vocabulary on Children's and Youth Culture",
"prefix": "1790"
},
"17900": {
"homepage": "http://vocab.datex.org/terms/",
"name": "Linked Datex II",
"prefix": "17900"
},
"17901": {
"homepage": "http://purl.org/net/dbm/ontology",
"name": "DBM Ontology",
"prefix": "17901"
},
"17902": {
"homepage": "http://ontology.cybershare.utep.edu/dbowl",
"name": "Relational to Ontology Mapping Primitive",
"prefix": "17902"
},
"17903": {
"homepage": "http://dbpedia.org/ontology/",
"name": "The DBpedia Ontology",
"prefix": "17903"
},
"17904": {
"homepage": "http://ontologi.es/doap-bugs",
"name": "DOAP Bugs",
"prefix": "17904"
},
"17905": {
"homepage": "http://purl.org/dc/dcam/",
"name": "DCMI Abstract Model",
"prefix": "17905"
},
"17907": {
"homepage": "http://purl.org/spar/datacite",
"name": "The DataCite Ontology",
"prefix": "17907"
},
"17908": {
"homepage": "http://ndl.go.jp/dcndl/terms/",
"name": "NDL Metadata Terms",
"prefix": "17908"
},
"17909": {
"homepage": "http://purl.org/dc/dcmitype/",
"name": "DCMI Type Vocabulary",
"prefix": "17909"
},
"1791": {
"description": "The Public Service Thesaurus (PST) has been developed as a list of descriptors, or controlled vocabulary, by which public sector resources may be indexed. It was developed to facilitate public sector compliance with the Irish Public Service Metadata Standard (IPSMS), and in so doing to enhance the capacity of public sector organisaitons to make their resources accessible and visible to their client base.\n\nCompliance can be achieved by using appropriate terms from the vocabulary in conjunction with the mandatory DC.Subject element.\n\nThe structure of the PST is such as to ensure ease of navigation around the vocabulary. It is represented at the top level by fourteen separate categories based on the wide areas of interest and involvement of public sector organisations. These top-level cateogries subdivide into second-level categories and so forth, each level in turn listing more specific subject sub-divisions.\n\nMany terms in the PST have been posted upwards in order to 1) limit the number of terms available for indexing, and consequently keep the thesaurus to a manageable size, and 2) to ensure as far as is practicable that resources sharing a common theme are returned together. This implies that the degree of specificity of terms available as indexing terms has been restricted. The PST, as an information retrieval thesaurus, is largely concerned with grouping like subject matter together, rather than allowing the naming of a particular object to the exclusion of others. In summary, a (preferred) term should be general enough that it might be used to index a number of items.",
"homepage": "http://www.gov.ie/webstandards/metastandards/pst/default.htm",
"name": "Irish Public Service Thesaurus",
"prefix": "1791"
},
"17910": {
"homepage": "https://code.google.com/archive/p/decision-ontology/",
"name": "Decision ontology",
"prefix": "17910"
},
"17911": {
"homepage": "http://www.demcare.eu/ontologies/demlab.owl",
"name": "Dem@Care Lab Ontology for Dementia Assessment",
"prefix": "17911"
},
"17912": {
"homepage": "http://purl.org/spar/deo",
"name": "The Discourse Elements Ontology",
"prefix": "17912"
},
"17913": {
"homepage": "http://ontologi.es/doap-deps",
"name": "DOAP Dependencies",
"prefix": "17913"
},
"17914": {
"description": "Ontology for healthcare metadata - especially metadata found in DICOM files (Digital Imaging and Communications in Medicine, see http://dicom.nema.org/).",
"homepage": "http://purl.org/healthcarevocab/v1",
"name": "Healthcare metadata - DICOM ontology",
"prefix": "17914"
},
"17915": {
"description": "The Design Intent Ontology (DIO) is a generic ontology that provides the conceptualisation needed to capture the knowledge generated during various phases of the overall design lifecycle. It provides definitions for design artifacts such as requirements, designs, design issues, solutions, justifications and evidence and relationships between them to represent the design process and how these things lead to design outcomes. It draws upon the paradigms of IBIS(Issue Based Information System), argumentation and design rationale. It is linked to W3C PROV by defining the actors in the design process as PROV agents and the design artifacts themselves are PROV entities. However DIO uses a modualrised version of PROV-O, based on Syntactic locality. DIO makes few assumptions about the design process used as the definitions of these activities properly belongs in the software lifecycle and data lifecycle models. The Figure below illustrates the conceptual entities in DIO and their relationships.",
"homepage": "https://w3id.org/dio",
"name": "The Design Intent Ontology",
"prefix": "17915"
},
"17916": {
"homepage": "http://rdf-vocabulary.ddialliance.org/discovery",
"name": "DDI-RDF Discovery Vocabulary",
"prefix": "17916"
},
"17917": {
"homepage": "http://purl.org/dita/ns",
"name": "DITA RDF ontology",
"prefix": "17917"
},
"17918": {
"homepage": "http://onto.dm2e.eu/schemas/dm2e",
"name": "DM2E model",
"prefix": "17918"
},
"17919": {
"homepage": "http://usefulinc.com/ns/doap",
"name": "Description of a Project vocabulary",
"prefix": "17919"
},
"1792": {
"description": "LEO aims to provide an agreed to semantic standard for any institution or organization that collects and manages data, information and knowledge in the field of Environmental Law and Governance. The development of a semantic Ontology for Multilateral Environmental Agreements (MEAs) and International Environmental Law was identified as a priority for MEA Secretariats and UNEP at the first meeting of the MEA Information and Knowledge Management (IKM) Initiative. Members to the MEA IKM Initiative agreed on the need for a βcontrolled vocabularyβ to allow for easier searching, locating and retrieving of MEA information such as decisions by MEA governing bodies and meeting documents, reports and national plans.\n\nGenerous financial support from the European Union provided for the review and enhancement of the draft InforMEA glossary through a Multi-Stakeholder process. The MEA IKM Initiative identified the IUCN Environmental Law Centre as collaborator in the development of the next version of the vocabulary and chose the FAOβs VOCbench system as the platform for the development and maintenance of the vocabulary. The IKM Initiative also reached out to organizations involved in the development of thesauri, such as the European Environment Agencyβs GEMET, the ECOLEX and the FAOlex glossary.",
"homepage": "http://leo.informea.org/",
"name": "Law & Environment Ontology",
"prefix": "1792"
},
"17920": {
"homepage": "http://www.w3.org/2000/10/swap/pim/doc",
"name": "Works, licences, derivatives and dependencies",
"prefix": "17920"
},
"17921": {
"homepage": "http://purl.org/spar/doco",
"name": "DoCO, the Document Components Ontology",
"prefix": "17921"
},
"17922": {
"homepage": "http://purl.org/ontology/dso",
"name": "Document Service Ontology",
"prefix": "17922"
},
"17923": {
"homepage": "http://elite.polito.it/ontologies/dogont.owl",
"name": "Ontology Modeling for Intelligent Domotic Environments",
"prefix": "17923"
},
"17924": {
"homepage": "http://purl.org/dpn",
"name": "Data Provider Node ontology",
"prefix": "17924"
},
"17925": {
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/dataquality",
"name": "OWL representation of ISO 19115 (Geographic Information - Metadata - Data quality package)",
"prefix": "17925"
},
"17926": {
"homepage": "http://semwebquality.org/ontologies/dq-constraints",
"name": "The Data Quality Constraints Library",
"prefix": "17926"
},
"17927": {
"homepage": "http://purl.org/dqm-vocabulary/v1/dqm",
"name": "The Data Quality Management Vocabulary",
"prefix": "17927"
},
"17928": {
"homepage": "http://purl.org/swan/2.0/discourse-relationships/",
"name": "Discourse relationships vocabulary",
"prefix": "17928"
},
"17929": {
"homepage": "http://vocab.data.gov/def/drm",
"name": "Data Reference Model",
"prefix": "17929"
},
"1793": {
"description": "The Europeana Food and Drink Classification scheme (EFD classification) is a multi-dimensional scheme for discovering and classifying Cultural Heritage Objects (CHO) related to Food and Drink (FD). To support the broadest possible range of re-use models, we are building upon existing terminologies to develop and apply a multilingual taxonomy for FD collections which will be used to tag, discover and aggregate relevant material by theme.",
"homepage": "http://vladimiralexiev.github.io/pubs/Europeana-Food-and-Drink-Classification-Scheme-%28D2.2%29.pdf",
"name": "Europeana Food and Drink Classification",
"prefix": "1793"
},
"17930": {
"description": "This vocabulary is used for modelling catalogs of datasets and its relationships with the datasets.",
"homepage": "http://purl.org/ctic/dcat",
"license": "CC BY-NC-SA 3.0",
"name": "Dataset Catalog Vocabulary",
"prefix": "17930"
},
"17931": {
"homepage": "http://purl.org/dsnotify/vocab/eventset/",
"name": "DSNotify Eventsets: A vocabulary for change events in linked data sources",
"prefix": "17931"
},
"17932": {
"homepage": "http://inference-web.org/2.0/ds.owl",
"name": "Data Structure Ontology",
"prefix": "17932"
},
"17933": {
"homepage": "http://www.linkedmodel.org/schema/dtype",
"name": "Datatype Ontology",
"prefix": "17933"
},
"17934": {
"name": "DOLCE+DnS Ultralite",
"prefix": "17934"
},
"17935": {
"homepage": "http://www.w3.org/ns/duv",
"name": "Dataset Usage Vocabulary",
"prefix": "17935"
},
"17936": {
"homepage": "http://purl.org/ontology/dvia",
"name": "The visualization vocabulary for LOD applications",
"prefix": "17936"
},
"17937": {
"homepage": "http://archivi.ibc.regione.emilia-romagna.it/ontology/eac-cpf/",
"name": "EAC-CPF Descriptions Ontology for Linked Archival Data",
"prefix": "17937"
},
"17938": {
"homepage": "http://www.w3.org/ns/earl",
"name": "Evaluation and Report Language",
"prefix": "17938"
},
"17939": {
"homepage": "http://linked.earth/ontology",
"name": "The Linked Earth Ontology",
"prefix": "17939"
},
"17940": {
"homepage": "http://www.ebu.ch/metadata/ontologies/ebucore/ebucore",
"name": "EBU Ontology",
"prefix": "17940"
},
"17941": {
"homepage": "https://vocab.eccenca.com/revision/",
"name": "RDF changes and revisions vocabulary",
"prefix": "17941"
},
"17942": {
"description": "The ECLAP vocabulary provide classes and properties for the description of multimedia content related with performing arts. It includes classes for the description of the kind of media used (Video, Audio, Document, etc.), classes for the description of annotations on media (One2One, Explosive), it includes properties for people involved in the creation process as performing arts professionals like (director, actor, mime, clown, etc.), and it includes properties relating the Users with content, groups and annotations (...).",
"homepage": "http://www.eclap.eu/schema/eclap/",
"license": "CC-BY-3.0",
"name": "ECLAP, Performing Arts Vocabulary",
"prefix": "17942"
},
"17943": {
"homepage": "http://purl.org/ontology/ecpo",
"name": "Enumeration and Chronology of Periodicals Ontology",
"prefix": "17943"
},
"17944": {
"homepage": "http://erlangen-crm.org/current/",
"name": "Erlangen CRM / OWL",
"prefix": "17944"
},
"17945": {
"homepage": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-edac.owl",
"name": "ELSEWeb EDAC Ontology",
"prefix": "17945"
},
"17946": {
"homepage": "http://www.europeana.eu/schemas/edm/",
"name": "Europeana Data Model vocabulary",
"prefix": "17946"
},
"17947": {
"homepage": "http://purl.org/eem",
"name": "The EPCIS Event Model",
"prefix": "17947"
},
"17948": {
"homepage": "http://purl.org/ctic/sector-publico/elecciones",
"prefix": "17948"
},
"17949": {
"homepage": "http://data.europa.eu/eli/ontology",
"name": "The European Legislation Identifier",
"prefix": "17949"
},
"1795": {
"description": "This hierarchic Vocabulary relies on the definitions of the Simplified Petrography in Salzburg. Another classification can be found in CIL Material Glossar. No Definitions can therefore be found here.\n\nMost of the Alternative Terms in Bulgarian, Turkish, Croatian, Suomi, Arabic and Modern Greek come from the EpiDoc Consortium efforts.\n\nThe vocabulary is hierarchically designed to allow for both precise and generic definition, as well as for several types of uncertainty. In many cases, for example for precious/exotic materials (onyx, gold, etc.) precision is possible and desirable but for most banal materials only basic distinctions will generally be possible. In many cases scholars in epigraphy do not seek to decided whether a base was of Proconnesian or Thasian marble, nor to decide exactly what kind of stone the local material was (generally a form of limestone), in such cases, according to us, we shall be able to be as precise as possible, but the best practice is to allow for different levels of depth of the information which might be meaningful only in some cases.\n\nA result of this approach has also been that this vocabulary should also be a fairly complete list of possible material on which an inscription from antiquity can be found.\n\nMany problems are involved with this kind of classification as well. 'Arcilla' for example is not in the same 'class' as 'terracotta, inscribed brick, etc', because it pertains to the material in which the inscription was written or carved in, that is, like 'stone, metal or wood'. There are also specific terms which could be assimilated but are not, like 'Lumaquela', the local name for the stone in which most of the inscriptions from Tarraco were carved in.",
"homepage": "https://www.eagle-network.eu/voc/material.html",
"name": "EAGLE Vocabulary Material",
"prefix": "1795"
},
"17950": {
"homepage": "http://ns.inria.fr/emoca",
"name": "Emotion Ontology for Context Awareness",
"prefix": "17950"
},
"17951": {
"homepage": "http://purl.org/ctic/empleo/oferta",
"prefix": "17951"
},
"17952": {
"homepage": "http://labs.mondeca.com/vocab/endpointStatus",
"name": "Vocabulary of endpoint status (availability, responseTime)",
"prefix": "17952"
},
"17953": {
"homepage": "http://eprints.org/ontology/",
"name": "EPrints Ontology",
"prefix": "17953"
},
"17954": {
"homepage": "http://purl.org/essglobal/vocab/",
"name": "ESSGlobal Vocabulary",
"prefix": "17954"
},
"17956": {
"homepage": "http://purl.org/net/ns/ex",
"name": "Example vocabulary",
"prefix": "17956"
},
"17957": {
"homepage": "http://www.w3.org/2003/12/exif/ns",
"name": "Exif data description vocabulary",
"prefix": "17957"
},
"17958": {
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/extent",
"name": "OWL representation of ISO 19115 (Geographic Information - Metadata - Extent package)",
"prefix": "17958"
},
"17959": {
"homepage": "http://purl.org/spar/fabio/",
"name": "FRBR-aligned Bibliographic Ontology",
"prefix": "17959"
},
"1796": {
"description": "Library of Congress Subject Headings (LCSH) has long included headings that represent the genre or form of musical works in combination with the mediums of performance (e.g., Sonatas (Trombone and organ); Concertos (Bassoon, clarinet, English horn, flute)), as well as headings that represent the mediums of performance alone (e.g., Bass clarinet and piano music). The structure of the headings can sometimes be of marginal utility to researchers, who may be most interested in finding music for a particular combination of instruments and are less focused on the genre of the music.\n\nOver the coming year, the concepts in the existing LC subject headings will be broken into their component parts. The forms and genres of musical works will be included in Library of Congress Genre/Form Terms for Library and Archival Materials (LCGFT) in 2014 or early 2015. The mediums of performance will be contained in the Library of Congress Medium of Performance Thesaurus for Music (LCMPT). When LCMPT and LCGFT terms for music are both implemented, the LC subject headings will cease to be assigned in new cataloging and will eventually be cancelled.\n\nLCMPT is a stand-alone vocabulary that provides terminology to describe the instruments, voices, etc., used in the performance of musical works. (...) The initial 802 LCMPT terms are based chiefly on existing LC subject headings, but some additional terms that do not already appear in LCSH have also been included. Authorized terms and references in LCMPT generally consist of single words and phrases, but parenthetical qualifiers are occasionally employed to differentiate among homonyms. All terms and references are in the singular form and are lowercased unless they are proper nouns (e.g., flute; saxophone ensemble; but Irish harp)\n\nThe thesaurus has three broadest terms: ensemble, instrument, and performer. Each of the other terms is hierarchically subordinate to one or more of these terms and exhibits the class/class member relationship. Most of the authorized terms have Used For (UF) references for synonyms. Scope notes are also provided in many cases, and may describe the mediumβs physical structure, the time period in which it was popular, and/or its geographic origin.",
"homepage": "http://id.loc.gov/authorities/performanceMediums.html",
"name": "Library of Congress Medium of Performance Thesaurus for Music",
"prefix": "1796"
},
"17960": {
"homepage": "http://vocab.data.gov/def/fea",
"name": "Federal Enterprise Architecture Vocabulary",
"prefix": "17960"
},
"17961": {
"homepage": "http://www.w3.org/TR/2003/PR-owl-guide-20031215/food",
"name": "Food Ontology in OWL",
"prefix": "17961"
},
"17962": {
"homepage": "http://iflastandards.info/ns/fr/frad/",
"name": "FRAD model",
"prefix": "17962"
},
"17963": {
"homepage": "http://purl.org/cerif/frapo/",
"name": "Funding, Research Administration and Projects Ontology",
"prefix": "17963"
},
"17964": {
"homepage": "http://streamreasoning.org/ontologies/frappe",
"name": "FraPPE: Frame, Pixel, Place, Event vocabulary",
"prefix": "17964"
},
"17965": {
"homepage": "http://purl.org/vocab/frbr/core",
"name": "Expression of Core FRBR Concepts in RDF",
"prefix": "17965"
},
"17966": {
"homepage": "http://purl.org/vocab/frbr/extended",
"name": "Extended FRBR",
"prefix": "17966"
},
"17967": {
"homepage": "http://iflastandards.info/ns/fr/frbr/frbrer/",
"name": "FRBRer model",
"prefix": "17967"
},
"17968": {
"homepage": "http://www.w3.org/2004/09/fresnel",
"name": "Fresnel Lens and Format Core Vocabulary",
"prefix": "17968"
},
"17969": {
"homepage": "http://data.ordnancesurvey.co.uk/ontology/50kGazetteer/",
"name": "50K Gazetteer Vocabulary",
"prefix": "17969"
},
"1797": {
"description": "This vocabulary will be used to describe the creators of, and contributors to, resources, and also the intended audience of resources. It will be created and maintained by the Policy and Standards Division, and be distinct from the other vocabularies that are maintained by that division: Library of Congress Subject Headings (LCSH), Library of Congress Genre/Form Terms for Library and Archival Materials (LCGFT), and the Library of Congress Medium of Performance Thesaurus for Music (LCMPT). (...) The development of LCDGT is necessitated by two circumstances: the genre/form project and the growing popularity of faceted displays and searching.\n\nThe genre/form project formed the original impetus for creating a demographic terms vocabulary. Some LC subject headingsβmost notably the form headings for literatureβinclude demographic information (e.g., Childrenβs stories, American, in which stories is the form, children are the audience demographic, and American, the creator demographic). The use of LCSH form headings for works of literature will be phased out as LC genre/form terms for literature are implemented, necessitating another method for bringing out the audience and creator/contributor information. (LCSH form headings will still be assigned to works about literature.\n\nNew discovery interfaces also make a new vocabulary desirable. Subject headings such as Childrenβs stories, American are assigned to works about American childrenβs stories, and also to works that are American childrenβs stories, so the computer cannot distinguish between the two types of works. LCGFT began to ameliorate this situation by allowing for a genre/form search, separate from a subject search. Users often want to know, though, what works a library has by a particular group (e.g., novels by lawyers), or for a particular group (e.g., handbooks for nurses). The demographic term vocabulary will fill the latter need. Together, LCSH, LCGFT, LCMPT, and LCDGT will allow for much more precision and flexibility in searching because terms within and across vocabularies can be mixed and matched to attain the level of specificity required.",
"name": "Library of Congress Demographic Group Terms",
"prefix": "1797"
},
"17970": {
"homepage": "http://data.totl.net/game/",
"name": "TotL Game Ontology",
"prefix": "17970"
},
"17971": {
"homepage": "http://www.oegov.org/core/owl/gc",
"name": "oeGOV Government Core Ontology",
"prefix": "17971"
},
"17972": {
"homepage": "http://vocab.data.gov/gd",
"name": "Government Data Vocabulary",
"prefix": "17972"
},
"17973": {
"homepage": "http://purl.org/gen/0.1",
"name": "Vocabulary for Linked Genealogical Data",
"prefix": "17973"
},
"17974": {
"description": "A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum.",
"homepage": "http://www.w3.org/2003/01/geo/wgs84_pos",
"name": "WGS84 Geo Positioning",
"prefix": "17974",
"wikidata_database": "Q11902211"
},
"17975": {
"homepage": "http://vocab.lenka.no/geo-deling",
"prefix": "17975"
},
"17976": {
"homepage": "http://www.mindswap.org/2003/owl/geo/geoFeatures20040307.owl",
"name": "Geo Features",
"prefix": "17976"
},
"17977": {
"homepage": "http://data.ign.fr/def/geofla",
"prefix": "17977"
},
"17978": {
"homepage": "http://data.ign.fr/def/geometrie",
"prefix": "17978"
},
"17979": {
"homepage": "http://aims.fao.org/aos/geopolitical.owl",
"name": "FAO Geopolitical Ontology",
"prefix": "17979"
},
"17980": {
"homepage": "http://rdf.geospecies.org/ont/geospecies",
"name": "GeoSpecies Ontology",
"prefix": "17980"
},
"17981": {
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19109/2005/feature",
"name": "OWL representation of ISO 19109 (General Feature Model)",
"prefix": "17981"
},
"17982": {
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19107/2003/geometry",
"name": "OWL representation of ISO 19107 (Geographic Information)",
"prefix": "17982"
},
"17983": {
"homepage": "http://www.opengis.net/ont/gml",
"name": "OGC Geometry",
"prefix": "17983"
},
"17984": {
"homepage": "http://www.geonames.org/ontology",
"name": "The Geonames ontology",
"prefix": "17984",
"wikidata_database": "Q29896506"
},
"17985": {
"homepage": "http://purl.org/linguistics/gold",
"name": "General Ontology for Linguistic Description",
"prefix": "17985"
},
"17986": {
"homepage": "http://gov.genealogy.net/ontology.owl",
"name": "Ontology for modelling historic administrative information",
"prefix": "17986"
},
"17987": {
"homepage": "http://purl.org/goodrelations/v1",
"name": "The GoodRelations Ontology for Semantic Web-based E-Commerce",
"prefix": "17987"
},
"17988": {
"homepage": "http://www.w3.org/2003/g/data-view",
"name": "Gleaning Resource Descriptions from Dialects of Languages Vocabulary",
"prefix": "17988"
},
"17989": {
"homepage": "http://www.w3.org/2006/gen/ont",
"name": "Generic Specific Ontology",
"prefix": "17989"
},
"1799": {
"description": "This glossary is designed to be a resource to inform people about the culture of βopen scholarshipβ. This resource was written by the community, and depends on the community to stay current.",
"homepage": "http://bit.ly/OpenResearchGlossary",
"license": "CC0-1.0",
"name": "Open Research Glossary",
"prefix": "1799"
},
"17990": {
"homepage": "http://www.opengis.net/ont/geosparql",
"name": "OGC GeoSPARQL",
"prefix": "17990"
},
"17991": {
"homepage": "http://vocab.gtfs.org/terms",
"name": "General Transit Feed Specification",
"prefix": "17991"
},
"17992": {
"homepage": "http://resource.geosciml.org/ontology/timescale/gts",
"name": "Geologic Timescale model",
"prefix": "17992"
},
"17993": {
"homepage": "http://vocab.getty.edu/ontology",
"name": "Getty Vocabulary Program ontology",
"prefix": "17993"
},
"17994": {
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19150/-2/2012/basic",
"name": "Ontology for conversion of ISO/TC 211",
"prefix": "17994"
},
"17995": {
"homepage": "http://sensormeasurement.appspot.com/ont/home/homeActivity",
"name": "Home Activity",
"prefix": "17995"
},
"17996": {
"homepage": "http://www.samos.gr/ontologies/helpdeskOnto.owl",
"name": "HelpDesk support Ontology",
"prefix": "17996"
},
"17997": {
"homepage": "http://purl.org/net/hifm/ontology",
"name": "HIFM Ontology",
"prefix": "17997"
},
"17998": {
"homepage": "http://purl.org/ontology/holding",
"name": "Holding Ontology",
"prefix": "17998"
},
"18": {
"abbreviation": "RAMEAU",
"description": "RAMEAU (Directory of Encyclopaedic and Unified Alphabet Authority and Subject Matter) is the material indexing language used in France by the Bibliothèque nationale de France, university libraries, numerous public and research libraries and several organizations private.\n\nIt has been elaborated since 1980, autonomously, in relation to the \"Directory of subject headings\" of the Université Laval in Quebec City, itself translated from the list of subject headings of the Library of Congress Subject Headings).\n\nThe RAMEAU pre-arranged indexing language consists of a vocabulary of interconnected terms and a syntax indicating the rules for constructing index headings. The set of authority records - the core of which consists of common names and geographical names - constitutes the RAMEAU authorities. They are supplemented by a RAMEAU indexing guide which ensures the correct use. The Creatives and Modifications Journal also informs users twice a year about the enhancements and evolutions of the indexing language.\n\nUnlike a thesaurus, the RAMEAU language is not built a priori but enriched as the needs of indexing, based on the proposals formulated by the network of its users through a National Proposal File BRANCH.",
"homepage": "http://rameau.bnf.fr/",
"name": "Encyclopedic and Unified Alphabetical Directory of Authority-Matter",
"prefix": "18",
"wikidata_database": "Q13421502"
},
"180": {
"description": "The Thesaurus of ERIC Descriptors (Thesaurus) is a controlled vocabulary β a carefully selected list of education-related words and phrases assigned to ERIC records to organize them by subject and make them easier to retrieve through a search. Searching by Descriptors involves selecting relevant terms from this controlled vocabulary to locate information on your topic. While you can also search ERIC using keywords of your choosing, you will get more precise search results if you use Thesaurus terms. That's because searching by keywords requires matching the exact words found in a record, while searching by Descriptors allows you to locate records indexed by subject, regardless of the terminology the author may have used. The ERIC Thesaurus will allow you to conduct systemic searches and save time by reducing guesswork and trial-and-error methods.",
"homepage": "https://eric.ed.gov/?ti=all",
"name": "Education Resources Information Center Thesaurus",
"prefix": "180"
},
"1800": {
"description": "Ein vom Imperial College London erstelltes Glossar, welches Begriffe zum Open Access verzeichnet.",
"homepage": "https://www.imperial.ac.uk/research-and-innovation/support-for-staff/scholarly-communication/open-access/glossary/",
"name": "Glossary of Open Access Terms",
"prefix": "1800"
},
"18000": {
"homepage": "http://iserve.kmi.open.ac.uk/ns/hrests",
"name": "hRESTS Ontology",
"prefix": "18000"
},
"18001": {
"homepage": "http://vcharpenay.github.io/hto/hto.xml",
"name": "Haystack Tagging Ontology",
"prefix": "18001"
},
"18002": {
"homepage": "http://www.w3.org/2011/http",
"name": "HTTP in RDF",
"prefix": "18002"
},
"18003": {
"homepage": "https://www.auto.tuwien.ac.at/downloads/thinkhome/ontology/WeatherOntology.owl",
"name": "Home Weather",
"prefix": "18003"
},
"18004": {
"homepage": "http://www.w3.org/ns/hydra/core",
"name": "The Hydra Core Vocabulary",
"prefix": "18004"
},
"18005": {
"homepage": "http://ontology.eil.utoronto.ca/icontact.owl",
"name": "International Contact Ontology: Addresses, phone numbers and emails",
"prefix": "18005"
},
"18006": {
"homepage": "http://rdf.insee.fr/def/demo",
"prefix": "18006"
},
"18007": {
"homepage": "http://www.identity.org/ontologies/identity.owl",
"name": "Ontology of digital identity",
"prefix": "18007"
},
"18008": {
"homepage": "http://rdf.insee.fr/def/geo",
"license": "CC-BY-3.0",
"prefix": "18008"
},
"18009": {
"homepage": "http://data.ign.fr/def/ignf",
"prefix": "18009"
},
"1801": {
"description": "Taxonomy for the content of CBS website.\" 4267 Terms, 422 Relationships Between Terms, 1463 Preferred Terms.",
"homepage": "http://taxonomie.cbs.nl/vocab/",
"name": "CBS Taxonomie",
"prefix": "1801"
},
"18010": {
"homepage": "http://vocab.resc.info/incident",
"name": "Vocabulary to describe incident response by emergency services",
"prefix": "18010"
},
"18011": {
"homepage": "http://www.ontologydesignpatterns.org/cp/owl/informationrealization.owl",
"name": "Information Realization",
"prefix": "18011"
},
"18012": {
"homepage": "http://purl.org/innovation/ns",
"name": "Ontology for Innovation",
"prefix": "18012"
},
"18013": {
"homepage": "http://reference.data.gov.uk/def/intervals",
"name": "Intervals Ontology",
"prefix": "18013"
},
"18014": {
"homepage": "http://www.ontologydesignpatterns.org/ont/dul/IOLite.owl",
"name": "Information Objects ontology",
"prefix": "18014"
},
"18015": {
"description": "The IoT lite Ontology is a lightweight ontology to represent Internet of Things resources, entities and services. The lightweight allow the representation and use of IoT platforms without consuming excessive processing time when querying the ontology. However it is also a meta ontology that can be extended in order to represent IoT concepts in a more detail way in different domains.",
"homepage": "http://purl.oclc.org/NET/UNIS/fiware/iot-lite",
"license": "CC-BY-3.0",
"name": "IoT lite Ontology",
"prefix": "18015"
},
"18016": {
"homepage": "http://www.irit.fr/recherches/MELODI/ontologies/IoT-O",
"name": "IoT-O",
"prefix": "18016"
},
"18017": {
"homepage": "http://purl.org/ipo/core",
"name": "IPO - Issue Procedure Ontology",
"prefix": "18017"
},
"18018": {
"homepage": "http://www.ontologydesignpatterns.org/ont/web/irw.owl",
"name": "The Identity of Resources on the Web ontology",
"prefix": "18018"
},
"18019": {
"homepage": "http://purl.org/ontology/is/core",
"name": "Info Service Ontology",
"prefix": "18019"
},
"1802": {
"homepage": "http://admin.tcda.infojus.gov.ar/escribanosba/",
"prefix": "1802"
},
"18020": {
"homepage": "http://iflastandards.info/ns/isbd/elements/",
"name": "ISBD elements",
"prefix": "18020"
},
"18021": {
"homepage": "http://purl.org/iso25964/skos-thes",
"name": "ISO 25964 SKOS extension",
"prefix": "18021"
},
"18022": {
"homepage": "http://dati.isprambiente.it/ontology/core",
"name": "Ispra Ontology",
"prefix": "18022"
},
"18023": {
"homepage": "http://spi-fm.uca.es/spdef/models/genericTools/itm/1.0",
"name": "Issue Tracking tool Model",
"prefix": "18023"
},
"18024": {
"homepage": "http://ontology.it/itsmo/v1",
"name": "IT Service Management Ontology",
"prefix": "18024"
},
"18025": {
"homepage": "http://w3id.org/charta77/jup",
"name": "Ontology of Building Accessibility",
"prefix": "18025"
},
"18026": {
"homepage": "http://rdfs.co/juso/",
"name": "Juso Ontology",
"prefix": "18026"
},
"18027": {
"description": "South Korea Extension to Juso Ontology is a Web vocabulary that extends Juso Ontology to descrbe geographical addresses and features in South Korea.\n\nThe master version of this vocabulary is maintained in the GitHub repository so others can contribute edits and improvements.\nMost of the descriptions given here are from Wikipedia or from the related ontologies and vocabularies.",
"homepage": "http://rdfs.co/juso/kr/",
"name": "South Korea Extension to Juso Ontology",
"prefix": "18027"
},
"18028": {
"homepage": "http://kdo.render-project.eu/kdo",
"name": "The Knowledge Diversity Ontology",
"prefix": "18028"
},
"18029": {
"homepage": "http://linkeddata.center/kees/v1",
"name": "KEES Ontology",
"prefix": "18029"
},
"1803": {
"homepage": "http://admin.tcda.infojus.gov.ar/mintrabajo2/",
"prefix": "1803"
},
"18030": {
"homepage": "http://purl.org/NET/c4dm/keys.owl",
"name": "Keys Ontology",
"prefix": "18030"
},
"18031": {
"homepage": "http://www.disit.org/km4city/schema",
"name": "km4city, the DISIT Knowledge Model for City and Mobility",
"prefix": "18031"
},
"18032": {
"homepage": "http://purl.org/net/vocab/2004/03/label",
"name": "label",
"prefix": "18032"
},
"18033": {
"homepage": "http://lawd.info/ontology/",
"name": "Linking Ancient World Data Ontology",
"prefix": "18033"
},
"18034": {
"homepage": "http://purl.org/vocab/lifecycle/schema",
"name": "Lifecycle Schema",
"prefix": "18034"
},
"18035": {
"homepage": "http://www.w3.org/ns/ldp",
"name": "Linked Data Platform",
"prefix": "18035"
},
"18036": {
"homepage": "http://purl.oclc.org/NET/ldr/ns",
"name": "Linked Data Rights (LDR)",
"prefix": "18036"
},
"18037": {
"homepage": "http://linked.opendata.cz/ontology/ldvm/",
"name": "Vocabulary for Linked Data Visualization Model",
"prefix": "18037"
},
"18038": {
"description": "The lexicon model for ontologies is designed to allow for descriptions of lexical information regarding ontological elements and other RDF resources. Lemon covers mapping of lexical decomposition, phrase structure, syntax, variation, morphology, and lexicon-ontology mapping.",
"homepage": "http://lemon-model.net/lemon",
"license": "CC-BY-3.0",
"name": "LExicon Model for ONtologies",
"prefix": "18038"
},
"18039": {
"homepage": "http://www.lexinfo.net/ontology/2.0/lexinfo",
"name": "LexInfo Ontology",
"prefix": "18039"
},
"1804": {
"description": "Controlled vocabulary of terms in Criminalistics Developed by staff of the Central Library of the Faculty of Law of the University of Buenos Aires Author: Maria Lia Miranda Lawyer Technical and linguistic assistance of Infojus: Diego Ferreyra and MarΓa OsΓ©s. 87 Terms.",
"homepage": "http://admin.tcda.infojus.gov.ar/criminalistica/",
"name": "Forensic science vocabulary",
"prefix": "1804"
},
"18040": {
"homepage": "http://linkedgeodata.org/ontology",
"name": "LinkedGeoData ontology",
"prefix": "18040"
},
"18041": {
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/lineage",
"name": "OWL representation of ISO 19115 (Geographic Information - Metadata - Lineage package)",
"prefix": "18041"
},
"18042": {
"homepage": "http://purl.org/library/",
"name": "Library extension of schema.org",
"prefix": "18042"
},
"18043": {
"homepage": "http://www.irit.fr/recherches/MELODI/ontologies/IoT-Lifecycle",
"name": "IoT-Lifecycle",
"prefix": "18043"
},
"18044": {
"homepage": "http://purl.org/limo-ontology/limo/",
"name": "Linked Statistical Models Vocabulary",
"prefix": "18044"
},
"18045": {
"homepage": "http://purl.org/LiMo/0.1",
"name": "License Model Ontology",
"prefix": "18045"
},
"18046": {
"homepage": "http://www.lingvoj.org/ontology",
"name": "The Lingvoj Ontology",
"prefix": "18046"
},
"18047": {
"homepage": "http://purl.org/net/lio",
"name": "Lightweight Image Ontology",
"prefix": "18047"
},
"18048": {
"homepage": "http://www.linklion.org/ontology",
"name": "LinkLion - the Link Discovery Portal",
"prefix": "18048"
},
"18049": {
"homepage": "http://www.ontologydesignpatterns.org/ont/lmm/LMM_L1.owl",
"name": "Lexical MetaModel Level 1",
"prefix": "18049"
},
"1805": {
"description": "Controlled Vocabulary on Castilian medieval poetry (from metric to general terminology of tratadΓstica) elaborated in the framework of the projects of the group PoeMetca, http://poemetca.linhd.es/.",
"homepage": "http://vocabularios.caicyt.gov.ar/pmc/",
"license": "CC BY-SA 3.0",
"name": "Spanish Medieval Poetry",
"prefix": "1805"
},
"18050": {
"homepage": "http://www.ontologydesignpatterns.org/ont/lmm/LMM_L2.owl",
"name": "Lexical MetaModel Level 2",
"prefix": "18050"
},
"18051": {
"homepage": "http://purl.org/ctic/infraestructuras/localizacion",
"prefix": "18051"
},
"18052": {
"homepage": "http://data.archiveshub.ac.uk/def/",
"name": "The LOCAH RDF Vocabulary",
"prefix": "18052"
},
"18053": {
"homepage": "http://www.w3.org/ns/locn",
"name": "ISA Programme Location Core Vocabulary",
"prefix": "18053"
},
"18054": {
"homepage": "http://linkedevents.org/ontology/",
"name": "Linking Open Descriptions of Events",
"prefix": "18054"
},
"18055": {
"homepage": "http://www.w3.org/2000/10/swap/log",
"name": "SWAP Logic Ontology",
"prefix": "18055"
},
"18056": {
"homepage": "http://data.opendiscoveryspace.eu/lom_ontology_ods.owl",
"name": "Learning Object Metadata Ontology",
"prefix": "18056"
},
"18057": {
"homepage": "http://loted.eu/ontology",
"name": "LOTED ontology",
"prefix": "18057"
},
"18058": {
"homepage": "http://linkedscience.org/lsc/ns",
"name": "Linked Science Core Vocabulary",
"prefix": "18058"
},
"18059": {
"homepage": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-lifemapper.owl",
"name": "ELSEWeb Lifemapper Ontology",
"prefix": "18059"
},
"1806": {
"homepage": "http://vocabularios.caicyt.gov.ar/biblioclastia/",
"prefix": "1806"
},
"18060": {
"homepage": "http://ontology.cybershare.utep.edu/ELSEWeb/mappings/elseweb-mappings.owl",
"name": "ELSEWeb Mappings Ontology",
"prefix": "18060"
},
"18061": {
"homepage": "http://lsq.aksw.org/vocab",
"name": "The Linked SPARQL Queries Vocabulary (LSQ(V))",
"prefix": "18061"
},
"18062": {
"homepage": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-data.owl",
"name": "ELSEWeb Data Ontology",
"prefix": "18062"
},
"18063": {
"homepage": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-modelling.owl",
"name": "ELSEWeb Modelling Ontology",
"prefix": "18063"
},
"18064": {
"homepage": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-lifemapper-parameters.owl",
"name": "ELSEWeb Lifemapper Parameters Ontology",
"prefix": "18064"
},
"18065": {
"homepage": "http://ns.inria.fr/ludo",
"name": "Ludo Ontology",
"prefix": "18065"
},
"18066": {
"homepage": "http://ns.inria.fr/ludo/v1/gamemodel",
"name": "Ludo Game Model Ontology",
"prefix": "18066"
},
"18067": {
"homepage": "http://ns.inria.fr/ludo/v1/gamepresentation",
"name": "Ludo - Game Presentation",
"prefix": "18067"
},
"18068": {
"homepage": "http://ns.inria.fr/ludo/v1/virtualcontext",
"name": "Ludo - Virtual Context",
"prefix": "18068"
},
"18069": {
"homepage": "http://ns.inria.fr/ludo/v1/xapi",
"name": "Experience API (xAPI)",
"prefix": "18069"
},
"18070": {
"abbreviation": "lv",
"homepage": "http://purl.org/lobid/lv",
"name": "lobid vocab",
"prefix": "18070"
},
"18071": {
"homepage": "http://lexvo.org/ontology",
"name": "Lexvo.org Ontology",
"prefix": "18071"
},
"18072": {
"homepage": "http://purl.org/linkingyou/",
"name": "Linking-you vocabulary",
"prefix": "18072"
},
"18073": {
"homepage": "http://purl.org/iot/vocab/m3-lite",
"name": "The Machine-to-Machine Measurement (M3) Lite Ontology",
"prefix": "18073"
},
"18074": {
"homepage": "http://www.w3.org/ns/ma-ont",
"name": "Ontology for Media Resources",
"prefix": "18074"
},
"18075": {
"homepage": "http://www.loc.gov/mads/rdf/v1",
"name": "Metadata Authority Description Schema",
"prefix": "18075"
},
"18076": {
"homepage": "http://www.gsi.dit.upm.es/ontologies/marl/ns",
"name": "Marl Ontology Specification",
"prefix": "18076"
},
"18077": {
"homepage": "http://securitytoolbox.appspot.com/MASO",
"prefix": "18077"
},
"18078": {
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/metadata",
"name": "OWL representation of ISO 19115",
"prefix": "18078"
},
"18079": {
"homepage": "http://semweb.datasciencelab.be/ns/multidimensional-interface/",
"name": "RDF vocabulary to describe a Multidimensional Interface",
"prefix": "18079"
},
"1808": {
"description": "Enter words into the search box, \"visualize a word,\" to look them up. Touch a node to see the definition of that word group and click and drag individual nodes to move them around to help clarify connections.\n\n It's a dictionary! It's a thesaurus!\n\n Great for writers, journalists, students, teachers, and artists.\n\n The online dictionary is available wherever thereβs an internet connection.\n\n No membership required.\n\nVisuwordsβ’ uses Princeton Universityβs WordNet, an opensource database built by University students and language researchers. Combined with a visualization tool and user interface built from a combination of modern web technologies, Visuwordsβ’ is available as a free resource to all patrons of the web.",
"homepage": "http://visuwords.com/",
"name": "Visuwordsβ’",
"prefix": "1808"
},
"18080": {
"homepage": "http://rdf.myexperiment.org/ontologies/base/",
"name": "The myExperiment Base Ontology",
"prefix": "18080"
},
"18081": {
"homepage": "http://purl.org/media",
"name": "The Media RDF Vocabulary",
"prefix": "18081"
},
"18082": {
"homepage": "http://mex.aksw.org/mex-algo",
"name": "MEX Algorithm Ontology",
"prefix": "18082"
},
"18083": {
"homepage": "http://mex.aksw.org/mex-core",
"name": "MEX Core Vocabulary",
"prefix": "18083"
},
"18084": {
"homepage": "http://mex.aksw.org/mex-perf",
"name": "MEX Performance Ontology",
"prefix": "18084"
},
"18085": {
"description": "The Muninn Military Ontology marks up information about military people, organizations and events.",
"homepage": "http://rdf.muninn-project.org/ontologies/military",
"license": "CC BY-SA 3.0",
"name": "Military Ontology Specification",
"prefix": "18085"
},
"18086": {
"homepage": "http://www.w3.org/ns/mls",
"name": "Machine Learning Schema",
"prefix": "18086"
},
"18087": {
"homepage": "http://www.observedchange.com/moac/ns",
"name": "Management of a Crisis Vocabulary",
"prefix": "18087"
},
"18088": {
"homepage": "http://moat-project.org/ns",
"name": "Meaning of a Tag Ontology",
"prefix": "18088"
},
"18089": {
"description": "The purpose of this list of relator terms and associated codes is to allow the relationship between an agent and a resource to be designated in bibliographic records.",
"homepage": "http://id.loc.gov/vocabulary/relators",
"name": "MARC Code List for Relators",
"prefix": "18089"
},
"1809": {
"description": "WordNetΒ is a large lexical database of English. Nouns, verbs, adjectives and adverbs are grouped into sets of cognitive synonyms (synsets), each expressing a distinct concept. Synsets are interlinked by means of conceptual-semantic and lexical relations. The resulting network of meaningfully related words and concepts can be navigated with the browser. WordNet is also freely and publicly available for download. WordNet's structure makes it a useful tool for computational linguistics and natural language processing.\n\n WordNet superficially resembles a thesaurus, in that it groups words together based on their meanings. However, there are some important distinctions. First, WordNet interlinks not just word formsβstrings of lettersβbut specific senses of words. As a result, words that are found in close proximity to one another in the network are semantically disambiguated. Second, WordNet labels the semantic relations among words, whereas the groupings of words in a thesaurus does not follow any explicit pattern other than meaning similarity.",
"homepage": "https://wordnet.princeton.edu/",
"name": "WordNet",
"prefix": "1809",
"wikidata_database": "Q533822"
},
"18090": {
"homepage": "http://iserve.kmi.open.ac.uk/ns/msm",
"name": "Minimal Service Model",
"prefix": "18090"
},
"18091": {
"homepage": "http://www.telegraphis.net/ontology/measurement/measurement",
"name": "Measurement Ontology",
"prefix": "18091"
},
"18092": {
"homepage": "http://www.ics.forth.gr/isl/MarineTLO/v4/marinetlo.owl",
"name": "MarineTLO Ontology",
"prefix": "18092"
},
"18093": {
"description": "A vocabulary, or music ontology, to describe classical music and performances. Classes (categories) for musical works, events, instruments and performers, as well as related properties are defined. Make sure to distinguish musical works (e.g. Opera) from performance events (Opera_Event), or works (String_Quartette) from performer (StringQuartetEnsemble in this vocab), whose natural language terms are used interchangeblly. The present version experiments more precise model to describe a musical work, its representations (performances, scores, etc) and a musical event to present a representation (a concert). Includes 30 keys as individuals.",
"homepage": "http://www.kanzaki.com/ns/music",
"name": "Music Vocabulary",
"prefix": "18093"
},
"18094": {
"homepage": "http://purl.org/muto/core",
"name": "Modular Unified Tagging Ontology (MUTO)",
"prefix": "18094"
},
"18095": {
"homepage": "http://purl.oclc.org/NET/mvco.owl",
"name": "Media Value Chain Ontology",
"prefix": "18095"
},
"18096": {
"homepage": "http://www.semanticdesktop.org/ontologies/2007/08/15/nao",
"name": "NEPOMUK Annotation Ontology",
"prefix": "18096"
},
"18097": {
"homepage": "http://www.semanticdesktop.org/ontologies/2007/04/02/ncal",
"name": "NEPOMUK Calendar Ontology",
"prefix": "18097"
},
"18098": {
"homepage": "http://www.semanticdesktop.org/ontologies/2007/03/22/nco",
"name": "NEPOMUK Contact Ontology",
"prefix": "18098"
},
"18099": {
"homepage": "http://www.semanticdesktop.org/ontologies/2007/03/22/nfo",
"name": "NEPOMUK File Ontology",
"prefix": "18099"
},
"181": {
"abbreviation": "AEO",
"description": "The AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology, to about 160 classes using the is_a relationship; it thus provides a detailed type classification for tissues. The ~100 new classes were chosen for their use in categorizing the major vertebrate and invertebrate anatomy ontologies at a granularity adequate for tissues of a single cell type.\n\nThe AEO is intended to be useful in increasing the amount of knowledge in anatomy ontologies, facilitating annotation and enabling interoperability across anatomy ontologies.\n\nAn important subcategory of the AEO is simple tissue (a synonym of the CARO portion of tissue), a recognisable anatomical entity composed predominantly to a single cell type. CARO had a only few epithelial classes here and these are inadequate for capturing the richness of anatomical tissue knowledge. The AEO has ~70 simple tissues and these are linked to their cell types (~100) as detailed in the cell type ontology through a has_part relationship. The AEO thus includes a subset of the cell type ontology.\n\nThe AEO has been refined through its use in annotating the ~2500 terms of the new version of the Ontology of Developing Human Anatomy and, while this has improved the ontology, it may have given it a mammalian bias.\n\nThe ontology can be used to classify most organisms as its terms are appropriate for most plant and fungal tissues. I plan to improve the ontology to include more non-animal anatomical terms.",
"name": "Ontology of Anatomical Entities",
"prefix": "181"
},
"1810": {
"description": "The Digital Humanities Thesaurus is a subject thesaurus covering the topic of digital humanities, and it is intended to be used for indexing Digital Humanities projects and articles. The terms in this thesaurus are arranged into hierarchical sections. Within each section terms are listed in alphabetical order. There is a search bar in the upper right hand corner, and also an 'Advanced Search' option in the top menu bar.\" 7568 Terms, 8166 Relations between terms, 323 Non preferred terms.",
"homepage": "http://vocabularyserver.com/dhthesaurus/index.php",
"name": "Digital Humanities Thesaurus",
"prefix": "1810"
},
"18100": {
"homepage": "http://geovocab.org/geometry",
"name": "NeoGeo Geometry Ontology",
"prefix": "18100"
},
"18101": {
"homepage": "http://www.semanticdesktop.org/ontologies/2007/01/19/nie",
"name": "NEPOMUK Information Element Core Ontology",
"prefix": "18101"
},
"18102": {
"homepage": "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core",
"name": "NLP Interchange Format",
"prefix": "18102"
},
"18103": {
"abbreviation": "nlon",
"description": "This specification describes National Library of Korea Ontology vocaburaries using W3C's RDF and OWL technology",
"homepage": "http://lod.nl.go.kr/ontology/",
"name": "National Library of Korea Ontology",
"prefix": "18103"
},
"18104": {
"homepage": "http://ns.nature.com/terms/",
"name": "Nature.com Core Ontology",
"prefix": "18104"
},
"18105": {
"homepage": "http://www.semanticdesktop.org/ontologies/2007/08/15/nrl",
"name": "NEPOMUK Representational Language",
"prefix": "18105"
},
"18107": {
"homepage": "http://ns.inria.fr/nicetag/2010/09/09/voc",
"name": "Nice Tag Ontology",
"prefix": "18107"
},
"18108": {
"homepage": "http://www.w3.org/ns/oa",
"name": "Open Annotation Data Model",
"prefix": "18108"
},
"18109": {
"description": "An ontology for the description of archival data (OAD, βOntology of Archival Descriptionβ) using the Web Ontology Language (OWL). This ontology represents the classes and properties needed to expose the archival resources as linked data.",
"homepage": "http://lod.xdams.org/reload/oad",
"license": "CC-BY-3.0",
"name": "Ontology for archival description",
"prefix": "18109"
},
"1811": {
"homepage": "http://vocabularyserver.com/redprodepaz/",
"prefix": "1811"
},
"18110": {
"homepage": "http://www.ics.forth.gr/isl/oae/core",
"name": "Open NEE Model",
"prefix": "18110"
},
"18111": {
"homepage": "http://data.lirmm.fr/ontologies/oan",
"prefix": "18111"
},
"18112": {
"homepage": "http://purl.obolibrary.org/obo/obi.owl",
"name": "Ontology for Biomedical Investigation",
"prefix": "18112"
},
"18113": {
"homepage": "http://rdf.geospecies.org/methods/observationMethod.rdf",
"name": "Observation Method Ontology",
"prefix": "18113"
},
"18114": {
"homepage": "http://delicias.dia.fi.upm.es/ontologies/ObjectWithStates.owl",
"name": "Object with states ontology",
"prefix": "18114"
},
"18115": {
"homepage": "http://contextus.net/ontology/ontomedia/core/expression",
"name": "OntoMedia Core",
"prefix": "18115"
},
"18116": {
"homepage": "http://vocab.deri.ie/odapp",
"name": "Open Data Applications Vocabulary",
"prefix": "18116"
},
"18117": {
"homepage": "http://semweb.mmlab.be/ns/odapps",
"name": "The vocabulary for (L)OD ideas and applications",
"prefix": "18117"
},
"18118": {
"homepage": "http://www.ontologydesignpatterns.org/cp/owl/participation.owl",
"name": "Ontology Design Pattern Participation",
"prefix": "18118"
},
"18119": {
"homepage": "http://www.w3.org/ns/odrl/2/",
"name": "The Open Digital Rights Language (ODRL) Ontology",
"prefix": "18119"
},
"1812": {
"description": "114 Terms.",
"homepage": "http://vocabularios.educacion.gov.ar/index.php?v=PRO",
"license": "CC BY-NC-SA 3.0",
"name": "Vocabulary on Production of Educational Materials",
"prefix": "1812"
},
"18120": {
"homepage": "http://schema.theodi.org/odrs",
"name": "Open Data Rights Statement Vocabulary",
"prefix": "18120"
},
"18121": {
"homepage": "http://reference.data.gov.uk/def/organogram",
"name": "Organogram Data Vocabulary",
"prefix": "18121"
},
"18122": {
"homepage": "http://www.oegov.org/core/owl/cc",
"name": "Extended Creative Commons Ontology",
"prefix": "18122"
},
"18123": {
"homepage": "http://owlrep.eu01.aws.af.cm/fridge",
"name": "Open Fridge vocabulary",
"prefix": "18123"
},
"18124": {
"homepage": "http://purl.org/opdm/refrigerator",
"name": "Fridge and Freezer Vocabulary",
"prefix": "18124"
},
"18125": {
"homepage": "http://ogp.me/ns",
"name": "Open Graph Protocol Vocabulary",
"prefix": "18125"
},
"18126": {
"homepage": "http://semweb.mmlab.be/ns/oh",
"name": "The Opening Hours vocabulary",
"prefix": "18126"
},
"18127": {
"homepage": "http://www.lingvoj.org/olca",
"name": "Ontology Loose Coupling Annotation",
"prefix": "18127"
},
"18128": {
"homepage": "http://purl.org/ontology/olo/core",
"name": "Ordered List Ontology",
"prefix": "18128"
},
"18129": {
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19156/2011/observation",
"name": "ISO 19156 Observation Model",
"prefix": "18129"
},
"1813": {
"description": "Over the last three years of our work with the Incluseum, weβve thought, written, and talked extensively of the power of words. (...) Working through the medium of the blog, however, we became dissatisfied with our ad-hoc and fractured way of organizing content. In other words, related content has not been systematically categorized and labelled as to make their relations visible. Moreover, we were concerned that our simple buckets (e.g., 'race/racism', 'gender', etc.) did not accurately capture how we wanted to be referring to the content in our blogposts. To address this situation, we partnered with Gabbie Barnes and Becca Fronczak, both students in the University of Washingtonβs Master in Library and Information Science program. They used their skills to develop a metadata schema for The Incluseum blog. A metadata schema helps create a standard for how things (i.e., information resources) should be described within a particular context to enhance user access. Here, their goal was also to ensure that the metadata schema would match The Incluseumβs values.",
"homepage": "https://drive.google.com/file/d/0Bzh2lQ7JEDUGbklKQlJ0TGY5bk0/view?usp=sharing",
"name": "Incluseum Metadata Schema",
"prefix": "1813"
},
"18130": {
"homepage": "http://def.seegrid.csiro.au/ontology/om/om-lite",
"name": "OWL for Observations",
"prefix": "18130"
},
"18131": {
"homepage": "http://open-multinet.info/ontology/omn",
"name": "Open-Multinet Upper Ontology",
"prefix": "18131"
},
"18132": {
"homepage": "http://open-multinet.info/ontology/omn-federation",
"name": "Open-Multinet Upper Federation Ontology",
"prefix": "18132"
},
"18133": {
"homepage": "http://open-multinet.info/ontology/omn-lifecycle",
"name": "Open-Multinet Upper Lifecycle Ontology",
"prefix": "18133"
},
"18134": {
"homepage": "http://www.ics.forth.gr/isl/oncm/core",
"name": "Open NEE Configuration Model",
"prefix": "18134"
},
"18135": {
"homepage": "http://purl.org/net/ns/ontology-annot",
"name": "Ontology annotation DLiser vocabulary",
"prefix": "18135"
},
"18136": {
"homepage": "http://www.ontologydesignpatterns.org/ont/dul/ontopic.owl",
"name": "Ontopic Ontology",
"prefix": "18136"
},
"18137": {
"homepage": "http://www.semanticweb.org/ontologies/2008/11/OntologySecurity.owl",
"name": "Ontology Security",
"prefix": "18137"
},
"18138": {
"homepage": "http://www.gsi.dit.upm.es/ontologies/onyx/ns",
"name": "Onyx Emotion Ontology",
"prefix": "18138"
},
"18139": {
"homepage": "http://purl.org/openorg/",
"name": "Open Organisations",
"prefix": "18139"
},
"1814": {
"description": "Media Types Scheme is derived from a controlled list of coded values representing content types principally used in RDA cataloging.",
"homepage": "http://id.loc.gov/vocabulary/mediaTypes",
"name": "Library of Congress Media Types Scheme",
"prefix": "1814"
},
"18140": {
"homepage": "http://environment.data.gov.au/def/op",
"name": "Observable properties",
"prefix": "18140"
},
"18141": {
"homepage": "http://ontology.eil.utoronto.ca/open311.owl",
"name": "Open 311 Ontology: An Ontology for publishing a city's non-emergency events.",
"prefix": "18141"
},
"18142": {
"homepage": "http://openprovenance.org/model/opmo",
"name": "Open Provenance Model",
"prefix": "18142"
},
"18143": {
"homepage": "http://purl.org/net/opmv/ns",
"name": "Open Provenance Model Vocabulary",
"prefix": "18143"
},
"18144": {
"homepage": "http://www.opmw.org/ontology/",
"name": "The OPMW Ontology",
"prefix": "18144"
},
"18145": {
"homepage": "http://online-presence.net/opo/ns",
"name": "Online Presence Ontology",
"prefix": "18145"
},
"18146": {
"homepage": "http://lsdis.cs.uga.edu/projects/semdis/opus",
"name": "SwetoDblp Ontology of Computer Science Publications",
"prefix": "18146"
},
"18147": {
"homepage": "http://www.openarchives.org/ore/terms/",
"name": "The OAI ORE terms vocabulary",
"prefix": "18147"
},
"18148": {
"homepage": "https://www.w3.org/TR/vocab-org/",
"name": "Core organization ontology",
"prefix": "18148"
},
"18149": {
"homepage": "http://datos.gob.es/def/sector-publico/organizacion",
"name": "Ontology about Spanish public organizations",
"prefix": "18149"
},
"1815": {
"description": "An umbrella scheme to collocate all the preservation vocabularies.",
"homepage": "http://id.loc.gov/vocabulary/preservation",
"name": "Preservation Schemes",
"prefix": "1815"
},
"18150": {
"homepage": "http://data.ordnancesurvey.co.uk/ontology/admingeo/",
"name": "The administrative geography and civil voting area ontology",
"prefix": "18150"
},
"18151": {
"homepage": "http://data.ordnancesurvey.co.uk/ontology/geometry/",
"name": "Ordnance Survey Geometry Ontology",
"prefix": "18151"
},
"18152": {
"homepage": "http://open-services.net/ns/core",
"name": "OSLC Core Vocabulary",
"prefix": "18152"
},
"18153": {
"homepage": "http://purl.org/oslo/ns/localgov",
"name": "OSLO Exchange Standard",
"prefix": "18153"
},
"18154": {
"homepage": "http://data.lirmm.fr/ontologies/osp",
"prefix": "18154"
},
"18155": {
"homepage": "http://contextus.net/ontology/ontomedia/core/space",
"name": "OntoMedia Space Representation",
"prefix": "18155"
},
"18156": {
"homepage": "http://data.ordnancesurvey.co.uk/ontology/spatialrelations/",
"name": "Spatial Relations Ontology",
"prefix": "18156"
},
"18157": {
"homepage": "http://www.ordnancesurvey.co.uk/ontology/Topography/v0.1/Topography.owl",
"name": "Ordnance Survey Topography Ontology",
"prefix": "18157"
},
"18158": {
"homepage": "http://open.vocab.org/terms",
"name": "OpenVocab",
"prefix": "18158"
},
"18159": {
"homepage": "http://www.w3.org/2002/07/owl",
"name": "The OWL 2 Schema vocabulary",
"prefix": "18159"
},
"1816": {
"description": "2135 Terms, 683 Relationships between terms, 519 Terms not preferred.",
"name": "Controlled Vocabulary for Arts of the Show",
"prefix": "1816"
},
"18160": {
"homepage": "http://purl.org/net/p-plan",
"name": "The P-PLAN Ontology",
"prefix": "18160"
},
"18161": {
"homepage": "http://reference.data.gov.uk/def/parliament",
"name": "Parliament Ontology",
"prefix": "18161"
},
"18162": {
"homepage": "http://purl.org/vocab/participation/schema",
"name": "Participation Schema",
"prefix": "18162"
},
"18163": {
"homepage": "http://data.lirmm.fr/ontologies/passim",
"name": "PASSIM ontology",
"prefix": "18163"
},
"18164": {
"homepage": "http://purl.org/hpi/patchr",
"name": "Patch Request Ontology",
"prefix": "18164"
},
"18165": {
"homepage": "http://www.essepuntato.it/2008/12/pattern",
"name": "The Pattern Ontology",
"prefix": "18165"
},
"18166": {
"homepage": "http://purl.org/pav/",
"name": "Provenance, Authoring and Versioning",
"prefix": "18166"
},
"18167": {
"homepage": "http://reference.data.gov.uk/def/payment",
"name": "Payments ontology",
"prefix": "18167"
},
"18168": {
"homepage": "http://purl.org/ontology/pbo/core",
"name": "Play Back Ontology",
"prefix": "18168"
},
"18169": {
"homepage": "http://purl.org/procurement/public-contracts",
"name": "Public Contracts Ontology",
"prefix": "18169"
},
"1817": {
"description": "The Ship Type List contains terms that are useful when registering a vessel, a map of a vessel or item attached to a vessel. The Data Type Ship Types are intended to be used with the Data Set Named Ship Types and the Data Set Series Manufactured Ships. The maritime heritage is a concern for many. We are therefore eight maritime museums that collaborate on common authorities and vocabulary in order to be able to describe the maritime heritage in a unified way. (...) The goal is for our cooperation to provide improved quality, searchability and usability in the information about the maritime heritage. Please use authorities and vocabulary and contact Malin Joakimson (mailto:Malin.Joakimson@maritima.se) if you and your institution want to take a more active part of the cooperation. The starting point for the list of ship types has been The Getty Research Institute's Art and Architecture Thesaurus and the terms linked To Vessel / Watercraf This material has since been translated, reproduced and supplemented to meet the needs of the maritime heritage in the Nordic waters. The terms have been linked to Gettys thesaurus and against Wikidata with the aim of facilitating links and searchability.",
"homepage": "http://kulturnav.org/c43d8eba-030b-4542-b1ac-6a31a0ba6d00",
"name": "Ship Types",
"prefix": "1817",
"wikidata_database": "Q20742915"
},
"18170": {
"homepage": "http://vocab.deri.ie/pdo",
"name": "Project Documents Ontology",
"prefix": "18170"
},
"18171": {
"homepage": "https://w3id.org/pep/",
"name": "Process Execution ontology.",
"prefix": "18171"
},
"18172": {
"homepage": "http://www.w3.org/ns/person",
"name": "ISA Programme Person Core Vocabulary",
"prefix": "18172"
},
"18173": {
"homepage": "http://www.ontotext.com/proton/protonext",
"name": "PROTON Extent module",
"prefix": "18173"
},
"18174": {
"homepage": "http://rdf-vocabulary.ddialliance.org/phdd",
"name": "Physical Data Description",
"prefix": "18174"
},
"18175": {
"homepage": "http://purl.org/ontology/places",
"name": "The Places Ontology",
"prefix": "18175"
},
"18176": {
"homepage": "http://cedric.cnam.fr/isid/ontologies/PersonLink.owl",
"name": "PersonLink Ontology",
"prefix": "18176"
},
"18177": {
"homepage": "http://purl.org/net/po",
"name": "Playlist Ontology",
"prefix": "18177"
},
"18178": {
"homepage": "http://inference-web.org/2.0/pml-provenance.owl",
"name": "PML2 provenance ontology",
"prefix": "18178"
},
"18179": {
"homepage": "http://data.press.net/ontology/asset/",
"name": "Press.net Asset Ontology",
"prefix": "18179"
},
"18180": {
"homepage": "http://data.press.net/ontology/classification/",
"name": "Press.net Classification Ontology",
"prefix": "18180"
},
"18181": {
"homepage": "http://data.press.net/ontology/event/",
"name": "Press.net Event Ontology",
"prefix": "18181"
},
"18182": {
"homepage": "http://data.press.net/ontology/identifier/",
"name": "SNaP Identifier Ontology",
"prefix": "18182"
},
"18183": {
"homepage": "http://data.press.net/ontology/stuff/",
"name": "Press.net Stuff Ontology",
"prefix": "18183"
},
"18184": {
"homepage": "http://data.press.net/ontology/tag/",
"name": "Press.net Tag Ontology",
"prefix": "18184"
},
"18185": {
"homepage": "http://dev.poderopedia.com/vocab/schema",
"name": "Poder Vocabulary",
"prefix": "18185"
},
"18186": {
"homepage": "http://data.ordnancesurvey.co.uk/ontology/postcode/",
"name": "Postcode Ontology",
"prefix": "18186"
},
"18187": {
"homepage": "http://data.lirmm.fr/ontologies/poste",
"prefix": "18187"
},
"18188": {
"homepage": "http://vocab.deri.ie/ppo",
"name": "Privacy Preference Ontology",
"prefix": "18188"
},
"18189": {
"homepage": "http://contsem.unizar.es/def/sector-publico/pproc",
"name": "PPROC ontology",
"prefix": "18189"
},
"1819": {
"description": "Thesaurus for fashion and fashion-related concepts in 10 languages based on the Art and Architecture Thesaurus (AAT)",
"name": "Europeana Fashion Vocabulary",
"prefix": "1819",
"wikidata_database": "Q29016777"
},
"18190": {
"homepage": "http://purl.org/ontology/prv/core",
"name": "Property Reification Vocabulary",
"prefix": "18190"
},
"18191": {
"homepage": "http://www.loc.gov/premis/rdf/v1",
"name": "PREMIS Ontology",
"prefix": "18191"
},
"18192": {
"homepage": "http://ns.inria.fr/prissma/v2",
"name": "Presentation of Resources for Interoperable Semantic and Shareable Mobile Adaptability",
"prefix": "18192"
},
"18193": {
"description": "PRO, the Publishing Roles Ontology, is an ontology written in OWL 2 DL for the characterization of the roles of agents (people, corporate bodies and computational agents) in the publication process. It permits one to specify how an agent has a role relating to a contextual entity, and the period of time during which that role is held.",
"homepage": "http://purl.org/spar/pro",
"license": "CC-BY-3.0",
"name": "The Publishing Roles Ontology",
"prefix": "18193"
},
"18194": {
"homepage": "http://purl.org/prog/",
"name": "The Event Programme Vocabulary",
"prefix": "18194"
},
"18195": {
"homepage": "http://www.w3.org/ns/prov",
"name": "W3C PROVenance Interchange",
"prefix": "18195"
},
"18196": {
"homepage": "http://ns.inria.fr/provoc",
"name": "Product Vocabulary",
"prefix": "18196"
},
"18197": {
"homepage": "http://purl.org/net/provenance/ns",
"name": "Provenance Vocabulary Core Ontology",
"prefix": "18197"
},
"18198": {
"description": "Extends the Provenance Vocabulary by defining subclasses of the types of provenance elements introduced in the core ontology.",
"homepage": "http://purl.org/net/provenance/types",
"name": "Provenance Vocabulary types",
"prefix": "18198"
},
"18199": {
"description": "PSO, the Publishing Status Ontology, is an ontology written in OWL 2 DL for characterizing the publication status of a document or other publication entity at each of the various stages in the publishing process (e.g. draft, submitted, under review, rejected, accepted for publication, proof, published, Version of Record, catalogued, archived).\n\nBecause it is based on the Time-indexed Value in Context ontology pattern (http://www.essepuntato.it/2012/04/tvc), it is easy to extends the set of specified statuses, simply by adding new individual to the class pso:Status or its sub-class pso:PublicationStatus.",
"homepage": "http://purl.org/spar/pso",
"license": "CC-BY-3.0",
"name": "The Publishing Status Ontology",
"prefix": "18199"
},
"182": {
"description": "The European Training Thesaurus (ETT) constitutes the controlled vocabulary of reference for vocational education and training (VET) in Europe. It is used to describe and access the knowledge of its institution, Cedefop. It contains over 2,500 terms (1550 are descriptors, and 950 non descriptors). Non-descriptors are in italics and contain a reference to the preferred term (descriptor). All terms are accessible through an alphabetical index in English (EN) and French (FR). Using ETT you can retrieve information and news from Cedefop's online catalogue on vocational training (VET-Bib); the ETV web site; the Training Institutions database, and ERO.",
"homepage": "http://libserver.cedefop.europa.eu/browse_subjects_alpha.aspx",
"name": "European Training Thesaurus",
"prefix": "182"
},
"1820": {
"description": "\"The lemmario-guide is aimed at compiling the Dress-Dresser Board.\n\n Contains terms related to:\n\n - single, complete garments and clothing items covering men's, feminine and infantile clothing and related to the main purposes of use and the various occasions of life\n\n Private and social; Were considered essential historical typologies of the 18th, 19th and 20th centuries, and those relating to garments still in use;\n\n - garments and items relating to underwear and hosiery;\n\n - elements of modeling and extending the feminine form from the 18th century to the present fashion;\n\n - structural and decorative components of furnishing items;\n\n - terms relating to the various sartorial processing;\n\n - lacing and / or closure systems in addition to the elements, applied or inserted, that determine them;\n\n - technique and textile decoration, main techniques and applications of lace and embroidery.\n\n Each lemma is accompanied by the acronym of the Dress-Dresser board field, for which the valuation can be used; The value \"\" descr \"\" indicates that the lemma is not included in a control vocabulary and can be used as a valid technical term in descriptive free text fields in the given form.\n\n The limbs that define the types of garments, if they are related to morphological typologies, are described within the main lymph while they generally have autonomous definitions when they also have a historical thickness.\n\n The terms relating to the historical or commercial name of the garment / garment element to be used for the OGTS field enhancement are defined within the reference limb and are to be understood as significant examples of terms that, if documented with reference to the good Object of cataloging, they must value the same OGTS field.\n\n Within the description of the main term are also given useful indications for the correct compilation of the clothing-dresser board.\n\n The acronyms of the Dress-Decoration Clothing Reference Card are:\n\n OGTD: definition\n\n OGTT: tailoring type\n\n OGTS: historical / commercial name \"\"",
"homepage": "http://www.iccd.beniculturali.it/siti_tematici/Scheda_VeAC/lemmario/",
"name": "Lemmary for Absorbing Abduction and Clothing",
"prefix": "1820"
},
"18200": {
"homepage": "http://www.ontotext.com/proton/protontop",
"name": "PROTON (Proto Ontology), Top Module",
"prefix": "18200"
},
"18201": {
"homepage": "https://vocab.eccenca.com/pubsub/",
"name": "Eccenca Publish-Subscribe Vocabulary",
"prefix": "18201"
},
"18202": {
"homepage": "http://purl.org/spar/pwo",
"name": "The Publishing Workflow Ontology",
"prefix": "18202"
},
"18203": {
"homepage": "http://purl.org/linked-data/cube",
"name": "The data cube vocabulary",
"prefix": "18203"
},
"18204": {
"homepage": "http://purl.org/qb4olap/cubes",
"name": "Vocabulary for publishing OLAP data cubes",
"prefix": "18204"
},
"18205": {
"homepage": "http://purl.oclc.org/NET/ssnx/qu/qu",
"name": "Quantity Kinds and Units",
"prefix": "18205"
},
"18206": {
"abbreviation": "QUDT",
"description": "QUDT is more than a set of vocabularies representing the various quantity and unit standards:\n\nMain QUDT Ontology\nQUDT Datatype Ontology\nQUDT Units Vocabulary\nQUDT QuantityKinds Vocabulary\nQUDT DimensionVectors Vocabulary\nQUDT Physical Constants Vocabulary\nQUDT Systems of Units Vocabulary",
"homepage": "http://qudt.org/",
"name": "Quantities, Units, Dimensions and Types",
"prefix": "18206"
},
"18207": {
"homepage": "http://guava.iis.sinica.edu.tw/r4r",
"name": "Relations for Reusing (R4R) Ontology",
"prefix": "18207"
},
"18208": {
"homepage": "http://www.w3.org/ns/radion",
"name": "Repository Asset Distribution",
"prefix": "18208"
},
"18209": {
"description": "A vocabulary to describe Web form widgets. Strongly aligned with the meta model of HTML Web forms.",
"homepage": "http://vocab.deri.ie/raul",
"name": "RAUL Vocabulary",
"prefix": "18209"
},
"1821": {
"description": "Discovery Programme for Irish Monuments",
"homepage": "http://vocabulary.locloud.eu/Irish_Monuments/",
"name": "Irish Monuments",
"prefix": "1821"
},
"18210": {
"homepage": "http://rdaregistry.info/Elements/a",
"name": "RDA Agent properties",
"prefix": "18210"
},
"18211": {
"homepage": "http://rdaregistry.info/Elements/c",
"name": "RDA Classes",
"prefix": "18211"
},
"18212": {
"homepage": "http://rdaregistry.info/Elements/e",
"name": "RDA Expression properties",
"prefix": "18212"
},
"18213": {
"homepage": "http://rdvocab.info/uri/schema/FRBRentitiesRDA",
"name": "FRBR Entities for RDA",
"prefix": "18213"
},
"18214": {
"homepage": "http://rdvocab.info/Elements",
"name": "RDA Group 1 Elements",
"prefix": "18214"
},
"18215": {
"homepage": "http://rdvocab.info/ElementsGr2",
"name": "RDA Group 2 Elements",
"prefix": "18215"
},
"18216": {
"homepage": "http://rdvocab.info/ElementsGr3",
"name": "RDA Group 3 Elements",
"prefix": "18216"
},
"18217": {
"homepage": "http://rdaregistry.info/Elements/i",
"name": "RDA Item properties",
"prefix": "18217"
},
"18218": {
"homepage": "http://rdaregistry.info/Elements/m",
"name": "RDA Manifestation properties",
"prefix": "18218"
},
"18219": {
"homepage": "http://rdvocab.info/RDARelationshipsWEMI",
"name": "RDA Relationships for Works, Expressions, Manifestations, Items",
"prefix": "18219"
},
"1822": {
"abbreviation": "NOMISMA",
"description": "Nomisma.org is a collaborative project to provide stable digital representations of numismatic concepts according to the principles of Linked Open Data. These take the form of http URIs that also provide access to reusable information about those concepts, along with links to other resources.",
"homepage": "http://nomisma.org/",
"license": "CC-BY-3.0",
"name": "Nomisma",
"prefix": "1822",
"wikidata_database": "Q24578999"
},
"18220": {
"homepage": "http://metadataregistry.org/uri/schema/RDARelationshipsGR2",
"name": "RDA Relationships GR2",
"prefix": "18220"
},
"18221": {
"homepage": "http://rdvocab.info/roles",
"name": "RDA Roles",
"prefix": "18221"
},
"18222": {
"homepage": "http://rdaregistry.info/Elements/u",
"name": "RDA Unconstrained properties",
"prefix": "18222"
},
"18223": {
"homepage": "http://rdaregistry.info/Elements/w",
"name": "RDA Work properties",
"prefix": "18223"
},
"18224": {
"homepage": "http://www.w3.org/1999/02/22-rdf-syntax-ns",
"name": "The RDF Concepts Vocabulary",
"prefix": "18224"
},
"18225": {
"homepage": "http://www.w3.org/ns/rdfa",
"name": "RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting",
"prefix": "18225"
},
"18226": {
"homepage": "http://www.w3.org/2004/03/trix/rdfg-1/",
"name": "Graph",
"prefix": "18226"
},
"18227": {
"homepage": "https://w3id.org/rdfp/",
"name": "The RDF Presentation ontology",
"prefix": "18227"
},
"18228": {
"homepage": "http://www.w3.org/2000/01/rdf-schema",
"name": "The RDF Schema vocabulary",
"prefix": "18228"
},
"18229": {
"homepage": "http://purl.org/ontology/rec/core",
"name": "Recommendation Ontology",
"prefix": "18229"
},
"18230": {
"homepage": "http://www.w3.org/2001/02pd/rec54",
"name": "Model of the W3C Process",
"prefix": "18230"
},
"18231": {
"homepage": "http://purl.org/reco",
"name": "RECommendations Ontology",
"prefix": "18231"
},
"18232": {
"homepage": "http://reegle.info/schema",
"name": "Renewable Energy and Energy Efficiency",
"prefix": "18232"
},
"18233": {
"homepage": "http://purl.org/vocab/relationship/",
"name": "Relationship",
"prefix": "18233"
},
"18234": {
"description": "Ontology for poetry description.",
"homepage": "http://www.purl.org/net/remetca",
"license": "CC-BY-3.0",
"name": "ReMetCa Ontology",
"prefix": "18234"
},
"18235": {
"homepage": "http://purl.org/stuff/rev",
"name": "Review Vocabulary",
"prefix": "18235"
},
"18236": {
"description": "This is a helper ontology for NIF 2.0 to be able to log errors and warning messages.",
"homepage": "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/rlog",
"license": "CC-BY-3.0",
"name": "RDF Logging Ontology",
"prefix": "18236"
},
"18237": {
"description": "The Wf4Ever Research Object Model provides a vocabulary for the description of workflow-centric Research Objects: aggregations of resources relating to scientific workflows.",
"homepage": "http://purl.org/wf4ever/ro",
"name": "The Research Object Ontology",
"prefix": "18237"
},
"18238": {
"homepage": "http://www.w3.org/ns/regorg",
"name": "Registered Organization Vocabulary",
"prefix": "18238"
},
"18239": {
"homepage": "http://www.w3.org/ns/r2rml",
"name": "RDB to RDF Mapping Language Schema",
"prefix": "18239"
},
"1824": {
"description": "Shelf Classification of Egyptology from the Library of the University of Trier",
"homepage": "https://www.uni-trier.de/index.php?id=4020",
"name": "Shelf Classification Egyptology",
"prefix": "1824"
},
"18240": {
"homepage": "http://purl.org/rss/1.0",
"name": "Vocabulary for Rich Site Summary (RSS) 1.0",
"prefix": "18240"
},
"18242": {
"homepage": "http://rdfunit.aksw.org/ns/core",
"name": "Test-Driven Data Debugging Ontology",
"prefix": "18242"
},
"18243": {
"homepage": "http://ns.inria.fr/s4ac/v2",
"name": "Social Semantic SPARQL Security For Access Control Ontology",
"prefix": "18243"
},
"18244": {
"homepage": "http://ontology.tno.nl/saref4ee/",
"name": "SAREF4EE: the EEbus/Energy@home extension of SAREF",
"prefix": "18244"
},
"18245": {
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19156/2011/sampling",
"name": "The Sampling Features Schema Vocabulary",
"prefix": "18245"
},
"18246": {
"homepage": "http://def.seegrid.csiro.au/ontology/om/sam-lite",
"name": "OWL for Sampling Features",
"prefix": "18246"
},
"18247": {
"homepage": "http://salt.semanticauthoring.org/ontologies/sao",
"name": "SALT Annotation Ontology",
"prefix": "18247"
},
"18248": {
"homepage": "http://ontology.tno.nl/saref/",
"name": "SAREF: the Smart Appliances REFerence ontology",
"prefix": "18248"
},
"18249": {
"homepage": "http://purl.org/saws/ontology",
"name": "Sharing Ancient Wisdoms Ontology",
"prefix": "18249"
},
"1825": {
"description": "Shelf Classification of General Linguistics and Literary Studies from the University Library Trier",
"homepage": "https://www.uni-trier.de/index.php?id=4632",
"name": "Shelf Classification General Linguistics and Literary Studies",
"prefix": "1825"
},
"18250": {
"homepage": "http://schema.org/",
"name": "Schema.org vocabulary",
"prefix": "18250"
},
"18251": {
"homepage": "http://lod.taxonconcept.org/ontology/sci_people.owl",
"name": "Scientific People Ontology",
"prefix": "18251"
},
"18252": {
"homepage": "http://purl.org/spar/scoro/",
"name": "Scholarly Contributions and Roles Ontology",
"prefix": "18252"
},
"18253": {
"description": "SCOT (Social Semantic Cloud of Tags) is an ontology for describing the structure and the semantics for tagging data across heterogenous users, sources, and applications.",
"homepage": "http://rdfs.org/scot/ns",
"name": "Social Semantic Cloud of Tags",
"prefix": "18253"
},
"18254": {
"homepage": "http://vocab.deri.ie/scovo",
"name": "The Statistical Core Vocabulary",
"prefix": "18254"
},
"18255": {
"homepage": "http://vocab.deri.ie/scsv",
"name": "Schema.org CSV",
"prefix": "18255"
},
"18256": {
"homepage": "http://www.w3.org/ns/sparql-service-description",
"name": "SPARQL 1.1 Service Description",
"prefix": "18256"
},
"18257": {
"homepage": "http://purl.org/linked-data/sdmx",
"name": "SDMX-RDF vocabulary",
"prefix": "18257"
},
"18258": {
"homepage": "http://purl.org/linked-data/sdmx/2009/code",
"name": "SDMX Code",
"prefix": "18258"
},
"18259": {
"homepage": "http://purl.org/linked-data/sdmx/2009/dimension",
"name": "SDMX Dimension",
"prefix": "18259"
},
"1826": {
"description": "Shelf Classification of English of the University Library Trier",
"homepage": "https://www.uni-trier.de/index.php?id=4639",
"name": "Shelf Classification English",
"prefix": "1826"
},
"18260": {
"homepage": "http://salt.semanticauthoring.org/ontologies/sdo",
"name": "SALT Document Ontology",
"prefix": "18260"
},
"18261": {
"homepage": "http://vocab.deri.ie/search",
"name": "Sindice Search Vocabulary",
"prefix": "18261"
},
"18262": {
"homepage": "http://purl.org/NET/seas",
"name": "SEAS ontology",
"prefix": "18262"
},
"18263": {
"homepage": "http://securitytoolbox.appspot.com/securityMain",
"name": "Security Ontology",
"prefix": "18263"
},
"18264": {
"homepage": "http://semanticweb.cs.vu.nl/2009/11/sem/",
"name": "The SEM Ontology",
"prefix": "18264"
},
"18265": {
"homepage": "http://www.lingvoj.org/semio.rdf",
"name": "Semio, an ontology of signs",
"prefix": "18265"
},
"18266": {
"homepage": "http://www.ontologydesignpatterns.org/cp/owl/sequence.owl",
"name": "Sequence Pattern",
"prefix": "18266"
},
"18267": {
"homepage": "http://purl.org/ontology/service",
"name": "The Service Ontology",
"prefix": "18267"
},
"18268": {
"homepage": "http://www.opengis.net/ont/sf",
"name": "Simplified Features Geometry",
"prefix": "18268"
},
"18269": {
"homepage": "http://dati.cdec.it/lod/shoah/",
"name": "Shoah Vocabulary Specification",
"prefix": "18269"
},
"1827": {
"description": "Shelf Classification of Archaeology of the University Library Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=4646",
"name": "Shelf Classification Archaeology",
"prefix": "1827"
},
"18270": {
"homepage": "http://paul.staroch.name/thesis/SmartHomeWeather.owl",
"name": "Smart Home Weather",
"prefix": "18270"
},
"18271": {
"homepage": "http://purl.org/ontology/similarity/",
"name": "The Similarity Ontology",
"prefix": "18271"
},
"18272": {
"homepage": "http://rdfs.org/sioc/ns",
"name": "Semantically-Interlinked Online Communities",
"prefix": "18272"
},
"18273": {
"homepage": "http://www.ontologydesignpatterns.org/cp/owl/situation.owl",
"name": "Situation Pattern",
"prefix": "18273"
},
"18274": {
"homepage": "http://www.w3.org/2004/02/skos/core",
"name": "Simple Knowledge Organization System",
"prefix": "18274"
},
"18275": {
"homepage": "http://www.w3.org/2008/05/skos-xl",
"name": "SKOS eXtension for Labels",
"prefix": "18275"
},
"18276": {
"homepage": "http://ns.cerise-project.nl/energy/def/cim-smartgrid",
"name": "CERISE CIM Profile for Smart Grids",
"prefix": "18276"
},
"18277": {
"homepage": "http://rdf.myexperiment.org/ontologies/snarm/",
"name": "Simple Network Access Rights Management Ontology",
"prefix": "18277"
},
"18278": {
"homepage": "http://purl.org/net/soron",
"name": "SORON: Social Relationships ONtology",
"prefix": "18278"
},
"18279": {
"homepage": "http://spinrdf.org/sp",
"name": "SPIN SPARQL Syntax",
"prefix": "18279"
},
"1828": {
"description": "Systematics of Bookstocks on Digital Humanities in the Freehand Area of ββthe University Library Trier",
"homepage": "https://www.uni-trier.de/index.php?id=45235",
"name": "Positioning system Digital Humanities",
"prefix": "1828"
},
"18280": {
"homepage": "http://geovocab.org/spatial",
"name": "NeoGeo Spatial Ontology",
"prefix": "18280"
},
"18281": {
"homepage": "http://spi-fm.uca.es/spdef/models/deployment/spcm/1.0",
"name": "Software Process Control Model",
"prefix": "18281"
},
"18282": {
"homepage": "http://kmi.open.ac.uk/projects/smartproducts/ontologies/food.owl",
"name": "SmartProducts Food Domain Model",
"prefix": "18282"
},
"18283": {
"homepage": "http://spinrdf.org/spin",
"name": "SPIN Inferencing Vocabulary",
"prefix": "18283"
},
"18285": {
"homepage": "http://spitfire-project.eu/ontology/ns",
"name": "SPITFIRE Ontology",
"prefix": "18285"
},
"18286": {
"homepage": "http://ns.inria.fr/ast/sql",
"name": "SQL Abstract Syntax Trees Vocabulary",
"prefix": "18286"
},
"18287": {
"homepage": "http://salt.semanticauthoring.org/ontologies/sro",
"name": "SALT Rhetorical Ontology",
"prefix": "18287"
},
"18288": {
"description": "This ontology describes sensors and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports. This ontology is developed by the W3C Semantic Sensor Networks Incubator Group (SSN-XG).",
"homepage": "http://www.w3.org/2005/Incubator/ssn/ssnx/ssn",
"name": "Semantic Sensor Network Ontology",
"prefix": "18288"
},
"18289": {
"homepage": "http://purl.org/ontology/ssso",
"name": "Simple Service Status Ontology",
"prefix": "18289"
},
"1829": {
"description": "Shelf classification of the education sciences at the library of the University of Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=6506",
"name": "Shelf classification Educational Sciences",
"prefix": "1829"
},
"18290": {
"homepage": "http://semweb.mmlab.be/ns/stoptimes#Ontology",
"name": "The Stop Times ontology",
"prefix": "18290"
},
"18291": {
"description": "A vocabulary to describe main security and cryptographic concepts: attacks, security mechanisms, OSI model, security protocols, security tools in numerous technologies: Web applications, network management, Sensor networks, Cellular (2G, 3G, 4G) and Wireless (Wifi), etc.",
"homepage": "http://securitytoolbox.appspot.com/stac",
"name": "Security Toolbox : Attacks and Countermeasures",
"prefix": "18291"
},
"18292": {
"homepage": "http://purl.org/net/step",
"name": "Semantic Trajectory Episodes",
"prefix": "18292"
},
"18293": {
"description": "Stories are present throughout our everyday lives and our history: books, film, television, and radio weave events into narrative and plot; myths and legends are passed between generations; news stories describe both ongoing and past events. These stories often share similar themes, characters, items, and locations: by providing an approach to linking these items together, stories can become powerfully navigable, discoverable, and open to new analysis and creation techniques. The Stories ontology was developed in collaboration with the BBC, with an aim to creating an ontology for narrative representation that could be applied across a diverse set of cases. These included accounts of events in Northern Ireland, the storylines of Doctor Who episodes, and key events of the Battle of Britain.\n\nThe Stories Ontology is built upon the oft-used Event and Timeline ontologies, thus ensuring interoperability with many existing datasets and allowing for the use of extension ontologies when needed.",
"homepage": "http://www.contextus.net/stories/",
"license": "CC-BY-3.0",
"name": "Stories Ontology",
"prefix": "18293"
},
"18294": {
"homepage": "http://purl.org/voc/summa/",
"name": "SUMMA Vocabulary",
"prefix": "18294"
},
"18295": {
"homepage": "http://data.semanticweb.org/ns/swc/ontology",
"name": "Semantic Web Conference Ontology",
"prefix": "18295"
},
"18296": {
"homepage": "http://www.w3.org/2004/03/trix/swp-1",
"name": "Graph Authority",
"prefix": "18296"
},
"18297": {
"homepage": "http://spi-fm.uca.es/spdef/models/deployment/swpm/1.0",
"name": "Software Work Product Model",
"prefix": "18297"
},
"18298": {
"homepage": "http://sw-portal.deri.org/ontologies/swportal",
"name": "Semantic Web Portal Ontology",
"prefix": "18298"
},
"18299": {
"homepage": "http://swrc.ontoware.org/ontology-07",
"name": "Semantic Web for Research Communities",
"prefix": "18299"
},
"183": {
"description": "Thesaurus for University Information Services.",
"homepage": "http://www.um.es/isgat/navegacion.php",
"name": "University Information",
"prefix": "183"
},
"1830": {
"description": "Shelf Classification of Ethnology at the Library of the University of Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=6563",
"name": "Shelf classification ethnology",
"prefix": "1830"
},
"18300": {
"description": "This document contains a proposal for a Semantic Web Rule Language (SWRL) based on a combination of the OWL DL and OWL Lite sublanguages of the OWL Web Ontology Language with the Unary/Binary Datalog RuleML sublanguages of the Rule Markup Language. SWRL includes a high-level abstract syntax for Horn-like rules in both the OWL DL and OWL Lite sublanguages of OWL. A model-theoretic semantics is given to provide the formal meaning for OWL ontologies including rules written in this abstract syntax. An XML syntax based on RuleML and the OWL XML Presentation Syntax as well as an RDF concrete syntax based on the OWL RDF/XML exchange syntax are also given, along with several examples.",
"homepage": "https://www.w3.org/Submission/SWRL/",
"license": "https://www.w3.org/Consortium/Legal/2015/doc-license",
"name": "Semantic Web Rule Language",
"prefix": "18300",
"wikidata_database": "Q3478367"
},
"18301": {
"homepage": "http://ns.bergnet.org/tac/0.1/triple-access-control",
"name": "TripleAccessControl Ontology",
"prefix": "18301"
},
"18302": {
"description": "An ontology that describes tags, as used in the popular del.icio.us and Flickr systems, and allows for relationships between tags to be described.",
"homepage": "http://www.holygoat.co.uk/owl/redwood/0.1/tags/",
"name": "Tag ontology",
"prefix": "18302"
},
"18303": {
"homepage": "http://vocab.deri.ie/tao",
"name": "Trust Assertion Ontology",
"prefix": "18303"
},
"18304": {
"homepage": "http://purl.org/biodiversity/taxon/",
"name": "TaxonMap Ontology",
"prefix": "18304"
},
"18305": {
"homepage": "http://www.w3.org/2006/time-entry",
"name": "Time Entry",
"prefix": "18305"
},
"18306": {
"homepage": "http://linkedscience.org/teach/ns",
"name": "Teaching Core Vocabulary Specification",
"prefix": "18306"
},
"18307": {
"homepage": "http://www.w3.org/2006/03/test-description",
"name": "Test Metadata",
"prefix": "18307"
},
"18308": {
"description": "An ontology for organising theatrical data.",
"homepage": "http://purl.org/theatre",
"name": "Theatre Ontology",
"prefix": "18308"
},
"18309": {
"homepage": "http://resource.geosciml.org/ontology/timescale/thors",
"name": "The Temporal Ordinal Reference Systems",
"prefix": "18309"
},
"1831": {
"description": "Shelf Classiification for German Studies at the University Library of Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=4820",
"name": "Shelf classification German Studies",
"prefix": "1831"
},
"18310": {
"homepage": "http://www.ontologydesignpatterns.org/cp/owl/timeinterval.owl",
"name": "The Time Interval Pattern",
"prefix": "18310"
},
"18311": {
"homepage": "http://www.w3.org/2006/time",
"name": "Time Ontology",
"prefix": "18311"
},
"18312": {
"homepage": "http://purl.org/tio/ns",
"name": "The Tickets Ontology",
"prefix": "18312"
},
"18313": {
"description": "A generic pattern usable for all situations that require a temporal indexing.",
"homepage": "http://www.ontologydesignpatterns.org/cp/owl/timeindexedsituation.owl",
"name": "Time Indexed Situation",
"prefix": "18313"
},
"18314": {
"homepage": "http://www.observedchange.com/tisc/ns",
"name": "Open Time and Space Core Vocabulary",
"prefix": "18314"
},
"18315": {
"homepage": "http://purl.org/NET/c4dm/timeline.owl",
"name": "The Timeline Ontology",
"prefix": "18315"
},
"18316": {
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19108/2002/temporal",
"name": "A vocabulary for temporal objects in Geographic Information",
"prefix": "18316"
},
"18317": {
"homepage": "http://www.w3.org/2001/sw/hcls/ns/transmed/",
"name": "Translational Medicine Ontology",
"prefix": "18317"
},
"18318": {
"homepage": "http://data.ign.fr/def/topo",
"prefix": "18318"
},
"18319": {
"homepage": "http://tour-pedia.org/download/tp.owl",
"name": "Tourpedia Ontology",
"prefix": "18319"
},
"1832": {
"description": "Shelf Classification of the Ancient History of the University Library of Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=4823",
"name": "Shelf Classification Ancient History",
"prefix": "1832"
},
"18320": {
"description": "An ontology that describes the management of the traffic in a straight road with two lanes, both in the same direction.",
"homepage": "http://www.sensormeasurement.appspot.com/ont/transport/traffic",
"name": "Road Traffic Management",
"prefix": "18320"
},
"18321": {
"homepage": "http://contextus.net/ontology/ontomedia/ext/common/trait",
"name": "OntoMedia Trait Representation",
"prefix": "18321"
},
"18322": {
"homepage": "http://vocab.org/transit/terms/",
"name": "TRANSIT",
"prefix": "18322"
},
"18323": {
"homepage": "http://linkeddata.finki.ukim.mk/lod/ontology/tao",
"name": "Transport Administration Ontology",
"prefix": "18323"
},
"18324": {
"description": "Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining subclasses and subproperties of SIOC terms.",
"homepage": "http://rdfs.org/sioc/types",
"name": "SIOC Types Ontology Module",
"prefix": "18324"
},
"18325": {
"homepage": "http://idi.fundacionctic.org/cruzar/turismo",
"prefix": "18325"
},
"18326": {
"homepage": "http://www.essepuntato.it/2012/04/tvc",
"name": "The Time-indexed Value in Context",
"prefix": "18326"
},
"18327": {
"homepage": "http://lod.taxonconcept.org/ontology/txn.owl",
"name": "TaxonConcept Ontology",
"prefix": "18327"
},
"18328": {
"homepage": "http://www.w3.org/2006/timezone",
"name": "Time Zone Ontology",
"prefix": "18328"
},
"18329": {
"homepage": "http://purl.org/olia/ubyCat.owl",
"name": "ubyCat.owl",
"prefix": "18329"
},
"1833": {
"description": "Shelf Classification for the Middle and New History of the University Library of Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=6251",
"name": "Shelf Classification Medieval and Modern History",
"prefix": "1833"
},
"18330": {
"homepage": "http://purl.org/uco/ns",
"name": "Used Cars Ontology",
"prefix": "18330"
},
"18331": {
"homepage": "http://purl.oclc.org/NET/muo/ucum/",
"name": "Units of measurement ontology",
"prefix": "18331"
},
"18332": {
"homepage": "http://www.w3.org/ns/ui",
"name": "A user interface ontology",
"prefix": "18332"
},
"18333": {
"homepage": "http://umbel.org/umbel",
"name": "Upper Mapping and Binding Exchange Layer",
"prefix": "18333"
},
"18334": {
"description": "An RDF vocabulary for extending some SKOS and ISO-THES functions in order to improve the linked data consumption of SKOS datasets.",
"homepage": "http://purl.org/umu/uneskos",
"name": "UNESKOS Vocabulary",
"prefix": "18334"
},
"18335": {
"homepage": "http://purl.uniprot.org/core/",
"name": "Uniprot Core Ontology",
"prefix": "18335"
},
"18336": {
"description": "This vocabulary describes the entities which may be derived from a URI and the relationships between them, such as Internet Domains, prototcols, file suffixes etc. It was initially issued as part of an April 1st gag, but has utility beyond the initial joke.",
"homepage": "http://uri4uri.net/vocab.html/",
"name": "URI Vocabulary",
"prefix": "18336"
},
"18337": {
"homepage": "http://code-research.eu/ontology/visual-analytics",
"name": "The Visual Analytics Vocabulary",
"prefix": "18337"
},
"18338": {
"homepage": "http://www.linkedmodel.org/schema/vaem",
"name": "Vocabulary for Attaching Essential Metadata",
"prefix": "18338"
},
"18339": {
"description": "Vagueness is a common human knowledge and language phenomenon, typically manifested by terms and concepts like High, Expert, Bad, Near, etc. It is a phenomenon related to our inability to precisely determine the extensions of such concepts in certain domains and contexts. That is because vague concepts have typically blurred boundaries which do not allow for a sharp distinction between the entities that fall within their extension and those that do no. For example, some people are borderline tall: not clearly 'tall' and not clearly 'not tall'.\n\nIn an OWL ontology vagueness may primarily appear in the definitions of classes, object and datatype properties, and datatypes. A class is vague if, in the given domain, context or application scenario, it admits borderline cases, namely if there are (or could be) individuals for which it is indeterminate whether they instantiate the class. Typical vague classes are attributions, namely classes that reflect qualitative states of entities (e.g., TallPerson, ExperiencedResearcher etc.). Similarly, an object property (relation) is vague if there are (or could be) pairs of individuals for which it is indeterminate whether they stand in the relation (e.g., hasGenre, hasIdeology etc.). The same applies for datatype properties and pairs of individuals and literal values. Finally, a vague datatype consists of a set of vague terms. An example is the datatype RestaurantPriceRange when this comprises the terms 'cheap', 'moderate' and 'expensive'.\n\nThe Vagueness Ontology enables the explicit identification and description of vague entities and (some of) their vagueness-related characteristics in OWL ontologies. Such a description is to be made by ontology creators and its goal is the narrowing of the possible interpretations that its vague entities may assume by human and software agents.",
"homepage": "http://www.essepuntato.it/2013/10/vagueness",
"name": "The Vagueness Ontology",
"prefix": "18339"
},
"1834": {
"description": "Shelf Classification der Informationswissenschaften der UniversitΓ€tsbibliothek Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=6256",
"name": "Shelf Classification Computer Science",
"prefix": "1834"
},
"18340": {
"homepage": "http://purl.org/vocab/vann/",
"name": "VANN: A vocabulary for annotating vocabulary descriptions",
"prefix": "18340"
},
"18341": {
"homepage": "http://www.w3.org/2006/vcard/ns",
"name": "An Ontology for vCards",
"prefix": "18341"
},
"18342": {
"homepage": "http://data.lirmm.fr/ontologies/vdpp",
"name": "Vocabulary for Dataset Publication Projects",
"prefix": "18342"
},
"18343": {
"homepage": "http://linkeddata.finki.ukim.mk/lod/ontology/veo",
"name": "Vehicle Emissions Ontology",
"prefix": "18343"
},
"18344": {
"description": "The Video Game Ontology is aimed at modelling video game related information. The main goal is to capture knowledge about events that happen in video games and information about players. This ontology has been created as a joint work by researchers at Lappeenranta University of Technology, Finland and Universidad Politecnica de Madrid, Spain.",
"homepage": "http://purl.org/net/VideoGameOntology",
"license": "CC BY-NC-SA 3.0",
"name": "The Video Game Ontology",
"prefix": "18344"
},
"18345": {
"description": "Derived from the DAML Wine ontology at http://www.daml.org/ontologies/76. Substantially changed, in particular the Region based relations.",
"homepage": "http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine",
"name": "Wine Ontology",
"prefix": "18345"
},
"18346": {
"homepage": "http://vivoweb.org/sites/vivoweb.org/files/vivo-isf-public-1.6.owl",
"name": "VIVO Core Ontology",
"prefix": "18346"
},
"18347": {
"homepage": "http://spi-fm.uca.es/spdef/models/genericTools/vmm/1.0",
"name": "Visual Modeling tool Model",
"prefix": "18347"
},
"18348": {
"description": "VOAF is a vocabulary specification providing elements allowing the description of vocabularies (RDFS vocabularies or OWL ontologies) used in the Linked Data Cloud. In particular it provides properties expressing the different ways such vocabularies can rely on, extend, specify, annotate or otherwise link to each other. It relies itself on Dublin Core and voiD. The name of the vocabulary makes an explicit reference to FOAF because VOAF can be used to define networks of vocabularies in a way similar to the one FOAF is used to define networks of people.",
"homepage": "http://lov.okfn.org/vocommons/voaf/",
"license": "CC-BY-3.0",
"name": "Vocabulary of a Friend",
"prefix": "18348"
},
"18349": {
"description": "VOAG stands for 'Vocabulary Of Attribution and Governance'. The ontology is intended to specify licensing, attribution, provenance and governance of an ontology. VOAG captures many common license types and their restrictions. Where a license requires attribution, VOAG provides resources that allow the attribution should be made. Provenance is defined in terms of source and pedigree. A miminal model of governance is provided based on how issues, releases and changes are managed. VOAG does not import, but makes uses of some concepts from VOID (http://vocab.deri.ie/void), notably void:Dataset.",
"homepage": "http://linkedmodel.org/doc/voag/1.0/",
"license": "CC BY-SA 3.0",
"name": "Vocabulary Of Attribution and Governance",
"prefix": "18349"
},
"1835": {
"description": "This is the classification system for romance at the University Library of Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=6531",
"name": "Shelf Classification Sinology",
"prefix": "1835"
},
"18350": {
"description": "An extension of W3C VoID that is able to represent these metrics for expressing the Connectivity Metrics of a Semantic Warehouse.",
"homepage": "http://www.ics.forth.gr/isl/VoIDWarehouse/VoID_Extension_Schema.owl",
"license": "CC-BY-3.0",
"name": "Void Warehouse Ontology",
"prefix": "18350"
},
"18352": {
"abbreviation": "vrank",
"homepage": "http://vocab.sti2.at/vrank",
"name": "Vocabulary for Ranking",
"prefix": "18352"
},
"18353": {
"homepage": "http://www.w3.org/2003/06/sw-vocab-status/ns",
"name": "SemWeb Vocab Status ontology",
"prefix": "18353"
},
"18354": {
"homepage": "http://vocab.sti2.at/vsearch/",
"name": "vSearch Vocabulary",
"prefix": "18354"
},
"18355": {
"homepage": "http://purl.org/vso/ns",
"name": "Vehicle Sales Ontology",
"prefix": "18355"
},
"18356": {
"homepage": "http://purl.org/vvo/ns",
"name": "Volkswagen Vehicles Ontology",
"prefix": "18356"
},
"18357": {
"homepage": "http://purl.org/wai",
"name": "Roles and Profiles Ontology",
"prefix": "18357"
},
"18358": {
"homepage": "http://www.w3.org/2007/05/powder-s",
"name": "Protocol for Web Description Resources",
"prefix": "18358"
},
"18359": {
"homepage": "http://purl.org/net/wf-invocation",
"name": "Workflow Invocation Ontology",
"prefix": "18359"
},
"1836": {
"description": "Shelf Classification of Canadian Studies of the University Library Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=6407",
"name": "Shelf Classification Canadian Studies",
"prefix": "1836"
},
"18360": {
"homepage": "http://purl.org/wf4ever/wfdesc",
"name": "The Wfdesc ontology",
"prefix": "18360"
},
"18361": {
"description": "Scientific workflows have been increasingly used in the last decade as an instrument for data intensive science. Workflows serve a dual function: first, as detailed documentation of the scientific method used for an experiment (i. e. the input sources and processing steps taken for the derivation of a certain data item), and second, as re-usable, executable artifacts for data-intensive analysis. Scientific workflows are composed of a variety of data manipulation activities such as Data Movement, data transformation, Data Analysis and Data Visualization to serve the goals of the scientific study. The composition is done through the constructs made available by the workflow system used, and is largely shaped by the function undertaken by the workflow and the environment in which the system operates. (...) This document specifies the classes and properties of the Workflow Motifs ontology, the OWL 2 encoding ot the aforementioned motif catalogue. The goal of this ontology is to provide the means to annotate workflows and their steps with the motifs of the vocabulary, without setting any restriction on how the workflows are defined themselves.",
"homepage": "http://purl.org/net/wf-motifs",
"license": "CC BY-NC-SA 3.0",
"name": "The Workflow Motif Ontology",
"prefix": "18361"
},
"18362": {
"description": "The wfprov ontology shows how to express minimal provenance information about the execution of a workflow described using the wfdesc ontology.",
"homepage": "http://purl.org/wf4ever/wfprov",
"license": "CC-BY-3.0",
"name": "The Wfprov Ontology",
"prefix": "18362"
},
"18363": {
"homepage": "http://vocab.org/whisky/terms",
"name": "Whisky Ontology",
"prefix": "18363"
},
"18364": {
"homepage": "http://www.kanzaki.com/ns/whois",
"name": "Who's who description vocabulary",
"prefix": "18364"
},
"18365": {
"description": "The Weighted Interests Vocabulary specification provides basic concepts and properties for describing describing preferences (interests) within contexts, their temporal dynamics and their origin on/ for the Semantic Web. This document contains a RDFa description of the Weighted Interests Vocabulary and some additional information and examples.",
"homepage": "http://purl.org/ontology/wi/core",
"license": "CC-BY-3.0",
"name": "The Weighted Interests Vocabulary",
"prefix": "18365"
},
"18366": {
"description": "A partir del anΓ‘lisis de diversos sistemas, como MediaWiki, Confluence o DokuWiki, se ha diseΓ±ado este vocabulario. TΓ©ngase en cuenta que este modelo no describe completamente el modelo conceptual de todos los tipos de sistemas wiki, sino sΓ³lo de los elementos principales.",
"homepage": "http://spi-fm.uca.es/spdef/models/genericTools/wikim/1.0",
"name": "WIKI tool Model",
"prefix": "18366"
},
"18367": {
"homepage": "http://www.wsmo.org/ns/wsmo-lite",
"name": "WSMO-Lite Ontology",
"prefix": "18367"
},
"18368": {
"description": "A simple vocabulary for describing biological species and related taxa. The vocabulary defines terms for describing the names and ranking of taxa, as well as providing support for describing their habitats, conservation status, and behavioural characteristics, etc.",
"homepage": "http://purl.org/ontology/wo/",
"license": "CC-BY-3.0",
"name": "BBC Wildlife Ontology",
"prefix": "18368"
},
"18369": {
"description": "The Weighting Ontology specification provides a vocabulary for describing weightings and their referenced scales, on/ for the Semantic Web.",
"homepage": "http://purl.org/ontology/wo/core",
"license": "CC-BY-3.0",
"name": "Weighting Ontology",
"prefix": "18369"
},
"1837": {
"description": "Shelf Classification of the art history of the Trier University Library.",
"homepage": "https://www.uni-trier.de/index.php?id=6414",
"name": "Shelf Classifictaion Art history",
"prefix": "1837"
},
"18370": {
"description": "RDF documents can make any number of statements. Without some kind of signature or other similar verification mechanism, there is no way to understand who made these statements. One way to document who made a set of statements is via the use of Digital Signatures: signing a document using Public Key Cryptography. The WOT, or Web Of Trust, schema is designed to facilitate the use of Public Key Cryptography tools such as PGP or GPG to sign RDF documents and document these signatures.",
"homepage": "http://xmlns.com/wot/0.1/",
"name": "Web Of Trust",
"prefix": "18370"
},
"18371": {
"description": "XAPI vocabularies are created and shared by Communities of Practice (CoPs) to help facilitate the reuse of Verbs and Activity Types. This schema was designed to enhance the semantic interoperability of xAPI by encouraging the adoption of RDF principles and publishing practices. This document defines a schema and provides descriptions of each of the classes and properties that are recommended for use when classifying and publishing datasets as RDF. By using RDF to describe xAPI vocabulary datasets, CoPs can increase discoverability and enable applications to easily consume metadata from multiple sources. Representing xAPI vocabulary datasets as RDF also further enables decentralized publishing of Verbs and Activity Types and can facilitate an open federated dataset search capability across applications, platforms, and CoPs.",
"homepage": "http://purl.org/xapi/ontology",
"name": "xAPI Controlled Vocabulary Ontology",
"prefix": "18371"
},
"18372": {
"description": "An attempt to publish XBRL standard following best practices on the Web. Not an official version from XBRL International and under development.",
"homepage": "https://w3id.org/vocab/xbrll",
"name": "A lightweight XBRL vocabulary",
"prefix": "18372"
},
"18373": {
"description": "This is a vocabulary collection utilized by XHTML Family modules and document types using XHTML Modularization, including XHTML Role and XHTML + RDFa as defined in rdfa-syntax.",
"homepage": "http://www.w3.org/1999/xhtml/vocab",
"name": "XHTML Vocabulary",
"prefix": "18373"
},
"18374": {
"description": "XKOS leverages the Simple Knowledge Organization System (SKOS) for managing statistical classifications and concept management systems, since SKOS is widely used. LOD is used to create Web artifacts that machines can interpret, so publishing machine-readable statistical classifications and other concept management systems as SKOS instances is desired. The XKOS developers found that SKOS was insufficient for the problem. No aspect of SKOS was found to be wrong, just incomplete. Therefore, an extension to SKOS, called XKOS, is proposed.\n\nXKOS extends SKOS for the needs of statistical classifications. It does so in two main directions. First, it defines a number of terms that enable the representation of statistical classifications with their structure and textual properties, as well as the relations between classifications. Second, it refines SKOS semantic properties to allow the use of more specific relations between concepts. Those specific relations can be used for the representation of classifications or for any other case where SKOS is employed. XKOS adds the extensions that are desirable to meet the requirements of the statistical community.",
"homepage": "http://www.ddialliance.org/Specification/RDF/XKOS",
"license": "CC BY-NC-SA 3.0",
"name": "XKOS",
"prefix": "18374"
},
"18375": {
"description": "XSD (XML Schema Definition), a recommendation of the World Wide Web Consortium (W3C), specifies how to formally describe the elements in an Extensible Markup Language (XML) document. It can be used by programmers to verify each piece of item content in a document. They can check if it adheres to the description of the element it is placed in.",
"homepage": "http://www.w3.org/2001/XMLSchema",
"name": "XML Schema",
"prefix": "18375",
"wikidata_database": "Q16342"
},
"18376": {
"description": "Extensions to SKOS and other standard vocabularies used by the German National Library of Economics (ZBW).",
"homepage": "http://zbw.eu/namespaces/zbw-extensions",
"name": "ZBW Extensions",
"prefix": "18376"
},
"18377": {
"description": "The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains 8246 drug entries including 2012 FDA-approved small molecule drugs, 229 FDA-approved biotech (protein/peptide) drugs, 94 nutraceuticals and over 6000 experimental drugs. Additionally, 4344 non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences are linked to these drug entries. Each DrugCard entry contains more than 200 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data.",
"homepage": "http://www.drugbank.ca/",
"license": "CC BY-NC 3.0",
"name": "DrugBank",
"prefix": "18377",
"wikidata_database": "Q1122544"
},
"18379": {
"description": "Kerameikos.org is a collaborative project dedicated to defining the intellectual concepts of pottery following the tenets of linked open data and the formulation of an ontology for representing and sharing ceramic data across disparate data systems. While the project is focused primarily on the definition of concepts within Greek black- and red-figure pottery, Kerameikos.org is extensible toward the definition of concepts in other fields of pottery studies.",
"homepage": "http://kerameikos.org/",
"license": "ODBL",
"name": "Kerameikos",
"prefix": "18379"
},
"1838": {
"description": "The technical system of Lusitanian book collections is supplemented by a geo-sign, with the exception of groups B, H, L, R and S, which shows whether the work is about Portugal, Portuguese-speaking Africa, Asia or America No geo-sign and stand at the beginning of a system group.",
"homepage": "https://www.uni-trier.de/index.php?id=6487",
"name": "Shelf Classification Lusitanistics",
"prefix": "1838"
},
"18386": {
"homepage": "http://apps.who.int/iris/bitstream/10665/39461/3/9789604520954_gre.pdf",
"name": "Lexicon of alcohol and drug terms",
"prefix": "18386"
},
"18387": {
"description": "Since the mid-1960s, an attempt has been made to simplify the legal drafting language in the common law countries. Particular emphasis was placed on the need to use simple language without redundancies and legalese so that legal texts are clear and understandable even by those who do not have legal training but do not lack legal integrity And validity.\n\nThe above effort has been systematically organized, among other things, through the creation of various organizations in the UK, such as the Plain English Campaign, Clarity and Plain Language Commission, which aimed to promote the change of the traditional legal writing style by introducing the use of simple English Languages.\n\nToday, the use of simple English in drafting legal texts has been adopted at the state level not only in the UK and the United States, but also in other countries of Anglo-American law, such as Australia, New Zealand and Canada. However, traditional English legal terminology is still widely used. The main reason for this approach is linked to the belief that the interpretation of these established legal expressions can not be challenged by the courts.\n\nRegardless of whether the author of a legal text chooses traditional or plain English, the translation of legal texts into English requires knowledge of the substantive differences between the civil law and the common law in order to achieve accurate performance Of legal terms and concepts, and in any case a specific expressive style should be chosen to ensure uniformity and consistency in the outcome. Finally, the choice of linguistic type between British English and American English is not only aesthetic, but it also implies knowledge of the differences in terminology between these two types of English.",
"name": "Law terminology",
"prefix": "18387"
},
"1839": {
"description": "Shelf Classification of the Mathematics of the University Library of Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=6495",
"name": "Shelf Classification Mathmatics",
"prefix": "1839"
},
"18393": {
"description": "Note that Widener uses two separate classification systems to shelve books: the Old Widener System and the Library of Congress System indicated by call numbers that begin with WID-LC. (...) In the Old Widener System, call numbers contain whole numbers and are separated by periods that do not confer a decimal value. (...) In Library of Congress WID-LC Classes, call numbers are separated by periods that do confer a decimal value.",
"name": "Widener System",
"prefix": "18393"
},
"18394": {
"description": "The beginning of the subject-classification system - books arranged by subject according to a classification schedule - is dated, rather too precisely, as 1890, because in that year the second library building (Chittenden Hall) was opened. The first library building, originally containing about 20,000 volumes, had reached its capacity of some 200,000 volumes in less than fifty years. The necessity of expanding into a second building made the year 1890 a natural time for making a radical change, which had undoubtedly been contemplated for several years. Although it may be obvious that all 200,000 books were not reclassified at once, it is difficult to realize that twenty-five years elapsed before the bulk of the books had been dealt with, and even today there are a few of the numbered-shelves books which still await reclassification. It is this very length of time occupied in the transition that accounts for much of the indigenous heterogeneity of the Yale Library's classification system. One element that caused delay was the choice of classification schedules. Although many more libraries were using subject classification schemes in 1890 than in 1701, especially in America, the Library of Congress schedules had not yet been published. Dewey's Decimal Classification had reached its third edition, but its rigidly topical structure had no great appeal for members of the Yale faculty, who preferred either a geographical or chronological approach to their material. Other available schemes were also rejected, and Addison Van Name, then Librarian, began work on a new system for Yale, based to a large extent on the classification recently devised by Hartwig for the University of Halle.",
"name": "Yale Library Classification",
"prefix": "18394"
},
"18395": {
"description": "This classification is designed solely to serve the purposes of the Yale Law School and its Library. It is published primarily for the use of the Yale Law Library staff now and in the future. In its preparation no thought was given to the question whether or not it might be adopted by other libraries. (...) The basis of procedure was that the classification should serve the Library, rather than that the Library should be bound by a preconceived theoretical classification. Although it does in fact in most instances facilitate access to the shelves by readers working as lawyers are accustomed to work, it does not purport to bring all material on a given subject together. This seemed to be neither possible nor desirable, and therefore emphasis has from the outset been laid on the subject side of the card catalogue to which one must, in any library, refer in order to find all material in the library on a given subject.",
"homepage": "https://hdl.handle.net/2027/mdp.39015036872680",
"name": "Yale Law Library Classification",
"prefix": "18395"
},
"18396": {
"description": "The Institute Libraryβs classification system is unique. It was created by our first professional librarian, William A. Borden, who served as librarian between 1897- and 1903-1910. After the establishment of the New Haven Free Public Library in 1887, the Institute Library began to withdraw from the public life of the city and focus primarily on expanding and circulating its collection of general-interest and popular literature. The librarian during this period, William A. Borden, made use of the Institute Library as a laboratory in which to experiment with new library technologies and practices. During the first six months of his engagement, he developed a new classification system for the libraryβs collection, which is unique to the Institute Library and remains in use today, together with Bordenβs original card catalog. In 1910, Borden accepted an invitation from the progressive Indian prince, Maharaja Savajirao Gaekwad III of Baroda, to create and direct a free public library system for the people of his state.",
"homepage": "http://institutelibrary.org/borden-classification/",
"name": "Institute Library Classification System",
"prefix": "18396"
},
"18398": {
"description": "This collection of glossaries is intended to assist two groups of people: 1) speakers of Modern Greek who need to read and translate works of philosophy written in English or to write philosophical works in English, and 2) speakers of English who need to to read and translate works of philosophy written in Modern Greek or to write philosophical works in Modern Greek. It gives standard and otherwise acceptable translations of over 2000 philosophical terms, but not their meanings. The current glossaries are presented in two separate pdf files, one for translating from English into Modern Greek and one for translating from Modern Greek into English.",
"homepage": "http://scholarship.claremont.edu/pomona_fac_pub/397/",
"name": "English-Greek Glossary of Philosophical Terms",
"prefix": "18398"
},
"18399": {
"description": "Identifies the type of aggregation used to combine related categories, usually within a common branch of a hierarchy, to provide information at a broader level than the level at which detailed observations are taken.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/AggregationMethod_1.0.html",
"license": "CC BY-SA 3.0",
"name": "Aggregation Method",
"prefix": "18399"
},
"184": {
"description": "Telemaque is the documentary base of the resource center of the INJEP.",
"homepage": "http://telemaque.injep.fr/ListThesau.htm",
"name": "National Institute of Youth and Popular Education Thesaurus",
"prefix": "184"
},
"1840": {
"description": "Shelf Classification of the Media Sciences of the University Library of Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=6503",
"name": "Shelf Classification Media science",
"prefix": "1840"
},
"18400": {
"description": "Describes the entity being analyzed in the study or in the variable.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/AnalysisUnit_1.0.html",
"license": "CC BY-SA 3.0",
"name": "Analysis Unit",
"prefix": "18400"
},
"18401": {
"description": "Standard set of characters upon which many character encodings are based (Wikipedia).",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/CharacterSet_1.0.html",
"license": "CC BY-SA 3.0",
"name": "Character Set",
"prefix": "18401",
"wikidata_database": "Q29149925"
},
"18402": {
"description": "Describes the degree of similarity between two items or schemes (collections of items).",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/CommonalityType_1.0.html",
"license": "CC BY-SA 3.0",
"name": "Commonality Type",
"prefix": "18402"
},
"18403": {
"description": "Includes a typology of data sources.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/DataSourceType_1.0.html",
"license": "CC-BY-3.0",
"name": "Data Source Type",
"prefix": "18403"
},
"18404": {
"description": "Identifies the type of data, which has a bearing on the acceptable data values, the operations that can be performed with the data, and the ways in which the data are stored. The present list is based on the W3C data types, and includes the terms relevant for documenting research data.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/DataType_1.0.html",
"license": "CC BY-SA 3.0",
"name": "Data Type",
"prefix": "18404",
"wikidata_database": "Q190087"
},
"18405": {
"description": "Specifies the type of date. The present list is based on ISO 8601 usage.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/DateType_1.0.html",
"license": "CC BY-SA 3.0",
"name": "Date Type",
"prefix": "18405"
},
"18406": {
"description": "Describes the physical format(s) of the data documented in the logical product(s) of a study unit.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/KindOfDataFormat_1.0.html",
"license": "CC-BY-3.0",
"name": "Kind of Data Format",
"prefix": "18406"
},
"18407": {
"description": "Describes the level of proficiency of an individual in a natural language.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/LanguageProficiency_1.0.html",
"license": "CC BY-SA 3.0",
"name": "Language Proficiency",
"prefix": "18407"
},
"18408": {
"description": "Specifies the event happening over the data life cycle that is considered significant enough to document.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/LifecycleEventType_1.0.html",
"license": "CC BY-SA 3.0",
"name": "Lifecycle Event Type",
"prefix": "18408"
},
"18409": {
"description": "The procedure, technique, or mode of inquiry used to attain the data.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/ModeOfCollection_2.0.html",
"license": "CC BY-SA 3.0",
"name": "Mode of Collection",
"prefix": "18409"
},
"1841": {
"description": "Shelf classification of the classical philology of the University Library of Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=6510",
"name": "Shelf Classification Classical Philology",
"prefix": "1841"
},
"18410": {
"description": "FRASER is both a digital library of economic history and a repository of the institutional history of the Federal Reserve System. As such, FRASER preserves and provides access to economic and banking data and policy documents.",
"homepage": "https://fraser.stlouisfed.org/subject/",
"name": "FRASER Subject Headings",
"prefix": "18410"
},
"18411": {
"description": "Specifies the type of numeric data.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/NumericType_1.0.html",
"license": "CC BY-SA 3.0",
"name": "Numeric Type",
"prefix": "18411"
},
"18412": {
"description": "Indicates the entity that provided the information carried by the variable.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/ResponseUnit_1.0.html",
"license": "CC BY-SA 3.0",
"name": "Response Unit",
"prefix": "18412"
},
"18413": {
"description": "Includes a typology of sampling methods.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/SamplingProcedure_1.0.html",
"license": "CC-BY-3.0",
"name": "Sampling Procedure",
"prefix": "18413"
},
"18414": {
"description": "Indicates the statistical software package used in the production/processing/dissemination of the data. Data collection software is not covered in this list.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/SoftwarePackage_1.0.html",
"license": "CC BY-SA 3.0",
"name": "Software Package",
"prefix": "18414"
},
"18415": {
"description": "Specifies the type of summary statistic. Summary statistics are a single number representation of the characteristics of a set of values.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/SummaryStatisticType_2.0.html",
"license": "CC BY-SA 3.0",
"name": "Summary Statistic Type",
"prefix": "18415"
},
"18416": {
"description": "Describes the time dimension of the data collection.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/TimeMethod_1.2.html",
"license": "CC BY-SA 3.0",
"name": "Time Method",
"prefix": "18416"
},
"18417": {
"description": "Time zone specification as an offset from UTC (Coordinated Universal Time) in terms of hours and minutes.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/TimeZone_1.0.html",
"license": "CC BY-SA 3.0",
"name": "Time Zone",
"prefix": "18417"
},
"18418": {
"description": "Identifies the type of address entered as contact information for an individual or an organization.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/TypeOfAddress_1.0.html",
"license": "CC BY-SA 3.0",
"name": "Type of Address",
"prefix": "18418"
},
"18419": {
"description": "Specifies the rationale for creating a concept group.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/TypeOfConceptGroup_1.0.html",
"license": "CC BY-SA 3.0",
"name": "Type of Concept Group",
"prefix": "18419"
},
"1842": {
"description": "Shelf Classification of the Philosophy of the University Library of Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=6513",
"name": "Shelf Classification Philosophy",
"prefix": "1842"
},
"18420": {
"description": "Includes a typology of notes.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/TypeOfNote_1.0.html",
"license": "CC BY-SA 3.0",
"name": "Type of Note",
"prefix": "18420"
},
"18421": {
"description": "Identifies the type of telephone entered as contact information for an individual or an organization.",
"homepage": "http://www.ddialliance.org/Specification/DDI-CV/TypeOfTelephone_1.0.html",
"license": "CC BY-SA 3.0",
"name": "Type of Telephone",
"prefix": "18421"
},
"18424": {
"description": "Our 1,569 fascinating Subject Files fill the drawers of four, five drawer horizontal file cabinets plus overflow boxes. Think of these files as 'Lesbians andβ¦'. The first file is 'Abortion' and the last is 'Youth'. In between are such topics as 'African-Ancestral Lesbians', 'Bars', 'Health Care', 'Marriage', 'Music Festivals', 'Publishers', 'Religion', 'Theatre', and 'Violence'. We have a complete listing of these files with cross-referencing plus a thesaurus to help you locate information related to your interest.\n\nEach file contains an assortment of papers β flyers, legal briefs, photocopies of newspaper articles, copies of the table of contents of books, event programs, and so on. When a particular topic, for e.g. 'Theatre' has a large number of file folders which are full to the brim, we move the overflow to large boxes stored upstairs. Subject files give you a good introduction to, and overview of a topic and point you towards other parts of the Archivesβ collections if you want more depth.",
"homepage": "http://lesbianherstoryarchives.org/tourcoll2.html",
"name": "Lesbian Herstory Archives Subject Files",
"prefix": "18424"
},
"18425": {
"description": "The SPCS maintains high standards for seed health and purity and operates by exerting official control over initial propagating material, the length of the multiplication chain, and application of strict tolerances for diseases, including those caused by viruses.",
"homepage": "https://www.sasa.gov.uk/sites/default/files/SPCS%20Leaflet%20English%20v13.pdf",
"name": "Scottish Seed Potato Classification Scheme",
"prefix": "18425"
},
"18426": {
"description": "The Seed Potato Classification Scheme (SPCS) provides classification of all potatoes produced and marketed in England and Wales, depending on the class of the parent seed, and the health of the crop and tubers. The aim of the SPCS is to provide assurance that seed potatoes delivered to buyers and growers meet specified minimum health and quality standards.",
"homepage": "https://www.gov.uk/guidance/the-seed-potato-classification-scheme",
"name": "Seed Potato Classification Scheme",
"prefix": "18426"
},
"18427": {
"description": "Plans, reports, photographs and architectural projects of Alfonso de Sierra Ochoa, last municipal architect during the Spanish protectorate in Morocco.",
"homepage": "https://academia6.poolparty.biz/FondoAlfonsodeSierraOchoa.html",
"name": "Fondo Alfonso de Sierra Ochoa",
"prefix": "18427"
},
"18428": {
"description": "English-Greek Glossary of Geomorphological Terms published by the Hellenic Geomorphological Society.",
"homepage": "http://geogclim.geol.uoa.gr/documents/EGE_Glossary_of_Geomorphological_Terms.pdf",
"name": "English-Greek Glossary of Geomorphological Terms",
"prefix": "18428"
},
"18429": {
"description": "English-Greek Glossary of Psychology published by the Hellenic Psychological Society.",
"homepage": "http://www.eleto.gr/download/Bodies/ELPSE_English-Greek-Glossary-of-psychology.pdf",
"name": "English-Greek Glossary of Psychology",
"prefix": "18429"
},
"1843": {
"description": "Shelf Classification of Political Science of the University Library of Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=6516",
"name": "Shelf Classification Political Science",
"prefix": "1843"
},
"18430": {
"description": "Metadata Dictionary is a terms and expressions necessary for the description data entity that includes both ISBD-item rules and the terminology of the RDA item's instructions. Stabilize the production of use of the vocabulary describing the meta information and unify the description is to promote the retrieval performance.\n\nMetadata Vocabulary is based on the structural hierarchy of categories in accordance with FRBR (Functional Requirements for Bibliographic Description)\n\nThe term refers to work independently on the cognitive or artistic content.\n\nThe term expression refers to cognitive or artistic work implement, which may be in the form of voice, image, motion, composed of letters, etc.\n\nThe term refers to the manifestation of work to get the expression of a phenotype (eg. An audio CD, book, map sheet, PDF file)\n\nThe term body refers to a single manifestation of completion (e.g. a single book, a CD-Audio library collections)\n\nThe term refers to an individual person or individual (alone or in combination with one or more other individuals) to establish identity.\n\nThe term entity refers to the organization or group of individuals and / or organizations that are known at a certain, and which is or can act as a single entity.\n\nThe term refers to a family of two or more persons, linked by family relationship, marriage, adoption, linked by a corresponding legal status, or that would otherwise occur as a family\n\nCategories of the concept model and includes item elements are Metadata vocabulary groups, one or more of which it is part. Each concept is included in a group.\n\nSearch applies to both categories of the concepts. an alphabetical listing are shown only terms of concepts.",
"homepage": "https://finto.fi/mts/",
"license": "CC0-1.0",
"name": "Metadata dictionary",
"prefix": "18430"
},
"18431": {
"description": "The general classification of public services consists of 27 main levels and about 180 lower-level categories. The terms used in heading headings describe the use of public services and situations.\n\nΒ The classification is intended specifically for systems and services that provide services to and from citizens and businesses. In the online service presentation platform, categories can be merged, typically for navigation and grouping purposes. In such composite classes, the terms of the classification remain unchanged.\n\nΒ You can and should also use the terms of a rating to use a limited topic or theme on web services whenever the topic provides these conditions.",
"homepage": "https://finto.fi/ptvl/",
"name": "Classification of public services",
"prefix": "18431"
},
"18432": {
"homepage": "https://finto.fi/keko/",
"license": "CC-BY-3.0",
"name": "Ontology for Education for Sustainable Development",
"prefix": "18432"
},
"18433": {
"homepage": "https://finto.fi/pto/",
"license": "CC0-1.0",
"name": "Finnish Geospatial Domain Ontology",
"prefix": "18433"
},
"18434": {
"homepage": "https://finto.fi/afo/",
"license": "CC-BY-3.0",
"name": "Natural resource and environment ontology",
"prefix": "18434"
},
"18435": {
"description": "The Finnish Presentation Composition (SEKO) is a single-language vocabulary covering music presentations. The vocabulary is intended for accurate indexing and retrieval of compositional compositions in the notes and avs.\n\nThe vocabulary is primarily intended for use in the presentation of a presentation set in the MARC 21 bibliographic records and authority records field 382 but may also be used in the artist's remarks (in MARC 21 bibliographic records field 511). The glossary is available in both the RDA description guidelines and the old Finnish inventory rules.\n\nSEKO is based on the Aidatrumpet to Zimbalome list of instruments. The program list has been completely redesigned, new terms have been added to the vocabulary and some of the old terms have been deleted.",
"homepage": "http://finto.fi/seko/",
"license": "CC0-1.0",
"name": "Finnish presentation composition vocabulary",
"prefix": "18435"
},
"18436": {
"description": "The Thesaurus of Mining and Related Matters is a bilingual (Spanish-English) controlled vocabulary for the indexing of sector information. It is an indispensable working tool for all those information units that analyze and process information related to the Area, with or without computer technology.",
"homepage": "http://dspace2.conicyt.cl/bitstream/handle/10533/91507/TESAURO_DE_LA_MINERIA_Y_MATERIAS_AFINES.pdf?sequence=1",
"license": "CC BY-NC-ND 3.0",
"name": "Thesaurus of Mining and Related Matter",
"prefix": "18436"
},
"18437": {
"description": "This vocabulary presents the conceptual organization of tourism in Argentina and in particular the vision that is offered by the Ministry of Tourism of the Nation, allowing navigation through its structure evidencing logical-semantic relationships between the terms.",
"homepage": "http://www.tesauroturistico.gob.ar/index.php?v=15",
"name": "Argentine Tourism Thesaurus",
"prefix": "18437"
},
"18438": {
"description": "Tourism, based on the automatic processing of the version published by the WORLD TOURISM ORGANIZATION.",
"homepage": "http://www.tesauroturistico.gob.ar/index.php?v=16",
"name": "Tourism Thesaurus",
"prefix": "18438"
},
"18439": {
"description": "The Tesauro of the National Archiving System is made up of the various controlled vocabularies present in the CAT SAN scheme as a support for a standardized description of the various resources - conservation institutes, archiving complexes, producer entities - coming from different systems belonging to the SAN. , The 'Tesauro SAN' therefore presents itself as a classification tool open to further evolution and integrable with other systems of national and international knowledge organization.",
"homepage": "http://san.beniculturali.it/web/san/dati-san-lod",
"license": "CC-BY-3.0",
"name": "Tesauro National Archiving System",
"prefix": "18439"
},
"1844": {
"description": "Shelf classification of psychology of the university library of Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=6520",
"name": "Shelf classification of psychology",
"prefix": "1844"
},
"18440": {
"description": "EIGEβs Gender Equality Glossary and Thesaurus is a specialised terminology tool focusing on the area of gender equality. It aims to foster a common understanding of gender equality terms across the EU and promote gender-fair and inclusive language to improve equality between women and men.\n\nThe Gender Equality Glossary and Thesaurus has been developed in cooperation with key stakeholders: European Commission, European Parliament and Council of Europe, as well as national machineries, academia and partners of EIGEβs Resource and Documentation Centre. The collection of terms was based on 92 sources from the European Union, Council of Europe and United Nations normative and policy documents, studies, reports and scientific articles.\n\nThe glossary contains over 400 terms in English with their definitions and sources. In the future, it will be linked with EuroVoc, the multi-lingual EU-wide thesaurus, and it will be available in all EU languages.",
"homepage": "http://eige.europa.eu/rdc/thesaurus",
"name": "Gender Equality Glossary and Thesaurus",
"prefix": "18440"
},
"18441": {
"description": "The Gender and Science Taxonomy provides a fixed set of key topics and keywords to classify all content on GenPORT. The taxonomy is organized around 7 top-level concepts, each holding itself several sub-categories. The taxonomy has been developed by the GenPORT Consortium in consultation with several stakeholders over the entire duration of the project. Currently, the taxonomy is fixed; however, it is available as standard compliant vocuabulary. GenPORT is currently exploring possibilities with other online sites (see for example EIGE's Gender Equality Glossary) to cross-reference content based on shared taxonomy terms.",
"homepage": "http://www.genderportal.eu/main-gender-and-science-taxonomy",
"name": "Gender and Science Taxonomy",
"prefix": "18441"
},
"18442": {
"description": "Welcome to Online Taxonomic Keys, a joint project of Fisheries and Oceans Canada and the Royal BC Museum. This project seeks to facilitate the development of, and make readily available, a variety of regional and global identification keys in a format that is concise and easy to use. The information presented is compiled from published and unpublished works from taxonomic specialists worldwide.\n\nTaxonomic keys are important tools used by scientists and other investigators to identify specific organisms based on defining characteristics. Up until the last decade, these keys were most often published as dichotomous keys, in which specimens are identified by choosing from a progressive series of pairs of options until a solution is reached. While dichotomous keys are still universally used, the online arena provides the opportunity to design and use keys based on a character matrix.\n\nThe identification keys on this site are based on a character matrix format. Specimens may be identified by selecting one or more character states (columns) for each character (rows). As selections are made a list of possible species identifications will appear at the bottom of the matrix. Clicking on the species name opens an information sheet with more information to help you understand the specimen youβve identified.\n\nThis library of identification keys is a work in progress, and will grow and expand as new keys become available.",
"homepage": "http://taxonomy.royalbcmuseum.bc.ca/Taxonomy/",
"name": "Online Taxonomic Key Application",
"prefix": "18442"
},
"18443": {
"description": "A puzzle should be classified by the problem that its designer intended the solver to encounter whilst attempting to solve it. In the case of a 3D interlocking assembly in the form of a cage with a ball in the centre: the fact that the instructions request the would-be solver to 'remove the ball' does not change the 3D assembly into an opening puzzle. The disassembly and/or reassembly of the cage remains the primary function of the puzzle. An interlocking puzzle should be classified according to its interior construction, rather than its outward appearance (e.g. a wooden cube, sphere, barrel, or teddy bear may all have similar Cartesian internal construction and so should all be classed as Interlocking-Cartesian). In cases where it seems possible to place a puzzle in more than one category, it must be classified in whichever is the most significant category. A few puzzles may have to be cross-referenced if it is absolutely necessary; however in most puzzles, which include two different classes of problem, one class will usually be dominant by virtue of the fact that in solving it, the secondary problem has also been solved.\n\nA good example of multiple-class puzzles is the 'Mazy Ball Game' made in Taiwan in the 1990s - It is based on a 3x3 sliding block puzzle under a clear plastic top - The pieces have L-shaped groves and a ball must be rolled up a ramp in the lower right onto one of the blocks - the ball must be moved from block to block and the blocks themselves slid around so that the ball can exit at the top left. Thus the puzzle requires Dexterity, Sequential movement and Routefinding. It would be classed as Routefinding because, if the route has been found, then the dexterity and sequence must have also been achieved.\n\nA puzzle will be referred to as 2D if its third dimension is irrelevant (e.g. thickness of paper or plywood or an operation involving a third dimension such as folding). Most standard jigsaws are 2D; however jigsaws with sloping cuts in fact have a relevant third dimension, so they must be classed as 3D.\n\nIt will be noted that the definition of 'A Puzzle' excludes the infants 'posting box' which whilst perhaps puzzling the infant was contrived only to educate and amuse; it also excludes the archer attempting to get a bullsβeye, the exercise of whose ingenuity is entirely incidental to the original warlike intent of the sport. Also excluded are puzzles that only require paper and pencil (e.g. crossword puzzles), unless they are on or part of some physical object. It is understood that specialist collectors will further subdivide the SubβClasses to suit their own specialised needs. For example, Tanglement Rigid & Tanglement Semi-Rigid is awaiting a thorough study of the topology of wire puzzles.\n\nThe full abbreviations consist of 3 characters, hyphen, plus up to 4 characters, such as 'INTβCART'. These are the standard abbreviations for the classes that have been chosen for relative ease of memory and conformity with most computer databases.",
"homepage": "http://www.puzzlemuseum.com/class/pzcla01.htm",
"name": "Classification of Mechanical Puzzles",
"prefix": "18443"
},
"18444": {
"description": "Insurance terms glossary published by the Global Insurance Group.",
"homepage": "http://www.glig.gr/asfalistikoi-oroi",
"name": "Insurance terms",
"prefix": "18444"
},
"18445": {
"description": "The Climate Bonds Taxonomy provides broad guidance for prospective green bond and climate bondβ―issuers and investors. Guided by the Climate Science Advisory Panel, the aim of the Taxonomy is to encourage common definitions across global markets, in a way that supports the growth of a cohesive thematic bond market. (...)\n\nThe Climate Bonds Taxonomy has been designed to be consistent with the Intergovernmental Panel on Climate Change (IPCC) AR5 report for both the emissions signature of a low-carbon economy required to avoid dangerous climate change and the selection of technologies and practices consistent with that signature. Wherever possible the Taxonomy references existing standards.\n\nThe Taxonomy is intended for broad guidance only. Detailed eligibility is required for certification, and these are being developed by Climate Bonds Standards expert committees.",
"homepage": "https://www.climatebonds.net/standards/taxonomy",
"name": "Climate Bonds Taxonomy",
"prefix": "18445"
},
"18446": {
"description": "Contextual taxonomy was developed in consultation with taxonomy experts from academia, ad measurement companies, and members of the IAB Networks & Exchanges Committee. This taxonomy defines contextual content categories on at least three different tiers.\n\nThe 'IAB Tech Lab Content Taxonomy' was previously called the 'Quality Assurance Guidelines (QAG) Taxonomy.'\n\nThe first tier is a broad level category defined as a targeting depth of either: category/portal, site section, or page. Tier 2 categories and greater are additional categories nested under Tier 1 categories. Both tier 1 and tier 2 categories are formerly established for the IQG Program (formerly QAG Program) so that content classification can be consistent across the industry.",
"homepage": "https://www.iab.com/guidelines/iab-quality-assurance-guidelines-qag-taxonomy/",
"name": "IAB Tech Lab Content Taxonomy",
"prefix": "18446"
},
"18447": {
"description": "The ADREP taxonomy is a set of definitions and descriptions used during the gathering and reporting of accident/incident data to ICAO.",
"homepage": "http://www.icao.int/safety/airnavigation/AIG/Pages/ADREP-Taxonomies.aspx",
"name": "Accident/Incident Data Reporting Taxonomy",
"prefix": "18447"
},
"18448": {
"description": "A wide range of models of PR and communication evaluation exist using a wide range of terms including inputs, outputs, outtakes, outflows, outgrowths, effects, results, and impact. An even wider range of metrics and methods for evaluation are proposed for each stage. The field is confusing for many practitioners.\n\nThis page presents a taxonomy of evaluation tailored to strategic public communication β a taxonomy being a mapping of a field to produce a categorisation of concepts and terms β in short, to show where things go and where they fit in relation to each other. This taxonomy identifies:\n\n1) The major stages of communication (such as inputs, outputs, etc.); 2) The key steps involved in each stage (such as distribution of information, reception by audiences, etc.); 3) Examples of metrics and milestones that can be generated or identified as part of evaluation at each stage; and 4) The most commonly used methods for generating these metrics and milestones.",
"homepage": "http://amecorg.com/amecframework/home/supporting-material/taxonomy/",
"prefix": "18448"
},
"18449": {
"homepage": "https://www.computer.org/web/tlt/taxonomy",
"name": "ACM Taxonomy for Learning Technologies",
"prefix": "18449"
},
"1845": {
"description": "Shelf Classification of Space and environmental sciences of the University Library Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=4817",
"name": "Shelf Classification Space and environmental sciences",
"prefix": "1845"
},
"18450": {
"description": "This TSC taxonomy is generated collectively by the editorial board in 2013 and is evolved from the ACM taxonomy on service computing and all submissions can use either this taxonomy or continue to use the version available in ScholarOne Manuscripts until it is updated.",
"homepage": "https://www.computer.org/web/tsc/taxonomy",
"name": "Taxonomy for Service Computing",
"prefix": "18450"
},
"18451": {
"description": "The Fallacy Files Taxonomy is a tree-like structure that classifies all of the fallacies in these files by the sub-fallacy relation. A sub-fallacy, which is a specific version of a more general fallacy, has whatever features the more general fallacy has, together with specific features which set it apart and make it worth naming in its own right. For example, instead of grouping together 'fallacies of relevance', there is one most general such fallacyβnamely, Red Herringβand all fallacies of relevance are sub-fallacies of it. Red Herring is itself a sub-fallacy of Informal Fallacy, which is a sub-fallacy of the most general logical fallacy of all: Logical Fallacy. Logical Fallacy is, thus, the top node of the Taxonomy, for every fallacy in the Taxonomy is a sub-fallacy of it. The sub-fallacy relationship is like a tree with a trunkβLogical Fallacyβwhich branches until it reaches leaves, that is, fallacies which have no sub-fallaciesβfor example, Appeal to Celebrity.",
"homepage": "http://www.fallacyfiles.org/taxonomy.html",
"name": "Taxonomy of the Logical Fallacies",
"prefix": "18451"
},
"18452": {
"description": "The first EPOC taxonomy of health systems interventions was developed in 2002, and included the following categories: (1) professional interventions; (2) financial interventions; (3) organisational interventions; and (4) regulatory interventions. This taxonomy was extensively revised and updated between 2013 and 2015 to address key gaps and also to bring the EPOC taxonomy into alignment with other taxonomies that were being used to classify health systems interventions in widely used online databases (Lavis 2015). Our starting point was a taxonomy for health systems arrangements developed for the Health Systems Evidence database (http://www.healthsystemsevidence.org) (Lavis 2015). We applied this taxonomy to all of the interventions included in four overviews of systematic reviews of health systems interventions of high relevance to low income countries (Ciapponi 2014; Herrera 2014; Pantoja 2014; Wiysonge 2014). The taxonomy was then revised iteratively to ensure that all of the included reviews were appropriately categorized and that all relevant health system arrangements and implementation strategies were included and organized logically.\n\nWe then applied the revised taxonomy to all of the interventions covered by EPOC reviews. Further minor revisions were made to the taxonomy at this stage to ensure appropriate categorisation of interventions and we also refined the definitions of each of the categories and subcategories.",
"homepage": "http://epoc.cochrane.org/sites/epoc.cochrane.org/files/public/uploads/epoc_taxonomy_13.12.16.pdf",
"name": "EPOC Taxonomy",
"prefix": "18452"
},
"18453": {
"description": "Fast-changing markets demand rapid development of new products and processes. Thousands of tools and methods are available to help innovators discover what users want and how to deliver on their expectations. The challenge is to figure out which ones to use when.\n\nLuma Institute has created a framework to help you choose the best tool for each step of the innovation process, based on the people youβre designing for and the complexity of the systems in which you operate. Luma distilled the portfolio down to 36 of the most effective tools for innovationβthe majority of them in common useβorganized in three categories: looking, understanding, and making. Each category contains three subcategories, and each subcategory contains four innovation tools. This hierarchical model makes it much easier to identify the tools you need and then put them to use.",
"homepage": "https://hbr.org/2014/01/a-taxonomy-of-innovation",
"name": "Taxonomy of Innovation",
"prefix": "18453"
},
"18454": {
"description": "In 2013, it became apparent that the publication ethics cases being brought to COPE for discussion and advice were becoming more complex. A new and more comprehensive classification scheme was therefore developed to make it easier to code cases, to aid searching, and to provide a finer level of detail for analysis. The resulting COPE Case Taxonomy comprises 18 main classification categories and 100 keywords and is designed to be descriptive not judgemental.\n\nAll the cases in COPEβs database were recoded and all new cases are being coded according to the new taxonomy (up to two classifications, denoting the main topics discussed, and 10 keywords can be assigned per case). It is important to note that classification and keyword coding denotes that a topic was raised and discussed, not that a particular form of publication misconduct had occurred.\n\nThe COPE Case Taxonomy is available, with appropriate attribution, for use by other organizations and individuals. Attribution should include the version date and number, and a link to the taxonomy on COPEβs website.",
"homepage": "http://publicationethics.org/cope-case-taxonomy",
"name": "COPE Case Taxonomy",
"prefix": "18454"
},
"18455": {
"homepage": "http://www.grnti.ru/",
"name": "Code of State Categories Scientific and Technical Information",
"prefix": "18455"
},
"18456": {
"description": "The thesaurus is intended for open access use by government, academic, and business records centers and archives for use in functional (function-based) classification of records and to aid in the arrangement and description (including electronic description) of archival materials. The thesaurus is meant for the proper classification of records of corporate bodies (governments, academic institutions, not-for-profit agencies, government offices, etc.) as functions or activities, and not for use for manuscripts, personal papers, or family papers, which require an occupational or genre thesaurus for proper classification and description.",
"homepage": "http://www2.archivists.org/sites/all/files/FunctionsThesaurus2010.pdf",
"name": "Functions and Activities Thesaurus for Business, Academic, Not-for-profit, and Government Entities",
"prefix": "18456"
},
"18457": {
"description": "Language used in the ISOC sub-bases of Anthropology, Archeology, Fine Arts and History. It is structured based on the different fields of content analysis used in this database: classification, descriptors, identifiers, place names, historical period, author keywords.",
"homepage": "http://archivos.cchs.csic.es/tematres/vocab/",
"license": "CC BY-NC 3.0",
"name": "Vocabulary of indexing ISOC Humanities - Cultural heritage",
"prefix": "18457"
},
"18459": {
"description": "A collection of 2000 administrative terms with English - Norwegian bokmΓ₯l/Norwegian bokmΓ₯l - English and English - Norwegian nynorsk/Norwegian nynorsk - English translations, from the Norwegian Institutions of Higher Education.\n\nThe termbase translates from Norwegian bokmΓ₯l/Norwegian nynorsk to British English and the other way round. (The base uses the Oxford University Press house style.)",
"homepage": "http://termbase.uhr.no/",
"license": "CC BY-NC-SA 3.0",
"name": "UHR's Termbase for Norwegian higher education institutions",
"prefix": "18459",
"wikidata_database": "Q28843616"
},
"1846": {
"description": "This is the classification system for legal science at the University Library of Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=6524",
"name": "Shelf Classification of Legal Science",
"prefix": "1846"
},
"18460": {
"description": "Collection of more than 3000 concepts from areas of both public and private law.",
"homepage": "http://www.terminologi.no/termbase_NOJU.xhtml",
"name": "Norwegian-German legal terminology",
"prefix": "18460"
},
"18462": {
"description": "In the COSMIN taxonomy three quality domains are distinguished, i.e. reliability, validity, and responsiveness. Each domain contains one or more measurement properties.\n\nThe domain reliability contains three measurement properties: internal consistency, reliability, and measurement error. The domain validity also contains three measurement properties: content validity, construct validity and criterion validity. The domain responsiveness contains only one measurement property, which is also called responsiveness. The term and definition of the domain and measurement property responsiveness are the same, but they are distinguished in the taxonomy for reasons of clarity. Some measurement properties contain one or more aspects, that were defined separately: Content validity includes face validity, and construct validity includes structural validity, hypotheses testing and cross-cultural validity.",
"homepage": "http://www.cosmin.nl/COSMIN%20taxonomy.html",
"name": "COSMIN Taxonomy of Measurement Properties",
"prefix": "18462"
},
"18463": {
"description": "It is difficult to provide a taxonomy of optimization because many of the subfields have multiple links. Shown here is one perspective, focused mainly on the subfields of deterministic optimization with a single objective function.",
"homepage": "https://neos-guide.org/content/optimization-taxonomy",
"name": "Optimization Taxonomy",
"prefix": "18463"
},
"18464": {
"description": "It is a uniform classification scheme of buildings across the globe. It will be used as a basis for assessing the risk from earthquakes within the scope of GEM. It also facilitates global collaboration and growing of our joint knowledge on the diversity and seismic vulnerability of all the buildings that exist around the globe.",
"homepage": "https://www.globalquakemodel.org/single-post/2017/05/17/GEM-Building-Taxonomy-Version-20",
"name": "GEM Building Taxonomy",
"prefix": "18464"
},
"18465": {
"description": "This document provides a standard taxonomy of medication errors to be used in combination with systems analysis in recording and tracking of medication errors. It is not intended to assess blame. The document is not all-inclusive, but can be expanded as new issues arise. The purpose of this taxonomy is to provide a standard language and structure of medication error-related data for use in developing databases analyzing medication error reports. (...)\n\nThe effectiveness of the taxonomy, and the resulting analysis of medication error reports, is dependent upon the amount and the quality of the data collected through medication error reports. For optimum application of the taxonomy, include as much information as possible in the instrument. However, if all the information described in the taxonomy is not collected, the information that is available should be categorized as shown in the taxonomy.",
"homepage": "http://www.nccmerp.org/sites/default/files/taxonomy2001-07-31.pdf",
"name": "NCC MERP Taxonomy of Medication Errors",
"prefix": "18465"
},
"18466": {
"description": "The goal of this project is simple, to maintain a free, community driven, open source taxonomy of potential threats to information systems. Our hope is that this taxonomy will serve as a resource for organizations attempting to prioritize their defenses and choose controls most appropriate for defending their information systems. We believe that the nature of a common internet and homogeneous systems leads to common threats to information systems. This taxonomy has been created to identify those threats in order to help organizations choose defenses most appropriate to defend such systems.",
"homepage": "https://www.auditscripts.com/resources/open_threat_taxonomy_v1.1a.pdf",
"license": "CC BY-SA 3.0",
"name": "Open Threat Taxonomy",
"prefix": "18466"
},
"18467": {
"homepage": "http://www.informationphilosopher.com/freedom/taxonomy.html",
"license": "CC-BY-3.0",
"name": "Taxonomy of Free Will Positions",
"prefix": "18467"
},
"18468": {
"description": "The Healthcare Provider Taxonomy Code Set is a hierarchical code set that consists of codes, descriptions, and definitions. Healthcare Provider Taxonomy Codes are designed to categorize the type, classification, and/or specialization of health care providers. The Code Set consists of two sections: Individuals and Groups of Individuals, and Non-Individuals. The Code Set is updated twice a year, effective April 1 and October 1. The 'Crosswalk β Medicare Provider/Supplier to Healthcare Provider Taxonomy' was updated because of changes made to the Healthcare Provider Taxonomy Code Set that will be implemented October 1, 2008. That Code Set is available from the Washington Publishing Company. The Code Set is maintained by the National Uniform Claim Committee. The Code Set is a Health Insurance Portability and Accountability (HIPAA) standard code set. As such, it is the only code set that may be used in HIPAA standard transactions to report the type/classification/specialization of a health care provider when such reporting is required.",
"homepage": "https://www.cms.gov/Medicare/Provider-Enrollment-and-Certification/MedicareProviderSupEnroll/Downloads/TaxonomyCrosswalk.pdf",
"name": "Healthcare Provider Taxonomy Code Set",
"prefix": "18468"
},
"18469": {
"description": "The Biomimicry Taxonomy is a classification system developed by the Biomimicry Institute to organize biological content on the website AskNature. The taxonomy categorizes the different ways that organisms and natural systems meet functional challenges into groups of related functions.\n\nUse the taxonomy to help you navigate AskNature or, when beginning a design challenge, as a tool to help you 'think functionally' and identify questions you can 'ask' nature.",
"homepage": "https://asknature.org/resource/biomimicry-taxonomy/#.WQD4QsakLIU",
"license": "CC BY-NC 3.0",
"name": "Biomimicry Taxonomy",
"prefix": "18469"
},
"1847": {
"description": "This is the classification system for romance at the University Library of Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=6534",
"name": "Shelf Classification Romanistik",
"prefix": "1847"
},
"18470": {
"homepage": "http://www.elderecho.com/tesauro/",
"name": "Thesaurus Elderecho.com",
"prefix": "18470"
},
"18471": {
"description": "In 1971, the Toulouse municipal library tested a systematic classification framework developed in 1969 by Henri-Jean MARTIN and Guy PARGUEZ for a study on the automation of cataloging by adding alphanumeric indices to the table frame (1865), the content of the former \"classification of booksellers,\" in which the subjects were divided into five classes: theology, law, science and the arts, belles-lettres, For a decade, the table was used and gradually modified in the presentation and in the content, in conjunction with the cataloging work of the old collection of the WB of Toulouse, then researchers and librarians Have used, which led us to draft a revised version in 1985, in collaboration with the Sibil network and after consulting the users The last update on the \"Brunet-Pargue Z \"took place in February 1994 in Toulouse during the colloquium organized by LIBER (League of European Research Libraries) (...).\n\nWhat is the value of this table? Provide an additional means of identifying books whose contents are poorly defined in an analytical catalog and using unconventional concepts. The advantage of the version developed in Toulouse, where all the rubrics \"mixtures\", in which Brunet inserted his dummy collections, was suppressed, is to encourage the reclassification and exploitation of thousands of brochures during the Despoil of these collections or bundles. The indexing of their contents allows the researcher to find small works, anonymous or of little known authors, who have escaped specialized bibliographies, and which can present a real interest for the human sciences.",
"name": "Systematic Classification Brunet-Parguez-Coulouma",
"prefix": "18471"
},
"18472": {
"description": "The BSI classification scheme is specific, and from the outset it has been chosen not to use pre-existing classifications such as CDU or Dewey, so BSI has developed its own tool.\n\nThe BSI classification scheme is a management tool that allows the distribution of documents: it is intended to classify documents all media and not knowledge. It does not attempt to describe precisely a specific knowledge. Its all media logic implies that a rating may contain only one or more media. The basic structure is a systematic and hierarchical classification, from the general to the particular. The notation of the indices is alphanumeric: one or more letters associated with the section, followed by a numerical index declined according to the decimal principle.\n\nDesigned to be able to adapt to the documentary policy, the editorial offer, the typology of documents and the evolution of knowledge, the classification plan is regularly reviewed.",
"homepage": "http://www.cite-sciences.fr/fr/au-programme/lieux-ressources/bibliotheque/toutes-les-collections/plan-de-classement/",
"name": "BSI Classification Plan",
"prefix": "18472"
},
"18473": {
"description": "The principles for classifying musical documents, often abbreviated to PCDM, are a musical classification system developed in public libraries in France since 1983, especially for collections of music-related documents. Public concern than Dewey's decimal classification.",
"homepage": "https://fr.wikipedia.org/wiki/Principes_de_classement_des_documents_musicaux",
"name": "Principles of Classification of Musical Documents",
"prefix": "18473"
},
"18474": {
"homepage": "http://pro.bpi.fr/plan-de-classement-de-la-bpi-1",
"license": "CC BY-SA 3.0",
"name": "Library Ranking Plan of the Bpi",
"prefix": "18474"
},
"18475": {
"description": "The fund Drioton was acquired by the NBU in 1961 with the amount in relation to war damage to the Second World War. Etienne Drioton (1889-1961) was Director General of the Department of Antiquities in Egypt (1936-1952) and Professor at the College de France (1957-1961). The works of his collection are kept in Joffre space and were cataloged in map styles in 1965-1970 years. A file created by authors and anonymous titles, systematic file (after a specific review, see below) and a concordance file is available to the coin store cabinet. In 2005 these catalogs were reverted and records of these books are available on the computer catalog of the NBU and on the Internet.",
"homepage": "http://www.bnu.fr/collections/patrimoine/le-fonds-egyptologique-du-chanoine-drioton",
"name": "Map of the Canotypes of Drioton",
"prefix": "18475"
},
"18476": {
"description": "In the 1970s, the Uniform Genre Format (UGI) was introduced and replaced by the Dutch Uniform Genre Classification (NUGI) in 1986. As of April 1, 2002, the Dutch-language Uniform Classification (NUR) was introduced because the old coding Under the auspices of the Dutch and Flemish Bookstores Association and with the support of the Dutch-Dutch publishing and bookstore (ONUB), this review has been completed. The publisher determines the NUR code of a book to be published. There are various tools To convert the old NUGI into the new NUR.",
"homepage": "http://www.boek.nl/nur",
"name": "Dutch Uniform Classification",
"prefix": "18476"
},
"18477": {
"description": "The Narcis Classification is a framework of codes with which institutes and experts are classified and can be retrieved. The D code classifies on scientific disciplines. The classification also contains an E code. This code includes some interdisciplinary research fields. The Narcis Classification has been revised in the year 2015.\n\nThe Narcis Classification is used among others in the scientific portal Narcis, https://www.narcis.nl.",
"homepage": "http://www.narcis.nl/classification",
"name": "NARCIS Classification",
"prefix": "18477"
},
"18478": {
"description": "Dictionary of computer architecture terms published by the Department of Informatics and Telecommunications.",
"homepage": "http://architecture.di.uoa.gr/lexico.html",
"name": "Dictionary of computer architecture terms",
"prefix": "18478"
},
"18479": {
"description": "This Strongs Greek-English Glossary has been generated based on βLexical Formβ glosses and Strongβs number assignment from the Lexham Greek-English Interlinear New Testament, available from Logos Bible Software (http://www.logos.com). Lexical Form glosses are general and relatively context-free; they are not formal definitions. While they serve some use for quick and easy lookup, if one is studying a particular word or word usage, one should further consult a formal Greek-English dictionary or lexicon.",
"homepage": "http://sblgnt.com/download/revint/99-Glossary.pdf",
"name": "Strongs Greek-English Glossary",
"prefix": "18479"
},
"1848": {
"description": "This is the classification system for Slavistics at the University Library of Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=6557",
"license": "CC-BY-3.0",
"name": "Shelf Classifications Slavistics",
"prefix": "1848"
},
"18480": {
"description": "Naval Headquarters Classification System of the Anna-Lindh-Library.",
"homepage": "https://www.fhs.se/Documents/Anna%20Lindhbiblioteket/Stabs/Marinstabens%20klassificeringssystem.pdf",
"name": "Naval Headquarters Classification System",
"prefix": "18480"
},
"18481": {
"description": "Shelf classification of the Anna Lindh Library.",
"homepage": "http://www.fhs.se/Documents/Anna%20Lindhbiblioteket/Stabs/fst_ocr.pdf",
"name": "Defense Staff Library's Classification System",
"prefix": "18481"
},
"18482": {
"description": "Military Staff Library's Classification System",
"homepage": "http://www.fhs.se/Documents/Anna%20Lindhbiblioteket/Stabs/MIL_ocr.pdf",
"name": "Military Staff Library's Classification System",
"prefix": "18482"
},
"18483": {
"description": "The Swedish Geotechnical Institute (SGI) is an expert agency that works for a safe, efficient and sustainable development and sustainable use of land and natural resources.",
"homepage": "http://www.swedgeo.se/en/research--learning/bibliotek/om-sgi-line/klassifikationssystem/",
"name": "International Geotechnical Classification System",
"prefix": "18483"
},
"18484": {
"description": "University libraries offer information search and information literacy teaching for their students and staff. In addition to study-related teaching, individual instruction is also available and can be booked from the information specialists of the academy libraries.\n\nThe library staff provides customer guidance for using the library and searching for material. You can ask for advice from the libraryβs customer service or by email. Detailed questions concerning information acquisition or thesis writing can be discussed in a private information specialist meeting.",
"homepage": "https://lib.uniarts.fi/sibelius-akatemian-kirjojen-luokitus",
"name": "Sibelius Academy book classification system",
"prefix": "18484"
},
"1849": {
"description": "This is the classification system for Theology at the University Library of Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=6569",
"name": "Aufstellungssystematik Theologie",
"prefix": "1849"
},
"18497": {
"abbreviation": "DNBSGR",
"name": "Subject Categories from the Deutsche Nationalbibliografie",
"prefix": "18497"
},
"18498": {
"abbreviation": "CDWA",
"description": "CDWA is a set of guidelines for the description of art, architecture, and other cultural works. CDWA also provides a framework to which existing art information systems may be mapped, upon which new systems may be developed, or upon which data may be linked in an open environment. CDWA is mapped to the Cultural Objects Name Authority (CONA) and CIDOC CRM.",
"homepage": "http://www.getty.edu/research/publications/electronic_publications/cdwa/",
"name": "Categories for the Description of Works of Art",
"prefix": "18498",
"wikidata_database": "Q5051819"
},
"18499": {
"description": "As members of the Finding Things team have written previously, weβve long understood the need for a GOV.UK taxonomy thatβs subject-based and site-wide, and weβve been working towards achieving this challenging aim for a while. When finished, the taxonomy will group together all content on the site in a meaningful and intuitive way, using a hierarchical structure. It will consist of many βtopicsβ and βsubtopicsβ, to which all content items will be tagged. Weβre not there yet, but we do now have a branch that covers the governmentβs education offering - and with all the relevant content tagged to it, thanks to the tireless work of publishers within the governmentβs education organisations. (...)\n\nSo why does government need a site-wide taxonomy? Because government has a lot of content: more than 300,000 individual items, in fact. With so much content it can be very difficult for users to find the thing theyβre looking for - or, if theyβre searching more broadly around a subject, to find things of real value or relevance. We also know from user research with professional users like teachers, accountants, lawyers and tax specialists that there are people who need to see everything about a topic so they can do their job properly. Without a subject-based taxonomy in place, these users might only get partial information and not the full picture. This new taxonomy will act as a framework for a redesigned navigation, with the 2 working in tandem to help users orientate themselves and explore the site more confidently and effectively.",
"homepage": "https://insidegovuk.blog.gov.uk/2017/03/21/presenting-our-new-taxonomy-beta/",
"name": "GOV.UK Taxonomy",
"prefix": "18499"
},
"185": {
"description": "517 terms.",
"homepage": "http://vocabularyserver.com/conole/",
"name": "Learning Activities",
"prefix": "185"
},
"1850": {
"description": "This is the classification system for Economics at the University Library of Trier.",
"homepage": "https://www.uni-trier.de/index.php?id=6459",
"name": "Shelf Classification Economics",
"prefix": "1850"
},
"18500": {
"description": "Search the Glossary for geography, science, and social studies terms.",
"homepage": "http://www.nationalgeographic.org/glossary/",
"name": "National Geographic Society Glossary",
"prefix": "18500"
},
"18501": {
"description": "Objectives of the Hierarchical Taxonomy of Psychopathology (HiTOP) are to advance the classification of psychopathology to maximize its usefulness for research and clinical practice. The HiTOP aims to address limitations of traditional nosologies, such as the DSM-5 and ICD-10, including arbitrary boundaries between psychopathology and normality, often unclear boundaries between disorders, frequent disorder co-occurrence, heterogeneity within disorders, and diagnostic instability.\n\nThe HiTOP approaches these problems by conducting an empirical search for psychopathology structures starting from the most basic building blocks and proceeding to the highest level of generality: combining individual signs and symptoms into homogeneous components or traits, assembling them into empirically-derived syndromes, and finally grouping them into psychopathology spectra (e.g., internalizing and externalizing).\n\nThis approach reduces within-disorder heterogeneity by grouping related symptoms together and assigning unrelated symptoms to different components. It makes comorbidity an explicit and predictable feature of the model by classifying related syndromes together. Finally, it describes psychiatric phenomenaally, addressing boundary problems and diagnostic instability. The HiTOP is not limited to dimensions, if evidence indicates existence of a natural boundary, this qualitative distinction will be incorporated in the model also.\n\nThe HiTOP system aims to significantly advance mental health research and care, providing an effective way to convey information on risk factors, etiology, pathophysiology, phenomenology, illness course, and treatment response, thus greatly improving the utility of the diagnosis of mental disorders. Dimensional measures have been developed to assess many aspects of the system, and several domains of the HiTOP are ready for clinical and research applications.",
"homepage": "https://medicine.stonybrookmedicine.edu/HITOP/AboutHiTOP",
"name": "Hierarchical Taxonomy of Psychopathology",
"prefix": "18501"
},
"18502": {
"description": "The Financial Accounting Foundation (FAF) and the Financial Accounting Standards Board (FASB) are responsible for the ongoing development and maintenance of the U.S. GAAP Financial Reporting Taxonomy (Taxonomy). As part of the ongoing development and maintenance of the Taxonomy, the Development\n\nTaxonomy is available for comment throughout the year. Additionally, the FASB publishes an annual release of the Taxonomy to address new reporting requirements.",
"homepage": "http://www.fasb.org/jsp/FASB/Page/LandingPage&cid=1176164131053",
"name": "US GAAP Financial Reporting Taxonomy",
"prefix": "18502"
},
"18503": {
"description": "There is no common way to describe or classify the βthingsβ that make up the IoT or the projects or systems and services based on them. To complicate matters, the range of projects and applications that the term IoT covers is vast. IoT applications could be made up of a simple sensor that reports whether a door is open or not (in the case of a simple security system) or whether a button has been pressed (in the case of a remote doorbell) to very sophisticated solutions that monitor dozens of phenomena, make complex calculations based on those phenomena, and then prompt a response (in the case of autonomous drones, for example). A means of classifying different IoT projects will be useful to properly understand the current state of IoT adoption, compare different IoT initiatives, and to inform decision making when it comes to policy development, and the definition research and market development initiatives.To this end, Digital Catapult has started to define a taxonomy that will provide an effective way of classifying IoT initiatives.",
"homepage": "https://iotuk.org.uk/wp-content/uploads/2017/01/IOT-Taxonomy-Report.pdf",
"name": "Internet of Things Taxonomy",
"prefix": "18503"
},
"18504": {
"description": "A comprehensive - an ever-growing - glossary of key terms in Human-Computer Interaction.",
"homepage": "https://www.interaction-design.org/literature/book/the-glossary-of-human-computer-interaction",
"name": "The Glossary of Human Computer Interaction",
"prefix": "18504"
},
"18505": {
"homepage": "http://www.natobilc.org/documents/Military%20Language/TriSvcBILC_005.pdf",
"name": "List of Useful Words of Armyβs Services - NATO Glossary",
"prefix": "18505"
},
"18506": {
"homepage": "http://www.redstar.gr/Foto_red/Lex.html",
"name": "Aviation Dictionary",
"prefix": "18506"
},
"18507": {
"homepage": "https://www.google.gr/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwiL-L7igovTAhVCbhQKHdW4D4AQFggaMAA&url=ftp%3A//ftp.mpic.de/WalterD/Transfer/Trockner/Compressor/Glossary/glossary/Mark%25202930%25207098%252051%2520%2520en---it-no-da-el-pt.pdf&usg=AFQjCNGbW-K2H0ILUA0dvjimzZOxkEoNfg&sig2=YAirWy67VGszyYLt_a3VYA",
"prefix": "18507"
},
"18508": {
"description": "The United States Code is a consolidation and codification by subject matter of the general and permanent laws of the United States.",
"name": "United States Code",
"prefix": "18508",
"wikidata_database": "Q1196092"
},
"18509": {
"homepage": "http://www.testapedia.com/proddir/dir_list.asp?dir_id=26",
"name": "Testapedia Taxonomy",
"prefix": "18509"
},
"1851": {
"description": "The Portico Library classification scheme is a fixed shelf classification. We do not use the Dewey Decimal System. As demonstrated in the list below, our classification is alphanumerical; subjects have been assigned a letter of the alphabet.",
"homepage": "http://www.theportico.org.uk/library/catalogue",
"name": "Portico Library Classification Scheme",
"prefix": "1851"
},
"18510": {
"description": "The GND subject categories are used to provide a broad classification of concepts in the Integrated Authority File.",
"homepage": "http://d-nb.info/standards/vocab/gnd/gnd-sc",
"license": "CC0-1.0",
"name": "GND subject categories",
"prefix": "18510"
},
"18512": {
"description": "The RePEc Author Service aims to link economists with their research output in the RePEc bibliographic database.",
"homepage": "https://authors.repec.org/",
"name": "RePEc Author Service",
"prefix": "18512",
"wikidata_database": "Q32075787"
},
"18514": {
"description": "Terminology used to record the broad date of a site, monument, building or structure. Covering the timeline of human existence.",
"homepage": "http://heritagedata.org/live/schemes/eh_period.html",
"license": "CC-BY-3.0",
"name": "Historic England Periods Authority File",
"prefix": "18514"
},
"18515": {
"abbreviation": "ISIL",
"description": "The International Standard Identifier for Libraries and Related Organisations (ISIL), ISO 15511, assigns unique identifiers to libraries and related organisations, such as archives and museums.",
"homepage": "http://biblstandard.dk/isil/",
"name": "International Standard Identifier for Libraries and Related Organizations",
"prefix": "18515",
"wikidata_database": "Q470458"
},
"18516": {
"description": "The current NUTS 2013 classification is valid from 1 January 2015 and lists 98 regions at NUTS 1, 276 regions at NUTS 2 and 1342 regions at NUTS 3 level.\n\nThe NUTS classification (Nomenclature of territorial units for statistics) is a hierarchical system for dividing up the economic territory of the EU for the purpose of :\n\nThe collection, development and harmonisation of European regional statistics\n\nSocio-economic analyses of the regions\n\n NUTS 1: major socio-economic regions\n\n NUTS 2: basic regions for the application of regional policies\n\n NUTS 3: small regions for specific diagnoses\n\n Regional typologies and local information corresponding to NUTS 3\n\nFraming of EU regional policies.\n\n Regions eligible for support from cohesion policy have been defined at NUTS 2 level.\n\n The Cohesion report has so far mainly been prepared at NUTS 2 level.",
"prefix": "18516",
"wikidata_database": "Q193083"
},
"18517": {
"description": "This vocabulary collects all writing techniques and types as attested in the EAGLE BPN. A major classification problem is faced on this respect by epigraphists. In same cases the distinction between the method used to produced a text is used as a principle for a definition, in some other the name of the writing technique is based on the result obtained, no matter of the method that was used. In particular Punctim, litt. Scariphatis and litt. Eminentibus are defintions of this second type.",
"homepage": "https://www.eagle-network.eu/voc/writing.html",
"name": "EAGLE Vocabulary - Execution Technique",
"prefix": "18517",
"wikidata_database": "Q19371183"
},
"18518": {
"description": "Translation of Physics terms based on the Coursework for Physics Grades 9 to 12.",
"homepage": "http://steinhardt.nyu.edu/metrocenter/resources/glossaries",
"prefix": "18518"
},
"18519": {
"description": "Translation of Living Environment terms based on the Coursework for Living Environment Grades 9 to 12.",
"homepage": "http://steinhardt.nyu.edu/metrocenter/resources/glossaries",
"prefix": "18519"
},
"1852": {
"description": "Systematics of the faculty library for natural sciences\n\nDate: 10/2015",
"homepage": "http://www.ubs.sbg.ac.at/fbn/systematik/systematik.htm",
"name": "Systematics of the faculty library for natural sciences",
"prefix": "1852"
},
"18521": {
"description": "In this vocabulary are described all terms which concern the type of text written on a stone according to its function and aim as a text. (Manzella 1987, pp. 110-111)",
"homepage": "http://www.eagle-network.eu/voc/typeins.html",
"prefix": "18521"
},
"18522": {
"description": "The classification of objects on which an inscription can be written is extremely complex in many cases. For example, within the scope of the inscription which would fall under Statue Base, there are few cases in which what survives is an βInscribed plaqueβ β an inscription once affixed to a base (made of a different material) β and in other cases our βstatue baseβ in a wider context would more naturally be defined in another way: in particular βTriumphal archβ (say, for the Arch of Constantine, that once supported statues), βCity gateβ (like those of Rome, with statues of the emperors), or βColumnar monumentβ (e.g. Trajanβs Column β which of course supported a statue).",
"homepage": "http://www.eagle-network.eu/voc/objtyp.html",
"prefix": "18522"
},
"18523": {
"description": "Terms in this vocabulary refer to any decoration surrounding an inscription. Hederae, crosses, and chi-rho monograms are probably among the most frequent decorations, but there are a number of classifiable features of decoration which support and are indeed vital in some cases, to the understanding of the inscribed text. Many artistic classification could be suggested, but for the purposes of epi- graphic research we offer a flat list of features which can be found surrounding an inscription.",
"homepage": "http://www.eagle-network.eu/voc/decor.html",
"prefix": "18523"
},
"18524": {
"description": "The common use among Members of the BPN is to insert, when this information is available two dates. A 'Not before' and 'Not after' dates. This is still a best practice and has been preserved as such in any encoding. There are nevertheless divergences on historical periods and indeed in the way computations are done. In many cases only a generic date is possible.\n\nIn this vocabulary we suggest a series of standardizations which equate some locution with a specific date interval, e.g. 'shortly after' with an interval of ca. 10 years. The Working Group has chosen to always explicitly suggest the corresponding TEI origDate element as a definition in this vocabulary.",
"homepage": "http://www.eagle-network.eu/voc/dates.html",
"prefix": "18524"
},
"18525": {
"description": "State of preservation (which could probably be abbreviated to 'Condition') is a small vocabulary describing the general condition in which the inscription was at the moment of the latest inspection. In many cases we wonβt know if an inscription still exists.",
"homepage": "http://www.eagle-network.eu/voc/statepreserv.html",
"prefix": "18525"
},
"18526": {
"description": "Literary terms and devices are a collection of universal artistic structures that are typical of all works of literature frequently employed by the writers to give meanings and a logical framework to their works through language. When such works are read by readers, they ultimately recognize and appreciate these literary structures. Due to their universality, they also allow the readers to compare a work of one writer to that of another and often across languages. They not only beautify the piece of literature but also give deeper meanings to it, testing the very understanding of the readers along with providing them enjoyment as they read. Additionally, literary terms and devices help ignite the readersβ imagination as they visualize the characters and scenes of the text.",
"homepage": "http://steinhardt.nyu.edu/metrocenter/resources/glossaries",
"prefix": "18526"
},
"18527": {
"homepage": "https://semantic-web.com/glossary/",
"name": "Semantic Web Company Glossary",
"prefix": "18527"
},
"18528": {
"homepage": "http://ΠΎΠΊΠ²ΡΠ΄.ΡΡ/",
"name": "Russian Economic Activities Classification System",
"prefix": "18528",
"wikidata_database": "Q19192441"
},
"1853": {
"description": "The open shelf music material in the Weston Library is classified according to the following sequence.",
"homepage": "http://ox.libguides.com/content.php?pid=246314&sid=2163279",
"license": "CC-BY-3.0",
"name": "Weston Library Music Open Shelf Classification",
"prefix": "1853"
},
"18531": {
"description": "This vocabulary describes the platform, versions of browsers and plug-ins that an item has been tested on and confirmed to support.",
"homepage": "http://vocabulary.curriculum.edu.au/technicalRequirement.html",
"name": "Technical Requirement",
"prefix": "18531"
},
"18532": {
"description": "The Australian Professional Standards for Teachers career stages guide the preparation, support and development of teachers. The stages reflect a continuum of a teacherβs developing professional expertise from undergraduate preparation through to being an exemplary practitioner and a leader in the profession.",
"homepage": "http://vocabulary.curriculum.edu.au/teachercareerstage.html",
"name": "Teacher career stage",
"prefix": "18532"
},
"18533": {
"description": "Skill level is defined as a function of the range and complexity of the set of tasks performed in a particular occupation. The greater the range and complexity of the set of tasks, the greater the skill level of an occupation.",
"homepage": "http://vocabulary.curriculum.edu.au/skillLevel.html",
"name": "Skill Level",
"prefix": "18533"
},
"18534": {
"description": "Modes refer to the various forms of communication β listening, speaking, reading, viewing and writing.",
"homepage": "http://vocabulary.curriculum.edu.au/languageModes.html",
"name": "Language Modes",
"prefix": "18534"
},
"18535": {
"description": "Elements used to organise the Australian Curriculum.",
"homepage": "http://vocabulary.curriculum.edu.au/curriculumElement.html",
"name": "Australian Curriculum Element",
"prefix": "18535"
},
"18536": {
"abbreviation": "LCNAF",
"description": "The Library of Congress Name Authority File (NAF) file provides authoritative data for names of persons, organizations, events, places, and titles. Its purpose is the identification of these entities and, through the use of such controlled vocabulary, to provide uniform access to bibliographic resources. Names descriptions also provide access to a controlled form of name through references from unused forms, e.g. a search under: Snodgrass, Quintus Curtius, 1835-1910 will lead users to the authoritative name for Mark Twain, which is, 'Twain, Mark, 1835-1910.' Names may also be used as subjects in bibliographic descriptions, so they may be combined with controlled values from subject heading schemes, such as LCSH.\n\nLibrary of Congress Names includes over 8 million descriptions created over many decades and according to different cataloging policies. LC Names is officially called the NACO Authority File and is a cooperative effort in which participants follow a common set of standards and guidelines.",
"homepage": "http://id.loc.gov/authorities/names.html",
"name": "Library of Congress Name Authority File",
"prefix": "18536",
"wikidata_database": "Q18912790"
},
"18537": {
"description": "The Library of Congress Subject Headings Supplemental Vocabularies: Childrenβs Headings (LCSHAC) is a thesaurus which is used in conjunction with LCSH. It is not a self-contained vocabulary, but is instead designed to complement LCSH and provide tailored subject access to children and young adults when LCSH does not provide suitable terminology, form, or scope for children. LCSHAC records can be identified by the LCCN prefix 'sj'.",
"homepage": "http://id.loc.gov/authorities/childrensSubjects.html",
"name": "Library of Congress Children's Subject Headings",
"prefix": "18537"
},
"18538": {
"description": "The Library of Congress Genre/Form Terms for Library and Archival Materials (LCGFT) is a thesaurus that describes what a work is versus what it is about. For instance, the subject heading Horror films, with appropriate subdivisions, would be assigned to a book about horror films. A cataloger assigning headings to the movie The Texas Chainsaw Massacre would also use Horror films, but it would be a genre/form term since the movie is a horror film, not a movie about horror films.\n\nThe thesaurus combines both genres and forms. Form is defined as a characteristic of works with a particular format and/or purpose. A 'short' is a particular form, for example, as is 'animation.' Genre refers to categories of works that are characterized by similar plots, themes, settings, situations, and characters. Examples of genres are westerns and thrillers. In the term Horror films 'horror' is the genre and 'films' is the form.",
"homepage": "http://id.loc.gov/authorities/genreForms.html",
"name": "Library of Congress Genre/Form Terms",
"prefix": "18538"
},
"18539": {
"description": "pbcoreAssetType is a broad definition of the type of intellectual content being described. Asset types might include those without associated instantiations (a collection or series), or those with instantiations (programs, episodes, clips, etc.)\n\nBest practice: The asset type should broadly describe all related instantiations β for example, if an asset includes many instantiations representing different generations of a program, the asset type βprogramβ remains accurate for all of them.",
"homepage": "http://pbcore.org/pbcore-controlled-vocabularies/pbcoreassettype-vocabulary/",
"license": "CC BY-NC-SA 3.0",
"name": "PBCoreAssetType Vocabulary",
"prefix": "18539"
},
"1854": {
"description": "Shelf Classification of the textbook collection of the University Library Leoben.",
"homepage": "http://bibliothek.unileoben.ac.at/de/411/",
"name": "Shelf Classification of the textbook collection of the University Library Leoben.",
"prefix": "1854"
},
"18540": {
"description": "dateType is an attribute that classifies by named type the date-related data of the element e.g., created, broadcast, dateAvailableStart.\n\nBest practice: Used to clarify how the date is related to the asset or instantiation. Date Created may be the most common, but the element could also be used to describe the Date Accessioned or Date Deaccessioned, for example. Can be used as an attribute of the following elements: pbcoreAssetDate, instantiationDate.",
"homepage": "http://pbcore.org/pbcore-controlled-vocabularies/datetype-vocabulary/",
"license": "CC BY-NC-SA 3.0",
"name": "@dateType Vocabulary",
"prefix": "18540"
},
"18541": {
"description": "@descriptionType is an attribute used to indicate the type of description being assigned to the element, such as βabstract,β βsummary,β or βphysical description.β Can be used as an attribute of the pbcoreDescription element.",
"homepage": "http://pbcore.org/pbcore-controlled-vocabularies/descriptiontype-vocabulary/",
"license": "CC BY-NC-SA 3.0",
"name": "@descriptionType Vocabulary",
"prefix": "18541"
},
"18542": {
"description": "@titleType is an attribute used to indicate the type of title being assigned to the asset, such as series title, episode title or project title. Can be used as an attribute of the pbcoreTitle element.",
"homepage": "http://pbcore.org/pbcore-controlled-vocabularies/titletype-vocabulary/",
"license": "CC BY-NC-SA 3.0",
"name": "@titleType Vocabulary",
"prefix": "18542"
},
"18543": {
"description": "pbcoreRelationType describes the relationship between the asset being describe by the pbcore document and any other asset. Ideally it would contain text from a controlled vocabulary for describing relationships. There is some depth to what a relationship could be. The assets can be related as different episodes in a series, different tapes in a box set, or different versions of an original, among others.\n\nBest practice: the assets may be related in that they are different discrete parts of a single intellectual unit, one may be a derivative of another, or they may be different versions that are distinct enough to be described as separate assets.",
"homepage": "http://pbcore.org/pbcore-controlled-vocabularies/pbcorerelationtype-vocabulary/",
"license": "CC BY-NC-SA 3.0",
"name": "pbcoreRelationType Vocabulary",
"prefix": "18543"
},
"18544": {
"description": "instantiationRelationType describes the relation between the instantiation being described and another instantiation.\n\nBest practice: The instantiations may be related in that they are different discrete parts of a single intellectual unit, they may be generationally related, one may be a derivative of another, they may be different versions.",
"homepage": "http://pbcore.org/pbcore-controlled-vocabularies/instatiationrelationtype-vocabulary/",
"license": "CC BY-NC-SA 3.0",
"name": "instantiationRelationType Vocabulary",
"prefix": "18544"
},
"18545": {
"description": "creatorRole is used to identify the role played by the person, people or organization(s) identified in the companion descriptor creator. The PBCore schema allows for creatorRole to be repeated in the pbcoreCreator container element. This can be useful when a single person or organization is associated with multiple roles in an asset.\n\ncontributorRole is used to identify the role played by the person, people or organizations identified in the companion element contributor. The PBCore schema allows for contributorRole to be repeated in the pbcoreContributor container element. This can be useful when a single person or organization is associated with multiple roles in an asset.",
"homepage": "http://pbcore.org/pbcore-controlled-vocabularies/creatorrole-and-contributorrole-vocabulary/",
"license": "CC BY-NC-SA 3.0",
"name": "creatorRole and contributorRole Vocabulary",
"prefix": "18545"
},
"18546": {
"description": "publisherRole is used to identify the role played by the specific publisher or publishing entity identified in the companion descriptor publisher. The PBCore schema allows for publisherRole to be repeated in the pbcorePublisher container element. This can be useful when a single person or organization is associated with multiple roles in an asset.",
"homepage": "http://pbcore.org/pbcore-controlled-vocabularies/publisherrole-vocabulary/",
"license": "CC BY-NC-SA 3.0",
"name": "publisherRole Vocabulary",
"prefix": "18546"
},
"18547": {
"description": "instantiationPhysical is used to identify the format of a particular instantiation as it exists in a physical form that occupies physical space (e.g. a tape on a shelf). This includes physical digital media, such as a DV tape, audio CD, or authored DVD, as well as analog media.\n\nBest practice: PBCore provides a controlled vocabulary for media objects, though any controlled vocabulary can be used so long as it is referenced. For digital storage carriers that contain file-based media, such as data CDs, LTO tapes or hard drives, use instantiationDigital to convey the mime type of the file instead of describing the carrier.",
"homepage": "http://pbcore.org/pbcore-controlled-vocabularies/instantiationphysical-audio-vocabulary/",
"license": "CC BY-NC-SA 3.0",
"name": "instantiationPhysical: Audio Vocabulary",
"prefix": "18547"
},
"18548": {
"description": "instantiationPhysical is used to identify the format of a particular instantiation as it exists in a physical form that occupies physical space (e.g. a tape on a shelf). This includes physical digital media, such as a DV tape, audio CD, or authored DVD, as well as analog media.\n\nBest practice: PBCore provides a controlled vocabulary for media objects, though any controlled vocabulary can be used so long as it is referenced. For digital storage carriers that contain file-based media, such as data CDs, LTO tapes or hard drives, use instantiationDigital to convey the mime type of the file instead of describing the carrier.\n\nThe Film vocabulary provides terms for moving image celluloid formats only.",
"homepage": "http://pbcore.org/pbcore-controlled-vocabularies/instantiationphysical-film-vocabulary/",
"license": "CC BY-NC-SA 3.0",
"name": "instantiationPhysical: Film Vocabulary",
"prefix": "18548"
},
"18549": {
"description": "instantiationPhysical is used to identify the format of a particular instantiation as it exists in a physical form that occupies physical space (e.g. a tape on a shelf). This includes physical digital media, such as a DV tape, audio CD, or authored DVD, as well as analog media.\n\nBest practice: PBCore provides a controlled vocabulary for media objects, though any controlled vocabulary can be used so long as it is referenced. For digital storage carriers that contain file-based media, such as data CDs, LTO tapes or hard drives, use instantiationDigital to convey the mime type of the file instead of describing the carrier.\n\nThe Video vocabulary provides terms for physical media formats for analog and digital video.",
"homepage": "http://pbcore.org/pbcore-controlled-vocabularies/instantiationphysical-video-vocabulary/",
"license": "CC BY-NC-SA 3.0",
"name": "instantiationPhysical: Video Vocabulary",
"prefix": "18549"
},
"1855": {
"description": "Shelf Classifications of the University Library of Leoben.",
"homepage": "http://bibliothek.unileoben.ac.at/de/412/",
"name": "Shelf Classification Main Library - departments of the university",
"prefix": "1855"
},
"18550": {
"description": "instantiationMediaType identifies the general, high level nature of the content of an instantiation. It uses categories that show how content is presented to an observer, e.g., as a sound, text or moving image.",
"homepage": "http://pbcore.org/pbcore-controlled-vocabularies/instantiationmediatype-vocabulary/",
"license": "CC BY-NC-SA 3.0",
"name": "instantiationMediaType Vocabulary",
"prefix": "18550"
},
"18551": {
"description": "instantiationGenerations identifies the use type and provenance of the instantiation. For example, the generation of a video tape may be an βOriginal Masterβ or βDub,β the generation of a film reel may be an βOriginal Negativeβ or βComposite Positive,β an audiotape may be a βMasterβ or βMix Element,β and an image may be a βPhotographβ or a βPhotocopy.β",
"homepage": "http://pbcore.org/pbcore-controlled-vocabularies/instantiationgenerations-vocabulary/",
"license": "CC BY-NC-SA 3.0",
"name": "instantiationGenerations Vocabulary",
"prefix": "18551"
},
"1856": {
"description": "Shelf classification Main Library - General and historical aspects of the University Library of Leoben.",
"homepage": "http://bibliothek.unileoben.ac.at/de/5324/",
"name": "Shelf Classification Main Library - General and Historical",
"prefix": "1856"
},
"18565": {
"homepage": "https://www.herder-institut.de/servicebereiche/bibliothek/benutzung/literatursuche.html",
"name": "Library Classification of the Herder Institute for Historical Research on East Central Europe",
"prefix": "18565"
},
"18566": {
"abbreviation": "ducal",
"description": "The ducal collection of the research library of Gotha counts 227.000 works. This classification scheme indexes the collection. It is structured by reference to scientific areas. There are 25 major groups and up to 10 minor groups.",
"homepage": "https://www2.uni-erfurt.de/bibliothek/cms/systematik/systematik.html",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Classification System of the Ducal Collection",
"pattern": "^[0-9][0-9]([.][0-9][0-9]([.][0-9])?)?$",
"prefix": "18566"
},
"18567": {
"homepage": "http://www.augustiner.de/files/engagement/BADAneu/Systematik.pdf",
"name": "Shelf Classification of Bibliotheca Augustiniana",
"prefix": "18567"
},
"18568": {
"description": "One of the easiest and most useful ways to search the historical databases created by the Bioethics Research Library at Georgetown University is to browse its classification scheme.\n\nDeveloped by the National Reference Center for Bioethics Literature to encompass the wide diversity found in the cross-disciplinary area of bioethics, it is used as a subject index to the extensive collection of periodical literature. Numbered from 1 to 22, beginning with general ethics, bioethics and philosophy of science, it becomes more specific as the numbers rise. Subdivisions within each main category point out specific topics within particular areas. The largest categories are 9 β Health Care, 18 β Human Experimentation, and 20 β Death and Dying.",
"homepage": "https://bioethics.georgetown.edu/library-materials/bioethics-research-library-databases/classification-scheme/",
"name": "Bioethics Research Library Numerical Classification List",
"prefix": "18568"
},
"18569": {
"description": "The Dickinson classification is a library classification scheme used to catalogue and classify musical compositions. It was developed by George Sherman Dickinson (1886 - 1964), and is used by many music libraries, primarily those at University at Buffalo, Vassar, and Columbia Universities.\n\nIt is fully detailed by Carol June Bradley in The Dickinson classification : a cataloguing & classification manual for music; including a reprint of the George Sherman Dickinson Classification of Musical Compositions published by Carlisle Books (1968).",
"homepage": "http://library.buffalo.edu/music/research/find-music/dickinson.html",
"name": "Dickinson Classification",
"prefix": "18569",
"wikidata_database": "Q5273753"
},
"1857": {
"description": "Shelf Classification of the specialized library for geosciences of the library of the Montsnuniversity Leoben",
"homepage": "http://bibliothek.unileoben.ac.at/de/5323/",
"name": "Shelf Classification Specialized library for geosciences",
"prefix": "1857"
},
"18570": {
"abbreviation": "KDC",
"description": "The Korean decimal classification (KDC) is a system of library classification used in South Korea. The main classes are the same as in the Dewey Decimal Classification but these are in a different order: Natural sciences 400; Technology and engineering 500; Arts 600; Language 700.",
"homepage": "http://www.kla.kr/jsp/fileboard/standardTool.do?procType=view&f_board_seq=19343",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Korean Decimal Classification",
"prefix": "18570",
"wikidata_database": "Q6431969"
},
"18571": {
"description": "The Garside Classification Scheme is one of those used in the libraries of UCL. It was devised by Kenneth Garside while he was deputy librarian there. Intellectually, it was based on the close relationship between the library and the teaching departments. The library at UCL rejected the major published classification schemes because 'none of them would generally acceptable to the teaching departments without such major modifications as would have destroyed its essential character.' Instead, it was modeled around the 'subject reading rooms' into which the collection had been divided. The intent was to utilise the expertise of the departments, and their teaching needs in drawing up the divisions within the scheme.",
"homepage": "http://www.ucl.ac.uk/library/subject-support/garside/#top",
"name": "Garside Classification",
"prefix": "18571",
"wikidata_database": "Q17015577"
},
"18572": {
"description": "The London Education Classification is a library classification and indexing thesaurus used at the UCL Institute of Education. It was devised by D.J. Foskett and Joy Foskett. It was devised to address deficiencies in general classification schemes in dealing with education. It was originally devised in 1963, and revised in 1974. It is a faceted classification, inspired by the work of S.R. Ranganathan and of the Classification Research Group.",
"homepage": "https://en.wikipedia.org/wiki/London_Education_Classification",
"name": "London Education Classification",
"prefix": "18572",
"wikidata_database": "Q28324905"
},
"18573": {
"description": "The Australian and New Zealand Standard Research Classification (ANZSRC) is jointly produced by the Australian Bureau of Statistics (ABS) and Statistics New Zealand (Statistics NZ). ANZSRC is the collective name for a set of three related classifications developed for use in the measurement and analysis of research and experimental development (R&D) undertaken in Australia and New Zealand. The three constituent classifications included in the ANZSRC are: Type of Activity (TOA), Fields of Research (FOR), and Socio-economic Objective (SEO). ANZSRC replaces the Australian Standard Research Classification (ASRC 1998) and introduces a new framework for measuring research and development activity in New Zealand. The use of the three constituent classifications in the ANZSRC ensures that R&D statistics collected are useful to governments, educational institutions, international organisations, scientific, professional or business organisations, business enterprises, community groups and private individuals in Australia and New Zealand.",
"homepage": "http://www.abs.gov.au/ausstats/abs@.nsf/mf/1297.0",
"license": "CC-BY-3.0",
"name": "Australian and New Zealand Standard Research Classification: Fields of Research",
"prefix": "18573",
"wikidata_database": "Q4824842"
},
"18574": {
"description": "The Australian and New Zealand Standard Research Classification (ANZSRC) is jointly produced by the Australian Bureau of Statistics (ABS) and Statistics New Zealand (Statistics NZ). ANZSRC is the collective name for a set of three related classifications developed for use in the measurement and analysis of research and experimental development (R&D) undertaken in Australia and New Zealand. The three constituent classifications included in the ANZSRC are: Type of Activity (TOA), Fields of Research (FOR), and Socio-economic Objective (SEO). ANZSRC replaces the Australian Standard Research Classification (ASRC 1998) and introduces a new framework for measuring research and development activity in New Zealand. The use of the three constituent classifications in the ANZSRC ensures that R&D statistics collected are useful to governments, educational institutions, international organisations, scientific, professional or business organisations, business enterprises, community groups and private individuals in Australia and New Zealand.",
"homepage": "http://www.abs.gov.au/ausstats/abs@.nsf/mf/1297.0",
"license": "CC-BY-3.0",
"name": "Australian and New Zealand Standard Research Classification: Socio-Economic Objective",
"prefix": "18574",
"wikidata_database": "Q4824842"
},
"18575": {
"description": "This is the translated text of a number of notations of the DoGi classification system. It reflects the structure of the Italian law and by no means is a comparison between civil and common law families' concepts. Only main entries have been translated into English as a vehicular language, to allow foreign users to identify the broad categories of the Italian law. Where no functional equivalents have been found, entries have not been translated. This is a work in progress and it will be updated on a continuing basis.",
"homepage": "http://www.ittig.cnr.it/dogi/consistenze/class2000.php",
"name": "DoGi Classification of branches of law",
"prefix": "18575"
},
"1858": {
"description": "Shelf Classification of the synthetic materials of the MontanuniversitΓ€t of the university Library Leoben.",
"homepage": "http://bibliothek.unileoben.ac.at/de/5320/",
"name": "Shelf Classification synthetic material library",
"prefix": "1858"
},
"18581": {
"description": "This file contains the CGI Waste Storage vocabulary, as defined by the IUGS Commission for Geoscience Information (CGI) Geoscience Terminology Working Group. The vocabulary defines concepts for categorizing approaches to material waste storage associated with Earth Resource extraction. By extension, this vocabulary includes all concepts in this conceptScheme, as well as concepts in any previous versions of the scheme.",
"homepage": "https://vocabs.ands.org.au/waste-storage",
"name": "CGI Waste Storage Vocabulary",
"prefix": "18581"
},
"18582": {
"description": "This file contains the CGI Vocabulary Relation vocabulary, as defined by the IUGS Commission for Geoscience Information (CGI) Geoscience Terminology Working Group. Use National Information Standards Organization (NISO), 2005, Guidelines for the construction, format, and management of monolingual controlled vocabularies: ANSI/NISO Z39.19-2005, Bethesda Md., NISO Press, 184 pages, ISBN: 1-880124-65-3. (accessed at http://www.niso.org/standards/resources/Z39-19-2005.pdf, 6/19/06) for semantic relationships between vocabulary terms, supplemented by Allen and Ferguson (1994) temporal relationships (1 dimensional topology) that are needed to express ordering relationships between time ordinal eras in a time scale or events in an event vocabulary. Narrower term relationship is deprecated in favor of usage of broader term links for hierarchical relationships. This makes searching easier because hierarchy links are always from a narrow (child) term to a broader (parent) terms. By extension, this vocabulary includes all concepts in this conceptScheme, as well as concepts in any previous versions of the scheme.",
"homepage": "https://vocabs.ands.org.au/vocabulary-relation",
"name": "Vocabulary Relation",
"prefix": "18582"
},
"18583": {
"description": "This file contains the CGI Value Qualifier vocabulary, as defined by the IUGS Commission for Geoscience Information (CGI) Geoscience Terminology Working Group. These terms are taken from the enumeration for values that may be assigned as the valueQualifier on CGI_Value. Definitions are proposed. This codelist includes qualifiers of several sorts: 1. frequence of occurrence--qualifiers that indicate how many occurrences of a described feature are expected to have a reported value. E.g. 'commonly red, sometimes brown'; 2. kinds of statistical procedure used to determine a single value to report based on a collection of observed values, e.g. mean, median, mode.; 3. kinds of nil values; 4. kind of value--a limiting value or the actual estimated value. By extension, this vocabulary includes all concepts in this conceptScheme, as well as concepts in any previous versions of the scheme.",
"homepage": "https://vocabs.ands.org.au/value-qualifier",
"name": "Value Qualifier",
"prefix": "18583"
},
"18584": {
"homepage": "https://vocabs.ands.org.au/viewById/182",
"name": "Geoscience Australia's Units of Measure",
"prefix": "18584"
},
"18585": {
"description": "This file contains the CGI UNFC Code vocabulary, as defined by the IUGS Commission for Geoscience Information (CGI) Geoscience Terminology Working Group. The vocabulary defines concepts for the categorisation of mineral reserves and resources according to the UN Framework Classification (2009). By extension, this vocabulary includes all concepts in this conceptScheme, as well as concepts in any previous versions of the scheme.",
"homepage": "https://vocabs.ands.org.au/unfc-code",
"name": "UNFC Code",
"prefix": "18585"
},
"18586": {
"description": "This concept scheme defines terms used to describe the type of mineral tenements granted in Australian and New Zealand jurisdictions (eg, exploration licence, mining lease).",
"homepage": "https://vocabs.ands.org.au/viewById/47",
"license": "CC-BY-3.0",
"name": "Tenement Type",
"prefix": "18586"
},
"18587": {
"description": "This concept scheme defines terms used to describe the status of mineral tenements in Australian and New Zealand jurisdictions (eg, granted, application, expired).",
"homepage": "https://vocabs.ands.org.au/viewById/48",
"license": "CC-BY-3.0",
"name": "Tenement Status",
"prefix": "18587"
},
"18588": {
"description": "This scheme specifies concepts used to categorize the stratigraphic rank of geologic units, as compiled by the IUGS Commission for Geoscience Information (CGI) Geoscience Terminology Working Group. By extension, it includes all concepts in this conceptScheme, as well as concepts in any previous versions of the scheme.",
"homepage": "https://vocabs.ands.org.au/stratigraphic-rank",
"license": "CC-BY-3.0",
"name": "Stratigraphic Rank",
"prefix": "18588"
},
"18589": {
"description": "This scheme specifies the concept space for Simple Lithology concepts, as defined by the IUGS Commission for Geoscience Information (CGI) Geoscience Terminology Working Group. By extension, it includes all concepts in this conceptScheme, as well as concepts in any previous versions of the scheme. This vocabulary is not designed to be a comprehensive list of all lithology terms.",
"license": "CC-BY-3.0",
"name": "Simple Lithology",
"prefix": "18589"
},
"1859": {
"description": "Shelf catagories of the technical University of Tampereen.",
"homepage": "http://www.tut.fi/fi/kirjasto/aineistot/hyllyluokat/",
"name": "Ordinary shelf categories",
"prefix": "1859"
},
"18590": {
"description": "This file contains the CGI Resource Assessment Category vocabulary, as defined by the IUGS Commission for Geoscience Information (CGI) Geoscience Terminology Working Group. The vocabulary defines concepts to describe methods and quality of resource assessment within an Earth Resource. By extension, this vocabulary includes all concepts in this conceptScheme, as well as concepts in any previous versions of the scheme.",
"homepage": "https://vocabs.ands.org.au/resource-assessment-category",
"name": "Resource Assessment Category",
"prefix": "18590"
},
"18591": {
"description": "The SummaryTypes Ontology is a categorization of summaries β including Short Summary, Long Summary and Standfirst β that are associated with specific articles. These summaries are written by editors, in contrast to abstracts which are written by the article authors.",
"homepage": "http://www.nature.com/ontologies/models/domain/summary-types/",
"license": "CC0-1.0",
"name": "NPG Summary Types Ontology",
"prefix": "18591"
},
"18592": {
"description": "The ReviewStates Ontology is a categorization of the various states that mark the review status of a publication. In particular, these indicate stages in the publishing workflow. For example, a siginificant state change for an article publication occurs when it is accepted for publication, whereby it transitions from an earlier 'Received' state to an 'Accepted' state. These state changes are managed by review-event objects which capture both the review-state and the date (or datetime) at which this event occurs.",
"homepage": "https://github.com/springernature/public-npg-domain-ontology/blob/master/npg-review-states-ontology.ttl",
"license": "CC0-1.0",
"name": "NPG Review States Ontology",
"prefix": "18592"
},
"18593": {
"description": "The ArticleTypes Ontology is a categorization of kinds of publication which are used to index and group content published on nature.com. This taxonomy is organised into a single tree using the SKOS vocabulary. It includes article-types that are directly applied to content, such as Article, Review Article, News, or Book Review plus higher-level groupings such as Research, News and Comment, or Amendments and Corrections. Categorization of content with the ArticleTypes Ontology is orthogonal to categorization with the Subjects Ontology.",
"homepage": "https://github.com/springernature/public-npg-domain-ontology/blob/master/npg-article-types-ontology.ttl",
"license": "CC0-1.0",
"name": "ArticleTypes Ontology",
"prefix": "18593"
},
"18594": {
"description": "The Blogs Ontology is the master catalogue of blogs from Macmillan Science and Education.",
"homepage": "https://github.com/springernature/public-npg-domain-ontology/blob/master/npg-blogs-ontology.ttl",
"license": "CC0-1.0",
"name": "NPG Blogs Ontology",
"prefix": "18594"
},
"18595": {
"description": "The Journals Ontology is the master catalogue of journals from Macmillan Science and Education, including the Nature Publishing Group and Palgrave Macmillan imprints.",
"homepage": "https://github.com/springernature/public-npg-domain-ontology/blob/master/npg-journals-ontology.ttl",
"license": "CC0-1.0",
"name": "NPG Journals Ontology",
"prefix": "18595"
},
"18596": {
"description": "The PublishStates Ontology is a categorization of the various states that mark the publishing status of a publication. In particular, these indicate stages in the publishing workflow. For example, a siginificant state change for an online article publication occurs when it is bound to an issue publication, whereby it transitions from an earlier 'Advance online publication' state to an 'Issue publication' state. These state changes are managed by publish-event objects which capture both the publish-state and the date (or datetime) at which this event occurs.",
"homepage": "https://github.com/springernature/public-npg-domain-ontology/blob/master/npg-publish-states-ontology.ttl",
"license": "CC0-1.0",
"name": "NPG Publish States Ontology",
"prefix": "18596"
},
"18597": {
"description": "The Relations Ontology is a catalogue of the kinds of relation which are used to manage our linked publications. This catalogue of relationships is organised as a SKOS concept scheme scheme although no concepts are supplied.\n\nThere will often exist a significant relationship between a pair of articles which are published separately. For example, a published article may subsequently be corrected via an erratum published as an article in its own right. This erratum can declare a relationship with the article it is amending by using a relations:isErratumOf relationship between itself and the article. It is then possible to add the inverse property relations:hasErratum on the original article to point to the erratum which has amended it in some way. The Relations Ontology lists many such pairs of relationships. All of these relationships are subproperties of the Core Ontology property :relation.",
"homepage": "https://github.com/springernature/public-npg-domain-ontology/blob/master/npg-relations-ontology.ttl",
"license": "CC0-1.0",
"name": "NPG Relations Ontology",
"prefix": "18597"
},
"18598": {
"description": "The SeverityLevels Ontology is a modelling of the syslog message severity values from RFC 5424. (...) This is used in conjunction with the SPIN vocabulary to label exceptions that we may create in our build process. This process makes extensive use of SPIN rules. Validation tests are applied to a given data model via a SPARQL construct query and any exceptions raised are added to the :Graph object associated to a class. This :Graph object is used to add RDF annotations about the class instance named graph.",
"homepage": "https://github.com/springernature/public-npg-domain-ontology/blob/master/npg-severity-levels-ontology.ttl",
"license": "CC0-1.0",
"name": "NPG Severity Levels Ontology",
"prefix": "18598"
},
"18599": {
"description": "WordNet-Affect is an extension of WordNet Domains. It includes a subset of synsets suitable to represent affective concepts correlated with affective word. This SKOS taxonomy mirrors the categories in WordNet-Affect and provides a semantic representation using the standard SKOS representation.",
"homepage": "https://www.gsi.dit.upm.es/ontologies/wnaffect/",
"license": "CC-BY-3.0",
"name": "WordNet-Affect Taxonomy",
"prefix": "18599"
},
"186": {
"description": "276 terms, 254 relationships between terms, 67 equivalent terms.",
"homepage": "http://www.vocabularyserver.com/comprender/",
"name": "Microthesaurus in Didactics of the Social Sciences",
"prefix": "186"
},
"1860": {
"homepage": "https://philosophie-gewi.uni-graz.at/de/institut/institutsbibliothek/aufstellungssystematik/",
"name": "Institute of Philosophy Institute Library",
"prefix": "1860"
},
"18600": {
"description": "DBLP is the most comprehensive computer science bibliography including information about authors, conferences, series, and journals",
"homepage": "http://dblp.org/",
"license": "http://www.opendatacommons.org/licenses/by/1.0",
"name": "Digital Bibliography & Library Project",
"prefix": "18600",
"wikidata_database": "Q1224715"
},
"18601": {
"description": "This file contains the CGI Reserve Assessment Category vocabulary, as defined by the IUGS Commission for Geoscience Information (CGI) Geoscience Terminology Working Group. The vocabulary defines concepts for classifying reserve types associated with Earth resource occurrences. By extension, this vocabulary includes all concepts in this conceptScheme, as well as concepts in any previous versions of the scheme.",
"homepage": "https://vocabs.ands.org.au/reserve-assessment-category",
"name": "Reserve Assessment Category",
"prefix": "18601"
},
"18602": {
"description": "The RIF-CS schema is a data interchange format that supports the electronic exchange of collection and service descriptions. It organises information about collections and services into a format used by the Australian National Data Service (ANDS) Collections Registry. More information on the RIF-CS Schema can be found at http://ands.org.au/guides/cpguide/cpgrifcs.html. With assistance from the RIF-CS Advisory Board and user community, ANDS has developed a suggested vocabulary for use with the RIF-CS Schema. The vocabulary is comprised of suggested terms for specific elements of the schema. Use of the ANDS vocabulary with the RIF-CS Schema is not mandatory but is however recommended. Use of consistent terminology improves data discoverability and the precision of search operations. The ANDS vocabularies are expected to be informed and developed further by the RIF-CS user community.",
"homepage": "https://vocabs.ands.org.au/rifcs",
"license": "CC-BY-3.0",
"name": "Registry Interchange Format - Collections and Services (Vocabularies)",
"prefix": "18602"
},
"18603": {
"description": "This file contains the CGI Raw Material Role vocabulary, as defined by the IUGS Commission for Geoscience Information (CGI) Geoscience Terminology Working Group. The vocabulary defines concepts for categorizing raw material relationships with Earth Resource occurrences. By extension, this vocabulary includes all concepts in this conceptScheme, as well as concepts in any previous versions of the scheme.",
"homepage": "https://vocabs.ands.org.au/raw-material-role",
"name": "Raw Material Role",
"prefix": "18603"
},
"18604": {
"description": "comprehensive list of the world's endangered languages",
"homepage": "http://www.unesco.org/languages-atlas/",
"name": "Atlas of the World's Languages in Danger",
"prefix": "18604",
"wikidata_database": "Q925553"
},
"18606": {
"description": "Chinese Agricultural Thesaurus (CAT) is the largest agricultural domain thesaurus in China, which is held and maintained by AII of CAAS. CAT was the important fruits of more than 100 professionalsβ six years hard work. The international and national standards were adopted while designing and constructing CAT. CAT covers areas including agriculture, forestry, biology, etc. It is organized in 40 main categories and contains more than 63 thousands concepts and most of them have English translation. In addition, CAT includes more than 130 thousands semantic relationships such as Use, UF, BT, NT and RT.\n\nCAT is now available as a Linked Data set published. The Linked Data version of CAT is in RDF/SKOS-XL, and is stored in Virtuoso triple store. Data is accessible to machines through a SPARQL endopoint, and to humans by means of a HTML pages generated with Virtuoso. From 2005, AII cooperated with FAO, started the CAT to AGROVOC mapping work, conforming to the Simple Knowledge Organization System (SKOS) mapping rules (skos: exactMatch, broadMatch and narrowMatch were mainly considered and applied). In addition, CAT has also been mapped to EUROVOC, NALT, LCSH automatically just based on the label string exact match. These mapping results could lay fundamental bases for higher level interoperability (e.g. cross-lingual information retrieval and knowledge discovery applications).",
"homepage": "http://cat.aii.caas.cn/",
"name": "Chinese Agricultural Thesaurus",
"prefix": "18606"
},
"18607": {
"description": "This file contains the CGI Proportion Term vocabulary, as defined by the IUGS Commission for Geoscience Information (CGI) Geoscience Terminology Working Group. This vocabulary provides terms that may be used to qualitatively express abundance of composition parts in a geologic unit or earth material description. Quantity that specifies the fraction of the geologic unit composed of the compound material. This vocabulary is used for GeologicUnit.GeologicUnitPart.proportion, GeologicUnit.compositionPart.proportion, and for compoundMaterial.ConsituentPart.proportion. By extension, this vocabulary includes all concepts in this conceptScheme, as well as concepts in any previous versions of the scheme.",
"homepage": "https://vocabs.ands.org.au/proportion-term",
"name": "Proportion Term",
"prefix": "18607"
},
"18608": {
"homepage": "http://mak.bn.org.pl/cgi-bin/makwww.exe?BM=19",
"prefix": "18608"
},
"18609": {
"homepage": "http://masp.art.br/pesquisa/pt/vocab/formulario.html",
"name": "Controlled Vocabulary of Arts",
"prefix": "18609"
},
"1861": {
"description": "HELECON-services are library's own content production and a special service for our customers. HELECON is a registered trademark. The service has a long tradition since 1975. Finnish Periodicals Index FINP founded what was then known as the Helsinki School of Economics. The databases are constantly updated and excerpt from a wide mass of information.",
"homepage": "http://web.lib.aalto.fi/fi/helevoc/",
"name": "Helecon Vocabulary",
"prefix": "1861"
},
"18610": {
"homepage": "http://masp.art.br/pesquisa/pt/autor/formulario.html",
"name": "Name Authority File",
"prefix": "18610"
},
"18611": {
"description": "This file contains the CGI Processing Activity vocabulary, as defined by the IUGS Commission for Geoscience Information (CGI) Geoscience Terminology Working Group. The vocabulary defines concepts to categorize processing activities associated with a mining activity. A miningActivity and subsequent processingActivity provide the linkage between a minedMaterial and a mine Product. By extension, this vocabulary includes all concepts in this conceptScheme, as well as concepts in any previous versions of the scheme.",
"homepage": "https://vocabs.ands.org.au/processing-activity",
"name": "Processing Activity",
"prefix": "18611"
},
"18612": {
"description": "This file contains the CGI Particle type vocabulary, as defined by the IUGS Commission for Geoscience Information (CGI) Geoscience Terminology Working Group. Used to specify particleType in particleTypeDescription associated with a compoundMaterial. Terms to specify the nature of individual particles of each constituent in an aggregation, based mostly on their genesis. Because the constituents are identifiable parts, the part units must have some definition. Examples include clasts, crystals, pore space, material fossil. Constituent type is determined based on the nature of the particles, and ideally is independent of the relationship between particles in a compound material aggregation. By extension, this vocabulary includes all concepts in this conceptScheme, as well as concepts in any previous versions of the scheme.",
"homepage": "https://vocabs.ands.org.au/viewById/88",
"name": "Particle Type",
"prefix": "18612"
},
"18613": {
"description": "This file contains the CGI Particle Shape vocabulary, as defined by the IUGS Commission for Geoscience Information (CGI) Geoscience Terminology Working Group. The Shape attribute describes, a) the development of crystal faces bounding particles in crystalline compond materials, and b) surface rounding of grains in sedimentary rocks. Roundness is a measure of the sharpness of the edges between surfaces bounding a particle (see Jackson, 1997; Wadell, 1932) and is an indication of the degree of abrasion of a clastic particle. Expressed by Wadell (1932) as the ratio of the average radius of curvature of the several edges or corners of the particle to the radius of curvature of the maximum inscribed sphere (or to one-half the nominal diameter of the particle). The value is more conveniently computed from a plane figure (a projection or cross section); thus, roundness may be defined as the ratio of the average radius of curvature of the corners of the particle image to the radius of the maximum inscribed circle. A perfectly rounded particle (such as a sphere) has a roundness value of 1.0; less-rounded particles have values less than 1.0. The corresponding concept in aggregates with crystalline as opposed to clastic grains is here referred to as crystallinity, and is the degree to which a mineral grain is bounded by crystal faces. Terms should be appropriate for the kind of compound material (eg: for crystalline rocks- euhedral, ideoblastic, subhedral, anhedral, xenoblastic; for sedimentary rocks - angular, rounded). By extension, this vocabulary includes all concepts in this conceptScheme, as well as concepts in any previous versions of the scheme.",
"homepage": "https://vocabs.ands.org.au/particle-shape",
"name": "Particle Shape",
"prefix": "18613"
},
"18614": {
"description": "This file contains the CGI Particle Aspect Ratio vocabulary, as defined by the IUGS Commission for Geoscience Information (CGI) Geoscience Terminology Working Group. AspectRatio describes the geometry of particles based on the ratios of lengths of long, intermediate and short axes of grains. Equates to sphericity in sedimentary rocks (ie: the degree to which the shape of a particle approximates a sphere). A quantitative specification is based on the ratio of lengths of long, intermediate and short axes of grain shape (Sneed and Folk, 1958; Zingg, 1935). This vocabulary includes terms for specifying average shape of some collection of particles.(eg: prolate, slightly flattened, very bladed, equant, acicular, tabular). Numeric shape values from Sneed and Folk (1958) are best understood by looking at the pictures of particles with the different shapes there and in Pettijohn et al. (1972). By extension, this vocabulary includes all concepts in this conceptScheme, as well as concepts in any previous versions of the scheme.",
"homepage": "https://vocabs.ands.org.au/particle-aspect-ratio",
"name": "Particle Aspect Ratio",
"prefix": "18614"
},
"18615": {
"description": "This scheme specifies concepts used to describe the method used to determine the planar or linear orientation of a GeologicFeature (eg, the dip of a fault), as defined by the IUGS Commission for Geoscience Information (CGI) Geoscience Terminology Working Group. By extension, it includes all concepts in this conceptScheme, as well as concepts in any previous versions of the scheme. Designed for use in the determinationMethod property in GeoSciML GSML_PlanarOrientation and GSML_LinearOrientation elements.",
"homepage": "https://vocabs.ands.org.au/orientation-determination-method",
"name": "Orientation Determination Method",
"prefix": "18615"
},
"18617": {
"description": "This file contains the CGI Observation Method (Mapped Feature) vocabulary, as defined by the IUGS Commission for Geoscience Information (CGI) Geoscience Terminology Working Group. These are terms that specify how a MappedFeature instance was mapped. MappedFeature ObservationMethod is essentially a metadata snippet indicating how the spatial extent of the mapped feature was determined, and the basis for association of the geometry with some GeologicFeature specification to define a MappedFeature. Observation method is a convenience property that provides a quick and dirty approach to shortcut use of more comprehensive observation and measurement construct when data are reported using a feature view (as opposed to observation view). By extension, this vocabulary includes all concepts in this conceptScheme, as well as concepts in any previous versions of the scheme.",
"homepage": "https://vocabs.ands.org.au/viewById/89",
"name": "Observation Method (Mapped Feature)",
"prefix": "18617"
},
"18618": {
"description": "Site status provides a description of whether an environmental monitoring site within the National Environmental Monitoring Sites Register is active, in-active, decommissioned etc.",
"homepage": "https://vocabs.ands.org.au/viewById/166",
"license": "CC-BY-3.0",
"name": "NEII Site Status",
"prefix": "18618"
},
"18619": {
"description": "Site licencing describes the type of licence that data are available under.",
"homepage": "https://vocabs.ands.org.au/viewById/171",
"license": "CC-BY-3.0",
"name": "NEII Licencing",
"prefix": "18619"
},
"1862": {
"description": "Systematics of the literature",
"homepage": "http://www.dkfz-heidelberg.de/zbi/iVerm/bibsyst.pdf",
"name": "Shelf classification DKZF-Central Library",
"prefix": "1862"
},
"18620": {
"homepage": "http://ordnokkelen.ra.no/multites/",
"name": "Thesaurus for Cultural Heritage",
"prefix": "18620"
},
"18621": {
"description": "The Glossaurus is a bilingual tool that acts as both a glossary and a thesaurus: terms associated with the principal media arts concepts used by DOCAM, together with their definitions, are structured in a tree diagram.",
"homepage": "http://www.docam.ca/en/glossaurus.html",
"name": "DOCAM Glossaurus",
"prefix": "18621"
},
"18622": {
"homepage": "http://www.termcat.cat/ca/Diccionaris_En_Linia/180/",
"name": "University management nomenclature",
"prefix": "18622"
},
"18623": {
"description": "For the recording of monuments related to the First World War in the UK. This thesaurus was constructed for the First World War Home Front Project and does not contain any additional terminology than that held in Monument Type.",
"homepage": "http://heritage-standards.org.uk/wp-content/uploads/2016/05/FWW_class_v20.pdf",
"name": "FISH First World War Thesaurus",
"prefix": "18623"
},
"18624": {
"description": "The Nippon Decimal Classification (NDC) or Nippon Decimal System (NDC) is a library classification based on the Dewey Decimal System. NDC was developed for mainly Japanese books and is maintained by the Japan Library Association since 1956.",
"name": "Nippon Decimal Classification",
"prefix": "18624",
"wikidata_database": "Q774896"
},
"18625": {
"description": "The Putnam Classification System was created by Herbert Putnam at the Minneapolis Central Library (1887-1891) before he moved to the Library of Congress",
"homepage": "https://archive.org/details/systemofclassifi00minnrich",
"name": "Putnam Classification System",
"prefix": "18625",
"wikidata_database": "Q25052493"
},
"18627": {
"abbreviation": "AADGENRES",
"description": "The genre headings by the Working Group on Rare Books (AAD) serves as the basis for a consistent tagging of rare books published until 1850 in the GBV Common Library Network. The authority file originates from the \"GΓΆttingen\" list and the VD17 list.",
"homepage": "http://aad.gbv.de/empfehlung/gattung.htm",
"license": "CC0-1.0",
"name": "Genre and subject headings for rare books by the AAD",
"prefix": "18627"
},
"18628": {
"description": "EDIRC is an index of economics institutions and part of the RePEc bibliographic database",
"homepage": "https://edirc.repec.org/",
"name": "Economics Departments, Institutes and Research Centers in the World",
"prefix": "18628",
"wikidata_database": "Q32079336"
},
"1863": {
"description": "Our system is organized according to different systematics, so you can also search directly on the shelf for a topic or a musical genre or occupation.",
"homepage": "https://www.hmt-rostock.de/fileadmin/hmt-rostock/2_Hochschule/Bibliothek/Von_A-Z/Theater-Schauspiel-Medien.pdf",
"name": "Systematic theater-acting media",
"prefix": "1863"
},
"18630": {
"description": "In 1999, MSCI and S&P Global developed the Global Industry Classification Standard (GICS), seeking to offer an efficient investment tool to capture the breadth, depth and evolution of industry sectors. GICS is a four-tiered, hierarchical industry classification system. It consists of 11 sectors, 24 industry groups, 68 industries and 157 sub-industries. Companies are classified quantitatively and qualitatively. Each company is assigned a single GICS classification at the sub-industry level according to its principal business activity. MSCI and S&P Global use revenues as a key factor in determining a firmβs principal business activity. Earnings and market perception, however, are also recognized as important and relevant information for classification purposes, and are taken into account during the annual review process.",
"homepage": "https://www.msci.com/gics",
"name": "Global Industry Classification Standard",
"prefix": "18630",
"wikidata_database": "Q2628939"
},
"18631": {
"description": "A vocabulary of geographic regions and their bounding box coordinates. Based on the Australian CSIRO geographic extents keywords.",
"homepage": "https://vocabs.ands.org.au/viewById/61",
"license": "CC-BY-3.0",
"name": "AODN Geographic Extents Vocabulary",
"prefix": "18631"
},
"18632": {
"description": "An AODN controlled vocabulary describing organisational entities.",
"homepage": "https://vocabs.ands.org.au/viewById/28",
"license": "CC-BY-3.0",
"name": "AODN Organisation Vocabulary",
"prefix": "18632"
},
"18633": {
"description": "A classification scheme to support faceted searching across parameter types in the AODN/IMOS Portal 1-2-3.",
"homepage": "https://vocabs.ands.org.au/viewById/24",
"license": "CC-BY-3.0",
"name": "AODN Parameter Category Vocabulary",
"prefix": "18633"
},
"18634": {
"description": "A classification scheme to support faceted searching across platform types in the AODN/IMOS Portal 1-2-3.",
"homepage": "https://vocabs.ands.org.au/viewById/26",
"license": "CC-BY-3.0",
"name": "AODN Platform Category Vocabulary",
"prefix": "18634"
},
"18635": {
"description": "A controlled vocabulary for platforms that can be used in Marine Community Profile metadata. This vocabulary will be used by the faceted search in the AODN/IMOS portal 1-2-3.",
"homepage": "https://vocabs.ands.org.au/viewById/25",
"license": "CC-BY-3.0",
"name": "AODN Platform Vocabulary",
"prefix": "18635"
},
"18636": {
"description": "An AODN controlled vocabulary describing sampling parameters.",
"homepage": "https://vocabs.ands.org.au/viewById/23",
"license": "CC-BY-3.0",
"name": "AODN Sampling Parameter Vocabulary",
"prefix": "18636"
},
"18637": {
"description": "A controlled vocabulary for units of measure that can be used in Marine Community Profile metadata.",
"homepage": "https://vocabs.ands.org.au/viewById/21",
"license": "CC-BY-3.0",
"name": "AODN Units of Measure Vocabulary",
"prefix": "18637"
},
"18638": {
"description": "This register contains a controlled vocabulary for XBT lines.",
"homepage": "https://vocabs.ands.org.au/viewById/122",
"license": "CC-BY-3.0",
"name": "AODN XBT line vocabulary",
"prefix": "18638"
},
"1864": {
"description": "The Morrison Collection: This collection was painstakingly amassed by George Ernest Morrison during his 20-year residency in Beijing. Contains approximately 24,000 volumes in Western languages dealing with China and its neighbors and includes about 1,000map/lithograph titles, about 7,200 pamphlets, and over 120 periodicals. Of particular value are 54 editions of Marco Polo's Description of the World including a copy of the first Latin printing in 1485. The reader will also find 500 dictionaries of Chinese The Library dialects, approximately 300 titles published in the West on Russo-Japanese War, reports of survey expeditions to Central Asia, books on China written by the earliest Christian missionaries to travel there.\n\nThe Morrison II Collection: Contains materials related to Southeast Asia collected by Morrison's son Alistair and his wife, Hedda.",
"homepage": "http://124.33.215.236/morisoncategory/",
"name": "Classification of the Morrison Collection in Toyo Bunko",
"prefix": "1864"
},
"18640": {
"description": "The RAL color standard defines a set of normed colors with unique numbers. It is mainly used in Europe.",
"homepage": "https://www.ral-farben.de/en/home/",
"name": "RAL color codes",
"prefix": "18640",
"wikidata_database": "Q369074"
},
"18641": {
"homepage": "https://archive.org/details/schemadesrealkat00univ",
"prefix": "18641"
},
"18642": {
"description": "Terms used for definitive but not necessarily comprehensive descriptions of measured phenomena in the CF conventions (a content standard for data stored in NetCDF).",
"homepage": "http://vocab.nerc.ac.uk/collection/P07/current/",
"name": "Climate and Forecast Standard Names",
"prefix": "18642"
},
"18643": {
"description": "Currency codes intended for use in any application of trade, commerce and banking, as well as in the public sector.",
"homepage": "http://www.currency-iso.org/en/home/tables/table-a1.html",
"name": "ISO 4271 Currency Codes",
"prefix": "18643",
"wikidata_database": "Q37431"
},
"18644": {
"description": "A thesaurus is a mostly hierarchical list of words used to standardize terminology. Our thesauri are used to index and find information in our databases. (...) We construct our thesauri with special attention to our local Flemish situation, but without losing sight of international thesauri such as the Art & Architecture Thesaurus and the thesauri of Historic England.",
"homepage": "https://thesaurus.onroerenderfgoed.be/conceptschemes/MATERIALEN",
"name": "Thesaurus Onroerend Erfgoed Materials",
"prefix": "18644"
},
"18645": {
"description": "A thesaurus is a mostly hierarchical list of words used to standardize terminology. Our thesauri are used to index and find information in our databases. (...) We construct our thesauri with special attention to our local Flemish situation, but without losing sight of international thesauri such as the Art & Architecture Thesaurus and the thesauri of Historic England.",
"homepage": "https://thesaurus.onroerenderfgoed.be/conceptschemes/STIJLEN_EN_CULTUREN",
"name": "Thesaurus Onroerend Erfgoed Styles and Cultures",
"prefix": "18645"
},
"18646": {
"description": "A thesaurus is a mostly hierarchical list of words used to standardize terminology. Our thesauri are used to index and find information in our databases. (...) We construct our thesauri with special attention to our local Flemish situation, but without losing sight of international thesauri such as the Art & Architecture Thesaurus and the thesauri of Historic England.",
"homepage": "https://thesaurus.onroerenderfgoed.be/conceptschemes/DATERINGEN",
"name": "Thesaurus Onroerend Erfgoed Periods",
"prefix": "18646"
},
"18647": {
"description": "A thesaurus is a mostly hierarchical list of words used to standardize terminology. Our thesauri are used to index and find information in our databases. (...) We construct our thesauri with special attention to our local Flemish situation, but without losing sight of international thesauri such as the Art & Architecture Thesaurus and the thesauri of Historic England.",
"homepage": "https://thesaurus.onroerenderfgoed.be/conceptschemes/ERFGOEDTYPES",
"name": "Thesaurus Onroerend Erfgoed Heritage Types",
"prefix": "18647"
},
"18648": {
"description": "A thesaurus is a mostly hierarchical list of words used to standardize terminology. Our thesauri are used to index and find information in our databases. (...) We construct our thesauri with special attention to our local Flemish situation, but without losing sight of international thesauri such as the Art & Architecture Thesaurus and the thesauri of Historic England.",
"homepage": "https://thesaurus.onroerenderfgoed.be/conceptschemes/WAARDETYPES",
"name": "Thesaurus Onroerend Erfgoed Value Types",
"prefix": "18648"
},
"18649": {
"description": "A thesaurus is a mostly hierarchical list of words used to standardize terminology. Our thesauri are used to index and find information in our databases. (...) We construct our thesauri with special attention to our local Flemish situation, but without losing sight of international thesauri such as the Art & Architecture Thesaurus and the thesauri of Historic England.",
"homepage": "https://thesaurus.onroerenderfgoed.be/conceptschemes/GEBEURTENISTYPES",
"name": "Thesaurus Onroerend Erfgoed Event Types",
"prefix": "18649"
},
"1865": {
"description": "The material is organized for subjects that reflect the library's specialized orientation, particularly attentive to religious-historical disciplines, related to the Byzantine religious and liturgical tradition. There are 31 classes, plus one dedicated to the Collections, identified by numbers, The order of which is sorted by format (from I to V) and then by progressive number.",
"homepage": "http://www.bibliotecagrottaferrata.beniculturali.it/index.php?it%2F106%2Fschemi-di-classificazione",
"name": "Classification Schemes",
"prefix": "1865"
},
"18650": {
"description": "A thesaurus is a mostly hierarchical list of words used to standardize terminology. Our thesauri are used to index and find information in our databases. (...) We construct our thesauri with special attention to our local Flemish situation, but without losing sight of international thesauri such as the Art & Architecture Thesaurus and the thesauri of Historic England.",
"homepage": "https://thesaurus.onroerenderfgoed.be/conceptschemes/BESLUITTYPES",
"name": "Thesaurus Onroerend Erfgoed Decree Types",
"prefix": "18650"
},
"18651": {
"description": "A thesaurus is a mostly hierarchical list of words used to standardize terminology. Our thesauri are used to index and find information in our databases. (...) We construct our thesauri with special attention to our local Flemish situation, but without losing sight of international thesauri such as the Art & Architecture Thesaurus and the thesauri of Historic England.",
"homepage": "https://thesaurus.onroerenderfgoed.be/conceptschemes/SOORTEN",
"name": "Thesaurus Onroerend Erfgoed Species",
"prefix": "18651"
},
"18652": {
"abbreviation": "CaLAThe",
"description": "Cadastre and Land Administration Thesaurus, shortly CaLAThe is a controlled vocabulary for the domain of cadastre and land administration. It is available at a dedicated web site: http://www.cadastralvocabulary.org, as well as through The Basic Register of Thesauri, Ontologies Classifications (BARTOC), the Definitions Server of the OGC, and from 2020 also linked with the LandVoc thesaurus. The initial 2011 version of CaLAThe was prepared based on terms and term relationships derived from DIS version of the ISO 19152:2012 Land Administration Domain Model (LADM). Moreover, it referred to existing thesauri, primarily the GEMET thesaurus, the AGROVOC thesaurus, and the STW Thesaurus for Economics. In the second version, terms rendering the dynamic or temporal aspects of the domain were added. Version 3 was supplemented with terms from the OGC Land and Infrastructure Conceptual Model Standard (LandInfra), and version 4 added code lists names and values from both standards. Version 5 started a multi-lingual itinerary by adding terms (SKOS: prefLabel) in Danish and Turkish, the native language of the authors. CaLAThe now comprises about 250 terms with a growing number of term definitions.",
"homepage": "http://cadastralvocabulary.org/",
"license": "CC BY-SA 3.0",
"name": "Cadastre and Land Administration Thesaurus",
"prefix": "18652"
},
"18653": {
"description": "The LIDO Terminology refers to LIDO β Lightweight Information Describing Objects, the XML Schema for contributing content to cultural heritage repositories, provided by the CIDOC LIDO Working Group.\n\nIt complements the LIDO v1.0 specification and is intended to further enhance the interoperability of LIDO data across different collections by introducing controlled type vocabularies for certain LIDO elements and attributes.\n\nThe LIDO Terminology is committed to the Linked Open Data paradigm by making each LIDO Term referenceable through a Uniform Resource Identifier (URI). It is recommended best practice to use the URI from the terminology.lido-schema.org/ namespace to indicate the type of a LIDO element or attribute. The primary objective of this practice is to support data providers in adapting or mapping their data structures to LIDO, thus facilitating the processing of LIDO data for service providers, increasing the interoperability of LIDO data, and supporting information retrieval across different collections.\n\nWork on the LIDO Terminology is carried out, on behalf of the CIDOC LIDO Working Group, by the LIDO Terminology Working Group: a joint effort of the Working Group Data ExchangeβSpecial Interest Group Documentation of the German Museums Association and the Working Group 'Data' of the German Digital Library.\"\n\n\"Indicates if the actor is an individual, a group of individuals, a family or an organization, such as a legal body, a corporation, or a firm.",
"homepage": "http://terminology.lido-schema.org/actor_type",
"license": "CC BY-SA 3.0",
"name": "LIDO Terminology Actor Type",
"prefix": "18653"
},
"18654": {
"description": "The LIDO Terminology refers to LIDO β Lightweight Information Describing Objects, the XML Schema for contributing content to cultural heritage repositories, provided by the CIDOC LIDO Working Group.\n\nIt complements the LIDO v1.0 specification and is intended to further enhance the interoperability of LIDO data across different collections by introducing controlled type vocabularies for certain LIDO elements and attributes.\n\nThe LIDO Terminology is committed to the Linked Open Data paradigm by making each LIDO Term referenceable through a Uniform Resource Identifier (URI). It is recommended best practice to use the URI from the terminology.lido-schema.org/ namespace to indicate the type of a LIDO element or attribute. The primary objective of this practice is to support data providers in adapting or mapping their data structures to LIDO, thus facilitating the processing of LIDO data for service providers, increasing the interoperability of LIDO data, and supporting information retrieval across different collections.\n\nWork on the LIDO Terminology is carried out, on behalf of the CIDOC LIDO Working Group, by the LIDO Terminology Working Group: a joint effort of the Working Group Data ExchangeβSpecial Interest Group Documentation of the German Museums Association and the Working Group 'Data' of the German Digital Library.\"\n\n\"The nature of the event associated with an object/work.",
"homepage": "http://terminology.lido-schema.org/eventType",
"license": "CC BY-SA 3.0",
"name": "LIDO Terminology Event Type",
"prefix": "18654"
},
"18655": {
"description": "The LIDO Terminology refers to LIDO β Lightweight Information Describing Objects, the XML Schema for contributing content to cultural heritage repositories, provided by the CIDOC LIDO Working Group.\n\nIt complements the LIDO v1.0 specification and is intended to further enhance the interoperability of LIDO data across different collections by introducing controlled type vocabularies for certain LIDO elements and attributes.\n\nThe LIDO Terminology is committed to the Linked Open Data paradigm by making each LIDO Term referenceable through a Uniform Resource Identifier (URI). It is recommended best practice to use the URI from the terminology.lido-schema.org/ namespace to indicate the type of a LIDO element or attribute. The primary objective of this practice is to support data providers in adapting or mapping their data structures to LIDO, thus facilitating the processing of LIDO data for service providers, increasing the interoperability of LIDO data, and supporting information retrieval across different collections.\n\nWork on the LIDO Terminology is carried out, on behalf of the CIDOC LIDO Working Group, by the LIDO Terminology Working Group: a joint effort of the Working Group Data ExchangeβSpecial Interest Group Documentation of the German Museums Association and the Working Group 'Data' of the German Digital Library.\"\n\n\"The type attribute of the LIDO Identifier Complex Type element qualifies the type of identifier used. Identifiers are assigned codes that are used to reference the resource being identified. Their scope may be either locally or globally unique and within that scope enable establishing comparison of equality. This vocabulary provides values for the type attribute of the following LIDO identifier elements: Published Object Identifier, LIDO Metadata Record-ID, Actor Identifier, Concept Identifier, Description/Descriptive Note Identifier, Event Identifier, Legal Body ID, Object Identifier, Place Identifier, Record Info ID, Record ID, Resource Identification Number.",
"homepage": "http://terminology.lido-schema.org/identifier_type",
"license": "CC BY-SA 3.0",
"name": "LIDO Terminology Identifier Type",
"prefix": "18655"
},
"18656": {
"description": "The LIDO Terminology refers to LIDO β Lightweight Information Describing Objects, the XML Schema for contributing content to cultural heritage repositories, provided by the CIDOC LIDO Working Group.\n\nIt complements the LIDO v1.0 specification and is intended to further enhance the interoperability of LIDO data across different collections by introducing controlled type vocabularies for certain LIDO elements and attributes.\n\nThe LIDO Terminology is committed to the Linked Open Data paradigm by making each LIDO Term referenceable through a Uniform Resource Identifier (URI). It is recommended best practice to use the URI from the terminology.lido-schema.org/ namespace to indicate the type of a LIDO element or attribute. The primary objective of this practice is to support data providers in adapting or mapping their data structures to LIDO, thus facilitating the processing of LIDO data for service providers, increasing the interoperability of LIDO data, and supporting information retrieval across different collections.\n\nWork on the LIDO Terminology is carried out, on behalf of the CIDOC LIDO Working Group, by the LIDO Terminology Working Group: a joint effort of the Working Group Data ExchangeβSpecial Interest Group Documentation of the German Museums Association and the Working Group 'Data' of the German Digital Library.\"\n\n\"The type attribute of the LIDO Record Metadata Date element designates the element as the point in time either for creation or modification date of the containing LIDO Record Info Set.\n\nIt should be expressed according to ISO 8601 in YYYY-MM-DD (e.g. 2016-07-11) or in the extended combined date and time format YYYY-MM-DD[Thh[:mm[:ss[Z|Β±hh:mm]]] (e.g. 2016-07-11T11:11:11Z) including timezone information (see ISO 8601).",
"homepage": "http://terminology.lido-schema.org/recordMetadataDate_type",
"license": "CC BY-SA 3.0",
"name": "LIDO Terminology Record Metadata Date Type",
"prefix": "18656"
},
"18657": {
"description": "The LIDO Terminology refers to LIDO β Lightweight Information Describing Objects, the XML Schema for contributing content to cultural heritage repositories, provided by the CIDOC LIDO Working Group.\n\nIt complements the LIDO v1.0 specification and is intended to further enhance the interoperability of LIDO data across different collections by introducing controlled type vocabularies for certain LIDO elements and attributes.\n\nThe LIDO Terminology is committed to the Linked Open Data paradigm by making each LIDO Term referenceable through a Uniform Resource Identifier (URI). It is recommended best practice to use the URI from the terminology.lido-schema.org/ namespace to indicate the type of a LIDO element or attribute. The primary objective of this practice is to support data providers in adapting or mapping their data structures to LIDO, thus facilitating the processing of LIDO data for service providers, increasing the interoperability of LIDO data, and supporting information retrieval across different collections.\n\nWork on the LIDO Terminology is carried out, on behalf of the CIDOC LIDO Working Group, by the LIDO Terminology Working Group: a joint effort of the Working Group Data ExchangeβSpecial Interest Group Documentation of the German Museums Association and the Working Group 'Data' of the German Digital Library.\"\n\n\"The LIDO Record Type element is an administrative metadata element that indicates the level of cataloging chosen for the record. It identifies the logical focus of the record, whether it is considered a single item, a constituent component of an item, or an object group that refers to a complex object consisting of distinct, identifiable parts.\n\nThe choice of the Record Type should take into account both the form or function of a document, an object or work of art, and the goal of the cataloging approach with respect to the logical arrangement of the whole and its parts.",
"homepage": "http://terminology.lido-schema.org/recordType",
"license": "CC BY-SA 3.0",
"name": "LIDO Terminology Record Type",
"prefix": "18657"
},
"18658": {
"description": "The LIDO Terminology refers to LIDO β Lightweight Information Describing Objects, the XML Schema for contributing content to cultural heritage repositories, provided by the CIDOC LIDO Working Group.\n\nIt complements the LIDO v1.0 specification and is intended to further enhance the interoperability of LIDO data across different collections by introducing controlled type vocabularies for certain LIDO elements and attributes.\n\nThe LIDO Terminology is committed to the Linked Open Data paradigm by making each LIDO Term referenceable through a Uniform Resource Identifier (URI). It is recommended best practice to use the URI from the terminology.lido-schema.org/ namespace to indicate the type of a LIDO element or attribute. The primary objective of this practice is to support data providers in adapting or mapping their data structures to LIDO, thus facilitating the processing of LIDO data for service providers, increasing the interoperability of LIDO data, and supporting information retrieval across different collections.\n\nWork on the LIDO Terminology is carried out, on behalf of the CIDOC LIDO Working Group, by the LIDO Terminology Working Group: a joint effort of the Working Group Data ExchangeβSpecial Interest Group Documentation of the German Museums Association and the Working Group 'Data' of the German Digital Library.\"\n\n\"The type attribute of the LIDO Custody/Repository Location Set element qualifies the given repository or location as a former or the current one.\n\nIt designates and identifies the institution of custody and, possibly, indicates the exact geographic location of the object. For stationary objects like buildings and monuments, it may be appropriate to indicate a location only.\n\nThe vocabulary for the type attribute of the LIDO element Custody/Repository Location Set may be extended, if necessary.",
"homepage": "http://terminology.lido-schema.org/repositorySet_type",
"license": "CC BY-SA 3.0",
"name": "LIDO Terminology Repository Set Type",
"prefix": "18658"
},
"18659": {
"description": "The LIDO Terminology refers to LIDO β Lightweight Information Describing Objects, the XML Schema for contributing content to cultural heritage repositories, provided by the CIDOC LIDO Working Group.\n\nIt complements the LIDO v1.0 specification and is intended to further enhance the interoperability of LIDO data across different collections by introducing controlled type vocabularies for certain LIDO elements and attributes.\n\nThe LIDO Terminology is committed to the Linked Open Data paradigm by making each LIDO Term referenceable through a Uniform Resource Identifier (URI). It is recommended best practice to use the URI from the terminology.lido-schema.org/ namespace to indicate the type of a LIDO element or attribute. The primary objective of this practice is to support data providers in adapting or mapping their data structures to LIDO, thus facilitating the processing of LIDO data for service providers, increasing the interoperability of LIDO data, and supporting information retrieval across different collections.\n\nWork on the LIDO Terminology is carried out, on behalf of the CIDOC LIDO Working Group, by the LIDO Terminology Working Group: a joint effort of the Working Group Data ExchangeβSpecial Interest Group Documentation of the German Museums Association and the Working Group 'Data' of the German Digital Library.\"\n\n\"The type attribute of the LIDO Resource Representation element qualifies the digital representation of a resource offered by the data provider for online presentation.",
"homepage": "http://terminology.lido-schema.org/resourceRepresentation_type",
"license": "CC BY-SA 3.0",
"name": "LIDO Terminology Resource Representation Type",
"prefix": "18659"
},
"1866": {
"homepage": "http://www.arcetri.astro.it/biblioteca/informazioni/188-servizi/biblioteca/297-schema-di-classificazione-della-biblioteca-di-arcetri",
"name": "Systematik der Bibliothek von Arcetri",
"prefix": "1866"
},
"18660": {
"description": "The LIDO Terminology refers to LIDO β Lightweight Information Describing Objects, the XML Schema for contributing content to cultural heritage repositories, provided by the CIDOC LIDO Working Group.\n\nIt complements the LIDO v1.0 specification and is intended to further enhance the interoperability of LIDO data across different collections by introducing controlled type vocabularies for certain LIDO elements and attributes.\n\nThe LIDO Terminology is committed to the Linked Open Data paradigm by making each LIDO Term referenceable through a Uniform Resource Identifier (URI). It is recommended best practice to use the URI from the terminology.lido-schema.org/ namespace to indicate the type of a LIDO element or attribute. The primary objective of this practice is to support data providers in adapting or mapping their data structures to LIDO, thus facilitating the processing of LIDO data for service providers, increasing the interoperability of LIDO data, and supporting information retrieval across different collections.\n\nWork on the LIDO Terminology is carried out, on behalf of the CIDOC LIDO Working Group, by the LIDO Terminology Working Group: a joint effort of the Working Group Data ExchangeβSpecial Interest Group Documentation of the German Museums Association and the Working Group 'Data' of the German Digital Library.\"\n\n\"A concept to index materials and/or technique.",
"homepage": "http://terminology.lido-schema.org/termMaterialsTech_type",
"license": "CC BY-SA 3.0",
"name": "LIDO Terminology Term Materials Tech Type",
"prefix": "18660"
},
"18661": {
"description": "This project is working with the Journal of Information Literacy (JIL) to develop a thesaurus for the field of information literacy based on a keyword list compiled by them, and then to publish it as a linked open thesaurus that adheres to the SKOS standard as recommended by the W3C. It is hoped that this will aid in the search process, helping to improve discoverability of articles published by JIL, and to allow for the possibility of the thesaurus to be utilized by other datasets. As action research combines theory and practice, it is the most suitable research strategy for this project. Self-reflection is helping in the development of best practice strategies with regards to creating domainspecific thesauri suitable for use as linked open data.",
"homepage": "http://csct-dev.uwe.ac.uk/il-thesaurus/vocab/",
"name": "Information Literacy Thesaurus",
"prefix": "18661"
},
"18663": {
"description": "The NASA Name Authority File from the NASA Goddard Library is a controlled vocabulary for mission and instrument names.",
"name": "NASA Name Authority File",
"prefix": "18663"
},
"18664": {
"description": "This website aims to create a comprehensive bibliography of Young Adult fiction with significant LGBTQ content published between 2000 and 2017 by major and minor presses in the United States, with a few exceptions. (...)\n\nThe website team created a controlled vocabulary to allow for searching among books. These facets were created with a combination of theoretical backing and practical interests. The facets are designed to allow users β whether teens, librarians, educators, or anyone interested β to find books that match a set of identities they want to read about, genres to explore, and a tool to warn for common trigger warnings and endings. The team welcomes feedback about our controlled vocabulary.",
"homepage": "http://queerbooksforteens.com/",
"name": "Queer Books for Teens Controlled Vocabulary",
"prefix": "18664"
},
"18665": {
"description": "CAMEO -- Conflict and Mediation Event Observations -- is the coding scheme we developed in conjunction with our research on third-party mediation. CAMEO has several new features not found in the WEIS system we have used in our earlier work:\n\nThe coding scheme is optimized for the study of mediation and contains a number of tertiary sub-categories specific to mediation; We have substantially expanded the categories for 'use of force' and can therefore make much finer distinctions between reported levels of violence; We have combined a number of WEIS categories that, in our experience, cannot be reliably differentiated in machine coding; We have developed a systematic hierarchical coding scheme for dealing with substate actors; We have developed a very extensive taxonomy for religious groups and ethnic groups.",
"homepage": "http://eventdata.parusanalytics.com/data.dir/cameo.html",
"license": "CC BY-NC-SA 3.0",
"name": "CAMEO Event Data Codebook",
"prefix": "18665"
},
"18666": {
"description": "The BC consists of 14 main topics which are arranged in 25 main classes. This is achieved by dividing some topics, such as History and Literature, into a number of main classes. (...) The BC uses an alphanumeric system of notation which, as Schleiermacher himself pointed out, is a system that was well known in Europe before 1800. Frederik Rostgaard (...) used letters of the roman alphabet to identify main classes, and long before Rostgaard the system had been used in medieval cloister libraries. In the BC, following the single capital letters, a series of arabic numbers is used to identify subclasses.",
"license": "CC0-1.0",
"name": "Bibliographic Classification of all the Sciences",
"prefix": "18666"
},
"18667": {
"description": "The Australian Health Thesaurus (AHT) is a taxonomy (or controlled vocabulary) of medical, health and human services related concepts, organised into a hierarchical structure. Other data, such as synonyms or alternative labels, are also applied to the concepts providing a rich reference source of health and related services information.",
"homepage": "https://www.healthdirect.gov.au/the-australian-health-thesaurus-aht",
"name": "Australian Health Thesaurus",
"prefix": "18667"
},
"18668": {
"description": "The International Trade Administrationβs (ITA) Thesaurus of International Trade Terms is a controlled and structured list of words and phrases used to tag and index information found on the ITAβs websites and databases. The thesaurus covers all subjects related to international trade and foreign investment with particular emphasis on exporting, trade promotion, market access and enforcement and compliance. The thesaurus is structured into six domains or micro-thesauri:\n\n Trade Topics\n\n Industries\n\n Countries\n\n World Regions\n\n Trade Regions\n\n U.S. Trade Initiatives\n\nThe thesaurus is available to the software developer community as a JSON endpoint. The thesaurus was developed by ITAβs staff of international trade specialists, consulting several authoritative sources and vocabularies covering the language of international trade and investment.",
"homepage": "https://developer.export.gov/taxonomy",
"name": "Thesaurus of International Trade Terms",
"prefix": "18668"
},
"1867": {
"description": "The Institute for Legal Information Theory and Techniques (ITTIG), the organ of the National Research Council, conducts research on computer science and computer law. He works in constant interaction with the academic world and with the public administrations. Creates and distributes legal databases. Design a special software and tools for interoperability of public data.",
"homepage": "http://www.ittig.cnr.it/risorse/biblioteca/biblioteca-classificazione/",
"name": "Institute of Theory and Techniques of Legal Information Library - Classification",
"prefix": "1867"
},
"18670": {
"description": "The ontology aims at modelling the data on cultural institutes or sites such as data regarding the agents that play a specific role on cultural institutes or sites, the sites themselves, the contact points, all multimedia files which describe the cultural institute or site and any other information useful to the public in order to access the institute or site. Moreover, the ontology represents events that can take place in specific cultural institutes or sites. The following figure illustrates some of the core elements of the ontology. The figure is not exaustive; however, it is included in order to help readers to understand some relationships among important concepts represented in the ontology. For each class, examples of their usage in turtle are provided; moreover, for only some of the classes, specific figures are reported that show the relationships and concepts connected to them. The alignment_xml.owl complements the ontology with the alignments with external ontologies such as FOAF, PRO, schma.org, dublin core, etc.",
"homepage": "http://dati.beniculturali.it/cultural-ON/ENG.html",
"name": "Cultural-ON",
"prefix": "18670"
},
"18671": {
"description": "LINKED HERITAGE WAS A 30 MONTHS EU PROJECT, STARTED ON 1st April 2011 AND ENDED THE 30th SEPTEMBER 2013.\n\nThe main goals were: 1) to contribute large quantities of new content to Europeana, from both the public and private sectors; 2) to demonstrate enhancement of quality of content, in terms of metadata richness, re-use potential and uniqueness; 3) to demonstrate enable improved search, retrieval and use of Europeana content.",
"homepage": "https://elearning.unipd.it/sba/mod/glossary/view.php?id=5",
"name": "Linked Heritage Glossary",
"prefix": "18671"
},
"18672": {
"description": "SKOS, the Simple Knowledge Organisation System, is a common data model for sharing controlled vocabularies such as code lists, thesauri, and taxonomies via the Web in a machine-readable format. Recently, six new controlled vocabularies, specified as part of the Asset Description Metadata Schema v1.00 (ADMS), have been published on the Web using the SKOS vocabulary.\n\nThe Asset Description Metadata Schema (v1.00) (ADMS) proposes six new controlled vocabularies (...), and specifies for each vocabulary and term corresponding purl.org term URIs (...):\n\n Asset Type: e.g. βdomain modelβ, βschemaβ, βtaxonomyβ;\n\n Interoperability Level: e.g. βlegal interoperabilityβ, βorganisational interoperabilityβ, βsemantic interoperabilityβ, and βtechnical interoperabilityβ;\n\n Licence Type: e.g. \"attribution\", and \"no derivative work\";\n\n Publisher Type: e.g. βcompanyβ, and βnational authorityβ;\n\n Representation Technique: e.g. βUMLβ, βXML Schemaβ, βSchematronβ, βOWLβ; and\n\n Status: e.g. βcompletedβ, and βunder developmentβ.\n\nThese six controlled vocabularies have been published as βLinked Dataβ on the Web using the data model of the Simple Knowledge Organisation System (SKOS). SKOS is a lightweight RDF vocabulary that allows representing the terms in a controlled vocabulary as instances of the class skos:Concepts. SKOS also defines properties for multi-lingual labels (skos:prefLabel), associated codes (skos:notation), and definitions (skos:definition).",
"homepage": "https://joinup.ec.europa.eu/document/skos-used-publish-controlled-vocabularies-defined-adms-web",
"name": "Controlled Vocabularies for the Asset Description Metadata Schema",
"prefix": "18672"
},
"18673": {
"description": "The AnaEE thesaurus aims to provide a controlled vocabulary for the semantic description of the study of continental ecosystems and their biodiversity. It has been developed within the framework of the AnaEE-France infrastructure through an iterative process combining both top down and bottom up approaches: import of concepts from other thesauri and collection of concepts used in the AnaEE data bases and/or modeling platforms.",
"homepage": "http://agroportal.lirmm.fr/ontologies/ANAEETHES",
"license": "CC-BY-3.0",
"name": "AnaEE Thesaurus",
"prefix": "18673"
},
"18674": {
"description": "(...) the Department of Egyptology of the University of Liege, in collaboration with the Berlin-Brandenburg Academy of Sciences and the Saxon Academy of Sciences in Leipzig (Thesaurus Linguae Aegyptiae), is now developing Thot, a set of resources for documenting and encoding ancient Egyptian resources in a shared, interoperable approach. Moving towards Web Semantic and Linked Open Data, the resources that will be pushed online progressively will consist in a set of thesauri covering most of the metadata relating to ancient Egyptian texts and monuments, as well as a proposal for a TEI interchange format that enables exchange and sharing of textual data. (.) A first set of resources will consist in a wide range of multilingual thesauri related to documentary and textual metadata, aiming at providing controlled vocabularies and terms so that Egyptological projects with text and object focus will interoperate with each other in an easier way.",
"homepage": "http://thot.philo.ulg.ac.be/concept/",
"name": "Thot - Thesauri & Ontology for documenting Ancient Egyptian Resources",
"prefix": "18674"
},
"18675": {
"description": "The FIBO vocabulary is distributed using the Simple Knowledge Organization System (SKOS). (...) The FIBO Vocabulary uses SKOS to provide a machine-readable dictionary of the FIBO terminology. (...) The FIBO Vocabulary is distributed as a machine-readable file in which the FIBO class hierarchy is rendered as a tree strucutre of broader and narrower terms. Properties in FIBO appear as properties in the FIBO vocabulary. Logical restrictions relating pairs of FIBO classes are rendered as simple relationships between corresponding concepts in FIBO Vocabulary. The FIBO Vocabulary therefore does not reflect the full richness of the FIBO Ontologies, and is provided to support knowledge organization applications that do not require the full logic of FIBO.\n\nThe FIBO Vocabulary machine-readable files are intended to provide input to a range of tools, usually characterized as Glossary or Vocabulary tools. These tools are generally used to provide further business-facing presentations of the content of these files.",
"homepage": "https://spec.edmcouncil.org/static/vocabulary/",
"name": "FIBO Vocabulary",
"prefix": "18675"
},
"18676": {
"description": "The Land Portal Foundation has taken the lead in the land governance sector to develop such a standardized vocabulary: LandVoc, the Linked Land Governance Thesaurus. LandVoc is mainly derived from FAO's Agrovoc (link is external), the standard Agriculture vocabulary, but links together many other vocabularies designed and/or used by land governance stakeholders on both a global and local level. LandVoc is always a working product, constantly being reviewed and improved. It is important to emphasize that LandVoc is not meant to serve as a glossary for land governance-related issues. The Thesaurus is purely meant to standardize the classification of content and resources, to improve the discoverability of and access to land-related information, from both global and grassroots sources, from all over the world.",
"homepage": "https://landvoc.org",
"license": "CC-BY-3.0",
"name": "LandVoc - the Linked Land Governance Thesaurus",
"prefix": "18676"
},
"18677": {
"description": "The Land Portal's Land Library contains highly curated metadata of over 20,000 land-related publications, articles and multimedia. The Land Portal aggregates this metadata from over 20 different sources, in addition to the resources that are added by users manually.\n\nIn order to combine these different databases that the Land Portal harvests metadata from, the Land Portal has needed to consolidate certain elements from these different databases to fit one standardized metadata structure in the Land Portal's Land Library.\n\nOne of the elements in metadata about resources that the Land Portal curates, is the type of resource. Many organizations and information providers use different terminologies to describe the types of resources they publish. The Land Portal has therefore created several broad categories of resource types, to be able to consolidate these various classifications.\n\nBelow you can find the list of resource types the Land Portal uses, along with a short description of what is meant with each category.",
"homepage": "https://landportal.org/library/resource-type/",
"license": "CC-BY-3.0",
"name": "Land Portal Resource Types",
"prefix": "18677"
},
"18678": {
"description": "Step by Step Classification (SSC) is a formula-based library classification scheme. The classification number (CN) of a document can be derived based on a single formula CN = I date. Each letter I date is an element representing discipline, area, time, and extra information respectively covered in the text of the classifying document. Each element is prefixed to the respective class number which is useful in locating a document in the library. To provide classification numbers certain devices like NDA, CD, and LDD are provided. Hence all types of documents in any physical form can be classified. SSC allows for sufficient space to classify newly emerging disciplines which may be developed in the future. Language is not a barrier to classify documents; classification numbers can be allotted to any language with the help of NDA numbers. This formula will be useful for deriving computerized classification numbers. The same formula may also be used in other fields as mentioned in theory.",
"homepage": "https://www.amazon.com/Step-Classification-Formula-Based-Volumes/dp/8193359798",
"name": "Step by Step Classification",
"prefix": "18678"
},
"18679": {
"homepage": "http://www.ib.hu-berlin.de/texte/thesaurus/titel.html",
"name": "Thesaurus for Subject Cataloging",
"prefix": "18679"
},
"1868": {
"description": "This classification scheme was elaborated mainly to help classify documents on the bookshelves and it is based on simple principles which do not require special classification skills (\"mark and park\"). The possibility to add a classification note to all the documents also provides users with a sort of classified catalogue, which represents an additional possibility of search.",
"homepage": "http://www.minori.it/minori/schema-di-classificazione-infanzia-e-adolescenza",
"name": "Classification scheme of childhood and adolescence",
"prefix": "1868"
},
"18680": {
"abbreviation": "NTA",
"homepage": "https://www.oclc.org/support/services/ggc/nta.en.html",
"license": "http://www.opendatacommons.org/licenses/by/1.0",
"name": "Dutch Thesaurus of Author Names",
"prefix": "18680"
},
"18681": {
"description": "It contains a total of 30 741 descriptors, of which 22 064 are valid descriptors and 8677 are forbidden terms. The INIS/ETDE Thesaurus contains the controlled terminology for indexing all information within the subject scopes of the International Nuclear Information System (INIS) and the Energy Technology Data Exchange (ETDE). The terminology is intended for use in subject descriptions for input or retrieval of information in these systems. The terminology in this thesaurus has its origin in the 1969 edition of the EURATOM Thesaurus. The structure subsequently given to that terminology was the result of a systematic study performed by subject specialists at the INIS Secretariat and several Member States. Further expansion of the thesaurus terminology was done by ETDE to incorporate information on all forms of energy.",
"homepage": "https://www.etde.org/edb/IAEA-INIS-ETDE-01-2013-08.pdf",
"name": "INIS/ETDE Thesaurus",
"prefix": "18681"
},
"18682": {
"description": "A list of access restriction types for ARCHE.",
"homepage": "https://vocabs.acdh.oeaw.ac.at/arche_access_restrictions/",
"license": "CC-BY-3.0",
"name": "ARCHE access restrictions",
"prefix": "18682"
},
"18683": {
"description": "A list to indicate the life cycle status of an object in ARCHE.",
"homepage": "https://vocabs.acdh.oeaw.ac.at/arche_lifecycle_status/",
"license": "CC-BY-3.0",
"name": "ARCHE life cycle status",
"prefix": "18683"
},
"18684": {
"description": "The general resource type an object can have based on controlled vocabulary of DataCite metadata schema 4.0.",
"homepage": "https://vocabs.acdh.oeaw.ac.at/arche_category/",
"license": "CC-BY-3.0",
"name": "ARCHE Resource Type Category",
"prefix": "18684"
},
"18685": {
"description": "Authoring tools are software and services that 'authors' (web developers, designers, writers, etc.) use to produce web content (static web pages, dynamic web applications, etc.). (...) ATAG is primarily for developers of authoring tools, including the following types of authoring tools:\n\n- web page authoring tools, for example, what-you-see-is-what-you-get (WYSIWYG) HTML editors\n\n- software for generating websites, for example, content management systems (CMS), courseware tools, content aggregators\n\n- software that converts to web content technologies, for example, word processors and other office document applications with \"Save as HTML\"\n\n- multimedia authoring tools\n\n- websites that let users add content, such as blogs, wikis, photo sharing sites, online forums, and social networking sites\n\nATAG and supporting resources are also intended to meet the needs of many different audiences, including policy makers, managers, and others.",
"homepage": "https://www.w3.org/TR/2015/REC-ATAG20-20150924/",
"name": "Authoring Tool Accessibility Guidelines",
"prefix": "18685"
},
"18686": {
"homepage": "http://data.bibliotheken.nl/id/dataset/brinkman",
"license": "http://www.opendatacommons.org/licenses/by/1.0",
"name": "Brinkman subjects",
"prefix": "18686"
},
"18687": {
"homepage": "http://data.bibliotheken.nl/doc/dataset/gtt",
"license": "http://www.opendatacommons.org/licenses/by/1.0",
"prefix": "18687"
},
"18688": {
"description": "This document describes requirements for some important aspects of the character model for W3C specifications. The two aspects discussed are string identity matching and string indexing. Both aspects are considered to be vital for the seamless interaction of many components of the current and future web architecture.",
"homepage": "https://www.w3.org/TR/2009/NOTE-charreq-20090915/",
"name": "Charreq",
"prefix": "18688"
},
"18689": {
"description": "This document describes CC/PP (Composite Capabilities/Preference Profiles) structure and vocabularies. A CC/PP profile is a description of device capabilities and user preferences. This is often referred to as a device's delivery context and can be used to guide the adaptation of content presented to that device.",
"homepage": "https://www.w3.org/TR/CCPP-struct-vocab/",
"name": "Composite Capability/Preference Profiles (CC/PP): Structure and Vocabularies",
"prefix": "18689"
},
"1869": {
"description": "The Italian Thesaurus on Childhood and Adolescence (Th.I.A.) contains all the terms used to enter the documents acquired by the Centre (bibliographic materials, rules and regulations, statistics and films) into a subject catalogue. The chosen topics derive from a list elaborated by Alfredo Carlo Moro, former Chairperson of the National Centre.\n\nThe Thesaurus has an interdisciplinary approach and it is divided into seven thematic fields: Culture, Education, Childhood and Adolescence, Institutions, Psychological processes, Health, Society. It is possible to browse for terms via an alphabetical and hierarchical index display.",
"homepage": "http://www.minori.it/thesaurus",
"name": "Italian Thesaurus on Childhood and Adolescence",
"prefix": "1869"
},
"18690": {
"description": "The Data Repositories taxonomy is a categorization of research data repositories that have been evaluated by the Scientific Data team as being suitable for archiving research data in conjunction with a Springer Nature publication.",
"homepage": "https://scigraph.springernature.com/explorer/taxonomies/",
"license": "CC-BY-3.0",
"name": "Data Repositories Taxonomy",
"prefix": "18690"
},
"18691": {
"description": "DHA taxonomy is a knowledge organization system designed to describe resources and subjects within activities of Digital Humanities Austria.",
"homepage": "https://vocabs.dariah.eu/dha_taxonomy/en/",
"license": "CC-BY-4.0",
"name": "DHA Taxonomy",
"prefix": "18691"
},
"18692": {
"description": "This specification defines the Document Object Model Level 2 Traversal and Range, platform- and language-neutral interfaces that allow programs and scripts to dynamically traverse and identify a range of content in a document. The Document Object Model Level 2 Traversal and Range build on the Document Object Model Level 2 Core [DOM Level 2 Core].",
"homepage": "https://www.w3.org/TR/2000/REC-DOM-Level-2-Traversal-Range-20001113/",
"name": "Document Object Model (DOM) Level 2 Traversal and Range Specification",
"prefix": "18692"
},
"18693": {
"description": "The Collection Description Frequency Vocabulary provides a set of terms that can be used as values of the dcterms:accrualPeriodicity property in descriptions of collections. It has been developed in association with the Dublin Core Collections Application Profile (DC Collections AP) but this vocabulary is independent of that profile and the terms defined here may be referenced in other metadata descriptions and used as the values of other properties.",
"homepage": "http://dublincore.org/groups/collections/frequency/",
"name": "Dublin Core Collection Description Frequency Vocabulary",
"prefix": "18693"
},
"18694": {
"description": "Controlled vocabulary used for indexing bibliographical records for the 'Prehistory and Protohistory' FRANCIS database (1972-2015, http://pascal-francis.inist.fr/).",
"homepage": "https://www.loterre.fr/skosmos/905/",
"license": "CC-BY-3.0",
"name": "Prehistory and Protohistory Vocabulary",
"prefix": "18694"
},
"18695": {
"description": "Controlled vocabulary used for indexing bibliographical records for the 'Art and Archaeology' FRANCIS database (1972-2015, http://pascal-francis.inist.fr/).",
"homepage": "https://www.loterre.fr/skosmos/27X/",
"license": "CC-BY-3.0",
"name": "Art and Archaeology Vocabulary",
"prefix": "18695"
},
"18697": {
"description": "Controlled vocabulary used for indexing bibliographical records for the 'History and Sciences of Religions' FRANCIS database (1972-2015, http://pascal-francis.inist.fr/).",
"homepage": "https://www.loterre.fr/skosmos/4V5/",
"license": "CC-BY-3.0",
"name": "History and Sciences of Religions Vocabulary",
"prefix": "18697"
},
"18698": {
"description": "Controlled vocabulary used for indexing bibliographical records for the 'Philosophy' FRANCIS database (1972-2015, http://pascal-francis.inist.fr/).",
"homepage": "https://www.loterre.fr/skosmos/73G/",
"license": "CC-BY-3.0",
"name": "Vocabulary of Philosophy",
"prefix": "18698"
},
"18699": {
"description": "Controlled vocabulary used for indexing bibliographical records for the 'Sociology' FRANCIS database (1972-2015, http://pascal-francis.inist.fr/).",
"homepage": "https://www.loterre.fr/skosmos/3JP/",
"license": "CC-BY-3.0",
"name": "Sociology Vocabulary",
"prefix": "18699"
},
"187": {
"description": "Contains 20,604 terms of the alphabetical corpus, permuted index, hierarchical indexes, list of controlled identifiers of characters and institutions.",
"homepage": "http://cuib.unam.mx/~tesauro/",
"name": "Mexican Macrothesaurus for Educational Content",
"prefix": "187"
},
"1870": {
"name": "Classification scheme",
"prefix": "1870"
},
"18700": {
"description": "Controlled vocabulary used for indexing bibliographical records dealing with 'Classical Thermodynamics / Heat Transfers' in the PASCAL database (1972-2015, http://pascal-francis.inist.fr/).",
"homepage": "https://www.loterre.fr/skosmos/1WB/",
"license": "CC-BY-3.0",
"name": "Vocabulary of Heat Transfers",
"prefix": "18700"
},
"18701": {
"description": "Vocabulary used for indexing bibliographical records dealing with βElectronicsβ in the PASCAL database, until 2014. This resource contains 4454 entries classified under 19 collections.",
"homepage": "https://www.loterre.fr/skosmos/RDR/",
"license": "CC-BY-3.0",
"name": "Electronics and Optoelectronics Vocabulary",
"prefix": "18701"
},
"18702": {
"description": "This bilingual thesaurus structures the key-concepts of biodiversity in its fundamental and applied ecological components. It uses the polyhierarchy and includes 400 associative relationships. Each descriptor has a large number of synonyms and searchable variants in English and French languages. The concepts are grouped by semantic categories, domains and EBV classes. Definitions are given with their source.",
"homepage": "https://www.loterre.fr/skosmos/BLH/",
"license": "CC-BY-3.0",
"name": "Biodiversity Thesaurus",
"prefix": "18702"
},
"18703": {
"description": "This bilingual (French-English) thesaurus, developed at Inist-CNRS, identifies the concepts of the cognitive psychology of human memory (memory systems and processes, empirical effects, memory disorders, study methods, theories and models), organized in the form of hierarchical (generic and specific terms), equivalence (synonyms) and association relationships.",
"homepage": "https://www.loterre.fr/skosmos/P66/",
"license": "CC-BY-3.0",
"name": "Thesaurus Cognitive psychology of human memory",
"prefix": "18703"
},
"18704": {
"description": "This thesaurus is based on the vocabulary used in scientific publications dealing with Blood Transfusion and neighbor fields. It contains more than 2000 concepts including various variants (synonyms, acronyms) divided into a number of microthesauri where the terms are grouped around a theme or a semantic field.",
"homepage": "https://www.loterre.fr/skosmos/W7B/",
"license": "CC-BY-3.0",
"name": "Thesaurus of Blood Transfusion",
"prefix": "18704"
},
"18705": {
"description": "ITIL is a set of detailed practices for IT service management that focuses on aligning IT services with the needs of business. It describes processes, procedures, tasks, and checklists which are not organization-specific but can be applied by an organization for establishing integration with the organizationβs strategy, delivering value, and maintaining a minimum level of competency.",
"homepage": "http://vocabulary.semantic-web.at/itil.html",
"name": "ITIL β Information Technology Infrastructure Library",
"prefix": "18705"
},
"18706": {
"description": "The top-level thesaurus proposed in DARIAH.",
"homepage": "https://vocabs.acdh.oeaw.ac.at/backbone_thesaurus/",
"name": "Backbone Thesaurus",
"prefix": "18706"
},
"18707": {
"description": "A concept scheme that defines the types of relationships between a learning resource and a node in an educational framework.",
"homepage": "https://www.dublincore.org/specifications/lrmi/concept_schemes/alignmentType/",
"license": "CC-BY-4.0",
"name": "LRMI Alignment Type Vocabulary",
"prefix": "18707"
},
"18708": {
"description": "A concept scheme that defines the primary or intended roles of the audience (beneficiary) of the resource being described.",
"homepage": "https://www.dublincore.org/specifications/lrmi/concept_schemes/educationalAudienceRole/",
"license": "CC-BY-4.0",
"name": "LRMI Educational Audience Role Vocabulary",
"prefix": "18708"
},
"18709": {
"description": "A concept scheme that enumerates the educational uses of a learning resource.",
"homepage": "https://www.dublincore.org/specifications/lrmi/concept_schemes/educationalUse/",
"license": "CC-BY-4.0",
"name": "LRMI Educational Use Vocabulary",
"prefix": "18709"
},
"1871": {
"description": "With the systematics of the bibliography of the musical writing system, you can call up a chronologically sorted overview of the publications for a specific area by clicking on the search results. You can search for the search result with any further search queries from the\" Advanced Search\" for example by keywords and slogans, type of material, year of publication or language.",
"homepage": "http://www.sim.spk-berlin.de/systematik_752.html",
"name": "Systematics of the bibliography of the musical writing",
"prefix": "1871"
},
"18710": {
"description": "Human Rights Terms is a controlled subject headings vocabulary covering mainly human rights literature, and is maintained by the Human Rights Library, part of the UiO Law Library.",
"homepage": "https://app.uio.no/ub/emnesok/mrtermer/",
"license": "CC0-1.0",
"name": "Human Rights Terms",
"prefix": "18710"
},
"18711": {
"license": "CC BY-SA 3.0",
"prefix": "18711"
},
"18712": {
"description": "The Subjects Ontology is a polyhierarchical categorization of scholarly subject areas which are used for the indexing of content by Macmillan Science and Education.",
"homepage": "https://github.com/springernature/public-npg-domain-ontology/blob/master/npg-subjects-ontology.ttl",
"license": "CC0-1.0",
"name": "NPG Subjects Ontology",
"prefix": "18712"
},
"18713": {
"homepage": "http://data.bibliotheken.nl/doc/dataset/kbcode",
"license": "http://www.opendatacommons.org/licenses/by/1.0",
"name": "Thesaurus KBcode",
"prefix": "18713"
},
"18715": {
"description": "This list is intended to be used with and supplement the Library of Congress subject headings. It addresses topics of significance to practicing planners and planning agencies. Library of Congress subject headings used by the APA Library are shown in italic type.",
"homepage": "https://planning-org-uploaded-media.s3.amazonaws.com/legacy_resources/library/pdf/subject.pdf",
"name": "American Planning Association Library Subject Headings",
"prefix": "18715"
},
"18716": {
"description": "The Basle Bibliography differs from all other music-oriented bibliography databases (e.g., RILM, BMS) above all due to its classification scheme (i.e., Index). With it, the recorded titles are assigned to precisely defined subject areas. This classification scheme was taken over into the digital version and can be used for searches. In this way, subject areas can be circumscribed with unparalleled precision.",
"homepage": "http://www.rimab.ch/content/bibliographie",
"name": "Basle Bibliography for Historical Performance Practice Classification Scheme",
"prefix": "18716"
},
"18717": {
"description": "The Wessex Classification Scheme is a revision of the National Library of Medicine (NLM) schedules incorporating current UK medical and health practice. The scheme was originally created by the librarians of the Wessex Regional Library and Information Network (WRLIN) and is now overseen by a working group of the SWIMS Network and other users of the scheme.",
"homepage": "http://www.swimsnetwork.nhs.uk/modules/cataloguing/wessex-scheme/wessex-classification-scheme-new/",
"name": "Wessex Classification Scheme",
"prefix": "18717"
},
"18718": {
"description": "This annotated index to the Wessex Classification Scheme was produced primarily for cataloguers within the SWIMS Network (formerly SWRLIN) Cataloguing Co-operative. The Classification Scheme has been adopted by other library networks in the UK and is widely used. Each indexing term in the annotated index refers to a suggested classification number or numbers within the Wessex Scheme. The index, however, should never be used as a classification tool on its own. It is essential that the actual schedules are checked to ensure that the context of the given classification number is appropriate for the document in hand. For example, TRANSACTIONAL ANALYSIS, originally a psychotherapeutic technique used for mental disorder, is now used in a number of other settings and it would be inappropriate to classify these in the Psychiatry Schedules. The terminology used in the annotated index is based on the NLM Medical Subject Headings (MeSH), and the tree structure in which it sits is indicated below the heading (e.g. L1).",
"homepage": "http://www.swimsnetwork.nhs.uk/modules/cataloguing/wessex-scheme/wessex-annotated-subject-headings-new/",
"name": "Wessex Annotated Subject Heading Index",
"prefix": "18718"
},
"18719": {
"homepage": "http://dmd.wepwawet.nl/bibliography.htm",
"name": "Systematic Bibliography on Deir el-MedΓna Classification Scheme",
"prefix": "18719"
},
"1872": {
"description": "Browse RILMβs Classification System which groups 87 classes under 12 super classes.",
"homepage": "http://www.rilm.org/searching/classes.php",
"name": "RILM Classification System",
"prefix": "1872"
},
"18720": {
"description": "This is the seventh edition (2016) of the Justice Thesaurus of the Dutch Ministry of Justice and Security.",
"name": "Justice Thesaurus",
"prefix": "18720"
},
"18721": {
"description": "The thesaurus DemoVoc, which aims to facilitate searching and indexing of documents in the field of population studies, is derived from the Popin thesaurus, created and maintained by CICRED (Committee for International Cooperation in National Research in Demography) from 1979 to 1993. Maintained by INED, DemoVoc consist of around 2500 descriptors and is updated on a yearly basis.",
"homepage": "http://thesaurus.web.ined.fr/navigateur/",
"license": "CC BY-NC-SA 3.0",
"name": "DemoVoc Thesaurus",
"prefix": "18721"
},
"18722": {
"description": "Thomas Jefferson created this classification for his private library. He sold his library to the Librarian of Congress in 1815 where its classification was used until replaced by the Library of Congress Classification (LCC) in 1897.",
"license": "CC0-1.0",
"name": "Jefferson's Library Classification",
"prefix": "18722",
"wikidata_database": "Q52789832"
},
"18723": {
"description": "MoTIF, the pilot thesaurus of Irish folklore, is intended to accompany the Thesaurus Construction Guidelines: An Introduction to Thesauri and Guidelines on Their Construction and act as a sample thesaurus and demonstration of the international principles and best practices outlined in that document. The pilot thesaurus should not be considered a tool for indexing and retrieval of content. Rather, it can act as a base from which such a tool can be constructed. (...) The core topics of the pilot thesaurus of Irish folklore include nature, animals, people, their occupations and activities primarily as they relate to the sustenance and support of the home and community. The thesaurus also covers the genres of folklore. As a pilot thesaurus the coverage of these topics should not be considered exhaustive but rather a sampling of the subject matter. (...) Just over 350 terms were selected from vocabulary resources at the beginning of the project. Following facet analysis additional terms were added to aid in the organisation of concepts bringing the number of preferred terms in the thesaurus to 522. The pilot thesaurus contains over 50 non- preferred terms.",
"homepage": "http://apps.dri.ie/motif/vocab/",
"license": "CC-BY-4.0",
"name": "MoTIF Pilot Thesaurus of Irish Folklore",
"prefix": "18723"
},
"18724": {
"homepage": "https://tesjmu.stm.jus.br/portalthes/",
"name": "Military Thesaurus of the Union",
"prefix": "18724"
},
"18725": {
"description": "(...) different terms and expressions from the world of carpets are explained and outlined.",
"homepage": "https://www.carpetencyclopedia.com/glossary",
"name": "Carpet Encyclopedia Glossary",
"prefix": "18725"
},
"18726": {
"homepage": "http://www.pi-schools.gr/lessons/tee/maritime/FILES/biblia/biblia/naytikh_texni_a/kef02.pdf",
"prefix": "18726"
},
"18727": {
"homepage": "http://elearn.ypa.gr/mod/glossary/view.php?id=753",
"name": "English-Greek Glossary of Air Traffic Management Terms",
"prefix": "18727"
},
"18728": {
"description": "(.) Wine Glossary is an informative resource of key wine terms. It lists key general terminology used within the wine Trade and includes descriptions related to viniculture, winemaking, grape varieties, wine tasting, and more.",
"homepage": "https://www.wineauctionprices.com/wine_glossary",
"name": "Wine Glossary",
"prefix": "18728"
},
"18729": {
"description": "A glossary of all the key sailing/yachting terminology used in sailing.",
"homepage": "http://www.sailinglatest.com/glossary",
"name": "Sailing Glossary/Terminology",
"prefix": "18729"
},
"1873": {
"homepage": "http://box.dar.unibo.it/files/biblioteca/merizzi/documentazione_musicologica.htm",
"name": "Classification scheme of historical-musicological documentation",
"prefix": "1873"
},
"18730": {
"description": "This glossary is to clarify some of the terms that may be specifically used in the discussion of debt and the political, economic and financial concepts that are involved.",
"homepage": "http://www.cadtm.org/Glossary",
"name": "Illegitimate Dept Glossary",
"prefix": "18730"
},
"18732": {
"homepage": "https://e-class.teilar.gr/modules/document/file.php/FURN112/%CE%91%CE%93%CE%93%CE%9B%CE%99%CE%9A%CE%97%20%CE%9F%CE%A1%CE%9F%CE%9B%CE%9F%CE%93%CE%99%CE%91%20%CE%94%CE%9F%CE%9C%CE%97%CE%A3%20%CE%9E%CE%A5%CE%9B%CE%9F%CE%A5.pdf",
"name": "English Wood Structure Terminology",
"prefix": "18732"
},
"18734": {
"homepage": "https://www.bfs.admin.ch/bfs/de/home/statistiken/kataloge-datenbanken/publikationen.assetdetail.5808569.html",
"license": "CC BY-NC 3.0",
"name": "Swiss Classification for Surgical Interventions",
"prefix": "18734"
},
"18736": {
"description": "The access-right authority table is a controlled vocabulary listing the access rights or restrictions to resources. It is designed for but not limited to DCAT descriptions of datasets. This authority table is maintained by the Publications Office of the European Union in the Metadata Registry (EU Vocabularies website).",
"license": "CC0-1.0",
"name": "Access Right Name Authority List",
"prefix": "18736"
},
"18737": {
"description": "This table provides the address types as used in the EU Whoiswho.",
"license": "CC0-1.0",
"name": "Address Type Name Authority List",
"prefix": "18737"
},
"18738": {
"description": "This table provides the various types of administrative territorial units within the Member States of the European Union. It is linked to the \"Administrative territorial units (ATU)\" table that provides the list of the subdivisions per country. The categorization of these types is based on national official information and with the kind contribution of the Committee of the Regions of the European Union for the translations in all official languages of the European Union. The ISO 3166-2 standard has also been used, even differences can be noticed. An administrative unit is defined for the purpose of administration with, according the country, a certain degree of autonomy. It refers to public administration for which the administrative law is applicable. The administrative territorial unit types must not be confused with the Nomenclature of Territorial Units for Statistics (NUTS). The NUTS is delineated according the population living in the territorial unit and is used in an economical / statistical environment. More information can be found on http://ec.europa.eu/eurostat/web/nuts/principles-and-characteristics. The administrative territorial unit types must not be confused with the jurisdiction territories designed for the Courts competence area. In certain countries, the subdivisions may be the same for the administrative, economical, statistical and jurisdiction units.",
"license": "CC0-1.0",
"name": "Administrative Territorial Units Types Name Authority List",
"prefix": "18738"
},
"18739": {
"description": "This table provides the list of the various administrative territorial units of the EU Member States. The name of each territorial unit can be found in the \"Administrative territorial unit types\" (ATTY) table. Due to the large volume of lowest level administrative units (local authority, municipality) in certain countries, these units have not yet been fully implemented. The lists of codes represent the administrative territorial units, based on national official / legal information and the ISO 3166-2 standard. Differences can be noticed due to the rapid changes occurring in the countries. The codes have been created, as far as possible, by integrating the code used in UNECE http://www.unece.org/cefact/locode/service/location.html. The administrative territorial units must not be confused with the Nomenclature of Territorial Units for Statistics (NUTS). The NUTS is delineated according to the population living in the territorial unit and is used in an economical / statistical environment. More information can be found on http://ec.europa.eu/eurostat/web/nuts/principles-and-characteristics. The administrative territorial units must not be confused with the jurisdiction territories designed for the competence area of Courts. In certain countries, the subdivisions may be the same for the administrative, economical, statistical and jurisdiction units.",
"license": "CC0-1.0",
"name": "Administrative Territorial Units Name Authority List",
"prefix": "18739"
},
"1874": {
"description": "To know the books owned by the CDEC Foundation library and to carry out a thematic research (eg 'Jews in Italy', 'Shoah', 'anti-Semitism', 'Jewish personalities'), you can consult online the Classification of the library with links to the OPAC catalog pages.",
"homepage": "http://www.cdec.it/applicazioni/new_criterio_biblio_2.asp?id_pagina=2&id=2",
"name": "CDEC Classification Scheme",
"prefix": "1874"
},
"18740": {
"description": "The browser authority table is a controlled vocabulary listing the different web browsers used in web crawling. It has been developed specifically for the EU Web Preservation project. The browser authority table is maintained by the Publications Office of the European Union in the Metadata Registry (EU Vocabularies website).",
"license": "CC0-1.0",
"name": "Browser Name Authority List",
"prefix": "18740"
},
"18741": {
"description": "The Capital classification NAL provides possible locality statuses.",
"license": "CC0-1.0",
"name": "Capital Classification Name Authority List",
"prefix": "18741"
},
"18742": {
"description": "This table provides the different names of the case law reports of the Court of Justice.",
"license": "CC0-1.0",
"name": "Case Report Name Authority List",
"prefix": "18742"
},
"18743": {
"description": "This table provides the different statuses used for a case at the Court of Justice.",
"license": "CC0-1.0",
"name": "Case Status Name Authority List",
"prefix": "18743"
},
"18744": {
"description": "This table is an internal table at the Publications Office and provides the various statuses used in a harmonized way amongst the various tables (NALs).",
"license": "CC0-1.0",
"name": "Concept Status Name Authority List",
"prefix": "18744"
},
"18745": {
"description": "The continent authority table is a controlled vocabulary providing a list of continents. This table is an internal table at the Publications Office of the European Union derived from the country authority table.",
"license": "CC0-1.0",
"name": "Continent Name Authority List",
"prefix": "18745"
},
"18746": {
"description": "The corporate-body-classification authority table is a controlled vocabulary providing types of corporate bodies. This authority table is maintained by the Publications Office of the European Union in the Metadata Registry (EU Vocabularies website).",
"license": "CC0-1.0",
"name": "Corporate Body Classification Name Authority List",
"prefix": "18746"
},
"18747": {
"description": "The Correction status NAL provides the possible statuses of proofreading of labels and descriptions.",
"license": "CC0-1.0",
"name": "Correction Status Name Authority List",
"prefix": "18747"
},
"18748": {
"description": "The Court type NAL provides a classification of courts.",
"license": "CC0-1.0",
"name": "Court Type Name Authority List",
"prefix": "18748"
},
"18749": {
"description": "The crawler table provides a list of programs used for web crawling designed for web archiving. It has been developed specifically for the EU Web Preservation.",
"license": "CC0-1.0",
"name": "Crawler Name Authority List",
"prefix": "18749"
},
"1875": {
"description": "The inner library is divided into several thematic areas. If you want to see the subdivision of the areas, download the list of sections in the Library.",
"homepage": "http://servizi.comune.fe.it/attach/artistife/docs/sezioni_biblioteca.pdf",
"name": "VIGOR Video Library Catalog classification of library sections",
"prefix": "1875"
},
"18750": {
"description": "The Data theme authority table was developed in the context of the revision of the DCAT application profile (DCAT-AP). The themes have been defined by the working group in charge of the revision of the DCAT-AP.",
"license": "CC0-1.0",
"name": "MDR data themes",
"prefix": "18750"
},
"18751": {
"description": "The dataset-status authority table is a controlled vocabulary providing possible statuses for datasets. It has been developed specifically for the EU Open Data Portal. This authority table is maintained by the Publications Office of the European Union in the Metadata Registry (EU Vocabularies website).",
"license": "CC0-1.0",
"name": "Dataset Status Name Authority List",
"prefix": "18751"
},
"18752": {
"description": "The dataset-type authority table is a controlled vocabulary providing possible types for categorising a dataset. It has been developed specifically for the EU Open Data Portal. This authority table is maintained by the Publications Office of the European Union in the Metadata Registry (EU Vocabularies website).",
"license": "CC0-1.0",
"name": "Dataset Type Name Authority List",
"prefix": "18752"
},
"18753": {
"description": "The distribution-type authority table is a controlled vocabulary providing possible distribution types. It has been developed specifically for the EU Open Data Portal. This authority table is maintained by the Publications Office of the European Union in the Metadata Registry (EU Vocabularies website).",
"license": "CC0-1.0",
"name": "Distribution Type Name Authority List",
"prefix": "18753"
},
"18754": {
"description": "This table provides possible documentation types. It has been developed specifically for the EU Open Data Portal.",
"license": "CC0-1.0",
"name": "Documentation Type Name Authority List",
"prefix": "18754"
},
"18755": {
"description": "This table provides possible statuses for amounts in the EU budget. It has been developed specifically for the EU budget as Linked Open Data project.",
"license": "CC0-1.0",
"name": "EU Budget Amount Status Name Authority List",
"prefix": "18755"
},
"18756": {
"description": "This table provides possible stages of the EU budget preparatory actions and pilot projects. It has been developed specifically for the EU budget as Linked Open Data project.",
"license": "CC0-1.0",
"name": "EU Budget Stage Name Authority List",
"prefix": "18756"
},
"18757": {
"description": "This table provides possible statuses of the EU budget preparatory actions and pilot projects. It has been developed specifically for the EU budget as Linked Open Data project.",
"license": "CC0-1.0",
"name": "EU Budget Status Name Authority List",
"prefix": "18757"
},
"18758": {
"description": "This table provides programmes financially supported by the EU. It has been developed specifically for the EU budget as Linked Open Data project.",
"license": "CC0-1.0",
"name": "EU Programme Name Authority List",
"prefix": "18758"
},
"18759": {
"description": "This table provides the accrual periodicities in the 24 official languages of the European Union.",
"license": "CC0-1.0",
"name": "Frequency Name Authority List",
"prefix": "18759"
},
"1876": {
"homepage": "http://www.biblioeconomia.unimore.it/site/home/informazioni/organizzazione-del-materiale-bibliografico/monografie/articolo117021668.html",
"prefix": "1876"
},
"18760": {
"description": "The Grammatical alternation NAL captures the phonological alternations based on whether the first letter of the succeeding word is a consonant or a vowel, completed with a syllable rule. It is used for but not limited to number forms in the Maltese language.",
"license": "CC0-1.0",
"name": "Grammatical Alternation Name Authority List",
"prefix": "18760"
},
"18761": {
"description": "The Grammatical consciousness NAL provides the grammatical features regarding consciousness of a substantive. This NAL is designed to capture number form variations in the Irish language.",
"license": "CC0-1.0",
"name": "Grammatical Consciousness Name Authority List",
"prefix": "18761"
},
"18762": {
"description": "The grammatical-gender authority table is a controlled vocabulary which provides the list of the grammatical genders in languages which have gender distinctions: \"male\", \"female\", \"neuter\" or \"utrum\".",
"license": "CC0-1.0",
"name": "Grammatical Gender Name Authority List",
"prefix": "18762"
},
"18763": {
"description": "This table provides the honorific titles used in addressing or referring to a person as used in the EU Whoiswho.",
"license": "CC0-1.0",
"name": "Honorific Name Authority List",
"prefix": "18763"
},
"18764": {
"description": "This table provides the list of human sexes.",
"license": "CC0-1.0",
"name": "Human Sex Name Authority List",
"prefix": "18764"
},
"18765": {
"description": "The NAL internal procedure lists the different procedures used in the context of data exchange between the institutions.",
"license": "CC0-1.0",
"name": "Internal Procedure Name Authority List",
"prefix": "18765"
},
"18766": {
"description": "This table provides the various forms of labels that are considered as 'alternative labels' in the SKOS format. It is an internal table used at the Publications Office of the EU.",
"license": "CC0-1.0",
"name": "Label Type Name Authority List",
"prefix": "18766"
},
"18767": {
"description": "The procjur-type authority table is a controlled vocabulary that provides the three different types of legal proceedings at the Court of Justice. It provides an authority code, the start-use date of the concept and labels in all official EU languages. The procjur-type authority table is updated in coordination with the Court of Justice of the European Union and maintained by the Publications Office of the European Union in the Metadata Registry (EU Vocabularies website).",
"license": "CC0-1.0",
"name": "Legal Proceeding Type Name Authority List",
"prefix": "18767"
},
"18768": {
"description": "The Licence authority table is a controlled vocabulary that lists the European Commission Reuse Notice and the European Union Public Licences. It also provides a list of standard licences available internationally, including the Creative Commons licences. It gives an authority code and labels in many official EU languages. The Licence authority table is maintained by the Publications Office of the European Union on the EU Vocabularies website.",
"license": "CC0-1.0",
"name": "Licence Name Authority List",
"prefix": "18768"
},
"18769": {
"description": "The Licence domain authority table is a controlled vocabulary that provides a list of domains covered by licences in the Licence authority table. The Licence domain authority table is maintained by the Publications Office of the European Union on the EU Vocabularies website.",
"license": "CC0-1.0",
"name": "Licence Domain Name Authority List",
"prefix": "18769"
},
"1877": {
"description": "The Library has a rich collection of periodicals in the field of economics and social sciences, consisting mainly of series, largely complete, of the most important journals of European and American economics. The entire collection of periodicals deals with Navata Nord ( From the Camp 4 to the Camp 17) and the North and South Ballatoons The current period of subscription periodicals is placed in exhibitors that extend the entire library at length.The exhibitors are provided, at the individual headings, Any online availability and / or indication of the cessation or disposal of the paper subscription.",
"homepage": "http://www.biblioeconomia.unimore.it/site/home/informazioni/organizzazione-del-materiale-bibliografico/periodici/articolo117021672.html",
"name": "Periodicals - Classification Schedule",
"prefix": "1877"
},
"18770": {
"description": "The Membership classification NAL provides a list of politico-economic units for classifying countries, localities or languages. This NAL focuses mainly on units with European relevance.",
"license": "CC0-1.0",
"name": "Membership Classification Name Authority List",
"prefix": "18770"
},
"18771": {
"description": "The Modification type NAL provides a list of modifications to the legal act resulting from instructions in the modifying act or corrigenda.",
"license": "CC0-1.0",
"name": "Modification Type Name Authority List",
"prefix": "18771"
},
"18772": {
"description": "The authority table notation type provides the list of notation types used in EU Vocabularies authority tables as well as in the context of DCAT-AP.",
"license": "CC0-1.0",
"name": "Notation Type Name Authority List",
"prefix": "18772"
},
"18773": {
"description": "The Numbers Named Authority List (NAL) is a controlled vocabulary listing a set of cardinal and ordinal numbers in the 24 official languages of the EU. The NAL is mainly used for numbering the issues. It contains numbers from 1 to 31, decimals from 40 to 100 and some bigger round number.\n\nThe NAL is under governance of the Interinstitutional Metadata Maintenance Committee (IMMC) and maintained by the Publications Office of the EU.",
"license": "CC0-1.0",
"name": "Number Name Authority List",
"prefix": "18773"
},
"18774": {
"description": "The organisation-type authority table is a controlled vocabulary listing the various types of organizations as used in the EU Whoiswho application. This authority table is maintained by the Publications Office of the European Union in the Metadata Registry (EU Vocabularies website).",
"license": "CC0-1.0",
"name": "Organization Type Name Authority List",
"prefix": "18774"
},
"18775": {
"description": "This table provides the position grade of the staff employed by the European institutions, bodies or agencies. It has been developed specifically for the EU budget as Linked Open Data project.",
"license": "CC0-1.0",
"name": "Position Grade Name Authority List",
"prefix": "18775"
},
"18776": {
"description": "This table provides the position status of the staff employed by the European institutions, bodies or agencies as used in the EU Whoiswho application.",
"license": "CC0-1.0",
"name": "Position Status Name Authority List",
"prefix": "18776"
},
"18777": {
"description": "This authority table provides the list of possible types of position of the staff employed by the EU institutions, bodies or agencies. It has been developed specifically for the EU budget as Linked Open Data project.t.",
"license": "CC0-1.0",
"name": "Position Type Name Authority List",
"prefix": "18777"
},
"18778": {
"description": "The Procedure nature authority table is a controlled vocabulary that provides a classification of procedures applicable to the adoption of legislation and other acts by the institutions of the European Union as defined by the treaties. The Procedure nature authority table is maintained by the Publications Office of the European Union on the EU Vocabularies website.",
"license": "CC0-1.0",
"name": "Procedure Nature Name Authority List",
"prefix": "18778"
},
"18779": {
"description": "This table provides the various product forms published at the Publications office, mainly those related to the general publications (brochures, leaflets, β¦) and the EU Open Data Portal (ODP)..",
"license": "CC0-1.0",
"name": "Product Form Name Authority List",
"prefix": "18779"
},
"1878": {
"description": "The Library has always paid particular attention to the acquisition of statistical documentation. In this area, our paper collection is among the most complete in Italy. It includes all ISTAT publications, publications by international organizations such as In addition to the statistical material, the Library includes in this section a large collection of Italian and international documentation on the activities of central banks, ministries, autonomous companies, international organizations (ad ILO, UN, World Bank, WTO, EIB), European Union, study centers, etc. The entire collection covers La Navata Sud (from Camp 3 to Camp 16) The current year of statistical publications and documentation in The subscription is not placed in exhibitors, but is placed on the shelves, following the previous vintages.",
"name": "Statistics and Documentation - Classification scheme",
"prefix": "1878"
},
"18780": {
"description": "This table provides the various themes used for the general publications.",
"license": "CC0-1.0",
"name": "Publication Theme Name Authority List",
"prefix": "18780"
},
"18782": {
"description": "The role-nature authority table is a controlled vocabulary that provides a list of values used for controlling the attribution of roles with the respective authority codes. Labels are available in English and in French. The role-nature authority table is maintained by the Publications Office of the European Union in the Metadata Registry (EU Vocabularies website).",
"license": "CC0-1.0",
"name": "Role Nature Name Authority List",
"prefix": "18782"
},
"18783": {
"description": "This table provides the quality of the interveners at the Court of Justice.",
"license": "CC0-1.0",
"name": "Role Qualifier Name Authority List",
"prefix": "18783"
},
"18785": {
"abbreviation": "BK",
"description": "German decimal classification system based on the Dutch Basic Classification (NBC)",
"homepage": "https://wiki.k10plus.de/display/K10PLUS/Basisklassifikation",
"license": "CC0-1.0",
"name": "Basic Classification",
"pattern": "^(0|1-2|3-4|5|7-8|[0-9]{2}(\\.[0-9]{2})?)$",
"prefix": "18785",
"wikidata_database": "Q29938469"
},
"18786": {
"description": "The script authority table is a controlled vocabulary providing a list of distinctive scripts. Each script is instantiated according to a writing system. This authority table is maintained by the Publications Office of the European Union in the Metadata Registry (EU Vocabularies website).",
"license": "CC0-1.0",
"name": "Script Name Authority List",
"prefix": "18786"
},
"18787": {
"description": "This table provides the sites referring to the premises occupied by the various EU institutions and bodies.",
"license": "CC0-1.0",
"name": "Site Name Authority List",
"prefix": "18787"
},
"18788": {
"description": "This table provides the subdivisions of acts used for legal citations. The subdivision authority table is part of the core metadata used in the exchange between the institutions involved in the legal decision making process and the Publications Office of the European Union. It is also used by EUR-Lex. It provides an authority code and labels in all official EU languages. The subdivision authority table is under governance of the Interinstitutional Metadata Maintenance Committee (IMMC) and maintained by the Publications Office of the European Union in the Metadata Registry (EU Vocabularies website).",
"license": "CC0-1.0",
"name": "Subdivision Name Authority List",
"prefix": "18788"
},
"18789": {
"description": "The Subdivision position NAL is used for the consolidation of legislation. It provides the possible positions in the subdivision of acts.",
"license": "CC0-1.0",
"name": "Subdivision Position Name Authority List",
"prefix": "18789"
},
"1879": {
"description": "The classification system results from the aggregation and standardization of 6 different international classification systems of scientific journals in various fields of social sciences (ISI, SCOPUS, ESF, AERES, CAPES and CERES).\n\nThe ClassifICS system is an open classification system that allows the further incorporation of any other scientific journals that may be referenced in at least one of the 6 classification systems contemplated.\n\nThe ClassifICS system is a dynamic classification system that may in the future incorporate other classification systems, namely those that result from the evaluation processes of Portuguese journals in the various fields of social sciences.\n\nThe main objectives of the classifICS are:\n\n- recognize and value the importance of the dissemination of scientific production in publications that are widely accepted by the international academic community, such as scientific journals with peer review;\n\n- provide information and identify publications that, due to the public recognition of their quality and excellence standards, should be chosen or privileged by researchers in the social sciences for the publication of their scientific work, with a view to their better dissemination And greater public impact;\n\n- establish clearly identifiable levels and levels of quality according to objective criteria that respect existing practices in monitoring and internal and external evaluation of research systems and institutions.",
"homepage": "http://www.ics.ul.pt/classifics/",
"name": "ClassifICS",
"prefix": "1879"
},
"18790": {
"description": "This table provides the target audiences used for the general publications.",
"license": "CC0-1.0",
"name": "Target Audience Name Authority List",
"prefix": "18790"
},
"18791": {
"description": "The time-period authority table is a controlled vocabulary which lists the periods of time in the 24 official languages of the EU. It enumerates the names of the seasons, months, weekdays and the main units of time when the issues are published. It also contains concepts for \"unlimited\" or \"unknown\" time periods. The NAL is under governance of the Interinstitutional Metadata Maintenance Committee (IMMC) and maintained by the Publications Office of the EU.",
"license": "CC0-1.0",
"name": "Time Period Name Authority List",
"prefix": "18791"
},
"18793": {
"description": "The Treaty classification NAL provides the list of types of treaties of the European Union and its predecessors.",
"license": "CC0-1.0",
"name": "Treaty Classification Name Authority List",
"prefix": "18793"
},
"18794": {
"description": "This table provides a list of the different applications or environments that make use of the various tables (NALs). It is an internal table used at the Publications Office of the EU.",
"license": "CC0-1.0",
"name": "Use Context Name Authority List",
"prefix": "18794"
},
"18795": {
"description": "The website-identifier table provides a list of websites (URL) included in the europa.eu domain and subdomains. It has been developed specifically for the EU Web Preservation, but will be used also for many other purposes. The table contains reference to copyright of the websites.",
"license": "CC0-1.0",
"name": "Website Identifier Name Authority List",
"prefix": "18795"
},
"18796": {
"description": "The Writing system NAL provides the list of the main writing systems. They are differentiated depending on what a symbol represents inside the system.",
"license": "CC0-1.0",
"name": "Writing System Name Authority List",
"prefix": "18796"
},
"18797": {
"abbreviation": "IxTheo",
"description": "The classification of Index Theologicus bibliography uses uppercase letter notations for topics of theological interest.",
"homepage": "https://www.ixtheo.de/Content/IxTheoClassification",
"license": "CC0-1.0",
"name": "IxTheo classification",
"pattern": "^[A-Z][A-Z]?[A-Z]$",
"prefix": "18797",
"wikidata_database": "Q57415367"
},
"18798": {
"description": "The technical complexity and material diversity used in the processes of conformation and decoration of objects require an approach from different disciplines. This thesaurus is dedicated to the techniques used for the manufacture and decoration of cultural goods and includes those terms that best describe the technical processes applied throughout history, in order to improve the knowledge and description of Cultural Heritage assets.",
"homepage": "http://tesauros.mecd.es/tesauros/tecnicas.html",
"license": "https://www.w3.org/Consortium/Legal/2015/doc-license",
"name": "Dictionary of Techniques",
"prefix": "18798"
},
"18799": {
"description": "The easiest way to search for a word in the dictionary is to use the form located on the homepage. Type the word or form in the box without worrying about DMF entries: proposals will be displayed. If the form is known to the DMF, the answer is displayed quickly. Otherwise, there is a waiting time, the lemmatizer analyzes the form to make proposals for entries. Options make it possible to search for the attestation of the form in the corpora, to propose an analysis if the form is known like a verbal graph. The option dictionaries quoted makes it possible to conveniently present the presence of the word in a given dictionary.",
"homepage": "http://www.atilf.fr/dmf/",
"name": "Middle French Dictionary",
"prefix": "18799"
},
"188": {
"description": "Titles (about 60,000) are indexed by the thesaurus developed for NICEM which contains 6,000 subject terms. The thesaurus hierarchy is shown at the left - click on a + sign to expand it until you find the subject you're looking for. Click on that term in the tree to launch a search.",
"homepage": "http://www.mediasleuth.com/MediaSleuthSearcher/navtree/",
"name": "National Information Center for Educational Media Thesaurus",
"prefix": "188"
},
"1880": {
"homepage": "http://www.edugracja.pl/system-klasyfikacji-umiejetnosci/",
"license": "CC-BY-3.0",
"name": "Skill Classification System",
"prefix": "1880"
},
"18800": {
"abbreviation": "HISCO",
"description": "Starting in the 1950s the International Labour Office has developed an International Standard Classification of Occupations (isco) allowing classification of occupational activities worldwide. Naturally, this system is not intended to deal with historical information. In recent years, a group of historians and sociologists have started to build upon the 1968 version of isco to create a classification scheme for occupational titles in the 19th and early 20th centuries, called hisco (...). It is tailored to cope with historical changes in the production process, and allows storage of information on product and status that could not be accommodated in isco. Large historical databases from which the hisco-data are taken and the international association of historians working on censuses have already agreed to adopt it, an many individual researchers are expected to do so as well.\n\nAltogether, the HISCO scheme was originally based on the coding of the 1,000 most frequent male and female occupational titles in datasets from eight different countries: Belgium, Britain, Canada, France, Germany, the Netherlands, Norway and Sweden. The occupational data which were employed to develop the scheme span the period 1690-1970, but are mostly from the nineteenth century. They contain titles declared by or recorded for people of all ages in parish and civil registration documents. The data used to create HISCO encompass the largest country in western Europe, the worldβs first industrial nation, the two most influential of the Scandinavian territories, and a newly-settled region of French-Canada. This, and an emphasis on variations within economies in sampling design, ensures that they provide a good mix of agricultural, industrial and commercial activities, of old and new technologies, of traditional and modern forms of organization. Moreover, the inclusion of two French-speaking populations, and a further region in which the official language was French, provides an effective test of the HISCO schemeβs sensitivity to the relationship between language and meaning. Nevertheless, the scheme is currently limited in coverage to the Northern European and Atlantic economies. Future development of the scheme will broaden its scope. To this end, the coding of new data into HISCO is being undertaken in several other countries.\n\nThe History of Work Information System has a coding section that helps users code their data in HISCO, and thus both make it comparable to other datasets, and make it of use to other scholars. The Provenance file lists all contributors to the HISCO-database.",
"homepage": "https://historyofwork.iisg.nl/",
"name": "Historical International Standard Classification of Occupations",
"prefix": "18800"
},
"18801": {
"description": "Video games are extremely popular materials held by both public libraries and academic libraries. There is a compelling need for a robust genre vocabulary for cataloging video games that will aid users in identifying video game titles by genre. (...) The OLAC video game genre vocabulary includes sixty-six genre terms, each with a scope note to help librarians choose the correct term when cataloging video games. The vocabulary is fully cross-referenced and includes authoritative sources to corroborate the usage of the genre term as applied to video games. (...) The OLAC video game genre vocabulary has been assigned the MARC source code of olacvggt for use in identifying the source of vocabulary genre terms assigned in bibliographic records for individual video game titles. The designated olacvggt code appears in the Genre/Form Code and Term Source Codes list which is maintained by the Library of Congress, http://www.loc.gov/standards/sourcelist/genre-form.html. (...) OLAC strongly encourages the cataloging community to embrace the use of the authorized OLAC terms in the OLAC video game genre vocabulary when cataloging video games for their collections.",
"homepage": "https://www.olacinc.org/olac-video-game-vocabulary",
"license": "CC BY-NC-SA 3.0",
"name": "OLAC Video Game Vocabulary",
"prefix": "18801"
},
"18802": {
"description": "The Lexicon of Greek Personal Names (LGPN) was established to collect and publish all ancient Greek personal names, drawing on the full range of written sources from the 8th century B.C. down to the late Roman Empire.",
"homepage": "http://www.lgpn.ox.ac.uk/",
"name": "Lexicon of Greek Personal Names",
"prefix": "18802"
},
"18803": {
"homepage": "http://www.woerterbuchnetz.de/",
"name": "Dictionary Network",
"prefix": "18803"
},
"18804": {
"abbreviation": "NDLSH",
"description": "Web NDL Authorities is a service by the National Diet Library (NDL), Japan, to access authority data created and maintained by the NDL. Name headings or Subject headings are assigned to the bibliographic data to distinguish different people with the same name or to identify people who use pseudonyms, nonstandard spellings, transliterated names, or other variants. To control these headings, authority data is organized to indicate alternative headings, synonyms, and the basis of choice for the headings.",
"homepage": "http://id.ndl.go.jp/auth/ndla",
"name": "Web NDL Authorities",
"prefix": "18804",
"wikidata_database": "Q2553334"
},
"18806": {
"description": "A vocabulary defining television, radio and associated media contributor roles.",
"homepage": "https://www.ebu.ch/metadata/ontologies/skos/ebu_RoleCodeCS.rdf",
"license": "CC BY-NC-SA 3.0",
"name": "EBU SKOS Classification Scheme for Role Codes",
"prefix": "18806",
"wikidata_database": "Q57837910"
},
"18807": {
"description": "The CINAHL subject headings are based on the MeSH headings, with additional specific nursing and allied health headings added as appropriate. Each year, the headings are updated and revised relative to terminology needed in these fields. In addition, new terms from MeSH may be added as well.",
"name": "CINAHL Subject Headings",
"prefix": "18807"
},
"18808": {
"description": "The Asset Description Metadata Schema (v1.00) (ADMS) proposes six new controlled vocabularies (...), and specifies for each vocabulary and term corresponding purl.org term URIs (...):\n\n Asset Type: e.g. 'domain model', 'schema', 'taxonomy';\n\n Interoperability Level: e.g. 'legal interoperability', 'organisational interoperability', 'semantic interoperability', and 'technical interoperability';\n\n Licence Type: e.g. 'attribution', and 'no derivative work';\n\n Publisher Type: e.g. 'company', and 'national authority';\n\n Representation Technique: e.g. 'UML', 'XML Schema', 'Schematron', 'OWL'; and\n\n Status: e.g. 'completed', and 'under development'.",
"homepage": "https://joinup.ec.europa.eu/document/skos-used-publish-controlled-vocabularies-defined-adms-web",
"name": "ADMS Controlled Vocabularies",
"prefix": "18808"
},
"18809": {
"description": "Vocabulary of accession methods.",
"homepage": "http://kulturnav.org/c4d0cd30-ba95-4864-8d1c-38b659b785b4",
"name": "Accession Method",
"prefix": "18809"
},
"1881": {
"description": "The Multilingual dictionary of cataloguing terms and concepts contains definitions for many terms and concepts used by the library cataloguing community. Terms and definitions are available in English and a variety of other languages.\n\nThe MulDiCat project was begun by Monika Muennich in 1998 for IFLA's Cataloguing Section. It was stored in a proprietary database developed by Bernard Eversberg in 2003. It has now re-emerged in part as a Word table and as a SKOS file on the new IFLA Namespace.\n\nIt is intended to be used for authoritative translations of IFLA cataloguing standards and related documents. The terms reflect international agreements on terms to use for these cataloguing and classification concepts -- in particular, the agreements reached during the IME ICC (IFLA Meetings of Experts on an International Cataloguing Code) that reviewed FRBR, FRAD, and ISBD terminology while developing the International Cataloguing Principles (ICP). As additional official translations of ICP are added to IFLANET, MulDiCat has been updated to include terms in these additional languages.\n\nOther terms will be added as IFLA reaches international agreement for them through the work of the Cataloguing Section and the Classification & Indexing Sections, as well as other units throughout IFLA interested and involved in bibliographic standards.",
"name": "Multilingual Dictionary of Cataloguing Terms and Concepts",
"prefix": "1881"
},
"18810": {
"homepage": "https://goo.gl/j9aZoW",
"name": "Controlled vocabulary for Mexico 1968: information resources",
"prefix": "18810"
},
"18811": {
"homepage": "https://github.com/judbd/Thesaurus-Lightroom-Collaboratif/blob/master/thesaurus_paris.txt",
"license": "http://www.wtfpl.net",
"name": "Thesaurus City of Paris",
"prefix": "18811"
},
"18812": {
"homepage": "https://github.com/judbd/Thesaurus-Lightroom-Collaboratif/blob/master/thesaurus_lyon.txt",
"license": "http://www.wtfpl.net",
"name": "Thesaurus City of Lyon",
"prefix": "18812"
},
"18813": {
"homepage": "https://github.com/judbd/Thesaurus-Lightroom-Collaboratif/blob/master/thesaurus_photo_culinaire.txt",
"license": "http://www.wtfpl.net",
"name": "Culinary Thesaurus",
"prefix": "18813"
},
"18814": {
"description": "This thesaurus lists all the French communes including metropolitan France and overseas regions and departments. The current communes (including those created in 2018) are attached to their department; the delegated, merged or associated communes are attached to the corresponding current commune. The different entries are mapped to l'INSEE, GeoNames, PACTOLS, Rameau, Wikidata et WikipΓ©dia.",
"homepage": "https://www.loterre.fr/skosmos/D63/",
"license": "CC-BY-3.0",
"name": "French Communes",
"prefix": "18814"
},
"18815": {
"description": "The Web-HCLCS is the webversion of the Helsinki City Library Classification System. It contains the tables and the index of HCLCS.",
"homepage": "http://finto.fi/hklj/",
"license": "CC0-1.0",
"name": "Helsinki City Library Classification System",
"prefix": "18815"
},
"18816": {
"description": "Money Aggregate Vocabulary, or MoneyAggVoc for short, is an attempt to catalogue money aggregate measures listed in the Exhibit 3 Definitions of Money in Reading 19 on Economics of the CFA Program Curriculum 2016 Level I (ISBN 978-1-942471-19-6) with some minor additions. Although the CFA Program Curriculum inspired the structure of the concepts in this vocabulary, the actual content was taken from open sources (DBpedia, Federal Reserve System, European Central Bank, Bank of Japan and Bank of England) and includes appropriate references.",
"homepage": "https://cadmiumkitty.github.io/moneyaggvoc/",
"license": "CC BY-SA 3.0",
"name": "Money Aggregate Vocabulary",
"prefix": "18816"
},
"18817": {
"description": "Subject authority headings for Filipiniana materials.This will contain terms on: 1. Works about the Philippines, its people and culture regardless of author, imprint, and language 2. Works written by Filipinos 3. Works written in Filipino or other native Philippine languages 4. Philippine Government publications such as yearbooks, annual reports, etc. 5. Other publications containing substantial content on the Philippines.",
"homepage": "http://rothmanlim.com/tematres/fisaf/",
"name": "Filipiniana Subject Authority File",
"prefix": "18817"
},
"18818": {
"description": "HurtLex is a multilingual computational lexicon of hate words. Starting from the Italian lexicon ''Le Parole per Ferire'' by Tullio de Mauro, we developed a computational lexicon and semi-automatically translated it into more than 50 languages.",
"prefix": "18818"
},
"18819": {
"description": "The UPIANA Classification Schedule forms part of a set of three special classification schedules developed by the Cataloging and Metadata Services Section of the University of the Philippines Diliman University Library. It was designed to meet an urgent need in the classification of its various special collections. While the University Library has chosen to adopt the United States Library of Congress Classification Schedules (LCC), catalogers have found it to be inadequate in handling most of the Filipiniana materials. (...) UPIANA is defined to include all officially published and/or unpublished materials emanating from and/or pertaining to the University of the Philippines System. The classification schedule developed in 1961 expanded the LC schedule for individual institutions offering higher education. Since then, it has undergone numerous revisions in order to incorporate the additions and changes in the University organization. Notable revisions of the schedule were carried out in 1975 by Vyva M. Aguirre as part of her Master of Library Science special problem, and by the C Section in 1982 and 2000. This present publication includes the additions and changes made as of March 2018. It does not cover serial publications which, as a standard practice, are not classified, nor does it provide for publications by individual faculty members, alumni, and students of the University on specific subject fields as these are preferably classified under the various classes in the LC Scheme. The UPIANA Classification Schedule is a customized scheme for the University of the Philippines System that may be adopted and or used as a model by other higher education institution libraries with similar needs. Like the LC Scheme, it is found to be functional and logically designed to serve as an organizing system for special and local collections. It is envisioned that libraries who are just beginning to develop similar schemes would find this tool useful for their own purpose.",
"homepage": "https://docs.google.com/document/d/1PYqt4L7-aTEkpilayhF-X9AHcmlJw583ugT86urDUqg/",
"name": "UPIANA Classification Scheme",
"prefix": "18819"
},
"1882": {
"description": "The language of the fashion world is plagued by foreign language and technicalities that appear frequently in the media due to the multitude of events and meetings held in this sector and the expansion of the specialized press. BBVA has produced this document, which contains and explains specific terms related to fashion, offers linguistic recommendations in cases where there may be doubts and alternatives are given in Spanish to avoid the abusive use of foreign languages. Conceived as a guide for the use of the lexicon in this area and does not pretend to exhaust the possibilities that may arise, since, in addition to the terms contained in this compilation, there are other alternatives used in different countries. Term is considered valid in Spanish, it is written in round and it is not necessary to highlight it ortho-typographically. Foreign language not adapted to Spanish spelling, it is appropriate to emphasize it in italics or, if this kind of letter is not available, to cross-reference it.",
"homepage": "http://www.fundeu.es/wp-content/uploads/2015/03/glosarioModaFundeu.pdf",
"license": "CC BY-ND 3.0",
"name": "Fashion Glossary",
"prefix": "1882"
},
"18820": {
"description": "The Gale Accounting Thesaurus is a subset of the master Gale Business Thesaurus in the narrower domain of accounting and its principles and procedures. This includes terms related to accounting, accounting firms, accounts receivable, auditing, and bookkeeping. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 173 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Accounting Thesaurus",
"prefix": "18820"
},
"18821": {
"description": "The Gale Advertising Thesaurus is a subset of the master Gale Business Thesaurus in the narrower domain of advertising. This includes terms related to corporate and political advertising, radio and television advertising, direct mail advertising, billboard advertising, product placement, and advertising agencies. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 92 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Advertising Thesaurus",
"prefix": "18821"
},
"18822": {
"description": "The Gale Aeronautics and Astronautics Thesaurus is a subset of the master Gale Technology Thesaurus in the narrower domain of design, construction, and operation of aircraft and spacecraft, and the technologies and processes that apply directly to the science of flight. Items in this thesaurus may overlap with terms related to fluid mechanics. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 449 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Aeronautics and Astronautics Thesaurus",
"prefix": "18822"
},
"18823": {
"description": "The Gale Agriculture Thesaurus is a subset of the master Gale Business Thesaurus in the narrower domain of the science or art of cultivating the soil, producing crops, and raising livestock. The Agriculture Thesaurus includes terms related to farms and farming, soils, seeds, crops, plowing, planting, irrigation, harvesting, fertilizers, herbicides, agricultural equipment and machinery, horticulture, viticulture, gardening, forests and forestry, logging, fishing and fisheries, ranching, and dairy farming. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 869 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Agriculture Thesaurus",
"prefix": "18823"
},
"18824": {
"description": "The Gale Alternative Medicine Thesaurus is a subset of the master Gale Health and Medicine Thesaurus in the narrower domain of herbal medicines, homeopathic treatments, and non-Western therapies such as acupuncture. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 898 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Alternative Medicine Thesaurus",
"prefix": "18824"
},
"18825": {
"description": "The Gale Anatomy Thesaurus is a subset of the master Gale Health and Medicine Thesaurus in the narrower domain of the human or animal body as a whole and all of the bodyβs systems, regions, and parts. It includes terms that represent the physiological processes that take place within the human or animal body. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,263 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Anatomy Thesaurus",
"prefix": "18825"
},
"18826": {
"description": "The Gale Anthropology Thesaurus is a subset of the master Gale Social Sciences Thesaurus in the narrower domain of the origin, development, and varieties of human beings and their societies. It also includes terms related to the field of anthropology and its sub-disciplines, such as human culture, archaeology, antiquities, ethnic groups, nationalities, social rituals, manners, and customs. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,920 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Anthropology Thesaurus",
"prefix": "18826"
},
"18827": {
"description": "The Gale Astronomy Thesaurus is a subset of the master Gale Science Thesaurus. Includes terms associated with the observation and study of celestial bodies and of many physical phenomena that occur beyond the earth's atmosphere. Specific areas include stars, galaxies, solar systems, comets, asteroids, meteoroids, nebulae, natural satellites, astrophysics, astrology, calendars, constellations, cosmology, eclipses, extraterrestrial radiation, and astronomical instruments and equipment. It does not include named space vehicles. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 488 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Astronomy Thesaurus",
"prefix": "18827"
},
"18828": {
"description": "The Gale Automotive Thesaurus is a subset of the master Gale Technology Thesaurus. This thesaurus includes subjects related to automotive fuels and equipment, brake parts, engine parts, fuel and exhaust systems, steering gear, automotive seating, and motor vehicle types. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 965 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Automotive Thesaurus",
"prefix": "18828"
},
"18829": {
"description": "The Gale Banking Thesaurus is a subset of the master Gale Business Thesaurus in the narrower domain of banking. This includes terms related to the banking industry, financial institutions, savings banks, savings and loan associations, and credit unions, as well as financial services such as bank accounts, ATMs, and bank loans. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 146 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Banking Thesaurus",
"prefix": "18829"
},
"1883": {
"homepage": "http://clasificacioncirc.es/",
"license": "CC BY-NC-ND 3.0",
"name": "Integrated Classification of Scientific Journals",
"prefix": "1883",
"wikidata_database": "Q21002668"
},
"18830": {
"description": "The Gale Biology Thesaurus a subset of the master Gale Science Thesaurus. This thesaurus includes subject areas related to animals, antibodies, biocatalysts, biological products, botany, genetics, microbiology, morphology, and physiology. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 13,382 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Biology Thesaurus",
"prefix": "18830"
},
"18831": {
"description": "The Gale Building and Construction Thesaurus is a subset of the master Gale Technology Thesaurus. This thesaurus includes subject areas related to building materials, civil engineering, construction methods and techniques, construction equipment, and material properties. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 577 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Building and Construction Thesaurus",
"prefix": "18831"
},
"18832": {
"description": "The Gale Business thesaurus is a large, general business thesaurus in the domains of accounting, advertising, agriculture, banking, commerce, currency and coinage, finance, human resources, industries, insurance, investments, management, marketing, labor, products and services, public relations, real estate, and taxation. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 6,936 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Business Thesaurus",
"prefix": "18832"
},
"18833": {
"description": "The Gale Chemical Technology Thesaurus is a subset of the master Gale Technology Thesaurus in the narrower domain of commercial and industrial applications of chemicals and chemical processes. It also may include terms related to social, economic, and environmental concerns about the use of chemicals. The thesaurus contains 533 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Chemical Technology Thesaurus",
"prefix": "18833"
},
"18834": {
"description": "The Gale Chemistry Thesaurus a subset of the master Gale Science Thesaurus. This thesaurus includes subject areas related to chemicals, chemical compounds, chemical elements, chemical equipment, and chemical reactions. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 2,040 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Chemistry Thesaurus",
"prefix": "18834"
},
"18835": {
"description": "The Gale Commerce Thesaurus is a subset of the master Gale Business Thesaurus in the narrower domain of the exchange of goods or commodities between different countries, or between different regions of the same country. This includes terms related to international trade, exports, imports, tariffs, balance of trade, free trade and protection, customs administration, interstate commerce, freight, shipping, trucking, commercial aviation, commercial policy, and commercial treaties. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 280 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Commerce Thesaurus",
"prefix": "18835"
},
"18836": {
"description": "The Gale Communications Thesaurus is a subset of the master Gale Technology Thesaurus in the narrower domain of voice, data, or both delivered through the air or over wire and cable. It includes communications equipment (satellite dishes, computer networking devices, cabling, transmission equipment, etc.), communications services (long distance phone service, internet access services, messaging services and technologies such as e-mail, instant messaging, voice mail, etc.); and communications technology (technologies, protocols, and standards in use and in development for the transmission, reception, encryption, and compression of any information in any form). All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 693 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Communications Thesaurus",
"prefix": "18836"
},
"18837": {
"description": "The Gale Computing Thesaurus is a subset of the master Gale Technology Thesaurus in the narrower domain of personal, business, and large-scale computing. Specific areas include computer software, peripherals, processes, programming languages, codes, and associated technologies. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,480 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Computing Thesaurus",
"prefix": "18837"
},
"18838": {
"description": "The Gale Currency and Coinage Thesaurus is a subset of the master Gale Business Thesaurus in the narrower domain of currency, government notes, and bank notes that are in circulation as a medium of exchange. This includes terms related to money, coins, paper money, counterfeiting, and foreign exchange. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 129 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Currency and Coinage Thesaurus",
"prefix": "18838"
},
"18839": {
"description": "The Gale Diseases Thesaurus is a subset of the master Gale Health and Medicine Thesaurus in the narrower domain of diseases, disorders, conditions and symptoms (both physical and psychological) that impact humans or animals. Terms are representative of the hereditary, congenital, and nutritional diseases and disorders. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 2,858 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Diseases Thesaurus",
"prefix": "18839"
},
"1884": {
"description": "The Compendium is popularly referred to as the 'Gold Book', in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC 'Colour Books' on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books.\n\nTerminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC's Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry.\n\nSome minor editorial changes were made to the originally published definitions, to harmonise the presentation and to clarify their applicability, if this is limited to a particular sub-discipline. Verbal definitions of terms from Quantities, Units and Symbols in Physical Chemistry (the IUPAC Green Book, in which definitions are generally given as mathematical expressions) were developed specially for this Compendium by the Physical Chemistry Division of IUPAC. Definitions of a few physicochemical terms not mentioned in the Green Book were added at the same time (referred to here as Physical Chemistry Division, unpublished).\n\nThe first reference given at the end of each definition is to the page of Pure Appl. Chem. or other source where the original definition appears; other references given designate other places where compatible definitions of the same term or additional information may be found, in other IUPAC documents. The complete reference citations are given in the appended list of source documents. Highlighted terms within individual definitions link to other entries where additional information is available.",
"homepage": "http://goldbook.iupac.org/",
"name": "IUPAC Compendium of Chemical Terminology",
"prefix": "1884",
"wikidata_database": "Q902163"
},
"18840": {
"description": "The Gale Drugs Thesaurus is a subset of the master Gale Health and Medicine Thesaurus in the narrower domain of chemicals and other substances that are administered (usually orally, topically, or subcutaneously) to diagnose, treat, or prevent human or animal diseases or disorders. This thesaurus includes both prescription and over-the-counter medications that are regulated by the United States Food and Drug Administration (FDA) or by any other national or supranational drug-regulatory authority. The thesaurus includes only generic names, not brand/trade names of specific drugs. Also included are terms that represent drug excipients and additives, but not chemical precursors to drugs. Terms related to herbal remedies, nutritional supplements, 'health foods', or any other foods, food products, or beverages that are thought to be therapeutic or health promoting or are marketed as such are not included. Neither are cosmetics or toiletries even if thought to be therapeutic or marketed as such. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 2,264 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Drugs Thesaurus",
"prefix": "18840"
},
"18841": {
"description": "The Gale Earth Sciences Thesaurus is a subset of the master Gale Science Thesaurus. Includes terms associated with the composition and structure of the Earth (or other astronomical bodies) and the physical process that shape and change the Earth (or other astronomical bodies). Specific areas include geology, physical geography, geophysics, geomatics, atmospheric sciences, oceanography, and related sciences, and terms associated with equipment and instruments used in those. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,449 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Earth Sciences Thesaurus",
"prefix": "18841"
},
"18842": {
"description": "The Gale Economics Thesaurus is a subset of the master Gale Social Sciences Thesaurus in the narrower domain of economic theories, principles, systems, policies, practices, concepts, and conditions. Also provided are terms related to the field of economics and its sub-disciplines including consumption, distribution, prices, costs, supply and demand, and economic development. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 570 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Economics Thesaurus",
"prefix": "18842"
},
"18843": {
"description": "The Gale Education Thesaurus is a subset of the master Gale Social Sciences Thesaurus in the narrower domain of teaching, training, and learning. It includes terms about educational institutions and facilities, students, programs, administration, policies and practices, concepts and theories; educational standards, testing; and specific types of school, training and trade schools, specialized training, and professional schools. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,080 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Education Thesaurus",
"prefix": "18843"
},
"18844": {
"description": "The Gale Electronics Thesaurus is a subset of the master Gale Technology Thesaurus in the narrower domain all electronic devices and components used by consumers and industry in the form of finished products or parts for manufacturing except computers, computer components, and peripherals specifically intended for use with stand-alone or networked computers. Consumer electronics (stereos, televisions, cell phones, tablets) are included, but computers are not, as they are in the Gale Computer Thesaurus. Industrial electronics (component parts and devices used in electronics manufacturing, from single transistors to assembly line robots) that usually perform a dedicated function are also included. Technical terms, terms for research and development, scientific theory, and other intangibles are also found in this thesaurus. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,026 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Electronics Thesaurus",
"prefix": "18844"
},
"18845": {
"description": "The Gale Energy Thesaurus is a subset of the master Gale Technology thesaurus in the narrower domain of the production, distribution, regulation, and uses of energy resources, including new sources/production methods and their environmental ramifications. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 702 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Energy Thesaurus",
"prefix": "18845"
},
"18846": {
"description": "The Gale Engineering Thesaurus is a subset of the master Gale Technology Thesaurus in the narrower domain of general engineering as well as specific engineering disciplines, such as civil engineering, and the systems created by practitioners in those disciplines, (e.g., water and sewer systems, public works, etc.). All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,211 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Engineering Thesaurus",
"prefix": "18846"
},
"18847": {
"description": "The Gale Facilities Thesaurus is a subset of the master Gale Business Thesaurus and includes subject areas related to a number of types of facilities, buildings, structures, and locations at which commercial or industrial enterprises conduct their manufacturing, distribution, or retail operations. Hospitals, other healthcare-related facilities, and laboratories are included, but recreational and educational facilities are not. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 154 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Facilities Thesaurus",
"prefix": "18847"
},
"18848": {
"description": "The Gale Finance Thesaurus is a subset of the master Gale Business Thesaurus in the narrower domain of international, domestic, corporate, and personal finance. This includes terms related to bankruptcy, budgets, capital, cash management, contracts, credit, debt, income, inflation, interest, mortgages, profit, property, public expenditures, savings, speculation, and wealth. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 733 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Finance Thesaurus",
"prefix": "18848"
},
"18849": {
"description": "The Gale Fine Arts Thesaurus is a subset of the master Gale Arts and Humanities Thesaurus. This thesaurus includes subject areas related to the visual arts, and their venues, practice, theory, and teaching, as well as art occupations, cultural movements, design, handicraft, and art types. Specific areas include drawing, painting, ceramics, fashion, photography, craftwork, architecture, design, sewing, textile arts, book arts, metal arts, and glasswork. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,426 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Fine Arts Thesaurus",
"prefix": "18849"
},
"1885": {
"description": "The Rules of Inorganic Nomenclature (the 'Red Book'), first published in 1958 by the International Union of Pure and Applied Chemistry (IUPAC), were most recently updated as Nomenclature of Inorganic Chemistry 1990. This new 2005 edition of the 'Red Book' clarifies and updates recommendations concerning the names and formulae of inorganic compounds and reflects major recent developments in inorganic chemistry. Moreover, it presents recommendations fully consistent with the principles of the nomenclature of organic chemistry. In order to choose the most appropriate of the various nomenclature systems described, a flowchart is provided to guide the reader to a section or chapter where rules can be found for a particular type of compound or species. Copious examples are supplemented by an extensive subject index.\n\nNomenclature of Inorganic Chemistry: IUPAC Recommendations 2005 is the definitive guide for scientists working in academia or industry, for scientific publishers of books, journals and databases, and for organisations requiring internationally approved nomenclature in a legal or regulatory environment.\n\nThe present book supersedes not only Red Book I but also, where appropriate, Nomenclature of Inorganic Chemistry II, IUPAC Recommendations 2000 (Red Book II).",
"name": "IUPAC Nomenclature of Inorganic Chemistry",
"prefix": "1885",
"wikidata_database": "Q2078184"
},
"18850": {
"description": "The Gale Food, Cooking and Nutrition Thesaurus is a subset of the master Gale Health and Medicine Thesaurus in the narrower domain of foods and beverages consumed by humans or animals; the noncommercial production, processing, cooking, and serving of those foods and beverages, and the related human or animal nutrition, including the non-medical study of nutrition and the non-medical application of nutritional principles. It includes all substances, natural and artificial, that are considered to be or are marketed or used as nutritional supplements as well as 'health foods' and all other foods, food products, and beverages that are thought to be therapeutic or health promoting or are marketed as such. It does not include terms whose scope is limited to the commercial production, processing, transportation, handling, marketing, or serving of human or animal foods, beverages, and related products, but can include terms whose meanings encompass both commercial and non-commercial activities. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,393 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Food, Cooking and Nutrition Thesaurus",
"prefix": "18850"
},
"18851": {
"description": "The Gale Geography Thesaurus is a subset of the master Gale Social Sciences Thesaurus in the narrower domain of the description, distribution, and interaction of the physical, biological, and geographical features found on the earthβs surface. Terms related to the field of geography and its sub-disciplines (topography, climate, population, travel/voyages, and maps/mapmaking) are also featured. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 384 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Geography Thesaurus",
"prefix": "18851"
},
"18852": {
"description": "The Gale Health and Medicine Thesaurus is a large thesaurus in the domains of alternative medicine, anatomy, diseases, drugs, food, cooking and nutrition, medical equipment, technologies and procedures, medical personnel, occupations and services, and pathogens. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 12,477 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Health and Medicine Thesaurus",
"prefix": "18852"
},
"18853": {
"description": "The Gale Herbs and Supplements Thesaurus is a subset of the master Gale Health and Medicine Thesaurus in the narrower domain of herbs, herbal remedies, and dietary supplements that affect human and animal health. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 379 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Herbs and Supplements Thesaurus",
"prefix": "18853"
},
"18854": {
"description": "The Gale History Thesaurus is a subset of the master Gale Social Sciences Thesaurus in the narrower domain of the description, analysis, and interpretation of past events involving human beings. It also supplies terms related to past events as they pertain to specific regions, nations, kingdoms, empires, dynasties, institutions, movements, ethnic groups, social groups, and forms of human settlement, association, and endeavor. Specific areas include ancient history, art history, cultural history, economic history, military history, music history, political history, religious history, social history, and world history. It includes eras and ages, but not named historical events. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,216 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale History Thesaurus",
"prefix": "18854"
},
"18855": {
"description": "The Gale Human Resource Management Thesaurus is a subset of the master Gale Business Thesaurus in the narrower domain of the field of management that has responsibility for recruiting, hiring, training, developing, compensating, managing, and supervising employees. It also includes descriptors associated with employer-employee relations in general and terms related to affirmative action, career development, benefits, compensation, employees and employers, employment, labor relations, labor unions, strikes, wages, and the work environment. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 304 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Human Resource Management Thesaurus",
"prefix": "18855"
},
"18856": {
"description": "The Gale Humanities Thesaurus contains the subject areas of fine arts, language, literature, performing arts, religion, and philosophy. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 7,434 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Humanities Thesaurus",
"prefix": "18856"
},
"18857": {
"description": "The Gale Industries Thesaurus is a subset of the master Gale Business Thesaurus in the narrower domain of distinct groups of productive or profit-making industries, enterprises, companies, and firms. This includes terms such as advertising agencies, airlines, automobile industry, clothing stores, drugstores, electric utilities, engineering services, health clubs, law firms, petroleum industry, supermarkets, and weapons industry. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 474 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Industries Thesaurus",
"prefix": "18857"
},
"18858": {
"description": "The Gale Insurance Thesaurus is a subset of the master Gale Business Thesaurus in the narrower domain of the business of insuring persons and property. This includes terms related to automobile insurance, business insurance, claims adjustment, group insurance, health insurance, insurance agents and brokers, insurance policies, life insurance, Medicare, and property and casualty insurance. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 106 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Insurance Thesaurus",
"prefix": "18858"
},
"18859": {
"description": "The Gale Investments Thesaurus is a subset of the master Gale Business thesaurus in the narrower domain of investing. Included are terms related to securities (stocks and bonds), commodities, financial instruments, financial markets, and portfolio management. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 248 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Investments Thesaurus",
"prefix": "18859"
},
"1886": {
"description": "Chemical nomenclature is used to identify a chemical species by means of written or spoken words and enables a common language for communication amongst chemists. Nomenclature for chemical compounds additionally contains an explicit or implied relationship to the structure of the compound, in order that the reader or listener can deduce the structure from the name. This purpose requires a system of principles and rules, the application of which gives rise to a systematic nomenclature. Of course, a wide range of traditional names, semisystematic or trivial, are also in use for a core group of common compounds. Detailing the latest rules and international practice, this new volume can be considered a guide to the essential organic chemical nomenclature, commonly described as the 'Blue Book'. An invaluable source of information for organic chemists everywhere and the definitive guide for scientists working in academia or industry, for scientific publishers of books, journals and databases, and for organisations requiring internationally approved nomenclature in a legal or regulatory environment.",
"name": "IUPAC Nomenclature of Organic Chemistry",
"prefix": "1886",
"wikidata_database": "Q192475"
},
"18860": {
"description": "The Gale Labor Thesaurus is a subset of the master Gale Business thesaurus in the narrower domain of labor. This includes terms associated with workers, the labor force, and labor relations. Specific areas include blue collar workers, child labor, migrant labor, skilled labor, labor unions, labor movement, and labor disputes. This thesaurus does not include terms associated with human resources or personnel management (which are in the Gale Human Resources Management Thesaurus) or terms for specific occupations or jobs (which are in the Gale Occupations Thesaurus). All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 282 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Labor Thesaurus",
"prefix": "18860"
},
"18861": {
"description": "The Gale Language Thesaurus is a subset of the master Gale Humanities Thesaurus. This thesaurus includes terms related to writing, linguistics, individual world languages, grammar, speech, signs and symbols, rhetoric, philology, onomasiology (naming), semantics, and lexicology. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 757 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Language Thesaurus",
"prefix": "18861"
},
"18862": {
"description": "The Gale Law Thesaurus is a subset of the master Gale Social Sciences Thesaurus in the narrower domain of the binding rules of human conduct established by authority, society, or custom. Terms related to the field of law and its sub-disciplines are also found here, including justice and administration; law enforcement and corrections; types of law, legislation, and regulation; courts, legal codes, concepts, and practices; attorneys and the legal profession. It does not include named laws or court cases. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 2,946 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Law Thesaurus",
"prefix": "18862"
},
"18863": {
"description": "The Gale Library Science Thesaurus is a subset of the master Gale Social Sciences thesaurus in the narrower domain of organizing knowledge and information, other than the purely philosophical terms. Also covered are library processes such as cataloging, as well as the business aspects such as abstracting and indexing services. Terms also describe kinds of libraries (e.g., government libraries, medical libraries) and cover related fields of information science, knowledge management, and information storage and retrieval. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 170 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Library Science Thesaurus",
"prefix": "18863"
},
"18864": {
"description": "The Gale Literature Thesaurus is a subset of the master Gale Humanities Thesaurus. This thesaurus includes subject areas related to authorship, literary criticism, cultural movements, fiction and nonfiction, literary forms and techniques, and literary occupations. Specific areas include literary genres, publishing, literary techniques, literary movements and groups, journalism, creative writing, reading, print formats such as books and periodicals, and oral traditions such as storytelling. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 2,049 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Literature Thesaurus",
"prefix": "18864"
},
"18865": {
"description": "The Gale Management Thesaurus is a subset of the master Gale Business Thesaurus in the narrower domain of business management. This includes terms related to corporations, businesses, executives, types of enterprises, and management and organizational theory. Most terms are not industry specific and this thesaurus does not include terms pertaining to business for which there are more specific terms, such as finance and accounting, marketing and advertising, commerce, human resources, investments, or public relations. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 585 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Management Thesaurus",
"prefix": "18865"
},
"18866": {
"description": "The Gale Marketing Thesaurus is a subset of the master Gale Business Thesaurus in the narrower domain of marketing. This includes terms related to sales, consumers, merchandizing, distribution, packaging, buying and selling, product development and introduction, and types of retailers. Marketing terms pertaining to specific types of products or industries are included. This thesaurus does not include terms dealing with advertising, which are in the Gale Advertising Thesaurus instead. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 550 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Marketing Thesaurus",
"prefix": "18866"
},
"18867": {
"description": "The Gale Materials Technology Thesaurus is a subset of the master Gale Technology Thesaurus in the narrower domain of the development, production, and use of metals, polymers, ceramics, semiconductors, and other materials in manufacturing, and the processes and technologies associated with them. Topics may include such things as film solar cells, super critical water oxidation, semiconductor developments, and other diverse processes and technologies. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,484 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Materials Technology Thesaurus",
"prefix": "18867"
},
"18868": {
"description": "The Gale Mathematics Thesaurus is a subset of the master Gale Science Thesaurus. This thesaurus includes terms associated with numbers and the use of numbers to count, measure, represent, or describe physical or abstract objects or the relationships or interrelations between such objects. Specific areas include number theory, arithmetic, algebra, geometry, calculus, statistics, discrete mathematics, mathematical analysis, and related fields. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 781 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Mathematics Thesaurus",
"prefix": "18868"
},
"18869": {
"description": "The Gale Medical Equipment, Technology and Procedures Thesaurus is a subset of the master Gale Health and Medicine Thesaurus in the narrower domain of equipment, supplies (except drugs), technologies, and procedures used to diagnose, treat, or prevent human or animal diseases and disorders. This thesaurus also includes medical specialties (e.g., Obstetrics). All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,884 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Medical Equipment, Technology and Procedures Thesaurus",
"prefix": "18869"
},
"18870": {
"description": "The Gale Medical Personnel, Occupations and Services Thesaurus is a subset of the master Gale Health and Medicine Thesaurus in the narrower domain of healthcare professionals and their assistants, healthcare educators and researchers, healthcare services, healthcare service administrators, support personnel, and public health workers and officials. Subject descriptors also feature items related to the education and training of personnel in a particular medical discipline (e.g., nursing school) as well as veterinarians and the veterinary works and the services they offer. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 664 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Medical Personnel, Occupations and Services Thesaurus",
"prefix": "18870"
},
"18871": {
"description": "The Gale Military and Naval Science Thesaurus is a subset of the master Gale Technology Thesaurus in the narrower domain of defense, training of soldiers, weaponry and armor, military strategy, ROTC, and military applications of various technologies as well as transportation, surveillance, and anything else the military owns or uses. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 669 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Military and Naval Science Thesaurus",
"prefix": "18871"
},
"18872": {
"description": "The Gale Occupations Thesaurus is a subset of the Gale Person Type Thesaurus and includes terms that represent vocational or professional pursuits. This thesaurus includes a full range of generic occupations covering subject areas such as agriculture, art, business, education, engineering, entertainment, government, information management, law, medicine, politics, science, sport, and transport. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,351 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Occupations Thesaurus",
"prefix": "18872"
},
"18873": {
"description": "The Gale Pathogens Thesaurus is a subset of the master Gale Health and Medicine Thesaurus in the narrower domain of organisms and substances that cause diseases or disorders in humans or animals. Examples include carcinogens, teratogens, and poisons. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 222 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Pathogens Thesaurus",
"prefix": "18873"
},
"18874": {
"description": "The Gale Performing Arts Thesaurus is a subset of the master Gale Humanities Thesaurus. This thesaurus includes subject areas related to acting and drama, comedy, entertainers, music, dance, films, opera, and theater. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,326 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Performing Arts Thesaurus",
"prefix": "18874"
},
"18875": {
"description": "The Gale Person Type Thesaurus focuses on describing people by a range of statuses and characteristics including gender, age, social role, nationality and ethnicity, and occupation. Includes terms that represent statuses, affiliations, personal qualities, etc. by which people can be categorized. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 4,420 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Person Type Thesaurus",
"prefix": "18875"
},
"18876": {
"description": "The Gale Physics Thesaurus is a subset of the master Gale Science Thesaurus. It includes terms associated with the study of matter, energy, and the interactions between matter and energy. Also included are terms associated with instruments and equipment used in physics research. Specific areas include mechanics, thermodynamics, forces, radiation, optics, acoustics, photonics, molecular physics, atomic physics, the phases of matter, quantum theory, and relativity and other areas of theoretical physics. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,240 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Physics Thesaurus",
"prefix": "18876"
},
"18877": {
"description": "The Gale Political Science Thesaurus is a subset of the master Gale Social Sciences Thesaurus in the narrower domain of the development, arrangement, and conduct of government, as well as the theories and the study of these processes. Also included are levels and kinds of government (local government, democracy, despotism, absolutism or tyranny), processes (elections), related activities (lobbyists, methods of change), movements (the American Civil Rights Movement), and actions such as misconduct in office. This thesaurus does not cover laws or legal procedures. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,797 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Political Science Thesaurus",
"prefix": "18877"
},
"18878": {
"description": "The Gale Products and Services Thesaurus comprises of all types of marketable products and services, as generic types, not brand names, both categories and highly specific things. Products include manufactured goods, processed goods, and raw materials, including plants, animals, and minerals if they are sold commercially. Services comprise all those that are available commercially. This thesaurus also features terms for broader classes of products such as animal products. This thesaurus does not include terms in fields related to product or services, only the products or services themselves. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 13,124 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Products and Services Thesaurus",
"prefix": "18878"
},
"18879": {
"description": "The Gale Psychology Thesaurus is a subset of the master Gale Social Sciences Thesaurus in the narrower domain of the study of the human psyche, emotions, reactions, mental processes, and individual behavior. Included are subdisciplines of psychology: psychopathology, human ecology, counseling, psychiatry, psychotherapy, peer counseling, sex therapy, child psychotherapy, and psychological disorders and treatments. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 2,007 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Psychology Thesaurus",
"prefix": "18879"
},
"1888": {
"description": "The 7th edition of the Health Thesaurus has been developed by the Departmental Library for use in all areas of the Department of Health. The Health Thesaurus is a living working tool which assists consistency and subject retrieval of health concepts. By standardising concepts to one single subject heading, the Thesaurus forms the basis for a common terminology within the Department.\n\nMeSH (medical Subject Headings) produced by the US National Library of Medicine has been used as the basis of the medical terms and the corresponding hierarchical schedules in the Health Thesaurus. We are very grateful for their permission to use MeSH in this way. For this edition 2004 MeSH has been used. Within the Department the Thesaurus has been used for the subject metadata element for the Departmental internet, to structure the relationship of terms in the Senior's Portal consumer website, to provide the automatic match of search terms for consumer health access in the HealthInsite gateway, and to give quality subject retrieval in the Library catalogue - which in turn allows easier access to Departmental and other publications. The Thesaurus is also used by a number of health related organisations in Australia. The Thesaurus can be used for classification or indexing of all types of documents and files, from personal files to corporate databases, and hence to assist in retrieval of corporate information. It is also used in Document management and Record management systems.",
"homepage": "http://www.health.gov.au/internet/main/publishing.nsf/Content/health-thesaurus.htm",
"name": "Health Thesaurus",
"prefix": "1888"
},
"18880": {
"description": "The Gale Public Relations Thesaurus is a subset of the master Gale Business Thesaurus in the narrower domain of public relations agencies. It includes terms in marketing communications, press relations, customer relations, investor relations, consumer education advertising, public service advertising, advocacy advertising, social cause advertising, corporate image, publicity, propaganda, and corporate social responsibility. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 47 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Public Relations Thesaurus",
"prefix": "18880"
},
"18881": {
"description": "The Gale Real Estate Thesaurus is a subset of the master Gale Business Thesaurus in the narrower domain of the business of developing, managing, financing, buying, selling, leasing, renting, and investing in real property. It includes terms related to office buildings, shopping centers, commercial property, and all types of housing. Also featured are terms related to real estate development, real estate agents and brokers, real estate management firms, real estate management, real estate investment, real estate investment trusts, title companies, mortgage banks, mortgage brokers, real estate lessors, and real property. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 318 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Real Estate Thesaurus",
"prefix": "18881"
},
"18882": {
"description": "The Gale Religion and Philosophy Thesaurus is a subset of the master Gale Humanities Thesaurus. This thesaurus includes subject areas related to world religions, religious law, religious occupations and organizations, rituals and symbolism, morality, philosophers, reasoning, and philosophical thought. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 2,364 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Religion and Philosophy Thesaurus",
"prefix": "18882"
},
"18883": {
"description": "The Gale Science Thesaurus contains the key subject areas of astronomy, biology, chemistry, earth sciences, mathematics, physics, and psychology. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 21,384 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Science Thesaurus",
"prefix": "18883"
},
"18884": {
"description": "The Gale Social Sciences thesaurus is a large thesaurus in the domain of anthropology, economics, education, geography, history, law, library science, political science, psychology, sociology, and sports/recreation. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 13,614 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Social Sciences Thesaurus",
"prefix": "18884"
},
"18885": {
"description": "The Gale Sociology Thesaurus is a subset of the master Gale Social Sciences Thesaurus in the narrower domain of the practice of sociology and the study of complex human societies, social groups (from families to nations), and the institutions, processes, movements, issues, and behavior related to those groupings. It includes subfields such as political sociology and methods of sociology. Also provided are terms for social arrangements like slavery, intergroup relations, and concubinage. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,716 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Sociology Thesaurus",
"prefix": "18885"
},
"18886": {
"description": "The Gale Sports and Recreation Thesaurus is a subset of the master Gale Social Sciences Thesaurus in the narrower domain of specific sports, sporting events, hobbies, and other recreational activities, whether engaged in by individuals or groups, amateurs, or professionals, for simple pleasure or competitive success. Also covered is the business of sports. Examples of subject descriptors in this thesaurus include sprinting, long-distance running races, arena football, windsurfing, safaris, bird watching, and stamp collecting. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,194 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Sports and Recreation Thesaurus",
"prefix": "18886"
},
"18887": {
"description": "The Gale Taxation Thesaurus is a subset of the master Gale Business Thesaurus in the narrower domain of the processes associated with the assessment and collection of federal, state, and municipal taxes. It includes terms related to tax administration, policy, law, rates, credits, exemptions, incentives, shelters, penalties, and liens. This thesaurus also includes terms related to income tax, corporate taxes, sales tax, withholding tax, estate taxes, social security taxes, use taxes, tariffs, tax treaties, tax reform, and tax planning. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 202 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Taxation Thesaurus",
"prefix": "18887"
},
"18888": {
"description": "The Gale Technology thesaurus is a large general technology thesaurus in the domains of aeronautics and astronautics, chemical technology, communications, computing, electronics, energy, engineering, materials, military and naval science, and transportation. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 10,031 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Technology Thesaurus",
"prefix": "18888"
},
"18889": {
"description": "The Gale Transportation Thesaurus is a subset of the master Gale Technology Thesaurus in the narrower domain of modes and mediums of transportation, except for those whose main application is military - such as troop transports, battleships, military aircraft, and tanks. Aside from the obligatory planes, trains, and automobiles, transportation also includes things such as forklifts, conveyor belts, and any other device or means for getting something or someone from one point to another including roads, tunnels, and bridges. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 1,397 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Transportation Thesaurus",
"prefix": "18889"
},
"1889": {
"description": "The IUPAC system of polymer nomenclature has aided the generation of unambiguous names that reflect the historical development of chemistry. However, the explosion in the circulation of information and the globalization of human activities mean that it is now necessary to have a common language for use in legal situations, patents, export-import regulations, and environmental health and safety information. Rather than recommending a 'unique name' for each structure, rules have been developed for assigning 'preferred IUPAC names', while continuing to allow alternatives in order to preserve the diversity and adaptability of nomenclature.\n\nThis new edition of the 'Purple Book' (...) collects into a single volume the most important papers on the nomenclature and terminology of most polymers, including Regular Single-Strand Organic Polymers, Regular Double-Strand (Ladder and Spiro) Organic Polymers, and Irregular Single-Strand Organic Polymers. The scope has been extended to include papers on terminology for polymers. It is a handy compendium for scientists and is invaluable for those professionals working in this field.",
"name": "IUPAC Compendium of Polymer Terminology and Nomenclature",
"prefix": "1889"
},
"18890": {
"description": "The Gale Wellness Thesaurus is a subset of the master Gale Health and Medicine Thesaurus in the narrower domain of wellness and fitness topics and issues. It includes terms associated with physical, mental, and emotional health, including terms related to diet, exercise, activities, products, and habits that affect human well-being. All thesaural relationships (BT/NT, RT, USE/UF) are included, and some terms have scope notes. The thesaurus contains 389 preferred terms/concepts (2019) and is continually updated.",
"homepage": "https://www.gale.com/license/partners/taxonomies-and-vocabularies",
"name": "Gale Wellness Thesaurus",
"prefix": "18890"
},
"18891": {
"abbreviation": "UBBI",
"description": "The classification system of Bielefeld University Library is a universal shelf classification developed in the 1960s with the foundation of the University.",
"homepage": "https://www.ub.uni-bielefeld.de/databases/systematik/",
"license": "CC0-1.0",
"name": "Bielefeld University Library Classification System",
"prefix": "18891",
"wikidata_database": "Q61809660"
},
"18892": {
"description": "This project, undertaken during the summer of 2018 intended to build a system that is reflective of the mission and values of the Out On The Shelves Library, namely to \"foster a free, accessible, and safe space for LGBTQ2IA+ people and their allies to discover and share stories and resources centering on LGBTQ2IA+ experiences\" (About: Out On The Shelves) To this end, goals for the new system β approved by the volunteer team at Out On The Shelves Library during the planning process β include updated language, logical order and arrangement to enhance the browsing experience, as well as ensuring it is a living system which is responsive to context and community. The final goal is that a historical record will be maintained to promote transparency in how and why the system came to be the way it is.",
"homepage": "https://outontheshelveslibrary.com/classification-system/",
"name": "Out On The Shelves Classification System",
"prefix": "18892"
},
"18893": {
"description": "The Thesaurus of Scientific Instruments in Portuguese aims at normalising and controlling terminology associated with historical collections of artefacts of science. It can be used freely by museums, institutions with scientific heritage, historians of science, conservators and restorers, among others.\n\nThe Thesaurus is regularly updated. Its first phase was developed by a network of Brazilian and Portuguese institutions between 2006 and 2013, coordinated by the National Museum of Natural History and Science (University of Lisbon) and the Museum of Astronomy and Related Sciences, Rio de Janeiro (MAST). It was financed by the Conselho Nacional de Desenvolvimento CientΓfico e TecnolΓ³gico (CNPq) in Brazil and the Fundação para a CiΓͺncia e Tecnologia (FCT) in Portugal.",
"homepage": "http://thesaurusonline.museus.ul.pt/",
"name": "Thesaurus of Scientific Instruments in Portuguese",
"prefix": "18893"
},
"18894": {
"description": "Bokbasen has a hierarchical thesaurus with controlled free-standing keywords. The thesaurus was established in the 1980s, and is continuously maintained and further developed by Bokbasen's catalog department. The file contains the five main categories of topics, form, genre, time and place, in BokmΓ₯l and Nynorsk.",
"homepage": "https://github.com/Bokbasen/metadata-thesaurus",
"name": "Bokbasen Thesaurus",
"prefix": "18894"
},
"18895": {
"description": "The PARTAGE PLUS VOCABULARY is a structured multilingual controlled vocabulary. It consists of components for the enrichment of metadata created for cultural heritage objects relating to Art Nouveau aesthetic production encompassing the visual arts, crafts and architecture, - referencing to and mainly based on the Art & Architecture Thesaurus of the Getty Research Institute. The controlled vocabulary contains 705 concepts represented by labels in 16 languages for the indexing of cultural heritage metadata, referring to object/work types; techniques; materials; actor roles and Art Nouveau style specific differentiation. (...) The vocabulary is available for free reuse.",
"name": "Partage Plus Vocabulary",
"prefix": "18895"
},
"18896": {
"license": "CC-BY-3.0",
"name": "WO2 Thesaurus",
"prefix": "18896"
},
"18897": {
"description": "This resource presents an attempt to link the large amount of different concept lists which are used in the linguistic literature, ranging from Swadesh lists in historical linguistics to naming tests in clinical studies and psycholinguistics. (...) This resource, our Concepticon, links concept labels from different conceptlists to concept sets. Each concept set is given a unique identifier, a unique label, and a human-readable definition. Concept sets are further structured by defining different relations between the concepts (...). The resource can be used for various purposes. Serving as a rich reference for new and existing databases in diachronic and synchronic linguistics, it allows researchers a quick access to studies on semantic change, cross-linguistic polysemies, and semantic associations.",
"homepage": "https://concepticon.clld.org/",
"license": "CC-BY-3.0",
"name": "Concepticon",
"prefix": "18897"
},
"18898": {
"description": "KBpedia is a comprehensive knowledge structure for promoting data interoperability and knowledge-based artificial intelligence, or KBAI. The KBpedia knowledge structure combines seven 'core' public knowledge bases β Wikipedia, Wikidata, schema.org, DBpedia, GeoNames, OpenCyc, and UMBEL β into an integrated whole. KBpedia's upper structure, or knowledge graph, is the KBpedia Knowledge Ontology. We base KKO on the universal categories and knowledge representation theories of the great 19th century American logician, polymath and scientist, Charles Sanders Peirce.\n\nKBpedia, written primarily in OWL 2, includes 55,000 reference concepts, mapped linkages to about 32 million entities (most from Wikidata), and 5,000 relations and properties, all organized according to about 70 modular typologies that can be readily substituted or expanded. We test candidates added to KBpedia using a rigorous (but still fallible) suite of logic and consistency tests β and best practices β before acceptance. The result is a flexible and computable knowledge graph that can be sliced-and-diced and configured for all sorts of machine learning tasks, including supervised, unsupervised and deep learning.\n\nKBpedia, KKO and its mapped information can drive multiple use cases such as providing a computable framework over Wikipedia and Wikidata, creating word embedding models, fine-grained entity recognition and tagging, relation and sentiment extractors, and categorization. Knowledge-based AI models may be set up and refined with unprecedented speed and accuracy by leveraging the integrated KBpedia structure.",
"homepage": "http://kbpedia.org/",
"license": "CC-BY-3.0",
"name": "KBpedia",
"prefix": "18898"
},
"18899": {
"description": "Controlled list of Subject Schemes",
"homepage": "http://id.loc.gov/vocabulary/subjectSchemes",
"name": "Library of Congress Subject Schemes",
"prefix": "18899"
},
"189": {
"description": "In each microthesaurus, the descriptors are organized in a hierarchical way and represent the semantic organization of a domain.",
"homepage": "http://www.uclouvain.be/promosanthes.html",
"name": "Promosanthes",
"prefix": "189"
},
"1890": {
"description": "The index of this edition contains ca 6,000 entries. The cross-references may help the readers to find the correct terms which they are looking for. (...) It is expected that the readers who are interested in IUPAC recommendations concerning analytical terms and definitions will be able to find them quickly and easily in the Compendium. In the text of the Compendium there are, occasionally, contradicting definitions which result from the fact that the experts of different fields - while trying to do their best-hold different views on certain key issues. One of the missions of this Compendium may be to stimulate a higher level of conformity and communication between the experts in rapidly developing areas of science.",
"name": "IUPAC Compendium of Analytical Nomenclature",
"prefix": "1890",
"wikidata_database": "Q2990408"
},
"18900": {
"description": "Controlled list of Classification Schemes",
"homepage": "http://id.loc.gov/vocabulary/classSchemes",
"name": "Library of Congress Classification Schemes",
"prefix": "18900"
},
"18901": {
"description": "A system of classification for Cultural Heritage Organizations developed by the Library of Congress.",
"homepage": "http://id.loc.gov/vocabulary/organizations",
"name": "Library of Congress Cultural Heritage Organizations",
"prefix": "18901"
},
"18902": {
"description": "This list includes terms that describe general categories, or genres that may be applied to various types of information resources. It has been compiled from controlled lists of values in various data elements in the MARC 21 Format for Bibliographic Data.",
"homepage": "http://id.loc.gov/vocabulary/marcgt",
"name": "Library of Congress MARC Genre Terms",
"prefix": "18902"
},
"18903": {
"homepage": "http://id.loc.gov/vocabulary/genreFormSchemes",
"name": "Library of Congress Genre/Form Schemes",
"prefix": "18903"
},
"18904": {
"description": "The MARC Code List for Countries contains a list of places and their associated two- or three-character lowercase alphabetic codes.",
"homepage": "http://id.loc.gov/vocabulary/countries",
"name": "Library of Congress MARC Countries",
"prefix": "18904"
},
"18905": {
"description": "The MARC Code List for Geographic Areas consists of a list of geographic areas and their associated one to seven-character codes.",
"homepage": "http://id.loc.gov/vocabulary/geographicAreas",
"name": "Library of Congress MARC Geographic Areas",
"prefix": "18905"
},
"18906": {
"description": "This list contains Resource Description and Access (RDA) terms and corresponding three-character lower case alphabetic codes for RDA Content types.",
"homepage": "http://id.loc.gov/vocabulary/contentTypes",
"name": "Library of Congress Content Types",
"prefix": "18906"
},
"18907": {
"description": "A list containing storage containers for data.",
"homepage": "http://id.loc.gov/vocabulary/carriers",
"name": "Library of Congress Carriers",
"prefix": "18907"
},
"18908": {
"description": "Convention Sources identifies standard rules or guidelines for describing bibliographic resources, commonly called cataloging rules, and assigns a code to each source. The purpose of this list is to enable the source of description guidelines in metadata records to be indicated by a code.",
"homepage": "http://id.loc.gov/vocabulary/descriptionConventions",
"name": "Library of Congress Description Conventions",
"prefix": "18908"
},
"18909": {
"description": "A list containing the degree of the level of an encoding.",
"homepage": "http://id.loc.gov/vocabulary/menclvl",
"name": "Library of Congress MARC Encoding Level",
"prefix": "18909"
},
"1891": {
"description": "The Biochemical Nomenclature and Related Documents (1992) presents IUPAC-IUBMB (International Union of Biochemistry and Molecular Biology) Joint Commissions' recommendations; it includes sections on amino acids, peptides and proteins, enzymes, nucleotides, nucleic acids and protein synthesis, carbohydrates, lipids, etc.",
"homepage": "http://www.chem.qmul.ac.uk/iupac/bibliog/white.html",
"name": "IUPAC Biochemical Nomenclature",
"prefix": "1891"
},
"18910": {
"description": "A list containing the file types on which data is saved on.",
"homepage": "http://id.loc.gov/vocabulary/mfiletype",
"name": "Library of Congress MARC File Type",
"prefix": "18910"
},
"18911": {
"description": "A list containing images of MARC data.",
"homepage": "http://id.loc.gov/vocabulary/millus",
"name": "Library of Congress MARC Illustrative Content",
"prefix": "18911"
},
"18912": {
"description": "A method or system used to represent the surface of the Earth or of a celestial sphere on a plane.",
"homepage": "http://id.loc.gov/vocabulary/mprojection",
"name": "Library of Congress Projection",
"prefix": "18912"
},
"18913": {
"description": "Used to encode the video content of a resource",
"homepage": "http://id.loc.gov/vocabulary/mvidformat",
"name": "Library of Congress Video Format",
"prefix": "18913"
},
"18914": {
"description": "There are three classification parts:\n\n- by subject group (\"FΓ€chergruppe\")\n\n- by study area (\"Studienbereiche\")\n\n- by field of study (\"Studienfelder\")\n\nEverything study-related inside the Hochschulkompass can be assigned to one or more fields of study. A field of study includes a partition of a knowledge- or topic area, where similar study courses are compiled.\n\nMultiple fields of study belong to a certain study area and multiple study areas belong to a subject group.\n\nIn the Hochschulkompass all possibilities for studying are structured around knowledge- or topic areas, meaning that you are able to start at subject group and go down the ladder step-by-step until you find the courses you want.",
"name": "Subject classification for higher education in Germany",
"prefix": "18914",
"wikidata_database": "Q1622262"
},
"18915": {
"abbreviation": "ZDB-FGS",
"description": "This classification was used in the German Union Catalogue of Serials until 2010 to classify journals. It was then replaced by the DDC.",
"name": "ZDB-Classification",
"pattern": "^[0-9]+$",
"prefix": "18915"
},
"18916": {
"description": "ISOcat ist ein Verzeichnis fΓΌr alle Konzepte, die Relevanz haben fΓΌr Linguistik und den Bereich Sprachquellen inklusive Metadatenkategorien usw..",
"name": "ISOCAT",
"prefix": "18916",
"wikidata_database": "Q5974188"
},
"18917": {
"description": "The german games-archive in Marburg (now Nuremberg) created a classification for board- and tablegames, which is used for archiving.",
"homepage": "http://www.michaelkleinschmidt.de/spiele/klassifikation/index.htm",
"name": "Classification of board games",
"prefix": "18917"
},
"18918": {
"description": "The german games-archive in Marburg (now Nuremberg) created a Classification, which differentiates classes between goals, mechanisms or both.",
"homepage": "http://www.michaelkleinschmidt.de/spiele/klassifikation/kartenspiele/index.htm",
"name": "Classification of card games",
"prefix": "18918"
},
"18919": {
"homepage": "https://www.destatis.de/DE/Methoden/Klassifikationen/Bildung/studenten-pruefungsstatistik.html",
"prefix": "18919"
},
"1892": {
"description": "The purpose of this manual is to improve the exchange of scientific information among the readers in different disciplines and across different nations. As the volume of scientific literature expands, each discipline has a tendency to retreat into its own jargon. This book attempts to provide a readable compilation of widely used terms and symbols from many sources together with brief understandable definitions. This Third Edition reflects the experience of the contributors with the previous editions and we are grateful for the many thoughtful comments we have received. Most of the material in this book is 'standard', but a few definitions and symbols are not universally accepted. In such cases, we have attempted to list acceptable alternatives.",
"name": "IUPAC Quantities, Units and Symbols in Physical Chemistry",
"prefix": "1892",
"wikidata_database": "Q779430"
},
"18920": {
"abbreviation": "DFΓ",
"homepage": "https://www.destatis.de/DE/Themen/Gesellschaft-Umwelt/Bildung-Forschung-Kultur/Hochschulen/Publikationen/_publikationen-innen-hochschulen-personal.html",
"pattern": "^[0-9]+$",
"prefix": "18920"
},
"18928": {
"abbreviation": "SSG",
"description": "The Sondersammelgebiets-Nummer was used in German libraries until 2015 to organize distributed collection of publications among disciplines. In 2016 it was replaced by FID codes.",
"homepage": "https://www.zeitschriftendatenbank.de/suche/fachgebiete/",
"pattern": "^[1-9]?[0-9](,[0-9]{1,3})?$",
"prefix": "18928",
"wikidata_database": "Q71786666"
},
"18929": {
"abbreviation": "FID",
"description": "The FID classification replaced the Sondersammelgebiets-Nummer (SSG) in 2016",
"homepage": "https://www.zeitschriftendatenbank.de/suche/fachgebiete/",
"name": "FID classification",
"pattern": "^FID-[A-Z]+$",
"prefix": "18929",
"wikidata_database": "Q71787657"
},
"1893": {
"description": "This page provides a survey of the different classes of meteorites. While the first part mirrors the systematic classification of meteorites, the second part represents an alphabetical index. Both parts contain direct hyperlinks leading to the respective descriptions of each class - just click on a name to get further information.",
"homepage": "http://www.meteorite.fr/en/classification/",
"name": "Meteorite Classification",
"prefix": "1893"
},
"1894": {
"abbreviation": "UMDNS",
"description": "Universal Medical Device Nomenclature Systemβ’ (UMDNS) is a standard, free of charge, monthly updated, international nomenclature and computer coding system to help you better manage medical devices. UMDNS is the worldwide nomenclature that has been officially adopted by many nations.\n\nThe purpose of UMDNS is to facilitate identifying, processing, filing, storing, retrieving, transferring, and communicating data about medical devices. The nomenclature is used in applications ranging from hospital inventory and work-order controls to national agency medical device regulatory systems and from e-commerce and procurement to medical device databases.",
"homepage": "https://www.ecri.org/components/UMDNS/",
"name": "Universal Medical Device Nomenclature Systemβ’",
"prefix": "1894"
},
"1895": {
"abbreviation": "UCUM",
"description": "The Unified Code for Units of Measure is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business. The purpose is to facilitate unambiguous electronic communication of quantities together with their units. The focus is on electronic communication, as opposed to communication between humans. A typical application of The Unified Code for Units of Measure are electronic data interchange (EDI) protocols, but there is nothing that prevents it from being used in other types of machine communication. How does it relate?\n\nThe Unified Code for Units of Measure is inspired by and heavily based on ISO 2955-1983, ANSI X3.50-1986, and HL7's extensions called ISO+. The respective ISO and ANSI standards are both entitled Representation of [...] units in systems with limited character sets where ISO 2955 refers to SI and other units provided by ISO 1000-1981, while ANSI X3.50 extends ISO 2955 to include U.S. customary units. Because these standards carry the restriction of limited character sets in their names they seem to be of less value today where graphical user interface and laser printers are in wide-spread use, which is why the european standard ENV 12435 in its clause 7.3 declares ISO 2955 obsolete.\n\nENV 12435 is dedicated exclusively to the communication of measurements between humans in display and print, and does not provide codes that can be used in communication between systems. It does not even provide a specification that would allow communication of units from one system to the screen or printer of another system. The issue about displaying units in the common style defined by the 9th ConfΓ©rence GΓ©nΓ©rale des Poids et Mesures (CGPM) in 1947 is not just the character set. Although The Unicode Standard and its predecessor ISO/IEC 10646 is the richest character set ever it is still not enough to specify the presentation of units because there are important typographical details such as superscripts, subscripts, roman and italics.\"\n\nSeveral URI namespaces and encoding methods have been proposed to map UCUM codes to URIs.",
"homepage": "http://unitsofmeasure.org/",
"name": "Unified Code for Units of Measure",
"prefix": "1895",
"wikidata_database": "Q2494286"
},
"1897": {
"description": "LOINC was initiated in 1994 by Clem McDonald, an investigator at the Regenstrief Institute, which is an internationally respected non-profit medical research organization associated with Indiana University. Regenstrief organized the LOINC committee to develop a common terminology for laboratory and clinical observations because there was a growing trend to send clinical data electronically from laboratories and other data producers to hospitals, physician's offices, and payers who use the data for clinical care and management purposes.\n\nAt the time, and still today, most laboratories and clinical services use HL7 to send their results electronically from their reporting systems to their care systems. However, the tests in these messages are identified by means of their internal, idiosyncratic code values. As a result, receiving care system cannot fully \"understand\" and properly file the results they receive unless they either adopt the producer's test codes (which is impossible if they receive results from multiple sources), or invest in the work to map each result producer's code system to their internal code system.\n\nHere's the problem that LOINC solves: LOINC provides universal codes and names that provide the global lingua franca for identifying tests and observations.",
"homepage": "http://loinc.org/",
"name": "LOINC",
"prefix": "1897",
"wikidata_database": "Q502480"
},
"1898": {
"description": "We know that some terms that we use, or that you may come across, may be unfamiliar to you, so we have come up with this glossary of terms to make things easier.",
"homepage": "http://www.palgrave.com/page/glossary-of-publishing-terms/",
"name": "Glossary of Academic Publishing Terms",
"prefix": "1898"
},
"1899": {
"abbreviation": "PhySH",
"description": "PhySH (Physics Subject Headings) is a physics classification scheme developed by the American Physical Society to organize journals, meetings, and other content by topic. The development of PhySH is motivated by the lack of a fully open, high quality classification scheme for physics. It is intended initially to meet the specific goals of the APS for our journal, meeting, and other content. A longer term goal is to make it available for use by the broader community. (...) Right now, the main use of PhySH is to classify manuscripts within the APS peer-review process and, ultimately, published journal articles. The assigned concepts will be used for ensuring articles are routed to the most appropriate handling editor who is knowledgeable in that area. They also help editors in finding similar articles previously submitted and in finding suitable referees.\n\nAs one might expect with something so new, the refinement of PhySH is still very much underway. The facets and disciplines have been identified and almost 3,000 concepts have been added to PhySH through an iterative process that is still ongoing. Many APS journal editors are involved in this process, primarily by lending their expertise in the various subfields in physics. The assignment of concepts to the various facets can be rather subjective. Thus, we expect to make many adjustments to PhySH as we receive feedback from the community (especially authors using PhySH to classify their submissions) and as we incorporate PhySH into the APS journal websites. As we iteratively refine PhySH over the coming months, the rate of new concept additions, concept reassignments within facets, and new relationships among concepts should abate significantly.",
"homepage": "https://physh.aps.org/",
"license": "CC0-1.0",
"name": "Physics Subject Headings",
"pattern": "^[0-9a-z-]+$",
"prefix": "1899",
"wikidata_database": "Q30523272"
},
"19": {
"abbreviation": "HASSET",
"description": "The Humanities and Social Science Electronic Thesaurus (HASSET) is the leading British English thesaurus for the social sciences. It was originally developed from the UNESCO thesaurus, becoming a separate product in 1997. HASSET is a working tool for the keyword annotation and retrieval of UK Data Service data. It consists of over 4,000 concepts and covers the core social science disciplines: politics, sociology, economics, education, law, crime, demography, health, employment, information and communication technology, history and, increasingly, environmental science.\nThe thesaurus can be used to find studies in the UK Data Service Data Catalogue. These studies include large-scale government surveys, international macrodata, business microdata, qualitative studies, historical studies and census data.\nRevisions to HASSET concepts and structures aim to keep abreast with developments in social science and humanities.",
"homepage": "http://hasset.ukdataservice.ac.uk/",
"license": "CC BY-SA 4.0",
"name": "Humanities and Social Science Electronic Thesaurus",
"pattern": "^[0-9a-f-]{36}$",
"prefix": "19",
"uri_format": "https://hasset.ukdataservice.ac.uk/$1"
},
"190": {
"description": "109 terms, 46 terms not preferred.",
"homepage": "http://fundacionevolucion.org.ar/repeal/",
"name": "School Networks and Educational Portals of Latin America",
"prefix": "190"
},
"19008": {
"description": "This table provides a list of options for the use of accessibility criteria for person with disabilities in the technical specifications within the domain of public procurement.",
"homepage": "http://publications.europa.eu/resource/authority/accessibility",
"license": "CC0-1.0",
"name": "Accessibility Name Authority List",
"prefix": "19008"
},
"19009": {
"description": "This table provides a list of the options pertinent to be chosen for a matter concerning the applicability of predefined fields. It is designed for but not restricted to the context of public procurement.",
"homepage": "http://publications.europa.eu/resource/authority/applicability",
"license": "CC0-1.0",
"name": "Applicability Name Authority List",
"prefix": "19009"
},
"19010": {
"description": "This table provides the list of rules to be taken into account for the award decisions within the in public procurement procedures. The initial values are those foreseen in the public procurement directives of 2014 (Directives 2014/23/EU, 2014/24/EU and 2014/25/EU). The translations provided are those used in the Commission Implementing Regulation (EU) 2015/1986 establishing standard forms for the publication of notices in the field of public procurement.",
"homepage": "http://publications.europa.eu/resource/authority/award-criterion-type",
"license": "CC0-1.0",
"name": "Award criterion type Name Authority List",
"prefix": "19010"
},
"19011": {
"description": "This table provides a list of the the type of procuring authorities within the domain of public procurement according to legislation.",
"homepage": "http://publications.europa.eu/resource/authority/buyer-legal-type",
"license": "CC0-1.0",
"name": "Buyer legal type Name Authority List",
"prefix": "19011"
},
"19012": {
"description": "This table provides the codes and values used in case of justification of correcions applied to a notice within the context of public procurement.",
"homepage": "http://publications.europa.eu/resource/authority/change-corrig-justification",
"license": "CC0-1.0",
"name": "Change corrig justification Name Authority List",
"prefix": "19012"
},
"19013": {
"description": "COM internal consultation type Named Authority List",
"homepage": "http://publications.europa.eu/resource/authority/com-internal-consultation-type",
"license": "CC0-1.0",
"name": "COM internal consultation type Name Authority List",
"prefix": "19013"
},
"19014": {
"description": "COM internal event Named Authority List",
"homepage": "http://publications.europa.eu/resource/authority/com-internal-event",
"license": "CC0-1.0",
"name": "COM internal event Name Authority List",
"prefix": "19014"
},
"19015": {
"description": "COM internal procedure Named Authority List",
"homepage": "http://publications.europa.eu/resource/authority/com-internal-procedure",
"license": "CC0-1.0",
"name": "COM internal procedure Name Authority List",
"prefix": "19015"
},
"19016": {
"description": "This table provides the justification for restricting access rights to resources within the context of public procurement.",
"homepage": "http://publications.europa.eu/resource/authority/communication-justification",
"license": "CC0-1.0",
"name": "Communication justification Name Authority List",
"prefix": "19016"
},
"19017": {
"description": "This table is an internal table at the Publications Office and provides the various statuses used in a harmonized way amongst the various tables (NALs).",
"homepage": "http://publications.europa.eu/resource/authority/concept-status",
"license": "CC0-1.0",
"name": "Concept status Name Authority List",
"prefix": "19017"
},
"19018": {
"description": "This table provides a list of different types of subjects and goods that can be acquired by means of a public contract such as works, supplies and services by one or more contracting authorities from economic operators.",
"homepage": "http://publications.europa.eu/resource/authority/contract-nature",
"license": "CC0-1.0",
"name": "Contract nature Name Authority List",
"prefix": "19018"
},
"19019": {
"description": "The Digital Europa Thesaurus (DET) is a multilingual thesaurus covering the main subject matters of the European Commission's public communications.",
"homepage": "http://publications.europa.eu/resource/authority/det",
"license": "CC0-1.0",
"name": "Digital Europa Thesaurus",
"prefix": "19019"
},
"1902": {
"description": "The celestial Emporium of benevolent knowledge is a certain Chinese encyclopedia fiction by the Argentine writer Jorge Luis Borges in the essay The analytical idiom of John Wilkins ... Borges says in said story: '(...) there is notoriously The reason is very simple: we do not know what the universe is' (...) This list, whose 'discovery' Borges attributes to Franz Kuhn, has given rise to a multiplicity of philosophical commentaries And literary, such as the beginning of the preface to Michel Foucault 's Words and Things, Louis Sass suggests that he reveals a schizophrenic thought.In contrast, linguist George Lakoff points out that the list is similar in many categorizations of non - Western cultures. ..).",
"name": "Celestial Emporium of Benevolent Knowledge",
"prefix": "1902",
"wikidata_database": "Q1966912"
},
"19020": {
"description": "This table provides the list of reasons for using a procedure which allows awarding contracts directly without the requirement of publishing a call for competition in the Official Journal of the European Union.",
"homepage": "http://publications.europa.eu/resource/authority/direct-award-justification",
"license": "CC0-1.0",
"name": "Direct award justification Name Authority List",
"prefix": "19020"
},
"19021": {
"description": "This technical table provides the codes used for internal purposes in the CELLAR application.",
"homepage": "http://publications.europa.eu/resource/authority/document-collection",
"license": "CC0-1.0",
"name": "Document collection Name Authority List",
"prefix": "19021"
},
"19022": {
"description": "This table provides a list wether a dynamic purchasing system is involved in a procurement and, in case of central purchasing bodies, whether it can be used by buyers not listed in the notice of the Official Journal of the European Union.",
"homepage": "http://publications.europa.eu/resource/authority/dps-usage",
"license": "CC0-1.0",
"name": "DPS usage Name Authority List",
"prefix": "19022"
},
"19023": {
"description": "This table provides the different categories in which the tenderers to whom a contract can be awarded are classified, according to their size (using as criteria the number of employees).",
"homepage": "http://publications.europa.eu/resource/authority/economic-operator-size",
"license": "CC0-1.0",
"name": "Economic operator size Name Authority List",
"prefix": "19023"
},
"19024": {
"description": "This table provides the information about whether a procurement includes (and how) an approach to reducing the environmental impacts of the work, supply or service used in the technical specifications, award criteria, selection criteria or contract performance conditions or not.",
"homepage": "http://publications.europa.eu/resource/authority/environmental-impact",
"license": "CC0-1.0",
"name": "Environmental impact Name Authority List",
"prefix": "19024"
},
"19025": {
"description": "The file-status authority table describes the different stages in the life cycle of an act (or in the decision-making process of an act) from the moment it is launched until the final step is completed.",
"homepage": "http://publications.europa.eu/resource/authority/file-status",
"license": "CC0-1.0",
"name": "File status Name Authority List",
"prefix": "19025"
},
"19026": {
"description": "This table provides the codes and values used for the type of forms according to procurement legislation.",
"homepage": "http://publications.europa.eu/resource/authority/form-type",
"license": "CC0-1.0",
"name": "Form type Name Authority List",
"prefix": "19026"
},
"19027": {
"description": "This table provides the list of codes to distinguish the different type framework agreement involved in a tender.",
"homepage": "http://publications.europa.eu/resource/authority/framework-agreement",
"license": "CC0-1.0",
"name": "Framework agreement Name Authority List",
"prefix": "19027"
},
"19028": {
"description": "The Grammatical number NAL provides the list of the grammatical numbers.",
"homepage": "http://publications.europa.eu/resource/authority/grammatical-number",
"license": "CC0-1.0",
"name": "Grammatical number Name Authority List",
"prefix": "19028"
},
"19029": {
"description": "This table provides the codes and values used for the type of innovative works, supplies or services being procured within the context of public procurement.",
"homepage": "http://publications.europa.eu/resource/authority/innovative-acquisition",
"license": "CC0-1.0",
"name": "Innovative acquisition Name Authority List",
"prefix": "19029"
},
"1903": {
"homepage": "http://sammlungen-archive.zhdk.ch/allcategories",
"name": "eMuseum Kategorien",
"prefix": "1903"
},
"19030": {
"description": "The Interinstitutional procedures NAL lists the different procedures used in the context of data exchange between the institutions involved in the legislative process.",
"homepage": "http://publications.europa.eu/resource/authority/procedure",
"license": "CC0-1.0",
"name": "Interinstitutional procedure Name Authority List",
"prefix": "19030"
},
"19031": {
"description": "This table provides the legal basis based on the legal acts used for a given public procurement procedure. The table is provided by the Publications Office.",
"homepage": "http://publications.europa.eu/resource/authority/legal-basis",
"license": "CC0-1.0",
"name": "Legal basis Name Authority List",
"prefix": "19031"
},
"19032": {
"description": "This table provides the list of main activities of the buyers.\n\n\t\t\t\t\t The codes associated with contracting authorities are derived from the top level of the Classification of the functions of the government (COFOG) from the United Nations Statistics Division.\n\n\t\t\t\t\t The codes associated with contracting entities are derived from sectors explicitly falling within the sectoral directive (2014/25/EU Art. 8 - Art. 14).",
"homepage": "http://publications.europa.eu/resource/authority/main-activity",
"license": "CC0-1.0",
"name": "Main activity Name Authority List",
"prefix": "19032"
},
"19033": {
"description": "Measurement unit",
"homepage": "http://publications.europa.eu/resource/authority/measurement-unit",
"license": "CC0-1.0",
"name": "Measurement unit Name Authority List",
"prefix": "19033"
},
"19034": {
"description": "This table provides the list of codes indicating wether tenderer-related information (complete or parcial) can be supplemented even after the submission deadline.",
"homepage": "http://publications.europa.eu/resource/authority/missing-info-submission",
"license": "CC0-1.0",
"name": "Missing info submission Name Authority List",
"prefix": "19034"
},
"19035": {
"description": "This table provides the main reasons for modifying a contract within the domain of public procurement.",
"homepage": "http://publications.europa.eu/resource/authority/modification-justification",
"license": "CC0-1.0",
"name": "Modification justification Name Authority List",
"prefix": "19035"
},
"19036": {
"description": "This table provides the list of reasons of the buyer for not choosing a winner in the procurement procedure.",
"homepage": "http://publications.europa.eu/resource/authority/non-award-justification",
"license": "CC0-1.0",
"name": "Non award justification Name Authority List",
"prefix": "19036"
},
"19037": {
"description": "This table provides a list of public procurement notices according to procurement legislation published once a project is approved.",
"homepage": "http://publications.europa.eu/resource/authority/notice-type",
"license": "CC0-1.0",
"name": "Notice type Name Authority List",
"prefix": "19037"
},
"19038": {
"description": "This table provides the codes linked to fix values within the context of public procurement.",
"homepage": "http://publications.europa.eu/resource/authority/number-fixed",
"license": "CC0-1.0",
"name": "Number fixed Name Authority List",
"prefix": "19038"
},
"19039": {
"description": "This table provides the codes linked to the type of threshold values within the context of public procurement.",
"homepage": "http://publications.europa.eu/resource/authority/number-threshold",
"license": "CC0-1.0",
"name": "Number threshold Name Authority List",
"prefix": "19039"
},
"19040": {
"description": "The Number type NAL provides the grammatical distinctions of numerals. The grammar distinguishes between cardinal and ordinal numbers.",
"homepage": "http://publications.europa.eu/resource/authority/number-type",
"license": "CC0-1.0",
"name": "Number type Name Authority List",
"prefix": "19040"
},
"19041": {
"description": "This table provides the codes linked to the type of weight values used in award criteria within the context of public procurement.",
"homepage": "http://publications.europa.eu/resource/authority/number-weight",
"license": "CC0-1.0",
"name": "Number weight Name Authority List",
"prefix": "19041"
},
"19042": {
"description": "This table provides the list of the different functions of the organisations in a procurement procedure.",
"homepage": "http://publications.europa.eu/resource/authority/organisation-role",
"license": "CC0-1.0",
"name": "Organisation role Name Authority List",
"prefix": "19042"
},
"19043": {
"description": "This table provides the list of the different sub-functions of the organisations in a procurement procedure.",
"homepage": "http://publications.europa.eu/resource/authority/organisation-subrole",
"license": "CC0-1.0",
"name": "Organisation subrole Name Authority List",
"prefix": "19043"
},
"19044": {
"description": "This table provides the broad geopolitical areas linked to the location of works and the place of performance or delivery within the context of public procurement.",
"homepage": "http://publications.europa.eu/resource/authority/other-place-service",
"license": "CC0-1.0",
"name": "Other place service Name Authority List",
"prefix": "19044"
},
"19045": {
"description": "This table provides the codes linked to the different values of permission and/or obligation.",
"homepage": "http://publications.europa.eu/resource/authority/permission",
"license": "CC0-1.0",
"name": "Permission Name Authority List",
"prefix": "19045"
},
"19046": {
"description": "The Procedure phase authority table is a controlled vocabulary listing phases of various decisional processes. It was originally created for AKN4EU specifications concerning documents pertaining to the ordinary legislative procedure, but it can be used for other purposes in the future, as a reference for phases of procedures of all nature β non legislative, legislative, internal, interinstitutional and judicial. It is part of the exchange between the institutions involved in the legal decision making process and the Publications Office of the European Union. It provides an authority code and the start-use date and a definition of each concept. The Procedure phase authority table is under governance of the Interinstitutional Metadata Maintenance Committee (IMMC) and maintained by the Publications Office of the European Union in the Metadata Registry (EU Vocabularies website).",
"homepage": "http://publications.europa.eu/resource/authority/procedure-phase",
"license": "CC0-1.0",
"name": "Procedure phase Name Authority List",
"prefix": "19046"
},
"19047": {
"description": "This table provides a list of activities leading to the conclusion of public contracts used in public procurement according to the legislation.",
"homepage": "http://publications.europa.eu/resource/authority/procurement-procedure-type",
"license": "CC0-1.0",
"name": "Procurement procedure type Name Authority List",
"prefix": "19047"
},
"19048": {
"description": "The table defines public event types. A public event is something that happens at a particular place and time, organised by an agent for a particular purpose, and is of interest to a general audience. This definition excludes natural events such as earthquakes or hurricanes.",
"homepage": "http://publications.europa.eu/resource/authority/public-event-type",
"license": "CC0-1.0",
"name": "Public event type Name Authority List",
"prefix": "19048"
},
"19049": {
"description": "This table provides the list of relevant categories used to classify tenders or requests to participate received within the context of public procurement.",
"homepage": "http://publications.europa.eu/resource/authority/received-submission-type",
"license": "CC0-1.0",
"name": "Received submission type Name Authority List",
"prefix": "19049"
},
"1905": {
"description": "It doesnβt take a rock expert to know that David Bowieβs musical influence has cast a large shadow ever since he broke out as a quasi-alien pop star with his 1972 classic The Rise and Fall of Ziggy Stardust and the Spiders From Mars. But one could have never heard a note of Bowieβs music (including his new album) and still be wowed by the extent to which the manβs various guises have, as you can see here, inspired a multitude of artists. If imitation is the sincerest form of flattery, Bowie should be blushing.",
"homepage": "http://www.vulture.com/2015/12/david-bowie-personas-imitators.html",
"name": "A Taxonomy of David Bowieβs Many Personas and Their Many Imitators",
"prefix": "1905"
},
"19050": {
"description": "This table provides the values used to indicate wether the participation in the procurement is reserved for specific organisations.",
"homepage": "http://publications.europa.eu/resource/authority/reserved-procurement",
"license": "CC0-1.0",
"name": "Reserved procurement Name Authority List",
"prefix": "19050"
},
"19051": {
"description": "This table provides the list of condictions that are concerned for evaluation purposes. In the domain of public procurement, selection criteria are normally based on a specific legal framework. This codelist is a subset of the ESPD codelist CriterionTaxonomy.",
"homepage": "http://publications.europa.eu/resource/authority/selection-criterion",
"license": "CC0-1.0",
"name": "Selection criterion Name Authority List",
"prefix": "19051"
},
"19052": {
"description": "This table provides the values linked to any social objective promoted by the technical specifications, award criteria, selection criteria or contract performance conditions included in a procurement.",
"homepage": "http://publications.europa.eu/resource/authority/social-objective",
"license": "CC0-1.0",
"name": "Social objective Name Authority List",
"prefix": "19052"
},
"19053": {
"description": "This table provides the information about whether a procurement aims to reduce environmental impact, fulfil social objectives and/or buy innovative works, supplies or services. These condictions are achived via either technical specifications, selection criteria, award criteria and contract terms.",
"homepage": "http://publications.europa.eu/resource/authority/strategic-procurement",
"license": "CC0-1.0",
"name": "Strategic procurement Name Authority List",
"prefix": "19053"
},
"19054": {
"description": "This table provides the list of codes and values used to indicate information regarding the share of parts of a contract to third parties. The share may refer to the portion of work, services or supplies and/or to the subject matter being subcontracted.",
"homepage": "http://publications.europa.eu/resource/authority/subcontracting-indication",
"license": "CC0-1.0",
"name": "Subcontracting indication Name Authority List",
"prefix": "19054"
},
"19055": {
"description": "This table provides the list of codes and values used for the obligation of the economic operator of sharing parts of the original contract to third parties. The share may refer to the portion of work, services or supplies.",
"homepage": "http://publications.europa.eu/resource/authority/subcontracting-obligation",
"license": "CC0-1.0",
"name": "Subcontracting obligation Name Authority List",
"prefix": "19055"
},
"19056": {
"description": "The Subject matter classification shows the concepts used for the indexation of notices published on EUR-Lex. The subject matter classification exists in parallel with two other classifications: the Directory of European Union Legislation and EuroVoc. Differently from these, the subject matter classification is aligned strictly to the evolution of European Union policies cited in the different treaties of the European Union that can be consulted at: http://eur-lex.europa.eu/collection/eu-law/treaties.html?locale=en.The content of the subject matter classification is managed by the GIL working group (Inter-institutional Group on Legislation).",
"homepage": "http://publications.europa.eu/resource/authority/subject-matter",
"license": "CC0-1.0",
"name": "Subject matter Name Authority List",
"prefix": "19056"
},
"19057": {
"description": "This table provides the list of codes and values indicating the application of criteria or other concepts and information.",
"homepage": "http://publications.europa.eu/resource/authority/usage",
"license": "CC0-1.0",
"name": "Usage Name Authority List",
"prefix": "19057"
},
"19058": {
"description": "This table provides the list of codes and values used to indicate whether a tenderer was chosen to be awarded with a contract and wether the competiotion is open.",
"homepage": "http://publications.europa.eu/resource/authority/winner-selection-status",
"license": "CC0-1.0",
"name": "Winner selection status Name Authority List",
"prefix": "19058"
},
"19059": {
"description": "The UNESP Thesaurus has vocabulary with specialized terms from the areas of knowledge of its teaching, research and extension activities. It is built with the combination of controlled vocabularies from the Library of Congress Subject Headings (LCSH), Terminology from the National Library of Brazil (BN) Medical Subject Headings (MeSH) and Health Sciences Descriptors (DeCS) in MARC21 authority records. The TemaTres software provides access to the Thesaurus UNESP, used to represent the content of the most significant information in books, dissertations, theses, monographs, course completion papers, journal articles, documents, legislation, etc. The UNESP (SΓ£o Paulo State University) Language Group, made up of library catalogers and researchers in the Knowledge Organization area, has been responsible for maintaining the UNESP Thesaurus since 2013. The maintenance work is continuous to correct keywords and consistency of hierarchical relationships between terms.\n\nTips for searching:\n\nStep 1 - Type a word, part of the word or phrase in the search box.\n\nStep 2 - Choose the keyword.\n\nStep 3 - The search result preview will show the keyword and its relationships that can be selected, if they are more specific or more generic.\n\nStep 4 - On the right side of the selected keyword, you have the access link for choosing the bibliographic records that contain the keyword.",
"homepage": "http://portal.biblioteca.unesp.br/tematres/vocab/",
"name": "Thesaurus Unesp",
"prefix": "19059"
},
"1906": {
"description": "The glossary supplements the more detailed material data sets and material group descriptions of the database, as well as additional information on processing and manufacturing techniques.",
"homepage": "http://www.materialarchiv.ch/",
"name": "Material Archive Glossary",
"prefix": "1906"
},
"19060": {
"description": "User-oriented vocabulary for public services in Norway, maintained by the Norwegian Digitalisation Agency. Los consists of around 500 concepts and over 2900 alternative labels (synonyms, former names, etc.) that can be used for categorization of content and resources across portals and to help users navigate.",
"license": "CC0-1.0",
"prefix": "19060"
},
"19062": {
"description": "The General Formal Ontology is an upper ontology developed by Onto-Med.",
"name": "General Formal Ontology",
"prefix": "19062",
"wikidata_database": "Q5532347"
},
"19063": {
"prefix": "19063",
"wikidata_database": "Q55118653"
},
"19064": {
"description": "The Unified Foundational Ontology (UFO) is an upper ontology that incorporating developments from GFO, DOLCE and the Ontology of Universals. UFO is the foundational ontology for the ontology modeling language OntoUML.",
"homepage": "https://www.onto-med.de/ontologies/gfo",
"prefix": "19064"
},
"1907": {
"description": "Library Systematics Last update: 29.07.2014",
"homepage": "http://www.landtag.rlp.de/icc/Internet-DE/med/601/6017b063-e613-e319-1989-54286d35f8f4",
"name": "Shelf classification of the Landtagsbibliothek Rheinland-Pfalz",
"prefix": "1907"
},
"1908": {
"description": "The 'Decimal Classification' was first printed by the National Petroleum Publishing Company, publishers of National Petroleum News, in 1928. A second edition appeared in serial form in The Petroleum Engineer in 1938 and was later reprinted in booklet form. During the intervening years since it was first available, many persons apparently have found this system useful in meeting their filing problems. Articles printed in The Petroleum Engineer have for many years been numbered in accordance with this decimal classification to facilitate orderly clipping and filing. It has also found use in oil company offices and libraries where filing of petroleum technology reference material is a day-to-day problem. (...) From the standpoint of one interested in some specialized industry, such as petroleum, the system developed by Dewey is too broad. Being all inclusive, it subordinates the particular things in which we are interested to the main divisions of knowledge in such a way that much of our material is widely scattered. The decimal classification given in the following pages is modeled after the plan used by Dewey, except that all knowledge is subordinated to the field of petroleum technology, to which the\n\nwhole classification applies. It is intended to provide an orderly and systematic arrangement of reference material for individuals whose chief interest lies in the field of petroleum technology. The main framework of the classification is indicated in the abridged list of 100 topics or subdivisions of petroleum technology (...). In the complete index, which appears on later pages, each division in this list is divided into ten subdivisions, thus providing 1, 000 topics with a number between 0 and 1, 000 assigned to each. Each number is followed by a decimal point, and additional digits may be added to the right of the decimal point if our needs require more detailed classification. The decimal point is used merely for convenience in reading and has no special significance. An effort has been made to include in the classification a number for every topic of any importance pertaining to the petroleum and related industries. When topics have been overlooked, it should be easy to extend the classification, where necessary, by providing a number that would place the topic in its proper sequence with relation to other topics.",
"homepage": "http://hdl.handle.net/2027/mdp.39015021085355",
"name": "Decimal System for Classifying Data Pertaining to the Petroleum Industry",
"prefix": "1908"
},
"1909": {
"description": "The HRCS is a system for classifying and analysing biomedical and health research funding. Its role is to faciliate research management by answering strategic questions about investment. (...) The Health Categories dimension of the HRCS captures the area of health or disease being studied. There are 21 separate categories which encompass all diseases, conditions and areas of health. (...) Research Activity Codes classify types of research activity. This dimension of the HRCS has 48 codes divided into eight overarching code groups which encompass all aspects of health related research activity ranging from basic to applied research.",
"homepage": "http://www.hrcsonline.net/",
"license": "CC BY-ND 3.0",
"name": "HCRS",
"prefix": "1909"
},
"191": {
"description": "Includes subject headings specific to Australia, New Zealand and Pacific Islands. Free 5 day trial, customers pay an annual subscription fee. SCIS Subject Headings is a comprehensive controlled vocabulary developed specifically to provide subject access in library catalogues in Australian and New Zealand schools. Both SCIS Subject Headings and Schools Online Thesaurus terms are used by SCIS Cataloguing Agencies when selecting or devising appropriate subject access for resources added to the SCIS database. SCIS Subject Headings may be used by library staff in schools to assist in conforming to SCIS standards when assigning subject headings to local resources. It can also be used by other organisations or services that require a controlled vocabulary specifically designed for the subject analysis of educational and curriculum materials.",
"homepage": "http://www2.curriculum.edu.au/scis/subject_headings.html",
"name": "SCIS Subject Headings",
"prefix": "191"
},
"1910": {
"description": "The Swedish-English dictionary contains translations of terms relevant to higher education. The starting point for the selection is that the terms are either specific to the university area or have a specific meaning in terms of education. Some terms contain, in addition to English translation, a definition or a remark. Does not contain translations of government names or government service titles. (...) The terms can be searched both in Swedish and English, but the dictionary is based on the Swedish terms. Definitions and remarks are only available in Swedish. Clickable terms have a definition or a remark The others have only one translation, sometimes synonyms and comparisons are also available. You will get the same information about the term, whether you are looking for Swedish or English. The English translation is based on British English. With / US /.",
"homepage": "https://www.uhr.se/publikationer/svensk-engelsk-ordbok/",
"name": "Swedish-English Dictionary of Higher Education",
"prefix": "1910"
},
"1911": {
"description": "Foreign Directory contains translations into English, German, French, Spanish and, to a certain extent Finnish and Russian, by names of authorities and organizations, EU agencies and countries. In addition, it contains government service titles.",
"homepage": "http://www.regeringen.se/informationsmaterial/2013/07/utrikes-namnbok/",
"name": "Foreign Name Book",
"prefix": "1911"
},
"1912": {
"description": "Charles Ammi Cutter (1837β1903), inspired by the decimal classification of his contemporary Melvil Dewey, originally developed his own classification scheme for the collections of the Boston Athenaeum, at which he served as librarian for two dozen years. He began work on it about 1880 and published the first schedules in the early 1890s. His five-volume catalogue of the Athenaeum collection is a classic in bibliographic history. The Cutter classification, although adopted by comparatively few libraries, mostly in New England, has been called one of the most logical and scholarly of American classifications. Its outline served as a basis for the Library of Congress classification, which also took over some of its features. It did not catch on as did Dewey's system because Cutter died before it was completely finished, making no provision for the kind of development necessary as the bounds of knowledge expanded and scholarly emphases changed throughout the 20th century.",
"homepage": "http://forbeslibrary.org/research/cutter-classification/",
"name": "Cutter Expansive Classification",
"prefix": "1912",
"wikidata_database": "Q5196943"
},
"1913": {
"homepage": "http://www.zlb.de/de/fachinformation/spezialbereiche/berlin-studien/berlin-systematik.html",
"name": "Berlin system",
"prefix": "1913"
},
"1914": {
"description": "This classification was prepared as a piece of the UDC (Universal Decimal Classification) which covers all knowledge in a fairly uniform way.",
"homepage": "http://www.mathontheweb.org/mathweb/Classif/RZhClassification.html",
"license": "https://www.w3.org/Consortium/Legal/2015/doc-license",
"prefix": "1914"
},
"1915": {
"abbreviation": "CoL",
"description": "The Catalogue of Life (CoL) is the nearest thing to a comprehensive catalogue of all known species of organisms on Earth. Continuous progress is made towards completion, and this edition contains 1,639,016 living and 5,763 extinct species. Please note that this is probably just over three quarters of the world's known species. This means that for many groups it continues to be deficient, and users will notice that many species are still missing from the Catalogue.\n\nThe present Catalogue is compiled with sectors provided by 157 taxonomic databases from around the world. Many of these contain taxonomic data and opinions from extensive networks of specialists, so that the complete work contains contributions from more than 3,000 specialists from throughout the taxonomic profession. Species 2000 and ITIS teams peer review databases, select appropriate sectors and integrate the sectors into a single coherent catalogue with a single hierarchical classification.",
"homepage": "http://www.catalogueoflife.org/col/",
"name": "Catalogue of Life",
"prefix": "1915",
"wikidata_database": "Q38840"
},
"1916": {
"description": "Wheelchair Rugby, with roots in wheelchair basketball and ice hockey, began in Canada in the 1970s as a counterpart to wheelchair basketball for persons with tetraplegia or tetra-equivalent function. The first classification system was medically based and there were three classes, largely determined by medical diagnosis and level of spinal cord injury. In 1991, the system was changed to a functional classification system unique to the sport of wheelchair rugby. This was done for many reasons, including the need to have a system that would accommodate the growing number of athletes both with and without spinal cord injury (such as polio, cerebral palsy, muscular dystrophy, multiple sclerosis and amputations).",
"homepage": "http://www.iwrf.com/?page=classification",
"name": "IWRF Functional Classification System",
"prefix": "1916"
},
"192": {
"description": "The Schools Online Thesaurus (ScOT) provides a controlled vocabulary of terms used in Australian and New Zealand schools. It encompasses all subject areas as well as terms describing educational and administrative processes. The thesaurus links non-preferred terms to curriculum terms. It also relates terms in a browsable structure. These features make ScOT an ideal vocabulary to integrate into search mechanisms of learning management systems.",
"homepage": "http://scot.curriculum.edu.au/",
"name": "Schools Online Thesaurus",
"prefix": "192"
},
"193": {
"description": "This multilingual glossary of terms used in education and training policy is intended for researchers and more generally for all those involved in education and training policy. It does not represent an exhaustive inventory of the terminology used by specialists; rather it identifies a selection of key terms that are essential for an understanding of current education and training policy in Europe.",
"homepage": "http://www.cedefop.europa.eu/EN/publications/13125.aspx",
"name": "Terminology of European Education and Training Policy",
"prefix": "193"
},
"1936": {
"description": "This file contains the thesaurus of clinical signs used for indexing rare disorders. Clinical signs are defined using a controlled vocabulary and classified by main organs and systems.",
"homepage": "http://www.orpha.net/consor/cgi-bin/Disease_DiagnosisAssistance.php",
"name": "Thesaurus of Clinical Signs",
"prefix": "1936"
},
"1937": {
"description": "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. HPO currently contains approximately 11,000 terms and over 115,000 annotations to hereditary diseases. The HPO also provides a large set of HPO annotations to approximately 4000 common diseases. (...) The HPO can be used for clinical diagnostics in human genetics (Phenomizer), bioinformatics research on the relationships between human phenotypic abnormalities and cellular and biochemical networks, for mapping between human and model organism phenotypes, and for providing a standardized vocabulary for clinical databases, among many other things. There exists an HPO web browser. The HPO project encourages input from the medical and genetics community with regards to the ontology itself and to clinical annotations.",
"homepage": "http://human-phenotype-ontology.github.io/",
"name": "Human Phenotype Ontology",
"prefix": "1937",
"wikidata_database": "Q17027854"
},
"1939": {
"description": "(...) a free, 'humble', modern, open-source, crowd-sourced replacement for the Dewey Decimal System. (...) The OSC will be: β’ Collaboratively written The OSC itself should be written socially--slowly, with great care and testing--but socially. See the Build the Open Shelves Classification group. β’ Collaboratively assigned As each level of OSC is proposed and ratified, members will be invited to catalog LibraryThing's books according to it. Using LibraryThing's fielded bibliographic wiki, Common Knowledge. And include: β’ Progressive development Written \"level-by-level\" (DDC's classes, divisions, etc.), in a process of discussion, schedule proposals, adoption of a tentative schedule, collaborative assignment of a large number of books, statistical testing, more discussion, revision and 'solidification'. β’ Public-library focus Academic collections, being larger, are less likely to change to a new system. Also, academic collections mostly use the Library of Congress System, which is already in the public domain. β’ Statistical testing As far as we are aware, no classification system has ever been tested statistically as it was built. Yet there are various interesting ways of doing just that. For example, it would be good to see how a proposed shelf-order matches up against other systems, like DDC, LCC, LCSH and tagging. If a statistical cluster in one of these systems ends up dispersed in OSC, why? (...) The OSC Project is a collaborative effort by LibraryThing members.",
"homepage": "https://wiki.librarything.com/index.php/Open_Shelves_Classification",
"name": "Open Shelves Classification",
"prefix": "1939"
},
"194": {
"homepage": "http://www.ciedelanus.com.ar/docs/CursoTesauro/TESAURO.doc",
"prefix": "194"
},
"1940": {
"abbreviation": "WD",
"description": "Wikidata is a free linked database that can be read and edited by both humans and machines. Wikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wikisource, and others. Wikidata also provides support to many other sites and services beyond just Wikimedia projects! The content of Wikidata is available under a free license, exported using standard formats, and can be interlinked to other open data sets on the linked data web.",
"homepage": "https://www.wikidata.org/wiki/Wikidata:Main_Page",
"license": "CC0-1.0",
"name": "Wikidata",
"pattern": "^Q[0-9]+$",
"prefix": "1940",
"wikidata_database": "Q2013"
},
"1941": {
"abbreviation": "KfM",
"description": "The classification makes it possible to record music (graphical music recordings, music prints, notes, acoustic music recordings, musical instruments, files). Facets of the classification may include the following: voices and musical instruments used in the recording in standardized abbreviation, genre, genre, form, stylistic direction, geographic reference, occasion, purpose, social carrier, Popularity, technical format).",
"homepage": "http://w3id.org/nkos/nkostype#classification_schema",
"name": "Classification for music libraries",
"prefix": "1941"
},
"1944": {
"abbreviation": "FUD",
"description": "The UB Dortmund presents its media in the Central Library according to the set-up system of economics and social sciences. There are also two other installation systems in the libraries architecture (10 main classes) and civil engineering and spatial planning (11 main classes).",
"homepage": "http://www.ub.tu-dortmund.de/Fachinformation/Wirtschaftswissenschaften/bw_syst.html",
"name": "Systematics of the University Library Dortmund",
"pattern": "^[A-Z]+([0-9]+)?$",
"prefix": "1944"
},
"1945": {
"abbreviation": "FUM",
"description": "The subject system of the Department of Religious Studies lists 17 topics of the religions divided into continents and religious groups. The notation consists of a three-digit number.",
"homepage": "https://www.uni-marburg.de/bis/ueber_uns/dezbib/bibgw/bibbr/brfachsys",
"name": "Subject classification system of the University of Marburg",
"pattern": "^([A-Z]+ )?[0-9]+ - ([A-Z]+ )?[0-9]+$",
"prefix": "1945"
},
"1946": {
"description": "The Billings Classification is a subject classification developed by John Shaw Billings in 1899. It was not an abstract experiment in the mapping of human knowledge, but rather a system devised specifically for the optimum arrangement of the Libraryβs collections. Dr. Billings envisioned a layout for the building, and while his classification scheme was in fact a division of human intellectual achievement into various subject areas designated by letter codes varying in number (usually three), it was fashioned in such a way as to maximize access to the unique holdings of the Library. The planned physical spaceβhow things would functionβall played a role in the construction of his classification. The majority of the Billings classmarks are not longer in use, as NYPL began using a fixed order system in the 1950s.",
"homepage": "http://billi.nypl.org/",
"name": "Billings Classification",
"prefix": "1946"
},
"1947": {
"description": "Fintech is a broad category describing an entire market. And itβs quite hard to try and get your head around this rapidly evolving market. But knowing the landscape can have great advantages:\n\n β’ If you are just starting out, it will give you a good idea of whatβs working and what is not, and more importantly, which segment provides the opportunity for fastest growth;\n\n β’ If you are already a Fintech pioneer, then knowing the landscape will help you explore market gaps for expansion or diversification;\n\n β’ You will have a much better handle on new and emerging competitors, threatening your business model; and\n\n β’ If you are an incumbent player, then knowledge of the landscape will help you identify acquisition or joint venture partnering opportunities, as a way to entering or getting exposure to the exciting world of\n\n Fintech.\n\n To make sense of this market and for your benefit, we have already started to map out the Fintech landscape, or Fintech taxonomy, as there just isnβt enough information out there. (...)\n\nThe map is divided across seven distinct functional lines covering the entire financial services landscape. The World Economic Forum research identified the first five and we added the last two categories to include suppliers and intermediaries.",
"homepage": "http://vedanvi.com/fintech-taxonomy-map/",
"name": "Fintech Taxonomy",
"prefix": "1947"
},
"1949": {
"description": "There are big changes underway in bird taxonomy. You've probably noticed that the checklist is always changing. Suddenly the ducks have replaced the loons in front of the NGS guide. Not too long ago the shrikes and vireos were next to the warblers, now they're next to the jays. Maybe you've heard that vultures are storks, or that they're not really storks after all, or that North American tanagers are now cardinals, or that saltators are tanagers, not cardinals. Then there are the Baltimore and Bullock's Orioles, or are they just Northern Orioles? Are they Slate-colored and Oregon Juncos, or maybe it's Dark-eyed Junco today. Not only are species being split or lumped, but everything is being rearranged. A new view of bird taxonomy takes shape as we watch.\n\nThere have always been questions and disagreements about bird taxonomy, and it has always been changing (see Bruce, 2003). Since Aristotle or before, people have tried to find a natural way to order all bird species (the very words 'genus' and 'species' carry the Aristotelean tradition). Early attempts were based on obvious similarities, such as grouping all waterbirds together. But what constitutes a natural order?\n\nLinnaeus simplified scientific nomenclature by naming each type bird with a genus and species, but was unable to tell us what order was natural. It is not until Darwin that we get a clearcut way to order the birds. They should be ordered according to descent. Birds with more recent common ancestors should be grouped together.\n\nThomas Huxley (1867) was the first to construct a comprehensive bird list on Darwinian lines. He focused on the characteristics of the bird's skull to determine common inherited features that he could base his taxonomy on. Numerous other ornithologists have used morphological traits to classify the birds, with Livezey and Zusi (2007) being the most recent effort of this type.\n\nMore recently, focus has shifted to molecular methods, the most important of which is to directly study the stuff of inheritanceβDNA. The culmination of the first wave of DNA based taxonomy were the publications by Sibley, Ahlquist, and Monroe (Sibley, Ahlquist, and Monroe, 1988; Sibley and Ahlquist, 1990; Sibley and Monroe, 1990). Sibley, Ahlquist, and Monroe used DNA hybridization to try to classify birds. This, together with increasing emphasis on cladistic methods, has revitalized interest in bird taxonomy. In the 1990's, DNA hybridization was replaced by the much more precise DNA sequencing, allowing direct examination of the genes themselves. This has opened the possibility of constructing a 'tree of life' showing the evolutionary relationships between all living organisms. It has brought the prospect of producing a completely accurate taxonomic tree of all living bird species, and touched off an onslaught of new research. This ongoing research is the driving force behind the checklist changes.\n\nThis set of web pages contains a guess at what the avian part of the tree of life might look like. It examines recent taxonomic changes, and possible changes to come. Some of the projected changes are pretty solid, others are guesses based on current research. Keep in mind that some of my guesses will turn out to be wrong, and some of the research they are based will be wrong or misleading. There will doubtless be taxonomic surprises before the entire avian tree is worked out, just as there have been a number of recent surprises.",
"homepage": "http://jboyd.net/Taxo/taxo1.html",
"name": "Aves - A Taxonomy in Flux",
"prefix": "1949"
},
"195": {
"description": "Thesaurus of European Educational System \"21 microthesauri, 4 unstructured lists, 1387 descriptors, 1371 non-descriptors and 312 explanatory notes, as a multilingual thesaurus, TESE is tailored to the needs of the Eurydice network, Lifelong Learning ', the European Union's action program on cooperation in the field of education. TESE is intended primarily to index Eurydice's bibliographic and electronic databases, but it is also intended to navigate the central website of the Eurydice Information Center of the Eurydice TESE is to be used in university libraries, the libraries of the Ministry of Education and various documentation centers (included in FENPROF, Em documentation center of the teachers' union). In Italy, TESE is used by the National Agency for the Development of the School Autonomy (formerly INDIRE) to index documents in a database for teachers, students and educators",
"homepage": "http://eacea.ec.europa.eu/education/eurydice/tese_de.php",
"name": "Thesaurus of European Education Systems",
"prefix": "195"
},
"1950": {
"description": "The AP News Taxonomy is a comprehensive set of standardized vocabularies for describing English-language news content. Terms in the vocabularies cover all aspects of news: subjects, people, places, organizations, and more. When you submit content to the automated AP Tagging Service, the data that comes back is drawn from these vocabularies. Publishers may also choose to integrate the AP News Taxonomy into their own publishing systems to support manual tagging. In addition to standardized terminology and unique IDs, the taxonomy stores a variety of details about the people, places, and topics it contains. This information can power enhanced search experiences, browsing and discovery, or informational displays.",
"homepage": "https://developer.ap.org/ap-metadata-services#apNewsTaxonomy",
"name": "AP News Taxonomy",
"prefix": "1950"
},
"1951": {
"description": "The European Union Telematics Controlled Terms (EUTCT) System is a Community repository and provider of controlled terms in multiple languages for the ongoing exchange of data between information systems and applications throughout the European Medicines Regulatory Network (EMRN).\n\n β’ It is intended that the EUTCT System will serve not only all current and future EU Telematics systems but, as far as is possible, the entire regulatory community for the pharmaceutical industry.\n\n β’ The system will also act as a medicinal products dictionary for use in validating information submitted to the Eudra family of applications electronically, for identification purposes.",
"homepage": "http://eutct.ema.europa.eu/eutct/",
"name": "European Union Telematics Controlled Terms",
"prefix": "1951"
},
"1952": {
"description": "For quite some time now, recruiting organizations have been capturing and monitoring performance data. Additionally, they have been using benchmark data to provide an objective lens through which information can be viewed and comparisons can be made. These comparisons are often used to drive the changes in behavior, strategy, or technology needed to improve performance. However, often the terminology and nomenclature of these metrics varies from company to company or analyst to analyst. In this article, we provide a glossary of the major talent acquisition metrics that companies should be tracking and compiling.",
"homepage": "http://trendline.dcrworkforce.com/a-glossary-of-talent-acquisition-terms.html",
"name": "Glossary of Talent Acquisition Metrics",
"prefix": "1952"
},
"1953": {
"description": "A taxonomy of Late Antique, Byzantine, and post-Byzantine sites, created as the basis for the places taxonomy for the collection management system mailto:AtoM@DO of the Image Collections and Fieldwork Archives of Dumbarton Oaks.",
"homepage": "http://koronis.at/tematres/vocab/",
"name": "AtoM-Places",
"prefix": "1953"
},
"1954": {
"description": "This service allows you to search by topics, navigating the different areas of knowledge and selecting the term or terms to make a query. The terms are hierarchically ordered showing the relationship of specificity between them.",
"homepage": "http://www.vocabularyserver.com/intal/tesauro/",
"name": "INTAL Documentation Center Thesaurus",
"prefix": "1954"
},
"1955": {
"description": "Beginning with the 111th Congress, all legislative measures are assigned at least one Subject term drawn from a new list of terms presented on this page. The Subject terms are designed to better group legislation, to improve consistency, and to shorten the time it takes to add Subject terms to bills. Subject terms can also be assigned from a large list of terms corresponding to geographic areas (foreign and domestic), U.S. government entities, and congressional committees. See the CRS Named-Entity Subject Terms for a complete list of those terms. Subject term assignment is cumulative; that is, it is added to in order to reflect revisions (if any) made to the measure as it moves through the legislative process.\n\nWhen looking at the Subject terms assigned to a bill or resolution, you will notice that the first term on the list appears out of alphabetical order. This is the Top Term for the measure, and it corresponds to the broad category that best describes the concerns of the measure's text. Top Terms are represented by the bold 'umbrella' terms on the list below.\n\nTerms assigned to legislation from the 110th and earlier Congresses came from a list that was based upon a thesaurus known as the Legislative Indexing Vocabulary (LIV). CRS plans to convert the LIV terms assigned to bills from the 93rd through the 110th Congresses to the new Subject terms as time and resources permit.",
"name": "CRS Legislative Subject Terms Used in THOMAS",
"prefix": "1955"
},
"1956": {
"description": "Legislative analysts from the Congressional Research Service (CRS) closely examine the content of each bill and resolution and assign (index) as many Subject terms as are required to describe the measure's substance and effects. Beginning with the 111th Congress, all legislative measures are assigned at least one Subject term drawn from the terms presented at CRS Legislative Subject Terms. Searchable Subjects also include a large number of terms corresponding to geographic areas (foreign and domestic), U.S. government entities, and congressional committees shown in the list below.",
"homepage": "http://thomas.loc.gov/help/terms-names.html",
"name": "CRS Named-Entity Subject Terms Used in THOMAS",
"prefix": "1956"
},
"1957": {
"description": "A thesaurus that originates from the humanities and social sciences, but has grown to cover most subjects. The vocabulary contains 17956 concepts, with terms in Norwegian BokmΓ₯l only. Mapping to Dewey is an ongoing project.",
"homepage": "https://www.ub.uio.no/bruk/sok-i-hele-biblioteket/emneord/humord/",
"license": "CC0-1.0",
"prefix": "1957",
"wikidata_database": "Q22927022"
},
"1958": {
"description": "The NPRIE Probation Thesaurus has been developed over many years by librarians and information managers within Probation trusts in England and Wales including Alida Teijken, Andrew Parkes, Cath Fell, Helen Parris, Hilary Lawrenson, Jill Whiteman, Judith Sawbridge, Kath Oates and Steve Burgess. The thesaurus covers general and technical terminology used in the Criminal Justice System in the United Kingdom; and also terms relating to law and social sciences. NPRIE (National Probation Research and Information Exchange) is no longer in existence and given the recent changes in the probation service and the reduction in number of libraries within probation, the thesaurus is no longer updated.",
"homepage": "http://www.thesauri.co.uk/NPRIE.html",
"name": "NPRIE Probation Thesaurus",
"prefix": "1958"
},
"1959": {
"description": "The mission of the Trust for Architectural Easements is to preserve Americaβs architectural heritage. We accomplish this mission primarily through the acceptance and stewardship of historic preservation easements. The Trust is one of the largest preservation easement holding organizations in the country, with protected properties in eight states.",
"homepage": "http://architecturaltrust.org/outreach/education/glossary-of-architectural-terms/",
"name": "Glossary of Architectural Terms",
"prefix": "1959"
},
"196": {
"description": "The thesaurus, in its current state, needs to be validated by the professionals of the reception / integration of the young people of the Center region. It is experimental, its elaboration (structuring and choice of the descriptors) There are surely synonyms to be included, additional associations to be inserted and application notes to be added This thesaurus allows several levels of use, from the simple classification of the documents To bibliographic research in the documentary holdings of the network, to the indexing of documents.",
"name": "Home and Insertion Thesaurus",
"prefix": "196"
},
"1960": {
"description": "Many definitions used in medically assisted reproduction (MAR) vary in different settings, making it difficult to standardize and compare procedures in different countries and regions. With the expansion of infertility interventions worldwide, including lower resource settings, the importance and value of a common nomenclature is critical. The objective is to develop an internationally accepted and continually updated set of definitions, which would be utilized to standardize and harmonize international data collection, and to assist in monitoring the availability, efficacy, and safety of assisted reproductive technology (ART) being practiced worldwide. (...) A consensus was reached on 87 terms,expanding the original glossary by 34 terms, which included definitions for numerous clinical and laboratory procedures.Special emphasis was placed in describing outcome measures such as cumulative delivery rates and other markers of safety and efficacy in ART. (...) Standardized terminology should assist in analysis of worldwide trends in MAR interventions and in the comparison of ART outcomes across countries and regions.This glossary will contribute to a more standardized communication among professionals responsible for ART practice, as well as those responsible for national, regional and international registries.",
"homepage": "http://www.who.int/reproductivehealth/publications/infertility/art_terminology.pdf",
"name": "Glossary on Assisted Reproductive Technology Terminology",
"prefix": "1960"
},
"1961": {
"description": "Concepts in the semantic web and social web domain.",
"name": "Social Semantic Web Thesaurus",
"prefix": "1961"
},
"1962": {
"description": "The goal of this project is to develop a database for historical persons, places and concepts - and relationships between them - for the collection of Swiss sources of law.\" The database is intended to allow all relevant information (ie, Which are contained in the printed registers) in a structured form, and it should also be possible to produce printed registers for individual volumes from these data.\n\n In order to enable as many future applications as possible, it is crucial that the information can be processed mechanically. For this purpose, they must not only exist as unstructured texts, but must be stored as structured data with precisely defined semantics. \"\"",
"homepage": "https://www.ssrq-sds-fds.ch/typo3/index.php?id=132",
"name": "Database of historical persons, things (lemma) and place names",
"prefix": "1962"
},
"1963": {
"description": "The Admiralty Scale (also called the NATO System) is used to rank the reliability of a source and the credibility of an information.",
"homepage": "https://github.com/MISP/misp-taxonomies/tree/master/admiralty-scale",
"name": "Admiralty Scale",
"prefix": "1963"
},
"1964": {
"description": "The Traffic Light Protocol - or short: TLP - was designed with the objective to create a favorable classification scheme for sharing sensitive information while keeping the control over its distribution at the same time.",
"name": "Traffic Light Protocol",
"prefix": "1964",
"wikidata_database": "Q7832459"
},
"1965": {
"description": "The Vocabulary for Event Recording and Incident Sharing (VERIS) is a set of metrics designed to provide a common language for describing security incidents in a structured and repeatable manner. VERIS is a response to one of the most critical and persistent challenges in the security industry - a lack of quality information. VERIS targets this problem by helping organizations to collect useful incident-related information and to share that information - anonymously and responsibly - with others. The overall goal is to lay a foundation from which we can constructively and cooperatively learn from our experiences to better measure and manage risk.",
"homepage": "http://veriscommunity.net/",
"name": "Vocabulary for Event Recording and Incident Sharing",
"prefix": "1965"
},
"1966": {
"description": "As of Dec. 31, 2016 discontinued.",
"homepage": "https://web.archive.org/web/20140518141250/https://glossar.ub.uni-kl.de/",
"name": "Glossary of terms of information competences",
"prefix": "1966"
},
"1967": {
"description": "It is an ordered relationship of the terms (related to each other) that are included or described individually in books, documents, etc., and which form part of the library catalog of the National Electoral Institute.",
"homepage": "http://www.ine.mx/archivos3/portal/historico/contenido/Tesauro_politico-electoral01/",
"name": "Electoral Political Thesaurus",
"prefix": "1967"
},
"1968": {
"description": "62880 Terms, 5732 Relationship between terms, 14643 Equivalent terms.",
"homepage": "http://www.serbi.ula.ve/tematres/vocab/",
"name": "Serbian thesaurus of matters",
"prefix": "1968"
},
"1969": {
"name": "Thesaurus Archives of the City Arganda del Rey",
"prefix": "1969"
},
"197": {
"abbreviation": "GHB",
"description": "According to this system, numerous university and technical college libraries provide their books freely accessible to the users. The GHB installation system is not updated since October 2004 and is frozen at the status of 25 June 2004. The libraries responsible for the specialist systems no longer undertake this task",
"homepage": "http://www.hbz-nrw.de/produkte_dienstl/ghb-sys/",
"name": "Comprehensive University Library System",
"pattern": "^[A-Z]+(-[A-Z]+)?$",
"prefix": "197",
"wikidata_database": "Q26903391"
},
"1970": {
"description": "Extended and up-to-date version of the glossary published in Claudio Gnoli, Vittorio Marino, and Luca Rosati, Hops, 2006. Collaboration with Fulvio Mazzocchi and Riccardo Ridi in the book 'Organizing knowledge: from libraries to the information architecture for the Web'.\n\nThe entries in Italian are written in round, while their English equivalents in italics. The illustration of terms is above all an explanatory purpose and does not pretend to constitute a perfect and exhaustive definition.",
"homepage": "http://www.iskoi.org/doc/glossario.htm",
"name": "Glossary of Knowledge Organization",
"prefix": "1970"
},
"1971": {
"description": "Confusion often arises when different people use terms to mean different things. In drawing up the following list I am grateful for suggestions and comments from three consultant colleagues who specialise in the development and use of thesauri and other forms of structured vocabulary for information retrieval: Stella Dextre Clarke, Alan Gilchrist and Ron Davies. I have tried as far as possible to maintain consistency with definitions which we drafted for the revised British standards for thesaurus construction (BS 8723:2005 Structured vocabularies for information retrieval) and have taken some account of the definitions in the USA national standard, Z39.19. I do not claim that these definitions are 'correct' and that other meanings are 'wrong', but I hope that they will be found to be a consistent and well-defined set which will aid communication by encouraging everyone to use the same words with the same meaning. Discussions about some of the definitions are continuing, and they may change. Some of the definitions, notes and examples are my personal suggestions, and my colleagues may not agree with them.",
"homepage": "http://www.willpowerinfo.co.uk/glossary.htm",
"name": "Glossary of Terms Relating to Thesauri and Other Forms of Structured Vocabulary for Information Retrieval",
"prefix": "1971"
},
"1972": {
"description": "This glossary is intended to foster development of a shared vocabulary within the new and rapidly evolving field of information architecture. It should serve as a valuable reference for anyone involved with or interested in the design of information architectures for web sites, intranets and other information systems.\n\nAlthough this may seem obvious, we want to make it clear that the terms in this glossary are defined in relation to the field of information architecture. We have attempted to be faithful to the ordinary usage of terms to the degree possible. However, as with any specialty, some common words are used in somewhat uncommon ways within this field, and it is those meanings we have tried to capture.\n\nDefining information architecture is an important and controversial challenge.",
"homepage": "http://argus-acia.com/white_papers/iaglossary.html",
"name": "Information Architecture Glossary",
"prefix": "1972"
},
"1973": {
"description": "JURISCAN is a database developed by the Government of the Canary Islands with the aim of disseminating knowledge and facilitating the consultation of the legal system of the Autonomous Community. (...) The consultation system allows from the simplest, with a minimum Of search arguments relating to the formal presentation of the provision, to the most complex one, in which elements related to the title, rank, subject matter or date of the arrangement can be combined.The search by subject is facilitated by a thesaurus Of about 3,000 terms that serves to standardize the terminology and structure the retrieval of documents.",
"homepage": "http://www.gobiernodecanarias.org/juriscan/tesauro.jsp",
"name": "JURISCAN Thesaurus",
"prefix": "1973"
},
"1974": {
"description": "The Thesaurus is an orderly and open set of terms of a thematic area, on which a synonymy and homonymy control has been made, which allows to find the key words (descriptors) to adequately synthesize the documents and facilitate their location In the Database, constituting a bridge between the terminology of the author and the specific interest of the reader.\n\nThe Argentine Psychoanalytic Association (APA) published the first version in 1990, which was followed by new editions that were enlarged and corrected: in 1997, the first revised edition was published; in 2006, the third edition was edited and enlarged.",
"homepage": "http://www.apdeba.org/tesauro-online/",
"name": "Tesauro Online",
"prefix": "1974"
},
"1975": {
"homepage": "http://www.invemar.org.co/redcostera1/invemar/docs/tesauro_ambiental/naveg.htm",
"name": "Environmental Thesaurus for Colombia",
"prefix": "1975"
},
"1976": {
"description": "The e-Science Thesaurus is a resource that supports and provides direction to the health sciences and science and technology library community by exploring the terminology, literature, and resources that describe and inform librarians about patron instruction, collection development, and research services related to e-Science and research data management principles and practice. The Thesaurus strives to describe the concepts, services, tools and resources required to create, curate, preserve and disseminate digital scholarship. (...) Through the NERβs e-Science Portal, the e-Science Thesaurus serves as a resource to provide an educational reference for health sciences and science and technology librarians wanting to explore e-Science, research data management and digital scholarship activities. The objective of this project is to inform the library community about emerging roles and services in e-Science and research data management by introducing vocabulary terms, formative literature, and relevant resources concerning these topics. Through this effort, the Thesaurus aspires to be a resource that will provide health sciences librarians with the opportunity to acquire professional knowledge about e-Science, research data management, and digital scholarship in order to become familiar with and implement these activities into their own professional practice.",
"homepage": "http://esciencelibrary.umassmed.edu/professional-educ/escience-thesaurus",
"license": "CC BY-NC-SA 3.0",
"name": "e-Science Thesaurus",
"prefix": "1976"
},
"1977": {
"description": "For a better understanding of the subject and adequate application of the descriptors in the process of analysis of environmental information, we considered it necessary to present in the first part of the thesaurus, the modules or large categories under which the descriptors have been grouped.\n\nThese categories offer an overview of the components of the environment and coincide with the organization that is given by the majority of specialists to study the Latin American environmental context.\n\nOur purpose has been to locate the user of the thesaurus, in the first term, in front of a spatial and historical sequence of the trajectory of the subject and to illustrate the inseparable result of the treatment of the same, if the socio-economic factors of the region are not considered.",
"homepage": "http://hdl.handle.net/11362/29455",
"name": "Thesaurus of the Environment for Latin America and the Caribbean",
"prefix": "1977"
},
"1978": {
"description": "The purpose of this project is the development of a system for the treatment and recovery of legal documentary information in criminal matters that allows the judicial officer and the legal operator to have updated, systematic and official information in the field of jurisprudence , Legislation and doctrine (...) This instrument is the result of the merger of the Criminologist Thesaurus and\n\nΒ Of the Criminal Legal Thesaurus elaborated by ILANUD in 1983 and 1985 respectively and includes the most important descriptors in both subjects. In parallel, and in order to facilitate its use, the manuals for the use and indexing of the Thesaurus were developed. In the preparation of this thesaurus, the valuable competition of prestigious specialists in Criminal Law, Criminology and Documentary Sciences of Latin America was counted, which allows to assure that it is a useful and reliable tool for the treatment and analysis of information.",
"homepage": "http://www.metabase.net/metarecursos/control/tesauro_criminal.pdf",
"name": "Thesaurus of Latin American Criminal Policy",
"prefix": "1978"
},
"1979": {
"description": "The current Thesaurus of Natural and Productive Resources of Chile, based on the Thesaurus prepared by IREN in 1979, has undergone numerous revisions and updates over the years. 1994, and in view of the many changes that have taken place since that year, the CIREN Documentation Center, in the middle of 2001, started the task of preparing a new edition, corrected and updated, in order to incorporate the new terminology that The terminology included is currently used in CIREN as a standardized terminological control tool for the assignment of keywords or descriptors used in the indexing and retrieval processes of Information, which allows us to deepen the analysis of the documentary collection in the section on the categories Thematic and specific topics to which the content of each information object processed and analyzed in the Bibliographic Information System (SIB), available in the CEDOC of CIREN and in the Map of originals of the Technical File Area or Central of Originals, refer to the content of each information object processed and analyzed. The catalogs of the databases that make up the SIB are available online at http://www.ciren.cl on the CEDOC website and at the Institutional INTRANET.",
"homepage": "http://www.ciren.cl/cedoc/images/tesauro_tematico.pdf",
"name": "Thesaurus of Natural and Productive Resources of Chile",
"prefix": "1979"
},
"198": {
"description": "The Brazilian Thesaurus of Education (Brased) is a controlled vocabulary that brings together terms and concepts, extracted from documents analyzed in the Information Center and Library in Education (Cibec), related to each other from a conceptual framework of the area.These terms, Called descriptors, are intended for indexing and retrieval of information.",
"homepage": "http://pergamum.inep.gov.br/pergamum/biblioteca/pesquisa_thesauro.php",
"name": "Thesaurus Brased",
"prefix": "198"
},
"1980": {
"abbreviation": "PsycTESTS",
"description": "Every record in PsycTESTS receives a PsycTESTS Classification, which is used to identify the general area of psychology that the measure is designed to assess. This field was added to PsycTESTS as a part of our November 2014 update. All records in the database at that time were updated with a PsycTESTS Classification.",
"homepage": "http://www.apa.org/pubs/databases/training/psyctests-class-codes.aspx",
"name": "PsycTESTS Classification System",
"prefix": "1980"
},
"1981": {
"description": "The system of the Saarland Library with a link to the library catalog.",
"homepage": "http://www.sulb.uni-saarland.de/de/suchen/sbo/systematik/",
"name": "Systematics of the Saarland Bibliography",
"prefix": "1981"
},
"1982": {
"description": "The present update extends the continuous bibliography of the author in the HethitologiePortal with a systematic classification that facilitates access and orientation in new scientific production according to different thematic and methodological aspects as well as specializations in the field of hittitology and anatolian archeology The necessary extension to related disciplines and adjacent areas.\n\nThus, the systematic bibliography of Hittitology is based, the last period of which was the starting point of this new data collection. Within the framework of a small project funded by the Deutsche Forschungsgemeinschaft (DFG), the extensive older part of the bibliography for the system was developed, corrected and supplemented between 2009 and the beginning of 2012. The processed material should, as far as possible, open up all the hitherto literature from the beginning, especially since the beginning of the 20th century.\n\nThe classification and arrangement system corresponds to that of the systematic bibliography of the Hethitology of V. SouΔek and J. SiegelovΓ‘, which divided the literature into nine large groups - general, archeology, writing, languages, geography, social, history, religion, cultural history. Within these groups a finer arrangement is then made according to the thematic orientation of the works to be treated, with the aim that the increasing amounts of data remain clear, accessible and user-friendly. The complete overview of the classification can be found in the introductory table. By clicking on the individual links in the decimal scheme, the individual topics can be opened.\n\nHowever, there are only a few publications focusing on a single problem. It is a great advantage of the electronic processing of bibliographical data that the works can be recorded in several relevant places and can be referenced by links. The basic classification, of course, is guided by the main theme. The broadening topics or the questions which are treated only in an additional way in the respective work are taken into account by the publication in the corresponding chapter 'under the line', ie. Only after the works in which the relevant problem circle is the focus.",
"homepage": "http://www.hethport.uni-wuerzburg.de/hetbibsys/obsah.php",
"name": "Systematics of the Hittite Bibliography",
"prefix": "1982"
},
"1983": {
"description": "The Bavarian Bibliography is the largest national bibliography in the German-speaking world. It compares as completely as possible all German and foreign-language publications, which have a relation to Bavaria.",
"homepage": "http://www.bayerische-bibliographie.de/",
"name": "Systematics of the Bavarian Bibliography",
"prefix": "1983"
},
"1984": {
"description": "Systematics of the Landesbibliographie Baden-WΓΌrttemberg with proof of possession of the respective library",
"homepage": "http://www.statistik.baden-wuerttemberg.de/LABI/LABI.asp?K4=5&T4=S",
"name": "Systematics of the country library Baden Wurttemberg",
"prefix": "1984"
},
"1985": {
"description": "The Hamburg bibliography documents all literature, whether printed or electronic, referring to Hamburg and personalities from Hamburg. It has books, magazines and series, maps and atlases, essays and periodicals.",
"homepage": "http://www.sub.uni-hamburg.de/hamburg/hamburg-bibliographie.html",
"name": "Systematics topics of the Hamburg-Bibliography",
"prefix": "1985"
},
"1986": {
"abbreviation": "MV",
"description": "The bibliography of Mecklenburg-Hither Pomerania is indexed by this classification scheme. It is segmented in 13 major groups from 1 to 13",
"homepage": "https://opac.lbs-wismar.gbv.de/DB=2.1/LBSSYST",
"license": "CC_MARK",
"name": "Systematics of the Mecklenburg-Vorpommern bibliography",
"pattern": "^[0-9\\.]+$",
"prefix": "1986"
},
"1987": {
"description": "The Lower Saxon Bibliography is a regional bibliography for the states of Lower Saxony and Bremen. It contains references to the literature on these countries and their regions since the year 1966.",
"homepage": "http://www.gwlb.de/nis/niedersaechsische_bibliographie/",
"name": "Systematics of the Lower Saxon Bibliography",
"prefix": "1987"
},
"1988": {
"description": "Association catalog of the university libraries of North Rhine-Westphalia and a large part of Rhineland-Palatinate",
"homepage": "https://nwbib.de/",
"name": "System of the North Rhine-Westphalian Bibliography",
"prefix": "1988"
},
"1989": {
"homepage": "https://nwbib.de/",
"name": "Spatial System of the North-West-Westphalian Bibliography",
"prefix": "1989"
},
"199": {
"description": "The thesaurus in health education was developed from version 2 of the BDSP (Public Health Databank) thesaurus used at the National Institute for Prevention and Education for Health and in some education committees This thesaurus BDSP 2 contains 5,200 descriptors and has wide-ranging possibilities for use in areas such as epidemiology, care or health technologies, but it has deficiencies, notably in education for health And Patient Education, in Psychology, Pedagogy and Sociology The Thesaurus in Health Education is a documentary tool gathering all the notions useful to characterize the content of documents in health education.",
"homepage": "http://www.inpes.sante.fr/CFESBases/catalogue/pdf/882.pdf",
"name": "Health Education Thesaurus",
"prefix": "199"
},
"1990": {
"description": "Rhineland-Palatinate Bibliography with bibliographical references from all areas of knowledge",
"homepage": "http://www.rlb.de/rpb04/notation.html",
"prefix": "1990"
},
"1991": {
"homepage": "http://www.rlb.de/rpb04/krverz.htm",
"name": "Local Systematics of the Rhineland-Palatinate Bibliography",
"prefix": "1991"
},
"1992": {
"abbreviation": "SHBSG",
"description": "The content development is carried out according to a systematically arranged system, adapted to the needs of a regional bibliography and the literature supply in Schleswig-Holstein.",
"homepage": "https://bibliographie.schleswig-holstein.de//content/index.xml",
"prefix": "1992"
},
"1993": {
"description": "The content development is carried out according to a systematically arranged system, adapted to the needs of a regional bibliography and the literature supply in Schleswig-Holstein.",
"homepage": "http://www.shlb.de/abacus-cgi/shbib.pl",
"name": "Systematics Time, epochs of the Schleswig-Holstein bibliography",
"prefix": "1993"
},
"1994": {
"description": "The Oldenburgische Bibliographie is the regional bibliography for the area of the old country Oldenburg. It lists books, essays and other media on all aspects of the territory of this territory in history and present. It also contains literature on the Principalities of Eutin and Birkenfeld for the period of their membership of the Oldenburgian state.",
"homepage": "http://134.106.84.190/olbib/",
"name": "Systematics of bibliography of Oldenburg",
"prefix": "1994"
},
"1995": {
"description": "System for the establishment of media in the free hand area of the Landesbibliothek Oldenburg",
"homepage": "http://www.lb-oldenburg.de/benutzun/neuinlbo/angebo2cfh.htm",
"name": "System of the country library Oldenburg",
"prefix": "1995"
},
"1996": {
"description": "There is a selection of reference works in the reading room, which are excluded from regular borrowing as a reference stock. These reference works are offered for use as a free-hand area of the Lesesaal in a systematic manner.",
"homepage": "http://www.noe.gv.at/Bildung/Landesbibliothek/SammlungenAbteilungen/Lesesaal.html",
"name": "Installation system of the state library NiederΓΆsterreich",
"prefix": "1996"
},
"1997": {
"description": "For the directory search, the table of contents, which is pre-presented to each printed bibliography, is presented, which provides a first content structuring and classification of the bibliographic single entries into a thematic framework And to improve the accuracy of the results for selected topics, but minor errors can also be caused by slight differences in the chapter names of the individual bibliographic pages forming the database of the present database.",
"homepage": "http://www.ooegeschichte.at/forschung/literatur/historische-bibliografie/verzeichnissuche.html",
"name": "Directory search of the Bibliography on Upper Austrian History",
"prefix": "1997"
},
"1998": {
"description": "Classification sheme of the bibliography portal on the history of East Central Europe.",
"homepage": "http://www.litdok.de/cgi-bin/litdok?t_syslist=x",
"name": "Classifications of the bibliography portal on the history of East Central Europe",
"prefix": "1998"
},
"1999": {
"description": "Welcome to the PhilPapers Bibliography, the most comprehensive bibliography of philosophy. The bibliography currently counts 5147 categories managed by 628 volunteer editors.",
"homepage": "http://philpapers.org/browse/all",
"name": "PhilPapers Categories",
"prefix": "1999"
},
"20": {
"description": "In IATE you can find EU-specific terminology and jargon, as well as terms from all sorts of areas, such as law, agriculture, information technology and many others. IATE has 8.4 million terms, including approximately 540 000 abbreviations and 130 000 phrases, and covers all 23 official EU languages.\n\nNew terms are added every day and the contents are constantly updated. IATE plays a major role in ensuring the quality of the written communication of the EU institutions and bodies.",
"homepage": "http://iate.europa.eu",
"name": "Inter-Active Terminology for Europe",
"prefix": "20",
"wikidata_database": "Q1520860"
},
"200": {
"description": "Unique controlled language for indexing, exchanging, searching for educational information, language for the various actors of education: pupils, documentalists, teachers, administrative staff, etc. Language specializing in the field of education and Education and contents of French general education; Reference language used in the colleges and lycΓ©es, the IUFM, the CAFA network, the CDI network of agricultural education and throughout the SCΓRΓN network ( CNDP-CRDP-CDDP-CLDP) Language enriched and updated by specialists in documentation and education, coordinated by the CNDP Total number of terms 21432, Number of descriptors 10310, Number of non-descriptors 11122, Number Of microthesaurus 68 + 10 annexes.",
"homepage": "http://www.cndp.fr/thesaurus-motbis/site/",
"name": "Thesaurus MOTBIS",
"prefix": "200"
},
"2000": {
"description": "Systematics for the International Archive Bibliography of the Archive School Marburg",
"homepage": "https://www.online.uni-marburg.de/archivschule/",
"name": "Systematics of the International Archives Bibliography",
"prefix": "2000"
},
"20000": {
"abbreviation": "bartoc-formats",
"description": "Data formats for Knowledge Organization Systems as listed in BARTOC.org",
"homepage": "http://bartoc.org/",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "BARTOC data formats",
"prefix": "20000"
},
"20001": {
"abbreviation": "bartoc-access",
"description": "This vocabulary is used to specify the access modes of a knowledge organization system listed in BARTOC.org: free (the vocabulary is freely available), registered (access requires registration), or licensed (access requires a personalized license).",
"homepage": "http://bartoc.org/",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "BARTOC access modes",
"prefix": "20001"
},
"20002": {
"abbreviation": "bartoc-api",
"description": "Vocabulary service API types",
"homepage": "http://bartoc.org/",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "BARTOC vocabulary API types",
"prefix": "20002"
},
"2001": {
"description": "The system was developed in 1995 and is a mirror of its time, it can be limited and very carefully changed. Each book is provided by us with a main rubric and up to 10 secondary rubrics. In combination with the other search criteria, the system proves to be an indispensable research tool.",
"homepage": "http://pw-portal.de/bibliografie/systematik",
"name": "Systematics of the Annotated Bibliography of Political Science",
"prefix": "2001"
},
"2002": {
"description": "The bibliography on the history of Silesia records the history of the historically working sciences on the past of the region and thus fulfills a scientific and a scientific-popular function. Both monographs and contributions from anthologies and journals (except for the daily press and weekly newspapers) are considered. Input into the database is primarily the history of scientific publications as well as contributions from other scientific disciplines concerning historical content. Literature with a country-specific character, as well as those dealing with problems of the present (publications in the field of political, economic or social sciences), will only be taken into account if their content has references to the history. The bibliography records the territory of historical Silesia and parts of the country that are historically related to Silesia. The parts of Silesia, which are now in the Czech Republic, are also part of the Lubusz region and part of Upper Lusatia. The online database contains the bibliographical material from the years 1990-2010. At present, it has more than 60,000 titles and is constantly being expanded.",
"homepage": "http://www.bhsl.pl/systematyka",
"name": "Bibliografia Historii ΕlΔ
ska Systematyka",
"prefix": "2002"
},
"2003": {
"description": "The list heading names and titles of the Library of Catalonia (LenΓ΄tre) contains authority records name, title, and name-title used for the classification of documents. The authority records can include, in addition to the heading, headings not accepted related headings and notes about the use of the header.\n\n Cataloging rules used by the library to choose and shape of name headings, name-title and title are the Anglo-American Cataloging Rules (Part II). The authorities used format is the MARC 21 Format for Authority Data.\n\n The list contains authority records created by the Library since 2000 - at that time the Library began implementing the guideline maintenance of authority records name, title, and name-title CD-P 010 Manual procedures of the Library of Catalonia: descriptive cataloging.\n\n The constant introduction of new headers and the need to review and update existing headings LenΓ΄tre make the organism live in a perpetual process of transformation and change. Updates the content of the database monthly fee.\n\n Hopefully LenΓ΄tre promotes the standardization of our catalogs to facilitate access to and exchange of bibliographic information.",
"homepage": "http://www.bnc.cat/lenoti/",
"prefix": "2003"
},
"2004": {
"description": "The catalog of names and titles authorities of Catalonia (canticle) is a catalog of cooperative authorities carried out in the Catalog of the Universities of Catalonia (CCUC) and is led by the Library of Catalonia.\n\nIts aim is to standardize access points of bibliographic catalogs, improve communication between the various catalogs and especially encourage the search and retrieval of information.\n\nHis records are available to authorities following types:\n\nβ’ Names of individuals and families\n\nβ’ Names of body\n\nβ’ Names of Congress\n\nβ’ Uniform Titles\n\nβ’ Combinations name-title when a main, added, subject added, or series added under the name of a person, entity or congress includes a uniform title\n\nExcluding records following authorities:\n\nβ’ thematic headings\n\nβ’ Geographical names\n\nβ’ Terms genre / form\n\nβ’ Names with subject subdivision\n\nCanticle gives special treatment to the authorities of the name and title linked to Catalan culture. These authorities are complete and authoritative work provides, in many cases, access to information from the Encyclopedia (Encyclopedia Catalan UAA).\n\nCatalan regional authority considers:\n\nβ’ persons and / or entities born and / or living in Catalonia,\n\nβ’ individuals and / or organizations that use the Catalan language as a means of expression,\n\nβ’ any person and / or organization of special interest to the Catalan culture\n\nβ’ authorities according AACR2r be established from reference works Catalan eg Greek and Latin classics, etc.\n\nβ’ securities linked to Catalan regional authorities, eg titles Catalan collections, anonymous classical works written in Catalan, etc.",
"homepage": "http://cantic.bnc.cat/",
"name": "Name and Title Authority File of Catalonia",
"prefix": "2004",
"wikidata_database": "Q8342938"
},
"20049": {
"abbreviation": "SDNB",
"description": "DDC-Subject groups and included DDC classes for the New Release Service and the Series A, B, C, H and O of the Deutsche Nationalbibliografie (based on DDC 23). Used since 2004.",
"homepage": "https://www.dnb.de/ddcindnb",
"pattern": "^[0-9]([0-9][0-9](\\.[0-9][0-9]?)?)?|[BKS]$",
"prefix": "20049",
"wikidata_database": "Q67011877"
},
"2005": {
"description": "The portal of the National Authority of the Czech Republic focuses on a fragmented information on the issue (in the broadest sense) of the creation and use of sets of national authorities of all types.\n\nNominated authorities include a set of personnel and corporate authorities (names of institutions and actions), gender, family, and author / author authority for use in both document and document processing.\n\nSubjects of authority include sets of thematic, geographical and formal authorities, making available a set of chronological authority terms is being prepared. Within this database is also published a set of Conspectus groups (Czech and English version) and a set of authorities for the places of release of old prints.\n\nIn 2006 a trial operation for the creation and use of name authorities for Czech book production and musical works (music and sound recordings) was launched. Under name titles, we include authorities for unified titles and methodology, as well as author / name authorities. Name authorities are used in both name and subject processing.",
"homepage": "http://aleph22.nkp.cz/F/?func=file&file_name=find-b&CON_LNG=CZE&local_base=aut",
"name": "Czech National Authority Database",
"prefix": "2005",
"wikidata_database": "Q13550863"
},
"20050": {
"abbreviation": "FKDigBib",
"homepage": "http://fkdigbib.de/ueber.html",
"pattern": "^[0-9]+$",
"prefix": "20050"
},
"20051": {
"description": "The Open Science Taxonomy has been developed in project FOSTER (Facilitate Open Science Training for European Research) to map basic concepts of Open Science.",
"homepage": "https://www.fosteropenscience.eu/about#download",
"license": "CC-BY-4.0",
"name": "Open Science Taxonomy",
"prefix": "20051"
},
"20052": {
"abbreviation": "UMLS",
"description": "The Unified Medical Language System (UMLS) is a compendium of many controlled vocabularies in the biomedical sciences.",
"homepage": "https://www.nlm.nih.gov/research/umls/index.html",
"name": "Unified Medical Language System",
"prefix": "20052",
"wikidata_database": "Q455338"
},
"20053": {
"description": "Collection of more than 6,000 words and terms in Catalan, Spanish and English related mainly with the welding and allied technologies. Elaborated by the ITCS (Institut Tècnic Català de la Soldadura).",
"homepage": "http://www.itcsoldadura.org/images/pdfs/vocabulari_ed3.pdf",
"name": "Joining vocabulary",
"prefix": "20053"
},
"20054": {
"description": "Dictionary of geographical terms in Catalan, with some 4,000 entries.",
"homepage": "https://publicacions.iec.cat/repository/pdf/00000238/00000007.pdf",
"name": "Contribution to the Catalan geographical terminology",
"prefix": "20054"
},
"20055": {
"description": "This book is a necessary reference for librarians, researchers, students, and general users of the library, including the overall literature and information science of Korea and the current status and operation of libraries. After the first publication of \"Library Studies and Information Studies Dictionary\" in 1986, the title was changed to \"Literature Information Dictionary\" in 1996 and the revised edition is published this time.",
"homepage": "http://www.kla.kr/jsp/fileboard/termdic.do",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Glossary of Library and Information Science",
"prefix": "20055"
},
"20056": {
"abbreviation": "KSIC",
"description": "The Korea Standard Industry Code (KSIC) is a systematic classification of industrial activities performed mainly by production units (business units, business units, etc.) according to their similarity. This Korean Standard Industrial Classification was prepared for statistical purposes, such as collecting, marking, and analyzing industry-related data, and the Statistics Act stipulates that all statistical agencies are required to use it for the accuracy and comparability of industrial statistical data.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Korea Standard Industry Code",
"prefix": "20056"
},
"20057": {
"abbreviation": "ESC",
"description": "The Educational Subjects Classification (ESC) is an extension of the International Standard Classification of Education (ISCED-2013). For example, it can be used for classifying by subject services that enable access to or discovery of educational resources. It is developed and maintained in the context of the OER Worldmap (OER = Open Educational Resources).",
"homepage": "https://w3id.org/class/esc/scheme",
"name": "Educational Subjects Classification",
"prefix": "20057"
},
"20058": {
"abbreviation": "Hist Ant",
"description": "local shelf classification ancient history at TIB library",
"homepage": "https://www.tib.eu/systematik/systemstelle.php?st_id=13",
"prefix": "20058"
},
"20059": {
"abbreviation": "FBR",
"description": "local shelf classification law at TIB library",
"homepage": "https://www.tib.eu/systematik/systemstelle.php?st_id=15",
"prefix": "20059"
},
"2006": {
"homepage": "http://baslerafrikabibliographien.faust-web.de/dothes.FAU?sid=EA53B6461&dm=1&thes=1",
"name": "Thesaurus of Basler Afrika Bibliographien",
"prefix": "2006"
},
"20060": {
"abbreviation": "FBS",
"description": "local shelf classification social sciences at TIB library",
"homepage": "https://www.tib.eu/systematik/systemstelle.php?st_id=9",
"prefix": "20060"
},
"20061": {
"abbreviation": "FBH",
"description": "local shelf classification economics at TIB library",
"homepage": "https://www.tib.eu/systematik/systemstelle.php?st_id=7",
"prefix": "20061"
},
"20062": {
"abbreviation": "Hist",
"description": "local shelf classification history at TIB library",
"homepage": "https://www.tib.eu/systematik/systemstelle.php?st_id=12",
"prefix": "20062"
},
"20063": {
"description": "local shelf classification mathematics at TIB library",
"homepage": "https://www.tib.eu/systematik/systemstelle.php?st_id=18",
"prefix": "20063"
},
"20064": {
"abbreviation": "RelGes",
"description": "local shelf classification history of religion at TIB library",
"prefix": "20064"
},
"20065": {
"abbreviation": "RelSys",
"description": "local shelf classification religion at TIB library",
"homepage": "https://www.tib.eu/systematik/systemstelle.php?st_id=10",
"prefix": "20065"
},
"20066": {
"description": "It is preparing and implementing development strategies at the pan-government level to enhance social benefits through the development of blockchain technology, support the development of source technology and manpower, survey the status of policy effects analysis, and establish a standardized classification system.\nIn order to prepare relevant statistics and utilize them for administrative purposes, the classification system for blockchain technology industry classification is prepared in a subdivided and updated form and the public notice is promoted.",
"homepage": "http://kostat.go.kr",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Blockchain Technology Industry Code",
"prefix": "20066"
},
"20067": {
"abbreviation": "SKTC",
"description": "The Korean Standard Trade Classification is a systematic classification of this product according to certain criteria and principles, such as its characteristics, characteristics of materials used in production, and production stages, in order to collect, analyze and compare data on products subject to foreign trade.",
"homepage": "http://kssc.kostat.go.kr/ksscNew_web/link.do?gubun=003",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Standard Korean Trade Classification",
"prefix": "20067"
},
"20068": {
"abbreviation": "KCEAP",
"description": "βΆ Purpose of classification\nSNA(System of National Account) is prepared, used as a standard for household expenditure surveys and consumer price surveys of consumer price surveys.\nβΆ Classification criteria\n* The Classification of Individual Consumption According to Purpose (COICOP) by Purpose, Classification of the Purposes of Non-Profit Institutions Serving Households(COPNI), and Classification of the Functions of Government (COFOG) established by the United Nations\n- Developed to meet international standards.\n* The Classification of Individual Consumption According to Purposes (COICOP) classifies all consumption expenditures by households, individual consumption expenditures by non-profit organizations and governments serving households.\n* The Classification of the Purposes of Non-Profit Institutions Serving Households\n(COPNI) is a classification of end-consumption, intermediate consumption, total capital formation, light transition and capital transfers spent by non-profit organizations.\n* The Classification of the Functions of Government (COFOG) is a classification of transactions concerning final consumption, intermediate consumption, total capital formation, current transfers and capital transfers spent by the government.\nβΆ Classification structure\n- COICOP-K consists of 15 divisions, 63 groups, 188 classes, and 353 tax categories.\n- COPNI-K consists of 9 divisions, 26 subgroups, and 30 classes.\n- COFOG-K consists of 10 divisions, 68 groups, and 108 classes.",
"homepage": "http://kssc.kostat.go.kr/ksscNew_web/index.jsp#",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Korean standard Classification of Expenditure According to Purpose",
"prefix": "20068"
},
"20069": {
"abbreviation": "COICOP-K",
"description": "Classification of all consumption expenditures by households, individual consumption expenditures by non-profit organizations and governments serving households",
"homepage": "http://kssc.kostat.go.kr/ksscNew_web/index.jsp#",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Korean Standard Classification of Individual Consumption According to Purpose",
"prefix": "20069"
},
"2007": {
"description": "Eesti mΓ€rksΓ΅nastik' (EMS) is a estonian subejct thesaurus structure",
"homepage": "http://ems.elnet.ee/",
"name": "Estonian Subject Thesaurus",
"prefix": "2007",
"wikidata_database": "Q12361632"
},
"20070": {
"abbreviation": "COPNI-K",
"description": "Classification of transactions concerning final consumption, intermediate consumption, total capital formation, current transfers and capital transfers spent by non-profit organizations",
"homepage": "http://kssc.kostat.go.kr/ksscNew_web/index.jsp#",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Korean Classification of the Purposes of Non-Profit Institutions Serving Households",
"prefix": "20070"
},
"20071": {
"abbreviation": "COFOG-K",
"description": "Classification of transactions concerning final consumption, intermediate consumption, total capital formation, current transfers and capital transfers spent by the government",
"homepage": "http://kssc.kostat.go.kr/ksscNew_web/index.jsp#",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Korean Classification of the Functions of Government",
"prefix": "20071"
},
"20072": {
"description": "- In order to foster the rapidly growing spatial information industry in various fields such as logistics and culture as a new growth engine, the scope of related industries is specified and prepared for the production of accurate industrial status statistics.\n- Prepare the spatial information industry (industries that produce, manage, process and distribute spatial information* or integrate with other industries to build systems or provide services) in Article 2 of the Space Information Industry Promotion Act.\n* Location information of natural or artificial objects in space, such as ground, underground, water, water, water, etc., and spatial cognition information related to them.\n- Businesses belonging to the spatial information industry are classified into six divisions, 16 divisions, and 20 groups, including manufacturing, wholesale and service industries, in accordance with the Korean Standard Industry Classification (KSIC, 10th).\nβ Including spatial information such as LBS* and ITS** games, related industries that are used in convergence or various combinations with or are used as linked industries\n* Location based services, ** Intelligent transport system\n- A project to utilize survey and satellite images as spatial information\n- Location-based service industry and equipment related to location determination, such as satellite measurement\n- Development of software for the production, management, processing, and distribution of spatial information\n- education, counseling, etc. related to spatial information",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Spatial information industry",
"prefix": "20072"
},
"20073": {
"description": "- Established to prepare the standards for basic surveys to establish tourism policies\n- Based on the Standard International Classification of Tourism Activities co-written by the World Tourism Organization and the United Nations Statistical Commission, it reflects the characteristics of the domestic industry.\n- Includes construction, automobile sales, transportation, lodging and restaurant business, real estate and mechanical equipment rental business, travel agencies and other travel assistance businesses, etc.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Tourism Industry",
"prefix": "20073"
},
"20074": {
"description": "- Establishment of design policies to enhance the competitiveness of the design industry and upgrading the forecast environment\n- Improving the reliability of design industry statistics defined as design companies and design utilization companies and enhancing the effectiveness of design policies such as time series prediction.\n- Prepare a classification system (plan) for the design industry, which is divided into 8 major categories, 42 middle categories, and 154 small groups, including the establishment of new service and experience designs.\n* The current Korean Standard Industrial Classification (KSIC, 9th) consists of four categories: interior design, product design, visual design, and other professional design.\n- It is a comprehensive design industry classification system that includes all design-related industries in addition to the existing professional design industry.\n* The classification structure consists of three stages: large, medium, and small. The classification code uses Arabic numerals (large, one digit, two digits, and three digits).",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Design industry",
"prefix": "20074"
},
"20075": {
"description": "- Statistical infrastructure to support the robot industry selected as a national strategic industry.\n- The National Science and Technology Committee selected the robot industry as a national strategic industry and established a project plan for \"Intelligent Robot Industry Vision and Development Strategy\" based on it, the Ministry of Commerce, Industry and Energy, the Ministry of Information and Communication, and the National Statistical Office worked together to enact it.\n- Manufacturing robots, service robots and related components, robot systems, robot embedded*, robot services, etc.\n*Means a product that does not appear to be a robot, but is technically a robot.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Robot industry",
"prefix": "20075"
},
"20076": {
"description": "- Provides a framework for analyzing industry-related and cost-benefit analysis of activities (logistics) related to freight transport that cannot be directly identified in the Korean Standard Industry Classification\n- Prepare the logistics business as prescribed by the Framework Act on Logistics Policy and the Restriction of Special Taxation Act based on the logistics industry.\n- Includes activities to directly transport freight, operation and lease of transportation support facilities, and transportation-related services;",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Logistics industry",
"prefix": "20076"
},
"20077": {
"abbreviation": "SSISC",
"description": "- Select items corresponding to the social service industry based on the Korean standard industry classification and prepare a social service industrial special code (SSISC) and use it as a means to prepare basic statistics for the relevant industries.\n- Development of new social services, integration and integration of social services, and establishment of a consumer-centered social service industry\n- Raise the status of social services included in the top five creative service industries along with major promising industries that have already established special categories such as IT, content, sports and tourism.\n- Article 32 of the Framework Act on Social Security, Article 5 of the Act on the Use of Social Services and the Management of Permissions, and Article 2 of the Enforcement Decree of the same Act\n- Under the Framework Act on Social Security, projects belonging to the social service industry are classified into 8 large, 15 middle, and 44 small groups in accordance with the Korean Standard Industry Classification (KSIC, 9th).",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Social Service Industrial Special Code",
"prefix": "20077"
},
"20078": {
"description": "- Select items corresponding to the fire industry based on the Korean standard industry classification and prepare a special classification of the fire industry, and use them as a means to prepare basic statistics for policymaking in related industries.\n- Classification system for systematic development of related industries by increasing the importance and scale of the fire industry\n- Prepare a classification system for the fire industry by dividing the design, construction, supervision, management, fire prevention, manufacturing, wholesale and retail, education, etc. into nine major categories, 21 divisions, and 38 minor categories.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Fire industry",
"prefix": "20078"
},
"20079": {
"description": "The existing special classification of fisheries in operation is expanded to special classification of marine fisheries in order to analyze the structure of the marine industry and understand the basic status such as market size, prepare national statistics related to marine fisheries, and support policies.\n- inclusion of secondary outputs processed as inputs from the results of collection, capture, form, collection and extraction of marine and fishery resources;\n- Include inputs mainly used in the production of primary and secondary outputs related to the marine fisheries industry.\n- Activities to provide goods and services necessary for the protection, preservation, development, management, leisure, sports, etc. of marine fishery resources are included.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Ocean and fishery industry",
"prefix": "20079"
},
"2008": {
"homepage": "http://www.fr.ch/bcu/a/bib_fri/plan_cl.htm",
"name": "Map of the Bibliography of Friborg",
"prefix": "2008"
},
"20080": {
"description": "As the national health promotion industry grows to foster healthy bodies and minds and use leisure time, it provides a basic framework for statistics and structural analysis of sports-related industries.\n- Manufacturing, construction, and related service industries that support sports activities under the National Sports Promotion Act\" and industries that produce and distribute goods and services to provide sports services.\"\n- Sports facility business under the \"Act on the Establishment and Use of Sports Facilities\"\n- Based on sports-related industries and products in the International Standard Industry Classification (ISIC Rev.4.0) and the Central Product Classification (CPC2.0)\n- Manufacturing, construction, distribution, and related services that support sports activities",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Sports industry",
"prefix": "20080"
},
"20081": {
"description": "- As the importance of the environment and energy industry increases, the framework for statistics and structural analysis of energy-related industries is provided.\n- Conversion of the current energy industry classification prepared in 2000 to the 9th Korea Standard Industry Classification System, which was revised and announced on December 28, 2007 in accordance with the UN's 3rd International Standard Industry Classification.\n- Acquisition, power generation and transmission of energy sources, electric gas and water supply projects",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Energy industry",
"prefix": "20081"
},
"20082": {
"description": "- Special classification of eLearning industries is established to analyze structures for eLearning industries, which are representative knowledge service industries, to understand the basic status such as market size, and to enhance the effectiveness of policies for fostering industries. Special classifications contribute to improving efficiency of research work and statistical utilization by enhancing reliability, stability, and international comparability of the eLearning industry survey (approval number 11528).\n- Established on the basis of Article 27 of the ELearning Industry Development Act (Statistics, etc.)\n- eLearning content, solutions and services included in the eLearning industry survey, plus additional hardware segments targeted at eLearning-related facilities and devices.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of e-learning industry",
"prefix": "20082"
},
"20083": {
"description": "- provide a classification system to establish a statistical foundation for structural analysis of the disaster safety industry, understanding the current status of the market, establishing and supporting policies for fostering the relevant industries, and supporting systematic development policies.\n- The Minister of Public Safety and Security classifies and manages industries in disaster prevention products and disaster prevention for fostering the disaster prevention business pursuant to Article 58 and for stable procurement and quality control of materials and materials needed for rapid recovery prevention projects.\n- By integrating the special classification and special classification of the disaster safety industry, the composition system of the disaster prevention, response, and recovery stages has been changed from the existing industrial activities to the disaster prevention and recovery system, consisting of 5 divisions, 16 divisions, and 71 small groups.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of disaster safety industry",
"prefix": "20083"
},
"20084": {
"description": "- Systematic production of the copyright industry statistics due to the expansion of the scope of the copyright industry and the increase of social interest\n- To establish a classification system necessary for establishing policies for the copyright industry based on the WIPO (World Intelligent Property Organization)'s Guide to Economic Contribution of Copyright-Based Industries.\n- Comprehensive scope is set according to the actual conditions of the domestic industry by referring to the comprehensive scope of the WIPO copyright industry.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of copyright-based industries",
"prefix": "20084"
},
"20085": {
"abbreviation": "ICT",
"description": "- Prepare in order to understand the current status of information and communication technology related industries and to utilize them for related policies.\n- Based on Korea Standard Industry Classification and OECD Classification of Information and Communication Technology Industry\n- Industries that realize or enable the processing and communication functions of information, including transmission and presentation, mainly through electronic means: OECD Committee for Science and Technology Industry (STI Committee)",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Information and Communication Technology",
"prefix": "20085"
},
"20086": {
"description": "- Establishes a statistical foundation for the intellectual property service industry, whose international value is increasing due to the increase in patent applications and disputes, and provides a basic classification system to support the establishment of systematic incubation policies for related industries.\n- prepare based on the intellectual property service industry as prescribed by the Framework Act on Intellectual Property and the Inventions Promotion Act.\n- Industrial activities such as intellectual property law proxy business, intellectual property assessment, rental and brokerage business, intellectual property distribution business, intellectual property information service business, intellectual property consulting, education, and promotion of intellectual property, etc.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of intellectual property industry",
"prefix": "20086"
},
"20087": {
"description": "- To support the policy, the Ministry of Culture decided to unify the promotion policy of the content industry following the reorganization of the government in 2008.\n- Referring to international standards prepared by the OECD (Content Media Industry Classification) and UNESCO (2009 UNESCO Framework for Cultural Statistics) and reflecting the characteristics of domestic industries\n- Includes music, film and video, animation industry, broadcasting industry, game industry, performance industry, craft and design industry, advertising industry, information service industry, intellectual property management, etc.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Contents Industry",
"prefix": "20087"
},
"20088": {
"description": "- prepared to understand the current status of environment-related industries and utilize them for policies based on the OECD's \"Environmental Goods and Services Industry\" and \"Korea Standard Industry Classification\"\n- Established in collaboration with the Ministry of Environment on the basis of the \"Environmental Goods and Services Industry\" stipulated by the OECD\n- Industries that produce goods and services that can measure, prevent, control, and minimize environmental hazards of water, air, and soil and problems related to waste, noise, and environmental systems.\n- Also included are clean technologies, goods and services that reduce environmental risks and minimize pollution and resource utilization.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Environment Industry",
"prefix": "20088"
},
"20089": {
"description": "The item classification table is the total income of all household members, including household owners, in income, mainly cash, securities and spot income brought into the household at the cost of labor and business, and consists of current and non-current income. It is classified as allocation of interest income, property, insurance, trust, etc. arising from interest on household income, such as current income, all cash, securities and spot remuneration paid for work, household owner's income, spouse's income, other household income, business income, property income, bonds, and savings.\nIn terms of expenditure, household expenditure, consumer expenditure, first foodstuffs (grain, rice, etc.), grain processing, meat, dairy, fish, dried fish, fish, fish farming, fish farming, vegetable algae, vegetables, seaweed, seafood, bread and maintenance, snacks. The second housing is classified as monthly rent, repair cost of housing facilities, and fire insurance, while the third mineral water is classified as water, electricity, fuel, and heating cost of apartments. The fourth furniture furniture is classified as general furniture, household appliances, and kitchenware, while the fifth clad shoes are classified as hanbok, outerwear, sweaters and shirts. The sixth health care is divided into medicines, health care supplies, and health care services, and the seventh education includes direct and indirect learning activities (hagwons, private lessons) for the products and related services needed for the curriculum. The eighth cultural entertainment is the expenditure on goods and services necessary for the purposes of culture, entertainment, hobbies, etc., classified as books, printed materials, cultural entertainment equipment, etc. The ninth traffic communication is classified as public transportation, personal transportation, etc. as a classification of expenditures on human transportation, transportation of goods, and services necessary for the delivery of information. The tenth consumer expenditure is classified as expenditure on goods and services not classified in the broad category from foodstuffs to transportation and communications, and transfer expenditure that cannot be included in households' free expenditures such as taxes, public pensions and social insurance.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of households total income and expenditures",
"prefix": "20089"
},
"2009": {
"description": "The Glarner Bibliography has been published annually since 1996. It shows the literature of Glaronensia.",
"homepage": "http://www.gl.ch/xml_1/internet/de/application/d1256/d33/d106/d124/f132.cfm",
"name": "Systematics of the Glarner Bibliography",
"prefix": "2009"
},
"20090": {
"abbreviation": "BEC",
"description": "Classification by Broad Economic Categories (BEC) identified by SKTC (Standard Korean Trade Classification), Harmonized Community and Coding System of Korea (HS-K), Korea Product Classification (KCP) Service, etc.\n\nThe development of the classification process was carried out in earnest by the United Nations Statistical Commission held in 1965, when the need for classification of import and export statistics such as the International Standard Trade Classification (SITC) was raised, and the classification was recommended in 1971 to reflect the opinions of UN member states and relevant international organizations.\nThe enacted BEC was basically composed of 19 categories to respond to the final classification of use used by the System of National Accounts (SNA), such as capital goods, intermediate goods, and consumer goods systems.\nThe enacted BEC has organized a classification system exclusively for goods. Since its enactment, it has been revised based on classification tables and explanatory materials four times, reflecting the revision results of SITC and HS, which are related product categories. The first and second amendments to the U.N. recommended were table amendments that reflected the SITC amendments, the third correction corrected errors in the BEC technology, and the fourth amendment was made with the relevant table amendments that reflected the HS amendments.\nThe revision of the BEC was carried out in parallel with the revision of the KCPC (Korea Goods and Service Classification) in March 2018, and the final revision classification system was finalized and operated in December 2018 after three rounds of meetings with statistical authorities and public opinion collection and classification experts. BEC's final revised classification system features a more detailed and structural system than the previous classification system, including a new service sector, a mix of economic activities and end uses, and a single system of general and special intermediate consumption to identify the international value chain.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification by Broad Economic Categories",
"prefix": "20090"
},
"20091": {
"abbreviation": "KCPC",
"description": "Based on internationally agreed concepts, definitions, principles, and rules, the KCPC organized a logical and consistent statistical classification system for products such as goods and services.\nIn addition, the revised KCPC strives to improve the suitability of reality by reflecting trends in domestic economic structure and production changes, and is designed to improve comparability and connectivity with industrial activity and trade-related statistics.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Korean central product classification",
"prefix": "20091"
},
"20092": {
"abbreviation": "KSCED",
"description": "- It is designed to improve comparability between domestic and foreign educational statistics, to identify education-related population trends, to efficiently allocate human and financial resources to education, to diagnose advantages and disadvantages of policies and institutions, and to benchmark outstanding overseas education policies and systems.\n- Korean standard education classification is largely divided into education level and education sector.\n- The education level sector was divided into the field of education programs and the field of number of education, and each unit was divided into three classes: large, medium, and small.\n- The large classification was classified in stages according to the curriculum of infant and primary and graduate schools based on the level of education.\n- Based on the nature of education, the division was divided into general education and vocational education from 2nd stage of electrical middle school (middle school) to 5th stage of professional education (or equivalent) and 8th stage of Ph.D. (or equivalent) courses.\n- In the case of small classification, the classification was subdivided based on the completion of each phase of the curriculum and qualification to the higher level of education. In the classification of the number of classes, the classification was subdivided based on the highest level of education learned by individuals.\n- The basic classification units in the field of education are education programs and related qualifications, and each unit is composed of three classes of major, minor and minor categories.\n- The large and middle categories are determined by the similarity of the purpose of learning and the theoretical knowledge underlying the area of the training program, and more specifically by the object of interest of the program.\n- Most of the classifications are divided into the tools and equipment used in the training program, along with the methods and techniques of the training program.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Korean Standard Classification of Education",
"prefix": "20092"
},
"20093": {
"description": "It is the job classification that systematically types what individuals are doing for income (economic activities) according to the type of work performed, and the Korean Standard Classification of Occupations (KSCO) is standardized to suit the job structure and status of Korea.\nThe Korean standard occupation classification is based on the ability to carry out the tasks and tasks of a given job, and is considering the job level and type of job. Skill level refers to the height of job performance, which is determined by regular education, vocational training, vocational experience, and innate ability and socio-cultural environment. Skill specialization relates to the field of knowledge required to perform a task, the tools and equipment used, the raw materials input, and the types of goods or services produced.\nAn occupation is a group of jobs that have similar task similarities. Distinguishing a set of tasks from other occupations and classifying them into the same profession presupposes a degree of similarity, which is equivalent to presenting job-specific job exclusivity that defines different tasks. However, it is very difficult to determine task-specific similarities and exclusivity due to the complexity of job performance conditions and the gap in job scope due to differences in the size of the enterprise.\nThe criteria for task similarity include knowledge, experience, and skill required by the person performing the task, as well as the skill requirements required by the person performing the task. Sometimes, the characteristics of companies where professionals mainly work, the process of production, or the final output, are important. Non-similar jobs can be called different jobs because the requirements of exclusivity are met, and if the labor market formation varies from job to job, it can be said that they have the most obvious exclusivity.\nIn addition, the size of employment by job is also a realistic criterion in the task categorization criterion. The Korean Standard Occupational Classification was established based on the employment of at least 1,000 people in the class unit, and 5,000 to 10,000 people are believed to be distributed in the class with a large number of employees.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Korean Standard classification of occupations",
"prefix": "20093"
},
"20094": {
"abbreviation": "KECO",
"description": "- prepared and utilized by the Ministry of Employment and Labor for administrative purposes for the delivery of job information such as job search and employment.\n- Same as the scope of the Korean standard job category\n- Match-linked 1:1 with the 7th Korea Standard Job Classification in the class (4-digit code) and have the same comprehensive range for each category\n- The Ministry of Employment and Labor (Korea Employment Information Service) has been used to provide information on job placement in the labor market, but it has difficulty in using it as an unauthorized classification, so it is requested to designate it as a special purpose classification of Korean standard occupations.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Korean Employment Classification of Occupations",
"prefix": "20094"
},
"20095": {
"abbreviation": "HRST",
"description": "Redesigning the concept of maximum consultation, consultation, and extended intention by combining the level of education above the level of professional education by the International Standard Education Classification with managers, experts and related workers",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Human Resources in Science and Technology",
"prefix": "20095"
},
"20096": {
"description": "In the digital economy, ICT (Information Communication Technology) personnel have emerged as a major force in the information age, providing a framework for efficient identification of personnel, enhancing statistical timeliness and international comparability, and providing basic data for ICT personnel policy.\nKorea Standard Job Classification (KSCO) selects and reclassifies items related to ICT (Information and Communication Technology (ICT) occupations.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Occupational Classification of Information and Communication Technology",
"prefix": "20096"
},
"20097": {
"description": "- Behavior classifications are divided into 9 sections, 42 divisions, and 138 subcategories according to the purpose of the respondents' actions.\n- Behavior classification code is composed of three digits, first of which represents a large category, second of which represents a middle category, and third of which represents a small category.\n- Korean behavioral classification code has been established according to the actual conditions of Korean society based on international standards.\n- International standards have not been applied, but the National Statistical Office has established and applied by itself.\n- International standards include the United Nations' Classification of Conduct (2012), but each country that conducts a survey on living hours has been classified according to the national characteristics and recommends that Korea uses its own classification system accordingly.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Korean Time Use Survey",
"prefix": "20097"
},
"20098": {
"abbreviation": "KCSE",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Korea Classification of Status in Employment",
"prefix": "20098"
},
"20099": {
"abbreviation": "KCD",
"description": "The Korean Standard Classification of Diseases (KCD) is a systematic classification of disease and death data in South Korea, including medical records and cause-of-death statistical surveys, based on similarities in their nature. Ensure consistent and comparative data by applying standardized criteria when preparing statistics that identify healthcare phenomena.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Korean Standard Classification of Diseases",
"prefix": "20099"
},
"201": {
"description": "For use in Electronic Database Searching. These terms are the terms commonly used by ERIC/CSMEE and ENC, this is not an exhaustive list and is by no means the only list of search language available. It is intended as a guideline for educators.",
"homepage": "https://archive.org/details/ERIC_ED462305",
"name": "Thesaurus of Environmental Education Terms",
"prefix": "201"
},
"2010": {
"description": "The purpose of the Basic Concepts Classification is first to identify an extensive and hierarchically organized set of βbasic conceptsβ: concepts that can readily be understood across disciplines and cultures. Second, all scholarly works can be classified in terms of combinations of these basic concepts. The Basic Concepts Classification thus provides a basis for a universal non-discipline-based classification.\n\nThere are three broad types of basic concept. Most basic concepts refer to real (or abstract) βthingsβ (phenomena) in the world (or to properties of those things). Yet there are also various relationships among things. Since the bulk of scholarly research -- and much of the general literature as well -- analyses how one or more things influence (or are related in other ways to) one or more other things, it is desirable to classify such works in terms of combinations of basic concepts. An important minority of scholarly works discusses the properties of one or more things or relationships. These adjective/adverbial properties form a third group of basic concepts. These properties can be combined with both things and relationships to more precisely capture the important elements of both types of work.",
"homepage": "https://sites.google.com/a/ualberta.ca/rick-szostak/research/basic-concepts-classification-web-version-2013",
"name": "Basic Concepts Classification",
"prefix": "2010"
},
"20100": {
"description": "- To understand the classification of Korean medicine, we need to understand the structure and purpose of the Korean Standard Disease Classification (KCD) and understand and utilize the unique concept of disease used in oriental medicine. For an understanding of the terms used in the classification of oriental medicine, see \"Standard Medical Glossary\" published in 2006 (issued by the Korean Medical Association, ISBN 89-).\n- The 3rd revision of the Classification of Korean Standard Diseases (Korean Medicine) is based on the Korea Standard Classification of Diseases (KCD), and is composed by adding the name of the disease, oriental diseases, and ideological diseases considering the special conditions of Korea.\n- In the 2nd revision of the Classification of Korean Standard Diseases (Korean Medicine), there were few considerations for connectivity with KCDs, and there were many overlapping contents with KCDs. Therefore, the 3rd revision of the Classification of Korean Standard Diseases (Limit) considers sufficient linkage with KCD while minimizing duplication with KCD.\n- As with the Korea Standard Classification of Disease Control and Prevention (KCD), a classification table for statistical assessment of the classification of Korean medicine in U-code is prepared.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Korean Standard Classification of Diseases(Oriental Medicine)",
"prefix": "20100"
},
"20101": {
"abbreviation": "KCF",
"description": "The overall purpose of the KCF is to provide a unified standard language and system to represent health and health-related states. The KCF defines components of health-related well-being states (e.g., education and labor). Therefore, KCF consists of health domains and health-related domains.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Korean Standard Classification of Functioning, Disability and Health",
"prefix": "20101"
},
"20102": {
"description": "The Patient Classification System is a system in which patients are classified into similar groups in terms of clinical significance and medical resource consumption using chronic diseases, procedures, and functional conditions. There are five subclassification systems.\nγ
Korean Diagnosis Related Group(KDRG)\nγ
Korean Rehabilitation Patient Group(KRPG)\nγ
Korean Outpatient Group(KOPG), 588 Classification System\nγ
Korean Diagnosis Related Group-Korean Medicine(KDRG-KM)\nγ
Korean Outpatient Group-Korean Medicine(KOPG-KM)",
"homepage": "http://biz.hira.or.kr",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Patient Classification System",
"prefix": "20102"
},
"20103": {
"abbreviation": "KDRG",
"description": "KDRG is a Korean version of DRG(Diagnosis Related Group), which is used as a payment unit for medical expenses for each disease group in Korea, and is used to calibrate patient composition when calculating relative indicators for comparison of hospital expenses.",
"homepage": "http://biz.hira.or.kr",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Korean Diagnosis Related Group",
"prefix": "20103"
},
"20104": {
"abbreviation": "KRPG",
"description": "The Rehabilitation Patient Classification System (KRPG) is a system that classifies inpatients who receive intensive rehabilitation treatment, and is the first of its kind developed in Korea after the acute period. Unlike the acute phase patient classification system, patients are classified as a variable to utilize the cause of damage, functional assessment (recognition function, ability to perform daily life, exercise and sensory functions).",
"homepage": "http://biz.hira.or.kr",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Korean Rehabilitation Patient Group",
"prefix": "20104"
},
"20105": {
"abbreviation": "KOPG",
"description": "The Outpatient Classification System (KOPG) is used as a correction tool for patient composition in comparison with hospital-to-patient care costs and has been continuously revised to reflect clinical reality since Ver 1.0 was developed in 2006.",
"homepage": "http://biz.hira.or.kr",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Korean Outpatient Group",
"prefix": "20105"
},
"20106": {
"abbreviation": "KDRG-KM",
"description": "Korean Diagnosis Related Group-KM (KDRG-KM) developed Ver 1.0 in January 2015 to use it as a correction tool for patient composition for comparison between medical institutions and has been continuously revised to reflect changing healthcare environments.",
"homepage": "http://biz.hira.or.kr",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Korean Diagnosis Related Group-KM",
"prefix": "20106"
},
"20107": {
"description": "Provides statistical standard terms and indicators alphabetically",
"homepage": "https://kostat.go.kr/understand/info/info_lge/1/index.action?bmode=languge&keyWord=0",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Statistical standarad terms and index",
"prefix": "20107"
},
"20108": {
"description": "- Systematic preparation of regional statistics by coding administrative districts nationwide according to administrative system and administrative order\n- Regional statistical data is not only used to enhance comparability but also to refer to administrative work.\n- The administrative districts across the country are classified into three categories: large (city, province), middle (Gu, city, county), and small (eup, myeon, dong) and each level of classification is assigned a code, and the jurisdiction is specified.",
"homepage": "http://kssc.kostat.go.kr/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of administrative districts",
"prefix": "20108"
},
"20109": {
"description": "A Comparison of Inter-Korean Languages on the Unification Ministry's North Korea Information Portal and information on terms used in real life in North Korea",
"homepage": "https://kosis.kr/bukhan/nkDicary/selectNkTerm.do?menuId=M_03_04",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Dictionary of North Korea",
"prefix": "20109"
},
"2011": {
"description": "The\" Bibliography on the History of the German Workers Movement \"is the oldest periodical publication of the library of the Friedrich Ebert Foundation. [...] The database version of the bibliography is a\" bibliography on the history of the German workers' movement and on the theory and practice of the political left \"Includes a series of publications on the history of the German workers' movement, programmatic literature on leftist parties and trade unions, and daily publications by prominent figures of the leftist political spectrum, including scientific and journalistic texts, digital, printed and non-fiction (articles from anthologies and periodicals) ) And monographic publications.",
"homepage": "http://library.fes.de/inhalt/ueberuns/bizga-system.htm",
"name": "Systematics of the Bibliography on the History of the German Workers' Movement",
"prefix": "2011"
},
"20110": {
"description": "A Comparison of Inter-Korean Languages on the Unification Ministry's North Korea Information Portal and information on terms used in real life in North Korea",
"homepage": "https://kosis.kr/bukhan/nkDicary/selectNkTerm.do?menuId=M_03_04_01",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of North Korea",
"prefix": "20110"
},
"20111": {
"description": "A Comparison of Inter-Korean Languages on the Unification Ministry's North Korea Information Portal and information on terms used in real life in North Korea",
"homepage": "https://kosis.kr/bukhan/nkDicary/selectLangCmpr.do?menuId=M_03_04_02",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of North Korea - A Comparison of Languages of South and North Korea",
"prefix": "20111"
},
"20112": {
"description": "A Comparison of Inter-Korean Languages on the Unification Ministry's North Korea Information Portal and information on terms used in real life in North Korea",
"homepage": "https://kosis.kr/bukhan/nkDicary/selectItTermCmpr.do?menuId=M_03_04_03",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of North Korea - Comparison of South and North Korean IT Terms",
"prefix": "20112"
},
"20113": {
"description": "A Comparison of Inter-Korean Languages on the Unification Ministry's North Korea Information Portal and information on terms used in real life in North Korea",
"homepage": "https://kosis.kr/bukhan/nkDicary/selectNkPatter.do?menuId=M_03_04_04",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of North Korea - resident slang",
"prefix": "20113"
},
"20114": {
"description": "A Comparison of Inter-Korean Languages on the Unification Ministry's North Korea Information Portal and information on terms used in real life in North Korea",
"homepage": "https://kosis.kr/bukhan/nkDicary/selectKnwldgDicaryList.do?menuId=M_03_04_05",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of North Korea - - North Korea Knowledge Dictionary",
"prefix": "20114"
},
"20115": {
"description": "It is classified for the efficiency of price calculation and management by reflecting item-specific characteristics such as function for use purposes, and the medical material code system consists of the code of the place. Treatment materials are classified into large group classification, and the large classification is classified into application and functional classification, which is the method of use of the type material specification, and the name of each supplier's product name, manufacture and import business.",
"homepage": "http://www.hira.or.kr/co/ebook/list.do?pgmid=HIRAA030402000000",
"license": "CC BY-NC 4.0",
"name": "Classification of Materials for Medical Treatment",
"prefix": "20115"
},
"20116": {
"description": "The difficult terms used by the Health Insurance Review and Assessment Service were easily solved.",
"homepage": "https://www.hira.or.kr/re/term/getExplainList.do?pgmid=HIRAA030407000000",
"license": "CC_MARK",
"name": "Terms that make health information easier to understand",
"prefix": "20116"
},
"20117": {
"description": "This is a manual on the disease classification system and the code relating to claims for medical care currently used by the Health Insurance Review and Assessment Service.\nTherefore, the main focus is only on basic information about how the structure of the disease classification system in use is constructed and what the classification codes (number, pharmacology, treatment materials, etc.) that exist within the classification system give content and meaning.",
"homepage": "https://biz.hira.or.kr/cms/CO/notice26/__icsFiles/afieldfile/2005/10/04/1172128_02.pdf",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Classification of Health Insurance Code",
"prefix": "20117"
},
"20118": {
"description": "Encourage foreigners to recognize Korean art by proposing a translation of high-quality Korean art terms.\nForeign language guidelines for major terms of 20th century Korean art that can be used for publishing and translating foreign language (English, Chinese, Japanese) related to Korean art and proposing recommendations for translation",
"homepage": "https://www.gokams.or.kr:442/visual-art/art-terms/index.asp",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Korean Art multilingual Terms",
"prefix": "20118"
},
"20119": {
"description": "Art terms cover art and culture terms that must be addressed in order to form Korean art in the 20th century, and include materials, techniques, ideas, papa, art movements, events, exhibitions, art organizations, educational institutions, museums, galleries, etc.",
"homepage": "https://www.gokams.or.kr:442/visual-art/art-terms/glossary/art_list.asp",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Korean Art multilingual Terms - subject",
"prefix": "20119"
},
"2012": {
"description": "Cataloging system which describes the bibliographic reference library of the University Library of the Ruhr University Bochum",
"homepage": "http://www.ub.ruhr-uni-bochum.de/informationen/systematikhb.html",
"name": "Installation system for the bibliographic reference library",
"prefix": "2012"
},
"20120": {
"description": "It is based on the website of the National Museum of Contemporary Art and the National Museum of Art, which currently has the largest number of DBs of writers based on people born between 1850 and 1970 and the person DB of the Korea Culture and Arts Council, and the Kim Dal-jin Institute of Art (see other writers' representative agencies and sites).\nKorean names, Chinese characters, Ahho (title), and English names are provided in the name of the person.",
"homepage": "https://www.gokams.or.kr:442/visual-art/art-terms/glossary/person_list.asp",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Korean Art multilingual Terms-Person",
"prefix": "20120"
},
"20121": {
"description": "The names of organizations and institutions include art organizations, academic societies, educational institutions, art galleries, museums, galleries, etc.\nThe names of the organizations and institutions were based on the Art Dictionary, the Korean National Cultural Encyclopedia DB, the National Museum of Art, and the major books, academic papers and newspapers of modern and contemporary Korean art, as well as the \"Korean Art Collection 1945-1999\" of the Kim Daljin Art Institute.",
"homepage": "https://www.gokams.or.kr:442/visual-art/art-terms/glossary/group_list.asp",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Korean Art multilingual Terms - organization and institution",
"prefix": "20121"
},
"20122": {
"description": "It guides you through difficult and hard life insurance terms. If you enter the search term you want in the term search window, you can see the description of the term and find it directly in the list.",
"homepage": "https://www.gokams.or.kr:442/visual-art/art-terms/glossary/group_list.asp",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Life insurance Terms",
"prefix": "20122"
},
"20123": {
"description": "It is a glossary of terms for pension insurance provided by IBK Pension Insurance. explain difficult terms in a term Select the appropriate consonant of the term you want to find in relation to the pension, or enter the word yourself for a description of the term.",
"homepage": "https://www.idblife.com/support/knowledge/insurance",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Terms of annuity insurance",
"prefix": "20123"
},
"20124": {
"description": "Search more easily with insurance dictionaries.",
"homepage": "https://www.kdblife.co.kr/ajax.do?scrId=HCSCT011M01P",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Insurance Term",
"prefix": "20124"
},
"20125": {
"description": "As stipulated in Articles 1 and 21 of the Game Industry Promotion Act (hereinafter referred to as the Game Industry Promotion Act), \"Video or related devices and devices designed to enhance entertainment, leisure, learning and exercise effects using computer programs or other information processing technology or machinery\" shall be classified as game management committee. In other words, those who intend to produce or distribute games for the purpose of distributing or providing them for use must receive a rating classification from the Game Board before making or distributing such games.",
"homepage": "https://www.grac.or.kr/Institution/EtcForm01.aspx",
"license": "CC_MARK",
"name": "Classification of game rating",
"prefix": "20125"
},
"20126": {
"description": "* 997 in 6 areas\nLabor economy (including employment, such as the labor market), labor education, labor law,\nLabor welfare (including employment insurance), labor-management relations, international labor, etc.\nLabor economy (227), labor education (242), labor law (146),\nLabor welfare (152), labor-management relations (198) and international labor (32)",
"homepage": "https://www.keli.kr/lmsV2/WordDictHome_list.do",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Employment and Labor Terminology",
"prefix": "20126"
},
"20127": {
"description": "Casino business, casino operation, casino terminology",
"homepage": "https://www.nl.go.kr/NL/contents/search.do?srchTarget=total&pageNum=1&pageSize=10&kwd=μΉ΄μ§λ
Έ+μ€λ¬΄+μ©μ΄+ν΄μ€#viewKey=CNTS-00082380317&viewType=C&category=λμ&pageIdx=2",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "The explanation of casino practical terminology",
"prefix": "20127"
},
"20128": {
"description": "Fair Trade Terminology",
"homepage": "https://www.ftc.go.kr/www/jargonSearchList.do?key=451",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Glossary of Fair Trade",
"prefix": "20128"
},
"20129": {
"description": "Imports of overseas Internet shopping (also known as direct overseas shopping) amounted to 1.7 trillion won in 2015. Consumers will choose to purchase directly overseas if the price of the goods is cheaper than in Korea, considering the price, tariffs and delivery costs of the goods. At this time, I wanted to know the estimated tariff amount of the goods I wanted to purchase, but it was difficult to check the tariff rate because the terms in the tariff rate table were different from the terms used in real life. The tariff rate requires the item number on the tariff rate table. However, many jargon is used in the tariff table because it follows the classification system under international agreements. This booklet explains the jargon of the tariff table in an encyclopedia definition and a picture of goods, and links the name of the tariff table used in daily life with the name of the tariff table through the index table, making it easier for the general public to understand the tariff table.",
"homepage": "https://unipass.customs.go.kr/clip/ebook/hs/ebook_0003/files/assets/basic-html/page-I.html",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "2016 Terms of Custom Tariff",
"prefix": "20129"
},
"2013": {
"description": "The goal of the Physics Instructional Resource Association (PIRA) Demonstration Classification Scheme is to create a logically organized and universally inclusive taxonomy giving a unique code to every lecture demonstration. (...) The topic and concept divisions of the structure loosely follow the standard textbook organization of chapter and section, although they were created to organize existing demonstrations, not cover the entirety of introductory physics, and therefore skip some areas of the curriculum covered by standard textbooks. As the standard curriculum changes over the years, categories have been created to contain the many demonstrations rendered obsolete by modern texts. Single concept films, videos, and computer programs are sometimes included but such resources have not been systematically identified.",
"homepage": "http://physicslearning.colorado.edu/Bib",
"name": "PIRA Demonstration Classification Scheme",
"prefix": "2013"
},
"20130": {
"description": "With the development of science and technology, new products such as superfoods are increasing as Internet of Things (IoT) products that incorporate smart technologies are emerging and public interest in healthy eating is increasing. When importing or exporting new products, the appropriate item number is reported to the customs office, and the item number (item classification) applied is a key factor in determining the country of origin and complex preferential tariffs between the countries in the free trade agreement (FTA). In particular, customs officials are having difficulty in determining the exact meaning of tariff rate table terminology when classifying items. Furthermore, in addition to the tariff rate table documentation, careful consideration is required, such as criteria for application of item classification, comments on HS classification, and regulations related to item classification by other departments. In order to easily understand the jargon (about 9,600) of the tariff rate table or tariff rate table manuals, the encyclopedia was defined, photographs, etc., and other departments' regulations on item classification (164), WCOHS classification opinions (94), etc. were published in advance.",
"homepage": "https://unipass.customs.go.kr/clip/ebook/hs/ebook_0001/autoalbum/page/191112094056351/view.html",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Terms of Custom Tariff(2019)",
"prefix": "20130"
},
"20131": {
"description": "Based on the component classification system used in the automotive HS guide book, the classification system was prepared in conjunction with the HS classification system in consideration of the accessibility and ease of access of parts manufacturers.",
"homepage": "https://unipass.customs.go.kr/clip/ctensrch/openULS0404001Q.do",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Classification of Automobile Parts",
"prefix": "20131"
},
"20132": {
"description": "The semiconductor guide systematically covers all the items used by semiconductor technology, from semiconductor devices to manufacturing and inspection equipment. This is a semiconductor HS guidebook published to help companies accurately report exports and imports and to establish item classification easily and systematically. Click on the list to see the semiconductor E-BOOK.",
"homepage": "https://unipass.customs.go.kr/clip/ctensrch/openULS0404010Q.do",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Semiconductor Guide",
"prefix": "20132"
},
"20133": {
"description": "Telephone was one of the greatest inventions of mankind, and it became a means of communication revolution that brought the whole world together. We tried to include the latest technical information such as smartphones and various cases of classification of items such as communication-related jargon, new manufacturing equipment, raw materials for each process, and various components.",
"homepage": "https://unipass.customs.go.kr/clip/ctensrch/openULS0404014Q.do",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Mobile Phone Parts Guide",
"prefix": "20133"
},
"20134": {
"description": "Item classification has been systematized for products related to display front and rear industries such as LCD, OLED, PDP, manufacturing and inspection equipment, and parts and materials. In order to support the accurate classification of items of the company, we published it through the process of the Korea Display Industry Association and the manufacturing industry. Click on the list to see the flat display E-BOOK.",
"homepage": "http://unipass.customs.go.kr/clip/ctensrch/openULS0404011Q.do",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Flat Panel Display Guide",
"prefix": "20134"
},
"20135": {
"description": "Insurance, loan, fund, trust, retirement pension terms",
"homepage": "https://www.kyobo.co.kr/webdocs/view.jsp?screenId=SCODCNLP004",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Insurance Terms",
"prefix": "20135"
},
"20136": {
"description": "Provides standardized records management terminology search according to standardization of records management terminology",
"homepage": "http://www.archives.go.kr/next/data/standardTermList.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terminology of standard records management",
"prefix": "20136"
},
"20137": {
"description": "μμ±μ¬μ , μμ±μ©μ΄",
"homepage": "http://nmsc.kma.go.kr/homepage/html/satellite/dic/listSatelliteDic.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of Satellite",
"prefix": "20137"
},
"20138": {
"description": "Satellite name",
"homepage": "http://nmsc.kma.go.kr/homepage/html/satellite/info/listSatelliteInfo.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "List of Satellite",
"prefix": "20138"
},
"20139": {
"abbreviation": "KS",
"description": "The term \"industrial standard\" means the standard for unifying and simplifying the type, shape, quality, production methods, methods of testing, inspection, measurement, methods of providing services related to industrial activities, etc. The Minister of Trade, Industry and Energy operates industrial standards under the Industrial Standardization Act, and the business standards announced accordingly are referred to as the Korean Industrial Standards (KS).\n\nKS (Korean Industrial Standards) is abbreviated to KS as national standards determined by the head of the National Institute of Technology and Standards and announced by the head of the competent department after deliberation by the Industrial Standards Council under the Industrial Standardization Act. Under the enactment of the Industrial Standardization Act 1961, 3,000 national standards have been in operation since 1962. In accordance with the WTO/TBT Agreement and the recommendations in APEC/SCSC, standards corresponding to international standards are complied with.\n\nThe Korean Industrial Standards are composed of 21 categories, from the basic sector (A) to the information sector (X), and can be classified into three main categories:\n\nο¬ Product standard: stipulating the improvement, dimensions, quality, etc. of a product\nο¬ Method standards : testing, analysis, inspection and measurement methods, working standards, etc.\nο¬ Standard for delivery : stipulated terms, technology, unit, sequence, etc.",
"homepage": "https://www.standard.go.kr/KSCI/standardIntro/getStandardSearchSubList.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Korean Industrial Standards",
"prefix": "20139"
},
"2014": {
"description": "The Library's classification system is unique, having been devised specifically for its purpose by the Founders (who based it upon the Bliss system), and formally copyrighted in 1990. It provides far more subcategories than would the Dewey decimal classification system. It is entirely alphabetical, the first two letters being the category code, the remaining three being the first three letters of the author's surname (with precedence rules for such names as macDonald, tenEyck or duMaurier).\n\n Because the system is lengthy and detailed it is not reproduced here. It covers all esoteric subjects, including (but of course not limited to):\n\n Astrology; Arthurian legend; fiction (SF, fantasy, historical and mythological); religions (comparitive, Paganism, Wicca, Hinduism, Buddhism, Islam, Taoism, Christianity and many others); occult teachings; magic (or magick) in numerous categories; divination; Tarot; Runes; reincarnation; Qabala (spelling optional); UFOs; ESP; astral projection; channelling; clairvoyance; philosophy; psychology; prophecy; Earth mysteries; environmental issues; sustainable living; alternative technology.\n\n The classification system is sufficiently flexible to allow the creation of new categories, which is done whenever a subject group appears to require subdivision.",
"homepage": "http://libraryofavalon.org.uk/old-website/classification.htm",
"name": "Library of Avalon Classification System",
"prefix": "2014"
},
"20140": {
"description": "Sites, definitions, and types of occurrences by type of cancer, and relevant statistics.\nRisk factors, prevention methods, and early examination by type of cancer\nGeneral symptoms, diagnostic methods, progressive stages, and diagnosis by cancer type\nTreatment methods by type of cancer, side effects of treatment, recurrence and transfer, and treatment status\nInformation on the daily life and diet of patients who are about to be treated for cancer.",
"homepage": "https://www.cancer.go.kr/lay1/program/S1T211C223/cancer/list.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of cancer",
"prefix": "20140"
},
"20141": {
"description": "Definitions and descriptions of human rights-related terms or words can be identified.",
"homepage": "https://www.humanrights.go.kr/site/program/dictionary/listDictionary?menuid=001003006",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of human rights",
"prefix": "20141"
},
"20142": {
"description": "The National Natural History Research Information System has been established, which allows users to view various national natural history resources such as biological samples, genetic resources, journals, papers, videos, photographs, and audio stored by universities, research institutes, science museums, and private collectors.\nDevelops the National Natural History Research Information System (NARIS) that can network national natural history resources to retrieve data, and contains vast amounts of data that can be easily found by classification, theme, and ecology through NARIS, and can be used by elementary school students, university professors, and researchers.",
"homepage": "https://www.naris.go.kr/resc/selectClassBySrch.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Natural history",
"prefix": "20142"
},
"20143": {
"description": "Taekwondo technical terms were not easy to name new technologies due to their lack of consistency and unity, and the same technology was sometimes called differently by different people. Also, it is hard to learn because the terms are long, and it is difficult for foreigners to follow in Korean. Meanwhile, the need for a standard vocabulary book for taekwondo has become more urgent as the terms of competition and demonstration have not been properly organized in the textbook, causing confusion of terms by team or demonstration team.\nAccordingly, Kukkiwon collects and reviews the various terms used in the painting and the stadium, selects 138 standard terms, and publishes a glossary with descriptions of each technique.\nThe standard terms in Taekwondo Technical Glossary have realized consistency, unity and simplicity of terms. In addition, we have expanded the method of technology, direction of technology, and technology that has not been included in the textbook. In the future, new technology names can be consistently established, and it is easy to learn and use as it can be short pronunciations of the command within five syllables at the training site. In addition, the Romanization of the National Institute of Korean Language, the name of Taekwondo technology can be called the same anywhere in the world by using the Romanization method.",
"homepage": "http://www.kukkiwon.or.kr/etribe/kor/front/education/word/terms_2011.pdf",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Terms of Taekwondo Skills",
"prefix": "20143"
},
"20144": {
"description": "It is a classification system for managing and searching the collection of Korean traditional music archives under the National Gugak Center. The Korean Decimal Classification Act (KDC) was established based on the classification of Gugak.",
"homepage": "https://archive.gugak.go.kr/portal/division/divisionMain",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Gugak: Korean Traditional Music",
"prefix": "20144"
},
"20145": {
"description": "- Gugak sisaurus is a type of dictionary that defines the association of terms (search terms) and improves the accuracy and reproducibility of searches.\n- Enter the terms you want to search directly or select from the alphabet/classification index and check the relevant terms (significant/upper/lower/relevant terms) checked.\n- Select terms to add or exclude from the search criteria and set AND/OR conditions to provide a more accurate search",
"homepage": "https://archive.gugak.go.kr/portal/division/thesaurusMain",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Thesaurus of Gugak: Korean Traditional Music",
"prefix": "20145"
},
"20146": {
"description": "- Consistently adopt terminology throughout the classification/genre.\n- easy and interesting terms suitable for elementary and secondary school education should be selected, but the scope of the terms should be understood by the general public who did not learn Gugak separately, and the theoretical depth should be understood by the first-year students of Gugak.\n- terms that satisfy the criteria such as practicality, feasibility, and unification of the Korean orthography shall be selected.",
"homepage": "http://www.gugak.go.kr/site/homepage/menu/viewMenu?menuid=001003001003&lang=ko",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Standard terms of Gugak",
"prefix": "20146"
},
"20147": {
"description": "(1) Standard language and other common non-standard words are included.\n(2) Not only general words but also jargon and proper nouns are included. Due to the large number of jargon and proper nouns, only a few were selected and included.\n(3) The principles or jargon and proper nouns shall contain only the units below the word, and idioms and proverbs.",
"homepage": "https://stdict.korean.go.kr/main/main.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Standard Korean Language Dictionary",
"prefix": "20147"
},
"20148": {
"description": "The Korean language basic dictionary is a Korean dictionary created by the National Institute of Korean Language in Korea, which is a basic dictionary for learning Korean on the Internet for foreign Korean learners. It is a dictionary that is the basis for translation when creating a Korean-language learning dictionary in the language of a region or country where there is a high demand for Korean learning.",
"homepage": "https://krdict.korean.go.kr/mainAction",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Basic Korean Dictionary",
"prefix": "20148"
},
"20149": {
"description": "β The Korean sign language dictionary provides sign language in three areas: 'Daily Life Sign', 'professional sign language' and 'Cultural Information Sign language'. Select the area you want to find so that you can see the corresponding sign language.\n- Daily life sign language (16 areas): personnel, conversation, time, hospital, designation, country name, family, occupation, food, fruits and vegetables, school life, company life, transportation, tourism, numbers, colors, sports\n- Professional terminology sign language (10 areas): law, transportation, medicine, information communication, Buddhism, Catholicism, Christianity, Korean language curriculum terms, economics, politics\n- Culture Information Sign Language: 'National Museum', 'National Folk Museum' and 'National Hangeul Museum' are described in Korean Sign Language\nβ‘ Click 'Korean Sign Language Dictionary' to go to the main screen.\nβ’ You can search for a sign by entering the word you want to find. The auto-complete search term feature makes it easy and fast to find the expression you want to find by entering just a small portion of the search term. If you do not want this feature, simply press 'Close search term auto-complete'.\nSelect 'Find More' for faster and more accurate representation searches.\nο¬ If you select 'Notices', you can view the entire list. If you select the title of the announcement, you can view the details of the announcement.\nβ£ On the main screen, users can see the 1st to 6th place of 'Frequently Seared Sign' and if '+ More' is selected, they can check the ranking from 1st to 100th.\nβ€ You can check the usage and contents of the Korean sign language dictionary through the Korean sign language video.\nChoose 'Favorite' to add your Korean sign language dictionary to your favorites list on your web browser.\nβ₯ you select 'Screen + -', you can zoom in or out on the Korean sign language dictionary.\nWhen the 'menu description sign' function is enabled, the menu description is provided as a sign language image. If you do not want to use this feature, you can select Off.\nβ¦ You can check the sign you've read again through 'The Sign I Saw'. Up to 12 can be saved.\nSelecting 'Delete All' will delete all history of the sign you have read.\nβ§ 'Finding a Hydrologic Dictionary' can be searched for a Korean sign language dictionary information, not in Korean.",
"homepage": "http://sldict.korean.go.kr/front/main/main.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Korean Sign Language Dictionary",
"prefix": "20149"
},
"2015": {
"description": "The DIMOC Controlled Vocabulary contains hierarchical terms covering DoD People, Places and Things. Terms come from authoritative sources such as the Military Services Fact Sheets. DIMOC will continue to add to the vocabulary and will partner with other agencies to ensure the most complete set of terms possible. Included in the Controlled Vocabulary is the DIMOC data schema in preparation for future uses.",
"homepage": "http://dimoc.synaptica.net/pvs/browse.asp",
"name": "DIMOC Controlled Vocabulary",
"prefix": "2015"
},
"20150": {
"description": "It is a specialized encyclopedia for collecting Korean folklore, and is currently working on a compilation project by dividing the subject into eight major categories.\n\"The Korean Folklore Dictionary\", \"The Korean Folk Religion Dictionary\", \"The Korean Folk Literature Dictionary\", \"The Korean Folk Art Dictionary\", \"The Korean Living Dictionary\", \"The Korean Biological Dictionary\", and \"The Korean Folklore Social Dictionary\" are collectively called the Korean Dictionary.",
"homepage": "https://folkency.nfm.go.kr/kr/main",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean Folk Culture",
"prefix": "20150"
},
"20151": {
"description": "This dictionary classifies the clothing life into a large number of hats, tops, bottoms, outerwear, underwear, large, shoes, ornaments, hair, makeup, fabrics, dyeing, patterns, and terms.\nThe dictionary consists of publications and publications, illustrations and table of contents, and texts and indexes. The table control arrangement was arranged in alphabetical order, and the writers' columns were prepared so that the subjects of each writer could be found.",
"homepage": "https://folkency.nfm.go.kr/kr/dic/61/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean Culture of Basic Necessities - clothing",
"prefix": "20151"
},
"20152": {
"description": "This dictionary systematically and comprehensively describes the dietary life that has been passed down in the life of our people.",
"homepage": "https://folkency.nfm.go.kr/kr/dic/61/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean Culture of Basic Necessities-food",
"prefix": "20152"
},
"20153": {
"description": "This dictionary systematically and comprehensively describes the housing life that has been passed down in the lives of our people.",
"homepage": "https://folkency.nfm.go.kr/kr/dic/61/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean Culture of Basic Necessities - housing",
"prefix": "20153"
},
"20154": {
"description": "The Korean folk drama dictionary deals with mask plays, puppet plays, and good plays, which were developed from rituals related to the lives of the Korean people and developed into entertainment.\nLike folk plays, folk play dictionaries, which reflect the public's feelings of life, aspirations, and customs of the time, dealt with both civilian and professional entertainment, and systematically and comprehensively explained the games designated as intangible cultural properties.",
"homepage": "http://folkency.nfm.go.kr/kr/dic/21/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean folk arts : folk dramas",
"prefix": "20154"
},
"20155": {
"description": "The Korean folk drama dictionary deals with mask plays, puppet plays, and good plays, which were developed from rituals related to the lives of the Korean people and developed into entertainment.\nLike folk plays, folk play dictionaries, which reflect the public's feelings of life, aspirations, and customs of the time, dealt with both civilian and professional entertainment, and systematically and comprehensively explained the games designated as intangible cultural properties.",
"homepage": "http://folkency.nfm.go.kr/kr/dic/21/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean folk arts : folk plays",
"prefix": "20155"
},
"20156": {
"description": "This dictionary classified folk dances into Nongak dance, mask dance, sound dance, nonsense dance, imitation dance, Gyobang dance, ritual dance, and new dance, and classified folk paintings into harmony, characterization, literary painting, landscape painting, and literary style.\nThe dictionary consists of publications and publications, illustrations and table of contents, and texts and indexes.\nThe table control arrangement was arranged in alphabetical order, and the writers' columns were prepared so that the subjects of each writer could be found.",
"homepage": "http://folkency.nfm.go.kr/kr/dic/21/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean folk arts : folk dance",
"prefix": "20156"
},
"20157": {
"description": "This dictionary classified folk dances into Nongak dance, mask dance, sound dance, nonsense dance, imitation dance, Gyobang dance, ritual dance, and new dance, and classified folk paintings into harmony, characterization, literary painting, landscape painting, and literary style.\nThe dictionary consists of publications and publications, illustrations and table of contents, and texts and indexes.\nThe table control arrangement was arranged in alphabetical order, and the writers' columns were prepared so that the subjects of each writer could be found.",
"homepage": "http://folkency.nfm.go.kr/kr/dic/21/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean folk arts : folk painting",
"prefix": "20157"
},
"20158": {
"description": "The newly published Korean Folk Art Dictionary, \"Music and Nongak,\" consisted of 240 items for table control, 3,200 manuscripts, 100 photos, 92 items for table control, 2,100 manuscripts, and 100 photographs for Nongak. The photographic materials were appropriately used by photographers, photographs of the head of the National Folk Museum of Korea, and photographs provided by other organizations.\nThis dictionary classified folk music into folk songs, japga, seonsori, pansori, Byeongchang, Sanjo, and religious music. Nongak was divided into Nongak names, organization, small tools, Jangdan, Play, Pangut, Jinpul, and terms.",
"homepage": "http://folkency.nfm.go.kr/kr/dic/21/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean folk arts : folk music",
"prefix": "20158"
},
"20159": {
"description": "The newly published Korean Folk Art Dictionary, \"Music and Nongak,\" consisted of 240 items for table control, 3,200 manuscripts, 100 photos, 92 items for table control, 2,100 manuscripts, and 100 photographs for Nongak. The photographic materials were appropriately used by photographers, photographs of the head of the National Folk Museum of Korea, and photographs provided by other organizations.\n\nThis dictionary classified folk music into folk songs, japga, seonsori, pansori, Byeongchang, Sanjo, and religious music. Nongak was divided into Nongak names, organization, small tools, Jangdan, Play, Pangut, Jinpul, and terms.",
"homepage": "http://folkency.nfm.go.kr/kr/dic/21/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean folk arts : Nongak",
"prefix": "20159"
},
"20160": {
"description": "This dictionary classifies lifelong rituals into birth rites, official rites, weddings, wedding ceremonies, public ceremonies, and rituals, and selected materials deemed essential for understanding the contents of the dictionary. The dictionary consists of publications and publications, illustrations and table of contents, and texts and indexes. The table control arrangement was arranged in alphabetical order, and the table of contents presented the order of each field along with the order of the alphabetical order. Kanada charye is a common dictionary search method that provides relatively convenient access to the heading. However, it is to make it easier to identify relevant procedures and terms in each field, ranging from birth rites to rituals. And the author's column included the title words and numbers written by the author so that they could find the title.",
"homepage": "http://folkency.nfm.go.kr/kr/dic/5/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean rites of passage",
"prefix": "20160"
},
"20161": {
"description": "The Korean Folk Literature Dictionary consists of a narrative, folk song, and pansori.\nIn 'Snowpiercer', the title of the individual narrative was mainly used as the title. In addition, terms and materials that are deemed essential to understanding the contents of the dictionary were also selected as well. In this dictionary, tales were divided into myth, legend, and folktales, and specific narratives were classified by placing a middle school section under the main tree and a small item under the middle section.\nThe dictionary consists of a publication and a summary of publication, illustration and table of contents, followed by text, index, and writer. The table control arrangement was arranged in alphabetical order, and the table of contents was largely arranged in alphabetical order and classified order. Kanada charye is a common dictionary search method that provides relatively convenient access to the heading. However, they also took turns in classification to make it easier to understand the nature of the narrative and related stories. In this way, the viewer can see at a glance what kind of narrative he or she is interested in and what kind of narrative is similar to that one. This enhances accessibility to the heading language and improves the functionality of references and learning, which are characteristics of encyclopedias. And in the last column of the author's name and affiliation, the author's title and number were written so that they could find the title through it.\nThis dictionary actively displays \"cross reference\" to strengthen its role as a guide to the dictionary so that readers can actively create a knowledge system. Interconnecting interrelated information functions to help readers proactively expand their knowledge. In particular, since the field of narrative has a lot of stories involved, cross-references that can immediately be used to find relevant headlines scattered can be used. In addition, the same story is often referred to differently, and in such cases, \"household control\" was set up so that the reader could easily access the heading.",
"homepage": "http://folkency.nfm.go.kr/kr/dic/4/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean folk literature : folktale",
"prefix": "20161"
},
"20162": {
"description": "The Korean Folk Literature Dictionary consists of a narrative, folk song, and pansori.\nThe title of the song is mainly based on the title of individual songs. In addition, terms and materials that require flowers to understand the contents of the dictionary were selected as headings.\nThe dictionary consists of a publication and a summary of publication, illustration and table of contents, followed by text, index, and writer. The table control arrangement was arranged in alphabetical order, and the table of contents was largely arranged in alphabetical order and classified order. Kanada charye is a common dictionary search method that provides relatively convenient access to the heading. However, they also took turns in classification to make it easier to understand the nature of the narrative and related stories. In this way, the viewer can see at a glance what kind of narrative he or she is interested in and what kind of narrative is similar to that one. This enhances accessibility to the heading language and improves the functionality of references and learning, which are characteristics of encyclopedias. And in the last column of the author's name and affiliation, the author's title and number were written so that they could find the title through it.\nThis dictionary actively displays \"cross reference\" to strengthen its role as a guide to the dictionary so that readers can actively create a knowledge system. Interconnecting interrelated information functions to help readers proactively expand their knowledge. In particular, since the field of narrative has a lot of stories involved, cross-references that can immediately be used to find relevant headlines scattered can be used. In addition, the same story is often referred to differently, and in such cases, \"household control\" was set up so that the reader could easily access the heading.",
"homepage": "http://folkency.nfm.go.kr/kr/dic/4/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean folk literature : Folk song",
"prefix": "20162"
},
"20163": {
"description": "The Korean Folk Literature Dictionary consists of a narrative, folk song, and pansori.\nThe title of \"Pansori\" is mainly based on the name and title of the work. In addition, terms and materials essential for understanding the contents of the dictionary were selected as headings. In this dictionary, the five madang, which carries pansori, is divided into one branch, and works that have not been transferred to the window and works created in modern times are divided into another branch.\nThe dictionary consists of a publication and a summary of publication, illustration and table of contents, followed by text, index, and writer. The table control arrangement was arranged in alphabetical order, and the table of contents was largely arranged in alphabetical order and classified order. Kanada charye is a common dictionary search method that provides relatively convenient access to the heading. However, they also took turns in classification to make it easier to understand the nature of the narrative and related stories. In this way, the viewer can see at a glance what kind of narrative he or she is interested in and what kind of narrative is similar to that one. This enhances accessibility to the heading language and improves the functionality of references and learning, which are characteristics of encyclopedias. And in the last column of the author's name and affiliation, the author's title and number were written so that they could find the title through it.\nThis dictionary actively displays \"cross reference\" to strengthen its role as a guide to the dictionary so that readers can actively create a knowledge system. Interconnecting interrelated information functions to help readers proactively expand their knowledge. In particular, since the field of narrative has a lot of stories involved, cross-references that can immediately be used to find relevant headlines scattered can be used. In addition, the same story is often referred to differently, and in such cases, \"household control\" was set up so that the reader could easily access the heading.",
"homepage": "http://folkency.nfm.go.kr/kr/dic/4/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean folk literature : Pansori(epic chant)",
"prefix": "20163"
},
"20164": {
"description": "The Korean Folklore and Faith Dictionary has set its direction to strengthen the independence of individual headlines. These directions are designed to address the topic of the heading, but also to describe the peripheral matters that are important to understand the heading, so that the control of the table alone can comprehensively and in depth understand the content. In other words, the independence of individual headings was strengthened without stratifying the volume and scope of the content.\nThe \"Muksok Sinpyeon\" and \"Village Sinpyeon\" were compiled in this direction, and the newly published home faith episode also followed this direction. In other words, a total of 248 headings were selected in seven categories, divided into sacrificial, physical, ritual, sacrificial, data, and terms.\nThe overall composition of the dictionary is the same as that of the \"Muksangpyeon\" and the \"Muksangpyeon.\" In other words, the table control arrangement was arranged in alphabetical order, and the table of contents was largely arranged in alphabetical order and by field. Kanada charye is a common dictionary search method that provides relatively convenient access to the title word. At the same time, the combination of turns by field is designed to make it easy to grasp the overall composition of the \"fake mind\" and to allow readers to see the areas of interest at a glance. For example, if you are interested in offering, you can see the offering at a glance through each field's turn, and through this, you can find the title word.",
"homepage": "http://folkency.nfm.go.kr/kr/dic/3/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean folklore and traditional culture : household religion",
"prefix": "20164"
},
"20165": {
"description": "The Korean Folklore and Faith Dictionary has set its direction to strengthen the independence of individual headlines. These directions are designed to address the topic of the heading, but also to describe the peripheral matters that are important to understand the heading, so that the control of the table alone can comprehensively and in depth understand the content. In other words, the independence of individual headings was strengthened without stratifying the volume and scope of the content.\nThe \"Muksok Sinpyeon\" and \"Village Sinpyeon\" were compiled in this direction, and the newly published home faith episode also followed this direction. In other words, a total of 248 headings were selected in seven categories, divided into sacrificial, physical, ritual, sacrificial, data, and terms.\nThe overall composition of the dictionary is the same as that of the \"Muksangpyeon\" and the \"Muksangpyeon.\" In other words, the table control arrangement was arranged in alphabetical order, and the table of contents was largely arranged in alphabetical order and by field. Kanada charye is a common dictionary search method that provides relatively convenient access to the title word. At the same time, the combination of turns by field is designed to make it easy to grasp the overall composition of the \"fake mind\" and to allow readers to see the areas of interest at a glance. For example, if you are interested in offering, you can see the offering at a glance through each field's turn, and through this, you can find the title word.",
"homepage": "http://folkency.nfm.go.kr/kr/dic/3/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean folklore and traditional culture : communal folk religion",
"prefix": "20165"
},
"20166": {
"description": "The Korean Folklore and Faith Dictionary has set its direction to strengthen the independence of individual headlines. These directions are designed to address the topic of the heading, but also to describe the peripheral matters that are important to understand the heading, so that the control of the table alone can comprehensively and in depth understand the content. In other words, the independence of individual headings was strengthened without stratifying the volume and scope of the content.\nThe \"Muksok Sinpyeon\" and \"Village Sinpyeon\" were compiled in this direction, and the newly published home faith episode also followed this direction. In other words, a total of 248 headings were selected in seven categories, divided into sacrificial, physical, ritual, sacrificial, data, and terms.\nThe overall composition of the dictionary is the same as that of the \"Muksangpyeon\" and the \"Muksangpyeon.\" In other words, the table control arrangement was arranged in alphabetical order, and the table of contents was largely arranged in alphabetical order and by field. Kanada charye is a common dictionary search method that provides relatively convenient access to the title word. At the same time, the combination of turns by field is designed to make it easy to grasp the overall composition of the \"fake mind\" and to allow readers to see the areas of interest at a glance. For example, if you are interested in offering, you can see the offering at a glance through each field's turn, and through this, you can find the title word.",
"homepage": "http://folkency.nfm.go.kr/kr/dic/3/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean folk beliefs : shamanism",
"prefix": "20166"
},
"20167": {
"description": "This dictionary was published in spring, summer, autumn, and winter according to the characteristics of seasonal customs. However, in the first lunar month, Jeongwol was decentralized because it was the period of the greatest custom among the seasonal customs.\nThis dictionary is largely divided into lunar and Gregorian periods, such as Lunar New Year's Day and the fifteenth of lunar January, and seasonal periods such as Ipchun and Woosoo, as well as monthly and daily activities. It is possible to visit and read the heading like a regular dictionary, and the entire system is organized organically, like a book. Therefore, it is also effective in finding fragmentary content and studying the overall customs of the lunar New Year. Spring, autumn, winter, appendices, and index works were published, with the first installment of the \"Encyclopedia of Korean seasonal customs\" as its head.",
"homepage": "http://folkency.nfm.go.kr/kr/dic/2/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean seasonal customs : January",
"prefix": "20167"
},
"20168": {
"description": "This dictionary was published in spring, summer, autumn, and winter according to the characteristics of seasonal customs. However, in the first lunar month, Jeongwol was decentralized because it was the period of the greatest custom among the seasonal customs.\nThis dictionary is largely divided into lunar and Gregorian periods, such as Lunar New Year's Day and the fifteenth of lunar January, and seasonal periods such as Ipchun and Woosoo, as well as monthly and daily activities. It is possible to visit and read the heading like a regular dictionary, and the entire system is organized organically, like a book. Therefore, it is also effective in finding fragmentary content and studying the overall customs of the lunar New Year. Spring, autumn, winter, appendices, and index works were published, with the first installment of the \"Encyclopedia of Korean seasonal customs\" as its head.",
"homepage": "http://folkency.nfm.go.kr/kr/dic/2/summary",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean seasonal customs : season",
"prefix": "20168"
},
"20169": {
"description": "The National Institute of Biological Resources has been conducting research to review existing and newly researched and discovered organisms, and based on the results, it publishes a list of national biological species every year. In addition, through continuous research, information on newly discovered natural organisms and taxonomic groups will be developed and updated periodically. The National Biological List is of great significance in identifying the existence of native organisms living on the Korean Peninsula, as reference materials for biological resource research, as well as basic information needed to establish policies.\nIt will be widely used and contribute greatly to the development of biological resources and biodiversity in Korea.\nIn addition, the Korean Taxonomic Serial Number (KTSN) is provided to all species that are managed or need to be managed by Korea to be efficient at the national level.\nIt is possible to manage biological resources, and furthermore, it has laid the foundation for handling various domestic procedures required by international laws related to biological resources, such as the Nagoya Protocol, in an efficient and unified manner.\nThe annual list of national species is freely downloadable and available to all citizens, and organizations that cannot maintain their own accurate records provide information services that can always receive the latest information through links.\n\nβ» In the list of national species, 7 households used the classification system of Cavalier-Smith (2004) and Van Baalen (2007) and the management system of the National Institute of Biological Resources of the Ministry of Environment.",
"homepage": "http://kbr.go.kr/content/view.do?menuKey=446&contentKey=14",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Korean Seasonal Customs : supplement",
"prefix": "20169"
},
"2017": {
"homepage": "https://www.psyndex.de/psychologie/testklassifikation.php",
"name": "Psychological Tests Classification",
"prefix": "2017"
},
"20170": {
"description": "Search Categories\nFirst grade in elementary school.It provides information on biological resources in 630 sixth-grade textbooks.",
"homepage": "https://species.nibr.go.kr/digital/enc/index.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Biodiversity",
"prefix": "20170"
},
"20171": {
"description": "National name authority service is a national bicycle data disclosure service that enables efficient access, sharing, and convergence of national knowledge information resources through the disclosure of authority data established by the National Library of Korea to promote the use of National name authority data.\nNational name authority data is a national asset that is the starting point for national knowledge resource sharing and convergence by enabling consistent list creation and bibliographic linkage by identifying and concentrating targets (name, title, topic name, etc.).\nAs a national library, the National Library of Korea is continuously striving to build high-quality National name authority data.\nWe plan to service personal and group name authority data established in the first stage and gradually expand the scope to 2nd stage subject name authority data and 3rd stage unification title authority data.",
"homepage": "http://www.nl.go.kr/authorities/main/index",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "National name authority service",
"prefix": "20171"
},
"20172": {
"description": "Glossary of Library Terms",
"homepage": "https://wl.nl.go.kr/usr/com/prm/BBSList.do?bbsId=BBSMSTR_000000000458&menuNo=13001&upperMenuId=13",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Glossary of Library Terms",
"prefix": "20172"
},
"20173": {
"description": "a glossary of practical terms in the library",
"homepage": "https://www.nl.go.kr/NL/contents/search.do?srchTarget=total&pageNum=1&pageSize=10&kwd=%EA%B5%AD%EB%A6%BD%EC%A4%91%EC%95%99%EB%8F%84%EC%84%9C%EA%B4%80+%EC%8B%A4%EB%AC%B4%EC%9A%A9%EC%96%B4+%ED%95%B4%EC%84%A4%EC%A7%91#viewKey=547392586&viewType=AH1&category=%EB%8F%84%EC%84%9C&pageIdx=1",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "a glossary of practical terms in the library",
"prefix": "20173"
},
"20174": {
"description": "The National Library of Korea is a national library that collects and preserves works permanently. In this process, we create and manage list information in MARC form, author and subject matter transfer for the management, preservation, and service of information resources. It is a service issued in linked open data format on the Web by converting data in the form of (KOR) MARC or DBMS to RDF format for bibliographic information, topic names, and low-profile data managed and preserved by the National Library of Korea.",
"homepage": "https://lod.nl.go.kr/home/index.jsp",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "National bibliography LOD",
"prefix": "20174"
},
"20175": {
"abbreviation": "CAPSS",
"description": "The CAPSS emission source classification system is based on the European CORINAIR emission source classification system (SNAP 97) and has changed the emission source classification system from 11 existing large categories to 13 large groups since 2007.\n\nFuel burning sources are divided into energy industry (01), non-industry (02), and manufacturing industry combustion (03) and emissions from manufacturing processes are included in the production process (04). Gasoline evaporation at gas stations and gas stations corresponds to energy transport and storage (05) and emissions from the use of paint, etc. (06) emissions. Automobiles are classified as non-road sources (07), aviation, ships, and construction machinery, and include sources of emissions from waste disposal (09) and agricultural activities (10). Other forest fires and fires are classified as other sources of cotton pollution (11), road recidivism, and construction activities, such as scattering dust (12), meat roasting, and charcoal kilns (13) as biological combustion sources.",
"homepage": "http://airemiss.nier.go.kr/mbshome/mbs/airemiss/subview.do?id=airemiss_020300000000",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Clean Air Poliy Support System",
"prefix": "20175"
},
"20176": {
"description": "Glossary of Chemical Information",
"homepage": "https://ncis.nier.go.kr/bbs/bbsDicList.do?bbsId=0006",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Glossary of Chemical information system",
"prefix": "20176"
},
"20177": {
"description": "Classification of chemical information",
"homepage": "https://ncis.nier.go.kr/ghcs/ghsClassLabelingCTabList.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Chemicla information system",
"prefix": "20177"
},
"20178": {
"description": "1. To make it easier for anyone to understand the land use information provided by the Land Use Regulation Information System, the terms related to the area, district, etc., building use under the Building Act, urban planning facilities under the National Land Planning and Utilization Act, and other relevant laws were selected.\n2. Each term consists of table control, terminology type, related laws, terminology description, and related terms (see 'Example of Term Preparation').\n3. The terms in the term list are arranged in alphabetical order for convenience of use, and consist of the words in table control, term descriptions, and reference terms (see 'Terms list description').\n4. In principle, the term description includes definitions of terms, background of introduction, location and decision criteria, subdivisions, and reference terms, and is prepared by referring to relevant statutes and relevant department policy data.\n5. In order to easily identify the link between terms, we have prepared a regional classification table, a building purpose classification table, and an urban planning facility classification table. You can find it in the term classification table.\n6. Terms are divided into legal and professional terms, and legal terms are faithfully reflected in the legal definitions, location, and decision criteria stipulated in the relevant statutes. The jargon was prepared using urban planning, architectural dictionaries, encyclopedias, and Korean dictionaries.7 However, various statistical data presented to assist the understanding were prepared based on the time when the relevant administrative agencies investigated and published.8. The term explanation was not limited to the specific laws, but rather summarized in various laws related to the terms. For example, in the case of roads, various laws such as the Building Act, the National Land Planning and Utilization Act, the Road Act, and the Private Investigation Act are operated differently in accordance with the purpose of legislation, and the contents prescribed by each law are mentioned together. Therefore, when using for a specific purpose, such as permission or permission, the definitions, location and decision criteria, behavioral restrictions, and permission criteria set forth in individual statutes must be checked and followed.",
"homepage": "http://luris.molit.go.kr/web/actreg/lawlanguage/WebLawLanguageList.jsp",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Land use regulation information Service",
"prefix": "20178"
},
"20179": {
"description": "Select the desired facility from among all facilities, including construction status and facility name.\nYou can check the basic procedures and cautions in the regulatory guide.",
"homepage": "http://luris.molit.go.kr/web/regguide/rgservice/RgGuideList.jsp",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classfication of land of regulation information service",
"prefix": "20179"
},
"2018": {
"description": "Geographic Information Systems have become indispensable tools in managing and displaying marine data and information. However, a unique georeferenced standard of marine place names and areas was not available, hampering several marine geographic applications, for example the linking of these locations to databases to integrate data. The purpose of Marine Regions is therefore to create a standard, relational list of geographic names, coupled with information and maps of the geographic location of these features. This will improve access and clarity of the different geographic, marine names such as seas, sandbanks, ridges and bays and display univocally the boundaries of marine biogeographic or managerial marine areas.\n\nMarine Regions is an integration of the VLIMAR Gazetteer and the VLIZ Maritime Boundaries Geodatabase. The VLIMAR Gazetteer is a database with geographic, mainly marine names such as seas, sandbanks, seamounts, ridges, bays or even standard sampling stations used in marine research. The geographic cover of the VLIMAR gazetteer is global but initially focused on the Belgian Continental Shelf and the Scheldt Estuary and the Southern Bight of the North Sea. Gradually more regional and global geographic information was added to VLIMAR and combining this information with the Maritime Boundaries database, representing the Exclusive Economic Zone (EEZ) of the world, led to the creation of marineregions.org.\n\nMarine Regions is managed by the Flanders Marine Institute. Funding for the creation of the VLIMAR gazetteer was provided initially through the EU Network of Excellence MarBEF, but also other European initiative such as EMODNet and Lifewatch provide the necessary funding for the maintenance and management of Marine Regions.\n\nWith the launch of marineregions.org, we are also aiming at the establishment of an international editorial board, responsible for the content, quality control and promotion of Marine Regions.",
"homepage": "http://www.marineregions.org/gazetteer.php",
"name": "Marine Gazetteer",
"prefix": "2018"
},
"20180": {
"description": "Glossary of Land, Infrastructure and Transport",
"homepage": "http://www.molit.go.kr/USR/dictionary/m_65/lst.jsp",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Glossary of Land, Infrastructure and Transport",
"prefix": "20180"
},
"20181": {
"homepage": "https://nlic.go.kr/nlic/nlic20201112_dicEditLi.action",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Dictionary of logistics",
"prefix": "20181"
},
"20182": {
"description": "Organize terms related to architectural administration in a way that is easy to understand\nThis dictionary is not case-sensitive and only searches for data within the site of the Setup.\nPlease click on the first letter of the term or enter a search term in the search method below.",
"homepage": "https://cloud.eais.go.kr/moct/awp/aeb03/AWPAEB03L01",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of Construction Administration",
"prefix": "20182"
},
"20183": {
"description": "By presenting the criteria necessary for systematic classification and unique code assignment of the construction project, the information generated during the construction project is used for various systems and application software such as PMIS to promote the interchange and utilization of construction information.",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Construction Information Classification",
"prefix": "20183"
},
"20184": {
"homepage": "https://www.airportal.go.kr/knowledge/library/KdMain01.jsp?df_search_target=e_subject&df_search_keyword=A&df_search_keyword2=B&class_code=1&SearchYN=N",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of Aviation",
"prefix": "20184"
},
"20185": {
"homepage": "http://www.climate.go.kr/home/explanation/explanation.php",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terminology of Atmosphere Watch",
"prefix": "20185"
},
"20186": {
"description": "κΈ°νμ©μ΄μ¬μ ",
"homepage": "http://www.climate.go.kr/home/06_community/06.html",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of Climate",
"prefix": "20186"
},
"20187": {
"description": "Climate abbreviation List",
"homepage": "http://www.climate.go.kr/home/06_community/07.html",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Climate abbreviation dictionary",
"prefix": "20187"
},
"20188": {
"description": "Screen description: This is the screen for the list of disease information for each classification search.\n1. Inquiry area\n- Enter the bottle/crop name search term and click the search button to view the list of 2.\n- Click the View Detailed Search button to activate the detailed inquiry area.\n2. Military Information List\n- Click on the name to go to the detail screen.\n- Click on the representative photo to show a pop-up that prints the original image.\n\n\nScreen description: Detailed screen of disease information for each classification search.\n1. Function button\n[Pesticide Information] A pop-up showing pesticide information is displayed.\n[Green agricultural materials] Pop-ups showing eco-friendly agricultural materials are printed.\n[Agricultural Technology Comprehensive Information] Pop-ups showing comprehensive agricultural technology information are printed.\n[Information/Time/Monthly Tab] Photographic information is classified and displayed for each tab.\n- When clicked by time, sub-tab (full/initial/medium/late/review) to check the damage photo information by symptom stage.\n- When clicking the monthly tab, sub-tab (January-December) should be used to check the damage picture information on a monthly basis.\nGo to the list screen before [List].",
"homepage": "https://ncpms.rda.go.kr/npms/SicknsInfoListRM.np",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "List of plant disease",
"prefix": "20188"
},
"20189": {
"description": "Screen description: This is the screen for the list of disease information for each classification search.\n1. Inquiry area\n- Enter the bottle/crop name search term and click the search button to view the list of 2.\n- Click the View Detailed Search button to activate the detailed inquiry area.\n2. Military Information List\n- Click on the name to go to the detail screen.\n- Click on the representative photo to show a pop-up that prints the original image.\n\n\nScreen description: Detailed screen of disease information for each classification search.\n1. Function button\n[Pesticide Information] A pop-up showing pesticide information is displayed.\n[Green agricultural materials] Pop-ups showing eco-friendly agricultural materials are printed.\n[Agricultural Technology Comprehensive Information] Pop-ups showing comprehensive agricultural technology information are printed.\n[Information/Time/Monthly Tab] Photographic information is classified and displayed for each tab.\n- When clicked by time, sub-tab (full/initial/medium/late/review) to check the damage photo information by symptom stage.\n- When clicking the monthly tab, sub-tab (January-December) should be used to check the damage picture information on a monthly basis.\nGo to the list screen before [List].",
"homepage": "https://ncpms.rda.go.kr/npms/PathogenInfoListRM.np",
"name": "List of phytopathogen",
"prefix": "20189"
},
"2019": {
"description": "This thesaurus does not claim to compete with the major instruments of the genre. It is simply a tool, bilingual Franco-Italian, voluntarily limited to less than 1500 words and elaborated ad hoc to facilitate, enrich - for example by crossing Terms and suggest searches in the PREALP database's iconographic documents.",
"homepage": "http://prealp.msh-alpes.fr/fr/thesaurus",
"name": "Thesaurus PREALP",
"prefix": "2019"
},
"20190": {
"description": "\nScreen description: This is the screen for the list of disease information for each classification search.\n1. Inquiry area\n- Enter the bottle/crop name search term and click the search button to view the list of 2.\n- Click the View Detailed Search button to activate the detailed inquiry area.\n2. Military Information List\n- Click on the name to go to the detail screen.\n- Click on the representative photo to show a pop-up that prints the original image.\n\n\nScreen description: Detailed screen of disease information for each classification search.\n1. Function button\n[Pesticide Information] A pop-up showing pesticide information is displayed.\n[Green agricultural materials] Pop-ups showing eco-friendly agricultural materials are printed.\n[Agricultural Technology Comprehensive Information] Pop-ups showing comprehensive agricultural technology information are printed.\n[Information/Time/Monthly Tab] Photographic information is classified and displayed for each tab.\n- When clicked by time, sub-tab (full/initial/medium/late/review) to check the damage photo information by symptom stage.\n- When clicking the monthly tab, sub-tab (January-December) should be used to check the damage picture information on a monthly basis.\nGo to the list screen before [List].",
"homepage": "https://ncpms.rda.go.kr/npms/HlsctIstguInfoListRM.np",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "List of insect damage information",
"prefix": "20190"
},
"20191": {
"description": "List\nScreen description: This is the screen for the list of disease information for each classification search.\n1. Inquiry area\n- Enter the bottle/crop name search term and click the search button to view the list of 2.\n- Click the View Detailed Search button to activate the detailed inquiry area.\n2. Military Information List\n- Click on the name to go to the detail screen.\n- Click on the representative photo to show a pop-up that prints the original image.\n\nClassification\nScreen description: Detailed screen of disease information for each classification search.\n1. Function button\n[Pesticide Information] A pop-up showing pesticide information is displayed.\n[Green agricultural materials] Pop-ups showing eco-friendly agricultural materials are printed.\n[Agricultural Technology Comprehensive Information] Pop-ups showing comprehensive agricultural technology information are printed.\n[Information/Time/Monthly Tab] Photographic information is classified and displayed for each tab.\n- When clicked by time, sub-tab (full/initial/medium/late/review) to check the damage photo information by symptom stage.\n- When clicking the monthly tab, sub-tab (January-December) should be used to check the damage picture information on a monthly basis.\nGo to the list screen before [List].",
"homepage": "https://ncpms.rda.go.kr/npms/WeedsInfoSearchR.np",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "List of weed information",
"prefix": "20191"
},
"20192": {
"description": "\nScreen description: This is the screen for the list of disease information for each classification search.\n1. Inquiry area\n- Enter the bottle/crop name search term and click the search button to view the list of 2.\n- Click the View Detailed Search button to activate the detailed inquiry area.\n2. Military Information List\n- Click on the name to go to the detail screen.\n- Click on the representative photo to show a pop-up that prints the original image.\n\n\nScreen description: Detailed screen of disease information for each classification search.\n1. Function button\n[Pesticide Information] A pop-up showing pesticide information is displayed.\n[Green agricultural materials] Pop-ups showing eco-friendly agricultural materials are printed.\n[Agricultural Technology Comprehensive Information] Pop-ups showing comprehensive agricultural technology information are printed.\n[Information/Time/Monthly Tab] Photographic information is classified and displayed for each tab.\n- When clicked by time, sub-tab (full/initial/medium/late/review) to check the damage photo information by symptom stage.\n- When clicking the monthly tab, sub-tab (January-December) should be used to check the damage picture information on a monthly basis.\nGo to the list screen before [List].",
"homepage": "https://ncpms.rda.go.kr/npms/EnmyInfoListRM.np",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "List of natural enemy insect information",
"prefix": "20192"
},
"20193": {
"description": "It provides basic information, pathogen information, and general information about pests by crop.\nGeneral information includes the environment of occurrence, symptom description, control method, introduction type, scientific name-identification, form, ecology, habitat, literature information, photographic information, etc.",
"homepage": "https://ncpms.rda.go.kr/npms/FoodImageListR.np",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Disease and pest information : Food crop",
"prefix": "20193"
},
"20194": {
"description": "It provides basic information, pathogen information, and general information about pests by crop.\nGeneral information includes the environment of occurrence, symptom description, control method, introduction type, scientific name-identification, form, ecology, habitat, literature information, photographic information, etc.",
"homepage": "https://ncpms.rda.go.kr/npms/FruitImageListR.np",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Disease and pest information : fruit trees",
"prefix": "20194"
},
"20195": {
"description": "It provides basic information, pathogen information, and general information about pests by crop.\nGeneral information includes the environment of occurrence, symptom description, control method, introduction type, scientific name-identification, form, ecology, habitat, literature information, photographic information, etc.",
"homepage": "https://ncpms.rda.go.kr/npms/VegitablesImageListR.np",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Information on pests: Vegetables",
"prefix": "20195"
},
"20196": {
"description": "It provides basic information, pathogen information, and general information about pests by crop.\nGeneral information includes the environment of occurrence, symptom description, control method, introduction type, scientific name-identification, form, ecology, habitat, literature information, photographic information, etc.",
"homepage": "https://ncpms.rda.go.kr/npms/FlowerImageListR.np",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Information on pests: Flower",
"prefix": "20196"
},
"20197": {
"description": "It provides basic information, pathogen information, and general information about pests by crop.\nGeneral information includes the environment of occurrence, symptom description, control method, introduction type, scientific name-identification, form, ecology, habitat, literature information, photographic information, etc.",
"homepage": "https://ncpms.rda.go.kr/npms/SpecialImageListR.np",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Information on pests: Special crops",
"prefix": "20197"
},
"20198": {
"description": "It provides basic information, pathogen information, and general information about pests by crop.\nGeneral information includes the environment of occurrence, symptom description, control method, introduction type, scientific name-identification, form, ecology, habitat, literature information, photographic information, etc.",
"homepage": "https://ncpms.rda.go.kr/npms/WeedsImgSearchR.np",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Disease and pest information: weeds",
"prefix": "20198"
},
"20199": {
"description": "Digital agricultural dictionaries can be searched in Korean, Chinese, English, Japanese, and Chinese characters.\nWith the Sisorus feature, you can see the meaning of the term as well as the information of the Sisorus built in multiple languages.\nμμ ) μ¬κ³Ό | Apple | ζ²ζ | γγγ | θΉζ.",
"homepage": "http://www.nongsaro.go.kr/portal/ps/psq/psqb/farmTermDicLst.ps?menuId=PS00064",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "agricultural terminology",
"prefix": "20199"
},
"202": {
"description": "Containing thousands of genocideβrelated concepts and experiences, the USC Shoah Foundation Institute Thesaurus is one of the first of its kind. It lists the indexing terms used to describe the Institute's video testimonies and arranges them hierarchically under broad headings. These terms have been assigned directly to digital time codes within testimonies where the specific topics are discussed, in much the same way that book index entries specify the page numbers where topics are covered. Because the Thesaurus currently contains more than 50,000 indexing terms, most of which are geographic in nature, we have abridged this document to make it more manageable in size - excluding the geographic indexing terms, the definitions and scope notes, as well as synonyms and quasiβsynonyms assigned as equivalent but nonβpreferred terms. USC Shoah Foundation Institute's indexing system.",
"homepage": "http://sfi.usc.edu/content/keyword-thesaurus",
"name": "USC Shoah Foundation Institute Thesaurus",
"prefix": "202"
},
"2020": {
"description": "The Taxonomy of subject areas used to index content on nature.com.",
"homepage": "http://www.nature.com/developers/hacks/#1",
"license": "CC0-1.0",
"name": "Nature Publishing Group Subject Ontology",
"prefix": "2020"
},
"20200": {
"description": "The Agricultural Science Library of the Rural Development Administration digitalizes terms and examples of agricultural ancient books of the Joseon Dynasty and provides search services, so please use them a lot.\n\nSearch functionality\n- Search terms [Terms/Examples of the High-Cultural Translation Report]\n- Term/ usage information provided by the Go-Nongseo General Statement",
"homepage": "http://lib.rda.go.kr/RDAWord/webIndex.jsp",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Old Agriculture Books Glossary",
"prefix": "20200"
},
"20201": {
"description": "It is not too much to say that all fields of entomology should start with accurate identification. If you don't know exactly what this study is about, no matter how hard you study and how good you get, you won't be able to disclose information or exchange information with other researchers, so it's just self-satisfaction. Therefore, they first go through compassion to find out what their materials are, and although they are often easily published in pictures or photographs, it is most desirable to compare them with professional literature or samples already sympathetic for accurate compassion.\nTo this end, the insect industry department of the National Institute of Agricultural Science collects samples from all over the country every year, focusing on pests that damage crops and natural enemy insects that parasitize or eat pests.\nAs evidence of the findings, the Insect Specimens Center samples and stores the material insects used in the study, making them available to other researchers and providing information related to insect and crop pests.",
"homepage": "http://www.nongsaro.go.kr/portal/ps/psw/pswb/pswbc/stleWordDicLst.ps?menuId=PS03280",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of Insect Form",
"prefix": "20201"
},
"20202": {
"description": "Provide a description of the terms of livestock",
"homepage": "http://www.nongsaro.go.kr/portal/ps/psg/psgd/stkrsTermDicLst.ps?menuId=PS03158",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of Livestock",
"prefix": "20202"
},
"20203": {
"description": "An easy-to-understand agricultural vocabulary house purifies, digitizes, and provides difficult Chinese character-oriented agricultural terms in easy-easy terms.",
"homepage": "http://lib.rda.go.kr/easydict/dictSearch.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Glossary of Ariculture",
"prefix": "20203"
},
"20204": {
"description": "It is a miniature version of the 2017 Tuberculosis and Respiratory Medicine Dictionary, which is based on terms directly related to Tuberculosis and Respiratory Science.\nThe reason for this is that medical terms are rapidly changing by sector, so it is reasonable to follow the medical terminology book of the Korean Medical Association, so we excluded them from the revision of this time.\nHowever, for readers who need it, the 2017 glossary was also available online.",
"homepage": "http://www.lungkorea.org/glossary_search.php",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Essential Tuberculosis and Respiratory Diseases Terminology",
"prefix": "20204"
},
"20205": {
"description": "We confirm that the following medical terminology principles have been applied to the publication of this glossary.\n1. Change difficult medical terms to easy-to-understand terms or Korean terms.\n2. If only the first term is possible, but it is deemed necessary to include the second and third terms (add existing terms in addition to the Korean terms in case of difficulty in meaningful communication), the same meaning shall be separated by commas, and the number of 1, 2 and 3 shall be appended if the meaning or use is different.\n3. Paste all Korean terms.\n4. Remove suffixes (~phase, ~sex, ~alcohol, ~yang, ~positive, ~symptoms, ~symptoms, ~type) after nouns, but keep them in parentheses if they are not familiar with these changes or are not distinguishable from similar foreign terms.\n5. In the case of scientific names, the generic name is (subject). If it is a species name, attach (species) and display it in italic font.\n6. Attach '-' after adjectives to distinguish between nouns.\n7. Erase 's after noun.\n8. Delete the '-' between nouns and maintain the '-' between proper nouns.\n9. Delete terms that were not used well in previous editions, and add new medical terms or new drug names based on Harrison's Internal Medicine Textbook (19 editions).\n10. Refer to the Korean Medical Association's Medical Terminology (5 editions), Harrison's Internal Medicine Textbook (19 editions), Wikipedia, PubMed, etc. as the basis for the wording.",
"homepage": "http://www.lungkorea.org/glossary_search.php",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Tuberculosis and Respiratory Diseases Medical Terminology",
"prefix": "20205"
},
"20206": {
"description": "The Korean language name of the domestic parasite is summarized and included in the \"Korean Animal Collection\" published by the Korean Society for Animal Classification in 1997. It's been a long time since the Korean animal book was published, and I think there are many problems for members of our society to use it.\nSo, we overcame the limitations of the list of animal species and decided to organize it because we needed to publish a systematic \"Parasite List\" at the conference level that is convenient for our members to use.",
"homepage": "http://www.parasitol.or.kr/parasitology/",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "List of Parasite Species",
"prefix": "20206"
},
"20207": {
"description": "The Korean Society of Parasite Studies wanted to increase the effectiveness of the parasite's academic vocabulary by adding terms based on the Korean Medical Association's \"Fiveth Book of Medicine (2009)\" and examining the validity of some terms. After completing this review, the fourth album of parasitic terms is a compilation of \"Parasite Korean names\" and \"Parasite General Terms\" and added terms to this book, referring to several recently published parasites, and incorporating new terms sent by members.",
"homepage": "http://www.parasitol.or.kr/parasitology/",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "The Korean Terminology of Parasites",
"prefix": "20207"
},
"20208": {
"description": "The revision of the Korean name for parasites in 1994 began with the principle of cooperating with the Korean Society for Animal Classification's decision to publish \"Korean Animal Master's Book.\" Accordingly, there have been significant revisions and supplementations to past academic glossary (Parasite Academic Terminology I, 1977). The Korean name for parasites of the progenitor subfamily and the epigenetic subfamily was widely collected according to the 1994 Korean Species of Species, but only the arthropod sentence was taken from the manuscript of the \"Korean insect masterpiece (1994).\nThe newly designated Korean word parasite may be more desirable if it is beautiful and easy to call, but it is not always possible, especially considering the principle of keeping usefulness and grammar. Previously used Korean parasites tried to strictly protect the permanence of the language by recognizing it as it was without any special errors.\nThere were many exceptions despite the fact that various principles, both large and small, were established and the work was carried out, and this is the characteristic of the term. As set forth this time, I hope that we will continue to observe what problems are there and share opinions to create more desirable Korean names and use each other in the future. And the parasite scientist who picked up the new parasite hopes that the parasite's Korean name will be carefully named and proposed so that the proposal will be respected.",
"homepage": "http://www.parasitol.or.kr/parasitology/",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "The Korean Terminology of Parasitology",
"prefix": "20208"
},
"20209": {
"description": "In this glossary, about 1,300 words related to lighting that are widely used in the field of stage lighting were selected and organized, and the current classification system was corrected to improve work efficiency, especially to help understand the vocabulary used at the performance site.",
"homepage": "https://www.staff.or.kr/Document/Term",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Stage Art Terms - Stage Lighting",
"prefix": "20209"
},
"2021": {
"description": "ORCID provides a persistent digital identifier that distinguishes you from every other researcher and, through integration in key research workflows such as manuscript and grant submission, supports automated linkages between you and your professional activities ensuring that your work is recognized.",
"homepage": "http://orcid.org/",
"license": "CC0-1.0",
"name": "ORCID",
"prefix": "2021",
"wikidata_database": "Q51044"
},
"20210": {
"description": "As the performance has become a daily life of modern people, interest in the stage is increasing, but even concert hall officials are using unpurified foreign terms, which makes it necessary to understand and disseminate the right words. Therefore, the National Theater's Stage Art Professional Qualification Committee is developing and distributing stage art collections in three fields, including stage machinery, lighting, and sound, in order to refine and standardize stage art terms.\nThe newly published glossary of terms in the field of stage sound has selected 1,500 common terms used on stage, including performance production, equipment operation, and performance progress, and illustrations and tables are inserted to help understand the situation.",
"homepage": "https://www.staff.or.kr/Document/Term",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Stage Art Terms - Stage Acoustics",
"prefix": "20210"
},
"20211": {
"description": "The characteristics of this glossary are that of the terms widely used in the field of stage art, foreign words have been rewritten in Korean as much as possible, and those used in the same meaning or more are unified into one. For example, 'the flooring' or 'the flooring plate' was unified as the 'the flooring'. In addition, the terms used in the Korean Industrial Standards were quoted as possible and new terms were developed considering the stage reality.\nThis glossary is arranged in Korean alphabetical order, and if the same term has multiple meanings, it is divided into numbers, and terms that have the same Korean notation but have different meanings depending on the field of use or use.",
"homepage": "https://www.staff.or.kr/Document/Term",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Stage Art Terms - Stage General, Mechanical, and Equipment",
"prefix": "20211"
},
"20212": {
"description": "Provides musical instrument information by dividing it into orchestras, air echoes, joules, body echoes, clanging, and electronic instruments.",
"homepage": "http://musichistory.or.kr/article/naver",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Encyclopedia of Musical Instruments",
"prefix": "20212"
},
"20213": {
"description": "Provides information divided into works, performers, performance organizations, composers, jazz, gugak, and world music",
"homepage": "http://musichistory.or.kr/article/daumkakao",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Encyclopedia of Classic music",
"prefix": "20213"
},
"20214": {
"description": "1. This dictionary selects and compiles 2,000 terms with universality, focusing on measurement and geodetic, photographic and telemetry, GIS, intellectual, map, and ISO/TC211 among the areas related to spatial information.\n2. Each term was arranged alphabetically.\n3. The text was organized in the order of Korean terms [Chinese, English abbreviations, English] glossary of terms (add additional explanations if necessary). If there are synonyms and related terms, they are added after the ο¬ and ο¬ codes, respectively, and if there are websites that refer to them, they are marked after the β sign.\n4. Terms were considered as one word and written in either case, such as words, abbreviations, synthesized words or phrases, or written in Korean or abbreviated words.\n5. In principle, the terms were written using Korean and Korean. However, if the Korean language did not fully express the meaning of the term or there was no Hangul to replace it, it was written as a foreign word.\n6. The terms were written in Gothic, and in the case of foreign words, all but abbreviations and proper nouns were written in lowercase.\n7. In principle, the glossary of terms was written in Korean and Korean, but generalized foreign words were written in Korean and foreign words were added in (). Ungeneralized foreign words were written in foreign words.\n8. Foreign words were written in accordance with the Korean Language Institute's foreign language notation.\n9. If the same term is used in two or more fields in different meanings, the original number (β . β‘, β’...) is used in different fields. ) is explained later.\n10. Pictures, photographs, and diagrams are inserted where necessary to help understand the terminology.\n11. English-Korean bands are arranged in alphabetical order of English terms.\n12. The contents described in the dictionary of this term are not legally effective in any case.",
"homepage": "http://www.nsdi.go.kr/lxportal/?menuno=2755",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Glossary of spatial information",
"prefix": "20214"
},
"20215": {
"description": "It contains 726 Korean food stories in various fields such as literature, proverbs, history, rituals, and folklore.",
"homepage": "https://www.kculture.or.kr/brd/board/640/L/menu/641",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Dictionary of Korean Food Culture",
"prefix": "20215"
},
"20216": {
"description": "Provide information on the description of the food ingredients, nutritional components, weaknesses, and folk remedies using the food.",
"homepage": "http://www.kculture.or.kr/www/jsp/prg/food/list.jsp",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Food Glossary",
"prefix": "20216"
},
"20217": {
"description": "* Purpose and Background\n- Prepare measures to estimate the size of the advertising industry in an objective and consistent manner\n- The classification and scope of the relevant business statistical survey is unclear, making the population representative vulnerable\n- Advertising industry classification of actual statistics is not linked to Korea Standard Industry Classification (KSIC)\nβ» It is a classification system created by the Korean Cultural Information Service for statistical production of related industries, not officially established.\n\n* Evidence\n- Referring to the advertising field among international standards prepared by the OECD (Content Media Industry Classification) and UNESCO (2009 UNESCO Framework for Cultural Statistics) and reflecting the characteristics of the domestic industry\n\n* Coverage\n- Comprehensive area based on value chain activities of production, infrastructure, distribution, and service in the advertising industry\n\n* Advertising industry classification (comprehensive domain and definition)\n- Core advertising industry: major industries that are fully engaged in the advertising industry, such as advertising production, advertising planning, advertising agency, and advertising services.\n- Interdependent advertising industry: Industries that maintain organic relationships with each other in revitalizing the advertising industry, such as the advertising production equipment industry and related research companies.\n- Part of the advertising industry: Partially involved in the advertising industry and only extracted elements attributable to advertising to assess economic contribution\n- Advertising support industry: An industry that has elements of the advertising industry but supports incidental work (not included in the core area)",
"homepage": "http://stat.mcst.go.kr/mcst/WebPortal/public/info/adver.html",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Advertising Industry",
"prefix": "20217"
},
"20218": {
"description": "* Purpose and Background\n- The importance of qualitative growth of national life increases, and the need for accurate market size estimation of the culture and arts industry arises.\n- Approval statistics are insufficient due to the lack of concept and scope of comprehensive scope for the culture and arts industry\n- the need for a separate classification of the culture and arts industry that reflects the characteristics of the culture, sports and tourism industry increases\nβ» It is a classification system created by the Korean Cultural Information Service for statistical production of related industries, not officially established.\n\n* Evidence\n- Based on the international standards prepared by UNESCO Framework for Cultural Statistics, it reflects the characteristics of the Korean culture and arts industry.\n\n* Coverage\n- Industrial activities that reflect social changes based on manufacturing, service, distribution and rental business, and supply businesses according to the cycle of cultural and artistic industries (creation, production, distribution, consumption and participation)\n\n* Culture and arts industry classification\n- Literature and publishing (large category): Translation services, literature provisioning, publishing, printing, publishing and distributing (division)\n- Performance (large category): Theater supply, dance supply, instrument distribution, musical instrument distribution, music reproduction, music distribution, music distribution, other performance provisioning, performance planning and production, performance clothing manufacturing, performance distribution (medium category)\n- Visual arts (large category): Art product manufacturing, art distribution, art distribution, art distribution, art specialization service, art supply, design, photography, photography, photography distribution, crafts distribution, crafts distribution, crafts distribution, exhibition services.\n* Cultural heritage and cultural facilities (large category): historic sites, literary and artistic facilities, library facilities, performance facilities, and exhibition facilities operations (medium category)",
"homepage": "http://stat.mcst.go.kr/mcst/WebPortal/public/info/cultureArt.html",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Culture and Art Industry",
"prefix": "20218"
},
"20219": {
"description": "It provides information by dividing it into plays, music, dance, art, video, culture, architecture, and festival culture.",
"homepage": "https://www.culture.go.kr/knowledge/encyclopediaList.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of Art Knowledge",
"prefix": "20219"
},
"2022": {
"description": "The IANA Language Subtag Registry contains language tags (abbreviated language codes) as defined by the Internet Engineering Task Force (IETF). These language tags are used in a number of modern computing standards, such as HTTP, HTML, XML, and RDF. Components of language tags are drawn from other standards such as ISO 639, ISO 15924 and ISO 3166-1.",
"homepage": "http://www.iana.org/assignments/language-subtag-registry/",
"license": "CC0-1.0",
"name": "IANA Language Subtag Registry",
"prefix": "2022",
"wikidata_database": "Q1059900"
},
"20220": {
"description": "Provides an explanation of the art terms appearing in the Art Knowledge White Paper",
"homepage": "https://www.culture.go.kr/knowledge/encyclopediaDictionary.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Glossary of art",
"prefix": "20220"
},
"20221": {
"description": "It is one of the national classification systems of occupations, focusing on the knowledge, ability, and temperament needed to perform jobs in each profession.",
"homepage": "https://www.career.go.kr/cnet/front/base/job/jobList.do#tab1",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Job Classifications",
"prefix": "20221"
},
"20222": {
"description": "It introduces not only fields directly related to science and technology, but also jobs that utilize advanced technology and future jobs in various fields.\nWe tried to expand the understanding of the world of work by presenting not only future jobs but also basic work in the field for each theme (topic).\nWe planned to link the results of career net interest test and aptitude test with future jobs.\nWe provided the trend of changing future jobs in a cartoon format so that teenagers can easily understand it.\nFuture jobs are presented in nine categories, including robots, food, shelter, health, connections, bio, design, play, energy, and safety. There are 50 future jobs offered by theme.\nIn order to select a future job, we have collected and analyzed professional literature at home and abroad extensively. After that, the survey was conducted on the related directors and finally listened to the opinions of professional experts and experts in science and technology experts.",
"homepage": "https://www.career.go.kr/cnet/front/base/guidebook/guideBookList.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Future job guidebook",
"prefix": "20222"
},
"20223": {
"description": "It provides information on new jobs that are gaining popularity abroad in various fields.\nYou can select the job you are interested in to find out more information.",
"homepage": "https://www.career.go.kr/cnet/front/base/base/newJob/newJobList.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of new job abroad",
"prefix": "20223"
},
"20224": {
"description": "Junior job information provides information about jobs that elementary and middle school students are interested in.\nClick on the job you are interested in to learn more about it.",
"homepage": "https://www.career.go.kr/cnet/front/base/juniorJob/juniorList.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Junior job information",
"prefix": "20224"
},
"20225": {
"description": "Classification of high school and university departments",
"homepage": "https://www.career.go.kr/cnet/front/base/major/FunivMajorList.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of curriculum information",
"prefix": "20225"
},
"20226": {
"description": "List of elementary, middle, high school, university, special/various schools, alternative schools",
"homepage": "https://www.career.go.kr/cnet/front/base/school/schoolUniversityList.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classfication of school information",
"prefix": "20226"
},
"20227": {
"description": "ICT integration classification",
"homepage": "https://spri.kr/posts/view/22345?code=stat_sw_classif",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Information & Communication Technology",
"prefix": "20227"
},
"20228": {
"description": "Classification System of SW Industry and Detailed Items in Wide Field",
"homepage": "https://spri.kr/posts/view/22347?code=stat_sw_classify",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification System of SW Industry",
"prefix": "20228"
},
"20229": {
"description": "Software industry, software detailed item classification system",
"homepage": "https://spri.kr/posts/view/22438?code=stat_sw_classify",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of cloud computing",
"prefix": "20229"
},
"2023": {
"description": "The MoEML Gazetteer of Early Modern London is a descriptive gazetteer in that each place is linked to an Encyclopedia page with a 'thick description' of place. (...) Until now, there has been no digital gazetteer and authority list for placenames in early modern London. Our gazetteer offers a standard for placenames ca. 1550-1650.1 Such a standard enables interoperability across digital projects that include early modern London placenames. Shakeosphere and DEEP have already used our gazetteer to identify toponyms in their data and link to MoEML. We hope that other scholars, editors, and researchers will adopt these authority names in secondary criticism, in modernized editions of early texts, and in datasets that include a geographic component. The gazetteer also allows us to aggregate many variant names that have been given to a place. We define place as a space that has been made meaningful by human activity or observation. The existence of a toponym is one sign that space has become place. Furthermore, toponyms often preserve a memory of why a place is significant. Thus, toponyms are intrinsically interesting to scholars of language, history, and onomastics (the study of the origin of proper names).",
"homepage": "https://mapoflondon.uvic.ca/gazetteer_a.htm",
"license": "CC BY-SA 3.0",
"name": "MoEML Gazetteer of Early Modern London",
"prefix": "2023"
},
"20230": {
"description": "Big data software, services, hardware, network, security, etc.",
"homepage": "https://spri.kr/posts/view/22439?code=stat_sw_classify",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of big data",
"prefix": "20230"
},
"20231": {
"description": "Internet of Things software, services, hardware, network, security, etc.",
"homepage": "https://spri.kr/posts/view/22440?code=stat_sw_classify",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of IoT",
"prefix": "20231"
},
"20232": {
"description": "Artificial intelligence software, services, hardware, etc.",
"homepage": "https://spri.kr/posts/view/22441?code=stat_sw_classify",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of artificial intelligence",
"prefix": "20232"
},
"20233": {
"description": "VR/AR/MR software, services, networks, etc.",
"homepage": "https://spri.kr/posts/view/22442?code=stat_sw_classify",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of VR/AR/MR",
"prefix": "20233"
},
"20234": {
"description": "SW Convergence New Service and Smart Service",
"homepage": "https://spri.kr/posts/view/22443?code=stat_sw_classify",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of software convergence new service",
"prefix": "20234"
},
"20235": {
"description": "Blockchain software, services, hardware, network, security, etc.",
"homepage": "https://spri.kr/posts/view/22444?code=stat_sw_classify",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Blockchain",
"prefix": "20235"
},
"20236": {
"description": "Toxicity information service system (Toxicity information service system) is an integrated and professional system that provides addiction information, tobacco information, and carcinogenic information for specialized treatment along with toxic information.\nThe Korea Food and Drug Administration (KFDA) has developed a system to make information on chemicals directly applied to human body, such as food medicine, easier for the general public and experts to access.\nIt consists of reliable toxic information on chemicals used directly in human body such as food and medicine, addiction information that provides treatment information to respond quickly to poisoning accidents at emergency medical centers in Korea, tobacco information that provides harmful information, and carcinogen classification in Korea and abroad.\nThrough Tox-info, we will contribute to relieving public anxiety and satisfying the public's right to know by providing rapid toxic information on hazardous materials.",
"homepage": "https://www.nifds.go.kr/toxinfo/intro/dictionary/list.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Toxicity information service system",
"prefix": "20236"
},
"20237": {
"description": "The Ministry of Food and Drug Safety's safety technology classification system is divided into six major categories: 1. Food Safety Management, 2. Nutrition Safety Management, 3. Medicines Safety Management, 4. Medical Supplies/Cosmetics Safety Management, 6. To strengthen its links to the National Science and Technology Classification System.",
"homepage": "https://www.khidi.or.kr/fileDownload?titleId=368174&fileId=9&fileDownType=C¶mMenuId=MENU01812",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Food and Drug Safety Technology",
"prefix": "20237"
},
"20238": {
"description": "Food and Drugs List",
"homepage": "https://www.mfds.go.kr/usr/lawdata_626/list.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of Food and Drug",
"prefix": "20238"
},
"20239": {
"description": "Korea has been using the international classification of industrial design (12 editions of Locarno classification) as the international design registration application system was implemented from July 1, 2014.\nDesign classification, or commodity classification, is prescribed by [Attachment 4] concerning Article 38 (1) and (3) of the Enforcement Rules of the same Act based on Article 40 (2) of the Design Protection Act.\nThe 12th edition of the Locarno category is the latest edition published in January 2019, with a list of 5,378 items in 218 groups of 32 species.\nWhen applying for design registration, the class (class) of the international classification shall be entered in the [goods and goods] entry box of the application.In this case, you can refer to the items in the list of items for each design item attached.\nThe list of design items includes the names of Locarno and the Korean classification of goods, and includes about 10,069 items.\nInternational classification shall be used only for management purposes, and it shall be noted that it shall be based on Korean classification when reviewing substance, such as prior design search.\nClass 2 (clothing and fashion miscellaneous goods), 5 (fabric products, artificial and natural sheet fabrics), 19 (textbooks, office supplies, art materials, and teaching materials) are some of the applications for review and the rest are design assessment applications.",
"homepage": "https://www.kipo.go.kr/kpo/BoardApp/UPatentApp?c=3001&catmenu=m06_07_04",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Design classification code",
"prefix": "20239"
},
"20240": {
"description": "The previous seven technology areas related to the Fourth Industrial Revolution* were expanded and improved to 16 technology sectors**, and the Advanced Patent Classification (CPC) system was added to the system. The details may be partially modified in the course of international standardization and revision.\n\n* Artificial intelligence (AI), big data, cloud, Internet of Things (IoT), intelligent robots, self-driving cars, 3D printing\n** Artificial intelligence (AI), big data, cloud computing, next-generation communications, Internet of Things (IoT), intelligent robots, drones, virtual augmented reality, smart cities, customized healthcare, innovative new drugs, advanced materials, renewable energy, 3D printing",
"homepage": "https://www.kipo.go.kr/ko/kpoContentView.do?menuCd=SCD0200271",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "New patent classification system",
"prefix": "20240"
},
"20241": {
"description": "Type classification: Enter the number of classification of goods or service industries according to the Enforcement Rules of the Trademark Act, and choose from 1-34 types of products and 35-45 types of service industries. If you know the classification, you can search by selecting the number shown in the product or service category at the bottom.\n\nPseudo-group code: An identification symbol indicating the similar range of goods or service industries starts with G (Goods) and S (Services), and consists of five to six letters and numbers. Some products are given at least two pseudo-group codes.\n(Ex.) Fertilizer: G0101, snack bar: S120602, cosmetics: G1201, S120907, S128302\n\nMultiple similarities: means a group of products belonging to two or more similar groups with properties and transaction status of the product itself.\n(e.g.) Multiple similarity codes for 'clothes' are G43030301, G450101, G450102, G4502, G450401, G4507\n\nDefinition of Symbols: The product name or symbol \"*\" shown is a generic name and is used when it can be classified as a different commodity depending on its purpose or material, so make sure that a similar product name exists in a different commodity. However, the symbol \"*\" shall not be entered when applying by using a form processor, etc.",
"homepage": "https://www.kipo.go.kr/kpo/HtmlApp?c=31064&catmenu=m06_07_03_01&version=11",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Product classification code",
"prefix": "20241"
},
"20242": {
"description": "Intellectual property rights such as patents and trademarks are very professional, making it difficult for the general public to easily understand related terms. In addition, overseas applications or lawsuits are also an important part of the related work, so it is necessary to systematically identify internationally accepted intellectual property terms.\nIn response, the Korean Intellectual Property Office revised the \"English-Korean Dictionary of Intellectual Property Rights\" published in 2008 to help the public understand difficult intellectual property terms and to reflect the changed intellectual property environment at home and abroad.\nIn this revised edition, the description of the term was revised to make it easier to understand, and new terms and precedents of intellectual property rights that have emerged in Korea and abroad have been included. In addition, we have added new Chinese terms for companies that are active or are planning to enter the Chinese market, which has become more economically important.\nIn the future, the Korean Intellectual Property Office will continue to reflect new terms and precedents in this dictionary in line with the changing environment of intellectual property rights, and will do its best to make it easier for the public to approach the intellectual property sector.",
"homepage": "http://www.kipris.or.kr/khome/guide/add_service/dictionary_new.jsp",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Glossary of intellectual Property Terms",
"prefix": "20242"
},
"20243": {
"description": "Legislation Standard Terms",
"homepage": "https://elaw.klri.re.kr/kor_service/wordSearch.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Legislation Standard Terms",
"prefix": "20243"
},
"20244": {
"description": "Provide a description of the latest legal terms",
"homepage": "https://elaw.klri.re.kr/kor_service/newUpdateWord.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "the latest Legislation Standard Terms",
"prefix": "20244"
},
"20245": {
"description": "Provide a description of the terms used in the statute",
"homepage": "https://www.klri.re.kr/kor/business/bizLawDicKeyword.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Legislation Terms",
"prefix": "20245"
},
"20246": {
"description": "This dictionary is a translation of the \"Radioactive Waste Dictionary\" published by the IAEA.",
"homepage": "https://wacid.kins.re.kr/GLOSSARY/glossary.aspx",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Radioactive Waste Terms",
"prefix": "20246"
},
"20247": {
"description": "Terminology related to nuclear nonproliferation and nuclear security with initial search",
"homepage": "https://www.kinac.re.kr/main/thesaurus?menuId=MENU00579",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Nuclear Terminology",
"prefix": "20247"
},
"20248": {
"description": "Dictionary of Terms and Conditions for Radioactive Waste Management Projects",
"homepage": "https://www.kinac.re.kr/main/thesaurus?menuId=MENU00579",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Glossary of the waste management business",
"prefix": "20248"
},
"20249": {
"description": "1,500 environmental terms",
"homepage": "http://me.go.kr/home/web/index.do?menuId=10448",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Glossary of environment",
"prefix": "20249"
},
"2025": {
"description": "Chiropractic Subject Headings (ChiroSH) is a thesaurus developed by librarians at chiropractic college libraries, intended for use by indexers for the Index to Chiropractic Literature (ICL) and by catalogers at chiropractic and natural health sciences libraries. The first draft of the thesaurus was developed from the subject authority files of the Texas Chiropractic College and Northwestern College of Chiropractic libraries, the subject thesaurus included in the first volume of CRAC: Chiropractic Research Abstracts Collection, and the subject lists included in ICL. ChiroSH is intended to be used in conjunction with the Medical Subject Headings (MeSH), published by the National Library of Medicine. Several ChiroSH headings are based upon MeSH headings, but most ChiroSH headings are unique to this thesaurus. Chiropractic terms with established medical headings are provided with 'See' references to direct users to MeSH, where they will find scope notes, accepted subheadings (qualifiers), and cross references.",
"homepage": "http://www.chiroindex.org/wp-content/uploads/2009/07/chirosh_6th_ed_2009.pdf",
"name": "Chiropractic Subject Headings",
"prefix": "2025"
},
"20250": {
"description": "This data provides overview and type of medical waste, medical institutions that generate medical waste, testing and inspection institutions, and RFID medical waste management system.",
"homepage": "http://www.me.go.kr/home/web/policy_data/read.do?menuId=10265&seq=6398",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of medical waste",
"prefix": "20250"
},
"20251": {
"description": "Automotive emissions terms",
"homepage": "https://emissiongrade.mecar.or.kr/www/fd/weather/dust04.do?_csrf=a710e348-0084-48ce-89f5-dec11029ac1e&first=T",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of vehicle emission gas",
"prefix": "20251"
},
"20252": {
"description": "Environmental education",
"homepage": "https://www.keep.go.kr/portal/145",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Environment Education Terms",
"prefix": "20252"
},
"20253": {
"description": "Medical equipment, pharmaceuticals, medical supplies manufacturing, wholesale and retail business",
"homepage": "https://khiss.go.kr/board?menuId=MENU00313&siteId=null",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of Pharmaceutical industry",
"prefix": "20253"
},
"20254": {
"description": "Medical equipment, pharmaceuticals, medical supplies manufacturing, wholesale and retail business",
"homepage": "https://khiss.go.kr/board?menuId=MENU00313&siteId=null",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Medical device Classification",
"prefix": "20254"
},
"20255": {
"description": "Medical equipment, pharmaceuticals, medical supplies manufacturing, wholesale and retail business\nWholesale and retail cosmetics, soap and cleaning agents",
"homepage": "https://khiss.go.kr/board?menuId=MENU00313&siteId=null",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of cosmetics industry",
"prefix": "20255"
},
"20256": {
"description": "Health and social welfare services (hospital, clinic, welfare facilities, etc.)",
"homepage": "https://khiss.go.kr/board?menuId=MENU00313&siteId=null",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "classification of healthcare industry",
"prefix": "20256"
},
"20257": {
"description": "Medications, medical devices, cosmetics, food, medical services, etc.",
"homepage": "https://khiss.go.kr/board?menuId=MENU00317&siteId=null",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Glossary of statistical terms for health industry",
"prefix": "20257"
},
"20258": {
"description": "It shows the number of terms registered by dictionary type and classification.",
"homepage": "http://dtims.dtaq.re.kr:8070/search/main/index.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Dictionary of defense scientific and technical terms",
"prefix": "20258"
},
"20259": {
"homepage": "https://dtims.krit.re.kr/vps/OINF_searchStndList.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Standard Classification of Defense Technology",
"prefix": "20259"
},
"2026": {
"description": "The Everglades Online Thesaurus is a structured vocabulary of concepts and terms relating to the south Florida environment. Designed as an information management tool for both researchers and metadata creators, the Thesaurus is intended to improve information retrieval across the many disparate information systems, databases, and web sites that provide Everglades-related information. The vocabulary provided by the Everglades Online Thesaurus expresses each relevant concept using a single βpreferred termβ, whereas in natural language many terms may exist to express that same concept. In this way, the Thesaurus offers the possibility of standardizing the terminology used to describe Everglades-related information β an important factor in predictable and successful resource discovery.",
"homepage": "http://digitalcommons.fiu.edu/glworks/1/",
"name": "Everglades Online Thesaurus",
"prefix": "2026"
},
"20260": {
"homepage": "https://dtims.krit.re.kr/vps/OINF_searchStndList.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Standard Classification of Weapon Systems",
"prefix": "20260"
},
"20261": {
"description": "Tax terminology",
"homepage": "https://txsi.hometax.go.kr/docs/customer/dictionary/wordList.jsp",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of tax",
"prefix": "20261"
},
"20262": {
"description": "Reference for tax code terms",
"homepage": "https://txsi.hometax.go.kr/docs_new/customer/dictionary/wordList.jsp",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Tax Law Terms",
"prefix": "20262"
},
"20263": {
"description": "Weather radar",
"homepage": "http://radar.kma.go.kr/lecture/dictionary/radar.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of Radar",
"prefix": "20263"
},
"20264": {
"description": "a meteorological lightning strike",
"homepage": "http://radar.kma.go.kr/lecture/dictionary/lightning.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of Lightning",
"prefix": "20264"
},
"20265": {
"homepage": "https://www.kahis.go.kr/home/lkdissinfo/disease_m8_01book.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of livestock diseases",
"prefix": "20265"
},
"20266": {
"homepage": "http://kvcc.kahis.go.kr/pms/web/disease/pmsDiseaseMain.do?iNo=4&iType=01&searchCondition=&searchKeyword=&searchKeyword1=&searchKeyword2=&searchKeyword3=",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Animal Disease Information",
"prefix": "20266"
},
"20267": {
"description": "The Medical Terminating Committee was born in 1976 and was formed to communicate and share information between the public and medical personnel, and has been working hard to standardize and maintain medical terminology and develop and disseminate Korean medical terms.\nThe pace of advancement in medicine is remarkable, and new technologies are being introduced and new diagnostic names and treatments are being introduced. As your enthusiasm and efforts to make good medical terms are concentrated, it seems that you have been negligent in introducing and deciding the terms needed for new medical technology. In the future, the Medical Terminology Committee will work harder to gather opinions from each conference and to introduce and standardize new medical terms for modern medicine.\nTo spread medical terminology, the Medical Terminating Commission has been running its website since 2001, providing infrastructure to search for the latest terminology in real time and access relevant information. In September 2015, the 5th album of medical terms of the Medical Association of Physicians was published as standard terms, and we hope that this homepage will help you search for and utilize standard medical terms.",
"homepage": "http://term.kma.org/index.asp",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Terms of medicine",
"prefix": "20267"
},
"20268": {
"description": "4,365 basic terms of the fourth chapter of the medical vocabulary book, 5 or more medical terminology developed by the Korea Advanced Institute of Science and Technology (KAIST), and 1 or more medical term used in the Korea Science Foundation Medical Research Information Center from 1998 to 1998.",
"homepage": "https://www.kamje.or.kr/func/download_file?file_name=035962dc9b5c16e6b617ba0c1f076628.pdf&file_path=../uploads/board/bo_workshop/38/&orig_name=5_%EC%9A%B0%EB%A6%AC%EB%A7%90_%EC%9D%98%ED%95%99%EC%9A%A9%EC%96%B4%EC%9D%98_%EA%B8%B0%EB%B3%B8%EC%9B%90%EC%B9%99,%ED%95%84%EC%88%98%EC%9D%98%ED%95%99%EC%9A%A9%EC%96%B4%EC%A7%91%EC%9D%84_%EC%A4%91%EC%8B%AC%EC%9C%BC%EB%A1%9C1.pdf",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Essential Medical Terminology",
"prefix": "20268"
},
"20269": {
"description": "The dictionary consists of a glossary of terms, abbreviations, numbers, and an English index, containing approximately 5,000 terms related to defense projects. Regarding defense projects, the title was written based on Janes, DTiMS Query Log, Defense Science and Technology Terms, and guidelines for each department of Defense Acquisition Program Administration.",
"homepage": "http://www.dapa.go.kr/dapa/wd/wdcry/list.do?menuId=326",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of defense business",
"prefix": "20269"
},
"2027": {
"description": "The Corporate Vocabulary is a purpose-built indexing tool which can be used for many applications across Natural England to search for and retrieve information more effectively. It facilitates accurate and consistent indexing and, by showing the relationships between different terms, it allows the most appropriate terms to be chosen, which improves the relevance of the information found.",
"homepage": "http://multites.net/natural/",
"name": "Natural England Corporate Vocabulary",
"prefix": "2027"
},
"20270": {
"description": "Terms related to electronic procurement can be searched through initial consonants and keywords",
"homepage": "http://www.d2b.go.kr/contents/info/termPop.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of defence e-procurement",
"prefix": "20270"
},
"20271": {
"description": "The encyclopedia is a content composed of the contents of major documents published by the court on key terms of important laws such as civil, criminal, and civil enforcement. The contents of the white paper dictionary may not be compatible with specific issues due to changes in precedents and statutes, so please use it as a reference only.",
"homepage": "http://gopenlaw.scourt.go.kr/view/index.jsp",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Encyclopedia of law",
"prefix": "20271"
},
"20272": {
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Thesaurus of law",
"prefix": "20272"
},
"20273": {
"homepage": "http://www.motie.go.kr/motie/py/gh/Publication/bbs/bbsView.do?bbs_seq_n=595&bbs_cd_n=30¤tPage=1&search_key_n=title_v&cate_n=&dept_v=&search_val_v=μ©μ΄",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Dictionary of Trade Policy Terms",
"prefix": "20273"
},
"20274": {
"homepage": "https://www.fta.go.kr/main/info/easy/word/",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of FTA",
"prefix": "20274"
},
"20275": {
"description": "Health education, health information, disease information",
"homepage": "https://health.cdc.go.kr/healthinfo/biz/health/gnrlzHealthInfo/gnrlzHealthInfo/gnrlzHealthInfoMain.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Glossary of health information",
"prefix": "20275"
},
"20276": {
"description": "infectious disease",
"homepage": "http://www.kdca.go.kr/npt/biz/npp/portal/nppLwcrIcdMain.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "List of legal communicable disease",
"prefix": "20276"
},
"20277": {
"description": "Terminology provided by the Han River Flood Control Office",
"homepage": "http://www.hrfco.go.kr/web/river/dictionaryList.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Water resource terms",
"prefix": "20277"
},
"20278": {
"description": "Flood terms provided by the Han River Flood Control Office",
"homepage": "http://www.hrfco.go.kr/web/riverPage/dictionary_2.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Flood terms",
"prefix": "20278"
},
"20279": {
"description": "The Korean Vocational Dictionary provides occupational and classification codes (regular education, skilled period, work strength, qualification, etc.) as a general occupation general manager of Korea (12,145 occupations, 16,442 occupations' name, as of the end of 2018).",
"homepage": "https://www.work.go.kr/consltJobCarpa/srch/jobDic/jobDicIntro.do?pageType=jobDicIntro",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Korean dictionary of occupations",
"prefix": "20279"
},
"20280": {
"description": "Search university department information",
"homepage": "https://www.work.go.kr/consltJobCarpa/srch/schdpt/schdptSrch.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Classification of department",
"prefix": "20280"
},
"20281": {
"description": "Annex 18 to the International Civil Aviation Organization and the Aviation Act mean substances or goods that are likely to emit explosive, toxic, corrosive, flammable gases or vapors that could harm people or aircraft.\nIn addition, dangerous goods shall be reported as dangerous goods as prescribed by the Aviation Act and transported in accordance with packaging, marking, and other strict procedures, and may be fined up to 20 million won or less for violations.",
"homepage": "https://avsec.ts2020.kr/avsc/main",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Dangerous Goods",
"prefix": "20281"
},
"20282": {
"homepage": "https://www.nl.go.kr/NL/contents/search.do?srchTarget=total&pageNum=1&pageSize=10&kwd=κΈ°λ‘νμ©μ΄μ¬μ !",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Word list of Energy",
"prefix": "20282"
},
"20283": {
"homepage": "http://www.kemco.or.kr/web/kem_home_new/info/dictionary/voca/kem_list.asp",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of Energy",
"prefix": "20283"
},
"20284": {
"description": "KEPCO implemented the term purification process to improve public understanding of electricity terms. Since May last year, we have organized an in-house T/F and have secured various in-house and external data to collect 3,000 power terms. Afterwards, the final 300 power terms were selected through heated meetings, including professors and ordinary people, the National Institute of Korean Language, and various associations related to the power industry. Through this work, difficult Chinese characters and abbreviations were improved to easy terms, awkward foreign words were changed according to the notation, and the appropriate representative terms were unified when mixed. In the wake of the purification of power terms, KEPCO will minimize the use of unnecessary foreign words and continue to improve them by identifying unidentified terms, Japanese expressions, Konglish, and authoritative terms. We will make efforts to purify unfamiliar and difficult words so that people can easily understand them and communicate them at the eyes of the people.",
"homepage": "https://home.kepco.co.kr/kepco/KO/D/htmlView/KODEHP001.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of Electric Power",
"prefix": "20284"
},
"20285": {
"description": "Terminology of Korea Electric Power Corporation's Electric Power",
"homepage": "https://home.kepco.co.kr/kepco/KO/E/A/KOEAPP001.po",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Terms of KEPCO",
"prefix": "20285"
},
"20286": {
"description": "The Korea Information and Communication Technology Association (TTA) describes and standardizes information and communication terms that are generated by the development of information and communication technology and convergence of technology with other fields. You can access the web directly with your PC or smartphone or download and use the information and communication terminology dictionary app from the mobile app.",
"homepage": "https://terms.tta.or.kr/intro.do",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Glossary of Information and Communications",
"prefix": "20286"
},
"20287": {
"abbreviation": "ISO639",
"description": "Comprehensive language code information, consisting of ISO 639-1, ISO 639-2 and IETF language types. Data is taken from the Library of Congress as the ISO 639-2 Registration Authority, and from the Unicode Common Locale Data Repository. The URIs have been assigned by BARTOC to get a common URI namespace.",
"homepage": "https://www.loc.gov/standards/iso639-2/",
"license": "http://opendatacommons.org/licenses/pddl/1.0",
"name": "ISO Language Codes (639-1 and 693-2) and IETF Language Types",
"pattern": "^[a-z]{2,3}$",
"prefix": "20287"
},
"20288": {
"abbreviation": "kdsf-ffk",
"homepage": "https://w3id.org/kdsf-ffk/",
"license": "CC BY-SA 4.0",
"prefix": "20288"
},
"20290": {
"abbreviation": "ASJC",
"description": "The All Science Journal Classification (ASJC) System is used in Scopus to classify journals and conference proceedings under four broad subject areas (life sciences, physical sciences, health sciences and social sciences and humanities) which are further divided into groups and 333 minor fields. In addition there is a class for multidisciplinary journals.",
"homepage": "https://service.elsevier.com/app/answers/detail/a_id/15181/supporthub/scopus/",
"name": "All Science Journal Classification Codes",
"pattern": "^[0-9]{4}$",
"prefix": "20290"
},
"20291": {
"name": "Test",
"prefix": "20291"
},
"20292": {
"abbreviation": "ICOM",
"description": "The development of professional standards is one of the core objectives of ICOM, particularly in the area of advancement, sharing, and communication of knowledge to the broad-ranging global museum community, but also to those who develop policies in relation to its work, to those responsible for managing the legal and social aspects of its profession, and not least to those to whom it is directed and who are expected to participate in and benefi t from it. Launched in 1993, under the supervision of AndrΓ© DesvallΓ©es, and with the collaboration of FranΓ§ois Mairesse from 2005 onwards, the Dictionary of Museologyis a monumental work resulting from many years of research, interrogation, analysis, revision and debate by ICOMβs International Committee for Museology (ICOFOM), which is particularly devoted to the process of developing our comprehension of the practice and theory of museums and the work that is undertaken within these institutions daily.",
"homepage": "http://icom-greece.mini.icom.museum/wp-content/uploads/sites/38/2018/12/Museology_WEB.pdf",
"name": "Key Concepts of Museology",
"prefix": "20292"
},
"20293": {
"description": "The Mathematical Dictionary was created by SolidarityNow as part of the project βComprehensive Service Provision for the Integration and Well-Being of Refugee Children and Familiesβ, supported by UNICEF with funding from the European Union Civil Protection and Humanitarian Aid Operations (DG-ECHO), and in collaboration with METAdrasi. METAdrasi realised this dictionary as part of the project \"Interpretation for Education of Refugee and Migrant Children in Greece\", supported by UNICEF with funding from the European Union Civil Protection and Humanitarian Aid Operations (DG-ECHO). The texts were translated in Arabic by SolidarityNow and edited by METAdrasi, while the translations in English, Farsi, Urdu and Turkish were realised by METAdrasi .",
"homepage": "https://www.solidaritynow.org/wp-content/uploads/2019/08/Mathematical-Dictionary-FINAL.pdf",
"name": "Mathematical Dictionary",
"prefix": "20293"
},
"20294": {
"description": "The glossary has been developed by the Human Rights National Implementation Division of the Directorate General of Human Rights and Rule of Law, under the HELP umbrella. It is intended to guide legal professionals from Council of Europe member states in using the correct terminology when they make Convention-based arguments in national proceedings and to correctly understand when reading judgments in English.",
"homepage": "https://rm.coe.int/glossary-of-the-european-convention-on-human-rights/16808ee7b5",
"name": "GLOSSARY of the European Convention on Human Rights",
"prefix": "20294"
},
"20295": {
"abbreviation": "IOM",
"description": "The IOM \"Glossary on Migration\" is as an accessible and comprehensive collection of migration-related terminology. Designed for all persons dealing with migration issues at the international level, the glossary aims at creating a common understanding of migration terms.\n\nThe governance of migration is multi-layered occurring at the national, regional and international levels, and in a world in which so many migration challenges and realties transcend national and regional borders, a common understanding of migration in order to effectively respond to such challenges is fundamental. At the foundation of any common understanding on migration is the use of a common \"language\". This Glossary provides a wide-set of terms pertaining to conceptual, legal, theoretical or practical matters of migration. It is addressed at policy makers, practitioners, scholars, students as well as to anyone who is interested in migration issues.",
"homepage": "https://blogs.sch.gr/par6gym/files/2014/06/Gloassari.pdf",
"name": "Glossary on Migration",
"prefix": "20295"
},
"20296": {
"abbreviation": "MLGT",
"description": "The ISO/TC 211 Multi-Lingual Glossary of Terms has been compiled from International Standards developed by ISO/TC 211. Its purpose is to encourage consistency in the use and interpretation of geospatial terms. It is being made freely available to all interested people and organizations.",
"homepage": "https://isotc211.geolexica.org/",
"name": "ISO/TC 211 Multi-Lingual Glossary of Terms",
"prefix": "20296"
},
"20297": {
"abbreviation": "ARK",
"homepage": "https://ark.staatsbibliothek-berlin.de/",
"name": "Classification of the Old Berlin State Library Catalog",
"prefix": "20297"
},
"20298": {
"abbreviation": "NSK",
"description": "Die Systematik des neuen Sachkatalog der Staatsbibliothek PreuΓischer Kulturbesitz wurde zur ErschlieΓung von Erwerbungen von 1945 bis 1999 im Haus Potsdamer StraΓe eingesetzt. Die NSK-Systematik basiert auf der Eppelsheimer Methode.",
"homepage": "https://staatsbibliothek-berlin.de/recherche/kataloge-der-staatsbibliothek/uebersicht-konventionelle-sachkataloge/",
"license": "CC BY-SA 4.0",
"name": "Classification of the New Berlin State Library Catalog",
"prefix": "20298"
},
"20299": {
"abbreviation": "CDT",
"description": "The Code on Dental Procedures and Nomenclature is used to provide for the efficient processing of dental claims, and to populate an Electronic Health Record.",
"homepage": "http://www.ada.org/en/publications/cdt",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Code on Dental Procedures and Nomenclature",
"prefix": "20299"
},
"203": {
"description": "This thesaurus is based on the original APSDEP Thesaurus, produced in 1993 by the International Labour Organisation's Asian and Pacific Skills Development Programme (ILO/APSDEP). Selected appropriate terms from the APSDEP thesaurus have been merged with terms from a supplement, produced at NCVER, containing recent Australian vocational education and training (VET) terms. This thesaurus is not currently being used in VOCEDplus.",
"homepage": "http://hdl.voced.edu.au/10707/6073",
"name": "VOCED Thesaurus",
"prefix": "203"
},
"2030": {
"abbreviation": "DEKLA",
"description": "Extension of the International Patent Classification published and internally used by the German Patent Office.",
"homepage": "http://dpma.de/service/klassifikationen/ipc/index.html",
"name": "Classification of the German Patent and Trademark Office",
"pattern": "^[A-H] [0-9]+ [A-Z]*( [0-9]*\\/[0-9]*)?$",
"prefix": "2030",
"wikidata_database": "Q26903402"
},
"20300": {
"description": "Olympic games glossary (English, Greek, French)",
"homepage": "http://repository.academyofathens.gr/document/201864.pdf",
"prefix": "20300"
},
"20301": {
"abbreviation": "DDB-HT",
"description": "Hierarchy type in the Deutschen Digitalen Bibliothek (DDB)",
"pattern": "^ht0[0-9][0-9]$",
"prefix": "20301"
},
"20302": {
"abbreviation": "NGL",
"description": "The Newspaper Genre List is an attempt to standardize terms used to designate genres of newspapers. The perspective and scope of the list reflects types of papers cataloged by members of the United States Newspaper Program.",
"homepage": "https://www.lib.washington.edu/gmm/collections/mcnews/ngl",
"license": "CC0-1.0",
"name": "Newspaper Genre List",
"prefix": "20302",
"wikidata_database": "Q106632466"
},
"20303": {
"abbreviation": "BBT",
"description": "The BBT is the research outcome of work undertaken by the DARIAH Thesaurus Maintenance WG in an effort to design and establish a coherent overarching thesaurus for the humanities, under which specialist thesauri and structured vocabularies used across scholarly communities can be aligned and form a thesaurus federation. It aims at enabling cross-disciplinary resource discovery while ensuring compatibility with thesauri that cover highly specific scientific domains and areas of knowledge in development. The BBT was created and funded by the DARIAH GR Developing a Greek Research Infrastructure for the Humanities project (2013-2015). Currently it receives funding by the APOLLONIS Greek Infrastructure for Humanities, Arts and Language Research and Innovation project (2017-2020).",
"homepage": "https://www.backbonethesaurus.eu/",
"license": "CC-BY-4.0",
"name": "Backbone Thesaurus",
"prefix": "20303"
},
"20304": {
"abbreviation": "PRECIS",
"description": "The PRECIS Subject Heading System was used 1974-1990 by the British Library. Development of PRECIS by Dereck Austin was influenced by the the Colon classification. The system is based on the Principle of Context Dependency and on the Principle of One-to One Relationship. The version of PRECIS used by the British Library is described in: PRECIS: a manual of concept analysis and subject indexing / Derek Austin (London: The Council for the British National Bibliography, 1974).",
"name": "PRECIS Subject Headings",
"prefix": "20304"
},
"20305": {
"abbreviation": "COMPASS",
"description": "The COMPuter Aided Subject System (COMPASS) is a subject indexing system developed by the British Library. With revision of UKMARC in 1990 COMPASS replaced PRECIS. COMPASS was used between 1991 and 1996.",
"name": "COMPuter Aided Subject System",
"prefix": "20305"
},
"20306": {
"description": "L-scheme is a controlled vocabulary for legal terms.",
"homepage": "http://data.ub.uio.no/skosmos/lskjema/",
"license": "CC0-1.0",
"prefix": "20306"
},
"20307": {
"description": "The Thesaurus is the intellectual property of the Academy of Athens (AA), the National and Kapodistrian University of Athens (UOA) and the Athens School of Fine Arts (ASFA). It was created as a collaborative effort and was compiled during the course of the project DARIAH GR: Developing a Greek Research Infrastructure for Arts and Humanities (2013-2015) and of the project APOLLONIS: Greek Infrastructure for Humanities, Arts and Language Research and Innovation (2017-2020). It is maintained by the Academy of Athens. It is the outcome of an attempt to create a multilingual structured thesaurus of use to humanities scholars. It is a specialist thesaurus based on the principles, methodology and hierarchies of the BBT.",
"homepage": "https://isl.ics.forth.gr/bbt-federated-thesaurus/HUMANITIES-THESAURUS/",
"license": "CC-BY-4.0",
"prefix": "20307"
},
"20308": {
"description": "PARTHENOS vocabularies is the research outcome of the H2020 Project βPARTHENOS Pooling Activities, Resources and Tools for Heritage E-research Networking, Optimization and Synergiesβ. It is provided under CC-BY 4.0 distribution license. This is a modified version that contains skos:broadMatch links from PARTHENOS concepts to BackBoneThesaurus (BBT) concepts.",
"homepage": "https://isl.ics.forth.gr/bbt-federated-thesaurus/PARTHENOS/",
"license": "CC-BY-4.0",
"prefix": "20308"
},
"20309": {
"description": "open and shared thesaurus covering INRAE's research fields. It serves as a controled vocabulary within the Institute for indexing and annotating documents, web pages, descriptions of activities, datasets, etc. for research or information analysis purposes.",
"homepage": "https://vocabulaires.irstea.fr/thesaurus-inrae/",
"license": "CC-BY-4.0",
"prefix": "20309"
},
"2031": {
"description": "Within the framework of the research project\" The Heritage of Schinkel - from the depot into the discourse \"funded by the Federal Ministry of Education and Research, a system for the art - technological description of drawings on paper in databases was developed in the Department of Conservation / Restoration of the Kupferstichkabinett Berlin 2010 (.), A publication of the model developed at the Kupferstichkabinett appears to be overdue (...).\n\nThe description system proposed here is intended to form the basis for a uniform, yet precise and differentiated art-technological recording of drawings on paper. It is limited to information that can be obtained by means of optical examination methods and is used for the purpose of object-taking, catalog or exhibition labeling.",
"name": "System for the description, input and processing of art-technical information for drawings on paper in databases",
"prefix": "2031"
},
"20310": {
"description": "List of thematic topics",
"homepage": "https://data.legilux.public.lu/vocabulaires/legal-subject-theme/",
"license": "CC-BY-4.0",
"prefix": "20310"
},
"20311": {
"description": "ScoLOMFR is a format for describing and sharing digital resources, ScoLOMFR helps you to build a free and paying resources offer for school education. Based on the LOMFR (2010) data schema, it is composed of fields organized in 9 elements and of a set of vocabularies common to the different actors of school education.",
"homepage": "https://www.reseau-canope.fr/scolomfr/data/scolomfr-7-0/",
"prefix": "20311"
},
"20312": {
"description": "This multilingual thesaurus structures, with a polyhierarchy, the main concepts of open science. It was initiated by building on existing glossaries and on the taxonomy proposed in the framework of the FOSTER project. It is enriched through a text-mining task of reference documents in the field. It is also available for download in PDF format, SKOS, CSV and JSON-LD.",
"homepage": "https://www.loterre.fr/skosmos/TSO/",
"license": "CC-BY-4.0",
"name": "Open science thesaurus",
"prefix": "20312"
},
"20313": {
"abbreviation": "CCT",
"description": "The Chinese Thesaurus (CT) was created by the Scientific and Technical Information Institute of China and the National Library of China for subject indexing of books and serials in library. It covers the social sciences, science and technology, and the humanities. In 1994 it was integrated into the Chinese Classified Thesaurus (CCT).",
"homepage": "https://ct.istic.ac.cn/site/organize/welcome",
"name": "Chinese Thesaurus",
"prefix": "20313"
},
"20314": {
"abbreviation": "CCT",
"description": "The Chinese Classified Thesaurus (CCT) was created 1986-1994 to to integrate the Chinese Library Classification (CLC) and the Chinese Thesaurus (CT).",
"homepage": "http://cct.nlc.cn/",
"name": "Chinese Classified Thesaurus",
"prefix": "20314"
},
"20315": {
"abbreviation": "NTSF",
"description": "Thesaurus containing genre and form terms, mostly applicable to printed and electronic publications, and covering literature for children as well as adults. Its terms are given in the languages Norwegian bokmΓ₯l, Norwegian nynorsk and partly in English. References to Libraryβ―ofβ―Congressβ―Genre/Form Terms are included whenever matching concepts are found.\n\nMarc source code: ntsf",
"homepage": "https://www.nb.no/nbvok/ntsf/",
"license": "CC0-1.0",
"prefix": "20315",
"wikidata_database": "Q107620287"
},
"20316": {
"abbreviation": "BIBBI",
"description": "Bibbi authorities is the integrated authority file of Biblioteksentralen, containing authorities for persons, corporations, place names, meetings/events and subjects.",
"homepage": "https://vokabular.bs.no/bibbi/",
"license": "CC0-1.0",
"name": "Bibbi authorities",
"pattern": "^[0-9]+$",
"prefix": "20316",
"wikidata_database": "Q107620603"
},
"20317": {
"homepage": "https://bergenbibliotek.no/musikkogfilm/emneord-for-musikk/",
"prefix": "20317"
},
"20318": {
"description": "Classification scheme used to classify literature in The Sami bibliography, a joint project between the National library of Norway, the Sami special library at the Sami Special Library at the Rovaniemi City Library, the Murmansk State Regional Universal Scientific Library, and Γjtte, Swedish Mountain- and Sami museum. \n\nThe classification scheme was developed by Anders LΓΆΓΆv at Norwegian Institute of Technology, starting in 1980. In 1991/1992 it was handed over to the National Library of Norway.",
"homepage": "https://www.nb.no/nbvok/loov/",
"name": "LΓΈΓΈv classification",
"pattern": "^[0-9]+$",
"prefix": "20318"
},
"20319": {
"description": "The CHIN Data Dictionaries contain a description of database fields for museum collection and archaeological site management and documentation. Each data field in the CHIN Data Dictionaries is described by a field label, a mnemonic, a name, a definition, entry rules, related fields, a data type, examples, a discipline, and a source. The CHIN Data Dictionaries are used: as the standard for Canadian institutions that contribute collections data to CHIN's Artefacts Canada, as guidelines for institutions which are developing or modifying a collections management system and to help cataloguers record information consistently, or to help users of collections databases with search strategies. The Canadian Heritage Information Network's Humanities Data Dictionary consists of 654 fields for collections in history, ethnology, archaeological specimens, and fine and decorative arts.",
"homepage": "https://app.pch.gc.ca/application/ddrcip-chindd/description-about.app?lang=en",
"name": "CHIN Humanities Data Dictionary",
"prefix": "20319"
},
"2032": {
"description": "The use of controlled vocabulary for cataloging is the basis for consistent object documentation, and the co-ordination of a common controlled vocabulary is all the more important when combining heterogeneous metadata from different collections in a portal to ensure optimal research conditions.\n\nThe controlled vocabulary for the description of technology and material, which is concatenated within the workgroup graphics, currently contains the basic stock of the vocabulary for indexing graphic sheets for the assembly in the planned graphics portal. Developed in accordance with the Art & Architecture Thesaurus Β (AAT) of the Getty Research Institute, the graphic vocabulary includes terms that have their analogies within the AAT facet of material and technology as well as in the field of technology also individual terms of the object facet provided They are media which are used in connection with a technique such as, for example, Tomb, feather etc.\n\nThe graphic vocabulary is under construction. It will continue to evolve as long as Graphic Collections demand more descriptors.",
"homepage": "http://www.arthistoricum.net/netzwerke/graphik-vernetzt/kontrolliertes-vokabular/",
"name": "Graphic vocabulary",
"prefix": "2032"
},
"20320": {
"description": "Artists in Canada, compiled and maintained by the National Gallery of Canada Library, is a bilingual union list that identifies the location of documentation files on Canadian artists. Twenty-three libraries and art galleries across Canada have contributed biographical information and lists of their documentation files to create this resource which contains information for over 42,700 artists.\n\nThe term \"artist\" is interpreted broadly in the visual arts field to include artisans along with painters, sculptors, printmakers, architects, and others. An artist \"in Canada\" denotes an artist born in Canada or an artist born elsewhere who has worked in Canada. The inclusion of an artist implies no selection process. An entry here indicates only the existence of a file, the size of which may range from one to hundreds of items, containing information in the form of press clippings, exhibition announcements, and other items.\n\nEach record in the database has information in up to 25 data fields. The data within these fields include brief biographical information on the artist, such as birth and/or death dates, place of birth and/or death, and artist technique.",
"homepage": "https://app.pch.gc.ca/application/aac-aic/description-about.app?lang=en",
"name": "Artists in Canada",
"prefix": "20320"
},
"20321": {
"description": "Wordlist for different types of threats to heritage assets (e.g. coastal erosion, flooding, vandalism).",
"homepage": "http://www.heritage-standards.org.uk/fish-vocabularies/",
"name": "Threat Types List",
"prefix": "20321"
},
"20322": {
"description": "This list relates to the MIDAS unit Management Proposal Outcome. It is intended to provide the option to audit the effectiveness of recommendations made in response to proposed work or planning applications (e.g. agreed, followed, withdrawn).",
"homepage": "http://www.heritage-standards.org.uk/fish-vocabularies/",
"name": "Consultation Outcome List",
"prefix": "20322"
},
"20323": {
"description": "This list relates to the MIDAS unit Management Proposal Type. The different contexts of consultations can be recorded, which in turn may determine the appropriate nature, method, procedure to be adopted by the inventory in response to the consultation (e.g. planning application, listed building consent, conservation area appraisal).",
"homepage": "http://www.heritage-standards.org.uk/fish-vocabularies/",
"prefix": "20323"
},
"20324": {
"description": "This list relates to the Event Type unit in MIDAS. It covers both investigative, data-gathering activities which involve a physical intervention in the site and survey events, ie those data-gathering events which do not have a damaging effect on the resource (e.g. field survey, soil samling, measured survey).",
"homepage": "http://www.heritage-standards.org.uk/fish-vocabularies/",
"name": "Event Type List",
"prefix": "20324"
},
"20325": {
"description": "This list relates to the MIDAS unit Management Proposal Outcome. It is intended to provide the option to audit the effectiveness of archaeological recommendations made in response to proposed work or planning applications by recording the final result of the planning application (e.g. approved with full condition, refused, amended).",
"homepage": "http://www.heritage-standards.org.uk/fish-vocabularies/",
"prefix": "20325"
},
"20326": {
"description": "This list relates to the MIDAS Management Proposal Work Proposed unit of information. It will offer the opportunity to audit the consultations received by SMRs by broad categories recommended by ALGAO (e.g. building extension, dredging, road construction).",
"homepage": "http://www.heritage-standards.org.uk/fish-vocabularies/",
"name": "Work Proposed List",
"prefix": "20326"
},
"20327": {
"description": "Fauna Europaea is Europe's main zoological taxonomic index. Scientific names and distributions of all living, currently known, multicellular, European land and freshwater animal species are available in one authoritative database. It is installed as a taxonomic backbone in a wide range of biodiversity services and actively contributes to biodiversity informatics innovations in various initiatives and EC programs. Fauna Europaea started in 2000 as an EC funded FP5 project and provides a unique taxonomic reference for many user-groups such as scientists, governments, industries, nature conservation communities and educational programs. Fauna Europaea was formally accepted as an INSPIRE standard for Europe, as part of the European Taxonomic Backbone established in PESI. Today it is hosted by the Museum fΓΌr Naturkunde in Berlin.",
"homepage": "https://fauna-eu.org/",
"license": "CC BY-SA 4.0",
"name": "Fauna Europaea",
"prefix": "20327"
},
"20328": {
"description": "Uberon is an anatomical ontology that represents body parts, organs and tissues in a variety of animal species, with a focus on vertebrates. It has been constructed to integrate seamlessly with other ontologies, such as the OBO Cell Ontology, the Gene Ontology, Trait and Phenotype ontologies, as well as other anatomical ontologies.\n\nThe ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. The figure below shows taxon-centric anatomy ontologies along the bottom axis; domain specific ontologies on the right hand side; orthogonal ontologies on the left axis.",
"homepage": "https://uberon.github.io/",
"name": "Uberon",
"prefix": "20328"
},
"20329": {
"description": "List of data formats and media forms used in BARTOC",
"homepage": "http://uri.gbv.de/terminology/bartoc_formatcatalog/",
"name": "Bartoc Formatcatalog",
"prefix": "20329"
},
"2033": {
"description": "EcoLexicon is a terminological resource developed by the LexiCon Research Group at the University of Granada.\n\nEcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology. Consequently, each concept appears in the context of a specialized frame that highlights its relation to other concepts, and makes explicit its designations in English, Spanish, German, French, Russian, and Greek. Through the convergence of conceptual, linguistic and graphical information, EcoLexicon meets the needs of different users groups (people interested in the Environment, students, translators, technical writers, etc.).",
"homepage": "http://ecolexicon.ugr.es/",
"name": "EcoLexicon",
"prefix": "2033"
},
"20330": {
"homepage": "http://uri.gbv.de/terminology/amh_datierung/",
"name": "ArchΓ€ologisches Museum Hamburg β Stadtmuseum Harburg/Helms-Museum: Age dating terms",
"prefix": "20330"
},
"20331": {
"abbreviation": "AMV",
"description": "Algorithm Metadata Vocabulary is a vocabulary for capturing and storing the metadata about the algorithms (a procedure or a set of rules that is followed step-by-step to solve a problem, especially by a computer). There are uncountable algorithms present in every area (e.g., Computer Science, Mathematics), which makes it hard for specialists, academicians, application engineers, and so forth to discover, distinguish, select, and reuse them. The snag faced by the researchers in the current time is the failure of getting relevant results when searching for algorithms in any search engine. AMV is represented as a semantic model and produced OWL file, which can be directly used by anyone interested to create and publish algorithm metadata as a knowledge graph, or to provide metadata service through SPARQL endpoint. The vocabulary may also be used to annotate the literature (e.g., research article, monographs, dissertation, technical reports) providing the algorithms.",
"homepage": "https://www.isibang.ac.in/ns/amv/",
"license": "CC0-1.0",
"name": "Algorithm Metadata Vocabulary",
"prefix": "20331"
},
"20332": {
"abbreviation": "CODO",
"description": "The purpose of CODO ontology to represent and reason information related to COVID-19 cases and patient information. The cases, such as active, recovered, deceased, migrated, etc. on a daily basis across the geo-location (district, state (province), and country), available resources and requirements. The patient and related information, such as nationality, symptom, suspected level of the disease, travel history, inter-personal relationships between patients, suspected transmission reason, tracking of patient test results, diagnosis, treatment facility, clinical facility, etc. The ontology has been produced by evaluating various COVID-19 resources, such as datasets, literature, services, etc.",
"homepage": "https://www.isibang.ac.in/ns/codo/",
"license": "CC-BY-4.0",
"prefix": "20332"
},
"20333": {
"abbreviation": "MOD",
"description": "Metadata for Ontology Description and publication was created by reviewing of standard existing metadata vocabularies (e.g., Dublin Core, OMV, DCAT, VoID) and selecting relevant properties for describing ontologies.",
"homepage": "https://www.isibang.ac.in/ns/mod/",
"license": "CC-BY-4.0",
"name": "Metadata for Ontology Description and publication",
"prefix": "20333"
},
"20334": {
"homepage": "http://uri.gbv.de/terminology/amh_eigentumsstatus/",
"name": "ArchΓ€ologisches Museum Hamburg β Stadtmuseum Harburg/Helms-Museum: Ownership status terms",
"prefix": "20334"
},
"20335": {
"homepage": "http://uri.gbv.de/terminology/amh_kulturgruppe/",
"name": "ArchΓ€ologisches Museum Hamburg β Stadtmuseum Harburg/Helms-Museum: Cultural groups",
"prefix": "20335"
},
"20336": {
"homepage": "http://uri.gbv.de/terminology/amh_material/",
"name": "ArchΓ€ologisches Museum Hamburg β Stadtmuseum Harburg/Helms-Museum: Material terms",
"prefix": "20336"
},
"20337": {
"homepage": "http://uri.gbv.de/terminology/amh_objektbezeichnung/",
"name": "ArchΓ€ologisches Museum Hamburg β Stadtmuseum Harburg/Helms-Museum: Object description terms",
"prefix": "20337"
},
"20338": {
"homepage": "http://uri.gbv.de/terminology/amh_personen/",
"name": "ArchΓ€ologisches Museum Hamburg β Stadtmuseum Harburg/Helms-Museum: Persons",
"prefix": "20338"
},
"20339": {
"homepage": "http://uri.gbv.de/terminology/amh_personenrollen/",
"name": "ArchΓ€ologischen Museum Hamburg β Stadtmuseum Harburg/Helms-Museum: Person roles",
"prefix": "20339"
},
"2034": {
"description": "The Textile Museum Thesaurus is a data management tool for cataloging and searching for textiles in The Textile Museumβs collection in its electronic database. The Thesaurus functions both as a controlled vocabulary for cataloging our collections and as an electronic querying aid structured to permit the highest level of success in retrieving the appropriate objects during searches. (...) The Textile Museum developed this Thesaurus because no currently available vocabulary resource meets our need to deal with textiles globally, or develops textile terminology to the level of detail necessary for textile specialists. The Textile Museum Thesaurus is, of course, idiosyncratic to its collection, software, data standards, and current curatorial staff preferences. This publication is intended to provide a model of an electronic thesaurus for cataloging textiles to the museum and textile fields. We expect that other institutions will adapt, expand, and/or draw from our Thesaurus as appropriate to their collections and needs.",
"homepage": "https://museum.gwu.edu/sites/g/files/zaxdzs3226/f/Textile%20Museum%20Thesaurus%20%28Final%29.pdf",
"name": "Textile Museum Thesaurus",
"prefix": "2034"
},
"20340": {
"homepage": "http://uri.gbv.de/terminology/amh_sachgruppe/",
"name": "ArchΓ€ologisches Museum Hamburg β Stadtmuseum Harburg/Helms-Museum: Subject groups",
"prefix": "20340"
},
"20341": {
"homepage": "http://uri.gbv.de/terminology/amh_technik/",
"name": "ArchΓ€ologisches Museum Hamburg β Stadtmuseum Harburg/Helms-Museum: Technique (craft) terms",
"prefix": "20341"
},
"20342": {
"homepage": "http://uri.gbv.de/terminology/amh_warenart/",
"name": "ArchΓ€ologisches Museum Hamburg β Stadtmuseum Harburg/Helms-Museum: Item types (exhibition types)",
"prefix": "20342"
},
"20343": {
"homepage": "http://uri.gbv.de/terminology/amh_wertart/",
"name": "ArchΓ€ologisches Museum Hamburg β Stadtmuseum Harburg/Helms-Museum: Value types",
"prefix": "20343"
},
"20344": {
"homepage": "http://uri.gbv.de/terminology/amh_wertgruppe/",
"name": "ArchΓ€ologisches Museum Hamburg β Stadtmuseum Harburg/Helms-Museum: Value groups",
"prefix": "20344"
},
"20345": {
"abbreviation": "bibliographic_publication_type",
"description": "Publication types from the K10plus format field PICA+ 200@ / Pica3 0500 Position 1.",
"name": "Physical publication types from K10plus format",
"prefix": "20345"
},
"20346": {
"license": "CC0-1.0",
"name": "Bibliographic relation type",
"prefix": "20346"
},
"20347": {
"homepage": "http://uri.gbv.de/terminology/bilddatenbank_typ_art/",
"name": "Type (bilddatenbank.gbv.de)",
"prefix": "20347"
},
"20348": {
"description": "Consists of the Getty-people-events and some entries from http://vocab.org/bio.",
"homepage": "http://uri.gbv.de/terminology/biographie_chronicle_event/",
"name": "Events in biographies or chronicles",
"prefix": "20348"
},
"20349": {
"name": "Phases in biographies or chronicles",
"prefix": "20349"
},
"2035": {
"description": "STRUNA is a database of Croatian Special Field Terminology. It was officially inaugurated on the web in February 2012. Its aim is to gradually make available to the public the standardized Croatian terminology for all professional domains.\n\nThe Development of Croatian Special Field Terminology project started in 2007 as part of the initial coordination project launched at the initiative of the Croatian Standard Language Council, and has since been financed by the Croatian Science Foundation. The program supports the strategic values of the Foundation and fits into two basic areas of the National Strategy for Science Development β development of information technology and sociocultural transition from an industrial to a knowledge-based society. The Institute of Croatian Language and Linguistics was chosen to serve as the national coordinator.\n\nGiven the pivotal role terminology plays in language development as well as professional communication, the objective of the program in a broader sense is to lay the foundation for the development of national terminology policy, to establish various forms of more structured education in this field, and to intensify long-term cooperation with national and international academic and other institutions dealing with different aspects of terminology work, with the Croatian Standards Institute and with other interested parties. (...)\n\nExperts from eighteen domains have so far joined the program with the aim of standardazing the terminology of their respective disciplines. Currently available for search are the terminologies of the following domains: aviation and air traffic, cartography and geoinformatics, chemistry, civil engineering, corrosion, dental medicine, marine engineering, mechanical engineering, polymers, and physics. Maritime terminology, anthropological terminology, and EU law terminology are in the final stage and the domains of phytomedicine, mathematics and archaeology in the process of joining the program.",
"homepage": "http://struna.ihjj.hr/",
"name": "STRUNA",
"prefix": "2035"
},
"20350": {
"description": "Art historical stylistic epochs and art movements with period specifications. Monohierarchical thesaurus according to DIN 1463-1 with GND reference.",
"homepage": "https://wiki.bsz-bw.de/display/MUSIS/BSZ-Thesauri#BSZThesauri-BSZ-Stilepochen",
"license": "CC BY-NC-ND 3.0",
"name": "BSZ - Stylistic epochs",
"prefix": "20350"
},
"20351": {
"homepage": "http://uri.gbv.de/terminology/citizenship_iso_3166/",
"name": "Citizenship (ISO 3166)",
"prefix": "20351"
},
"20352": {
"homepage": "http://uri.gbv.de/terminology/collection_type/",
"license": "CC0-1.0",
"name": "Type of collection",
"prefix": "20352"
},
"20353": {
"name": "Relations between corporations",
"prefix": "20353"
},
"20354": {
"name": "CSS-Color-Names",
"prefix": "20354"
},
"20355": {
"name": "Filetypes",
"prefix": "20355"
},
"20356": {
"description": "FSO vocabulary for persons and entities.",
"homepage": "http://uri.gbv.de/terminology/fso_actor/",
"name": "FSO: Person",
"prefix": "20356"
},
"20357": {
"description": "FSO vocabulary for recording the function of persons and entities in the context of a unit of distortion.",
"homepage": "http://uri.gbv.de/terminology/fso_actor_role/",
"name": "FSO: Person role",
"prefix": "20357"
},
"20358": {
"description": "FSO vocabulary for recording the state of development.",
"homepage": "http://uri.gbv.de/terminology/fso_status_description/",
"name": "FSO: Status of description",
"prefix": "20358"
},
"20359": {
"description": "FSO vocabulary for recording the type of remark.",
"homepage": "http://uri.gbv.de/terminology/fso_annotation_role/",
"name": "FSO: Annotation role",
"prefix": "20359"
},
"2036": {
"description": "The database contains over 338,000 terms, searchable under both Irish and English versions. More than 2.3 million unique visitors used the website between 2006 and mid 2014. They made 9.8 million visits and 56 million searches in that time. According to annual user surveys carried out by Fiontar since 2010, the site is primarily used by translators and interpreters and by university students. (...).\n\nThe first phase of the work was done with funding from INTERREG III A (2004-7). Phase I of the work consisted of digitising and integrating existing paper and electronic lists. Fiontar continues to manage and develop this resource with project funding from Foras na Gaeilge. Many resources have been added under subsequent phases, including collections of sports, arts and legal terms, tools for translation memories and other resources for translators, and a link facility to The New Corpus for Ireland.\n\nPhase V of the project began on 1 June 2014 and, among other things, a collection of computing terms is being developed. Hosting of the National Terminology Database for Irish was transferred from DCU to Tibus in May 2014. Fiontar is responsible for the application, but Tibus is now responsible for the site-hosting (availability, speed, etc). The web address for the National Terminology Database for Irish changed from focal.ie to tearma.ie on 1 March 2015.",
"homepage": "http://www.tearma.ie/",
"name": "National Terminology Database for Irish",
"prefix": "2036"
},
"20360": {
"description": "FSO vocabulary for recording the classification of the contents of units of description.",
"homepage": "http://uri.gbv.de/terminology/fso_content_type/",
"name": "FSO: Content type",
"prefix": "20360"
},
"20361": {
"description": "FSO vocabulary for recording the perimeter units for stocks.",
"homepage": "http://uri.gbv.de/terminology/fso_extent_unit_collection/",
"name": "FSO: Unit of extent (collection)",
"prefix": "20361"
},
"20362": {
"description": "FSO vocabulary for recording the circumference units for units of distortion.",
"homepage": "http://uri.gbv.de/terminology/fso_extent_unit_item/",
"name": "FSO: Unit of extent (item)",
"prefix": "20362"
},
"20363": {
"description": "FSO vocabulary for recording the format of reproduction forms in units of distortion.",
"homepage": "http://uri.gbv.de/terminology/fso_format/",
"name": "FSO: Format",
"prefix": "20363"
},
"20364": {
"description": "FSO vocabulary for keywords.",
"homepage": "http://uri.gbv.de/terminology/fso_keyword/",
"name": "FSO: Keyword",
"prefix": "20364"
},
"20365": {
"description": "FSO vocabulary for keywords related to persons or entities.",
"homepage": "http://uri.gbv.de/terminology/fso_keyword_person/",
"name": "FSO: Keyword (person)",
"prefix": "20365"
},
"20366": {
"description": "FSO vocabulary for keywords related to places.",
"homepage": "http://uri.gbv.de/terminology/fso_keyword_place/",
"name": "FSO: Keyword (place)",
"prefix": "20366"
},
"20367": {
"description": "FSO vocabulary for recording the types of material occurring in units of distortion.",
"homepage": "http://uri.gbv.de/terminology/fso_material/",
"name": "FSO: Material",
"prefix": "20367"
},
"20368": {
"description": "FSO vocabulary for recording the role of a name variation of persons and entities in the context of a unit of record.",
"homepage": "http://uri.gbv.de/terminology/fso_name_role/",
"name": "FSO: Name role",
"prefix": "20368"
},
"20369": {
"description": "FSO vocabulary for recording the object type.",
"homepage": "http://uri.gbv.de/terminology/fso_object_type/",
"name": "FSO: Object type",
"prefix": "20369"
},
"2037": {
"abbreviation": "EAD",
"description": "EAD stands for Encoded Archival Description, and is a non-proprietary de facto standard for the encoding of finding aids for use in a networked (online) environment. Finding aids are inventories, indexes, or guides that are created by archival and manuscript repositories to provide information about specific collections. While the finding aids may vary somewhat in style, their common purpose is to provide detailed description of the content and intellectual organization of collections of archival materials. EAD allows the standardization of collection information in finding aids within and across repositories.",
"homepage": "https://www.loc.gov/ead/",
"license": "CC-BY-3.0",
"name": "Encoded Archival Description",
"prefix": "2037",
"wikidata_database": "Q1340077"
},
"20370": {
"description": "FSO vocabulary for places.",
"homepage": "http://uri.gbv.de/terminology/fso_place/",
"name": "FSO: Place",
"prefix": "20370"
},
"20371": {
"description": "FSO vocabulary for recording the role of a place in the context of a unit of distortion.",
"homepage": "http://uri.gbv.de/terminology/fso_place_function/",
"name": "FSO: Place function",
"prefix": "20371"
},
"20372": {
"description": "FSO vocabulary for recording the role of a place name variant of persons and entities in the context of a unit of record.",
"homepage": "http://uri.gbv.de/terminology/fso_place_name_role/",
"name": "FSO: Place name role",
"prefix": "20372"
},
"20373": {
"description": "FSO vocabulary for recording the form of reproduction of units of distortion.",
"homepage": "http://uri.gbv.de/terminology/fso_reproduction_form/",
"prefix": "20373"
},
"20374": {
"description": "FSO vocabulary for recording the title role.",
"homepage": "http://uri.gbv.de/terminology/fso_title_type/",
"name": "FSO: Type of title",
"prefix": "20374"
},
"20375": {
"description": "A list of genders.",
"homepage": "http://uri.gbv.de/terminology/gender/",
"license": "CC0-1.0",
"name": "Gender",
"prefix": "20375"
},
"20376": {
"homepage": "http://uri.gbv.de/terminology/historic_flag/",
"name": "Historic Flag",
"prefix": "20376"
},
"20377": {
"homepage": "http://uri.gbv.de/terminology/ikmk_besitzer/",
"license": "CC BY-NC-SA 4.0",
"name": "Owners from IKMK",
"prefix": "20377"
},
"20378": {
"homepage": "http://uri.gbv.de/terminology/ikmk_herstellungstyp/",
"license": "CC BY-NC-SA 4.0",
"name": "Production type from IKMK",
"prefix": "20378"
},
"20379": {
"homepage": "http://uri.gbv.de/terminology/ikmk_land/",
"license": "CC BY-NC-SA 4.0",
"name": "Country from IKMK",
"prefix": "20379"
},
"2038": {
"description": "Consistent, harmonised and easily accessible terminology is an extremely important stronghold for ensuring true multilingualism in the European Union and throughout the world. From EU legislation and trade to the needs and mobility of every EU citizen, terminology is the key for easy, fast and reliable communications. However, new EU member countries face the issue of terminology resource fragmentation across different institutions, inconsistency and lack of coordination in terminology development, as well as structural and technical incompatibility.\n\nThe EuroTermBank project results in a centralized online terminology bank for languages of new EU member countries interlinked to other terminology banks and resources. Although EuroTermBank is addressed directly towards Estonia, Hungary, Latvia, Lithuania, and Poland, the project is open to other new EU member states and interested countries and organizations outside EU. It also enables exchange of terminology data with existing national and EU terminology databases by establishing cooperative relationships, aligning methodologies and standards, designing and implementing data exchange mechanisms and procedures.",
"homepage": "http://www.eurotermbank.com/",
"name": "EuroTermBank",
"prefix": "2038"
},
"20380": {
"homepage": "http://uri.gbv.de/terminology/ikmk_material/",
"license": "CC BY-NC-SA 4.0",
"name": "Material from IKMK",
"prefix": "20380"
},
"20381": {
"homepage": "http://uri.gbv.de/terminology/ikmk_muenzstand/",
"license": "CC BY-NC-SA 4.0",
"name": "Coin stand from IKMK",
"prefix": "20381"
},
"20382": {
"homepage": "http://uri.gbv.de/terminology/ikmk_nominal/",
"license": "CC BY-NC-SA 4.0",
"name": "Nominal from IKMK",
"prefix": "20382"
},
"20383": {
"homepage": "http://uri.gbv.de/terminology/ikmk_ort/",
"license": "CC BY-NC-SA 4.0",
"name": "Location from IKMK",
"prefix": "20383"
},
"20384": {
"homepage": "http://uri.gbv.de/terminology/ikmk_person_koerperschaft/",
"license": "CC BY-NC-SA 4.0",
"name": "Person / corporation from IKMK",
"prefix": "20384"
},
"20385": {
"homepage": "http://uri.gbv.de/terminology/ikmk_personentyp/",
"license": "CC BY-NC-SA 4.0",
"name": "Type of person from IKMK",
"prefix": "20385"
},
"20386": {
"homepage": "http://uri.gbv.de/terminology/ikmk_region/",
"license": "CC BY-NC-SA 4.0",
"name": "Region from IKMK",
"prefix": "20386"
},
"20387": {
"homepage": "http://uri.gbv.de/terminology/ikmk_sachbegriff/",
"license": "CC BY-NC-SA 4.0",
"name": "Subject terms from IKMK",
"prefix": "20387"
},
"20388": {
"homepage": "http://uri.gbv.de/terminology/ikmk_typenquelle/",
"license": "CC BY-NC-SA 4.0",
"name": "Type source from IKMK",
"prefix": "20388"
},
"20389": {
"homepage": "http://uri.gbv.de/terminology/ikmk_waehrung/",
"license": "CC BY-NC-SA 4.0",
"name": "Currency from IKMK",
"prefix": "20389"
},
"2039": {
"description": "At its grand opening, Rikstermbanken contained more than 50 000 term records, and it will continue to grow contentwise. Although it is a Swedish term bank, it does not only contain Swedish terms but also terms in other languages, e.g. English, French, German, and Finnish, to name a few. Terminologicentrum TNC (The Swedish Centre for Terminology) has designed the term bank and its software, and is also the responsible body for the term bank and its content. The Swedish Ministry of Industry, Employment and Communications has contributed financially to its realization. More than 70 organizations β mostly public bodies but also associations and private companies β have contributed as suppliers of terminology collections. The terminology in Rikstermbanken belongs to various domains β geology, economics, planning and construction, cleaning, and interior decoration. Most of TNCβs own glossaries are also included. Thus, Rikstermbanken hopefully represents the accurate and actual terminology usage of these various domains.",
"homepage": "http://www.rikstermbanken.se/",
"name": "SwedenΒ΄s national term bank",
"prefix": "2039",
"wikidata_database": "Q9310430"
},
"20390": {
"homepage": "http://uri.gbv.de/terminology/ikmk_zugangsart/",
"license": "CC BY-NC-SA 4.0",
"name": "Access type from IKMK",
"prefix": "20390"
},
"20391": {
"abbreviation": "EuroSciVoc",
"description": "EuroSciVoc is a multilingual taxonomy that represents all the main fields of science that were discovered from CORDIS content and organised through a semi-automatic process based on NLP techniques. It contains more than 1000 categories in 6 languages (English, French, German, Italian, Polish and Spanish) and each category is enriched with relevant keywords extracted from the textual description of CORDIS projects.\n\nEuroSciVoc is managed by the Publications Office of the EU, and is currently used by the CORDIS website. It is specifically developed as a reference vocabulary for the Open Science community and is aligned with Linked Open Data standards.",
"homepage": "https://op.europa.eu/web/eu-vocabularies/concept-scheme/-/resource?uri=http://data.europa.eu/8mn/euroscivoc/40c0f173-baa3-48a3-9fe6-d6e8fb366a00",
"name": "The European Science Vocabulary",
"pattern": "^[0-9a-f-]+$",
"prefix": "20391"
},
"20392": {
"abbreviation": "EURIO",
"description": "EURIO (EUropean Research Information Ontology) conceptualises, formally encodes and makes available in an open, structured and machine-readable format data about resarch projects funded by the EU's framework programmes for research and innovation.",
"homepage": "https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/eurio&version=1.0",
"name": "EUropean Research Information Ontology",
"prefix": "20392"
},
"20393": {
"abbreviation": "BLL",
"description": "The Bibliography of Linguistic Literature (BLL) is one of the most comprehensive linguistic bibliographies worldwide. It covers general linguistics with all its neighbouring disciplines and subdomains as well as English, German and Romance linguistics. The BLL dates back as far as 1971 and lists circa 500,000 bibliographic references. Furthermore, the BLL provides a hierarchically categorised thesaurus of domain-specific index terms in German and English. The BLL Thesaurus comprises more than 9,000 subject terms.",
"homepage": "https://data.linguistik.de/bll/index.html",
"license": "CC-BY-4.0",
"name": "BLL-Thesaurus",
"prefix": "20393"
},
"20394": {
"abbreviation": "EuroSciVoc",
"description": "European Science Vocabulary (EuroSciVoc) is the taxonomy of fields of science based on OECD's 2015 Frascati Manual taxonomy. It was extended with fields of science categories extracted from CORDIS content through a semi-automatic process developed with Natural Language Processing (NLP) techniques.",
"homepage": "https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/euroscivoc",
"name": "European Science Vocabulary",
"prefix": "20394"
},
"20395": {
"abbreviation": "EURIO",
"description": "EURIO (EUropean Research Information Ontology) conceptualises, formally encodes and makes available in an open, structured and machine-readable format data about resarch projects funded by the EU's framework programmes for research and innovation.",
"homepage": "https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/eurio",
"prefix": "20395"
},
"20396": {
"abbreviation": "MSC2020",
"description": "Mathematical Reviews (MR) and zbMATH collaborate on maintaining the Mathematics Subject Classification, which is used by these reviewing services, publishers, funding agencies, and others to categorize items in the mathematical sciences literature. It is a taxonomy created by and for mathematical researchers. Every ten years, the two editorial groups solicit input from the mathematics community. For the current revision, we received over 350 comments and suggestions from more than 100 different people. MR and zbMATH carefully considered this input from the community, and used it in the preparation of our joint revision of the classification.",
"homepage": "https://msc2020.org/",
"license": "CC BY-NC-SA 4.0",
"name": "Mathematics Subject Classification System",
"pattern": "^[0-9]{2}(-XX|-[0-9]{2}|[A-Z](xx|[0-9]{2}))$",
"prefix": "20396"
},
"20397": {
"description": "This classification scheme was used to classifie the collection of the GΓΆttingen State and University Library till 1945. It has its origin in the 18th century.",
"homepage": "https://www.univerlag.uni-goettingen.de/handle/3/GBS3?locale-attribute=en",
"license": "CC BY-ND 3.0",
"name": "Classification of the classified book catalogue of the GΓΆttingen State and University Library",
"prefix": "20397"
},
"20398": {
"license": "http://rightsstatements.org/vocab/InC/1.0",
"prefix": "20398"
},
"204": {
"description": "The thesaurus used for the database CINAHL is probably the most advanced in the field of nursing sciences, but it is not a comprehensive thesaurus in English. The Thesaurus developed for the database WISE is based on a keyword collection, which was built between 2001 and 2009. The terms in this collection were not systematized, and as part of the development of the database, the intention was to begin with a systematization of these terms, which is divided into two levels. On the lower level, subjects differentiate these topics. Keywords can be assigned to several categories. The search in the database WISE can thus be concentrated on specific topics, since the assignment of individual keywords becomes clear.",
"homepage": "http://www.dip.de/datenbank-wise/informationen-zu-wise/thesaurus/",
"name": "Database for scientific papers in nursing Thesaurus",
"prefix": "204"
},
"2040": {
"description": "The Melvil Decimal System (MDS) is based on the 1922 public domain edition of Dewey Decimal System with class labels adjusted to modern language.",
"homepage": "http://blog.librarything.com/main/2010/08/introducing-the-melvil-decimal-system/",
"license": "CC0-1.0",
"name": "Melvil Decimal System",
"prefix": "2040",
"wikidata_database": "Q25373158"
},
"20400": {
"abbreviation": "BC",
"description": "This classification scheme structures a collection of cartographic contents. The database consists of 62.000 titles.",
"homepage": "https://bc.staatsbibliothek-berlin.de/DB=1.67/",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Classification scheme of the Bibliographia Cartographia",
"pattern": "^[A-Z]([.](.+)?)?$",
"prefix": "20400"
},
"20402": {
"abbreviation": "m4i",
"description": "The ontology Metadata4Ing is developed within the NFDI Consortium NFDI4Ing with the aim of providing a thorough framework for the semantic description of research data, with a particular focus on engineering sciences and neighbouring disciplines. This ontology allows a description of the whole data generation process (experiment, observation, simulation), embracing the object of investigation, all sample and data manipulation procedures, a summary of the data files and the informaton contained, and all personal and institutional roles. The subordinate classes and relations can be built according to the two principles of inheritance and modularity. \"Inheritance\" means that a subclass inherits all properties of its superordinate class, possibly adding some new ones. Modularity means that all expansions are independent of each other; this makes possible for instance to generate expanded ontologies for any possible combinations of method Γ object of research.\"",
"homepage": "https://w3id.org/nfdi4ing/metadata4ing",
"license": "CC-BY-4.0",
"name": "Metadata4Ing",
"prefix": "20402"
},
"20403": {
"abbreviation": "ARM",
"description": "The ontology housed in this repository is being developed as an extension of the BIBFRAME ontology for generalized bibliographic description to provide specialized modeling in the archives, art and rare materials domains.",
"homepage": "https://art-and-rare-materials-bf-ext.github.io/arm/v1.0/",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Art and Rare Materials (ARM) BIBFRAME Ontology Extensions",
"prefix": "20403"
},
"20404": {
"abbreviation": "retrohab",
"description": "In the 1980s, the Duke August Library made an attempt to retrospectively classify its old holdings. This was based on the system designed by Otto Hartwig (1830-1902) for the library of the University of Halle, but adapted to the WolfenbΓΌttel collection profile. The classification was carried out for medicine and natural sciences, partly also for theology and law. A card catalogue was created, which was converted into electronic form in the course of the catalogue enrichment.",
"homepage": "http://dev.hab.de/signaturen/public/skos.php?notation=MN",
"license": "CC0-1.0",
"name": "Retrospective classification of medical, scientific, legal and theological prints",
"pattern": "^[A-Z]+( [A-Z][a-z]*)*(.[0-9]+)*$",
"prefix": "20404"
},
"20405": {
"abbreviation": "gessner",
"description": "In the mid-16th century, the learned physician Conrad Gessner (1516-1565) published his βBibliotheca Universalisβ, a comprehensive bibliography that claimed to list all books printed in Latin, Greek and Hebrew in alphabetical order. In a second part, the βPandectaeβ, published from 1548 onwards, he also developed a universal system of knowledge. He compiled numerous loci communes for all 21 main groups and grouped them into superordinate tituli. No tituli and loci communes are available for the field of medicine, as this was not published due to economic reasons. The 21 main groups were used by several early modern libraries to organise their collections.",
"license": "CC0-1.0",
"name": "21 Books of Universal Knowledge or Universal Partitioning",
"pattern": "^[A-Z][a-z]*([0-9]*.*)*$",
"prefix": "20405"
},
"20406": {
"abbreviation": "brunfels",
"description": "In 1532, a student of the learned physician and theologian Otto Brunfels (1488-1534) published an extensive and widely recognised loci communes collection on the field of medicine, which he had compiled on the basis of Brunfels' lessons. The most important statements, especially those of the traditional authorities, are compiled in 106 chapters. The small-scale structure allows precise access to special contemporary medical topics.",
"license": "CC0-1.0",
"name": "Theses or loci communes of the whole medical field",
"pattern": "^[A-Z][a-z]*([0-9]*.*)*$",
"prefix": "20406"
},
"20407": {
"abbreviation": "thuana",
"description": "The catalogue of the Bibliotheca Thuana was first published in 1679 in two parts. It is based on the influential classification system of the Paris libraries and is designed to be universal in accordance with Jacques Auguste de Thouβs book collection. Contemporarily, the catalogue was widely recognised, especially because of its strong subdivision. In the detail of its classification, it anticipates the professionalised, deep classifications of the 19th century.",
"license": "CC0-1.0",
"name": "Catalogue of the Thuana Library",
"pattern": "^[A-Z][a-z]*([0-9]*.*)*$",
"prefix": "20407"
},
"20408": {
"abbreviation": "TID",
"name": "Terminology of documentation",
"prefix": "20408"
},
"20409": {
"abbreviation": "FMT",
"description": "FrauenMediaThesaurus is used by Feminist Archive and Library FrauenMediaTurm",
"homepage": "https://frauenmediaturm.de/feministisches-archiv/feministischer-thesaurus/",
"prefix": "20409"
},
"2041": {
"description": "The IFRS Taxonomyβ’ is the global standard issued by the IFRS Foundation to mark up electronic IFRS financial statements. By providing the IFRS Taxonomy, the IASB can ensure that the taxonomy used is an accurate representation of the International Financial Reporting Standards ('the Standards').\n\nA taxonomy is a classification system of some kind of knowledge or business domain. The content of the IFRS Taxonomy is designed to accurately reflect the presentation and disclosure requirements of the Standards as issued by the IASB. Its content also includes elements from the accompanying materials to the Standards (Implementation Guidance and Illustrative Examples) and elements for disclosures that are not required, but that are commonly reported in practice by entities (Common Practice).\n\nThe IFRS Taxonomy Updates occur throughout the year in line with the publication of new or amended Standards issued by the IASB. Updates may also be released as a result of common practice projects or technology updates. Each year an annual compilation of all Updates is produced (the Annual IFRS Taxonomy).\n\nThe IFRS Taxonomy is developed through a formal system of due process. This ensures transparency and compliance with best practice, and also provides quality assurance and opportunities to engage with stakeholders.",
"homepage": "http://www.ifrs.org/XBRL/IFRS-Taxonomy/Pages/IFRS-Taxonomy.aspx",
"prefix": "2041"
},
"20410": {
"abbreviation": "NFDICO",
"description": "The NFDICO core ontology describes all resouces (datasets, data providers, persons, projects and other entities) in the data domain of NFDI4Culture (see: https://nfdi4culture.de/resource/about.html). It serves as the basis for the NFDI4Culture Knowledge Graph (see: https://nfdi4culture.de/resources/knowledge-graph.html) and contains mappings to numerous external vocabularies and ontologies.",
"homepage": "https://nfdi4culture.de/ontology",
"name": "NFDI4Culture Ontology",
"prefix": "20410"
},
"20411": {
"description": "The iDAI.world Thesaurus brings together and harmonises all thesauri and vocabularies of the libraries and the projects of the German Archaeological Institute. It was developed between 2015 and 2019, since 2020 it is continuously updated and implemented. The core structure is based on the BBT.",
"homepage": "http://thesauri.dainst.org/de.html",
"license": "CC-BY-4.0",
"name": "iDAI.world Thesaurus",
"prefix": "20411"
},
"20412": {
"description": "The βVICAV Taxonomy of Arabic Dialectsβ provides a classification scheme for Arabic dialects used in the VICAV application and sources.",
"homepage": "https://vocabs.dariah.eu/vicav_dialects_taxonomy/",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "VICAV Taxonomy of Arabic Dialects",
"prefix": "20412"
},
"20413": {
"description": "Taxonomy within the project \"Intertextuality in the Legal Papers of Karl Kraus β A Scholarly Digital Edition\".",
"homepage": "https://vocabs.dariah.eu/legalkraus/en/",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"prefix": "20413"
},
"20414": {
"description": "The travel!digital Thesaurus is a knowledge organization system for the travel!digital Corpus, a unique collection of historical Baedeker travel guides published between 1875 and 1914. The digital full-texts and the thesaurus were created within the travel!digital project (Project-Nr.: ΓAW0204, 1.12.2014-30.11.2017) at the ACDH - Austrian Centre for Digital Humanities of the Austrian Academy of Sciences. Exclusively reflecting the vocabulary contained in the travel guides, the thesaurus uses spellings and translations from there. The primary language is German (4908 entries), followed by English (177), Arabic (81), French (52), Spanish (25) and other languages with less than 25 entries. The focus is on group designations (amongst others geographical oriented designations, ethnic/national, religious and social communities as well as professions) and selected sights.",
"homepage": "https://vocabs.dariah.eu/traveldigital_thesaurus/en/",
"license": "CC-BY-4.0",
"name": "travel!digital Thesaurus",
"prefix": "20414"
},
"20415": {
"description": "DEFC thesaurus is a knowledge organization system designed for Digitizing Early Farming Cultures project.",
"homepage": "https://vocabs.dariah.eu/defc_thesaurus/en/",
"license": "CC-BY-4.0",
"name": "DEFC Thesaurus",
"prefix": "20415"
},
"20416": {
"description": "The Iron-Age-Danube thesaurus is based on controlled vocabulary of Iron-Age-Danube database created in the frame of the Interreg Iron-Age-Danube project (www.iron-age-danube.eu). The purpose of the database is to gain an overview of archaeology of Iron Age sites, their touristic potential, and cultural protection status. The database is limited to the sites located in the Danube region including Austria, Hungary, Croatia, and Slovenia.\nTo avoid misconceptions and ambiguities resulting from the use of different translations for the same concept throughout the literature, the Iron-Age-Danube thesaurus offers a unified terminology and translations of its concepts to German, Hungarian, Croatian, and Slovenian language. In addition, a special attention was given to the possibility of linked data and reuse of existing standards, therefore many concepts in Iron-Age-Danube thesaurus are linked to existing vocabularies of Forum on Information Standards in Heritage (FISH) and Ontology Lookup Service (OLS).",
"homepage": "https://vocabs.dariah.eu/iad_thesaurus/en/",
"license": "CC-BY-4.0",
"name": "Iron-Age-Danube thesaurus",
"prefix": "20416"
},
"20417": {
"description": "A list of licenses that can be used for acdh:hasLicense in ARCHE.",
"homepage": "https://vocabs.dariah.eu/arche_licenses/en/",
"license": "CC-BY-4.0",
"name": "ARCHE Licenses",
"prefix": "20417"
},
"20418": {
"description": "A list of sets for the OAI-PMH protocol for ARCHE. They are used to denote which object is going to be delivered to which aggregator.",
"homepage": "https://vocabs.dariah.eu/arche_oaiphmsets/en/",
"license": "CC-BY-4.0",
"name": "ARCHE OAI Sets",
"prefix": "20418"
},
"20419": {
"description": "The sheer number of metadata standards in the cultural heritage sector is overwhelming, and their inter-relationships further complicate the situation. This visual map of the metadata landscape is intended to assist planners with the selection and implementation of metadata standards.\n\nEach of the 105 standards listed here is evaluated on its strength of application to defined categories in each of four axes: community, domain, function, and purpose. The strength of a standard in a given category is determined by a mixture of its adoption in that category, its design intent, and its overall appropriateness for use in that category.\n\nThe standards represented here are among those most heavily used or publicized in the cultural heritage community, though certainly not all standards that might be relevant are included. A small set of the metadata standards plotted on the main visualization also appear as highlights above the graphic. These represent the most commonly known or discussed standards for cultural heritage metadata.",
"homepage": "http://jennriley.com/metadatamap/seeingstandards_glossary_pamphlet.pdf",
"license": "CC BY-NC 3.0",
"name": "Glossary of metadata standards",
"prefix": "20419"
},
"20420": {
"description": "The Elective Studies category scheme provides the ability to categorize elective studies at the variable level.",
"homepage": "https://lod.gesis.org/KategorienschemaWahlstudien/",
"name": "Elective Studies category scheme",
"prefix": "20420"
},
"20421": {
"description": "The classification of the State Library of Schleswig-Holstein is used to classify the holdings of this library.",
"homepage": "https://katalog.ub.uni-kiel.de/LNG=DU/DB=3/",
"prefix": "20421"
},
"20422": {
"description": "A taxonomy to the dataset of OpenAIRE.",
"homepage": "https://explore.openaire.eu/fields-of-science",
"license": "CC-BY-4.0",
"name": "Fields of Science",
"prefix": "20422"
},
"20423": {
"abbreviation": "WHG",
"description": "World Historical Gazetteer (WHG) is providing a collection of content and services that permit world historians, their students, and the general public to do spatial and temporal reasoning and visualization in a data rich environment at global and trans-regional scales.",
"homepage": "https://whgazetteer.org/",
"name": "World Historical Gazetteer",
"prefix": "20423"
},
"20424": {
"description": "ARCHIDICT is an illustrative multilingual dictionary for architects, builders, construction workers, designers, architectural technologists and all those interested in architecture and design. An innovative tool, vital not only for mastering terms in a foreign language, but also for understanding and learning the technology and the profession itself, all with the aid of illustrated graphics. Unique and unified design of technical illustrations provides a clear understanding of the interweaving terminology and the subjects discussed. This allows the drawings to act as the principle medium in explaining building techniques using the correct associated vocabulary.",
"homepage": "https://archidict.com/el/",
"name": "Illustrative Multilingual Dictionary for Architects, Builders and Construction Workers",
"prefix": "20424"
},
"20425": {
"abbreviation": "T-PRO",
"description": "The thesaurus of provenance terms is used in German libraries to describe the provenance of (rare) books.",
"homepage": "https://provenienz.gbv.de/T-PRO_Thesaurus_der_Provenienzbegriffe",
"name": "Thesaurus of provenance terms",
"pattern": "^[0-9a-f-]+$",
"prefix": "20425"
},
"20426": {
"abbreviation": "KSDF",
"homepage": "https://www.kerndatensatz-forschung.de/",
"prefix": "20426"
},
"20427": {
"homepage": "https://edoc.hu-berlin.de/handle/18452/24965",
"prefix": "20427"
},
"20428": {
"abbreviation": "semapv",
"description": "The Semantic Mapping Vocabulary provides and defines terms used for creating and maintaining semantic mappings, in particular mapping metadata.",
"homepage": "https://mapping-commons.github.io/semantic-mapping-vocabulary/",
"license": "CC0-1.0",
"name": "Semantic Mapping Vocabulary",
"prefix": "20428"
},
"20429": {
"abbreviation": "MMV",
"description": "Vocabulary for tagging mismatches in mappings between knowledge organization systems or semantic artifacts.",
"homepage": "https://github.com/gbv/jskos-data/tree/master/mismatch",
"license": "CC_MARK",
"name": "Mapping Mismatch Vocabulary",
"prefix": "20429"
},
"20430": {
"abbreviation": "OBV",
"description": "The OBV classes are used in the Austrian Library Network (OBV) as broad classification.",
"name": "OBV classes",
"pattern": "^[0-9][0-9]$",
"prefix": "20430"
},
"20431": {
"description": "Pleiades gives scholars, students, and enthusiasts worldwide the ability to use, create, and share historical geographic information about the ancient world in digital form. At present, Pleiades has extensive coverage for the Greek and Roman world, and is expanding into Ancient Near Eastern, Byzantine, Celtic, and Early Medieval geography",
"homepage": "https://pleiades.stoa.org/home",
"license": "CC-BY-3.0",
"name": "Pleiades",
"prefix": "20431",
"wikidata_database": "Q24423804"
},
"20432": {
"name": "Biblissima iconography thesaurus",
"pattern": "^Q[1-9]+[0-9]*$",
"prefix": "20432"
},
"20433": {
"description": "Controlled vocabulary of types of functional texts by Eckard Rolf (1993) in its online version by FactGrid (2023)",
"homepage": "https://blog.factgrid.de/archives/3061",
"license": "CC0-1.0",
"name": "Types of functional texts",
"prefix": "20433"
},
"20434": {
"abbreviation": "arXiv",
"description": "Subject categories of arXiv.org repository.",
"homepage": "https://arxiv.org/category_taxonomy",
"name": "arXiv categories",
"prefix": "20434"
},
"20435": {
"abbreviation": "GOV",
"description": "gazetteer used in German genealogy",
"homepage": "http://www.gov.genealogy.net/",
"prefix": "20435"
},
"20436": {
"abbreviation": "lemon",
"description": "The aim of the lexicon model for ontologies (lemon) is to provide rich linguistic grounding for ontologies. Rich linguistic grounding includes the representation of morphological and syntactic properties of lexical entries as well as the syntax-semantics interface, i.e. the meaning of these lexical entries with respect to an ontology or vocabulary.\n\nLemon consists of a core model (ontolex) and modules for syntax and semantics (synsem), decomposition (decomp), variation and translation (vartrans), and linguistic metadata (lime).",
"homepage": "https://www.w3.org/2016/05/ontolex/",
"license": "CC0-1.0",
"name": "Lexicon Model for Ontologies",
"prefix": "20436"
},
"20437": {
"abbreviation": "OhdAB",
"homepage": "https://www.geschichte.uni-halle.de/struktur/hist-data/ontologie/",
"prefix": "20437"
},
"20438": {
"description": "The aim of this work is the creation of a \"Thesaurus of Geology\" exclusively nourished with terms from the ICYT database of the CSIC. This vocabulary comes from the scientific geological literature in Spanish and obviously does not cover all aspects of geology, which entails important limitations when it comes to prioritising terms and presenting a complete and uniform thesaurus. The purpose of this Thesaurus is to structure the terminology used in the discipline of geology to be used in the ICYT Database as a vocabulary control tool, the dissemination and use of which will help to carry out bibliographic searches and improve the indexing of documents. It is presented in three languages: English, French and Spanish.",
"homepage": "http://libros.csic.es/download.php?id=305&pdf=products_pdfcomple&PHPSESSID=8830d9fb7082e1586a16f6872c49862b",
"license": "CC-BY-3.0",
"name": "Geology thesaurus",
"prefix": "20438"
},
"20439": {
"description": "Concise dictionary of mathematics and statistics with encyclopedic supplements, intended to be useful in helping to write and understand mathematics and also including biographies of the most important mathematicians in history.",
"homepage": "https://cit.iec.cat/DME",
"license": "CC-BY-3.0",
"name": "Dictionary of mathematics and statistics",
"prefix": "20439"
},
"20440": {
"description": "Thesaurus about silk developed by SILKNOW, \"a research project that improves the understanding, conservation and dissemination of European silk heritage from the 15th to the 19th century\".",
"homepage": "https://skosmos.silknow.org/thesaurus/",
"license": "CC-BY-3.0",
"name": "Silk heritage thesaurus",
"prefix": "20440"
},
"20441": {
"description": "The purpose of the \"Multilingual archival terminology\" is to support archivists, records managers and information managers in the use of records-related terms, from the traditional ones to those related to the preservation of authentic records in digital systems. Founded on archival, diplomatic and records and information knowledge, the 320 initial terms express concepts that are central to both the ICA [International Council on Archives] (many of the terms chosen appear in existing ICA dictionaries), and the InterPARES project.",
"homepage": "http://www.ciscra.org/mat/",
"name": "Multilingual archival terminology",
"prefix": "20441"
},
"20442": {
"description": "The terminology was drawn from a number of subfields, including e-transactions, marketing, security, cryptography, communications, customer and business products and services, consumer protection, as well as information technologies.",
"homepage": "https://publications.gc.ca/site/archivee-archived.html?url=https://publications.gc.ca/collections/collection_2007/pwgsc-tpsgc/S53-35-2004.pdf",
"name": "Panlatin electronic commerce glossary",
"prefix": "20442"
},
"20443": {
"description": "This glossary aims to facilitate communication between the agents of the wood sector in the various territories on both sides of the Pyrenees.",
"homepage": "https://www.coopwoodplus.eu/dictionnaires/",
"license": "CC-BY-4.0",
"name": "Wood glossary",
"prefix": "20443"
},
"20444": {
"abbreviation": "CM",
"description": "Types of controlled methods in psychological studies as used in PubPsych bibliographical database",
"homepage": "https://psyndex.de/ueber/inhalte-aufbau/schlagwoerter-klassifikationen/",
"name": "Controlled Method",
"pattern": "^[0-9]+$",
"prefix": "20444"
},
"20445": {
"description": "Glossary of academic terms, especially from Psychology with easy to understand explanation",
"homepage": "https://w3id.org/zpid/vocabs/klarsaurus/",
"prefix": "20445"
},
"20446": {
"abbreviation": "fivs",
"description": "Topic classification of the German Information Network for International Relations and Area Studies (FIV). There is also a regional classification and the European Thesaurus.",
"name": "FIV General Classification",
"pattern": "^S[A-Z]([0-9][0-9](\\.[0-9][0-9])?)?$",
"prefix": "20446"
},
"20447": {
"abbreviation": "fivr",
"description": "Regional classification (countries and areas) of the German Information Network for International Relations and Area Studies (FIV). There is also a general subject classification and the European Thesaurus.",
"pattern": "^R[A-Z]([0-9][0-9](\\.[0-9][0-9])?)?$",
"prefix": "20447"
},
"20448": {
"abbreviation": "cit",
"homepage": "https://chineseiconography.org/terms/",
"license": "CC-BY-4.0",
"name": "Chinese Iconography Thesaurus",
"pattern": "^CIT[0-9]+$",
"prefix": "20448"
},
"20449": {
"abbreviation": "ABNE",
"description": "Subject indexing file of the National Library of Spain.",
"homepage": "http://catalogo.bne.es/uhtbin/authoritybrowse.cgi",
"prefix": "20449"
},
"20450": {
"abbreviation": "EMBNE",
"description": "Part of the Autoridades de la Biblioteca Nacional de EspaΓ±a.",
"prefix": "20450"
},
"20451": {
"abbreviation": "UCD",
"description": "Categorization of measures used in Astronomy",
"homepage": "https://vizier.cds.unistra.fr/doc/UCD/inVizieR.htx",
"name": "Uniform Content Descriptors",
"prefix": "20451"
},
"20452": {
"abbreviation": "KldB",
"description": "The German classification of occupations was last revised in 2020. In large parts compatible with the International Standard Classification of Occupations (ISCO).",
"homepage": "https://statistik.arbeitsagentur.de/DE/Navigation/Grundlagen/Klassifikationen/Klassifikation-der-Berufe/Klassifikation-der-Berufe-Nav.html",
"name": "German classification of occupations",
"prefix": "20452",
"wikidata_database": "Q1744612"
},
"20453": {
"prefix": "20453"
},
"20454": {
"abbreviation": "DHB",
"description": "The Classification of the Bibliography of German History (DHB-Systematik) is a faceted classification scheme partially following the Dewey Decimal Classification (DDC). It enables the single or multiple labelling of titles in three facets: region, subject and epoch. The DHB-Systematik employs short mnemonics instead of the numeric DDC-scheme. Example: the classification βG:de S:ge Z:40β translates to: region = Germany, subject = history, epoch = 19th century.",
"homepage": "https://www.historicum.net/metaopac/start.do?View=dhb",
"name": "Classification of the Bibliography of German History",
"pattern": "^[A-Z]:?(.+)?$",
"prefix": "20454"
},
"20455": {
"homepage": "https://aibook.gr/glossary-en/",
"name": "Artificial intelligence glossary",
"prefix": "20455"
},
"20456": {
"homepage": "https://aibook.gr/glossary-en/",
"name": "Artificial intelligence glossary",
"prefix": "20456"
},
"20457": {
"homepage": "https://rm.coe.int/16806f7d5b",
"name": "Spatial development glossary",
"prefix": "20457"
},
"20458": {
"description": "This European Position Paper on the Anatomical Terminology of the Internal Nose and Paranasal Sinuses was conceived to re-evaluate the anatomical terms in common usage by endoscopic sinus surgeons and to compare this with the official Terminologica Anatomica. The text is a concise summary of all the structures encountered during routine endoscopic surgery in the nasal cavity, paranasal sinuses and at the interface with the orbit and skull base but does not provide a comprehensive text for advanced skull base surgery. It draws on a detailed review of the literature and provides a consensus where several options are available, defining the anatomical structure in simple terms and in English. It is recognised that this is an area of great variation and some indication of the frequency with which these variants are encountered is given in the text and table. All major anatomical points are illustrated, drawing on the expertise of the multi-national and multi-disciplinary contributors to this project.",
"homepage": "https://www.researchgate.net/publication/320056097_E_Ellenike_antistoichia_sten_EUROPAIKE_THESE_GIA_TEN_ANATOMIKE_OROLOGIA_ANGLIKE_TOU_ESOTERIKOU_TES_RINOS_KAI_PARARRINIKON_KOLPON",
"name": "European Position Paper on the Anatomical Terminology of the Internal Nose and Paranasal Sinuses",
"prefix": "20458"
},
"20459": {
"description": "It's recommended to use Geonames, Wikidata or the GND (entity Geographika).",
"homepage": "https://museumsvokabular.de/node/6",
"license": "CC-BY-3.0",
"name": "Geography file",
"prefix": "20459"
},
"20460": {
"abbreviation": "UNECE Rec 20",
"description": "Recommendation 20 Provides three character alphabetic and alphanumeric codes for representing units of measurement for length, area, volume/capacity, mass (weight), time, and other quantities used in international trade. The codes are intended for use in manual and/or automated systems for the exchange of information between participants in international trade.",
"homepage": "https://service.unece.org/trade/uncefact/vocabulary/rec20/",
"license": "CC_MARK",
"name": "Codes for Units Of Measure Used in International Trade",
"prefix": "20460"
},
"20461": {
"abbreviation": "CCO",
"description": "A manual to help you describe, document, and catalog cultural artifacts (like art and architecture) and visual media that represent them.",
"homepage": "https://www.vraweb.org/cco",
"license": "CC BY-NC-SA 3.0",
"name": "Cataloging Cultural Objects",
"prefix": "20461"
},
"20462": {
"description": "The thesaurus contains data about technical terms and classes from the Thesaurus of the Vienna Museum of Science and Technology.",
"homepage": "https://data.tmw.at/thesaurus",
"name": "Thesaurus of the Vienna Museum of Science and Technology",
"prefix": "20462"
},
"20463": {
"description": "For the indexing of information from the historical record and for the quantitatively evaluable description of the characteristics of building components, an extensive digital vocabulary was developed in the project \"Die NΓΌrnberger GroΓkirchen β Best Practice fΓΌr die digitale Erfassung komplexer Baudenkmale\", which contains several thousand terms for the designation of building components, materials, damage, traces of processing and static interactions.\n\nIt is available in SKOS format and contains definitions, alternative terms and foreign-language translations for each term. The individual terms are thematically related to each other within an ontology and linked to external standard data such as the GND or the Getty AAT.",
"homepage": "https://hist-arch-vocab.org/",
"name": "Bamberg vocabulary for historical architecture",
"prefix": "20463"
},
"20464": {
"abbreviation": "ISNI",
"description": "ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. As ISO 27729, it is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, and ISWC.\n\nThe mission of the ISNI International Agency (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described.\n\nBy achieving these goals, the ISNI will act as a bridge identifier across multiple domains and become a critical component in Linked Data and Semantic Web applications.",
"homepage": "https://isni.org/",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "International Standard Name Identifier",
"prefix": "20464"
},
"20465": {
"description": "Source: This list was derived from a controlled list of coded values in the MARC 21 Format for Bibliographic Data from field 048 (Number of Musical Instruments or Voices Codes).",
"homepage": "https://www.loc.gov/standards/valuelist/marcmusperf.html",
"license": "CC-BY-4.0",
"name": "MARC Instruments and Voices Code List",
"prefix": "20465"
},
"20466": {
"abbreviation": "MOP",
"description": "Instruments and/or voices, devices and other performers which make up a musical work.",
"homepage": "https://www.iflastandards.info/unimarc/terms/mop",
"license": "CC-BY-4.0",
"name": "UNIMARC: Medium of performance",
"prefix": "20466"
},
"20467": {
"description": "Thesaurus for the identification and description of scenes and figures of the\nChristian iconography; connections with the iconographic class ifications\nIconClass and RΓ©au.\nSpecific for art and art history area.\nManaged by the Ministry of Culture and Communication (MCC/DAPA)\nUsed as an internal index and information retrieval tool for the national\nheritage databases (MΓ©moire, MΓ©rimΓ©e, P alissy)",
"homepage": "http://www2.culture.gouv.fr/culture/inventai/extranet/sysdesc.htm",
"name": "Thesaurus for Illustrations",
"prefix": "20467"
},
"20468": {
"description": "The Dating Systematics of the BSZ contains, for a large part, time definitions, sources and definitions of the term, the archaeological and historical periods of the respective period.\"",
"homepage": "https://wiki.bsz-bw.de/display/MUSIS/BSZ-Thesauri",
"license": "CC BY-NC-ND 3.0",
"name": "BSZ periods AD",
"prefix": "20468"
},
"20469": {
"description": "Maritime thesaurus based on the NAVIS I-III databases.",
"homepage": "https://archaeology.link/",
"name": "Navis.one Maritime Thesaurus",
"prefix": "20469"
},
"20470": {
"abbreviation": "LADO",
"description": "A linked ontology for archaeological data.",
"homepage": "https://archaeology.link/",
"license": "CC-BY-4.0",
"name": "Linked Archaeological Data Ontology",
"prefix": "20470"
},
"20471": {
"description": "The MiMoText ontology is dedicated to the domain of literary history and historiography β a broad and far-reaching field of knowledge which we do not intend to address in its entirety. The scope and coverage of the ontology result from the practical requirements of the realization of our knowledge graph and the associated concerns. An essential particularity of our domain is that we model perspectives rather than facts. Therefore, the possibilities of the linked open data paradigm to let complementary and also contradictory statements coexist are very useful to us. This particularity has the consequence that 'reification' (i.e., statements about statements) is an important modeling dimension that includes, among other things, the unambiguous referencing of each statement, including linkage to the dataset to which it can be traced.",
"homepage": "https://mimotext.uni-trier.de/english/",
"license": "CC_MARK",
"name": "MiMoText Ontology",
"prefix": "20471"
},
"20472": {
"homepage": "https://www.boekman.nl/en/thesaurus/",
"name": "Cultural Policies Thesaurus",
"prefix": "20472"
},
"20473": {
"description": "iDAI.chronontology is a web service that combines concepts of time with dating. The ChronOntology project was funded by the German Research Foundation (DFG) from 2015 to 2018. The long-term availability of the data is guaranteed by the DAI as part of iDAI.welt.",
"homepage": "https://chronontology.dainst.org/",
"license": "CC-BY-4.0",
"name": "iDAI.chronontology",
"prefix": "20473"
},
"20474": {
"abbreviation": "ROR",
"description": "ROR is a global, community-led registry of open persistent identifiers for research organizations",
"homepage": "https://ror.org/",
"license": "CC-BY-4.0",
"name": "Research Organization Registry",
"prefix": "20474",
"wikidata_database": "Q110235640"
},
"20475": {
"abbreviation": "OFR",
"description": "It is good practice for authors to acknowledge support for and contributions to their research in their published articles. This support may be financial, such as a grant or salary award; or practical, such as the use or loan of specialist facilities and equipment. They do this by listing the funding agency and the grant number somewhere in their article - usually the first or last page, or in the acknowledgments or footnotes section. Members contribute by depositing the funding acknowledgements from their publications as part of their standard metadata, together with the unique funder IDs listed in the OFR. The deposit should include funder names, funder IDs, and associated grant numbers.\n\nThis means that anyone can make connections, for example, to identify which funders invest in certain fields of research. Funding data is also used by funders to track the publications that result from their grants.",
"homepage": "https://www.crossref.org/documentation/funder-registry/",
"license": "CC_MARK",
"name": "Open Funder Registry",
"prefix": "20475"
},
"20476": {
"description": "This GRAPHIS Image Region vocabulary contains all concepts GRAPHIS currently provides its users to annotate image regions. Image regions are shapes like rectangles, circles or any possible polygon that can be marked and saved within an image. The IPTC Photo Metadata Standard (https://iptc.org/standards/photo-metadata/iptc-standard) has enabled storing these image regions since its 2019.1 version (see https://iptc.org/std/photometadata/specification/IPTC-PhotoMetadata#image-region, https://www.iptc.org/std/photometadata/specification/IPTC-PhotoMetadata-2019.1.html).",
"homepage": "https://vocabs.dariah.eu/graphis_imgreg_browse/en/index",
"license": "CC_MARK",
"name": "GRAPHIS Image Region",
"prefix": "20476"
},
"20477": {
"description": "The INDIGO Graffiti Thesaurus is a curated academic resource centred on contemporary graffiti terminology, with a spatial focus on the Danube Canal in Vienna, Austria. It is not just a compilation of terms, but also a specialised tool that organises and categorises graffiti-related concepts within a controlled vocabulary. More specifically, it takes the form of a thesaurus, where concepts are connected to each other through equivalence, hierarchical, and associative relationships.\n\nBy leveraging the Simple Knowledge Organization System (SKOS) data model, the thesaurus ensures consistency and precision in its representation of information. The use of SKOS not only makes the thesaurus accessible but also interoperable, allowing for seamless integration with other widely used resources such as Wikidata and the Getty Art & Architecture Thesaurus (AAT) of the J. Paul Getty Trust and Getty Research Institute. The thesaurus is inspired by the AAT and therefore also contains information provided under the ODC Attribution License by the Getty Research Institute. Moreover, the content systematically reflects the structure of the AAT by using facets, hierarchy names, and guide terms.\n\nThe thesaurus is made available through the Vocabs service of the Austrian Centre for Digital Humanities and Cultural Heritage (ACDH-CH), which utilises Skosmos, an open-source software tailored for publishing vocabularies. For enhanced accessibility, the thesaurus can be queried via a REST API (Representational State Transfer Application Programming Interface), facilitating its interaction with data over the World Wide Web. Moreover, its availability in diverse data formats, including TSV (Tab-Separated Values) and JSON (JavaScript Object Notation), caters to a wide range of academic and technological preferences.\n\nWith its unique focus on the graffiti culture of the Danube Canal, the thesaurus offers a deep insight into Vienna's Danube Canal contemporary graffiti world and serves as a valuable tool for all those interested in this form of creativity.",
"homepage": "https://projectindigo.eu/",
"license": "http://www.opendatacommons.org/licenses/by/1.0",
"name": "INDIGO Graffiti Thesaurus",
"prefix": "20477"
},
"20478": {
"abbreviation": "ScAPA",
"description": "List of archaeological periods & ages for cultural heritage use in Scotland.",
"homepage": "https://www.heritagedata.org/blog/vocabularies-provided/",
"license": "CC-BY-3.0",
"name": "ScAPA : Scottish Archaeological Periods & Ages",
"prefix": "20478"
},
"20479": {
"description": "The type of ownership or legal status of property of an object in the collection, e.g. property, loan, or foreign property etc.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Status of property (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20479"
},
"20480": {
"description": "The owner of the collection in question.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Owner (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20480"
},
"20481": {
"description": "The weight of a (numismatic) object. This is usually given in grams (g), usually with one decimal place, more rarely with two decimal places.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Weight",
"pattern": "^{0-9}+$",
"prefix": "20481"
},
"20482": {
"description": "The technique of manufacture, e.g. struck or cast.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Manufacture (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20482"
},
"20483": {
"description": "A notable, characteristic or unusual physical feature of an individual numismatic object which distinguishes it from other examples of the same group, or of a group of numismatic objects that marks it out from other groups, and which is related to the process of production of a numismatic object.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Peculiarity of production (MK Berlin)",
"pattern": "^{0-9}+$",
"prefix": "20483"
},
"20484": {
"description": "A corporation, public or private, which is related to an object in the collection.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Corporation (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20484"
},
"20485": {
"description": "A modern state or country to which certain regions, places (as mints, places of issue for paper money), and find places are being assigned to.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Country (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20485"
},
"20486": {
"abbreviation": "mk-material",
"description": "The physical material from which an object is made.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Material (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20486"
},
"20487": {
"description": "The legal status of the person, ethnic, or institutional authority under which any numismatic object is issued. This term can be described more closely at a secondary level (Archbishopric - Archbishopric Cologne, Swiss Federation - Canton of GraubΓΌnden etc.).",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Class/status (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20487"
},
"20488": {
"description": "Term indicating the value of a coin or banknote within a certain denominational system.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Denomination (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20488"
},
"20489": {
"description": "Term to describe the physical status of an object, e.g. present, damaged, lost, stolen...",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Object status (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20489"
},
"20490": {
"description": "The location or place, in which a coin was minted, paper money issued or an object found.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Location (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20490"
},
"20491": {
"description": "A period in time and in the history of humans, also used here to categorizing certain periods in art history.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Period (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20491"
},
"20492": {
"description": "Any individual in his or her relationship or role to an object in question.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Person (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20492"
},
"20493": {
"description": "A region either historic or contemporary within a modern state.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Region (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20493"
},
"20494": {
"description": "The type of a numismatic object, e.g. coin, medal, token etc.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Item (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20494"
},
"20495": {
"description": "Any features which arise subsequent to the actual production of a numismatic object; for example halving, chop-marking, etc.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Secondary Treatment (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20495"
},
"20496": {
"description": "The relationship between the orientation of obverse and reverse of a (struck) coin or medal. Often expressed as hours of the clock (from 1 to 12 h) or degrees in a circle.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Die-axis (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20496"
},
"20497": {
"description": "Term to describe the role of an individual or corporation regarding a numismatic object, e.g. authority, sitter, previous owner etc.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Type for person and corporation (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20497"
},
"20498": {
"description": "A website, portal or digital resource which either represents a database to browse a certain collection or allows for a systematic presentation of types or concepts in relation to individual numismatic objects.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Type of Source (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20498"
},
"20499": {
"description": "A system of monetary units in common use, issued by a state, city, or any other legal authority, consisting of various subunits and multiples (denominations).",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Currency (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20499"
},
"205": {
"description": "Applied in the library database.",
"homepage": "http://ecf.base-alexandrie.fr/ListRecord.htm",
"name": "School of the Freudian Cause Thesaurus",
"prefix": "205"
},
"2050": {
"description": "In a PokΓ©mon's PokΓ©dex information, the category (...) (Japanese: ει‘ classification) is a name which identifies the PokΓ©mon based on one of its defining biological characteristics. Most often, the defining traits are part of the PokΓ©monβs physiology, special abilities, or behavior. It was previously also known as species. (...) Because of how brief and uninformative the description of a PokΓ©mon often is in its category, and how little the category relates to other data, it is not often regarded as an important piece of information about a PokΓ©mon. Before Generation III, the category was shown by just seeing the PokΓ©mon, rather than upon catching it. In PokΓ©mon games prior to Generation III, the character limit for a category name was ten characters. This has since increased from Generation III onwards, with the longest English category name being observed to be thirteen characters long. In other languages, the longest category name is Pachirisu's German category 'ElektrohΓΆrnchen' which is 15 characters long. This includes spaces but does not include 'PokΓ©mon'.",
"homepage": "http://bulbapedia.bulbagarden.net/wiki/Pok%C3%A9mon_category",
"license": "CC BY-NC-SA 3.0",
"name": "PokΓ©mon Category",
"prefix": "2050",
"wikidata_database": "Q25935882"
},
"20500": {
"description": "The type of accession of an object into the collection: e.g. purchased, donated etc.",
"homepage": "https://ikmk.smb.museum/ndp/home",
"license": "CC-BY-3.0",
"name": "Accession (MK Berlin)",
"pattern": "^[0-9]+$",
"prefix": "20500"
},
"20501": {
"description": "A vocabulary for all areas of catalysis initiated in NFDI4Cat. Starting with photocatalysis we add more and more terms from other areas of catalysis and related disciplines like chemical engineering or materials science.",
"homepage": "https://github.com/nfdi4cat/voc4cat",
"license": "CC_MARK",
"name": "voc4cat",
"prefix": "20501"
},
"20502": {
"description": "Thesaurus for the identification and description of elements of architecture.\nConnections with the terms used in the AAT and Royal Commission on the\nHistorical Monuments of England1.\nSpecific for art and art history area.\nManaged by the Ministry of Culture and Communication (MCC/DAPA)\nUsed as an internal index and information retrieval tool for the national\nheritage databases (MΓ©moire, MΓ©rimΓ©e, P alissy)",
"homepage": "http://www.culture.gouv.fr/culture/inventai/extranet/sysdesc.htm",
"name": "Architecture Thesaurus",
"prefix": "20502"
},
"20503": {
"abbreviation": "AKL",
"description": "The Allgemeines KΓΌnstlerlexikon (AKL) is a name authority file. Designed as International Database of Artists.",
"homepage": "https://www.degruyter.com/database/akl/html?lang=de",
"name": "Artists of the world",
"prefix": "20503"
},
"20504": {
"abbreviation": "MICHAEL",
"description": "Through the multilingual MICHAEL service you can find and explore digital collections from museums, archives, libraries and other cultural institutions from across Europe. Whether you are interested in art or archaeology, family history or planning holidays, the Romans or modern History, MICHAEL can show you what is available.",
"homepage": "http://www.michael-culture.org/",
"name": "Multilingual Inventory of Cultural Heritage in Europe",
"prefix": "20504"
},
"20505": {
"abbreviation": "RA",
"description": "The terminological tool presented here constitutes a reworking, edited by the ICCU and the VAST-LAB Laboratory within the framework of the EU project ARIADNE (Advanced Research Infrastructure for Archaeological Dataset Networking in Europe), of the standard thesaurus released by the ICCD for the definition of movable archaeological property, functional for the compilation of the RA - Archaeological Finds catalog card, for which please refer to the institutional page http://www.iccd.beniculturali.it/index.php?it/473/standard-catalografici/Standard/74.",
"homepage": "https://vast-lab.org/thesaurus/ra/vocab/",
"name": "Thesaurus Archaeological Finds",
"prefix": "20505"
},
"20506": {
"abbreviation": "DiGA Thesaurus",
"description": "The DiGA Thesaurus is a resource for the standard description of Gandharan Buddhist art. It draws upon the βRepertorio terminologico per la schedatura delle sculture dellβarte gandharicaβ published by Domenico Faccenna and Anna Filigenzi in 2007 (IsIAO, Rome). This printed resource has been revised, expanded and restructured to fit a digital use. It now covers the following categories: animals, architecture, ceremonial objects, decorative motifs, everyday objects, figures (general features), figures (protagonists), means of transports, musical instruments, narratives, the sculptor's work, vegetation, weapons. Concerning the new categories of βnarrativesβ and βfiguresβ, these are based on a variety of complementary sources.",
"homepage": "https://w3id.org/diga/terms",
"license": "CC_MARK",
"name": "The Digitization of Gandharan Artefacts Thesaurus",
"prefix": "20506"
},
"20507": {
"abbreviation": "DiGA Gazetteer",
"description": "The DiGA Gazetteer is a resource for the standard description of Gandharan Buddhist art.",
"homepage": "https://w3id.org/diga/gazetteer",
"license": "CC_MARK",
"name": "The Digitization of Gandharan Artefacts Gazetteer",
"prefix": "20507"
},
"20508": {
"description": "This concept scheme contains skos concepts for analysis methods used to produce observation results with information about the physical properties, chemical or isotopic composition, crystallography, or molecular structure of material samples. Based on spreadsheet compilation of method vocabularies from Geo.X, GEOROC, PetDB and OSIRIS-REx. Definitions added and updated based on web research, and SKOS serialization by S.M. Richard. Note that although there are high-level method categories for 'Physical property measurement', 'Geochronology technique', and 'Bioanalytical method', these are placeholders and only include a few examples that are relevant to analytical methods in geo- or cosmochemistry.",
"homepage": "https://vocabs.ardc.edu.au/viewById/650",
"license": "CC-BY-3.0",
"name": "Analytical methods for geochemistry and cosmochemistry",
"prefix": "20508"
},
"20509": {
"abbreviation": "CHMO",
"description": "CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI).",
"homepage": "https://github.com/rsc-ontologies/rsc-cmo",
"license": "CC-BY-4.0",
"name": "Chemical Methods Ontology",
"prefix": "20509"
},
"20510": {
"abbreviation": "SWEET",
"description": "The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research). Originally developed by NASA Jet Propulsion Labs under Rob Raskin, SWEET is now officially under the governance of the ESIP foundation.",
"homepage": "http://sweetontology.net/sweetAll",
"license": "CC_MARK",
"name": "Semantic Web for Earth and Environment Technology Ontology",
"prefix": "20510"
},
"20511": {
"abbreviation": "TEATER",
"description": "The Thesaurus of Archaeological Terminology is a web thesaurus aimed at making the terminology of archaeology and the related disciplines more available. TEATER is intended for a wide sphere of users ranging from the lay public to amateur archaeologists, beginning students of archaeology, librarians of not only archaeological institutions and professional archaeologists. The entries are available in an interactive interface that enables both full-text searching and hierarchical browsing. TEATERβs content is available in three language versions β Czech, English and German. Entries can be exported from TEATER in .json format or linked using their PURL. More information on the possibilities of use of the thesaurus by various groups of users, the search application, the structure and selection of the entries is available in the Help section.",
"homepage": "https://teater.aiscr.cz/",
"license": "CC BY-NC 4.0",
"name": "Thesaurus of Archaeological Terminology",
"pattern": "^[0-9]+$",
"prefix": "20511"
},
"20512": {
"abbreviation": "IAMO-BibSys",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"pattern": "^([A-Z] ([0-9]{1,2}(.[0-9](.[0-9]{1,2})?)?)?|.[0-9](.[0-9]{1,2})?|Anmerkung)$",
"prefix": "20512"
},
"20513": {
"abbreviation": "IAMO-Thes",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"prefix": "20513"
},
"20514": {
"description": "The SPDX License List is an integral part of the SPDX Specification. The SPDX License List itself is a list of commonly found licenses and exceptions used in free and open or collaborative software, data, hardware, or documentation. The SPDX License List includes a standardized short identifier, the full name, the license text, and a canonical permanent URL for each license and exception.\n\nThe purpose of the SPDX License List is to enable efficient and reliable identification of such licenses and exceptions in an SPDX document, in source files or elsewhere.",
"homepage": "https://spdx.org/licenses/",
"license": "CC0-1.0",
"name": "SPDX License List",
"pattern": "^.+$",
"prefix": "20514"
},
"20515": {
"description": "mimetype.io is an open-source Gatsby-based project that provides a comprehensive database and resources related to various MIME types.",
"homepage": "https://mimetype.io/all-types",
"license": "http://www.opendatacommons.org/licenses/by/1.0",
"name": "MIME types",
"prefix": "20515"
},
"20516": {
"description": "Persons and institutions of the german vocabulary of museum-digital.",
"homepage": "https://term.museum-digital.de/",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "md:term Persons and Institutions",
"prefix": "20516"
},
"20517": {
"description": "Geographic terms of the german vocabulary of museum-digital.",
"homepage": "https://term.museum-digital.de/",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "md:term places",
"prefix": "20517"
},
"20518": {
"description": "Terms concerning times of the german vocabulary of museum-digital.",
"homepage": "https://term.museum-digital.de/",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "md:term Times",
"prefix": "20518"
},
"20519": {
"description": "Tags of the german vocabulary of museum-digital.",
"homepage": "https://term.museum-digital.de/",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "md:term tags",
"prefix": "20519"
},
"2053": {
"abbreviation": "VIAF",
"description": "The Virtual International Authority File (VIAF) is an international service designed to provide convenient access to the world's major name authority files. Its creators envision the VIAF as a building block for the Semantic Web to enable switching of the displayed form of names for persons to the preferred language and script of the Web user. VIAF began as a joint project with the Library of Congress (LC), the Deutsche Nationalbibliothek (DNB), the Bibliothèque nationale de France (BNF) and OCLC. It has, over the past decade, become a cooperative effort involving an expanding number of other national libraries and other agencies. (...)\n\nVIAF helps to make library authority files less expensive to maintain and more generally useful to the library domain and beyond. To achieve this, VIAF matches and links the authority files of national libraries and groups all authority records for a given entity into a merged 'super' authority record that brings together the different names for that entity. By linking disparate names for the same person or organization, VIAF provides a convenient means for a wider community of libraries and other agencies to repurpose bibliographic data produced by libraries serving different language communities.",
"homepage": "http://viaf.org/",
"license": "http://www.opendatacommons.org/licenses/by/1.0",
"name": "Virtual International Authority File",
"pattern": "^[1-9]\\d(\\d{0,7}|\\d{17,20})]$",
"prefix": "2053",
"wikidata_database": "Q54919"
},
"2055": {
"description": "The following represents a linear or flat taxonomy of key Configuration Types or Categorizations that are used by Information Technology (IT) organizations and professionals to help define, structure, organize, and understand various forms of Data, Information, and Knowledge that are specifically associated with 'Configurations' and Configuration Management. Such information is often used as a foundation for work that needs to be performed as well as data modeling, especially in the design, definition, and implementation of other Taxonomies and Ontologies. Such constructs are also often used as mechanisms to provide clarity and standardize terminology for communications between business stakeholders and IT organizations.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/configuration_taxonomy.html",
"name": "Configuration Taxonomy",
"prefix": "2055"
},
"2056": {
"description": "The following represents a linear or flat taxonomy of the different Configuration Item types that are tracked and managed as part of the Configuration Management discipline and its related set of processes. Such Items may be composed of other smaller Configuration Items that they depend on and may also be used as dependencies for the construction of greater Items. In other words, some may be composed of pieces and/or act as pieces for others. Tracking of such dependencies is critical for most IT organizations and, as a result, some of the Configuration Items may be tracked in dedicated domain based systems and others may be tracked in formal Configuration Management Databases (CMDBs).",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/configuration_item_taxonomy.html",
"name": "Configuration Item Taxonomy",
"prefix": "2056"
},
"2057": {
"description": "The following represents a linear or flat taxonomy of the many different Configuration Management types that are tracked, managed and performed as part of the Configuration Management discipline and its related set of processes. These areas of Configuration Management concern themselves with their corresponding Configuration Types and, also, their correlating Configuration Item Types. While the Foundation acknowledges that each category has a different level of importance to different enterprises, the taxonomy serves to highlight just how many different areas of Configuration Management exist and that must be dealt with by many enterprises. Examples of how some of these types of Configuration Management categories fit into an enterprise can be seen in the IT Deployment Framework, which calls out the different, Deployment related Configuration Management Types.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/configuration_management_taxonomy.html",
"name": "Configuration Management Taxonomy",
"prefix": "2057"
},
"2058": {
"description": "The following represents a linear or flat taxonomy of key Data Entities that are used by Information Technology (IT) organizations and professionals to help define, structure, organize, and understand various forms of Data, Information, and Knowledge. Such information is often used as a foundation for data modeling, especially in the design, definition, and implementation of other Taxonomies and Ontologies. Such constructs are also often used as mechanisms to provide clarity and standardize terminology for communications between business stakeholders and IT organizations.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/data_entity_taxonomy.html",
"name": "Data Entity Taxonomy",
"prefix": "2058"
},
"2059": {
"description": "The following represents a linear or flat representation of the different enterprise Discipline related Document types or classifications. Such types are used by IT Professionals and the enterprises they provide services to as a means of identifying, defining, classifying, organizing, storing, and publishing different enterprise documents. This taxonomy is critical to multiple enterprise Disciplines such as Document Management, Artifact Management, and Records Management. Such taxonomies are commonly used in Document Management Systems as a means of tagging Documents as a means of assisting in organization and search.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/management_document_taxonomy.html",
"name": "Document Taxonomy",
"prefix": "2059"
},
"206": {
"description": "The conceptual list was prepared by deaf and hearing students of the Department of Psychology at the University of Hamburg, taking into account suggestions from deaf pedagogy as well as psychological and psychotherapeutic work with deaf people, including the introductory literature of the seven subject areas of general psychology, biopsychology, differential psychology , Developmental and pedagogic psychology, clinical psychology, cognitive psychology and social psychology, and was compared with already existing psychological specialties, with the aim of selecting a basic vocabulary for a psychological study at a predefined upper limit of about 1000 terms Of the employees from their studies were included in the selection.Systematic aspects could only be considered to a very limited extent Nter are references to the existing sign language variants for this entry. If you click on one of the reference pictures, the display will jump to the part of the lexicon entry belonging to this variant below. These include supplementary information on the lemma: common abbreviations (ABK), synonyms (AUCH), or, in the case of conceptual pairs, the connotation (eg 'Efference': 'AUCH: Gegenbegriff: Afferenz'). Below the definition text are listed the top terms to which the respective term can be assigned. The subject areas, with the exception of the applied psychology, are divided into a total of 37 terms. An upper term was recorded if at least 4 items could be assigned to it. The upper concepts were not further hierarchized among themselves, since this would have been possible only in very few cases. They also do not always agree with the terms of the technical terms, e.g. (Learning, observation, learning, distributed, etc.) are to be found under the heading 'learning and learning theories'. The lemmas, which could not be assigned to a specific concept within a discipline, are to be found under an umbrella term which is nominally identical to the subject area. The lexicon is primarily intended for deaf students and interpreters. However, it also offers valuable information and suggestions for all persons who use sign language in psychological contexts (psychologists, medical practitioners, educators, social workers / social workers and others).",
"homepage": "http://www.sign-lang.uni-hamburg.de/projekte/plex/plex/lemmata/indizes/deutscha.htm",
"name": "Professional sign language dictionary Psychology Alphabetical index",
"prefix": "206"
},
"2060": {
"description": "The following represents a linear or flat representation of the different File Plan Types or Categories that are used by Information Technology (IT) organizations, professionals and their business clients, such as Records Management Organizations, to help identify, define, manage, and support the many different File Plan Types that are used to facilitate, both, File Plan Management and Records Management solutions.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/file_plan_taxonomy.html",
"name": "File Plan Taxonomy",
"prefix": "2060"
},
"2061": {
"description": "The following represents a hierarchical taxonomy of key Enterprise and Information Technology (IT) Glossary Types or Categorizations, along with dynamic HTML links to their semantically grouped Term/Definition pairs. These Glossaries are used by IT organizations, IT professionals and the various enterprises they support to help standardize language, semantics, understanding and communications between individuals and systems and represent the very foundation for Enterprise Knowledge Management.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/hierarchical_glossary_taxonomy.html",
"name": "Glossary Taxonomy",
"prefix": "2061"
},
"2062": {
"description": "The following represents a linear or flat representation of key forms of Governance that are used by Information Technology (IT) organizations and professionals to help manage themselves and to help define, structure, organize, and understand various forms of Data, Information, and Knowledge within their enterprises. Such information is often used as a foundation for data modeling, especially in the design, definition, and implementation of other Taxonomies and Ontologies. Such constructs are also often used as mechanisms to provide clarity and standardize terminology for communications between business stakeholders and IT organizations.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/governance_taxonomy.html",
"name": "Governance Taxonomy",
"prefix": "2062"
},
"2063": {
"description": "The following represents a linear or flat taxonomy of key Inventories that are used and should be maintained by Information Technology (IT) organizations and professionals. Such Inventories help define, structure, organize, and understand various forms of Data, Information, and Knowledge that are important to IT Organizations, IT Professionals, and their Business Stakeholders. Specifically, maintaining current and up to date Inventories is a best practice that ensures better transparency into the enterprise and which leads to good operational metrics for better decision making.\n\nSuch a Taxonomy is often used as a foundation for data modeling, especially in the design, definition, and implementation of other Taxonomies and Ontologies. These constructs are also often used as mechanisms to provide clarity and standardize terminology for communications between business stakeholders and IT organizations.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/inventory_taxonomy.html",
"name": "Inventory Taxonomy",
"prefix": "2063"
},
"2064": {
"description": "The following represents a linear or flat taxonomy of key IT Disciplines that are used by Information Technology (IT) organizations and professionals to help define, structure, organize, and understand various forms of Data, Information, and Knowledge associated with the many Discplines performed by IT Organizations and their IT Professionals, both, for themselves and for their business stakeholders. Such information is often used as a foundation for data modeling, especially in the design, definition, and implementation of other Taxonomies and Ontologies. Such constructs are also often used as mechanisms to provide clarity and standardize terminology for communications between business stakeholders and IT organizations.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/it_discipline_taxonomy.html",
"name": "IT Discipline Taxonomy",
"prefix": "2064"
},
"2065": {
"description": "The following represents a linear or flat taxonomy of key Enterprise Knowledge Management types or categories that are important to most enterprises, Information Technology (IT) Organizations, IT Professionals, and Knowledge Management Professionals who support or provide services to enterprises.\n\nA Knowledge Taxonomy is often used as a foundation for understanding the types of Knowledge that an enterprise needs to identify, measure, collect, persist, share, teach, and/or develop and improve, over time.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/enterprise_knowledge_taxonomy.html",
"name": "Knowledge Management Taxonomy",
"prefix": "2065"
},
"2066": {
"description": "The following represents a linear or flat representation of the different Categories or Types of Policies that are common to most enterprises. This Taxonomy is associated with the IT Disciplines known as Policy Management.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/policy_taxonomy.html",
"name": "Policy Taxonomy",
"prefix": "2066"
},
"2067": {
"description": "The following represents a linear or flat taxonomy of different Process types or categorizations that are used by Information Technology (IT) professionals to help identify, define, classify, structure, organize, track and understand various Processes. These Process types or categorizations are associated with the IT Discipline called Process Management.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/process_taxonomy.html",
"name": "Process Taxonomy",
"prefix": "2067"
},
"2068": {
"description": "The following represents a linear or flat taxonomy of different Record types or categorizations that are used by Information Technology (IT) professionals in order to help define, structure, organize, track and understand various forms of Data, Information, and Knowledge. These Record types or categorizations are associated with the IT Discipline called Records Management and its related processes.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/records_taxonomy.html",
"name": "Records Taxonomy",
"prefix": "2068"
},
"2069": {
"description": "The following represents a linear or flat taxonomy of different Records Management types or categorizations that are used by Information Technology (IT) professionals in order to help define, structure, organize, track and understand various forms of Data, Information, and Knowledge. These Record Management types or categorizations are associated with the IT Discipline called Records Management and all of its related processes and solutions. They also help to highlight the importance and complexity of Records Management.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/records_management_taxonomy.html",
"name": "Records Management Taxonomy",
"prefix": "2069"
},
"207": {
"description": "The version presented by the TESAURO ISOC DE PSICOLOGIA, like the previous one, can be improved, since the thesaurus, although it is a controlled language, has to reflect the natural language of a discipline and, therefore, must incorporate the terms This issue, like the previous one, is considered to be a very useful tool for all Documentation Centers and Libraries specializing in Psychology or related sciences .",
"homepage": "http://thes.cindoc.csic.es/index_PSICO_esp.php",
"name": "ISOC Psychology Thesaurus",
"prefix": "207"
},
"2070": {
"description": "The following represents a linear or flat taxonomy of different Roadmap types or categorizations that are used by Information Technology (IT) professionals, their organizations and the business they support, in order to help with the definition and understanding of Work and Delivery that is critical to the implementation and oversight of Strategy. These Roadmap types or categorizations are associated with the IT Discipline called Roadmap Management and its related processes, and they represent the inventory of all Roadmaps that mature enterprises strive to define and maintain, regularly.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/roadmaps_taxonomy.html",
"name": "Roadmap Taxonomy",
"prefix": "2070"
},
"2071": {
"description": "The following represents a linear or flat representation of the different Service Types or Categories that are used by Information Technology (IT) organizations, professionals and their business clients to help define, deploy and manage the many different Services that are used to facilitate Work Management or Service Management solutions.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/service_taxonomy.html",
"name": "Service Taxonomy",
"prefix": "2071"
},
"2072": {
"description": "The following represents a linear or flat taxonomy of the many different key Taxonomy types or categorizations that are used by Information Technology (IT) organizations and professionals to help define, structure, organize, and understand various forms of Data, Information, and Knowledge. Such a Taxonomy is often used as a foundation for activities like data modeling (i.e. the design, definition and development of other Taxonomies and Ontologies). Such constructs are also often used as mechanisms to provide clarity and standardize terminology for communications between business stakeholders and IT organizations.\n\nNote: Each of these Taxonomy types or categorizations is directly aligned with the specific form of Taxonomy Management.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/taxonomy_taxonomy.html",
"name": "Taxonomy Taxonomy",
"prefix": "2072"
},
"2073": {
"description": "The following represents a linear or flat representation of the different Unique Identifier Types that are used by Information Technology (IT) organizations and professionals (especially Data professionals) to help create Data Solutions that allow unique identification of instances of Data Entities or Data Items. This Taxonomy is associated with the IT Disciplines known as Unique Identifier Management and Data Management.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/unique_identifier_taxonomy.html",
"name": "Unique Identifier (ID) Taxonomy",
"prefix": "2073"
},
"2074": {
"description": "The IF4ITβs IT Glossary is intended to be a centralized, thorough, public and freely available repository of Information Technology 'Operations' (or 'Operational') terms. By Operations/Operational we mean that these terms address how Information Technology resources 'work' and the concepts they need to perform their work. The glossary consists of thousands of of terms that are consistent with how IT leaders lead and how IT workers work, across all industries. Weβre proud of the fact that the IF4IT Glossary is the most thorough operations glossary in the world and that it is constantly growing at a rate that outpaces any other glossary source that is available to the IT community.",
"homepage": "http://www.if4it.com/it-glossary/",
"name": "Information Technology Glossary of Terms and Phrases",
"prefix": "2074"
},
"2075": {
"description": "A common language that conveys the complex reality of current social and cultural valuesβethical, aesthetic, scientific and technologicalβremains a constant concern for those in charge of transmitting a message to society, particularly in the field of museology. In this context, the International Committee of ICOM for Museology (ICOFOM) developed the booklet βKey Concepts of Museologyβ, an avant-premiΓ¨re of the complete Dictionary of Museology, a reference tool that will provide museum professionals worldwide with a common language. The booklet, distributed during the 22nd ICOM General Conference, presents 21 fundamental concepts of museology.",
"homepage": "http://icom.museum/professional-standards/key-concepts-of-museology/",
"name": "Key Concepts of Museology",
"prefix": "2075"
},
"2076": {
"description": "SNORRE contains terms and definitions which have been extracted from national, European or international standards and which have been quality assured by subject specialists and linguists. Consequently, the term base provides a valuable tool for translators, technical writers and others interpreting or producing technical text. (...) The terms in SNORRE have been extracted from standards from a wide variety of standardization areas. Examples include Quality, Services, Transport, Food technology, Sports equipment and facilities, Company organization and management, Textile and leather technology, and Shipbuilding and marine structures. The majority of the terms have been extracted from translations. The database therefore comprises a vast amount of building and civil engineering terminology, as this is the standardization area in which most translations are produced. SNORRE also contains many environmental terms. (...) The term base has more than 50 000 entries and more than 200 000 terms and 30 000 definitions. SNORRE is a multilingual terminological database that contains terminology in Norwegian BokmΓ₯l, Norwegian Nynorsk and English. Many entries also include German and/or French terms. The following elements are normally to be found in a SNORRE database entry: terms and definitions, notes, sources and subject fields. (...) The SNORRE user interface enables users to make simple search requests among terms, definitions etc. in various languages. Advanced search features are also available. Furthermore, the search results page offers filter functionality that makes it possible to narrow down search results according to source, language and category (terms/definitions), as well as free text search. Users may access term lists based on subject area and lists containing all terms that have been extracted from a specific source. Moreover, the term entries are linked to a product information page where users may collect background information about the referenced sources (standards) and also get a preview of the documents (five pages). (...) SNORRE is the result of a project that was carried out in co-operation with the Language Council of Norway with financial support from the Norwegian Ministry of Culture. The main project objective was to make terminology from standards publicly accessible. The intension was to strengthen the position of the Norwegian language (BokmΓ₯l and Nynorsk) through providing the public with valuable Norwegian terminology.",
"homepage": "http://www.termbasen.no/",
"prefix": "2076"
},
"2077": {
"description": "UNTERM is a multilingual terminology database maintained jointly by the main duty stations and regional commissions of the United Nations system. (...) UNTERM provides terminology and nomenclature in subjects relevant to the work of the United Nations. Information is provided in the six UN official languages, and there are also entries in German and Portuguese. (...) This database is a linguistic tool created primarily to facilitate the work of United Nations staff members and other people around the world who participate or are interested in the Organization's activities. The inclusion of an item in this database should not be construed as an endorsement by the United Nations of any particular position, entity or programme.",
"homepage": "https://unterm.un.org/",
"name": "UNTERM",
"prefix": "2077"
},
"208": {
"description": "8222 terms, 5613 postable index terms, 2609 nonpostable terms. Each record in APA's databases contains controlled vocabulary terms from the Thesaurus of Psychological Index Terms.",
"homepage": "http://www.apa.org/pubs/databases/training/thesaurus.aspx",
"name": "Thesaurus of Psychological Index Terms",
"prefix": "208"
},
"209": {
"description": "The HealthPsy thesaurus contains 3373 descriptors and 1562 synonyms (non-descriptors). It is organized into 30 semantic fields, hierarchized in seven levels and consists of three parts: a hierarchical list, a structured alphabetical list and a permuted list.",
"homepage": "https://www.ascodocpsy.org/archives_santepsy/Thesaurus/",
"name": "ThΓ©saurus SantΓ©Psy",
"prefix": "209"
},
"21": {
"description": "11497 terms, 12386 relationships between terms, 5408 equivalent terms, headings of subjects structured by different thematic areas.",
"homepage": "https://confrides.cpd.ua.es/tematres/vocab/",
"name": "Subject index",
"prefix": "21"
},
"211": {
"abbreviation": "CABT",
"description": "The CAB Thesaurus is the essential search tool for all users of the CAB ABSTRACTSβ’ and Global Health databases and related products. The CAB Thesaurus is not only an invaluable aid for database users but it has many potential uses by individuals and organizations indexing their own information resources for both internal use and on the Internet.\n\nIts strengths include: Controlled vocabulary that has been in constant use since 1983; Regularly updated (current version released July 2017) (...); Broad coverage of pure and applied life sciences, technology and social sciences (...); Total number of terms approaching 2.7 million; Specific terminology for all subjects covered; Includes about 241,900 plant, animal and microorganism names; Broad, narrow and related terms to help users find relevant terminology; Cross-references from non-preferred synonyms to preferred terms; Multi-lingual, with Dutch, Portuguese and Spanish equivalents for most English terms, plus lesser content in Danish, Finnish, French, German, Italian, Norwegian and Swedish; American and British spelling variants; Relevant CAS registry numbers for chemicals; Commission notation for enzymes.",
"homepage": "http://www.cabi.org/cabthesaurus/",
"license": "CC BY-NC-ND 3.0",
"name": "CAB Thesaurus",
"prefix": "211"
},
"212": {
"description": "The Canadian Immigration and Citizenship Indexing Terms is a bilingual standardized vocabulary developed to facilitate the indexing and retrieval of resources available from Citizenship and Immigration Canada (CIC). In addition to the indexing and searching functions, the Indexing Terms is meant to clarify terminology and provide a standard, common language for use within the fields of citizenship and immigration. The Canadian Immigration and Citizenship Indexing Terms is meant to be used as a source of standardized terminology for the production of indexes to information resources in all media. The standardization of the external form and the meaning of index terms will result in a consistent representation of a particular concept or subject within the index.",
"name": "Canadian Immigration and Citizenship Indexing Terms",
"prefix": "212"
},
"213": {
"description": "An integrated controlled environmental vocabulary. Use it for creation of metadata and construction of queries, both online and in stand-alone systems.",
"name": "California Environmental Resources Evaluation System Thesaurus",
"prefix": "213"
},
"214": {
"description": "The terms are organised hierarchically according to their specificity. Each term is associated with a facet code, which is a combination of letters or numbers that indicates the place of the term in the hierarchy. The CIS Thesaurus represents a slight variation from the \"classic\" thesaurus paradigm: because terms and their facets are not generally added to the thesaurus unless they have been used to index a document, it may happen that there is no generic term covering one or more terms at a particular level in the thesaurus, although there may be an even broader term further up the hierarchy. Used to index the CIS bulletin and database. It can also supply 'meta' tags for indexing Web pages, and its system of facet codes has been used to organize occupational safety and health libraries.",
"homepage": "http://www.ilo.org/safework/info/publications/WCMS_112576/",
"name": "Occupational Safety and Health Thesaurus",
"prefix": "214"
},
"215": {
"description": "The keyword list of the DZA serves as a basis for the content development of the literature in GeroLit and was created by the staff of the library with regard to the specialized literature.",
"homepage": "http://www.dza.de/fileadmin/dza/pdf/Schlagwortliste_Bibliothek.pdf",
"name": "German Center of Gerontology tag list",
"prefix": "215"
},
"216": {
"description": "BFO grows out of a philosophical orientation which overlaps with that of DOLCE and SUMO. Unlike these, however, it is narrowly focused on the task of providing a genuine upper ontology which can be used in support of domain ontologies developed for scientific research, as for example in biomedicine within the framework of the OBO Foundry. Thus BFO does not contain physical, chemical, biological or other terms which would properly fall within the special sciences domains.\n\nThe BFO project was initiated in 2002. The theory behind BFO was developed initially by Barry Smith and Pierre Grenon and presented in a series of publications listed here. Since then important contributions to BFO have been made by many people, including: Werner Ceusters, Chris Mungall, Fabian Neuhaus, Holger Stenzhorn, Alan Ruttenberg, Mathias Brochausen, Bjoern Peters, Kerry Trentelman, and by more than hundred other members of the BFO Discussion Group. Its development has been carried out under the auspices of the project Forms of Life sponsored by the Volkswagen Foundation.",
"homepage": "http://www.ifomis.org/bfo/",
"prefix": "216",
"wikidata_database": "Q4866972"
},
"217": {
"description": "The ontology consists of concepts or terms (nodes) that are linked by three types of relationships (edges). That means the ontology appears as a direct acyclic graph. The parent and child terms are connected to each other by is_a and part_of relationships. The former is a relation in which the child term is a more restrictive concept than its parent (thus divination is_a traditional_practice). The latter is used to show the inclusion relationships between concepts, for example that a potion_type is part_of a potion.",
"homepage": "http://purl.bioontology.org/ontology/ATMO",
"name": "African Traditional Medicine Ontology",
"prefix": "217"
},
"218": {
"description": "The goal of the Newborn Screening Coding and Terminology Guide is to promote and facilitate the use of electronic health data standards in recording and transmitting newborn screening test results. The Web site includes standard codes and terminology for newborn tests and the conditions for which they screen, and links to other related sites. The codes and vocabulary standards are provided in a series of tables that you can view on the Web and/or download for your own use. These tables cover conditions recommended for screening by the Secretary's Advisory Committee on Heritable Disorders in Newborns and Children (SACHDNC) or by a state within the U.S.\n\nUse of these standards can speed the delivery of newborn screening reports, facilitate the care and follow-up of infants with positive test results, enable the use (and comparison) of data from different laboratories, and support the development of strategies for improving the newborn screening process.",
"homepage": "http://newbornscreeningcodes.nlm.nih.gov/",
"name": "Newborn Screening Coding and Terminology Guide",
"prefix": "218"
},
"219": {
"description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events. AERO focuses on signs reported by clinicians as part of adverse event reporting forms, whether causality to the medical intervention as been established or not. Official releases will be marked as such, and will comply with ID and deprecation policies.",
"homepage": "http://code.google.com/p/adverse-event-reporting-ontology/",
"name": "Adverse Event Reporting Ontology",
"prefix": "219"
},
"22": {
"description": "Until September 2007 subject terms used in Index New Zealand were from the Index New Zealand Thesaurus, which is based on the APAIS thesaurus, created by the National Library of Australia. This version was released in November 2005 and contains over 1,200 preferred terms. The Index New Zealand Thesaurus has been designed to describe journal and newspaper articles about New Zealand and the South Pacific in the areas of social sciences and humanities.",
"homepage": "http://natlib-primo.hosted.exlibrisgroup.com/primo_library/libweb/action/search.do?mode=Basic&tab=innz",
"name": "Index New Zealand Thesaurus",
"prefix": "22"
},
"220": {
"abbreviation": "BSSC",
"description": "The BIC Standard Subject Categories scheme (BSSC) was created in the mid-1990s and used as the standard classification scheme for the UK book trade and other English language markets. In 2017 its development was frozen and in 2024 it was marked as obsolete. It has since been replaced by Thema classification.",
"homepage": "http://www.bic.org.uk/7/BIC-Standard-Subject-Categories/",
"name": "Book Industry Communication Standard Subject Categories",
"prefix": "220"
},
"221": {
"description": "This manual contains the descriptions of the Classification Units (CUs) used by the Workplace Safety and Insurance Board (WSIB) to classify the business activities of employers in Ontario.",
"homepage": "http://www.wsib.on.ca/en/community/WSIB/230/PolicyHome/24345?vgnextoid=1238b411be12e110VgnVCM1000000e18120aRCRD",
"name": "Employer Classification Manual",
"prefix": "221"
},
"222": {
"description": "The name 'Central Product Classification' is intended to indicate that the purpose of CPC is to provide a framework for international comparison of various kinds of statistics dealing with goods, services and assets. Basically, CPC is intended to be used for different types of statistics, for example, industrial statistics and national accounts, price statistics, foreign trade statistics (including trade in services) and balance-of-payments statistics.",
"homepage": "http://unstats.un.org/unsd/cr/registry/cpc-2.asp",
"name": "Central Product Classification",
"prefix": "222",
"wikidata_database": "Q1053950"
},
"223": {
"abbreviation": "PsycINFO",
"description": "Every record in PsycINFOΒ databases receives a classification code, which is used to categorize the document according to the primary subject matter. These classification codes can help you target your search by allowing you to restrict retrieval to a specific category. There are 22 major categories and 135 subcategories, and a list of codes. Each record is assigned to one or two classifications.\n\nNOTE: This classification code system was designed to describe the content of the PsycINFO database, not the field of psychology.",
"homepage": "http://www.apa.org/pubs/databases/training/class-codes.aspx",
"name": "PsycINFO Classification Categories and Codes",
"prefix": "223"
},
"224": {
"description": "Classification of underweight/overweight based on the Body Mass Index (BMI)",
"homepage": "http://apps.who.int/bmi/index.jsp?introPage=intro_3.html",
"name": "International Classification of adult underweight, overweight and obesity according to BMI",
"prefix": "224",
"wikidata_database": "Q30002147"
},
"225": {
"description": "The classification seeks to provide the basis on which data from time-use surveys would be coded and presented in categories that would be meaningful in the assessment of national labour inputs into production of all goods and all types of services; in the compilation of household satellite accounts; and in examining trends in the broad uses of time.",
"homepage": "http://unstats.un.org/unsd/cr/registry/regcst.asp?Cl=231&Lg=1",
"name": "International Classification of Activities for Time-Use Statistics",
"prefix": "225"
},
"226": {
"description": "In principle, COPNI classifies individual outlays of NPISHs according to the purpose they serve. In most countries, however, there is little information about the activities of NPISHs and so, for practical reasons, the NPISHs themselves will usually constitute the units of classification. Many, perhaps most, NPISHs have a single purpose and can be unambiguously allocated to one of the purposes listed in the classification. Even if a broadly defined NPISH performs two or more functions - such as a religious organization running hospitals and schools as well as organizing religious ceremonies - it will usually be possible to distinguish separate units for each function. If it is not possible to identify a separate unit for each function, or to have an estimation related to each one, then the NPISH as a whole will have to be assigned to the purpose that predominates in terms of employment or total expenditure.",
"homepage": "http://unstats.un.org/unsd/cr/registry/regcst.asp?Cl=6&%3BLg=1",
"name": "Classification of the Purposes of Non-Profit Institutions Serving Households",
"prefix": "226"
},
"227": {
"description": "Developed by the OECD, the Classification of the Functions of Government (COFOG) classifies government expenditure data from the System of National Accounts by the purpose for which the funds are used.",
"homepage": "http://unstats.un.org/unsd/cr/registry/regcst.asp?Cl=4&%3BLg=1",
"name": "Classification of the Functions of Government",
"prefix": "227",
"wikidata_database": "Q5128413"
},
"228": {
"description": "The present fourth revision has been prepared to take into account the more detailed description of commodities provided by the 2002 edition of the Harmonized Commodity Description and Coding System, and information relevant to determining main end-use which has become available since the publication of the original BEC.",
"homepage": "http://unstats.un.org/unsd/cr/registry/regcst.asp",
"prefix": "228",
"wikidata_database": "Q4971877"
},
"229": {
"abbreviation": "DOCUTES",
"description": "The purpose of this web site is the online publication of the Thesauri of Sciences of the Documenation 'DOCUTES' prepared by the Library and Documentation Department of the University of LeΓ³n thanks to the Research Project granted by the Ministry of Education and Culture of the Junta de Castilla y LeΓ³n in the year 2000. The project falls within the category of grants awarded for the 'Empowerment of practices and tutorial action through the creation of suitable material.' For the preparation of the thesaurus has been employed The thesaurus construction program MULTITES, a specific software that enables and optimizes the automated processing of the terms as well as the electronic edition of the thesaurus. Since the project was granted in support of the teaching material, it seemed appropriate to develop a website for Introduce the thesaurus online and also insert contents related to the documentary languages ββqu E help students understand the thesaurus within the broader context of terminological tools.",
"homepage": "http://eprints.rclis.org/5875/",
"name": "Thesaurus of Documentation Sciences",
"prefix": "229"
},
"23": {
"description": "The Integrated Public Sector Vocabulary (IPSV) is an 'encoding scheme' for populating the e-GMS Subject element of metadata. It is fully compliant with ISO 2788 and BS 8723, the International and British Standards for monolingual thesauri. The vocabulary was developed with the backing of the ODPM (Office of the Deputy Prime Minister) and the eGU (Cabinet Office e-Government Unit). Version 1.00 was released in April 2005; Version 2.00 supersedes it, as of 3 April 2006.\n\nVersion 1 was developed by merging three earlier lists: the GCL (Government Category List), LGCL (Local Government Category List) and seamlessUK taxonomy. It had 2732 preferred terms and 4230 non-preferred. Version 2 is much bigger, with 3080 preferred terms and 4843 non-preferred. As a result, IPSV now covers internal-facing as well as public-oriented topics. You can still refer back to the superseded version if necessary. IPSV is just one of a family of lists you can obtain from the esd-standards site.\n\nTwo subsets of IPSV are now available:\n\nThe Internal Vocabulary covers only the 'internal-facing' topics. It has 756 preferred terms and 1333 non-preferred.\n\nThe Abridged version covers the whole scope of IPSV but is limited to the upper levels. It has 549 preferred terms and 1472 non-preferred.",
"homepage": "http://id.esd.org.uk/list/subjects",
"name": "Integrated Public Sector Vocabulary",
"prefix": "23"
},
"230": {
"description": "The DZI uses a thesaurus - a structured list of words - with a short and concise description of all content.These descriptors are assigned according to a uniform principle and reduce complex contents to simple basic forms.the DZI thesaurus does not contain any except the target group 'Migrantin' Feminine forms and also plural formations such as 'human rights', 'living conditions' or 'psychological consequences' are rare. The thesaurus concepts describe the target group (child, adolescents, chronically ill, etc.) and the field of activity.",
"homepage": "http://www.dzi.de/wp-content/uploads/2010/05/Alphabetischer-Thesaurus-gesamt.pdf",
"name": "German Central Institute for Social Issues Thesaurus",
"prefix": "230"
},
"231": {
"description": "3516 terms, 2100 relationships between terms, 520 terms not preferred.",
"homepage": "http://vocabularyserver.com/tee/es/",
"name": "European Education Thesaurus",
"prefix": "231"
},
"232": {
"description": "Since 1998, the International Bureau of Education has concentrated its activities on the adaptation of educational content to the challenges of the twenty-first century, focusing on the strengthening of capacity-building in the area of curriculum change. In 2000, thanks to the collaboration of the National Foundation for Educational Research in England and Wales (NFER), work began on updating the Thesaurus, taking into account the terminology of the IBEβs new framework programme and the report to UNESCO of the International Commission on Education for the Twenty- First Century, Learning: the treasure within, also known as the Delors report. Many new descriptors were introduced, while changes were made to the terms dealing with teaching and learning methods, and to the educational technology terms. Some descriptors and identifiers were eliminated. At the same time the number of explanatory notes was increased. In 2002, further developments took place with the introduction of new descriptors relating to curriculum and to HIV/AIDS education, in line with the IBEβs new activities. This latest October 2007 revision includes the addition of over 130 new terms, presented in the same format as the 2002 revision, and also available on the Internet in English only. The IBE is indebted to colleagues in the UNESCO Institute of Lifelong Learning, Hamburg, the UNESCO Regional Office for Education in Latin America and the Caribbean, Santiago, and the Caribbean Educational Research Information Service (CERIS), University of the West Indies who collaborated with suggestions for new terms and modifications.\n\nThe UNESCO-IBE Education Thesaurus is an important indexing tool in the education field. Its descriptors are used for indexing materials in the electronic catalogue IBEDOCS, and the Thesaurus is the principal tool in many educational documentation centres around the world.",
"homepage": "http://www.ibe.unesco.org/en/services/online-materials/unesco-ibe-education-thesaurus.html",
"name": "UNESCO-IBE Education Thesaurus",
"prefix": "232"
},
"233": {
"description": "1383 terms, 2106 relations between terms, 178 non-preferred terms.",
"homepage": "http://www.vocabularyserver.com/hpmulti/en/index.php",
"name": "Multilingual European Thesaurus on Health Promotion",
"prefix": "233"
},
"234": {
"description": "A controlled and hierarchical vocabulary developed for European School Sector.",
"homepage": "http://lreforschools.eun.org/web/guest/lre-thesaurus",
"license": "CC BY-NC 3.0",
"name": "Learning Resource Exchange Thesaurus",
"prefix": "234"
},
"235": {
"description": "Family Thesaurus is arranged in an alphabetical sequence showing the hierarchical relationship of each main term to other terms. Non-used terms or cross-references are listed to guide users to the preferred terms. Main terms are shown in bold and non-used terms in a lighter typeface. The Thesaurus facilitates post-coordinated indexing, whereby complex subjects are represented by several different headings, rather than one single heading. Post-coordinated systems rely on the use of boolean operators - such as and, or, not - to combine the separate headings for searching. In constructing terms, punctuation is used minimally and hyphens avoided where possible. For phrases, direct order or natural language is preferred. To distinguish meaning in homographs, a qualifying term appears in brackets-for example: Dependency (Economics), Dependency (Personality), Dependency (Physical).",
"homepage": "https://aifs.gov.au/our-work/resources/aifs-library",
"name": "Family Thesaurus",
"prefix": "235"
},
"236": {
"description": "The scope of SITC, Revision 4, remains the same as that of SITC, Revision 3, that is to say SITC, Revision 4, covers all goods classifiable in HS except for monetary gold, gold coin and current coin. All SITC, Revision 4, basic headings (except for 911.0 and 931.0) are defined in terms of HS07 subheadings. Since SITC is now recommended only for analytical purposes, there was no need - except in several special cases - to create new basic headings in SITC, Revision 4, that would be in one-to-one correspondence with the new HS07 subheadings.\n\nSITC, Revision 4, retains the overall structure of SITC, Revision 3, and consists of the same number of sections, divisions and groups. The changes made were at the level of basic headings and some subgroups. SITC, Revision 4, contains 2,970 basic headings.",
"name": "Standard International Trade Classification",
"prefix": "236",
"wikidata_database": "Q1667852"
},
"237": {
"description": "1543 terms, 40 relations between terms, 307 non-preferred terms.",
"homepage": "http://www.vocabularyserver.com/fonz/",
"name": "Functions of New Zealand Thesaurus",
"prefix": "237"
},
"238": {
"description": "In order to provide you with a differentiated search, we have now brought this search index into a transparent form, so please make use of this index, which lists all keywords both thematically and alphabetically, with each index being an index Number, which can be entered into the search form as a substitute for this.",
"homepage": "http://db.genderinn.uni-koeln.de/cgi-bin/n/suchindex",
"name": "Gender Inn search index",
"prefix": "238"
},
"239": {
"abbreviation": "ISIC",
"description": "The International Standard Industrial Classification of All Economic Activities (ISIC) is the international reference classification of productive activities. Its main purpose is to provide a set of activity categories that can be utilized for the collection and reporting of statistics according to such activities. Since the adoption of the original version of ISIC in 1948, the majority of countries around the world have used ISIC as their national activity classification or have developed national classifications derived from ISIC. ISIC has therefore provided guidance to countries in developing national activity classifications and has become an important tool for comparing statistical data on economic activities at the international level. Wide use has been made of ISIC, both nationally and internationally, in classifying data according to kind of economic activity in the fields of economic and social statistics, such as for statistics on national accounts, demography of enterprises, employment and others. In addition, ISIC is increasingly used for non-statistical purposes.",
"homepage": "http://unstats.un.org/unsd/cr/registry/isic-4.asp",
"name": "International Standard Industrial Classification of All Economic Activities",
"prefix": "239",
"wikidata_database": "Q1666934"
},
"24": {
"description": "IRIS (Illinois Researcher Information Service) has been replaced by the grants database service GrantForward, hosted and managed by Cazoodle, Inc. GrantForward features enhanced search and user account interfaces, as well as an administrative console for generating usage reports and managing grants for your institution. IRIS' Subject Keywords have been renamed 'Categories' within the Grant Forward system. These categories represent a curated list of disciplines that a grant belongs to. These categories can be queried directly in the Advanced Search. Additionally, categories are auto-completed for ease-of-use so that the user does not need to navigate a complicated hierarchy of subject lists.",
"homepage": "http://grantforward.com/",
"name": "Illinois Researcher Information Service Keyword Thesaurus",
"prefix": "24"
},
"240": {
"description": "369 terms.",
"name": "Geography and Urbanism Thesaurus",
"prefix": "240"
},
"241": {
"abbreviation": "DDC",
"description": "The Dewey Decimal Classification (DDC) system, devised by library pioneer Melvil Dewey in the 1870s and owned by OCLC since 1988, provides a dynamic structure for the organization of library collections. Now in its 23rd edition, and available in print and Web versions, the DDC is the world's most widely used library classification system.",
"homepage": "http://www.oclc.org/dewey/",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "Dewey Decimal Classification",
"pattern": "^(([0-9][0-9]?|[0-9]{3}(-[0-9]{3})?|[0-9]{3}(-[0-9]{3}(:[0-9]+)?)?|[0-9]{3}\\.[0-9]+(-[0-9]{3}\\.[0-9]+(:[0-9]+)?)?|T[1-9][A-Z]?--[0-9]+(-T[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?|[1-9][A-Z]?--[0-9]+(-[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?)?)$",
"prefix": "241",
"uri_format": "http://dewey.info/class/$1/e23/",
"wikidata_database": "Q48460"
},
"242": {
"description": "The ICPSR Thesaurus is a controlled vocabulary system composed of three separate lists: Subject Thesaurus, Personal Names Authority List, and Geographic Names Thesaurus. Subject Thesaurus is an alphabetical listing of social science subject terms. The scope of this thesaurus is multidisciplinary and is intended to reflect the subject range of the ICPSR archive. Social science disciplines represented include: political science, sociology, history, economics, education, criminal justice, gerontology, demography, public health, law, and international relations. Personal Names Authority List provides controlled name forms and spellings. Unlike the Subject and the Geographic lists, it is non-hierarchical (there are no broader/narrower, or related term designations). This list is designed to provide name form consistency and, through the use of a \"description\" (DSC) note field, enable users to distinguish between same or similar names and to determine whether the person/name is appropriate to their indexing or searching needs. Geographic Names Thesaurus provides guidance on the preferred and/or current names of geographic and geopolitical entities. It is hierarchically arranged using broader/narrower notation, allowing one to navigate the relationships among region, continent, country, and in some cases, cities. Scope notes briefly detailing the history of country name changes are included along with instructions and restrictions for their use and application. Organization Names Authority List is an alphabetical authority list of name forms for organizations listed in ICPSR metadata as funding agencies or as corporate authors/principal investigators.",
"homepage": "https://www.vocabularyserver.com/icpsr/index.php",
"license": "CC BY-NC 3.0",
"name": "Inter-University Consortium for Political and Social Research Thesaurus",
"prefix": "242"
},
"243": {
"description": "The ILO Thesaurus is a compilation of more than 4000 terms relating to the world of work. The ILO Thesaurus contains terms on a wide variety of topics related to economic and social development. Areas of major interest to the ILO are treated in detail. These include labour and employment policy, labour standards, labour administration, labour relations, vocational training, social protection, working conditions, wages, occupational safety and health, small enterprise, the informal economy and human rights in the workplace. The ILO Thesaurus is used primarily for the content analysis of material selected for inclusion in Labordoc. Familiarity with the ILO Thesaurus makes it easier to find material in Labordoc on a specific subject. The ILO Thesaurus is also used by other departments in the ILO for indexing and retrieving their own specific or local material. Staff of the International Labour Standards Department use it to summarize the contents of major labour legislation included in their database NATLEX. A number of specialized libraries in ILO partner institutions - governments, employers' organizations, trade unions - use the ILO Thesaurus as a tool for indexing and retrieval. As well, several ILO field offices use the facet numbers in the ILO Thesaurus to arrange their collections. Editors and translators also use the ILO Thesaurus as a specialized glossary.",
"homepage": "http://ilo.multites.net/",
"name": "International Labour Organization Thesaurus",
"prefix": "243"
},
"244": {
"description": "The ILO Taxonomy was designed by the ILO Library as a tool for retrieving information from the ILO website. Its structure therefore closely reflects the work programme of the ILO and is used by ILO departments and Field Offices for describing the content of their web pages and for searching the ILO web site. It is also well suited for use as a subject classification system for arranging collections in small libraries or labour information centres. The main difference between the ILO Taxonomy and the ILO Thesaurus is its purpose. As mentioned above, the Taxonomy was designed to facilitate information retrieval from the ILO website. The Thesaurus, on the other hand, is designed to cover a much greater range of subjects and is not specific to the work of the ILO. The ILO Taxonomy is more flexible in use than the ILO Thesaurus; if necessary, the user can add, modify or remove terms. Because of its simple structure, the Taxonomy can be easily tailored to local environments. As with the ILO Thesaurus, the ILO Taxonomy can be used as a subject classification system for collection arrangement in small libraries or labour information centres. The ILO Taxonomy comprises 400 labour-related terms arranged into 25 subject groups.",
"homepage": "http://www.ilo.org/public/english/support/lib/tools/taxonomy.htm",
"prefix": "244"
},
"245": {
"description": "The Thesaurus is an adaptation of the Third Edition of the Population Information Network (POPIN), containing subject, period and geographic keywords, structured by semantic relationships, searchable via a database module, Keywords materials, containing all significant words in alphabetical order This version of the POPIN thesaurus is composed of the keywords that are actually used for indexing and retrieving documents. The original thesaurus was abandoned because it was out-of-scope. The new keywords were also included in the third edition, which were deemed essential to reflect the evolution of terminology.",
"homepage": "http://bibliotheque.web.ined.fr/popin/",
"name": "National Institute for Demographic Studies Thesaurus",
"prefix": "245"
},
"246": {
"description": "It is possible to search through a query with a few letters of a word either in the set of keywords or in one of the 4 categories proposed: anthropo (names of personalities), geography (names of cities, regions, Countries ...), subjects (common names) and organizations (company name, political party, NGO ...) The list of answers allows to visualize the key word, to know its father and its category .The notice of each keyword allows to bounce on the articles associated with it.",
"homepage": "http://signal.sciencespo-lyon.fr/",
"name": "Institute of Political Studies of Lyon Keywords",
"prefix": "246"
},
"248": {
"abbreviation": "etiras",
"description": "You will find here alphabetically and systematically ordered keywords (descriptors) that you can use for your search in the portal content of IREON. The display of upper, lower and related terms, as well as synonyms (non-descriptors) to a keyword, facilitates the selection of relevant ones The European Thesaurus contains about 8,200 descriptors in nine languages as well as numerous non-descriptors for each language version. The European Thesaurus is a multilingual thesaurus that maps all the main aspects of the field of international relations and countries And the search for literature and facts in the field of international relations and country studies.",
"homepage": "https://fiviblk.de/thesaurus/",
"name": "European Thesaurus International Relations and National Customers",
"prefix": "248",
"wikidata_database": "Q1377962"
},
"249": {
"description": "The ISSA provides access to information, expert advice, business standards, practical guidelines and platforms for members to build and promote dynamic social security systems worldwide. The vision of dynamic social security provides a framework for the ISSA's action. Dynamic social security refers to social security systems that are accessible, sustainable, adequate, socially inclusive and economically productive, and that are based on performing, well-governed, proactive and innovative social security institutions. In line with the nature of the ISSA as an association of social security institutions, the vision of promoting dynamic social security ties social security improvements to the capacities and performance of these institutions.",
"homepage": "http://www.issa.int/content/download/135919/2764020/file/thesaurus-en.pdf",
"name": "International Social Security Association Social Security Thesaurus",
"prefix": "249"
},
"25": {
"description": "The 'Risk Thesaurus' is a set of terms chosen for their ability to facilitate the description of the major hazards theme. It allows to consult the terms attached to a descriptor (or keyword) and to more easily identify a subject in It is easy and quick to use: it allows you to translate your keywords into a structured language (descriptors) and provides a restricted and more relevant set of answers. To the descriptors that have been assigned to the documents.",
"homepage": "http://www.irma-grenoble.com/05documentation/00bibliotheque_recherchethesaurus.php",
"name": "Institute of Major Hazards Thesaurus",
"prefix": "25"
},
"250": {
"description": "The Thesaurus grew out of the Draft Thesaurus of Refugee Terminology compiled in English for the UNHCR by Piers Campbell in 1986. In 1988, the then chief of the UNHCR Centre for Documentation on Refugees (CDR), Hans Thoolen, invited Jean Aitchison, a respected expert in the field of thesauri, to provide the technical expertise for the revision and restructuring of this draft. She worked closely with the CDR and with an international working group, and the result of their collaboration was the first edition of the International Thesaurus of Refugee Terminology, in three separate language editions, published in 1989. The Spanish version was translated by the Latin American Information Center on Migration (CIMAL) in Santiago de Chile and published by the Instituto Interamericano de Derechos Humanos (IIDH) in Costa Rica. The French edition was translated by Documentation Réfugiés in Paris and published by La Documentation française (France). The English edition was published by UNHCR. We hope this new version will serve as a more efficient medium for identifying relevant indexing terminology and as a value-added mechanism for managing refugee- and forced migration-related information. It is intended as a tool for use by organizations that process information concerning refugees.",
"homepage": "http://www.refugeethesaurus.org/",
"name": "International Thesaurus of Refugee Terminology",
"prefix": "250"
},
"251": {
"description": "2478 terms, 1124 relations between terms, 442 equivalent terms.",
"homepage": "http://vocabularyserver.com/kemlu/",
"name": "Vocabulary of Social Studies of Science",
"prefix": "251"
},
"252": {
"description": "The Code of Federal Regulations (CFR) annual edition is the codification of the general and permanent rules published in the Federal Register by the departments and agencies of the Federal Government. It is divided into 50 titles that represent broad areas subject to Federal regulation. The 50 subject matter titles contain one or more individual volumes, which are updated once each calendar year, on a staggered basis. The annual update cycle is as follows: titles 1-16 are revised as of January 1; titles 17-27 are revised as of April 1; titles 28-41 are revised as of July 1; and titles 42-50 are revised as of October 1. Each title is divided into chapters, which usually bear the name of the issuing agency. Each chapter is further subdivided into parts that cover specific regulatory areas. Large parts may be subdivided into subparts. All parts are organized in sections, and most citations to the CFR refer to material at the section level.\n\nThe Electronic Code of Federal Regulations (e-CFR) is a regularly updated, unofficial editorial compilation of CFR material and Federal Register amendments produced by the National Archives and Records Administration's Office of the Federal Register (OFR) and the Government Printing Office.",
"name": "Code of Federal Regulations",
"prefix": "252",
"wikidata_database": "Q1065972"
},
"253": {
"description": "The Food and Drug Administration (FDA) has established classifications for approximately 1,700 different generic types of devices and grouped them into 16 medical specialties referred to as panels. Each of these generic types of devices is assigned to one of three regulatory classes based on the level of control necessary to assure the safety and effectiveness of the device.",
"homepage": "http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfPCD/classification.cfm",
"name": "Product Classification",
"prefix": "253"
},
"254": {
"description": "The Gross Motor Function Classification System (GMFCS) is a 5 level classification system that describes the gross motor function of children and youth with cerebral palsy on the basis of their self-initiated movement with particular emphasis on sitting, walking, and wheeled mobility. Distinctions between levels are based on functional abilities, the need for assistive technology, including hand-held mobility devices (walkers, crutches, or canes) or wheeled mobility, and to a much lesser extent, quality of movement.\n\nThe focus of the GMFCS is on determining which level best represents the child's or youth's present abilities and limitations in gross motor function. Emphasis is on usual performance in home, school, and community settings (i.e., what they do), rather than what they are known to be able to do at their best (capability). It is therefore important to classify current performance in gross motor function and not to include judgments about the quality of movement or prognosis for improvement.\n\nThe GMFCS - E&R includes an age band for youth 12 to 18 years of age and emphasizes the concepts inherent in the World Health Organization's International Classification of Functioning, Disability and Health (ICF). We encourage users to be aware of the impact that environmental and personal factors may have on what children and youth are observed or reported to do. The descriptions for the 6 to 12 year and 12 to 18 year age bands reflect the potential impact of environment factors (e.g., distances in school and community) and personal factors (e.g., energy demands and social preferences) on methods of mobility.",
"homepage": "https://canchild.ca/en/resources/42-gross-motor-function-classification-system-expanded-revised-gmfcs-e-r",
"name": "Gross Motor Function Classification System",
"prefix": "254",
"wikidata_database": "Q5610509"
},
"255": {
"description": "This section contains the group coverage qualification standards, associated individual occupational requirements (IOR), and individual qualification standards covering white collar occupations in the Federal competitive service. These standards describe the minimum qualification requirements (for example, educational, medical, age, experience, etc.) for each occupational series. You may search for information about specific qualification requirements using either the Index by Series Number or Index by Series Title.\n\nThe standards are written broadly for Governmentwide application and are not intended to provide detailed information about specific qualification requirements for individual positions at a particular agency. Such information (i.e., a description of the specialized experience requirements for a particular position) should be included in the vacancy announcements issued by the agency.",
"homepage": "http://www.opm.gov/policy-data-oversight/classification-qualifications/general-schedule-qualification-standards/",
"name": "General Schedule Qualification Standards",
"prefix": "255"
},
"256": {
"description": "Job grading standards provide information used in determining the occupational series and title of jobs performing trades, craft, and labor work in the Federal Government. They also provide grading criteria for positions classified under the Federal Wage System (FWS).",
"homepage": "http://www.opm.gov/policy-data-oversight/classification-qualifications/classifying-federal-wage-system-positions/",
"name": "Job Grading Standards for Trades, Craft, and Labor Positions",
"prefix": "256"
},
"257": {
"description": "The total number of search terms covered in KOSSDA Thesaurus is 17,389, including 2,357 preferred terms(descriptors), 2,364 non-preferred terms, and as many as 25,766 terms of hierarchical(broader terms and narrower terms) and associative relationships(related terms). KOSSDA Thesaurus has been developed specifically for and by KOSSDA.",
"homepage": "http://www.kossda.or.kr/eng/w02_06s.asp",
"name": "Korea Social Science Data Archive Thesaurus",
"prefix": "257"
},
"258": {
"description": "Subject words are chosen from a consistent female perspective, ie the subject word of women is always implied.\" The author of the author refers to female writers, the term \"police\" means female police officers (or possibly male police in relation to female colleagues / criminals). Want to search for records of male criminals, Writers etc are added: men to the keyword, eg criminals: men. Other texts about men can be found by searching for manhood, men's role, fathers, etc. The topic indexation began in the late 1950s and the number of subjects grows as needed. The indexing, performed on KvinnSam, is to make the literature possible to retrieve. User-friendliness has always been at the center.",
"homepage": "http://www.ub.gu.se/kvinn/kvinnsam/listor/amnesord.html",
"name": "WOMEN'S PROPERTY List of topics",
"prefix": "258"
},
"259": {
"description": "236 terms, 34 relations between terms, 5 equivalent terms",
"homepage": "http://www.vocabularyserver.com/politicaspublicas/",
"name": "Documentary Language in Public Policies of the Capital District",
"prefix": "259"
},
"26": {
"description": "The LACBD Thesaurus was compiled from the subject indexes that accompany the two bibliographies to provide a controlled vocabulary that spans one hundred years of Los Angeles subject matter. This specificity means that some terms and names one might expect in a thesaurus about Los Angeles will not be present. Likewise, general subject hierarchies that may have been constructed to place orphan terms were not developed, although the current structure allows for future development. Part one of the LACBD thesaurus is a common subject thesaurus. Index subject headings from the bibliographies were compiled into a hierarchical thesaurus. Some terms were created or added from other vocabularies to collocate legacy index terms.\n\nPart two is the LACBD Geographic Names Thesaurus. Buildings, streets, institutions and neighborhoods are among the many kinds of geographic names included. Only places that are named in the source bibliographies have been included in the thesaurus, although contemporary names may have been added to provide access for todayβs users. Facet nodes based upon the LACBD Subject thesaurus group the geographic names into helpful categories. Part three is the LACBD Personal Names Authority List. Peoplesβ names that are indexed in the bibliographies are included in this list. As with the geographic names, facet nodes based upon the LACBD Subject thesaurus group the personal names into categories. There are some persons who elude categorization, and they are grouped under an 'unclassified names' heading. Developed as a companion resource for the Los Angeles Comprehensive Bibliographic Database (LACBD).",
"name": "Los Angeles Comprehensive Bibliographic Database Thesaurus",
"prefix": "26"
},
"260": {
"description": "1112 terms, 624 relations between terms, 65 equivalent terms.",
"homepage": "http://vocabularyserver.com/emergencias/",
"name": "Microthesaurus in Prevention and Emergency Care of Bogota",
"prefix": "260"
},
"261": {
"description": "A-Z links show index terms in alphabetical order, one section at a time. Subject Index lists a hierarchy of subject terms (some index terms are not listed).",
"name": "Montague Institute Review Index and Thesaurus",
"prefix": "261"
},
"262": {
"description": "Der Thesaurus ist hierarchisch aufgebaut und umfasst bis zu vier Gliederungsebenen. Der Grad der Feinheit in der Unterteilung richtet sich nach dem Ausbau der Forschungsschwerpunkte des MZES. Mit dem hier vorgestellten Thesaurus wird die inhaltliche Erschliessung des Bestandes verfeinert, da bislang nur eine Recherche nach Stichworten (sogenannten Keywords, die das System selbst generiert) und groben Standortsystematikgruppen ('Classifications') mΓΆglich war. Den Benutzerinnen und Benutzern erlaubt der Thesaurus zusammen mit den Standardoptionen des Programms (Title, Author, Corporate Body u. a.) eine komfortable Recherche nach allen wichtigen bibliographischen Angaben und inhaltlichen Fragestellungen.",
"name": "Thesaurus der Bibliothek des Mannheimer Zentrums fΓΌr EuropΓ€ische Sozialforschung",
"prefix": "262"
},
"263": {
"description": "The Thesaurus is displayed in a hierarchical and alphabetical fashion. The Thesaurus contains 1330 subject terms, including descriptors, and cross-references. At its core, the Thesaurus is meant to provide standardized terminology in the field of peace and security studies. As a controlled vocabulary, the Thesaurus addresses the information retrieval needs of the international affairs community by providing context for search terms.",
"homepage": "http://vocabularyserver.com/psst/index.php",
"name": "Peace and Security Studies Thesaurus",
"prefix": "263"
},
"264": {
"description": "549 terms, 2 relations between terms, 16 equivalent terms.",
"homepage": "http://www.vocabularyserver.com/hidrocarburos/",
"name": "Hydrocarbon Thesaurus",
"prefix": "264"
},
"265": {
"description": "The thesauri base that the ITESO Library makes available to the user is a project under construction and permanent improvement, so that at each stage it reflects the thesauri developed until that moment by the Classification and Development Area of ββCollections. Not only explains why there are thesauri of some subjects and not others, but also an open invitation to receive suggestions and comments that allow them to improve them and adapt them to the needs of users. Through this page the user can access the collection of Books in the library, making use of developed thesauri.Thus, you will have a general idea of ββthe thematic organization of the collection.Line searches can be done by entering directly by the discipline in question (in the Start menu), Where the main branches are opened and thus, successively, until reaching the more specific levels.Also, Can be searched by specific words, writing them as is usually done on the Internet or choosing from the Alphabetical Index. There is also a Contextual Index that places a term in any part of the thematic entry (s) in which it is found. When doing searches you must keep in mind that the capital letters are without accent, but that in the rest of the word you have to include the accent if it is appropriate, otherwise the term is not located.",
"homepage": "http://quijote.biblio.iteso.mx/catia/tesauro/",
"name": "Library Dr. Jorge Villalobos Padilla, S.J. Thesaurus",
"prefix": "265"
},
"266": {
"description": "The POPIN Thesaurus provides alphabetical, thematic or subject, and permuted arrangements of terms. As a result of this work, the Third Edition of the POPIN Thesaurus contains approximately 100 new descriptors or terms, all of which are provided in all three languages. A total of some 240 descriptors have been deleted in order to give the thesaurus a more specific subject focus. Some 56 existing descriptors have been clarified by the addition of Scope Notes (SN) in some or all of the languages concerned. Many of the terms in all three languages have also been changed in accordance with the guidelines laid down by the POPIN Thesaurus Management Working Group, primarily to achieve closer comparability between the POPIN Thesaurus and the Macrothesaurus. A few changes in facet titles have also been made, but no major changes to the thematic organisation of the thesaurus were attempted. The POPIN Thesaurus is designed primarily for individual organisations and networks wishing to index material acquired by libraries and documentation centres and for the corresponding retrieval of such material. Second, the thesaurus may be used as a terminological guide for the standardisation of index entries such as subject headings. Third, wherever a computerized search is conducted of bibliographic databases in other subject areas, the thesaurus can be used as a search aid together with other subject-related vocabularies. Fourth, the thesaurus can be used to obtain linguistic equivalencies for translation purposes.",
"homepage": "http://www.cicred.org/OLD2004/thesaurus/INTEGRAL/",
"name": "Population Multilingual Thesaurus",
"prefix": "266"
},
"267": {
"description": "The POPLINE Keyword Guide is a compilation of 2,000+ keywords used to index documents represented in the POPLINE database. Use POPLINE keywords to build more targeted searches of the more than 340,000 records contained in the POPLINE database. Familiarity with this vocabulary will make you a better POPLINE searcher. POPLINE keywords are capitalized. In addition, commonly used synonyms and closely related concepts are included to help find the most relevant POPLINE keyword for the subject you are researching. In todayβs fluid information technology/knowledge management environment, the opportunities for POPLINE users to repurpose our thesaurus are almost limitless. Taxonomic structure now provides the foundation for many IT/KM innovations beyond traditional library and database applications.",
"homepage": "http://www.popline.org/Online_Thesaurus/POPLINE_Online_Thesaurus.htm",
"name": "POPLINE Keyword Guide",
"prefix": "267"
},
"268": {
"description": "The Population/Fertility Control Thesaurus is presented in four sections: an alphabetical list, a descriptor list, a category list and a hierarchical list. The four types of displays should be helpful in term selection both for indexing and for retrieval.",
"homepage": "http://pdf.usaid.gov/pdf_docs/pnaap426.pdf",
"name": "Population/Fertility Control Thesaurus",
"prefix": "268"
},
"269": {
"description": "Position classification standards provide information used in determining the occupational series and title for positions performing white collar work in the Federal Government. They also provide grading criteria for positions classified under the General Schedule (GS) Classification System.",
"homepage": "https://www.opm.gov/policy-data-oversight/classification-qualifications/classifying-general-schedule-positions/",
"name": "Position Classification Standards for White Collar Work",
"prefix": "269"
},
"27": {
"description": "The Local Government Category List (LGCL) was developed by the LAWs Project to define the subject matter of local government and related community resources according to a common vocabulary. The list builds on the work of the prior APLAWS project and has been refined following extensive dialogs with users. The list is provided as a 'scheme' for populating the e-GMS 'subject.category' element. It also offers 'lower level' terms to make it suitable for powering search engines and populating 'subject.refinement'. Category terms are mapped to Government Category List terms and to Local Government Service List services. It provides a controlled vocabulary suitable to apply to subject metadata.",
"homepage": "http://standards.esd.org.uk/?uri=list/subjects&tab=children",
"name": "Local Government Category List",
"prefix": "27"
},
"270": {
"description": "This thesaurus, the implementation of which was envisaged at the first meetings of the\" GREDIN \"group, was developed during the working sessions which took place from 1976 and which benefited from the participation of a very large number Librarians and documentalists in the social and medico-social sector, in order to take into account the entries of the different vocabularies used within the organizations in their diversities and their disciplinary, administrative and ideological specificities.\n\nOnce the choices of terms chosen as descriptors and \"synonyms\" have been made, a small group with the identity of \"Commission Documentary Language\" has attached itself to the realization of the thesaurus itself by distributing these lexical units in semantic fields which Group them according to their proximity of meaning and by constructing the different constitutive tables of such languages: list of records, alphabetical list of descriptors, permuted list (KWIC index) and list of descriptors by semantic fields.\n\nThis work allowed the creation of a distributed database by harmonizing not only the format of the records of the references entered by each documentalist of the network, but also their indexing, the adoption of a standardized vocabulary considerably reducing the risk of dispersion Information on different concepts but designating objects or principles that are very close to each other.",
"homepage": "http://www.documentation-sociale.org/prisme/produits-services/thesaurus-sas/",
"name": "PRISME Thesaurus",
"prefix": "270"
},
"271": {
"description": "Each course in the AMCAS application must be classified strictly on the primary content of the course.",
"homepage": "https://students-residents.aamc.org/applying-medical-school/article/course-classification-guide/",
"name": "American Medical College Application Service Course Classification Guide",
"prefix": "271"
},
"272": {
"description": "The Health Development Agency and England's Public Health Observatories (PHO's) have developed a unified Public Health Language (PHL) [formally known as the National Public Health Language] to facilitate interoperability. The first version of this language was officially launched at a conference on the 20th December 2004. The PHL is the result of integrating the former HDA's 'Public Health Information Thesaurus' with the PHOs 'Public Health Information Tagging System' (PHITS), which are no longer active as they have been superseded by the PHL. The Public Health Language has been adopted by many organisations and can now be considered as 'the' Public Health Language for the UK and Ireland. Now at Version 2.0 (and the PHL sub-set of SNOMED CT).",
"homepage": "http://www.multites.com/nphl2/NPHL-top-term.pdf",
"name": "Public Health Language",
"prefix": "272"
},
"273": {
"description": "11006 terms, 534 relations between terms, 2243 non-preferred terms.",
"homepage": "http://www.safetylit.org/thes/",
"name": "SafetyLit Thesaurus",
"prefix": "273"
},
"274": {
"description": "The International Classification of Sleep Disorders is the authoritative text for clinicians to access information about sleep disorders, criteria for diagnosis and other relevant information imperative for the treatment of their patients. This second edition provides the most current nosology of sleep medicine and is designed in a more user-friendly format. It is an invaluable resource for all clinicians. Disorders are grouped into eight categories.",
"homepage": "http://www.aasmnet.org/store/product.aspx?pid=1026",
"name": "International Classification of Sleep Disorders",
"prefix": "274",
"wikidata_database": "Q1666423"
},
"275": {
"description": "This is the discussion basis for a semiotic thesaurus of library science, which serves as the basis for a terminology of modern library science.",
"homepage": "https://web.archive.org/web/20170811170611/http://www.ib.hu-berlin.de/~wumsta/infopub/textbook/definitions/thesauindex.html",
"name": "Semiotics thesaurus of library science",
"prefix": "275"
},
"276": {
"description": "SIPRI is an independent international institute dedicated to research into conflict, armaments, arms control and disarmament. Established in 1966, SIPRI provides data, analysis and recommendations, based on open sources, to policymakers, researchers, media and the interested public. SIPRI is named as one of the world's leading think tanks in the international 'Think Tank Index'.",
"name": "Stockholm International Peace Research Institute Library Thesaurus",
"prefix": "276"
},
"277": {
"description": "20,000+ terms.",
"name": "SocINDEX Thesaurus",
"prefix": "277"
},
"278": {
"description": "The Government Activity Thesaurus is the result of efforts to bring together the terms that the French language spoken in Quebec offers to name the concepts used in the Administration, to communicate about government activity and to promote the use of Programs and public services The thesaurus is a standardized mechanism that promotes the development of a general semantic base of important vocabulary components in the functioning of public services and the description of government activity. Of structuring a vocabulary will make it possible, on the one hand, to increase internal coherence by reducing the differences in the meaning of terms according to their use by public organizations and, on the other hand, to link the terms used in Quebec society Language or professional level. The thesaurus will be used to index the S documents issued by various departments and agencies. Its content is destined to be enriched by more and more specific terms.",
"name": "Thesaurus of the Governmental Activity of QuΓ©bec",
"prefix": "278"
},
"279": {
"description": "The classification of childhood cancer is based on tumor morphology and primary site with an emphasis on morphology rather than the emphasis on primary site for adults.\n\nIn the ICCC, there are certain combinations of histologies, behaviors, and/or sites that are not considered in the schema, and for these we have added a group for unknown ICCC, which includes in situ tumors and some malignant tumors. Therefore, when we produce all sites based on ICCC, we will exclude these cases.",
"homepage": "http://seer.cancer.gov/iccc/",
"name": "International Classification of Childhood Cancer",
"prefix": "279"
},
"28": {
"description": "The Thesaurus of the Italian Culture Portal is a controlled vocabulary, designed to subject indexing and classification of very heterogeneous resources, from cultural extremely different domains data-source. The Thesaurus is an 'open system' to evolution, so as to ensure the best organization of the information imported from the Italian Culture Portal.",
"homepage": "http://www.culturaitalia.it/pico/thesaurus/4.3/thesaurus_4.3.0.skos.xml",
"license": "CC-BY-3.0",
"name": "PICO Thesaurus",
"prefix": "28"
},
"280": {
"homepage": "http://vocabularyserver.com/piupc/",
"prefix": "280"
},
"281": {
"description": "The thesaurus presented here has been prepared by the National Institute of Women with the aim of providing the libraries and documentation centers of the country, with a total of 3,104 terms, of which 2,573 are descriptors and 531 are non-descriptors, Dedicated to the theme of gender and women, a complete and updated tool for the classification of their materials. Also available to users and users of these centers and libraries, a search tool that has been made specifically To catalog and access literature on gender and women.",
"homepage": "http://www.oei.es/genero/documentos/bibliografia/Bib_5.pdf",
"name": "Gender Thesaurus: Language with Equity",
"prefix": "281"
},
"282": {
"description": "The final terminological universe consists of just over 4,000 descriptors and 700 NO-preferred terms (which refer to some of the main descriptors) that are grouped and hierarchically articulated in 12 families or semantic fields.",
"homepage": "http://thes.cindoc.csic.es/index_SOCIO_esp.php",
"name": "Thesaurus of Sociology",
"prefix": "282"
},
"283": {
"description": "It collects more than 14400 political-administrative toponyms representing 196 countries. This toponyms thesaurus should serve as an essential complement for the indexing and retrieval in the Social and Human Sciences databases and is therefore designed as a tool Of documentary work and only secondarily as a work of geographical reference.",
"name": "ISOC Thesaurus of Place Names",
"prefix": "283"
},
"284": {
"description": "2332 terms, 207 relationships between terms, 95 equivalent terms. Result of the work done by the CDTE throughout its almost 50 years of existence, the Thesaurus that can be downloaded here is a unique worldwide catalog of related terms of use Frequent in the tourist industry.",
"name": "Tourism Thesaurus",
"prefix": "284"
},
"285": {
"description": "The AUE Thesaurus of Architectural, Urban and Environmental Terms, first published in 1999, is a working tool used today by all the CAUEs as well as by certain partners in these fields. The AUE Thesaurus was the fruit of the collaboration of the AAU, the Oise, the RhΓ΄ne and the Val-d'Oise, and has been regularly updated to allow this The fourth edition 2008, enriched with more than 150 terms. Of the 25 tables that prioritize the 4,500 terms present in the thesaurus, the Landscape and Energy Have been widely complemented and restructured. A sharing tool, free of access, capable of receiving data from different software.",
"homepage": "http://www.caue69.fr/modules/smartsection/item.php?itemid=86",
"name": "Thesaurus for Architecture, Urban Planning and the Environment",
"prefix": "285"
},
"286": {
"description": "Coordination SUD ensures a double mission to support the professionalization of French NGOs and to represent their positions with public and private institutions in France, Europe and the world.",
"homepage": "http://www.r020.com.ar/tematresView/view_thesaurus.php",
"prefix": "286"
},
"287": {
"description": "The IDRC Library Thesaurus consists of four main parts: the alphabetical list, the facet list, the ANY tables, and the full names of the organizations, the latter two sections being a new element in this work. The IDRC Library has two basic needs: (i) to make a good list of descriptors available to IDRC indexing and retrieval specialists; (ii) to inform other Macrothesaurus users of IDRC's contribution to the update of this valuable instrument, widely used today for indexing and seeking information on economic and social development.",
"name": "Thesaurus of the Library of the International Development Research Center",
"prefix": "287"
},
"288": {
"description": "All the texts, speeches, interviews, press releases, press conferences ... are listed in the Public Speeches Collection and are indexed: keywords that account for the content are selected by the documentalists of the This list is standardized and structured: the keywords are ranked by thematic area and hierarchized from the most generic to the most precise, and the Thesaurus Public Information Is provided here.This regularly updated Thesaurus contains approximately 6000 terms in 26 thematic areas and includes additional lists with own names or keywords, and the keywords are intended for use with keywords Or thematic names. The thematic areas are highly structured and go down to five levels of specific terms.",
"name": "Public Information Thesaurus",
"prefix": "288"
},
"289": {
"description": "Total number of terms: 849, Total number of descriptors: 645, Total number of non-descriptors: 204. We have developed this thesaurus on women to facilitate indexing and research in the service computerization project .",
"homepage": "http://maridoc.free.fr/produits_doc/thesaurus.htm",
"name": "Thesaurus Women",
"prefix": "289"
},
"29": {
"abbreviation": "PSH",
"description": "Polythematic Structured Subject Heading System (PSH) is a bilingual CzechβEnglish controlled vocabulary of subject headings which is used for organizing and searching the documents by subject. It is developed and maintained at the National Library of Technology of Prague. PSH contains over 13 900 subject headings in its latest version PSH 4.0 and is divided into 44 thematic sections which cover the main fields of human knowledge. Each subject heading is included in a hierarchy of six (or - under special circumstances - seven) levels according to its semantic content and specificity. The whole system is a tree structure and it represents various concepts from the most general to more specific ones. There are hierarchical, associative and equivalence relations in PSH.",
"homepage": "http://psh.ntkcz.cz/skos/",
"license": "CC BY-SA 3.0",
"name": "Polythematic Structured Subject",
"prefix": "29",
"wikidata_database": "Q7227098"
},
"290": {
"description": "This edition of the Thesaurus contains 2,095 main terms, including 228 geographical terms, as well as 753 nonpostable cross-references. The Thesaurus of Aging Terminology is divided into three sections: Relational Terms, Rotated Terms, and Geographical Terms. The Relational Terms section indicates all levels of relationship among Thesaurus terms. The Rotated Terms section provides an alphabetized columnar listing of all words found within Thesaurus terms. The Geographical Terms section provides a ready reference list of state, province, country, regional, and continent names searchable as Descriptors. Used to index journal articles, books, book chapters, videos, and dissertations cited in the AgeLine Database.",
"homepage": "http://assets.aarp.org/rgcenter/general/thesaurus.pdf",
"name": "Thesaurus of Aging Terminology",
"prefix": "290"
},
"291": {
"description": "The Thesaurus of Political Science Indexing Terms contains an alphabetical listing of Main Term descriptors used for indexing and searching the PS database and printed index, beginning with the May 2002 issue. Efforts were made to preserve the terminology of the controlled vocabularies used in the backfiles of ABC POL SCI and IFI/Plenum Political Science Abstracts. Associated term relationships are displayed under each Main Term. These may include a Descriptor Code, Scope Note, Use For and Use references, Broader Terms and Narrower Terms, and Related Terms. The thesaurus terms are used by indexers to describe the contents of publications in a consistent, comprehensive, and concise manner. These terms are listed in the Descriptors field (DE=) of each record added to the database. A searcher uses these terms to retrieve the most precise set of relevant documents.",
"name": "Thesaurus of Political Science Indexing Terms",
"prefix": "291"
},
"292": {
"description": "The Thesaurus of Sociological Indexing Terms contains an alphabetical listing of Main Term descriptors used for indexing and searching the SA database and printed index, beginning with the April 1986 issue. It also references discontinued terms from the former Descriptor Authority File, which are used for accessing information prior to 1986. Associated term relationships are displayed under each Main Term. These may include a Descriptor Code, Scope Note, History Note, Use For and Use references, Broader Terms and Narrower Terms, and Related Terms. The thesaurus terms are used by indexers to describe the contents of publications in a consistent, comprehensive and concise manner.",
"name": "Thesaurus of Sociological Indexing Terms",
"prefix": "292"
},
"293": {
"description": "This fourth edition consists of 12825 terms, or 7144 descriptors, divided into 57 subdomains (also called 'fields' or 'micro-thesaurus') and 5681 synonyms, or 'non-descriptors', which refer to a valid descriptor The BDSP thesaurus can be freely used in documentation centers or libraries working in the health and social sectors.",
"homepage": "http://asp.bdsp.ehesp.fr/Thesaurus/",
"license": "CC-BY-3.0",
"name": "Public Health Thesaurus",
"prefix": "293"
},
"294": {
"abbreviation": "TheSoz",
"description": "The thesaurus currently contains about 12,000 entries, of which about 8,000 descriptors and around 4,000 synonyms, covers all disciplines of social sciences.The thesaurus is available in interactive form with its own user interface in the Fachportal sowiport The thesaurus of social sciences is a central one Instrument for content-oriented searches in the databases SOFIS and SOLIS.",
"license": "CC BY-NC-ND 3.0",
"name": "Thesaurus for the Social Sciences",
"prefix": "294",
"wikidata_database": "Q15850664"
},
"295": {
"description": "The thesaurus contains a total of 6796 terms including 5367 descriptors and 1429 non-descriptors (synonyms), descriptors are written in the form of substantives in the singular, unless use requires the use of the plural, a monohierarchical thesaurus , That is to say that each term belongs only to a semantic field, and is hierarchized at four levels from the generic term, but in some semantic fields the hierarchy can comprise up to 6 The thesaurus is used for the selection of the relevant keywords and their standardized writing, but also as a tool for classifying information. The documentalists of the ministries use them daily to feed the documentary databases, For specialized uses, it is possible to envisage the creation of lists of aid to the research by selecting the relevant terms In research, it is used to navigate from one concept to the other and to modulate the answers thanks to the semantic links established between the terms: for example to pass from the notion of sanitary engineering to that of treatment of the \" Water and then to the types of water treatment. It also allows you to automatically switch from an acronym to its meaning. By putting the main documentary resources of the ministries on the intranet, it becomes the instrument for more efficient access by users to ministry documentation.",
"homepage": "http://www.social-sante.gouv.fr/espaces",
"prefix": "295"
},
"296": {
"homepage": "http://notx.documentation.developpement-durable.gouv.fr/Urbanisme/thesaurus/navigation.xhtml",
"prefix": "296",
"wikidata_database": "Q3552180"
},
"297": {
"description": "The Classification of Instructional Programs (CIP) provides a taxonomic scheme that supports the accurate tracking and reporting of fields of study and program completions activity. CIP was originally developed by the U.S. Department of Education's National Center for Education Statistics (NCES) in 1980, with revisions occurring in 1985, 1990, and 2000. The 2000 edition (CIP-2000) is the third revision of the taxonomy and presents an updated taxonomy of instructional program classifications and descriptions.",
"homepage": "http://nces.ed.gov/ipeds/cipcode/",
"name": "Classification of Instructional Programs",
"prefix": "297",
"wikidata_database": "Q5128393"
},
"298": {
"description": "Since 1990 our collective knowledge of snow and the techniques we use to observe its characteristics have evolved. Thus, in 2003, the current classification (Colbeck et al., 1990) needed an update, but the users of the 1990 classification felt that corrections and additions should be kept to a minimum. Following the spirit of the previous editions, the Working Group on Snow Classification took care to again provide a concise document usable by user groups of quite different specialties: snow scientists, practitioners, scientists from other fields, as well as interested lay persons. However,\n\nclassification schemes typically become more technical as knowledge, measurement techniques, and observation methods evolve. The classification deals primarily with seasonal snow, even though many concepts in the present snow classification can also be applied to firn, which is the first stage in the formation of glacier ice. Definitions and tools are provided mainly to describe point observations of the snowpack, e.g., from snow pit work. However, the classification does not attempt to classify snow covers from a climatic point of view.",
"homepage": "http://www.cryosphericsciences.org/snowClassification.html",
"name": "International Classification for Seasonal Snow on the Ground",
"prefix": "298"
},
"299": {
"description": "This Local Government Classification Scheme (LGCS) is published on behalf of the Records Management Society of Great Britain, Local Government Group. Its objective is to promote improved records management practices within local government.\n\n Use - A fileplan with retention schedules it supports local authorities in the areas of Data Protection, Freedom of Information and the Local Government Act.",
"homepage": "https://joinup.ec.europa.eu/catalogue/asset_release/local-government-classification-scheme",
"name": "Local Government Classification Scheme",
"prefix": "299"
},
"30": {
"description": "From 1999 until April 2005, the DSP thesaurus was adopted as the Government of Canada Core Subject Thesaurus (CST) and during that period the two vocabularies were identical. In 2005, Library and Archives Canada assumed responsibility for the CST and the DSP thesaurus has been maintained and developed independently since then. The PDS thesaurus is a bilingual vocabulary consisting of two separate data files, English and French. The English and French versions of the thesaurus were developed and are maintained simultaneously and neither language is to be considered the dominant or source language in this vocabulary. Neither language is a translation of the other; they are each in a relationship of equivalence. The English thesaurus and the French thesaurus are identical in their coverage but their respective relational structures are not identical due to the natural conceptual and terminological differences between the two languages. The English vocabulary contains 2157 postable terms and 1698 non-postable terms. All postable terms are assigned to one or more of nineteen subject catagories.\n\nUsed as a source of subject descriptors for DSP catalogue records. As of 2009, the PDS Subject Thesaurus is also being used by Publishing and Depository Services as a source of descriptors for web metadata on the Publications Canada web site.",
"homepage": "http://publications.gc.ca/collections/collection_2010/tpsgc-pwgsc/P109-1-2010-eng.pdf",
"name": "Publishing and Depository Services Program Subject Thesaurus",
"prefix": "30"
},
"301": {
"description": "The Thesaurus Care and Welfare: the language of the social domain.\n\nMore than 35,000 terms in health and well-being, both language and language of the citizen. The terms describe a wide range of subjects of overlapping sectors: from voluntary work to local social policy, from youth care to elderly care, from social services to medical care, from education to leisure activities, etc.\n\nThe Thesaurus Care and Welfare is used by organizations as a dictionary; The definitions clarify the meaning of terms and the terms can be shown in conjunction with each other because of the relationships between the terms. In addition, organizations set up the Thesaurus Care and Welfare for consistent content metadata of websites, databases, social cards and / or for enrichment of their search engine, which makes it easier and easier for users to find the requested information.",
"homepage": "http://www.thesauruszorgenwelzijn.nl/",
"name": "Thesaurus Care and Welfare",
"prefix": "301"
},
"302": {
"description": "The TRT Web site allows users to access terminology through Alphabetical, Hierarchical, Keyword In Context or Keyword Out of Context displays. The full display shows relationship of terms including SN (Scope Notes), UF (used for terms), BT (Broader Term), NT (Narrower Term), and RT (Related Term). Through the use of the TRT's standardized vocabulary, the transportation community's access to information has been improved. A tool to improve the indexing and retrieval of transportation information. The TRT's purpose is to provide a common and consistent language between producers and users of transportation information. The thesaurus is currently also used as an indexing tool for federal, state and university collections.",
"homepage": "http://trt.trb.org/trt.asp",
"name": "Transportation Research Thesaurus",
"prefix": "302"
},
"303": {
"abbreviation": "TWSE",
"homepage": "http://www.twse.info/",
"name": "Thesaurus for economic and social development",
"prefix": "303"
},
"304": {
"description": "The Womenβs Thesaurus is a useful tool for searching by subject. It consists of terms about women, gender, gender equality and feminism. It also includes synonyms along with broader, more specific and related terms. The Thesaurus is a good starting point for searches involving theses, research, articles, programmes and policy memoranda. (...)\n\nThe online Womenβs Thesaurus is an up-to-date version of the publication The Womenβs Thesaurus: A List of Controlled Terms for Indexing Information on the Position of Women and Womenβs Studies (1992), which was compiled by Gusta Drenthe and Maria van der Sommen. It was jointly published by the International Archives for the Womenβs Movement (now known as Atria) and the Anna Maria van Schurman Centre (AMSC), the Graduate School for Advanced Research on Womenβs Studies at Utrecht University. Both The Womenβs Thesaurus and its English-language equivalent, The European Womenβs Thesaurus (1998), are used not only by Atria but also by many other womenβs information centres both at home and abroad. Atria maintains the online Womenβs Thesaurus and the European Womenβs Thesaurus.",
"homepage": "https://collectie.atria.nl/en/thesaurus",
"name": "Women's thesaurus",
"prefix": "304"
},
"305": {
"description": "AGROVOC is a controlled vocabulary covering all areas of interest of the Food and Agriculture Organization (FAO) of the United Nations, including food, nutrition, agriculture, fisheries, forestry, environment etc. It is published by FAO and edited by a community of experts.\n\nAGROVOC consists of over 40,900 concepts available in up to 42 languages: Arabic, Belarusian, Chinese, Czech, English, Estonian, French, German, Hindi, Hungarian, Italian, Japanese, Korean, Lao, Malay, Norwegian BokmΓ₯l, Persian, Polish, Portuguese, Russian, Slovak, Spanish, Swahili, Telugu, Thai, Turkish, Ukrainian and others.\n\nYou can use AGROVOC to look up the common name of a plant in a language that you do not master, or to find relations between a commodity and the crop from which it is produced. Your library can use AGROVOC to index its documents, or you can use it from inside your content management system (e.g., Drupal) to organize your documents or web site. You can also use AGROVOC as an hub to access many other vocabularies available on the web.\n\nTo date, AGROVOC is used by researchers, librarians and information managers for indexing, retrieving and organizing data in agricultural information systems and Web pages. Currently, AGROVOC is an SKOS-XL concept scheme and a Linked Open Data (LOD) set aligned with 16 other multilingual knowledge organization systems related to agriculture.\n\nYou may download AGROVOC, access its Web Services or SPARQL endpoint.",
"homepage": "http://www.fao.org/agrovoc/",
"license": "CC BY-SA 3.0",
"name": "AGROVOC",
"prefix": "305",
"wikidata_database": "Q292649"
},
"306": {
"description": "The scope of AOHST is to cover concepts relevant to OHS in Australia at national, State and local level. Some concepts are international, but the emphasis is given to the Australian context wherever necessary. The aim is to limit the size of the thesaurus to no more than 3,000 terms. This is to ensure that it is relatively easy to review and keep up-to-date. The terminology currently included in AOHST is OHS specific. This means that certain areas which are peripheral to the NOHSCβs priorities, such as compensation and insurance, are less developed at this stage. However, the thesaurus is structured in such a way as to allow the inclusion or exclusion of other categories, as required. The AOHST is of particular importance in the online environment in providing subject access to documents, databases and web sites.",
"name": "Australian Occupational Health and Safety Thesaurus",
"prefix": "306"
},
"307": {
"description": "The Business Thesaurus is a controlled vocabulary of terms that assists in the effective searching of this business content. There are over 12,000 valid terms in the Business Thesaurus. Additionally, there are over 15,000 synonyms and non-preferred terms that lead to these preferred terms. General keyword searches interact with the Business Thesaurus as a result of the back-end processing that associates business thesaurus terms to each record. For the more advanced user, the Business Thesaurus is a feature that can be browsed alphabetically or searched by relevancy ranking. The Business Thesaurus is a subject specific thesaurus and is a sub-set of the EBSCO Publishing Comprehensive Subject Index (CSI), which is a vocabulary database of subject headings used across EBSCO databases. Originally based on the Library of Congress system of subject headings, the CSI has been revised and expanded to provide a consistent, interrelated vocabulary to describe a wide range of topics. Business Thesaurus terms are drawn from a variety of sources. CSI editors have expanded on the Library of Congress list of subject headings by reviewing current terminology from other field-specific glossaries and encyclopedias as well as from news outlets and business-related publications.",
"name": "Business Thesaurus",
"prefix": "307"
},
"308": {
"description": "Concept Space is a visual interface to a formal framework for describing business literature. It is based on a hierarchical map of the business studies subject area. The graphical interface helps you to pinpoint your topic precisely, which leads to more focused, relevant search results. Concept Space is a point and click interface to a subset of the resources available to staff and students at London Business School.",
"homepage": "http://conceptspace.london.edu/",
"name": "Concept Space",
"prefix": "308"
},
"309": {
"description": "The CRA's Controlled Subject Vocabulary (CRA CSV) has been developed to help Content managers, Librarians and Metadata developers in the Agency to select controlled subject terms for metadata requirements under TBITS 39.1 & 2. The CRACSV is to be used as a source of standardized terminology for the indexing and retrieval of CRA information resources in various formats, once it has been approved by Library and Archives Canada. Its main function to standardize the external form and meaning of index terms, thus ensuring that a particular concept or subject will always be represented in the same way in CRA Web site metadata resources. (...) The intended audience for use of the CRACSV consists primarily of those who have the responsibility for building, enhancing or revising Web pages within the CRA Web site. This includes Web developers, librarians, content providers, indexers, Web technologists and communications personnel. It is anticipated that indexers will use this Web site as an authoritative source of controlled vocabulary.",
"homepage": "http://www.cra-arc.gc.ca/csv_vcs/english/menu-e.html",
"name": "Canada Revenue Agency Controlled Subject Vocabulary",
"prefix": "309"
},
"31": {
"description": "1937 terms, 1302 relations between terms, 832 non-preferred terms. Created for use with the NZGLS metadata standard.",
"homepage": "http://www.vocabularyserver.com/sonz/",
"name": "Subjects of New Zealand Thesaurus",
"prefix": "31"
},
"310": {
"description": "1471 terms.",
"homepage": "http://alexandrie.ira-lyon.gouv.fr/ListRecord.htm",
"name": "Lyon Regional Administrative Institute Thesaurus",
"prefix": "310"
},
"311": {
"description": "An early tool for the referencing of development terms, that became an indispensable tool for the libraries and documentation centres of both developing and developed countries cataloguing work on economic development.",
"homepage": "http://www.oecd-ilibrary.org/development/macrothesaurus-for-information-processing-in-the-field-of-economic-and-social-development_9789264162990-en",
"name": "Macrothesaurus for Information Processing in the Field of Economic and Social Development",
"prefix": "311"
},
"312": {
"description": "Thesaurus is a database of selected and controlled subject that is partly organized hierarchically. Subjects are searchable in free text in the database where the index is used as an additional search help.",
"homepage": "http://was.prv.se/TesaurusExternWeb/browseTreeExternal.jsp",
"name": "Patent and Registration Office Thesaurus",
"prefix": "312"
},
"313": {
"abbreviation": "STW",
"description": "The STW Thesaurus for Economics is the world's most comprehensive bilingual thesaurus for representing and searching for economics-related content. With more than 6,000 subject headings in English and German and more than 20,000 synonyms it covers all economics-related subject areas and, on a broader level, the most important related subject fields. The STW is published and continuously further developed by the ZBW according to the latest changes in the economic terminology.\n\nAs a generally re-usable concept system it is used by universities, research institutes, public institutions and companies for knowledge organization and for research and development in computer and information science as well as in the area of Linked Data and Semantic Web technologies. It has been published as one of the first thesauri in the Linked Open Data Cloud and is linked to other vocabularies through mappings. The STW is part of cross-linked information environments and web services for processing and linking economic literature, research data, author profiles and educational material.",
"homepage": "http://zbw.eu/stw/versions/latest/",
"license": "CC-BY-4.0",
"name": "STW Thesaurus for Economics",
"pattern": "^[0-9]+-[0-9]$",
"prefix": "313",
"wikidata_database": "Q26903352"
},
"314": {
"description": "First edition of the ISOC Thesaurus of Economy published in 1995, prepared by the Centro de InformaciΓ³n y DocumentaciΓ³n CientΓfica (CINDOC). It contains 6.792 terms, 5.464 are descriptors and 1.328 non-descriptors or synonyms. These terms are structured in 13 topics. Three kinds of relations are established between the terms: of hierarchy, equivalence and association. The thesaurus has three index: one hierarchical, one alphabetical and a third permuted (KWIC). It is completed by two annexes, one with names of persons, institutions, political parties, etc., and another with the name of national currencies. This edition presents the translation of all descriptors into English and French.",
"homepage": "https://digital.csic.es/handle/10261/30257",
"name": "ISOC Thesaurus for Economics",
"prefix": "314"
},
"315": {
"description": "This Thesaurus is the result of cooperation between the European Conference of Ministers of Transport (ECMT) and UIC. It was published in 1995.",
"name": "Transport Thesaurus",
"prefix": "315"
},
"316": {
"description": "The thesaurus is organized into 17 subject categories, indicated by the 'Subject Category' designation. The subject categories are used to browse the Thesaurus in a specific discipline or subject area. The subject scope of agriculture is broadly defined in the thesaurus, and includes terminology in the supporting biological, physical and social sciences. Biological nomenclature comprises a majority of the terms in the thesaurus and is located in the 'Taxonomic Classification of Organisms' Subject Category. Political geography is mainly described at the country level. The NAL Agricultural Thesaurus includes hierarchical, equivalence and associative relationships among concepts. English Total Terms - 128,253 Lead-in Terms - 60,959 Preferred Terms - 67,294 Subject Categories - 17 Scope Notes - 759 Definitions - 5,223 Spanish Total Terms - 105,432 Lead-in Terms - 38,138 Preferred Terms - 67,294 Subject Categories - 17 Scope Notes - 759 Definitions - 5,223. The thesaurus is primarily used for indexing and for improving retrieval of agricultural information. Currently, the thesaurus is the indexing vocabulary for the National Agricultural Library's bibliographic database of citations to agricultural resources, AGRICOLA. The Food Safety Research Information Office (FSRIO) and Agricultural Network Information Center (AgNIC) also use the NALT as the indexing vocabulary for their information systems. In addition, the NALT is used as an aid for locating information at the Agricultural Research Service, Economic Research Service and AgNIC web sites and databases.",
"homepage": "http://agclass.nal.usda.gov/dne/search.shtml",
"name": "United States Department of Agriculture Thesaurus",
"prefix": "316",
"wikidata_database": "Q17364107"
},
"317": {
"description": "The Enterprise Topic Thesaurus is a thesaurus which represents the concepts and terms used to describe the World Bank Groupβs topical knowledge domains and areas of expertise β the βwhat we doβ and βwhat we knowβ aspect of the Bankβs work. The Enterprise Topic Thesaurus provides an enterprise-wide, application-independent framework for describing all of the Bankβs areas of expertise and knowledge domains, current as well as historical, representing the vocabularies used by domain experts and domain novices, and Bank staff and Bank clients.",
"homepage": "http://vocabulary.worldbank.org/thesaurus.html",
"name": "World Bank Thesaurus",
"prefix": "317"
},
"318": {
"description": "This Database accommodates all pieces of legislation enacted in Palestine since the mid 1900s until nowadays. The Legislation Database features all items of legislation, which were enforced in Palestine under the Ottoman rule until 1917; legislation under the British Mandate until 1948; legislation under the Egyptian Administration in the Gaza Strip as well as the Jordanian rule over the West Bank until 1967; and military orders issued by the Israeli occupation authorities from 1967 onwards. In addition, the Legislation Database contains recent pieces of legislation enacted by the Palestinian National Authority (PNA), which have been published in the Palestinian Official Gazette since 1994. The Database is further upgraded on an ongoing basis. \n\nSo far, AL MUQTAFI includes approximately 13,000 pieces of legislation, collated from over a period of 150 years of Palestine's contemporary history. More than 50,000 pages of legislation are accessible to users, either to view online or to print out. Moreover, full texts of about 1,200 regulations published in the Palestinian Official Gazette are now provided on the AL MUQTAFI Databank.",
"homepage": "http://muqtafi.birzeit.edu/en/legalLexicon/legal_lexicon2.aspx",
"name": "Al-Muqtafi Legal Thesaurus",
"prefix": "318"
},
"319": {
"description": "The Systematic Thesaurus is subdivided into five chapters, like the branches of a tree (hence the branched, hierarchical structure of the Thesaurus). The major branches of this 'tree' are subdivided into ever finer branches, and thus the subjects covered by the branches become more and more specific. The Systematic Thesaurus is a system of classification in the field of constitutional law, which is used to index decisions of constitutional courts and equivalent bodies (in the Bulletin on Constitutional Case-Law and the database CODICES) as well as individual articles of constitutions and laws on the courts (in the database CODICES).",
"homepage": "http://www.venice.coe.int/webforms/documents/?pdf=CDL-JU%282011%29013-e",
"name": "European Commission for Democracy Through Law Systematic Thesaurus",
"prefix": "319"
},
"32": {
"description": "The Statistics Canada Thesaurus was developed to provide subject access to Statistics Canada's information resources. The Thesaurus is a bilingual, fully structured, indexing and information retrieval tool which conforms to internationally accepted standards and conventions for thesaurus construction. It consists of descriptors and non-descriptors, accompanied by their hierarchical, associative and prescriptive relationships. The scope of the Thesaurus is dynamic and reflects subjects that have been addresssed at one time or another in Statistics Canada sources. Terms were selected from various Statistics Canada products, including publications, databases and related sources. The following types of concepts have been excluded from the Thesaurus: geographical names, titles (e.g., of surveys), proper names (e.g., of companies) and acronyms, except where they are in common usage. In the Thesaurus, French and English have equal weight, neither being the dominant or \"source\" language. The French and English versions are parallel except for non-descriptors in which correlation between the French and English versions of the Thesaurus may or may not occur. Exact equivalence is mandatory only for preferred terms (descriptors). Descriptors in French are in the masculine form; for example, \"acteurs\" is preferred, not \"actrices\"; \"techniciens\" is preferred, not \"techniciennes\" or \"technicien(ne)s\". In general, terms are in the form of nouns or noun phrases. The plural form is preferred over the singular; this convention has been observed in both English and French. Terms are in direct (not inverted) format, as they would be in natural speech; for example, \"primary education\" not \"education, primary\"; \"age of head of household\" not \"head of household - age\". Terms may be accompanied, as required, by scope notes which provide a brief explanation of intended coverage or proper usage of a term. The relationships contained in the Thesaurus are hierarchical (broader/narrower), associative (related) or prescriptive (use/used for).",
"homepage": "http://www47.statcan.ca/th_r000-eng.htm",
"name": "Statistics Canada Thesaurus",
"prefix": "32"
},
"320": {
"description": "This fourth edition of the GAQ Thesaurus lists more than 2500 terms which are used to index GAO documents and to retrieve information from the GAO documents database. The thesaurus is divided into two parts: an alphabetical thesaurus of subject terms and a keyword out of context (KWOC) index. Used to index GAO documents and to retrieve information from the GAO documents database.",
"homepage": "http://www.gao.gov/assets/200/199243.pdf",
"name": "U.S. Government Accountability Office Thesaurus",
"prefix": "320"
},
"321": {
"description": "From 2007 through 2009, members of the working group discussed the terms that should be included in the thesaurus and used a wiki to help organize the various phases of the project. Their starting point was William Benemannβs Genre terms for law materials: a thesaurus (Buffalo, N.Y.: William S. Hein, 2006). The working group decided to modify the style and wording of some of Benemannβs terms, remove others altogether, and add additional headings. The group also added many cross references and scope notes and reviewed the corresponding LC subject headings for possible harmonization of the two lists. In October 2009 the AALL Cataloging and Classification Committee approved the thesaurus. AALLβs thesaurus also includes approximately twenty terms that are not specific to law. Instead, they represent genres and forms of general reference works that are heavily collected by law and other libraries (e.g., academic theses, dictionaries, and directories). Incorporated into Library of Congress Genre/Form Terms for Library and Archival Materials (LCGFT).",
"homepage": "http://vocabularyserver.com/lawgenre/",
"name": "Genre/Form Terms for Law Materials",
"prefix": "321"
},
"322": {
"description": "A collection of 48 lists with terminology. The Micro-thesauri are intended for use in conjunction with HURIDOCS Standard Formats manuals, and in particular with the HURIDOCS Events Standard Formats: a tool for documenting human rights violations. The Micro-thesauri can be used as a starting point for developing oneβs own index terms for libraries and documentation centres, as keywords for organising information on websites, or as controlled vocabularies for databases to record violations.",
"homepage": "http://www.huridocs.org/resource/micro-thesauri/",
"name": "Human Rights Information and Documentation Systems Micro-Thesauri",
"prefix": "322"
},
"323": {
"description": "The following represents a linear or flat taxonomy of key Enterprise Capability Types or Categorizations that are used by Information Technology (IT) organizations, its professionals and their business constituents to help define, structure, organize, and understand the Capabilities that are required by an enterprise for successful operation. Such information (i.e. these Capability Categories) are key to the enterprise IT Discipline known as Capability Management and usually feeds other activities, such as design, data modeling, standards development and support. Such constructs are also often used as mechanisms to provide clarity and standardize terminology for communications between business stakeholders and IT organizations.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/capability_taxonomy.html",
"name": "Capability Taxonomy",
"prefix": "323"
},
"324": {
"description": "The following represents a linear or flat representation of the different Software Types or Software Categories that are used by Information Technology (IT) organizations and professionals to help build solutions that enable their businesses to operate successfully. This Taxonomy is associated with the IT Discipline known as Software Management.",
"homepage": "http://www.if4it.com/SYNTHESIZED/FRAMEWORKS/TAXONOMY/management_software_taxonomy.html",
"name": "Software Taxonomy",
"prefix": "324"
},
"325": {
"description": "This site is a support tool which allows licensed subscribers to search the AIRS/211 LA County Taxonomy in a variety of ways, print the Taxonomy in various formats, download the file that will allow them to incorporate the Taxonomy in their database initially and keep it updated over time as the Taxonomy changes and grows, view recent changes and additions, and develop, save and share customized versions of the Taxonomy through the Filters function. Separate versions of the Taxonomy are available to U.S. and Canadian subscribers. To change the view of the Taxonomy that is being displayed, click on 'change' and select the locale you wish to see.",
"homepage": "https://211taxonomy.org/",
"name": "AIRS/211 LA County Taxonomy of Human Services",
"prefix": "325"
},
"327": {
"description": "All notations are principally in three places and consist in the first position of a capital letter, in the second position of a digit for additional subdivision and in the third position of a digit to characterize the educational institution.",
"homepage": "http://www.iwi-iuk.org/projects/zdm/",
"name": "Subject Classification Scheme",
"prefix": "327"
},
"328": {
"description": "The classification of outlays of producers by purpose (COPP) is used to classify expenditures by producers (intermediate consumption, compensation of employees, etc) by purpose (e.g. outlays on repair and maintenance or outlays on sales promotion).",
"homepage": "http://unstats.un.org/unsd/cr/registry/regcst.asp?Cl=7&%3BLg=1",
"name": "Classification of the Outlays of Producers According to Purpose",
"prefix": "328"
},
"329": {
"description": "The Locarno Classification (LOC) is an international classification used for the purposes of the registration of industrial designs. It was set up by an agreement concluded at a diplomatic conference held in Locarno in 1968: the Locarno Agreement Establishing an International Classification for Industrial Designs. The Locarno Classification comprises a list of classes and subclasses with explanatory notes and an alphabetical list of goods in which industrial designs are incorporated, with an indication of the classes and subclasses into which they fall.",
"homepage": "http://www.wipo.int/classifications/locarno/",
"license": "CC-BY-3.0",
"name": "International Classification for Industrial Designs",
"prefix": "329"
},
"33": {
"description": "It contains a total of 3216 terms, comprising 1430 Preferred terms and 1786 Non-preferred terms (entry terms or reference points). The structure is hierarchical, using a 'tree' structure that starts with broad concepts (top terms) which are then broken down into narrower concepts. The structure is fairly flat, with 571 top terms, and a maximum of 3-4 steps in each hierarchy. Subject thesaurus terms are used to describe the subject matter of resources - they describe what resources are about. This thesaurus is designed for post-coordinate retrieval - that is, each term represents a single concept, and as many terms as necessary may be used to describe a resource. This provides for flexibility and precision during resource discovery, because the searcher is able to combine terms to satisfy the particular enquiry. In indexing and retrieval, composite concepts may require the use of two or more keywords. For example, a resource dealing with 'computer network security' would have the TAGS terms 'Computer networks' and 'Security measures' assigned as Subject metadata.\n\nTAGS is a thesaurus of subject terms for use by Australian Government agencies which: covers, at a high level, subject concepts representing the scope of Australian Government activities; provides a potential source of terminology for portal browse lists; and provides a subject vocabulary which is broader than the detailed vocabularies already adopted by some agencies, but which is able to function as an introduction to those detailed vocabularies, or to serve as a controlled vocabulary for those agencies without a specialised one.",
"homepage": "https://www.finance.gov.au/agimo-archive/tags.html",
"name": "Thesaurus of Australian Government Subjects",
"prefix": "33"
},
"330": {
"description": "The Nice Classification (NCL) is an international classification of goods and services applied for the registration of trademarks and service marks. It was established by an international, multilateral agreement concluded at a Diplomatic Conference held in Nice in 1957: the Nice Agreement Concerning the International Classification of Goods and Services for the Purposes of the Registration of Marks. The Electronic Forum has been available since May 2010. It has been developed in order to facilitate the process of submission and discussion of proposals for changes to the Nice, Vienna and Locarno Classifications by the countries of the respective Unions and by certain organizations specialized in the field of trademarks or industrial designs. Access to the information posted on the electronic forum is open to the public. The Nice Classification is based on the Classification prepared by the United International Bureaux for the Protection of Intellectual Property (BIRPI) - predecessor of WIPO - in 1935. It was that Classification, consisting of a list of 34 classes and an alphabetical list of goods, that was adopted under the Nice Agreement and later expanded to embrace also eleven classes covering services and an alphabetical list of those services.",
"homepage": "http://www.wipo.int/classifications/nice/",
"license": "CC-BY-3.0",
"name": "International Classification of Goods and Services for the Purposes of the Registration of Marks",
"prefix": "330",
"wikidata_database": "Q193988"
},
"331": {
"description": "The Vienna Classification constitutes a hierarchical system that proceeds from the general to the particular, classifying the figurative elements of marks into categories, divisions and sections, on the basis of their shape. This publication contains the seventh edition of the Classification, which comprises a total of: 29 categories, 145 divisions, 806 main sections, and 903 auxiliary sections.\n\nThe examples of figurative elements relating to certain divisions, are included for information purposes only, and are therefore not an integral part of the Classification.",
"homepage": "http://www.wipo.int/classifications/vienna/",
"license": "CC-BY-3.0",
"name": "International Classification of the Figurative Elements of Marks",
"prefix": "331"
},
"332": {
"description": "The CPV establishes a single classification system for public procurement aimed at standardising the references used by contracting authorities and entities to describe the subject of procurement contracts. The CPV consists of a main vocabulary for defining the subject of a contract, and a supplementary vocabulary for adding further qualitative information. The main vocabulary is based on a tree structure comprising codes of up to 9 digits (an 8 digit code plus a check digit) associated with a wording that describes the type of supplies, works or services forming the subject of the contract.\n\nThe main vocabulary is based on a tree structure comprising codes of up to nine digits associated with a wording that describes the supplies, works or services forming the subject of the contract.\n\n* The first two digits identify the divisions (XX000000-Y);\n\n* The first three digits identify the groups (XXX00000-Y);\n\n* The first four digits identify the classes (XXXX0000-Y);\n\n* The first five digits identify the categories (XXXXX000-Y);\n\nEach of the last three digits gives a greater degree of precision within each category. A ninth digit serves to verify the previous digits.\n\nThe supplementary vocabulary may be used to expand the description of the subject of a contract. The items are made up of an alphanumeric code with a corresponding wording allowing further details to be added regarding the specific nature or destination of the goods to be purchased.\n\nThe alphanumeric code is made up of:\n\n* a first level comprising a letter corresponding to a section;\n\n* a second level comprising four digits, the first three of which denote a subdivision and the last one being for verification purposes.",
"homepage": "http://simap.ted.europa.eu/web/simap/cpv",
"name": "Common Procurement Vocabulary",
"prefix": "332",
"wikidata_database": "Q1500936"
},
"333": {
"description": "The Harmonised European Time Use (HETUS) activity coding list is based on international practices and previous classifications of daily activities used in Europe. The coding system and index were tested and revised on the basis of time use pilot surveys in 18 countries. The final system was completed in 2000 and revised in 2008. The European activity coding list allows several groupings of activities depending on the purpose of the analysis.",
"homepage": "http://ec.europa.eu/eurostat/ramon/nomenclatures/index.cfm",
"name": "Activity Coding List for Harmonised European Time Use Surveys",
"prefix": "333"
},
"334": {
"description": "This classification is designed to cover the wood and wood-based products for which FAO and ECE collect statistics on a regular basis. Included is wood taken from forests or from trees outside the forest, bark and cork; charcoal; wood and wood-based materials resulting from the first processing of the wood available from forest operations (including sawnwood, railway sleepers, veneer sheets, wood pulp and wood residues); and materials resulting from further processing of some of these materials (e.g. wood-base panels, paper and paperboard); waste paper and recoverable wood products.\n\nManufactured articles of wood and paper (as opposed to materials) are excluded as outside the regular data collection programmes of FAO and ECE. Moreover, this classification does not attempt to cover non-wood forest products such as small ornamental trees cut for special purposes; nuts, berries, seeds, roots, or other parts of plants gathered in forest areas; gums, balsams, lacs, etc.; wood derivatives such as turpentine, tall oil, sulphite dye and other chemicals. Forestry operations and services such as reforestation, forest protection (including fire protection and fire fighting) are also excluded, along with other forest-based activities such as protection and management of watersheds, of forest wildlife and of forest recreational areas.\n\nCriteria of classification: Considerations incorporated in the formulation of subdivisions in the classification include: a) chief component material; b) stage of manufacture; c) technology applied in production; d) purpose or intended use.\n\nSo far as possible, each group is confined to only one stage of manufacture i.e.: a) crude materials; b) products of first processing; c) products of further processing.\n\nAn important consideration was the harmonization with the major international classifications.",
"homepage": "http://ec.europa.eu/eurostat/ramon/nomenclatures/index.cfm?TargetUrl=ACT_OTH_DFLT_LAYOUT&StrNom=FORESTPROD&StrLanguageCode=EN",
"name": "Classification of Forest Products",
"prefix": "334"
},
"335": {
"abbreviation": "SfB",
"description": "The goal is to be able to work permanently with a current system, which is closely aligned with the practice, and which is designed in a work-based manner.\n\nAfter several printouts and various conventionally prepared updates, the SfB has been freely accessible since 2009 in an online version. In the future, SfB-Online will receive an update every year. The content processing is still done in the tried and tested cooperation, but internally in an online procedure based on a wiki. The ekz provides for the hosting of the SfB-Online and the technical support. Characteristic for SfB-Online is the simple search for class texts and the comfortable navigation due to the strongly pronounced linking. The structure of SfB-Online also provides that more information about the systematization language can be stored more than before.\n\nThe goal of this online publication is to provide the updates and changes not only to the four libraries, but to all SfB users in a timely and free manner. Close co-ordination with ekz ensures that their services are based on the current foundation and that the libraries have the same.",
"homepage": "http://www.sfb-online.de",
"name": "SfB classification",
"pattern": "^[A-Z][A-Za-zΓ€]* [0-9]+(.[0-9]| [A-Z] - [A-Z])?$",
"prefix": "335",
"wikidata_database": "Q2377005"
},
"336": {
"description": "The classification schema above genus level is limited in FishBase to classes, orders, families and subfamilies ranks (the latter not yet displayed). It has the advantage to keep it simple; it has the disadvantage to ignore some important clades in fish phylogeny like Chondrichthyes, Teleostei, Acanthomorpha, Percomorpha.\n\n In general, it follows Nelson's Fishes of the World (2006) with the noticeable exception of Elasmobranchii and Holocephali being elevated to class rank (see foot note). Also at family level, FishBase may follow Eschmeyer's Catalog of Fishes that is updated more frequently to integrate new stable groupings.\n\n Number of taxa from Orders to Species are given for what they are, a useful tool for information and database management. The design of some analyses (so-called Biodiversity analyses) that uses these numbers must be carefully assessed before processing.\n\n Catalog of Fishes gives also number of species, including available names in the sense of the International Code of Zoological Nomenclature, which we don't have. Possible discrepancies between the species and genera numbers are explained in Bailly (2010). Finally, Wiley and Johnson (2010) just published a new classification for Teleostei. They propose to stabilize several hypotheses published recently or some (long) time ago by listing the known evidences (synapomorphies). FishBase will follow this new arrangement as soon as the ichthyological community endorses it, e.g., as published in a next version of Fishes of the World. In the meantime, to avoid confusion for non-specialists, we hold on the current one.\n\n Total count of Genera: 4991. Total count of Species: 32233.",
"homepage": "http://fishbase.sinica.edu.tw/tools/Classification/ClassificationList.php",
"license": "CC BY-NC 3.0",
"name": "FishBase Classification",
"prefix": "336"
},
"337": {
"description": "We present an updated classification for the entire Crustacea Decapoda, listing all known families and genera organized by higher taxonomic groups and including estimates of the number of species in every genus. All taxonomic names are also linked to the verified literature in which they were described, the first compilation of its kind for the Decapoda. To arrive at this compilation, we began with the classification scheme provided by Martin & Davis (2001) for extant families, updated the higher classification and included the fossil taxa. The resultant framework was then populated with the currently valid genera and an estimate of species numbers within each genus. Our resulting classification, spanning both extant (living) and fossil taxa, is the first comprehensive estimate of taxonomic diversity within the entire Decapoda. The classification consists of 233 families of decapods containing 2,725 genera and an estimated 17,635 species (including both extant and fossil species). Of the families in our classification, 53 are exclusively fossil, 109 contain both fossil and extant species, and 71 are extant only. The current estimate for extant species is 14,756, whereas 2,979 species are known exclusively as fossils.",
"homepage": "http://www.researchgate.net/publication/39064758_A_Classification_of_Living_and_Fossil_Genera_of_Decapod_Crustaceans",
"name": "Classification of Living and Fossil Genera of Decapod Crustaceans",
"prefix": "337"
},
"338": {
"description": "This volume is an attempt to provide the reader, whether a seasoned systematist or a beginning student, with a glimpse into the enormous variety of extant crustaceans. The sheer number of categories that humans have constructed to contain and order this group is some indication of the incredible amount of morphological diversity they exhibit. But this is only a small part of the overall picture. Even if one were to grasp the full range of taxonomic diversity as presented in this classification, such knowledge would shed no light on the actual biology of these fascinating animals: their behavior, feeding, locomotion, reproduction; their relationships to other organisms; their adaptations to the environment; and other facets of their existence that fall under the heading of biodiversity. By producing this volume we are attempting to update an existing classification, produced by Tom Bowman and Larry Abele (1982), in order to arrange and update the Crustacea collection of the Natural History Museum of Los Angeles County. This enormous and diverse collection contains an estimated four to five million specimens, making it the second largest collection of Crustacea in the Americas. While undertaking this task, it occurred to us that others might benefit from our efforts, and that perhaps a general update on the number and arrangement of the living crustacean families, along with an explanation of the systematic and classificatory changes suggested during the last two decades, might be a welcome addition to the literature.",
"name": "Classification of the Recent Crustacea",
"prefix": "338"
},
"339": {
"description": "The goal of the GHS is to identify the intrinsic hazards found in substances and mixtures and to convey hazard information about these hazards. The criteria for hazard classification are harmonized. Hazard statements, symbols and signal words have been standardized and harmonized and now form an integrated hazard communication system. The GHS will allow the hazard communication elements of the existing systems to converge. Competent authorities will decide how to apply the various elements of the GHS based on the needs of the competent authority and the target audience.",
"homepage": "http://www.unece.org/trans/danger/publi/ghs/ghs_rev03/03files_e.html",
"name": "Globally Harmonized System of Classification and Labelling of Chemicals",
"prefix": "339",
"wikidata_database": "Q899146"
},
"34": {
"description": "The OIA thesaurus has been developed and updated from the Thesaurus of Social Issues (1993).\" The thesaurus is presented in two indexes, alphabetical and hierarchical.",
"homepage": "http://www.observatoriodelainfancia.es/oia/comun/tesauro/tesauro_jerarquico.aspx",
"name": "Thesaurus of the Board of Andalusia",
"prefix": "34"
},
"340": {
"description": "This document sets out a classification system to distinguish between the more and the less hazardous forms of selected pesticides based on acute risk to human health (that is the risk of single or multiple exposures over a relatively short period of time). It takes into consideration the toxicity of the technical active substance and also describes methods for the classification of formulations.\n\n The document lists common technical grade pesticides and recommended classifications together with a listing of active ingredients believed to be obsolete or discontinued for use as pesticides, pesticides subject to the prior informed consent procedure (Rotterdam Convention), limitations to trade because of the Stockholm convention (POPs), and gaseous or volatile fumigants not classified under these recommendations.\n\n This document replaces the 2004 edition of the classification. Since the previous edition of the classification was published, the Globally Harmonized System of Classification and Labelling of Chemicals (GHS) has been further developed and is now being widely used for the classification and labeling of chemicals worldwide. For this revision of the classification, the WHO Hazard Classes have been aligned in an appropriate way with the GHS Acute Toxicity Hazard Categories for acute oral or dermal toxicity as the starting point for allocating pesticides to a WHO Hazard Class. As has always been the case, the classification of some pesticides has been adjusted to take account of severe hazards to health other than acute toxicity. The GHS Acute Toxicity Hazard Category for each pesticide is now presented alongside the existing information.",
"homepage": "http://www.who.int/ipcs/publications/pesticides_hazard/en/",
"name": "Classification of Pesticides by Hazard",
"prefix": "340"
},
"341": {
"description": "The design and conceptual foundation of the CEMAS classification scheme follows traditional ideas and attempts to remain clinically pragmatic. The scheme describes three broad categories of abnormalities: 1) Horizontal Deviations, 2) Vertical Deviations and Special Forms of Strabismus, and finally, 3) Nystagmus and Other Ocular Oscillations and is comprised of eight major areas.",
"homepage": "https://nei.nih.gov/sites/default/files/nei-pdfs/cemas.pdf",
"name": "Classification of Eye Movement Abnormalities and Strabismus",
"prefix": "341"
},
"342": {
"description": "The Australian Bureau of Statistics (ABS) is decommissioning the Australian and New Zealand Standard Product Classification (ANZSPC) as the Australian statistical standard for products. ANZSPC was produced in 2001 as a collaboration between the Australian Bureau of Statistics (ABS) and Statistics New Zealand. It was intended that the ANZSPC become the statistical standard for the collection and presentation of product statistics in both countries. However, the recent review of product classifications, focusing on the use of ANZSPC within the ABS, found that: ANZSPC has not been adopted widely within the ABS, rather a range of collection specific classifications have been developed; a range of product classifications are required to account for different conceptual bases such as industry of origin, end use and material composition; and ANZSPC is no longer internationally comparable given the impending release of Central Product Classification (CPC) V2.0.\n\nFurthermore, consultation with Statistics New Zealand revealed that the adoption of ANZSPC throughout New Zealand has also been nominal, therefore decommissioning the ANZSPC is seen as a logical and practical approach by Statistics New Zealand.\n\nThe ABS plans to adopt the international CPC V2.0 as the overarching framework for product classifications, that is, product classifications used within the ABS will concord with CPC V2.0 to at least 3 digit level. The CPC is a multipurpose classification covering all goods and services and recent developments to increase the level of detail and comparability with other international standards has positioned it well to fulfil the function of an overarching reference product classification for Australia and New Zealand, taking on the role intended for the ANZSPC.",
"homepage": "http://www.abs.gov.au/ausstats/abs@.nsf/mf/1254.0.55.001",
"license": "CC-BY-3.0",
"name": "Australian and New Zealand Standard Product Classification",
"prefix": "342"
},
"343": {
"description": "836 terms, 322 relations between terms, 463 non-preferred terms.",
"homepage": "http://vocabularyserver.com/ip/",
"name": "Intellectual Property Subject Thesaurus",
"prefix": "343"
},
"344": {
"description": "The International Children's Rights Thesaurus consists of a core of several hundred terms that express the specific rights and concerns of the Convention on the Rights of the Child together with a number of more general terms that set these issues in their economic and social context. The criterion for inclusion of descriptors in the Thesaurus is their usefulness for indexing and retrieving documents on issues covered by the CRC. The International Children's Rights Thesaurus has been created as a tool for indexing and retrieving documents from the point of view of the Convention on the Rights of the Child (CRC).",
"homepage": "http://www.unicef-irc.org/php/Thesaurus/",
"name": "International Children's Rights Thesaurus",
"prefix": "344"
},
"345": {
"description": "JURIVOC, the juridical thesaurus of the Federal Supreme Court and the former Federal Insurance Court (now the Social Departments of the Federal Supreme Court), was created in cooperation with the Swiss legal libraries. The main part is made up of juridical terms. Moreover, it contains terms borrowed from other fields (eg, geography, medicine, etc.), insofar as they are necessary for the specification of a legal indexing aspect. JURIVOC is systematic, ie the terms (descriptors) are subdivided into hierarchies, which are essentially based on the foundations of the systematic collection of legal rights in federal law. JURIVOC is monohierarchic, which means that each term (descriptor) is assigned to a single generic term. This thesaurus does not claim to be strictly scientific, but meets the practical needs of an intellectual indexation of legal documents.",
"homepage": "https://www.bger.ch/ext/jurivoc/live/de/jurivoc/Jurivoc.jsp?interfaceLanguage=german",
"name": "JURIVOC",
"prefix": "345"
},
"346": {
"description": "Over 10,000 terms. More than half of the terms are approved indexing terms while the remainder are USE references to lead users to authorized terms. The access vocabulary has been improved with the gain of over 100 new terms over the previous edition. The format employed in this vocabulary facilitates the assignment of indexing terms to a document at the most appropriate levels of specificity or generality and from a variety of points of view. Cross references show both hierarchical and collateral relations among terms. The former provide a choice of indexing levels for many concepts, while the latter assist in leading the user to relevant indexing terms reflecting other aspects of the topic. The great variety of subject areas of research assigned to the Congressional Research Service make this indexing vocabulary a mixture of general and specific, popular and technical terminology. Current terminology is aimed for as well as an optimum degree of compatibility with Library of Congress Subject Headings (LCSH). Collaboration with the staff of the Library's Cataloging Policy and Support Office has resulted in achieving a high degree of compatibility between the two systems, and many LIV indexing terms are found in the current edition of the LCSH and in the online and card catalogs of the Library. For use with the THOMAS Bill Summary & Status Databases prior to the 111th Congress.",
"homepage": "http://www.loc.gov/lexico/servlet/lexico",
"name": "Legislative Indexing Vocabulary",
"prefix": "346"
},
"347": {
"description": "Use Thesaurus Term Search to search for materials in the NCJRS Abstracts Database using an NCJRS controlled vocabulary. This controlled vocabulary is used to assign relevant indexing terms to the documents in the NCJRS collection.",
"homepage": "https://www.ncjrs.gov/app/search/thesaurussearch.aspx",
"name": "National Criminal Justice Thesaurus",
"prefix": "347"
},
"348": {
"description": "Subjects dealt with most completely are those having to do with the main activities of City government. For example, public works, transportation, and housing are each a main focus of City activities, so there are many terms present to permit specific indexing. Geographical concepts are also an emphasis; terms are included for most Seattle neighborhoods and for major geographic features. Topics which are included in only the briefest way (i.e. few terms) are those which only indirectly relate to Seattle City government's activities. This thesaurus consists of two main parts. The first is the subject classification, which shows the relationships between subject terms in outline form. The classification displays a hierarchical arrangement of broader and narrower terms and shows the conceptual scheme used in classifying documents. Geographic names other than those for neighborhood districts are not included in the subject classification. The second part of the thesaurus is an alphabetical list of terms. It contains both the approved subject terms and other words people commonly use to describe City activities. This part of the thesaurus gives the approved subject term to use in place of unapproved 'lead-in' words. Approved or authorized indexing terms are shown in bold type. The entry for each main term includes references to broader, narrower and related terms. Some terms also have short definitions, or scope notes. A code in the form 'AB 0123' follows each main term in the alphabetical list and precedes each term in the hierarchical subject classification. This notation allow a user to find the location of a term in the hierarchy. The thesaurus contains 1713 authorized terms and 601 lead-in or unauthorized words. The collection of terms in this thesaurus has been designed to permit clear indexing and classification of records in the Seattle City Clerk's office, but it is of limited scope.",
"homepage": "http://clerk.seattle.gov/~public/thesaurus/newtoc.htm",
"name": "Seattle City Clerk Thesaurus",
"prefix": "348"
},
"349": {
"description": "In order to select the desired descriptor in the Thesaurus, it is presented in the form of drop-down lists linked in several hierarchical levels according to its structure. The Thesaurus is divided into 7 chapters which are subdivided into sub-chapters within Of which the descriptors around which the norms are grouped are classified 2068 terms.",
"homepage": "http://www.mcu.es/archivos/lhe/Consultas/consultaTesauro.jsp",
"license": "https://www.w3.org/Consortium/Legal/2015/doc-license",
"name": "Thesaurus of Historical Legislation of Spain",
"prefix": "349"
},
"35": {
"description": "The purpose of a thesaurus is to gather the terminology used in a discipline or a portion of it. It is at this moment when we should mention the complexity involved in the development of a thesaurus of Urbanism, given the nature of this discipline. As a multidisciplinary science forms its theoretical corpus from the disciplines that begin to study the urban and territorial problems from their different perspectives.The result is a series of knowledge of very diverse nature united by the common denominator of the city and the territory. Interdisciplinarity is evident in the selection of the 15 thematic areas around which articulates the totality of the terms of this thesaurus.\n\nThis Urbanization Thesaurus was created to be used in the URBISOC Database, a database developed in CINDOC, specialized in Urban Planning and Territorial Planning. But it is also born with the desire to become the instrument of control of vocabulary of other bases specialized in identical subjects that do not have a thesaurus of their own and do not have the necessary means to elaborate it. Their dissemination and use in these other information systems will prove their usefulness.",
"name": "ISOC Urban Planning Thesaurus",
"prefix": "35"
},
"350": {
"description": "As a result of these phases, the Thesaurus has been configured in 24 sub-abbreviations that include a total of 1,702 terms, of which 829 correspond to descriptors and 873 to referrals. As a programmatic goal of normalization of automated legal terminology, with a view to obtaining Sensitive improvements in the treatment, recovery, exchange and compatibilization of legal information resources of all kinds, it is intended to stimulate the use of this Industrial Property Thesaurus, which will allow to be able to present, with all the guarantees, in the local, autonomous, national forums Or international companies a product suitable for incorporation into the automated systems of management of legal information related to Industrial Property.",
"homepage": "http://thes.cindoc.csic.es/index_PROIND_esp.php",
"name": "Industrial Property Thesaurus",
"prefix": "350"
},
"351": {
"description": "The new version features 15,814 entries, of which 8,186 systematize different subjects, 6,359 refer to the national toponymy and 1,269 to the international toponymy. It is also an extension of focus: the new thesaurus carries with it all the riches and specificities of our language and As a working tool, it allows us to standardize the technical treatment of the contents in the information systems existing in the Electoral Court. As a tool to help in the search for information, it guarantees to the various social actors involved in the electoral process the Access to the information requested.",
"homepage": "http://www.tse.jus.br/hotsites/catalogo-publicacoes/pdf/tesauro/Tesauro_web_v2.pdf",
"name": "Electoral Justice Thesaurus",
"prefix": "351"
},
"352": {
"description": "The Thesaurus SAIJ of Argentine Law (TSDA) is a thesaurus of Law and, more precisely, of Argentine Law, which was taken into account not only the academic voices but also the current customs and customs, beyond the technicalities. It is only a compendium of theoretical terms since in the compilation of voices also the local idioms were taken into account, like for example Corralito financier.The TSDA is characterized by contain terminology with a high degree of conceptual specificity presenting not only legal terms but Also non-legal voices, which were duly standardized by the tool, to relate to one or more terms with transcendence in the field of law.",
"homepage": "http://admin.tcda.infojus.gov.ar/saij/index.php",
"name": "SAIJ Thesaurus of Argentine Law",
"prefix": "352"
},
"353": {
"description": "The ASCC classifies domestically produced transportable goods. Links are specified to the Harmonized System (HS), the Standard International Trade Classification (SITC) and the Australian Standard Industrial Classification (ASIC). The commodities are those collected in respect of 1989-90.",
"homepage": "http://www.abs.gov.au/ausstats/abs@.nsf/mf/1254.0",
"license": "CC0-1.0",
"name": "Australian and New Zealand Standard Commodity Classification",
"prefix": "353"
},
"354": {
"description": "This publication describes the suite of economic sector classifications used by the Australian Bureau of Statistics (ABS) to produce Australia's official economic sector statistics.\n\nThe classifications are: Standard Institutional Sector Classification of Australia (SISCA); Public/Private Classification; Level of Government Classification; Jurisdiction Classification; Type of Legal Organisation (TOLO). They are used in the compilation and publication of the National Accounts, Government Finance and International Accounts statistics as well as other component economic indicators. The purpose of sector classification is to identify and group all economic units which share common organisational and operational characteristics. Units within the same sector may be expected to react in a sufficiently similar fashion to market, fiscal and monetary forces to make aggregation meaningful for the purpose of economic analysis. Sector classifications provide an integrated framework for the collection, analysis and dissemination of sector data for the economy.",
"homepage": "http://www.abs.gov.au/ausstats/abs@.nsf/mf/1218.0",
"license": "CC-BY-3.0",
"name": "Standard Economic Sector Classifications of Australia",
"prefix": "354"
},
"355": {
"description": "The scope of the SACC is all countries, as defined above, currently existing in the world. Most countries are separately identified in the classification, even though many of them are statistically insignificant in the Australian context. A small number of geographic areas have not been separately identified but have been included in residual (not elsewhere classified) categories. Most of these entities have no permanent civilian population and are not significant in terms of social or economic statistics. This comprehensive coverage makes the classification useful for a range of applications and increases its longevity.",
"homepage": "http://www.abs.gov.au/AUSSTATS/abs@.nsf/Lookup/1269.0Main+Features1Second%20Edition?OpenDocument",
"license": "CC-BY-3.0",
"name": "Standard Australian Classification of Countries",
"prefix": "355"
},
"356": {
"description": "The scope of the classification is all religions and subsets of religions in the world as defined above. In practice, only those religious groups that have a significant number of affiliated persons in Australia are separately identified in the classification structure. However, all other religions are covered and are included in the most appropriate residual category (Miscellaneous, Other, or Not elsewhere classified categories) of the classification. The code structure of the classification also allows the identification of religious groups not separately identified, if such a need arises. (...)\n\nThe classification structure also includes a broad group that covers 'Secular Beliefs and Other Spiritual Beliefs and No Religious Affiliation' which could be considered to be inconsistent with the basis of the classification as described above and outside the scope of the religion topic. This broad group has been included for practical reasons and to make the classification more useful. Many statistical and administrative applications need to accommodate the whole range of responses to a question on religion, including personal spiritual beliefs, secular beliefs and the response 'No Religion'.",
"homepage": "http://www.abs.gov.au/ausstats/abs@.nsf/mf/1266.0",
"license": "CC-BY-3.0",
"name": "Australian Standard Classification of Religious Groups",
"prefix": "356"
},
"357": {
"description": "All world languages are in scope of the classification. Languages with significant numbers of speakers in Australia are separately identified within the classification structure. Actively spoken Australian Indigenous languages are also separately identified. Languages which are not separately identified are included in the most appropriate residual category of the classification. Extinct or dead languages spoken for religious or academic purposes are included in the most appropriate residual category of the classification. However, if sufficient numbers of an extinct or dead language are spoken in Australia, it is separately identified in the classification, for example Latin. Sign languages are defined as a communication system using gestures rather than speech or writing (The Macquarie Dictionary (Fifth Edition, 2009), and are included in the classification. Languages excluded from the classification cover those not commonly used as a means of communicating between people, such as computer languages.",
"homepage": "http://www.abs.gov.au/AUSSTATS/abs@.nsf/Lookup/1267.0Main+Features12011?OpenDocument",
"license": "CC-BY-3.0",
"name": "Australian Standard Classification of Languages",
"prefix": "357"
},
"358": {
"description": "The Australian Standard Classification of Education (ASCED) is a new Australian standard classification and replaces the ABS Classification of Qualifications (ABSCQ). ASCED is comprised of two component classifications, Level of Education and Field of Education. It provides a basis for comparable administrative and statistical data on educational activities and attainment classified by level and field. The publication provides details of the conceptual basis of ASCED, the structure of the classification, definitions for all categories of level and field and concordances with other education classifications.",
"homepage": "http://www.abs.gov.au/ausstats/abs@.nsf/0/F501C031BD9AC9C5CA256AAF001FCA33",
"license": "CC-BY-3.0",
"name": "Australian Standard Classification of Education",
"prefix": "358"
},
"36": {
"description": "It consists of a controlled and structured vocabulary consisting of more than 10,000 terms (descriptors and non descriptors) and about 77,000 semantic relationships that refer to development, both in its scientific and technological, as well as in economic and social, in the The SPINES Thesaurus, developed within the framework of the intergovernmental cooperation program in the field of scientific and technical information, was conceived as a key instrument of an international information exchange system.",
"homepage": "http://vocabularios.caicyt.gov.ar/spines/",
"name": "SPINES Thesaurus",
"prefix": "36"
},
"360": {
"description": "The Australian Standard Classification of Drugs of Concern (ASCDC) is the Australian statistical standard for classifying data relating to drugs which are considered to be of concern in Australian society. The ASCDC is essentially a classification of type of drug of concern based on the chemical structure, mechanism of action and effect on physiological activity of the drugs of concern. The classification of Type of Drug is described as the 'main classification structure' throughout the ASCDC document. The ASCDC is intended for use in the collection, classification, storage and dissemination of all statistical, administrative and service delivery data relating to drugs of concern. There are two additional classifications, Form of Drug and Method of Drug Use.\n\nThe ASCDC assists government planners, policy analysts and social researchers by providing a consistent framework for the classification of drug-related data. The use of the standard definitions, classifications and coding procedures detailed in the ASCDC helps to ensure the comparability and compatibility of data derived from a range of different statistical, administrative and service provision systems at both the state and national level.\n\nThe ASCDC is designed to collect, classify and disseminate data on drugs of concern. Because most drugs have the potential to be considered of concern in certain circumstances or contexts, the scope of the classification is all drugs. However, only those drugs noted by key stakeholders in the health, welfare, and crime and justice sectors to be of current concern in the Australian context of harm minimisation are identified in the main classification structure. This includes all drugs of concern which may be identified using the criteria listed above (see Identifying the Base Level Units of the Classification, above).\n\nIt should also be noted that the main classification structure of the ASCDC does not distinguish between drugs of concern on the basis of their legality. Further, it is not a suitable vehicle for the classification of the different chemical or physical forms in which a drug may be available, and should not be used to determine the different methods of drug use. These are correlative variables for which the 'Form of Drug' and 'Method of Drug Use' classifications have been developed.",
"homepage": "http://www.abs.gov.au/ausstats/abs@.nsf/mf/1248.0",
"license": "CC-BY-3.0",
"name": "Australian Standard Classification of Drugs of Concern",
"prefix": "360"
},
"361": {
"description": "The Australian Standard Classification of Cultural and Ethnic Groups (ASCCEG) is the Australian statistical standard for classifying ancestry data within the Australian population. ASCCEG has been developed based on the geographic area in which a group originated, developed or settled noting, similarity of groups in terms of social and cultural characteristics. ASCCEG is intended for use in the collection, aggregation and dissemination of data relating to the cultural diversity of the Australian population.\n\n The Australian Bureau of Statistics (ABS) developed ASCCEG to satisfy wide community interest in the ethnic and cultural composition of the Australian population and the characteristics of particular migrant community groups. The classification is intended to provide a standard to meet a growing statistical, administrative and service delivery need for data relating to these interests. The adoption of ASCCEG by statistical, administrative and service delivery agencies improved the comparability and compatibility of data on ethnicity from diverse sources.",
"homepage": "http://www.abs.gov.au/ausstats/abs@.nsf/mf/1249.0",
"license": "CC-BY-3.0",
"name": "Australian Standard Classification of Cultural and Ethnic Groups",
"prefix": "361"
},
"362": {
"description": "The Australian Culture and Leisure Classifications (ACLC) are part of the commitment of the Australian Bureau of Statistics (ABS) to develop national standards for culture and leisure information. They comprise three separate classifications, covering culture and leisure related industries, products and occupations.\n\nThe classifications of the ACLC focus on the economic side of culture and leisure activities - that is, the way culture and leisure activities are linked to the economy through direct expenditure and employment. The ACLC does this through three classifications: Industry, Product and Occupation. The Industry Classification lists industries consisting of organisations for which the main activity is the production or provision of culture and leisure goods and services, and is based on the Australian and New Zealand Standard Industrial Classification (ANZSIC). The Product Classification consists of a list of culture and leisure goods and services (together known as products). These products are the primary outputs of the industries listed in the Industry Classification; in addition, they may also be produced by other industries (for example, museum services may be provided by a business in the mining industry). The Occupation Classification, which is based on the Australian and New Zealand Standard Classification of Occupations (ANZSCO), lists occupations which are predominantly culture or leisure in nature.\n\nThese classifications are adopted by the ABS and organisations outside of the ABS for survey design, organising administrative data and disseminating culture and leisure information.\n\nThis is the second edition of the ACLC, following the first edition developed in 2001. This edition reflects a minor review undertaken to update ACLC concordances to the new editions of standard ABS classifications. A summary of the changes can be found in the appendices of the publication.",
"homepage": "http://www.abs.gov.au/ausstats/abs@.nsf/mf/4902.0",
"license": "CC-BY-3.0",
"name": "Australian Culture and Leisure Classifications",
"prefix": "362"
},
"363": {
"description": "The Australian and New Zealand Standard Classification of Occupations (ANZSCO) First Edition (cat. no. 1220.0) was released in September 2006. Revision 1 is the first update to ANZSCO First Edition and includes minor changes to the classification structure and definitional changes for some occupations. This product comprises an explanation of the conceptual basis of the classification, the classification structure and definitions for all levels of the classification (major, sub-major, minor and unit groups and occupations). The primary purpose of this product is to aid in the interpretation of ABS and Statistics New Zealand occupation statistics classified to ANZSCO.",
"homepage": "http://www.abs.gov.au/ausstats/abs@.nsf/mf/1220.0",
"license": "CC-BY-3.0",
"name": "Australian and New Zealand Standard Classification of Occupations",
"prefix": "363"
},
"364": {
"description": "The Australian and New Zealand Standard Industrial Classification (ANZSIC) 2006 (cat no. 1292.0) was released in February 2006. As a result of using this new classification in statistical collections, the ABS identified some areas where clarifications are needed. Revisions to ANZSIC 2006 are shown in this release. The revisions to ANZSIC 2006 are minor, maintaining the scope, concepts and structure. It concentrates on the revision of primary activities to capture new and emerging activities, clarifies class definitions to overcome practical difficulties in implementation and corrects minor errors and omissions. The minor revisions facilitate the consistent interpretation of the classification by all concerned and allow the inclusion of activities especially for industries that are subject to frequent changes (e.g. information technology).",
"homepage": "http://www.abs.gov.au/ausstats/abs@.nsf/mf/1292.0",
"license": "CC-BY-3.0",
"name": "Australian and New Zealand Standard Industrial Classification",
"prefix": "364",
"wikidata_database": "Q4824846"
},
"365": {
"description": "The ASGS brings all the regions for which the ABS publishes statistics within the one framework and will be used by the ABS for the collection and dissemination of geographically classified statistics from 1 July 2011. It is the framework for understanding and interpreting the geographical context of statistics published by the ABS. The ABS also encourages the use of the ASGS by other organisations to improve the comparability and usefulness of statistics generally.\n\n While there are superficial similarities between the ASGS and the Australian Standard Geographical Classification (ASGC), it is important to recognise that the two are fundamentally different and there are significant differences between their respective regions, both in their geographical extent and their conceptual foundation. As a whole, the ASGS represents a more comprehensive, flexible and consistent way of defining Australia's statistical geography than the ASGC.",
"homepage": "http://www.abs.gov.au/ausstats/abs@.nsf/mf/1270.0.55.001",
"license": "CC-BY-3.0",
"name": "Australian Statistical Geography Standard",
"prefix": "365"
},
"366": {
"description": "12122 terms, 27831 terms between terms, 2759 non-preferred terms. The documentary should develop and use documentary languages for indexing and retrieval of information, in order to guarantee the final quality of the product of bibliographic processing. Conceptual framework to support the construction of documentary languages of specialized areas of human knowledge, considering that in the Documentation, the construction of specialized lexicons does not have a theoretical basis for this The documentalist who wishes to develop documentary languages has to unite Terminology and Documentation \"Terminology will provide the methodology for searching and using terms and the Documentation the conceptual bases for structuring the documentary language.",
"homepage": "http://www.vocabularyserver.com/tejut/",
"name": "Thesaurus in Labor Law",
"prefix": "366"
},
"367": {
"description": "This thesaurus does not focus as heavily on synonyms as other traditional thesauri. Instead, it takes a human rights approach by cross-referencing related ESC rights, concepts, terminology in order to reflect the interrelationships between many rights. The Categorical Index presents rights, terminology and potential violations in a structured and logical format. The Thematic Index offers many routes to identifying and locating material, and the full entries (Alphabetical Thesaurus) serve as an access point for the plethora of documents relating to ESC rights. The principal goal of this thesaurus is to serve as a tool to introduce readers to economic, social and cultural rights, related concepts, issues, and potential violations of these rights. It is not a definitive resource, nor do we believe that one could ever exist concerning ESC rights.",
"homepage": "https://www.huridocs.org/resource/thesaurus-of-economic-social-and-cultural-rights/",
"name": "Thesaurus of Economic, Social and Cultural Rights",
"prefix": "367"
},
"368": {
"description": "Triblex is the case law database of the ILO Administrative Tribunal. Triblex allows users to browse Tribunal case law by session, organization or keyword. The site also features an advanced search function which allows users to search by term, date, organization, session, keyword, or judgment number. Triblex also offers the enabling statute and rules of the Administrative Tribunal. Because researching Administrative Tribunal case law can be challenging to the unfamiliar researcher, one of Triblex's most useful features is its in-depth 'About us' section. This section provides a wealth of explanatory information on the Tribunal, its composition, and its history.",
"homepage": "http://www.ilo.org/dyn/triblex/triblexmain.byKeyword",
"name": "TRIBLEX Case-Law Database Thesaurus Keywords",
"prefix": "368"
},
"369": {
"description": "UTU is a 'universal' tree structure that allows for the organization and incorporation of the different sources of law, namely legislation, jurisprudence and doctrine, which includes all branches of law. Of a universal legal thesaurus UTU is accessible to all and can therefore be used by all The structure developed is a tree structure, implying that the presented classification adopts an analytical approach to the law as opposed to a register In the development of the tree for the different branches of the law, the starting point chosen is, as far as possible, the basic legislative text which Governs the matter.",
"name": "Thesaurus of Belgian law",
"prefix": "369"
},
"37": {
"description": "The approximately 1,300 terms in this thesaurus come from many sources; before weeding, there were nearly 5,000 seed terms that originated in several existing controlled and uncontrolled vocabularies. A few terms have been added by the editor to fill obvious omissions in the hierarchy, and reference has been made both to the Education Resources Information Center (ERIC) thesaurus and to Helen Willa Samuelsβs Varsity Letters for enlightenment and clarity, although neither of these sources was incorporated. LCSH is the preferred term unless the editor found a strong sense of the term's abandonment in contemporary usage by comparing the LCSH term with the terms used in the other thesauri. Some terms may inspire controversy; in such cases the policy of preferring LCSH over other terms was the rule. Submission of the terms in this thesaurus as new terms or as cross- references to the Library of Congress through the Subject Authority Cooperative Program of the Program for Cooperative Cataloging (SACO) are encouraged.\n\nThis thesaurus is a set of terms for use by any college or university archives in the United States for describing its holdings.",
"homepage": "http://www.archivists.org/publications/epubs/thesaurus.asp",
"name": "Thesaurus for Use in College and University Archives",
"prefix": "37"
},
"370": {
"description": "The Thesaurus contains approximately 12,200 legal concepts and aims to be a suitable instrument to: maximize the use of case law, reaching increasing levels of accessibility for internal users, ministers and servers, and other organs of the judiciary, lawyers and the general public; Greater uniformity and flexibility in the processing of information, facilitating the exchange of information between systems and databases, enabling a more comprehensive integration.",
"homepage": "http://www.stj.jus.br/SCON/thesaurus/",
"name": "Legal Vocabulary",
"prefix": "370"
},
"371": {
"description": "At present, only our Topic Terms are accessible online, but we will be adding our other vocabularies in the near future. This thesaurus of topic terms is exportable in various XML schemas. We welcome others to use and adapt these terms for their own purposes. Included in the Topics are broad concepts (e.g. Accountability, Due Process, Womenβs Rights) as well as more literal or visually descriptive terms (e.g. Scenics and Beauty Shots, Crowds). Some terms are applicable in both senses (e.g. Water). In some cases, terms are selected because of frequency of use or currency within the human rights community (e.g. Sex Workers). Some terms are also selected because content creators prefer to use them (e.g. Feminicide). 334 terms, 194 relations between terms, 24 non-preferred terms. The WITNESS thesauri were developed to meet the unique needs of audiovisual content in a human rights context.",
"homepage": "http://bartoc.org/sites/default/files/skos_files/WITNESS.csv",
"name": "WITNESS Media Archive Topic Terms",
"prefix": "371"
},
"372": {
"abbreviation": "YSA",
"description": "Outdated, do not use.\n\nThe maintenance of General Finnish Thesaurus YSA and its Swedish language counterpart AllΓ€rs ended in 2019. The vocabulary replacing these two is General Finnish Ontology YSO. Updates to YSO are no longer added to YSA or AllΓ€rs. YSO is a trilingual (Finnish, Swedish, English) machine-readable version of YSA and AllΓ€rs, enhanced with linked data capabilities. All YSA and AllΓ€rs concepts incude a link to a corresponding YSO concept.\n\nThe YSA (General Finnish Thesaurus) is a general vocabulary covering all fields of science and information in the world, containing the most common terms in the various fields, and also contains geographic names and lists of names, including names of plants, sports and animals.In 2012 YSA had almost 31,000 terms, Of which about 5 700 geographic names. YSA has been used in databases since 1987.",
"homepage": "http://finto.fi/ysa/fi/",
"license": "CC0-1.0",
"name": "Finnish General Thesaurus",
"prefix": "372",
"wikidata_database": "Q5409964"
},
"373": {
"abbreviation": "MUSA",
"description": "Outdated, please, do not use.\n\nThe Finnish Music Thesaurus (MUSA) was one of the language specific vocabularies for music indexing, which complied with the principles and structure of the Finnish General Thesaurus (YSA). The Music Thesaurus was intended for for indexing and information retrieval of books and articles on music, as well as all recorded music (printed music, sound recordings, etc.). Glossary guided content describers and information seekers to use a common language. The compiling of the Music Thesaurus followed the Finnish thesaurus preparation and maintenance instructions (SFS 5471). The Thesaurus included the Swedish language music terms in CILLA which were availabe by swithcinge the language in the user interface.",
"homepage": "http://finto.fi/musa/",
"license": "CC0-1.0",
"name": "Finnish Music Thesaurus",
"prefix": "373"
},
"374": {
"description": "The Anthropological Index Online is an online bibliographic index which catalogues the contents of anthropology journals in The Centre for Anthropology Library at the The British Museum (formerly the Museum of Mankind Library, incorporating the Royal Anthropological Institute Library) which receives periodicals in all branches of anthropology, from academic institutions and publishers around the world. The AIO provides a searchable index to the contents of over 770 journals, published in more than 40 languages. The index staff provide English keywords for all entries so consistent searching is possible. Many of the journals indexed are catalogued only in the AIO so it provides unique access to some of the more obscure anthropology publications.",
"homepage": "https://aio.therai.org.uk/aio.php?action=keywordindex",
"name": "Anthropological Index Online Keywords",
"prefix": "374"
},
"375": {
"description": "Thematic index can be displayed by each of the Tags topic category includes Clicking on key words, you will get a Finnish subject heading, its Swedish and English equivalents, see also -., References and Sciences by subject category See also -.. Reference and the class to continue searching within the thesaurus alphabetical index scroll to display the list of that start with the same letter of the key words Klikaamalla key words, you will get the English word thing, its Swedish and English equivalents, see also -.. and the references to the subject matter of the word class See also -. the reference to the category and to continue searching within the thesaurus",
"homepage": "http://www.eduskunta.fi/kirjasto/EKS/",
"name": "Library of Parliament Thesaurus",
"prefix": "375"
},
"376": {
"description": "Design and communication thesaurus is in Finnish design, communication, and arts and crafts specialty vocabulary. The dictionary contains about 2500 actual key words and almost 400 control term, which control the approved free word use. Index comprises of keywords use, repair and further instructions, and the alphabetical dictionary part and attachments. Design and communication thesaurus is constructed tesaurustyyppinen, that is, it refers to the most common semantic relationships between key words. Design and communication vocabulary for use in books and articles, but also other data types, indexing and search for information, for example. catalogs, databases and bibliographies libraries derived materials. Glossary help Added information and knowledge-seekers to use a common language. glossary is intended for use with VESA-network terminology http://vesa.lib.helsinki.fi/ysa/index.html (a Finnish General siasanasto) in parallel with the design and communication of specific terminology.",
"name": "Design and communication Thesaurus",
"prefix": "376"
},
"377": {
"description": "Abbreviations for this subject word: hand = use the following term, the left column term is not used, instead the right-hand column term is used LT = broader term RT = parallel term ST = narrower term see YSA = see General Finnish keyword KT = The library's cataloging information is usually marked with one or more keyword descriptive content, which can be used to find books on the subject or subject matter to be explored, and library purchases have been listed in HELKA since 1992. Earlier books have been cataloged retrospectively but Since content descriptors are only available in some of the material, a directory card kept in the library is still a useful utility.",
"homepage": "https://blogs.helsinki.fi/teolasiasanasto/",
"name": "Theological Thesaurus",
"prefix": "377"
},
"378": {
"description": "Applied in the court software OpenJustitia.",
"homepage": "http://tds.eurospider.com/TDS/",
"name": "Thesaurus of Swiss Law",
"prefix": "378"
},
"379": {
"description": "Thesaurus for the curricular materials of the biology subjects of the baccalaureate of the Spanish educational system (17-18 years) 462 terms, 320 relations between terms, 52 equivalent terms.",
"homepage": "http://doteine.uc3m.es/tesauros/biologia/",
"name": "Thesaurus of Biology",
"prefix": "379"
},
"38": {
"description": "UKAT is a subject thesaurus which has been created for the archive sector in the United Kingdom. It is a controlled vocabulary which archives can use when indexing their collections and catalogues. UKAT was created between June 2003 and August 2004 from subject terms contributed by individual archives, archive projects and users of archives. The backbone of UKAT is the UNESCO Thesaurus. However, while UNESCO covers a broad range of subject areas, it often lacks the depth of detailed terminology required by archives for indexing. It was therefore decided that UKAT should extend and adapt UNESCO to incorporate indexing terms which repositories and projects had devised themselves or incorporated from other schemes, such as Library of Congress Subject Headings or the British Education Thesaurus. UKAT has thus been created as a thesaurus conforming to international standards, with the coherent structure of UNESCO, but also significantly enhanced to include terms of relevance to the archive community and its users. Particular emphasis has been given to incorporating terms reflecting the histories and experiences of groups which are under-represented among archive users, to encourage their participation in the archival heritage in line with national priorities for the sector.\n\nThe key aims of UKAT are: to improve access to archives by subject; to ensure that users of archives can carry out effective subject searches of the national archives network; and to promote the involvement in archives by groups which are under-represented among archive users, by providing subject terms which reflect their histories and experiences.",
"homepage": "http://www.ukat.org.uk/",
"name": "UK Archival Thesaurus",
"prefix": "38"
},
"380": {
"description": "Although the database will be updated in the future (edited by DeeAnn M. Reeder and Kristofer M. Helgen), it is not, and will not be continuously updated. The names are organized in a hierarchy that includes Order, Suborder, Family, Subfamily, Genus, Species and Subspecies. Records include the following fields: Scientific name, Author's name and year described, Original publication citation, Common name, Type Species, Type Locality, Distribution, Comments, Status, Synonyms. It is hoped that this database on the World Wide Web can be used as a convenient on-line reference for identifying or verifying recognized scientific names and for taxonomic research.",
"homepage": "https://www.departments.bucknell.edu/biology/resources/msw3/",
"prefix": "380",
"wikidata_database": "Q1538807"
},
"381": {
"description": "The current vocabulary has 2890 concepts, of which 274 are 'TopConcepts'. The goal is to provide a general vocabulary foundation to which other, more specialised, vocabularies can be added as needed, and to provide a good 'lingua franca' for the creation of vocabulary mappings.",
"homepage": "http://www.ivoa.net/rdf/Vocabularies/vocabularies-20091007/IVOAT/",
"name": "International Virtual Observatory Alliance Thesaurus",
"prefix": "381"
},
"382": {
"description": "It can be used for indexing information; for searching or retrieving information; and as a translation tool for English, French and Spanish water and sanitation terms. The thesaurus originates from the collaboration of IRC with organisations from the United Kingdom, France, Peru, Jordan, Burkina Faso and Thailand.",
"homepage": "http://www.ircwash.org/thesaurus",
"name": "InterWATER Thesaurus",
"prefix": "382"
},
"383": {
"description": "The Multilingual Thesaurus contains 5823 key terms expressed as descriptors (preferred terms) or non-descriptors (non-preferred terms) in the language versions of the MT. The Multilingual Thesaurus (MT) is compatible with major international and national bibliographic databases and indexing vocabularies. The English (American) version of the MT is compatible with the AGI (American Geological Institute) GeoRef Thesaurus, the French version with the INIST/BRGM (Institute de l'Information Scientifique et Technique/Bureau de Recherches Géologiques et Minières) PASCAL/GEODE Lexique, and the German with the BGR (Bundesanstalt für Geowissenschaften und Rohstoffe) GEOLINE Thesaurus. The other language versions are compatible with national thesauri used in Russia (VSEGEI), Spain (ITGE/GEOMINER), Italy (CNR/GEODOC) and Finland (Geological Survey of Finland/FINGEO). The MT gives the documentary equivalents of major geoscience concepts in the languages included at present. The MT is also an operational tool for the development and management of other national geoscience thesauri in a manner that ensures compatibility with other major geoscience information systems. A most interesting aspect of the MT is the possibility of developing multilingual search facilities, i.e. searches can be performed in any of the languages of the MT, and documents may be retrieved that contain the corresponding term in any of the other languages of the MT. At the Geological Survey of Finland the MT has been already been used to enable such multilingual searches. The Finnish index terms or English index terms used in the databases to describe the content can be linked through the thesaurus function of the TRIP system to the corresponding terms in all languages of the MT making all terms for the same concept synomyms irrespective of the language.",
"homepage": "http://www.sciencedirect.com/science/book/9780080364315",
"name": "Multilingual Thesaurus of Geosciences",
"prefix": "383"
},
"384": {
"description": "The concepts that characterize the DeCS vocabulary are organized in a tree structure allowing a search on broader or narrower terms or on all terms from the same tree within the hierarchical structure. DeCS is a dynamic vocabulary totaling 30,895 descriptors, of which 26,664 come from MeSH, and 4658 are exclusively DeCS. There is an addition of 2051 hierarchic codes from DeCS categories in 1491 MeSH descriptors. The following are the DeCS categories and their total number of descriptors: Health Surveillance (828); Homeopathy (1,944), Public Health (3,491); and Science and Health (219). The sum is greater than the total number of descriptors, since a descriptor may occur more than once in the hierarchy. By being dynamic, it records a permanent process of change including the development of new areas of terminology. With the creation of the national, institutional and thematic VHLs, search strategies were made available in the various topics in order to facilitate the retrieval of the existing literature. DeCS was created to serve as a unique language in indexing articles from scientific journals, books, congress proceedings, technical reports, and other types of materials, as well as for searching and retrieving subjects from scientific literature from information sources available on the Virtual Health Library (VHL) such as LILACS, MEDLINE, and others.",
"homepage": "http://decs.bvs.br/I/homepagei.htm",
"name": "Health Sciences Descriptors",
"prefix": "384",
"wikidata_database": "Q5690673"
},
"385": {
"description": "The CIRRIE Thesaurus is an alphabetical listing of approved terms for searching the CIRRIE Database.",
"homepage": "http://www.naric.com/cirrie_sql/database/thesaurus/",
"name": "Center for International Rehabilitation Research Information and Exchange Thesaurus",
"prefix": "385"
},
"386": {
"description": "The foundation of the database is the original Bioethics Thesaurus, which was developed at the Kennedy Institute of Ethics and was used to index BIOETHICSLINE from 1975-2000. It has been updated extensively, particularly to include new genetics terms for the GenETHX database, and new Islamic ethics terms for the Islamic Medical and Scientific Ethics database. Here you can search the thesaurus terminology as a database to get more detailed information about each term or phrase, review a full list of lead terms and cross references, or choose a letter below to retrieve all the entries beginning with a particular letter of the alphabet.",
"homepage": "http://bioethics.georgetown.edu/databases/bt/",
"name": "Bioethics Thesaurus Database",
"prefix": "386"
},
"387": {
"description": "The ASFA Thesaurus is an indexing and searching tool. It contains the subject descriptors used to index the records which are contained in the Aquatic Sciences and Fisheries Abstracts (ASFA) bibliographic database.",
"homepage": "http://www4.fao.org/asfa/asfa.htm",
"name": "Aquatic Sciences and Fisheries Abstracts Thesaurus",
"prefix": "387"
},
"388": {
"description": "The Alzheimer's disease thesaurus is used for indexing and online searching of materials cited in the ADEAR database.",
"name": "Alzheimer's Disease Thesaurus",
"prefix": "388"
},
"389": {
"description": "The Hierarchical Listing With Definitions contains all subject terms and USE cross references currently approved for use, and displays the full hierarchical structure for each term along with a definition when available. In addition, the listing has been developed to serve as an orthographic authority for upper/lowercase forms of all terms and cross references. The term-added date, displayed for all terms added after April 1988, is also given. The listing includes terms appearing in the NASA Thesaurus, Preliminary Edition (December 1967), the NASA Thesaurus Alphabetical Update (September 1971), the NASA Thesaurus (1982, 1985, 1988, 1994, and 1998 editions), and other terms approved for use through the end of January 2012. Over 18,400 terms, 4,300 definitions, and approximately 4,500 USE references are contained in the Hierarchical Listing With Definitions. The Rotated Term Display is a ready-reference tool that provides thousands of additional 'access points' to the thesaurus terminology. It contains the postable terms and nonpostable terms found in the Hierarchical Listing arranged in a KWIC (key-word-in-context) index. It is a useful companion to the Volume 1 listing, containing approximately 52,000 entries.",
"name": "NASA Thesaurus",
"prefix": "389"
},
"39": {
"description": "The multilingual UNBIS Thesaurus contains the terminology used in subject analysis of documents and other materials relevant to United Nations programmes and activities. It is multidisciplinary in scope, reflecting the Organizationβs wide-ranging concerns. The terms included are meant to reflect accurately, clearly, concisely and with a sufficient degree of specificity, matters of importance and interest to the United Nations. In addition, since the inception of the Thesaurus in 1981, two primary criteria in the selection of descriptors have been: a) consistency with the terminology used by the Organization itself as reflected in its documents; and b) compatibility with terms included in thesauri produced or utilized within the UN System, in order to facilitate exchange of information with other organizations. The organizations of the United Nations System, such as the World Bank, ILO, WHO, FAO, IAEA and Unesco, are lead agencies in their particular areas of activity and their choice of descriptors has been preferred.\n\nIt is used as the subject authority of the United Nations Bibliographic Information System (UNBIS) and has been incorporated as the subject lexicon of the United Nations Official Document System.",
"homepage": "http://metadata.un.org/thesaurus/",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "United Nations Bibliographical Information System Thesaurus",
"prefix": "39"
},
"390": {
"description": "The Feature Type Thesaurus contains a hierarchical scheme of terms for typing gazetteer entries; that is, for typing named geographic places. It is intended for general use for many types of gazetteers and as a shared vocabulary for interoperability among gazetteers. It has been designed to be used with the Alexandria Digital Library (ADL) Gazetteer.",
"name": "Alexandria Digital Library Feature Type Thesaurus",
"prefix": "390"
},
"391": {
"abbreviation": "MeSH",
"description": "MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. MeSH descriptors are arranged in both an alphabetic and a hierarchical structure. At the most general level of the hierarchical structure are very broad headings such as 'Anatomy' or 'Mental Disorders'. More specific headings are found at more narrow levels of the twelve-level hierarchy, such as 'Ankle' and 'Conduct Disorder'. There are 26,142 descriptors in 2011 MeSH. There are also over 177,000 entry terms that assist in finding the most appropriate MeSH Heading, for example, 'Vitamin C' is an entry term to 'Ascorbic Acid'. In addition to these headings, there are more than 199,000 headings called Supplementary Concept Records (formerly Supplementary Chemical Records) within a separate thesaurus. The MeSH thesaurus is used by NLM for indexing articles from 5,400 of the world's leading biomedical journals for the MEDLINEΒ/PubMEDΒ database. It is also used for the NLM-produced database that includes cataloging of books, documents, and audiovisuals acquired by the Library. Each bibliographic reference is associated with a set of MeSH terms that describe the content of the item. Similarly, search queries use MeSH vocabulary to find items on a desired topic.",
"homepage": "http://www.nlm.nih.gov/mesh/",
"name": "Medical Subject Headings",
"prefix": "391",
"wikidata_database": "Q199897"
},
"392": {
"description": "This thesaurus functions as a means for indexing articles, photos, and web pages on some of the basic identifying characteristics of herbs. It is designed for the hobbyist or recreational gardener rather than scientist or medical reference. The preferred terminology is that of a home gardener rather than a herbalists or botanists since they are the targeted end-user. (...) This mini-thesaurus contains preferred terms selected based on common usage, and the cross-references are made from the non-preferred terms. Scope notes have been added where necessary. In the hierarchical display, facets appear in bold text, in the alphabetical display preferred terms appear in bold text. This thesaurus functions as a means for indexing articles, photos, and web pages on some of the basic identifying characteristics of herbs. It is designed for the hobbyist or recreational gardener rather than scientist or medical reference. The preferred terminology is that of a home gardener rather than a herbalists or botanists since they are the targeted end-user.",
"homepage": "https://www.toriorr.com/herb-thesaurus-project",
"name": "Herb Thesaurus",
"prefix": "392"
},
"393": {
"description": "The main aim in producing this reference work is to try to standardise the terminology in the field of astronomy for the purposes of aiding unambiguous library cataloguing and more precise recall of data from computer databases. The thesaurus is intended for use by astronomy librarians and scientists. Its compilation was originally requested during a meeting of Commission 5 (Documentation) of the International Astronomical Union at the New Delhi General Assembly of the IAU in 1984. Vocabulary control has become essential in the use of online databases, particularly where those responsible for data input and for searching databases are nonspecialists. Consistency, particularly in the input to computerised databases, is imperative if there is to be high precision recall in information retrieval. Conversely, for those accessing databases (the output process), the selection of relevant terms or those most specific to the information request, will result in higher precision recall. The thesaurus is also designed to give the librarian, cataloguer or indexer, as well as the astronomer, a context for astronomical terms with which they may not be familiar. It is envisaged that the thesaurus will be used for the following main purposes: 1. Assigning keyterms to scientific papers; this is usually best done by the authors themselves, rather than by non-specialists. If the thesaurus is to serve as originally intended by Commission 5 of the IAU - to standardise the astronomical terminology -, then authors should use only the upper case terms in the thesaurus in their keyterm lists. 2. Extraction of references from databases, when the use of the same list of terms as is used by the authors can be expected to result in high precision recall of relevant data. 3. Assisting in the updating of library classification schemes. 4. It may be included in 'intelligent' databases, to help the user select alternatives or extensions to a searcher's initial list, as in proximity searching. Other uses suggested to us have been as a source of terms for exclusion as passwords for observatory computers and as a supplementary dictionary of words used by a spelling checker for word processors.",
"homepage": "http://www.mso.anu.edu.au/library/thesaurus/",
"name": "The Astronomy Thesaurus",
"prefix": "393"
},
"394": {
"description": "Initial development of the AOD Thesaurus started with collecting terms and term relationships from many sources; search requests received for ETOH and NCADI databases; document titles and index terms; more than 40 special thesauri; and NIAAA's Reports to Congress on Alcohol and Health and other publications. Major sources used for reference and guidance included the World Health Organization's (WHO's) Lexicon of Alcohol and Drug Terms, developed jointly with NIAAA; NLM's Medical Subject HeadingsInternational Classification of Diseases, 9th and 10th Revisions; the DSMβIII and draft DSMβIV; the Thesaurus of Psychological Indexing Terms (PsyclNFO); the Thesaurus of ERIC Descriptors; and the Thesaurus of Sociological Indexing Terms (Sociological Abstracts). The multitude of terms collected from these sources were organized into hierarchies, which revealed many synonyms and near-synonyms. A conceptual analysis process known as semantic factoring further clarified the structure and led to a smaller vocabulary of conceptual building blocks. The resulting structure was thoroughly field-tested through a query formulation and indexing test. Analyzing the results from multiple indexers for important terms missed, different indexers using different terms to express the same idea, terms assigned erroneously, and terms needed but missing from the Thesaurus, the developers identified areas requiring clarification, redundancies between areas, missing cross-references, the need for more or better scope notes, and areas where detail could be reduced. Further refinements were made in the second edition based on indexing and searching experience: Descriptors were added, overly specific descriptors were pruned, the structure was improved, and many scope notes and relationships were added. Thesaurus maintenance for this edition started with identifying key, recent sources in the AOD field, including a wide variety of publications such as NIAAAβs Ninth Report to the U.S. Congress on Alcohol and Health, a number of issues of Alcohol Health & Research World, the Institute of Medicineβs Reducing Risks for Mental Disorders: Frontiers for Preventive Intervention Research, the draft International Classification of Preventive Trials, and of course, the most recent editions of various thesauri: NLMβs Medical Subject Headings, the Thesaurus of Psychological Terms, and the Thesaurus of Sociological Indexing Terms. Terms and term relationships from the preceding publications in addition to many other sources, including the entire Identifier (ID) field from the ETOH database, which is used to assign terms or concepts that are not in the AOD Thesaurus or for terms that are not designated ETOH descriptors. An analysis of the terms in this field helped the thesaurus development team identify missing concepts and thesaurus terms that should be designated ETOH descriptors. NIAAA is committed to the maintenance of the AOD Thesaurus as an ongoing process driven by user feedback. Users are strongly encouraged to comment on any aspect of the thesaurus. The thesaurus presents a structured collection of concepts and terms intended to facilitate indexing and retrieval, support research and program planning through conceptual structure and definitions, and improve communication through standardized terminology. The thesaurus provides guidance to the indexers for request-oriented (or user-centered) indexing. It organizes concepts collected from search requests into an easily grasped hierarchical structure that serves as a framework or checklist in analyzing documents. The logical structure of the Thesaurus communicates user interests to the indexer. Its controlled vocabulary expresses each concept unambiguously through one term, called a descriptor, that is used in indexing and can thus be used with confidence in searching. Synonyms lead to descriptors: polydrug use leads to AA2.6 multiple drug use; chemical abuse, drug abuse, and substance abuse all lead to GC2 AOD abuse; nerve cellneurocyte both lead to and XX2.2 neuron. The thesaurus is also very useful for free-text searching (searching based on words in the title or abstract). An exhaustive free-text search must include all terms that might be used to express the searched-for concept. This requires query term expansion: In synonym expansion, expand the query term XX2.2 neuron by adding the synonyms nerve cell and neurocyte; in hierarchic expansion, add narrower terms, such as XX2.2.2.4 dendrite and XX2.2.2.6 axon (with its synonyms, such as nerve fiber and neurite).",
"homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/AOD/",
"name": "The Alcohol and Other Drugs Thesaurus",
"prefix": "394"
},
"395": {
"description": "The terms in the Joint Thesaurus are listed alphabetically. For each alphabetical entry, a 'word block', containing the terms associated with this particular entry, is displayed. In the word block, terms that have a hierarchical relationship to the entry are identified by the symbols BT for Broader Term, and NT for Narrower Term; a term with an affinitive relationship is identified by RT, for Related Term; terms with a preferential relationship are identified by USE or SEE, and UF for Used For, and SF for Seen For. In case of multiple USE relationships for a forbidden term, all listed descriptors should be used to index or search a given concept. In case of multiple SEE relationships, one or more of the listed descriptors should be considered for indexing or searching this concept. Over the years the INIS/ETDE Thesaurus has evolved as a result of systematic study and it contains over 30 000 terms. Using the Joint Thesaurus as a starting point, INIS, in cooperation with the Member States, has developed INIS Multilingual Thesaurus with navigation capabilities including the full thesaurus hierarchy. It is available in all official languages of the IAEA. It represents a unique multilingual thesaurus in the nuclear field and serves as a major tool for indexing and describing nuclear information and knowledge in a structured form, which assists in multilingual and semantic searches of the INIS Database.",
"name": "INIS Interactive Multilingual Thesaurus",
"prefix": "395"
},
"396": {
"description": "481 terms, 132 relations between terms, 120 non-preferred terms.",
"homepage": "http://www.vocabularyserver.com/animals/",
"name": "Animal Use Alternatives Thesaurus Terminology",
"prefix": "396"
},
"397": {
"description": "The ASGC provides seven hierarchies of geographical areas. Each structure is designed to suit different statistical purposes. This edition has four current structures. The Main Structure and the Statistical Region Structure cover the whole of Australia. The Local Government Area Structure and the Statistical District Structure cover only part of Australia. The three remaining structures, Urban Centres and Localities, Section of State and Remoteness Structures, have not been included as Census Collection Districts are no longer defined. These structures are now defined in the new Australian Statistical Geography Standard (ASGS). The ASGS has been released concurrently with the ASGC to ensure a smooth transition to the new statistical geography. The ASGS and the ASGC will both be current for 2011 however, from 1 July 2012 the ASGS will replace the ASGC. The ASGS brings all the regions for which the ABS publishes statistics within the one framework and will be used by the ABS for the collection and dissemination of geographically classified statistics progressively from 1 July 2011. The ASGS is a more comprehensive, flexible and consistent way of defining Australia's statistical geography.",
"homepage": "http://www.abs.gov.au/websitedbs/D3310114.nsf/home/Australian+Standard+Geographical+Classification+%28ASGC%29",
"license": "CC-BY-3.0",
"name": "Australian Standard Geographical Classification",
"prefix": "397"
},
"398": {
"description": "Here are mineral lists (IMA approved mineral names and varieties names) sorted either alphabetically or arranged systematically. As every science, mineralogy is changing: new analysis often modify formulas and other datas; new minerals are discovered; others are discredited. So, consider these lists as dynamic and subject to change and error. Comments, corrections and additions are welcome. It follows Strunz classification schemes (Mineralogical Tables, VIIIth edition) and has been modified according to the systematic numbers published in the 'Lapis Mineralienverzeichnis'. It shows similarities well enough, especially when completed with space group, density, etc.",
"homepage": "http://athena.unige.ch/athena/mineral/min_lists.html",
"name": "Mineral Lists",
"prefix": "398"
},
"399": {
"description": "Organisms are classified in a hierarchical tree structure. Our taxonomy database contains every node (taxon) of the tree. UniProtKB taxonomy data is manually curated: next to manually verified organism names, we provide a selection of external links, organism strains and viral host information.",
"homepage": "http://www.uniprot.org/taxonomy/",
"prefix": "399"
},
"40": {
"description": "The UNESCO Thesaurus is a controlled and structured list of concepts used in subject analysis and retrieval of documents and publications in the fields of education, culture, natural sciences, social and human sciences, communication and information. Continuously enriched and updated, its multidisciplinary terminology reflects the evolution of UNESCO's programmes and activities. The first edition of the Thesaurus was released in English in 1977, with French and Spanish translations in 1983 and 1984. The second revised and restructured version was released in 1995. Today the Thesaurus is available in English, French, Russian and Spanish. Concepts are grouped into 7 broad subject areas which are broken down into microthesauri. The UNESCO Thesaurus is compliant with the ISO 25964 standard.",
"homepage": "http://vocabularies.unesco.org/browser/thesaurus/en/",
"license": "CC BY-SA 3.0",
"name": "UNESCO Thesaurus",
"prefix": "40",
"wikidata_database": "Q2467479"
},
"400": {
"description": "The Tree of Life Web Project is a collection of information about biodiversity compiled collaboratively by hundreds of expert and amateur contributors. Its goal is to contain a page with pictures, text, and other information for every species and for each group of organisms, living or extinct. Connections between Tree of Life web pages follow phylogenetic branching patterns between groups of organisms, so visitors can browse the hierarchy of life and learn about phylogeny and evolution as well as the characteristics of individual groups.",
"homepage": "http://tolweb.org/tree/phylogeny.html",
"prefix": "400",
"wikidata_database": "Q2300489"
},
"401": {
"description": "TRANSFACΒ provides data on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. 5 superclasses, 33 classes, 76 families, 91 subfamilies.",
"homepage": "http://www.gene-regulation.com/pub/databases/transfac/clSM.html",
"name": "Transcription Factor Classification",
"prefix": "401"
},
"402": {
"description": "This table provides a classification of HTTP-based APIs. The classification achieves an explicit differentiation between the various kinds of uses of HTTP and provides a foundation to analyse and describe the system properties induced. Providing distinct names for the API 'styles' overcomes the useless situation where APIs are named 'RESTful' and 'not so RESTful','almost RESTful', or 'unRESTful'. An API either adheres to REST's interface constraints or it does not and if it does not, there is no sense in referring to 'REST' in the API's name. Especially so because mentioning REST might cause the false impression that the achieved system would share the same system properties as RESTful systems. They do not - and it is important to understand that the system being designed might not have the expected properties. For example, caching and visibility can be ruined by tunneling operations though action names in URIs.\n\nThe most important distinction to be made today is the one between the two HTTP-based API kinds HTTP-based Type I and HTTP-based Type II on the one hand and REST on the other hand. The former two, while not RESTful due to their violation of the hypermdia constraint, can be a reasonable design choice if the tight coupling they induce is acceptable for the given system. This might be the case if the expected life time of the system does not warrant the considerable work of designing a proper media type. However, it must be explicitly understood that both API kinds, 'HTTP-based Type I' and 'HTTP-based Type II' lead to systems in which clients and servers are coupled by their original design and that the evolvability properties of RESTful systems are in no way induced.",
"homepage": "https://web.archive.org/web/20110824015753/http://www.nordsc.com/ext/classification_of_http_based_apis.html",
"license": "CC BY-NC 3.0",
"name": "Classification of HTTP-based APIs",
"prefix": "402"
},
"403": {
"description": "A substance is dangerous goods when (a) it is listed by name in Schedule 1 and is in any form, state or concentration that meets the criteria in this Part for inclusion in at least one of the 9 classes of dangerous goods; or (b) it is not listed by name in Schedule 1 but meets the criteria in this Part for inclusion in at least one of the 9 classes of dangerous goods.",
"homepage": "http://www.tc.gc.ca/eng/tdg/clear-part2-339.htm",
"name": "Transportation of Dangerous Goods Regulations Classification",
"prefix": "403"
},
"404": {
"description": "This website contains (or will contain) a wealth of information on the various families of the Pentatomoidea (especially the Pentatomidae), and even some information that will be of general interest to Heteropterists. More information on each of these families is presented within the Systematics section of this website.",
"homepage": "http://www.ndsu.nodak.edu/ndsu/rider/Pentatomoidea/Classification/classification.htm",
"name": "Pentatomoidea Classification",
"prefix": "404"
},
"405": {
"description": "The Industry Classification Benchmark (ICB) is a definitive system categorizing over 70,000 companies and 75,000 securities worldwide, enabling the comparison of companies across four levels of classification and national boundaries. The ICB system is supported by the ICB Database, an unrivalled data source for global sector analysis, which is maintained by FTSE Group. 10 industries, 19 supersectors, 41 sectors, 114 subsectors.",
"homepage": "http://www.icbenchmark.com/",
"name": "Industry Classification Benchmark",
"prefix": "405",
"wikidata_database": "Q1317652"
},
"406": {
"description": "The European Socio-economic Classification (ESeC) is an occupationally based classification but has rules to provide coverage of the whole adult population. The information required to create ESeC is:\n\n* occupation coded to the minor groups (i.e. 3-digit groups) of the International Standard Classification of Occupations 1988 (ISCO88 (COM))\n\n* details of employment status, i.e. whether an employer, self-employed or employee;\n\n* number of employees at the workplace\n\n* whether a worker is a supervisor.",
"homepage": "https://www.iser.essex.ac.uk/archives/esec",
"name": "European Socio-economic Classification",
"prefix": "406"
},
"407": {
"description": "The ICNPΒ is a unified nursing language system. It is a compositional terminology for nursing practice that facilitates the development of and the cross-mapping among local terms and existing terminologies.",
"homepage": "http://www.icn.ch/what-we-do/international-classification-for-nursing-practice-icnpr/",
"name": "International Classification for Nursing Practice",
"prefix": "407",
"wikidata_database": "Q1666418"
},
"408": {
"description": "This classification is hierarchical and you must decide how detailed you want to make your diagnosis. This can range from the first-digit level to the fourth. First one gets a rough idea about which group the patient belongs to. Is it for example 1. Migraine or 2. Tension-type headache or 3. Cluster headache and other trigeminal autonomic cephalalgias? Then one obtains information allowing a more detailed diagnosis. The desired detail depends on the purpose. In general practice only the first- or second-digit diagnoses are usually applied whilst in specialist practice and headache centres a diagnosis at the third- or fourth-digit levels is appropriate.",
"homepage": "http://ihs-classification.org/",
"name": "International Classification of Headache Disorders",
"prefix": "408",
"wikidata_database": "Q2976581"
},
"409": {
"description": "1072 terms, 148 relations between terms, 223 non-preferred terms.",
"homepage": "http://vocabularyserver.com/parasitology/",
"name": "Thesaurus of Parasitology",
"prefix": "409"
},
"41": {
"description": "Purpose: The USAID Thesaurus is a tool for the indexing and retrieval of technical and project document information processed by the Development Experience Clearinghouse (DEC) of the U.S. Agency for International Development. [...]\"\n\n\"Subject Coverage: The USAID Thesaurus is multidisciplinary in scope. Subjects like agriculture, communications, culture, demography, economics, education, energy, government and law, health, housing, industry, labor, management, natural resources, science and technology, sociology and psychology, trade, and transportation are all covered. [...].",
"homepage": "https://data.usaid.gov/Information-and-Communications-Technology-Services/USAID-Thesaurus/abaj-3t2b",
"license": "http://rightsstatements.org/vocab/InC/1.0",
"name": "U.S. Agency for International Development Thesaurus",
"prefix": "41"
},
"410": {
"description": "EMWIS is an initiative of the Euro-Mediterranean Partnership. It provides a strategic tool for exchanging information and knowledge in the water sector between and within the Euro Mediterranean partnership countries. All the countries involved in the Euro-Mediterranean Partnership are concerned: The 27 EU member states; The 10 Mediterranean Partner Countries (Algeria, Egypt, Israel, Jordan, Lebanon, Morocco, Palestine, Syria, Tunisia and Turkey). At the conference of the Euro-Med Water Directors (Rome, Nov. 2005), it was decided to open EMWIS to the Mediterranean countries not signatories of the Barcelona Declaration, i.e. Balkan countries and Libya.",
"homepage": "https://web.archive.org/web/20170309070207/http://www.semide.net/portal_thesaurus/",
"name": "SEMIDE Thesaurus",
"prefix": "410"
},
"412": {
"description": "The Health Canada Controlled Subject Vocabulary was developed to provide subject access to Health Canada's information resources. The Controlled Vocabulary is a bilingual, structured, indexing and information retrieval tool for both publishers and users of the documents and information published on the Health Canada Web site. The terms listed in the controlled vocabulary are used in the Dublin Core metadata record for the SUBJECT element, where appropriate and feasible, in order to provide accurate and comprehensive results when searching the Health Canada Web site. The Health Canada Controlled Subject Vocabulary ('gchccv') has been registered with Library and Archives Canada for this purpose. The scope of the Controlled Vocabulary is dynamic and reflects subjects that have been addressed at one time or another in Health Canada sources. Terms were selected from the Government of Canada's Core Subject thesaurus and various Health Canada products, including publications, databases and related sources. The following types of concepts have been excluded from the Controlled Vocabulary: geographical names, titles (e.g., of programs), proper names (e.g., of companies) and acronyms, except where they are in common usage. The Controlled Vocabulary is a set of preferred terms that can be used to catalogue documents. It standardizes the words associated with a given subject matter, allowing for more precise searches and preventing ambiguous database indexing.",
"homepage": "http://www.hc-sc.gc.ca/home-accueil/search-recherche/hccv-vcsc-intro-eng.php",
"name": "Health Canada Controlled Subject Vocabulary",
"prefix": "412"
},
"413": {
"description": "The indexing terms listed in the thesaurus are those found in the RCDC Bibliographic Data Base and therefore are the terms used to generate the keyword index in this volume. The keywords are arranged alphabetically. Numbers, dashes, parentheses and super- and sub-scripts are ignored in ordering the terms except when required to distinguish two terms. Thus, '1-propanol' precedes '2-propanol' (following 'propane') and 'H2O+' precedes 'H2O-' and 'H2O2+' (all three precede 'hole'). Arrangement is word by word, thus 'hole traps' precedes 'holes'. The name of any element may be used as a keyword, but the names have been omitted from the listing. In addition, the following terms may be used: 1. 'element name' followed by a one- to three-digit number, specifying a nuclide, e.g. cobalt-60. 2. 'element name' followed by 'ions', e.g. vanadium ions. 3. 'element name' followed by 'compounds', e.g. nickel compounds. 4. 'element name' followed by 'atoms', e.g., oxygen atoms. None of the terms represented by 1 through 4 appear in the thesaurus with the exception of several in group 3 for which narrower terms have neen designated as keywords. Another exception occurs in the indexing of halogen, nitrogen and sulfur compounds; element symbols rather than element names have been used (Br, Cl, F, I, N, S) and the keywords appear as Br compounds, organic and Br compounds, inorganic, etc. Keywords which are the names of specific compounds or classes of compounds are used to define the primary subject of the investigation (or reactant). Products are indexed only by terms such as 'hydrogen formation', 'alkane formation', etc. The addition of -a or -s to a chemical name indicates that the compound was used as an additive or solvent, respectively. Thus, the keyword index may contain 'ethanol-s' as well as 'ethanol'. Each keyword entry contains a listing of broader (BT), narrower (NT) and related (RT) terms, as well as synonyms (see the USE and USED FOR (UF) terms). The narrower terms are always used when applicable, so to find all information on a particular keyword the narrower terms should also be consulted. This thesaurus was developed as a guide for the indexer and has been published to aid the users of the information services provided by the Radiation Chemistry Data Center.",
"homepage": "http://kinetics.nist.gov/solution/",
"name": "Radiation Chemistry Data Center Thesaurus",
"prefix": "413"
},
"414": {
"description": "The USGS Thesaurus is the principal controlled vocabulary supporting Science Topics. It is designed as a formal thesaurus conforming to ANSI/NISO Z39.19, with rigid adherence to the hierarchical (BT, NT) term relationships, generic non-hierarchical (RT) relationships, and lead-in term relationships linking non-preferred terms to descriptors either singly (UF) or in a compound USE-WITH relationship. The thesaurus is faceted, meaning its top terms delineate general aspects of information resources: Sciences: Major educational fields, fields of study, and professional groupings within USGS. Methods: Techniques, methods, procedures, or strategies for research, management, collection, or analysis of scientific information in USGS Topics: Themes, subjects, and concerns for which USGS information resources are relevant Product types: General representation of the information in a resource, such as a map or data set Time periods: Geologic time periods and seasons of the year USGS: Activities, processes, and organizational concepts relevant to USGS itself The thesaurus is limited in depth and specificity of coverage. It does not attempt to replicate existing controlled vocabularies such as GeoRef. The intention is to provide sufficient contextual cues for the information seeker to determine the relevance of a resource for his or her concern, not to locate precisely the answer to a specific user question. Each information resource in the Science Topics catalog is categorized using several index terms. Consequently a document will be listed under each category for which it would be considered a relevant resource. Approximately 1200 web resources are listed in the catalog.",
"homepage": "https://www2.usgs.gov/science/about/",
"name": "U.S. Geological Survey Thesaurus",
"prefix": "414"
},
"415": {
"description": "Comprehensive and polyhierarchically structured, Emtree provides a consistent description of all biomedical terminology, allowing unrivaled drug and disease indexing. Over 56,000 preferred terms (of which more than 27,000 are drugs and chemicals) - more than twice as large as MeSH; More than 230,000 synonyms (with over 144,000 drugs and chemical synonyms); 7,500 explosion terms (terms that define the hierarchical structure); 78 subheadings (64 drug subheadings and 14 disease subheadings); 20,300 links to CAS registry numbers; All MeSH terms; Easy to search: each term has on average more than four synonyms, enabling easy mapping of your search terms; Comprehensive drug searching: Emtree includes chemical names, trade names, and laboratory/research codes as well as generic names; Up-to-date: the latest drugs, diseases, organisms and procedures are indexed as candidate terms throughout the year, and the most frequently used terms are added annually to Emtree. This means you can search using even the newest terms; Explosion (tree) searching: facilitated by Emtree's extensive hierarchical structure, with up to 12 levels, you can broaden and narrow your search; Polyhierarchical structure: no need to know 'where' terms are located in the Emtree structure, the Emtree tool will guide you; Natural language terminology: no need to know 'how' terms are defined in Emtree, just use natural language; Inclusive terminology: includes all MeSH terms and many Enzyme Commission (EC) numbers, so you can search using these terms as well.",
"name": "Emtree",
"prefix": "415"
},
"417": {
"description": "The Thesaurus contains scope notes and cross references that explain the indexing system with its use of broad, narrow, and related subject terms. The Tall Timbers Fire Ecology Thesaurus is the tool created by the library for indexing database records. A list of words or phrases (i.e., keywords) that are used to describe topics covered by citations listed in the Tall Timbers Fire Ecology Database.",
"homepage": "http://www.talltimbers.org/images/fedb/FEDB-thesaurus.pdf",
"name": "E.V. Komarek Fire Ecology Thesaurus",
"prefix": "417"
},
"418": {
"description": "The State Disability Observatory (OED) has developed the first Thesaurus of Disability in the Spanish language, a tool that is constructed from terms extracted from natural language, related to some discipline of knowledge and interrelated to define the context As a documentary language, a thesaurus chooses a single term for each concept, defining its form, its use, its context, its relations and conferring to the other terms the property of no 1420 terms, 644 relationships between terms, 446 equivalent terms This thesaurus, developed by the OED technical team, has a systematic and alphabetic presentation and is born with the objective To offer, as a pioneer in its field, a reference, nonexistent at present, for any information management service In the field of disability.",
"homepage": "http://tesauro.observatoriodeladiscapacidad.es/",
"name": "Thesaurus of Disability",
"prefix": "418"
},
"419": {
"description": "6828 terms, 5571 equivalent terms.",
"homepage": "http://webserv.fq.edu.uy/tematres/",
"name": "Medicinal Plant Thesaurus",
"prefix": "419"
},
"42": {
"description": "A collection of Utah-specific independent controlled vocabulary terms divided into discrete, mutually exclusive facets (i.e. node labels) with smaller controlled vocabularies. Each facet has 'labels' organized into sub-hierarchies. 10320 terms, 1736 relations between terms, 4849 non-preferred terms.",
"homepage": "https://vocabularyserver.com/utahtaxonomy/",
"name": "Utah Taxonomy",
"prefix": "42"
},
"420": {
"description": "1954 terms, 1534 relations between terms, 989 equivalent terms.",
"homepage": "http://translaworks.com/tematres/",
"name": "Multilingual synoptic thesaurus of affections of the soft tissues of the oral cavity",
"prefix": "420"
},
"421": {
"description": "The Thesaurus provides a broad multidisciplinary subject term vocabulary that aids in information search and retrieval. Subject terms, called Descriptors, are organized into hierarchies, where series of narrower terms are linked to broader terms. After performing a Thesaurus search, a user can insert a Descriptor directly into the Technical Reports Guided Search page. 16463 terms, 8598 relations between terms, 2278 non-preferred terms.",
"name": "Defense Technical Information Center Thesaurus",
"prefix": "421"
},
"423": {
"description": "This thesaurus consists of 1079 descriptors organized by preferential, non-preferential, generic and specific terms. The documentalists who index the documents referenced in NosoBase use the NosoBase thesaurus to fill in the word (s).",
"homepage": "http://nosobase.chu-lyon.fr/Base/thesaurus.html",
"name": "NosoBase Thesaurus",
"prefix": "423"
},
"424": {
"description": "Generic terms (Higher Terms) associated with specific keywords are indicated by the use of the abbreviation 'h.t.'. This means that whenever the specific term appears in the file, the corresponding Higher Term(s) will also appear and can be searched instead of the specific keyword if a broader search is desired. The abbreviation 's.a.' (see also) is used to indicate a related term which may also be worth considering in a search. Some terms have been altered since the start of the database and this is indicated by the use of the word 'was'. This Thesaurus is designed to facilitate searching of the Derwent Biotechnology Abstracts online database. The Thesaurus is intended to guide the searcher in the selection of correct search terms.",
"homepage": "http://ip-science.thomsonreuters.com/m/pdfs/mgr/bio_thes.pdf",
"name": "Derwent Biotechnology Abstracts Thesaurus",
"prefix": "424"
},
"425": {
"description": "The Thesaurus contains all searchable keywords except the newest drug names and novel concepts that have arisen since publication. The Thesaurus is laid out in two columns; the left column contains the look-up term and the right column either contains the higher terms of a keyword, the generic name of a proprietary drug name, or refers the seacher to the correct term or alternative terms to use. Higher terms associated with specific keywords are indicated by the abbreviation h.t. and are found in the right column of the Thesaurus. Whenever the specific keyword appears in the database, the corresponding higher terms also appear and can be searched instead of the specific term if a broader search is required. The abbreviation βs.a.β (see also) is used to indicate a related term which may be worth considering in a search. This Thesaurus is designed to facilitate searching of the Derwent Drug File. The aim of the Thesaurus is to guide the searcher in the selection of correct search terms.",
"name": "Derwent Drug File Thesaurus",
"prefix": "425"
},
"426": {
"description": "The thesaurus includes preferred terms, non-preferred terms, related terms and scope notes where available. The Australian Emergency Management Terms Thesaurus provides a list of terms commonly used across the emergency management sector. The thesaurus includes terms likely to be used by the sector, but not those relating to specific areas of particular emergency services.",
"homepage": "https://www.aidr.org.au/media/1499/manual-4-australian-emergency-management-thesaurus.pdf",
"name": "Australian Emergency Management Terms Thesaurus",
"prefix": "426"
},
"427": {
"homepage": "http://finto.fi/afo/fi/",
"license": "CC-BY-3.0",
"name": "AFO - Natural resource and environment ontology",
"prefix": "427"
},
"428": {
"description": "256 terms. The support of transnational sustainable flood risk management will be carried out by the community acting over a web-based communication site, which will provide substantial information and an integrated multilingual thesaurus for the partners and decision makers.",
"homepage": "http://www.ceframe.eu/thesaurus/",
"name": "Central European Flood Risk Assessment and Management in Centrope Thesaurus",
"prefix": "428"
},
"429": {
"description": "It facilitates searching and retrieving information by linking similar documents and on-line resources with unique terms. It standardizes descriptions, and so assists in efforts to make information interoperable. Because most terms are taken from official Convention documents, UNEP's ENVOC, and FAOβs AGROVOC, the translation of these terms is facilitated. The CBD Controlled Vocabulary was developed in 2003 with the intent to establish a list of terms to be used as descriptors (i.e. metadata) for CBD documents and web pages.",
"homepage": "http://www.cbd.int/doc/lists/cbd-voc.pdf",
"name": "Convention on Biological Diversity Controlled Vocabulary",
"prefix": "429"
},
"43": {
"description": "In general, the Unesco Thesaurus is taken as a guide, and when it has been necessary, some of its relations (alternatives of synonyms and of the relation UP or USE) have been modified or those of other thesauri have been incorporated. Extracted from other thesauri or reference works, and which have not been integrated with those of the Unesco Thesaurus, only the source has been annotated.The terms that are joined by the asterisk for example History * Argentina must be interpreted as Argentine history. Descriptors with the note 'Not used by this Library' or 'Not used by this Library' are listed in order to present the relationships with other terms that are used 3865 terms, 3884 relations between terms, 400 equivalent terms This list (under construction) contains the indexing terms used by this Library from 1992 to the present and their corresponding relationships.",
"homepage": "http://intranetsid.uncu.edu.ar/ffyl/macro/vocab/index.php",
"name": "Controlled Vocabulary of the Library of the Faculty of Philosophy and Letters (UNCUYO)",
"prefix": "43"
},
"430": {
"abbreviation": "GND",
"description": "GND is a standard file for people, bodies, conferences, geographics, subject - matter and work titles, mainly for the cataloging of literature in libraries, but increasingly also for archives, museums, projects and web applications Is co-operated by the Deutsche Nationalbibliothek, all German-speaking library associations, the Zeitungsdatenatenbank (ZDB) and numerous other institutions. The GND is either co-organized or by direct agreement with the Deutsche Nationalbibliothek.\n\nThe OGND provides access to the GND (common standard file), in which the previous standard file names (PND), slogan standard file (SWD) and common corporate file (GKD) as well as the single unit title file of the Deutsches Musikarchiv were merged into a common standard file (GND). The OGND is updated online from the GND of the cataloging database of the SΓΌdwestdeutschen Bibliotheksverbundes (SWB). The objective of the GND project, which has been running for several years, has been a standard file, which includes all types of entities, as a common, clear reference system for libraries' bibliographic data, as well as data for other standard data users such as archives, museums, projects and scientific and cultural institutions.",
"homepage": "http://www.dnb.de/gnd",
"license": "CC0-1.0",
"name": "Integrated Authority File",
"pattern": "^[0-9X]+(-[0-9X])?$",
"prefix": "430",
"wikidata_database": "Q36578"
},
"431": {
"description": "To facilitate its use, the thesaurus is presented in three parts: A multilingual main part on AIDS and HIV infection A multilingual geographical part describing the countries and major regions of the world A monolingual part containing the annexes of Belgium, Spain, France, the Netherlands, Portugal and Switzerland The thesaurus is presented in each language version in the following forms: Main part on AIDS and HIV infection: structured alphabetical list (In the language of the language version with indication of the terms in the other languages), hierarchical list by microthesaurus (in the language version of the language version), lexical exchange (in the language of the linguistic version) Geographical part: structured alphabetical list (In the language of the linguistic version with indication of the terms in the other languages), hierarchical list by microthesaurus (in the language of the verse Linguistic ion) Annexes country: structured alphabetical list (in the language or languages ββof the country); Hierarchical list by microthesaurus (in the language or languages ββof the country). The main users of the thesaurus are database managers, librarians and documentalists, researchers, teachers, students, social workers, stakeholders, and anyone seeking information on AIDS and HIV / Infection.",
"homepage": "http://dossierdoc.typepad.com/descripteurs/2005/09/thsaurus_multil.html",
"name": "European multilingual thesaurus on AIDS and HIV infection",
"prefix": "431"
},
"432": {
"description": "The HIV / AIDS Treatment Thesaurus is presented in alphabetical order, which combines in a single alphabetical list descriptors and non-descriptors accompanied by semantic links, as designated by the EA (English equivalent), EM (Employ), EP (employee for), TG (generic term), TS (specific term) and TA (associate term) Sometimes an explanatory note (BN) is used to specify the use of a given term, To refer the user to the European multilingual thesaurus on AIDS and HIV infection. Thesauri have traditionally been used in library catalogs and indexes, but they can also be used or adapted for others Thesaurus is used to standardize the storage and retrieval of information during indexing and, To search databases or filing systems. The HIV / AIDS Treatment Thesaurus can serve as an information management model for service organizations and other AIDS community groups that are exploring the possibilities of new information technologies.",
"homepage": "http://www.catie.ca/pdf/Thesaurus/french_thesaurus.pdf",
"prefix": "432"
},
"433": {
"description": "549 terms.",
"homepage": "http://vocabularyserver.com/music/",
"name": "MusicMoz Music Styles",
"prefix": "433"
},
"434": {
"description": "506 terms.",
"homepage": "http://vocabularyserver.com/instruments/",
"name": "Instruments Tree",
"prefix": "434"
},
"435": {
"description": "The thesaurus contains terms, as used in the text publications and geological maps of the Federal Institution, all of which have their own http web addresses, which can be used as hyperlinks for online texts, in web applications, or as attributes for geodata Single term can also have several alternative names, and is defined in its meaning (semantics) by superior, subordinate, and related terms.\n\nIn terms of content, the thesaurus is supervised by a dedicated editorial team, with expert experts on various topics. The existing subject areas are continually being expanded, and are also available in German as well as in English.\n\nThe terms of the thesaurus are published on the web machine-readable (XML, RDF, SKOS) and linked to other terms published in the web (Wikipedia, GeoSciML, Freebase). The thesaurus can be freely used and corresponds to the standards of the Semantic Web or LinkedOpenData. For web programmers, there are also SparQL endpoints and a REST interface to the thesaurus.\n\nWith the creation of semantic and technically interoperable geodata, the Geologische Bundesanstalt implements the legal obligations of the EU Directive 2007/2 / EC INSPIRE or the GeoData Infrastructure Act 2010 GeoDIG. Thesaurus data are attributed to thesaurus terms, while the thesaurus is linked to INSPIRE terminology and other internationally standardized vocabularies.",
"homepage": "http://resource.geolba.ac.at/",
"name": "Geological Federal Institution Thesaurus",
"prefix": "435"
},
"436": {
"description": "The DEH thesaurus is broadly based on a subset of the Thesaurus of Environmental Protection Terms, Department of Environmental Protection, WA, 1995. Over the years, current specific Commonwealth terminology has been incorporated into the thesaurus. The Department of the Environment and Heritage thesaurus is used to provide access to DEH web resources.",
"homepage": "http://www.environment.gov.au/",
"license": "CC-BY-3.0",
"name": "Department of the Environment and Heritage Thesaurus",
"prefix": "436"
},
"437": {
"description": "The 'UAG Thesaurus' is based on TEMATRES, which is free software for thesaurus management and on the academic structure of the UAG, since it is considered to be the academic areas and their various faculties, schools, departments, academic degrees and Materials that request and generate information resources with which the collections of the Library Network are developed, and that these in turn are the basis for teaching, learning and research in the various educational programs of the UAG. The above is the documentary wealth of libraries, which is one of the indicators of the educational quality of the UAG. This tool is intended to consolidate a system of organization and retrieval of information from the origin of the discipline or Specific UAG school to the end user. Also some parts of the UAG structure, especially its departments are addressed by a code, to the dis Cipline and subdiscipline of the UNESCO International Nomenclature for Science and Technology, in order to recover various types of information stored in the UNIVERSIA library that is classified on the basis of this nomenclature. To have a terminological control instrument that works as a tool to index general documents, based on the academic-scientific structure of the UAG. The thesaurus also allows you to concentrate meaningful keywords for a community, through which a vocabulary of controlled terms is organized, which later serve to classify, organize and retrieve information.",
"homepage": "http://tesauro.uag.mx/tematres/",
"name": "Thesaurus of the Autonomous University of Guadalajara",
"prefix": "437"
},
"438": {
"description": "The Finnish maritime libraries have together created the maritime thesaurus. This is the first Finnish maritime thesaurus, and it is on the network freely available to everyone. The thesaurus is based on the STCW Code themes (Standard of Training, Certification and Watchkeeping). If the word is Swedish or English counterparts, they are also given terminology. due to the internationality of English terms is broad and not all of the words have equivalents in Finnish. the shipping industry is commonly used in a variety of abbreviations. They are given in full without the Finnish-language expression but the original language equivalents. If a foreign language your keyword missing Finnish counterpart, the term has been added to the list only in Swedish or English. The thesaurus is not designed as a full word terms in the field of book v Publications of indexing tool. Therefore, the details of the desired avoided, and the vocabulary is limited. In practice maritime professionals use slang words more often than actual terms. As a result, the list of words is being completed with the maritime slang. Terminology, slang word for each item is placed on clarification of the nature of the word.",
"homepage": "http://merisanasto.kyamk.fi/",
"prefix": "438"
},
"439": {
"description": "2994 terms, 249 relationships between terms, 916 equivalent terms.",
"homepage": "http://www.vocabularyserver.com/tesamat/",
"name": "Thesaurus of Mathematical Sciences",
"prefix": "439"
},
"44": {
"description": "6101 terms, 1641 relations between terms, 709 equivalent terms.",
"homepage": "http://www.vocabularyserver.com/filo/",
"name": "Vocabulary of the Central Library of the FFyL",
"prefix": "44"
},
"440": {
"description": "T-REX is a classification and thesaurus of information science at the same time, which has two possibilities: 1. Search for a classification, 2. Browse the top-down classification. In addition to the concepts belonging to the central area of ββ'information science' itself, there are 'auxiliary sciences' and 'post-biodiversities'. 'Aid sciences' Are those whose results are needed directly for the development of information systems that explicitly work on information systems and in which information scientists can collaborate (eg information linguistics and information technology).",
"homepage": "http://server02.is.uni-sb.de/trex/",
"name": "Terminosaurus Rex",
"prefix": "440"
},
"441": {
"description": "You can browse this alphabetical list of Subject headings or you can select a letter to jump to a specific portion of the list.",
"homepage": "http://cedb.asce.org/CEDBsearch/",
"name": "Civil Engineering Database Subject Headings",
"prefix": "441"
},
"442": {
"description": "This thesaurus consists of a list of 'preferred terms' and 'non-preferred terms' each with an indication of the keyword(s) to be used in indexing. It will also show relations between terms: 'broader terms' (BTs), 'narrower terms' (NTs) and 'related terms' (RTs). Many terms will include 'scope notes' (SNs) clarifying their intended use (the subject areas that they cover). Below is a list of the different types of entries that appear in the thesaurus: SC 'subject category' - broad subject area (processes, materials, applications, etc.) SN 'scope note' - explaining the meaning of a term USE points from non-preferred term to preferred term UF 'used for' - the opposite of USE UA 'use and' - for cases where a concept is expressed by two keywords used together UFA 'used for' - the opposite of UA NT 'narrower term' - the opposite of BT BT 'broader term' - generic-specific, part-whole, etc. RT 'related term' - similar terms, terms in same subject area, opposites HIS 'history' - date added, term(s) used before that date. The purpose of a thesaurus, in information retrieval, is to make it easier to retrieve a maximum number of items that are relevant to your enquiry, and a minimum number of items that are not relevant to your enquiry: to give you more of what you want, and less of what you don't want.",
"homepage": "http://www.iiwelding.org/WorkingUnits/Commission_VI/Commission_VI_WG1/Pages/Thesaurus.aspx",
"name": "The International Welding Thesaurus",
"prefix": "442"
},
"443": {
"abbreviation": "NSogg",
"description": "Nuovo soggettario, edited by the National Central Library of Florence (Biblioteca nazionale centrale di Firenze), is a subject indexing tool for various types of information resources. It has been developed in compliance with the International Federation of Library Associations and Institutions (IFLA) recommendations and other international standards in the field of subject indexing. This tool has been created for general and specialized Italian libraries, especially those participating in the National Library Service (SBN), and for museums, multimedia libraries, archives and documentation centres. The Nuovo soggettario system has been used by the Italian National Bibliography (Bibliografia Nazionale Italiana, BNI) since 2007, and is in continual evolution.",
"homepage": "http://thes.bncf.firenze.sbn.it/novita.php?menuR=2&menuS=2",
"license": "CC-BY-3.0",
"name": "BNCF Thesaurus",
"prefix": "443",
"wikidata_database": "Q16583225"
},
"444": {
"description": "Includes about 1,000 descriptors plus. 300 geographical terms, 800 synonyms. The terminology Subjects 'information sciences' and their peripheral regions is structured and hierarchically compiled alphabetically with broader and narrower terms and related terms and combined in this thesaurus. The INFODATA- Thesaurus serves as a tool for the content development of all relevant specialist information and its retrieval by means of different search strategies. A search in the full-text database INFODATA-eDepot is possible directly via the individual descriptors.",
"homepage": "http://www.infodata-edepot.de/thesaurus/START.HTM",
"name": "INFODATA-Thesaurus",
"prefix": "444",
"wikidata_database": "Q1654169"
},
"445": {
"abbreviation": "ICD-O",
"description": "Used principally in tumour or cancer registries for coding the site (topography) and the histology (morphology) of neoplasms, usually obtained from a pathology report.\n\nA multi-axial classification of the site, morphology, behaviour, and grading of neoplasms. The topography axis uses the ICD-10 classification of malignant neoplasms (except those categories which relate to secondary neoplasms and to specified morphological types of tumours) for all types of tumours, thereby providing greater site detail for non-malignant tumours than is provided in ICD-10. In contrast to ICD-10, the ICD-O includes topography for sites of haematopoietic and reticuloendothelial tumours. The morphology axis provides five-digit codes ranging from M-8000/0 to M-9989/3. The first four digits indicate the specific histological term. The fifth digit after the slash (/) is the behaviour code, which indicates whether a tumour is malignant, benign, in situ, or uncertain (whether benign or malignant). A separate one-digit code is also provided for histologic grading (differentiation).",
"homepage": "http://www.who.int/classifications/icd/adaptations/oncology/",
"name": "International Classification of Diseases for Oncology",
"prefix": "445",
"wikidata_database": "Q1430635"
},
"446": {
"description": "The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. These domains are classified from body, individual and societal perspectives by means of two lists: a list of body functions and structure, and a list of domains of activity and participation. Since an individual's functioning and disability occurs in a context, the ICF also includes a list of environmental factors.\n\nThe ICF is WHO's framework for measuring health and disability at both individual and population levels. The ICF was officially endorsed by all 191 WHO Member States in the Fifty-fourth World Health Assembly on 22 May 2001 (resolution WHA 54.21). Unlike its predecessor, which was endorsed for field trail purposes only, the ICF was endorsed for use in Member States as the international standard to describe and measure health and disability.\n\nThe ICF puts the notions of 'health' and 'disability' in a new light. It acknowledges that every human being can experience a decrement in health and thereby experience some degree of disability. Disability is not something that only happens to a minority of humanity. The ICF thus 'mainstreams' the experience of disability and recognises it as a universal human experience. By shifting the focus from cause to impact it places all health conditions on an equal footing allowing them to be compared using a common metric - the ruler of health and disability. Furthermore ICF takes into account the social aspects of disability and does not see disability only as a 'medical' or 'biological' dysfunction. By including Contextual Factors, in which environmental factors are listed ICF allows to records the impact of the environment on the person's functioning.",
"homepage": "http://www.who.int/classifications/icf/",
"name": "International Classification of Functioning, Disability and Health",
"prefix": "446",
"wikidata_database": "Q917426"
},
"447": {
"abbreviation": "ICD",
"description": "The International Classification of Diseases (ICD) is the standard diagnostic tool for epidemiology, health management and clinical purposes. This includes the analysis of the general health situation of population groups. It is used to monitor the incidence and prevalence of diseases and other health problems. It is used to classify diseases and other health problems recorded on many types of health and vital records including death certificates and health records. In addition to enabling the storage and retrieval of diagnostic information for clinical, epidemiological and quality purposes, these records also provide the basis for the compilation of national mortality and morbidity statistics by WHO Member States. It is used for reimbursement and resource allocation decision-making by countries. ICD-10 was endorsed by the Forty-third World Health Assembly in May 1990 and came into use in WHO Member States as from 1994. The 11th revision of the classification has already started and will continue until 2015.",
"homepage": "https://www.who.int/standards/classifications/classification-of-diseases",
"name": "International Statistical Classification of Diseases",
"prefix": "447",
"wikidata_database": "Q50018"
},
"448": {
"abbreviation": "EDMA",
"description": "An effective product classification system is critical to the functioning of any industry in the knowledge-based markets of today. A classification scheme assigns a code to each product type or class, allowing quick identification of the product in a language-independent fashion (the specific name of the product is actually not mentioned).\n\nEDMA has been following the development of the European IVD market for many years. In order to allow for the easy compilation and consolidation of market data, EDMA has created a specific product classification scheme for IVDs. This European Diagnostic Market Statistics (EDMS) programme, based on the independent audit of invoiced sales, is the authoritative source of IVD market statistics in Europe. Its objective information serves as a valuable basis for decision-making in the IVD industry.",
"homepage": "https://www.dimdi.de/dynamic/de/medizinprodukte/bezeichnungssysteme/edma-ivd-classification/",
"name": "Global InVitro Diagnostic Classification",
"prefix": "448"
},
"449": {
"abbreviation": "ATC",
"description": "In the Anatomical Therapeutic Chemical (ATC) classification system, the active substances are divided into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels. The drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The 2nd, 3rd and 4th levels are often used to identify pharmacological subgroups when that is considered more appropriate than therapeutic or chemical subgroups.",
"name": "Anatomical Therapeutic Chemical Classification System",
"prefix": "449",
"wikidata_database": "Q192093"
},
"45": {
"description": "6637 terms, 312 relationships between terms, 864 equivalent terms.",
"homepage": "http://www.bnm.me.gov.ar/vocabularios/tesauro/",
"name": "General Vocabulary of the National Library of Teachers",
"prefix": "45"
},
"450": {
"abbreviation": "OPS",
"description": "The Operations and Procedures Key (OPS) is the official classification for encrypting operations, procedures and general medical procedures in the inpatient area and for outpatient surgery.",
"homepage": "https://www.dimdi.de/dynamic/de/klassifikationen/ops/",
"name": "Operation and procedure keys",
"prefix": "450",
"wikidata_database": "Q2026515"
},
"451": {
"description": "The Dating Systematics of the BSZ for the period from the Palaeolithic to the Migration Period contains, for a large part, time definitions, sources and definitions of the term, the archaeological and historical periods of the respective period.",
"homepage": "https://wiki.bsz-bw.de/display/MUSIS/BSZ-Thesauri",
"name": "BSZ periods BC",
"prefix": "451"
},
"452": {
"description": "Scope: 62 main groups, with about 9000 items down to the fourth hierarchy level.",
"homepage": "https://museumsvokabular.de/node/6",
"license": "CC BY-NC-SA 3.0",
"name": "Coarse systematics",
"prefix": "452"
},
"453": {
"description": "Keywords in this Thesaurus are referred to as preferred terms. Preferred terms are used in indexing the Australian Transport Index (ATRI) and are shown in bold type. Non-preferred terms are not used for indexing and are shown in italics; their role in the Thesaurus is to lead to the preferred term. Terms in the Thesaurus are listed in a single alphabetical sequence and appear in word-by-word order, so that 'Access road' appears before 'Accessibility'. This Thesaurus is designed to assist Australian researchers to access Australian and overseas literature on land transport. However, it may also be useful to those involved in metadata and knowledge management within the land transport arena.",
"homepage": "http://www.arrb.com.au/admin/file/content2/c7/ATRI_2013.pdf",
"name": "Australian Transport Index Thesaurus",
"prefix": "453"
},
"454": {
"abbreviation": "LCSH",
"description": "LCSH in this service includes all Library of Congress Subject Headings, free-floating subdivisions (topical and form), Genre/Form headings, Children's (AC) headings, and validation strings for which authority records have been created. The content includes a few name headings (personal and corporate), such as William Shakespeare, Jesus Christ, and Harvard University, and geographic headings that are added to LCSH as they are needed to establish subdivisions, provide a pattern for subdivision practice, or provide reference structure for other terms. This content is expanded beyond the print issue of LCSH (the 'red books') with inclusion of validation strings. *Validation strings: Some authority records are for headings that have been built by adding subdivisions. These records are the result of an ongoing project to programmatically create authority records for valid subject strings from subject heading strings found in bibliographic records. The authority records for these subject strings were created so the entire string could be machine-validated. The strings do not have broader, narrower, or related terms. Library of Congress Subject Headings (LCSH) has been actively maintained since 1898 to catalog materials held at the Library of Congress. By virtue of cooperative cataloging other libraries around the United States also use LCSH to provide subject access to their collections. In addition LCSH is used internationally, often in translation.",
"homepage": "http://id.loc.gov/authorities/subjects.html",
"license": "CC0-1.0",
"name": "Library of Congress Subject Headings",
"prefix": "454",
"wikidata_database": "Q1823134"
},
"455": {
"description": "Terminology and monitored by SHKS. Experts nominated, which handles all of the vocabulary of terms and their translations, and decide on the publication terms Hoidokki continuously developed and an expert calls for the missing information of terms obtained by thermally proposals term proposal can be made using this system in such a way that fulfills the proposed term of the form and. send it to a group of experts for consideration. vocabulary may be used for information retrieval, and to index publications of nursing science.",
"homepage": "http://www.hoidokki.fi/",
"name": "Hoidokki online dictionary",
"prefix": "455"
},
"456": {
"description": "The properties-source index provides databases, reference works, and websites for physico-chemical and other material-related properties (data, definition, measurement), realized as a system of two entangled thesauri for physical properties and chemical systems , 347 synonyms, 126 facets, the following are given: property names, synonyms and translations, a definition and common symbols and physical units according to the IUPAC \"Green Book.\" 326 descriptors, 70 synonyms Sources: Round 830 Sources: Databases, reference books, websites, etc. Associations: 6200 assignments of physical properties, chemical systems, and sources, a tool to find recommended sources for a physico-chemical or other substance-related property.",
"homepage": "http://www.eqi.ethz.ch/",
"name": "Properties Source Index",
"prefix": "456"
},
"457": {
"description": "The Rice Thesaurus now contains 3,807 terms (descriptors and nondescriptors). It aims to make available standard terms used in rice production and ultimately, to facilitate the search and retrieval of rice information.",
"homepage": "http://agclass.nal.usda.gov/irri/rice_search.shtml",
"name": "International Rice Research Institute Rice Thesaurus",
"prefix": "457"
},
"458": {
"description": "The Thesaurus of the University of Barcelona (THUB) is a tool that facilitates the consultation by subjects in the Catalog because: it normalizes the way to access the indexes of subjects; unambiguously identifies the term sought; Group the catalog documents from the accepted forms. THUB is the structured and controlled vocabulary that is used as a basic tool for indexing and retrieval by subjects of all the information resources of the CRAI of the University of Barcelona. THUB is a multidisciplinary thesaurus in Catalan that includes terms that design concepts of the various specialties that are the field of action and interest of the UB. The THUB can also be a useful tool for terminological research for its hierarchical and associative structure, and the classification by categories, which are the basis of Microtesaurus UB. (...) The THUB is used in the indexing and conceptual recovery of all the information resources of the CRAI of the UB in the different search applications available. It is therefore the vocabulary for the indexation of these resources described in: the Catalog of the libraries of the UB and the Collective Catalog of the Universities of Catalonia (CCUC); the Digital Deposit of the UB and the set of external repositories in which the UB participates: RACO, RECERCAT, TDX and MDX; the Digital Memory of Catalonia, a consortium repository for the description of patrimonial collections; Other databases of the institution, such as the UBTV.\n\nCurrently (November 2018) the THUB contains 27,537 descriptors, of which: 20,905 are thematic descriptors, 6,414 are geographical descriptors, 218 are genre / form descriptors. The thesaurus incorporates in addition equivalences of the preferred terms in Spanish, English and French. At present, 80% of THUB authority records contain equivalences in these three languages ββthat are the basis of the current multilingual structure. (Translated by Google Translate)",
"homepage": "http://crai.ub.edu/ca/recursos-d-informacio/thub",
"license": "CC0-1.0",
"name": "Thesaurus of the University of Barcelona",
"prefix": "458"
},
"459": {
"abbreviation": "ICONCLASS",
"description": "Iconclass is a subject-specific classification system. It is a hierarchically ordered collection of definitions of objects, people, events and abstract ideas that serve as the subject of an image. Art historians, researchers and curators use it to describe, classify and examine the subject of images represented in various media such as paintings, drawings and photographs. Numerous institutions across the world use Iconclass to describe and classify their collections in a standardized manner. In turn, users ranging from art historians to museum visitors use Iconclass to search and retrieve images from these collections. And as a research tool, Iconclass is also used to identify the significance of entire scenes or individual elements represented within an image. ICONCLASS applications used around the world have made it the most widely accepted classification system for visual documents. The three main components of Iconclass are: Classification System: 28,000 hierarchically ordered definitions divided into ten main divisions. Each definition consists of an alphanumeric classification code (notation) and the description of the iconographic subject (textual correlate). The definitions are used to index, catalogue and describe the subjects of images represented in works of art, reproductions, photographs and other sources. Alphabetical Index: 14,000 keywords used for locating the notation and its textual correlate needed to describe and/or index an image. Bibliography: 40,000 references to books and articles of iconographical interest (not yet online).",
"homepage": "http://www.iconclass.org/",
"license": "ODBL",
"name": "Iconclass",
"prefix": "459",
"wikidata_database": "Q1502787"
},
"46": {
"description": "The thesaurus was designed to describe services commonly provided by state governments in general. The participating states hope that by using this vocabulary it will be possible to develop methods making it easier to search for information across states. It is designed to be small and general in nature rather than large and specific.\n\nThis thesaurus is a suggested controlled vocabulary for use in creating metatag information for the Dublin Core Subject field (DC.Subject) for state government web pages.",
"name": "Wisconsin Thesaurus",
"prefix": "46"
},
"460": {
"description": "eHRAF World Cultures is an online cross-cultural database that contains information on all aspects of cultural and social life. This ethnographic database is unique because each culture or ethnic group contains a variety of source documents (books, articles, and dissertations) that have been indexed and organized according to HRAF's comprehensive culture and subject classification systems: the Outline of World Cultures and the Outline of Cultural Materials (OCM). These retrieval systems extend search capability well beyond keyword searching thus allowing for precise culture and subject retrieval, even in a foreign language.",
"homepage": "http://hraf.yale.edu/online-databases/ehraf-world-cultures/outline-of-cultural-materials/",
"name": "Outline of Cultural Materials",
"prefix": "460"
},
"461": {
"description": "The Classification of individual consumption by purpose, abbreviated as COICOP, is a nomenclature developed by the United Nations Statistics Division to classify and analyze individual consumption expenditures incurred by households, non-profit institutions serving households and general government according to their purpose.",
"homepage": "http://unstats.un.org/unsd/cr/registry/regcst.asp?Cl=5",
"name": "Classification of Individual Consumption According to Purpose",
"prefix": "461"
},
"462": {
"description": "The Bibliographic Classification (BC2 or Bliss) is the leading example of a fully faceted classification scheme. It provides a detailed classification for use in libraries and information services of all kinds, having a broad and detailed structure and order. The vocabulary in each class is comprehensive and complemented by an exceptionally brief faceted notation considering the detail available, providing indexing to any depth the classifier wishes. The structure of the subject within each class is clearly and simply laid out with rules provided for the quick and consistent placing of any item. A thorough A-Z index is provided in each volume. Users can access a subject catalogue record via any part of the whole, depending upon the primary interest of the user.",
"homepage": "http://www.blissclassification.org.uk/",
"name": "The Bliss Bibliographic Classification",
"prefix": "462",
"wikidata_database": "Q1114454"
},
"463": {
"description": "Founded in 1983, on the initiative of AFERA, Professor Jean Bossy and the BibliothΓ¨que de MΓ©decine de NΓmes. 20000 references in acupuncture and traditional Chinese medicine: articles stripped from our collections of paper or online journals, congress , Books, dissertations and theses A database enhanced by the new acquisitions of the BU MΓ©decine de NΓmes: more than 1000 new references per year Indexed by acupuncturists with the help of a thesaurus created by Team of acupuncturists and librarians.",
"homepage": "http://www.acubase.fr/",
"name": "Acupuncture Thesaurus",
"prefix": "463"
},
"464": {
"description": "The Open Family Services subject vocabulary provides a way of categorising family services within the Open Family Services Directory (formerly DfE Family Information Directory). The 'Guidance' tab describes how the list is used and links to guidance and complementary controlled vocabulary files. The 'Formats' makes the list available in a variety of formats including its native ZThes XML format.",
"homepage": "https://joinup.ec.europa.eu/catalogue/asset_release/open-family-services-directory",
"name": "Open Family Services Directory",
"prefix": "464"
},
"465": {
"description": "The Joint Academic Coding System (JACS) is owned and maintained by the Universities and Colleges Admissions Service (UCAS) and the Higher Education Statistics Agency (HESA) and is used for subject coding of provision across higher education in the UK. JACS was first introduced in 2002/03 (UCAS year of entry 2002 and reporting year 2002/03 HESA) to replace the two different classifications systems previously used by the two organisations. JACS is currently used to code the subjects of both higher education courses and the individual modules within them across the full range of higher education provision.",
"homepage": "https://www.hesa.ac.uk/support/documentation/jacs",
"name": "Joint Academic Coding System",
"prefix": "465",
"wikidata_database": "Q6269063"
},
"466": {
"description": "The ANSM provides health professionals with all the drug interactions identified by the ad hoc working group and grouped together in a Thesaurus. This Thesaurus provides healthcare professionals with reliable, pragmatic reference information , With deliberately simple labels using key words, and should be used as a pharmacotherapeutic prescribing guide.The interaction is defined by a pair of protagonists 'a + b' which can be an active substance, The first protagonist of the interaction ('a') appears grayed out in the Thesaurus. The first protagonist of the interaction ('a') appears gray in the Thesaurus. When the interaction concerns a therapeutic class, the various substances which make up this class are cited in When the interaction concerns a single substance, the various therapeutic classes including this substance, which are also subject to class interactions, are cited within the gray area. These couples appear 'in mirror', each interaction being mentioned twice, depending on whether the research is on one or the other of the protagonists. All therapeutic substances or classes in the Thesaurus are listed in alphabetical order. Two indexes accompany this Thesaurus. The index of all the substances mentioned in the Thesaurus specifies, where appropriate, the therapeutic classes and / or whether they have their own interactions. The index of therapeutic classes mentions all the classes present in the Thesaurus. \"b",
"homepage": "http://ansm.sante.fr/Dossiers-thematiques/Interactions-medicamenteuses/Interactions-medicamenteuses/(offset)/Dossiers-thematiques/Interactions-medicamenteuses/Interactions-medicamenteuses/(offset)/0",
"name": "Drug Interactions Thesaurus",
"prefix": "466"
},
"467": {
"description": "The fund is mainly focused on the pedagogy of adults with low knowledge.",
"homepage": "http://www.illettrisme.org/ressources-documentaires/au-centre-de-documentation/plan-de-classement",
"name": "Center Ressources Illettrisme Provence-Alpes-CΓ΄te d'Azur Ranking Plan",
"prefix": "467"
},
"468": {
"description": "SHIC is a subject classification widely used by UK museums. It was created nearly 20 years ago by the SHIC Working Party which continues to develop it today. The first published edition appeared in 1983 and a revised second edition was published in 1993 with further updates in 1996. The Social History and Industrial Classification (SHIC) is designed to make links between a wide variety of museum material - objects, photographs, archival material, tape recordings, information files - according to the sphere of human activity with which they are primarily associated. The aim of the Classification is to make relationships between objects, etc. via their context. A carpenter's hammer, for example, is used with other carpenter's tools, and is therefore classified alongside those related items.",
"homepage": "http://www.shcg.org.uk/About-SHIC",
"name": "Social History and Industrial Classification",
"prefix": "468",
"wikidata_database": "Q7550666"
},
"469": {
"description": "The U.S. Geological Survey Library classification system has been designed for earth science libraries. It is a tool for assigning call numbers to earth science and allied pure science materials in order to collect these materials into related subject groups on the library shelves and arrange them alphabetically by author and title. The classification can be used as a retrieval system to access materials through the subject and geographic numbers. The classification scheme has been developed over the years since 1904 to meet the ever-changing needs of increased specialization and the development of new areas of research in the earth sciences. The purpose of this publication is to provide the earth science community with a classification and retrieval system for earth science materials, to offer sufficient explanation of its structure and use, and to enable library staff and clientele to classify or access research materials in a library collection.",
"homepage": "http://pubs.usgs.gov/bul/b2010/",
"name": "U.S. Geological Survey Library Classification System",
"prefix": "469",
"wikidata_database": "Q7889905"
},
"47": {
"description": "Applied in Gnomon online - EichstΓ€tter Information system for classical antiquity science.",
"name": "Gnomon Thesaurus",
"prefix": "47"
},
"470": {
"description": "The thesaurus of occupational therapy subject headings is a reference guide for use with OT SEARCH, an online bibliographic database which indexes the holdings of the Wilma L. West Library. This compilation consists of a controlled vocabulary based on the National Library of Medicineβs Medical Subject Headings (MeSH). OT Search users will find this tool useful in performing compact and efficient search strategies. In comparison to a broad keyword search, a search strategy utilizing valid subject headings will generate the most pertinent references related to a particular topic. It is, therefore, advisable to select appropriate terms from the thesaurus before performing your search in OT SEARCH. This thesaurus comprises two major sections: I. Alphabetical Subject Listing: A listing of all the subject terms in alphabetical order. Each entry consists of a hierarchical tree number, a note and annotation when appropriate, and a definition of the term proper. While approved subject headings are printed in capital letters (e.g. SENSORY INTEGRATIVE DYSFUNCTION), related terms are printed in lower case (e.g. Early intervention programs), with a reference to the approved subject headings (e.g. Tactile Defensiveness, use SENSORY INTEGRATIVE DYSFUNCTION). In some cases, the searcher is directed to related terms by a 'see also' reference (e.g. NURSING HOMES, see also HOMES FOR THE AGED). Some subject headings are inverted for focus purposes (e.g. health insurance is listed in the thesaurus as INSURANCE, HEALTH). II. Hierarchical Classification Scheme: A listing of tree numbers in hierarchical order. Each term is assigned a unique alphanumeric number which places it in an hierarchical classification scheme or 'tree' with a broader, narrower, or related term. The hierarchical classification scheme consists of a number of tables which classify the subject headings into several categorical layers. The major categories cover broader concepts such as anatomy, diseases, chemicals and drugs, procedures and techniques, equipment and supplies, behavior and behavior mechanisms, biological sciences, physical sciences, social sciences, technology, humanities, information sciences, persons, health care and geographic names. These categories are further broken into a strata of categories. Each table consists of an array of tree numbers and matching subject headings which are indented according to their hierarchical structure. A hyphen [-] is used to represent the status of the terms in the hierarchical scheme. The more indented the term is, the narrower in scope.",
"name": "Thesaurus of Occupational Therapy Subject Headings",
"prefix": "470"
},
"471": {
"description": "The primary purpose for which BSO has been compiled is to serve as an exchange or switching language for use in an information network covering all subjects and in principle extending to users anywhere in the world.",
"homepage": "http://www.ucl.ac.uk/fatks/bso/",
"name": "Broad System of Ordering",
"prefix": "471"
},
"472": {
"abbreviation": "ILC",
"description": "The Integrative Levels Classification (ILC) is a knowledge organization system featuring experimental innovations. Although drawing from the heritage of bibliographic classifications, it is different from most of them in allowing to represent any combination of concepts without the ties of traditional disciplines. Phenomena of the world are listed in the ILC schedule according to the natural sequence of integrative levels; each concept can then be freely combined with others by meaningful relationships (facets). This makes ILC suitable to order and connect knowledge in a variety of media, including directories, websites, encyclopedias, audio-visual archives, printed collections, museum specimens, etc. The expressivity of its notation makes it especially fit to be integrated in computer-based automation to produce clever search and dynamic displays of knowledge items. ILC is being developed progressively since 2004. A first stable edition (ILC 1) is available for those interested in testing or using it. This includes 7052 classes (concepts) covering the whole spectrum of knowledge broadly, plus deeper specificity in certain domains (e.g. cetaceans, countries, ...) that have already been worked out in detail. The combination mechanisms allow to use the existing classes to generate meanings that approximate well enough the contents of most general collections. A special feature (deictics) is also available to define extensions fitting your local needs in ways compatible with the general system. The ILC research project takes its theoretical and technical foundations from the work developed in the 1960s by the Classification Research Group (CRG) in London, particularly in the persons of Douglas J. Foskett and Derek Austin, under a NATO grant. At the time this did not produce a finished system for contingent reasons, but it did leave us with a precious heritage of advanced techniques (freely faceted classification) that are now being implemented in ILC. The system is currently developed and managed by an international team led by Claudio Gnoli and including researchers, librarians, computer scientists, and philosophers.",
"homepage": "http://www.iskoi.org/ilc/",
"license": "CC BY-SA 3.0",
"name": "Integrative Levels Classification",
"prefix": "472"
},
"473": {
"abbreviation": "PACS",
"description": "The Physics and Astronomy Classification SchemeΒ (PACS) was developed by the American Institute of Physics (AIP) and has been used in Physical Review since 1975 to identify fields and sub-fields of physics. It is used in a variety of ways, for example, in the online journals as a tool in searching for articles by subject. PACS is arranged hierarchically, by subdivision of the whole spectrum of subject matter in physics- and astronomy-related sciences into segments and then repeating the process of subdivision down to four levels. The latest edition of PACS is the 2010 edition.",
"homepage": "http://publish.aps.org/PACS",
"name": "Physics and Astronomy Classification Scheme",
"prefix": "473",
"wikidata_database": "Q1457979"
},
"474": {
"abbreviation": "MSC2010",
"description": "The Mathematics Subject Classification (MSC2010) is the previous version of the MSC2020. It has been used by Mathematical Reviews (MR) and Zentralblatt fΓΌr Mathematik (Zbl) since 2010. There has been a previous version of MSC2010 as well, the MSC2000.\n\n\"The Mathematics Subject Classification (MSC) underwent a general revision, with some additions and changes, and corrections of existing errors, thus creating MSC2010 as a successor to the previous MSC2000. Mathematical Reviews (MR) and Zentralblatt fΓΌr Mathematik (Zbl) carefully considered all feedback and used it in preparing their joint MSC revision.\n\nThe Final MSC2010 revision was made public here [http://msc2010.org/Default.html] in May 2009, and deployed in production in July 2009 by MR for MathSciNet and Zbl for zbMATH.",
"homepage": "http://msc2010.org/mscwork/",
"license": "CC BY-NC-SA 3.0",
"name": "Mathematics Subject Classification",
"pattern": "^[0-9]{2}(-XX|-[0-9]{2}|[A-Z](xx|[0-9]{2}))$",
"prefix": "474",
"wikidata_database": "Q967960"
},
"475": {
"abbreviation": "CSS",
"description": "ACM's first classification system for the computing field was published in 1964. Then, in 1982, the ACM published an entirely new system. New versions based on the 1982 system followed, in 1983, 1987, 1991, and 1998. The 2012 scheme utilizes a new poly-hierarchical structure and a more in-depth approach than the 1998 version. It no longer uses the letter-and-number coding of the previous versions. The old scheme has been mapped to the new, and both the 1998 and 2012 terms are available on Citation Pages of all indexed articles in the ACM Digital Library. The 2012 ACM Computing Classification System has been developed as a poly-hierarchical ontology that can be utilized in semantic web applications. It replaces the traditional 1998 version of the ACM Computing Classification System (CCS), which has served as the de facto standard classification system for the computing field. It is being integrated into the search capabilities and visual topic displays of the ACM Digital Library. It relies on a semantic vocabulary as the single source of categories and concepts that reflect the state of the art of the computing discipline and is receptive to structural change as it evolves in the future. ACM will a provide tools to facilitate the application of 2012 CCS categories to forthcoming papers and a process to ensure that the CCS stays current and relevant. The new classification system will play a key role in the development of a people search interface in the ACM Digital Library to supplement its current traditional bibliographic search.",
"homepage": "http://www.acm.org/about/class/",
"name": "Association for Computing Machinery Computing Classification System",
"prefix": "475",
"wikidata_database": "Q288530"
},
"476": {
"description": "The North American Industry Classification System (NAICS) is the standard used by Federal statistical agencies in classifying business establishments for the purpose of collecting, analyzing, and publishing statistical data related to the U.S. business economy. NAICS was developed under the auspices of the Office of Management and Budget (OMB), and adopted in 1997 to replace the Standard Industrial Classification (SIC) system. It was developed jointly by the U.S. Economic Classification Policy Committee (ECPC), Statistics Canada, and Mexico's Instituto Nacional de Estadistica y Geografia, to allow for a high level of comparability in business statistics among the North American countries.",
"homepage": "http://www.census.gov/eos/www/naics/",
"name": "North American Industry Classification System",
"prefix": "476",
"wikidata_database": "Q3509282"
},
"477": {
"description": "This guide serves as a crosswalk between the 2000 Census job codes and the ten (10) job categories on the Employer Information Report EEO-1, and is designed to assist employers in correctly classifying employees according to the ten (10) job categories on the EEO-1 report. Each job category is explained in the EEO-1 Instruction Booklet with a definition and examples of the types of jobs included in the category.",
"homepage": "http://www.eeoc.gov/employers/eeo1survey/jobclassguide.cfm",
"name": "EEO-1 Job Classification Guide",
"prefix": "477"
},
"478": {
"description": "NLCD 1992 was a success, and its success had a lot to do with building the momentum for NLCD 2001. NLCD 2001 improves upon NLCD 1992 in three important ways. Whereas NLCD 1992 was simply a land-cover data set, NLCD 2001 is a land-cover database comprised of three elements: land cover, impervious surface and canopy density. Second, NLCD 2001 used improved classification algorithms, which have resulted in data with more precise rendering of spatial boundaries between the 16 classes (an additional nine classes are available in coastal areas and another four classes in Alaska only). Third, NLCD 2001 also includes Alaska, Hawaii, and Puerto Rico. NLCD 1992 was restricted to the conterminous United States.",
"homepage": "http://www.epa.gov/mrlc/classification.html",
"name": "National Land Cover Data Classification Schemes",
"prefix": "478"
},
"479": {
"description": "The South American Classification Committee is an official committee of the American Ornithologists' Union whose mission is to create a standard classification, with English names, for the bird species of South America. This classification is subject to constant revision by the proposal system to allow incorporation of new data. The SACC hopes to have this classification published as a printed document within a year or so. The starting point for the classification was a pre-publication draft of Dickinson (2003); the published version differed in a few minor ways from the version used for the starting point (as noted in the Notes sections below). The classification herein consists mainly of the ranks Order, Family, Genus, and Species. Most traditional subfamilies are omitted unless supported by multiple independent data sets that mark major, deep branches within a family. Subspecies are omitted for now; a future edition will also include the Subspecies rank as designating diagnosable populations (equivalent to phylogenetic species sensu Cracraft) within taxa accorded species rank, as well as synopses of distribution. We recognize the importance of this level of classification for many kinds of analyses but are unable to provide a comprehensive evaluation of which currently recognized subspecies represent valid taxonomic units in terms of diagnosability. See Dickinson (2003) for a preliminary assessment of valid subspecies of South American birds, as well as various volumes of the Handbook of the Birds of World (Lynx Edicions, Barcelona). The region covered by the list is: (1) continental South America and all islands within 1200 km of its shores eastward into the Atlantic and westward into the Pacific oceans (including Malpelo, the Galapagos islands, San Felix and San Ambrosio, the Juan Fernandez islands, Fernando de Noronha, Trindade, Martin Vaz, SΓ£o Pedro and SΓ£o Paulo Archipelago, and the Falklands/Malvinas); (2) islands in the Caribbean Sea close to South America and not covered by the AOU Checklist (including Netherlands Antilles, Trinidad and Tobago); and (3) waters within 200 nautical miles of the coasts of these land areas, including the islands. A species is included on the list if the evidence for its occurrence in the area is supported by tangible evidence that is available for verification, namely a museum specimen or an archived or published photograph, videotape, or sound recording. The main list currently includes 3,330 species (3094 native breeding species, 1 of which is extinct; 147 nonbreeding residents; 75 vagrants; 14 established, introduced species). Of these, 103 newly discovered species have been described since the publication of Meyer de Schauensee's (1970) classic compilation of the species of birds of South America (i.e., at a rate of 2.5 species per year). Species whose presence is supported only by sight records, or by unpublished or non-archived tangible evidence, are placed on the Hypothetical List.",
"homepage": "http://www.museum.lsu.edu/~Remsen/SACCWordFiles/SACCBaseline01.html",
"name": "A Classification of the Bird Species of South America",
"prefix": "479"
},
"48": {
"description": "The HEREIN network also offers a unique multilingual thesaurus, covering concepts and terms in the domain of heritage policies and programmes, with the aim of harmonising the description and the understanding of heritage policies throughout Europe.\n\nThe HEREIN Thesaurus, available in 14 languages, consists of about 700 terms connected by relationships such as hierarchy, equivalences, related terms and non-preferred terms. It is already possible to look at the different categories and search for words, their relationships and their equivalents in all available languages, although the thesaurus tool is still under development and a user interface is not available at this stage.",
"homepage": "http://www.herein-system.eu/herein-thesaurus",
"name": "European Heritage Network Multilingual Thesaurus",
"prefix": "48"
},
"480": {
"description": "Classification and retrieval of literature and research projects 14 main classes with a total of 145 subclasses.",
"homepage": "http://www.gesis.org/forschung/sozialwissenschaftliche-forschung/",
"name": "Classification of Social Sciences",
"prefix": "480"
},
"481": {
"description": "In order to ensure global uniformity when describing the habitat in which a taxon occurs, the threats to a taxon, what conservation actions are in place or are needed, and whether or not the taxon is utilized, a set of standard terms (called Classification Schemes; formerly referred to as Authority Files) have been developed for documenting taxa on the IUCN Red List. These Classification Schemes are still being developed and tested and not all of them have been implemented in this version of the IUCN Red List.",
"homepage": "http://www.iucnredlist.org/technical-documents/classification-schemes",
"name": "International Union for Conservation of Nature and Natural Resources Red List of Threatened Species Classification Schemes",
"prefix": "481"
},
"482": {
"description": "Classifying vegetation is a critical to sound ecological science and efficient land assessment, management and planning. The National Vegetation Classification (NVC) is a central organizing framework for how all vegetation in the United States is inventoried and studied, from broad scale formations (biomes) to fine-scale plant communities. The purpose of the NVC is to produce uniform statistics about vegetation resources across the nation, based on vegetation data gathered at local, regional, or national levels. The latest classification standard was published in 2008 by the Federal Geographic Data Committee and provides the basis for ongoing refinement of the NVC. We invite your participation in this dynamic process and hope you will make use of the considerable resources of this web portal.",
"homepage": "http://usnvc.org/",
"name": "U.S. National Vegetation Classification",
"prefix": "482",
"wikidata_database": "Q7863249"
},
"483": {
"description": "The TC-DB website details a comprehensive classification system for membrane transport proteins known as the Transport Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information. Descriptions, TC numbers, and examples of over 600 families of transport proteins are provided. Transport systems are classified on the basis of five criteria, and each of these criteria corresponds to one of the five numbers or letters within the TC# for a particular type of transporter. Thus a TC# normally has five components as follows: V.W.X.Y.Z. V (a number) corresponds to the transporter class (i.e., channel, carrier (porter), primary active transporter or group translocator); W (a lettter) corresponds to the transporter subclass which in the case of primary active transporters refers to the energy source used to drive transport; X (a number) corresponds to the transporter family (sometimes actually a superfamily); Y (a number) corresponds to the subfamily in which a transporter is found, and Z corresponds to the substrate or range of substrates transported. Any two transport systems in the same subfamily of a transporter family that transport the same substrate(s) are given the same TC#, regardless of whether they are orthologues (e.g., arose in distinct organisms by speciation) or paralogues (e.g., arose within a single organism by gene duplication). Sequenced homologues of unknown function are not normally assigned a TC# unless they represent a unique (sub)family or are from an unrepresented organismal kingdom. If multiple dissimilar subunits are present, they are numbered S1, S2, S3...Sn. Classification categories 8 and 9 are reserved for accessory transport proteins and incompletely characterized (families of) transporters, respectively. Mechanisms of bulk transport via endocytosis, exocytosis and intracellular trafficking, observed in eukaryotes and prokaryotes (Lonhienne et al., 2010) are not included in TCDB.",
"homepage": "http://www.tcdb.org/",
"license": "CC BY-SA 3.0",
"name": "Transporter Classification System",
"prefix": "483",
"wikidata_database": "Q142667"
},
"484": {
"abbreviation": "WZ",
"description": "The European Classification of Economic Activity (NACE) is designed to provide a uniform statistical recording of the economic activities of enterprises, establishments and other statistical units in the European Union, which is based on a classification of the economic sectors (WZ) The new system was created with the intensive participation of data users and data producers in the economy, research, administration and society in order to meet the changing requirements and requirements. As a result, a hierarchically structured economic classification with 21 sections, 88 departments, 272 groups, 615 classes and 839 subclasses was created.",
"homepage": "https://www.destatis.de/DE/Publikationen/Verzeichnis/KlassifikationWZ08.html",
"name": "Classification of economic activities",
"prefix": "484"
},
"485": {
"description": "The JEL Classification Codes Guide is now available online. Additionally, you may download an xml file of JEL Codes. JEL Codes are 3-digit, but EconLit searches require the use the four digit codes consisting of the 3-digit JEL code plus a 0. The EconLit subject descriptors are the same as the Journal of Economic Literature (JEL) classification codes.",
"homepage": "http://www.aeaweb.org/jel/jel_class_system.php",
"name": "Journal of Economic Literature Classification System",
"prefix": "485",
"wikidata_database": "Q1501332"
},
"486": {
"abbreviation": "LCC",
"description": "The Library of Congress Classification (LCC) is a classification system that was first developed in the late nineteenth and early twentieth centuries to organize and arrange the book collections of the Library of Congress. Over the course of the twentieth century, the system was adopted for use by other libraries as well, especially large academic libraries in the United States. It is currently one of the most widely used library classification systems in the world. The Library's Cataloging Policy and Support Office maintains and develops the system, posting weekly lists of updates on its Web site. The system divides all knowledge into twenty-one basic classes, each identified by a single letter of the alphabet. Most of these alphabetical classes are further divided into more specific subclasses, identified by two-letter, or occasionally three-letter, combinations. For example, class N, Art, has subclasses NA, Architecture; NB, Sculpture, ND, Painting; as well as several other subclasses. Each subclass includes a loosely hierarchical arrangement of the topics pertinent to the subclass, going from the general to the more specific. Individual topics are often broken down by specific places, time periods, or bibliographic forms (such as periodicals, biographies, etc.). Each topic (often referred to as a caption) is assigned a single number or a span of numbers. Whole numbers used in LCC may range from one to four digits in length, and may be further extended by the use of decimal numbers. Some subtopics appear in alphabetical, rather than hierarchical, lists and are represented by decimal numbers that combine a letter of the alphabet with a numeral , e.g. .B72 or .K535. Relationships among topics in LCC are shown not by the numbers that are assigned to them, but by indenting subtopics under the larger topics that they are a part of, much like an outline. In this respect, it is different from more strictly hierarchical classification systems, such as the Dewey Decimal Classification, where hierarchical relationships among topics are shown by numbers that can be continuously subdivided.",
"homepage": "http://www.loc.gov/catdir/cpso/lcc.html",
"license": "CC0-1.0",
"name": "Library of Congress Classification",
"pattern": "^[A-Z]{1,3}(\\d+(\\.\\d+)?( *\\.?[A-Z]{0,3}\\d*([ -]\\.?[A-Z]{0,3}\\d+)?)?( *\\d+[a-z]*)?)?$",
"prefix": "486",
"wikidata_database": "Q621080"
},
"487": {
"description": "Scope: On the basis of\" furniture \"as\" furniture of the private household, movable inventory \"7 basic types of furniture divided into subordinate form types. An alphabetical register also allows access to the synonymous terms.",
"homepage": "https://museumsvokabular.de/node/6",
"license": "CC BY-NC-SA 3.0",
"name": "Furniture",
"prefix": "487"
},
"488": {
"homepage": "http://www.ccohs.ca/oshanswers/legisl/whmis_classifi.html",
"prefix": "488"
},
"489": {
"description": "These so-called. 'Hessian system' is a system of cultural and historical museums. It consists of 18 main groups. Each main group has subgroups (previously up to 12), and each subgroup names are led by concrete objects example, belong to this subgroup.",
"homepage": "https://museumsverband-hessen.de/de/veroeffentlichungen/arbeitshilfen-und-handreichungen",
"license": "CC BY-NC-SA 3.0",
"name": "Nomenclature for inventorying cultural history collections in museums",
"prefix": "489"
},
"49": {
"description": "Physical evidence, usually portable, resulting from past human activity or environmental remains that can be recovered from archaeological fieldwork. English Heritage takes a leading role in setting standards for recording the built and buried heritage. By setting standards that can be adopted by everyone, we can make sure that all records are consistent. In other words, if everyone uses the same words to describe the same monument, archaeological object, building material, etc, then anyone using this common language can easily index, retrieve and understand these records. With this aim in mind, English Heritage is continually developing new thesauri to provide structure and guidelines for the standardisation of terms to be used when creating new records of the past. Now, in our drive to disseminate these standards and promote their wider use, we are making available seven separate online thesauri. A tailor-made suite of programs has been developed, which uses a database to create a series of web pages for any chosen thesaurus. These can be easily accessed using a frames-capable browser and regularly updated as new terms are submitted and approved by our Data Standards Unit.\n\nNational cultural heritage thesauri and vocabularies have acted as standards for use by both national organizations and local authority Historic Environment Records but until now have lacked the persistent Linked Open Data (LOD) URIs that would allow them to act as vocabulary hubs for the Web of Data. The AHRC funded SENESCHAL project aims to make such vocabularies available online as Semantic Web resources. SENESCHAL will start with major vocabularies as exemplars and project partners will continue to make other vocabularies available. Other organizations are welcome to make use of the data and services which will be open licensed.\n\nRESTful web services will be developed for the project to make the vocabulary resources programmatically accessible and searchable. These will include the provision to βfeed backβ new terms (concepts) suggested by users.",
"homepage": "http://www.heritagedata.org/blog/vocabularies-provided/",
"license": "CC-BY-3.0",
"name": "FISH Archaeological Objects Thesaurus",
"prefix": "49"
},
"490": {
"description": "The European Classification System (ECLA) is an extension of the IPC and is used by the EPO. Both the IPC and ECLA are divided into eight sections, A-H, which in turn are sub-divided into classes, sub-classes, groups and sub-groups. There are approximately 135 000 classification entries in ECLA.\" \"ECLA has been replaced by the Cooperative Patent Classification (CPC) as of January 1, 2013.",
"homepage": "http://www.epo.org/searching/essentials/classification/cpc.html",
"name": "European Classification System",
"prefix": "490",
"wikidata_database": "Q11544935"
},
"491": {
"description": "A typology for museums and collections: 12 basic shapes of vessels as well as a hierarchy of these types of forms, the forms are represented by extensive drawings and photographs, each of which is presented in alphabetical order with numerous concrete object names Phrases and each illustrated by a photo.",
"homepage": "https://museumsvokabular.de/node/6",
"license": "CC BY-NC-SA 3.0",
"name": "Vessels and forms",
"prefix": "491"
},
"492": {
"description": "The third edition of the Australian and New Zealand Standard Offence Classification (ANZSOC) has been developed for use within Australia and in New Zealand for the production and analysis of crime and justice statistics. It replaces the second edition of the Australian Standard Offence Classification (ASOC) and incorporates a title change from ASOC to ANZSOC and corrects some minor typographical errors only. The classification content and structure, which was updated in the second edition of ASOC following a review of the first edition of ASOC released in 1997, remains unchanged. The revised title ANZSOC reflects the international use of the framework to classify criminal behaviour and highlights the collaborative work occurring between Australia and New Zealand. The title change from ASOC to ANZSOC is also in accordance with the agreed policy between the Australian Bureau of Statistics (ABS) and Statistics New Zealand to harmonise classifications where possible. The objective of the ANZSOC is to provide a uniform national statistical framework for classifying criminal behaviour in the production and analysis of crime and justice statistics. The ANZSOC is used in Australian Bureau of Statistics statistical collections, Statistics New Zealand statistical collections, Australian police, criminal courts and corrective services agencies and New Zealand police and justice agencies.",
"homepage": "http://www.abs.gov.au/ausstats/abs@.nsf/mf/1234.0",
"license": "CC-BY-3.0",
"name": "Australian and New Zealand Standard Offence Classification",
"prefix": "492"
},
"493": {
"description": "Scope. 20 manufacturing / processing modes offered on the first hierarchical level Some of them are other businesses associated (10 in total) on the second level of the hierarchy, the word collection is consistently adjectival total number of entries:.. 30.",
"homepage": "https://museumsvokabular.de/node/6",
"license": "CC BY-NC-SA 3.0",
"name": "System for techniques for the production of lace and embroidery",
"prefix": "493"
},
"494": {
"description": "This system lists the types of lace and embroidery (products) in high specialization and gives an exact description of each entry. Four main groups, sub-groups up to the fourth level, about 150 entries.",
"homepage": "https://museumsvokabular.de/node/6",
"license": "CC BY-NC-SA 3.0",
"name": "System for lace and embroidery",
"prefix": "494"
},
"495": {
"abbreviation": "TUM",
"description": "The book stock of the University Library of the Technical University of Munich will be developed from the year 1982 onwards, in addition to the verbal classification of subjects by subject headings are characterized by a three-digit, mnemonic letter code, the subclasses by a three-digit numeric code, the systematic (not strictly) hierarchical.",
"homepage": "http://www.ub.tum.de/systematik",
"name": "TUM classification",
"pattern": "^[A-Z]{3}( [0-9]{3})?$",
"prefix": "495",
"wikidata_database": "Q2385549"
},
"496": {
"abbreviation": "UDC",
"description": "The Universal Decimal Classification (UDC) is the world's foremost multilingual classification scheme for all fields of knowledge, a sophisticated indexing and retrieval tool. It was adapted by Paul Otlet and Nobel Prizewinner Henri La Fontaine from the Decimal Classification of Melvil Dewey, and first published (in French) between 1904 and 1907. Since then, it has been extensively revised and developed, and has become a highly flexible and effective system for organizing bibliographic records for all kinds of information in any medium (it is well suited to multi-media information collections). It is structured in such a way that new developments and new fields of knowledge can be readily incorporated. The code itself is independent of any particular language or script (consisting of arabic numerals and common punctuation marks), and the accompanying class descriptions have appeared in many translated versions. UDC is in worldwide use, and has been published in whole or in part in 40 different languages. The Multilingual Universal Decimal Classification Summary - UDC Summary (udcS) for short - represents a selection of around 2,600 classes extracted from the UDC Master Reference File (UDC MRF) 2011 which contains over 70,000 classes. The selection comprises main numbers, common auxiliary numbers and special auxiliary numbers and it represents even coverage of all areas of knowledge as contained by the scheme. UDC is updated annually and UDC Summary represents always the latest version of UDC. The UDC Summary is held in a multilingual database that mirrors the structure of the UDC MRF database and in that respect represents the full set of data and can be used as a UDC demonstrator for training, research, various information organization and retrieval purposes.",
"homepage": "https://udc-hub.com/",
"license": "CC BY-SA 3.0",
"name": "Universal Decimal Classification",
"pattern": "^[0-9]+.[0-9]*.[0-9]*$",
"prefix": "496",
"wikidata_database": "Q243350"
},
"497": {
"description": "Scope: 4 main groups with subdivision up to the 5th hierarchical level.",
"homepage": "https://museumsvokabular.de/node/6",
"license": "CC BY-NC-SA 3.0",
"name": "Thesaurus for farm equipment, field orders - Agricultural transport - Utility tools (woodworking)",
"prefix": "497"
},
"498": {
"description": "The project purpose is to develop and maintain a reference structured terminology in the domain of the cryosphere environment. The identification of the potential sources of terminology was carried out with the assistance of experts of the Arabba Avalanche Centre. The result consists of a certain number of lists of terms, usually contained in glossaries where they are supplied with one or more definitions and scarcely organised within a structure. In certain cases they are clustered in thematic areas. The terms of these lists were selected according to their pertinence and relevance.\n\nAt present we are working on a database of around 3.700 terms. The thematic areas, covered at present, deal with snow and ice physics, snow and ice morphology, snow and ice radiometry, remote sensing and GIS in cryosphere environment, sea ice, avalanches and glaciers. Concerning the vertical structure we adopted the Classification Scheme already in use for the development of the EARTh Thesaurus. The hierarchical setup is based on facets; according to its intrinsic features, the structure can be used as a semantic reference system, stable and partially independent from the context.\n\nSince the facet structure tends to scatter the terms under the more general referral category, we are implementing a thematic structure that will cluster the terms in themes representing specific sectors. The possibility of applying different thematic schemes allows the exploration of concepts according to different perspectives, which is able to emphasize particular and contingent aspects.",
"name": "SnowTerm Thesaurus",
"prefix": "498"
},
"499": {
"description": "The project aims at developing a controlled and structured terminology system related to GIS and remote sensing. The first phase corresponds to the identification of potential sources of terminology, the selection of proper terms, their extraction and the creation of a terminology database. Terms have been classified according to the EARTh upper structure. The semantic classification foresees the allocation of each term in a relation tree starting from the more general concept represented by the category. The result is a terminology system containing about 3.500 terms. The system can be considered as a prototype of domain semantic map, open to future integrations and updating. The use of the system by a user community would allow a better management of information and ease the information and data sharing, due both to the use of a common language and to the better semantic comprehension of data.",
"name": "Earth Observation Thesaurus",
"prefix": "499"
},
"50": {
"description": "An indexing tool to aid the recording of aircraft remains and crash sites, listing aircraft types by form, function and manufacturer. English Heritage takes a leading role in setting standards for recording the built and buried heritage. By setting standards that can be adopted by everyone, we can make sure that all records are consistent. In other words, if everyone uses the same words to describe the same monument, archaeological object, building material, etc, then anyone using this common language can easily index, retrieve and understand these records. With this aim in mind, English Heritage is continually developing new thesauri to provide structure and guidelines for the standardisation of terms to be used when creating new records of the past. Now, in our drive to disseminate these standards and promote their wider use, we are making available seven separate online thesauri. A tailor-made suite of programs has been developed, which uses a database to create a series of web pages for any chosen thesaurus. These can be easily accessed using a frames-capable browser and regularly updated as new terms are submitted and approved by our Data Standards Unit.",
"homepage": "http://thesaurus.historicengland.org.uk/thesaurus.asp?thes_no=225&thes_name=FISH%20Historic%20Aircraft%20Type%20Thesaurus",
"name": "English Heritage Aircraft Type Thesaurus",
"prefix": "50"
},
"500": {
"description": "The EARTh terminological content is derived form various multilingual and monolingual sources of controlled environmental terminology: GEMET - GEneral Multilingual Environmental Thesaurus; The UNEP-Infoterra EnVoc thesaurus; the Italian Earth Sciences Thesaurus; EnvDev, the Terminological Bulletin for the Rio de Janeiro Conference on Environment and Development, plus other documents concerning specific sectors. The selection, as well as the semantic and morphological processing of this terminology, is still in progress, and requires the management of problems connected with the utilization of multiple sources, developed in different operational fields and characterized by different approaches, concerning conceptual structuring and terminological representation. The thesaurus is constantly updated. At present it contains about 14.500 terms (...).",
"name": "Environmental Applications Reference Thesaurus",
"prefix": "500"
},
"501": {
"description": "The classification of therapeutic services (CTD) in medical rehabilitation has been a tried and tested instrument for the documentation of the therapeutic services in the rehabilitation discharge reports since 1997. It contributes significantly to the quality assurance of the medical rehabilitation of the pension insurance as well as to the further development of the rehabilitative care practices Rehabilitation guidelines that provide recommendations for the treatment of therapies for defined patient groups.",
"homepage": "http://www.deutsche-rentenversicherung.de/Allgemein/de/Inhalt/5_Services/03_broschueren_und_mehr/01_broschueren/01_national/KTL.html",
"name": "Classification of therapeutic services in medical rehabilitation",
"prefix": "501",
"wikidata_database": "Q1744633"
},
"502": {
"description": "APQC's Process Classification FrameworkSM (PCF) is a taxonomy of business processes that allows organizations to objectively track and compare their performance internally and externally with organizations from any industry. It also forms the basis for a variety of projects related to business processes. APQC's PCF was developed in the early 1990s by APQC and a group of members from a number of industries and countries throughout the world. Originally envisioned as a tool to aid in performance improvement projects, the framework evolved into the broad taxonomy that it is today. Organizations can use the PCF's common terminology to name, organize, and map their processes. It is also helpful as a tool for explaining a business in terms of horizontal processes rather than vertical functions. It is designed as a framework and global standard to be customized for use in any organization. Thus, the PCF does not list all processes within a specific organization, and every process listed in the framework does not exist in all organizations.",
"homepage": "http://www.apqc.org/knowledge-base/documents/apqc-process-classification-framework-pcf-cross-industry-pdf-version-600",
"name": "Process Classification Framework",
"prefix": "502"
},
"503": {
"description": "Country is a key variable for determining a range of social and economic statistics including country of birth, country of residence, migration, international trade and balance of payments. The National Statistics Country Classification, including the definition and coding index is designed to be the standard harmonised framework used by National Statistics' users and producers involved in the collection and processing of country-related statistical data. The National Statistics Country Classification is based on ISO 3166-1, adapted to meet data needs of United Kingdom National Statistics' users and producers.",
"homepage": "http://www.ons.gov.uk/ons/guide-method/classifications/current-standard-classifications/national-statistics-country-classification/index.html",
"name": "National Statistics Country Classification",
"prefix": "503"
},
"504": {
"abbreviation": "ISCED",
"description": "As national education systems vary in terms of structure and curricular content, it can be difficult to benchmark performance across countries over time or monitor progress towards national and international goals. In order to understand and properly interpret the inputs, processes and outcomes of education systems from a global perspective, it is vital to ensure that data are comparable. This can be done by applying the International Standard Classification of Education (ISCED), the standard framework used to categorise and report cross-nationally comparable education statistics.\n\nUNESCO developed the International Standard Classification of Education (ISCED) to facilitate comparisons of education statistics and indicators across countries on the basis of uniform and internationally agreed definitions. In 2011, a revision to ISCED was formally adopted by UNESCO Member States. The product of extensive international and regional consultations among education and statistical experts, ISCED 2011 takes into account significant changes in education systems worldwide since the last ISCED revision in 1997.",
"homepage": "http://www.uis.unesco.org/Education/Pages/international-standard-classification-of-education.aspx",
"name": "International Standard Classification of Education",
"prefix": "504",
"wikidata_database": "Q1390351"
},
"505": {
"abbreviation": "OBG",
"description": "The Preamble file (OBG) is a hierarchical collection of object names for cultural history museums, divided into 45 main groups and subgroups Of the Landesstelle for the non-state museums in Bavaria. Since 2008, the OBG is run in the web-based vocabulary administration tool xTree.",
"homepage": "https://museumsvokabular.de/sites/museumsvokabular/files/vocabulary/downloads/OBG%20Beschreibung-20220512.pdf",
"license": "CC BY-NC-SA 3.0",
"name": "Preamble file",
"prefix": "505"
},
"506": {
"description": "Over 10000 Meteorites from A-Z are listed by classification.",
"homepage": "http://class.meteorites.com.au/",
"name": "Meteorite Classification List",
"prefix": "506"
},
"507": {
"abbreviation": "ICTV",
"description": "Taxonomy lies at the uneasy interface between biology and logic. The processing of information follows somewhat different rules in these two systems and the role of taxonomy is to reconcile them as tidily as possible. To this end, the Virology Division of the International Union of Microbiological Societies (IUMS) charged the International Committee on Taxonomy of Viruses (ICTV) with the task of developing, refining, and maintaining a universal virus taxonomy. The goal of this undertaking is to categorize the multitude of known viruses into a single classification scheme that reflects their evolutionary relationships, i.e. their individual phylogenies.",
"homepage": "https://talk.ictvonline.org/taxonomy",
"name": "Virus Taxonomy",
"prefix": "507"
},
"508": {
"description": "Companies often use different names for the same invention, and additional variation may be introduced when the patent application is translated into different languages. Also some keywords can appear in many different contexts within patent titles. For example the word 'valve' can be either mechanical or electrical. So a subject classification system is essential for effective patent searching.\n\nDWPI categorizes patent documents using a simple classification system for all technologies. This unique classification is consistently applied to all patents by Thomson Scientific subject experts, enabling effective and precise searching in a particular area of technology. Patents are divided into three broad areas: Chemical, Engineering, and Electronic and Electrical Engineering. Each of these is then further divided into Sections and Classes which describe the technical area, or areas, covered by the patent.",
"homepage": "http://ip-science.thomsonreuters.com/scientific/support/patents/dwpiref/reftools/classification/",
"name": "Derwent World Patents Index Classification System",
"prefix": "508"
},
"509": {
"description": "The NCBI Taxonomy database is a curated set of names and classifications for all of the organisms that are represented in GenBank. When new sequences are submitted to GenBank, the submission is checked for new organism names, which are then classified and added to the Taxonomy database. As of April 2003, there were 176,890 total taxa represented.\n\nThere are two main tools for viewing the information in the Taxonomy database: the Taxonomy Browser, and Taxonomy Entrez. Both systems allow searching of the Taxonomy database for names, and both link to the relevant sequence data. However, the Taxonomy Browser provides a hierarchical view of the classification (the best display for most casual users interested in exploring our classification), whereas Entrez Taxonomy provides a uniform indexing, search, and retrieval engine with a common mechanism for linking between the Taxonomy and other relevant Entrez databases.\n\nOrganismal taxonomy is a powerful organizing principle in the study of biological systems. Inheritance, homology by common descent, and the conservation of sequence and structure in the determination of function are all central ideas in biology that are directly related to the evolutionary history of any group of organisms. Because of this, taxonomy plays an important cross-linking role in many of the NCBI tools and databases.\n\nThe NCBITaxon ontology is an automatic translation of the NCBI taxonomy (a taxonomic classification of living organisms and associated artifacts) database into obo/owl.",
"homepage": "http://www.ncbi.nlm.nih.gov/taxonomy",
"name": "National Center for Biotechnology Information Taxonomy",
"prefix": "509"
},
"51": {
"description": "Used for recording the techniques, recovery methods and materials associated with the archaeological sciences. English Heritage takes a leading role in setting standards for recording the built and buried heritage. By setting standards that can be adopted by everyone, we can make sure that all records are consistent. In other words, if everyone uses the same words to describe the same monument, archaeological object, building material, etc, then anyone using this common language can easily index, retrieve and understand these records. With this aim in mind, English Heritage is continually developing new thesauri to provide structure and guidelines for the standardisation of terms to be used when creating new records of the past. Now, in our drive to disseminate these standards and promote their wider use, we are making available seven separate online thesauri. A tailor-made suite of programs has been developed, which uses a database to create a series of web pages for any chosen thesaurus. These can be easily accessed using a frames-capable browser and regularly updated as new terms are submitted and approved by our Data Standards Unit.\n\nNational cultural heritage thesauri and vocabularies have acted as standards for use by both national organizations and local authority Historic Environment Records but until now have lacked the persistent Linked Open Data (LOD) URIs that would allow them to act as vocabulary hubs for the Web of Data. The AHRC funded SENESCHAL project aims to make such vocabularies available online as Semantic Web resources. SENESCHAL will start with major vocabularies as exemplars and project partners will continue to make other vocabularies available. Other organizations are welcome to make use of the data and services which will be open licensed.\n\nRESTful web services will be developed for the project to make the vocabulary resources programmatically accessible and searchable. These will include the provision to βfeed backβ new terms (concepts) suggested by users.",
"homepage": "http://www.heritagedata.org/blog/vocabularies-provided/",
"license": "CC-BY-3.0",
"name": "FISH Archaeological Sciences Thesaurus",
"prefix": "51"
},
"510": {
"description": "In the new 'Worldwide Bioclimatic Classification System' proposed, five macrobioclimates, twenty-seven bioclimates and five bioclimatic variants are recognized. The five macrobioclimates are: Tropical, Mediterranean, Temperate, Boreal and Polar. Each of them, and every one of their subordinate units or bioclimates, is represented by a characteristic group of plant formations, biocenosis and plant communities. Within almost every bioclimate, a number of variations in the seasonal rainfall patterns of rain allows us to recognize the bioclimatic variants. Additionally, within every bioclimate, variations in the thermic and ombrothermic values make it possible to distinguish the bioclimatic belts: thermotypes and ombrotypes. If macrobioclimates, bioclimates, bioclimatic variants as well as bioclimatic belts (thermo- and ombrotypes) are taken into account, about three hundred isobioclimates find territorial representation on the Earth.",
"homepage": "http://www.globalbioclimatics.org/",
"name": "Worldwide Bioclimatic Classification System",
"prefix": "510"
},
"511": {
"description": "For the news industry - but also far beyond - it is a strict requirement being able to assert something about the content of a news item, to apply so called metadata. This could be achieved either by free-text human language (e.g. by a headline or a caption) or by codes, NewsCodes. Codes have the advantage that they can be easily shared among users and as each code requires an explicit and comprehensive definition not only the codes but also their semantics can be shared among users. Further NewsCodes are language agnostic, thus the code is the same for describing content in different languages, only the definition of the code should be translated to help with understanding its semantics. As the world is only one single big object all codes could be put into a single vocabulary. But such a vocabulary can hardly be managed. For that reason the IPTC decided to split concepts of the same type into a specific controlled vocabulary. Each vocabulary has a description of its scope.",
"homepage": "http://www.iptc.org/site/NewsCodes/View_NewsCodes/",
"name": "NewsCodes",
"prefix": "511"
},
"512": {
"description": "The International Patent Classification (IPC), established by the Strasbourg Agreement 1971, provides for a hierarchical system of language independent symbols for the classification of patents and utility models according to the different areas of technology to which they pertain.\n\nThe IPC divides technology into eight sections with approximately 70,000 subdivisions. Each subdivision has a symbol consisting of Arabic numerals and letters of the Latin alphabet.\n\nThe appropriate IPC symbols are indicated on each patent document, of which more than 1,000,000 were issued each year in the last 10 years. The IPC symbols are allotted by the national or regional industrial property office that publishes the patent document. For PCT documents, IPC symbols are allotted by the International Searching Authority (ISA).\n\nThe Classification is indispensable for the retrieval of patent documents in the search for 'prior art.' Such retrieval is needed by patent-issuing authorities, potential inventors, research and development units, and others concerned with the application or development of technology.",
"homepage": "http://www.wipo.int/classifications/ipc/en/",
"license": "CC-BY-3.0",
"name": "International Patent Classification",
"prefix": "512",
"wikidata_database": "Q1667423"
},
"513": {
"description": "The USPC is a system for organizing all U.S. patent documents and many other technical documents into relatively small collections based on common subject matter. Each subject matter division in the USPC includes a major component called a class and a minor component called a subclass. A class generally delineates one technology from another. Subclasses delineate processes, structural features, and functional features of the subject matter encompassed within the scope of a class. Every class has a unique alphanumeric identifier, as do most subclasses.\n\nA class/subclass pair of identifiers uniquely identifies a subclass within a class (for example, the identifier '2/456' represents Class 2, Apparel, subclass 456, Body cover). This unique identifier is called a classification symbol, or simply a classification, or USPC classification, to distinguish it from classifications of other patent classification schemes. A subclass represents the smallest division of subject matter in the USPC under which documents may be collected.",
"homepage": "http://www.uspto.gov/web/patents/classification/selectnumwithtitle.htm",
"name": "United States Patent Classification",
"prefix": "513",
"wikidata_database": "Q7890868"
},
"514": {
"description": "The Cooperative Patent Classification (CPC) effort is a joint partnership between the United States Patent and Trademark Office (USPTO) and the European Patent Office (EPO) where the Offices have agreed to harmonize their existing classification systems (European Classification (ECLA) and United States Patent Classification (USPC) respectively) and migrate towards a common classification scheme.",
"homepage": "http://worldwide.espacenet.com/classification?locale=en_EP",
"name": "Cooperative Patent Classification",
"prefix": "514",
"wikidata_database": "Q1765777"
},
"515": {
"description": "An Emergency Classification is a set of plant conditions which indicate a level of risk to the public. Both nuclear power plants and research and test reactors use the four emergency classifications listed below in order of increasing severity. The vast majority of events reported to the NRC are routine in nature and do not require activation of our incident response program. Recognizing that security-related events may involve different response actions from the licensees, the NRC issued Bulletin 2005-02, Emergency Preparedness and Response Actions for Security-Based Events. This bulletin identifies minor changes to the emergency classification levels to reflect emphasis of post-9/11 conditions.",
"homepage": "http://www.nrc.gov/about-nrc/emerg-preparedness/about-emerg-preparedness/emerg-classification.html",
"name": "Emergency Classification",
"prefix": "515"
},
"516": {
"description": "Development of the Biocomplexity Thesaurus began in 2002-2003 through a partnership between the former USGS NBII Program and ProQuest (formerly CSA), a worldwide information company with more than 30 years experience as a leading bibliographic database provider. The original Biocomplexity Thesaurus, first made available online in 2003, was a merger of five individual thesauri:\n\n* the CSA Aquatic Sciences and Fisheries Thesaurus\n\n* the CSA Life Sciences Thesaurus\n\n* the CSA Pollution Thesaurus\n\n* the CSA Sociological Thesaurus\n\n* the CERES/NBII Thesaurus\n\nIn 2004, the CSA Ecotourism Thesaurus was also merged into the Biocomplexity Thesaurus. Merging and reconciliation of the terms in these thesauri was performed by Jessica Milstead, a leading expert in the development of scientific thesauri. In 2007, USGS assumed editorial management of the Biocomplexity Thesaurus, and now leads expansion of the thesaurus, addition or modification of terms, and development of tools and services to enable the use of the Thesaurus in both CSAS and external applications. In 2008, USGS significantly expanded the Biocomplexity Thesaurus to include terminology that supports the fire ecology and management communities. More than 2,000 new concepts were added to the Thesaurus. This expansion was made possible by the very generous contributions of the following terminologies by their managing organizations:\n\n* E.V. Komarek Fire Ecology Thesaurus, Tall Timbers Research Station\n\n* Fire Effects Information System (FEIS) Glossary\n\n* Northwest and Alaska Fire Effects Clearinghouse Glossary\n\n* National Wildfire Coordinating Group Glossary of Wildland Fire Terminology\n\n* Encyclopedia of Southern Fire Science\n\n* Wildland Fire Lessons Learned Center Topics\n\nThe USGS Core Science Analytics & Synthesis (CSAS) Program is committed to maintaining and expanding the Biocomplexity Thesaurus to support science informatics initiatives within USGS, and externally.",
"homepage": "http://www.usgs.gov/core_science_systems/csas/biocomplexity_thesaurus/index.html",
"name": "Biocomplexity Thesaurus",
"prefix": "516"
},
"517": {
"description": "The Alpha-Numeric System for Classification of Recordings (ANSCR) is composed of 46 major categories into which all sound recordings are organized.",
"homepage": "http://www.calstatela.edu/library/guides/anscr_class.htm",
"name": "Alpha-Numeric System for Classification of Recordings",
"prefix": "517"
},
"518": {
"description": "Library stocks are freely accessible according to this system.",
"homepage": "http://www.drze.de/bibliothek/systematik",
"name": "Systematics of the special library of the German Reference Center for Ethics in the Biosciences",
"prefix": "518"
},
"519": {
"description": "The Australian and New Zealand Standard Research Classification (ANZSRC) is jointly produced by the Australian Bureau of Statistics (ABS) and Statistics New Zealand (Statistics NZ). ANZSRC is the collective name for a set of three related classifications developed for use in the measurement and analysis of research and experimental development (R&D) undertaken in Australia and New Zealand. The three constituent classifications included in the ANZSRC are: Type of Activity (TOA), Fields of Research (FOR), and Socio-economic Objective (SEO). ANZSRC replaces the Australian Standard Research Classification (ASRC 1998) and introduces a new framework for measuring research and development activity in New Zealand. The use of the three constituent classifications in the ANZSRC ensures that R&D statistics collected are useful to governments, educational institutions, international organisations, scientific, professional or business organisations, business enterprises, community groups and private individuals in Australia and New Zealand.",
"homepage": "http://www.abs.gov.au/ausstats/abs@.nsf/mf/1297.0",
"license": "CC-BY-3.0",
"name": "Australian and New Zealand Standard Research Classification: Type of Activity",
"prefix": "519",
"wikidata_database": "Q4824842"
},
"52": {
"description": "Types of cargo being carried by ships when they went down. English Heritage takes a leading role in setting standards for recording the built and buried heritage. By setting standards that can be adopted by everyone, we can make sure that all records are consistent. In other words, if everyone uses the same words to describe the same monument, archaeological object, building material, etc, then anyone using this common language can easily index, retrieve and understand these records. With this aim in mind, English Heritage is continually developing new thesauri to provide structure and guidelines for the standardisation of terms to be used when creating new records of the past. Now, in our drive to disseminate these standards and promote their wider use, we are making available seven separate online thesauri. A tailor-made suite of programs has been developed, which uses a database to create a series of web pages for any chosen thesaurus. These can be easily accessed using a frames-capable browser and regularly updated as new terms are submitted and approved by our Data Standards Unit.\n\nNational cultural heritage thesauri and vocabularies have acted as standards for use by both national organizations and local authority Historic Environment Records but until now have lacked the persistent Linked Open Data (LOD) URIs that would allow them to act as vocabulary hubs for the Web of Data. The AHRC funded SENESCHAL project aims to make such vocabularies available online as Semantic Web resources. SENESCHAL will start with major vocabularies as exemplars and project partners will continue to make other vocabularies available. Other organizations are welcome to make use of the data and services which will be open licensed.\n\nRESTful web services will be developed for the project to make the vocabulary resources programmatically accessible and searchable. These will include the provision to βfeed backβ new terms (concepts) suggested by users.",
"homepage": "http://thesaurus.historicengland.org.uk/thesaurus.asp?thes_no=77&thes_name=FISH%20Maritime%20Cargo%20Types%20Thesaurus",
"name": "English Heritage Cargo Types Thesaurus",
"prefix": "52"
},
"520": {
"abbreviation": "DFG",
"description": "German Research Foundation (DFG) classification of scientific disciplines, research areas, review boards, and subject areas. The vocabulary is reviewed by the Senate of the DFG every four years (2016-2019, 2020-2024, ...)",
"homepage": "http://www.dfg.de/dfg_profil/gremien/fachkollegien/faecher/",
"name": "Systematics of the subjects and colleges of the German Research Association",
"prefix": "520",
"wikidata_database": "Q110439023"
},
"521": {
"description": "The publication Keys to Soil Taxonomy serves two purposes. It provides the taxonomic keys necessary for the classification of soils in a form that can be used easily in the field. It also acquaints users of the taxonomic system with recent changes in the system. The eleventh edition of the Keys to Soil Taxonomy incorporates all changes approved since the publication of the second edition of Soil Taxonomy: A Basic System of Soil Classification for Making and Interpreting Soil Surveys (1999). One of the most significant changes in the eleventh edition is the addition of the suborders Wassents and Wassists for subaqueous Entisols and Histosols. We plan to continue issuing updated editions of the Keys to Soil Taxonomy as changes warrant new editions. Since it was first published 35 years ago, Soil Taxonomy: A Basic System of Soil Classification for Making and Interpreting Soil Surveys has been used to support soil survey efforts in many countries around the world. It has been translated into several languages. Soil scientists from many nations have contributed significantly to the development of the taxonomic system. The authors encourage the continued use of soil taxonomy internationally and look forward to future collaborations with the international soil science community so we can continue to make improvements. Through continued communication and collaboration, we hope that our efforts will eventually result in a truly universal soil classification system.",
"homepage": "http://www.nrcs.usda.gov/wps/portal/nrcs/main/soils/survey/class/taxonomy/",
"name": "Soil Taxonomy",
"prefix": "521",
"wikidata_database": "Q512060"
},
"522": {
"description": "The MK Spectral classification system was founded by W. W. Morgan and P. C. Keenan in the year 1943, with the publication of the first photographic spectral classification atlas, 'An Atlas of Stellar Spectra' (Morgan, Keenan & Kellman 1943). Since that time, the MK system has been extensively revised and refined by Morgan, Keenan and others. In the late 1970's, two important spectral atlases, summarizing the development of the MK system up until that time, were published. These atlases, the Revised MK Spectral Atlas for Stars Earlier than the Sun by Morgan, Abt & Tapscott (1978) and An Atlas of Spectra of the Cooler Stars: Types G, K, M, S and C, by Keenan & McNeil (1976), are the inspiration for this new digital spectral classification atlas. Indeed, some of the pages in this atlas are 'digitized' versions of pages from those two atlases. The MK spectral classification system is a natural, empirical system of spectral classification which uses in the classification process only the directly observable features in the spectrum. The MK system is defined by a set of standard stars, and classification on the system is carried out by the comparison of the program star with the standard stars, taking into account all of the features in the spectrum. The use of standards is vital because it maintains the autonomy of the system as well as ensuring that different observers will classify stars on the same system. When the MK system was first defined, it was based on photographic spectra in the blue-violet part of the spectrum. This was done by necessity, as photographic emulsions in the 1940's were sensitive only to blue-violet light. However, it was a fortunate choice, as the blue-violet portion of the spectrum (essentially from the Ca II K-line to Hbeta) contains a high density of astrophysically important atomic lines and molecular bands, which allow accurate classification of the star in a two-dimensional temperature, luminosity grid. Classification systems can and have been set up in the red, IR and the ultraviolet. These should remain independent of the traditional MK system, as different parts of the spectrum can sample different levels in the atmosphere of the star. The current spectral atlas should be considered an ongoing work which will likely be completed only in a number of years. The spectra in this atlas have been obtained with the Gray/Miller spectrograph on the 0.8 meter telescope of the Dark Sky Observatory, using a CCD detector. Two spectral resolutions have been used in this atlas. Most of the illustrations use spectra obtained with the 1200g/mm grating, which gives a spectral resolution of 1.8 Γ
/2 pixels and a spectral range of 3800 Γ
- 4600 Γ
, but some illustrations, especially those of the later-type stars (K, M, C and S) use spectra obtained with the 600g/mm grating. These have a resolution of 3.6 Γ
/2 pixels, and a spectral range of 3800 Γ
- 5600 Γ
. The higher resolution spectra are presented in a rectified intensity versus wavelength format, in which the spectral continuum has been normalized to unity. The 3.6 Γ
resolution spectra, for the most part, are presented in a flux versus wavelength format; this format provides additional information on the energy distribution of the star, and is to be preferred for the cooler stars, as these stars have essentially no continuum points in their spectra. For ease of illustration, the fluxes have been normalized to unity at one consistent point in the spectrum. Since the publication of the two most recent photographic spectral atlases mentioned in the paragraphs above, the MK system has undergone extensive revision and refinement. Important work in refining and extending the MK system to dimensions beyond the traditional two-dimensional temperature/luminosity grid has been carried out by Keenan and co-workers in the addition of abundance indices for the late-type stars, by Gray (1989), in the extension of the MK system to metal-weak F and G-type stars, by Henry, Kirkpatrick & coworkers in their careful redefinition and extension of the MK system to the M-type dwarfs and most lately the \"L-type\" stars, and by Walborn in the classification of the O-type stars. Later editions of this atlas will attempt to illustrate more fully these developments.",
"homepage": "http://ned.ipac.caltech.edu/level5/Gray/frames.html",
"name": "Digital Spectral Classification Atlas",
"prefix": "522"
},
"523": {
"description": "The Atlas of Stellar Spectra and the accompanying outline have been prepared from the viewpoint of the practical stellar astronomer. Problems connected with the astrophysical interpretation of the spectral sequence are not touched on; as a consequence, emphasis is placed on ``ordinary'' stars. These are the stars most important statistically and the only ones suitable for large-scale investigations of galactic structure. The plan of the Atlas can be stated as follows: a) To set up a classification system as precise as possible which can be extended to stars of the eighth to twelfth magnitude with good systematic accuracy. The system should be as closely correlated with color temperature (or color equivalent) as is possible. The criteria used for classification should be those which change most smoothly with color equivalent. b) Such a system as described under (a) requires a classification according to stellar luminosity, that is, the system should be two-dimensional. We thus introduce a vertical spectral type, or luminosity class; then, for a normal star, the spectrum is uniquely located when a spectral type and a luminosity class are determined. The actual process of classification is carried out in the following manner: (1) an approximate spectral type is determined; (2) the luminosity class is determined; (3) by comparison with stars of similar luminosity an accurate spectral type is found.",
"homepage": "http://ned.ipac.caltech.edu/level5/ASS_Atlas/frames.html",
"name": "Atlas of Stellar Spectra",
"prefix": "523"
},
"524": {
"description": "The United Nations Standard Products and Services CodeΒ (UNSPSCΒ) provides an open, global multi-sector standard for efficient, accurate classification of products and services. Search the code on this website to locate commodity codes that can be used by your company. The UNSPSC offers a single global classification system that can be used for: Company-wide visibility of spend analysis, Cost-effective procurement optimization, Full exploitation of electronic commerce capabilities. The UNSPSC is a hierarchical classification with five levels. These levels allow analysis by drilling down or rolling up to analyze expenditures. Each level in the hierarchy has its own unique number.",
"homepage": "http://www.unspsc.org/",
"name": "United Nations Standard Products and Services Code",
"prefix": "524",
"wikidata_database": "Q1361569"
},
"525": {
"description": "The HTS comprises a hierarchical structure for describing all goods in trade for duty, quota, and statistical purposes. This structure is based upon the international Harmonized Commodity Description and Coding System (HS), administered by the World Customs Organization in Brussels; the 4- and 6-digit HS product categories are subdivided into 8-digit unique U.S. rate lines and 10-digit non-legal statistical reporting categories.",
"homepage": "http://hts.usitc.gov/",
"name": "Harmonized Tariff Schedule of the United States",
"prefix": "525",
"wikidata_database": "Q16841257"
},
"526": {
"description": "The National Taxonomy of Exempt Entities (NTEE) system is used by the IRS and NCCS to classify nonprofit organizations. It is also used by the Foundation Center to classify both grants and grant recipients (typically nonprofits or governments). NCCS and the IRS use the NTEE-CC system, described below, while the Foundation Center uses a slightly different version with more codes, as well as 'population/beneficiary' codes to indicate the type of population served and 'auspice' codes to indicate religious or governmental affiliation. The original NTEE was developed by NCCS during the 1980s with the collaboration of major nonprofit organizations. According to Russy D. Sumariwalla, one of the principal developers of the system, the use of such a system: facilitates the collection, tabulation, presentation, and analysis of data by the types of organizations and their activities; promotes uniformity and comparability in the presentation of statistical and other data collected by various public and private agencies; provides better quality information as the basis for public policy debate and decision-making for the nonprofit sector and for society at large. In the mid-1990s, the IRS decided to begin classifying new organizations using the NTEE system. The 'IRS determination specialists' - the individuals who decide whether or not an organization is eligible to receive federal tax exempt status - would classify the organizations based on descriptive data in the organizations' applications for recognition of tax-exempt status (Forms 1023 and 1024). Before beginning, they requested a simplified version of the NTEE to ease classification and to provide a better fit into the North American Industry Classification System (NAICS), the new federal government economic classification system that replaced the Standard Industrial Classification (SIC) codes in 1999. The National Taxonomy of Exempt Entities-Core Codes (NTEE-CC) was created to meet this need. Designed by a team of experts, the NTEE-CC includes approximately two-thirds, or about 400, of the 645 categories in the original NTEE. Though the majority of the differences in the NTEE-CC are a result of collapsing lesser-used codes, improvements were also included. With its ease of use and consistent hierarchical logic, the NTEE-CC serves as the best instrument for tax-exempt status determination, NAICS linkage, and nonprofit organizational classification. Unlike the system used the Foundation Center, the NTEE-CC system eliminated the so-called Common Codes that permitted the 4th character of the NTEE to indicate if an organization primarily serve any of a dozen or so functions other than direct service. These categories include: alliances, advocacy, management and technical assistance, research, policy analysis, fundraising and other types of support for other nonprofit organizations. At the same time, the NTEE-CC system added 3-character categories - all in the 01-19 range within each major group (e.g., A01, B01, A19, B19, etc.) - for organizations that fulfilled these specialized functions.",
"homepage": "http://nccs.urban.org/classification/NTEE.cfm",
"name": "National Taxonomy of Exempt Entities",
"prefix": "526",
"wikidata_database": "Q178110"
},
"527": {
"description": "In 2012, in order to better meet the needs of the philanthropic sector, the Foundation Center began an extensive revision of our Philanthropy Classification System (PCS), reexamining both the terms included in the taxonomy and the overall structure. The goal was not to create yet another standard, but to work towards creating a more broadly adopted standard that more accurately reflects the work of the field and can serve as a more relevant tool for a 21st Century global philanthropy community.\n\nThe Center consulted partner organizations, received feedback from the sector to complete the final revisions, and released the first version of the PCS in December 2014. The Center will be recoding our entire database over the next 4 months and the PCS will be reflected in our online products during the second quarter of 2015. Until that time we will continue to publish data using our prior Grants Classification System.\n\nThe Philanthropy Classification System (PCS) describes the work of grantmakers, recipient organizations and the philanthropic transactions between those entities. The Centerβs Classification System in based on the National Taxonomy of Exempt Entities (NTEE) and has been expanded over the last three decades to include the emerging work we have evidenced while capturing and indexing the work of the sector on a global scale.\n\nThe facets of the PCS illuminate the work and answer the following questions about philanthropy:\n\n Who? = Population Served\n\n What? = Subject and Organization Type\n\n How? = Support Strategy and Transaction Type\n\n Where? = Geographic Area Served (geotree.foundationcenter.org)\n\nOur newly designed site lets you explore each facet of the taxonomy through the Visual Navigation tool, Quick Search, A-Z search or a hierarchy view.",
"homepage": "http://taxonomy.foundationcenter.org/",
"license": "CC BY-NC 3.0",
"name": "Philanthropy Classification System",
"prefix": "527"
},
"528": {
"abbreviation": "NLM",
"description": "The NLM Classification covers the field of medicine and related sciences. The scheme is a system of classification intended to be used for the shelf arrangement of all library materials, regardless of format. Designed as a broad classification, it is suitable for both large and small library collections and may be adapted to handle specialized collections of any size. The NLM Classification is a system of mixed notation patterned after the Library of Congress (LC) Classification where alphabetical letters which denote broad subject categories are further subdivided by numbers. The NLM Classification utilizes schedules QS-QZ and W-WZ, permanently excluded from the LC Classification Schedules and is intended to be used with the LC schedules which supplement the NLM Classification for subjects bordering on medicine and for general reference materials. The LC schedules for Human Anatomy (QM), Microbiology (QR), and Medicine (R) are not used at all by the National Library of Medicine since they overlap the NLM Classification. The headings for the individual schedules are given in brief form (e.g., WE - Musculoskeletal System; WG - Cardiovascular System) and together they provide an outline of the subjects that constitute the NLM Classification. These headings are interpreted broadly and include the physiological system, the specialty or specialties connected with them, the regions of the body chiefly concerned and subordinate related fields. The Classification is hierarchical, and within each schedule, division by organ usually has priority. Each main schedule, as well as some sections within a schedule, begins with a group of form numbers ranging generally from 1-49 which are used to classify materials by publication type, e.g., dictionaries, atlases, laboratory manuals, etc. The main schedules QS-QZ, W-WY, and WZ (excluding WZ 220-270) are used to classify works published after 1913; the 19th century schedule is used for works published 1801-1913; and WZ 220-270 is used to provide century groupings for works published before 1801 and Americana. Geographic subdivision is provided for certain subjects in the NLM schedules by the application of Table G notations.",
"homepage": "http://www.nlm.nih.gov/class/",
"name": "National Library of Medicine Classification",
"pattern": "^[A-Z]+ [0-9]+(.[0-9](.[A-Z0-9]+)?)?$",
"prefix": "528",
"wikidata_database": "Q986957"
},
"529": {
"description": "Shelf Classification for the inventory of the Chemistry Biology Pharmacy Information Center, accessible via StarTree, alphabetical lists, search and navigation in the classification. It is based on practical criteria (investigated and mediated knowledge areas, size and segmentation of the stock in the participating departments) And was developed partly in collaboration with the institutes. 1366 Descriptors, 239 Synonyms.",
"homepage": "http://www.clicaps.ethz.ch/topics.php",
"name": "CLICAPS Shelf Classification",
"prefix": "529"
},
"53": {
"description": "Elements of a monument relating to the built or buried heritage. English Heritage takes a leading role in setting standards for recording the built and buried heritage. By setting standards that can be adopted by everyone, we can make sure that all records are consistent. In other words, if everyone uses the same words to describe the same monument, archaeological object, building material, etc, then anyone using this common language can easily index, retrieve and understand these records. With this aim in mind, English Heritage is continually developing new thesauri to provide structure and guidelines for the standardisation of terms to be used when creating new records of the past. Now, in our drive to disseminate these standards and promote their wider use, we are making available seven separate online thesauri. A tailor-made suite of programs has been developed, which uses a database to create a series of web pages for any chosen thesaurus. These can be easily accessed using a frames-capable browser and regularly updated as new terms are submitted and approved by our Data Standards Unit.\n\nNational cultural heritage thesauri and vocabularies have acted as standards for use by both national organizations and local authority Historic Environment Records but until now have lacked the persistent Linked Open Data (LOD) URIs that would allow them to act as vocabulary hubs for the Web of Data. The AHRC funded SENESCHAL project aims to make such vocabularies available online as Semantic Web resources. SENESCHAL will start with major vocabularies as exemplars and project partners will continue to make other vocabularies available. Other organizations are welcome to make use of the data and services which will be open licensed.\n\nRESTful web services will be developed for the project to make the vocabulary resources programmatically accessible and searchable. These will include the provision to βfeed backβ new terms (concepts) suggested by users.",
"homepage": "http://www.heritagedata.org/blog/vocabularies-provided/",
"license": "CC-BY-3.0",
"name": "Components (EH)",
"prefix": "53"
},
"530": {
"description": "Human Resources, within the Finance and Administration Division, provides system-wide leadership, consultative services, and coordination of major human resources functions in cooperation with the seven public universities that comprise the Oregon University System. Human Resource performs a wide range of Chancellor's Office and system-wide responsibilities, including conducting and reporting system wide compensations and benefit survey findings, participating in system wide projects and task forces. The Human Resources department works closely with OUS leadership and Chancellorβs office department heads on CO staffing, compensation, leave administration, and employment policy. The department also disseminates collective bargaining agreement and benefits information to the campuses, and works closely with campus services for Chancellor's office benefits administration.",
"homepage": "http://www.ous.edu/dept/hr/classification-specs/",
"name": "Oregon University System Human Resources Classification Specifications",
"prefix": "530"
},
"531": {
"description": "In the naming of garments we worked always from the objects themselves and their relation to the body and not to any theory of classification which introduced other factors. The terms themselves and their grouping do not take account of special Function, but the naming has to be seen within the context of the list of basic information where function appears as a separate entry, following the name of the object. So the basic term for bathing or wedding dress alike is Dress. The lists of basic information and basic terms are now published as a guide to recording, setting out what information should be recorded from dress to lead into the many different aspects of its study and recommending a vocabulary of basic terms for identifying and recording its garments and accessories. The versions in different languages are not translations but the result of working together with common identification of the main types of garment with appropriate naming in each language.",
"homepage": "http://www.collectionslink.org.uk/assets/thesaurus_icombts/vbt00e.htm",
"name": "Vocabulary of Basic Terms for Cataloguing Costume",
"prefix": "531"
},
"532": {
"description": "The classification rules of the VDP define the quality of a wine in particular according to the terroir, the origin in connection with the quality, the maintenance of this particular terroir is the focus - and this is accompanied by the renouncement of all area, generic and simple position designations Terroir is defined by a 'magical triangle' of the first quality and character of the vineyard, the second hand of the winemaker, and the 3rd quality of the grapes, which is recognizable in the wine, and the quality of a vineyard is defined Through the soil (topographical location, climate and microclimate), and the use of appropriate grape varieties is defined as a terroir.",
"homepage": "http://www.vdp.de/de/der-vdp/klassifikation/",
"name": "Association of German PrΓ€dikatsweingΓΌter e. V. Classification model",
"prefix": "532"
},
"533": {
"abbreviation": "RVK",
"description": "The Regensburger Verbundklassifikation (RVK) is a classification scheme for academic libraries. In the 1960s the University of Regensburg Library developed the RVK as an in-house classification scheme for its own extensive holdings on the open shelves. Since then the RVK evolved step by step into a classification which is currently developed cooperatively by a network of 130 academic libraries and institutions in Germany, Austria, Italy and Switzerland. The University of Regensburg Library maintains the RVK as a tool for the organization of knowledge with regard to its technical and organisational requirements.",
"homepage": "http://rvk.uni-regensburg.de/",
"license": "CC0-1.0",
"name": "Regensburger Association Classification",
"pattern": "^(LD,)?[A-Z]([A-Z]( [0-9]+([a-z]|\\.[0-9]+)?( [A-Z][0-9]*)?)?)?( - [A-Z]([A-Z]( [0-9]+([a-z]|\\.[0-9]+)?( [A-Z][0-9]*)?)?)?)?$",
"prefix": "533",
"wikidata_database": "Q2137453"
},
"534": {
"abbreviation": "SOC",
"description": "The 2010 Standard Occupational Classification (SOC) system is used by Federal statistical agencies to classify workers into occupational categories for the purpose of collecting, calculating, or disseminating data. All workers are classified into one of 840 detailed occupations according to their occupational definition. To facilitate classification, detailed occupations are combined to form 461 broad occupations, 97 minor groups, and 23 major groups. Detailed occupations in the SOC with similar job duties, and in some cases skills, education, and/or training, are grouped together.",
"homepage": "http://www.bls.gov/soc/",
"name": "Standard Occupational Classification",
"prefix": "534",
"wikidata_database": "Q7598269"
},
"535": {
"description": "SCOP contains the domains of all PDB entries available at the time of the current release's construction. For each of these entries a coordinate file is available and can be displayed via the various graphical interfaces. The sequence of each protein chain has also been extracted. The release also contains many literature references. These are structures that have been published in sufficient detail to be classified in SCOP, but where the coordinates are not yet available from PDB. Whereas PDB entries are identified by a 4 letter code starting with a digit, these literature entries have been given 4 letter codes starting with the letter s followed by 3 digits, e.g. s149. This code is arbitrary and may change between releases. Entries included in SCOP in this way tend only to be those structures that are significantly different from any structure already in PDB. In the absence of a PDB header, a pseudo header file has been constructed. These header files contain the reference; the SWISSPROT identifier for the sequence; the fragment of the sequence for which structural information exists (where known) and the domain classification of each part of this sequence fragment in SCOP. (Note that occassionally some of this information is incomplete where there was insufficient information about the sequence in the orginal reference.)",
"homepage": "http://scop.mrc-lmb.cam.ac.uk/scop/",
"name": "Structural Classification of Proteins",
"prefix": "535",
"wikidata_database": "Q4832556"
},
"536": {
"description": "Estimated # species in Lamiales = 22,000. The goal of this project is to produce a working infraordinal classification of the Lamiales to genus with information on distribution and species richness. All recognized taxa will be clades; adherence to Linnaean ranks is optional. Synonymy is very incomplete (comprehensive synonymy is not a goal of the project, but could be incorporated). Although I anticipate producing a publishable version of this classification at a future date, my near-term goal is to produce a web-accessible version, which will be available to the public and which will be updated regularly through input from systematists familiar with taxa within the Lamiales.",
"homepage": "http://depts.washington.edu/phylo/classifications/",
"name": "A Synoptical Classification of the Lamiales",
"prefix": "536"
},
"537": {
"description": "Non-profit institutions in the satellite account are classified by primary area of activity according to the International Classification of Non-profit Organizations (ICNPO). It is the classification system recommended in the United Nations (UN) Handbook on Non-profit Institutions in the System of National Accounts. The ICNPO system groups organizations into 12 major activity groups, including a catch-all 'not elsewhere classified' category. These 12 major activity groups are further divided into 24 subgroups. Satellite account estimates are published at the major group level.",
"homepage": "http://www.statcan.gc.ca/pub/13-015-x/2009000/sect13-eng.htm",
"name": "The International Classification of Non-profit Organizations",
"prefix": "537"
},
"538": {
"description": "The Carnegie Classificationβ’ has been the leading framework for recognizing and describing institutional diversity in U.S. higher education for the past four decades. Starting in 1970, the Carnegie Commission on Higher Education developed a classification of colleges and universities to support its program of research and policy analysis. Derived from empirical data on colleges and universities, the Carnegie Classification was originally published in 1973, and subsequently updated in 1976, 1987, 1994, 2000, 2005, and 2010 to reflect changes among colleges and universities. This framework has been widely used in the study of higher education, both as a way to represent and control for institutional differences, and also in the design of research studies to ensure adequate representation of sampled institutions, students, or faculty. To ensure continuity of the classification framework and to allow comparison across years, the 2010 Classification update retains the same structure of six parallel classifications, initially adopted in 2005. They are as follows: Basic Classification (the traditional Carnegie Classification Framework), Undergraduate and Graduate Instructional Program classifications, Enrollment Profile and Undergraduate Profile classifications, and Size & Setting classification. These classifications provide different lenses through which to view U.S. colleges and universities, offering researchers greater analytic flexibility. These classifications were updated using the most recent national data available as of 2010, and collectively they depict the most current landscape of U.S. colleges and universities.",
"homepage": "http://carnegieclassifications.iu.edu/",
"license": "CC BY-NC-SA 3.0",
"name": "The Carnegie Classification of Institutions of Higher Education",
"prefix": "538",
"wikidata_database": "Q4223026"
},
"539": {
"description": "The classification for Community Engagement is an elective classification, meaning it is based on voluntary participation by institutions. Whereas the Foundation's all-inclusive classifications involve secondary analysis of existing national data sources available for all institutions, elective classifications involve additional data collection and documentation, with substantial effort invested by participating institutions. Elective classifications enable the Foundation's classification system to recognize important aspects of institutional mission and action that are not represented in the national data. Because of their voluntary nature, elective classifications do not represent a comprehensive national assessment: an institution's absence from the Community Engagement classification should not be interpreted as reflecting a judgment about the institution's commitment to its community.",
"license": "CC BY-NC-SA 3.0",
"name": "Community Engagement Elective Classification",
"prefix": "539"
},
"54": {
"description": "A development of the ALGAO events wordlist. The thesaurus is an indexing tool to be used for recording archaeological and architectural investigative, data collection exercises; from intrusive interventions into the resource to non damaging survey events. The Event Types Thesaurus includes 128 terms. Of these, there are 83 preferred terms, 37 non-preferred terms and 8 non-index terms. The terms are divided into two classes: INTRUSIVE EVENT and NON INTRUSIVE EVENT. The former covering events that have a physical impact upon the archaeological resource and the latter covering events that record the resource but do not have a physical impact upon it. In order to ease retrieval the terms sit in hierarchies under a number of non index grouping terms, for example ARCHAEOLOGICAL INTERVENTION, ENVIRONMENTAL INTERVENTION, HERITAGE ASSESSMENT and REMOTE SENSING etc.\n\nEnglish Heritage takes a leading role in setting standards for recording the built and buried heritage. By setting standards that can be adopted by everyone, we can make sure that all records are consistent. In other words, if everyone uses the same words to describe the same monument, archaeological object, building material, etc, then anyone using this common language can easily index, retrieve and understand these records. With this aim in mind, English Heritage is continually developing new thesauri to provide structure and guidelines for the standardisation of terms to be used when creating new records of the past. Now, in our drive to disseminate these standards and promote their wider use, we are making available seven separate online thesauri. A tailor-made suite of programs has been developed, which uses a database to create a series of web pages for any chosen thesaurus. These can be easily accessed using a frames-capable browser and regularly updated as new terms are submitted and approved by our Data Standards Unit.\n\nNational cultural heritage thesauri and vocabularies have acted as standards for use by both national organizations and local authority Historic Environment Records but until now have lacked the persistent Linked Open Data (LOD) URIs that would allow them to act as vocabulary hubs for the Web of Data. The AHRC funded SENESCHAL project aims to make such vocabularies available online as Semantic Web resources. SENESCHAL will start with major vocabularies as exemplars and project partners will continue to make other vocabularies available. Other organizations are welcome to make use of the data and services which will be open licensed.\n\nRESTful web services will be developed for the project to make the vocabulary resources programmatically accessible and searchable. These will include the provision to βfeed backβ new terms (concepts) suggested by users.",
"homepage": "http://www.heritagedata.org/blog/vocabularies-provided/",
"license": "CC-BY-3.0",
"name": "FISH Event Types Thesaurus",
"prefix": "54"
},
"540": {
"abbreviation": "NOC",
"description": "The National Occupational Classification (NOC) 2011 provides a standardized language for describing the work performed by Canadians in the labour market. It is used for many applications including defining and collecting statistics, managing information databases, analyzing labour market trends and extracting practical career planning information. More importantly, it gives statisticians, labour market analysts, career counsellors, employers and individual job seekers a consistent way to collect data and describe and understand the nature of work. The NOC is developed in collaboration with Statistics Canada. The NOC tool classifies occupations with a four-digit code according to skill type and skill level. The digits of the NOC code reflect important information about the occupation it represents (e.g., 3113 Dentists - '31' indicates that this is a health occupation and it requires university level education). For a complete overview of the classification system, please consult the on-line NOC Training Tutorial (See related links section). The classification system also supports a variety of career information sources published by the Government of Canada and others. For example, Job Futures, the widely-used source of information about occupational outlooks, and the national JobBankΒ, an electronic listing of jobs, work or business opportunities provided by Canadian employers are both organized according to NOC definitions. By providing a standard way of organizing labour market information, the NOC helps all Canadians to be better informed about the world of work.",
"homepage": "http://www.cic.gc.ca/english/immigrate/skilled/noc.asp",
"name": "National Occupational Classification",
"prefix": "540",
"wikidata_database": "Q6974608"
},
"541": {
"description": "The helmsman presents deadlines in two languages: Polish and English and their definitions derived from the dictionary and encyclopaedical literature, the literature of the subject, library and bibliographic documentation, norms and standards, for example, what means an access point, resource, or what is understood today. You can also submit suggested terms (Menu - Notification) that you think should appear in this dictionary. \"We encourage you to work together.\" 1307 Terms, 2520 Relations Between Terms, 62 Terms Equivalent.",
"homepage": "http://sternik.bn.org.pl/vocab/index.php",
"name": "Terminology Dictionary of Bibliography and Cataloging",
"prefix": "541"
},
"542": {
"description": "On the other hand, the SNS (year of publication 2005) is used for the determination and allocation of slogans in the case of material media (verbal material closure), and on the other hand it provides assistance in the allocation of DK notations (classificatory material closure), which contains 13,000 terms (4700 keywords, 8300 references) , The DK-notations of the \"Kleine DK-Tafel fΓΌr Schul- und Gemeindelibliotheken\" are attached to the slogans.",
"homepage": "http://www.sabclp.ch/bestellungmitglieder/mitgliederd/schlagwortnormdatei.htm",
"name": "Subject headings Switzerland for General Public Libraries",
"prefix": "542"
},
"543": {
"description": "The intention of the ACGT Master Ontology (MO) is to represent the domain of cancer research and management in a computationally tractable manner. The ACGT MO is built being maintained, using the ProtΓ©gΓ©-OWL free open-source ontology editor, Version 4. It is written in OWL-DL and presented as an .owl file. The ACGT MO is re-using Basic Formal Ontology (BFO) as upper level and the OBO Relation Ontology.",
"homepage": "http://www.ifomis.org/acgt/1.0",
"name": "Advancing Clinico-Genomic Trials on Cancer Master Ontology",
"prefix": "543"
},
"544": {
"abbreviation": "CPO",
"description": "The Cell Phenotype Ontology (CPO) is an ontology to describe phenotypes on the cellular scale. It contains a rich classification of cellular component abnormalities, including links to morphological and physiological abnormalities. Based on the Gene Ontology's classification of cellular processes, CPO provides a large number of formally as well as textually defined classes to characterize process abnormalities.",
"homepage": "https://code.google.com/archive/p/cell-phenotype/",
"name": "Cell Phenotype Ontology",
"prefix": "544"
},
"545": {
"description": "The Neglected Tropical Diseases (NTDs) are a set of diseases which persist in exactly the physical, psychosocial and economic situation of the poorest, most marginalized populations of the developing world. Most NTDs diseases are chronic diseases which are related to poverty as a promoter of parasitic, bacterial, and also viral or fungal infections. Although of major healthcare impact in developing and threshold countries NTDs are still seen as a rare event in developed countries.\n\nIn the main target countries of Latin America, Asia and Sub-Saharan Africa, the distribution of NTD is controlled by climatic conditions like Temperature (15Β° C and 40Β° C), humidity and altitude (below 2200 meters). In these regions, most of the population (around 2.7 billion people) lives on the basis of about $ 2.00 per day. This population is considered the poorest in the world, and is also listed as most vulnerable to NTDs.\n\nAmong the NTDs, the vector-borne diseases (Dengue fever, Leishmaniasis, Chagas disease, American Trypanosomiasis, African Trypanosomiasis, Lymphatic Filariasis, Yellow Fever, among others) have resulted in a high level of mortality in poorer regions. These infections persist for a long time and can cause severe disability and disfigurement, resulting in fundamental economic, social and political burden. Some of these diseases affect developed countries as well.\n\nEnvisioning the maintenance of health quality through health policy efforts, ontologies could play an important role in the management of information processed by health systems. If data in Clinical Information Systems and health databases would be standardized via ontologies data mining and even secondary data usage would be easier. Ontologically accessed data is integratively queryable and hence easy to compare. In particular such formalized data, if grouped, could produce new epidemiological information, to help in decision-making process. As keys challenges for infectious disease management the World Health Organization indicated an urgent need for diagnostic tools, new more effective medicines and pesticides, and the promotion of integrated vector management.\n\nA prerequisite in the fight against vector-borne diseases it has recently been recognized that efforts are needed to facilitate the access to epidemiological knowledge about these diseases in a structured way. Controlled terminologies supported by ontologies help the user to systematically use this knowledge and permit large scale automated analysis approaches like logical and rule-based machine reasoning. At this level our effort concentrates on the most important point for vector-borne disease control is the transmission path, as it drives prevention strategies and decision support. It is also important to have an integration with tools to improve health policy related outcomes.",
"homepage": "http://www.cin.ufpe.br/~ntdo/",
"name": "Neglected Tropical Disease Ontology",
"prefix": "545"
},
"546": {
"description": "The Minimal Anatomy Terminology (MAT) is an OBO format terminology using broader-than relationships designed for annotating and searching tissue-associated data and timelines from organisms. Identifiers from >20 anatomy ontologies are mapped to each MAT term to facilitate access to and interoperability across tissue-associated data resources.",
"homepage": "http://www.ebi.ac.uk/microarray-srv/mat/",
"name": "Minimal Anatomy Terminology",
"prefix": "546"
},
"547": {
"description": "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic entities, it aims at building a comprehensive classification of the functional modules of MGE's at the protein, gene, and higher levels. There are 122154 proteins found in 2326 MGEs. Total number of host is 811 (Version 0.4).",
"homepage": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC308818/pdf/gkh084.pdf",
"name": "A Classification of Mobile Genetic Elements",
"prefix": "547",
"wikidata_database": "Q5128407"
},
"548": {
"description": "MeGO is a Gene Ontology under construction dedicated to the functions of mobile genetic elements. The terms defined in MeGO are used to annotate phage and plasmid protein families in ACLAME.\n\nPlease note that some terms in the ontology are there transiently as markers or awaiting future incorporation in the sequence ontology (SO). The phage ontology PhiGO has now been incorporated in MeGO and can thus be accessed in MeGO version 1.0 and up.",
"homepage": "http://aclame.ulb.ac.be/Classification/mego.html",
"name": "Mobile Genetic Element Ontology",
"prefix": "548"
},
"549": {
"abbreviation": "EMAPA",
"description": "The ontology of mouse developmental anatomy was originally developed by Jonathan Bard and his colleagues as part of the Edinburgh Mouse Atlas Project (EMAP) (http://www.emouseatlas.org) in order to provide a structured controlled vocabulary of stage-specific anatomical structures for the developing laboratory mouse.\n\nThe developmental mouse anatomy ontology has subsequently been substantially extended and refined in a collaborative effort between EMAP and the Gene Expression Database (GXD) project, part of the Mouse Genome Informatics (MGI) resource at The Jackson Laboratory. Both GXD and the Edinburgh Mouse Atlas of Gene Expression (EMAGE) database project currently use this anatomy ontology to describe patterns of gene expression in the mouse embryo.\n\nPrevious versions, such as the one posted on the OBO Foundry site under the filename EMAP.obo, listed the anatomical entities for each developmental stage (Theiler Stages 1 through 26) separately. Stage-specific instances were presented as uniparental hierarchical trees organized using part-of relationships only (i.e. as a strict partonomy). These hierarchies have been used for annotation of expression in both the EMAGE and GXD databases, and the associated identifiers for the stage-specific instances are preserved.",
"homepage": "http://www.obofoundry.org/wiki/index.php/EMAPA:Main_Page",
"name": "Ontology of Mouse Developmental Anatomy",
"prefix": "549"
},
"55": {
"description": "Terminology covering the existing physical remains of a monument, or the means by which a monument has been identified where no physical remains exist. English Heritage takes a leading role in setting standards for recording the built and buried heritage. By setting standards that can be adopted by everyone, we can make sure that all records are consistent. In other words, if everyone uses the same words to describe the same monument, archaeological object, building material, etc, then anyone using this common language can easily index, retrieve and understand these records. With this aim in mind, English Heritage is continually developing new thesauri to provide structure and guidelines for the standardisation of terms to be used when creating new records of the past. Now, in our drive to disseminate these standards and promote their wider use, we are making available seven separate online thesauri. A tailor-made suite of programs has been developed, which uses a database to create a series of web pages for any chosen thesaurus. These can be easily accessed using a frames-capable browser and regularly updated as new terms are submitted and approved by our Data Standards Unit.\n\nNational cultural heritage thesauri and vocabularies have acted as standards for use by both national organizations and local authority Historic Environment Records but until now have lacked the persistent Linked Open Data (LOD) URIs that would allow them to act as vocabulary hubs for the Web of Data. The AHRC funded SENESCHAL project aims to make such vocabularies available online as Semantic Web resources. SENESCHAL will start with major vocabularies as exemplars and project partners will continue to make other vocabularies available. Other organizations are welcome to make use of the data and services which will be open licensed.\n\nRESTful web services will be developed for the project to make the vocabulary resources programmatically accessible and searchable. These will include the provision to βfeed backβ new terms (concepts) suggested by users.",
"homepage": "http://www.heritagedata.org/blog/vocabularies-provided/",
"license": "CC-BY-3.0",
"name": "Evidence (EH)",
"prefix": "55"
},
"550": {
"description": "Data generated from cancer nanotechnology research are so diverse and large in volume that it is difficult to share and efficiently use them without informatics tools. In particular, ontologies that provide a unifying knowledge framework for annotating the data are required to facilitate the semantic integration, knowledge-based searching, unambiguous interpretation, mining and inferencing of the data using informatics methods. Here, we discuss the design and development of NanoParticle Ontology (NPO), which is developed within the framework of the Basic Formal Ontology (BFO), and implemented in the Ontology Web Language (OWL) using well-defined ontology design principles. The NPO is developed to represent the knowledge underlying the description, preparation, and characterization of nanomaterials in cancer nanotechnology research.",
"homepage": "http://www.nano-ontology.org/",
"name": "NanoParticle Ontology for Cancer Nanotechnology Research",
"prefix": "550"
},
"551": {
"description": "The Neurobehavior Ontology (NBO) consists of two main components, an ontology of behavioral processes and an ontology of behavioral phenotypes. The behavioral process branch of NBO contains a classification of behavior processes complementing and extending GOβs process ontology. The behavior phenotype branch of NBO consists of a classification of both normal and abnormal behavioral characteristics of organisms. NBOβs prime application is to provide the vocabulary that is required to integrate behavior observations within and across species. It is currently being applied by several model organism communities as well as in the description of human behavior-related disease phenotypes.",
"homepage": "http://code.google.com/p/behavior-ontology/",
"name": "Neurobehavior Ontology",
"prefix": "551"
},
"552": {
"description": "The Mental Functioning Ontology is an ontology for mental functioning, including mental processes such as cognition and traits such as intelligence, and related diseases and disorders. It is developed in the context of the Ontology for General Medical Science and the Basic Formal Ontology. The project is being developed in collaboration between the University of Geneva, Switzerland, and the University at Buffalo, USA. The project is being developed with full involvement of all relevant communities, following best practices laid out by the OBO Foundry. Efforts are currently underway to align with related projects including the Behaviour Ontology, the Cognitive Atlas, the Cognitive Paradigm Ontology and the Neural Electro Magnetic Ontologies.",
"homepage": "http://code.google.com/p/mental-functioning-ontology/",
"name": "Mental Functioning Ontology",
"prefix": "552"
},
"553": {
"description": "The goal of DDI project is to develop an ontology for the description of drug discovery investigations. The Pharmaceutical industry is an information based industry. The aim of DDI is to add value to the information generated in the drug pipeline by making the information easier to reuse, integrate, curate, retrieve, and reason with. DDI aims to follow to the Open Biomedical Ontologies Foundry (OBO) principles, to use relations laid down in the OBO Relation Ontology, and to be compliant with Ontology for biomedical investigations (OBI).",
"homepage": "http://code.google.com/p/ddi-ontology/",
"name": "Ontology for Drug Discovery Investigations",
"prefix": "553"
},
"554": {
"description": "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats.",
"homepage": "http://code.google.com/p/ogms/",
"name": "Ontology for General Medical Science",
"prefix": "554"
},
"555": {
"description": "The domain of data mining (DM) deals with analyzing different types of data. The data typically used in data mining is in the format of a single table, with primitive datatypes as attributes. However, structured (complex) data, such as graphs, sequences, networks, text, image, multimedia and relational data, are receiving an increasing amount of interest in data mining. A major challenge is to treat and represent the mining of different types of structured data in a uniform fashion.\n\nA theoretical framework that unifies different data mining tasks, on different types of data can help to formalize the knowledge about the domain and provide a base for future research, unification and standardization. Next, automation and overall support of the Knowledge Discovery in Databases (KDD) process is also an important challenge in the domain of data mining. A formalization of the domain of data mining is a solution that addresses these challenges. It can directly support the development of a general framework for data mining, support the representation of the process of mining structured data, and allow the representation of the complete process of knowledge discovery.\n\nWe propose a reference modular ontology for the domain of data mining OntoDM, directly motivated by the need for formalization of the data mining domain. The OntoDM ontology is designed and implemented by following ontology best practices and design principles. Its distinguishing feature is that it uses Basic Formal Ontology (BFO) as an upper-level ontology and a template, a set of formally defined relations from Relational Ontology (RO) and other state-of-the-art ontologies, and reuses classes and relations from the Ontology of Biomedical Investigations (OBI), the Information Artifact Ontology (IAO), and the Software Ontology (SWO). This will ensure compatibility and connections with other ontologies and allow cross-domain reasoning capabilities.",
"homepage": "http://ontodm.com/",
"name": "Ontology of Data Mining",
"prefix": "555"
},
"556": {
"description": "Using realistic ontology BFO as its top ontology's framwork, OGI formalized the genomic element by defining an upper class 'genetic interval'. The definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) that have a liner primary sequence sturcture. It is either a proper part of an chromosome or a RNA molecule or an artificial genetic interval.\"\n\nThe 'genetic sequence' is also formalized in OGI, the differences between 'genetic sequence' and 'genetic interval' is that, 'genetic squence' refers to a liner sequence with only primary structure, whereas 'genetic interval' refers to the 3D sequence in reality, which has not only 3D structure, but also need to have the 'genetic sequence' as its primary structure'. From this aspect we make a distinction between a modelled sequence and a real sequence object as realm.",
"homepage": "https://code.google.com/p/ontology-for-genetic-interval/",
"name": "Ontology for Genetic Interval",
"prefix": "556"
},
"557": {
"description": "ICPC (International Classification of Primary Care) is a clinical coding system. The first version of ICPC published in 1987 is referred to as ICPC-1. The version in the 1993 publication βThe International Classification of Primary Care in the European Community: With a Multi-Language Layerβ is known as ICPC-1. The second version from 1998 is referred to as ICPC-2. ICPC-2e is an electronic version from year 2000 of the revised and corrected chapters 10 and 11 of the ICPC-2 book. The full revision cycle is currently 11 years, however, mapping to other classifications may be reviewed at shorter intervals to adjust for changes in other classifications and changed usage.",
"homepage": "http://www.kith.no/templates/kith_WebPage____1062.aspx",
"name": "International Classification of Primary Care",
"prefix": "557",
"wikidata_database": "Q723530"
},
"558": {
"abbreviation": "ChEBI",
"description": "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on βsmallβ chemical compounds. The term βmolecular entityβ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms. ChEBI incorporates an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified.",
"homepage": "http://www.ebi.ac.uk/chebi/",
"name": "Chemical Entities of Biological Interest",
"prefix": "558",
"wikidata_database": "Q902623"
},
"559": {
"description": "The Dengue ontology (IDODEN) is an extension of the Infectious Disease Ontology (IDO) for dengue fever.",
"homepage": "http://code.google.com/p/dengue-fever-ontology/",
"name": "Dengue Ontology",
"prefix": "559"
},
"56": {
"description": "Construction materials for monuments relating to the built and buried heritage. English Heritage takes a leading role in setting standards for recording the built and buried heritage. By setting standards that can be adopted by everyone, we can make sure that all records are consistent. In other words, if everyone uses the same words to describe the same monument, archaeological object, building material, etc, then anyone using this common language can easily index, retrieve and understand these records. With this aim in mind, English Heritage is continually developing new thesauri to provide structure and guidelines for the standardisation of terms to be used when creating new records of the past. Now, in our drive to disseminate these standards and promote their wider use, we are making available seven separate online thesauri. A tailor-made suite of programs has been developed, which uses a database to create a series of web pages for any chosen thesaurus. These can be easily accessed using a frames-capable browser and regularly updated as new terms are submitted and approved by our Data Standards Unit.\n\n National cultural heritage thesauri and vocabularies have acted as standards for use by both national organizations and local authority Historic Environment Records but until now have lacked the persistent Linked Open Data (LOD) URIs that would allow them to act as vocabulary hubs for the Web of Data. The AHRC funded SENESCHAL project aims to make such vocabularies available online as Semantic Web resources. SENESCHAL will start with major vocabularies as exemplars and project partners will continue to make other vocabularies available. Other organizations are welcome to make use of the data and services which will be open licensed.\n\n RESTful web services will be developed for the project to make the vocabulary resources programmatically accessible and searchable. These will include the provision to βfeed backβ new terms (concepts) suggested by users.",
"homepage": "http://www.heritagedata.org/blog/vocabularies-provided/",
"license": "CC-BY-3.0",
"name": "FISH Building Materials Thesaurus",
"prefix": "56",
"wikidata_database": "Q28934016"
},
"560": {
"description": "The eagle-i research resource ontology (ERO) models research resources such as instruments, protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/). Currently, ERO consists of over 2100 classes of which 1200 were created within the ERO namespace, while the rest come from existent ontologies such as the Ontology for Biomedical Investigation (OBI), the uber-anatomy ontology (Uberon), VIVO, the Ontology for Clinical Research (OCRe), the Sequence Ontology (SO), the Software Ontology (SWO) and we include terms from the NCBI Taxonomy as well.",
"homepage": "https://open.med.harvard.edu/wiki/display/eaglei/Ontology",
"name": "eagle-i Research Resource Ontology",
"prefix": "560"
},
"561": {
"description": "The Swiss Centre for Affective Sciences, in collaboration with the University at Buffalo, is developing an Emotion Ontology to describe affective phenomena. This project is a branch of the broader Mental Functioning ontology effort. The Centre brings together scientists from neuroscience and psychology, together with economists, historians, philosophers as well as scholars in the humanities, in a multi-disciplinary effort to understand how affective phenomena, such as motives, attitudes, moods, and emotions, affect the individual and society.\n\nInterdisciplinary research is inherently plagued by the difficulties of integration and standardisation of terminology, knowledge and disparate theoretical frameworks in order to compare results across disciplines which historically have evolved separately. In the context of this multi-disciplinary research environment, to assist the integration and computational processing of results in the affective sciences, we are developing the Emotion Ontology to aid in disambiguation and standardised reporting of research results.\n\nThe ontology will represent all relevant aspects of affective phenomena including their bearers, the different types of emotions, moods, etc., their different parts and dimensions of variation, their facial and vocal expressions, and the role of emotions and affective phenomena in general in influencing human behavior.\n\nProper delineation of the upper levels is essential to ensure the unambiguous interpretation of the entities in the ontology which contributes to the usability and interoperability of the fully populated ontology. To achieve this, we will draw on the Basic Formal Ontology, the domain-independent upper ontology advocated by the OBO Foundry. Subsequent phases of the project will identify, define and place all relevant affective phenomena within the ontology, and link this ontology to neighbouring efforts in the domains of neural and social informatics, such as the Neuroscience Information Framework. Finally, we will develop software applications which make use of the ontology to directly support the work of Affective Science researchers both in Switzerland and globally.",
"homepage": "https://code.google.com/archive/p/emotion-ontology/",
"license": "Apache 2.0 License",
"name": "Emotion Ontology",
"prefix": "561"
},
"562": {
"description": "The Environment Ontology (EnvO) provides a controlled, structured vocabulary that is designed to support the annotation of any organism or biological sample with environment descriptors. EnvO contains terms for biomes, environmental features, and environmental material.\" EnvO enables \"a concise, standardised, and comprehensive description of environment that is key to the integration, archiving and federated searching of environmental data. As a tool for the life sciences, we see EnvO bringing benefits similar to those of the Gene Ontology (GO). Through promoting consistent annotation grounded in an ontological framework, we hope to facilitate the semantic retrieval of any biological record anchored to EnvO. Records contained in sequence databases, 'omic data repositories, tissue banks and museum collections are prime candidates for EnvO annotation. However, EnvO is also suitable for the annotation of any record that has an environmental component. For example, you can use EnvO terms to provide information on the environment of remote sensing devices or simply to tag a picture that you took at the weekend. Further, the EnvO project is closely tied with GAZ, a first step towards an open source gazetteer constructed on ontological principles. GAZ describes places and place names as well as the relations between them and, when linked with EnvO descriptors, provides a basis to infer environment from place names.",
"homepage": "http://www.environmentontology.org/",
"name": "Environment Ontology",
"prefix": "562"
},
"563": {
"description": "The Crop Ontology (CO) current objective is to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. Development of crop-specific trait ontologies and the germplasm ontologies began in 2008 for chickpea, maize, Musa, potato, rice and wheat, and in 2010 for cassava. The GCP Crop Ontology is a global public good, available to be used freely by all.",
"homepage": "http://www.cropontology.org/",
"name": "Crop Ontology",
"prefix": "563"
},
"564": {
"description": "CNO is a controlled vocabulary composed of classes representing general concepts related to computational neuroscience. These concepts are organized in a hierarchy of concepts and related to each other using logical relations. One of the main relations is the hierarchical relation named βis aβ relation. Knowing the relations between classes allows us to create simple sentences such as: βa model is a thingβ, βa leaky integrate-and-fire is a modelβ, βvoltage is a elementary model componentβ, β¦ The first step for CNO development was to create a list of relevant terms and concepts from textbooks and from the different expertise of the MSM Task Force members. Based on this list of terms, we developed a first version of the Computational Neuroscience Ontology (CNO), using the OWL-DL standard proposed by W3C. The core of CNO is currently (January 2013) composed of 221 terms and 2 datatype properties. As Computational Neuroscience model are very diverse, CNO is still in development to integrate the most relevant concepts for annotating as many Computational Neuroscience models as possible. However, CNO aims to be a tool for the community and therefore contribution of the community would be highly valuable to bring CNO to a more mature distribution.",
"homepage": "http://purl.bioontology.org/ontology/CNO",
"name": "Computational Neurosciences Ontology",
"prefix": "564"
},
"565": {
"description": "CDAO stands for \"Comparative Data Analysis Ontology\", a formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science. In general, ontologies are designed to support formal or automated reasoning. Our aim in developing CDAO is to provide the language support for representing, and reasoning over, phylogenetic data and metadata. When CDAO is fully developed and supported by software, it will be possible for one researcher to represent information with conceptual richness, and for another research (or a computer) to access that same conceptual richness. The current version of CDAO is a kind of free-floating ontology not linked into an \"upper\" ontology. The reason for this is that, when we first began to develop CDAO, we did not understand where the concepts and relations would fit in terms of available upper ontologies. We're still not entirely sure.",
"homepage": "http://sourceforge.net/projects/cdao/",
"name": "Comparative Data Analysis Ontology",
"prefix": "565"
},
"57": {
"description": "Craft types which survive as wrecks for the RCHME's maritime record and can be used to describe types of ship. English Heritage takes a leading role in setting standards for recording the built and buried heritage. By setting standards that can be adopted by everyone, we can make sure that all records are consistent. In other words, if everyone uses the same words to describe the same monument, archaeological object, building material, etc, then anyone using this common language can easily index, retrieve and understand these records. With this aim in mind, English Heritage is continually developing new thesauri to provide structure and guidelines for the standardisation of terms to be used when creating new records of the past. Now, in our drive to disseminate these standards and promote their wider use, we are making available seven separate online thesauri. A tailor-made suite of programs has been developed, which uses a database to create a series of web pages for any chosen thesaurus. These can be easily accessed using a frames-capable browser and regularly updated as new terms are submitted and approved by our Data Standards Unit.\n\n National cultural heritage thesauri and vocabularies have acted as standards for use by both national organizations and local authority Historic Environment Records but until now have lacked the persistent Linked Open Data (LOD) URIs that would allow them to act as vocabulary hubs for the Web of Data. The AHRC funded SENESCHAL project aims to make such vocabularies available online as Semantic Web resources. SENESCHAL will start with major vocabularies as exemplars and project partners will continue to make other vocabularies available. Other organizations are welcome to make use of the data and services which will be open licensed.\n\n RESTful web services will be developed for the project to make the vocabulary resources programmatically accessible and searchable. These will include the provision to βfeed backβ new terms (concepts) suggested by users.",
"homepage": "http://www.heritagedata.org/blog/vocabularies-provided/",
"license": "CC-BY-3.0",
"name": "FISH Maritime Craft Types Thesaurus",
"prefix": "57"
},
"570": {
"description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team. We also add terms for external users when requested.",
"homepage": "http://www.ebi.ac.uk/efo/",
"name": "Experimental Factor Ontology",
"prefix": "570",
"wikidata_database": "Q16251642"
},
"571": {
"abbreviation": "FMA",
"description": "The Foundational Model of Anatomy Ontology (FMA) is an evolving computer-based knowledge source for biomedical informatics; it is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. Its ontological framework can be applied and extended to all other species.",
"homepage": "http://sig.biostr.washington.edu/projects/fm/",
"name": "Foundational Model of Anatomy",
"prefix": "571",
"wikidata_database": "Q1406710"
},
"572": {
"abbreviation": "GO",
"description": "The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data.",
"homepage": "http://www.geneontology.org/",
"name": "Gene Ontology",
"prefix": "572",
"wikidata_database": "Q135085"
},
"573": {
"description": "The Genomic Clinical Decision Support (Genomic CDS) project aims to create and maintain an integrated, ontology-based knowledge base of clinically relevant pharmacogenomic information. This knowledge base is used to implement clinical decision support algorithms for improving quality of care, e.g., for providing drug dosage recommendations and comparisons of the efficacy of different treatment options.",
"name": "Genomic Clinical Decision Support Ontology",
"prefix": "573"
},
"575": {
"abbreviation": "GlycO",
"description": "The Glycomics Ontology (GlycO) focuses on the glycoproteomics domain to model the structure and functions of glycans and glycoconjugates, the enzymes involved in their biosynthesis and modification, and the metabolic pathways in which they participate. GlycO is intended to provide both a schema and a sufficiently large knowledge base, which will allow classification of concepts commonly encountered in the field of glycobiology in order to facilitate automated reasoning and information analysis in this domain. The GlycO schema exploits the expressiveness of OWL-DL to place restrictions on relationships, thus making it suitable to be used as a means to classify new instance data. These logical restrictions are necessary due to the chemical nature of glycans, which have complex, branched structures that cannot be represented in any simple way. Glycans are thus distinguished from DNA (e.g., genes) and proteins, which can be represented (at least in their most basic forms) as simple character strings. The structural knowledge in GlycO is modularized, in that larger structures are semantically composed from smaller canonical building blocks. In particular, glycan instances are modeled by linking together several instances of canonical monosaccharide residues, which embody knowledge of their chemical structure (e.g., Ξ²-D-GlcpNAc) and context (e.g., attached directly to the Asn residue of a protein). This bottom-up semantic modeling of large molecular structures using smaller building blocks allows structures in GlycO to be placed in a biochemical context by describing the specific interactions of its component parts with proteins, enzymes and other biochemical entities.",
"homepage": "http://glycomics.ccrc.uga.edu/core4/informatics-ontologies.html",
"name": "Glycomics Ontology",
"prefix": "575"
},
"576": {
"abbreviation": "DO",
"description": "The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts through collaborative efforts of researchers at Northwestern University, Center for Genetic Medicine and the University of Maryland School of Medicine, Institute for Genome Sciences.\n\nThe Disease Ontology semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCIβs thesaurus, SNOMED and OMIM.",
"homepage": "http://disease-ontology.org/",
"name": "Disease Ontology",
"prefix": "576",
"wikidata_database": "Q5282129"
},
"577": {
"description": "The Fission Yeast Phenotype Ontology (FYPO) is a formal ontology of phenotypes observed in fission yeast. FYPO is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the online fission yeast resource. Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions.",
"homepage": "http://www.pombase.org/browse-curation/fission-yeast-phenotype-ontology",
"name": "Fission Yeast Phenotype Ontology",
"prefix": "577"
},
"578": {
"description": "The (Computer-Based Patient Record) CPR ontology burrows its name from the Institute of Medicine term used to define medical records systems of the future and the important features that distinguish them for EHRs of today. In particular, it defines a set of requirements including a Record Content category, which states: Uniform core data elements, standardized coding systems and formats, a common data dictionary, and information on outcomes of care and functional status.\n\nThe requirement of a set of uniform core elements is meant to be directly addressed by this ontology. In addition, it attempts to define a minimal set of terms that provide grounded, ontologically commitment for the representations shared between many of the healthcare information (such as HL7 RIM), process and terminological models via the use of foundational ontologies.\n\nIn addition, a major influencing principle is that as far as the application of ontology for the benefit of medical informatics is concerned, a pragmatic approach is necessary - one that compromises between a purely 'realist' approach and a cognitive approach that refrains from committing to a representation of the intrinsic nature of the world. For those aspects of reality for which there is significant consensus on the underlying science and use of terminology, an ontology should try as much as possible to capture the constraints that reflect this consensus. However, where such constraints do not provide any direct benefit in the use ontology in a CPR, we should refrain from any further formalization. The general motivation is to allow ontologies to facilitate the use of computer reasoning in playing an important role in the scientific method, but at the same time protect against an excessive attempt to reduce every aspect of clinical medicine to metaphysical distinctions that do not have any legitimate benefit.",
"homepage": "http://code.google.com/p/cpr-ontology/",
"name": "Computer-Based Patient Record Ontology",
"prefix": "578"
},
"579": {
"description": "The use of alternate and even competitive terminologies can often impede scientific discoveries. While the experimental psychology and cognitive neuroscience literature may refer to certain behavioral paradigms by name (eg. the Stroop paradigm or the Sternberg paradigm) or by function (a working memory task, a visual attention task), these paradigms can vary tremendously in the stimuli that are presented to the subject, the response expected from the subject, and the instructions given to the subject. This means that an automated reasoning system using names of paradigms would not realize that data from these different experiments could be compared and used.\n\nCogPO was developed directly from the taxonomy created for the BrainMap Database. Its design concentrates on what can be observed directly: categorization of each paradigm in terms of (1) the stimulus presented to the subjects, (2) the requested instructions, and (3) the returned response. All paradigms are essentially composed of these three orthogonal components, and formalizing an ontology around them is a clear and direct approach to describing paradigms. CogPO seeks to represent stimuli, responses, and instructions that define the conditions of the experiment in a standardized format, with well-defined terms and relationships between them. CogPO is being built to be compliant with OBO Foundry principles, and uses the Basic Formal Ontology (BFO) as its upper level ontology.",
"homepage": "http://www.cogpo.org/",
"name": "Cognitive Paradigm Ontology",
"prefix": "579"
},
"58": {
"description": "Maritime ports, countries and bodies of water from and to which ships may have sailed or been registered. English Heritage takes a leading role in setting standards for recording the built and buried heritage. By setting standards that can be adopted by everyone, we can make sure that all records are consistent. In other words, if everyone uses the same words to describe the same monument, archaeological object, building material, etc, then anyone using this common language can easily index, retrieve and understand these records. With this aim in mind, English Heritage is continually developing new thesauri to provide structure and guidelines for the standardisation of terms to be used when creating new records of the past. Now, in our drive to disseminate these standards and promote their wider use, we are making available seven separate online thesauri. A tailor-made suite of programs has been developed, which uses a database to create a series of web pages for any chosen thesaurus. These can be easily accessed using a frames-capable browser and regularly updated as new terms are submitted and approved by our Data Standards Unit.",
"homepage": "http://heritage-standards.org.uk/wp-content/uploads/2016/05/MarPlaceName_class.pdf",
"name": "English Heritage Maritime Place Name Thesaurus",
"prefix": "58"
},
"580": {
"description": "XeO has been created to help plant scientists in documenting and sharing metadata describing the abiotic environment.",
"homepage": "http://xeo.codeplex.com/",
"name": "XEML Environment Ontology",
"prefix": "580"
},
"581": {
"abbreviation": "XAO",
"description": "The Xenopus Anatomical Ontology describes Xenopus anatomy and development as a controlled vocabulary of terms, organized in a graphical structure. Tissues are shown as being part of other tissues and the timing of their development is indicated by start and end stages. The lineage of tissues is represented by develops from relationships between different tissues at different developmental stages. Many items have been classified according to the Common Anatomy Reference Ontology. The ontology is listed at the Open Biomedical Ontologies (OBO Foundry).",
"homepage": "http://xenbase.org/anatomy/xao.do?method=display",
"name": "Xenopus Anatomical Ontology",
"prefix": "581"
},
"582": {
"description": "The IDO ontologies are designed as a set of interoperable ontologies that will together provide coverage of the infectious disease domain. At the core of the set is a general Infectious Disease Ontology (IDO-Core) of entities relevant to both biomedical and clinical aspects of most infectious diseases. Sub-domain specific extensions of IDO-Core complete the set providing ontology coverage of entities relevant to specific pathogens or diseases.",
"homepage": "https://code.google.com/p/infectious-disease-ontology/",
"name": "Infectious Disease Ontology",
"prefix": "582"
},
"583": {
"description": "The Information Artifact Ontology (IAO) is a new ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch.\n\nAn information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon.",
"homepage": "http://code.google.com/p/information-artifact-ontology/",
"name": "Information Artifact Ontology",
"prefix": "583"
},
"584": {
"description": "ICECI is a free practical tool for classifying the circumstances in which injuries occur. Thus, it can be used in surveillance and research to support injury and trauma prevention and control efforts throughout the world. Using this tool, one can code the key factors that may be involved in causing injuries. Consequently, injuries can be both counted and described to yield useful information for setting priorities, making policy decisions, and guiding prevention.\n\nPurpose/Definition: To enable classifying external causes of injuries. It is designed to help researchers and prevention practitioners to describe, measure and monitor the occurrence of injuries and to investigate their circumstances of occurrence using an internally agreed classification. Criteria underlying the classification are: a separate coding axis for each main concept, usefulness for injury prevention, useability in may types of settings (many parts of the world; emergency departments and other places where data are collected), comparability and complementarity with the ICD-10.",
"name": "International Classification of External Causes of Injury",
"prefix": "584",
"wikidata_database": "Q16948198"
},
"585": {
"description": "To enable the accurate and repeatable execution of a computational simulation task, it is important to identify both the algorithm used and the initial setup. These minimum information requirements are described by the MIASE guidelines. Since the details of some algorithms are not always publicly available, and many are implemented only in a limited number of simulation tools, it is crucial to identify alternative algorithms with similar characteristics that may be used to provide comparable results in an equivalent simulation experiment. The Kinetic Simulation Algorithm Ontology (KiSAO) was developed to address this issue by describing existing algorithms and their inter-relationships through their characteristics and parameters. The use of KiSAO in conjunction with simulation descriptions, such as SED-ML, will allow simulation software to automatically choose the best algorithm available to perform a simulation and unambiguously refer to it.",
"homepage": "http://biomodels.net/kisao/",
"name": "Kinetic Simulation Algorithm Ontology",
"prefix": "585",
"wikidata_database": "Q17062520"
},
"59": {
"description": "Types of monuments relating to the built and buried heritage in England. English Heritage takes a leading role in setting standards for recording the built and buried heritage. By setting standards that can be adopted by everyone, we can make sure that all records are consistent. In other words, if everyone uses the same words to describe the same monument, archaeological object, building material, etc, then anyone using this common language can easily index, retrieve and understand these records. With this aim in mind, English Heritage is continually developing new thesauri to provide structure and guidelines for the standardisation of terms to be used when creating new records of the past. Now, in our drive to disseminate these standards and promote their wider use, we are making available seven separate online thesauri. A tailor-made suite of programs has been developed, which uses a database to create a series of web pages for any chosen thesaurus. These can be easily accessed using a frames-capable browser and regularly updated as new terms are submitted and approved by our Data Standards Unit.\n\nNational cultural heritage thesauri and vocabularies have acted as standards for use by both national organizations and local authority Historic Environment Records but until now have lacked the persistent Linked Open Data (LOD) URIs that would allow them to act as vocabulary hubs for the Web of Data. The AHRC funded SENESCHAL project aims to make such vocabularies available online as Semantic Web resources. SENESCHAL will start with major vocabularies as exemplars and project partners will continue to make other vocabularies available. Other organizations are welcome to make use of the data and services which will be open licensed.\n\nRESTful web services will be developed for the project to make the vocabulary resources programmatically accessible and searchable. These will include the provision to βfeed backβ new terms (concepts) suggested by users.",
"homepage": "http://www.heritagedata.org/blog/vocabularies-provided/",
"license": "CC-BY-3.0",
"name": "FISH Thesaurus of Monument Types",
"prefix": "59"
},
"60": {
"abbreviation": "THRED",
"description": "Terminology for the description of archive type and format. English Heritage takes a leading role in setting standards for recording the built and buried heritage. By setting standards that can be adopted by everyone, we can make sure that all records are consistent. In other words, if everyone uses the same words to describe the same monument, archaeological object, building material, etc, then anyone using this common language can easily index, retrieve and understand these records. With this aim in mind, English Heritage is continually developing new thesauri to provide structure and guidelines for the standardisation of terms to be used when creating new records of the past. Now, in our drive to disseminate these standards and promote their wider use, we are making available seven separate online thesauri. A tailor-made suite of programs has been developed, which uses a database to create a series of web pages for any chosen thesaurus. These can be easily accessed using a frames-capable browser and regularly updated as new terms are submitted and approved by our Data Standards Unit.",
"homepage": "http://thesaurus.historicengland.org.uk/thesaurus.asp?thes_no=547&thes_name=EH%20And%20National%20Trust%20Resource%20Description%20Thesaurus",
"name": "English Heritage National Trust Thred Thesaurus",
"prefix": "60"
},
"61": {
"description": "Types of defensive monuments relating to the 20th century in Great Britain and Northern Ireland. English Heritage takes a leading role in setting standards for recording the built and buried heritage. By setting standards that can be adopted by everyone, we can make sure that all records are consistent. In other words, if everyone uses the same words to describe the same monument, archaeological object, building material, etc, then anyone using this common language can easily index, retrieve and understand these records. With this aim in mind, English Heritage is continually developing new thesauri to provide structure and guidelines for the standardisation of terms to be used when creating new records of the past. Now, in our drive to disseminate these standards and promote their wider use, we are making available seven separate online thesauri. A tailor-made suite of programs has been developed, which uses a database to create a series of web pages for any chosen thesaurus. These can be easily accessed using a frames-capable browser and regularly updated as new terms are submitted and approved by our Data Standards Unit.",
"homepage": "http://thesaurus.historicengland.org.uk/thesaurus.asp?thes_no=365&thes_name=Defence%20of%20Britain%20Thesaurus",
"name": "English Heritage Defence Of Britain Thesaurus",
"prefix": "61"
},
"62": {
"description": "Applied in the Numismatic Image Database EichstΓ€tt.",
"homepage": "http://www.nbeonline.de/",
"name": "Numismatic image database Thesaurus",
"prefix": "62"
},
"63": {
"description": "The PACTOLS (Peoples, Anthroponyms, Chronology, Toponymies, Works, Places and Subjects) thesauri, specializing in the sciences of antiquity and archeology from prehistory to the industrial era, are poly-hierarchical, evolutive and multilingual. PACTOLS is a thesaurus managed by the FRANTIQ program and is used to interrogate the indexed collective catalog (CCI) and other external bases.",
"homepage": "http://pactols.frantiq.fr/opentheso/",
"prefix": "63"
},
"64": {
"description": "The AJRP aims to provide a resource for historians and others interested in the Australia-Japan relationship, especially in war, from 1901 to 1957.",
"homepage": "http://ajrp.awm.gov.au/AJRP/AJRP2.nsf/Web-Thesauri/Area",
"name": "Australia-Japan Research Project Area Thesaurus",
"prefix": "64"
},
"65": {
"description": "The AJRP aims to provide a resource for historians and others interested in the Australia-Japan relationship, especially in war, from 1901 to 1957.",
"homepage": "http://ajrp.awm.gov.au/AJRP/AJRP2.nsf/Web-Thesauri/Keyword",
"name": "Australia-Japan Research Project Keyword Thesaurus",
"prefix": "65"
},
"654": {
"description": "The NCI Thesaurus is a reference terminology and biomedical ontology used in a growing number of NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities. The NCI Thesaurus provides definitions, synonyms, and other information on nearly 10,000 cancers and related diseases, 8,000 single agents and combination therapies, and a wide range of other topics related to cancer and biomedical research. It is maintained by a multidisciplinary team of editors, who add about 900 new entries each month and is published monthly by NCI.",
"homepage": "http://ncit.nci.nih.gov/",
"name": "National Cancer Institute Thesaurus",
"prefix": "654"
},
"655": {
"description": "NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. NCIm features: Maps 4,000,000 terms from more than 75 sources into 2,000,000 biomedical concepts that represent their meaning; Displays preferred terms, synonyms, definitions, and other information from each source; Links to NCI Thesaurus and other related information sources; Contains 22,000,000 cross-links between content elements; Updated frequently by a team of biomedical terminology and subject matter experts.\n\nNCIm contains most public domain terminologies from the National Library of Medicine's UMLS Metathesaurus, as well as many other biomedical terminologies created by or of interest to NCI and its partners.",
"homepage": "http://ncim.nci.nih.gov/ncimbrowser/",
"name": "National Cancer Institute Metathesaurus",
"prefix": "655",
"wikidata_database": "Q6953141"
},
"656": {
"description": "The goal of the MAO project is to develop a controlled, structured vocabulary, that will provide a common language not only for the construction of multiple alignments, but also for the numerous applications that exploit the information available in an integrated, global multiple alignment of a protein family. An important issue in the development of MAO is the interoperability with existing information sources, in order to maximise itsβ applicability and utility. Therefore, links should be provided to other kinds of information, including databases such as UniProt, PDB or InterPro, as well as existing ontologies such as GO or the HUPO Proteomics Standards Initiative (PSI).\n\nA vocabulary of terms is provided in the form of a hierarchical network of concepts, together with precise, explanatory definitions of each term and the inter-relations between the different concepts. The aim is to include the great majority of the concepts relevant to multiple sequence alignments, ranging from fundamental concepts such as βsequenceβ or βresidueβ to more complex concepts such as structural environment, functional activity or evolutionary context.\n\nThe MAO is represented as a Directed Acyclic Graph (DAG), in which each node stands for a concept and the links connecting the nodes represent the relationship between them. Two hierarchical relations are defined: βis_aβ and βpart_ofβ. The nodes can also have other information attached to them in the form of names (defined by the relation βis_nameβ), annotations (defined by βis_annotationβ) or other attributes. An attribute is generally a simple string or number variable that contains additional information about the concept.",
"homepage": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1180671/",
"name": "Multiple Alignment Ontology",
"prefix": "656"
},
"657": {
"description": "The goal of the COSMO working group was to develop a foundation ontology by a collaborative process that will allow it to represent all of the basic (βprimitiveβ) ontology elements that all members felt were needed for their applications. Interoperability could then be achieved among ontology-based applications using the foundation ontology by creating any specialized domain ontology element as a combination of the primitive ontology elements, and when one system wishes to communicate information to others, it must transmit not only the data, but also any logical specifications of the ontology elements required to interpret the data (if they are not already in the foundation ontology or some public extension). Any system that can properly interpret the primitive elements will be able to properly interpret ontology elements created as a combination of those primitives.\n\nThe development of COSMO is fully open, and any comments or suggestions from any sources are welcome. After some discussion and input from members in 2006, the development of the COSMO has been continued primarily by Patrick Cassidy, the chairman of the COSMO Working Group (no longer active). Contributions and suggestions from any interested party are still welcome and encouraged. Many of the types (OWL classes) in the current COSMO have been taken from the OpenCyc OWL version 0.78, and from the SUMO. Other elements were taken from other ontologies (such as BFO and DOLCE) or developed specifically for COSMO.\n\nThe development of the COSMO started as a merger of basic elements from Cyc, SUMO, and DOLCE, and continued up to revision 589 (2008-02-19), at which point the names (labels) of the elements of the COSMO were compared with the words in the Longman defining vocabulary, and out of the 2201 Longman words, it was discovered that 1817 were not present as labels for COSMO elements. At this point, a systematic supplementation of the COSMO was begun, to assure that the concepts represented by the Longman vocabulary were all represented in some form in the COSMO. The new elements are being added by alphabetical inspection of the list of missing Longman words.\n\nAt version 0.65 (April 2010) the COSMO had 7339 types (OWL classes), 808 relations, and 2039 restrictions, and all of the words in the Longman defining vocabulary had some correlated ontology element in the COSMO. The formal mapping of the Longman words to the ontology elements is at present (rev945) only partly complete, and is continuing. The mapping consists of a relation βxxxxβ on the ontology element to the Longman word(s) that represent that element in English.",
"homepage": "http://www.micra.com/COSMO/",
"name": "COSMO Ontology",
"prefix": "657"
},
"658": {
"description": "Objects made by human activity.",
"name": "Archaeological Objects Thesaurus (Scotland)",
"prefix": "658"
},
"659": {
"description": "Types of craft that survive as wrecks, or are documented as losses, in Scottish maritime waters.",
"name": "Maritime Craft Thesaurus (Scotland)",
"prefix": "659"
},
"66": {
"description": "The AJRP aims to provide a resource for historians and others interested in the Australia-Japan relationship, especially in war, from 1901 to 1957.",
"homepage": "http://ajrp.awm.gov.au/AJRP/AJRP2.nsf/Web-Thesauri/Unit-Names",
"name": "Australia-Japan Research Project Unit Name Thesaurus",
"prefix": "66"
},
"660": {
"description": "Monument types relating to the archaeological and built heritage of Scotland. The terminology also includes Scottish Gaelic translations for some terms.",
"name": "Monument Type Thesaurus (Scotland)",
"prefix": "660"
},
"661": {
"description": "Classification of monument types in Wales by function.",
"homepage": "http://www.heritagedata.org/blog/vocabularies-provided/",
"name": "Monument Thesaurus (Wales)",
"prefix": "661"
},
"662": {
"description": "A list of periods for use in Wales.",
"homepage": "http://www.heritagedata.org/blog/vocabularies-provided/",
"name": "Period (Wales)",
"prefix": "662"
},
"663": {
"description": "JITA Classification System has been built for E-LIS on the basis of NewsAgentTopic Classification Scheme and RIS Classification Schema.",
"homepage": "http://eprints.rclis.org/view/subjects/subjects.html",
"name": "JITA Classification System of Library and Information Science",
"prefix": "663",
"wikidata_database": "Q1676606"
},
"665": {
"description": "Thesaurus for indexing different types of farmsteads, related buildings, areas and layouts.",
"homepage": "http://heritage-standards.org.uk/wp-content/uploads/2016/05/farmsteads_class_v20.pdf",
"name": "Forum on Information Standards in Heritage Farmstead Types",
"prefix": "665"
},
"666": {
"description": "Thesaurus for indexing types of crime and incidents against heritage assets.",
"homepage": "http://heritage-standards.org.uk/wp-content/uploads/2016/05/HeritCrime_class_v20.pdf",
"name": "Forum on Information Standards in Heritage Heritage Crime",
"prefix": "666"
},
"667": {
"description": "Thesaurus for mapping current and past land use or character of rural areas.",
"homepage": "http://heritage-standards.org.uk/wp-content/uploads/2016/05/HistoricCharactFull_-Aug2015.pdf",
"name": "Forum on Information Standards in Heritage Historic Landscape Characterisation",
"prefix": "667"
},
"668": {
"description": "Wordlist for indexing types of loss of vessels or aircraft.",
"homepage": "http://heritage-standards.org.uk/wp-content/uploads/2016/05/MannerOfLoss_v19.zip",
"name": "Forum on Information Standards in Heritage Manner of Loss",
"prefix": "668"
},
"669": {
"description": "Thesaurus of non-structural, movable items on vessels.",
"homepage": "http://heritage-standards.org.uk/wp-content/uploads/2016/05/MarFixFit_class_v20.pdf",
"name": "Forum on Information Standards in Heritage Maritime Fixtures and Fittings",
"prefix": "669"
},
"67": {
"description": "A thematic index of more than 1500 keywords 'Matter' and 1800 keywords 'Geography'.",
"homepage": "http://bihr.droz.org/",
"name": "International Bibliography of Humanism and Renaissance Thesaurus",
"prefix": "67"
},
"671": {
"description": "By the late 1950's it had become evident that the nomenclature of enzymology, in the absence of any guiding authority, in a period when the number of known enzymes was increasing rapidly, was getting out of hand. The naming of enzymes by individual workers had proved far from satisfactory in practice. In many cases the same enzymes became known by several different names, while conversely the same name was sometimes given to different enzymes. Many of the names conveyed little or no idea of the nature of the reactions catalysed, and similar names were sometimes given to enzymes of quite different types. To meet this situation, various attempts to bring order into the general nomenclature of enzymes, or into that of particular groups of enzymes, were made by individuals or small groups of specialists, but none of the resulting nomenclatures met with general approval. (...) The Enzyme List in the sixth edition (1992) contains 3540 entries, of which 178 record enzymes which are now transferred elsewhere in the list, and 166 have been deleted completely. Thus the number of enzymes actually listed is 3196, an increase of 29% on the 1984 edition.",
"homepage": "https://www.abbexa.com/enzyme-commission-number",
"name": "Enzyme Nomenclature",
"prefix": "671",
"wikidata_database": "Q741108"
},
"672": {
"abbreviation": "kfsb",
"description": "SAB is a classification system that primarily classifies books, but also other media. It is used in many Swedish public libraries, school libraries and research libraries. The first edition came in 1921 and was based on the classification used in the accession libraries of the scientific libraries. The system is also called\" SAB System Classification System \",\" SAB System \"and\" SAB Classification System \". The abbreviation SAB stands for the\" Swedish Public Library Association. \"SAB collaborated with the Swedish Library Society (SBS) and formed the current Swedish Library Association. To keep up with the development of new subject areas. The Swedish Library Association Committee for Classification Systems for Swedish Libraries (formerly SAB's Cataloging and Classification Committee) decides on changes, corrections and application instructions to SAB's classification system. On which, for example, you specify the contents of a signature or add new topics. Sometimes there are proper audits where the entire system is being revised. The major audits usually result in a new edition of the classification system. The last eighth edition began in 2002 and was taken in autumn 2006.",
"homepage": "http://www.kb.se/katalogisering/Klassifikation/SAB-praxis/",
"name": "Classification system for Swedish libraries",
"prefix": "672",
"wikidata_database": "Q10659446"
},
"673": {
"description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System was designed to classify proteins (and their genes) in order to facilitate high-throughput analysis. Proteins have been classified according to: Family and subfamily: families are groups of evolutionarily related proteins; subfamilies are related proteins that also have the same function. Molecular function: the function of the protein by itself or with directly interacting proteins at a biochemical level, e.g. a protein kinase. Biological process: the function of the protein in the context of a larger network of proteins that interact to accomplish a process at the level of the cell or organism, e.g. mitosis. Pathway: similar to biological process, but a pathway also explicitly specifies the relationships between the interacting molecules. (...) Version 8.1 (release date June 1, 2013) contains 7729 protein families, divided into 68,992 functionally distinct protein subfamilies.",
"name": "PANTHER Classification System",
"prefix": "673",
"wikidata_database": "Q16335194"
},
"674": {
"description": "The scope of AGRIS and CARIS coincides with the scope of FAO and covers agriculture and its related fields, including fisheries, forestry, food, veterinary science and rural development. The AGRIS/CARIS Categorization Scheme is the basic manual for the categorization of agricultural literature and agricultural research projects to be included respectively in AGRIS and CARIS, and gives a breakdown of the AGRIS/CARIS subject scope into a number of main fields which are further subdivided into specific subject categories. Each subject category is represented by a code.",
"homepage": "http://www.fao.org/docrep/003/u1808e/u1808e00.htm",
"name": "AGRIS/CARIS Categorization Scheme",
"prefix": "674"
},
"675": {
"description": "This thesaurus was based on EUROVOC, the thesaurus of the European Parliament and the Office for Official Publications of the European Union. The EUROVOC has been 'helvetized', meaning that expressions required in Switzerland have been supplemented, ambiguous or incomprehensible names have been deleted, and in some cases the hierarchical structure changed. Polyhierarchies (more than a generic term for the same sub-term) have been omitted altogether in the interests of clearer use. However, most of the EUROVOC descriptors were adopted, mainly based on version 2, supplemented by version 2.1 and the French version 3 draft. We did not adopt the distinction between domains, microthesauri and descriptors; all descriptors in Helvetosaurus are equivalent keywords that are embedded in a hierarchy. Helvetization was in German; the French version has been deferred for cost-benefit considerations, in agreement with the French-speaking staff of the documentation center.\n\nAs sources for the Helvetization we mainly used documents of the parliamentary services and the federal administration, such as provisional list of keywords, registers and dossier divisions. In order to check how many times a word had been used, we were able to use databases of the parliamentary services, which are e.g. the parliamentary initiatives since 1983 contained in the full text.\"\n\n The thesaurus is no longer forwarded.",
"homepage": "https://helvetosaurus.sozialarchiv.ch/",
"name": "Helvetosaurus",
"prefix": "675"
},
"676": {
"description": "List of nationalities for indexing foreign vessels and aircraft.",
"homepage": "http://heritage-standards.org.uk/wp-content/uploads/2016/05/National_class_v20.pdf",
"name": "Forum on Information Standards in Heritage Nationality",
"prefix": "676"
},
"677": {
"description": "Thesaurus of the substance or substances out of which an object is or can be made.",
"homepage": "http://heritage-standards.org.uk/wp-content/uploads/2016/05/ObjMat_class_v20.pdf",
"name": "Forum on Information Standards in Heritage Object Material",
"prefix": "677"
},
"678": {
"description": "Our thesauri provide thematic structuring of legal content with standardized slogans, thus facilitating the search for similar terms and related topics, particularly facilitating the incorporation into new subjects, as well as the functional enhancement of electronic legal systems and databases.\n\nThesauri mainly contain vocabularies on legal issues, but these are supplemented by subject terms in neighboring fields such as economics, sociology or politics.\n\nThe thesaurus information is also available in RDF format via a SPARQL endpoint to facilitate a diverse reuse by the legal community and the Semantic Web Community.",
"homepage": "http://vocabulary.wolterskluwer.de/arbeitsrecht.html",
"name": "Wolters Kluwer Germany labor law Thesaurus",
"prefix": "678"
},
"679": {
"homepage": "http://vocabulary.wolterskluwer.de/court.html",
"prefix": "679"
},
"68": {
"description": "From the beginning, we saw that the thesauri we knew did not solve our specific needs, which is why we decided to create one again: the need to organize and interpret the material, which at first seemed technical And even boring, was the basis of our project.That was when the responsibility for its elaboration was taken up by the whole group of researchers, not to choose and classify words that would name the historical experiences of women Catalonia from the 9th to the 18th centuries, but to design, from the diversity of our experiences, semantic fields and concrete terms of an own language that gave meaning and meaning to the lives of women of the past and of history. Collective needs, converting an amalgam of personal needs into a common desire to make the world. The process of realizing the thesaurus has been Complex and enriching, sometimes harsh, in the sense that it has meant, at least for some of the women we have participated in, a rethinking of our being in history and in the world in political relation with other women, and not just as historians . The work, which originally emerged as a group work, became a work of relationship, through the discussion of individual knowledge and proposals with the rest of the team. We started the thesaurus by creating semantic fields and concepts from criticism to androcentric history, especially from the study of gender relations, in which the past and present social subordination of women is revealed and denounced, and a critical reconstruction is made Of social relations between the sexes, as defined by the patriarchal symbolic order. In this way, we defined a large section of our thesaurus that we call 'patriarchal order'. We did it relatively quickly, since we all knew too well 'the master's house', but arguing a lot, given the diversity of our analyzes and our experiences. 1420 terms.\n\nIt arose from the need that the specialists in women's history felt - and felt - to be able to count on the basic instruments of work to develop more rigorously our research, and to guide the historians and historians interested in the subject.",
"name": "Thesaurus of Women's History",
"prefix": "68"
},
"680": {
"description": "The WB Business Taxonomy (or Business Classification Scheme - BCS) is a hierarchy of controlled terms used to describe the Bankβs business; simply put, it describes in specifically what the Bank does.",
"homepage": "http://vocabulary.worldbank.org/BusinessTaxonomy.html",
"name": "World Bank Business Taxonomy",
"prefix": "680"
},
"681": {
"description": "The WBG Taxonomy is a classification schema which represents the concepts used to describe the World Bank Groupβs topical knowledge domains and areas of expertise - expertise β the βwhat we doβ and βwhat we knowβ aspect of the Bankβs work. The WBG Taxonomy provides an enterprise-wide, application-independent framework for describing all of the Bankβs areas of expertise and knowledge domains, current as well as historical, representing the language used by domain experts and domain novices, and Bank staff and Bank clients.",
"homepage": "http://vocabulary.worldbank.org/taxonomy.html",
"name": "World Bank Group Topical Taxonomy",
"prefix": "681"
},
"682": {
"homepage": "https://bartoc-skosmos.unibas.ch/SolarSystem/en/",
"prefix": "682"
},
"683": {
"description": "ESCO identifies and categorises skills/competences, qualifications and occupations relevant for the EU labour market and education and training, in 22 European languages. It provides occupational profiles showing which competences and qualifications are relevant for an occupation. ESCO is developed in an open IT format that can be used by third parties' software. It can be accessed through the ESCO portal and is available free of charge to everyone.",
"homepage": "https://ec.europa.eu/esco/portal/home",
"name": "Multilingual Classification of European Skills, Competences, Qualifications and Occupations",
"prefix": "683",
"wikidata_database": "Q42417229"
},
"684": {
"description": "FATHUM is a faceted classification designed to accommodate the humanities and was developed for the FATKS project (http://www.ucl.ac.uk/fatks). During this one year project, the following parts of the humanities vocabulary were developed: broad knowledge classification (300 concepts); generally applicable concepts (3000 concepts); religion (2200 concepts); the arts (300 terms). A contextual subject alphabetical index (chain index) contains 9300 entries. The classification is designed so that concepts can be freely combined in the process of indexing.",
"homepage": "http://www.ucl.ac.uk/fatks/database.htm",
"name": "Facet Analytical Theory in Managing Knowledge Structure for Humanities",
"prefix": "684"
},
"685": {
"description": "This classification scheme replaces the one previously used since Volume 44, Issue 1, March 2004 of the Bulletin.",
"homepage": "http://bollettino.aib.it/index.php/bollettinoaib/pages/view/classif",
"license": "CC BY-SA 3.0",
"name": "Letteratura Professionale Italiana Schema di Classificazione",
"prefix": "685"
},
"686": {
"description": "Its function is the elimination of barriers between legal information that is characterized by being voluminous and complex and is expressed in legislation, jurisprudence, doctrine, legal research data, legal databases, user queries, legal information for the citizen In general, legal literature for law professionals, and others.",
"homepage": "http://admin.tcda.infojus.gov.ar/tcda/",
"name": "Thesaurus Cooperativo de Derecho Argentino",
"prefix": "686"
},
"687": {
"description": "-",
"homepage": "http://tcda.infojus.gov.ar/index.php",
"name": "Thesaurus of the National Social Security Administration",
"prefix": "687"
},
"688": {
"homepage": "http://tcda.infojus.gov.ar/index.php",
"name": "Subject index",
"prefix": "688"
},
"689": {
"description": "Based on the Multilingual Thesaurus International Public Administration Society for the International Encyclopaedia of Public Administration.",
"homepage": "http://admin.tcda.infojus.gov.ar/inap/",
"name": "Public Administration Thesaurus",
"prefix": "689"
},
"69": {
"description": "The History of Catalonia Thesaurus is a controlled vocabulary of terminology in Catalan, on the history of Catalonia. The ability to create our own documentary language also allows us to make a critical assessment of the terminology used in the Catalan historiography. The compilation of the concepts used and the subsequent analysis of these (equivalence relations, hierarchy and association) allow the reduction of the meanings of the terms to a single meaning, removing ambiguities and synonyms in a donor or other content. terminology included in the first stage of creating the database was collected in the Thesaurus of Contemporary History of Catalonia. the adaptation of the documentary language to the needs of the database extended to all historical periods, implied the incorporation of new terminology and the integration of new subject areas and structures (different types of admin istraciΓ³, new social movements ...) The terminology contained in different databases county has been the starting point of this restructuring thesaurus in which this working language, as a tool that naixΓ© strict documentary, s it has become a tool that provides information on the nature of the discipline and on important aspects of our history and peculiar. It should be mentioned that the terminology provided for each region reflects in part the particularities of its territory and history and enriches extremely thesaurus. 4395 terms, relations between terms 8142, 1018 equivalent terms.\n\nIt was created to serve as an instrument in document analysis and retrieval Fund Local History of Catalonia.",
"homepage": "http://www.vocabularyserver.com/historia_catalunya/",
"name": "Thesaurus History of Catalonia",
"prefix": "69"
},
"690": {
"description": "The Intellectual Property Services Classification (IPSC) defines types of business activities that are executed by companies active in the IP market. Each main category is divided in several sub-categories.",
"homepage": "http://ipib.ci.moez.fraunhofer.de/ipst",
"license": "CC-BY-3.0",
"name": "Intellectual Property Services Classification",
"prefix": "690"
},
"691": {
"description": "2025 terms, 3764 relations between terms, 90 non preferred terms.",
"name": "Geothermal Energy Thesaurus",
"prefix": "691"
},
"692": {
"description": "2085 terms, 1154 relations between terms, 27 non preferred terms.",
"name": "GeoRiskVoc",
"prefix": "692"
},
"693": {
"description": "The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modelling. It consists of seven orthogonal vocabularies defining: reaction participants roles (e.g. \"substrate\"), quantitative parameters (e.g. \"Michaelis constant\"), classification of mathematical expressions describing the system (e.g. \"mass action rate law\"), modelling framework used (e.g. \"logical framework\"), the nature of the entity (e.g. \"macromolecule\"), the type of interaction (e.g. \"process\"), as well as a branch to define the different types of metadata that may be present within a model. SBO terms can be used to introduce a layer of semantic information into the standard description of a model, or to annotate the results of biochemical experiments in order to facilitate their efficient reuse.",
"homepage": "http://www.ebi.ac.uk/sbo/",
"name": "Systems Biology Ontology",
"prefix": "693",
"wikidata_database": "Q2377160"
},
"694": {
"description": "Sub-classification to the International Standard Classification of Education (ISCED-97) by field of education which has been created with the double objective of providing more detail and precision for the purpose of collecting policy-relevant data on fields of vocational education and training, while simultaneously maintaining the logic and structure of ISCED. The Classification on 'Fields of Training' has been replaced since the beginning of 1999 by the 'Classification of fields of education and training'.",
"homepage": "http://ec.europa.eu/eurostat/ramon/nomenclatures/index.cfm",
"name": "Classification of Fields of Training",
"prefix": "694"
},
"695": {
"description": "The CSO Standard Fields of Education Classification is a classification of the various fields of study which can be undertaken. This classification was derived from a joint project with Eurostat and UNESCO. It is based on the International Standard Classification of Education - ISCED 1997 (Fields of Education). In 1999, Eurostat and UNESCO further elaborated on the ISCED 1997 and provided a third level of about 80 categories called 'Detailed Fields'. This additional level was added to allow the EUORSTAT Classification of Training developed in 1997-98 to be integrated with ISCED 1997 and features subjects which would normally be covered as part of vocational education.",
"homepage": "http://www.cso.ie/en/surveysandmethodology/classifications/fieldsofeducationclassification/",
"license": "CC-BY-3.0",
"name": "CSO Standard Fields of Education Classification",
"prefix": "695"
},
"696": {
"prefix": "696",
"wikidata_database": "Q941910"
},
"697": {
"homepage": "https://www.baspo.admin.ch/content/baspo-internet/de/bildung-und-forschung/sportmediathek/_jcr_content/contentPar/downloadlist/downloadItems/38_1462285488353.download/Systematik.pdf",
"license": "CC BY-NC-SA 3.0",
"prefix": "697",
"wikidata_database": "Q15848220"
},
"698": {
"homepage": "http://d-nb.info/standards/elementset/gnd",
"name": "GND Ontology",
"prefix": "698",
"wikidata_database": "Q36578"
},
"699": {
"description": "The Sports Media Center of the Federal Office of Sports FOSPO is the largest sports media library in Switzerland. More than 46,000 titles in German, French, Italian and English are available to students of the EidgenΓΆssische Hochschule fΓΌr Sport Magglingen EHSM and the interested public. Print documents with year of publication since 1990 (14'000 documents) as well as all DVDs, CD-ROMs and DVD-ROMs are freely accessible and thematically arranged.",
"homepage": "https://www.baspo.admin.ch/content/baspo-internet/de/bildung-und-forschung/sportmediathek/_jcr_content/contentPar/downloadlist/downloadItems/98_1481555475433.download/Schlagw%C3%B6rter%20deutsch-franz.pdf",
"license": "CC BY-NC-SA 3.0",
"name": "Sports media librarry Magglingen Keyword index",
"prefix": "699",
"wikidata_database": "Q15848220"
},
"7": {
"description": "The Australian Governments' Interactive Functions Thesaurus (AGIFT) is a three-level hierarchical thesaurus that describes the business functions carried out across Australian, state and local governments in Australia. It contains 25 high-level functions, each with second and third level terms, as well as non-preferred terms and related terms. Its main purpose is to describe web-based resources to aid online discovery of government information and services.",
"homepage": "http://www.naa.gov.au/agift/",
"license": "CC BY-NC-ND 3.0",
"name": "Australian Governments' Interactive Functions Thesaurus",
"prefix": "7"
},
"70": {
"description": "The Thesaurus Locorum lists in 40,063 entries the names of the places recorded in the archives and libraries of Hesse, Thuringia, Saxony and Silesia in the catalogs of the Research Center for Personnel Records The database contains the entire German-speaking area of the Early Modern Age, which allows the identification of early-modern names, as they appear in different sources, not just in the preaching of the dead, with their modern place names It gives an overview of the various, sometimes very different, German and Latin names of a place in the early modern period.",
"homepage": "http://www.personalschriften.de/datenbanken/thelo.html",
"name": "Thesaurus Locorum",
"prefix": "70"
},
"700": {
"description": "The Basler Bibliography is the Bibliography of the Canton of Basel-Stadt and of the Basel Region. It has comprehensively compiled both independent publications as well as contributions to specialist journals or collections (see Ausgewertete Fachzeitschriften), which refer to the city and region of Basel.",
"homepage": "https://ub.unibas.ch/de/ub-als-kantonsbibliothek/klassifikation-basler-bibliographie/",
"name": "Systematics Basler Bibliography",
"prefix": "700"
},
"701": {
"description": "This outline supplements the topical classification of the 'Outline of Cultural Materials' with a new outline organizing and classifying the known cultures of the world. The new system: (1) expedites the beginning of actual processing of information into the Human Relations Area Files, (2) permits excerpting of sources processed that pertain to cultures other than those for which files have been established, and (3) assures that societies selected for processing approach the ideal of a representative sample of the world's cultures. Thus, this outline is a reference to files of materials on 400 cultures covering eight geographical regions of the earth. Used in conjunction with the 'Outline of Cultural Materials', researchers can locate data on a cross-section of the world's cultures in 79 major divisions of information pertaining to cultural background. A sample and index of world cultures are included.",
"homepage": "http://hraf.yale.edu/resources/reference/outline-of-world-cultures-list/",
"name": "Outline of World Cultures",
"prefix": "701"
},
"702": {
"homepage": "http://www.unibe.ch/unibe/portal/content/e809/e962/e963/e6331/e6368/e34776/e40798/e40799/Aufstellungssystematikaktuellschwarz-weiss_ger.pdf",
"name": "Law Library of Bern",
"prefix": "702"
},
"703": {
"description": "PRODCOM is the title of the EU production statistics for Mining, Quarrying and Manufacturing, i.e. Sections B and C of the Statistical Classification of Economic Activities in the European Community (NACE Rev. 2). The title comes from the French 'PRODuction COMmunautaire' (Community production). The headings of the PRODCOM list are derived from the Harmonized System (HS) or the Combined Nomenclature (CN), which thus enables comparisons to be made between production statistics and foreign trade statistics. PRODCOM headings are coded using an eight-digit numerical code, the first six digits of which are, in general, identical to those of the CPA code. The PRODCOM list is therefore linked to, and consistent with, the central product classification.",
"homepage": "http://ec.europa.eu/eurostat/ramon/nomenclatures/index.cfm",
"name": "PRODCOM List",
"prefix": "703"
},
"704": {
"abbreviation": "TaDiRAH",
"description": "This taxonomy of digital research activities in the humanities has been developed for use by community-driven sites and projects that aim to structure information relevant to digital humanities and make it more easily discoverable. The taxonomy is expected to be particularly useful to endeavors aiming to collect information on digital humanities tools, methods, projects, or readings.",
"homepage": "https://github.com/dhtaxonomy/TaDiRAH",
"license": "CC0-1.0",
"name": "Taxonomy of Digital Research Activities in the Humanities",
"prefix": "704"
},
"705": {
"description": "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.",
"name": "Vital Sign Ontology",
"prefix": "705"
},
"706": {
"description": "The TErminology for the Description of DYnamics (TEDDY) project aims to provide an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.",
"homepage": "http://co.mbine.org/standards/teddy/",
"name": "TErminology for the Description of DYnamics",
"prefix": "706",
"wikidata_database": "Q21159923"
},
"707": {
"abbreviation": "FAST",
"description": "FAST subject headings were developed by adapting the Library of Congress Subject Headings (LCSH) with a simplified syntax, retaining the very rich vocabulary of LCSH while making the schema easier to understand, control, apply, and use.",
"homepage": "http://fast.oclc.org/searchfast/",
"license": "http://www.opendatacommons.org/licenses/by/1.0",
"name": "Faceted Application of Subject Terminology",
"prefix": "707",
"wikidata_database": "Q3294867"
},
"708": {
"description": "Web Service Interaction Ontology (WSIO) enables automated interaction with more complex Web services that are typical for example within life sciences. WSIO is however independent of the application domain and relevant for both SOAP and REST Web services, and for batch execution engines in general. If the interaction scenario with a Web service is nontrivial (and incorporates session handling), annotation with WSIO concepts will enable automatic generation of client programs, scripts, or interactive applications with a graphical user interface. WSIO also enables automation of different ways of data transfer and data un-/compression or en-/decoding. We strongly discourage providers from developing complex interaction and data-transfer/compression scenarios, however when needed, WSIO may enable smooth automated interaction with them. Future versions will support more interaction scenarios. WSIO aims to serve also as a means to standardise the complex interaction scenarios primarily within both SOAP and REST Web services, and secondarily to apply also to batch execution infrastructure in general.",
"homepage": "http://purl.bioontology.org/ontology/WSIO",
"name": "Web Service Interaction Ontology",
"prefix": "708"
},
"709": {
"description": "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. This includes a set of 'universal' terms, that are applicable across various biological and technological domains, and domain-specific terms relevant only to a given domain. This ontology will support the consistent annotation of biomedical investigations, regardless of the particular field of study. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).",
"homepage": "http://obi.sourceforge.net/ontologyInformation/",
"name": "Ontology for Biomedical Investigations",
"prefix": "709",
"wikidata_database": "Q7095051"
},
"71": {
"description": "The Thesaurus Professionum is a database of professional terms of the Early Modern Period, which currently records 28,877 historical professional names from funeral pretexts and other mourning libraries in Hessian, Saxon, Silesian and Thuringian libraries and archives, which were recorded in the catalogs of the Research Center for Personnel Records The database contains the entire German-speaking area of the early modern period, with the help of the search for registries, one can search specifically for the abolition of abbreviated or translations of foreign-language occupational terms, as they appear in the sources The database also provides the opportunity to systematically search for the early-modern names of a particular profession from seven main professions.",
"homepage": "http://www.personalschriften.de/datenbanken/thepro.html",
"name": "Thesaurus Professionum",
"prefix": "71"
},
"710": {
"description": "The Sport Ontology is a simple lightweight ontology for publishing data about competitive sports events. The terms in this ontology allow data to be published about: The structure of sports tournaments as a series of events, the competing of agents in a competition, the type of discipline a event involves, the award associated with the competition and how received it ...etc. Whilst it originates in a specific BBC use case, the Sport Ontology should be applicable to a wide range of competitive sporting events data publishing use cases. Care has been taken to try and ensure interoperability with more general ontologies in use. In particular it draws heavily upon the events ontology.",
"homepage": "http://www.bbc.co.uk/ontologies/sport/",
"name": "Sport Ontology",
"prefix": "710"
},
"711": {
"description": "The Music Ontology Specification provides main concepts and properties fo describing music (i.e. artists, albums and tracks) on the Semantic Web. This vocabulary defines 54 classes and 153 properties. Music Ontology data can be published by anyone as part of a web site or an API and linked with existing data, therefore creating a music-related web of data.",
"homepage": "http://purl.org/ontology/mo/",
"name": "Music Ontology",
"prefix": "711"
},
"712": {
"description": "FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people's heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world. FOAF does not compete with socially-oriented Web sites; rather it provides an approach in which different sites can tell different parts of the larger story, and by which users can retain some control over their information in a non-proprietary format.",
"homepage": "http://xmlns.com/foaf/0.1/",
"name": "Friend of a Friend vocabulary",
"prefix": "712",
"wikidata_database": "Q1389366"
},
"713": {
"description": "This ontology is centered around the notion of event, seen here as the way by which cognitive agents classify arbitrary time/space regions (...). This ontology has already been proven useful in a wide range of context, due to its simplicity and usability: from talks in a conference, to description of a concert, or chords being played in a Jazz piece (when used with the Timeline ontology), festivals, etc.",
"homepage": "http://motools.sf.net/event/event.html",
"license": "CC-BY-3.0",
"name": "Event Ontology",
"prefix": "713"
},
"714": {
"description": "This ontology is centered around the notion of timeline, seen here as a way to identify a temporal backbone. A timeline may support a signal, a video, a score, a work, etc. This ontology, used with the Event ontology, can be used to annotate sections of a signal, a video, or any temporal object. For example, it can be used to express: This shot holds between this frame and that frame, in this video; This performance happened at that particular date; In this song, the first chorus is before the second verse; A new structural segment starts at 2 minutes and 43 seconds, on this signal; This signal is a sampled version of this one; This part of the score corresponds to this section in an actual performance (in progress...).",
"homepage": "http://motools.sf.net/timeline/timeline.html",
"name": "Timeline Ontology",
"prefix": "714"
},
"715": {
"description": "CSA Mechanical & Transportation Engineering Abstracts provides citations, abstracts, and indexing of the serials literature in mechanical and transportation engineering and their complementary fields, including forensic engineering, management and marketing of engineering services, engineering education, theoretical mechanics and dynamics, and mathematics and computation.",
"name": "Mechanical & Transportation Engineering Abstracts Classification Codes",
"prefix": "715"
},
"716": {
"description": "As a result of the mission entrusted to it by the MILDT to develop a national resource center on drugs, OFDT provides a database in its documentary service covering different fields (products, uses and Consequences of these uses, public responses and drug markets) and is aimed primarily at decision-makers and professionals in the health, social and law enforcement sectors.",
"homepage": "http://bdoc.ofdt.fr/pmb/opac_css/",
"name": "Thesaurus TOXIBASE",
"prefix": "716"
},
"717": {
"description": "The Aerospace & High Technology Database provides bibliographic coverage of basic and applied research in aeronautics, astronautics, and space sciences. The database also covers technology development and applications in complementary and supporting fields such as chemistry, geosciences, physics, communications, and electronics.",
"homepage": "http://www.lib.vt.edu/help/handouts/databases/aerospace-eng.pdf",
"name": "Aerospace & High Technology Database Classification",
"prefix": "717"
},
"718": {
"description": "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own sublassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's (LM_ID) which reflects their position in the classification hierarchy.",
"homepage": "http://www.lipidmaps.org/data/classification/LM_classification_exp.php",
"name": "Lipid Classification System",
"prefix": "718"
},
"719": {
"description": "The FormacodeΒ thesaurus is an indispensable tool for indexing and retrieving information on the training offer. It is a reference tool for all those involved in vocational training.\n\nThe FormacodeΒ thesaurus allows: to index the fields of training but also the public, the teaching methods and methods, the types of certifications ...; To manage databases on training provision; Easier to explore training databases; To establish a crossroads between the \"job\" and \"training\" nomenclatures (Rome, NSF and GFE);\n\n14 major domains, 63 semantic fields, 3207 keywords, 5 annexes, correspondences.",
"homepage": "http://formacode.centre-inffo.fr/",
"name": "Formacode",
"prefix": "719"
},
"72": {
"description": "The revised thesaurus remains a mono-hierarchical thesaurus, that is, a given descriptor is linked to only one thematic branch. Descriptors for the different modes of transport are in a transport hierarchy in Chapter 3 COMMUNICATIONS, whereas the terms relating to transport infrastructure are in a 'communication channel' hierarchy in Chapter 6 EQUIPMENT. 'Rail transport' is referred to as an associated term in the hierarchy of 'communication channels' and 'railway networks' Is a term associated with 'rail transport' in the 'transport' hierarchy The 1997 edition consisted of 1015 descriptors and non-descriptors. And 460 new descriptors for the thesaurus, 15 new terms for the list of Actions authorities, 64 new document typologies and 122 new descriptors for the historical context. The working group also proposes the deletion of 18 descriptors and 11 non-descriptors, the transformation of 8 descriptors into non-descriptors and 7 non-descriptors into descriptors, the displacement of 36 descriptors in the hierarchy, and the addition of 306 Non-descriptive synonymy terms of the 'employ' type. At the same time, in response to requests from the services for a structured version of the thesaurus for integration into archival software, the Archives of France management has carried out tests to convert the thesaurus to the SKOS format (Simple System d Organization of knowledge), a format allowing the easy publication of structured vocabularies for their use in the semantic Web.\n\nThe revised thesaurus is not restricted to archives in the strict sense but must in principle be applicable to all resources held by public or private archives (including iconographic collections and libraries).",
"license": "CC BY-SA 3.0",
"name": "Thesaurus for the Indexation of Local Archives",
"prefix": "72"
},
"720": {
"abbreviation": "WoRMS",
"description": "The aim of a World Register of Marine Species (WoRMS) is to provide an authoritative and comprehensive list of names of marine organisms, including information on synonymy. While highest priority goes to valid names, other names in use are included so that this register can serve as a guide to interpret taxonomic literature. The content of WoRMS is controlled by taxonomic experts, not by database managers. WoRMS has an editorial management system where each taxonomic group is represented by an expert who has the authority over the content, and is responsible for controlling the quality of the information. Each of these main taxonomic editors can invite several specialists of smaller groups within their area of responsibility to join them. This register of marine species grew out of the European Register of Marine Species (ERMS), and its combination with several other species registers maintained at the Flanders Marine Institute (VLIZ). Rather than building separate registers for all projects, and to make sure taxonomy used in these different projects is consistent, VLIZ developed a consolidated database called βAphiaβ. A list of marine species registers included in Aphia is available below. MarineSpecies.org is the web interface for this database. The WoRMS is an idea that is being developed, and will combine information from Aphia with other authoritative marine species lists which are maintained by others (e.g. AlgaeBase, FishBase, Hexacorallia, NeMys). Resources to build MarineSpecies.org and Aphia were provided mainly by the EU Network of Excellence βMarine Biodiversity and Ecosystem Functioningβ (MarBEF), and also by the EU funded Species 2000 Europe and ERMS projects. Intellectual property rights of the European part of the register is managed through the Society for the Management of Electronic Biodiversity Data (SMEBD). Similar solutions are now being investigated for the other parts of the register. Aphia contains valid species names, synonyms and vernacular names, and extra information such as literature and biogeographic data. Besides species names, Aphia also contains the higher classification in which each scientific name is linked to its parent taxon. The classification used is a βcompromiseβ between established systems and recent changes. Its aim is to aid data management, rather than suggest any taxonomic or phylogenetic opinion on species relationships. Keeping WoRMS up-to-date is a continuous process. New information is entered daily by the taxonomic editors and by the members of our data management team. Often data also come in from contributions of large datasets, such as global or regional species lists. No database of this size is without errors and omissions. We canβt promise to make no errors, but we do promise to follow up and give feedback on any communications pointing out errors. Feedback is very welcome!",
"homepage": "http://www.marinespecies.org/",
"license": "CC-BY-3.0",
"name": "World Register of Marine Species",
"prefix": "720",
"wikidata_database": "Q604063"
},
"721": {
"description": "CiTO, the Citation Typing Ontology, is an ontology written in OWL 2 DL to enable characterization of the nature or type of citations, both factually and rhetorically, and to permit these descriptions to be published on the Web. The citations characterized may be either direct and explicit (as in the reference list of a journal article), indirect (e.g. a citation to a more recent paper by the same research group on the same topic), or implicit (e.g. as in artistic quotations or parodies, or in cases of plagiarism). CiTO contains the object property cito:cites and its sub-properties, and its inverse property cito:isCitedBy, from the original Citation Typing Ontology, CiTO v1.6. Upon the creation of version 2.0 of CiTO, a number of new sub-properties of cito:cites were added, and the inverse properties of all the sub-properties of cito:cites were created, all of which are sub-properties of cito:isCitedBy. The ontology has also been integrated with the SWAN Discourse Relationships Ontology by making cito:cites a sub-property of http://purl.org/swan/2.0/discourse-relationships/refersTo. Restrictions of domain and range present in the previous version of CiTO were removed from the object properties when creating CiTO v 2.0, permitting its independent use in other contexts, in addition to conventional bibliographic citations.",
"homepage": "http://purl.org/spar/cito/",
"license": "CC-BY-3.0",
"name": "Citation Typing Ontology",
"prefix": "721"
},
"722": {
"description": "Project development of a multilingual thesaurus managed by Flora software: French, English, Spanish, German, Italian 3330 descriptors and 954 non-descriptors are distributed in 39 semantic fields.",
"homepage": "http://www.sportdocs.insep.fr/flora_insep/jsp/index.jsp",
"name": "Thesaurus Heracles",
"prefix": "722"
},
"723": {
"description": "The terms of this thesaurus and many others are defined in the Sustainable Development Dictionaries, a nomenclature of over 1,100 terms and abbreviations and more than 1,000 definitions The vocabulary of sustainable development from French official sources, Foreign and International Cooperation: SD 21000, Brundtland Commission, Earth Summit, Framework Convention on Climate Change, Convention on Biodiversity, Work of the United Nations Environment Program, Federal Council for Sustainable Development, Etc. The expertise of sustainable development actors, in particular Christian Brodhag, in particular a member of the French delegation, presented at the Johannesburg World Summit on Sustainable Development in 2002 and Florent Breuil, engineer Armines and Environment expert. Fundamental vocabulary of sustainable development, as well as the notions derived from the most recent Environmental, scientific and economic issues. The English equivalents for each term. An index of English words to access their French equivalents. A selection of websites to access official information.",
"homepage": "http://wwwv1.agora21.org/encyclopedie/thesdd.pdf",
"name": "French Thesaurus Sustainable Development",
"prefix": "723"
},
"724": {
"abbreviation": "InPhO",
"description": "The InPhO analyzes over 37 million words of philosophical content from: Stanford Encyclopedia of Philosophy; Internet Encyclopedia of Philosophy; PhilPapers; HathiTrust/Google Books Collection. The InPhO is constructed by a novel 3-step semi-automated process, called dynamic ontology: 1. Data Mining β Natural language processing (NLP) techniques generate statistical hypothesis about the relationships among philosophically-salient topics. 2. Expert Feedback β These hypotheses are evaluated by domain experts through online interfaces. 3. Machine Reasoning β Our machine reasoning program uses feedback and statistical measures to populate the ontology.",
"homepage": "https://inpho.cogs.indiana.edu/",
"license": "CC BY-NC-SA 3.0",
"name": "Indiana Philosophy Ontology",
"prefix": "724",
"wikidata_database": "Q6023365"
},
"725": {
"homepage": "http://purl.org/dc/terms/",
"license": "CC-BY-3.0",
"name": "DCMI Metadata Terms",
"prefix": "725",
"wikidata_database": "Q624610"
},
"726": {
"description": "PRISM Publishing Requirements for Industry Standard Metadata defines an XML/RDF metadata vocabulary for managing, aggregating, post-processing, multi-purposing and aggregating magazine, news, catalog, book, and mainstream journal content. PRISM recommends the use of certain existing standards, such as XML, RDF, the Dublin Core, and various ISO specifications for locations, languages, and date/time formats. In addition PRISM provides a framework for the interchange and preservation of content and metadata, a collection of elements to describe that content, and a set of controlled vocabularies listing the values for those elements.\n\nMetadata is an exceedingly broad category of information covering everything from an article's country of origin to the fonts used in its layout.PRISM's scope is driven by the needs of publishers to receive, track, and deliver multi-part content. The focus is on additional uses for the content, so metadata concerning the content's appearance is outside PRISM's scope.",
"homepage": "http://prismstandard.org/Pam_1.0/PAMGuide1_0.pdf",
"name": "Publishing Requirements for Industry Standard Metadata",
"prefix": "726",
"wikidata_database": "Q7258111"
},
"727": {
"homepage": "http://www.nbdbiblion.nl/product/siso-online",
"prefix": "727",
"wikidata_database": "Q2582270"
},
"728": {
"description": "1418 terms, 546 relationships between terms, 277 equivalent terms.",
"name": "Thesaurus Music Colombia",
"prefix": "728"
},
"729": {
"description": "UniProtKB Keywords constitute a controlled vocabulary with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest. Keywords are classified in 10 categories: Biological process, Cellular component, Coding sequence diversity, Developmental stage, Disease, Domain, Ligand, Molecular function, Post-translational modification, Technical term. An entry often contains several keywords. Inside a category, the keywords are stored in alphabetical order. Keywords can be used to retrieve subsets of protein entries or to generate indexes of entries based on functional, structural, or other categories.",
"homepage": "http://www.uniprot.org/keywords/",
"license": "CC BY-ND 3.0",
"name": "UniProtKB Keywords",
"prefix": "729"
},
"73": {
"description": "Subject terms used in RHSV cataloguing projects.",
"homepage": "http://collections.historyvictoria.com.au/rhsvdatabases/ThesApr11/",
"name": "Victorian Local History Thesaurus",
"prefix": "73"
},
"730": {
"abbreviation": "BOS",
"description": "Bremen 's online system allows for the complete presentation of all about 53 Bremen professional systems in the sense of a virtual book shelf with a link to the stock of the individual class, thereby enabling thematic browsing within the individual subject systematics (example informatics) and subsequent presentation of the stock of a notation .. class designations are mitindexiert within the e-LIB searched in a thematic search, therefore, are also classes of Bremer system as hits available are the classes selected, the user will receive all verorteten there title - regardless of the initial term.",
"homepage": "http://www.suub.uni-bremen.de/fachinformationen/bremer-online-systematik/",
"name": "Bremer Online Systematics",
"pattern": "^[a-z]{3}( [0-9]{3}(\\.[0-9]+)?( [a-z]+)?)?$",
"prefix": "730"
},
"731": {
"description": "The thesaurus of municipal archives aims to reflect the municipal administration, agglutinating and amalgamating, from its logical and semantic concept, the disciplines, activities and functions of the institution. The intrinsic variety of the municipal administration advises the development of a list of In this way, the terms of the thesaurus will be bound to this area and will be terms that appear in the documents generated by the municipal institution. Is understood as a context, but also as an organic and functional structure of the areas that make it possible to carry out the activities according to the functions entrusted to them.Thus, the organizational picture has been taken into account as a reference, not as a determinant, of thematic dimension When choosing families, although sometimes some Sections of the table may coincide with the denomination of the families. That is, the local administration has been understood as a theme, without obviating its organic structure.",
"homepage": "http://arquivosdegalicia.xunta.es/export/sites/default/arquivos-de-galicia/resources/normativa/Tesauro_archivos_municipales.pdf",
"name": "Thesaurus of Municipal Archives",
"prefix": "731"
},
"732": {
"abbreviation": "ASB",
"description": "The General System for Public Libraries (ASB) is a classification that is used by many public libraries, especially in the old federal states of Germany, albeit with different, often in-house variants (ASB) was originally developed in the 1950s, according to the circumstances (in many places conversion from the theken library to the freehand library), it is an answer \"This was especially the case with the Association of Libraries of the State of North Rhine-Westphalia, supported by speakers from the magazine BΓΌcherei und Bildung.",
"homepage": "http://asb-kab-online.ekz.de/",
"name": "General Systematic for Public Libraries",
"pattern": "^[A-Z][a-z]*( [0-9]+)?$",
"prefix": "732",
"wikidata_database": "Q1571087"
},
"733": {
"description": "The list of subject headings in Catalan (LEMAC) is a controlled language used for cataloging and indexing of documents theme. It contains records subject authority adapted the Library of Congress Subject Headings (LCSH) and from the translation of the list of subject headings for Libraries Carmen and Jorge Rovira Aguayo preliminary edition published by the Library Service of the Government of Catalonia in 1988. Other lists of subject headings that also serve as a basis for the adaptation of records LEMAC December celebrities include Répertoire-matière (RVM Laval) and RAMEAU: Industry directory to Autorité et matière encyclopedic alphabetical unifié (RAMEAU). the records can be viewed as a thesaurus and MARC format. the constant introduction of new terms and the need to review and update existing headings LEMAC make the organism live in a perpetual process transformation and change. Updates the content of the database will be made fortnightly.\n\nThe LEMAC includes the following types of headings and subdivisions: Headings subject and form; Headings personal name, corporate and securities that serve as a model; Geographical names of political and administrative jurisdictions and subdivisions followed by non-jurisdictional geographic names; Subdivisions under geographical names, language names and subdivisions under common or free application.",
"name": "List of subject headings in Catalan",
"prefix": "733",
"wikidata_database": "Q199303"
},
"734": {
"description": "The main tool used by the TRACES database to describe the contents of the documents Thesaurus Language and Literature, a documentary language that allows both controlled indexing evenly and reliably retrieve documents easily and tour information each user needs.\n\nUnlike free languages, thesaurus provides a set of hierarchically structured terms, and to control the proper use of scientific terminology used. Only in this way can avoid the use of synonyms to designate the same concept (see, for instance, the terms Interference and linguistic barbarisms), and you can retrieve documents from the terms may not appear in the original document.\n\nTherefore, when in 1987 he started talking about the possibility of a bibliographic database, one of the initial tasks was to draft a first version of the thesaurus, which included scientific terminology required for indexing documents. Over the years, this first draft has been modified and extended: the thematic areas have been rethought general, if you have added new sub needed and have been constantly added new descriptors necessary for the description of documents. This dynamic process ensures the adequacy of the thesaurus to the evolution of scientific disciplines specific to the database, and corrects defects that demonstrates its use constantly.",
"homepage": "http://projectetraces.uab.cat/index.php/project/el-tesaurus/",
"name": "Thesaurus Language and Literature",
"prefix": "734"
},
"735": {
"description": "The implementation of the ARCHIVOS thesaurus has the purpose of having a tool for the treatment of information related to archival documentation. This instrument will be used both in the indexing process of documents and in the retrospective search of information.\n\nThe thesaurus covers the terminology of the documentation of the File of the DiputaciΓ³n and of the municipalities of the province of Alicante attached to the Plan of Assistance to Municipal Archives of the DiputaciΓ³n de Alicante. These institutions produce documents referring to any subject and historical periods, so we can say that this is a multidisciplinary thesaurus.\n\nDescriptors: 2.428, No descriptors: 600, Application notes 285.",
"homepage": "http://www.archivo.diputacionalicante.es/tesauro.htm",
"name": "Thesaurus of Archives",
"prefix": "735"
},
"736": {
"description": "Under the same premises and structure as the Thesaurus of Archives, and with the same objective of facilitating documentary description and the search for archival information, we have developed the thesaurus of place names. Although most of the documentation analyzed has a scope In order to be able to accommodate any geographical term, we have chosen to divide the thesaurus of place names into three families, , Domains or micro thesauri: MT of the province of Alicante, MT of Autonomous Communities and MT of Countries.",
"homepage": "http://www.archivo.diputacionalicante.es/tesauro.htm",
"name": "Toponymic thesaurus of the Province Alicante",
"prefix": "736"
},
"737": {
"description": "This is a control initiative on the thematic terminology used in the library in the absence of updates, regionalisms and / or localisms in the field of social sciences in Thesauri.This vocabulary contains mainly descriptors of the Macrotesauro on economic and social development of the OECD. In addition, for the areas not included in this thesaurus, descriptors of the Unesco Thesaurus of Education, the ISOC Thesaurus of Psychology and the SAIJ Tesauro of Argentine Law were added. According to the specific needs for indexing in the library.",
"homepage": "http://vocabularios.caicyt.gov.ar/portal/index.php?v=FLACSO",
"name": "Vocabulary Controlled FLACSO Argentina",
"prefix": "737"
},
"738": {
"description": "It is an initiative of exchange and cooperation of the working group SOCIABLES The Library\" Norberto Rodriguez Bustamante \"of the Faculty of Social Sciences of the UBA was the one who called it, integrating to the same the following libraries of the area of social sciences belonging to these institutions : Cultural Cooperation Center, Latin American Faculty of Social Sciences, Gino Germani Research Institute - UBA, National University of General Sarmiento, National University of LanΓΊs and National University of Quilmes. Vocabulary is a development based on the \"Macrotesauro sobre desarrollo Economic and social development. \"Its main purpose is to provide a semantic tool that is up-to-date and includes localisms and regionalisms in the disciplinary field of the social sciences.",
"homepage": "http://vocabularios.caicyt.gov.ar/portal/index.php",
"name": "Latin American Vocabulary of Social Sciences",
"prefix": "738"
},
"739": {
"description": "Based on the DECS vocabulary developed and maintained by the Pan American Health Organization. Argentinean localization carried out by CAICYT / CONICET with the support of CONICET's network of institutional libraries.",
"homepage": "http://vocabularios.caicyt.gov.ar/portal/index.php",
"name": "Vocabulary of Health Sciences for Argentina",
"prefix": "739"
},
"74": {
"description": "3166 terms, 554 relationships between terms, 77 equivalent terms.",
"name": "Vocabulary of Argentine and American History",
"prefix": "74"
},
"740": {
"description": "Classification of areas and technologies used in the field of CONICET for the structuring and management of its activities and projects, based on the Revised Field of Science and Technology (FOS). Classification the Frascati Manual 2002 \", with adaptations for Uruguay, originally developed by the OECD.",
"homepage": "http://www.caicyt-conicet.gov.ar/comcient/ark%3A/16680081/rsctf#?c=0&m=0&s=0&cv=0",
"license": "CC BY-SA 3.0",
"name": "CONICET Classification by areas and technologies",
"prefix": "740"
},
"741": {
"description": "The ICS (International Classification for Standards) is intended to serve as a structure for catalogues of international, regional and national standards and other normative documents, and as a basis for standing-order systems for international, regional and national standards. It may also be used for classifying standards and normative documents in databases, libraries, etc. The ICS should facilitate the harmonization of information and ordering tools such as catalogues, selective lists, bibliographies, and databases on magnetic and optical media, thus promoting the world-wide dissemination of international, regional and national standards and other normative documents.",
"name": "International Classification for Standards",
"prefix": "741",
"wikidata_database": "Q1510727"
},
"742": {
"abbreviation": "ΓSΓB",
"description": "The system is an important tool for the attractive presentation of the stock and the targeted collection of thematic resources, which helps to facilitate access to information, education and culture to the users of libraries Public libraries \"(ΓSΓB), which is now available in a completely revised form (ΓSΓB'04) The WWW version offers the complete systematics with all the explanations, references and terms of the keyword register, characterized by comfortable search and navigation possibilities Is continuously updated.",
"homepage": "https://www.bvoe.at/serviceangebote/systematik/online-version",
"name": "Austrian classification for public libraries",
"pattern": "^[A-Z]{1,2}(\\.([A-Z0-9]{1,3}(\\.[0-9A-Z]{1,3})?)?)?$",
"prefix": "742",
"wikidata_database": "Q305980"
},
"743": {
"abbreviation": "ESSB",
"description": "The system of systematics for South Tyrolean libraries (ESSB) is the most widely used system for linguistic literature in South Tyrol's public libraries and school libraries. It was published in 1982 by the local library in Bolzano, and is based on the general system of public libraries , Which was thoroughly revised from 2001 to 2005 and published in a new version at the beginning of 2006. Since then, it has been updated twice a year and adapted to the latest developments.",
"homepage": "https://bvs.bz.it/dienstleistungen/medienbearbeitung/inhaltliche-erschliessung/essb",
"name": "Unit system for South Tyrolean libraries",
"pattern": "^[A-Z]([a-z]|Γ€)( [0-9]+(\\.[0-9](\\.[0-9])?)?)?$",
"prefix": "743",
"wikidata_database": "Q1278277"
},
"744": {
"description": "The Fons of the IEA bibliographical document is a special feature in the field of territorial political autonomy in Spain and abroad, in the political, constitutional, administrative and financial aspects. Tesaurus temà tic: Tables els registres estan informats amb unes paraules Which correspond to the matèries de què tracten. Totes aquestes paraules clau are recollides in a tesaurus temà tic d'elaboració interna.",
"homepage": "http://governacio.gencat.cat/web/.content/iea/documents/serveis/arxius/tesaurus_iea.pdf",
"name": "Fons Documental i BibliogrΓ fic Tesaurus temΓ tic",
"prefix": "744"
},
"745": {
"abbreviation": "NBC",
"description": "The Dutch Basic Classification (NBC) is originally a Dutch library classification scheme developed for academic libraries. This rating is late 80's developed under the leadership of the Royal Library (Netherlands), in use since 1990 and has since been updated. the purpose of the basic rating is originally threefold: Organize or categorization of scientific publications on research areas, search or subject indexing of books and journals by academic libraries, the Collection Development Coordination in Dutch research libraries in practice the Basic classification is used together with a detailed word system. consisting of keywords, description of place and time, type keyword, genre, keyword and personal name as subject. The current basic classification (3rd revised edition 1998) is divided into five categories, 48 ββcategories and about 2250 part sections. Headings are indicated with two numbers, sub-areas are indicated by two more digits after which the column to which they belong, separated by a dot.",
"homepage": "http://www.kb.nl/sites/default/files/docs/bc04.pdf",
"name": "Dutch Basic Classification",
"pattern": "^[0-9]{2}\\.[0-9]{2}$",
"prefix": "745",
"wikidata_database": "Q810226"
},
"746": {
"description": "The New Zealand Standard Classification of NonβProfit Organisations (NZSCNPO) has been developed to assist in the study of the nonβprofit sector in the New Zealand context. Designed to meet the requirements of the satellite account for nonβprofit institutions (NPISA), the classification may be applied by various organisations throughout New Zealand to encourage standardisation and data comparability. The classification is based on the International Classification of Non Profit Organisations (ICNPO) to ensure international comparability of data on nonβprofit organisations. Some changes to the international classification have been made to reflect the operation of nonβprofit institutions (NPIs) in the New Zealand context and the needs of users. The standard classification of non-profit organisation is a hierarchical classification of two levels. Level 1 of the classification has 11 categories and level 2 of the classification has 43 categories β excluding residual categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/non-profit-organisation.aspx",
"name": "New Zealand Standard Classification of NonβProfit Organisations",
"prefix": "746"
},
"747": {
"description": "The Activity Classification for the Time Use Survey (ACTUS) was developed to assist in the study of time use in the New Zealand context. This classification was designed to meet the requirements of the Statistics New Zealand Time Use Survey 2009/10. ACTUS is based on the activity classification used for the Statistics New Zealand Time Use Survey 1998/99. Changes to this classification have been made to reflect the needs of users and to improve international comparability with time use surveys in Australia, Canada, the United States of America, and the United Kingdom. ACTUS is a hierarchical classification of four levels. Level one of the classification has four categories. Level two has 11 categories, level three has 71 categories, and level four has 126 categories β excluding residual categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/activity-time-use-survey.aspx",
"license": "CC-BY-3.0",
"name": "Activity Classification for the Time Use Survey",
"prefix": "747"
},
"748": {
"description": "The standard classification of accommodation is a hierarchical classification of three levels. Level 1 of the classification has five categories, level 2 has 11 categories and level 3 has 18 categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/accommodation.aspx",
"license": "CC-BY-3.0",
"name": "New Zealand Accommodation Classification",
"prefix": "748"
},
"749": {
"description": "Age is a flat classification with single-year categories from 0 years to 119 years inclusive, plus a category for 120 years and over. Classifications for date of birth are required because age is derived from the day, month and year a person is born. Date of birth is derived from three flat classifications: date of birth day, date of birth month and date of birth year. Day has single categories 01 to 31 (representing the days of the month). Month has single categories 01 to 12 (representing the months of the year). Year has single categories (representing 120 years back from the current year). For example, in 2007, the year classification range starts with 1887, which is 120 years from 2007.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/age.aspx",
"license": "CC-BY-3.0",
"name": "Age β New Zealand Standard Classification",
"prefix": "749"
},
"75": {
"abbreviation": "AAT",
"description": "The AAT is a structured vocabulary currently containing around 131,000 terms and other information about concepts. Terms for any concept may include the plural form of the term, singular form, natural order, inverted order, spelling variants, scientific and common forms, various forms of speech, and synonyms that have various etymological roots. Among these terms, one is flagged as the preferred term, or descriptor. There may be multiple descriptors reflecting usage in multiple languages. Preferences for individual contributors may differ and are noted.\n\nThe primary users of the Getty vocabularies include museums, art libraries, archives, visual resource collection catalogers, conservation specialists, archaeological projects, bibliographic projects concerned with art, researchers in art and art history, and the information specialists who are dealing with the needs of these users. In addition, a significant number of users of the Getty vocabularies are students or members of the general public.",
"homepage": "http://www.getty.edu/research/tools/vocabularies/aat/",
"license": "http://www.opendatacommons.org/licenses/by/1.0",
"name": "Getty Art and Architecture Thesaurus",
"prefix": "75",
"wikidata_database": "Q611299"
},
"750": {
"description": "Air Routes is a hierarchical classification of four levels. Level 1 of the classification has nine categories, Level 2 has 25 categories, Level 3 has 102 categories and Level 4 has 465 categories - excluding supplementary categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/air-routes.aspx",
"license": "CC-BY-3.0",
"name": "Air Routes Classification",
"prefix": "750"
},
"751": {
"description": "The standard classification of area unit is a flat classification and contains 2,020 categories. It is released annually on the 1st of January, but there are not always changes from the previous classification. To facilitate time series analysis of data, correspondence files between area units 2006 and 2013 and area units 2001 and 2006 are available.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/area-unit.aspx",
"license": "CC-BY-3.0",
"name": "Standard Classification of Area Unit",
"prefix": "751"
},
"752": {
"description": "In order to structure the information on rural culture has created the first Catalan Thesaurus of rural culture, which has been agreed with Red Roots - cultivation of knowledge.\" The thesaurus is built based on existing documentation database Roots - cultivation of knowledge. in our thesaurus 12 subject areas are subdivided into 45 sub-major.",
"homepage": "http://www.arrelsconreusabers.cat/tesaurus/",
"name": "Thesaurus of Rural Catalan Culture",
"prefix": "752"
},
"753": {
"description": "PUC-Minas and the Federal University of Minas Gerais provided a Thesaurus in Information Science. The thesaurus was prepared as part of the doctoral work of Manoel Palhares, under the guidance of Profa. Dr. Maria Aparecida Moura at the School of Information Science at UFMG.",
"homepage": "http://icei.pucminas.br/ci/tci/",
"name": "Thesaurus in Information Science",
"prefix": "753"
},
"754": {
"description": "The present Thesaurus of hydraulic engineering is directed to the technicians and professionals who must submerge in the problems that the location of the information in this field represents, and to the professionals of the documentation which they approach subjects of hydraulic Engineering.\n\nThe Thesaurus represents a documentary tool that, thanks to itΒ΄s characteristic of the specific language normalization, allows the conversion of the technical language of a document to the own controlled documentary language, essential way for all user who accedes to a data base looking for information and needs to prepare a strategy for the documentary consultation.\n\nFurthermore, the Thesaurus means a fundamental tool for the information retrieval officer that must link certain document or contribute with references to a data base. DonΒ΄t exist thesaurus in Castilian language on hydraulic Engineering, the present documentary tool not only means an important advance to guarantee the quality in the index-linking processes and information retrieval of the data bases, but it represents a contribution in the field of the scientific terminology in ours language.",
"homepage": "http://hispagua.cedex.es/documentacion/tesauro",
"name": "Thesaurus of Hydraulic Engineering",
"prefix": "754"
},
"755": {
"description": "The inventory of the library's library is developed in this form up to and including the acquisition year 2011. A classification of the library consists of three parts: alphanumeric notation, for example A 01.05, verbal description of the notation, for example growth theory, further explanations (in italics)\".",
"homepage": "http://www.libit.de/bbkwo/Buba/Klassifikation/Thematische_Suche_Zentrale_Klassifikation.HTML",
"name": "Deutsche Bundesbank Classification Library Head office",
"prefix": "755"
},
"756": {
"description": "A classification of the Numismatic Library consists of two parts: alphanumeric notation, for example D.2; verbal description of the notation, for example, coin technology.",
"homepage": "http://www.libit.de/bbkwo/Buba/Klassifikation/Klassifikation_NB_A-Z.HTML",
"license": "https://www.w3.org/Consortium/Legal/2015/doc-license",
"name": "Deutsche Bundesbank Classification Numismatic specialist library",
"prefix": "756"
},
"757": {
"homepage": "http://www.libit.de/bbkwo/Buba/Klassifikation/Schlagwort%C3%BCbersicht_WEB_OpenUrl.pdf",
"prefix": "757"
},
"758": {
"description": "The standard classification of broad economic categories is a hierarchical classification of five levels. Level 1 of the classification has seven categories, level 2 has 15 categories, level 3 has 44 categories, level 4 has 90 categories and level 5 of the classification has 74 categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/broad-economic-categories.aspx",
"name": "Broad Economic Categories β New Zealand Standard Classification",
"prefix": "758"
},
"759": {
"description": "The classification of business type is a flat classification with 15 categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/business-type.aspx",
"license": "CC-BY-3.0",
"name": "Business Type β New Zealand Standard Classification",
"prefix": "759"
},
"76": {
"description": "The editors of ARTbibliographies Modern (ABM) use the controlled vocabulary featured in this Thesaurus in order to index entries in the database with the appropriate subject terms.",
"name": "ARTbibliographies Modern Thesaurus",
"prefix": "76"
},
"77": {
"description": "The Australian Pictorial Thesaurus (APT) is a hierarchical thesaurus of over 15,000 Australian subject terms for the indexing of images and other original material collections. The APT uses contemporary Australian words and phrases to describe objects, people, places, activities and concepts [depicted in an image]. The range and depth of APT terms facilitate the precise indexing of images and collections. The APT arranges terms hierarchically. This means that terms are organised within a table of linked terms. That is: terms which are similar but broader in their application; terms which are similar but narrower in their application; and terms which are related. This allows the user to move around the thesaurus by following its hyperlinks, to choose the most appropriate term.\n\nIt ensures the common description of pictorial collections across Australian libraries, museums and archives.\"\n\n\"The Australian Pictorial Thesaurus will no longer be available from 31 August 2015. Please refer to other indexing tools such as the Library of Congress Subject Headings and the Art and Architecture Thesaurus.",
"homepage": "http://www.vocabularyserver.com/apt/",
"name": "Australian Pictorial Thesaurus",
"prefix": "77"
},
"782": {
"description": "411 Terms, 20 Relations between Terms, 12 Equivalent Terms.",
"homepage": "http://www.vocabularyserver.com/rarothes/",
"name": "Ancient and Rare Book Thesaurus",
"prefix": "782"
},
"783": {
"description": "NewsIndexer uses a broad and deep taxonomy to reflect the news media's evolving coverage of topics. Developed by our team of expert taxonomists, NewsIndexer supports automatic news filtering or assists human indexers in tagging subjects for individual news articles. Identification of the topics and concepts in each article inline, as well as for the article as a whole, leverages search and discovery while maintaining high accuracy, precision, and recall. The result is an unparalleled tool for enhancing discoverability of content.\n\nOnline searches for news articles often yield a flood of erroneous hits and useless links. To retain the faith of readers, online searches must yield more useful results. News publishers have needed better ways of indexing articles, and have sought indexing software to make the process easier.\n\nNewsIndexer terms have been mapped to the GICS, IPTC and ICB systems to support RSS and topical news feeds to all customers. The export options comply with the NITF (News Industry Text Format) standards of the IPTC (International Press Telecommunications Council).\n\nNewsIndexer terms have all been mapped to the GICS, IPTC and ICB systems as well to ensure that the data from all newsfeeds can be fully tagged and presented to support RSS and topical news feeds to all customers. The export options are mapped for compliance with the NITF (News Industry Text Format) standards of the IPTC (International Press Telecommunications Council).",
"homepage": "http://www.newsindexer.com/",
"name": "NewsIndexer",
"prefix": "783"
},
"784": {
"description": "Thesaurus of the Forest File of the General Directorate of Environment of the Autonomous Community of the Region of Murcia.",
"homepage": "http://www.um.es/isgat/navegacion.php",
"name": "Forest File Thesaurus",
"prefix": "784"
},
"785": {
"description": "Child dependency is an important variable in determining the composition of families and households. Census and many other surveys (eg Household Labour Force Survey, New Zealand Income Survey, and Household Economic Survey) use the child dependency classifications to derive information about dependent and non-dependent children. Three classifications are included in the scope of this standard: dependent child under 18 indicator classification; dependent young person indicator classification; child dependency status classification.\n\nThe 'Dependent child under 18 indicator' and 'Dependent young person indicator' classifications are flat classifications each with three categories.\n\nThe standard classification of child dependency status (master version) is a hierarchical classification of three levels. Level 1 of the classification has two categories, level 2 has nine categories, and level 3 has 15 categories.\n\nThe alternate version of the standard classification of child dependency status is a hierarchical classification of two levels. Level 1 of the classification has four categories and level 2 has seven categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/child-dependency.aspx",
"license": "CC-BY-3.0",
"name": "Child Dependency Status Standard Classification",
"prefix": "785"
},
"786": {
"description": "Information on cigarette smoking behaviour is used by both government and private health sector agencies, special interest groups, researchers, other organisations and individuals to plan health promotion programmes, identify and monitor changes in smoking prevalence and withdrawal rates and to identify at risk groups in the population.\n\nCigarette smoking behaviour is a flat classification with three categories β excluding residual categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/cigarette-smoking-behaviour.aspx",
"license": "CC-BY-3.0",
"name": "Cigarette Smoking Behaviour Classification",
"prefix": "786"
},
"787": {
"description": "Country is a key variable for determining population and economic statistics that relate to birthplace, country of residence, overseas trade, and balance of payments data. There are two types of country classifications: the four-numeric classification and the two-alpha classification. Statistics NZ maintains the four-numeric classification according to the numeric codes and names assigned by the UN Statistical Division and the International Organization for Standardization. The four-numeric classification of a country is a hierarchical classification with three levels. There are nine major groups in level 1, 27 minor groups in level 2, and 244 countries in level 3. There are no residual categories as supplementary codes are used instead.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/country.aspx",
"license": "CC-BY-3.0",
"name": "Country β New Zealand Standard Classification",
"prefix": "787"
},
"788": {
"description": "Currency is a flat classification with 62 categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/currency.aspx",
"license": "CC-BY-3.0",
"name": "Currency β Standard Classification",
"prefix": "788"
},
"789": {
"description": "Dwelling address is a key variable for determining the geographic characteristics of the population. Dwelling address allows comparisons of outputs from different surveys on a regional basis. It is mandatory for the Census of Population and Dwellings to collect particulars as to the location of dwellings under the Statistics Act 1975. Dwelling address is a flat classification of over 46,000 categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/dwelling-address.aspx",
"license": "CC-BY-3.0",
"name": "Dwelling Address Classification",
"prefix": "789"
},
"790": {
"description": "Dwelling occupancy status provides information on whether dwellings are occupied or unoccupied, or are under construction. Dwelling occupancy status provides an indication of the housing stock available in New Zealand for habitation. Information on dwelling occupancy status can be used to evaluate, appraise, and predict urban infrastructure requirements, such as transport, sewerage, and water.\n\nDwelling occupancy status is a hierarchical classification with two levels. Level 1 of the classification has three categories (excluding residual categories), and level 2 of the classification has four categories. At level 2, the category 'unoccupied dwelling', is split into 'residents away' and 'empty dwelling'.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/dwelling-occupancy-status.aspx",
"license": "CC-BY-3.0",
"name": "Dwelling Occupancy Status β Standard Classification",
"prefix": "790"
},
"791": {
"description": "Information on the types of energy consumed in occupied New Zealand private dwellings is used for marketing research and to monitor changes, over time, in the energy types used by New Zealand households. It is an indicator of the habitability of houses, when used in conjunction with information on dampness and insulation levels and is an important variable in deriving the deprivation index. The information may also be combined with other variables to help forecast and plan energy requirements and distribution, enable natural resource accounting, and monitor trends in energy efficiency and conservation.\n\nEnergy Types Used in Private Dwellings is a hierarchical classification with 2 levels. It has nine categories at the highest level and 26 categories at the second level β excluding residual categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/energy-privte-dwell.aspx",
"license": "CC-BY-3.0",
"name": "Energy Types Used in Private Dwellings β Standard Classification",
"prefix": "791"
},
"792": {
"description": "The standard classification of ethnicity is a hierarchical classification of four levels. Level 1 of the classification has six categories and is used solely for output. Level 2 has 21 categories, level 3 has 36 categories and level 4 has 233 categories β excluding residual categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/ethnicity.aspx",
"license": "CC-BY-3.0",
"name": "Ethnicity New Zealand Standard Classification",
"prefix": "792"
},
"793": {
"description": "Family type is a key variable for determining the demographic characteristics of a population. Five classifications are included in the scope of this statistical standard: family type classification; family nucleus containing birth/biological, adopted children classification; family nucleus containing step children classification; family nucleus containing grandparent(s) in a parent role classification; family nucleus containing other children classification.\n\nFamily type is a hierarchical classification with three levels. Level 1 of the classification has three categories. Level 2 of the classification has 10 categories, and level 3 has 12 categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/family-type.aspx",
"license": "CC-BY-3.0",
"name": "Family Type",
"prefix": "793"
},
"794": {
"description": "Fertility is one of the main ways through which the size and/or composition of a population may change. Statistics on fertility are required to provide basic demographic information, and to inform the study of differences and changes in reproductive patterns, family size and structure in various age, ethnic and other sub-groups, including geographic areas, of the New Zealand population. This information provides central government agencies, local authorities, health authorities, researchers, private organisations and businesses with valuable information required for planning current and future social and community services, facilities and products. A statistical standard for fertility is required to clearly define the concepts being measured and to ensure that collections of this data will be consistent across surveys and over time.\n\nFertility is a flat classification in number of children categories from no children to nine children plus a category for ten or more children. The classification has 11 categories β excluding residual categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/fertility.aspx",
"license": "CC-BY-3.0",
"name": "Fertility β Standard Classification",
"prefix": "794"
},
"795": {
"description": "The main purpose of classifying financial assets and liabilities is to provide consistent and relevant statistics that support economic analysis and macroeconomic management for New Zealand. As these classes have economic-based meanings, their definitions can vary from accounting and taxation definitions. Financial assets and liabilities will respond differently to fiscal and monetary policy depending on their type, and under various economic conditions. Financial asset and liability statistics are useful for assessing: liquidity and financial soundness of sectors; exposure to financial risks; sensitivity to monetary and fiscal policy; leverage within the economy or institutional sectors; the composition of a sectorβs assets and liabilities; claims on other sectors, including the rest of the world.\n\nThe Statistical Classification of Financial Assets and Liabilities 2013 (SCFAL), which underpins this statistical standard, is largely based on the classification of financial assets and liabilities in the System of National Accounts 2008 (2008 SNA). Therefore the concepts and definitions within this standard also align closely with the 2008 SNA manual. It provides a standard system for classifying the financial assets and liabilities of all institutional units within the economy. Because of the symmetry of financial assets and liabilities, the same classification is used for both assets and liabilities.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/financial-assets-and-liabilities-new.aspx",
"license": "CC-BY-3.0",
"name": "Statistical Classification of Financial Assets and Liabilities",
"prefix": "795"
},
"796": {
"description": "In 1993, the Ministry of Cultural Affairs approached Statistics New Zealand to discuss strategies for improving the range and quality of statistical information available on New Zealand's cultural sector. With its responsibility for collecting statistics relevant to the needs of government, business and the community, Statistics New Zealand agreed that improvement was needed. In order to define what was meant by 'cultural statistics' and to provide direction for future work, it was agreed that the first priority should be the production of a framework for cultural statistics. The two organisations jointly commenced work on the framework at the beginning of 1994.\n\nThe standard classification of framework for cultural statistics is a hierarchical classification of three levels. Level 1 of the classification has nine categories, level 2 has 24 categories and level 3 has 70 categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/framework-for-cultural-statistics.aspx",
"license": "CC-BY-3.0",
"name": "New Zealand Framework for Cultural Statistics",
"prefix": "796"
},
"797": {
"description": "Access to general electoral district is a flat classification with 64 categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/general-electoral-district.aspx",
"license": "CC-BY-3.0",
"name": "Classification of General Electoral District",
"prefix": "797"
},
"798": {
"description": "The hours worked in employment variable is used to produce information on the nature of employment, the relationship between labour supply and income and to analyse changes in employment characteristics over time. The standard classification of hours worked in employment is a flat classification of hour categories from 1 hour to 168 hours and residual categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/hours-worked-in-employment.aspx",
"name": "Hours Worked in Employment Per Week β Standard Classification",
"prefix": "798"
},
"799": {
"description": "Household composition is a key variable for determining the demographic characteristics of a population. Household composition is a hierarchical classification with three levels. Level 1 of the classification has six categories. Level 2 of the classification has 19 categories, and level 3 has 31 categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/household-composition.aspx",
"license": "CC-BY-3.0",
"name": "Household Composition Standard Classification",
"prefix": "799"
},
"8": {
"description": "2989 terms, 804 relationships between terms, 378 non-preferred terms, referential study for archival description of the AHSP collection structured in vectors.",
"homepage": "http://www.arquiamigos.org.br/thesaurus/",
"name": "Historical Archive of SΓ£o Paulo Archival Description",
"prefix": "8"
},
"800": {
"description": "Income bands are a convenient and alternate way of collecting income information when income is not the prime focus of a survey. Bands reduce respondent burden by providing a simple way to obtain contextual information about income. Income bands are often tabulated with other variables such as age, occupation and education qualifications to provide information on the relationship between these variables and the income distribution of the population.\n\nIn addition, when income information has been collected as dollar amounts, it may be output as income bands. This provides statistics on the distribution of income across the population, which is not provided by average income.\n\nIncome band statistics are used extensively within Statistics New Zealand, across government, and by other agencies and academics for: formulating social and economic policy; calculating school deciles; use as an indicator for poverty statistics and the New Zealand Index of Deprivation; research and planning; monitoring programmes.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/income-bands.aspx",
"license": "CC-BY-3.0",
"name": "Income Bands - Standard Classification",
"prefix": "800"
},
"801": {
"description": "Terms 5128, Relationship between terms ?, Non-preferred terms 282.",
"homepage": "http://thesaurus.bhlscielo.org/vocab/",
"name": "Thesaurus of Biodiversity",
"prefix": "801"
},
"802": {
"description": "Terms 238, Relationships between terms 60, Equivalent terms 15.",
"homepage": "http://vocabularyserver.com/ts/",
"name": "Social work",
"prefix": "802"
},
"803": {
"description": "The main purpose of classifying statistics by institutional sectors is to provide information that supports economic analysis and macroeconomic management. This is done by grouping economic units that have similar roles and which respond to economic events and interventions in a similar manner. Institutional sector statistics are useful for: monitoring the effects of fiscal and monetary policy; analysing investment and consumption behaviour; studying the source and disposal of incomes and the origin of savings; identifying the direction and method of transfer of savings from one sector to another; recognising the funding sources of investment and, consequently, borrowing and lending between sectors. The statistical standard was developed in 2013.\n\nThe statistical classification for institutional sectors is a hierarchical classification with three levels. The sector level has six categories. The subsector level has 18 categories. The group level of the classification has 21 categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/institutional-sector.aspx",
"license": "CC-BY-3.0",
"name": "Statistical Classification for Institutional Sectors",
"prefix": "803"
},
"804": {
"description": "Statistics on the size and demographic characteristics of Iwi affiliates are needed: to allow the Crown and Iwi to monitor the performance of Treaty of Waitangi obligations; to assist in allocating resources and funds to Iwi; to assist Iwi in planning social and economic developments; to assist Waitangi Tribunal decisions on land ownership, fishing rights, etc; to assist central, regional and local government agencies planning and providing services to Iwi in areas such as housing, health, social welfare and special assistance programmes; to assist local government in the administration of the Resource Management Act 1991.\n\nIwi is a hierarchical classification with two levels. Level 1 represents Iwi region (rohe) and is to be used for summary purposes only, and does not imply any future or present confederation of Iwi. Level 2 shows individual Iwi. Level 1 has 14 categories and level 2 has 128 categories β excluding residual categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/iwi.aspx",
"license": "CC-BY-3.0",
"name": "Iwi β New Zealand Standard Classification",
"prefix": "804"
},
"805": {
"description": "For the classification of documents to the library.",
"homepage": "http://www.esmuc.cat/L-Escola/Serveis/Biblioteca/Trobar-informacio/Classificacio-dels-documents",
"name": "Classification of documents Catalonia College of Music",
"prefix": "805"
},
"806": {
"description": "Labour force status is a key labour market variable. It allows analysis of the employed, unemployed and those persons not in the labour force. Labour force status is derived from the following classifications: job indicator 1, 2 and 3; found work; seeking work; job search methods; available for work.\n\nLabour force status is a flat classification with three categories β excluding residual categories. Job indicator 1, 2 and 3, found work, seeking work and available for work are all flat classifications with two categories β excluding residual categories. The job search classification is a flat classification of nine categories β excluding residual categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/labour-force-status.aspx",
"name": "Labour Force Status β Standard Classification",
"prefix": "806"
},
"807": {
"description": "The standard classification of language is a hierarchical classification of three levels. Level 1 of the classification has 24 categories, level 2 of the classification has 43 categories and level 3 has 134 categories β excluding residual categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/language.aspx",
"name": "Language β Standard Classification",
"prefix": "807"
},
"808": {
"description": "Legally registered relationship status is a key variable for determining the demographic characteristics of a population. The standard classification of legally registered relationship status is a hierarchical classification of four levels. Excluding residual categories, level 1 has three categories, level 2 has eight categories, level 3 has 16 categories, and level 4 has 24 categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/legally-registered-relationship-status.aspx",
"name": "Legally Registered Relationship Status β Standard Classification",
"prefix": "808"
},
"809": {
"description": "The New Zealand Standard Trade Classification β Level of Processing is a hierarchical classification of five levels. Level one of the classification has 3 categories. Level two has 5 categories, level three has 20 categories, level 4 has 59 categories, and level 5 has 208 categories β excluding residual categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/level-of-processing-trade.aspx",
"name": "New Zealand Standard Trade Classification β Level of Processing",
"prefix": "809"
},
"810": {
"description": "Living arrangements is a key variable for deriving complex household and family data. Living arrangements is a hierarchical classification with three levels. Level 1 has seven categories, level 2 has 18 categories and level 3 contains 34 categories β excluding residual categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/living-arrangements.aspx",
"name": "Living Arrangements β New Zealand Standard Classification",
"prefix": "810"
},
"811": {
"description": "Main means of travel to work is a key variable in monitoring changes in travel patterns and in planning transport services. Main means of travel to work is a flat classification with 15 categories β excluding residual categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/main-means-of-travel-to-work.aspx",
"license": "CC-BY-3.0",
"name": "Main Means of Travel to Work β Standard Classification",
"prefix": "811"
},
"812": {
"description": "MΔori descent is a key variable in meeting the demand for information on the number, distribution and characteristics of the tangata whenua. MΔori descent is a flat classification with two categories β excluding residual categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/maori-descent.aspx",
"license": "CC-BY-3.0",
"name": "MΔori Descent β Standard Classification",
"prefix": "812"
},
"813": {
"description": "MΔori electoral district is a flat classification with eight categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/maori-electoral-district.aspx",
"license": "CC-BY-3.0",
"name": "MΔori Electoral District",
"prefix": "813"
},
"814": {
"description": "Number of children is a hierarchical classification of two levels. Level 1 of the classification has six categories and level 2 has 17 categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/number-of-children.aspx",
"name": "Number of children - Standard classification",
"prefix": "814"
},
"815": {
"description": "The proposed classification is based on the decimal classification used in libraries. The collection of various items that can be recorded on sound recordings is divided into eight main classes according to a decimal division (100, 200, 300, 400, etc.) similar to Dewey or UDC. they use two tables: 1) Table geographic subdivisions of two figures, aimed at the classification of traditional music and national, to be ordered by countries, regions, continents or ethnic groups. 2) Table subdivisions instrumental also two figures used to specify\n\nnumeric codes of the three classes (classical music) and 4 (new musical languages).",
"homepage": "http://www.xtec.cat/crp-terrassa/puntedu/classificacio-enregistraments-sonors-classes.pdf",
"name": "Rating of sound recordings",
"prefix": "815"
},
"816": {
"homepage": "http://books.google.cat/books",
"prefix": "816"
},
"817": {
"description": "The keywords were assigned after reading according to a thesaurus constantly updated by specialists, depending on the evolution of the disciplines.",
"homepage": "http://societies.africamuseum.be/fr/tp_allkw",
"name": "Center for Humanities Documentation List of keywords",
"prefix": "817"
},
"818": {
"description": "The Semanticscience Integrated Ontology (SIO) provides a simple, integrated ontology of types and relations for rich description of objects, processes and their attributes.",
"homepage": "http://semanticscience.org/ontology/sio.owl",
"name": "Semanticscience Integrated Ontology",
"prefix": "818"
},
"819": {
"description": "The terms have been chosen as representative of the lexicon of the field where we are working -religion- has reached them by means of inductive or deductive analysis used according to the sources. These sources were basically written: reference works treated, specialized vocabularies, list headings, etc. \".",
"homepage": "http://archive-org.com/page/1217119/2013-01-23/http://www.bibliotecaepiscopalbcn.org/FOTOSBARRA/File/Thesaurus.pdf",
"name": "Catalan Thesaurus religion",
"prefix": "819"
},
"82": {
"prefix": "82"
},
"820": {
"abbreviation": "UAT",
"description": "The Unified Astronomy Thesaurus (UAT) is an open, interoperable and community-supported thesaurus which unifies the existing divergent and isolated Astronomy & Astrophysics thesauri into a single high-quality, freely-available open thesaurus formalizing astronomical concepts and their inter-relationships. The UAT builds upon the existing IAU Thesaurus with major contributions from the Astronomy portions of the thesauri developed by the Institute of Physics Publishing and the American Institute of Physics. We expect that the Unified Astronomy Thesaurus will be further enhanced and updated through a collaborative effort involving broad community participation.\n\nWhile the AAS has assumed formal ownership of the UAT, the work will be available under a Creative Commons License, ensuring its widest use while protecting the intellectual property of the contributors. We envision that development and maintenance will be stewarded by a broad group of parties having a direct stake in it. This includes professional associations (IVOA, IAU), learned societies (AAS, RAS), publishers (IOP, AIP), librarians and other curators working for major astronomy institutes and data archives.\n\nThe main impetus behind the creation of a single thesaurus has been the wish to support semantic enrichment of the literature, but we expect that use of the UAT (along with other vocabularies and ontologies currently being developed in our community) will be much broader and will have a positive impact on the discovery of a wide range of astronomy resources, including data products and services.",
"license": "CC BY-SA 3.0",
"name": "Unified Astronomy Thesaurus",
"prefix": "820",
"wikidata_database": "Q24254757"
},
"821": {
"description": "The 11th edition of the GeoRef Thesaurus contains more than 30,800 controlled vocabulary terms and the complete GeoRef indexing structure. The Thesaurus is an indispensable tool for efficient searching of the GeoRef database.",
"homepage": "http://www.americangeosciences.org/sites/default/files/Introduction.pdf",
"name": "GeoRef Thesaurus",
"prefix": "821"
},
"822": {
"description": "The re3data.org schema is a list of metadata properties describing a research data repository regarding its general scope, content and infrastructure as well as its compliance with technical, metadata and quality standards. The schema includes required metadata properties and optional properties providing additional information. The schema is designed to recommend a standard for describing a research data repository; provide the basis for interoperability between research data repositories and re3data.org; be one of the first steps towards the goal of a certificate for research data repositories.",
"homepage": "http://www.re3data.org/schema/",
"license": "CC-BY-3.0",
"name": "Schema for the description of research data repositories",
"prefix": "822"
},
"823": {
"description": "This thesaurus is directed, in particular, to the professionals of the documentation and, in general, to all those interested in the world of comics, whether professionals or amateurs. The objective of this work is to establish the conceptual framework of the discipline through their associative and hierarchical relationships, and disseminate, therefore, standardization of concepts made. Thus, aspires to become the basic work for indexing and reference service around the center, specializing in the discipline or producer base specialized data therein, for precisely the information demands of users.",
"homepage": "http://hdl.handle.net/10760/6733",
"name": "Thesaurus on the world of comics",
"prefix": "823"
},
"824": {
"description": "In the description of the contents of each document registered in the database, the thesaurus was used. The systematic thesaurus provides the hierarchically ordered relationship of the descriptors, indicating the respective related terms.",
"homepage": "http://www.fcsh.unl.pt/silveira/html/tresframe.html",
"name": "Bibliography of Contemporary History of Portugal Thesaurus",
"prefix": "824"
},
"825": {
"description": "To describe representations of objects, museums in France use the iconographic Thesaurus, a descriptive system of François Garnier's representations (Paris, leopard d'or, 1984, out of print). Homogeneous, extremely diverse and very numerous Each representation is treated as a document of general interest independently of any technical, stylistic or aesthetic notion The main meanings of representation are translated using a limited number of descriptors. The iconographic thesaurus consists of closed lists and open lists.\n\nClosed lists: their vocabulary is limited to about 3,200 descriptors. These have been selected in such a way as to allow essential regrouping, but also to avoid as much as possible the ambiguities due to the form (homographs, for example: grenade) and to the bottom (multiple designations for the same object). They are organized hierarchically.\n\nThe terms relate to human life, its surroundings and its manifestations, irrespective of any eventual singularity. Open lists: they are constantly enriched. The main open lists concern: animals, vegetables and minerals, geographical places, personalities (heads of state, popes, saints, mythological beings ...), nationalities, religious orders, currents of thought, periods , The ornaments ...",
"homepage": "http://www.culture.gouv.fr/public/mistral/jocrepr_fr",
"name": "Joconde Thesaurus of subjects represented",
"prefix": "825"
},
"826": {
"description": "The Thesaurus is a subject index of the catalogues and administrative histories in this archive. You can use this to find datasets and documents dealing with subjects that you're interested in.",
"homepage": "http://webarchive.nationalarchives.gov.uk/20101104101827/http://www.ndad.nationalarchives.gov.uk/search/thesaurus.html",
"name": "The National Archives Thesaurus",
"prefix": "826"
},
"827": {
"description": "All keywords in the Archives.",
"homepage": "https://www.asso-epra.fr/phonotheque",
"name": "EPRA Sound Library Thesaurus",
"prefix": "827"
},
"828": {
"description": "The 2012 edition contains 18,755 terms of which 9,722 terms are preferred terms (called Controlled Indexing, Descriptors or Subject Headings on various platforms). 9,033 terms are lead-ins (synonyms) - terms that advise the searcher which controlled term they should use for searching.",
"homepage": "http://www.theiet.org/resources/inspec/about/records/ithesaurus.cfm",
"name": "Inspec Thesaurus",
"prefix": "828",
"wikidata_database": "Q24254710"
},
"829": {
"description": "Inspec Classification is a powerful search tool, which enables you to limit your search to predetermined sections of the Inspec Database.",
"homepage": "http://www.theiet.org/resources/inspec/about/records/iclass.cfm",
"name": "Inspec Classification",
"prefix": "829",
"wikidata_database": "Q24254702"
},
"83": {
"description": "More than simply a resource for art students and art historians, Art Full Text rounds out the research experience for those studying other fields, such as womenβs, media or cultural studies; history; anthropology; industrial design; and other related areas of study. Researchers are able to track the careers of artists and review their materials and methods, and can find books by and about artists, as well as interviews, profiles and much more. Indexing of art reproductions provides examples of styles and art movements, including works by emerging artists.",
"name": "Art Full Text Thesaurus",
"prefix": "83"
},
"830": {
"description": "These national priorities have been defined by The Australian Curriculum, Assessment and Reporting Authority (ACARA). They may include local, regional or global issues. Total concepts: 38.",
"homepage": "http://vocabulary.curriculum.edu.au/crossCurriculum.html",
"name": "Australian Cross-curriculum Priority",
"prefix": "830"
},
"831": {
"description": "This is a national vocabulary dividing learning areas into a core set of strands and further subdivisions.",
"homepage": "http://vocabulary.curriculum.edu.au/framework.html",
"name": "Australian Curriculum Framework",
"prefix": "831"
},
"832": {
"description": "This is a national vocabulary identifying important general capabilities that schools should help students develop, in addition to content of particular learning areas. Total concepts: 40.",
"homepage": "http://vocabulary.curriculum.edu.au/generalCapability.html",
"name": "Australian General Capability",
"prefix": "832"
},
"833": {
"description": "The development of professional standards for teachers that can guide professional learning, practice and engagement, facilitates the improvement of teacher quality and contributes positively to the public standing of the profession. The key elements of quality teaching are described in the Standards. They articulate what teachers are expected to know and be able to do at four career stages: Graduate, Proficient, Highly Accomplished and Lead. The Standards and their descriptors represent an analysis of effective, contemporary practice by teachers throughout Australia. Total concepts: 192.",
"homepage": "http://vocabulary.curriculum.edu.au/teacherstandards.html",
"name": "Australian Professional Standards for Teachers",
"prefix": "833"
},
"834": {
"description": "The thesaurus field corresponds to the keywords used for the indexing of the documents. The thesaurus search is used to navigate between the subjects of the books in the library The thesaurus is a hierarchical classification of the keywords established by the library.",
"homepage": "http://abiodoc.docressources.fr/opac/index.php",
"name": "Biobase Thesaurus",
"prefix": "834"
},
"835": {
"description": "Glossary currently includes key words 2211 and 2541 case the relationship between the words.",
"homepage": "http://www.puhaas.net/",
"name": "Defense Administration Thesaurus",
"prefix": "835"
},
"836": {
"description": "Palli @ Doc is the database of the CNDR Palliative Care, in the form of bibliographic records. It is intended to be exhaustive in the fields of palliative care, accompaniment",
"name": "National Resource Palliative Care Center Thesaurus",
"prefix": "836"
},
"837": {
"description": "Welcome to the Revised Edition of the Australian Soil Classification. The information provided here is intended as an on-line facility for all interested parties to assist with soil classification work. It is recommended, however, if any extended work is to be undertaken, that obtaining the book would be beneficial as it is convenient to use in the field where most soil description and classification takes place.",
"homepage": "http://www.clw.csiro.au/aclep/asc_re_on_line/soilhome.htm",
"name": "Australian Soil Classification",
"prefix": "837",
"wikidata_database": "Q4824694"
},
"838": {
"homepage": "http://www.fao.org/soils-portal/soil-survey/soil-classification/world-reference-base/",
"prefix": "838",
"wikidata_database": "Q2167138"
},
"839": {
"description": "The New Zealand Soil Classification was developed in the 1980s. The top three levels of the classification ( orders, groups, and subgroups) were described by Hewitt (1993) and the fourth level (soilforms) by Clayden and Webb (1994). The new classification grew out of the N ew Zealand Genetic Soil Classification and, where possible, preserved its useful features. The new classification was also influenced by local experience in testing the United States soil classification system \"Soil Taxonomy\" (Soil Survey Staff 1975, 1996; Leamy et al. 1983). The resulting classification represents the best attempt to classify New Zealand soils, at our current state of knowledge.",
"homepage": "http://soils.landcareresearch.co.nz/contents/SoilNames_NZSoilClassification_About.aspx",
"name": "New Zealand Soil Classification",
"prefix": "839"
},
"84": {
"description": "For more convenience, it is recommended to print the thesaurus. Note that this section and the associated lexicon include the contents of the fields 'Literary Source' and 'Theme represented'.",
"homepage": "http://www.culture.gouv.fr/documentation/arcade/",
"name": "Base Arcade Thesaurus",
"prefix": "84"
},
"840": {
"description": "Social Insurance terminology is assembled terminological entries and kΓ€sitekaavioina data in almost 500 concept. Glossary explaining the contents of the concepts defined, and by means of the additional observations, and provides recommendations to the relationship between the Finnish and Swedish terms. Concepts illustrated concept diagrams. KELA terminology credits, the concept of the descriptions and the concept diagrams are translated Swedish.\n\nKela terminology glossary describes the Finnish social security system from the perspective of law. Glossary is intended for professionals who need to know which are the recommended terms Kela manages social security and what they mean. Glossary is a good tool for law drafters, for example, information officers, journalists and translators. Glossary can also support data management and create conditions for the development mm. information retrieval, data transfer, archiving and data modeling.",
"homepage": "http://www.tsk.fi/tsk/en/the_terminological_vocabulary_of_kela_%E2%80%93_benefitrelated_concepts_3rd_edition_tsk_46-843.html",
"name": "Kela terminology glossary",
"prefix": "840"
},
"841": {
"description": "Glossary of Social Welfare economic classifications are summarized in terminological entries and kΓ€sitekaavioina information on more than 200 concept, which relates to social welfare customers of private individuals on revenue, expenditure, assets and liabilities. The glossary explains the contents of concepts, definitions and allows them additional observations, and provides recommendations for Finnish-language terms. Relations between the concepts illustrated in the concept diagrams through.\n\nGlossary is intended for professionals who need information on what social welfare in economic terms appear in the ratings mean. Glossary is also beneficial to social services for citizens seeking and social care partners. Vocabulary is an important part of the development of public administration in accordance with the overall architecture of data management, which will create better conditions for the current interoperability of information systems and use of the information.",
"homepage": "http://www.tsk.fi/tsk/fi/sosiaalihuollon_taloudellisten_luokitusten_sanasto-845.html",
"name": "Social Welfare economic classifications glossary",
"prefix": "841"
},
"842": {
"description": "The Social Welfare Clients document vocabulary Version 2.0 includes a Finnish information 290 concept, which are mainly social welfare client documents. The concepts of content explaining the definitions and additional remarks through, and customer documents, names are given recommendations. In addition, some of the concept of relationships is illustrated by the concept of system diagrams.\n\nGlossary has been prepared in support of Social Welfare document structures and the use of modeling. The aim has been to clarify the social welfare document type classification concepts of terminology work means. The vocabulary is aimed specifically at experts in social welfare and development of information systems who need information on social welfare client documents in the name of recommendations and on the purpose of various customer documents are used. Glossary thereby supports data management and creates the preconditions for the development of, inter alia, data retrieval, data transfer and archiving.",
"homepage": "http://www.thl.fi/attachments/tiedonhallinta/Sosiaalihuollon_asiakasasiakirjasanasto_v2%200.pdf",
"name": "Social Welfare Clients vocabulary document",
"prefix": "842"
},
"843": {
"description": "Social care data components vocabulary Version 2.0 includes a Finnish-language information on most of the social welfare client information model data components. The glossary presented concepts related to a total of 249 public information components, information components, classes, and information components in the field. The concepts of content explaining the definitions and allows them additional comments, and the Finnish-language terms that will make recommendations. Some of the relations between the concepts The concept is illustrated in schematic form.\n\nInformation semantic components are sets of data that is used for document-based content structuring. Information System Modeling The aim is to ensure that the same type of information stored in documents in an integrated manner. Another basic idea is reusability: Data of the component structure is defined once, and then it is used in several different document. Social Welfare data of the components of terminology is intended to support social services and more generally in the public sector information architecture work, as well as data definitions for users, such as suppliers of information systems and document structures designers.",
"homepage": "http://www.thl.fi/attachments/tiedonhallinta/tietokomponenttisanasto_v2%200.pdf",
"name": "Social Welfare data components glossary",
"prefix": "843"
},
"844": {
"description": "As a whole vocabulary contains 128 concept, the content of which is described in Finnish and using the English language definitions and additional comments. Definitions and notes have been prepared in Finnish and translated into Finnish into English. Concepts Finnish term recommendations and their English equivalents are given. Relationships between concepts are illustrated in a conceptual diagram in , which is hoped to give the reader an overall picture of the vocabulary of each subject area.\n\nReal Estate Business Glossary is intended for all actors and partners in the field in both domestic and international markets. Vocabulary objective is to facilitate the independent information of citizens and facilitate communication between experts and citizens.",
"homepage": "http://www.tsk.fi/tiedostot/pdf/Kiinteistoliiketoiminnan_sanasto2.pdf",
"name": "Real estate vocabulary",
"prefix": "844"
},
"845": {
"description": "This is a national vocabulary identifying levels in the school sector, including years preceding formal schooling. Levels are coupled with typical age ranges. Total concepts: 19.",
"homepage": "http://vocabulary.curriculum.edu.au/schoolLevel",
"name": "Australian School Level",
"prefix": "845"
},
"846": {
"description": "In use since 1988, the Thesaurus of the Journal des dΓ©bats is a documentary tool composed of more than 4500 descriptors used to index the Journal of Debates to the National Assembly of Quebec.These descriptors cover the vast field of information Political, economic and social issues arising from the discussions and work of Quebec parliamentarians.\n\nLet us recall that a thesaurus is a list of organized authority of descriptors and non-descriptors obeying their own terminological rules and linked by semantic relations (hierarchical, associative or equivalence). This controlled set of terms serves not only for the indexing of documents, but also a posteriori facilitates the search for information in these same documents.\n\nThis is true of the Thesaurus of the Journal des dΓ©bats. Designed to regularize and standardize the indexing of the Journal of Debates, it can also be used to locate information by suggesting various avenues of research.\n\nThe Thesaurus of the Journal des dΓ©bats is an evolving tool. An update is periodically carried out to adapt it to its documentary function. There is addition of descriptors if, during the indexing or the documentary search, one finds that notions or relations between the notions have not been sufficiently specified. A descriptor is removed if it is subsequently found to be inadequate. If this descriptor has been used for indexing and is replaced by another more relevant term, a reference to the preferred term is added.",
"homepage": "http://www.assnat.qc.ca/thesaurus/mtwdk.exe",
"name": "Thesaurus of the Journal of Debates",
"prefix": "846"
},
"847": {
"description": "The vocabulary of the documentation you have access to here corresponds to the paper edition, coordinated by Arlette Boulogne and published by the ADBS in 2004. It offers a technical vocabulary in the field of information-documentation. Does not cover all the requirements of the professional exercise, in particular it does not include all the terms related to the use of information technologies and the Internet. Of a search form.",
"homepage": "http://www.adbs.fr/vocabulaire-de-la-documentation-41820.htm",
"name": "Vocabulary of documentation",
"prefix": "847"
},
"848": {
"description": "This is a multi-part standard that specifies learning object metadata. This part specifies a conceptual data schema that defines the structure of a metadata instance for a learning object. For this standard, a learning object is defined as any entity - digital or non-digital - that may be used for learning, education, or training. For this standard, a metadata instance for a learning object describes relevant characteristics of the learning object to which it applies. Such characteristics may be grouped in general, life cycle, meta-metadata, educational, technical, educational, rights, relation, annotation, and classification categories. The conceptual data schema specified in this part permits linguistic diversity of both learning objects and the metadata instances that describe them.\n\nThe purpose of this multi-part standard is to facilitate search, evaluation, acquisition, and use of learning objects, for instance by learners or instructors or automated software processes. This multi-part standard also facilitates the sharing and exchange of learning objects, by enabling the development of catalogs and inventories while taking into account the diversity of cultural and lingual contexts in which the learning objects and their metadata are reused.",
"homepage": "http://biblio.educa.ch/sites/default/files/20130328/lom_1484_12_1_v1_final_draft_0.pdf",
"name": "IEEE Standard for Learning Object Metadata",
"prefix": "848",
"wikidata_database": "Q1196964"
},
"849": {
"description": "Listed are terms relevant to the Indexing of professional materials in the field of exceptional child education. Entries are approved descriptors appearing in the 'Thesaurus of ERIC Descriptors' used by the Educational Resources Information Center (ERIC) Clearinghouses, and were selected on the basis of particular need to the Clearinghouse on Exceptional Children. For selected terms, additional information is provided in scope notes, which define the term, clarify specific usage, or indicate selected similar terms.",
"homepage": "http://files.eric.ed.gov/fulltext/ED052554.pdf",
"name": "Thesaurus for Exceptional Child Education",
"prefix": "849"
},
"85": {
"description": "The Beethoven Thesaurus is a list of approximately 9,000 subject and category (formerly known as genre) terms. The thesaurus groups these terms together in nine sections (or hierarchies). Terms are listed in alphabetical order within each section, with instructions on the scope of the terms, their relationships with other terms in the Thesaurus, and unused synonyms. Each listing might also include instructions to the indexer on how to apply the term to a particular subject area. In order to facilitate use by the largest audience possible, the Thesaurus terms were derived from Library of Congress Subject Headings (LCSH) and subdivisions whenever possible. Additional headings more specific to Beethoven studies were created when necessary to lead users to subjects that they cannot search with LCSHs. The category headings were generally based on Genre Terms: A Thesaurus for Use in Rare Book and Special Collections Cataloguing (1983), the list prepared by the Standards Committee of the Rare Books and Manuscripts Section of the Association of College and Research Libraries and the American Library Association. As needed, these Category terms were supplemented with music and Beethoven-related terms. Used for searching the Beethoven Gateway.",
"homepage": "http://bvc.sjlibrary.org/",
"name": "Beethoven Thesaurus",
"prefix": "85"
},
"850": {
"description": "The importance of producing a thesaurus with this specific theme is that it will facilitate the access to the information of the researchers related to philosophy, also adding a much wider and more inclusive vision where the work of both women philosophers and Male philosophers are represented in a working instrument (in this case, the thesaurus) in an equitable and fair way, recognizing the differences and without exclusions or discrimination, such as those related to sex that is the subject of interest in this work gender).",
"homepage": "http://132.248.9.9/libroe_2007/tesauro1/Index.html",
"name": "Thesaurus specializing in Philosophy, with a gender focus",
"prefix": "850"
},
"851": {
"description": "The Myobase thesaurus is a structured list of keywords related to the clinical, scientific, psycho-social aspects of the neuromuscular domain. These keywords, which are linked by synonymy, hierarchy and association relationships, are added to The Myobase Thesaurus is an indispensable tool for describing documents and finding them efficiently.",
"homepage": "http://www.myobase.org/opac/",
"name": "Thesaurus Myobase",
"prefix": "851"
},
"852": {
"description": "This thesaurus has been developed according to a thematic classification at two hierarchical levels: each chapter is associated with a limited number of keywords (generally less than 50) In order to avoid redundancy of keywords, each of these Is allocated to one or two themes maximum.",
"homepage": "http://www.fondationbiodiversite.fr/fr/documents-frb/comprendre-la-biodiversite/thesaurus.html",
"name": "Thesaurus Foundation for Biodiversity Research",
"prefix": "852"
},
"853": {
"description": "Terminology Center TSK coordinated by the banking and financial sector glossary project publishes glossary of materials in the field for public use published recommendations have been born Terminology Center, as well as a number of banking and cooperation with financial experts from the banking and financial terminology bank has been opened in February 2002. It contains terminology, definitions of concepts and descriptions as well.. The concept of the charts in Finnish, Swedish and English. The glossary is published 13.6.2014 a total of 989 concept. glossary accumulating constantly, so be sure to visit the site later on.",
"homepage": "http://www.tsk.fi/tsk/pankkisanasto/",
"name": "Bank and Finance Terminology",
"prefix": "853"
},
"854": {
"description": "The ESC's Terminology Projects' Thesis proposes recommendations on Finnish-language IT terminology, followed by a number of IT professionals, language and communications professionals.\" Termites in IT terminology include Finnish and English terms and Finnish definitions and conceptual concepts.",
"homepage": "http://www.tsk.fi/tsk/termitalkoot/",
"name": "Terminals for information technology",
"prefix": "854"
},
"855": {
"description": "Many social media concepts to missing Finnish terms or used in the terms is the standard deviation, and on the other hand the contents of a number of concepts have different interpretations of these reasons Terminology Center TSK. Started operations in spring 2009 on the initiative of FICORA Terminology Working Group glossary of the project, the purpose of which was to compile a glossary for publication of key concepts related to social media. the enclosed, the project led to a glossary is intended for all Internet and social media users, both private individuals and the organization, as well as social media content services, and producers. vocabulary the aim is to facilitate the communication officers, journalists and translators work.\n\nThe dictionary contains 62 concept, the content of which is described in the specification and in the means of additional observations. The concepts are given in Finnish term recommendations and to those in Swedish and English equivalents. relationships between concepts are illustrated in the concept diagrams, which we hope will give the reader an overall picture of each subject area. 5 except the vocabulary is included in the brief descriptions of the 13 social media website. It is not intended to be a comprehensive list of services, but an idea of ββthe types of services the vocabulary of writing has been in use. A glossary is intended to facilitate and harmonize the social media communication clarifying the concepts and terminology of foreign origin. Vocabulary also aims to contribute to the consolidation of the English terminology proposal by the preferred terms, and also provide a defined concepts judiciously selected Swedish and English terms. because of the limited resources allocated to work in the glossary Glossary efforts have been made to focus on concepts related to the vocabulary of accounting at the date of the general public on existing forms of social media. Social media phenomena and the concept of field is expanding and is constantly changing, and it has also changed during the drafting of the vocabulary so that a glossary cover the latest release moments phenomena. Social media concepts is a very large user base - of different ages and backgrounds social media services users, active content providers, enterprises, public administration, academics - and concepts has not been possible to achieve a consensus between all the users in the glossary of the project. at various points in the vocabulary is from other glossaries wealth of information about the potential of concepts in different configurations, unlike his, far from living side by side with the synonymous term Terminology Center (one or some of which may in the future to establish itself in language use), as well as, for example, on what basis a specific term have been recommended. Some of the Internet and social media related to the basic concepts are not included in the dictionary, as defined in the Terminology Center TSK. The term, coordinated by the Information Technology voluntary work project in the database 1, the term",
"homepage": "http://www.tsk.fi/tsk/fi/sosiaalisen_median_sanasto_tsk_40-513.html",
"name": "Social media Glossary",
"prefix": "855"
},
"856": {
"description": "Broadband Glossary The project started Terminology Center TSK at the beginning of 2011 the initiative of the Finnish Communications Regulatory Authority The terminology working group of the project was to compile a glossary for publication of key concepts related to broadband, thereby facilitating and harmonizing the broadband communication attached, the project led to a glossary is intended for all broadband services, users and broadband service providers Vocabulary aim... to facilitate the work of the communicators, suppliers and translators. the dictionary contains 60 concept, the content of which is described in the specification and in the additional notes through. concepts Finnish term recommendations and to the Swedish and English equivalents are given. relationships between concepts are illustrated in a conceptual diagram in which, should provide the reader due to the wide target audience complete picture of each subject area. Vocabulary has tried to avoid definitions The technical details. They have sought to highlight the most relevant information about accessibility for ordinary users. The glossary does not deal with individual business broadband solutions. The main vocabulary is selected in the media and the devices manual for details include the concepts. The subjects have been treated with broadband connections and services, terminals and other telecommunication network equipment and information security.",
"homepage": "http://www.tsk.fi/tsk/fi/laajakaistasanasto_tsk_43-654.html",
"name": "broadband Glossary",
"prefix": "856"
},
"857": {
"description": "The BIBFRAME Model is a conceptual/practical model that balances the needs of those recording detailed bibliographic description, the needs of those describing other cultural materials, and those who do not require such a detailed level of description. There are four high-level classes, or entitities, in the BIBFRAME Model: BIBFRAME Work; BIBFRAME Instance; BIBFRAME Authority; BIBFRAME Annotation. BIBFRAME Work identifies the conceptual essence of something; a BIBFRAME Instance reflects the material embodiment of a Work; a BIBFRAME Authority identifies a thing or concept associated with a BIBFRAME Work or Instance; and a BIBFRAME Annotation provides a new way to expand the description of a BIBFRAME Work, Instance, or Authority. You can read more about the BIBFRAME Model here.\n\nThe BIBFRAME Vocabulary is the key to the description of resources. Like the MARC format has a defined set of elements and attributes, the BIBFRAME Vocabulary has a defined set of classes and properties. A class identifies a type of BIBFRAME resource (much like a MARC field might bundle a single concept); properties serve a means to further describe a BIBFRAME resource (much like MARC subfields more specifically identify aspects of the concept).",
"homepage": "http://bibframe.org/vocab",
"name": "BIBFRAME",
"prefix": "857",
"wikidata_database": "Q17050075"
},
"858": {
"description": "This thesaurus is the result of systematic work involving a multidisciplinary team with extensive experience in the area of Brazilian popular culture.\" Its first version, sponsored by Unesco, resulted in 2,092 terms, selected from the CNFCP's documentary and museological collections.",
"homepage": "http://www.cnfcp.gov.br/tesauro/",
"name": "Thesaurus of Folklore and Brasilian Popular Culture",
"prefix": "858"
},
"859": {
"description": "The present thesaurus has been constructed as an instrument to facilitate the use of information technologies to assist in the management of human rights knowledge and to achieve greater communication and integration among users of the Joint Library of the Court and This thesaurus has been conceived not only as a guide for the construction of the database, but as a conceptual reference tool useful for guiding and facilitating the selection, retrieval, analysis, indexing and dissemination of information. This thesaurus consolidates the meanings of terms used in different databases and other specialized thesauri.This way the thesaurus helps to maximize a great diversity of terminology existing in the region and to represent their relations. The selection of terms included in each of them, allows And there is consistency and consistency at the time of the search, while reducing the percentage of errors that occur when processing and indexing documents, facilitating the identification of linguistic equivalents and convergence with other controlled vocabularies.",
"homepage": "http://www.corteidh.or.cr/index.php/es/biblioteca/biblioteca-tesauro",
"license": "CC BY-NC-ND 3.0",
"name": "Thesaurus on human rights",
"prefix": "859"
},
"86": {
"description": "Subject or key words, including dating by quarter century, e.g., 1500-1 (first quarter of sixteenth century); and school, e.g., Lombard, Central Italian, Roman, Emilian, etc. (Non-Italian schools are listed as English, French, Spanish, etc.). Subject or keywords are also terms not generally found in the title of the drawing, e.g., Allegory, Musical Instruments - Stringed, Mythology, Saints, Genre, Religious Orders - Franciscans, Landscapes, etc.",
"homepage": "http://www.italnet.nd.edu/ambrosiana/eng/subject_keys.shtml",
"name": "Biblioteca Ambrosiana Subject Keys",
"prefix": "86"
},
"860": {
"description": "The Keyword Catalog is a hierarchical, controlled vocabulary composed of commonly used key words, synonyms and phrases. It is mainly aimed at stock photographers who wish to easily find appropriate keywords to tag their growing image collections. It covers a very broad sweep of subjects and is divided into 40 convenient main categories, subcategories, headings and subheadings. The keywords have been systematically arranged in order to make it as easy as possible to find the keywords and associated words. If a word is spelled differently in British English and American English (as in colour | color), both versions are included. You can load all of the categories into your keywording application or on a need to use basis in order to streamline the navigation. You can use the Keyword Catalog with Adobe Bridge, Photoshop Lightroom, BreezeBrowser Pro, Photo Mechanic, etc.",
"homepage": "http://keyword-catalog.com/",
"name": "Keyword Catalog",
"prefix": "860"
},
"861": {
"description": "This basic list of Enhancement Terms for electronic photo archiving has its roots in the Library of Congress Thesaurus for Graphic Materials (1987 edition). A task force from the Special Libraries Association-News Division selected words from that list in 1994. Tribune Company news librarians refined that list, to which other newspapers, most notably the Columbus Dispatch and the Toronto Star and Sun, made additions. Another task force from the S.L.A. News Division considered all these changes and authorized this list, which was accepted by the S.L.A. News Division at its annual meeting in June, 1998.",
"homepage": "http://www.ibiblio.org/slanews/archiving/terms/photowords.htm",
"name": "Key Words for Digital Newsphoto Archives",
"prefix": "861"
},
"862": {
"description": "Colon classification (CC) is a system of library classification developed by S. R. Ranganathan. It was the first ever faceted (or analytico-synthetic) classification. The first edition was published in 1933. Since then six more editions have been published. It is especially used in libraries in India. Its name 'colon classification' comes from the use of colons to separate facets in class numbers. However, many other classification schemes, some of which are completely unrelated, also use colons and other punctuation in various functions. They should not be confused with colon classification.",
"homepage": "http://www.iskoi.org/doc/colon.htm",
"name": "Colon Classification",
"prefix": "862",
"wikidata_database": "Q1110558"
},
"863": {
"description": "Every document that is abstracted for the REHABDATA database is tagged with up to 8 keywords or descriptors from the REHABDATA Thesaurus, a taxonomy developed over more than 30 years by rehabilitation professionals, researchers, and librarians.",
"homepage": "http://www.naric.com/",
"name": "REHABDATA Thesaurus",
"prefix": "863"
},
"864": {
"description": "While it was conceived in 1952, the first published edition of this classification system appeared in 1962. Since then, its use has spread widely throughout the United States, Israel and other parts of the Jewish world. Libraries of all kinds, in synagogues and community centers, in Hebrew schools, on college campuses and in research institutions, have adopted the scheme and worked with it. As a result, a body of experience in applying the system to all these diverse institutions developed, clearly demonstrating the need for minimal changes in the system from time to time while reaffirming the utility of its basic organizing principles. Meanwhile, the intervening years have been full of events deeply significant in contemporary Jewish history, all of which need to be reflected in an up-to-date classification scheme.",
"homepage": "https://sites.google.com/site/mtevansco/elazar-classification",
"name": "A Classification System for Libraries of Judaica",
"prefix": "864"
},
"865": {
"description": "The lack of a satisfactory classification scheme for the average Jewish library has long been a problem to the Jewish librarian. Many solutions have been suggested and attempted, with varying degrees of success. The classification scheme of the Library of Congress, which has now been adopted by most of the great scholarly Jewish libraries of the country, suffers from the drawbacks of being unknown to most of the general public. On the other hand, the Dewey Decimal System as it stands, although familiar even to school children, presents certain difficulties when applied to a specialized collection. The excessive subdivision required in certain numbers, the lack of provision for certain subject areas which do not fit satisfactorily into the Dewey system, are drawbacks which librarians in the Jewish field have long struggled with. It was to meet these objections that the author devised the present scheme. Although based upon the Dewey system, certain areas have been drastically revised, most notably in the fields of religion, Jewish education, and history. In every case, whether or not explicitly stated, the number refers only to the Jewish aspect of the subject in question. Since the scheme is intended only for Judaica collections, the letter 'z' has been added throughout, to distinguish it from the regular Dewey system. This will be useful in the case of librarians with 'mixed' collections, i.e., containing books of a general as well as of a Jewish nature. This classification scheme is intended primarily for a small Judaica library, such as one in a synagogue or school. Very large or very scholarly collections will probably find the Library of Congress classification more suited to their needs.",
"homepage": "http://jewishlibraries.org/content.php",
"name": "Weine Classification Scheme and Relative Index for Judaica Libraries",
"prefix": "865"
},
"866": {
"description": "The thesaurus on German-Jewish history is used by the Jewish Museum Berlin to close the collections, including an archive, which currently contains 7,500 descriptors, including art and culture, business and transport, education, history, law and justice; The vocabulary is partially mapped to GND and AAT. \"This is the first time that the German language has been translated into German, English, French, German, Italian, and Spanish.",
"name": "Thesaurus for German-Jewish history",
"prefix": "866"
},
"867": {
"description": "Understanding the basic principles of the classification system will make browsing and finding materials in the Pendlebury Library a lot easier. Every item in the library has a specific and unique shelf number. It is this number that is crucial for locating the item on the shelves. There actually are three different classification systems; one for bound volumes (books and scores), one for unbound music and one for other media (CDs, Videos, DVDs, Microfilms etc.).",
"homepage": "http://pendlebury.mus.cam.ac.uk/library-collections/classification-system",
"name": "Pendlebury Library of Music Classification System",
"prefix": "867"
},
"868": {
"description": "The U.S. Superintendent of Documents developed this system (also called SuDocs) for the arrangement of federal government publications. Arrangement is basically by issuing agency. The Documents Library uses this classification system. The Superintendent of Documents (SuDocs) classification system for publications generally groups together documents by issuing agency. SuDocs numbers consist of a letter, designating the particular issuing agency, followed by numbers identifying subordinate bureaus within the agencies and specific publications.",
"homepage": "http://www.library.illinois.edu/doc/researchtools/guides/usfederal/sudoclist.html",
"name": "Superintendent of Documents Classification System",
"prefix": "868"
},
"869": {
"description": "The following is a list of terms used to index the holdings of the Society Library. If you are having problems with a subject search, please check this list for the terms which most closely match what you are looking for. Terms in UPPERCASE in this list are the only subject terms used in our catalog records. Note: Brackets [] indicate headings used to group related terms -- the bracketed words are typically not used as subject terms.",
"homepage": "http://library.sandiegozoo.org/thesaurus.htm",
"name": "San Diego Zoo Global Library Subject Terms (Thesaurus)",
"prefix": "869"
},
"87": {
"description": "With more than 25,000 documents, the Vincent-Warren Dance Library holds Canada's largest and most important dance collection in Canada, acquiring, conserving and distributing information in all its forms Dance, its history and its development, and thus supports the pedagogical mission of the Γcole supΓ©rieure de ballet du QuΓ©bec.",
"homepage": "http://esbq.asp.visard.ca/",
"name": "Vincent-Warren Dance Library Thesaurus",
"prefix": "87"
},
"870": {
"description": "The purpose of developing this thesaurus is to provide the maternal and child health (MCH) professional community with a standard vocabulary in MCH program development and management, including health services, research, training, and program administration. The vocabulary focuses on public health; clinical medical terms such as the names of diseases and therapeutic procedures are excluded except when they are germane to public health or MCH. The vocabulary contained here will allow for the indexing and retrieval of a wide variety of materials including government documents, technical reports, educational materials, audiovisual materials, programs, and grants. The thesaurus will be useful to MCH resource centers, libraries, special collections, and databases in organizations such as government agencies; universities and schools of public health; nonprofit and professional organizations that provide information to health professionals, families, and the public; special projects funded by MCHB; and other agencies with programs funded under Title V of the Social Security Act.",
"name": "Maternal and Child Health Thesaurus",
"prefix": "870"
},
"871": {
"description": "In 1931, the growing collection was transferred from Widener Library to the Harvard-Yenching Institute, founded in 1928. By the time of his retirement in 1964, [Alfred Kaiming] Chiu had built the library into a resource of hundreds of thousands of publications and an unparalleled collection of rare books and manuscripts. He also devised the first successful system for cataloging books in Chinese and Japanese. Known as the \"Harvard-Yenching Classification System,\" it was adopted worldwide and remained in use for the next 40 years.",
"homepage": "http://library.unimelb.edu.au/collections/classification",
"name": "Harvard-Yenching Classification",
"prefix": "871",
"wikidata_database": "Q5676674"
},
"872": {
"description": "In a nut-shell, a geodemographic classification system is an attempt to simplify a large and complex body of information about people, where and how they live, work or recreate. It is developed on geographical ideas that similar people with similar characteristics are more likely to live within the same locality and that such area types will be distributed in different locations across geographical space. The Nigerian LGA classification system encapsulates spatially referenced datasets for the year 2006 sourced from the National Bureau of Statistics (NBS) for each of the 774 LGAs in the country. Every LGA has been placed in one of 6 Super-groups, and into one of 23 Groups and finally into one of 57 Sub-groups. This hierarchical structure of Super-groups, Groups and Sub-groups allows for greater flexibility and means that analysis, visualisation and reporting can be done at any of the three levels.\n\nThe Nigerian system is the first African open source geodemographic classification system recognised in academic literature. It therefore leads the way for a new era of unbiased approach to understanding a wide range of issues within the public sector, private sector and indeed the academia.",
"homepage": "http://www.nigerianlgaclassification.com/",
"name": "Nigerian Local Government Area Geodemographic Classification System and Profiler",
"prefix": "872"
},
"873": {
"description": "We present below a picture frame classification applies to all funds of the former municipalities of Plan added to Barcelona in the late nineteenth century and the first quarter of the twentieth century. Towns Plan were similar institutions that had enjoyed powers parallel and identical functions fulfilled in a physical space and a similar time period. (...) the picture frame is a first approach we propose - solidly documented - to cope with the description and management of those series and many more common funds villages that remain attached to the different municipal archives district. We opted for a table with functional organic references, given the lack of information necessary to rebuild the organizational structure of almost all the hamlets.",
"homepage": "http://w110.bcn.cat/fitxers/arxiumunicipal/pdf/poblesagregats.873.pdf",
"name": "Picture of the classification of the documentary hamlets",
"prefix": "873"
},
"874": {
"description": "EUROSION document elaborated by the Group of the Institute of Environmental Science and Technology (UAB) on 16 March 2004, in collaboration with the Ministry of Land Infrastructure and Transport (ETSECCPB - UPC). (...) Each geospatial data producer organization has designed models of the real world according to their own criteria and needs. the theme of these data sets has to be expressed in a single word in order to then use it to retrieve that information. the purpose of the thesaurus is to prevent each data set can be described differently by each organization (known semantic problem.) this document aims to systematize the description of the topics of data sets and start a path towards standardization in this field, so that we all understand when we talk about a particular topic. we classified the most common issues that can occur and, which may be susceptible to be studied.",
"homepage": "http://cartocat.cat/geoportal/eng/meta-d/tesaurus_idecostes.pdf",
"name": "Thesaurus of the coast",
"prefix": "874"
},
"875": {
"description": "The Current Road Classification System was developed over 30 years ago and has six road classes named from Classes A to E and a Special Purpose Road class. Each class is defined by the functional criteria related to administrative level of centres the roads connect. The system covers only 61,936km of the entire road network of 160,886km while the rest 98,950km are not classified.\n\n(...) The current road classification system was developed over 30 years ago. Since then the road network has grown rapidly and changed in character. (...) The new classification system covers all public roads and extends to the presently unclassified rural and urban roads. The main thrust of the approach is to make the classification more objective and consistent by specifying quantifiable parameters (traffic, population, spacing) to guide the selection of appropriate road classes. It is also a dynamic system where road classes can be periodically reviewed to adapt to changes in traffic, function etc. The proposed Road Classification System sees Kenya's road network as being composed of two distinct networks i.e. the Rural Roads Network (outside Cities and Municipalities) and the Urban Roads Network (within Cities and Municipalities) for all public roads with 9m or more road reserves. Although the new classification system retains A,B,C,D and E classes, the system has been extended to include additional classes. It should be noted that presently classified roads do not necessarily retain their road classes under the new classification.",
"homepage": "https://en.wikipedia.org/wiki/Transport_in_Kenya",
"name": "Road Network Classification",
"prefix": "875"
},
"876": {
"description": "The National Diet Library classification table was created as a classification table for the purpose of efficiently managing and utilizing all the collections collected from domestic and overseas in this way. .\n\n (1) Although it is a general classification table covering all fields of knowledge, we focus on the social science department reflecting the library composition of our library.\n\n (2) Enumerated type drainage classification table considering the convenience of the use of the staff of the hotel and the archive management. In general, a separate document group is included in the classification system so that the discharge position of the material can be clearly indicated by the classification symbol itself. However, bibliographic categorization is also considered, such as preparing symbols for bibliographic classification.\n\n (3) The symbolic law has a high division ability to systematize enormous collections, a brief expression power for storage and payment, and acceptability capable of dealing with the emergence of new themes and new material groups It is a mixture non-decimal type of alphabet and integer. \"\"",
"homepage": "http://www.ndl.go.jp/jp/library/data/ndl_ndlc.html",
"name": "National Diet Library Classification Table",
"prefix": "876"
},
"877": {
"description": "Internet Call Dictionary (ESC 37) defines Finnish about 80 concepts related to Internet telephone calls and recommendations from Finnish terms. Terminology is of responses in Swedish and English. The terms shall also illustrates the concept diagrams. Vocabulary target group of consumers. The objective is to cover the vocabulary to which the consumer impinges purchasing equipment and services for making internet calls. efforts have been made to avoid technical details and to raise the consumer most relevant information in the definition of terms. consumers in addition to the dictionary it is hoped to be useful also for translators, reporters and information. Vocabulary the aim is to standardize and facilitate internet calls dealing with communications. Internet Call Glossary project was launched in autumn 2006 Communications Regulatory Authority initiative terminology Working Group. Glossary Glossary drafted, led by Finland, a working group k uuluivat Finnet Association, the Consumer Agency, the Ministry of Transport and Communications, Nokia, SW Television / Welho, TeliaSonera Finland Oyj and the Finnish Communications Regulatory Authority. The project was funded by the Finnet Association, the Consumer Agency, the Ministry of Transport and Communications Agency, SW Television Oy / Welho, TeliaSonera Finland Oyj and the Finnish Communications Regulatory Authority.",
"homepage": "http://www.tsk.fi/tsk/fi/internetpuhelusanasto_tsk_37-192.html",
"name": "Internet Call Dictionary",
"prefix": "877"
},
"879": {
"description": "This document provides a trilingual thesaurus, which will allow the producer data document metadata in three different languages: Catalan, Spanish and English. [...] This paper aims to systematize the description of the topics of data sets and start a path towards standardization in this field, so that we all understand when we talk about a particular topic.",
"homepage": "http://www.geoportal.cat/geoportal/cat/participar/publicar-metad/ttemesv2.pdf",
"name": "Thesaurus issues",
"prefix": "879"
},
"88": {
"description": "To enable a thematical and geographical searching for archive material with different language background a multilingual thesaurus is available. This thesaurus includes thematical and geographical terms. Every term is available in the four languages English, French, German and Dutch. By using one thesaurus term on searching, the translation of this term is included and search results for all four languages are returned.",
"homepage": "http://www.birth-of-tv.org/birth/thesaurix.do",
"name": "BIRTH Television Archive Multilingual Thesaurus",
"prefix": "88"
},
"880": {
"description": "ECLAS covers the EU's official publications as well as documents of most intergovernmental organizations, commercial, academic and government presses, and selected periodical articles of lasting interest. Material is found on European integration, the political objectives and activities of the Union institutions and material on Member States of the EU, in particular their institutional, legal and socioeconomic structures or technical material necessary to the work of the various Commission departments, ranging from legal documentation to scientific and technical research papers. When conducting a search it is important to know the terms used by ECLAS - therefore it is useful to search the ECLAS Thesaurus first before conducting a search with the appropriate terms. (...) Only the English and French versions are currently complete.",
"homepage": "http://ec.europa.eu/eclas/F/SVKGVQF493QR5DUX5PXJX64T8RAUYV7883QM936E6MFGUNT1DV-16222?func=file&file_name=theseng.htm",
"name": "European Commission Libraries Catalogue Thesaurus",
"prefix": "880"
},
"881": {
"description": "A list of keywords or subject headings such as this is known technically as a thesaurus. This is an introduction to the thesaurus for the SoyaScan database, created one record at a time by Soyinfo Center starting in 1985. Keywords, also widely called subject headings, are a 'controlled vocabulary'. You must chose from a given list β as in a dropdown menu. (...) In the body of the Thesaurus, the subject headings and cross references are listed alphabetically.",
"homepage": "http://www.soyinfocenter.com/searchdbkeywords-thesaurus.php",
"name": "Thesaurus for SoyaScan Database of Soybeans and Soyfoods",
"prefix": "881"
},
"882": {
"description": "This document provides a trilingual thesaurus, which will allow the producer data document metadata in three different languages: Catalan, Spanish and English. Each organization producing geospatial data has designed models of the real world according to their own criteria and needs. This means that the same object may be described differently by each organization (known semantic problem concerning the terminology and concept models of the territory). This document aims to systematize the description of phenomena and begin a path to standardization in this field, so that we all understand when we talk about a particular object or phenomenon. we classified the most common phenomena that can appear on the map, and that may be susceptible to be studied.",
"homepage": "http://www.geoportal.cat/geoportal/cat/participar/publicar-metad/Tobjectesv2.pdf",
"name": "Thesaurus objects",
"prefix": "882"
},
"883": {
"description": "Although there are many specialized thesauri in the health and the social sciences, the HIV/AIDS Thesaurus is unique in its character and focus.\n\n1. Community-based - We have tried as much as possible to make the thesaurus reflect the language and values of community-based AIDS service organizations, rather than the terminology of technical or medical professions. The thesaurus is, therefore, not based on existing systems such as Library of Congress Subject Headings (LCSH) or Medical Subject Headings (MeSH). For example, we use the term 'Poppers' rather than the more technical term 'Amyl Nitrates', and 'Drug Use' rather than the more judgmental term 'Drug Abuse'.\n\n2. Comprehensive - Resource centres in AIDS service organizations tend to collect a broad range of HIV/AIDS material. The thesaurus reflects this broad scope by covering all aspects of HIV/AIDS: everything from basic science and treatment to prevention, the arts and the psychological, social, and political aspects of the epidemic.\n\n3. Based on Literary Warrant - 'Literary warrant' is a concept librarians use to decide whether the creation of a subject term is justified by the quantity of literature available. We only created subject terms when there were sufficient numbers of books, periodical articles, videos, and audio tapes to warrant the heading. Other subject tools take theory as their point of departure not the production and publication of information. We avoided creating terms simply on the basis of theoretical considerations or out of a sense of symmetry. For instance, we allow for the headings 'Hepatitis B' and 'Hepatitis C', but do not include terms for other types of hepatitis (e.g. hepatitis A, hepatitis D, etc.). This decision was made because 'Hepatitis B' and 'Hepatitis C' are warranted by the number of books and videos on that topic, while books specific to other types of hepatitis are rare in our collection.\n\n4. Based on a Psychosocial, Consumer Health Collection - The first edition of the thesaurus was developed to describe the broad subject scope of books. Narrower terms are added to the second edition so that the thesaurus can be used to describe the more specific content of periodical articles. The thesaurus still remains, however, a list of terms used to describe a psychosocial, consumer health focused collection. The overall depth of the thesaurus has not greatly increased and terms are still more general than terms that would be used to describe articles in a medical or treatment focused collection.",
"homepage": "http://www.actoronto.org/home.nsf/pages/thesaurusterms",
"name": "HIV/AIDS Thesaurus",
"prefix": "883"
},
"884": {
"description": "The most evident wealth of cultural heritage is its own set of materials and techniques, which are properly integrated, making cultural objects, documents of an irreplaceable value on technical evolutions, craftsmanship, social meanings and identity symbols of the community. Tesauro is the first part of a great work of compilation and systematization of the terminology related to the materiality of cultural property. The aim is to serve as a source of knowledge for cataloging and as a tool for terminology normalization of cultural heritage assets.",
"homepage": "http://tesauros.mecd.es/tesauros/materias.html",
"license": "https://www.w3.org/Consortium/Legal/2015/doc-license",
"name": "Dictionary of Materials",
"prefix": "884"
},
"885": {
"description": "The Thesaurus and Dictionary of Denominations of Cultural Property, due to its wide range of themes and the large number of descriptors it gathers, is being the subject of independent publication of its different sections. So far, two sections have been published: Objects associated with rites , Cults and beliefs and objects of artistic expression.the character of this Thesaurus and Dictionary of Denominations of Cultural Property is multidisciplinary and has counted on the advice and the collaboration of experts of different specialties.",
"homepage": "http://tesauros.mecd.es/tesauros/bienesculturales.html",
"license": "https://www.w3.org/Consortium/Legal/2015/doc-license",
"name": "Thesaurus and Dictionary of Denominations of Cultural Property",
"prefix": "885"
},
"886": {
"description": "The identification of geographical landmarks - countries, cities, and regions - is basic when it comes to dealing with the cataloging of a cultural asset. This Geographical Thesaurus, which locates the main geographical facts spread over five continents, including its seas and oceans, is a fundamental tool for identifying and describing cultural heritage collections, making it possible to identify each cultural asset based on its place of origin, production, emission and acquisition, as well as to complete its contextualization with reference geographical descriptors.",
"homepage": "http://tesauros.mecd.es/tesauros/geografico.html",
"license": "https://www.w3.org/Consortium/Legal/2015/doc-license",
"name": "Geographic Dictionary",
"prefix": "886"
},
"887": {
"description": "Ceramic materials are very present among man-made objects to respond to their most diverse needs. Among the cultural goods that we document and protect as cultural heritage, we find a large number of ceramic objects.This thesaurus contains terminology referring both to denominations of ceramic objects and to materials and techniques for the elaboration and decoration thereof, as well as specific formal descriptors.",
"homepage": "http://tesauros.mecd.es/tesauros/ceramica.html",
"license": "https://www.w3.org/Consortium/Legal/2015/doc-license",
"name": "Dictionary of Ceramics",
"prefix": "887"
},
"888": {
"description": "The coin has accompanied Humanity in its last twenty-six centuries of history. Its long life, abundance and diffusion have led to its wide presence in the collections of museums, in addition to its great demand as a resource and source of research. Terminology referred to numismatic concepts, denominations of monetary objects, their specific formal descriptors, as well as materials and manufacturing processes of them.",
"homepage": "http://tesauros.mecd.es/tesauros/numismatica.html",
"license": "https://www.w3.org/Consortium/Legal/2015/doc-license",
"name": "Numismatic Dictionary",
"prefix": "888"
},
"889": {
"description": "The furniture has been an important part of the home environment of man throughout history. Although its role has been primarily functional, has been enriched with other meanings of social and cultural aspects that make the furniture an essential element of cultural heritage. This includes thesaurus terminology referring to designations of furniture, their types, specific formal descriptors, as well as materials and processing techniques and decorating them.",
"homepage": "http://tesauros.mecd.es/tesauros/mobiliario.html",
"license": "https://www.w3.org/Consortium/Legal/2015/doc-license",
"name": "Furniture Dictionary",
"prefix": "889"
},
"89": {
"description": "The decision to publish The British Museum materials thesaurus was based on the interest shown in it over the years by visiting documentation specialists, and their requests for copies. In my opinion, the thesaurus is unique, due to the great range of terms included, the inevitable consequence of documenting world-wide collections from almost any historical period, a great variety of cultures, and covering almost any type of object. The eclectic nature of the listing precluded the possibility of importing a thesaurus into our documentation system, and we therefore had to devise our own version. The greatest difficulty lay in providing an overall structure which could accommodate specialised terminology, archaic or local names for certain materials, and everyday nomenclature as well. Our thesaurus indicates one approach, no doubt there are many others (indeed we tried several before settling on the current structure). I am reassured by the fact that our users regularly retrieve records by material, using the thesaurus as a retrieval tool.\n\nThree Top Terms are provided - 'Organic', 'Inorganic' and 'Processed Material' and are generally mutually exclusive. 'Organic' is defined as naturally occurring animal and plant material, and naturally occurring substances derived from them. 'Inorganic' is defined as naturally occurring material which, for the purposes of this thesaurus, is not of organic origin, i.e. mainly minerals and stones. 'Processed material' may be regarded as material which has been manufactured or has undergone some form of processing (such as smelting) to alter it from its original natural state. The definitions of the three categories are provided for general guidance, rather than as strict formulations. It is accepted that there are grey areas, particularly in deciding whether a substance is processed or not. However the primary intention is to group materials in a way which is meaningful to the average user. 2129 terms, 513 relations between terms, 284 non-preferred terms. It is stressed that the final listing is not intended as a scientific classification system, rather it is a reflection of the terminology, both current and historical, in use in curatorial departments in The British Museum.",
"name": "British Museum Materials Thesaurus",
"prefix": "89"
},
"890": {
"description": "A long tradition of cooperation brings together documentalists from the major French management schools, and many exchanges and common achievements have made it possible to establish a wide network of information, training and mutual assistance. Are constituted in association (ACIEGE, Association of the managers of the information centers of the schools of management).\n\nMost of them use the Management Thesaurus based on the work of the Van Dijk Office and Georges Sandeau for their documentary system, the third edition of which is dated from 1986. As early as 1976, the need for permanent maintenance work , In order to ensure its relevance to the evolution of the fields covered, to adapt it to the requirements of the increasing level of management techniques, without neglecting the pedagogical function in training future managers in research and The rational use of information.\n\nThe working group composed of representatives of ten grandes Γ©coles is the guarantor of the continuous evolution of the thesaurus and ensures its control, in accordance with the maintenance rules: the proposed amendments are examined at a bi-annual meeting which validates the creation, The deletion of descriptors or equivalent terms and the establishment of judicious links between descriptors. These operations are essential to ensure the operational character of this documentary tool, in constant contact with reality, in the interests of coherence and a proven methodology. Each semantic field has been fully resumed, analyzed, and restructured in depth. This tool is intended to be alive and particularly adapted to the use of the information resources of schools of management. The Management Thesaurus is now available in three languages: French, English and Spanish and in various formats.",
"homepage": "http://bibliotheque.tbs-education.fr/thesaurus/thesaurus.html",
"license": "CC BY-NC-ND 3.0",
"name": "Management Thesaurus",
"prefix": "890"
},
"891": {
"description": "The panlatine lexicon of economic marketing was developed within the Panlatine Network of Terminology (Realiter) and coordinated by Prof. Dr. Angela Bidu VrΔnceanu, University of Bucharest. The final synthesis and editing of the material was made by Roxana Cioloaneanu. The field of economic marketing is relatively new and its dynamics is continuous.The applicative interest of this field is complex and refers to aspects of economy, trade, advertising, communication The list of illustrative terms for this field has been selected and limited to about 150 terms, Since marketing is a complex and heterogeneous domain whose limits are difficult to establish, we have tried to cover different areas of marketing by selecting terms belonging to\n\nOf its various sub-areas, such as: marketing research, promotion policy, consumer behavior, distribution policy. This selection is also motivated by the diachronic evolution of marketing, discussed in the literature as being carried out in three stages: 1) 1900-1920: marketing deals with selling products on the market (sale); 2) The 1950s added a dimension, namely, the advertisement; 3) Due to the economic growth of the 50s and 60s, which led to an increase in competition, sales orientation of marketing has turned into customer orientation (consumer behavior) (see Zollondz 2007: 14-20). The elaboration of the marketing lexicon had as its starting point the Romanian language, the terms being selected from the Romanian specialized dictionaries and checked in specialized texts (scientific texts, didactic texts) and in economic press articles. For each term, equivalents were given in six languages\n\nRomance (taking into account their territorial distribution where appropriate): Catalan, Spanish (Spain, Argentina, Mexico), French (France, Canada), Galician, Italian, Portuguese (Brazil). Also for each term the English equivalent is provided. The terms in the Pantellean Lexicon of Economic Marketing can be consulted in each of the above-mentioned languages ββby using the alphabetical index for each language. All terms benefit from indicating the appropriate grammatical category. For some terms, quasi (synonyms) and / or writing variants have been recorded. (Cvasi) the synonyms in Romanian appear immediately under the title-term, and for the other Romance languages, they are listed one below the other. The arrow (β) means the reference to another title-term\n\n(Quasi) synonym from the list. The inventory of terms includes both simple terms and terminological terms. The latter were taken over as such by the Romanian specialized dictionaries. For some simple terms, with circulation in other specialized languages, as well as in the common language, deconfiguring contexts, extracts from specialized texts and articles in the press and marked\n\nIn square brackets []. Each of the contributors to the Panlatine Lexicon of Economic Marketing project is responsible for the terms provided as equivalents in that language. We believe that the panlatine lexicon of marketing will facilitate interlingual communication and will satisfy the complex (extralinguistic, linguistic and terminological) interest in this field. The target audience is represented by specialists\n\nIn several areas: economics, commerce, advertising, media and, last but not least, terminologists and linguists.",
"homepage": "http://www.realiter.net/wp-content/uploads/2013/06/Lex_pan_MkEc.pdf",
"name": "The panlatine lexicon of economic marketing",
"prefix": "891"
},
"892": {
"description": "The Secretariat for Information, the Department of Documentation and Information of the Senate, keeps the terminological control (...) The terms are presented in alphabetical order and can be: Authorized Terms:. Terms chosen to represent the concepts, terms Unauthorized : Synonyms or almost synonyms and alternative forms whose use is not authorized. The words are not accentuated, except for 'Γ' and 'Γ'.",
"homepage": "http://www.senado.gov.br/publicacoes/thes/",
"name": "Thesaurus of Senado Federal",
"prefix": "892"
},
"893": {
"description": "China Library Book Classification\" is a representative of China after the founding of a large-scale comprehensive classification, referred to as \"since the law.\" Since the fourth edition in 1999 changed its name to \"China Library Classification \"Abbreviation is unchanged, the English translation of the Chinese Library Classification, the English abbreviation for the CLC.\" Chinese law \"and other domestic classification, compared to the preparation of late, but the development of fast, it not only systematically summed up our classification At present, the \"China map\" has been widely used in the various types of libraries, the major domestic large bibliography, search journals, machine readable database, and \"China\" in the preparation of foreign classification of the theory and technology. National Standard Book Number \"and so on are recorded\" in the law \"classification number.",
"homepage": "http://clc.nlc.cn/",
"name": "Chinese Library Classification",
"prefix": "893",
"wikidata_database": "Q5100524"
},
"894": {
"description": "The Info-Muse classification system for ethnology, history and historical archaeology museums is largely based on the classification system for Parks Canada Service collections, itself based in part on The Revised Nomenclature for Museum Cataloging. This system is the fruit of collaboration between Parks Canada, the MusΓ©e de la civilisation and the SociΓ©tΓ© des musΓ©es quΓ©bΓ©cois. The definitions of terms are drawn mainly from the Parks Canada document. The classification system makes it possible to group objects in a collection by their original function. It divides them up into a hierarchy in which the smallest unit is the object name, the intermediate unit is the sub-category and the largest unit is the category. This structure makes it possible to organize information on object identification in a logical, meaningful manner. Using a standardized system to divide up information makes it simpler to search for and access records. To maximize system performance, standardized terms must be used to identify the objects. Using the classification system gives a better overview of collections, so that users can spot similarities and differences, groupings and contrasts within a collection itself. In addition to offering better understanding of the content of collections, the classification system promotes reflection on guidelines for collecting, research options and ideal means of sharing the knowledge gained.",
"homepage": "http://www.smq.qc.ca/publicsspec/guidesel/doccoll/en/classificationethno/",
"name": "Info-Muse Classification System for Ethnology, History and Historical Archaeology Museums",
"prefix": "894"
},
"895": {
"description": "Since 1995, the Info-Muse classification system for fine arts and decorative arts collections has been based on the Art & Architecture Thesaurus (AAT), with the approval of AAT authorities. The system is based on painstaking research work done by ThΓ©rΓ¨se LabbΓ©, at the time a museology consultant, who successfully completed this job for the Info-Muse Network. Representatives of the David M. Stewart Foundation, the MusΓ©e d'art contemporain de MontrΓ©al, the David M. Stewart Museum, the Montreal Museum of Decorative Arts, the MusΓ©e des SΕurs grises de MontrΓ©al, the MusΓ©e du QuΓ©bec, CHIN and the Info-Muse Network also contributed. The system was revised again in 2006 to reflect changes relating to the increasing diversity of practices in contemporary art. ThΓ©rΓ¨se LabbΓ©, researcher-documentalist at the MusΓ©e national des beaux-arts du QuΓ©bec, agreed to lead a discussion group on the subject. Representatives of the Leonard & Bina Ellen Gallery, the MinistΓ¨re de la Culture et des Communications du QuΓ©bec, the MusΓ©e d'art contemporain de MontrΓ©al, the Montreal Museum of Fine Arts and the City of Gatineau were involved in the work.\n\nThe two subdivisions of the AAT's 'Art' subgroup, namely 'Fine Arts' and 'Decorative Arts', correspond to the categories in the Info-Muse classification system. The 'Fine Arts' sub-categories have to do with the various artistic disciplines and the 'Decorative Arts' sub-categories refer to the various families or groups of applied arts and their use in industry.",
"homepage": "http://www.smq.qc.ca/publicsspec/guidesel/doccoll/en/classificationarts/",
"name": "Info-Muse Classification System for Fine Arts and Decorative Arts museums",
"prefix": "895"
},
"896": {
"description": "The standard classification of Meshblock is a flat classification and contains 46,643 categories in 2014. The classification is released annually on 1 January.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/meshblock.aspx",
"license": "CC-BY-3.0",
"name": "Classification of Meshblock",
"prefix": "896"
},
"897": {
"description": "Religious affiliation is a variable of strong interest to religious organisations, social scientists, and can be used as an explanatory variable in studies on topics such as marriage formation and dissolution, fertility and income. In Australia and in Britain, religion is a variable that is used to derive measures of ethnicity. In New Zealand, religious affiliation is of particular significance for data users interested in MΔori and in Pacific Island peoples. It is a variable of historical interest as well; religious affiliation has been collected in the New Zealand Census of Population and Dwellings since 1851.\n\nThe standard classification of religious affiliation is a hierarchical classification of three levels. Level 1 of the classification has nine categories, level 2 has 40 categories and level 3 has 84 categories β excluding residual categories.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/religious-affiliation.aspx",
"license": "CC-BY-3.0",
"name": "Religious Affiliation β New Zealand Standard Classification",
"prefix": "897"
},
"898": {
"description": "The standard classification of territorial authority is a flat classification and contains 68 categories. It is released annually on the 1st of January, and on occasion mid year, but there are not always changes from the previous classification.",
"homepage": "http://www.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/territorial-authority.aspx",
"license": "CC-BY-3.0",
"name": "Standard Classification of Territorial Authority",
"prefix": "898"
},
"899": {
"description": "The Zoological Record Thesaurus contains controlled terms used to index records. It also contains uncontrolled terms as entry points to controlled (preferred) terms. The five major hierarchies in the thesaurus are: Subject; Geographical; Palaeontological; Systematic; Taxa Notes. You can expand each hierarchy to browse for controlled terms and to see their positions in the hierarchy. You can also search the entire combined thesaurus to find the appropriate controlled term(s) for your search.",
"homepage": "https://images.webofknowledge.com/WOK50B6/help/ZOOREC/hsa_zrthesaurus.html",
"name": "Zoological Record Thesaurus",
"prefix": "899"
},
"9": {
"description": "AIM25 uses subject terms taken from the UNESCO thesaurus, with the inclusion of terms at a more detailed level or for cross referring purposes from other thesauri where appropriate. These include, for instance, terms from Library of Congress Subject Headings (LCSH), Medical Subject Headings (MeSH) and the Australian Human Services and Health Thesaurus (HSH). The AIM25 version of the UNESCO Thesaurus also includes more specialised subject terms contributed by AIM25 repositories, the Public Record Office, the AIM25 Project team, the British Education Thesaurus, Library of Congress subject terms, and the SOAS Missionary thesaurus, where they are considered to be helpful in locating descriptions. The provenance of subject terms is marked against each term in the alphabetical or hierarchical lists. For example UNESCO terms are marked with a [U] and AIM25 added terms are marked with [A]. Personal and corporate names are formulated according to the Rules for the construction of personal, place and corporate names developed and published by the UK National Council on Archives (1997). Place names are fitted into the country groupings given in section 7 of the UNESCO Thesaurus, with the addition of Seas, Oceans and Arctic Regions. Descriptions are also indexed by subjects and by names of persons, corporate organizations, and places associated with the description and these indexing terms or 'index entries' are listed at the end of each description. Subject thesaurus and Name index assisted searching uses these index entries. The index entries are limited to those available in the database, so they guarantee at least one hit on a relevant description.",
"homepage": "http://www.aim25.ac.uk/browse.htm",
"name": "Archives in London and the M25 Area Thesaurus",
"prefix": "9"
},
"90": {
"description": "A Collections Data Management Section (CDMS) Working Party was set up in the 1980s to analyse the terms used to record object names in the British Museum, and to incorporate them into an on-line thesaurus. Hierarchical and other standard thesaural relationships were added, as well as explanatory notes where appropriate. The thesaurus architecture is based on ISO 2788. Curatorial advice has been sought at all stages of the project, and a number of publications were consulted, which are listed in the bibliography. Members of the Working Party also contributed extensively to the Museum Documentation Association (mda) Terminology Working Group and to the mda Archaeological Objects Thesaurus Working Party. The initial entries were generated from the object name indexes to the databases, consisting of terms taken from a variety of documentary sources (such as registers, file cards and catalogues). Hence the terms in the thesaurus are not full descriptions of the objects; these are entered in the Description field. The choice of Top Terms and Broad Terms was determined by common retrieval enquiries and by the nature of the British Museum's collections, and includes functional object name categories (e.g. vessel) as well as those referring to an activity (e.g. dance equipment) or concept (e.g. religious/ritual equipment). The addition of the word 'equipment' allows for object names describing ancillary equipment to be included in each category. Thus for example, the music equipment hierarchy incorporates music-book as well as musical instrument.\n\nThe thesaurus reflects the nature of the British Museum collections, and was originally set up as an internal reference tool. Some areas of terminology may be more specific than others, depending on the level of documentation available, or the size of particular collections.",
"homepage": "http://old.collectionstrust.org.uk/assets/thesaurus_bmon/Objintro.htm",
"name": "British Museum Object Names Thesaurus",
"prefix": "90"
},
"900": {
"description": "The FIS Educational Literature Database is the most comprehensive compilation of literary literatures in the German-speaking world, with a focus on educational science research and education, but also provides a comprehensive range of pedagogical practice (kindergarten, school, special education, etc.) From all disciplines of educational science, as well as from educational scripts and practical texts and materials. \"Both printed and online published essays, anthologies, anthologies, and monographs have been explored in terms of content and partial abstracts since the year 1980.",
"homepage": "http://www.fachportal-paedagogik.de/fis_bildung/fis_sws.html",
"name": "Register of the FIS education literature database",
"prefix": "900"
},
"901": {
"description": "This classification functional groups the documents to reflect the functions and activities of the University following a hierarchical structure and logic. It is a picture flexible, which allows you to add new features without the need to structure it or encode it again. the divisions are from general concepts to specific activities. the documents of the University are divided into two categories: document management and operating documents. the documents that are characteristic of any administrative documents with specific functions of the UPC. within these categories there are twelve kinds of documents. there are eight kinds of documents management equal in any administration.",
"homepage": "http://www.upc.edu/oda/gestio_documental/quadre-de-classificacio",
"name": "Classification UPC",
"prefix": "901"
},
"902": {
"description": "Verkko-Kaunokki is the subject matter of fictive material and its content and functionality is managed by the Helsingin kaupunginkirjasto - Central Library of the Public Libraries, based on the Kaunokki: fiktiv aineistanius published by BTJ Finland, published by BTJ Finland.",
"homepage": "http://kaunokki.kirjastot.fi/",
"name": "Domain of fiction",
"prefix": "902"
},
"903": {
"description": "The WebPLC is the webversion of the Finnish Public Libraries Classification System. It contains the tables and the index of the PLC.",
"homepage": "http://ykl.kirjastot.fi/",
"license": "CC0-1.0",
"name": "Finnish Public Libraries Classification System",
"prefix": "903",
"wikidata_database": "Q11902814"
},
"904": {
"homepage": "http://www.agroweb.bf.uni-lj.si/geslovnik.htm",
"name": "Agrotezaver: Flora in Favna",
"prefix": "904"
},
"905": {
"description": "The definitions used in this glossary are identical to those in the published document, see G.P. Moss Pure and Applied Chemistry, 68, 2193-2222 (1996) [Copyright IUPAC; reproduced with the permission of IUPAC]. If you use any of these definitions please cite this reference as their source. In setting up the World Wide Web version some errors have been detected. The changes have been marked by which is a link to details of the change and where it applies. (...)\n\nThis is a glossary of the more important, and most widely-used, stereochemical terms. It extends the list of those defined in the IUPAC Nomenclature of Organic Chemistry, Section E: Stereochemistry (Recommendations 1974) and includes some terms from the Glossary of Terms used in Physical Organic Chemistry (Recommendations 1994). Additional terms have been added from inorganic and macromolecular chemistry. Some misleading terms are included together with guidance on correct usage or acceptable alternatives.\n\nMany of the symbols used in stereochemical nomenclature are mentioned but details of their assignment or their incorporation into chemical names are left to the appropriate recommendations. Terminology related to techniques used in the determination of stereochemistry are largely excluded as well as terms used to describe reaction mechanisms.",
"homepage": "http://www.chem.qmul.ac.uk/iupac/stereo/",
"name": "Basic Terminology of Stereochemistry",
"prefix": "905"
},
"906": {
"description": "This is a hierarchical system which consists of (1) biogeographic regions, i.e. major taxa; (2) biotic provinces withinthe regions. Further, each province is characterized by a (3) major biome or biome-complex. As discussed above, we re-name the first two items (biogeographical realm, biogeographical province).",
"homepage": "https://portals.iucn.org/library/efiles/documents/OP-018.pdf",
"name": "Classification of the Biogeographical Provinces of the World",
"prefix": "906"
},
"907": {
"description": "More than 1400 terms useful in wildland and related resource planning are defined. The purpose of the work is to facilitate communication between professionals, not to provide them with exhaustive vocabularies of each other's specialties. Definitions are drawn from many sources, including public laws and government manuals, but are not intended to establish legally binding definitions. A list of terms and list of sources are included.",
"homepage": "http://www.treesearch.fs.fed.us/pubs/26935",
"name": "Wildland Planning Glossary",
"prefix": "907"
},
"908": {
"description": "The system comprises forty-six main groups, which are represented by a two letter code. This code is based on the French version of the descriptors. Each main group can be divided into thirty-four subgroups which are represented both by the digits 1 to 9 and the letters A to Z (βIβ was omitted in order to avoid confusion). The result is a three character code of high mnemonic value, especially since the third character is inheritable in meaning.",
"name": "Classification Lenoch",
"prefix": "908"
},
"909": {
"description": "Lapponica thesaurus is within Rovaniemi library's decades-edited a special vocabulary that is used to Lapland collection and the wider pohjoiskalottikokoelman for indexing. A special feature thesaurus is especially terminology in relation to the Sami people. The reason for drawing up Special Case glossary has been the need for the terms that have been difficult to describe the more general subject headings form. Thesauruses is involved also the wider Arctic region and words related somewhat to the northern Finno-Ugric kindred peoples of terms.",
"homepage": "http://finto.fi/lapponica/",
"name": "Lapponica",
"prefix": "909"
},
"91": {
"description": "There are 15,331 files in the TC/CS. Most of the descriptor terms in the TC/CS are in plural form (i.e. cars). The thesaurus uses the convention: if you can answer the question 'how much ____?' (how much rain), then the term will be listed in the singular form. If you can answer the question 'how many ____?' (i.e. how many cars), then it will be listed in the plural form. If you are unsure, then append a '*' wildcard to the desired words in your search strategy; for example 'survey*'. There are 15,331 files in the TC/CS. Each of the descriptor terms in the electronic TC.CS are contained in a self-standing file. That is, a term such as 'thesaurus' is stored in a file named 'thesaurus.html', and the BT,WT,NT, etc. are external crosslinks contained in the file. In all cases, any CTCS descriptor can only point to a BT, GT or WT that is one level above, or a NT or PT that is one level below, or a RT or AT that is on the same level. There are 10 levels in this hierarchy, going from terms such as 'Knowledge' and 'Research' at the top level down to the nuts and bolts at the bottom level.",
"name": "Canadian Thesaurus of Construction Science and Technology",
"prefix": "91"
},
"910": {
"abbreviation": "YSO",
"description": "General Finnish Upper Ontology YSO is a trilingual ontology consisting mainly of general concepts. YSO has been founded on the basis of concepts in Finnish cultural sphere. As an indexing tool it is best applicable when indexed material is interdiscliplinary and its themes vary to a great extent.\n\nYSO's hierarchical construction is founded on parent-child relationships. In addition to this, some concepts are supplemented with associative and part-whole relations.\n\nEach concept in YSO is issued to at least one thematic group and some concepts have also been grouped with a non-hierarchical collection label (such as \"clothes by materials\").\n\nFollowing the international standards for thesauri, the terms for concepts are usually plural nouns. Terms in singular are usually mass nouns or terms referring to actions or abstract concepts. Some terms carry a different meaning when used in plural and in singular. For example, ballet refers to an art form and ballets to individual works of art.\n\nYSO is based on General Finnish Thesaurus (YSA) and General Finnish Thesaurus in Swedish (AllΓ€rs). Concepts in YSO and concepts in YSA and AllΓ€rs have been linked to each other with equivalence relationships. YSO has also been linked to Library of Congress Subject Headings (LCSH).",
"homepage": "http://finto.fi/yso/",
"license": "CC-BY-3.0",
"name": "General Finnish Ontology",
"prefix": "910",
"wikidata_database": "Q27303896"
},
"911": {
"description": "This glossary is intended as a resource to facilitate communication within the UB around academic subjects and teachers. The need for it is the fact that often, certain terms are given different meanings and also often arise and spread new words that accompany the process of change in which they are immersed universities.",
"homepage": "http://diposit.ub.edu/dspace/bitstream/2445/3141/4/Glossari.pdf",
"name": "Glossary for academics and teaching at the University of Barcelona",
"prefix": "911"
},
"912": {
"homepage": "http://finto.fi/muso/",
"license": "CC-BY-3.0",
"name": "Ontology for Music",
"prefix": "912"
},
"913": {
"homepage": "http://finto.fi/valo/",
"license": "CC-BY-3.0",
"name": "The Finnish Ontology of Photography",
"prefix": "913"
},
"914": {
"homepage": "http://finto.fi/kulo/",
"license": "CC-BY-3.0",
"prefix": "914"
},
"915": {
"homepage": "http://finto.fi/maotao/",
"license": "CC-BY-3.0",
"name": "Ontology for Museum Domain and Applied Arts",
"prefix": "915"
},
"916": {
"description": "List of concepts, terms and acronyms of Psychology and Educational Sciences",
"homepage": "http://cv.uoc.edu/moduls/UW_10000_01100/",
"name": "List of concepts, terms and acronyms of Psychology and Educational Sciences",
"prefix": "916"
},
"917": {
"description": "KOKO is a collection of Finnish core ontologies, which have been merged together. The ontologies include the Finnish General Upper Ontology YSO and ontologies that extend and refine YSO such as the Ontology for Museum Domain, the Ontology of Applied Arts, and the Finnish Ontology of Photography.",
"homepage": "http://finto.fi/koko/",
"license": "CC-BY-3.0",
"name": "KOKO Ontology",
"prefix": "917"
},
"918": {
"description": "Please, do not use.\n\nMaintenance of The Names of Finnish Corporate Bodies (Suomalaiset yhteisΓΆnimet) ended in December 2020. You can find the names of the Finnish corporate bodies in KANTO (http://finto.fi/finaf/en/), where you can see the names of persons associated with Finnish publications as well.\n\nThe Finnish community names cover the reference names of the National Library of Finland in the description of the national bibliography of the National Library of Finland and the target communities of the Finnish publishing houses, and the names of the music material are not yet available. Can also be linked to a previous or recent name in the Community The following are the rules and policies of the Finnish Listing Rules for the search part of the list: Updates of name forms are made when the same entity appears differently in the following publication. The name tag has been revised. Finnish community names are intended for use with books, articles, electronic material and other material Type indexing and data retrieval. Uniform form names help data writers and seekers find just the right community. On the one hand, they can tie together the various variants of the above mentioned names and, on the other hand, distinguish between the same names (eg Nokia City and Nokia).",
"homepage": "http://finto.fi/cn/fi/",
"license": "CC0-1.0",
"name": "Names of Finnish Corporate Bodies",
"prefix": "918"
},
"919": {
"homepage": "http://finto.fi/juho/",
"license": "CC-BY-3.0",
"prefix": "919"
},
"92": {
"description": "13 semantic fields are proposed, and a navigation in the subdivisions of each is possible to search for the exact correct subject.",
"homepage": "http://www.cineressource.net/thesaurus/",
"name": "Cine-Resources Thesaurus",
"prefix": "92"
},
"920": {
"homepage": "http://finto.fi/jupo/",
"license": "CC-BY-3.0",
"prefix": "920"
},
"921": {
"description": "On development activities in statistics Research and Statistics Finland, in 2007, introduced by the discipline classification was revised in 2010 by dividing classes into smaller and earlier given the most appropriate entities Discipline classification is based on the OECD Discipline rating OKM used..., Published by R & D activities in support of statistics Frascati-Manual FOS classification",
"homepage": "http://finto.fi/okm-tieteenala/",
"name": "A discipline classification used in higher education research collection",
"prefix": "921"
},
"922": {
"homepage": "http://finto.fi/liito/",
"license": "CC-BY-3.0",
"prefix": "922"
},
"923": {
"homepage": "http://finto.fi/mero/fi/",
"license": "CC-BY-3.0",
"prefix": "923"
},
"924": {
"homepage": "http://finto.fi/puho/",
"license": "CC-BY-3.0",
"prefix": "924"
},
"925": {
"homepage": "http://finto.fi/tsr/",
"license": "CC-BY-3.0",
"name": "TSR ontology",
"prefix": "925"
},
"926": {
"homepage": "http://finto.fi/afo/fi/",
"prefix": "926"
},
"927": {
"homepage": "http://finto.fi/kassu/fi/",
"license": "CC-BY-3.0",
"name": "Finnish Names of Plants",
"prefix": "927"
},
"928": {
"homepage": "http://finto.fi/tero/",
"license": "CC-BY-3.0",
"name": "Finnish Ontology of Health and Welfare",
"prefix": "928"
},
"929": {
"description": "KAUNO is an ontology for works of fiction. Its Finnish terms are based on Kaunokki thesaurus and Swedish on Bella thesaurus. The ontology is maintained by Helsinki City Library.",
"homepage": "http://finto.fi/kauno/",
"license": "CC-BY-3.0",
"name": "Ontology for Fiction",
"prefix": "929"
},
"93": {
"description": "Used in the database 'Communication & Mass Media Complete'.",
"name": "Communication Thesaurus",
"prefix": "93"
},
"930": {
"homepage": "http://finto.fi/kito/",
"license": "CC-BY-3.0",
"prefix": "930"
},
"931": {
"homepage": "http://finto.fi/kto/",
"license": "CC-BY-3.0",
"prefix": "931"
},
"932": {
"description": "911 Terms, 462 Relations between terms, 196 Non preferred terms.",
"homepage": "http://vocab.lternet.edu/vocab/vocab/",
"name": "Long Term Ecological Research Network Controlled Vocabulary",
"prefix": "932"
},
"933": {
"homepage": "http://www.vocabularyserver.com/clacso/",
"prefix": "933"
},
"934": {
"description": "190 Terms, Relationships between Terms, 18 Equivalent Terms.",
"homepage": "http://www.vocabularyserver.com/literaturainfantil/index.php",
"name": "Colombian Contemporary Children's Literature",
"prefix": "934"
},
"935": {
"description": "127 Terms, 60 Relations between terms, 15 Non preferred terms.\" \"This Standard presents guidelines and conventions for the contents, display, construction, testing, maintenance, and management of monolingual controlled vocabularies. This Standard focuses on controlled vocabularies that are used for the representation of content objects in knowledge organization systems including lists, synonym rings, taxonomies, and thesauri. This Standard should be regarded as a set of recommendations based on preferred techniques and procedures. Optional procedures are, however, sometimes described, e.g., for the display of terms in a controlled vocabulary. The primary purpose of vocabulary control is to achieve consistency in the description of content objects and to facilitate retrieval. Vocabulary control is accomplished by three principal methods: defining the scope, or meaning, of terms; using the equivalence relationship to link synonymous and nearly synonymous terms; and distinguishing among homographs.",
"homepage": "http://vocabularyserver.com/glossaries/z3919/",
"name": "Guidelines for the Construction, Format, and Management of Monolingual Controlled Vocabularies",
"prefix": "935"
},
"936": {
"homepage": "http://mek.oszk.hu/00700/00769/",
"name": "OSZKΓ Thesaurus / KΓΆztaurusz",
"prefix": "936"
},
"937": {
"homepage": "http://id.sgcb.mcu.es/",
"prefix": "937"
},
"939": {
"description": "This publication offers a list of subject headings in the service of the standardization and effectiveness of Spanish public libraries. It is a Spanish list and at the same time universal, by not translating or adapting a foreign list of headings or that of a It was based on the idea of ββan ideal collection scheme for public libraries of our time, which also managed to manage the guidelines for the acquisitions of the library. Thesaurus was considered as a basic framework for the writing of the headings and These were later verified in the file of headings of matter of the National Library. Finally, the headings were related to each other and it was verified the existence of a certain rigor in the application of norms, which turns this List into a documented language 'checked'.\"\n\n\"The List of Headings of Matters for Public Libraries has been crossed with the List of headings of matter in Galician (LEMAG) and with the Llista de encapΓ§alaments de material de la Biblioteca de Catalunya (LEMAC), obtaining 4,834 links (...) In short, the number of links to other lists of subject headings is: 11,100 to LCSH, 6,660 to RAMEAU, 7,572 to GND, in addition to the aforementioned LEMAG and LEMAC.",
"homepage": "http://id.sgcb.mcu.es/",
"name": "List of Subject Headings for Public Libraries",
"prefix": "939"
},
"94": {
"abbreviation": "CONA",
"description": "The focus of CONA is works cataloged in scholarly literature, museum collections, visual resources collections, archives, libraries, and indexing projects with a primary emphasis on art, architecture, or archaeology. There are many fields in CONA, however through titles/names (equivalence relationships), as well as hierarchical and associative relationships, the basic structure of CONA is that of a thesaurus in compliance with ISO and NISO standards. Although it may be displayed as a list, CONA is a hierarchical database; its trees branch from a root called Top of the CONA hierarchy (Subject_ID: 700000000). There may be multiple broader contexts, making CONA polyhierarchical. In addition to the hierarchical relationships (e.g., between a print and the larger volume to which it belongs), CONA has equivalence relationships (between equivalent titles/names) and associative relationships (e.g., between a sketch and the final work). The primary top divisions of CONA are the facets Built Work and Movable Work. With the exception of performance art, CONA records unique physical works. However, CONA may include works that were never built or that no longer exist, for example designs for a building that was not constructed or a work that has been destroyed.\n\nThe primary users of the Getty vocabularies include museums, art libraries, archives, visual resource collection catalogers, bibliographic projects concerned with art, researchers in art and art history, and the information specialists who are dealing with the needs of these users. In addition, a significant number of users of the Getty vocabularies are students or members of the general public.",
"homepage": "http://www.getty.edu/research/tools/vocabularies/cona/",
"name": "The Cultural Objects Names Authority",
"prefix": "94",
"wikidata_database": "Q11409212"
},
"940": {
"description": "The Roles name authority list (NAL) or authority table is a controlled vocabulary listing the roles relevant for the descriptive metadata used at the Publications Office and the core metadata used in the data exchange between the institutions involved in the legal decision making process. It is also used by EUR-Lex. \n\nThe table provides an authority code, the start-use date and labels in all official EU languages. \n\nThe Roles NAL is part of the Core Metadata (CM) used in the exchange between the institutions involved in the legal decision making process and the Publications Office of the EU. The NAL is under governance of the Interinstitutional Metadata Maintenance Committee (IMMC) and maintained by the Publications Office of the EU in its Metadata Registry (MDR).",
"license": "CC0-1.0",
"name": "Roles Name Authority List",
"prefix": "940"
},
"941": {
"description": "The Places name authority list (NAL) or Common Authority Table (CAT) is a controlled vocabulary listing locations relevant for the descriptive metadata used at the Publications Office and the core metadata used in the data exchange between the institutions involved in the legal decision making process. \n\nIn this authority table (AT) the authority codes are constructed based on UN/LOCODE codes. The AT uses the classification (membership classification) and the authority codes of the country AT. This AT also provides ISO 3166-2 codes, as well as geographical coordinates. \n\nEuropean capitals of culture are also included. The original name of each locality is given. Descriptions for each concept are provided. \n\nCorporate body AT uses this AT to identify the seat of each concept (LOC_id), and site AT uses it to identify the location of each site (loc_code). \n\nThe NAL is maintained by the Publications Office of the European Union on the EU Vocabularies website.",
"license": "CC0-1.0",
"name": "Places Name Authority List",
"prefix": "941"
},
"942": {
"description": "The Interinstitutional procedures name authority list (NAL) is a controlled vocabulary listing the procedures that are part of the legal decision making process with their authority code and label(s) in the 24 official languages of the EU (when available). The Inter-institutional procedures NAL lists the different procedures used in the context of data exchange between the institutions involved in the legislative process.\n\nThe NAL is under governance of the Interinstitutional Metadata Maintenance Committee (IMMC) and maintained by the Publications Office of the EU in its Metadata Registry (MDR).",
"license": "CC0-1.0",
"name": "Interinstitutional procedures Name Authority List",
"prefix": "942"
},
"943": {
"description": "This authority table is a controlled vocabulary showing the composition of the courts of the European Union according to the case they are seized with (Articles 251, 254 and 257 of the Treaty on Functioning of the European Union (TFEU). It provides an authority code, the start-use date of the concept and labels in all official EU languages. The concepts are used for the production of reports of cases before the Court and to publish case-law on the EUR-Lex site. \n\nThe authority table is used in an IMMC extension for which only one institution is the source (Court of Justice). It is maintained by the Publications Office of the European Union on the EU Vocabularies website.\n\nMore detailed information can be obtained from the Statute of the Court of Justice common to all courts, as well as from the respective Rules of Procedure of the courts, available on the website of the Court of Justice of the European Union: \n\nStatute of the Court of Justice (1-9-2016): https://curia.europa.eu/jcms/jcms/p1_219149/en/ \n\nRules of Procedure of the Statute of the Court of Justice (25-9-2012): https://curia.europa.eu/jcms/upload/docs/application/pdf/2012-10/rp_en.pdf \n\nRules of procedure of the General Court (4-3-2015): https://curia.europa.eu/jcms/upload/docs/application/pdf/2018-11/tra-doc-en-div-t-0000-2018-201810296-05_01.pdf\n\nRules of Procedure of the European Union Civil Service Tribunal (1-7-2011): http://curia.europa.eu/jcms/upload/docs/application/pdf/2010-04/rp_14_04_2010_en.pdf\n\nThese concepts are used for the production of reports of cases before the Court and to publish the case-law on the EUR-Lex site: http://eur-lex.europa.eu/collection/eu-law/eu-case-law.html",
"license": "CC0-1.0",
"name": "Formation of the Court Name Authority List",
"prefix": "943"
},
"944": {
"description": "This table presents concepts relating to the results of a case or procedure following the delivery of the decision. They are to be used together with the table of proceedings.\n\nMore detailed information can be consulted in the Rules of Procedure of these courts, available on the website of the Court of Justice of the European Union:\n\nRules of Procedure of the Court of Justice (18-6-2013): http://curia.europa.eu/jcms/upload/docs/application/pdf/2012-10/rp_en.pdf\n\nRules of Procedure of the General Court (1-7-2013): http://curia.europa.eu/jcms/upload/docs/application/pdf/2008-09/txt7_2008-09-25_14-08-6_431.pdf\n\nRules of Procedure of the European Union Civil Service Tribunal (1-7-2011): http://curia.europa.eu/jcms/upload/docs/application/pdf/2010-04/rp_14_04_2010_en.pdf\n\nThese concepts are used for the production of reports of cases before the Court and to publish the case-law on the EUR-Lex site: http://eur-lex.europa.eu/collection/eu-law/eu-case-law.html",
"license": "CC0-1.0",
"name": "Legal proceeding result Name Authority List",
"prefix": "944"
},
"945": {
"description": "The treaty authority table is a controlled vocabulary listing the different EU treaties, including treaties and protocols, accession treaties, Schengen Convention and Charter of Fundamental Rights. It provides an authority code, the start-use date of the concept and labels in all official EU languages. \n\nThe treaty authority table gives the day and the location of the signature of a treaty with reference to place authority table, excluding the consolidated versions as well as the acts concerning the conditions of accession and the Charter of Fundamental Rights of the European Union.\n\nThis table is part of the core metadata used in the exchange between the institutions involved in the legal decision-making process and the Publications Office of the European Union. It is also used by EUR-Lex. The treaty authority table is under governance of the Interinstitutional Metadata Maintenance Committee (IMMC) and maintained by the Publications Office of the European Union in the Metadata Registry (EU Vocabularies website).",
"license": "CC0-1.0",
"name": "Treaties Name Authority List",
"prefix": "945"
},
"946": {
"description": "This table presents concepts relating to different legal remedies available to an applicant before the EU Courts (Court of Justice, the General Court and the Civil Service Tribunal) (Articles 260, 263, 268 and 270 of the Treaty on the Functioning of the European Union).\n\nThis table presents concepts relating to different legal remedies available to an applicant before the EU Courts (Court of Justice, the General Court and the Civil Service Tribunal) (Articles 260, 263, 268 and 270 of the Treaty on the Functioning of the European Union).\n\nThe authority table is used together with the procresult authority table (legal proceeding result). The table provides an authority code, the start-use date of the concept and labels in all official EU languages. \n\nThese concepts are used for the production of reports of cases before the Court and to publish the case-law on the EUR-Lex site: http://eur-lex.europa.eu/collection/eu-law/eu-case-law.html. The concepts are put in alphabetical order.\n\nMore detailed information can be consulted in the Rules of Procedure of these courts, available on the website of the Court of Justice of the European Union:\n\nRules of Procedure of the Court of Justice (18-6-2013): http://curia.europa.eu/jcms/upload/docs/application/pdf/2012-10/rp_en.pdf\n\nRules of Procedure of the General Court (1-7-2013): http://curia.europa.eu/jcms/upload/docs/application/pdf/2008-09/txt7_2008-09-25_14-08-6_431.pdf\n\nRules of Procedure of the European Union Civil Service Tribunal (1-7-2011): http://curia.europa.eu/jcms/upload/docs/application/pdf/2010-04/rp_14_04_2010_en.pdf",
"license": "CC0-1.0",
"name": "Legal proceeding Name Authority List",
"prefix": "946"
},
"947": {
"description": "The Resource types named authority list (NAL) or Common Authority Table (CAT) is a controlled vocabulary listing resource or document types with their authority code and label(s) in the 24 official languages of the EU (when available). \n\nThe resource type authority table (AT) lists the different types of document (e.g. directive, regulation, etc.) used in the context of data exchange between the European institutions involved in the legal decision-making process. Set up in order to harmonise the various types of documents used by different systems and, in particular, used in the \"Core Metadata and Extension Metadata XML schemas\", the AT is part of the \"Core Metadata\". As regards the \"Core Metadata\", the AT is related to the event and corporate-body (Agent) authority tables. \n\nThe NAL is under the governance of the Interinstitutional Metadata Maintenance Committee (IMMC) and maintained by the Publications Office of the EU in its Metadata Registry (MDR).",
"license": "CC0-1.0",
"prefix": "947"
},
"948": {
"description": "The multilingual authority table is a controlled vocabulary based on the language authority table. It contains language combinations used for catalogue purposes. The EU publications use two-character codes, the first two positions of the three-character authority code. \n\nThe codes are alphanumeric in order to not confuse with ISO codes that are strictly alphabetic.",
"license": "CC0-1.0",
"name": "Multilingual Name Authority List",
"prefix": "948"
},
"949": {
"description": "The Language authority table is a controlled vocabulary that lists concepts associated with languages.\n\nIts main scope is to support activities associated with publication process.\n\nThe concepts included are correlated with the ISO 639 international standard. This standard is issued in several parts:\n\nISO 639-1 contains strictly two alphabetic letters (alpha-2),\n\nISO 639-2/B (B = bibliographic) is used for bibliographic purpose (alpha-3),\n\nISO 639-2/T (T = terminology) is used for technical purpose (alpha-3),\n\nISO 639-3 covers all the languages and macro-languages of the world (alpha-3); the values are compliant with ISO 639-2/T.\n\nIf an authority code is needed for a language without assigned ISO code, an alphanumeric code is created in order to not confuse with ISO codes that are strictly alphabetic.\n\nContributions to the Language authority table are accepted following a review made by EU Vocabularies team of the Publications Office of the EU.\n\nThe Language authority table is maintained by the Publications Office of the European Union on the EU Vocabularies website.",
"license": "CC0-1.0",
"name": "Language Name Authority List",
"prefix": "949"
},
"95": {
"description": "The CRTC Thesaurus contains the preferred terms used to index CRTC information resources on its website. Describing web resources using controlled terminology improves the ability of users to find the information they need when search engines are metadata-enabled.",
"homepage": "http://www.crtc.gc.ca/eng/irct-tcir.htm",
"name": "Canadian Radio-television and Telecommunications Commission Thesaurus",
"prefix": "95"
},
"950": {
"description": "The File types name authority list (NAL) or Common Authority Table (CAT) is a controlled vocabulary listing file types (...) with their authority code and label(s) in the 24 official languages of the EU (when available). The File types NAL is part of the Core Metadata (CM) used in the data exchange between the institutions involved in the legal decision making process and the Publications Office of the EU. The NAL is under governance of the Interinstitutional Metadata Maintenance Committee (IMMC) and maintained by the Publications Office of the EU in its Metadata Registry (MDR).",
"license": "CC0-1.0",
"name": "File Type Name Authority List",
"prefix": "950"
},
"951": {
"description": "This country codes authority table is intended to provide a code related to the names of the countries β in a short and in a long form β in the 24 official languages of the European Union.These codes are used for the documentary metadata and may present slight differences with those used for the production of documents at a stylistic level.\n\nThe \"Authority code\" relays on the ISO 3166-1/alpha-3 positions. If the ISO code doesn't exist, an alpha-numeric code is created. A traceability of this codes creation is ensured and historical relationships are also offered as from 1950 till now with the date(s) of event(s).\n\nA country code comparison is provided between ISO codes, IANA codes (Internet ccTLDS β Country-code Top-level Domains), and TIR (Transport International par la Route) Vehicle system codes.\n\nCodes marked in italic are obsolete and should not be used, excepted in the case of back-log work.\n\nISO 3166 is the International standard for country codes. The purpose of ISO 3166 is to establish codes for the representation of names of countries. This standard exists in three forms:\n\nISO 3166-1 (2006) contains a two-letter code which is recommended as the general purpose code, a three-letter code which has better mnenomic properties and a numeric-3 code which can be useful if script independence of the codes is important.\n\nISO 3166-2 (2007) gives codes for the names of the principal subdivisions (e.g provinces or states) of all countries coded in ISO 3166-1. This code is based on the two-letter code element from ISO 3166-1 followed by a separator and a further string of up to three alphanumeric characters.\n\nISO 3166-3 (1999) contains a four-letter code for those country names which have been deleted from ISO 3166-1 since its first publication in 1974. The code elements for formerly used country names have a length of four alphabetical characters (alpha-4 code elements).\n\nThe ISO 3166-1 is also used by the EU Geonomenclature of the Statistical Office, the UN/LOCODE, the World Intellectual Property Organisation (WIPO), the International Atomic Energy Agency (IAEA), the Internet Assigned Authority Numbers (IANA) and more other organisations.",
"homepage": "https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/country",
"license": "CC0-1.0",
"name": "Country Name Authority List",
"prefix": "951"
},
"952": {
"description": "The Currencies name authority list (NAL) or Common Authority Table (CAT) is a controlled vocabulary listing currencies with their authority code and label(s) in the 24 official languages of the EU (when available). The list is based on the ISO standard ISO 4217. This NAL is maintained by the Publications Office of the EU in its Metadata Registry (MDR).",
"license": "CC0-1.0",
"name": "Currencies Name Authority List",
"prefix": "952"
},
"953": {
"description": "The Event authority table (AT) is a controlled vocabulary listing the events that are part of the legal decision making process. It was created in order to harmonize and to trace historically the various events triggered by an agent within the procedures and associated to a resource type. The various sources of information were extracted from Pegase and Prelex. The Event AT is part of the core metadata used in the exchange between the institutions involved in the legal decision making process and the Publications Office of the European Union. It is also used by EUR-Lex. It provides an authority code, the start-use date of the concept and labels in all official EU languages. Codes in italic are deprecated and should not be used, except in the case of back-log work. The Event AT is under governance of the Interinstitutional Metadata Maintenance Committee (IMMC) and maintained by the Publications Office of the European Union on EU Vocabularies website.",
"license": "CC0-1.0",
"name": "Event Name Authority List",
"prefix": "953"
},
"954": {
"description": "The Corporate bodies name authority list (NAL) or Common Authority Table (CAT) is a controlled vocabulary listing corporate entities such as European institutions and bodies with their authority code and label(s) in the 24 official languages of the EU (when available). The list covers as well subdivisions of the different institutions such as DG's. The Corporate bodies NAL is part of the Core Metadata (CM) used in the data exchange between the institutions involved in the legal decision making process and the Publications Office of the EU. The NAL is under governance of the Interinstitutional Metadata Maintenance Committee (IMMC) and maintained by the Publications Office of the EU in its Metadata Registry (MDR).\n\nThis table provides the varying names of EU corporate bodies for a given time span. Some other corporate bodies are also included as far as they are used in the various systems in the Publications Office. They are classified accordingly in \"EU\" | \"INT (for international)\" | \"Other\". The traceability of the chronological modifications is ensured when possible.\n\nFor the EU Corporate bodies, the legal basis is also indicated, as far as they are known.\n\nAs the official languages have changed over the time, the translations are provided in the existing official languages for a given period. The names are provided under the labels and in a longer form (e.g. Committee of the Regions | Committee of the Regions of the European Union).\n\nA bi-directional vertical relationship shows how the entities are connected in a parent-child relationship.\n\nA bi-directional horizontal relationship is establish between the entities, starting at a given date and, if the case occurs, the link to the successor and the predecessor.",
"license": "CC0-1.0",
"name": "Corporate bodies Name Authority List",
"prefix": "954"
},
"955": {
"description": "Recently, various groups within the osteopathic profession discovered that the current sources of osteopathic terminology were inadequate to meet their needs. They determined that, especially in the digital age, an authoritative osteopathic thesaurus was essential to the increasing number of professional activities requiring accurate, consistent descriptive terminology. (...) The Authorized Osteopathic Thesaurus (AOT) is the official thesaurus for osteopathic medicine, defining the meaning and interrelationships of those terms that have a unique meaning in osteopathic medicine.\n\nThe goal of the AOT is to standardize the unique diagnostic, therapeutic, and theoretical concepts and terminology of osteopathic philosophy, principles and practice. The Thesaurus includes the preferred form of each term; its definition; references as needed to broader, narrower, and related terms; synonyms; and archaic forms of the term. Abbreviations and acronyms are also included.\n\nThis first edition of the AOT is derived in part from the September 2003 edition of the Glossary of osteopathic terminology.Published biannually by the American Association of Colleges of Osteopathic Medicine's Educational Council on Osteopathic Principles (ECOP) since 1981, the Glossary was the largest pre-existing authoritative source of osteopathic terms.\n\nThe other primary source was the OSTMED Β subject authority file and bibliographic index to the literature of osteopathic medicine. The 2004 Edition is the first edition of the AOT. We anticipate regularly updating and revising the AOT. Future editions will include more terms and reflect further development of modern osteopathic teaching. This edition consists of:\n\nTotal Number of Terms 471, Uniquely Osteopathic Terms 240, MeSH Terms 27, Non-Preferred Terms (Synonyms) 231.",
"homepage": "http://www.aacom.org/news-and-events/publications/osteopathic-thesaurus",
"name": "Authorized Osteopathic Thesaurus",
"prefix": "955"
},
"956": {
"description": "Thesagro is the responsibility of the National Agricultural Library - BINAGRI, an agency of the Executive Secretariat of the Ministry of Agriculture, Livestock and Supply. Its first edition was published in June 1979. It is a vocabulary specialized in agriculture and related areas, used for Indexing and retrieval of documents in accordance with UNESCO directives, ie standards established by the United Nations Information System - Unisist of the document Principles directeurs pour LΓ©tablissement et dΓ©veloppement le thesaurus monolingues (SC / WS / 555, Paris, 1973). National is updated periodically. We will always be providing the latest version for download.",
"homepage": "http://snida.agricultura.gov.br:81/binagri/html/Cen_Thes1.html",
"name": "National Agricultural Thesaurus",
"prefix": "956"
},
"957": {
"description": "The Harmonized System is an international nomenclature for the classification of products. It allows participating countries to classify traded goods on a common basis for customs purposes. At the international level, the Harmonized System (HS) for classifying goods is a six-digit code system.\n\nThe HS comprises approximately 5,300 article/product descriptions that appear as headings and subheadings, arranged in 99 chapters, grouped in 21 sections. The six digits can be broken down into three parts. The first two digits (HS-2) identify the chapter the goods are classified in, e.g. 09 = Coffee, Tea, MatΓ© and Spices. The next two digits (HS-4) identify groupings within that chapter, e.g. 09.02 = Tea, whether or not flavoured. The next two digits (HS-6) are even more specific, e.g. 09.02.10 Green tea (not fermented)... Up to the HS-6 digit level, all countries classify products in the same way (a few exceptions exist where some countries apply old versions of the HS).\n\nThe Harmonized System was introduced in 1988 and has been adopted by most of the countries worldwide. It has undergone several changes in the classification of products. These changes are called revisions and happened in 1996, 2002 and 2007.",
"homepage": "http://ec.europa.eu/eurostat/ramon/nomenclatures/index.cfm",
"name": "Harmonized Commodity Description and Coding System",
"prefix": "957",
"wikidata_database": "Q2294130"
},
"958": {
"homepage": "http://ec.europa.eu/eurostat/ramon/nomenclatures/index.cfm?TargetUrl=LST_NOM_DTL&StrNom=CLUSTERS93&StrLanguageCode=EN&IntPcKey=&StrLayoutCode=HIERARCHIC&IntCurrentPage=1",
"name": "Classification for Land Use Statistics",
"prefix": "958"
},
"96": {
"description": "Used in the 'Database of Virtual Art'.",
"homepage": "https://www.digitalartarchive.at/nc/database/database-info/keywords.html",
"name": "Database of Virtual Art Keywords",
"prefix": "96"
},
"960": {
"description": "CEPA is a functional classification used to classifiy activities, products, outlays and other transactions whose primary purpose is environmental protection. It is a hierarchic classification with 3 levels (level 1: 9 categories, level 2: 46 categories, level 3: 20 categories).",
"homepage": "http://ec.europa.eu/eurostat/ramon/nomenclatures/index.cfm?TargetUrl=LST_NOM_DTL&StrNom=CEPA_2000&StrLanguageCode=EN&IntPcKey=&StrLayoutCode=HIERARCHIC&CFID=1378067&CFTOKEN=f3ca17a821ad668f-D41B1650-C434-C401-4A424D82324A27AE&jsessionid=ee30991268c4351339",
"name": "Classification of Environmental Protection Activities and Expenditure",
"prefix": "960"
},
"961": {
"description": "The BISAC Subject Headings List, also known as the BISAC Subject Codes List, is a standard used by many companies throughout the supply chain to categorize books based on topical content. The Subject Heading applied to a book can determine where the work is shelved in a brick and mortar store or the genre(s) under which it can be searched for in an internal database.",
"homepage": "http://bisg.org/page/bisacedition",
"name": "BISAC Subject Headings",
"prefix": "961",
"wikidata_database": "Q56646988"
},
"962": {
"description": "A systematic set-up system provides thematic access to the titles of the Hessian Bibliography.",
"homepage": "http://prodopac.rz.uni-frankfurt.de/HEBCGI/hessBib.pl?cat=sachgebiete&port=80",
"name": "Subject areas of the Hessian Bibliography",
"prefix": "962"
},
"963": {
"description": "Resources are classified at study level by one or more of topics taken from the CESSDA classification.",
"homepage": "http://www.cessda.net/catalogue/",
"name": "Consortium of European Social Science Data Archives Topic Classification",
"prefix": "963"
},
"964": {
"description": "The Finnish Social Science Data Archive uses the CESSDA topic classification in its descriptors as well as its own classification.",
"homepage": "http://www.fsd.uta.fi/fi/aineistot/arkistointi/FSD_topcClas.html",
"name": "Disciplines of the Information Archives",
"prefix": "964"
},
"965": {
"description": "The National Vegetation Classification (NVC) is one of the key common standards developed for the country nature conservation agencies. The original project aimed to produce a comprehensive classification and description of the plant communities of Britain, each systematically named and arranged and with standardised descriptions for each.\n\n It was originally commissioned in 1975 by the Nature Conservancy Council (NCC) and was intended as a new classification, not an attempt to fit British plant communities into some existing scheme derived from elsewhere in Europe. The general approach adopted was phytosociological and, therefore, concentrated on the rigorous recording of floristic data. It did, nevertheless, try to avoid over-scrupulous selection of samples, rejection of awkward data and preoccupation with the hierarchical taxonomy of vegetation types.",
"homepage": "http://jncc.defra.gov.uk/page-4259",
"name": "National Vegetation Classification",
"prefix": "965",
"wikidata_database": "Q4970539"
},
"966": {
"description": "The New Zealand Threat Classification System's long-term goal is to list all extant species that exist here according to their threat of extinction. The system is made up of manuals and corresponding taxa status lists. The status of each species group (birds, plants, reptiles, etc.) is assessed over a 3-year cycle.",
"homepage": "http://www.doc.govt.nz/publications/conservation/nz-threat-classification-system/",
"name": "New Zealand Threat Classification System",
"prefix": "966",
"wikidata_database": "Q17055563"
},
"967": {
"description": "In February 1999, the statistical agencies of Canada, Mexico, and the United States launched a joint multi-phase initiative (...) to develop a comprehensive demand-oriented product classification system to complement the new supply-oriented industry classification system introduced in 1997. The industry classification system is known as the North American Industry Classification System (NAICS); the product classification is known as the North American Product Classification System (NAPCS). The long-term objective of NAPCS is to develop a market-oriented, or demand-based, hierarchical classification system for products (goods and services) that (a) is not industry-of-origin based but can be linked to the NAICS industry structure, (b) is consistent across the three NAICS countries, and (c) promotes improvements in the identification and classification of service products across international classification systems, such as the Central Product Classification System of the United Nations. (...)\n\nThe products developed under Phases I - III are assembled into 102 product lists that identify and define the significant products produced by about 370 US service industries. These lists include 98 that are at the trilateral level; three at the bilateral level (US and Mexico for NAICS 55-Management of Companies and Enterprises, NAICS 621210-Offices of Dentists, and NAICS 621610-Home Health Care Services); and one at the US-only level (for NAICS 621-2 (except 6212, 6, and 9)-Health Care Services of Physicians, Health Care Practitioners (except Dentists) and Hospitals). Product lines developed from all 102 lists were incorporated into product collection forms developed for the 2007 and 2012 Economic Censuses, and they are being incorporated incrementally into the Service Annual Survey (beginning in 2001).",
"homepage": "http://www.census.gov/eos/www/napcs/",
"name": "North American Product Classification System",
"prefix": "967",
"wikidata_database": "Q7053849"
},
"968": {
"description": "The purpose of the grading system is simply to assess the degree of a patientβs 'sickness' or 'physical state' prior to selecting the anesthetic or prior to performing surgery. Describing patientsβ preoperative physical status is used for recordkeeping, for communicating between colleagues, and to create a uniform system for statistical analysis. The grading system is not intended for use as a measure to predict operative risk.",
"homepage": "http://www.asahq.org/resources/clinical-information/asa-physical-status-classification-system",
"name": "American Society of Anesthesiologists Physical Status Classification System",
"prefix": "968",
"wikidata_database": "Q297199"
},
"969": {
"description": "CSLB licenses contractors in 43 classifications.",
"homepage": "http://www.cslb.ca.gov/About_Us/Library/Licensing_Classifications/",
"name": "Contractors State License Board Licensing Classifications",
"prefix": "969"
},
"97": {
"description": "The thesaurus consists of an alphabetical part, descriptor to descriptor with all its relations, and the thesaurus consists of an alphabetical part, descriptor to descriptor with all its relations, and The main purpose of our thesaurus is to serve as a terminological tool in the indexing and retrieval of information, Of a set of documents, those related to the field of research of Contemporary History of Spain and forming part of an automated information system. This thesaurus, due to the specific and specialized level of the subjects in the sources used, articles of magazines , Allows its use for the analysis of a great variety of documentary types, such as l Ibros, articles, conference proceedings, doctoral theses or chapters of compilations.",
"homepage": "http://thes.cindoc.csic.es/alfa_esp.php",
"name": "Thesaurus of Contemporary History of Spain",
"prefix": "97"
},
"970": {
"description": "ISCO is a tool for organizing jobs into a clearly defined set of groups according to the tasks and duties undertaken in the job. Its main aims are to provide: a basis for the international reporting, comparison and exchange of statistical and administrative data about occupations; a model for the development of national and regional classifications of occupations; and a system that can be used directly in countries that have not developed their own national classifications.\n\nIt is intended for use in statistical applications and in a variety of client oriented applications. Client oriented applications include the matching of job seekers with job vacancies, the management of short or long term migration of workers between countries and the development of vocational training programmes and guidance.\n\nThe first version of ISCO was adopted in 1957 by the Ninth International Conference of Labour Statisticians (ICLS). It is known as ISCO-58. This version was superseded by ISCO-68, which was adopted by the Eleventh ICLS in 1966. The third version, ISCO-88, was adopted by the Fourteenth ICLS in 1987. Many current national occupational classifications are based on one of these three ISCO versions.\n\nISCO has recently been updated to take into account developments in the world of work since 1988 and to make improvements in light of experience gained in using ISCO-88. The updating did not change the basic principles and top structure of ISCO-88 but significant structural changes were made in some areas. The updated classification was adopted in December 2007 and is known as ISCO-08. Many countries are now updating their national classification either based on ISCO-08 or to improve alignment with the new international statistical standard.",
"homepage": "http://www.ilo.org/public/english/bureau/stat/isco/",
"name": "International Standard Classification of Occupations",
"prefix": "970",
"wikidata_database": "Q1233766"
},
"971": {
"description": "The Nursing Interventions Classification (NIC) is a comprehensive, research-based, standardized classification of interventions that nurses perform. It is useful for clinical documentation, communication of care across settings, integration of data across systems and settings, effectiveness research, productivity measurement, competency evaluation, reimbursement, and curricular design. The Classification includes the interventions that nurses do on behalf of patients, both independent and collaborative interventions, both direct and indirect care. An intervention is defined as \"any treatment, based upon clinical judgment and knowledge, that a nurse performs to enhance patient/client outcomes.\" While an individual nurse will have expertise in only a limited number of interventions reflecting on her or his specialty, the entire classification captures the expertise of all nurses. NIC can be used in all settings (from acute care intensive care units, to home care, to hospice, to primary care) and all specialties (from critical care to ambulatory care and long term care). While the entire classification describes the domain of nursing, some of the interventions in the classification are also done by other providers. NIC can be used by other non-physician providers to describe their treatments.\n\nNIC interventions include both the physiological (e.g. Acid-Base Management) and the psychosocial (e.g. Anxiety Reduction). Interventions are included for illness treatment (e.g. Hyperglycemia Management), illness prevention (e.g. Fall Prevention), and health promotion (e.g. Exercise Promotion). Most of the interventions are for use with individuals but many are for use with families (e.g. Family Integrity Promotion), and some are for use with entire communities (e.g. Environmental Management: Community). Indirect care interventions (e.g. Supply Management) are also included. Each intervention as it appears in the classification is listed with a label name, a definition, a set of activities to carry out the intervention, and background readings.\n\nThe 554 interventions in NIC (6th ed.) are grouped into thirty classes and seven domains for ease of use. (...) Each intervention has a unique number (code). The classification is continually updated with an ongoing process for feedback and review. In the back of the book, there are instructions for how users can submit suggestions for modifications to existing interventions or propose a new intervention. All contributors whose changes are included in the next edition are acknowledged in the book. New editions of the classification are planned for approximately every 5 years. The classification was first published in 1992, the second edition in 1996, the third edition in 2000, the fourth edition in 2004, the fifth edition in 2008, and the 6th edition in 2013.",
"name": "Nursing Interventions Classification",
"prefix": "971",
"wikidata_database": "Q260842"
},
"972": {
"description": "The Nursing Outcomes Classification (NOC) is a comprehensive, standardized classification of patient/client outcomes developed to evaluate the effects of interventions provided by nurses or other health care professionals. Standardized outcomes are essential for documentation in electronic records, for use in clinical information systems, for the development of nursing knowledge and the education of professional nurses. An outcome is a measurable individual, family, or community state, behavior or perception that is measured along a continuum and is responsive to nursing interventions. The outcomes are developed for use in all settings and with all patient populations. Clinical sites used to test the NOC included tertiary care hospitals, community hospitals, community agencies, nursing centers, and a nursing home. The outcomes are developed for use in all settings and can be used across the care continuum to follow patient outcomes throughout an illness episode or over an extended period of care. Since the outcomes describe patient/client status, other disciplines may find them useful for the evaluation of their interventions.\n\nThe 490 outcomes in Nursing Outcomes Classification (NOC) (5th ed.) are listed in alphabetical order. Each outcome has a definition, a list of indicators that can be used to evaluate patient status in relation to the outcome, a target outcome rating, scale(s) to measure patient status, and a short list of references used in the development and refinement of the outcome. A five-point Likert scale is used with all outcomes and indicators. A rating of a '5' is always the best possible score and '1' is always the worst possible score. Examples of measurement scales used with the outcomes are: 1=Extremely compromised to 5= Not compromised and 1=Never demonstrated to 5=Consistently demonstrated. The NOC outcomes are grouped in a coded taxonomy that organizes the outcomes within a conceptual framework to facilitate identifying an outcome. The 490 outcomes are grouped into thirty-two classes and seven domains for ease of use. The seven domains are: Functional Health, Physiologic Health, Psychosocial Health, Health Knowledge & Behavior, Perceived Health, Family Health, and Community Health. Each outcome has a unique code number that facilitates its use in computerized clinical information systems and allows manipulation of data to answer questions about nursing care quality and effectiveness. The classification is continually updated to include new outcomes and to revise outcomes based on new research or user feedback.",
"homepage": "http://www.rncasemanager.com/articles/NursingOutcomesClassificationLabelsDefinitions.pdf",
"name": "Nursing Outcomes Classification",
"prefix": "972",
"wikidata_database": "Q2005404"
},
"973": {
"description": "The Human Genome Project (HGP) was an international 13-year effort, 1990 to 2003. Primary goals were to discover the complete set of human genes and make them accessible for further biological study, and determine the complete sequence of DNA bases in the human genome.",
"homepage": "http://web.ornl.gov/sci/techresources/Human_Genome/glossary.shtml",
"name": "Human Genome Project Glossary",
"prefix": "973"
},
"974": {
"description": "You can browse though the hierarchy by clicking on the names below and drilling down. At each level the numbers of current species are given for each taxon. Only currently accepted names are currently included. Should you find any errors, please click on the little envelope icon, and you can send me an e-mail via the site. In order to make calculations of the numbers of species of living algae, note that 68 or so species of flowering plants (seagrasses) are included for the present (under the Phylum Magnoliophyta), and about 2000 fossil algae, mainly calcium- and silica- secreting forms. A few fungal names are included. We are currently revising the classification to take account of some recent phylogenetic studies; however, because of difficulties with the Botanical and Zoological Codes, this may seem very inconsistent in places.\n\nPlants vs Animals\n\nThe age-old question of what is an animal and what is a plant creates classification problems for botanists and zoologists alike, and in many groups the differences are quite unclear. The classification of organisms currently included in AlgaeBase adopted here closely follows a draft classification by Dennis Gordon (Principal Scientist, Aquatic Biodiversity & Biosecurity, National Institute of Water & Atmospheric Research, Wellington, New Zealand) and colleagues (including AlgaeBase) in July 2011, with the exception of the euglenoid flagellates and the dinoflagellates for which AlgaeBase has mostly retained the ICBN (botanical) suffixes; however, we have occasionally added the equivalent taxa in zoology. We have largely adopted this classification for the sake of conformity.\n\nFlowering Plants\n\nFor the marine flowering plants we follow Angiosperm Phylogeny Group III system in respect of the Angiosperms in which all seagrasses are in one order, the Alismatales. The family Cymodoceaceae is not recognised currently in this system, but we have retained it for the present. The seagrasses are, of course, not algae, but are included here for convenience.",
"homepage": "http://www.algaebase.org/browse/taxonomy/",
"name": "AlgaeBase Taxonomy",
"prefix": "974"
},
"975": {
"description": "The National Plant Germplasm System of the Agricultural Research Service, U.S. Department of Agriculture maintains a computer database, the Germplasm Resources Information Network (GRIN), for the management of and as a source of information on its 568,489 germplasm accessions. The taxonomic portion of GRIN provides the classification and nomenclature for these genetic resources and many other economic plants on a worldwide basis. Included in GRIN TAXONOMY are scientific names for 26,968 genera (14,279 accepted) and 1,375 infragenera (1,316 accepted) and 103,161 species or infraspecies (61,241 accepted) with common names, geographical distributions, literature references, and economic impacts. Generally recognized standards for abbreviating author's names and botanical literature have been adopted in GRIN. The scientific names are verified, in accordance with the international rules of botanical nomenclature, by taxonomists of the National Germplasm Resources Laboratory using available taxonomic literature and consultations with taxonomic specialists. Included in GRIN TAXONOMY are federal- and state-regulated noxious weeds and federally and internationally listed threatened and endangered plants.",
"homepage": "https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomyquery.aspx",
"name": "GRIN Taxonomy for Plants",
"prefix": "975"
},
"976": {
"description": "Each entry consists of a term (in bold), a definition of the term, and a number in parentheses indicating the source of the definition. Clicking on the speaker icon will give you the pronunciation of the term. (Be sure to close the window for the sound player after each use.) The pencil icon will give you a drawing, and the camera icon will give you a photograph.",
"homepage": "http://www.plantpath.cornell.edu/glossary/",
"name": "On-Line Glossary of Technical Terms in Plant Pathology",
"prefix": "976"
},
"977": {
"description": "In 1999, FAO published the first French version of the multilingual land tenure thesaurus. Its main purpose was to be put to the test of the ground, that is to say, subject to constructive criticism from users Search for new information and insights from land experts, both in terms of substance and form, a number of strengths and gaps have been identified since 1999 by the editorial team and Many other land specialists, and this second version takes into account as much as possible these returns from the land, while the \"land\" discipline, like the disciplines that nourish it, is constantly evolving and a period of five years Can certainly be considered sufficiently long to perceive mutations or trends in the conceptual bases as well as in the approaches.This also justifies the draft of a later version As it also announces the draft of a third version. More than forty new terms have thus been added as main entry or as secondary entry. About the same number of terms have also been completed and exemplified. References to websites where additional information or illustrations can be found are also included.\n\nFinally, it is important to mention the recent edition of the 2003 and 2003 versions of the thesaurus, which, more than mere translations of the French version, are real adaptations to the geographic and cultural worlds of Spanish and English. This second French version of course benefited from the editorial experience gained with the preparation of the Spanish and English versions. A Chinese version was also released very recently.",
"homepage": "http://www.fao.org/docrep/005/x2038f/x2038f00.htm",
"name": "Multilingual Property Thesaurus",
"prefix": "977"
},
"978": {
"description": "This Thesaurus is a compilation of many sources used in general for computer applications and has been developed by an international team of Egyptologists in seven languages and consists of 15 sections and aims to provide a documentation standard to describe Many museums have already adopted it, and it is becoming an increasingly recognized international standard.",
"homepage": "http://projetrosette.info/page.php?Id=290",
"license": "https://www.w3.org/Consortium/Legal/2015/doc-license",
"name": "Multilingual Egyptian Thesaurus",
"prefix": "978"
},
"979": {
"description": "The 'Glossary of Biotechnology for Food and Agriculture' is a revised, augmented version of the 'Glossary of Biotechnology and Genetic Engineering' published by FAO in 1999. The idea for such a collection of terminology associated with the rapidly expanding fields related to or deriving from biotechnology and genetic engineering, was stimulated by the difficulty of communicating effectively in discussions at intergovernmental level. On various occasions, simple differences of interpretation of terminology have threatened to de-rail negotiations of international importance. This Glossary tries to provide a consolidated, comprehensive and yet accessible list of terms and acronyms that are used regularly in biotechnology for food and agriculture and that represent a convenient reference source for researchers, students and technicians. (...) The second edition contained 3,196 terms and related definitions (about 450 new terms, about 100 terms were deleted). A number of definitions were improved to enhance the coherence of the Glossary. The second edition also has a slightly modified title, that reflects more precisely the scope of the Glossary, limited to terms involving biotechnology for food and agriculture. (...) However, FAO does not consider that the process is completed, and inputs from users (suggestions of new terms, comments on current terms, etc.) are encouraged. The new glossary management system introduced in 2012 allows the addition of new terms and definitions as well as their simultaneous translation into Arabic, Chinese, French, Russian, and Spanish, enabling us to keep pace with new developments in the fast progressing field of agricultural biotechnologies.",
"homepage": "http://www.fao.org/biotech/biotech-glossary/",
"name": "FAO Glossary of Biotechnology for Food and Agriculture",
"prefix": "979"
},
"98": {
"description": "Guidelines on Subject Access to Individual Works of Fiction, Drama, Etc., 2nd edition, was published in 2000. The Guidelines constitute a recommendation for national standard practice in the provision of genre and subject access to individual works of fiction, drama, poetry, humor, and folklore in all formats.",
"name": "Guidelines on Subject Access to Individual Works of Fiction, Drama, etc. Genre Terms",
"prefix": "98"
},
"980": {
"description": "Manure management, utilisation and the potential impacts on the environment are topics of high relevance across Europe. It is well recognised that internationally coordinated research and development and exchange of experience can greatly benefit science, technology transfer and the development of the corresponding policy framework across Europe. A major handicap in international collaboration, and a major source of misunderstandings, in these areas is the lack of a standardised terminology. This is not only true for the translation between different languages but also within most languages. (...) The glossary comprises mainly terms concerning manures produced by farm livestock but also includes relevant, broader terms concerning fertilisers, crops, feeding livestock and wider environmental issues. There are also some terms concerning other types of organic materials that are commonly applied to agricultural land. Similarly, although it is primarily a glossary of terms used in Europe, some terms in common use in North America are included.",
"homepage": "http://www.ramiran.net/DOC/Glossary2003.pdf",
"name": "Glossary of terms on livestock manure management",
"prefix": "980"
},
"981": {
"description": "Thesaulangue is above all a documentary tool for scientific indexing, a homogenization of the linguistic indexing on the terminological level, intended to facilitate all bibliographic searches and to promote the relevance of the results of an automated request on the bibliographic database of Documentation and futures center on HAL (hyper online article) which provides an interface allowing authors to deposit manuscripts of scientific articles in all disciplines on the basis of the CCSD (Center for Direct Scientific Communication - UPS 2275). (...) Thesaulangue must be understood by the linguistic community as a terminological reserve of the history of epistemological approaches, such as the conservatory of valuable data accumulated in the course of research, as a place of living memory offered to Future researchers.",
"homepage": "https://apps.atilf.fr/revues/thesaulangue.pdf",
"name": "Thesaulangue",
"prefix": "981"
},
"982": {
"description": "Keywords (German, English): alphabetically arranged list for the reproduction of the content of a publication, synonymously used terms are placed behind the keyword in brackets (\" also includes \"), references to similar keywords are listed under\") (German, English) or systematically (German, English) Parasitology / Diseases (German, English): For diseases the respective pathogens are used as keywords, diseases are listed as synonyms.",
"homepage": "http://www.wildtier.ch/index.php",
"name": "Swiss Wildlife Information Service Keyword catalogs (Thesaurus)",
"prefix": "982"
},
"983": {
"description": "The Hegoa Documentation Center aims to set up and disseminate a specialized fund for international development and cooperation. It has a digital and in-person library with more than 19,700 bibliographic records structured in 8 major topics, classified and controlled by a specific Thesaurus with 1,100 Descriptors or keywords that facilitate the retrieval of information.",
"homepage": "http://biblioteca.hegoa.efaber.net/tesauro/tematico",
"name": "Thesaurus Institute of Studies on Development and International Cooperation",
"prefix": "983"
},
"984": {
"description": "37525 terms, 7076 relationships between terms, 4469 equivalent terms.",
"homepage": "http://bibliotesauro.aecid.es/vocab/",
"prefix": "984"
},
"985": {
"homepage": "http://www.iamm.fr/ressources/opac_css/index.php",
"prefix": "985"
},
"986": {
"description": "Documentation Center of the EESP",
"homepage": "http://www.eesp.ch/homedirs/groups/6/Cdoc/thesaurus.pdf",
"name": "Thesaurus of the High School of Social Work and Health Lausanne",
"prefix": "986"
},
"987": {
"description": "The Bernard Liou Library is the scientific library of the Department of underwater and underwater archaeological research (DRASSM).",
"homepage": "http://www.bibliotheque-bernard-liou-drassm-culture.fr/ListThesau.htm",
"name": "Thesaurus of the Bernard Liou Library",
"prefix": "987"
},
"988": {
"description": "The Thesaurus of Industrial Technology and Applied Sciences developed in the Technical Processes Sector of the INTI Library began to be compiled in 1981, starting with the terminology proper to the monographic works of the technical staff of the Institute.After a first collection Of terms, the respective hierarchical and horizontal relationships mentioned above were compared by comparing the terms selected with their equivalents in other thesauri (eg Root Thesaurus (BSI), Macrothesaurus (OECD), Thesaurus of Engineering and Scientific Terms ), Agrovoc (FAO), FSTA thesaurus, and others), as well as new terms from the books and monographic series found in the bibliographic database of the Library The descriptors or keywords thus compiled were recorded in a Microisis support database. With respect to the thematic areas it covers, they correspond fundamentally to The branches of industrial technology, applied sciences and related areas, covering basically the subjects in which INTI deploys its research, development and technical assistance activities.\n\nΒ Currently the Thesaurus gathers about 5400 descriptors, although it should be mentioned that the update is continuous given that as new material is incorporated, new terms are emerging, which, after an evaluation, are included with the same methodology.",
"homepage": "http://www-biblio.inti.gov.ar/index.php",
"name": "Thesaurus of Industrial Technology and Applied Sciences",
"prefix": "988"
},
"989": {
"description": "The first version of this Thesaurus of Library and Documentation was published three years ago, specifically in the spring of 2002. Since its publication, this thesaurus has been used in the indexing tasks of the various CINDOC databases and in the Assignment of materials of the articles collected in the journal portal Temaria, which allowed to gather the comments and suggestions of the specialized staff on the terminology used and its hierarchical presentation.These suggestions have served to better develop the version now presented .\n\nWith respect to the one presented in 2002, in the present version of the Thesaurus of Library and Documentation the following changes have been made: the number of terms in the different thematic areas has increased; Some terms have been relocated in the alphabetical and hierarchical indexes; The presentation of some descriptors has been modified; And more outreach notes have been added to better determine the meaning and use of the terms. A new annex has also been added with the Spanish and Catalan equivalents of the descriptors.",
"homepage": "http://digital.csic.es/bitstream/10261/30255/1/Tesauro%20de%20Biblioteconomia%20y%20Documentacion.pdf",
"name": "Librarianship and Documentation Thesaurus",
"prefix": "989"
},
"99": {
"description": "The IEEE Taxonomy comprises the first three hierarchical 'levels' under each term-family (or branch) that is formed from the top-most terms of the IEEE Thesaurus. In this document these term-families are arranged alphabetically and denoted by boldface type. Each term family's hierarchy goes to no more than three sublevels, denoted by indents (grouping of four dots) preceding the next level terms. A term can appear in more than one hierarchical branch and can appear more than once in any particular hierarchy. The IEEE Taxonomy is defined in this way so that it is always a subset of the IEEE Thesaurus.\n\nThe IEEE Thesaurus is a tool to improve and enhance the indexing and retrieval of articles and other material from IEEE periodicals, conferences, standards, and other publications that are made available on IEEE Xplore. It provides a common and consistent language for authors, researchers and online discovery.",
"license": "CC BY-ND 3.0",
"name": "The Institute of Electrical and Electronics Engineers Taxonomy",
"prefix": "99"
},
"990": {
"description": "The ICYT Thesaurus of Animal Biology, developed within the framework of this project, was born from the concrete need to standardize, update and structure the scientific terms used for documentary analysis in the field of Animal Biology.There is no other thesaurus on this This option was more appropriate than the translation and adaptation of a thesaurus in a foreign language, because it was better adapted to the specific needs of that database. As the first results in the development of the thesaurus, were presented at the 46th IDF Congress and Conference, held in Madrid in October 1992.\n\nThe appearance of this thesaurus presents a multiple interest. On the one hand, it is the first thesaurus on Animal Biology created in Spanish language, and represents an advance in the standardization of scientific terminology in Spanish. Secondly, since it was developed from the documentary language of the ICYT database, it has a practical and immediate practical application, since its implementation in the DBMS facilitates both the documentary analysis and the recovery of the scientific literature Spanish in this field. Finally, it provides documentalists, researchers and users in general with a reference frame of reference and a tool that makes the process of retrieving information from bibliographic databases more user-friendly, while increasing the relevance of such retrieval.\n\nThe presentation of a scientific work, of the characteristics of the present, generally implies an invitation to make a recapitulation about the avatars that, during its gestation, have been taking place, and the perspectives and future projects related to The same, which, in a necessarily schematic form, will constitute the basic content of this presentation.",
"homepage": "http://digital.csic.es/handle/10261/32544",
"name": "Thesaurus of Animal Biology",
"prefix": "990"
},
"991": {
"description": "This is a web interface for consultation online vocabulary conditioning and psychology of learning, indicating the frequency of use of words and their English equivalents, and Louis Garcia Sevilla and Adriana Garau and flowers . This vocabulary was awarded the Prize MariΓ AguilΓ³ IX in 1978, the Institute of Catalan Studies.",
"homepage": "http://cit.iec.cat/VPCA/default.asp",
"license": "CC BY-NC-ND 3.0",
"name": "Vocabulary of the psychology of learning and conditioning",
"prefix": "991"
},
"992": {
"homepage": "http://bibliotheque.insee.net/opac/index.php",
"name": "Thesaurus Insee",
"prefix": "992"
},
"993": {
"description": "Contemporary Women's Issues (CWI), a multidisciplinary, full-text database that brings together relevant content from mainstream periodicals, \"gray\" literature, and the alternative press -- with a focus on the critical issues and events that influence women's lives in more than 190 countries. Contemporary Women's Issues includes English-language titles from East and West Africa, Asia, and South and Central America, the Caribbean, North America and Europe. Contemporary Women's Issues compiles into a single collection, often overlooked and hard-to-find newsletters and NGO research reports to which most libraries do not subscribe, plus ephemeral literature from leading research institutes and grass roots organizations that is rarely indexed or cataloged. Contemporary Women's Issues records are indexed by 17 categories, including subject, region, article type and publication type.",
"homepage": "http://search.rdsinc.com/help/cwi_thesaurus_index.html",
"name": "Contemporary Women's Issues Subject Thesaurus",
"prefix": "993"
},
"994": {
"description": "The statistical classifications are grouped into typologies of family anomalies, principally economic classificacions (economic and product activitats) and demographic and social classifications (occupations, education and health). Products (transportable goods or merchandises and goods not transportable or stable) categorize productions per se to produce statistics that relate to the operations to which they are sotmeten (producció, comerç exterior i transport).",
"homepage": "http://www.idescat.cat/Classif/",
"license": "CC-BY-3.0",
"name": "Catalan classification of productes per activitats",
"prefix": "994"
},
"995": {
"description": "Thesaurus of cultural heritage\" was created within the framework of the project \"Dictionary of hierarchical terminology of cultural heritage - a tool supporting the creation and use of databases of monuments of art\", realized by the Documentary Museum of Art Monuments of the Institute of Art History of the University of WrocΕaw in 2007-2009 under the supervision of prof. Project No. N 17 0004 04. The aim of the project was to develop and make available a hierarchical dictionary of terms used to describe works of visual art and tools enabling its further development based on the cooperation of related institutions. Over the course of the project, more than 8000 concepts were introduced to the vocabulary, primarily concerning the classification of material and formal works of art and the material and technique of their implementation.",
"homepage": "http://sai.bu.uni.wroc.pl:8080/The2/",
"name": "Thesaurus of cultural heritage",
"prefix": "995"
},
"996": {
"description": "The Italian on Bioethics Thesaurus born in the SIBIL project (Information System for Bioethics Online), which has produced, among other things an archive of bioethics literature produced in Italy from 1995 to present. This thesaurus, built in order to make effective indexing and retrieval of documents, it is the first product of its kind in Italian, and with its approximately 1,000 terms encompasses all the essential concepts of bioethics specialist language and related disciplines.",
"homepage": "http://www.iss.it/binary/sibi/cont/thesa.1151313180.pdf",
"name": "Thesaurus Italian on Bioethics",
"prefix": "996"
},
"997": {
"description": "The objective of creating an Italian thesaurus of earth sciences stems from the desire to do justice to terminology and documentary complexity of our prestigious national heritage, muffled still largely imported from indexing tools and therefore often improper. Such an objective presented at the same time an ambitious and conscious challenge, as it means, resources and expertise, as anything but discounted amount, formed intermediate battles to win for the 'dream realization'. Now the Thist was finally realized with the help of many, technicians and scholars have directed their patient work and their backgrounds in order to collectively prepostoci.\n\nThe Thist, born precisely at random from the conviction of the need to do justice to the vast and rich Italian expertise in a specific and crucial scientific sector, see today, to the satisfaction of those who have taken care of growth and development, its publication. Being an instrument in constant evolution as a thesaurus, it also wants to be the first of other issues that will follow. We believe we can reasonably say that will be a valuable tool not only for experts, but also for those working in the world of conservation and dissemination of documentary material. (...) At present the Thist presents 10350 103850 descriptors linked by hierarchical relations, membership and equivalence.",
"homepage": "http://www.isprambiente.gov.it/contentfiles/00000000/26-143650-thist.pdf",
"name": "Italian thesaurus of Earth Sciences",
"prefix": "997"
},
"998": {
"description": "It contains the list of descriptors that define the topics of the articles and help them to search the Archive. Information about characters, institutions or legislation is found under the indexes index.You can consult the thesaurus from the Hierarchical List or Of the Alphabet.",
"homepage": "http://www.march.es/ceacs/biblioteca/proyectos/linz/Herramientas/",
"name": "Archive Linz of the Spanish Transition Thesaurus",
"prefix": "998"
},
"999": {
"description": "When the IDRC Library began to index the material in its collection and to build a data base using the ISIS computer systems, the OECD's Macrothesaurus was selected as the source of descriptors for indexing and retrieval. At that time it was hoped that the international and other organizations also using the Macrothesaurus would construct a joint operation to keep it up to date and to modify it in the light of experience. These hopes have not so far been realized, and, while there have been considerable ad hoc consultations among some of the major users of the Macrothesaurus, each has had to make modifications unilaterally to meet individual requirements. IDRC's policy has been to stay as close as possible to the Macrothesaurus, and to make changes only when necessary. Nevertheless, hundreds of changes in matters of detail have had to be introduced over the years since operations began; the original structure of the Macrothesaurus has, however, been retained.",
"homepage": "https://idl-bnc-idrc.dspacedirect.org/bitstream/handle/10625/837/IDL-837.pdf",
"name": "International Development Research Centre Library Thesaurus",
"prefix": "999"
}
} ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9539669
bioregistry-0.11.12/src/bioregistry/external/biocontext/ 0000755 0001751 0000177 00000000000 14655546227 022774 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/biocontext/__init__.py 0000644 0001751 0000177 00000004736 14655542206 025110 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download BioContext."""
import json
from pathlib import Path
from typing import Any, Dict, Mapping, Sequence
from pystow.utils import download
from bioregistry.constants import RAW_DIRECTORY, URI_FORMAT_KEY
from bioregistry.external.alignment_utils import Aligner
__all__ = [
"get_biocontext",
"BioContextAligner",
]
DIRECTORY = Path(__file__).parent.resolve()
RAW_PATH = RAW_DIRECTORY / "biocontext.json"
PROCESSED_PATH = DIRECTORY / "processed.json"
URL = "https://raw.githubusercontent.com/prefixcommons/biocontext/master/registry/commons_context.jsonld"
SKIP_PARTS = {"identifiers.org", "purl.obolibrary.org"}
def get_biocontext(force_download: bool = False) -> Mapping[str, Mapping[str, Any]]:
"""Get the BioContext context map.
:param force_download: If true, forces download. If false and the file
is already cached, reuses it.
:returns: The biocontext data dictionary
.. seealso:: https://github.com/prefixcommons/biocontext
"""
if PROCESSED_PATH.exists() and not force_download:
with PROCESSED_PATH.open() as file:
return json.load(file)
download(url=URL, path=RAW_PATH, force=force_download)
with RAW_PATH.open() as file:
data = json.load(file)
rv = {
prefix: {URI_FORMAT_KEY: f"{uri_prefix.strip()}$1"}
for prefix, uri_prefix in data["@context"].items()
}
with PROCESSED_PATH.open("w") as file:
json.dump(rv, file, indent=2, sort_keys=True)
return rv
class BioContextAligner(Aligner):
"""Aligner for BioContext."""
key = "biocontext"
getter = get_biocontext
curation_header = [URI_FORMAT_KEY]
def get_skip(self) -> Mapping[str, str]:
"""Get entries for BioContext that should be skipped."""
return {
"fbql": "not a real resource, as far as I can tell",
}
def prepare_external(self, external_id, external_entry) -> Dict[str, Any]:
"""Prepare BioContext data to be added to the BioContext for each BioPortal registry entry."""
uri_format = external_entry[URI_FORMAT_KEY]
if any(p in uri_format for p in SKIP_PARTS):
return {}
return {URI_FORMAT_KEY: uri_format}
def get_curation_row(self, external_id, external_entry) -> Sequence[str]:
"""Prepare curation rows for unaligned BioContext registry entries."""
formatter = external_entry[URI_FORMAT_KEY]
return [formatter]
if __name__ == "__main__":
BioContextAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254391.0
bioregistry-0.11.12/src/bioregistry/external/biocontext/processed.json 0000644 0001751 0000177 00000222241 14655543167 025661 0 ustar 00runner docker {
"": {
"uri_format": "https://monarchinitiative.org/$1"
},
"2D-PAGE.PROTEIN": {
"uri_format": "http://identifiers.org/2d-page.protein/$1"
},
"3DMET": {
"uri_format": "http://identifiers.org/3dmet/$1"
},
"AAO": {
"uri_format": "http://purl.obolibrary.org/obo/AAO_$1"
},
"ABS": {
"uri_format": "http://identifiers.org/abs/$1"
},
"ACEVIEW.WORM": {
"uri_format": "http://identifiers.org/aceview.worm/$1"
},
"ACLAME": {
"uri_format": "http://identifiers.org/aclame/$1"
},
"ADW": {
"uri_format": "http://purl.obolibrary.org/obo/ADW_$1"
},
"AEO": {
"uri_format": "http://purl.obolibrary.org/obo/AEO_$1"
},
"AERO": {
"uri_format": "http://purl.obolibrary.org/obo/AERO_$1"
},
"AFFY.PROBESET": {
"uri_format": "http://identifiers.org/affy.probeset/$1"
},
"AFTOL.TAXONOMY": {
"uri_format": "http://identifiers.org/aftol.taxonomy/$1"
},
"AGD": {
"uri_format": "http://identifiers.org/agd/$1"
},
"AGRICOLA": {
"uri_format": "http://identifiers.org/agricola/$1"
},
"AGRO": {
"uri_format": "http://purl.obolibrary.org/obo/AGRO_$1"
},
"ALLERGOME": {
"uri_format": "http://identifiers.org/allergome/$1"
},
"AMOEBADB": {
"uri_format": "http://identifiers.org/amoebadb/$1"
},
"ANTIBODYREGISTRY": {
"uri_format": "http://identifiers.org/antibodyregistry/$1"
},
"ANTWEB": {
"uri_format": "http://identifiers.org/antweb/$1"
},
"AOP": {
"uri_format": "http://identifiers.org/aop/$1"
},
"AOP.EVENTS": {
"uri_format": "http://identifiers.org/aop.events/$1"
},
"AOP.RELATIONSHIPS": {
"uri_format": "http://identifiers.org/aop.relationships/$1"
},
"AOP.STRESSOR": {
"uri_format": "http://identifiers.org/aop.stressor/$1"
},
"APB": {
"uri_format": "http://pb.apf.edu.au/phenbank/strain.html?id=$1"
},
"APD": {
"uri_format": "http://identifiers.org/apd/$1"
},
"APHIDBASE.TRANSCRIPT": {
"uri_format": "http://identifiers.org/aphidbase.transcript/$1"
},
"APID.INTERACTIONS": {
"uri_format": "http://identifiers.org/apid.interactions/$1"
},
"APO": {
"uri_format": "http://purl.obolibrary.org/obo/APO_$1"
},
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"PW": {
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"PX": {
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"PomBase": {
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"uri_format": "http://www2.brc.riken.jp/lab/animal/detail.php?brc_no=RBRC$1"
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"REACT": {
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"RGDRef": {
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"RICENETDB.COMPOUND": {
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"RICENETDB.MIRNA": {
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"RNACENTRAL": {
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"RNAMODS": {
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"RNAO": {
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"RXCUI": {
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"RXNO": {
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"SABIORK.EC": {
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"SABIORK.KINETICRECORD": {
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"SCIENCESIGNALING.PATH": {
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"SCIENCESIGNALING.PDC": {
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"SCRETF": {
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"SDBS": {
"uri_format": "http://identifiers.org/sdbs/$1"
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"SEED": {
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"SHEEPQTLDB": {
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"SIDER.DRUG": {
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"SIDER.EFFECT": {
"uri_format": "http://identifiers.org/sider.effect/$1"
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"WBbt": {
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"WD_Entity": {
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"WORMPEP": {
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"WORMS": {
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"WormBase": {
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"XAO": {
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"XCO": {
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"XL": {
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"Xenbase": {
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"YDPM": {
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"YEASTINTRON": {
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"YETFASCO": {
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"YID": {
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"YRCPDR": {
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"ZECO": {
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"ZFA": {
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"ZFIN": {
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"ZFIN.EXPRESSION": {
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"ZFIN.PHENOTYPE": {
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"ZFS": {
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"ZINC": {
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"ZP": {
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"catfishQTL": {
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},
"cattleQTL": {
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},
"chickenQTL": {
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"dbSNP": {
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"dbSNPIndividual": {
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"dbVar": {
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"dc": {
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"dcat": {
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"dcterms": {
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"dictyBase": {
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"faldo": {
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"foaf": {
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"horseQTL": {
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"idot": {
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"oa": {
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"oboInOwl": {
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"owl": {
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"pav": {
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},
"pigQTL": {
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"prov": {
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},
"rainbow_troutQTL": {
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},
"rdf": {
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},
"rdfs": {
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},
"sheepQTL": {
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},
"skos": {
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},
"void": {
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},
"xml": {
"uri_format": "http://www.w3.org/XML/1998/namespace$1"
},
"xsd": {
"uri_format": "http://www.w3.org/2001/XMLSchema#$1"
}
} ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9539669
bioregistry-0.11.12/src/bioregistry/external/biolink/ 0000755 0001751 0000177 00000000000 14655546227 022245 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/biolink/__init__.py 0000644 0001751 0000177 00000004740 14655542206 024354 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download Biolink."""
import json
from pathlib import Path
from typing import Any, Dict, Mapping, Sequence
import yaml
from pystow.utils import download
from bioregistry.constants import RAW_DIRECTORY, URI_FORMAT_KEY
from bioregistry.external.alignment_utils import Aligner
__all__ = [
"get_biolink",
"BiolinkAligner",
]
URL = "https://raw.githubusercontent.com/biolink/biolink-model/master/biolink-model.yaml"
DIRECTORY = Path(__file__).parent.resolve()
RAW_PATH = RAW_DIRECTORY / "biolink.yaml"
PROCESSED_PATH = DIRECTORY / "processed.json"
PROCESSING_BIOLINK_PATH = DIRECTORY / "processing_biolink.json"
def get_biolink(force_download: bool = False):
"""Get Biolink."""
if PROCESSED_PATH.exists() and not force_download:
with PROCESSED_PATH.open() as file:
return json.load(file)
download(url=URL, path=RAW_PATH, force=True)
with RAW_PATH.open() as file:
data = yaml.safe_load(file)
rv = {
prefix: {URI_FORMAT_KEY: f"{uri_prefix}$1"}
for prefix, uri_prefix in data["prefixes"].items()
}
with PROCESSED_PATH.open("w") as file:
json.dump(rv, file, indent=2, sort_keys=True)
return rv
class BiolinkAligner(Aligner):
"""Aligner for Biolink."""
key = "biolink"
getter = get_biolink
curation_header = [URI_FORMAT_KEY, "identifiers", "purl"]
def get_skip(self) -> Mapping[str, str]:
"""Get the skipped Biolink identifiers."""
with PROCESSING_BIOLINK_PATH.open() as file:
j = json.load(file)
return {entry["prefix"]: entry["reason"] for entry in j["skip"]}
def prepare_external(self, external_id, external_entry) -> Dict[str, Any]:
"""Prepare Biolink data to be added to the Biolink for each BioPortal registry entry."""
uri_format = external_entry[URI_FORMAT_KEY]
return {
URI_FORMAT_KEY: uri_format,
"is_identifiers": uri_format.startswith("http://identifiers.org"),
"is_obo": uri_format.startswith("http://purl.obolibrary.org"),
}
def get_curation_row(self, external_id, external_entry) -> Sequence[str]:
"""Prepare curation rows for unaligned Biolink registry entries."""
uri_format = external_entry[URI_FORMAT_KEY]
return [
uri_format,
uri_format.startswith("http://identifiers.org"),
uri_format.startswith("http://purl.obolibrary.org"),
]
if __name__ == "__main__":
BiolinkAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254826.0
bioregistry-0.11.12/src/bioregistry/external/biolink/processed.json 0000644 0001751 0000177 00000024242 14655544052 025125 0 ustar 00runner docker {
"AGRKB": {
"uri_format": "https://www.alliancegenome.org/$1"
},
"AspGD": {
"uri_format": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1"
},
"CAID": {
"uri_format": "http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1"
},
"CHADO": {
"uri_format": "http://gmod.org/wiki/Chado/$1"
},
"CHEMBL.MECHANISM": {
"uri_format": "https://www.ebi.ac.uk/chembl/mechanism/inspect/$1"
},
"CID": {
"uri_format": "http://pubchem.ncbi.nlm.nih.gov/compound/$1"
},
"CLINVAR": {
"uri_format": "http://identifiers.org/clinvar$1"
},
"COAR_RESOURCE": {
"uri_format": "http://purl.org/coar/resource_type/$1"
},
"COG": {
"uri_format": "https://www.ncbi.nlm.nih.gov/research/cog-project/$1"
},
"CPT": {
"uri_format": "https://www.ama-assn.org/practice-management/cpt/$1"
},
"CTD": {
"uri_format": "http://ctdbase.org/$1"
},
"CTD.CHEMICAL": {
"uri_format": "http://ctdbase.org/detail.go?type=chem&acc=$1"
},
"CTD.DISEASE": {
"uri_format": "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1"
},
"CTD.GENE": {
"uri_format": "http://ctdbase.org/detail.go?type=gene&acc=$1"
},
"ChemBank": {
"uri_format": "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$1"
},
"ComplexPortal": {
"uri_format": "https://www.ebi.ac.uk/complexportal/complex/$1"
},
"DGIdb": {
"uri_format": "https://www.dgidb.org/interaction_types$1"
},
"DOID-PROPERTY": {
"uri_format": "http://purl.obolibrary.org/obo/doid#$1"
},
"DrugCentral": {
"uri_format": "http://drugcentral.org/drugcard/$1"
},
"ECTO": {
"uri_format": "http://purl.obolibrary.org/obo/ECTO_$1"
},
"EDAM-DATA": {
"uri_format": "http://edamontology.org/data_$1"
},
"EDAM-FORMAT": {
"uri_format": "http://edamontology.org/format_$1"
},
"EDAM-OPERATION": {
"uri_format": "http://edamontology.org/operation_$1"
},
"EDAM-TOPIC": {
"uri_format": "http://edamontology.org/topic_$1"
},
"EFO": {
"uri_format": "http://www.ebi.ac.uk/efo/EFO_$1"
},
"ExO": {
"uri_format": "http://purl.obolibrary.org/obo/ExO_$1"
},
"FYECO": {
"uri_format": "https://www.pombase.org/term/$1"
},
"FYPO": {
"uri_format": "http://purl.obolibrary.org/obo/FYPO_$1"
},
"GOP": {
"uri_format": "http://purl.obolibrary.org/obo/go#$1"
},
"GOREL": {
"uri_format": "http://purl.obolibrary.org/obo/GOREL_$1"
},
"GSID": {
"uri_format": "https://scholar.google.com/citations?user=$1"
},
"GTEx": {
"uri_format": "https://www.gtexportal.org/home/gene/$1"
},
"GTOPDB": {
"uri_format": "https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1"
},
"HANCESTRO": {
"uri_format": "http://www.ebi.ac.uk/ancestro/ancestro_$1"
},
"HCPCS": {
"uri_format": "http://purl.bioontology.org/ontology/HCPCS/$1"
},
"HsapDv": {
"uri_format": "http://purl.obolibrary.org/obo/HsapDv_$1"
},
"ICD10": {
"uri_format": "https://icd.codes/icd9cm/$1"
},
"ICD9": {
"uri_format": "http://translator.ncats.nih.gov/ICD9_$1"
},
"INO": {
"uri_format": "http://purl.obolibrary.org/obo/INO_$1"
},
"KEGG": {
"uri_format": "http://www.kegg.jp/entry/$1"
},
"KEGG.BRITE": {
"uri_format": "https://bioregistry.io/kegg.brite:$1"
},
"KEGG.GENES": {
"uri_format": "https://bioregistry.io/kegg.genes:bsu:$1"
},
"KEGG.PATHWAY": {
"uri_format": "https://bioregistry.io/kegg.pathway:$1"
},
"KEGG.RCLASS": {
"uri_format": "https://www.genome.jp/dbget-bin/www_bget?rc:$1"
},
"LOINC": {
"uri_format": "http://loinc.org/rdf/$1"
},
"MAXO": {
"uri_format": "http://purl.obolibrary.org/obo/MAXO_$1"
},
"MESH": {
"uri_format": "http://id.nlm.nih.gov/mesh/$1"
},
"METANETX.REACTION": {
"uri_format": "https://www.metanetx.org/equa_info/$1"
},
"MI": {
"uri_format": "http://purl.obolibrary.org/obo/MI_$1"
},
"MSigDB": {
"uri_format": "https://www.gsea-msigdb.org/gsea/msigdb/$1"
},
"MmusDv": {
"uri_format": "http://purl.obolibrary.org/obo/MMUSDV_$1"
},
"NBO-PROPERTY": {
"uri_format": "http://purl.obolibrary.org/obo/nbo#$1"
},
"NCBIGene": {
"uri_format": "http://identifiers.org/ncbigene/$1"
},
"NCIT-OBO": {
"uri_format": "http://purl.obolibrary.org/obo/ncit#$1"
},
"NDDF": {
"uri_format": "http://purl.bioontology.org/ontology/NDDF/$1"
},
"NLMID": {
"uri_format": "https://www.ncbi.nlm.nih.gov/nlmcatalog/?term=$1"
},
"OBAN": {
"uri_format": "http://purl.org/oban/$1"
},
"OMIM.PS": {
"uri_format": "https://www.omim.org/phenotypicSeries/$1"
},
"ORCID": {
"uri_format": "https://orcid.org/$1"
},
"PANTHER.FAMILY": {
"uri_format": "http://www.pantherdb.org/panther/family.do?clsAccession=$1"
},
"PHARMGKB.DISEASE": {
"uri_format": "https://www.pharmgkb.org/disease/$1"
},
"PHARMGKB.DRUG": {
"uri_format": "https://www.pharmgkb.org/chemical/$1"
},
"PHARMGKB.GENE": {
"uri_format": "https://www.pharmgkb.org/gene/$1"
},
"PHARMGKB.PATHWAYS": {
"uri_format": "https://www.pharmgkb.org/pathway/$1"
},
"PHARMGKB.VARIANT": {
"uri_format": "https://www.pharmgkb.org/variant/$1"
},
"PHAROS": {
"uri_format": "http://pharos.nih.gov$1"
},
"PMC": {
"uri_format": "http://europepmc.org/articles/PMC$1"
},
"PathWhiz": {
"uri_format": "http://smpdb.ca/pathways/#$1"
},
"PomBase": {
"uri_format": "https://www.pombase.org/gene/$1"
},
"REPODB": {
"uri_format": "http://apps.chiragjpgroup.org/repoDB/$1"
},
"RO": {
"uri_format": "http://purl.obolibrary.org/obo/RO_$1"
},
"RXCUI": {
"uri_format": "https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1"
},
"RXNORM": {
"uri_format": "http://purl.bioontology.org/ontology/RXNORM/$1"
},
"ResearchID": {
"uri_format": "https://publons.com/researcher/$1"
},
"SEED.REACTION": {
"uri_format": "https://modelseed.org/biochem/reactions/$1"
},
"SEMMEDDB": {
"uri_format": "https://skr3.nlm.nih.gov/SemMedDB$1"
},
"SIO": {
"uri_format": "http://semanticscience.org/resource/SIO_$1"
},
"SNOMEDCT": {
"uri_format": "http://snomed.info/id/$1"
},
"SPDI": {
"uri_format": "https://api.ncbi.nlm.nih.gov/variation/v0/spdi/$1"
},
"STY": {
"uri_format": "http://purl.bioontology.org/ontology/STY/$1"
},
"ScopusID": {
"uri_format": "https://www.scopus.com/authid/detail.uri?authorId=$1"
},
"UBERGRAPH": {
"uri_format": "http://translator.renci.org/ubergraph-axioms.ofn#$1"
},
"UBERON_CORE": {
"uri_format": "http://purl.obolibrary.org/obo/uberon/core#$1"
},
"UBERON_NONAMESPACE": {
"uri_format": "http://purl.obolibrary.org/obo/core#$1"
},
"UMLSSG": {
"uri_format": "https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt$1"
},
"UNIPROT.ISOFORM": {
"uri_format": "http://purl.uniprot.org/isoforms/$1"
},
"UO-PROPERTY": {
"uri_format": "http://purl.obolibrary.org/obo/uo#$1"
},
"UniProtKB": {
"uri_format": "http://purl.uniprot.org/uniprot/$1"
},
"VANDF": {
"uri_format": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/$1"
},
"VMC": {
"uri_format": "https://github.com/ga4gh/vr-spec/$1"
},
"WBVocab": {
"uri_format": "http://bio2rdf.org/wormbase_vocabulary$1"
},
"WBbt": {
"uri_format": "http://purl.obolibrary.org/obo/WBbt_$1"
},
"WBls": {
"uri_format": "http://purl.obolibrary.org/obo/WBls_$1"
},
"WIKIDATA": {
"uri_format": "https://www.wikidata.org/entity/$1"
},
"WIKIDATA_PROPERTY": {
"uri_format": "https://www.wikidata.org/prop/$1"
},
"XPO": {
"uri_format": "http://purl.obolibrary.org/obo/XPO_$1"
},
"Xenbase": {
"uri_format": "http://www.xenbase.org/gene/showgene.do?method=display&geneId=$1"
},
"apollo": {
"uri_format": "https://github.com/GMOD/Apollo$1"
},
"biolink": {
"uri_format": "https://w3id.org/biolink/vocab/$1"
},
"bioschemas": {
"uri_format": "https://bioschemas.org/$1"
},
"dcat": {
"uri_format": "http://www.w3.org/ns/dcat#$1"
},
"dcid": {
"uri_format": "https://datacommons.org/browser/$1"
},
"dct": {
"uri_format": "http://purl.org/dc/terms/$1"
},
"doi": {
"uri_format": "https://doi.org/$1"
},
"fabio": {
"uri_format": "http://purl.org/spar/fabio/$1"
},
"foaf": {
"uri_format": "http://xmlns.com/foaf/0.1/$1"
},
"foodb.compound": {
"uri_format": "http://foodb.ca/compounds/$1"
},
"foodb.food": {
"uri_format": "http://foodb.ca/foods/$1"
},
"gff3": {
"uri_format": "https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#$1"
},
"gpi": {
"uri_format": "https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#$1"
},
"gtpo": {
"uri_format": "https://rdf.guidetopharmacology.org/ns/gtpo#$1"
},
"interpro": {
"uri_format": "https://www.ebi.ac.uk/interpro/entry/$1"
},
"isbn": {
"uri_format": "https://www.isbn-international.org/identifier/$1"
},
"isni": {
"uri_format": "https://isni.org/isni/$1"
},
"issn": {
"uri_format": "https://portal.issn.org/resource/ISSN/$1"
},
"linkml": {
"uri_format": "https://w3id.org/linkml/$1"
},
"medgen": {
"uri_format": "https://www.ncbi.nlm.nih.gov/medgen/$1"
},
"metacyc.reaction": {
"uri_format": "http://identifiers.org/metacyc.reaction:$1"
},
"mirbase": {
"uri_format": "http://identifiers.org/mirbase$1"
},
"mmmp.biomaps": {
"uri_format": "https://bioregistry.io/mmmp.biomaps:$1"
},
"ncats.bioplanet": {
"uri_format": "https://tripod.nih.gov/bioplanet/detail.jsp?pid=$1"
},
"ncats.drug": {
"uri_format": "https://drugs.ncats.io/drug/$1"
},
"orphanet": {
"uri_format": "http://www.orpha.net/ORDO/Orphanet_$1"
},
"os": {
"uri_format": "https://github.com/cmungall/owlstar/blob/master/owlstar.ttl$1"
},
"pav": {
"uri_format": "http://purl.org/pav/$1"
},
"prov": {
"uri_format": "http://www.w3.org/ns/prov#$1"
},
"qud": {
"uri_format": "http://qudt.org/1.1/schema/qudt#$1"
},
"schema": {
"uri_format": "http://schema.org/$1"
},
"wgs": {
"uri_format": "http://www.w3.org/2003/01/geo/wgs84_pos$1"
}
} ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/biolink/processing_biolink.json 0000644 0001751 0000177 00000000774 14655542206 027024 0 ustar 00runner docker {
"skip": [
{
"prefix": "RTXKG1",
"reason": "This is a file server with a few files in it"
},
{
"prefix": "CHADO",
"reason": "This is a wiki with no entries"
},
{
"prefix": "REPODB",
"reason": "This isn't actually a resource that resolves things or has its own entities"
},
{
"prefix": "CHEMBL.MECHANISM",
"reason": "This is an outdated notion from an older vesion of ChEBML. Maybe it's supposed to refer to targets?"
}
]
}
././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9579668
bioregistry-0.11.12/src/bioregistry/external/bioportal/ 0000755 0001751 0000177 00000000000 14655546227 022611 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/bioportal/__init__.py 0000644 0001751 0000177 00000016024 14655542206 024716 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download the NCBO BioPortal registry.
Get an API key by logging up, signing in, and navigating to https://bioportal.bioontology.org/account.
"""
import json
import math
from dataclasses import dataclass, field
from pathlib import Path
from typing import Optional
import pystow
import requests
from tqdm import tqdm
from tqdm.contrib.concurrent import thread_map
from bioregistry.constants import EMAIL_RE, RAW_DIRECTORY
from bioregistry.license_standardizer import standardize_license
from bioregistry.utils import removeprefix
__all__ = [
"get_bioportal",
"get_agroportal",
"get_ecoportal",
]
BIOPORTAL_BASE_URL = "https://data.bioontology.org"
ECOPORTAL_BASE_URL = "http://ecoportal.lifewatch.eu:8080"
AGROPORTAL_BASE_URL = "http://data.agroportal.lirmm.fr"
DIRECTORY = Path(__file__).parent.resolve()
@dataclass
class OntoPortalClient:
"""A client for an OntoPortal site, like BioPortal."""
metaprefix: str
base_url: str
api_key: Optional[str] = None
raw_path: Path = field(init=False)
processed_path: Path = field(init=False)
max_workers: int = 2
def __post_init__(self):
self.raw_path = RAW_DIRECTORY.joinpath(self.metaprefix).with_suffix(".json")
self.processed_path = DIRECTORY.joinpath(self.metaprefix).with_suffix(".json")
def query(self, url: str, **params) -> requests.Response:
"""Query the given endpoint on the OntoPortal site.
:param url: URL to query
:param params: Kwargs to give as params to :func:`requests.get`
:returns: The response from :func:`requests.get`
The rate limit is 15 queries per second. See:
https://www.bioontology.org/wiki/Annotator_Optimizing_and_Troublehooting
"""
if self.api_key is None:
self.api_key = pystow.get_config(self.metaprefix, "api_key", raise_on_missing=True)
params.setdefault("apikey", self.api_key)
return requests.get(url, params=params)
def download(self, force_download: bool = False):
"""Get the full dump of the OntoPortal site's registry."""
if self.processed_path.exists() and not force_download:
with self.processed_path.open() as file:
return json.load(file)
# see https://data.bioontology.org/documentation#Ontology
res = self.query(self.base_url + "/ontologies", summaryOnly=False, notes=True)
records = res.json()
records = thread_map(
self._preprocess,
records,
unit="ontology",
max_workers=self.max_workers,
desc=f"Preprocessing {self.metaprefix}",
)
with self.raw_path.open("w") as file:
json.dump(records, file, indent=2, sort_keys=True, ensure_ascii=False)
records = thread_map(
self.process, records, disable=True, description=f"Processing {self.metaprefix}"
)
rv = {result["prefix"]: result for result in records}
with self.processed_path.open("w") as file:
json.dump(rv, file, indent=2, sort_keys=True, ensure_ascii=False)
return rv
def _preprocess(self, record):
record.pop("@context", None)
prefix = record["acronym"]
url = f"{self.base_url}/ontologies/{prefix}/latest_submission"
res = self.query(url, display="all")
if res.status_code != 200:
tqdm.write(
f"{self.metaprefix}:{prefix} had issue getting submission details: {res.text}"
)
return record
res_json = res.json()
for key in [
"homepage",
"publication",
"version",
"description",
"exampleIdentifier",
"repository",
]:
value = res_json.get(key)
if value:
if isinstance(value, list) and len(value) == 1:
value = value[0]
if isinstance(value, float) and not math.isnan(value):
value = str(value)
if not isinstance(value, str):
tqdm.write(f"got non-string value ({type(value)}) for {key}: {value}")
continue
record[key] = (
(value or "")
.strip()
.replace("\r\n", " ")
.replace("\r", " ")
.strip()
.replace(" ", " ")
.replace(" ", " ")
.replace(" ", " ")
)
license_stub = res_json.get("hasLicense")
if license_stub:
record["license"] = standardize_license(license_stub)
contacts = [
{k: v.strip() for k, v in contact.items() if not k.startswith("@")}
for contact in res_json.get("contact", [])
]
contacts = [contact for contact in contacts if EMAIL_RE.match(contact.get("email", ""))]
if contacts:
contact = contacts[0]
# TODO consider sorting contacts in a canonical order?
# contact = min(contacts, key=lambda c: len(c["email"]))
record["contact"] = {k: v for k, v in contact.items() if k != "id"}
name = record["contact"].get("name")
if name:
record["contact"]["name"] = removeprefix(removeprefix(name, "Dr. "), "Dr ")
return {k: v for k, v in record.items() if v}
def process(self, entry):
"""Process a record from the OntoPortal site's API."""
prefix = entry["acronym"]
rv = {
"prefix": prefix,
"name": entry["name"].strip(),
"description": entry.get("description"),
"contact": entry.get("contact"),
"homepage": entry.get("homepage"),
"version": entry.get("version"),
"publication": entry.get("publication"),
"repository": entry.get("repository"),
"example_uri": entry.get("exampleIdentifier"),
"license": entry.get("license"),
}
return {k: v for k, v in rv.items() if v}
bioportal_client = OntoPortalClient(
metaprefix="bioportal",
base_url=BIOPORTAL_BASE_URL,
)
def get_bioportal(force_download: bool = False):
"""Get the BioPortal registry."""
return bioportal_client.download(force_download=force_download)
ecoportal_client = OntoPortalClient(
metaprefix="ecoportal",
base_url=ECOPORTAL_BASE_URL,
)
def get_ecoportal(force_download: bool = False):
"""Get the EcoPortal registry."""
return ecoportal_client.download(force_download=force_download)
agroportal_client = OntoPortalClient(
metaprefix="agroportal",
base_url=AGROPORTAL_BASE_URL,
)
def get_agroportal(force_download: bool = False):
"""Get the AgroPortal registry."""
return agroportal_client.download(force_download=force_download)
if __name__ == "__main__":
print("EcoPortal has", len(get_ecoportal(force_download=True))) # noqa:T201
print("AgroPortal has", len(get_agroportal(force_download=True))) # noqa:T201
print("BioPortal has", len(get_bioportal(force_download=True))) # noqa:T201
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254532.0
bioregistry-0.11.12/src/bioregistry/external/bioportal/agroportal.json 0000644 0001751 0000177 00000475512 14655543404 025666 0 ustar 00runner docker {
"AAO": {
"contact": {
"email": "cavoc@ml.affrc.go.jp",
"name": "Akane Takezaki"
},
"description": "Agriculture Activity ontology (AAO) is an ontology that describes agricultural work using attributes such as purpose, behavior, objective, and its attribute values.",
"name": "Agriculture Activity Ontology",
"prefix": "AAO"
},
"ADW": {
"contact": {
"email": "adw.staff@umich.edu",
"name": "Animal Diversity Web technical staff"
},
"description": "An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.",
"homepage": "https://bioportal.bioontology.org/ontologies/ADW",
"name": "Animal Natural History and Life History Ontology",
"prefix": "ADW"
},
"AEO": {
"contact": {
"email": "anne.tireau@supagro.inra.fr",
"name": "Tireau Anne"
},
"description": "AEO is an ontology aimed to represent objects related to agricultural practices.",
"example_uri": "http://purl.org/dc/dcam/VocabularyEncodingScheme",
"homepage": "http://lovinra.inra.fr/",
"license": "CC-BY-4.0",
"name": "Agricultural Experiments Ontology",
"prefix": "AEO",
"version": "Version 3.3 created by UMR MISTEA"
},
"AFEO": {
"contact": {
"email": "anne.tireau@inrae.fr",
"name": "Tireau Anne"
},
"description": "The Agri-Food Experiment Ontology (AFEO), a new ontology network was developed based on two existing ontology resources, i.e., OAE (Ontology for Agriculture Experiment) and OFPE (Ontology for Food Processing Experiment).",
"example_uri": "http://www.mistea.supagro.inra.fr/ontologies/2016/v1/afeo#Must",
"homepage": "http://opensilex.org/vocabulary/2016/v1/afeo.owl",
"license": "CC-BY-4.0",
"name": "Agri-Food Experiment Ontology",
"prefix": "AFEO",
"version": "4.2 May 2022\nchange import"
},
"AFO": {
"contact": {
"email": "Eero.Hyvonen@tkk.fI",
"name": "Eero HyvΓΆnen"
},
"description": "The Agriculture and Forestry Ontology (AFO) is based on the Agriforest thesaurus maintained by the Viikki Campus Library, University of Helsinki. The combination of AFO and the Finnish General Upper Ontology YSO has been created in the FinnONTO project by the Viikki Science Library in cooperation with the Semantic Computing Research Group. The ontology was created by aligning the Agriculture and Forestry Ontology with the Finnish General Upper Ontology (YSO) using the top ontology and other modelling principles of YSO. This way the equivalent and differing concepts and their links to more general concepts could be explicitly described. This combination of ontologies can be used for describing resources especially in domain of agriculture, forestry, veterinary medicine, food science, environmental science and biology.",
"example_uri": "http://www.yso.fi/onto/yso/p16591",
"license": "CC-BY-4.0",
"name": "Agriculture and Forestry Ontology",
"prefix": "AFO"
},
"AGFOOD": {
"contact": {
"email": "contact-terminologietal@inist.fr",
"name": "Inist"
},
"description": "This bilingual vocabulary contains 3117 concepts covering the domains of agri-food science and technology, ranging \"from farm to table\", as well as nutritional and environmental aspects, taking into account the ongoing agricultural and food transition. The terminology is enriched with a large number of alternative entries (3230 in English or French) and hidden terms for easy searching., Ce vocabulaire bilingue comprend 3117 concepts des domaines de la science et de la technologie agroalimentaire, allant Β« de la ferme Γ la table Β», ainsi que des aspects nutritionnels et environnementaux, tenant compte de la transition agricole et alimentaire en cours. La terminologie est enrichie dβun grand nombre dβaccΓ¨s synonymes (3230 en franΓ§ais ou en anglais) et de formes cachΓ©es facilitant la recherche. Il est alignΓ© avec lβontologie FoodOn., taking into account the ongoing agricultural and food transition. The terminology is enriched with a large number of alternative entries (3230 in English or French) and hidden terms for easy searching. It has been aligned with the FoodOn ontology., Este vocabulario bilingΓΌe (francΓ©s e inglΓ©s) contiene 3117 conceptos que abarcan los Γ‘mbitos de la ciencia y la tecnologΓa agroalimentarias, que van \"de la granja a la mesa\", asΓ como aspectos nutricionales y medioambientales, teniendo en cuenta la transiciΓ³n agrΓcola y alimentaria en curso. La terminologΓa se enriquece con un gran nΓΊmero de entradas alternativas (3230 en francΓ©s o inglΓ©s) y tΓ©rminos ocultos para facilitar la bΓΊsqueda. Se ha alineado con la ontologΓa FoodOn.",
"example_uri": "http://data.loterre.fr/ark:/67375/Q1W-S6NXBHHH-3",
"homepage": "http://www.inist.fr",
"license": "CC-BY-4.0",
"name": "Agri-food vocabulary",
"prefix": "AGFOOD",
"version": "1.1"
},
"AGRO": {
"contact": {
"email": "c.aubert@cgiar.org",
"name": "CΓ©line Aubert"
},
"description": "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities",
"example_uri": "http://purl.obolibrary.org/obo/AGRO_00000002",
"homepage": "https://bigdata.cgiar.org/resources/agronomy-ontology/",
"license": "CC-BY-4.0",
"name": "Agronomy Ontology",
"prefix": "AGRO",
"publication": "http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf",
"repository": "https://github.com/AgriculturalSemantics/agro",
"version": "1.0"
},
"AGRONTOLOGY": {
"contact": {
"email": "AGROVOC@fao.org",
"name": "AGROVOC"
},
"description": "Agrontology is the Web Ontology Language (OWL) vocabulary providing a set of domain properties to the AGROVOC thesaurus.",
"example_uri": "http://purl.org/dc/terms/BibliographicResource",
"homepage": "https://www.fao.org/agrovoc/agrontology",
"license": "CC-BY-4.0",
"name": "AgrOntology",
"prefix": "AGRONTOLOGY"
},
"AGRORDF": {
"contact": {
"email": "ktbl@ktbl.de",
"name": "KBTL"
},
"description": "agroXML is an XML dialect for representing and describing farm work. It provides elements and XML data types for representing data on work processes on the farm including accompanying operating supplies like fertilizers, pesticides, crops and the like. It can be used within farm management information systems as a file format for documentation purposes but also within web services and interfaces between the farm and external stakeholders as a means to exchange data in a structured, standardized and easy to use way. It covers topics relevant to on farm activity including βcropβ, βcropSpeciesβ, βchemical substanceβ, βharvestDateβ, βenginePowerβ. There exists an XML version and an RDF version.",
"example_uri": "http://www.agroxml.de/rdf/vocabulary/workprocess#Fertilization",
"homepage": "http://www.openagramap.org",
"license": "W3C",
"name": "AGRORDF",
"prefix": "AGRORDF",
"publication": "https://pdfs.semanticscholar.org/3000/185f2a8f3d7b7d3032b7613aa17b010b5b95.pdf",
"version": "1.5"
},
"AGROVOC": {
"contact": {
"email": "AGROVOC@fao.org",
"name": "AGROVOC"
},
"description": "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is a large Linked Open Data set about agriculture, available for public use, and its highest impact is through facilitating the access and visibility of data across domains and languages.",
"example_uri": "http://aims.fao.org/aos/agrovoc/c_38445",
"homepage": "http://www.fao.org/agrovoc/",
"license": "CC-BY-4.0",
"name": "AGROVOC",
"prefix": "AGROVOC",
"publication": "https://www.fao.org/agrovoc/publications",
"version": "2024-04"
},
"AHOL": {
"contact": {
"email": "matthieu.reichstadt@inrae.fr",
"name": "Matthieu Reichstadt"
},
"description": "AHOL dΓ©finit et organise les caractΓ¨res phΓ©notypiques des animaux dβΓ©levage, en prenant en compte les prΓ©occupations sociΓ©tales et les grands types de production (lait, Εuf, viande, fertilitΓ©, alimentation)., AHOL (Animal Health Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). AHOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientific and educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the AHOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production",
"example_uri": "http://opendata.inra.fr/AHOL/AHOL_0005114",
"homepage": "http://www.atol-ontology.com/",
"license": "CC-BY-4.0",
"name": "Animal Health Ontology for Livestock",
"prefix": "AHOL"
},
"ANAEETHES": {
"contact": {
"email": "christian.pichot@inrae.fr",
"name": "Christian Pichot"
},
"description": "The AnaEE thesaurus aims to provide a controlled vocabulary for the semantic description of the study of continental ecosystems and their biodiversity. It has been developed within the framework of the AnaEE-France infrastructure through an iterative process combining both top down and bottom up approaches: import of concepts from other thesauri and collection of concepts used in the AnaEE data bases and/or modeling platforms.",
"example_uri": "http://opendata.inra.fr/anaeeThes/c2_942",
"homepage": "https://www.anaee-france.fr",
"license": "CC-BY-4.0",
"name": "AnaEE Thesaurus",
"prefix": "ANAEETHES",
"version": "2.0"
},
"ANDO": {
"contact": {
"email": "sophie.aubin@inra.fr",
"name": "Sophie Aubin"
},
"description": "L'ontologie des maladies animales est un référentiel de maladies touchant des animaux de rente et d'agents pathogènes ainsi que des relations qu'ils entretiennent. Ce référentiel est en français avec des équivalents anglais. Il contient plus de 500 couples maladie-hôtes et plus de 500 agents pathogènes associés. Il a été constitué au fil des ans par un travail de veille réglementaire à l'INRA., The Animal Diseases Ontology includes information on diseases of production animals and their related pathogenic agents in French and English. This version contains more than 500 pairs of host-disease and their more than 500 associated pathogens.",
"example_uri": "http://opendata.inra.fr/AnimalDiseasesOnto/MA67",
"license": "CC BY-SA 4.0",
"name": "Animal Disease Ontology",
"prefix": "ANDO",
"publication": "https://hal.inrae.fr/hal-02746898",
"version": "3.1"
},
"ANT": {
"contact": {
"email": "ifpri@cgiar.org",
"name": "International Food Policy Research Institute"
},
"description": "Agricultural ontology for CRP mapping.",
"example_uri": "http://aims.fao.org/aos/geopolitical.owl#area",
"name": "Agricultural and Nutrition Technology Ontology",
"prefix": "ANT",
"version": "1.0"
},
"AQFO": {
"contact": {
"email": "m.a.laporte@cgiar.org",
"name": "Marie-AngΓ©lique Laporte"
},
"description": "The Aquatic Food Ontology (AQFO) is currently being developed to enable easy aggregation and analysis of data generated by the CGIAR Initiative on Aquatic Foods. The ontology covers two domains - aquaculture and small scale fisheries. The development of AQFO is currently led by WorldFish and supported by the Alliance of Bioversity and CIAT.",
"example_uri": "http://w3id.org/aqfo/aqfo_00002088",
"license": "CC-BY-4.0",
"name": "Aquatic Food Ontology",
"prefix": "AQFO"
},
"ASCOPAIN-T": {
"contact": {
"email": "vocabulaires-ouverts@inrae.fr",
"name": "VO@INRAE"
},
"description": "The AsCoPain-T terminology lists and defines the main quality assessment descriptors used by bread-making professionals and those used in scientific studies. It aims at linking professional and scientific terminologies, as language can vary greatly to denote similar processing operations and observations that are made on the dough and bread.\nThe AsCoPain-T terminology is the result of successive efforts: expert knowledge collected by the INRA AsCoPain project first resulted in the definition of the relations between bread-making control variables and the different states of the dough and bread. These relations were implemented into the expert system used to predict the state of the dough throughout the kneading process. The terminology collected during this work was then published in the form of a glossary in a document referenced by the FAO (see http://prodinra.inra.fr/record/48319).\nThe recent adaptation of its content to the semantic web standards now allows unforeseen uses, in particular by applications. The terminology is available in French. Its translation in English will soon be under way. , La terminologie AsCoPain-T dΓ©finit les descripteurs qualitΓ© utilisΓ©s usuellement par les professionnels de la panification et ceux issus des travaux scientifiques. Son objectif est dβΓ©tablir un lien entre terminologies professionnelles et scientifiques ; le langage employΓ© pour caractΓ©riser les mΓͺmes opΓ©rations de la transformation et les nΓ©cessaires observations de la pΓ’te Γ©tant trΓ¨s variΓ©. \nLa terminologie AsCoPain-T est issue dβun travail prΓ©alable de recueil de connaissances dans le cadre du projet INRA AsCoPain qui a permis dβintΓ©grer les relations entre des variables de contrΓ΄le du procΓ©dΓ© de panification et des Γ©tats de la pΓ’te et du pain dans un systΓ¨me expert de prΓ©diction de lβΓ©tat de la pΓ’te tout au long de lβopΓ©ration de pΓ©trissage. Ce travail a aussi produit un glossaire terminologique publiΓ© dans un document rΓ©fΓ©rencΓ© par la FAO (voir http://prodinra.inra.fr/record/48319). \nLβadaptation de son contenu aux standards du web sΓ©mantique permet dβenvisager de nouveaux usages de la terminologie, notamment son utilisation par des programmes informatiques. La terminologie est disponible en franΓ§ais et une version en anglais est en projet.",
"example_uri": "http://opendata.inra.fr/AsCoPainT/contiguite",
"license": "CC-BY-4.0",
"name": "Terminology of French bread descriptors",
"prefix": "ASCOPAIN-T",
"publication": "http://prodinra.inra.fr/record/48319",
"version": "1.0"
},
"ASFA": {
"contact": {
"email": "tamsin.vicary@fao.org",
"name": "Tamsin Vicary"
},
"description": "The ASFA Thesaurus contains over 5000 terms related to aquatic sciences, fisheries and aquaculture. The thesaurus covers all topics within ASFAβs subject scope: science, technology, management, and conservation of marine, brackish water, and freshwater resources and environments, including their socio-economic and legal aspects. Maintained by ASFA partners and available in 40 languages, the ASFA thesaurus is an AGROVOCβs sub-scheme.",
"example_uri": "http://aims.fao.org/aos/agrovoc/c_02e0df9b",
"homepage": "https://www.fao.org/asfa/en",
"license": "CC-BY-3.0",
"name": "ASFA Thesaurus",
"prefix": "ASFA",
"version": "2.0"
},
"ATC": {
"contact": {
"email": "catherine.roussey@irstea.fr",
"name": "Catherine Roussey"
},
"description": "This ontology is a module that is based on skos vocabulary, linnean taxonomy ODP and classification ODP. The module was enriched by specialising taxonomic relationship based on the AOS ontology. Taxon ranks are linked to their agrovoc concepts. Some disjoint axioms between ranks were added.",
"example_uri": "http://ontology.irstea.fr/agronomictaxon/core#FamilyRank",
"homepage": "http://ontology.irstea.fr/pmwiki.php/Site/AgronomicTaxon",
"license": "CC-BY-4.0",
"name": "AgronomicTaxon",
"prefix": "ATC",
"version": "1.0"
},
"ATOL": {
"contact": {
"email": "matthieu.reichstadt@inrae.fr",
"name": "Matthieu Reichstadt"
},
"description": "ATOL dΓ©finit et organise les caractΓ¨res phΓ©notypiques des animaux dβΓ©levage, en prenant en compte les prΓ©occupations sociΓ©tales et les grands types de production (lait, Εuf, viande, fertilitΓ©, alimentation)., ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientific and educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production",
"example_uri": "http://opendata.inra.fr/ATOL/ATOL_0000455",
"homepage": "http://www.atol-ontology.com/",
"license": "CC-BY-4.0",
"name": "Animal Trait Ontology for Livestock",
"prefix": "ATOL",
"publication": "http://www.atol-ontology.com/rb/fr/6",
"version": "6.0"
},
"AWS": {
"contact": {
"email": "bernard.vatant@mondeca.com",
"name": "Bernard Vatant"
},
"description": "This ontology is part of the Agriculture Meteorology example showcasing the ontology developed by the W3C Semantic Sensor Networks incubator group (SSN-XG). It is published here in order to generalize the potential usage and the alignment with other standardization efforts of the SSN ontology.",
"example_uri": "http://purl.oclc.org/NET/ssnx/qu/dim#SurfaceTension",
"license": "http://www.w3.org/Consortium/Legal/2002/copyright-software-20021231.html",
"name": "Ontology for Meteorological Sensors",
"prefix": "AWS"
},
"BAGO": {
"contact": {
"email": "catherine.roussey@inrae.fr",
"name": "Catherine Roussey"
},
"description": "This ontology and related knowledge graph was build during the D2KAB project. The goal is to model all the living organisms involved in cultivated plant disease appearance. The ontology and its documentation represent the point of view of some french researchers from differents intstitutions., This ontology and related knowledge graph was build during the D2KAB project. The goal is to model all the living organisms involved in cultivated plant disease appearance. The ontology and its documentation represent the point of view of some french researchers from differents institutions.",
"name": "Bio AGgressor Ontology",
"prefix": "BAGO"
},
"BCO": {
"contact": {
"email": "rwalls2008@gmail.com",
"name": "Ramona Walls"
},
"description": "The goal of the BCO is to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. The BCO covers distinctions between individuals, organisms, voucher specimens, lots, samples, the relations between these entities, and the processes governing the creation and use of \"samples\". Also within scope are properties including collector, location, time, storage environment, containers, institution, and collection identifiers.",
"example_uri": "http://purl.obolibrary.org/obo/bco_0000036",
"homepage": "https://github.com/BiodiversityOntologies",
"license": "CC0-1.0",
"name": "Biological Collections Ontology",
"prefix": "BCO",
"repository": "https://github.com/BiodiversityOntologies/bco"
},
"BDG": {
"contact": {
"email": "nikola.tulechki@ontotext.com",
"name": "Nikola Tulechki"
},
"description": "Ontology, semantic model and semantic data for the H2020 BigDataGrapes EU project. BigDataGrapes ontology is used for representing observations about soil, weather, agriculture, viticulture, wine making, etc. It also contains extra units of measure based on QUDT 2.0.",
"example_uri": "http://purl.org/linked-data/cube#DataStructureDefinition",
"license": "CC-BY-4.0",
"name": "BigDataGrapes Ontology",
"prefix": "BDG",
"repository": "https://github.com/BigDataGrapes-EU/ontology",
"version": "1.0"
},
"BFO": {
"contact": {
"email": "phismith@buffalo.edu",
"name": "Barry Smith"
},
"description": "BFO grows out of a philosophical orientation which overlaps with that of DOLCE and SUMO. Unlike these, however, it is narrowly focused on the task of providing a genuine upper ontology which can be used in support of domain ontologies developed for scientific research, as for example in biomedicine within the framework of the OBO Foundry. Thus BFO does not contain physical, chemical, biological or other terms which would properly fall within the special sciences domains. BFO is the upper level ontology upon which OBO Foundry ontologies are built.",
"example_uri": "http://purl.obolibrary.org/obo/BFO_0000140",
"homepage": "http://ifomis.org/bfo",
"license": "CC-BY-4.0",
"name": "Basic Formal Ontology",
"prefix": "BFO",
"publication": "http://ifomis.uni-saarland.de/bfo/publications",
"repository": "https://github.com/BFO-ontology/BFO",
"version": "1.1"
},
"BIODIVTHES": {
"contact": {
"email": "contact-terminologietal@inist.fr",
"name": "Biodiversity Thesaurus contact"
},
"description": "This bilingual thesaurus organizes the key concepts of biodiversity sciences, in their basic and applied ecological components. It uses polyhierarchy and includes 818 reciprocal associative relationships. The 1654 French and English descriptors (designating 827 concepts) are enriched with a large number of synonyms (1860) and hidden variants (7020) in both languages. Concepts are grouped into 82 collections, by semantic categories, thematic fields and EBV classes (Essential Biodiversity Variables). Definitions are given with their sources. It could be utilized as a controlled vocabulary to enrich metadata of biodiversity data portals, enhancing semantic interoperability. It aims to extend (via narrower concepts, and synonyms) generic environmental science thesauri/ontologies., Ce thésaurus entièrement bilingue organise les concepts clés des sciences de la biodiversité, dans leurs composantes écologiques fondamentales et appliquées. Il utilise la polyhiérarchie et comprend 818 relations associatives réciproques. Les 1654 descripteurs français et anglais (désignant 827 concepts) sont accompagnés d'un grand nombre de synonymes (1860) et de variantes cachées (7020) dans les 2 langues. Les concepts sont regroupés en 82 collections, par catégories sémantiques, domaines thématiques et classes de VEB (variables essentielles de biodiversité). Les définitions sont données avec leurs sources. Cette ressource est alignée sur les thésaurus internationaux AGROVOC, GEMET (GEneral Multilingual Environmental Thesaurus) et EnvThes (Environmental Thesaurus), ainsi que sur l'ontologie ENVO (Environment Ontology)., thematic fields and EBV classes (Essential Biodiversity Variables). Definitions are given with their sources. This resource is aligned with the international thesauri AGROVOC, GEMET (GEneral Multilingual Environmental Thesaurus) and EnvThes (Environmental Thesaurus), as well as with the ontology ENVO (Environment Ontology).",
"example_uri": "http://data.loterre.fr/ark:/67375/BLH-FHNG3BCR-H",
"homepage": "http://www.inist.fr",
"license": "CC-BY-4.0",
"name": "Biodiversity Thesaurus",
"prefix": "BIODIVTHES",
"publication": "https://hal.archives-ouvertes.fr/hal-02907484",
"version": "2.1"
},
"BIOREFINERY": {
"contact": {
"email": "patrice.buche@inrae.fr",
"name": "Patrice Buche"
},
"description": "The biorefinery ontology (BIOREFINERY) is dedicated to the description of biomass transformation processes and characterisation of samples.",
"example_uri": "http://opendata.inra.fr/BIORAF/sulfuric_acid",
"homepage": "https://www6.inra.fr/cati-icat-atweb/Ontologies/Biorefinery",
"license": "CC-BY-4.0",
"name": "Biorefinery",
"prefix": "BIOREFINERY",
"publication": "http://prodinra.inra.fr/record/359143",
"version": "V-2023/01/12"
},
"BIPOM": {
"contact": {
"email": "anne.goelzer@inrae.fr",
"name": "Anne Goelzer"
},
"description": "BiPOm is an ontology based on systemic representation of metabolic processes. BiPOm is an ontological model carrying the main biological processes and molecular roles/functions at a high level of genericity where the usual annotated resources are treated as instances. BiPOm, 1) contains biological knowledge as instances and 2) uses automatic reasoning through Semantic Web Rule Language (SWRL) in order to automatically infer, formalize and refine properties of molecules.",
"name": "Biological interlocked Process Ontology for metabolism",
"prefix": "BIPOM",
"version": "Core 2020-04-15"
},
"BIPON": {
"contact": {
"email": "anne.goelzer@inrae.fr",
"name": "Anne Goelzer"
},
"description": "BiPON is an ontology permitting a multi-scale systemic representation of bacterial cellular processes and the coupling to their mathematical models. BiPON is further composed of two sub- ontologies, bioBiPON and modelBiPON. bioBiPON aims at organizing the systemic description of biological information while modelBiPON aims at describing the mathematical models (including parameters) associated to each biological process.",
"license": "CC-BY-4.0",
"name": "Bacterial interlocked Process ONtology",
"prefix": "BIPON",
"version": "2017-11-08-bis"
},
"BOHLMANN": {
"contact": {
"email": "d.fichtmueller@bgbm.org",
"name": "David Fichtmueller"
},
"description": "An ontology listing the natural substances that occur in the plant family of Compositae (Asteraceae)., An ontology listing the natural substances that occur in the plant family of Compositae (Asteraceae)",
"name": "Bohlmann Ontology",
"prefix": "BOHLMANN",
"version": "1.1.0"
},
"C3PO": {
"contact": {
"email": "florence.amardeilh@elzeard.co",
"name": "Florence Amardeilh"
},
"description": "Crop Planning and Production Process Ontology aims at representing vegetable farming crop management knowledge. The ontology is composed of several modules, each one representing specific domain of interest for vegetable agriculture planning",
"example_uri": "http://www.elzeard.co/ontologies/c3po/cropManagement#Prick",
"homepage": "https://www.elzeard.co/ontologies/c3po/",
"license": "CC-BY-4.0",
"name": "Crop Planning and Production Process Ontology",
"prefix": "C3PO",
"publication": "https://doi.org/10.3389/frai.2023.1187090",
"repository": "https://gitlab.com/serre-des-savoirs/c3po"
},
"CASO": {
"contact": {
"email": "catherine.roussey@irstea.fr",
"name": "Catherine Roussey"
},
"description": "CASO (Context Aware System Observation) is an ontology for context aware system and observation services. Its goal is to describe all the processing of the context.",
"example_uri": "http://www.w3id.org/def/caso#Observation",
"homepage": "https://w3id.org/def/caso",
"license": "CC-BY-4.0",
"name": "Context-Aware System Ontology",
"prefix": "CASO",
"version": "1.2.0"
},
"CCON": {
"name": "Cerrado Concepts and Plant Community Dynamics",
"prefix": "CCON"
},
"CD": {
"contact": {
"email": "swami.neha@gmail.com",
"name": "Neha Kaushik"
},
"description": "A basic ontology for crop-disease-pesticide information, mostly pertaining to Indian Agriculture",
"example_uri": "http://www.semanticweb.org/mac/ontologies/2018/4/untitled-ontology-24#Pest",
"name": "Crop Disease",
"prefix": "CD"
},
"CDAO": {
"contact": {
"email": "balhoff@nescent.org",
"name": "Jim Balhoff"
},
"description": "The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character.",
"example_uri": "http://purl.obolibrary.org/obo/CDAO_0000098",
"homepage": "http://www.evolutionaryontology.org/",
"license": "CC0-1.0",
"name": "Comparative Data Analysis Ontology",
"prefix": "CDAO",
"publication": "http://www.evolutionaryontology.org",
"repository": "https://sourceforge.net/projects/cdao/",
"version": "2013-02-01"
},
"CDNO": {
"contact": {
"email": "landreshdz@gmail.com",
"name": "Liliana AndrΓ©sβHernΓ‘ndez"
},
"description": "The CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. These terms are intended primarily to be associated with datasets that quantify concentration of chemical nutritional components derived from samples taken from any stage in the production of food raw materials (including from crops, livestock, fisheries) and through processing and supply chains. Additional knowledge associated with these dietary sources may be represented by terms that describe functional, physical and other attributes. Whilst recognising that dietary nutrients within food substrates may be present as complex and dynamic physical and chemical structures or mixtures, CDNO focuses on components typically quantified in an analytical chemistry laboratory. The primary CDNO class βdietary nutritional componentβ contains hierarchical sets of terms organised to reflect commonly used classifications of chemical food composition. This class does not represent an exhaustive classification of chemical components, but focuses on structuring terms according to widely accepted categories. This class is independent of, but may be used in conjunction with, classes that describe βanalytical methodsβ for quantification, βphysical propertiesβ or βdietary functionβ. Quantification data may be used and reported in research literature, to inform food composition tables and labelling, or for supply chain quality assurance and control. More specifically, terms within the βnutritional component concentrationβ class may be used to represent quantification of components described in the βdietary nutritional componentβ class. Concentration data are intended to be described in conjunction with post-composed metadata concepts, such as represented by the Food Ontology (FoodOn) βFood product by organismβ, which derives from some food or anatomical entity and a NCBI organismal classification ontology (NCBITaxon) entity. The common vocabulary and relationships defined within CDNO should facilitate description, communication and exchange of material entity-derived nutritional composition datasets typically generated by analytical laboratories. The organisation of the vocabulary is structured to reflect common categories variously used by those involved in crop, livestock or other organismal production, associated R&D and breeding, as well as the food processing and supply sector, and nutritionists, inlcuding compilers and users of food composition databases. The CDNO therefore supports characterisation of genetic diversity and management of biodiversity collections, as well as sharing of knowledge relating to dietary composition between a wider set of researchers, breeders, farmers, processors and other stakeholders. Further development of the functional class should also assist in understanding how interactions between organismal genetic and environmental variation contribute to human diet and health in the farm to fork continuum., None",
"example_uri": "http://purl.obolibrary.org/obo/CDNO_0200815",
"homepage": "https://cdno.info/",
"license": "CC-BY-3.0",
"name": "Compositional Dietary Nutrition Ontology",
"prefix": "CDNO",
"repository": "https://github.com/Southern-Cross-Plant-Science/cdno"
},
"CGO": {
"contact": {
"email": "jack.verhoosel@tno.nl",
"name": "Jack Verhoosel"
},
"description": "This ontology defines common concepts in the greenhouse domain and covers three main aspects of the greenhouse, namely (1) greenhouse construction concepts, (2) real-time measurements and action concepts and (3) dynamic objects and situation concepts. The construction concepts are defined together with main greenhouse construction companies. The real-time measurements and action concepts are based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group. The dynamic objects and situation concepts are defined based on the DOLCE+DnS Ultralite (DUL) ontology. The definition and usage of units are based on the Ontology of Measurements (OM). This ontology does not describe generic concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.",
"example_uri": "http://www.ontology-of-units-of-measure.org/resource/om-2/LuminousFluxUnit",
"homepage": "https://gitlab.com/ddings/common-greenhouse-ontology",
"license": "CC-BY-4.0",
"name": "Common Greenhouse Ontology",
"prefix": "CGO",
"publication": "https://gitlab.com/ddings/common-greenhouse-ontology",
"repository": "https://gitlab.com/ddings/common-greenhouse-ontology/-/blob/main/Ontologies/Versions/CGO-v2.2.ttl",
"version": "2.3"
},
"CIQUAL": {
"contact": {
"email": "patrice.buche@inrae.fr",
"name": "Buche"
},
"description": "This ontology contains a OWL representation of Ciqual food terms using Langual thesaurus. Ciqual is the nutritional database managed by ANSES in France.",
"example_uri": "https://ico.iate.inra.fr/meatylab/origin_databases/2/foods/13549",
"license": "CC-BY-4.0",
"name": "CIQUAL",
"prefix": "CIQUAL"
},
"CL": {
"contact": {
"email": "addiehl@buffalo.edu",
"name": "Alex Diehl"
},
"description": "An ontology of cell types.",
"example_uri": "http://purl.obolibrary.org/obo/CL_0000000",
"homepage": "https://cell-ontology.github.io/",
"license": "CC-BY-4.0",
"name": "Cell Ontology",
"prefix": "CL",
"repository": "https://github.com/obophenotype/cell-ontology",
"version": "2024-07-10"
},
"CLC": {
"contact": {
"email": "phil.archer@gs1.org",
"name": "Phil Archer"
},
"description": "This is the human-readable version of the SKOS concept scheme developed from the Corine Land Cover Classes published by the European Environment Agency. In any variance between the EEA documentation and this document, the original documentation is authoritative.",
"example_uri": "http://www.w3.org/2015/03/corine#clc123",
"homepage": "https://www.w3.org/2015/03/corine",
"name": "Corine Land Cover Nomenclature",
"prefix": "CLC",
"version": "2015"
},
"CO_020": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "FAO/Bioversity Multi-Crop Passport Descriptors V.2.1 [MCPD V.2.1] standard",
"example_uri": "http://www.cropontology.org/rdf/CO_020:0000015",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Multi-Crop Passport Ontology",
"prefix": "CO_020",
"repository": "https://github.com/bioversity/multi-crop-passport-descriptor-ontology"
},
"CO_121": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Defines growth stages of wheat",
"example_uri": "http://www.cropontology.org/rdf/CO_121:0000072",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Wheat Plant Anatomy and Development Ontology",
"prefix": "CO_121",
"publication": "http://pantheon.generationcp.org/index.php?option=com_content&task=view&id=472&Itemid=35",
"repository": "https://github.com/bioversity/wheat-plant-anatomy-and-development-ontology",
"version": "1.0"
},
"CO_125": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project (http://www.cropontology.org), created in 2008 by the CGIAR, as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://purl.obolibrary.org/obo/CO_125_0000122",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Banana Anatomy",
"prefix": "CO_125",
"repository": "https://github.com/bioversity/banana-anatomy-ontology"
},
"CO_320": {
"contact": {
"email": "j.detras@cgiar.org",
"name": "Jeffrey A. Detras"
},
"description": "Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables",
"example_uri": "http://www.cropontology.org/rdf/CO_320:0000600/5",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Rice Ontology",
"prefix": "CO_320",
"repository": "https://github.com/Planteome/CO_320-rice-traits",
"version": "March 2016"
},
"CO_321": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Wheat Trait Dictionary in template v5.",
"example_uri": "http://www.cropontology.org/rdf/CO_321:0000238",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Wheat Ontology",
"prefix": "CO_321",
"repository": "https://github.com/Planteome/CO_321-wheat-traits",
"version": "Feb 2016"
},
"CO_322": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project (http://www.cropontology.org),as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_322:0000850",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Maize Ontology",
"prefix": "CO_322",
"repository": "https://github.com/Planteome/CO_322-maize-traits",
"version": "September 2016"
},
"CO_323": {
"contact": {
"email": "r.verma@cgiar.org",
"name": "Ramesh Verna"
},
"description": "Reference Plant Ontologies are being developed in the context of the Plantome project and are being integrated with the Crop Ontology, which provides harmonized breeder's trait names, measurement methods, scales, and standard variables for many crops. The barley Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"example_uri": "http://www.cropontology.org/rdf/CO_323:0000005/4",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Barley Ontology",
"prefix": "CO_323",
"repository": "https://github.com/Planteome/CO_323-barley-traits",
"version": "1.2"
},
"CO_324": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Sorghum TDv5 Ontology",
"example_uri": "http://www.cropontology.org/rdf/CO_324:0000660",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Sorghum Ontology",
"prefix": "CO_324",
"repository": "https://github.com/Planteome/CO_324-sorghum-traits",
"version": "1.0"
},
"CO_325": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Banana Trait Dictionary in template 5 - characterization and breeding variables, drought experiment variables.",
"example_uri": "http://www.cropontology.org/rdf/CO_325:0000267",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Banana Ontology",
"prefix": "CO_325",
"repository": "https://github.com/Planteome/CO_325-banana-traits",
"version": "April 2019"
},
"CO_326": {
"contact": {
"email": "coming@coming.com",
"name": "Stephanie Bocs Sidibe"
},
"description": "Coconut Ontology v1.0 - Coconut trait dictionary started by CIRAD, based on the \"Guidelines for collecting coconut germplasm characterisation data during prospecting missions\", COGENT (to be published); the \"Descriptors for Coconut, (Cocos nucifera L.)\", IPGRI (1995); and the \"Manual on standardized research techniques in coconut breeding\", IPGRI (1996).",
"homepage": "https://cropontology.org/term/CO_326:ROOT",
"license": "CC-BY-4.0",
"name": "Coconut Ontology",
"prefix": "CO_326",
"version": "1.0"
},
"CO_327": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Pearl millet Trait Dictionary in template 5.",
"example_uri": "http://www.cropontology.org/rdf/CO_327:0000185",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Pearl Millet Ontology",
"prefix": "CO_327",
"repository": "https://github.com/Planteome/CO_327-pearl-millet-traits",
"version": "April 2016"
},
"CO_330": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "(to come)",
"example_uri": "http://www.cropontology.org/rdf/CO_330:0000056/2",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Potato Ontology",
"prefix": "CO_330",
"repository": "https://github.com/Planteome/CO_330-potato-traits",
"version": "december 2017"
},
"CO_331": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Sweet Potato Trait Dictionary in template v5",
"example_uri": "http://www.cropontology.org/rdf/CO_331:0000601/1",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Sweet Potato Ontology",
"prefix": "CO_331",
"repository": "https://github.com/Planteome/CO_331-sweetpotato-traits",
"version": "June 2016"
},
"CO_333": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRA, Geves, ITB, UnversitΓ© d'Angers) and breeding companies (Florimond Desprez).",
"example_uri": "http://www.cropontology.org/rdf/CO_333:0001137",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Beet Ontology",
"prefix": "CO_333",
"repository": "https://forgemia.inra.fr/urgi-is/ontologies/-/tree/develop/Beet",
"version": "November 2017"
},
"CO_334": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project, as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_334:0100676",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Cassava Ontology",
"prefix": "CO_334",
"publication": "http://www.cropontology.org/",
"repository": "https://github.com/Planteome/CO_334-cassava-traits",
"version": "February 2016"
},
"CO_335": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project, as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_335:0000475/4",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Common Bean Ontology",
"prefix": "CO_335",
"repository": "https://github.com/Planteome/CO_335-common-bean-traits",
"version": "August 2014"
},
"CO_336": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Soybean Trait Dictionary in template v5",
"example_uri": "http://www.cropontology.org/rdf/CO_336:0000230/2",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Soybean Ontology",
"prefix": "CO_336",
"repository": "https://github.com/Planteome/CO_336-soybean-traits",
"version": "July 2015"
},
"CO_337": {
"contact": {
"email": "tm.shah@cgiar.org",
"name": "Trushar Shah"
},
"description": "This ontology is a part of the the Crop Ontology project , as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_337:0000006",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Groundnut Ontology",
"prefix": "CO_337",
"repository": "https://github.com/Planteome/CO_337-groundnut-traits",
"version": "Sept 2015"
},
"CO_338": {
"contact": {
"email": "tm.shah@cgiar.org",
"name": "Trushar Shah"
},
"description": "This ontology is a part of the the Crop Ontology project, as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_338:0000344",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Chickpea Ontology",
"prefix": "CO_338",
"repository": "https://github.com/Planteome/CO_338-chickpea-traits",
"version": "July 2015"
},
"CO_339": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project, as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_339:0000117",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Lentil Ontology",
"prefix": "CO_339",
"repository": "https://github.com/Planteome/CO_339-lentil-traits",
"version": "July 2015"
},
"CO_340": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project (http://www.cropontology.org), created in 2008 by the CGIAR, as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_340:0000388/4",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Cowpea Ontology",
"prefix": "CO_340",
"publication": "http://www.cropontology.org/",
"repository": "https://github.com/Planteome/CO_340-cowpea-traits",
"version": "August 2015"
},
"CO_341": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Pigeonpea Trait Dictionary in template v5",
"example_uri": "http://www.cropontology.org/rdf/CO_341:0000015",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Pigeon Pea Ontology",
"prefix": "CO_341",
"repository": "https://github.com/Planteome/CO_341-pigeonpea-traits",
"version": "July 2015"
},
"CO_343": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Yam trait ontology",
"example_uri": "http://www.cropontology.org/rdf/CO_343:0000357",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Yam Ontology",
"prefix": "CO_343",
"repository": "https://github.com/Planteome/CO_343-yam-traits",
"version": "Feb 2017"
},
"CO_345": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project (http://www.cropontology.org), as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_345:0000044",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Brachiaria Ontology",
"prefix": "CO_345",
"repository": "https://github.com/Planteome/CO_345-brachiaria-traits",
"version": "Oct 2016"
},
"CO_346": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project , as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_346:0000095",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Mungbean Ontology",
"prefix": "CO_346",
"repository": "https://agroportal.lirmm.fr/ontologies/CO_346",
"version": "Oct 2016"
},
"CO_347": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project, as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_347:0000108",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Castor Bean Ontology",
"prefix": "CO_347",
"repository": "https://github.com/Planteome/CO_347-castorbean-traits",
"version": "March 2017"
},
"CO_348": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "helpdesk cropontology"
},
"description": "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France).",
"example_uri": "http://www.cropontology.org/rdf/CO_348:1000012",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Brassica Ontology",
"prefix": "CO_348",
"repository": "https://github.com/Brassica-Trait-Ontology/brato",
"version": "November 2017"
},
"CO_350": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Oat trait dictionary commissioned by Oat Global (http://oatglobal.org/) to hold the traits used in the T3/Oat database (http://triticeaetoolbox.org/oat/).",
"example_uri": "http://www.cropontology.org/rdf/CO_350:0000091",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Oat Ontology",
"prefix": "CO_350",
"repository": "https://github.com/Planteome/CO_350-oat-traits",
"version": "1.0"
},
"CO_356": {
"contact": {
"email": "cyril.pommier@inrae.fr",
"name": "Cyril Pommier"
},
"description": "Grape Ontology including OIV and bioversity descriptors.",
"example_uri": "http://www.cropontology.org/rdf/CO_356:1000182",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Vitis Ontology",
"prefix": "CO_356",
"repository": "https://forgemia.inra.fr/urgi-is/ontologies/-/tree/develop/Vitis"
},
"CO_357": {
"name": "Woody Plant Ontology",
"prefix": "CO_357"
},
"CO_358": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project, as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_358:0000215",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Cotton Ontology",
"prefix": "CO_358",
"repository": "https://github.com/Planteome/CO_358-cotton-traits",
"version": "2020-01-03"
},
"CO_359": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "To add",
"example_uri": "https://cropontology.org/rdf/CO_359:0000568",
"homepage": "https://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Sunflower Ontology",
"prefix": "CO_359",
"repository": "https://github.com/Planteome/CO_359-sunflower-traits",
"version": "2019-12-16"
},
"CO_360": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Sugar Kelp trait ontology",
"example_uri": "http://www.cropontology.org/rdf/CO_360:0000085",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Sugar Kelp Ontology",
"prefix": "CO_360",
"repository": "https://github.com/Planteome/CO_360-sugar-kelp-traits",
"version": "June 2019"
},
"CO_365": {
"contact": {
"email": "ICARDA-ethiopia@cgiar.org",
"name": "ICARDA Ethiopia"
},
"description": "to add",
"example_uri": "http://www.cropontology.org/rdf/CO_365:0000146",
"homepage": "http://www.cropontology.org",
"license": "CC-BY-4.0",
"name": "Fababean Ontology",
"prefix": "CO_365",
"repository": "https://github.com/Planteome/CO_365-faba-bean-traits",
"version": "2019-10-15"
},
"CO_366": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "This ontology is a part of the the Crop Ontology project , as an essential source of traits and variables to support the standardization of the breeding databases.",
"example_uri": "http://www.cropontology.org/rdf/CO_366:0000253/9",
"homepage": "http://www.cropontology.org",
"license": "CC-BY-4.0",
"name": "Bambara Groundnut Ontology",
"prefix": "CO_366",
"repository": "https://github.com/Planteome/CO_366-bambara-goundnut-traits",
"version": "2019-12-23"
},
"CO_367": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Quinoa Ontology database of the Crop Ontology (CO_367) of the Generation Challenge Program (GCP) describe traits variables of Quinoa Germinate Database http://germinate.quinoadb.org. Quinoa Phenotyping Consortium Creation Date 23.05.2021",
"homepage": "https://cropontology.org/term/CO_367:ROOT",
"license": "CC-BY-4.0",
"name": "Quinoa Ontology",
"prefix": "CO_367",
"publication": "https://doi.org/10.3390/plants10091759"
},
"CO_369": {
"contact": {
"email": "coming@coming.com",
"name": "Bryce Meyering"
},
"description": "This ontology describes a standard trait lexicon used in phenotyping the forage and pulse crop, Sainfoin (Onobrychis viciifolia), with the intention of increasing trait consistency across different breeding programs.",
"homepage": "https://cropontology.org/term/CO_369:ROOT",
"license": "CC-BY-4.0",
"name": "Sainfoin Ontology",
"prefix": "CO_369",
"publication": "https://doi.org/10.3389/fpls.2023.1177406",
"repository": "https://github.com/Planteome/CO_369-sainfoin-traits"
},
"CO_370": {
"contact": {
"email": "ekaterina.chuprikova@eurac.edu",
"name": "Ekaterina Chuprikova"
},
"description": "Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales.",
"example_uri": "https://cropontology.org/rdf/CO_370:0001028",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Apple Ontology",
"prefix": "CO_370",
"publication": "https://doi.org/10.5194/egusphere-egu21-15804",
"repository": "https://github.com/echuprikova/AppleCropOntology",
"version": "1.1"
},
"CO_371": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Blueberry (Vaccinium) ontology defines crop traits and variables to support the standardization of phenotypic data collection for blueberry breeding programs in the USA. The ontology provides a description of agronomic, biochemical, morphological, phenological, physiological, quality, abiotic and biotic stress traits with their methods and scales used for each trait.",
"homepage": "https://cropontology.org/term/CO_371:ROOT",
"license": "CC-BY-4.0",
"name": "Blueberry Ontology",
"prefix": "CO_371",
"repository": "https://github.com/Planteome/CO_371-blueberry-traits"
},
"CO_715": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Describes experimental design, environmental conditions and methods associated with the crop study/experiment/trail and their evaluation",
"example_uri": "http://purl.obolibrary.org/obo/CO_715_0000054",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Crop Research Ontology",
"prefix": "CO_715",
"repository": "https://github.com/bioversity/crop-research-ontology",
"version": "1.0"
},
"CROPUSAGE": {
"contact": {
"email": "catherine.roussey@inrae.fr",
"name": "Catherine Roussey"
},
"description": "An RDF vocabulary for describing the basic structure and content of concept schemes such as thesauri, classification schemes, subject heading lists, taxonomies, 'folksonomies', other types of controlled vocabulary, and also concept schemes embedded in glossaries and terminologies., Les sources utilisées sont le registre parcellaire, le larousse agricole, wikipédia, le catalogue officiel des espèces et variétés de plantes cultivées en France du GEVES, les fiches \"les plantes fourragères pour les pairies\" du GNIS, la base Ephy, la liste des cultures à utiliser pour renseigner le descriptif des parcelles et les statistiques agricoles annuelle de l'Agreste, les tables du catalogue de l'Acta publié en 2021. Concernant les légumes et leur classification nous avons cherché les points communs entre plusieurs sources: Wikipedia, Bonduelle, FranceAgriMer, Encyclopedia Universalis, AM Nagelseim, la ferme du Bec Hellouin. A notre qu'il n'existe pas de consensus sur la classification des legumes. Cette classification est utilisée pour organiser les Bulletins de Santé du Végétal (BSV) et les fiches GECO. Cette classification n'est pas complète et aura besoin d'évoluer au cours du temps en fonction des besoins. auteur est catherine roussey de l'INRAE catherine.roussey@inrae.fr, les tables du catalogue de l'Acta publié en 2021. \nConcernant les légumes et leur classification nous avons cherché les points communs entre plusieurs sources: Wikipedia, la ferme du Bec Hellouin. A notre qu'il n'existe pas de consensus sur la classification des legumes.\n\nCette classification est utilisée pour organiser les Bulletins de Santé du Végétal (BSV) et les fiches GECO. Cette classification n'est pas complète et aura besoin d'évoluer au cours du temps en fonction des besoins.\nauteur est catherine roussey de l'INRAE catherine.roussey@inrae.fr",
"example_uri": "http://ontology.inrae.fr/frenchcropusage/Ray_grass",
"homepage": "http://ontology.inrae.fr/pmwiki.php/Site/FrenchCropUsage",
"license": "CC-BY-4.0",
"name": "French Crop Usage thesaurus (Classification des plantes cultivΓ©es en France en fonction des usages)",
"prefix": "CROPUSAGE",
"repository": "https://gitlab.irstea.fr/copain/frenchcropusage",
"version": "3.3"
},
"CSOPRA": {
"contact": {
"email": "manuel.martin@inrae.fr",
"name": "Manuel Martin"
},
"description": "This ontology was created to support the development of the csopra libraries and the modelToolBox, which enables the modeling of soil organic changes, as a result of soil management, such as agricultural practices. It also aims at enabling interoperability between various data sources and various crop or biogeochemical models.",
"name": "Soil organic carbon storage and agricultural practices modeling",
"prefix": "CSOPRA",
"version": "2.0"
},
"CVO": {
"contact": {
"email": "akane@affrc.go.jp",
"name": "Akane Takezaki"
},
"description": "Crop Vocabulary provides taxonomy of crops in farming. Terms are mainly collected in agricultural documents published by Japanese Government. Crop is basically classified by plant but some are classified by cultivation method, edible parts, and and so on. Links to AGROVOC and NCBI taxonomy are included.",
"example_uri": "http://www.w3.org/2004/02/skos/core#Concept",
"homepage": "http://www.cavoc.org/cvo.php",
"license": "CC0-1.0",
"name": "Crop Vocabulary",
"prefix": "CVO",
"version": "2.03"
},
"DATA4CPLUS": {
"contact": {
"email": "julien.demenois@cirad.fr",
"name": "Julien Demenois"
},
"description": "DATA4C+ is a thesaurus classifying and defining land management practices in agriculture and forestry for soil carbon storage. DATA4C+ thesaurus is focussed on land management practices identified in the scientific literature as drivers of soil organic carbon (SOC) changes. DATA4C+ thesaurus aim was to fill the gap of lack of a comprehensive thesaurus for land management practices which directly or indirectly affect SOC dynamics. DATA4C+ thesaurus was developped by Cirad, INRAE and IRD during the ANR DATA4C+ project (https://www.data4c-plus-project.fr/en, Projet ANR- 19-DATA-0005). DATA4C+ thesaurus contains 224 classified and defined terms related to land management practices in agriculture and forestry. DATA4C+ thesaurus is organized as a hierarchical tree reflecting the drivers of SOC storage. To have access to the definition of a given term, the user must click on it in the tree. Then a βpop upβ appears with the definition of the term and the source of the definition. A link to the source of the definition (URL or DOI) is given for each term. By clicking on this link, a new web page appears.",
"example_uri": "http://data4c-plus.net/admin/thesaurus/read/100",
"homepage": "http://data4c-plus.net/admin/thesaurus/index",
"license": "CC-BY-4.0",
"name": "Thesaurus to define land management practices in agriculture and forestry for soil carbon storage",
"prefix": "DATA4CPLUS",
"publication": "https://soil.copernicus.org/articles/9/89/2023/",
"version": "version 0.2 - February 2023"
},
"DEMETER-AIM": {
"contact": {
"email": "rpalma@man.poznan.pl",
"name": "Raul Palma"
},
"description": "The DEMETER Agri Profile is a master profile importing focused specific profiles/modules of DEMETER AIM.",
"example_uri": "http://purl.oclc.org/NET/ssnx/qu/dim#Concentration",
"homepage": "https://gitlab.com/demeterproject/wp2/agriculturalinformationmodel/domainspecificontologies",
"license": "CC-BY-4.0",
"name": "DEMETER Agriculture Information Model",
"prefix": "DEMETER-AIM",
"repository": "https://github.com/rapw3k/DEMETER/tree/master/models",
"version": "3.0"
},
"DSW": {
"contact": {
"email": "steve.baskauf@vanderbilt.edu",
"name": "Steve Baskauf"
},
"description": "Version 0.4 to 1.0 fixed reversed dsw:locates and dsw:locatedAt. Added labels. Changed comments and descriptions to conform to DC and DwC precedent. Added subClassOf relations to RO hasEvidence and isEvidenceFor. Specified preferred direction for inverse object property pairs., Changes from version 0.2.1 to version 0.3: removal of all functional and inverse function properties of object property terms, use of dwctype classes, deprecation of terms replaced by dwciri: terms, removal of references to TDWG Ontology., Changes from version 0.3 to 0.4 change DwC class namespace from dwctype: to dwc: to follow class proposal, removed references to TDWG TaxonConcept ontology; deprecated terms that now have equivalent terms in Darwin Core., Change from version 1.0 to 1.0.1 Add CC0 license.",
"example_uri": "http://xmlns.com/foaf/0.1/Agent",
"homepage": "https://github.com/darwin-sw/",
"license": "CC0-1.0",
"name": "Darwin-SW",
"prefix": "DSW",
"repository": "https://github.com/darwin-sw/dsw",
"version": "1.0.1"
},
"DURUM_WHEAT": {
"contact": {
"email": "patrice.buche@inra.fr",
"name": "Patrice Buche"
},
"description": "The durum wheat ontology (DURUM_WHEAT) is dedicated to the sustainability analysis of the durum wheat chain.Current data available on this ontology concern durum wheat quality criteria criteria used in different countries (Moisture content rate, chemical content, etc.).",
"example_uri": "http://opendata.inra.fr/resources/Durum_Wheat#rgt_musclur",
"homepage": "http://lovinra.inra.fr/",
"license": "CC-BY-4.0",
"name": "Durum Wheat",
"prefix": "DURUM_WHEAT",
"version": "V-2019/07/04"
},
"E-PHY": {
"contact": {
"email": "syphax.bouazzouni@lirmm.fr",
"name": "Syphax Bouazzouni"
},
"description": "Le catalogue des produits phytopharmaceutiques de lβANSES en une base de connaissances OWL dont le modΓ¨le ontologique est celui de la base de donnΓ©es E-Phy (https://ephy.anses.fr/) et les instances sont les produits qui y sont listΓ©s, alignΓ©es avec dβautres ressources sΓ©mantiques tel que le thΓ©saurus French Crop Usage pour les cultures et lβontologie CHEBI pour les familles chimiques. Cependant considΓ©rant que nos organismes ne sont pas des autoritΓ©s pour ce catalogue, notre modΓ¨le de donnΓ©es est volontairement βbridΓ©β pour Γͺtre complΓ¨tement rΓ©tro-compatible avec la base dβorigine de faΓ§on Γ facilement mettre Γ jour notre ontologie Γ partir de nouveaux exports de lβANSES., E-Phy est une base de connaissances (ontologie+instances) tirΓ©e de la base de donnΓ©es E-Phy de l'ANSES (https://ephy.anses.fr) qui contient le catalogue des produits phytopharmaceutiques et de leurs usages, des matiΓ¨res fertilisantes et des supports de culture autorisΓ©s en France. Cette base de connaissances a Γ©tΓ© crΓ©e dans le cadre du projet ANR D2KAB par le LIRMM et l'INRAE. Elle a vocation Γ proposer une version RDF de la base de donnΓ©es E-Phy.",
"license": "https://creativecommons.org/licenses/by-nd/4.0",
"name": "Catalogue des produits phytopharmaceutiques et de leurs usages, des matières fertilisantes et des supports de culture autorisés en France",
"prefix": "E-PHY",
"version": "1.1"
},
"EBO": {
"contact": {
"email": "emilie.fernandez@inrae.fr",
"name": "Emilie Fernandez"
},
"description": "An ontology for describing environmental biorefinery data for the information system EnviBIS, using the application core ontology OESO and the core ontology PO2.",
"example_uri": "http://www.opensilex.org/vocabulary/oeso#PhDThesis",
"license": "CC-BY-4.0",
"name": "Environmental Biorefinery Ontology",
"prefix": "EBO",
"version": "Version 2 (2023) created by LBE - INRAE"
},
"ECTO": {
"contact": {
"email": "annethessen@gmail.com",
"name": "Anne Thessen"
},
"description": "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology).",
"example_uri": "http://purl.obolibrary.org/obo/ECTO_9000201",
"homepage": "https://github.com/EnvironmentOntology/environmental-exposure-ontology",
"license": "CC0-1.0",
"name": "Environmental Conditions, Treatments and Exposures Ontology",
"prefix": "ECTO",
"publication": "https://doi.org/10.1186/s13326-023-00283-x",
"repository": "https://github.com/EnvironmentOntology/environmental-exposure-ontology",
"version": "2023-02-14"
},
"EDAM": {
"name": "EDAM bioinformatics operations, data types, formats, identifiers and topics",
"prefix": "EDAM"
},
"EFO": {
"contact": {
"email": "efo-users@lists.sourceforge.net",
"name": "EFO User List"
},
"description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for projects such as the GWAS catalog. It combines parts of several biological ontologies, such as UBERON anatomy, ChEBI chemical compounds, and Cell Ontology. EFO is developed by the EMBL-EBI Samples, Phenotypes and Ontologies Team (SPOT). We also add terms for external users when requested.",
"example_uri": "http://www.orpha.net/ORDO/Orphanet_1390",
"homepage": "http://www.ebi.ac.uk/efo/",
"license": "Apache 2.0 License",
"name": "Experimental Factor Ontology",
"prefix": "EFO",
"repository": "https://github.com/EBISPOT/efo",
"version": "3.68.0"
},
"ENVO": {
"contact": {
"email": "pier.buttigieg@awi.de",
"name": "Pier Luigi Buttigieg (ORCID: orcid.org/0000-0002-4366-3088)"
},
"description": "ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities",
"example_uri": "http://purl.obolibrary.org/obo/ENVO_00005746",
"homepage": "http://environmentontology.org/",
"license": "CC0-1.0",
"name": "Environment Ontology",
"prefix": "ENVO",
"publication": "https://doi.org/10.1186/s13326-016-0097-6",
"repository": "https://github.com/EnvironmentOntology/envo",
"version": "2024-07-01"
},
"EO": {
"contact": {
"email": "cooperl@science.oregonstate.edu",
"name": "Laurel Cooper"
},
"description": "The Plant Environment Ontology describes the treatments,growing conditions, and/or study types used in various types of plant biology experiments. The subjects of the studies may also include in vitro plant structures (PO:0000004). A plant treatment is the most specific,and may be a component of a plant growing condition, and the plant study type. The broadest classes are the plant study types where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own and it may also involve instances of biotic and abiotic treatments and different growing conditions.",
"example_uri": "http://purl.obolibrary.org/obo/EO_0007263",
"homepage": "http://planteome.org/",
"license": "CC-BY-4.0",
"name": "Plant Environment Ontology",
"prefix": "EO",
"publication": "http://wiki.plantontology.org/index.php/Category:Publications",
"repository": "https://github.com/Planteome/plant-experimental-conditions-ontology",
"version": "releases/2023-11-10"
},
"EOL": {
"contact": {
"email": "matthieu.reichstadt@inrae.fr",
"name": "Matthieu Reichstadt"
},
"description": "L'ontologie EOL décrit les conditions d'environnement des élevages d'animaux domestiques. Elle décrit plus particulièrement les modalités de l'alimentation, de l'environnement, de la structure des élevages et des systèmes d'élevage., The EOL ontology describes environmental conditions of livestock breeding. It includes feeding modalities, the structure of breeding systems and their environment.",
"example_uri": "http://opendata.inra.fr/EOL/EOL_0000301",
"homepage": "http://www.atol-ontology.com/",
"license": "CC-BY-4.0",
"name": "Environment Ontology for Livestock",
"prefix": "EOL",
"publication": "http://www.atol-ontology.com/rb/fr/6"
},
"FALDO": {
"contact": {
"email": "jerven.bolleman@isb-sib.ch",
"name": "Jerven Bolleman"
},
"description": "FALDO is the Feature Annotation Location Description Ontology. It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources. The aim of this ontology is to describe the position of a sequence region or a feature. It does not aim to describe features or regions itself, but instead depends on resources such as the Sequence Ontology or the UniProt core ontolgy.",
"example_uri": "http://biohackathon.org/resource/faldo#CollectionOfRegions",
"homepage": "http://aber-owl.net/ontology/FALDO/#/",
"license": "CC0-1.0",
"name": "Feature Annotation Location Description Ontology",
"prefix": "FALDO",
"repository": "https://github.com/OBF/FALDO",
"version": "Created at the Biohackathon 2012 and 2013"
},
"FCUO": {
"contact": {
"email": "catherine.roussey@inrae.fr",
"name": "Catherine ROUSSEY"
},
"description": "This ontology specialized the skos model to create a new class Crop subclass of skos:Concept. fcuo:Crop is a defined class. Thus a reasoner like Hermit should be used to classify all the instances of skos:Concept that belongs to the scheme fcuo:thesaurus_FrenchCropUsage as an instance of Crop. FCUO contains also new objet properties and annotation properties dedicated to FCU alignement with taxonomy like TAXREF-LD., ontologie associée au thésaurus Usage des plantes cultivées en France et définissant des relations d'alignements entre les usgaes des plantes définies dans ce thésaurus et les taxonomies scientifiques comme NCBI taxon ou TAXREF-LD., ontology related to the thesaurus French Crop Usage. This ontology defines mapping relations between FCU thesaurus and scientific taxonomies like TAXREF-LD or NCBI taxon., Les sources utilisées sont le registre parcellaire, le larousse agricole, wikipédia, le catalogue officiel des espèces et variétés de plantes cultivées en France du GEVES, les fiches \"les plantes fourragères pour les pairies\" du GNIS, la base Ephy, la liste des cultures à utiliser pour renseigner le descriptif des parcelles et les statistiques agricoles annuelle de l'Agreste, les tables du catalogue de l'Acta publié en 2021. \nConcernant les légumes et leur classification nous avons cherché les points communs entre plusieurs sources: Wikipedia, Bonduelle, FranceAgriMer, Encyclopedia Universalis, AM Nagelseim, la ferme du Bec Hellouin. A notre qu'il n'existe pas de consensus sur la classification des legumes.\n\nCette classification est utilisée pour organiser les Bulletins de Santé du Végétal (BSV) et les fiches GECO. Cette classification n'est pas complète et aura besoin d'évoluer au cours du temps en fonction des besoins.\nauteur est catherine roussey de l'INRAE catherine.roussey@inrae.fr",
"homepage": "http://ontology.inrae.fr/pmwiki.php/Site/FrenchCropUsage",
"license": "CC-BY-4.0",
"name": "French Crop Usage Ontology",
"prefix": "FCUO",
"repository": "https://forgemia.inra.fr/bsv/frenchcropusage",
"version": "1.1"
},
"FLAIR": {
"contact": {
"email": "xavier.delpuech@vignevin.com",
"name": "Xavier DELPUECH"
},
"description": "Ce fichier au format RDF contient les Γ©lΓ©ments d'une modΓ©lisation de l'analyse sensorielle des vins. Cette ontologie a Γ©tΓ© construite lors du projet CASDAR VITISDATACROP (France, 2021-2023). Contacter Xavier DELPUECH pour toute modification dans ce fichier.",
"example_uri": "http://data.vignevin.com/def/wine.descriptors#driedVegetal",
"homepage": "https://github.com/XavierDelpuech/flair",
"license": "CC-BY-4.0",
"name": "Wine Descriptors Ontology",
"prefix": "FLAIR",
"repository": "https://github.com/XavierDelpuech/flair",
"version": "1.1"
},
"FLOPO": {
"contact": {
"email": "robert.hoehndorf@kaust.edu.sa",
"name": "Robert Hoehndorf"
},
"description": "The Flora Phenotype Ontology (FLOPO) is an ontology of phenotypes reported in Floras. The original version was developed at the pro-iBiosphere Hackathon in Leiden. This is the pre-classified version of the ontology. The Flora Phenotype Ontology is generated from the Flora Malesiana, Flora Gabon, Flora of Central Africa, and a collection of Kew's African Floras. Every class in the ontology has at least one taxon annotation. The (draft) taxon annotation are available at http://jagannath.pdn.cam.ac.uk/plant/flora/clean-rerun/",
"example_uri": "http://purl.obolibrary.org/obo/FLOPO_0000003",
"homepage": "https://github.com/flora-phenotype-ontology",
"license": "CC0-1.0",
"name": "Flora Phenotype Ontology",
"prefix": "FLOPO",
"repository": "https://github.com/flora-phenotype-ontology/flopoontology/",
"version": "0.9"
},
"FOBI": {
"contact": {
"email": "polcaes@gmail.com",
"name": "Pol Castellano Escuder"
},
"description": "FOBI (Food-Biomarker Ontology) is an ontology composed of two interconnected sub-ontologies. One is a βFood Ontologyβ consisting of raw foods and multi-component foods while the second is a βBiomarker Ontologyβ containing food intake biomarkers classified by their chemical classes. These two sub-ontologies are conceptually independent but interconnected by different properties. This allows data and information regarding foods and food biomarkers to be visualized in a bidirectional way, going from metabolomics to nutritional data or vice versa. Potential applications of this ontology include the annotation of foods and biomarkers using a well-defined and consistent nomenclature, the standardized reporting of metabolomics workflows (e.g. metabolite identification, experimental design), or the application of different enrichment analysis approaches to analyze nutrimetabolomic data.",
"example_uri": "http://purl.obolibrary.org/obo/FOBI_040001",
"homepage": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology",
"name": "Food-Biomarker Ontology",
"prefix": "FOBI",
"repository": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology",
"version": "1.0.0"
},
"FOODEX2": {
"contact": {
"email": "data@food.gov.uk",
"name": "UK Food Standard Agency"
},
"description": "Food Type identifiers, supporting codes and vocabularies based on the EFSA FoodEx2 (https://www.efsa.europa.eu/en/data/data-standardisation) that are being tested in the development of the FSA's code and data standards repository. These codes may be used within FSA data.",
"example_uri": "http://data.food.gov.uk/codes/foodtype/id/A0TMC",
"homepage": "https://data.food.gov.uk/codes/_foodtype",
"name": "Food Classification and Description System (from FSA Food Type identifiers)",
"prefix": "FOODEX2",
"version": "2"
},
"FOODIE": {
"contact": {
"email": "rpalma@man.poznan.pl",
"name": "Raul Palma"
},
"description": "This release 4.6.3 added missing crop property; release 4.6.2 fixes model regarding DoseUnit that cannot be a codelist, and is defined as datatype, FOODIE ontology has been generated from FOODIE application schema (UML model), Revision 4.6.1, and translated into an ontology according to ISO/DIS 19150-2 using ShapeChange plus several pre and post processing changes. This is a revision of v4.3.2, manually updated to v4.6.1.",
"example_uri": "http://www.opengis.net/ont/gml#CompositeSurface",
"homepage": "http://foodie-cloud.github.io/model/FOODIE.html",
"name": "FOODIE Core Ontology",
"prefix": "FOODIE",
"publication": "https://link.springer.com/chapter/10.1007/978-3-319-33245-1_13",
"repository": "https://git.man.poznan.pl/stash/projects/FOOD/repos/model/",
"version": "4.6.3"
},
"FOODON": {
"contact": {
"email": "damion_dooley@sfu.ca",
"name": "Damion Dooley"
},
"description": "FoodOn is a consortium-driven project to build a comprehensive and easily accessible global farm-to-fork ontology about food, that accurately and consistently describes foods commonly known in cultures from around the world., that accurately and consistently describes foods commonly known in cultures from around the world. See https://foodon.org for more details.",
"example_uri": "http://purl.obolibrary.org/obo/FOODON_03412974",
"homepage": "https://foodon.org",
"license": "CC-BY-3.0",
"name": "FoodOn",
"prefix": "FOODON",
"repository": "https://github.com/FoodOntology/foodon",
"version": "2024-07-12"
},
"GACS": {
"contact": {
"email": "tom@tombaker.org",
"name": "Tom Baker"
},
"description": "The Global Agricultural Concept Scheme (GACS) is a hub for concepts related to agriculture, in multiple languages, for use in Linked Data. The idea for GACS emerged out of discussions at the World Congress of IAALD, the International Association of Agricultural Information Specialists, in July 2013. The Food and Agricultural Organization of the United Nations (FAO), CAB International (CABI), and the National Agricultural Library of the USA (NAL) agreed in October 2013 to explore the feasibility of developing a shared concept scheme by integrating their three thesauri: the AGROVOC Concept Scheme, the CAB Thesaurus (CABT), and NAL Thesaurus (NALT). In the GACS vision, the integration of these three thesauri is but the first step towards the realization of a hub that links to and from the concept schemes beyond the initial three, and in multiple language areas.",
"example_uri": "http://id.agrisemantics.org/gacs/C15137",
"homepage": "http://agrisemantics.org/gacs/",
"name": "Global Agricultural Concept Scheme",
"prefix": "GACS",
"publication": "http://eprints.rclis.org/30221/",
"version": "Beta 1.6"
},
"GALLONT": {
"contact": {
"email": "adeans@psu.edu",
"name": "Andy Deans"
},
"description": "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls., None",
"example_uri": "http://purl.obolibrary.org/obo/GALLONT_0000008",
"homepage": "https://adeans.github.io/gallont/",
"license": "CC0-1.0",
"name": "Plant Gall Ontology",
"prefix": "GALLONT",
"publication": "https://doi.org/10.3897/arphapreprints.e128953",
"repository": "https://github.com/adeans/gallont",
"version": "2024-04-19"
},
"GAO": {
"contact": {
"email": "cyril.pommier@inrae.fr",
"name": "Cyril Pommier"
},
"description": "Describes a list of organs classified by biological function, DΓ©crit une liste d'organes classΓ© par fonction biologique, Describes a list of organs classified by biological function, DΓ©crit une liste d'organes classΓ© par fonction biologique",
"example_uri": "http://opendata.inra.fr/gao:30080",
"license": "https://www.etalab.gouv.fr/licence-ouverte-open-licence",
"name": "Grapevine Anatomy Ontology",
"prefix": "GAO",
"version": "1.0"
},
"GECO": {
"contact": {
"email": "geco@acta.asso.fr",
"name": "GECO support"
},
"description": "Agroecology knowledge management is an application ontology for the description and organization of knowledge to design innovative crop systems. , Gestion des connaissances en agroΓ©cologie est une ontologie dβapplication dΓ©crivant et organisant les connaissances permettant de concevoir des systΓ¨mes de culture innovants.",
"example_uri": "http://www.geco.ecophytopic.fr/geco/TypeConcept/Facteur_De_Contexte",
"homepage": "https://geco.ecophytopic.fr/",
"name": "Agroecology Knowledge Management (GECO ontology)",
"prefix": "GECO"
},
"GEMET": {
"contact": {
"email": "helpdesk@eionet.europa.eu",
"name": "Eionet Helpdesk"
},
"description": "The basic idea for the development of GEMET was to use the best of the presently available excellent multilingual thesauri, in order to save time, energy and funds. GEMET was conceived as a βgeneralβ thesaurus, aimed to define a common general language, a core of general terminology for the environment. Specific thesauri and descriptor systems (e.g. on Nature Conservation, on Wastes, on Energy, etc.) have been excluded from the first step of development of the thesaurus and have been taken into account only for their structure and upper level terminology.",
"example_uri": "http://www.eionet.europa.eu/gemet/concept/5580",
"homepage": "http://www.eionet.europa.eu/gemet/en/about/",
"license": "http://creativecommons.org/licenses/by/2.5/dk",
"name": "GEneral Multilingual Environmental Thesaurus",
"prefix": "GEMET",
"publication": "http://www.eionet.europa.eu/gemet/en/about/#chapter-VII",
"version": "4.2.3"
},
"GFVO": {
"contact": {
"email": "kim@codamono.com",
"name": "Joachim Baran"
},
"description": "The Genomic Feature and Variation Ontology (GFVO) is modeled to represent genomic data using the Resource Description Format (RDF). It is captures the contents of data files that adhere to the Generic Feature Format Version 3 (GFF3, http://www.sequenceontology.org/resources/gff3.html), the General Transfer Format (GTF, http://mblab.wustl.edu/GTF22.html), the Genome Variation Format Version 1 (GVF, http://www.sequenceontology.org/resources/gvf.html), and the Variant Call Format (VCF, http://vcftools.sourceforge.net/specs.html). The creation of the ontology was inspired by previous work of Robert Hoehndorf on RDF2OWL (http://code.google.com/p/rdf2owl).",
"example_uri": "http://www.biointerchange.org/gfvo#BaseQuality",
"homepage": "https://github.com/BioInterchange/Ontologies",
"name": "Genomic Feature and Variation Ontology",
"prefix": "GFVO",
"repository": "https://github.com/BioInterchange/Ontologies",
"version": "1.0.2"
},
"GO": {
"contact": {
"email": "go@geneontology.org",
"name": "Gene Ontology"
},
"description": "The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms.",
"example_uri": "http://purl.obolibrary.org/obo/GO_0015219",
"homepage": "http://www.geneontology.org/",
"license": "CC-BY-4.0",
"name": "Gene Ontology",
"prefix": "GO",
"publication": "http://geneontology.org/page/publications",
"repository": "https://sourceforge.net/projects/geneontology/",
"version": "2024-06-17"
},
"GR-TAX": {
"contact": {
"email": "gr-tax@contact.com",
"name": "gr-tax"
},
"description": "It is a representation of the taxonomy tree in the ontology format. Each term in this ontology can represent subspecies, species, genus, order, class or any rank in the classification. Primarily derived from NCBI Taxonomy, the revisions were made as and when/where required in the rankings. The rank of genome types was added by this project. This taxonomy ontology focuses on the Poaceae (Gramineae) family of plant taxonomy only.",
"example_uri": "http://purl.obolibrary.org/obo/GR_tax_079425",
"homepage": "http://www.gramene.org/",
"name": "Gramene Taxonomy Ontology",
"prefix": "GR-TAX",
"version": "2013"
},
"ICC": {
"contact": {
"email": "faq-hq@fao.org",
"name": "Food and Agriculture Organization of the United Nations (FAO)"
},
"description": "The Indicative Crop Classification (ICC) was developed for the 2020 round of agricultural censuses.",
"example_uri": "http://stats-class.fao.uniroma2.it/ICC/ICC_v1.1/4-04-03",
"homepage": "http://www.fao.org/world-census-agriculture/wcarounds/wca2010/en",
"name": "Indicative Crop Classification",
"prefix": "ICC",
"version": "1.1"
},
"INFRARISK": {
"contact": {
"email": "dumitru.roman@sintef.no",
"name": "Dumitru Roman"
},
"description": "The InfraRisk Ontology: Enabling Semantic Interoperability for Critical Infrastructures at Risk from Natural Hazards. This InfraRisk ontology may be used for representing relevant information about natural hazard events and their impact on infrastructure components. Earthquakes, landslides, and other natural hazard events have severe negative socio-economic impacts.",
"example_uri": "https://www.infrarisk-fp7.eu/vocabs/#Road",
"homepage": "http://vocabs.datagraft.net/infrarisk.html",
"license": "CC-BY-3.0",
"name": "InfraRisk Ontology",
"prefix": "INFRARISK",
"version": "1.0"
},
"INIA-RDM": {
"contact": {
"email": "antonio@spadial.com",
"name": "Antonio J. SΓ‘nchez-Padial"
},
"description": "This ontology is used to describe datasets hosted on Spanish National Institute for Agricultural and Food Research and Technology (INIA) Research Data Repository. It combines terms from dataset ontologies such as DCAT, with some specific terms in Agriculture Research, e.g., keywords based on AGROVOC.",
"example_uri": "http://purl.org/dc/terms/BibliographicResource",
"homepage": "http://data.inia.es/def/",
"license": "http://purl.org/NET/rdflicense/cc-by4.0",
"name": "INIA Research Datasets",
"prefix": "INIA-RDM",
"version": "0.0.2"
},
"INRAETHES": {
"contact": {
"email": "thesaurusINRAE@inrae.fr",
"name": "ComitΓ© ThΓ©saurus INRAE"
},
"description": "INRAE Thesaurus is the open and shared thesaurus covering INRAE's research fields. It serves as a controled vocabulary within the institute for indexing and annotating documents, web pages, descriptions of activities, datasets, etc. for research or information analysis purposes. It is maintained by an editorial committee under the responsibility of INRAE DipSO.",
"example_uri": "http://opendata.inrae.fr/thesaurusINRAE/c_10060",
"homepage": "https://thesaurus.inrae.fr",
"license": "CC-BY-4.0",
"name": "INRAE Thesaurus",
"prefix": "INRAETHES",
"repository": "https://forgemia.inra.fr/dipso/thesaurus-inrae/-/tree/main",
"version": "2.0"
},
"IRRIG": {
"contact": {
"email": "Catherine.roussey@irstea.fr",
"name": "Catherine Roussey"
},
"description": "IRRIG is an Irrigation Ontology for experimentation in TSCF, Irstea Clermont-Fd.",
"example_uri": "http://www.w3id.org/def/irrig#RootZoneDailyAverageMoistureObservation",
"homepage": "https://w3id.org/def/irrig",
"license": "CC-BY-4.0",
"name": "Irrigation Ontology",
"prefix": "IRRIG",
"repository": "https://github.com/Irstea/irrig",
"version": "1.0.0"
},
"LANDVOC": {
"contact": {
"email": "info@landvoc.org",
"name": "Land Portal Foundation"
},
"description": "LandVoc is a thesaurus (controlled vocabulary) covering 310 concepts related to all areas of interest to the land community including land administration, land governance, land use and cover etc. It is built by the Land Portal Foundation and relies on a subset of AGROVOC concepts.",
"example_uri": "http://aims.fao.org/aos/agrovoc/c_aca7ac6d",
"homepage": "http://landvoc.org",
"license": "CC-BY-3.0",
"name": "Linked Land Governance Thesaurus",
"prefix": "LANDVOC",
"version": "2.0"
},
"LBO": {
"contact": {
"email": "jreecy@iastate.edu",
"name": "Jim Reecy"
},
"description": "A vocabulary for buffalo, cattle, chicken, goat, horse, pig, and sheep breeds.",
"example_uri": "http://purl.obolibrary.org/obo/LBO_0000700",
"name": "Livestock Breed Ontology",
"prefix": "LBO",
"repository": "https://github.com/AnimalGenome/livestock-breed-ontology",
"version": "9.5"
},
"LEXEAU": {
"contact": {
"email": "jeanlouisjanin@gmail.com",
"name": "Jean-Louis Janin"
},
"description": "L'ontologie LEXEAU est la source d'un lexique de l'eau bilingue des services de l'eau et du dΓ©veloppement durable. Elle a Γ©tΓ© conΓ§ue et dΓ©veloppΓ©e dans le cadre d'un projet global (projet LexeauΒ) pour amΓ©liorer l'intercomprΓ©hension des acteurs du domaine : usagers de l'eau publics et privΓ©s, Γ©lus europΓ©ens, nationaux et locaux, dirigeants et salariΓ©s d'entreprise, ingΓ©nieurs et scientifiques, techniciens de maintenance, juristes, fonctionnaires, journalistes, etc. Les entitΓ©s du lexique sont des unitΓ©s lexicales, des entitΓ©s du monde et des acronymes. Les unitΓ©s lexicales sont spΓ©cifiques (propres au domaine de l'eau) ou auxiliaires (partagΓ©es avec d'autres domaines de connaissance). Les unitΓ©s lexicales spΓ©cifiques sont prΓ©fixΓ©es \"1-TS\", \"2-TA\" ou \"3-C\" lorsqu'elles sont utilisΓ©es, respectivement, dans la strate discursive spΓ©cifique technico-scientifique, technico-administrative ou courante. Les unitΓ©s lexicales auxiliaires sont prΓ©fixΓ©es \"A\". Les unitΓ©s lexicales sont dΓ©rivΓ©es des libellΓ©s des classes de l'ontologie et des entitΓ©s contrΓ΄lΓ©es. Les entitΓ©s du monde du lexique sont des objets concrets, \"rΓ©fΓ©rents\" de l'unitΓ© lexicale dΓ©rivΓ©e du libellΓ© de leur classe d'origine dans l'ontologie. Les articles du lexique sont introduits en commentaire (annotation \"comment\") du libellΓ© de l'unitΓ© lexicale (sous le libellΓ© de la classe), du libellΓ© de l'entitΓ© contrΓ΄lΓ©e, rΓ©putΓ© libellΓ© de l'unitΓ© lexicale, ou du libellΓ© de l'entitΓ© monde. Les relations lexicales qui suivent chaque article sont dΓ©rivΓ©es de la hiΓ©rarchie des classes, de l'instanciation des classes et des \"assertions de propriΓ©tΓ©\" associΓ©es aux propriΓ©tΓ©s de l'ontologie. Un graphe conceptuel est Γ©ditΓ© pour chaque unitΓ© lexicale et exportΓ© comme \"image\" (format \"png\"). L'Γ©dition Γ©lectronique du lexique avec des liens hypertexte, y compris les graphes conceptuels, est directement issue de l'ontologie. Elle est disponible sur demande. Face Γ la transition Γ©nergΓ©tique et Γ l'adaptation climatique, la structure de l'ontologie est bien adaptΓ©e Γ la mise Γ jour du lexique des services de l'eau et du dΓ©veloppement durable et Γ son extension Γ d'autres thΓ¨mes tels que le dessalement de l'eau, le recyclage des eaux usΓ©es, l'exploitation pΓ©renne des eaux souterraine, la protection du littoral, ainsi que la prΓ©vention et la rΓ©paration des dommages liΓ©s aux sΓ©cheresses et aux inondations. Bordeaux, le 7 juin 2024 Jean-Louis Janin",
"license": "CC-BY-4.0",
"name": "A stratified lexicon of water related geophysical and textual data",
"prefix": "LEXEAU",
"version": "1.8"
},
"LHO": {
"contact": {
"email": "miel.hostens@ugent.be",
"name": "Miel Hostens"
},
"description": "The Livestock Health Ontology (LHO) contains information on the health and well-being of livestock animal species such as cattle, pigs, and poultry. Furthermore, it represents the explicit structured and standardized framework for specific domain knowledge and data integration of livestock species. During the development process, knowledge can be retrieved from domain experts, and after the retrieving process, the prototype is designed for reasoning and planning of data related to cattle, pigs, and poultry. Moreover, LHO contains information regarding farms Identifications, their samples, geolocation, breed, diagnostic tests, Pathogen identifications, and Pathogen results for specific bacteria such as Histophilus Somni (HS), Mannheimia Haemolytica (MH), Pasteurella Multocida (PM), Bovine Coronavirus (BCV) bacterial mycoplasma and aerobic culture results for the respiratory diseases in cattle. This information is represented as concepts of classes, subclasses, and their relationship in the form of object and data properties. For pigs, it includes farm type, age, weight, pig stages and pathogens like PRRS, SwineInfluenza, and M_Hyponemoniea. In poultry, LHO incorporates farm type, with specific pathogen names such as Infectious Bronchitis (IB), providing a concise overview of health aspects across livestock species. Incorporating pathogen identification results, whether positive or negative, within the Livestock Health Ontology (LHO), not only enhances data organization but also supports projects like DECIDE EU Horizon 2020. By providing a structured framework for analyzing disease emergence and options for diagnostic confirmation, LHO contributes to the development of robust data-driven decision-support tools in livestock health management.",
"name": "Livestock Health Ontology",
"prefix": "LHO",
"version": "V1.1"
},
"LPT": {
"contact": {
"email": "jreecy@iastate.edu",
"name": "Jim Reecy"
},
"description": "The Livestock Product Trait (LPT) Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.",
"example_uri": "http://purl.obolibrary.org/obo/LPT_0000156",
"homepage": "https://www.animalgenome.org/bioinfo/projects/lpt/",
"name": "Livestock Product Trait Ontology",
"prefix": "LPT",
"repository": "https://github.com/AnimalGenome/livestock-product-trait-ontology",
"version": "4.3"
},
"MEAT-T": {
"contact": {
"email": "vocabulaires-ouverts@inrae.fr",
"name": "Vocabulaires Ouverts"
},
"description": "The meat thesaurus describes different facets of the meat production chain, such as the meat market, breed, slaughtering, culinary preparations, etc. It contains terms and definitions in French and English. It was derived and adapted from the Dictionnaire de la viande, AcadΓ©mie de la viande (France). Publisher, Autres voix, 2012. ISBN, 2918237086, 9782918237082",
"example_uri": "http://opendata.inrae.fr/ThViande/C707",
"license": "CC-BY-4.0",
"name": "Meat Thesaurus",
"prefix": "MEAT-T",
"version": "0.1"
},
"MICROFILTRATION": {
"contact": {
"email": "patrice.buche@inrae.fr",
"name": "Patrice Buche"
},
"description": "The Microfiltration ontology (MICROFILTRATION) is dedicated to the description of milk transformation itineraries for microfiltration purposes and characterisation of associated samples.",
"example_uri": "http://opendata.inra.fr/resources/MICROFILTRATION#rotation_speed",
"license": "CC-BY-4.0",
"name": "Milk Microfiltration Ontology",
"prefix": "MICROFILTRATION",
"version": "V-2020/04/08"
},
"MILKOLIGO": {
"contact": {
"email": "sylvie.combes@inrae.fr",
"name": "Sylvie Combes"
},
"description": "This thesaurus gathers milk oligosaccharide synonyms., This dataset is a thesaurus gathering milk oligosaccharide synonyms",
"example_uri": "http://opendata.inrae.fr/holooligo/oligo_165",
"homepage": "https://doi.org/10.57745/RA5DAC",
"license": "https://spdx.org/licenses/etalab-2.0.html",
"name": "Milk Oligosaccharide Thesaurus - HoloOLIGO project",
"prefix": "MILKOLIGO",
"publication": "http://dx.doi.org/10.2139/ssrn.4596815",
"version": "1.0"
},
"MS2O": {
"contact": {
"email": "juliette.dibie-barthelemy@inrae.fr",
"name": "Juliette Dibie"
},
"description": "The Multi-scale Multi-step ontology (MSΒ²O) is an ontology to describe transformation processes., Multi-scale Multi-step ontology (MSΒ²O) est une ontologie permettant de dΓ©crire des processus de transformation.",
"example_uri": "http://opendata.inra.fr/ms2o/Product",
"homepage": "http://lovinra.inra.fr/2015/12/16/multi-scale-multi-step-ontology/",
"license": "CC-BY-4.0",
"name": "Multi-scale Multi-step ontology",
"prefix": "MS2O",
"version": "0.2"
},
"NALT": {
"contact": {
"email": "sujata.suri@ars.usda.gov",
"name": "Sujata Suri"
},
"description": "The Thesaurus is an online vocabulary of agricultural terms in English and Spanish and is cooperatively produced by the National Agricultural Library, USDA and the Inter-American Institute for Cooperation on Agriculture as well as other Latin American agricultural institutions belonging to the Agriculture Information and Documentation Service of the Americas (SIDALC). The NAL Agricultural Thesaurus (NALT) was first published in 1967 and converted to SKOS in 2019 then released by the National Agricultural Library in 2002, with in-depth coverage of agriculture, biology, and related disciplines. The Spanish language version of NALT was first published in May 2007 under the Spanish language name \"Tesauro AgrΓcola\", and was created in cooperation with the Inter-American Institute for Cooperation on Agriculture (IICA) and other Latin American agricultural institutions belonging to the Agriculture Information and Documentation Service of the Americas (SIDALC). In 2022 NALT was redesigned as part of the Library's \"NALT for the Machine Age\" initiative, and is a state-of-the-art multischeme concept space with added structural features for enhanced scalability and machine readability. Inaugural schemes included NALT Core, and NALT Full.",
"example_uri": "http://lod.nal.usda.gov/nalt/38813",
"homepage": "https://agclass.nal.usda.gov/agt.shtml",
"license": "CC-BY-4.0",
"name": "National Agricultural Library Thesaurus",
"prefix": "NALT",
"publication": "https://agclass.nal.usda.gov/bib.shtml"
},
"NCBITAXON": {
"contact": {
"email": "info@ncbi.nlm.nih.gov",
"name": "NCBI information"
},
"description": "The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.",
"example_uri": "http://purl.bioontology.org/ontology/NCBITAXON/201174",
"homepage": "https://www.ncbi.nlm.nih.gov/",
"name": "National Center for Biotechnology Information (NCBI) Organismal Classification",
"prefix": "NCBITAXON",
"repository": "https://github.com/obophenotype/ncbitaxon",
"version": "2023ab"
},
"OBA": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "The Ontology of Biological Attributes (OBA) is a formalised, species-independent collection of interoperable phenotypic trait categories that is intended to fulfil a data integration role. OBA is a standardised representational framework for observable attributes that are characteristics of biological entities, organisms, or parts of organisms. It is collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO., A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO.",
"example_uri": "http://purl.obolibrary.org/obo/OBA_0000005",
"homepage": "https://github.com/obophenotype/bio-attribute-ontology",
"license": "CC0-1.0",
"name": "Ontology of Biological Attributes",
"prefix": "OBA",
"publication": "https://doi.org/10.1007/s00335-023-09992-1",
"repository": "https://github.com/obophenotype/bio-attribute-ontology",
"version": "2024-06-27"
},
"OBOE": {
"contact": {
"email": "mecum@nceas.ucsb.edu",
"name": "Bryce Mecum"
},
"description": "The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations.",
"example_uri": "http://ecoinformatics.org/oboe/oboe.1.2/oboe-characteristics.owl#SpectralRadiance",
"homepage": "https://github.com/NCEAS/oboe/",
"license": "CC-BY-3.0",
"name": "The Extensible Observation Ontology",
"prefix": "OBOE",
"publication": "https://doi.org/10.1016/j.ecoinf.2007.05.004",
"repository": "https://github.com/NCEAS/oboe",
"version": "Version 1.2"
},
"OEEV": {
"contact": {
"email": "llorenc.cabrera-bosquet@inra.fr",
"name": "Llorenç Cabrera-Bosquet"
},
"description": "The Ontology of Experimental Events (OEEv), characterises events that occur during an experiment, e.g. dates of sowing, application of a given treatment, harvesting, measurements or sampling for -omic measurements, or any category of technical problem.",
"example_uri": "http://www.phenome-fppn.fr/vocabulary/2018/oeev#Fertilization",
"license": "CC-BY-4.0",
"name": "Ontology of Experimental Events",
"prefix": "OEEV",
"version": "Version 3.1 (2018-06-06) created by INRA - MISTEA - LEPSE"
},
"OEPO": {
"contact": {
"email": "llorenc.cabrera-bosquet@inra.fr",
"name": "Llorenç Cabrera-Bosquet"
},
"description": "The Ontology for Experimental Phenotypic Objects (OEPO), allows assigning types (e.g. Experimental organization and context, Environment type, Germplasm, Physical Object) to objects involved in phenotyping experiments and defining specialization hierarchy between them according to the specificities of the installations and experiments.",
"example_uri": "http://www.phenome-fppn.fr/vocabulary/2018/oepo#AirMixer",
"license": "CC-BY-4.0",
"name": "Ontology for Experimental Phenotypic Objects",
"prefix": "OEPO",
"version": "releases/2017-12-12"
},
"OESO-CORE": {
"contact": {
"email": "anne.tireau@inrae.fr",
"name": "Anne Tireau"
},
"description": "The Ontology for Experimental Scientific Objects (OESO), allows assigning types (e.g. Experimental organization and context, Environment type, Germplasm, Physical Object) to objects involved in experiments and defining specialization hierarchy between them according to the specificities of the installations and experiments. OESO core contains the main concept for OpenSILEX application. This core ontology should be extend with the application domain concepts.",
"example_uri": "http://vegetalunit.inrae.fr/arbo/id/project/prumel",
"homepage": "http://opensilex.org/vocabulary/oeso.owl",
"license": "CC-BY-4.0",
"name": "Ontology for Experimental Scientific Objects Core",
"prefix": "OESO-CORE",
"publication": "https://hal.inrae.fr/hal-02788853",
"repository": "https://github.com/OpenSILEX",
"version": "Version 3.2.1 (2021-10-20) created by INRAE"
},
"OFPE": {
"contact": {
"email": "anne.tireau@inra.fr",
"name": "Tireau Anne"
},
"description": "OFPE is a generic ontology specialized for food processing experiments, where raw materials are transformed into final products. It includes different classes that represent products and activities during food transformation processes, which can be classified into four main concepts, i.e., Product, Operation, Attribute, and Observation., OFPE is a generic ontology\nspecialized for food processing experiments, where raw ma-\nterials are transformed into final products. It includes dif-\nferent classes that represent products and activities during\nfood transformation processes, which can be classified into\nfour main concepts, and\nObservation.",
"example_uri": "http://www.mistea.supagro.inra.fr/ontologies/2016/v4/ontofp#IntermediateProduct",
"license": "CC-BY-4.0",
"name": "Ontology for Food Processing Experiment",
"prefix": "OFPE",
"version": "4.0 august 2016"
},
"OFSMR": {
"contact": {
"email": "scuberog@hotmail.com",
"name": "Salvador Cubero GonzΓ‘lez"
},
"description": "Food-matrix ontology for Open Food Safety Model Repository",
"name": "Open Predictive Microbiology Ontology",
"prefix": "OFSMR",
"version": "0.4"
},
"OM": {
"contact": {
"email": "hajo.rijgersberg@wur.nl",
"name": "Hajo Rijgersberg"
},
"description": "The Ontology of units of Measure (OM) 2.0 models concepts and relations important to scientific research. It has a strong focus on units, quantities, measurements, and dimensions.",
"example_uri": "http://www.wurvoc.org/vocabularies/om-1.8/Molar_energy",
"homepage": "http://www.ontology-of-units-of-measure.org/",
"license": "CC-BY-4.0",
"name": "Ontology of units of Measure",
"prefix": "OM",
"repository": "https://github.com/HajoRijgersberg/OM",
"version": "2.0.57"
},
"ONS": {
"contact": {
"email": "francesco.vitali.bio@gmail.com",
"name": "Francesco Vitali"
},
"description": "ONS was developed under the ENPADASI European project, to assist the standardized description of (human) nutritional studies. As such, it includes and covers classes and relations that are commonly encountered while conducting, storing, harmonizing, integrating, describing and querying for nutritional studies. ONS main objective and long-term goal, is to represent a comprehensive resource for the description of concepts in the broader human nutrition domain, representing a solid and extensible formal ontology framework, where integration of new information can be easily achieved by the addition of extra modules.",
"example_uri": "http://purl.obolibrary.org/obo/ONS_0000083",
"name": "Ontology for Nutritional Studies",
"prefix": "ONS",
"version": "Relese version 1.0"
},
"ONTOAGROHIDRO": {
"contact": {
"email": "olgafernanda@gmail.com",
"name": "Olga Fernanda"
},
"description": "OntoAgroHidro is an ontology that represents knowledge about impacts of agricultural activities and climatic changes on water resources.",
"name": "OntoAgroHidro",
"prefix": "ONTOAGROHIDRO"
},
"ONTOBIOTOPE": {
"contact": {
"email": "claire.nedellec@inrae.fr",
"name": "Claire NΓ©dellec"
},
"description": "OntoBiotope is an ontology of microorganism habitats, phenotypes and use. Its modeling principle and its lexicon reflect the biotope classification used by biologists to describe microorganism isolation sites, phenotypes and uses. OntoBiotope is developed and maintained by the Bibliome group of MaIAGE lab and microbiologists from INRAE (French National Research Institute for Agriculture, Food and Environment) from all fields of applied microbiology. OntoBiotope classes are used in the Bacteria Biotope reference dataset of BioNLP shared task to annotate the habitats and phenotype entities. It is also used to index the data of the Omnicrobe DataBase",
"example_uri": "http://purl.obolibrary.org/obo/OBT_001929",
"license": "http://creativecommons.org/licenses/by-nd/4.0",
"name": "OntoBiotope",
"prefix": "ONTOBIOTOPE",
"publication": "https://arxiv.org/abs/1805.04107",
"version": "Oct 2021"
},
"OWSD": {
"contact": {
"email": "arnaud.charleroy@inrae.fr",
"name": "Arnaud Charleroy"
},
"description": "Les descripteurs d'analyse sensorielle du vin, une nouvelle ontologie, dΓ©crit une liste de groupes de descripteurs (classes) utilisΓ©s pour classer les descripteurs sensoriels (instances)., The Wine Sensory analysis Descriptors, a new ontology describes a list of descriptors groups (classes) used to classify sensorial descriptors (instances).",
"example_uri": "http://opendata.inrae.fr/owsd#yeast_sf_o",
"homepage": "http://opendata.inrae.fr/owsd",
"license": "https://www.etalab.gouv.fr/licence-ouverte-open-licence",
"name": "Ontology for the management of Wine Sensory analysis Descriptors",
"prefix": "OWSD",
"version": "1"
},
"PATO": {
"contact": {
"email": "g.gkoutos@gmail.com",
"name": "George Gkoutos"
},
"description": "An ontology of phenotypic qualities (properties, attributes or characteristics). This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested.",
"example_uri": "http://purl.obolibrary.org/obo/PATO_0001464",
"homepage": "https://github.com/pato-ontology",
"license": "CC-BY-3.0",
"name": "Phenotype And Trait Ontology",
"prefix": "PATO",
"repository": "https://github.com/pato-ontology/pato/",
"version": "2024-03-28"
},
"PCO": {
"contact": {
"email": "rwalls2008@gmail.com",
"name": "Ramona Walls"
},
"description": "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology.",
"example_uri": "http://purl.obolibrary.org/obo/PCO_0000061",
"homepage": "https://github.com/PopulationAndCommunityOntology/pco",
"license": "CC0-1.0",
"name": "Population and Community Ontology",
"prefix": "PCO",
"repository": "https://github.com/PopulationAndCommunityOntology/pco",
"version": "2013-10-03"
},
"PDO_CAS": {
"contact": {
"email": "openresources@mail.las.ac.cn",
"name": "National Science Library, Chinese Academy of Sciences"
},
"description": "Plant Diversity Ontology (PDO) is the outcome of the construction tasks of domain ontology of science in the project of Scientific & Technological Knowledge Organization Systems (STKOS). The structure of PDO centers on species, including micro level of molecular, cell and tissue, medium level of plant organs, species and population, and macro level of ecosystem. The classes of PDO also capture the habitat, environmental conditions and expand the general characteristics of plants, completing the instances richness for plant species, geographical, classification and morphology. Furthermore, PDO builds the relationships among species, region, morphology, plant organs, developmental stage, revealing the list of species in an area, the morphology and life form of plants, and development process of species. In sum, PDO shows a growth process or development stage of a species and its structure characteristics in particular space and time scale, realizing the description of species diversity, ecosystem diversity and genetic diversity. At present, PDO has been applied to the platform of Go to Selected Open Access Journals (GoOA) developed by National Science Library of Chinese Academy of Sciences, supporting concept retrieval and concept extension for GoOA.",
"name": "Plant Diversity Ontology",
"prefix": "PDO_CAS"
},
"PEAO": {
"contact": {
"email": "peaoteam@gmail.com",
"name": "PEAO Team"
},
"description": "The Plant domain has been the subject of several attempts to structure and formally define terms and corresponding relations, such as their anatomical features, developmental stages, and the application of particular experimental procedures to a biological problem. However, a focus on experimental assays in order to describe the whole experimental procedure, to the best of our knowledge, has only been attempted in the context of a very general description based on classical views of the scientific method. In this study, we focus on the development and proposal of an ontology dedicated to the description of these experimental procedures, regardless of the scientific questions that prompted the assays. This ontology includes entities from three distinct realms (biological, physical and data), which include both experimental products, their relations and the protocols describing their manipulation.",
"example_uri": "http://purl.obolibrary.org/obo/EO_0007263",
"homepage": "https://bitbucket.org/PlantExpAssay/ontology",
"name": "Plant Experimental Assay Ontology",
"prefix": "PEAO",
"repository": "https://bitbucket.org/PlantExpAssay/ontology/src/"
},
"PECO": {
"contact": {
"email": "jaiswalp@oregonstate.edu",
"name": "Pankaj Jaiswal"
},
"description": "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.",
"example_uri": "http://purl.obolibrary.org/obo/PECO_0007359",
"homepage": "https://planteome.org/",
"license": "CC-BY-4.0",
"name": "Plant Experimental Conditions Ontology",
"prefix": "PECO",
"repository": "https://github.com/Planteome/plant-experimental-conditions-ontology",
"version": "July 2023"
},
"PO": {
"contact": {
"email": "cooperl@science.oregonstate.edu",
"name": "Laurel Cooper"
},
"description": "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data., An ontology that describes plant anatomy, morphology, and growth and development in plants.",
"example_uri": "http://purl.obolibrary.org/obo/PO_0025270",
"homepage": "https://planteome.org/",
"license": "CC-BY-4.0",
"name": "Plant Ontology",
"prefix": "PO",
"repository": "https://github.com/Planteome/plant-ontology",
"version": "July 2023"
},
"PO2": {
"contact": {
"email": "stephane.dervaux@inrae.fr",
"name": "Stephane Dervaux"
},
"description": "A core ontology for modeling transformation processes and their observations. PO2 is part of an interdisciplinary project called Delicious concerning the production and transformation processes in food science. The project combines data from different disciplines like food composition, food structure, sensorial perception and nutrition.",
"example_uri": "http://opendata.inra.fr/PO2/computedSeriesResult",
"homepage": "http://lovinra.inra.fr/2016/08/03/process-and-observation-ontology/",
"license": "CC-BY-4.0",
"name": "Process and Observation Ontology",
"prefix": "PO2",
"version": "2.0"
},
"POLAPGEN_BARLEY": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
"name": "Crop Ontology Helpdesk"
},
"description": "Barley Trait Ontology template v 4, 6 June 2013 submitted by the Institute of Plant Genetics Poznan on behalf of Polapgen Consortium Poland",
"example_uri": "http://www.cropontology.org/rdf/POLAPGEN_BARLEY:0000381",
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"name": "Barley Trait POLAPGEN Ontology",
"prefix": "POLAPGEN_BARLEY",
"version": "2013-06-06"
},
"PPDO": {
"contact": {
"email": "catherine.roussey@inrae.fr",
"name": "roussey"
},
"description": "This RDF file contains an extension of the SKOS model to model the development stages (or phenological stages) of cultivated plants. This model defines classes representing the main stages and the secondary stages (2 and 3 digits). The general BBCH scale is represented as an instance of skos:ConceptScheme. A new scale was created, intitled, BBCH global scale, that gather all the stages existing in all BBCh cales. It was built during the ANR D2KAB project., that gather all the stages existing in all BBCh cales. It was built during the ANR D2KAB project. Contact Catherine Roussey (catherine.roussey@inrae.fr) for any modification in this file. This extension of SKOS model was build using 4 versions of BBCH monograph: * Growth stages of mono- and dicotyledonous plants BBCH Monograph edited by Uwe Meier Julius Kühn-Institut (JKI) Quedlinburg 2018 DOI: 10.5073/20180906-074619 ISBN: 978-3-95547-071-5 * Stades phénologiques des mono-et dicotylédones cultivées BBCH Monographie rédigé par Uwe Meier Instituto Julius Kühn (JKI, siglas en alomÑn) Quedlinburg, 2018 DOI: 10.5073/20180906-075455 ISBN: 978-3-95547-072-2 * Estadios de las plantas mono-y dicotyledóneas BBCH Monografia Elaborado por Uwe Meier Instituto Julius Kühn (JKI, 2018 DOI: 10.5073/20180906-075743 ISBN: 978-3-95547-069-2 * Entwicklungsstadien mono- und dikotyler Pflanzen BBCH Monografie bearbeitet von Uwe Meier Julius Kühn-Institut (JKI) Quedlinburg 2018 DOI: 10.5073/20180906-075119 ISBN: 978-3-95547-070-8 All versions are licensed under a Creative Commons Attribution 4.0 International License., Ce fichier RDF contient une extension du modèle SKOS pour modeliser les stades de développement (ou stades phénologiques) des plantes cultivées. Ce modèle défini des classes représentant les stades principaux et les stades secondaires (à 2 et 3 chiffres). l'échelle BBCH générale est représentée sous forme d'une instance de skos:ConceptScheme. Une nouvelle échelle a été créée, appelée échelle BBCH globale, regroupant tous les stades existant dans toutes les échelles BBCH. L'ontologie a été construite pendant le projet ANR D2KAB. Contacter Catherine Roussey (catherine.roussey@inrae.fr) pour toute modification dans ce fichier. Ce modele skos a été construit en utilisant 4 versions de la monographie BBCH toutes sous licence Creative Commons Attribution 4.0 International: * Growth stages of mono- and dicotyledonous plants BBCH Monograph edited by Uwe Meier Julius Kühn-Institut (JKI) Quedlinburg 2018 DOI: 10.5073/20180906-074619 ISBN: 978-3-95547-071-5 * Stades phénologiques des mono-et dicotylédones cultivées BBCH Monographie rédigé par Uwe Meier Instituto Julius Kühn (JKI, 2018 DOI: 10.5073/20180906-075743 ISBN: 978-3-95547-069-2 * Entwicklungsstadien mono- und dikotyler Pflanzen BBCH Monografie bearbeitet von Uwe Meier Julius Kühn-Institut (JKI) Quedlinburg 2018 DOI: 10.5073/20180906-075119 ISBN: 978-3-95547-070-8, that gather all the stages existing in all BBCh cales. It was built during the ANR D2KAB project. Contact Catherine Roussey (catherine.roussey@inrae.fr) for any modification in this file. This extension of SKOS model was build using 4 versions of BBCH monograph. All versions are licensed under a Creative Commons Attribution 4.0 International License., regroupant tous les stades existant dans toutes les échelles BBCH. L'ontologie a été construite pendant le projet ANR D2KAB. Contacter Catherine Roussey (catherine.roussey@inrae.fr) pour toute modification dans ce fichier. Ce modele skos a été construit en utilisant 4 versions de la monographie BBCH toutes sous licence Creative Commons Attribution 4.0 International.",
"example_uri": "http://ontology.inrae.fr/ppdo/ontology/SecondaryStage03",
"homepage": "http://ontology.irstea.fr/pmwiki.php/Site/Ppdo",
"license": "CC-BY-4.0",
"name": "BBCH-based Plant Phenological Description Ontology",
"prefix": "PPDO",
"repository": "https://gitlab.irstea.fr/copain/phenologicalstages",
"version": "1.3"
},
"PPEO": {
"contact": {
"email": "cyril.pommier@inrae.fr",
"name": "Cyril Pommier"
},
"description": "The Plant Phenotyping Experiment Ontology (PPEO) is an implementation of the Minimal Information About Plant Phenotyping Experiment. It lists and organises all the informations necessary to describe and reuse a phenotyping dataset following FAIR principles (Findable Interoperable Accessible Reusable). It has been initiated with experts from Elixir, Emphasis, Bioversity International - CGIAR and RDA.",
"example_uri": "https://raw.githubusercontent.com/MIAPPE/MIAPPE-ontology/master/MIAPPE.owl#MIAPPE_000011",
"homepage": "http://purl.org/ppeo",
"license": "CC-BY-4.0",
"name": "Plant Phenotype Experiment Ontology",
"prefix": "PPEO",
"repository": "https://github.com/MIAPPE/MIAPPE-ontology",
"version": "1.1-beta"
},
"PPO": {
"contact": {
"email": "rlwalls2008@gmail.com",
"name": "Ramona Walls"
},
"description": "Plant phenology β the timing of plant life-cycle events, such as flowering or leafing-out β has cascading effects on multiple levels of biological organization, from individuals to ecosystems, and is crucial for understanding the links between climate and biological communities. Plant phenology data are collected and used by many different types of researchers, from plant breeders to ecosystem ecologists. Today, thanks to data digitization and aggregation initiatives, phenology monitoring networks, and the efforts of citizen scientists, more phenologically relevant data is available than ever before. Unfortunately, combining these data in large-scale analyses remains prohibitively difficult, mostly because the individuals and organizations producing the data are using non-standardized terminologies and metrics during data collection and processing. Lack of standardization remains particularly problematic for historical datasets, which are crucial for time-based analyses. The Plant Phenology Ontology (PPO) is a collaborative effort to help solve these problems by developing the standardized terminology, definitions, and relations that are needed for large-scale data integration. The PPO builds on the widely used Plant Ontology (PO) and Phenotype and Trait Ontology (PATO) to promote broad reuse of phenological data. The initial use case for the PPO is integration of citizen science data from the USA National Phenology Network (USA-NPN) and the Pan-European Phenology Network (PEP), but work is also planned for integrating data from herbaria.",
"example_uri": "http://purl.obolibrary.org/obo/PPO_0007001",
"homepage": "http://www.obofoundry.org/ontology/ppo.html",
"license": "CC-BY-3.0",
"name": "Plant Phenology Ontology",
"prefix": "PPO",
"repository": "https://github.com/PlantPhenoOntology",
"version": "2018-10-26"
},
"PR": {
"contact": {
"email": "pirmail@georgetown.edu",
"name": "Protein Information Resource"
},
"description": "An ontological representation of protein-related entities. The PRotein Ontology (PRO) formally defines taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes., The PRotein Ontology (PRO) formally defines taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes.",
"example_uri": "http://purl.obolibrary.org/obo/PR_Q9UIG8-3",
"license": "CC-BY-4.0",
"name": "Protein Ontology",
"prefix": "PR"
},
"PSO": {
"contact": {
"email": "cooperl@oregonstate.edu",
"name": "Laurel Cooper"
},
"description": "The Plant Stress Ontology (PSO) describes biotic and abiotic stresses that a plant may encounter. An ontology containing biotic and abiotic plant stresses. Part of the Planteome suite of reference ontologies.",
"example_uri": "http://purl.obolibrary.org/obo/PSO_0000013",
"homepage": "https://planteome.org/",
"license": "CC-BY-4.0",
"name": "Plant Stress Ontology",
"prefix": "PSO",
"repository": "https://github.com/Planteome/plant-stress-ontology",
"version": "2023-11-14"
},
"RO": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies., RO chemical module.",
"example_uri": "http://purl.obolibrary.org/obo/RO_0002533",
"homepage": "https://github.com/oborel/obo-relations/",
"license": "CC0-1.0",
"name": "Relations Ontology",
"prefix": "RO",
"repository": "http://purl.obolibrary.org/obo/ro.owl",
"version": "2024-04-24"
},
"SAREF": {
"contact": {
"email": "maxime.lefrancois@emse.fr",
"name": "Maxime Lefrançois"
},
"description": "The Smart Applications REFerence ontology (SAREF) is intended to enable interoperability between solutions from different providers and among various activity sectors in the Internet of Things (IoT), thus contributing to the development of the global digital market.",
"example_uri": "https://saref.etsi.org/core/Command",
"homepage": "https://saref.etsi.org/",
"license": "https://forge.etsi.org/etsi-software-license",
"name": "Smart Applications REFerence ontology",
"prefix": "SAREF",
"publication": "https://www.etsi.org/deliver/etsi_ts/103200_103299/103264/03.01.01_60/ts_103264v030101p.pdf",
"version": "v3.1.1"
},
"SAREF4AGRI": {
"contact": {
"email": "mpoveda@fi.upm.es",
"name": "Maria Poveda-Villalon"
},
"description": "SAREF4AGRI is an extension of SAREF for the agriculture and food domain. SAREF4AGRI is specified and published by ETSI in the TS 103 410-6 associated to this ontology file. The list of use cases, standards and requirements that guided the creation of SAREF4AGRI are described in the associated ETSI TR 103 511., This ontology extends the SAREF ontology for the Agricultural domain. This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx), which was established with the goal to create three SAREF extensions, one of them for the Agricultural domain.",
"example_uri": "https://saref.etsi.org/core/State",
"license": "https://forge.etsi.org/etsi-software-license",
"name": "SAREF4AGRI: an extension of SAREF for the agriculture and food domain",
"prefix": "SAREF4AGRI",
"version": "v1.1.2"
},
"SAREF4ENVI": {
"contact": {
"email": "maxime.lefrancois@emse.fr",
"name": "Maxime Lefrançois"
},
"description": "The present document is the technical specification of SAREF4ENVI, an extension of SAREF [1] for the environment domain. The extension was created in collaboration with domain experts in the field of light pollution currently working in the STARS4ALL European H2020 project (http://www.stars4all.eu/index.php/lpi/). The STARS4ALL project is composed by partners such as Universidad PolitΓ©cnica de Madrid, Universidad Complutense de Madrid, ESCP Europe, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Instituto de AstrofΓsica de Canarias, University of Southampton, Europan Crowdfunding Network, and CEFRIEL (SocietΓ Consortile a Responsabilita Limitata). SAREF4ENVI has two main aims: on the one hand, to be the basis for enabling the use of SAREF in the environment domain and, on the other hand, to exemplify how to enable interoperability between environmental devices in cooperation. SAREF4ENVI is an OWL-DL ontology that extends SAREF with 32 classes (24 defined in SAREF4ENVI and 7 reused from the time, SAREF and geo ontologies), 24 object properties (22 defined in SAREF4ENVI and 2 reused from the SAREF and geo ontologies), 13 data type properties (9 defined in SAREF4ENVI and 4 reused from the SAREF ontology), and 24 individuals (9 defined in SAREF4ENVI and 12 reused from the OM ontology). SAREF4ENVI focuses on extending SAREF for photometers to solve the lack of interoperability between sensors that can measure and share information about light pollution. Such extension involves the following use cases (more details can be found in ETSI TR 103 411 [i.1]): Use case 1: Monitor light pollution in a city, through the data collected by photometers about the magnitude of the light emitted in a given area. Use case 2: Adjust lampposts light intensity due to high pollution, after identifying the most contaminating lampposts and therefore the areas where more energy is being thrown away. Use case 3: Register a photometer, in which a new collection of photometers is incorporated into an existing sensor network., This ontology extends the SAREF ontology for the environment domain, specifically for the light pollution domain, including concepts like photometers, light, etc.",
"example_uri": "https://saref.etsi.org/saref4envi/DigitalRepresentation",
"homepage": "https://saref.etsi.org/saref4envi/",
"license": "https://forge.etsi.org/etsi-software-license",
"name": "SAREF4ENVI: an extension of SAREF for the environment domain",
"prefix": "SAREF4ENVI",
"version": "v1.1.2"
},
"SDGIO": {
"contact": {
"email": "pier.buttigieg@awi.de",
"name": "Pier Luigi Buttigieg (ORCID: orcid.org/0000-0002-4366-3088)"
},
"description": "The SDGIO aims to provide a semantic bridge between 1) the Sustainable Development Goals, their targets, and indicators and 2) the large array of entities they refer to. It will import classes from numerous exisitng ontologies and map to vocabularies such as GEMET to promote interoperability. New classes will be minted and defined where no external class exists.",
"example_uri": "http://purl.unep.org/sdg/SDGIO_00010073",
"homepage": "https://github.com/SDG-InterfaceOntology/sdgio",
"name": "Sustainable Development Goals Interface Ontology",
"prefix": "SDGIO",
"publication": "http://ceur-ws.org/Vol-1747/IT201_ICBO2016.pdf",
"repository": "https://github.com/SDG-InterfaceOntology",
"version": "2018-05-11"
},
"SEONT": {
"contact": {
"email": "m.a.laporte@cgiar.org",
"name": "Marie Angelique Laporte"
},
"description": "This ontology is the socio-economic ontology developed by CGIAR and partners. Socio-economic ontology team gratefully acknowledges the Platform for big data in agriculture (https://bigdata.cgiar.org) and CGIAR Research program on Policies, Instiutions and Markets(http://pim.cgiar.org/) for their financial support to implement this ontology., None",
"homepage": "https://github.com/AgriculturalSemantics/SEONT?tab=readme-ov-file",
"license": "https://creativecommons.org/licenses/unspecified",
"name": "Socio-Economic Ontology",
"prefix": "SEONT",
"repository": "https://github.com/AgriculturalSemantics/SEOnt"
},
"SFWO": {
"contact": {
"email": "mickael.hedde@inrae.fr",
"name": "MickaΓ«l Hedde"
},
"description": "The Soil Food Web Ontology (SFWO) is a OWL ontology which provides a standardised terminology and a logical formalisation of the domain of soil trophic ecology. It proposes a reference vocabulary to describe information about trophic interactions, feeding-related functional traits, and feeding processes of soil biota. By harmonizing the definitions of trophic groups, SFWO provides a common, logically-sound framework for soil-associated consumers classification across taxonomic groups and trophic levels. The Soil Food Web Ontology aims at being a reference ontology for soil trophic ecology, and a resource for ontology-driven applications in the field, including: trophic trait datasets standardization, trophic data integration and knowledge graph construction, automated soil food web reconstruction using OWL reasoning, and trophic information extraction., The Soil Food Web Ontology (SFWO) describes concepts related to the trophic ecology of soil organisms, including diets, food resources, trophic processes, and trophic groups, across taxonomic groups and trophic levels. SFWO aims at being both a reference ontology -including a standardised vocabulary- for soil trophic ecology, and an application ontology, with a focus on reasoning-based applications.",
"example_uri": "http://purl.org/sfwo/SFWO_0000128",
"license": "CC-BY-4.0",
"name": "Soil Food Web Ontology",
"prefix": "SFWO",
"publication": "https://doi.org/10.1016/j.ecoinf.2023.102360",
"version": "2023-09-22"
},
"SIO": {
"contact": {
"email": "michel.dumontier@gmail.com",
"name": "Michel Dumontier"
},
"description": "The semanticscience integrated ontology (SIO) provides a simple, integrated ontology (types, relations) for objects, processes and their attributes. This project provides foundational support for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects. website: http://semanticscience.org email: sio-ontology@googlegroups.com mailing list: http://groups.google.com/group/sio-ontology , processes and their attributes. This project provides foundational support for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.",
"example_uri": "http://semanticscience.org/resource/SIO_000837",
"homepage": "http://sio.semanticscience.org/",
"license": "CC-BY-4.0",
"name": "Semanticscience Integrated Ontology",
"prefix": "SIO",
"publication": "http://www.jbiomedsem.com/content/5/1/14",
"repository": "https://github.com/micheldumontier/semanticscience",
"version": "1.59"
},
"SIREN": {
"contact": {
"email": "patrice.buche@inrae.fr",
"name": "Buche"
},
"description": "This ontology contains a OWL representation of SIREN food terms using Langual thesaurus. SIREN is the Scientific Information and Retrieval Exchange Network of the US Food and Drug administration.",
"example_uri": "http://purl.obolibrary.org/obo/FOODON_03306963",
"name": "SIREN",
"prefix": "SIREN"
},
"SNPO": {
"contact": {
"email": "adrien.coulet@loria.fr",
"name": "Adrien Coulet"
},
"description": "SNP-Ontology is a domain ontology that provides a formal representation (OWL-DL) of genomic variations. Despite its name, SNP-Ontology, is not limited to the representation of SNPs but it encompasses genomic variations in a broader meaning. SNP-Ontology is general enough to enable the representation of variations observed in genome of various species. Latest versions of SNP-Ontology include the representation of haplotype and of CNV. The unambiguous representation of genomic variations provided by SNP-Ontology enables to integrate heterogeneous data related to genomic variations. To achieve this goal SNP-Ontology enables (1) to represent one variation in accordance with various ways that exist for describing it, (2) to represent the equivalence between two distinct descriptions of one variation, and (3) to represent correspondence between a genomic variation and its outcome at the transcriptome and proteome levels.",
"example_uri": "http://www.loria.fr/~coulet/ontology/snpontology/version1.6/snpontology_full.owl#haplotype",
"homepage": "https://members.loria.fr/ACoulet/files/snpontology1.6_description.html",
"name": "Single-Nucleotide Polymorphism (SNP) Ontology",
"prefix": "SNPO",
"publication": "http://hal.inria.fr/inria-00067863/en",
"version": "version: full 1.6\nrelease: 14/03/2017"
},
"SO": {
"contact": {
"email": "barry.moore@genetics.utah.edu",
"name": "Barry Moore (Software Developer)"
},
"description": "A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases.",
"example_uri": "http://purl.obolibrary.org/obo/SO_0001673",
"homepage": "http://www.sequenceontology.org/",
"name": "Sequence Types and Features Ontology",
"prefix": "SO",
"publication": "http://www.sequenceontology.org/?page_id=296",
"repository": "https://github.com/The-Sequence-Ontology/SO-Ontologies"
},
"SOIL": {
"contact": {
"email": "giovanni.labate@crea.gov.it",
"name": "Giovanni L'Abate"
},
"description": "This vocabulary is a first formalization of the INSPIRE data model into an RDFs vocabulary.Developed by the Italian Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA) in collaboration with the Global Forum on Agricultural Research (GFAR) and the Food and Agriculture Organization of the United Nations (FAO).",
"example_uri": "http://vocabularies.aginfra.eu/soil#coverageByDomainAndRange",
"homepage": "http://vocabularies.aginfra.eu/soil",
"name": "agINFRA Soil Vocabulary",
"prefix": "SOIL",
"version": "V-2014"
},
"SOSA": {
"contact": {
"email": "simon.cox@csiro.au",
"name": "Simon Cox"
},
"description": "This ontology is based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group.",
"example_uri": "http://www.w3.org/ns/sosa/Observation",
"homepage": "https://www.w3.org/TR/vocab-ssn/",
"license": "http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document",
"name": "Sensor, Observation, Sample, and Actuator Ontology",
"prefix": "SOSA",
"repository": "https://github.com/w3c/sdw",
"version": "V-2017"
},
"SOY": {
"contact": {
"email": "rex.nelson@ars.usda.gov",
"name": "Rex Nelson"
},
"description": "Soybean Growth and Trait Ontology",
"example_uri": "http://purl.obolibrary.org/obo/SOY:0000249",
"homepage": "https://www.soybase.org/",
"name": "Soy Ontology",
"prefix": "SOY",
"repository": "https://github.com/Planteome/soybase-ontology",
"version": "V10 revision 2.4"
},
"SPO-FDM": {
"contact": {
"email": "e.motta@open.ac.uk",
"name": "Enrico Motta"
},
"description": "SmartProducts Network of Ontologies (SPO) provides a clear specification of the conceptual model underlying the work on the SmartProducts project, and maximises interoperability not just among all SmartProducts applications, but also between these and other applications in related domains. SPO Food ontologies have been designed according to a smart kitchen application scenario. Food Domain Model (FDM) defines concepts and properties specific for the Philips use case (cooking domain)",
"name": "SmartProducts Network of Ontologies Food Domain Model",
"prefix": "SPO-FDM"
},
"SPO-FND": {
"contact": {
"email": "e.motta@open.ac.uk",
"name": "Enrico Motta"
},
"description": "SmartProducts Network of Ontologies (SPO) provides a clear specification of the conceptual model underlying the work on the SmartProducts project, and maximises interoperability not just among all SmartProducts applications, but also between these and other applications in related domains. SPO Food ontologies have been designed according to a smart kitchen application scenario. Food Nutrition Data (FND) contains nutritional information from Freebase and defines individuals for a \"dummy\" test scenario for Philips",
"name": "SmartProducts Network of Ontologies Food Nutrition Data",
"prefix": "SPO-FND"
},
"SPO-FTM": {
"contact": {
"email": "e.motta@open.ac.uk",
"name": "Enrico Motta"
},
"description": "SmartProducts Network of Ontologies (SPO) provides a clear specification of the conceptual model underlying the work on the SmartProducts project, and maximises interoperability not just among all SmartProducts applications, but also between these and other applications in related domains. SPO Food ontologies have been designed according to a smart kitchen application scenario. Food Taxonomy Model (FTM) contains food taxonomy constructed using PowerAqua and edited manually",
"name": "SmartProducts Network of Ontologies Food Taxonomy Model",
"prefix": "SPO-FTM"
},
"SPTO": {
"contact": {
"email": "nm249@cornell.edu",
"name": "Naama Menda"
},
"description": "Solanaceae crop phenotypes and traits, developed in collaboration with the research community, especially for breeder traits of agronomic importance.",
"example_uri": "http://www.cropontology.org/rdf/SP:0000334",
"homepage": "https://solgenomics.net/",
"license": "CC-BY-4.0",
"name": "Solanaceae Phenotype Ontology",
"prefix": "SPTO",
"repository": "https://github.com/solgenomics/sgn/blob/master/ontology/SP.obo"
},
"SSN": {
"contact": {
"email": "simon.cox@csiro.au",
"name": "Simon Cox"
},
"description": "This ontology describes sensors, actuators and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.",
"example_uri": "http://www.w3.org/ns/ssn/Stimulus",
"homepage": "https://www.w3.org/TR/vocab-ssn/",
"license": "http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document",
"name": "Semantic Sensor Network Ontology",
"prefix": "SSN",
"publication": "https://doi.org/10.3233/SW-180320",
"repository": "https://github.com/w3c/sdw",
"version": "New modular version of the SSN ontology. \n\nThis ontology was originally developed in 2009-2011 by the W3C Semantic Sensor Networks Incubator Group (SSN-XG). For more information on the group's activities see: http://www.w3.org/2005/Incubator/ssn/. The ontology was revised and modularized in 2015-2017 by the W3C/OGC Spatial Data on the Web Working Group, see: https://www.w3.org/2015/spatial/wiki/Semantic_Sensor_Network_Ontology. \n\nIn particular, (a) the scope is extended to include actuation and sampling; (b) the core concepts and properties are factored out into the SOSA ontology. The SSN ontology imports SOSA and adds formal axiomatization consistent with the text definitions in SOSA, and adds classes and properties to accommodate the scope of the original SSN ontology."
},
"STY": {
"contact": {
"email": "olivier@nlm.nih.gov",
"name": "Olivier Bodenreider"
},
"description": "The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types. This section of the documentation provides an overview of the Semantic Network, and describes the files of the Semantic Network. Sample records illustrate structure and content of these files.",
"example_uri": "http://purl.bioontology.org/ontology/STY/T057",
"homepage": "https://lhncbc.nlm.nih.gov/semanticnetwork/",
"license": "CC0-1.0",
"name": "UMLS Semantic Network",
"prefix": "STY",
"version": "12 (2022AA)"
},
"TAXRANK": {
"contact": {
"email": "peter.midford@gmail.com",
"name": "Peter Midford"
},
"description": "A vocabulary of taxonomic ranks developed as part of Phenoscape's Vertebrate Taxonomy Ontology. It provides terms for taxonomic ranks drawn from both the NCBI taxonomy database and from a rank vocabulary developed for the TDWG biodiversity information standards group. Cross references to appearances of each term in each source are provided. Consistent with its intended use as a vocabulary of labels, there is no relation specifying an ordering of the rank terms.",
"name": "Taxonomic Rank Ontology",
"prefix": "TAXRANK"
},
"TAXREF-LD": {
"contact": {
"email": "gargo@mnhn.fr",
"name": "Olivier Gargominy"
},
"description": "Representation of the TAXREF taxonomic register as linked data. This resource is at the same time an ontology of classes depicting the taxa and a thesaurus (SKOS concept scheme) of the scientific names attached to the taxa., ReprΓ©sentation du rΓ©fΓ©rentiel taxonomique TAXREF comme un jeu de donnΓ©es liΓ©es. Cette ressource est Γ la fois une ontologies des classes reprΓ©sentant les taxons, et un thΓ©saurus (SKOS concept scheme) des noms scientifiques dΓ©signant ces taxons.",
"example_uri": "http://taxref.mnhn.fr/lod/taxon/60878",
"homepage": "https://inpn.mnhn.fr/programme/referentiel-taxonomique-taxref?lg=en",
"license": "https://creativecommons.org/licenses/by/3.0/fr",
"name": "TAXREF-LD",
"prefix": "TAXREF-LD",
"publication": "https://hal.science/hal-01617708",
"repository": "https://github.com/frmichel/taxref-ld",
"version": "15.2"
},
"THESAE": {
"contact": {
"email": "veronique.batifol@inrae.fr",
"name": "VΓ©ronique Batifol"
},
"description": "ThΓ©saurus d'AgroΓ©cologie is a thesaurus in French containing 556 concepts denoting the issues, levers, indicators and agricultural production systems involved in an agro-ecological approach. This thesaurus, based on the results of a territorial watch on the scale of the Midi-PyrΓ©nΓ©es region, is the result of expert work carried out by researchers and specialists in scientific and technical information from the Institut National de la Recherche Agronomique, Le ThΓ©saurus d'AgroΓ©cologie est un thΓ©saurus en franΓ§ais prΓ©sentant 556 concepts dΓ©notant les enjeux, leviers, indicateurs et systΓ¨mes de production agricoles impliquΓ©s dans une dΓ©marche agroΓ©cologique. Ce thΓ©saurus, basΓ© sur les rΓ©sultats d'une veille territoriale Γ l'Γ©chelle de la rΓ©gion Midi-PyrΓ©nΓ©es est issu dβun travail dβexpertise rΓ©alisΓ© par des chercheurs et des spΓ©cialistes de lβinformation scientifique et technique de lβInstitut National de la Recherche Agronomique",
"example_uri": "http://opendata.inra.fr/ThesAE/engraissement_a_l_herbe",
"name": "Agroecology Thesaurus",
"prefix": "THESAE"
},
"TO": {
"contact": {
"email": "cooperl@science.oregonstate.edu",
"name": "Laurel Cooper"
},
"description": "An ontology that describes phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant.",
"example_uri": "http://purl.obolibrary.org/obo/TO_0000064",
"homepage": "https://planteome.org/",
"license": "CC-BY-4.0",
"name": "Plant Trait Ontology",
"prefix": "TO",
"publication": "https://planteome.org/references",
"repository": "https://github.com/Planteome/plant-trait-ontology",
"version": "July 2023"
},
"TOP": {
"contact": {
"email": "baptiste.laporte@fondationbiodiversite.fr",
"name": "Baptiste Laporte"
},
"description": "The Thesaurus Of Plant characteristics (TOP), aims to harmonize and formalize concepts for plant characteristics widely used in ecology. TOP concentrates on two types of plant characteristics: traits and environmental associations. Characteristics are modelled as the βQualityβ of an βEntityβ used in the context of Open Biological Ontologies. Whenever possible, the Entities and Qualities are taken from existing terminology standards, mainly the Plant Ontology (PO) and Phenotypic Quality Ontology (PATO) ontologies. TOP provides names, definitions, units, synonyms and related terms for about 850 plant characteristics.",
"example_uri": "http://top-thesaurus.org/trait#TOP598",
"homepage": "http://top-thesaurus.org",
"name": "Thesaurus of Plant Characteristics",
"prefix": "TOP",
"version": "1.0"
},
"TRANSFORMON": {
"contact": {
"email": "magalie.weber@inrae.fr",
"name": "Magalie Weber"
},
"description": "Domain ontology on food and bioproduct processing and characterization. The ontology is a specialization of the PO2 ontology (Process and Observation Ontology).",
"example_uri": "http://opendata.inrae.fr/PO2/Ontology/TransformON/Step/FwCv01",
"license": "http://publications.europa.eu/resource/authority/access-right/PUBLIC",
"name": "PO2/TransformON",
"prefix": "TRANSFORMON",
"version": "4.0"
},
"TRANSMAT": {
"contact": {
"email": "patrice.buche@inrae.fr",
"name": "Patrice Buche"
},
"description": "The Matter Transfer ontology is dedicated to matter transfer (e.g. O2, CO2, H2O) and mechanical properties of materials (eg food packaging tensile strength).",
"example_uri": "http://opendata.inra.fr/resources/hSC9z#_2wtpercent_cloisite_30b_pla_4032d_",
"homepage": "https://www6.inra.fr/cati-icat-atweb/Ontologies/Transmat",
"license": "CC-BY-4.0",
"name": "Matter Transfer Ontology",
"prefix": "TRANSMAT",
"version": "101"
},
"TRIPHASE": {
"contact": {
"email": "claire.nedellec@inrae.fr",
"name": "Claire NΓ©dellec"
},
"description": "TODO, TriPhase est un thésaurus couvrant le domaine de la physiologie animale et de l'élevage conçu par l'INRA. , TriPhase is a large thesaurus in the domain of animal physiology and livestock designed by INRA.",
"example_uri": "https://opendata.inra.fr/Triphase/ID_0000003",
"license": "CC-BY-4.0",
"name": "Thesaurus for Animal Physiology and Livestock Systems",
"prefix": "TRIPHASE",
"publication": "local:Avril, P., Bernard, E., Corvaisier, M., Girard, A., Golik, W., NΓ©dellec, C., Touze, M.-L., Wacrenier, N. (2016). Analyser la production scientifique d'un dΓ©partement de recherche : construction d'une ressource termino-ontologique par des documentalistes. Cahier des Techniques de l'INRA (89), 1-12.\nhttps://prodinra.inra.fr/record/386562",
"version": "1.2"
},
"UC_SENSE": {
"contact": {
"email": "mclange@ucdavis.edu",
"name": "Matthew Lange"
},
"description": "uc_Sense is an ontology for unambiguous characterization (UC) of sensory experiences and their descriptive terms. The uc_Sense ontology provides terms gathered from food and beverage flavor wheels in order to provide a vocabulary that will distinguish how a sensory event is perceived and how the same event is processed by an individual.",
"example_uri": "http://www.semanticweb.org/mateolan/ontologies/2016/3/untitled-ontology-5#perceived_milk_chocolate",
"name": "Unambiguous Characterization of Sensory Experiences Ontology",
"prefix": "UC_SENSE",
"publication": "https://ceur-ws.org/Vol-1747/IP11_ICBO2016.pdf",
"repository": "https://github.com/agroportal/uc_Sense"
},
"UO": {
"contact": {
"email": "g.gkoutos@gmail.com",
"name": "George Gkoutos"
},
"description": "Units Ontology (UO) is an ontology currently being used in many scientific resources for the standardized description of units of measurements. Metrical units for use in conjunction with PATO",
"example_uri": "http://purl.obolibrary.org/obo/UO_0000294",
"homepage": "https://github.com/bio-ontology-research-group/unit-ontology",
"license": "CC-BY-3.0",
"name": "Units of Measurement Ontology",
"prefix": "UO",
"publication": "https://doi.org/10.1093/database/bas033",
"repository": "https://github.com/bio-ontology-research-group/unit-ontology",
"version": "2023-05-25"
},
"USE": {
"contact": {
"email": "claire.nedellec@inrae.fr",
"name": "Claire NΓ©dellec"
},
"description": "The Use ontology is a subpart of the Ontobiotope ontology. It defines the uses and applications of microorganisms. Microorganisms are linked to the classes of the Use ontology by the relationship \"is studied for\". See examples in the Florilege database.",
"example_uri": "http://purl.obolibrary.org/obo/EC_0000026",
"homepage": "http://migale.jouy.inra.fr/florilege/#&searchByUse",
"license": "CC-BY-4.0",
"name": "Ontobiotope_Use",
"prefix": "USE",
"version": "V2"
},
"VARIO": {
"contact": {
"email": "mauno.vihinen@med.lu.se",
"name": "Mauno Vihinen"
},
"description": "Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations. VariO allows unambiguous description of variation effects as well as computerized analyses over databases utilizing the ontology for annotation. VariO is a position specific ontology that can be used to describe effects of variations on DNA, RNA and/or protein level, whatever is appropriate.",
"example_uri": "http://purl.obolibrary.org/obo/VariO_0117",
"homepage": "http://variationontology.org/",
"name": "Variation Ontology",
"prefix": "VARIO",
"publication": "http://genome.cshlp.org/content/early/2013/10/25/gr.157495.113.abstract",
"version": "2017-02-06"
},
"VT": {
"contact": {
"email": "jreecy@iastate.edu",
"name": "Jim Reecy"
},
"description": "The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.",
"example_uri": "http://purl.obolibrary.org/obo/VT_1000047",
"homepage": "https://www.animalgenome.org/bioinfo/projects/vt/",
"license": "CC-BY-4.0",
"name": "Vertebrate Trait Ontology",
"prefix": "VT",
"repository": "https://github.com/AnimalGenome/vertebrate-trait-ontology",
"version": "2024-07-22"
},
"WCACROPS": {
"contact": {
"email": "Caterina.Caracciolo@fao.org",
"name": "Caterina Caracciolo"
},
"description": "The more granular crop classification used in the FAO WCA. Used in the 2010 round of agricultural censuses.",
"example_uri": "http://stats-class.fao.uniroma2.it/WCA_CropList/Manioc_(cassava)",
"homepage": "http://stats-class.fao.uniroma2.it/skosmos_demo/WCACrops/en/",
"name": "FAO WCA Crop",
"prefix": "WCACROPS",
"version": "1.0"
},
"WHEATPHENOTYPE": {
"contact": {
"email": "claire.nedellec@inrae.fr",
"name": "Claire NΓ©dellec"
},
"description": "WheatPhenotype (also called Wheat Treat Ontology) is an ontology in OBO format that describes the traits of soft wheat (Triticum aestivum) and the environmental factors that affect these traits. Traits include traits of resistance, development, nutritional, baking quality, etc. Environmental factors include biotic and abiotic factors.",
"example_uri": "http://purl.obolibrary.org/obo/WTO_0000569",
"name": "Wheat Trait and Phenotype Ontology",
"prefix": "WHEATPHENOTYPE",
"publication": "https://dx.doi.org/10.5808/GI.2020.18.2.e14",
"version": "3.2"
},
"WHEAT_TAX": {
"contact": {
"email": "catherine.roussey@irstea.fr",
"name": "Catherine Roussey"
},
"description": "Manually built by Catherine Roussey, inspired by https://fr.wikipedia.org/wiki/TaxonomiedublΓ©. Each species proposed into the wheat species table have been validated with European Wheat data base http://genbank.vurv.cz/ewdb/. The taxon name and its ranking was firstly validated with the use of taxref reference table from INPN. NCBI's taxonomy have been used when not found in taxref. Then links to agrovoc's thesaurus, NAL and CABI Have been added. Links to ITIS database have been added, and also the links to DBpedia. Be warned : DBpedia contains two missing species :triticum zhukovsyi and triticum compactum erinaceum which are not in taxref. triticum zhukovsyi is in European Wheat data base. Links to TAXREF-LD have also been added.",
"example_uri": "http://ontology.irstea.fr/agronomictaxon/core#FamilyRank",
"homepage": "http://ontology.irstea.fr/pmwiki.php/Site/AgronomicTaxon",
"license": "CC-BY-4.0",
"name": "Wheat Taxa Gold Standard",
"prefix": "WHEAT_TAX"
},
"XEO": {
"contact": {
"email": "billiau@mpimp-golm.mpg.de",
"name": "Kenny Billiau"
},
"description": "XeO has been created to help plant scientists in documenting and sharing metadata describing the abiotic environment.",
"homepage": "https://xeo.codeplex.com/",
"license": "https://opensource.org/licenses/MIT",
"name": "XEML Environment Ontology",
"prefix": "XEO",
"repository": "https://xeo.codeplex.com/SourceControl/latest",
"version": "1.6"
}
} ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/bioportal/agroportal.py 0000644 0001751 0000177 00000000254 14655542206 025327 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Align the AgroPortal with the Bioregistry."""
from .bioportal import AgroPortalAligner
if __name__ == "__main__":
AgroPortalAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254800.0
bioregistry-0.11.12/src/bioregistry/external/bioportal/bioportal.json 0000644 0001751 0000177 00002435071 14655544020 025500 0 ustar 00runner docker {
"ABA-AMB": {
"contact": {
"email": "chinhda@alleninstitute.org",
"name": "Allen Institute for Brain Science"
},
"description": "Allen Brain Atlas P56 Mouse Ontology",
"homepage": "http://www.brain-map.org",
"name": "Allen Brain Atlas (ABA) Adult Mouse Brain Ontology",
"prefix": "ABA-AMB",
"publication": "http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470054085.html",
"version": "1"
},
"ABD": {
"contact": {
"email": "adaughton@lanl.gov",
"name": "Ashlynn Daughton"
},
"description": "Our disease ontology provides information on infectious diseases, disease synonyms, transmission pathways, disease agents, affected populations and disease properties. Diseases have been grouped into syndromic disease categories, such that programmers can look through relevant categories, as well as at specific diseases. Organisms, linked to both agents and populations, are structured hierarchically, to provide multiple levels of organism resolution. In addition, both disease transmission and relevant disease properties are available to search. Disease properties include tags like 'notifiable diseases' and 'economic importance' to flag particular disease characteristics that may be of interest, but are not captured elsewhere.",
"homepage": "http://brd.bsvgateway.org/disease",
"name": "Anthology of Biosurveillance Diseases",
"prefix": "ABD",
"publication": "http://brd.bsvgateway.org/reference"
},
"ACESO": {
"contact": {
"email": "shabann@uthsc.edu",
"name": "Arash Shaban-Nejad"
},
"description": "An ontology to help describe data about Adverse Childhood Experiences.",
"name": "Adverse Childhood Experiences Ontology",
"prefix": "ACESO",
"version": "Light"
},
"ACGT-MO": {
"contact": {
"email": "mbrochhausen@gmail.com",
"name": "Mathias Brochhausen"
},
"description": "The intention of the ACGT Master Ontology (MO) is to represent the domain of cancer research and management in a computationally tractable manner.",
"homepage": "http://www.ifomis.org/acgt",
"name": "Cancer Research and Management ACGT Master Ontology",
"prefix": "ACGT-MO",
"publication": "http://www.ifomis.org/acgt",
"version": "1.1"
},
"ACVD_ONTOLOGY": {
"contact": {
"email": "ma.hetong@imicams.ac.cn",
"name": "hetong"
},
"description": "The ontology describes the related aspects of atherosclerotic cerebrovascular disease, and provides a clear set of cross-lingual concepts and terms with an explicit hierarchical structure, helping scientific researchers to quickly retrieve relevant medical literature, assisting data scientists to efficiently identify relevant contents in electronic health records, and providing a clear domain framework for academic reference. The current ontology included 10 top-level classes, respectively clinical manifestation, comorbidity, complication, diagnosis, model of atherosclerotic cerebrovascular disease, pathogenesis, prevention, rehabilitation, risk factor, and treatment. Totally, there are 1715 concepts in the 11-level ontology, covering 4588 Chinese terms, 6617 English terms, and 972 definitions.",
"name": "Atherosclerotic Cerebrovascular Disease Ontology",
"prefix": "ACVD_ONTOLOGY",
"version": "1.0"
},
"AD-DROP": {
"contact": {
"email": "vincent643@gmail.com",
"name": "Henry Vincent"
},
"description": "Alzheimer Disease Relevance Ontology by Process (AD-DROP) aimed at classifying Disease Relevant Process according to their specificity, frequency and pathogenic intensity properties toward AD",
"name": "Alzheimer Disease Relevance Ontology by Process",
"prefix": "AD-DROP",
"version": "alpha"
},
"ADALAB": {
"contact": {
"email": "jacek.grzebyta@brunel.ac.uk",
"name": "Jacek Grzebyta"
},
"description": "AdaLab ontology",
"name": "AdaLab ontology",
"prefix": "ADALAB",
"version": "0.9.2"
},
"ADALAB-META": {
"contact": {
"email": "jacek.grzebyta@brunel.ac.uk",
"name": "Jacek Grzebyta"
},
"description": "AdaLab meta ontology.",
"name": "AdaLab-meta ontology",
"prefix": "ADALAB-META",
"version": "0.9.2"
},
"ADAR": {
"contact": {
"email": "peleg.mor@gmail.com",
"name": "Mor Peleg"
},
"description": "The autism DSM-ADI-R (ADAR) ontology extends an ontology by Tu et al. with additional SWRL rules to infer phenotypes from ADI-R items. It includes OWL class definitions representing DSM IV diagnostic criteria for autistic disorder and ASD criteria for Autism Spectrum Disorder OWL Reasoners can thus infer autism-related phenotypes from ADI-R questionnaire results Tu SW, Tennakoon L, Connor MO, Das A. Using an Integrated Ontology and Information Model for Querying and Reasoning about Phenotypesβ―: The Case of Autism. AMIA Annu Symp Proc 2008;727β31",
"name": "Autism DSM-ADI-R ontology",
"prefix": "ADAR",
"version": "1.1"
},
"ADCAD": {
"contact": {
"email": "mecum@nceas.ucsb.edu",
"name": "Bryce Mecum"
},
"description": "Ontology to support disciplinary annotation of datasets housed at the Arctic Data Center (https://arcticdata.io)",
"homepage": "https://github.com/NCEAS/adc-disciplines",
"name": "Arctic Data Center Academic Disciplines Ontology",
"prefix": "ADCAD",
"version": "Version 1.0.0"
},
"ADHER_INTCARE_EN": {
"contact": {
"email": "ester.roman.exts@juntadeandalucia.es",
"name": "Esther RomΓ‘n VillarΓ‘n"
},
"description": "This ontology includes concepts in English related to adherence to therapeutic plans in the context of integrated care. Includes maps with Snomed CT, bibliographic references and definitions from the Dictionary of the Royal Academy of Medicine of Spain. Ontology developed with the support of the project StandICT.eu. The equivalent ontology in Spanish is ADHER_INTCARE_SP.",
"name": "Adherence and Integrated Care",
"prefix": "ADHER_INTCARE_EN",
"version": "English 051319"
},
"ADHER_INTCARE_SP": {
"contact": {
"email": "carlos.parra.sspa@juntadeandalucia.es",
"name": "Carlos Luis Parra-CalderΓ³n"
},
"description": "This ontology includes concepts in Spanish related to adherence to therapeutic plans in the context of integrated care. Includes maps with Snomed CT, bibliographic references and definitions from the Dictionary of the Royal Academy of Medicine of Spain. Ontology developed with the support of the project StandICT.eu.",
"name": "Adherence and Integrated Care in Spanish",
"prefix": "ADHER_INTCARE_SP",
"version": "Spanish 052319"
},
"ADMF": {
"contact": {
"email": "pautorrentduran@gmail.com",
"name": "Pau Torrent Duran"
},
"description": "Alzheimer main ontologies",
"name": "alzhaimer dessiese main factors",
"prefix": "ADMF"
},
"ADMIN": {
"contact": {
"email": "philip.shields@live.vu.edu.au",
"name": "Philip Shields"
},
"description": "This is an ontology showing a nurse administrator's process domain",
"name": "Nurse Administrator",
"prefix": "ADMIN"
},
"ADMO": {
"contact": {
"email": "vincent.henry@inria.fr",
"name": "Henry Vincent"
},
"description": "Alzheimerβs disease (AD) pathophysiology is still imperfectly understood and current paradigms have not led to curative outcome. Omics technologies offer great promises for improving our understanding and generating new hypotheses. However, integration and interpretation of such data pose major challenges, calling for adequate knowledge models. AlzPathway is a disease map that gives a detailed and broad account of AD pathophysiology. However, AlzPathway lacks formalism, which can lead to ambiguity and misinterpretation. Ontologies are an adequate framework to overcome this limitation, through their axiomatic definitions and logical reasoning prop-erties. We introduce the AD Map Ontology (ADMO), an ontological upper model based on systems biology terms. We then propose to convert AlzPathway into an ontology and to integrate it into ADMO.",
"name": "Alzheimer Disease Map Ontology",
"prefix": "ADMO",
"version": "beta"
},
"ADO": {
"contact": {
"email": "alpha.tom.kodamullil@scai.fraunhofer.de",
"name": "Alpha Tom Kodamullil"
},
"description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer's Disease, structured by upper level Basic Formal Ontology (BFO). This ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining.",
"homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO",
"name": "Alzheimer's Disease Ontology",
"prefix": "ADO",
"publication": "https://pubmed.ncbi.nlm.nih.gov/23830913/",
"version": "2.0.1"
},
"ADW": {
"contact": {
"email": "adw.staff@umich.edu",
"name": "Animal Diversity Web technical staff"
},
"description": "An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.",
"homepage": "http://www.animaldiversity.org",
"name": "Animal Natural History and Life History Ontology",
"prefix": "ADW",
"version": "10/11/04"
},
"AEO": {
"contact": {
"email": "J.Bard@ed.ac.uk",
"name": "Jonathan Bard"
},
"description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology, to about 200 classes using the is_a relationship; it thus provides a detailed type classification for tissues. The new classes were chosen for their use in categorizing the major vertebrate and invertebrate anatomy ontologies at a granularity adequate for tissues of a single cell type. The ontology should be useful in increasing the amount of knowledge in anatomy ontologies, facilitating annotation and enabling interoperability across anatomy ontologies",
"homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology/",
"name": "Anatomical Entity Ontology",
"prefix": "AEO"
},
"AERO": {
"contact": {
"email": "mcourtot@gmail.com",
"name": "Melanie Courtot"
},
"description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events.",
"homepage": "http://purl.obolibrary.org/obo/aero",
"name": "Adverse Event Reporting Ontology",
"prefix": "AERO",
"version": "unknown"
},
"AFO": {
"contact": {
"email": "more.info@allotrope.org",
"name": "Allotrope Foundation"
},
"description": "Allotrope Merged Ontology Suite
The AFO is an ontology suite that provides a standard vocabulary and semantic model for the representation of laboratory analytical processes. The AFO suite is aligned at the upper layer to the Basic Formal Ontology (BFO). The core domains modeled include: Equipment, Material, Process, and Results.
This version of Allotrope Foundation Ontology (AFO) has been prepared specifically for publication on the NCBO platform.
license: http://purl.allotrope.org/voc/creative-commons-attribution-license
rights: http://purl.allotrope.org/voc/copyright
Please get the latest version of AFO from http://purl.allotrope.org
",
"homepage": "http://purl.allotrope.org",
"name": "Allotrope Merged Ontology Suite",
"prefix": "AFO",
"publication": "http://www.allotrope.org",
"version": "REC/2024/06"
},
"AFPO": {
"contact": {
"email": "mcmelek@msn.com",
"name": "Melek Chaouch"
},
"description": "AfPO is a tool which enables to annotate the African individuals, and brings together knowledge accumulated about existing populations with their genetic fingerprint in a standardized format.",
"homepage": "https://github.com/h3abionet/afpo",
"name": "African Population Ontology",
"prefix": "AFPO",
"version": "2024-03-21"
},
"AGRO": {
"contact": {
"email": "m.a.laporte@cgiar.org",
"name": "Marie-AngΓ©lique Laporte"
},
"description": "AGRO, the AGRonomy Ontology, describes agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments. AGRO is being built using traits identified by agronomists, the ICASA variables, and other existing ontologies such as ENVO, UO, and PATO, IAO, and CHEBI. Further, AGRO will power an Agronomy Management System and fieldbook modeled on a CGIAR Breeding Management System to capture agronomic data.",
"homepage": "https://github.com/AgriculturalSemantics/agro",
"name": "AGRonomy Ontology",
"prefix": "AGRO"
},
"AGROCYMAC": {
"contact": {
"email": "gema.herreras@ug.edu.ec",
"name": "Gema Herrera"
},
"description": "Agrocymac es una ontologΓa creada para estructurar informaciΓ³n sobre el control y monitoreo de plagas, malezas y enfermedades que afectan especΓficamente a los cultivos de Arroz, CafΓ© y Cacao.",
"name": "Control y Monitoreo de afecciones en los cultivos",
"prefix": "AGROCYMAC"
},
"AGROMOP": {
"contact": {
"email": "pedrovelez5.1995@hotmail.com",
"name": "Pedro"
},
"description": "Ontologia con informaciΓ³n relevante al cuidado del cacao de manera orgΓ‘nica contra plagas y enfermedades.",
"name": "Control de Cacao",
"prefix": "AGROMOP",
"version": "1.1"
},
"AHOL": {
"contact": {
"email": "jeremy.yon@inra.fr",
"name": "JΓ©rΓ©my Yon"
},
"description": "AHOL (Animal Health Ontology for Livestock) is an ontology of characteristics defining health issues of livestock in their environment (EOL) linked to their phenotypes (ATOL). AHOL aims to: - provide a reference ontology of health traits of farm animals for the international scientific and educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the AHOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production",
"homepage": "http://147.99.156.182/ontologies/visualisation/ontologie/",
"name": "Animal Health Ontology for Livestock",
"prefix": "AHOL",
"version": "1.0"
},
"AHSO": {
"contact": {
"email": "ahso@datadrivensurveillance.org",
"name": "Karl Hammar"
},
"description": "(Work in progress - please contact ahso@datadrivensurveillance.org before using this ontology) This is an ontology for health surveillance, assuming that surveillance data is recorded at three main levels: SAMPLE data - data about specific collected samples; OBSERVATIONS, which can aggregate several samples; and OBSERVATIONAL CONTEXT, which is the context in which the observations were made (for instance clinical observation, surveillance sampling, etc). HEALTH EVENT is the occurrence in the real World to be modeled. This occurrence is an abstract concept, as it generally cannot be determined what are its boundaries in time, space, or population units. We assume that several OBSERVATIONS are derived from each health event, and recorded in the same or different databases - for instance clinical journal, laboratory database, abattoir. At the same time or not. AHSO attempts to model these time specific observations. The ontology is focused on the modeling of the animal and health information connected to a single observation, made at a specific point on time. All the information recorded is relative to that specific point in time. For instance, an animal belongs to a herd, which belongs to an owner, AT THE TIME OF THE OBSERVATION. We do not attempt to model how that animal changed herds on time. Similarly, we do not model clinical progression. It is up to those using the data to create definitions of when two observations should be connected to the same event.",
"homepage": "http://datadrivensurveillance.org/ahso",
"name": "Animal Health Surveillance Ontology",
"prefix": "AHSO",
"version": "0.1.0"
},
"AI-RHEUM": {
"contact": {
"email": "custserv@nlm.nih.gov",
"name": "NLM Customer Service"
},
"description": "AI/RHEUM is used for the diagnosis of rheumatologic diseases. AI/RHEUM contains findings, such as clinical signs, symptoms, laboratory test results, radiologic observations, tissue biopsy results, and intermediate diagnosis hypotheses. Findings and hypotheses, which include definitions, are used to reach diagnostic conclusions with definite, probable, or possible certainty. AI/RHEUM is used by clinicians and informatics researchers.",
"name": "Artificial Intelligence Rheumatology Consultant System Ontology",
"prefix": "AI-RHEUM",
"version": "2023AB"
},
"AIO": {
"contact": {
"email": "MJoachimiak@lbl.gov",
"name": "marcin pawel joachimiak"
},
"description": "This ontology models classes and relationships describing deep learning networks, their component layers and activation functions, as well as potential biases.",
"homepage": "https://github.com/berkeleybop/artificial-intelligence-ontology",
"name": "Artificial Intelligence Ontology",
"prefix": "AIO",
"publication": "https://arxiv.org/abs/2404.03044",
"version": "2024-08-09"
},
"AISM": {
"contact": {
"email": "entiminae@gmail.com",
"name": "Jennifer C. GirΓ³n"
},
"description": "The AISM contains terms used in insect biodiversity research for describing structures of the exoskeleton and the skeletomuscular system. It aims to serve as the basic backbone of generalized terms to be expanded with order-specific terminology.",
"homepage": "https://github.com/insect-morphology/aism",
"name": "Ontology for the Anatomy of the Insect SkeletoMuscular system",
"prefix": "AISM",
"publication": "GirΓ³n, J. C., S. Tarasov, L. A. GonzΓ‘lez MontaΓ±a, N. Matentzoglu, A. D. Smith, M. Koch, B. E. Boudinot, P. Bouchard, R. Burks, L. Vogt, M. Yoder, D. Osumi-Sutherland, F. Friedrich, R. Beutel, I. MikΓ³ (2022) Formalizing insect morphological data: a model-based, extensible insect anatomy ontology and its potential applications in biodiversity research and informatics. Preprints. https://doi.org/10.20944/preprints202201.0254.v1",
"version": "2023-04-14"
},
"ALLERGIDOC": {
"contact": {
"email": "marcin.trzmielewski@univ-montp3.fr",
"name": "Marcin Trzmielewski"
},
"description": "The ALLERGIDOC Ontology represents and articulates scientific, clinical and generalist knowledge of the allergy domain, through user-oriented main classes (facets) closely linked to informational targets of allergy professionals. It has been constructed by Marcin Trzmielewski (under the direction of CΓ©line Paganelli) for the Allergy Unit of the Montpellier University Hospital, as a part of a thesis in Information Science and Communication Studies at the Paul-ValΓ©ry University of Montpellier 3. The ontology was created according to a constructivist approach, that relied on one hand, on the study of the informational practices of allergy employees; and on the other hand, on a terminological and linguistic analysis of documents that employees use in their daily activities.",
"homepage": "https://allergo.infodocs.eu/allergidoc1",
"name": "Allergy Ontology",
"prefix": "ALLERGIDOC",
"publication": "doi.org/10.5771/0943-7444-2024-3-151",
"version": "1.0"
},
"ALLERGYDETECTOR": {
"contact": {
"email": "nquevedo@hotmail.com",
"name": "Nelson Quevedo"
},
"description": "Allergy Detection Ontology.",
"name": "Allergy Detector II",
"prefix": "ALLERGYDETECTOR",
"version": "0.0.1"
},
"AMINO-ACID": {
"contact": {
"email": "admin@co-ode.org",
"name": "Nick Drummond, Georgina Moulton, Robert Stevens, Phil Lord"
},
"description": "An ontology of amino acids and their properties. Inferred version.",
"homepage": "http://www.co-ode.org/ontologies/amino-acid/2009/02/16/",
"name": "Amino Acid Ontology",
"prefix": "AMINO-ACID",
"version": "version 1.2, copyright The University of\n\t\t\tManchester, Nick Drummond, Georgina Moulton, Robert Stevens, Phil Lord"
},
"AMPHX": {
"contact": {
"email": "hescriva@obs-banyuls.fr",
"name": "Hector Escriva"
},
"description": "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).",
"homepage": "https://github.com/EBISPOT/amphx_ontology",
"name": "The Amphioxus Development and Anatomy Ontology",
"prefix": "AMPHX"
},
"AO": {
"contact": {
"email": "s.shinneman@surrey.ac.uk",
"name": "Stacy Shinneman"
},
"description": "Asthma ontology",
"homepage": "www.clininf.eu",
"name": "Asthma Ontology",
"prefix": "AO",
"version": "1.3"
},
"APACOMPUTER": {
"contact": {
"email": "iangalloway75@gmail.com",
"name": "Ian Galloway"
},
"description": "APA Computer Cluster",
"name": "Computer Cluster",
"prefix": "APACOMPUTER"
},
"APADISORDERS": {
"contact": {
"email": "alexgarciac@gmail.com",
"name": "alexander Garcia"
},
"description": "APA Disorders cluster, owls loaded from urls.",
"name": "Disorders cluster",
"prefix": "APADISORDERS"
},
"APAEDUCLUSTER": {
"contact": {
"email": "alexgarciac@gmail.com",
"name": "alexander Garcia"
},
"description": "APA Educational Cluster, URI based ontology load",
"name": "Educational Cluster",
"prefix": "APAEDUCLUSTER"
},
"APANEUROCLUSTER": {
"contact": {
"email": "alexgarciac@gmail.com",
"name": "alexander Garcia"
},
"description": "APA Neuropsychology and Neurology Cluster",
"name": "APA Neuro Cluster",
"prefix": "APANEUROCLUSTER"
},
"APAOCUEMPLOY": {
"contact": {
"email": "alexgarciac@gmail.com",
"name": "alexander Garcia"
},
"description": "APA Occupational and Employment Cluster",
"name": "APA Occupational and Employment cluster",
"prefix": "APAOCUEMPLOY"
},
"APAONTO": {
"contact": {
"email": "alexgarciac@gmail.com",
"name": "alexander garcia"
},
"description": "APA thesaurus . Flat ontology file",
"name": "Psychology Ontology",
"prefix": "APAONTO",
"version": "4"
},
"APASTATISTICAL": {
"contact": {
"email": "alexgarciac@gmail.com",
"name": "alexander Garcia"
},
"description": "APA Statistical Cluster",
"name": "APA Statistical Cluster",
"prefix": "APASTATISTICAL"
},
"APATANDT": {
"contact": {
"email": "alexgarciac@gmail.com",
"name": "alexander Garcia"
},
"description": "APA Tests and Testing Cluster",
"name": "APA Tests and Testing cluster",
"prefix": "APATANDT"
},
"APATREATMENT": {
"contact": {
"email": "alexgarciac@gmail.com",
"name": "alexander Garcia"
},
"description": "APA Treatment Cluster",
"name": "APA Treatment Cluster",
"prefix": "APATREATMENT"
},
"APO": {
"contact": {
"email": "sgd-helpdesk@lists.stanford.edu",
"name": "Saccharomyces Genome Database"
},
"description": "A structured controlled vocabulary for the phenotypes of Ascomycete fungi",
"homepage": "http://www.yeastgenome.org/",
"name": "Ascomycete Phenotype Ontology",
"prefix": "APO",
"version": "releases/2024-08-03"
},
"APOLLO-SV": {
"contact": {
"email": "hoganwr@gmail.com",
"name": "William Hogan"
},
"description": "Apollo-SV, developed as an OWL specification, defines the terms and relations necessary for interoperation between epidemic simulators and public health application software that interface with these simulators.",
"homepage": "https://github.com/ApolloDev/apollo-sv",
"name": "Apollo Structured Vocabulary",
"prefix": "APOLLO-SV",
"version": "2024-04-19"
},
"APRO": {
"contact": {
"email": "zhangqiang_dh@163.com",
"name": "Qiang Zhang"
},
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εθθδΊζη¨ζ§εζ©ε±ζ§οΌζ―ζθ·¨ι’εηζ₯θ―’εεζγ APRO (Ancient Poet Resource Ontology) is an ontology designed to systematically organize and describe information related to ancient Chinese poets and their works. The ontology encompasses the life, works, historical context, and related events of ancient poets, as well as emotional and stylistic characteristics associated with their works. Integrating elements of historical, literary, and cultural studies, APRO provides a rich framework for analyzing and exploring the richness and complexity of ancient Chinese poetry. Key features and components include: Person Class: Contains basic information about ancient poets, such as their names, courtesy names, art names, birth and death dates, major achievements, and life events. Work Class: Details the main works of the poets, including the name of the work, time of creation, genre, theme, and style. Event Class: Records significant historical events related to the poets and their works. Emotion Class: Covers the emotional tendencies and stylistic features expressed in the works. Resource Class: Pertains to various resources associated with the poets and their works, such as literature, research papers, and educational materials. Time and Place Class: Specifies the times and places of the poets' activities, as well as the background of the creation of their works. The APRO ontology is suitable for literary researchers, historians, educators, and anyone interested in ancient Chinese poetry, for use in teaching, academic research, and cultural heritage preservation. The design of the ontology takes into account ease of use and extensibility, supporting cross-disciplinary queries and analysis.",
"name": "Ancient Poet Resource Ontology",
"prefix": "APRO"
},
"ARCRC": {
"contact": {
"email": "mecum@nceas.ucsb.edu",
"name": "Bryce Mecum"
},
"description": "An ontology associated with the National Oceanic and Atmospheric Administration's (NOAA) Arctic Report Card: https://arctic.noaa.gov/Report-Card project.",
"homepage": "https://github.com/DataONEorg/sem-prov-ontologies/tree/master/arctic-report-card",
"name": "Arctic Report Card",
"prefix": "ARCRC",
"version": "0.10.0"
},
"ARO": {
"contact": {
"email": "mcarthua@mcmaster.ca",
"name": "Andrew G. McArthur"
},
"description": "The Antibiotic Resistance Ontology describes antibiotic resistance genes and mutations, their products, mechanisms, and associated phenotypes, as well as antibiotics and their molecular targets. It is integrated with the Comprehensive Antibiotic Resistance Database, a curated resource containing high quality reference data on the molecular basis of antimicrobial resistance.",
"homepage": "https://github.com/arpcard/aro",
"name": "Antibiotic Resistance Ontology",
"prefix": "ARO"
},
"ASDF": {
"name": "testiiii1",
"prefix": "ASDF"
},
"ASDPTO": {
"contact": {
"email": "Alexa_McCray@hms.harvard.edu",
"name": "Alexa T McCray"
},
"description": "Autism Spectrum Disorder Phenotype Ontology encapsulates the Autism Spectrum Disorder behavioral phenotype, informed by the standard ASD assessment instruments and the currently known characteristics of this disorder. http://www.ncbi.nlm.nih.gov/pubmed/24163114",
"name": "Autism Spectrum Disorder Phenotype Ontology",
"prefix": "ASDPTO",
"version": "1"
},
"ASPECT": {
"contact": {
"email": "niva@dtu.dk",
"name": "Nikola Vasiljevic"
},
"description": "This is a taxonomy (i.e. controlled vocabulary) of variables, parameters, and constants used in the wind energy community.",
"homepage": "http://purl.org/aspect",
"name": "ASPECT: wind energy vAriableS, ParametErs and ConsTants",
"prefix": "ASPECT",
"version": "0.1.0"
},
"ASSAYNODE": {
"contact": {
"email": "aleka.aktau@gmail.com",
"name": "Aliya Aktau"
},
"description": "An ontology providing controlled vocabularies for Sequence Analysis and sequencing instrument model.",
"name": "Assaynode",
"prefix": "ASSAYNODE",
"version": "1.0"
},
"ATC": {
"contact": {
"email": "whocc@fhi.no",
"name": "WHO Collaborating Centre for Drug Statistics Methodology"
},
"description": "The Anatomical Therapeutic Chemical (ATC) Classification System is used for the classification of active ingredients of drugs according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. It is controlled by the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC), and was first published in 1976.",
"homepage": "http://www.who.int/classifications/atcddd/en/",
"name": "Anatomical Therapeutic Chemical Classification",
"prefix": "ATC",
"publication": "http://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System",
"version": "2023AB"
},
"ATO": {
"contact": {
"email": "sbhdbe@mst.edu",
"name": "AmphiAnat list"
},
"description": "A taxonomy of Amphibia",
"homepage": "http://www.amphibanat.org",
"name": "Amphibian Taxonomy Ontology",
"prefix": "ATO",
"version": "See Remote Site"
},
"ATOL": {
"contact": {
"email": "matthieu.reichstadt@clermont.inra.fr",
"name": "Reichstadt Matthieu"
},
"description": "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientific and educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production",
"homepage": "www.atol-ontology.com",
"name": "Animal Trait Ontology for Livestock",
"prefix": "ATOL",
"version": "6.0"
},
"ATOM": {
"contact": {
"email": "tgbugs@gmail.com",
"name": "Tom Gillespie"
},
"description": "An ontology model for anatomical atlases.",
"homepage": "https://github.com/SciCrunch/NIF-Ontology",
"name": "Atlas Ontology Model",
"prefix": "ATOM",
"publication": "https://doi.org/10.1101/2023.01.22.525049",
"version": "2023-04-27"
},
"AURA": {
"contact": {
"email": "vinay.chaudhri@sri.com",
"name": "Vinay Chaudhri"
},
"description": "KB_Bio_101 is the ontology of the AURA + Inquire project @ SRI International, Menlo Park. This work is owned by Vulcan Inc. and is licensed for use under the Creative Commons Attribution-NonCommerical-ShareAlike 3.0 license (http://creativecommons.org/licenses/by-nc-sa/3.0/). Vulcan Inc., June 2013",
"homepage": "http://www.ai.sri.com/people/chaudhri",
"name": "KB_Bio_101",
"prefix": "AURA",
"publication": "http://www.ai.sri.com/software/AURA",
"version": "1.0"
},
"BAO": {
"contact": {
"email": "sschurer@med.miami.edu",
"name": "Stephan Schurer"
},
"description": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 1000 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc.). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation.",
"homepage": "http://www.bioassayontology.org/",
"name": "BioAssay Ontology",
"prefix": "BAO",
"publication": "http://www.bioassayontology.org/",
"version": "2.8.11"
},
"BAO-GPCR": {
"contact": {
"email": "sschurer@med.miami.edu",
"name": "Stephan Schurer"
},
"description": "The G protein-coupled receptors (GPCRs) ontology (http://www.bioassayontology.org/bao_gpcr) describes pharmacology, biochemistry and physiology of these important and therapeutically promising class of academic and pharmaceutical research targets. Incorporation and comparison of various small molecule screening data sets, such as those deposited in PubChem, ChEMBL, KEGG, PDSP, and/or IUPHAR databases, requires a formalized electronic organization system. In order to bridge the gap between the overflow of HTS data and the bottleneck of integrated analysis tools, herein, we provide the first comprehensive GPCR ontology. The development and utility of GPCR ontology was based on previously developed BioAssay Ontology (BAO). The GPCR ontology contains information about biochemical, pharmacological, and functional properties of individual GPCRs as well as GPCR-selective ligands inclusive of their HTS screening results and other records. This provides the first all-inclusive GPCR ontology with all available data to model the relationship between the GPCR binding sites and their physiologic and pharmacologic role in physiology via small molecule chemical structures. We developed this system using emerging semantic technologies, by leveraging existing and descriptive domain level ontologies.",
"homepage": "http://www.bioassayontology.org/",
"name": "G Protein-Coupled Receptor BioAssays Ontology",
"prefix": "BAO-GPCR",
"publication": "http://www.schurerlab.org/home/publications",
"version": "1.1"
},
"BCGO": {
"contact": {
"email": "alex27bulzan@yahoo.com",
"name": "Alexandra Bulzan"
},
"description": "assigns a grade to a tumor starting from the 3 criteria of the NGS",
"name": "Breast Cancer Grading Ontology",
"prefix": "BCGO",
"version": "1.5"
},
"BCI-O": {
"contact": {
"email": "srodriguez@pet.cs.nctu.edu.tw",
"name": "Sergio JosΓ© RodrΓguez MΓ©ndez"
},
"description": "The BCI ontology specifies a foundational metadata model set for real-world multimodal Brain-Computer Interaction (BCI) data capture activities. Its structure depicts a conceptual framework that BCI applications can extend and use in their implementations, to define core concepts that capture a relevant and interoperable metadata vocabulary. This ontology is aligned to the Semantic Sensor Network Ontology (SSN): a domain-independent and end-to-end model for sensor/actuator applications. Hence, its structure has been normalized to assist its use in conjunction with other ontologies or linked data resources to specify any particular definitions (such as units of measurement, time and time series, and location and mobility), that specialized applications in the BCI domain might need. Its spec provides general alignment data modeling guidelines for core concepts, to help BCI applications in their design.",
"homepage": "http://lov.okfn.org/dataset/lov/vocabs/bci",
"name": "Brain-Computer Interaction (BCI) Ontology",
"prefix": "BCI-O",
"publication": "https://github.com/perma-id/w3id.org/tree/master/BCI-ontology",
"version": "0.9.6"
},
"BCLION": {
"contact": {
"email": "zonghui0228@163.com",
"name": "Hui Zong"
},
"description": "The Breast Cancer Lifestyle Ontology (BCLION) captures various factors related to lifestyle choices and behaviors that may influence the risk of developing breast cancer. It provides a structured representation of these factors in a hierarchical manner, allowing for a comprehensive understanding of the different aspects of breast cancer lifestyle.",
"name": "Breast Cancer Lifestyle Ontology",
"prefix": "BCLION",
"version": "1.0"
},
"BCO": {
"contact": {
"email": "bco-discuss@googlegroups.com",
"name": "bco-discuss list"
},
"description": "BCO supports the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. A key feature of BCO is an ontological interpretation of Darwin Core terms.",
"homepage": "https://github.com/BiodiversityOntologies/bcom/p/bco/",
"name": "Biological Collections Ontology",
"prefix": "BCO",
"version": "2021-11-14"
},
"BCON": {
"contact": {
"email": "zonghui0228@163.com",
"name": "Hui Zong"
},
"description": "The Breast Cancer Ontology (BCON) aims to capture the diverse aspects of breast cancer, including its molecular biology, pathology, epidemiology, clinical data, and lifestyle factors. By representing this knowledge in a standardized and machine-readable format, the ontology enables researchers, clinicians, and other stakeholders to access, share, and analyze breast cancer-related information more effectively. It serves as a valuable resource for organizing existing knowledge, discovering new insights, and supporting decision-making processes in the field of breast cancer research and healthcare.",
"name": "Breast Cancer Ontology",
"prefix": "BCON",
"version": "1.0"
},
"BCS7": {
"contact": {
"email": "cancer.staging.ontology@gmail.com",
"name": "Cancer Staging Ontology Developers, Tetherless World Constellation, Rensselaer Polytechnic Institute"
},
"description": "Breast Cancer Staging axioms as per the AJCC 7th Edition Guidelines.",
"homepage": "https://cancer-staging-ontology.github.io",
"name": "Breast Cancer Staging - 7th Edition",
"prefix": "BCS7",
"version": "version 0.1"
},
"BCS8": {
"contact": {
"email": "cancer.staging.ontology@gmail.com",
"name": "Cancer Staging Ontology Developers, Tetherless World Constellation, Rensselaer Polytechnic Institute"
},
"description": "Breast Cancer Staging axioms as per the AJCC 8th Edition Guidelines.",
"homepage": "https://cancer-staging-ontology.github.io",
"name": "Breast Cancer Staging - 8th Edition",
"prefix": "BCS8",
"version": "version 0.1"
},
"BCSR-ONTO": {
"contact": {
"email": "erohrer@fing.edu.uy",
"name": "Edelweis Rohrer"
},
"description": "BCSR-Onto represents knowledge about risk assessment and recommendations by diverse guidelines for breast cancer screening both for women at high and average risk of developing breast cancer.",
"name": "Breast cancer screening recommendation ontology",
"prefix": "BCSR-ONTO",
"version": "2.1"
},
"BCTEO": {
"contact": {
"email": "federica.viti@itb.cnr.it",
"name": "Federica Viti / Alessandro Orro"
},
"description": "Ontology that describes the field of Tissue Engineering for what concerns bone and cartilage tissues.",
"name": "Bone and Cartilage Tissue Engineering Ontology",
"prefix": "BCTEO",
"publication": "Federica Viti, Silvia Scaglione, Alessandro Orro, Luciano Milanesi \"Guidelines for managing data and processes in bone and cartilage tissue engineering\", BMC Bioinformatics, in press.",
"version": "releases/2013-08"
},
"BCTT": {
"contact": {
"email": "remove@aon.at",
"name": "no"
},
"description": "BCT Taxonomy v0.4",
"homepage": "http://www.ucl.ac.uk/behaviour-change-techniques",
"name": "Behaviour Change Technique Taxonomy",
"prefix": "BCTT",
"version": "0.4"
},
"BDO": {
"contact": {
"email": "tudor.groza@uq.edu.au",
"name": "Tudor Groza"
},
"description": "The Bone Dysplasia ontology provides a comprehensive and formal representation of the different domain concepts involved in documenting the full complexity of the skeletal dysplasia domain. It captures and combines the genetic features that discriminate the bone dysplasias with the multitude of phenotypic characteristics manifested by patients and required to be taken into account in order to support the diagnosis process.",
"name": "Bone Dysplasia Ontology",
"prefix": "BDO",
"version": "1.5"
},
"BE": {
"contact": {
"email": "benjamin_gyori@hms.harvard.edu",
"name": "Benjamin Gyori"
},
"description": "Bioentities is a collection of resources for grounding biological entities from text and describing their hierarchical relationships, focusing on protein families and complexes.",
"homepage": "http://github.com/sorgerlab/bioentities",
"name": "Bioentities",
"prefix": "BE",
"version": "1.0"
},
"BERO": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "Biological and Environmental Research Ontology (BERO) is an application ontology developed by the combination of many ontologies (base or subsets) namely : ChEBI, ECOCORE, EDAM, ENVO, GO, MeSH, MOP, NCBITaxon, NCIT, OBI, OMO, PATO, PO and TO.",
"homepage": "https://github.com/berkeleybop/bero",
"name": "Biological and Environmental Research Ontology",
"prefix": "BERO",
"version": "2022-12-23"
},
"BFLC": {
"contact": {
"email": "nlorimer@stanford.edu",
"name": "Nancy Lorimer"
},
"description": "An experimental extension to BIBFRAME 2.0 primarily for use by the Library of Congress, but with additions also applicable for other users",
"homepage": "http://id.loc.gov/ontologies/bflc.html",
"name": "LC BIBFRAME 2.0 Vocabulary Extension",
"prefix": "BFLC",
"version": "1.2.0"
},
"BFO": {
"contact": {
"email": "phismith@buffalo.edu",
"name": "Barry Smith"
},
"description": "BFO grows out of a philosophical orientation which overlaps with that of DOLCE and SUMO. Unlike these, however, it is narrowly focused on the task of providing a genuine upper ontology which can be used in support of domain ontologies developed for scientific research, as for example in biomedicine within the framework of the OBO Foundry. Thus BFO does not contain physical, chemical, biological or other terms which would properly fall within the special sciences domains.",
"homepage": "http://www.ifomis.org/bfo",
"name": "Basic Formal Ontology",
"prefix": "BFO",
"version": "2.0"
},
"BHN": {
"description": "L'activité innovante de biologie et d'anatomo-pathologie réalisée notamment dans les Centres Hospitalo-Universitaires est habituellement appelée \"activité hors nomenclature\" (BHN pour la biologie hors nomenclature et PHN pour l'anatomo-pathologie hors nomenclature). Ce caractère \"hors nomenclature\" signifie que l'assurance maladie n'a pas encore intégré ces actes dans la Nomenclature des Actes de Biologie Médicale (NABM) ou la Nomenclature Générale des Actes Professionnels (NGAP).",
"homepage": "http://www.chu-montpellier.fr/publication/inter_pub/R300/rubrique.jsp",
"name": "Biologie Hors Nomenclature",
"prefix": "BHN",
"version": "3.2"
},
"BHO": {
"contact": {
"email": "smollah@rockefeller.edu",
"name": "Shamim Mollah"
},
"description": "An application ontology devoted to the standardized recording of phenotypic data related to hemorrhagic disorders.",
"homepage": "http://www.rockefeller.edu/ccts/bioinformatics.php",
"name": "Bleeding History Phenotype Ontology",
"prefix": "BHO",
"publication": "http://www.rockefeller.edu/ccts/bioinformatics.php",
"version": "0.4"
},
"BIBFRAME": {
"contact": {
"email": "khes@loc.gov",
"name": "Kirk Hess"
},
"description": "Initiated by the Library of Congress, BIBFRAME provides a foundation for the future of bibliographic description, both on the web, and in the broader networked world. In addition to being a replacement for MARC, BIBFRAME serves as a general model for expressing and connecting bibliographic data. A major focus of the initiative will be to determine a transition path for the MARC 21 formats while preserving a robust data exchange that has supported resource sharing and cataloging cost savings in recent decades.",
"homepage": "https://www.loc.gov/bibframe/",
"name": "BIBFRAME 2.0",
"prefix": "BIBFRAME",
"version": "2.2.0"
},
"BIBLIOTEK-O": {
"contact": {
"email": "jgraybeal@stanford.edu",
"name": "John Graybeal"
},
"description": "An ontology recommendation for modeling bibliographic metadata",
"homepage": "http://bibliotek-o.org/",
"name": "The Biblioteko Ontology",
"prefix": "BIBLIOTEK-O",
"version": "Version 1.1.0"
},
"BIFO": {
"contact": {
"email": "TRAMARAJ@depaul.edu",
"name": "Thiru Ramaraj"
},
"description": "BIFO is intended to provide a biofilm ontology capable of understanding fundamental terminologies the relations between common biofilm terminologies following the guidelines of the Basic Formal Ontology (BFO).",
"homepage": "https://github.com/biofilmDB/ontology",
"name": "Biofilm Ontology",
"prefix": "BIFO",
"publication": "https://github.com/biofilmDB/ontology"
},
"BIM": {
"contact": {
"email": "nagy1989@gmail.com",
"name": "Mate Levente Nagy"
},
"description": "Biomedical images published within the scientific literature play a central role in reporting and facilitating life science discoveries. Existing ontologies and vocabularies describing biomedical images, particularly sequence images, do not provide sufficient semantic representation for image annotations generated automatically and/or semi-automatically. We present an open ontology for the annotation of biomedical images (BIM) scripted in OWL/RDF. The BIM ontology provides semantic vocabularies to describe the manually curated image annotations as well as annotations generated by online bioinformatics services using content extracted from images by the Semantic Enrichment of Biomedical Images (SEBI) system. The BIM ontology is represented in three parts; (i) image vocabularies - which holds vocabularies for the annotation of an image and/or region of interests (ROI) inside an image, as well as vocabularies to represent the pre and post processing states of an image, (ii) text entities - covers annotations from the text that are associated with an image (e.g. image captions) and provides semantic representation for NLP algorithm outputs, (iii) a provenance model - that contributes towards the maintenance of annotation versioning. To illustrate the BIM ontologyβs utility, we provide three annotation cases generated by BIM in conjunction with the SEBI image annotation engine.",
"homepage": "https://sites.google.com/site/bimontology/",
"name": "Biomedical Image Ontology",
"prefix": "BIM",
"publication": "https://code.google.com/p/bio-ont/",
"version": "1.3"
},
"BIN": {
"contact": {
"email": "pbruha@kiv.zcu.cz",
"name": "Petr BrΕ―ha"
},
"description": "This ontology was created as a part of VΓtΔzslav Vacek's masters thesis and is describing the terminology used within the Body in Numbers (BiN) project that is currently underway (as of 2019-05-01) at the University of West Bohemia, Czech Republic and focuses on the terminology used during the data collection process.",
"name": "Body in Numbers project terminology",
"prefix": "BIN",
"version": "1.1"
},
"BIODIVTHES": {
"contact": {
"email": "dominique.vachez@inist.fr",
"name": "Dominique Vachez"
},
"description": "This bilingual thesaurus organizes the key concepts of biodiversity sciences, in their basic and applied ecological components. It uses polyhierarchy and includes 818 reciprocal associative relationships. The 1654 French and English descriptors (designating 827 concepts) are enriched with a large number of synonyms (1860) and hidden variants (7020) in both languages. Concepts are grouped into 82 collections, by semantic categories, thematic fields and EBV classes (Essential Biodiversity Variables). Definitions are given with their sources. This resource is aligned with the international thesauri AGROVOC, GEMET (GEneral Multilingual Environmental Thesaurus) and EnvThes (Environmental Thesaurus), as well as with the ontology ENVO (Environment Ontology).",
"homepage": "https://www.loterre.fr/skosmos/BLH/en/",
"name": "Biodiversity Thesaurus",
"prefix": "BIODIVTHES",
"version": "2.1"
},
"BIOLINK": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations",
"homepage": "https://biolink.github.io/biolink-model/",
"name": "Biolink Model",
"prefix": "BIOLINK",
"version": "2.2.13"
},
"BIOMO": {
"contact": {
"email": "mikel.egana@ehu.es",
"name": "Mikel EgaΓ±a Aranguren"
},
"description": "The BIOMO ontology maps the HDF5 based BIOM format (http://biom-format.org/) to OWL, offering a method to convert a BIOM file to RDF and therefore publish it as Linked Data",
"homepage": "http://github.com/mikel-egana-aranguren/biom-ld",
"name": "Biological Observation Matrix Ontology",
"prefix": "BIOMO",
"version": "0.0.1"
},
"BIOMODELS": {
"contact": {
"email": "robert.hoehndorf@kaust.edu.sa",
"name": "Robert Hoehndorf"
},
"description": "OWL Representation of the models in the BioModels repository.",
"homepage": "https://code.google.com/p/sbmlharvester/",
"name": "BioModels Ontology",
"prefix": "BIOMODELS",
"publication": "http://www.biomedcentral.com/1752-0509/5/124",
"version": "21"
},
"BIPOM": {
"contact": {
"email": "anne.goelzer@inrae.fr",
"name": "Anne Goelzer"
},
"description": "BiPOm is an ontology based on systemic representation of metabolic processes. BiPOm is an ontological model carrying the main biological processes and molecular roles/functions at a high level of genericity where the usual annotated resources are treated as instances. BiPOm, 1) contains biological knowledge as instances and 2) uses automatic reasoning through Semantic Web Rule Language (SWRL) in order to automatically infer, formalize and refine properties of molecules.",
"name": "Biological interlocked Process Ontology for metabolism",
"prefix": "BIPOM",
"version": "Core"
},
"BIPON": {
"contact": {
"email": "anne.goelzer@inra.fr",
"name": "Anne Goelzer"
},
"description": "BiPON is an ontology permitting a multi-scale systemic representation of bacterial cellular processes and the coupling to their mathematical models. BiPON is further composed of two sub- ontologies, bioBiPON and modelBiPON. bioBiPON aims at organizing the systemic description of biological information while modelBiPON aims at describing the mathematical models (including parameters) associated to each biological process.",
"name": "Bacterial interlocked Process ONtology",
"prefix": "BIPON",
"version": "2017-11-08-bis"
},
"BIRNLEX": {
"contact": {
"email": "wbug@ncmir.ucsd.edu",
"name": "William Bug"
},
"description": "The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design.",
"homepage": "http://xwiki.nbirn.net:8080/xwiki/bin/view/%20BIRN-OTF-Public/Home",
"name": "Biomedical Informatics Research Network Project Lexicon",
"prefix": "BIRNLEX",
"version": "1.3.1"
},
"BIRTHONTO": {
"contact": {
"email": "abhilashcb@iiitdwd.ac.in",
"name": "Abhilash C B"
},
"description": "US Birth ontology is a formal representation of the concepts, properties, and relationships that are relevant to the domain of US birth data Competency questions are: 1. What is the total number of live births in the United States for a given year? 2. What is the distribution of birth weight for babies born to mothers of different ages? 3. What is the prevalence of preterm births among babies born to mothers who smoke during pregnancy? 4. What is the relationship between maternal age and the likelihood of having a multiple birth? 5. What is the difference in birth outcomes between mothers who receive prenatal care and those who do not? 6. What is the trend in the rate of low birth weight babies over time? 7. What is the impact of socioeconomic status on birth outcomes, such as birth weight and gestational age? 8. What is the relationship between the mother's race and ethnicity and the likelihood of having a preterm birth? 9. What are the common risk factors for adverse birth outcomes, and how do they interact with each other? US Birth ontology can be used to facilitate data integration, analysis, and sharing across different data sources and systems. It can help to ensure that data is consistent, interoperable, and reusable, and can facilitate data discovery and reuse. The ontology can be used by researchers, healthcare professionals, and policymakers to ask and answer questions about birth outcomes, risk factors, and trends in the US birth data.",
"homepage": "https://koolgax99.github.io/abhilash-US-birth-onto/index-en.html",
"name": "BirthOnto: Birth Data Analysis",
"prefix": "BIRTHONTO",
"version": "1.1"
},
"BKO": {
"contact": {
"email": "adrienrougny@gmail.com",
"name": "Adrien Rougny"
},
"description": "The BricKs Ontology (BKO) provides Systems Biology Graphical Notation representations of recurring concepts in molecular networks. These representations, called bricks, are associated in the ontology with terms describing the concepts. Part of these terms are borrowed from the Gene Ontology and the Systems Biology Ontology. The bricks can be used for both the template-based construction of molecular networks maps as well as for their annotation.",
"homepage": "http://sbgnbricks.org",
"name": "Bricks ontology",
"prefix": "BKO",
"version": "13:07:2018 10:45"
},
"BLLM": {
"name": "Large Language Model Ontology",
"prefix": "BLLM"
},
"BMONT": {
"contact": {
"email": "alpha.tom.kodamullil@scai.fraunhofer.de",
"name": "Alpha Tom Kodamullil"
},
"description": "The Biomarker Ontology (BMONT) is a comprehensive knowledge representation involving a variety of fields of medical and biological aspects. BMONT is built in line with Basic Formal Ontology (BFO) and Open Biological and Biomedical Ontology (OBO) principles. Entities and definitions are added by reviewing the biomarker ontology (created by Fraunhofer SCAI 10 years ago and used for the validation of the companion biomarker for a anticancer drug), as well as collected from scientific publications and books from different fields capturing various diseases.",
"name": "The Biomarker Ontology",
"prefix": "BMONT",
"version": "Version Release: 0.5.4"
},
"BMS-LM": {
"contact": {
"email": "araboudi.fealinx@gmail.com",
"name": "Amel Raboudi"
},
"description": "Biomedical research data reuse and sharing is essential for fostering research progress. To this aim, data producers need to master data management and reporting through standard and rich metadata, as encouraged by open data initiatives such as the FAIR (Findable, Accessible, Interoperable, Reusable) guidelines. This helps data re-users to understand and reuse the shared data with confidence. Therefore, dedicated frameworks are required. The provenance reporting throughout a biomedical study lifecycle has been proposed as a way to increase confidence in data while reusing it. The Biomedical Study - Lifecycle Management (BMS-LM) data model has implemented provenance and lifecycle traceability for several multimodal-imaging techniques but this is not enough for data understanding while reusing it. Actually, in the large scope of biomedical research, a multitude of metadata sources, also called Knowledge Organization Systems (KOSs), are available for data annotation. In addition, data producers uses local terminologies or KOSs, containing vernacular terms for data reporting. The result is a set of heterogeneous KOSs (local and published) with different formats and levels of granularity. To manage the inherent heterogeneity, semantic interoperability is encouraged by the Research Data Management (RDM) community. Ontologies, and more specifically top ontologies such as BFO and DOLCE, make explicit the metadata semantics and enhance semantic interoperability. Based on the BMS-LM data model and the BFO top ontology, the BioMedical Study - Lifecycle Management (BMS-LM) core ontology is proposed together with an associated framework for semantic interoperability between heterogeneous KOSs. It is made of four ontological levels: top/core/domain/local and aims to build bridges between local and published KOSs. In this paper, the conversion of the BMS-LM data model to a core ontology is detailed. The implementation of its semantic interoperability in a specific domain context is explained and illustrated with examples from small animal preclinical research.",
"name": "BioMedical Study Lifecycle Management",
"prefix": "BMS-LM",
"publication": "https://doi.org/10.1016/j.jbi.2022.104007",
"version": "Version 1.1"
},
"BMT": {
"contact": {
"email": "jison@ebi.ac.uk",
"name": "Jon Ison"
},
"description": "An ontology of biological and biomedical topics, created from merging the EDAM Topics sub-ontology with auxiliary topics that are out of scope of EDAM.",
"name": "Biomedical Topics",
"prefix": "BMT",
"version": "1.4"
},
"BNO": {
"contact": {
"email": "cameron@rockefeller.edu",
"name": "Cameron Coffran, Diane Meehan, Andrea Ronning"
},
"description": "The Bionutrition Ontology relates concepts and terminologies used for human nutrition in a clinical and biomedical setting.",
"name": "Bionutrition Ontology",
"prefix": "BNO",
"version": "0.2"
},
"BOF": {
"contact": {
"email": "francolamping@gmail.com",
"name": "Franco"
},
"description": "An ontology of biodiversity of INPA",
"name": "Biodiversity Ontology",
"prefix": "BOF",
"version": "1.2"
},
"BOSHI": {
"name": "boshra",
"prefix": "BOSHI"
},
"BP": {
"contact": {
"email": "demir@cbio.mskcc.org",
"name": "Emek Demir"
},
"description": "The BioPAX ontology (www.biopax.org) is a standard language for formally representing biological pathways. BioPAX Level 3 supports the representation of metabolic pathways, signal transduction pathways, protein-protein interaction networks, gene regulatory networks and genetic interactions.",
"homepage": "www.biopax.org",
"name": "BioPAX Ontology of Biological Pathways",
"prefix": "BP",
"version": "Level3 v1.0"
},
"BP-METADATA": {
"contact": {
"email": "noy@stanford.edu",
"name": "Natasha Noy"
},
"description": "This ontology represents the structure that BioPortal uses to represent all of its metadata (ontology details, mappings, notes, reviews, views)",
"homepage": "http://www.bioontology.org/wiki/index.php/BioPortal_Metadata",
"name": "BioPortal Metadata Ontology",
"prefix": "BP-METADATA",
"publication": "http://ceur-ws.org/Vol-524/swese2009_5.pdf",
"version": "0.9.5"
},
"BPFORMS": {
"contact": {
"email": "info@karrlab.org",
"name": "Karr Lab"
},
"description": "BpForms is an ontology of molecularly-concrete DNA, RNA, and protein residues and crosslinks which can be composed into molecularly-concrete forms of DNA, RNA, proteins, and complexes. The ontology can be used with the BpForms grammar and software tools for polymers and the BcForms grammar and software tools for complexes. See https://www.bpforms.org and https://www.bcforms.org for more information.",
"homepage": "https://www.bpforms.org",
"name": "Ontology of chemically concrete, composable DNA, RNA, and protein residue and crosslinks",
"prefix": "BPFORMS",
"publication": "https://arxiv.org/abs/1903.10042",
"version": "0.0.9"
},
"BPT": {
"contact": {
"email": "nesterova.anastasia@gmail.com",
"name": "Anastasia Nesterova"
},
"description": "Biological Pathway Taxonomy (BPT) - hierarchical taxonomy of cellular and molecular mechanisms, metabolic reactions, and diseases that can be shown as signaling pathways. BPT was created manually based on the Elsevier Pathway Collection available for public usage. ο ο ο There are 3 types of entities in BPT β pathway, group, and folder of pathways and groups. ο ο ο Group is the list of genes and proteins associated with biological function and diseases. ο ο ο Pathway is an interactive model of molecular interactions in human and mammalian cells described in the literature. Each model was reconstructed based on facts published in peer-reviewed journals, with manually quality control. ο ο ο BPT pathway entity includes several properties such as link to the model in Pathway Studio software which allows reading supported sentences from published articles and additional information about members. A list of members for each model can be provided by request. Property βnetworkβ describes maps without logical causal relationships between members to distinguish them from actual models of molecular mechanisms (βsignalingβ). ο ο ο The index folder contains all pathways and groups sorted alphabetically.",
"name": "Biological Pathway Taxonomy",
"prefix": "BPT",
"publication": "Nesterova, A.P., Klimov, E.A., Zharkova, M., Sozin, S., Sobolev, V., Ivanikova, N.V., Shkrob, M., Yuryev, A., 2020. Introduction, in: Disease Pathways. Elsevier, pp. 3β32. https://doi.org/10.1016/b978-0-12-817086-1.00001-4",
"version": "synonymes2022"
},
"BRAIN-COF": {
"contact": {
"email": "devesh.singh@dzne.de",
"name": "Devesh Singh"
},
"description": "BRAIN-COF is an ontology for representing neuroanatomical concepts aligned with the DesikanβKillianyβTourville (DKT) brain atlas. Using hierarchical relationships, our ontology explicitly encodes a priori neuroanatomical relationships amongst brain regions. Brain-COF implements computationally efficient calculation of volumetric deviation indicative of disease pathology.",
"homepage": "https://explaination.net/",
"name": "Computational Ontology Framework for Brain Profiles",
"prefix": "BRAIN-COF",
"publication": "http://dx.doi.org/10.1007/978-3-658-44037-4_43",
"version": "3"
},
"BRCT": {
"contact": {
"email": "alpha.tom.kodamullil@scai.fraunhofer.de",
"name": "Alpha Tom Kodamullil"
},
"description": "The BRCT stands for Brain Region and Cell Type terminology, which was built with the purpose of organizing the knowledge domain of brain anatomy with a top-down granularity, from gross regions to cell types. This resource has been created for use in the IMI-funded AETIONOMY project (www.aetionomy.org).",
"name": "Brain Region & Cell Type terminology",
"prefix": "BRCT",
"version": "3.0"
},
"BRIDG": {
"contact": {
"email": "clynch@surewest.net",
"name": "Cecil Lynch"
},
"description": "The Biomedical Research Integrated Domain Group (BRIDG) Model is a collaborative effort engaging stakeholders from the Clinical Data Interchange Standards Consortium (CDISC), the HL7 Regulated Clinical Research Information Management Technical Committee (RCRIM TC), the National Cancer Institute (NCI) and its Cancer Biomedical Informatics Grid (caBIGΒ), and the US Food and Drug Administration (FDA). The BRIDG model is an instance of a Domain Analysis Model (DAM). The goal of the BRIDG Model is to produce a shared view of the dynamic and static semantics for the domain of protocol-driven research and its associated regulatory artifacts. This domain of interest is further defined as: Protocol-driven research and its associated regulatory artifacts: i.e. the data, organization, resources, rules, and processes involved in the formal assessment of the utility, impact, or other pharmacological, physiological, or psychological effects of a drug, procedure, process, or device on a human, animal, or other subject or substance plus all associated regulatory artifacts required for or derived from this effort, including data specifically associated with post-marketing adverse event reporting. This OWL version of the BRIDG model is create by the National Cancer Institute (NCI). Source repository: https://ncisvn.nci.nih.gov/WebSVN/listing.php?repname=bridg-model&path=%2Ftrunk%2FModel+-+OWL%2F&",
"homepage": "http://www.bridgmodel.org/",
"name": "Biomedical Research Integrated Domain Group Model",
"prefix": "BRIDG",
"version": "3.2"
},
"BRO": {
"contact": {
"email": "bro-discuss@googlegroups.com",
"name": "Trish Whetzel, Csongor Nyulas, Natasha Noy"
},
"description": "A controlled terminology of resources, which is used to improve the sensitivity and specificity of web searches.",
"homepage": "http://www.ncbcs.org/biositemaps/",
"name": "Biomedical Resource Ontology",
"prefix": "BRO",
"version": "3.2.1"
},
"BRSO": {
"contact": {
"email": "kwsm@dbcls.rois.ac.jp",
"name": "Shuichi Kawashima"
},
"description": "Biological Resource Schema Ontology",
"homepage": "https://github.com/dbcls/brso",
"name": "Biological Resource Schema Ontology",
"prefix": "BRSO",
"version": "0.02"
},
"BSAO": {
"contact": {
"email": "contact@bioself-communication.com",
"name": "Delphine DAUGA"
},
"description": "The first ontology describing the anatomy and the development of Botryllus schlosseri. Working group : Lucia Manni, Fabio Gasparini, Kohji Hotta, Katherine J. Ishizuka J, Lorenzo Ricci, Stefano Tiozzo, Ayelet Voskoboynik, Delphine Dauga",
"name": "Botryllus schlosseri anatomy and development ontology",
"prefix": "BSAO",
"version": "Version 1"
},
"BSPO": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies.",
"homepage": "https://github.com/obophenotype/biological-spatial-ontology",
"name": "Spatial Ontology",
"prefix": "BSPO",
"version": "2023-05-27"
},
"BT": {
"contact": {
"email": "stefan.schulz@medunigraz.at",
"name": "Stefan Schulz"
},
"description": "A top-domain ontology that provides definitions for the foundational entities of biomedicine as a basic vocabulary to unambiguously describe facts in this domain. The original BioTop is no longer maintained, because it duplicated much content of other ontologies. The currently maintained version is BioTopLite 2, abbreviated as BTL2",
"homepage": "http://purl.org/biotop",
"name": "BioTop Ontology",
"prefix": "BT",
"version": "Last modification\nApr 24, 2012 by Stefan Schulz"
},
"BT-ONTOLOGY": {
"contact": {
"email": "stefano.marchesin@unipd.it",
"name": "Stefano Marchesin"
},
"description": "BrainTeaser Ontology (BTO) whose purpose is to jointly model both Amyotrophic Lateral Sclerosis (ALS) and Multiple Sclerosis (MS). The BTO serves multiple purposes: - to provide a unified and comprehensive conceptual view about ALS and MS, which are typically dealt with separately, allowing us to coherently integrate the data coming from the different medical partners in the project; - to seamlessly represent both retrospective data and prospective data, produced during the lifetime of BRAINTEASER - to allow for sharing and re-using the BRAINTEASER datasets according to Open Science and FAIR principles. For more details, visit the BTO documentation page: https://brainteaser.dei.unipd.it/ontology/",
"homepage": "https://brainteaser.dei.unipd.it/ontology/",
"name": "BrainTeaser Ontology (BTO)",
"prefix": "BT-ONTOLOGY",
"version": "2.0"
},
"BTO": {
"contact": {
"email": "a.chang@tu-bs.de",
"name": "BrendaTissue Administrators"
},
"description": "A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.",
"homepage": "http://www.brenda-enzymes.info",
"name": "BRENDA Tissue and Enzyme Source Ontology",
"prefix": "BTO",
"version": "releases/2021-10-26"
},
"BTO-BFO": {
"contact": {
"email": "hossein.beygi-nasrabadi@bam.de",
"name": "Hossein Beygi Nasrabadi"
},
"description": "Brinell Test Ontology (BTO) has developed for representing the Brinell testing process, testing equipment requirements, test pieces charactristics, and related testing parameters and their measurement procedure according to DIN EN ISO 6506-1 standard., KupferDigital project (www.materialdigital.de/project/1)",
"name": "Brinell Test Ontology-BFO",
"prefix": "BTO-BFO",
"version": "5.0.4 (BFO, IOF. MSEO)"
},
"BTO-EMMO": {
"contact": {
"email": "hossein.beygi-nasrabadi@bam.de",
"name": "Hossein Beygi Nasrabadi"
},
"description": "Brinell Test Ontology (BTO) has developed for representing the Brinell testing process, testing equipment requirements, test pieces charactristics, and related testing parameters and their measurement procedure according to DIN EN ISO 6506-1 standard. Versions info: V2 developed using BFO+CCO top-level ontologies. V3 developed using EMMO+CHAMEO top-level ontologies. V4 developed using PROVO+PMDco top-level ontologies. V5 developed using BFO+IOF top-level ontologies.",
"homepage": "https://gitlab.com/kupferdigital/process-graphs/brinell-hardness-test/",
"name": "Brinell Test Ontology-EMMO",
"prefix": "BTO-EMMO",
"publication": "https://gitlab.com/kupferdigital/process-graphs/brinell-hardness-test/",
"version": "3.0.4 (EMMO, CHAMEO, MT)"
},
"BTO-PROVO": {
"contact": {
"email": "hossein.beygi-nasrabadi@bam.de",
"name": "Hossein Beygi Nasrabadi"
},
"description": "Brinell Test Ontology (BTO) has developed for representing the Brinell testing process, testing equipment requirements, test pieces charactristics, and related testing parameters and their measurement procedure according to DIN EN ISO 6506-1 standard. Versions info: V4 developed using PROVO+PMDco top-level ontologies.",
"homepage": "https://gitlab.com/kupferdigital/process-graphs/brinell-hardness-test/",
"name": "Brinell Test Ontology-PROVO",
"prefix": "BTO-PROVO",
"publication": "https://gitlab.com/kupferdigital/process-graphs/brinell-hardness-test/",
"version": "4.0.4 (PROV, PMDco)"
},
"BTO_ONTOLOGY": {
"contact": {
"email": "subhashis.das@dcu.ie",
"name": "SUBHASHIS DAS"
},
"description": "The purpose of this work is to develop an ontology-based framework for developing an information retrieval system to cater to specific queries of users. For creating such an ontology, information was obtained from a wide range of information sources involved with brain tumour study and research. The information thus obtained was compiled and analysed to provide a standard, reliable and relevant information base to aid our proposed system. Facet-based methodology has been used for ontology formalization for quite some time. Ontology formalization involves different steps such as identification of the terminology, analysis, synthesis, standardization and ordering. A vast majority of the ontologies being developed nowadays lack flexibility. This becomes a formidable constraint when it comes to interoperability. We found that a facet-based method provides a distinct guideline for the development of a robust and flexible model concerning the domain of brain tumours. Our attempt has been to bridge library and information science and computer science, which itself involved an experimental approach. It was discovered that a faceted approach is really enduring, as it helps in the achievement of properties like navigation, exploration and faceted browsing. Computer-based brain tumour ontology supports the work of researchers towards gathering information on brain tumour research and allows users across the world to intelligently access new scientific information quickly and efficiently.",
"homepage": "https://github.com/subhashishhh/BTO-Ontology/blob/master/BrainTumour_ontology.owl",
"name": "Brain Tumour Ontology",
"prefix": "BTO_ONTOLOGY",
"publication": "Das, Subhashis, and Sayon Roy. \"Faceted Ontological Model for Brain Tumour Study.\" KO KNOWLEDGE ORGANIZATION 43, no. 1 (2016): 3-12.",
"version": "1"
},
"C19M": {
"name": "COVID-19",
"prefix": "C19M"
},
"CABRO": {
"contact": {
"email": "dimitriszikos@gmail.com",
"name": "Dimitrios Zikos"
},
"description": "a web ontology for the semantic representation of the computer assisted brain trauma rehabilitation domain. This is a novel and emerging domain, since it employs the use of robotic devices, adaptation software and machine learning to facilitate interactive, adaptive and personalized rehabilitation care, patient monitoring and assisted living.",
"name": "Computer Assisted Brain Injury Rehabilitation Ontology",
"prefix": "CABRO",
"version": "0.5"
},
"CANCO": {
"contact": {
"email": "zeginis@uom.gr",
"name": "Dimitris Zeginis"
},
"description": "The Cancer Chemoprevention Ontology constitutes a vocabulary that is able to describe and semantically interconnect the different paradigms of the cancer chemoprevention domain.",
"name": "Cancer Chemoprevention Ontology",
"prefix": "CANCO",
"publication": "http://www.semantic-web-journal.net/content/collaborative-development-common-semantic-model-interlinking-cancer-chemoprevention-linked-d",
"version": "0.3"
},
"CANONT": {
"contact": {
"email": "andre.stander@up.ac.za",
"name": "Andre Stander"
},
"description": "Providing an upper-level ontology for cancer.",
"name": "Upper-Level Cancer Ontology",
"prefix": "CANONT",
"version": "unknown"
},
"CAO": {
"contact": {
"email": "linikujp@gmail.com",
"name": "Asiyah Yu Lin"
},
"description": "CAO ontology is designed for supporting the COG enrichment study by using Fisher's exact test",
"homepage": "http://cao.sourceforge.net/",
"name": "Clusters of Orthologous Groups (COG) Analysis Ontology",
"prefix": "CAO",
"publication": "http://www.hegroup.org/docs/OntoCOG_ICBO-2011_Proceeding.pdf",
"version": "1.4"
},
"CARELEX": {
"contact": {
"email": "admin@carelex.org",
"name": "Jennifer Alpert Palchak"
},
"description": "Contains controlled vocabulary terms from National Cancer Institute used to classify clinical trial electronic content (documents, images, etc). A Content model contains content classification categories (classes) and metadata properties (data properties). Data properties should be assigned to each Content Type. This model has been published as part of the new OASIS eTMF Standard, a draft specification available at: http://oasis-open.org/committees/etmf. CareLex is a non-profit organization formed to promote eClinical application and content interoperability for the life sciences and healthcare industries. For more info go to www.CareLex.Org",
"homepage": "http://www.carelex.org",
"name": "Content Archive Resource Exchange Lexicon",
"prefix": "CARELEX",
"publication": "http://carelex.org/publications/",
"version": "1.02"
},
"CARO": {
"contact": {
"email": "haendel@ohsu.edu",
"name": "Melissa Haendel"
},
"description": "The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO will be described in Anatomy Ontologies for Bioinformatics: Principles and Practice Albert Burger, Duncan Davidson and Richard Baldock (Editors)",
"homepage": "https://github.com/obophenotype/caro/",
"name": "Common Anatomy Reference Ontology",
"prefix": "CARO",
"version": "2023-03-15"
},
"CAROLIO": {
"contact": {
"email": "msaban@luc.edu",
"name": "Michael Saban"
},
"description": "We present CaroliO, an ontology for Caroli's disease and syndrome, aimed at enhancing the diagnosis and treatment of these rare liver conditions. Our work addresses the pressing need for structured knowledge resources in the field of rare diseases, which often present significant diagnostic and treatment challenges due to limited information. We developed our ontology in two versions: CaroliO VB, which is the Basic ontology; and CaroliO VA, the Applied Version, which includes more complex axioms i.e. closure axioms and axioms that indicate combinations of scenarios among symptoms, signs, treatments, and outcomes. The Basic Version follows the underlying Open World Assumption and is suitable for ontologists and future researches, while the Applied Version includes more complex axioms to better reflect real world decision making in diagnosis and choosing treatments for Caroliβs disease and syndrome based on our current knowledge.",
"homepage": "https://github.com/TootooniLab/CaroliO",
"name": "Caroli's Disease and Syndrome Ontology",
"prefix": "CAROLIO",
"version": "2.2"
},
"CARRE": {
"contact": {
"email": "allan.third@open.ac.uk",
"name": "Allan Third"
},
"description": "Clinical risk factors, evidence and observables",
"homepage": "http://www.carre-project.eu",
"name": "CARRE Risk Factor ontology",
"prefix": "CARRE",
"version": "0.2"
},
"CASE-BASE-ONTO": {
"contact": {
"email": "ayatollahi.h@iums.ac.ir",
"name": "Haleh Ayatollahi"
},
"description": "The case-base ontology was developed for a CBR system to diagnose gastric dystemperament in the Persian medicine.",
"name": "Case-base ontology for gastric dystemperament in Persian medicine",
"prefix": "CASE-BASE-ONTO",
"version": "1.0"
},
"CBO": {
"contact": {
"email": "JSluka@indiana.edu",
"name": "James P. Sluka"
},
"description": "The Cell Behavior Ontology (CBO) describes multi-cell computational models. In particular to describe both the existential behaviors of cells (spatiality, growth, movement, adhesion, death, ...) and computational models of those behaviors. Funding: US National Institute of Health grant R01GM76692, US Environmental Protection Agency grant R835001, Indiana University, Bloomington (IUB) and the Biocomplexity Institute at IUB all provided support for this work. This work used the Protege resource, supported by grant LM007885 from the US National Library of Medicine to Stanford University.",
"homepage": "http://cbo.biocomplexity.indiana.edu/cbo/",
"name": "Cell Behavior Ontology",
"prefix": "CBO",
"publication": "http://bioinformatics.oxfordjournals.org/content/early/2014/05/18/bioinformatics.btu210.long",
"version": "Version 1.1.2 added license info.\nVersion 1.1.1 added fuding sources.\nVersion 1.1.0 added classes for OMERO-Tiff files similar to those for VTK files \nVersion 1.0.0 is the initial release of the Cell Behavior Ontology (CBO). \nVersion 1.0.1 added Journal citation for the Cell Behavior Ontology (CBO). \nVersion 1.0.2 corrected a few annotations that had \"snap:process\" that should be \"span:process\".\nVersion 1.0.3 corrected/changed class \"SpacialExclusive\" to \"SpatialExclusive\" and property \"has_Quality\" to \"has_quality\"."
},
"CCF": {
"contact": {
"email": "anitac@ebi.ac.uk",
"name": "Anita R. Caron"
},
"description": "The Common Coordinate Framework (CCF) Ontology is an application ontology built to support the development of the Human Reference Atlas (HRA). It unifies vocabulary for HRA construction and usageβmaking it possible to ingest external data sources; supporting uniform tissue sample registration that includes the spatial positioning and semantic annotations within 3D reference organs; and supporting user-formulated cross-domain queries over tissue donor properties, anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology consists of three major ontologies. The Biological Structure Ontology records anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships between them. The ASCT+B tables are authored by human experts using templated Google Sheets. The biomarkers, cell types, and anatomical structures are mapped to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible. All relationships between anatomical structures and from cell types to anatomical structures are valid Uberon and CL relationships. The Spatial Ontology defines the shape, size, location, and rotation of experimental tissue and data major anatomical structures in the 3D Reference Object Library. The Specimen Ontology captures the sex, age, and other information on donors that provided tissue data used in the construction of the HRA.",
"homepage": "https://lod.humanatlas.io/vocab/ccf/latest",
"name": "Human Reference Atlas Common Coordinate Framework Ontology",
"prefix": "CCF",
"publication": "https://hubmapconsortium.github.io/ccf/",
"version": "3.0.0"
},
"CCO": {
"contact": {
"email": "mironov@bio.ntnu.no",
"name": "Vladimir Mironov"
},
"description": "An application ontology integrating knowledge about the eukaryotic cell cycle.",
"homepage": "http://www.semantic-systems-biology.org/cco/",
"name": "Cell Cycle Ontology",
"prefix": "CCO",
"publication": "http://genomebiology.com/2009/10/5/R58",
"version": "2.10"
},
"CCON": {
"contact": {
"email": "souza.a@outlook.com",
"name": "Adriano Souza"
},
"description": "The ontology of Cerrado wood plant dynamics was created in order to represent the set of concepts about the dynamics, that is, changes over time of the wood vegetation structure, of Cerrado. Ccon describes the main parameters used to measure the changes, such as mortality rate and recruitment rate.",
"name": "Cerrado concepts and plant community dynamics",
"prefix": "CCON",
"version": "0.9.3"
},
"CCONT": {
"contact": {
"email": "matthias.ganzinger@med.uni-heidelberg.de",
"name": "Matthias Ganzinger"
},
"description": "CCONT is an ontology for the formal representation of cell lines and their correspnding culture conditions.",
"name": "Cell Culture Ontology",
"prefix": "CCONT",
"publication": "http://www.ncbi.nlm.nih.gov/pubmed/23144907",
"version": "1.1"
},
"CCTOO": {
"contact": {
"email": "f.lin@garvan.org.au",
"name": "Frank Lin"
},
"description": "The Cancer Care: Treatment Outcomes Ontology (CCTOO) catalogues various clinical endpoints used in evaluating outcomes of cancer treatment. In addition to a vocabulary list, CCTOO also curates the dependencies between individual concepts, in form of production rules, for translating clinical findings recorded in the electronic medical records (EMR) into literature-based concepts. An earlier version of this ontology was presented as a scientific abstract alongside the American Society of Clinical Oncology annual meeting 2017, Chicago, USA (J Clin Oncol 2017; 35 suppl; abstr e18137). Full paper on http://ascopubs.org/doi/abs/10.1200/CCI.18.00026",
"name": "Cancer Care: Treatment Outcome Ontology",
"prefix": "CCTOO",
"publication": "http://ascopubs.org/doi/full/10.1200/CCI.18.00026",
"version": "releases/2018-05-11"
},
"CDAO": {
"contact": {
"email": "balhoff@renci.org",
"name": "Jim Balhoff"
},
"description": "A formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science.",
"homepage": "https://github.com/evoinfo/cdao",
"name": "Comparative Data Analysis Ontology",
"prefix": "CDAO",
"version": "$Revision$"
},
"CDMONTO": {
"contact": {
"email": "benali.khaled@univ-bechar.dz",
"name": "Khaled Benali"
},
"description": "The Common Diabetes Medications Ontology (CDMOnto) is an ontology-based decision support system that has been developed with the objective of providing appropriate treatment suggestions for diabetic patients. The CDMOnto Ontology serves as a foundation for shared semantics, domain-specific, standard, and interoperable knowledge pertinent to common diabetes medications. It encompasses the knowledge of diabetes medications and offers a unified terminology that can be disseminated and processed by medical professionals, pharmacists, and diabetic patients.",
"name": "Common Diabetes Medications Ontology",
"prefix": "CDMONTO",
"version": "2"
},
"CDNO": {
"contact": {
"email": "l.andres.hernandez.18@student.scu.edu.au",
"name": "Liliana Andres Hernandez"
},
"description": "CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet.",
"homepage": "https://github.com/Southern-Cross-Plant-Science/cdno",
"name": "Compositional Dietary Nutrition Ontology",
"prefix": "CDNO"
},
"CDO": {
"contact": {
"email": "hujie@njmu.edu.cn",
"name": "Jie Hu"
},
"description": "Note: The abbreviation of Chinese Diabetes Mellitus Ontology was changed to CDMO. CDMO is an OWL 2 ontology designed to cover the diabetes mellitus knowledge represented in Chinese language. The ontology is based on BFO and OGMS. In addition, the top hierarchical structure was adapted from SNOMED-CT, and strive for mapping with other medical ontologies in English, such as SNOMED-CT, HPO, DOID, DRON.",
"name": "Chinese Diabetes Mellitus Ontology",
"prefix": "CDO",
"version": "3.0"
},
"CDOH": {
"contact": {
"email": "nk495@njit.edu",
"name": "Navya Martin"
},
"description": "Commercial factors including the production, distribution, and marketing of goods and services, may exert a substantial influence on health outcomes. This ontology covers concepts and relationships relevant to non-clinical factors resulting from commercial determinants of health(CDoH).",
"name": "Commercial determinant of Health Ontology",
"prefix": "CDOH",
"version": "v1"
},
"CDPEO": {
"contact": {
"email": "zheyu_zju@qq.com",
"name": "ZHEYU WANG"
},
"description": "This ontology is used to recommend personalized education materials to chronic disease patients. The constructed ontology mainly consists of two levels. Level 1 includes 5 terms: demographic, disease, vital sign, lifestyle and medication, which describe the characteristics contained in the patient data, as well as the topics of education materials. Leve 2 contains the detailed elements for each Level 1 class. The patient profile class is used to generate the instance of patient data, using object properties to connect to the specific characteristic class. The patient data will be mapped to a vector space generated from the Level 2 classes. SWRL rules are added to implement the semantic logic of mapping from patient original data to the ontology vector space. The pulblication of the ontology is in preperation.",
"name": "Chronic Disease Patient Education Ontology",
"prefix": "CDPEO",
"version": "1.0.0"
},
"CEDARPC": {
"contact": {
"email": "marcosmr@stanford.edu",
"name": "Marcos Martinez Romero"
},
"description": "CEDAR Provisional Classes",
"homepage": "http://metadatacenter.org/",
"name": "CEDAR Provisional Classes",
"prefix": "CEDARPC"
},
"CEDARVS": {
"contact": {
"email": "jgraybeal@stanford.edu",
"name": "John Graybeal"
},
"description": "Value Sets used by the CEDAR project",
"homepage": "http://cedar.stanford.edu",
"name": "CEDAR Value Sets",
"prefix": "CEDARVS",
"version": "0.2.2"
},
"CEPH": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "An anatomical and developmental ontology for cephalopods",
"homepage": "https://github.com/obophenotype/cephalopod-ontology",
"name": "Cephalopod Ontology",
"prefix": "CEPH"
},
"CHD": {
"contact": {
"email": "cmoschop@esat.kuleuven.be",
"name": "Charalampos Moschopoulos"
},
"description": "An ontology that describes the Congenital Heart Defects data.",
"homepage": "http://homes.esat.kuleuven.be/~bioiuser/chdwiki",
"name": "Congenital Heart Defects Ontology",
"prefix": "CHD",
"version": "1.1"
},
"CHEAR": {
"contact": {
"email": "mccusj2@rpi.edu",
"name": "James McCusker"
},
"description": "Children's health and wellbeing are influenced by interactions between environmental and genetic factors. NIEHS is establishing an infrastructure, the Children's Health Exposure Analysis Resource (CHEAR), to provide the extramural research community access to laboratory and data analyses that add or expand the inclusion of environmental exposures in children's health research. The goal of CHEAR is to provide tools so researchers can assess the full range of environmental exposures which may affect children's health. We anticipate that CHEAR will be used by children's health researchers conducting epidemiological or clinical studies that currently have limited consideration of environmental exposures, or those who have collected exposure data but seek more extensive analyses.",
"name": "Children's Health Exposure Analysis Resource",
"prefix": "CHEAR",
"version": "2.8"
},
"CHEBI": {
"contact": {
"email": "gowen@ebi.ac.uk",
"name": "Gareth Owen"
},
"description": "A structured classification of chemical compounds of biological relevance.",
"homepage": "http://www.ebi.ac.uk/chebi",
"name": "Chemical Entities of Biological Interest Ontology",
"prefix": "CHEBI",
"version": "236"
},
"CHEMBIO": {
"contact": {
"email": "binchen@indiana.edu",
"name": "Bin Chen, Ying Ding, David Wild"
},
"description": "Ontology for Systems Chemical Biology and Chemogenomics",
"homepage": "http://chem2bio2rdf.org/owl",
"name": "Systems Chemical Biology and Chemogenomics Ontology",
"prefix": "CHEMBIO",
"version": "1.1"
},
"CHEMINF": {
"contact": {
"email": "egon.willighagen@maastrichtuniversity.nl",
"name": "Egon Willighagen"
},
"description": "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.",
"homepage": "https://github.com/semanticchemistry/semanticchemistry",
"name": "Chemical Information Ontology",
"prefix": "CHEMINF",
"publication": "https://github.com/semanticchemistry/semanticchemistry",
"version": "2.1.0"
},
"CHEMROF": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "CHEMROF is an ontological framework for Chemical Entities Mixtures Reactions Ontological Framework. This OWL ontology is an automated Translation of the source LinkML schema, https://w3id.org/chemrof",
"homepage": "https://w3id.org/chemrof",
"name": "CHEMROF",
"prefix": "CHEMROF"
},
"CHIRO": {
"contact": {
"email": "vasilevs@ohsu.edu",
"name": "Nicole Vasilevsky"
},
"description": "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.",
"homepage": "https://github.com/obophenotype/chiro",
"name": "CHEBI Integrated Role Ontology",
"prefix": "CHIRO"
},
"CHMO": {
"contact": {
"email": "batchelorc@rsc.org",
"name": "Colin Batchelor"
},
"description": "CMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI).",
"homepage": "https://code.google.com/p/rsc-cmo/",
"name": "Chemical Methods Ontology",
"prefix": "CHMO",
"version": "releases/2014-11-20"
},
"CHO": {
"contact": {
"email": "alice.rogier@inria.fr",
"name": "Alice Rogier"
},
"description": "ChemoOnto, an ontology to qualify the course of chemotherapies",
"homepage": "https://team.inria.fr/heka/team-members/rogier/",
"name": "ChemoOnto",
"prefix": "CHO",
"publication": "https://www.iscb.org/ismbeccb2023-programme/tracks/bio-ontologies",
"version": "Version: 1.0.1\nDate: Dec 12, 2024\nAuthor: Alice Rogier, Inria Paris, CRC (Inserm, Univ. Paris-CitΓ©)\nLicence: MIT License"
},
"CHR": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "Ontological representation of chromosomes in major species",
"homepage": "https://github.com/monarch-initiative/monochrom/",
"name": "Monochrom",
"prefix": "CHR",
"version": "2024-08-06"
},
"CHRO": {
"contact": {
"email": "ahnm@wustl.edu",
"name": "Minyoung Ahn"
},
"description": "Functional and biochemical description of covalent histone modifiers and chromatin remodeler proteins.",
"name": "Chromatin Regulator Ontology",
"prefix": "CHRO",
"version": "2023-08-18"
},
"CIDO": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun Oliver He"
},
"description": "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.",
"homepage": "https://github.com/CIDO-ontology/cido",
"name": "Coronavirus Infectious Disease Ontology",
"prefix": "CIDO",
"publication": "He Y, Yu H, Ong E, Wang Y, Liu Y, Huffman A, Huang H, Beverley J, Hur J, Yang X, Chen L, Omenn GS, Athey B, Smith B. CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. Scientific Data. (2020) 7:181 | https://doi.org/10.1038/s41597-020-0523-6.",
"version": "2024-02-16"
},
"CIDOC-CRM": {
"contact": {
"email": "patrick.le-boeuf@bnf.fr",
"name": "Patrick Le BΕuf"
},
"description": "The CIDOC Conceptual Reference Model (CRM) provides definitions and a formal structure for describing the implicit and explicit concepts and relationships used in cultural heritage documentation. The CIDOC CRM is intended to promote a shared understanding of cultural heritage information by providing a common and extensible semantic framework that any cultural heritage information can be mapped to. It is intended to be a common language for domain experts and implementers to formulate requirements for information systems and to serve as a guide for good practice of conceptual modelling. In this way, it can provide the \"semantic glue\" needed to mediate between different sources of cultural heritage information, such as that published by museums, libraries and archives.",
"homepage": "http://www.cidoc-crm.org/",
"name": "CIDOC Conceptual Reference Model",
"prefix": "CIDOC-CRM",
"version": "v6.2"
},
"CIINTEADO": {
"contact": {
"email": "contact@bioself.fr",
"name": "Delphine Dauga"
},
"description": "The first ontology describing the anatomy and the development of Ciona intestinalis, based on the Hotta developmental table.",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Ciona intestinalis Anatomy and Development Ontology",
"prefix": "CIINTEADO",
"version": "Version 1"
},
"CIO": {
"contact": {
"email": "frederic.bastian@unil.ch",
"name": "Frederic Bastian"
},
"description": "An ontology to capture confidence information about annotations",
"homepage": "https://github.com/BgeeDB/confidence-information-ontology",
"name": "Confidence Information Ontology",
"prefix": "CIO"
},
"CISAVIADO": {
"contact": {
"email": "contact@bioself.fr",
"name": "Delphine Dauga"
},
"description": "The first ontology describing the anatomy and the development of Ciona savignyi, based on the Hotta developmental table.",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Ciona savignyi Anatomy and Development Ontology",
"prefix": "CISAVIADO"
},
"CKDO": {
"contact": {
"email": "nicholascole@nhs.net",
"name": "Nicholas Cole"
},
"description": "The Chronic Kidney Disease Ontology was developed to assist routine data studies and case identification of CKD in primary care.",
"homepage": "clininf.eu",
"name": "Chronic Kidney Disease Ontology",
"prefix": "CKDO",
"publication": "https://bmcnephrol.biomedcentral.com/articles/10.1186/s12882-018-0882-9",
"version": "v1.0"
},
"CL": {
"contact": {
"email": "addiehl@buffalo.edu",
"name": "Alexander Diehl"
},
"description": "The Cell Ontology is a structured controlled vocabulary for cell types in animals. The Cell Ontology is designed as a structured controlled vocabulary for cell types. This ontology was constructed for use by the model organism and other bioinformatics databases, where there is a need for a controlled vocabulary of cell types. This ontology is not organism specific. It covers cell types from prokaryotes to mammals. However, it excludes plant cell types, which are covered by PO.",
"homepage": "https://obophenotype.github.io/cell-ontology/",
"name": "Cell Ontology",
"prefix": "CL",
"publication": "https://www.ncbi.nlm.nih.gov/pubmed/27377652",
"version": "2024-07-10"
},
"CLAO": {
"contact": {
"email": "lagonzalezmo@unal.edu.co",
"name": "Luis A. GonzΓ‘lez-MontaΓ±a"
},
"description": "Collembola Anatomy Ontology (CLAO) includes anatomical terms to refer to sclerites, anatomical systems, cell components, and chaetotaxy. CLAO is directed towards building semantic annotations or the production of morphological data employing a standardized language. CLAO is intended as a complementary tool to morhological descriptions during taxonomic work, before obtaining phylogenetic characters.",
"homepage": "http://github/luis-gonzalez-m",
"name": "Collembola Anatomy Ontology",
"prefix": "CLAO",
"version": "2021-09-27"
},
"CLO": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "The Cell Line Ontology (CLO) is a community-based ontology in domain of biological cell lines with a focus on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications.",
"homepage": "http://www.clo-ontology.org/",
"name": "Cell Line Ontology",
"prefix": "CLO",
"publication": "http://www.jbiomedsem.com/content/5/1/37",
"version": "2.1.188"
},
"CLYH": {
"contact": {
"email": "lucas.leclere@obs-vlfr.fr",
"name": "Lucas Leclere"
},
"description": "The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle.",
"homepage": "https://github.com/EBISPOT/clyh_ontology",
"name": "Clytia hemisphaerica Development and Anatomy Ontology",
"prefix": "CLYH"
},
"CMDO": {
"contact": {
"email": "kirarang@gmail.com",
"name": "Yu Rang Park"
},
"description": "The Clinical MetaData Ontology is designed to be used to classify Common Data Elements (CDEs) from different studies and clinical documents. CDEs can be efficiently searched, shared and reused by using our ontology.",
"homepage": "http://www.snubi.org/software/cmo/",
"name": "Clinical MetaData Ontology",
"prefix": "CMDO",
"version": "1.1.4"
},
"CMECS": {
"contact": {
"email": "kate.rose@noaa.gov",
"name": "Kate Rose"
},
"description": "The Coastal and Marine Ecological Classification Standard (CMECS, FGDC-STD-018-2012) is collection of defined terms (\"units\") used to describe and classify marine ecological data. It is a national scheme for classifying and integrating observational data collected in coastal, marine, and lacustrine environments in U.S. waters. CMECS was published by the U.S. Federal Geographic Data Committee (FGDC) in 2012.",
"homepage": "https://github.com/NCEI-NOAAGov/cmecs",
"name": "Coastal and Marine Ecological Classification Standard Catalog",
"prefix": "CMECS",
"version": "1.1.0"
},
"CMO": {
"contact": {
"email": "akwitek@mcw.edu",
"name": "Anne Kwitek"
},
"description": "The Clinical Measurement Ontology is designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs.",
"homepage": "https://rgd.mcw.edu/rgdweb/ontology/search.html",
"name": "Clinical Measurement Ontology",
"prefix": "CMO",
"publication": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361058/",
"version": "2.221"
},
"CMPO": {
"contact": {
"email": "jupp@ebi.ac.uk",
"name": "Simon Jupp"
},
"description": "The Cellular Microscopy Phenotype Ontology (CMPO) is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is an application ontology developed in OWL that contains precomposed phenotypes descriptions that are defined using the Gene Ontology (GO) and the Phenotype Trait Ontology (PATO).",
"homepage": "https://github.com/EBISPOT/CMPO",
"name": "Cellular microscopy phenotype ontology",
"prefix": "CMPO",
"version": "1.3"
},
"CMR-QA": {
"contact": {
"email": "vcarapella@gmail.com",
"name": "Valentina Carapella"
},
"description": "CMR-QA ontology aims at defining the semantics of free-text quality assessment annotations associated to Cardiac Magnetic Resonance (CMR) Imaging.",
"homepage": "https://github.com/ernestojimenezruiz/CMR-QA-Semantic-Layer/",
"name": "Cardiovascular Magnetic Resonance Quality Assessment Ontology",
"prefix": "CMR-QA",
"publication": "https://github.com/ernestojimenezruiz/CMR-QA-Semantic-Layer/",
"version": "0.4.5"
},
"CN": {
"contact": {
"email": "demaidim@cs.man.ac.uk",
"name": "monademaidi"
},
"description": "Computer networks ontology",
"name": "computer network",
"prefix": "CN"
},
"CNO": {
"contact": {
"email": "ylefranc@gmail.com",
"name": "Yann Le Franc"
},
"description": "CNO is a controlled vocabulary of terms used in Computational Neurosciences to describe models of the nervous system. This first release of CNO is an alpha version and should be further aligned with other ontologies accessible on Bioportal and should be made compliant with the OBO foundry recommendations. This work is licensed under the Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. If you have any comments, questions or suggestions, please contact Yann Le Franc at ylefranc(at)gmail.com.",
"name": "Computational Neuroscience Ontology",
"prefix": "CNO",
"version": "version 0.5"
},
"CO": {
"name": "Crop Ontology",
"prefix": "CO"
},
"CO-WHEAT": {
"contact": {
"email": "R.Shrestha2@cgiar.org",
"name": "Rosemary Shrestha; Elizabeth Arnaud"
},
"description": "This ontology defines traits of the International Wheat Information System (IWIS) database and wheat descriptor.",
"homepage": "http://cropontology.org/",
"name": "Wheat Trait Ontology",
"prefix": "CO-WHEAT",
"publication": "http://pantheon.generationcp.org/",
"version": "08.11.2010"
},
"COB": {
"contact": {
"email": "bpeters@lji.org",
"name": "Bjoern Peters"
},
"description": "The Core Ontology for Biology and Biomedicine (COB) brings together key terms from a wide range of OBO projects into a single, small ontology. The goal is to improve interoperabilty and reuse across the OBO community through better coordination of key terms.",
"homepage": "https://github.com/OBOFoundry/COB",
"name": "Core Ontology for Biology and Biomedicine",
"prefix": "COB",
"version": "2023-11-16"
},
"CODO": {
"description": "The initial version, CODO ontology v1.0 to v1.3, encompasses pivotal features such as classes like patients, clinical findings, symptoms, and properties like relationships between patients, travel history, and test results. It facilitates tracking specific pandemic cases, detailing how patients may have been infected, and identifying potential contacts at risk due to their connection with the infected individual. CODO also enables monitoring of clinical tests, travel history, available resources, and actual needs like ICU beds and invasive ventilators. With capabilities for advanced analytics, contact tracing, trend studies, and growth projections based on daily COVID-19 data, CODO supports the organization and representation of COVID-19 data on a daily basis. It allows semantic querying and data retrieval and aids in behavior analysis of the disease and transmission routes. In contrast, Version 1.4, also known as CODO_COVIDRO 1.4 or COVID-19 Drug and Risk Ontology (COViDRO), presents a formal model specifically designed to tackle the multifaceted challenges associated with COVID-19 treatment, risk factors, and drug interactions. The knowledge embedded in the COViDRO model is extracted from diverse medical literature and treatment guidelines provided by reputable organizations such as the World Health Organization (WHO), the National Institutes of Health (NIH), the Food and Drug Administration (FDA), and the Centers for Disease Control and Prevention (CDC). The model incorporates information on therapeutics, adverse effects, and drug interactions from authoritative medical literature, making a significant contribution to patient care, research, and public health strategies. COViDRO, or COVID-19 Drug and Risk Ontology 1.4, seamlessly integrates into knowledge graph information systems or recommender systems. It assists healthcare professionals in suggesting appropriate treatments by considering a comprehensive set of factors, abbreviated as \"PRADiCT\" (Patient Risk factors, Adverse effects, Drug interaction, Clinical findings, and Treatment procedure). These factors encompass patient risk level, risk factors (such as underlying health conditions, age, immunocompromised state, and occupation), drug interactions, drug adverse effects, clinical findings (including diagnosis, signs, symptoms, and status), and treatment procedures. By offering a standardized framework for organizing and integrating data from diverse sources like clinical trials, medical literature, and real-world patient data, COViDRO enhances informed decision-making, thereby elevating the quality of patient care. It stands as a patient-centric solution, facilitating COVID-19 treatment options and personalized care based on individual patient characteristics. CODO V1.5 extends the previous CODO V1.4 with the focus on COVID-19 Virus Genomics for representation of genomic sequence data. VGO model comprises 261 classes, 55 object properties, and 14 data properties. Designed to streamline the use and dissemination of COVID-19 genomic sequence data, VGO serves as a robust resource for researchers and healthcare professionals. It incorporates data from the Global Initiative on Sharing All Influenza Data (GISAID), which facilitates efficient querying and visualization of genomic data, thereby improving both accessibility and usability. VGO includes a variety of classes that represent COVID-19-related data such as variants, mutations, amino acids, genes, proteins, genome sequencing, samples, hosts, sampling strategies, and assembly methods. Furthermore, VGO supports automated reasoning, enhancing its functionality for in-depth analysis and interpretation. By integrating GISAID data into the VGO knowledge graph, the model not only enriches its conceptual representation but also optimizes the querying and visualization processes, making genomic data more accessible and usable for the scientific and medical communities.",
"homepage": "https://github.com/biswanathdutta/CODO",
"name": "CODO: an Ontology for collection and analysis of COviD-19 data",
"prefix": "CODO",
"publication": "https://www.isibang.ac.in/~bisu/covid19project.html",
"version": "1.5"
},
"COGAT": {
"contact": {
"email": "poldrack@gmail.com",
"name": "Russell Poldrack"
},
"description": "The Cognitive Atlas is a collaborative knowledge building project that aims to develop an ontology that characterizes the state of current thought in cognitive science. It defines a set of mental concepts along with a set of mental tasks, and the measurement relations between those classes.",
"homepage": "http://www.cognitiveatlas.org",
"name": "Cognitive Atlas Ontology",
"prefix": "COGAT",
"version": "0.4"
},
"COGPO": {
"contact": {
"email": "jturner@mrn.org",
"name": "Jessica Turner"
},
"description": "This ontology is used to describe the experimental conditions within cognitive/behavioral experiments, primarily in humans.",
"homepage": "http://www.cogpo.org",
"name": "Cognitive Paradigm Ontology",
"prefix": "COGPO",
"version": "1"
},
"COHSI2STUDY": {
"contact": {
"email": "aleka.aktau@gmail.com",
"name": "Aliya Aktau"
},
"description": "These ontologies are created under the CoHSI2 Study.",
"name": "cohsi2study",
"prefix": "COHSI2STUDY",
"version": "0.2.8"
},
"COHSI2TERMSWEEKX": {
"contact": {
"email": "aleka.aktau@gmail.com",
"name": "Aliya Aktau"
},
"description": "Vocabularies are created to descibe week X report for CoHSI2 study",
"name": "cohsi2termsweekx",
"prefix": "COHSI2TERMSWEEKX"
},
"COID": {
"contact": {
"email": "samanfapc@gmail.com",
"name": "Samantha Pendleton"
},
"description": "A domain ontology for inflammatory diseases, with ICD-10 used as a foundation. Ontology is expanded to include medical therapies, anatomy, and symptoms. With the addition of synonyms and lay terms derived from embedding models.",
"homepage": "https://github.com/sap218/coid",
"name": "Combined Ontology for Inflammatory Diseases",
"prefix": "COID",
"version": "1.0.0"
},
"COKPME": {
"contact": {
"email": "abhilashcb@iiitdwd.ac.in",
"name": "Abhilash C B"
},
"description": "The ontology will be used by analysts for finding the relative and precautionary measures that can be put in action for controlling the spread. Also, it should be able to handle the competence question like: ο Which properties of the patient should be considered for modeling ο Which properties of patient changes ο Which properties of patient confirm COVID positive ο Do the symptom of the patient change over time *** ο Do the treatment provided depends on the category of patient ο Do other comorbid conditions derive any interestingness **** ο Which symptom is high in a particular district? (Or) Does the geographical location influence the patient category These keep change over an iterative process of ontology development",
"name": "COKPME - COVID19 Ontology for analyzing the Karnataka Private Medical Establishments Data",
"prefix": "COKPME",
"version": "1.0"
},
"COLAO": {
"contact": {
"email": "entiminae@gmail.com",
"name": "Jennifer C. GirΓ³n"
},
"description": "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. It has been built using the Ontology Develoment Kit with the Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) as a backbone. The project is open for collaboration.",
"homepage": "https://github.com/insect-morphology/colao",
"name": "Coleoptera Anatomy Ontology",
"prefix": "COLAO",
"version": "2024-06-21"
},
"COMET": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "A collection of common metadata elements and terms for constructing LinkML Schemas and Data Models",
"homepage": "https://github.com/linkml/linkml-common",
"name": "LinkML Common Metadata Elements and Terms",
"prefix": "COMET"
},
"COMODI": {
"contact": {
"email": "comodi-on-bioportal@binfalse.de",
"name": "martin scharm"
},
"description": "An ontology to characterise differences in versions of computational models in biology",
"homepage": "http://comodi.sems.uni-rostock.de",
"name": "COMODI",
"prefix": "COMODI",
"publication": "http://comodi.sems.uni-rostock.de"
},
"CONDOR": {
"contact": {
"email": "asanoverden@gmail.com",
"name": "mojtaba.nayyeri@ki.uni-stuttgart.de"
},
"description": "The CONDOR is a comprehensive framework designed to encapsulate the multifaceted aspects of liver cancer patient care. It encompasses essential elements ranging from patient profiles to disease classifications and treatment options. This ontology aims to streamline the process of liver cancer analysis and treatment, enabling more personalized and effective patient care strategies.",
"homepage": "https://www.ki.uni-stuttgart.de/departments/ac/research/projects/ATLAS/",
"name": "Liver Cancer Ontology Diagnosis Treatment",
"prefix": "CONDOR",
"version": "0.1"
},
"CONTSONTO": {
"contact": {
"email": "subhashis.das@dcu.ie",
"name": "creator: Subhashis Das"
},
"description": "The Ontology of Continuity of care (ContSOnto) is an emerging research area consisting of the extension of a healthcare ontology to inform the continuity of care domain. This field is positioned at the confluence of health informatics, nursing informatics, process modelling, and artificial intelligence. This research relating to ContSOnto is underpinned by health informatics standard ISO 13940 Systems of Concepts for Continuity of Care ContSOnto focuses on how information flows from different information systems across and between services for clinical applications and health care professionals to use. Figure 14.2 provides an illustration (see https://contsys.org/pages/Guest%20blog/FormalOntology)of how the different classes and relationships in the standard are represented. Subject of care refers to the individual service user and health care actors can be human or non-human, for example, a health care professional or an organisation.",
"homepage": "http://purl.org/net/for-coc",
"name": "Continuity of care",
"prefix": "CONTSONTO",
"publication": "https://contsys.org/pages/Guest%20blog/FormalOntology",
"version": "1.5"
},
"COPDO": {
"contact": {
"email": "l.rayner@surrey.ac.uk",
"name": "Louise Rayner"
},
"description": "The COPD Ontology is a biomedical ontology used for modelling concepts associated to chronic obstructive pulmonary disease in routine clinical databases.",
"homepage": "clininf.eu",
"name": "COPD Ontology",
"prefix": "COPDO",
"version": "1"
},
"COSTART": {
"contact": {
"email": "info@ntis.gov",
"name": "U.S. Food and Drug Administration Center for Drug Evaluation and Research"
},
"description": "Coding Symbols for Thesaurus of Adverse Reaction Terms (COSTART). 5th ed. Rockville (MD). COSTART is used for coding, filing, and retrieving post-marketing adverse drug and biologic experience reports. COSTART is organized in body system and pathophysiology hierarchies, as well as a separate fetal/neonatal category of less than 20 terms. COSTART has been superseded by the Medical Dictionary for Regulatory Activities (MedDRA) Terminology. For more information about MedDRA in the Metathesaurus, see the MedDRA source synopsis. COSTART was last updated in the Metathesaurus in 1999.",
"homepage": "http://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/CST/",
"name": "Coding Symbols for a Thesaurus of Adverse Reaction Terms",
"prefix": "COSTART",
"version": "2023AB"
},
"COVID-19": {
"contact": {
"email": "alpha.tom.kodamullil@scai.fraunhofer.de",
"name": "Alpha Tom Kodamullil"
},
"description": "The COVID-19 ontology covers the role of molecular and cellular entities in virus-host-interactions, in the virus life cycle, as well as a wide spectrum of medical and epidemiological concepts linked to COVID-19.",
"name": "COVID-19 Ontology",
"prefix": "COVID-19",
"publication": "Sargsyan A, Kodamullil AT, Baksi S, Darms J, Madan S, Gebel S, Keminer O, Jose GM, Balabin H, DeLong LN, Kohler M, Jacobs M, Hofmann-Apitius M. The COVID-19 Ontology. Bioinformatics. 2020 Dec 21:btaa1057. doi: 10.1093/bioinformatics/btaa1057. PMID: 33346828; PMCID: PMC7799333.",
"version": "Version Release: 1.0.0"
},
"COVID-19-ONT-PM": {
"contact": {
"email": "hanfeib@gmail.com",
"name": "Hanfei Bao"
},
"description": "This ontology will focus on the COVID-19 fields in order to help the hard efforts against the outbreak of the pandemic. It is expected, through the ontology, to understand the medical events or conditions and make medical decisions in more integrated or systematic ways, based on more engineered or calculation methods. This ontology will also be involved in the explorations on the Pattern Medicines (PMs) and so called the Generalized Biology Mechanics (GBM), raised by the author in his Biomedical Knowledge Integration (BMKI), a pilot topic full of challenges.",
"homepage": "https://blog.51.ca/u-345129/2020/11/13/the-preliminary-researches-on-the-data-dynamics-of-covid-19/",
"name": "COVID-19OntologyInPatternMedicine",
"prefix": "COVID-19-ONT-PM",
"publication": "https://blog.51.ca/u-345129/2020/11/13/the-preliminary-researches-on-the-data-dynamics-of-covid-19/",
"version": "007"
},
"COVID19": {
"contact": {
"email": "john.williams@phc.ox.ac.uk",
"name": "John Williams"
},
"description": "The COVID-19 Surveillance Ontology is an application ontology used to support SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) surveillance in primary care. The ontology facilitates monitoring of COVID-19 cases and related respiratory conditions using data from multiple brands of computerised medical record systems.",
"homepage": "https://orchid.phc.ox.ac.uk/index.php/cov-19/",
"name": "COVID-19 Surveillance Ontology",
"prefix": "COVID19",
"publication": "https://publichealth.jmir.org/2020/4/e21434/",
"version": "V1.0"
},
"COVID19-IBO": {
"contact": {
"email": "archanamca92@gmail.com",
"name": "Archana"
},
"description": "Covid19 Impact on Banking Ontology (Covid19-IBO) provides semantic information about the impact of the Covid-19 on the banking sector of India",
"name": "Covid19 Impact on Banking Ontology",
"prefix": "COVID19-IBO",
"version": "1.5"
},
"COVIDCRFRAPID": {
"contact": {
"email": "luiz.bonino@go-fair.org",
"name": "Luiz Bonino"
},
"description": "This is a semantic data model for the WHO's COVID-19 case record form RAPID version from April 8 2020. It aims at providing semantic references to the questions and answers of the form. Changes in the version 1.1.4: - Corrected: Urea_(BUN) to remove the \"()\", which may cause resolution and validation issues; Changes in the version 1.1.3: - Corrected: Chloroquine/hydroxychloroquine to remove the \"/\", which may cause resolution issues; Changes in version 1.1.2: - Corrected: Cough with haemoptysis because the IRI was mispelled; - Corrected: CPAP/NIV Mask to remove the \"/\", which may cause resolution issues; - Added: missing \"part of\" property for section 1g. - Added: \"has other measurement unit label\" property for the laboratory results that may use a different unit than specified in the CRF; - Added: missing \"has value\" for the Which coronavirus question; - Added: missing possibility to enter the name of a specific antibiotic in section 3c of the CRF; - Added: missing question on testing the presence of other pathogenic of public health interest from section 3a of the CRF. Changes in version 1.1.1: - Added: Facility Name to identify the care facility in which the case is reported from. Changes in version 1.1.0: - This version covers the modifications introduced by the WHO COVID-19 Rapid CRF from April 8, 2020. The model maintains backward compatibility with the WHO COVID-19 Rapid CRF from March 23, 2020.",
"homepage": "http://purl.org/vodan/whocovid19crfsemdatamodel/",
"name": "WHO COVID-19 Rapid Version CRF semantic data model",
"prefix": "COVIDCRFRAPID",
"version": "1.1.4"
},
"CPRO": {
"contact": {
"email": "chimezie@gmail.com",
"name": "Chimezie Ogbuji"
},
"description": "A uniform core set of data elements (whose formal semantics are captured in OWL) for use in a Computer-Based Patient Record (CPR)",
"homepage": "https://code.google.com/p/cpr-ontology/",
"name": "Computer-Based Patient Record Ontology",
"prefix": "CPRO",
"publication": "https://www.researchgate.net/publication/235463154_A_Framework_Ontology_for_Computer-Based_Patient_Record_Systems?ev=prf_pub",
"version": "Last modification: July 31th, 2011 Chimezie Ogbuji"
},
"CPT": {
"contact": {
"email": "Intellectual.PropertyServices@ama-assn.org",
"name": "American Medical Association"
},
"description": "CPT is a list of descriptive terms and identifying numeric codes for medical services and procedures that are provided by physicians and health care professionals.",
"homepage": "https://www.ama-assn.org/practice-management/cpt-current-procedural-terminology",
"name": "CPT - Current Procedural Terminology",
"prefix": "CPT",
"version": "2020AB"
},
"CPTAC": {
"contact": {
"email": "fanzhan@iupui.edu",
"name": "Fan Zhang"
},
"description": "a basic ontology which describes the proteomics pipeline infrastructure for CPTAC project",
"name": "CPTAC Proteomics Pipeline Infrastructure Ontology",
"prefix": "CPTAC",
"version": "alpha 1.1"
},
"CRENO": {
"contact": {
"email": "muamith@utmb.edu",
"name": "Tuan Amith"
},
"description": "This work undertakes the possibility of using the Web Ontology Language (OWL2) to describe concepts related to \"culture\", \"race\", \"ethnicity\", and \"nationality\" - concepts that are sometimes misunderstood/misused due to lack of standardization and biases. The project also attempts to link data relating to these broad concepts to health data, like cancer rates, and shed light on understanding health disparities that impact certain communities. This work is early in development and preliminary.",
"homepage": "https://github.com/UTHealth-Ontology/CRENO",
"name": "Culture, Race, Ethnicity and Nationality Ontology",
"prefix": "CRENO",
"publication": "http://www.ncbi.nlm.nih.gov/pmc/articles/pmc10283130/",
"version": "0.6"
},
"CRISP": {
"contact": {
"email": "af8d@nih.gov",
"name": "Anita Ghebeles"
},
"description": "Computer Retrieval of Information on Scientific Projects (CRISP)",
"name": "Computer Retrieval of Information on Scientific Projects Thesaurus",
"prefix": "CRISP",
"version": "2023AB"
},
"CRO": {
"contact": {
"email": "whimar@ohsu.edu",
"name": "Marijane White"
},
"description": "The Contributor Role Ontology (CRO) is an extension of the CASRAI Contributor Roles Taxonomy (CRediT).",
"homepage": "https://github.com/data2health/contributor-role-ontology",
"name": "Contributor Role Ontology",
"prefix": "CRO",
"publication": "https://github.com/data2health/contributor-role-ontology",
"version": "v2019-08-16"
},
"CRYOEM": {
"contact": {
"email": "coss@cnb.csic.es",
"name": "Carlos Oscar Sorzano"
},
"description": "Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles",
"homepage": "http://scipion.i2pc.es/ontology/cryoem",
"name": "Cryo Electron Microscopy",
"prefix": "CRYOEM",
"version": "2021-03-09"
},
"CS": {
"contact": {
"email": "a.r.dirkson@liacs.leidenuniv.nl",
"name": "Anne Dirkson"
},
"description": "This is an ontology of possible coping strategies that patients advise for managing side effects they experience. It was created based on a forum for patients with a GastroIntestinal Stromal Tumor (GIST) . This ontology can be found here: https://github.com/AnneDirkson/CopingStratExtract.",
"name": "Coping Strategies for Adverse Drug Events Ontology",
"prefix": "CS"
},
"CSEO": {
"contact": {
"email": "sam.ansari@pmi.com",
"name": "Sam Ansari"
},
"description": "The CSEO has potential to become a widely used standard within the academic and industrial community. Mainly because of the emerging need of systems toxicology to controlled vocabularies and also the lack of suitable ontologies for this domain, the CSEO prepares the ground for integrative systems-based research in the exposure science.",
"homepage": "https://publicwiki-01.fraunhofer.de/CSEO-Wiki/index.php/Main_Page",
"name": "Cigarette Smoke Exposure Ontology",
"prefix": "CSEO",
"publication": "http://www.jbiomedsem.com/content/5/1/31/abstract",
"version": "1.0"
},
"CSO": {
"contact": {
"email": "cameron@rockefeller.edu",
"name": "Cameron Coffran"
},
"description": "Ontology to describe general clinical studies.",
"name": "Clinical Study Ontology",
"prefix": "CSO"
},
"CSSO": {
"contact": {
"email": "hmori@bio.titech.ac.jp",
"name": "MicrobeDB.jp Project Team"
},
"description": "An ontology for describing clinical signs and symptoms.",
"homepage": "http://mdb.bio.titech.ac.jp/csso",
"name": "Clinical Signs and Symptoms Ontology",
"prefix": "CSSO",
"version": "Version 0.6"
},
"CST": {
"contact": {
"email": "cancer.staging.ontology@gmail.com",
"name": "Oshani Seneviratne"
},
"description": "This ontology consists of cancer staging terms that specify higher-level terms that are useful in classifying cancer, specifically breast cancer, according to the AJCC 7th and 8th editions.",
"name": "Cancer Staging Terms",
"prefix": "CST"
},
"CSTD": {
"contact": {
"email": "hsiehjulien@gmail.com",
"name": "Julien Wen Hsieh"
},
"description": "This is an knowledge domain about smell and taste disoders. The aim of this ontology domain is the facilitate high throughput and deep-phenotyping assessment in clinical smell and taste research.",
"name": "Clinical smell and taste disorders",
"prefix": "CSTD",
"version": "1"
},
"CTCAE": {
"contact": {
"email": "ncictcaehelp@mail.nih.gov",
"name": "CTCAE Help"
},
"description": "Common Terminology Criteria for Adverse Events (CTCAE) is widely accepted throughout the oncology community as the standard classification and severity grading scale for adverse events in cancer therapy clinical trials and other oncology settings. Version 5 was published by the NCI Cancer Therapy Evaluation Program (CTEP) in November 2017. It is organized by MedDRA System Organ Class and mapped to MedDRA LLTs with corresponding MedDRA codes, and harmonized with MedDRA at the Adverse Event (AE) level including revised AE terms and severity indicators to reflect clinical effects identified with current oncology interventions.Severity grades are assigned and most are defined to clarify the meaning of the term. CTCAE is designed to integrate into information networks for safety data exchange, and is the primary standard for data management for AE data collection, analysis, and patient outcomes associated with cancer research and care.",
"homepage": "https://nciterms.nci.nih.gov/ncitbrowser/pages/vocabulary.jsf?dictionary=CTCAE_v5&version=5.0",
"name": "Common Terminology Criteria for Adverse Events",
"prefix": "CTCAE",
"version": "5.0"
},
"CTENO": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "An anatomical and developmental ontology for ctenophores (Comb Jellies)",
"homepage": "https://github.com/obophenotype/ctenophore-ontology",
"name": "Ctenophore Ontology",
"prefix": "CTENO"
},
"CTGO": {
"contact": {
"email": "gedman4b@yahoo.com",
"name": "Scott Josephson"
},
"description": "The Clinical Trials Gov Ontology (CTGO) is based on the AACT database schema for Aggregate Analysis of ClinicalTrials.gov. AACT contains information about clinical studies that have been registered at ClinicalTrials.gov. AACT includes all of the protocol and results data elements for studies publicly available at ClinicalTrials.gov.",
"homepage": "http://mraas.ai/ontologies/ctgo.ttl",
"name": "Clinical Trials Gov Ontology",
"prefix": "CTGO",
"version": "1.0"
},
"CTO": {
"contact": {
"email": "alpha.tom.kodamullil@scai.fraunhofer.de",
"name": "Alpha Tom Kodamullil"
},
"description": "Clinical Trial Ontology (CTO) is designed to formally represent and integrate all terms used to describe and register the clinical trials. The development of CTO was done as a collaborative project among Fraunhofer SCAI, Germany; University of Michigan; Center for Devices and Radiological Health, FDA; and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda. Respective related projects are described below: At Fraunhofer SCAI, the work was supported and funded from the EUβs Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 785907 (Human Brain Project SGA2 by the HBP Medical Informatics Platform) and No. 826421 (VirtualBrainCloud), and a Fraunhofer internal funding MAVO project \"Human Brain Pharmacome\". At University of Michigan, the work was supported by the NIH-NIDDK U2C Project (1U2CDK114886) and a grant from the Michigan MedicineβPeking University Health Sciences Center Joint Institute for Clinical and Translational Research (U063430). At NCBI side, thhe work of QL and EB was supported by the Intramural Research Program of the National Library of Medicine, National Institutes of Health.",
"name": "Clinical Trials Ontology",
"prefix": "CTO",
"version": "Version Release: 1.0.0"
},
"CTO-NDD": {
"contact": {
"email": "alpha.tom.kodamullil@scai.fraunhofer.de",
"name": "Alpha Tom Kodamullil"
},
"description": "The CTO-NDD stands for Clinical Trial Ontology-Neurodegenerative Diseases, which was built with the purpose of organizing the knowledge domain of clinical trials in neurodegeneration field. This resource has been created for use in the IMI-funded AETIONOMY project (www.aetionomy.org).",
"name": "Clinical Trials Ontology - Neurodegenerative Diseases",
"prefix": "CTO-NDD",
"version": "0.6"
},
"CTONT": {
"contact": {
"email": "rshankar@stanford.edu",
"name": "Ravi Shankar, Stanford Medical Informatics"
},
"name": "Epoch Clinical Trial Ontology",
"prefix": "CTONT",
"publication": "http://smi.stanford.edu/smi-web/research/projectDetail.jsp?projectId=9",
"version": "\n \n | \n Version\n | \n \n 0.97\n | \n
\n \n | \n Date\n | \n \n 3/2/2007
\n | \n
\n
\n
"
},
"CTU_BEREADY_GEM": {
"contact": {
"email": "muriel.helmers@ctu.unibe.ch",
"name": "Muriel Helmers"
},
"description": "Ontology used for project 1694, BEReady (be ready for future pandemics)",
"homepage": "http://www.ctu.unibe.ch",
"name": "CTU Bern BEReady Gemeinden",
"prefix": "CTU_BEREADY_GEM",
"version": "gem_onto_1level_v0_01"
},
"CTX": {
"contact": {
"email": "maria.taboada@usc.es",
"name": "Maria Taboada"
},
"description": "The ontology represents CTX phenotypes, genetic variants, and bidirectional relationships between them though a patient model. The CTX ontology was build reusing the Human Phenotype Ontology (HPO) and the Snomed ct ontologies. A set of temporal clinical manifestations are semantically annotated with a domain phenotype ontology and registered with a time-stamped value.",
"homepage": "http://www.usc.es/keam/~mariataboada/",
"name": "Cerebrotendinous Xanthomatosis Ontology",
"prefix": "CTX",
"publication": "http://www.usc.es/keam/publications.html",
"version": "vtemp2"
},
"CU-VO": {
"contact": {
"email": "jdr2160@cumc.columbia.edu",
"name": "Joseph D. Romano"
},
"description": "An ontology of venoms and venom-related compounds, designed to facilitate the discovery of novel venom-derived therapeutics.",
"name": "Venom Ontology",
"prefix": "CU-VO",
"version": "1.0"
},
"CVAO": {
"contact": {
"email": "erfanir@gmail.com",
"name": "Erfan Younesi"
},
"description": "Stroke ontology",
"name": "STO",
"prefix": "CVAO",
"version": "2017-11-01"
},
"CVDO": {
"contact": {
"email": "adrien.barton@gmail.com",
"name": "Adrien Barton"
},
"description": "CVDO is an ontology based on the OGMS model of disease, designed to describe entities related to cardiovascular diseases (including the diseases themselves, the underlying disorders, and the related pathological processes). It is being developed at Sherbrooke University (Canada) and the INSERM research institute (Institut National de la SantΓ© et de la Recherche MΓ©dicale).",
"homepage": "https://github.com/OpenLHS/CVDO",
"name": "Cardiovascular Disease Ontology",
"prefix": "CVDO",
"version": "2024-05-17"
},
"CWD": {
"contact": {
"email": "rfurberg@rti.org",
"name": "Robert Furberg"
},
"description": "Consumer Wearable Devices (CWD) enable passive, low-burden, longitudinal collection of data relevant to health behaviors, human performance, and biometrics. Such data are increasingly used to tailor clinical and public health interventions and as outcome measures in clinical trials. The uptake of CWD in research applications warrants an examination of the data collected from these products. This ontology was developed based on a review of publicly available documentation and data sets from three CWD vendors and is open for researchers to modify + extend as new features become available.",
"name": "Consumer Wearable Device",
"prefix": "CWD"
},
"CYTO": {
"contact": {
"email": "demetrios.sarantis@yale.edu",
"name": "Kleinstein Lab, Yale School of Medicine, Demetrios Sarantis"
},
"description": "It is flat ontology showing cytokine synonyms. It has been produced by merging cytokine branches, using SOMA (Synonym Ontology Mapping Approach) method, of 10 Bioportal ontologies.",
"name": "CYTOKINE",
"prefix": "CYTO",
"version": "Cytokines"
},
"DATACITE": {
"contact": {
"email": "sparontologies@gmail.com",
"name": "SPAR Ontologies"
},
"description": "The DataCite Ontology (DataCite) is an ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF.",
"homepage": "http://www.sparontologies.net/ontologies/datacite",
"name": "SPAR DataCite Ontology",
"prefix": "DATACITE",
"publication": "http://dx.doi.org/10.6084/m9.figshare.2075356",
"version": "1.2"
},
"DATACITE-VOCAB": {
"contact": {
"email": "me@thisisnikola.com",
"name": "Nikola Vasiljevic"
},
"description": "Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is Datacite Controlled Vocabulary. This controlled vocabulary is produced based on description of Datacite Schema V4.4. The work of creating this controlled vocabulary is part of FAIRware project which if funded by RoRi. sheet2rdf is used to build Datacite Controlled Vocabulary, while PURL, is used to persist and resolve identifiers via BioPortal for the vocabulary terms.",
"homepage": "https://github.com/metadatacenter/datacite-controlled-vocabulary",
"name": "DATACITE V4.4",
"prefix": "DATACITE-VOCAB",
"publication": "https://github.com/metadatacenter/datacite-controlled-vocabulary",
"version": "0.1.0"
},
"DC": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kim Durante"
},
"description": "The Dublin Core Schema is a small set of vocabulary terms that can be used to describe several kinds of resources. Dublin Core Metadata may be used for multiple purposes, from simple resource description, to combining metadata vocabularies of different metadata standards, to providing interoperability for metadata vocabularies in the Linked Data cloud and Semantic Web implementations.",
"homepage": "http://dublincore.org",
"name": "Dublin Core",
"prefix": "DC"
},
"DCAT": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "kdurante"
},
"description": "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web.",
"homepage": "https://www.w3.org/TR/vocab-dcat/",
"name": "Data Catalog Vocabulary",
"prefix": "DCAT"
},
"DCAT-FDC": {
"contact": {
"email": "nikola@fairdatacollective.com",
"name": "Nikola Vasiljevic"
},
"description": "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web. This document defines the schema and provides examples for its use. DCAT enables a publisher to describe datasets and data services in a catalog using a standard model and vocabulary that facilitates the consumption and aggregation of metadata from multiple catalogs. This can increase the discoverability of datasets and data services. It also makes it possible to have a decentralized approach to publishing data catalogs and makes federated search for datasets across catalogs in multiple sites possible using the same query mechanism and structure. Aggregated DCAT metadata can serve as a manifest file as part of the digital preservation process. The namespace for DCAT terms is http://www.w3.org/ns/dcat# The suggested prefix for the DCAT namespace is dcat",
"homepage": "https://www.w3.org/TR/vocab-dcat-3/",
"name": "Data Catalog Vocabulary (DCAT)",
"prefix": "DCAT-FDC",
"publication": "https://www.w3.org/TR/vocab-dcat-3/",
"version": "Toto je aktualizovanΓ‘ kopie slovnΓku DCAT verze 2.0, pΕevzatΓ‘ z https://www.w3.org/ns/dcat.ttl"
},
"DCAT3": {
"contact": {
"email": "alexskr@stanford.edu",
"name": "Alex Skrenchuk"
},
"description": "DCAT",
"name": "DCAT3",
"prefix": "DCAT3",
"version": "3"
},
"DCCDFV": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kim Durante"
},
"description": "The Collection Description Accrual Policy Vocabulary provides a set of terms that can be used as values of the dcterms:accrualPolicy property in descriptions of collections.",
"homepage": "http://dublincore.org/groups/collections/accrual-policy/",
"name": "Dublin Core Collection Description Frequency Vocabulary",
"prefix": "DCCDFV"
},
"DCM": {
"contact": {
"email": "dclunie@dclunie.com",
"name": "David Clunie"
},
"description": "DICOM Controlled Terminology (PS3.16 2024 Annex D)",
"homepage": "http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html",
"name": "DICOM Controlled Terminology",
"prefix": "DCM",
"version": "2024c_20240617"
},
"DCMITYPE": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kim Durante"
},
"description": "The DCMI Type Vocabulary provides a general, cross-domain list of approved terms that may be used as values for the Resource Type element to identify the genre of a resource",
"homepage": "http://dublincore.org/documents/dcmi-type-vocabulary",
"name": "DCMI Type Vocabulary",
"prefix": "DCMITYPE"
},
"DCO": {
"contact": {
"email": "elze@infai.org",
"name": "Romy Elze"
},
"description": "Dispedia Core Ontology is a schema for information brokering and knowledge management in the complex field of rare diseases. On the one hand, the Dispedia schema uses semantic technologies to describe patients affected by rare diseases, and on the other hand, to record expertise concerning these particular diseases in machine-processable form. In addition to the differentiated attribution of facts to the individual need for information, Dispedia enables information brokering which adjusts to the type of recipient, its character as well as its personal attitude. The schema was initially geared to an exemplified disease, Amyotrophe Lateralsclerose (ALS).",
"homepage": "www.dispedia.de",
"name": "Dispedia Core Ontology",
"prefix": "DCO",
"version": "0.7.0.0002"
},
"DCT": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kim Durante"
},
"description": "Specification of all metadata terms maintained by the Dublin Core Metadata Initiative. Included are the fifteen terms of the Dublin Core Metadata Element Set",
"name": "DC Terms",
"prefix": "DCT"
},
"DCTERMS": {
"contact": {
"email": "futo@stanford.edu",
"name": "Michelle Futornick"
},
"description": "DCMI properties in the /terms/ namespace",
"homepage": "http://dublincore.org/documents/dcmi-terms/",
"name": "DCMI Metadata Terms: properties in /terms/ namespace",
"prefix": "DCTERMS"
},
"DDANAT": {
"contact": {
"email": "pfey@northwestern.edu",
"name": "Petra Fey"
},
"description": "A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum.",
"homepage": "http://dictybase.org/",
"name": "Dictyostelium Discoideum Anatomy Ontology",
"prefix": "DDANAT",
"publication": "http://www.biomedcentral.com/1471-2164/9/130",
"version": "1.19"
},
"DDI": {
"contact": {
"email": "soldatova.larisa@gmail.com",
"name": "Larisa Soldatova; Da Qi (ddq@aber.ac.uk)"
},
"description": "The goal of DDI project is to develop an ontology for the description of drug discovery investigations. DDI aims to follow to the OBO (Open Biomedical Ontologies) Foundry principles, uses relations laid down in the OBO Relation Ontology, and be compliant with Ontology for biomedical investigations (OBI).",
"homepage": "http://purl.org/ddi/home",
"name": "Ontology for Drug Discovery Investigations",
"prefix": "DDI",
"version": "$Revision$"
},
"DDIEM": {
"contact": {
"email": "pns12@cam.ac.uk",
"name": "Paul Schofield"
},
"description": "DDIEM Ontology for the Drug Database for Inborn Errors of Metabolism. The DDIEM database is a database of therapeutic strategies and treatments for inborn errors of metabolism. These strategies are classified by mechanism and outcome using the DDIEM Ontology. The DDIEM database also includes descriptions of the phenotypes addressed by the treatment, together with drugs and procedures applied.",
"homepage": "http://ddiem.phenomebrowser.net/",
"name": "Drug Database for Inborn Errors of Metabolism (DDIEM) Ontology",
"prefix": "DDIEM",
"version": "1.2"
},
"DDPHENO": {
"contact": {
"email": "pfey@northwestern.edu",
"name": "Petra Fey"
},
"description": "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum.",
"homepage": "http://dictybase.org/",
"name": "Dictyostelium Discoideum Phenotype Ontology",
"prefix": "DDPHENO"
},
"DDSS": {
"contact": {
"email": "safaa.menad1@univ-rouen.fr",
"name": "menad"
},
"description": "This resource encompasses mappings from different ontologies: the Disease Ontology (DOID), the Symptom Ontology (SYMP), the Drug Ontology (DRON), and entities from OpenFDA for side effects.",
"name": "Health_ontology",
"prefix": "DDSS"
},
"DEB": {
"contact": {
"email": "osnat.hakimi@gmail.com",
"name": "Osnat Hakimi"
},
"description": "An ontology developed to facilitate information curation in the area of medical devices, experimental scaffolds and biomaterials. The ontology was designed to complement existing medical vocabularies, with emphasis on material processing, structures and features associated with biomaterials and experimental scaffolds. It is used as part of an automated text mining pipeline which populates the database of Experimental Biomaterials and their Biological Effect (DEBBIE). DEBBIE is an EU Horizon 2020 funded project. For more information visit https://projectdebbie.github.io/",
"homepage": "https://projectdebbie.github.io/",
"name": "Devices, Experimental scaffolds and Biomaterials Ontology",
"prefix": "DEB",
"publication": "https://onlinelibrary.wiley.com/doi/10.1002/adfm.201909910",
"version": "4.0"
},
"DECIDE": {
"contact": {
"email": "Saba.Noor@UGent.be",
"name": "Saba Noor"
},
"description": "Ontology is developed for decision support tools for different animal species as a part of DECIDE project (https://decideproject.eu).",
"homepage": "https://github.com/decide-project-eu",
"name": "DECIDE ONTOLOGY",
"prefix": "DECIDE"
},
"DERMLEX": {
"contact": {
"email": "nlevinthal@aad.org",
"name": "Naomi Levinthal"
},
"description": "Version 1.0 of the American Academy of Dermatology's DermLex: The Dermatology Lexicon, a standardized terminology of dermatologic diagnoses, therapies, procedures, and laboratory tests.",
"homepage": "http://www.aad.org/research/lexicon/",
"name": "Dermatology Lexicon",
"prefix": "DERMLEX",
"version": "1"
},
"DERMO": {
"contact": {
"email": "pns12@cam.ac.uk",
"name": "Paul Schofield"
},
"description": "Ontology of human dermatologic disease",
"name": "Human Dermatological Disease Ontology",
"prefix": "DERMO",
"version": "1.19"
},
"DFO": {
"contact": {
"email": "e.j.hyde@umcg.nl",
"name": "Eleanor Hyde"
},
"description": "The Databank Family Ontology describes groups of data banks with similar record prompts and originators.",
"homepage": "https://w3id.org/dfo",
"name": "Databank Family Ontology",
"prefix": "DFO",
"publication": "forthcoming",
"version": "0.1"
},
"DIAB": {
"contact": {
"email": "philipp.gormanns@helmholtz-muenchen.de",
"name": "Philipp"
},
"description": "Diabetes ontology",
"name": "BioMedBridges Diabetes Ontology",
"prefix": "DIAB",
"version": "2.0"
},
"DIAGONT": {
"contact": {
"email": "amrapali.j.zaveri@gmail.com",
"name": "Amrapali Zaveri"
},
"description": "We built a computational diagnostic ontology containing 91 elements, including classes and sub-classes, which are required to conduct SR-MA (Systematic Review - Meta Analysis) for diagnostic studies, that will assist in standardized reporting of diagnostic articles. We also report high percentage of agreement among five observers as a result of the inter-observer agreement that we conducted among them to tag 13 articles using the diagnostic ontology. Moreover, we extend our existing repository CERR-N (Center of Excellence in Research Reporting in Neurosurgery) to include diagnostic studies.",
"name": "Diagnostic Ontology",
"prefix": "DIAGONT",
"version": "2.0"
},
"DIDEO": {
"contact": {
"email": "mbrochhausen@gmail.com",
"name": "Mathias Brochhausen"
},
"description": "The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology. DIDEO is created as part of an NIH-funded project aiming towards developing a new knowledge base for potential drug drug interaction information. In DIDEO we represent PDDIs as information content entities and we aim to also provide the evidence for those entities using nano- and micro publication approaches.",
"homepage": "https://github.com/DIDEO/DIDEO",
"name": "Drug Interaction and Evidence Ontology",
"prefix": "DIDEO",
"publication": "https://dikb.org",
"version": "release version 2017-11-17"
},
"DIKB": {
"contact": {
"email": "rdb20@pitt.edu",
"name": "Richard D Boyce"
},
"description": "An evidence taxonomy for pharmacologic studies that, when combined with a set of inclusion criteria, enable drug experts to specify what their confidence in a drug mechanism assertion would be if it were supported by a specific set of evidence. Boyce R, Collins C, Horn J, Kalet I. Computing with evidence Part I: A drug-mechanism evidence taxonomy oriented toward confidence assignment. J Biomed Inform. 2009 Dec;42(6):979-89. Epub 2009 May 10. PubMed PMID: 19435613; PubMed Central PMCID: PMC2783801.",
"homepage": "http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/front-page.html",
"name": "Drug Interaction Knowledge Base Ontology",
"prefix": "DIKB",
"publication": "http://www.ncbi.nlm.nih.gov/pubmed/19435613",
"version": "Version 1.6"
},
"DILON": {
"contact": {
"email": "ifilgood@snu.ac.kr",
"name": "Hyeoneui Kim"
},
"description": "DILON was created to represent dietary lifestyle data. Concepts were pulled from Korean dietary assessment scales and English assessment scales. Concepts are labeled in English and Korean translations are also provided.",
"name": "Dietary lifestyle ontology",
"prefix": "DILON",
"version": "2"
},
"DINTO": {
"contact": {
"email": "maria.herrero@kcl.ac.uk",
"name": "Maria Herrero"
},
"description": "DINTO is an OWL ontology that systematically organizes all drug-drug interaction (DDI) related information. Drug-drug interactions (DDIs) form a significant risk group for adverse effects associated with pharmaceutical treatment. These interactions are often reported in the literature, however, they are sparsely represented in machine-readable resources, such as online databases, thesauri or ontologies. DINTO is an ontology that describes and categorizes DDIs and all the possible mechanisms that can lead to them (including both pharmacodynamic and pharmacokinetic DDI mechanisms).",
"homepage": "http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto",
"name": "The Drug-Drug Interactions Ontology",
"prefix": "DINTO",
"version": "1.3"
},
"DISDRIV": {
"contact": {
"email": "lynn.schriml@gmail.com",
"name": "Lynn Schriml"
},
"description": "Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. Built in collaboration with EnvO, ExO, ECTO and ChEBI.",
"homepage": "https://disease-ontology.org/",
"name": "Disease Drivers Ontology",
"prefix": "DISDRIV"
},
"DLORO": {
"contact": {
"email": "amkalet@uw.edu",
"name": "alan kalet"
},
"description": "Dependency Layered Ontology for Radiation Oncology",
"homepage": "https://ont2bn.radonc.washington.edu/IROK/",
"name": "Dependency Layered Ontology for Radiation Oncology",
"prefix": "DLORO",
"version": "1.2"
},
"DMDSONT": {
"contact": {
"email": "duygu.celik@emu.edu.tr",
"name": "Duygu Celik Ertugrul"
},
"description": "Diabetes Mellitus Diagnosis and Support Ontology (DMDSOnt) is created using OWL 2.0 according to the directions given in the IDFβs guidelines (2022). As required and directed in the IDFβs guidelines, DMDSOnt contains concepts and relations about the signs and symptoms observed in DM, active lifestyle expected from patients, genetic conditions of patients, physical activities to be followed, laboratory tests, other factors/criteria in the diagnosis of DM, and supportive treatment recommendations for the proper management of DM risk. IDF:\tAmerican Diabetes Association Professional Practice Committee. (2022). 2.Classification and diagnosis of diabetes: standards of medical care in diabetesβ2022. Diabetes Care, 45, (Supplement_1), S17-S38, DOI: /10.2337/dc22-S002, http://diabetesjournals.org/care/article-pdf/45/Supplement_1/S17/637547/dc22s002.pdf.",
"name": "Diabetes Mellitus Diagnosis and Support Ontology",
"prefix": "DMDSONT",
"version": "ver 1.0"
},
"DMTO": {
"contact": {
"email": "farmankanju@gmail.com",
"name": "2. Farman Ali"
},
"description": "DMTO is an OWL 2 ontology for creating customized treatment plans for diabetic patients. The ontology is based on BFO and OGMS. In addition, it extends the DDO ontology by adding the treatment classes and axioms to the existing diagnosis part.",
"name": "Diabetes Mellitus Treatment Ontology",
"prefix": "DMTO",
"publication": "https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-018-0176-y",
"version": "2015-11-20"
},
"DOCCC": {
"description": "Diagnosis Ontology of Clinical Care Classification (CCC)",
"name": "Diagnosis Ontology of Clinical Care Classification",
"prefix": "DOCCC",
"version": "20131004"
},
"DOID": {
"contact": {
"email": "lynn.schriml@gmail.com",
"name": "Lynn Schriml"
},
"description": "Creating a comprehensive classification of human diseases organized by etiology.",
"homepage": "https://disease-ontology.org/",
"name": "Human Disease Ontology",
"prefix": "DOID",
"publication": "https://disease-ontology.org/community/publications",
"version": "2024-07-31"
},
"DOREMUS-KEYS": {
"contact": {
"email": "nlorimer@stanford.edu",
"name": "Nancy Lorimer"
},
"description": "The sum of relations, melodic and harmonic, existing between the tones of a scale or musical system.",
"name": "Doremus List of Keys",
"prefix": "DOREMUS-KEYS"
},
"DOVES": {
"contact": {
"email": "benjamin.rosner@uscf.edu",
"name": "Benjamin Rosner"
},
"description": "The Digital medicine Outcomes Value Set (DOVeS) ontology aims to provide users with a set of ontologically structured healthcare outcomes (clinical, operational, economic, technical, and others) tailored to digital medicine and digital therapeutic applications.",
"name": "Digital medicine Outcomes Value Set (DOVeS) Ontology",
"prefix": "DOVES",
"version": "releases/2023-03-01"
},
"DPCO": {
"contact": {
"email": "rashidsabbir@gmail.com",
"name": "Sabbir Rashid"
},
"description": "The Diabetes Pharmacology Ontology contains the classes needed to describe antihyperglycemic therapies, pharmacotherapy factors, and diagnostic factors.",
"homepage": "https://tetherless-world.github.io/diabetes-pharmacology-ontology/",
"name": "Diabetes Pharmacology Ontology",
"prefix": "DPCO",
"version": "1.0"
},
"DPO": {
"contact": {
"email": "cp390@cam.ac.uk",
"name": "Clare Pilgrim"
},
"description": "An ontology of commonly encountered and/or high level Drosophila phenotypes. It has significant formalisation - utilising terms from GO, CL, PATO and the Drosophila anatomy ontology. It has been used by FlyBase for > 159000 annotations of phenotype.",
"homepage": "http://purl.obolibrary.org/obo/fbcv",
"name": "Drosophila Phenotype Ontology",
"prefix": "DPO",
"version": "2024-08-08"
},
"DRANPTO": {
"contact": {
"email": "zz889@uowmail.edu.au",
"name": "Zhenyu Zhang"
},
"description": "DRANPTO is developed for representing the domain knowledge specific to non-pharmacological intervention for agitation in dementia, particularly for the long-term care setting.",
"name": "Dementia-Related Agitation Non-Pharmacological Treatment Ontology",
"prefix": "DRANPTO",
"publication": "https://doi.org/10.1002/trc2.12061",
"version": "Version 1.0"
},
"DREAMDNPTO": {
"contact": {
"email": "zz889@uowmail.edu.au",
"name": "Zhenyu Zhang"
},
"description": "DREAMDNPTO represents the domain knowledge specific to the non-pharmacological treatment of emotional and mood disturbances (e.g., depression and anxiety in dementia) in people with dementia living in the long-term care setting.",
"name": "Dementia-Related Emotional And Mood Disturbance Non-Pharmacological Treatment Ontology",
"prefix": "DREAMDNPTO",
"version": "v1.0"
},
"DRMO": {
"contact": {
"email": "niveditadgp@gmail.com",
"name": "NIVEDITA DUTTA"
},
"description": "The DrMO ontology is a domain ontology that represents knowledge underlying the composition, characterization and standardization of different materials involved in the dental restoration procedure. It will assist dentists in selecting appropriate materials based on up-to-date scientific knowledge to satisfy a patientβs specific requirements, without jeopardizing their clinical time. It reuses several ontologies from the OBO foundry, especially the Oral Health and Disease (OHD) Ontology. However, the dental restoration domain is complex and also requires concepts from materials science and engineering. Thus, DrMO also incorporates knowledge from the Devices, Experimental scaffolds, and Biomaterials (DEB) and Functionally Graded Materials (FGM) ontologies to provide more comprehensive knowledge of this area of dental material than previous ontologies. However, much of the terminology from FGM is different than that used in clinical dentistry. Thus, DrMO has changed the appropriate classes to make them consistent with terminology common in dentistry. DrMO also follows ontology design best practices by reusing meta-data properties from the Dublin Core vocabulary. It captures knowledge from a large set of the most recent and influential papers in Dental Materials and related fields. Links to these papers are included in the ontology as meta-data defined with Dublin Core. It is implemented in OWL2 and was developed with the ProtΓ©gΓ© 5.5 ontology editor. The ontology was created using the Ontology Development 101 methodology by Natalya et.al. Several domain experts in addition to Dr. Dutta also provided their expertise. The ontology is available on GitHub and licensed via an open source license. The GitHub project includes a corresponding file of SPARQL queries that answer the competency questions defined as part of the ontology development methodology.",
"name": "Dental Restorative Material Ontology",
"prefix": "DRMO"
},
"DRON": {
"contact": {
"email": "hoganwr@gmail.com",
"name": "William Hogan"
},
"description": "We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive).",
"homepage": "https://github.com/ufbmi/dron",
"name": "The Drug Ontology",
"prefix": "DRON",
"version": "2024-08-05"
},
"DRPSNPTO": {
"contact": {
"email": "zz889@uowmail.edu.au",
"name": "Zhenyu Zhang"
},
"description": "The DRPSNPTO ontology represents the domain knowledge specific to non-pharmacological treatment of psychotic symptoms in dementia in the long-term care setting.",
"name": "Dementia-Related Psychotic Symptoms Non-Pharmacological Treatment Ontology",
"prefix": "DRPSNPTO",
"version": "v1.0"
},
"DSEO": {
"contact": {
"email": "lfierro@isi.edu",
"name": "Lily Fierro"
},
"description": "Simple ISA hierarchical taxonomy denoting subfields of study in data science for use in educational applications.",
"homepage": "http://bigdatau.org/about_erudite",
"name": "Data Science Education Ontology",
"prefix": "DSEO",
"version": "1.1"
},
"DSIP": {
"contact": {
"email": "hfwlw0416@outlook.com",
"name": "ZiyiXu"
},
"description": "Here is the mock data about pharmacy management in the Data Science in Practice.",
"name": "Pharmacy mock data",
"prefix": "DSIP"
},
"DSIP1V": {
"contact": {
"email": "alexchang526@gmail.com",
"name": "Chih-Chieh Chang"
},
"description": "This is vocabularies for the DSIP Group 1 FieldLabs",
"name": "DSIP1_vocabulary",
"prefix": "DSIP1V"
},
"DSIP2324_DEMO": {
"contact": {
"email": "rens@renskievit.com",
"name": "Rens Kievit"
},
"description": "This is an ontology made for the purposes of demonstrating the process of vocabulary creation for the Data Science in Practice course. Update V0.2: Fixed Leiden University coupling to DBpedia",
"name": "DSIP2324_Demonstration",
"prefix": "DSIP2324_DEMO",
"version": "0.2"
},
"DSIP7": {
"contact": {
"email": "senjutibala15@gmail.com",
"name": "Senjuti Bala"
},
"description": "The Human Trafficking Vocabulary is an essential resource for researchers and analysts working with raw interview data gathered from refugees affected by human trafficking. It offers a standardized framework for categorizing and understanding various aspects of human trafficking incidents. The vocabulary includes terms for describing the nationality and location of human traffickers, the number of times traffickers are mentioned by independent sources, the type of observation obtained (first-hand or second-hand), and more. This vocabulary was created as part of Data Science in Practice Fieldlab-7, with guidance from Kai Smiths. It is continuously updated to reflect new insights and developments in the field of human trafficking research.",
"name": "DSIP_FieldLab_7",
"prefix": "DSIP7"
},
"DSIP8": {
"contact": {
"email": "s3790525@vuw.leidenuniv.nl",
"name": "Hedy Ho"
},
"description": "refugee datapod updated ontology after feedback",
"name": "DSIP8REFUGEE",
"prefix": "DSIP8"
},
"DSIPF7": {
"contact": {
"email": "senjutibala15@gmail.com",
"name": "Senjuti Bala"
},
"description": "The Human Trafficking Vocabulary is an essential resource for researchers and analysts working with raw interview data gathered from refugees affected by human trafficking. It offers a standardized framework for categorizing and understanding various aspects of human trafficking incidents. The vocabulary includes terms for describing the nationality and location of human traffickers, the number of times traffickers are mentioned by independent sources, the type of observation obtained (first-hand or second-hand), and more. This vocabulary was created as part of Data Science in Practice Fieldlab-7, with guidance from Kai Smiths. It is continuously updated to reflect new insights and developments in the field of human trafficking research.",
"name": "DSIP FiledLab7",
"prefix": "DSIPF7"
},
"DSIPFL7": {
"contact": {
"email": "r.suryaparthipan@gmail.com",
"name": "Parthipan Ramakrishnan"
},
"description": "The Human Trafficking Vocabulary is an essential resource for researchers and analysts working with raw interview data gathered from refugees affected by human trafficking. It offers a standardized framework for categorizing and understanding various aspects of human trafficking incidents. The vocabulary includes terms for describing the nationality and location of human traffickers, the number of times traffickers are mentioned by independent sources, the type of observation obtained (first-hand or second-hand), and more. This vocabulary was created as part of Data Science in Practice Fieldlab-7, with guidance from Kai Smiths. It is continuously updated to reflect new insights and developments in the field of human trafficking research.",
"name": "DSIP_Fieldlab_7",
"prefix": "DSIPFL7",
"version": "latest_v1"
},
"DSIP_FL_7": {
"contact": {
"email": "r.suryaparthipan@gmail.com",
"name": "Parthipan Ramakrishnan"
},
"description": "The Human Trafficking Vocabulary is an essential resource for researchers and analysts working with raw interview data gathered from refugees affected by human trafficking. It offers a standardized framework for categorizing and understanding various aspects of human trafficking incidents. The vocabulary includes terms for describing the nationality and location of human traffickers, the number of times traffickers are mentioned by independent sources, the type of observation obtained (first-hand or second-hand), and more. This vocabulary was created as part of Data Science in Practice Fieldlab-7, with guidance from Kai Smiths. It is continuously updated to reflect new insights and developments in the field of human trafficking research.",
"name": "DSIP_FL_7",
"prefix": "DSIP_FL_7",
"version": "v1"
},
"DTO": {
"contact": {
"email": "sschurer@med.miami.edu",
"name": "Stephan Schurer"
},
"description": "Drug Target Ontology (DTO) is being developed at the University of Miami in the research group of Stephan SchΓΌrer. DTO is supported by grant U54CA189205 (Illuminating the Druggable Genome Knowledge Management Center, Tudor Oprea, PI) awarded by the NCI through the NIH Common Fund. It is a component of the Illuminating the Druggable Genome (IDG) project (https://commonfund.nih.gov/idg). The DTO project develops a novel semantic framework to formalize knowledge about drug targets with a focus on the current IDG protein families. The DTO is developed as a reference for drug targets with the longer-term goal to create a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The first version of the DTO consists of asserted class hierarchies of the four IDG protein families, GPCRs, kinases, ion channels, and nuclear hormone receptors. Protein classes are linked to tissue and disease via different levels of confidence. DTO also contains drug target development level classifications developed in the IDG project (http://targetcentral.ws/), and functional and qualitative annotations and classifications for kinase proteins, GPCR ligands and ion channels. DTO is modeled in OWL2-DL to enable further classification by inference reasoning and SPARQL queries. DTO is implemented following a modularization approach. DTO is used as the organizational framework for drug targets in the IDG PHAROS User Interface Portal (https://pharos.nih.gov) and also the Tin-X Target Importance and Novelty Explorer (http://newdrugtargets.org).",
"homepage": "http://drugtargetontology.org/",
"name": "Drug Target Ontology",
"prefix": "DTO",
"publication": "http://drugtargetontology.org/",
"version": "1.1.1"
},
"DUO": {
"contact": {
"email": "mcourtot@ebi.ac.uk",
"name": "Melanie Courtot"
},
"description": "An ontology based on the consent codes decsription from the Dyke et al. paper at http://dx.doi.org/10.1371/journal.pgen.1005772. It allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage. This resource is based on the OBO Foundry principles, and its use is under review by the Broad Institute ad the European Genome-phenome Archive (EGA) at EMBL-EBI.",
"homepage": "https://github.com/EBISPOT/DUO",
"name": "The Data Use Ontology",
"prefix": "DUO"
},
"E-PPO": {
"contact": {
"email": "patceeng@gmail.com",
"name": "Patience U. Usip"
},
"description": "The Enhanced Personal Profile Ontology (e-PPO) provides personal profile of personnel that are required for software requirement engineering task selection. Properties of the ontology includes static and dynamic features. Name, gender, date of birth, etc. are static in nature and may not change. Other static properties such as educational qualification and skills acquired can be updated while others including area of specialization and profession are dynamic and can be changed. Also, areas of specializations cannot be out of the scope of oneβs profession, although one personnel can have multiple profession and skills, more than one profession can share things in common such as the same professional qualification may be required.",
"name": "Enhanced Personal Profile Ontology",
"prefix": "E-PPO"
},
"EBP": {
"contact": {
"email": "tylerwheeler4@gmail.com",
"name": "Tyler Wheeler"
},
"description": "Clinical practice guidelines, behaviour change theories, and associated behaviour change strategies for the management of hypertension.",
"name": "EmpowerBP",
"prefix": "EBP",
"version": "2.5"
},
"ECAO": {
"contact": {
"email": "ettensohn@cmu.edu",
"name": "Charles Ettensohn"
},
"description": "An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586).",
"homepage": "https://github.com/echinoderm-ontology/ecao_ontology",
"name": "The Echinoderm Anatomy and Development Ontology",
"prefix": "ECAO"
},
"ECDO": {
"contact": {
"email": "lars.schrijver@hotmail.com",
"name": "Lars Schrijver"
},
"description": "This is an ontology for elderly dementia care in the Netherlands.",
"name": "Elderly Care Dementia Ontology",
"prefix": "ECDO"
},
"ECG": {
"contact": {
"email": "rwinslow@jhu.edu",
"name": "Raimond L. Winslow, PhD & Stephen Granite"
},
"description": "The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms.",
"homepage": "http://www.cvrgrid.org",
"name": "Electrocardiography Ontology",
"prefix": "ECG",
"version": "1"
},
"ECM4M-MD-VOCABS": {
"contact": {
"email": "jgraybeal@stanford.edu",
"name": "John Graybeal"
},
"description": "Collection of EarthCube M4M vocabularies for sample metadata definitions.",
"homepage": "https://github.com/go-fair-us/EarthCubeM4M",
"name": "EarthCube M4M Metadata Vocabulary",
"prefix": "ECM4M-MD-VOCABS",
"version": "0.1.2"
},
"ECO": {
"contact": {
"email": "mgiglio@som.umaryland.edu",
"name": "Michelle Giglio"
},
"description": "An ontology of evidence types for supporting conclusions in scientific research",
"homepage": "https://github.com/evidenceontology/evidenceontology",
"name": "Evidence and Conclusion Ontology",
"prefix": "ECO",
"publication": "https://github.com/evidenceontology/evidenceontology",
"version": "releases/2024-07-19"
},
"ECOCORE": {
"homepage": "https://github.com/EcologicalSemantics/ecocore",
"name": "An ontology of core ecological entities",
"prefix": "ECOCORE",
"version": "2022-03-09"
},
"ECOSIM": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "An ontology of variables for earth system simulation, derived from the ecosim framework.",
"homepage": "https://github.com/cmungall/ecosim-ontology",
"name": "ecosim ontology",
"prefix": "ECOSIM"
},
"ECP": {
"contact": {
"email": "portokallidis@gmail.com",
"name": "Nick Portokallidis"
},
"description": "Our focus in this work is to define in a formal way (ontology-based) and platform independent representative metadata and relationships of care plans. This approach has as goal to work as an umbrella over all these systems and provides some advantages regarding the management, the organization and the searching of formal care plans.",
"homepage": "http://iris.med.duth.gr/research/ecp/ontology",
"name": "Electronic Care Plan",
"prefix": "ECP",
"version": "0.6"
},
"ECSO": {
"contact": {
"email": "mecum@nceas.ucsb.edu",
"name": "Bryce Mecum"
},
"description": "DataONE ontology of Carbon Flux measurements for MsTMIP and LTER Use Cases",
"homepage": "https://github.com/DataONEorg/sem-prov-ontologies",
"name": "The Ecosystem Ontology",
"prefix": "ECSO",
"version": "0.9"
},
"ECTO": {
"homepage": "https://github.com/EnvironmentOntology/environmental-exposure-ontology",
"name": "Environmental conditions, treatments and exposures ontology",
"prefix": "ECTO",
"version": "2023-02-14"
},
"EDAM": {
"contact": {
"email": "matus.kalas@uib.no",
"name": "MatΓΊΕ‘ KalaΕ‘"
},
"description": "EDAM is a domain ontology of data analysis and data management in bio- and other sciences, and science-based applications. It comprises concepts related to analysis, modelling, optimisation, and data life-cycle. Targetting usability by diverse users, the structure of EDAM is relatively simple, divided into 4 main sections: Topic, Operation, Data (incl. Identifier), and Format. EDAM is particularly suitable for semantic annotations and categorisation of diverse resources related to data analysis and management: e.g. tools, workflows, learning materials, or standards. EDAM is also useful in data management itself, for recording provenance metadata of processed data. As a reference article (citation), please use https://doi.org/10.7490/f1000research.1118900.1",
"homepage": "http://edamontology.org",
"name": "EDAM - Bioscientific data analysis ontology",
"prefix": "EDAM",
"publication": "https://doi.org/10.7490/f1000research.1118900.1",
"version": "unstable(1.26_dev)"
},
"EDAM-BIOIMAGING": {
"contact": {
"email": "drmatuskalas@duck.com",
"name": "MatΓΊΕ‘ KalaΕ‘"
},
"description": "Bioimage informatics operations, types of data, data formats, and bioimaging topics. EDAM Bioimaging is an extension of the EDAM ontology (edamontology.org) for image analysis, bioimage informatics, bioimaging, and imaging in general. It is being developed in collaboration between the ELIXIR Research Infrastructure and the NEUBIAS and COMULIS COST Actions (neubias.org CA15124, comulis.eu CA17121, funded by the Horizon 2020 Framework Programme of the European Union), in coordination with the Euro-BioImaging Research Infrastructure (PP2) and the Global BioImaging network.",
"homepage": "https://webprotege.stanford.edu/#projects/2ce704bf-83ed-4d2e-985f-84c4841fac71/edit/Classes",
"name": "EDAM Bioimaging Ontology",
"prefix": "EDAM-BIOIMAGING",
"publication": "https://github.com/edamontology/edam-bioimaging#citing",
"version": "alpha06"
},
"EDDA": {
"contact": {
"email": "tanja.bekhuis@tcbinfosci.com",
"name": "Tanja Bekhuis"
},
"description": "The EDDA Study Designs Taxonomy (v2.0) was developed by the Evidence in Documents, Discovery, and Analytics (EDDA) Group: Tanja Bekhuis (Principal Scientist); Eugene Tseytlin (Systems Developer); Ashleigh Faith (Taxonomist); Faina Linkov (Epidemiologist). The EDDA Group is a division of TCB Research & Indexing LLC. This work was made possible, in part, by the US National Library of Medicine, National Institutes of Health, grant no. R00LM010943. Foundational research is described in Bekhuis T, Demner Fushman D, Crowley RS. Comparative effectiveness research designs: an analysis of terms and coverage in Medical Subject Headings (MeSH) and Emtree. Journal of the Medical Library Association (JMLA). 2013 April;101(2):92-100. PMC3634392. Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries. A PDF of this taxonomy is available in ResearchGate DOI: 10.13140/RG.2.1.3769.2406/1. The EDDA Study Designs Taxonomy by Tanja Bekhuis and Eugene Tseytlin is licensed under a Creative Commons AttributionβNonCommercialβShareAlike 4.0 International License (CC BY-NC-SA 4.0). For information about this license, see https://creativecommons.org/licenses/by-nc-sa/4.0/.",
"name": "EDDA Study Designs Taxonomy",
"prefix": "EDDA",
"version": "2.0"
},
"EDDA_PT": {
"contact": {
"email": "tanja.bekhuis@tcbinfosci.com",
"name": "Tanja Bekhuis"
},
"description": "The EDDA Publication Types Taxonomy (v1.0) was developed by Tanja Bekhuis (Principal Scientist) and Eugene Tseytlin (Systems Developer) of the Evidence in Documents, Discovery, and Analytics (EDDA) Group. The EDDA Group is a division of TCB Research & Indexing LLC. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCIT, Emtree, and dictionaries. The EDDA Publication Types Taxonomy by Tanja Bekhuis and Eugene Tseytlin is licensed under a Creative Commons AttributionβNonCommercialβShareAlike 4.0 International License (CC BY-NC-SA 4.0). For information about this license, see https://creativecommons.org/licenses/by-nc-sa/4.0/.",
"name": "EDDA Publication Types Taxonomy",
"prefix": "EDDA_PT",
"version": "1.0"
},
"EDEM-CONNECTONTO": {
"contact": {
"email": "christiane.pinkert@dzne.de",
"name": "Christiane Pinkert"
},
"description": "The EDEM-CONNECTONTO has been created to incorporate domain knowledge about the various types of agitation observed in people with dementia (PwD), as well as the dyadic relationship existing between PwD and their informal caregivers. Furthermore, it offers a structured framework for non-pharmacological interventions, enabling caregivers to effectively manage and mitigate the bidirectional effects of agitation in PwD.",
"name": "eDEM-Connect: Ontology of Dementia-related Agitation and Relationship between Informal Caregivers and Persons with Dementia",
"prefix": "EDEM-CONNECTONTO",
"version": "Version 1.0"
},
"EFO": {
"contact": {
"email": "efo-users@ebi.ac.uk",
"name": "EFO User List"
},
"description": "The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental variables in multiple resources at the EBI and Open Targets. The ontology has been developed to increase the richness of the annotations that are currently made in resources and to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology pulls together classes from reference ontologies such as disease, cell line, cell type and anatomy and adds axiomatisation as necessary to connect areas such as disease to phenotype. Contact EFO users list for information: efo-users@ebi.ac.uk.",
"homepage": "http://www.ebi.ac.uk/efo",
"name": "Experimental Factor Ontology",
"prefix": "EFO",
"version": "3.68.0"
},
"EGO": {
"contact": {
"email": "yongqunhe@med.umich.edu",
"name": "Oliver He"
},
"description": "The Epigenome Ontology (EGO) a biomedical ontology for integrative epigenome knowledge representation and data analysis.",
"homepage": "https://github.com/EGO-ontology",
"name": "Epigenome Ontology",
"prefix": "EGO",
"version": "Arbor version; 1.0.1"
},
"EHDA": {
"contact": {
"email": "J.Bard@ed.ac.uk",
"name": "Jonathan Bard"
},
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once.",
"homepage": "http://obofoundry.org/ontology/ehda.html",
"name": "Human Developmental Anatomy Ontology, timed version",
"prefix": "EHDA",
"version": "unknown"
},
"EHDAA": {
"contact": {
"email": "J.Bard@ed.ac.uk",
"name": "Jonathan Bard"
},
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release.",
"homepage": "http://obofoundry.org/ontology/ehdaa.html",
"name": "Human Developmental Anatomy Ontology, abstract version 1",
"prefix": "EHDAA",
"version": "unknown"
},
"EHDAA2": {
"contact": {
"email": "J.Bard@ed.ac.uk",
"name": "EMAP Administrators"
},
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release.",
"homepage": "http://genex.hgu.mrc.ac.uk/",
"name": "Human Developmental Anatomy Ontology, abstract version 2",
"prefix": "EHDAA2",
"version": "releases/2024-01-11"
},
"ELD": {
"contact": {
"email": "aleka.aktau@gmail.com",
"name": "Aliya Aktau"
},
"description": "This is the list of Ethiopian Diseases approved by MOH Ethiopia",
"name": "EthiopianListOfDiseases",
"prefix": "ELD",
"version": "4"
},
"ELECTRICA": {
"contact": {
"email": "f.maikore@sheffield.ac.uk",
"name": "Fatima Maikore"
},
"description": "An ontology to help describe data for ELEctronic tool for Clinicians, Trainers and Researchers In Child Abuse",
"homepage": "https://github.com/fatibaba/electrica",
"name": "Ontology for ELEctronic tool for Clinicians, Trainers and Researchers In Child Abuse",
"prefix": "ELECTRICA",
"version": "2024-07-06"
},
"ELIG": {
"contact": {
"email": "mab7036@dbmi.columbia.edu",
"name": "Mary Regina Boland"
},
"description": "We derived a set of 1,437 eligibility features that were organized into a feature hierarchy using 80 breast cancer trials.",
"name": "Eligibility Feature Hierarchy",
"prefix": "ELIG",
"version": "v. 1.0"
},
"ELTER_CL": {
"contact": {
"email": "barbara.magagna@gmail.com",
"name": "Barbara Magagna"
},
"description": "eLTER Controlled Lists are used in different environmental projects related to the eLTER community.",
"name": "eLTER Controlled Lists",
"prefix": "ELTER_CL",
"version": "1.1.1"
},
"EMAP": {
"contact": {
"email": "Terry.Hayamizu@jax.org",
"name": "Terry Hayamizu"
},
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).",
"homepage": "http://emouseatlas.org/",
"name": "Mouse Gross Anatomy and Development Ontology",
"prefix": "EMAP",
"version": "unknown"
},
"EMAPA": {
"contact": {
"email": "Terry.Hayamizu@jax.org",
"name": "Terry Hayamizu"
},
"description": "Abstract (i.e. non-stage specific) stage-specific anatomical structures of the mouse.",
"homepage": "http://emouseatlas.org/",
"name": "Mouse gross anatomy and development, timed",
"prefix": "EMAPA"
},
"EMIF-AD": {
"contact": {
"email": "i.bermejo@maastrichtuniversity.nl",
"name": "Inigo Bermejo"
},
"description": "Ontology developed as part of European Medical Information Framework' s (EMIF) Alzheimerβs disease (AD) project.",
"homepage": "http://www.emif.eu/emif-ad-2/",
"name": "EMIF-AD ontology",
"prefix": "EMIF-AD",
"version": "0.0.2"
},
"EMO": {
"contact": {
"email": "gemma.l.holliday@gmail.com",
"name": "Gemma Holliday"
},
"description": "This ontology describes the components of an enzyme and its reaction mechanism including the roles that the components play in the reaction mechanism.",
"name": "Enzyme Mechanism Ontology",
"prefix": "EMO"
},
"ENM": {
"contact": {
"email": "hastings@ebi.ac.uk",
"name": "Janna Hastings"
},
"description": "The eNanoMapper ontology covers the full scope of terminology needed to support research into nanomaterial safety. It builds on multiple pre-existing external ontologies such as the NanoParticle Ontology.",
"homepage": "https://github.com/enanomapper/ontologies",
"name": "eNanoMapper",
"prefix": "ENM",
"publication": "https://scholar.google.com/scholar?hl=nl&as_sdt=0%2C5&q=enanomapper+ontology&btnG=&oq=enano",
"version": "10.0"
},
"ENTITY": {
"contact": {
"email": "jhanit@gmail.com",
"name": "Nitin"
},
"description": "Entity Membership",
"name": "ISO-15926-2_2003_entityMembership",
"prefix": "ENTITY",
"version": "Created 2008-07-14. Version 1.0."
},
"ENVO": {
"description": "Official PURL: http://purl.obolibrary.org/obo/envo.owl The most up-to-date information about ENVO is available here: http://www.obofoundry.org/ontology/envo.html EnvO is an OBO Foundry and Library ontology for the concise, controlled description of environmental entities such as ecosystems, environmental processes, and environmental qualities. It closely interoperates with a broad collection of other OBO ontologies and is used in a diverse range of projects.",
"homepage": "http://environmentontology.org/",
"name": "Environment Ontology",
"prefix": "ENVO",
"publication": "http://environmentontology.org/",
"version": "2024-07-01"
},
"ENVS_VARIABLES": {
"contact": {
"email": "pedro.carvalho@envs.au.dk",
"name": "Pedro Carvalho"
},
"description": "Quantitative and qualitative variables describing environmental state",
"homepage": "https://github.com/m4m-dk/workshop-2-vocabulary",
"name": "ENVS variables",
"prefix": "ENVS_VARIABLES",
"publication": "https://github.com/m4m-dk/workshop-2-vocabulary",
"version": "0.1.1"
},
"ENVTHES": {
"contact": {
"email": "barbara.magagna@gmail.com",
"name": "Barbara Magagna"
},
"description": "EnvThes",
"name": "Thesaurus for long-term ecological research, monitoring, experiments",
"prefix": "ENVTHES",
"version": "5.0.5"
},
"EO": {
"contact": {
"email": "z.tippu@surrey.ac.uk",
"name": "Zayed Tippu"
},
"description": "The Ethnicity Ontology (EO) has been developed by extending the Basic Formal Ontology 2 standard in order to have a common reference for ethnicity concepts for semantic integration of datasets. It attempts to utilise iterated proxy markers for ethnicity such language spoken and interpreter requirements in order to support health care research studies.",
"homepage": "www.ClinInf.eu",
"name": "Ethnicity Ontoloy",
"prefix": "EO",
"version": "1.0"
},
"EO1": {
"contact": {
"email": "oliveri.leo@gmail.com",
"name": "Leonardo Oliveri"
},
"description": "Ontology with some information about patient's origin and disabilities",
"name": "Example Ontology",
"prefix": "EO1"
},
"EOL": {
"contact": {
"email": "matthieu.reichstadt@clermont.inra.fr",
"name": "Reichstadt Matthieu"
},
"description": "L'ontologie EOL décrit les conditions d'environnement des élevages d'animaux domestiques. Elle décrit plus particulièrement les modalités de l'alimentation, de l'environnement, de la structure des élevages et des systèmes d'élevage",
"name": "Environment Ontology for Livestock",
"prefix": "EOL"
},
"EP": {
"contact": {
"email": "rwinslow@jhu.edu",
"name": "Raimond L. Winslow, PhD"
},
"description": "The Cardiac Electrophysiology Ontology contains terms describing single-channel electrophysiological experiments and data obtained using voltage-clamp, current clamp and fluorescence imaging techniques applied at the cell level and multi-channel fluorescence imaging techniques applied at the cell, tissue and whole heart levels.",
"homepage": "http://www.cvrgrid.org",
"name": "Cardiac Electrophysiology Ontology",
"prefix": "EP",
"version": "1"
},
"EPIE": {
"contact": {
"email": "PATUserSupport@mail.nih.gov",
"name": "PATUserSupport"
},
"description": "Biological entities associated with changes in the regulation of gene activity without alteration of genetic structure. Development of this terminology was funded by the National Institute of Child Health and Human Development in support of the Placental Atlas Tool (PAT) with final verification by the PAT External Scientific Panel. This terminology was developed through a combination of resources including existing biomedical ontology resources, such as the Gene Ontology and the National Cancer Institute Thesaurus, web-based content, and epigenetic literature.",
"name": "Epigenetic Entity",
"prefix": "EPIE",
"version": "1.3"
},
"EPILONT": {
"contact": {
"email": "dourado@dei.uc.pt",
"name": "Antonio Dourado"
},
"description": "Ontology about the epilepsy domain and epileptic seizures. Based on the diagnosis proposed by the International League Against Epilepsy (ILAE).",
"homepage": "www.epilepsiae.eu",
"name": "Epilepsy Ontology",
"prefix": "EPILONT",
"version": "V1"
},
"EPIO": {
"contact": {
"email": "alpha.tom.kodamullil@scai.fraunhofer.de",
"name": "Alpha Tom Kodanullil"
},
"description": "The Epilepsy Ontology (EPO) is an assembly of structured knowledge on various aspects of epilepsy, developed according to basic formal ontology (BFO) and Open Biological and Biomedical Ontology (OBO) Foundry principles. Entities and definitions are collected from the latest International League against Epilepsy (ILAE) classification, as well as from domain-specific ontologies such as Epilepsy Ontology (EPILONT), Epilepsy Syndrome Seizure Ontology (ESSO), Epilepsy Semiology(EPISEM) and Epilepsy and Seizure Ontology (EPSO) and scientific literature. This ontology is intended to be used for data management and for text mining purposes. The current release of the ontology is publicly available and is a community based effort to assemble various facets of the complex disease Epilepsy.",
"name": "EpilepsyOntology",
"prefix": "EPIO",
"version": "Version Release: 1.0.0"
},
"EPIP": {
"contact": {
"email": "PATUserSupport@mail.nih.gov",
"name": "PATUserSupport"
},
"description": "Biological processes associated with changes in the regulation of gene activity without alteration of genetic structure. Development of this terminology was funded by the National Institute of Child Health and Human Development in support of the Placental Atlas Tool (PAT) with final verification by the PAT External Scientific Panel. This terminology was developed through a combination of resources including existing biomedical ontology resources, such as the Gene Ontology and the National Cancer Institute Thesaurus, web-based content, and epigenetic literature.",
"name": "Epigenetic Process",
"prefix": "EPIP",
"version": "1.3"
},
"EPISEM": {
"contact": {
"email": "dhier@uic.edu",
"name": "Daniel B Hier"
},
"description": "An ontology designed to capture the semiology of epilepsy including ictal, post-ictal, inter-ictal, and aura signs. For the branches entitled \"disease\", \"etiologic factor\", \"epidemiologic factor\"--see ESSO ontology on this website for origin of terms.",
"name": "Epilepsy Semiology",
"prefix": "EPISEM",
"version": "5.0"
},
"EPO": {
"contact": {
"email": "ferdinand.dhombres@inserm.fr",
"name": "Ferdinand Dhombres"
},
"description": "The early pregnancy ontology contains the concepts to describe ectopic pregnancy ultrasound images, organized into several subsumption hierarchies for types of ectopic pregnancies and the signs, anatomical structures and technical elements of imaging associated with ectopic pregnancy. Version 1.1 was used for ultrasound image annotations (Dhombres et al. Developing a knowledge base to support the annotation of ultrasound images of ectopic pregnancy. J Biomed Semantics, 2017)",
"name": "Early Pregnancy Ontology",
"prefix": "EPO",
"version": "1.1"
},
"EPSO": {
"contact": {
"email": "satyasahoo@ieee.org",
"name": "Satya Sahoo"
},
"description": "The Epilepsy Ontology (BioPortal ID: EpSO) is an application ontology developed to support epilepsy research, patient care, and health system management. The updated version of the Epilepsy Ontology adds Dravet Syndrome (DS) related terms covering both model systems and patients with DS. This version expands on the prior version of the ontology, which focused on neuropathology terms, including immunohistochemistry, microscopy, and anatomical description, related to epilepsy. This work has been funded in part by the Dravet Syndrome Foundation (DSF), International League Against Epilepsy (ILAE), and the US National Institutes of Health (NIH). Some of the funding agencies retain intellectual ownership of the ontology, together with the Case Western Reserve University and other collaborating institutions. Contributors: Satya S. Sahoo, Jeffrey Buchhalter, Samden D. Lhatoo, Katja Kobow, Deepak K. Gupta, Alireza Bozorgi, Aman Dabir, Bilal Gonen, Hans O. Luders, Kenneth Loparo, Veronica Hood",
"homepage": "https://bmhinformatics.case.edu/",
"name": "Epilepsy and Seizure Ontology",
"prefix": "EPSO",
"publication": "https://bmhinformatics.case.edu/",
"version": "3"
},
"ERO": {
"contact": {
"email": "carlotorniai@gmail.com",
"name": "Carlo Torniai"
},
"description": "This ontology models research resources such instruments. protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/).",
"homepage": "http://code.google.com/p/eagle-i/",
"name": "Eagle-I Research Resource Ontology",
"prefix": "ERO",
"publication": "http://code.google.com/p/eagle-i/wiki/Publications",
"version": "2013-08-02"
},
"ESFO": {
"contact": {
"email": "sfld-help@cgl.ucsf.edu",
"name": "Shoshana Brown"
},
"description": "The ESFO provides a new paradigm for organizing enzyme sequence, structure, and function information, whereby specific elements of enzyme sequence and structure are mapped to specific conserved aspects of function, thus facilitating the functional annotation of uncharacterized enzymes. The ESFO helps prevent misannotation by emphasizing annotation of enzymes only at the level of functional granularity warranted by available information.",
"homepage": "http://sfld.rbvi.ucsf.edu/",
"name": "Enzyme Structure Function Ontology",
"prefix": "ESFO",
"version": "1"
},
"ESO_C": {
"contact": {
"email": "leilei_25@126.com",
"name": "Lei Chen"
},
"description": "Semiology of Epilepsy",
"name": "Epilepsy Semiology Ontology",
"prefix": "ESO_C",
"version": "1.0"
},
"ESSO": {
"contact": {
"email": "Jeffrey.Buchhalter@albertahealthservices.ca",
"name": "Jeffrey Buchhalter"
},
"description": "This ontology contains epilepsy syndromes, seizure types, and data elements associated with them.",
"name": "Epilepsy Syndrome Seizure Ontology",
"prefix": "ESSO",
"version": "1.03"
},
"ETANC": {
"contact": {
"email": "tigist.habtamu@aau.edu.et",
"name": "Tigist"
},
"description": "Ethiopian Antenatal care (ANC) register vocabulary",
"name": "ETHIOPIANC",
"prefix": "ETANC",
"version": "0.2"
},
"ETHANC": {
"contact": {
"email": "aleka.aktau@gmail.com",
"name": "Aliya Aktau"
},
"description": "Antenatal care registry for Ethiopia",
"name": "ETHANC",
"prefix": "ETHANC",
"version": "14"
},
"ETHOPD": {
"contact": {
"email": "tigist.habtamu@aau.edu.et",
"name": "Tigist"
},
"description": "This is an Ethiopian Out Patient Department register vocabulary",
"name": "Ethiopian OPD",
"prefix": "ETHOPD",
"version": "0.3"
},
"EUPATH": {
"contact": {
"email": "stoeckrt@pennmedicine.upenn.edu",
"name": "Chris Stoeckert"
},
"description": "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.",
"homepage": "https://github.com/EuPath-ontology/EuPath-ontology",
"name": "VEuPathDB Ontology",
"prefix": "EUPATH",
"publication": "https://pdfs.semanticscholar.org/888e/a51dbb138122d39c42f863f2a1ada7976db4.pdf",
"version": "2023-05-30"
},
"EVI": {
"contact": {
"email": "ma3xy@virginia.edu",
"name": "Sadnan Al Manir"
},
"description": "The Evidence Graph ontology extends core concepts from the W3C Provenance Ontology PROV-O and Bioschemas' Profiles to describe evidence for correctness of findings in biomedical publications. The semantic data model in EVI is expressed using OWL2 Web Ontology Language.",
"homepage": "https://evidencegraph.github.io/EVI/",
"name": "Evidence Graph Ontology",
"prefix": "EVI",
"version": "1.1"
},
"EXACT": {
"contact": {
"email": "soldatova.larisa@gmail.com",
"name": "Larisa Soldatova"
},
"description": "EXACT aims to explicitly define the semantics of experimental protocols in order to ensure their reproducibility, and to support computer applications that assist biologists in the preparation, maintenance, submission and sharing of experimental protocols.",
"homepage": "https://github.com/larisa-soldatova/EXACT",
"name": "An ontology for experimental actions",
"prefix": "EXACT",
"version": "2"
},
"EXMO": {
"contact": {
"email": "xyz19940216@163.com",
"name": "Xingyun Liu"
},
"description": "A core reference ontology built upon BFO about exercise medicine. This ontology contains the related terms for healthy people, people with chronic conditions and people living with diability to exercise.",
"homepage": "https://github.com/DarkKnight0-0/exmo",
"name": "Exercise Medicine Ontology",
"prefix": "EXMO",
"version": "1.1"
},
"EXO": {
"contact": {
"email": "annethessen@gmail.com",
"name": "Anne Thessen"
},
"description": "Significant progress has been made over the last several years in collecting and improving access to genomic, toxicology, and health data to promote understanding about environmental influences on human health. The resulting information resources, however, lack extensive and reliable exposure data, which are required to translate molecular insights, elucidate environmental contributions to diseases, and assess human health risks at the individual and population levels. We report our development of an Exposure Ontology, ExO, designed to address this information gap by facilitating centralization and integration of exposure data to inform understanding of environmental health. Like other widely used ontologies, ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics.",
"homepage": "https://github.com/CTDbase/exposure-ontology",
"name": "Exposure Ontology",
"prefix": "EXO",
"version": "releases/2022-06-29"
},
"EXON": {
"contact": {
"email": "scuberog@hotmail.com",
"name": "Salvador Cubero"
},
"description": "Experiment focused in the compatibility with proteg'e software to create and upload ontologies on Bioportal",
"name": "Experimental Ontology",
"prefix": "EXON"
},
"EXTRACT": {
"contact": {
"email": "nikola@fairdatacollective.com",
"name": "Nikola Vasiljevic"
},
"description": "Controlled vocabularies such as taxonomies allow an accurate and controlled approach in describing datasets. One of such controlled vocabulary is Wind Energy Taxonomy of External Conditions. This taxonomy is the result of EERA JP WIND IRPWind Open Data initiative that took place in 2017 in which wind energy experts generated the first version of the taxonomy as an input for defining and structuring wind energy metadata.",
"homepage": "https://github.com/DTUWindEnergy/EXTRACT-taxonomy",
"name": "EXTeRnAl Conditions Taxonomy (EXTRACT)",
"prefix": "EXTRACT",
"publication": "https://github.com/DTUWindEnergy/EXTRACT-taxonomy",
"version": "v0.1.0"
},
"FALDO": {
"contact": {
"email": "faldo@googlegroups.com",
"name": "FALDO group"
},
"description": "FALDO is the Feature Annotation Location Description Ontology. It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources. The aim of this ontology is to describe the position of a sequence region or a feature. It does not aim to describe features or regions itself, but instead depends on resources such as the Sequence Ontology or the UniProt core ontolgy.",
"homepage": "http://biohackathon.org/resource/faldo",
"name": "Feature Annotation Location Description Ontology",
"prefix": "FALDO",
"publication": "https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0067-z",
"version": "Created at the Biohackathon 2012 and 2013"
},
"FALL": {
"contact": {
"email": "johnny_khawaja@hotmail.com",
"name": "johnny"
},
"description": "fall detection scenario",
"name": "MyOntoServiceFull_FallDetection",
"prefix": "FALL",
"version": "1"
},
"FALLS": {
"contact": {
"email": "subhashis.das@dcu.ie",
"name": "Subhashis Das"
},
"description": "This ontology is about a falls prevention intervention record.",
"name": "falls prevention",
"prefix": "FALLS",
"version": "0.1"
},
"FAO": {
"contact": {
"email": "dinglis@stanford.edu",
"name": "Diane Inglis"
},
"description": "A structured controlled vocabulary for the anatomy of fungi.",
"homepage": "https://github.com/obophenotype/fungal-anatomy-ontology",
"name": "Fungal Gross Anatomy Ontology",
"prefix": "FAO"
},
"FARMACI": {
"name": "FARMACI AIFA",
"prefix": "FARMACI"
},
"FAST-CHRONO": {
"contact": {
"email": "nlorimer@stanford.edu",
"name": "Nancy Lorimer"
},
"description": "FAST is an enumerative, faceted subject heading schema derived from the Library of Congress Subject Headings (LCSH). The purpose of adapting the LCSH with a simplified syntax to create FAST is to retain the very rich vocabulary of LCSH while making the schema easier to understand, control, apply, and use. This facet includes chronological terms derived from LCSH.",
"name": "FAST (Faceted Access of Subject Terminology) Chronological Facet",
"prefix": "FAST-CHRONO"
},
"FAST-EVENT": {
"contact": {
"email": "futo@stanford.edu",
"name": "Michelle Futornick"
},
"description": "FAST is an enumerative, faceted subject heading schema derived from the Library of Congress Subject Headings (LCSH). The purpose of adapting the LCSH with a simplified syntax to create FAST is to retain the very rich vocabulary of LCSH while making the schema easier to understand, control, apply, and use. The schema maintains upward compatibility with LCSH, and any valid set of LC subject headings can be converted to FAST headings. This is the Event facet.",
"homepage": "http://www.oclc.org/research/themes/data-science/fast/download.html",
"name": "FAST (Faceted Application of Subject Terminology) Event",
"prefix": "FAST-EVENT"
},
"FAST-EVENT-SKOS": {
"contact": {
"email": "futo@stanford.edu",
"name": "Michelle Futornick"
},
"description": "This is a test of submitting FAST-EVENT with Format dropdown set to SKOS (instead of OWL)",
"name": "FAST (Faceted Application of Subject Terminology) Event Facet",
"prefix": "FAST-EVENT-SKOS"
},
"FAST-FORMGENRE": {
"contact": {
"email": "futo@stanford.edu",
"name": "Michelle Futornick"
},
"description": "FAST is an enumerative, faceted subject heading schema derived from the Library of Congress Subject Headings (LCSH). The purpose of adapting the LCSH with a simplified syntax to create FAST is to retain the very rich vocabulary of LCSH while making the schema easier to understand, control, apply, and use.",
"name": "FAST (Faceted Application of Subject Terminology) FormGenre facet",
"prefix": "FAST-FORMGENRE"
},
"FAST-GENREFORM": {
"contact": {
"email": "nlorimer@stanford.edu",
"name": "Nancy Lorimer"
},
"description": "FAST is an enumerative, faceted subject heading schema derived from the Library of Congress Subject Headings (LCSH).",
"homepage": "http://www.oclc.org/research/themes/data-science/fast/download.html",
"name": "FAST (Faceted Access of Subject Terminology) GenreForm",
"prefix": "FAST-GENREFORM"
},
"FAST-TITLE": {
"contact": {
"email": "futo@stanford.edu",
"name": "Michelle Futornick"
},
"description": "FAST (Faceted Application of Subject Terminology) is an enumerative, faceted subject heading schema derived from the Library of Congress Subject Headings (LCSH). The purpose of adapting the LCSH with a simplified syntax to create FAST is to retain the very rich vocabulary of LCSH while making the schema easier to understand, control, apply, and use.",
"homepage": "http://www.oclc.org/research/themes/data-science/fast/download.html",
"name": "FAST (Faceted Application of Subject Terminology) Title Facet",
"prefix": "FAST-TITLE"
},
"FASTO": {
"contact": {
"email": "shaker_elsapagh@yahoo.com",
"name": "Shaker El-Sappagh"
},
"description": "FHIR And SSN based Type 1 diabetes Ontology (FASTO) is an OWL 2 ontology for real time management of insulin for diabetes patients especially type 1 diabetics. The ontology is based on BFO as the top-level ontology, SSN sensor ontology, and HL7 FHIR standard. This ontology can support the development of mobile health applications. It supports the interoperability between clinical decision support systems on a cloud environment, distributed electronic health records, mobile devices, and wireless body area networks.",
"name": "HL7 FHIR and SSN ontology based Type 1 Diabetes Mellitus Ontology",
"prefix": "FASTO",
"publication": "https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-019-0806-z",
"version": "2015-11-20"
},
"FB-BT": {
"contact": {
"email": "cp390@cam.ac.uk",
"name": "Claire Pilgrim"
},
"description": "An ontology representing the gross anatomy of Drosophila melanogaster",
"homepage": "http://purl.obolibrary.org/obo/fbbt",
"name": "Drosophila Gross Anatomy Ontology",
"prefix": "FB-BT",
"version": "fbbt/releases/2024-08-08"
},
"FB-CV": {
"contact": {
"email": "cp390@cam.ac.uk",
"name": "Clare Pilgrim"
},
"description": "A structured controlled vocabulary used for various aspects of annotation by FlyBase. It includes the Drosophila Phenotype Ontology (DPO) which is also released separately. This ontology is maintained by FlyBase for various aspects of annotation not covered, or not yet covered, by other OBO ontologies. If and when community ontologies are available for the domains here covered FlyBase will use them.",
"homepage": "http://purl.obolibrary.org/obo/fbcv",
"name": "FlyBase Controlled Vocabulary",
"prefix": "FB-CV",
"version": "2024-08-08"
},
"FB-DV": {
"contact": {
"email": "mmc46@gen.cam.ac.uk",
"name": "Marta Costa"
},
"description": "A structured controlled vocabulary of the development of Drosophila melanogaster.",
"homepage": "http://sourceforge.net/p/fbbtdv/wiki/Home/",
"name": "Drosophila Development Ontology",
"prefix": "FB-DV",
"version": "fbdv/releases/2024-08-07"
},
"FB-SP": {
"contact": {
"email": "mmc46@gen.cam.ac.uk",
"name": "Marta Costa"
},
"description": "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.",
"homepage": "http://www.flybase.org/",
"name": "Fly Taxonomy",
"prefix": "FB-SP"
},
"FBbi": {
"contact": {
"email": "chris@bio.umass.edu",
"name": "Chris Woodcock"
},
"description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.",
"homepage": "http://cellimagelibrary.org/",
"name": "Biological Imaging Methods Ontology",
"prefix": "FBbi"
},
"FCC1": {
"contact": {
"email": "diwale.varsha@gmail.com",
"name": "Varsha Diwale"
},
"description": "Fernald Community Cohort meta data",
"homepage": "http://www.semanticweb.org/diwaleva/ontologies/2019/9/fcc-ontology",
"name": "Fernald Community Cohort N",
"prefix": "FCC1",
"version": "1.0"
},
"FDC-GDMT": {
"contact": {
"email": "jgraybeal@stanford.edu",
"name": "John Graybeal"
},
"description": "Controlled terms and semantic properties used in the FAIR Data Collective's Generic Dataset Metadata Template.",
"homepage": "https://github.com/fair-data-collective/generic-dataset-metadata-template",
"name": "Ontology for Generic Dataset Metadata Template",
"prefix": "FDC-GDMT",
"version": "v0.3.7"
},
"FDSAJFAHSJK": {
"contact": {
"email": "akaren.kan@gmail.com",
"name": "akaren.kan"
},
"description": "dasf",
"name": "OWL_XML_Tool5",
"prefix": "FDSAJFAHSJK"
},
"FDT-O": {
"contact": {
"email": "l.o.boninodasailvasantos@utwente.nl",
"name": "Luiz Bonino"
},
"description": "The FAIR Data Train Ontology provides the definitions of concepts and relations used in the FAIR Data Train environment.",
"name": "FAIR Data Train Ontology",
"prefix": "FDT-O",
"version": "- Refactored FHIR API and FHIR Train as sub-classes of REST API and REST Train, respectively."
},
"FENICS": {
"contact": {
"email": "David.Lewis-Smith@newcastle.ac.uk",
"name": "David Lewis-Smith"
},
"description": "The Functional Epilepsy Nomenclature for Ion Channels (FENICS) is allowing the consistent evaluation of electrophysiology experiments on Ion Channels in the context of neurological disorders, in particular epilepsy.",
"name": "Functional Electrophysiology Nomenclature for Ion Channels",
"prefix": "FENICS",
"version": "0.0.5"
},
"FG": {
"contact": {
"email": "jam.belien@amsterdamumc.nl",
"name": "Jeroen A.M. BeliΓ«n"
},
"description": "The FAIR Genomes semantic metadata schema to power reuse of NGS data in research and healthcare.",
"homepage": "https://w3id.org/fair-genomes",
"name": "FAIR Genomes",
"prefix": "FG",
"version": "1.2-Minor"
},
"FGNHNS": {
"contact": {
"email": "higuchi@nibiohn.go.jp",
"name": "HIGUCHI, Chihiro"
},
"description": "Ontology of food groups of the National Health and Nutrition Examination Survey issued by the Ministry of Health, Labour and Welfare. Foods are divided into major, medium, and minor categories, and the English and Japanese names of foods belonging to the minor categories are noted.",
"name": "FoodGroupNHNS",
"prefix": "FGNHNS",
"version": "0.169"
},
"FHHO": {
"contact": {
"email": "jpeace@unc.edu",
"name": "Jane Peace"
},
"description": "The FHHO facilitates representing the family health histories of persons related by biological and/or social family relationships (e.g. step, adoptive) who share genetic, behavioral, and/or environmental risk factors for disease. SWRL rules are included to compute 3 generations of biological relationships based on parentage and family history findings based on personal health findings.",
"homepage": "http://healthsystems.engr.wisc.edu/Alumni/JanePeace.html",
"name": "Family Health History Ontology",
"prefix": "FHHO",
"publication": "http://healthsystems.engr.wisc.edu/Alumni/JanePeace.html",
"version": "1"
},
"FIDEO": {
"contact": {
"email": "georgeta.bordea@u-bordeaux.fr",
"name": "Georgeta Bordea"
},
"description": "The Food Interactions with Drugs Evidence Ontology (FIDEO) is an ontology used for annotation and retrieval of scientific articles about food-drug interactions.",
"homepage": "https://gitub.u-bordeaux.fr/erias/fideo",
"name": "Food Interactions with Drugs Evidence Ontology",
"prefix": "FIDEO",
"publication": "http://www.informatik.uni-leipzig.de/~loebe/tmp/ICBO2020/paperL.pdf",
"version": "2023-12-18"
},
"FIRE": {
"contact": {
"email": "souza.a@outlook.com",
"name": "Adriano Souza"
},
"description": "The ontology of Fire was created in order to represent the set of concepts about the fire occurring in natural vegetation, its characteristics, causes and effects, with focus on Cerrado vegetation domain. The fire plays a determinant role on the structure and composition of Cerrado physiognomies.",
"name": "Fire Ontology",
"prefix": "FIRE",
"version": "0.8"
},
"FISH-AST": {
"contact": {
"email": "futo@stanford.edu",
"name": "Michelle"
},
"description": "Terminology used for recording the techniques, recovery methods and materials associated with archaeological sciences. Maintained by Historic England on behalf of the FISH Terminology Working Group.",
"homepage": "http://heritagedata.org/live/schemes/560.html",
"name": "FISH Archaeological Sciences Thesaurus",
"prefix": "FISH-AST"
},
"FISHO": {
"contact": {
"email": "23.mohdnajib@gmail.com",
"name": "Mohd Najib"
},
"description": "This Fish Ontology is an ontology created as how the author views the fish structure following the book \"The Diversity of Fishes: Biology, Evolution and Ecology\" as the main reference, which covers one part of view on ichthyology, with an emphasis on diversity and adaptation. This ontology is created with the mindset of categorizing fish automatically based on the attributes and terms mined from the fish specimen. Most of the basic organization from this ontology follows Nelson's research due to its synthetic and broad approach, while recognizing that Nelson's conclusions are one of many alternative interpretations of the literature, which is mostly agreed by our main references, and many fish and fisheries researchers. Most of the classification used in this ontology is in no means completed and just following the recent classification provided by the books For now our work focused more on two group of fish which is early jawless fish, and advanced jawed fishes. The classification from both of this group are structured following the reference.",
"homepage": "https://mohdnajib1985.github.io/FOWebPage/",
"name": "Fish Ontology",
"prefix": "FISHO",
"publication": "https://peerj.com/preprints/3020/",
"version": "Version 1.0.3 (Possible addition)\n\n-Considering to add more fish study related terms in the ontology such as fish immune sytem, and Fish Locomotion and Feeding Behavior.\n-Also focused on completing other classification of fish, and adding more relationships between the classes.\n\n\nVersion 1.0.2\n\n-Added a lot of annotations and metadata for fish terms, and added several more subclasses for the ontology. \n\n\nVersion 1.0.1\n\n-Change the structure and the hierarchy of a lot of classes to follow the main references. Several classes are deleted and marked as \"deprecated\" or \"In Review\" in case they might be useful later.\n\n\nVersion 1.0.0\n\n-The first version of the fish ontology is created."
},
"FITBIT": {
"name": "Fitbit Vocabulary",
"prefix": "FITBIT"
},
"FIT_BIT": {
"contact": {
"email": "harryeshun19@gmail.com",
"name": "Harold"
},
"description": "This contains vocabulary information for Fitbit data for a single source user from the online API",
"name": "Fitbit Vocabularies",
"prefix": "FIT_BIT"
},
"FIX": {
"contact": {
"email": "chebi-help@ebi.ac.uk",
"name": "Chebi Administrators"
},
"description": "FIX consists of two ontologies: methods and properties (but not objects, which are subject of the chemical ontology). The methods are applied to study the properties.",
"name": "Physico-Chemical Methods and Properties",
"prefix": "FIX",
"version": "1.2"
},
"FLDLB3": {
"contact": {
"email": "rensanderson7@gmail.com",
"name": "Rens Anderson"
},
"description": "This is the final ontology of fieldlab 3 check 3",
"homepage": "https://github.com/Rens-byte/Fieldlab3-2/tree/main",
"name": "FIELDLAB3_2023_2",
"prefix": "FLDLB3",
"version": "3"
},
"FLOPO": {
"contact": {
"email": "leechuck@leechuck.de",
"name": "Robert Hoehndorf"
},
"description": "The Flora Phenotype Ontology is an ontology of phenotypes reported in Floras. The original version was developed at the pro-iBiosphere Hackathon in Leiden. This is the pre-classified version of the ontology; the original OWL file is at https://github.com/flora-phenotype-ontology/flopoontology/blob/master/ontology/flopo.owl The Flora Phenotype Ontology is generated from the Flora Malesiana, Flora Gabon, Flora of Central Africa, and a collection of Kew's African Floras. Every class in the ontology has at least one taxon annotation. The (draft) taxon annotation are available at http://jagannath.pdn.cam.ac.uk/plant/flora/clean-rerun/",
"homepage": "http://wiki.pro-ibiosphere.eu/wiki/Traits_Task_Group",
"name": "Flora Phenotype Ontology",
"prefix": "FLOPO",
"version": "0.9"
},
"FLU": {
"contact": {
"email": "burkesquires@gmail.com",
"name": "Burke Squires"
},
"description": "Starting in the fall of 2007, a collaborative group of influenza researchers have established an influenza ontology. The influenza ontology is an application ontology. Consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS)",
"homepage": "http://purl.obolibrary.org/obo/flu/",
"name": "Influenza Ontology",
"prefix": "FLU",
"version": "0.9.0"
},
"FLYGLYCODB": {
"contact": {
"email": "kkiyoko@soka.ac.jp",
"name": "Kiyoko F. Aoki-Kinoshita"
},
"description": "Ontology to describe glycogenes of Drosophila. Includes mutants, activity, references and links to FlyBase and UniProt.",
"homepage": "http://fly.glycoinfo.org",
"name": "FlyGlycoDB",
"prefix": "FLYGLYCODB",
"version": "1.0.0"
},
"FMA": {
"contact": {
"email": "mejino@uw.edu",
"name": "Onard Mejino"
},
"description": "FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. For a description of how this OWL version is generated, see: \"Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy\" by N. F. Noy, M. A. Musen, J. L. Mejino Jr., C. Rosse (https://www.sciencedirect.com/science/article/pii/S0169023X03001253).",
"homepage": "http://si.washington.edu/projects/fma",
"name": "Foundational Model of Anatomy",
"prefix": "FMA",
"publication": "http://sigpubs.si.washington.edu/view/subjects/FMA.html",
"version": "5.0.0"
},
"FMPM": {
"contact": {
"email": "scuberog@hotmail.com",
"name": "Salvador Cubero GonzΓ‘lez"
},
"description": "Food matrix ontology for predictive microbiology.",
"name": "Food Matrix for Predictive Microbiology",
"prefix": "FMPM",
"version": "0.9.2"
},
"FNS-H": {
"contact": {
"email": "pance.panov@ijs.si",
"name": "Pance Panov"
},
"description": "Application ontology for the FNS-Cloud project ontology PURL: https://purl.org/fns-h",
"homepage": "https://github.com/panovp/FNS-Harmony",
"name": "FNS-Harmony",
"prefix": "FNS-H",
"version": "1.3"
},
"FO": {
"contact": {
"email": "kwsm@dbcls.rois.ac.jp",
"name": "Shuichi Kawashima"
},
"description": "Fern Ontology (FO) is a controlled and structured vocabulary of fern specific anatomy and lifecycle.",
"name": "Fern Ontology",
"prefix": "FO",
"version": "0.05"
},
"FOAF": {
"contact": {
"email": "rafael.goncalves@stanford.edu",
"name": "Rafael Gonçalves"
},
"description": "Friend of a Friend Vocabulary",
"name": "Friend of a Friend Vocabulary",
"prefix": "FOAF",
"version": "0.99"
},
"FOBI": {
"contact": {
"email": "polcaes@gmail.com",
"name": "Pol Castellano Escuder"
},
"description": "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data.",
"homepage": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology",
"name": "FOBI (Food-Biomarker Ontology)",
"prefix": "FOBI"
},
"FOO": {
"contact": {
"email": "hamednh@cardiff.ac.uk",
"name": "NAEIMA HAMED"
},
"description": "The Forest Observatory Ontology (FOO) ( is an ontology for describing wildlife data generated by sensors. FOO's scope evolves around the Internet of Things (IoT) and wildlife habitats. To illustrate our datasets of interest, we modelled the concept to represent \"sensors observing animals and land\". These sensors generate observations. For example, the animal GPS collar tracks an elephant and records its geo-location observations for different and equally spaced time intervals and temperature every specified time interval. We adopted classes and properties from SOSA and BBC wildlife ontologies to model the domain coverage.",
"homepage": "ontology.forest-observatory.org",
"name": "Forest Observatory Ontology",
"prefix": "FOO",
"publication": "https://link.springer.com/chapter/10.1007/978-3-031-43458-7_29",
"version": "BBC Wildlife Ontology Reused 26 June 2024"
},
"FOODON": {
"contact": {
"email": "damion_dooley@sfu.ca",
"name": "Damion Dooley"
},
"description": "FoodOn is an ontology built to represent entities which bear a βfood roleβ and is initially focused on categorizing and processing of food for humans. We aim to develop semantics for food safety, food security, the agricultural and animal husbandry practices linked to food production, culinary, nutritional and chemical ingredients and processes. FoodOn belongs to the OBOFoundry.org family of ontologies.",
"homepage": "http://foodon.org",
"name": "The FoodOn Food Ontology",
"prefix": "FOODON",
"publication": "https://www.nature.com/articles/s41538-018-0032-6",
"version": "2024-06-17"
},
"FOUR-M_VOCABS": {
"contact": {
"email": "powellk@health.missouri.edu",
"name": "Kimberly Powell"
},
"description": "Vocabulary for the 4M nursing framework",
"name": "AGE-FRIENDLY 4M VOCABULARY",
"prefix": "FOUR-M_VOCABS",
"version": "1"
},
"FOVT": {
"contact": {
"email": "rlwalls2008@gmail.com",
"name": "Ramona Walls"
},
"description": "FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA).",
"homepage": "https://github.com/futres/fovt",
"name": "FuTRES Ontology of Vertebrate Traits",
"prefix": "FOVT",
"version": "2023-05-31"
},
"FPLX": {
"homepage": "https://github.com/sorgerlab/famplex",
"name": "FamPlex",
"prefix": "FPLX",
"publication": "https://www.biorxiv.org/content/early/2018/03/26/225698",
"version": "1.0"
},
"FRMO": {
"contact": {
"email": "ftuhaifa@gmail.com",
"name": "Fatimah Altuhaifa"
},
"description": "We have developed an ontology representing major fall risk management entities to support approaches to text mining, data descriptions and linkage in the context of fall risk management. This ontology contains concepts related to fall risk factors, fall risk interventions, and fall consequences. Title: Developing an Ontology Representing Fall Risk Management Domain Knowledge Link to the article: https://link.springer.com/article/10.1007/s10916-024-02062-2",
"name": "Fall Risk Management Ontology",
"prefix": "FRMO",
"publication": "https://link.springer.com/article/10.1007/s10916-024-02062-2",
"version": "09.10"
},
"FTC": {
"contact": {
"email": "samuel.croset@gmail.com",
"name": "Samuel Croset"
},
"description": "The Functional Therapeutic Chemical Classification System (FTC) defines over 20'000 mechanisms and modes of action for approuved drugs. The resource abstracts away from the traditional chemical structure-based approach and focuses solely on the mode of action of drugs. The classification sorts therapeutic agents based on their function in the human body.",
"homepage": "https://www.ebi.ac.uk/chembl/ftc",
"name": "Functional Therapeutic Chemical Classification System",
"prefix": "FTC",
"publication": "https://www.ebi.ac.uk/chembl/ftc",
"version": "1"
},
"FYPO": {
"contact": {
"email": "vw253@cam.ac.uk",
"name": "Valerie Wood"
},
"description": "Fission Yeast Phenotype Ontology",
"homepage": "https://github.com/pombase/fypo",
"name": "Fission Yeast Phenotype Ontology",
"prefix": "FYPO",
"version": "2024-08-01"
},
"G-PROV": {
"contact": {
"email": "agun@rpi.edu",
"name": "Nkechinyere Agu"
},
"description": "The ontology provides the vocabulary for enabling provenance in clinical decision support systems.",
"homepage": "https://tetherless-world.github.io/GProv/",
"name": "Guideline Provenance",
"prefix": "G-PROV",
"version": "1"
},
"G4-DSIP": {
"contact": {
"email": "jasper.mosseveld@gmail.com",
"name": "Jasper van Mosseveld"
},
"description": "Group 4 Data Science in Practice",
"name": "Group 4-Data Science in Practice",
"prefix": "G4-DSIP",
"version": "1.0.0"
},
"GALEN": {
"contact": {
"email": "j@deltaflow.com",
"name": "Julian Seidenberg"
},
"description": "A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.",
"homepage": "http://www.co-ode.org/galen/",
"name": "Galen Ontology",
"prefix": "GALEN",
"version": "1.1"
},
"GALLONT": {
"contact": {
"email": "adeans@psu.edu",
"name": "Andy Deans"
},
"description": "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls.",
"homepage": "https://adeans.github.io/gallont/",
"name": "Plant Gall Ontology",
"prefix": "GALLONT",
"version": "2024-04-19"
},
"GAMUTS": {
"contact": {
"email": "ckahn@upenn.edu",
"name": "Charles E. Kahn, Jr."
},
"description": "In radiology, a \"gamut\" is the set of conditions that can cause a specified imaging finding. The Radiology Gamuts Ontology (RGO) links more than 16,000 diseases and imaging findings. The causal relation (may_cause; inverse, may_be_caused_by) connects findings and possible causes. This work is made available under provisions of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) license.",
"homepage": "https://www.gamuts.net/",
"name": "Radiology Gamuts Ontology",
"prefix": "GAMUTS",
"publication": "https://www.gamuts.net/about.php",
"version": "2.0"
},
"GAZ": {
"contact": {
"email": "lschriml@som.umaryland.edu",
"name": "Lynne Schriml"
},
"description": "GAZ is a large, ontologically-oriented resource listing place names which can be treated as instances of environments.",
"homepage": "http://environmentontology.github.io/gaz/",
"name": "Gazetteer",
"prefix": "GAZ",
"version": "$Revision: 1.512 $"
},
"GB": {
"contact": {
"email": "bdkouiti5013@gmail.com",
"name": "Koichi Arakawa"
},
"description": "GlycanBind is an ontology for representing glycan and pathogen binding interaction data in RDF. Many of the terms are based on the data originally contained in the SugarBind database.",
"name": "GlycanBind",
"prefix": "GB",
"version": "1.1.1"
},
"GBM": {
"contact": {
"email": "cameron@rockefeller.edu",
"name": "Cameron Coffran"
},
"description": "Ontology of Glioblastoma",
"name": "Glioblastoma",
"prefix": "GBM"
},
"GBOL": {
"contact": {
"email": "jesse.vandam@wur.nl",
"name": "Jesse van Dam"
},
"description": "Genome Biology Ontology Language (GBOL)",
"homepage": "http://gbol.life",
"name": "GBOL",
"prefix": "GBOL",
"publication": "https://www.biorxiv.org/content/early/2017/09/05/184747",
"version": "1"
},
"GCBO": {
"contact": {
"email": "christian.kindermann@stanford.edu",
"name": "Christian Kindermann"
},
"description": "An initial version of the Global Code Book Ontology",
"name": "Global Code Book Ontology",
"prefix": "GCBO",
"version": "2024-05-01"
},
"GCO": {
"contact": {
"email": "z.tatum@lumc.nl",
"name": "Zuotian Tatum"
},
"description": "The Genome Component Ontology is intended to define the abstract division of the total genetic information of an organism by its physical separation into different components, thereby providing a high level reference point to which more specific descriptions of the characteristics of these components can be linked.",
"name": "Genome Component Ontology",
"prefix": "GCO",
"version": "0.2"
},
"GDCO": {
"contact": {
"email": "jcumming@uoguelph.ca",
"name": "Joel Cummings"
},
"description": "The Data Collection Ontology (DCO) is an ontology designed for data collection providing classes and relations on top of the Basic Formal Ontology (BFO) to facilitate data collection processes, subjects, and data anaylsis through the use of classifiers. DCO is based on the notion of reasoning to validate incoming data through their definitions based on classifiers.",
"name": "Data Collection Ontology",
"prefix": "GDCO",
"version": "1.0"
},
"GDMT": {
"contact": {
"email": "horridge@stanford.edu",
"name": "Matthew Horridge"
},
"description": "An initial version of the Generic Dataset Metadata Template vocabulary",
"homepage": "https://github.com/bmir-radx/gdmt",
"name": "Generic Dataset Metadata Template Vocabulary",
"prefix": "GDMT",
"version": "1.0.0-alpha"
},
"GECCO": {
"contact": {
"email": "alpha.tom.kodamullil@scai.fraunhofer.de",
"name": "Alpha Tom Kodamullil"
},
"description": "To ensure the interoperability and compatibility among COVID-19 datasets, we present here a Common Data Model (CDM) which has been built from 11 different COVID-19 datasets from various geographical locations. The current version of the CDM holds 4639 data variables related to COVID-19 such as basic patient information (age, biological sex, and diagnosis) as well as disease-specific data variables, for example, Anosmia and Dispnea. Each of the data variables in the data model is associated with specific data types, variable mappings, value ranges, data units, and data encodings that could be used for standardizing any dataset.",
"name": "COVID-19 Common Datamodel",
"prefix": "GECCO",
"version": "1.0.0"
},
"GECKO": {
"contact": {
"email": "rbca.jackson@gmail.com",
"name": "Rebecca Jackson"
},
"description": "An ontology to represent genomics cohort attributes.",
"homepage": "https://github.com/IHCC-cohorts/GECKO",
"name": "Genomics Cohorts Knowledge Ontology",
"prefix": "GECKO"
},
"GENDER": {
"contact": {
"email": "vinutha_rk@yahoo.com",
"name": "Vinutha Venkatesh"
},
"description": "This vocabulary makes up the different gender identities - Female, Male and Other.",
"name": "Gender Identity",
"prefix": "GENDER"
},
"GENE-CDS": {
"contact": {
"email": "samwald@gmx.at",
"name": "Matthias Samwald"
},
"description": "The Genomic CDS ontology aims to unify several functionalities in a single resource, being: * A knowledge base for clinical pharmacogenomics/pharmacogenetics that can be used for question-answering (e.g., which SNPs are associated with this drug?) * A rule base for clinical decision support (e.g., inferring that a patient with a specific set of SNPs requires a lowered dose of warfarin and generating a CDS message that can be viewed by clinicians) * A tool for checking data consistency (e.g., highlighting which allele definitions in PharmGKB are overlapping, or which clinical decision support rules are matching the same group of patients)",
"homepage": "http://samwald.info",
"name": "Genomic Clinical Decision Support Ontology",
"prefix": "GENE-CDS",
"version": "0.8.0"
},
"GENEPIO": {
"contact": {
"email": "damion_dooley@sfu.ca",
"name": "Damion Dooley"
},
"description": "The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information required to support data sharing and integration for foodborne infectious disease surveillance and outbreak investigations.",
"homepage": "https://genepio.org/",
"name": "Genomic Epidemiology Application Ontology",
"prefix": "GENEPIO"
},
"GENEVIEVE": {
"name": "Charlotte",
"prefix": "GENEVIEVE"
},
"GENO": {
"contact": {
"email": "mhb120@gmail.com",
"name": "Matthew Brush"
},
"description": "An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases.",
"homepage": "https://github.com/monarch-initiative/GENO-ontology/",
"name": "Genotype Ontology",
"prefix": "GENO",
"version": "2023-10-08"
},
"GEO": {
"contact": {
"email": "hoganwr@gmail.com",
"name": "William Hogan"
},
"description": "An ontology of geographical entities implemented in Web Ontology Language 2 (OWL2) and based on Basic Formal Ontology (BFO).",
"homepage": "https://github.com/ufbmi/geographical-entity-ontology/",
"name": "Geographical Entity Ontology",
"prefix": "GEO",
"version": "production version 2018-02-23"
},
"GEOSPARQL": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kim Durante"
},
"description": "The OGC GeoSPARQL standard supports representing and querying geospatial data on the Semantic Web. GeoSPARQL defines a vocabulary for representing geospatial data in RDF, and it defines an extension to the SPARQL query language for processing geospatial data. In addition, GeoSPARQL is designed to accommodate systems based on qualitative spatial reasoning and systems based on quantitative spatial computations.",
"name": "GeoSPARQL",
"prefix": "GEOSPARQL",
"version": "OGC GeoSPARQL 1.0"
},
"GEOSPECIES": {
"contact": {
"email": "pdevries@wisc.edu",
"name": "Peter J. DeVries"
},
"description": "This ontology was designed to help integrate species concepts with species occurrences, gene sequences, images, references and geographical information. See also Taxonconcept.org",
"homepage": "http://lod.geospecies.org/",
"name": "GeoSpecies Ontology",
"prefix": "GEOSPECIES",
"publication": "http://about.geospecies.org/",
"version": "2012-10-02"
},
"GEXO": {
"contact": {
"email": "vladimir.n.mironov@gmail.com",
"name": "Vladimir Mironov"
},
"description": "An application ontology for the domain of gene expression. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, and orthology relations using ontological properties from RO and ISO.",
"homepage": "http://www.semantic-systems-biology.org/apo",
"name": "Gene Expression Ontology",
"prefix": "GEXO",
"publication": "http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0386-y",
"version": "2015"
},
"GFF-M4M": {
"contact": {
"email": "barbara.magagna@gmail.com",
"name": "Barbara Magagna"
},
"description": "Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is M4M Vocabulary. This controlled vocabulary is produced in Metadata 4 Machine (M4M) Workshop. sheet2rdf is used to build and serve M4M Vocabulary, while PURL is used to persist identifiers for the vocabulary: http://purl.org/m4m/",
"homepage": "https://github.com/gofair-foundation/m4m-vocabulary",
"name": "GO FAIR M4M",
"prefix": "GFF-M4M",
"publication": "https://github.com/gofair-foundation/m4m-vocabulary",
"version": "0.0.5"
},
"GFFO": {
"contact": {
"email": "carsten.fortmann-grote@evolbio.mpg.de",
"name": "Carsten Fortmann-Grote"
},
"description": "An ontology to represent genome feature annotations in gff3 format.",
"homepage": "https://github.com/mpievolbio-scicomp/GenomeFeatureFormatOntology",
"name": "Genetic Feature Format Ontology",
"prefix": "GFFO",
"version": "0.0.1"
},
"GFO": {
"contact": {
"email": "heinrich.herre@imise.uni-leipzig.de",
"name": "Heinrich Herre"
},
"description": "The General Formal Ontology (GFO) is a top-level ontology integrating objects and processes.",
"homepage": "http://www.onto-med.de/ontologies/gfo/",
"name": "General Formal Ontology",
"prefix": "GFO",
"version": "Version 1.0 ($Revision: 1.13 $)"
},
"GFO-BIO": {
"contact": {
"email": "leechuck@leechuck.de",
"name": "Robert Hoehndorf"
},
"description": "GFO-Bio is a biological core ontology built on the General Formal Ontology.",
"homepage": "http://www.onto-med.de/ontologies/gfo-bio/",
"name": "General Formal Ontology for Biology",
"prefix": "GFO-BIO",
"version": "1.1"
},
"GFVO": {
"contact": {
"email": "kim@codamono.com",
"name": "Joachim Baran"
},
"description": "The Genomic Feature and Variation Ontology (GFVO) is modeled to represent genomic data using the Resource Description Format (RDF) or Linked Data using JSON (JSON-LD). It is captures the contents of data files that adhere to the Generic Feature Format Version 3 (GFF3, http://www.sequenceontology.org/resources/gff3.html), the General Transfer Format (GTF, http://mblab.wustl.edu/GTF22.html), the Genome Variation Format Version 1 (GVF, http://www.sequenceontology.org/resources/gvf.html), and the Variant Call Format (VCF, http://vcftools.sourceforge.net/specs.html), as well as the FASTA format (http://en.wikipedia.org/wiki/FASTA_format). The creation of the ontology was inspired by previous work of Robert Hoehndorf on RDF2OWL (http://code.google.com/p/rdf2owl). NOTE: GFVO in BioPortal is a simplified version without ontology imports and having class/property equivalences removed. The full ontology is available at: http://www.biointerchange.org/gfvo",
"homepage": "https://www.codamono.com/biointerchange/",
"name": "Genomic Feature and Variation Ontology",
"prefix": "GFVO",
"publication": "https://peerj.com/articles/933/",
"version": "1.0.6"
},
"GLYCO": {
"contact": {
"email": "will@ccrc.uga.edu",
"name": "Will York"
},
"description": "The GlycO ontology provides an up-to-date knowledge base of experimentally verified glycan structures. Glycan (oligosaccharide or polysaccharide) structures are represented as trees of monosaccharide residues. Linkage to proteins and lipids is supported as well. Insertion of a new glycan is controlled by curation process that includes matching the new glycan against a canonical glyco-tree (a highly branched representation for a family of glycans).",
"homepage": "http://glycomics.ccrc.uga.edu/core4/informatics-ontologies.html",
"name": "Glycomics Ontology",
"prefix": "GLYCO",
"publication": "http://glycomics.ccrc.uga.edu/core4/informatics-ontologies.html",
"version": "4.6.0.0"
},
"GLYCOCOO": {
"contact": {
"email": "issaku@noguchi.or.jp",
"name": "Issaku Yamada"
},
"description": "GlycoConjugate Ontology (GlycoCoO) as a standard semantic framework to describe and represent glycoconjugate data in RDF.",
"homepage": "https://github.com/glycoinfo/GlycoCoO",
"name": "GlycoConjugate Ontology",
"prefix": "GLYCOCOO",
"publication": "https://academic.oup.com/glycob/article/31/7/741/6144622",
"version": "1.1.3"
},
"GLYCORDF": {
"contact": {
"email": "rene@ccrc.uga.edu",
"name": "Rene Ranzinger"
},
"description": "GlycoRDF is a standard representation for storing Glycomcis data (glycan structures, publication information, biological source information, experimental data) in RDF.",
"homepage": "https://github.com/glycoinfo/GlycoRDF",
"name": "GlycoRDF",
"prefix": "GLYCORDF",
"publication": "http://bioinformatics.oxfordjournals.org/content/31/6/919.long",
"version": "1.2.1"
},
"GML": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kim Durante"
},
"description": "The Geography Markup Language (GML) is an RDF encoding for the transport and storage of geographic information, including both the geometry and properties of geographic features. Vocabulary terms are declared using OWL language to support RDF applications.",
"name": "Ontology for Geography Markup Language (GML3.0)",
"prefix": "GML",
"version": "version 1.0"
},
"GMM": {
"contact": {
"email": "kristina.gruden@nib.si",
"name": "Kristina Gruden"
},
"description": "GoMapMan is an open web-accessible resource for gene functional annotations in the plant sciences. It was developed to facilitate improvement, consolidation and visualization of gene annotations across several plant species.",
"homepage": "http://www.gomapman.org/",
"name": "GoMapMan",
"prefix": "GMM",
"version": "1.2"
},
"GMO": {
"contact": {
"email": "shuichi.kawashima@gmail.com",
"name": "Shuichi Kawashima"
},
"description": "A structured controlled vocabulary for describing ingredients that constitute microbial growth media used in biological research centers.",
"name": "Growth Medium Ontology",
"prefix": "GMO",
"version": "0.22 Beta"
},
"GNO": {
"contact": {
"email": "nje5@georgetown.edu",
"name": "Nathan Edwards"
},
"description": "An ontology for glycans based on GlyTouCan, but organized by subsumption.",
"homepage": "https://github.com/glygen-glycan-data/GNOme",
"name": "Glycan Naming Ontology",
"prefix": "GNO",
"version": "V2.2.0"
},
"GO": {
"description": "Provides structured controlled vocabularies for the annotation of gene products with respect to their molecular function, cellular component, and biological role. The Gene Ontology consists of three Vocabularies.",
"homepage": "http://www.geneontology.org",
"name": "Gene Ontology",
"prefix": "GO",
"version": "releases/2024-06-17"
},
"GO-EXT": {
"contact": {
"email": "go@geneontology.org",
"name": "Gene Ontology Consortium"
},
"description": "Gene Ontology Extension",
"homepage": "http://www.geneontology.org",
"name": "Gene Ontology Extension",
"prefix": "GO-EXT",
"version": "2"
},
"GO-PLUS": {
"contact": {
"email": "go-friends@lists.stanford.edu",
"name": "GO Mailing List"
},
"description": "This is the fully axiomatised version of the GO. It includes cross ontology relationships (axioms) and imports additional required ontologies including ChEBI, cell ontology and Uberon. It also includes a complete set of relationship types including some not in go.obo/go.owl. This version is only available in OWL.",
"homepage": "http://geneontology.org",
"name": "go-plus",
"prefix": "GO-PLUS",
"publication": "http://www.geneontology.org/page/publications",
"version": "2024-06-17"
},
"GOLDTERMS": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "A rendering of the JGI GOLD ecosystem classification (https://gold.jgi.doe.gov/ecosystem_classification)",
"homepage": "https://github.com/cmungall/gold-ontology",
"name": "GOLD Ecosystem Classification",
"prefix": "GOLDTERMS",
"publication": "https://pubmed.ncbi.nlm.nih.gov/20653767/"
},
"GPML": {
"contact": {
"email": "wikipathways-devel@googlegroups.com",
"name": "WikiPathways Team"
},
"description": "GPML is the file format used to store pathway content at WikiPathways. GPML is short for Graphical Pathway Markup Language, and it is a custom XML format compatible with pathway visualization and analysis tools such as Cytoscape and PathVisio. Get it as RDFa in HTML: http://vocabularies.wikipathways.org/gpml Or get it translated to RDF/XML from either of these URLs: http://getschema.org/rdfaliteextractor?url=http%3A%2F%2Fvocabularies.wikipathways.org%2Fgpml&out=rdf or http://rdf-translator.appspot.com/convert/rdfa/xml/http%3A%2F%2Fvocabularies.wikipathways.org%2Fgpml",
"name": "Graphical Pathway Markup Language",
"prefix": "GPML",
"version": "2013a"
},
"GRO": {
"contact": {
"email": "vlee@ebi.ac.uk",
"name": "Vivian Lee"
},
"description": "The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes.",
"homepage": "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html",
"name": "Gene Regulation Ontology",
"prefix": "GRO",
"version": "0.5"
},
"GRO-CPD": {
"contact": {
"email": "po-discuss@plantontology.org",
"name": "Plant Ontology Administrators"
},
"description": "A structured controlled vocabulary for describing cereal plant development and growth stages. Please note that this ontology has now been superseded by the Plant Ontology.",
"homepage": "http://www.gramene.org/plant_ontology/",
"name": "Cereal Plant Development Ontology",
"prefix": "GRO-CPD",
"version": "1.6"
},
"GRO-CPGA": {
"contact": {
"email": "jaiswalp@oregonstate.edu",
"name": "Pankaj Jaiswal"
},
"description": "A structured controlled vocabulary for the anatomy of Gramineae. Please note that this ontology has now been superseded by the Plant Ontology.",
"homepage": "https://planteome.org/",
"name": "Cereal Plant Gross Anatomy Ontology",
"prefix": "GRO-CPGA",
"publication": "https://planteome.org/pub",
"version": "unknown"
},
"GSSO": {
"contact": {
"email": "gsso.ontology@gmail.com",
"name": "Clair Kronk"
},
"description": "The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology.",
"homepage": "https://gsso.research.cchmc.org/",
"name": "Gender, Sex, and Sexual Orientation Ontology",
"prefix": "GSSO",
"publication": "https://doi.org/10.1093/jamia/ocaa061",
"version": "2.0.6"
},
"GVO": {
"contact": {
"email": "tf@nig.ac.jp",
"name": "Takatomo Fujisawa"
},
"description": "The Genome Variation Ontology (GVO) is an ontology for the systematic description of various genomic variations, including complex structural variations in genomes.",
"homepage": "http://genome-variation.org/resource/gvo",
"name": "Genome Variation Ontology",
"prefix": "GVO",
"version": "2021-11-18"
},
"HAAURAADO": {
"contact": {
"email": "contact@bioself.fr",
"name": "Delphine Dauga"
},
"description": "The first ontology describing the anatomy and the development of Halocynthia aurantium.",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Halocynthia aurantium Anatomy and Development Ontology",
"prefix": "HAAURAADO"
},
"HAMIDEHSGH": {
"contact": {
"email": "sabbaghi.opt@gmail.com",
"name": "Hamideh Sabbaghi"
},
"description": "Inherited retinal dystrophy (IRD) as one of the rare ocular diseases encompasses different types of hereditary retinal degenerations appearing by involvement of the different layers of the posterior ocular segment. In respect of the importance of the classification systems regarding the recorded history of biologic and natural sciences, there is no classification regarding the IRD diagnoses. Therefore, we aimed to present a novel classification in this regard.",
"name": "Inherited Retinal Dystrophy",
"prefix": "HAMIDEHSGH"
},
"HANCESTRO": {
"contact": {
"email": "dwelter.ontologist@gmail.com",
"name": "Danielle Welter"
},
"description": "The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies. Please note that as of v2.0 (released July 2018), HANCESTRO (formerly ANCESTRO) has undergone some major changes including a revised namespace.",
"homepage": "https://github.com/EBISPOT/hancestro",
"name": "Human Ancestry Ontology",
"prefix": "HANCESTRO",
"publication": "https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1396-2",
"version": "2024-06-21"
},
"HAO": {
"contact": {
"email": "diapriid@gmail.com",
"name": "HAO developers"
},
"description": "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, sawflies and ants)",
"homepage": "http://hymao.org",
"name": "Hymenoptera Anatomy Ontology",
"prefix": "HAO",
"version": "2023-06-01"
},
"HAROREADO": {
"contact": {
"email": "contact@bioself.fr",
"name": "Delphine Dauga"
},
"description": "The first ontology describing the anatomy and the development of Halocynthia roretzi.",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Halocynthia roretzi Anatomy and Development Ontology",
"prefix": "HAROREADO"
},
"HASCO": {
"contact": {
"email": "pp3223@gmail.com",
"name": "Paulo Pinheiro"
},
"description": "The Human-Aware Science Ontology (HAScO) integrates a collection of well-established science-related ontologies, and aims to address issues related to data annotation for large data ecosystem, where data can come from diverse data sources including sensors, lab results, and questionnaires. The HAScO has been used to annotate data collections to facilitate data exploration and analysis for numerous scientific projects. Data files produced by scientific studies are processed to identify and annotate the objects (a gene, for instance) with the appropriate ontological terms.",
"homepage": "http://www.hadatac.org/hasco-ontology/",
"name": "Human-Aware Science Ontology",
"prefix": "HASCO",
"publication": "http://ceur-ws.org/Vol-2228/paper4.pdf",
"version": "0.9"
},
"HC": {
"name": "Habronattus Courtship Ontology",
"prefix": "HC"
},
"HCDR": {
"contact": {
"email": "ga1179@nyu.edu",
"name": "Gavin Arneson"
},
"description": "This ontology utilizes the European Typology of Homelessness and Housing Exclusion (ETHOS), a respected conceptual framework used to define degrees of housing insecurity and homelessness internationally, to conceptualize, define, and link homelessness in SNOMED, Read CTV3, and Read 2 codes to clinical data extraction. The ontology uses the ETHOS as a general framework, leading to endpoints represented by codes from across the three databases. This is useful for researchers and medical professionals seeking to understand how homelessness is represented in clinical data, how homelessness is defined internationally, and what types of services are available for homeless individuals.",
"name": "Homelessness and Clinical Data Recording",
"prefix": "HCDR",
"version": "1"
},
"HCODONONT": {
"contact": {
"email": "hanfeib@gmail.com",
"name": "Hanfei Bao"
},
"description": "This ontology contains the information of the frequency of usage and the relative frequency of usage of Human Gene Codons, to be used to the operations by The Project Of HIV Ontology.",
"homepage": "http://blog.51.ca/u-345129/",
"name": "HGeneCodonOntology",
"prefix": "HCODONONT",
"version": "2"
},
"HCPCS": {
"contact": {
"email": "Cynthia.Hake@cms.hhs.gov",
"name": "Cynthia Hake"
},
"description": "Healthcare Common Procedure Coding System",
"homepage": "http://cms.hhs.gov",
"name": "Healthcare Common Procedure Coding System",
"prefix": "HCPCS",
"publication": "http://cms.hhs.gov",
"version": "2023AB"
},
"HDMPONTO": {
"contact": {
"email": "mantx626@gmail.com",
"name": "Man Tianxing"
},
"description": "A Hierarchical Data Mining Process Ontology, by combined OntoKDD and DMWF.",
"name": "HierarchicalDMProcessOnto",
"prefix": "HDMPONTO"
},
"HECON": {
"contact": {
"email": "alba.morales-tirado@open.ac.uk",
"name": "Alba Morales Tirado"
},
"description": "Health Condition Evolution Ontology (HECON), is a formal model representation of the evolution of medical events over time.",
"homepage": "http://kmi.open.ac.uk/conrad/HECON",
"name": "HECON: Health Condition Evolution Ontology",
"prefix": "HECON",
"version": "0.1"
},
"HED": {
"contact": {
"email": "kay.robbins@utsa.edu",
"name": "Kay Robbins"
},
"description": "HED (Hierarchical Event Descriptors) is a standardized vocabulary for describing what happens during experiments and a framework for mapping these terms and other metadata onto the experimental timeline to enable analysis. HED is a subtag system organized by the top-level categories: Event, Agent, Action, Item, Property, and Relation. Users create HED annotations as comma-separated, parenthesized lists of terms. See https://www.hed-resource.org for documentation, tutorials and other resources. Recently we have created an ontology representation of the HED vocabulary (HED schema) to provide a better mechanism for linking the HED terms to terms from other ontologies and to provide better provenance information. The HED tags as well as auxiliary information such as types of units and types of values are represented as classes. The HED schema attributes are represented either as DataProperty or ObjectProperty depending on their range. Some additional attributes that are not inherited are represented as AnnotationProperty. HED is the standard used for event annotation in BIDS (Brain Imaging Data Structure) a standard for storing neuroimaging repository and is used by datasets on several repositories such as openNeuro and Nemar.",
"homepage": "www.hedtags.org",
"name": "Hierarchical Event Descriptors",
"prefix": "HED",
"version": "releases/2024-06-10"
},
"HEIO": {
"contact": {
"email": "jmcmurray@wlu.ca",
"name": "Josephine McMurray"
},
"description": "The purpose of this ontology is to develop a model for regional healthcare system interoperability and information exchange quantification (measured by the electronic health information exchange (eHIE) indicator). The eHIE is hypothesized as a leading measure of regional healthcare system integration. A publication associated with this ontology is currently under review.",
"name": "Regional Healthcare System Interoperability and Information Exchange Measurement Ontology",
"prefix": "HEIO",
"version": "Version 1.15"
},
"HELIFIT": {
"contact": {
"email": "carloallocca@gmail.com",
"name": "Carlo Allocca"
},
"description": "This an ontology for healthcare.",
"name": "HeLiFit-Ontology",
"prefix": "HELIFIT",
"version": "1.6.4"
},
"HENECON": {
"contact": {
"email": "eestevez@lst.tfo.upm.es",
"name": "EstefanΓa EstΓ©vez Priego"
},
"description": "HeNeCOn (Head and Neck Cancer Ontology) is the first ontology specifically focused on the Head and Neck Cancer (HNC) domain. It provides a clinically reliable data model for HNC processes during all phases of the disease: prognosis, treatment, and follow-up. The ontology is established based on an annotated dataset to provide formal reference descriptions, contains 170 clinical variables organized into a taxonomy, and is expanded and mapped to formalize and integrate multiple databases into the HeNeCOn ontology. The outcomes of this iterative process were reviewed and validated by clinicians and statisticians. HeNeCOn, with roughly 500 classes, is a very specific ontology which includes a taxonomy with a hierarchical structure, semantic definitions of 283 medical terms and detailed relations between them, which makes it a reference data model.",
"name": "Head and Neck Cancer Ontology",
"prefix": "HENECON",
"version": "2.0"
},
"HENEGEO": {
"contact": {
"email": "eestevez@lst.tfo.upm.es",
"name": "EstefanΓa EstΓ©vez Priego"
},
"description": "HeNeGeO (Head and Neck Cancer - Clinical and Gene Ontology) presents a data model that encompasses both clinical and genomic aspects of Head and Neck Cancer (HNC) across every stage of the disease, covering prognosis, treatment and follow-up. This ontology builds upon the foundation laid by HENECON (Head and Neck Cancer Ontology) and has been significantly expanded with a focus on information pertaining to cancer recurrence, alongside a comprehensive list of genes that offer valuable insights throughout the entire head and neck cancer progression. To enhance clarity, novel medical terms have been thoughtfully annotated with their respective semantic meanings. This comprehensive update includes the incorporation of 29,770 genes, featuring essential details such as NCBI GeneID (EntrezID), gene symbol, gene name, gene alias, and the HGNC ID. The development of this ontology underwent rigorous review and validation by experts in both clinical and genomic domains.",
"name": "Head and Neck Cancer - Clinical and Gene Ontology",
"prefix": "HENEGEO",
"version": "1.0"
},
"HFO": {
"contact": {
"email": "liqin.j.wang@gmail.com",
"name": "Liqin Wang"
},
"description": "Heart failure ontology is an attempt to define heart-failure-relevant information including the causes and risk factors, signs and symptoms, diagnostic tests and results, and treatment.",
"name": "Heart Failure Ontology",
"prefix": "HFO",
"publication": "http://www.sciencedirect.com/science/article/pii/S0933365716300689",
"version": "version 1.0"
},
"HGNC": {
"contact": {
"email": "hgnc@genenames.org",
"name": "Elspeth Bruford"
},
"description": "Human Genome Organisation (HUGO) Gene Nomenclature Committee at the European Bioinformatics Institute approves a gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database.",
"homepage": "http://www.genenames.org/",
"name": "HUGO Gene Nomenclature",
"prefix": "HGNC",
"publication": "http://www.genenames.org/",
"version": "July2010"
},
"HGNC-NR": {
"contact": {
"email": "johardi@stanford.edu",
"name": "Josef Hardi"
},
"description": "HUGO Gene Nomenclature Committee Ontology with recurring uploads",
"name": "HGNC New Releases Ontology",
"prefix": "HGNC-NR",
"version": "2024-03-04"
},
"HHEAR": {
"contact": {
"email": "paulo@psemantica.com",
"name": "Paulo Pinheiro"
},
"description": "The Human Health Exposure Analysis Resource (HHEAR) measures exposures that cover the breadth of the βexposome,β which encompasses all environmental exposures including chemical, physical, and biological stressors, as well as lifestyle and social environments, from conception through adulthood.",
"homepage": "https://hhearprogram.org",
"name": "Human Health Exposure Analysis Resource",
"prefix": "HHEAR",
"version": "1.11"
},
"HHEARP": {
"contact": {
"email": "js5406@cumc.columbia.edu",
"name": "Jeanette Stingone"
},
"description": "An ontology of properties used to annotate the studies included in the Human Health Exposure Analysis Resource (HHEAR) knowledge graph; visit https://hheardatacenter.mssm.edu for more information regarding HHEAR.",
"name": "HHEAR Properties",
"prefix": "HHEARP",
"version": "0.0.3"
},
"HHEARVS": {
"contact": {
"email": "js5406@cumc.columbia.edu",
"name": "Jeanette Stingone"
},
"description": "A SKOS ontology of concept schemes and concepts to be used in CEDAR metadata templates",
"name": "HHEAR Value Sets",
"prefix": "HHEARVS",
"version": "0.0.12"
},
"HINO": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun \"Oliver\" He"
},
"description": "The Human Interaction Network Ontology (HINO) is an INO extension for the domain of human interaction networks. It has currently incoporated Reactome reactions and pathways. Like INO, HINO aligns with BFO. HINO is developed by following the OBO Foundry principles.",
"homepage": "http://www.ino-ontology.org/",
"name": "Human Interaction Network Ontology",
"prefix": "HINO",
"version": "Vision Release: 1.0.69"
},
"HIO": {
"contact": {
"email": "giant.plankton@gmail.com",
"name": "Jade Hotchkiss"
},
"description": "The Hearing Impairment Ontology (HIO) is a common controlled hearing impairment (HI) vocabulary, which is expected to enhance collaborative research. This ontology is currently the most comprehensive and standardized human- and machine-readable resource that unambiguously defines HI concepts and terminology for researchers, patients and clinicians in order to help process, reuse and re-apply existing HI knowledge in biomedical research and health-care systems. In the context of big data analytics, this ontology may facilitate a retrospective data harmonization and contribute to mapping HI datasets to functional knowledge to enable the subsequent HI research translation into clinical applications and policy guidelines. The HIO will allow researchers, clinicians and patients to readily access standardized HI-related knowledge in a single location and promote HI data integration, interoperability and sharing, including epidemiological, socio-environmental, biomedical, genetic and phenotypic datasets.",
"name": "Hearing Impairment Ontology",
"prefix": "HIO",
"version": "1"
},
"HIV": {
"contact": {
"email": "martin.schiller@unlv.edu",
"name": "Martin Schiller"
},
"description": "The HIV ontology encompasses all knowledge about HIV",
"name": "HIV ontology",
"prefix": "HIV",
"version": "2.6"
},
"HIVCRS": {
"contact": {
"email": "hanfeib@gmail.com",
"name": "Hanfei Bao"
},
"description": "The Ontology to express the ternary relations of HIV1",
"homepage": "http://blog.51.ca/u-345129/",
"name": "HIVCompoundRels",
"prefix": "HIVCRS",
"version": "1"
},
"HIVHPV": {
"name": "HIVHPV",
"prefix": "HIVHPV"
},
"HIVHPVFGS": {
"contact": {
"email": "fabianjennrich@duck.com",
"name": "Fabian Jennrich"
},
"description": "Vocabulary for testing and vaccination records for HIV, HPV, and FGS in Uganda.",
"name": "HIV, HPV, FGS vocabulary",
"prefix": "HIVHPVFGS"
},
"HIVHPVSCHISTOSOM": {
"contact": {
"email": "mariam.basajja@gmail.com",
"name": "Mariam Basajja"
},
"description": "This is the ontology containing the controlled terms and semantic properties used in the HIV, HPV and Schistosomiasis dataset obtained from the MOH Uganda",
"name": "HIVHPVSchistosomiasis",
"prefix": "HIVHPVSCHISTOSOM",
"version": "1.1"
},
"HIVHPVSTOM": {
"contact": {
"email": "nc1635718843@gmail.com",
"name": "Cong Ning"
},
"description": "The data of HIVHPV and Schistosomiasis",
"name": "HIVHPVStom",
"prefix": "HIVHPVSTOM"
},
"HIVMT": {
"contact": {
"email": "hanfeib@gmail.com",
"name": "Hanfei Bao"
},
"description": "This is an ontology about the mutations Of HIV1 and the relations between them and the clinical practices. And it has imported the main ontology: https://bioportal.bioontology.org/ontologies/HIVO004.",
"homepage": "https://blog.51.ca/u-345129/",
"name": "HIVMutation",
"prefix": "HIVMT",
"version": "01"
},
"HIVO004": {
"contact": {
"email": "hanfeib@gmail.com",
"name": "Hanfei Bao"
},
"description": "A Project of Biomedical Ontology for Systems Biomedicine. The Project includes, so far, a main ontology (HIVOnt0**.owl) which is imported by several other sub ontologies AIDSClinic0**.owl, etc. The goals of the Project include: (1). To pilot the novel researches on AIDS and HIV or other diseases by viruses, by means of the ontology and other biomedical informatics technologies, connecting the insights of the Biomedical Knowledge Integration (BMKI), systems biomedicine, complexity sciences etc. (2). To Carry out the methodology explorations for the goals above.",
"homepage": "http://biomedinteg.org",
"name": "HIVOntologymain.owl",
"prefix": "HIVO004",
"publication": "https://biomedinteg.org/publications/",
"version": "020"
},
"HL7": {
"contact": {
"email": "mnm@lists.hl7.org",
"name": "Methodology and Modelling Committee"
},
"description": "This version is the first update to Normative RIM, Release 3. It is based on changes approved in Harmonization in November 2010. This release of the RIM is bound to HL7 Abstract Data Types Release 2.",
"homepage": "http://www.hl7.org",
"name": "Health Level Seven Reference Implementation Model, Version 3",
"prefix": "HL7",
"publication": "http://www.hl7.org",
"version": "2023AB"
},
"HMADO": {
"contact": {
"email": "hmori@nig.ac.jp",
"name": "Hiroshi Mori"
},
"description": "Human Microbiome Associated Disease Ontology.",
"name": "Human Microbiome Associated Disease Ontology",
"prefix": "HMADO"
},
"HMIS033B": {
"contact": {
"email": "ncirak@sabanciuniv.edu",
"name": "Nurullah Cirak"
},
"description": "Ontology for Uganda HMIS 033b Health Unit wekkly Epidemiological Surveillance report",
"name": "HMIS 033",
"prefix": "HMIS033B"
},
"HMISLAB0115": {
"contact": {
"email": "Leendert1@live.nl",
"name": "Leendert Van der Plas"
},
"description": "Assignment for group 5 of DSIP",
"name": "HMIS LAB 011 5",
"prefix": "HMISLAB0115"
},
"HNS": {
"contact": {
"email": "subhashis.das@dcu.ie",
"name": "SUBHASHIS DAS"
},
"description": "The purpose of this research is to develop an ontology with subsequent testing and evaluation, for identifying utility and value. The domain that has been chosen is human nervous system (HNS) disorders. It is hypothesized here that an ontology-based patient records management system is more effective in meeting and addressing complex information needs of health-care personnel. Therefore, this study has been based on the premise that developing an ontology and using it as a component of the search interface in hospital records management systems will lead to more efficient and effective management of health-care. It is proposed here to develop an ontology of the domain of HNS disorders using a standard vocabulary such as MeSH or SNOMED CT. The principal classes of an ontology include facet analysis for arranging concepts based on their common characteristics to build mutually exclusive classes. We combine faceted theory with description logic, which helps us to better query and retrieve data by implementing an ontological model. ProtΓ©gΓ© 5.2.0 was used as ontology editor. The use of ontologies for domain modelling will be of acute help to doctors for searching patient records. In this paper we show how the faceted approach helps us to build a flexible model and retrieve better information. We use the medical domain as a case study to show examples and implementation.",
"homepage": "https://github.com/subhashishhh/HNS-Ontology/blob/master/HNS_ontology.owl",
"name": "HNS_Ontolgoy",
"prefix": "HNS",
"publication": "https://www.ergon-verlag.de/isko_ko/downloads/ko_46_2019_3_c.pdf",
"version": "4.0"
},
"HO": {
"contact": {
"email": "claudia.mazo@correounivalle.edu.co",
"name": "Claudia Mazo"
},
"description": "A Histological Ontology of the Human Cardiovascular System v. 1.1",
"name": "Histological Ontology",
"prefix": "HO",
"version": "1.1"
},
"HOIP": {
"contact": {
"email": "yuki.yamagata@riken.jp",
"name": "Yuki Yamagata"
},
"description": "Homeostasis imbalance process ontology (HoIP) is an ontology that systematizes a wide variety of terms involving homeostasis imbalance courses and processes. HoIP focuses on the course of COVID-19 infectious processes and cellular senescence.",
"homepage": "https://github.com/yuki-yamagata/hoip",
"name": "Homeostasis imbalance process ontology",
"prefix": "HOIP",
"publication": "https://doi.org/10.1101/2023.03.09.531883",
"version": "2024/04/03"
},
"HOM": {
"contact": {
"email": "bgee@sib.swiss",
"name": "Bgee team"
},
"description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.",
"homepage": "https://bgee.org",
"name": "Ontology of Homology and Related Concepts in Biology",
"prefix": "HOM",
"publication": "http://dx.doi.org/10.1016/j.tig.2009.12.012",
"version": "releases/2015-01-07"
},
"HOME": {
"contact": {
"email": "nk495@njit.edu",
"name": "Navya Martin"
},
"description": "An ontology to record the physical, emotional and psychological effects resulting from differences in treatment that citizens receive based on their identity when entering healthcare institutions. We present the first version of such a Health Ontology for Minority Equity (HOME)",
"name": "Health Ontology for Minority Equity",
"prefix": "HOME",
"version": "1"
},
"HOOM": {
"contact": {
"email": "david.lagorce@inserm.fr",
"name": "David Lagorce"
},
"description": "Orphanet provides phenotypic annotations of the rare diseases in the Orphanet nomenclature using the Human Phenotype Ontology (HPO). HOOM is a module that qualifies the annotation between a clinical entity and phenotypic abnormalities according to a frequency and by integrating the notion of diagnostic criterion. In ORDO a clinical entity is either a group of rare disorders, a rare disorder or a subtype of disorder. The phenomes branch of ORDO has been refactored as a logical import of HPO, and the HPO-ORDO phenotype disease-annotations have been provided in a series of triples in OBAN format in which associations, frequency and provenance are modeled. HOOM is provided as an OWL (Ontologies Web Languages) file, using OBAN, the Orphanet Rare Disease Ontology (ORDO), and HPO ontological models. HOOM provides extra possibilities for researchers, pharmaceutical companies and others wishing to co-analyse rare and common disease phenotype associations, or re-use the integrated ontologies in genomic variants repositories or match-making tools.",
"homepage": "https://www.orphadata.com",
"name": "HPO - ORDO Ontological Module",
"prefix": "HOOM",
"version": "2.2"
},
"HORD": {
"contact": {
"email": "laia.subirats@gmail.com",
"name": "Laia Subirats"
},
"description": "This ontology describes the bio-psico-social state of a person of rare diseses in a holistic way. It considers several contents such as disease, psychological, social, environmental state of the person.",
"homepage": "https://sites.google.com/site/laiasubirats",
"name": "Holistic Ontology of Rare Diseases",
"prefix": "HORD",
"publication": "https://sites.google.com/site/laiasubirats/publications",
"version": "4.0"
},
"HP": {
"contact": {
"email": "dr.sebastian.koehler@gmail.com",
"name": "Sebastian KΓΆhler"
},
"description": "The Human Phenotype Ontology is being developed to provide a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. Our goal is to provide resource for the computational analysis of the human phenome, with a current focus on monogenic diseases listed in the Online Mendelian Inheritance in Man (OMIM) and Orphanet databases, for which annotations are also provided. Please see documentation and license information at http://www.human-phenotype-ontology.org",
"homepage": "http://www.human-phenotype-ontology.org",
"name": "Human Phenotype Ontology",
"prefix": "HP",
"publication": "http://human-phenotype-ontology.github.io/license.html",
"version": "hp/releases/2024-07-01"
},
"HPIO": {
"contact": {
"email": "ina.hulsegge@wur.nl",
"name": "Wageningen UR Livestock Research"
},
"description": "Ontology for host pathogen interactions in farmed animals",
"name": "Host Pathogen Interactions Ontology",
"prefix": "HPIO",
"version": "1"
},
"HP_O": {
"contact": {
"email": "marcinkgolec@gmail.com",
"name": "Marcin Golec"
},
"description": "Hypersensitivity Pneumonitis Ontology involves the domain of knowledge of 1. diseases caused by organic dusts exposure including hypersensitivity pneumonitis as well as 2. organic dusts.",
"homepage": "https://hypontology.herokuapp.com/",
"name": "Hypersensitivity pneumonitis ontology",
"prefix": "HP_O",
"version": "1.0"
},
"HRA": {
"contact": {
"email": "katy@iu.edu",
"name": "Katy BΓΆrner"
},
"description": "The Human Reference Atlas (HRA) is a comprehensive, high-resolution, three-dimensional atlas of all the cells in the healthy human body. The Human Reference Atlas provides standard terminologies and data structures for describing specimens, biological structures, and spatial positions linked to existing ontologies.",
"name": "Human Reference Atlas",
"prefix": "HRA",
"version": "2.1.0"
},
"HRAVS": {
"contact": {
"email": "johardi@stanford.edu",
"name": "Josef Hardi"
},
"description": "A collection of curated and standardized values used by the HuBMAP (Human BioMolecular Atlas Program) and SenNet (Cellular Senescence Network) metadata records to ensure uniformity in the description of samples and single-cell data produced by the consortium.",
"name": "HuBMAP Research Attributes Value Set",
"prefix": "HRAVS",
"version": "2.5.10"
},
"HRDO": {
"contact": {
"email": "ferdinand.dhombres@inserm.fr",
"name": "Ferdinand Dhombres"
},
"description": "This resource was designed during a PhD in medical informatics (funded by INSERM, 2010-2012). Its components are (i) a core ontology consistent with a metamodel (disorders and groups of disorders, genes, clinical signs and their relations) and (ii) an instantiation of this metamodel with Orphanet Data (available on http://orphadata.org). Research experiments demonstrated (i) efficient classifications generation based on SPARQL Construct, (ii) perspectives in semantic audit of a knowledge base, (iii) semantic comparison with OMIM (www.omim.org) using proximity measurements and (iv) opened perspectives in knowledge sharing (LORD, http://lord.bndmr.fr). Current production services of Orphanet developed ORDO, released in 2014, an ontology synchronized with their production database. This ontology is now available on Bioportal.",
"name": "Disease core ontology applied to Rare Diseases",
"prefix": "HRDO",
"version": "V2"
},
"HSAPDV": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "Life cycle stages for Human. HsapDv was developed by the Bgee group with assistance from the core Uberon developers and the Human developmental anatomy ontology (EHDAA2) developers. Currently it includes both embryonic (Carnegie) stages and adult stages.",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv",
"name": "Human Developmental Stages Ontology",
"prefix": "HSAPDV"
},
"HSCLO38": {
"contact": {
"email": "taylordm@chop.edu",
"name": "Deanne Taylor"
},
"description": "HSCLO38's purpose is to simplify the integration of genomic experimental data at different resolution scales within biomedical knowledge graphs. It defines chromosomal locations within the GRCh38 release for chr 1-22, X,Y and M. HSCLO38 provides 3,431,153 classes at five distinct resolution levels: whole chromosome, 1 megabase pair (Mbp), 100 kilobase pairs (kbp), 10 kbp, and 1 kbp. Each node within these class levels is interconnected to its scale parent and to the immediate neighbors on either side to support mapping and association between genomic datasets and features. For example, the 1kbp element HSCLO38:chr1.20517001-20518000 is_a connected to its \"scale parent\" HSCLO38:chr1.20510001-20520000 as well as to the 5' neighbor HSCLO38:chr1.20516001-20517000 and 3' neighbor HSCLO38:chr1.20518001-20519000. We provide knowledge-graph-ready files for HSCLO38 on the project home page.",
"homepage": "https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/GENCODEHSCLO.md",
"name": "Homo sapiens Chromosomal Location Ontology for GRCh38",
"prefix": "HSCLO38"
},
"HSO": {
"contact": {
"email": "fernanda.dorea@sva.se",
"name": "Fernanda DΓ³rea"
},
"description": "This is an ontology to support (one) health surveillance, focused on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc.",
"homepage": "http://datadrivensurveillance.org/ontology/",
"name": "Health Surveillance Ontology",
"prefix": "HSO",
"version": "3.1.1"
},
"HSPO": {
"contact": {
"email": "natasha.mulligan@ie.ibm.com",
"name": "HSPO Team https://github.com/IBM/hspo-ontology"
},
"description": "The HSPO is an ontology that aims to represent and link together information about an individual from multiple domains. This work is motivated by the need to better understand the drivers of health outcomes that may arise from other domains including, but not limited to, the social determinants of health (e.g. ethnicity, transportation, education). This ontology can also describe a group of individuals that share similar characteristics (i.e. a cohort). Through this ontology we attempt to define a number of social contexts or social domains which can be useful to organise information coming from different terminologies such as ICD and SNOMED. Git Repository, Documentation and License details: https://github.com/IBM/hspo-ontology Apache License 2.0",
"homepage": "https://github.com/IBM/hspo-ontology",
"name": "Health and Social Person-centric Ontology",
"prefix": "HSPO",
"publication": "https://github.com/IBM/hspo-ontology",
"version": "0.1.0"
},
"HTN": {
"contact": {
"email": "aellenhicks@gmail.com",
"name": "Amanda Hicks"
},
"description": "The Hypertension Ontology is a realism-based reference ontology for semantically managing clinical data about hypertension. Definitions of hypertension and elevated blood pressure are highly sensitive to context. Thresholds may vary according to population, guidelines, or clinical context. Variations in the clinical interpretation of blood pressure pose challenges to using blood pressure data for cohort identification, semantic data integration across data sets, and semantically enriching clinical data for clinical decision support applications. The Hypertension Ontology provides a framework for connecting clinical data to context-sensitive definitions of elevated blood pressure and hypertension.",
"homepage": "https://github.com/aellenhicks/htn_owl",
"name": "Hypertension Ontology",
"prefix": "HTN"
},
"HTO": {
"contact": {
"email": "horridge@stanford.edu",
"name": "Matthew Horridge"
},
"description": "This is just a test ontology. Called the Horridge Test Ontology (HTO)",
"name": "Horridge Test Ontology",
"prefix": "HTO",
"version": "0.0.1"
},
"HUPSON": {
"contact": {
"email": "michaela.guendel@scai-extern.fraunhofer.de",
"name": "Michaela Guendel"
},
"description": "Large biomedical simulation initiatives, such as the Virtual Physiological Human (VPH), are substantially dependent on controlled vocabularies to facilitate the exchange of information, of data and of models. Hindering these initiatives is a lack of a comprehensive ontology that covers the essential concepts of the simulation domain. We propose a first version of a newly constructed ontology, HuPSON, as a basis for shared semantics and interoperability of simulations, of models, of algorithms and of other resources in this domain. The ontology is based on the Basic Formal Ontology, and adheres to the MIREOT principles.",
"homepage": "http://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads.html",
"name": "Human Physiology Simulation Ontology",
"prefix": "HUPSON",
"publication": "http://www.jbiomedsem.com/content/4/1/35",
"version": "1.1.1"
},
"I-ADOPT": {
"contact": {
"email": "barbara.magagna@gmail.com",
"name": "Barbara Magagna"
},
"description": "The I-ADOPT Framework is an ontology designed to facilitate interoperability between existing variable description models (including ontologies, taxonomy, and structured controlled vocabularies). One of the challenges in representing semantic descriptions of variables is getting people to agree about what they mean when describing the components that define the variables. The I-ADOPT ontology addresses this by providing core components and their relations that can be applied to define machine-interpretable variable descriptions that re-use FAIR vocabulary terms. This first version of the ontology has been developed by a core group of terminology experts and users from the Research Data Alliance (RDA) InteroperAble Descriptions of Observable Property Terminology (I-ADOPT) Working Group.",
"homepage": "https://www.rd-alliance.org/group/interoperable-descriptions-observable-property-terminology-wg-i-adopt-wg/wiki/i-adopt-0",
"name": "I-ADOPT Framework Ontology",
"prefix": "I-ADOPT",
"publication": "http://ceur-ws.org/Vol-2969/paper10-s4biodiv.pdf",
"version": "1.0.3"
},
"I2SV": {
"contact": {
"email": "i2s@anu.edu.au",
"name": "Gabriele Bammer"
},
"description": "Terms used to describe research concepts, methods and processes for addressing complex societal and environmental problems, especially investigations involving integration across different disciplinary and stakeholder perspectives, as well as implementation of findings into policy and practice change. The terms were originally developed for the Integration and Implementation Insights blog (http://i2Insights.org).",
"homepage": "https://i2insights.org/index/integration-and-implementation-sciences-vocabulary/",
"name": "Integration and Implementation Sciences Vocabulary",
"prefix": "I2SV",
"version": "1.0.0"
},
"IAML-MOP": {
"contact": {
"email": "nlorimer@stanford.edu",
"name": "Nancy Lorimer"
},
"description": "Instruments and/or voices, devices and other performers which make up a musical work.",
"name": "IAML Medium of Performance Vocabulary",
"prefix": "IAML-MOP"
},
"IAO": {
"contact": {
"email": "alanruttenberg@gmail.com",
"name": "Alan Ruttenberg"
},
"description": "The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI consortium.
To import
Latest released version: http://purl.obolibrary.org/obo/iao.owl
Other versions
Developer (live) version: http://purl.obolibrary.org/obo/iao/dev/iao.owl
Ontology metadata properties and classes only: http://purl.obolibrary.org/obo/iao/dev/iao.owl
Dated versions
Please note: The ontology metrics displayed by BioPortal do not distinguish IAO-developed terms from terms imported from other ontologies.
Tracker: http://purl.obolibrary.org/obo/iao/tracker
Discussion group: http://groups.google.com/group/information-ontology",
"homepage": "http://purl.obolibrary.org/obo/iao",
"name": "Information Artifact Ontology",
"prefix": "IAO",
"publication": "http://purl.obolibrary.org/obo/iao/reports",
"version": "2022-11-07"
},
"IBD": {
"contact": {
"email": "archanamca92@gmail.com",
"name": "Archana PATEL"
},
"description": "Indian Biodiversity Ontology contains the semantic information about the domain of Indian Biodiversity",
"name": "Indian Biodiversity Ontology",
"prefix": "IBD",
"version": "1.1"
},
"IBIO": {
"contact": {
"email": "iamvishallama@gmail.com",
"name": "Vishal Lama"
},
"description": "Conceptualization of knowledge of Indian Biodiversity domain.",
"name": "IndianBiodiversity",
"prefix": "IBIO"
},
"IBO": {
"contact": {
"email": "proemnaamdouni@gmail.com",
"name": "Emna Amdouni"
},
"description": "The Imaging Biomarker Ontology describes radiological measurements that characterize biological processes (such as anisotropic water diffusion in a particular tissue region) of imaged subjects (such as neuro-imaging observations) and help clinicians, particularly in the assessment of therapeutic responses and the early prediction of pathologies. IBO reuses several OBO ontologies namely BFO, IAO, PATO, GO, FMA, and OGMS.",
"name": "Imaging Biomarker Ontology",
"prefix": "IBO",
"publication": "maging Biomarker Ontology (IBO): A Biomedical Ontology to Annotate and Share Imaging Biomarker Data (DOI: 10.1007/s13740-018-0093-3)"
},
"ICD-O-3": {
"contact": {
"email": "nicholas.nicholson@ec.europa.eu",
"name": "Nicholas Nicholson"
},
"description": "Ontology used for oncology research derived from the European Cancer Information System (ECIS)",
"homepage": "https://data.jrc.ec.europa.eu/dataset/88ff4ec5-1832-403e-abe1-64928592568f",
"name": "International Classification of Diseases for Oncology, 3rd edition",
"prefix": "ICD-O-3",
"version": "OCD-O Revision 3.2 (complete)"
},
"ICD10": {
"contact": {
"email": "info@who.int",
"name": "World Health Organization"
},
"description": "International Statistical Classification of Diseases and Related Health Problems (ICD-10). 10th rev. Geneva",
"name": "International Classification of Diseases, Version 10",
"prefix": "ICD10",
"version": "2023AB"
},
"ICD10CM": {
"contact": {
"email": "pbrooks@hcfa.gov",
"name": "Patricia Brooks"
},
"description": "International Classification of Diseases, 10th Edition, Clinical Modification, 2011_01",
"homepage": "http://www.cms.hhs.gov/",
"name": "International Classification of Diseases, Version 10 - Clinical Modification",
"prefix": "ICD10CM",
"publication": "http://www.cms.hhs.gov/",
"version": "2023AB"
},
"ICD10PCS": {
"contact": {
"email": "patricia.brooks2@cms.hhs.gov",
"name": "Pat Brooks"
},
"description": "ICD-10-PCS, 2009",
"homepage": "http://www.cms.hhs.gov",
"name": "International Classification of Diseases, Version 10 - Procedure Coding System",
"prefix": "ICD10PCS",
"publication": "http://www.cms.hhs.gov",
"version": "2023AB"
},
"ICD11-BODYSYSTEM": {
"contact": {
"email": "swt@stanford.edu",
"name": "Samson Tu"
},
"description": "This is a set of body-system terms used in the ICD 11 revision",
"name": "Body System Terms from ICD11",
"prefix": "ICD11-BODYSYSTEM",
"version": "1"
},
"ICD9CM": {
"contact": {
"email": "pbrooks@hcfa.gov",
"name": "Patricia Brooks"
},
"description": "The ICD is the international standard diagnostic classification for all general epidemiological, many health management purposes and clinical use.",
"homepage": "http://www.cms.hhs.gov/",
"name": "International Classification of Diseases, Version 9 - Clinical Modification",
"prefix": "ICD9CM",
"version": "2023AB"
},
"ICDO": {
"contact": {
"email": "wanlingeric@qq.com",
"name": "Ling Wan"
},
"description": "A biomedical ontology for logical representation of the terms and relations related to the International Classification of Diseases (ICD)",
"homepage": "https://github.com/icdo/ICDO",
"name": "International Classification of Diseases Ontology",
"prefix": "ICDO",
"version": "1.0.83"
},
"ICECI": {
"contact": {
"email": "swt@stanford.edu",
"name": "Samson Tu"
},
"description": "The International Classification of External Causes of Injury (ICECI) is a system of classifications to enable systematic description of how injuries occur. It is designed especially to assist injury prevention. The ICECI was originally designed for use in settings in which information is recorded in a way that allows statistical reporting--for example, injury surveillance based on collection of information about cases attending a sample of hospital emergency departments. It has also been found useful for other purposes. For example, it has been used as a reference classification during revision of another classification, to record risk-factor exposure of children in a cohort study, as the basis for special-purpose classifications and in a growing number of other ways.",
"name": "International Classification of External Causes of Injuries",
"prefix": "ICECI",
"version": "Original Source: 1.2; OWL version 1.02"
},
"ICEO": {
"homepage": "https://github.com/ontoice/ICEO",
"name": "Integrative and Conjugative Element Ontology",
"prefix": "ICEO",
"version": "2.1"
},
"ICF": {
"contact": {
"email": "info@who.int",
"name": "The World Health Organization"
},
"description": "The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. These domains are classified from body, individual and societal perspectives by means of two lists: a list of body functions and structure, and a list of domains of activity and participation. Since an individual's functioning and disability occurs in a context, the ICF also includes a list of environmental factors.
Source: http://www.who.int/classifications/icf/en/",
"homepage": "http://www.who.int/classifications/icf/en/",
"name": "International Classification of Functioning, Disability and Health",
"prefix": "ICF",
"version": "1.0.2"
},
"ICHOM-PROMS-PCB": {
"contact": {
"email": "f.heddema@pharmaccess.org",
"name": "Femke Heddema"
},
"description": "The ICHOM Set of Patient-Centered Outcome Measures for Pregnancy And Childbirth is the result of hard work by a group of leading physicians, measurement experts and patients. It is a recommendation of the outcomes that matter most to persons experiencing Pregnancy And Childbirth.",
"name": "ICHOM Set Pregnancy and Childbirth",
"prefix": "ICHOM-PROMS-PCB"
},
"ICNP": {
"contact": {
"email": "laville@icn.ch",
"name": "Katia Laville"
},
"description": "International Classification for Nursing Practice",
"homepage": "https://www.icn.ch/what-we-do/projects/ehealth-icnp",
"name": "International Classification for Nursing Practice",
"prefix": "ICNP",
"version": "classified"
},
"ICO": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "Informed Consent Ontology (ICO) is a community-based ontology in the domain of informed consent. It is an OBO library ontology and developed by following the OBO Foundry principles.",
"homepage": "https://github.com/ICO-ontology/ICO",
"name": "Informed Consent Ontology",
"prefix": "ICO",
"publication": "http://ceur-ws.org/Vol-1327/icbo2014_paper_54.pdf",
"version": "1.0.187"
},
"ICPC2P": {
"contact": {
"email": "fmrc@fmrc.org.au",
"name": "Prof Helena Britt"
},
"description": "ICPC-2 PLUS",
"homepage": "http://www.fmrc.org.au/",
"name": "International Classification of Primary Care - 2 PLUS",
"prefix": "ICPC2P",
"publication": "http://www.fmrc.org.au/",
"version": "2023AB"
},
"ICPS": {
"contact": {
"email": "ocorcho@fi.upm.es",
"name": "Oscar Corcho"
},
"description": "Ontology network about Patient Safety Incident. This work has been carried out by the Ontological Engineering Group, using sources from the University of Saint Etienne and the Australian Patient Safety Foundation, and supported by the World Health Organisation under the International Classification for Patient Safety programme.",
"homepage": "http://www.oeg-upm.net/",
"name": "International Classification for Patient Safety",
"prefix": "ICPS",
"version": "Created by Aldo Gangemi and Valentina Presutti"
},
"ICW": {
"contact": {
"email": "john.robinson@wellzesta.com",
"name": "John Robinson"
},
"description": "The International Classification of Wellness (ICW) is Wellness taxonomy. ICW provides a scheme for classifying Wellness events (activities) in which persons (users) can participate. ICW furthers the goals of preventative medicine and population health by supporting goal setting, quantifying user engagement in wellness activities, and correlating user engagement in wellness activities with health outcomes.",
"name": "International Classification of Wellness",
"prefix": "ICW",
"version": "1.2"
},
"ID-AMR": {
"description": "DEMO vocabulary for collections of terms for the ZonMW ID&AMR programme. These terms are based on vocabularies provided for describing project and data content metadata. This submission was created using sheet2rdf GitHub workflow.",
"homepage": "https://raw.githubusercontent.com/gofair-foundation/vocabs_archive/main/M4M17.ttl",
"name": "Infectious Diseases and Antimicrobial Resistance",
"prefix": "ID-AMR",
"version": "1.2.1"
},
"IDEM": {
"contact": {
"email": "nikola@fairdatacollective.com",
"name": "Nikola Vasiljevic"
},
"description": "Controlled vocabularies such as taxonomies allow an accurate and controlled approach in describing datasets. One of such controlled vocabulary is Wind Energy Taxonomy of Models. This taxonomy is the result of EERA JP WIND IRPWind Open Data initiative that took place in 2017 in which wind energy experts generated the first version of the taxonomy as an input for defining and structuring wind energy metadata. The report of this work is available at Zenodo: https://www.zenodo.org/record/1199489#.XSD6haeQ3RY In 2018, the taxonomy of topics was improved during the internal project of DTU Wind Energy titled 'FAIR Digitalization': https://www.zenodo.org/record/1493874#.XSD7TaeQ3RY In 2021, the taxonomy was converted into FAIR machine-actionable controlled vocabulary using sheet2rdf. The controlled vocabulary is served to humans and machines using an instace of OntoStack hosted by DTU Wind Energy. sheet2rdf and OntoStack are developed by FAIR Data Collective. Additionally, in 2021, the persistent URL purl.org/idem has been registered for the taxonomy. This allows us to: If there is a needed to move the taxonomy to another domain (currently under data.windenergy.dtu.dk) URLs will be still resolvable and unchanged Use short URls as PIDs for the taxonomy terms and properties.",
"homepage": "https://github.com/DTUWindEnergy/IDEM-taxonomy",
"name": "IDEM: wInD Energy Models Taxonomy",
"prefix": "IDEM",
"publication": "https://github.com/DTUWindEnergy/IDEM-taxonomy",
"version": "v0.1.0"
},
"IDG_GL": {
"contact": {
"email": "dvidovic@med.miami.edu",
"name": "Dusica Vidovic"
},
"description": "List of genes studied under the IDG project",
"name": "IDG gene list",
"prefix": "IDG_GL",
"version": "1.0"
},
"IDO": {
"contact": {
"email": "johnbeverley2021@u.northwestern.edu",
"name": "John Beverley"
},
"description": "The IDO ontologies are designed as a set of interoperable ontologies that will together provide coverage of the infectious disease domain. At the core of the set is a general Infectious Disease Ontology (IDO-Core) of entities relevant to both biomedical and clinical aspects of most infectious diseases. Sub-domain specific extensions of IDO-Core complete the set providing ontology coverage of entities relevant to specific pathogens or diseases.
To import,
Latest version: http://purl.obolibrary.org/obo/ido.owl
This version (2010-12-02): http://purl.obolibrary.org/obo/ido/2010-12-02/ido.owl
Previous versions:
2010-05-26 http://purl.obolibrary.org/obo/ido/2010-05-26/ido.owl
2009-08-14 http://purl.obolibrary.org/obo/ido/2009-08-14/ido.owl
Latest release notes at http://infectiousdiseaseontology.org/page/Download
Please note: The ontology metrics displayed by BioPortal do not distinguish IDO-developed terms from terms imported from other ontologies.",
"homepage": "http://infectiousdiseaseontology.org",
"name": "Infectious Disease Ontology",
"prefix": "IDO",
"publication": "http://infectiousdiseaseontology.org/page/Publications",
"version": "8-3-20"
},
"IDO-COVID-19": {
"contact": {
"email": "johnbeverley2021@u.northwestern.edu",
"name": "John Beverley"
},
"description": "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease.",
"homepage": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19",
"name": "The COVID-19 Infectious Disease Ontology",
"prefix": "IDO-COVID-19",
"version": "8-3-2020"
},
"IDOBRU": {
"contact": {
"email": "linikujp@gmail.com",
"name": "Asiyah Yu Lin"
},
"description": "Brucellosis Ontology is a biomedical ontology in the domain of zoonotic disease brucellosis that is caused by Brucella, a facultative intracellular baterium.",
"homepage": "http://www.phidias.us/bbp/idobru/index.php",
"name": "Brucellosis Ontology",
"prefix": "IDOBRU",
"version": "Arbor version; 1.2.92"
},
"IDODEN": {
"contact": {
"email": "elvira@imbb.forth.gr",
"name": "Elvira Mitraka"
},
"description": "An ontology for dengue fever.",
"homepage": "http://code.google.com/p/dengue-fever-ontology/",
"name": "Dengue Fever Ontology",
"prefix": "IDODEN",
"version": "0.15b"
},
"IDOMAL": {
"contact": {
"email": "topalis@imbb.forth.gr",
"name": "Pantelis Topalis"
},
"description": "An application ontology for malaria extending the infectious disease ontology (IDO)",
"homepage": "http://anobase.vectorbase.org/idomal/IDOMAL.obo",
"name": "Malaria Ontology",
"prefix": "IDOMAL",
"publication": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2925367/?tool=pubmed",
"version": "1.3.9"
},
"IDQA": {
"contact": {
"email": "thomas.schrader@computer.org",
"name": "Thomas Schrader"
},
"description": "Image and Data Quality Assessment for scientific data management",
"homepage": "http://idqa.wordpress.com",
"name": "Image and Data Quality Assessment Ontology",
"prefix": "IDQA",
"version": "v50"
},
"IFAR": {
"contact": {
"email": "esanborn@rockefeller.edu",
"name": "Erica Sanborn"
},
"description": "An application ontology devoted to the standardized recording of data related to Fanconi Anemia (FA). This ontology was created using an OWL file provided by Dr. Ada Hamish (and Francois Schiettecatte) at the Centers for Mendelian Genetics, with their permission. Their original ontology can be found at: http://phenodb.net/help/features. Modifications were made using HPO, OMIM, NCI, and SNOMED. Novel classes pertaining to FA were added and defined as appropriate.",
"homepage": "http://lab.rockefeller.edu/smogorzewska/ifar/",
"name": "Fanconi Anemia Ontology",
"prefix": "IFAR",
"publication": "http://lab.rockefeller.edu/smogorzewska/ifarpublications",
"version": "3"
},
"IK": {
"name": "Irabi kassim",
"prefix": "IK"
},
"ILLNESSINJURY": {
"contact": {
"email": "dastacey@uoguelph.ca",
"name": "Deborah Stacey"
},
"description": "This list of Illness and Injury (Morbidity and Mortality) classifications is an abbreviated version of the World Health Organization's (WHO) Startup Mortality List (ICD-10-SMoL). ICD-10-SMoL is the WHO's application of ICD-10 for low-resource settings initial cause of death collection. ICD-10-SMoL was chosen because it is a simplified version of the ICD-10. ICD (International Classification of Diseases) \"is the foundation for the identification of health trends and statistics globally, and the international standard for reporting diseases and health conditions. It is the diagnostic classification standard for all clinical and research purposes. ICD defines the universe of diseases, disorders, injuries and other related health conditions\" [http://www.who.int/classifications/icd/en/]. Version 1.0 of this ontology was compiled for the Canadian Writing Research Collaboratory (CWRC) ontology project and reflects the need to have causes of death and health issues organized in a way to allow for analysis of cultural data. A simplified list was deemed sufficient since the domain under study (cultural documents) will not have detailed medical information with regards to cause of death or health issues. But instead of accepting a list of general usage terms for causes of death or health issues that appear in some sources (e.g. Wikipedia, Wikidatak, etc.), a standardized, medical classification was selected so that it could be of use for future analysis regarding questions involving the intersection of health and culture. ICD-10-SMoL was chosen since it was the latest version of this list (June, 2018). A stable version of ICD-11 was to be available in June 2018 but there was no ICD-11-SMoL available at this time. To obtain the ICD10-SMoL: http://www.who.int/healthinfo/civil_registration/ICD_10_SMoL.pdf?ua=1",
"name": "Illness and Injury",
"prefix": "ILLNESSINJURY",
"version": "1.0.2"
},
"IMGT-ONTOLOGY": {
"contact": {
"email": "Veronique.Giudicelli@igh.cnrs.fr",
"name": "VΓ©ronique Giudicelli, Patrice Duroux, Professor Marie-Paule Lefranc"
},
"description": "IMGT-ONTOLOGY is the first ontology for immunogenetics and immunoinformatics. It provides a semantic specification of the terms to be used in immunogenetics and immunoinformatics and manages the related knowledge, thus allowing the standardization for immunogenetics data from genome, proteome, genetics, two-dimensional (2D) and three-dimensional (3D) structures. IMGT-ONTOLOGY manages the knowledge through diverse facets relying on seven axioms, \"IDENTIFICATION\", \"CLASSIFICATION\", \"DESCRIPTION\", \"NUMEROTATION\", \"LOCALIZATION\", \"ORIENTATION\" and \"OBTENTION\". These axioms postulate that any object, any process and any relation can be identified, classified, described, numbered, localized and orientated, and the way it is obtained can be characterized. The axioms constitute the Formal IMGT-ONTOLOGY, also designated as IMGT-Kaleidoscope. As the same axioms can be used to generate concepts for multi-scale level approaches, the Formal IMGT-ONTOLOGY represents a paradigm for system biology ontologies, which need to identify, to classify, to describe, to number, to localize and to orientate objects, processes and relations at the molecule, cell, tissue, organ, organism or population levels. IMGTΒ, the international ImMunoGeneTics information systemΒ, has been built on IMGT-ONTOLOGY. The version 1.0.3 of IMGT-ONTOLOGY includes the concepts of IDENTIFICATION and an update of the concepts of CLASSIFICATION.",
"homepage": "http://www.imgt.org/",
"name": "Immunogenetics Ontology",
"prefix": "IMGT-ONTOLOGY",
"publication": "http://www.imgt.org/IMGTindex/ontology.php",
"version": "1.0.3"
},
"IMOBO": {
"contact": {
"email": "xyz19940216@163.com",
"name": "Xingyun Liu"
},
"description": "Intelligent Medicine oriented Biobank Ontology (IMOBO) is an ontology developed to facilitate the annotation and modeling of biobank repositories, metadata, and biobanking administration, supporting the paradigm shift towards AI in medicine. IMOBO focuses on AI modeling in both clinical applications and healthcare, with a specific emphasis on engaging clinical doctors and patients in data collection. Its goal is to structure knowledge for the future patient-centered medical paradigm. As measurement technologies and medical artificial intelligence continue to evolve, IMOBO will continually enhance its content and structure.",
"name": "Intelligent Medicine oriented Biobank Ontology",
"prefix": "IMOBO",
"version": "0.1"
},
"INBANCIDO": {
"contact": {
"email": "archanamca92@gmail.com",
"name": "Archana Patel"
},
"description": "InBan-CIDO ontology is an extension of the CIDO ontology to show the impact of Covid-19 on the Indian economy sector.",
"name": "Assessment of Indian Economy During Covid-19",
"prefix": "INBANCIDO",
"version": "1.0.214"
},
"INBIO": {
"contact": {
"email": "alsayed.algergawy@uni-jena.de",
"name": "Alsayed Algergawy"
},
"description": "The Invasion Biology Ontology (INBIO) contains terms and concepts relevant in the field of invasion biology, which is a research area dealing with the translocation, establishment, spread, impact and management of species outside of their native ranges, where they are called non-native or alien species. This first version of the ontology covers terms and concepts needed to describe twelve major invasion hypotheses building the hierarchical hypothesis network (see also Jeschke JM, Heger T (Eds) (2018) Invasion Biology: Hypotheses and Evidence. CABI, Wallingford, UK).",
"name": "Invasion Biology Ontology",
"prefix": "INBIO",
"version": "1.1"
},
"INBIODIV": {
"contact": {
"email": "archanamca92@gmail.com",
"name": "Archana PATEL"
},
"description": "InBiodiv-O: An Ontology for Indian Biodiversity Knowledge Management",
"name": "An Ontology for Indian Biodiversity Knowledge Management",
"prefix": "INBIODIV",
"version": "1.1"
},
"INCENTIVE": {
"description": "DEMO vocabulary only! Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is INCENTIVE Controlled Vocabulary. This controlled vocabulary is a result of Metadata 4 Machine (M4M) Workshop 18 and 22 (M4M.18 and M4M.22) provided to the INCENTIVE community. sheet2rdf and OntoStack are used to build and serve INCENTIVE Controlled Vocabulary, while PURL is used to persist identifiers for the vocabulary terms.",
"homepage": "https://raw.githubusercontent.com/gofair-foundation/vocabs_archive/main/M4M22.ttl",
"name": "INCENTIVE Community Controlled Vocabulary",
"prefix": "INCENTIVE",
"version": "0.1.3"
},
"INCENTIVE-VARS": {
"contact": {
"email": "nikola@fairdatacollective.com",
"name": "Nikola Vasiljevic"
},
"description": "Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is INCENTIVE Variables. This controlled vocabulary is a result of Metadata 4 Machine (M4M) Workshop 18 (M4M.18) provided to the INCENTIVE community (https://zenodo.org/communities/incentive/about/). sheet2rdf and OntoStack, developed by FAIR Data Collective, are used to build and serve INCENTIVE Variable, while PURL is used to persist identifiers for the vocabulary terms and properties: http://purl.org/incentive/variables/",
"homepage": "https://github.com/fair-data-collective/M4M18-vocabulary",
"name": "INCENTIVE Variables",
"prefix": "INCENTIVE-VARS",
"publication": "https://zenodo.org/communities/incentive/about/",
"version": "0.1.0"
},
"INFECTION_TRANS": {
"contact": {
"email": "e.slavco@uu.nl",
"name": "Elena Slavco"
},
"description": "The Infection Transmission Ontology is developed in order to make transmission data reusable and interoperable. The ontology captures every step of analysing data from the transmission process, especially for quantification of trans- mission parameters. It is applicable to animal and human (hospital) data from both experimental and observational stud- ies. The lack of a common terminology in the infection transmission experiments leads to repetition of costly experiments. By developing a domain ontology we can reuse and combine the transmission data, which leads to the improvement of an estimation of transmission parameters and prediction of outcomes of yet unobserved situations.",
"homepage": "https://raw.githubusercontent.com/UtrechtUniversity/summer-fair/master/src/create_ontology/map_ontology/infection_trans.owl#",
"name": "Infection Transmission Ontology",
"prefix": "INFECTION_TRANS",
"version": "1.0.2"
},
"INFRA-EN": {
"contact": {
"email": "Patrick@alerti.com",
"name": "Patrick Chassany"
},
"description": "Ontologie des infrastructures de transports (aΓ©roport, gare..)",
"name": "Infrastructure",
"prefix": "INFRA-EN",
"version": "1.0"
},
"INFRARISK": {
"contact": {
"email": "dumitru.roman@sintef.no",
"name": "Dumitru Roman"
},
"description": "The InfraRisk Ontology: Enabling Semantic Interoperability for Critical Infrastructures at Risk from Natural Hazards. This InfraRisk ontology may be used for representing relevant information about natural hazard events and their impact on infrastructure components. Earthquakes, landslides, and other natural hazard events have severe negative socio-economic impacts.",
"homepage": "https://www.infrarisk-fp7.eu",
"name": "InfraRisk Ontology",
"prefix": "INFRARISK",
"publication": "http://dx.doi.org/10.1007/978-3-319-69459-7_31",
"version": "1.0"
},
"INJURYTYPES": {
"contact": {
"email": "vinutha_rk@yahoo.com",
"name": "Vinutha Venkatesh"
},
"description": "This class is associated with the different injury types.",
"name": "Injury Types",
"prefix": "INJURYTYPES"
},
"INO": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun \"Oliver\" He"
},
"description": "The Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles.",
"homepage": "https://github.com/INO-ontology/ino",
"name": "Interaction Network Ontology",
"prefix": "INO",
"publication": "https://www.ncbi.nlm.nih.gov/pubmed/25785184",
"version": "1.1.13"
},
"INSECTH": {
"contact": {
"email": "spolavar@gmail.com",
"name": "Sridevi Polavaram"
},
"description": "NeuroMorpho.Org insect brain regions ontology is compiled to create data annotation standard for depositing insect data. Currently at v6.2, NeuroMorpho.Org hosts over 17k neuronal reconstructions mostly from the fly. The insect ontology follows the standard nomenclature of the insect brain (Ito et al., 2013) and the virtualfly.org.",
"name": "insectH",
"prefix": "INSECTH",
"version": "0.1"
},
"INSNAME": {
"contact": {
"email": "aleka.aktau@gmail.com",
"name": "Aliya Aktau"
},
"description": "This is the list of facilities participating in FAIRification of data.",
"name": "VODANAINSNAMES",
"prefix": "INSNAME",
"version": "5"
},
"INTO": {
"contact": {
"email": "archanamca92@gmail.com",
"name": "Archana PATEL"
},
"description": "Creating the largest comprehensive knowledge base of terrorism and related activities, people and agencies involved, and extremist movements; and providing a platform to the society, the government, and the military personnel in order to combat the evolving threat of the global menace of terrorism.",
"name": "Indian Terrorism Ontology",
"prefix": "INTO",
"version": "1.1"
},
"INTVEETYPE": {
"contact": {
"email": "vinutha_rk@yahoo.com",
"name": "Vinutha Venkatesh"
},
"description": "This class refers to the different types of Interviewees.",
"name": "Interviewee Type",
"prefix": "INTVEETYPE"
},
"INTVMODE": {
"contact": {
"email": "vinutha_rk@yahoo.com",
"name": "Vinutha Venkatesh"
},
"description": "This class refers to the different modes of Interview",
"name": "Interview Mode",
"prefix": "INTVMODE"
},
"INVERSEROLES": {
"contact": {
"email": "jhanit@gmail.com",
"name": "Nitin"
},
"description": "ISO inverse roles ontology for oil and gas",
"name": "ISO-15926-2_2003_inverseRoles",
"prefix": "INVERSEROLES",
"version": "Generated 2008-09-03T19:12:44.687+02:00"
},
"IOBC": {
"contact": {
"email": "kushida@biosciencedbc.jp",
"name": "Tatsuya Kushida"
},
"description": "Interlinking Ontology for Biological Concepts (IOBC) contains approximately 80,000 biological concepts such as biological phenomena, diseases, molecular functions, gene products, chemicals, and medical cares, and approximately 20,000 related concepts such as earth science and environmental science. The concepts are structured by thirty-five relations such as has function, has role, has quality, and precedes. Each concept has both of English and Japanese labels. For further information including the developmental method, see papers in the PUBLICATIONS PAGE. The license for this ontology is specified in the Creative Commons Attribution-NonCommercial 4.0 International. If you use data from this ontology, please be sure attribute this ontology as follows: \"Interlinking Ontology for Biological Concepts Β© National Bioscience Database Center licensed under CC Attribution-NonCommercial 4.0 International\".",
"homepage": "https://github.com/kushidat/IOBC",
"name": "Interlinking Ontology for Biological Concepts",
"prefix": "IOBC",
"publication": "http://purl.jp/bio/4/publications/iobc",
"version": "version 1.6.0"
},
"IPD": {
"contact": {
"email": "s217003@stn.nagaokaut.ac.jp",
"name": "Xiaodong Feng"
},
"description": "IPD-Onto divides product injury into five unified classes (host, vector, agent, environment, and consequences) and constructs the accident process through the object properties (lead to, touch, accident, etc.)IPD-Onto is used to realise the transformation and reorganisation from product injury to injury information, to reproduce the process of accident occurrence, and realise human-computer interactions to meet the needs of data query.",
"name": "injury process description ontology",
"prefix": "IPD",
"version": "1.0"
},
"IRD": {
"contact": {
"email": "sabbaghi.opt@gmail.com",
"name": "Hamideh Sabbaghi"
},
"description": "Inherited retinal dystrophy (IRD) as one of the rare ocular diseases encompasses different types of hereditary retinal degenerations appearing by involvement of the different layers of the posterior ocular segment. In respect of the importance of the classification systems regarding the recorded history of biologic and natural sciences, there is no classification regarding the IRD diagnoses. Therefore, a novel classification for this type of hereditary ocular disease was developed and presented.",
"name": "Inherited Retinal Dystrophies",
"prefix": "IRD"
},
"IRDG": {
"contact": {
"email": "emmanuel.roux@ird.fr",
"name": "Emmanuel Roux"
},
"description": "Ontology used to describe the data system in the cross-border surveillance system of malaria between French Guiana and Brazil. Developed by the IRD and the Fiocruz and funding by the Bill and Melinda Gates Foundation (GCE Round 18, Grant ID OPP1171795)",
"name": "Data harmonization ontology for cross border malaria surveillance",
"prefix": "IRDG"
},
"ISO-15926-2_2003": {
"contact": {
"email": "jhanit@gmail.com",
"name": "Nitin"
},
"description": "This ontology describes gas and oil field process level descriptions",
"name": "ISO-15926-2_2003_oil",
"prefix": "ISO-15926-2_2003",
"version": "Generated 2008-02-21T17:29:19.558+01:00"
},
"ISO-ANNOTATIONS": {
"contact": {
"email": "jhanit@gmail.com",
"name": "Nitin"
},
"description": "Oil and Gas Annotations",
"name": "ISO-15926-2_2003_annotations",
"prefix": "ISO-ANNOTATIONS"
},
"ISO-FOOD": {
"contact": {
"email": "tome.eftimov@ijs.si",
"name": "Tome Eftimov"
},
"description": "To link and harmonize different knowledge repositories with respect to isotopic data, we propose an ISO-FOOD ontology as a domain ontology for describing isotopic data within Food Science. The ISO-FOOD ontology consists of metadata and provenance data that needs to be stored together with data elements in order to describe isotopic measurements with all necessary information required for future analysis. The new domain has been linked with existing ontologies, such as Units of Measurements Ontology, Food, Nutrient and the Bibliographic Ontology. So linked ontology consists of several superclasses, and for each of these the relevant subclasses, object properties and data properties are defined. To show how such an ontology can be used in practice, it was populated with 20 isotopic measurements of Slovenian food samples. Describing data in this way offers a powerful technique for organizing and sharing stable isotope data across Food Science.",
"homepage": "http://cs.ijs.si/repository/ISO-FOOD/ISO-FOOD_Ontology.zip",
"name": "A formal representation of the knowledge within the domain of Isotopes for Food Science",
"prefix": "ISO-FOOD"
},
"ISO19108TO": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kimberly Durante"
},
"description": "ISO 19108 Temporal Objects",
"name": "ISO 19108 Temporal Objects",
"prefix": "ISO19108TO",
"version": "2006-10-15"
},
"ISO19110": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "kdurante"
},
"description": "ISO 19110:2005 Methodology for feature cataloguing",
"name": "ISO 19110 Methodology for Feature Cataloguing",
"prefix": "ISO19110",
"version": "2005-02-15"
},
"ISO19115": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "kim durante"
},
"description": "ISO19115:2003",
"name": "ISO 19115",
"prefix": "ISO19115",
"version": "version 1.10"
},
"ISO19115CC": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kimberly Durante"
},
"description": "ISO 19115 Common Classes",
"name": "ISO 19115 Common Classes",
"prefix": "ISO19115CC",
"version": "2014"
},
"ISO19115CI": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kim Durante"
},
"description": "Citation and responsible part ontology",
"name": "ISO 19115 Citation Information",
"prefix": "ISO19115CI",
"version": "2014"
},
"ISO19115CON": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kim Durante"
},
"description": "ISO Schema for Constraints - Access and Use Restrictions",
"name": "ISO 19115 Constraints Information",
"prefix": "ISO19115CON",
"version": "2014"
},
"ISO19115DI": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kimberly Durante"
},
"description": "ISO 19115 Distribution Information",
"name": "ISO 19115 Distribution Information",
"prefix": "ISO19115DI",
"version": "2014"
},
"ISO19115DTC": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kim Durante"
},
"description": "ISO 19115 Date Type Codes",
"name": "ISO 19115 Date Type Code",
"prefix": "ISO19115DTC",
"version": "2.0"
},
"ISO19115EX": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kimberly Durante"
},
"description": "ISO 19115 Extent Information",
"name": "ISO 19115 Extent Information",
"prefix": "ISO19115EX",
"version": "2014"
},
"ISO19115ID": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kim Durante"
},
"description": "ISO 19115-1:2014 Identification Information Section for describing Geospatial Datasets",
"name": "ISO 19115 Identification Information",
"prefix": "ISO19115ID",
"version": "2003-05-0"
},
"ISO19115MI": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kim Durante"
},
"description": "ISO 19115 Metadata Information section",
"name": "ISO 19115 Metadata Information",
"prefix": "ISO19115MI",
"version": "2014"
},
"ISO19115PR": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kim Durante"
},
"description": "ISO 19115 codelists",
"name": "ISO 19115 Codelists",
"prefix": "ISO19115PR",
"version": "2.0"
},
"ISO19115ROLES": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kim Durante"
},
"description": "Role Codes for use in ISO 19115-1:2014 metadata",
"name": "ISO 19115 Role Codes",
"prefix": "ISO19115ROLES",
"version": "2.0"
},
"ISO19115SRS": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kimberly Durante"
},
"description": "ISO 19115 Spatial reference systems",
"name": "ISO 19115 Reference Systems",
"prefix": "ISO19115SRS",
"version": "2014"
},
"ISO19115TCC": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "kdurante"
},
"description": "ISO 19115 Topic Category Codes",
"name": "ISO 19115 Topic Categories",
"prefix": "ISO19115TCC"
},
"ISO639-1": {
"contact": {
"email": "jgraybeal@stanford.edu",
"name": "John Graybeal"
},
"description": "Language codes from ISO 639-1, as expressed in https://www.w3schools.com/tags/ref_language_codes.asp and converted to SKOS using http://labs.sparna.fr/skos-play/convert.",
"name": "ISO 639-1: Codes for the Representation of Names of Languages - Part 1: Two-letter codes for languages",
"prefix": "ISO639-1",
"version": "1.0.0"
},
"ISO639-2": {
"contact": {
"email": "kdurante@stanford.edu",
"name": "Kim Durante"
},
"description": "ISO 639-2 is part of the ISO 639 language code family, which provides also a two-character code set (ISO 639-1) for the representation of names of languages. ISO 639-2 contains codes for all languages contained in ISO 639-1 and several hundred additional languages. The ISO 639-2 (Bibliographic) codes were devised for use in bibliographic metadata, e.g., for libraries, information services, and publishers, and ISO 639-2 (Terminology) targets terminology, lexicography, and linguistic applications. The lists are the same except for 20 languages that have different Bibliographic and Terminology codes. The list contains over 500 discrete codes.",
"homepage": "http://id.loc.gov/vocabulary/iso639-2.html",
"name": "ISO 639-2: Codes for the Representation of Names of Languages",
"prefix": "ISO639-2"
},
"ISPO": {
"contact": {
"email": "huarui@bjtu.edu.cn",
"name": "RuiHua"
},
"description": "ISPO delivers an integrated controlled vocabulary for symptom phenotypes, with both clinical and biomedical literature synonyms in Chinese and English languages, it would enhance the semantic interoperability among heterogeneous medical data sources and clinical decision support systems. Furthermore, symptom ontology would propose a standard vocabulary for teasing the symptom-gene associations and thus become a vital requirement for symptom science and TCM biological discovery.",
"homepage": "https://github.com/HuaRui0420/ISPO",
"name": "Integrated Ontology for Symptom Phenotype Terminologies",
"prefix": "ISPO",
"version": "2023V1"
},
"ISSVA": {
"contact": {
"email": "info@issva.org",
"name": "The International Society for the Study of Vascular Anomalies"
},
"description": "The International Society for the Study of Vascular Anomalies (ISSVA) is a multidisciplinary international society of physicians, scientists, and health care providers united by an interest in vascular anomalies. The Society aims to promote the highest standards of care for patients with vascular anomalies by advancing clinical and scientific knowledge concerning causes, diagnosis and treatment, and by education of physicians, health care providers, patients and the community. The Society encourages the free flow of information between its members and interested groups, through workshop meetings and teaching programs, and by the dissemination of a classification scheme and pertinent scientific data. The updated classification was approved at the May, 2018 General Assembly in Amsterdam, the Netherlands and can be found at https://www.issva.org/classification. What is the ISSVA Ontology? The ISSVA ontology has been created to represent a sharable semantic data model of the ISSVA classification. This ontological representation of the ISSVA classification is machine-readable and facilitates interoperability between systems that capture data about vascular anomalies. It is structured hierarchically and contains all concepts of the ISSVA classification and the relationships between them. The ontology is available in the Web Ontology Language (OWL) format, and can be browsed and downloaded online: https://bioportal.bioontology.org/ontologies/ISSVA How to Use the ISSVA Ontology? The ISSVA ontology does not substitute the ISSVA classification, instead, it should be used as an additional component to facilitate interoperability. Every concept in the ISSVA ontology has a unique code that should be attached to the corresponding data element. In the context of databases, the ISSVA ontology codes could be added as an extra column to the existing data. Mappings to Other Ontologies? The ISSVA ontology contains machine-readable mappings to equivalent concepts in other ontologies, namely: the Orphanet Rare Disease Ontology (ORDO), SNOMED Clinical Terms (SNOMED CT), National Cancer Institute thesaurus (NCIT), and the Human Phenotype Ontology (HPO). This means that data annotated with codes from the ISSVA ontology are interoperable with data annotated with the aforementioned ontologies, without any extra effort, as long as there exists a mapping between the concepts. Issue Reporting Please contact ISSVA at info@issva.org in case you have any issues and/or feature requests for the ISSVA ontology. The ontology can then be updated accordingly.",
"homepage": "https://www.issva.org",
"name": "International Society for the Study of Vascular Anomalies (ISSVA) Ontology",
"prefix": "ISSVA",
"version": "1.1.3"
},
"ITEMAS": {
"contact": {
"email": "silviaseda@gmail.com",
"name": "Silvia SΓ‘nchez Seda"
},
"description": "The defined ontology is focused on addressing medical innovation technology in public healthcare institutions. This ontology is currently only in Spanish language. It has been developed the Platform for Innovation Medical and Health Technology (ITEMAS) a network composed by 67 Spanish healthcare organizations (including hospitals, healthcare centers, Ministry of Health, Social Services and Equality and more than 100 organizations focused on medical technology innovation. The ITEMAS Platform has been by Carlos III National Health Institute (PT13/0006/0036), both co-funded by FEDER from European Regional Development Funds (European Union).",
"homepage": "www.itemas.org",
"name": "Medical Technology Innovation in healthcare centers",
"prefix": "ITEMAS",
"version": "3.0"
},
"ITO": {
"description": "The Intelligence Task Ontology and Knowledge Graph (ITO) provides a comprehensive, curated model of artificial intelligence tasks, benchmarks and benchmark results, including the biomedical domain. NOTE: The version uploaded to BioPortal has all instances and benchmark data removed because of performance issues with the BioPortal class browser. Please refer to https://github.com/OpenBioLink/ITO/ for downloading the full version of the ontology and dataset.",
"homepage": "https://github.com/OpenBioLink/ITO/",
"name": "Intelligence Task Ontology",
"prefix": "ITO",
"version": "1.12 (PWC export dated 2022-07-30) - internal, just a minor fix"
},
"IXNO": {
"contact": {
"email": "cmattin@mdibl.org",
"name": "Carolyn Mattingly"
},
"description": "The Interaction ontology (IxnO) was developed to enable curation of chemical-gene and chemical-protein interactions for the Comparative Toxicogenomics Database (CTD). CTD is a freely available resource that aims to promote understanding and novel hypothesis development about the effects of the environment on human health.",
"homepage": "http://ctd.mdibl.org",
"name": "Interaction Ontology",
"prefix": "IXNO",
"version": "1"
},
"JERM": {
"contact": {
"email": "stuart.owen@manchester.ac.uk",
"name": "Stuart Owen"
},
"description": "The JERM ontology is an application ontology that describes the relationships between the data, models and other research assets that can be shared through the FAIRDOM platform, for sharing Systems and Synthetic Biology experiments. JERM 2 includes a new model for describing Biosamples, developed during the ELIXIR-lead Biosamples club",
"homepage": "https://fair-dom.org/",
"name": "Just Enough Results Model Ontology",
"prefix": "JERM",
"publication": "https://fair-dom.org/publications/",
"version": "2"
},
"KENYAANC": {
"contact": {
"email": "wmnandwa77@gmail.com",
"name": "William Muhadi Nandwa"
},
"description": "Ontology on kenyan ANC terms.",
"name": "kenyaancfile",
"prefix": "KENYAANC",
"version": "1"
},
"KGCL": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "Knowledge Graph Change Language ontology.",
"homepage": "https://github.com/INCATools/kgcl",
"name": "Knowledge Graph Change Language",
"prefix": "KGCL",
"version": "0.1.0"
},
"KISAO": {
"contact": {
"email": "sed-ml-editors@googlegroups.com",
"name": "SED-ML Editors"
},
"description": "The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology of algorithms for simulating and analyzing biological models, as well as the characteristics of these algorithms, their input parameters, and their outputs. In addition, KiSAO captures relationships among algorithms, their parameters, and their outputs.",
"homepage": "http://biomodels.net/kisao/",
"name": "Kinetic Simulation Algorithm Ontology",
"prefix": "KISAO",
"publication": "https://doi.org/10.1038/msb.2011.77",
"version": "2.34"
},
"KORO": {
"contact": {
"email": "ajflynn@umich.edu",
"name": "Allen Flynn"
},
"description": "An ontology to define the parts of a Knowledge Object and their relations built using the Basic Formal Ontology and Information Artifact Ontology",
"name": "Knowledge Object Reference Ontology",
"prefix": "KORO",
"version": "1.3"
},
"KTAO": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "The Kidney Tissue Atlas Ontology (KTAO) is an ontology that integrates kidney-related cell types, cell states, locations, gene markers, disease, etc., and their relations. KTAO is developed to support the NIH-NIDDK-funed Kidney Precision Medicine Project (KPMP).",
"homepage": "https://github.com/KPMP/KTAO",
"name": "Kidney Tissue Atlas Ontology",
"prefix": "KTAO",
"version": "Vision Release: 1.0.121"
},
"KUSIIMA": {
"name": "naava",
"prefix": "KUSIIMA"
},
"LABO": {
"contact": {
"email": "paul.fabry@usherbrooke.ca",
"name": "Paul Fabry"
},
"description": "LABO is an ontology of informational entities describing laboratory tests prescriptions and reporting documents. LABO is a component of a core ontological model, along with the ontology of drug prescriptions PDRO, that aims to enable interoperability between various clinical data sources in the context of a Learning Health System.",
"homepage": "https://github.com/OpenLHS/LABO",
"name": "clinical LABoratory Ontology",
"prefix": "LABO"
},
"LAND-SURFACE": {
"contact": {
"email": "Andrew.Biggs@resources.qld.gov.au",
"name": "Andrew Biggs"
},
"description": "Machine-readable representation of the classifiers described in chapter 7 Land Surface, by R.C. McDonald, R.F. Isbell and J.G. Speight, in Australian soil and land survey field handbook (3rd edn). Land surface is concerned mainly with surface phenomena affecting land use and soil development that have traditionally been noted at the point of soil observation.",
"name": "Land Surface classifiers",
"prefix": "LAND-SURFACE",
"version": "3rd Edition"
},
"LANDFORM": {
"contact": {
"email": "andrew.biggs@resources.qld.gov.au",
"name": "Andrew Biggs"
},
"description": "Machine-readable representation of the classifiers described in chapter 5 Landform, by J.G. Speight, in Australian soil and land survey field handbook (3rd edn). In this technique for describing landforms, the whole land surface is viewed as a mosaic of tiles of odd shapes and sizes. The scheme is intended to produce a record of observations rather than inferences. The data was converted from the print representation to this linked-data form by Linda Gregory assisted by Simon J D Cox.",
"name": "Landform classifiers",
"prefix": "LANDFORM",
"version": "3rd edition"
},
"LBO": {
"contact": {
"email": "jreecy@iastate.edu",
"name": "Jim Reecy"
},
"description": "A vocabulary for buffalo, cattle, chicken, goat, horse, pig, and sheep breeds.",
"homepage": "https://www.animalgenome.org/bioinfo/projects/lbo/",
"name": "Livestock Breed Ontology",
"prefix": "LBO",
"version": "9.5"
},
"LC-CARRIERS": {
"contact": {
"email": "nlorimer@stanford.edu",
"name": "Nancy Lorimer"
},
"description": "Carriers Scheme is derived from a controlled list of values representing the format of the storage medium and its media type, which is principally used in RDA cataloging.",
"homepage": "http://id.loc.gov/vocabulary/carriers.html",
"name": "Library of Congress Carriers Scheme",
"prefix": "LC-CARRIERS"
},
"LC-MEDIA": {
"contact": {
"email": "nlorimer@stanford.edu",
"name": "Nancy Lorimer"
},
"description": "Media Types Scheme is derived from a controlled list of values reflecting the general type of intermediation device required to view, play, run, etc., the content of a resource, which is principally used in RDA cataloging.",
"homepage": "http://id.loc.gov/vocabulary/mediaTypes.html",
"name": "Library of Congress Media Types Scheme",
"prefix": "LC-MEDIA"
},
"LCDGT": {
"contact": {
"email": "futo@stanford.edu",
"name": "Michelle Futornick"
},
"description": "The Library of Congress Demographic Group Terms (LCDGT) is designed to describe the characteristics of the intended audiences of resources, and also the creators of, and contributors to, those resources.",
"homepage": "http://id.loc.gov/authorities/demographicTerms.html",
"name": "Library of Congress Demographic Group Terms",
"prefix": "LCDGT"
},
"LCGFT": {
"contact": {
"email": "nlorimer@stanford.edu",
"name": "Nancy Lorimer"
},
"description": "The Library of Congress Genre/Form Terms for Library and Archival Materials (LCGFT) is a thesaurus that describes what a work is versus what it is about. For instance, the subject heading Horror films, with appropriate subdivisions, would be assigned to a book about horror films. A cataloger assigning headings to the movie The Texas Chainsaw Massacre would also use Horror films, but it would be a genre/form term since the movie is a horror film, not a movie about horror films. The thesaurus combines both genres and forms. Form is defined as a characteristic of works with a particular format and/or purpose. A \"short\" is a particular form, for example, as is \"animation.\" Genre refers to categories of works that are characterized by similar plots, themes, settings, situations, and characters. Examples of genres are westerns and thrillers. In the term Horror films\"horror\" is the genre and \"films\" is the form.",
"homepage": "http://id.loc.gov/authorities/genreForms.html",
"name": "Library of Congress Genre/Form Thesaurus for Library and Archival Materials",
"prefix": "LCGFT",
"version": "2017-09-05"
},
"LDA": {
"contact": {
"email": "hari.cohly@jsums.edu",
"name": "Hari Cohly"
},
"description": "We present the short review of language terms used in the domain of autism and populate them into ontology available for consultation and sharing. The language terms were obtained via text mining and automatic retrieval of terms from the corpus of PubMed abstracts.",
"name": "Ontology of Language Disorder in Autism",
"prefix": "LDA",
"version": "12-15-2008"
},
"LDBASE": {
"contact": {
"email": "Jessica.Logan@vanderbilt.edu",
"name": "Jessica Logan"
},
"description": "LDbase is an NIH-funded behavioral research data repository. The LDbase taxonomy includes project descriptors for projects in the fields of educational and developmental sciences. Developed as a collaboration between researchers and librarians, this first-of-its-kind project-oriented data repository contains decades of knowledge and includes data on individuals across the full range of abilities. The LDbase ontology is used to describe research projects in the developmental sciences.",
"homepage": "LDbase.org",
"name": "LDbase",
"prefix": "LDBASE",
"version": "0.0.1"
},
"LEGALAPA": {
"contact": {
"email": "alexgarciac@gmail.com",
"name": "alexander garcia"
},
"description": "this is a test with the legal cluster of apa ontology",
"name": "legalapa",
"prefix": "LEGALAPA",
"version": "01"
},
"LEGALAPATEST2": {
"contact": {
"email": "alexgarciac@gmail.com",
"name": "alexander garcia"
},
"description": "Legal cluster for APA ontology",
"name": "apalegal",
"prefix": "LEGALAPATEST2",
"version": "1"
},
"LEPAO": {
"contact": {
"email": "lagonzalezmo@unal.edu.co",
"name": "Luis A. Gonzalez-Montana"
},
"description": "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. LEPAO is developed in part by BIOfid (The Specialised Information Service Biodiversity Research).",
"homepage": "https://github.com/insect-morphology/lepao",
"name": "Lepidoptera Anatomy Ontology",
"prefix": "LEPAO",
"version": "2023-02-18"
},
"LHN": {
"contact": {
"email": "peteremidford@yahoo.com",
"name": "Peter Midford"
},
"description": "A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms. An ontology for Loggerhead sea turtle (Caretta caretta) nesting behavior, based on the published ethogram of Hailman and Elowson.",
"homepage": "http://www.mesquiteproject.org/ontology/Loggerhead/index.html",
"name": "Loggerhead Nesting Ontology",
"prefix": "LHN"
},
"LICO": {
"contact": {
"email": "suzan.uskudarli@boun.edu.tr",
"name": "S Uskudarli"
},
"description": "Liver Case Ontology (LiCO) is a case-centric ontology for liver patient cases called lico (Liver Case Ontology) that integrates several ontologies and lexicons developed for sub-disciplines of medicine such as RadLex (Radiology Lexicon), SNOMED CT (Systematized Nomenclature of Medicine, Clinical Terms), LOINC (The Logical Observation Identifier Names and Codes). It is an extension of ONLIRA (Ontology of the Liver for Radiology) that represents the liver and lesions from a radiological perspective.",
"name": "Liver Case Ontology (LiCO)",
"prefix": "LICO",
"publication": "https://vavlab.boun.edu.tr/publications-patents?field_tags_tid%5B%5D=68&field_tags_tid%5B%5D=70",
"version": "changes\n* Segments and Regions are modelling as Classes in order to identify which patient (liver) they belong to.\n* Redundant restrictions are removed"
},
"LIFO": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "The Life Ontology (LifO) is an ontology of the life of organism. LifO represents the life processes of organisms and related entities and relations. LifO is a general purpose ontology that covers the common features associated with different organisms such as unicellular prokaryotes (e.g., E. coli) and multicellular organisms (e.g., human).",
"homepage": "https://github.com/lifeontology/lifo",
"name": "Life Ontology",
"prefix": "LIFO",
"version": "Vision Release: 1.0.17"
},
"LION": {
"contact": {
"email": "m.r.molenaar@uu.nl",
"name": "Martijn Molenaar"
},
"description": "Lipid ontology (LION) associates >50,000 lipid species to biophysical, chemical, and cell biological features.",
"homepage": "www.lipidontology.com",
"name": "LipidOntology",
"prefix": "LION",
"publication": "https://doi.org/10.1093/gigascience/giz061",
"version": "1.1"
},
"LIPRO": {
"contact": {
"email": "bakerc@unb.ca",
"name": "Christipher Baker"
},
"description": "Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied. The ontology describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define membership requirements for sub classes of lipid according to appropriate functional groups.",
"name": "Lipid Ontology",
"prefix": "LIPRO",
"version": "See Remote Site"
},
"LOINC": {
"contact": {
"email": "loinc@regenstrief.org",
"name": "LOINC Support"
},
"description": "Logical Observation Identifier Names and Codes (LOINC)",
"homepage": "http://loinc.org/downloads",
"name": "Logical Observation Identifier Names and Codes",
"prefix": "LOINC",
"publication": "http://loinc.org/downloads",
"version": "2023AB"
},
"LONGCOVID": {
"contact": {
"email": "nikhil.mayor@nhs.net",
"name": "Nik Mayor"
},
"description": "Oxford-RCGP RSC Long COVID-19 (LC) Phenotype Ontology",
"homepage": "https://orchid.phc.ox.ac.uk/",
"name": "Long Covid Phenotype Ontology",
"prefix": "LONGCOVID",
"version": "20220106"
},
"LPT": {
"contact": {
"email": "jreecy@iastate.edu",
"name": "Jim Reecy"
},
"description": "The Livestock Product Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.",
"homepage": "https://www.animalgenome.org/bioinfo/projects/lpt/",
"name": "Livestock Product Trait Ontology",
"prefix": "LPT",
"version": "4.3"
},
"LSFC": {
"name": "LSFC",
"prefix": "LSFC"
},
"LUNGMAP-HUMAN": {
"contact": {
"email": "hpan@rti.org",
"name": "Huaqin (Helen) Pan"
},
"description": "Anatomic Ontology for Human Lung Maturation (LungMAP Human Anatomy (LMHA) Developed by Susan E Wert, Gail H. Deutsch, Helen Pan, and the NHLBI Molecular Atlas of Lung Development Program Consortium Ontology Subcommittee",
"homepage": "https://www.lungmap.net/breath-ontology-browser/",
"name": "Anatomic Ontology for Human Lung Maturation",
"prefix": "LUNGMAP-HUMAN",
"version": "1.4"
},
"LUNGMAP-MOUSE": {
"contact": {
"email": "hpan@rti.org",
"name": "Helen Pan"
},
"description": "Anatomic ontology for Mouse Lung Maturation (LungMAP Mouse Anatomy (LMMA) Developed by Susan E Wert, Gail H. Deutsch, Helen Pan, and the NHLBI Molecular Atlas of Lung Development Program Consortium Ontology Subcommittee",
"homepage": "https://lungmap.net/breath-ontology-browser/",
"name": "Anatomic Ontology for Mouse Lung Maturation",
"prefix": "LUNGMAP-MOUSE",
"version": "1.2"
},
"LUNGMAP_H_CELL": {
"contact": {
"email": "hpan@rti.org",
"name": "Huaqin (Helen) Pan"
},
"description": "Cell Ontology for Human Lung Maturation (LungMAP Human Anatomy (LMHA)) Developed by Susan E Wert, Gail H. Deutsch, Helen Pan, and the NHLBI Molecular Atlas of Lung Development Program Consortium Ontology Subcommittee",
"homepage": "https://www.lungmap.net/breath-ontology-browser/",
"name": "Cell Ontology for Human Lung Maturation",
"prefix": "LUNGMAP_H_CELL",
"version": "3.2"
},
"LUNGMAP_M_CELL": {
"contact": {
"email": "hpan@rti.org",
"name": "Huaqin (Helen) Pan"
},
"description": "Cell Ontology for Mouse Lung Maturation (LungMAP Mouse Anatomy (LMMA)) Developed by Susan E Wert, Gail H. Deutsch, Helen Pan, and the NHLBI Molecular Atlas of Lung Development Program Consortium Ontology Subcommittee",
"homepage": "https://www.lungmap.net/breath-ontology-browser/",
"name": "Cell Ontology for Mouse Lung Maturation",
"prefix": "LUNGMAP_M_CELL",
"version": "3.2"
},
"M": {
"name": "May",
"prefix": "M"
},
"M4M-20-SUBJECTS": {
"description": "Demo vocabulary only! Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is Psychology Subjects. This controlled vocabulary is produced in Metadata 4 Machine (M4M) Workshop 20 (M4M.20 FAIRware Psychology), which one of deliverables of FAIRware project which if funded by RoRi. sheet2rdf is used to build and serve Psychology Subjects, while PURL is used to persist identifiers for the vocabulary, which resolve on BioPortal (Stanford's ontology service).",
"homepage": "https://raw.githubusercontent.com/gofair-foundation/vocabs_archive/main/M4M20_subjects.ttl",
"name": "M4M.20 FAIRWare Subjects",
"prefix": "M4M-20-SUBJECTS",
"version": "0.1.3"
},
"M4M-20-VARIABLES": {
"description": "DEMO vocabulary only! Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is Psychology Variables. This controlled vocabulary is produced in Metadata 4 Machine (M4M) Workshop 20 (M4M.20 FAIRware Psychology), which is one of deliverables of FAIRware project funded by RoRi. sheet2rdf is used to build and serve Psychology Variables, while PURL is used to persist identifiers for the vocabulary, which resolve on BioPortal (Stanford's ontology service):",
"homepage": "https://raw.githubusercontent.com/gofair-foundation/vocabs_archive/main/M4M20_variables.ttl",
"name": "M4M.20 FAIRWare Variables",
"prefix": "M4M-20-VARIABLES",
"version": "0.1.3"
},
"M4M-21-SUBJECTS": {
"description": "DEMO vocabulary only! Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is Neuroscience Subjects. This controlled vocabulary is produced in Metadata 4 Machine (M4M) Workshop 21 (M4M.21 FAIRware Neuroscience), which is one of deliverables of FAIRware project funded by RoRi. sheet2rdf is used to build and serve Neuroscience Subjects, while PURL is used to persist identifiers for the vocabulary, which resolve on BioPortal (Stanford's ontology service).",
"homepage": "https://raw.githubusercontent.com/gofair-foundation/vocabs_archive/main/M4M21_subjects.ttl",
"name": "M4M.21 FAIRWare Subjects",
"prefix": "M4M-21-SUBJECTS",
"version": "0.1.2"
},
"M4M-21-VARIABLES": {
"description": "DEMO vocabulary only! Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is Neuroscience Variables. This controlled vocabulary is produced in Metadata 4 Machine (M4M) Workshop 21 (M4M.21 FAIRware Neuroscience), which is one of deliverables of FAIRware project funded by RoRi. sheet2rdf is used to build and serve Neuroscience Variables, while PURL is used to persist identifiers for the vocabulary, which resolve on BioPortal (Stanford's ontology service).",
"homepage": "https://raw.githubusercontent.com/gofair-foundation/vocabs_archive/main/M4M21_variables.ttl",
"name": "M4M.21 FAIRWare Variables",
"prefix": "M4M-21-VARIABLES",
"version": "0.1.2"
},
"M4M-CHAR": {
"contact": {
"email": "martin.oconnor@stanford.edu",
"name": "Martin O'Connor"
},
"description": "M4M Charlotseville Vocabulary",
"name": "M4M-CHAR",
"prefix": "M4M-CHAR",
"version": "0.0.1"
},
"M4M19-SUBS": {
"description": "DEMO vocabulary only. Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is NICEST-2 Subjects. This controlled vocabulary is a result of Metadata 4 Machine (M4M) Workshop 19 (M4M.19 funded by EOSC-Nordic ) provided to the NICEST-2 project. sheet2rdf and OntoStack, developed by FAIR Data Collective, are used to build and serve NICEST-2 Subjects, while PURL will be used to persist identifiers for the vocabulary terms and properties:",
"homepage": "https://raw.githubusercontent.com/gofair-foundation/vocabs_archive/main/M4M19_subjects.ttl",
"name": "M4M19 Subjects",
"prefix": "M4M19-SUBS",
"version": "0.1.0"
},
"M4M19-VARS": {
"description": "DEMO vocabulary only. Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is NICEST-2 Variables. This controlled vocabulary is a result of Metadata 4 Machine (M4M) Workshop 19 (M4M.19 funded by EOSC-Nordic ) provided to the NICEST-2 project. sheet2rdf and OntoStack, developed by FAIR Data Collective, are used to build and serve NICEST-2 Subjects, while PURL will be used to persist identifiers for the vocabulary terms and properties: http://purl.org/m4m19/variables/",
"homepage": "https://raw.githubusercontent.com/gofair-foundation/vocabs_archive/main/m4m19_vars.ttl",
"name": "M4M19 Variables",
"prefix": "M4M19-VARS",
"version": "0.2.0"
},
"MA": {
"contact": {
"email": "Terry.Hayamizu@jax.org",
"name": "Terry Hayamizu"
},
"description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus).",
"homepage": "http://www.informatics.jax.org/searches/AMA_form.shtml",
"name": "Mouse Adult Gross Anatomy Ontology",
"prefix": "MA",
"version": "releases/2017-02-07"
},
"MACROALGAETRAITS": {
"contact": {
"email": "ilaria.rosati@cnr.it",
"name": "Ilaria Rosati"
},
"description": "The Macroalgae Traits Thesaurus contains several concepts on demographic and functional traits. It has been developed and published by LifeWatch Italy, the Italian node of the e-science European infrastructure for biodiversity and ecosystem research (LifeWatch ERIC). It reflects the agreement of a scientific expert community to fix semantic properties (e.g. label, definition) of approximately 100 traits.",
"homepage": "http://thesauri.lifewatchitaly.eu/Macroalgae/index.php",
"name": "Macroalgae Traits Thesaurus",
"prefix": "MACROALGAETRAITS"
},
"MADS-RDF": {
"contact": {
"email": "nlorimer@stanford.edu",
"name": "Nancy Lorimer"
},
"description": "MADS/RDF (Metadata Authority Description Schema in RDF) is a knowledge organization system (KOS) designed for use with controlled values for names (personal, corporate, geographic, etc.), thesauri, taxonomies, subject heading systems, and other controlled value lists. It is closely related to SKOS, the Simple Knowledge Organization System and a widely supported and adopted RDF vocabulary. MADS/RDF has been fully mapped to SKOS. It is presented as an OWL ontology. The MADS/RDF is designed as a data model for authority and vocabulary data used within the library and information science (LIS) community, which is inclusive of museums, archives, and other cultural institutions. For example, MADS/RDF provides a means to record data from the Machine Readable Cataloging (MARC) Authorities format in RDF for use in semantic applications and Linked Data projects.",
"homepage": "http://www.loc.gov/standards/mads/rdf/",
"name": "Metadata Authority Description Schema in RDF",
"prefix": "MADS-RDF",
"version": "1.0"
},
"MAMO": {
"contact": {
"email": "mamo-ontology-discuss@lists.sourceforge.net",
"name": "mamo-ontology-discuss"
},
"description": "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.",
"homepage": "http://co.mbine.org/standards/mamo",
"name": "Mathematical Modelling Ontology",
"prefix": "MAMO",
"version": "2023-02-03"
},
"MAMO-SCR-ONTO": {
"contact": {
"email": "erohrer@gmail.com",
"name": "Edelweis Rohrer"
},
"description": "The Mammography Screening Ontology (MAMO-SCR-Onto) is designed to provide mammography application recommendations for the early detection of breast cancer in patients at average risk of the disease.",
"name": "Mammography Screening Ontology",
"prefix": "MAMO-SCR-ONTO",
"version": "1.0"
},
"MARC-LANGUAGES": {
"contact": {
"email": "nlorimer@stanford.edu",
"name": "Nancy Lorimer"
},
"description": "MARC List for Languages provides three-character lowercase alphabetic strings that serve as the identifiers of languages and language groups. The codes are usually based on the first three letters of the English form or, in some cases, vernacular form of the corresponding language name. The codes are varied where necessary to resolve conflicts and are not intended to be abbreviations of a language name. When the name of a language is changed in the list, the original code is generally retained. The codes in this list are equivalent to those of ISO 639-2 (Bibliographic) codes and some codes from ISO 639-5, although the language name labels may differ. They are linked to the equivalent codes in ISO 639-2 and ISO 639-5 and the corresponding two-character codes in ISO 639-1.",
"homepage": "http://id.loc.gov/vocabulary/languages.html",
"name": "MARC List for Languages",
"prefix": "MARC-LANGUAGES"
},
"MARC-RELATORS": {
"contact": {
"email": "nlorimer@stanford.edu",
"name": "Nancy Lorimer"
},
"description": "Relator terms and their associated codes designate the relationship between a name and a bibliographic resource. The relator codes are three-character lowercase alphabetic strings that serve as identifiers. Either the term or the code may be used as controlled values.",
"name": "MARC Code List for Relators",
"prefix": "MARC-RELATORS"
},
"MAT": {
"contact": {
"email": "J.Bard@ed.ac.uk",
"name": "Jonathan Bard"
},
"description": "A minimal set of terms for anatomy.",
"name": "Minimal Anatomical Terminology",
"prefix": "MAT",
"version": "1.1"
},
"MATERIALSMINE": {
"contact": {
"email": "rashidsabbir@gmail.com",
"name": "Sabbir Rashid"
},
"description": "A materials ontology to support data publication involving nanomaterials and metamaterials.",
"homepage": "https://materialsmine.org/nm/",
"name": "MaterialsMine Ontology",
"prefix": "MATERIALSMINE",
"version": "1.1"
},
"MATR": {
"contact": {
"email": "jhanit@gmail.com",
"name": "Nitin"
},
"description": "List of material Objects from SWEET ontology",
"name": "Material",
"prefix": "MATR",
"version": "2.3"
},
"MATRCOMPOUND": {
"contact": {
"email": "nitin@biginfolabs.com",
"name": "Nitin"
},
"description": "Material Compound details from SWEET ontology",
"name": "Material Compound",
"prefix": "MATRCOMPOUND",
"version": "2.3"
},
"MATRELEMENT": {
"contact": {
"email": "jhanit@gmail.com",
"name": "Nitin"
},
"description": "Material Element part of SWEET ontology",
"name": "Material Element",
"prefix": "MATRELEMENT",
"version": "2.3"
},
"MATRROCK": {
"contact": {
"email": "jhanit@gmail.com",
"name": "Nitin"
},
"description": "RocK material",
"name": "Material Rock",
"prefix": "MATRROCK",
"version": "2.3"
},
"MATRROCKIGNEOUS": {
"contact": {
"email": "jhanit@gmail.com",
"name": "Nitin"
},
"description": "matrRockIgneous",
"name": "Material Rock Igneouus",
"prefix": "MATRROCKIGNEOUS",
"version": "2.3"
},
"MAXO": {
"contact": {
"email": "Leigh.Carmody@jax.org",
"name": "Leigh Carmody"
},
"description": "The Medical Action Ontology (MAxO) provides a structured vocabulary for medical procedures, interventions, therapies, and treatments for disease with an emphasis on rare disease (RD). It is often difficult to find relevant clinical literature about strategies to manage RD patients. Responding to this need, MAxO provides a vocabulary to annotate diseases and phenotypes with recommended treatments and interventions.",
"homepage": "https://github.com/monarch-initiative/MAxO",
"name": "Medical Action Ontology",
"prefix": "MAXO",
"version": "2024-07-29"
},
"MCBCC": {
"contact": {
"email": "arathi@molecularconnections.com",
"name": "Arathi Raghunath"
},
"description": "Contains a comprehensive list of cell lines derived from breast tissue, both normal and pathological. The ontology in built in OWL with cross relation to classes- genetic variation, pathological condition, genes, chemicals and drugs. The relations built enable semantic query across different classes",
"homepage": "www.molecularconnections.com",
"name": "Breast Tissue Cell Lines Ontology",
"prefix": "MCBCC",
"version": "2"
},
"MCCL": {
"contact": {
"email": "usha@molecularconnections.com",
"name": "Usha Mahadevan"
},
"description": "Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive of machine-interpretable definitions of basic concepts in the domain and relations among them. The need for ontologies that provide a systematic arrangement of available data and allow cross talk across various related domains is gaining momentum. In this backdrop, we have developed a comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format.",
"homepage": "http://www.molecularconnections.com",
"name": "Cell Line Ontology [by Mahadevan]",
"prefix": "MCCL",
"version": "2"
},
"MCCV": {
"contact": {
"email": "shuichi.kawashima@gmail.com",
"name": "Shuichi Kawashima"
},
"description": "Structured controlled vocabulary for describing meta information of microbial calture collection maintained in biological research centers",
"name": "Microbial Culture Collection Vocabulary",
"prefix": "MCCV",
"version": "Version 0.99 beta"
},
"MCHVODANATERMS": {
"contact": {
"email": "mariam.basajja@gmail.com",
"name": "Mariam Basajja"
},
"description": "Ontology containing the controlled terms and semantic properties used in the Maternal Child Health Care generic template used within different facilities in VODANA",
"name": "MCHVODANATERMS",
"prefix": "MCHVODANATERMS",
"version": "3.0"
},
"MCO": {
"contact": {
"email": "citlalli.mejiaalmonte@gmail.com",
"name": "Citlalli MejΓa-Almonte"
},
"description": "Microbial Conditions Ontology contains terms to describe growth conditions in microbiological experiments. The first version is based on gene regulation experiments in Escherichia coli K-12. It is being used in RegulonDB to link growth conditions to gene regulation data.",
"homepage": "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology",
"name": "Microbial Conditions Ontology",
"prefix": "MCO"
},
"MCRO": {
"contact": {
"email": "muamith@utmb.edu",
"name": "Tuan Amith"
},
"description": "An ontology representing the structure of model card reports - reports that describe basic characteristics of machine learning models for the public and consumers.",
"homepage": "https://github.com/UTHealth-Ontology/MCRO",
"name": "Model Card Report Ontology",
"prefix": "MCRO",
"version": "2023-03-07"
},
"MDDB": {
"contact": {
"email": "keckert@drugfacts.com",
"name": "Karen Eckert"
},
"description": "Master Drug Data Base, 2009_08_05",
"homepage": "http://www.medispan.com",
"name": "Master Drug Data Base Clinical Drugs",
"prefix": "MDDB",
"publication": "http://www.medispan.com",
"version": "2017AA"
},
"MDM": {
"contact": {
"email": "bernd.mueller@zbmed.de",
"name": "Bernd MΓΌller"
},
"description": "The Mapping of Drug Names and MeSH 2022 (MDM) provides owl:sameAs relationships as well as owl:equivalentClass of similar concepts for Drug Names from the DrugBank vocabulary (released 2022-01-03 under version 5.1.9: https://go.drugbank.com/releases/latest#open-data) and the Medical Subject Headings (2022 version: http://id.nlm.nih.gov/mesh/). Two concepts are considered similar if they share the same concept name or a common synonym. Additional synonyms are generated using the Snowball stemming algorithm. The software implementation is available on github within the Maven project SNoKE in the module snoke.ontology: https://github.com/bernd-mueller/snoke/tree/master/snoke.ontology",
"homepage": "https://www.zbmed.de/",
"name": "Mapping of Drug Names and MeSH 2022",
"prefix": "MDM",
"version": "0.330"
},
"MEDDRA": {
"contact": {
"email": "mssohelp@meddra.org",
"name": "MedDRA MSSO"
},
"description": "MedDRA is an international medical terminology with an emphasis on use for data entry, retrieval, analysis, and display. It applies to all phases of drug development, excluding animal toxicology, and to the health effects and malfunction of devices. An appendix includes concept descriptions which describe how a medical concept is interpreted, used, and classified within the MedDRA terminology. It is not intended as a medical definition. The concept descriptions are intended to aid the consistent and accurate use of MedDRA in coding, retrieval, and analysis.",
"homepage": "https://www.meddra.org/",
"name": "Medical Dictionary for Regulatory Activities Terminology (MedDRA)",
"prefix": "MEDDRA",
"publication": "https://www.meddra.org/msso-presentations",
"version": "2023AB"
},
"MEDEON": {
"contact": {
"email": "yang.gong@uth.tmc.edu",
"name": "Yang Gong"
},
"description": "This is a demo version of the patient safety ontology.",
"name": "Medical Error Ontology",
"prefix": "MEDEON"
},
"MEDLINEPLUS": {
"contact": {
"email": "custserv@nlm.nih.gov",
"name": "NLM Customer Service"
},
"description": "MedlinePlus Health Topics;National Library of Medicine;June 14, 2008;Bethesda, MD",
"homepage": "http://www.nlm.nih.gov/medlineplus/xmldescription.html",
"name": "MedlinePlus Health Topics",
"prefix": "MEDLINEPLUS",
"publication": "http://www.nlm.nih.gov/medlineplus/xmldescription.html",
"version": "2023AB"
},
"MEDO": {
"contact": {
"email": "parkinson@ebi.ac.uk",
"name": "Helen Parkinson"
},
"description": "A representation of experimental design for high-throughput mouse analysis pipelines.",
"name": "Mouse Experimental Design Ontology",
"prefix": "MEDO",
"version": "1.0"
},
"MEGO": {
"contact": {
"email": "ariane.toussaint@ulb.ac.be",
"name": "Ariane Toussaint"
},
"description": "MeGO is a Gene Ontology under construction dedicated to the functions of mobile genetic elements. The terms defined in MeGO are used to annotate phage and plasmid protein families in ACLAME.",
"homepage": "http://aclame.ulb.ac.be",
"name": "Mobile Genetic Element Ontology",
"prefix": "MEGO",
"publication": "http://aclame.ulb.ac.be/Resources/publications.html",
"version": "2_1"
},
"MELLO-D": {
"contact": {
"email": "saan2mari@gmail.com",
"name": "Jisan LEE"
},
"description": "MEdical LifeLog Ontology for the people with Disability",
"name": "MEdical LifeLog Ontology for people with Disability",
"prefix": "MELLO-D",
"version": "1.5"
},
"MELO": {
"contact": {
"email": "kang.hongyu@imicams.ac.cn",
"name": "Hongyu Kang"
},
"description": "Ontology of melanoma disease, composed of terms of disease, drug, symptoms, molecular abnormalityοΌanatomical structure, diagnosis, treatment and relationships between them.",
"name": "Melanoma Ontology",
"prefix": "MELO",
"version": "1.0"
},
"MEO": {
"contact": {
"email": "hmori@nig.ac.jp",
"name": "MicrobeDB.jp Project Team"
},
"description": "An Ontology for organismal habitats (especially focused on microbes)",
"homepage": "http://microbedb.jp",
"name": "Metagenome and Microbes Environmental Ontology",
"prefix": "MEO",
"version": "0.9"
},
"MEPO": {
"contact": {
"email": "bernd.mueller@zbmed.de",
"name": "Bernd MΓΌller"
},
"description": "The Mapping of Epilepsy Ontologies (MEPO) provides owl:sameAs relationships of similar concepts for the ontologies EpSO, ESSO, EPILONT, EPISEM, and FENICS. Two concepts are considered similar if they share the same concept name or the same synonym. Additional synonyms for each of the concepts are generated using the Snowball stemming algorithm. The software implementation is available on github within the Maven project snoke in the module snoke.ontology: https://github.com/bernd-mueller/snoke/tree/master/snoke.ontology",
"homepage": "https://www.zbmed.de/",
"name": "Mapping of Epilepsy Ontologies",
"prefix": "MEPO",
"publication": "https://pubmed.ncbi.nlm.nih.gov/35073996/",
"version": "0.6"
},
"MERA": {
"contact": {
"email": "portokallidis@gmail.com",
"name": "Nick Portokallidis"
},
"description": "The educational resource ontology is designed in order to provide structure to resources aggregated by the educational resource aggregator. The aim of the educational resource aggregator is to harvest educational resources from 3rd party repositories, present these to the medical expert for annotation and rating, and output the results of the annotation (together with resource metadata) to the CARRE public RDF repository. The main parts of this aggregator are: the Resource Retriever, the Resource Rating, the Resource Metadata Processing, and the User Application. The educational metadata involve the Resource Metadata processing module.This module is a combination of 3 services that collect data per article, making multiple SPARQL requests to enrich the data and finally store it as a unique identified resource into the local datastore. Then data is transformed into RDF triples in order to be inserted to CARRE educational repository. The ontology is developed using the ProtΓ©gΓ© v5.0 , a free, open-source ontology editor from the Stanford University. The ontology is available on CARRE rdf repository among the other ontologies. CARRE url : http://carre.kmi.open.ac.uk/ontology/educational.owl",
"homepage": "https://edu.carre-project.eu",
"name": "Medical Educational Resource Aggregator",
"prefix": "MERA",
"version": "0.0.1"
},
"MESH": {
"contact": {
"email": "custserv@nlm.nih.gov",
"name": "NLM Customer Service"
},
"description": "Medical Subject Headings (MeSH);National Library of Medicine; 2011",
"homepage": "http://www.nlm.nih.gov/mesh",
"name": "Medical Subject Headings",
"prefix": "MESH",
"publication": "http://www.nlm.nih.gov/mesh",
"version": "2023AB"
},
"METABUS": {
"contact": {
"email": "metabus@frankbosco.com",
"name": "Frank Bosco"
},
"description": "The metaBUS hierarchical taxonomy of ~5,000 constructs studied in applied psychology, organizational behavior, and human resource management.",
"homepage": "http://www.metabus.org",
"name": "metaBUS controlled vocabulary for organizational and applied psychology research",
"prefix": "METABUS",
"publication": "http://www.metabus.org/publications",
"version": "0.1"
},
"MF": {
"description": "The Mental Functioning Ontology is an ontology for mental functioning, including mental processes such as cognition and traits such as intelligence, and related diseases and disorders. It is developed in the context of the Ontology for General Medical Science and the Basic Formal Ontology. The project is being developed in collaboration between the University of Geneva, Switzerland, and the University at Buffalo, USA.\\r\\n\\r\\nThe project is being developed with full involvement of all relevant communities, following best practices laid out by the OBO Foundry. Efforts are currently underway to align with related projects including the Behaviour Ontology, the Cognitive Atlas, the Cognitive Paradigm Ontology and the Neural Electro Magnetic Ontologies.",
"homepage": "https://github.com/jannahastings/mental-functioning-ontology/",
"name": "Mental Functioning Ontology",
"prefix": "MF",
"publication": "https://github.com/jannahastings/mental-functioning-ontology/",
"version": "2022-07-19"
},
"MFMO": {
"contact": {
"email": "druzinsk@uic.edu",
"name": "Robert Druzinsky"
},
"description": "An antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors.",
"homepage": "http://feedexp.org/",
"name": "Mammalian Feeding Muscle Ontology",
"prefix": "MFMO"
},
"MFO": {
"contact": {
"email": "Thorsten.Henrich@embl-heidelberg.de",
"name": "Medaka_ontology Administrators"
},
"description": "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.",
"name": "Medaka Fish Anatomy and Development Ontology",
"prefix": "MFO"
},
"MFOEM": {
"contact": {
"email": "janna.hastings@gmail.com",
"name": "Janna Hastings"
},
"description": "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings, designed to support interdisciplinary research by providing unified annotations. The ontology is a domain specialisation of the broader Mental Functioning Ontology.",
"homepage": "https://github.com/jannahastings/emotion-ontology",
"name": "Emotion Ontology",
"prefix": "MFOEM",
"publication": "https://github.com/jannahastings/emotion-ontology",
"version": "2022-07-19"
},
"MFOMD": {
"contact": {
"email": "janna.hastings@gmail.com",
"name": "Janna Hastings"
},
"description": "An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable.",
"homepage": "https://github.com/jannahastings/mental-functioning-ontology",
"name": "MFO Mental Disease Ontology",
"prefix": "MFOMD",
"version": "2020-04-26"
},
"MGBD": {
"contact": {
"email": "matthew.burns2@uhn.ca",
"name": "Matthew Burns"
},
"description": "MGB Drug List",
"name": "MGB Drug List",
"prefix": "MGBD",
"version": "0.6"
},
"MHC": {
"contact": {
"email": "david_deluca@dfci.harvard.edu",
"name": "David S. DeLuca"
},
"description": "The MaHCO contains terms necessary for describing and categorizing concepts related to MHC, in general, and for a number of model species, and also for humans.",
"homepage": "http://purl.org/stemnet/",
"name": "Major Histocompatibility Complex Ontology",
"prefix": "MHC",
"publication": "http://purl.org/stemnet/",
"version": "1.0.1"
},
"MHCRO": {
"contact": {
"email": "bpeters@liai.org",
"name": "Bjoern Peters"
},
"description": "The MHC Restriction Ontology (MRO) is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions.",
"homepage": "https://github.com/IEDB/MRO",
"name": "MHC Restriction Ontology",
"prefix": "MHCRO",
"version": "2024-08-02"
},
"MI": {
"contact": {
"email": "orchard@ebi.ac.uk",
"name": "Sandra Orchard"
},
"description": "A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Developed by the HUPO Proteomics Standards Initiative.",
"homepage": "https://github.com/HUPO-PSI/psi-mi-CV",
"name": "Molecular Interactions",
"prefix": "MI"
},
"MIAPA": {
"contact": {
"email": "hlapp@drycafe.net",
"name": "Hilmar Lapp"
},
"description": "An application ontology to formalize annotation of phylogenetic data according to the emerging Minimum Information About a Phylogenetic Analysis (MIAPA) metadata reporting standard.",
"homepage": "http://www.evoio.org/wiki/MIAPA",
"name": "MIAPA Ontology",
"prefix": "MIAPA"
},
"MIDO": {
"contact": {
"email": "agun@rpi.edu",
"name": "Nkechinyere Agu"
},
"description": "MIDO is an OWL 2 ontology for creating a standardized format for modeling data in medical imaging tasks such as Disease Classification/ Diagnosis as well as Disease localization/segmentation",
"name": "Medical Imaging and Diagnostic Ontology",
"prefix": "MIDO",
"version": "2015-11-20"
},
"MIM": {
"contact": {
"email": "anders.riutta@gladstone.ucsf.edu",
"name": "Anders Riutta"
},
"description": "The Molecular Interaction Map (MIM) notation seeks to provide a standardized method to draw diagrams for bioregulatory networks with features similar to technical diagrams in other fields. This vocabulary uses the term hierarchy from the Formal MIM Notation Specification. Where possible, Systems Biology Ontology (SBO) and Biological Pathway Exchange (BioPAX) terms and IRIs are used. If no SBO or BioPAX term is available, a new term and IRI are created. This is currently only a partial implementation. Many elements still need to be added to cover the full the specification.",
"homepage": "http://discover.nci.nih.gov/mim/",
"name": "Molecular Interaction Map",
"prefix": "MIM",
"version": "10:30:2014 16:04"
},
"MINERAL": {
"contact": {
"email": "jhanit@gmail.com",
"name": "Nitin"
},
"description": "Material Mineral",
"name": "Material Mineral",
"prefix": "MINERAL",
"version": "2.3"
},
"MINI-FAST-1": {
"contact": {
"email": "futo@stanford.edu",
"name": "michelle"
},
"description": "Test of SKOS vocab to see if skos/core#Concept is required",
"name": "mini fast test",
"prefix": "MINI-FAST-1"
},
"MIO": {
"contact": {
"email": "zhancy999@163.com",
"name": "Chaoying Zhan"
},
"description": "The myocardial infarction ontology (MIO) is a disease-specific ontology that characterizes the knowledge field of myocardial infarction.",
"name": "Myocardial Infarction Ontology",
"prefix": "MIO",
"version": "V1.0.0"
},
"MIRNAO": {
"contact": {
"email": "vdritsou@gmail.com",
"name": "Vicky Dritsou"
},
"description": "An application ontology for microRNAs.",
"homepage": "https://code.google.com/archive/p/mirna-ontology/",
"name": "MicroRNA Ontology",
"prefix": "MIRNAO",
"version": "1.7"
},
"MIRO": {
"contact": {
"email": "louis@imbb.forth.gr",
"name": "C. Louis"
},
"description": "Application ontology for entities related to insecticide resistance in mosquitos.",
"homepage": "http://www.anobase.org",
"name": "Mosquito Insecticide Resistance",
"prefix": "MIRO",
"version": "releases/2014-05-14"
},
"MIXS": {
"contact": {
"email": "rlwalls2008@gmail.com",
"name": "Ramona Walls"
},
"description": "An OWL representation of the Minimum Information for any (x) Standard (MIxS), managed by the Genomic Standards Consortium.",
"homepage": "https://github.com/GenomicsStandardsConsortium/mixs",
"name": "Minimal Information about any Sequence Ontology",
"prefix": "MIXS",
"version": "6.1.0"
},
"MIXSCV": {
"contact": {
"email": "douginator2000@gmail.com",
"name": "Doug Wendel"
},
"description": "Controlled vocabularies for the MIxS family of metadata checklists. See http://gensc.org/gc_wiki/index.php/MIxS for details on the MIxS checklists.",
"name": "Minimal Information about any Sequence (MIxS) Controlled Vocabularies",
"prefix": "MIXSCV",
"version": "1"
},
"MLTX": {
"contact": {
"email": "isadatathing@gmail.com",
"name": "Ashleigh Faith"
},
"description": "The machine learning methodology taxonomy mapping project is focused on gathering the terminology focused on machine learning and mapping the controlled and users' natural language to form a mapping file across these terminologies. This work was originally associated with dissertation research.",
"name": "Machine Learning Methodology Taxonomy Mapping",
"prefix": "MLTX",
"version": "1"
},
"MM": {
"name": "mm",
"prefix": "MM"
},
"MMO": {
"contact": {
"email": "akwitek@mcw.edu",
"name": "Anne Kwitek"
},
"description": "The Measurement Method Ontology is designed to represent the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms.",
"homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000",
"name": "Measurement Method Ontology",
"prefix": "MMO",
"publication": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361058/",
"version": "2.109"
},
"MMUSDV": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "Life cycle stages for Mus Musculus. MmusDv was developed by the Bgee group with assistance from the core Uberon developers and the Mouse anatomy ontology developers. Currently it includes both embryonic stages and adult stages.",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv",
"name": "Mouse Developmental Stages",
"prefix": "MMUSDV"
},
"MNR": {
"contact": {
"email": "nitin@biginfolabs.com",
"name": "Nitin"
},
"description": "Natural Resource",
"name": "Material Natural Resource",
"prefix": "MNR",
"version": "2.3"
},
"MNV": {
"contact": {
"email": "ghardallou.m@gmail.com",
"name": "Ghardallou"
},
"description": "migrants ontologies",
"name": "VODANA Migrants",
"prefix": "MNV",
"version": "1.0"
},
"MO": {
"contact": {
"email": "stoeckrt@pcbi.upenn.edu",
"name": "Chris Stoeckert"
},
"description": "Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1.",
"homepage": "http://mged.sourceforge.net/ontologies/MGEDontology.php",
"name": "Microarray and Gene Expression Data Ontology",
"prefix": "MO",
"version": "1.3.1.1"
},
"MOC": {
"contact": {
"email": "jhanit@gmail.com",
"name": "Nitin"
},
"description": "Organic Compound",
"name": "Material Organic Compound",
"prefix": "MOC",
"version": "2.3"
},
"MODSCI": {
"contact": {
"email": "sm_fathalla@yahoo.com",
"name": "SaidFathalla"
},
"description": "ModSci is a reference ontology for modelling different types of modern sciences and related entities, such as scientific discoveries, renowned scientists, instruments, phenomena ... etc.",
"homepage": "https://saidfathalla.github.io/Science-knowledge-graph-ontologies/doc/ModSci_doc/index-en.html",
"name": "Modern Science Ontology",
"prefix": "MODSCI",
"version": "1.0"
},
"MOMCARE": {
"contact": {
"email": "f.heddema@pharmaccess.org",
"name": "Femke Heddema"
},
"description": "MomCare Vocabulary",
"name": "MomCareVocabulary",
"prefix": "MOMCARE",
"version": "1.1"
},
"MONDO": {
"contact": {
"email": "nicole@tislab.org",
"name": "Nicole Vasilevsky"
},
"description": "The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. It is a semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.",
"homepage": "https://monarch-initiative.github.io/mondo",
"name": "Mondo Disease Ontology",
"prefix": "MONDO",
"publication": "https://mondo.monarchinitiative.org/pages/resources/",
"version": "releases/2024-05-08"
},
"MONO": {
"contact": {
"email": "sarinder@um.edu.my",
"name": "Sarinder Kaur"
},
"description": "Monogenean Ontology",
"name": "Monogenean Ontology",
"prefix": "MONO"
},
"MOOCCIADO": {
"contact": {
"email": "contact@bioself.fr",
"name": "Delphine Dauga"
},
"description": "The first ontology describing the anatomy and the development of Molgula occidentalis.",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Molgula occidentalis Anatomy and Development Ontology",
"prefix": "MOOCCIADO"
},
"MOOCCUADO": {
"contact": {
"email": "contact@bioself.fr",
"name": "Delphine Dauga"
},
"description": "The first ontology describing the anatomy and the development of Molgula occulta.",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Molgula occulta Anatomy and Development Ontology",
"prefix": "MOOCCUADO"
},
"MOOCULADO": {
"contact": {
"email": "contact@bioself.fr",
"name": "Delphine Dauga"
},
"description": "The first ontology describing the anatomy and the development of Molgula oculata.",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Molgula oculata Anatomy and Development Ontology",
"prefix": "MOOCULADO"
},
"MOP": {
"contact": {
"email": "batchelorc@rsc.org",
"name": "Colin Batchelor"
},
"description": "Processes at the molecular level.",
"homepage": "https://github.com/rsc-ontologies/rxno",
"name": "Molecular Process Ontology",
"prefix": "MOP"
},
"MOSAIC": {
"contact": {
"email": "mecum@nceas.ucsb.edu",
"name": "Bryce Mecum"
},
"description": "Ontology to support Semantic Annotation of MOSAiC datasets housed in the Arctic Data Center (https://arcticdata.io).",
"homepage": "https://github.com/DataONEorg/sem-prov-ontologies",
"name": "The MOSAiC Ontology",
"prefix": "MOSAIC",
"version": "Version 1.0.1"
},
"MP": {
"contact": {
"email": "pheno@jax.org",
"name": "JAX phenotype list"
},
"description": "Standard terms for annotating mammalian phenotypic data.",
"homepage": "http://www.informatics.jax.org/searches/MP_form.shtml",
"name": "Mammalian Phenotype Ontology",
"prefix": "MP",
"version": "2024-07-02"
},
"MPATH": {
"contact": {
"email": "pns12@cam.ac.uk",
"name": "Mouse_pathology Administrators"
},
"description": "A structured controlled vocabulary of mutant and transgenic mouse pathological lesions and processes",
"homepage": "http://www.pathbase.net",
"name": "Mouse Pathology Ontology",
"prefix": "MPATH",
"version": "2020-05-19"
},
"MPIO": {
"contact": {
"email": "mbrochhausen@uams.edu",
"name": "Mathias Brochhausen"
},
"description": "MPIO (Minimum PDDI Information Ontology) is an OWL representation of minimum information regarding potential drug-drug interaction information. It is based on and meant to be use in alignment with DIDEO or DINTO.",
"homepage": "https://github.com/MPIO-Developers/MPIO",
"name": "Minimum PDDI Information Ontology",
"prefix": "MPIO",
"version": "2023-10-17"
},
"MPO": {
"contact": {
"email": "shuichi.kawashima@gmail.com",
"name": "Shuichi Kawashima"
},
"description": "An ontology for describing microbial phenotypes",
"name": "Microbial Phenotype Ontology",
"prefix": "MPO",
"version": "Version 0.74 alpha"
},
"MRO": {
"contact": {
"email": "sanju.tiwari.2007@gmail.com",
"name": "Sanju Tiwari"
},
"description": "It is an ontology for Military concepts",
"name": "Defen",
"prefix": "MRO"
},
"MS": {
"contact": {
"email": "gerhard.mayer@rub.de",
"name": "Gerhard Mayer"
},
"description": "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry. Developed by the HUPO Proteomics Standards Initiative (PSI).",
"homepage": "http://www.psidev.info/groups/controlled-vocabularies",
"name": "Mass Spectrometry Ontology",
"prefix": "MS",
"publication": "http://database.oxfordjournals.org/content/2013/bat009.long",
"version": "4.1.169"
},
"MSO": {
"contact": {
"email": "ashutosh.malhotra@scai.fraunhofer.de",
"name": "Ashutosh Malhotra"
},
"description": "Multiple sclerosis ontology integrated with Basic formal ontology.",
"homepage": "http://www.scai.fraunhofer.de/de/geschaeftsfelder/bioinformatik/downloads.html",
"name": "Multiple sclerosis ontology",
"prefix": "MSO"
},
"MSR": {
"contact": {
"email": "yasanmo@gmail.com",
"name": "Yasmine AnchΓ©n"
},
"description": "This is an ontology that represents a variety of entities and classifications that share the knowledge of the recommendations provided by the guideline from the American Cancer Society on Breast Cancer Screening for Women at Average Risk. This ontology was developed as part of an ontology course on UdelaR Univeristy. Mentored by Regina Motz and Edelweis Rohrer",
"name": "Mammography screening recommendation",
"prefix": "MSR",
"version": "0.0.1"
},
"MSTDE": {
"contact": {
"email": "custserv@nlm.nih.gov",
"name": "NLM Customer Service"
},
"description": "Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy. Bethesda, MD: National Library of Medicine, 2001.",
"name": "Minimal Standard Terminology of Digestive Endoscopy",
"prefix": "MSTDE",
"version": "2023AB"
},
"MSTDE-FRE": {
"contact": {
"email": "custserv@nlm.nih.gov",
"name": "NLM Customer Service"
},
"description": "Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy, French Translation, 2001",
"name": "Minimal Standard Terminology of Digestive Endoscopy, French",
"prefix": "MSTDE-FRE",
"version": "2023AB"
},
"MSV": {
"contact": {
"email": "hmori@nig.ac.jp",
"name": "MicrobeDB.jp Project Team"
},
"description": "An ontology for metagenome sample metadata. This ontology mainly defines predicates.",
"homepage": "http://microbedb.jp",
"name": "Metagenome Sample Vocabulary",
"prefix": "MSV",
"version": "0.2"
},
"MVAONT": {
"contact": {
"email": "rjeyakodi02@gmail.com",
"name": "G.Jeyakodi, Dr.P. Shanthi Bala, Department of Computer Science, Pondicherry University, Puducherry, India"
},
"description": "MVAont is about the description of Indian Mosquito Vectors and their Associations with Biocontrol Agents",
"name": "Mosquito Vector Association Ontology with Biocontrol Agents",
"prefix": "MVAONT",
"publication": "https://journals.lww.com/jvbd/abstract/9000/mbors__mosquito_vector_biocontrol_ontology_and.99949.aspx",
"version": "Version2"
},
"MWLA": {
"contact": {
"email": "gdrosato@ee.duth.gr",
"name": "George Drosatos"
},
"description": "This ontology designed and developed in order to represent the detected intentions from the Web Lifestyle Data Aggregator. In particular, it seeks to represent what is involved in the gathering of data from the web and social lifestyle of user on the Internet. We decided, therefore, to develop the ontology using the ProtΓ©gΓ© v5.0, a free, open-source ontology editor from the Stanford University. The outcome of ProtΓ©gΓ© is available on the following URL: http://carre.kmi.open.ac.uk/ontology/lifestyle.owl The presented ontology is generic and can support different type of providers (e.g. web searches, Facebook, Twitter etc.). Additionally, the predefined intentions are also generic supporting the majority of intentions in the Web. In the context of CARRE, we utilize, as a first attempt, the web searches as provider and we only upload the relevant intentions (health and travel) to CARRE in the private RDF repository. A user (representing an individual person whose data is being represented using the terms of this ontology) has connections. A connection represents that a Web Lifestyle Data Aggregator of a particular personal computer of user provides intentions for particulars providers. A connection is therefore associated with a UUID (Universal Unique Identifier) that represents an installation of the aggregator. A provider can be the web searches, Facebook or Twitter. A measurement is associated with a provider and a connection in order to declare the connection (i.e. the Web Lifestyle Data Aggregator of a particular personal computer) from which a measurement came. Every measurement must have a date at which the detected intention was taken, a weight which defines the importance of an intention and of course the detected intention that is only relevant to CARRE.",
"homepage": "https://www.carre-project.eu/innovation/web-lifestyle-data-aggregator/",
"name": "Medical Web Lifestyle Aggregator",
"prefix": "MWLA",
"version": "0.0.1"
},
"MWS22": {
"contact": {
"email": "skysnour@gmail.com",
"name": "Nour"
},
"description": "This ontology is about svu university",
"name": "Svu ontology",
"prefix": "MWS22"
},
"MY_SYRIANCINEMA": {
"contact": {
"email": "rahaf.enzawi@gmail.com",
"name": "Rahaf Enzawi"
},
"description": "I have an anthology that describes Syrian cinema It contains the film's class, the actor's class, the director's class, the producer's class, and other classes Each class has the necessary properties There are several relationships between classes The project is a practical assignment in the Semantic Web course for a graduate student in the Master of Web Science program",
"homepage": "https://www.facebook.com/share/Lahi4gL4qiX647wW/?mibextid=qi2Omg",
"name": "MWS-WSM Syrian Cinema Ontology",
"prefix": "MY_SYRIANCINEMA",
"publication": "https://www.facebook.com/share/Lahi4gL4qiX647wW/?mibextid=qi2Omg",
"version": "4.3"
},
"N-CDOH": {
"contact": {
"email": "nk495@njit.edu",
"name": "Navya"
},
"description": "Supporting ontology reuse by integrating CDoH with an existing SDoH ontology. We are presenting an overarching conception for all non-clinical determinants of health (N-CDoH).",
"name": "Non Clinical Determinants of Health",
"prefix": "N-CDOH",
"version": "v1"
},
"NANDO": {
"contact": {
"email": "kninomiya-mope@g.ecc.u-tokyo.ac.jp",
"name": "Kota Ninomiya"
},
"description": "Creating a comprehensive hierarchical controlled vocabulary for intractable and rare disease (i.e., nanbyo) representation in Japan.",
"homepage": "https://nanbyodata.jp",
"name": "Nanbyo Disease Ontology",
"prefix": "NANDO",
"version": "2023-11-28"
},
"NATPRO": {
"contact": {
"email": "batistar@cs.man.ac.uk",
"name": "Riza Theresa Batista-Navarro"
},
"description": "An ontology for describing biological activities of natural products.",
"name": "Natural Products Ontology",
"prefix": "NATPRO",
"version": "unknown"
},
"NBO": {
"contact": {
"email": "g.gkoutos@gmail.com",
"name": "George Gkoutos"
},
"description": "The Neurobehavior Ontology (NBO) consists of two main components, an ontology of behavioral processes and an ontology of behavioral phenotypes. The behavioral process branch of NBO contains a classification of behavior processes complementing and extending GOβs process ontology. The behavior phenotype branch of NBO consists of a classification of both normal and abnormal behavioral characteristics of organisms.",
"homepage": "https://github.com/obo-behavior/behavior-ontology/",
"name": "Neuro Behavior Ontology",
"prefix": "NBO",
"version": "2023-07-04"
},
"NCBITAXON": {
"contact": {
"email": "info@ncbi.nlm.nih.gov",
"name": "NCBI information"
},
"description": "The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases.",
"homepage": "http://www.ncbi.nlm.nih.gov/taxonomy",
"name": "National Center for Biotechnology Information (NCBI) Organismal Classification",
"prefix": "NCBITAXON",
"version": "2023AB"
},
"NCCNEHR": {
"contact": {
"email": "Lamb@nccn.org",
"name": "Peter Lamb"
},
"description": "The NCCN EHR Oncology Advisory Group was formed to address the high variance in oncology history documentation within EHR systems. Specifically, there is a lack of standardization in the names of oncology history categories across institutions. Moreover, no synonym list or mapping currently exists between the varied category names. Furthermore, oncology history documentation is often inconsistent, incomplete, and not updated appropriately. The NCCN EHR Oncology Advisory Group has established best practices and is working with EHR vendors to implement and enhance tools for documentation of oncology history. This ontology is a result of the work of the group, and provides users with a list of oncology history categories and synonyms. It is our sincere hope that this work can form the basis of improving standardization and interoperability of oncology history documentation within EHR systems.",
"homepage": "https://www.nccn.org/",
"name": "NCCN EHR Oncology Categories",
"prefix": "NCCNEHR",
"version": "1.0.0"
},
"NCCO": {
"description": "Nursing Care Coordination Ontology contains activities that nurses use while coordinating care among patients.",
"name": "Nursing Care Coordination Ontology",
"prefix": "NCCO",
"version": "1.0"
},
"NCIT": {
"contact": {
"email": "ncithesaurus@mail.nih.gov",
"name": "NCI Thesaurus Mailbox"
},
"description": "Vocabulary for clinical care, translational and basic research, and public information and administrative activities.",
"homepage": "https://ncithesaurus.nci.nih.gov/ncitbrowser/",
"name": "National Cancer Institute Thesaurus",
"prefix": "NCIT",
"version": "24.01e"
},
"NCOD": {
"contact": {
"email": "tigist.habtamu@aau.edu.et",
"name": "Tigist Habtamu Shiferaw"
},
"description": "National Disease classification of Ethiopia",
"name": "NCoD",
"prefix": "NCOD",
"version": "0.1.1"
},
"NCRO": {
"contact": {
"email": "huang@southalabama.edu",
"name": "Jingshan Huang"
},
"description": "The NCRO is a reference ontology in the non-coding RNA (ncRNA) field, aiming to provide a common set of terms and relations that will facilitate the curation, analysis, exchange, sharing, and management of ncRNA structural, functional, and sequence data.",
"name": "Non-coding RNA Ontology",
"prefix": "NCRO",
"version": "Working version 06102015"
},
"NDDF": {
"contact": {
"email": "cs@firstdatabank.com",
"name": "First DataBank Customer Support"
},
"description": "National Drug Data File Plus Source Vocabulary",
"name": "National Drug Data File",
"prefix": "NDDF",
"version": "2023AB"
},
"NDDO": {
"contact": {
"email": "ilin.tolovski@ijs.si",
"name": "Ilin Tolovski"
},
"description": "Neurodegenerative Disease Data Ontology (NDDO) is an ontology for describing data on neurodegenerative disease patients.",
"homepage": "http://www.ontodm.com/doku.php?id=nddo",
"name": "Neurodegenerative Disease Data Ontology",
"prefix": "NDDO",
"version": "0.2"
},
"NDFRT": {
"contact": {
"email": "michael.lincoln@va.gov",
"name": "Michael J. Lincoln MD"
},
"description": "National Drug File - Reference Terminology Public Inferred Edition, 2008_03_11",
"homepage": "http://www.va.gov",
"name": "National Drug File - Reference Terminology",
"prefix": "NDFRT",
"publication": "http://www.va.gov",
"version": "2018AA"
},
"NEIC-ONTO": {
"contact": {
"email": "wolmar.n.akerstrom@uu.se",
"name": "Wolmar"
},
"description": "Terms used to describe different aspects of NeIC activities",
"name": "Unoffical NeIC Organisation Vocabulary",
"prefix": "NEIC-ONTO",
"version": "0.2.2"
},
"NEICBEER": {
"contact": {
"email": "wolmar.n.akerstrom@nbis.se",
"name": "Wolmar Nyberg Γ
kerstrΓΆm"
},
"description": "This vocabulary is used to create a machine actionable dataset of beer and beer consumption",
"name": "The NeIC PaRI beer vocabulary",
"prefix": "NEICBEER",
"version": "0.1.0"
},
"NEIO": {
"contact": {
"email": "wdduncan@gmail.com",
"name": "Bill Duncan"
},
"description": "The Neural Electronic Interface Ontology represents the types of devices used to interface with the central nervous system to enhance (or augment) stimuli from a subject's external environment, the conditions under which these devices should be employed, the assessment of a subject's sensory ability, and the metrics for evaluating the performance.",
"homepage": "https://github.com/uflcod/neural-electronic-interface-ontology/",
"name": "Neural Electronic Interface Ontology",
"prefix": "NEIO",
"version": "2024-06-25"
},
"NEMO": {
"contact": {
"email": "gfrishkoff@gsu.edu",
"name": "Gwen Frishkoff"
},
"description": "Neural ElectroMagnetic Ontology (NEMO) describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters). Working (unstable), Release (stable), and Old (archival) versions of NEMO can be found on sourceforge: http://sourceforge.net/projects/nemoontologies/.",
"homepage": "http://nemo.nic.uoregon.edu",
"name": "Neural ElectroMagnetic Ontology",
"prefix": "NEMO",
"publication": "http://nemo.nic.uoregon.edu/wiki/Publications",
"version": "v3.10"
},
"NEO": {
"contact": {
"email": "dhier@uic.edu",
"name": "Daniel B Hier MD"
},
"description": "An ontology to capture findings from the neurological examination. The ontology is based on concepts from UMLS Metathesaurus and SNOMED CT. Only abnormal findings are included. The purpose of the ontology is to act as a limited vocabulary for coding the neurological examination for big data projects or machine learning. Hier DB, Brint SU. A Neuro-ontology for the neurological examination. BMC Med Inform Decis Mak. 2020;20(1):47. Published 2020 Mar 4. doi:10.1186/s12911-020-1066-7",
"homepage": "https://doi.org/10.1186/s12911-020-1066-7",
"name": "Neurologic Examination Ontology",
"prefix": "NEO",
"publication": "https://doi.org/10.1186/s12911-020-1066-7",
"version": "49.0"
},
"NEOMARK3": {
"contact": {
"email": "mortega@lst.tfo.upm.es",
"name": "Marta Ortega"
},
"description": "Ontology that describes the medical information necessary for early detection of the oral cancer reoccurrence extracted from the NeoMark Project.",
"homepage": "http://www.neomark.eu/portal/",
"name": "Neomark Oral Cancer Ontology, version 3",
"prefix": "NEOMARK3",
"version": "3.1"
},
"NEOMARK4": {
"contact": {
"email": "dsalvi@lst.tfo.upm.es",
"name": "Dario Salvi"
},
"description": "Ontology that describes the medical information necessary for early detection of the oral cancer reoccurrence extracted from the NeoMark Project.",
"homepage": "http://www.neomark.eu",
"name": "Neomark Oral Cancer Ontology, version 4",
"prefix": "NEOMARK4",
"publication": "http://www.neomark.eu/portal/index.php?option=com_content&view=article&id=86&Itemid=96",
"version": "4.1"
},
"NERO": {
"contact": {
"email": "robert.stevens@manchester.ac.uk",
"name": "Prof. Robert Stevens"
},
"description": "Named Entity Recognition Ontology (NERO) developed specifically for describing textual entities in biomedical texts, which accounts for diverse levels of ambiguity, bridging the scientific sublanguages of molecular biology, genetics, biochemistry, and medicine. The annotation of natural science texts is more challenging than in other domains. Biomedical language is replete with ambiguity distinct from that observed in news articles or informal text online. In biomedical texts, alternative meanings are not always clearly separated. For example, in some biomedical contexts, the words for a named entity may refer to a gene or a protein with nearly equal probability; for example, βa mutant hemoglobin Ξ±_2β can refer to either a gene or a protein. If the author meant gene-or-protein A, and we force an annotator to choose either interpretation gene A or protein A, the resulting annotation is of limited utility because the choice between gene and protein is random if the meanings are equally likely based on context. NERO attempts to minimize unwarranted, arbitrary annotative semantic label assignments for textual entities. NERO defines ambiguous concepts, such as GeneOrProtein, which subsumes both Gene and Protein using the following axiom: EquivalentTo: βGeneβ or βProtein.β There are no biological entities that are either a gene or a protein, but there are lexical entities that can correspond to either or both of these entities.",
"name": "Named Entity Recognition Ontology",
"prefix": "NERO",
"version": "The main developer of NERO is Prof. Robert Stevens, the University of Manchester"
},
"NEUDIGS": {
"contact": {
"email": "gullyburns@gmail.com",
"name": "Gully Burns"
},
"description": "Neuroscience Domain Insight Graphs provide a framework for expressing linked open data about neuronal populations expressed as statements about (A) distributions of subcellular components, (B) measurable physiological changes under various experimental conditions. The goal of this representation is to provide a computable language for reasoning over experimental neuroscientific findings.",
"homepage": "http://dig.isi.edu",
"name": "Neuroscience Domain Insight Graph",
"prefix": "NEUDIGS",
"version": "0.0.1"
},
"NEUMORE": {
"contact": {
"email": "huang@usouthal.edu",
"name": "Jingshan Huang"
},
"description": "Neural Functional Motor Recovery Ontology",
"homepage": "http://cis.usouthal.edu/~huang/",
"name": "Neural Motor Recovery Ontology",
"prefix": "NEUMORE",
"version": "0.1"
},
"NEUROBRG": {
"contact": {
"email": "Jessica.Turner@osumc.edu",
"name": "Jessica Turner"
},
"description": "NeuroBridge ontology is being developed as part of the NeuroBridge project to implement FAIR principles for neuroimaging and neurophysiology data using computable provenance metadata. The NeuroBridge ontology extends the W3C PROV ontology and the ProvCaRe ontology with terms from the SchizConnect and Data Bridge ontology aligned and merged into the original class structure of the ProvCaRe ontology.",
"homepage": "https://portal.neurobridges.org/",
"name": "NeuroBridge Ontology",
"prefix": "NEUROBRG",
"publication": "https://neurobridges.org/",
"version": "1.0 (Release 2023)"
},
"NGBO": {
"contact": {
"email": "dal.alghamdi92@gmail.com",
"name": "Dalia Alghamdi"
},
"description": "The Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.",
"homepage": "https://github.com/Dalalghamdi/NGBO",
"name": "Next Generation Biobanking Ontology",
"prefix": "NGBO",
"version": "2022-10-05"
},
"NGSONTO": {
"contact": {
"email": "mickaelsilva@medicina.ulisboa.pt",
"name": "mickael silva"
},
"description": "The NGSOnto ontology aims at capturing the workflow of all the processes involved in a Next Generation Sequencing, in order to ensure the reproducibility of the entire process, through the use of a controled and specific vocabulary.",
"name": "NGS ontology",
"prefix": "NGSONTO",
"version": "1.2"
},
"NHSQI2009": {
"name": "NHS Quality Indicators",
"prefix": "NHSQI2009"
},
"NIC": {
"name": "Nursing Interventions Classification",
"prefix": "NIC"
},
"NIDM-RESULTS": {
"contact": {
"email": "incf-nidash-nidm@googlegroups.com",
"name": "NIDM development team"
},
"description": "NIDM-Results is a data model that enable sharing neuroimaging results using a common descriptive standard across neuroimaging software. NIDM-Results focuses on mass-univariate studies and is mostly targeted at fMRI but is also suitable for anatomical MRI (with Voxel-Based Morphometry), and Positron Emission Tomography (PET). NIDM-Results packs provide a lightweight solution to share maps generated by neuroimaging studies along with their metadata. Export to NIDM-Results is natively implemented in SPM, NeuroVault and CBRAIN and a Python library is ready for integration in FSL. NeuroVault additionally can import NIDM-Results packs.",
"homepage": "http://nidm.nidash.org/specs/nidm-results.html",
"name": "NIDM-Results",
"prefix": "NIDM-RESULTS",
"version": "Recommendation version 2013-04-30"
},
"NIFCELL": {
"contact": {
"email": "smtifahim@gmail.com",
"name": "Fahim Imam"
},
"description": "Cell types from NIFSTD",
"homepage": "http://neuinfo.org/",
"name": "Neuroscience Information Framework (NIF) Cell Ontology",
"prefix": "NIFCELL",
"version": "v.1.10 - July 17, 2013"
},
"NIFDYS": {
"contact": {
"email": "smtifahim@gmail.com",
"name": "Fahim Imam"
},
"description": "This ontology contains the former BIRNLex-Disease, version 1.3.2. -- The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. It is built using the organizational framework provided by the foundational Basic Formal Ontology (BFO). It uses an abstract biomedical layer on top of that - OBO-UBO which has been constructed as a proposal to the OBO Foundry. This is meant to support creating a sharable view of core biomedical objects such as biomaterial_entity, and organismal_entity that all biomedical ontologies are likely to need and want to use with the same intended meaning. The BIRNLex biomaterial entities have already been factored to separately maintained ontology - BIRNLexBiomaterialEntity.owl which this BIRNLex-Main.owl file imports. The Ontology of Biomedical Investigation (OBI) is also imported and forms the foundation for the formal description of all experiment-related artifacts. The BIRNLex will serve as the basis for construction of a formal ontology for the multiscale investigation of neurological disease.",
"homepage": "http://neuinfo.org/",
"name": "Neuroscience Information Framework (NIF) Dysfunction Ontlogy",
"prefix": "NIFDYS",
"version": "1.5 (December, 2012)"
},
"NIFSTD": {
"contact": {
"email": "tgbugs@gmail.com",
"name": "Tom Gillespie"
},
"description": "NIF Standard ontology (NIFSTD) is a core component of Neuroscience Information Framework (NIF) project (http://neuinfo.org), a semantically enhanced portal for accessing and integrating neuroscience data, tools and information. NIFSTD includes a set of modular ontologies that provide a comprehensive collection of terminologies to describe neuroscience data and resources.",
"homepage": "http://ontology.neuinfo.org",
"name": "Neuroscience Information Framework (NIF) Standard Ontology",
"prefix": "NIFSTD",
"publication": "http://neuinfo.org/about/publications.shtm",
"version": "3.1 - January 15, 2018"
},
"NIFSUBCELL": {
"contact": {
"email": "tgbugs@gmail.com",
"name": "Tom Gillespie"
},
"description": "http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl",
"name": "Neuroscience Information Framework (NIF) Subcellular Ontology",
"prefix": "NIFSUBCELL",
"version": "1.3 (May 2012)"
},
"NIGO": {
"contact": {
"email": "erubin@bgu.ac.il",
"name": "Eitan Rubin"
},
"description": "The Neural-Immune Gene Ontology (NIGO) is a subset of GO directed for neurological and immunological systems. NIGO was created by clipping those GO terms that are not associated to any gene in human, rat and mouse, and by clipping terms not found to be relevant to the neural and/or immune domains.",
"name": "Neural-Immune Gene Ontology",
"prefix": "NIGO",
"publication": "http://www.biomedcentral.com/1471-2105/11/458",
"version": "v1"
},
"NIHSS": {
"contact": {
"email": "vcelak@kiv.zcu.cz",
"name": "Petr Vcelak"
},
"description": "Domain ontology for National Institutes of Health Stroke Scale (NIHSS). Scores range from 0-42. Patients are given more points for greater deficiencies. A score of 0 indicates that the test is normal.",
"name": "National Institutes of Health Stroke Scale Ontology",
"prefix": "NIHSS",
"version": "2024/06"
},
"NIO": {
"contact": {
"email": "albagvb@dia.uned.es",
"name": "Alba GΓ³mez-ValadΓ©s"
},
"description": "An integrative ontology of the four main domains of neuropsychological diseases, brain areas, cognitive functions and neuropsychological tests",
"name": "Neuropsychological Integrative Ontology",
"prefix": "NIO",
"version": "v15\nHeneka comments / shifs / modifications integrated"
},
"NIST_GEL": {
"contact": {
"email": "sierra.miller@nist.gov",
"name": "Sierra D. Miller"
},
"description": "Genome editing technology is a fast-growing and rapidly advancing global bioscience field with applications in many biotechnology sectors. Genome editing is used to modify the nucleic acids of a genetic code, which can be composed of DNA or RNA, in a site-specific manner. Modifications can include insertion, deletion or alteration of nucleic acids. The technology operates by biochemical principles generally applicable to every kind of cell. Examples of genome editing technology applications with global significance include human cell-based therapeutics, agriculture, microbial based therapeutics, synthetic biology and biomanufacturing. While genome editing technology is being actively utilized, there is a need for international standardization in terms and definitions for this field, so as to enhance interpretation and communication of concepts, data and results. This document has been developed to provide a unified standard set of terms and definitions that serve the needs of biotechnology stakeholders and act as a reference for genome editing technology.",
"homepage": "https://www.nist.gov/programs-projects/nist-genome-editing-lexicon",
"name": "NIST Genome Editing Lexicon",
"prefix": "NIST_GEL",
"publication": "https://www.iso.org/standard/80679.html?browse=tc",
"version": "2.2"
},
"NLMVS": {
"contact": {
"email": "manuelso@stanford.edu",
"name": "Manuel Salvadores"
},
"description": "NIH NLM Value Set as a SKOS terminology",
"homepage": "https://github.com/ncbo/NLMVS2RDF",
"name": "NIH NLM Value Sets",
"prefix": "NLMVS",
"version": "1.0"
},
"NLN": {
"contact": {
"email": "whimar@ohsu.edu",
"name": "Marijane White"
},
"description": "The NLighten ontology is an ontology designed to model clinical research/trials educational resourcses. It includes a model of educational resources and a taxonomy of clinical research competencies. The educational resource model reuses many schema.org concepts, the taxonomy is based on a variety of domain competency frameworks, and the ontology is designed to work with the eagle-i software platform.",
"homepage": "https://github.com/NLightenGroup/nlighten-ontology",
"name": "NLighten Ontology",
"prefix": "NLN",
"version": "2018-02-28"
},
"NMDCO": {
"contact": {
"email": "mamillerpa@gmail.com",
"name": "Mark Miller"
},
"description": "The NMDC Ontology (NMDCO) is used by the National Microbiome Data Collaborative (NMDC, https://microbiomedata.org) to annotate multi-omic microbiome metadata. It merges a number of ontologies relevant to the NMDC (such as the plant and environment ontologies) into a single ontology. The ontology can be download from Github at https://github.com/microbiomedata/nmdc-ontology.",
"homepage": "https://github.com/microbiomedata/nmdc-ontology",
"name": "NMDC Ontology",
"prefix": "NMDCO",
"version": "2024-03-15"
},
"NMOBR": {
"contact": {
"email": "spolavar@gmail.com",
"name": "Sridevi Polavaram"
},
"description": "The species, brain regions and cell types are integrated into a single ontology for enabling OntoSearch functionality to mine the latest v7.0 release of NeuroMorpho.Org.",
"name": "NeuroMorpho.Org brain region ontologies",
"prefix": "NMOBR",
"version": "2.0"
},
"NMOSP": {
"contact": {
"email": "spolavar@gmu.edu",
"name": "Sridevi Polavaram"
},
"description": "The species ontology of NeuroMorpho.Org was updated (OntoSearch v1.3) to map the new species and strains added in NeuroMorpho.Org v6.3 release.",
"homepage": "NeuroMorpho.Org",
"name": "NeuroMorpho.Org species ontology",
"prefix": "NMOSP",
"version": "1.3"
},
"NMR": {
"contact": {
"email": "dschober@ipb-halle.de",
"name": "Daniel Schober"
},
"description": "This is the new msi-sanctioned nmr CV, created within the COSMOS EU project, to support the nmrML data standard for nuclear magnetic resonance data in metabolomics with meaningful raw data descriptors.",
"homepage": "http://nmrml.org/cv/",
"name": "NMR-Controlled Vocabulary",
"prefix": "NMR",
"version": "1.1.0"
},
"NND_CH": {
"contact": {
"email": "n.j.mekkes@umcg.nl",
"name": "Nienke Mekkes"
},
"description": "Netherlands Neurogenetics Database Clinical History ontology. This ontology describes clinical signs, symptoms and findings from the most common neurodegenerative and psychiatric disorders in the Netherlands Brain Bank and can be used for cross-disorder brain research. These attributes encompass 19 groupings, including βDisturbances in mood and behaviorβ, βExtrapyramidal signsβ, βCognitive and memory impairmentβ in 5 broad domains: Psychiatric, Cognitive, Motor, Sensory/autonomic, and General.",
"name": "NND_Clinical_history",
"prefix": "NND_CH",
"version": "1"
},
"NND_ND": {
"contact": {
"email": "n.j.mekkes@umcg.nl",
"name": "Nienke Mekkes"
},
"description": "Netherlands Neurogenetics Database Neuropathological Diagnosis ontology. This ontology describes the most common neurodegenerative and psychiatric disorders in the Netherlands Brain Bank and can be used for cross-disorder brain research.",
"name": "NND_Neuropathological_Diagnosis",
"prefix": "NND_ND",
"version": "2023-03-31"
},
"NOMEN": {
"contact": {
"email": "diapriid@gmail.com",
"name": "Matt Yoder"
},
"description": "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature.",
"homepage": "https://github.com/SpeciesFileGroup/nomen",
"name": "NOMEN - A nomenclatural ontology for biological names",
"prefix": "NOMEN"
},
"NONRCTO": {
"contact": {
"email": "amrapali.zaveri@gmail.com",
"name": "Amrapali Zaveri"
},
"description": "We built an ontology to help the systematic review and meta-analysis process of non randomized clinical trials.",
"name": "Non-Randomized Controlled Trials Ontology",
"prefix": "NONRCTO",
"version": "2.0"
},
"NPI": {
"contact": {
"email": "the-loc.nguyen@lirmm.fr",
"name": "The Loc NGUYEN"
},
"description": "Terminologies of Non-Pharmacological Interventions",
"homepage": "http://www.cepsplatform.eu",
"name": "Non-Pharmacological Interventions (NPIs)",
"prefix": "NPI",
"version": "Version 8"
},
"NPO": {
"contact": {
"email": "nathan.baker@pnl.gov",
"name": "Nathan Baker"
},
"description": "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.",
"homepage": "http://www.nano-ontology.org",
"name": "NanoParticle Ontology",
"prefix": "NPO",
"publication": "http://www.nano-ontology.org",
"version": "2011-12-08 (yyyy-mm-dd)"
},
"NPOKB": {
"contact": {
"email": "tgbugs@gmail.com",
"name": "Tom Gillespie"
},
"description": "An ontology of neuron types based on the phenotypic dimensions of cells that can be measure experimentally.",
"homepage": "https://github.com/SciCrunch/NIF-Ontology",
"name": "Neuron Phenotype Ontology",
"prefix": "NPOKB",
"version": "2024-08-01"
},
"NRO": {
"contact": {
"email": "chenjiafeng@sr.gxmu.edu.cn",
"name": "ChenJiafeng"
},
"description": "The neural reprogramming ontology encompasses the domain of neural regenerative cell reprogramming knowledge. As research progresses, researchers and specialists in the field of reprogramming could continue to expand the bounds of this foundation, so adding to its depth.",
"name": "NeuralReprogrammingOntology",
"prefix": "NRO",
"version": "1.0.0"
},
"NXDX": {
"contact": {
"email": "2277162907@qq.com",
"name": "zinzingzin"
},
"description": "A test for ontology submission",
"name": "Test NXDX",
"prefix": "NXDX",
"version": "2021/8/10"
},
"O-REXTECH": {
"contact": {
"email": "smrTucson@gmail.com",
"name": "Stephen M Richard"
},
"description": "second draft, M4M workshop, testing SKOS-Play and workflows. Add top concepts and more hierarchy.",
"name": "OSIRIS-REx Analytical Technique",
"prefix": "O-REXTECH",
"version": "0.0.2"
},
"OA": {
"description": "The Web Annotation Data Model specification describes a structured model and format to enable annotations to be shared and reused across different hardware and software platforms. Annotations are typically used to convey information about a resource or associations between resources. Simple examples include a comment or tag on a single web page or image, or a blog post about a news article.",
"homepage": "https://www.w3.org/TR/annotation-model/",
"name": "Web Annotation Ontology",
"prefix": "OA",
"version": "2016-11-12T21:28:11Z"
},
"OAE": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun \"Oliver\" He"
},
"description": "The Ontology of Adverse Events (OAE) is a community-based biomedical ontology in the domain of adverse events. OAE is developed to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. Its development follows the OBO Foundry principles.",
"homepage": "http://www.oae-ontology.org/",
"name": "Ontology of Adverse Events",
"prefix": "OAE",
"publication": "http://www.ncbi.nlm.nih.gov/pubmed/25093068",
"version": "1.2.47"
},
"OARCS": {
"contact": {
"email": "mjyoder@illinois.edu",
"name": "Matt Yoder"
},
"description": "OArCS is an ontology describing the Arthropod ciruclatory system.",
"homepage": "https://github.com/aszool/oarcs",
"name": "Ontology of Arthropod Circulatory Systems",
"prefix": "OARCS",
"version": "2019-04-18"
},
"OBA": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO.",
"homepage": "https://github.com/obophenotype/bio-attribute-ontology",
"name": "Ontology of Biological Attributes",
"prefix": "OBA",
"version": "2024-06-27"
},
"OBCS": {
"contact": {
"email": "jiezheng@upenn.edu",
"name": "Jie Zheng"
},
"description": "The Ontology of Biological and Clinical Statistics (OBCS) is a biomedical ontology in the domain of biological and clinical statistics. OBCS is primarily targeted for statistical representation in the fields in biological, biomedical, and clinical domains. OBCS uses the Basic Formal Ontology (BFO) as the upper level ontology. OBCS imports all biostatistics related terms in the Ontology for Biomedical Investigations (OBI) including all logical axioms.",
"homepage": "https://github.com/obcs/obcs",
"name": "Ontology of Biological and Clinical Statistics",
"prefix": "OBCS",
"publication": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5024438/",
"version": "2023-12-08"
},
"OBI": {
"contact": {
"email": "bpeters@liai.org",
"name": "Bjoern Peters"
},
"description": "OBI is an ontology of investigations, the protocols and instrumentation used, the material used, the data generated and the types of analysis performed on it.
To import,
Latest version: http://purl.obolibrary.org/obo/obi.owl
Latest release notes at http://purl.obolibrary.org/obo/obi/release-notes.html
Note: BFO 2.0 pre-Graz release (not official release version) was used in this release.",
"homepage": "http://purl.obolibrary.org/obo/obi",
"name": "Ontology for Biomedical Investigations",
"prefix": "OBI",
"publication": "http://purl.obolibrary.org/obo/obi/Technical_Reports",
"version": "2024-06-10"
},
"OBIB": {
"contact": {
"email": "jiezheng@upenn.edu",
"name": "Jie Zheng"
},
"description": "The ontology for Biobanking (OBIB) is an ontology built for annotation and modeling of biobank repository and biobanking administration. It is developed based on subset of Ontology for Biomedical Investigations (OBI) using Basic Formal Ontology (BFO) as top ontology and following OBO Foundry principles. The first version of the ontology is merged of two existing biobank related ontologies, OMIABIS and biobank ontology.",
"homepage": "https://github.com/biobanking/biobanking/wiki",
"name": "Ontology for Biobanking",
"prefix": "OBIB",
"version": "2023-04-05"
},
"OBIWS": {
"contact": {
"email": "jiezheng@pcbi.upenn.edu",
"name": "jie zheng"
},
"description": "The Bioinformatics Web Services ontology (OBIws) is an ontology that extends the Ontology for Biomedical Investigations (OBI) to build an Ontology that supports consistent annotation of Bioinformatics Web services.",
"homepage": "http://code.google.com/p/obi-webservice/",
"name": "Bioinformatics Web Service Ontology",
"prefix": "OBIWS",
"version": "Release v1.1"
},
"OBI_BCGO": {
"contact": {
"email": "jiezheng@upenn.edu",
"name": "Jie Zheng"
},
"description": "Beta Cell Genomics Ontology (BCGO) is an application ontology built for the Beta Cell Genomics database (http://genomics.betacell.org/gbco/) aiming to support database annotation, complicated semantic queries, and automated cell type classification. The ontology is developed using Basic Formal Ontology (BFO) as upper ontology, Ontology for Biomedical Investigations (OBI) as ontology framework and integrated subsets of multiple OBO Foundry (candidate) ontologies. Current the BCGO contains 2383 classes including terms referencing to 24 various OBO Foundry ontologies including CL, CLO, UBERON, GO, PRO, UO, etc.",
"homepage": "https://github.com/obi-bcgo/bcgo",
"name": "Beta Cell Genomics Ontology",
"prefix": "OBI_BCGO",
"version": "2015-07-08"
},
"OBI_IEE": {
"contact": {
"email": "drbff@protonmail.com",
"name": "Brenda Farrell"
},
"description": "Inner Ear Electrophysiology (IEE) is an application ontology created to describe electrophysiology and biophysical data collections of the anatomical entities and cells (e.g., outer hair cells) of the inner ear. The ontology is developed with The Ontology for Biomedical Investigations (OBI) and integrated subsets of multiple OBO ontologies, especially, PATO, FMA, CHEBI, and OBA.",
"name": "The Ontology for Biomedical Investigation based Inner Ear Electrophysiology",
"prefix": "OBI_IEE",
"version": "2018-05-23"
},
"OBOE": {
"contact": {
"email": "mecum@nceas.ucsb.edu",
"name": "Bryce Mecum"
},
"description": "The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations. The main concepts in OBOE include: - Observation: an event in which one or more measurements are taken - Measurement: the measured value of a property for a specific object or phenomenon (e.g., 3.2) - Entity: an object or phenomenon on which measurements are made (e.g., Quercus rubrum) - Characteristic: the property being measured (e.g., VolumetricDensity) - Standard: units and controlled vocabularies for interpreting measured values (e.g., g/cm^3) - Protocol: the procedures followed to obtain measurements (e.g., DensityProtocol2014) OBOE can characterize the context of an observation (e.g., space and time), as well as dependencies such as nested experimental observations. It includes an extensive set of unit definitions (e.g., grams of carbon per liter of seawater), and can facilitate automatic unit conversions (e.g., pounds to kilograms). OBOE can be easily extended to create Entities and Characteristics for specific research domains, making it both broadly applicable and highly customizable. OBOE is being used to improve data interpretation, facilitate reuse, and create precise and effective systems for data search and discovery.",
"homepage": "https://github.com/NCEAS/oboe",
"name": "The Extensible Observation Ontology",
"prefix": "OBOE",
"publication": "Madin, J., S. Bowers, M. Schildhauer, S. Krivov, D. Pennington, and F. Villa. 2007. An ontology for describing and synthesizing ecological observation data. Ecological Informatics 2:279β296. doi:10.1016/j.ecoinf.2007.05.004",
"version": "Version 1.2"
},
"OBOE-SBC": {
"contact": {
"email": "leinfelder@nceas.ucsb.edu",
"name": "Ben Leinfelder"
},
"description": "Extensible Observation Ontology for the Santa Barbara Coastal Long Term Ecological Research project (SBC-LTER). OBOE SBC extends core concepts defined in the OBOE suite that are particular to the Santa Barbara Coastal Long Term Ecological Research project's data collection activities. These include specific measurement protocols, sites, etc. This is mean as a case study ontology for the Semtools project.",
"homepage": "https://semtools.ecoinformatics.org/",
"name": "Santa Barbara Coastal Observation Ontology",
"prefix": "OBOE-SBC",
"version": "Version 1.0"
},
"OBOREL": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "A collection of relations intended primarily for standardization across ontologies in the OBO Foundry and wider OBO library. It incorporates ROCore upper-level relations such as part of as well as biology-specific relationship types such as develops from.",
"homepage": "https://github.com/oborel/obo-relations/",
"name": "Relations Ontology",
"prefix": "OBOREL",
"version": "2024-04-24"
},
"OBS": {
"contact": {
"email": "thib64du@hotmail.fr",
"name": "Thibaut"
},
"description": "Application ontology for covariate selection support.",
"name": "OntoBioStat",
"prefix": "OBS",
"publication": "https://pubmed.ncbi.nlm.nih.gov/34042854/"
},
"OCCO": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun (Oliver) He"
},
"description": "This Occupaton Ontology (OccO) is an ontology in the domain of human occupations. Current OccO version is developed based on the US Bureau of Labor Statistics Standard Occupation Classification (SOC) and the related O*Net System. The OccO development follows the principles of the Open Biological and Biomedical (OBO) Foundry.",
"homepage": "https://hegroup.org/",
"name": "Occupation Ontology",
"prefix": "OCCO",
"version": "2023-08-20"
},
"OCD": {
"contact": {
"email": "muhajaba@cardiff.ac.uk",
"name": "Areej"
},
"description": "The Obsessive Compulsive Disorder Ontology (OCD) is a domain-specific ontology for representing the knowledge of OCD.",
"name": "OCD ontology",
"prefix": "OCD"
},
"OCDM": {
"contact": {
"email": "detwiler@sig.biostr.washington.edu",
"name": "Todd Detwiler"
},
"description": "The Ontology of Craniofacial Development and Malformation (OCDM) is a mechanism for representing knowledge about craniofacial development and malformation, and for using that knowledge to facilitate integrating craniofacial data obtained via multiple techniques from multiple labs and at multiple levels of granularity. The OCDM is a project of the NIDCR-sponsored FaceBase Consortium, whose goal is to promote and enable research into the genetic and epigenetic causes of specific craniofacial abnormalities through the provision of publicly accessible, integrated craniofacial data.",
"homepage": "https://www.facebase.org/ocdm/",
"name": "Ontology of Craniofacial Development and Malformation",
"prefix": "OCDM",
"version": "1.10.0"
},
"OCE": {
"contact": {
"email": "liukaiyong163@163.com",
"name": "Kaiyong Liu"
},
"description": "The Ontology of Chemical Elements (OCE) is a community-based ontology in the domain of chemical elements. OCE systematically represents and annotates the known 118 chemical elements and their charactistics and relations with other entities. OCE imports the basic chemical element information from ChEBI and adds more classes, annotations, and axioms. OCE specifically focuses on adding all the related information from the Periodic Table of Chemical Elements.",
"homepage": "https://github.com/ontologyofchemicalelements/OCE",
"name": "Ontology of Chemical Elements",
"prefix": "OCE",
"version": "Vision Release: 1.0.29"
},
"OCHV": {
"contact": {
"email": "muhammad.f.amith@uth.tmc.edu",
"name": "Tuan Amith"
},
"description": "A SKOS-encoded implementation of the \"Open Access, Collaborative Consumer Health Vocabulary Initiative\" by the University of Utah (consumerhealthvocab.org and layhealthinformatics.com)",
"name": "Ontology of Consumer Health Vocabulary",
"prefix": "OCHV",
"version": "1"
},
"OCIMIDO": {
"contact": {
"email": "samanfapc@gmail.com",
"name": "Samantha Pendleton"
},
"description": "Application ontology for Ocular Immune-mediated Inflammatory Diseases, built from domain experts in ophthalmology, clinical guidelines, and enhanced with patient-preferred terms.",
"homepage": "https://github.com/sap218/ocimido",
"name": "Ocular Immune-Mediated Inflammatory Diseases Ontology",
"prefix": "OCIMIDO",
"publication": "https://doi.org/10.1016/j.compbiomed.2021.104542",
"version": "1.2"
},
"OCMR": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "OCMR is a biomedical ontology that represents anti-rheumatism traditional Chinese medicines and related information.",
"homepage": "https://github.com/biomedontology/ocmr",
"name": "Ontology of Chinese Medicine for Rheumatism",
"prefix": "OCMR",
"version": "Vision Release; 1.0.11"
},
"OCO": {
"contact": {
"email": "bisu@drtc.isibang.ac.in",
"name": "Biswanath Dutta"
},
"description": "Open healthCare Ontology (OpenCare) is an integrated metadata vocabulary expressed as an ontological data model, to facilitate the effective reasoning of patient-specific electronic health record (EHR) data. The OpenCare model identifies the concepts and semantic types in the EHR data with the aim of enabling the representation of clinical data in a way that is accessible and usable by researchers and healthcare facility users. The development of OpenCare and its components is formalized using the Ontology Web Language (OWL). This framework aims to enhance the accessibility and user-friendliness of EHR clinical data.",
"homepage": "https://w3id.org/opencare",
"name": "OpenCareOntology",
"prefix": "OCO",
"version": "1.1"
},
"OCRE": {
"contact": {
"email": "ida.sim@ucsf.edu",
"name": "Ida Sim"
},
"description": "OCRe is an ontology designed to support systematic description of, and interoperable queries on, human studies and study elements.",
"homepage": "http://rctbank.ucsf.edu/home/ocre",
"name": "Ontology of Clinical Research",
"prefix": "OCRE",
"publication": "http://rctbank.ucsf.edu/home/ocre",
"version": "Revision 315"
},
"OCVDAE": {
"contact": {
"email": "wang.liwei@mayo.edu",
"name": "Liwei Wang"
},
"description": "OCVDAE is a biomedical ontology of cardiovascular disease drug-associated adverse events",
"name": "Ontology of Cardiovascular Drug Adverse Events",
"prefix": "OCVDAE",
"version": "Vision Release; 1.0.4"
},
"ODAE": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "The Ontology of Drug Adverse Events (ODAE) is a biomedical ontology in the area of drug adverse events, developed by following OBO Foundry principles (e.g., openness, collaboration).",
"homepage": "https://github.com/ODAE-ontology/ODAE",
"name": "Ontology of Drug Adverse Events",
"prefix": "ODAE",
"version": "Vision Release: 1.0.08"
},
"ODHT": {
"contact": {
"email": "spencer@prism.bio",
"name": "Spencer Hey"
},
"description": "This is an ontology of digital health technologies (DHTs) with a specific focus on DHT use in clinical trials. It was created as part of a collaborative project between Prism.Bio and Janssen Clinical Innovation on digital sustainability for the clinical trials enterprise.",
"name": "Digital Health Technologies",
"prefix": "ODHT",
"version": "0.2"
},
"ODNAE": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "ODNAE is an extension of OAE with a focus on drug-associated neuropathy adverse events.",
"homepage": "https://github.com/odnae/odnae",
"name": "Ontology of Drug Neuropathy Adverse Events",
"prefix": "ODNAE",
"version": "Vision Release; 1.0.13"
},
"OF": {
"contact": {
"email": "vikas@hotmail.it",
"name": "Vikas"
},
"description": "This is an ontology with SWRL rules of nutrition for diabetic patient. We can import the value of Blood Sugar and Weight by .xls and use that like instance for generate the rules with rule engine Jess.",
"name": "OntoFood",
"prefix": "OF",
"version": "1.0"
},
"OFSMR": {
"contact": {
"email": "scuberog@hotmail.com",
"name": "Salvador"
},
"description": "Food-matrix ontology for Open Food Safety Model Repository",
"homepage": "https://sites.google.com/site/openfsmr/open-fsmr-detailfilter",
"name": "Open Predictive Microbiology Ontology",
"prefix": "OFSMR",
"version": "0.4"
},
"OGDI": {
"contact": {
"email": "linikujp@gmail.com",
"name": "Yu Lin"
},
"description": "It is the ontology used to model the scientific investigation, especially Genome-Wide Association Study (GWAS), to find out genetic susceptibility factor to disease, such as Diabetes. It models the genetic varaints, polymorphisms, statistical measurement, populations and other elements that are essential to determine a genetic susceptibility factor in GWAS study. It must be used with other two ontologies, in the case of Diabetes, :Ontology of Geographical Region (OGR) and Ontology of Glucose Metabolism Disorder (OGMD) .",
"name": "Ontology for Genetic Disease Investigations",
"prefix": "OGDI",
"publication": "http://www.med.kobe-u.ac.jp/journal/contents/55/E53.pdf, http://www.academia.edu/213769/Ontology_of_Genetic_Susceptibility_Factors_to_Diabetes_Mellitus_OGSF-DM_",
"version": "1.0"
},
"OGG": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets.",
"homepage": "https://bitbucket.org/hegroup/ogg",
"name": "Ontology of Genes and Genomes",
"prefix": "OGG",
"version": "Vision Release: 1.0.59"
},
"OGG-MM": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "OGG-Mm is the OGG Mus musculus (mouse) subset. The OGG (Ontology of Genes and Genomes) is a formal ontology of genes and genomes of biological organisms. OGG is developed by following OBO Foundry principles and aligning with the BFO top ontology.",
"homepage": "https://bitbucket.org/hegroup/ogg-mm",
"name": "Ontology of Genes and Genomes - Mouse",
"prefix": "OGG-MM",
"version": "Vision Release: 1.0.66"
},
"OGI": {
"contact": {
"email": "linikujp@gmail.com",
"name": "Yu Lin"
},
"description": "Using BFO as its framwork, OGI formalized the genomic element by defining an upper class 'genetic interval'. The definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.",
"homepage": "https://code.google.com/p/ontology-for-genetic-interval/",
"name": "Ontology for Genetic Interval",
"prefix": "OGI",
"version": "2.0"
},
"OGMD": {
"contact": {
"email": "linikujp@gmail.com",
"name": "Yu Lin"
},
"description": "Including the disease names. phenotypes and their classifications involved in Glucose Metabolism Disorder, Diabetes. (OBO and OWL format are available in sourceforge.) OWL file is downloadable as the different view here.",
"homepage": "http://sourceforge.net/projects/ogmd/",
"name": "Ontology of Glucose Metabolism Disorder",
"prefix": "OGMD",
"publication": "http://www.med.kobe-u.ac.jp/journal/contents/55/E53.pdf",
"version": "1"
},
"OGMS": {
"contact": {
"email": "rscheuermann@jcvi.org",
"name": "Richard Scheuermann"
},
"description": "The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. See http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf",
"homepage": "https://github.com/OGMS/ogms",
"name": "Ontology for General Medical Science",
"prefix": "OGMS",
"publication": "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf",
"version": "2021-08-19"
},
"OGR": {
"contact": {
"email": "linikujp@gmail.com",
"name": "Yu Lin"
},
"description": "This OWL ontology classified the geograhical regions related vocabularies extracted from UMLS. It used with other ontologies to represent the genetic susceptibility factors of diabetes.",
"name": "Ontology of Geographical Region",
"prefix": "OGR",
"publication": "http://www.med.kobe-u.ac.jp/journal/contents/55/E53.pdf",
"version": "1.1"
},
"OGROUP": {
"contact": {
"email": "marcelo.lucas@ymail.com",
"name": "Marcelo L Silva"
},
"description": "Ontology to help prossessing the information from orthologous groups in order to infer new functional annotations. The ontology integrates definitions from diverse ontologies.",
"name": "Orthologous Group Ontology",
"prefix": "OGROUP",
"version": "1.0"
},
"OGSF": {
"contact": {
"email": "linikujp@gmail.com",
"name": "Asiyah Yu Lin"
},
"description": "Ontology for Genetic Susceptibility Factor (OGSF) is an application ontology to model/represent the notion of genetic susceptibility to a specific disease or an adverse event or a pathological biological process. It is developed using BFO2.0's framwork. The ontology is under the domain of genetic epidemiology.",
"homepage": "https://code.google.com/p/ogsf/",
"name": "Ontology for Genetic Susceptibility Factor",
"prefix": "OGSF",
"version": "2.0"
},
"OHD": {
"contact": {
"email": "wdduncan@gmail.com",
"name": "Bill Duncan"
},
"description": "The Oral Health and Disease Ontology is intended as a BFO and OBO Foundry compliant ontology for the oral health domain. It is currently used to represent the content of dental practice health records and is intended to be further developed for use in translation medicine. It demonstrates a principled split between billing codes as information entities and what the codes are about, such as dental procedures, materials, and patients. OHD is structured using BFO uses terms from OGMS, OBI, IAO and FMA. In addition it uses terms from CARO, OMRSE, NCBITaxon, and a subset of terms from the Current Dental Terminology (CDT) OHD is in early development and subject to change without notice.",
"homepage": "https://github.com/oral-health-and-disease-ontologies/ohd-ontology",
"name": "The Oral Health and Disease Ontology",
"prefix": "OHD",
"version": "2024-06-21"
},
"OHMI": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.",
"homepage": "https://github.com/ohmi-ontology/ohmi",
"name": "Ontology of Host-Microbe Interactions",
"prefix": "OHMI",
"version": "2019-09-17"
},
"OHPI": {
"contact": {
"email": "edong@umich.edu",
"name": "Edison Ong"
},
"description": "The Ontology of Host-Pathogen Interactions (OHPI) is a biomedical ontology of the host-pathogen interactions. Its development follows the OBO Foundry Principles.",
"homepage": "https://github.com/OHPI/ohpi/",
"name": "Ontology of Host-Pathogen Interactions",
"prefix": "OHPI",
"publication": "https://www.ncbi.nlm.nih.gov/pubmed/30365026",
"version": "1.0.26"
},
"OLAM": {
"contact": {
"email": "yongqunh@med.umich.udu",
"name": "Oliver He"
},
"description": "The OLAM is community-based biomedical ontology in the field of laboratory animal medicine, with the aim to ontologically represent entities and the relations among the entities related to laboratory animal medicine.",
"homepage": "https://github.com/olam-ontology/OLAM",
"name": "Ontology of Laboratory Animal Medicine",
"prefix": "OLAM",
"version": "Vision Release: 1.0.20"
},
"OLATDV": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "Life cycle stages for Medaka. OlatDv is based on the original medaka stage ontology MFO by Thorsten Henrich. Currently it includes only pre-adult stages.",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv",
"name": "Medaka Developmental Stages",
"prefix": "OLATDV"
},
"OM": {
"contact": {
"email": "hajo.rijgersberg@wur.nl",
"name": "Hajo Rijgersberg"
},
"description": "The Ontology of units of Measure (OM) 2.0 models concepts and relations important to scientific research. It has a strong focus on units, quantities, measurements, and dimensions. OM is modelled in OWL 2 - Web Ontology Language. The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units metre and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant or the quantity vaselife. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology and Typography.",
"homepage": "https://github.com/HajoRijgersberg/OM",
"name": "Ontology of units of Measure",
"prefix": "OM",
"publication": "https://github.com/HajoRijgersberg/OM/blob/master/README.md#papers-on-om",
"version": "2.0.57"
},
"OMDO": {
"contact": {
"email": "rongrongchinese@163.com",
"name": "Rongrong Wu"
},
"description": "The OligoMetastatic Disease Ontology(OMDO) is a disease-specific ontology that characterizes the knowledge field of oligometastatic disease/oligometastatic cancer.",
"name": "OligoMetastatic Disease Ontology",
"prefix": "OMDO"
},
"OMIM": {
"contact": {
"email": "custserv@nlm.nih.gov",
"name": "NLM Customer Service"
},
"description": "Online Mendelian Inheritance in Man, OMIM (TM). McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine",
"homepage": "http://www.ncbi.nlm.nih.gov/omim/",
"name": "Online Mendelian Inheritance in Man",
"prefix": "OMIM",
"publication": "http://www.ncbi.nlm.nih.gov/omim/",
"version": "2023AB"
},
"OMIT": {
"contact": {
"email": "huang@southalabama.edu",
"name": "Jingshan Huang"
},
"description": "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). OMIT has reused and extended a set of well-established concepts from existing bio-ontologies, e.g., Gene Ontology, Sequence Ontology, Protein Ontology, NCBI Organism Taxonomy, Human Disease Ontology, Foundational Model of Anatomy, and so forth.",
"homepage": "http://omnisearch.soc.southalabama.edu/",
"name": "Ontology for MicroRNA Target",
"prefix": "OMIT",
"version": "OBO 4.0-12122013-2338"
},
"OMO": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "The OBO Metadata Ontology (OMO) specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO) before.",
"homepage": "https://github.com/information-artifact-ontology/ontology-metadata",
"name": "OBO Metadata Ontology",
"prefix": "OMO"
},
"OMP": {
"contact": {
"email": "d-siegele@tamu.edu",
"name": "Deborah A. Siegele"
},
"description": "OMP is a formal ontology of phenotypes observed in all microbes: bacteria, archaea, protists, fungi, and viruses. OMP is being developed to be compatible with other microbial phenotype ontologies, such as the Fission Yeast Phenotype Ontology (FYPO) and the Ascomycete Phenotype Ontology (APO), and aims to standardize the capture of phenotypic information to allow improved cross-species data mining and analysis.",
"homepage": "microbialphenotypes.org",
"name": "Ontology of Microbial Phenotypes",
"prefix": "OMP",
"publication": "https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-014-0294-3",
"version": "releases/2019-06-07"
},
"OMRSE": {
"contact": {
"email": "hoganwr@gmail.com",
"name": "Bill Hogan"
},
"description": "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations.",
"homepage": "https://github.com/mcwdsi/OMRSE",
"name": "Ontology for Modeling and Representation of Social Entities",
"prefix": "OMRSE",
"publication": "https://github.com/mcwdsi/OMRSE#list-of-publications",
"version": "2024-03-22"
},
"OMV": {
"contact": {
"email": "jbgraybeal@sonic.net",
"name": "John Graybeal"
},
"description": "A standard for ontology metadata; a vocabulary of terms and definitions describing ontologies which specifies reusability-enhancing ontology features for human and machine processing purposes.",
"homepage": "http://omv2.sourceforge.net/index.html",
"name": "Ontology Metadata Vocabulary",
"prefix": "OMV",
"version": "2.4.1"
},
"ONE": {
"contact": {
"email": "Chen.Yang@UGent.be",
"name": "Chen Yang"
},
"description": "Nutritional epidemiology is a specific research area. The generic ontologies for food science, nutrition science or medical science failed to cover the specific characteristics of nutritional epidemiologic studies. As a result, we developed the ontology for nutritional epidemiology (ONE) in order to describe nutritional epidemiologic studies accurately.",
"homepage": "https://github.com/cyang0128/Nutritional-epidemiological-ontologies",
"name": "Ontology for Nutritional Epidemiology",
"prefix": "ONE",
"publication": "https://www.mdpi.com/2072-6643/11/6/1300",
"version": "V2.2"
},
"ONL-DP": {
"contact": {
"email": "bernard.gibaud@univ-rennes1.fr",
"name": "Bernard Gibaud"
},
"description": "This ontology is a module of the OntoNeuroLOG ontology, developed in the context of the NeuroLOG project, a french project supported by ANR (ANR-06-TLOG-024 grant) aiming at integrating distributed heterogeous resources in neuroimaging. If covers the domain of Datasets and the processing of datasets. It includes a detailed taxonomy of datasets in the area of neuroimaging (and especially MR imaging) as well as a taxonomy of medical image processing.",
"homepage": "http://neurolog.unice.fr/ontoneurolog/v3.0/Documentation_OntoNeuroLOGv3.pdf",
"name": "Dataset processing",
"prefix": "ONL-DP",
"version": "V1"
},
"ONL-MR-DA": {
"contact": {
"email": "bernard.gibaud@univ-rennes1.fr",
"name": "Bernard Gibaud"
},
"description": "This ontology is a module of the OntoNeuroLOG ontology, developed in the context of the NeuroLOG project, a french project supported by ANR (ANR-06-TLOG-024 grant) aiming at integrating distributed heterogeneous resources in neuroimaging. If covers the domain of Magnetic Resonance Imaging (MRI) dataset acquisition, i.e. MRI protocols, and MRI sequence parameters. In particular, it includes a multi-axial classification of MR sequences.",
"homepage": "http://neurolog.unice.fr/ontoneurolog/v3.0/Documentation_OntoNeuroLOGv3.pdf",
"name": "Magnetic Resonance Dataset Acquisition Ontology",
"prefix": "ONL-MR-DA",
"version": "V1"
},
"ONL-MSA": {
"contact": {
"email": "bernard.gibaud@univ-rennes1.fr",
"name": "Bernard Gibaud"
},
"description": "This ontology is a module of the OntoNeuroLOG ontology, developed in the context of the NeuroLOG project, a french project supported by ANR (ANR-06-TLOG-024 grant) aiming at integrating distributed heterogeous resources in neuroimaging. This MSA ontology module covers the field of mental state assessments, i.e. instruments, instrument variables, assessments, and resulting scores. It includes a generic domain core ontology, that provides a general model of such entities and a general taxonomy of behavioural, neurosychological and neuroclinical instruments, that can be easily extended to model any particular kind of instrument. It also includes such extensions for 8 relatively standard instruments, namely: (1) the Beck-depression-inventory-(BDI-II), (2) the Expanded-Disability-Status-Scale, (3) the Controlled-oral-word-association-test, (4) the Free-and-Cued-Selective-Reminding-Test-with-Immediate-Recall-16-item-version-(The-GrΓΆber-and-Buschke-test), (5) the Mini-Mental-State, (6) the Stroop-color-and-word-test, (7) the Trail-making-test-(TMT), (8) the Wechsler-Adult-Intelligence-Scale-third-edition, (9) the Clinical-Dementia-Rating-scale, (10) the Category-verbal-fluency, (11) the Rey-Osterrieth-Complex-Figure-Test-(CFT).",
"homepage": "http://neurolog.unice.fr/ontoneurolog/v3.0/Documentation_OntoNeuroLOGv3.pdf",
"name": "Mental State Assessment",
"prefix": "ONL-MSA",
"version": "v1"
},
"ONL-TASKS": {
"contact": {
"email": "maxis81@gmail.com",
"name": "Maxim Bakaev"
},
"description": "This ontology is an extension of the OntoNeuroLOG ontology, developed in the context of a project supported by Russian Foundation for Basic Research (19-29-01017 grant). The ontology organizes tests that are used for assessing cognitive reserves with the focus on keywords that can be employed in mining of PubMed publications.",
"name": "Cognitive Reserves Assessment Tasks",
"prefix": "ONL-TASKS",
"publication": "http://ceur-ws.org/Vol-2648/paper3.pdf"
},
"ONLIRA": {
"contact": {
"email": "neda.marvasti@gmail.com",
"name": "neda barzegarmarvasti"
},
"description": "ONLIRA (Ontology of the Liver for Radiology) focuses on a semantic specification of imaging observations of CT scans for the liver. ONLIRA extends RadLex with semantic relationships that describe and relate the concepts. Thus, automated processing tasks, such as identifying similar patients, are supported.",
"homepage": "http://vavlab.ee.boun.edu.tr/pages.php?p=research/CARERA/carera.html",
"name": "Ontology of Liver for Radiology",
"prefix": "ONLIRA",
"publication": "http://vavlab.ee.boun.edu.tr/pages.php?p=research/CARERA/carera.html",
"version": "changes\n* Segments and Regions are modelling as Classes in order to identify which patient (liver) they belong to.\n* Redundant restrictions are removed"
},
"ONS": {
"contact": {
"email": "francesco.vitali@ibba.cnr.it",
"name": "Francesco Vitali"
},
"description": "Ontology For Nutritional Studies (ONS) is the first systematic effort to provide a formal ontology framework for the description of nutritional studies.",
"homepage": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies",
"name": "Ontology for Nutritional Studies",
"prefix": "ONS",
"publication": "https://doi.org/10.1186/s12263-018-0601-y",
"version": "2024-07-03"
},
"ONSTR": {
"contact": {
"email": "snez.sn@gmail.com",
"name": "Rani Singh, Snezana Nikolic"
},
"description": "Ontology for Newborn Screening Follow-up and Translational Research (ONSTR) is an application ontology covering the domain of newborn screening, follow-up and translational research pertaining to patients diagnosed with inheritable and congenital diseases mainly identified through newborn dried blood spot screening. ONSTR is a central component of the project Newborn Screening Follow-up Data Integration Collaborative (NBSDC). ONSTR uses the Basic Formal Ontology v2 (BFO2, v2012-07-20) as top-level ontology and extends the classes imported from OBO Foundry ontologies and candidate ontologies. For latest release notes please see: http://onstr.googlecode.com/svn/tags/currentRelease/2013-05-02/ NBSDC project page: https://nbsdc.org (under construction).",
"homepage": "http://code.google.com/p/onstr/",
"name": "Ontology for Newborn Screening Follow-up and Translational Research",
"prefix": "ONSTR",
"publication": "https://nbsdc.org/publications.php",
"version": "0.4"
},
"ONTOAD": {
"contact": {
"email": "Khadim.Drame@isped.u-bordeaux2.fr",
"name": "Khadim DramΓ©"
},
"description": "OntoAD is a bilingual (English-French) domain ontology for modeling knowledge about Alzheimer's Disease and Related Syndromes.",
"name": "Bilingual Ontology of Alzheimer's Disease and Related Diseases",
"prefix": "ONTOAD",
"version": "1.0"
},
"ONTOAVIDA": {
"contact": {
"email": "fortuna@ebd.csic.es",
"name": "Miguel A. Fortuna"
},
"description": "OntoAvida develops an integrated vocabulary for the description of the most widely-used computational approach for studying evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment).",
"homepage": "https://gitlab.com/fortunalab/ontoavida",
"name": "OntoAvida: ontology for Avida digital evolution platform",
"prefix": "ONTOAVIDA"
},
"ONTODM-ALGORITHM": {
"contact": {
"email": "pance.panov@ijs.si",
"name": "PanΔe Panov"
},
"description": "OntoDM-algorithms is an ontology for data mining and machine learning entities.",
"name": "OntoDM-core/algorithms",
"prefix": "ONTODM-ALGORITHM",
"version": "0.1"
},
"ONTODM-CORE": {
"contact": {
"email": "pance.panov@ijs.si",
"name": "Pance Panov"
},
"description": "OntoDM is a generic ontology for the domain of data mining. The ontology includes the information processing processes that occur in the domain of data mining, participants in the processes and their specifications. OntoDM is highly transferable and extendable due to its adherence to accepted standards, and compliance with existing ontology resources. The generality in scope allows wide number of applications of the ontology, such as semantic annotation of data mining scenarios, ontology based support for QSARs, etc.",
"homepage": "www.ontodm.com",
"name": "Ontology of Core Data Mining Entities",
"prefix": "ONTODM-CORE",
"publication": "http://link.springer.com/article/10.1007/s10618-014-0363-0#",
"version": "2.0"
},
"ONTODM-KDD": {
"contact": {
"email": "pance.panov@ijs.si",
"name": "Pance Panov"
},
"description": "OntoDM-KDD is an ontology for representing data mining investigations. Its goal is to allow the representation of knowledge discovery processes and be general enough to represent the data mining investigations. The ontology is based on the CRISP-DM process methodology.",
"homepage": "www.ontodm.com",
"name": "Ontology of Data Mining Investigations",
"prefix": "ONTODM-KDD",
"publication": "www.ontodm.com",
"version": "0.1"
},
"ONTODT": {
"contact": {
"email": "pance.panov@ijs.si",
"name": "Pance Panov"
},
"description": "This ontology contains entities such as: datatype, datatype generator, datatype qualiy and others giving the possibility to represent arbitrary complex datatypes. This is an important fact for a general data mining ontology that wants to represent and query over modelling algorithms for mining structured data. The ontology was first developed under the OntoDM (Ontology of Data Mining is available at http://kt.ijs.si/panovp/OntoDM) ontology, but for generality and reuse purpose it was decided to export it as a separate ontology. Additionaly, the OntoDT ontology is based on and ISO/IEC 11404 (http://www.iso.org/iso/catalogue_detail.htm?csnumber=39479) standard and can be reused used independently by any domain ontology that requires representation and reasoning about general purpose datatypes.",
"homepage": "http://www.ontodt.com",
"name": "Ontology of Datatypes",
"prefix": "ONTODT",
"publication": "http://www.sciencedirect.com/science/article/pii/S0020025515005800",
"version": "2.0"
},
"ONTOKBCF": {
"contact": {
"email": "xjing2007@googlemail.com",
"name": "Xia Jing"
},
"description": "OntoKBCF is an ontological knowledge base model for cystic fibrosis. There are molecular genetic information (i.e. gene mutations) and health information included in OntoKBCF. The purposes of OntoKBCF include management of molecular genetic information and health information and embedding OntoKBCF into EHR settings.",
"name": "Ontological Knowledge Base Model for Cystic Fibrosis",
"prefix": "ONTOKBCF",
"version": "1301"
},
"ONTOLURGENCES": {
"contact": {
"email": "Jean.Charlet@upmc.fr",
"name": "Jean Charlet"
},
"description": "Emergency care ontology build during LERUDI project. http://www.ncbi.nlm.nih.gov/pubmed/25160343 (v4.0)",
"name": "Emergency care ontology",
"prefix": "ONTOLURGENCES",
"version": "3.0.4"
},
"ONTOMA": {
"contact": {
"email": "martinsanou@lavima.org",
"name": "SANOU MARTIN"
},
"description": "Common concepts for communication between traditional medicine and western medicine. (In French)",
"homepage": "www.lavima.org",
"name": "Ontology of Alternative Medicine, French",
"prefix": "ONTOMA",
"publication": "www.lavima.org/ontoma_1_1.html",
"version": "Version 1.1Date: 11-2011"
},
"ONTONEO": {
"contact": {
"email": "fernanda.farinelli@gmail.com",
"name": "Fernanda Farinelli"
},
"description": "The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby.",
"homepage": "https://ontoneo.com/",
"name": "Obstetric and Neonatal Ontology",
"prefix": "ONTONEO",
"publication": "https://github.com/ontoneo-project/Ontoneo",
"version": "2021-04-29"
},
"ONTOPARON": {
"contact": {
"email": "jean.charlet@upmc.fr",
"name": "Jean Charlet"
},
"description": "Ontology of ALS (amyotrophic lateral sclerosis), social module + coordination module + medical module developped by neurologists (ICM) and knowledge engineers (LIMICS). This version (11/15/2018) is upload with inferred axioms but without equivalent classe axioms. It serves in this version in a Gate pipeline for a semantic annotation task. This version (03/20/2019) is upload with object properties, inferred axioms and equivalent classes axioms. This version (11/10/2020) is uploaded with small corrections.",
"name": "Ontology of Amyotrophic Lateral Sclerosis, all modules",
"prefix": "ONTOPARON",
"version": "1.1"
},
"ONTOPARON_SOCIAL": {
"contact": {
"email": "jean.charlet@upmc.fr",
"name": "Jean Charlet"
},
"description": "Ontology of ALS (amyotrophic lateral sclerosis), social module developped by neurologist (ICM) and knowledge engineers (LIMICS). Complete version available at http://bioportal.bioontology.org/ontologies/ONTOPARON",
"name": "Ontology of amyotrophic lateral sclerosis, social module",
"prefix": "ONTOPARON_SOCIAL",
"version": "1.0"
},
"ONTOPBM": {
"contact": {
"email": "ilin.tolovski@ijs.si",
"name": "Ilin Tolovski"
},
"description": "OntoPBM is an ontology of core entities for process-based modeling of dynamical systems.",
"name": "Ontology for Process-Based Modeling of Dynamical Systems (OntoPBM)",
"prefix": "ONTOPBM",
"version": "0.1"
},
"ONTOPNEUMO": {
"contact": {
"email": "jean.charlet@upmc.fr",
"name": "Jean Charlet"
},
"description": "Ontology of pneumology (french version). The ONTOPNEUMO ontology was developped by Audrey Baneyx, under the direction of Jean Charlet about knowledge engineering expertise and by FranΓ§ois-Xavier Blanc in collaboration with Bruno Housset about medical expertise. The OWL compliant ONTOPNEUMO ontology is available under Creative Commons license βAttribution-Non-Commercial-No Derivative Works 2.0 UKβ. Details of this license are accessible at : http://creativecommons.org/licenses/ by-nc-nd/2.0/uk/.",
"name": "Ontology of Pneumology",
"prefix": "ONTOPNEUMO",
"version": "0.1"
},
"ONTOPSYCHIA": {
"contact": {
"email": "Jean.Charlet@upmc.fr",
"name": "Jean Charlet"
},
"description": "Ontology of social and environmental determinants for psychiatry",
"name": "OntoPsychia, social module",
"prefix": "ONTOPSYCHIA",
"version": "1.0"
},
"ONTOREPLICOV": {
"contact": {
"email": "ladwissam@hotmail.com",
"name": "Wissame Laddada"
},
"description": "OntoRepliCov is an ontology designed to describe the different stages of the SARS-CoV-2 replication process.",
"name": "OntoRepliCov",
"prefix": "ONTOREPLICOV",
"version": "0"
},
"ONTOSIM": {
"contact": {
"email": "dciriaco@ime.usp.br",
"name": "Debora Lina Ciriaco"
},
"description": "[pt] A Ontologia do SIM foi desenvolvida no contexto do projeto DIASUS. Ela buscou resgatar a estrutura presente na ficha de preenchimento da Declaração de Γbito - DO, do Sistema de Informação de Mortalidade - SIM, do Sistema Γnico de SaΓΊde, do Brasil. [en] The SIM Ontology was developed in the context of DIASUS project. This ontology intent to rescue the data structure presented in Death Certificate form, from Information System on Mortality - SIM, from Brazilian Public Health System - SUS.",
"name": "The Ontology of Information System on Mortality",
"prefix": "ONTOSIM",
"version": "1.0.0"
},
"ONTOSINASC": {
"contact": {
"email": "dciriaco@ime.usp.br",
"name": "Debora Lina Ciriaco"
},
"description": "[pt] A Ontologia do SINASC foi desenvolvida no contexto do projeto DIASUS. Ela buscou resgatar a estrutura presente na ficha de preenchimento da Declaração de Nascido Vivo - DN, do Sistema de Informação de Nascidos Vivos - SINASC, do Sistema Γnico de SaΓΊde, do Brasil. [en] The SINASC Ontology was developed in the context of DIASUS project. This ontology intent to rescue the data structure presented in Live Birth Certificate form, from Information System on Live Births - SINASC, from Brazilian Public Health System - SUS.",
"name": "Ontology of Information System on Live Births",
"prefix": "ONTOSINASC",
"version": "1.0.0"
},
"ONTOTOX": {
"contact": {
"email": "alice.rogier@inserm.fr",
"name": "Alice Rogier"
},
"description": "OntoTox is an ontology designed to represent chemotherapy toxicities extracted from various data in Clinical Data Warehouses. OntoTox can integrate toxicities and grading information extracted from heterogeneous sources. Examples of OntoTox instantiations can be found in GitHub : https://github.com/TeamHeka/OntoTox",
"homepage": "https://github.com/TeamHeka/OntoTox",
"name": "Chemotherapy Toxicities Ontology",
"prefix": "ONTOTOX",
"version": "1.0"
},
"ONTOTOXNUC": {
"contact": {
"email": "marie-therese.menager@cea.fr",
"name": "Marie-Thérèse Ménager"
},
"description": "Ontology of nuclear toxicity developed during ToxNuc project <>.",
"name": "Ontology of Nuclear Toxicity",
"prefix": "ONTOTOXNUC",
"version": "1.0"
},
"ONTRISCAL": {
"contact": {
"email": "evaldo.oliveira@gmail.com",
"name": "EVALDO DE OLIVEIRA DA SILVA"
},
"description": "This ontology organizes concepts and properties of risk stratification in mental health. Stratification aims to determine the patient's risk level by scoring signs and symptoms. Psychotherapeutic treatments aim to minimize patient risk by producing qualitative data reported in therapeutic sessions. Thus, the ONTRISCAL is applied in projects that organize the knowledge about quali-quanti data produced by risk stratification and mental health treatments. Quali-quanti data, semantically annotated by ONTRISCAL, can be ingested into knowledge graphs. Domain specialists can use knowledge graphs to navigate the ONTRISCAL concepts, analyze psychotherapeutic treatments, and control risks in mental health. This is a non-profit and open-source project.",
"name": "Ontology of Risk Stratification in Mental Health",
"prefix": "ONTRISCAL",
"version": "1.0"
},
"OOEVV": {
"contact": {
"email": "gully@usc.edu",
"name": "Gully Burns"
},
"description": "The ontology of experimental variables and values provides a lightweight representation of (a) the variables used to measure experimental properties and (b) the measurement scales that form the complex data types supporting that data. Many different variables measure the same thing, here we use a lightweight representation driven by a small number of classes and a large number of variables to focus only on providing a vocabulary of variables that may be extended for consolidation to standardized variables for specific things and functions to map between values from different measurements scales. We use the base ontology description to provide a very lightweight representation of the basic elements of an experimental design and we use views to instantiate it for specific domains.",
"homepage": "http://bmkeg.isi.edu",
"name": "Ontology of Experimental Variables and Values",
"prefix": "OOEVV",
"publication": "http://www.isi.edu/research_groups/bmkeg/publications",
"version": "0.0.4"
},
"OOSTT": {
"contact": {
"email": "MBrochhausen@uams.edu",
"name": "Mathias Brochhausen"
},
"description": "The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2). It is developed collaboratively by domain and ontology experts in the NIH-funded CAFE (Comparative Assessment Framework for Environments of trauma care) project (1R01GM111324-01A1). It will be used as the ontology backbone of a graphical user interface comparing graphical representations of organizational structures.",
"homepage": "https://github.com/OOSTT/OOSTT",
"name": "Ontology of Organizational Structures of Trauma centers and Trauma systems",
"prefix": "OOSTT",
"version": "release version - 2024-01-25"
},
"OPB": {
"contact": {
"email": "dcook@u.washington.edu",
"name": "Daniel L. Cook"
},
"description": "The OPB is a reference ontology of classical physics and thermodynamics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (atoms to organisms) and multiple physical domains (fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.",
"homepage": "https://sites.google.com/site/semanticsofbiologicalprocesses/projects/the-ontology-of-physics-for-biology-opb",
"name": "Ontology of Physics for Biology",
"prefix": "OPB",
"publication": "http://dx.plos.org/10.1371/journal.pone.0028708",
"version": "1.2"
},
"OPD-NAMBOBI": {
"contact": {
"email": "amnambobi@gmail.com",
"name": "Nambobi Mutwalibi"
},
"description": "Objective:\t\tTo\treport cases of notifiable diseases, other diseases of\tpublic health importance.",
"name": "SELECTED OTHER PRIORITY DISEASES UNDER IDSR (INTEGRATED DISEASE SURVEILLANCE AND RESPONSES)",
"prefix": "OPD-NAMBOBI"
},
"OPDE": {
"contact": {
"email": "getu.tadele@gmail.com",
"name": "Getu Tadele Taye"
},
"description": "This is an OPD Registry Form in Ethiopia.",
"name": "OPD-Ethiopia",
"prefix": "OPDE"
},
"OPDRE": {
"contact": {
"email": "getu.tadele@gmail.com",
"name": "Getu Tadele Taye"
},
"description": "Out patient registry that is used in health facilities in Ethiopia.",
"name": "OPD Regitry Ethiopia",
"prefix": "OPDRE",
"version": "0.0.1"
},
"OPDRONT": {
"contact": {
"email": "jayyil0617@gmail.com",
"name": "Jay"
},
"description": "Vocabulary creation for OPD Register: MINISTRY OF HEALTH AND CHILD CARE",
"name": "OPD Register Ontology",
"prefix": "OPDRONT",
"version": "0.0.1"
},
"OPDT": {
"contact": {
"email": "christine99x@gmail.com",
"name": "Cheng"
},
"description": "opd test for group 2",
"name": "opd_test",
"prefix": "OPDT"
},
"OPDZIMBABWE": {
"contact": {
"email": "aleka.aktau@gmail.com",
"name": "Aliya Aktau"
},
"description": "OPD Terms that are used in Zimbabwe.",
"name": "OPDZimbabwe",
"prefix": "OPDZIMBABWE",
"version": "1.1"
},
"OPE": {
"contact": {
"email": "foustjc@stanford.edu",
"name": "Juan-Carlos Foust"
},
"description": "The Ontology of Physical Exercises (OPE) provides a reference for describing an exercise in terms of functional movements, engaged musculoskeletal system parts, related equipment or monitoring devices, intended health outcomes, as well as target ailments for which the exercise might be employed as a treatment or preventative measure.",
"name": "Ontology of Physical Exercises",
"prefix": "OPE",
"version": "0.0.1"
},
"OPL": {
"contact": {
"email": "preets79@gmail.com",
"name": "Priti Parikh"
},
"description": "The Ontology for Parasite LifeCycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.",
"homepage": "http://knoesis.wright.edu/trykipedia/parasitelifecycle",
"name": "Ontology for Parasite LifeCycle",
"prefix": "OPL",
"publication": "http://knoesis.wright.edu/trykipedia/parasitelifecycle",
"version": "2023-08-28"
},
"OPMI": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "The Ontology of Precision Medicine and Investigation (OPMI) is an application ontology to support precision medicine and its related investigations. OPMI is community-driven and developed by following the OBO Foundry ontology development principles. OPMI reuses, aligns, and integrates related terms from existing OBO ontologies.",
"homepage": "https://github.com/OPMI/opmi",
"name": "Ontology of Precision Medicine and Investigation",
"prefix": "OPMI",
"version": "Vision Release: 1.0.166"
},
"OPTIMAL": {
"contact": {
"email": "livitckaia@gmail.com",
"name": "Kristina Livitckaia"
},
"description": "OPTImAL is a reusable formal model of factors affecting CVD patient adherence to physical activity and exercise. The basis for this model relies on the analysis of data/evidence published in the scientific literature and enables identification of adherence based on the patient profile. In the model, the patient profile is seen from the perspective of 60 multidimensional aspects (320 factors). Each factor is associated with defined adherence to a particular patient activity behavior.",
"name": "OPTImAL: An ontology for patient adherence modeling in physical activity domain",
"prefix": "OPTIMAL",
"version": "1"
},
"OPTION-ONTOLOGY": {
"contact": {
"email": "ana.kostovska@ijs.si",
"name": "Ana Kostovska"
},
"description": "OPTImization Algorithm Benchmarking ONtology",
"name": "Optimization Algorithm Benchmarking Ontology",
"prefix": "OPTION-ONTOLOGY",
"version": "1.0.0"
},
"ORCS": {
"contact": {
"email": "hoganwr@gmail.com",
"name": "William R. Hogan"
},
"description": "The Ontology for Representing CDM Semantics (ORCS) is an application ontology that was developed to transform common-data-model-based data into ontologically-based data such as RDF, RDF*, OWL2, or Referent Tracking tuples. Although initially developed for such transformations of PCORnet Common Data Model (CDM) based data, ongoing and future work involves other CDMs such as OMOP.",
"homepage": "https://github.com/ufbmi/ORCS",
"name": "Ontology for Representing CDM Semantics",
"prefix": "ORCS",
"version": "2021-11-13"
},
"ORDO": {
"contact": {
"email": "ordo.orphanet@inserm.fr",
"name": "Ana Rath"
},
"description": "The Orphanet Rare Disease ontology (ORDO) is jointly developed by Orphanet and the EBI to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It derived from the Orphanet database (www.orpha.net ) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, SNOMED CT, UMLS, MedDRA),databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10). The ontology will be maintained by Orphanet and further populated with new data. Orphanet classifications can be browsed in the OLS view. The Orphanet Rare Disease Ontology is updated monthly and follows the OBO guidelines on deprecation of terms. It constitutes the official ontology of rare diseases produced and maintained by Orphanet (INSERM, US14).",
"homepage": "https://www.orpha.net",
"name": "Orphanet Rare Disease Ontology",
"prefix": "ORDO",
"version": "4.5"
},
"OREX-SAM": {
"contact": {
"email": "smrTucson@gmail.com",
"name": "Stephen M Richard"
},
"description": "Sample types from JSC-SAMIS Interface Control Document. Edited by S.M. Richard. These sample types are limited to those expected from the OSIRIS-REx sample return, this is not an exhaustive sample type categorization.",
"name": "OSIRIS-REx sample type",
"prefix": "OREX-SAM",
"version": "0.2.0"
},
"OREX-WG": {
"contact": {
"email": "smrTucson@gmail.com",
"name": "Stephen M Richard"
},
"description": "Workgroups organized to analyzed samples returned by OSIRIS-REx mission from asteroid Bennu. Mostly for reference in other metadata records.",
"name": "OSIRIS-REx sample analysis workgroups",
"prefix": "OREX-WG",
"version": "0.1.0"
},
"ORNASEQ": {
"contact": {
"email": "safisher@upenn.edu",
"name": "Stephen Fisher"
},
"description": "This is an application ontology used to annotate next-generation sequencing experiments performed on RNA (RNAseq). It uses terms from BFO, CHEBI, CL, GENEPIO, GO, IAO, NCBITaxon, NCIT, OBI, OBIws, OGMS, OMIABIS, SO, TAXRANK, and UBERON as well as EFO.",
"homepage": "http://kim.bio.upenn.edu/software/ornaseq.shtml",
"name": "Ontology of RNA Sequencing",
"prefix": "ORNASEQ"
},
"ORTH": {
"contact": {
"email": "jfernand@um.es",
"name": "Jesualdo TomΓ‘s FernΓ‘ndez-Breis"
},
"description": "Orthology Ontology",
"homepage": "https://github.com/qfo/OrthologyOntology",
"name": "Orthology Ontology",
"prefix": "ORTH",
"publication": "http://www.jbiomedsem.com/content/7/1/34",
"version": "2.0"
},
"OVAE": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "The Ontology of Vaccine Adverse Events (OVAE) is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the Ontology of Adverse Events (OAE) and the Vaccine Ontology (VO). OVAE is aimed to represent and analyze various vaccine-specific adverse events.",
"homepage": "http://www.violinet.org/ovae",
"name": "Ontology of Vaccine Adverse Events",
"prefix": "OVAE",
"version": "Vision Release: 1.0.34"
},
"OntoVIP": {
"contact": {
"email": "bernard.gibaud@univ-rennes1.fr",
"name": "Bernard Gibaud"
},
"description": "The OntoVIP ontology was developed in the context of the Virtual Imaging Platform project (VIP), a french project supported by ANR (ANR-09-COSI-03 grant) aiming at sharing medical image simulation resources. This ontology describes the content of the models used in medical image simulation. This ontology can be used to annotate such models in order to highlight the different entities that are present in the 3D scene to be imaged, i.e. anatomical structures, pathological structures, foreign bodies, contrast agents etc. The model allows also to associate to these entities information about their physical qualities, which are used in the medical image simulation process (to mimick physical phenomena involved in CT, MR, US and PET imaging). This ontology partly relies on the OntoNeuroLOG ontology (ONL-DP ONL-MR-DA), as well as PATO, RadLex, FMA and ChEBI.",
"homepage": "http://vip.creatis.insa-lyon.fr/ontovip/v1.0/Documentation_OntoVIPv1.pdf",
"name": "Medical image simulation",
"prefix": "OntoVIP",
"version": "v1"
},
"PACO": {
"contact": {
"email": "rtaira@ucla.edu",
"name": "Ricky Taira"
},
"description": "Physical Activity Concept Ontology (PACO) contains various concepts that are required to describe one's physical activity.",
"name": "Physical Activity Ontology",
"prefix": "PACO",
"version": "0.2"
},
"PAE": {
"contact": {
"email": "jaiswalp@science.oregonstate.edu",
"name": "Pankaj Jaiswal"
},
"description": "REPLACED BY: Plant Ontology (PO). A controlled vocabulary of plant morphological and anatomical structures representing organs, tissues, cell types, and their biological relationships based on spatial and developmental organization. Note that this has been subsumed into the PO. This file is created by filtering plant_ontology_assert.obo to contain only terms from the plant anatomical entity branch of the PO. For more information, please see: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/",
"homepage": "http://www.plantontology.org",
"name": "Plant Anatomy",
"prefix": "PAE",
"version": "Release #20"
},
"PAINO": {
"contact": {
"email": "jaya.1.chaturvedi@kcl.ac.uk",
"name": "Jaya Chaturvedi"
},
"description": "A lexicon of pain terms that have been reviewed by 2 clinicians and a patient and public involvement group of people with lived experiences of chronic pain.",
"name": "Pain Ontology",
"prefix": "PAINO",
"publication": "https://www.frontiersin.org/articles/10.3389/fdgth.2021.778305/full",
"version": "1.0.0"
},
"PANDA": {
"contact": {
"email": "larisa.soldatova@brunel.ac.uk",
"name": "Larisa Soldatova"
},
"description": "Probabilistic Knowledge Assembly (PANDA) Ontology has been developed in the context of the DARPA's Big Mechanism research program. It provides a semantic interface for capturing information on molecular interactions extracted from scientific texts.",
"name": "Probabilistic Knowledge Assembly Ontology",
"prefix": "PANDA",
"version": "0.9"
},
"PANET": {
"contact": {
"email": "mriyayi@hotmail.com",
"name": "Daniel Iyayi"
},
"description": "The PaNET ontology provides a taxonomy and thesaurus of photon and neutron (PaN) experimental techniques, based mainly on accelerator-based light sources and neutron facilities. The primary use of the ontology is to enhance the FAIRness of PaN data catalogues services. The ontology defines specific techniques in terms of more general technique classes and provides synonyms and references.",
"name": "PaN Experimental technique",
"prefix": "PANET",
"publication": "https://doi.org/10.5281/zenodo.4806026",
"version": "1.0.0-3-g6a0b629-dirty"
},
"PARTUMDO": {
"contact": {
"email": "bolandm@upenn.edu",
"name": "Mary Regina Boland"
},
"description": "This ontology is for use in extracting postpartum depression condition codes, and also comorbidities and diseases often mistaken for postpartum depression. The ontology describes not only the codes but also the relationships between these various diseases/risk factors for use in automatically extracting relevant patient populations from Electronic Health Records",
"name": "postpartum depression ontology",
"prefix": "PARTUMDO"
},
"PATAXO": {
"contact": {
"email": "li.yixuan727@gmail.com",
"name": "Yixuan LI"
},
"description": "PATAXO is a bilingual Chinese-English technical taxonomy for patent-related technology domains using the International Patent Classification (IPC).",
"name": "Technical Taxonomies for Patents",
"prefix": "PATAXO",
"version": "1.0.0"
},
"PATCT": {
"contact": {
"email": "PATUserSupport@mail.nih.gov",
"name": "PATUserSupport"
},
"description": "Cell types associated with placental structure and function. This Cell Type ontology builds on the Cell Ontology (CL) as well as the BRENDA Tissue and Enzyme Source Ontology (BTO) and was further developed by PAT External Scientific Panel Members and contributions from other subject matter experts.",
"name": "Placental Cell Type",
"prefix": "PATCT",
"version": "1.0"
},
"PATEL": {
"contact": {
"email": "archanamca92@gmail.com",
"name": "Archana"
},
"description": "Covid19 Impact on Banking Ontology (Covid19-IBO) provides semantic information about the impact of the Covid-19 on the banking sector of India",
"name": "Archana Patel",
"prefix": "PATEL",
"version": "1"
},
"PATGV": {
"contact": {
"email": "PATUserSupport@mail.nih.gov",
"name": "PATUserSupport"
},
"description": "Includes variations of DNA sequence, chromosomal structure and copy number, as well as RNA and translational variation. The Genetic Variation ontology expands on work done for Variation Ontology (VariO) and Sequence Types and Features Ontology (SO) which can be found on NCBO. This ontology was further developed by PAT External Scientific Panel Members and contributions from other subject matter experts.",
"name": "Placental Genetic Variance",
"prefix": "PATGV",
"version": "1.0"
},
"PATHLEX": {
"contact": {
"email": "christel.daniel@crc.jussieu.fr",
"name": "Christel Daniel"
},
"description": "PathLex, a comprehensive lexiconβa unified language of anatomic pathology termsβfor standardized indexing and retrieval of anatomic pathology information resources.",
"name": "Anatomic Pathology Lexicon",
"prefix": "PATHLEX",
"version": "1.2"
},
"PATIT": {
"contact": {
"email": "PATUserSupport@mail.nih.gov",
"name": "PATUserSupport"
},
"description": "Experimental methods and observation types used in placental research. The PAT Investigative Techniques ontology builds on work done for a handful of existing ontologies, including the Ontology for Biomedical Investigations (OBI) and NCI Thesaurus (NCIT), and was further developed by PAT External Scientific Panel Members and contributions from other subject matter experts.",
"name": "Placental Investigative Technique",
"prefix": "PATIT",
"version": "1.0"
},
"PATMHC": {
"contact": {
"email": "PATUserSupport@mail.nih.gov",
"name": "PATUserSupport"
},
"description": "Physical and psychological disorders in the mother that occur during pregnancy, childbirth, and the postpartum period. These include both pre-existing and gestational maternal health conditions that may result in adverse pregnancy outcomes. The Maternal Conditions Ontology builds on the work done for a handful of existing ontologies, including the Human Phenotype Ontology (HPO) and NCI Thesaurus (NCIT), and was further developed by PAT External Scientific Panel Members and contributions from other subject matter experts.",
"name": "Placental Maternal Health Conditions",
"prefix": "PATMHC",
"version": "1.0"
},
"PATO": {
"contact": {
"email": "g.gkoutos@gmail.com",
"name": "George Gkoutos"
},
"description": "Phenotypic qualities (properties). This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested.",
"homepage": "https://github.com/pato-ontology/pato/",
"name": "Phenotypic Quality Ontology",
"prefix": "PATO",
"version": "2024-03-28"
},
"PAV": {
"contact": {
"email": "stian@soiland-reyes.com",
"name": "Stian Soiland-Reyes"
},
"description": "PAV is a lightweight ontology for tracking Provenance, Authoring and Versioning. PAV specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources. This ontology describes the defined PAV properties and their usage. Note that PAV does not define any explicit classes or domain/ranges, as every property is meant to be used directly on the described online resource.",
"homepage": "https://github.com/pav-ontology/pav/",
"name": "PAV Provenance, Authoring and Versioning",
"prefix": "PAV",
"publication": "https://github.com/pav-ontology/pav/wiki/Publications",
"version": "2.3.1"
},
"PAYMENTMODE": {
"contact": {
"email": "vinutha_rk@yahoo.com",
"name": "Vinutha Venkatesh"
},
"description": "This class refers to the different payment methods.",
"name": "Payment Mode",
"prefix": "PAYMENTMODE"
},
"PAYOR": {
"contact": {
"email": "vinutha_rk@yahoo.com",
"name": "Vinutha Venkatesh"
},
"description": "This class refers to the entity that made the payment on behalf of the interviewee.",
"name": "Payor",
"prefix": "PAYOR"
},
"PBPKO": {
"name": "Physiologically Based Pharmacokinetic ontology",
"prefix": "PBPKO"
},
"PCALION": {
"contact": {
"email": "743434289@qq.com",
"name": "Chunjiang Yu"
},
"description": "PCLiON:Prostate Cancer Lifestyle Ontology",
"homepage": "http://pcaontology.net/PCaLifeStyleDefault.aspx",
"name": "Prostate Cancer Lifestyle Ontology",
"prefix": "PCALION",
"publication": "http://pcaontology.net/PCaLifeStyleDefault.aspx",
"version": "3.0"
},
"PCAO": {
"contact": {
"email": "743434289@qq.com",
"name": "Chunjiang Yu"
},
"description": "Here, we introduce the Prostate cancer ontology (PCaO) as a comprehensive semantic framework covering the whole breadth of the PCaβs knowledge domain. This ontology with a subclass-based taxonomic hierarchy not only covers the broad spectrum of major biomedical concepts from molecular to clinical features of the disease, but also the different views on disease features held by molecular biologists, clinicians and drug developers. PCaO organized under three biological viewpoints, i.e., epidemiology, diagnosis, and treatment. Note: The prostate cancer ontology version 1.0 (PCAO 1.0) was published by Hua Min in 2009 (PMID: 19497389).",
"homepage": "http://pcaontology.net",
"name": "Prostate Cancer Ontology",
"prefix": "PCAO",
"publication": "http://pcaontology.net",
"version": "2.0"
},
"PCL": {
"contact": {
"email": "davidos@ebi.ac.uk",
"name": "David Osumi-Sutherland"
},
"description": "Cell types that are provisionally defined by experimental techniques such as single cell or single nucleus transcriptomics rather than a straightforward & coherent set of properties.",
"homepage": "https://github.com/obophenotype/provisional_cell_ontology",
"name": "Provisional Cell Ontology",
"prefix": "PCL",
"publication": "https://doi.org/10.1101/2021.10.10.463703",
"version": "2024-07-11"
},
"PCMO": {
"description": "Pediatric Consultation and Monitoring Ontology consists of 10 main classes, 10 sub-classes, 39 properties (object-type and sub-object-type properties, data type), numerous OWL individuals and almost 90 SWRL rules (medical cases based on ARTI based diseases for pediatric patients). Almost all the rules of the knowledge base consider: -Body temperature -Currently observed number of the local, major, and minor symptoms -Medications used and time of use in recent period (has drug and has drug time properties) -Presence of medical cold treatment applied in recent period β only one of medical case will be inferencing result. Project Funding: βThis research project was funded in 2014 by the National Science Foundation- The Scientific and Technological Research Council of Turkey (TUBITAK) under 1501 type funding program with the β3140417β grant number. The titled βMobile Pediatric Consultation and Monitoring Systemβ project was successfully completed by the end of 2015. The project was completed by collaboration of the AcΔ±badem Hospitals Group, Istanbul Aydin University and Semantica Internet and Software Services Trd. Ltd. Company in Turkeyβ.",
"name": "Pediatric Consultation and Monitoring Ontology",
"prefix": "PCMO",
"version": "v.4.0"
},
"PCO": {
"contact": {
"email": "rlwalls2008@gmail.com",
"name": "Ramona Walls"
},
"description": "The Population and Community Ontology (PCO) models material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. The PCO is complient with the Basic Formal Ontology (BFO) and is designed to be compatible with other OBO Foundry ontologies.",
"homepage": "https://github.com/PopulationAndCommunityOntology/pco",
"name": "Population and Community Ontology",
"prefix": "PCO",
"version": "2013-10-03"
},
"PDO": {
"contact": {
"email": "hmori@bio.titech.ac.jp",
"name": "MicrobeDB.jp Project Team"
},
"description": "An ontology for describing both human infectious diseases caused by microbes and the diseases that is related to microbial infection.",
"homepage": "http://mdb.bio.titech.ac.jp/pdo",
"name": "Pathogenic Disease Ontology",
"prefix": "PDO",
"version": "Version 0.7"
},
"PDON": {
"contact": {
"email": "erfan.younesi@scai.fraunhofer.de",
"name": "Erfan Younesi"
},
"description": "Here, we introduce the Parkinsonβs disease ontology (PDO) as a comprehensive semantic framework covering the whole breadth of the Parkinsonβs knowledge domain. This ontology with a subclass-based taxonomic hierarchy not only covers the broad spectrum of major biomedical concepts from molecular to clinical features of the disease, but also the different views on disease features held by molecular biologists, clinicians and drug developers. This resource has been created for use in the IMI-funded AETIONOMY project (www.aetionomy.org).",
"name": "Parkinson's Disease Ontology",
"prefix": "PDON",
"version": "1.0"
},
"PDO_CAS": {
"contact": {
"email": "openresources@mail.las.ac.cn",
"name": "Ma Yumeng, Huang Jinxia, Liu Fenghong,Xu Zheping, Guo Jinjing, Cui Jinzhong, Sun Tan"
},
"description": "Plant Diversity Ontology (PDO) is the outcome of the construction tasks of domain ontology of science in the project of Scientific & Technological Knowledge Organization Systems (STKOS). The structure of PDO centers on species, including micro level of molecular, cell and tissue, medium level of plant organs, species and population, and macro level of ecosystem. The classes of PDO also capture the habitat, environmental conditions and expand the general characteristics of plants, completing the instances richness for plant species, geographical, classification and morphology. Furthermore, PDO builds the relationships among species, region, morphology, plant organs, developmental stage, revealing the list of species in an area, the morphology and life form of plants, and development process of species. In sum, PDO shows a growth process or development stage of a species and its structure characteristics in particular space and time scale, realizing the description of species diversity, ecosystem diversity and genetic diversity. At present, PDO has been applied to the platform of Go to Selected Open Access Journals (GoOA) developed by National Science Library of Chinese Academy of Sciences, supporting concept retrieval and concept extension for GoOA.",
"homepage": "http://gooa.las.ac.cn/external/index.jsp",
"name": "Plant Diversity Ontology",
"prefix": "PDO_CAS",
"publication": "http://124.16.154.130:8080/lis/CN/10.13266/j.issn.0252-3116.2015.03.017"
},
"PDQ": {
"contact": {
"email": "volker@mail.nih.gov",
"name": "Volker Englisch"
},
"description": "Physician Data Query (PDQ) Terminology is part of NCI's comprehensive cancer information database, which contains expert summaries on a wide range of cancer topics, a listing of some 30,000 cancer clinical trials from around the world, a directory of genetics services professionals, the NCI Dictionary of Cancer Terms, and the NCI Drug Dictionary.",
"name": "Physician Data Query",
"prefix": "PDQ",
"version": "2023AB"
},
"PDRO": {
"contact": {
"email": "ryeyan.taseen@gmail.com",
"name": "Ryeyan Taseen"
},
"description": "PDRO is a realist ontology that aims to represent the domain of drug prescriptions. Such an ontology is currently missing in the OBOFoundry and is highly relevant to the domains of existing ontologies like DRON, OMRSE and OAE. PDROβs central focus is the structure of a drug prescription, which is represented as a mereology of informational entities. Our current use cases are (1) refining this structure (e.g., adding closure axioms, cardinality, datatype bindings, etc) for prospectively standardizing local electronic prescriptions and (2) annotating prescription data of differing EHRs for detecting inappropriate prescriptions using a central semantic framework. Future ontological work will include aligning PDRO more closely with the Document Acts Ontology.",
"homepage": "https://github.com/OpenLHS/PDRO",
"name": "The Prescription of Drugs Ontology",
"prefix": "PDRO"
},
"PDUMDV": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "Life cycle stages for Platynereis dumerilii.",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies",
"name": "Platynereis Developmental Stages",
"prefix": "PDUMDV"
},
"PE": {
"contact": {
"email": "liqin.j.wang@gmail.com",
"name": "Liqin Wang"
},
"description": "A controlled vocabulary of PE-relevant information. Currently, only treatment information is available.",
"name": "Pulmonary Embolism Ontology",
"prefix": "PE",
"publication": "http://www.sciencedirect.com/science/article/pii/S0933365716300689",
"version": "version 1.0"
},
"PE-O": {
"contact": {
"email": "samizuno@med.tohoku.ac.jp",
"name": "Satoshi Mizuno"
},
"description": "The PEO incorporates a wide range of key concepts and terms of PE from clinical and biomedical research in structuring the knowledge base that is specific to PE.",
"name": "Pre-eclampsia Ontology",
"prefix": "PE-O",
"version": "v15\nHeneka comments / shifs / modifications integrated"
},
"PEAO": {
"contact": {
"email": "peaoteam@gmail.com",
"name": "PEAO Team"
},
"description": "The Plant domain has been the subject of several attempts to structure and formally define terms and corresponding relations, such as their anatomical features, developmental stages, and the application of particular experimental procedures to a biological problem. However, a focus on experimental assays in order to describe the whole experimental procedure, to the best of our knowledge, has only been attempted in the context of a very general description based on classical views of the scientific method. In this study, we focus on the development and proposal of an ontology dedicated to the description of these experimental procedures, regardless of the scientific questions that prompted the assays. This ontology includes entities from three distinct realms (biological, physical and data), which include both experimental products, their relations and the protocols describing their manipulation. The final outcome is a useful and comprehensive ontology in the plant domain, to be used as a log book by experimentalists, providing a formal relation between entities.",
"homepage": "https://bitbucket.org/PlantExpAssay/ontology",
"name": "Plant Experimental Assay Ontology",
"prefix": "PEAO"
},
"PECO": {
"contact": {
"email": "jaiswalp@science.oregonstate.edu",
"name": "Pankaj Jaiswal"
},
"description": "The Plant Experimental Conditions Ontology describes the treatments, growing conditions, and/or study types used in plant biology experiments. The subjects of the studies may also include in vitro plant structures (PO:0000004). A plant treatment is the most specific,and may be a component of a plant growing condition, and the plant study type. The broadest classes are the plant study types where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own and it may also involve instances of biotic and abiotic treatments and different growing conditions.",
"homepage": "http://browser.planteome.org/amigo/term/EO:0007359",
"name": "Plant Experimental Conditions Ontology",
"prefix": "PECO",
"publication": "http://planteome.org/pub",
"version": "releases/2023-11-10"
},
"PEDTERM": {
"contact": {
"email": "srivastava_ranjana@bah.com",
"name": "Ranjana Srivastava"
},
"description": "Terms associated with pediatrics, representing information related to child health and development from pre-birth through 21 years of age; contributed by the National Institute of Child Health and Human Development.",
"name": "Pediatric Terminology",
"prefix": "PEDTERM",
"version": "Version 2.0"
},
"PEO": {
"contact": {
"email": "priti@knoesis.org",
"name": "Priti Parikh"
},
"description": "The Parasite Experiment Ontology (PEO) models provenance metadata associated with experiment protocols used in parasite research. The PEO extends the upper-level Provenir ontology (http://knoesis.wright.edu/provenir/provenir.owl) to represent parasite domain-specific provenance terms. The PEO (v 1.0) includes Proteome, Microarray, Gene Knockout, and Strain Creation experiment terms along with other terms that are used in pathway.",
"homepage": "http://wiki.knoesis.org/index.php/Parasite_Experiment_ontology",
"name": "Parasite Experiment Ontology",
"prefix": "PEO",
"publication": "http://wiki.knoesis.org/index.php/Parasite_Experiment_ontology",
"version": "1"
},
"PESONT": {
"contact": {
"email": "patceeng@gmail.com",
"name": "Patience U. Usip"
},
"description": "Preposition-enabled Spatial Ontology (PeSONT) is a model that describes health service with related concepts, sub-concepts, attributes, and relations among concepts. Inferences of new knowledge are possible using queries. PeSONT classifies linguistic place terms using (Bennett and Agarwal, 2007) and uses prepositions of English language for location identification. Its implementation is to further the application of the PeNLP parser on human related problems by classifying place-like terms in natural language and for extracting geolocations.",
"name": "Preposition_enabled Spatial Ontology",
"prefix": "PESONT"
},
"PGHD-BP": {
"contact": {
"email": "rens@renskievit.com",
"name": "Rens Kievit"
},
"description": "Ontology containing terms describing the ancillary information surrounding the collection of Blood Pressure data and the communication via Interactive Voice Response in the context of the VODAN-Africa project.",
"homepage": "https://github.com/RenVit318/pghd",
"name": "PGHD Auxillary - BP",
"prefix": "PGHD-BP",
"version": "1.1"
},
"PGHD_CONNECT": {
"contact": {
"email": "rens@renskievit.com",
"name": "Rens"
},
"description": "Overarching ontology containg terms to describe the various types of Patient Generated Health Data that are generated on a specific patients. Meant for implementation in the VODAN-Africa project.",
"homepage": "https://github.com/RenVit318/pghd",
"name": "PGHD_CONNECT",
"prefix": "PGHD_CONNECT",
"version": "1.0"
},
"PGXO": {
"contact": {
"email": "adrien.coulet@loria.fr",
"name": "Adrien Coulet"
},
"description": "PGxO: a lite Pharmacogenomic Ontology. This ontology aims at providing a small set of concepts and roles that may type elements of pharmacogenomic relationships. Its concepts has been mapped to other existing ontologies. Mappings are not included in this version for lisibility purposes. Mapping are available on demand.",
"homepage": "https://members.loria.fr/ACoulet/",
"name": "PGxO",
"prefix": "PGXO",
"publication": "https://peerj.com/preprints/3140/",
"version": "0.4"
},
"PHAGE": {
"contact": {
"email": "diallo.abdoulaye@uqam.ca",
"name": "UniversitΓ© du QuΓ©bec Γ MontrΓ©al, Laboratoire de bioinformatique et LATECE"
},
"description": "This ontology represents the seven steps of phylogenetic analyses. Each root concept step is composed from a set of resource annotations (to represent the data-flow) and programs (to represent the control flow). Object properties serve to represent relations to annotate data (e.g. has_RetrievedInDatabase, has_ModeledBy, etc.) and reorder the sequence of programs (e.g. has_InputOutput).This ontology has been collected in a semi-automated way from well-known databases such as NCBI, GeneOntology, UniProtKB and Felsensteinβs Web site through Web crawling and mapping techniques.",
"name": "Phylogenetics Ontology",
"prefix": "PHAGE",
"version": "5.0"
},
"PHARE": {
"contact": {
"email": "adrien.coulet@loria.fr",
"name": "Adrien Coulet"
},
"description": "The PHArmacogenomic RElationships Ontology (or PHARE) proposes concepts and roles to represent relationships of pharmacogenomics interest.",
"homepage": "http://bioportal.bioontology.org/ontologies/45138",
"name": "Pharmacogenomic Relationships Ontology",
"prefix": "PHARE",
"publication": "http://www.jbiomedsem.com/content/2/S2/S10",
"version": "version id: 110114"
},
"PHARMGKB": {
"name": "PharmGKB Ontology",
"prefix": "PHARMGKB"
},
"PHENOMEBLAST": {
"name": "PhenomeBLAST Ontology",
"prefix": "PHENOMEBLAST"
},
"PHENX": {
"contact": {
"email": "yingqin@rti.org",
"name": "PhenX Admin"
},
"description": "Standard measures related to complex diseases, phenotypic traits and environmental exposures",
"name": "PhenX Phenotypic Terms",
"prefix": "PHENX",
"version": "1.2"
},
"PHFUMIADO": {
"contact": {
"email": "contact@bioself.fr",
"name": "Delphine Dauga"
},
"description": "The first ontology describing the anatomy and the development of Phallusia fumigata.",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Phallusia fumigata Anatomy and Development Ontology",
"prefix": "PHFUMIADO"
},
"PHIPO": {
"contact": {
"email": "alayne.cuzick@rothamsted.ac.uk",
"name": "Alayne Cuzick"
},
"description": "PHIPO is a formal ontology of species-neutral phenotypes observed in pathogen-host interactions. PHIPO is being developed to support the comprehensive and detailed representation of phenotypes in PHI-base, the multi-species Pathogen-Host Interactions database available online at http://www.phi-base.org. PHIPO is pre-composed and logically defined.",
"homepage": "https://github.com/PHI-base/phipo",
"name": "Pathogen Host Interaction Phenotype Ontology",
"prefix": "PHIPO",
"version": "2024-04-04"
},
"PHMAMMADO": {
"contact": {
"email": "contact@bioself.fr",
"name": "Delphine Dauga"
},
"description": "The first ontology describing the anatomy and the development of Phallusia mammillata.",
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Phallusia mammillata Anatomy and Development Ontology",
"prefix": "PHMAMMADO"
},
"PHYLONT": {
"contact": {
"email": "mp@uga.edu",
"name": "maryam panahiazar"
},
"description": "Ontology for Phylogenetic Analysis",
"name": "Phylogenetic Ontology",
"prefix": "PHYLONT",
"version": "ver8"
},
"PIERO": {
"contact": {
"email": "maskot@bio.titech.ac.jp",
"name": "Masaaki Kotera"
},
"description": "Enzyme Reaction Ontology for annotating Partial Information of chemical transformation",
"homepage": "http://reactionontology.org",
"name": "Enzyme Reaction Ontology for annotating Partial Information of chemical transformation",
"prefix": "PIERO"
},
"PINO": {
"contact": {
"email": "zhe@fsu.edu",
"name": "Zhe He"
},
"description": "An ontology about pregnancy information needs across all stages of pregnancy",
"homepage": "https://github.com/henryhezhe2003/Pregnancy_Infomation_Needs_Ontology",
"name": "Pregnancy Information Needs Ontology",
"prefix": "PINO",
"publication": "To be published in JMIR Pediatrics and Parenting soon.",
"version": "1.1"
},
"PLANA": {
"contact": {
"email": "smr@stowers.org",
"name": "Sofia Robb"
},
"description": "Anatomy ontology for planaria and terms specific to the developmental stages of the planarian Schmidtea mediterranea.",
"homepage": "https://github.com/obophenotype/planaria-ontology",
"name": "Planarian Anatomy and Developmental Stage Ontolgoy",
"prefix": "PLANA",
"version": "2023-03-13"
},
"PLANP": {
"contact": {
"email": "smr@stowers.org",
"name": "Sofia Robb"
},
"description": "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea. Many of the phenotypes were seen durning RNAi experiments.",
"homepage": "https://github.com/obophenotype/planarian-phenotype-ontology",
"name": "Planarian Phenotype Ontology",
"prefix": "PLANP"
},
"PLANTSO": {
"contact": {
"email": "cooperl@science.oregonstate.edu",
"name": "Laurel Cooper"
},
"description": "This ontology describes biotic and abiotic stresses that a plant may encounter.",
"homepage": "https://github.com/Planteome/plant-stress-ontology",
"name": "Plant Stress Ontology",
"prefix": "PLANTSO",
"version": "2023-11-14"
},
"PLIO": {
"contact": {
"email": "erfan.younesi@scai.fraunhofer.de",
"name": "Erfan Younesi"
},
"description": "The protein--ligand interaction ontology (PLIO) was developed around three main concepts, namely target, ligand and interaction, and was enriched by adding synonyms, useful annotations and references.",
"name": "Protein-ligand interaction ontology",
"prefix": "PLIO",
"publication": "http://www.ncbi.nlm.nih.gov/pubmed/21546398",
"version": "1.0"
},
"PLOSTHES": {
"contact": {
"email": "subjectareas@plos.org",
"name": "PLOS Taxonomy Team"
},
"description": "The PLOS Thesaurus includes over 10,000 Subject Area terms covering the wide range of research topics included the PLOS journals. It was initially built for PLOS in 2012 by Access Innovations (http://www.accessinn.com/). The entire corpus of PLOS articles was analysed to ensure that the thesaurus covers relevant research domains comprehensively. Updates are released several times a year.",
"homepage": "https://github.com/PLOS/plos-thesaurus",
"name": "PLOS Thesaurus",
"prefix": "PLOSTHES",
"publication": "http://www.plos.org/",
"version": "plosthes.2017-1"
},
"PMA": {
"contact": {
"email": "martinji@mail.nih.gov",
"name": "Jim Martin"
},
"description": "The Portfolio Management Application (PMA) is a system for tracking grants and producing reports - Users can access grant data through a query interface and a variety of pre-defined forms and reports",
"name": "Portfolio Management Application",
"prefix": "PMA",
"version": "0.9.1"
},
"PMAPP-PMO": {
"contact": {
"email": "li.jiao@imicams.ac.cn",
"name": "Jiao Li"
},
"description": "The Precision Medicine Ontology (PMO) has been developed as a standardized ontology for human precision medicine with consistent, reusable and sustainable descriptions of human disease terms, genomic molecular, phenotype characteristics and related medical vocabulary disease concepts through collaborative efforts of researchers at Institute of Medical Information, Chinese Academy of Medical Sciences. The Precision Medicine Ontology focuses on the development of a high level patients-centric ontology for the academic research, thus, it systematically integrates biomedicine vocabularies from GO, NCBI Gene, DrugBank, HPO, MeSH, SNOMED CT, etc. This work is supported by the National Key Research and Development Program of China (Precision Medicine Knowledge Base, Grant No. 2016YFC0901901).",
"homepage": "http://www.phoc.org.cn/pmo/",
"name": "PMO Precision Medicine Ontology",
"prefix": "PMAPP-PMO",
"publication": "https://www.aimspress.com/article/10.3934/mbe.2020227/fulltext.html",
"version": "4.0"
},
"PMD": {
"description": "PMD is an ontology that represents classification and related information of Persian medicine diseases. Persian medicine also known as Iranian traditional medicine is one of famous and most ancient forms of traditional medicines. This ontology is based on the top-level ontology GFO (General Formal Ontology)",
"name": "Persian Medicine Diseases Ontology",
"prefix": "PMD",
"version": "1.0"
},
"PMDO": {
"contact": {
"email": "satyasahoo@ieee.org",
"name": "Satya S. Sahoo"
},
"description": "The Parkinson Movement Disorder Ontology (PMDO) uses a systematic analysis of movement disorder instruments, extensive review of literature led by movement disorder specialists, and the AMP PD knowledge portal with an iterative ontology engineering process. The current version of PMDO is focused on parkinsonian disorders with classes representing three broad categories of: (1) neurological findings, (2) treatment plans, and (3) instruments used to evaluate various traits of PD. Release notes (v1.0): This version models the MDS Clinical Diagnostic Criteria for Parkinsonβs Disease (2015), including: 1. Essential criteria (1) 2. Supportive criteria (4) 3. Absolute exclusion criteria (9) 4. Red flags (10)",
"homepage": "https://bmhinformatics.case.edu/",
"name": "Parkinson and Movement Disorder Ontology",
"prefix": "PMDO",
"publication": "https://www.medrxiv.org/content/medrxiv/early/2020/11/12/2020.11.09.20228577.full.pdf",
"version": "1.1"
},
"PMO": {
"contact": {
"email": "nlorimer@stanford.edu",
"name": "Nancy Lorimer"
},
"description": "An extension to the Library of Congress BIBFRAME ontology for performed music.",
"name": "Performed Music Ontology",
"prefix": "PMO",
"version": "1.0"
},
"PMO-SPEED": {
"contact": {
"email": "nlorimer@stanford.edu",
"name": "Nancy Lorimer"
},
"description": "Vocabulary for playing speeds of audio carriers, e.g., audio discs, audio cassettes, piano/organ rolls, primarily for use with the Performed Music Ontology, or other similar music ontologies.",
"homepage": "https://github.com/LD4P/PerformedMusicOntology/tree/master/Vocabularies",
"name": "PMO Playing Speed Vocabulary",
"prefix": "PMO-SPEED",
"version": "1.0"
},
"PMR": {
"contact": {
"email": "laia.subirats@gmail.com",
"name": "Laia Subirats"
},
"description": "Knowledge representation related to computer-based decision support in rehabilitation; concepts and relationships in the rehabilitation domain, integrating clinical practice, the ICD (specifically its 11th revision), the clinical investigator record ontology, the ICF and SNOMED CT.",
"homepage": "https://sites.google.com/site/laiasubirats",
"name": "Physical Medicine and Rehabilitation",
"prefix": "PMR",
"publication": "https://sites.google.com/site/laiasubirats/publications",
"version": "1.6"
},
"PNADO": {
"contact": {
"email": "sabrina.azzi@uqo.ca",
"name": "Sabrina Azzi"
},
"description": "Pneumonia Diagnosis Ontology (PNADO) provides the necessary knowledge to diagnose infective pneumonia. It covers symptoms and clinical signs, clinical history, pathogens, laboratory tests and results, imaging, differential diagnosis, complications and pneumonia types.",
"name": "Pneumonia Diagnosis Ontology",
"prefix": "PNADO",
"version": "Version 1.0, 2021/02/01"
},
"PO": {
"contact": {
"email": "jaiswalp@oregonstate.edu",
"name": "Pankaj Jaiswal"
},
"description": "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plants.",
"homepage": "http://planteome.org",
"name": "Plant Ontology",
"prefix": "PO",
"publication": "http://planteome.org/pub",
"version": "releases/2024-04-17"
},
"PORO": {
"contact": {
"email": "thacker@uab.edu",
"name": "Bob Thacker"
},
"description": "An ontology covering the anatomy of Porifera (sponges)",
"name": "Porifera Ontology",
"prefix": "PORO",
"version": "unknown"
},
"PP": {
"contact": {
"email": "peaoteam@gmail.com",
"name": "PEAO Team"
},
"description": "To answer the need for a workflow representing a sequence of data transformations, a high-level process ontology was defined, denoted Pipeline Patterns (PP) ontology. Every concept is generically a Data (class from EDAM), which can be further specified as an Entry (P:00002) or an Exit (P:00009). All Entries can be subjected to an Operation (class from EDAM) producing an Intermediate (P:00010). An Intermediate has a TemporalEntity associated to represent its time of creation. Some Entries are specifically of the type Exit, meaning that they will represent concepts that exit the current category and be passed to the next one on the workflow. Additionally, in order to permit the treatment of a set of objects as a single entity, this high-level ontology considers the concept of List (P:00004) and more specifically an Aggregate (P:00005), containing a set of Data or Entry, respectively. The concept Intermediate is an Entry, allowing for the successive application of an operation to an Element. This is particularly useful in the case of the application of sequential set of operations.",
"homepage": "https://bitbucket.org/PlantExpAssay/ontology",
"name": "Pipeline Patterns Ontology",
"prefix": "PP",
"version": "1.0"
},
"PPLC": {
"contact": {
"email": "raymondw.redline@UHhospitals.org",
"name": "Raymond W. Redline, MD"
},
"description": "Placental pathology: current terminology with definitions, short descriptions, and representative images pertaining to the cause, origin and nature of placental disease. The Placental Pathology Lesion Classification was developed by a PAT External Scientific Panel Member, placental pathologist Dr. Raymond Redline. This terminology is a continuation of the effort of the Amsterdam Placental Lesion Consensus Group.",
"name": "Placental Pathology Lesion Classification",
"prefix": "PPLC",
"version": "1.0"
},
"PPO": {
"contact": {
"email": "rlwalls2008@gmail.com",
"name": "Ramona Walls"
},
"description": "An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales.",
"homepage": "https://github.com/PlantPhenoOntology/PPO",
"name": "Plant Phenology Ontology",
"prefix": "PPO"
},
"PR": {
"contact": {
"email": "dan5@georgetown.edu",
"name": "Darren Natale"
},
"description": "PRO provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp).",
"homepage": "http://proconsortium.org",
"name": "Protein Ontology",
"prefix": "PR",
"publication": "https://proconsortium.org/pro_pub.shtml",
"version": "69.0"
},
"PREGONTO": {
"contact": {
"email": "h.s.liyanage@surrey.ac.uk",
"name": "Harshana Liyanage"
},
"description": "The pregnancy ontology is a biomedical ontology used for identifying pregnancies in routine health databases. The ontology was primarily developed for conducting surveillance of vaccine uptake in pregnant women in the UK.",
"name": "Pregnancy Ontology",
"prefix": "PREGONTO"
},
"PREMEDONTO": {
"contact": {
"email": "n.s.tawfik@uu.nl",
"name": "Noha Tawfik"
},
"description": "Precision MedicinePreMedOnto is an application ontology built for the precision medicine domain on top of gold standard biomedical ontologies. The ontology learning process involves mining the PubMed repository to extract domain specific texts, abstracts and vocabulary as sources of data. The information gathered is clustered and outlined to determine main modules. It reuses terms and concepts from NCIT, MESH and IOBC to construct the ontology hierarchy.",
"name": "Precision Medicine Ontology",
"prefix": "PREMEDONTO"
},
"PREO": {
"contact": {
"email": "maulik@maulik-kamdar.com",
"name": "Maulik Kamdar"
},
"description": "The Presence Ontology is a systematic vocabulary of terms with defined relationships that models the encounters taking place every day among providers, patients, and family members or friends in environments such as hospitals and clinics. The Presence Ontology provides a conceptual model for the human experience in medicine. This is a preliminary approach, but further use of methods we have developed here may aid in providing clarity and consensus to topics in healthcare. The ontology is also a model for interdisciplinary collaboration, as it was developed in conjunction with experts from bioinformatics, medicine, anthropology, business, and communication sciences through multiple iterative stages.",
"homepage": "http://med.stanford.edu/presence/about.html",
"name": "Presence Ontology",
"prefix": "PREO",
"version": "1.0.0"
},
"PROCCHEMICAL": {
"contact": {
"email": "jhanit@gmail.com",
"name": "Nitin"
},
"description": "Chemical process",
"name": "Chemical Process",
"prefix": "PROCCHEMICAL",
"version": "2.3"
},
"PROCO": {
"contact": {
"email": "wes_schafer@merck.com",
"name": "Wes Schafer"
},
"description": "PROCO covers process chemistry, the chemical field concerned with scaling up laboratory syntheses to commercially viable processes.",
"homepage": "https://github.com/proco-ontology/PROCO",
"name": "Process Chemistry Ontology",
"prefix": "PROCO",
"version": "PROCO release 20220414"
},
"PROJ": {
"contact": {
"email": "simon.cox@csiro.au",
"name": "Simon Cox"
},
"description": "The PROJECT ontology is a profile of PROV-O which is designed to enable publication of information describing projects, including research projects. It is not designed to support project management, though sub-activities are included. As far as possible PROJECT is intended to be domain-neutral, and it is expected that domains and applications will specialize or extend this ontology for more specific purposes. The ontology gives terms to support the representation of: project planning, funding, goals project stakeholders and relationships project activities and timeline Primary documentation is at http://linked.data.gov.au/def/project",
"homepage": "http://linked.data.gov.au/def/project",
"name": "Project ontology",
"prefix": "PROJ",
"version": "2020"
},
"PROPREO": {
"contact": {
"email": "satyasahoo@ieee.org",
"name": "Satya S. Sahoo"
},
"description": "A comprehensive proteomics data and process provenance ontology.",
"homepage": "http://knoesis.wright.edu/research/semsci/application_domain/sem_life_sci/glycomics/resources/ontologies/propreo/",
"name": "Proteomics Data and Process Provenance Ontology",
"prefix": "PROPREO",
"publication": "http://knoesis.wright.edu/research/semsci/application_domain/sem_life_sci/glycomics/resources/ontologies/propreo/",
"version": "1.1"
},
"PROVO": {
"contact": {
"email": "lebot@rpi.edu",
"name": "Timothy Lebo"
},
"description": "The PROV Ontology (PROV-O) expresses the PROV Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes, properties, and restrictions that can be used to represent and interchange provenance information generated in different systems and under different contexts. It can also be specialized to create new classes and properties to model provenance information for different applications and domains.",
"homepage": "http://www.w3.org/TR/prov-o/",
"name": "Provenance Ontology",
"prefix": "PROVO",
"version": "Recommendation version 2013-04-30"
},
"PSDO": {
"contact": {
"email": "zachll@umich.edu",
"name": "Zach Landis-Lewis"
},
"description": "The Performance Summary Display Ontology (PSDO) is a lightweight application ontology used to reproducibly study visualizations of clinical performance and their associated outcomes in healthcare quality improvement settings. PSDO extends boundaries of visual representation artifacts by the IAO in the domain of distributed representations. PSDO describes dimensional representations of relational information displays that can be used to study the influence of feedback interventions on clinical practice.",
"homepage": "https://github.com/Display-Lab/psdo",
"name": "Performance Summary Display Ontology",
"prefix": "PSDO",
"publication": "https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf",
"version": "1.0.1"
},
"PSDS": {
"contact": {
"email": "jaiswalp@oregonstate.edu",
"name": "Pankaj Jaiswal"
},
"description": "REPLACED BY: Plant Ontology (PO). A controlled vocabulary of growth and developmental stages in various plants. Note that this has been subsumed into the Plant Ontology (PO). This file is created by filtering plant_ontology_assert.obo to contain only terms from the plant structure development stage branch of the PO. For more information, please see: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/",
"homepage": "http://www.plantontology.org",
"name": "Plant Structure Development Stage",
"prefix": "PSDS",
"version": "Release #20"
},
"PSIMOD": {
"contact": {
"email": "sylvie.ricard-blum@univ-lyon1.fr",
"name": "Sylvie Ricard-Blum"
},
"description": "PSI-MOD is an ontology consisting of terms that describe protein chemical modifications, logically linked by an is_a relationship in such a way as to form a direct acyclic graph (DAG). The PSI-MOD ontology has more than 45 top-level nodes, and provides alternative hierarchical paths for classifying protein modifications either by the molecular structure of the modification, or by the amino acid residue that is modified.",
"homepage": "http://www.psidev.info/MOD",
"name": "Protein Modification Ontology",
"prefix": "PSIMOD",
"version": "1.031.6"
},
"PSO": {
"contact": {
"email": "schrader@th-brandenburg.de",
"name": "Thomas Schrader"
},
"description": "It is the ontology embedding PRIME (Prospective Risk Analysis in Medical Environments) in related issues of patient safety research and activities. It classifies terms and express relations between them. The ontology building in an ongoing process. Any comments are welcome.",
"name": "PatientSafetyOntology",
"prefix": "PSO",
"version": "008:2017-08-04: Einarbeitung der ZustΓ€nde"
},
"PSO_2": {
"contact": {
"email": "thomas.schrader@computer.org",
"name": "Thomas Schrader"
},
"description": "This is a revised version of the Patient Safety Ontology",
"name": "PatientSafetyOntologyRevisted",
"prefix": "PSO_2",
"version": "005"
},
"PTO": {
"contact": {
"email": "jaiswalp@oregonstate.edu",
"name": "Pankaj Jaiswal"
},
"description": "A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part.",
"homepage": "http://www.planteome.org",
"name": "Plant Trait Ontology",
"prefix": "PTO",
"version": "July 2023"
},
"PTRANS": {
"contact": {
"email": "lynn.schriml@gmail.com",
"name": "Lynn Schriml"
},
"description": "The Pathogen Transmission Ontology describes the transmission methods of human disease pathogens from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.",
"homepage": "https://github.com/DiseaseOntology/PathogenTransmissionOntology",
"name": "Pathogen Transmission Ontology",
"prefix": "PTRANS",
"version": "releases/2022-10-10"
},
"PTS": {
"contact": {
"email": "alpha.tom.kodamullil@scai.fraunhofer.de",
"name": "Alpha Tom Kodamullil"
},
"description": "Pathwas terminology systems integrates biological Events and various Pathway types.",
"name": "Pathway Terminology System",
"prefix": "PTS",
"version": "1.0"
},
"PVONTO": {
"contact": {
"email": "jhuan@ittc.ku.edu",
"name": "Jingshan Huang, huang@usouthal.edu; Jun (Luke) Huan"
},
"description": "A pharmacovigilance ontology to connect known facts on drugs, disease, ADEs, and their molecular mechanisms.",
"homepage": "http://people.eecs.ku.edu/~jhuan/",
"name": "Pharmacovigilance Ontology",
"prefix": "PVONTO",
"version": "0.1"
},
"PW": {
"contact": {
"email": "gthayman@mcw.edu",
"name": "G. Thomas Hayman"
},
"description": "The goal of the Pathway Ontology is to cover all types of biological pathways, including altered and disease pathways, and to capture the relationships between them within the hierarchical structure of a Directed Acyclic Graph (DAG). The five nodes of the ontology are: classic metabolic, regulatory, signaling, drug and disease pathways. An extensive survey of the review literature along with searches of existing pathway databases have been used to choose terms and their position within the tree. The ontology is continually expanding along with the development of Pathway and Disease Portals at RGD. Mapping of pathways in other databases to terms in PW as synonyms further increased the content of the ontology. It also provided the means to bring in annotations made by these databases and link to their sites via automatic pipelines built at RGD. The ontology allows for the standardized annotation of rat as well as human and mouse genes to pathway terms. It also serves as a vehicle to connect between genes and ontology reports, between reports and interactive pathway diagrams, between pathways that directly connect to one another within a diagram or between pathways that in some fashion are globally related in pathway suites and suite networks. Metabolic, regulatory or signaling pathway terms have associated terms for the altered version of the pathway and the level at which the alteration(s) may occur. Proteins with mutations known to affect a particular pathway can be annotated to the normal and altered version(s) of the pathway and to a disease pathway, if known. Both the provision of terms for the altered versions of pathways and the representation of disease pathway diagrams as a collection of altered pathways are unique to the PW ontology and RGD's pathway data. The Pathway ontology is distributed under the terms of the Creative Commons Attribution license version 3.0 Unported (CC BY 3.0), see http://creativecommons.org/licenses/by/3.0 for details.",
"homepage": "https://rgd.mcw.edu/rgdweb/ontology/search.html",
"name": "Pathway Ontology",
"prefix": "PW",
"publication": "http://rgd.mcw.edu/wg/home/pathway2/molecular-pathways/#pwrpubs",
"version": "7.85"
},
"QUDT": {
"description": "The QUDT, or 'Quantity, Unit, Dimension and Type' collection of ontologies define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems. The goal of the QUDT ontology is to provide a unified model of, measurable quantities, units for measuring different kinds of quantities, the numerical values of quantities in different units of measure and the data structures and data types used to store and manipulate these objects in software. This OWL schema is a foundation for a basic treatment of units.",
"homepage": "http://qudt.org/",
"name": "Quantities, Units, Dimensions, and Types Ontology",
"prefix": "QUDT"
},
"QUDT2": {
"contact": {
"email": "jgraybeal@stanford.edu",
"name": "John Graybeal"
},
"description": "The QUDT, or \"Quantity, Unit, Dimension and Type\" schema defines the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems. The goal of the QUDT ontology is to provide a unified model of, measurable quantities, units for measuring different kinds of quantities, the numerical values of quantities in different units of measure and the data structures and data types used to store and manipulate these objects in software. Except for unit prefixes, all units are specified in separate vocabularies.",
"homepage": "http://qudt.org/doc/2016/DOC_SCHEMA-QUDT-v2.0.html",
"name": "Quantities, Units, Dimensions and Types (QUDT) Schema - Version 2.0",
"prefix": "QUDT2",
"version": "2.0"
},
"QUDT2-1": {
"contact": {
"email": "steve.ray@qudt.org",
"name": "Steve Ray"
},
"description": "QUDT presents a unified architecture for the conceptual representation of quantities, quantity kinds, units, dimensions, and data types, which lie at the core of all scientific and engineering inquiry. But the QUDT specification is more than a core architecture and a list of these concepts, because it implements international standards and thus provides the foundation for system interoperability. In order to provide for interoperability and data exchange between information systems, the specification needs to be available in a machine processable form, with no ambiguities. For these reasons, the QUDT approach to specifying these concepts is to use precise semantically grounded specifications in an ontology model with translation into machine-processable representations.",
"homepage": "qudt.org",
"name": "Quantities, Units, Dimensions and Types (QUDT Version 2.1)",
"prefix": "QUDT2-1",
"version": "2.1"
},
"RADLEX": {
"contact": {
"email": "radlex-feedback@lists.rsna.org",
"name": "Radiological Society of North America"
},
"description": "RadLex OWL, as downloaded from BioPortal, includes a set of puns in order to facilitate browsing and display. The base RadLex ontology, without puns, is available at http://radlex.org/",
"homepage": "https://www.rsna.org/practice-tools/data-tools-and-standards/radlex-radiology-lexicon",
"name": "Radiology Lexicon",
"prefix": "RADLEX",
"version": "4.1"
},
"RADMO": {
"name": "RADx Metadata Ontology",
"prefix": "RADMO"
},
"RADXTT-MVREASONS": {
"contact": {
"email": "jgraybeal@stanford.edu",
"name": "John Graybeal"
},
"description": "These concepts define the different reasons values might be missing from the RADx data record. The concepts have been approved by the RADx Executive Committee to fill in fields that do not have a value in them. The concepts in this vocabulary were developed by the RADx Missing Values Tiger Team. The protocols for managing these concepts in the RADx Data Hub environment are still being developed and will be improved and described as part of the RADx program.",
"homepage": "https://github.com/bmir-radx/radx-missing-value-reasons",
"name": "RADx Tiger Team Missing Value Reasons",
"prefix": "RADXTT-MVREASONS",
"version": "0.1.2"
},
"RAO": {
"contact": {
"email": "liqin.j.wang@gmail.com",
"name": "Liqin Wang"
},
"description": "A controlled vocabulary of RA-relevant information. Currently, only treatment information is available.",
"name": "Rheumatoid Arthritis ontology",
"prefix": "RAO",
"publication": "http://www.sciencedirect.com/science/article/pii/S0933365716300689",
"version": "Version 1.0"
},
"RB": {
"contact": {
"email": "acallaha@stanford.edu",
"name": "Alison Callahan"
},
"description": "The RegenBase ontology describes biological entities and processes studied in spinal cord injury (SCI) research.",
"homepage": "https://regenbase.cs.miami.edu",
"name": "RegenBase ontology",
"prefix": "RB",
"version": "1.0"
},
"RBO": {
"contact": {
"email": "kristen.m.peach@nasa.gov",
"name": "Kristen Peach"
},
"description": "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.",
"homepage": "https://github.com/Radiobiology-Informatics-Consortium/RBO/tree/master/src/ontology",
"name": "Radiation Biology Ontology",
"prefix": "RBO",
"publication": "https://doi.org/10.1080/09553002.2023.2173823",
"version": "2024-05-31"
},
"RCD": {
"contact": {
"email": "helpdesk3@nhsccc.exec.nhs.uk",
"name": "NHS Information Authority Loughborough"
},
"description": "Clinical Terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre",
"name": "Read Codes, Clinical Terms Version 3 (CTV3)",
"prefix": "RCD",
"version": "2023AB"
},
"RCTONT": {
"contact": {
"email": "amrapali.j.zaveri@gmail.com",
"name": "Amrapali Zaveri"
},
"description": "We developed and evaluated an ontology specifically for Randomized Controlled Trials in order to facilitate the production of systematic reviews and metaanalysis.",
"name": "Randomized Controlled Trials Ontology",
"prefix": "RCTONT",
"publication": "http://www.ncbi.nlm.nih.gov/pubmed/20953737",
"version": "2.0"
},
"RCTV2": {
"contact": {
"email": "fennie.liang@kcl.ac.uk",
"name": "Fennie Liang"
},
"description": "NHS UK Read Codes Version 2",
"name": "Read Clinical Terminology Version 2",
"prefix": "RCTV2",
"version": "2015"
},
"RDA-CONTENT": {
"contact": {
"email": "nlorimer@stanford.edu",
"name": "Nancy Lorimer"
},
"description": "A categorization reflecting the fundamental form of communication in which the content is expressed and the human sense through which it is intended to be perceived. Required data for RDA (Resource Description and Access)",
"homepage": "http://www.rdaregistry.info/termList/RDAContentType/",
"name": "RDA Content type",
"prefix": "RDA-CONTENT"
},
"RDA-ISSUANCE": {
"contact": {
"email": "nlorimer@stanford.edu",
"name": "Nancy Lorimer"
},
"description": "RDA vocabulary for mode of issuance of a resource (single unit, multipart monograph, etc.)",
"homepage": "https://www.rdaregistry.info/termList/ModeIssue/",
"name": "RDA Mode of Issuance",
"prefix": "RDA-ISSUANCE",
"version": "1.0"
},
"RDFS": {
"contact": {
"email": "danbri@w3.org",
"name": "Dan Brickley"
},
"description": "RDF Schema provides a data-modelling vocabulary for RDF data",
"name": "The RDF Schema vocabulary",
"prefix": "RDFS",
"version": "1.1"
},
"RDL": {
"contact": {
"email": "jhanit@gmail.com",
"name": "Nitin"
},
"description": "RDL",
"name": "RDL",
"prefix": "RDL",
"version": "Generated 2013-03-28T19:01:04.897+01:00"
},
"RDO": {
"contact": {
"email": "archanamca92@gmail.com",
"name": "Archana Patel"
},
"description": "Facilitating Biodiversity information",
"name": "Reusable Biodiversity Ontology",
"prefix": "RDO",
"version": "1.1"
},
"REGN_BRO": {
"contact": {
"email": "taimoor.mirza9595@gmail.com",
"name": "taimoor mirza"
},
"description": "A controlled terminology of resources, which is used to improve the sensitivity and specificity of web searches.",
"name": "REGN_BRO",
"prefix": "REGN_BRO",
"version": "1.1"
},
"REGN_GO": {
"contact": {
"email": "taimoor.mirza9595@gmail.com",
"name": "taimoor mirza"
},
"description": "Provides structured controlled vocabularies for the annotation of gene products with respect to their molecular function, cellular component, and biological role. The Gene Ontology consists of three Vocabularies.",
"name": "REGN_GO",
"prefix": "REGN_GO",
"version": "2023-01-01"
},
"REPO": {
"contact": {
"email": "ina.hulsegge@wur.nl",
"name": "Wageningen UR Livestock Research"
},
"description": "Ontology for livestock reproductive traits and phenotypes",
"name": "Reproductive Trait and Phenotype Ontology",
"prefix": "REPO",
"version": "1.1"
},
"REPOS": {
"contact": {
"email": "destyrodiah@gmail.com",
"name": "desty"
},
"description": "Repository OWL",
"name": "repository",
"prefix": "REPOS"
},
"REPRODUCE-ME": {
"contact": {
"email": "sheeba.samuel@uni-jena.de",
"name": "Sheeba Samuel"
},
"description": "The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials and settings required for its reproducibility.",
"homepage": "https://w3id.org/reproduceme/research",
"name": "REPRODUCE-ME",
"prefix": "REPRODUCE-ME",
"publication": "https://w3id.org/reproduceme/research",
"version": "1.1"
},
"RETO": {
"contact": {
"email": "vladimir.n.mironov@gmail.com",
"name": "Vladimir Mironov"
},
"description": "An application ontology for the domain of gene transcription regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI and orthological properties from RO and SIO.",
"homepage": "http://www.semantic-systems-biology.org/apo/",
"name": "Regulation of Transcription Ontology",
"prefix": "RETO",
"publication": "http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0386-y",
"version": "2015"
},
"REX": {
"contact": {
"email": "chebi-help@ebi.ac.uk",
"name": "Chebi Administrators"
},
"description": "REX is an ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. REX includes both microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes. Some biochemical processes from Gene Ontology (GO Biological process) can be described as instances of REX.",
"homepage": "http://www.ebi.ac.uk/~kirill/REX/",
"name": "Physico-Chemical Process",
"prefix": "REX",
"version": "1.13"
},
"REXO": {
"contact": {
"email": "vladimir.n.mironov@gmail.com",
"name": "Vladimir Mironov"
},
"description": "An application ontology for the domain of gene expression regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, and orthology relations using ontological properties from RO and ISO.",
"homepage": "http://www.semantic-systems-biology.org/apo",
"name": "Regulation of Gene Expression Ontolology",
"prefix": "REXO",
"publication": "http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0386-y",
"version": "2015"
},
"RGD": {
"name": "RRB Group D",
"prefix": "RGD"
},
"RH-MESH": {
"contact": {
"email": "leechuck@leechuck.de",
"name": "Robert Hoehndorf"
},
"description": "Medical Subjects Headings Thesaurus 2014, Modified version. This is an OWL representation of MeSH so that it can be integrated with other ontologies represented in OWL. It contains all terms that are in MeSH and in the MeSH concept tree, including the pharmacological actions (represented as subclass relations). Concepts in the MeSH concept tree are merged with MeSH term ids. --------------------------
Note that, while this ontology is composed of MeSH terms, it does not correspond directly to UMLS MeSH. In particular, a single term in UMLS MeSH often results in multiple classes in this ontology. For example, in MeSH there is a single term with the label \"Heart\". The internal code (unique identifier) for this term is A07.541. In this ontology there are two entirely different terms, both of which have the label \"Heart\". The codes for these terms are A07.541 and D006321.",
"homepage": "https://code.google.com/p/pharmgkb-owl/",
"name": "Robert Hoehndorf Version of MeSH",
"prefix": "RH-MESH",
"publication": "http://leechuck.de/publications.html",
"version": "2014"
},
"RNAO": {
"contact": {
"email": "BatchelorC@rsc.org",
"name": "Colin Batchelor"
},
"description": "The central aim of the RNA Ontology Consortium (ROC) is to develop an ontology to capture all aspects of RNA - from primary sequence to alignments, secondary and tertiary structure from base pairing and base stacking to sophisticated motifs.",
"homepage": "https://github.com/BGSU-RNA/rnao",
"name": "RNA Ontology",
"prefix": "RNAO",
"version": "r113"
},
"RNPRIO": {
"contact": {
"email": "sfarzaneh@ucsd.edu",
"name": "Seena Farzaneh"
},
"description": "Ontology for Inventories of Clinical Data Research Networks, Patient-Powered Research Networks, and Patient Registries",
"name": "Research Network and Patient Registry Inventory Ontology",
"prefix": "RNPRIO",
"version": "1"
},
"RNRMU": {
"contact": {
"email": "bogopol2@gmail.com",
"name": "Gennady Bogopolskiy"
},
"description": "The terms of RNRMU",
"name": "RNRMU",
"prefix": "RNRMU",
"version": "0.1"
},
"RO": {
"contact": {
"email": "alberto.traverso@maastro.nl",
"name": "Alberto Traverso"
},
"description": "The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual",
"name": "Radiomics Ontology",
"prefix": "RO",
"version": "2.1"
},
"ROCKNROLLTEST": {
"contact": {
"email": "niva@dtu.dk",
"name": "Nikola Vasiljevic"
},
"description": "This Vocabulary describes some few terms of high level geologic concept hierarchy. This vocabulary is not complete and half randomly made up, but based on the USGS North American Geological Map Data Model. It is a test before the M4M workshop.",
"name": "ROCK-N-ROLL-TEST",
"prefix": "ROCKNROLLTEST"
},
"ROLEO": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "The Role Ontology (RoleO) is an ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO development follows the OBO Foundry principles. RoleO has represented all the occupations defined in the Standard Occupational Classification (SOC) System from the USA Bureau of Labor Statistics.",
"homepage": "https://github.com/roleontology/roleo",
"name": "Role Ontology",
"prefix": "ROLEO",
"version": "Vision Release: 1.0.16"
},
"ROO": {
"contact": {
"email": "andre.dekker@maastro.nl",
"name": "Andre Dekker"
},
"description": "The Radiation Oncology Ontology aims to cover the radiation oncology domain with a strong focus on re-using existing ontologies. From release 0.5 forward the ROO has changed its naming scheme from all entities starting with numbers to all entities starting with C(lasses) or P(redicates). This change was needed for better compatibility to web standards. Releases 0.4.1-0.4.3. include the necessary axioms to go from the original naming scheme to the new naming scheme.
0.4.1: Added new entities with equivalence to the old entities
0.4.2: Added deprecated property to the old entities
0.4.3: Removed axioms with the old entities except annotations
0.5: Removed all old entities, the new base",
"homepage": "http://www.cancerdata.org/roo",
"name": "Radiation Oncology Ontology",
"prefix": "ROO",
"version": "0.5"
},
"ROS": {
"contact": {
"email": "jean-emmanuel.bibault@aphp.fr",
"name": "Jean-Emmanuel Bibault"
},
"description": "This ontology describes commonly contoured (anatomical and treatment planning) structures for radiation treatment planning. 22000 structures labels (created over a 16 years period in our radiation department) were extracted, classified and categorized to produce this ontology. Lymph nodes delineation international guidelines are provided. This ontology was created to ease and standardize the integration of radiation oncology data into clinical datawarehouses for multicentric studies. The high granularity of this ontology will allow precise dosimetric evaluations.",
"homepage": "http://www.twitter.com/jebibault",
"name": "Radiation Oncology Structures Ontology",
"prefix": "ROS",
"version": "1.2.2"
},
"RPO": {
"contact": {
"email": "sujatha@rcai.riken.jp",
"name": "Sujatha Mohan"
},
"description": "RAPID phenotype ontology presents controlled vocabulary of ontology class structures and entities of observed phenotypic terms for primary immunodeficiency diseases (PIDs) that facilitate global sharing and free exchange of PID data with usersβ communities",
"homepage": "http://rapid.rcai.riken.jp/ontology/v1.0/phenomer.php",
"name": "Resource of Asian Primary Immunodeficiency Diseases (RAPID) Phenotype Ontology",
"prefix": "RPO",
"version": "Version 1.0"
},
"RS": {
"contact": {
"email": "akwitek@mcw.edu",
"name": "Anne Kwitek"
},
"description": "This ontology defines the hierarchical display of the different rat strains as derived from the parental strains",
"homepage": "http://rgd.mcw.edu/rgdweb/search/strains.html",
"name": "Rat Strain Ontology",
"prefix": "RS",
"publication": "http://www.ncbi.nlm.nih.gov/pubmed/23603846",
"version": "6.229"
},
"RSA": {
"contact": {
"email": "z.tatum@lumc.nl",
"name": "Zuotian Tatum"
},
"description": "An ontology for sequence annotations and how to preserve them with reference sequences",
"name": "Reference Sequence Annotation",
"prefix": "RSA",
"version": "0.6"
},
"RVO": {
"contact": {
"email": "k.bandara@unsw.edu.au",
"name": "Madhushi Bandara"
},
"description": "RVO, Research Variable Ontology, proposes a schema that can be use to record empirical data analytics research and can be use as a knowledge-base to support knowledge exploration phase of a new analytics research to learn and get recommendation. RVO is designed around the research variables, which form the basis of the hypothesis that analysts test through building a model.",
"homepage": "http://w3id.org/rv-ontology/info",
"name": "Research Variable Ontology",
"prefix": "RVO",
"version": "1.0"
},
"RXNO": {
"contact": {
"email": "batchelorc@rsc.org",
"name": "Colin Batchelor"
},
"description": "RXNO, the name reaction ontology, connects organic name reactions such as the Diels-Alder cyclization and the Cannizzaro reaction to their roles in an organic synthesis.",
"homepage": "https://code.google.com/p/rxno/",
"name": "Name Reaction Ontology",
"prefix": "RXNO",
"version": "releases/2021-12-16"
},
"RXNORM": {
"contact": {
"email": "custserv@nlm.nih.gov",
"name": "NLM Customer Service"
},
"description": "RxNorm Vocabulary",
"name": "RxNORM",
"prefix": "RXNORM",
"version": "2023AB"
},
"SALMON": {
"contact": {
"email": "jones@nceas.ucsb.edu",
"name": "Matthew Jones"
},
"description": "An ontology representing knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. This ontology is considered to be in the early stages of development, though it is based upon considerable previous work. Contributions of all kinds are welcome and encouraged, including alignments, updates to existing terms, and new terms.",
"homepage": "https://github.com/DataONEorg/sem-prov-ontologies/",
"name": "Salmon Ontology",
"prefix": "SALMON",
"version": "0.3.2"
},
"SAO": {
"contact": {
"email": "mmartone@ucsd.edu",
"name": "Maryann Martone"
},
"description": "SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules.",
"name": "Subcellular Anatomy Ontology",
"prefix": "SAO",
"version": "Version 1.2"
},
"SARSMUTONTO": {
"contact": {
"email": "j.bakkas@uca.ac.ma",
"name": "Jamal BAKKAS"
},
"description": "The SARSMutOnto ontology provides a list of all SARS-CoV-2 Pango lineages while maintaining their hierarchy (lineage/sublineage) describing in detail all lineage mutations",
"homepage": "https://github.com/jbakkas/SARSMutOnto",
"name": "Ontology for SARS-CoV-2 lineages and mutations",
"prefix": "SARSMUTONTO",
"version": "1.1"
},
"SASAP": {
"contact": {
"email": "mecum@nceas.ucsb.edu",
"name": "Bryce Mecum"
},
"description": "An ontology which represents information about the State of Alaska's Salmon and People (SASAP) project, as well as knowledge about salmon, features of their habitats, salmon stakeholders, and related entities.",
"homepage": "https://github.com/DataONEorg/sem-prov-ontologies",
"name": "The State of Alaska's Salmon and People Ontology",
"prefix": "SASAP",
"version": "0.3.1"
},
"SATO": {
"contact": {
"email": "peleg.mor@gmail.com",
"name": "Mor Peleg"
},
"description": "Designing effective theory-driven digital behaviour change interventions (DBCI) is a challenging task. To ease the design process, and assist with knowledge sharing and evaluation of the DBCI, we propose the SATO (IDEASexpAnded wiTh BCIO) design workflow based on the IDEAS (Integrate, Design, Assess, and Share) framework and aligned with the Behaviour Change Intervention Ontology (BCIO). BCIO is a structural representation of the knowledge in behaviour change domain supporting evaluation of behaviour change interventions (BCIs) but it is not straightforward to utilise it during DBCI design. IDEAS (Integrate, Design, Assess, and Share) framework guides multi-disciplinary teams through the mobile health (mHealth) application development life-cycle but it is not aligned with BCIO entities. SATO couples BCIO entities with workflow steps and extends IDEAS Integrate stage with consideration of customisation and personalisation. The SATO ontology provides the extensions of BCIO along with examples of a BCI Scenario of Fatigue Reduction.",
"name": "SATO (IDEAS expAnded wiTh BCIO): workflow for designers of patient-centered mobile health behaviour change intervention applications",
"prefix": "SATO",
"version": "v2"
},
"SBO": {
"contact": {
"email": "sheriff@ebi.ac.uk",
"name": "Rahuman Sheriff"
},
"description": "The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. The ontology consists of six orthogonal vocabularies defining: the roles of reaction participants (eg. \"substrate\"), quantitative parameters (eg. \"Michaelis constant\"), a precise classification of mathematical expressions that describe the system (eg. \"mass action rate law\"), the modeling framework used (eg. \"logical framework\"), and a branch each to describe entity (eg. \"macromolecule\") and interaction (eg. \"process\") types, and a branch to define the different types of metadata that may be present within a model. SBO terms can be used to introduce a layer of semantic information into the standard description of a model, or to annotate the results of biochemical experiments in order to facilitate their efficient reuse. SBO is an Open Biomedical Ontologies (OBO) candidate ontology, and is free for use. More information about SBO can be found from the project FAQ, at http://www.ebi.ac.uk/sbo/ SBO is a project of the BioModels.net effort and is developed through community collaboration.",
"homepage": "https://github.com/EBI-BioModels/SBO",
"name": "Systems Biology Ontology",
"prefix": "SBO",
"version": "28:08:2021 03:13"
},
"SBOL": {
"contact": {
"email": "jacqueline.quinn@autodesk.com",
"name": "Jacqueline Quinn"
},
"description": "Synthetic Biology Open Language Visual (SBOLv) is an ontology to represent standardized graphical notation for synthetic biology.",
"homepage": "www.sbolstandard.org/visual",
"name": "Synthetic Biology Open Language Visual Ontology",
"prefix": "SBOL",
"version": "unknown"
},
"SCDO": {
"contact": {
"email": "giant.plankton@gmail.com",
"name": "Jade Hotchkiss"
},
"description": "The Sickle Cell Disease Ontology (SCDO) project is a collaboration between H3ABioNet (Pan African Bioinformatics Network) and SPAN (Sickle Cell Disease Pan African Network). The SCDO is currently under development and its purpose is to: 1) establish community standardized SCD terms and descriptions, 2) establish canonical and hierarchical representation of knowledge on SCD, 3) links to other ontologies and bodies of work such as DO, PhenX, MeSH, ICD, NCIβs thesaurus, SNOMED and OMIM. Once complete, we anticipate that the ontology will: 1) be the most comprehensive collection of knowledge on SCD, 2) facilitate exploration of new scientific questions and ideas, 3) facilitate seamless data sharing and collaborations including meta-analysis within the SCD community, 4) support the building of databasing and clinical informatics in SCD.",
"homepage": "http://scdontology.h3abionet.org",
"name": "Sickle Cell Disease Ontology",
"prefix": "SCDO",
"publication": "https://scdontology.h3abionet.org",
"version": "2021-04-15"
},
"SCHEMA": {
"contact": {
"email": "johardi@stanford.edu",
"name": "Josef Hardi"
},
"description": "A collection of schemas that webmasters can use to markup HTML pages in ways recognized by major search providers, and that can also be used for structured data interoperability (e.g. in JSON). This representation includes all layers, as presented in the experimental OWL file at https://schema.org/docs/schemaorg.owl. Versions containing -fixes in their names include the fixes described at https://github.com/schemaorg/schemaorg/issues/1611#issuecomment-299292010.",
"homepage": "http://schema.org/",
"name": "Schema.org core and all extension vocabularies",
"prefix": "SCHEMA",
"version": "3.4 fixes"
},
"SCIO": {
"contact": {
"email": "mhartung@cit-ec.uni-bielefeld.de",
"name": "Matthias Hartung"
},
"description": "Representation of pre-clinical studies in the domain of spinal cord injury therapies",
"homepage": "http://www.psink.de",
"name": "Spinal Cord Injury Ontology",
"prefix": "SCIO",
"publication": "https://pub.uni-bielefeld.de/publication/2913603",
"version": "1"
},
"SCO": {
"contact": {
"email": "charis@rpi.edu",
"name": "Shruthi Chari"
},
"description": "The Study Cohort Ontology (SCO) is developed to model overall structure and patterns of cohort variables and control/intervention groups defined within the structured population descriptions (commonly referred to as Table1's or Cohort Summary Tables)of observational case studies and clinical trials. We maintain only domain agnostic and commonly occuring subject variables and interventions in SCO, and we have a suite of ontologies (Diseases, Medications, LabResults etc) to encode Diabetes related terminology. We have adopted a bottom-up approach to modeling and we have revised the structure of SCO upon investigation of a few research studies (11 to be precise) from the Pharmacological Interventions (Chapter 8) and Cardiovascular Complications (Chapter 9) of the American Diabetes Association (ADA)βs Standards of Medical Care 2018 CPG. We enable deep drive visualizations driven off queries to knowledge graphs modeled on SCO, to help assist physician visualize the similarity of a patient to a study group, at a quick glance. We welcome contributions and suggestions to extend SCO to represent cohort descriptions of publications targeted to other diseases, and we plan to release set of tools to make this process seamless.",
"homepage": "https://tetherless-world.github.io/study-cohort-ontology/",
"name": "Study Cohort Ontology",
"prefix": "SCO",
"publication": "https://link.springer.com/chapter/10.1007/978-3-030-30796-7_4",
"version": "1.1.0"
},
"SCO_F23": {
"name": "Syrian Cinema Ontology - ahmad - F23",
"prefix": "SCO_F23"
},
"SD3": {
"contact": {
"email": "mcivorwr@anes.upmc.edu",
"name": "William R. McIvor, MD"
},
"description": "The taxonomy will facilitate quality assurance in scenario delivery, permit standardized descriptors of simulation delivery deviations, and enable researchers to quantify the impact that scenario delivery and documentation deviations have upon participant performance. Though created specifically for high-fidelity mannequin-based simulation, the taxonomy can be applied to other simulation modalities.",
"name": "Simulation Delivery and Documentation Deviations",
"prefix": "SD3",
"version": "1.0"
},
"SDO": {
"contact": {
"email": "sivaram.arabandi@gmail.com",
"name": "Sivaram Arabandi"
},
"description": "An application ontology for the domain of Sleep Medicine.",
"homepage": "https://mimi.case.edu/concepts",
"name": "Sleep Domain Ontology",
"prefix": "SDO",
"version": "Last modification: Feb. 11, 2013 Sivaram Arabandi"
},
"SDOHO": {
"contact": {
"email": "Yifang.Dang.1@uth.tmc.edu",
"name": "Yifang Dang"
},
"description": "SDoHO aims to represent fundamental SDoH factors and their relationships in a standardized and measurable way. It has well-designed hierarchies, practical objective properties, and versatile functionalities, and the comprehensive semantic and coverage evaluation achieved promising performance compared to the existing ontologies relevant to SDoH.",
"homepage": "https://github.com/Tao-AI-group/SDoHO",
"name": "social determinants of health ontology-TaoLab",
"prefix": "SDOHO",
"publication": "https://pubmed.ncbi.nlm.nih.gov/37301740/",
"version": "SDoHO_1005"
},
"SEDI": {
"description": "An ontology for DICOM as used in the SeDI project.",
"homepage": "https://semantic-dicom.org",
"name": "Semantic DICOM Ontology",
"prefix": "SEDI",
"version": "0.6 alpha"
},
"SENSO": {
"contact": {
"email": "mecum@nceas.ucsb.edu",
"name": "Bryce Mecum"
},
"description": "The SENSO ontology is designed to provide classification terms for labeling sensitive data for data archival and sharing.",
"homepage": "https://github.com/DataONEorg/sem-prov-ontologies",
"name": "Sensitive Data Ontology",
"prefix": "SENSO",
"version": "Version 0.1.0"
},
"SEP": {
"contact": {
"email": "psidev-gps-dev@lists.sourceforge.net",
"name": "SEP developers"
},
"description": "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments, such as, and including, gel electrophoresis, column chromatography, capillary electrophoresis, centrifugation and so on. Developed jointly by the HUPO Proteomics Standards Initiative and The Metabolomics Standards Initiative.",
"homepage": "http://psidev.info/index.php?q=node/312",
"name": "Sample Processing and Separation Techniques Ontology",
"prefix": "SEP",
"version": "1.070708"
},
"SEPIO": {
"contact": {
"email": "mhb120@gmail.com",
"name": "Matthew Brush"
},
"description": "The Scientific Evidence and Provenance Information Ontology (SEPIO) was developed to support description of evidence and provenance information for scientific claims. The core model represents the relationships between claims, their evidence lines, the information items that comprise these lines of evidence, and the methods, tools, and agents involved in the creation of these entities. Use cases driving SEPIO development include integration of scientific claims and their associated evidence/provenance metadata, and support for the discovery, analysis, and evaluation of claims based on this metadata.",
"homepage": "https://github.com/monarch-initiative/SEPIO-ontology",
"name": "Scientific Evidence and Provenance Information Ontology",
"prefix": "SEPIO",
"version": "2023-06-13"
},
"SEPON": {
"contact": {
"email": "zhangchi8359@wchscu.cn",
"name": "ZHANG CHI"
},
"description": "The Sepsis Ontology (SEPON) is a disease-specific ontology that defines the concepts and relationships between concepts in the field of sepsis and related diseases, contributing to data standardization and providing precise and personalized diagnosis, treatment and prognosis recommandations for sepsis.",
"name": "Sepsis Ontology",
"prefix": "SEPON",
"version": "V1.0.0"
},
"SHR": {
"contact": {
"email": "hassan.shojaee@gmail.com",
"name": "Hassan Shojaee"
},
"description": "The goal of SHR project is to develop an ontology for the description of student health records. Student health records are created for entering college students in order to provide better health services will be formed. This file contains various sections such as history of disease, family history of disease, public examinations and ... .",
"homepage": "http://www.shojaee.com/shr/",
"name": "Student Health Record Ontology",
"prefix": "SHR",
"version": "1.1"
},
"SIBO": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "Social behavior in insects.",
"homepage": "https://github.com/obophenotype/sibo",
"name": "Social Insect Behavior Ontology",
"prefix": "SIBO"
},
"SIMM": {
"contact": {
"email": "giulia.panzarella3@gmail.com",
"name": "Giulia Panzarella"
},
"description": "MAATrica is a novel metric for assessing the coherence of methodologies in research papers within the fields of medicinal and nutraceutical chemistry. MAATrica employs user-controlled and customizable ontologies (in silico, in vitro and in vivo), enabling personalized analysis of research papers in the fields of medicinal and nutraceutical chemistry.",
"name": "In Silico Methodologies Ontology for MAATrica metric",
"prefix": "SIMM"
},
"SIMON": {
"contact": {
"email": "mdebellissf@gmail.com",
"name": "Michael DeBellis"
},
"description": "The SImple Measurement ONtology (SIMON) is a small vocabulary (3 top level classes: PunnedClass, Measurement, and Unit) to represent measurements and units. It uses the pattern to represent N-ary relations and a recursive structure to make the representation of various measurements and units (e.g., \"5 kilograms\", \"4 miles per hour\", \"5 meters per second per second\" straight forward and obvious. It utilizes the Semantic Web Rule Language (SWRL) to automatically order measurements of the same type (e.g., Speed) regardles of units. E.g., that 5 kilometers per hour is greater than 5 meters per hour. It does this by transforming all measures of a specific type (e.g., distance, mass, speed, acceleration) to canonical units. The canonical units can be modified by changing a few rules. I also include on the github page some SPARQL transformations that generate the rdfs:label for each measurement instance so the developer doesn't have to take the effort and potential error prone risk of doing this manually. The version included here is the version after the SWRL rules have run and with the inferences exported and also after the SPARQL transforms have generated all the rdfs:label values. Although there are other vocabularies that address this problem they are either much more complex (addressing many additional issues besides units and measures) and/or do not automatically order measures of different units.",
"homepage": "https://github.com/mdebellis/SIMON-A-Simple-Measurement-Vocabulary",
"name": "Simple Measurement Ontology",
"prefix": "SIMON",
"publication": "First paper is pending review",
"version": "1.0"
},
"SIO": {
"contact": {
"email": "michel.dumontier@gmail.com",
"name": "Michel Dumontier"
},
"description": "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. It provides vocabulary for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.",
"homepage": "http://sio.semanticscience.org",
"name": "Semanticscience Integrated Ontology",
"prefix": "SIO",
"publication": "http://sio.semanticscience.org",
"version": "1.59"
},
"SITBAC": {
"contact": {
"email": "morpeleg@is.haifa.ac.il",
"name": "Mor Peleg"
},
"description": "Context-based healthcare access-control policies",
"homepage": "http://mis.hevra.haifa.ac.il/~morpeleg/",
"name": "Situation-Based Access Control Ontology",
"prefix": "SITBAC",
"version": "1.3"
},
"SK": {
"contact": {
"email": "Sandeepak525@gmail.com",
"name": "sandeepak bhandari"
},
"description": "An abstraction based approach.",
"name": "Digital Forensic",
"prefix": "SK"
},
"SLSO": {
"contact": {
"email": "daniel.c.berrios@nasa.gov",
"name": "Dan Berrios"
},
"description": "The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive (located at https://nlsp.nasa.gov) and other systems that contain space life science research data. Many kinds of scientific research in space involve specialized equipment, experimental procedures, specimens and specimen collection apparatus, supporting operational structures, and references to specific space environments and their characteristics. Often such research is extremely costly compared with planetary/terrestrial investigations, and the community supporting space life sciences is accustomed to the use of various specialized concepts and terminologies when dealing with this kind of research and data. However, the underlying conceptual models (and especially the specific labeled relationships in these models) have never been made explicit. The SLSO attempts to provide definition and organization of these models for the space research community. The SLSO was developed ab inicio using the Ontology Development Kit and imports an extends many concepts from the Basic Formal Ontology (BFO), the Ontology of Biomedical Investigations (OBI), the Environmental Ontology (ENVO), and other OBO Foundry ontologies. Projects at NASA such as the Open Science Data Repository (https://osdr.nasa.gov/) are already using many OBO ontologies, including the Radiation Biology Ontology (https://github.com/Radiobiology-Informatics-Consortium/RBO) and OBI, to index space biology investigation data. With the development of the SLSO, this practice can be extended to include all life science research in space or addressing space effects. Furthermore, the SLSO has a component that imports concepts from the Science Data Discovery Ontology, which was developed to support NASA's Science Discovery Engine (https://sciencediscoveryengine.nasa.gov). These links in the imported SDDO to concepts underlying a broad spectrum of space research (astrophysics, heliophysics, etc.) can ultimately be used to provide key capabilities for discovering and analyzing space life science data and how they relate to other kinds of scientific data regarding space environments.",
"homepage": "https://github.com/nasa/LSDAO/tree/master/src/ontology",
"name": "Space Life Sciences Ontology",
"prefix": "SLSO",
"version": "2024-05-17"
},
"SMASH": {
"contact": {
"email": "csehao@cs.uoregon.edu",
"name": "Hao Wang"
},
"description": "The SMASH (Semantic Mining of Activity, Social, and Health data) system ontology describes concepts used in describing the semantic features of healthcare data and social networks. The SMASH system primarily addresses the research topic of sustained weight loss with continued intervention with frequent social contacts.",
"name": "SMASH Ontology",
"prefix": "SMASH"
},
"SMO": {
"contact": {
"email": "7855b87500@emailnax.com",
"name": "ADM SVU"
},
"description": "Syrian Movies Ontology, For Education.",
"name": "Syrian Movies Ontology",
"prefix": "SMO"
},
"SNMI": {
"contact": {
"email": "info@ihtsdo.org",
"name": "IHTSDO"
},
"description": "Cote, Roger A., editor. Systematized Nomenclature of Human and Veterinary Medicine: SNOMED International. Northfield (IL): College of American Pathologists; Schaumburg (IL): American Veterinary Medical Association, Version 3.5, 1998.",
"name": "Systematized Nomenclature of Medicine, International Version",
"prefix": "SNMI",
"version": "2023AB"
},
"SNOMEDCT": {
"contact": {
"email": "custserv@nlm.nih.gov",
"name": "NLM Customer Service"
},
"description": "SNOMED Clinical Terms",
"homepage": "http://www.snomed.org",
"name": "SNOMED CT",
"prefix": "SNOMEDCT",
"publication": "http://www.snomed.org",
"version": "2023AB"
},
"SNPO": {
"contact": {
"email": "adrien.coulet@loria.fr",
"name": "Adrien Coulet"
},
"description": "SNP-Ontology is a domain ontology that provides a formal representation (OWL-DL) of genomic variations. Despite its name, SNP-Ontology, is not limited to the representation of SNPs but it encompasses genomic variations in a broader meaning. SNP-Ontology is general enough to enable the representation of variations observed in genome of various species. Latest versions of SNP-Ontology include the representation of haplotype and of CNV. The unambiguous representation of genomic variations provided by SNP-Ontology enables to integrate heterogeneous data related to genomic variations. To achieve this goal SNP-Ontology enables (1) to represent one variation in accordance with various ways that exist for describing it, (2) to represent the equivalence between two distinct descriptions of one variation, and (3) to represent correspondence between a genomic variation and its outcome at the transcriptome and proteome levels.",
"homepage": "https://members.loria.fr/ACoulet/files/snpontology1.6_description.html",
"name": "Single-Nucleotide Polymorphism (SNP) Ontology",
"prefix": "SNPO",
"publication": "http://hal.inria.fr/inria-00067863/en",
"version": "version: full 1.6\nrelease: 14/03/2017"
},
"SO": {
"contact": {
"email": "song-devel@lists.sourceforge.net",
"name": "SO Administrators"
},
"description": "SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/",
"homepage": "http://www.sequenceontology.org",
"name": "Sequence Types and Features Ontology",
"prefix": "SO",
"version": "unknown"
},
"SOCPRES": {
"contact": {
"email": "u.hoang@surrey.ac.uk",
"name": "Uy Hoang"
},
"description": "The social prescribing ontology specifies concepts associated to social prescribing practices and the well being of social prescribing recipients. The ontology will be primary used to harmonise data related social prescribing processes across various parts of the health system.",
"name": "Social Prescribing Ontology",
"prefix": "SOCPRES"
},
"SOHO": {
"contact": {
"email": "nk495@njit.edu",
"name": "Navya Martin"
},
"description": "SOHO has terminologies covering societal factors, such as where a person was born, grew up, works, lives, etc., along with socio-economic and community factors that affect an individualβs health.",
"name": "Social Determinants of Health Ontology",
"prefix": "SOHO",
"version": "3"
},
"SOIL-PROF": {
"contact": {
"email": "andrew.biggs@resources.qld.gov.au",
"name": "Andrew Biggs"
},
"description": "Machine-readable representation of the classifiers described in chapter 8 Soil Profile, by R.C. McDonald and R.F. Isbell, in Australian soil and land survey field handbook (3rd edn). A soil profile is a vertical section of a soil from the soil surface through all its horizons to parent material, other consolidated substrate material or selected depth in unconsolidated material. The data was converted from the print representation to this linked-data form by Linda Gregory assisted by Simon J D Cox.",
"homepage": "http://registry.it.csiro.au/def/soil/au/asls/soil-prof",
"name": "Soil Profile classifiers",
"prefix": "SOIL-PROF",
"version": "3rd edition"
},
"SOPHARM": {
"contact": {
"email": "adrien.coulet@loria.fr",
"name": "Adrien Coulet"
},
"description": "SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. SO-Pharm articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables to represent pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables to represent patient and more largely panel included in trials, and populations. SO-Pharm enables the representation of measured items on this patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains.",
"homepage": "https://members.loria.fr/ACoulet/files/sopharm2.0_description.php",
"name": "Suggested Ontology for Pharmacogenomics",
"prefix": "SOPHARM",
"publication": "http://hal.inria.fr/inria-00089824/en/",
"version": "Version: SO-Pharm 2.2\nRelease: 02 Mar 2017"
},
"SOS": {
"contact": {
"email": "dalton.bc96@gmail.com",
"name": "Dalton Costa"
},
"description": "Um teste",
"name": "emergΓͺncia",
"prefix": "SOS"
},
"SOY": {
"contact": {
"email": "nelsonrt@iastate.edu",
"name": "Rex Nelson"
},
"description": "Growth, trait and development ontology for soybean",
"homepage": "soybase.org",
"name": "Soy Ontology",
"prefix": "SOY",
"version": "unknown"
},
"SP": {
"contact": {
"email": "oxgiraldo@gmail.com",
"name": "Olga Giraldo"
},
"description": "The SeMAntic RepresenTation for Protocols, SMART Protocols, provides a structured OWL vocabulary of experimental protocols. SMART Protocols ontology includes two modules, SP-document and SP-workflow. SP-document, aims to provide a structured vocabulary of concepts to represent information necessary and sufficient for reporting an experimental protocol. SP-Workflow represents: i) the executable elements of a protocol, protocol instructions; ii) the experimental actions and material entities that participates in instructions (sample/specimen, organisms, reagents, instruments); and iii) the order of execution of the instructions.",
"homepage": "https://smartprotocols.github.io/",
"name": "SMART Protocols",
"prefix": "SP",
"version": "4.0"
},
"SPD": {
"contact": {
"email": "michalik@uni-greifswald.de",
"name": "Peter Michalik"
},
"description": "An ontology for spider anatomy.",
"name": "Spider Anatomy Ontology",
"prefix": "SPD",
"version": "1.1"
},
"SPO": {
"contact": {
"email": "tariq.abdulla@gmail.com",
"name": "Tariq Abdulla"
},
"homepage": "www.lboro.ac.uk",
"name": "Skin Physiology Ontology",
"prefix": "SPO",
"publication": "www.lboro.ac.uk",
"version": "2"
},
"SPTO": {
"contact": {
"email": "nm249@cornell.edu",
"name": "Naama Menda"
},
"description": "Solanaceae crop phenotypes and traits, developed in collaboration with the research community, especially for breeder traits of agronomic importance.",
"homepage": "solgenomics.net",
"name": "Solanaceae Phenotype Ontology",
"prefix": "SPTO",
"publication": "http://www.ncbi.nlm.nih.gov/pubmed/18539779",
"version": "unknown"
},
"SP_ONTOLOGY": {
"contact": {
"email": "carlos.parra.sspa@juntadeandalucia.es",
"name": "Carlos Luis Parra CalderΓ³n"
},
"description": "The ontology developed for the SmartPITeS project contains decision rules established in clinical practice on which a software developed for clinical decision support for the pharmacological prescription and de-prescription of complex chronic patients is based. Specifically patients with atrial fibrillation under treatment with anticoagulants.",
"name": "SmartPITeS Proyect Ontology for Complex Chronic Patients",
"prefix": "SP_ONTOLOGY"
},
"SSE": {
"contact": {
"email": "surse@mskcc.org",
"name": "Nita McNeil"
},
"description": "Memorial Sloan-Kettering Cancer Center Surgical Secondary Events Ontology (Adverse Events)",
"homepage": "https://www.mskcc.org/departments/surgery/surgical-secondary-events-system",
"name": "Surgical Secondary Events",
"prefix": "SSE",
"publication": "https://www.mskcc.org/departments/surgery/surgical-secondary-events-system/surgical-secondary-events-system-references",
"version": "1.1"
},
"SSN": {
"contact": {
"email": "jgraybeal@stanford.edu",
"name": "John Graybeal"
},
"description": "This ontology describes sensors, actuators and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.",
"homepage": "https://www.w3.org/TR/vocab-ssn/",
"name": "Semantic Sensor Network Ontology",
"prefix": "SSN",
"version": "New modular version of the SSN ontology. \n\nThis ontology was originally developed in 2009-2011 by the W3C Semantic Sensor Networks Incubator Group (SSN-XG). For more information on the group's activities see: http://www.w3.org/2005/Incubator/ssn/. The ontology was revised and modularized in 2015-2017 by the W3C/OGC Spatial Data on the Web Working Group, see: https://www.w3.org/2015/spatial/wiki/Semantic_Sensor_Network_Ontology. \n\nIn particular, (a) the scope is extended to include actuation and sampling; (b) the core concepts and properties are factored out into the SOSA ontology. The SSN ontology imports SOSA and adds formal axiomatization consistent with the text definitions in SOSA, and adds classes and properties to accommodate the scope of the original SSN ontology."
},
"SSO": {
"contact": {
"email": "anna.okhmatovskaia@mcgill.ca",
"name": "Anya Okhmatovskaia, David L Buckeridge"
},
"description": "The SSO encodes agreement among experts about how Emergency Department (ED) chief complaints are grouped into syndromes of public health importance (consensus definitions).",
"name": "Syndromic Surveillance Ontology",
"prefix": "SSO",
"version": "1"
},
"STATO": {
"contact": {
"email": "alejandra.gonzalez.beltran@gmail.com",
"name": "Alejandra Gonzalez-Beltran"
},
"description": "STATO is a general-purpose STATistics Ontology. Its aim is to provide coverage for processes such as statistical tests, their conditions of applications, and information needed or resulting from statistical methods, such as probability distributions, variable, spread and variation metrics. STATO also covers aspects of experimental design and description of plots and graphical representations commonly used to provide visual cues of data distribution or layout and to assist review of the results.",
"homepage": "http://stato-ontology.org/",
"name": "Statistics Ontology",
"prefix": "STATO",
"publication": "http://stato-ontology.org/",
"version": "2024-07-07"
},
"STMSO": {
"contact": {
"email": "misaghzahiri@yahoo.com",
"name": "misagh zahiri"
},
"description": "STMSO is the first comprehensive semantic representation of symptomatic treatment of MS and provides a major step toward the development of intelligent Clinical Decision Support System (CDSS) for MS symptomatic treatment.",
"name": "symptomatic treatment of multiple sclerosis ontology",
"prefix": "STMSO"
},
"STO-DRAFT": {
"contact": {
"email": "erfan.younesi@gmx.de",
"name": "Erfan Younesi"
},
"description": "The Stroke Ontology (STO) covers the knowledge domain of stroke based on expert views and translational continuum of stroke research.",
"name": "The Stroke Ontology",
"prefix": "STO-DRAFT",
"version": "2017-11-01"
},
"STY": {
"contact": {
"email": "support@bioontology.org",
"name": "bioportal"
},
"description": "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types. This section of the documentation provides an overview of the Semantic Network, and describes the files of the Semantic Network. Sample records illustrate structure and content of these files. The Semantic Network is distributed as one of the UMLS Knowledge Sources and as an open source resource available on the Semantic Network Web site, subject to these terms and conditions.",
"homepage": "https://semanticnetwork.nlm.nih.gov/",
"name": "Semantic Types Ontology",
"prefix": "STY",
"version": "2023AB"
},
"SUGARBIND": {
"contact": {
"email": "bdkouiti5013@gmail.com",
"name": "Koichi Arakawa"
},
"description": "Ontology for representing glycan and pathogen binding interaction data in RDF. Many of the terms are based on the data originally contained in the SugarBind database.",
"name": "SugarBind",
"prefix": "SUGARBIND",
"version": "2023-06-20"
},
"SURGICAL": {
"contact": {
"email": "philip.shields@live.vu.edu.au",
"name": "Philip Shields"
},
"description": "This is an ontology of a surgical nurse's process domain",
"name": "Nurse Surgical",
"prefix": "SURGICAL"
},
"SVU_MWS_WSM": {
"contact": {
"email": "rahaf.enzawi@gmail.com",
"name": "Rahaf Enzawi"
},
"description": "Syrian Cinema Othology this othology releted to Protege project which is a practical assignment in the Semantic Web course for a graduate student in the Master of Web Science program with Dr.Bassel Al Khatib This ontology conten seven class Each class has the necessary data properties and several object properties which represent relationship between classes",
"homepage": "rahaf_246783@svuonline.org",
"name": "Syrian Cinema Ontology",
"prefix": "SVU_MWS_WSM",
"publication": "rahaf_246783@svuonline.org",
"version": "1.0"
},
"SVU_MWS_WSM_F23": {
"contact": {
"email": "rahaf.enzawi@gmail.com",
"name": "Rahaf Enzawi"
},
"description": "This ontology releted to Protege project which is a practical assignment in the Semantic Web course for a graduate student in the Master of Web Science program with Dr.Bassel Al Khatib This ontology contens seven class Each class has the necessary data properties and several object properties which represent relationship between classes",
"homepage": "rahaf_246783@svuonline.org",
"name": "MWS-WSM-F23 Syrian Cinema Ontology",
"prefix": "SVU_MWS_WSM_F23",
"publication": "rahaf_246783@svuonline.org",
"version": "1.0"
},
"SWEET": {
"description": "The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research). Originally developed by NASA Jet Propulsion Labs under Rob Raskin, SWEET is now officially under the governance of the ESIP foundation.",
"homepage": "https://github.com/ESIPFed/sweet/blob/master/README.md",
"name": "Semantic Web for Earth and Environment Technology Ontology",
"prefix": "SWEET",
"version": "3.6.0"
},
"SWO": {
"contact": {
"email": "james@scibite.com",
"name": "James Malone"
},
"description": "The Software Ontology (SWO) describes software used in research, primarily Bioinformatics. The SWO covers areas such as the software type, licence, manufacturer of the software, the input and output data types and the uses (i.e. objectives) to which the software can be put.",
"homepage": "https://github.com/allysonlister/swo",
"name": "Software Ontology",
"prefix": "SWO",
"publication": "https://doi.org/10.1186/2041-1480-5-25",
"version": "2023-03-05"
},
"SYMP": {
"contact": {
"email": "lynn.schriml@gmail.com",
"name": "Lynn Schriml"
},
"description": "The symptom ontology was designed around the guiding concept of a symptom being: \"A perceived change in function, sensation or appearance reported by a patient indicative of a disease\". Understanding the close relationship of Signs and Symptoms, where Signs are the objective observation of an illness, the Symptom Ontology will work to broaden it's scope to capture and document in a more robust manor these two sets of terms. Understanding that at times, the same term may be both a Sign and a Symptom",
"homepage": "https://disease-ontology.org",
"name": "Symptom Ontology",
"prefix": "SYMP",
"version": "2024-05-17"
},
"SYRIAN-CINEMA": {
"contact": {
"email": "m.m.shahmeh@gmail.com",
"name": "Mouaz Al-Shahmeh"
},
"description": "Syrian Cenima antology by Mouaz Al-Shahmeh - 216212",
"name": "Syrian Cinema",
"prefix": "SYRIAN-CINEMA",
"version": "1.0.0"
},
"T4FS": {
"contact": {
"email": "allyson.lister@oerc.ox.ac.uk",
"name": "Allyson Lister"
},
"description": "A terminology for the skills necessary to make data FAIR and to keep it FAIR",
"homepage": "https://github.com/terms4fairskills/FAIRterminology",
"name": "terms4FAIRskills",
"prefix": "T4FS",
"version": "2023-03-02"
},
"TADS": {
"contact": {
"email": "dsonensh@odu.edu",
"name": "Daniel Sonenshine"
},
"description": "The anatomy of the Tick, Families: Ixodidae, Argassidae",
"homepage": "http://www.anobase.org",
"name": "Tick Gross Anatomy Ontology",
"prefix": "TADS",
"version": "1.21"
},
"TAO": {
"contact": {
"email": "wasila.dahdul@usd.edu",
"name": "Wasila Dahdul"
},
"description": "TAO is a multispecies anatomy ontology for teleost fishes. Originally seeded from ZFA, but intended to cover terms relevant to other taxa.",
"homepage": "https://www.nescent.org/phenoscape/Main_Page",
"name": "Teleost Anatomy Ontology",
"prefix": "TAO",
"publication": "http://dx.doi.org/10.1093/sysbio/syq013",
"version": "2012-08-10"
},
"TAON": {
"name": "Therapeutic Antibody Ontology",
"prefix": "TAON"
},
"TAXRANK": {
"contact": {
"email": "peteremidford@yahoo.com",
"name": "Peter Midford"
},
"description": "A vocabulary of taxonomic ranks intended to replace the sets of rank terms found in the Teleost Taxonomy Ontology, the OBO translation of the NCBI taxonomy and similar OBO taxonomy ontologies. It provides terms for taxonomic ranks drawn from both the NCBI taxonomy database and from a rank vocabulary developed for the TDWG biodiversity information standards group. Cross references to appearances of each term in each source are provided. Consistent with its intended use as a vocabulary of labels, there is no relation specifying an ordering of the rank terms.",
"homepage": "https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary",
"name": "Taxonomic Rank Vocabulary",
"prefix": "TAXRANK",
"version": "unknown"
},
"TCDO": {
"contact": {
"email": "zhuyan166@126.com",
"name": "Yan Zhu"
},
"description": "More than 400 popular TCD decoction pieces (TCD-DP) were selected from authoritative textbooks, standards and terminologies, as well as their crudes, Chinese medicinal material (CMM). The TCD-DP entities are categorized in 23 upper level terms by their clinical effects. Their properties like nature, flavor, toxicity and meridian entries are also defined formally by logical relations. CMMβs species is mapped to the NCBITaxon taxonomy ontology, which establishes a link between traditional medicine and modern biomedical science. TCDO contains over 1,500 terms, including terms drawn from existing ontologies and more than 1,000 TCD-specific terms, labeled in both Chinese and English.",
"homepage": "https://github.com/TCMOntology/TCDO",
"name": "Traditional Chinese Drug Ontology",
"prefix": "TCDO",
"version": "0.05"
},
"TCO": {
"contact": {
"email": "xyz19940216@163.com",
"name": "XingyunLiu"
},
"description": "Thyroid cancer ontology (TCO) contains 578 concepts organized under 6 biological viewpoints, i.e., Anatomy and Histoembryology, Basic Information of Patient, Cellular or Molecular Interactions, Clinical Aspects, Etiology, Pathology",
"name": "Thyroid Cancer Ontology",
"prefix": "TCO",
"version": "1.0"
},
"TDWGSPEC": {
"contact": {
"email": "kimberlydurante@gmail.com",
"name": "Kim Durante"
},
"description": "Biodiversity Information Standards (TDWG) is an international not-for-profit group that develops standards and protocols for sharing biodiversity data. They have a detailed collection of vocabularies and ontologies for studies of biological organisms.",
"name": "TDWG Specimen LSID Ontology",
"prefix": "TDWGSPEC",
"version": "0.3"
},
"TEDDY": {
"contact": {
"email": "biomodels-net-support@lists.sf.net",
"name": "BioModels.net team"
},
"description": "The TErminology for the Description of DYnamics (TEDDY) project aims to provide an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.",
"homepage": "http://teddyontology.sourceforge.net/",
"name": "Terminology for the Description of Dynamics",
"prefix": "TEDDY",
"publication": "http://www.nature.com/msb/journal/v7/n1/full/msb201177.html",
"version": "rel-2014-04-24 (inferred)"
},
"TEMPO": {
"description": "TempO is a lightweight ontology for describing temporal validity and efficacy according to a tritemporal data model.",
"homepage": "https://github.com/hroptatyr/tempo/",
"name": "TempO",
"prefix": "TEMPO",
"version": "0.1"
},
"TEO": {
"contact": {
"email": "tao.cui@mayo.edu",
"name": "Cui Tao"
},
"description": "The Time Event Ontology (TEO) is an ontology for representing events, time, and their relationships.",
"name": "Time Event Ontology",
"prefix": "TEO",
"version": "1.0.8"
},
"TEPHRAM4MEXAMPLE": {
"contact": {
"email": "nhoebel@kmotifs.com",
"name": "Nancy Hoebelheinrich"
},
"description": "Test of a Tephra controlled vocabulary for Station to be used for a M4M workshop.",
"name": "Tephra M4M Example",
"prefix": "TEPHRAM4MEXAMPLE",
"version": "0.1.1"
},
"TEST-M4M20-PAV": {
"contact": {
"email": "me@thisisnikola.com",
"name": "Nikola Vasiljevic"
},
"description": "Test",
"name": "test-m4m20-subjects-pav",
"prefix": "TEST-M4M20-PAV",
"version": "0.1.0"
},
"TESTEX": {
"contact": {
"email": "felipe.leza@databiology.com",
"name": "felipe"
},
"description": "first ontology creation format",
"name": "test1",
"prefix": "TESTEX",
"version": "0.0.1"
},
"TEST_A": {
"contact": {
"email": "felipe.leza@databiology.com",
"name": "Felipe Leza"
},
"description": "This is an example ontology created by owlready2 python library",
"name": "TEST_A",
"prefix": "TEST_A"
},
"TEST_CBI": {
"contact": {
"email": "ranjanp@ornl.gov",
"name": "Priya Ranjan"
},
"description": "Testing CBI ontology",
"name": "test_cbi",
"prefix": "TEST_CBI"
},
"TGMA": {
"contact": {
"email": "louis@imbb.forth.gr",
"name": "C. Louis"
},
"description": "A structured controlled vocabulary of the anatomy of mosquitoes.",
"homepage": "http://www.anobase.org",
"name": "Mosquito Gross Anatomy Ontology",
"prefix": "TGMA",
"version": "releases/2013-06-03"
},
"THREE-ST": {
"contact": {
"email": "esther.meerwijk@gmail.com",
"name": "Esther L Meerwijk"
},
"description": "This ontology contains classes, sub-classes, and relationships that map onto the 3-Step Theory of suicide (3ST). The classes represent the four factors that make up the central tenets of the theory: 1) psychological pain, 2) hopelessness, 3) connectedness, and 4) capacity for suicide. The instances of each subclass are terms that were found in VA clinical notes and indicate presence or absence of the associated 3ST factor. The terms are intended to be used in an NLP pipeline to extract 3ST information from clinical progress notes. Psychological pain, hopelessness, and capacity for suicide are major risk factors for suicide, whereas connectedness is a protective factor. In brief, the theory holds that suicide only occurs if pain and hopelessness outweigh connectedness and only then if the capacity for suicide is present.",
"name": "3-Step Theory of suicide",
"prefix": "THREE-ST",
"version": "1.0.1"
},
"TIME": {
"contact": {
"email": "chris.little@metoffice.gov.uk",
"name": "Chris Little"
},
"description": "OWL-Time is an OWL-2 DL ontology of temporal concepts, for describing the temporal properties of resources in the world or described in Web pages. The ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. Time positions and durations may be expressed using either the conventional (Gregorian) calendar and clock, or using another temporal reference system such as Unix-time, geologic time, or different calendars.",
"homepage": "https://www.w3.org/TR/owl-time/",
"name": "OWL-Time",
"prefix": "TIME",
"version": "2017"
},
"TIMEBANK": {
"contact": {
"email": "tobias.grubenmann@live.com",
"name": "Tobias Grubenmann"
},
"description": "The Timebank Ontology is used to describe Timebank systems for Peer-to-Peer Service Exchange. A Timebank allows user to store virtual money, often called a Time Dollar, into a bank account. This virtual currency can be earned by helping fellow Timebank users and spent by requesting help from others. The main goal of the ontology is to facilitate the matching between helpers and requesters of help.",
"homepage": "https://w3id.org/timebank",
"name": "Timebank Ontology",
"prefix": "TIMEBANK",
"version": "0.3"
},
"TM-CONST": {
"contact": {
"email": "tudorache@stanford.edu",
"name": "Tania Tudorache"
},
"description": "The value set for the Constitution property of the International Classification of Traditional Medicine (ICTM).",
"homepage": "https://sites.google.com/site/whoictm/home",
"name": "Traditional Medicine Constitution Value Set",
"prefix": "TM-CONST",
"version": "1"
},
"TM-MER": {
"contact": {
"email": "tudorache@stanford.edu",
"name": "Tania Tudorache"
},
"description": "The meridian value set used in the International Classification of Traditional Medicine.",
"homepage": "https://sites.google.com/site/whoictm/home",
"name": "Traditional Medicine Meridian Value Sets",
"prefix": "TM-MER",
"version": "1"
},
"TM-OTHER-FACTORS": {
"contact": {
"email": "tudorache@stanford.edu",
"name": "Tania Tudorache"
},
"description": "The value set for the Other Factors property of the International Classification of Traditional Medicine (ICTM).",
"homepage": "https://sites.google.com/site/whoictm/home",
"name": "Traditional Medicine Other Factors Value Set",
"prefix": "TM-OTHER-FACTORS",
"version": "1"
},
"TM-SIGNS-AND-SYMPTS": {
"contact": {
"email": "tudorache@stanford.edu",
"name": "Tania Tudorache"
},
"description": "The value set for the Signs and Symptoms property of the International Classification of Traditional Medicine (ICTM).",
"homepage": "https://sites.google.com/site/whoictm/home",
"name": "Traditional Medicine Signs and Symptoms Value Set",
"prefix": "TM-SIGNS-AND-SYMPTS",
"version": "1"
},
"TMA": {
"contact": {
"email": "borromeocd@upmc.edu",
"name": "Chuck Borromeo"
},
"description": "Tissue microarrays (TMA) are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential. The Resource Description Framework (RDF) provides a flexible method to represent knowledge in triples, which take the form Subject-Predicate-Object. All data resources are described using Uniform Resource Identifiers (URI), which are global in scope. We present an OWL (Web Ontology Language) schema that expands upon the TMA data exchange specification to address this issue and assist in data sharing and integration.",
"name": "Tissue Microarray Ontology",
"prefix": "TMA",
"version": "1.0.0"
},
"TML": {
"contact": {
"email": "l.soldatova@gmail.com",
"name": "Larisa Soldatova"
},
"description": "a set of metadata to record transformative machine learning experiments with LINCS dataset",
"name": "trasformative machine learning metadata",
"prefix": "TML",
"version": "0.1"
},
"TMO": {
"contact": {
"email": "tmo-administration@googlegroups.com",
"name": "TMO task in W3C's HCLS IG"
},
"description": "This project focuses on the development of a high level patient-centric ontology for the pharmaceutical industry. The ontology should enable silos in discovery research, hypothesis management, experimental studies, compounds, formulation, drug development, market size, competitive data, population data, etc. to be brought together. This would enable scientists to answer new questions, and to answer existing scientific questions more quickly. This will help pharmaceutical companies to model patient-centric information, which is essential for the tailoring of drugs, and for early detection of compounds that may have sub-optimal safety profiles. The ontology should link to existing publicly available domain ontologies.",
"homepage": "http://esw.w3.org/HCLSIG/PharmaOntology",
"name": "Translational Medicine Ontology",
"prefix": "TMO",
"publication": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102889/",
"version": "1.0.2"
},
"TOK": {
"contact": {
"email": "Nizar.Ghoula@unige.ch",
"name": "Nizar ghoula"
},
"description": "An Ontology describing Resources having different formats. This Ontology can be used to annotate and describe Terminological, Ontological Knowledge resources.",
"homepage": "http://cui.unige.ch/~ghoula/",
"name": "Terminological and Ontological Knowledge Resources Ontology",
"prefix": "TOK",
"publication": "http://cui.unige.ch/~ghoula/",
"version": "0.2.1"
},
"TOP-MENELAS": {
"contact": {
"email": "jean.charlet@upmc.fr",
"name": "Jean Charlet"
},
"description": "The two main goals MENELAS contributes to are to (i) Provide better account of and better access to medical information through natural languages in order to help physicians in their daily practice, and to (ii) Enhance European cooperation by multilingual access to standardised medical nomenclatures. The major achievements of MENELAS are the realisation of its two functional systems: (i) The Document Indexing System encodes free text PDSs into both an internal representation (a set of Conceptual Graphs) and international nomenclature codes (ICD-9-CM). Instances of the Document Indexing System have been realised for French, English and Dutch ; (ii) The Consultation System allows users to access the information contained in PDSs previously indexed by the Document Indexing System. The test domain for the project was coronary diseases. The existing prototype shows promising results for information retrieval from natural language PDSs and for automatically encoding PDSs into an existing classification such as ICD-9-CM. A set of components, tools, knowledge bases and methods has also been produced by the project. These include language-independent ontology and models for the domain of coronary diseases; conceptual description of the relevant ICD-9-CM codes. This ontology includes a top-ontology, a top-domain ontology and a domain ontology (Coronay diseases surgery). The menelas-top ontology here is the part of the whole ontology without any reference to medical domain.",
"name": "Menelas Project Top-Level Ontology",
"prefix": "TOP-MENELAS",
"version": "1.0"
},
"TP4": {
"contact": {
"email": "oualidzizi02@gmail.com",
"name": "ZIZI Oualid"
},
"description": "relation familiales",
"name": "Oualid",
"prefix": "TP4"
},
"TP_REL_FAM": {
"contact": {
"email": "oualidzizi02@gmail.com",
"name": "ZIZI Oualid"
},
"description": "TP4 concernant les relations familiales",
"name": "Relation familiales",
"prefix": "TP_REL_FAM"
},
"TRAK": {
"contact": {
"email": "i.spasic@cs.cardiff.ac.uk",
"name": "Irena Spasic"
},
"description": "TRAK (Taxonomy for RehAbilitation of Knee conditions) is an ontology that formally models information relevant for the rehabilitation of knee conditions. TRAK provides the framework that can be used to collect coded data in sufficient detail to support epidemiologic studies so that the most effective treatment components can be identified, new interventions developed and the quality of future randomized control trials improved to incorporate a control intervention that is well defined and reflects clinical practice.",
"homepage": "http://www.cs.cf.ac.uk/trak",
"name": "Taxonomy for Rehabilitation of Knee Conditions",
"prefix": "TRAK",
"version": "unknown"
},
"TRANS": {
"contact": {
"email": "philip.shields@live.vu.edu.au",
"name": "Philip Shields"
},
"description": "This is an ontology of a transitional care nurse's process domain",
"name": "Nurse Transitional",
"prefix": "TRANS"
},
"TRIAGE": {
"contact": {
"email": "philip.shields@live.vu.edu.au",
"name": "Philip Shields"
},
"description": "An ontology showing the process domain of a triage nurse.",
"name": "Nurse triage",
"prefix": "TRIAGE"
},
"TRON": {
"contact": {
"email": "ontology@ibeetle-base.uni-goettingen.de",
"name": "JΓΌrgen DΓΆnitz, Daniela Grossmann"
},
"description": "TrOn is an ontology about the anatomical structures of the red flour beetle Tribolium castaneum in the developmental stages larva, pupa and adult.",
"homepage": "http://ibeetle-base.uni-goettingen.de/ontology/overview.jsf",
"name": "Tribolium Ontology",
"prefix": "TRON",
"version": "unknown"
},
"TST7": {
"contact": {
"email": "rensanderson7@gmail.com",
"name": "Rens Anderson"
},
"description": "Final skos",
"homepage": "https://cedar.metadatacenter.org/templates/edit/https://repo.metadatacenter.org/templates/1bcab355-0b9f-4449-9f12-99c3552df353?folderId=https:%2F%2Frepo.metadatacenter.org%2Ffolders%2Fe4bd3d33-b817-4357-aed7-812b84200c88",
"name": "FIELDLAB3_2023",
"prefix": "TST7"
},
"TTO": {
"contact": {
"email": "peteremidford@yahoo.com",
"name": "Peter Midford"
},
"description": "The Teleost taxonomy ontology is being used to facilitate annotation of phenotypes, particularly for taxa that are not covered by NCBI because no submissions of molecular data have been made. Taxonomy ontologies can also be valuable in annotating legacy data, where authors make phenotype or ecological assertions (e.g., host-parasite associations) that refer to groups that are reorganized or no longer recognized. The taxonomy ontology serves as the source of taxa for our project's use for identifying evolutionary changes that match the phenotype of a zebrafish mutant.",
"homepage": "http://obofoundry.org/ontology/tto.html",
"name": "Teleost Taxonomy Ontology",
"prefix": "TTO",
"version": "unknown"
},
"TXPO": {
"contact": {
"email": "yuki.yamagata@riken.jp",
"name": "Yuki Yamagata"
},
"description": "TOXic Process Ontology (TXPO) includes entities related to toxic mechanisms (toxic courses) and processes, mainly focusing on hepatotoxicity. Application system TOXPILOT: https://toxpilot.nibiohn.go.jp",
"homepage": "https://toxpilot.nibiohn.go.jp",
"name": "Toxic Process Ontology",
"prefix": "TXPO",
"publication": "https://pubmed.ncbi.nlm.nih.gov/32883995/",
"version": "2022/12/07"
},
"TYPON": {
"contact": {
"email": "phyloviz@kdbio.inesc-id.pt",
"name": "PHYLOViZ Team"
},
"description": "TyPon provides a comprehensive description of the existing microbial typing methods for the identification of bacterial Isolates and their classification. Such a description constitutes an universal format for the exchange of information on the microbial typing field, providing a vehicle for the integration of the numerous disparate online databases. In its current version, TyPon describes most used microbial typing methods but it is, and always will be, a work in progress given the constant advances in the microbial typing field.",
"homepage": "http://www.phyloviz.net/typon/",
"name": "Microbial Typing Ontology",
"prefix": "TYPON",
"publication": "https://bitbucket.org/phyloviz/typon/wiki",
"version": "20140929"
},
"UBERON": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.",
"homepage": "http://uberon.org",
"name": "Uber Anatomy Ontology",
"prefix": "UBERON",
"publication": "http://genomebiology.com/content/13/1/R5",
"version": "2023-07-25"
},
"UGANDA_DISEASES": {
"contact": {
"email": "mariam.basajja@gmail.com",
"name": "Mariam Basajja"
},
"description": "This is the seventh version of the Uganda diseases",
"name": "Uganda_diseases",
"prefix": "UGANDA_DISEASES",
"version": "7"
},
"UHC-METADATA": {
"contact": {
"email": "rl627@drexel.edu",
"name": "Ran Li"
},
"description": "Draft of onotlogy for UHC meta hub",
"name": "UHC Metadata",
"prefix": "UHC-METADATA",
"version": "v0.0.1"
},
"UMMS": {
"contact": {
"email": "lekha.rajas@gmail.com",
"name": "Rajas Mukund Gokhale"
},
"description": "This is an in-progress ontology for the numerous use cases of UMMS Enterprise Data & Analytics dept",
"name": "FirstOntologyForUMMS",
"prefix": "UMMS",
"version": "0.3"
},
"UNITSONT": {
"contact": {
"email": "sivaram.arabandi@gmail.com",
"name": "Sivaram Arabandi"
},
"description": "A small ontology for the units of measurement developed during the development of the Sleep Domain Ontology (SDO). It supports the use of SDO within the PhysioMIMI application.",
"homepage": "https://mimi.case.edu/concepts",
"name": "Units Ontology",
"prefix": "UNITSONT",
"version": "1.0"
},
"UO": {
"contact": {
"email": "g.gkoutos@gmail.com",
"name": "George Gkoutos"
},
"description": "Metrical units for use in conjunction with PATO",
"homepage": "https://github.com/bio-ontology-research-group/unit-ontology",
"name": "Units of Measurement Ontology",
"prefix": "UO",
"version": "2023-05-25"
},
"UPA": {
"contact": {
"email": "Anne.Morgat@sib.swiss",
"name": "Anne Morgat"
},
"description": "UniPathway (http://www.unipathway.org) is a fully manually curated resource for the representation and annotation of metabolic pathways. UniPathway provides explicit representations of enzyme-catalyzed and spontaneous chemical reactions, as well as a hierarchical representation of metabolic pathways. This hierarchy uses linear subpathways as the basic building block for the assembly of larger and more complex pathways, including species-specific pathway variants. All of the pathway data in UniPathway has been extensively cross-linked to existing pathway resources such as KEGG and MetaCyc, as well as sequence resources such as the UniProt KnowledgeBase (UniProtKB), for which UniPathway provides a controlled vocabulary for pathway annotation. We introduce here the basic concepts underlying the UniPathway resource, with the aim of allowing users to fully exploit the information provided by UniPathway.",
"homepage": "https://github.com/geneontology/unipathway",
"name": "Unipathway",
"prefix": "UPA",
"publication": "https://www.ncbi.nlm.nih.gov/pubmed/22102589",
"version": "UniPathway Release 2015_03"
},
"UPHENO": {
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall"
},
"description": "Combined phenotype ontology",
"name": "Combined Phenotype Ontology",
"prefix": "UPHENO"
},
"VANDF": {
"contact": {
"email": "michael.lincoln@med.va.gov",
"name": "Michael Lincoln"
},
"description": "NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes.",
"homepage": "http://www.pbm.va.gov/NationalFormulary.aspx",
"name": "Veterans Health Administration National Drug File",
"prefix": "VANDF",
"version": "2023AB"
},
"VARIO": {
"contact": {
"email": "mauno.vihinen@med.lu.se",
"name": "Mauno Vihinen"
},
"description": "Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations. Ontology is unreachable as of 2024, but continues to be available on BioPortal as a retired ontology.",
"homepage": "http://variationontology.org",
"name": "Variation Ontology",
"prefix": "VARIO",
"publication": "https://obofoundry.org/ontology/vario",
"version": "2018-11-09"
},
"VBO": {
"contact": {
"email": "Sabrina@tislab.org",
"name": "Sabrina Toro"
},
"description": "Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.",
"homepage": "https://github.com/monarch-initiative/vertebrate-breed-ontology",
"name": "Vertebrate Breed Ontology",
"prefix": "VBO",
"version": "2024-05-22"
},
"VDOT": {
"contact": {
"email": "ulf.schwarz@ifomis.uni-saarland.de",
"name": "Ulf Schwarz"
},
"description": "VDOT is a middle-layer ontology for the health care domain with special emphasis on viral infections and transplantation medicine.",
"name": "Viral Disease Ontology Trunk",
"prefix": "VDOT",
"version": "Initial Version\nrelease date 28/02/2017"
},
"VEO": {
"contact": {
"email": "rlin29@jhu.edu",
"name": "Rebecca Lin"
},
"description": "Visual Emotion Ontology (VEO) is an ontology that links visualizations with specific emotions from the Ortony, Clore, and Collins' description of human emotions.",
"name": "Visualized Emotion Ontology",
"prefix": "VEO",
"publication": "https://doi.org/10.1186/s12911-018-0634-6",
"version": "0.5"
},
"VFB_DRIVERS": {
"contact": {
"email": "cp390@cam.ac.uk",
"name": "Clare Pilgrim"
},
"description": "An ontology of Drosophila melanogaster drivers and expression patterns.",
"name": "vfb_drivers",
"prefix": "VFB_DRIVERS",
"version": "2024-08-05"
},
"VHOG": {
"contact": {
"email": "bgee@isb-sib.ch",
"name": "Bgee team"
},
"description": "vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 \"historical homology\". Each mapping has been manually reviewed, and we provide confidence codes and references when available.",
"homepage": "http://bgee.unil.ch",
"name": "Vertebrate Homologous Organ Group Ontology",
"prefix": "VHOG",
"publication": "http://www.unil.ch/dee/page31219_en.html",
"version": "unknown"
},
"VICO": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He"
},
"description": "The Vaccination Informed Consent Ontology (VICO) is a community-driven ontology in the domain of vaccination/immunization informed consent.",
"homepage": "https://github.com/VICO-ontology",
"name": "Vaccination Informed Consent Ontology",
"prefix": "VICO",
"version": "Arbor version; 1.0.52"
},
"VIDO": {
"contact": {
"email": "johnbeve@buffalo.edu",
"name": "John Beverley"
},
"description": "The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc.",
"homepage": "https://github.com/infectious-disease-ontology-extensions/ido-virus",
"name": "Virus Infectious Disease Ontology",
"prefix": "VIDO",
"publication": "https://osf.io/5bx8c",
"version": "10-27-2022"
},
"VIMM": {
"contact": {
"email": "giulia.panzarella3@gmail.com",
"name": "Giulia Panzarella"
},
"description": "MAATrica is a novel metric for assessing the coherence of methodologies in research papers within the fields of medicinal and nutraceutical chemistry. MAATrica employs user-controlled and customizable ontologies (in silico, in vitro and in vivo), enabling personalized analysis of research papers in the fields of medicinal and nutraceutical chemistry. Here we present the in vitro ontology we developed for the scope.",
"name": "In Vitro Methodologies Ontology for MAATrica metric",
"prefix": "VIMM"
},
"VIO": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun He"
},
"description": "VIO is an VO-extended ontology with the aim to standardize the metadata types in various vaccine investigation studies.",
"homepage": "https://github.com/vaccineontology/VIO",
"name": "Vaccine Investigation Ontology",
"prefix": "VIO",
"publication": "https://sites.google.com/site/vdosworkshop/VDOS-2018",
"version": "Vision Release: 1.0.01"
},
"VIVO": {
"contact": {
"email": "sjm222@cornell.edu",
"name": "Stella Mitchell"
},
"description": "The VIVO ontology represents researchers in the context of their experience, outputs, interests, accomplishments, and associated institutions.",
"homepage": "http://vivoweb.org/ontology/core",
"name": "VIVO Ontology for Researcher Discovery",
"prefix": "VIVO",
"version": "version 1.7"
},
"VIVO-ISF": {
"contact": {
"email": "vivo-ontology@lists.sourceforge.net",
"name": "VIVO-ISF Listserv"
},
"description": "The Integrated Semantic Framework ontology modules for VIVO (the VIVO-ISF ontology) provide a set of types (classes) and relationships (properties) to represent researchers and the full context in which they work.",
"homepage": "vivoweb.org",
"name": "VIVO-Integrated Semantic Framework",
"prefix": "VIVO-ISF",
"version": "1.6"
},
"VO": {
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqunh He"
},
"description": "A biomedical ontology in the vaccine domain",
"homepage": "https://github.com/vaccineontology/VO",
"name": "Vaccine Ontology",
"prefix": "VO",
"version": "2024-07-13"
},
"VODANA-GENERAL": {
"contact": {
"email": "aleka.aktau@gmail.com",
"name": "Aliya Aktau"
},
"description": "VODANA's General list of terms that are used within Outpatient Department Registration and Antenatal Care Templates.",
"name": "VODANATERMS",
"prefix": "VODANA-GENERAL",
"version": "8"
},
"VODANA-MI": {
"contact": {
"email": "ghardallou.m@gmail.com",
"name": "Ghardallou"
},
"description": "Migrants Interviews Ontologies",
"name": "VODANA-MIGRANTS-INTERVIEWS",
"prefix": "VODANA-MI",
"version": "2.0"
},
"VODANA-MIGRANTS": {
"contact": {
"email": "ghardallou.m@gmail.com",
"name": "Ghardallou"
},
"description": "migrants ontologies",
"name": "VODANA MIGRANTS VOCABULARY",
"prefix": "VODANA-MIGRANTS",
"version": "1"
},
"VODANA-MPA": {
"contact": {
"email": "ghardallou.m@gmail.com",
"name": "Ghardallou"
},
"description": "migrants Press Articles ontologies",
"name": "VODANA-MIGRANTS-PRESS ARTICLES",
"prefix": "VODANA-MPA",
"version": "2"
},
"VODANACOVID": {
"contact": {
"email": "m.basajja@liacs.leidenuniv.nl",
"name": "Mariam Basajja"
},
"description": "Ontology containing the controlled terms and semantic properties used in the COVID-19 generic template used within different facilities in VODANA",
"name": "VODANA-COVIDTERMS",
"prefix": "VODANACOVID",
"version": "3.0"
},
"VODANADISEASES": {
"contact": {
"email": "aleka.aktau@gmail.com",
"name": "Aliya Aktau"
},
"description": "Vodana disease terms based on WHO's ICD-11 standards intended for coding health information for FAIR implementation countries in Africa",
"name": "VODANADiseases",
"prefix": "VODANADISEASES",
"version": "2.0.1"
},
"VODANAKENYA": {
"contact": {
"email": "wmnandwa77@gmail.com",
"name": "William Muhadi Nandwa"
},
"description": "Ontology containing the controlled terms and semantic properties used in the Ontology for Out-patient Claim Form NHIS",
"name": "VODANA KENYA",
"prefix": "VODANAKENYA",
"version": "0.1.1"
},
"VODANAMFLCODE": {
"contact": {
"email": "mariam.basajja@gmail.com",
"name": "Mariam Basajja"
},
"description": "This is the list of VODANA health facilities with VODANA MFL Code.",
"name": "VODANAFACILITIESLIST",
"prefix": "VODANAMFLCODE",
"version": "4.0"
},
"VODANANIGERIA": {
"contact": {
"email": "mariam.basajja@gmail.com",
"name": "Mariam Basajja"
},
"description": "This ontology contains controlled terms and properties of the out patient register claim report used to collect out patient information within different facilities in Nigeria.",
"name": "VODANANIGERIA",
"prefix": "VODANANIGERIA",
"version": "2.0"
},
"VODANAUGANDA": {
"contact": {
"email": "mariam.basajja@gmail.com",
"name": "Mariam Basajja"
},
"description": "This is an ontology comprising of controlled vocabulary terms and properties about the data collected using the Out Patient Register 002 in different health facilities in Uganda.",
"name": "VODANAUGANDA",
"prefix": "VODANAUGANDA",
"version": "2.0"
},
"VODANETHIOPIA_OR": {
"contact": {
"email": "aleka.aktau@gmail.com",
"name": "Aliya Aktau"
},
"description": "These are terms of Outpatient Register Ethiopia",
"name": "ETHIOPIA_OUTPATIENT",
"prefix": "VODANETHIOPIA_OR",
"version": "2"
},
"VODAN_ANC": {
"contact": {
"email": "tesfitgebremeskel@gmail.com",
"name": "Tesfit Gebremeskel"
},
"description": "This is a general comment that will be ignored. The converter will detect automatically the line containing the column titles below, so you can have a header as long as you want.",
"homepage": "https://vodan-totafrica.info/ANC",
"name": "VODAN ANC Vocabulary",
"prefix": "VODAN_ANC",
"version": "VI"
},
"VRD": {
"contact": {
"email": "aleka.aktau@gmail.com",
"name": "Aliya Aktau"
},
"description": "This is test",
"name": "Vaccineresearchdata",
"prefix": "VRD",
"version": "2.0"
},
"VSAO": {
"contact": {
"email": "wasila.dahdul@usd.edu",
"name": "Wasila Dahdul"
},
"description": "VSAO is an anatomy ontology covering the vertebrate skeletal system. VSAO integrates terms for skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system.",
"homepage": "http://phenoscape.org/wiki/Main_Page",
"name": "Vertebrate Skeletal Anatomy Ontology",
"prefix": "VSAO",
"publication": "http://dx.plos.org/10.1371/journal.pone.0051070",
"version": "2012-11-06"
},
"VSO": {
"contact": {
"email": "albertgoldfain@gmail.com",
"name": "Albert Goldfain"
},
"description": "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.",
"homepage": "http://code.google.com/p/vital-sign-ontology/",
"name": "Vital Sign Ontology",
"prefix": "VSO",
"publication": "http://ontology.buffalo.edu/smith/articles/Vital_Sign_Ontology.pdf",
"version": "2012-04-25"
},
"VT": {
"contact": {
"email": "jreecy@iastate.edu",
"name": "Jim Reecy"
},
"description": "The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.",
"homepage": "https://www.animalgenome.org/bioinfo/projects/vt/",
"name": "Vertebrate Trait Ontology",
"prefix": "VT",
"publication": "https://www.animalgenome.org/bioinfo/projects/vt/",
"version": "releases/2024-07-22"
},
"VTO": {
"contact": {
"email": "balhoff@renci.org",
"name": "James Balhoff"
},
"description": "The Vertebrate Taxonomy Ontology includes both extinct and extant vertebrates, aiming to provide one comprehensive hierarchy. The hierarchy backbone for extant taxa is based on the NCBI taxonomy. Since the NCBI taxonomy only includes species associated with archived genetic data, to complement this, we also incorporate taxonomic information across the vertebrates from the Paleobiology Database (PaleoDB). The Teleost Taxonomy Ontology (TTO) and AmphibiaWeb (AWeb) are incorporated to provide a more authoritative hierarchy and a richer set of names for specific taxonomic groups.",
"homepage": "http://code.google.com/p/vertebrate-taxonomy-ontology/",
"name": "Vertebrate Taxonomy Ontology",
"prefix": "VTO",
"version": "unknown"
},
"VVMM": {
"contact": {
"email": "giulia.panzarella3@gmail.com",
"name": "Giulia Panzarella"
},
"description": "MAATrica is a novel metric for assessing the coherence of methodologies in research papers within the fields of medicinal and nutraceutical chemistry. MAATrica employs user-controlled and customizable ontologies (in silico, in vitro and in vivo), enabling personalized analysis of research papers in the fields of medicinal and nutraceutical chemistry. Here we present the in vivo ontology we developed for the scope.",
"name": "In Vivo Methodologies Ontology for MAATrica metric",
"prefix": "VVMM"
},
"WB-BT": {
"contact": {
"email": "raymond@caltech.edu",
"name": "Raymond Lee"
},
"description": "A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.",
"homepage": "http://www.wormbase.org/",
"name": "C. elegans Gross Anatomy Vocabulary",
"prefix": "WB-BT",
"version": "releases/2024-07-01"
},
"WB-LS": {
"contact": {
"email": "wchen@its.caltech.edu",
"name": "Worm_development Administrators"
},
"description": "A structured controlled vocabulary of the development of Caenorhabditis elegans.",
"homepage": "http://www.wormbase.org/",
"name": "C. elegans Development Vocabulary",
"prefix": "WB-LS",
"version": "unknown"
},
"WB-PHENOTYPE": {
"contact": {
"email": "garys@caltech.edu",
"name": "Gary Schindelman"
},
"description": "A structured controlled vocabulary of Caenorhabditis elegans phenotypes",
"homepage": "http://www.wormbase.org/",
"name": "C. elegans Phenotype Vocabulary",
"prefix": "WB-PHENOTYPE",
"version": "releases/2024-06-05"
},
"WC": {
"contact": {
"email": "info@karrlab.org",
"name": "Karr Lab"
},
"description": "Ontology for whole-cell (WC) modeling See https://wholecell.org for more information about WC modeling",
"homepage": "https://github.com/karrlab/wc_onto",
"name": "Whole-cell modeling ontology",
"prefix": "WC",
"version": "0.0.1"
},
"WEAR": {
"contact": {
"email": "nikola@fairdatacollective.com",
"name": "Nikola Vasiljevic"
},
"description": "Controlled vocabularies such as taxonomies allow an accurate and controlled approach in describing datasets. One of such controlled vocabulary is Wind Energy Taxonomy of Activities. This taxonomy is the result of EERA JP WIND IRPWind Open Data initiative that took place in 2017 in which wind energy experts generated the first version of the taxonomy as an input for defining and structuring wind energy metadata. The report of this work is available at Zenodo: https://www.zenodo.org/record/1199489#.XSD6haeQ3RY In 2018, the taxonomy of topics was improved during the internal project of DTU Wind Energy titled 'FAIR Digitalization': https://www.zenodo.org/record/1493874#.XSD7TaeQ3RY In 2021, the taxonomy was converted into FAIR machine-actionable controlled vocabulary using sheet2rdf. The controlled vocabulary is served to humans and machines using an instace of OntoStack hosted by DTU Wind Energy. sheet2rdf and OntoStack are developed by FAIR Data Collective. Additionally, in 2021, the persistent URL purl.org/wear has been registered for the taxonomy. This allows us to: If there is a needed to move the taxonomy to another domain (currently under data.windenergy.dtu.dk) URLs will be still resolvable and unchanged Use short URls as PIDs for the taxonomy terms and properties.",
"homepage": "https://github.com/DTUWindEnergy/WEAR-taxonomy",
"name": "WEAR: Wind Energy mAteRials Taxonomy",
"prefix": "WEAR",
"publication": "https://github.com/DTUWindEnergy/WEAR-taxonomy",
"version": "v0.1.0"
},
"WEAVE": {
"contact": {
"email": "nikola@fairdatacollective.com",
"name": "Nikola Vasiljevic"
},
"description": "Controlled vocabularies such as taxonomies allow an accurate and controlled approach in describing datasets. One of such controlled vocabulary is Wind Energy Taxonomy of Activities. This taxonomy is the result of EERA JP WIND IRPWind Open Data initiative that took place in 2017 in which wind energy experts generated the first version of the taxonomy as an input for defining and structuring wind energy metadata. The report of this work is available at Zenodo: https://www.zenodo.org/record/1199489#.XSD6haeQ3RY In 2018, the taxonomy of topics was improved during the internal project of DTU Wind Energy titled 'FAIR Digitalization': https://www.zenodo.org/record/1493874#.XSD7TaeQ3RY In 2021, the taxonomy was converted into FAIR machine-actionable controlled vocabulary using sheet2rdf. The controlled vocabulary is served to humans and machines using an instace of OntoStack hosted by DTU Wind Energy. sheet2rdf and OntoStack are developed by FAIR Data Collective. Additionally, in 2021, the persistent URL purl.org/weave has been registered for the taxonomy. This allows us to: If there is a needed to move the taxonomy to another domain (currently under data.windenergy.dtu.dk) URLs will be still resolvable and unchanged Use short URls as PIDs for the taxonomy terms and properties such as: purl.org/weave/Measurements",
"homepage": "https://github.com/DTUWindEnergy/WEAVE-taxonomy#weave-wind-energy-activities",
"name": "WEAVE: Wind Energy ActiVitiEs",
"prefix": "WEAVE",
"publication": "https://github.com/DTUWindEnergy/WEAVE-taxonomy#weave-wind-energy-activities",
"version": "v0.1.0"
},
"WETAXTOPICS": {
"contact": {
"email": "anse@dtu.dk",
"name": "Anna Maria Sempreviva"
},
"description": "Controlled vocabularies such as taxonomies allow an accurate and controlled approach in describing datasets. One of such controlled vocabulary is Wind Energy Taxonomy of Topics. This taxonomy is the result of EERA JP WIND IRPWind Open Data initiative that took place in 2017 in which wind energy experts generated the first version of the taxonomy as an input for defining and structuring wind energy metadata. The report of this work is available at Zenodo: https://www.zenodo.org/record/1199489#.XSD6haeQ3RY In 2018, the taxonomy of topics was improved during the internal project of DTU Wind Energy titled 'FAIR Digitalization': https://www.zenodo.org/record/1493874#.XSD7TaeQ3RY In 2020, the definition of taxonomy terms were added and the taxonomy was converted into FAIR machine-actionable controlled vocabulary using sheet2rdf. The controlled vocabulary is served to humans and machines using an instace of OntoStack hosted by DTU Wind Energy.",
"homepage": "http://purl.org/neat/",
"name": "NEAT: wiNd Energy tAxonomy of Topics",
"prefix": "WETAXTOPICS",
"publication": "https://www.zenodo.org/record/1199489#.XSD6haeQ3RY",
"version": "v0.1.1"
},
"WHO-ART": {
"contact": {
"email": "support@who.int",
"name": "WHO Collaborating Centre for International Drug Monitoring"
},
"description": "WHO Adverse Reaction Terminology, 1997",
"homepage": "http://www.who.int/",
"name": "World Health Organization (WHO) Adverse Reaction Terminology",
"prefix": "WHO-ART",
"publication": "http://www.who.int/",
"version": "2023AA"
},
"WIKIPATHWAYS": {
"contact": {
"email": "egon.willighagen@gmail.com",
"name": "Egon Willighagen"
},
"description": "The WP ontology for WikiPathways.",
"homepage": "https://www.wikipathways.org/",
"name": "WikiPathways",
"prefix": "WIKIPATHWAYS",
"publication": "https://scholia.toolforge.org/topic/Q7999828"
},
"WSIO": {
"contact": {
"email": "matus.kalas@uib.no",
"name": "Matus Kalas"
},
"description": "Web Service Interaction Ontology (WSIO) enables automated interaction with more complex Web services that are typical for example within life sciences. WSIO is however independent of the application domain and relevant for both SOAP and REST Web services, and for batch execution engines in general. If the interaction scenario with a Web service is nontrivial (and incorporates session handling), annotation with WSIO concepts will enable automatic generation of client programs, scripts, or interactive applications with a graphical user interface. WSIO also enables automation of different ways of data transfer and data un-/compression or en-/decoding. We strongly discourage providers from developing complex interaction and data-transfer/compression scenarios, however when needed, WSIO may enable smooth automated interaction with them. Future versions will support more interaction scenarios. WSIO aims to serve also as a means to standardise the complex interaction scenarios primarily within both SOAP and REST Web services, and secondarily to apply also to batch execution infrastructure in general.",
"homepage": "http://wsio.org",
"name": "Web-Service Interaction Ontology",
"prefix": "WSIO",
"version": "beta2"
},
"WWECA": {
"contact": {
"email": "Yilinxia_99@163.com",
"name": "Xia Yilin"
},
"description": "This is an ontology for the management of women of child-bearing age with epilepsy.",
"name": "Women with Epilepsy of Child-bearing Age Ontology",
"prefix": "WWECA",
"version": "3.0"
},
"XAO": {
"contact": {
"email": "Virgilio.Ponferrada@cchmc.org",
"name": "VG Ponferrada"
},
"description": "A structured, controlled vocabulary of the anatomy and development of the African clawed frogs (Xenopus laevis and tropicalis).",
"homepage": "http://www.xenbase.org/anatomy/xao.do?method=display",
"name": "Xenopus Anatomy Ontology",
"prefix": "XAO",
"publication": "http://www.jbiomedsem.com/content/4/1/31/abstract",
"version": "releases/2022-08-29"
},
"XCO": {
"contact": {
"email": "akwitek@mcw.edu",
"name": "Anne Kwitek"
},
"description": "The Experimental Conditions Ontology is designed to represent the conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.",
"homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000",
"name": "Experimental Conditions Ontology",
"prefix": "XCO",
"publication": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361058/",
"version": "4.177"
},
"XEO": {
"contact": {
"email": "billiau@mpimp-golm.mpg.de",
"name": "Kenny Billiau"
},
"description": "XeO has been created to help plant scientists in documenting and sharing metadata describing the abiotic environment.",
"homepage": "http://xeo.codeplex.com/",
"name": "XEML Environment Ontology",
"prefix": "XEO",
"version": "1.6"
},
"XLMOD": {
"contact": {
"email": "gerhard.mayer@rub.de",
"name": "Gerhard Mayer"
},
"description": "XLMOD is an ontology for cross-linking mass spectrometry reagents and GC-MS derivatization reagents.",
"homepage": "https://github.com/HUPO-PSI/mzIdentML/tree/master/cv",
"name": "mass spectrometry cross-linking and derivatization reagents",
"prefix": "XLMOD",
"version": "release/2019-10-28"
},
"XPO": {
"contact": {
"email": "esegerd3@gmail.com",
"name": "Erik Segerdell"
},
"description": "An ontology of anatomical, cellular, and gene function phenotypes in Xenopus, the African clawed frogs. The Xenopus Phenotype Ontology represents and standardizes anatomical, cellular, and gene function phenotypes in Xenopus, the African clawed frogs. The XPO is being designed primarily to support phenotype curation in Xenbase, the model organism database for Xenopus, and to facilitate mappings between frog phenotypes and human disease.",
"homepage": "https://github.com/obophenotype/xenopus-phenotype-ontology",
"name": "Xenopus Phenotype Ontology",
"prefix": "XPO",
"version": "2024-04-18"
},
"XREF-FUNDER-REG": {
"contact": {
"email": "jgraybeal@stanford.edu",
"name": "John Graybeal"
},
"description": "The Funder Registry provides a common taxonomy of international funding body names that funding data participants should use to normalize funder names and IDs for deposit with Crossref. The list can be used to present authors with a pre-populated \"Funder Name\" option at the time of submission, and can also be used to match funder names extracted from papers. The list is available to download as an RDF file, and is freely available under a CC0 license waiver. This information was obtained from a GitLab repository created by Bryan Vickery (see Homepage). The first version downloaded was 1.34.",
"homepage": "https://gitlab.com/crossref/open_funder_registry",
"name": "CrossRef Funder Registry",
"prefix": "XREF-FUNDER-REG"
},
"ZAHRAHADDAD": {
"contact": {
"email": "fkh510@gmail.com",
"name": "khosravi"
},
"description": "Ψ§ΩΨͺΩΩΩΪΫ Ψ§Ψ±ΨͺΨ¨Ψ§Ψ·Ψ§Ψͺ Ψ¨Ω Ψ²Ψ¨Ψ§Ω ΩΨ§Ψ±Ψ³Ϋ",
"name": "Ψ§Ψ±ΨͺΨ¨Ψ§Ψ·Ψ§Ψͺ",
"prefix": "ZAHRAHADDAD"
},
"ZEA": {
"contact": {
"email": "Leszek@missouri.edu",
"name": "Leszek Vincent"
},
"homepage": "http://www.maizemap.org/",
"name": "Maize Gross Anatomy Ontology",
"prefix": "ZEA",
"version": "1.2"
},
"ZECO": {
"contact": {
"email": "ybradford@zfin.org",
"name": "Yvonne Bradford"
},
"description": "This ontology is designed to represent the experimental conditions applied to zebrafish and has been developed to facilitate experiment condition annotation at ZFIN.",
"homepage": "https://github.com/ybradford/zebrafish-experimental-conditions-ontology",
"name": "Zebrafish Experimental Conditions Ontology",
"prefix": "ZECO",
"version": "2022-02-14"
},
"ZFA": {
"contact": {
"email": "zfinadmin@zfin.org",
"name": "ZFIN administrators"
},
"description": "A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio).",
"homepage": "http://zfin.org/zf_info/anatomy/dict/sum.html",
"name": "Zebrafish Anatomy and Development Ontology",
"prefix": "ZFA",
"publication": "http://www.jbiomedsem.com/content/5/1/12",
"version": "releases/2022-12-09"
},
"ZFS": {
"contact": {
"email": "zfinadmin@zfin.org",
"name": "ZFIN administrators"
},
"description": "An ontology of developmental stages of the Zebrafish (Danio rerio). Note that ZFA includes the leaf nodes of this ontology.",
"name": "Zebrafish Developmental Stages",
"prefix": "ZFS"
},
"ZONMW-ADMIN-MD": {
"contact": {
"email": "jgraybeal@stanford.edu",
"name": "John Graybeal"
},
"description": "Collections of terms for the ZonMW COVID Training project. These terms are based on vocabularies provided for describing project-level metadata. This submission was created using SKOS Play from an Excel spreadsheet.",
"homepage": "https://github.com/fair-data-collective/zonmw-project-admin/tree/main/ontology",
"name": "ZonMW Administrative Metadata Vocabulary",
"prefix": "ZONMW-ADMIN-MD",
"version": "1.2.0a"
},
"ZONMW-CONTENT": {
"description": "DEMO-vocabulary with collections of terms for the ZonMW COVID19 programme created in M4M.14 facilitated by GO FAIR Foundation. These terms are based on vocabularies provided for describing project and data content metadata. This submission was created using sheet2rdf GitHub workflow.",
"homepage": "https://raw.githubusercontent.com/gofair-foundation/vocabs_archive/main/zonmw_content.ttl",
"name": "ZonMW COVID-19",
"prefix": "ZONMW-CONTENT",
"version": "2.4.0"
},
"ZONMW-GENERIC": {
"description": "DEMO Vocabulary for general-purpose terms for the ZonMw Community built in M4M.14",
"homepage": "https://raw.githubusercontent.com/gofair-foundation/vocabs_archive/main/zonmw_generic.ttl",
"name": "ZonMw Generic Terms",
"prefix": "ZONMW-GENERIC",
"version": "1.5.0"
},
"ZP": {
"contact": {
"email": "ybradford@zfin.org",
"name": "Yvonne Bradford"
},
"description": "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.",
"homepage": "https://github.com/obophenotype/zebrafish-phenotype-ontology",
"name": "Zebrafish Phenotype Ontology",
"prefix": "ZP",
"version": "2024-04-18"
},
"pseudo": {
"contact": {
"email": "yhl3@gersteinlab.org",
"name": "Gerstein Lab"
},
"name": "Pseudogene",
"prefix": "pseudo",
"version": "0.1"
},
"suicideo": {
"contact": {
"email": "alexgarciac@gmail.com",
"name": "alexander garcia"
},
"description": "ontology for suicidology",
"name": "suicideonto",
"prefix": "suicideo",
"version": "2"
}
} ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/bioportal/bioportal.py 0000644 0001751 0000177 00000001661 14655542206 025153 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Align the BioPortal with the Bioregistry."""
from bioregistry.external.alignment_utils import Aligner
from bioregistry.external.bioportal import get_agroportal, get_bioportal, get_ecoportal
__all__ = [
# Base class
"OntoPortalAligner",
# Concrete classes
"BioPortalAligner",
"AgroPortalAligner",
"EcoPortalAligner",
]
class OntoPortalAligner(Aligner):
"""Aligner for OntoPortal."""
curation_header = ("name", "homepage", "description")
class BioPortalAligner(OntoPortalAligner):
"""Aligner for BioPortal."""
key = "bioportal"
getter = get_bioportal
class EcoPortalAligner(OntoPortalAligner):
"""Aligner for EcoPortal."""
key = "ecoportal"
getter = get_ecoportal
class AgroPortalAligner(OntoPortalAligner):
"""Aligner for AgroPortal."""
key = "agroportal"
getter = get_agroportal
if __name__ == "__main__":
BioPortalAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/bioportal/ecoportal.json 0000644 0001751 0000177 00000055605 14655542206 025500 0 ustar 00runner docker {
"ACFORMAT": {
"contact": {
"email": "steve.baskauf@vanderbilt.edu",
"name": "Steve Baskauf"
},
"description": "Audubon Core borrows the Dublin Core terms dc:format and dcterms:format to provide information about the physical or electronic format of a media item. This controlled vocabulary provides values for those two terms.",
"name": "Audubon Core Controlled Vocabulary for Dublin Core format",
"prefix": "ACFORMAT",
"publication": "https://ac.tdwg.org/format/",
"version": "2020-10-13"
},
"ACSUBTYPE": {
"contact": {
"email": "steve.baskauf@vanderbilt.edu",
"name": "Steve Baskauf"
},
"description": "Audubon Core uses the terms ac:subtype and ac:subtypeLiteral to refine the type of a media item to a level more specific than the Dublin Core Type Vocabulary, http://purl.org/dc/dcmitype/. This controlled vocabulary provides values for ac:subtype and ac:subtypeLiteral.",
"homepage": "http://rs.tdwg.org/ac/doc/subtype/",
"name": "Audubon Core subtype Controlled Vocabulary",
"prefix": "ACSUBTYPE",
"publication": "http://rs.tdwg.org/ac/doc/subtype/",
"version": "2020-10-13"
},
"ACTRIS_CL": {
"contact": {
"email": "mf@nilu.no",
"name": "Markus Fiebig"
},
"description": "Lists of controlled terms used in ACTRIS",
"homepage": "https://vocabulary.actris.nilu.no/skosmos/actris_ctrl_lists/en/",
"license": "CC0-1.0",
"name": "ACTRIS Controlled Lists",
"prefix": "ACTRIS_CL",
"version": "1.0.0"
},
"ACTRIS_VOCAB": {
"contact": {
"email": "mf@nilu.no",
"name": "Markus Fiebig"
},
"description": "Controlled vocabulary of terms used in ACTRIS",
"homepage": "https://vocabulary.actris.nilu.no/skosmos/actris_vocab/en/",
"license": "CC0-1.0",
"name": "ACTRIS Vocabulary",
"prefix": "ACTRIS_VOCAB",
"publication": "https://vocabulary.actris.nilu.no/skosmos/actris_vocab/en/",
"version": "1.1.1"
},
"ACVARIANT": {
"contact": {
"email": "steve.baskauf@vanderbilt.edu",
"name": "Steve Baskauf"
},
"description": "Audubon Core uses the terms ac:variant and ac:variantLiteral to provide information about the size, extent, and availability of the Service Access Point of a media item. This controlled vocabulary provides values for those terms.",
"name": "Audubon Core variant Controlled Vocabulary",
"prefix": "ACVARIANT",
"publication": "http://rs.tdwg.org/ac/doc/variant/",
"version": "2020-10-13"
},
"AGROVOC": {
"contact": {
"email": "agrovoc@fao.org",
"name": "AGROVOC Team"
},
"description": "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is a large Linked Open Data set about agriculture, available for public use, and its highest impact is through facilitating the access and visibility of data across domains and languages.",
"homepage": "http://www.fao.org/agrovoc/",
"license": "CC-BY-4.0",
"name": "AGROVOC",
"prefix": "AGROVOC",
"publication": "https://www.fao.org/agrovoc/publications",
"version": "2024-04"
},
"ALIENSPECIES": {
"contact": {
"email": "ilaria.rosati@cnr.it",
"name": "Ilaria Rosati"
},
"description": "The Alien Species Thesaurus is an initiative to deal with the semantics about alien and invasive species. It has been developed and published by LifeWatch Italy, the Italian node of the e-science European infrastructure for biodiversity and ecosystem research (LifeWatch ERIC). It is developed on the basis of already existing glossaries created within the framework of international initiatives aimed at the study of alien and invasive species. The terms (or concepts) are shared very broadly by the scientific community, and their definitions derive from guidelines prepared by relevant international organizations, and only in few occasions by peer reviewed papers. The Thesaurus currently consists of 157 terms.",
"name": "Alien Species Thesaurus",
"prefix": "ALIENSPECIES",
"publication": "https://www.lifewatchitaly.eu/publications/#1590425563910-01d9d51a-b764",
"version": "2.5"
},
"BCO": {
"contact": {
"email": "rlwalls2008@gmail.com",
"name": "Ramona Walls"
},
"description": "The BCO supports the interoperability of biodiversity and biodiversity related data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. A key aspect of the BCO is distinguishing among material samples (i.e. specimens), observing processes, and data about either of those entities.",
"homepage": "https://github.com/BiodiversityOntologies/bco",
"name": "BioCollections Ontology",
"prefix": "BCO",
"publication": "https://github.com/BiodiversityOntologies/bco",
"version": "2021-11-14"
},
"BIODIVTHES": {
"contact": {
"email": "contact-terminologietal@inist.fr",
"name": "Loterre contact"
},
"description": "This bilingual thesaurus organizes the key concepts of biodiversity sciences, in their basic and applied ecological components. It uses polyhierarchy and includes 818 reciprocal associative relationships. The 1654 French and English descriptors (designating 827 concepts) are enriched with a large number of synonyms (1860) and hidden variants (7020) in both languages. Concepts are grouped into 82 collections, by semantic categories, thematic fields and EBV classes (Essential Biodiversity Variables). Definitions are given with their sources. This resource is aligned with the international thesauri AGROVOC, GEMET (GEneral Multilingual Environmental Thesaurus) and EnvThes (Environmental Thesaurus), as well as with the ontology ENVO (Environment Ontology).",
"name": "Biodiversity Thesaurus",
"prefix": "BIODIVTHES",
"publication": "https://hal.archives-ouvertes.fr/hal-02907484",
"version": "2.1"
},
"CPMETA": {
"contact": {
"email": "oleg.mirzov@nateko.lu.se",
"name": "Oleg Mirzov"
},
"description": "OWL vocabulary describing metadata of two environmental research infrastructures: ICOS and SITES, as well as of a pilot project ICOS Cities",
"homepage": "https://github.com/ICOS-Carbon-Portal/meta/blob/master/src/main/resources/owl/cpmeta.owl",
"license": "CC0-1.0",
"name": "Ontology of Integrated Carbon Observation System (ICOS)",
"prefix": "CPMETA",
"version": "1.1"
},
"DSW": {
"contact": {
"email": "steve.baskauf@vanderbilt.edu",
"name": "Steve Baskauf"
},
"description": "Darwin-SW (DSW) is an RDF vocabulary designed to complement the Biodiversity Information Standards (TDWG) Darwin Core Standard. DSW is based on a model derived from a community discussion about the relationships among the main Darwin Core classes.",
"homepage": "https://github.com/darwin-sw/dsw",
"name": "Darwin-SW",
"prefix": "DSW",
"publication": "http://www.semantic-web-journal.net/content/darwin-sw-darwin-core-based-terms-expressing-biodiversity-data-rdf-1",
"version": "1.0.1"
},
"DWCDOE": {
"contact": {
"email": "steve.baskauf@vanderbilt.edu",
"name": "Steve Baskauf"
},
"description": "The Darwin Core term degreeOfEstablishment provides information about degree to which an Organism survives, reproduces, and expands its range at the given place and time. The Degree of Establishment Controlled Vocabulary provides term that should be used as values for dwc:degreeOfEstablishment and dwciri:degreeOfEstablishment",
"example_uri": "http://xmlns.com/foaf/0.1/document",
"name": "Darwin Core Degree Of Establishment Controlled Vocabulary",
"prefix": "DWCDOE",
"version": "1.0"
},
"DWCEM": {
"contact": {
"email": "tuco@berkeley.edu",
"name": "John Wieczorek"
},
"description": "The Darwin Core term establishmentMeans provides information about whether an organism or organisms have been introduced to a given place and time through the direct or indirect activity of modern humans. The Establishment Means Controlled Vocabulary provides terms that should be used as values for dwc:establishmentMeans and dwciri:establishmentMeans.",
"homepage": "http://rs.tdwg.org/dwc/doc/em/",
"name": "Darwin Core Establishment Means Controlled Vocabulary",
"prefix": "DWCEM",
"publication": "https://doi.org/10.3897/biss.3.38084",
"version": "2021-09-01"
},
"DWCPW": {
"contact": {
"email": "tuco@berkeley.edu",
"name": "John Wieczorek"
},
"description": "The Darwin Core term pathway provides information about the process by which an Organism came to be in a given place at a given time. The Pathway Controlled Vocabulary provides terms that should be used as values for dwc:pathway and dwciri:pathway.",
"homepage": "http://rs.tdwg.org/dwc/doc/pw/",
"name": "Darwin Core Pathway Controlled Vocabulary",
"prefix": "DWCPW",
"publication": "https://doi.org/10.3897/biss.3.38084",
"version": "2021-09-01"
},
"ECSO": {
"contact": {
"email": "mecum@nceas.ucsb.edu",
"name": "Bryce Mecum"
},
"description": "DataONE ontology of Carbon Flux measurements for MsTMIP and LTER Use Cases",
"homepage": "https://bioportal.bioontology.org/ontologies/ECSO",
"name": "The Ecosystem Ontology",
"prefix": "ECSO",
"repository": "https://github.com/DataONEorg/sem-prov-ontologies/tree/ECSO8-add_non-carbon_measurements",
"version": "0.9.1"
},
"ELTER_CL": {
"description": "eLTER_CL is a thesaurus for controlled lists used by the eLTER community",
"license": "CC-BY-4.0",
"name": "eLTER Controlled Lists",
"prefix": "ELTER_CL",
"version": "1.1.0"
},
"ENDEMISMS": {
"contact": {
"email": "stefano.de.felici@uniroma2.it",
"name": "Stefano De Felici"
},
"description": "Thesaurus on endemisms",
"name": "Endemisms Thesaurus",
"prefix": "ENDEMISMS",
"publication": "http://www.lifewatchitaly.eu/web/lifewatch-italia/reports",
"version": "2.0"
},
"ENVTHES": {
"description": "EnvThes compiles a set of terms in order to describe in a harmonised way data resulting from observations and measurements of ecosystem processes across different domain specific sciences. It is used by DEIMS-SDR for common keywords for annotation and quering metadata purposes.",
"license": "CC-BY-4.0",
"name": "Environmental Thesaurus",
"prefix": "ENVTHES",
"publication": "https://www.w3.org/2013/share-psi/wiki/images/0/00/Schentz_et_al_SemanticDataIntegrationforLTER.pdf",
"version": "5.0.5"
},
"EURIO": {
"contact": {
"email": "OP-EU-VOCABULARIES@publications.europa.eu",
"name": "Publications Office of the European Union"
},
"description": "EURIO (EUropean Research Information Ontology) conceptualises, formally encodes and makes available in an open, structured and machine-readable format data about resarch projects funded by the EU's framework programmes for research and innovation.",
"homepage": "https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/eurio",
"name": "eurio",
"prefix": "EURIO",
"publication": "https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/eurio",
"version": "v1.1 - 15 October 2021"
},
"EUROSCIVOC": {
"contact": {
"email": "OP-EU-VOCABULARIES@publications.europa.eu",
"name": "Publications Office of the European Union"
},
"description": "European Science Vocabulary (EuroSciVoc) is the taxonomy of fields of science based on OECD's 2015 Frascati Manual taxonomy. It was extended with fields of science categories extracted from CORDIS content through a semi-automatic process developed with Natural Language Processing (NLP) techniques.",
"homepage": "https://op.europa.eu/s/y4UK",
"name": "EuroSciVoc",
"prefix": "EUROSCIVOC",
"publication": "https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/euroscivoc",
"version": "1.3"
},
"EUROVOC": {
"contact": {
"email": "OP-EU-VOCABULARIES@publications.europa.eu",
"name": "Publications Office of the European Union"
},
"description": "EuroVoc is a multilingual, multidisciplinary thesaurus covering the activities of the EU. It contains terms in 24 EU languages, plus in three languages of countries which are candidate for EU accession. EuroVoc is managed by the Publications Office of the European Union, which moved forward to ontology-based thesaurus management and semantic web technologies conformant to W3C recommendations as well as latest trends in thesaurus standards. EuroVoc users include the European Union institutions, the Publications Office of the EU, national and regional parliaments in Europe, plus national governments and private users around the world. EcoPortal is currently hosting the core concepts of EuroVoc, including all their attributes, except alternative labels.",
"homepage": "https://op.europa.eu/s/y4TH",
"name": "EuroVoc Core Concepts",
"prefix": "EUROVOC",
"publication": "https://op.europa.eu/en/web/eu-vocabularies/dataset/-/resource?uri=http://publications.europa.eu/resource/dataset/eurovoc",
"version": "20211217-0"
},
"FISHTRAITS": {
"contact": {
"email": "ilaria.rosati@cnr.it",
"name": "Ilaria Rosati"
},
"description": "The Fish Traits Thesaurus is the first initiative to deal with the semantics of fish functional traits. It has been developed by LifeWatch Italy, the Italian node of the e-science European infrastructure for biodiversity and ecosystem research (LifeWatch ERIC). FishTraits reflects the agreement of a scientific expert community to fix semantic properties (e.g. label, definition, relationships) of approximately 220 concepts.",
"name": "Fish Traits Thesaurus",
"prefix": "FISHTRAITS",
"publication": "http://www.lifewatchitaly.eu/web/lifewatch-italia/reports",
"version": "1.5"
},
"I-ADOPT": {
"description": "The I-ADOPT Framework is an ontology designed to facilitate interoperability between existing variable description models (including ontologies, taxonomy, and structured controlled vocabularies). One of the challenges in representing semantic descriptions of variables is getting people to agree about what they mean when describing the components that define the variables. The I-ADOPT ontology addresses this by providing core components and their relations that can be applied to define machine-interpretable variable descriptions that re-use FAIR vocabulary terms. It was developed by a core group of terminology experts and users from the Research Data Alliance (RDA) InteroperAble Descriptions of Observable Property Terminology (I-ADOPT) Working Group. The first published versions of the ontology up to v0.9.1 satisfied the basic cross-domain interoperability requirements. It defines four classes or \"concepts\" (Variable, Property, Entity, Constraint), and six object properties (hasProperty, hasObjectOfInterest, hasContextObject, hasMatrix, hasConstraint, constrains). The Variable is the top concept. It represents the description of something observed or mathematically derived. It minimally consists of one entity (the ObjectOfInterest) and its Property; a Property being a type of characteristic (i.e. a quantity or a quality). More complex variables can involve additional entities, for example an entity may have the role of Matrix and/or of ContextObject(s). The framework does not capture units, instruments, methods, and geographical location information; however its usage recommendation will make explicit reference to these by connecting the I-ADOPT framework to existing and complementary ontologies. This new version of the ontology (v1.0) adds one optional new class (VariableSet) and four optional new object properties (hasApplicableProperty, hasApplicableObjectOfInterest, hasApplicableMatrix, hasApplicableContextObject). This was necessary in order to enable flexibility in assigning optional and user-defined machine-interpretable categorizations of I-ADOPT variables under one or multiple coarser grouping concepts to facilitate dataset discovery and dataset aggregation. With the introduction of these concepts and properties, the framework enables different user communities or product developers to develop their own grouping criteria. While the Variable class must be connected to at least two classes via the mandatory properties hasProperty and hasObjectOIfInterest, the VariableSet class can have either of the new properties. Additionally, the VariableSet class can also be optionally connected to the Variable class using the property [ro:hasMember](http://purl.obolibrary.org/obo/RO_0002351) from the [OBO Relations Ontology](https://obofoundry.org/ontology/ro.html).",
"name": "I-ADOPT Framework ontology",
"prefix": "I-ADOPT",
"publication": "https://doi.org/10.15497/RDA00071/2",
"version": "1.0.3"
},
"LUPO": {
"contact": {
"email": "xeni.kechagioglou@lifewatch.eu",
"name": "Xeni Kechagioglou"
},
"description": "The LifeWatch ERIC UpperΒ Ontology (LUPO) is the model defining the core set of LifeWatch ERIC elements (Actors, Services and Infrastructure) and describing their high-level arrangement. LUPO is extendable and will foster, connect and describe lower level models of its core elements, with the vision to provide functionalities that facilitate the uptake, re-use and enrichment of LifeWatch ERIC resources by an ever broader community.",
"name": "LifeWatch ERIC Upper Ontology",
"prefix": "LUPO",
"publication": "http://ecoportal.lifewatch.eu/ontologies/LUPO",
"version": "v1.0 2021/04/07"
},
"MACROALGAETRAITS": {
"contact": {
"email": "caterina.bergami@ismar.cnr.it",
"name": "Caterina Bergami"
},
"description": "The Macroalgae Traits Thesaurus contains several concepts on demographic and functional traits. It has been developed and published by LifeWatch Italy, the Italian node of the e-science European infrastructure for biodiversity and ecosystem research (LifeWatch ERIC). It reflects the agreement of a scientific expert community to fix semantic properties (e.g. label, definition) of approximately 100 traits.",
"name": "Macroalgae Traits Thesaurus",
"prefix": "MACROALGAETRAITS",
"version": "1.5"
},
"MR": {
"contact": {
"email": "info@marineregions.org",
"name": "Marine Regions Data Management team"
},
"description": "The Marine Regions ontology provides definitions for the classes and properties used in the Marine Regions dataset.",
"homepage": "https://www.marineregions.org/",
"name": "Marine Regions ontology",
"prefix": "MR",
"publication": "http://www.vliz.be/en/imis?refid=346947",
"version": "1"
},
"MRPTCODELIST": {
"contact": {
"email": "info@marineregions.org",
"name": "Marine Regions Data Management team"
},
"description": "The Marine Regions PlaceType code list provides definitions for the PlaceTypes used in the Marine Regions dataset.",
"homepage": "https://www.marineregions.org/",
"name": "Marine Regions PlaceTypes code list",
"prefix": "MRPTCODELIST",
"publication": "http://www.vliz.be/en/imis?refid=346947",
"version": "1"
},
"OBOE": {
"contact": {
"email": "joshua.madin@mq.edu.au",
"name": "Joshua Madin"
},
"description": "The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations.",
"homepage": "https://github.com/NCEAS/oboe/",
"license": "CC-BY-3.0",
"name": "The Extensible Observation Ontology",
"prefix": "OBOE",
"publication": "https://doi.org/10.1016/j.ecoinf.2007.05.004",
"repository": "https://github.com/NCEAS/oboe",
"version": "1.2"
},
"PCO": {
"contact": {
"email": "rlwalls2008@gmail.com",
"name": "Ramona Walls"
},
"description": "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology.",
"homepage": "https://github.com/PopulationAndCommunityOntology/pco",
"name": "Population and Community Ontology",
"prefix": "PCO",
"publication": "https://github.com/PopulationAndCommunityOntology/pco",
"version": "2021-05-03"
},
"PHYTOTRAITS": {
"contact": {
"email": "elena.stanca@unisalento.it",
"name": "Elena Stanca"
},
"description": "The Phytoplankton Traits Thesaurus is the first initiative to deal with the semantics of phytoplankton functional traits focusing on morpho-functional traits. It has been developed and published by LifeWatch Italy, the Italian node of the e-science European infrastructure for biodiversity and ecosystem research (LifeWatch ERIC). PhytoTraits reflects the agreement of a scientific expert community to fix semantic properties (e.g. label, definition) of approximately 120 traits.",
"name": "Phytoplankton Traits Thesaurus",
"prefix": "PHYTOTRAITS",
"publication": "https://doi.org/10.1016/j.ecoinf.2017.10.014",
"version": "1.5"
},
"STY": {
"contact": {
"email": "gs_bouazzoun@esi.dz",
"name": "Syphax Bouazzouni"
},
"description": "The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types. This section of the documentation provides an overview of the Semantic Network, and describes the files of the Semantic Network. Sample records illustrate structure and content of these files.",
"example_uri": "http://purl.bioontology.org/ontology/STY/T057",
"name": "STY",
"prefix": "STY"
},
"ZOOPLANKTRAITS": {
"contact": {
"email": "caterina.bergami@ismar.cnr.it",
"name": "Caterina Bergami"
},
"description": "The Zooplankton Traits Thesaurus contains several concepts mainly on zooplankton morpho-functional traits. It has been developed and published by LifeWatch Italy, the Italian node of the e-science European infrastructure for biodiversity and ecosystem research (LifeWatch ERIC). It reflects the agreement of a scientific expert community to fix semantic properties (e.g. label, definition) of approximately 90 traits.",
"name": "Zooplankton Traits Thesaurus",
"prefix": "ZOOPLANKTRAITS",
"publication": "https://doi.org/10.1016/j.ecoinf.2017.10.014",
"version": "1.5"
}
} ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/bioportal/ecoportal.py 0000644 0001751 0000177 00000000251 14655542206 025142 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Align the EcoPortal with the Bioregistry."""
from .bioportal import EcoPortalAligner
if __name__ == "__main__":
EcoPortalAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9579668
bioregistry-0.11.12/src/bioregistry/external/cellosaurus/ 0000755 0001751 0000177 00000000000 14655546227 023157 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/cellosaurus/__init__.py 0000644 0001751 0000177 00000005340 14655542206 025263 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download the Cellosaurus registry."""
import itertools as itt
import json
from pathlib import Path
from typing import Mapping
from pystow.utils import download
from bioregistry.constants import RAW_DIRECTORY, URI_FORMAT_KEY
from bioregistry.external.alignment_utils import Aligner
__all__ = [
"get_cellosaurus",
"CellosaurusAligner",
]
URL = "https://ftp.expasy.org/databases/cellosaurus/cellosaurus_xrefs.txt"
DIRECTORY = Path(__file__).parent.resolve()
RAW_PATH = RAW_DIRECTORY / "cellosaurus.txt"
PROCESSED_PATH = DIRECTORY / "processed.json"
KEYMAP = {
"Abbrev": "prefix",
"Cat": "category",
"Db_URL": URI_FORMAT_KEY,
"Name": "name",
"Server": "homepage",
}
def get_cellosaurus(force_download: bool = False, keep_missing_uri: bool = True):
"""Get the Cellosaurus registry."""
if PROCESSED_PATH.exists() and not force_download:
with PROCESSED_PATH.open() as file:
return json.load(file)
download(url=URL, path=RAW_PATH, force=True)
with RAW_PATH.open(encoding="ISO8859-1") as file:
lines = [line.rstrip() for line in file]
# Get up until the third big line break and chomp two extra lines
# for the line break
break_line_idxs = [i for i, line in enumerate(lines) if line.startswith("------")]
lines = lines[break_line_idxs[3] + 2 :]
rv = {}
for cond, slines in itt.groupby(lines, lambda line: line == "//"):
if cond:
continue
d = {}
for line in slines:
if line[6] != ":": # strip notes out
continue
key, value = (s.strip() for s in line.split(":", 1))
mapped_key = KEYMAP.get(key)
if mapped_key is None:
continue
if mapped_key == URI_FORMAT_KEY:
value = _process_db_url(value)
if value is None:
continue
d[mapped_key] = value
if not keep_missing_uri and URI_FORMAT_KEY not in d:
continue
rv[d.pop("prefix")] = d
with PROCESSED_PATH.open("w") as file:
json.dump(rv, file, indent=2, sort_keys=True)
return rv
def _process_db_url(value):
if value in {"https://%s", "None"}:
return
return value.rstrip("/").replace("%s", "$1")
class CellosaurusAligner(Aligner):
"""Aligner for the Cellosaurus."""
key = "cellosaurus"
getter = get_cellosaurus
curation_header = ("name", "homepage", "category", URI_FORMAT_KEY)
def get_skip(self) -> Mapping[str, str]:
"""Get the skipped Cellosaurus identifiers."""
return {
"CCTCC": "dead site",
"CCLV": "stub website, URL dead",
}
if __name__ == "__main__":
CellosaurusAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254804.0
bioregistry-0.11.12/src/bioregistry/external/cellosaurus/processed.json 0000644 0001751 0000177 00000074354 14655544024 026047 0 ustar 00runner docker {
"4DN": {
"category": "Biological sample resources",
"homepage": "https://data.4dnucleome.org/",
"name": "4D Nucleome Data Portal",
"uri_format": "https://data.4dnucleome.org/biosources/$1"
},
"ABCD": {
"category": "Biological sample resources",
"homepage": "https://web.expasy.org/abcd/",
"name": "AntiBodies Chemically Defined database",
"uri_format": "https://web.expasy.org/abcd/$1"
},
"ABM": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.abmgood.com/Cell-Biology.html",
"name": "Applied Biological Materials cell line products",
"uri_format": "https://www.abmgood.com/catalogsearch/result/?cat=&q=$1"
},
"ATCC": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.atcc.org/",
"name": "American Type Culture Collection",
"uri_format": "https://www.atcc.org/Products/$1"
},
"Abcam": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.abcam.com/nav/cell-lines-and-lysates",
"name": "Abcam cell line products",
"uri_format": "https://www.abcam.com/$1.html"
},
"AddexBio": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.addexbio.com/productshow?id=4",
"name": "AddexBio cell line products",
"uri_format": "https://www.addexbio.com/productdetail?pid=$1"
},
"ArrayExpress": {
"category": "Gene expression databases",
"homepage": "https://www.ebi.ac.uk/biostudies/arrayexpress",
"name": "ArrayExpress Archive of Functional Genomics",
"uri_format": "https://www.ebi.ac.uk/biostudies/ArrayExpress/studies/$1"
},
"BCGO": {
"category": "Anatomy/cell type resources",
"homepage": "https://github.com/obi-bcgo/bcgo",
"name": "Beta Cell Genomics Ontology",
"uri_format": "http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/$1"
},
"BCRC": {
"category": "Cell line collections (Providers)",
"homepage": "https://catalog.bcrc.firdi.org.tw/",
"name": "Taiwan Bioresource Collection and Research Center",
"uri_format": "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1"
},
"BCRJ": {
"category": "Cell line collections (Providers)",
"homepage": "https://bcrj.org.br/pesquisa/",
"name": "Banco de Celulas do Rio de Janeiro",
"uri_format": "http://bcrj.org.br/celula/$1"
},
"BEI_Resources": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.beiresources.org/Home.aspx",
"name": "BEI Resources cell line products",
"uri_format": "https://www.beiresources.org/Catalog/cellBanks/$1.aspx"
},
"BTO": {
"category": "Anatomy/cell type resources",
"homepage": "https://bioportal.bioontology.org/ontologies/BTO",
"name": "BRENDA Tissue Ontology",
"uri_format": "https://bioportal.bioontology.org/ontologies/BTO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_$1"
},
"BioGRID_ORCS_Cell_line": {
"category": "CRISP screens repositories",
"homepage": "https://orcs.thebiogrid.org/",
"name": "BioGRID Open Repository of CRISPR Screens cell lines",
"uri_format": "https://orcs.thebiogrid.org/Search?searchType=10&search=$1&organism=all"
},
"BioSample": {
"category": "Biological sample resources",
"homepage": "https://www.ncbi.nlm.nih.gov/biosample",
"name": "BioSample database",
"uri_format": "https://www.ncbi.nlm.nih.gov/biosample/?term=$1"
},
"BioSamples": {
"category": "Biological sample resources",
"homepage": "https://www.ebi.ac.uk/biosamples/",
"name": "BioSamples database",
"uri_format": "https://www.ebi.ac.uk/biosamples/samples/$1"
},
"CBA": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/",
"name": "CellBank Australia",
"uri_format": "https://www.cellbankaustralia.com/$1"
},
"CCLV": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.fli.de/en/services/collection-of-cell-lines-in-veterinary-medicine-cclv/",
"name": "Collection of Cell Lines in Veterinary Medicine"
},
"CCRID": {
"category": "Cell line databases/resources",
"homepage": "http://cellresource.cn/",
"name": "Chinese Cell Resource Information Database",
"uri_format": "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1"
},
"CCTCC": {
"category": "Cell line collections (Providers)",
"homepage": "http://www.cctcc.org/",
"name": "China Center for Type Culture Collection"
},
"CGH-DB": {
"category": "Cell line databases/resources",
"homepage": "http://www.cghtmd.jp/CGHDatabase/index_e.jsp",
"name": "CGH Data Base",
"uri_format": "http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en"
},
"CL": {
"category": "Anatomy/cell type resources",
"homepage": "https://obophenotype.github.io/cell-ontology/",
"name": "Cell Ontology",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http://purl.obolibrary.org/obo/$1"
},
"CLDB": {
"category": "Cell line databases/resources",
"homepage": "http://bioinformatics.hsanmartino.it/cldb/",
"name": "Cell Line Data Base",
"uri_format": "http://bioinformatics.hsanmartino.it/cldb/$1.html"
},
"CLO": {
"category": "Cell line databases/resources",
"homepage": "http://www.clo-ontology.org",
"name": "Cell Line Ontology",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/clo/terms?iri=http://purl.obolibrary.org/obo/$1"
},
"CLS": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.cytion.com/",
"name": "Cell Lines Service",
"uri_format": "https://www.cytion.com/$1"
},
"CancerTools": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.cancertools.org/cell-lines",
"name": "CancerTools.org",
"uri_format": "https://www.cancertools.org/cell-lines/$1"
},
"Cell_Biolabs": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.cellbiolabs.com",
"name": "Cell Biolabs cell line products",
"uri_format": "https://www.cellbiolabs.com/search?keywords=$1"
},
"Cell_Model_Passport": {
"category": "Cell line databases/resources",
"homepage": "https://cellmodelpassports.sanger.ac.uk/",
"name": "Sanger Cell Model Passports",
"uri_format": "https://cellmodelpassports.sanger.ac.uk/passports/$1"
},
"CelloPub": {
"category": "Reference resources",
"homepage": "https://www.cellosaurus.org/",
"name": "Cellosaurus Publication",
"uri_format": "https://www.cellosaurus.org/cellopub/$1"
},
"Cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://www.cellosaurus.org/",
"name": "Cellosaurus - a knowledge resource on cell lines",
"uri_format": "https://www.cellosaurus.org/$1"
},
"ChEBI": {
"category": "Chemistry resources",
"homepage": "https://www.ebi.ac.uk/chebi/",
"name": "Chemical Entities of Biological Interest",
"uri_format": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=$1"
},
"ChEMBL-Cells": {
"category": "Chemistry resources",
"homepage": "https://www.ebi.ac.uk/chembldb",
"name": "ChEMBL database of bioactive drug-like small molecules - Cell lines section",
"uri_format": "https://www.ebi.ac.uk/chembldb/cell/inspect/$1"
},
"ChEMBL-Targets": {
"category": "Chemistry resources",
"homepage": "https://www.ebi.ac.uk/chembldb",
"name": "ChEMBL database of bioactive drug-like small molecules - Targets section",
"uri_format": "https://www.ebi.ac.uk/chembldb/target/inspect/$1"
},
"ClinVar": {
"category": "Polymorphism and mutation databases",
"homepage": "https://www.ncbi.nlm.nih.gov/clinvar/",
"name": "ClinVar",
"uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1"
},
"ColonAtlas": {
"category": "Cell line databases/resources",
"homepage": "http://www.coloncanceratlas.org",
"name": "Colorectal Cancer Atlas",
"uri_format": "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1"
},
"Coriell": {
"category": "Cell line collections (Providers)",
"homepage": "https://catalog.coriell.org",
"name": "Coriell Institute Biorepositories",
"uri_format": "https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=$1&Product=CC"
},
"Cosmic": {
"category": "Polymorphism and mutation databases",
"homepage": "https://cancer.sanger.ac.uk/cosmic",
"name": "Catalogue of somatic mutations in cancer",
"uri_format": "https://cancer.sanger.ac.uk/cosmic/sample/overview?id=$1"
},
"Cosmic-CLP": {
"category": "Cell line databases/resources",
"homepage": "https://cancer.sanger.ac.uk/cell_lines",
"name": "COSMIC Cell lines Project",
"uri_format": "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1"
},
"DGRC": {
"category": "Cell line collections (Providers)",
"homepage": "https://dgrc.bio.indiana.edu/cells/Catalog",
"name": "Drosophila Genomics Resource Center",
"uri_format": "https://dgrc.bio.indiana.edu/product/View?product=$1"
},
"DOI": {
"category": "Reference resources",
"homepage": "https://dx.doi.org",
"name": "Digital Object Identifier",
"uri_format": "https://dx.doi.org/$1"
},
"DSHB": {
"category": "Cell line collections (Providers)",
"homepage": "https://dshb.biology.uiowa.edu/",
"name": "Developmental Studies Hybridoma Bank",
"uri_format": "https://dshb.biology.uiowa.edu/$1"
},
"DSMZ": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.dsmz.de/collection/catalogue/human-and-animal-cell-lines/catalogue",
"name": "Deutsche Sammlung von Mikroorganismen und Zellkulturen",
"uri_format": "https://www.dsmz.de/collection/catalogue/details/culture/$1"
},
"DSMZCellDive": {
"category": "Cell line databases/resources",
"homepage": "https://celldive.dsmz.de/",
"name": "DSMZ Tools for Diving into Cell Line Data",
"uri_format": "https://celldive.dsmz.de/celllines/$1"
},
"DepMap": {
"category": "Cell line databases/resources",
"homepage": "https://depmap.org/portal/",
"name": "Cancer Dependency Map",
"uri_format": "https://depmap.org/portal/cell_line/$1"
},
"DiscoverX": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.discoverx.com/product-category/cell-lines-primary-cells/",
"name": "DiscoverX cell line products",
"uri_format": "https://www.discoverx.com/?post_type=product&s=$1"
},
"DrugBank": {
"category": "Chemistry resources",
"homepage": "https://go.drugbank.com/",
"name": "DrugBank database",
"uri_format": "https://go.drugbank.com/drugs/$1"
},
"EBiSC": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.ebisc.org",
"name": "European Bank for induced pluripotent Stem Cells",
"uri_format": "https://cells.ebisc.org/$1"
},
"ECACC": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.culturecollections.org.uk/about-us/ecacc/",
"name": "European Collection of Cell Cultures",
"uri_format": "https://www.culturecollections.org.uk/products/celllines/detail.jsp?refId=$1"
},
"EFO": {
"category": "Experimental variables resources",
"homepage": "https://www.ebi.ac.uk/efo/",
"name": "Experimental Factor Ontology",
"uri_format": "https://www.ebi.ac.uk/efo/$1"
},
"EGA": {
"category": "Sequence databases",
"homepage": "https://ega-archive.org/",
"name": "European Genome-Phenome Archive",
"uri_format": "https://ega-archive.org/studies/$1"
},
"ENCODE": {
"category": "Biological sample resources",
"homepage": "https://www.encodeproject.org",
"name": "Encyclopedia of DNA Elements",
"uri_format": "https://www.encodeproject.org/biosamples/$1"
},
"ESTDAB": {
"category": "Cell line databases/resources",
"homepage": "https://www.ebi.ac.uk/ipd/estdab/",
"name": "European Searchable Tumour Line Database"
},
"FCDI": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.fujifilmcdi.com/cirm-ipsc-products/",
"name": "FujiFilm Cellular Dynamics, Inc"
},
"FCS-free": {
"category": "Cell line databases/resources",
"homepage": "https://fcs-free.org/",
"name": "Fetal Calf Serum-Free Database",
"uri_format": "https://fcs-free.org/fcs-database?$1"
},
"FlyBase_Cell_line": {
"category": "Cell line databases/resources",
"homepage": "https://flybase.org/cgi-bin/cvreport.pl?id=FBbt%3A00005329",
"name": "Drosophila genome database; cell line entry",
"uri_format": "https://flybase.org/reports/$1.html"
},
"FlyBase_Gene": {
"category": "Organism-specific databases",
"homepage": "https://flybase.org",
"name": "Drosophila genome database; gene entry",
"uri_format": "https://flybase.org/reports/$1.html"
},
"GDSC": {
"category": "Chemistry resources",
"homepage": "https://www.cancerrxgene.org",
"name": "Genomics of Drug Sensitivity in Cancer Project",
"uri_format": "https://www.cancerrxgene.org/translation/CellLine/$1"
},
"GEO": {
"category": "Gene expression databases",
"homepage": "https://www.ncbi.nlm.nih.gov/geo/",
"name": "Gene Expression Omnibus",
"uri_format": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1"
},
"GeneCopoeia": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.genecopoeia.com/",
"name": "GeneCopoeia cell line products",
"uri_format": "https://www.genecopoeia.com/product/search3/?s=$1"
},
"HGNC": {
"category": "Organism-specific databases",
"homepage": "https://www.genenames.org",
"name": "Human Gene Nomenclature Committee Database",
"uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$1"
},
"HIVReagentProgram": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.hivreagentprogram.org/",
"name": "NIH HIV Reagent Program",
"uri_format": "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx"
},
"HipSci": {
"category": "Cell line databases/resources",
"homepage": "https://www.hipsci.org",
"name": "Human Induced Pluripotent Stem Cells Initiative",
"uri_format": "https://www.hipsci.org/lines/#/lines/$1"
},
"Horizon_Discovery": {
"category": "Cell line collections (Providers)",
"homepage": "https://horizondiscovery.com/",
"name": "Horizon Discovery cell line collection",
"uri_format": "https://horizondiscovery.com/en/search?searchterm=$1"
},
"Hysigen": {
"category": "Cell line collections (Providers)",
"homepage": "https://hysigen.com/",
"name": "Hysigen cell line collection",
"uri_format": "https://hysigen.com/$1.html"
},
"IARC_TP53": {
"category": "Polymorphism and mutation databases",
"homepage": "https://tp53.isb-cgc.org/explore_cl",
"name": "IARC TP53 Database"
},
"IBRC": {
"category": "Cell line collections (Providers)",
"homepage": "http://www.en.ibrc.ir/",
"name": "Iranian Biological Research Center cell line collection"
},
"ICLC": {
"category": "Cell line collections (Providers)",
"homepage": "http://www.iclc.it",
"name": "Interlab Cell Line Collection",
"uri_format": "http://www.iclc.it/details/det_list.php?line_id=$1"
},
"ICLDB": {
"category": "Cell line databases/resources",
"homepage": "https://entomology.ca.uky.edu/aginsectcellsdatabase",
"name": "Insect Cell Lines DataBase",
"uri_format": "https://entomology.ca.uky.edu/content/$1"
},
"IGRhCellID": {
"category": "Cell line databases/resources",
"homepage": "http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi",
"name": "Integrated Genomic Resources of human Cell Lines for Identification",
"uri_format": "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1"
},
"IGSR": {
"category": "Biological sample resources",
"homepage": "https://www.internationalgenome.org/",
"name": "International Genome Sample Resource",
"uri_format": "https://www.internationalgenome.org/data-portal/sample/$1"
},
"IHW": {
"category": "Cell line databases/resources",
"homepage": "https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html",
"name": "International Histocompatibility Workshop cell lines"
},
"IPD-IMGT/HLA": {
"category": "Cell line databases/resources",
"homepage": "https://www.ebi.ac.uk/ipd/imgt/hla/",
"name": "IPD-IMGT/HLA database",
"uri_format": "https://www.ebi.ac.uk/ipd/imgt/hla/cells/cell/?cellid=$1"
},
"ISCR": {
"category": "Cell line databases/resources",
"homepage": "https://www.umassmed.edu/iscr/",
"name": "International Stem Cell Registry"
},
"IZSLER": {
"category": "Cell line collections (Providers)",
"homepage": "http://www.ibvr.org/Services/CellCultures.aspx",
"name": "Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna biobank"
},
"Imanis": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.imanislife.com/collections/cell-lines/",
"name": "Imanis Life Sciences cell line products",
"uri_format": "https://www.imanislife.com/?s=$1"
},
"Innoprot": {
"category": "Cell line collections (Providers)",
"homepage": "https://innoprot.com/",
"name": "Innoprot cell line products",
"uri_format": "https://innoprot.com/?s=$1&lang=en"
},
"JCRB": {
"category": "Cell line collections (Providers)",
"homepage": "http://cellbank.nibiohn.go.jp/english/",
"name": "Japanese Collection of Research Bioresources Cell Bank",
"uri_format": "http://cellbank.nibiohn.go.jp//~cellbank/en/search_res_det.cgi?RNO=$1"
},
"KCB": {
"category": "Cell line collections (Providers)",
"homepage": "http://www.kmcellbank.com/",
"name": "Kunming Cell Bank of Type Culture Collection"
},
"KCLB": {
"category": "Cell line collections (Providers)",
"homepage": "https://cellbank.snu.ac.kr/eng/",
"name": "Korean Cell Line Bank",
"uri_format": "https://cellbank.snu.ac.kr/main/tmpl/sub_main.php?m_cd=6&m_id=0201&strQ=$1"
},
"KYinno": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.kyinno.com/",
"name": "KYinno cell lines",
"uri_format": "https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf"
},
"Kerafast": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.kerafast.com/",
"name": "Kerafast cell lines",
"uri_format": "https://www.kerafast.com/Search?SearchTerm="$1""
},
"LIMORE": {
"category": "Cell line databases/resources",
"homepage": "https://www.picb.ac.cn/limore/home",
"name": "Liver Cancer Model Repository",
"uri_format": "https://www.picb.ac.cn/limore/cellLines/single?para=$1"
},
"LINCS_HMS": {
"category": "Cell line databases/resources",
"homepage": "http://lincs.hms.harvard.edu/db/cells/",
"name": "Harvard Medical School (HMS) LINCS Center",
"uri_format": "http://lincs.hms.harvard.edu/db/cells/$1"
},
"LINCS_LDP": {
"category": "Cell line databases/resources",
"homepage": "http://lincsportal.ccs.miami.edu/cells/",
"name": "LINCS Data Portal",
"uri_format": "http://lincsportal.ccs.miami.edu/cells/#/view/$1"
},
"LiGeA": {
"category": "Polymorphism and mutation databases",
"homepage": "http://hpc-bioinformatics.cineca.it/fusion/main",
"name": "Cancer cell LInes GEne fusions portAl",
"uri_format": "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1"
},
"Lonza": {
"category": "Cell line databases/resources",
"homepage": "https://knowledge.lonza.com",
"name": "Lonza Cell and Transfection Database",
"uri_format": "https://knowledge.lonza.com/cell?id=$1"
},
"MCCL": {
"category": "Cell line databases/resources",
"homepage": "https://bioportal.bioontology.org/ontologies/MCCL",
"name": "Molecular Connection Cell Line ontology"
},
"MGI": {
"category": "Organism-specific databases",
"homepage": "http://www.informatics.jax.org",
"name": "Mouse Genome Database (MGD) from Mouse Genome Informatics",
"uri_format": "http://www.informatics.jax.org/marker/$1"
},
"MMRRC": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.mmrrc.org/",
"name": "Mutant Mouse Resource & Research Centers",
"uri_format": "https://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1"
},
"MeSH": {
"category": "Medical resources",
"homepage": "https://www.ncbi.nlm.nih.gov/mesh",
"name": "Medical Subject Headings",
"uri_format": "https://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?field=uid&term=$1"
},
"MetaboLights": {
"category": "Metabolomic databases",
"homepage": "https://www.ebi.ac.uk/metabolights/",
"name": "MetaboLights database for metabolomics experiments and derived information",
"uri_format": "https://www.ebi.ac.uk/metabolights/$1"
},
"Millipore": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.merckmillipore.com/",
"name": "Merck Millipore (EMD Millipore)",
"uri_format": "https://www.merckmillipore.com/catalogue/item/$1"
},
"NCBI_Iran": {
"category": "Cell line collections (Providers)",
"homepage": "https://en.pasteur.ac.ir/Department%20of%20Cell%20Bank",
"name": "National Cell Bank of Iran"
},
"NCBI_TaxID": {
"category": "Taxonomy",
"homepage": "https://www.ncbi.nlm.nih.gov/taxonomy",
"name": "NCBI taxonomy database",
"uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1&lvl=3"
},
"NCI-DTP": {
"category": "Cell line collections (Providers)",
"homepage": "https://dtp.cancer.gov/repositories/",
"name": "NCI Development Therapeutics Program"
},
"NCIt": {
"category": "Medical resources",
"homepage": "https://ncit.nci.nih.gov/ncitbrowser",
"name": "NCI thesaurus",
"uri_format": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=$1"
},
"NHCDR": {
"category": "Cell line collections (Providers)",
"homepage": "https://stemcells.nindsgenetics.org",
"name": "NINDS Human Cell and Data Repository",
"uri_format": "https://stemcells.nindsgenetics.org?line=$1"
},
"NIHhESC": {
"category": "Cell line databases/resources",
"homepage": "https://grants.nih.gov/stem_cells/registry/current.htm",
"name": "NIH Human Embryonic Stem Cell Registry",
"uri_format": "https://grants.nih.gov/stem_cells/registry/current.htm?ID=$1"
},
"NISES": {
"category": "Cell line collections (Providers)",
"homepage": "https://web.archive.org/web/20160709065305/https://www.gene.affrc.go.jp/ex-nises/NISESCells/CellindexE1.html",
"name": "National Institute of Sericultural and Entomological Science Cell Database"
},
"NRFC": {
"category": "Cell line collections (Providers)",
"homepage": "https://mail.nbfgr.res.in/nrfc/",
"name": "National Repository of Fish Cell Line"
},
"ORDO": {
"category": "Medical resources",
"homepage": "https://www.ebi.ac.uk/ols/ontologies/ordo",
"name": "Orphanet Rare Disease Ontology",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/ordo/terms?iri=http://www.orpha.net/ORDO/$1"
},
"PRIDE": {
"category": "Proteomic databases",
"homepage": "https://www.ebi.ac.uk/pride/archive/",
"name": "PRoteomics IDEntifications archive",
"uri_format": "https://www.ebi.ac.uk/pride/archive/projects/$1"
},
"Patent": {
"category": "Reference resources",
"homepage": "https://patents.google.com",
"name": "Google Patents",
"uri_format": "https://patents.google.com/patent/$1"
},
"PerkinElmer": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.perkinelmer.com/",
"name": "PerkinElmer cell line collection",
"uri_format": "https://www.perkinelmer.com/searchresult?searchName=$1"
},
"PharmacoDB": {
"category": "Chemistry resources",
"homepage": "https://pharmacodb.ca/",
"name": "PharmacoDB integrative pharmacogenomic database",
"uri_format": "https://pharmacodb.ca/cell_lines/$1"
},
"Progenetix": {
"category": "Polymorphism and mutation databases",
"homepage": "https://progenetix.org/",
"name": "Cancer genome data @ progenetix.org",
"uri_format": "https://progenetix.org/biosamples/by-curie/cellosaurus:$1"
},
"PubChem": {
"category": "Chemistry resources",
"homepage": "https://pubchem.ncbi.nlm.nih.gov",
"name": "PubChem compound database",
"uri_format": "https://pubchem.ncbi.nlm.nih.gov/compound/$1"
},
"PubChem_Cell_line": {
"category": "Chemistry resources",
"homepage": "https://pubchem.ncbi.nlm.nih.gov",
"name": "PubChem compound database; cell line pages",
"uri_format": "https://pubchem.ncbi.nlm.nih.gov/cell/$1"
},
"PubMed": {
"category": "Reference resources",
"homepage": "https://www.ncbi.nlm.nih.gov/pubmed",
"name": "PubMed",
"uri_format": "https://www.ncbi.nlm.nih.gov/pubmed/$1"
},
"RCB": {
"category": "Cell line collections (Providers)",
"homepage": "https://cell.brc.riken.jp/en/rcb",
"name": "RIKEN Bioresource Center Cell Bank",
"uri_format": "http://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1&lang=En"
},
"RGD": {
"category": "Organism-specific databases",
"homepage": "https://rgd.mcw.edu",
"name": "Rat Genome Database",
"uri_format": "https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1"
},
"RIKEN_BRC_EPD": {
"category": "Cell line collections (Providers)",
"homepage": "https://epd.brc.riken.jp/en/",
"name": "RIKEN BRC Experimental Plant Division cell lines",
"uri_format": "https://plant.rtc.riken.jp/resource/cell_line/cell_line_detail.html?brcno=%S"
},
"RSCB": {
"category": "Cell line collections (Providers)",
"homepage": "https://web.archive.org/web/20201001144644/http://www.royaninstitute.org/cmsen/index.php?option=com_content&task=view&id=205&Itemid=40",
"name": "Royan Stem Cell Bank"
},
"Rockland": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.rockland.com/categories/cell-lines-and-lysates/",
"name": "Rockland cell line products",
"uri_format": "https://www.rockland.com/search/?searchString=$1"
},
"SKIP": {
"category": "Cell line databases/resources",
"homepage": "https://www.skip.stemcellinformatics.org/en/",
"name": "Stemcell Knowledge and Information Portal",
"uri_format": "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1"
},
"SKY/M-FISH/CGH": {
"category": "Cell line databases/resources",
"homepage": "https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd136/",
"name": "SKY/M-FISH and CGH database"
},
"SLKBase": {
"category": "Cell line databases/resources",
"homepage": "https://sumlineknowledgebase.com/",
"name": "SUM Breast Cancer Cell Line Knowledge Base",
"uri_format": "https://sumlineknowledgebase.com/?page_id=$1"
},
"TKG": {
"category": "Cell line collections (Providers)",
"homepage": "http://www2.idac.tohoku.ac.jp/dep/ccr/",
"name": "Tohoku University cell line catalog",
"uri_format": "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvo10%n/$1.html"
},
"TNGB": {
"category": "Cell line collections (Providers)",
"homepage": "http://biobanknetwork.telethon.it/",
"name": "Telethon Network of Genetic Biobanks",
"uri_format": "http://biobanknetwork.telethon.it/Sample/View?sampleId=$1"
},
"TOKU-E": {
"category": "Cell line databases/resources",
"homepage": "http://cell-lines.toku-e.com",
"name": "TOKU-E Cell-culture Database",
"uri_format": "http://cell-lines.toku-e.com/Cell-Lines_$1.html"
},
"UBERON": {
"category": "Anatomy/cell type resources",
"homepage": "https://uberon.github.io/",
"name": "Uber-anatomy ontology",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http://purl.obolibrary.org/obo/$1"
},
"Ubigene": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.ubigene.us/",
"name": "Ubigene Biosciences cell line products",
"uri_format": "https://www.ubigene.us/product/?cate=0&mykeyword=$1"
},
"UniProtKB": {
"category": "Sequence databases",
"name": "UniProt knowledgebase",
"uri_format": "https://www.uniprot.org/uniprotkb/$1/entry"
},
"VGNC": {
"category": "Organism-specific databases",
"homepage": "https://vertebrate.genenames.org/",
"name": "Vertebrate Gene Nomenclature Committee Database",
"uri_format": "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/VGNC:$1"
},
"WiCell": {
"category": "Cell line collections (Providers)",
"homepage": "https://www.wicell.org",
"name": "WiCell Research Institute Cell Collection",
"uri_format": "https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true"
},
"Wikidata": {
"category": "Encyclopedic resources",
"homepage": "https://www.wikidata.org/wiki/Wikidata:Main_Page",
"name": "Wikidata",
"uri_format": "https://www.wikidata.org/wiki/$1"
},
"Ximbio": {
"category": "Cell line collections (Providers)",
"homepage": "https://ximbio.com",
"name": "Ximbio reagents online portal",
"uri_format": "https://ximbio.com/reagent/$1"
},
"cancercelllines": {
"category": "Cell line databases/resources",
"homepage": "https://cancercelllines.org/",
"name": "cancercelllines.org - cancer cell line oncogenomic online resource",
"uri_format": "https://cancercelllines.org/cellline/?id=cellosaurus:$1"
},
"dbGAP": {
"category": "Sequence databases",
"homepage": "https://www.ncbi.nlm.nih.gov/gap/",
"name": "Database of Genotypes and Phenotypes",
"uri_format": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1"
},
"dbMHC": {
"category": "Cell line databases/resources",
"homepage": "https://www.ncbi.nlm.nih.gov/gv/mhc/",
"name": "dbMHC database"
},
"dbSNP": {
"category": "Polymorphism and mutation databases",
"homepage": "https://www.ncbi.nlm.nih.gov/snp/",
"name": "Single Nucleotide Polymorphism database",
"uri_format": "https://www.ncbi.nlm.nih.gov/snp/$1"
},
"hPSCreg": {
"category": "Cell line databases/resources",
"homepage": "https://hpscreg.eu",
"name": "Human Pluripotent Stem Cell Registry",
"uri_format": "https://hpscreg.eu/cell-line/$1"
}
} ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9579668
bioregistry-0.11.12/src/bioregistry/external/cheminf/ 0000755 0001751 0000177 00000000000 14655546227 022227 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/cheminf/__init__.py 0000644 0001751 0000177 00000003401 14655542206 024327 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download the Chemical Information Ontology registry (children of ``CHEMINF:000464``).
To convert CHEMINF from OWL to OBO Graph JSON, do the following:
.. code-block:: sh
$ robot convert --input cheminf.owl --format json --output cheminf.json
See the OBO Foundry workflow for preparing a docker container that has ROBOT available
"""
import json
from pathlib import Path
from typing import Mapping
from bioregistry.external.alignment_utils import Aligner
from bioregistry.utils import get_ols_descendants
__all__ = [
"get_cheminf",
"ChemInfAligner",
]
DIRECTORY = Path(__file__).parent.resolve()
PROCESSED_PATH = DIRECTORY / "processed.json"
BASE_URL = "http%253A%252F%252Fsemanticscience.org%252Fresource%252FCHEMINF_000464"
SKIP = {
"000467": "Not enough information available on this term.",
"000234": "PubChem Conformer isn't actually an identifier, just a part of PubChem Compound database",
"000303": "Double mapping onto `genbank`",
}
def get_cheminf(force_download: bool = False):
"""Get the Chemical Information Ontology registry."""
if PROCESSED_PATH.exists() and not force_download:
with PROCESSED_PATH.open() as file:
return json.load(file)
rv = get_ols_descendants(ontology="cheminf", uri=BASE_URL, force_download=force_download)
with PROCESSED_PATH.open("w") as file:
json.dump(rv, file, indent=2, sort_keys=True)
return rv
class ChemInfAligner(Aligner):
"""Aligner for the Chemical Information Ontology."""
key = "cheminf"
getter = get_cheminf
curation_header = ("name", "description")
def get_skip(self) -> Mapping[str, str]:
"""Get the skipped identifiers."""
return SKIP
if __name__ == "__main__":
ChemInfAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254962.0
bioregistry-0.11.12/src/bioregistry/external/cheminf/processed.json 0000644 0001751 0000177 00000006344 14655544262 025115 0 ustar 00runner docker {
"000140": {
"description": [],
"name": "PubChem compound identifier (CID)",
"obsolete": false
},
"000141": {
"description": [],
"name": "PubChem substance identifier (SID)",
"obsolete": false
},
"000234": {
"description": [],
"name": "PubChem conformer",
"obsolete": false
},
"000302": {
"description": [],
"name": "PubChem Identifier",
"obsolete": false
},
"000303": {
"description": [],
"name": "GenBank Protein Identifier",
"obsolete": false
},
"000304": {
"description": [],
"name": "GenBank Nucleotide Identifier",
"obsolete": false
},
"000405": {
"description": "Database identifier used by ChemSpider.",
"name": "ChemSpider",
"obsolete": false
},
"000406": {
"description": "Database identifier used by DrugBank.",
"name": "DrugBank",
"obsolete": false
},
"000407": {
"description": "Database identifier used by ChEBI.",
"name": "ChEBI",
"obsolete": false
},
"000408": {
"description": "Database identifier used by Human Metabolome Database.",
"name": "HMDB",
"obsolete": false
},
"000409": {
"description": "Database identifier used by KEGG.",
"name": "KEGG",
"obsolete": false
},
"000411": {
"description": "Database identifier used by Reactome.",
"name": "Reactome",
"obsolete": false
},
"000412": {
"description": "Identifier used by the ChEMBL database for compounds, assays, target, etc.",
"name": "ChEMBL",
"obsolete": false
},
"000446": {
"description": "Identifier used by the Chemical Abstracts Service database.",
"name": "CAS registry number",
"obsolete": false
},
"000447": {
"description": "A seven-digit identifier for chemical substances for regulatory purposes within the European Union.",
"name": "EC number",
"obsolete": false
},
"000467": {
"description": "A chemical database identifier which has been validated by a curator.",
"name": "validated chemical database",
"obsolete": false
},
"000563": {
"description": "Identifier used by the USA Food and Drug Administration.",
"name": "Unique Ingredient Identifier",
"obsolete": false
},
"000564": {
"description": "Identifier used by the LipidMaps database, http://www.lipidmaps.org/.",
"name": "LipidMaps",
"obsolete": false
},
"000565": {
"description": "Identifier used by the Cancer Chemotherapy National Service Center.",
"name": "National Service Center number",
"obsolete": false
},
"000566": {
"description": "Identifier used by the RTECS database (http://www.cdc.gov/niosh/rtecs/).",
"name": "RTECS",
"obsolete": false
},
"000569": {
"description": "Identifier used by the European Registry of Materials (https://nanocommons.github.io/identifiers/).",
"name": "European Registry of Materials",
"obsolete": false
},
"000570": {
"description": [],
"name": "SwissLipids",
"obsolete": false
},
"000571": {
"description": [],
"name": "MolMeDB",
"obsolete": false
},
"000572": {
"description": [],
"name": "PDB ligand",
"obsolete": false
},
"000573": {
"description": [],
"name": "PDB structure",
"obsolete": false
}
} ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9579668
bioregistry-0.11.12/src/bioregistry/external/cropoct/ 0000755 0001751 0000177 00000000000 14655546227 022267 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/cropoct/__init__.py 0000644 0001751 0000177 00000004150 14655542206 024371 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download registry information from CROPOCT."""
import io
import json
import logging
from pathlib import Path
import yaml
from pystow.utils import download
from bioregistry.constants import RAW_DIRECTORY
from bioregistry.external.alignment_utils import Aligner
__all__ = [
"get_cropoct",
"CropOCTAligner",
]
logger = logging.getLogger(__name__)
DIRECTORY = Path(__file__).parent.resolve()
RAW_PATH = RAW_DIRECTORY / "cropoct.yaml"
PROCESSED_PATH = DIRECTORY / "processed.json"
CROPOCT_URL = "https://cropontology.org/metadata"
def get_cropoct(force_download: bool = False):
"""Get the CropOCT registry."""
if PROCESSED_PATH.exists() and not force_download:
with PROCESSED_PATH.open() as file:
return json.load(file)
download(url=CROPOCT_URL, path=RAW_PATH, force=True)
lines = []
with RAW_PATH.open() as file:
next(file) # throw away header
for i, line in enumerate(file):
line = line.rstrip()
line = line.replace(" : ", ": ")
if line.count('"') > 2:
logger.debug("issue on line %s: %s", i, line)
continue
lines.append(line)
fixed = "\n".join(lines)
RAW_PATH.write_text(
yaml.safe_dump(
yaml.safe_load(io.StringIO(fixed)),
indent=2,
)
)
with RAW_PATH.open() as file:
data = yaml.safe_load(file)
rv = {record["id"]: _process(record) for record in data["ontologies"]}
with PROCESSED_PATH.open("w") as file:
json.dump(rv, file, indent=2, sort_keys=True)
return rv
def _process(record):
rv = {
"prefix": record["id"],
"name": record["title"],
"homepage": record["homepage"],
"download_owl": record.get("ontology_purl"),
"description": record.get("description"),
}
return {k: v for k, v in rv.items() if k and v}
class CropOCTAligner(Aligner):
"""Aligner for CropOCT."""
key = "cropoct"
getter = get_cropoct
curation_header = ["name", "homepage", "description"]
if __name__ == "__main__":
CropOCTAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254815.0
bioregistry-0.11.12/src/bioregistry/external/cropoct/processed.json 0000644 0001751 0000177 00000030000 14655544037 025137 0 ustar 00runner docker {
"CO_320": {
"description": "Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables",
"download_owl": "http://cropontology.org/rdf/CO_320.owl",
"homepage": "http://cropontology.org/term/CO_320:ROOT",
"name": "Rice ontology",
"prefix": "CO_320"
},
"CO_321": {
"description": "July 2018",
"download_owl": "http://cropontology.org/rdf/CO_321.owl",
"homepage": "http://cropontology.org/term/CO_321:ROOT",
"name": "Wheat ontology",
"prefix": "CO_321"
},
"CO_322": {
"description": "Maize Trait Dictionary in template 5 - CIMMYT- September 2016- Updated nov 2023 Updated Nov 2023 with the traits and variables for on farm comparative ranking of varieties",
"download_owl": "http://cropontology.org/rdf/CO_322.owl",
"homepage": "http://cropontology.org/term/CO_322:ROOT",
"name": "Maize ontology",
"prefix": "CO_322"
},
"CO_323": {
"description": "ICARDA - TDv5 - Sept 2018",
"download_owl": "http://cropontology.org/rdf/CO_323.owl",
"homepage": "http://cropontology.org/term/CO_323:ROOT",
"name": "Barley ontology",
"prefix": "CO_323"
},
"CO_324": {
"description": "Sorghum TDv5 - Oct 2019- Updated January 2024 with the Traits of 1000Farms project trials using comparative ranking by farmers method",
"download_owl": "http://cropontology.org/rdf/CO_324.owl",
"homepage": "http://cropontology.org/term/CO_324:ROOT",
"name": "Sorghum ontology",
"prefix": "CO_324"
},
"CO_325": {
"description": "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019",
"download_owl": "http://cropontology.org/rdf/CO_325.owl",
"homepage": "http://cropontology.org/term/CO_325:ROOT",
"name": "Banana ontology",
"prefix": "CO_325"
},
"CO_326": {
"download_owl": "http://cropontology.org/rdf/CO_326.owl",
"homepage": "http://cropontology.org/term/CO_326:ROOT",
"name": "Coconut ontology",
"prefix": "CO_326"
},
"CO_327": {
"description": "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016 - Updated with onfarm trial traits from 1000Farms project, 2024",
"download_owl": "http://cropontology.org/rdf/CO_327.owl",
"homepage": "http://cropontology.org/term/CO_327:ROOT",
"name": "Pearl millet ontology",
"prefix": "CO_327"
},
"CO_330": {
"description": "CIP - potato ontology - december 2018",
"download_owl": "http://cropontology.org/rdf/CO_330.owl",
"homepage": "http://cropontology.org/term/CO_330:ROOT",
"name": "Potato ontology",
"prefix": "CO_330"
},
"CO_331": {
"description": "Sweetpotato Trait Dictionary in template v5 - CIP - November 2019",
"download_owl": "http://cropontology.org/rdf/CO_331.owl",
"homepage": "http://cropontology.org/term/CO_331:ROOT",
"name": "Sweet Potato ontology",
"prefix": "CO_331"
},
"CO_333": {
"description": "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017.",
"download_owl": "http://cropontology.org/rdf/CO_333.owl",
"homepage": "http://cropontology.org/term/CO_333:ROOT",
"name": "Beet Ontology ontology",
"prefix": "CO_333"
},
"CO_334": {
"description": "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016, and in 2023 for the traits from on farm trials",
"download_owl": "http://cropontology.org/rdf/CO_334.owl",
"homepage": "http://cropontology.org/term/CO_334:ROOT",
"name": "Cassava ontology",
"prefix": "CO_334"
},
"CO_335": {
"description": "CIAT Common bean trait dictionary - Updated version Nov. 2023, with the traits and variables for on farm comparative ranking of varieties",
"download_owl": "http://cropontology.org/rdf/CO_335.owl",
"homepage": "http://cropontology.org/term/CO_335:ROOT",
"name": "Common bean ontology",
"prefix": "CO_335"
},
"CO_336": {
"description": "Soybean Trait Dictionary in template v5 - IITA - July 2015",
"download_owl": "http://cropontology.org/rdf/CO_336.owl",
"homepage": "http://cropontology.org/term/CO_336:ROOT",
"name": "Soybean ontology",
"prefix": "CO_336"
},
"CO_337": {
"description": "Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015 -Updated Nov 2023 with traits from the on farm trials for the comparative ranking of varieties",
"download_owl": "http://cropontology.org/rdf/CO_337.owl",
"homepage": "http://cropontology.org/term/CO_337:ROOT",
"name": "Groundnut ontology",
"prefix": "CO_337"
},
"CO_338": {
"description": "Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015",
"download_owl": "http://cropontology.org/rdf/CO_338.owl",
"homepage": "http://cropontology.org/term/CO_338:ROOT",
"name": "Chickpea ontology",
"prefix": "CO_338"
},
"CO_339": {
"description": "Lentil Trait Dictionary in template v5 - ICARDA - July 2015",
"download_owl": "http://cropontology.org/rdf/CO_339.owl",
"homepage": "http://cropontology.org/term/CO_339:ROOT",
"name": "Lentil ontology",
"prefix": "CO_339"
},
"CO_340": {
"description": "Cowpea Trait Dictionary - IITA - August 2015 - Updated Nov 2023 with the traits and variables for on farm comparative ranking of varieties",
"download_owl": "http://cropontology.org/rdf/CO_340.owl",
"homepage": "http://cropontology.org/term/CO_340:ROOT",
"name": "Cowpea ontology",
"prefix": "CO_340"
},
"CO_341": {
"description": "Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015",
"download_owl": "http://cropontology.org/rdf/CO_341.owl",
"homepage": "http://cropontology.org/term/CO_341:ROOT",
"name": "Pigeonpea ontology",
"prefix": "CO_341"
},
"CO_343": {
"description": "version 2019 - pvs",
"download_owl": "http://cropontology.org/rdf/CO_343.owl",
"homepage": "http://cropontology.org/term/CO_343:ROOT",
"name": "Yam ontology",
"prefix": "CO_343"
},
"CO_345": {
"description": "Brachiaria (forages) ontology TD v5 - Version Oct 2016",
"download_owl": "http://cropontology.org/rdf/CO_345.owl",
"homepage": "http://cropontology.org/term/CO_345:ROOT",
"name": "Brachiaria ontology",
"prefix": "CO_345"
},
"CO_346": {
"description": "oct 2016",
"download_owl": "http://cropontology.org/rdf/CO_346.owl",
"homepage": "http://cropontology.org/term/CO_346:ROOT",
"name": "Mungbean ontology",
"prefix": "CO_346"
},
"CO_347": {
"description": "March 2017 version ",
"download_owl": "http://cropontology.org/rdf/CO_347.owl",
"homepage": "http://cropontology.org/term/CO_347:ROOT",
"name": "Castor bean ontology",
"prefix": "CO_347"
},
"CO_348": {
"description": "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France).",
"download_owl": "http://cropontology.org/rdf/CO_348.owl",
"homepage": "http://cropontology.org/term/CO_348:ROOT",
"name": "Brassica ontology",
"prefix": "CO_348"
},
"CO_350": {
"description": "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo",
"download_owl": "http://cropontology.org/rdf/CO_350.owl",
"homepage": "http://cropontology.org/term/CO_350:ROOT",
"name": "Oat ontology",
"prefix": "CO_350"
},
"CO_356": {
"description": "Grape Ontology including OIV and bioversity descriptors. INRA July 2017",
"download_owl": "http://cropontology.org/rdf/CO_356.owl",
"homepage": "http://cropontology.org/term/CO_356:ROOT",
"name": "Vitis ontology",
"prefix": "CO_356"
},
"CO_357": {
"description": "This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (ITQB NOVA/IBET) - Version 2 submitted on Jun 2020 by INRAE.",
"download_owl": "http://cropontology.org/rdf/CO_357.owl",
"homepage": "http://cropontology.org/term/CO_357:ROOT",
"name": "Woody Plant Ontology ontology",
"prefix": "CO_357"
},
"CO_358": {
"description": "Cotton ontology from CottonGen database - June 2019",
"download_owl": "http://cropontology.org/rdf/CO_358.owl",
"homepage": "http://cropontology.org/term/CO_358:ROOT",
"name": "Cotton ontology",
"prefix": "CO_358"
},
"CO_359": {
"description": "December 2019",
"download_owl": "http://cropontology.org/rdf/CO_359.owl",
"homepage": "http://cropontology.org/term/CO_359:ROOT",
"name": "Sunflower ontology",
"prefix": "CO_359"
},
"CO_360": {
"description": "Sugar Kelp trait ontology",
"download_owl": "http://cropontology.org/rdf/CO_360.owl",
"homepage": "http://cropontology.org/term/CO_360:ROOT",
"name": "Sugar Kelp trait ontology",
"prefix": "CO_360"
},
"CO_365": {
"description": "developed by ICARDA - Dec 2018",
"download_owl": "http://cropontology.org/rdf/CO_365.owl",
"homepage": "http://cropontology.org/term/CO_365:ROOT",
"name": "Fababean ontology",
"prefix": "CO_365"
},
"CO_366": {
"description": "version Dec 2019",
"download_owl": "http://cropontology.org/rdf/CO_366.owl",
"homepage": "http://cropontology.org/term/CO_366:ROOT",
"name": "Bambara groundnut ontology",
"prefix": "CO_366"
},
"CO_367": {
"description": "Curator name: Clara S. Stanschewski; Curator Affiliation: King Abdullah University of Science and Technology; Contributing Scientists or Crop expert group: The Salt Lab and the Quinoa Phenotyping Consortium Creation Date: 23.05.2021",
"download_owl": "http://cropontology.org/rdf/CO_367.owl",
"homepage": "http://cropontology.org/term/CO_367:ROOT",
"name": "Quinoa Ontology ontology",
"prefix": "CO_367"
},
"CO_369": {
"description": "This ontology describes a standard trait lexicon used in phenotyping the forage and pulse crop, Sainfoin (Onobrychis viciifolia), with the intention of increasing trait consistency across different breeding programs. Submitted on behalf of the Sainfoin Consortium on November 3rd, 2022. Version 1.0.",
"download_owl": "http://cropontology.org/rdf/CO_369.owl",
"homepage": "http://cropontology.org/term/CO_369:ROOT",
"name": "Sainfoin ontology",
"prefix": "CO_369"
},
"CO_370": {
"description": "Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales.",
"download_owl": "http://cropontology.org/rdf/CO_370.owl",
"homepage": "http://cropontology.org/term/CO_370:ROOT",
"name": "Apple ontology",
"prefix": "CO_370"
},
"CO_371": {
"description": "Blueberry (Vaccinium) ontology defines crop traits and variables to support the standardization of phenotypic data collection for blueberry breeding programs in the USA. The ontology provides a description of agronomic, biochemical, morphological, phenological, physiological, quality, abiotic and biotic stress traits with their methods and scales used for each trait.",
"download_owl": "http://cropontology.org/rdf/CO_371.owl",
"homepage": "http://cropontology.org/term/CO_371:ROOT",
"name": "Blueberry ontology",
"prefix": "CO_371"
},
"CO_372": {
"description": "Strawberry trait ontology by USDA, GDR, 24 June 2024",
"download_owl": "http://cropontology.org/rdf/CO_372.owl",
"homepage": "http://cropontology.org/term/CO_372:ROOT",
"name": "Strawberry ontology",
"prefix": "CO_372"
}
}././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9579668
bioregistry-0.11.12/src/bioregistry/external/edam/ 0000755 0001751 0000177 00000000000 14655546227 021524 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/edam/__init__.py 0000644 0001751 0000177 00000003112 14655542206 023623 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Import accessions from EDAM."""
import json
from pathlib import Path
from typing import Mapping
from bioregistry.external.alignment_utils import Aligner
from bioregistry.utils import get_ols_descendants
__all__ = [
"get_edam",
"EDAMAligner",
]
DIRECTORY = Path(__file__).parent.resolve()
PROCESSED_PATH = DIRECTORY / "processed.json"
EDAM_PARENT_IRI = "http%253A%252F%252Fedamontology.org%252Fdata_2091"
def get_edam(force_download: bool = False):
"""Get the EDAM registry."""
if PROCESSED_PATH.exists() and not force_download:
return json.loads(PROCESSED_PATH.read_text())
rv = get_ols_descendants(
ontology="edam",
uri=EDAM_PARENT_IRI,
force_download=force_download,
get_identifier=_get_identifier,
)
PROCESSED_PATH.write_text(json.dumps(rv, indent=2, sort_keys=True))
return rv
def _get_identifier(term, ontology: str) -> str:
# note that this prefix doesn't match the ontology name
return term["obo_id"][len("data:") :]
class EDAMAligner(Aligner):
"""Aligner for the EDAM ontology."""
key = "edam"
getter = get_edam
alt_key_match = "name"
curation_header = ("name", "description")
def get_skip(self) -> Mapping[str, str]:
"""Get entries that should be skipped and their reasons."""
return {
"1164": "MIRIAM URI not relevant",
"1175": "BioPAX ontologies aren't globally unique",
"2582": "GO sub-hierarchy",
"2583": "GO sub-hierarchy",
}
if __name__ == "__main__":
EDAMAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254381.0
bioregistry-0.11.12/src/bioregistry/external/edam/processed.json 0000644 0001751 0000177 00000131060 14655543155 024404 0 ustar 00runner docker {
"1002": {
"description": "CAS registry number of a chemical compound; a unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service.",
"name": "CAS number",
"obsolete": false
},
"1003": {
"description": "Beilstein registry number of a chemical compound.",
"name": "Chemical registry number (Beilstein)",
"obsolete": false
},
"1004": {
"description": "Gmelin registry number of a chemical compound.",
"name": "Chemical registry number (Gmelin)",
"obsolete": false
},
"1011": {
"description": "An Enzyme Commission (EC) number of an enzyme.",
"name": "EC number",
"obsolete": false
},
"1027": {
"description": "An NCBI unique identifier of a gene.",
"name": "Gene ID (NCBI)",
"obsolete": false
},
"1031": {
"description": "Identifier of a gene or feature from the CGD database.",
"name": "Gene ID (CGD)",
"obsolete": false
},
"1032": {
"description": "Identifier of a gene from DictyBase.",
"name": "Gene ID (DictyBase)",
"obsolete": false
},
"1033": {
"description": "Unique identifier for a gene (or other feature) from the Ensembl database.",
"name": "Ensembl gene",
"obsolete": false
},
"1034": {
"description": "Identifier of an entry from the SGD database.",
"name": "Gene ID (SGD)",
"obsolete": false
},
"1035": {
"description": "Identifier of a gene from the GeneDB database.",
"name": "Gene ID (GeneDB)",
"obsolete": false
},
"1036": {
"description": "Identifier of an entry from the TIGR database.",
"name": "TIGR",
"obsolete": false
},
"1037": {
"description": "Identifier of an gene from the TAIR database.",
"name": "TAIR accession (gene)",
"obsolete": false
},
"1039": {
"description": "Identifier of a protein domain (or other node) from the SCOP database.",
"name": "SCOP domain",
"obsolete": false
},
"1040": {
"description": "Identifier of a protein domain from CATH.",
"name": "CATH domain",
"obsolete": false
},
"1041": {
"description": "A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification.",
"name": "SCOP concise classification string (sccs)",
"obsolete": false
},
"1042": {
"description": "Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229.",
"name": "SCOP sunid",
"obsolete": false
},
"1043": {
"description": "A code number identifying a node from the CATH database.",
"name": "CATH node",
"obsolete": false
},
"1066": {
"description": "Identifier of a molecular sequence alignment, for example a record from an alignment database.",
"name": "Sequence alignment",
"obsolete": false
},
"1089": {
"description": "Identifier of an object from the FlyBase database.",
"name": "FlyBase",
"obsolete": false
},
"1098": {
"description": "Accession number of a RefSeq database entry.",
"name": "RefSeq",
"obsolete": false
},
"1100": {
"description": "An identifier of PIR sequence database entry.",
"name": "PIR",
"obsolete": false
},
"1102": {
"description": "Primary identifier of a Gramene database entry.",
"name": "Gramene primary",
"obsolete": false
},
"1103": {
"description": "Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases.",
"name": "EMBL/GenBank/DDBJ",
"obsolete": false
},
"1104": {
"description": "A unique identifier of an entry (gene cluster) from the NCBI UniGene database.",
"name": "Sequence cluster ID (UniGene)",
"obsolete": false
},
"1105": {
"description": "Identifier of a dbEST database entry.",
"name": "dbEST",
"obsolete": false
},
"1106": {
"description": "Identifier of a dbSNP database entry.",
"name": "dbSNP",
"obsolete": false
},
"1113": {
"description": "Unique identifier of an entry from the COG database.",
"name": "Sequence cluster ID (COG)",
"obsolete": false
},
"1118": {
"description": "Unique identifier or name of a HMMER hidden Markov model.",
"name": "HMMER hidden Markov model",
"obsolete": false
},
"1119": {
"description": "Unique identifier or name of a profile from the JASPAR database.",
"name": "JASPAR profile",
"obsolete": false
},
"1123": {
"description": "Accession number of an entry from the TreeBASE database.",
"name": "TreeBASE study accession number",
"obsolete": false
},
"1124": {
"description": "Accession number of an entry from the TreeFam database.",
"name": "TreeFam accession number",
"obsolete": false
},
"1127": {
"description": "An identifier of an entry from the PDB database.",
"name": "PDB",
"obsolete": false
},
"1128": {
"description": "Identifier of an entry from the AAindex database.",
"name": "AAindex",
"obsolete": false
},
"1129": {
"description": "Accession number of an entry from the BIND database.",
"name": "BIND accession number",
"obsolete": false
},
"1130": {
"description": "Accession number of an entry from the IntAct database.",
"name": "IntAct accession number",
"obsolete": false
},
"1133": {
"description": "Primary accession number of an InterPro entry.",
"name": "InterPro",
"obsolete": false
},
"1134": {
"description": "Secondary accession number of an InterPro entry.",
"name": "InterPro secondary",
"obsolete": false
},
"1135": {
"description": "Unique identifier of an entry from the Gene3D database.",
"name": "Gene3D",
"obsolete": false
},
"1136": {
"description": "Unique identifier of an entry from the PIRSF database.",
"name": "PIRSF",
"obsolete": false
},
"1137": {
"description": "The unique identifier of an entry in the PRINTS database.",
"name": "PRINTS code",
"obsolete": false
},
"1138": {
"description": "Accession number of a Pfam entry.",
"name": "Pfam accession number",
"obsolete": false
},
"1139": {
"description": "Accession number of an entry from the SMART database.",
"name": "SMART accession number",
"obsolete": false
},
"1140": {
"description": "Unique identifier (number) of a hidden Markov model from the Superfamily database.",
"name": "Superfamily hidden Markov model number",
"obsolete": false
},
"1141": {
"description": "Accession number of an entry (family) from the TIGRFam database.",
"name": "TIGRFam",
"obsolete": false
},
"1142": {
"description": "A ProDom domain family accession number.",
"name": "ProDom accession number",
"obsolete": false
},
"1143": {
"description": "Identifier of an entry from the TRANSFAC database.",
"name": "TRANSFAC accession number",
"obsolete": false
},
"1146": {
"description": "Identifier of an entry from the EMDB electron microscopy database.",
"name": "EMDB",
"obsolete": false
},
"1147": {
"description": "Accession number of an entry from the GEO database.",
"name": "GEO accession number",
"obsolete": false
},
"1148": {
"description": "Identifier of an entry from the GermOnline database.",
"name": "GermOnline",
"obsolete": false
},
"1149": {
"description": "Identifier of an entry from the EMAGE database.",
"name": "EMAGE",
"obsolete": false
},
"1151": {
"description": "Identifier of an entry from the HGVbase database.",
"name": "HGVbase",
"obsolete": false
},
"1153": {
"description": "Identifier of an entry from the OMIM database.",
"name": "OMIM",
"obsolete": false
},
"1154": {
"description": "Unique identifier of an object from one of the KEGG databases (excluding the GENES division).",
"name": "KEGG object",
"obsolete": false
},
"1155": {
"description": "Identifier of an entry from the Reactome database.",
"name": "Pathway ID (reactome)",
"obsolete": false
},
"1157": {
"description": "Identifier of an pathway from the BioCyc biological pathways database.",
"name": "Pathway ID (BioCyc)",
"obsolete": false
},
"1158": {
"description": "Identifier of an entry from the INOH database.",
"name": "Pathway ID (INOH)",
"obsolete": false
},
"1159": {
"description": "Identifier of an entry from the PATIKA database.",
"name": "Pathway ID (PATIKA)",
"obsolete": false
},
"1160": {
"description": "Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB.",
"name": "Pathway ID (CPDB)",
"obsolete": false
},
"1161": {
"description": "Identifier of a biological pathway from the Panther Pathways database.",
"name": "Pathway ID (Panther)",
"obsolete": false
},
"1162": {
"description": "Unique identifier of a MIRIAM data resource.",
"name": "MIRIAM",
"obsolete": false
},
"1164": {
"description": "The URI (URL or URN) of a data entity from the MIRIAM database.",
"name": "MIRIAM URI",
"obsolete": false
},
"1167": {
"description": "Unique identifier of a Taverna workflow.",
"name": "Taverna workflow",
"obsolete": false
},
"1171": {
"description": "Unique identifier of an entry from the BioModel database.",
"name": "BioModel",
"obsolete": false
},
"1172": {
"description": "Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure.",
"name": "PubChem C",
"obsolete": false
},
"1173": {
"description": "Identifier of an entry from the ChemSpider database.",
"name": "ChemSpider",
"obsolete": false
},
"1174": {
"description": "Identifier of an entry from the ChEBI database.",
"name": "ChEBI",
"obsolete": false
},
"1175": {
"description": "An identifier of a concept from the BioPax ontology.",
"name": "BioPax concept",
"obsolete": false
},
"1176": {
"description": "An identifier of a concept from The Gene Ontology.",
"name": "GO concept",
"obsolete": false
},
"1177": {
"description": "An identifier of a concept from the MeSH vocabulary.",
"name": "MeSH concept",
"obsolete": false
},
"1178": {
"description": "An identifier of a concept from the HGNC controlled vocabulary.",
"name": "HGNC concept",
"obsolete": false
},
"1179": {
"description": "A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database.",
"name": "NCBI taxonomy",
"obsolete": false
},
"1180": {
"description": "An identifier of a concept from the Plant Ontology (PO).",
"name": "Plant Ontology concept",
"obsolete": false
},
"1181": {
"description": "An identifier of a concept from the UMLS vocabulary.",
"name": "UMLS concept",
"obsolete": false
},
"1182": {
"description": "An identifier of a concept from Foundational Model of Anatomy.",
"name": "FMA concept",
"obsolete": false
},
"1183": {
"description": "An identifier of a concept from the EMAP mouse ontology.",
"name": "EMAP concept",
"obsolete": false
},
"1184": {
"description": "An identifier of a concept from the ChEBI ontology.",
"name": "ChEBI concept",
"obsolete": false
},
"1185": {
"description": "An identifier of a concept from the MGED ontology.",
"name": "MGED concept",
"obsolete": false
},
"1186": {
"description": "An identifier of a concept from the myGrid ontology.",
"name": "myGrid concept",
"obsolete": false
},
"1187": {
"description": "PubMed unique identifier of an article.",
"name": "PubMed",
"obsolete": false
},
"1188": {
"description": "Digital Object Identifier (DOI) of a published article.",
"name": "DOI",
"obsolete": false
},
"1189": {
"description": "Medline UI (unique identifier) of an article.",
"name": "Medline UI",
"obsolete": false
},
"1794": {
"description": "Identifier of a gene from PlasmoDB Plasmodium Genome Resource.",
"name": "Gene ID (PlasmoDB)",
"obsolete": false
},
"1795": {
"description": "Identifier of a gene from EcoGene Database.",
"name": "Gene ID (EcoGene)",
"obsolete": false
},
"1796": {
"description": "Gene identifier from FlyBase database.",
"name": "Gene ID (FlyBase)",
"obsolete": false
},
"1802": {
"description": "Gene identifier from Gramene database.",
"name": "Gene ID (Gramene)",
"obsolete": false
},
"1803": {
"description": "Gene identifier from Virginia Bioinformatics Institute microbial database.",
"name": "Gene ID (Virginia microbial)",
"obsolete": false
},
"1804": {
"description": "Gene identifier from Sol Genomics Network.",
"name": "Gene ID (SGN)",
"obsolete": false
},
"1805": {
"description": "Gene identifier used by WormBase database.",
"name": "Gene ID (WormBase)",
"obsolete": false
},
"1873": {
"description": "A unique identifier for an organism used in the iHOP database.",
"name": "iHOP organism",
"obsolete": false
},
"1885": {
"description": "Identifier of a gene from the GeneFarm database.",
"name": "Gene ID (GeneFarm)",
"obsolete": false
},
"1886": {
"description": "The blattner identifier for a gene.",
"name": "Blattner number",
"obsolete": false
},
"1891": {
"description": "A unique identifier of a protein or gene used in the iHOP database.",
"name": "iHOP symbol",
"obsolete": false
},
"1895": {
"description": "Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases)",
"name": "Locus ID (AGI)",
"obsolete": false
},
"1896": {
"description": "Identifier for loci from ASPGD (Aspergillus Genome Database).",
"name": "Locus ID (ASPGD)",
"obsolete": false
},
"1897": {
"description": "Identifier for loci from Magnaporthe grisea Database at the Broad Institute.",
"name": "Locus ID (MGG)",
"obsolete": false
},
"1898": {
"description": "Identifier for loci from CGD (Candida Genome Database).",
"name": "Locus ID (CGD)",
"obsolete": false
},
"1899": {
"description": "Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute.",
"name": "Locus ID (CMR)",
"obsolete": false
},
"1900": {
"description": "Identifier for loci from NCBI database.",
"name": "NCBI locus tag",
"obsolete": false
},
"1901": {
"description": "Identifier for loci from SGD (Saccharomyces Genome Database).",
"name": "Locus ID (SGD)",
"obsolete": false
},
"1902": {
"description": "Identifier of loci from Maize Mapping Project.",
"name": "Locus ID (MMP)",
"obsolete": false
},
"1903": {
"description": "Identifier of locus from DictyBase (Dictyostelium discoideum).",
"name": "Locus ID (DictyBase)",
"obsolete": false
},
"1904": {
"description": "Identifier of a locus from EntrezGene database.",
"name": "Locus ID (EntrezGene)",
"obsolete": false
},
"1905": {
"description": "Identifier of locus from MaizeGDB (Maize genome database).",
"name": "Locus ID (MaizeGDB)",
"obsolete": false
},
"1907": {
"description": "Identifier of a gene from the KOME database.",
"name": "Gene ID (KOME)",
"obsolete": false
},
"1908": {
"description": "Identifier of a locus from the Tropgene database.",
"name": "Locus ID (Tropgene)",
"obsolete": false
},
"2102": {
"description": "A three-letter code used in the KEGG databases to uniquely identify organisms.",
"name": "KEGG organism code",
"obsolete": false
},
"2104": {
"description": "Identifier of an object from one of the BioCyc databases.",
"name": "BioCyc",
"obsolete": false
},
"2105": {
"description": "Identifier of a compound from the BioCyc chemical compounds database.",
"name": "Compound ID (BioCyc)",
"obsolete": false
},
"2106": {
"description": "Identifier of a biological reaction from the BioCyc reactions database.",
"name": "Reaction ID (BioCyc)",
"obsolete": false
},
"2107": {
"description": "Identifier of an enzyme from the BioCyc enzymes database.",
"name": "Enzyme ID (BioCyc)",
"obsolete": false
},
"2112": {
"description": "Primary identifier of an object from the FlyBase database.",
"name": "FlyBase primary",
"obsolete": false
},
"2114": {
"description": "Protein identifier used by WormBase database.",
"name": "WormBase wormpep",
"obsolete": false
},
"2174": {
"description": "Secondary identifier of an object from the FlyBase database.",
"name": "FlyBase secondary",
"obsolete": false
},
"2209": {
"description": "A unique identifier of a specific mutation catalogued in a database.",
"name": "Mutation",
"obsolete": false
},
"2220": {
"description": "Unique identifier of a sequence cluster from the SYSTERS database.",
"name": "Sequence cluster ID (SYSTERS)",
"obsolete": false
},
"2285": {
"description": "Identifier for genetic elements in MIPS database.",
"name": "Gene ID (MIPS)",
"obsolete": false
},
"2290": {
"description": "An accession number of an entry from the EMBL sequence database.",
"name": "EMBL",
"obsolete": false
},
"2292": {
"description": "Accession number of an entry from the GenBank sequence database.",
"name": "GenBank",
"obsolete": false
},
"2293": {
"description": "Secondary (internal) identifier of a Gramene database entry.",
"name": "Gramene secondary",
"obsolete": false
},
"2297": {
"description": "Identifier of an E. coli K-12 gene from EcoGene Database.",
"name": "Gene ID (ECK)",
"obsolete": false
},
"2298": {
"description": "Identifier for a gene approved by the HUGO Gene Nomenclature Committee.",
"name": "Gene ID (HGNC)",
"obsolete": false
},
"2302": {
"description": "Unique identifier of an entry from the STRING database of protein-protein interactions.",
"name": "STRING",
"obsolete": false
},
"2309": {
"description": "Identifier of a biological reaction from the SABIO-RK reactions database.",
"name": "Reaction ID (SABIO-RK)",
"obsolete": false
},
"2314": {
"description": "A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record.",
"name": "GI number",
"obsolete": false
},
"2315": {
"description": "An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number.",
"name": "NCBI version",
"obsolete": false
},
"2325": {
"description": "Identifier of an enzyme from the REBASE enzymes database.",
"name": "REBASE enzyme number",
"obsolete": false
},
"2326": {
"description": "Unique identifier of a drug from the DrugBank database.",
"name": "DrugBank",
"obsolete": false
},
"2327": {
"description": "A unique identifier assigned to NCBI protein sequence records.",
"name": "GI number (protein)",
"obsolete": false
},
"2343": {
"description": "Identifier of a pathway from the KEGG pathway database.",
"name": "Pathway ID (KEGG)",
"obsolete": false
},
"2344": {
"description": "Identifier of a pathway from the NCI-Nature pathway database.",
"name": "Pathway ID (NCI-Nature)",
"obsolete": false
},
"2345": {
"description": "Identifier of a pathway from the ConsensusPathDB pathway database.",
"name": "Pathway ID (ConsensusPathDB)",
"obsolete": false
},
"2346": {
"description": "Unique identifier of an entry from the UniRef database.",
"name": "Sequence cluster ID (UniRef)",
"obsolete": false
},
"2347": {
"description": "Unique identifier of an entry from the UniRef100 database.",
"name": "Sequence cluster ID (UniRef100)",
"obsolete": false
},
"2348": {
"description": "Unique identifier of an entry from the UniRef90 database.",
"name": "Sequence cluster ID (UniRef90)",
"obsolete": false
},
"2349": {
"description": "Unique identifier of an entry from the UniRef50 database.",
"name": "Sequence cluster ID (UniRef50)",
"obsolete": false
},
"2356": {
"description": "Stable accession number of an entry (RNA family) from the RFAM database.",
"name": "RFAM",
"obsolete": false
},
"2367": {
"description": "Identifier of an object from the ASTD database.",
"name": "ASTD",
"obsolete": false
},
"2368": {
"description": "Identifier of an exon from the ASTD database.",
"name": "ASTD ID (exon)",
"obsolete": false
},
"2369": {
"description": "Identifier of an intron from the ASTD database.",
"name": "ASTD ID (intron)",
"obsolete": false
},
"2370": {
"description": "Identifier of a polyA signal from the ASTD database.",
"name": "ASTD ID (polya)",
"obsolete": false
},
"2371": {
"description": "Identifier of a transcription start site from the ASTD database.",
"name": "ASTD ID (tss)",
"obsolete": false
},
"2374": {
"description": "Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database.",
"name": "Spot serial number",
"obsolete": false
},
"2375": {
"description": "Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database.",
"name": "Spot ID (HSC-2DPAGE)",
"obsolete": false
},
"2380": {
"description": "A unique identifier of an item from the CABRI database.",
"name": "CABRI",
"obsolete": false
},
"2383": {
"description": "Identifier of an entry from the EGA database.",
"name": "EGA",
"obsolete": false
},
"2384": {
"description": "Identifier of a protein entry catalogued in the International Protein Index (IPI) database.",
"name": "IPI protein",
"obsolete": false
},
"2385": {
"description": "Accession number of a protein from the RefSeq database.",
"name": "RefSeq accession (protein)",
"obsolete": false
},
"2386": {
"description": "Identifier of an entry (promoter) from the EPD database.",
"name": "EPD",
"obsolete": false
},
"2387": {
"description": "Identifier of an entry from the TAIR database.",
"name": "TAIR",
"obsolete": false
},
"2388": {
"description": "Identifier of an Arabidopsis thaliana gene from the TAIR database.",
"name": "TAIR accession (At gene)",
"obsolete": false
},
"2389": {
"description": "Identifier of an entry from the UniSTS database.",
"name": "UniSTS",
"obsolete": false
},
"2390": {
"description": "Identifier of an entry from the UNITE database.",
"name": "UNITE",
"obsolete": false
},
"2391": {
"description": "Identifier of an entry from the UTR database.",
"name": "UTR",
"obsolete": false
},
"2392": {
"description": "Accession number of a UniParc (protein sequence) database entry.",
"name": "UniParc",
"obsolete": false
},
"2393": {
"description": "Identifier of an entry from the Rouge or HUGE databases.",
"name": "mFLJ/mKIAA number",
"obsolete": false
},
"2398": {
"description": "Unique identifier for a protein from the Ensembl database.",
"name": "Ensembl protein",
"obsolete": false
},
"2578": {
"description": "Unique identifier of a toxin from the ArachnoServer database.",
"name": "ArachnoServer",
"obsolete": false
},
"2580": {
"description": "Unique identifier of a monomer from the BindingDB database.",
"name": "BindingDB Monomer",
"obsolete": false
},
"2582": {
"description": "An identifier of a 'biological process' concept from the the Gene Ontology.",
"name": "GO concept ID (biological process)",
"obsolete": false
},
"2583": {
"description": "An identifier of a 'molecular function' concept from the the Gene Ontology.",
"name": "GO concept ID (molecular function)",
"obsolete": false
},
"2588": {
"description": "Unique identifier of a blot from a Northern Blot from the BlotBase database.",
"name": "BlotBase blot",
"obsolete": false
},
"2591": {
"description": "Identifier of an entry from the Brite database of biological hierarchies.",
"name": "Brite hierarchy",
"obsolete": false
},
"2593": {
"description": "A unique identifier for an organism used in the BRENDA database.",
"name": "BRENDA organism",
"obsolete": false
},
"2605": {
"description": "Unique identifier of a chemical compound from the KEGG database.",
"name": "Compound ID (KEGG)",
"obsolete": false
},
"2608": {
"description": "Identifier of a biological reaction from the KEGG reactions database.",
"name": "Reaction ID (KEGG)",
"obsolete": false
},
"2609": {
"description": "Unique identifier of a drug from the KEGG Drug database.",
"name": "Drug ID (KEGG)",
"obsolete": false
},
"2610": {
"description": "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database.",
"name": "Ensembl",
"obsolete": false
},
"2611": {
"description": "An identifier of a disease from the International Classification of Diseases (ICD) database.",
"name": "ICD",
"obsolete": false
},
"2612": {
"description": "Unique identifier of a sequence cluster from the CluSTr database.",
"name": "Sequence cluster ID (CluSTr)",
"obsolete": false
},
"2613": {
"description": "Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND).",
"name": "KEGG Glycan",
"obsolete": false
},
"2614": {
"description": "A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins.",
"name": "TCDB",
"obsolete": false
},
"2615": {
"description": "Unique identifier of an entry from the MINT database of protein-protein interactions.",
"name": "MINT",
"obsolete": false
},
"2616": {
"description": "Unique identifier of an entry from the DIP database of protein-protein interactions.",
"name": "DIP",
"obsolete": false
},
"2617": {
"description": "Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database.",
"name": "Signaling Gateway protein",
"obsolete": false
},
"2619": {
"description": "Identifier of a protein modification catalogued in the RESID database.",
"name": "RESID",
"obsolete": false
},
"2620": {
"description": "Identifier of an entry from the RGD database.",
"name": "RGD",
"obsolete": false
},
"2621": {
"description": "Identifier of a protein sequence from the TAIR database.",
"name": "TAIR accession (protein)",
"obsolete": false
},
"2622": {
"description": "Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB).",
"name": "Compound ID (HMDB)",
"obsolete": false
},
"2625": {
"description": "Identifier of an entry from the LIPID MAPS database.",
"name": "LIPID MAPS",
"obsolete": false
},
"2626": {
"description": "Identifier of a peptide from the PeptideAtlas peptide databases.",
"name": "PeptideAtlas",
"obsolete": false
},
"2628": {
"description": "A unique identifier of an interaction from the BioGRID database.",
"name": "BioGRID interaction",
"obsolete": false
},
"2629": {
"description": "Unique identifier of a peptidase enzyme from the MEROPS database.",
"name": "Enzyme ID (MEROPS)",
"obsolete": false
},
"2631": {
"description": "An identifier of a mobile genetic element from the Aclame database.",
"name": "ACLAME",
"obsolete": false
},
"2632": {
"description": "Identifier of an entry from the Saccharomyces genome database (SGD).",
"name": "SGD",
"obsolete": false
},
"2634": {
"description": "The International Standard Book Number (ISBN) is for identifying printed books.",
"name": "ISBN",
"obsolete": false
},
"2635": {
"description": "Identifier of a metabolite from the 3DMET database.",
"name": "Compound ID (3DMET)",
"obsolete": false
},
"2636": {
"description": "A unique identifier of an interaction from the MatrixDB database.",
"name": "MatrixDB interaction",
"obsolete": false
},
"2637": {
"description": "A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database.",
"name": "cPath",
"obsolete": false
},
"2638": {
"description": "Identifier of an assay from the PubChem database.",
"name": "PubChem bioassay",
"obsolete": false
},
"2639": {
"description": "Identifier of an entry from the PubChem database.",
"name": "PubChem",
"obsolete": false
},
"2641": {
"description": "Identifier of an enzyme reaction mechanism from the MACie database.",
"name": "Reaction ID (MACie)",
"obsolete": false
},
"2642": {
"description": "Identifier for a gene from the miRBase database.",
"name": "Gene ID (miRBase)",
"obsolete": false
},
"2643": {
"description": "Identifier for a gene from the Zebrafish information network genome (ZFIN) database.",
"name": "Gene ID (ZFIN)",
"obsolete": false
},
"2644": {
"description": "Identifier of an enzyme-catalysed reaction from the Rhea database.",
"name": "Reaction ID (Rhea)",
"obsolete": false
},
"2645": {
"description": "Identifier of a biological pathway from the Unipathway database.",
"name": "Pathway ID (Unipathway)",
"obsolete": false
},
"2646": {
"description": "Identifier of a small molecular from the ChEMBL database.",
"name": "Compound ID (ChEMBL)",
"obsolete": false
},
"2647": {
"description": "Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database.",
"name": "LGICdb",
"obsolete": false
},
"2648": {
"description": "Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database.",
"name": "Reaction kinetics ID (SABIO-RK)",
"obsolete": false
},
"2649": {
"description": "Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).",
"name": "PharmGKB",
"obsolete": false
},
"2650": {
"description": "Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).",
"name": "Pathway ID (PharmGKB)",
"obsolete": false
},
"2651": {
"description": "Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).",
"name": "Disease ID (PharmGKB)",
"obsolete": false
},
"2652": {
"description": "Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).",
"name": "Drug ID (PharmGKB)",
"obsolete": false
},
"2653": {
"description": "Identifier of a drug from the Therapeutic Target Database (TTD).",
"name": "Drug ID (TTD)",
"obsolete": false
},
"2654": {
"description": "Identifier of a target protein from the Therapeutic Target Database (TTD).",
"name": "Target ID (TTD)",
"obsolete": false
},
"2656": {
"description": "A unique identifier of a neuron from the NeuronDB database.",
"name": "NeuronDB",
"obsolete": false
},
"2657": {
"description": "A unique identifier of a neuron from the NeuroMorpho database.",
"name": "NeuroMorpho",
"obsolete": false
},
"2658": {
"description": "Identifier of a chemical from the ChemIDplus database.",
"name": "Compound ID (ChemIDplus)",
"obsolete": false
},
"2659": {
"description": "Identifier of a pathway from the Small Molecule Pathway Database (SMPDB).",
"name": "Pathway ID (SMPDB)",
"obsolete": false
},
"2660": {
"description": "Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology.",
"name": "BioNumbers",
"obsolete": false
},
"2662": {
"description": "Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database.",
"name": "T3DB",
"obsolete": false
},
"2664": {
"description": "Identifier of an entry from the GlycomeDB database.",
"name": "GlycomeDB",
"obsolete": false
},
"2665": {
"description": "Identifier of an entry from the LipidBank database.",
"name": "LipidBank",
"obsolete": false
},
"2666": {
"description": "Identifier of a conserved domain from the Conserved Domain Database.",
"name": "CDD",
"obsolete": false
},
"2667": {
"description": "An identifier of an entry from the MMDB database.",
"name": "MMDB",
"obsolete": false
},
"2668": {
"description": "Unique identifier of an entry from the iRefIndex database of protein-protein interactions.",
"name": "iRefIndex",
"obsolete": false
},
"2669": {
"description": "Unique identifier of an entry from the ModelDB database.",
"name": "ModelDB",
"obsolete": false
},
"2670": {
"description": "Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS).",
"name": "Pathway ID (DQCS)",
"obsolete": false
},
"2700": {
"description": "Identifier of a protein domain (or other node) from the CATH database.",
"name": "CATH",
"obsolete": false
},
"2701": {
"description": "A code number identifying a family from the CATH database.",
"name": "CATH node ID (family)",
"obsolete": false
},
"2702": {
"description": "Identifier of an enzyme from the CAZy enzymes database.",
"name": "Enzyme ID (CAZy)",
"obsolete": false
},
"2704": {
"description": "A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence).",
"name": "Clone ID (IMAGE)",
"obsolete": false
},
"2705": {
"description": "An identifier of a 'cellular component' concept from the Gene Ontology.",
"name": "GO concept ID (cellular component)",
"obsolete": false
},
"2709": {
"description": "An identifier of a gene expression profile from the CleanEx database.",
"name": "CleanEx entry name",
"obsolete": false
},
"2713": {
"description": "Unique identifier for a protein complex from the CORUM database.",
"name": "Protein ID (CORUM)",
"obsolete": false
},
"2714": {
"description": "Unique identifier of a position-specific scoring matrix from the CDD database.",
"name": "CDD PSSM-",
"obsolete": false
},
"2715": {
"description": "Unique identifier for a protein from the CuticleDB database.",
"name": "Protein ID (CuticleDB)",
"obsolete": false
},
"2716": {
"description": "Identifier of a predicted transcription factor from the DBD database.",
"name": "DBD",
"obsolete": false
},
"2719": {
"description": "Identifier of an oligonucleotide probe from the dbProbe database.",
"name": "dbProbe",
"obsolete": false
},
"2721": {
"description": "Identifier of an dinucleotide property from the DiProDB database.",
"name": "DiProDB",
"obsolete": false
},
"2723": {
"description": "Unique identifier for a protein from the DisProt database.",
"name": "Protein ID (DisProt)",
"obsolete": false
},
"2725": {
"description": "Unique identifier for a gene transcript from the Ensembl database.",
"name": "Ensembl transcript",
"obsolete": false
},
"2729": {
"description": "Identifier of an EST sequence from the COGEME database.",
"name": "COGEME EST",
"obsolete": false
},
"2730": {
"description": "Identifier of a unisequence from the COGEME database.",
"name": "COGEME unisequence",
"obsolete": false
},
"2731": {
"description": "Accession number of an entry (family) from the TIGRFam database.",
"name": "Protein family ID (GeneFarm)",
"obsolete": false
},
"2736": {
"description": "A feature identifier as used in the SwissRegulon database.",
"name": "Sequence feature ID (SwissRegulon)",
"obsolete": false
},
"2737": {
"description": "A unique identifier of gene in the NMPDR database.",
"name": "FIG",
"obsolete": false
},
"2738": {
"description": "A unique identifier of gene in the Xenbase database.",
"name": "Gene ID (Xenbase)",
"obsolete": false
},
"2739": {
"description": "A unique identifier of gene in the Genolist database.",
"name": "Gene ID (Genolist)",
"obsolete": false
},
"2741": {
"description": "Identifier of an entry (promoter) from the ABS database.",
"name": "ABS",
"obsolete": false
},
"2742": {
"description": "Identifier of a transcription factor from the AraC-XylS database.",
"name": "AraC-XylS",
"obsolete": false
},
"2744": {
"description": "Identifier of a locus from the PseudoCAP database.",
"name": "Locus ID (PseudoCAP)",
"obsolete": false
},
"2745": {
"description": "Identifier of a locus from the UTR database.",
"name": "Locus ID (UTR)",
"obsolete": false
},
"2746": {
"description": "Unique identifier of a monosaccharide from the MonosaccharideDB database.",
"name": "MonosaccharideDB",
"obsolete": false
},
"2751": {
"description": "An identifier of a particular genome.",
"name": "GenomeReviews",
"obsolete": false
},
"2752": {
"description": "Identifier of an entry from the GlycosciencesDB database.",
"name": "GlycoMap",
"obsolete": false
},
"2756": {
"description": "Identifier of a membrane transport proteins from the transport classification database (TCDB).",
"name": "TC",
"obsolete": false
},
"2758": {
"description": "Accession number of a Pfam clan.",
"name": "Pfam clan",
"obsolete": false
},
"2759": {
"description": "Identifier for a gene from the VectorBase database.",
"name": "Gene ID (VectorBase)",
"obsolete": false
},
"2766": {
"description": "Name of a protein family from the HAMAP database.",
"name": "HAMAP",
"obsolete": false
},
"2770": {
"description": "Identifier of an RNA transcript from the H-InvDB database.",
"name": "HIT",
"obsolete": false
},
"2771": {
"description": "A unique identifier of gene cluster in the H-InvDB database.",
"name": "HIX",
"obsolete": false
},
"2772": {
"description": "Identifier of a antibody from the HPA database.",
"name": "HPA antibody id",
"obsolete": false
},
"2773": {
"description": "Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database.",
"name": "IMGT/HLA",
"obsolete": false
},
"2774": {
"description": "A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI).",
"name": "Gene ID (JCVI)",
"obsolete": false
},
"2776": {
"description": "Identifier of a physical entity from the ConsensusPathDB database.",
"name": "ConsensusPathDB entity",
"obsolete": false
},
"2778": {
"description": "The number of a strain of algae and protozoa from the CCAP database.",
"name": "CCAP strain number",
"obsolete": false
},
"2780": {
"description": "A stock number from The Arabidopsis information resource (TAIR).",
"name": "Stock number (TAIR)",
"obsolete": false
},
"2781": {
"description": "Identifier of an entry from the RNA editing database (REDIdb).",
"name": "REDIdb",
"obsolete": false
},
"2783": {
"description": "Accession number of an entry (family) from the PANTHER database.",
"name": "Protein family ID (PANTHER)",
"obsolete": false
},
"2784": {
"description": "A unique identifier for a virus from the RNAVirusDB database.",
"name": "RNAVirusDB",
"obsolete": false
},
"2786": {
"description": "An identifier of a genome project assigned by NCBI.",
"name": "NCBI Genome Project",
"obsolete": false
},
"2787": {
"description": "A unique identifier of a whole genome assigned by the NCBI.",
"name": "NCBI genome",
"obsolete": false
},
"2789": {
"description": "Unique identifier for a membrane protein from the TopDB database.",
"name": "Protein ID (TopDB)",
"obsolete": false
},
"2792": {
"description": "Unique identifier for a peroxidase protein from the PeroxiBase database.",
"name": "Protein ID (PeroxiBase)",
"obsolete": false
},
"2793": {
"description": "Identifier of an entry from the SISYPHUS database of tertiary structure alignments.",
"name": "SISYPHUS",
"obsolete": false
},
"2794": {
"description": "Accession of an open reading frame (catalogued in a database).",
"name": "ORF",
"obsolete": false
},
"2796": {
"description": "Identifier of an entry from the GlycosciencesDB database.",
"name": "Linucs",
"obsolete": false
},
"2797": {
"description": "Unique identifier for a ligand-gated ion channel protein from the LGICdb database.",
"name": "Protein ID (LGICdb)",
"obsolete": false
},
"2798": {
"description": "Identifier of an EST sequence from the MaizeDB database.",
"name": "MaizeDB",
"obsolete": false
},
"2799": {
"description": "A unique identifier of gene in the MfunGD database.",
"name": "Gene ID (MfunGD)",
"obsolete": false
},
"2800": {
"description": "An identifier of a disease from the Orpha database.",
"name": "Orpha number",
"obsolete": false
},
"2802": {
"description": "Unique identifier for a protein from the EcID database.",
"name": "Protein ID (EcID)",
"obsolete": false
},
"2803": {
"description": "A unique identifier of a cDNA molecule catalogued in the RefSeq database.",
"name": "Clone ID (RefSeq)",
"obsolete": false
},
"2804": {
"description": "Unique identifier for a cone snail toxin protein from the ConoServer database.",
"name": "Protein ID (ConoServer)",
"obsolete": false
},
"2805": {
"description": "Identifier of a GeneSNP database entry.",
"name": "GeneSNP",
"obsolete": false
},
"2835": {
"description": "Identifier for a gene from the VBASE2 database.",
"name": "Gene ID (VBASE2)",
"obsolete": false
},
"2836": {
"description": "A unique identifier for a virus from the DPVweb database.",
"name": "DPVweb",
"obsolete": false
},
"2837": {
"description": "Identifier of a pathway from the BioSystems pathway database.",
"name": "Pathway ID (BioSystems)",
"obsolete": false
},
"2915": {
"description": "Identifier of a Gramene database entry.",
"name": "Gramene",
"obsolete": false
},
"2916": {
"description": "An identifier of an entry from the DDBJ sequence database.",
"name": "DDBJ",
"obsolete": false
},
"3021": {
"description": "Accession number of a UniProt (protein sequence) database entry.",
"name": "UniProt",
"obsolete": false
},
"3022": {
"description": "Identifier of a genetic code in the NCBI list of genetic codes.",
"name": "NCBI genetic code",
"obsolete": false
},
"3029": {
"description": "EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators.",
"name": "Protein ID (EMBL/GenBank/DDBJ)",
"obsolete": false
},
"3103": {
"description": "Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC).",
"name": "ATC code",
"obsolete": false
},
"3238": {
"description": "Cell type ontology concept ID.",
"name": "Cell type ontology",
"obsolete": false
},
"3264": {
"description": "Identifier of a COSMIC database entry.",
"name": "COSMIC",
"obsolete": false
},
"3265": {
"description": "Identifier of a HGMD database entry.",
"name": "HGMD",
"obsolete": false
},
"3270": {
"description": "Unique identifier for a gene tree from the Ensembl database.",
"name": "Ensembl gene tree",
"obsolete": false
},
"3274": {
"description": "Identifier of an object from the MGI database.",
"name": "MGI",
"obsolete": false
},
"3757": {
"description": "Identifier of a protein modification catalogued in the Unimod database.",
"name": "Unimod",
"obsolete": false
},
"3769": {
"description": "An identifier of a concept from the BRENDA ontology.",
"name": "BRENDA ontology concept",
"obsolete": false
},
"3856": {
"description": "Identifier of an entry from the RNA central database of annotated human miRNAs.",
"name": "RNA central",
"obsolete": false
},
"3952": {
"description": "Identifier of a pathway from the WikiPathways pathway database.",
"name": "Pathway ID (WikiPathways)",
"obsolete": false
}
} ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9579668
bioregistry-0.11.12/src/bioregistry/external/fairsharing/ 0000755 0001751 0000177 00000000000 14655546227 023113 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/fairsharing/__init__.py 0000644 0001751 0000177 00000012177 14655542206 025225 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Scraper for FAIRsharing.
.. seealso:: https://beta.fairsharing.org/API_doc
"""
import json
import logging
import re
from pathlib import Path
from typing import Any, MutableMapping, Optional, Set
from bioregistry.constants import ORCID_PATTERN
from bioregistry.external.alignment_utils import Aligner
from bioregistry.license_standardizer import standardize_license
from bioregistry.utils import removeprefix, removesuffix
__all__ = [
"get_fairsharing",
"FairsharingAligner",
]
logger = logging.getLogger(__name__)
DIRECTORY = Path(__file__).parent.resolve()
PROCESSED_PATH = DIRECTORY / "processed.json"
ALLOWED_TYPES = {
"terminology_artefact",
"identifier_schema",
# "knowledgebase",
# "knowledgebase_and_repository",
# "repository",
}
ORCID_RE = re.compile(ORCID_PATTERN)
def get_fairsharing(
*, force_download: bool = False, force_reload: bool = False, use_tqdm: bool = False
):
"""Get the FAIRsharing registry."""
if PROCESSED_PATH.exists() and not force_download and not force_reload:
with PROCESSED_PATH.open() as file:
return json.load(file)
from fairsharing_client import load_fairsharing
data = load_fairsharing(force_download=force_download, use_tqdm=use_tqdm)
rv = {}
for prefix, record in data.items():
new_record = _process_record(record)
if new_record:
rv[prefix] = new_record
with PROCESSED_PATH.open("w") as file:
json.dump(rv, file, indent=2, ensure_ascii=False, sort_keys=True)
return rv
KEEP = {
"description",
"name",
"subjects",
"user_defined_tags",
"domains",
}
def _process_record(record: MutableMapping[str, Any]) -> Optional[MutableMapping[str, Any]]:
if record.get("record_type") not in ALLOWED_TYPES:
return None
rv = {key: record[key] for key in KEEP if record[key]}
abbreviation = record.get("abbreviation")
if abbreviation:
for suf in [
" CT",
" CV",
" Controlled Vocabulary",
" Terminology",
" Ontology",
" Thesaurus",
" Vocabulary",
" Taxonomy",
]:
rv["abbreviation"] = removesuffix(abbreviation, suf)
metadata = record.get("metadata", {})
url_for_logo = record.get("url_for_logo")
if url_for_logo is not None:
rv["logo"] = "https://api.fairsharing.org" + url_for_logo
homepage = metadata.get("homepage")
if homepage:
rv["homepage"] = homepage
rv["publications"] = list(
filter(
None,
(_process_publication(publication) for publication in record.get("publications", [])),
)
)
contacts = [
{removeprefix(k, "contact_"): v for k, v in contact.items()}
for contact in metadata.get("contacts", [])
# make sure ORCID is available and valid
if (orcid := contact.get("contact_orcid")) and ORCID_RE.match(orcid)
]
for contact in contacts:
contact["name"] = removeprefix(removeprefix(contact["name"], "Dr. "), "Dr ")
if "orcid" in contact:
contact["orcid"] = contact["orcid"].replace(" ", "")
if contacts:
rv["contact"] = contacts[0]
for support_link in metadata.get("support_links", []):
if support_link["type"] == "Twitter":
rv["twitter"] = removeprefix(support_link["url"], "https://twitter.com/")
if support_link["type"] == "Github":
rv["repository"] = support_link["url"]
missed = set()
for license_link in record.get("licence_links", []):
url = license_link.get("licence_url")
if not url:
continue
license_standard = standardize_license(url)
if license_standard == url:
if license_standard not in missed and license_standard not in SKIP_LICENSES:
missed.add(license_standard)
logger.debug("Need to curate license URL: %s", license_standard)
continue
else:
rv["license"] = license_standard
rv = {k: v for k, v in rv.items() if k and v}
return rv
#: Licenses that are one-off and don't need curating
SKIP_LICENSES: Set[str] = set()
def _process_publication(publication):
rv = {}
doi = publication.get("doi")
if doi:
doi = doi.rstrip(".").lower()
doi = removeprefix(doi, "doi:")
doi = removeprefix(doi, "https://doi.org/")
if "/" not in doi:
doi = None
else:
rv["doi"] = doi
pubmed = publication.get("pubmed_id")
if pubmed:
rv["pubmed"] = str(pubmed)
if not doi and not pubmed:
return
title = publication.get("title")
if title:
title = title.replace(" ", " ").rstrip(".")
rv["title"] = title
year = publication.get("year")
if year:
rv["year"] = int(year)
return rv
class FairsharingAligner(Aligner):
"""Aligner for the FAIRsharing."""
key = "fairsharing"
alt_key_match = "abbreviation"
skip_deprecated = True
getter = get_fairsharing
curation_header = ("abbreviation", "name", "description")
if __name__ == "__main__":
FairsharingAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254377.0
bioregistry-0.11.12/src/bioregistry/external/fairsharing/processed.json 0000644 0001751 0000177 00003217205 14655543151 026000 0 ustar 00runner docker {
"FAIRsharing.00adc9": {
"abbreviation": "LCSHAC",
"description": "The Library of Congress Subject Headings Supplemental Vocabularies: Childrenβs Headings (LCSHAC) is a thesaurus which is used in conjunction with LCSH. It is not a self-contained vocabulary, but is instead designed to complement LCSH and provide tailored subject access to children and young adults when LCSH does not provide suitable terminology, form, or scope for children.",
"homepage": "https://id.loc.gov/authorities/childrensSubjects.html",
"license": "https://www.loc.gov/legal",
"name": "Library of Congress Subject Headings Supplemental Vocabularies: Childrenβs Headings",
"subjects": [
"Humanities and Social Science",
"Literary Studies"
]
},
"FAIRsharing.01e983": {
"description": "Controlled, standardized and multilingual vocabulary for archaeology, from prehistory to the contemporary period and for the sciences of antiquity in all their aspects.",
"homepage": "https://pactols.frantiq.fr/opentheso/",
"license": "ODBL",
"name": "PACTOLS: Peuples et Cultures, Anthroponymes, Chronologie relative, Toponymes, Oeuvres, Lieux, Sujets",
"repository": "https://github.com/frantiq/PACTOLS",
"subjects": [
"Archaeology"
]
},
"FAIRsharing.07f04a": {
"description": "DCAT-AP is a DCAT profile for sharing information about Catalogues containing Datasets and Data Services descriptions in Europe, under maintenance by the SEMIC action, Interoperable Europe.\n\nThis Application Profile provides a minimal common basis within Europe to share Datasets and Data Services cross-border and cross-domain. ",
"homepage": "https://op.europa.eu/en/web/eu-vocabularies/dcat-ap",
"license": "CC-BY-4.0",
"name": "DCAT Application profile for data portals in Europe",
"subjects": [
"Data Management",
"Subject Agnostic"
]
},
"FAIRsharing.093230": {
"abbreviation": " PSO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Publishing Status Ontology (PSO) is an ontology designed to characterise the publication status of documents at each stage of the publishing process (draft, submitted, under review, etc.).\n\n",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/pso",
"license": "CC-BY-4.0",
"name": "Publishing Status Ontology",
"publications": [
{
"doi": "10.1145/2362499.2362502",
"title": "Scholarly publishing and Linked Data: describing roles, statuses, temporal and contextual extents",
"year": 2012
}
],
"repository": "https://github.com/sparontologies/pso",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"FAIRsharing.0a2576": {
"abbreviation": "FRAPO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Funding, Research Administration and Projects Ontology (FRAPO) is an ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc.",
"domains": [
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/frapo",
"license": "CC-BY-4.0",
"name": "Funding, Research Administration and Projects Ontology ",
"repository": "https://github.com/sparontologies/frapo",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies",
"user_defined_tags": [
"Funding bodies",
"grant application",
"research project"
]
},
"FAIRsharing.0b7e54": {
"abbreviation": "hdl",
"description": "The Handle System is the Corporation for National Research Initiatives's proprietary registry assigning persistent identifiers, or handles, to information resources, and for resolving \"those handles into the information necessary to locate, access, and otherwise make use of the resources\". As with handles used elsewhere in computing, Handle System handles are opaque, and encode no information about the underlying resource, being bound only to metadata regarding the resource. Consequently, the handles are not rendered invalid by changes to the metadata.",
"domains": [
"Centrally registered identifier"
],
"homepage": "http://handle.net",
"name": "Handle",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.0d9792": {
"abbreviation": "LiCO",
"contact": {
"email": "suzan.uskudarli@boun.edu.tr",
"name": "Suzan Uskudarli",
"orcid": "0000-0002-0106-0182"
},
"description": "Liver Case Ontology (LiCO) is a case-centric ontology for liver patient cases.",
"domains": [
"Liver disease",
"Patient care",
"Liver"
],
"homepage": "https://bioportal.bioontology.org/ontologies/LICO",
"license": "CC0-1.0",
"name": "Liver Case Ontology",
"publications": [
{
"doi": "10.1016/j.eswa.2018.02.001",
"title": "Towards an ontology-driven clinical experience sharing ecosystem: Demonstration with liver cases",
"year": 2018
}
],
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.0dd54d": {
"description": "This vocabulary gathers the main concepts describing fluid mechanics. It is derived from the vocabulary used until 2015 to index the bibliographic references of the PASCAL database (https://pascal-francis.inist.fr/) produced by Inist, and has been enhanced with more recent concepts.",
"homepage": "https://skosmos.loterre.fr/2QZ/en/",
"license": "CC-BY-4.0",
"name": "Fluid mechanics vocabulary",
"subjects": [
"Physics",
"Fluid Mechanics"
]
},
"FAIRsharing.0e2b98": {
"abbreviation": "PreMedOnto",
"description": "The PreMedOnto ontology can be used for NLP (Natural Language Processing) applications in the Precision Medicine domain.",
"domains": [
"Disease"
],
"homepage": "https://bioportal.bioontology.org/ontologies/PREMEDONTO",
"license": "CC0-1.0",
"name": "Precision Medicine Ontology",
"publications": [
{
"doi": "10.1007/978-3-030-23281-8_28",
"title": "PreMedOnto: A Computer Assisted Ontology for Precision Medicine",
"year": 2019
}
],
"subjects": [
"Genomics",
"Biomedical Science"
]
},
"FAIRsharing.10960p": {
"abbreviation": "ICW",
"description": "Record does not exist anymore: International Classification of Wellness. The record with identifier content https://doi.org/10.25504/FAIRsharing.10960p was invalid.",
"homepage": "http://bioportal.bioontology.org/ontologies/ICW",
"name": "International Classification of Wellness"
},
"FAIRsharing.10gr18": {
"abbreviation": "VT",
"description": "The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.",
"domains": [
"Phenotype",
"Morphology"
],
"homepage": "https://github.com/AnimalGenome/vertebrate-trait-ontology",
"license": "CC-BY-4.0",
"name": "Vertebrate Trait Ontology",
"publications": [
{
"doi": "10.1186/2041-1480-4-13",
"pubmed": "23937709",
"title": "The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species",
"year": 2013
}
],
"repository": "https://github.com/AnimalGenome/vertebrate-trait-ontology/issues",
"subjects": [
"Animal Physiology",
"Developmental Biology",
"Physiology",
"Biology"
]
},
"FAIRsharing.10zsxb": {
"abbreviation": "ICD-9-CM",
"description": "The ICD is the international standard diagnostic classification for all general epidemiological, many health management purposes and clinical use. The International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) is an adaption created by the U.S. National Center for Health Statistics (NCHS) and used in assigning diagnostic and procedure codes associated with inpatient, outpatient, and physician office utilization in the United States. The ICD-9-CM is based on the ICD-9 but provides for additional morbidity detail.",
"domains": [
"Disease",
"Diagnosis",
"Morbidity"
],
"homepage": "https://www.cdc.gov/nchs/icd/icd9cm.htm",
"name": "International Classification of Diseases, Ninth Revision, Clinical Modification",
"subjects": [
"Medicine",
"Health Science",
"Biomedical Science",
"Epidemiology",
"Preclinical Studies"
]
},
"FAIRsharing.119q9t": {
"contact": {
"email": "olivier@nlm.nih.gov",
"name": "Olivier Bodenreider",
"orcid": "0000-0003-4769-4217"
},
"description": "The UMLS Semantic Network is one of three UMLS Knowledge Sources developed as part of the Unified Medical Language System project. The network provides a consistent categorization of all concepts represented in the UMLS Metathesaurus. The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types. The Network provides information about the set of basic semantic types, or categories, which may be assigned to these concepts, and it defines the set of relationships that may hold between the semantic types. The Semantic Network contains 127 semantic types and 54 relationships. The Semantic Network serves as an authority for the semantic types that are assigned to concepts in the Metathesaurus. The Network defines these types, both with textual descriptions and by means of the information inherent in its hierarchies.",
"domains": [
"Annotation"
],
"homepage": "https://lhncbc.nlm.nih.gov/semanticnetwork/",
"license": "https://creativecommons.org/licenses/by-nc-nd/2.5/ch",
"name": "The UMLS Semantic Network",
"publications": [
{
"doi": "10.1002/cfg.255",
"pubmed": "18629109",
"title": "An upper-level ontology for the biomedical domain",
"year": 2008
}
],
"subjects": [
"Data Integration",
"Biomedical Science"
]
},
"FAIRsharing.11d3c6": {
"abbreviation": "PIC",
"description": "Persistent identifier for an organization",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://www.wikidata.org/wiki/Q22693425",
"name": "Participant Identification Code",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.124cf2": {
"description": "This vocabulary gathers the main concepts describing the microscopic and macroscopic properties of condensed matter. It is derived from the vocabulary used until 2015 to index the bibliographic references of the PASCAL database (http://pascal-francis.inist.fr/), which has been enhanced with more recent concepts.",
"homepage": "https://skosmos.loterre.fr/NHT/en/",
"license": "CC-BY-4.0",
"name": "Condensed matter physics vocabulary",
"subjects": [
"Experimental Condensed Matter Physics",
"Solid-State Chemistry",
"Condensed Matter Physics",
"Theoretical Condensed Matter Physics",
"Surface Science"
],
"user_defined_tags": [
"thin films",
"crystal growth"
]
},
"FAIRsharing.1413b5": {
"abbreviation": "TGN",
"description": "The Thesaurus of Geographic Names (TGN) is a terminology that focuses on places relevant to art, architecture, and related disciplines, recording names, relationships, place types, dates, notes, and coordinates for current and historical cities, nations, empires, archaeological sites, lost settlements, and physical features. The TGN is one of 5 Getty Vocabularies intended to provide terminology and other information about the objects, artists, concepts, and places important to various disciplines that specialize in art, architecture, and other material culture.",
"domains": [
"Geographical location"
],
"homepage": "http://www.getty.edu/research/tools/vocabularies/tgn/index.html",
"license": "http://opendatacommons.org/licenses/by/1.0",
"name": "Thesaurus of Geographic Names",
"subjects": [
"Culture",
"Geography",
"Art History",
"Architecture",
"Ancient Cultures",
"Fine Arts",
"History",
"Human Geography"
]
},
"FAIRsharing.1414v8": {
"abbreviation": "BTO",
"description": "A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.",
"domains": [
"Reaction data",
"Cell",
"Enzyme",
"Organ"
],
"homepage": "http://www.brenda-enzymes.info",
"name": "BRENDA tissue / enzyme source",
"publications": [
{
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"title": "The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources",
"year": 2010
},
{
"doi": "10.1093/nar/gky1048",
"pubmed": "30395242",
"title": "BRENDA in 2019: a European ELIXIR core data resource",
"year": 2018
},
{
"doi": "10.1093/nar/gkh081",
"pubmed": "14681450",
"title": "BRENDA, the enzyme database: updates and major new developments",
"year": 2003
},
{
"doi": "10.1093/nar/gku1068",
"pubmed": "25378310",
"title": "BRENDA in 2015: exciting developments in its 25th year of existence",
"year": 2014
},
{
"doi": "10.1093/nar/gks1049",
"pubmed": "23203881",
"title": "BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA",
"year": 2012
}
],
"subjects": [
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},
"FAIRsharing.162003": {
"abbreviation": "DoCO",
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"name": "Silvio Peroni",
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"name": "Document Components Ontology ",
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{
"doi": "10.3233/sw-150177",
"title": "The Document Components Ontology (DoCO)",
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"domains": [
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"homepage": "https://www.onto-med.de/ontologies/gfo/",
"name": "General Formal Ontology",
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"abbreviation": "XAO",
"contact": {
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"name": "Erik Segerdell",
"orcid": "0000-0002-9611-1279"
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"description": "The Xenopus Anatomical Ontology (XAO) describes Xenopus anatomy and embryological development using a 'controlled vocabulary' of anatomy terms that are organized in an hierarchy with a graphical structure. XAO terms describe gene expression, and the XAO is constantly being updated in response to the latest published Xenopus research.",
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"homepage": "http://www.xenbase.org/anatomy/xao.do?method=display",
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"name": "Xenopus Anatomy Ontology",
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{
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"year": 2013
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{
"doi": "10.1186/1471-213x-8-92",
"pubmed": "18817563",
"title": "An ontology for Xenopus anatomy and development",
"year": 2008
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"Life Science"
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},
"FAIRsharing.18je7e": {
"abbreviation": "ONSTR",
"description": "Ontology for Newborn Screening Follow-up and Translational Research (ONSTR) is an application ontology for representing data entities, practices and knowledge in the domain of newborn screening and short-Ββ and long-Ββterm follow-Ββup of patients diagnosed with inheritable and congenital disorders. No project homepage could be found, and the resource has not been updated recently. Please get in touch if you have information about this resource.",
"homepage": "http://code.google.com/p/onstr/",
"name": "Ontology for Newborn Screening Follow-up and Translational Research",
"subjects": [
"Medicine",
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"abbreviation": "ATC",
"description": "The Anatomical Therapeutic Chemical (ATC) Classification System is used for the classification of active ingredients of drugs according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. It is controlled by the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC), and was first published in 1976.",
"domains": [
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"homepage": "http://www.whocc.no/atc/structure_and_principles/",
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"publications": [
{
"doi": "10.1007/s002280000200",
"pubmed": "11214783",
"title": "Different versions of the anatomical therapeutic chemical classification system and the defined daily dose--are drug utilisation data comparable?",
"year": 2001
},
{
"pubmed": "7368387",
"title": "[New classification of drugs. The Medical list and the Drug catalogue are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code) in 1981]",
"year": 1980
}
],
"subjects": [
"Chemical Biology",
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"user_defined_tags": [
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"abbreviation": "BCT",
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"homepage": "https://www.ucl.ac.uk/pals/research/clinical-educational-and-health-psychology/research-groups/behaviour-change-techniques/resources/bcttv1-publications",
"name": "Behaviour Change Technique Taxonomy",
"publications": [
{
"doi": "10.1007/s12160-013-9486-6",
"title": "The Behavior Change Technique Taxonomy (v1) of 93 Hierarchically Clustered Techniques: Building an International Consensus for the Reporting of Behavior Change Interventions",
"year": 2013
},
{
"doi": "10.1186/s13012-016-0448-9",
"title": "Reporting behaviour change interventions: do the behaviour change technique taxonomy v1, and training in its use, improve the quality of intervention descriptions?",
"year": 2016
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"subjects": [
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},
"FAIRsharing.1bdf3c": {
"abbreviation": "EMMO",
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"email": "gerhard@goldbeck-consulting.com",
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},
"description": "EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) for applied sciences. It is based on physics, analytical philosophy and information and communication technologies. It has been instigated by materials science to provide a framework for knowledge capture that is consistent with scientific principles and methodologies.",
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"license": "CC-BY-4.0",
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"name": "Elementary Multiperspective Material Ontology ",
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"Philosophy",
"Physics",
"Communication Science"
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"abbreviation": "CO_360",
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Sugar Kelp Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Marine environment",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_360:ROOT",
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"name": "Sugar Kelp Trait Ontology",
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"user_defined_tags": [
"Plant Phenotypes and Traits"
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},
"FAIRsharing.1d817c": {
"abbreviation": "AGLDWG PID Namespace",
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"email": "nick@kurrawong.net",
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"description": "The Australian Government Linked Data Working Group (AGLDWG) advocates the use of Linked Data as a particular set of technologies to be used for Internet-distributed, machine-readable data and, due to this, advocates the use of Internationalized Resource Identifiers (IRIs) as identifiers for things.\n\nThe linked.data.gov.au namespace was implemented by the AGLDWG to govern Linked Data resources for Australia. The namespace uses pattern which can be used to create individual PIDs for infinitely many persistent identifiers for Australian Government Linked Data resources. The namespace uses a domain name that is not coupled to a particular agency's name or function. Use of this namespace was initiated in 2016 and then strengthened in 2018 with multiple Australian government agencies signing a Memorandum of Understanding to reserve the use of linked.data.gov.au for PID IRIs and to ensure its operational stability. The AGLDWG has adopted the IS0 19135 for IRI registration procedure and roles and issued Guidelines that details its PID allocation process.",
"domains": [
"Centrally registered identifier"
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"homepage": "https://www.linked.data.gov.au/guidelines",
"license": "CC-BY-4.0",
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"abbreviation": "MEDO",
"description": "Record does not exist anymore: Mouse Experimental Design Ontology. The record with identifier content 10.25504/FAIRsharing.1dppze was invalid.",
"homepage": "http://bioportal.bioontology.org/ontologies/MEDO",
"name": "Mouse Experimental Design Ontology"
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"FAIRsharing.1e1cb8": {
"abbreviation": "SBOL-VO",
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"orcid": "0000-0002-2454-7188"
},
"description": "Ontology for mapping ontological terms to SBOL Visual glyphs.",
"domains": [
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],
"homepage": "https://vows.sbolstandard.org",
"license": "CC0-1.0",
"name": "Synthetic Biology Open Language Visual 2 Ontology",
"publications": [
{
"doi": "10.1021/acssynbio.0c00046",
"title": "SBOL Visual 2 Ontology",
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}
],
"repository": "https://github.com/dissys/sbol-visual-ontology",
"subjects": [
"Genetics",
"Synthetic Biology"
]
},
"FAIRsharing.1esk4f": {
"abbreviation": "AI/RHEUM",
"description": "AI/RHEUM is used for the diagnosis of rheumatologic diseases. AI/RHEUM contains findings, such as clinical signs, symptoms, laboratory test results, radiologic observations, tissue biopsy results, and intermediate diagnosis hypotheses. Findings and hypotheses, which include definitions, are used to reach diagnostic conclusions with definite, probable, or possible certainty. AI/RHEUM is used by clinicians and informatics researchers.",
"domains": [
"Diagnosis"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1430",
"name": "Artificial Intelligence Rheumatology Consultant System Ontology",
"publications": [
{
"pubmed": "3537610",
"title": "Anatomy of a knowledge-based consultant system: AI/RHEUM",
"year": 1986
},
{
"doi": "10.1007/bf00996349",
"pubmed": "3320252",
"title": "AI/LEARN network. The use of computer-generated graphics to augment the educational utility of a knowledge-based diagnostic system (AI/RHEUM)",
"year": 1987
},
{
"doi": "10.1007/bf00993283",
"pubmed": "6352842",
"title": "AI/RHEUM. A consultant system for rheumatology",
"year": 1983
},
{
"doi": "10.1007/bf00993009",
"pubmed": "3330560",
"title": "AI/LEARN: an interactive videodisk system for teaching medical concepts and reasoning",
"year": 1987
},
{
"doi": "10.1002/art.1780310210",
"pubmed": "3279963",
"title": "The AI/RHEUM knowledge-based computer consultant system in rheumatology. Performance in the diagnosis of 59 connective tissue disease patients from Japan",
"year": 1988
},
{
"pubmed": "1406331",
"title": "Validation of the AI/RHEUM knowledge base with data from consecutive rheumatological outpatients",
"year": 1992
}
],
"subjects": [
"Radiology",
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.1evfpc": {
"abbreviation": "CRISP",
"description": "CRISP is a terminology used for indexing biomedical information. CRISP contains over 8,000 preferred terms that are grouped hierarchically into 11 domains.",
"domains": [
"Food",
"Disease"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1526",
"name": "Computer Retrieval of Information on Scientific Projects Thesaurus",
"publications": [
{
"pubmed": "8718842",
"title": "Taking a bite out of CRISP. Strategies on using and conducting searches in the Computer Retrieval of Information on Scientific Projects database",
"year": 1996
}
],
"subjects": [
"Anatomy",
"Social Science",
"Medicine",
"Chemical Biology",
"Biomedical Science",
"Biology"
]
},
"FAIRsharing.1f6445": {
"description": "Permanent links are saved publications links that enable users to bookmark a publication and go back to it later or share it by clicking on the permanent link function on the top right of the search result or publication detail page. Each general publication of data.europa.eu has a permanent link and automatic redirections based on publications identifiers.",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://op.europa.eu/en/web/webtools/permanents-links-and-short-url",
"name": "EU Permanent links",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.1g5j3h": {
"abbreviation": "BMT",
"description": "Record does not exist anymore: Biomedical Topics. The record with identifier content 10.25504/FAIRsharing.1g5j3h was invalid.",
"domains": [
"Classification"
],
"homepage": "http://bioportal.bioontology.org/ontologies/BMT",
"name": "Biomedical Topics",
"subjects": [
"Engineering Science",
"Life Science"
]
},
"FAIRsharing.1gr4tz": {
"abbreviation": "EFO",
"contact": {
"email": "siiraa@ebi.ac.uk",
"name": "Sirarat Sarntivijai",
"orcid": "0000-0002-2548-641X"
},
"description": "The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental variables in multiple resources at the EBI and the Centre for Therapeutic Target Validation. The ontology has been developed to increase the richness of the annotations that are currently made in resources and to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology pulls together classes from reference ontologies such as disease, cell line, cell type and anatomy and adds axiomatisation as necessary to connect areas such as disease to phenotype.",
"domains": [
"Experimental measurement",
"Assay",
"Independent variable",
"Study design",
"Genome-wide association study"
],
"homepage": "https://www.ebi.ac.uk/efo/",
"license": "Apache 2.0 License",
"name": "Experimental Factor Ontology",
"publications": [
{
"doi": "10.1093/bioinformatics/btq099",
"pubmed": "20200009",
"title": "Modeling sample variables with an Experimental Factor Ontology",
"year": 2010
}
],
"repository": "https://github.com/EBISPOT/efo",
"subjects": [
"Functional Genomics"
],
"user_defined_tags": [
"Experimental condition"
]
},
"FAIRsharing.1h49c6": {
"abbreviation": "UNITSONT",
"contact": {
"email": "sivaram.arabandi@gmail.com",
"name": "Sivaram Arabandi",
"orcid": "0000-0002-2973-6228"
},
"description": "An ontology for the units of measurement developed during the development of the Sleep Domain Ontology (SDO). It supports the use of SDO within the PhysioMIMI application. No official homepage for this resource can be found.",
"domains": [
"Sleep",
"Unit",
"Measurement"
],
"homepage": "http://bioportal.bioontology.org/ontologies/UNITSONT",
"name": "Sleep Domain Units Ontology",
"subjects": [
"Health Science"
]
},
"FAIRsharing.1rj558": {
"abbreviation": "TTO",
"contact": {
"email": "pmabee@usd.edu",
"name": "Paula Mabee",
"orcid": "0000-0002-8455-3213"
},
"description": "This is an ontology of taxonomic terms (names of taxonomic groups) used in the systematics of fish, including non-teleost groups such as Chondrichthys (sharks and rays), Sarcopterygii (lungfish and coelacanths), lampreys, and hagfish.",
"domains": [
"Taxonomic classification"
],
"homepage": "https://wiki.phenoscape.org/wiki/Ontologies#Teleost_Taxonomy_Ontology_.28TTO.29",
"license": "CC0-1.0",
"name": "Teleost Taxonomy Ontology",
"subjects": [
"Life Science"
]
},
"FAIRsharing.1sgm8q": {
"contact": {
"email": "robert.hoehndorf@kaust.edu.sa",
"name": "Robert Hoehndorf",
"orcid": "0000-0001-8149-5890"
},
"description": "The BioModels Ontology is an OWL Representation of the models in the BioModels repository. This resource has not been updated recently within BioPortal, and no official homepage can be found, therefore we have marked its status as Uncertain. Please get in touch with us if you have any information on this project.",
"domains": [
"Mathematical model",
"Network model",
"Molecular entity",
"Modeling and simulation",
"Enzymatic reaction",
"Pathway model"
],
"homepage": "http://bioportal.bioontology.org/ontologies/BIOMODELS",
"name": "BioModels Ontology",
"publications": [
{
"doi": "10.1186/1752-0509-5-124",
"pubmed": "21835028",
"title": "Integrating systems biology models and biomedical ontologies",
"year": 2011
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.1vrrdh": {
"abbreviation": "OBOREL",
"description": "Record does not exist anymore: Open Biological and Biomedical Ontologies Relationship Types. The record with identifier content 10.25504/FAIRsharing.1vrrdh was invalid. It was a duplicate of https://doi.org/10.25504/FAIRsharing.9c2azc",
"homepage": "http://www.obofoundry.org/ro",
"name": "Open Biological and Biomedical Ontologies Relationship Types"
},
"FAIRsharing.1wm8em": {
"abbreviation": "HRDO",
"description": "This resource was designed during a PhD in medical informatics (funded by INSERM, 2010-2012). Its components are (i) a core ontology consistent with a metamodel (disorders and groups of disorders, genes, clinical signs and their relations) and (ii) an instantiation of this metamodel with Orphanet Data (available on http://orphadata.org). Research experiments demonstrated (i) efficient classifications generation based on SPARQL Construct, (ii) perspectives in semantic audit of a knowledge base, (iii) semantic comparison with OMIM (www.omim.org) using proximity measurements and (iv) opened perspectives in knowledge sharing (LORD, http://lord.bndmr.fr). Current production services of Orphanet developed ORDO, released in 2014, an ontology synchronized with their production database. This ontology is now available on Bioportal.",
"domains": [
"Rare disease"
],
"homepage": "http://bioportal.bioontology.org/ontologies/HRDO",
"name": "Disease core ontology applied to Rare Diseases",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.1xr6v0": {
"abbreviation": "SSE",
"description": "Memorial Sloan-Kettering Cancer Center Surgical Secondary Events Ontology (Adverse Events)",
"domains": [
"Adverse Reaction"
],
"homepage": "http://www.mskcc.org/sse",
"name": "Surgical Secondary Events",
"subjects": [
"Surgery"
],
"user_defined_tags": [
"Adverse outcome pathways"
]
},
"FAIRsharing.1z28wz": {
"abbreviation": "suicideo",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/suicideo",
"name": "suicideonto",
"subjects": [
"Psychology",
"Social and Behavioural Science"
]
},
"FAIRsharing.21gwxs": {
"abbreviation": "WHO-ART",
"description": "The World Health Organization Adverse Drug Reaction Terminology (WHO-ART) was developed and maintained by the WHO Collaborating Centre for International Drug Monitoring Uppsala Monitoring Centre (UMC). The WHO-ART collection is used for coding clinical information related to adverse drug reactions as a standardization collection of vocabulary/terminology for adverse reactions. ",
"domains": [
"Adverse Reaction"
],
"homepage": "https://who-umc.org/vigibase/vigibase-services/who-art/",
"name": "WHO Adverse Reaction Terminology",
"subjects": [
"Medicine",
"Biomedical Science",
"Ontology and Terminology"
]
},
"FAIRsharing.22j4p7": {
"abbreviation": "PO_PAE",
"description": "Plant Anatomy is a controlled vocabulary of plant morphological and anatomical structures representing organs, tissues, cell types, and their biological relationships based on spatial and developmental organization. This standard is now part of PO.",
"homepage": "http://bioportal.bioontology.org/ontologies/1108",
"name": "Plant Anatomy",
"subjects": [
"Anatomy"
]
},
"FAIRsharing.23th83": {
"abbreviation": "GeoSpecies",
"contact": {
"email": "pdevries@wisc.edu",
"name": "Peter J. DeVries",
"orcid": "0000-0003-4637-5281"
},
"description": "This ontology was designed to help integrate species concepts with species occurrences, gene sequences, images, references and geographical information.",
"domains": [
"Citation",
"Taxonomic classification",
"Geographical location",
"Image",
"Sequence",
"Gene"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1247",
"name": "GeoSpecies Ontology",
"subjects": [
"Life Science"
]
},
"FAIRsharing.24yjfc": {
"abbreviation": "HC",
"description": "A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms. An ontology for courtship behavior of the spider Habronattus californicus.",
"domains": [
"Behavior"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1020",
"name": "Habronattus Courtship Ontology",
"subjects": [
"Life Science"
]
},
"FAIRsharing.2626f9": {
"description": "The bibcode (also known as the refcode) is a compact identifier used by several astronomical data systems to uniquely specify literature references.",
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"Centrally registered identifier"
],
"homepage": "https://en.wikipedia.org/wiki/Bibcode",
"name": "Bibcode Identifier",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.26ffrf": {
"abbreviation": "APANEUROCLUSTER",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/APANEUROCLUSTER",
"name": "APA Neuro Cluster",
"subjects": [
"Neurology"
]
},
"FAIRsharing.2787qk": {
"abbreviation": "CIINTEADO",
"contact": {
"email": "contact@bioself-communication.com",
"name": "Delphine Dauga",
"orcid": "0000-0003-3152-1194"
},
"description": "The first ontology describing the anatomy and the development of Ciona intestinalis, based on the Hotta developmental table.",
"domains": [
"Cell",
"Life cycle",
"Life cycle stage"
],
"homepage": "https://www.aniseed.fr/aniseed/anatomy/find_devstage",
"name": "Ciona intestinalis Anatomy and Development Ontology",
"subjects": [
"Anatomy",
"Developmental Biology"
],
"user_defined_tags": [
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},
"FAIRsharing.27rndz": {
"abbreviation": "GEO",
"description": "The Geographical Entity Ontology (GEO) is an ontology of geographical entities (such as sovereign states and their administrative subdivisions) as well as various geographical regions (including but not limited to the specific ones over which the governments have jurisdiction).",
"domains": [
"Geographical location"
],
"homepage": "https://github.com/mcwdsi/geographical-entity-ontology",
"license": "CC-BY-4.0",
"name": "Geographical Entity Ontology",
"subjects": [
"Human Geography",
"Physical Geography"
]
},
"FAIRsharing.27w8k0": {
"abbreviation": "UCUM",
"description": "The Unified Code for Units of Measure is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business. The purpose is to facilitate unambiguous electronic communication of quantities together with their units. The focus is on electronic communication, as opposed to communication between humans. A typical application of The Unified Code for Units of Measure are electronic data interchange (EDI) protocols, but there is nothing that prevents it from being used in other types of machine communication.",
"domains": [
"Data identity and mapping",
"Unit",
"Measurement"
],
"homepage": "https://ucum.org/trac",
"name": "The Unified Code for Units of Measure",
"publications": [
{
"doi": "10.1136/jamia.1999.0060151",
"pubmed": "10094068",
"title": "Units of measure in clinical information systems",
"year": 1999
}
],
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.284e1z": {
"abbreviation": "OBI",
"contact": {
"email": "bpeters@lji.org",
"name": "Bjoern Peters",
"orcid": "0000-0002-8457-6693"
},
"description": "The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI fosters clear communication about scientific investigations by defining more than 2500 terms for assays, devices, objectives, and more.",
"domains": [
"Reagent",
"Report",
"Assay",
"Protocol",
"Device",
"Data transformation",
"Study design"
],
"homepage": "http://obi-ontology.org/",
"license": "CC-BY-3.0",
"name": "Ontology for Biomedical Investigations",
"publications": [
{
"doi": "10.1186/2041-1480-4-s1-s6",
"pubmed": "23734660",
"title": "Query enhancement through the practical application of ontology: the IEDB and OBI",
"year": 2013
},
{
"doi": "10.4056/sigs.1994602",
"pubmed": "22180825",
"title": "Minimum Information about a Genotyping Experiment (MIGEN)",
"year": 2011
},
{
"doi": "10.1093/database/bau132",
"pubmed": "25632945",
"title": "Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach",
"year": 2015
},
{
"doi": "10.1371/journal.pone.0154556",
"pubmed": "27128319",
"title": "The Ontology for Biomedical Investigations",
"year": 2016
},
{
"doi": "10.1186/2041-1480-1-s1-s7",
"pubmed": "20626927",
"title": "Modeling biomedical experimental processes with OBI",
"year": 2010
}
],
"repository": "https://github.com/obi-ontology/obi",
"subjects": [
"Functional Genomics",
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.29924b": {
"abbreviation": "ISO 27729:2012 ISNI",
"description": "ISO 27729:2012 specifies the International Standard Name Identifier (ISNI) for the identification of public identities of parties, i.e. the identities used publicly by parties involved throughout the media content industries in the creation, production, management and content distribution chains. ISNIs uniquely identify public identities across multiple fields of creative activity and provides a tool for disambiguating public identities that might otherwise be confused. An ISNI is made up of 16 digits, the last character being a check character. The check character may be either a decimal digit or the character βXβ.",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://www.iso.org/standard/44292.html",
"name": "ISO 27729:2012 Information and documentation β International standard name identifier",
"subjects": [
"Informatics"
]
},
"FAIRsharing.29c262": {
"abbreviation": "UMDNS",
"description": "The Universal Medical Device Nomenclature System (UMDNS) is a standard worldwide nomenclature for medical devices.",
"domains": [
"Device"
],
"homepage": "https://www.ecri.org/solutions/umdns",
"name": "Universal Medical Device Nomenclature System of ECRI institute",
"publications": [
{
"pubmed": "10184630",
"title": "The Universal Medical Device Nomenclature System",
"year": 1996
}
],
"subjects": [
"Medicine"
],
"user_defined_tags": [
"medical devices"
]
},
"FAIRsharing.2QpmkQ": {
"description": "Controlled vocabulary used for indexing bibliographical records for the \"Prehistory and Protohistory\" FRANCIS database (1972-2015). It consists of 3093 entries mainly in 2 languages (English and French) grouped under 107 collections",
"homepage": "https://www.loterre.fr/skosmos/905/en/",
"license": "CC-BY-4.0",
"name": "Prehistory and Protohistory Vocabulary",
"subjects": [
"Humanities",
"Prehistory",
"Ancient History"
],
"user_defined_tags": [
"Protohistory"
]
},
"FAIRsharing.2ZShyL": {
"description": "The Ethnology vocabulary is a controlled vocabulary used for indexing the bibliographical records for the now-archived \"Ethnology\" FRANCIS database (1972 - 2015, http://pascal-francis.inist.fr/). This resource contains over 9000 classes, with each class available in English and French.",
"domains": [
"Bibliography"
],
"homepage": "https://www.loterre.fr/skosmos/KW5/en/",
"license": "CC-BY-4.0",
"name": "Ethnology vocabulary",
"subjects": [
"Humanities and Social Science",
"Social Anthropology"
],
"user_defined_tags": [
"Ethnology"
]
},
"FAIRsharing.2b04ae": {
"abbreviation": "CO_357",
"description": "The Woody Plant Ontology lists reference variables used for experimentations and observations on woody plants (forest trees and shrubs, and possibly fruit trees). It is an international initiative based on various communities (French, Portuguese and European). Terms are collected from various sources and organized following the Crop Ontology standard which provides harmonized variables composed by a triplet: (i) a trait, the studied character, (ii) a method, the measurement protocol and (iii) a scale, the unit of measurement or scoring scale. ",
"domains": [
"Phenotype"
],
"homepage": "https://doi.org/10.15454/JB2WCE",
"license": "CC-BY-4.0",
"name": "Woody Plant Ontology",
"subjects": [
"Botany",
"Life Science"
]
},
"FAIRsharing.2b0d92": {
"description": "The Identifiers.org Resolution Service provides consistent access to life science data using Compact Identifiers. Compact Identifiers consist of an assigned unique prefix and a local provider designated accession number (prefix:accession). The resolving location of Compact Identifiers is determined using information that is stored in the Identifiers.org Registry.\n",
"domains": [
"Data retrieval",
"Centrally registered identifier"
],
"homepage": "https://docs.identifiers.org/pages/identification_scheme.html",
"license": "CC-BY-4.0",
"name": "Identifiers.org namespace",
"publications": [
{
"doi": "10.1093/nar/gkr1097",
"pubmed": "22140103",
"title": "Identifiers.org and MIRIAM Registry: community resources to provide persistent identification",
"year": 2012
},
{
"doi": "10.1038/sdata.2018.29",
"pubmed": "29737976",
"title": "Uniform resolution of compact identifiers for biomedical data",
"year": 2018
},
{
"doi": "10.1093/bioinformatics/btaa864",
"pubmed": "33031499",
"title": "Identifiers.org: Compact Identifier services in the cloud",
"year": 2021
}
],
"subjects": [
"Knowledge and Information Systems",
"Life Science"
]
},
"FAIRsharing.2b4316": {
"abbreviation": "PMC ID",
"description": "Identifier schema for PubMed Central, a U.S. National Institutes of Health's National Library of Medicine (NIH/NLM) free full-text archive of biomedical and life sciences journal literature.",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmc",
"name": "PubMed Central Identifier",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.2b9b61": {
"abbreviation": "PMID",
"description": "The PubMed Unique Identifier (PMID) is a 1- to 8-digit accession number with no leading zeros for managing and disseminating records at the PubMed repository. The PMID is a unique reference number for PubMed citations and is a distinctly different number from the PMCID and is used only for PubMed records. PMIDs are not reused after records are deleted. Prior to the 2004 version of PubMed (available December 3, 2003), many records contained a MEDLINE Unique Identifier in addition to the PMID. NLM no longer displays the MEDLINE Unique Identifier. The PMID has become the unique identifier for the MEDLINE record.",
"domains": [
"Citation",
"Bibliography",
"Publication"
],
"homepage": "https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmid",
"name": "PubMed Unique Identifier",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.2basyz": {
"abbreviation": "CVDO",
"description": "CVDO is an ontology based on the OGMS model of disease, designed to describe entities related to cardiovascular diseases (including the diseases themselves, the underlying disorders, and the related pathological processes).",
"domains": [
"Cardiovascular disease"
],
"homepage": "https://github.com/OpenLHS/CVDO",
"license": "CC-BY-4.0",
"name": "Cardiovascular Disease Ontology",
"subjects": [
"Cardiology"
]
},
"FAIRsharing.2bf47f": {
"abbreviation": "DIDs",
"description": "Decentralized identifiers (DIDs) are a new type of identifier that enables verifiable, decentralized digital identity. A DID refers to any subject (e.g., a person, organization, thing, data model, abstract entity, etc.) as determined by the controller of the DID. In contrast to typical, federated identifiers, DIDs have been designed so that they may be decoupled from centralized registries, identity providers, and certificate authorities. Specifically, while other parties might be used to help enable the discovery of information related to a DID, the design enables the controller of a DID to prove control over it without requiring permission from any other party. DIDs are URIs that associate a DID subject with a DID document allowing trustable interactions associated with that subject.",
"domains": [
"Resource metadata"
],
"homepage": "https://www.w3.org/TR/did-core/",
"name": "Decentralized Identifiers",
"repository": "https://github.com/w3c/did-core/",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.2c9203": {
"abbreviation": "scm",
"description": "This vocabulary contains of two Concept Schemes of soil chemical testing methods based on the publications Australian Laboratory Handbook of Soil and Water Chemical Methods (1992), Rayment, G.E and Higginson, F.R. and Soil Chemical Methods Australasia (2011), George E Rayment and David J Lyons. The vocabulary is designed to be expandable to contain other Concept Schemes of soil chemical methods. The data was converted from a HTML representation ( Australian Laboratory Handbook of Soil and Water Chemical Methods, 1992) and hard-copy (Soil Chemical Methods Australasia, 2011) to 'linked-data' format. It includes the chemical procedures and the units of measure and result code-lists associated with each procedure, as defined by the texts. ",
"domains": [
"Cropping systems",
"Sustainability",
"Agroecosystem"
],
"homepage": "https://github.com/ANZSoilData/def-au-scm",
"license": "CC-BY-4.0",
"name": "A linked data (RDF) representation of Soil Chemical Methods, Australasia. ",
"subjects": [
"Soil Science",
"Agriculture"
],
"user_defined_tags": [
"biogeochemistry",
"soil carbon",
"Soil pH"
]
},
"FAIRsharing.2d1735": {
"abbreviation": "GRID Identifier",
"description": "Identifier schema for GRID",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://bioregistry.io/registry/grid",
"name": "Global Research Identifier Database Identifier",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.2d9c1a": {
"abbreviation": "GA PID",
"description": "The Geoscience Australia Persistent Identifier (GA PID) is a persistent identifier scheme with a root and structure of http://pid.geoscience.gov.au/[sample|site|survey]/{IGSN} . The subdomain is managed by Geoscience Australia on behalf of the Australian geoscience community.",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://pid.geoscience.gov.au/",
"license": "CC-BY-4.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdU1CIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--d8ab4505fc82083346042dd279c4ed9d968f4c88/geoscience_inline.jpg?disposition=inline",
"name": "Geoscience Australia Persistent Identifier",
"subjects": [
"Earth Science"
]
},
"FAIRsharing.2etax0": {
"abbreviation": "IMR",
"description": "A structured controlled vocabulary of concrete protein names and generic (abstract) protein names. This ontology is a INOH pathway annotation ontology, one of a set of ontologies intended to be used in pathway data annotation to ease data integration. IMR is part of the BioPAX working group.",
"domains": [
"Protein"
],
"homepage": "http://purl.bioontology.org/ontology/IMR",
"name": "INOH Molecule Role",
"publications": [
{
"doi": "10.1002/cfg.432",
"pubmed": "18629146",
"title": "The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature",
"year": 2008
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.2f3180": {
"abbreviation": "FaBiO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "FaBiO, the FRBR-aligned Bibliographic Ontology, is an ontology for recording and publishing on the Semantic Web descriptions of entities that are published or potentially publishable, and that contain or are referred to by bibliographic references, or entities used to define such bibliographic references. FaBiO entities are primarily textual publications such as books, magazines, newspapers and journals, and items of their content such as poems, conference papers and editorials. However, they also include blogs, web pages, datasets, computer algorithms, experimental protocols, formal specifications and vocabularies, legal records, governmental papers, technical and commercial reports and similar publications, and also anthologies, catalogues and similar collections.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Publication",
"Protocol",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/fabio",
"license": "CC-BY-4.0",
"name": "FRBR-aligned Bibliographic Ontology",
"publications": [
{
"doi": "10.1016/j.websem.2012.08.001",
"title": "FaBiO and CiTO: Ontologies for describing bibliographic resources and citations",
"year": 2012
}
],
"repository": "https://github.com/sparontologies/fabio",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"FAIRsharing.2ffmsb": {
"abbreviation": "EDDA",
"description": "Terminology of study designs and publication types (beta version). Developed by the Evidence in Documents, Discovery, and Analysis (EDDA) Group. Tanja Bekhuis (PI); Eugene Tseytlin (Systems Developer); Ashleigh Faith (Taxonomist). Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pennsylvania, US. This work was made possible, in part, by the US National Library of Medicine, National Institutes of Health, grant no. R00LM010943. Based on research described in Bekhuis T, Demner-Fushman D, Crowley RS. Comparative effectiveness research designs: an analysis of terms and coverage in Medical Subject Headings (MeSH) and Emtree. Journal of the Medical Library Association (JMLA). 2013 April;101(2):92-100. PMC3634392. The terminology appearing in JMLA has been enriched with terms from MeSH, NCI Thesaurus (NCIT), and Emtree, the controlled vocabularies for MEDLINE, the National Cancer Institute, and Embase, respectively, as well as from published research literature. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCIT, Emtree, and medical dictionaries. A class for Publication Type is included because investigators consider type and design when screening reports for inclusion in comparative effectiveness research. EDDA Study Designs and Publications by Tanja Bekhuis is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.",
"homepage": "http://edda.dbmi.pitt.edu/",
"name": "EDDA Study Designs Taxonomy",
"subjects": [
"Medicine"
]
},
"FAIRsharing.2fnz2n": {
"abbreviation": "GLYCORDF",
"description": "GlycoRDF is a standard representation for storing Glycomcis data (glycan structures, publication information, biological source information, experimental data) in RDF. The RDF language is defined by an OWL ontology and documented in the ontology and generated WORD files. Its GitHub repository also contains source code for the generation of RDF data for glycomics databases.",
"domains": [
"Molecular structure"
],
"homepage": "http://www.glycoinfo.org/GlycoRDF/",
"name": "GlycoRDF",
"publications": [
{
"doi": "10.1186/2041-1480-4-39",
"pubmed": "24280648",
"title": "Introducing glycomics data into the Semantic Web",
"year": 2013
},
{
"doi": "10.1093/bioinformatics/btu732",
"pubmed": "25388145",
"title": "GlycoRDF: an ontology to standardize glycomics data in RDF",
"year": 2014
}
],
"repository": "https://github.com/ReneRanzinger/GlycoRDF/blob/master/ontology/documentation.docx",
"subjects": [
"Life Science",
"Glycomics"
],
"user_defined_tags": [
"Glycan Annotation"
]
},
"FAIRsharing.2gpf81": {
"abbreviation": "ENM",
"contact": {
"email": "egon.willighagen@maastrichtuniversity.nl",
"name": "Egon Willighagen",
"orcid": "0000-0001-7542-0286"
},
"description": "The eNanoMapper ontology covers the full scope of terminology needed to support research into nanomaterial safety. It builds on multiple pre-existing external ontologies such as the NanoParticle Ontology.",
"domains": [
"Chemical entity",
"Nanoparticle"
],
"homepage": "https://github.com/enanomapper/ontologies",
"license": "CC-BY-3.0",
"name": "eNanoMapper Ontology",
"publications": [
{
"doi": "10.1186/s13326-015-0005-5",
"pubmed": "25815161",
"title": "eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment",
"year": 2015
}
],
"subjects": [
"Health Science"
],
"user_defined_tags": [
"Nanosafety"
]
},
"FAIRsharing.2h33ax": {
"abbreviation": "ICPC-2",
"description": "The International Classification of Primary Care, 2nd Edition (ICPC-2) classifies patient data and clinical activity in the domains of General/Family Practice and primary care, taking into account the frequency distribution of problems seen in these domains. It allows classification of the patientβs reason for encounter (RFE), the problems/diagnosis managed, interventions, and the ordering of these data in an episode of care structure.",
"domains": [
"Electronic health record",
"Patient care",
"Diagnosis"
],
"homepage": "https://www.who.int/standards/classifications/other-classifications/international-classification-of-primary-care",
"name": "International Classification of Primary Care, 2nd Edition",
"publications": [
{
"doi": "10.3109/02813438609013970",
"pubmed": "3961309",
"title": "International classification of primary care",
"year": 1986
}
],
"subjects": [
"Social Science",
"Medicine",
"Psychology",
"Primary Health Care",
"Physiology",
"Biomedical Science",
"Epidemiology"
]
},
"FAIRsharing.2hzttx": {
"abbreviation": "BCGO",
"description": "Breast Cancer Grading Ontology assigns a grade to a tumor starting from the 3 criteria of the NGS.",
"domains": [
"Cancer",
"Tumor",
"Tumor grading",
"Disease",
"Diagnosis",
"Mammary gland"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1304",
"name": "Breast Cancer Grading Ontology",
"subjects": [
"Medicine",
"Health Science",
"Biomedical Science"
]
},
"FAIRsharing.2jkxp5": {
"abbreviation": "CO_320",
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The IBP Rice Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology. Based on SES, Rice Descriptor and IRIS DB.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_320:ROOT",
"license": "CC-BY-4.0",
"name": "Rice Ontology",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.2m4ms9": {
"abbreviation": "PSI-MOD",
"description": "PSI-MOD is an ontology consisting of terms that describe protein chemical modifications, logically linked by an is_a relationship in such a way as to form a direct acyclic graph (DAG). The PSI-MOD ontology has more than 45 top-level nodes, and provides alternative hierarchical paths for classifying protein modifications either by the molecular structure of the modification, or by the amino acid residue that is modified.",
"domains": [
"Enzymatic reaction",
"Protein"
],
"homepage": "http://www.psidev.info/groups/protein-modifications",
"license": "CC-BY-4.0",
"name": "Protein MODification",
"publications": [
{
"doi": "10.1038/nbt0808-864",
"pubmed": "18688235",
"title": "The PSI-MOD community standard for representation of protein modification data",
"year": 2008
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.2mk2zb": {
"abbreviation": "LOINC",
"description": "LOINC is a common language (set of identifiers, names, and codes) for clinical and laboratory observations. LOINC is a catalog of measurements, including laboratory tests, clinical measures like vital signs and anthropomorphic measures, standardized survey instruments, and more. LOINC enables the exchange and aggregation of clinical results for care delivery, outcomes management, and research by providing a set of universal codes and structured names to unambiguously identify things you can measure or observe.",
"domains": [
"Genetic polymorphism",
"Assay",
"Phenotype",
"Diagnosis",
"Genetic disorder"
],
"homepage": "https://loinc.org/",
"license": "https://loinc.org/terms-of-use",
"name": "Logical Observation Identifier Names and Codes",
"publications": [
{
"doi": "10.1016/s1386-5056(98)00089-6",
"pubmed": "9749897",
"title": "Combining laboratory data sets from multiple institutions using the logical observation identifier names and codes (LOINC)",
"year": 1998
},
{
"doi": "10.1016/j.jbi.2012.01.005",
"pubmed": "22285984",
"title": "Enabling international adoption of LOINC through translation",
"year": 2012
},
{
"doi": "10.1093/jamia/ocu012",
"pubmed": "25656513",
"title": "Supporting interoperability of genetic data with LOINC",
"year": 2015
}
],
"subjects": [
"Life Science",
"Biomedical Science",
"Preclinical Studies"
],
"twitter": "LOINC"
},
"FAIRsharing.2ndf9r": {
"abbreviation": "PLOSTHES",
"description": "The PLOS Thesaurus includes over 10,000 Subject Area terms covering the wide range of research topics included the PLOS journals. The terms are applied programmatically to publications to aid record search and discovery.",
"domains": [
"Publication"
],
"homepage": "https://github.com/PLOS/plos-thesaurus",
"license": "CC0-1.0",
"name": "PLOS Thesaurus",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.2q8c28": {
"abbreviation": "IDOMAL",
"contact": {
"email": "topalis@imbb.forth.gr",
"name": "Pantelis Topalis",
"orcid": "0000-0002-1635-4810"
},
"description": "An application ontology for malaria extending the infectious disease ontology (IDO). With about half a billion cases, of which nearly one million fatal ones, malaria constitutes one of the major infectious diseases worldwide. A recently revived effort to eliminate the disease also focuses on IT resources for its efficient control, which prominently includes the control of the mosquito vectors that transmit the Plasmodium pathogens. As part of this effort, IDOMAL has been developed and it is continually being updated.",
"domains": [
"Malaria",
"Pathogen",
"Intervention design",
"Disease"
],
"homepage": "https://www.vectorbase.org/ontology-browser",
"license": "CC0-1.0",
"name": "Infection Disease Ontology Malaria",
"publications": [
{
"doi": "10.1186/2041-1480-4-16",
"pubmed": "24034841",
"title": "IDOMAL: the malaria ontology revisited",
"year": 2013
},
{
"doi": "10.1186/1475-2875-9-230",
"pubmed": "20698959",
"title": "IDOMAL: an ontology for malaria",
"year": 2010
}
],
"subjects": [
"Molecular Infection Biology",
"Life Science",
"Biomedical Science"
],
"twitter": "VectorBase"
},
"FAIRsharing.2rm2b3": {
"abbreviation": "PROV-O",
"description": "The PROV Ontology (PROV-O) expresses the PROV Data Model using the OWL2 Web Ontology Language (OWL2). It is intended for the Linked Data and Semantic Web community. It provides a set of classes, properties, and restrictions that can be used to represent and interchange provenance information generated in different systems and under different contexts. It can also be specialized to create new classes and properties to model provenance information for different applications and domains. PROV-O is one serialization of PROV-DM, the other two being PROV-N and PROV-XML. PROV-DM and PROV-O define how to represent provenance on the World Wide Web, and as such additional documentation has been included in this record for PROV-AQ (Access and Query), a note which describes how standard web protocols may be used to locate, retrieve and query provenance records. PROV-DC provides a mapping from Dublin Core to PROV-O, and is listed in this record. For the purpose of this specification, provenance is defined as a record that describes the people, institutions, entities, and activities involved in producing, influencing, or delivering a piece of data or a thing. In particular, the provenance of information is crucial in deciding whether information is to be trusted, how it should be integrated with other diverse information sources, and how to give credit to its originators when reusing it. In an open and inclusive environment such as the Web, where users find information that is often contradictory or questionable, provenance can help those users to make trust judgements.",
"domains": [
"Resource metadata"
],
"homepage": "http://www.w3.org/TR/prov-o/",
"name": "W3C Provenance Ontology",
"subjects": [
"Data Management",
"Subject Agnostic"
],
"user_defined_tags": [
"Metadata standardization"
]
},
"FAIRsharing.2rzyrx": {
"abbreviation": "DCO",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Rare disease"
],
"homepage": "https://bioportal.bioontology.org/ontologies/DCO",
"name": "Dispedia Core Ontology",
"subjects": [
"Medicine",
"Health Science"
]
},
"FAIRsharing.2xahkx": {
"abbreviation": "NIFDYS",
"contact": {
"email": "smtifahim@gmail.com",
"name": "Fahim Imam",
"orcid": "0000-0003-4752-543X"
},
"description": "This ontology contains the former BIRNLex-Disease, version 1.3.2. -- The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. It is built using the organizational framework provided by the foundational Basic Formal Ontology (BFO). It uses an abstract biomedical layer on top of that - OBO-UBO which has been constructed as a proposal to the OBO Foundry. This is meant to support creating a sharable view of core biomedical objects such as biomaterial_entity, and organismal_entity that all biomedical ontologies are likely to need and want to use with the same intended meaning. The BIRNLex was intended to serve as the basis for construction of a formal ontology for the multiscale investigation of neurological disease.",
"domains": [
"Protocol",
"Study design",
"Disease",
"Brain"
],
"homepage": "http://bioportal.bioontology.org/ontologies/NIFDYS?p=summary",
"license": "CC-BY-4.0",
"name": "Neuroscience Information Framework Dysfunction",
"repository": "https://github.com/SciCrunch/NIF-Ontology",
"subjects": [
"Anatomy",
"Neurobiology",
"Biomedical Science"
]
},
"FAIRsharing.309v57": {
"abbreviation": "LBO",
"description": "The Livestock Breed Ontology (LBO) is a controlled vocabulary for the unambiguous description of breeds. Its utility include proper identification of inherited variation sources in genetics/genomic studies. ",
"homepage": "https://www.animalgenome.org/bioinfo/projects/lbo/",
"license": "CC BY-NC 4.0",
"name": "Livestock Breed Ontology",
"repository": "https://github.com/AnimalGenome/livestock-breed-ontology",
"subjects": [
"Animal Breeding",
"Genomics",
"Genetics",
"Animal Husbandry"
]
},
"FAIRsharing.30vmv9": {
"contact": {
"email": "d.brooks@auckland.ac.nz",
"name": "David Brooks",
"orcid": "0000-0002-6758-2186"
},
"description": "An ontology for working with biosignals. This ontology defines concepts to describe the storage and exchange of biosignals, regardless of their underlying data format, and provides terms for common biosignal metadata.",
"homepage": "https://www.biosignalml.org/ontologies/2011/04/biosignalml.html",
"license": "CC BY-SA 3.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdDRDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--32639c60324da5b96c71282e1dd4d9d86eb932a5/BSMLLogo3.png?disposition=inline",
"name": "BioSignalML Ontology",
"publications": [
{
"doi": "10.1109/iembs.2011.6091372",
"pubmed": "22255626",
"title": "BioSignalML--a meta-model for biosignals",
"year": 2012
}
],
"subjects": [
"Life Science",
"Electrophysiology"
]
},
"FAIRsharing.31apg2": {
"abbreviation": "CO_340",
"description": "The Cowpea Trait Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_340:ROOT",
"license": "CC-BY-4.0",
"name": "IBP Cowpea Trait Ontology",
"publications": [
{
"doi": "10.3389/fphys.2012.00326",
"pubmed": "22934074",
"title": "Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice",
"year": 2012
}
],
"subjects": [
"Botany",
"Agriculture"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.31venv": {
"abbreviation": "DCO-DEBUGIT",
"description": "The Debugit Core Ontology (dco) covers the complete conceptual space of the domain of interest in the DebugIT project. It focuses on the management of antibiotics resistance within hospitals and infectious diseases to cover the clinical monitoring use cases. The ontology shall provide a semantic reference as logically defined classes in a formal and computer understandable format. It is supposed to formally represent all basic kinds of entities in the domain of interest, together with their invariant and context-independent properties. The ontology is therefore distinct from the representation of clinical knowledge as targeted by the DebugIT WP 4. Instead, it has a supportive semantic glue Function as it provides standardized and formally described meaning identifiers across the whole project, hence serving the Interoperability platform as well.",
"domains": [
"Antimicrobial"
],
"homepage": "http://dx.doi.org/10.3233/978-1-60750-588-4-1060",
"name": "DebugIT Core Ontology",
"subjects": [
"Infectious Disease Medicine",
"Biomedical Science"
],
"user_defined_tags": [
"Antimicrobial resistance"
]
},
"FAIRsharing.322dc0": {
"description": "Identifier schema for BioSamples. The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation.",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://registry.identifiers.org/registry/biosample",
"name": "BioSamples identifier",
"publications": [
{
"doi": "10.1093/nar/gkr1163",
"pubmed": "22139929",
"title": "BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata",
"year": 2011
}
],
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.33aa85": {
"abbreviation": "ISO 639-3",
"description": "ISO 639-3 provides a comprehensive set of identifiers for all languages for use in a wide range of applications, including linguistics, lexicography and internationalization of information systems. It attempts to represent all known full languages. ISO 639 provides three language code sets: one is a two-letter code (ISO 639-1) and two others are three-letter codes (ISO 639-2 and ISO 639-3) for the representation of names of languages. The three-letter codes in ISO 639-2 and ISO 639-3 are complementary and compatible. The two codes have been devised for different purposes. The set of individual languages listed in ISO 639-2 is a subset of those listed in ISO 639-3. The codes differ in that ISO 639-2 includes code elements representing some individual languages and also collections of languages, while ISO 639-3 includes code elements for all known individual languages but not for collections of languages. Overall, the set of individual languages listed in ISO 639-3 is much larger than the set of individual languages listed in ISO 639-2.",
"homepage": "https://www.iso.org/standard/39534.html",
"name": "ISO 639-3 Codes for the representation of names of languages - Part 3: Alpha-3 code for comprehensive coverage of languages",
"subjects": [
"Informatics",
"Computer Science",
"Linguistics"
],
"user_defined_tags": [
"Language"
]
},
"FAIRsharing.33mxgr": {
"abbreviation": "FALL",
"description": "This resource is no longer available because its underlying source material is not suitable for FAIRsharing. ",
"homepage": "http://bioportal.bioontology.org/ontologies/FALL",
"name": "MyOntoServiceFull_FallDetection",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.343864": {
"abbreviation": "FIP",
"contact": {
"email": "kuhntobias@gmail.com",
"name": "Tobias Kuhn",
"orcid": "0000-0002-1267-0234"
},
"description": "The FAIR Implementation Profile (FIP) Ontology is an extension of the FAIR Principles Vocabulary, implemented as a formal vocabulary, for describing Nanopublication schema classes, properties and data properties designed for machine-actionable FAIR implementations at the discretion of individual communities of practice. ",
"domains": [
"FAIR"
],
"homepage": "https://peta-pico.github.io/FAIR-nanopubs/fip/index-en.html",
"license": "CC0-1.0",
"name": "FAIR Implementation Profile Ontology",
"publications": [
{
"doi": "10.1007/978-3-030-65847-2_13",
"title": "Reusable FAIR Implementation Profiles as Accelerators of FAIR Convergence",
"year": 2020
},
{
"doi": "10.1007/978-3-030-65847-2_13",
"title": "Reusable FAIR Implementation Profiles as Accelerators of FAIR Convergence",
"year": 2020
},
{
"doi": "10.3897/rio.8.e94150",
"title": "The Comparative Anatomy of Nanopublications and FAIR Digital Objects",
"year": 2022
},
{
"doi": "10.3897/rio.8.e94451",
"title": "FIPs and Practice",
"year": 2022
}
],
"repository": "https://peta-pico.github.io/FAIR-nanopubs/principles/index-en.html",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.35e1c3": {
"abbreviation": "CO_350",
"contact": {
"email": "jeanluc.work@gmail.com",
"name": "Jean-Luc Jannink",
"orcid": "0000-0003-4849-628X"
},
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Oat Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology. The Oat Trait Dictionary was commissioned by Oat Global (http://oatglobal.org/) to hold the traits used in the T3/Oat database (http://triticeaetoolbox.org/oat/).",
"domains": [
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_350:ROOT",
"license": "CC-BY-4.0",
"name": "Oat Trait Ontology",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.36bc7b": {
"abbreviation": "MAMBO",
"description": "MAMBO (Materials And Molecules Basic Ontology) is a domain ontology for molecular materials. Its main targets are: i) Allowing the retrieval of structured information regarding molecular materials and related applications (i.e. devices based on molecular materials), ii) Supporting the development of new, complex workflows for modelling systems based on molecular materials (computational modelling and data-driven techniques), iii) Integrating data generated via computational simulations and empirical experiments.",
"domains": [
"Data model",
"Machine learning",
"Knowledge representation"
],
"homepage": "https://github.com/daimoners/MAMBO",
"name": "Materials And Molecules Basic Ontology",
"subjects": [
"Nanotechnology",
"Materials Science"
]
},
"FAIRsharing.36pf8q": {
"abbreviation": "RxNORM",
"description": "RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, MediSpan, Gold Standard Drug Database, and Multum. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary. RxNorm now includes the National Drug File - Reference Terminology (NDF-RT) from the Veterans Health Administration. NDF-RT is a terminology used to code clinical drug properties, including mechanism of action, physiologic effect, and therapeutic category.",
"domains": [
"Drug name",
"Drug"
],
"homepage": "https://www.nlm.nih.gov/research/umls/rxnorm/",
"name": "RxNORM",
"publications": [
{
"pubmed": "18998891",
"title": "RxTerms - a drug interface terminology derived from RxNorm",
"year": 2008
},
{
"doi": "10.1136/amiajnl-2011-000116",
"pubmed": "21515544",
"title": "Normalized names for clinical drugs: RxNorm at 6 years",
"year": 2011
},
{
"doi": "10.1109/mitp.2005.122",
"title": "RxNorm: prescription for electronic drug information exchange",
"year": 2005
}
],
"subjects": [
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.38ph3j": {
"abbreviation": "ONTOPSYCHIA",
"description": "Ontology of social and environmental determinants for psychiatry",
"domains": [
"Monitoring",
"Treatment"
],
"homepage": "http://bioportal.bioontology.org/ontologies/ONTOPSYCHIA",
"name": "OntoPsychia, social module",
"subjects": [
"Psychiatry",
"Clinical Psychology",
"Systems Medicine",
"Medical Informatics"
]
},
"FAIRsharing.3929xa": {
"abbreviation": "APACOMPUTER",
"description": "This resource is no longer available because its underlying source material is not suitable for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/APACOMPUTER",
"name": "Computer Cluster",
"subjects": [
"Computer Science"
]
},
"FAIRsharing.398b24": {
"abbreviation": "NPU",
"description": "NPU terminology is a coding system and terminology for the identification and communication of examination results, covering most fields of clinical laboratory science.",
"homepage": "https://www.npu-terminology.org",
"license": "CC0-1.0",
"name": "Nomenclature for Properties and Units terminology",
"subjects": [
"Clinical Studies",
"Toxicology",
"Medical Virology",
"Pharmacology",
"Clinical Immunology"
]
},
"FAIRsharing.39fd58": {
"abbreviation": "DEO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Discourse Elements Ontology (DEO) is an ontology that provides a structured vocabulary for rhetorical elements within documents (e.g., Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix). It is imported by DoCO.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/deo",
"license": "CC-BY-4.0",
"name": "Discourse Elements Ontology",
"publications": [
{
"doi": "10.3233/sw-150177",
"title": "The Document Components Ontology (DoCO)",
"year": 2016
}
],
"repository": "https://github.com/sparontologies/deo",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"FAIRsharing.39ff0a": {
"abbreviation": "RDA Vocabularies",
"description": "Resource Description and Access Vocabularies (RDA) Vocabularies is a representation of the RDA entities, elements, relationship designators, and controlled terms in RDF (Resource Description Framework). RDA is a standard for descriptive cataloging of bibliographic data. It is intended for use by libraries and other cultural organizations such as museums and archives. The Vocabularies are intended to support linked data applications using RDA.",
"domains": [
"Citation",
"Bibliography",
"Literature curation"
],
"homepage": "http://www.rdaregistry.info/",
"license": "CC-BY-4.0",
"name": "Resource Description and Access Vocabularies",
"repository": "https://github.com/RDARegistry/RDA-Vocabularies",
"subjects": [
"Humanities and Social Science"
]
},
"FAIRsharing.3a96ae": {
"abbreviation": "CAT",
"description": "The Chinese Agricultural Thesaurus (CAT) is an agricultural domain thesaurus. A number of international and national standards were adopted during its design and construction. CAT covers areas including agriculture, forestry, and biology. It is organized in 40 main categories, with most of the concepts having an English translation. The website is now longer resolving, and we cannot find a new homepage. Please get in touch with us if you have any information. ",
"homepage": "http://cat.aii.caas.cn/",
"name": "Chinese Agricultural Thesaurus",
"subjects": [
"Forest Management",
"Agriculture",
"Biology"
]
},
"FAIRsharing.3c59dd": {
"abbreviation": "GND Identifier",
"description": "Identifier schema for Gemeinsame Normdatei (GND)",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://bioregistry.io/registry/gnd",
"license": "https://creativecommons.org/licenses/by/1.0",
"name": "Gemeinsame Normdatei Identifier",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.3cf5bc": {
"abbreviation": "OPMV",
"description": "OPMV, the Open Provenance Model Vocabulary, is a lightweight provenance vocabulary created to aid responsible data publishing and interoperability between provenance information on the Semantic Web. The Open Provenance Model Vocabulary is closely based on OPM data model. OPMV can be used together with other provenance-related RDF/OWL vocabularies/ontologies, such as Dublin Core, FOAF, the Changeset Vocabulary, and the Provenance Vocabulary.",
"domains": [
"Resource metadata"
],
"homepage": "http://purl.org/net/opmv/ns",
"license": "https://creativecommons.org/licenses/by/1.0",
"name": "Open Provenance Model Vocabulary",
"subjects": [
"Data Management",
"Computer Science"
]
},
"FAIRsharing.3d5b53": {
"abbreviation": "ND",
"contact": {
"email": "addiehl@buffalo.edu",
"name": "Alexander D Diehl ",
"orcid": "0000-0001-9990-8331"
},
"description": "Representation of aspects of neurological diseases that are relevant to their treatment and study.",
"domains": [
"Disease"
],
"homepage": "https://github.com/addiehl/neurological-disease-ontology/blob/master/src/ontology/ND.owl",
"license": "CC0-1.0",
"name": "Neurological Disease Ontology",
"publications": [
{
"doi": "10.1186/2041-1480-4-42",
"pubmed": "24314207",
"title": "The neurological disease ontology",
"year": 2013
}
],
"subjects": [
"Neurology",
"Biomedical Science"
],
"user_defined_tags": [
"neurology disease"
]
},
"FAIRsharing.3da56b": {
"abbreviation": "GECKO",
"contact": {
"email": "mcourtot@gmail.com",
"name": "MΓ©lanie Courtot",
"orcid": "0000-0002-9551-6370"
},
"description": "GECKO is an ontology to represent genomics cohort attributes. The GECKO is maintained by the CINECA project, and standardises attributes commonly used for genomics cohort description as well as individual-level data items.",
"domains": [
"Experimental measurement",
"Biological sample"
],
"homepage": "https://github.com/IHCC-cohorts/GECKO",
"license": "CC-BY-4.0",
"name": "Genomics Cohorts Knowledge Ontology",
"subjects": [
"Genomics",
"Statistics",
"Life Science"
],
"user_defined_tags": [
"Survey"
]
},
"FAIRsharing.3de58a": {
"abbreviation": "OCO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The OpenCitations Ontology (OCO) is not yet another bibliographic ontology; instead, it is a place where existing and complementary ontological entities from several other ontologies are grouped to provide descriptive metadata for the OpenCitations Indexes and other OpenCitations datasets. This model is freely available for third parties to use to model their data, either for their independent use or to permit their data, conformed to the OpenCitations Data Model, to be published on their behalf by OpenCitations.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Publication",
"Protocol",
"Data model"
],
"homepage": "https://w3id.org/oc/ontology",
"license": "CC-BY-4.0",
"name": "OpenCitations Ontology",
"publications": [
{
"doi": "10.6084/m9.figshare.3443876.v7",
"title": "The OpenCitations Data Model",
"year": 2022
},
{
"doi": "10.1007/978-3-030-62466-8_28",
"title": "The OpenCitations Data Model",
"year": 2020
}
],
"repository": "https://github.com/opencitations/ontology",
"subjects": [
"Subject Agnostic"
],
"twitter": "opencitations",
"user_defined_tags": [
"none"
]
},
"FAIRsharing.3dm6gm": {
"abbreviation": "EHDA",
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy (EMAP ontology) and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once. The EHDA; Hunter et al. 2003 is less complete than later versions: it comprises a set of ontologies, one for each Carnegie stage (CS) (1β20) that only includes basic part_of data. Its structure was derived from the original EMAP ontology, and its content was based partly on this and partly on a limited study of sectioned human material.",
"domains": [
"Life cycle",
"Life cycle stage"
],
"homepage": "http://obofoundry.org/ontology/ehda.html",
"name": "Edinburgh Human Developmental Anatomy",
"publications": [
{
"doi": "10.1046/j.1469-7580.2003.00224.x",
"pubmed": "14620375",
"title": "An ontology of human developmental anatomy",
"year": 2003
}
],
"subjects": [
"Anatomy",
"Developmental Biology",
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.3e0sn4": {
"abbreviation": "GeXO",
"contact": {
"email": "kuiper@bio.ntnu.no",
"name": "Martin Kuiper",
"orcid": "0000-0002-1171-9876"
},
"description": "An application ontology for the domain of gene expression. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, and orthology relations using ontological properties from RO and ISO.",
"domains": [
"Expression data",
"Gene expression"
],
"homepage": "https://www.biogateway.eu/tools/#GeXKB",
"name": "Gene Expression Ontology",
"publications": [
{
"doi": "10.1186/s12859-014-0386-y",
"pubmed": "25490885",
"title": "Finding gene regulatory network candidates using the gene expression knowledge base",
"year": 2014
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.3e603c": {
"abbreviation": "PURL",
"description": "PURLs are Web addresses or Uniform Resource Locators (URLs) that act as permanent identifiers in the face of a dynamic and changing Web infrastructure. Instead of resolving directly to Web resources (documents, data, services, people, etc.). PURLs allow third party control over both URL resolution and resource metadata provision. A URL is simply an address of a resource on the World Wide Web. A Persistent URL is an address on the World Wide Web that causes a redirection to another Web resource. If a Web resource changes location (and hence URL), a PURL pointing to it can be updated. A user of a PURL always uses the same Web address, even though the resource in question may have moved. PURLs may be used by publishers to manage their own information space or by Web users to manage theirs; a PURL service is independent of the publisher of information. Please note that the referenced homepage contains links to an archived google code site, and may not refer to the current specification location. Please get in touch with us if you have more information.",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://code.google.com/archive/p/persistenturls/",
"license": "Apache 2.0 License",
"name": "Persistent Uniform Resource Locator",
"subjects": [
"Knowledge and Information Systems",
"Subject Agnostic"
]
},
"FAIRsharing.3e88d6": {
"abbreviation": "PRO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Publishing Roles Ontology (PRO) is an ontology for the characterisation of the roles of agents β people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/pro",
"license": "CC-BY-4.0",
"name": "Publishing Roles Ontology",
"publications": [
{
"doi": "10.1145/2362499.2362502",
"title": "Scholarly publishing and Linked Data: describing roles, statuses, temporal and contextual extents",
"year": 2012
}
],
"repository": "https://github.com/sparontologies/pro",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"FAIRsharing.3fc9zf": {
"abbreviation": "openEHR",
"contact": {
"email": "k.atalag@auckland.ac.nz",
"name": "Koray Atalag",
"orcid": "0000-0003-0517-4803"
},
"description": "openEHR is an open standard that uses a novel two-level modelling methodology to represent health information and meta-data by preserving the semantics during when it were created. It enables semantic interoperability and makes it possible to link disparate data sources easily and safely. It also allows for terminology binding which provides the bridge between the 'terminology' and 'information model' this making it much more useful than using these standards separately. Although openEHR is a de-facto standard that is developed by volunteers openly, ISO and CEN adopted it (ISO/EN 13606) so it is a full international standard. It has relationship and mappings between other standards, such as HL7.",
"domains": [
"Electronic health record"
],
"homepage": "http://www.openehr.org",
"name": "openEHR Health Record Specification",
"subjects": [
"Medicine",
"Health Science",
"Biomedical Science"
]
},
"FAIRsharing.3ftws4": {
"abbreviation": "OGR",
"description": "This OWL ontology classified the geograhical regions related vocabularies extracted from UMLS. It must be used with other two ontologies, in the case of diabetes: the Ontology of Glucose Metabolism Disorder (OGMD) and the Ontology for Genetic Disease Investigations (OGDI). Together, these three ontologies form the Ontology for Genetic Susceptibility Factor (OGSF), which is the project where information about this ontology is stored.",
"domains": [
"Geographical location",
"Diabetes mellitus"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1087",
"name": "Ontology of Geographical Region",
"subjects": [
"Earth Science",
"Biomedical Science"
]
},
"FAIRsharing.3fyavr": {
"abbreviation": "OBIws",
"description": "The Bioinformatics Web Services ontology (OBIws) is an ontology that extends the Ontology for Biomedical Investigations (OBI) to build an ontology that supports consistent annotation of bioinformatics Web services. We follow a systematic methodology for enriching OBI with terms to support Web service annotation. This process involves the design of ontology analysis diagrams for Web services and their subsequent analysis to discover terms that need to be added to the ontology. Current OBIws ontology is focusing on sequence analysis web services. With developed patterns of modeling web services, OBIws can be extended easily to support annotations of different kind web services.",
"domains": [
"Web service"
],
"homepage": "https://github.com/obi-webservice/OBIws",
"name": "Bioinformatics Web Service Ontology",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.3kcgmr": {
"abbreviation": "CARO",
"contact": {
"email": "haendel@ohsu.edu",
"name": "Melissa Haendel",
"orcid": "0000-0001-9114-8737"
},
"description": "The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies.",
"domains": [
"Annotation"
],
"homepage": "http://bioportal.bioontology.org/ontologies/CARO?p=summary",
"name": "Common Anatomy Reference Ontology",
"publications": [
{
"doi": "10.1007/978-1-84628-885-2_16",
"title": "CARO β The Common Anatomy Reference Ontology",
"year": 2008
}
],
"subjects": [
"Anatomy",
"Life Science"
],
"user_defined_tags": [
"Interoperability"
]
},
"FAIRsharing.3kfn3j": {
"abbreviation": "ABA-AMB",
"description": "The Adult Mouse Brain ontology is used within the Allen Brain Map Project to describe and annotate data from the project.",
"homepage": "http://www.brain-map.org",
"license": "https://alleninstitute.org/legal/citation-policy",
"name": "Allen Brain Atlas Adult Mouse Brain Ontology",
"subjects": [
"Neuroscience"
]
},
"FAIRsharing.3ngg40": {
"abbreviation": "PO",
"contact": {
"email": "jaiswalp@science.oregonstate.edu",
"name": "Pankaj Jaiswal",
"orcid": "0000-0002-1005-8383"
},
"description": "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plants.",
"domains": [
"Expression data",
"Plant development stage",
"Life cycle"
],
"homepage": "http://plantontology.org/",
"license": "CC-BY-4.0",
"name": "Plant Ontology",
"publications": [
{
"doi": "10.1002/cfg.496",
"pubmed": "18629207",
"title": "Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages",
"year": 2008
},
{
"doi": "10.1002/cfg.154",
"pubmed": "18628842",
"title": "The Plant Ontology Consortium and plant ontologies",
"year": 2008
},
{
"doi": "10.1007/978-1-4939-3167-5_5",
"pubmed": "26519402",
"title": "The Plant Ontology: A Tool for Plant Genomics",
"year": 2015
},
{
"doi": "10.1093/pcp/pcs163",
"pubmed": "23220694",
"title": "The plant ontology as a tool for comparative plant anatomy and genomic analyses",
"year": 2012
},
{
"doi": "10.1093/nar/gkm908",
"pubmed": "18194960",
"title": "The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations",
"year": 2008
},
{
"doi": "10.1371/journal.pbio.1002033",
"pubmed": "25562316",
"title": "Finding our way through phenotypes",
"year": 2015
}
],
"repository": "https://github.com/Planteome/plant-ontology",
"subjects": [
"Botany",
"Life Science",
"Plant Anatomy"
]
},
"FAIRsharing.3nx7t": {
"abbreviation": "DCES",
"description": "The Dublin Metadata Element Set, which is often called Dublin Core (DC), is a standardized metadata scheme for description of any kind of resource such as documents in electronic and non-electronic form, digital materials (such as video, sound, images, etc) and composite media like web pages. Dublin Core Metadata may be used for multiple purposes, from simple resource description, to combining metadata vocabularies of different metadata standards, to providing interoperability for metadata vocabularies in the Linked Data cloud and Semantic Web implementations. Please note that this version of the specification for the Dublin Core Element Set 1.1 is somewhat out of date, although it is not officially deprecated. The DCMI Metadata Terms specification is linked to this record and is the current documentation that should be used for the Dublin Core Element Set 1.1. This document, an excerpt from the more comprehensive document \"DCMI Metadata Terms\" [DCTERMS] provides an abbreviated reference version of the fifteen element descriptions that have been formally endorsed in the following standards: ISO Standard 15836:2009 of February 2009 [ISO15836], ANSI/NISO Standard Z39.85-2012 of February 2013 [NISOZ3985], and IETF RFC 5013 of August 2007 [RFC5013].",
"domains": [
"Resource metadata",
"Annotation"
],
"homepage": "https://www.dublincore.org/specifications/dublin-core/dces/",
"license": "CC-BY-3.0",
"name": "Dublin Core Metadata Element Set",
"subjects": [
"Life Science",
"Subject Agnostic",
"Biomedical Science"
],
"user_defined_tags": [
"Metadata standardization"
]
},
"FAIRsharing.3prt32": {
"abbreviation": "BCTEO",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Tissue"
],
"homepage": "http://bioportal.bioontology.org/ontologies/BCTEO",
"name": "Bone and Cartilage Tissue Engineering Ontology",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.3qdg66": {
"abbreviation": "GENE-CDS",
"description": "The Genomic CDS ontology aims to unify several functionalities in a single resource, being: * A knowledge base for clinical pharmacogenomics/pharmacogenetics that can be used for question-answering (e.g., which SNPs are associated with this drug?) * A rule base for clinical decision support (e.g., inferring that a patient with a specific set of SNPs requires a lowered dose of warfarin and generating a CDS message that can be viewed by clinicians) * A tool for checking data consistency (e.g., highlighting which allele definitions in PharmGKB are overlapping, or which clinical decision support rules are matching the same group of patients).",
"homepage": "http://samwald.info",
"name": "Genomic Clinical Decision Support Ontology",
"subjects": [
"Genomics",
"Health Science",
"Proteomics"
]
},
"FAIRsharing.3vf3hp": {
"abbreviation": "EUFUT",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/1702",
"name": "Eurofut",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.3wbgm0": {
"abbreviation": "MPATH",
"contact": {
"email": "pns12@cam.ac.uk",
"name": "Paul Schofield",
"orcid": "0000-0002-5111-7263"
},
"description": "Mouse PATHology (MPATH) ontology is a structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes. This resource was developed by the Pathology Consortium of Pathbase (www.pathbase.net).",
"domains": [
"Mutation",
"Histology",
"Phenotype",
"Disease",
"Genetic strain"
],
"homepage": "https://github.com/PaulNSchofield/mpath",
"name": "Mouse PATHology",
"publications": [
{
"doi": "10.1177/0300985810374845",
"pubmed": "20587689",
"title": "Pathbase and the MPATH ontology. Community resources for mouse histopathology",
"year": 2010
}
],
"subjects": [
"Anatomy",
"Biomedical Science"
]
},
"FAIRsharing.3x8jd5": {
"abbreviation": "ROO",
"description": "The Radiation Oncology Ontology (ROO) aims to cover the radiation oncology domain with a strong focus on re-using existing ontologies. ROO models terms including: uniform and non-uniform margins; ROI target volumes and organs-at-risk; dose-volume histogram parameters (Dx, Vx, MLD, etc.); and on-line / off-line setup protocols. ROO represents clinical data (and their relationships) in the radiation oncology domain following FAIR principles.",
"domains": [
"Cancer",
"Radiotherapy"
],
"homepage": "https://www.cancerdata.org/roo-information",
"license": "CC BY-NC 3.0",
"name": "Radiation Oncology Ontology",
"publications": [
{
"doi": "10.1002/mp.12879",
"pubmed": "30144092",
"title": "The radiation oncology ontology (ROO): Publishing linked data in radiation oncology using semantic web and ontology techniques",
"year": 2018
}
],
"repository": "https://github.com/RadiationOncologyOntology/ROO",
"subjects": [
"Oncology",
"Health Science",
"Biomedical Science"
]
},
"FAIRsharing.3ychgy": {
"abbreviation": "ImmDis",
"description": "The Immune Disorder Ontology was generated as part of the Bioinformatics Integration Support Contract (BISC) funded by the Division of Allergy, Immunology and Transplantation (DAIT) within NIAID. The ontology is based on the National Library of Medicine (NLM) Medical Subject Headings; National Cancer Institute Thesaurus; International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM); ICD-10; and other open source public databases.",
"domains": [
"Disease",
"Immune system"
],
"homepage": "http://bioportal.bioontology.org/ontologies/3127",
"name": "Immune Disorder Ontology",
"subjects": [
"Immunology",
"Biomedical Science"
]
},
"FAIRsharing.41b655": {
"abbreviation": "Ringgold ID",
"description": "The Ringgold ID is a Persistent Identifier (PID) that assigns a unique numerical identifier to organizations for use across the scholarly communications sector. Ringgold assigns each organization an Identify Database record ID, and includes organizations which are part of the scholarly ecosystem β licensees, publishers, intermediaries, and funders β as well as those which license and create scholarly content β universities, hospitals, corporations, and government entities. Ringgold is a part of the Copyright Clearance Center (CCC) and contains 600,000+ records encompassing publishers, funders, research organizations, universities, intermediaries, and more.",
"domains": [
"Quality control",
"Centrally registered identifier"
],
"homepage": "https://www.ringgold.com/ringgold-identifier/",
"license": "https://www.copyright.com/terms-conditions",
"name": "Ringgold Identifier",
"subjects": [
"Data Management"
],
"twitter": "ringgoldinc"
},
"FAIRsharing.424420": {
"abbreviation": "GGDonto",
"contact": {
"email": "h.narimatsu@aist.go.jp",
"name": "Hisashi Narimatsu",
"orcid": "0000-0002-8402-133X"
},
"description": "Focused on the molecular etiology, pathogenesis, and clinical manifestations of genetic diseases and disorders of glycan metabolism and developed as a knowledge-base for this scientific field, GGDonto provides comprehensive information on various topics, including links to aid the integration with other scientific resources. The availability and accessibility of this knowledge will help users better understand how genetic defects impact the metabolism of glycans as well as how this impaired metabolism affects various biological functions and human health. In this way, GGDonto will be useful in fields related to glycoscience, including cell biology, biotechnology, and biomedical, and pharmaceutical research.",
"domains": [
"Genetic disorder"
],
"homepage": "http://acgg.asia/db/diseases/html/ggdonto.html",
"name": "Genetic Glyco-Diseases Ontology",
"publications": [
{
"doi": "10.1186/s13326-018-0182-0",
"pubmed": "29669592",
"title": "GGDonto ontology as a knowledge-base for genetic diseases and disorders of glycan metabolism and their causative genes",
"year": 2018
}
],
"subjects": [
"Biomedical Science"
],
"user_defined_tags": [
"Glycan sequences"
]
},
"FAIRsharing.43m9f6": {
"abbreviation": "SYN",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/SYN",
"name": "Sage Bionetworks Synapse Ontology",
"subjects": [
"Medicine"
]
},
"FAIRsharing.446bv0": {
"abbreviation": "OoEVV",
"contact": {
"email": "gully@usc.edu",
"name": "Gully Burn",
"orcid": "0000-0003-1493-865X"
},
"description": "The Ontology of Experimental Variables and Values (OoEVV) provides a lightweight representation of (a) the variables used to measure experimental properties and (b) the measurement scales that form the complex data types supporting that data. Many different variables measure the same thing, here we use a lightweight representation driven by a small number of classes and a large number of variables to focus only on providing a vocabulary of variables that may be extended for consolidation to standardized variables for specific things and functions to map between values from different measurements scales. We use the base ontology description to provide a very lightweight representation of the basic elements of an experimental design and we use views to instantiate it for specific domains.",
"domains": [
"Resource metadata",
"Experimental measurement",
"Protocol",
"Independent variable",
"Study design",
"Experimentally determined",
"Measurement"
],
"homepage": "https://bioportal.bioontology.org/ontologies/OOEVV",
"name": "Ontology of Experimental Variables and Values",
"publications": [
{
"doi": "10.1016/j.neuroimage.2013.05.024",
"pubmed": "23684873",
"title": "Modeling functional Magnetic Resonance Imaging (fMRI) experimental variables in the Ontology of Experimental Variables and Values (OoEVV)",
"year": 2013
}
],
"subjects": [
"Natural Science",
"Life Science"
],
"user_defined_tags": [
"Experimental condition"
]
},
"FAIRsharing.457f35": {
"abbreviation": "PDB Identifier",
"contact": {
"email": "harukin@protein.osaka-u.ac.jp",
"name": "Haruki Nakamura",
"orcid": "0000-0001-6690-5863"
},
"description": "Identifier schema for Protein Data Bank",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://registry.identifiers.org/registry/pdb",
"name": "Protein Data Bank Identifier",
"publications": [
{
"doi": "10.1007/978-1-4939-7000-1_26",
"pubmed": "28573592",
"title": "Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive",
"year": 2017
}
],
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.46rwe6": {
"abbreviation": "CSSO",
"description": "An ontology for describing clinical signs and symptoms.",
"homepage": "http://mdb.bio.titech.ac.jp/csso",
"name": "Clinical Signs and Symptoms Ontology",
"subjects": [
"Medicine",
"Clinical Studies"
]
},
"FAIRsharing.4877h0": {
"abbreviation": "ORTH",
"description": "ORTH ontology is designed to describe sequence homology data such as gene region, gene and protein-centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures in a single terminology.",
"domains": [
"Protein",
"Sequence",
"Gene",
"Homologous",
"Orthologous",
"Paralogous"
],
"homepage": "https://github.com/qfo/OrthologyOntology",
"license": "CC-BY-4.0",
"name": "Orthology Ontology",
"publications": [
{
"doi": "10.1186/s13326-016-0077-x",
"title": "The Orthology Ontology: development and applications",
"year": 2016
}
],
"subjects": [
"Comparative Genomics"
]
},
"FAIRsharing.48b735": {
"abbreviation": "Linguistics",
"description": "Controlled vocabulary used for indexing the records included in the FRANCIS bibliographical database \"Linguistics\" (1972-2015, http://pascal-francis.inist.fr/). It contains 6113 terminological entries grouped into 49 collections. It is aligned with Wikidata. The \"glottonyms\" collection is furthermore hierarchically organized according to the geographical origin of the languages and enriched with ISO 639-3 and Glottolog codes.",
"homepage": "https://skosmos.loterre.fr/X64/en/",
"license": "CC-BY-4.0",
"name": "Linguistics vocabulary",
"subjects": [
"Linguistics"
],
"user_defined_tags": [
"Language"
]
},
"FAIRsharing.493qns": {
"abbreviation": "PDUMDV",
"description": "Life cycle stages for Platynereis dumerilii. The status of this resource is \"in development\", confirmed via developer remarks within the GitHub project stating that the ontology is not ready.",
"domains": [
"Life cycle stage"
],
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/tree/master/src/pdumdv",
"name": "Platynereis Developmental Stages",
"repository": "https://github.com/obophenotype/developmental-stage-ontologies/wiki",
"subjects": [
"Developmental Biology",
"Life Science"
]
},
"FAIRsharing.495736": {
"abbreviation": "ISO 639-1:2002",
"description": "This part of ISO 639 provides a code consisting of language code elements comprising two-letter language identifiers for the representation of names of languages. The language identifiers according to this part of ISO 639 were devised originally for use in terminology, lexicography and linguistics, but may be adopted for any application requiring the expression of language in two-letter coded form, especially in computerized systems. Languages designed exclusively for machine use, such as computer-programming languages, are not included in this code.",
"homepage": "https://www.iso.org/standard/22109.html",
"name": "ISO 639-1:2002 Codes for the representation of names of languages β Part 1: Alpha-2 code",
"subjects": [
"Informatics",
"Linguistics"
],
"user_defined_tags": [
"Language"
]
},
"FAIRsharing.49bmk": {
"abbreviation": "anaeeThes",
"contact": {
"email": "christian.pichot@inrae.fr",
"name": "Christian Pichot",
"orcid": "0000-0003-1636-9438"
},
"description": "The anaeeThes thesaurus aims at providing a controlled vocabulary for the semantic description of the study of continental ecosystems and their biodiversity. The thesaurus consists of concepts handled in different main thematic areas: abiotic (e.g. atmosphere, climate, hydrosphere, litosphere); biotic (e.g. animals, plants, micro-organisms, biodiversity); chemical compounds; experimentation and observation (e.g. instrument, method, protocol, measurement, quality, infrastructure); ecosystems (e.g. type, structure, functioning); modeling (e.g. formalism, platform, type of model, computer language); disciplines (disciplinary and scientific fields); and unit (units of the international system, inherited from the OBOE-standards ontology).",
"domains": [
"Experimental measurement",
"Ecosystem",
"Modeling and simulation",
"Protocol",
"Device",
"Unit"
],
"homepage": "https://lovinra.inra.fr/2017/03/13/thesaurus-anaee/",
"license": "CC-BY-4.0",
"name": "AnaEE Thesaurus",
"subjects": [
"Soil Science",
"Agricultural Engineering",
"Ecology",
"Biodiversity",
"Atmospheric Science",
"Ecosystem Science"
]
},
"FAIRsharing.4bcrzk": {
"abbreviation": "CYTO",
"description": "It is flat ontology showing cytokine synonyms. It has been produced by merging cytokine branches, using SOMA (Synonym Ontology Mapping Approach) method, of 10 Bioportal ontologies.",
"domains": [
"Immune system"
],
"homepage": "http://bioportal.bioontology.org/ontologies/CYTO",
"name": "CYTOKINE",
"subjects": [
"Molecular Infection Biology",
"Immunology"
],
"user_defined_tags": [
"Synonyms"
]
},
"FAIRsharing.4c0b6b": {
"abbreviation": "UBERON",
"description": "Uberon is an integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies. It represents a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.",
"homepage": "http://uberon.org/",
"license": "CC-BY-3.0",
"name": "UBER anatomy ONtology",
"publications": [
{
"doi": "10.1186/2041-1480-5-21",
"pubmed": "25009735",
"title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon",
"year": 2014
},
{
"doi": "10.1186/gb-2012-13-1-r5",
"pubmed": "22293552",
"title": "Uberon, an integrative multi-species anatomy ontology",
"year": 2012
}
],
"repository": "https://github.com/obophenotype/uberon/wiki/Manual",
"subjects": [
"Anatomy",
"Taxonomy",
"Developmental Biology",
"Life Science"
],
"twitter": "uberanat"
},
"FAIRsharing.4c7f91": {
"abbreviation": "MSIO",
"contact": {
"email": "philippe.rocca-serra@oerc.ox.ac.uk",
"name": "Philippe Rocca-Serra",
"orcid": "0000-0001-9853-5668"
},
"description": "The Metabolomics Standards Initiative Ontology (MSIO) aims to support metabolomic experimental annotations for mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy techniques to identify, measure and quantify small molecules known as metabolites. MSIO covers metabolite profiling, targeted or untargeted, and tracer based applications. MSIO leverages other existing resource terms from other ontology collections such as CHEBI, DUO, NMRCV, OBI, and STATO.",
"domains": [
"Mass spectrum",
"Experimental measurement",
"Annotation",
"Nuclear Magnetic Resonance (NMR) spectroscopy",
"Omics data analysis"
],
"homepage": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO",
"license": "CC-BY-3.0",
"name": "Metabolomics Standards Initiative Ontology",
"publications": [
{
"doi": "10.1007/s11306-007-0069-z",
"title": "Metabolomics standards initiative: ontology working group work in progress",
"year": 2007
}
],
"repository": "https://raw.githubusercontent.com/ISA-tools/MSIO/master/MSIO-edit.owl",
"subjects": [
"Metabolomics",
"Omics"
]
},
"FAIRsharing.4cvwxa": {
"abbreviation": "NCIt",
"description": "NCI Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities. NCIt features: stable, unique codes for biomedical concepts; preferred terms, synonyms, research codes, external source codes, and other information; over 100,000 textual definitions; links to NCI Metathesaurus and other information sources; and over 400,000 cross-links between concepts, providing formal logic-based definition of many concepts. NCIt is a widely recognized standard for biomedical coding and reference, used by a broad variety of public and private partners both nationally and internationally including the Clinical Data Interchange Standards Consortium Terminology (CDISC), the U.S. Food and Drug Administration (FDA), the Federal Medication Terminologies (FMT), and the National Council for Prescription Drug Programs (NCPDP).",
"domains": [
"Cancer",
"Disease"
],
"homepage": "https://ncit.nci.nih.gov",
"license": "CC-BY-4.0",
"name": "NCI Thesaurus",
"publications": [
{
"doi": "10.3233/978-1-60750-949-3-33",
"pubmed": "15360769",
"title": "NCI Thesaurus: using science-based terminology to integrate cancer research results",
"year": 2004
}
],
"repository": "https://github.com/NCI-Thesaurus/thesaurus-obo-edition",
"subjects": [
"Biomedical Science",
"Translational Medicine",
"Preclinical Studies"
]
},
"FAIRsharing.4ded1f": {
"abbreviation": "TEO",
"description": "The Time Event Ontology (TEO) is an ontology for representing events, time, and their relationships.",
"domains": [
"Measurement"
],
"homepage": "http://bioportal.bioontology.org/ontologies/TEO",
"name": "Time Event Ontology",
"subjects": [
"Physics"
],
"user_defined_tags": [
"Events"
]
},
"FAIRsharing.4dvtcz": {
"abbreviation": "CLO",
"contact": {
"email": "Sirarat.Sarntivijai@fda.hhs.gov",
"name": "Sirarat Sarntivijai",
"orcid": "0000-0002-2548-641X"
},
"description": "The Cell Line Ontology (CLO) is a community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. Thousands of cell lines have been artificially developed and used for different applications. Integration of data from multiple sources is a challenge, confounded by lack of consistent naming conventions, contamination of cell lines, and provision of the same cell lines by multiple commercial sources but with different biological attributes. CLO is a community-based effort to represent all cell lines in a standard ontology approach.",
"domains": [
"Cell line",
"Cell",
"Morphology"
],
"homepage": "https://github.com/CLO-ontology/CLO",
"license": "CC-BY-3.0",
"name": "Cell Line Ontology",
"publications": [
{
"doi": "10.1186/2041-1480-5-37",
"pubmed": "25852852",
"title": "CLO: The cell line ontology",
"year": 2014
}
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},
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"abbreviation": "CO_327",
"description": "The goal of the CGIAR Pearl Millet Ontology is to help improve food security for subsistence smallholder farmers in East and West Africa with productive and nutritious pearl millet food and fodder production technologies.",
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"abbreviation": "UKAT",
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"abbreviation": "CO_330",
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Potato Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
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"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Sweet Potato Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
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"Food"
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"homepage": "https://cropontology.org/term/CO_331:ROOT",
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"Agriculture",
"Life Science"
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"description": "Health Indicators Ontology is an ontology of a number of health related indicator terms and description as well as health status classifications.",
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"name": "Health Indicators Ontology",
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"doi": "10.1016/j.compbiomed.2005.07.003",
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"title": "A pilot ontological model of public health indicators",
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},
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"abbreviation": "MOOCCUADO",
"contact": {
"email": "contact@bioself.communication.com",
"name": "Delphine Dauga",
"orcid": "0000-0003-3152-1194"
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"description": "The first ontology describing the anatomy and the development of Molgula occulta.",
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"abbreviation": "LCGFT",
"description": "The Library of Congress Genre/Form Terms for Library and Archival Materials (LCGFT) is a thesaurus that describes what a work is versus what it is about. For instance, the subject heading Horror films, with appropriate subdivisions, would be assigned to a book about horror films. A cataloger assigning headings to the movie The Texas Chainsaw Massacre would also use Horror films, but it would be a genre/form term since the movie is a horror film, not a movie about horror films. The thesaurus combines both genres and forms. Form is defined as a characteristic of works with a particular format and/or purpose. A \"short\" is a particular form, for example, as is \"animation.\" Genre refers to categories of works that are characterized by similar plots, themes, settings, situations, and characters.",
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"abbreviation": "MF",
"contact": {
"email": "hastings@ebi.ac.uk",
"name": "Janna Hastings",
"orcid": "0000-0002-3469-4923"
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"description": "The Mental Functioning Ontology is an ontology for mental functioning, including mental processes such as cognition and traits such as intelligence, and related diseases and disorders. It is developed in the context of the Ontology for General Medical Science and the Basic Formal Ontology. The project is being developed in collaboration between the University of Geneva, Switzerland, and the University at Buffalo, USA. The project is being developed with full involvement of all relevant communities, following best practices laid out by the OBO Foundry. Efforts are currently underway to align with related projects including the Behaviour Ontology, the Cognitive Atlas, the Cognitive Paradigm Ontology and the Neural Electro Magnetic Ontologies.",
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"Cognition",
"Mental health"
],
"homepage": "https://github.com/jannahastings/mental-functioning-ontology",
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"abbreviation": "JERM",
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"email": "kwolstencroft@cs.man.ac.uk",
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"description": "The JERM provides a framework to describe SEEK assets and the relationships between assets and the experiments that created them. All assets are related to the scientists that created them and the projects they originate from, so the model captures provenance information as well as physical links between assets. JERM definitions for each type of data in SEEK is different, but highly overlapping and they comply with existing minimal information guidelines where they are available.",
"domains": [
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"Biological sample",
"Assay",
"Protocol"
],
"homepage": "https://jermontology.org/",
"name": "Just Enough Results Model Ontology",
"repository": "https://github.com/FAIRdom/JERMOntology",
"subjects": [
"Life Science"
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"FAIRsharing.4ndncv": {
"abbreviation": "PRO",
"contact": {
"email": "dan5@georgetown.edu",
"name": "Darren Natale",
"orcid": "0000-0001-5809-9523"
},
"description": "Protein Ontology (PRO) provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp).",
"domains": [
"Annotation",
"PTM site prediction",
"Protein acetylation",
"Phosphorylation",
"Methylation",
"Protein-containing complex",
"Glycosylation",
"Data model",
"Protein",
"Biocuration"
],
"homepage": "https://proconsortium.org/",
"license": "CC-BY-4.0",
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"name": "PRotein Ontology",
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"doi": "10.1093/nar/gkt1173",
"pubmed": "24270789",
"title": "Protein Ontology: a controlled structured network of protein entities",
"year": 2013
},
{
"doi": "10.1093/nar/gkq907",
"pubmed": "20935045",
"title": "The Protein Ontology: a structured representation of protein forms and complexes",
"year": 2010
},
{
"doi": "10.1186/1471-2105-8-s9-s1",
"pubmed": "18047702",
"title": "Framework for a protein ontology",
"year": 2007
},
{
"doi": "10.1186/1471-2105-12-371",
"pubmed": "21929785",
"title": "The representation of protein complexes in the Protein Ontology (PRO)",
"year": 2011
},
{
"doi": "10.1093/nar/gkw1075",
"pubmed": "27899649",
"title": "Protein Ontology (PRO): enhancing and scaling up the representation of protein entities",
"year": 2016
}
],
"subjects": [
"Biology"
]
},
"FAIRsharing.4qyf0f": {
"abbreviation": "ReTO",
"description": "An application ontology for the domain of gene transcription regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI and orthological properties from RO and SIO.",
"domains": [
"Regulation of gene expression",
"Transcript"
],
"homepage": "https://bioportal.bioontology.org/ontologies/RETO",
"name": "Regulation of Transcription Ontolology",
"subjects": [
"Life Science",
"Transcriptomics"
]
},
"FAIRsharing.4vr0ys": {
"abbreviation": "FYPO",
"contact": {
"email": "vw253@cam.ac.uk",
"name": "Valerie Wood",
"orcid": "0000-0001-6330-7526"
},
"description": "FYPO is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the online fission yeast resource (www.pombase.org). Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions.",
"domains": [
"Gene Ontology enrichment",
"Phenotype"
],
"homepage": "http://sourceforge.net/apps/trac/pombase/wiki/FissionYeastPhenotypeOntology",
"license": "CC-BY-3.0",
"name": "Fission Yeast Phenotype Ontology",
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{
"doi": "10.1093/bioinformatics/btt266",
"pubmed": "23658422",
"title": "FYPO: the fission yeast phenotype ontology",
"year": 2013
}
],
"subjects": [
"Genetics",
"Phylogenetics",
"Life Science"
]
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"abbreviation": "EDDA_PT",
"description": "The EDDA Publication Types Taxonomy (v1.0) was developed by Tanja Bekhuis (Principal Scientist) and Eugene Tseytlin (Systems Developer) of the Evidence in Documents, Discovery, and Analytics (EDDA) Group. The EDDA Group is a division of TCB Research & Indexing LLC. V",
"domains": [
"Bibliography",
"Publication"
],
"homepage": "http://bioportal.bioontology.org/ontologies/EDDA_PT",
"license": "CC BY-NC-SA 4.0",
"name": "EDDA Publication Types Taxonomy",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.4yrcbc": {
"abbreviation": "FISH-AST",
"description": "Terminology used for recording the techniques, recovery methods and materials associated with archaeological sciences. Maintained by Historic England on behalf of the FISH Terminology Working Group.",
"domains": [
"Microscopy"
],
"homepage": "http://heritagedata.org/live/schemes/560.html",
"license": "CC-BY-3.0",
"name": "FISH Archaeological Sciences Thesaurus",
"subjects": [
"Archaeology",
"Mineralogy"
],
"user_defined_tags": [
"Soil pH"
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},
"FAIRsharing.4zegak": {
"abbreviation": "RoleO",
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Oliver He",
"orcid": "0000-0001-9189-9661"
},
"description": "The Role Ontology (RoleO) is a ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles.",
"homepage": "https://sourceforge.net/projects/roleo/",
"name": "Role Ontology",
"subjects": [
"Computer Science"
]
},
"FAIRsharing.504c6c": {
"abbreviation": "RO",
"description": "The Radiomics Ontology (RO) aims to cover the radiomics feature domain as well as the full spectrum of radiomics computational details. Radiomics is a research area concerned with the extraction of large amount of features from radiographic medical images. The current version of the RO includes all the possible steps that should be documented when performing a radiomic study. RO shares IRIs with the IBSI reference manual.",
"domains": [
"Medical imaging"
],
"homepage": "https://github.com/albytrav/RadiomicsOntologyIBSI",
"name": "Radiomics Ontology",
"repository": "https://github.com/albytrav/RadiomicsOntologyIBSI/wiki/1.-Home",
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"Computer Science",
"Biomedical Science"
],
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},
"FAIRsharing.5164e7": {
"abbreviation": "Marine Regions",
"contact": {
"email": "info@marineregions.org",
"name": "Lennert Schepers",
"orcid": "0000-0002-6145-8248"
},
"description": "The purpose of Marine Regions is to create a standard, relational list of geographic names, coupled with information and maps of the geographic location of these features. The objectives are to capture all geographic marine names worldwide, including ocean basins, seas, seamounts, sandbanks, ridges, bays and other marine geographical place names and attributes, and to display univocally the boundaries of marine biogeographic or other managed marine areas in order to facilitate marine data management, marine (bio)geographic research and the management of marine areas.",
"domains": [
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"Marine environment"
],
"homepage": "https://marineregions.org",
"license": "CC-BY-4.0",
"name": "Marine Regions",
"subjects": [
"Environmental Science",
"Geography",
"Geophysics",
"Data Management",
"Marine Biology",
"Earth Science",
"Oceanography"
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"twitter": "marineregions",
"user_defined_tags": [
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"maritime policy"
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},
"FAIRsharing.5403x": {
"abbreviation": "MFO",
"description": "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.",
"domains": [
"Cell cycle"
],
"homepage": "http://www.obofoundry.org/ontology/mfo.html",
"name": "Medaka Fish Ontology",
"publications": [
{
"doi": "10.1093/bioinformatics/bti478",
"pubmed": "15879458",
"title": "MEPD: a resource for medaka gene expression patterns",
"year": 2005
}
],
"subjects": [
"Anatomy",
"Developmental Biology",
"Life Science"
]
},
"FAIRsharing.546873": {
"description": "Identifier schema for BioProject. BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a projectβs scope, material, objectives, funding source and general relevance categories.",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://registry.identifiers.org/registry/bioproject",
"name": "BioProject identifier",
"publications": [
{
"doi": "10.1093/nar/gkr1163",
"pubmed": "22139929",
"title": "BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata",
"year": 2011
}
],
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.54pw8x": {
"abbreviation": "PD_ST",
"description": "Developmental stages of Platynereis.",
"domains": [
"Life cycle",
"Life cycle stage"
],
"homepage": "http://www.obofoundry.org/ontology/pd_st.html",
"name": "Platynereis Developmental STage",
"publications": [
{
"doi": "10.1186/1742-9994-7-31",
"pubmed": "21192805",
"title": "The normal development of Platynereis dumerilii (Nereididae, Annelida)",
"year": 2011
}
],
"subjects": [
"Developmental Biology"
]
},
"FAIRsharing.560f4e": {
"abbreviation": "Ecotoxicology",
"description": "This bilingual, French-English thesaurus structures the key concepts of ecotoxicology, the study of the impact of pollutants on ecosystems, with searchable synonyms. The resource area includes risks to human health. It also contains terms from geography, animal and plant taxonomy and chemical compounds. It uses polyhierarchy. Concepts are grouped into semantic categories. Definitions are given for some concepts.",
"homepage": "https://skosmos.loterre.fr/3WV/en/",
"license": "CC-BY-4.0",
"name": "Ecotoxicology thesaurus",
"subjects": [
"Toxicology",
"Global Health",
"Medical Toxicology",
"Ecology"
],
"user_defined_tags": [
"plants"
]
},
"FAIRsharing.5744rq": {
"abbreviation": "sepCV",
"description": "The sepCV is a controlled vocabulary for teminology associated with sample preparation and sample processing for proteomics. The sepCV was originally designed to provide terminology for the MIAPE GE reporting guidelines and the gelML data transfer format. It has now been expanded to include terminology for gel image informatics to support the MIAPE GI reporting guidelines and the GelInfoML data transfer format. In addition it includes relevant terminology for general sample processing to support the data transfer format of spML. The sepCV is beign jointly developed by the Proteomics Standards Intiative (PSI) and the Metabolomics Standards Intitative (MSI).",
"domains": [
"Sample preparation for assay",
"Material processing",
"Protein"
],
"homepage": "http://www.psidev.info/sepcv",
"name": "Sample processing and separations controlled vocabulary",
"repository": "https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo",
"subjects": [
"Proteomics",
"Life Science"
]
},
"FAIRsharing.5794af": {
"abbreviation": "EPPO Codes",
"description": "European and Mediterranean Plant Protection Organization (EPPO) Codes are computer codes developed for plants, pests (including pathogens) which are important in agriculture and plant protection. EPPO codes constitute a harmonized coding system which aims to facilitate the management of plant and pest names in computerized databases, as well as data exchange between IT systems.",
"domains": [
"Centrally registered identifier",
"Pathogen"
],
"homepage": "https://www.eppo.int/RESOURCES/eppo_databases/eppo_codes",
"name": "European and Mediterranean Plant Protection Organization Codes",
"subjects": [
"Botany",
"Taxonomy",
"Agriculture"
],
"twitter": "EPPOnews"
},
"FAIRsharing.58b6f9": {
"abbreviation": "RInChI",
"description": "The aim of the RInChI project, in the same vein as InChI, is to create a unique data string to describe a reaction. Reaction InChIs, or RInChIs, are such data strings.",
"domains": [
"Reaction data",
"Centrally registered identifier"
],
"homepage": "http://www-rinchi.ch.cam.ac.uk/",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBcUlFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--e03d046e3a37448b0cd9e13b86fa57a003ff3190/inchi-wheel.png?disposition=inline",
"name": "Reaction InChI",
"publications": [
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"doi": "10.1186/s13321-017-0210-6",
"title": "A possible extension to the RInChI as a means of providing machine readable process data",
"year": 2017
},
{
"doi": "10.1186/1758-2946-5-45",
"title": "International chemical identifier for reactions (RInChI)",
"year": 2013
}
],
"repository": "https://github.com/IUPAC-InChI/RInChI",
"subjects": [
"Cheminformatics",
"Chemistry",
"Analytical Chemistry"
]
},
"FAIRsharing.595710": {
"abbreviation": "AFO",
"description": "The Agriculture and Forestry Ontology (AFO), also known as the Agriforest Ontology, combines the concepts of the Agriforest Thesaurus with The Finnish General Upper Ontology (YSO). This combination of ontologies can be used for describing resources especially in domain of agriculture, forestry, veterinary medicine, food science, environmental science and biology.",
"domains": [
"Food"
],
"homepage": "https://seco.cs.aalto.fi/ontologies/afo/",
"license": "CC-BY-4.0",
"name": "Agriculture and Forestry Ontology",
"subjects": [
"Environmental Science",
"Forest Management",
"Agricultural Engineering",
"Agriculture",
"Veterinary Medicine",
"Food Chemistry",
"Biology"
]
},
"FAIRsharing.5970hq": {
"abbreviation": "OBOE",
"contact": {
"email": "mecum@nceas.ucsb.edu",
"name": "Bryce Mecum",
"orcid": "0000-0002-0381-3766"
},
"description": "OBOE is a suite of OWL-DL ontologies for modeling and representing scientific observations. The OBOE model is designed as a generic data model with a number of constructs for defining observational data. Key features of OBOE include its ability to represent a wide range of measurement types, a mechanism for specifying measurement context, and the ability to associate the type of entity (e.g., sample, organism, etc.) being measured. OBOE is being used and developed within the Semtools project for describing a wide variety of ecological data stored within the Knowledge Network for Biodiversity (KNB) as well as extensions for ontology-based data annotation and discovery within the MetaCat software infrastructure.",
"homepage": "https://github.com/NCEAS/oboe/",
"license": "CC-BY-3.0",
"name": "OBOE: The Extensible Observation Ontology",
"repository": "https://github.com/NCEAS/oboe/issues",
"subjects": [
"Environmental Science",
"Ecology",
"Biodiversity"
],
"user_defined_tags": [
"Observations"
]
},
"FAIRsharing.5NhJFK": {
"abbreviation": "VGNC",
"description": "The VGNC approves both a short-form abbreviation known as a gene symbol, and also a longer and more descriptive name. Each symbol is unique and the committee ensures that each gene is only given one approved gene symbol. This allows for clear and unambiguous reference to genes in scientific communications, and facilitates electronic data retrieval from databases and publications.",
"homepage": "https://vertebrate.genenames.org/download/statistics-and-files/",
"name": "VGNC Gene Symbols, Gene Names and IDs",
"subjects": [
"Life Science"
]
},
"FAIRsharing.5a4y1y": {
"abbreviation": "ONTONEO",
"description": "The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby.",
"domains": [
"Electronic health record"
],
"homepage": "https://ontoneo.com/",
"name": "Obstetric and Neonatal Ontology",
"publications": [
{
"doi": "10.1002/asi.23900",
"title": "Ontologies for the representation of electronic medical records: The obstetric and neonatal ontology",
"year": 2017
}
],
"subjects": [
"Obstetrics"
]
},
"FAIRsharing.5anxc5": {
"abbreviation": "ALLERGYDETECTOR",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Allergen"
],
"homepage": "http://bioportal.bioontology.org/ontologies/ALLERGYDETECTOR",
"name": "Allergy Detector II",
"subjects": [
"Immunology"
]
},
"FAIRsharing.5bd3ef": {
"abbreviation": "USGS Thesaurus",
"description": "The United States Geological Survey Thesaurus (USGS Thesaurus) is a controlled vocabulary providing category terms for scientific information products generated by the U.S. Geological Survey. It is designed as a formal thesaurus conforming to ANSI/NISO Z39.19. The thesaurus is limited in depth and specificity of coverage. It does not attempt to replicate existing controlled vocabularies. The intention is to provide sufficient contextual cues for the information seeker to determine the relevance of a resource, not to precisely locate the answer to a specific user question.",
"homepage": "https://apps.usgs.gov/thesaurus/",
"name": "United States Geological Survey Thesaurus",
"subjects": [
"Engineering Science",
"Data Management",
"Natural Science"
]
},
"FAIRsharing.5c7cec": {
"abbreviation": "CESSDA Vocabulary",
"description": "CESSDA Vocabulary Service enables users to discover, browse, and download controlled vocabularies in a variety of languages. The service is provided by the Consortium of European Social Science Data Archives (CESSDA). The majority of the source (English) vocabularies included in the service have been created by the DDI Alliance. The Data Documentation Initiative (DDI) is an international standard for describing data produced by surveys and other observational methods in the social, behavioural, economic, and health sciences.",
"homepage": "https://vocabularies.cessda.eu/#!discover",
"name": "CESSDA Vocabulary",
"subjects": [
"Economics",
"Social Science",
"Public Health",
"Social and Behavioural Science"
],
"twitter": "CESSDA_Data"
},
"FAIRsharing.5cmtw3": {
"abbreviation": "MIRNAO",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "https://code.google.com/p/mirna-ontology/",
"name": "MicroRNA Ontology",
"subjects": [
"Genomics"
]
},
"FAIRsharing.5dnjs2": {
"abbreviation": "DUO",
"description": "The Data Use Ontology (DUO) describes data use requirements and limitations. DUO allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage. This resource is based on the OBO Foundry principles, and developed using the W3C Web Ontology Language. It is used in production by the European Genome-phenome Archive (EGA) at EMBL-EBI and CRG as well as the Broad Institute for the Data Use Oversight System (DUOS).",
"homepage": "https://raw.githubusercontent.com/EBISPOT/DUO/master/duo.owl",
"license": "CC-BY-3.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdmdCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--9a42083efa91d79ee5c7ed8e7868db0f7faf0b76/DUO_logo_white_background.png?disposition=inline",
"name": "The Data Use Ontology",
"publications": [
{
"doi": "10.1016/j.xgen.2021.100028",
"title": "The Data Use Ontology to streamline responsible access to human biomedical datasets",
"year": 2021
}
],
"repository": "https://github.com/EBISPOT/duo/issues",
"subjects": [
"Subject Agnostic",
"Biomedical Science"
],
"user_defined_tags": [
"Metadata standardization"
]
},
"FAIRsharing.5dvejq": {
"abbreviation": "TM-OTHER-FACTORS",
"description": "The value set for the Other Factors property of the International Classification of Traditional Medicine (ICTM). The World Health Organization, in consultation with a large group of stakeholders in the areas of Traditional Medicine or Complementary and Alternative Medicine and Health Information Systems, has developed a collaborative project plan to produce an international standard terminology and classification system for Traditional Medicine. This resource is part of an effort to produce an international standard for information on TM that is ready for electronic health records and that will serve as a standard for scientific comparability and communication.",
"homepage": "https://sites.google.com/site/whoictm/home",
"license": "https://creativecommons.org/licenses/by-nc-sa/3.0/igo",
"name": "Traditional Medicine Other Factors Value Set",
"subjects": [
"Traditional Medicine"
]
},
"FAIRsharing.5e52cd": {
"description": "A classification system for Science developed by the ERC (European Research Council) with the aim of characterising the research projects supported by ERC funding in 2021 and 2022. The contribution of Inist relates to the French translation of the headings and the creation of the RDF-SKOS version published on Loterre.",
"domains": [
"Classification"
],
"homepage": "https://skosmos.loterre.fr/ERC/en/",
"license": "CC-BY-4.0",
"name": "ERC Panel structure",
"subjects": [
"Engineering Science",
"Chemistry",
"Humanities and Social Science",
"Astrophysics and Astronomy",
"Earth Science",
"Mathematics",
"Life Science",
"Physics"
]
},
"FAIRsharing.5e5n7c": {
"abbreviation": "APAOCUEMPLOY",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/APAOCUEMPLOY",
"name": "APA Occupational and Employment cluster",
"subjects": [
"Humanities and Social Science"
]
},
"FAIRsharing.5hbs1x": {
"abbreviation": "MINI-FAST-1",
"description": "Record does not exist anymore: mini fast test. The record with identifier content 10.25504/FAIRsharing.5hbs1x was invalid.",
"homepage": "http://bioportal.bioontology.org/ontologies/MINI-FAST-1",
"name": "mini fast test"
},
"FAIRsharing.5k1aqq": {
"abbreviation": "ELIG",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Cancer"
],
"homepage": "http://bioportal.bioontology.org/ontologies/ELIG",
"name": "Eligibility Feature Hierarchy",
"subjects": [
"Medicine",
"Clinical Studies"
]
},
"FAIRsharing.5p12xh": {
"abbreviation": "OBCS",
"description": "The Ontology of Biological and Clinical Statistics (OBCS) is a biomedical ontology in the domain of biological and clinical statistics. OBCS is primarily targeted for statistical representation in the fields in biological, biomedical, and clinical domains. OBCS uses the Basic Formal Ontology (BFO) as the upper level ontology. OBCS imports all biostatistics related terms in the Ontology for Biomedical Investigations (OBI) including all logical axioms.",
"domains": [
"Vaccine"
],
"homepage": "https://github.com/obcs/obcs",
"license": "CC-BY-3.0",
"name": "Ontology of Biological and Clinical Statistics",
"publications": [
{
"doi": "10.1186/s13326-016-0100-2",
"pubmed": "27627881",
"title": "The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis",
"year": 2016
}
],
"repository": "https://github.com/obcs/obcs/issues",
"subjects": [
"Medicine",
"Statistics",
"Biomedical Science",
"Biology",
"Medical Informatics"
]
},
"FAIRsharing.5x3gnz": {
"abbreviation": "COSTART",
"description": "Coding Symbols for Thesaurus of Adverse Reaction Terms (COSTART). 5th ed. Rockville (MD). COSTART is used for coding, filing, and retrieving post-marketing adverse drug and biologic experience reports. COSTART is organized in body system and pathophysiology hierarchies, as well as a separate fetal/neonatal category of less than 20 terms. COSTART has been superseded by the Medical Dictionary for Regulatory Activities (MedDRA) Terminology.",
"domains": [
"Drug",
"Approved drug"
],
"homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/CST/",
"name": "Coding Symbols for a Thesaurus of Adverse Reaction Terms",
"subjects": [
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.5yn03x": {
"abbreviation": "ONL-DP",
"description": "This ontology is a module of the OntoNeuroLOG ontology, developed in the context of the NeuroLOG project, a french project supported by ANR (ANR-06-TLOG-024 grant) aiming at integrating distributed heterogeous resources in neuroimaging. If covers the domain of Datasets and the processing of datasets. It includes a detailed taxonomy of datasets in the area of neuroimaging (and especially MR imaging) as well as a taxonomy of medical image processing.",
"domains": [
"Bioimaging"
],
"homepage": "http://neurolog.unice.fr/ontoneurolog/v3.0/Documentation_OntoNeuroLOGv3.pdf",
"name": "Dataset processing",
"subjects": [
"Neurology"
]
},
"FAIRsharing.619eqr": {
"abbreviation": "CTX",
"contact": {
"email": "maria.taboada@usc.es",
"name": "Maria Taboada",
"orcid": "0000-0002-2353-596X"
},
"description": "The ontology represents CTX phenotypes, genetic variants, and bidirectional relationships between them though a patient model. The CTX ontology was build reusing the Human Phenotype Ontology (HPO) and the Snomed ct ontologies. A set of temporal clinical manifestations are semantically annotated with a domain phenotype ontology and registered with a time-stamped value.",
"domains": [
"Lipid",
"Phenotype",
"Disease",
"Brain"
],
"homepage": "http://bioportal.bioontology.org/ontologies/CTX",
"name": "Cerebrotendinous Xanthomatosis Ontology",
"publications": [
{
"doi": "10.1097/mol.0b013e328362df13",
"pubmed": "23759795",
"title": "Cerebrotendinous xanthomatosis",
"year": 2013
}
],
"subjects": [
"Genetics",
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.61b58c": {
"abbreviation": "HAL ID",
"description": "Identifier for an article in the HAL (Hyper Articles en Ligne) open access repository.",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://www.wikidata.org/wiki/Property:P7864",
"name": "Hyper Article en Ligne identifier",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.62qk8w": {
"abbreviation": "ChEBI",
"contact": {
"email": "venkat@ebi.ac.uk",
"name": "Venkat",
"orcid": "0000-0002-6850-9888"
},
"description": "Chemical Entities of Biological Interest (ChEBI) is a free dictionary that describes 'smallβ chemical compounds. These compound includes distinct synthetic or natural atoms, molecules, ions, ion pair, radicals, radical ions, complexes, conformers, etc.. These molecular entities can interact with or affect the processes of living organisms.",
"domains": [
"Molecular structure",
"Taxonomic classification",
"Molecular entity",
"Small molecule",
"Natural product"
],
"homepage": "http://www.ebi.ac.uk/chebi/",
"license": "CC-BY-4.0",
"name": "Chemical Entities of Biological Interest",
"publications": [
{
"doi": "10.1002/0471250953.bi1409s26",
"pubmed": "19496059",
"title": "ChEBI: an open bioinformatics and cheminformatics resource",
"year": 2009
},
{
"doi": "10.1093/nar/gkm791",
"pubmed": "17932057",
"title": "ChEBI: a database and ontology for chemical entities of biological interest",
"year": 2007
},
{
"doi": "10.1093/nar/gkv1031",
"pubmed": "26467479",
"title": "ChEBI in 2016: Improved services and an expanding collection of metabolites",
"year": 2015
},
{
"doi": "10.1093/nar/gkp886",
"pubmed": "19854951",
"title": "Chemical Entities of Biological Interest: an update",
"year": 2009
},
{
"doi": "10.1093/nar/gks1146",
"pubmed": "23180789",
"title": "The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013",
"year": 2012
}
],
"subjects": [
"Biochemistry",
"Chemistry"
],
"twitter": "chebit"
},
"FAIRsharing.63f902": {
"description": "The arXiv identifier provides a complete and unique citation for an arXiv article. ",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://info.arxiv.org/help/arxiv_identifier.html",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBZ29EIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--9e967b057f22cede612603c4dcf259c72dac5307/Capture%20d%E2%80%99e%CC%81cran%202023-10-04%20a%CC%80%2014.05.24.png?disposition=inline",
"name": "arXiv identifier",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.640fde": {
"description": "Identifier schema for EU Clinical Trial Register",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://registry.identifiers.org/registry/euclinicaltrials",
"name": "EU Clinical Trials Identifier",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.64f3va": {
"abbreviation": "PFO",
"description": "The Phenotype Fragment Ontology, together with a processing pipeline, enable the automatic decomposition and conceptualization of phenotype descriptions for the human skeletal phenome.",
"domains": [
"Phenotype"
],
"homepage": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3572876/",
"name": "Phenotype Fragment Ontology",
"publications": [
{
"doi": "10.4137/bii.s10729",
"pubmed": "23440304",
"title": "Decomposing phenotype descriptions for the human skeletal phenome",
"year": 2013
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.658tcg": {
"abbreviation": "OMOP Standardized Vocabularies",
"description": "The OMOP Standardized Vocabularies combine a number of different vocabularies that are used for different aspects of recording healthcare information. These different purposes cause the vocabularies to come with different formats, quality, comprehensiveness and coverage, and life cycle. Even though the content of the vocabularies are left intact, the new format and structural elements will result in a different representation of each vocabulary than its native form.",
"domains": [
"Data identity and mapping"
],
"homepage": "https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:sidebar",
"name": "Observational Medical Outcomes Partnership Standardized Vocabularies",
"publications": [
{
"doi": "10.1146/annurev-statistics-022513-115645",
"title": "A Systematic Statistical Approach to Evaluating Evidence from Observational Studies",
"year": 2014
}
],
"repository": "https://github.com/OHDSI/OMOP-Standardized-Vocabularies",
"subjects": [
"Medicine",
"Clinical Studies",
"Health Science",
"Preclinical Studies"
]
},
"FAIRsharing.65xkbs": {
"abbreviation": "VariO",
"description": "Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations. VariO allows unambiguous description of variation effects as well as computerized analyses over databases utilizing the ontology for annotation. VariO is a position specific ontology that can be used to describe effects of variations on DNA, RNA and/or proteins.",
"domains": [
"DNA structural variation",
"Deoxyribonucleic acid",
"Ribonucleic acid",
"Protein",
"Sequence variant"
],
"homepage": "http://variationontology.org",
"name": "Variation Ontology",
"publications": [
{
"doi": "10.1101/gr.157495.113",
"pubmed": "24162187",
"title": "Variation Ontology for annotation of variation effects and mechanisms",
"year": 2013
},
{
"doi": "10.1007/s00439-015-1529-6",
"pubmed": "25616435",
"title": "Types and effects of protein variations",
"year": 2015
},
{
"doi": "10.1186/2041-1480-5-9",
"pubmed": "24533660",
"title": "Variation ontology: annotator guide",
"year": 2014
},
{
"doi": "10.1002/humu.22954",
"pubmed": "26773573",
"title": "VariOtator, a Software Tool for Variation Annotation with the Variation Ontology",
"year": 2016
},
{
"doi": "10.1186/s12864-018-5262-0",
"pubmed": "30591019",
"title": "Systematics for types and effects of DNA variations",
"year": 2018
}
],
"subjects": [
"Genetics"
]
},
"FAIRsharing.6627e9": {
"abbreviation": "EMDN",
"description": "The European Medical Device Nomenclature (EMDN) is the nomenclature of use by manufacturers when registering their medical devices in the EUDAMED database.",
"homepage": "https://webgate.ec.europa.eu/dyna2/emdn/",
"license": "CC-BY-4.0",
"name": "European Medical Device Nomenclature",
"subjects": [
"Medicine"
],
"user_defined_tags": [
"medical devices"
]
},
"FAIRsharing.6641pb": {
"abbreviation": "OFPE",
"description": "OFPE is a generic ontology specialized for food processing experiments, where raw materials are transformed into ο¬nal products. It includes different classes that represent products and activities during food transformation processes, which can be classiο¬ed into four main concepts: Product, Operation, Attribute, and Observation. FAIRsharing is unable to contact the developers of this resource, and cannot find a project homepage. Therefore this record's status has been marked as Uncertain. Please get in touch if you have any information regarding this resource.",
"domains": [
"Food"
],
"homepage": "http://agroportal.lirmm.fr/ontologies/OFPE",
"license": "CC-BY-4.0",
"name": "Ontology for Food Processing Experiment",
"subjects": [
"Agricultural Engineering",
"Life Science",
"Nutritional Science"
]
},
"FAIRsharing.669cnk": {
"abbreviation": "MFMO",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://feedexp.org/",
"name": "Mammalian Feeding Muscle Ontology",
"subjects": [
"Anatomy"
]
},
"FAIRsharing.66q7yz": {
"abbreviation": "WSIO",
"description": "Web Service Interaction Ontology (WSIO) enables automated interaction with more complex Web services that are typical for example within life sciences. WSIO is however independent of the application domain and relevant for both SOAP and REST Web services, and for batch execution engines in general.",
"homepage": "http://wsio.org/",
"name": "Web-Service Interaction Ontology",
"subjects": [
"Computer Science",
"Subject Agnostic"
]
},
"FAIRsharing.67sssf": {
"abbreviation": "InterLex",
"description": "The InterLex terminology is a lexicon of biomedical terms built on the foundation of NeuroLex and contains all of the existing NeuroLex terms. The initial entries in NeuroLex were built from the NIFSTD ontologies and BIRNLex (Biomedical Informatics Research Network Project Lexicon). Final content review from NeuroLex is still ongoing.",
"domains": [
"Imaging",
"Brain"
],
"homepage": "https://scicrunch.org/scicrunch/interlex/dashboard",
"license": "CC-BY-3.0",
"name": "InterLex",
"publications": [
{
"doi": "10.3389/fninf.2013.00018",
"pubmed": "24009581",
"title": "NeuroLex.org: an online framework for neuroscience knowledge",
"year": 2013
}
],
"subjects": [
"Anatomy",
"Neurobiology",
"Biomedical Science"
]
},
"FAIRsharing.68thre": {
"abbreviation": "MEO",
"description": "An Ontology for organismal habitats (especially focused on microbes)",
"domains": [
"Metagenome"
],
"homepage": "https://bioportal.bioontology.org/ontologies/MEO",
"license": "CC-BY-4.0",
"name": "Metagenome/Microbes Environmental Ontology",
"subjects": [
"Genomics",
"Microbiology"
]
},
"FAIRsharing.69226e": {
"abbreviation": "HASSET",
"contact": {
"email": "matthew@essex.ac.uk",
"name": "Matthew Woollard",
"orcid": "0000-0002-1077-4312"
},
"description": "The Humanities and Social Science Electronic Thesaurus (HASSET) is the leading British English thesaurus for the social sciences. HASSET has been compiled at the UK Data Archive for over forty years. It was developed initially as an information retrieval tool to access data deposited in the UK Data Archive. Its scope has now expanded to cover the collections held by the UK Data Service.",
"homepage": "https://hasset.ukdataservice.ac.uk/",
"license": "https://creativecommons.org/licenses/by-nc-nd/4.0",
"name": "Humanities and Social Science Electronic Thesaurus",
"subjects": [
"Economics",
"Environmental Science",
"Demographics",
"Social Science",
"Health Science",
"Public Law",
"Biomedical Science",
"Political Science",
"Epidemiology",
"Communication Science"
],
"twitter": "UKDataService",
"user_defined_tags": [
"Sociology"
]
},
"FAIRsharing.69734m": {
"abbreviation": "MERA",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "https://edu.carre-project.eu",
"name": "Medical Educational Resource Aggregator",
"subjects": [
"Medicine"
]
},
"FAIRsharing.6a8d27": {
"abbreviation": "BCTEO",
"contact": {
"email": "federica.viti@itb.cnr.it",
"name": "Federica Viti",
"orcid": "0000-0002-9651-8896"
},
"description": "Ontology for the field of Tissue Engineering, especially bone and cartilage tissues.",
"domains": [
"Bone"
],
"homepage": "https://bioportal.bioontology.org/ontologies/BCTEO",
"license": "CC0-1.0",
"name": "Bone and Cartilage Tissue Engineering Ontology",
"publications": [
{
"doi": "10.1186/1471-2105-15-s1-s14",
"pubmed": "24564199",
"title": "Guidelines for managing data and processes in bone and cartilage tissue engineering",
"year": 2014
}
],
"subjects": [
"Bioengineering"
]
},
"FAIRsharing.6a97fa": {
"abbreviation": "CaLAThe",
"description": "The Cadastre and Land Administration Thesaurus (CaLAThe) is a thesaurus for the domain of cadastre and land administration. The domain regards the surveying and mapping of land, including the boundaries of land parcels, as performed by the profession of surveyors. From a public point of view, the domain provides the technical base for taxation of land and buildings, and for land use planning; from a private point of view, the domain supports security in ownership and other land-related rights. CaLAThe is hosted at the OGC Definitions Server.",
"homepage": "http://www.cadastralvocabulary.org/",
"license": "CC BY-SA 3.0",
"name": "Cadastre and Land Administration Thesaurus",
"subjects": [
"Urban Planning",
"Earth Science"
],
"user_defined_tags": [
"Survey"
]
},
"FAIRsharing.6ax9gn": {
"abbreviation": "REPO",
"contact": {
"email": "ina.hulsegge@wur.nl",
"name": "Ina Hulsegge",
"orcid": "0000-0002-7015-6540"
},
"description": "Ontology for livestock reproductive traits and phenotypes.",
"domains": [
"Phenotype"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1552",
"name": "Reproductive trait and phenotype ontology",
"publications": [
{
"doi": "10.2527/jas.2011-4251",
"pubmed": "22228038",
"title": "Contributions to an animal trait ontology",
"year": 2012
}
],
"subjects": [
"Life Science"
],
"user_defined_tags": [
"Livestock",
"Trait modelling data"
]
},
"FAIRsharing.6b77ac": {
"abbreviation": "ECTO",
"description": "The Environmental Conditions, Treatments, and Exposures Ontology (ECTO) is a species-agnostic ontology focused on exposure events that occur as a result of natural and experimental processes, such as diet, work, or research activities.",
"domains": [
"Diet",
"Exposure"
],
"homepage": "https://github.com/EnvironmentOntology/environmental-exposure-ontology",
"license": "CC0-1.0",
"name": "Environmental Conditions, Treatments, and exposures Ontology",
"publications": [
{
"doi": "10.1186/s13326-023-00283-x",
"pubmed": "36823605",
"title": "The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond",
"year": 2023
}
],
"subjects": [
"Environmental Science"
]
},
"FAIRsharing.6bc7h9": {
"abbreviation": "SO",
"contact": {
"email": "keilbeck@fruitfly.org",
"name": "Karen Eilbeck",
"orcid": "0000-0002-0831-6427"
},
"description": "SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. The Sequence Ontology is a set of terms and relationships used to describe the features and attributes of biological sequence. SO includes different kinds of features which can be located on the sequence.",
"domains": [
"Sequence annotation",
"Deoxyribonucleic acid",
"Ribonucleic acid",
"Sequence",
"Sequence feature",
"Gene",
"Genome"
],
"homepage": "http://www.sequenceontology.org/",
"license": "CC-BY-4.0",
"name": "Sequence Ontology",
"publications": [
{
"doi": "10.1186/gb-2010-11-8-r88",
"pubmed": "20796305",
"title": "A standard variation file format for human genome sequences",
"year": 2010
},
{
"doi": "10.1186/gb-2005-6-5-r44",
"pubmed": "15892872",
"title": "The Sequence Ontology: a tool for the unification of genome annotations",
"year": 2005
},
{
"doi": "10.1016/j.jbi.2010.03.002",
"pubmed": "20226267",
"title": "Evolution of the Sequence Ontology terms and relationships",
"year": 2010
}
],
"repository": "https://github.com/The-Sequence-Ontology/SO-Ontologies",
"subjects": [
"Bioinformatics",
"Life Science",
"Biology"
]
},
"FAIRsharing.6brn4p": {
"abbreviation": "IMGT Ontology",
"contact": {
"email": "Veronique.Giudicelli@igh.cnrs.fr",
"name": "VΓ©ronique Giudicelli",
"orcid": "0000-0002-2258-468X"
},
"description": "IMGT-ONTOLOGY provides a specific vocabulary of the terminology to be used in immunogenetics and immunoinformatics. The ontology allows for the standardization for immunogenetics data from genome, proteome, genetics, two-dimensional and three-dimensional structures.",
"domains": [
"Molecular structure",
"Proteome",
"Cellular component",
"Biological process",
"Immunoglobulin complex",
"Antibody",
"Structure"
],
"homepage": "https://www.imgt.org/download/IMGT-ONTOLOGY/",
"license": "https://creativecommons.org/licenses/by-nc-nd/4.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdU1DIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--8a182a30111a331dc7f589ae66886d77014f3d3b/logo2_IMGT.png?disposition=inline",
"name": "ImMunoGeneTics Ontology",
"publications": [
{
"doi": "10.3389/fgene.2012.00079",
"pubmed": "22654892",
"title": "IMGT-ONTOLOGY 2012",
"year": 2012
},
{
"doi": "10.1093/bioinformatics/15.12.1047",
"pubmed": "10745995",
"title": "Ontology for immunogenetics: the IMGT-ONTOLOGY",
"year": 2000
},
{
"doi": "10.3389/fimmu.2014.00022",
"pubmed": "24600447",
"title": "Immunoglobulin and T Cell Receptor Genes: IMGT((R)) and the Birth and Rise of Immunoinformatics",
"year": 2014
}
],
"subjects": [
"Informatics",
"Immunogenetics",
"Genetics",
"Immunology",
"Biomedical Science"
]
},
"FAIRsharing.6bxcr4": {
"abbreviation": "SNMI",
"description": "Cote, Roger A., editor. Systematized Nomenclature of Human and Veterinary Medicine: SNOMED International. Northfield (IL): College of American Pathologists; Schaumburg (IL): American Veterinary Medical Association, Version 3.5, 1998.",
"domains": [
"Drug interaction",
"Disease",
"Morphology"
],
"homepage": "http://bioportal.bioontology.org/ontologies/SNMI",
"name": "Systematized Nomenclature of Medicine, International Version",
"publications": [
{
"doi": "10.1002/hep.1840190535",
"title": "SNOMED International (systematized Nomenclature of Human and Veterinary Medicine). 3rd Ed",
"year": 1994
}
],
"repository": "https://github.com/IHTSDO",
"subjects": [
"Anatomy",
"Occupational Medicine",
"Pharmacology",
"Veterinary Medicine",
"Biomedical Science",
"Translational Medicine"
]
},
"FAIRsharing.6ca1c5": {
"abbreviation": "KTAO",
"contact": {
"email": "yongqunh@umich.edu",
"name": "Yongqun He",
"orcid": "0000-0001-9189-9661"
},
"description": "The Kidney Tissue Atlas Ontology (KTAO) is an ontology that integrates kidney-related cell types, cell states, locations, gene markers, disease, etc., and their relations. KTAO is developed to support the NIH-NIDDK-funded Kidney Precision Medicine Project (KPMP, http://kpmp.org). The KTAO development is also supported by the KPMP project. ",
"domains": [
"Kidney disease"
],
"homepage": "https://github.com/KPMP/KTAO",
"name": "Kidney Tissue Atlas Ontology",
"publications": [
{
"doi": "10.1126/sciadv.abn4965",
"title": "A reference tissue atlas for the human kidney",
"year": 2022
},
{
"doi": "10.1038/s41581-020-00335-w",
"title": "Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project",
"year": 2020
}
],
"subjects": [
"Clinical Studies",
"Nephrology",
"Biomedical Science",
"Omics",
"Translational Medicine"
]
},
"FAIRsharing.6ccbe6": {
"abbreviation": "XLMOD",
"contact": {
"email": "lutz.fischer@tu-berlin.de",
"name": "Lutz Fischer",
"orcid": "0000-0003-4978-0864"
},
"description": "The XLMOD ontology is a structured, controlled vocabulary for cross-linking reagents and cross-linker related post-translational modifications used in cross-linking mass spectrometry experiments and derivatization reagents for GC-MS. Developed by the HUPO Proteomics Standards Initiative (PSI).",
"domains": [
"Mass spectrum",
"Experimental measurement",
"Mass spectrometry assay"
],
"homepage": "https://github.com/HUPO-PSI/xlmod-CV",
"license": "CC-BY-3.0",
"name": "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary",
"repository": "https://github.com/HUPO-PSI/xlmod-CV",
"subjects": [
"Chemical Biology",
"Metabolomics",
"Omics"
]
},
"FAIRsharing.6dba71": {
"abbreviation": "GeoNames Ontology",
"description": "The GeoNames Ontology makes it possible to add geospatial semantic information to the Word Wide Web. It maps to the DB schema that is used by GeoNames data export.",
"domains": [
"Geographical location"
],
"homepage": "http://www.geonames.org/ontology/documentation.html",
"license": "CC-BY-4.0",
"name": "GeoNames Ontology",
"subjects": [
"Geography",
"Geoinformatics"
]
},
"FAIRsharing.6dfe9b": {
"abbreviation": "FiveStars",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Five Stars of Online Research Articles Ontology (FiveStars) is an ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/fivestars",
"license": "CC-BY-4.0",
"name": "Five Stars of Online Research Articles Ontology ",
"publications": [
{
"doi": "10.1045/january2012-shotton",
"title": "The Five Stars of Online Journal Articles - a Framework for Article Evaluation",
"year": 2012
}
],
"repository": "https://github.com/sparontologies/fivestars",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"FAIRsharing.6ehjqt": {
"abbreviation": "MATRROCK",
"description": "This resource is no longer available because its underlying source material does not exist.",
"homepage": "http://bioportal.bioontology.org/ontologies/MATRROCK",
"name": "Material Rock"
},
"FAIRsharing.6gs502": {
"abbreviation": "STUFF",
"description": "Multiple domain ontologies have various representations of types of stuff--also called matter, mass, or substance--such as milk, alcohol, and mud. This is modelled in a range of different ways that are not quite compatible with each other as they do not adhere to a single structured approach, at times not even within an ontology itself. The Stuff Ontology is a 'bridging' core ontology describing categories of stuff and formalised in OWL for purposes of implementability. It stands on its own, but there are also versions that link to the DOLCE and BFO foundational ontologies, and one with examples to illustrate classification of stuffs (among others, mayonnaise and gold). This then also resolves the main type of interoperability issues with stuffs in domain ontologies, thereby also contributing to better ontology quality.",
"domains": [
"Knowledge representation"
],
"homepage": "http://www.meteck.org/stuff.html",
"name": "Stuff Ontology",
"subjects": [
"Computer Science"
]
},
"FAIRsharing.6hna78": {
"abbreviation": "ExO",
"description": "Exposure Ontology (ExO) is designed to facilitate the centralization and integration of exposure data to inform understanding of environmental health. ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics.",
"domains": [
"Disease",
"Exposure"
],
"homepage": "https://github.com/CTDbase/exposure-ontology",
"license": "CC-BY-4.0",
"name": "Exposure Ontology",
"publications": [
{
"doi": "10.1021/es2033857",
"pubmed": "22324457",
"title": "Providing the missing link: the exposure science ontology ExO",
"year": 2012
}
],
"repository": "https://github.com/CTDbase/exposure-ontology",
"subjects": [
"Environmental Science",
"Epigenetics",
"Toxicology"
]
},
"FAIRsharing.6mck": {
"abbreviation": "CHEAR",
"description": "Children's health and wellbeing are influenced by interactions between environmental and genetic factors. NIEHS is establishing an infrastructure, the Children's Health Exposure Analysis Resource (CHEAR), to provide the extramural research community access to laboratory and data analyses that add or expand the inclusion of environmental exposures in children's health research. The goal of CHEAR is to provide tools so researchers can assess the full range of environmental exposures which may affect children's health. We anticipate that CHEAR will be used by children's health researchers conducting epidemiological or clinical studies that currently have limited consideration of environmental exposures, or those who have collected exposure data but seek more extensive analyses.",
"domains": [
"Exposure"
],
"homepage": "http://bioportal.bioontology.org/ontologies/CHEAR",
"name": "Children's Health Exposure Analysis Resource",
"subjects": [
"Genetics",
"Health Science",
"Pediatrics"
]
},
"FAIRsharing.6mmbzs": {
"abbreviation": "PLIO",
"description": "The protein--ligand interaction ontology (PLIO) was developed around three main concepts, namely target, ligand and interaction, and was enriched by adding synonyms, useful annotations and references. PLIO represents knowledge about the interaction of proteins and ligands (including drugs) and has a different scope and conceptual resolution than, for example, the molecular interaction ontology. An important feature of PLIO is that it links directly from an ontology framework describing proteinβligand interactions to the mathematical formulas relevant for the computation of some of the entities represented in the ontology.",
"domains": [
"Protein interaction",
"Ligand",
"Binding",
"Ligand binding domain binding",
"Protein"
],
"homepage": "https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads.html",
"name": "Protein-ligand interaction ontology",
"publications": [
{
"doi": "10.1093/bioinformatics/btr256",
"pubmed": "21546398",
"title": "PLIO: an ontology for formal description of protein-ligand interactions",
"year": 2011
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.6qd09b": {
"abbreviation": "PROCCHEMICAL",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/PROCCHEMICAL",
"name": "Chemical Process",
"subjects": [
"Chemistry"
]
},
"FAIRsharing.6s2sfz": {
"abbreviation": "BT",
"description": "A top-domain ontology that provides definitions for the foundational entities of biomedicine as a basic vocabulary to unambiguously describe facts in this domain. This ontology is no longer maintained, as it duplicated much of the content in other ontologies. Though not maintained, this ontology remains available for use. The currently maintained version is BioTopLite 2 (BTL2).",
"homepage": "http://biotopontology.github.io/",
"name": "BioTop",
"publications": [
{
"doi": "10.1093/bioinformatics/btp194",
"pubmed": "19478019",
"title": "Alignment of the UMLS semantic network with BioTop: methodology and assessment",
"year": 2009
}
],
"repository": "https://github.com/BioTopOntology/biotop",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.6t5q3m": {
"abbreviation": "ATMO",
"contact": {
"email": "ghislain.atemezing@gmail.com",
"name": "Ghislain Atemezing",
"orcid": "0000-0002-9553-8123"
},
"description": "African Traditional Medicine Ontology (ATMO) describes the actors' function (healer, fetishist or soothsayer); the different types of proposed process treatment, the symptom's roles and the disease consideration.",
"domains": [
"Disease process modeling"
],
"homepage": "http://ontohub.org/bioportal/ATMO///symbols?kind=Class",
"name": "African Traditional Medicine",
"publications": [
{
"doi": "10.1007/978-3-540-85863-8_39",
"title": "An Ontology for African Traditional Medicine",
"year": 2009
},
{
"doi": "10.4236/iim.2011.36030",
"title": "Towards a βDeepβ Ontology for African Traditional Medicine",
"year": 2011
}
],
"subjects": [
"Medicine",
"Traditional Medicine",
"Biomedical Science"
]
},
"FAIRsharing.6tgyxf": {
"abbreviation": "FBcv",
"contact": {
"email": "cp390@cam.ac.uk",
"name": "Clare Pilgrim",
"orcid": "0000-0002-1373-1705"
},
"description": "A structured controlled vocabulary developed and used by FlyBase, including the Drosophila phenotype ontology. It is used in annotation and classification of data related to Drosophila, including phenotypes and expression.",
"domains": [
"Expression data",
"Phenotype"
],
"homepage": "https://github.com/FlyBase/flybase-controlled-vocabulary",
"license": "CC-BY-4.0",
"name": "FlyBase Controlled Vocabulary",
"publications": [
{
"doi": "10.1186/2041-1480-4-30",
"pubmed": "24138933",
"title": "The Drosophila phenotype ontology",
"year": 2013
}
],
"repository": "https://github.com/FlyBase/flybase-controlled-vocabulary",
"subjects": [
"Life Science"
]
},
"FAIRsharing.6ttpnv": {
"abbreviation": "ZEA",
"description": "A structured controlled vocabulary for the anatomy of Zea mays.",
"homepage": "http://bioportal.bioontology.org/ontologies/1050",
"name": "Maize gross anatomy",
"subjects": [
"Anatomy",
"Life Science"
]
},
"FAIRsharing.6xfgaq": {
"abbreviation": "VIVO",
"description": "The VIVO Ontology provides a set of concepts to represent researchers and the full context in which they work. It is used as part of the VIVO project, which uses a collection of ontologies to represent scholarship.",
"domains": [
"Resource metadata",
"Protocol",
"Study design"
],
"homepage": "https://wiki.lyrasis.org/display/VIVODOC111x/Ontology+Reference",
"license": "CC-BY-4.0",
"name": "VIVO Ontology",
"subjects": [
"Natural Science"
],
"user_defined_tags": [
"Researcher data"
]
},
"FAIRsharing.6xq0ee": {
"abbreviation": "GO",
"contact": {
"email": "suzia@stanford.edu",
"name": "Suzi Aleksander",
"orcid": "0000-0001-6787-2901"
},
"description": "The Gene Ontology (GO) is a structured vocabulary for use by the research community for the annotation of genes, gene products and sequences. The GO defines concepts/classes used to describe gene function and relationships between these concepts.",
"domains": [
"Expression data",
"Gene Ontology enrichment",
"Annotation",
"Sequence annotation",
"Gene functional annotation",
"Molecular function",
"Cellular component",
"Biological process",
"Data model",
"Protein",
"Transcript",
"Gene",
"Knowledge representation",
"Biocuration"
],
"homepage": "http://www.geneontology.org",
"license": "CC-BY-4.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBY0k9IiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--17999ec75f811e894e6a645034077964b591019b/gologo.png?disposition=inline",
"name": "Gene Ontology",
"publications": [
{
"doi": "10.1093/nar/gky1055",
"pubmed": "30395331",
"title": "The Gene Ontology Resource: 20 years and still GOing strong",
"year": 2018
},
{
"doi": "10.1093/nar/gkr1028",
"pubmed": "22102568",
"title": "The Gene Ontology: enhancements for 2011",
"year": 2011
},
{
"doi": "10.1093/nar/gkp1018",
"pubmed": "19920128",
"title": "The Gene Ontology in 2010: extensions and refinements",
"year": 2009
},
{
"doi": "10.1093/nar/gku1179",
"pubmed": "25428369",
"title": "Gene Ontology Consortium: going forward",
"year": 2014
},
{
"doi": "10.1093/nar/gks1050",
"pubmed": "23161678",
"title": "Gene Ontology annotations and resources",
"year": 2012
},
{
"doi": "10.1038/75556",
"pubmed": "10802651",
"title": "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium",
"year": 2000
},
{
"doi": "10.1093/nar/gkh036",
"pubmed": "14681407",
"title": "The Gene Ontology (GO) database and informatics resource",
"year": 2003
},
{
"doi": "10.1186/1471-2164-14-513",
"pubmed": "23895341",
"title": "Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology",
"year": 2013
},
{
"doi": "10.1093/nar/gkaa1113",
"title": "The Gene Ontology resource: enriching a GOld mine",
"year": 2020
}
],
"subjects": [
"Life Science"
],
"twitter": "news4go"
},
"FAIRsharing.6xwdvb": {
"abbreviation": "ICECI",
"description": "The International Classification of External Causes of Injury (ICECI) was created to enable the classification of external causes of injuries. It is designed to help researchers and prevention practitioners to describe, measure and monitor the occurrence of injuries and to investigate their circumstances of occurrence using an internally agreed classification. Criteria underlying the classification are: a separate coding axis for each main concept, usefulness for injury prevention, useability in may types of settings (many parts of the world; emergency departments and other places where data are collected), comparability and complementarity with the ICD-10.",
"domains": [
"Electronic health record",
"Classification",
"Injury"
],
"homepage": "https://www.who.int/standards/classifications/other-classifications/international-classification-of-external-causes-of-injury",
"name": "International Classification of External Causes of Injury",
"subjects": [
"Primary Health Care",
"Biomedical Science"
]
},
"FAIRsharing.6yNXYK": {
"abbreviation": "PECO",
"description": "PECO is a structured, controlled vocabulary for the representation of plant experimental conditions. It describes the treatments, growing conditions, and/or study types used in various types of plant biology experiments.",
"domains": [
"Experimental measurement",
"Study design",
"Experimentally determined"
],
"homepage": "https://github.com/Planteome/plant-experimental-conditions-ontology",
"license": "CC-BY-4.0",
"name": "Plant Experimental Condition Ontology",
"publications": [
{
"doi": "10.1093/nar/gkx1152",
"pubmed": "29186578",
"title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics",
"year": 2017
}
],
"repository": "https://github.com/Planteome/plant-experimental-conditions-ontology/issues",
"subjects": [
"Botany"
],
"user_defined_tags": [
"Experimental condition"
]
},
"FAIRsharing.707262": {
"abbreviation": "UNBIS Thesaurus",
"description": "The UNBIS Thesaurus is a multilingual database of the controlled vocabulary used to describe UN documents and other materials in the Dag HammarskjΓΆld Library's collection. The UNBIS Thesaurus grows as new topics are introduced to the agenda of the Organization and evolves as the language in the UN documents shifts over time. Controlled vocabulary makes subject searches possible by identifying documents on the same concept, even as terminology changes. UNBIS Thesaurus terms are used in the UN Digital Library as well as other UN programmes, funds and regional commissions. These groups use the UNBIS Thesaurus for the description of bibliographic materials and web content. The UNBIS Thesaurus is available in the six official UN languages (Arabic, Chinese, English, French, Russian and Spanish).",
"domains": [
"Bibliography",
"Transport"
],
"homepage": "https://metadata.un.org/thesaurus/?lang=en",
"name": "UNBIS Thesaurus",
"subjects": [
"Economics",
"Fisheries Science",
"Environmental Science",
"Forest Management",
"Engineering Science",
"Geography",
"Education Science",
"Health Science",
"Global Health",
"Natural Science",
"Agriculture",
"Subject Agnostic",
"Political Science"
],
"user_defined_tags": [
"Employment",
"Humanitarian Studies",
"Trade"
]
},
"FAIRsharing.725a75": {
"abbreviation": "ThesoTM",
"description": "The ThesoTM (Thesaurus of Text Mining) thesaurus is a bilingual (French-English) terminology resource based on transformation into SKOS of an ontology of open source text mining tools. It contains more than 1,300 concepts with their definitions and possibly an associated bibliography.\n\nIt is based on the reuse of classes and properties from existing ontologies:\nβ’ BFO (Basic Formal Ontology): a high-level ontology, modeling the main categories of reality\nβ’ IAO (Information Artifact Ontology): a core ontology, modeling artifactual information entities\nβ’ SWO (Software Ontology): software modeling\nβ’ OMTD-Share (from the OpenMinTed project): modeling of automatic language processing tasks.\n\nNew classes and properties have been introduced where necessary. The following are documented for the various tools: languages and input data types; possible operating systems, underlying programming languages, user interfaces and tasks performed; design countries, licenses used and fields of application; and all useful access information: home page, repositories and download locations.",
"domains": [
"Text mining",
"Software"
],
"homepage": "https://skosmos.loterre.fr/LTK/en/",
"license": "CC-BY-4.0",
"name": "ThesoTM thesaurus",
"subjects": [
"Engineering Science",
"Computer Science"
],
"user_defined_tags": [
"Open Science",
"open source software"
]
},
"FAIRsharing.72b7ef": {
"description": "This is a semantic data model for the WHO's COVID-19 case record form RAPID version from April 8 2020. It aims at providing semantic references to the questions and answers of the form. The model maintains backward compatibility with the WHO COVID-19 Rapid CRF from March 23, 2020.",
"domains": [
"Electronic health record",
"Hospital"
],
"homepage": "https://bioportal.bioontology.org/ontologies/COVIDCRFRAPID",
"name": "WHO COVID-19 Rapid Version CRF semantic data model",
"subjects": [
"Clinical Studies",
"Primary Health Care"
],
"user_defined_tags": [
"COVID-19"
]
},
"FAIRsharing.73122f": {
"contact": {
"email": "linda.gregory@csiro.au",
"name": "Linda Gregory",
"orcid": "0000-0002-0693-1899"
},
"description": "Classifiers described in chapter 9 Substrate, by R.C. McDonald and R.F. Isbell, in Australian Soil and Land Survey Field Handbook (3rd edn)\n\nThis vocabulary deals with materials and masses of earth or rock that do not show pedological development. They are not soils, but typically underlie them.\n\nThe data was converted from the print representation to this linked-data form by Linda Gregory assisted by Simon J D Cox",
"domains": [
"Agroecosystem",
"Classification"
],
"homepage": "https://github.com/ANZSoilData/def-au-asls-substrate",
"license": "CC-BY-4.0",
"name": "ASLS Substrate classifiers",
"subjects": [
"Agroecology"
],
"user_defined_tags": [
"vegetation classification"
]
},
"FAIRsharing.737p4k": {
"abbreviation": "ISO-15926-2_2003",
"description": "This resource is no longer available because its underlying source material is not suitable for FAIRsharing: ISO-15926-2_2003_oil. The record with identifier content 10.25504/FAIRsharing.737p4k was invalid.",
"domains": [
"Data retrieval"
],
"homepage": "http://bioportal.bioontology.org/ontologies/ISO-15926-2_2003",
"name": "ISO-15926-2_2003_oil",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.73c2f5": {
"description": "Bilingual thesaurus (English-French) of more than 2500 inorganic compounds, classified by chemical elements and families of compounds. The compounds come from the controlled vocabulary used for indexing bibliographic references in the PASCAL database (1972-2015).",
"domains": [
"Chemical entity"
],
"homepage": "https://skosmos.loterre.fr/RVQ/en/",
"name": "Inorganic compounds",
"subjects": [
"Inorganic Molecular Chemistry",
"Chemistry",
"Solid-State Chemistry"
]
},
"FAIRsharing.741b75": {
"description": "Identifier schema for ClinicalTrials.gov",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://registry.identifiers.org/registry/clinicaltrials",
"name": "ClinicalTrials.gov Identifier",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.75r2zd": {
"abbreviation": "OCRe",
"contact": {
"email": "ida.sim@ucsf.edu",
"name": "Ida Sim",
"orcid": "0000-0002-1045-8459"
},
"description": "OCRe is an OWL ontology designed to support the systematic description of, and interoperable queries on, human studies and study elements. Please note that, while this ontology is available for use, it is currently not being actively developed.",
"domains": [
"Treatment"
],
"homepage": "https://sites.google.com/site/humanstudyome/home/ocre",
"name": "Ontology of Clinical Research",
"subjects": [
"Life Science",
"Biomedical Science",
"Preclinical Studies"
],
"user_defined_tags": [
"Interoperability"
]
},
"FAIRsharing.75rf2e": {
"abbreviation": "NCCO",
"description": "Nursing Care Coordination Ontology contains activities that nurses use while coordinating care among patients.",
"domains": [
"Nurse"
],
"homepage": "http://bioportal.bioontology.org/ontologies/NCCO",
"name": "Nursing Care Coordination Ontology",
"subjects": [
"Medicine"
]
},
"FAIRsharing.766499": {
"abbreviation": "Microsoft Academic ID",
"description": "Identifier for an object or topic in the Microsoft Academic Graph",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://www.wikidata.org/wiki/Property:P6366",
"name": "Microsoft Academic Graph Identifier",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.778n2k": {
"abbreviation": "MRO",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/MRO",
"name": "Defen",
"subjects": [
"Social Science",
"Political Science"
],
"user_defined_tags": [
"Defence and intelligence"
]
},
"FAIRsharing.77jqpc": {
"abbreviation": "APADISORDERS",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/APADISORDERS",
"name": "Disorders cluster",
"subjects": [
"Psychiatry"
]
},
"FAIRsharing.77v8xn": {
"abbreviation": "CANONT",
"description": "Providing an upper-level ontology for cancer.",
"domains": [
"Cancer"
],
"homepage": "http://bioportal.bioontology.org/ontologies/CANONT",
"name": "Upper-Level Cancer Ontology",
"subjects": [
"Oncology"
]
},
"FAIRsharing.7e0974": {
"abbreviation": "OMIABIS",
"description": "OMIABIS is an open-source ontology of biobank administration. OMIABIS stands for Ontologized MIABIS where MIABIS is the Minimum Information About BIobank data Sharing.",
"domains": [
"Biobank"
],
"homepage": "https://github.com/OMIABIS/omiabis-dev",
"name": "Ontologized MIABIS",
"subjects": [
"Health Science"
]
},
"FAIRsharing.7e4ddf": {
"contact": {
"email": "blepori@usi.ch",
"name": "Benadetto Lepori",
"orcid": "0000-0002-4178-4687"
},
"description": "OrgReg, short for 'Organizational Register', is a central infrastructure within the Research Infrastructure for Science and Innovation Studies (RISIS). Its primary role is to establish a comprehensive and distinctive list of organizations involved in the research and higher education system, including higher education institutions, public research organizations, research hospitals, public administration entities, and private non-profit organizations. By assigning a unique identifier to each organization based on its organizational identity, the register enables temporal tracking and consistent identification, promoting interoperability with other datasets within RISIS and links with external data sources on the Internet. Additionally, OrgReg integrates indicators of research output through its connection with the KNOWMAK database, providing a regional perspective through EUROSTAT's NUTS classification. These identifiers are meant to uniquely identify organizations included in the register across time. This also implies that, when an organization ceases to exist, the corresponding code is not reassigned. ID will have the following format: ISO-Country code + 4 digits numeric (e.g. FR0001). A specific code INT is included to track supranational organizations, including international organizations based on treaties, CERN (PRO) or the UN system agencies, as well as those organizations which are directly part of the European Union structure, like the Joint Research Center or the European Research Council.",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://doi.org/10.5281/zenodo.6396703",
"name": "OrgReg Identifier",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.7e9cff": {
"abbreviation": "CO_343",
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Yam Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_343:ROOT",
"license": "CC-BY-4.0",
"name": "Yam Ontology",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.7f1646": {
"abbreviation": "Climate change",
"description": "\nThis thesaurus is dedicated to the field of \"Climate Change\", one of the six Societal Challenges defined in the Contract of Objectives and Performance 2019-2023 signed by the CNRS with the French Government. It was developed on the basis of terminological extractions from a corpus of scientific articles written in French and English, and by mining of IPCC reports. It therefore considers climate change from two complementary perspectives: scientific research dedicated to climate knowledge and the societal or political aspects of climate change. It is mapped to the Environment and sustainable development published on TerMef, to the GEMET and EnvThes thesauri and to Wikipedia.",
"domains": [
"Climate"
],
"homepage": "https://skosmos.loterre.fr/CHC/en/",
"license": "CC-BY-4.0",
"name": "Climate change thesaurus",
"subjects": [
"Meteorology",
"Ecology"
],
"user_defined_tags": [
"Climate change",
"Paleoclimatology"
]
},
"FAIRsharing.7f5f06": {
"abbreviation": "UTN",
"description": "As part of the WHO Registry Criteria for linking related records on the ICTRP Search Portal, the WHO Universal Trial Number (UTN) is assigned to unambiguously identify a trial, even though it may have multiple registration records (that is, the trial may appear on more than one registry database). WHO UTN assignments are obtained early in the history of the trial, and help to uniquely identify clinical trials registered in WHO Primary Registries, of which are displayed on the WHO International Clinical Trials Registry Platform's (ICTRP) through the search portal.",
"domains": [
"Centrally registered identifier",
"Protocol"
],
"homepage": "https://www.who.int/clinical-trials-registry-platform/unambiguous-trial-identification/the-universal-trial-number-(utn)",
"name": "Universal Trial Number",
"subjects": [
"Clinical Studies",
"Global Health"
]
},
"FAIRsharing.7hxvhz": {
"abbreviation": "DIKB-Evidence",
"description": "An evidence taxonomy for pharmacologic studies that, when combined with a set of inclusion criteria, enable drug experts to specify what their confidence in a drug mechanism assertion would be if it were supported by a specific set of evidence.",
"domains": [
"Evidence",
"Drug interaction"
],
"homepage": "https://dikb.org/",
"license": "CC BY-NC-SA 3.0",
"name": "Drug Interaction Knowledge Base Evidence Ontology",
"publications": [
{
"doi": "10.1016/j.jbi.2009.05.001",
"pubmed": "19435613",
"title": "Computing with evidence Part I: A drug-mechanism evidence taxonomy oriented toward confidence assignment",
"year": 2009
},
{
"doi": "10.1016/j.jbi.2015.04.006",
"pubmed": "25917055",
"title": "Toward a complete dataset of drug-drug interaction information from publicly available sources",
"year": 2015
}
],
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.7k29h0": {
"abbreviation": "HORD",
"description": "This ontology describes the bio-psico-social state of a person of rare diseses in a holistic way. It considers several contents such as disease, psychological, social, environmental state of the person.",
"domains": [
"Rare disease"
],
"homepage": "https://sites.google.com/site/laiasubirats",
"name": "Holistic Ontology of Rare Diseases",
"subjects": [
"Primary Health Care"
]
},
"FAIRsharing.7ky72t": {
"abbreviation": "NatPrO",
"contact": {
"email": "batistar@cs.man.ac.uk",
"name": "Riza Theresa Batista-Navarro",
"orcid": "0000-0001-6693-7531"
},
"description": "An ontology for describing biological activities of natural products.",
"homepage": "http://bioportal.bioontology.org/ontologies/3004",
"name": "Natural Products Ontology",
"subjects": [
"Environmental Science",
"Life Science"
]
},
"FAIRsharing.7m85ax": {
"abbreviation": "TRAK",
"description": "TRAK (Taxonomy for RehAbilitation of Knee conditions) is an ontology that formally models information relevant for the rehabilitation of knee conditions. TRAK provides the framework that can be used to collect coded data in sufficient detail to support epidemiologic studies so that the most effective treatment components can be identified, new interventions developed and the quality of future randomized control trials improved to incorporate a control intervention that is well defined and reflects clinical practice.",
"homepage": "http://www.cs.cf.ac.uk/trak",
"name": "Taxonomy for Rehabilitation of Knee Conditions",
"publications": [
{
"doi": "10.1016/j.jbi.2013.04.009",
"pubmed": "23665300",
"title": "TRAK ontology: defining standard care for the rehabilitation of knee conditions",
"year": 2013
},
{
"doi": "10.1186/s13326-015-0033-1",
"pubmed": "26347806",
"title": "KneeTex: an ontology-driven system for information extraction from MRI reports",
"year": 2015
},
{
"doi": "10.2196/resprot.4091",
"pubmed": "26474643",
"title": "TRAK App Suite: A Web-Based Intervention for Delivering Standard Care for the Rehabilitation of Knee Conditions",
"year": 2015
}
],
"subjects": [
"Anatomy",
"Biomedical Science",
"Pain Medicine",
"Pathology"
],
"user_defined_tags": [
"Rehabilitation Medicine"
]
},
"FAIRsharing.7p0xdg": {
"abbreviation": "DSEO",
"description": "Simple SKOS Taxonomy denoting subfields of study in data science for use in educational applications.",
"homepage": "http://bigdatau.org/about_erudite",
"name": "Data Science Education Ontology",
"subjects": [
"Knowledge and Information Systems",
"Education Science"
],
"user_defined_tags": [
"data science"
]
},
"FAIRsharing.7rmkwr": {
"abbreviation": "ONTOLURGENCES",
"description": "OntolUrgences is a termino-ontological resource developed to index and retrieve information in electronic Emergency Medical Record.",
"homepage": "https://bioportal.bioontology.org/ontologies/ONTOLURGENCES",
"name": "Emergency care ontology",
"publications": [
{
"pubmed": "25160343",
"title": "Describing localized diseases in medical ontology: an FMA-based algorithm",
"year": 2014
}
],
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.7rngj0": {
"abbreviation": "ICF",
"description": "The International Classification of Functioning, Disability and Health (ICF) is a classification of health and health-related domains. As the functioning and disability of an individual occurs in a context, ICF also includes a list of environmental factors. ICF is the WHO framework for measuring health and disability at both individual and population levels. ICF was officially endorsed by all 191 WHO Member States in the Fifty-fourth World Health Assembly on 22 May 2001 (resolution WHA 54.21) as the international standard to describe and measure health and disability.",
"domains": [
"Electronic health record"
],
"homepage": "https://www.who.int/standards/classifications/international-classification-of-functioning-disability-and-health",
"license": "https://creativecommons.org/licenses/by-nc-sa/3.0/igo",
"name": "International Classification of Functioning, Disability and Health",
"subjects": [
"Medicine",
"Health Science",
"Primary Health Care",
"Biomedical Science"
]
},
"FAIRsharing.7s74s8": {
"abbreviation": "SDO",
"contact": {
"email": "sivaram.arabandi@gmail.com",
"name": "Sivaram Arabandi",
"orcid": "0000-0002-2973-6228"
},
"description": "An application ontology for the domain of Sleep Medicine.",
"domains": [
"Sleep",
"Phenotype",
"Disease"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1651",
"name": "Sleep Domain Ontology",
"subjects": [
"Neurobiology",
"Health Science",
"Biomedical Science"
]
},
"FAIRsharing.7y955w": {
"abbreviation": "GO-EXT",
"description": "Gene Ontology Extension",
"domains": [
"Expression data",
"Gene Ontology enrichment",
"Annotation",
"Sequence annotation",
"Gene functional annotation",
"Molecular function",
"Cellular component",
"Biological process",
"Data model",
"Protein",
"Transcript",
"Gene",
"Knowledge representation",
"Biocuration"
],
"homepage": "http://www.geneontology.org",
"name": "Gene Ontology Extension",
"subjects": [
"Life Science"
]
},
"FAIRsharing.7zxrs6": {
"abbreviation": "EHDAA2",
"description": "The EHDAA2 ontology is a human developmental anatomy covering the first 49 days [Carnegie stages (CS)1β20], primarily structured around the parts of organ systems and their development. The ontology includes more than 2000 anatomical entities (AEs) that range from the whole embryo, through organ systems and organ parts down to simple or leaf tissues (groups of cells with the same morphological phenotype), as well as features such as cavities. It represents a complete rebuilding of the EHDA intended to meet current standards. The intention has been to include as much information about human developmental anatomy as is practical and as is available in the literature.",
"domains": [
"Animal organ development",
"Life cycle stage"
],
"homepage": "http://bioportal.bioontology.org/ontologies/EHDAA2",
"name": "Edinburgh human developmental anatomy abstract version 2",
"publications": [
{
"doi": "10.1111/j.1469-7580.2012.01566.x",
"pubmed": "22973865",
"title": "A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20)",
"year": 2012
}
],
"subjects": [
"Anatomy",
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.80d8cg": {
"abbreviation": "EXACT",
"description": "EXACT aims to explicitly define the semantics of experimental protocols in order to ensure their reproducibility, and to support computer applications that assist biologists in the preparation, maintenance, submission and sharing of experimental protocols.",
"domains": [
"Experimental measurement",
"Protocol",
"Study design"
],
"homepage": "https://github.com/larisa-soldatova/EXACT",
"name": "An ontology for experimental actions",
"publications": [
{
"doi": "10.1093/bioinformatics/btn156",
"title": "The EXACT description of biomedical protocols",
"year": 2008
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.81amet": {
"abbreviation": "ADALAB-META",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/ADALAB-META",
"name": "AdaLab-meta ontology",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.81dc5f": {
"abbreviation": "UNESCO Thesaurus",
"description": "The UNESCO Thesaurus is a controlled and structured list of concepts used in subject analysis and retrieval of documents and publications in the fields of education, culture, natural sciences, social and human sciences, communication and information. Continuously enriched and updated, its multidisciplinary terminology reflects the evolution of UNESCO's programmes and activities. It is available in English, French, Spanish, Russian, and Arabic.",
"domains": [
"Report",
"Publication"
],
"homepage": "http://vocabularies.unesco.org",
"license": "https://creativecommons.org/licenses/by-sa/3.0/igo",
"name": "UNESCO Thesaurus",
"subjects": [
"Culture",
"Education Science",
"Subject Agnostic",
"Political Science",
"Communication Science"
]
},
"FAIRsharing.82n9jp": {
"abbreviation": "ECP",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://iris.med.duth.gr/research/ecp/ontology",
"name": "Electronic Care Plan",
"subjects": [
"Life Science"
]
},
"FAIRsharing.82t0w2": {
"abbreviation": "LSM",
"description": "An ontology of CD markers for lymphocyte classification in the cell ontology, and other categories of surface and secreted proteins useful for discriminating between lymphocyte subsets by flow cytometry, ELISPOT, ELISA and other assays typically used for phenotypic identification of individual lymphocytes or lymphocyte populations have been included.",
"homepage": "http://bioportal.bioontology.org/ontologies/1520",
"name": "Leukocyte Surface Markers",
"subjects": [
"Life Science"
]
},
"FAIRsharing.8337e2": {
"abbreviation": "GND",
"description": "The Integrated Authority File (GND) is a service facilitating the collaborative use and administration of authority data. These authority data represent and describe entities, i.e. persons, corporate bodies, conferences and events, geographic entities, topics and works relating to cultural and academic collections. Libraries in particular use the GND to catalogue publications. However, archives, museums, cultural and academic institutions, and researchers involved in research projects are also increasingly working with the GND. Authority data make cataloguing easier, offer definitive search entries and forge links between different information resources. Every entity in the GND features a unique and stable identifier (GND ID). This makes it possible to link the authority data with both each other and external data sets and web resources. This results in a cross-organisational, machine-readable data network.",
"domains": [
"Publication"
],
"homepage": "https://www.dnb.de/EN/Professionell/Standardisierung/GND/gnd_node.html",
"license": "CC0-1.0",
"name": "Integrated Authority File",
"subjects": [
"Knowledge and Information Systems",
"Culture",
"Social Science"
],
"twitter": "gndnet"
},
"FAIRsharing.83ded0": {
"abbreviation": "ePIC Identifier",
"contact": {
"email": "ulrich.schwardmann@gwdg.de",
"name": "Ulrich Schwardmann (GWDG)",
"orcid": "0000-0001-6337-8674"
},
"description": "ePIC is to set up and maintain a reliable joint service for registering, storing and resolving persistent identifiers based on handles for the research community. ePIC was founded in 2009 by a consortium of European partners in order to provide PID services for the European Research Community, based on the handle system, for the allocation and resolution of persistent identifiers. The consortium signed a Memorandum of Understanding aiming to provide long term reliability for the PID services. Meanwhile ePIC is also an international consortium and open to partners from the research community worldwide.",
"domains": [
"Resource metadata",
"Data retrieval",
"Web service"
],
"homepage": "https://doc.pidconsortium.net/docs/generate",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBZWs9IiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--a5a2f1d8312aa3f747d81df9779634ceb2c0ee24/ePIC-head.png?disposition=inline",
"name": "Persistent Identifier Consortium for eResearch",
"subjects": [
"Subject Agnostic"
],
"user_defined_tags": [
"Document metadata",
"Metadata standardization"
]
},
"FAIRsharing.8532n8": {
"abbreviation": "DermLex",
"description": "DermLex: The Dermatology Lexicon standardized terminology of dermatologic diagnoses, therapies, procedures, and laboratory tests.",
"domains": [
"Patient care",
"Disease"
],
"homepage": "https://www.aad.org/dermlex/Default.aspx",
"name": "DermLex: The Dermatology Lexicon",
"subjects": [
"Medicine",
"Health Science",
"Dermatology",
"Biomedical Science"
]
},
"FAIRsharing.85k1jm": {
"abbreviation": "ICD-10-PCS",
"description": "The ICD-10 Procedure Coding System (ICD-10-PCS) is an international system of medical classification used for procedural coding. The ICD-10-PCS is a procedure classification published by the United States for classifying procedures performed in hospital inpatient health care settings. The ICD-10-PCS replaces the procedural coding portion (Volume 3) of ICD-9-CM.",
"domains": [
"Electronic health record",
"Hospital",
"Disease",
"Diagnosis",
"Classification",
"Morbidity"
],
"homepage": "https://www.cms.gov/Medicare/Coding/ICD10/2020-ICD-10-PCS",
"name": "International Classification of Diseases Version 10 - Procedure Coding System",
"subjects": [
"Health Science",
"Biomedical Science",
"Epidemiology"
]
},
"FAIRsharing.88246d": {
"description": "Controlled vocabulary used for indexing bibliographical records for the \"History of Science and Technology\" FRANCIS database (1972 to 2015, https://pascal-francis.inist.fr/). This resource contains 3757 terminological entries grouped into 117 collections. ",
"homepage": "https://skosmos.loterre.fr/XD4/en/",
"license": "CC-BY-4.0",
"name": "History of Science and Technology",
"subjects": [
"History of Science",
"History"
]
},
"FAIRsharing.89e853": {
"abbreviation": "ITO",
"contact": {
"email": "matthias.samwald@meduniwien.ac.at",
"name": "Matthias Samwald",
"orcid": "0000-0002-4855-2571"
},
"description": "The Intelligence Task Ontology and Knowledge Graph (ITO) provides comprehensive, curated and interlinked data of artificial intelligence tasks, benchmarks, AI performance metrics, benchmark results and research papers. ITO ontology aims to support 1) Manual curation of AI task classification hierarchies and performance metrics, enabling more precise analyses; 2) Representing data as a graph, facilitating network-based query and analysis; 3) Allowing for easy integration and enrichment with external data, as well as simple extensibility for modeling related knowledge domains from other domains; 4) Allowing for automated deductive inference and automated knowledge base consistency checking; 5) Allowing for ongoing, collaborative expert curation of underlying ontological models. ITO aims to enable precise and network-based analyses of the global landscape of AI tasks and capabilities based on technologies that allow for easy integration and enrichment with external data, automated inference and continuous, collaborative expert curation of underlying ontological models. ",
"domains": [
"Natural language processing",
"Machine learning"
],
"homepage": "https://github.com/OpenBioLink/ITO",
"license": "CC-BY-4.0",
"name": "Intelligence Task Ontology and Knowledge Graph",
"publications": [
{
"doi": "10.48550/arxiv.2110.01434",
"title": "A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks",
"year": 2021
},
{
"doi": "10.1038/s41597-022-01435-x",
"title": "A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks",
"year": 2022
},
{
"doi": "10.5281/zenodo.5561989",
"title": "Intelligence Task Ontology and Knowledge Graph (ITO)",
"year": 2022
}
],
"subjects": [
"Artificial Intelligence"
]
},
"FAIRsharing.89qcm2": {
"abbreviation": "NIF_GrossAnatomy",
"description": "The \"Neuroscience Information Framework Gross Anatomy\" was developed as part of the NIF Standard Ontologies. It extended NeuroNames by including terms from BIRNLex, SumsDB, BrainMap.org, etc.; for multi-scale\nrepresentation of the nervous system and macroscopic anatomy. For more information, see the article \"Development and use of Ontologies Inside the Neuroscience Information Framework: A Practical Approach\" \nFT Imam et al, Front Genet 2012 Jun 22; 3:111. doi: 10.3389/fgene.2012.00111. eCollection 2012 https://pubmed.ncbi.nlm.nih.gov/22737162/",
"homepage": "http://purl.bioontology.org/ontology/nif",
"name": "Neuroscience Information Framework Gross Anatomy",
"subjects": [
"Anatomy",
"Life Science",
"Neuroscience"
]
},
"FAIRsharing.8DrzMv": {
"description": "Controlled vocabulary used for indexing bibliographical records for the \"Sociology\" FRANCIS database (1972-2015). It consists of 5275 entries in 2 languages (English, French).",
"homepage": "https://www.loterre.fr/skosmos/3JP/en/",
"license": "CC-BY-4.0",
"name": "Sociology Vocabulary",
"subjects": [
"Sociological Theory",
"Humanities and Social Science"
],
"user_defined_tags": [
"Sociology"
]
},
"FAIRsharing.8a7a0w": {
"abbreviation": "vHOG",
"description": "vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. A mapping to species-specific anatomical ontologies is also provided. This mapping represents homology-strict relationships, in the sense of HOM:0000007 historical homology. Each mapping has been manually reviewed, and we provide confidence codes and references when available.",
"domains": [
"Homologous",
"Organ",
"Life cycle stage"
],
"homepage": "http://bioportal.bioontology.org/ontologies/VHOG?p=summary",
"name": "verteberate Homologous Organ Groups",
"publications": [
{
"doi": "10.1186/2041-1480-5-21",
"pubmed": "25009735",
"title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon",
"year": 2014
},
{
"doi": "10.1093/bioinformatics/bts048",
"pubmed": "22285560",
"title": "vHOG, a multispecies vertebrate ontology of homologous organs groups",
"year": 2012
}
],
"subjects": [
"Anatomy",
"Developmental Biology",
"Life Science"
]
},
"FAIRsharing.8ajxrw": {
"abbreviation": "neuDIGs",
"description": "Neuroscience Domain Insight Graphs (neuDIGs) was created to serve the needs of systems-level neuroscience: an advanced, complex scientific subject. The goal is to provide a large-scale, practical, common representation for neuroscientific knowledge that is primarily concerned with properties and characteristics of neuron populations that may (or may not) be explicitly identified by name.",
"domains": [
"Neuron"
],
"homepage": "https://github.com/SciKnowEngine/SciDIG",
"name": "Neuroscience Domain Insight Graphs",
"repository": "http://usc-isi-i2.github.io/dig/",
"subjects": [
"Life Science",
"Biomedical Science",
"Neuroscience"
]
},
"FAIRsharing.8b6wfq": {
"abbreviation": "DOID",
"contact": {
"email": "lynn.schriml@gmail.com",
"name": "Lynn Schriml",
"orcid": "0000-0001-8910-9851"
},
"description": "The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics, underlying mechanisms and related medical vocabulary disease concepts.",
"domains": [
"Disease process modeling",
"Infection",
"Disease phenotype",
"Disease",
"Classification",
"Genetic disorder",
"Mental health"
],
"homepage": "http://www.disease-ontology.org",
"license": "CC0-1.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBWkU9IiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--cfd1eca9383fe170c6035a80aa48bff273f7607c/DO_blue_logo.png?disposition=inline",
"name": "Disease Ontology",
"publications": [
{
"doi": "10.1093/nar/gkr972",
"pubmed": "22080554",
"title": "Disease Ontology: a backbone for disease semantic integration",
"year": 2011
},
{
"doi": "10.1093/database/baw015",
"pubmed": "26989148",
"title": "Wikidata as a semantic framework for the Gene Wiki initiative",
"year": 2016
},
{
"doi": "10.1093/nar/gku1011",
"pubmed": "25348409",
"title": "Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data",
"year": 2014
},
{
"doi": "10.1093/bioinformatics/btp193",
"pubmed": "19478018",
"title": "From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations",
"year": 2009
},
{
"doi": "10.1093/nar/gkab1063",
"pubmed": "34755882",
"title": "The Human Disease Ontology 2022 update",
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{
"doi": "10.1093/nar/gky1032",
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{
"doi": "10.1242/dmm.032839",
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{
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{
"doi": "10.1093/database/bav032",
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{
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{
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"title": "COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model",
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{
"doi": "10.7554/elife.52614",
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{
"doi": "10.1093/nar/gky1036",
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"title": "ECO, the Evidence & Conclusion Ontology: community standard for evidence information",
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{
"doi": "10.1016/j.ajhg.2015.05.020",
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"title": "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease",
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{
"doi": "10.1093/nar/gkad1051",
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"title": "The DO-KB Knowledgebase: a 20-year journey developing the disease open science ecosystem",
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"description": "Identifier schema for Ensembl",
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{
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"abbreviation": "AIO",
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"email": "MJoachimiak@lbl.gov",
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"description": "The Artificial Intelligence Ontology (AIO) is a systematized collection of terms covering artificial intelligence (AI) concepts, methodologies, and interrelations aimed to address the rapidly evolving landscape of AI terminolgy by providing a comprehensive framework that encompasses both technical and ethical aspects of AI technologies. The primary audience for this collection includes AI researchers, developers, and educators seeking to standardize terminology and concepts within the AI domain.",
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"Machine learning",
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"abbreviation": "BODC PUV",
"description": "The British Oceanographic Data Centre Parameter Usage Vocabulary (BODC PUV) is a controlled vocabulary for labelling variables in databases and data files in oceanography and related domains. It is a collection of unique and persistent identifiers attached to structurally logical labels and textual definitions. This vocabulary is also frequently referred to as the PO1 PUV.",
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"abbreviation": "NIGO",
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"description": "The Neural-Immune Gene Ontology (NIGO) is a subset of GO directed for neurological and immunological systems. NIGO was created by clipping those GO terms that are not associated to any gene in human, rat and mouse, and by clipping terms not found to be relevant to the neural and/or immune domains.",
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"abbreviation": "EMAP",
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{
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{
"doi": "10.1016/s0925-4773(98)00069-0",
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"abbreviation": "BCO",
"description": "The Biological Collections Ontology (BCO) supports the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. The BCO covers distinctions between individuals, organisms, voucher specimens, lots, samples, the relations between these entities, and the processes governing the creation and use of \"samples\". Also within scope are properties including collector, location, time, storage environment, containers, institution, and collection identifiers.",
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"abbreviation": "MSO",
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"homepage": "http://www.scai.fraunhofer.de/de/geschaeftsfelder/bioinformatik/downloads.html",
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"abbreviation": "NDDF",
"description": "The National Drug Data File vocabulary supports clinical research and patient care. Please note that we have been unable to confirm the current status of NDDF and its relationship with FDB MedKnowledge. Until that time, the FAIRsharing team has marked this resource as having an Uncertain status. Please get in touch if you have any information.",
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"abbreviation": "TDWGSPEC",
"description": "The TDWG Specimen LSID Ontology was designed to represent records of specimens, and contain information specific to the specimen. Biodiversity Information Standards (TDWG) is an international not-for-profit group that develops standards and protocols for sharing biodiversity data. They have a detailed collection of vocabularies and ontologies for studies of biological organisms.",
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"abbreviation": "VICO",
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"description": "The Vaccination Informed Consent Ontology (VICO) is a community-driven ontology in the domain of vaccination/immunization informed consent. It extends the Informed Consent Ontology and integrates related OBO foundry ontologies, such as the Vaccine Ontology, with a focus on vaccination screening questionnaires in the vaccination informed consent domain. VICO could support a platform for vaccination informed consent data standardization, data integration, and data queries.",
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"abbreviation": "TADS",
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"name": "Daniel Sonenshine",
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"description": "This ontology covers all the terms relevant for the gross anatomy of the tick (family Ixodida).",
"homepage": "https://www.vectorbase.org/ontology-types/tick-anatomy",
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"abbreviation": "PDO",
"description": "An ontology for describing both human infectious diseases caused by microbes and the diseases that is related to microbial infection.",
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"homepage": "http://mdb.bio.titech.ac.jp/pdo",
"name": "Pathogenic Disease Ontology",
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"abbreviation": "PHAGE",
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"homepage": "http://bioportal.bioontology.org/ontologies/PHAGE",
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"abbreviation": "NDFRT",
"description": "The National Drug File Reference Terminology contains a novel reference hierarchy to describe physiologic effects (PE) of drugs.",
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"title": "Adequacy of representation of the National Drug File Reference Terminology Physiologic Effects reference hierarchy for commonly prescribed medications",
"year": 2004
}
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"Health Science",
"Physiology",
"Biomedical Science"
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},
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"abbreviation": "GEMET",
"description": "The GEneral Multilingual Environmental Thesaurus (GEMET) was created as a βgeneralβ environmental thesaurus, aimed to define a common general language with a core of general terminology for the environment. It is the reference vocabulary of the European Environment Agency (EEA) and its Network (Eionet).",
"homepage": "https://www.eionet.europa.eu/gemet/en/themes/",
"name": "GEneral Multilingual Environmental Thesaurus",
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"Ecology",
"Biodiversity"
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"abbreviation": "POLAPGEN_BARLEY",
"description": "The Crop Ontology's (CO) current objective is to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The POLAPGEN Barley Ontology is one of CO terminologies, with a focus on traits used in genetics and bioinformatics.",
"homepage": "https://cropontology.org/term/POLAPGEN_BARLEY:ROOT",
"license": "CC-BY-4.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaXNCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--ccbb560936b5114f8775c9ff8132ee4fa79d6bb9/16a1deec-90a3-4f48-a266-e7288056fe70.jpeg?disposition=inline",
"name": "Barley Trait Ontology",
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"Bioinformatics",
"Genetics",
"Agriculture"
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},
"FAIRsharing.9228fv": {
"abbreviation": "CROPUSAGE",
"description": "A thesaurus about crops cultivated in France. The hierarchy is based on the final destination of the crop (human food, animal breeding, food industry) and the cultivated system. The hierachy is not based on scientific agronomic taxon like (species, genus). We are interested on categorize the usage of the crop, not on the plant classification.",
"domains": [
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"homepage": "http://ontology.inrae.fr/cropusage",
"license": "CC-BY-4.0",
"name": "French Crop Usage",
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{
"doi": "10.1016/j.compag.2017.10.022",
"title": "A methodology for the publication of agricultural alert bulletins as LOD",
"year": 2017
}
],
"subjects": [
"Botany",
"Agricultural Engineering",
"Agriculture",
"Life Science"
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},
"FAIRsharing.93ee19": {
"abbreviation": "AEO",
"description": "The AEO ontology of anatomical structures is a resource to facilitate the increase in knowledge in anatomy ontologies, supporting annotation and enabling compatibility with other anatomy ontologies. The ontology can be used to classify most organisms as its terms are appropriate for most plant and fungal tissues. It is envisaged that in future the ontology will include more non-animal anatomical terms.",
"homepage": "http://www.obofoundry.org/ontology/aeo.html",
"name": "Anatomical Entity Ontology",
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{
"doi": "10.3389/fgene.2012.00018",
"pubmed": "22347883",
"title": "The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs",
"year": 2012
}
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"subjects": [
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"Life Science"
]
},
"FAIRsharing.93g1th": {
"abbreviation": "PORO",
"description": "An ontology covering the anatomy of Porifera (sponges)",
"domains": [
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"homepage": "http://bioportal.bioontology.org/ontologies/PORO",
"name": "Porifera Ontology",
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"Taxonomy",
"Phylogeny"
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},
"FAIRsharing.945c78": {
"abbreviation": "MAxO",
"contact": {
"email": "Leigh.Carmody@jax.org",
"name": "Leigh Carmody",
"orcid": "0000-0001-7941-2961"
},
"description": "The Medical Action Ontology (MAxO) is being developed to provide a structured vocabulary for medical procedures, interventions, therapies, and treatments for rare diseases.",
"domains": [
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],
"homepage": "https://github.com/monarch-initiative/MAxO",
"license": "CC-BY-4.0",
"name": "Medical Action Ontology",
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"title": "The Medical Action Ontology: A Tool for Annotating and Analyzing Treatments and Clinical Management of Human Disease",
"year": 2023
}
],
"subjects": [
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},
"FAIRsharing.94ca5a": {
"abbreviation": "OEEV",
"description": "The Ontology of Experimental Events (OEEv) characterizes events that occur during an experiment; for example, moving of plants, dates of sowing, application of a given treatment, harvesting, measurements or sampling for βomic measurements, or any category of technical problem. The OEEv ontology contains four groups of events, namely Faciility Management, Scientific Object Management, Trouble and Displacement",
"domains": [
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"Protocol",
"Study design"
],
"homepage": "https://github.com/OpenSILEX/ontology-vocabularies",
"name": "Ontology of Experimental Events",
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{
"doi": "10.1111/nph.15385",
"pubmed": "30152011",
"title": "Dealing with multi-source and multi-scale information in plant phenomics: the ontology-driven Phenotyping Hybrid Information System",
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"Agriculture"
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"abbreviation": "NALT",
"description": "The National Agricultural Library Thesaurus (NALT) is an online vocabulary of agricultural terms in English and Spanish. The Agricultural Thesaurus and Glossary were first released by the National Agricultural Library in 2002. In 2007, NAL and the Inter-American Institute for Cooperation on Agriculture (IICA) collaborated to develop the Spanish version of the NAL Agricultural Thesaurus and Glossary, named Tesauro Agricola y Glosario. The thesaurus is primarily used for indexing and for improving retrieval of agricultural information. The subject scope of agriculture is broadly defined in the thesaurus, and includes terminology in the supporting biological, physical and social sciences. Biological nomenclature comprises a majority of the terms in the thesaurus, with political geography mainly described at the country level.",
"domains": [
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"Geographical location",
"Food"
],
"homepage": "https://agclass.nal.usda.gov/",
"license": "CC0-1.0",
"name": "National Agricultural Library Thesaurus",
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"Botany",
"Economics",
"Environmental Science",
"Engineering Science",
"Animal Genetics",
"Plant Breeding",
"Social Science",
"Health Science",
"Animal Husbandry",
"Entomology",
"Agricultural Engineering",
"Earth Science",
"Agriculture",
"Life Science",
"Nutritional Science",
"Jurisprudence",
"Biology",
"Pathology"
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},
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"abbreviation": "GMDN",
"description": "The Global Medical Device Nomenclature (GMDN) is a system of internationally agreed generic descriptors used to identify all medical device products.",
"domains": [
"Device"
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"homepage": "https://www.gmdnagency.org",
"name": "Global Medical Device Nomenclature",
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{
"doi": "10.4103/0975-1483.71637",
"pubmed": "21264103",
"title": "Global medical device nomenclature: the concept for reducing device-related medical errors",
"year": 2010
}
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"user_defined_tags": [
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},
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"abbreviation": "ICD 11",
"description": "The International Classification of Diseases (ICD) was created to allow the recording, reporting and grouping of conditions and factors that influence health. It contains categories for diseases, health related conditions, and external causes of illness or death. The purpose of the ICD is to allow the systematic recording, analysis, interpretation and comparison of mortality and morbidity data collected in different countries or areas and at different times. The ICD is used to translate diagnoses of diseases and other health problems into an alphanumeric code, which allows storage, retrieval, and analysis of the data. The ICD has become the international standard diagnostic classification for all general epidemiological and many health management purposes. ICD-11 was released in 2018 to allow Member States to prepare for implementation, including translating ICD into their national languages. Member States will start reporting using ICD-11 on 1 January 2022.",
"domains": [
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"Disease",
"Diagnosis",
"Morbidity"
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"homepage": "https://icd.who.int/en",
"license": "http://www.who.int/about/licensing/copyright_form/en",
"name": "International Classification of Diseases Version 11",
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"Global Health",
"Biomedical Science",
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"abbreviation": "GML3.0",
"description": "The Geography Markup Language (GML) is an RDF encoding for the transport and storage of geographic information, including both the geometry and properties of geographic features. Vocabulary terms are declared using OWL language to support RDF applications.",
"homepage": "http://bioportal.bioontology.org/ontologies/GML",
"name": "Ontology for Geography Markup Language",
"subjects": [
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},
"FAIRsharing.981c26": {
"abbreviation": "URN",
"description": "A Uniform Resource Name (URN) is a Uniform Resource Identifier (URI) that is assigned under the \"urn\" URI scheme and a particular URN namespace, with the intent that the URN will be a persistent, location-independent resource identifier.",
"domains": [
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"homepage": "https://datatracker.ietf.org/doc/html/rfc8141",
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"FAIRsharing.9918b9": {
"abbreviation": "PATHLEX",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/PATHLEX",
"name": "Anatomic Pathology Lexicon",
"subjects": [
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"Pathology"
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},
"FAIRsharing.99da5f": {
"abbreviation": "BiRO",
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"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "the Bibliographic Reference Ontology (BiRO) is an ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively.\n\n",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/biro",
"license": "CC-BY-4.0",
"name": "Bibliographic Reference Ontology ",
"repository": "https://github.com/sparontologies/biro",
"subjects": [
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"twitter": "sparontologies"
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"FAIRsharing.99t4hg": {
"abbreviation": "ADMIN",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Nurse"
],
"homepage": "http://bioportal.bioontology.org/ontologies/ADMIN",
"name": "Nurse Administrator",
"subjects": [
"Medicine"
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},
"FAIRsharing.9c1p18": {
"abbreviation": "DDPHENO",
"contact": {
"email": "pfey@northwestern.edu",
"name": "Petra Fey",
"orcid": "0000-0002-4532-2703"
},
"description": "A structured controlled vocabulary of phenotypes of the social amoeba Dictyostelium discoideum. The Dicty Phenotype Ontology is a hierarchical controlled vocabulary used for annotating strains with phenotypes. Terms from the Dicty Phenotype Ontology are required when annotating phenotypes within dictyBase. The phenotype ontology consists of two composite terms: (1) the anatomical part or the biological process changed in the mutant, and (2) a quality describing that modification. For example, a βdelayed aggregationβ phenotype qualifies the βaggregationβ (biological process) as being βdelayedβ, or the βdecreased spore sizeβ qualifies the βsporeβ to be of βdecreased sizeβ.",
"domains": [
"Phenotype"
],
"homepage": "https://github.com/dictyBase/migration-data/blob/master/ontologies/dicty_phenotypes.obo",
"name": "Dictyostelium Phenotype Ontology",
"publications": [
{
"doi": "10.1007/978-1-62703-302-2_4",
"pubmed": "23494302",
"title": "One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012",
"year": 2013
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.9c2azc": {
"abbreviation": "OBO_REL",
"description": "This record describes the original relations ontology (ID space \"OBO_REL\"), which was a direct translation of the 2005 RO paper into OBO format. It suffered a number of problems, such as lack of clarity in the semantics of class level relations. The OBO Relations Ontology (RO) has replaced this resource, and a description of how the two resources differ can be found at https://github.com/oborel/obo-relations/wiki/DifferencesWithOldRO.",
"homepage": "http://purl.bioontology.org/ontology/OBO_REL",
"name": "OBO ReLationship",
"publications": [
{
"doi": "10.1186/gb-2005-6-5-r46",
"pubmed": "15892874",
"title": "Relations in biomedical ontologies",
"year": 2005
}
],
"repository": "https://github.com/oborel/obo-relations/",
"subjects": [
"Life Science"
],
"user_defined_tags": [
"Relations"
]
},
"FAIRsharing.9d08ks": {
"abbreviation": "NMOBR",
"description": "The NeuroMorpho.Org brain region ontologies adopts and integrates relevant portions of available taxonomies (or lineages) \"as needed\" based on the existing knowledge that is openly accessible. For standardization purposes, cell types and other experimental metadata hierarchies are also added to OntoSearch v2.0. Concepts with insufficient knowledge are not classified as hierarchies, such as molecular, firing, and \"other\" unclassifiable properties of cell types. The species, brain regions and cell types are integrated into a single ontology for enabling OntoSearch functionality to mine NeuroMorpho.Org.",
"homepage": "http://bioportal.bioontology.org/ontologies/NMOBR",
"name": "NeuroMorpho.Org brain region ontologies",
"subjects": [
"Computational Neuroscience",
"Neuroscience"
]
},
"FAIRsharing.9d38e2": {
"abbreviation": "URL",
"description": "URL (Uniform Resource Locator) β the typical \"address\" of web content. It is a kind of URI (Uniform Resource Identifier) that begins with \"http://\" and consists of a string of characters used to identify or name a resource on the Internet. Such identification enables interaction with representations of the resource over a network, typically the World Wide Web, using the HTTP protocol. Well-managed URL redirection can make URLs as persistent as any identifier. Resolution depends on HTTP redirection and can be managed through an API or a user interface. A URL is a type of URI that identifies a resource via a representation of its primary access mechanism (e.g., its network \"location\"), rather than by some other attributes it may have (see https://www.w3.org/TR/uri-clarification/#contemporary).",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://tools.ietf.org/html/rfc1630",
"name": "Uniform Resource Locator",
"subjects": [
"Knowledge and Information Systems",
"Subject Agnostic"
]
},
"FAIRsharing.9e9683": {
"abbreviation": "CO_345",
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Brachiaria Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_345:ROOT",
"license": "CC-BY-4.0",
"name": "Brachiaria Ontology",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.9gqfpm": {
"abbreviation": "INHAND",
"description": "Standard reference for nomenclature and diagnostic criteria in toxicologic pathology.",
"domains": [
"Disease",
"Toxicity"
],
"homepage": "http://www.goreni.org/",
"name": "International Harmonization of Nomenclature and Diagnostic criteria",
"publications": [
{
"doi": "10.1177/0192623309353423",
"pubmed": "20032296",
"title": "Proliferative and nonproliferative lesions of the rat and mouse respiratory tract",
"year": 2010
}
],
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.9j4wh2": {
"abbreviation": "CHMO",
"description": "CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy; prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis; and synthesise materials such as epitaxy and continuous vapour deposition. It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI).",
"domains": [
"Chromatography",
"Electron microscopy",
"Assay",
"Mass spectrometry assay"
],
"homepage": "https://github.com/rsc-ontologies/rsc-cmo",
"license": "CC-BY-4.0",
"name": "Chemical Methods Ontology",
"repository": "https://github.com/rsc-ontologies/rsc-cmo/issues",
"subjects": [
"Chemistry"
]
},
"FAIRsharing.9pm45h": {
"abbreviation": "DDO",
"description": "An ontology for diagnosis of diabetes containing the diabetes related complications, symptoms, drugs, lab tests, etc.",
"domains": [
"Diagnosis",
"Diabetes mellitus"
],
"homepage": "https://link.springer.com/content/pdf/10.1186/s40535-016-0021-2.pdf",
"name": "Diabetes Mellitus Diagnosis Ontology",
"subjects": [
"Biomedical Science",
"Diabetology"
]
},
"FAIRsharing.9psjsk": {
"abbreviation": "OPE",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/OPE",
"name": "Ontology of Physical Exercises",
"subjects": [
"Health Science"
]
},
"FAIRsharing.9rhr9j": {
"abbreviation": "VEuPathDB Ontology",
"description": "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource. The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.",
"domains": [
"Microbiome"
],
"homepage": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology",
"license": "CC-BY-4.0",
"name": "Eukaryotic Pathogen, Host & Vector Genomics Resource Ontology",
"repository": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology",
"subjects": [
"Functional Genomics",
"Biomedical Science",
"Epidemiology",
"Population Genetics"
]
},
"FAIRsharing.9sza27": {
"abbreviation": "GMO",
"description": "A structured controlled vocabulary for describing ingredients that constitute microbial growth media used in biological research centers.",
"homepage": "https://github.com/skwsm/gmo",
"name": "Growth Medium Onotology",
"subjects": [
"Microbiology"
]
},
"FAIRsharing.9te3ev": {
"abbreviation": "PDRO",
"description": "PDRO is a realist ontology that aims to represent the domain of drug prescriptions. Such an ontology is currently missing in the OBOFoundry and is highly relevant to the domains of existing ontologies like DRON, OMRSE and OAE. PDROβs central focus is the structure of a drug prescription, which is represented as a mereology of informational entities. Our current use cases are (1) refining this structure (e.g., adding closure axioms, cardinality, datatype bindings, etc) for prospectively standardizing local electronic prescriptions and (2) annotating prescription data of differing EHRs for detecting inappropriate prescriptions using a central semantic framework. Future ontological work will include aligning PDRO more closely with the Document Acts Ontology.",
"domains": [
"Drug"
],
"homepage": "https://github.com/OpenLHS/PDRO",
"license": "CC-BY-4.0",
"name": "The Prescription of Drugs Ontology",
"subjects": [
"Primary Health Care"
]
},
"FAIRsharing.9thw6y": {
"abbreviation": "HIVCRS",
"description": "The Ontology to express the ternary relations of HIV1",
"homepage": "http://blog.51.ca/u-345129/",
"name": "HIVCompoundRels",
"subjects": [
"Medicine"
]
},
"FAIRsharing.9vtwjs": {
"abbreviation": "DCMI Metadata Terms",
"description": "This document is an up-to-date, authoritative specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. Included are the fifteen terms of the Dublin Core Metadata Element Set, which have also been published as a separate specification.",
"domains": [
"Resource metadata"
],
"homepage": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/",
"license": "CC-BY-3.0",
"name": "Dublin Core Metadata Initiative Terms",
"subjects": [
"Subject Agnostic"
],
"user_defined_tags": [
"Metadata standardization"
]
},
"FAIRsharing.9w8ea0": {
"abbreviation": "RO",
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"description": "RO is a collection of relations intended primarily for standardization across ontologies in the OBO Foundry and wider OBO library. It incorporates ROCore upper-level relations such as part of as well as biology-specific relationship types such as develops from. The predecessor of RO was OBO_REL. Many of the relations in OBO_REL have been ceded to BFO.",
"homepage": "https://github.com/oborel/obo-relations/",
"license": "CC0-1.0",
"name": "OBO Relations Ontology",
"repository": "https://github.com/oborel/obo-relations/wiki/ROAndBFO",
"subjects": [
"Life Science"
],
"user_defined_tags": [
"Relations"
]
},
"FAIRsharing.9xcr4z": {
"abbreviation": "CIDOC-CRM",
"description": "The CIDOC Conceptual Reference Model (CRM) provides definitions and a formal structure for describing the implicit and explicit concepts and relationships used in cultural heritage documentation. The overall scope of the CIDOC CRM can be summarised in simple terms as the curated, factual knowledge\nabout the past at a human scale. The CIDOC CRM is intended to promote a shared understanding of cultural heritage information by providing a common and extensible semantic framework that any cultural heritage information can be mapped to. It is intended to be a common language for domain experts and implementers to formulate requirements for information systems and to serve as a guide for good practice of conceptual modelling. In this way, it can provide the \"semantic glue\" needed to mediate between different sources of cultural heritage information, such as that published by museums, libraries and archives. The ISO 21127:2014 specification (Information and documentation β A reference ontology for the interchange of cultural heritage information) was created from the CIDOC CRM, although the CIDOC CRM Special Interest Group continues to maintain this original document as well.",
"domains": [
"Resource collection"
],
"homepage": "https://www.cidoc-crm.org/",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBZUk9IiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--057a21005e538cb21742ec8a475bf44a6228c707/cidoc.png?disposition=inline",
"name": "CIDOC Conceptual Reference Model",
"subjects": [
"Culture",
"Humanities and Social Science",
"Cultural Studies",
"Anthropology"
]
},
"FAIRsharing.9y3gv0": {
"abbreviation": "ESFO",
"description": "The ESFO provides a new paradigm for organizing enzyme sequence, structure, and function information, whereby specific elements of enzyme sequence and structure are mapped to specific conserved aspects of function, thus facilitating the functional annotation of uncharacterized enzymes. The ESFO helps prevent misannotation by emphasizing annotation of enzymes only at the level of functional granularity warranted by available information. The archive is a static snapshot of the data in the SFLD as of April 2019, and will not be updated",
"domains": [
"Molecular structure",
"Protein structure",
"DNA sequence data",
"Annotation",
"Function analysis",
"Enzyme",
"Sequence alignment"
],
"homepage": "http://sfld.rbvi.ucsf.edu/archive/django/index.html",
"name": "Enzyme Structure Function Ontology",
"publications": [
{
"doi": "10.1093/database/bax006",
"pubmed": "28365730",
"title": "Biocuration in the structure-function linkage database: the anatomy of a superfamily",
"year": 2017
}
],
"subjects": [
"Enzymology",
"Life Science"
]
},
"FAIRsharing.9y8f0n": {
"abbreviation": "DIDEO",
"contact": {
"email": "rdb20@pitt.edu",
"name": "Richard D. Boyce",
"orcid": "0000-0002-2993-2085"
},
"description": "A domain ontology for potential drug-drug interactions (PDDIs) that covers the material entities and processes in the domain of discourse for PDDI evidence and knowledge claims. The representation enables the integration of drug interaction mechanisms, effects, risk factors, severity, and management options with the chemical and pharmacological properties (e.g., chemical structure, function, pharmacokinetic and pharmacodynamic properties) of the interacting drugs. It also has a rich and detailed set evidence entities related to pharmacology. See below for publications about DIDEO. A description of the goals of the project can be found in the following workshop paper located in the docs/DIDEO-discussion-ICBO-Brochhausen-2014.pdf: Brochhausen, M., Schneider, J., Malone, D., Empey, PE., Hogan WR., and Boyce, RD. Towards a foundational representation of potential drug-drug interaction knowledge. The 1st International Drug-Drug Interaction Knowledge Representation Workshop (DIKR 2014). Collocated with the 2014 International Conference on Biomedical Ontology (ICBO 2014). October 6th, Houston, Texas. United States.",
"domains": [
"Evidence",
"Drug interaction",
"Natural product"
],
"homepage": "https://github.com/DIDEO/DIDEO",
"license": "CC-BY-4.0",
"name": "The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology",
"publications": [
{
"doi": "10.1016/j.knosys.2016.10.006",
"title": "Conceptual models of drug-drug interactions : A summary of recent efforts",
"year": 2016
},
{
"doi": "10.1186/s13326-018-0183-z",
"pubmed": "29743102",
"title": "Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse",
"year": 2018
},
{
"pubmed": "29295242",
"title": "Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies to Improve Evidence Base Curation",
"year": 2018
}
],
"subjects": [
"Biochemistry"
]
},
"FAIRsharing.9yHHCp": {
"description": "Vocabulary used for indexing bibliographical records dealing with βElectronicsβ in the PASCAL database, until 2014. This resource consists of 4454 entries in 3 languages (English, French and Spanish) classified under 19 collections.",
"homepage": "https://www.loterre.fr/skosmos/RDR/en/",
"license": "CC-BY-4.0",
"name": "Electronics and Optoelectronics Vocabulary",
"subjects": [
"Engineering Science",
"Component Engineering"
],
"user_defined_tags": [
"Electronics",
"Optoelectronics",
"Semiconductor electronics"
]
},
"FAIRsharing.9yf7w3": {
"abbreviation": "GDCO",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/GDCO",
"name": "Data Collection Ontology",
"subjects": [
"Data Mining",
"Data Quality",
"Subject Agnostic"
]
},
"FAIRsharing.9zpcgj": {
"description": "Amino Acid Ontology is an ontology of amino acids and their properties. It captures how biochemists talk about amino acids; that is, it is a conceptualisation of amino acids. This ontology smoothens out the way in which amino acids are described as the chemical reality tends to obscure rather than reveal what may be considered important features of amino acids. This ontology serves as a demonstration of a move towards a sort of mass production of axiomatically rich ontologies.",
"domains": [
"Amino acid sequence"
],
"homepage": "https://bioportal.bioontology.org/ontologies/AMINO-ACID",
"name": "Amino Acid Ontology",
"subjects": [
"Proteomics",
"Life Science"
]
},
"FAIRsharing.A29ckB": {
"abbreviation": "Biodiversity",
"description": "This bilingual thesaurus organizes the key concepts of biodiversity sciences, in their basic and applied ecological components. It uses polyhierarchy and includes 818 reciprocal associative relationships. The 1654 French and English descriptors (designating 827 concepts) are enriched with a large number of synonyms (1860) and hidden variants (7020) in both languages. Concepts are grouped into 82 collections, by semantic categories, thematic fields and EBV classes (Essential Biodiversity Variables). Definitions are given with their sources. This resource is aligned with the international thesauri AGROVOC, GEMET (GEneral Multilingual Environmental Thesaurus) and EnvThes (Environmental Thesaurus), as well as with the ontology ENVO (Environment Ontology).",
"domains": [
"Climate",
"Ecosystem"
],
"homepage": "https://skosmos.loterre.fr/BLH/en/",
"license": "CC-BY-4.0",
"name": "Biodiversity Thesaurus",
"subjects": [
"Agroecology",
"Environmental Science",
"Ecology",
"Biodiversity",
"Ecosystem Science"
]
},
"FAIRsharing.ATwSZG": {
"abbreviation": "RRID",
"description": "Research Resource Identifiers (#RRID) are ID numbers assigned to help researchers cite key resources (antibodies, model organisms and software projects) in the biomedical literature to improve transparency of research methods. \n\n\n\n",
"domains": [
"Citation",
"Resource metadata",
"Annotation",
"Data retrieval",
"Centrally registered identifier"
],
"homepage": "https://www.rrids.org/",
"name": "Research Resource Identifier",
"publications": [
{
"doi": "10.12688/f1000research.6555.2",
"pubmed": "26594330",
"title": "The Resource Identification Initiative: A cultural shift in publishing",
"year": 2015
},
{
"doi": "10.1016/j.neuron.2016.04.030",
"pubmed": "27151636",
"title": "RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods",
"year": 2016
},
{
"doi": "10.1002/cne.23913",
"pubmed": "26599696",
"title": "The Resource Identification Initiative: A Cultural Shift in Publishing",
"year": 2015
},
{
"doi": "10.7717/peerj.148",
"pubmed": "24032093",
"title": "On the reproducibility of science: unique identification of research resources in the biomedical literature",
"year": 2013
},
{
"doi": "10.1038/nmeth.3995",
"pubmed": "27595404",
"title": "A proposal for validation of antibodies",
"year": 2016
}
],
"subjects": [
"Knowledge and Information Systems",
"Chemistry",
"Life Science"
]
},
"FAIRsharing.DbFnKV": {
"abbreviation": "RGO",
"contact": {
"email": "ckahn@upenn.edu",
"name": "Charles E. Kahn, Jr., MD, MS",
"orcid": "0000-0002-6654-7434"
},
"description": "The Radiology Gamuts Ontology (RGO) is a knowledge resource for radiology diagnosis. RGO hosts more than 2,000 differential-diagnosis listings for imaging findings in all body systems. One can view all of the causes of an finding, then click on one of the diagnoses to view all of the findings that it causes.",
"domains": [
"Medical imaging",
"Disease",
"Diagnosis"
],
"homepage": "https://www.gamuts.net",
"license": "https://creativecommons.org/licenses/by-nc-nd/4.0",
"name": "Radiology Gamuts Ontology",
"publications": [
{
"doi": "10.1093/jamia/ocy161",
"pubmed": "30624645",
"title": "Integrating ontologies of human diseases, phenotypes, and radiological diagnosis",
"year": 2019
},
{
"doi": "10.1007/s10278-019-00186-3",
"pubmed": "30706210",
"title": "Integrating an Ontology of Radiology Differential Diagnosis with ICD-10-CM, RadLex, and SNOMED CT",
"year": 2019
},
{
"doi": "10.1148/rg.341135036",
"pubmed": "24428295",
"title": "Informatics in radiology: radiology gamuts ontology: differential diagnosis for the Semantic Web",
"year": 2014
}
],
"subjects": [
"Radiology",
"Biomedical Science"
]
},
"FAIRsharing.FSIfv8": {
"abbreviation": "DRAO",
"description": "The Domain Resource Application Ontology (DRAO) is an application ontology describing cross-discipline research domains used within FAIRsharing records by curators and the user community. It is built in conjunction with the Subject Resource Application Ontology (SRAO), which describes higher-level subject areas / disciplines. All classes within DRAO come from over 50 publicly-available ontologies.",
"domains": [
"Resource metadata",
"Classification",
"FAIR"
],
"homepage": "https://github.com/FAIRsharing/domain-ontology",
"license": "CC BY-SA 4.0",
"name": "Domain Resource Application Ontology",
"repository": "https://github.com/FAIRsharing/domain-ontology/blob/master/Development.md",
"subjects": [
"Environmental Science",
"Humanities",
"Natural Science",
"Earth Science",
"Agriculture",
"Life Science",
"Computer Science",
"Biomedical Science"
],
"twitter": "FAIRsharing_org",
"user_defined_tags": [
"Metadata standardization"
]
},
"FAIRsharing.FrSPDi": {
"description": "This thesaurus is based on the vocabulary used in scientific publications for Artificial nutrition and neighbor fields. It contains more than 2500 concepts in two languages (English and French), including various variants (synonyms, acronyms) divided into a number of microthesauri where the terms are grouped around a theme or a semantic field.",
"homepage": "https://www.loterre.fr/skosmos/BL8/en/",
"license": "CC-BY-4.0",
"name": "Artificial Nutrition Thesaurus",
"subjects": [
"Medicine",
"Nutritional Science"
],
"user_defined_tags": [
"Artificial nutrition"
]
},
"FAIRsharing.GOZFxU": {
"description": "Vocabulary used for indexing bibliographical records dealing with the field \"Signal theory and processing\" in the PASCAL database, until 2014. This resource contains 2483 entries in 3 languages (English, French, and Spanish), grouped in 84 collections.",
"homepage": "https://www.loterre.fr/skosmos/SN8/en/",
"license": "CC-BY-4.0",
"name": "Signal theory and processing vocabulary",
"subjects": [
"Engineering Science"
],
"user_defined_tags": [
"Signal processing",
"Signal theory"
]
},
"FAIRsharing.GWEIFA": {
"abbreviation": "landform",
"description": "Machine-readable representation of the classifiers described in chapter 5 Landform, by J.G. Speight, in Australian soil and land survey field handbook (3rd edn). In this technique for describing landforms, the whole land surface is viewed as a mosaic of tiles of odd shapes and sizes. The scheme is intended to produce a record of observations rather than inferences. The data was converted from the print representation to this linked-data form by Linda Gregory assisted by Simon J D Cox.",
"homepage": "https://github.com/ANZSoilData/def-au-asls-landform",
"license": "https://creativecommons.org/licenses/by/3.0/au",
"name": "ASLS - Landform classifiers",
"subjects": [
"Soil Science",
"Earth Science"
],
"user_defined_tags": [
"soil carbon",
"Soil pH",
"Soil texture"
]
},
"FAIRsharing.IUZaXe": {
"abbreviation": "land-surface",
"description": "Machine-readable representation of the classifiers described in chapter 7 Land Surface, by R.C. McDonald, R.F. Isbell and J.G. Speight, in Australian soil and land survey field handbook (3rd edn). Land surface is concerned mainly with surface phenomena affecting land use and soil development that have traditionally been noted at the point of soil observation. The data was converted from the print representation to this linked-data form by Linda Gregory and Simon J D Cox.",
"homepage": "https://github.com/ANZSoilData/def-au-asls-land-surface",
"license": "https://creativecommons.org/licenses/by/3.0/au",
"name": "ASLS - Land Surface classifiers",
"subjects": [
"Soil Science",
"Earth Science"
],
"user_defined_tags": [
"soil carbon",
"Soil pH",
"Soil texture"
]
},
"FAIRsharing.L4Q3H9": {
"abbreviation": "IVOA Identifier",
"description": "An IVOA Identifier is a globally unique name for a resource within the Virtual Observatory. This name can be used to retrieve a unique description of the resource from an IVOA-compliant registry or to identify an entity like a dataset or a protocol without dereferencing the identifier. This document describes the syntax for IVOA Identifiers as well as how they are created. The syntax has been defined to encourage global-uniqueness naturally and to maximize the freedom of resource providers to control the character content of an identifier.",
"domains": [
"Centrally registered identifier"
],
"homepage": "http://www.ivoa.net/documents/IVOAIdentifiers/index.html",
"name": "IVOA Identifier",
"subjects": [
"Astrophysics and Astronomy"
]
},
"FAIRsharing.LQfdaV": {
"abbreviation": "AAT",
"description": "The Getty Art & Architecture Thesaurus (AAT) is a thesaurus containing generic terms, dates, relationships, sources, and notes for work types, roles, materials, styles, cultures, techniques, and other concepts related to art, architecture, and other cultural heritage. The AAT is one of 5 Getty Vocabularies intended to provide terminology and other information about the objects, artists, concepts, and places important to various disciplines that specialize in art, architecture, and other material culture. The AAT contains generic terms; it contains no iconographic subjects and no proper names. That is, each concept is a case of many (a generic thing), not a case of one (a specific thing).",
"homepage": "http://www.getty.edu/research/tools/vocabularies/aat/index.html",
"license": "http://opendatacommons.org/licenses/by/1.0",
"name": "Art & Architecture Thesaurus",
"subjects": [
"Culture",
"Art History",
"Architecture",
"Art",
"Fine Arts",
"History",
"Cultural Studies",
"Building Design"
],
"user_defined_tags": [
"Built Environment"
]
},
"FAIRsharing.LcyXdU": {
"description": "This bilingual thesaurus (French-English), developed at Inist-CNRS, covers the concepts from the cognitive psychology of human memory (memory systems and processes, empirical effects, memory disorders, study methods, theories and models), organized in the form of hierarchical (generic and specific terms), equivalence (synonyms) and association relationships. Most of the concepts are presented with a definition and a bibliography. Notes have been added to some of them (only in French for the moment). The resource is mapped to the Cognitive Atlas, Wikipedia, wikidata and the SantΓ© Psy thesaurus. This resource consists of 870 terminological entries grouped into 18 collections.",
"homepage": "https://www.loterre.fr/skosmos/P66/en/",
"license": "CC-BY-4.0",
"name": "Thesaurus Cognitive psychology of human memory",
"subjects": [
"Psychology",
"Cognitive Neuroscience"
],
"user_defined_tags": [
"Human memory"
]
},
"FAIRsharing.LwAk3f": {
"description": "The thesaurus of Blood Transfusion consists of 2032 entries, in English and French.",
"homepage": "https://www.loterre.fr/skosmos/W7B/en/",
"license": "CC-BY-4.0",
"name": "Thesaurus of Blood Transfusion",
"subjects": [
"Medicine",
"Transfusion Medicine"
]
},
"FAIRsharing.Mghsr2": {
"abbreviation": "GCMD Keywords",
"description": "Global Change Master Directory (GCMD) Keywords are a hierarchical set of controlled Earth Science vocabularies that help ensure Earth Science data, services, and variables are described in a consistent and comprehensive manner and allow for the precise searching of metadata and subsequent retrieval of data, services, and variables. Initiated over twenty years ago, GCMD Keywords are periodically analyzed for relevancy and will continue to be refined and expanded in response to user needs.",
"domains": [
"Geographical location",
"Device"
],
"homepage": "https://earthdata.nasa.gov/earth-observation-data/find-data/gcmd/gcmd-keywords",
"name": "Global Change Master Directory Keywords",
"subjects": [
"Earth Science"
]
},
"FAIRsharing.NIvbz9": {
"description": "Controlled vocabulary used for indexing bibliographical records for the \"Art and Archaeology\" FRANCIS database (1972-2015). It consists of 1960 entries available in mainly 2 languages (English, French) and grouped into 133 collections.",
"homepage": "https://www.loterre.fr/skosmos/27X/en/",
"license": "CC-BY-4.0",
"name": "Art and Archaeology Vocabulary",
"subjects": [
"Archaeology",
"Humanities",
"Art"
]
},
"FAIRsharing.OrNi1L": {
"abbreviation": "ORCID iD Identifier Schema",
"description": "The ORCID Identifier Schema is an https URI with a 16-digit number that is compatible with the ISO Standard (ISO 27729), also known as the International Standard Name Identifier (ISNI), e.g. https://orcid.org/0000-0001-2345-6789 Initially ORCID iDs will be randomly assigned by the ORCID Registry from a block of numbers that will not conflict with ISNI-formatted numbers assigned in other ways. ORCID iDs always require all 16 digits of the identifier; they can not be shortened to remove leading zeros if they exist. No information about a person is encoded in the ORCID iD. The identifiers were designed to be usable in situations where personally-identifiable information should/can not be shared. Also, since the ORCID iD is designed to be a career-long identifier, no information that can change over a person's career is embedded in the iD, e.g., country, institution, field of study.",
"domains": [
"Citation",
"Bibliography",
"Publication",
"Centrally registered identifier"
],
"homepage": "https://support.orcid.org/hc/en-us/articles/360006897674-Structure-of-the-ORCID-Identifier",
"name": "Open Researcher and Contributor iD Identifier Schema",
"publications": [
{
"doi": "10.23640/07243.22250740.v1",
"title": "ORCID 2022 Annual Report",
"year": 2023
}
],
"repository": "https://github.com/ORCID",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.OsiqlF": {
"abbreviation": "IUPAC Gold Book",
"contact": {
"email": "schalk@unf.edu",
"name": "Stuart Chalk",
"orcid": "0000-0002-0703-7776"
},
"description": "The IUPAC Gold Book is a database of ~7000 chemical concepts derived from IUPAC's Recommendations published in Pure and Applied Chemistry.",
"homepage": "https://goldbook.iupac.org/",
"license": "https://creativecommons.org/licenses/by-nc-nd/4.0",
"name": "IUPAC Compendium of Chemical Terminology",
"subjects": [
"Synthetic Chemistry",
"Organic Chemistry",
"Biochemistry",
"Polymer Chemistry",
"Synthesis Chemistry",
"Chemistry",
"Molecular Physical Chemistry",
"Theoretical Chemistry",
"Solid-State Chemistry",
"Physical Chemistry",
"Clinical Chemistry",
"Analytical Chemistry",
"Food Chemistry",
"Computational Chemistry",
"Medicinal Chemistry"
]
},
"FAIRsharing.PB6595": {
"abbreviation": "QID",
"description": "Wikidata is a document-oriented database, focused on items, which represent any kind of topic, concept, or object. Each item is allocated a unique, persistent identifier (a QID), which is a positive integer prefixed with the upper-case letter Q.",
"homepage": "https://www.wikidata.org/wiki/Q43649390",
"name": "Wikidata Identifier",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.QxlUSp": {
"abbreviation": "soil-prof",
"description": "Machine-readable representation of the classifiers described in chapter 8 Soil Profile, by R.C. McDonald and R.F. Isbell, in Australian soil and land survey field handbook (3rd edn). A soil profile is a vertical section of a soil from the soil surface through all its horizons to parent material, other consolidated substrate material or selected depth in unconsolidated material. The data was converted from the print representation to this linked-data form by Linda Gregory assisted by Simon J D Cox.",
"homepage": "https://github.com/ANZSoilData/def-au-asls-soil-prof",
"license": "https://creativecommons.org/licenses/by/3.0/au",
"name": "ASLS - Soil Profile classifiers",
"subjects": [
"Soil Science",
"Earth Science"
],
"user_defined_tags": [
"soil carbon"
]
},
"FAIRsharing.RlEMBA": {
"abbreviation": "P-PLAN",
"description": "The Ontology for Provenance and Plans (P-Plan) is an extension of the PROV-O ontology [PROV-O] created to represent the plans that guided the execution of scientific processes. P-Plan describes how the plans are composed and their correspondence to provenance records that describe the execution itself.",
"domains": [
"Resource metadata"
],
"homepage": "http://purl.org/net/p-plan",
"license": "CC BY-NC-SA 2.0",
"name": "Ontology for Provenance and Plans",
"subjects": [
"Data Management",
"Computer Science"
]
},
"FAIRsharing.S6BoUk": {
"abbreviation": "w3id",
"description": "A secure, permanent URL re-direction service for Web applications run by the W3C Permanent Identifier Community Group. Web applications that deal with Linked Data often need to specify and use URLs that are very stable. They utilize services such as this one to ensure that applications using their URLs will always be re-directed to a working website. This website operates like a switchboard, connecting requests for information with the true location of the information on the Web. The switchboard can be reconfigured to point to a new location if the old location stops working.",
"domains": [
"Resource metadata",
"Centrally registered identifier",
"Web service"
],
"homepage": "https://w3id.org/",
"name": "w3id.org",
"repository": "https://github.com/perma-id",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.TrcBD2": {
"description": "Controlled vocabulary used for indexing bibliographical records dealing with chemistry in the PASCAL database (1972-2015). It is aligned with the terms of the ChEBI (Chemical Entities of Biological Interest), RXNO (name reaction ontology), MOP (molecular process ontology), REX (Physico-chemical process), FIX (Physico-chemical methods and properties), ontologies and the terms of the IUPAC Gold Book. This resource contains 9150 entries in 2 languages (English and French) grouped under 21 collections.",
"homepage": "https://www.loterre.fr/skosmos/37T/en/",
"license": "CC-BY-4.0",
"name": "Chemistry vocabulary",
"subjects": [
"Organic Chemistry",
"Inorganic Molecular Chemistry",
"Organic Molecular Chemistry",
"Molecular Chemistry",
"Chemistry",
"Molecular Physical Chemistry",
"Theoretical Chemistry",
"Solid-State Chemistry",
"Physical Chemistry",
"Analytical Chemistry",
"Computational Chemistry"
]
},
"FAIRsharing.U7rBYm": {
"description": "Earth and Universe Sciences controlled vocabulary used for indexing bibliographical records for the PASCAL database. This resource contains 10835 entries grouped into 60 collections, in two languages (English and French).",
"homepage": "https://www.loterre.fr/skosmos/26L/en/",
"license": "CC-BY-4.0",
"name": "Vocabulary of Earth Sciences",
"subjects": [
"Astrophysics and Astronomy",
"Cosmology",
"Earth Science"
],
"user_defined_tags": [
"Cosmology"
]
},
"FAIRsharing.USxx0K": {
"abbreviation": "ONE",
"contact": {
"email": "carl.lachat@ugent.be",
"name": "Carl Lachat",
"orcid": "0000-0002-1389-8855"
},
"description": "The ontology for nutritional epidemiology (ONE) describes nutritional epidemiologic studies, and was created to improve on how generic ontologies for food science, nutrition science or medical science covered the specific characteristics of nutritional epidemiologic studies.",
"domains": [
"Diet"
],
"homepage": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies",
"license": "CC-BY-4.0",
"name": "Ontology for Nutritional epidemiology",
"publications": [
{
"pubmed": "31181762",
"title": "An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content",
"year": 2019
}
],
"repository": "https://github.com/cyang0128/Nutritional-Epidemiologic-ontologies",
"subjects": [
"Nutritional Science",
"Metabolomics",
"Epidemiology"
]
},
"FAIRsharing.X0q5BG": {
"contact": {
"email": "delphine.dauga@contact-communication.com",
"name": "Delphine Dauga",
"orcid": "0000-0003-3152-1194"
},
"description": "The first ontology describing the anatomy and the development of Ciona robusta, based on the Hotta developmental tables.",
"domains": [
"Life cycle",
"Life cycle stage"
],
"homepage": "https://www.aniseed.fr/aniseed/anatomy/find_devstage?module=aniseed&action=anatomy:find_devstage",
"name": "Ciona robusta Anatomy and Development Ontology",
"publications": [
{
"doi": "10.1101/gr.108175.110",
"pubmed": "20647237",
"title": "The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program",
"year": 2010
},
{
"doi": "10.1038/s41598-020-73544-9",
"pubmed": "33087765",
"title": "The ontology of the anatomy and development of the solitary ascidian Ciona: the swimming larva and its metamorphosis",
"year": 2020
}
],
"subjects": [
"Anatomy",
"Developmental Biology"
]
},
"FAIRsharing.XYFbZD": {
"description": "The Human Diseases Thesaurus describes human diseases, and is part of the Medicine vocabulary used from 1972 to 2015 for indexing bibliographical records in the now-archived PASCAL database (http://pascal-francis.inist.fr/). It is available in English and French.",
"domains": [
"Disease"
],
"homepage": "https://www.loterre.fr/skosmos/VH8/en/",
"license": "CC-BY-4.0",
"name": "Human Diseases Thesaurus",
"subjects": [
"Medicine",
"Life Science",
"Pathology"
]
},
"FAIRsharing.XfpPv7": {
"description": "Controlled vocabulary used for indexing bibliographical records for the \"History and Sciences of Religions\" FRANCIS database (1972-2015). It consists of 4579 entries available in 3 languages (English, French, and Spanish).",
"homepage": "https://www.loterre.fr/skosmos/4V5/en/",
"license": "CC-BY-4.0",
"name": "History and Sciences of Religions Vocabulary",
"subjects": [
"Religious Studies",
"Humanities and Social Science",
"History"
]
},
"FAIRsharing.XuvIC0": {
"abbreviation": "OPMW-PROV",
"description": "OPMW is an ontology for describing workflows based on the Open Provenance Model. It has been designed as a profile for OPM, extending and reusing OPM's core ontologies OPMV (OPM-Vocabulary) and OPMO (OPM-Ontology). Since the publication of the PROV-O standard, the ontology also extends the W3C recommendation. The OPMW profile was originally created as an extension of OPM to represent abstract workflows in addition to workflow execution traces. This requirement was motivated by the goal of publishing workflows of scientific articles.",
"domains": [
"Resource metadata"
],
"homepage": "https://www.opmw.org/",
"name": "Open Provenance Model for Workflows Ontology",
"subjects": [
"Data Management",
"Computer Science"
]
},
"FAIRsharing.XykycZ": {
"abbreviation": "TFClass",
"description": "TFClass is a resource that classifies eukaryotic transcription factors (TFs) according to their DNA-binding domains. Combining information from different resources, manually checking the retrieved mammalian TF sequences and applying extensive phylogenetic analyses, >39,000 TFs from up to 41 mammalian species were assigned to the Superclasses, Classes, Families and Subfamilies of TFClass. TFClass provides corresponding sequence collections in FASTA format; sequence logos and phylogenetic trees at different classification levels; predicted TF binding sites for human, mouse, dog and cow genomes; and links to several external databases.",
"domains": [
"Expression data",
"Transcription factor binding site prediction",
"Binding",
"Transcription factor",
"Binding site"
],
"homepage": "http://tfclass.bioinf.med.uni-goettingen.de/index.jsf",
"name": "Transcription Factor Class",
"publications": [
{
"doi": "10.1093/nar/gkx987",
"pubmed": "29087517",
"title": "TFClass: expanding the classification of human transcription factors to their mammalian orthologs",
"year": 2017
}
],
"subjects": [
"Bioinformatics",
"Phylogenetics",
"Transcriptomics"
]
},
"FAIRsharing.YKGuWm": {
"description": "This bilingual thesaurus (French-English), developed at Inist-CNRS, covers the concepts from the emerging COVID-19 outbreak which reminds the past SARS coronavirus outbreak and Middle East coronavirus outbreak. This thesaurus is based on the vocabulary used in scientific publications for SARS-CoV-2 and other coronaviruses, like SARS-CoV and MERS-CoV. It provides a support to explore the coronavirus infectious diseases.",
"homepage": "https://www.loterre.fr/skosmos/C0X/en/",
"license": "CC-BY-4.0",
"name": "Covid-19 Thesaurus",
"subjects": [
"Virology",
"Biomedical Science",
"Epidemiology"
],
"user_defined_tags": [
"COVID-19"
]
},
"FAIRsharing.YovxU6": {
"description": "Controlled vocabulary used for indexing bibliographical records for the \"Philosophy\" FRANCIS database (1972-2015). It consists of 4435 entries in mainly 2 languages (English and French) grouped into 102 collections.",
"homepage": "https://www.loterre.fr/skosmos/73G/en/",
"license": "CC-BY-4.0",
"name": "Vocabulary of Philosophy",
"subjects": [
"Humanities",
"Philosophy",
"Classical Philology",
"Practical Philosophy",
"Theoretical Philosophy"
]
},
"FAIRsharing.Yvc76F": {
"abbreviation": "IGSN (GeoSample)",
"description": "The IGSN is a globally unique persistent identifier for physical specimens. The IGSN registration service will facilitate the discovery, access, and sharing of samples, ensure preservation and access of sample data, aid identification of samples in the literature, and advance the exchange of digital sample data among interoperable data systems. ",
"homepage": "https://igsn.github.io/",
"name": "International GeoSample Number",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.ZZZvAw": {
"abbreviation": "VOUnits",
"description": "VOUnits is a recommended syntax for writing the string representation of unit labels. In addition, it describes a set of recognised and deprecated units, which is as far as possible consistent with other relevant standards (BIPM, ISO/IEC and the IAU). The intention is that units written to conform to this specification will likely also be parsable by other well-known parsers. To this end, we include machine-readable grammars for other units syntaxes.",
"domains": [
"Unit"
],
"homepage": "http://ivoa.net/documents/VOUnits/index.html",
"name": "Units in the Virtual Observatory",
"subjects": [
"Astrophysics and Astronomy"
]
},
"FAIRsharing.ZkwSlo": {
"abbreviation": "AHOL",
"description": "The AHOL ontology (Animal Health Ontology for Livestock) was built collaboratively within a network of experts in the livestock health field, in order to describe production diseases. Its structure is based on the type of disease: communicable, non communicable, genetic, metabolic, physical or psychological. The properties of each disease are related to associated symptoms (the expression of a phenotypical character), the affected organism (livestock, poultry, mammals, fishes) or the one causing the disease (virus, bacteria, fungus, parasite).",
"domains": [
"Phenotype",
"Disease"
],
"homepage": "http://www.atol-ontology.com/en/a-ahol/",
"license": "CC-BY-4.0",
"name": "Animal Health Ontology for Livestock",
"subjects": [
"Fisheries Science",
"Animal Husbandry"
],
"user_defined_tags": [
"Livestock"
]
},
"FAIRsharing.a08d34": {
"abbreviation": "PANET",
"description": "The PaNET ontology provides a taxonomy and thesaurus of photon and neutron (PaN) experimental techniques, based mainly on accelerator-based light sources and neutron facilities. The primary use of the ontology is to enhance the FAIRness of PaN data catalogues services. The ontology defines specific techniques in terms of more general technique classes and provides synonyms and references.",
"homepage": "https://github.com/ExPaNDS-eu/ExPaNDS-experimental-techniques-ontology",
"license": "CC-BY-4.0",
"name": "PaN Experimental technique",
"publications": [
{
"doi": "10.5281/zenodo.4806026",
"title": "ExPaNDS ontologies v1.0",
"year": 2021
}
],
"subjects": [
"Physics"
],
"user_defined_tags": [
"Neutron Science",
"photon science"
]
},
"FAIRsharing.a0c8ff": {
"description": "Controlled vocabulary used for indexing bibliographical records for the \"Litterature\" FRANCIS database (1972-2015, http://pascal-francis.inist.fr/). This resource contains 11059 entries grouped into 63 collections, each entry being described by an english and a french preferred term.",
"homepage": "https://skosmos.loterre.fr/P21/en/",
"license": "CC-BY-4.0",
"name": "Litterature Vocabulary",
"subjects": [
"Humanities"
],
"user_defined_tags": [
"litterature"
]
},
"FAIRsharing.a0r156": {
"abbreviation": "OGMD",
"description": "Ontology of Glucose Metabolism Disorder includes disease names, phenotypes and their classifications involved in Glucose Metabolism Disorder, Diabetes. It must be used with other two ontologies, in the case of Diabetes: the Ontology of Geographical Region (OGR) and the Ontology for Genetic Disease Investigations (OGDI). Together, these three ontologies form the Ontology for Genetic Susceptibility Factor (OGSF), which is the project where information about this ontology is stored.",
"domains": [
"Glucose",
"Disease process modeling",
"Glucose metabolic process",
"Phenotype",
"Disease",
"Diabetes mellitus"
],
"homepage": "https://code.google.com/p/ogsf/",
"name": "Ontology of Glucose Metabolism Disorder",
"publications": [
{
"doi": "10.1186/2041-1480-5-19",
"pubmed": "24963371",
"title": "The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events",
"year": 2014
},
{
"pubmed": "20847592",
"title": "Ontology driven modeling for the knowledge of genetic susceptibility to disease",
"year": 2009
}
],
"subjects": [
"Genetics",
"Metabolomics",
"Biomedical Science"
]
},
"FAIRsharing.a0yy2x": {
"abbreviation": "IEV",
"description": "INOH Event Ontology (IEV) is a structured controlled vocabulary of pathway centric biological processes used to annotate biological processes, pathways, sub-pathways in the INOH pathway data. .",
"domains": [
"Mathematical model",
"Enzymatic reaction",
"Pathway model"
],
"homepage": "http://www.obofoundry.org/ontology/iev.html",
"license": "https://creativecommons.org/licenses/by/2.1/jp",
"name": "Integrating Network Objects with Hierarchies Event Ontology",
"publications": [
{
"doi": "10.1002/cfg.432",
"pubmed": "18629146",
"title": "The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature",
"year": 2008
},
{
"doi": "10.1093/database/bar052",
"pubmed": "22120663",
"title": "INOH: ontology-based highly structured database of signal transduction pathways",
"year": 2011
},
{
"pubmed": "17094236",
"title": "Event ontology: a pathway-centric ontology for biological processes",
"year": 2006
}
],
"subjects": [
"Biology"
]
},
"FAIRsharing.a14123": {
"abbreviation": "CO_335",
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Common Bean Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Food"
],
"homepage": "https://cropontology.org/term/CO_335:ROOT",
"license": "CC-BY-4.0",
"name": "Common Bean Ontology",
"subjects": [
"Botany",
"Agriculture"
]
},
"FAIRsharing.a15ac6": {
"abbreviation": "VIAF",
"description": "The VIAFΒ (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web.",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://viaf.org/",
"name": "Virtual International Authority File",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.a1e399": {
"abbreviation": "LM ID",
"description": "The LIPID MAPSΒ Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPSΒ Structure Database (LMSD) have been classified using this system and have been assigned a unique LIPID MAPSΒ ID (LM_ID). LMSD can be searched by lipid class, common name, systematic name or synonym, mass, InChIKey or LIPID MAPSΒ ID with the search box in the banner, or alternatively, by LIPID MAPSΒ ID, systematic or common name, mass, formula, category, main class, subclass data, or structure or sub-structure with one of the search interfaces in the LMSD database section. Each LMSD record contains an image of the molecular structure, common and systematic names, links to external databases, Wikipedia pages (where available), other annotations and links to structure viewing tools. In addition to LMSD search interfaces, you can drill down through the classification hierarchy below to the LMSD record for an individual lipid. LM IDs are comprised of a unique 12 character identifier string based on the classification schema: two fixed database designation characters, a two letter lipid category code, two digit lipid species class code, two digit lipid species subclass code, and a unique four character identifier within a subclass.",
"domains": [
"Annotation",
"Small molecule"
],
"homepage": "https://www.lipidmaps.org/databases/lmsd/browse",
"name": "LIPID MAPSΒ Lipid Classification System Identifier",
"publications": [
{
"doi": "10.1194/jlr.r800095-jlr200",
"pubmed": "19098281",
"title": "Update of the LIPID MAPS comprehensive classification system for lipids",
"year": 2008
},
{
"doi": "10.1194/jlr.s120001025",
"pubmed": "33037133",
"title": "Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures",
"year": 2020
}
],
"subjects": [
"Environmental Science",
"Molecular Chemistry",
"Life Science",
"Metabolomics",
"Biomedical Science"
],
"user_defined_tags": [
"lipidomics"
]
},
"FAIRsharing.a1j1a7": {
"abbreviation": "PE-O",
"description": "The PEO incorporates a wide range of key concepts and terms of PE from clinical and biomedical research in structuring the knowledge base that is specific to PE.",
"homepage": "http://bioportal.bioontology.org/ontologies/PE-O",
"name": "Pre-eclampsia Ontology",
"publications": [
{
"doi": "10.1371/journal.pone.0162828",
"title": "The Pre-Eclampsia Ontology: A Disease Ontology Representing the Domain Knowledge Specific to Pre-Eclampsia",
"year": 2016
}
],
"subjects": [
"Gynecology",
"Obstetrics"
]
},
"FAIRsharing.a3d34f": {
"abbreviation": "CETAF Stable Identifier",
"description": "The Stable Identifiers of the Consortium of European Taxonomic Facilities (CETAF) are globally unique, consistent and reliable identifiers for specimens in natural and botanical collections. These identifiers are used in the world wide web to redirect users and systems to images, websites and metadata of the physical objects and to integrate them with the semantic web. The CETAF identifier system is based on HTTP-URIs and Linked Data principles. It is simple and future-proof. Each collection object as well as its associated information resources (e.g. multimedia, RDF, webpages) are identified by stable HTTP-URIs that will never change. The URI Syntax for the objects is chosen and maintained by the institution owning them. This flexibility is one of the main advantages of the CETAF Stable Identifier system as it allows e.g. to include branding and local scope identifiers into the CETAF Stable Identifier URI.",
"homepage": "https://cetaf.org/best-practices/cetaf-stable-identifiers-csi-2/",
"license": "CC BY-SA 4.0",
"name": "Consortium of European Taxonomic Facilities Stable Identifier",
"publications": [
{
"doi": "10.1371/journal.pone.0261130",
"title": "A botanical demonstration of the potential of linking data using unique identifiers for people",
"year": 2021
},
{
"doi": "10.1093/database/bax003",
"title": "Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects",
"year": 2017
}
],
"subjects": [
"Taxonomy",
"Biodiversity"
]
},
"FAIRsharing.a3d659": {
"description": "RefSeq Identifiers for RNA and protein products come in two categories: those generated by the eukaryotic genome annotation pipeline that use accession prefixes XM_, XR_, and XP_; and those mainly derived from GenBank cDNA and EST data and are supported by the RefSeq eukaryotic curation group, which use accession prefixes NM_, NR_, and NP_.",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://www.ncbi.nlm.nih.gov/refseq/about/",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBamtFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--9dde9d9bb4456b42f37e21fc0f2ec72452993705/Screenshot%20from%202024-04-16%2013-36-53.png?disposition=inline",
"name": "RefSeq RNA and protein product Identifier",
"subjects": [
"Knowledge and Information Systems",
"Life Science"
]
},
"FAIRsharing.a4dcb9": {
"abbreviation": "AGI Glossary of Geology",
"description": "The American Geosciences Institute (AGI) Glossary of Geology is a reference vocabulary for the earth sciences. Information includes terms and definitions together with term history; the meaning of abbreviations, prefixes and acronyms common in the geoscience vocabulary; the dates many terms were first used; the preferred term of two or more synonyms; and in some cases a syllabification guide and background information. The Glossary is available in print, e-book or via online subscription. Online subscriptions are available for institutions only, and not to individuals.",
"homepage": "https://www.americangeosciences.org/pubs/glossary",
"name": "American Geosciences Institute Glossary of Geology",
"subjects": [
"Geology",
"Earth Science"
]
},
"FAIRsharing.a4ww64": {
"abbreviation": "ECSO",
"description": "DataONE ontology of Carbon Flux measurements for MsTMIP and LTER Use Cases",
"domains": [
"Ecosystem"
],
"homepage": "http://bioportal.bioontology.org/ontologies/ECSO",
"name": "The Ecosystem Ontology",
"subjects": [
"Earth Science",
"Ecosystem Science"
]
},
"FAIRsharing.a557he": {
"abbreviation": "OCVDAE",
"description": "With increased usage of cardiovascular drugs (CVDs) for treating cardiovascular diseases, it is important to analyze CVD-associated adverse events (AEs). The Ontology of Cardiovascular Drug Adverse Events (OCVDAE) is an ontology of adverse events associated with cardiovascular disease drugs. It extends the Ontology of Adverse Events (OAE) and NDF-RT. OCVDAE includes 194 CVDs, CVD ingredients, mechanisms of actions (MoAs), and CVD-associated 736 AEs.",
"domains": [
"Adverse Reaction",
"Cardiovascular disease",
"Approved drug"
],
"homepage": "http://bioportal.bioontology.org/ontologies/OCVDAE",
"name": "Ontology of Cardiovascular Drug Adverse Events",
"publications": [
{
"doi": "10.1038/s41598-017-12580-4",
"pubmed": "29061976",
"title": "Ontology-based systematical representation and drug class effect analysis of package insert-reported adverse events associated with cardiovascular drugs used in China",
"year": 2017
}
],
"repository": "https://github.com/OCVDAE/OCVDAE",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.a57627": {
"abbreviation": "ANZCTR Identifier",
"description": "Identifier schema for Australian New Zealand Clinical Trials Registry",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://bioregistry.io/registry/anzctr",
"name": "Australian New Zealand Clinical Trials Registry Identifier",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.a5e1jd": {
"abbreviation": "EMO",
"contact": {
"email": "gemma.l.holliday@gmail.com",
"name": "Gemma Holliday",
"orcid": "0000-0002-6731-6398"
},
"description": "The \"Enzyme Mechanism Ontology \" describes the components of an enzyme and its reaction mechanism including the roles that the components play in the reaction mechanism.",
"domains": [
"Mathematical model",
"Network model",
"Molecular entity",
"Enzymatic reaction",
"Enzyme",
"Pathway model"
],
"homepage": "http://bioportal.bioontology.org/ontologies/EMO",
"name": "Enzyme Mechanism Ontology",
"subjects": [
"Life Science"
]
},
"FAIRsharing.a67ec3": {
"abbreviation": "re3data Identifier",
"description": "This record describes the identifier schema for Re3data, a registry of research data repositories.",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://bioregistry.io/registry/re3data",
"name": "Registry of Research Data Repositories Identifier",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.a6r7zs": {
"abbreviation": "EDAM",
"description": "EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within bioscientific data analysis and data management (including computational biology, bioinformatics, and bioimage informatics). EDAM includes topics, operations, types of data and data identifiers, and data formats, relevant in data analysis and data management in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use. EDAM is particularly suitable for semantic annotations and categorisation of diverse resources related to data analysis and management: e.g. tools, workflows, learning materials, or standards. EDAM is also useful in data management itself, for recording provenance metadata of processed bioscientific data.",
"domains": [
"Analysis",
"Data acquisition",
"Data transformation"
],
"homepage": "http://edamontology.org",
"license": "CC BY-SA 4.0",
"name": "The bioscientific data analysis and management ontology",
"publications": [
{
"doi": "10.1093/bioinformatics/btt113",
"pubmed": "23479348",
"title": "EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats",
"year": 2013
},
{
"doi": "10.7490/f1000research.1118900.1",
"title": "EDAM: the bioscientific data analysis ontology (update 2021)",
"year": 2021
},
{
"doi": "10.5281/zenodo.3899895",
"title": "edamontology/edamontology: EDAM 1.25",
"year": 2020
}
],
"repository": "https://github.com/edamontology/edamontology",
"subjects": [
"Bioinformatics",
"Life Science",
"Subject Agnostic"
],
"twitter": "edamontology"
},
"FAIRsharing.a7154f": {
"description": "\nThis bilingual vocabulary (French and English) contains 3117 concepts covering the domains of agri-food science and technology, ranging \"from farm to table\", as well as nutritional and environmental aspects, taking into account the ongoing agricultural and food transition. The terminology is enriched with a large number of alternative entries (3230 in English or French) and hidden terms for easy searching. It has been aligned with the FoodOn ontology. ",
"domains": [
"Food"
],
"homepage": "https://skosmos.loterre.fr/Q1W/en/",
"license": "CC-BY-4.0",
"name": "Agri-food vocabulary",
"subjects": [
"Animal Nutrition",
"Food Process Engineering",
"Agriculture"
]
},
"FAIRsharing.a8diI4": {
"abbreviation": "UCD1+ Vocabulary",
"description": "This document describes the list of controlled terms used to build the Unified Content Descriptors, Version 1+ (UCD1+). The document describing the UCD1+ can be found at the URL: http://www.ivoa.net/Documents/latest/UCD.html. This document reviews the structure of the UCD1+ and presents the current vocabulary. This version contains new UCD words for the planetary data community as proposed in the Technical Note by Cecconi et al. The suggested list of line labels under the em.line branch is not included. A general solution is currently under study to deal with lists of element instances such spectral lines, chemical elements, elementary particles, etc. using either utypes or a vocabulary.",
"homepage": "http://www.ivoa.net/documents/UCD1+/",
"name": "The UCD1+ controlled vocabulary",
"subjects": [
"Astrophysics and Astronomy"
]
},
"FAIRsharing.aVmpKl": {
"abbreviation": "CIDO",
"description": "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment. Its development follows the OBO Foundry Principles.",
"domains": [
"Drug",
"Drug interaction",
"Infection",
"Disease"
],
"homepage": "https://github.com/cido-ontology/cido",
"license": "CC-BY-4.0",
"name": "Coronavirus Infectious Disease Ontology",
"publications": [
{
"doi": "10.1038/s41597-020-0523-6",
"pubmed": "32533075",
"title": "CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis",
"year": 2020
}
],
"repository": "https://github.com/CIDO-ontology/cido/issues",
"subjects": [
"Drug Discovery",
"Bioinformatics",
"Drug Repositioning",
"Virology",
"Epidemiology"
],
"user_defined_tags": [
"COVID-19"
]
},
"FAIRsharing.aae3v6": {
"abbreviation": "IDO",
"contact": {
"email": "Lindsay.Cowell@utsouthwestern.edu",
"name": "Lindsay Cowell",
"orcid": "0000-0003-1617-8244"
},
"description": "The IDO ontologies are designed as a set of interoperable ontologies that will together provide coverage of the infectious disease domain. At the core of the set is a general Infectious Disease Ontology (IDO-Core) of entities relevant to both biomedical and clinical aspects of most infectious diseases. Sub-domain specific extensions of IDO-Core complete the set providing ontology coverage of entities relevant to specific pathogens or diseases. Please note that, while the ontology remains available at https://github.com/infectious-disease-ontology/infectious-disease-ontology, it has not been updated in 5 years and should be used with care. Further, the original homepages provided by the resource developers (http://infectiousdiseaseontology.org/ and https://www.bioontology.org//wiki/Index.php/Infectious_Disease_Ontology) are either unavailable or empty.",
"domains": [
"Disease process modeling",
"Disease",
"Classification"
],
"homepage": "https://github.com/infectious-disease-ontology/infectious-disease-ontology",
"license": "https://creativecommons.org/licenses/by/3.0/us",
"name": "Infectious Disease Ontology Core",
"publications": [
{
"doi": "10.1186/s13326-021-00245-1",
"pubmed": "34275487",
"title": "The Infectious Disease Ontology in the age of COVID-19",
"year": 2021
}
],
"repository": "https://github.com/infectious-disease-ontology/infectious-disease-ontology",
"subjects": [
"Molecular Infection Biology",
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.abxd9x": {
"abbreviation": "TAO",
"contact": {
"email": "wasila.dahdul@usd.edu",
"name": "Wasila Dahdul",
"orcid": "0000-0003-3162-7490"
},
"description": "TAO is a multi-species ontology for teleost fishes that was initialized with terms from the Zebrafish Anatomical Ontology (ZFA). The development of the TAO focused on the skeletal system because it varies significantly across fishes, is well-preserved in fossil specimens, and it is often the focus of morphologically-based evolutionary studies in ichthyology. Note that TAO is a deprecated ontology and has been superceded by Uberon.",
"domains": [
"Morphology",
"Structure"
],
"homepage": "http://purl.bioontology.org/ontology/TAO",
"name": "Teleost Anatomy Ontology",
"publications": [
{
"doi": "10.1093/sysbio/syq013",
"pubmed": "20547776",
"title": "The teleost anatomy ontology: anatomical representation for the genomics age",
"year": 2010
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"FAIRsharing.acd824": {
"abbreviation": "ELSST",
"contact": {
"email": "carsten.thiel@cessda.eu",
"name": "Carsten Thiel ",
"orcid": "0000-0003-0804-8992"
},
"description": "The European Language Social Science Thesaurus (ELSST) is a broad-based, multilingual thesaurus for the social sciences. It is owned and published by the Consortium of European Social Science Data Archives (CESSDA) and its national Service Providers. The thesaurus consists of over 3,300 concepts and covers the core social science disciplines: politics, sociology, economics, education, law, crime, demography, health, employment, information, communication technology, and environmental science.\nELSST is used for data discovery within CESSDA and facilitates access to data resources across Europe, independent of domain, resource, language, or vocabulary.\n\nELSST is currently available in 16 languages: Danish, Dutch, Czech, English, Finnish, French, German, Greek, Hungarian, Icelandic, Lithuanian, Norwegian, Romanian, Slovenian, Spanish, and Swedish",
"homepage": "https://thesauri.cessda.eu/en/",
"license": "CC BY-SA 4.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaFFDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--ee784912b873e09e9d907ebf15f37fb26c0ce50d/Screenshot%20from%202022-11-22%2021-00-34.png?disposition=inline",
"name": "European Language Social Science Thesaurus",
"subjects": [
"Economics",
"Social Science"
],
"twitter": "CESSDA_Data/"
},
"FAIRsharing.ad3137": {
"abbreviation": "MedDRA",
"description": "MedDRA is a multilingual terminology allowing most users to operate in their native languages. MedDRA can be used to analyse individual medical events (e.g., βInfluenzaβ) or issues involving a system, organ or etiology (e.g., infections) using its hierarchical structure. MedDRA can be used for signal detection and monitoring of clinical syndromes whose symptoms encompass numerous systems or organs using its multi-axial hierarchy or through the special feature of Standardised MedDRA Queries. The ability to communicate adverse event data is another strength of MedDRA and has lead to MedDRA being an integral part of the ICH e-submission standards: eCTD (ICH M8) and ICSRs (ICH E2B).",
"domains": [
"Disease"
],
"homepage": "http://www.meddra.org/",
"name": "Medical Dictionary for Regulatory Activities Terminology",
"publications": [
{
"doi": "10.2165/00002018-199920020-00002",
"pubmed": "10082069",
"title": "The medical dictionary for regulatory activities (MedDRA)",
"year": 1999
},
{
"doi": "10.1016/s1386-5056(00)00062-9",
"pubmed": "10961570",
"title": "The use of a medical dictionary for regulatory activities terminology (MedDRA) in prescription-event monitoring in Japan (J-PEM)",
"year": 2000
}
],
"subjects": [
"Medicine",
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.ae8hpt": {
"abbreviation": "DOLCE",
"description": "DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering) is a foundational ontology developed as part of the WonderWeb Foundational Ontologies Library (WFOL). The development of this library has been guided by the need of a reliable set of foundational ontologies that can serve as 1) astarting point for building other ontologies, 2) a reference point for easy and rigorous comparisons among different ontological approaches, and 3) a rigorous basis for analyzing, harmonizing and integrating existing ontologies and metadata standards (by manually mapping them into some general module(s) in the library). DOLCE is the first module of WFOL and it is not a candidate for a universal standard ontology. Rather, it is intended as a starting point for comparing and elucidating the relationships with the other modules of the library, and also for clarifying the hidden assumptions underlying existing ontologies or linguistic resources such as WordNet. As reflected by its acronym, DOLCE has a clear cognitive bias, in the sense that it aims at capturing the ontological categories underlying natural language and human commonsense. DOLCE is an ontology that focuses on particulars in the sense that its domain of discourse is restricted to them. The project is complete, though the ontology remains available for use.",
"domains": [
"Classification"
],
"homepage": "http://www.loa.istc.cnr.it/dolce/overview.html",
"name": "Descriptive Ontology for Linguistic and Cognitive Engineering",
"subjects": [
"Knowledge and Information Systems",
"Computer Science",
"Subject Agnostic",
"Linguistics"
]
},
"FAIRsharing.aef0q5": {
"abbreviation": "CogAt",
"contact": {
"email": "poldrack@mail.utexas.edu",
"name": "Russell Poldrack",
"orcid": "0000-0001-6755-0259"
},
"description": "The Cognitive Atlas is a collaborative knowledge building project that aims to develop a knowledge base (or ontology) that characterizes the state of current thought in cognitive science. Cognitive neuroscience aims to map mental processes onto brain function, which begs the question of what \"mental processes\" exist and how they relate to the tasks that are used to manipulate and measure them.",
"domains": [
"Behavior",
"Cognition",
"Mental health"
],
"homepage": "http://www.cognitiveatlas.org/",
"license": "https://creativecommons.org/licenses/by-sa/3.0/us",
"name": "Cognitive Atlas",
"publications": [
{
"doi": "10.3389/fninf.2011.00017",
"pubmed": "21922006",
"title": "The cognitive atlas: toward a knowledge foundation for cognitive neuroscience",
"year": 2011
}
],
"subjects": [
"Neurobiology",
"Cognitive Neuroscience",
"Biomedical Science"
]
},
"FAIRsharing.aej2a8": {
"abbreviation": "GALEN",
"description": "A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.",
"homepage": "http://bioportal.bioontology.org/ontologies/1055",
"name": "Galen Ontology",
"subjects": [
"Medicine",
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.af5655": {
"abbreviation": "CO_333",
"description": "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution and breeding company within the project. Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Beet Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_333:ROOT",
"license": "CC-BY-4.0",
"name": "Beet Ontology",
"subjects": [
"Botany",
"Plant Breeding",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.af7a2d": {
"abbreviation": "CO_348",
"description": "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Brassica Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_348:ROOT",
"license": "CC-BY-4.0",
"name": "Brassica Ontology",
"repository": "https://github.com/Brassica-Trait-Ontology/brato",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.agvc7y": {
"abbreviation": "WB-PHENOTYPE",
"contact": {
"email": "garys@caltech.edu",
"name": "Gary Schindelman",
"orcid": "0000-0001-7883-4388"
},
"description": "A structured controlled vocabulary of Caenorhabditis elegans phenotypes .",
"domains": [
"Phenotype"
],
"homepage": "https://wormbase.org/tools/ontology_browser#o_browser",
"name": "C. elegans phenotype",
"publications": [
{
"doi": "10.1186/1471-2105-12-32",
"pubmed": "21261995",
"title": "Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community",
"year": 2011
}
],
"repository": "https://github.com/obophenotype/c-elegans-phenotype-ontology",
"subjects": [
"Anatomy",
"Life Science"
]
},
"FAIRsharing.akmeb9": {
"abbreviation": "VTO",
"description": "The Vertebrate Taxonomy Ontology includes both extinct and extant vertebrates, aiming to provide one comprehensive hierarchy. The hierarchy backbone for extant taxa is based on the NCBI taxonomy. Since the NCBI taxonomy only includes species associated with archived genetic data, to complement this, we also incorporate taxonomic information across the vertebrates from the Paleobiology Database (PaleoDB). The Teleost Taxonomy Ontology (TTO) and AmphibiaWeb (AWeb) are incorporated to provide a more authoritative hierarchy and a richer set of names for specific taxonomic groups.",
"domains": [
"Bone"
],
"homepage": "https://gitlab.com/phenoscape/vto",
"name": "Vertebrate Taxonomy Ontology",
"subjects": [
"Taxonomy"
]
},
"FAIRsharing.amcv1e": {
"abbreviation": "HGNC",
"description": "The HGNC approves both a short-form abbreviation known as a gene symbol, and also a longer and more descriptive name. Each symbol is unique and the committee ensures that each gene is only given one approved gene symbol. This allows for clear and unambiguous reference to genes in scientific communications, and facilitates electronic data retrieval from databases and publications.",
"domains": [
"Gene name",
"Protein",
"Pseudogene",
"Non-coding RNA"
],
"homepage": "https://www.genenames.org/",
"name": "HGNC Gene Symbols, Gene Names and IDs",
"publications": [
{
"doi": "10.1159/000131404",
"pubmed": "295268",
"title": "International system for human gene nomenclature (1979) ISGN (1979)",
"year": 1979
},
{
"doi": "10.1093/nar/gky930",
"pubmed": "30304474",
"title": "Genenames.org: the HGNC and VGNC resources in 2019",
"year": 2018
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.amf6me": {
"abbreviation": "VIVO-ISF",
"description": "The VIVO Integrated Semantic Framework ontology (VIVO-ISF Ontology, sometimes also known as the VIVO Ontology) represents researchers in the context of their experience, outputs, interests, accomplishments, and associated institutions. VIVO-ISF provides a set of types (classes) and relationships (properties) to represent researchers and the full context in which they work. The larger VIVO software is an open source platform for research discovery. Content in any local VIVO installation may be maintained manually, brought into VIVO in automated ways from local systems of record, such as HR, grants, course, and faculty activity databases, or from database providers such as publication aggregators and funding agencies.",
"domains": [
"Protocol",
"Study design"
],
"homepage": "https://wiki.lyrasis.org/display/VIVODOC110x/Ontology+Reference",
"license": "CC-BY-4.0",
"name": "VIVO Integrated Semantic Framework Ontology",
"repository": "https://github.com/openrif/vivo-isf-ontology",
"subjects": [
"Life Science",
"Biomedical Science"
],
"user_defined_tags": [
"Researcher data"
]
},
"FAIRsharing.an9ct0": {
"abbreviation": "DIAB",
"description": "The BioMedBridges diabetes-specific ontology enables users to integrate data resources related to prediabetes, diabetes, and late consequences/complications of diabetes. Data integration between mouse disease models and human studies is hindered by fundamental differences in the ontologies used by the respective communities to describe the same phenotypes. Common standards and ontologies to bridge the phenotype gap between mouse and human open extensive mouse phenotype data to clinical researchers. \n\nTo develop a comprehensive set of terms to describe Type 2 diabetes and obesity phenotypes in mouse and human, Type 2 Diabetes-related phenotypes were mined from the literature for use as new phenotype terms. Expert clinicians/diabetologists then curated the mined terms and categorised them by temporal disease stages. The ontology was then used for the annotation of mouse and human datasets with specific terminology representing Type 2 Diabetes progression, which will ultimately support translational research.",
"domains": [
"Diabetes mellitus"
],
"homepage": "http://www.biomedbridges.eu/unlocking-data-mouse-disease-models-diabetes-ontology",
"name": "BioMedBridges Diabetes Ontology",
"repository": "https://github.com/vasant32/DiabetesOntology",
"subjects": [
"Diabetology"
]
},
"FAIRsharing.anpj91": {
"abbreviation": "AGROVOC",
"description": "AGROVOC is a controlled vocabulary covering all areas of interest of the Food and Agriculture Organization (FAO) of the United Nations, including food, nutrition, agriculture, fisheries, forestry, environment etc. It is published by FAO and edited by a community of experts. AGROVOC consists of over 41,000 concepts available in up to 42 languages. AGROVOC uses semantic web technologies, linking to other multilingual knowledge organization systems and building bridges between datasets. Your library can use AGROVOC to index its documents or datasets, or you can use it from inside your content management system (e.g., Drupal) to organize your documents or web site. You can also use AGROVOC as an hub to access many other vocabularies available on the web. To date, AGROVOC is used by researchers, librarians and information managers for indexing, retrieving and organizing data in agricultural information systems and Web pages. Currently, AGROVOC is an SKOS-XL concept scheme and a Linked Open Data (LOD*) set aligned with over 20 other multilingual knowledge organization systems related to agriculture. You may browse AGROVOC, access its Web Services or SPARQL endpoint.",
"domains": [
"Food"
],
"homepage": "http://www.fao.org/agrovoc/",
"license": "CC-BY-3.0-IGO",
"name": "AGROVOC",
"publications": [
{
"doi": "10.3390/engproc2021009017",
"title": "How Agricultural Digital Innovation Can Benefit from Semantics: The Case of the AGROVOC Multilingual Thesaurus",
"year": 2021
},
{
"doi": "10.4060/cb2838en",
"title": "AGROVOC β Semantic data interoperability on food and agriculture",
"year": 2021
},
{
"doi": "10.1016/j.compag.2020.105965",
"title": "AGROVOC: The linked data concept hub for food and agriculture",
"year": 2022
}
],
"subjects": [
"Botany",
"Fisheries Science",
"Environmental Science",
"Forest Management",
"Data Management",
"Agriculture",
"Nutritional Science"
],
"twitter": "FAOAIMS",
"user_defined_tags": [
"thesaurus"
]
},
"FAIRsharing.aqnss4": {
"abbreviation": "thesaurus",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/3034",
"name": "thesaurus",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.as08v3": {
"abbreviation": "CareLex CV",
"description": "Contains controlled vocabulary terms from National Cancer Institute used to classify clinical trial electronic content (documents, images, etc). A Content model contains content classification categories (classes) and metadata properties (data properties). Data properties should be assigned to each Content Type. This model has been published as part of the new OASIS eTMF Standard, a draft specification available at: http://oasis-open.org/committees/etmf. CareLex is a non-profit organization formed to promote eClinical application and content interoperability for the life sciences and healthcare industries.",
"domains": [
"Cancer",
"Classification"
],
"homepage": "http://www.carelex.org/",
"name": "CareLex Controlled Vocabulary",
"subjects": [
"Life Science",
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.asg057": {
"abbreviation": "PEO",
"contact": {
"email": "priti@knoesis.org",
"name": "Priti Parikh",
"orcid": "0000-0002-1086-4190"
},
"description": "The Parasite Experiment Ontology (PEO) models the processes, instruments, parameters, and sample details that will be used to annotate experimental results with βprovenanceβ metadata (derivation history of results). The ontology was created to enable publication of results in journals, conferences with details of the method used to arrive at the result. Please note that the homepage is no longer active, and the ontology has not been updated in BioPortal since 2011. Until we can ascertain the current status of the ontology, we have marked this record as \"Uncertain\".",
"domains": [
"Drug",
"Drug combination effect modeling",
"Parasite",
"Life cycle"
],
"homepage": "http://bioportal.bioontology.org/ontologies/PEO",
"name": "Parasite Experiment Ontology",
"subjects": [
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.askzq4": {
"abbreviation": "IDODEN",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://code.google.com/p/dengue-fever-ontology/",
"name": "Dengue Fever Ontology",
"subjects": [
"Medicine"
]
},
"FAIRsharing.av8nfd": {
"abbreviation": "OFSMR",
"description": "This is the food-matrix ontology for the Open Food Safety Model Repository. Transferring predictive microbial models from research into real world food manufacturing or risk assessment applications is still a challenge for members of the food safety modelling community. This ontology supports the repository where existing predictive models previously published in the scientific literature were re-implemented using Predictive Modelling in Food Markup Language (PMF-ML), which is based on SBML.",
"homepage": "https://sites.google.com/site/openfsmr/",
"name": "Open Food Safety Model Ontology",
"publications": [
{
"doi": "10.1016/j.profoo.2016.02.098",
"title": "Towards Community Driven Food Safety Model Repositories",
"year": 2016
}
],
"subjects": [
"Life Science",
"Systems Biology"
]
},
"FAIRsharing.ay74mj": {
"abbreviation": "SYMP",
"contact": {
"email": "lynn.schriml@gmail.com",
"name": "Lynn Schriml",
"orcid": "0000-0001-8910-9851"
},
"description": "The symptom ontology was designed around the guiding concept of a symptom being: \"A perceived change in function, sensation or appearance reported by a patient indicative of a disease\". There is a close relationship between Signs and Symptoms, where Signs are the objective observation of an illness. The Symptom Ontology will work to broaden its scope to capture and document in a more robust manor these two sets of terms. At times, the same term may be both a Sign and a Symptom.",
"domains": [
"Patient care",
"Disease",
"Diagnosis"
],
"homepage": "https://disease-ontology.org/resources/symptom-ontology",
"license": "CC0-1.0",
"name": "Symptom Ontology",
"publications": [
{
"doi": "10.1093/nar/gkp832",
"pubmed": "19850722",
"title": "GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database",
"year": 2010
},
{
"doi": "10.1093/nar/gkad1051",
"pubmed": "37953304",
"title": "The DO-KB Knowledgebase: a 20-year journey developing the disease open science ecosystem",
"year": 2023
}
],
"repository": "https://github.com/DiseaseOntology/SymptomOntology/issues",
"subjects": [
"Life Science",
"Biomedical Science",
"Pain Medicine"
]
},
"FAIRsharing.ayjdsm": {
"abbreviation": "ATO",
"description": "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource",
"domains": [
"Taxonomic classification"
],
"homepage": "http://purl.bioontology.org/ontology/ATO",
"name": "Amphibian Taxonomy Ontology",
"subjects": [
"Taxonomy"
]
},
"FAIRsharing.azj141": {
"abbreviation": "MATRROCKIGNEOUS",
"description": "Material Rock Igneous component of SWEET ontology. SWEET is a highly modular ontology suite with many separate ontologies covering Earth system science. SWEET is a mid-level ontology and consists of nine top-level concepts that can be used as a foundation for domain-specific ontologies that extend these top-level SWEET components. ",
"homepage": "http://bioportal.bioontology.org/ontologies/MATRROCKIGNEOUS",
"name": "Material Rock Igneous",
"subjects": [
"Environmental Science",
"Earth Science"
]
},
"FAIRsharing.azq2t6": {
"abbreviation": "MIM",
"description": "A Molecular Interaction Map (MIM) is a diagram convention that is capable of unambiguous representation of networks containing multi-protein complexes, protein modifications, and enzymes that are substrates of other enzymes. This graphical representation makes it possible to view all of the many interactions in which a given molecule may be involved, and it can portray competing interactions, which are common in bioregulatory networks. In order to facilitate linkage to databases, each molecular species is represented only once in a diagram. ",
"domains": [
"Network model"
],
"homepage": "http://discover.nci.nih.gov/mim/",
"name": "Molecular Interaction Map",
"subjects": [
"Proteomics",
"Enzymology"
]
},
"FAIRsharing.azqskx": {
"abbreviation": "ENVO",
"description": "The Environment Ontology (EnvO) provides a controlled, structured vocabulary that is designed to support the annotation of any organism or biological sample with environment descriptors. EnvO contains terms ranging from astronomical objects, through planetary scale biomes, to nanomaterials. Further, these terms are interlinked with logical axioms describing their composition, colocalisation, and relationships to environmental and biological processes. Using ENVO terms for an environmental description allows a comprehensive description of environment that is key to machine-assisted integration, archiving and federated searching of environmental data.",
"domains": [
"Environmental material",
"Marine metagenome",
"Microbiome"
],
"homepage": "http://environmentontology.org/",
"license": "CC-BY-3.0",
"name": "Environment Ontology",
"publications": [
{
"doi": "10.1186/s13326-016-0097-6",
"pubmed": "27664130",
"title": "The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation",
"year": 2016
},
{
"doi": "10.1186/2041-1480-4-43",
"pubmed": "24330602",
"title": "The environment ontology: contextualising biological and biomedical entities",
"year": 2013
},
{
"doi": "10.1093/database/baw005",
"pubmed": "26896844",
"title": "EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation",
"year": 2016
},
{
"doi": "10.7717/peerj.1470",
"pubmed": "26713234",
"title": "Emerging semantics to link phenotype and environment",
"year": 2015
}
],
"repository": "https://github.com/EnvironmentOntology/envo",
"subjects": [
"Environmental Science",
"Ecology",
"Life Science",
"Nutritional Science",
"Epidemiology"
],
"twitter": "envoTweets"
},
"FAIRsharing.azr389": {
"abbreviation": "ECG",
"contact": {
"email": "rwinslow@jhu.edu",
"name": "Raimond Winslow",
"orcid": "0000-0003-1719-1651"
},
"description": "The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms. This ontology was developed and is being maintained by the CardioVascular Research Grid (www.cvrg.org).",
"domains": [
"Heart",
"Electrocardiography"
],
"homepage": "http://wiki.cvrgrid.org/index.php/Ontology_Development",
"name": "ElectroCardioGraphy Ontology",
"publications": [
{
"doi": "10.1016/j.jbi.2010.08.007",
"pubmed": "20800107",
"title": "Using an ECG reference ontology for semantic interoperability of ECG data",
"year": 2010
}
],
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.b084yh": {
"abbreviation": "OMIM Ontology",
"description": "OMIM is a comprehensive, authoritative compendium of human genes and genetic phenotypes as well as the relationship between them, that is freely available and updated daily. The OMIM ontology contains terms used within the OMIM database.",
"domains": [
"Disease process modeling",
"Phenotype",
"Disease",
"Genetic disorder",
"Genotype"
],
"homepage": "http://omim.org/",
"name": "Online Mendelian Inheritance in Man Ontology",
"publications": [
{
"doi": "10.1093/nar/gku1205",
"pubmed": "25428349",
"title": "OMIM.org: Online Mendelian Inheritance in Man (OMIM(R)), an online catalog of human genes and genetic disorders",
"year": 2014
}
],
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.b1xD9f": {
"abbreviation": "SRAO",
"description": "The Subject Resource Application Ontology (SRAO) is an application ontology describing subject areas / academic disciplines used within FAIRsharing records by curators and the user community. It is built in conjunction with the Domain Resource Application Ontology (DRAO), which contains more specific domain terms and other descriptors. All classes within SRAO come from publicly-available ontologies and controlled vocabularies.",
"domains": [
"Resource metadata",
"Classification",
"FAIR"
],
"homepage": "https://github.com/FAIRsharing/subject-ontology",
"license": "CC BY-SA 4.0",
"name": "Subject Resource Application Ontology",
"repository": "https://github.com/FAIRsharing/subject-ontology/issues",
"subjects": [
"Environmental Science",
"Humanities",
"Natural Science",
"Earth Science",
"Agriculture",
"Life Science",
"Computer Science",
"Biomedical Science"
],
"twitter": "FAIRsharing_org",
"user_defined_tags": [
"Metadata standardization"
]
},
"FAIRsharing.b220d4": {
"abbreviation": "CiTO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Citation Typing Ontology (CiTO) is an ontology that enables the characterization of the nature or type of citations, both factually and rhetorically. It is intended to allow authors (or others) to mark citation links and to capture citation intent when someone cites a particular publication. In particular, CiTO allows the creation of metadata describing citations that are distinct from metadata describing the cited works themselves, and permits the motives of an author when referring to another document to be captured.\n",
"domains": [
"Citation",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/cito",
"license": "CC-BY-4.0",
"name": "Citation Typing Ontology ",
"publications": [
{
"doi": "10.1016/j.websem.2012.08.001",
"title": "FaBiO and CiTO: Ontologies for describing bibliographic resources and citations",
"year": 2012
}
],
"repository": "https://github.com/sparontologies/cito",
"subjects": [
"Knowledge and Information Systems"
],
"twitter": "sparontologies"
},
"FAIRsharing.b2979t": {
"abbreviation": "MONDO",
"description": "MonDO (Monarch Disease Ontology) is a semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.",
"domains": [
"Biocuration"
],
"homepage": "https://github.com/monarch-initiative/mondo-build",
"license": "CC-BY-4.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdGtDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--898bdc43b92d38a40469367c9d28eae876b63f8b/mondo_logo_black-stacked.png?disposition=inline",
"name": "Monarch Disease Ontology",
"publications": [
{
"doi": "10.1101/2022.04.13.22273750",
"title": "Mondo: Unifying diseases for the world, by the world",
"year": 2022
},
{
"doi": "10.1093/nar/gkw1128",
"pubmed": "27899636",
"title": "The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species",
"year": 2016
}
],
"repository": "https://github.com/monarch-initiative/mondo",
"subjects": [
"Medicine",
"Infectious Disease Medicine"
],
"twitter": "MonarchInit"
},
"FAIRsharing.b34b43": {
"abbreviation": "FRBR",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/frbr",
"license": "CC-BY-4.0",
"name": "Essential FRBR in OWL2 DL Ontology ",
"repository": "https://github.com/sparontologies/frbr",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"FAIRsharing.b3c5ck": {
"abbreviation": "Lexeau",
"description": "This terminology is also known as the Lexique bilingue des textes et des donnΓ©es sur l'eau. The Lexeau project is in the research and developement stage, using existing software to test the lexicon model and user interface on specific themes of the water domain such as flooding. This resource does not have a specific homepage, and currently is only available via AgroPortal.",
"homepage": "http://agroportal.lirmm.fr/ontologies/LEXEAU",
"name": "Bilingual lexicon of water related texts and data",
"subjects": [
"Environmental Science",
"Earth Science",
"Water Management",
"Water Research"
]
},
"FAIRsharing.b3ca98": {
"description": "Identifier schema for Global Biodiversity Information Facility",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://bioregistry.io/registry/gbif",
"name": "Global Biodiversity Information Facility Identifier",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.b403jy": {
"abbreviation": "PE",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/PE",
"name": "Pulmonary Embolism Ontology",
"subjects": [
"Medicine"
]
},
"FAIRsharing.b4929b": {
"abbreviation": "HED",
"contact": {
"email": "Kay.Robbins@utsa.edu",
"name": "Kay Robbins",
"orcid": "0000-0002-7147-5797"
},
"description": "HED (Hierarchical Event Descriptors) is a framework for using a controlled yet extensible vocabulary to systematically describe experiment events of all types (perceptual, action, experiment control, task β¦).\n\nThe goals of HED are to enable and support its users to store and share recorded data in a fully analysis-ready format, and to support efficient (and/or extended cross-study) data search and analysis.\n\nHED may be used to annotate any type of data β but particularly data acquired in functional brain imaging (EEG, MEG, fNIRS, fMRI), multimodal (aka MoBI, mobile brain/body imaging), psychophysiological (ECG, EMG, GSR), or purely behavioral experiments.",
"domains": [
"Resource metadata",
"Annotation",
"Data retrieval",
"Analysis",
"Magnetic resonance imaging",
"Functional magnetic resonance imaging",
"Electroencephalography"
],
"homepage": "https://www.hedtags.org",
"license": "CC-BY-4.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBblVDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--2a5cc32eef94b2fa87d5380e467450f660019028/croppedWideLogo.png?disposition=inline",
"name": "Hierarchical Event Descriptors",
"publications": [
{
"doi": "10.1007/s12021-021-09537-4",
"pubmed": "34970709",
"title": "Building FAIR Functionality: Annotating Events in Time Series Data Using Hierarchical Event Descriptors (HED)",
"year": 2022
}
],
"repository": "https://github.com/hed-standard",
"subjects": [
"Neurophysiology",
"Computational Neuroscience",
"Cognitive Neuroscience",
"Electrophysiology"
],
"twitter": "HEDStandard",
"user_defined_tags": [
"Document metadata",
"Image analysis",
"Metadata standardization"
]
},
"FAIRsharing.b4sa0w": {
"abbreviation": "OOSTT",
"description": "The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2). It is developed collaboratively by domain and ontology experts in the NIH-funded CAFE (Comparative Assessment Framework for Environments of trauma care) project (1R01GM111324-01A1). It will be used as the ontology backbone of a graphical user interface comparing graphical representations of organizational structures.",
"homepage": "https://github.com/OOSTT/OOSTT",
"license": "CC-BY-4.0",
"name": "Ontology of Organizational Structures of Trauma centers and Trauma systems",
"repository": "https://github.com/OOSTT/OOSTT/",
"subjects": [
"Traumatology"
]
},
"FAIRsharing.b549b8": {
"abbreviation": "USI",
"contact": {
"email": "edeutsch@systemsbiology.org",
"name": "Eric Deutsch",
"orcid": "0000-0001-8732-0928"
},
"description": "The Universal Spectrum Identifier (USI) is multi-part key identifier for identifying mass spectra contained in public data repositories, primarily focused on proteomics. The USI provides a standardized mechanism for encoding a virtual path to any single mass spectrum generated by a mass spectrometer contained/deposited to public proteomics dataset repositories for enabling greater transparency of spectral evidence. With more than 1 billion USI identifications from over 3 billion spectra already available through ProteomeXchange repositories, Universal Spectrum Identifier encodes the dataset, the MS Run, the scan number and the proposed peptidoform and charge of the ions responsible for the spectrum. The USI identifier is comprised of five key components (and an optional sixth component) in defining an abstract path to a specified spectrum. The USI core components include: 1) the prefix βmzspecβ to make clear that the following string is a USI and to aid in automated mapping of a USI string to a URL, 2) the subsequent dataset submission or dataset collection identifier assigned by the primary repository archive, 3) the mass spectrometry run name (or root name of the raw vendor format file) such as an mzML file (with or without the file extension), 4) a type flag (such as βscanβ, βindexβ or βnativeIdβ as defined in the current mzML specification) for indicating how to interpret the fifth component, 5) the index value (based on the flag type) within the specified MS run, and optionally 6) any relevant information for interpretation of the spectrum if available. ",
"domains": [
"Mass spectrum",
"Data retrieval",
"Data identity and mapping",
"Omics data analysis"
],
"homepage": "http://psidev.info/usi",
"license": "Apache 2.0 License",
"name": "HUPO-PSI Universal Spectrum Identifier",
"publications": [
{
"doi": "10.1038/s41592-021-01184-6",
"pubmed": "34183830",
"title": "Universal Spectrum Identifier for mass spectra",
"year": 2021
}
],
"repository": "https://github.com/HUPO-PSI/usi/tree/master/Specification",
"subjects": [
"Data Governance",
"Proteomics",
"Metabolomics"
],
"user_defined_tags": [
"lipidomics"
]
},
"FAIRsharing.b5yzzf": {
"abbreviation": "DLORO",
"description": "Dependency Layered Ontology for Radiation Oncology",
"homepage": "https://ont2bn.radonc.washington.edu/IROK/",
"name": "Dependency Layered Ontology for Radiation Oncology",
"publications": [
{
"doi": "10.1002/mp.12340",
"title": "Developing Bayesian networks from a dependencyβlayered ontology: A proofβofβconcept in radiation oncology",
"year": 2017
}
],
"subjects": [
"Radiation Oncology"
]
},
"FAIRsharing.b70tzs": {
"abbreviation": "ENTITY",
"description": "This resource is no longer available because its underlying source material is not suitable for FAIRsharing: ISO-15926-2_2003_entityMembership. The record with identifier content 10.25504/FAIRsharing.b70tzs was invalid.",
"domains": [
"Data retrieval"
],
"homepage": "http://bioportal.bioontology.org/ontologies/ENTITY",
"name": "ISO-15926-2_2003_entityMembership",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.b7evv9": {
"abbreviation": "MeGO",
"description": "MeGO is dedicated to the functions of mobile genetic elements. The terms defined in MeGO are used to annotate phage and plasmid protein families in ACLAME. MeGO is a non-OBO ontology expanded from the Phage Ontology (PhiGO). ",
"domains": [
"Gene Ontology enrichment",
"Plasmid",
"Transcript",
"Mobile genetic element"
],
"homepage": "http://bioportal.bioontology.org/ontologies/MEGO/?p=summary",
"name": "MeGO",
"publications": [
{
"doi": "10.2144/05382rr04",
"pubmed": "15727134",
"title": "MEGO: gene functional module expression based on gene ontology",
"year": 2005
}
],
"subjects": [
"Genetics"
]
},
"FAIRsharing.b7gm54": {
"abbreviation": "CN",
"description": "This resource is no longer available because its underlying source material is not suitable for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/CN",
"name": "computer network",
"subjects": [
"Computer Science"
]
},
"FAIRsharing.b8233y": {
"abbreviation": "DwC_translations",
"contact": {
"email": "gtuco.btuco@gmail.com",
"name": "John Wieczorek",
"orcid": "0000-0003-1144-0290"
},
"description": "The Darwin Core is meant to serve a global community. Access to the documents describing the standard in multiple languages will facilitate open access and global adoption. This resource is meant to be an index to all translations of Darwin Core documents. Anyone interested in providing translations to be hosted with the corpus of the standard should contact the Darwin Core Task Group.",
"homepage": "https://tdwg.github.io/rs.tdwg.org/",
"license": "CC-BY-4.0",
"name": "Darwin Core translations",
"publications": [
{
"doi": "10.1371/journal.pone.0029715",
"pubmed": "22238640",
"title": "Darwin Core: an evolving community-developed biodiversity data standard",
"year": 2012
}
],
"subjects": [
"Biodiversity"
],
"user_defined_tags": [
"Data standards"
]
},
"FAIRsharing.b82qvn": {
"abbreviation": "CHD",
"description": "Congenital Heart Defects Ontology (CHD) is a standard that represents the ontology of CHD.",
"domains": [
"Annotation",
"Heart"
],
"homepage": "https://bioportal.bioontology.org/ontologies/CHD/?p=summary",
"name": "Congenital Heart Defects Ontology",
"subjects": [
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.b91873": {
"abbreviation": "OEO",
"description": "The Open Energy Ontology (OEO) is a domain ontology within the field of energy system modelling. The goal of OEO is to ease cooperation and exchange of information across the energy systems analysis domain. It is designed to map the complexity of this research area and to collect, connect and structure the ambiguous terminology of those adjacent domains the energy systems analysis domain needs information from.",
"homepage": "https://openenergy-platform.org/ontology/",
"license": "CC0-1.0",
"name": "Open Energy Ontology",
"publications": [
{
"doi": "10.1016/j.egyai.2021.100074",
"title": "Introducing the Open Energy Ontology: Enhancing data interpretation and interfacing in energy systems analysis",
"year": 2021
}
],
"repository": "https://github.com/OpenEnergyPlatform/ontology",
"subjects": [
"Energy Engineering"
]
},
"FAIRsharing.b9znd5": {
"abbreviation": "ICO",
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun He",
"orcid": "0000-0001-9189-9661"
},
"description": "Informed Consent Ontology (ICO) represents the documentations and processes involved in informed consent. ICO aims to support informed consent data integration and reasoning in the clinical research space. The core terms of ICO covers informed consent forms, the component inside the informed consent form, and various informed consent processes.",
"homepage": "https://github.com/ICO-ontology/ICO",
"name": "Informed Consent Ontology",
"repository": "https://github.com/ICO-ontology/ICO/issues",
"subjects": [
"Medicine",
"Clinical Studies",
"Health Science",
"Biomedical Science"
]
},
"FAIRsharing.ba68c5": {
"description": "This tri-lingual thesaurus (French, English, Spanish) structures, with a polyhierarchy, the main concepts of open science. It was initiated by building on existing glossaries and on the taxonomy proposed in the framework of the FOSTER project. It is enriched through a text-mining task of reference documents in the field.",
"domains": [
"FAIR"
],
"homepage": "https://www.loterre.fr/skosmos/TSO/en/",
"license": "CC-BY-4.0",
"name": "Open science thesaurus",
"subjects": [
"Knowledge and Information Systems"
],
"user_defined_tags": [
"Open Access",
"Open Science",
"open scholarship"
]
},
"FAIRsharing.bc8ayj": {
"abbreviation": "ZFS",
"description": "An ontology of developmental stages of the Zebrafish (Danio rerio). Note that ZFA includes the leaf nodes of this ontology.",
"domains": [
"Aging",
"Life cycle"
],
"homepage": "http://bioportal.bioontology.org/ontologies/ZFS",
"name": "Zebrafish Developmental Stages",
"subjects": [
"Anatomy",
"Zoology",
"Marine Biology",
"Developmental Biology"
]
},
"FAIRsharing.bdf6ab": {
"abbreviation": "ISRCTN Identifier",
"description": "Identifier schema for International Traditional Medicine Clinical Trial Registry",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://bioregistry.io/registry/isrctn",
"name": "International Traditional Medicine Clinical Trial Registry Identifier",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.beb855": {
"abbreviation": "C4O",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Citation Counting and Context Characterisation Ontology (C4O) is an ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date;",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/c4o",
"license": "CC-BY-4.0",
"name": "Citation Counting and Context Characterization Ontology ",
"repository": "https://github.com/sparontologies/c4o",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"FAIRsharing.bey51s": {
"abbreviation": "CO_125",
"description": "The Banana Anatomy Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype",
"Morphology"
],
"homepage": "https://cropontology.org/term/CO_125:ROOT",
"license": "CC-BY-4.0",
"name": "Banana Anatomy Ontology",
"subjects": [
"Botany",
"Agriculture",
"Plant Anatomy"
]
},
"FAIRsharing.bf8dsb": {
"abbreviation": "MEDLINEPLUS",
"description": "This resource provides information on the symptoms, causes, treatment and prevention for a wide range of diseases, illnesses, health conditions and wellness issues. MedlinePlus health topics are regularly reviewed, and links are updated daily.",
"domains": [
"Disease"
],
"homepage": "http://www.nlm.nih.gov/medlineplus/xmldescription.html",
"name": "MedlinePlus Health Topics",
"subjects": [
"Medicine",
"Health Science",
"Biomedical Science"
]
},
"FAIRsharing.bfcfd0": {
"abbreviation": "PCL",
"contact": {
"email": "davidos@ebi.ac.uk",
"name": "David Osumi-Sutherland",
"orcid": "0000-0002-7073-9172"
},
"description": "PCL is an ontology created to record claims of potential new cell types derived from single cell data analysis, where there is no additional evidence that supports the addition of corresponding classically defined cell type to the Cell Ontology (CL). PCL hence provides a place for terms that might not be ready for CL.",
"domains": [
"Annotation",
"Cell"
],
"homepage": "https://github.com/obophenotype/provisional_cell_ontology",
"license": "CC-BY-4.0",
"name": "Provisional Cell Ontology",
"publications": [
{
"doi": "10.1101/2021.10.10.463703",
"title": "Brain Data Standards Ontology: A data-driven ontology of transcriptomically defined cell types in the primary motor cortex",
"year": 2021
}
],
"repository": "https://github.com/obophenotype/provisional_cell_ontology/issues",
"subjects": [
"Anatomy",
"Life Science",
"Cell Biology"
]
},
"FAIRsharing.bg7bb6": {
"abbreviation": "OHD",
"description": "The Oral Health and Disease Ontology is intended as a BFO and OBO Foundry compliant ontology for the oral health domain. It is currently used to represent the content of dental practice health records and is intended to be further developed for use in translation medicine. It demonstrates a principled split between billing codes as information entities and what the codes are about, such as dental procedures, materials, and patients. OHD is structured using BFO uses terms from OGMS, OBI, IAO and FMA. In addition it uses terms from CARO, OMRSE, NCBITaxon, and a subset of terms from the Current Dental Terminology (CDT) OHD is in early development and subject to change without notice.",
"homepage": "https://github.com/oral-health-and-disease-ontologies/ohd-ontology",
"name": "The Oral Health and Disease Ontology",
"subjects": [
"Medicine",
"Dentistry",
"Oral Surgery"
]
},
"FAIRsharing.bgkyd7": {
"abbreviation": "MMO",
"contact": {
"email": "shimoyama@mcw.edu",
"name": "Mary Shimoyama",
"orcid": "0000-0003-1176-0796"
},
"description": "The Measurement Method Ontology is designed to represent the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms.",
"domains": [
"Model organism",
"Phenotype"
],
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000",
"name": "Measurement Method Ontology",
"publications": [
{
"doi": "10.3389/fgene.2012.00087",
"pubmed": "22654893",
"title": "Three ontologies to define phenotype measurement data",
"year": 2012
},
{
"doi": "10.1186/2041-1480-4-26",
"pubmed": "24103152",
"title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications",
"year": 2013
}
],
"subjects": [
"Life Science",
"Biomedical Science",
"Preclinical Studies"
],
"twitter": "ratgenome"
},
"FAIRsharing.bgx54j": {
"abbreviation": "MHC",
"contact": {
"email": "david_deluca@dfci.harvard.edu",
"name": "David S. DeLuca",
"orcid": "0000-0002-0141-9116"
},
"description": "MHC, or major histocompatibility complex is a gene complex found in jawed vertebrates. The genes found on this region of the genome include several important genes which encode proteins which are responsible for presenting peptides on the cell surface for inspection by cells of the immune system. In human, such genes are called HLA (human leukocyte antigen). MaHCO contains terms necessary for describing and categorizing concepts related to MHC, in general, and for a number of model species, and also for humans.",
"domains": [
"Major histocompatibility complex",
"Immune system"
],
"homepage": "http://www.bioinformatics.org/mahco/wiki/",
"name": "MaHCO",
"publications": [
{
"doi": "10.1093/bioinformatics/btp306",
"pubmed": "19429601",
"title": "MaHCO: an ontology of the major histocompatibility complex for immunoinformatic applications and text mining",
"year": 2009
}
],
"subjects": [
"Health Science",
"Biomedical Science"
]
},
"FAIRsharing.bke5k": {
"abbreviation": "RAO",
"description": "A controlled vocabulary of RA-relevant information. Currently, only treatment information is available.",
"homepage": "http://bioportal.bioontology.org/ontologies/RAO",
"name": "Rheumatoid Arthritis ontology",
"subjects": [
"Rheumatology"
]
},
"FAIRsharing.bkejsq": {
"abbreviation": "HUPSON",
"description": "Large biomedical simulation initiatives, such as the Virtual Physiological Human (VPH), are substantially dependent on controlled vocabularies to facilitate the exchange of information, of data and of models. Hindering these initiatives is a lack of a comprehensive ontology that covers the essential concepts of the simulation domain. We propose a first version of a newly constructed ontology, HuPSON, as a basis for shared semantics and interoperability of simulations, of models, of algorithms and of other resources in this domain. The ontology is based on the Basic Formal Ontology, and adheres to the MIREOT principles.",
"domains": [
"Modeling and simulation",
"Algorithm"
],
"homepage": "http://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads.html",
"name": "Human Physiology Simulation Ontology",
"subjects": [
"Systems Biology",
"Medical Informatics"
]
},
"FAIRsharing.bnx9cf": {
"abbreviation": "MCCL",
"description": "The Molecular Connections Cell Line Ontology models primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. The ontology covers all cell lines from sources such ATCC, DSMZ, ECACC, ICLC. This ontology has been developed as an extension of the sub class βcell line cellβ which is a part of the major class βexperimentally modified cellβ of the Cell type [CL] ontology that already existed in OBO foundry. Disease ontology with which the cell line relates to has been exported from βHuman Diseaseβ [DOID] ontology and the organ/tissue details relate to the βFoundational model of anatomyβ [FMA] ontology. There appears to be no official homepage.",
"domains": [
"Cell line",
"Cell",
"Protein"
],
"homepage": "https://bioportal.bioontology.org/ontologies/MCCL",
"name": "Molecular Connections Cell Line Ontology",
"subjects": [
"Anatomy",
"Health Science",
"Life Science"
]
},
"FAIRsharing.brhpb0": {
"abbreviation": "MicrO",
"description": "MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The ontology was built to support the ongoing development of a natural language processing algorithm, MicroPIE (or, Microbial Phenomics Information Extractor). FAIRsharing curators have been unable to contact the project developers, and as such this record has been marked as Uncertain. Please contact us if you have any information on this resource.",
"domains": [
"Assay",
"Cell culture",
"Phenotype"
],
"homepage": "https://github.com/carrineblank/MicrO",
"license": "CC BY 2.0",
"name": "Ontology of Prokaryotic Phenotypic and Metabolic Characters",
"publications": [
{
"doi": "10.1186/s13326-016-0060-6",
"pubmed": "27076900",
"title": "MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions",
"year": 2016
}
],
"repository": "https://github.com/carrineblank/MicrO/issues",
"subjects": [
"Bioinformatics",
"Microbiology"
]
},
"FAIRsharing.bst9e4": {
"abbreviation": "TM-CONST",
"description": "The value set for the Constitution property of the International Classification of Traditional Medicine (ICTM). The World Health Organization, in consultation with a large group of stakeholders in the areas of Traditional Medicine or Complementary and Alternative Medicine and Health Information Systems, has developed a collaborative project plan to produce an international standard terminology and classification system for Traditional Medicine. This resource is part of an effort to produce an international standard for information on TM that is ready for electronic health records and that will serve as a standard for scientific comparability and communication.",
"homepage": "https://sites.google.com/site/whoictm/home",
"name": "Traditional Medicine Constitution Value Set",
"subjects": [
"Traditional Medicine"
]
},
"FAIRsharing.bxc508": {
"abbreviation": "OBIB",
"description": "The ontology for Biobanking (OBIB) is an ontology built for annotation and modeling of biobank repository and biobanking administration. It is developed based on subset of Ontology for Biomedical Investigations (OBI) using Basic Formal Ontology (BFO) as top ontology and following OBO Foundry principles. The first version of the ontology is merged of two existing biobank related ontologies, OMIABIS and biobank ontology.",
"domains": [
"Biobank"
],
"homepage": "https://github.com/biobanking/biobanking/wiki",
"license": "CC-BY-4.0",
"name": "Ontology for Biobanking",
"publications": [
{
"doi": "10.1186/s13326-016-0068-y",
"title": "OBIB-a novel ontology for biobanking",
"year": 2016
}
],
"subjects": [
"Health Science"
]
},
"FAIRsharing.c06f1e": {
"abbreviation": "DataCite",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The DataCite Ontology (DataCite) is an ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/datacite",
"license": "CC-BY-4.0",
"name": "DataCite Ontology ",
"repository": "https://github.com/sparontologies/datacite",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"FAIRsharing.c0bvcy": {
"abbreviation": "SSN",
"description": "The Semantic Sensor Network (SSN) ontology is an ontology for describing sensors and their observations, the involved procedures, the studied features of interest, the samples used to do so, and the observed properties, as well as actuators. SSN follows a horizontal and vertical modularization architecture by including a lightweight but self-contained core ontology called SOSA (Sensor, Observation, Sample, and Actuator) for its elementary classes and properties. With their different scope and different degrees of axiomatization, SSN (http://www.w3.org/ns/ssn/) and SOSA (http://www.w3.org/ns/sosa/) are able to support a wide range of applications and use cases, including satellite imagery, large-scale scientific monitoring, industrial and household infrastructures, social sensing, citizen science, observation-driven ontology engineering, and the Web of Things. ",
"domains": [
"Resource metadata",
"Imaging",
"Monitoring"
],
"homepage": "https://www.w3.org/TR/vocab-ssn/",
"name": "Semantic Sensor Network Ontology",
"publications": [
{
"doi": "10.1016/j.websem.2012.05.003",
"title": "The SSN ontology of the W3C semantic sensor network incubator group",
"year": 2012
},
{
"doi": "10.3233/sw-180320",
"title": "The Modular SSN Ontology: A Joint W3C and OGC Standard Specifying the Semantics of Sensors, Observations, Sampling, and Actuation",
"year": 2019
},
{
"doi": "10.1016/j.websem.2018.06.003",
"title": "SOSA: A lightweight ontology for sensors, observations, samples, and actuators",
"year": 2018
}
],
"repository": "https://github.com/w3c/sdw/issues",
"subjects": [
"Remote Sensing"
],
"user_defined_tags": [
"Sensor data",
"Web of Things",
"ontology"
]
},
"FAIRsharing.c26a4e": {
"abbreviation": "ERM Identifier",
"contact": {
"email": "egon.willighagen@maastrichtuniversity.nl",
"name": "Egon Willighagen",
"orcid": "0000-0001-7542-0286"
},
"description": "Identifier project to uniquely identify nanomaterials, allowing them to identify materials in experimental designs, data, reports, project deliverables, and scholarly publications.",
"domains": [
"Chemical entity"
],
"homepage": "https://nanocommons.github.io/identifiers/",
"license": "CC0-1.0",
"name": "European Registry of Materials Identifier",
"publications": [
{
"doi": "10.1186/s13321-022-00614-7",
"title": "European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials",
"year": 2022
}
],
"subjects": [
"Nanotechnology",
"Materials Informatics"
]
},
"FAIRsharing.c2yb5w": {
"abbreviation": "MADS/RDF",
"description": "MADS/RDF is a knowledge organization system (KOS) designed for use with controlled values for names (personal, corporate, geographic, etc.), thesauri, taxonomies, subject heading systems, and other controlled value lists. It is closely related to SKOS, the Simple Knowledge Organization System and a widely supported and adopted RDF vocabulary. MADS/RDF has been fully mapped to SKOS. It is presented as an OWL ontology. While SKOS is very broad in its application, MADS/RDF is designed specifically to support authority data as used by and needed in the LIS community and its technology systems. For example, MADS/RDF provides a means to record data from the Machine Readable Cataloging (MARC) Authorities format in RDF for use in semantic applications and Linked Data projects.",
"domains": [
"Citation",
"Bibliography"
],
"homepage": "http://id.loc.gov/ontologies/madsrdf/v1.html",
"license": "https://www.loc.gov/legal",
"name": "Metadata Authority Description Schema in RDF",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.c496e6": {
"abbreviation": "ICHI",
"description": "The International Classification of Health Interventions (ICHI) is for reporting and analysing health interventions for clinical and statistical purposes.",
"homepage": "https://www.who.int/standards/classifications/international-classification-of-health-interventions",
"name": "International Classification of Health Interventions",
"subjects": [
"Clinical Studies",
"Statistics",
"Global Health"
]
},
"FAIRsharing.c4e46c": {
"abbreviation": "PWO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Publishing Workflow Ontology (PWO) is a simple ontology for describing the steps in the workflow associated with the publication of a document or other publication entity.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/pwo",
"license": "CC-BY-4.0",
"name": " Publishing Workflow Ontology ",
"publications": [
{
"doi": "10.3233/sw-160230",
"title": "The Publishing Workflow Ontology (PWO)",
"year": 2014
}
],
"repository": "https://github.com/sparontologies/pwo",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"FAIRsharing.c5qpnc": {
"abbreviation": "NPI",
"description": "Terminologies of Non-Pharmacological Interventions",
"homepage": "https://bioportal.bioontology.org/ontologies/NPI",
"name": "Non-Pharmacological Interventions",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.c6vhm3": {
"abbreviation": "HSAPDV",
"description": "Life cycle stages for Human. HsapDv was developed by the Bgee group with assistance from the core Uberon developers and the Human developmental anatomy ontology (EHDAA2) developers. Currently it includes both embryonic (Carnegie) stages and adult stages.",
"domains": [
"Life cycle stage"
],
"homepage": "https://obofoundry.org/ontology/hsapdv.html",
"license": "CC-BY-3.0",
"name": "Human Developmental Stages Ontology",
"repository": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv",
"subjects": [
"Anatomy",
"Developmental Biology"
]
},
"FAIRsharing.c7c940": {
"abbreviation": "Educational Sciences",
"description": "Controlled vocabulary used for indexing bibliographical records for the \"Educational sciences\" FRANCIS database (1972-2015, http://pascal-francis.inist.fr/). This resource contains 2681 entries grouped into 52 collections, each entry being described by an English and a French preferred term.",
"homepage": "https://skosmos.loterre.fr/216/en/",
"license": "CC BY-NC 4.0",
"name": "Educational Sciences Vocabulary",
"subjects": [
"Education Science",
"Humanities and Social Science",
"Educational Psychology"
]
},
"FAIRsharing.c7f365": {
"abbreviation": "IGSN (Generic)",
"description": "An IGSN ID is a globally unique and persistent identifier for physical samples in all scientific fields. An IGSN ID can be applied to an individual sample, an aggregation of samples, or to a feature-of-interest (the real-world feature that the sample is taken from). From 2021, IGSN IDs are functionally DOIs and are registered with metadata encoded in the DataCite Metadata Schema. The IGSN ID, previously known as an \"International GeoSample Number\", naming schema has changed, to reflects the expanding scope and utilization as a partnership agreement between DataCite and the IGSN e.V.",
"domains": [
"Citation"
],
"homepage": "https://www.igsn.org",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaVVDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--4d19e53906f86cdaca6a9752fde1dd82276b7f22/igsn-original.jpg?disposition=inline",
"name": "International Generic Sample Number",
"publications": [
{
"doi": "10.5334/dsj-2017-002",
"title": "Utilizing the International Geo Sample Number Concept in Continental Scientific Drilling During ICDP Expedition COSC-1",
"year": 2017
},
{
"doi": "10.5334/dsj-2021-033",
"title": "Towards Globally Unique Identification of Physical Samples: Governance and Technical Implementation of the IGSN Global Sample Number",
"year": 2021
},
{
"doi": "10.5334/dsj-2023-005",
"title": "Scaling Identifiers and their Metadata to Gigascale: An Architecture to Tackle the Challenges of Volume and Variety",
"year": 2023
},
{
"doi": "10.1007/978-3-030-85040-1_162",
"title": "International Generic Sample Number",
"year": 2023
},
{
"doi": "10.5281/zenodo.5118289",
"title": "IGSN 2040 Summary Report: Defining the Future of the IGSN as a Global Persistent Identifier for Material Samples",
"year": 2021
}
],
"subjects": [
"Geochemistry",
"Hydrogeology",
"Environmental Science",
"Geology",
"Earth Science"
],
"user_defined_tags": [
"physical samples"
]
},
"FAIRsharing.c7f4d7": {
"abbreviation": "CO_356",
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Vitis Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_356:ROOT",
"license": "CC BY-SA 4.0",
"name": "Vitis Ontology",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.c86b48": {
"abbreviation": "SCoRO",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The Scholarly Contributions and Roles Ontology (SCoRO) is an ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator)",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/scoro",
"license": "CC-BY-4.0",
"name": "Scholarly Contributions and Roles Ontology ",
"publications": [
{
"doi": "10.3233/sw-150177",
"title": "The Document Components Ontology (DoCO)",
"year": 2016
}
],
"repository": "https://github.com/sparontologies/deo",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"FAIRsharing.c86z66": {
"abbreviation": "OlatDv",
"description": "Life cycle stages for Medaka. OlatDv is based on the original medaka stage ontology MFO by Thorsten Henrich. Currently it includes only pre-adult stages.",
"domains": [
"Life cycle stage"
],
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv",
"license": "CC-BY-3.0",
"name": "Medaka Stage Ontology",
"repository": "https://github.com/obophenotype/developmental-stage-ontologies/issues",
"subjects": [
"Aquaculture",
"Developmental Biology",
"Life Science"
]
},
"FAIRsharing.c9v5sz": {
"abbreviation": "PTS",
"description": "Pathwas terminology systems integrates biological Events and various Pathway types.",
"homepage": "http://bioportal.bioontology.org/ontologies/PTS",
"name": "Pathway Terminology System",
"subjects": [
"Biology"
]
},
"FAIRsharing.ca63ce": {
"abbreviation": "FO",
"description": "Fern Ontology (FO) is a controlled and structured vocabulary of fern specific anatomy and lifecycle.",
"domains": [
"Plant development stage"
],
"homepage": "http://bioportal.bioontology.org/ontologies/FO",
"name": "Fern Ontology",
"subjects": [
"Life Science",
"Plant Anatomy",
"Plant Cell Biology"
]
},
"FAIRsharing.cakne1": {
"abbreviation": "NIDM-Results",
"description": "NIDM-Results is a data model that enable sharing neuroimaging results using a common descriptive standard across neuroimaging software. NIDM-Results focuses on mass-univariate studies and is mostly targeted at fMRI but is also suitable for anatomical MRI (with Voxel-Based Morphometry), and Positron Emission Tomography (PET). NIDM-Results packs provide a lightweight solution to share maps generated by neuroimaging studies along with their metadata. Export to NIDM-Results is natively implemented in SPM, NeuroVault and CBRAIN and a Python library is ready for integration in FSL. NeuroVault additionally can import NIDM-Results packs.",
"domains": [
"Magnetic resonance imaging",
"Positron emission tomography",
"Functional magnetic resonance imaging",
"Brain",
"Brain imaging"
],
"homepage": "http://nidm.nidash.org/specs/nidm-results.html",
"license": "CC0-1.0",
"name": "NIDM-Results",
"subjects": [
"Neurobiology",
"Computational Neuroscience",
"Neurology"
]
},
"FAIRsharing.cbz72b": {
"abbreviation": "BO",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/3059",
"name": "BOOK",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.cc3f2x": {
"abbreviation": "OMP",
"description": "The Ontology of Microbial Phenotypes (OMP) is a community ontology for annotating microbial phenotypes, including bacteria, archaea, protists, fungi, and viruses. It has been created to help with standardized capture of essential phenotypic information. OMP is designed to be compatible with other microbial phenotype ontologies, such as the Fission Yeast Phenotype Ontology (FYPO) and the Ascomycete Phenotype Ontology (APO), and aims to standardize the capture of phenotypic information to allow improved cross-species data mining and analysis.",
"domains": [
"Phenotype"
],
"homepage": "https://microbialphenotypes.org",
"license": "CC-BY-3.0",
"name": "Ontology of Microbial Phenotypes",
"publications": [
{
"doi": "10.1186/s12866-014-0294-3",
"pubmed": "25433798",
"title": "An ontology for microbial phenotypes",
"year": 2014
}
],
"repository": "https://github.com/microbialphenotypes/OMP-ontology",
"subjects": [
"Data Mining",
"Microbiology",
"Biology"
]
},
"FAIRsharing.cd7603": {
"abbreviation": "TNM",
"description": "The TNM Classification of Malignant Tumors (TNM) is a global standard for classifying the anatomical extent of the spread of malignant tumours (cancer).",
"domains": [
"Cancer"
],
"homepage": "https://www.uicc.org/what-we-do/sharing-knowledge/tnm",
"name": "Tumor Node Metastasis",
"subjects": [
"Oncology"
],
"twitter": "uicc"
},
"FAIRsharing.cdc4cb": {
"description": "Engineering sciences vocabulary used for indexing bibliographical records for the PASCAL database until 2014 (https://pascal-francis.inist.fr/). This vocabulary contains 8746 concepts, all of which have an English and a French preferred label.",
"homepage": "https://skosmos.loterre.fr/QJP/en/",
"license": "CC-BY-4.0",
"name": "Engineering sciences vocabulary",
"subjects": [
"Engineering Science"
]
},
"FAIRsharing.cfe09b": {
"description": "The DDI Agency Identifier is part of a free globally-unique identifier system for metadata-producing organizations. In concert with the DDI Agency Registry, the DDI Agency Identifier acts as both a namespace in a globally-unique id and a pointer for distributed service resolution.\nBased on ISO/IEC 11179 Part 6 International Registration Data Identifiers (11179 IRDIs), DDI agency identifiers are used as the Registration Authority (11179 RA) in a IRDI and in DDI URNs.",
"domains": [
"Resource metadata",
"Centrally registered identifier"
],
"homepage": "https://registry.ddialliance.org/",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBZ2dDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--a87e9d8c4f63f4465f2c282dad5ebdfdf9144344/logo.png?disposition=inline",
"name": "DDI Agency Identifier",
"repository": "https://github.com/Colectica/ddiregistry",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.cga8gf": {
"abbreviation": "CU-VO",
"description": "Record does not exist anymore: Venom Ontology. The record with identifier content 10.25504/FAIRsharing.cga8gf was invalid.",
"homepage": "http://bioportal.bioontology.org/ontologies/CU-VO",
"name": "Venom Ontology",
"subjects": [
"Biology"
]
},
"FAIRsharing.cjzx96": {
"abbreviation": "GTO",
"description": "The Genetic Test Ontology (GTO) was created with the aim of filling the gap between the large volume of available genetic tests and insufficient usage of these genetic tests. The GTO was built on top of a meta-ontology by populating specific genetic testing data. Literature data from SemMedDB has been extracted and integrated into the GTO to provide scientific evidence.",
"homepage": "http://qianzhu-lab.umbc.edu/",
"name": "Genetic Testing Ontology",
"subjects": [
"Genetics",
"Human Genetics"
]
},
"FAIRsharing.ckd4rf": {
"abbreviation": "ADO",
"description": "The Alzheimer's Disease Ontology (ADO) is an ontology representing relevant knowledge on Alzheimerβs disease. ADO was developed with the purpose of containing information relevant to four main biological viewsβpreclinical, clinical, etiological, and molecular/cellular mechanismsβand contains synonyms and references.",
"homepage": "https://bioportal.bioontology.org/ontologies/ADO",
"name": "Alzheimer's Disease Ontology",
"publications": [
{
"doi": "10.1016/j.jalz.2013.02.009",
"pubmed": "23830913",
"title": "ADO: a disease ontology representing the domain knowledge specific to Alzheimer's disease",
"year": 2013
}
],
"subjects": [
"Health Science"
],
"user_defined_tags": [
"Alzheimerβs disease"
]
},
"FAIRsharing.ckrs1g": {
"abbreviation": "PDQ",
"description": "Physician Data Query (PDQ) Terminology is part of NCI's comprehensive cancer information database, which contains expert summaries on a wide range of cancer topics, a listing of some 30,000 cancer clinical trials from around the world, a directory of genetics services professionals, the NCI Dictionary of Cancer Terms, and the NCI Drug Dictionary.",
"domains": [
"Drug",
"Cancer",
"Treatment"
],
"homepage": "https://www.cancer.gov/publications/pdq",
"name": "Physician Data Query",
"publications": [
{
"doi": "10.1093/jnci/djx022",
"title": "PDQ (Physician Data Query) (February 2017)",
"year": 2017
},
{
"doi": "10.1080/08858198609527818",
"pubmed": "3079208",
"title": "The Physician Data Query (PDQ) cancer information system",
"year": 1986
},
{
"doi": "10.1016/0305-7372(91)90010-w",
"pubmed": "1804524",
"title": "The PDQ (Physician Data Query), the cancer database, in oncological clinical practice",
"year": 1991
},
{
"doi": "10.1093/jnci/djs025",
"pubmed": "22271770",
"title": "Physician data query (PDQ(R)) update (February 2012)",
"year": 2012
},
{
"doi": "10.1093/jnci/djs231",
"pubmed": "22517987",
"title": "Physician Data Query (PDQ(R)) update (May 2012 )",
"year": 2012
},
{
"doi": "10.1093/jnci/djw336",
"title": "PDQ (Physician Data Query) (January 2017)",
"year": 2017
},
{
"doi": "10.1093/jnci/djx047",
"title": "PDQ (Physician Data Query) (March 2017)",
"year": 2017
},
{
"doi": "10.1007/s13187-013-0536-3",
"pubmed": "23996204",
"title": "NCI's Physician Data Query (PDQ(R)) cancer information summaries: history, editorial processes, influence, and reach",
"year": 2013
}
],
"subjects": [
"Oncology",
"Medicine",
"Genetics",
"Health Science",
"Life Science",
"Pharmacogenomics",
"Biomedical Science"
]
},
"FAIRsharing.cnbjkn": {
"abbreviation": "SNPO",
"contact": {
"email": "adrien.coulet@loria.fr",
"name": "Adrien Coulet",
"orcid": "0000-0002-1466-062X"
},
"description": "The SNP Ontology is a domain ontology that provides a formal representation (OWL-DL) of genomic variations. Despite its name, SNP-Ontology, is not limited to the representation of SNPs but it encompasses genomic variations in a broader meaning. The SNP Ontology is general enough to enable the representation of variations observed in the genome of various species.",
"domains": [
"Deoxyribonucleic acid",
"Genetic polymorphism",
"Single nucleotide polymorphism",
"Genome",
"Sequence variant",
"Genotype"
],
"homepage": "https://members.loria.fr/ACoulet/files/snpontology1.6_description.html",
"name": "Single Nucleotide Polymorphism Ontology",
"subjects": [
"Genomics",
"Proteomics"
]
},
"FAIRsharing.cp0ybc": {
"abbreviation": "RO",
"contact": {
"email": "ro-model-dev@googlegroups.com",
"name": "Stian Soiland-Reyes",
"orcid": "0000-0001-9842-9718"
},
"description": "The Wf4Ever Research Object Model provides a vocabulary for the description of workflow-centric Research Objects: aggregations of resources relating to scientific workflows.",
"domains": [
"Resource metadata",
"Reproducibility",
"Workflow"
],
"homepage": "https://w3id.org/ro/",
"license": "CC-BY-3.0",
"name": "Wf4Ever Research Object Model 1.0",
"publications": [
{
"doi": "10.1186/2041-1480-5-41",
"pubmed": "25276335",
"title": "Structuring research methods and data with the research object model: genomics workflows as a case study",
"year": 2014
}
],
"repository": "https://github.com/ResearchObject/ro-tutorials",
"subjects": [
"Natural Science"
],
"user_defined_tags": [
"Research object"
]
},
"FAIRsharing.crq91b": {
"abbreviation": "SURGICAL",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Nurse"
],
"homepage": "http://bioportal.bioontology.org/ontologies/SURGICAL",
"name": "Nurse Surgical",
"subjects": [
"Health Science"
]
},
"FAIRsharing.ct3xa3": {
"abbreviation": "PO PSDS",
"description": "A controlled vocabulary of growth and developmental stages in various plants. Note that this has been subsumed into the Plant Ontology (PO).",
"domains": [
"Structure",
"Life cycle",
"Life cycle stage"
],
"homepage": "http://browser.planteome.org/amigo/term/PO:0009012#display-lineage-tab",
"license": "CC-BY-4.0",
"name": "Plant Structure Development Stage",
"publications": [
{
"doi": "10.1093/nar/gkm908",
"pubmed": "18194960",
"title": "The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations",
"year": 2008
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"FAIRsharing.ctqJoR": {
"description": "This trilingual thesaurus (French, English, Spanish) deals with the 118 chemical elements of the periodic table recognized by the IUPAC. It is aligned with ChEBI, wikidata, wikipedia, DBpedia.",
"domains": [
"Chemical entity"
],
"homepage": "https://www.loterre.fr/skosmos/8HQ/en/",
"license": "CC-BY-4.0",
"name": "Inist Periodic Table of the Elements Trilingual Thesaurus",
"subjects": [
"Chemistry"
],
"user_defined_tags": [
"chemical element"
]
},
"FAIRsharing.cyv30a": {
"abbreviation": "TOK",
"description": "An Ontology describing resources with different formats. This Ontology can be used to annotate and describe terminological / ontological knowledge resources.",
"domains": [
"Taxonomic classification"
],
"homepage": "http://bioportal.bioontology.org/ontologies/TOK",
"name": "Terminological and Ontological Knowledge Resources Ontology",
"subjects": [
"Life Science"
]
},
"FAIRsharing.cz9cnp": {
"abbreviation": "OHMI",
"description": "OHMI is aimed to ontologically represent various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions.",
"domains": [
"Host",
"Microbiome"
],
"homepage": "https://github.com/ohmi-ontology/ohmi",
"name": "Ontology of Host-Microbe Interactions",
"subjects": [
"Life Science"
]
},
"FAIRsharing.czzmpg": {
"abbreviation": "CO_321",
"contact": {
"email": "R.Shrestha2@cgiar.org",
"name": "Rosemary Shrestha",
"orcid": "0000-0002-9399-8003"
},
"description": "This ontology defines traits of the International Wheat Information System (IWIS) database and wheat descriptor. The Wheat Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_321:ROOT",
"license": "CC-BY-4.0",
"name": "Wheat Ontology",
"publications": [
{
"doi": "10.1093/aobpla/plq008",
"pubmed": "22476066",
"title": "Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature",
"year": 2010
}
],
"subjects": [
"Agriculture",
"Life Science"
]
},
"FAIRsharing.d092a4": {
"abbreviation": "TheSoz",
"description": "The Thesaurus for the Social Sciences (TheSoz) isa SKOS-based German thesaurus for the social sciences. It is intended as an aid for indexing documents and research information as well as for search term recommendation. The TheSoz is available in three languages (German, English and French). The thesaurus covers all topics and sub-disciplines of the social sciences, including sociology, employment re-search, pedagogics and political science.",
"homepage": "https://lod.gesis.org/thesoz/en/index",
"license": "CC BY-NC-ND 3.0",
"name": "Thesaurus for the Social Sciences",
"subjects": [
"Economics",
"Social Science",
"Education Science",
"Political Science"
],
"user_defined_tags": [
"Employment"
]
},
"FAIRsharing.d099fb": {
"abbreviation": "minid",
"contact": {
"email": "foster@uchicago.edu",
"name": "Ian Foster",
"orcid": "0000-0003-2129-5269"
},
"description": "A Minimal Viable Identifier (minid) provides a lightweight way of uniquely and unambiguously identifying research data products and is sufficiently simple to create and use to make data easily findable, accessible, interoperable, and reusable (FAIR). ",
"domains": [
"Citation",
"Data retrieval",
"Publication"
],
"homepage": "https://github.com/fair-research/minid",
"license": "CC-BY-3.0",
"name": "Minimal Viable Identifier",
"publications": [
{
"doi": "10.1371/journal.pone.0294883",
"title": "Correction: Reproducible big data science: A case study in continuous FAIRness",
"year": 2023
},
{
"doi": "10.1371/journal.pone.0213013",
"pubmed": "30973881",
"title": "Reproducible big data science: A case study in continuous FAIRness",
"year": 2019
}
],
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.d0a681": {
"abbreviation": "EuroVoc",
"description": "EuroVoc is a multilingual, multidisciplinary thesaurus covering the activities of the EU, the European Parliament in particular. It contains terms in 23 official EU languages, plus in three languages of countries which are candidates for EU accession. The aim of the thesaurus is to provide the information management and dissemination services with a coherent indexing tool for the effective management of their documentary resources and to enable users to carry out documentary searches using a controlled vocabulary.",
"domains": [
"Food",
"Transport"
],
"homepage": "https://op.europa.eu/en/web/eu-vocabularies/th-dataset/-/resource/dataset/eurovoc",
"name": "EuroVoc",
"subjects": [
"Economics",
"Fisheries Science",
"Public Finance",
"Environmental Science",
"Forest Management",
"Transportation Planning",
"Social Science",
"Geography",
"Energy Engineering",
"Business Administration",
"Agriculture",
"Social Policy",
"Linguistics",
"Political Science"
],
"user_defined_tags": [
"Employment",
"International Relations",
"Trade"
]
},
"FAIRsharing.d1zzym": {
"abbreviation": "EO",
"description": "The Ethnicity Ontology (EO) has been developed by extending BFO to have a common reference for ethnicity concepts for semantic integration of datasets. It attempts to utilise iterated proxy markers for ethnicity such language spoken and interpreter requirements in order to support health care research studies.",
"homepage": "http://bioportal.bioontology.org/ontologies/EO",
"name": "Ethnicity Ontology",
"publications": [
{
"doi": "10.14236/jhi.v23i4.920",
"pubmed": "28346128",
"title": "Ethnicity Recording in Primary Care Computerised Medical Record Systems: An Ontological Approach",
"year": 2017
}
],
"subjects": [
"Health Science",
"Social Anthropology",
"Medical Informatics"
],
"user_defined_tags": [
"Language"
]
},
"FAIRsharing.d261e1": {
"abbreviation": "URI",
"contact": {
"email": "connolly@w3.org",
"name": "Dan Connolly",
"orcid": "0000-0002-0928-7103"
},
"description": "A Uniform Resource Identifier (URI) is a compact sequence of characters that identifies an abstract or physical resource. This specification defines the generic URI syntax and a process for resolving URI references that might be in relative form, along with guidelines and security considerations for the use of URIs on the Internet. The URI syntax defines a grammar that is a superset of all valid URIs, allowing an implementation to parse the common components of a URI reference without knowing the scheme-specific requirements of every possible identifier. This specification does not define a generative grammar for URIs; that task is performed by the individual specifications of each URI scheme.",
"domains": [
"Web service"
],
"homepage": "https://www.rfc-editor.org/rfc/rfc3986",
"name": "Uniform Resource Identifier",
"publications": [
{
"doi": "10.17487/rfc3986",
"title": "Uniform Resource Identifier (URI): Generic Syntax",
"year": 2005
}
],
"subjects": [
"Knowledge and Information Systems",
"Subject Agnostic"
]
},
"FAIRsharing.d2d84f": {
"abbreviation": "OPMI",
"contact": {
"email": "yongqunh@umich.edu",
"name": "Yongqun He",
"orcid": "0000-0001-9189-9661"
},
"description": "The Ontology of Precision Medicine and Investigation (OPMI) ontology is an application ontology to support precision medicine and related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles. OPMI reuses, aligns, and integrates related terms from existing ontologies in the OBO ontology library. OPMI aims to represent and standardize the entities associated with precision medicine, including all the data/metadata types, investigation processes, and analysis in various aspects of clinical, pathological, and molecular studies to be conducted in KPMP. The Kidney Tissue Atlas Ontology (KTAO) is a more kidney-specific complementary addition to OMPI precision medicine-related terms that can be used in parallel. ",
"domains": [
"Disease"
],
"homepage": "https://github.com/OPMI/opmi",
"license": "CC-BY-4.0",
"name": "Ontology of Precision Medicine and Investigation",
"subjects": [
"Clinical Studies",
"Omics"
]
},
"FAIRsharing.d31795": {
"abbreviation": "LCSH",
"description": "The Library of Congress Subject Headings (LCSH) provides catalog headings for materials held at the Library of Congress. Libraries throughout the United States use LCSH to provide subject access to their collections. LCSH is also used internationally, often in translation. The LCSH online resource includes all Library of Congress Subject Headings, free-floating subdivisions (topical and form), Genre/Form headings, Children's (AC) headings, and validation strings for which authority records have been created.",
"homepage": "https://id.loc.gov/authorities/subjects.html",
"license": "https://www.loc.gov/legal",
"name": "Library of Congress Subject Headings",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.d3pqw7": {
"abbreviation": "QUDT",
"description": "The QUDT, or 'Quantity, Unit, Dimension and Type' collection of ontologies define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems. QUDT provides a unified model of measurable quantities, units for measuring different kinds of quantities, the numerical values of quantities in different units of measure and the data structures and data types used to store and manipulate these objects in software. This OWL schema is a foundation for a basic treatment of units. Originally developed by TopQuadrant for the NASA Exploration Initiatives Ontology Models (NExIOM) project, they now form the basis of the NASA QUDT Handbook. QUDT aims to improve interoperability of data and the specification of information structures through industry standards for Units of Measure, Quantity Kinds, Dimensions and Data Types.",
"domains": [
"Experimental measurement",
"Unit"
],
"homepage": "http://qudt.org/",
"license": "CC-BY-4.0",
"name": "Quantities, Units, Dimensions and Types",
"repository": "https://github.com/qudt/qudt-public-repo/blob/master/docs/2020-04-28%20Intro%20to%20QUDT.pdf",
"subjects": [
"Astrophysics and Astronomy"
]
},
"FAIRsharing.d50st0": {
"abbreviation": "OntoMA",
"description": "Common concepts for communication between traditional medicine and western medicine. (In French)",
"homepage": "http://bioportal.bioontology.org/ontologies/3090",
"name": "Ontology of Alternative Medicine, French",
"subjects": [
"Traditional Medicine"
]
},
"FAIRsharing.d5a210": {
"abbreviation": "JCBN - Amino Acids and Peptides",
"description": "The Nomenclature and Symbolism for Amino Acids and Peptides, created by the IUPAC-IUB Joint Commission on Biochemical Nomenclature, formalizes the naming scheme for amino acids, non-peptide derivatives of amino acids and peptides as well as peptide derivatives. It also describes the 3-letter and 1-letter symbols for amino acids.",
"domains": [
"Peptide identification",
"Peptide",
"Classification",
"Protein",
"Amino acid sequence"
],
"homepage": "https://www.qmul.ac.uk/sbcs/iupac/misc/naabb.html",
"name": "IUPAC-IUB Joint Commission on Biochemical Nomenclature - Nomenclature and Symbolism for Amino Acids and Peptides",
"subjects": [
"Biochemistry"
]
},
"FAIRsharing.d5c06e": {
"abbreviation": "DEB",
"contact": {
"email": "osnat.hakimi@gmail.com",
"name": "Osnat Hakimi",
"orcid": "0000-0002-8839-4846"
},
"description": "The Devices, Experimental scaffolds and Biomaterials Ontology (DEB) is an open resource for organizing information about biomaterials, their design, manufacture and biological testing.",
"homepage": "https://projectdebbie.github.io/",
"license": "CC0-1.0",
"name": "Devices, Experimental Scaffolds, and Biomaterials Ontology",
"publications": [
{
"doi": "10.1002/adfm.201909910",
"title": "The Devices, Experimental Scaffolds, and Biomaterials Ontology (DEB): A Tool for Mapping, Annotation, and Analysis of Biomaterials Data",
"year": 2020
}
],
"repository": "https://github.com/ProjectDebbie/Ontology_DEB",
"subjects": [
"Biomaterials",
"Biomedical Science"
],
"user_defined_tags": [
"medical devices"
]
},
"FAIRsharing.d5ff6e": {
"abbreviation": "SDGIO",
"contact": {
"email": "pier.buttigieg@awi.de",
"name": "Pier Luigi Buttigieg",
"orcid": "0000-0002-4366-3088"
},
"description": "The Sustainable Development Goals Interface Ontology (SDGIO) aims to provide a semantic bridge between 1) the Sustainable Development Goals, their targets, and indicators and 2) the large array of entities they refer to. SDGIO will reuse existing ontologies where appropriate.",
"domains": [
"Sustainability"
],
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{
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{
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"title": "InChI version 1.06: now more than 99.99% reliable",
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"abbreviation": "ODNAE",
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"abbreviation": "DINTO",
"description": "DINTO is an OWL ontology that systematically organizes all drug-drug interaction (DDI) related information.",
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"abbreviation": "FIBO",
"description": "The Financial Industry Business Ontology (FIBO) is the global standard ontology for efficient and unambiguous financial services. FIBO is developed as an ontology in the Web Ontology Language (OWL). The language is codified by the World Wide Web Consortium (W3C), and it is based on Description Logic.",
"homepage": "https://spec.edmcouncil.org/fibo/",
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{
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"title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications",
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"abbreviation": "ICPS",
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"abbreviation": "MFOEM",
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"pubmed": "25937879",
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"homepage": "https://data.inrae.fr/dataset.xhtml?persistentId=doi:10.15454/1.4822495904463706E12",
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"description": "The Sorghum Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
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"homepage": "https://cropontology.org/term/CO_324:ROOT",
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"FAIRsharing.dyj433": {
"abbreviation": "PSO",
"description": "It is the ontology embedding PRIME (Prospective Risk Analysis in Medical Environments) in related issues of patient safety research and activities. It classifies terms and express relations between them. The ontology building in an ongoing process. Any comments are welcome.",
"domains": [
"Monitoring",
"Hospital"
],
"homepage": "http://bioportal.bioontology.org/ontologies/PSO",
"name": "PatientSafetyOntology",
"subjects": [
"Occupational Medicine",
"Medical Informatics"
]
},
"FAIRsharing.dyqz3y": {
"abbreviation": "APO",
"contact": {
"email": "cherry@stanford.edu",
"name": "J. Michael Cherry",
"orcid": "0000-0001-9163-5180"
},
"description": "Ascomycete Phenotype Ontology is a structured controlled vocabulary for the phenotypes of Ascomycete fungi.",
"domains": [
"Mutation",
"Study design",
"Phenotype",
"Morphology",
"Life cycle stage"
],
"homepage": "http://bioportal.bioontology.org/ontologies/APO?p=summary",
"name": "Ascomycete Phenotype Ontology",
"subjects": [
"Life Science",
"Cell Biology"
],
"twitter": "yeastgenome"
},
"FAIRsharing.dzxae": {
"abbreviation": "FOODON",
"contact": {
"email": "damion.dooley@bccdc.ca",
"name": "Damion Dooley",
"orcid": "0000-0002-8844-9165"
},
"description": "The need to represent knowledge about food is central to many human activities including agriculture, medicine, food safety inspection, shopping patterns, and sustainable development. FoodOn is built to interoperate with the OBO Library and to represent entities which bear a food role. Initially the ontology will focus on the human-centric categorization and handling of food, but in the future it will also encompass materials in natural ecosystems and food webs. We aim to develop semantics for food safety, food security, the agricultural and animal husbandry practices linked to food production, culinary, nutritional and chemical ingredients and processes.",
"domains": [
"Sustainability",
"Food",
"Disease"
],
"homepage": "https://foodon.org/",
"license": "CC-BY-3.0",
"name": "Food Ontology",
"publications": [
{
"doi": "10.3389/fmicb.2017.01068",
"pubmed": "28694792",
"title": "Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance",
"year": 2017
},
{
"doi": "10.1038/s41538-018-0032-6",
"pubmed": "31304272",
"title": "FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration",
"year": 2019
}
],
"repository": "https://github.com/FoodOntology/foodon",
"subjects": [
"Botany",
"Environmental Science",
"Medicine",
"Agriculture"
]
},
"FAIRsharing.e1c595": {
"abbreviation": "Brick",
"description": "Brick is an open-source effort to standardize semantic descriptions of the physical, logical and virtual assets in buildings and the relationships between them. Brick consists of an extensible dictionary of terms and concepts in and around buildings, a set of relationships for linking and composing concepts together, and a flexible data model permitting seamless integration of Brick with existing tools and databases. Through the use of powerful Semantic Web technology, Brick can describe the broad set of idiosyncratic and custom features, assets and subsystems found across the building stock in a consistent matter. Adopting Brick as the canonical description of a building enables the following: 1) Brick lowers the cost of deploying analytics, energy efficiency measures and intelligent controls across buildings, 2) Brick presents an integrated, cross-vendor representation of the multitude of subsystems in modern buildings: HVAC, lighting, fire, security and so on, 3) Brick simplifies the development of smart analytics and control applications, and 4) Brick reduces the reliance upon the non-standard, unstructured labels endemic to building management systems.\n",
"domains": [
"Data model"
],
"homepage": "https://brickschema.org/",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBYXc9IiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--5c7080d13b18a371dfa46816c406e7c896c6f921/Brick.png?disposition=inline",
"name": "Brick - A Uniform Metadata Schema For Buildings",
"publications": [
{
"doi": "10.1145/2993422.2993577",
"title": "Brick",
"year": 2016
},
{
"doi": "10.1016/j.apenergy.2018.02.091",
"title": "Brick : Metadata schema for portable smart building applications",
"year": 2018
},
{
"doi": "10.1145/3408308.3427627",
"title": "Shepherding Metadata Through the Building Lifecycle",
"year": 2020
},
{
"doi": "10.1145/3137133.3141449",
"title": "HodDB",
"year": 2018
},
{
"doi": "10.1145/3276774.3276794",
"title": "Plaster",
"year": 2018
},
{
"doi": "10.1145/3276774.3276795",
"title": "Scrabble",
"year": 2018
},
{
"doi": "10.1145/3276774.3276796",
"title": "Mortar",
"year": 2018
},
{
"doi": "10.1145/3199666",
"title": "Design and Analysis of a Query Processor for Brick",
"year": 2018
},
{
"doi": "10.1016/j.aei.2018.04.010",
"title": "A large-scale evaluation of automated metadata inference approaches on sensors from air handling units",
"year": 2018
},
{
"doi": "10.1145/3360322.3360862",
"title": "Beyond a House of Sticks",
"year": 2019
},
{
"doi": "10.1145/3408308.3431125",
"title": "Interactive Metadata Integration with Brick",
"year": 2020
}
],
"repository": "https://github.com/BrickSchema/brick",
"subjects": [
"Building Informatics",
"Industrial Engineering",
"Energy Engineering",
"Systems Engineering",
"Power Engineering",
"Building Design"
],
"user_defined_tags": [
"building information modeling"
]
},
"FAIRsharing.e1yjxM": {
"abbreviation": "Glossary",
"description": "CDISC Glossary seeks to harmonize definitions (including acronyms, abbreviations, and initials) used in the various standards initiatives undertaken by CDISC in clinical research. Glossary also serves the community of clinical researchers by selecting and defining terms pertaining to clinical research, particularly eClinical investigations, sponsored by the pharmaceutical industry or a federal agency.",
"homepage": "https://www.cdisc.org/standards/glossary",
"name": "CDISC Glossary",
"subjects": [
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.e21b3k": {
"abbreviation": "PPIO",
"description": "Record does not exist anymore: Protein-Protein Interaction Ontology. The record with identifier content https://doi.org/10.25504/FAIRsharing.e21b3k was invalid.",
"homepage": "http://psidev.sf.net",
"name": "Protein-Protein Interaction Ontology"
},
"FAIRsharing.e2zy7j": {
"abbreviation": "apollo-ls",
"contact": {
"email": "juest4@pitt.edu",
"name": "Jeremy Espino",
"orcid": "0000-0001-8104-2656"
},
"description": "The Apollo Location Service (LS) Database issues persistent identifiers for locations for specific time intervals, including intervals that start in the past and are still open at present (i.e., the identifier should be used to refer to the location today). Temporally specific location identifiers are particularly important in epidemiology because the epidemiological record includes locations that do not presently exist, location names that have changed and location names whose political boundaries have changed.",
"domains": [
"Geographical location"
],
"homepage": "http://betaweb.rods.pitt.edu/ls",
"name": "Apollo Location Code",
"subjects": [
"Epidemiology"
],
"user_defined_tags": [
"Geographic Information System (GIS)"
]
},
"FAIRsharing.e3t0yw": {
"abbreviation": "CIO",
"description": "The Confidence Information Ontology (CIO) is an ontology to capture confidence information about annotations. Please note that the last update to the ontology files were in 2015.",
"domains": [
"Annotation"
],
"homepage": "https://github.com/BgeeDB/confidence-information-ontology",
"license": "CC0-1.0",
"name": "Confidence Information Ontology",
"publications": [
{
"doi": "10.1093/database/bav043",
"title": "The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations",
"year": 2015
}
],
"subjects": [
"Biology"
]
},
"FAIRsharing.e45arr": {
"abbreviation": "OntoBiotope",
"contact": {
"email": "claire.nedellec@jouy.inra.fr",
"name": "Claire NΓ©dellec",
"orcid": "0000-0002-0577-0595"
},
"description": "OntoBiotope is an ontology of microorganism habitats. Its modeling principle and its lexicon reflect the biotope classification used by biologists to describe microorganism isolation sites (e.g. GenBank, GOLD, ATCC). OntoBiotope is developed and maintained by the Meta-omics of Microbial Ecosystems (MEM) network in which 30 microbiologists from INRA (French National Institute for Agricultural Research) from all fields of applied microbiology participate. The relevance of OntoBiotope terms is evaluated through the PubMedBiotope semantic search engine. It identifies and categorizes microbial biotopes in all PubMed abstracts by applying the ToMap method (Text to Ontology Mapping) to the OntoBiotope ontology. It also indexes 3,35 millions relations between taxa and their habitats.",
"domains": [
"Text mining",
"Ecosystem"
],
"homepage": "http://dx.doi.org/10.15454/1.4382640528105164E12",
"license": "CC-BY-4.0",
"name": "OntoBiotope",
"subjects": [
"Genomics",
"Life Science"
],
"user_defined_tags": [
"Natural Resources, Earth and Environment"
]
},
"FAIRsharing.e68dba": {
"abbreviation": "PaST Thesaurus",
"description": "The Paleoenvironmental Standard Terms (PaST) Thesaurus is a thesaurus of standard terms used for defining measured variables by the World Data Service for Paleoclimatology. These terms describe the quantity measured, the material on which it was measured, reported error, units, analytical or statistical methods, transformations made to raw data, reconstructed seasonality, data type, and data format. Standard terms organize heterogeneous paleoclimate datasets and improve the findability, interoperability, and reusability of data.",
"domains": [
"Climate"
],
"homepage": "https://www.ncdc.noaa.gov/data-access/paleoclimatology-data/past-thesaurus",
"name": "Paleoenvironmental Standard Terms Thesaurus",
"subjects": [
"Earth Science"
],
"user_defined_tags": [
"Paleoceanography",
"Paleoclimatology",
"Paleolimnology"
]
},
"FAIRsharing.e7e609": {
"abbreviation": "FR",
"contact": {
"email": "silvio.peroni@unibo.it",
"name": "Silvio Peroni",
"orcid": "0000-0003-0530-4305"
},
"description": "The FAIR* Reviews Ontology (FR) enables the description of reviews of scientific articles and other scholarly resources.",
"domains": [
"Citation",
"Bibliography",
"Report",
"Data model"
],
"homepage": "http://www.sparontologies.net/ontologies/fr",
"license": "CC-BY-4.0",
"name": "FAIR* Reviews Ontology ",
"repository": "https://github.com/sparontologies/fr",
"subjects": [
"Subject Agnostic"
],
"twitter": "sparontologies"
},
"FAIRsharing.e8a48f": {
"abbreviation": "EXDOC",
"contact": {
"email": "philipp.hagedorn-n6v@ruhr-uni-bochum.de",
"name": "Philipp Hagedorn",
"orcid": "0000-0002-6249-243X"
},
"description": "This ontology provides an extension for document types for the ISO 21597-1:2020 Container ontology. It includes the ExternalDatabase class as a subclass of the ct:ExternalDocument. This class can be used to provide information and connection details from an existing relational database, e.g., to retrieve data from DB and convert it into payload triples using R2RML mappings (see W3C R2RML Recommendation). ",
"domains": [
"Resource metadata"
],
"homepage": "https://icdd.vm.rub.de/ontology/icdd/ExtendedDocument",
"license": "CC-BY-4.0",
"name": "Extension for document types for the ISO 21597 ICDD Part 1 Container ontology",
"subjects": [
"Construction Engineering"
],
"user_defined_tags": [
"Document metadata"
]
},
"FAIRsharing.e96vf2": {
"abbreviation": "PTSD",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Phenotype"
],
"homepage": "http://bioportal.bioontology.org/ontologies/3024",
"name": "PTSD",
"subjects": [
"Life Science"
]
},
"FAIRsharing.e9efac": {
"abbreviation": "ASLS-vegetation",
"contact": {
"email": "simon.cox@csiro.au",
"name": "Simon Cox",
"orcid": "0000-0002-3884-3420"
},
"description": "Classifiers described in chapter 6 Vegetation, by R.J. Hnatiuk, R. Thackway and J. Walker in Australian Soil and Land Survey Field Handbook (3rd edn). \nThe data was converted from the print representation to this linked-data form by Simon J D Cox https://orcid.org/0000-0002-3884-3420",
"domains": [
"Agroecosystem"
],
"homepage": "https://github.com/ANZSoilData/def-au-asls-veg",
"license": "CC-BY-4.0",
"name": "ASLS Vegetation classifiers",
"subjects": [
"Agroecology"
],
"user_defined_tags": [
"vegetation classification"
]
},
"FAIRsharing.e9sg7": {
"abbreviation": "sam-lite",
"contact": {
"email": "dr.shorthair@pm.me",
"name": "Simon Cox",
"orcid": "0000-0002-3884-3420"
},
"description": "An OWL representation of the Sampling Features Schema described in clauses 9-11 of ISO 19156:2011 Geographic Information - Observations and Measurements.",
"domains": [
"Experimental measurement",
"Geographical location",
"Observation design"
],
"homepage": "https://www.semantic-web-journal.net/system/files/swj1237.pdf",
"license": "https://creativecommons.org/licenses/by/3.0/au",
"name": "Sampling Features OWL implementation",
"publications": [
{
"doi": "10.3233/sw-160214",
"title": "Ontology for observations and sampling features, with alignments to existing models",
"year": 2017
}
],
"subjects": [
"Earth Science"
]
},
"FAIRsharing.ea3z77": {
"abbreviation": "NeuMORE",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Neuron"
],
"homepage": "http://neumore.cis.usouthal.edu/",
"name": "Neural Motor Recovery Ontology",
"subjects": [
"Computational Neuroscience",
"Neurology",
"Biomedical Science",
"Neuroscience",
"Medical Informatics"
],
"user_defined_tags": [
"Neuroinformatics",
"neurology disease"
]
},
"FAIRsharing.eawbqb": {
"abbreviation": "CCONT",
"contact": {
"email": "matthias.ganzinger@med.uni-heidelberg.de",
"name": "Matthias Ganzinger",
"orcid": "0000-0002-2716-5425"
},
"description": "Cell Culture Ontology (CCONT) is an ontology for the formal representation of cell lines and their corresponding culture conditions.",
"domains": [
"Cell line",
"Cell",
"Disease process modeling",
"Cell culture"
],
"homepage": "http://bioportal.bioontology.org/ontologies/3108",
"name": "Cell Culture Ontology",
"publications": [
{
"doi": "10.1371/journal.pone.0048584",
"pubmed": "23144907",
"title": "On the ontology based representation of cell lines",
"year": 2012
}
],
"subjects": [
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.eb12a9": {
"abbreviation": "CMDO",
"contact": {
"email": "juhan@snu.ac.kr",
"name": "Ju Han Kim",
"orcid": "0000-0002-3186-0770"
},
"description": "The Clinical MetaData Ontology is designed to be used to classify Common Data Elements (CDEs) from different studies and clinical documents.",
"homepage": "https://bioportal.bioontology.org/ontologies/CMDO",
"license": "CC0-1.0",
"name": "Clinical MetaData Ontology",
"publications": [
{
"doi": "10.1186/s12911-019-0877-x",
"pubmed": "31429750",
"title": "Clinical MetaData ontology: a simple classification scheme for data elements of clinical data based on semantics",
"year": 2019
}
],
"subjects": [
"Clinical Studies"
]
},
"FAIRsharing.ec6bec": {
"abbreviation": "SVO",
"description": "The Scientific Variables Ontology (SVO) outlines the required and optional components for creating machine-interpretable scientific variable concepts. SVO comprises an upper ontology (SVU) that contains a set of modular conceptual categories and relationships between them, as well as a lower ontology (SVL) that contains instances within each category. SVL can be manually or automatically populated with concepts from a wide range of fields to create custom variables. Originally, SVO was created to express the set of CSDMS standard names in ontology form. The current ontology is designed to be terminology agnostic and can be augmented to include an unlimited number of synonymous terms. SVO is designed to balance a linguistic model of the world with a scientific model. SVO attempts to provide a template for retrieving information about a variable from free-form text. One of the primary goals of SVO is to work towards automated ontology generation of scientific variables following ideas laid out in an upper ontology of higher level concepts.",
"domains": [
"Experimental measurement",
"Report",
"Assay",
"Data transformation"
],
"homepage": "https://scientificvariablesontology.org/",
"name": "Scientific Variables Ontology",
"subjects": [
"Engineering Science",
"Natural Science"
],
"user_defined_tags": [
"Experimental condition"
]
},
"FAIRsharing.ech3sa": {
"abbreviation": "ISO639-2:1998",
"description": "ISO 639-2:1998 provides two sets of three-letter alphabetic codes for the representation of names of languages, one for terminology applications and the other for bibliographic applications. The code sets are the same except for twenty-five languages that have variant language codes because of the criteria used for formulating them. The language codes were devised originally for use by libraries, information services, and publishers to indicate language in the exchange of information, especially in computerized systems. ISO 639-2 represents all languages contained in ISO 639-1 and in addition any other language as well as language groups as they may be coded for special purposes when more specificity in coding is needed. The languages listed in ISO 639-1 are a subset of the languages listed in ISO 639-2; every language code in the two-letter code set has a corresponding language code in the alpha-3 list, but not necessarily vice versa.",
"homepage": "https://www.iso.org/standard/4767.html",
"name": "ISO 639-2: Codes for the Representation of Names of Languages Part 2: Alpha-3 Code",
"subjects": [
"Computer Science",
"Linguistics"
],
"user_defined_tags": [
"Language"
]
},
"FAIRsharing.eefm1j": {
"abbreviation": "MOC",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/MOC",
"name": "Material Organic Compound",
"subjects": [
"Organic Chemistry"
]
},
"FAIRsharing.eeyne8": {
"abbreviation": "CO_322",
"description": "The Maize Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_322:ROOT",
"license": "CC-BY-4.0",
"name": "Maize Ontology",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.eff3b2": {
"abbreviation": "GGBN",
"description": "The GGBN Data Standard is a set of terms and controlled vocabularies designed to represent sample facts. It does not cover e.g., scientific name, geography, or physiological facts. This allows combining the GGBN Data Standard with other complementary standards, such as DwC, ABCD or MIxS. Potentially, the standard can be used not only for non-human genomic samples but also human samples. It builds upon existing standards commonly used within the communities extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard is intended to be used with ABCD or Darwin Core and is not a stand-alone solution. It is intended to replace the DNA extension for Access to Biological Collection Data (ABCDDNA), however that specification has not been formally deprecated.",
"domains": [
"Biological sample annotation",
"Biological sample",
"Genome",
"FAIR"
],
"homepage": "https://wiki.ggbn.org/ggbn/GGBN_Data_Standard",
"license": "CC BY-SA 3.0",
"name": "Global Genome Biodiversity Network Data Standard",
"publications": [
{
"doi": "10.1093/database/baw125",
"pubmed": "27694206",
"title": "The Global Genome Biodiversity Network (GGBN) Data Standard specification",
"year": 2016
}
],
"subjects": [
"Genomics",
"Biodiversity"
]
},
"FAIRsharing.efv7gw": {
"abbreviation": "HOM",
"contact": {
"email": "julien.roux@unil.ch",
"name": "Julien Roux",
"orcid": "0000-0002-4192-5099"
},
"description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.",
"domains": [
"Molecular entity",
"Homologous",
"Life cycle stage"
],
"homepage": "http://bioportal.bioontology.org/ontologies/HOM/?p=summary",
"name": "HOMology",
"publications": [
{
"doi": "10.1016/j.tig.2009.12.012",
"pubmed": "20116127",
"title": "An ontology to clarify homology-related concepts",
"year": 2010
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"FAIRsharing.egv2cz": {
"abbreviation": "OGSF",
"contact": {
"email": "linikujp@gmail.com",
"name": "Asiyah Yu Lin",
"orcid": "0000-0003-2620-0345"
},
"description": "Ontology for Genetic Susceptibility Factor (OGSF) is an application ontology to model/represent the notion of genetic susceptibility to a specific disease or an adverse event or a pathological biological process. It is developed using BFO 2.0's framework. The ontology is under the domain of genetic epidemiology. OGSF is built from a combination of three ontologies: the Ontology of Geographical Region (OGR), the Ontology of Glucose Metabolism (OGMD), and the Ontology of Genetic Disease Investigations (OGDI). ",
"domains": [
"Adverse Reaction",
"Disease",
"Genetic disorder"
],
"homepage": "https://github.com/linikujp/OGSF",
"name": "Ontology for Genetic Susceptibility Factor",
"publications": [
{
"doi": "10.1186/2041-1480-5-19",
"pubmed": "24963371",
"title": "The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events",
"year": 2014
},
{
"pubmed": "20847592",
"title": "Ontology driven modeling for the knowledge of genetic susceptibility to disease",
"year": 2009
}
],
"subjects": [
"Genetics",
"Biomedical Science",
"Epidemiology"
]
},
"FAIRsharing.ehe3yp": {
"abbreviation": "CO_341",
"contact": {
"email": "e.arnaud@cgiar.org",
"name": "Elizabeth Arnaud",
"orcid": "0000-0002-6020-5919"
},
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Pigeon Pea Ontology is one of these reference plant ontologies integrated within the Crop Ontology.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_341:ROOT",
"license": "CC-BY-4.0",
"name": "Pigeon Pea Ontology",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.emw6am": {
"abbreviation": "ONL-MR-DA",
"description": "The OntoNeuroLOG Magnetic Resonance Dataset Acquisition (ONL-MR-DA) ontology is one of the modules in the OntoNeuroLOG ontology version 3.0, developed in the context of the NeuroLOG project., a French project supported by ANR (ANR-06-TLOG-024 grant) aiming at integrating distributed heterogeneous resources in neuroimaging. DOLCE was used as the upper-level ontology for each of the modules within this ontology. This ontology covers the domain of Magnetic Resonance Imaging (MRI) dataset acquisition, i.e. MRI protocols, and MRI sequence parameters. In particular, it includes a multi-axial classification of MR sequences. The project and its funding has been completed, and the last release (3.0) as of 2013 is expected to be the final one. However, it continues to be available for use.",
"domains": [
"Magnetic resonance imaging",
"Protocol",
"Brain imaging"
],
"homepage": "http://neurolog.unice.fr/public_namespace/ontology",
"name": "Magnetic Resonance Dataset Acquisition Ontology",
"publications": [
{
"doi": "10.1016/j.jbi.2008.03.002",
"pubmed": "18440282",
"title": "Towards an ontology for sharing medical images and regions of interest in neuroimaging",
"year": 2008
}
],
"subjects": [
"Biomedical Science",
"Neuroscience"
]
},
"FAIRsharing.eqgjeq": {
"abbreviation": "BILA",
"description": "This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource.",
"homepage": "http://purl.bioontology.org/ontology/BILA",
"name": "Bilateria anatomy",
"subjects": [
"Anatomy"
]
},
"FAIRsharing.erb60y": {
"abbreviation": "PANDA",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Molecular interaction"
],
"homepage": "http://bioportal.bioontology.org/ontologies/PANDA",
"name": "Probabilistic Knowledge Assembly Ontology",
"subjects": [
"Molecular biology"
]
},
"FAIRsharing.evzkcj": {
"abbreviation": "phenomeblast-owl",
"contact": {
"email": "robert.hoehndorf@kaust.edu.sa",
"name": "Robert Hoehndorf",
"orcid": "0000-0001-8149-5890"
},
"description": "PhenomeBLAST is an ontology-based tool that provides a practical implementation of cross-species alignments of phenotypes using ontologies. Both a command-line tool and a web-server are available.",
"domains": [
"Molecular interaction",
"Phenotype"
],
"homepage": "https://code.google.com/archive/p/phenomeblast/",
"name": "PhenomeBLAST ontology",
"publications": [
{
"doi": "10.1093/nar/gkr538",
"pubmed": "21737429",
"title": "PhenomeNET: a whole-phenome approach to disease gene discovery",
"year": 2011
},
{
"doi": "10.1007/s00335-012-9404-4",
"pubmed": "22814867",
"title": "Computational tools for comparative phenomics: the role and promise of ontologies",
"year": 2012
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"FAIRsharing.exmkp8": {
"abbreviation": "NIFSUBCELL",
"contact": {
"email": "smtifahim@gmail.com",
"name": "Fahim Imam",
"orcid": "0000-0003-4752-543X"
},
"description": "NIF has developed a comprehensive vocabulary for annotating and searching neuroscience resources. A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology that can be used to describe and retrieve neuroscience-relevant resources. NeuroLex is built from our core OWL ontology, NIFSTD, in a modular fashion, with separate modules covering major domains of neuroscience: anatomy, cell, subcellular (the standard described in this record), molecule, function and dysfunction.",
"homepage": "https://neuinfo.org/about/nifvocabularies",
"name": "Neuroscience Information Framework Subcellular Ontology",
"subjects": [
"Neurobiology",
"Life Science",
"Biomedical Science"
],
"twitter": "neuinfo"
},
"FAIRsharing.ez2nhb": {
"abbreviation": "OPL",
"description": "OPL models the life cycle stage details of T.cruzi and two related kinetoplastids, Trypanosoma brucei and Leishmania major. In addition, the ontology also models necessary contextual details such as host information, vector information, strain and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.",
"domains": [
"Parasite",
"Host",
"Life cycle",
"Life cycle stage"
],
"homepage": "https://bioportal.bioontology.org/ontologies/OPL",
"name": "Ontology for Parasite LifeCycle",
"publications": [
{
"doi": "10.1186/2041-1480-3-5",
"pubmed": "22621763",
"title": "The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms",
"year": 2012
}
],
"repository": "https://github.com/OPL-ontology/OPL",
"subjects": [
"Anatomy",
"Developmental Biology",
"Life Science"
]
},
"FAIRsharing.ezwdhz": {
"abbreviation": "PATO",
"contact": {
"email": "g.gkoutos@gmail.com",
"name": "George Gkoutos",
"orcid": "0000-0002-2061-091X"
},
"description": "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily phenotype annotation. This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes.",
"domains": [
"Phenotype"
],
"homepage": "https://github.com/pato-ontology/pato/",
"license": "CC-BY-3.0",
"name": "Phenotypic QualiTy Ontology",
"publications": [
{
"doi": "10.1186/gb-2004-6-1-r8",
"pubmed": "15642100",
"title": "Using ontologies to describe mouse phenotypes",
"year": 2005
},
{
"doi": "10.1186/gb-2010-11-1-r2",
"pubmed": "20064205",
"title": "Integrating phenotype ontologies across multiple species",
"year": 2010
}
],
"repository": "https://github.com/pato-ontology/pato/blob/master/CHANGES.md",
"subjects": [
"Biodiversity",
"Biology"
]
},
"FAIRsharing.f1292d": {
"abbreviation": "ADL",
"description": "The Activities of Daily Living Ontology is available for use in the SPHERE (Sensor Platform for HEalth in a Residential Environment) system to capture and express daily behaviour and activities among patients. While this ontology is available, please note that it has not been updated since 2016.",
"domains": [
"Behavior",
"Patient care"
],
"homepage": "https://doi.org/10.5523/bris.1234ym4ulx3r11i2z5b13g93n7",
"license": "https://www.nationalarchives.gov.uk/doc/non-commercial-government-licence/version/2",
"name": "SPHERE Activities of Daily Living",
"publications": [
{
"pubmed": "30037001",
"title": "Activities of Daily Living Ontology for Ubiquitous Systems: Development and Evaluation",
"year": 2018
}
],
"subjects": [
"Medicine",
"Clinical Studies",
"Medicines Research and Development",
"Behavioural Biology",
"Social and Behavioural Science"
]
},
"FAIRsharing.f21eae": {
"abbreviation": "STW Thesaurus for Economics",
"description": "The Standard-Thesaurus Wirtschaft (STW) Thesaurus for Economics contains terms relating to economics as well as technical terms used in law, sociology, politics, and geographic names. The STW Thesaurus for Economics is a bilingual thesaurus (German, English) for representing and searching economics-related content. It is used by universities, research institutes, public institutions and companies for knowledge organization and for research and development in computer and information science as well as in the area of Linked Data and Semantic Web technologies. The STW Thesaurus for Economics is part of the Linked Open Data Cloud and other information environments and web services for processing and linking economic literature, research data, author profiles and educational material.",
"homepage": "https://zbw.eu/stw/version/latest/about.en.html",
"license": "ODBL",
"name": "Standard-Thesaurus Wirtschaft Thesaurus for Economics",
"subjects": [
"Economics",
"Political Science"
]
},
"FAIRsharing.f55kb7": {
"abbreviation": "OGROUP",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/OGROUP",
"name": "Orthologous Group Ontology",
"subjects": [
"Genomics"
]
},
"FAIRsharing.f69084": {
"abbreviation": "CO_323",
"description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. The Barley Ontology is one of these reference plant ontologies integrated within the Crop Ontology. Its focus is on traits and variable used in field trials for breeding.",
"domains": [
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_323:ROOT",
"license": "CC-BY-4.0",
"name": "Barley Ontology",
"subjects": [
"Botany",
"Agriculture"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.f73143": {
"abbreviation": "ROR ID",
"description": "The Research Organization Registry (ROR) ID schema is the specification of the identifier for institutions in ROR. ROR is a global, community-led registry of open persistent identifiers for research organizations. ROR makes it easy for anyone or any system to disambiguate institution names and connect research organizations to researchers and research outputs.",
"domains": [
"Citation",
"Data retrieval"
],
"homepage": "https://ror.readme.io/docs/ror-identifier-pattern",
"license": "CC0-1.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBZ3NDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--5c0df1fa712279f60346a8a58f10ba3f5b33674c/download.png?disposition=inline",
"name": "Research Organization Registry ID Schema",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.f73xhd": {
"abbreviation": "PW",
"contact": {
"email": "vpetri@mcw.edu",
"name": "Victoria Petri",
"orcid": "0000-0002-5540-8498"
},
"description": "The goal of the Pathway Ontology is to cover all types of biological pathways, including altered and disease pathways, and to capture the relationships between them within the hierarchical structure of a Directed Acyclic Graph (DAG). The five nodes of the ontology are: classic metabolic, regulatory, signaling, drug and disease pathways. An extensive survey of the review literature along with searches of existing pathway databases have been used to choose terms and their position within the tree. The ontology is continually expanding along with the development of Pathway and Disease Portals at RGD.",
"domains": [
"Mathematical model",
"Network model",
"Molecular entity",
"Drug",
"Signaling",
"Biological regulation",
"Enzymatic reaction",
"Disease",
"Pathway model"
],
"homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=PW:0000001",
"license": "CC-BY-4.0",
"name": "Pathway Ontology",
"publications": [
{
"doi": "10.1186/2041-1480-5-7",
"pubmed": "24499703",
"title": "The pathway ontology - updates and applications",
"year": 2014
},
{
"doi": "10.1186/s40246-014-0017-8",
"pubmed": "25265995",
"title": "Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease",
"year": 2014
}
],
"subjects": [
"Drug Metabolism",
"Life Science"
]
},
"FAIRsharing.f7ymbr": {
"abbreviation": "ONLIRA",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Liver"
],
"homepage": "http://vavlab.ee.boun.edu.tr/pages.php?p=research/CARERA/carera.html",
"name": "Ontology of Liver for Radiology",
"subjects": [
"Radiology"
]
},
"FAIRsharing.f84009": {
"abbreviation": "ULAN",
"description": "The Union List of Artist Names (ULAN) contains names, relationships, notes, sources, and biographical information for artists, architects, firms, studios, repositories, patrons, and other individuals and corporate bodies, both named and anonymous. Names are included when they are required for the documentation, collection, and discovery of information about art, architecture, and other material culture where the works are of the type collected by art museums and other repositories for visual cultural heritage, or that are architecture. The ULAN is one of 5 Getty Vocabularies intended to provide terminology and other information about the objects, artists, concepts, and places important to various disciplines that specialize in art, architecture, and other material culture.",
"homepage": "http://www.getty.edu/research/tools/vocabularies/ulan/index.html",
"license": "http://opendatacommons.org/licenses/by/1.0",
"name": "Union List of Artist Names",
"subjects": [
"Culture",
"Art History",
"Architecture",
"Art",
"History"
]
},
"FAIRsharing.f8b3ec": {
"abbreviation": "m4i",
"description": "The ontology Metadata4Ing is developed within the NFDI Consortium NFDI4Ing with the aim of providing a framework for the semantic description of research data, with a particular focus on engineering sciences and neighbouring disciplines. This ontology allows a thorough description of the whole data generation process (experiment, observation, simulation), embracing the object of investigation, all sample and data manipulation procedures, a summary of the data files and the information contained, and all personal and institutional roles. The subordinate classes and relations can be built according to the two principles of inheritance and modularity. \"Inheritance\" means that a subclass inherits all properties of its superordinate class, possibly adding some new ones. Modularity means that all expansions are independent of each other; this makes possible for instance to generate expanded ontologies for any possible combinations of method Γ object of research.",
"homepage": "http://metadata4ing.org",
"license": "CC-BY-4.0",
"name": "Metadata4Ing",
"subjects": [
"Engineering Science"
]
},
"FAIRsharing.f8cd83": {
"abbreviation": "CF Standard Names",
"description": "The Climate and Forecast Standard Names Parameter Vocabulary (CF Standard Names) is intended for use with climate and forecast data in the atmosphere, surface and ocean domains. The CF Standard Names are the list of standard names used by the CF conventions. The list includes the units recommended for each standard name (most common prefixes can be used with the units, e.g. kilo (k), hecto (h), Mega (M), etc). If a standard_name metadata attribute is associated with a data variable, its value must be chosen from the list published in the standard name table. It is not compulsory within the CF conventions to assign a standard name to a data variable, but including one helps data users to understand the contents of a netCDF file. A CF standard name is not a netCDF variable name, but instead a value for the standard_name variable attribute. A standard_name attribute identifies the physical quantity of a variable.",
"domains": [
"Climate"
],
"homepage": "http://cfconventions.org/Data/cf-standard-names/current/build/cf-standard-name-table.html",
"name": "Climate and Forecast Standard Names Parameter Vocabulary",
"subjects": [
"Atmospheric Science",
"Oceanography",
"Hydrology"
],
"user_defined_tags": [
"Carbon cycle",
"Forecasting",
"Sea ice"
]
},
"FAIRsharing.f928f1": {
"abbreviation": "ARK Identifier",
"description": "Archival Resource Keys (ARKs) serve as persistent identifiers, or stable, trusted references for information objects. Among other things, they aim to be web addresses (URLs) that donβt return 404 Page Not Found errors. The ARK Alliance is an open global community supporting the ARK infrastructure on behalf of research and scholarship. End users, especially researchers, rely on ARKs for long term access to the global scientific and cultural record. Since 2001 some 8.2 billion ARKs have been created by over 1000 organizations β libraries, data centers, archives, museums, publishers, government agencies, and vendors. They identify anything digital, physical, or abstract. ARKs are open, mainstream, non-paywalled, decentralized persistent identifiers that can be created by an organization as soon as it is registered with a NAAN (Name Assigning Authority Number). Once registered, an ARK organization can create unlimited numbers of ARKs and publicize them via the n2t.net global resolver or via their own local resolver.",
"domains": [
"Data retrieval",
"Centrally registered identifier"
],
"homepage": "https://arks.org/",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaThDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--c69281eac0647c6b7a664f0932bee0d5fd27781d/gold_boat_arka.png?disposition=inline",
"name": "Archival Resource Key Identifier",
"subjects": [
"Data Management",
"Subject Agnostic"
],
"twitter": "arks_org"
},
"FAIRsharing.faej7j": {
"abbreviation": "PHMAMMADO",
"contact": {
"email": "contact@bioself-communication.com",
"name": "Delphine Dauga",
"orcid": "0000-0003-3152-1194"
},
"description": "The first ontology describing the anatomy and the development of Phallusia mammillata.",
"domains": [
"Cell",
"Life cycle",
"Life cycle stage"
],
"homepage": "https://aniseed.fr/aniseed/anatomy/find_devstage?module=aniseed&action=anatomy:find_devstage",
"name": "Phallusia mammillata Anatomy and Development Ontology",
"subjects": [
"Anatomy",
"Developmental Biology"
],
"user_defined_tags": [
"Morphogenesis"
]
},
"FAIRsharing.fajtj3": {
"abbreviation": "BIOREFINERY",
"description": "The Biorefinery ontology (BIOREFINERY) is dedicated to the determination of the best match treatment-biomass allowing the achievement of best constituent extraction yields with minimum environmental impact. It describes characteristics of biomass relevant for bio-refinery and unitary operations to transform biomass in glucose.",
"homepage": "https://www6.inrae.fr/cati-icat-atweb/Ontologies/Biorefinery",
"license": "CC-BY-4.0",
"name": "Biorefinery",
"subjects": [
"Agricultural Engineering",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Biomass"
]
},
"FAIRsharing.farr39": {
"abbreviation": "BAO-GPCR",
"description": "The G protein-coupled receptors (GPCRs) ontology describes pharmacology, biochemistry and physiology of these important and therapeutically promising class of academic and pharmaceutical research targets. Incorporation and comparison of various small molecule screening data sets, such as those deposited in PubChem, ChEMBL, KEGG, PDSP, and/or IUPHAR databases, requires a formalized electronic organization system. In order to bridge the gap between the overflow of HTS data and the bottleneck of integrated analysis tools, herein, we provide the first comprehensive GPCR ontology. The development and utility of GPCR ontology was based on previously developed BioAssay Ontology (BAO). The GPCR ontology contains information about biochemical, pharmacological, and functional properties of individual GPCRs as well as GPCR-selective ligands inclusive of their HTS screening results and other records. This ontology aims to model the relationship between the GPCR binding sites and their physiologic and pharmacologic role in physiology via small molecule chemical structures. ",
"domains": [
"Small molecule binding",
"Small molecule",
"Receptor",
"Assay"
],
"homepage": "http://www.bioassayontology.org/",
"license": "https://creativecommons.org/licenses/by/3.0/us",
"name": "G Protein-Coupled Receptor BioAssays Ontology",
"publications": [
{
"doi": "10.1186/2041-1480-5-s1-s5",
"pubmed": "25093074",
"title": "Evolving BioAssay Ontology (BAO): modularization, integration and applications",
"year": 2014
},
{
"doi": "10.1371/journal.pone.0049198",
"pubmed": "23155465",
"title": "Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO)",
"year": 2012
},
{
"doi": "10.1186/1471-2105-12-257",
"pubmed": "21702939",
"title": "BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results",
"year": 2011
}
],
"subjects": [
"Biochemistry",
"Biomedical Science"
]
},
"FAIRsharing.fb6837": {
"abbreviation": "SRA Identifier",
"description": "Identifier schema for Sequence Read Archive",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://bioregistry.io/registry/insdc.sra",
"name": "Sequence Read Archive Identifier",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.fb99fa": {
"abbreviation": "T4FS",
"contact": {
"email": "allyson.lister@oerc.ox.ac.uk",
"name": "Allyson Lister",
"orcid": "0000-0002-7702-4495"
},
"description": "terms4FAIRskills terminology is designed to capture the necessary competencies, skills and knowledge associated with how to make data FAIR and to keep it FAIR. terms4FAIRskills terms can be implemented to serve a variety of use-case applications such as 1) creation and assessment of stewardship curricula, 2) annotation for the discovery and evaluation of various FAIR-enabling materials/resources (e.g.training, etc.) , and 3) formalisation of job descriptions and CVs for recognising structured FAIR competencies for hire. User integrations include implementations from the FAIR Cookbook, FAIRsFAIR Competency Centre, FAIRassist, and Semaphora. terms4FAIRskills provides user flexibility for terms by FAIR trainers for FAIR data skills, researchers and/or data managers working to identify FAIR gaps for teams requiring support, managers recruiting specific FAIR implementation competencies, and developments leveraging FAIR competency-based reward structures and training plans.",
"domains": [
"Curated information",
"Digital curation",
"FAIR"
],
"homepage": "https://github.com/terms4fairskills/FAIRterminology",
"license": "CC-BY-4.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBZ1VDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--692c3b4cc5ea2f7aa8cc80267dad833f16dcccbb/terms4FAIRskills.png?disposition=inline",
"name": "terms4FAIRskills",
"publications": [
{
"doi": "10.5281/zenodo.4772741",
"title": "EOSC Co-creation funded project 074: Delivery of a proof of concept for terms4FAIRskills: Technical report",
"year": 2021
}
],
"repository": "https://github.com/terms4fairskills",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.fbn4sh": {
"abbreviation": "RSA",
"description": "An ontology for sequence annotations and how to preserve them with reference sequences.",
"domains": [
"Sequence"
],
"homepage": "http://bioportal.bioontology.org/ontologies/RSA",
"name": "Reference Sequence Annotation",
"subjects": [
"Genomics"
]
},
"FAIRsharing.fd6003": {
"description": "UniProt protein identifiers are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'. UniProtKB accession numbers consist of 6 or 10 alphanumeric characters in the format.",
"domains": [
"Data retrieval",
"Publication",
"Centrally registered identifier"
],
"homepage": "https://www.uniprot.org/help/accession_numbers",
"name": "UniProt Protein Identifier",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.fe4816": {
"abbreviation": "CRediT",
"contact": {
"email": "info@casrai.org",
"name": "Liz Allen",
"orcid": "0000-0002-9298-3168"
},
"description": "CRediT (Contributor Roles Taxonomy) is a high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributorβs specific contribution to the scholarly output.",
"domains": [
"Citation",
"Resource metadata",
"Publication",
"Classification"
],
"homepage": "https://credit.niso.org/",
"license": "https://creativecommons.org/licenses/by-nd/2.0/uk",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaUFCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--af4f02374db4f42007e6674ea2055ccaa36aa830/credit-icon-499x500-1.png?disposition=inline",
"name": "Contributor Roles Taxonomy",
"publications": [
{
"doi": "10.1038/508312a",
"title": "Publishing: Credit where credit is due",
"year": 2014
},
{
"doi": "10.3789/ansi.niso.z39.104-2022",
"title": "ANSI/NISO Z39.104-2022, CRediT, Contributor Roles Taxonomy",
"year": 2022
},
{
"doi": "10.1002/leap.1210",
"title": "How can we ensure visibility and diversity in research contributions? How the Contributor Role Taxonomy (CRediT) is helping the shift from authorship to contributorship",
"year": 2019
},
{
"doi": "10.1087/20150211",
"title": "Beyond authorship: attribution, contribution, collaboration, and credit",
"year": 2015
},
{
"doi": "10.1038/d41586-019-01715-4",
"title": "Credit data generators for data reuse",
"year": 2019
}
],
"subjects": [
"Data Quality",
"Subject Agnostic"
],
"twitter": "contrib_roles"
},
"FAIRsharing.fee65c": {
"description": "The iDAI.world thesaurus collects and unifies all thesauri and vocabularies of the libraries and the projects of the German Archaeological Institute. It was developed between 2015 and 2019, since 2020 it is continuously updated and implemented. The core structure is based on the BackBoneThesaurus (https://vocabs.dariah.eu/bbt/en/). Please note that while a majority of this site is in German, the thesaurus itself is mainly multi-lingual. ",
"homepage": "http://thesauri.dainst.org/de.html",
"license": "CC-BY-4.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaUVCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--995fabc4dabdddfd4f5b258f72ef1d27e147d5b8/iDAI.thesauri_blau.png?disposition=inline",
"name": "iDAI.world Thesaurus",
"publications": [
{
"doi": "10.34780/7aqi-ei1b ",
"title": "iDAI.thesauri",
"year": 2017
}
],
"subjects": [
"Archaeology",
"Humanities",
"Prehistory",
"Ancient Cultures",
"Ancient History",
"Construction History"
]
},
"FAIRsharing.fgd5gq": {
"abbreviation": "CO_346",
"description": "The Mungbean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe data.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_346:ROOT",
"license": "CC-BY-4.0",
"name": "Mungbean Ontology",
"subjects": [
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.fgmzk8": {
"abbreviation": "PEAO",
"description": "The Plant Experimental Assay Ontology (PEAO) was created to describe experimental procedures within plant research, regardless of the scientific questions that prompted the assays. This ontology models entities from three distinct realms (biological, physical and data), which include experimental products, their relations and the protocols describing their manipulation. PEAO is intended to be used as a log book by experimentalists, providing a formal relation between entities.",
"domains": [
"Experimental measurement",
"Assay",
"Protocol",
"Study design",
"Experimentally determined"
],
"homepage": "https://bitbucket.org/PlantExpAssay/ontology",
"name": "Plant Experimental Assay Ontology",
"subjects": [
"Botany",
"Life Science"
],
"user_defined_tags": [
"Experimental condition"
]
},
"FAIRsharing.fhn1zb": {
"abbreviation": "TM-SIGNS-AND-SYMPTS",
"description": "The World Health Organization, in consultation with a large group of stakeholders in the areas of Traditional Medicine or Complementary and Alternative Medicine and Health Information Systems, has developed a collaborative project plan to produce an international standard terminology and classification system for Traditional Medicine. This resource is part of an effort to produce an international standard for information on TM that is ready for electronic health records and that will serve as a standard for scientific comparability and communication.",
"domains": [
"Electronic health record"
],
"homepage": "https://sites.google.com/site/whoictm/home",
"name": "Traditional Medicine Signs and Symptoms Value Set",
"subjects": [
"Medicine",
"Traditional Medicine",
"Health Science"
]
},
"FAIRsharing.fj07xj": {
"abbreviation": "NCBITAXON",
"description": "The NCBI Taxonomy is a database of taxonomic information. It does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts.",
"domains": [
"Taxonomic classification"
],
"homepage": "https://www.ncbi.nlm.nih.gov/taxonomy",
"license": "CC0-1.0",
"name": "NCBI Taxonomy",
"publications": [
{
"doi": "10.1093/nar/gkx1094",
"pubmed": "29140468",
"title": "GenBank",
"year": 2017
},
{
"doi": "10.1093/nar/gkr1178",
"pubmed": "22139910",
"title": "The NCBI Taxonomy database",
"year": 2011
},
{
"doi": "10.1093/database/baaa062",
"pubmed": "32761142",
"title": "NCBI Taxonomy: a comprehensive update on curation, resources and tools",
"year": 2020
}
],
"repository": "https://github.com/obophenotype/ncbitaxon",
"subjects": [
"Taxonomy",
"Phylogenetics",
"Life Science"
]
},
"FAIRsharing.fmz635": {
"abbreviation": "GR-TAX",
"description": "Gramene Taxonomy Ontology (GR-TAX) is a representation of the taxonomy tree in the ontology format. Each term in this ontology can represent subspecies, species, genus, order, class or any rank in the classification. Primarily derived from NCBI Taxonomy, the revisions were made as and when/where required in the rankings. The rank of genome types was added by this project. This taxonomy ontology focuses on the Poaceae (Gramineae) family of plant taxonomy only.",
"domains": [
"Taxonomic classification"
],
"homepage": "http://archive.gramene.org/db/ontology/search_term?id=GR_tax:017502",
"name": "Gramene Taxonomy Ontology",
"subjects": [
"Botany"
]
},
"FAIRsharing.fpwvra": {
"abbreviation": "BIOMO",
"description": "The BIOMO ontology maps the HDF5 based BIOM format (http://biom-format.org/) to OWL, offering a method to convert a BIOM file to RDF and therefore publish it as Linked Data",
"domains": [
"Microbiome"
],
"homepage": "http://github.com/mikel-egana-aranguren/biom-ld",
"name": "Biological Observation Matrix Ontology",
"subjects": [
"Genomics"
]
},
"FAIRsharing.fr3ng0": {
"abbreviation": "EHDAA",
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy (EMAP ontology) and incorporates each Carnegie stage of development (CS1-20). This abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). This ontology was made computationally and later deemed \"incoherent\" by the authors because the stage-dependent hierarchical structures were not integrated.",
"domains": [
"Life cycle stage"
],
"homepage": "http://obofoundry.org/ontology/ehdaa.html",
"name": "Edinburgh Human Developmental Anatomy Abstract",
"publications": [
{
"doi": "10.1046/j.1469-7580.2003.00224.x",
"pubmed": "14620375",
"title": "An ontology of human developmental anatomy",
"year": 2003
},
{
"doi": "10.1111/j.1469-7580.2012.01566.x",
"pubmed": "22973865",
"title": "A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20)",
"year": 2012
}
],
"subjects": [
"Anatomy",
"Developmental Biology",
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.frp1rm": {
"abbreviation": "ACGT-MO",
"contact": {
"email": "mbrochhausen@gmail.com",
"name": "Mathias Brochhausen",
"orcid": "0000-0003-1834-3856"
},
"description": "The ACGT Master Ontology, which has been developed within the FP6-IST project \"Advancing Clinico-Genomic Trials\", has the aim to represent the domain of cancer research and management in a computationally tractable manner. The ACGT MO is built being maintained, using the ProtΓ©gΓ©-OWL free open-source ontology editor, Version 4. It is written in OWL-DL and presented as an .owl file. The ACGT MO is re-using Basic Formal Ontology (BFO) as upper level and the OBO Relation Ontology. Although this resource is available at the stated homepage, it has not been updated in a number of years, and we could not get in touch with the contacts provided.",
"domains": [
"Cancer",
"Tumor",
"Disease"
],
"homepage": "https://www.uni-saarland.de/institut/ifomis/activities/acgt-master-ontology.html",
"name": "Cancer Research and Management ACGT Master Ontology",
"publications": [
{
"doi": "10.1016/j.jbi.2010.04.008",
"pubmed": "20438862",
"title": "The ACGT Master Ontology and its applications--towards an ontology-driven cancer research and management system",
"year": 2010
}
],
"repository": "https://github.com/IFOMIS/ACGT",
"subjects": [
"Medicine",
"Health Science",
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.fsk662": {
"abbreviation": "HPIO",
"contact": {
"email": "ina.hulsegge@wur.nl",
"name": "Ina Hulsegge",
"orcid": "0000-0002-7015-6540"
},
"description": "Ontology for host pathogen interactions in farmed animals.",
"domains": [
"Animal research",
"Pathogen"
],
"homepage": "http://bioportal.bioontology.org/ontologies/HPIO",
"name": "Host Pathogen Interactions Ontology",
"publications": [
{
"doi": "10.2527/jas.2011-4251",
"pubmed": "22228038",
"title": "Contributions to an animal trait ontology",
"year": 2012
}
],
"subjects": [
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.ft8113": {
"abbreviation": "NORREG",
"description": "Record does not exist anymore: Norwegian national quality registries- Variabelbibliotek for medisinske kvalitetsregistre. The record with identifier content https://doi.org/10.25504/FAIRsharing.ft8113 was invalid.",
"homepage": "https://docs.google.com/spreadsheets/d/1w2NatnnDfacYqrs24HDxQuEBM_xmGxL8-DilqAHVFDM/edit#gid=1014457671",
"name": "Norwegian national quality registries- Variabelbibliotek for medisinske kvalitetsregistre"
},
"FAIRsharing.fvw159": {
"abbreviation": "CEPATHAMIL",
"description": "Record does not exist anymore: caracepathaml. The record with identifier content https://doi.org/10.25504/FAIRsharing.fvw159 was invalid.",
"homepage": "https://www.jualbukucaracepathamil.website/",
"name": "caracepathaml"
},
"FAIRsharing.fw8k2k": {
"abbreviation": "TRIPHASE",
"description": "TriPhase is a large thesaurus in the domain of animal physiology and livestock designed by INRA. This resource has been marked as Uncertain as we cannot find a homepage, publication or other documentation for it. Please contact us if you have any information regarding this resource.",
"homepage": "http://agroportal.lirmm.fr/ontologies/TRIPHASE",
"license": "CC BY-SA 3.0",
"name": "Thesaurus for Animal Physiology and Livestock Systems",
"subjects": [
"Animal Physiology",
"Animal Husbandry",
"Life Science"
],
"user_defined_tags": [
"Livestock"
]
},
"FAIRsharing.fyiMub": {
"description": "Terminology resource derived from a controlled vocabulary used for indexing bibliographical records for the PASCAL database of Inist (1972-2015, http://pascal-francis.inist.fr/), in the fields of Electrical engineering and Electro-energetics. It is aligned with wikidata. This resource contains 6630 entries grouped into 34 collections.",
"homepage": "https://www.loterre.fr/skosmos/BJW/en/",
"license": "CC-BY-4.0",
"name": "Electrical engineering and Electro-energetics vocabulary",
"subjects": [
"Energy Engineering",
"Electrical Engineering"
],
"user_defined_tags": [
"Electro-energetics"
]
},
"FAIRsharing.g0a7s0": {
"abbreviation": "REX",
"description": "REX is an ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. REX includes both microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes. Some biochemical processes from Gene Ontology (GO Biological process) can be described as instances of REX.",
"domains": [
"Reaction data",
"Enzymatic reaction"
],
"homepage": "http://purl.bioontology.org/ontology/REX",
"name": "Physico-chemical process",
"subjects": [
"Chemistry",
"Life Science"
]
},
"FAIRsharing.g1qrqs": {
"abbreviation": "PLANA",
"description": "Anatomy ontology for planaria and terms specific to the developmental stages of the planarian Schmidtea mediterranea. As the regenerative flatworm Schmidtea mediterranea gains popularity as a developmental research organism the need for standard nomenclature and a centralized repository of anatomical terms has become increasingly apparent. Utilization of a controlled vocabulary creates opportunities to catalogue genes and expression data for computational searches across research groups and cross-species comparisons, all while establishing a framework for integration of new terms. We created a Planarian Anatomy Ontology containing 327 terms and definitions for cellular organelles, cell types, tissues, organ systems, anatomical entities, life cycle stages and developmental processes described in the literature. Where possible, extant terms and definitions from Uberon and other open source anatomy ontologies were imported into the ontology to strengthen cross-species queries.",
"domains": [
"Organelle",
"Organ",
"Tissue"
],
"homepage": "https://planosphere.stowers.org/anatomyontology",
"license": "CC-BY-3.0",
"name": "Planarian Anatomy and Developmental Stage Ontology",
"repository": "https://github.com/obophenotype/planaria-ontology",
"subjects": [
"Anatomy",
"Developmental Biology",
"Life Science"
]
},
"FAIRsharing.g201pt": {
"abbreviation": "AFEO",
"contact": {
"email": "anne.tireau@supagro.inra.fr",
"name": "Anne Tireau",
"orcid": "0000-0001-8501-6922"
},
"description": "The Agri-Food Experiment Ontology (AFEO) is based on two existing ontology resources, OAE (Ontology for Agriculture Experiment) and OFPE (Ontology for Food Processing Experiment). It covers various viticultural practices, winemaking products and operations. FAIRsharing is unable to contact the developers of this resource, and cannot find a project homepage. Therefore this record's status has been marked as Uncertain. Please get in touch if you have any information regarding this resource.",
"domains": [
"Food"
],
"homepage": "http://agroportal.lirmm.fr/ontologies/AFEO",
"license": "CC-BY-4.0",
"name": "Agri-Food Experiment Ontology",
"publications": [
{
"doi": "10.1016/j.compag.2017.06.020",
"title": "A generic ontological network for Agri-food experiment integration β Application to viticulture and winemaking",
"year": 2017
}
],
"subjects": [
"Agricultural Engineering",
"Agriculture",
"Life Science",
"Nutritional Science"
]
},
"FAIRsharing.g593w1": {
"abbreviation": "EDAM-BIOIMAGING",
"description": "Bioimaging operations, data types, formats, identifiers and topics. EDAM-Bioimaging is an extension to the EDAM ontology (edamontology.org) for bioimaging, developed in collaboration with partners from NEUBIAS (neubias.org).",
"domains": [
"Bioimaging"
],
"homepage": "http://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING",
"name": "EDAM Bioimaging Ontology",
"subjects": [
"Bioinformatics"
]
},
"FAIRsharing.g75npx": {
"abbreviation": "CEEROntology",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/1675",
"name": "CEEROntology",
"subjects": [
"Medicine"
]
},
"FAIRsharing.g78mbm": {
"abbreviation": "LPT",
"description": "The Livestock Product Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.",
"domains": [
"Phenotype"
],
"homepage": "https://www.animalgenome.org/bioinfo/projects/lpt/",
"name": "Livestock Product Trait Ontology",
"repository": "https://github.com/AnimalGenome/livestock-product-trait-ontology ",
"subjects": [
"Animal Husbandry"
]
},
"FAIRsharing.g7b4rj": {
"abbreviation": "WIKIPATHWAYS",
"description": "WikiPathways simplifies the contribution and maintenance of biological pathway information. It is an open and collaborative platform that curates pathways, complementing existing databases like KEGG, Reactome, and Pathway Commons. The web-based format makes it easy for anyone to participate, from students to experts. The community takes on peer review, editorial curation, and maintenance tasks.",
"domains": [
"Reaction data",
"Protein interaction",
"Signaling",
"Biological regulation",
"Molecular interaction",
"Genetic interaction",
"Drug interaction",
"Pathway model"
],
"homepage": "http://www.wikipathways.org/",
"name": "WikiPathways",
"subjects": [
"Virology",
"Epidemiology"
]
},
"FAIRsharing.g7y77y": {
"abbreviation": "CISAVIADO",
"contact": {
"email": "contact@bioself-communication.com",
"name": "Delphine Dauga",
"orcid": "0000-0003-3152-1194"
},
"description": "The first ontology describing the anatomy and the development of Ciona savignyi, based on the Hotta developmental table.",
"domains": [
"Cell",
"Life cycle",
"Life cycle stage"
],
"homepage": "https://www.aniseed.fr/aniseed/anatomy/find_devstage?module=aniseed&action=anatomy:find_devstage",
"name": "Ciona savignyi Anatomy and Development Ontology",
"subjects": [
"Anatomy",
"Developmental Biology"
],
"user_defined_tags": [
"Morphogenesis"
]
},
"FAIRsharing.gaqfk4": {
"abbreviation": "HCODONONT",
"description": "This ontology contains the information of the frequency of usage and the relative frequency of usage of Human Gene Codons, to be used to the operations by The Project Of HIV Ontology.",
"homepage": "http://blog.51.ca/u-345129/",
"name": "HGeneCodonOntology",
"subjects": [
"Genomics"
]
},
"FAIRsharing.gd8hqn": {
"abbreviation": "MOOCCIADO",
"contact": {
"email": "contact@bioself.communication.com",
"name": "Delphine Dauga",
"orcid": "0000-0003-3152-1194"
},
"description": "The first ontology describing the anatomy and the development of Molgula occidentalis.",
"domains": [
"Cell",
"Life cycle",
"Life cycle stage"
],
"homepage": "http://www.aniseed.cnrs.fr/",
"name": "Molgula occidentalis Anatomy and Development Ontology",
"subjects": [
"Anatomy",
"Developmental Biology"
],
"user_defined_tags": [
"Morphogenesis"
]
},
"FAIRsharing.gdrs2p": {
"abbreviation": "SEDI",
"description": "An ontology for DICOM as used in the SeDI project.",
"homepage": "http://semantic-dicom.org",
"name": "Semantic DICOM Ontology",
"subjects": [
"Medicine"
]
},
"FAIRsharing.gdszhh": {
"abbreviation": "CO_325",
"contact": {
"email": "e.arnaud@cgiar.org",
"name": "Elizabeth Arnaud",
"orcid": "0000-0002-6020-5919"
},
"description": "The Banana Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_325:ROOT",
"license": "CC-BY-4.0",
"name": "Banana Ontology",
"subjects": [
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.ge8y23": {
"abbreviation": "CO_337",
"description": "The Groundnut Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_337:ROOT",
"license": "CC-BY-4.0",
"name": "Groundnut Ontology",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.gjn0y": {
"abbreviation": "QIBO",
"contact": {
"email": "termite@stanford.edu",
"name": "David Paik",
"orcid": "0000-0002-7830-312X"
},
"description": "An ontology that describes various concepts in quantitative imaging biomarkers.",
"domains": [
"Biomarker",
"Imaging"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1671",
"name": "Quantitative Imaging Biomarker Ontology",
"publications": [
{
"doi": "10.1007/s10278-013-9599-2",
"pubmed": "23589184",
"title": "Quantitative imaging biomarker ontology (QIBO) for knowledge representation of biomedical imaging biomarkers",
"year": 2013
}
],
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.gkw1w8": {
"abbreviation": "APAONTO",
"description": "Record does not exist anymore: Psychology Ontology. The record with identifier content 10.25504/FAIRsharing.gkw1w8 was invalid.",
"domains": [
"Behavior"
],
"homepage": "http://bioportal.bioontology.org/ontologies/APAONTO",
"name": "Psychology Ontology",
"subjects": [
"Psychology"
]
},
"FAIRsharing.gq1xtx": {
"abbreviation": "IAO",
"contact": {
"email": "alanruttenberg@gmail.com",
"name": "Alan Ruttenberg",
"orcid": "0000-0002-1604-3078"
},
"description": "The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch.",
"domains": [
"Drug report",
"Experimental measurement",
"Data identity and mapping",
"Reagent",
"Assay",
"Protocol",
"Study design"
],
"homepage": "https://github.com/information-artifact-ontology/IAO/",
"license": "CC-BY-3.0",
"name": "Information Artifact Ontology",
"publications": [
{
"doi": "10.3233/978-1-61499-101-4-68",
"pubmed": "22874154",
"title": "An information artifact ontology perspective on data collections and associated representational artifacts",
"year": 2012
}
],
"repository": "https://github.com/information-artifact-ontology/IAO/wiki/Meeting_notes",
"subjects": [
"Knowledge and Information Systems",
"Data Management",
"Subject Agnostic",
"Biomedical Science"
]
},
"FAIRsharing.gt5K7W": {
"description": "Controlled vocabulary used for indexing bibliographical records dealing with βClassical Thermodynamics / Heat Transfersβ in the PASCAL database (1972 Γ 2015). This vocabulary reflects the content of the indexed articles, including the experimental and/or theoretical context in which the heat transfer phenomena were studied. The resource is aligned with Rameau and LCSH. It consists of 1462 entries in 2 languages (English, French) grouped under 7 collections.",
"homepage": "https://www.loterre.fr/skosmos/1WB/en/",
"license": "CC-BY-4.0",
"name": "Vocabulary of Heat Transfers",
"subjects": [
"Thermodynamics",
"Physical Chemistry"
],
"user_defined_tags": [
"Heat transfers"
]
},
"FAIRsharing.gvr3p6": {
"abbreviation": "APAEDUCLUSTER",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/APAEDUCLUSTER",
"name": "Educational Cluster",
"subjects": [
"Education Science"
]
},
"FAIRsharing.h0can5": {
"abbreviation": "DOCCC",
"description": "Record does not exist anymore: Diagnosis Ontology of Clinical Care Classification. The record with identifier content 10.25504/FAIRsharing.h0can5 was invalid.",
"homepage": "http://bioportal.bioontology.org/ontologies/DOCCC",
"name": "Diagnosis Ontology of Clinical Care Classification"
},
"FAIRsharing.h1gmb7": {
"abbreviation": "DURUM_WHEAT",
"description": "The durum wheat ontology (DURUM_WHEAT) is dedicated to the sustainability analysis of the durum wheat chain. Current data available on this ontology concern durum wheat quality control criteria used in different countries (Moisture content rate, chemical content, etc.).",
"domains": [
"Food",
"Quality control"
],
"homepage": "https://www6.inrae.fr/cati-icat-atweb/Ontologies/Durum-wheat",
"license": "CC-BY-4.0",
"name": "Durum Wheat",
"subjects": [
"Agriculture",
"Life Science"
]
},
"FAIRsharing.h4rs6h": {
"abbreviation": "GO-PLUS",
"description": "This is the fully axiomatised version of the Gene Ontology (GO). It includes cross-ontology relationships (axioms) and imports additional required ontologies including ChEBI, Cell Ontology and Uberon. It also includes a complete set of relationship types including some not in go.obo/go.owl. This version is only available in OWL format.",
"domains": [
"Gene functional annotation",
"Molecular function",
"Cellular component",
"Biological process"
],
"homepage": "http://geneontology.org/docs/download-ontology/#go_plus_owl",
"name": "GO-PLUS",
"subjects": [
"Genomics"
]
},
"FAIRsharing.h94kv6": {
"abbreviation": "OntoVIP",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Imaging"
],
"homepage": "http://vip.creatis.insa-lyon.fr/ontovip/v1.0/Documentation_OntoVIPv1.pdf",
"name": "Medical image simulation",
"subjects": [
"Medical Physics",
"Medical Informatics"
]
},
"FAIRsharing.hFLKCn": {
"abbreviation": "DOI",
"description": "The digital object identifier (DOI) system originated in a joint initiative of three trade associations in the publishing industry (International Publishers Association; International Association of Scientific, Technical and Medical Publishers; Association of American Publishers). The system was announced at the Frankfurt Book Fair 1997. The International DOIΒ Foundation (IDF) was created to develop and manage the DOI system, also in 1997. The DOI system was adopted as International Standard ISO 26324 in 2012. The DOI system implements the Handle System and adds a number of new features. The DOI system provides an infrastructure for persistent unique identification of objects of any type. The DOI system is designed to work over the Internet. A DOI name is permanently assigned to an object to provide a resolvable persistent network link to current information about that object, including where the object, or information about it, can be found on the Internet. While information about an object can change over time, its DOI name will not change. A DOI name can be resolved within the DOI system to values of one or more types of data relating to the object identified by that DOI name, such as a URL, an e-mail address, other identifiers and descriptive metadata. The DOI system enables the construction of automated services and transactions. Applications of the DOI system include but are not limited to managing information and documentation location and access; managing metadata; facilitating electronic transactions; persistent unique identification of any form of any data; and commercial and non-commercial transactions. The content of an object associated with a DOI name is described unambiguously by DOI metadata, based on a structured extensible data model that enables the object to be associated with metadata of any desired degree of precision and granularity to support description and services. The data model supports interoperability between DOI applications. The scope of the DOI system is not defined by reference to the type of content (format, etc.) of the referent, but by reference to the functionalities it provides and the context of use. The DOI system provides, within networks of DOI applications, for unique identification, persistence, resolution, metadata and semantic interoperability.",
"domains": [
"Centrally registered identifier"
],
"homepage": "https://www.doi.org",
"name": "Digital Object Identifier",
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.hakg7c": {
"abbreviation": "PPO",
"description": "An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales.",
"domains": [
"Phenotype",
"Life cycle"
],
"homepage": "https://github.com/PlantPhenoOntology/PPO",
"license": "CC-BY-3.0",
"name": "Plant Phenology Ontology",
"publications": [
{
"doi": "10.3389/fpls.2018.00517",
"pubmed": "29765382",
"title": "The Plant Phenology Ontology: A New Informatics Resource for Large-Scale Integration of Plant Phenology Data",
"year": 2018
}
],
"repository": "https://github.com/PlantPhenoOntology/ppo/raw/master/documentation/ppo.pdf",
"subjects": [
"Botany"
],
"user_defined_tags": [
"Phenology"
]
},
"FAIRsharing.haxp7g": {
"abbreviation": "FALDO",
"description": "The Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences for data resources represented in RDF and/or OWL. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned βomicsβ areas. Using the same data format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types.",
"domains": [
"Nucleic acid sequence",
"Sequence annotation",
"Gene feature",
"Sequence feature",
"Binding site"
],
"homepage": "http://biohackathon.org/resource/faldo",
"license": "CC0-1.0",
"name": "Feature Annotation Location Description Ontology",
"publications": [
{
"doi": "10.1186/s13326-016-0067-z",
"pubmed": "27296299",
"title": "FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation",
"year": 2016
}
],
"repository": "https://github.com/OBF/FALDO",
"subjects": [
"Genetics"
]
},
"FAIRsharing.hgsFLe": {
"abbreviation": "DwC-germplasm",
"contact": {
"email": "dag.endresen@gmail.com",
"name": "Dag Endresen",
"orcid": "0000-0002-2352-5497"
},
"description": "The Darwin Core germplasm extension (DwC-germplasm) was developed to provide a bridge between the established standards in use by the genebank community for plant genetic resources for food and agriculture (PGRFA) and the standards maintained by the Biodiversity Information Standards/Taxonomic Databases Working Group (TDWG). The DwC-germplasm provides an extension to the Darwin Core standard of the TDWG for occurrences. Darwin Core can be seen as an extension to the Dublin Core Metadata Data Initiative (DCMI) terms.",
"domains": [
"Resource metadata",
"Food"
],
"homepage": "https://github.com/dagendresen/darwincore-germplasm",
"license": "CC0-1.0",
"name": "Darwin Core Germplasm",
"subjects": [
"Genetics",
"Biodiversity",
"Agriculture",
"Biology",
"Plant Genetics"
],
"user_defined_tags": [
"Metadata standardization"
]
},
"FAIRsharing.hmhzhy": {
"abbreviation": "CNO_ACRONYM",
"description": "Record does not exist anymore: CNO_NAME. The record with identifier content 10.25504/FAIRsharing.hmhzhy was invalid.",
"homepage": "http://bioportal.bioontology.org/ontologies/CNO_ACRONYM",
"name": "CNO_NAME"
},
"FAIRsharing.hpmpyx": {
"abbreviation": "CanCO",
"description": "The Cancer Chemoprevention Ontology constitutes a vocabulary that is able to describe and semantically interconnect the different paradigms of the cancer chemoprevention domain.",
"domains": [
"Cancer"
],
"homepage": "http://bioportal.bioontology.org/ontologies/CANCO",
"name": "Cancer Chemoprevention Ontology",
"subjects": [
"Cheminformatics",
"Medicine",
"Health Science",
"Biomedical Science"
]
},
"FAIRsharing.hpvbxb": {
"abbreviation": "ICD-10-CM",
"description": "The International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) is a morbidity classification for classifying diagnoses and reason for visits in all American health care settings. The ICD-10-CM is based on the ICD-10, the statistical classification of disease published by the World Health Organization (WHO) which replaces ICD-9. ICD-10-CM replaced ICD-9-CM Volumes 1 and 2 from October 2015 onwards.",
"domains": [
"Electronic health record",
"Disease",
"Diagnosis",
"Morbidity"
],
"homepage": "https://www.cdc.gov/nchs/icd/icd10cm.htm",
"name": "International Classification of Diseases, Tenth Revision, Clinical Modification",
"subjects": [
"Medicine",
"Health Science",
"Biomedical Science"
]
},
"FAIRsharing.hqyeb7": {
"abbreviation": "FIRE",
"description": "The ontology of Fire was created in order to represent the set of concepts about the fire occurring in natural vegetation, its characteristics, causes and effects, with focus on Cerrado vegetation domain. The fire plays a determinant role on the structure and composition of Cerrado physiognomies.",
"domains": [
"Combustion",
"Climate",
"Ecosystem"
],
"homepage": "http://bioportal.bioontology.org/ontologies/FIRE",
"name": "Fire Ontology",
"subjects": [
"Plant Ecology",
"Environmental Science",
"Population Dynamics",
"Meteorology",
"Biodiversity",
"Ecosystem Science"
]
},
"FAIRsharing.hs43fc": {
"abbreviation": "FISHO",
"description": "This Fish Ontology is an ontology created as how the author views the fish structure following the book \"The Diversity of Fishes: Biology, Evolution and Ecology\" as the main reference, which covers one part of view on ichthyology, with an emphasis on diversity and adaptation. This ontology is created with the mindset of categorizing fish automatically based on the attributes and terms mined from the fish specimen. Most of the basic organization from this ontology follows Nelson's research due to its synthetic and broad approach, while recognizing that Nelson's conclusions are one of many alternative interpretations of the literature, which is mostly agreed by our main references, and many fish and fisheries researchers. Most of the classification used in this ontology is in no means completed and just following the recent classification provided by the books For now our work focused more on two group of fish which is early jawless fish, and advanced jawed fishes. The classification from both of this group are structured following the reference.",
"homepage": "https://mohdnajib1985.github.io/FOWebPage/",
"name": "Fish Ontology",
"subjects": [
"Fisheries Science"
]
},
"FAIRsharing.htq39f": {
"abbreviation": "COMODI",
"description": "An ontology to characterise differences in versions of computational models in biology",
"homepage": "http://comodi.sems.uni-rostock.de",
"name": "COMODI",
"publications": [
{
"doi": "10.1186/s13326-016-0080-2",
"pubmed": "27401413",
"title": "COMODI: an ontology to characterise differences in versions of computational models in biology",
"year": 2016
}
],
"subjects": [
"Computational Biology"
]
},
"FAIRsharing.hve0ac": {
"abbreviation": "TRANSMAT",
"description": "The Matter Transfer ontology is dedicated to matter transfer (eg O2, CO2, H2O) and mechanical properties of materials especially with respect to food, bacteria and packaging fields.",
"domains": [
"Food"
],
"homepage": "https://www6.inrae.fr/cati-icat-atweb/Ontologies/Transmat",
"license": "CC-BY-4.0",
"name": "Matter Transfer Ontology",
"subjects": [
"Engineering Science",
"Materials Science"
]
},
"FAIRsharing.hw3bh2": {
"abbreviation": "TIME",
"contact": {
"email": "simon.cox@csiro.au",
"name": "Simon Cox, Chris Little",
"orcid": "0000-0002-3884-3420"
},
"description": "OWL-Time is an OWL-2 DL ontology of temporal concepts, for describing the temporal properties of resources in the world or described in Web pages. The ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. Time positions and durations may be expressed using either the conventional (Gregorian) calendar and clock, or using another temporal reference system such as Unix-time, geologic time, or different calendars.",
"domains": [
"Resource metadata",
"Data model"
],
"homepage": "https://www.w3.org/TR/owl-time/",
"license": "CC-BY-4.0",
"name": "OWL-Time",
"subjects": [
"Subject Agnostic"
],
"user_defined_tags": [
"Data coordination",
"Metadata standardization"
]
},
"FAIRsharing.hw5gr6": {
"abbreviation": "HEIO",
"description": "The purpose of this ontology is to develop a model for regional healthcare system interoperability and information exchange quantification (measured by the electronic health information exchange (eHIE) indicator). The eHIE is hypothesized as a leading measure of regional healthcare system integration. A publication associated with this ontology is currently under review.",
"domains": [
"Hospital"
],
"homepage": "http://bioportal.bioontology.org/ontologies/HEIO",
"name": "Regional Healthcare System Interoperability and Information Exchange Measurement Ontology",
"subjects": [
"Knowledge and Information Systems",
"Data Management",
"Medical Informatics"
]
},
"FAIRsharing.j01xzz": {
"abbreviation": "NMOSP",
"description": "The species ontology of NeuroMorpho.Org was updated (OntoSearch v1.3) to map the new species and strains added in NeuroMorpho.Org v6.3 release.",
"homepage": "https://bioportal.bioontology.org/ontologies/NMOSP",
"name": "NeuroMorpho.Org species ontology",
"subjects": [
"Computational Neuroscience",
"Neuroscience"
]
},
"FAIRsharing.j09az5": {
"abbreviation": "ISO19108TO",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/ISO19108TO",
"name": "ISO 19108 Temporal Objects",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.j0fa1d": {
"abbreviation": "EMAPA",
"description": "The ontology of mouse developmental anatomy was originally developed by Jonathan Bard and his colleagues as part of the Edinburgh Mouse Atlas Project (EMAP) in order to provide a structured controlled vocabulary of stage-specific anatomical structures for the developing laboratory mouse.\n\nInitial versions listed anatomical entities for each developmental stage (Theiler Stages 1 through 26) separately. Stage-specific instances were presented as uniparental hierarchies organized solely using part-of relationships (i.e. as a strict partonomy). An βabstractβ (i.e. non-stage-specific) representation of the mouse developmental anatomy ontology was subsequently developed.\n\nThe mouse developmental anatomy ontology has been substantially extended and refined over many years in a collaborative effort between EMAP and the Gene Expression Database (GXD) project, part of the Mouse Genome Informatics (MGI) resource at The Jackson Laboratory. The ontology continues to be maintained and expanded by GXD.",
"homepage": "https://www.informatics.jax.org/vocab/gxd/anatomy",
"license": "CC-BY-4.0",
"name": "Mouse Developmental Anatomy Ontology",
"publications": [
{
"doi": "10.1186/2041-1480-4-15",
"pubmed": "23972281",
"title": "EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update",
"year": 2013
}
],
"repository": "https://github.com/obophenotype/mouse-anatomy-ontology",
"subjects": [
"Anatomy",
"Developmental Biology"
]
},
"FAIRsharing.j2cgnn": {
"abbreviation": "ADAR",
"description": "The Autism DSM-ADI-R (ADAR) ontology uses SWRL rules to infer phenotypes from ADI-R items. It includes OWL class definitions representing DSM IV diagnostic criteria for autistic disorder and ASD criteria for Autism Spectrum Disorder. The goal is to create an ontology that will allow data integration and reasoning with subject data to classify subjects, and based on this classification, to infer new knowledge on Autism Spectrum Disorder (ASD) and related neurodevelopmental disorders (NDD). They extended an existing autism ontology to allow automatic inference of ASD phenotypes and Diagnostic & Statistical Manual of Mental Disorders (DSM) criteria based on subjectsβ Autism Diagnostic Interview-Revised (ADI-R) assessment data.",
"domains": [
"Autistic disorder",
"Phenotype",
"Diagnosis",
"Classification"
],
"homepage": "http://bioportal.bioontology.org/ontologies/ADAR",
"name": "Autism DSM-ADI-R ontology",
"publications": [
{
"doi": "10.1016/j.jbi.2015.06.026",
"pubmed": "26151311",
"title": "An ontology for Autism Spectrum Disorder (ASD) to infer ASD phenotypes from Autism Diagnostic Interview-Revised data",
"year": 2015
}
],
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.j2np9m": {
"abbreviation": "TOP-MENELAS",
"description": "The two main goals MENELAS contributes to are to (i) Provide better account of and better access to medical information through natural languages in order to help physicians in their daily practice, and to (ii) Enhance European cooperation by multilingual access to standardised medical nomenclatures. The major achievements of MENELAS are the realisation of its two functional systems: (i) The Document Indexing System encodes free text PDSs into both an internal representation (a set of Conceptual Graphs) and international nomenclature codes (ICD-9-CM). Instances of the Document Indexing System have been realised for French, English and Dutch ; (ii) The Consultation System allows users to access the information contained in PDSs previously indexed by the Document Indexing System. The test domain for the project was coronary diseases. The existing prototype shows promising results for information retrieval from natural language PDSs and for automatically encoding PDSs into an existing classification such as ICD-9-CM. A set of components, tools, knowledge bases and methods has also been produced by the project. These include language-independent ontology and models for the domain of coronary diseases; conceptual description of the relevant ICD-9-CM codes. This ontology includes a top-ontology, a top-domain ontology and a domain ontology (Coronay diseases surgery). The menelas-top ontology here is the part of the whole ontology without any reference to medical domain.",
"domains": [
"Cardiovascular disease"
],
"homepage": "https://bioportal.lirmm.fr/ontologies/TOP-MENELAS",
"name": "Menelas Project Top-Level Ontology",
"subjects": [
"Vascular Surgery",
"Biomedical Science"
]
},
"FAIRsharing.j4encb": {
"abbreviation": "XEO",
"description": "XeO has been created to help plant scientists in documenting and sharing metadata describing the abiotic environment.",
"domains": [
"Experimental measurement",
"Experimentally determined"
],
"homepage": "http://xeo.codeplex.com/",
"name": "XEML Environment Ontology",
"subjects": [
"Botany"
]
},
"FAIRsharing.j75srj": {
"abbreviation": "CO_336",
"contact": {
"email": "e.arnaud@cgiar.org",
"name": "Elizabeth Arnaud",
"orcid": "0000-0002-6020-5919"
},
"description": "The Soybean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_336:ROOT",
"license": "CC-BY-4.0",
"name": "Soybean Ontology",
"subjects": [
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.j9e8qd": {
"abbreviation": "PSI-PAR CV",
"description": "The scopes of molecular interactions and protein affinity reagents are largely overlapping but are also partially unique. This fact is reflected in the PSI-PAR CV, which contains the majority of the terms from the PSI-MI CV and an additional βΌ200 new terms as of its creation in 2009.",
"domains": [
"Molecular interaction",
"Affinity",
"Protein"
],
"homepage": "http://www.psidev.info/psi-par",
"name": "Protein Affinity Reagent Controlled Vocabulary",
"publications": [
{
"doi": "10.1038/nbt0710-650",
"pubmed": "20622827",
"title": "Minimum information about a protein affinity reagent (MIAPAR)",
"year": 2010
},
{
"doi": "10.1074/mcp.m900185-mcp200",
"pubmed": "19674966",
"title": "A community standard format for the representation of protein affinity reagents",
"year": 2009
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.j9y503": {
"abbreviation": "CL",
"contact": {
"email": "addiehl@buffalo.edu",
"name": "Alexander Diehl",
"orcid": "0000-0001-9990-8331"
},
"description": "The Cell Ontology (CL) is a candidate OBO Foundry ontology for the representation of cell types. First described in 2005, the CL integrates cell types from the prokaryotic, fungal, and eukaryotic organisms. As a core component of the OBO Foundry, the CL merges information contained in species-specific anatomical ontologies as well as referencing other OBO Foundry ontologies such as the Protein Ontology (PR) for uniquely expressed biomarkers and the Gene Ontology (GO) for the biological processes a cell type participates in. The CL is under continuous revision to expand representation of cell types and to better integrate with other biomedical ontologies.",
"domains": [
"Annotation",
"Cell",
"Morphology"
],
"homepage": "https://github.com/obophenotype/cell-ontology",
"license": "CC-BY-3.0",
"name": "Cell Ontology",
"publications": [
{
"doi": "10.1186/1471-2105-12-6",
"pubmed": "21208450",
"title": "Logical development of the cell ontology",
"year": 2011
},
{
"doi": "10.1186/s13326-016-0088-7",
"pubmed": "27377652",
"title": "The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability",
"year": 2016
}
],
"repository": "https://github.com/obophenotype/cell-ontology/blob/master/src/ontology/README.txt",
"subjects": [
"Anatomy",
"Life Science",
"Cell Biology"
]
},
"FAIRsharing.jE0WcA": {
"abbreviation": "DDIEM Ontology",
"contact": {
"email": "robert.hoehndorf@kaust.edu.sa",
"name": "Robert Hoehndorf",
"orcid": "0000-0001-8149-5890"
},
"description": "DDIEM Ontology for the Drug Database for Inborn Errors of Metabolism. The DDIEM database is a database of therapeutic strategies and treatments for inborn errors of metabolism. These strategies are classified by mechanism and outcome using the DDIEM Ontology.",
"domains": [
"Drug",
"Phenotype",
"Disease",
"Genetic disorder"
],
"homepage": "http://aber-owl.net/ontology/DDIEM/",
"license": "CC-BY-4.0",
"name": "Drug Database for Inborn Errors of Metabolism Ontology",
"repository": "https://github.com/bio-ontology-research-group/DDIEM",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.jT49Da": {
"description": "The Provenance Vocabulary provides classes and properties for describing provenance of Web data. The vocabulary focuses on two main use cases: 1.) It enables consumers of Web data to describe provenance of data retrieved from the Web and of data derived from such Web data. 2.) It enables providers of Web data to publish provenance-related metadata about their data. Notice, the vocabulary is not intended for describing provenance of other kinds of Web content. The Provenance Vocabulary is designed as a Web data specific specialization of the W3C PROV Ontology (PROV-O); classes and properties provided by the vocabulary are domain specific extensions of the more general concepts introduced in PROV-O. As a consequence, any Provenance Vocabulary based description of provenance can be easily interpreted and exchanged according to the W3C PROV family of standards. While this vocabulary is in a stable state, it is not being actively developed at this time.",
"domains": [
"Resource metadata"
],
"homepage": "http://purl.org/net/provenance/ns",
"license": "https://creativecommons.org/licenses/by/1.0",
"name": "Provenance Vocabulary",
"subjects": [
"Data Management",
"Computer Science"
]
},
"FAIRsharing.jcg19w": {
"abbreviation": "KiSAO",
"contact": {
"email": "lenov@ebi.ac.uk",
"name": "Nicolas Le Novère",
"orcid": "0000-0002-6309-7327"
},
"description": "The Kinetic Simulation Algorithm Ontology aims at providing support in unambiguously referring to simulation algorithms when describing a simulation experiment. It describes and classifies existing algorithms and their inter-relationships through the algorithm characteristics and parameters.",
"domains": [
"Kinetic model",
"Modeling and simulation",
"Algorithm"
],
"homepage": "http://co.mbine.org/standards/kisao",
"name": "Kinetic Simulation Algorithm Ontology",
"publications": [
{
"doi": "10.1038/msb.2011.77",
"pubmed": "22027554",
"title": "Controlled vocabularies and semantics in systems biology",
"year": 2011
}
],
"subjects": [
"Bioinformatics",
"Computer Science"
]
},
"FAIRsharing.jcj3gv": {
"abbreviation": "MONO",
"description": "The Monogenean Ontology is an ontology describing the anatomy of Monogeneans, small worms that parasitise aquatic animals such as fish and frogs.",
"homepage": "http://bioportal.bioontology.org/ontologies/MONO",
"name": "Monogenean Ontology",
"subjects": [
"Anatomy"
]
},
"FAIRsharing.jedbbt": {
"abbreviation": "BIRNLEX",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Study design",
"Disease"
],
"homepage": "http://xwiki.nbirn.net:8080/xwiki/bin/view/%20BIRN-OTF-Public/Home",
"name": "Biomedical Informatics Research Network Project Lexicon",
"subjects": [
"Anatomy",
"Biomedical Science"
]
},
"FAIRsharing.jh4xht": {
"abbreviation": "SWEET",
"description": "The Semantic Web for Earth and Environmental Terminology is a mature foundation ontology originally developed at the NASA Jet Propulsion Laboratory. Containing over 11000 concepts organized into ~200 ontologies, its top-level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), and Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research). Since 2017, SWEET has been under the governance of the ESIP foundation.",
"homepage": "http://sweetontology.net/",
"license": "CC0-1.0",
"name": "Semantic Web for Earth and Environmental Terminology Ontology",
"repository": "https://github.com/ESIPFed/sweet/wiki/SWEET-IRI-Patterns-for-Ontologies-and-their-Terms",
"subjects": [
"Environmental Science",
"Geology",
"Geography",
"Earth Science"
]
},
"FAIRsharing.jj4n9f": {
"abbreviation": "SPTO",
"contact": {
"email": "nm249@cornell.edu",
"name": "Naama Menda",
"orcid": "0000-0002-9117-8116"
},
"description": "Solanaceae crop phenotypes and traits, developed in collaboration with the research community, especially for breeder traits of agronomic importance.",
"domains": [
"Phenotype",
"Genotype"
],
"homepage": "https://solgenomics.net/search/phenotypes/traits",
"license": "CC-BY-4.0",
"name": "Solanaceae Phenotype Ontology",
"publications": [
{
"doi": "10.1104/pp.108.119560",
"pubmed": "18539779",
"title": "A community-based annotation framework for linking solanaceae genomes with phenomes",
"year": 2008
}
],
"subjects": [
"Botany",
"Genomics",
"Genetics",
"Phenomics"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.jjb2p2": {
"abbreviation": "VSO",
"description": "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.",
"domains": [
"Experimental measurement",
"Blood"
],
"homepage": "https://code.google.com/p/vital-sign-ontology/",
"name": "Vital Sign Ontology",
"subjects": [
"Health Science",
"Biomedical Science"
]
},
"FAIRsharing.jkj6ah": {
"abbreviation": "TMA",
"description": "Tissue microarrays (TMA) are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential.",
"domains": [
"Expression data",
"Cellular localization",
"Microarray experiment",
"Histology",
"Tissue"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1494",
"name": "Tissue Microarray Ontology",
"publications": [
{
"doi": "10.1186/1471-2105-9-s4-s4",
"pubmed": "18460177",
"title": "Ontology-based, Tissue MicroArray oriented, image centered tissue bank",
"year": 2008
},
{
"pubmed": "17476071",
"title": "Tissue MicroArray: a distributed Grid approach for image analysis",
"year": 2007
}
],
"subjects": [
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.jkt8ye": {
"abbreviation": "i2b2-patvisdims",
"description": "This database is a tool for describing patient information and facts such as patient health history, diagnosis, medication etc...This is supported by the i2b2 software. Datasets are gathered from a variety of sources. The i2b2 team merged with the TranSMART Foundation in 2017.",
"domains": [
"Phenotype"
],
"homepage": "https://www.i2b2.org",
"name": "i2b2-patient_visit_dimensions",
"subjects": [
"Medicine",
"Health Science"
]
},
"FAIRsharing.jmg2st": {
"abbreviation": "NIFCELL",
"description": "NIF has developed a comprehensive vocabulary for annotating and searching neuroscience resources.",
"domains": [
"Cell",
"Neuron",
"Phenotype"
],
"homepage": "https://neuinfo.org/about/nifvocabularies",
"name": "Neuroscience Information Framework Cell",
"subjects": [
"Neurobiology",
"Life Science",
"Neuroscience"
],
"twitter": "neuinfo"
},
"FAIRsharing.jprvcd": {
"abbreviation": "nihss",
"description": "Domain ontology for describing the standardized neurological examination of stroke patients according to the National Institutes of Health Stroke Scale (NIHSS). The ontology is intended for describing the assessment of a patient after a stroke. A patient with more limitations is evaluated with more points (worse condition). An evaluation (score) with a value of 0 (zero) indicates a normal state.",
"domains": [
"Cardiovascular disease"
],
"homepage": "http://bioportal.bioontology.org/ontologies/NIHSS",
"name": "Stroke Scale Ontology",
"subjects": [
"Health Science",
"Neuroscience"
],
"user_defined_tags": [
"stroke"
]
},
"FAIRsharing.jpxsv1": {
"abbreviation": "MPO",
"description": "An ontology for describing microbial phenotypes",
"domains": [
"Phenotype"
],
"homepage": "http://bioportal.bioontology.org/ontologies/MPO",
"name": "Microbial Phenotype Ontology",
"subjects": [
"Anatomy",
"Microbiology"
]
},
"FAIRsharing.jrxhh7": {
"abbreviation": "GRO_CPD",
"description": "A structured controlled vocabulary for describing cereal plant development and growth stages. Please note that this ontology has now been superseded by the Plant Ontology.",
"homepage": "http://bioportal.bioontology.org/ontologies/1047",
"name": "Cereal Plant Development",
"subjects": [
"Anatomy",
"Agriculture"
]
},
"FAIRsharing.js20q3": {
"abbreviation": "CO_338",
"description": "Development of crop-specific trait ontologies including the Chickpea Ontology began in 2008 as part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_338:ROOT",
"license": "CC-BY-4.0",
"name": "Chickpea Ontology",
"subjects": [
"Botany",
"Agriculture"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.jt4pzr": {
"abbreviation": "SEP",
"description": "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments, such as, and including, gel electrophoresis, column chromatography, capillary electrophoresis, centrifugation and so on. Developed jointly by the HUPO Proteomics Standards Initiative and The Metabolomics Standards Initiative.",
"domains": [
"Chromatography",
"Electrophoresis"
],
"homepage": "http://psidev.info/index.php?q=node/312",
"name": "Sample Processing and Separation Techniques Ontology",
"subjects": [
"Proteomics",
"Life Science"
]
},
"FAIRsharing.jtz0dv": {
"abbreviation": "DMTO",
"description": "The Diabetes Mellitus Treatment Ontology (DMTO) was created to model type 2 diabetes mellitus (T2DM) treatment. It models T2DM patientsβ current conditions, previous profiles, and T2DM-related aspects, including complications, symptoms, lab tests, interactions, treatment plan (TP) frameworks, and glucose-related diseases and medications.",
"domains": [
"Diabetes mellitus",
"Treatment"
],
"homepage": "http://bioportal.bioontology.org/ontologies/DMTO",
"name": "Diabetes Mellitus Treatment Ontology",
"publications": [
{
"doi": "10.1186/s13326-018-0176-y",
"pubmed": "29409535",
"title": "DMTO: a realistic ontology for standard diabetes mellitus treatment",
"year": 2018
}
],
"subjects": [
"Biomedical Science",
"Diabetology"
]
},
"FAIRsharing.jvgfka": {
"abbreviation": "TM-MER",
"description": "The meridian value set used in the International Classification of Traditional Medicine. The value set for the Signs and Symptoms property of the International Classification of Traditional Medicine (ICTM). The World Health Organization, in consultation with a large group of stakeholders in the areas of Traditional Medicine or Complementary and Alternative Medicine and Health Information Systems, has developed a collaborative project plan to produce an international standard terminology and classification system for Traditional Medicine. This resource is part of an effort to produce an international standard for information on TM that is ready for electronic health records and that will serve as a standard for scientific comparability and communication.",
"homepage": "https://bioportal.bioontology.org/ontologies/TM-MER",
"name": "Traditional Medicine Meridian Value Sets",
"subjects": [
"Traditional Medicine"
]
},
"FAIRsharing.jw50ht": {
"abbreviation": "TRIAGE",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Nurse"
],
"homepage": "http://bioportal.bioontology.org/ontologies/TRIAGE",
"name": "Nurse triage",
"subjects": [
"Health Science"
]
},
"FAIRsharing.jy3bvk": {
"abbreviation": "PedTerm",
"description": "Terms associated with pediatrics, representing information related to child health and development from pre-birth through 21 years of age; contributed by the National Institute of Child Health and Human Development.",
"domains": [
"Disease",
"Infant"
],
"homepage": "https://www.cancer.gov/research/resources/terminology/pediatric",
"name": "Pediatric Terminology",
"publications": [
{
"doi": "10.1542/peds.2013-1504",
"pubmed": "24534404",
"title": "Building a common pediatric research terminology for accelerating child health research",
"year": 2014
}
],
"subjects": [
"Medicine",
"Health Science",
"Pediatrics",
"Biomedical Science"
]
},
"FAIRsharing.jz4ea7": {
"abbreviation": "TRANS",
"contact": {
"email": "lschriml@som.umaryland.edu",
"name": "Lynn M. Schriml",
"orcid": "0000-0001-8910-9851"
},
"description": "This vocabulary describes a process that is the means of how a pathogen is transmitted from one host, reservoir, or source to another host. This transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.",
"domains": [
"Pathogen",
"Host",
"Infection"
],
"homepage": "https://disease-ontology.org/resources/pathogen-transmission-ontology",
"license": "CC0-1.0",
"name": "Pathogen Transmission Ontology",
"publications": [
{
"doi": "10.1093/nar/gkab1063",
"pubmed": "34755882",
"title": "The Human Disease Ontology 2022 update",
"year": 2022
},
{
"doi": "10.1093/nar/gkp832",
"pubmed": "19850722",
"title": "GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database",
"year": 2010
},
{
"doi": "10.1093/nar/gkad1051",
"pubmed": "37953304",
"title": "The DO-KB Knowledgebase: a 20-year journey developing the disease open science ecosystem",
"year": 2023
}
],
"repository": "https://github.com/DiseaseOntology/PathogenTransmissionOntology/issues",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.k008w7": {
"abbreviation": "DERMO",
"description": "DermO is an Ontology of cutaneous disease, constructed manually by domain experts. With more than 3000 terms, DermO represents the most comprehensive formal dermatological disease terminology available. The disease entities are categorized in 20 upper level terms, which use a variety of features such as anatomical location, heritability, affected cell or tissue type, or etiology, as the features for classification, in line with professional practice and nosology in dermatology.",
"domains": [
"Disease"
],
"homepage": "http://bioportal.bioontology.org/ontologies/DERMO",
"name": "Human Dermatological Disease Ontology",
"publications": [
{
"doi": "10.1186/s13326-016-0085-x",
"pubmed": "27296450",
"title": "DermO; an ontology for the description of dermatologic disease",
"year": 2016
}
],
"subjects": [
"Dermatology"
]
},
"FAIRsharing.k2dq5j": {
"abbreviation": "AO",
"description": "An ontology which describes the medical terminology for asthmatic conditions.",
"homepage": "http://bioportal.bioontology.org/ontologies/AO",
"name": "Asthma Ontology",
"publications": [
{
"doi": "10.1136/bmjopen-2018-024372",
"pubmed": "30679295",
"title": "Determinants of inter-practice variation in childhood asthma and respiratory infections: cross-sectional study of a national sentinel network",
"year": 2019
}
],
"subjects": [
"Medicine"
]
},
"FAIRsharing.k3fp3g": {
"abbreviation": "Read v2",
"description": "Read Codes are a coded thesaurus of clinical terms. They have been used in the NHS since 1985. There are two versions: version 2 (v2) and version 3 (CTV3 or v3). Both versions provide a standard vocabulary for clinicians to record patient findings and procedures, in health and social care IT systems across primary and secondary care. The Read Codes were developed in 1985 by Dr. James Read. The U.K. National Health Service Centre for Coding and Classification (NHS CCC) acquired and now maintains the Read Codes. Read Codes contain hundreds of thousands of terms, synonyms, and abbreviations covering all aspects of patient care including signs and symptoms, treatments and therapies, investigations, occupations, diagnoses, and drugs and appliances. Read Codes are used by healthcare professionals in computerized information systems. Read Codes are now known as Clinical Terms. PLEASE NOTE: the retirement of Read v2 and v3 (CTV3) clinical terminologies has been scheduled. The last release of Read v2 was April 2016, and as such this record has been marked with a \"Deprecated\" status. CTV3 is due to be retired after the April 2018 release.",
"domains": [
"Drug",
"Diagnosis",
"Treatment"
],
"homepage": "https://digital.nhs.uk/article/1104/Read-Codes",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Read Clinical Terminology Version 2",
"subjects": [
"Medicine",
"Primary Health Care",
"Preclinical Studies"
]
},
"FAIRsharing.k7NfCn": {
"abbreviation": "WTO",
"contact": {
"email": "claire.nedellec@inrae.fr",
"name": "Claire Nedellec",
"orcid": "0000-0002-0577-0595"
},
"description": "Wheat Trait Ontology is an ontology of wheat traits and environmental factors that affect these traits. They include resistance to disease, development, nutrition, bread quality, etc. Environmental factors include biotic and abiotic factors. An alternative title is the Wheat Phenotype Ontology.",
"domains": [
"Food",
"Disease",
"Plant development stage"
],
"homepage": "https://doi.org/10.15454/1.4382637738008071E12",
"name": "Wheat Trait Ontology",
"publications": [
{
"doi": "10.5808/gi.2020.18.2.e14",
"title": "WTO, an ontology for wheat traits and phenotypes in scientific publications",
"year": 2020
}
],
"subjects": [
"Botany",
"Plant Nutrition",
"Plant Breeding",
"Food Process Engineering",
"Agriculture"
]
},
"FAIRsharing.k893xa": {
"abbreviation": "MRO",
"description": "MHC molecules form a highly diverse family of proteins that play a key role in cellular immune recognition. No consistent nomenclature exists across different vertebrate species. To correctly represent MHC related data in The Immune Epitope Database (IEDB), we built upon a previously established MHC ontology (MaHCO) and created MRO to represent MHC molecules as they relate to immunological experiments. MRO models MHC protein chains from 16 species, deals with different approaches used to identify MHC, such as direct sequencing verses serotyping, relates engineered MHC molecules to naturally occurring ones, connects genetic loci, alleles, protein chains and multichain proteins, and establishes evidence codes for MHC restriction.",
"domains": [
"Major histocompatibility complex",
"Immune system"
],
"homepage": "https://github.com/IEDB/MRO",
"license": "CC-BY-3.0",
"name": "MHC Restriction Ontology",
"publications": [
{
"doi": "10.1186/s13326-016-0045-5",
"pubmed": "26759709",
"title": "An ontology for major histocompatibility restriction",
"year": 2016
}
],
"repository": "https://github.com/IEDB/MRO/issues",
"subjects": [
"Immunology"
]
},
"FAIRsharing.kay31r": {
"abbreviation": "CDAO",
"contact": {
"email": "balhoff@gmail.com",
"name": "Jim Balhoff",
"orcid": "0000-0002-8688-6599"
},
"description": "Comparative Data Analysis Ontology (CDAO) is a formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types).",
"domains": [
"Evolution"
],
"homepage": "https://github.com/evoinfo/cdao",
"license": "CC0-1.0",
"name": "Comparative Data Analysis Ontology",
"publications": [
{
"doi": "10.4137/ebo.s2320",
"pubmed": "19812726",
"title": "Initial implementation of a comparative data analysis ontology",
"year": 2009
}
],
"repository": "https://github.com/evoinfo/cdao/issues",
"subjects": [
"Molecular biology",
"Bioinformatics",
"Taxonomy",
"Phylogenetics",
"Evolutionary Biology",
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.kbtt7f": {
"abbreviation": "HP",
"description": "The Human Phenotype Ontology has been developed to provide a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. The goal is to provide resource for the computational analysis of the human phenome, with a focus on monogenic diseases listed in the Online Mendelian Inheritance in Man (OMIM) and Orphanet databases, for which annotations are also provided.",
"domains": [
"Phenotype",
"Disease"
],
"homepage": "https://hpo.jax.org/",
"license": "hpo",
"name": "Human Phenotype Ontology",
"publications": [
{
"doi": "10.1093/nar/gkt1026",
"pubmed": "24217912",
"title": "The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data",
"year": 2013
},
{
"doi": "10.1093/nar/gkw1039",
"pubmed": "27899602",
"title": "The Human Phenotype Ontology in 2017",
"year": 2016
},
{
"doi": "10.1111/j.1399-0004.2010.01436.x",
"pubmed": "20412080",
"title": "The human phenotype ontology",
"year": 2010
},
{
"doi": "10.1093/nar/gky1105",
"pubmed": "30476213",
"title": "Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources",
"year": 2018
},
{
"doi": "10.1016/j.ajhg.2008.09.017",
"pubmed": "18950739",
"title": "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease",
"year": 2008
}
],
"subjects": [
"Genetics",
"Phenomics",
"Biomedical Science",
"Preclinical Studies"
],
"twitter": "hp_ontology"
},
"FAIRsharing.kbz5jh": {
"abbreviation": "MAMO",
"contact": {
"email": "n.lenovere@gmail.com",
"name": "Nicolas Le Novere",
"orcid": "0000-0002-6309-7327"
},
"description": "Classification of the types of mathematical models used mostly in the life sciences, the types of variables, the types of readout and other relevant features.",
"domains": [
"Modeling and simulation"
],
"homepage": "http://co.mbine.org/standards/mamo",
"name": "Mathematical Modelling Ontology",
"subjects": [
"Mathematics",
"Computational Biology",
"Systems Biology"
]
},
"FAIRsharing.kd6sg8": {
"description": "The RegenBase ontology describes biological entities and processes studied in spinal cord injury (SCI) research. The project aims to improve the replicability of SCI research findings through a minimum information standard for describing SCI experiments and their results, and this ontology to formally describe SCI concepts and the relationships between them. ",
"homepage": "https://regenbase.org/regenbase-ontology.html",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdklDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--a3ccd509fd2fd8ae5e38c934f0e5ce0caff6a49d/1424801361.png?disposition=inline",
"name": "RegenBase ontology",
"publications": [
{
"doi": "10.4103/1673-5374.125322",
"title": "Facilitating transparency in spinal cord injury studies using data standards and ontologies",
"year": 2014
}
],
"subjects": [
"Anatomy",
"Medicine",
"Neurobiology",
"Biomedical Science",
"Translational Medicine"
],
"user_defined_tags": [
"Spinal Cord",
"Spinal Cord Injury"
]
},
"FAIRsharing.kfs4pj": {
"abbreviation": "Pseudo",
"description": "This ontology is about human pseudogenes, extending the existing SO framework to incorporate additional attributes. Relationships between pseudogenes and segmental duplications are defined in this standard. To answer research questions and to annotate pseudogenes appropriately, a series of logical rules using SWRL was created.",
"domains": [
"Pseudogene",
"Gene"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1135",
"name": "Pseudogene",
"publications": [
{
"doi": "10.1093/bioinformatics/btq173",
"pubmed": "20529940",
"title": "Using semantic web rules to reason on an ontology of pseudogenes",
"year": 2010
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.kg1x4z": {
"abbreviation": "MP",
"contact": {
"email": "susan.bello@jax.org",
"name": "Susan M. Bello",
"orcid": "0000-0003-4606-0597"
},
"description": "The observable morphological, physiological, behavioral and other characteristics of mammalian organisms that are manifested through development and lifespan.",
"domains": [
"Behavior",
"Phenotype"
],
"homepage": "https://www.informatics.jax.org/vocab/mp_ontology/",
"license": "CC-BY-4.0",
"name": "Mammalian Phenotype Ontology",
"publications": [
{
"doi": "10.1186/gb-2004-6-1-r7",
"pubmed": "15642099",
"title": "The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information",
"year": 2005
},
{
"doi": "10.1002/wsbm.44",
"pubmed": "20052305",
"title": "The mammalian phenotype ontology: enabling robust annotation and comparative analysis",
"year": 2010
},
{
"doi": "10.1007/s00335-012-9421-3",
"pubmed": "22961259",
"title": "The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data",
"year": 2012
},
{
"doi": "10.1186/s13326-015-0009-1",
"pubmed": "25825651",
"title": "Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens",
"year": 2015
}
],
"repository": "https://github.com/obophenotype/mammalian-phenotype-ontology",
"subjects": [
"Developmental Biology",
"Life Science",
"Physiology"
]
},
"FAIRsharing.kj336a": {
"abbreviation": "MCCV",
"description": "Structured controlled vocabulary for describing meta information of microbial calture collection maintained in biological research centers",
"domains": [
"Sequence",
"Genetic strain"
],
"homepage": "http://bioportal.bioontology.org/ontologies/MCCV",
"name": "Microbial Culture Collection Vocabulary",
"subjects": [
"Taxonomy",
"Microbiology"
]
},
"FAIRsharing.kj3m5n": {
"abbreviation": "HAO",
"contact": {
"email": "andy_deans@ncsu.edu",
"name": "Andrew R Deans",
"orcid": "0000-0002-2119-4663"
},
"description": "The Hymenoptera Anatomy Ontology is a structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)",
"domains": [
"Image"
],
"homepage": "http://portal.hymao.org/projects/32/public/ontology/",
"name": "Hymenoptera Anatomy Ontology",
"publications": [
{
"doi": "10.1371/journal.pone.0015991",
"pubmed": "21209921",
"title": "A gross anatomy ontology for hymenoptera",
"year": 2011
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"FAIRsharing.kkq6pw": {
"abbreviation": "SCDO",
"description": "The Sickle Cell Disease Ontology (SCDO) project is a collaboration between H3ABioNet (Pan African Bioinformatics Network) and SPAN (Sickle Cell Disease Pan African Network). The SCDO is currently under development and its purpose is to: 1) establish community standardized SCD terms and descriptions, 2) establish canonical and hierarchical representation of knowledge on SCD, 3) links to other ontologies and bodies of work such as DO, PhenX MeSH, ICD, NCIβs thesaurus, SNOMED and OMIM. ",
"domains": [
"Genetic disorder"
],
"homepage": "http://scdontology.h3abionet.org",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBbWtCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--69320a8be8ca6a407eaf142714307b4c7e6b5f45/cropped-Screenshot-from-2020-05-23-20-20-32-2.png?disposition=inline",
"name": "Sickle Cell Disease Ontology",
"publications": [
{
"doi": "10.1093/database/baac014",
"pubmed": "35363306",
"title": "The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation",
"year": 2022
},
{
"doi": "10.1089/omi.2020.0153",
"pubmed": "33021900",
"title": "The Sickle Cell Disease Ontology: Enabling Collaborative Research and Co-Designing of New Planetary Health Applications",
"year": 2020
},
{
"doi": "10.1093/database/baz118",
"pubmed": "31769834",
"title": "The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation",
"year": 2019
}
],
"subjects": [
"Biomedical Science"
],
"user_defined_tags": [
"sickle cell disease"
]
},
"FAIRsharing.kn0d5v": {
"abbreviation": "DC_CL",
"contact": {
"email": "Lindsay.Cowell@utsouthwestern.edu",
"name": "Lindsay Cowell",
"orcid": "0000-0003-1617-8244"
},
"description": "\"Dendritic cell\" is a standard, specialising in the fields described under \"scope and data types\", below. Until this entry is claimed, more information on this project can be found at http://purl.bioontology.org/ontology/DC_CL. This text was generated automatically. If you work on the project responsible for \"Dendritic cell\" then please consider helping us by claiming this record and updating it appropriately.",
"domains": [
"Annotation",
"Dendritic cell",
"Morphology"
],
"homepage": "http://purl.bioontology.org/ontology/DC_CL",
"name": "Dendritic cell",
"subjects": [
"Anatomy"
]
},
"FAIRsharing.knp11s": {
"abbreviation": "CMPO",
"description": "Cellular Microscopy Phenotype Ontology (CMPO) is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations",
"domains": [
"Cell",
"Microscopy",
"Cellular component",
"Phenotype"
],
"homepage": "http://www.ebi.ac.uk/cmpo/",
"license": "Apache 2.0 License",
"name": "Cellular Microscopy Phenotype Ontology",
"publications": [
{
"doi": "10.1186/s13326-016-0074-0",
"pubmed": "27195102",
"title": "The cellular microscopy phenotype ontology",
"year": 2016
}
],
"repository": "https://github.com/EBISPOT/CMPO",
"subjects": [
"Cell Biology"
]
},
"FAIRsharing.kpbna7": {
"abbreviation": "GENO",
"description": "An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases.",
"domains": [
"Disease phenotype",
"Genotype"
],
"homepage": "https://github.com/monarch-initiative/GENO-ontology/",
"license": "CC-BY-4.0",
"name": "Genotype Ontology",
"subjects": [
"Genomics"
]
},
"FAIRsharing.kqt2h2": {
"abbreviation": "RNAO",
"contact": {
"email": "BatchelorC@rsc.org",
"name": "Colin Batchelor",
"orcid": "0000-0001-5985-7429"
},
"description": "RNAO is a controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures. The central aim of the RNA Ontology Consortium (ROC) is to develop an ontology to capture all aspects of RNA - from primary sequence to alignments, secondary and tertiary structure, and from base pairing and base stacking interactions to sophisticated motifs.",
"domains": [
"RNA secondary structure",
"Molecular structure",
"Ribonucleic acid",
"Sequence motif"
],
"homepage": "https://github.com/bgsu-rna/rnao",
"name": "RNA Ontology",
"publications": [
{
"doi": "10.1261/rna.2343206",
"pubmed": "16484377",
"title": "The RNA Ontology Consortium: an open invitation to the RNA community",
"year": 2006
},
{
"doi": "10.3233/ao-2011-0082",
"title": "The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data",
"year": 2011
}
],
"subjects": [
"Biochemistry",
"Life Science"
]
},
"FAIRsharing.ktk1sg": {
"abbreviation": "ONL-MSA",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Bioimaging"
],
"homepage": "http://neurolog.unice.fr/ontoneurolog/v3.0/Documentation_OntoNeuroLOGv3.pdf",
"name": "Mental State Assessment",
"subjects": [
"Neuroscience"
]
},
"FAIRsharing.kw3mn5": {
"abbreviation": "IDQA",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Imaging"
],
"homepage": "http://idqa.wordpress.com",
"name": "Image and Data Quality Assessment Ontology",
"subjects": [
"Data Quality"
]
},
"FAIRsharing.kwwh11": {
"abbreviation": "FDA-MedDevice",
"description": "Record does not exist anymore: FDA Medical Devices. The record with identifier content 10.25504/FAIRsharing.kwwh11 was invalid.",
"homepage": "http://www.fda.gov/MedicalDevices/default.htm",
"name": "FDA Medical Devices",
"subjects": [
"Medicine",
"Health Science",
"Biomedical Science"
]
},
"FAIRsharing.kx2md1": {
"abbreviation": "ONTIE",
"description": "The Ontology of Immune Epitopes (ONTIE) is an effort to represent terms in the immunology domain in a formal ontology with the specific goal of representing experiments that identify and characterize immune epitopes. ONTIE has been developed as a subset of OBI (Ontology of Biomedical Investigations) and includes terms relating to experiments involving immune epitopes. This file contains the minimal amount of upper ontology terms and axioms from BFO (Basic Formal Ontology), IAO (Information Artifact Ontology) and OBI, in order to view and reason upon ONTIE. It is currently at version 0.1 beta. ONTIE covers terms regarding immune responses, adaptive immune receptors, immune epitope assays, MHC molecules, and infectious diseases. ONTIE is (at this development stage) a virtual ontology, drawing together terms from multiple reference ontologies. We are actively working on adding more terms to ONTIE either through term requests or through active contribution to external ontologies.",
"domains": [
"Infection",
"Major histocompatibility complex"
],
"homepage": "http://ontology.iedb.org",
"name": "Ontology of Immune Epitopes",
"subjects": [
"Immunology",
"Life Science"
]
},
"FAIRsharing.kx4bgf": {
"abbreviation": "NGSONTO",
"description": "The NGSOnto ontology aims at capturing the workflow of all the processes involved in a Next Generation Sequencing, in order to ensure the reproducibility of the entire process, through the use of a controled and specific vocabulary.",
"domains": [
"Next generation DNA sequencing"
],
"homepage": "https://github.com/mickaelsilva/NGSOnto",
"name": "NGS ontology",
"subjects": [
"Biology"
]
},
"FAIRsharing.kz1ygb": {
"abbreviation": "PKO",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/1409",
"name": "PKO_Re",
"subjects": [
"Biology"
]
},
"FAIRsharing.lWbenx": {
"abbreviation": "RefMet",
"contact": {
"email": "christine@sdsc.edu",
"name": "Christine Kirkpatrick",
"orcid": "0000-0002-4451-8042"
},
"description": "RefMet provides a standardized reference nomenclature for both discrete metabolite structures and metabolite species identified by spectroscopic techniques in metabolomics experiments. This is an essential prerequisite for the ability to compare and contrast metabolite data across different experiments and studies. Over 200,000 names from a set of over 1,100 MS and NMR studies on the Metabolomics Workbench has been used to generate a highly curated analytical chemistry-centric list of common names for metabolite structures and isobaric species. Additionally, the vast majority of these names have been linked to a metabolite classification system using a combination of LIPID MAPS and ClassyFire classification methods. A name-conversion user interface is provided where users can submit a list of metabolite names and map them to the corresponding RefMet names. New metabolites are constantly being added to RefMet, however very new metabolite names generated by metabolomics experiments may not currently map to RefMet identifiers. Nevertheless, RefMet has the ability to greatly increase the data-sharing potential of metabolomics experiments and facilitate \"meta-analysis\" and systems biology objectives for the majority of commonly encountered metabolite species.",
"domains": [
"Metabolite",
"Classification"
],
"homepage": "https://www.metabolomicsworkbench.org/databases/refmet/index.php",
"name": "Reference list of Metabolite names",
"subjects": [
"Metabolomics",
"Systems Biology"
]
},
"FAIRsharing.m0e1s0": {
"abbreviation": "SOY",
"description": "This is a community-curated controlled vocabulary for soybean field growth stages (Soybean Whole Plant Growth Ontology), plant structure names (Soybean Structure Ontology), development (Soybean Development Ontology) and plant traits (Soybean Trait Ontology). Where applicable, soybean specific terms have been associated with their Plant Ontology (PO) and Gramene Plant Trait Ontology (TO) synonyms to facilitate cross species comparisons. Currently, there are 4 divisions to SOY terms, soybean structural terms (Soybean Structure Ontology), developmental stages (Soybean Developmental Ontology), whole plant development terms (Soybean Whole Plant Growth Stages) and trait terms (Soybean Trait Ontology). For the trait, structure and development terms the old SoyTO and SoyGRO accessions have been added to their records as synonyms for continuity.",
"domains": [
"Phenotype",
"Life cycle stage"
],
"homepage": "https://soybase.org/ontology.php",
"name": "SoyOntology",
"publications": [
{
"doi": "10.1093/nar/gkp798",
"pubmed": "20008513",
"title": "SoyBase, the USDA-ARS soybean genetics and genomics database",
"year": 2009
}
],
"subjects": [
"Botany",
"Anatomy",
"Agriculture",
"Developmental Biology"
],
"twitter": "SoyBaseDatabase"
},
"FAIRsharing.m0pprb": {
"abbreviation": "RCTONT",
"contact": {
"email": "amrapali.j.zaveri@gmail.com",
"name": "Amrapali Zaveri",
"orcid": "0000-0003-3239-4588"
},
"description": "An ontology specifically for Randomized Controlled Trials in order to facilitate the production of systematic reviews and metaanalysis.",
"domains": [
"Evidence",
"Systematic review"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1676",
"license": "CC BY-SA 3.0",
"name": "Randomized Controlled Trials Ontology",
"publications": [
{
"doi": "10.1007/s12021-010-9079-5",
"pubmed": "20953737",
"title": "Achieving high research reporting quality through the use of computational ontologies",
"year": 2010
}
],
"subjects": [
"Neurobiology",
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.m283c": {
"abbreviation": "core",
"description": "The UniProt core is an OWL ontology that describes the predicates, classes and concepts used to model the UniProt data in RDF.",
"domains": [
"Annotation",
"Protein"
],
"homepage": "http://purl.uniprot.org/core/",
"license": "CC-BY-4.0",
"name": "Uniprot Core Ontology",
"subjects": [
"Life Science"
]
},
"FAIRsharing.m3wzgs": {
"abbreviation": "FBsp",
"description": "\"Fly taxonomy\" provides taxonomic information about the Fruit fly family (Drosophilidae). This information is a combination of NCBI TAXON data and from the following paper: Grimaldi, D.A.\"A phylogenetic, revised classification of Genera in the Drosophilidae (Diptera)\" Bulletin of the American Museum of Natural History. New York: New York . American Museum of Natural History, 1990.",
"domains": [
"Taxonomic classification"
],
"homepage": "http://flybase.org/static_pages/allied-data/phylogeny/Drosophilidae-Tree/Drosophilidae.html",
"name": "Fly taxonomy",
"publications": [
{
"doi": "10.1093/nar/gkv1046",
"pubmed": "26467478",
"title": "FlyBase: establishing a Gene Group resource for Drosophila melanogaster",
"year": 2015
}
],
"subjects": [
"Life Science"
],
"twitter": "flybasedotorg"
},
"FAIRsharing.m40bhw": {
"abbreviation": "AgrO",
"description": "AgrO, the Agronomy Ontology, describes agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments. AgrO is being built by CGIAR using traits identified by agronomists, the ICASA variables, and other existing ontologies such as ENVO, UO, and PATO. It will complement existing crop, livestock, and fish ontologies to enable harmonized approaches to data collection, facilitating easier data sharing and reuse. A key use case for AgrO is the Agronomy Field Information Management System (AgroFIMS). AgroFIMS enables digital collection of agronomic data that is semantically described a priori with agronomic terms from AgrO.",
"domains": [
"Cropping systems"
],
"homepage": "https://bigdata.cgiar.org/resources/agronomy-ontology/",
"license": "CC-BY-4.0",
"name": "Agronomy Ontology",
"repository": "https://github.com/AgriculturalSemantics/agro/issues/",
"subjects": [
"Farming Systems Research",
"Plant Breeding",
"Agronomy",
"Agriculture"
]
},
"FAIRsharing.m5gatp": {
"abbreviation": "ONTOTOXNUC",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/ONTOTOXNUC",
"name": "Ontology of Nuclear Toxicity",
"subjects": [
"Toxicology",
"Chemistry"
]
},
"FAIRsharing.mb5dc": {
"abbreviation": "HAAURAADO",
"contact": {
"email": "contact@bioself-communication.com",
"name": "Delphine Dauga",
"orcid": "0000-0003-3152-1194"
},
"description": "The first ontology describing the anatomy and the development of Halocynthia aurantium.",
"domains": [
"Cell",
"Life cycle",
"Life cycle stage"
],
"homepage": "https://www.aniseed.fr/aniseed/anatomy/find_devstage?module=aniseed&action=anatomy:find_devstage",
"name": "Halocynthia aurantium Anatomy and Development Ontology",
"subjects": [
"Anatomy",
"Developmental Biology"
],
"user_defined_tags": [
"Morphogenesis"
]
},
"FAIRsharing.mc998w": {
"abbreviation": "NeoMark4",
"contact": {
"email": "dsalvi@lst.tfo.upm.es",
"name": "Dario Salvi",
"orcid": "0000-0002-9203-1124"
},
"description": "An ontology that describes the medical information necessary for early detection of the oral cancer reoccurrence extracted from the NeoMark Project.",
"domains": [
"Biomarker",
"Cancer"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1686",
"name": "Neomark Oral Cancer Ontology version 4",
"publications": [
{
"doi": "10.1109/tbme.2012.2216879",
"pubmed": "22955869",
"title": "Merging person-specific bio-markers for predicting oral cancer recurrence through an ontology",
"year": 2012
}
],
"subjects": [
"Anatomy",
"Oncology",
"Genomics",
"Proteomics",
"Biomedical Science"
]
},
"FAIRsharing.mct09a": {
"abbreviation": "MOP",
"description": "The Molecular Process Ontology (MOP) was created to work together with the Name Reaction Ontology (RXNO). MOP describes underlying molecular processes in organic reactions such as cyclization, methylation and demethylation.",
"domains": [
"Reaction data"
],
"homepage": "https://github.com/rsc-ontologies/rxno",
"license": "CC-BY-4.0",
"name": "Molecular Process Ontology",
"subjects": [
"Molecular Chemistry"
]
},
"FAIRsharing.md3e78": {
"abbreviation": "AC",
"contact": {
"email": "secretary@tdwg.org",
"name": "Patricia Mergen",
"orcid": "0000-0003-2848-8231"
},
"description": "The Audubon Core Multimedia Resources Metadata schema (βAC schemaβ, or simply βACβ) is a set of metadata vocabularies for describing biodiversity-related multimedia resources and collections. The specification is independent of how these vocabularies may be represented for machine use. An Audubon Core record is a description of a multimedia resource using the Audubon Core terms. Two kinds of terms are specified by AC: record-level terms and access-level terms.",
"domains": [
"Image",
"Multimedia"
],
"homepage": "https://ac.tdwg.org/introduction/",
"license": "CC-BY-4.0",
"name": "Audubon Core Multimedia Resources Metadata Schema",
"publications": [
{
"doi": "10.17161/bi.v8i2.4117",
"title": "Discovery and publishing of primary Biodiversity Data associated with multimedia resources: The Audubon Core Strategies and approaches",
"year": 2013
}
],
"repository": "https://github.com/tdwg/ac",
"subjects": [
"Biodiversity"
]
},
"FAIRsharing.mf91p5": {
"abbreviation": "OMIT",
"description": "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). Please note that, although the ontology is available at the stated GitHub repository, it has not been updated in a number of years and you may wish to carefully review the ontology before use.",
"domains": [
"Annotation",
"Computational biological predictions",
"Gene prediction",
"Molecular entity",
"Cell",
"Regulation of gene expression",
"Molecular interaction",
"Protein",
"Micro RNA",
"Gene"
],
"homepage": "https://github.com/OmniSearch/omit",
"license": "CC-BY-3.0",
"name": "Ontology for MicroRNA Target",
"publications": [
{
"doi": "10.1371/journal.pone.0100855",
"pubmed": "25025130",
"title": "OMIT: dynamic, semi-automated ontology development for the microRNA domain",
"year": 2014
},
{
"doi": "10.1007/s11095-011-0573-8",
"pubmed": "21879385",
"title": "OMIT: a domain-specific knowledge base for microRNA target prediction",
"year": 2011
},
{
"doi": "10.1186/s13326-016-0064-2",
"pubmed": "27175225",
"title": "OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data",
"year": 2016
}
],
"repository": "https://github.com/OmniSearch/omit",
"subjects": [
"Life Science",
"Biology"
]
},
"FAIRsharing.mgxgza": {
"abbreviation": "CTENO",
"description": "An anatomical and developmental ontology for ctenophores (Comb Jellies). Please note that, while available, this ontology has not been updated since 2016.",
"homepage": "https://github.com/obophenotype/ctenophore-ontology",
"license": "CC-BY-3.0",
"name": "Ctenophore Ontology",
"subjects": [
"Anatomy",
"Developmental Biology"
]
},
"FAIRsharing.mjnypw": {
"abbreviation": "UO",
"contact": {
"email": "geg18@aber.ac.uk",
"name": "George Gkoutos",
"orcid": "0000-0002-2061-091X"
},
"description": "The Units Ontology (UO) models metrical units for use in conjunction with PATO. Units are basic scientific tools that render meaning to numerical data. Their standardization and formalization caters for the report, exchange, process, reproducibility and integration of quantitative measurements. The Units Ontology is an ontology currently being used for the standardized description of units of measurements.",
"domains": [
"Unit",
"Measurement"
],
"homepage": "https://github.com/bio-ontology-research-group/unit-ontology",
"license": "CC-BY-3.0",
"name": "Units Ontology",
"publications": [
{
"doi": "10.1093/database/bas033",
"pubmed": "23060432",
"title": "The Units Ontology: a tool for integrating units of measurement in science",
"year": 2012
}
],
"repository": "https://github.com/bio-ontology-research-group/unit-ontology/issues",
"subjects": [
"Mathematics",
"Life Science"
]
},
"FAIRsharing.mm72as": {
"abbreviation": "INO",
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun He",
"orcid": "0000-0001-9189-9661"
},
"description": "The Interaction Network Ontology (INO) aims to standardize interaction network annotation, integrate various interaction network data, and support computer-assisted reasoning. It models general interactions (e.g., molecular interactions) and interaction networks (e.g., Bayesian network). INO is aligned with the Basic Formal Ontology (BFO) and imports terms from 10 other existing ontologies, and includes over 500 terms. In terms of interaction-related terms, INO imports and aligns PSI-MI and GO interaction terms and includes over 100 newly generated ontology terms.",
"domains": [
"Network model",
"Molecular interaction"
],
"homepage": "https://sourceforge.net/projects/ino/",
"license": "CC-BY-4.0",
"name": "Interaction Network Ontology",
"publications": [
{
"doi": "10.1186/s13040-016-0118-0",
"pubmed": "28031747",
"title": "The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature",
"year": 2016
},
{
"doi": "10.1186/2041-1480-6-2",
"pubmed": "25785184",
"title": "Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions",
"year": 2015
},
{
"doi": "10.1186/2041-1480-2-s2-s8",
"pubmed": "21624163",
"title": "Mining of vaccine-associated IFN-gamma gene interaction networks using the Vaccine Ontology",
"year": 2011
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.mp0rwf": {
"abbreviation": "OBA",
"description": "A collection of biological attributes / traits covering all kingdoms of life. It is interoperable with a number of other community ontologies.",
"homepage": "https://github.com/obophenotype/bio-attribute-ontology",
"license": "CC0-1.0",
"name": "Ontology of Biological Attributes",
"subjects": [
"Biology"
]
},
"FAIRsharing.mp8js2": {
"abbreviation": "MWLA",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "https://www.carre-project.eu/innovation/web-lifestyle-data-aggregator/",
"name": "Medical Web Lifestyle Aggregator",
"subjects": [
"Health Science"
]
},
"FAIRsharing.mpxb4a": {
"abbreviation": "NLMVS",
"description": "Record does not exist anymore: NIH NLM Value Sets. The record with identifier content 10.25504/FAIRsharing.mpxb4a was invalid.",
"homepage": "https://github.com/ncbo/NLMVS2RDF",
"name": "NIH NLM Value Sets"
},
"FAIRsharing.msgwvy": {
"abbreviation": "PMA",
"contact": {
"email": "martinji@mail.nih.gov",
"name": "Jim Martin",
"orcid": "0000-0002-3891-0347"
},
"description": "The Portfolio Management Application (PMA) is a system for tracking grants and producing reports - Users can access grant data through a query interface and a variety of pre-defined forms and reports",
"domains": [
"Electronic health record"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1497",
"name": "Portfolio Management Application",
"subjects": [
"Medicine",
"Health Science"
]
},
"FAIRsharing.mtf81z": {
"abbreviation": "ICD-O-3",
"description": "The International Classification of Diseases for Oncology, 3rd Edition (ICD-O-3) is used principally in tumour or cancer registries for coding the site (topography) and the histology (morphology) of neoplasms, usually obtained from a pathology report. It provides a multi-axial classification of the site, morphology, behaviour, and grading of neoplasms. The topography axis uses the ICD-10 classification of malignant neoplasms (except those categories which relate to secondary neoplasms and to specified morphological types of tumours) for all types of tumours, thereby providing greater site detail for non-malignant tumours than is provided in ICD-10. In contrast to ICD-10, the ICD-O-3 includes topography for sites of haematopoietic and reticuloendothelial tumours.",
"domains": [
"Cancer",
"Tumor",
"Electronic health record",
"Histology",
"Disease",
"Classification",
"Morphology"
],
"homepage": "https://www.who.int/standards/classifications/other-classifications/international-classification-of-diseases-for-oncology",
"name": "International Classification of Diseases for Oncology, 3rd Edition",
"subjects": [
"Oncology",
"Health Science",
"Global Health",
"Pathology"
]
},
"FAIRsharing.mtmsgm": {
"abbreviation": "GRO CPGA",
"description": "Cereal plant gross anatomy is a structured controlled vocabulary for the anatomy of Gramineae. Please note that this ontology has now been superseded by the Plant Ontology.",
"domains": [
"Morphology",
"Structure"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1001",
"name": "Cereal Plant Gross Anatomy Ontology",
"subjects": [
"Anatomy",
"Life Science"
]
},
"FAIRsharing.mtvxae": {
"abbreviation": "FHHO",
"description": "The FHHO facilitates representing the family health histories of persons related by biological and/or social family relationships (e.g. step, adoptive) who share genetic, behavioral, and/or environmental risk factors for disease. SWRL rules are included to compute 3 generations of biological relationships based on parentage and family history findings based on personal health findings.",
"homepage": "http://bioportal.bioontology.org/ontologies/1126",
"name": "Family Health History Ontology",
"subjects": [
"Medicine",
"Health Science",
"Human Genetics",
"Biomedical Science"
]
},
"FAIRsharing.mvp707": {
"abbreviation": "GBM",
"description": "Record does not exist anymore: Glioblastoma. The record with identifier content 10.25504/FAIRsharing.mvp707 was invalid.",
"homepage": "http://bioportal.bioontology.org/ontologies/GBM",
"name": "Glioblastoma"
},
"FAIRsharing.mx4fvx": {
"abbreviation": "invertebrata",
"description": "This resource is no longer available because its underlying source material is not suitable for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/1658",
"name": "Hewan Invertebrata",
"subjects": [
"Life Science"
]
},
"FAIRsharing.mxx5rp": {
"abbreviation": "AAO",
"contact": {
"email": "david.c.blackburn@gmail.com",
"name": "David Blackburn",
"orcid": "0000-0002-1810-9886"
},
"description": "A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO has been integrated into Uberon.",
"homepage": "http://bioportal.bioontology.org/ontologies/AAO",
"name": "Amphibian gross Anatomy Ontology",
"publications": [
{
"doi": "10.1186/2041-1480-5-21",
"pubmed": "25009735",
"title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon",
"year": 2014
},
{
"doi": "10.1142/9789812772435_0035",
"title": "AN ANATOMICAL ONTOLOGY FOR AMPHIBIANS",
"year": 2006
}
],
"subjects": [
"Anatomy"
]
},
"FAIRsharing.mye76w": {
"abbreviation": "BAO",
"description": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.",
"domains": [
"Molecular entity",
"Chemical entity",
"Reagent",
"Cell",
"Biological process",
"Assay",
"Protein",
"Target"
],
"homepage": "http://bioassayontology.org",
"license": "CC-BY-4.0",
"name": "BioAssay Ontology",
"publications": [
{
"doi": "10.1186/2041-1480-5-s1-s5",
"pubmed": "25093074",
"title": "Evolving BioAssay Ontology (BAO): modularization, integration and applications",
"year": 2014
},
{
"doi": "10:1371/journal.pone.0049198",
"pubmed": "10",
"title": "Digitoxin metabolism by rat liver microsomes",
"year": 1975
},
{
"doi": "10.1371/journal.pone.0049198",
"pubmed": "23155465",
"title": "Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO)",
"year": 2012
},
{
"doi": "10.1186/1471-2105-12-257",
"pubmed": "21702939",
"title": "BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results",
"year": 2011
}
],
"repository": "https://github.com/BioAssayOntology/BAO/wiki",
"subjects": [
"Biochemistry",
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.n511c4": {
"abbreviation": "LEGALAPATEST2",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/LEGALAPATEST2",
"name": "apalegal",
"subjects": [
"Humanities",
"Psychology"
]
},
"FAIRsharing.n66krd": {
"abbreviation": "NEMO",
"description": "Neural ElectroMagnetic Ontology (NEMO) describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters). FAIRsharing curators have been unable to contact the project developers, and as such this record has been marked as Uncertain. Please contact us if you have any information on this resource.",
"domains": [
"Neuron",
"Imaging",
"Cognition",
"Electroencephalography",
"Brain"
],
"homepage": "http://aimlab.cs.uoregon.edu/NEMO/web/index.html",
"name": "Neural ElectroMagnetic Ontologies",
"publications": [
{
"doi": "10.4056/sigs.2025347",
"pubmed": "22180824",
"title": "Minimal Information for Neural Electromagnetic Ontologies (MINEMO): A standards-compliant method for analysis and integration of event-related potentials (ERP) data",
"year": 2011
},
{
"doi": "10.1038/npre.2009.3458.1",
"title": "Development of Neural Electromagnetic Ontologies (NEMO): Ontology-based Tools for Representation and Integration of Event-related Brain Potentials",
"year": 2009
}
],
"subjects": [
"Neurobiology",
"Cognitive Neuroscience",
"Life Science"
],
"user_defined_tags": [
"Interoperability"
]
},
"FAIRsharing.n7vyyc": {
"abbreviation": "ADALAB",
"description": "Record does not exist anymore: AdaLab ontology. The record with identifier content 10.25504/FAIRsharing.n7vyyc was invalid.",
"homepage": "http://bioportal.bioontology.org/ontologies/ADALAB",
"name": "AdaLab ontology"
},
"FAIRsharing.nK2JoH": {
"abbreviation": "French Communes",
"description": "This thesaurus lists all the French communes including metropolitan France and overseas regions and departments. The current communes (including those created in 2018) are attached to their department; the delegated, merged or associated communes are attached to the corresponding current commune. The different entries are mapped to l'INSEE, GeoNames, PACTOLS, Rameau, Wikidata and Wikipedia. Available in English and French.",
"homepage": "https://www.loterre.fr/skosmos/D63/en/",
"license": "CC-BY-4.0",
"name": "French Communes",
"subjects": [
"Geography"
],
"user_defined_tags": [
"Communes",
"France"
]
},
"FAIRsharing.na5xp": {
"abbreviation": "STATO",
"contact": {
"email": "philippe.rocca-serra@oerc.ox.ac.uk",
"name": "Philippe Rocca-Serra",
"orcid": "0000-0001-9853-5668"
},
"description": "STATO is a general-purpose STATistics Ontology. Its aim is to provide coverage for processes such as statistical tests, their conditions of applications, and information needed or resulting from statistical methods, such as probability distributions, variable, spread and variation metrics. STATO also covers aspects of experimental design and description of plots and graphical representations commonly used to provide visual cues of data distribution or layout and to assist review of the results.",
"domains": [
"Experimental measurement",
"Graph",
"Protocol",
"Study design"
],
"homepage": "http://stato-ontology.org/",
"license": "CC-BY-3.0",
"name": "Statistics Ontology",
"repository": "https://github.com/ISA-tools/stato",
"subjects": [
"Statistics",
"Data Visualization"
]
},
"FAIRsharing.nbfwwv": {
"abbreviation": "PAV",
"contact": {
"email": "stian@soiland-reyes.com",
"name": "Stian Soiland-Reyes",
"orcid": "0000-0001-9842-9718"
},
"description": "PAV is a lightweight ontology for tracking Provenance, Authoring and Versioning. PAV specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources. This ontology describes the defined PAV properties and their usage. Note that PAV does not define any explicit classes or domain/ranges, as every property is meant to be used directly on the described online resource.",
"domains": [
"Citation",
"Resource metadata"
],
"homepage": "https://github.com/pav-ontology/pav/",
"license": "Apache 2.0 License",
"name": "Provenance, Authoring and Versioning Ontology",
"publications": [
{
"doi": "10.1186/2041-1480-4-37",
"pubmed": "24267948",
"title": "PAV ontology: provenance, authoring and versioning",
"year": 2013
}
],
"repository": "http://pav-ontology.github.io/pav/",
"subjects": [
"Data Management",
"Subject Agnostic"
]
},
"FAIRsharing.nc71b5": {
"abbreviation": "OCDM",
"description": "The Ontology of Craniofacial Development and Malformation (OCDM) is a mechanism for representing knowledge about craniofacial development and malformation, and for using that knowledge to facilitate integrating craniofacial data obtained via multiple techniques from multiple labs and at multiple levels of granularity. The OCDM is a project of the NIDCR-sponsored FaceBase Consortium, whose goal is to promote and enable research into the genetic and epigenetic causes of specific craniofacial abnormalities through the provision of publicly accessible, integrated craniofacial data. The OCDM is based on the Foundational Model of Anatomy (FMA) and includes modules to represent adult and developmental craniofacial anatomy in human, mouse and zebrafish, mappings between homologous structures in the different species, and associated malformations.",
"domains": [
"Abnormal craniofacial development",
"Craniofacial phenotype"
],
"homepage": "https://www.facebase.org/ocdm/",
"name": "Ontology of Craniofacial Development and Malformation",
"subjects": [
"Anatomy",
"Medicine",
"Epigenetics",
"Genetics",
"Developmental Biology"
]
},
"FAIRsharing.nesfnr": {
"abbreviation": "NTDO",
"description": "The Neglected Tropical Disease Ontology (NTDO) models Neglected Tropical Diseases (NTD), a specific set of diseases which persist among marginalized populations of the developing world. The NTDO focuses on vector-borne disease control as the transmission path, as this drives prevention strategies and decision support. NTDO includes information about the disease, its causative agents (when available), dispositions, and the geographic location the disease happens.",
"domains": [
"Tropical",
"Disease"
],
"homepage": "http://www.cin.ufpe.br/~ntdo",
"name": "Neglected Tropical Disease Ontology",
"publications": [
{
"doi": "10.1093/bioinformatics/btr226",
"pubmed": "21685092",
"title": "Ontology patterns for tabular representations of biomedical knowledge on neglected tropical diseases",
"year": 2011
},
{
"doi": "10.1186/2041-1480-3-s2-s7",
"pubmed": "23046681",
"title": "Towards an ontological representation of morbidity and mortality in Description Logics",
"year": 2012
}
],
"subjects": [
"Infectious Disease Medicine",
"Tropical Medicine"
],
"user_defined_tags": [
"tropical disease"
]
},
"FAIRsharing.newa3z": {
"abbreviation": "BSPO",
"contact": {
"email": "cjmungall@lbl.gov",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"description": "This ontology represents spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies.",
"homepage": "http://bioportal.bioontology.org/ontologies/BSPO",
"license": "CC-BY-3.0",
"name": "Biological SPatial Ontology",
"publications": [
{
"doi": "10.1186/2041-1480-5-34",
"pubmed": "25140222",
"title": "Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology",
"year": 2014
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"FAIRsharing.nft558": {
"abbreviation": "PDO_CAS",
"description": "Plant Diversity Ontology (PDO) is the outcome of the construction tasks of domain ontology of science in the project of Scientific & Technological Knowledge Organization Systems (STKOS). The structure of PDO centers on species, including micro level of molecular, cell and tissue, medium level of plant organs, species and population, and macro level of ecosystem. The classes of PDO also capture the habitat, environmental conditions and expand the general characteristics of plants, completing the instances richness for plant species, geographical, classification and morphology. Furthermore, PDO builds the relationships among species, region, morphology, plant organs, developmental stage, revealing the list of species in an area, the morphology and life form of plants, and development process of species. In sum, PDO shows a growth process or development stage of a species and its structure characteristics in particular space and time scale, realizing the description of species diversity, ecosystem diversity and genetic diversity. At present, PDO has been applied to the platform of Go to Selected Open Access Journals (GoOA) developed by National Science Library of Chinese Academy of Sciences, supporting concept retrieval and concept extension for GoOA.",
"homepage": "http://gooa.las.ac.cn/external/index.jsp",
"name": "Plant Diversity Ontology",
"subjects": [
"Biodiversity"
]
},
"FAIRsharing.ngn3a6": {
"abbreviation": "GCO",
"description": "The Genome Component Ontology is intended to define the abstract division of the total genetic information of an organism by its physical separation into different components, thereby providing a high level reference point to which more specific descriptions of the characteristics of these components can be linked.",
"domains": [
"Genome"
],
"homepage": "http://bioportal.bioontology.org/ontologies/GCO",
"name": "Genome Component Ontology",
"subjects": [
"Genomics"
]
},
"FAIRsharing.ngv2xx": {
"abbreviation": "Apollo-SV",
"contact": {
"email": "hoganwr@gmail.com",
"name": "William Hogan",
"orcid": "0000-0002-9881-1017"
},
"description": "An ontology of infectious disease epidemiology and ecology (a.k.a. population biology).",
"domains": [
"Pathogen",
"Infection"
],
"homepage": "http://purl.obolibrary.org/obo/apollo_sv.owl",
"license": "CC-BY-3.0",
"name": "Apollo-SV",
"publications": [
{
"pubmed": "24551417",
"title": "Apollo: giving application developers a single point of access to public health models using structured vocabularies and Web services",
"year": 2014
},
{
"doi": "10.1186/s13326-016-0092-y",
"pubmed": "27538448",
"title": "The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation",
"year": 2016
}
],
"repository": "https://github.com/ApolloDev/apollo-sv",
"subjects": [
"Ecology",
"Biomedical Science",
"Epidemiology",
"Population Genetics"
]
},
"FAIRsharing.nj16g": {
"abbreviation": "ICD-10",
"description": "The ICD is the international standard diagnostic classification for all general epidemiological, many health management purposes and clinical use. ICD-10 is the 10th revision of the International Statistical Classification of Diseases and Related Health Problems (ICD), a medical classification list by the World Health Organization (WHO). It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases.",
"domains": [
"Disease",
"Diagnosis"
],
"homepage": "http://www.who.int/classifications/icd/en/",
"license": "http://www.who.int/about/licensing/copyright_form/en",
"name": "International Classification of Diseases Version 10",
"subjects": [
"Health Science",
"Global Health",
"Biomedical Science",
"Epidemiology"
]
},
"FAIRsharing.np2wfz": {
"abbreviation": "ZECO",
"description": "This ontology is designed to represent the experimental conditions applied to zebrafish and has been developed to facilitate experiment condition annotation at ZFIN.",
"domains": [
"Expression data",
"Bibliography",
"Model organism",
"Disease process modeling",
"Mutation",
"Phenotype",
"Gene",
"Allele",
"Genome"
],
"homepage": "https://github.com/ybradford/zebrafish-experimental-conditions-ontology",
"name": "Zebrafish Experimental Conditions Ontology",
"subjects": [
"Genomics",
"Animal Physiology",
"Genetics",
"Developmental Biology"
]
},
"FAIRsharing.nttge3": {
"abbreviation": "SOPHARM",
"contact": {
"email": "Adrien.Coulet@loria.fr",
"name": "Adrien Coulet",
"orcid": "0000-0002-1466-062X"
},
"description": "SO-Pharm is a formal ontology that represent domain knowledge in pharmacogenomics. To achieve this goal, SO-Pharm articulates ontologies from sub domains of phamacogenomics (i.e. genotype, phenotype, drug, trial representations). SO-Pharm enables to support knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics.",
"domains": [
"Drug",
"Chemical entity",
"Phenotype",
"Genotype"
],
"homepage": "http://bioportal.bioontology.org/ontologies/SOPHARM",
"name": "Suggested Ontology for PHARMacogenomics",
"publications": [
{
"doi": "10.1007/978-1-4419-7046-6_36",
"pubmed": "21431576",
"title": "Ontology-based knowledge discovery in pharmacogenomics",
"year": 2011
}
],
"subjects": [
"Life Science",
"Pharmacogenomics",
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.nvytcd": {
"abbreviation": "INVERSEROLES",
"description": "This resource is no longer available because its underlying source material is not suitable for FAIRsharing: ISO-15926-2_2003_inverseRoles. The record with identifier content 10.25504/FAIRsharing.nvytcd was invalid.",
"domains": [
"Data retrieval"
],
"homepage": "http://bioportal.bioontology.org/ontologies/INVERSEROLES",
"name": "ISO-15926-2_2003_inverseRoles",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.nwgynk": {
"abbreviation": "ERO",
"contact": {
"email": "carlotorniai@gmail.com",
"name": "Carlo Torniai",
"orcid": "0000-0002-3734-1859"
},
"description": "A unique feature of the eagle-i software is that the data collection and search tools are completely driven by ontologies. These ontologies are a set of modules that are written in the OWL language and edited and managed using ProtΓ©gΓ©. Beginning in 2009, the eagle-i Research Resource Ontology (ERO) was developed alongside the eagle-i applications to model various biomedical research resources such as instruments, Core Facilities, protocols, reagents, animal models and biospecimens. It has now been integrated into the VIVO-ISF Ontology, which leverages and expands upon both the eagle-i and VIVO ontologies to create a semantic framework that describes not only scientific resources but research activities and clinical activities.",
"domains": [
"Reagent",
"Biological sample",
"Protocol",
"Study design"
],
"homepage": "https://open.catalyst.harvard.edu/wiki/display/eaglei/Ontology",
"name": "eagle-i Research Resource Ontology",
"publications": [
{
"doi": "10.1109/jcdl.2017.7991571",
"pubmed": "29599662",
"title": "Automating data citation: the eagle-i experience",
"year": 2018
},
{
"doi": "10.1093/database/bar067",
"pubmed": "22434835",
"title": "Research resources: curating the new eagle-i discovery system",
"year": 2012
}
],
"subjects": [
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.ny3z9j": {
"abbreviation": "FBbi",
"description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.",
"domains": [
"Imaging",
"Image",
"Assay"
],
"homepage": "http://flybase.org/vocabularies",
"name": "Biological Imaging methods Ontology",
"subjects": [
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.ny6hcb": {
"abbreviation": "SitBAC",
"contact": {
"email": "morpeleg@is.haifa.ac.il",
"name": "Mor Peleg",
"orcid": "0000-0002-5612-768X"
},
"description": "Context-based healthcare access-control policies.",
"domains": [
"Data retrieval",
"Electronic health record"
],
"homepage": "http://bioportal.bioontology.org/ontologies/SITBAC?p=summary",
"name": "Situation-Based Access Control",
"publications": [
{
"doi": "10.1016/j.jbi.2008.03.014",
"pubmed": "18511349",
"title": "Situation-Based Access Control: privacy management via modeling of patient data access scenarios",
"year": 2008
}
],
"subjects": [
"Medicine",
"Biomedical Science"
]
},
"FAIRsharing.ny9vnm": {
"abbreviation": "FLOPO",
"contact": {
"email": "robert.hoehndorf@kaust.edu.sa",
"name": "Robert Hoehndorf",
"orcid": "0000-0001-8149-5890"
},
"description": "The Flora Phenotype Ontology is a domain ontology for the description of plant characters. FLOPO contains more than 25000 phenotype and traits classes, the creation of FLOPO is data-driven: For each trait/phenotype class exists a taxon annotation in the underlying Floras.",
"domains": [
"Phenotype",
"Life cycle stage"
],
"homepage": "https://github.com/flora-phenotype-ontology/flopoontology",
"license": "CC0-1.0",
"name": "Flora Phenotype Ontology",
"publications": [
{
"doi": "10.3897/bdj.2.e1125",
"pubmed": "25057255",
"title": "Enriched biodiversity data as a resource and service",
"year": 2014
},
{
"doi": "10.1186/s13326-016-0107-8",
"pubmed": "27842607",
"title": "The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants",
"year": 2016
}
],
"repository": "https://github.com/flora-phenotype-ontology/flopoontology",
"subjects": [
"Botany",
"Biodiversity",
"Plant Anatomy"
]
},
"FAIRsharing.nygmp7": {
"abbreviation": "TRANS",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/TRANS",
"name": "Nurse Transitional",
"subjects": [
"Health Science"
]
},
"FAIRsharing.oaxyMK": {
"abbreviation": "PICO",
"description": "The PICO ontology provides a model for describing evidence in a consistent way focusing on complex populations, detailed interventions and their comparisons as well as the outcomes considered. The PICO ontology was originally designed to model the questions asked and answered in Cochrane's systematic reviews. The PICO model can be used to describe healthcare evidence as well as used in other evidence-based domains. It aims to provide a model for describing evidence in a consistent way.",
"domains": [
"Evidence"
],
"homepage": "https://data.cochrane.org/ontologies/pico/index-en.html",
"license": "https://creativecommons.org/licenses/by-nc-nd/4.0",
"name": "Cochrane Patient/Population/Problem Intervention Comparison Outcome Ontology",
"subjects": [
"Demographics",
"Clinical Studies",
"Health Science",
"Medical Informatics"
]
},
"FAIRsharing.ochiOn": {
"abbreviation": "IVOA UCD",
"description": "The IVOA Standard for Unified Content Descriptors document describes the current understanding of the IVOA controlled vocabulary for describing astronomical data quantities, called Unified Content Descriptors (UCDs). The present document defines a new standard (named UCD1+) improving the first generation of UCDs (UCD1). The basic idea is to adopt a new syntax and vocabulary requiring little effort for people to adapt software already using UCD1. This document also addresses the questions of maintenance and evolution of the UCD1+. Examples of use cases within the Virtual Observatory and tools for using UCD1+ are also described.",
"homepage": "http://www.ivoa.net/documents/latest/UCD.html",
"name": "IVOA Standard for Unified Content Descriptors",
"subjects": [
"Astrophysics and Astronomy"
]
},
"FAIRsharing.p1dodf": {
"abbreviation": "GACS",
"description": "The Global Agricultural Concept Scheme (GACS) is a SKOS concept scheme with concepts and related terms used in the field of agriculture, broadly defined. GACS is developed by the Food and Agriculture Organization of the United Nations (FAO), the Centre for Agriculture and Biosciences International (CABI), and the USDA National Agricultural Library (NAL), GACS was formed at the intersection of most-frequently-used concepts from their three respective thesauri -- the AGROVOC Concept Scheme, CAB Thesaurus, and the NAL Thesaurus, for which GACS provides a mapping hub. GACS is seen as an important step towards linking and integrating agricultural data of all types to address the long-term challenge of global food security.",
"homepage": "https://agrisemantics.github.io/gacs-qip/",
"name": "Global Agricultural Concept Scheme",
"subjects": [
"Food Security",
"Agricultural Engineering",
"Agriculture"
]
},
"FAIRsharing.p1nva": {
"abbreviation": "AURA",
"description": "KB-Bio-101 contains knowledge about processes and mechanisms, and was created from an introductory textbook in biology.",
"domains": [
"Chromosome"
],
"homepage": "https://bioportal.bioontology.org/ontologies/AURA",
"license": "CC BY-NC 3.0",
"name": "KB_Bio_101",
"subjects": [
"Biology"
]
},
"FAIRsharing.p1sejz": {
"abbreviation": "TAXRANK",
"contact": {
"email": "peteremidford@yahoo.com",
"name": "Peter E. Midford",
"orcid": "0000-0001-6512-3296"
},
"description": "This is a vocabulary of taxonomic ranks intended to replace the sets of rank terms found in the Teleost Taxonomy Ontology, the OBO translation of the NCBI taxonomy and similar OBO taxonomy ontologies. It provides terms for taxonomic ranks drawn from both the NCBI taxonomy database and from a rank vocabulary developed for the TDWG biodiversity information standards group. Each term contains cross reference links to the resources that use the terms. Consistent with its intended use as a vocabulary, there is no relation specifying an ordering of the rank terms. Likewise, all terms are directly descended from the term 'taxonomic rank' (TAXRANK:0000000).",
"domains": [
"Taxonomic classification"
],
"homepage": "https://wiki.phenoscape.org/wiki/Ontologies#Taxonomic_Rank_Vocabulary_.28TAXRANK.29",
"license": "CC0-1.0",
"name": "Taxonomic Rank Vocabulary",
"repository": "https://github.com/phenoscape/taxrank",
"subjects": [
"Taxonomy",
"Life Science"
]
},
"FAIRsharing.p1ss22": {
"abbreviation": "DCM",
"description": "DICOM Controlled Terminology (PS3.16 2017c Annex D)",
"domains": [
"Imaging"
],
"homepage": "http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html",
"name": "DICOM Controlled Terminology",
"subjects": [
"Life Science"
]
},
"FAIRsharing.p4zyjr": {
"abbreviation": "SMASH",
"description": "The goal of the Semantic Mining of Activity, Social, and Health data (SMASH) Ontology is to develop a formal and expressive Semantic Web ontology for the concepts and relationships used in describing the semantic features of healthcare data and social networks. The SMASH ontology focuses on defining concepts and relationships for discovering factors associated with sustained weight loss, especially those related to continued intervention with frequent social contacts. The smash ontology covers the three domains: biomarker measures, physical activities, and social activities. ",
"domains": [
"Biomarker"
],
"homepage": "http://aimlab.cs.uoregon.edu/smash/ontologies.html",
"name": "Semantic Mining of Activity, Social, and Health data Ontology",
"subjects": [
"Primary Health Care",
"Social and Behavioural Science"
]
},
"FAIRsharing.p51kqa": {
"abbreviation": "VSAO",
"description": "VSAO is an anatomy ontology covering the vertebrate skeletal system. VSAO integrates terms for skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. Note that VSAO is a deprecated ontology and has been superceded by Uberon.",
"domains": [
"Cell",
"Molecular interaction",
"Organ",
"Tissue",
"Bone"
],
"homepage": "https://wiki.phenoscape.org/wiki/Ontologies#Vertebrate_Skeletal_Anatomy_Ontology_.28VSAO.29",
"name": "Vertebrate Skeletal Anatomy Ontology",
"publications": [
{
"doi": "10.1371/journal.pone.0051070",
"pubmed": "23251424",
"title": "A unified anatomy ontology of the vertebrate skeletal system",
"year": 2012
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"FAIRsharing.p52pzj": {
"abbreviation": "FBdv",
"contact": {
"email": "cp390@cam.ac.uk",
"name": "Clare Pilgrim",
"orcid": "0000-0002-1373-1705"
},
"description": "An ontology of the developmental stages of Drosophila melanogaster. It provides a controlled vocabulary for use in annotation and classification of data related to Drosophila, such as gene expression, phenotypes and images.",
"domains": [
"Life cycle",
"Life cycle stage"
],
"homepage": "http://flybase.org/vocabularies",
"license": "CC-BY-4.0",
"name": "Drosophila developmental ontology",
"repository": "https://github.com/FlyBase/drosophila-anatomy-developmental-ontology",
"subjects": [
"Developmental Biology",
"Life Science"
]
},
"FAIRsharing.p58bm4": {
"abbreviation": "CEPH",
"description": "An anatomical and developmental ontology for cephalopods",
"domains": [
"Life cycle"
],
"homepage": "https://github.com/obophenotype/cephalopod-ontology",
"name": "Cephalopod Ontology",
"subjects": [
"Fisheries Science",
"Anatomy",
"Zoology"
]
},
"FAIRsharing.p5df9c": {
"abbreviation": "FAST",
"description": "FAST (Faceted Application of Subject Terminology) is a nine-facet vocabulary derived from the Library of Congress Subject Headings (LCSH), and is one of the library domain's most widely used subject terminology schemas. The broad purpose of adapting the LCSH with a simplified syntax to create FAST is to retain the rich vocabulary of LCSH while making the schema easier to understand, control, apply, and use. The schema maintains upward compatibility with LCSH, and any valid set of LC subject headings can be converted to FAST headings.",
"homepage": "https://www.oclc.org/research/themes/data-science/fast.html",
"license": "http://opendatacommons.org/licenses/by/1.0",
"name": "Faceted Application of Subject Terminology",
"subjects": [
"Subject Agnostic"
],
"user_defined_tags": [
"Metadata standardization"
]
},
"FAIRsharing.p63yyx": {
"abbreviation": "RBMS",
"description": "These thesauri provide standardized vocabulary for retrieving special collections materials by form, genre, or by various physical characteristics that are typically of interest to researchers and special collections librarians, and for relating materials to individuals or corporate bodies.",
"domains": [
"Resource collection"
],
"homepage": "http://rbms.info/vocabularies/",
"name": "RBMS Controlled Vocabularies",
"subjects": [
"Literary Studies",
"Anthropology"
]
},
"FAIRsharing.p6412v": {
"abbreviation": "Epilepsy Ontology",
"contact": {
"email": "dourado@dei.uc.pt",
"name": "Antonio Dourado",
"orcid": "0000-0002-5445-6893"
},
"description": "Ontology about the epilepsy domain and epileptic seizures. Based on the diagnosis proposed by the International League Against Epilepsy (ILAE).",
"domains": [
"Epilepsy",
"Disease"
],
"homepage": "http://www.epilepsiae.eu/",
"name": "Epilepsy Ontology",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.p9xm4v": {
"abbreviation": "ABA",
"description": "ABA Adult Mouse Brain is a standardised collection of the expression patterns of thousands of adult brain genes. This resource can be used for a vast array of research on brain organisation and function. There are lighter versions of this ontology that are customised for the NeuroMorpho.Org brain regions.",
"domains": [
"Gene expression",
"Brain",
"Brain imaging"
],
"homepage": "http://mouse.brain-map.org",
"name": "ABA Adult Mouse Brain",
"publications": [
{
"doi": "10.1038/nature05453",
"pubmed": "17151600",
"title": "Genome-wide atlas of gene expression in the adult mouse brain",
"year": 2006
}
],
"subjects": [
"Neuroscience"
]
},
"FAIRsharing.pa6njw": {
"abbreviation": "SHR",
"description": "The goal of the SHR project is to develop an ontology for the description of student health records. Student health records are created for entering college students in order to provide better health services will be formed. This file contains various sections such as history of disease, family history of disease and public examinations.",
"domains": [
"Electronic health record"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1665",
"name": "Student Health Record",
"subjects": [
"Medicine",
"Health Science",
"Biomedical Science"
]
},
"FAIRsharing.pbbnwa": {
"abbreviation": "ORDO",
"contact": {
"email": "ordo.orphanet@inserm.fr",
"name": "Ana Rath",
"orcid": "0000-0003-4308-6337"
},
"description": "Orphanet Rare Diseases Ontology (ORDO) provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.",
"domains": [
"Rare disease",
"Phenotype",
"Disease",
"Diagnosis",
"Gene"
],
"homepage": "http://www.orphadata.org/cgi-bin/inc/ordo_orphanet.inc.php",
"license": "CC-BY-4.0",
"name": "Orphanet Rare Diseases Ontology",
"publications": [
{
"pubmed": "22874158",
"title": "Rare diseases knowledge management: the contribution of proximity measurements in OntoOrpha and OMIM",
"year": 2012
}
],
"subjects": [
"Health Science",
"Biomedical Science"
]
},
"FAIRsharing.pdwqcr": {
"abbreviation": "MA",
"description": "The Anatomy Ontology for the Adult Mouse is organized spatially and functionally, using \"is a\" and \"part of\" relationships to describe the anatomy of the postnatal mouse. Anatomical terms are arranged as a hierarchy from body region or organ system to tissue substructure. Modeling the anatomy hierarchically makes it possible to record expression results from assays with differing spatial resolution in a consistent and integrated manner. Organizing the anatomical terms as a Directed Acyclic Graph (DAG), i.e., in which a term can have more than one parent, allows presentation of the anatomy from multiple perspectives. In various locations, this ontology is also referred to as: 'Mouse Adult Gross Anatomy ontology', 'Adult Mouse Anatomy', 'Mouse Anatomy' or 'Mouse anatomical entity'. ",
"domains": [
"Organ",
"Tissue"
],
"homepage": "http://www.informatics.jax.org/vocab/gxd/ma_ontology/",
"license": "CC-BY-4.0",
"name": "Mouse Adult Gross Anatomy Ontology",
"publications": [
{
"doi": "10.1186/gb-2005-6-3-r29",
"pubmed": "15774030",
"title": "The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data",
"year": 2005
}
],
"repository": "https://github.com/obophenotype/mouse-anatomy-ontology",
"subjects": [
"Anatomy"
]
},
"FAIRsharing.peabnh": {
"abbreviation": "BHO",
"contact": {
"email": "smollah@rockefeller.edu",
"name": "Shamim Mollah",
"orcid": "0000-0001-9178-8339"
},
"description": "An application ontology devoted to the standardized recording of phenotypic data related to hemorrhagic disorders.",
"domains": [
"Patient care",
"Phenotype",
"Blood"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1116",
"name": "Bleeding History Phenotype",
"subjects": [
"Medicine",
"Biomedical Science"
]
},
"FAIRsharing.pf2qyq": {
"abbreviation": "DDI",
"contact": {
"email": "soldatova.larisa@gmail.com",
"name": "Larisa Soldatova",
"orcid": "0000-0001-6489-3029"
},
"description": "The goal of DDI project is to develop an ontology for the description of drug discovery investigations. The Pharmaceutical industry is an information based industry. The aim of DDI is to add value to the information generated in the drug pipeline by making the information easier to reuse, integrate, curate, retrieve, and reason with. DDI aims to follow to the Open Biomedical Ontologies Foundry (OBO) principles, to use relations laid down in the OBO Relation Ontology, and to be compliant with the Ontology for biomedical investigations (OBI).",
"homepage": "https://code.google.com/p/ddi-ontology/",
"name": "Ontology for Drug Discovery Investigations",
"subjects": [
"Drug Discovery",
"Biomedical Science"
]
},
"FAIRsharing.phk7dd": {
"abbreviation": "WB-BT",
"contact": {
"email": "raymond@caltech.edu",
"name": "Raymond Lee",
"orcid": "0000-0002-8151-7479"
},
"description": "A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.",
"domains": [
"Cell"
],
"homepage": "https://www.wormbase.org/tools/ontology_browser",
"name": "C. elegans gross anatomy",
"publications": [
{
"doi": "10.1002/cfg.248",
"pubmed": "18629098",
"title": "Building a cell and anatomy ontology of Caenorhabditis elegans",
"year": 2008
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"FAIRsharing.pk6cwg": {
"description": "The Epoch Clinical Trial Ontology is a standard, originally curated from data in BioPortal. It encodes knowledge about the clinical trial domain that is relevant to trial management applications. It has been created to support semantic interoperation of clinical trial software applications. Epoch is a suite of clinical trial ontologies that formally represents protocol entities relevant to the clinical trials management applications they support. However, information on this standard appears to no longer be available. If you work on this standard, or know of it's current status, please get in touch with our team.",
"domains": [
"Chemical entity",
"Treatment"
],
"homepage": "http://bioportal.bioontology.org/ontologies/CTONT",
"name": "Epoch Clinical Trial Ontology",
"publications": [
{
"pubmed": "18693919",
"title": "An ontology-based architecture for integration of clinical trials management applications",
"year": 2008
}
],
"subjects": [
"Life Science",
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.pkt5s4": {
"abbreviation": "SBRO",
"description": "\"Smoking Behavior Risk Ontology\" is a standard, specialising in the fields described under \"scope and data types\", below. Until this entry is claimed, more information on this project can be found at http://bioportal.bioontology.org/ontologies/1249. This text was generated automatically. If you work on the project responsible for \"Smoking Behavior Risk Ontology\" then please consider helping us by claiming this record and updating it appropriately.",
"domains": [
"Behavior",
"Phenotype",
"Exposure"
],
"homepage": "http://bioportal.bioontology.org/ontologies/SBRO",
"name": "Smoking Behavior Risk Ontology",
"publications": [
{
"doi": "10.1097/fpc.0b013e32832e2ced",
"pubmed": "19525886",
"title": "A systems biology network model for genetic association studies of nicotine addiction and treatment",
"year": 2009
}
],
"subjects": [
"Medicine",
"Health Science",
"Pharmacogenomics",
"Biomedical Science"
]
},
"FAIRsharing.pktgc6": {
"abbreviation": "NBO",
"description": "The Neurobehavior Ontology (NBO) consists of two main components, an ontology of behavioral processes and an ontology of behavioral phenotypes. The behavioral process branch of NBO contains a classification of behavior processes complementing and extending GOβs process ontology. The behavior phenotype branch of NBO consists of a classification of both normal and abnormal behavioral characteristics of organisms .",
"domains": [
"Behavior",
"Phenotype"
],
"homepage": "https://github.com/obo-behavior/behavior-ontology/",
"license": "CC-BY-3.0",
"name": "Neuro Behavior Ontology",
"publications": [
{
"doi": "10.1016/b978-0-12-388408-4.00004-6",
"pubmed": "23195121",
"title": "The neurobehavior ontology: an ontology for annotation and integration of behavior and behavioral phenotypes",
"year": 2012
}
],
"repository": "https://github.com/obo-behavior/behavior-ontology/issues",
"subjects": [
"Social and Behavioural Science",
"Systemic Neuroscience"
]
},
"FAIRsharing.ple9HR": {
"description": "The Cochrane Core Vocabulary ontology describes the entities and concepts that exist in the domain of evidence-based healthcare. It is used for the construction of the Cochrane Linked Data Vocabulary containing some 400k terms including Interventions (Drugs, Procedures etc), Populations (Age, Sex, Condition), and Clinical outcomes. *Please note our web pages are currently under review*",
"domains": [
"Intervention design"
],
"homepage": "https://data.cochrane.org/ontologies/core/index-en.html",
"license": "https://creativecommons.org/licenses/by-nc-nd/4.0",
"name": "Cochrane Core Vocabulary Ontology",
"subjects": [
"Demographics",
"Clinical Studies",
"Health Science",
"Medical Informatics"
]
},
"FAIRsharing.pmvppd": {
"abbreviation": "MCBCC",
"description": "List of cell lines derived from breast tissue, both normal and pathological. The ontology in built in OWL with cross relation to classes- genetic variation, pathological condition, genes, chemicals and drugs.",
"domains": [
"Cell line",
"Cell",
"Genetic polymorphism",
"Drug interaction",
"Disease",
"Tissue",
"Mammary gland",
"Chemical-gene association"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1438",
"name": "Breast tissue cell lines",
"subjects": [
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.pmygc7": {
"description": "A Value Set in CEDAR is like a very simple ontology; it consists only of a set of terms that have identifiers and labels. Value Sets tend to be smaller than ontologies as well, and organized around a single topic. This record described the initial set of value sets uploaded to BioPortal.",
"domains": [
"Resource metadata",
"Experimental measurement",
"Protocol",
"Study design",
"Machine learning",
"FAIR",
"Biocuration"
],
"homepage": "https://metadatacenter.github.io/cedar-manual/sections/c3/2_defining_your_answers_with%20term_lists/#searching-for-ontologies-and-value-sets",
"name": "CEDAR Value Sets",
"subjects": [
"Data Integration",
"Data Governance"
]
},
"FAIRsharing.pn1sen": {
"abbreviation": "PIERO",
"description": "PIERO stands for \"Enzyme Reaction Ontology for annotating Partial Information of chemical transformation\", which allows the extraction of partial reaction characteristics (or transformations) of the enzymatic reactions. ",
"homepage": "http://reactionontology.genome.jp/",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaFlFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--80c044d69ca4031cb9b8d1b0cacb1999069b3476/piero-logo.png?disposition=inline",
"name": "Enzyme Reaction Ontology for annotating Partial Information of chemical transformation",
"publications": [
{
"doi": "10.1142/s0219720014420013",
"title": "PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB enzyme list",
"year": 2014
}
],
"subjects": [
"Biochemistry",
"Enzymology"
]
},
"FAIRsharing.ps501f": {
"contact": {
"email": "noy@stanford.edu",
"name": "Natasha Noy",
"orcid": "0000-0002-7437-0624"
},
"description": "This ontology represents the structure that BioPortal uses to represent all of its metadata (ontology details, mappings, notes, reviews, views).",
"homepage": "http://www.bioontology.org/wiki/index.php/BioPortal_Metadata",
"name": "BioPortal Metadata",
"subjects": [
"Life Science",
"Biomedical Science",
"Biology"
]
},
"FAIRsharing.pxj1sx": {
"abbreviation": "ONTOKBCF",
"description": "OntoKBCF is an ontological knowledge base model for cystic fibrosis. There are molecular genetic information (i.e. gene mutations) and health information included in OntoKBCF. The purposes of OntoKBCF include management of molecular genetic information and health information and embedding OntoKBCF into EHR settings.",
"homepage": "http://bioportal.bioontology.org/ontologies/ONTOKBCF",
"name": "Ontological Knowledge Base Model for Cystic Fibrosis",
"subjects": [
"Molecular Genetics"
]
},
"FAIRsharing.pyhdJS": {
"abbreviation": "BTL2",
"description": "BioTopLite 2 (BTL2) is a simplified, high-level version of BioTop, a top-domain ontology that provides definitions for the foundational entities of biomedicine. BioTop imports BTL2 as its upper-level ontology.",
"homepage": "http://biotopontology.github.io/",
"name": "BioTopLite 2",
"publications": [
{
"pubmed": "28423831",
"title": "The BioTop Family of Upper Level Ontological Resources for Biomedicine",
"year": 2017
}
],
"repository": "https://github.com/BioTopOntology/biotop/issues",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.pzxjh": {
"abbreviation": "CCON",
"description": "The ontology of Cerrado wood plant dynamics was created in order to represent the set of concepts about the dynamics, that is, changes over time of the wood vegetation structure, of Cerrado. Ccon describes the main parameters used to measure the changes, such as mortality rate and recruitment rate.",
"domains": [
"Ecosystem"
],
"homepage": "http://bioportal.bioontology.org/ontologies/CCON",
"name": "Cerrado concepts and plant community dynamics",
"subjects": [
"Plant Ecology",
"Population Dynamics",
"Biodiversity",
"Ecosystem Science"
]
},
"FAIRsharing.q053vb": {
"abbreviation": "MFOMD",
"description": "An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable.",
"domains": [
"Disease"
],
"homepage": "https://github.com/jannahastings/mental-functioning-ontology",
"name": "MFO Mental Disease Ontology",
"subjects": [
"Psychiatry"
]
},
"FAIRsharing.q09hck": {
"abbreviation": "SIBO",
"description": "The Social Inset Behavior Ontology mostly contains terms related to Chemical, Anatomy, Behavior, Species. The most developed use cases are for Pogonomyrmex harvester ant foraging and apis mellifera honeybee colony defense.\n",
"homepage": "https://github.com/obophenotype/sibo",
"license": "CC-BY-3.0",
"name": "Social Inset Behavior Ontology",
"subjects": [
"Biology"
]
},
"FAIRsharing.q47I0t": {
"abbreviation": "CryoEM Ontology",
"contact": {
"email": "coss@cnb.csic.es",
"name": "Carlos Oscar S. Sorzano",
"orcid": "0000-0002-9473-283X"
},
"description": "The CryoEM Ontology for describing objects and workflows in Single Particle Analysis by Cryo Electron Microscopy.",
"domains": [
"Electron microscopy"
],
"homepage": "http://scipion.i2pc.es/ontology/cryoem",
"license": "CC-BY-3.0",
"name": "CryoEM Ontology",
"subjects": [
"Structural Biology"
]
},
"FAIRsharing.q5tfhf": {
"abbreviation": "BIOA",
"description": "There is currently no information avauilable on the BioActivity Ontology. Please contact us if you know more about this ontology.",
"domains": [
"Molecular entity",
"Bioactivity"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1684",
"name": "BioActivity Ontology",
"subjects": [
"Life Science"
]
},
"FAIRsharing.q5xf99": {
"abbreviation": "COPDO",
"description": "The COPD Ontology is a biomedical ontology used for modelling concepts associated to chronic obstructive pulmonary disease in routine clinical databases. There are a no plans to revise this ontology in the near future and therefore the version shown in the BioPortal link should be considered the final version.",
"domains": [
"Disease"
],
"homepage": "https://clininf.eu",
"name": "COPD Ontology",
"subjects": [
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.qcceez": {
"abbreviation": "OPB",
"description": "The Ontology of Physics for Biology is a reference of classical physics as applied to the dynamics of biological systems. This resource provides a reference ontology of physical properties (e.g., pressure, chemical concentration) and principles (e.g., Ohmβs law, Fickeβs law) by which the physical meaning of biosimulation models may be annotated.",
"domains": [
"Mathematical model",
"Concentration",
"Kinetic model"
],
"homepage": "https://sites.google.com/site/semanticsofbiologicalprocesses/projects/the-ontology-of-physics-for-biology-opb",
"name": "Ontology of Physics for Biology",
"publications": [
{
"doi": "10.1371/journal.pone.0028708",
"pubmed": "22216106",
"title": "Physical properties of biological entities: an introduction to the ontology of physics for biology",
"year": 2012
},
{
"doi": "10.1186/2041-1480-4-41",
"pubmed": "24295137",
"title": "Ontology of physics for biology: representing physical dependencies as a basis for biological processes",
"year": 2013
}
],
"subjects": [
"Life Science",
"Physics"
]
},
"FAIRsharing.qdcgfc": {
"abbreviation": "OntoPneumo",
"description": "OntoPneumo is an ontology for describing pneumology (french version). Their goal is to use natural language within the ontology to express the meaning of each concept using differential principles inherited from Differential Semantics theory. OntoPneumo is used in software for pneumologists that represents medical knowledge to describe the medical diagnoses in the form of graphs and to propose the proper French DRG (Diagnosis Related Group) code.",
"domains": [
"Diagnosis"
],
"homepage": "http://bioportal.bioontology.org/ontologies/ONTOPNEUMO",
"license": "https://creativecommons.org/licenses/by-nc-nd/2.0/uk",
"name": "Ontology of Pneumology",
"publications": [
{
"doi": "10.3233/ao-2008-0056",
"title": "OntoPneumo: An ontology of pneumology domain",
"year": 2008
}
],
"subjects": [
"Medicine"
]
},
"FAIRsharing.qdjc1z": {
"abbreviation": "PVONTO",
"contact": {
"email": "jhuan@ittc.ku.edu",
"name": "Jun (Luke) Huan",
"orcid": "0000-0003-4929-2617"
},
"description": "The pharmacovigilance ontology connects known facts on drugs, disease, ADEs, and their molecular mechanisms.",
"domains": [
"Drug",
"Molecular interaction",
"Disease"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1567",
"name": "Pharmacovigilance Ontology",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.qeb7hb": {
"abbreviation": "PHARE",
"contact": {
"email": "adrien.coulet@loria.fr",
"name": "Adrien Coulet",
"orcid": "0000-0002-1466-062X"
},
"description": "The PHArmacogenomic RElationships Ontology (or PHARE) proposes concepts and roles to represent relationships of pharmacogenomics interest.",
"domains": [
"Chemical entity",
"Molecular interaction",
"Phenotype"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1550",
"name": "Pharmacogenomic Relationships Ontology",
"publications": [
{
"doi": "10.1186/2041-1480-2-s2-s10",
"pubmed": "21624156",
"title": "Integration and publication of heterogeneous text-mined relationships on the Semantic Web",
"year": 2011
}
],
"subjects": [
"Pharmacology",
"Pharmacogenomics",
"Biomedical Science"
]
},
"FAIRsharing.qnkw45": {
"abbreviation": "MESH",
"description": "The Medical Subject Headings (MeSHΒ) thesaurus is a controlled vocabulary produced by the National Library of Medicine and used for indexing, cataloging, and searching for biomedical and health-related information and documents. MeSH includes the subject descriptors appearing in MEDLINEΒ/PubMedΒ and other NLM databases. MeSH provides a consistent way to find content with different terminology but the same concepts. Many synonyms, near-synonyms, and closely related concepts are included as entry terms to help users find the most relevant MeSH descriptor for the concept they are seeking. In NLM's online databases, many terms entered by searchers are automatically mapped to MeSH descriptors to facilitate retrieval of relevant information. Various online systems provide access to MeSH and the vocabulary is available in several NLM online systems. These include the MeSH Browser, containing the complete contents of the MeSH vocabulary; the MeSH Entrez databases, which are designed to assist those searching MEDLINEΒ/PubMedΒ; and the UMLS MetathesaurusΒ with links to many other controlled vocabularies. MeSH Records contain three types: Descriptors, Qualifiers, and Supplementary Concept Records (SCRs).",
"domains": [
"Data retrieval",
"Data model",
"Literature curation"
],
"homepage": "http://www.nlm.nih.gov/mesh/",
"name": "Medical Subject Headings",
"publications": [
{
"pubmed": "13982385",
"title": "Medical subject headings",
"year": 1963
}
],
"subjects": [
"Bioinformatics",
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.qp211a": {
"abbreviation": "CTO",
"contact": {
"email": "erfan.younesi@scai.fraunhofer.de",
"name": "Erfan Younesi",
"orcid": "0000-0001-8793-2692"
},
"description": "The Clinical Trials Ontology (CTO) is also known as the Clinical Trial Ontology-Neurodegenerative Diseases (CTO-NDD), and describes clinical trials in the field of neurodegeneration. This resource has been created for use in the IMI-funded AETIONOMY project (www.aetionomy.org).",
"domains": [
"Disease"
],
"homepage": "http://bioportal.bioontology.org/ontologies/CTO",
"name": "Clinical Trials Ontology",
"subjects": [
"Neurobiology",
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.qqy0dr": {
"abbreviation": "OCMR",
"description": "OCMR is a biomedical ontology that represents anti-rheumatism traditional Chinese medicines and related information.",
"homepage": "https://github.com/biomedontology/ocmr",
"license": "Apache 2.0 License",
"name": "Ontology of Chinese Medicine for Rheumatism",
"subjects": [
"Traditional Medicine",
"Biomedical Science"
]
},
"FAIRsharing.qrpwmw": {
"description": "There is no information currently available for Basic Vertebrate Anatomy ontology.",
"homepage": "http://bioportal.bioontology.org/ontologies/1056",
"name": "Basic Vertebrate Anatomy",
"subjects": [
"Anatomy"
]
},
"FAIRsharing.qrrvyk": {
"abbreviation": "CO_347",
"description": "The Castor Bean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe data.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_347:ROOT",
"license": "CC-BY-4.0",
"name": "Castor Bean Ontology",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.qs4x5m": {
"abbreviation": "MO",
"contact": {
"email": "stoeckrt@pcbi.upenn.edu",
"name": "Chris Stoeckert",
"orcid": "0000-0002-5714-991X"
},
"description": "The MGED Ontology is a top level container for the MGEDCoreOntology and the MGEDExtendedOntology. The MGED ontology describes microarray experiments and is split into the MGEDCoreOntology, which supports MAGE-OM v1.0 and is organized consistently with MAGE, and the MGEDExtendedOntology, which expands MAGE v1.0 and contains concepts and relationships which are not included in MAGE. Until this entry is claimed, more information on this project can be found at http://purl.bioontology.org/ontology/MO. If you work on the project responsible for \"MGED Ontology\" then please consider helping us by claiming this record and updating it appropriately.",
"domains": [
"Expression data",
"Assay",
"DNA microarray",
"Transcript"
],
"homepage": "http://mged.sourceforge.net/ontologies/MGEDontology.php",
"name": "Microarray and Gene Expression Data Ontology",
"publications": [
{
"doi": "10.1093/bioinformatics/btl005",
"pubmed": "16428806",
"title": "The MGED Ontology: a resource for semantics-based description of microarray experiments",
"year": 2006
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.qtb9yb": {
"abbreviation": "MAT",
"description": "Minimal set of terms for anatomy.",
"homepage": "http://bioportal.bioontology.org/ontologies/MAT?p=summary",
"name": "Minimal Anatomical Terminology",
"subjects": [
"Anatomy",
"Life Science"
]
},
"FAIRsharing.qtwya6": {
"description": "Material Element component of SWEET ontology. SWEET is a highly modular ontology suite with many separate ontologies covering Earth system science. SWEET is a mid-level ontology and consists of nine top-level concepts that can be used as a foundation for domain-specific ontologies that extend these top-level SWEET components. ",
"homepage": "https://github.com/ESIPFed/sweet/blob/master/src/matrElement.ttl",
"license": "CC0-1.0",
"name": "Material Element component of the SWEET ontology",
"subjects": [
"Earth Science"
]
},
"FAIRsharing.qwz9f2": {
"abbreviation": "CEDARPC",
"description": "This resource is no longer available because its underlying source material is not suitable for FAIRsharing. ",
"homepage": "http://metadatacenter.org/",
"name": "CEDAR Provisional Classes",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.r1rjvx": {
"abbreviation": "PO2",
"description": "A core ontology for modeling transformation processes and their observations. PO2 is part of an interdisciplinary project called Delicious concerning the production and transformation processes in food science. The project combines data from different disciplines like food composition, food structure, sensorial perception and nutrition.",
"domains": [
"Food",
"Sense of smell",
"Sense of taste"
],
"homepage": "http://dx.doi.org/10.15454/1.4702114192525708E12",
"license": "CC-BY-4.0",
"name": "Process and Observation Ontology",
"publications": [
{
"doi": "10.1007/978-3-319-49157-8_13",
"title": "PO2 - A Process and Observation Ontology in Food Science. Application to Dairy Gels",
"year": 2016
}
],
"subjects": [
"Agricultural Engineering",
"Life Science"
]
},
"FAIRsharing.r30na3": {
"abbreviation": "BRD Disease Ontology",
"description": "Our disease ontology provides information on infectious diseases, disease synonyms, transmission pathways, disease agents, affected populations and disease properties. Diseases have been grouped into syndromic disease categories, such that programmers can look through relevant categories, as well as at specific diseases. Organisms, linked to both agents and populations, are structured hierarchically, to provide multiple levels of organism resolution. In addition, both disease transmission and relevant disease properties are available to search. Disease properties include tags like 'notifiable diseases' and 'economic importance' to flag particular disease characteristics that may be of interest, but are not captured elsewhere.",
"domains": [
"Disease course",
"Infectious disease"
],
"homepage": "http://brd.bsvgateway.org/disease",
"name": "Biosurveillance Resource Directory Disease Ontology",
"publications": [
{
"doi": "10.1371/journal.pone.0083730",
"title": "Advancing a Framework to Enable Characterization and Evaluation of Data Streams Useful for Biosurveillance",
"year": 2014
}
],
"subjects": [
"Infectious Disease Medicine"
]
},
"FAIRsharing.r34hjr": {
"abbreviation": "MSTDE-FRE",
"description": "Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy, French Translation, 2001",
"homepage": "http://bioportal.bioontology.org/ontologies/MSTDE-FRE",
"name": "Minimal Standard Terminology of Digestive Endoscopy, French",
"subjects": [
"Gastroenterology"
],
"user_defined_tags": [
"endoscopy"
]
},
"FAIRsharing.r41qhx": {
"abbreviation": "UPHENO",
"description": "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology. Version 2 is the active release of the ontology, while version 1 should be considered deprecated. ",
"domains": [
"Phenotype"
],
"homepage": "https://github.com/obophenotype/upheno",
"license": "CC0-1.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBa01CIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--3f5258d2bcf30a7e127b5a9fe209b27e25e88883/up.png?disposition=inline",
"name": "Unified phenotype ontology",
"subjects": [
"Evolutionary Biology",
"Phenomics"
]
},
"FAIRsharing.r7Kwy7": {
"abbreviation": "CAS RN",
"description": "Identifier used by the Chemical Abstracts Service Registry. A CAS Registry Number is a numeric identifier that can contain up to 10 digits, divided by hyphens into three parts. The right-most digit is a check digit used to verify the validity and uniqueness of the entire number.",
"domains": [
"Chemical entity"
],
"homepage": "https://www.cas.org/support/documentation/chemical-substances/faqs#2",
"name": "CAS Registry Number",
"publications": [
{
"doi": "10.1021/acs.jcim.2c00268",
"title": "CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community",
"year": 2022
}
],
"subjects": [
"Cheminformatics"
]
},
"FAIRsharing.rab28f": {
"abbreviation": "SPO",
"description": "The Skin Physiology Ontology is an ontology with 339 terms. We have struggled to find any further information about this ontology. If you know more, please do contact the FAIRsharing team.",
"domains": [
"Biological process"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1122",
"name": "Skin Physiology Ontology",
"subjects": [
"Dermatology",
"Life Science",
"Physiology",
"Biomedical Science"
]
},
"FAIRsharing.rbp5wp": {
"abbreviation": "CO_715",
"contact": {
"email": "r.shrestha2@cgiar.org",
"name": "Rosemary Shrestha",
"orcid": "0000-0002-9399-8003"
},
"description": "The IBP Crop Research Ontology describes experimental design, environmental conditions and methods associated with the crop study/experiment/trait and their evaluation. It has been adapted from the database management system (DMS) and germplasm management system (GMS) of the International Crop Information System (ICIS) model. This ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms.",
"domains": [
"Study design"
],
"homepage": "https://cropontology.org/term/CO_715:ROOT",
"license": "CC-BY-4.0",
"name": "IBP Crop Research Ontology",
"subjects": [
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Method descriptions",
"Species-environment interaction"
]
},
"FAIRsharing.rbpqg": {
"abbreviation": "PGXO",
"description": "PGxO is a lightweight and simple Pharmacogenomic Ontology to reconcile and trace knowledge in pharmacogenomics (PGx).",
"domains": [
"Electronic health record"
],
"homepage": "https://pgxo.loria.fr",
"license": "CC BY-NC 4.0",
"name": "PGxO",
"publications": [
{
"doi": "10.1186/s12859-019-2693-9",
"title": "PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison",
"year": 2019
}
],
"repository": "https://github.com/practikpharma/PGxO",
"subjects": [
"Pharmacogenomics"
]
},
"FAIRsharing.recas1": {
"abbreviation": "ReXO",
"contact": {
"email": "kuiper@bio.ntnu.no",
"name": "Martin Kuiper",
"orcid": "0000-0002-1171-9876"
},
"description": "An application ontology for the domain of gene expression regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, and orthology relations using ontological properties from RO and ISO.",
"domains": [
"Expression data",
"Regulation of gene expression",
"Orthologous"
],
"homepage": "https://bioportal.bioontology.org/ontologies/REXO",
"name": "Regulation of Gene Expression Ontolology",
"publications": [
{
"doi": "10.1186/s12859-014-0386-y",
"pubmed": "25490885",
"title": "Finding gene regulatory network candidates using the gene expression knowledge base",
"year": 2014
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.reenq1": {
"abbreviation": "CONA",
"description": "The Cultural Objects Name Authority (CONA) compiles titles, creator attributions, physical characteristics, depicted subjects, and other metadata about visual works, such as architecture, painting, sculpture, and many other types of works. CONA may contain information about objects that are ceremonial or utilitarian in nature, but are not necessarily labeled as art according to traditional Western aesthetics. Architecture, destroyed works, and works depicted in visual surrogates or other works are also included. CONA also includes Getty Iconography Authority (IA) , which resides in the same editorial system as CONA. The IA includes proper names and other information for named events, themes and narratives from religion/mythology, legendary and fictional characters, themes from literature, works of literature and performing arts, and legendary and fictional places. CONA and IA are part of 5 Getty Vocabularies intended to provide terminology and other information about the objects, artists, concepts, and places important to various disciplines that specialize in art, architecture, and other material culture.",
"homepage": "http://www.getty.edu/research/tools/vocabularies/cona/index.html",
"license": "http://opendatacommons.org/licenses/by/1.0",
"name": "Cultural Objects Name Authority",
"subjects": [
"Culture",
"Art History",
"Architecture",
"Literary Studies",
"Art",
"Fine Arts",
"History",
"Cultural Studies"
]
},
"FAIRsharing.ret599": {
"abbreviation": "SSO",
"description": "Most syndromic surveillance systems use data from ED visits, often free-text chief complaints. Classification of chief complaints into syndromes is often inconsistent, due to the lack of agreement about the concepts that define a syndrome and how individual terms or strings map to these concepts. The Syndromic Surveillance Ontology addresses this problem by formally encoding a set of consensus definitions for syndromes in terms of ED chief complaints in a standard shareable format. The goal of the project is to ensure that consensus syndrome definitions are disseminated broadly, maintained collaboratively, and incorporated easily into automated systems.",
"domains": [
"Taxonomic classification"
],
"homepage": "http://surveillance.mcgill.ca/projects/sso/",
"name": "Syndromic Surveillance Ontology",
"subjects": [
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.rf4pmz": {
"abbreviation": "Chem2Bio2RDF",
"description": "Chem2Bio2RDF has been created by aggregating data from multiple chemogenomics repositories and is cross-linked into Bio2RDF and LODD. There is also a linked-path generation tool to facilitate SPARQL query generation, and have created extended SPARQL functions to address specific chemical/biological search needs. Chem2Bio2RDF can be used to investigate polypharmacology, identification of potential multiple pathway inhibitors, and the association of pathways with adverse drug reactions. ",
"domains": [
"Drug"
],
"homepage": "http://cheminfov.informatics.indiana.edu:8080/c2b2r/",
"name": "Ontology for Systems Chemical Biology and Chemogenomics",
"publications": [
{
"doi": "10.1186/1471-2105-11-255",
"pubmed": "20478034",
"title": "Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data",
"year": 2010
}
],
"subjects": [
"Genomics"
],
"user_defined_tags": [
"Chemogenomics"
]
},
"FAIRsharing.rfLD2u": {
"abbreviation": "EC Number",
"description": "In its report in 1961, the first Enzyme Commission devised a system for enzyme classification that also serves as a basis for assigning code numbers. These code numbers, prefixed by EC, contain four elements separated by points / full stops and are now widely in use. The first number shows to which of the six main divisions (classes) the enzyme belongs and therefore identifies the class of reaction catalysed. The second number indicates the subclass, and generally contains information about the type of compound or group involved. The third figure gives the sub-subclass, which further specifies the type of reaction involved. The fourth figure is the serial number of the enzyme in its sub-subclass.",
"domains": [
"Enzyme Commission number",
"Centrally registered identifier",
"Enzyme",
"Classification"
],
"homepage": "https://www.qmul.ac.uk/sbcs/iubmb/enzyme/rules.html",
"name": "Enzyme Commission Number",
"subjects": [
"Biochemistry",
"Enzymology"
]
},
"FAIRsharing.rfec93": {
"abbreviation": "ONS",
"description": "Ontology For Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies. It is the first systematic effort to provide a formal ontology framework for the description of nutritional studies.",
"homepage": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies",
"license": "CC-BY-4.0",
"name": "Ontology for Nutritional Studies",
"repository": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies/issues",
"subjects": [
"Nutritional Science",
"Biomedical Science"
]
},
"FAIRsharing.rfrsk4": {
"abbreviation": "TRON",
"description": "TrOn is an ontology about the anatomical structures of the red flour beetle Tribolium castaneum in the developmental stages larva, pupa and adult.",
"domains": [
"Life cycle",
"Life cycle stage"
],
"homepage": "http://ibeetle-base.uni-goettingen.de/ontology/overview.jsf",
"name": "Tribolium Ontology",
"subjects": [
"Anatomy",
"Developmental Biology"
]
},
"FAIRsharing.rhhrtx": {
"abbreviation": "BDO",
"contact": {
"email": "tudor.groza@uq.edu.au",
"name": "Tudor Groza",
"orcid": "0000-0003-2267-8333"
},
"description": "The Bone Dysplasia ontology provides a comprehensive and formal representation of the different domain concepts involved in documenting the full complexity of the skeletal dysplasia domain. It captures and combines the genetic features that discriminate the bone dysplasias with the multitude of phenotypic characteristics manifested by patients and required to be taken into account in order to support the diagnosis process.",
"domains": [
"Bone disease",
"Mutation analysis",
"Phenotype",
"Bone",
"Genotype"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1613",
"name": "Bone Dysplasia Ontology",
"publications": [
{
"doi": "10.1186/1471-2105-13-50",
"pubmed": "22449239",
"title": "The Bone Dysplasia Ontology: integrating genotype and phenotype information in the skeletal dysplasia domain",
"year": 2012
}
],
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.rja8qp": {
"abbreviation": "HANCESTRO",
"description": "The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies.",
"domains": [
"Genome-wide association study"
],
"homepage": "https://github.com/EBISPOT/hancestro",
"license": "CC-BY-4.0",
"name": "Human Ancestry Ontology",
"publications": [
{
"doi": "10.1186/s13059-018-1396-2",
"pubmed": "29448949",
"title": "A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog",
"year": 2018
}
],
"repository": "https://github.com/EBISPOT/ancestro/issues",
"subjects": [
"Demographics",
"Human Genetics",
"Population Genetics"
]
},
"FAIRsharing.rm5xc3": {
"abbreviation": "GCC",
"description": "Gastroenterology Clinical Cases is an ontology to describe clinical case terminologies associated with Gastroenterology. The link for this record no longer works and there is no current information available at present.",
"domains": [
"Disease",
"Lower digestive tract"
],
"homepage": "http://bioportal.bioontology.org/ontologies/3017",
"name": "Gastroenterology Clinical Cases",
"subjects": [
"Medicine",
"Gastroenterology"
]
},
"FAIRsharing.rnckxp": {
"abbreviation": "BOF",
"description": "An ontology of biodiversity of INPA, available via BioPortal.",
"homepage": "http://bioportal.bioontology.org/ontologies/BOF",
"name": "Biodiversity Ontology",
"subjects": [
"Biodiversity"
]
},
"FAIRsharing.rrms81": {
"abbreviation": "TAHE",
"description": "\"Terminology of Anatomy of Human Embryology\" is a standard, specialising in the fields described under \"scope and data types\", below. Until this entry is claimed, more information on this project can be found at http://bioportal.bioontology.org/ontologies/1536. This text was generated automatically. If you work on the project responsible for \"Terminology of Anatomy of Human Embryology\" then please consider helping us by claiming this record and updating it appropriately.",
"homepage": "http://bioportal.bioontology.org/ontologies/1536",
"name": "Terminology of Anatomy of Human Embryology",
"subjects": [
"Anatomy",
"Embryology",
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.rtzdrx": {
"abbreviation": "BIPON",
"description": "BiPON is an ontology permitting a multi-scale systemic representation of bacterial cellular processes and the coupling to their mathematical models. BiPON is further composed of two sub- ontologies, bioBiPON and modelBiPON. bioBiPON aims at organizing the systemic description of biological information while modelBiPON aims at describing the mathematical models (including parameters) associated to each biological process.",
"domains": [
"Mathematical model"
],
"homepage": "http://bioportal.bioontology.org/ontologies/BIPON",
"name": "Bacterial interlocked Process ONtology",
"subjects": [
"Microbiology"
]
},
"FAIRsharing.rvssy8": {
"abbreviation": "TAHH",
"description": "\"Terminology of Anatomy of Human Histology\" is a standard, specialising in the fields described under \"scope and data types\", below. Until this entry is claimed, more information on this project can be found at http://bioportal.bioontology.org/ontologies/1535. This text was generated automatically. If you work on the project responsible for \"Terminology of Anatomy of Human Histology\" then please consider helping us by claiming this record and updating it appropriately.",
"domains": [
"Histology"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1535",
"name": "Terminology of Anatomy of Human Histology",
"subjects": [
"Anatomy",
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.rvz0m9": {
"abbreviation": "OGMS",
"contact": {
"email": "rscheuermann@jcvi.org",
"name": "Richard Scheuermann",
"orcid": "0000-0003-1355-892X"
},
"description": "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies.",
"domains": [
"Cancer",
"Disease phenotype",
"Disease",
"Diagnosis"
],
"homepage": "https://github.com/OGMS/ogms",
"name": "Ontology for General Medical Science",
"publications": [
{
"doi": "10.1186/2041-1480-4-42",
"pubmed": "24314207",
"title": "The neurological disease ontology",
"year": 2013
}
],
"repository": "https://github.com/OGMS/ogms/issues",
"subjects": [
"Medicine",
"Biomedical Science"
]
},
"FAIRsharing.rxazmf": {
"abbreviation": "NEOMARK3",
"description": "An ontology that describes the medical information necessary for early detection of the oral cancer reoccurrence extracted from the NeoMark Project.",
"domains": [
"Cancer"
],
"homepage": "http://purl.bioontology.org/ontology/NEOMARK3",
"name": "Neomark Oral Cancer-Centred Ontology",
"subjects": [
"Oncology",
"Medicine",
"Biomedical Science"
]
},
"FAIRsharing.ry1ezg": {
"abbreviation": "CO_339",
"description": "The Lentil Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_339:ROOT",
"license": "CC-BY-4.0",
"name": "Lentil Ontology",
"subjects": [
"Botany",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.rycy2x": {
"abbreviation": "AERO",
"contact": {
"email": "mcourtot@gmail.com",
"name": "Melanie Courtot",
"orcid": "0000-0002-9551-6370"
},
"description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events.",
"domains": [
"Electronic health record",
"Adverse Reaction"
],
"homepage": "http://purl.obolibrary.org/obo/aero",
"license": "CC-BY-3.0",
"name": "Adverse Event Reporting ontology",
"subjects": [
"Medicine",
"Health Science",
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.s0gpch": {
"abbreviation": "DATASRC-ORTHO",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/1698",
"name": "HOM-DATASRC-ORTHO",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.s12wda": {
"abbreviation": "BRO_ACRONYM",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/BRO_ACRONYM",
"name": "Bro_Name",
"subjects": [
"Medicine"
]
},
"FAIRsharing.s19src": {
"abbreviation": "SBO",
"description": "The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modelling. It consists of seven orthogonal vocabularies defining: reaction participants roles (e.g. \"substrate\"), quantitative parameters (e.g. \"Michaelis constant\"), classification of mathematical expressions describing the system (e.g. \"mass action rate law\"), modelling framework used (e.g. \"logical framework\"), the nature of the entity (e.g. \"macromolecule\"), the type of interaction (e.g. \"process\"), as well as a branch to define the different types of metadata that may be present within a model. Use of such terms introduces a layer of semantic information into the standard description of a model, facilitating its interpretation and efficient reuse.",
"domains": [
"Mathematical model",
"Modeling and simulation",
"Molecular interaction",
"Pathway model"
],
"homepage": "http://www.ebi.ac.uk/sbo/",
"name": "Systems Biology Ontology",
"publications": [
{
"doi": "10.1038/msb.2011.77",
"pubmed": "22027554",
"title": "Controlled vocabularies and semantics in systems biology",
"year": 2011
}
],
"subjects": [
"Systems Biology"
],
"twitter": "biomodels"
},
"FAIRsharing.s39p61": {
"abbreviation": "ontologia",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/3035",
"name": "Ontologia proj alternativa",
"subjects": [
"Biology"
]
},
"FAIRsharing.s3r6sk": {
"abbreviation": "ZFA",
"description": "A structured controlled vocabulary of the anatomy and development of the Zebrafish. If you work on the project responsible for \"Zebrafish anatomy and development\" then please consider helping us by claiming this record and updating it appropriately.",
"domains": [
"Morphology",
"Structure",
"Life cycle",
"Life cycle stage"
],
"homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources",
"name": "Zebrafish anatomy and development",
"publications": [
{
"doi": "10.1186/2041-1480-5-12",
"pubmed": "24568621",
"title": "The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio",
"year": 2014
}
],
"subjects": [
"Anatomy",
"Developmental Biology",
"Life Science"
]
},
"FAIRsharing.s54t82": {
"abbreviation": "MATRCOMPOUND",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/MATRCOMPOUND",
"name": "Material Compound",
"subjects": [
"Chemistry"
]
},
"FAIRsharing.s63y3p": {
"abbreviation": "SP",
"description": "The SeMAntic RepresenTation for Protocols, SMART Protocols, provides a structured OWL vocabulary of experimental protocols. SMART Protocols ontology includes two modules, SP-document and SP-workflow. SP-document, aims to provide a structured vocabulary of concepts to represent information necessary and sufficient for reporting an experimental protocol. SP-Workflow represents: i) the executable elements of a protocol, protocol instructions; ii) the experimental actions and material entities that participates in instructions (sample/specimen, organisms, reagents, instruments); and iii) the order of execution of the instructions.",
"domains": [
"Protocol"
],
"homepage": "https://smartprotocols.github.io/",
"name": "SMART Protocols",
"publications": [
{
"doi": "10.1186/s13326-017-0160-y",
"title": "Using semantics for representing experimental protocols",
"year": 2017
}
],
"subjects": [
"Biomedical Science",
"Biology"
]
},
"FAIRsharing.s6zfkg": {
"abbreviation": "NIC",
"description": "The Nursing Interventions Classification (NIC) is a comprehensive, research-based, standardized classification of interventions that nurses perform. It is useful for clinical documentation, communication of care across settings, integration of data across systems and settings, effectiveness research, productivity measurement, competency evaluation, reimbursement, and curricular design. The Classification includes the interventions that nurses do on behalf of patients, both independent and collaborative interventions, both direct and indirect care.",
"domains": [
"Nurse"
],
"homepage": "http://www.nursing.uiowa.edu/cncce/nursing-interventions-classification-overview",
"name": "Nursing Interventions Classification",
"publications": [
{
"pubmed": "8591448",
"title": "Nursing interventions classification (NIC)",
"year": 1995
}
],
"subjects": [
"Medicine",
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.s7ryc2": {
"abbreviation": "OntoDM-KDD",
"description": "OntoDM-KDD is an ontology for representing data mining investigations. Its goal is to allow the representation of knowledge discovery processes and be general enough to represent the data mining investigations. The ontology is based on the CRISP-DM process methodology.",
"homepage": "http://www.ontodm.com/doku.php?id=ontodm-kdd",
"name": "Ontology for Data Mining Investigations",
"publications": [
{
"doi": "10.1007/978-3-642-40897-7_9",
"title": "OntoDM-KDD: Ontology for Representing the Knowledge Discovery Process",
"year": 2013
}
],
"subjects": [
"Data Mining",
"Life Science"
]
},
"FAIRsharing.s8g6nh": {
"abbreviation": "NonRCTOntology",
"contact": {
"email": "amrapali.j.zaveri@gmail.com",
"name": "Amrapali Zaver",
"orcid": "0000-0003-3239-4588"
},
"description": "Non Randomized Controlled Trials Ontology is an ontology to help the systematic review and meta-analysis process of non randomized clinical trials.",
"domains": [
"Non-randomized controlled trials"
],
"homepage": "http://bioportal.bioontology.org/ontologies/3012",
"license": "CC BY-SA 3.0",
"name": "Non Randomized Controlled Trials Ontology",
"publications": [
{
"doi": "10.1016/j.jbi.2004.03.001",
"pubmed": "15120657",
"title": "An ontology of randomized controlled trials for evidence-based practice: content specification and evaluation using the competency decomposition method",
"year": 2004
}
],
"subjects": [
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.s8nf87": {
"abbreviation": "CAMRQ",
"description": "\"Quadrupedal Gait\" is a standard that was, until recently, listed on BioPortal. The entry there has now been deleted and we have been unable to find any record of this standard. If you know more, please do not hesitate to contact us.",
"domains": [
"Diagnosis"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1657",
"name": "Quadrupedal Gait",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.sbbbf6": {
"abbreviation": "GBOL",
"contact": {
"email": "jasper.koehorst@wur.nl",
"name": "Jasper Koehorst",
"orcid": "0000-0001-8172-8981"
},
"description": "To enable interoperability of genome annotations, we have developed the Genome Biology Ontology Language (GBOL) and associated stack (GBOL stack). GBOL is provenance centered and provides a consistent representation of genome derived automated predictions linked to the dataset-wise and element-wise provenance of predicted elements. GBOL is modular in design, extendible and is integrated with existing ontologies. Interoperability of linked data can only be guaranteed through the application of tools that provide the means for a continuous validation of generated linked data. The GBOL stack enforces consistency within and between the OWL and ShEx definitions. Genome wide large scale functional analyses can then easily be achieved using SPARQL queries. Additionally, modules have been developed to serialize the linked data (RDF) and to generate a plain text format files with integrated support for data provenance that that mimic the indentation structure of GenBank and EMBL formats.",
"domains": [
"Annotation",
"Genome"
],
"homepage": "http://gbol.life",
"name": "Genome Biology Ontology Language",
"publications": [
{
"doi": "10.1101/184747",
"title": "Interoperable genome annotation with GBOL, an extendable infrastructure for functional data mining",
"year": 2017
}
],
"subjects": [
"Functional Genomics",
"Life Science"
]
},
"FAIRsharing.sdjk2h": {
"abbreviation": "CPT",
"description": "The Current Procedural Terminology (CPT), a product of the American Medical Association (AMA), are a list of descriptive terms and identifying numeric codes for medical services and procedures that are provided by physicians and health care professionals. CPT codes are used by healthcare professionals for billing of medical services and procedures to public and private health insurance programs.\n\n",
"domains": [
"Electronic health record"
],
"homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/CPT/metarepresentation.html",
"name": "Metathesaurus Current Procedural Terminology",
"subjects": [
"Clinical Studies",
"Biomedical Science"
]
},
"FAIRsharing.sec0c9": {
"abbreviation": "RAPID Phenotype Ontology",
"description": "RAPID phenotype ontology presents controlled vocabulary of ontology class structures and entities of observed phenotypic terms for primary immunodeficiency diseases (PIDs) that facilitate global sharing and free exchange of PID data with usersβ communities",
"domains": [
"Phenotype"
],
"homepage": "http://web16.kazusa.or.jp/rapid/",
"name": "Resource of Asian Primary Immunodeficiency Diseases Phenotype Ontology",
"publications": [
{
"doi": "10.1093/nar/gkn682",
"pubmed": "18842635",
"title": "RAPID: Resource of Asian Primary Immunodeficiency Diseases",
"year": 2008
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.sgk7s0": {
"abbreviation": "OntoDM-core",
"contact": {
"email": "pance.panov@ijs.si",
"name": "Pance Panov",
"orcid": "0000-0002-7685-9140"
},
"description": "OntoDM is a generic ontology for the domain of data mining. The ontology includes the information processing processes that occur in the domain of data mining, participants in the processes and their specifications. OntoDM is highly transferable and extendable due to its adherence to accepted standards, and compliance with existing ontology resources. The generality in scope allows wide number of applications of the ontology, such as semantic annotation of data mining scenarios, ontology based support for QSARs, etc.",
"homepage": "http://www.ontodm.com/doku.php?id=ontodm-core",
"name": "Ontology of Core Data Mining Entities",
"publications": [
{
"doi": "10.1007/s10618-014-0363-0",
"title": "Ontology of core data mining entities",
"year": 2014
}
],
"subjects": [
"Data Mining",
"Life Science"
],
"user_defined_tags": [
"Semantic"
]
},
"FAIRsharing.shm2f2": {
"abbreviation": "RadLex",
"description": "RadLex is a comprehensive lexiconβa unified language of radiology termsβfor standardized indexing and retrieval of radiology information resources. With more than 68,000 terms, RadLex satisfies the needs of software developers, system vendors and radiology users by adopting the best features of existing terminology systems while producing new terms to fill critical gaps. RadLex also provides a comprehensive and technology-friendly replacement for the ACR Index for Radiological Diagnoses. It unifies and supplements other lexicons and standards, such as SNOMED-CT and DICOM. RadLex development has received support from both the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the cancer Biomedical Informatics Grid (caBIG) project.",
"domains": [
"Medical imaging",
"Diagnosis"
],
"homepage": "https://www.rsna.org/en/practice-tools/data-tools-and-standards/radlex-radiology-lexicon",
"name": "Radiology Lexicon",
"publications": [
{
"doi": "10.2214/ajr.174.5.1741463",
"pubmed": "10789815",
"title": "Radiology lexicon",
"year": 2000
},
{
"doi": "10.1016/j.jvir.2008.10.022",
"pubmed": "19081735",
"title": "The IR RadLex project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology",
"year": 2008
},
{
"doi": "10.1016/j.jvir.2009.04.031",
"pubmed": "19560008",
"title": "The IR Radlex Project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology",
"year": 2009
}
],
"subjects": [
"Anatomy",
"Radiology",
"Clinical Studies",
"Biomedical Science",
"Medical Informatics"
]
},
"FAIRsharing.shpqgt": {
"abbreviation": "HAROREADO",
"contact": {
"email": "contact@bioelf-communication.com",
"name": "Delphine Dauga",
"orcid": "0000-0003-3152-1194"
},
"description": "The first ontology describing the anatomy and the development of Halocynthia roretzi.",
"domains": [
"Cell",
"Life cycle",
"Life cycle stage"
],
"homepage": "https://aniseed.fr/aniseed/anatomy/find_devstage?module=aniseed&action=anatomy:find_devstage",
"name": "Halocynthia roretzi Anatomy and Development Ontology",
"subjects": [
"Anatomy",
"Developmental Biology"
],
"user_defined_tags": [
"Morphogenesis"
]
},
"FAIRsharing.sjf113": {
"abbreviation": "MIRO",
"description": "Monitoring of insect vector populations with respect to their susceptibility to one or more insecticides is a crucial element of the strategies used for the control of arthropod-borne diseases. This management task can nowadays be achieved more efficiently when assisted by IT (Information Technology) tools, ranging from modern integrated databases to GIS (Geographic Information System). MIRO is an application ontology that can be used for the purpose of controlling mosquitoes and, thus, the diseases that they transmit.",
"domains": [
"Insecticide resistance",
"Mutation",
"Phenotype"
],
"homepage": "https://www.vectorbase.org/ontology-browser",
"name": "Mosquito Insecticide Resistance Ontology",
"publications": [
{
"doi": "10.1371/journal.pntd.0000465",
"pubmed": "19547750",
"title": "MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide resistance in mosquito disease vectors",
"year": 2009
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.sjhvyy": {
"abbreviation": "CHEMINF",
"contact": {
"email": "egon.willighagen@gmail.com",
"name": "Egon Willighagen",
"orcid": "0000-0001-7542-0286"
},
"description": "The Chemical Information Ontology (CHEMINF) aims to establish a standard in representing chemical information. In particular, it aims to produce an ontology to represent chemical structure and to richly describe chemical properties, whether intrinsic or computed.",
"domains": [
"Molecular structure",
"Molecular entity"
],
"homepage": "https://github.com/semanticchemistry/semanticchemistry",
"license": "CC0-1.0",
"name": "CHEMical INFormation Ontology",
"publications": [
{
"doi": "10.1371/journal.pone.0025513",
"pubmed": "21991315",
"title": "The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web",
"year": 2011
}
],
"repository": "https://github.com/semanticchemistry/semanticchemistry/issues",
"subjects": [
"Biochemistry",
"Chemistry",
"Life Science"
]
},
"FAIRsharing.sm90nh": {
"abbreviation": "WBLS",
"description": "A structured controlled vocabulary of the development of Caenorhabditis elegans. This resource is also referred to as the Life Stage ontology on the wormbase database.",
"domains": [
"Life cycle",
"Life cycle stage"
],
"homepage": "https://www.wormbase.org/tools/ontology_browser",
"name": "C. elegans development",
"repository": "https://github.com/obophenotype/c-elegans-development-ontology",
"subjects": [
"Developmental Biology",
"Life Science"
]
},
"FAIRsharing.sp3szt": {
"abbreviation": "SWO",
"contact": {
"email": "allyson.lister@oerc.ox.ac.uk",
"name": "Allyson Lister",
"orcid": "0000-0002-7702-4495"
},
"description": "The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. SWO also covers software manufacturer, input and output data types and the uses (i.e. objectives) to which the software can be put.",
"domains": [
"Algorithm",
"Workflow",
"Software"
],
"homepage": "https://github.com/allysonlister/swo",
"license": "CC-BY-4.0",
"name": "SoftWare Ontology",
"publications": [
{
"doi": "10.1186/2041-1480-5-25",
"pubmed": "25068035",
"title": "The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation",
"year": 2014
}
],
"repository": "https://github.com/allysonlister/swo/issues",
"subjects": [
"Bioinformatics",
"Computer Science"
]
},
"FAIRsharing.sp7hvb": {
"abbreviation": "ProPreO",
"description": "A comprehensive proteomics data and process provenance ontology.",
"homepage": "http://bioportal.bioontology.org/ontologies/PROPREO",
"name": "Proteomics data and process provenance",
"subjects": [
"Proteomics",
"Life Science"
]
},
"FAIRsharing.spjjv8": {
"abbreviation": "FTC",
"description": "The Functional Therapeutic Chemical Classification System (FTC) defines over 20,000 mechanisms and modes of action for approved drugs. The resource abstracts away from the traditional chemical structure-based approach and focuses solely on the mode of action of drugs. The classification sorts therapeutic agents based on their function in the human body. Please note that this resource is no longer actively maintained (source: https://github.com/loopasam/ftc/issues/1).",
"domains": [
"Drug",
"Classification",
"Approved drug"
],
"homepage": "https://github.com/loopasam/ftc",
"license": "CC-BY-3.0",
"name": "Functional Therapeutic Chemical Classification System",
"publications": [
{
"doi": "10.1093/bioinformatics/btt628",
"pubmed": "24177719",
"title": "The functional therapeutic chemical classification system",
"year": 2013
}
],
"repository": "https://github.com/loopasam/ftc/issues",
"subjects": [
"Drug Repositioning"
]
},
"FAIRsharing.sszk3y": {
"abbreviation": "RH-MeSH",
"contact": {
"email": "leechuck@leechuck.de",
"name": "Robert Hoehndorf",
"orcid": "0000-0001-8149-5890"
},
"description": "A modified version of the Medical Subjects Headings Thesaurus (MeSH) 2014. This is an OWL representation of MeSH so that it can be integrated with other ontologies represented in OWL. It contains all terms that are in MeSH and in the MeSH concept tree, including the pharmacological actions (represented as subclass relations). Concepts in the MeSH concept tree are merged with MeSH term ids. Note that, while this ontology is composed of MeSH terms, it does not correspond directly to UMLS MeSH. In particular, a single term in UMLS MeSH often results in multiple classes in this ontology.",
"domains": [
"Phenotype"
],
"homepage": "https://code.google.com/p/pharmgkb-owl/",
"name": "Robert Hoehndorf's Version of MeSH",
"subjects": [
"Bioinformatics",
"Biomedical Science"
]
},
"FAIRsharing.str8m4": {
"abbreviation": "CSEO",
"description": "The Cigarette Smoke Exposure Ontology (CSEO) is a specialized ontology of environmental exposure with particular focus on the description of the experimental elements and the impact that environmental exposure, e.g. cigarette smoke, poses to biological systems. The scope of CSEO is centered on the following elements: Exposure experiment, Exposure condition, Test system, Sampling, and Disease outcome.",
"domains": [
"Environmental contaminant",
"Disease course",
"Exposure"
],
"homepage": "https://publicwiki-01.fraunhofer.de/CSEO-Wiki/index.php/Main_Page",
"name": "Cigarette Smoke Exposure Ontology",
"publications": [
{
"doi": "10.1186/2041-1480-5-31",
"pubmed": "25093069",
"title": "CSEO - the Cigarette Smoke Exposure Ontology",
"year": 2014
}
],
"subjects": [
"Life Science",
"Biomedical Science"
],
"user_defined_tags": [
"Species-environment interaction"
]
},
"FAIRsharing.sw9xbj": {
"abbreviation": "eVOC",
"description": "Expressed Sequence Annotation for Humans provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment. This record is no longer being maintained.",
"domains": [
"Sequence feature",
"Transcript"
],
"homepage": "http://www.obofoundry.org/ontology/ev.html",
"name": "Expressed Sequence Annotation for Humans",
"subjects": [
"Genomics",
"Life Science"
]
},
"FAIRsharing.sxh2dp": {
"abbreviation": "PSI-MS CV",
"description": "The PSI-MS Controlled Vocabulary is developed in common with the PSI-Proteomics Informatics group. It consists of a large collection of structured terms covering description and use of Mass Spectrometry instrumentation as well as Protein Identification and Quantitation software. The source of the terms are multiple: they include vocabulary and definitions in chapter 12 of the IUPAC nomenclature book, instrument and software vendors and developers and other user-submitted terms. Although its structure and use is linked to mzML, mzIdentML and mzQuantML, it is dynamically maintained in a OBO format. The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MSβrelated data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. Owing to the range of topics covered by the CV, collaborative development across several PSI working groups, including proteomics research groups, instrument manufacturers and software vendors, was necessary.",
"domains": [
"Mass spectrometry assay",
"Protein"
],
"homepage": "http://www.psidev.info/groups/mass-spectrometry#controlled",
"license": "CC-BY-4.0",
"name": "HUPO PSI Mass Spectrometry Controlled Vocabulary",
"publications": [
{
"doi": "10.1093/database/bat009",
"pubmed": "23482073",
"title": "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary",
"year": 2013
}
],
"repository": "https://github.com/HUPO-PSI/psi-ms-CV",
"subjects": [
"Proteomics",
"Life Science"
]
},
"FAIRsharing.szexty": {
"abbreviation": "INSECTH",
"description": "NeuroMorpho.Org insect brain regions ontology is compiled to create data annotation standard for depositing insect data. Currently at v6.2, NeuroMorpho.Org hosts over 17k neuronal reconstructions mostly from the fly. The insect ontology follows the standard nomenclature of the insect brain (Ito et al., 2013) and the virtualfly.org.",
"homepage": "http://bioportal.bioontology.org/ontologies/INSECTH",
"name": "insectH",
"subjects": [
"Entomology"
]
},
"FAIRsharing.szrmev": {
"abbreviation": "CDISC CT",
"description": "CDISC Controlled Terminology is the set of codelists and valid values used with data items within CDISC-defined datasets. Controlled Terminology provides the values required for submission to FDA and PMDA in CDISC-compliant datasets. Controlled Terminology does not tell you WHAT to collect; it tells you IF you collected a particular data item, how you should submit it in your electronic dataset.",
"homepage": "https://www.cdisc.org/standards/terminology",
"name": "CDISC Controlled Terminology",
"subjects": [
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.t6y94s": {
"abbreviation": "OF",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/OF",
"name": "OntoFood",
"subjects": [
"Nutritional Science"
]
},
"FAIRsharing.t955dp": {
"abbreviation": "CTV3",
"description": "Read Codes are a coded thesaurus of clinical terms. They have been used in the NHS since 1985. There are two versions: version 2 (v2) and version 3 (CTV3 or v3). Both versions provide a standard vocabulary for clinicians to record patient findings and procedures, in health and social care IT systems across primary and secondary care. The Read Codes were developed in 1985 by Dr. James Read. The U.K. National Health Service Centre for Coding and Classification (NHS CCC) acquired and now maintains the Read Codes. Read Codes contain hundreds of thousands of terms, synonyms, and abbreviations covering all aspects of patient care including signs and symptoms, treatments and therapies, investigations, occupations, diagnoses, and drugs and appliances. Read Codes are used by healthcare professionals in computerized information systems. Read Codes are now known as Clinical Terms. Clinical Terms Version 3 (CTV3) has been merged with the Systematized Nomenclature of Medicine β Reference Terminology (SNOMED RT), resulting in the creation of SNOMED β Clinical Terms (SNOMED CT). PLEASE NOTE: the retirement of Read v2 and v3 (CTV3) clinical terminologies has been scheduled. The last release of Read v2 was April 2016, with CTV3 due to be retired after the April 2018 release. Organisations should be well underway with their preparations to ensure they can use the dictionary of medicines and devices (dm+d) for medicines and SNOMED CT for clinical content. SNOMED CT is adopted across primary care and the wider NHS.",
"domains": [
"Drug",
"Diagnosis",
"Treatment"
],
"homepage": "https://digital.nhs.uk/article/1104/Read-Codes",
"license": "http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3",
"name": "Read Codes Clinical Terms Version 3",
"subjects": [
"Medicine",
"Primary Health Care",
"Preclinical Studies"
]
},
"FAIRsharing.t9fvdn": {
"abbreviation": "ADW",
"description": "An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.",
"domains": [
"Taxonomic classification"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1530",
"name": "Animal natural history and life history",
"subjects": [
"Anatomy",
"Life Science"
]
},
"FAIRsharing.tb6w4b": {
"abbreviation": "CPO",
"contact": {
"email": "rh497@cam.ac.uk",
"name": "Robert Hoehndorf",
"orcid": "0000-0001-8149-5890"
},
"description": "The CPO is an ontology of morphological and physiological phenotypic characteristics of cells, cell components and cellular processes. Its prime application is to provide terms and uniform definition patterns for the annotation of cellular phenotypes. The CPO can be used for the annotation of observed abnormalities in domains, such as systems microscopy, in which cellular abnormalities are observed and for which no phenotype ontology has been created.",
"domains": [
"Cell",
"Cell morphology",
"Phenotype",
"Morphology"
],
"homepage": "https://code.google.com/archive/p/cell-phenotype/",
"name": "Cell Phenotype Ontology",
"publications": [
{
"doi": "10.1093/bioinformatics/bts250",
"pubmed": "22539675",
"title": "Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology",
"year": 2012
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"FAIRsharing.tbep2b": {
"abbreviation": "PhyMeRe",
"contact": {
"email": "laia.subirats@gmail.com",
"name": "Laia Subirats",
"orcid": "0000-0001-8646-5463"
},
"description": "Knowledge representation related to computer-based decision support in rehabilitation; concepts and relationships in the rehabilitation domain, integrating clinical practice, the ICD (specifically its 11th revision), the clinical investigator record ontology, the ICF and SNOMED CT.",
"homepage": "https://bioportal.bioontology.org/ontologies/PMR",
"name": "Physical Medicine and Rehabilitation",
"subjects": [
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.tc2jbF": {
"description": "Terminology resource used for indexing bibliographical records dealing with βOpticsβ in the PASCAL database, until 2014. It consists of 3177 entries in 4 languages (English, French, Spanish and German).",
"homepage": "https://www.loterre.fr/skosmos/FMC/en/",
"license": "CC-BY-4.0",
"name": "Optics terminology resource",
"subjects": [
"Atomic, Molecular, Optical and Plasma Physics"
],
"user_defined_tags": [
"Optics"
]
},
"FAIRsharing.tcbwad": {
"abbreviation": "HIV",
"description": "The HIV ontology encompasses all knowledge about HIV",
"domains": [
"Protein interaction",
"Mutation"
],
"homepage": "http://bioportal.bioontology.org/ontologies/HIV",
"name": "HIV ontology",
"subjects": [
"Functional Genomics",
"Proteomics",
"Medical Virology",
"Epidemiology"
]
},
"FAIRsharing.tepvv5": {
"abbreviation": "FOODIE",
"description": "The FOODIE project is focused on building an open and interoperable agricultural specialized platform on the cloud for the management, discovery and large-scale integration of data relevant for farming production. The FOODIE ontology is an INSPIRE-based vocabulary for the publication of Agricultural Linked Data. The ontology provides a semantic representation of the FOODIE core data model, which was specified in UML by extending and specializing the INSPIRE data model for Agricultural and Aquaculture Facilities (AF), which is in turn based on the ISO/OGC standards for geographical information.",
"domains": [
"Food"
],
"homepage": "http://foodie-cloud.github.io/model/FOODIE.html",
"name": "FOODIE core ontology",
"repository": "https://github.com/FOODIE-cloud/ontology",
"subjects": [
"Farming Systems Research",
"Agriculture"
]
},
"FAIRsharing.tghhc4": {
"abbreviation": "PP",
"description": "To answer the need for a workflow representing a sequence of data transformations, a high-level process ontology was defined, denoted Pipeline Patterns (PP) ontology. Every concept is generically a Data (class from EDAM), which can be further specified as an Entry (P:00002) or an Exit (P:00009). All Entries can be subjected to an Operation (class from EDAM) producing an Intermediate (P:00010). An Intermediate has a TemporalEntity associated to represent its time of creation. Some Entries are specifically of the type Exit, meaning that they will represent concepts that exit the current category and be passed to the next one on the workflow. Additionally, in order to permit the treatment of a set of objects as a single entity, this high-level ontology considers the concept of List (P:00004) and more specifically an Aggregate (P:00005), containing a set of Data or Entry, respectively. The concept Intermediate is an Entry, allowing for the successive application of an operation to an Element. This is particularly useful in the case of the application of sequential set of operations.",
"domains": [
"Assay",
"Study design"
],
"homepage": "https://bitbucket.org/PlantExpAssay/ontology",
"license": "CC-BY-4.0",
"name": "Pipeline Patterns Ontology",
"subjects": [
"Botany"
]
},
"FAIRsharing.th72sy": {
"abbreviation": "CO_121",
"description": "The IBP Wheat Plant Anatomy and Development Ontology defines growth stages of wheat and is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. Although this ontology seems to have a stable status on its homepage, it is listed as Retired in AgroPortal. Therefore we have marked its record status as Uncertain. Please get in touch if you have information regarding the current status of this resource.",
"domains": [
"Food"
],
"homepage": "https://cropontology.org/term/CO_121:ROOT",
"license": "CC-BY-4.0",
"name": "IBP Wheat Plant Anatomy and Development Ontology",
"subjects": [
"Botany",
"Agriculture",
"Plant Anatomy",
"Plant Cell Biology"
]
},
"FAIRsharing.tke3y2": {
"abbreviation": "DTO",
"description": "Drug Target Ontology (DTO) is developed as a reference for drug targets with the longer-term goal to create a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The first version of the DTO consists of asserted class hierarchies of the four IDG protein families, GPCRs, kinases, ion channels, and nuclear hormone receptors. Protein classes are linked to tissue and disease via different levels of confidence. DTO also contains drug target development classifications, a large collection of cell lines from the LINCS project and relevant cell-disease and cell-tissue relations. DTO is modeled in OWL2-DL to enable further classification by inference reasoning and SPARQL queries. DTO is implemented following a modularization approach. DTO will serve as the organizational framework for drug targets in the IDG PHAROS User Interface Portal (https://pharos.nih.gov).",
"domains": [
"Disease",
"Protein"
],
"homepage": "http://drugtargetontology.org/",
"license": "CC-BY-3.0",
"name": "Drug Target Ontology",
"publications": [
{
"doi": "10.1186/s13326-017-0161-x",
"pubmed": "29122012",
"title": "Drug target ontology to classify and integrate drug discovery data",
"year": 2017
}
],
"repository": "https://github.com/DrugTargetOntology/DTO",
"subjects": [
"Drug Discovery",
"Biomedical Science"
],
"user_defined_tags": [
"Drug Target"
]
},
"FAIRsharing.tn7et": {
"description": "The glycobiology of Drosophila has been extensively studied in recent years, and much information has accumulated regarding glycan-related genes and proteins in Drosophila. The FlyGlycoDB ontology describes glycogenes of Drosophila and includes mutants, activity, references and links to FlyBase and UniProt. It is part of the FlyGlycoDB database.",
"domains": [
"Mutation",
"Protein",
"Gene"
],
"homepage": "http://fly.glycoinfo.org",
"license": "CC-BY-4.0",
"name": "FlyGlycoDB Ontology",
"subjects": [
"Life Science",
"Glycomics"
],
"user_defined_tags": [
"Glycan Annotation",
"Glycan sequences"
]
},
"FAIRsharing.ts6zgq": {
"abbreviation": "NCCNEHR",
"description": "The NCCN EHR Oncology Advisory Group was formed to address the high variance in oncology history documentation within EHR systems. Specifically, there is a lack of standardization in the names of oncology history categories across institutions. Moreover, no synonym list or mapping currently exists between the varied category names. Furthermore, oncology history documentation is often inconsistent, incomplete, and not updated appropriately. The NCCN EHR Oncology Advisory Group has established best practices and is working with EHR vendors to implement and enhance tools for documentation of oncology history. This ontology is a result of the work of the group, and provides users with a list of oncology history categories and synonyms. It is our sincere hope that this work can form the basis of improving standardization and interoperability of oncology history documentation within EHR systems.",
"homepage": "https://www.nccn.org/",
"name": "NCCN EHR Oncology Categories",
"subjects": [
"Oncology"
]
},
"FAIRsharing.ttprgy": {
"abbreviation": "EPSO",
"description": "The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. ",
"domains": [
"Epilepsy",
"Patient care"
],
"homepage": "https://bioportal.bioontology.org/ontologies/EPSO",
"license": "CC BY-SA 3.0",
"name": "Epilepsy and Seizure Ontology",
"publications": [
{
"doi": "10.1136/amiajnl-2013-001696",
"title": "Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care",
"year": 2013
}
],
"subjects": [
"Neurology"
]
},
"FAIRsharing.tw4q8x": {
"abbreviation": "OAE",
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun \"Oliver\" He",
"orcid": "0000-0001-9189-9661"
},
"description": "The Ontology of Adverse Events (OAE) is a community-driven ontology that is developed to standardize and integrate data on biomedical adverse events (e.g., vaccine and drug adverse events) and support computer-assisted reasoning. As a result of a medical intervention, events may occur which lie outside the intended consequences of the intervention. Some of these events are adverse events, in the sense that they are pathological bodily processes. For many such adverse events it is unclear whether they are causal consequences of the medical intervention which preceded them, since adverse events may also occur due to other reasons (for example a natural viral infection). OAE was created to represent the whole process from initial medical intervention to subsequent outcomes.",
"domains": [
"Drug",
"Adverse Reaction",
"Vaccine"
],
"homepage": "https://github.com/oae-ontology",
"license": "CC-BY-3.0",
"name": "Ontology of Adverse Events",
"publications": [
{
"doi": "10.1186/2041-1480-5-29",
"pubmed": "25093068",
"title": "OAE: The Ontology of Adverse Events",
"year": 2014
}
],
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.twp7vn": {
"abbreviation": "BNO",
"description": "The Bionutrition Ontology relates concepts and terminologies used for human nutrition in a clinical and biomedical setting.",
"homepage": "http://bioportal.bioontology.org/ontologies/BNO",
"name": "Bionutrition Ontology",
"subjects": [
"Nutritional Science"
]
},
"FAIRsharing.tz3682": {
"abbreviation": "PHFUMIADO",
"contact": {
"email": "contact@bioself-communication.com",
"name": "Delphine Dauga",
"orcid": "0000-0003-3152-1194"
},
"description": "The first ontology describing the anatomy and the development of Phallusia fumigata.",
"domains": [
"Cell",
"Life cycle",
"Life cycle stage"
],
"homepage": "https://aniseed.fr/aniseed/anatomy/find_devstage?module=aniseed&action=anatomy:find_devstage",
"name": "Phallusia fumigata Anatomy and Development Ontology",
"subjects": [
"Anatomy",
"Developmental Biology"
],
"user_defined_tags": [
"Morphogenesis"
]
},
"FAIRsharing.tz6hz6": {
"abbreviation": "OCHV",
"description": "A SKOS-encoded implementation of the \"Open Access, Collaborative Consumer Health Vocabulary Initiative\" by the University of Utah (consumerhealthvocab.org and layhealthinformatics.com)",
"homepage": "http://bioportal.bioontology.org/ontologies/OCHV",
"name": "Ontology of Consumer Health Vocabulary",
"subjects": [
"Health Science"
]
},
"FAIRsharing.v06c4q": {
"abbreviation": "CO_334",
"description": "Crop-specific trait ontologies enhance the interoperability and effectiveness of data exchange between the data sources which adopt it, by providing standard concepts that are use to describe phenotypes stored in those sources. As one of them, the Cassava Ontology is actively used and shared in different databases such as the BMS (Breeding Management system) of the IBP or the CassavaBase. Cassava, a major staple crop, is the main source of calories for 500 million people across the globe. A perennial woody shrub native to Latin America, cassava is primarily grown as an annual crop in the humid tropics. A cash crop as well as a subsistence crop, cassava's large edible starchy roots are a source of low-cost carbohydrates for millions. Cassava end products range from fresh roots cooked, boiled, baked or fried at the household level, to highly processed starch as a food additive.",
"domains": [
"Food",
"Phenotype"
],
"homepage": "https://cropontology.org/term/CO_334:ROOT",
"license": "CC-BY-4.0",
"name": "IBP Cassava Trait Ontology",
"repository": "https://github.com/Planteome/ibp-cassava-traits",
"subjects": [
"Botany",
"Agriculture",
"Nutritional Science"
],
"user_defined_tags": [
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.v248nq": {
"abbreviation": "GLYCO",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://glycomics.ccrc.uga.edu/core4/informatics-ontologies.html",
"name": "Glycomics Ontology",
"subjects": [
"Life Science"
]
},
"FAIRsharing.v5ymcw": {
"abbreviation": "ROS",
"description": "This ontology describes commonly contoured (anatomical and treatment planning) structures for radiation treatment planning. 22000 structures labels (created over a 16 years period in our radiation department) were extracted, classified and categorized to produce this ontology. Lymph nodes delineation international guidelines are provided. This ontology was created to ease and standardize the integration of radiation oncology data into clinical datawarehouses for multicentric studies. The high granularity of this ontology will allow precise dosimetric evaluations.",
"homepage": "https://github.com/jebibault/Radiation-Oncology-Structures-Ontology",
"name": "Radiation Oncology Structures Ontology",
"subjects": [
"Radiation Oncology"
]
},
"FAIRsharing.v665h": {
"abbreviation": "MST",
"description": "The Minimal Standard Terminology (MST) for gastrointestinal endoscopy is the result of a continuous work by WEO, the European Society of Gastrointestinal Endoscopy (ESGE), the American Society of Gastrointestinal Endoscopy (ASGE) and a large group of international collaborators. Standardization of the language of gastrointestinal endoscopy is becoming increasingly important on account of international collaboration, standardized documentation requirements, and computer-based reporting. The MST offers a selection of terms and attributes for appropriate description of findings, procedures and complications with regards to gastrointestinal endoscopy. It does not offer a complete reference for the endoscopic report.",
"homepage": "https://www.worldendo.org/resources/minimal-standard-terminology-mst/",
"license": "https://www.worldendo.org/resources/minimal-standard-terminology-mst",
"name": "Minimal Standard Terminology for Gastrointestinal Endoscopy",
"publications": [
{
"doi": "10.1055/s-0029-1214949",
"title": "Minimal standard terminology for gastrointestinal endoscopy β MST 3.0",
"year": 2009
}
],
"subjects": [
"Gastroenterology"
],
"user_defined_tags": [
"endoscopy"
]
},
"FAIRsharing.vajn3f": {
"abbreviation": "RS",
"description": "This ontology defines the hierarchical display of the different rat strains as derived from the parental strains.",
"domains": [
"Mutation",
"Genetic strain"
],
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457",
"name": "Rat Strain Ontology",
"publications": [
{
"doi": "10.1093/database/bat015",
"pubmed": "23603846",
"title": "PhenoMiner: quantitative phenotype curation at the rat genome database",
"year": 2013
},
{
"doi": "10.1186/2041-1480-4-36",
"pubmed": "24267899",
"title": "Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD",
"year": 2013
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.vb7991": {
"abbreviation": "OGG-MM",
"description": "OGG-Mm is the OGG Mus musculus (mouse) subset. The OGG (Ontology of Genes and Genomes) is a formal ontology of genes and genomes of biological organisms. OGG is developed by following OBO Foundry principles and aligning with the BFO top-level ontology.",
"domains": [
"Gene",
"Genome"
],
"homepage": "https://bitbucket.org/hegroup/ogg-mm",
"name": "Ontology of Genes and Genomes - Mouse",
"subjects": [
"Genomics"
]
},
"FAIRsharing.vbejb6": {
"abbreviation": "GFVO",
"description": "The Genomic Feature and Variation Ontology (GFVO) is modeled to represent genomic data using the Resource Description Format (RDF) or Linked Data using JSON (JSON-LD). The GFVO specifically addresses genomic data as it is regularly shared using the GFF3 (incl. FASTA), GTF, GVF and VCF file formats. GFVO simplifies data integration and enables linking of genomic annotations across datasets through common semantics of genomic types and relations. NOTE: GFVO in BioPortal is a simplified version without ontology imports and having class/property equivalences removed.",
"domains": [
"Genome annotation",
"Sequence feature",
"Sequence variant"
],
"homepage": "https://github.com/BioInterchange/Ontologies",
"license": "CC0-1.0",
"name": "Genomic Feature and Variation Ontology",
"publications": [
{
"doi": "10.7717/peerj.933",
"pubmed": "26019997",
"title": "GFVO: the Genomic Feature and Variation Ontology",
"year": 2015
}
],
"repository": "https://github.com/BioInterchange/Ontologies/issues",
"subjects": [
"Genomics"
]
},
"FAIRsharing.vc9xtj": {
"abbreviation": "GFO-BIO",
"description": "GFO-Bio is a biological core ontology based on the top-level ontology General Formal Ontology (GFO).",
"homepage": "http://www.onto-med.de/ontologies/gfo-bio/index.jsp",
"name": "General Formal Ontology: Biology",
"subjects": [
"Life Science"
]
},
"FAIRsharing.vdenk6": {
"abbreviation": "PHYLONT",
"description": "Ontology for Phylogenetic Analysis",
"domains": [
"Mathematical model",
"Evolution"
],
"homepage": "http://bioportal.bioontology.org/ontologies/PHYLONT",
"name": "Phylogenetic Ontology",
"subjects": [
"Phylogenetics"
]
},
"FAIRsharing.vekcbe": {
"abbreviation": "HIVO004",
"description": "This ontology does not appear to have a project homepage, and complete metadata cannot be found. Please get in touch with us if you have any information.",
"homepage": "https://bioportal.bioontology.org/ontologies/HIVO004",
"name": "HIVOntologymain.owl",
"subjects": [
"Infectious Disease Medicine",
"Virology"
]
},
"FAIRsharing.vgw1m6": {
"abbreviation": "NIFSTD",
"contact": {
"email": "tgbugs@gmail.com",
"name": "Tom Gillespie",
"orcid": "0000-0002-7509-4801"
},
"description": "NIF Standard ontology (NIFSTD) is a core component of Neuroscience Information Framework (NIF) project (http://neuinfo.org), a semantically enhanced portal for accessing and integrating neuroscience data, tools and information. NIFSTD includes a set of modular ontologies that provide a comprehensive collection of terminologies to describe neuroscience data and resources.",
"homepage": "http://ontology.neuinfo.org",
"license": "CC-BY-4.0",
"name": "Neuroscience Information Framework Standard Ontology",
"publications": [
{
"doi": "10.1007/s12021-008-9032-z",
"pubmed": "18975148",
"title": "The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience",
"year": 2008
}
],
"subjects": [
"Neuroscience"
]
},
"FAIRsharing.vgx074": {
"abbreviation": "MDDB",
"description": "Master Drug Data Base provides comprehensive and current drug information from a single source. The resource provides pricing and descriptive drug information on name brand, generic, prescription and OTC medications, and herbal products. It includes industry standard identifiers for all brand and generic drugs on the market including National Drug Code (NDC), Universal Product Code (UPC) and Health Related Item (HRI) numbers.",
"domains": [
"Drug",
"Chemical entity",
"Approved drug"
],
"homepage": "http://bioportal.bioontology.org/ontologies/MDDB",
"name": "Master Drug Data Base Clinical Drugs",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.vh9jbb": {
"abbreviation": "OGI",
"description": "Using BFO (Basic Formal Ontology) as its upper-level ontology, the Ontology for Genetic Interval (OGI) represents gene as an entity with its 3D shape, topography, and primary DNA sequence as the foundation for its 3D structure. There is no official homepage for this resource, and it is not currently in active development. However, the maintainer has described it as available for use via BioPortal and OBO Foundry.",
"domains": [
"Molecular structure",
"Nucleic acid sequence",
"Deoxyribonucleic acid"
],
"homepage": "http://purl.bioontology.org/ontology/OGI",
"name": "Ontology for Genetic Interval",
"subjects": [
"Genetics",
"Life Science"
]
},
"FAIRsharing.vhgehd": {
"abbreviation": "SAO",
"description": "SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules.",
"domains": [
"Cell",
"Cellular component"
],
"homepage": "http://purl.bioontology.org/ontology/SAO",
"name": "Subcellular Anatomy Ontology",
"subjects": [
"Anatomy",
"Life Science"
]
},
"FAIRsharing.vm1x6q": {
"abbreviation": "MEDEON",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/MEDEON",
"name": "Medical Error Ontology",
"subjects": [
"Health Science"
]
},
"FAIRsharing.vm4688": {
"abbreviation": "RDL",
"description": "Record does not exist anymore: RDL. The record with identifier content 10.25504/FAIRsharing.vm4688 was invalid.",
"homepage": "http://bioportal.bioontology.org/ontologies/RDL",
"name": "RDL"
},
"FAIRsharing.vmsc5w": {
"abbreviation": "SD3",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Modeling and simulation"
],
"homepage": "http://bioportal.bioontology.org/ontologies/SD3",
"name": "Simulation Delivery and Documentation Deviations",
"subjects": [
"Medicine"
]
},
"FAIRsharing.vppyga": {
"abbreviation": "NCRO",
"description": "The NCRO is a reference ontology in the non-coding RNA (ncRNA) field, aiming to provide a common set of terms and relations that will facilitate the curation, analysis, exchange, sharing, and management of ncRNA structural, functional, and sequence data.",
"domains": [
"Non-coding RNA"
],
"homepage": "http://bioportal.bioontology.org/ontologies/NCRO",
"name": "Non-coding RNA Ontology",
"publications": [
{
"doi": "10.1186/s13326-016-0066-0",
"title": "The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology",
"year": 2016
}
],
"subjects": [
"Genomics"
]
},
"FAIRsharing.vpy0jx": {
"abbreviation": "KORO",
"description": "An ontology to define the parts of a Knowledge Object and their relations built using the Basic Formal Ontology and Information Artifact Ontology",
"domains": [
"Knowledge representation"
],
"homepage": "http://bioportal.bioontology.org/ontologies/KORO",
"name": "Knowledge Object Reference Ontology",
"publications": [
{
"doi": "10.1002/lrh2.10054",
"title": "The Knowledge Object Reference Ontology (KORO): A formalism to support management and sharing of computable biomedical knowledge for learning health systems",
"year": 2018
}
],
"subjects": [
"Knowledge and Information Systems"
]
},
"FAIRsharing.vq28qp": {
"abbreviation": "PCO",
"contact": {
"email": "rlwalls2008@gmail.com",
"name": "Ramona Walls",
"orcid": "0000-0001-8815-0078"
},
"description": "Population and Community Ontology (PCO) is an ontology standard for describing the collective and interacting species of any taxa such as humans or plants. PCO has useful application in community health care, plant pathology, behavioral studies, sociology, and ecology. The PCO is compliant with the Basic Formal Ontology (BFO) and is designed to be compatible with other OBO Foundry ontologies.",
"domains": [
"Evolution"
],
"homepage": "https://github.com/PopulationAndCommunityOntology/pco",
"license": "CC0-1.0",
"name": "Population and Community Ontology",
"repository": "https://github.com/PopulationAndCommunityOntology/pco/issues",
"subjects": [
"Ecology",
"Biodiversity",
"Community Care",
"Social and Behavioural Science",
"Population Genetics"
]
},
"FAIRsharing.vv9tsb": {
"abbreviation": "ENTITYCANDIDATES",
"description": "Record does not exist anymore: ISO-15926-2_2003_entityMembershipCandidates. The record with identifier content 10.25504/FAIRsharing.vv9tsb was invalid.",
"homepage": "http://bioportal.bioontology.org/ontologies/ENTITYCANDIDATES",
"name": "ISO-15926-2_2003_entityMembershipCandidates"
},
"FAIRsharing.vxpUJ6": {
"abbreviation": "OHPI",
"contact": {
"email": "edong@umich.edu",
"name": "Edison Ong",
"orcid": "0000-0002-5159-414X"
},
"description": "OHPI is a community-driven ontology of host-pathogen interactions (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs in the Victors database become less virulence inside a host organism or host cells. It is also developed to represent manually curated HPI knowledge available in the PHIDIAS resource.",
"domains": [
"Pathogen",
"Host",
"Infection"
],
"homepage": "https://github.com/OHPI/ohpi",
"license": "CC-BY-4.0",
"name": "Ontology of Host-Pathogen Interactions",
"publications": [
{
"doi": "10.1093/nar/gky999",
"pubmed": "30365026",
"title": "Victors: a web-based knowledge base of virulence factors in human and animal pathogens",
"year": 2018
}
],
"repository": "https://github.com/OHPI/ohpi/issues",
"subjects": [
"Bioinformatics",
"Biomedical Science"
]
},
"FAIRsharing.vxyt0f": {
"abbreviation": "LiPrO",
"description": "Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied. The ontology describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL).",
"domains": [
"Lipid"
],
"homepage": "http://purl.bioontology.org/ontology/LiPrO",
"name": "Lipid Ontology",
"publications": [
{
"doi": "10.1186/1471-2105-9-s1-s5",
"pubmed": "18315858",
"title": "Towards ontology-driven navigation of the lipid bibliosphere",
"year": 2008
}
],
"subjects": [
"Biochemistry",
"Life Science"
]
},
"FAIRsharing.vy0p71": {
"abbreviation": "NPO",
"contact": {
"email": "nathan.baker@pnl.gov",
"name": "Nathan Baker",
"orcid": "0000-0002-5892-6506"
},
"description": "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.",
"domains": [
"Molecular entity",
"Nanoparticle",
"Structure"
],
"homepage": "http://www.nano-ontology.org",
"name": "NanoParticle Ontology",
"publications": [
{
"doi": "10.1016/j.jbi.2010.03.001",
"pubmed": "20211274",
"title": "NanoParticle Ontology for cancer nanotechnology research",
"year": 2010
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.vywjrq": {
"abbreviation": "NEWT",
"description": "While the original homepage was http://www.ebi.ac.uk/newt/, this link no longer works as NEWT is deprecated. Therefore, to have a valid homepage, a link has been provided to the resource that should be used instead.",
"domains": [
"Taxonomic classification"
],
"homepage": "http://www.uniprot.org/taxonomy/",
"name": "New Taxonomy database",
"publications": [
{
"doi": "10.1093/nar/gkg516",
"pubmed": "12824428",
"title": "NEWT, a new taxonomy portal",
"year": 2003
}
],
"subjects": [
"Taxonomy",
"Life Science"
]
},
"FAIRsharing.vzrsab": {
"abbreviation": "Uniprot Tisslist",
"description": "The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues in the \"TISSUE\" topic of the RC line type. It also contains cross-references to other ontologies where tissue types are specified.",
"domains": [
"Organ",
"Tissue"
],
"homepage": "https://www.uniprot.org/docs/tisslist",
"license": "CC-BY-4.0",
"name": "Uniprot Tissues controlled vocabulary",
"subjects": [
"Life Science"
]
},
"FAIRsharing.w2mrnx": {
"abbreviation": "CABRO",
"description": "CABRO is a web ontology for the semantic representation of the computer assisted brain trauma rehabilitation domain. This research area employs the use of robotic devices, adaptation software and machine learning to facilitate interactive, adaptive and personalized rehabilitation care, patient monitoring and assisted living.",
"domains": [
"Monitoring",
"Brain",
"Injury"
],
"homepage": "http://bioportal.bioontology.org/ontologies/CABRO",
"name": "Computer Assisted Brain Injury Rehabilitation Ontology",
"publications": [
{
"pubmed": "23823389",
"title": "A web ontology for brain trauma patient computer-assisted rehabilitation",
"year": 2013
}
],
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.w4tncg": {
"abbreviation": "RXNO",
"description": "The Name Reaction Ontology (RXNO) connects organic name reactions such as the Diels-Alder cyclization and the Cannizzaro reaction to their roles in organic synthesis.",
"domains": [
"Reaction data"
],
"homepage": "https://github.com/rsc-ontologies/rxno/",
"license": "CC-BY-4.0",
"name": "Name Reaction Ontology",
"subjects": [
"Molecular Chemistry"
]
},
"FAIRsharing.w4x6n4": {
"abbreviation": "OVAE",
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqunh He",
"orcid": "0000-0001-9189-9661"
},
"description": "The Ontology of Vaccine Adverse Events (OVAE) is a biomedical ontology in the area of vaccine adverse events. While they are extremely useful in decreasing infection prevalence in human populations, vaccines may also induce some unintended adverse events. As vaccine usage increases, the risk of adverse events proportionally increases. To protect public health, it is necessary to represent, study, and analyze various vaccine adverse events (VAES). Two existing ontologies are closely related to the VAE studies. The Ontology of Adverse Events (OAE) is a community-based biomedical ontology in the area of adverse events. The Vaccine Ontology (VO) represents various vaccines, vaccine components, and vaccinations. Both OAE and VO are OBO Foundry candidate ontologies and are developed by following the OBO Foundry principles. To better represent various VAEs and support vaccine safety study, we developed the Ontology of Vaccine Adverse Events (OVAE) as an extension of the biomedical ontologies OAE and VO.",
"domains": [
"Adverse Reaction",
"Vaccine"
],
"homepage": "https://github.com/OVAE-Ontology/ovae",
"license": "Apache 2.0 License",
"name": "Ontology of Vaccine Adverse Events",
"publications": [
{
"doi": "10.1186/2041-1480-4-40",
"pubmed": "24279920",
"title": "The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines",
"year": 2013
}
],
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.w5kj3q": {
"contact": {
"email": "peteremidford@yahoo.com",
"name": "Peter Midford",
"orcid": "0000-0001-6512-3296"
},
"description": "A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms. An ontology for Loggerhead sea turtle (Caretta caretta) nesting behavior, based on the published ethogram of Hailman and Elowson.",
"domains": [
"Behavior"
],
"homepage": "http://obofoundry.org/ontology/loggerhead.html",
"name": "Loggerhead Nesting Ontology",
"publications": [
{
"doi": "10.1093/bioinformatics/bth433",
"pubmed": "15284105",
"title": "Ontologies for behavior",
"year": 2004
}
],
"subjects": [
"Behavioural Biology",
"Life Science"
]
},
"FAIRsharing.w5ntfd": {
"abbreviation": "DrOn",
"contact": {
"email": "hoganwr@gmail.com",
"name": "William Hogan",
"orcid": "0000-0002-9881-1017"
},
"description": "An ontology of drug products and packaged drug products.",
"domains": [
"Drug",
"Small molecule",
"Approved drug"
],
"homepage": "https://github.com/mcwdsi/dron",
"license": "CC-BY-4.0",
"name": "The Drug Ontology",
"publications": [
{
"doi": "10.1186/s13326-016-0048-2",
"pubmed": "27096073",
"title": "An accurate and precise representation of drug ingredients",
"year": 2016
},
{
"doi": "10.1186/s13326-017-0121-5",
"pubmed": "28253937",
"title": "Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request",
"year": 2017
},
{
"doi": "10.1186/2041-1480-4-44",
"pubmed": "24345026",
"title": "Building a drug ontology based on RxNorm and other sources",
"year": 2013
}
],
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.w69t6r": {
"abbreviation": "TO",
"contact": {
"email": "cooperl@science.oregonstate.edu",
"name": "Laurel Cooper",
"orcid": "0000-0002-6379-8932"
},
"description": "A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part. The TO is part of the Planteome Project.",
"domains": [
"Phenotype",
"Structure",
"Life cycle"
],
"homepage": "http://browser.planteome.org/amigo/term/TO:0000387#display-lineage-tab",
"license": "CC-BY-4.0",
"name": "Plant Trait Ontology",
"publications": [
{
"doi": "10.1093/nar/gkx1152",
"pubmed": "29186578",
"title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics",
"year": 2017
}
],
"repository": "https://github.com/Planteome/plant-trait-ontology",
"subjects": [
"Botany"
]
},
"FAIRsharing.w7a76x": {
"abbreviation": "EO",
"description": "EO is a structured, controlled vocabulary for the representation of plant environmental conditions. EO has now been replaced by PECO. If you are using classes like EO:nnnnnn then you should be able to substitute this for PECO:nnnnnn, as all of the numeric parts of the ID are preserved. For a more robust mechanism, peco.obo contains alt_ids, and peco.owl contains the equivalent replaced_by assertions, which point from an obsoleted EO class to the corresponding PECO class.",
"homepage": "http://browser.planteome.org/amigo/term/EO:0007359",
"license": "CC-BY-4.0",
"name": "Plant Environmental Ontology",
"subjects": [
"Botany",
"Environmental Science"
]
},
"FAIRsharing.w7bw2y": {
"abbreviation": "EOL",
"description": "The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems.",
"homepage": "http://www.atol-ontology.com/en/eol-2/",
"license": "CC-BY-4.0",
"name": "Environment Ontology for Livestock",
"subjects": [
"Environmental Science",
"Animal Husbandry",
"Agriculture"
],
"user_defined_tags": [
"Livestock",
"Species-environment interaction"
]
},
"FAIRsharing.w7kfdn": {
"abbreviation": "EP",
"contact": {
"email": "rwinslow@jhu.edu",
"name": "Raimond L. Winslow",
"orcid": "0000-0003-1719-1651"
},
"description": "The Cardiac Electrophysiology Ontology contains terms describing single-channel electrophysiological experiments and data obtained using voltage-clamp, current clamp and fluorescence imaging techniques applied at the cell level and multi-channel fluorescence imaging techniques applied at the cell, tissue and whole heart levels. This tool is part of the Cardiovascular Research Grid project (http://wiki.cvrgrid.org/index.php/Main_Page) which is part funded by the NIH. ",
"domains": [
"Experimental measurement",
"Protocol",
"Study design",
"Experimentally determined",
"Cardiovascular disease",
"Electrocardiography"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1142",
"name": "Cardiac Electrophysiology Ontology",
"subjects": [
"Biomedical Science",
"Electrophysiology"
]
},
"FAIRsharing.w8g777": {
"abbreviation": "HINO",
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun He",
"orcid": "0000-0001-9189-9661"
},
"description": "The Human Interaction Network Ontology (HINO) is an INO extension for the domain of human interaction networks. It has incorporated Reactome reactions and pathways. Like INO, HINO aligns with BFO. HINO is developed following the OBO Foundry principles. Please note that the homepage listed is an indirect homepage only, as no project-specific homepage could be found.",
"domains": [
"Network model",
"Molecular interaction",
"Pathway model"
],
"homepage": "http://www.hegroup.org/onenettheory.html",
"name": "Human Interaction Network Ontology",
"subjects": [
"Life Science"
]
},
"FAIRsharing.w9jvbt": {
"abbreviation": "TEDDY",
"description": "The TErminology for the Description of DYnamics (TEDDY) project aims to provide an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.",
"domains": [
"Modeling and simulation"
],
"homepage": "http://co.mbine.org/standards/teddy",
"name": "TErminology for the Description of DYnamics",
"publications": [
{
"doi": "10.1038/msb.2011.77",
"pubmed": "22027554",
"title": "Controlled vocabularies and semantics in systems biology",
"year": 2011
}
],
"subjects": [
"Neurophysiology",
"Synthetic Biology",
"Systems Biology"
]
},
"FAIRsharing.wcfkac": {
"abbreviation": "Field",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/1369",
"name": "PhysicalFields",
"subjects": [
"Physics"
]
},
"FAIRsharing.wcpd6f": {
"abbreviation": "BFO",
"description": "The Basic Formal Ontology (BFO, also known via its ISO label as 'ISO/IEC 21838-2:2021 Information technology β Top-level ontologies (TLO) β Part 2: Basic Formal Ontology (BFO)') is an ontology that is conformant to the requirements specified for top-level ontologies in ISO/IEC 21838β1. BFO is a small, upper level ontology that is designed for use in supporting information retrieval, analysis and integration in scientific and other domains. BFO is a genuine upper ontology. Thus it does not contain physical, chemical, biological or other terms which would properly fall within the coverage domains of the special sciences. BFO is used by more than 250 ontology-driven endeavors throughout the world. ",
"domains": [
"Data retrieval"
],
"homepage": "https://www.iso.org/standard/74572.html",
"license": "CC-BY-4.0",
"name": "Basic Formal Ontology",
"repository": "https://github.com/bfo-ontology/BFO",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.wd68xv": {
"abbreviation": "BRCT",
"contact": {
"email": "erfan.younesi@scai.fraunhofer.de",
"name": "Erfan Younesi",
"orcid": "0000-0001-8793-2692"
},
"description": "The Brain Region and Cell Type terminology (BRCT) describes brain anatomy with a top-down granularity, from gross regions to cell types. This resource has been created for use in the IMI-funded AETIONOMY project (www.aetionomy.org).",
"domains": [
"Neuron",
"Brain"
],
"homepage": "http://bioportal.bioontology.org/ontologies/BRCT",
"name": "Brain Region & Cell Type Terminology",
"subjects": [
"Anatomy",
"Neurobiology",
"Biomedical Science"
]
},
"FAIRsharing.wd8j2q": {
"abbreviation": "bibliotek-o",
"description": "bibliotek-o is an ontology framework for modeling bibliographic metadata based on the Library of Congress BIBFRAME ontology. It includes: the bibliotek-o ontology, which defines extensions and modifications to BIBFRAME and is intended to be used as a supplement to the core BIBFRAME ontology; a set of external ontology fragments (including BIBFRAME) intended for use with the bibliotek-o ontology; and a data model and application profile - i.e., a set of recommended models and patterns for expressing bibliographic metadata using BIBFRAME, the bibliotek-o ontology, and other external ontologies. bibliotek-o 2017-07-06 Release of Version 1.1.0 will remain frozen until further notice.",
"domains": [
"Citation",
"Bibliography"
],
"homepage": "https://github.com/ld4l-labs/bibliotek-o",
"license": "CC0-1.0",
"name": "bibliotek-o",
"repository": "https://github.com/ld4l-labs/bibliotek-o",
"subjects": [
"Computer Science",
"Subject Agnostic"
]
},
"FAIRsharing.wf28wm": {
"abbreviation": "UP",
"description": "The taxonomy database that is maintained by the UniProt group is based on the NCBI taxonomy database, which is supplemented with data specific to the UniProt Knowledgebase (UniProtKB). While the NCBI taxonomy is updated daily to be in sync with GenBank/EMBL-Bank/DDBJ, the UniProt taxonomy is updated only at UniProt releases to be in sync with UniProtKB. It may therefore happen that for the time period of a UniProt release, you can find new taxa at the NCBI that are not yet in UniProt (and vice versa for deleted taxa). Species with manually annotated and reviewed protein sequences in the Swiss-Prot section of UniProtKB are named according to UniProt nomenclature. In particular, we have adopted a systematic convention for naming viral and bacterial strains and isolates.",
"domains": [
"Taxonomic classification"
],
"homepage": "http://www.uniprot.org/taxonomy/",
"license": "CC-BY-4.0",
"name": "UniProt Taxonomy",
"subjects": [
"Biology"
]
},
"FAIRsharing.wfyvvz": {
"abbreviation": "APATREATMENT",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Treatment"
],
"homepage": "http://bioportal.bioontology.org/ontologies/APATREATMENT",
"name": "APA Treatment Cluster",
"subjects": [
"Medicine"
]
},
"FAIRsharing.wgfrmg": {
"abbreviation": "CO",
"contact": {
"email": "earnaud@cgiar.org",
"name": "Elizabeth Arnaud",
"orcid": "0000-0002-6020-5919"
},
"description": "Created in 2008 by the CGIAR, the Crop Ontology (CO; http://www.cropontology.org) is an essential source of traits and variables to support the standardization of the breeding databases such as the Integrated Breeding Platformβs BMS (IBP; https://www.integratedbreeding.net/) and the Boyce Thompson Instituteβs Breedbase (https://breedbase.org/) (Arnaud et al., 2020). By providing descriptions of agronomic, morphological, physiological, quality, and stress traits along with their definitions and relationships, also including a standard nomenclature for composing the variables, the CO enables digital capture and aggregation of crop trait data, as well as comparison across projects and locations (Shrestha et al, 2012). The crop ontologies follow a conceptual model that defines a phenotypic variable as a combination of a trait, a method and a scale. This model aims at supporting the creation and management of breedersβ field books and the generation of annotated trial data. Annotated data are interpretable, interoperable and reusable. The development of a crop-specific ontology is a community-driven effort which is usually coordinated by a curator (or curators) nominated from within the community itself. COβs Traits that are properly described following the guidelines are progressively mapped to the Planteome species-neutral Trait Ontology (TO) maintained by Oregon State University.",
"domains": [
"Phenotype"
],
"homepage": "http://www.cropontology.org/",
"license": "CC-BY-4.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBCZz09IiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--776cb0c3be592f850fc0c898de73963446bb0785/Capture%20d%E2%80%99e%CC%81cran%202022-01-26%20a%CC%80%2013.41.07.png?disposition=inline",
"name": "Crop Ontology",
"publications": [
{
"doi": "10.1093/aobpla/plq008",
"pubmed": "22476066",
"title": "Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature",
"year": 2010
},
{
"doi": "10.3389/fphys.2012.00326",
"pubmed": "22934074",
"title": "Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice",
"year": 2012
}
],
"subjects": [
"Anatomy",
"Plant Breeding",
"Agriculture"
],
"user_defined_tags": [
"Metadata standardization",
"Plant Phenotypes and Traits"
]
},
"FAIRsharing.wkdjpb": {
"abbreviation": "GAZ",
"description": "A controlled vocabulary following ontological rules that describes named geographical locations. GAZ represents a first step towards an open source gazetteer, constructed on ontological principles, that describes places and place names and the relations between them.",
"domains": [
"Geographical location"
],
"homepage": "http://environmentontology.github.io/gaz/",
"license": "CC0-1.0",
"name": "Gazetteer",
"subjects": [
"Environmental Science"
]
},
"FAIRsharing.wp0134": {
"abbreviation": "CAO",
"description": "CAO ontology is designed for supporting the COG enrichment study by using Fisher's exact test. It is used for the ontology based application for statistical analysis on COG db.",
"domains": [
"Annotation",
"Protein",
"Transcript",
"Gene",
"Amino acid sequence",
"Orthologous"
],
"homepage": "http://sourceforge.net/projects/cao/",
"name": "Clusters of Orthologous Groups (COG) Analysis Ontology",
"publications": [
{
"doi": "10.1126/science.278.5338.631",
"pubmed": "9381173",
"title": "A genomic perspective on protein families",
"year": 1997
}
],
"subjects": [
"Genetics",
"Phylogenetics",
"Life Science"
]
},
"FAIRsharing.wpxab1": {
"abbreviation": "CPT",
"description": "Current Procedural Terminology is a medical nomenclature used to report medical procedures and services under public and private health insurance programs.",
"homepage": "https://www.ama-assn.org/practice-management/cpt/ama-cpt-licensing-overview",
"name": "Current Procedural Terminology",
"publications": [
{
"doi": "10.1136/neurintsurg-2014-011156",
"pubmed": "24589819",
"title": "Current procedural terminology; a primer",
"year": 2014
},
{
"doi": "10.1016/j.jacr.2007.10.004",
"pubmed": "18359442",
"title": "CPT: an open system that describes all that you do",
"year": 2008
}
],
"subjects": [
"Medicine",
"Health Science",
"Biomedical Science"
]
},
"FAIRsharing.wqy605": {
"abbreviation": "OMV",
"description": "A standard for ontology metadata; a vocabulary of terms and definitions describing ontologies which specifies reusability-enhancing ontology features for human and machine processing purposes.",
"homepage": "http://omv2.sourceforge.net/index.html",
"name": "Ontology Metadata Vocabulary",
"subjects": [
"Subject Agnostic"
],
"user_defined_tags": [
"Metadata standardization"
]
},
"FAIRsharing.wsfk5z": {
"abbreviation": "ATOL",
"description": "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment. ATOL aims to: provide a reference ontology of phenotypic traits of farm animals for the international scientific and educational - communities, farmers, etc.; deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; represent traits as generic as possible for livestock vertebrates; make the ATOL ontology as operational as possible and closely related to measurement techniques; and structure the ontology in relation to animal production.",
"domains": [
"Phenotype"
],
"homepage": "http://www.atol-ontology.com/en/atol-2/",
"license": "CC-BY-4.0",
"name": "Animal Trait Ontology for Livestock",
"subjects": [
"Animal Husbandry",
"Agriculture",
"Life Science"
],
"user_defined_tags": [
"Livestock"
]
},
"FAIRsharing.wvpgwn": {
"abbreviation": "ECO",
"contact": {
"email": "mchibucos@som.umaryland.edu",
"name": "Marcos Chibucos",
"orcid": "0000-0001-9586-0780"
},
"description": "The Evidence and Conclusion Ontology (ECO) contains terms that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has function Y as supported by evidence Z). Capture of this information allows tracking of annotation provenance, establishment of quality control measures, and query of eviden",
"domains": [
"Evidence",
"Resource metadata",
"Biological sample annotation",
"Text mining",
"Assay",
"Curated information",
"Digital curation",
"Study design",
"Literature curation",
"Biocuration"
],
"homepage": "https://evidenceontology.org/",
"license": "CC0-1.0",
"name": "Evidence and Conclusion Ontology",
"publications": [
{
"doi": "10.1142/9789812704856_0019",
"pubmed": "14992503",
"title": "An evidence ontology for use in pathway/genome databases",
"year": 2004
},
{
"doi": "10.1093/nar/gky1036",
"pubmed": "30407590",
"title": "ECO, the Evidence & Conclusion Ontology: community standard for evidence information",
"year": 2018
},
{
"doi": "10.1007/978-1-4939-3743-1_18",
"pubmed": "27812948",
"title": "The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations",
"year": 2016
}
],
"repository": "https://github.com/evidenceontology/evidenceontology",
"subjects": [
"Computational Biology",
"Life Science"
]
},
"FAIRsharing.wwy1ns": {
"abbreviation": "FIX",
"description": "FIX consists of two ontologies: methods and properties (but not objects, which are subject of the chemical ontology). The methods are applied to study the properties. While this ontology is available via BioPortal and the OBO Foundry, we cannot find a home page or a publication for the resource, and the resource itself is no longer maintained.",
"domains": [
"Experimental measurement",
"Protocol"
],
"homepage": "http://purl.bioontology.org/ontology/FIX",
"name": "Physico-chemical methods and properties",
"subjects": [
"Chemistry"
]
},
"FAIRsharing.x05a9p": {
"abbreviation": "thealternativa",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/3037",
"name": "thesaurus alternativa",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.x13tv8": {
"abbreviation": "OBOE SBC",
"contact": {
"email": "mecum@nceas.ucsb.edu",
"name": "Bryce Mecum",
"orcid": "0000-0002-0381-3766"
},
"description": "Extensible Observation Ontology for the Santa Barbara Coastal Long Term Ecological Research project (SBC-LTER). OBOE SBC extends core concepts defined in the OBOE suite that are particular to the Santa Barbara Coastal Long Term Ecological Research project's data collection activities. These include specific measurement protocols, sites, etc. This is mean as a case study ontology for the Semtools project.",
"domains": [
"Protocol"
],
"homepage": "https://semtools.ecoinformatics.org/oboe/annotation-bake-off-sbc-oboe-extension-and-eml-datasets",
"name": "Santa Barbara Coastal Observation Ontology",
"subjects": [
"Environmental Science"
]
},
"FAIRsharing.x39h5y": {
"abbreviation": "XCO",
"contact": {
"email": "shimoyama@mcw.edu",
"name": "Mary Shimoyama",
"orcid": "0000-0003-1176-0796"
},
"description": "The Experimental Conditions Ontology is designed to represent the conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.",
"domains": [
"Experimental measurement",
"Assay",
"Protocol",
"Study design",
"Experimentally determined"
],
"homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000",
"license": "CC-BY-4.0",
"name": "Experimental Conditions Ontology",
"publications": [
{
"doi": "10.3389/fgene.2012.00087",
"pubmed": "22654893",
"title": "Three ontologies to define phenotype measurement data",
"year": 2012
}
],
"subjects": [
"Life Science",
"Biomedical Science"
],
"twitter": "ratgenome",
"user_defined_tags": [
"Experimental condition"
]
},
"FAIRsharing.x56jsy": {
"abbreviation": "FMA",
"description": "The Foundational Model of Anatomy Ontology (FMA) is an evolving computer-based knowledge source for biomedical informatics; it is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. Its ontological framework can be applied and extended to all other species",
"domains": [
"Phenotype",
"Brain imaging"
],
"homepage": "http://si.washington.edu/projects/fma",
"license": "CC-BY-3.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBYTg9IiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--16f323877b0cea5b9b3df9ea964ed441ad10cff1/fma.png?disposition=inline",
"name": "Foundational Model of Anatomy",
"publications": [
{
"doi": "10.1016/j.jbi.2003.11.007",
"pubmed": "14759820",
"title": "A reference ontology for biomedical informatics: the Foundational Model of Anatomy",
"year": 2004
},
{
"doi": "10.1016/j.artmed.2016.04.003",
"pubmed": "27235801",
"title": "From frames to OWL2: Converting the Foundational Model of Anatomy",
"year": 2016
}
],
"subjects": [
"Anatomy",
"Radiology",
"Biomedical Science"
]
},
"FAIRsharing.x68yjk": {
"abbreviation": "CARRE",
"description": "The βcoreβ of the CARRE Risk Factor Ontology is the semantic representation of the CARRE data model for risk (D.2.2), intended to represent current medical knowledge regarding cardiorenal risk factors. This core relates to public data; that is to say, data from the medical literature regarding conditions, genetics, demographics and the environment, how these factors interact and the studies and evidence quality relating to their interactions. Please note that, while available, this resource has not been updated since 2014.",
"homepage": "https://www.carre-project.eu/innovation/risk-factor-ontology/",
"name": "CARRE Risk Factor ontology",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.x6sgd3": {
"abbreviation": "Body System",
"contact": {
"email": "swt@stanford.edu",
"name": "Samson Tu",
"orcid": "0000-0002-0295-7821"
},
"description": "This is a set of body-system terms used in the ICD 11 revision",
"homepage": "http://bioportal.bioontology.org/ontologies/1487",
"name": "Body System",
"subjects": [
"Anatomy",
"Biomedical Science"
]
},
"FAIRsharing.x81wz8": {
"abbreviation": "HCPCS",
"description": "Each year, in the United States, health care insurers process over 5 billion claims for payment. For Medicare and other health insurance programs to ensure that these claims are processed in an orderly and consistent manner, standardized coding systems are essential. The HCPCS is divided into two principal subsystems, referred to as level I and level II of the HCPCS. Level I of the HCPCS is comprised of CPT (Current Procedural Terminology), a numeric coding system maintained by the American Medical Association (AMA). Level II of the HCPCS is a standardized coding system that is used primarily to identify products, supplies, and services not included in the CPT codes, such as ambulance services and durable medical equipment, prosthetics, orthotics, and supplies (DMEPOS) when used outside a physician's office.",
"homepage": "https://www.cms.gov/medicare/coding/medhcpcsgeninfo/index.html",
"name": "Healthcare Common Procedure Coding System",
"subjects": [
"Business Administration",
"Biomedical Science"
]
},
"FAIRsharing.x9s8e": {
"abbreviation": "RPO",
"description": "The Resource of Asian Primary Immunodeficiency Diseases (RAPID) Phenotype Ontology (RPO) is a controlled vocabulary for phenotypic terms for primary immunodeficiency diseases (PIDs) used within the RAPID database. It is intended to facilitate global sharing and free exchange of PID data with usersβ communities. Please note that, while available via BioPortal, the RAPID phenotype ontology is no longer being updated.",
"domains": [
"Phenotype",
"Immune system"
],
"homepage": "https://bioportal.bioontology.org/ontologies/RPO",
"name": "Resource of Asian Primary Immunodeficiency Diseases Phenotype Ontology",
"subjects": [
"Immunogenetics",
"Immunology"
]
},
"FAIRsharing.xeh248": {
"abbreviation": "OGDI",
"description": "This ontology is used to model scientific investigation, especially Genome-Wide Association Studies (GWAS), to discover genetic susceptibility factors to disease, such as Diabetes. It models the genetic variants, polymorphisms, statistical measurement, populations and other elements that are essential to determine a genetic susceptibility factor in GWAS study. It must be used with other two ontologies, in the case of Diabetes: Ontology of Geographical Region (OGR) and Ontology of Glucose Metabolism (OGMD). Together, these three ontologies form the Ontology for Genetic Susceptibility Factor (OGSF), which is the project where information about this ontology is stored.",
"domains": [
"Genetic polymorphism",
"Assay",
"Genome",
"Sequence variant",
"Genome-wide association study",
"Diabetes mellitus"
],
"homepage": "https://code.google.com/archive/p/ogsf/",
"name": "Ontology for Genetic Disease Investigations",
"publications": [
{
"doi": "10.1186/2041-1480-5-19",
"pubmed": "24963371",
"title": "The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events",
"year": 2014
}
],
"subjects": [
"Statistics",
"Biomedical Science"
]
},
"FAIRsharing.xfje21": {
"abbreviation": "MSV",
"description": "An ontology for metagenome sample metadata. This ontology mainly defines predicates.",
"domains": [
"Metagenome"
],
"homepage": "http://mdb.bio.titech.ac.jp/msv",
"name": "Metagenome Sample Vocabulary",
"subjects": [
"Metagenomics"
]
},
"FAIRsharing.xg0685": {
"contact": {
"email": "amrapali.j.zaveri@gmail.com",
"name": "Amrapali Zaveri",
"orcid": "0000-0003-3239-4588"
},
"description": "The Diagnostic Ontology is a computational diagnostic ontology containing 91 elements, including classes and sub-classes, which are required to conduct Systematic Reviews - Meta Analysis (SR-MA) for diagnostic studies, which will assist in standardized reporting of diagnostic articles. SR-MA are studies that aggregate several studies to come to one conclusion for a particular research question.",
"domains": [
"Systematic review",
"Diagnosis"
],
"homepage": "http://bioportal.bioontology.org/ontologies/3013",
"license": "CC BY-SA 3.0",
"name": "Diagnostic Ontology",
"publications": [
{
"doi": "10.1371/journal.pone.0036759",
"pubmed": "22629329",
"title": "Center of excellence in research reporting in neurosurgery--diagnostic ontology",
"year": 2012
}
],
"subjects": [
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.xhpn6z": {
"abbreviation": "BSAO",
"contact": {
"email": "contact@bioself-communication.com",
"name": "Delphine DAUGA",
"orcid": "0000-0003-3152-1194"
},
"description": "The Botryllus schlosseri Ontology of Development and Anatomy (BODA) is the first ontology describing the anatomy and the development of Botryllus schlosseri. It is based on studies that investigate the anatomy, blastogenesis and regeneration of this organism. BODA features allow the users to easily search and identify anatomical structures in the colony, to define the developmental stage, and to follow the morphogenetic events of a tissue and/or organ of interest throughout asexual development.",
"domains": [
"Cell",
"Life cycle",
"Life cycle stage"
],
"homepage": "http://bioportal.bioontology.org/ontologies/BSAO",
"name": "Botryllus schlosseri anatomy and development ontology",
"publications": [
{
"doi": "10.1371/journal.pone.0096434",
"pubmed": "24789338",
"title": "Ontology for the asexual development and anatomy of the colonial chordate Botryllus schlosseri",
"year": 2014
}
],
"subjects": [
"Anatomy",
"Developmental Biology",
"Life Science"
],
"user_defined_tags": [
"Asexual reproduction",
"Morphogenesis"
]
},
"FAIRsharing.xhwrnr": {
"abbreviation": "CCO",
"contact": {
"email": "kuiper@bio.ntnu.no",
"name": "Martin Kuiper",
"orcid": "0000-0002-1171-9876"
},
"description": "CCO contains genes, proteins, interactions (comprising genes or proteins that participate in them), processes from the cell cycle subtree of GO, molecular functions (GO), taxa, and ontological constructs (like an upper level ontology and relationships) to stick everything together.",
"domains": [
"Cell",
"Molecular function",
"Cell cycle"
],
"homepage": "https://www.biogateway.eu/tools/#CCO",
"name": "Cell Cycle Ontology",
"publications": [
{
"doi": "10.1186/gb-2009-10-5-r58",
"pubmed": "19480664",
"title": "The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process",
"year": 2009
}
],
"subjects": [
"Functional Genomics",
"Genomics",
"Proteomics",
"Life Science"
]
},
"FAIRsharing.xj5egt": {
"abbreviation": "BIBFRAME",
"description": "Initiated by the Library of Congress, BIBFRAME provides a foundation for the future of bibliographic description, both on the web, and in the broader networked world. This site presents general information about the project, including presentations, FAQs, and links to working documents. In addition to being a replacement for MARC, BIBFRAME serves as a general model for expressing and connecting bibliographic data. A major focus of the initiative will be to determine a transition path for the MARC 21 formats while preserving a robust data exchange that has supported resource sharing and cataloging cost savings in recent decades.",
"domains": [
"Citation",
"Bibliography"
],
"homepage": "https://www.loc.gov/bibframe/",
"name": "BIBFRAME 2.0",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.xjj977": {
"abbreviation": "FLU",
"contact": {
"email": "burkesquires@gmail.com",
"name": "Burke Squires",
"orcid": "0000-0001-9666-6285"
},
"description": "The influenza ontology is an application ontology. Consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS).",
"domains": [
"Disease"
],
"homepage": "http://influenzaontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page",
"name": "Influenza Ontology",
"subjects": [
"Virology",
"Biomedical Science"
]
},
"FAIRsharing.xm7tkj": {
"abbreviation": "nmrCV",
"description": "nmrCV is a MSI-sanctioned NMR controlled vocabulary, created within the COSMOS EU project, to support the nmrML data standard for nuclear magnetic resonance data in metabolomics with standardized meaningful data descriptors. This CV is the successor of the (now deprecated) 'NMR-instrument specific component of metabolomics investigations' CV of 2006. This standard is currently financed via the PhenoMeNal EU project. It is a simple taxonomy build according to the same design principles as its role model artefact, the Mass Spec CV of PSI.",
"domains": [
"Molecular structure",
"Chemical structure",
"Metabolite",
"Nuclear Magnetic Resonance (NMR) spectroscopy",
"Chemical screen",
"Assay"
],
"homepage": "http://nmrml.org/cv/",
"license": "CC0-1.0",
"name": "Nuclear Magnetic Resonance Controlled Vocabulary",
"publications": [
{
"doi": "10.1038/nbt0807-846b",
"pubmed": "17687353",
"title": "The metabolomics standards initiative",
"year": 2007
},
{
"doi": "10.1021/acs.analchem.7b02795",
"pubmed": "29035042",
"title": "nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data",
"year": 2017
}
],
"repository": "https://github.com/nmrML/nmrML/tree/master/xml-schemata",
"subjects": [
"Chemistry",
"Metabolomics"
]
},
"FAIRsharing.xmmsmr": {
"abbreviation": "EGO",
"description": "The Epigenome Ontology (EGO) a biomedical ontology for integrative epigenome knowledge representation and data analysis.",
"homepage": "https://github.com/EGO-ontology",
"license": "CC0-1.0",
"name": "Epigenome Ontology",
"subjects": [
"Epigenomics"
]
},
"FAIRsharing.xn3pb3": {
"abbreviation": "VANDF",
"description": "Veterans Health Administration National Drug File is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies.",
"domains": [
"Drug",
"Drug interaction"
],
"homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/",
"name": "Veterans Health Administration National Drug File",
"publications": [
{
"pubmed": "12463886",
"title": "A semantic normal form for clinical drugs in the UMLS: early experiences with the VANDF",
"year": 2002
}
],
"subjects": [
"Pharmacology",
"Biomedical Science"
]
},
"FAIRsharing.xs4ge6": {
"abbreviation": "IDOBRU",
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun He",
"orcid": "0000-0001-9189-9661"
},
"description": "The Brucellosis Ontology is an extension of the Infectious Disease Ontology. It is a biomedical ontology describing the zoonotic disease brucellosis that is caused by Brucella, a facultative intracellular bacterium. The ontology is intended as an aid in brucellosis-related data standardization and integration.",
"domains": [
"Pathogen",
"Infection"
],
"homepage": "http://www.phidias.us/bbp/idobru/index.php",
"name": "Brucellosis Ontology",
"publications": [
{
"doi": "10.1186/2041-1480-2-9",
"pubmed": "22041276",
"title": "Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology",
"year": 2011
}
],
"subjects": [
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.xs6t67": {
"abbreviation": "FAO",
"contact": {
"email": "dinglis@stanford.edu",
"name": "Diane Inglis",
"orcid": "0000-0003-3166-4638"
},
"description": "A structured controlled vocabulary for the anatomy of fungi.",
"homepage": "https://github.com/obophenotype/fungal-anatomy-ontology",
"name": "Fungal Gross Anatomy Ontology",
"subjects": [
"Anatomy",
"Life Science",
"Microbiology"
]
},
"FAIRsharing.xvf5y3": {
"abbreviation": "DwC",
"description": "Darwin Core (DwC) is a vocabulary that includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing identifiers, labels, and definitions. The Darwin Core is primarily based on the observation, specimen and samples of taxa. The Darwin Core standard is comprised of one vocabulary (the Darwin Core vocabulary), and six associated documents. The vocabulary itself is composed of four term lists: Darwin Core terms borrowed from the Dublin Core legacy and terms namespace, Darwin Core IRI-value Term Analogs, and the core terms defined by Darwin Core.",
"domains": [
"Taxonomic classification",
"Biological sample annotation",
"Geographical location"
],
"homepage": "http://www.tdwg.org/standards/450",
"license": "https://creativecommons.org/licenses/by/3.0/us",
"name": "Darwin Core",
"publications": [
{
"doi": "10.1371/journal.pone.0029715",
"pubmed": "22238640",
"title": "Darwin Core: an evolving community-developed biodiversity data standard",
"year": 2012
},
{
"doi": "10.3897/bdj.2.e1039",
"pubmed": "24723785",
"title": "Linking multiple biodiversity informatics platforms with Darwin Core Archives",
"year": 2014
},
{
"doi": "10.1371/journal.pone.0102623",
"pubmed": "25099149",
"title": "The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet",
"year": 2014
}
],
"repository": "https://github.com/tdwg/dwc",
"subjects": [
"Biodiversity",
"Life Science"
]
},
"FAIRsharing.xx2wv5": {
"abbreviation": "PharmGKB-owl",
"description": "The PharmGKB Ontology imports genetic sequence data, collected in relational format, into the OWL, and aims to automate the process of updating the links between the ontology and data acquisition when the ontology changes. They have linked PharmGKB with data acquisition from a relational model of genetic sequence information.",
"homepage": "https://code.google.com/p/pharmgkb-owl/",
"name": "Pharmacogenomics Ontology",
"publications": [
{
"doi": "10.1385/1-59259-957-5:179",
"pubmed": "16100408",
"title": "PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base",
"year": 2005
}
],
"subjects": [
"Pharmacogenomics",
"Biomedical Science"
]
},
"FAIRsharing.xyj0nr": {
"abbreviation": "CogPO",
"description": "This ontology is used to describe the experimental conditions within cognitive/behavioral experiments, primarily in humans. CogPO is a framework for the formal representation of the cognitive paradigms used in behavioral experiments, driven by cognitive neuroscience and neuroimaging examples.",
"domains": [
"Imaging",
"Behavior",
"Cognition",
"Assay",
"Brain imaging"
],
"homepage": "http://www.cogpo.org",
"name": "Cognitive Paradigm Ontology",
"publications": [
{
"doi": "10.1007/s12021-011-9126-x",
"pubmed": "21643732",
"title": "The cognitive paradigm ontology: design and application",
"year": 2011
}
],
"subjects": [
"Neurobiology",
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.y0kqgt": {
"abbreviation": "LCMPT",
"description": "The Library of Congress Medium of Performance Thesaurus (LCMPT) for Music is a stand-alone vocabulary that provides terminology to describe the instruments, voices, etc., used in the performance of musical works. The core terms in LCMPT are based chiefly on existing LC subject headings (LCSH), but some additional terms that do not already appear in LCSH have also been included.",
"domains": [
"Classification"
],
"homepage": "https://id.loc.gov/authorities/performanceMediums.html",
"license": "https://www.loc.gov/legal",
"name": "Library of Congress Medium of Performance Thesaurus for Music",
"subjects": [
"Fine Arts",
"Musicology"
]
},
"FAIRsharing.y1mmbv": {
"abbreviation": "GenEpiO",
"description": "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research food-borne pathogens, infectious disease surveillance and outbreak investigations. This includes descriptions of the genomics, laboratory, clinical and epidemiological contextual information required to support data sharing and integration for food-borne infectious disease surveillance and outbreak investigations.",
"domains": [
"Food",
"Pathogen",
"Genome"
],
"homepage": "https://genepio.org/",
"license": "CC-BY-3.0",
"name": "Genomic Epidemiology Ontology",
"repository": "https://github.com/GenEpiO/genepio",
"subjects": [
"Genomics",
"Epidemiology"
]
},
"FAIRsharing.y2dt83": {
"abbreviation": "CBO",
"contact": {
"email": "JSluka@indiana.edu",
"name": "James P. Sluka",
"orcid": "0000-0002-5901-1404"
},
"description": "The Cell Behavior Ontology (CBO) describes multi-cell computational models. In particular to describe both the existential behaviors of cells (spatiality, growth, movement, adhesion, death, ...) and computational models of those behaviors.",
"domains": [
"Mathematical model",
"Cell",
"Cell adhesion"
],
"homepage": "http://cbo.biocomplexity.indiana.edu/cbo/",
"name": "Cell Behavior Ontology",
"publications": [
{
"doi": "10.1093/bioinformatics/btu210",
"pubmed": "24755304",
"title": "The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents",
"year": 2014
}
],
"subjects": [
"Life Science",
"Systems Biology"
]
},
"FAIRsharing.y2qkst": {
"abbreviation": "FBbt",
"contact": {
"email": "cp390@cam.ac.uk",
"name": "Clare Pilgrim",
"orcid": "0000-0002-1373-1705"
},
"description": "An ontology of the anatomy of Drosophila melanogaster. It can be used for annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotype and images. It was originally developed by FlyBase, who continue to maintain it and use it for curation.",
"domains": [
"Gene expression",
"Image",
"Phenotype",
"Life cycle stage"
],
"homepage": "http://flybase.org/vocabularies",
"license": "CC-BY-4.0",
"name": "Drosophila anatomy ontology",
"publications": [
{
"doi": "10.1093/nar/gkj068",
"pubmed": "16381917",
"title": "FlyBase: anatomical data, images and queries",
"year": 2005
},
{
"doi": "10.1186/2041-1480-4-32",
"pubmed": "24139062",
"title": "The Drosophila anatomy ontology",
"year": 2013
},
{
"doi": "10.1093/bioinformatics/bts113",
"pubmed": "22402613",
"title": "A strategy for building neuro-anatomy ontologies",
"year": 2012
},
{
"doi": "10.1093/bioinformatics/btr677",
"pubmed": "22180411",
"title": "The Virtual Fly Brain Browser and Query Interface",
"year": 2011
}
],
"repository": "https://github.com/FlyBase/drosophila-anatomy-developmental-ontology",
"subjects": [
"Anatomy",
"Developmental Biology",
"Life Science"
]
},
"FAIRsharing.y3vp4j": {
"abbreviation": "LDA",
"description": "Language terms used in the domain of autism. The language terms were obtained via text mining and automatic retrieval of terms from the corpus of PubMed abstracts.",
"domains": [
"Text mining",
"Autistic disorder",
"Language disorder",
"Natural language processing",
"Disease"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1398",
"name": "Ontology of Language Disorder in Autism",
"subjects": [
"Biomedical Science"
]
},
"FAIRsharing.y47s7f": {
"abbreviation": "ICNP",
"description": "The International Classification for Nursing Practice (INCP) was accepted by WHO within the WHO Family of International Classifications (FIC) to extend the coverage of the domain of nursing practice as an essential and complementary part of professional health services. ICNP classifies patient data and clinical activity in the domain of nursing and can be used for decision-making and policy development aimed at improving health status and health care delivery. ICNP can represent diagnoses, interventions, and outcomes. A number of subsets are available to provide precoordinated concepts for select health priorities, including nursing outcome indicators, paediatric pain management, palliative care, and partnering with patients and families to promote adherence to treatment.",
"domains": [
"Electronic health record",
"Patient care",
"Hospital",
"Nurse"
],
"homepage": "https://www.who.int/standards/classifications/other-classifications/international-classification-for-nursing-practice",
"name": "International Classification for Nursing Practice",
"publications": [
{
"doi": "10.3233/978-1-60750-909-7-45",
"pubmed": "15460220",
"title": "The International Classification For Nursing Practice",
"year": 2004
}
],
"subjects": [
"Clinical Studies",
"Primary Health Care",
"Biomedical Science"
]
},
"FAIRsharing.y4RpVy": {
"abbreviation": "DDI CVs",
"description": "The Data Documentation Initiative (DDI) Controlled Vocabularies Group (CVG) has created a set of controlled vocabularies (CVs) that can be used with DDI as well as for other purposes and applications. The DDI CVs are used to aid in the description and documentation of data in the social science research community. The published DDI-CVs work with both versions of the DDI specification (DDI-L and DDI-C).",
"homepage": "https://ddialliance.org/controlled-vocabularies",
"name": "Data Documentation Initiative Controlled Vocabularies",
"subjects": [
"Humanities and Social Science"
],
"twitter": "DDIAlliance"
},
"FAIRsharing.y4z3tx": {
"abbreviation": "CSO",
"description": "Ontology to describe general clinical studies.",
"domains": [
"Monitoring",
"Hospital"
],
"homepage": "http://bioportal.bioontology.org/ontologies/CSO",
"name": "Clinical Study Ontology",
"subjects": [
"Clinical Studies",
"Medical Informatics"
]
},
"FAIRsharing.y5jcwa": {
"abbreviation": "PhenX",
"description": "Standard measures related to complex diseases, phenotypic traits and environmental exposures.",
"domains": [
"Phenotype",
"Disease",
"Exposure"
],
"homepage": "https://www.phenx.org/",
"name": "PhenX Phenotypic Terms",
"publications": [
{
"doi": "10.1097/mol.0b013e3283377395",
"pubmed": "20154612",
"title": "PhenX: a toolkit for interdisciplinary genetics research",
"year": 2010
},
{
"doi": "10.1093/aje/kwr193",
"pubmed": "21749974",
"title": "The PhenX Toolkit: get the most from your measures",
"year": 2011
},
{
"doi": "10.1038/gim.2016.199",
"pubmed": "28079902",
"title": "PhenX measures for phenotyping rare genetic conditions",
"year": 2017
}
],
"subjects": [
"Environmental Science",
"Life Science",
"Biomedical Science"
]
},
"FAIRsharing.y9d8rt": {
"abbreviation": "CPTAC",
"description": "A basic ontology which describes the proteomics pipeline infrastructure for CPTAC project",
"domains": [
"Data acquisition",
"Data transformation",
"Protein"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1192",
"name": "Proteomics Pipeline Infrastructure for CPTAC",
"subjects": [
"Genomics",
"Proteomics",
"Life Science"
]
},
"FAIRsharing.yIYItV": {
"abbreviation": "TFClass Schema",
"contact": {
"email": "edgar.wingender@bioinf.med.uni-goettingen.de",
"name": "Edgar Wingender",
"orcid": "0000-0002-7729-8453"
},
"description": "The TFClass Schema is an identifier schema for classifying transcription factors according to a six-level schema, four of which are abstractions according to different criteria, while the fifth level represents TF genes and the sixth individual gene products. The first four levels of the TFClass schema are Superclass, Class, Family and Subfamily, with Subfamily an optional category. Two lower levels represent physical entities (i.e. genes and gene products) and have been termed Genera and Species (or \"molecular species\", to avoid confusion with biological species).",
"domains": [
"Expression data",
"Centrally registered identifier",
"Transcription factor"
],
"homepage": "http://www.edgar-wingender.de/TFClass_schema.html",
"name": "Transcription Factor Class Schema",
"publications": [
{
"doi": "10.1093/nar/gks1123",
"pubmed": "23180794",
"title": "TFClass: an expandable hierarchical classification of human transcription factors",
"year": 2012
}
],
"subjects": [
"Life Science",
"Transcriptomics"
]
},
"FAIRsharing.ya2wjp": {
"abbreviation": "IxnO",
"contact": {
"email": "cmattin@mdibl.org",
"name": "Carolyn Mattingly",
"orcid": "0000-0002-2146-9436"
},
"description": "The Interaction ontology (IxnO) was developed to enable curation of chemical-gene and chemical-protein interactions for the Comparative Toxicogenomics Database (CTD). CTD is a freely available resource that aims to promote understanding and novel hypothesis development about the effects of the environment on human health.",
"domains": [
"Chemical-disease association",
"Chemical-gene association"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1614",
"name": "Interaction Ontology",
"subjects": [
"Environmental Science",
"Medicine",
"Health Science",
"Biomedical Science"
]
},
"FAIRsharing.yc237s": {
"abbreviation": "MS2O",
"description": "The Multi-scale Multi-step ontology (MS2O) is an ontology to describe transformation processes. MS2O was created for an interdisciplinary project concerning transformation processes in food science. The use case concerns the production of stabilized micro-organisms performed at INRA (French National Institute for Agricultural Research). Experimental observations are available for some inputs of the production processes, at different steps and at a certain scale.",
"homepage": "http://dx.doi.org/10.15454/1.4502762931471938E12",
"license": "CC-BY-4.0",
"name": "Multi-Scale Multi-Step Ontology",
"publications": [
{
"doi": "10.1007/978-3-319-40985-6_13",
"title": "M2SO - A Multi-scale and Multi-step Ontology for Transformation Processes: Application to Micro-Organisms",
"year": 2016
}
],
"subjects": [
"Materials Engineering",
"Agricultural Engineering",
"Materials Science"
],
"user_defined_tags": [
"Processing"
]
},
"FAIRsharing.ydnwd9": {
"abbreviation": "OntoDT",
"contact": {
"email": "pance.panov@ijs.si",
"name": "Pance Panov",
"orcid": "0000-0002-7685-9140"
},
"description": "This ontology contains entities such as: datatype, datatype generator, datatype quality and others giving the possibility to represent arbitrary complex datatypes. This is an important fact for a general data mining ontology that wants to represent and query over modeling algorithms for mining structured data. The ontology was first developed under the OntoDM (Ontology of Data Mining is available at http://kt.ijs.si/panovp/OntoDM) ontology, but for generality and reuse purpose it was decided to export it as a separate ontology. Additionally, the OntoDT ontology is based on and ISO/IEC 11404 (http://www.iso.org/iso/catalogue_detail.htm?csnumber=39479) standard and can be reused used independently by any domain ontology that requires representation and reasoning about general purpose datatypes.",
"homepage": "http://www.ontodm.com/doku.php?id=ontodt",
"name": "Ontology of General Purpose Datatypes",
"publications": [
{
"doi": "10.1016/j.ins.2015.08.006",
"title": "Generic ontology of datatypes",
"year": 2016
}
],
"subjects": [
"Data Mining",
"Data Management",
"Life Science",
"Computer Science",
"Subject Agnostic"
],
"user_defined_tags": [
"data science"
]
},
"FAIRsharing.yecp83": {
"abbreviation": "SPD",
"contact": {
"email": "ramirez@macn.gov.ar",
"name": "Martin Ramirez",
"orcid": "0000-0002-0358-0130"
},
"description": "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).",
"domains": [
"Behavior"
],
"homepage": "https://github.com/obophenotype/spider-ontology",
"license": "CC-BY-3.0",
"name": "Spider Anatomy Ontology",
"publications": [
{
"doi": "10.3390/d11100202",
"title": "The Spider Anatomy Ontology (SPD)βA Versatile Tool to Link Anatomy with Cross-Disciplinary Data",
"year": 2019
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"FAIRsharing.yg0zpm": {
"abbreviation": "CPR",
"description": "A uniform core set of data elements (whose formal semantics are captured in OWL) for use in a Computer-Based Patient Record (CPR).",
"domains": [
"Electronic health record",
"Patient care"
],
"homepage": "https://code.google.com/archive/p/cpr-ontology/",
"license": "Apache 2.0 License",
"name": "Computer-based Patient Record Ontology",
"subjects": [
"Medicine",
"Biomedical Science",
"Medical Informatics"
]
},
"FAIRsharing.yhxj0x": {
"abbreviation": "APATANDT",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/APATANDT",
"name": "APA Tests and Testing cluster",
"subjects": [
"Psychology"
]
},
"FAIRsharing.yjr7et": {
"abbreviation": "ASDPTO",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"domains": [
"Autistic disorder"
],
"homepage": "http://bioportal.bioontology.org/ontologies/ASDPTO",
"name": "Autism Spectrum Disorder Phenotype Ontology",
"subjects": [
"Psychiatry"
],
"user_defined_tags": [
"neurology disease"
]
},
"FAIRsharing.ypfgeq": {
"abbreviation": "TMO",
"description": "This project focuses on the development of a high level patient-centric ontology for the pharmaceutical industry. The ontology should enable silos in discovery research, hypothesis management, experimental studies, compounds, formulation, drug development, market size, competitive data, population data, etc. to be brought together. This would enable scientists to answer new questions, and to answer existing scientific questions more quickly. This will help pharmaceutical companies to model patient-centric information, which is essential for the tailoring of drugs, and for early detection of compounds that may have sub-optimal safety profiles. The ontology should link to existing publicly available domain ontologies.",
"domains": [
"Drug"
],
"homepage": "https://www.w3.org/wiki/HCLSIG/PharmaOntology/Ontology",
"license": "CC-BY-3.0",
"name": "Translational Medicine Ontology",
"subjects": [
"Clinical Studies",
"Drug Development",
"Biomedical Science",
"Translational Medicine"
]
},
"FAIRsharing.ypkpgf": {
"abbreviation": "ISO-ANNOTATIONS",
"description": "This resource is no longer available because its underlying source material is not suitable for FAIRsharing: ISO-15926-2_2003_annotations. The record with identifier content 10.25504/FAIRsharing.ypkpgf was invalid.",
"domains": [
"Data retrieval"
],
"homepage": "http://bioportal.bioontology.org/ontologies/ISO-ANNOTATIONS",
"name": "ISO-15926-2_2003_annotations",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.ypqwvr": {
"abbreviation": "SCIO",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "https://bioportal.bioontology.org/ontologies/SCIO",
"name": "Spinal Cord Injury Ontology",
"subjects": [
"Life Science"
],
"user_defined_tags": [
"Spinal Cord",
"Spinal Cord Injury"
]
},
"FAIRsharing.yqn857": {
"abbreviation": "OArCS",
"description": "OArCS is a structural model for the description of anatomical features (morphemes) using ontologies. Its domain is the Arthropod ciruclatory system. This ontology has not been updated recently, and therefore has been marked as uncertain. Please get in touch with us if you have any information.",
"homepage": "https://github.com/aszool/oarcs",
"name": "Ontology of Arthropod Circulatory Systems",
"publications": [
{
"doi": "10.1093/sysbio/syw108",
"title": "The first organ-based free ontology for arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its integration into a novel formalization scheme for morphological descriptions",
"year": 2017
}
],
"subjects": [
"Anatomy",
"Angiology"
]
},
"FAIRsharing.yr6mb8": {
"abbreviation": "POL",
"description": "\"Pilot Ontology\" is a standard, specialising in the fields described under \"scope and data types\", below. Until this entry is claimed, more information on this project can be found at http://bioportal.bioontology.org/ontologies/1399. This text was generated automatically. If you work on the project responsible for \"Pilot Ontology\" then please consider helping us by claiming this record and updating it appropriately.",
"homepage": "http://bioportal.bioontology.org/ontologies/1399",
"name": "Pilot Ontology",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.ytfz9g": {
"abbreviation": "uni-ece",
"description": "This resource is no longer available because its underlying source material is not in scope for FAIRsharing.",
"homepage": "http://bioportal.bioontology.org/ontologies/3048",
"name": "uni-ece",
"subjects": [
"Subject Agnostic"
]
},
"FAIRsharing.z0p37e": {
"abbreviation": "OMRSE",
"contact": {
"email": "hoganwr@gmail.com",
"name": "William Hogan",
"orcid": "0000-0002-9881-1017"
},
"description": "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations. For more information on the social entities represented in OMRSE, please visit our wiki page or list of publications. OMRSE is designed to be a mid-level ontology that bridges the gap between BFO, which it reuses for its top-level hierarchy, and more specific domain or application ontologies. For this reason, we are always open to working with ontology developers who want to build interoperability between their projects and OMRSE.",
"domains": [
"Patient care",
"Hospital"
],
"homepage": "https://github.com/mcwdsi/OMRSE",
"license": "CC-BY-4.0",
"name": "Ontology for Modeling and Representation of Social Entities",
"publications": [
{
"doi": "10.1186/s13326-016-0087-8",
"pubmed": "27406187",
"title": "The ontology of medically related social entities: recent developments",
"year": 2016
}
],
"repository": "https://github.com/mcwdsi/OMRSE/issues",
"subjects": [
"Demographics",
"Social Science",
"Health Science",
"Biomedical Science"
]
},
"FAIRsharing.z2cz7s": {
"abbreviation": "MOOCULADO",
"contact": {
"email": "contact@bioself.communication.com",
"name": "Delphine Dauga",
"orcid": "0000-0003-3152-1194"
},
"description": "The first ontology describing the anatomy and the development of Molgula oculata.",
"domains": [
"Cell",
"Life cycle",
"Life cycle stage"
],
"homepage": "https://www.aniseed.fr/aniseed/anatomy/find_devstage?module=aniseed&action=anatomy:find_devstage",
"name": "Molgula oculata Anatomy and Development Ontology",
"subjects": [
"Anatomy",
"Developmental Biology"
],
"user_defined_tags": [
"Morphogenesis"
]
},
"FAIRsharing.z656ab": {
"abbreviation": "DDANAT",
"contact": {
"email": "pgaudet@northwestern.edu",
"name": "Pascale Gaudet",
"orcid": "0000-0003-1813-6857"
},
"description": "The Dictyostelium Anatomy Ontology ontology describes the anatomy of the slime mold. It defines the structural makeup of Dictyostelium and its composing parts including the different cell types, throughout its life cycle. It has two main goals: (1) promote the consistent annotation of Dictyostelium-specific events, such as phenotypes and gene expression information; and (2) encourage researchers to use the same terms with the same intended meaning.",
"domains": [
"Cell"
],
"homepage": "http://dictybase.org/Dicty_Info/dicty_anatomy_ontology.html",
"name": "Dictyostelium Anatomy Ontology",
"publications": [
{
"doi": "10.1186/1471-2164-9-130",
"pubmed": "18366659",
"title": "An anatomy ontology to represent biological knowledge in Dictyostelium discoideum",
"year": 2008
}
],
"subjects": [
"Anatomy",
"Life Science"
]
},
"FAIRsharing.z8nb52": {
"abbreviation": "LEGALAPA",
"description": "Record does not exist anymore: legalapa. The record with identifier content 10.25504/FAIRsharing.z8nb52 was invalid.",
"homepage": "http://bioportal.bioontology.org/ontologies/LEGALAPA",
"name": "legalapa"
},
"FAIRsharing.zbff4z": {
"abbreviation": "GRO",
"description": "The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes.",
"domains": [
"Deoxyribonucleic acid",
"Molecular entity",
"Regulation of gene expression",
"Gene"
],
"homepage": "http://purl.bioontology.org/ontology/GRO",
"name": "Gene Regulation Ontology",
"publications": [
{
"pubmed": "18487700",
"title": "Gene Regulation Ontology (GRO): design principles and use cases",
"year": 2008
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.zc2tfa": {
"abbreviation": "IFAR",
"description": "An application ontology devoted to the standardized recording of data related to Fanconi Anemia (FA). This ontology was created using an OWL file provided by Dr. Ada Hamish (and Francois Schiettecatte) at the Centers for Mendelian Genetics, with their permission. Their original ontology can be found at: http://phenodb.net/help/features. Modifications were made using HPO, OMIM, NCI, and SNOMED. Novel classes pertaining to FA were added and defined as appropriate.",
"homepage": "http://lab.rockefeller.edu/smogorzewska/ifar/",
"name": "Fanconi Anemia Ontology",
"subjects": [
"Medicine"
]
},
"FAIRsharing.zcfp65": {
"abbreviation": "BRO",
"description": "Biomedical Resource Ontology (BRO) enables semantic annotation and discovery of biomedical resources. The biomedical research community relies on a diverse set of resources, both within their own institutions and at other research centers. Without effective means to locate and query these resources, it is challenging, if not impossible, for investigators to be aware of the myriad resources available, or to effectively perform resource discovery when the need arises.",
"domains": [
"Resource metadata"
],
"homepage": "http://bioportal.bioontology.org/ontologies/BRO",
"name": "Biomedical Resource Ontology",
"publications": [
{
"doi": "10.1016/j.jbi.2010.10.003",
"pubmed": "20955817",
"title": "The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research",
"year": 2010
}
],
"subjects": [
"Health Science",
"Social and Behavioural Science",
"Biomedical Science"
]
},
"FAIRsharing.zchb68": {
"abbreviation": "MMUSDV",
"description": "Life cycle stages for Mus Musculus. MmusDv was developed by the Bgee group with assistance from the core Uberon developers and the Mouse anatomy ontology developers. Currently it includes both embryonic stages and adult stages. ",
"domains": [
"Life cycle stage"
],
"homepage": "https://obofoundry.org/ontology/mmusdv.html",
"license": "CC-BY-3.0",
"name": "Mouse Developmental Stages",
"repository": "https://github.com/obophenotype/developmental-stage-ontologies",
"subjects": [
"Anatomy",
"Developmental Biology",
"Embryology"
]
},
"FAIRsharing.zkdn1d": {
"abbreviation": "CO_020",
"description": "The FAO/IPGRI Multi-Crop Passport Descriptor is part of the Crop Ontology (CO) project. The ontology has been adapted from the December 2015 version of the FAO/Bioversity Multi-Crop Passport Descriptors. Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breedersβ trait names, measurement methods, scales and standard variables for many crops. This ontology is one of these reference plant ontologies integrated within the Crop Ontology. This ontology is currently unavailable from the Crop Ontology site, and therefore has been marked as uncertain. Please get in touch with us if you have information on this resource.",
"domains": [
"Food"
],
"homepage": "http://www.cropontology.org/ontology/CO_020/FAO-Bioversity%20Multi-Crop%20Passport%20Descriptors",
"license": "CC-BY-4.0",
"name": "Food and Agriculture Organization (FAO)-IPGRI-Bioversity Multi-Crop Passport Descriptor",
"subjects": [
"Botany",
"Agriculture",
"Plant Genetics"
]
},
"FAIRsharing.zmx7nn": {
"abbreviation": "OGG",
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqun He",
"orcid": "0000-0001-9189-9661"
},
"description": "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms. Each gene in OGG has over 10 annotation items, includes gene-associated Gene Ontology (GO) and PubMed article information. OGG has represented genes in human, two viruses, and four bacteria. Additionally, 7 OGG subsets are developed to represent genes and genomes of 7 model systems including mouse, fruit fly, zebrafish, yeast, A. thaliana, C. elegans, and P. falciparum.",
"domains": [
"Gene name",
"Gene",
"Genome"
],
"homepage": "https://bitbucket.org/hegroup/ogg",
"license": "CC-BY-3.0",
"name": "Ontology of Genes and Genomes",
"subjects": [
"Life Science",
"Biology"
]
},
"FAIRsharing.zn05ta": {
"abbreviation": "PDON",
"contact": {
"email": "erfan.younesi@scai.fraunhofer.de",
"name": "Erfan Younesi",
"orcid": "0000-0001-8793-2692"
},
"description": "The Parkinson's Disease Ontology (PDO) was created to represent and model the Parkinson's Disease knowledge domain. This ontology with a covers major biomedical concepts from molecular to clinical features of the disease as well as the different views on disease features held by molecular biologists, clinicians and drug developers. This resource has been created for use in the IMI-funded AETIONOMY project (www.aetionomy.org).",
"domains": [
"Parkinson's disease",
"Disease"
],
"homepage": "http://bioportal.bioontology.org/ontologies/PDON",
"license": "CC0-1.0",
"name": "Parkinson's Disease Ontology",
"publications": [
{
"doi": "10.1186/s12976-015-0017-y",
"pubmed": "26395080",
"title": "PDON: Parkinson's disease ontology for representation and modeling of the Parkinson's disease knowledge domain",
"year": 2015
}
],
"subjects": [
"Drug Discovery",
"Molecular biology",
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.znrhmd": {
"abbreviation": "HFO",
"description": "Heart failure ontology is an attempt to define heart-failure-relevant information including the causes and risk factors, signs and symptoms, diagnostic tests and results, and treatment.",
"domains": [
"Heart"
],
"homepage": "http://bioportal.bioontology.org/ontologies/HFO",
"name": "Heart Failure Ontology",
"subjects": [
"Human Biology"
]
},
"FAIRsharing.zsnv69": {
"abbreviation": "MAO",
"description": "MAO is an ontology for multiple alignments of nucleic and protein sequences. MAO is designed to improve interoperation and data sharing between different alignment protocols for the construction of a high quality, reliable multiple alignment in order to facilitate knowledge extraction and the presentation of the most pertinent information to the biologist.",
"domains": [
"Nucleic acid sequence",
"Amino acid sequence"
],
"homepage": "http://bioportal.bioontology.org/ontologies/1026",
"name": "Multiple alignment",
"publications": [
{
"doi": "10.1093/nar/gki735",
"pubmed": "16043635",
"title": "MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences",
"year": 2005
}
],
"subjects": [
"Life Science"
]
},
"FAIRsharing.zve9cc": {
"abbreviation": "PxO",
"description": "The Proteasix Ontology (PxO) is an ontology that supports the Proteasix tool; an open-source peptide-centric tool that can be used to predict automatically and in a large-scale fashion in silico the proteases involved in the generation of proteolytic cleavage fragments (peptides). PxO aims to describe the known proteases and their target cleavage sites, to enable the description of proteolytic cleavage fragments as the outputs of observed and predicted proteolysis, and to use knowledge about the function, species and cellular location of a protease and protein substrate to support the prioritisation of proteases in observed and predicted proteolysis. Although the Proteasix project website remains active, download / browse links to the ontology are no longer available and the owners of the resource have not confirmed its current status. Therefore we have marked this resource with an Uncertain status. Please get in touch if you can provide FAIRsharing with up-to-date information regarding this resource.",
"domains": [
"Proteolytic digest",
"Protein cleavage site prediction",
"Protease cleavage",
"Protease site"
],
"homepage": "https://dx.doi.org/10.1186%2Fs13326-016-0078-9",
"name": "Proteasix Ontology",
"publications": [
{
"doi": "10.1186/s13326-016-0078-9",
"pubmed": "27259807",
"title": "The Proteasix Ontology",
"year": 2016
}
],
"subjects": [
"Biology"
]
},
"FAIRsharing.zvytda": {
"abbreviation": "ICPC-2 PLUS",
"description": "The International Classification of Primary Care Version 2 PLUS (ICPC-2 PLUS, also known as the BEACH coding system) is a clinical terminology which extends the International Classification of Primary Care, Version 2 (ICPC-2). ICPC-2 PLUS can be used in age-sex disease registers, morbidity registers and full electronic health records in primary care. Primarily used in Australia, ICPC-2 PLUS is used within software packages and electronic health record (EHR) systems. It is also used in research projects, including the BEACH (Bettering the Evaluation And Care of Health) program, the national study of general practice activity. The terminology is therefore often referred to as the BEACH coding system. ICPC-2 PLUS has been specifically designed by the FMRC for use in computerised clinical systems, recall systems, disease registers and secondary coding of clinical data. It is not part of the ICPC-2 standard. Charges apply for end users of ICPC-2 PLUS. All end users must sign an ICPC-2 PLUS end user contract before being given access to ICPC-2 PLUS. The World Organization of Family Doctors (WONCA) and the WONCA International Classification Committee (WICC) have no control over it although they do have control over the ICPC classification which the PLUS extension makes use of.",
"domains": [
"Electronic health record"
],
"homepage": "http://sydney.edu.au/health-sciences/ncch/icpc-2-plus/overview.shtml",
"name": "International Classification of Primary Care Version 2 PLUS",
"subjects": [
"Medicine",
"Primary Health Care",
"Biomedical Science",
"Preclinical Studies"
]
},
"FAIRsharing.zwtww5": {
"abbreviation": "VO",
"contact": {
"email": "yongqunh@med.umich.edu",
"name": "Yongqunh He",
"orcid": "0000-0001-9189-9661"
},
"description": "The Vaccine Ontology (VO) was created as part of an international community-based effort to represent vaccine knowledge and to support automated reasoning. VO describes the detailed classification and definitions of vaccine components and vaccine administration processes. To ensure consistent representation of vaccine knowledge and to support automated reasoning, a community-based effort to develop the Vaccine Ontology (VO) has been initiated. This international collaborative VO development effort has been joined by many institutes and disciplines around the world. The Vaccine Ontology is also being used in a variety of applications by many user groups in academia and industry.",
"domains": [
"Biological process",
"Pathogen",
"Vaccine",
"Vaccination"
],
"homepage": "https://github.com/vaccineontology/VO",
"license": "CC-BY-3.0",
"logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaUFDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--0d3898a5618b34c0bc948bb0d101e906f212f05f/vo_banner.png?disposition=inline",
"name": "The Vaccine Ontology",
"publications": [
{
"doi": "10.1186/1745-7580-6-s1-s5",
"pubmed": "20875156",
"title": "Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN",
"year": 2010
},
{
"doi": "10.1186/2041-1480-3-17",
"pubmed": "23256535",
"title": "Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses",
"year": 2012
},
{
"doi": "10.2174/1381612826666201125112131",
"pubmed": "33238868",
"title": "Ontology-based Precision Vaccinology for Deep Mechanism Understanding and Precision Vaccine Development",
"year": 2020
}
],
"repository": "https://github.com/vaccineontology",
"subjects": [
"Pathobiochemistry",
"Biomedical Science"
]
}
} ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9619668
bioregistry-0.11.12/src/bioregistry/external/go/ 0000755 0001751 0000177 00000000000 14655546227 021223 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/go/__init__.py 0000644 0001751 0000177 00000007224 14655542206 023332 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download the Gene Ontology registry."""
import json
import logging
from pathlib import Path
from typing import Any, Dict, Mapping
import yaml
from pystow.utils import download
from bioregistry.constants import RAW_DIRECTORY, URI_FORMAT_KEY
from bioregistry.external.alignment_utils import Aligner
__all__ = [
"get_go",
"GoAligner",
]
logger = logging.getLogger(__name__)
# Xrefs from GO that aren't generally useful
SKIP = {
"TO_GIT",
"OBO_SF_PO",
"OBO_SF2_PO",
"OBO_SF2_PECO",
"PECO_GIT",
"PO_GIT",
"PSO_GIT",
"EO_GIT",
}
# The key is redundant of the value
REDUNDANT = {
"AspGD": "AspGD_LOCUS",
}
DIRECTORY = Path(__file__).parent.resolve()
RAW_PATH = RAW_DIRECTORY / "go.yml"
PROCESSED_PATH = DIRECTORY / "processed.json"
GO_URL = "https://raw.githubusercontent.com/geneontology/go-site/master/metadata/db-xrefs.yaml"
PROCESSING_GO_PATH = DIRECTORY / "processing_go.json"
def get_go(force_download: bool = False):
"""Get the GO registry."""
if PROCESSED_PATH.exists() and not force_download:
with PROCESSED_PATH.open() as file:
return json.load(file)
download(url=GO_URL, path=RAW_PATH, force=True)
with RAW_PATH.open() as file:
entries = yaml.full_load(file)
entries = [
entry
for entry in entries
if entry["database"] not in SKIP and entry["database"] not in REDUNDANT
]
rv = {entry["database"]: entry for entry in entries}
with PROCESSED_PATH.open("w") as file:
json.dump(rv, file, indent=2, sort_keys=True)
return rv
class GoAligner(Aligner):
"""An aligner for the Gene Ontology (GO) registry."""
key = "go"
getter = get_go
curation_header = "name", "description"
def get_skip(self) -> Mapping[str, str]:
"""Get the skipped GO identifiers."""
with PROCESSING_GO_PATH.open() as file:
j = json.load(file)
return j["skip"]
def prepare_external(
self, external_id: str, external_entry: Mapping[str, Any]
) -> Dict[str, Any]:
"""Prepare GO data to be added to the bioregistry for each GO registry entry."""
rv = {
"name": external_entry["name"],
}
description = external_entry.get("description")
if description:
rv["description"] = description
homepages = [
homepage
for homepage in external_entry.get("generic_urls", [])
if not any(
homepage.startswith(homepage_prefix)
for homepage_prefix in [
"http://purl.obolibrary.org",
]
)
]
if len(homepages) > 1:
logger.info(f"{external_id} multiple homepages {homepages}")
if homepages:
rv["homepage"] = homepages[0]
entity_types = external_entry.get("entity_types", [])
if len(entity_types) > 1:
logger.info(f"{external_id} multiple entity types")
# TODO handle
elif len(entity_types) == 1:
entity_type = entity_types[0]
uri_format = entity_type.get("url_syntax")
if uri_format and not any(
uri_format.startswith(formatter_prefix)
for formatter_prefix in [
"http://purl.obolibrary.org",
"https://purl.obolibrary.org",
]
):
uri_format = uri_format.replace("[example_id]", "$1")
rv[URI_FORMAT_KEY] = uri_format
if "synonyms" in external_entry:
rv["synonyms"] = external_entry["synonyms"]
return rv
if __name__ == "__main__":
GoAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254817.0
bioregistry-0.11.12/src/bioregistry/external/go/processed.json 0000644 0001751 0000177 00000433444 14655544041 024111 0 ustar 00runner docker {
"AGI_LocusCode": {
"database": "AGI_LocusCode",
"description": "Comprises TAIR, TIGR and MIPS",
"entity_types": [
{
"example_id": "AGI_LocusCode:At2g17950",
"example_url": "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=At2g17950",
"id_syntax": "A[Tt][MmCc0-5][Gg][0-9]{5}(\\.[0-9]{1})?",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "http://arabidopsis.org/servlets/TairObject?type=locus&name=[example_id]"
}
],
"generic_urls": [
"http://www.arabidopsis.org"
],
"name": "Arabidopsis Genome Initiative"
},
"AGRICOLA_ID": {
"database": "AGRICOLA_ID",
"entity_types": [
{
"example_id": "AGRICOLA_NAL:TP248.2 P76 v.14",
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://agricola.nal.usda.gov/"
],
"name": "AGRICultural OnLine Access"
},
"AGRICOLA_IND": {
"database": "AGRICOLA_IND",
"entity_types": [
{
"example_id": "AGRICOLA_IND:IND23252955",
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://agricola.nal.usda.gov/"
],
"name": "AGRICultural OnLine Access"
},
"APweb": {
"database": "APweb",
"entity_types": [
{
"example_id": "APweb:Glossary",
"example_url": "http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html"
}
],
"generic_urls": [
"http://www.mobot.org/mobot/research/apweb/"
],
"name": "Angiosperm Phylogeny Website"
},
"ARBA": {
"database": "ARBA",
"entity_types": [
{
"example_id": "ARBA:ARBA00000001",
"example_url": "https://www.uniprot.org/arba/ARBA00000001",
"id_syntax": "ARBA[0-9]{8}",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.uniprot.org/arba/[example_id]"
}
],
"generic_urls": [
"https://www.uniprot.org/arba/"
],
"name": "ARBA machine learning models for automatic annotation of UniProtKB unreviewed entries"
},
"ARUK-UCL": {
"database": "ARUK-UCL",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"https://www.ucl.ac.uk/cardiovascular/research/pre-clinical-and-fundamental-science/functional-gene-annotation/neurological-gene-0"
],
"name": "Alzheimers Research Gene Ontology Initiative"
},
"ASAP": {
"database": "ASAP",
"entity_types": [
{
"example_id": "ASAP:ABF-0014586",
"example_url": "https://asap.genetics.wisc.edu/asap/feature_info.php?FeatureID=ABF-0014586",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "https://asap.genetics.wisc.edu/asap/feature_info.php?FeatureID=[example_id]"
}
],
"generic_urls": [
"https://asap.genetics.wisc.edu/asap/ASAP1.htm"
],
"name": "A Systematic Annotation Package for Community Analysis of Genomes"
},
"AgBase": {
"database": "AgBase",
"entity_types": [
{
"example_id": "P02264",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://agbase.arizona.edu/cgi-bin/getEntry.pl?db_pick=all&database=Swiss-Prot&gb_acc=[example_id]"
}
],
"generic_urls": [
"http://www.agbase.msstate.edu/"
],
"name": "AgBase resource for functional analysis of agricultural plant and animal gene products"
},
"AlphaFold": {
"database": "AlphaFold",
"entity_types": [
{
"example_id": "AlphaFold:Q5VSL9",
"example_url": "https://alphafold.ebi.ac.uk/entry/Q5VSL9",
"id_syntax": "([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z]([0-9][A-Z][A-Z0-9]{2}){1,2}[0-9])((-[0-9]+)|-PRO_[0-9]{10}|-VAR_[0-9]{6}){0,1}",
"type_id": "PR:000000001",
"type_name": "protein",
"url_syntax": "https://alphafold.ebi.ac.uk/entry/[example_id]"
}
],
"generic_urls": [
"https://alphafold.ebi.ac.uk/"
],
"name": "AlphaFold Protein Structure Database"
},
"Alzheimers_University_of_Toronto": {
"database": "Alzheimers_University_of_Toronto",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.ims.utoronto.ca/"
],
"name": "Alzheimers Project at University of Toronto"
},
"Animal_CorrDB": {
"database": "Animal_CorrDB",
"description": "A database with curated publicly available trait correlation and inheritability data in livestock animal species. The link ID is called The link ID is called Corr_ID on CorrDB data downloads.",
"entity_types": [
{
"example_id": "Animal_CorrDB:37232",
"example_url": "https://www.animalgenome.org/CorrDB/q/?id=37232",
"id_syntax": "\\d+",
"type_id": "CorrID:000000",
"type_name": "Correlation",
"url_syntax": "https://www.animalgenome.org/CorrDB/q/?id=[example_id]"
}
],
"generic_urls": [
"https://www.animalgenome.org/CorrDB"
],
"name": "CorrDB"
},
"Animal_QTLdb": {
"database": "Animal_QTLdb",
"description": "A database with curated publicly available trait mapping data (QTL and SNP associations) in livestock animal species. The link ID is called QTL_ID on QTLdb data dpownloads.",
"entity_types": [
{
"example_id": "Animal_QTLdb:23155",
"example_url": "https://www.animalgenome.org/QTLdb/q?id=23155",
"id_syntax": "\\d+",
"type_id": "QTL_ID:0000000",
"type_name": "QTL",
"url_syntax": "https://www.animalgenome.org/QTLdb/q?id=[example_id]"
}
],
"generic_urls": [
"https://www.animalgenome.org/QTLdb"
],
"name": "QTLdb"
},
"AspGD_LOCUS": {
"database": "AspGD_LOCUS",
"entity_types": [
{
"example_id": "AspGD_LOCUS:AN10942",
"example_url": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=AN10942",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=[example_id]"
}
],
"generic_urls": [
"http://www.aspergillusgenome.org/"
],
"name": "Aspergillus Genome Database",
"rdf_uri_prefix": "http://identifiers.org/aspgd.locus/"
},
"AspGD_REF": {
"database": "AspGD_REF",
"entity_types": [
{
"example_id": "AspGD_REF:90",
"example_url": "http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=90",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=[example_id]"
}
],
"generic_urls": [
"http://www.aspergillusgenome.org/"
],
"name": "Aspergillus Genome Database"
},
"BFO": {
"database": "BFO",
"description": "An upper ontology used by Open Bio Ontologies (OBO) Foundry. BFO contains upper-level classes as well as core relations such as part_of (BFO_0000050)",
"entity_types": [
{
"example_id": "BFO:0000066",
"example_url": "http://purl.obolibrary.org/obo/BFO_0000066",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://purl.obolibrary.org/obo/BFO_[example_id]"
}
],
"generic_urls": [
"http://purl.obolibrary.org/obo/bfo"
],
"name": "Basic Formal Ontology",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/BFO_"
},
"BHF-UCL": {
"database": "BHF-UCL",
"description": "The Cardiovascular Gene Ontology Annotation Initiative is supported by the British Heart Foundation (BHF) and located at University College London (UCL).",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"https://www.ucl.ac.uk/cardiovascular/research/pre-clinical-and-fundamental-science/functional-gene-annotation/cardiovascular-gene"
],
"name": "Cardiovascular Gene Ontology Annotation Initiative"
},
"BIOMD": {
"database": "BIOMD",
"entity_types": [
{
"example_id": "BIOMD:BIOMD0000000045",
"example_url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000045",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.ebi.ac.uk/biomodels/[example_id]"
}
],
"generic_urls": [
"https://www.ebi.ac.uk/biomodels/"
],
"name": "BioModels Database",
"synonyms": [
"BIOMDID"
]
},
"BRENDA": {
"database": "BRENDA",
"entity_types": [
{
"example_id": "BRENDA:4.2.1.3",
"example_url": "https://www.brenda-enzymes.info/enzyme.php?ecno=4.2.1.3",
"type_id": "GO:0003824",
"type_name": "catalytic activity",
"url_syntax": "https://www.brenda-enzymes.info/enzyme.php?ecno=[example_id]"
}
],
"generic_urls": [
"http://www.brenda-enzymes.info"
],
"name": "BRENDA, The Comprehensive Enzyme Information System"
},
"BTO": {
"database": "BTO",
"description": "A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.",
"entity_types": [
{
"example_id": "BTO_0002164",
"example_url": "http://purl.obolibrary.org/obo/BTO_0002164",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://purl.obolibrary.org/obo/BTO_[example_id]"
}
],
"generic_urls": [
"http://purl.obolibrary.org/obo/bto"
],
"name": "BRENDA tissue / enzyme ontology",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/BTO_"
},
"BioCyc": {
"database": "BioCyc",
"entity_types": [
{
"example_id": "BioCyc:PWY-5271",
"example_url": "http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-5271",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=[example_id]"
}
],
"generic_urls": [
"http://biocyc.org/"
],
"name": "BioCyc collection of metabolic pathway databases"
},
"CACAO": {
"database": "CACAO",
"description": "The Community Assessment of Community Annotation with Ontologies (CACAO) is a project to do large-scale manual community annotation of gene function using the Gene Ontology as a multi-institution student competition.",
"entity_types": [
{
"example_id": "MYCS2:A0QNF5",
"example_url": "https://gowiki.tamu.edu/wiki/index.php/MYCS2:A0QNF5",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://gowiki.tamu.edu/wiki/index.php/[example_id]"
}
],
"generic_urls": [
"http://gowiki.tamu.edu/wiki/index.php/Category:CACAO"
],
"name": "Community Assessment of Community Annotation with Ontologies"
},
"CAFA": {
"database": "CAFA",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://biofunctionprediction.org/cafa/"
],
"name": "Critical Assessment of Protein Function Annotation"
},
"CARO": {
"database": "CARO",
"description": "An upper ontology for anatomy used by OBO Foundry ontologies. Used to facilitate interoperability between existing anatomy ontologies for different species",
"entity_types": [
{
"example_id": "CARO:0020003",
"example_url": "http://purl.obolibrary.org/obo/CARO_0020003",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://purl.obolibrary.org/obo/CARO_[example_id]"
}
],
"generic_urls": [
"http://purl.obolibrary.org/obo/caro"
],
"name": "Common Anatomy Reference Ontology",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/CARO_"
},
"CAS": {
"database": "CAS",
"description": "CAS REGISTRY is the most authoritative collection of disclosed chemical substance information, containing more than 54 million organic and inorganic substances and 62 million sequences. CAS REGISTRY covers substances identified from the scientific literature from 1957 to the present, with additional substances going back to the early 1900s.",
"entity_types": [
{
"example_id": "CAS:58-08-2",
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.cas.org/expertise/cascontent/registry/index.html"
],
"name": "CAS Chemical Registry",
"rdf_uri_prefix": "http://identifiers.org/cas/"
},
"CASGEN": {
"database": "CASGEN",
"entity_types": [
{
"example_id": "CASGEN:1040",
"example_url": "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?genid=1040",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?genid=[example_id]"
}
],
"generic_urls": [
"https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp"
],
"name": "Catalog of Fishes genus database",
"synonyms": [
"CAS_GEN"
]
},
"CASREF": {
"database": "CASREF",
"entity_types": [
{
"example_id": "CASREF:2031",
"example_url": "https://researcharchive.calacademy.org/research/ichthyology/catalog/getref.asp?id=2031",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://researcharchive.calacademy.org/research/ichthyology/catalog/getref.asp?id=[example_id]"
}
],
"generic_urls": [
"https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp"
],
"name": "Catalog of Fishes publications database"
},
"CASSPC": {
"database": "CASSPC",
"entity_types": [
{
"example_url": "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=1979",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=[example_id]"
}
],
"generic_urls": [
"https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp"
],
"name": "Catalog of Fishes species database",
"synonyms": [
"CAS_SPC"
]
},
"CAZY": {
"database": "CAZY",
"description": "The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.",
"entity_types": [
{
"example_id": "CAZY:PL11",
"example_url": "http://www.cazy.org/PL11.html",
"id_syntax": "(CE|GH|GT|PL)\\d+",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.cazy.org/[example_id].html"
}
],
"generic_urls": [
"http://www.cazy.org/"
],
"name": "Carbohydrate Active EnZYmes"
},
"CDD": {
"database": "CDD",
"entity_types": [
{
"example_id": "CDD:34222",
"example_url": "http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=34222",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=[example_id]"
}
],
"generic_urls": [
"https://www.ncbi.nlm.nih.gov/cdd"
],
"name": "Conserved Domain Database at NCBI"
},
"CGD": {
"database": "CGD",
"entity_types": [
{
"example_id": "CGD:CAL0000179664",
"example_url": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=CAL0000179664",
"id_syntax": "(CAL|CAF)[0-9]{10}",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=[example_id]"
}
],
"generic_urls": [
"http://www.candidagenome.org/"
],
"name": "Candida Genome Database",
"rdf_uri_prefix": "http://identifiers.org/cgd/",
"synonyms": [
"CGDID"
]
},
"CGD_LOCUS": {
"database": "CGD_LOCUS",
"entity_types": [
{
"example_id": "CGD_LOCUS:HWP1",
"example_url": "http://www.candidagenome.org/cgi-bin/locus.pl?locus=HWP1",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.candidagenome.org/cgi-bin/locus.pl?locus=[example_id]"
}
],
"generic_urls": [
"http://www.candidagenome.org/"
],
"name": "Candida Genome Database"
},
"CGD_REF": {
"database": "CGD_REF",
"entity_types": [
{
"example_id": "CGD_REF:1490",
"example_url": "http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=1490",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=[example_id]"
}
],
"generic_urls": [
"http://www.candidagenome.org/"
],
"name": "Candida Genome Database"
},
"CGSC": {
"database": "CGSC",
"entity_types": [
{
"example_id": "CGSC:rbsK",
"example_url": "http://cgsc.biology.yale.edu/Site.php?ID=315",
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://cgsc.biology.yale.edu/"
],
"name": "CGSC"
},
"CHEBI": {
"database": "CHEBI",
"entity_types": [
{
"example_id": "CHEBI:17234",
"example_url": "http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17234",
"id_syntax": "[0-9]{1,6}",
"type_id": "CHEBI:24431",
"type_name": "chemical entity",
"url_syntax": "http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:[example_id]"
}
],
"generic_urls": [
"http://www.ebi.ac.uk/chebi/"
],
"name": "Chemical Entities of Biological Interest",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/CHEBI_",
"synonyms": [
"ChEBI"
]
},
"CL": {
"database": "CL",
"entity_types": [
{
"example_id": "CL:0000041",
"example_url": "http://purl.obolibrary.org/obo/CL_0000041",
"id_syntax": "[0-9]{7}",
"type_id": "GO:0005623",
"type_name": "cell",
"url_syntax": "http://purl.obolibrary.org/obo/CL_[example_id]"
}
],
"generic_urls": [
"http://cellontology.org"
],
"name": "Cell Type Ontology",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/CL_"
},
"COG": {
"database": "COG",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.ncbi.nlm.nih.gov/COG/"
],
"name": "NCBI Clusters of Orthologous Groups"
},
"COG_Cluster": {
"database": "COG_Cluster",
"entity_types": [
{
"example_id": "COG_Cluster:COG0001",
"example_url": "http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=COG0001",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=[example_id]"
}
],
"generic_urls": [
"http://www.ncbi.nlm.nih.gov/COG/"
],
"name": "NCBI COG cluster"
},
"COG_Function": {
"database": "COG_Function",
"entity_types": [
{
"example_id": "COG_Function:H",
"example_url": "http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=H",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=[example_id]"
}
],
"generic_urls": [
"http://www.ncbi.nlm.nih.gov/COG/"
],
"name": "NCBI COG function"
},
"COG_Pathway": {
"database": "COG_Pathway",
"entity_types": [
{
"example_id": "COG_Pathway:14",
"example_url": "http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=14",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=[example_id]"
}
],
"generic_urls": [
"http://www.ncbi.nlm.nih.gov/COG/"
],
"name": "NCBI COG pathway"
},
"CORIELL": {
"database": "CORIELL",
"description": "The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world.",
"entity_types": [
{
"example_id": "GM07892",
"example_url": "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07892",
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"type_id": "BET:0000000",
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"name": "Database of transcription factor binding sites (TFBS) in the Bacteria domain"
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"id_syntax": "[0-9]{7}",
"type_id": "CARO:0000000",
"type_name": "anatomical entity"
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"name": "Digital Object Identifier"
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"id_syntax": "\\d{7}",
"type_id": "BET:0000000",
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"type_id": "SO:0000704",
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"id_syntax": "([A-Z]{1}[0-9]{5})|([A-Z]{2}[0-9]{6})|([A-Z]{4}[0-9]{8,9})",
"type_id": "BET:0000000",
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"url_syntax": "http://www.ebi.ac.uk/ena/data/view/[example_id]"
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],
"generic_urls": [
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"name": "European Nucleotide Archive"
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"id_syntax": "ENS[A-Z0-9]{10,17}",
"type_id": "SO:0000704",
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"url_syntax": "http://www.ensembl.org/id/[example_id]"
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{
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"id_syntax": "ENS[A-Z0-9]{10,17}",
"type_id": "PR:000000001",
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"url_syntax": "http://www.ensembl.org/id/[example_id]"
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"id_syntax": "ENS[A-Z0-9]{10,17}",
"type_id": "SO:0000673",
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"url_syntax": "http://www.ensembl.org/id/[example_id]"
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"name": "Ensembl database of automatically annotated genomic data",
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"synonyms": [
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"id_syntax": "ENSG[0-9]{9,16}",
"type_id": "SO:0000704",
"type_name": "gene",
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"name": "Ensembl database of automatically annotated genomic data"
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"url_syntax": "http://www.ensembl.org/id/[example_id]"
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"name": "Ensembl database of automatically annotated genomic data"
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"id_syntax": "ENST[0-9]{9,16}",
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"url_syntax": "http://www.ensembl.org/id/[example_id]"
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],
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"name": "Ensembl database of automatically annotated genomic data"
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"example_url": "https://enzyme.expasy.org/EC/1.1.1.1",
"type_id": "BET:0000000",
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"generic_urls": [
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"name": "Swiss Institute of Bioinformatics enzyme database"
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"id_syntax": "EB[0-9]{4}",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "https://www.york.ac.uk/res/thomas/Gene.cfm?&recordID=[example_id]"
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"generic_urls": [
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"name": "EchoBASE post-genomic database for Escherichia coli"
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"id_syntax": "^[A-Za-z0-9+_.%-:]+$",
"type_id": "GO:0008150",
"type_name": "biological_process",
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"id_syntax": "^[A-Za-z0-9+_.%-:]+$",
"type_id": "PR:000000001",
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{
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"id_syntax": "^[A-Za-z0-9+_.%-:]+$",
"type_id": "CHEBI:33697",
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"id_syntax": "^[A-Za-z0-9+_.%-:]+$",
"type_id": "GO:0032991",
"type_name": "protein-containing complex",
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"generic_urls": [
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"name": "Scientific database for the bacterium Escherichia coli K-12 MG1655"
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"type_name": "entity",
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"name": "Scientific database for the bacterium Escherichia coli K-12 MG1655",
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"type_id": "SO:0000704",
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"example_url": "http://www.ensemblgenomes.org/id/YOR197W",
"type_id": "SO:0000704",
"type_name": "gene",
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"name": "Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi."
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"example_url": "http://www.ensemblgenomes.org/id/FBgn0052693",
"type_id": "SO:0000704",
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"type_id": "SO:0000704",
"type_name": "gene",
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}
],
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"name": "Ensembl Plants, the Ensembl database for accessing genome-scale data from plants.",
"synonyms": [
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"example_url": "http://www.ensemblgenomes.org/id/PFL2550w",
"type_id": "SO:0000704",
"type_name": "gene",
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],
"generic_urls": [
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"name": "Ensembl Protists, the Ensembl database for accessing genome-scale data from protists."
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"example_url": "http://eupathdb.org/gene/LtaP17.1490",
"type_id": "BET:0000000",
"type_name": "gene",
"url_syntax": "http://eupathdb.org/gene/[example_id]"
}
],
"generic_urls": [
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"name": "The Eukaryotic Pathogen Database"
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"entity_types": [
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"type_id": "BET:0000000",
"type_name": "entity"
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],
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"name": "Eurofungbase community annotation"
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"example_url": "http://flybase.org/reports/FBgn0000024.html",
"id_syntax": "FBgn[0-9]{7}",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "http://flybase.org/reports/[example_id].html"
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{
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"example_url": "https://flybase.org/reports/FBrf0193169.htm",
"id_syntax": "FB:FBrf[0-9]{7}",
"type_id": "BET:0000000",
"type_name": "reference",
"url_syntax": "http://flybase.org/reports/[example_id].htm"
}
],
"generic_urls": [
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],
"name": "FlyBase",
"rdf_uri_prefix": "http://identifiers.org/flybase/",
"synonyms": [
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"example_url": "http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:00007002",
"id_syntax": "[0-9]{8}",
"type_id": "GO:0005623",
"type_name": "cell",
"url_syntax": "http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:[example_id]"
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{
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"example_url": "http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:10000000",
"id_syntax": "[0-9]{8}",
"type_id": "UBERON:0001062",
"type_name": "anatomical entity",
"url_syntax": "http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:[example_id]"
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],
"generic_urls": [
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"name": "Drosophila gross anatomy",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/FBbt_"
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"example_url": "http://flybase.org/cgi-bin/fbcvq.html?query=FBdv:00007012",
"id_syntax": "[0-9]{8}",
"type_id": "UBERON:0000105",
"type_name": "life cycle stage",
"url_syntax": "http://flybase.org/cgi-bin/fbcvq.html?query=FBdv:[example_id]"
}
],
"generic_urls": [
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],
"name": "Drosophila development",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/FBdv_"
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"FMA": {
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"entity_types": [
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"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
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],
"name": "Foundational Model of Anatomy",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/FMA_"
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"FYPO": {
"database": "FYPO",
"entity_types": [
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"id_syntax": "\\d{7}",
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
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],
"name": "Fission Yeast Phenotype Ontology",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/FYPO_"
},
"GEO": {
"database": "GEO",
"entity_types": [
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"example_url": "http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS2223",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=[example_id]"
}
],
"generic_urls": [
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],
"name": "NCBI Gene Expression Omnibus"
},
"GO": {
"database": "GO",
"entity_types": [
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"example_url": "http://amigo.geneontology.org/amigo/term/GO:0004352",
"id_syntax": "\\d{7}",
"type_id": "GO:0003674",
"type_name": "molecular_function",
"url_syntax": "http://amigo.geneontology.org/amigo/term/GO:[example_id]"
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{
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"example_url": "http://amigo.geneontology.org/amigo/term/GO:0044767",
"id_syntax": "\\d{7}",
"type_id": "GO:0008150",
"type_name": "biological_process",
"url_syntax": "http://amigo.geneontology.org/amigo/term/GO:[example_id]"
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{
"example_id": "GO:0005634",
"example_url": "http://amigo.geneontology.org/amigo/term/GO:0005634",
"id_syntax": "\\d{7}",
"type_id": "GO:0005575",
"type_name": "cellular_component",
"url_syntax": "http://amigo.geneontology.org/amigo/term/GO:[example_id]"
},
{
"example_id": "GO:0044776",
"example_url": "http://amigo.geneontology.org/amigo/term/GO:0044776",
"id_syntax": "\\d{7}",
"type_id": "GO:0032991",
"type_name": "macromolecular complex",
"url_syntax": "http://amigo.geneontology.org/amigo/term/GO:[example_id]"
}
],
"generic_urls": [
"http://amigo.geneontology.org/"
],
"name": "Gene Ontology Database",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/GO_"
},
"GOC": {
"database": "GOC",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.geneontology.org/"
],
"name": "Gene Ontology Consortium"
},
"GOC-OWL": {
"database": "GOC-OWL",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.geneontology.org/"
],
"name": "Gene Ontology Consortium - Logical inferences"
},
"GONUTS": {
"database": "GONUTS",
"description": "Third party documentation for GO and community annotation system.",
"entity_types": [
{
"example_id": "GONUTS:MOUSE:CD28",
"example_url": "https://gowiki.tamu.edu/wiki/index.php/MOUSE:CD28",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://gowiki.tamu.edu/wiki/index.php/[example_id]"
}
],
"generic_urls": [
"http://gowiki.tamu.edu"
],
"name": "Gene Ontology Normal Usage Tracking System (GONUTS)"
},
"GOREL": {
"database": "GOREL",
"description": "Additional relations pending addition into RO",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://purl.obolibrary.org/obo/ro"
],
"name": "GO Extensions to OBO Relation Ontology Ontology"
},
"GO_Central": {
"database": "GO_Central",
"description": "Manual annotation from PAINT curators into the UniProt Protein2GO curation tool.",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.geneontology.org/GO.refgenome.shtml"
],
"name": "GO Central",
"synonyms": [
"GO_CENTRAL"
]
},
"GO_Noctua": {
"database": "GO_Noctua",
"description": "Manual annotation derived from LEGO annotations",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"https://github.com/geneontology/noctua-models"
],
"name": "GO Noctua"
},
"GO_REF": {
"database": "GO_REF",
"entity_types": [
{
"example_id": "0000001",
"example_url": "http://purl.obolibrary.org/obo/go/references/0000001",
"id_syntax": "\\d{7}",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://purl.obolibrary.org/obo/go/references/[example_id]"
}
],
"generic_urls": [
"http://geneontology.org/gorefs"
],
"name": "Gene Ontology Database references"
},
"GR": {
"database": "GR",
"entity_types": [
{
"example_id": "GR:sd1",
"example_url": "http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=sd1",
"id_syntax": "[A-Z][0-9][A-Z0-9]{3}[0-9]",
"type_id": "PR:000000001",
"type_name": "protein",
"url_syntax": "http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=[example_id]"
}
],
"generic_urls": [
"http://www.gramene.org/"
],
"name": "Gramene"
},
"GRIN": {
"database": "GRIN",
"entity_types": [
{
"example_id": "GRIN:1882640",
"example_url": "https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=1882640",
"type_id": "BET:0000000",
"type_name": "germplasm",
"url_syntax": "https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=[example_id]"
}
],
"generic_urls": [
"https://www.ars-grin.gov/"
],
"name": "Germplasm Resources Information Network",
"synonyms": [
"grin"
]
},
"GRINDesc": {
"database": "GRINDesc",
"entity_types": [
{
"example_id": "GRINdesc:89033",
"example_url": "https://npgsweb.ars-grin.gov/gringlobal/descriptordetail.aspx?id=89033",
"type_id": "BET:0000000",
"type_name": "germplasm descriptors",
"url_syntax": "https://npgsweb.ars-grin.gov/gringlobal/descriptordetail.aspx?id=[example_id]"
}
],
"generic_urls": [
"https://www.ars-grin.gov/"
],
"name": "Germplasm Resources Information Network"
},
"GR_Ensembl": {
"database": "GR_Ensembl",
"entity_types": [
{
"example_id": "GR_Ensembl:At1g10040",
"example_url": "http://gramene.org/?idList=At1g10040",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://gramene.org/?idList=[example_id]"
}
],
"generic_urls": [
"http://www.gramene.org/"
],
"name": "Gramene"
},
"GR_GENE": {
"database": "GR_GENE",
"entity_types": [
{
"example_id": "GR_GENE:GR:0060198",
"example_url": "http://www.gramene.org/db/genes/search_gene?acc=GR:0060198",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.gramene.org/db/genes/search_gene?acc=[example_id]"
}
],
"generic_urls": [
"http://www.gramene.org/"
],
"name": "Gramene",
"rdf_uri_prefix": "http://identifiers.org/gramene.gene/",
"synonyms": [
"GR_gene"
]
},
"GR_MUT": {
"database": "GR_MUT",
"entity_types": [
{
"example_id": "GR_MUT:GR:0060198",
"example_url": "http://www.gramene.org/db/genes/search_gene?acc=GR:0060198",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.gramene.org/db/genes/search_gene?acc=[example_id]"
}
],
"generic_urls": [
"http://www.gramene.org/"
],
"name": "A Comparative Mapping Resource for Grains"
},
"GR_PROTEIN": {
"database": "GR_PROTEIN",
"entity_types": [
{
"example_id": "GR_PROTEIN:Q6VSV0",
"example_url": "http://www.gramene.org/db/protein/protein_search?acc=Q6VSV0",
"id_syntax": "[A-Z][0-9][A-Z0-9]{3}[0-9]",
"type_id": "PR:000000001",
"type_name": "protein",
"url_syntax": "http://www.gramene.org/db/protein/protein_search?acc=[example_id]"
}
],
"generic_urls": [
"http://www.gramene.org/"
],
"name": "Gramene",
"rdf_uri_prefix": "http://identifiers.org/gramene.protein/",
"synonyms": [
"GR_protein"
]
},
"GR_QTL": {
"database": "GR_QTL",
"entity_types": [
{
"example_id": "GR_QTL:CQU7",
"example_url": "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=CQU7",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=[example_id]"
}
],
"generic_urls": [
"http://www.gramene.org/"
],
"name": "Gramene",
"rdf_uri_prefix": "http://identifiers.org/gramene.qtl/"
},
"GR_REF": {
"database": "GR_REF",
"entity_types": [
{
"example_id": "GR_REF:659",
"example_url": "http://www.gramene.org/db/literature/pub_search?ref_id=659",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.gramene.org/db/literature/pub_search?ref_id=[example_id]"
}
],
"generic_urls": [
"http://www.gramene.org/"
],
"name": "Gramene"
},
"GenBank": {
"database": "GenBank",
"description": "The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.",
"entity_types": [
{
"example_id": "GB:AA816246",
"example_url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AA816246",
"id_syntax": "([A-Z]{2}[0-9]{6})|([A-Z]{1}[0-9]{5})",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=[example_id]"
},
{
"example_id": "GB:AA816246",
"example_url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AA816246",
"id_syntax": "([A-Z]{2}[0-9]{6})|([A-Z]{1}[0-9]{5})",
"type_id": "PR:000000001",
"type_name": "protein",
"url_syntax": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=[example_id]"
}
],
"generic_urls": [
"http://www.ncbi.nlm.nih.gov/Genbank/"
],
"name": "GenBank",
"synonyms": [
"GB"
]
},
"Gene3D": {
"database": "Gene3D",
"entity_types": [
{
"example_id": "Gene3D:3.30.390.30",
"example_url": "http://gene3d.biochem.ucl.ac.uk/search?mode=family&sterm=3.30.390.30",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://gene3d.biochem.ucl.ac.uk/search?mode=family&sterm=[example_id]"
}
],
"generic_urls": [
"http://gene3d.biochem.ucl.ac.uk/Gene3D/"
],
"name": "Domain Architecture Classification"
},
"GeneDB": {
"database": "GeneDB",
"entity_types": [
{
"example_id": "PF3D7_1467300",
"example_url": "http://www.genedb.org/gene/PF3D7_1467300",
"id_syntax": "((LmjF|LinJ|LmxM)\\.[0-9]{2}\\.[0-9]{4})|(PF3D7_[0-9]{7})|(Tb[0-9]+\\.[A-Za-z0-9]+\\.[0-9]+)|(TcCLB\\.[0-9]{6}\\.[0-9]+)",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "http://www.genedb.org/gene/[example_id]"
}
],
"generic_urls": [
"http://www.genedb.org/gene/"
],
"name": "GeneDB",
"rdf_uri_prefix": "http://identifiers.org/genedb/"
},
"Genesys-pgr": {
"database": "Genesys-pgr",
"entity_types": [
{
"example_id": "Genesys-pgr:CM1015-16",
"example_url": "https://www.genesys-pgr.org/acn/search?q=CM1015-16",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.genesys-pgr.org/acn/search?q=[example_id]"
}
],
"generic_urls": [
"https://www.genesys-pgr.org/"
],
"name": "Gene DB, Genesys"
},
"H-invDB": {
"database": "H-invDB",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.h-invitational.jp/"
],
"name": "H-invitational Database"
},
"H-invDB_cDNA": {
"database": "H-invDB_cDNA",
"entity_types": [
{
"example_id": "H-invDB_cDNA:AK093148",
"example_url": "http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=AK093149",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=[example_id]"
}
],
"generic_urls": [
"http://www.h-invitational.jp/"
],
"name": "H-invitational Database"
},
"H-invDB_locus": {
"database": "H-invDB_locus",
"entity_types": [
{
"example_id": "H-invDB_locus:HIX0014446",
"example_url": "http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=HIX0014446",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=[example_id]"
}
],
"generic_urls": [
"http://www.h-invitational.jp/"
],
"name": "H-invitational Database"
},
"HAMAP": {
"database": "HAMAP",
"entity_types": [
{
"example_id": "HAMAP:MF_00031",
"example_url": "http://hamap.expasy.org/unirule/MF_00131",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://hamap.expasy.org/unirule/[example_id]"
}
],
"generic_urls": [
"http://hamap.expasy.org/"
],
"name": "High-quality Automated and Manual Annotation of microbial Proteomes"
},
"HGNC": {
"database": "HGNC",
"entity_types": [
{
"example_id": "HGNC:29",
"example_url": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:29",
"id_syntax": "[0-9]+",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:[example_id]"
}
],
"generic_urls": [
"http://www.genenames.org/"
],
"name": "HUGO Gene Nomenclature Committee",
"rdf_uri_prefix": "http://identifiers.org/hgnc/"
},
"HGNC-UCL": {
"database": "HGNC-UCL",
"description": "While based at UCL, HGNC provided GO annotations for proteins during the process of assigning approved gene names and symbols",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"https://www.ucl.ac.uk/cardiovascular/hgnc-gene-annotation"
],
"name": "UCL-based HGNC"
},
"HPA": {
"database": "HPA",
"entity_types": [
{
"example_id": "HPA:HPA000237",
"example_url": "http://www.proteinatlas.org/tissue_profile.php?antibody_id=HPA000237",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.proteinatlas.org/tissue_profile.php?antibody_id=[example_id]"
}
],
"generic_urls": [
"http://www.proteinatlas.org/"
],
"name": "Human Protein Atlas tissue profile information"
},
"HPA_antibody": {
"database": "HPA_antibody",
"entity_types": [
{
"example_id": "HPA_antibody:HPA000237",
"example_url": "http://www.proteinatlas.org/antibody_info.php?antibody_id=HPA000237",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.proteinatlas.org/antibody_info.php?antibody_id=[example_id]"
}
],
"generic_urls": [
"http://www.proteinatlas.org/"
],
"name": "Human Protein Atlas antibody information"
},
"HUGO": {
"database": "HUGO",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.hugo-international.org/"
],
"name": "Human Genome Organisation"
},
"IAO": {
"database": "IAO",
"description": "Ontology of information entities, including ontology metadata relations.",
"generic_urls": [
"http://purl.obolibrary.org/obo/iao"
],
"name": "Information Artifact Ontology",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/IAO_"
},
"IMG": {
"database": "IMG",
"entity_types": [
{
"example_id": "IMG:640008772",
"example_url": "http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=640008772",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=[example_id]"
}
],
"generic_urls": [
"http://img.jgi.doe.gov"
],
"name": "Integrated Microbial Genomes; JGI web site for genome annotation"
},
"IMGT_HLA": {
"database": "IMGT_HLA",
"entity_types": [
{
"example_id": "IMGT_HLA:HLA00031",
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.ebi.ac.uk/imgt/hla"
],
"name": "IMGT/HLA human major histocompatibility complex sequence database"
},
"IMGT_LIGM": {
"database": "IMGT_LIGM",
"description": "Database of immunoglobulins and T cell receptors from human and other vertebrates, with translation for fully annotated sequences.",
"entity_types": [
{
"example_id": "IMGT_LIGM:U03895",
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.imgt.org/"
],
"name": "ImMunoGeneTics database covering immunoglobulins and T-cell receptors"
},
"IRGC": {
"database": "IRGC",
"entity_types": [
{
"example_id": "IRGC:10012",
"example_url": "https://www.genesys-pgr.org/acn/search?q=IRGC+10013",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.genesys-pgr.org/acn/search?q=IRGC+[example_id]"
}
],
"generic_urls": [
"https://www.genesys-pgr.org"
],
"name": "International Rice Genebank Collection"
},
"IRIC": {
"database": "IRIC",
"entity_types": [
{
"example_id": "IRIS_313-8922",
"example_url": "https://oryzasnp.org/_variety.zul?irisid=IRIS_313-8922",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://oryzasnp.org/_variety.zul?irisid=[example_id]"
}
],
"generic_urls": [
"https://oryzasnp.org"
],
"name": "International Rice Research Institute"
},
"ISBN": {
"database": "ISBN",
"entity_types": [
{
"example_id": "ISBN:0781702534",
"example_url": "https://www.worldcat.org/search?q=bn%3A0781702534",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.worldcat.org/search?q=bn%3A[example_id]"
}
],
"generic_urls": [
"https://www.worldcat.org"
],
"name": "International Standard Book Number"
},
"ISSN": {
"database": "ISSN",
"entity_types": [
{
"example_id": "ISSN:1234-1231",
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.issn.org/"
],
"name": "International Standard Serial Number"
},
"IUPHAR/BPS": {
"database": "IUPHAR/BPS",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"https://www.guidetopharmacology.org/"
],
"name": "IUPHAR/BPS Guide to Pharmacology"
},
"IUPHAR_GPCR": {
"database": "IUPHAR_GPCR",
"entity_types": [
{
"example_id": "IUPHAR_GPCR:13",
"example_url": "https://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=13",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=[example_id]"
}
],
"generic_urls": [
"http://www.iuphar.org/"
],
"name": "International Union of Pharmacology"
},
"IUPHAR_RECEPTOR": {
"database": "IUPHAR_RECEPTOR",
"entity_types": [
{
"example_id": "IUPHAR_RECEPTOR:56",
"example_url": "https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=56",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=[example_id]"
}
],
"generic_urls": [
"http://www.iuphar.org/"
],
"name": "International Union of Pharmacology"
},
"IntAct": {
"database": "IntAct",
"entity_types": [
{
"example_id": "IntAct:EBI-17086",
"example_url": "https://www.ebi.ac.uk/intact/pages/interactions/interactions.xhtml?query=EBI-17086",
"id_syntax": "EBI-[0-9]+",
"type_id": "BET:0000013",
"type_name": "molecular interaction",
"url_syntax": "https://www.ebi.ac.uk/intact/pages/interactions/interactions.xhtml?query=[example_id]"
},
{
"example_id": "IntAct:EBI-10205244",
"example_url": "http://www.ebi.ac.uk/complexportal/complex/EBI-10205244",
"id_syntax": "EBI-[0-9]+",
"type_id": "GO:0032991",
"type_name": "protein-containing complex",
"url_syntax": "http://www.ebi.ac.uk/complexportal/complex/[example_id]"
}
],
"generic_urls": [
"https://www.ebi.ac.uk/intact/"
],
"name": "IntAct protein interaction database",
"rdf_uri_prefix": "http://identifiers.org/intact/"
},
"InterPro": {
"database": "InterPro",
"entity_types": [
{
"example_id": "InterPro:IPR000001",
"example_url": "http://www.ebi.ac.uk/interpro/entry/IPR015421",
"id_syntax": "IPR\\d{6}",
"type_id": "SO:0000839",
"type_name": "polypeptide region",
"url_syntax": "http://www.ebi.ac.uk/interpro/entry/[example_id]"
}
],
"generic_urls": [
"http://www.ebi.ac.uk/interpro/"
],
"name": "InterPro database of protein domains and motifs",
"rdf_uri_prefix": "http://identifiers.org/interpro/",
"synonyms": [
"INTERPRO",
"IPR"
]
},
"JSTOR": {
"database": "JSTOR",
"entity_types": [
{
"example_id": "JSTOR:3093870",
"example_url": "https://www.jstor.org/stable/3093870",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.jstor.org/stable/[example_id]"
}
],
"generic_urls": [
"https://www.jstor.org/"
],
"name": "Digital archive of scholarly articles"
},
"Jaiswal_Lab": {
"database": "Jaiswal_Lab",
"entity_types": [
{
"example_id": "Jaiswal_Lab:gene00002",
"example_url": "http://wiki.plantontology.org/index.php/PO_REF:00008",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://wiki.plantontology.org/index.php/PO_REF:00008"
}
],
"generic_urls": [
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],
"name": "Jaiswal_Lab"
},
"JaponicusDB": {
"database": "JaponicusDB",
"entity_types": [
{
"example_id": "JaponicusDB:SJAG_01143",
"example_url": "https://www.japonicusdb.org/gene/SJAG_01143",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "https://www.japonicusdb.org/gene/[example_id]"
}
],
"generic_urls": [
"https://www.japonicusdb.org/"
],
"name": "JaponicusDB"
},
"KEGG": {
"database": "KEGG",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.genome.ad.jp/kegg/"
],
"name": "Kyoto Encyclopedia of Genes and Genomes"
},
"KEGG_ENZYME": {
"database": "KEGG_ENZYME",
"entity_types": [
{
"example_id": "KEGG_ENZYME:2.1.1.4",
"example_url": "http://www.genome.jp/dbget-bin/www_bget?ec:2.1.1.4",
"id_syntax": "\\d(\\.\\d{1,2}){2}\\.\\d{1,3}",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.genome.jp/dbget-bin/www_bget?ec:[example_id]"
}
],
"generic_urls": [
"http://www.genome.jp/dbget-bin/www_bfind?enzyme"
],
"name": "KEGG Enzyme Database",
"rdf_uri_prefix": "http://identifiers.org/kegg.enzyme/"
},
"KEGG_LIGAND": {
"database": "KEGG_LIGAND",
"entity_types": [
{
"example_id": "KEGG_LIGAND:C00577",
"example_url": "http://www.genome.jp/dbget-bin/www_bget?cpd:C00577",
"id_syntax": "C\\d{5}",
"type_id": "CHEBI:24431",
"type_name": "chemical entity",
"url_syntax": "http://www.genome.jp/dbget-bin/www_bget?cpd:[example_id]"
}
],
"generic_urls": [
"http://www.genome.ad.jp/kegg/docs/upd_ligand.html"
],
"name": "KEGG LIGAND Database"
},
"KEGG_PATHWAY": {
"database": "KEGG_PATHWAY",
"entity_types": [
{
"example_id": "KEGG_PATHWAY:ot00020",
"example_url": "http://www.genome.jp/dbget-bin/www_bget?path:ot00020",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.genome.jp/dbget-bin/www_bget?path:[example_id]"
}
],
"generic_urls": [
"http://www.genome.jp/kegg/pathway.html"
],
"name": "KEGG Pathways Database",
"rdf_uri_prefix": "http://identifiers.org/kegg.pathway/"
},
"KEGG_REACTION": {
"database": "KEGG_REACTION",
"entity_types": [
{
"example_id": "KEGG:R02328",
"example_url": "http://www.genome.jp/dbget-bin/www_bget?rn:R02328",
"id_syntax": "R\\d+",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.genome.jp/dbget-bin/www_bget?rn:[example_id]"
}
],
"generic_urls": [
"http://www.genome.jp/kegg/reaction/"
],
"name": "KEGG Reaction Database"
},
"LIFEdb": {
"database": "LIFEdb",
"description": "LifeDB is a database for information on protein localization, interaction, functional assays and expression.",
"entity_types": [
{
"example_id": "LIFEdb:DKFZp564O1716",
"example_url": "https://www.dkfz.de/en/mga/Groups/LIFEdb-Database.html?ID=DKFZp564O1716",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.dkfz.de/en/mga/Groups/LIFEdb-Database.html?ID=[example_id]"
}
],
"generic_urls": [
"http://www.lifedb.de/"
],
"name": "LifeDB"
},
"MA": {
"database": "MA",
"description": "Adult Mouse Anatomical Dictionary; part of Gene Expression Database",
"entity_types": [
{
"example_id": "MA:0000003",
"example_url": "http://www.informatics.jax.org/searches/AMA.cgi?id=MA:0000003",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.informatics.jax.org/searches/AMA.cgi?id=MA:[example_id]"
}
],
"generic_urls": [
"http://www.informatics.jax.org/"
],
"name": "Adult Mouse Anatomical Dictionary",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/MA_"
},
"MACSC_REF": {
"database": "MACSC_REF",
"entity_types": [
{
"example_id": "MACSC_REF:78112",
"example_url": "http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=78112",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=[example_id]"
}
],
"generic_urls": [
"http://www.maizegdb.org/"
],
"name": "Maize Genetics and Genomics Database"
},
"MEDLINE": {
"database": "MEDLINE",
"entity_types": [
{
"example_id": "MEDLINE:20572430",
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.nlm.nih.gov/databases/databases_medline.html"
],
"name": "Medline literature database"
},
"MEROPS": {
"database": "MEROPS",
"entity_types": [
{
"example_id": "MEROPS:A08.001",
"example_url": "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=A08.001",
"id_syntax": "^[SCTAGMNU]\\d{2}\\.([AB]\\d{2}|\\d{3}|[A-Z]{3})$",
"type_id": "PR:000000001",
"type_name": "protein",
"url_syntax": "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=[example_id]"
}
],
"generic_urls": [
"https://www.ebi.ac.uk/merops/"
],
"name": "MEROPS peptidase database"
},
"MEROPS_fam": {
"database": "MEROPS_fam",
"entity_types": [
{
"example_id": "MEROPS_fam:M18",
"example_url": "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=M18",
"id_syntax": "^[SCTAGMNU]\\d+$",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=[example_id]"
},
{
"example_id": "MEROPS_fam:M18",
"example_url": "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=M18",
"id_syntax": "^[SCTAGMNU]\\d+$",
"type_id": "NCIT:C20130",
"type_name": "protein family",
"url_syntax": "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=[example_id]"
}
],
"generic_urls": [
"https://www.ebi.ac.uk/merops"
],
"name": "MEROPS peptidase database"
},
"MGCSC_GENETIC_STOCKS": {
"database": "MGCSC_GENETIC_STOCKS",
"entity_types": [
{
"example_id": "MGCSC_GENETIC_STOCKS:78112",
"example_url": "http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=78112",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.maizegdb.org/cgi-bin/displaystockrecord.cgi?id=[example_id]"
}
],
"generic_urls": [
"http://www.maizegdb.org"
],
"name": "Maize Genetics and Genomics Database"
},
"MGD": {
"database": "MGD",
"entity_types": [
{
"example_id": "MGD:Adcy9",
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.informatics.jax.org/"
],
"name": "Mouse Genome Database"
},
"MGI": {
"database": "MGI",
"entity_types": [
{
"example_id": "MGI:MGI:1345277",
"example_url": "http://www.informatics.jax.org/accession/MGI:1345277",
"id_syntax": "MGI:[0-9]{5,}",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "http://www.informatics.jax.org/accession/[example_id]"
},
{
"example_id": "MGI:MGI:3590672",
"example_url": "http://www.informatics.jax.org/accession/MGI:3590672",
"id_syntax": "MGI:[0-9]{5,}",
"type_id": "VariO:0001",
"type_name": "variation",
"url_syntax": "http://www.informatics.jax.org/accession/[example_id]"
}
],
"generic_urls": [
"http://www.informatics.jax.org/"
],
"name": "Mouse Genome Informatics",
"rdf_uri_prefix": "http://identifiers.org/MGI/"
},
"MIPS_funcat": {
"database": "MIPS_funcat",
"entity_types": [
{
"example_id": "MIPS_funcat:11.02",
"example_url": "http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=11.02",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=[example_id]"
}
],
"generic_urls": [
"http://mips.gsf.de/proj/funcatDB/"
],
"name": "MIPS Functional Catalogue"
},
"MITRE": {
"database": "MITRE",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.mitre.org/"
],
"name": "The MITRE Corporation"
},
"MaizeGDB": {
"database": "MaizeGDB",
"entity_types": [
{
"example_id": "MaizeGDB:12098",
"example_url": "https://maizegdb.org/gene_center/gene/12098",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://maizegdb.org/gene_center/gene/[example_id]"
}
],
"generic_urls": [
"https://www.maizegdb.org/"
],
"name": "MaizeGDB"
},
"MaizeGDB_Locus": {
"database": "MaizeGDB_Locus",
"entity_types": [
{
"example_id": "MaizeGDB_Locus:25011",
"example_url": "https://www.maizegdb.org/gene_center/gene/25011",
"id_syntax": "[A-Za-z][A-Za-z0-9]*",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "https://www.maizegdb.org/gene_center/gene/[example_id]"
}
],
"generic_urls": [
"https://www.maizegdb.org/"
],
"name": "MaizeGDB",
"rdf_uri_prefix": "http://identifiers.org/maizegdb.locus/"
},
"MaizeGDB_QTL": {
"database": "MaizeGDB_QTL",
"entity_types": [
{
"example_id": "MaizeGDB_QTL:78112",
"example_url": "https://www.maizegdb.org/data_center/trait?id=78112",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.maizegdb.org/data_center/trait?id=[example_id]"
}
],
"generic_urls": [
"https://www.maizegdb.org/"
],
"name": "Maize Genetics and Genomics Database"
},
"MaizeGDB_REF": {
"database": "MaizeGDB_REF",
"entity_types": [
{
"example_id": "MaizeGDB_REF:9021423",
"example_url": "http://maizegdb.org/data_center/reference?id=9021423",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://maizegdb.org/data_center/reference?id=[example_id]"
}
],
"generic_urls": [
"https://www.maizegdb.org/"
],
"name": "Maize Genetics and Genomics Database"
},
"MaizeGDB_stock": {
"database": "MaizeGDB_stock",
"entity_types": [
{
"example_id": "MaizeGDB_stock:282110",
"example_url": "https://maizegdb.org/data_center/stock?id=282110",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://maizegdb.org/data_center/stock?id=[example_id]"
}
],
"generic_urls": [
"https://www.maizegdb.org/"
],
"name": "Maize Genetics and Genomics Database"
},
"MeSH": {
"database": "MeSH",
"entity_types": [
{
"example_id": "MeSH:D017209",
"example_url": "http://id.nlm.nih.gov/mesh/D017209",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://id.nlm.nih.gov/mesh/[example_id]"
}
],
"generic_urls": [
"https://meshb.nlm.nih.gov"
],
"name": "Medical Subject Headings",
"synonyms": [
"MESH",
"MSH"
]
},
"MetaCyc": {
"database": "MetaCyc",
"entity_types": [
{
"example_id": "MetaCyc:GLUTDEG-PWY",
"example_url": "https://biocyc.org/META/NEW-IMAGE?type=NIL&object=GLUTDEG-PWY",
"id_syntax": "^[A-Za-z0-9+_.%-:]+$",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://biocyc.org/META/NEW-IMAGE?type=NIL&object=[example_id]"
}
],
"generic_urls": [
"https://metacyc.org/"
],
"name": "Metabolic Encyclopedia of metabolic and other pathways",
"rdf_uri_prefix": "http://identifiers.org/metacyc.reaction/",
"synonyms": [
"METACYC"
]
},
"ModBase": {
"database": "ModBase",
"entity_types": [
{
"example_id": "ModBase:P10815",
"example_url": "http://salilab.org/modbase/searchbyid?databaseID=P04848",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://salilab.org/modbase/searchbyid?databaseID=[example_id]"
}
],
"generic_urls": [
"http://modbase.compbio.ucsf.edu/"
],
"name": "ModBase comprehensive Database of Comparative Protein Structure Models"
},
"NASC_code": {
"database": "NASC_code",
"entity_types": [
{
"example_id": "NASC_code:N3371",
"example_url": "http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=N3371",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=[example_id]"
}
],
"generic_urls": [
"http://arabidopsis.info"
],
"name": "Nottingham Arabidopsis Stock Centre Seeds Database",
"synonyms": [
"NASC"
]
},
"NC-IUBMB": {
"database": "NC-IUBMB",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.chem.qmw.ac.uk/iubmb/"
],
"name": "Nomenclature Committee of the International Union of Biochemistry and Molecular Biology"
},
"NCBI": {
"database": "NCBI",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.ncbi.nlm.nih.gov/"
],
"name": "National Center for Biotechnology Information"
},
"NCBIGene": {
"database": "NCBIGene",
"entity_types": [
{
"example_id": "NCBI_Gene:4771",
"example_url": "https://www.ncbi.nlm.nih.gov/gene/4771",
"id_syntax": "\\d+",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "https://www.ncbi.nlm.nih.gov/gene/[example_id]"
}
],
"generic_urls": [
"http://www.ncbi.nlm.nih.gov/"
],
"name": "NCBI Gene",
"rdf_uri_prefix": "http://identifiers.org/ncbigene/",
"synonyms": [
"GeneID",
"LocusID",
"NCBI_Gene"
]
},
"NCBITaxon": {
"database": "NCBITaxon",
"entity_types": [
{
"example_id": "NCBITaxon:7227",
"example_url": "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3702",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=[example_id]"
}
],
"generic_urls": [
"http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/"
],
"name": "NCBI Taxonomy",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/NCBITaxon_",
"synonyms": [
"taxon",
"ncbi_taxid"
]
},
"NCBI_GP": {
"database": "NCBI_GP",
"entity_types": [
{
"example_id": "NCBI_GP:EAL72968",
"example_url": "https://www.ncbi.nlm.nih.gov/protein/EAL72968",
"id_syntax": "[A-Z]{3}[0-9]{5}(\\.[0-9]+)?",
"type_id": "PR:000000001",
"type_name": "protein",
"url_syntax": "https://www.ncbi.nlm.nih.gov/protein/[example_id]"
}
],
"generic_urls": [
"http://www.ncbi.nlm.nih.gov/"
],
"name": "NCBI GenPept"
},
"NCBI_NP": {
"database": "NCBI_NP",
"generic_urls": [
"https://www.ncbi.nlm.nih.gov/protein"
],
"name": "NCBI Protein"
},
"NCBI_gi": {
"database": "NCBI_gi",
"entity_types": [
{
"example_id": "NCBI_gi:113194944",
"example_url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=113194944",
"id_syntax": "[0-9]{5,}",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id]"
}
],
"generic_urls": [
"http://www.ncbi.nlm.nih.gov/"
],
"name": "NCBI databases"
},
"NCBI_locus_tag": {
"database": "NCBI_locus_tag",
"entity_types": [
{
"example_id": "NCBI_locus_tag:CTN_0547",
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.ncbi.nlm.nih.gov/"
],
"name": "NCBI locus tag"
},
"NIF_Subcellular": {
"database": "NIF_Subcellular",
"entity_types": [
{
"example_id": "NIF_Subcellular:sao1186862860",
"example_url": "http://www.neurolex.org/wiki/sao1770195789",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.neurolex.org/wiki/[example_id]"
}
],
"generic_urls": [
"http://www.neurolex.org/wiki"
],
"name": "Neuroscience Information Framework standard ontology, subcellular hierarchy"
},
"NTNU_SB": {
"database": "NTNU_SB",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.ntnu.edu/nt/systemsbiology"
],
"name": "Norwegian University of Science and Technology, Systems Biology team"
},
"OBI": {
"database": "OBI",
"entity_types": [
{
"example_id": "OBI:0000038",
"example_url": "http://purl.obolibrary.org/obo/OBI_0000038",
"id_syntax": "\\d{7}",
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://obi-ontology.org/"
],
"name": "Ontology for Biomedical Investigations"
},
"OMIM": {
"database": "OMIM",
"entity_types": [
{
"example_id": "OMIM:190198",
"example_url": "https://omim.org/entry/190198",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://omim.org/entry/[example_id]"
}
],
"generic_urls": [
"https://omim.org/"
],
"name": "Mendelian Inheritance in Man",
"synonyms": [
"MIM"
]
},
"OMSSA": {
"database": "OMSSA",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://pubchem.ncbi.nlm.nih.gov/omssa/"
],
"name": "Open Mass Spectrometry Search Algorithm"
},
"PANTHER": {
"database": "PANTHER",
"entity_types": [
{
"example_id": "PANTHER:PTHR11455",
"example_url": "http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR10000",
"id_syntax": "PTN[0-9]{9}|PTHR[0-9]{5}|PTHR[0-9]{5}:SF[0-9]+",
"type_id": "NCIT:C20130",
"type_name": "protein family",
"url_syntax": "http://www.pantherdb.org/panther/lookupId.jsp?id=[example_id]"
}
],
"generic_urls": [
"http://www.pantherdb.org/"
],
"name": "Protein ANalysis THrough Evolutionary Relationships Classification System",
"rdf_uri_prefix": "http://identifiers.org/panther.family/"
},
"PATO": {
"database": "PATO",
"entity_types": [
{
"example_id": "PATO:0001420",
"example_url": "http://purl.obolibrary.org/obo/PATO_0001420",
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.obofoundry.org/ontology/pato.html"
],
"name": "Phenotypic quality ontology",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/PATO_"
},
"PATRIC": {
"database": "PATRIC",
"description": "PathoSystems Resource Integration Center at the Virginia Bioinformatics Institute",
"entity_types": [
{
"example_id": "PATRIC:fig%7C83332.12.peg.11",
"example_url": "https://www.patricbrc.org/view/Feature/fig%7C83332.12.peg.1",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.patricbrc.org/view/Feature/[example_id]"
}
],
"generic_urls": [
"https://www.patricbrc.org"
],
"name": "PathoSystems Resource Integration Center"
},
"PDB": {
"database": "PDB",
"entity_types": [
{
"example_id": "PDB:1A4U",
"example_url": "https://www.rcsb.org/structure/1A4U",
"id_syntax": "[A-Za-z0-9]{4}",
"type_id": "PR:000000001",
"type_name": "protein",
"url_syntax": "https://www.rcsb.org/structure/[example_id]"
}
],
"generic_urls": [
"https://www.rcsb.org/pdb/"
],
"name": "Protein Data Bank"
},
"PHI-base": {
"database": "PHI-base",
"description": "PHI-base catalogues experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts.",
"entity_types": [
{
"example_id": "PHI:3",
"example_url": "http://www.phi-base.org/searchFacet.htm?queryTerm=PHI:3",
"id_syntax": "PHI:[0-9]+",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.phi-base.org/searchFacet.htm?queryTerm=PHI:[example_id]"
}
],
"generic_urls": [
"http://www.phi-base.org/"
],
"name": "Pathogen-Host Interactions Database"
},
"PIR": {
"database": "PIR",
"entity_types": [
{
"example_id": "PIR:I49499",
"example_url": "https://proteininformationresource.org/cgi-bin/nbrfget?uid=I49499",
"id_syntax": "[A-Z]{1}[0-9]{5}",
"type_id": "PR:000000001",
"type_name": "protein",
"url_syntax": "https://proteininformationresource.org/cgi-bin/nbrfget?uid=[example_id]"
}
],
"generic_urls": [
"https://proteininformationresource.org/"
],
"name": "Protein Information Resource"
},
"PIRSF": {
"database": "PIRSF",
"entity_types": [
{
"example_id": "PIRSF:SF002327",
"example_url": "http://pir.georgetown.edu/cgi-bin/ipcSF?id=SF002327",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://pir.georgetown.edu/cgi-bin/ipcSF?id=[example_id]"
}
],
"generic_urls": [
"http://pir.georgetown.edu/pirsf/"
],
"name": "PIR Superfamily Classification System"
},
"PMCID": {
"database": "PMCID",
"entity_types": [
{
"example_id": "PMCID:PMC201377",
"example_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC201377/",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.ncbi.nlm.nih.gov/pmc/articles/[example_id]"
}
],
"generic_urls": [
"https://www.ncbi.nlm.nih.gov/pmc/"
],
"name": "Pubmed Central",
"synonyms": [
"PMC"
]
},
"PMID": {
"database": "PMID",
"entity_types": [
{
"example_id": "PMID:31931324",
"example_url": "https://www.ncbi.nlm.nih.gov/pubmed/31931324",
"id_syntax": "[0-9]+",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.ncbi.nlm.nih.gov/pubmed/[example_id]"
}
],
"generic_urls": [
"https://www.ncbi.nlm.nih.gov/pubmed"
],
"name": "PubMed",
"synonyms": [
"PUBMED"
]
},
"PO": {
"database": "PO",
"entity_types": [
{
"example_id": "PO:0009004",
"example_url": "http://browser.planteome.org/amigo/term/PO:0009004",
"id_syntax": "[0-9]{7}",
"type_id": "PO:0025131",
"type_name": "plant anatomical entity",
"url_syntax": "http://browser.planteome.org/amigo/term/PO:[example_id]"
},
{
"example_id": "PO:0025131",
"example_url": "http://browser.planteome.org/amigo/term/PO:0025131",
"id_syntax": "[0-9]{7}",
"type_id": "PO:0009012",
"type_name": "plant structure development stage",
"url_syntax": "http://browser.planteome.org/amigo/term/PO:[example_id]"
}
],
"generic_urls": [
"http://www.planteome.org/"
],
"name": "Plant Ontology",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/PO_"
},
"POC": {
"database": "POC",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.plantontology.org/"
],
"name": "Plant Ontology Consortium"
},
"PO_REF": {
"database": "PO_REF",
"entity_types": [
{
"example_id": "PO_REF:00001",
"example_url": "http://planteome.org/po_ref/00001",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://planteome.org/po_ref/[example_id]"
}
],
"generic_urls": [
"http://planteome.org/po_ref"
],
"name": "Plant Ontology custom references"
},
"PPI": {
"database": "PPI",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.pseudomonas-syringae.org/"
],
"name": "Pseudomonas syringae community annotation project"
},
"PR": {
"database": "PR",
"entity_types": [
{
"example_id": "PR:Q64445",
"example_url": "https://purl.obolibrary.org/obo/PR_000060258",
"id_syntax": "([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}){1}(-[0-9]+){0,1}|[0-9]{9}",
"type_id": "PR:000000001",
"type_name": "protein",
"url_syntax": "https://purl.obolibrary.org/obo/PR_[example_id]"
}
],
"generic_urls": [
"https://proconsortium.org/"
],
"name": "Protein Ontology",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/PR_",
"synonyms": [
"PRO"
]
},
"PRINTS": {
"database": "PRINTS",
"entity_types": [
{
"example_id": "PRINTS:PR00025",
"example_url": "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=PR00025",
"id_syntax": "PR[0-9]{5}",
"type_id": "SO:0000839",
"type_name": "polypeptide region",
"url_syntax": "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=[example_id]"
}
],
"generic_urls": [
"http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/"
],
"name": "PRINTS compendium of protein fingerprints"
},
"PSI-MI": {
"database": "PSI-MI",
"entity_types": [
{
"example_id": "MI_0018",
"example_url": "http://purl.obolibrary.org/obo/MI_0018",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://purl.obolibrary.org/obo/"
}
],
"generic_urls": [
"http://www.psidev.info/"
],
"name": "Proteomic Standard Initiative for Molecular Interaction",
"synonyms": [
"MI"
]
},
"PSI-MOD": {
"database": "PSI-MOD",
"entity_types": [
{
"example_id": "MOD_00219",
"example_url": "http://purl.obolibrary.org/obo/MOD_00219",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://purl.obolibrary.org/obo/[example_id]"
}
],
"generic_urls": [
"http://www.psidev.info/groups/protein-modifications"
],
"name": "Proteomics Standards Initiative protein modification ontology",
"synonyms": [
"MOD"
]
},
"PSORT": {
"database": "PSORT",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"https://www.psort.org/"
],
"name": "PSORT protein subcellular localization databases and prediction tools for bacteria"
},
"ParkinsonsUK-UCL": {
"database": "ParkinsonsUK-UCL",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"https://www.ucl.ac.uk/cardiovascular/research/pre-clinical-and-fundamental-science/functional-gene-annotation/neurological-gene"
],
"name": "Parkinsons Disease Gene Ontology Initiative"
},
"Pfam": {
"database": "Pfam",
"description": "Pfam is a collection of protein families represented by sequence alignments and hidden Markov models (HMMs)",
"entity_types": [
{
"example_id": "Pfam:PF00046",
"example_url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF00069",
"id_syntax": "PF[0-9]{5}",
"type_id": "SO:0000110",
"type_name": "sequence feature",
"url_syntax": "https://www.ebi.ac.uk/interpro/entry/pfam/[example_id]"
},
{
"example_id": "Pfam:PF00046",
"example_url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF00069",
"id_syntax": "PF[0-9]{5}",
"type_id": "SO:0000839",
"type_name": "polypeptide region",
"url_syntax": "https://www.ebi.ac.uk/interpro/entry/pfam/[example_id]"
}
],
"generic_urls": [
"https://www.ebi.ac.uk/interpro/entry/pfam"
],
"name": "Pfam database of protein families"
},
"PharmGKB": {
"database": "PharmGKB",
"entity_types": [
{
"example_id": "PharmGKB:PA267",
"example_url": "https://www.pharmgkb.org/do/serve?objId=PA267",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.pharmgkb.org/do/serve?objId=[example_id]"
}
],
"generic_urls": [
"https://www.pharmgkb.org"
],
"name": "Pharmacogenetics and Pharmacogenomics Knowledge Base"
},
"PhenoScape": {
"database": "PhenoScape",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://phenoscape.org/"
],
"name": "PhenoScape Knowledgebase"
},
"PlantSystematics_image_archive": {
"database": "PlantSystematics_image_archive",
"entity_types": [
{
"example_id": "PlantSystematics_image_archivee:37658",
"example_url": "http://www.plantsystematics.org/imagebyid_37658.html",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.plantsystematics.org/imagebyid_[example_id].html"
}
],
"generic_urls": [
"http://plantsystematics.org"
],
"name": "PlantSystematics.org"
},
"PlasmoDB": {
"database": "PlasmoDB",
"entity_types": [
{
"example_id": "PF3D7_1467300",
"example_url": "https://plasmodb.org/plasmo/app/record/gene/PF3D7_1467300",
"id_syntax": "PF3D7_[0-9]{7}",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "https://plasmodb.org/plasmo/app/record/gene/[example_id]"
}
],
"generic_urls": [
"https://plasmodb.org"
],
"name": "PlasmoDB",
"rdf_uri_prefix": "http://identifiers.org/plasmodb/"
},
"PomBase": {
"database": "PomBase",
"entity_types": [
{
"example_id": "PomBase:SPBC11B10.09",
"example_url": "https://www.pombase.org/gene/SPBC11B10.09",
"id_syntax": "S\\w+(\\.)?\\w+(\\.)?",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "https://www.pombase.org/gene/[example_id]"
}
],
"generic_urls": [
"https://www.pombase.org/"
],
"name": "PomBase",
"rdf_uri_prefix": "http://identifiers.org/pombase/"
},
"Pompep": {
"database": "Pompep",
"entity_types": [
{
"example_id": "Pompep:SPAC890.04C",
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"https://www.pombase.org/downloads/protein-datasets"
],
"name": "Schizosaccharomyces pombe protein data"
},
"Prosite": {
"database": "Prosite",
"entity_types": [
{
"example_id": "PDOC00314",
"example_url": "https://prosite.expasy.org/PDOC00314",
"id_syntax": "PDOC[0-9]{5}",
"type_id": "SO:0000839",
"type_name": "polypeptide region",
"url_syntax": "https://prosite.expasy.org/[example_id]"
}
],
"generic_urls": [
"https://prosite.expasy.org/"
],
"name": "Prosite database of protein families and domains"
},
"PseudoCAP": {
"database": "PseudoCAP",
"entity_types": [
{
"example_id": "PseudoCAP:PA4756",
"example_url": "http://www.pseudomonas.com/feature/show?locus_tag=PA4756",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.pseudomonas.com/feature/show?locus_tag=[example_id]"
}
],
"generic_urls": [
"http://www.pseudomonas.com"
],
"name": "Pseudomonas Genome Project"
},
"PubChem_BioAssay": {
"database": "PubChem_BioAssay",
"entity_types": [
{
"example_id": "PubChem_BioAssay:177",
"example_url": "https://pubchem.ncbi.nlm.nih.gov/bioassay/177",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://pubchem.ncbi.nlm.nih.gov/bioassay/[example_id]"
}
],
"generic_urls": [
"https://pubchem.ncbi.nlm.nih.gov"
],
"name": "NCBI PubChem database of bioassay records"
},
"PubChem_Compound": {
"database": "PubChem_Compound",
"entity_types": [
{
"example_id": "PubChem_Compound:159296",
"example_url": "https://pubchem.ncbi.nlm.nih.gov/compound/159296",
"id_syntax": "[0-9]+",
"type_id": "CHEBI:24431",
"type_name": "chemical entity",
"url_syntax": "https://pubchem.ncbi.nlm.nih.gov/compound/[example_id]"
}
],
"generic_urls": [
"https://pubchem.ncbi.nlm.nih.gov"
],
"name": "NCBI PubChem database of chemical structures"
},
"PubChem_Substance": {
"database": "PubChem_Substance",
"entity_types": [
{
"example_id": "PubChem_Substance:4594",
"example_url": "https://pubchem.ncbi.nlm.nih.gov/substance/4594",
"id_syntax": "[0-9]{4,}",
"type_id": "CHEBI:24431",
"type_name": "chemical entity",
"url_syntax": "https://pubchem.ncbi.nlm.nih.gov/substance/[example_id]"
}
],
"generic_urls": [
"https://pubchem.ncbi.nlm.nih.gov"
],
"name": "NCBI PubChem database of chemical substances"
},
"RAP-DB": {
"database": "RAP-DB",
"entity_types": [
{
"example_id": "RAP-DB:Os01t0100600-01",
"example_url": "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=Os01t0100600-01",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=[example_id]"
}
],
"generic_urls": [
"https://rapdb.dna.affrc.go.jp"
],
"name": "Rice annotation Project database"
},
"REBASE": {
"database": "REBASE",
"entity_types": [
{
"example_id": "REBASE:EcoRI",
"example_url": "http://rebase.neb.com/rebase/enz/EcoRI.html",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://rebase.neb.com/rebase/enz/[example_id].html"
}
],
"generic_urls": [
"http://rebase.neb.com/rebase/rebase.html"
],
"name": "REBASE restriction enzyme database"
},
"RESID": {
"database": "RESID",
"entity_types": [
{
"example_id": "RESID:AA0062",
"example_url": "https://proteininformationresource.org/cgi-bin/resid?id=AA0062",
"id_syntax": "AA[0-9]{4}",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://proteininformationresource.org/cgi-bin/resid?id=[example_id]"
}
],
"generic_urls": [
"https://proteininformationresource.org/resid/resid.shtml"
],
"name": "RESID Database of Protein Modifications"
},
"RGD": {
"database": "RGD",
"entity_types": [
{
"example_id": "RGD:2004",
"example_url": "https://rgd.mcw.edu/rgdweb/search/search.html?term=2004",
"id_syntax": "[0-9]{4,7}",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "https://rgd.mcw.edu/rgdweb/search/search.html?term=[example_id]"
}
],
"generic_urls": [
"https://rgd.mcw.edu/"
],
"name": "Rat Genome Database",
"rdf_uri_prefix": "http://identifiers.org/rgd/",
"synonyms": [
"RAD",
"RGDID"
]
},
"RHEA": {
"database": "RHEA",
"description": "Rhea is a manually annotated database of chemical reactions. All data in Rhea is freely accessible and available for anyone to use.",
"entity_types": [
{
"example_id": "RHEA:25811",
"example_url": "https://www.rhea-db.org/rhea/25811",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.rhea-db.org/rhea/[example_id]"
}
],
"generic_urls": [
"https://www.rhea-db.org"
],
"name": "Rhea, the Annotated Reactions Database"
},
"RNAcentral": {
"database": "RNAcentral",
"description": "An international database of ncRNA sequences",
"entity_types": [
{
"example_id": "RNAcentral:URS000047C79B_9606",
"example_url": "https://rnacentral.org/rna/URS000047C79B_9606",
"id_syntax": "URS[0-9A-F]{10}([_\\/][0-9]+){0,1}",
"type_id": "CHEBI:33697",
"type_name": "ribonucleic acid",
"url_syntax": "https://rnacentral.org/rna/[example_id]"
}
],
"generic_urls": [
"https://rnacentral.org"
],
"name": "RNAcentral"
},
"RNAmods": {
"database": "RNAmods",
"entity_types": [
{
"example_id": "RNAmods:20",
"example_url": "https://mods.rna.albany.edu/mods/modifications/view/20",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://mods.rna.albany.edu/mods/modifications/view/[example_id]"
}
],
"generic_urls": [
"https://mods.rna.albany.edu/"
],
"name": "RNA Modification Database",
"synonyms": [
"RNAMDB"
]
},
"RO": {
"database": "RO",
"description": "A collection of relations used across OBO ontologies",
"entity_types": [
{
"example_id": "RO:0002211",
"example_url": "http://purl.obolibrary.org/obo/RO_0002211",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://purl.obolibrary.org/obo/RO_[example_id]"
}
],
"generic_urls": [
"http://purl.obolibrary.org/obo/ro"
],
"name": "OBO Relation Ontology Ontology",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/RO_"
},
"Reactome": {
"database": "Reactome",
"entity_types": [
{
"example_id": "Reactome:R-HSA-109582",
"example_url": "https://www.reactome.org/content/detail/R-HSA-109582",
"id_syntax": "R-[A-Z]{3}-[0-9]+(-[0-9]+){0,1}(\\.[0-9]+){0,1}",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.reactome.org/content/detail/[example_id]"
}
],
"generic_urls": [
"https://www.reactome.org/"
],
"name": "Reactome - a curated knowledgebase of biological pathways",
"rdf_uri_prefix": "http://identifiers.org/reactome/",
"synonyms": [
"REACTOME",
"REAC"
]
},
"RefGenome": {
"database": "RefGenome",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.geneontology.org/GO.refgenome.shtml"
],
"name": "GO Reference Genomes",
"synonyms": [
"REFGENOME"
]
},
"RefSeq": {
"database": "RefSeq",
"entity_types": [
{
"example_id": "RefSeq:XP_001068954",
"example_url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=XP_001068954",
"id_syntax": "(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+(\\.[0-9]+){0,1}",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id]"
},
{
"example_id": "RefSeq:XP_001068954",
"example_url": "https://www.ncbi.nlm.nih.gov/protein/NP_001121125",
"id_syntax": "(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+(\\.[0-9]+){0,1}",
"type_id": "PR:000000001",
"type_name": "protein",
"url_syntax": "https://www.ncbi.nlm.nih.gov/protein/[example_id]"
}
],
"generic_urls": [
"http://www.ncbi.nlm.nih.gov/RefSeq/"
],
"name": "RefSeq"
},
"Rfam": {
"database": "Rfam",
"entity_types": [
{
"example_id": "Rfam:RF00012",
"example_url": "https://rfam.org/family/RF00012",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://rfam.org/family/[example_id]"
}
],
"generic_urls": [
"https://rfam.org"
],
"name": "Rfam database of RNA families"
},
"RiceSES": {
"database": "RiceSES",
"entity_types": [
{
"example_id": "RiceSES:bakanae-diseases-bak",
"example_url": "http://www.knowledgebank.irri.org/extension/crop-damage-diseases/bakanae-diseases-bak.html",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.knowledgebank.irri.org/extension/crop-damage-diseases/[example_id].html"
}
],
"generic_urls": [
"http://www.ncbi.nlm.nih.gov/PubMed/"
],
"name": "Rice Knowledge Bank"
},
"SABIO-RK": {
"database": "SABIO-RK",
"description": "The SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.",
"entity_types": [
{
"example_id": "SABIO-RK:1858",
"example_url": "http://sabio.villa-bosch.de/reacdetails.jsp?reactid=1858",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://sabio.villa-bosch.de/reacdetails.jsp?reactid=[example_id]"
}
],
"generic_urls": [
"http://sabio.villa-bosch.de/"
],
"name": "SABIO Reaction Kinetics"
},
"SEED": {
"database": "SEED",
"description": "Project to annotate the first 1000 sequenced genomes, develop detailed metabolic reconstructions, and construct the corresponding stoichiometric matrices",
"entity_types": [
{
"example_id": "SEED:fig|83331.1.peg.1",
"example_url": "http://www.theseed.org/linkin.cgi?id=fig|83331.1.peg.1",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.theseed.org/linkin.cgi?id=[example_id]"
}
],
"generic_urls": [
"http://www.theseed.org"
],
"name": "The SEED;"
},
"SGD": {
"database": "SGD",
"entity_types": [
{
"example_id": "SGD:S000006169",
"example_url": "https://www.yeastgenome.org/search?q=S000006169&is_quick=true",
"id_syntax": "S[0-9]{9}",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "https://www.yeastgenome.org/search?q=[example_id]&is_quick=true"
}
],
"generic_urls": [
"http://www.yeastgenome.org/"
],
"name": "Saccharomyces Genome Database",
"rdf_uri_prefix": "http://identifiers.org/sgd/",
"synonyms": [
"SGDID"
]
},
"SGD_LOCUS": {
"database": "SGD_LOCUS",
"entity_types": [
{
"example_id": "SGD_LOCUS:GAL4",
"example_url": "https://www.yeastgenome.org/search?q=S000006169&is_quick=true",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.yeastgenome.org/search?q=[example_id]&is_quick=true"
}
],
"generic_urls": [
"http://www.yeastgenome.org/"
],
"name": "Saccharomyces Genome Database"
},
"SGD_PWY": {
"database": "SGD_PWY",
"entity_types": [
{
"example_id": "SGD_PWY:CYSTEINE-SYN2-PWY",
"example_url": "https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=NIL&object=SERSYN-PWY",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.yeastgenome.org/locus/[example_id]"
}
],
"generic_urls": [
"https://pathway.yeastgenome.org/"
],
"name": "Saccharomyces Genome Database YeastPathways"
},
"SGD_REF": {
"database": "SGD_REF",
"entity_types": [
{
"example_id": "SGD_REF:S000049602",
"example_url": "http://www.yeastgenome.org/reference/S000049602/overview",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.yeastgenome.org/reference/[example_id]/overview"
}
],
"generic_urls": [
"http://www.yeastgenome.org/"
],
"name": "Saccharomyces Genome Database"
},
"SGN": {
"database": "SGN",
"entity_types": [
{
"example_id": "SGN_gene:7740",
"example_url": "http://solgenomics.net/phenome/locus_display.pl?locus_id=7740",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "http://solgenomics.net/phenome/locus_display.pl?locus_id=[example_id]"
}
],
"generic_urls": [
"https://www.sgn.cornell.edu/"
],
"name": "Sol Genomics Network",
"rdf_uri_prefix": "http://identifiers.org/sgn/",
"synonyms": [
"SGN_gene"
]
},
"SGN_germplasm": {
"database": "SGN_germplasm",
"entity_types": [
{
"example_id": "SGN_germplasm:6583",
"example_url": "http://solgenomics.net/stock/6583/view/",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://solgenomics.net/stock/[example_id]/view/"
}
],
"generic_urls": [
"https://solgenomics.net/"
],
"name": "Sol Genomics Network"
},
"SGN_ref": {
"database": "SGN_ref",
"entity_types": [
{
"example_id": "SGN_ref:861",
"example_url": "https://sgn.cornell.edu/chado/publication.pl?pub_id=861",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://sgn.cornell.edu/chado/publication.pl?pub_id=[example_id]"
}
],
"generic_urls": [
"https://www.sgn.cornell.edu/"
],
"name": "Sol Genomics Network"
},
"SMART": {
"database": "SMART",
"entity_types": [
{
"example_id": "SMART:SM00005",
"example_url": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00005",
"type_id": "SO:0000839",
"type_name": "polypeptide region",
"url_syntax": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=[example_id]"
}
],
"generic_urls": [
"http://smart.embl-heidelberg.de/"
],
"name": "Simple Modular Architecture Research Tool"
},
"SO": {
"database": "SO",
"entity_types": [
{
"example_id": "SO:0000400",
"example_url": "http://www.sequenceontology.org/browser/current_svn/term/SO:0000400",
"id_syntax": "\\d{7}",
"type_id": "SO:0000400",
"type_name": "sequence attribute",
"url_syntax": "http://www.sequenceontology.org/browser/current_svn/term/SO:[example_id]"
},
{
"example_id": "SO:0000307",
"example_url": "http://www.sequenceontology.org/browser/current_svn/term/SO:0000307",
"id_syntax": "\\d{7}",
"type_id": "SO:0000110",
"type_name": "sequence feature",
"url_syntax": "http://www.sequenceontology.org/browser/current_svn/term/SO:[example_id]"
},
{
"example_id": "SO:0001166",
"example_url": "http://www.sequenceontology.org/browser/current_svn/term/SO:0001166",
"id_syntax": "\\d{7}",
"type_id": "SO:0001683",
"type_name": "sequence motif",
"url_syntax": "http://www.sequenceontology.org/browser/current_svn/term/SO:[example_id]"
}
],
"generic_urls": [
"http://www.sequenceontology.org/"
],
"name": "Sequence Ontology",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/SO_"
},
"SOY_QTL": {
"database": "SOY_QTL",
"entity_types": [
{
"example_id": "Seedling, abnormal+1-1",
"example_url": "https://www.soybase.org/sbt/search/search_results.php?category=QTLName&search_term=Seedling,+abnormal+1-1",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.soybase.org/sbt/search/search_results.php?category=QTLName&search_term=[example_id]"
}
],
"generic_urls": [
"https://soybase.org/"
],
"name": "SoyBase"
},
"SOY_ref": {
"database": "SOY_ref",
"entity_types": [
{
"example_id": "SOY ref:SoyBase6597900",
"example_url": "https://www.soybase.org/sbt/search/search_results.php?category=Soybase_ID&search_term=SoyBase3142000126",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.soybase.org/sbt/search/search_results.php?category=Soybase_ID&search_term=[example_id]"
}
],
"generic_urls": [
"https://soybase.org/"
],
"name": "SoyBase"
},
"SUPERFAMILY": {
"database": "SUPERFAMILY",
"description": "A database of structural and functional protein annotations for completely sequenced genomes",
"entity_types": [
{
"example_id": "SUPERFAMILY:56994",
"example_url": "http://supfam.org/scop/56994",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://supfam.org/scop/[example_id]"
}
],
"generic_urls": [
"http://supfam.org/"
],
"name": "SUPERFAMILY protein annotation database"
},
"SYSCILIA_CCNET": {
"database": "SYSCILIA_CCNET",
"description": "A systems biology approach to dissect cilia function and its disruption in human genetic disease",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://syscilia.org/"
],
"name": "Syscilia"
},
"Sanger": {
"database": "Sanger",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.sanger.ac.uk/"
],
"name": "Wellcome Trust Sanger Institute"
},
"Soy_gene": {
"database": "Soy_gene",
"entity_types": [
{
"example_id": "Glyma18g02210",
"example_url": "https://www.soybase.org/sbt/search/search_results.php?category=FeatureName&search_term=Glyma18g02210",
"type_id": "BET:0000000",
"type_name": "gene",
"url_syntax": "https://www.soybase.org/sbt/search/search_results.php?category=FeatureName&search_term=[example_id]"
}
],
"generic_urls": [
"https://soybase.org/"
],
"name": "SoyBase"
},
"SynGO": {
"database": "SynGO",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"https://www.syngoportal.org/"
],
"name": "The Synapse Gene Ontology and Annotation Initiative"
},
"SynGO-UCL": {
"database": "SynGO-UCL",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"https://www.ucl.ac.uk/cardiovascular/research/pre-clinical-and-fundamental-science/functional-gene-annotation/neurological-gene-2"
],
"name": "The Synapse Gene Ontology and Annotation Initiative at UCL"
},
"TAIR": {
"database": "TAIR",
"entity_types": [
{
"example_id": "TAIR:gene:2062713",
"example_url": "http://arabidopsis.org/servlets/TairObject?accession=gene:2062713",
"id_syntax": "gene:[0-9]{7,12}",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "http://arabidopsis.org/servlets/TairObject?accession=[example_id]"
},
{
"example_id": "TAIR:Communication:1345790",
"example_url": "http://arabidopsis.org/servlets/TairObject?type=communication&id=1345790",
"id_syntax": "Communication:[0-9]{7,12}",
"type_id": "BET:0000000",
"type_name": "communication",
"url_syntax": "http://arabidopsis.org/servlets/TairObject?type=communication&id=[example_id]"
},
{
"example_id": "TAIR:locus:2146653",
"example_url": "http://arabidopsis.org/servlets/TairObject?accession=locus:2146653",
"id_syntax": "locus:[0-9]{7,12}",
"type_id": "SO:0000185",
"type_name": "primary transcript",
"url_syntax": "http://arabidopsis.org/servlets/TairObject?accession=[example_id]"
}
],
"generic_urls": [
"http://www.arabidopsis.org/"
],
"name": "The Arabidopsis Information Resource",
"rdf_uri_prefix": "http://identifiers.org/tair.locus/"
},
"TC": {
"database": "TC",
"entity_types": [
{
"example_id": "TC:9.A.4.1.1",
"example_url": "http://www.tcdb.org/tcdb/index.php?tc=9.A.4.1.1",
"id_syntax": "[0-9]+\\.[A-Z](\\.[0-9]+)+",
"type_id": "PR:000000001",
"type_name": "protein",
"url_syntax": "http://www.tcdb.org/tcdb/index.php?tc=[example_id]"
}
],
"generic_urls": [
"http://www.tcdb.org/"
],
"name": "Transport Protein Database"
},
"TFClass": {
"database": "TFClass",
"entity_types": [
{
"example_id": "TFCLASS_FAMILY:2.1.1",
"example_url": "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=2.1.1",
"id_syntax": "\\d+(\\.\\d+){2,3}",
"type_id": "PR:000000001",
"type_name": "protein",
"url_syntax": "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=[example_id]"
}
],
"generic_urls": [
"http://tfclass.bioinf.med.uni-goettingen.de/"
],
"name": "TFClass is a resource for the classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains",
"synonyms": [
"TFCLASS_FAMILY",
"tfclass"
]
},
"TGD": {
"database": "TGD",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.ciliate.org/"
],
"name": "Tetrahymena Genome Database",
"rdf_uri_prefix": "http://identifiers.org/tgd/"
},
"TGD_LOCUS": {
"database": "TGD_LOCUS",
"entity_types": [
{
"example_id": "TGD_LOCUS:PDD1",
"example_url": "http://db.ciliate.org/cgi-bin/locus.pl?locus=PDD1",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://db.ciliate.org/cgi-bin/locus.pl?locus=[example_id]"
}
],
"generic_urls": [
"http://www.ciliate.org/"
],
"name": "Tetrahymena Genome Database"
},
"TGD_REF": {
"database": "TGD_REF",
"entity_types": [
{
"example_id": "TGD_REF:T000005818",
"example_url": "http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=T000005818",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=[example_id]"
}
],
"generic_urls": [
"http://www.ciliate.org/"
],
"name": "Tetrahymena Genome Database"
},
"TIGRFAMS": {
"database": "TIGRFAMS",
"entity_types": [
{
"example_id": "TIGRFAMS:TIGR00254",
"example_url": "http://tigrfams.jcvi.org/cgi-bin/HmmReportPage.cgi?acc=TIGR00254",
"id_syntax": "TIGR[0-9]{5}",
"type_id": "SO:0000839",
"type_name": "polypeptide region",
"url_syntax": "http://tigrfams.jcvi.org/cgi-bin/HmmReportPage.cgi?acc=[example_id]"
}
],
"generic_urls": [
"http://tigrfams.jcvi.org/cgi-bin/index.cgi"
],
"name": "TIGRFAMs HMM collection at the J. Craig Venter Institute",
"synonyms": [
"TIGR_TIGRFAMS"
]
},
"TRANSFAC": {
"database": "TRANSFAC",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://www.gene-regulation.com/pub/databases.html#transfac"
],
"name": "TRANSFAC database of eukaryotic transcription factors"
},
"TreeGenes": {
"database": "TreeGenes",
"entity_types": [
{
"example_id": "TreeGenes:254",
"example_url": "http://dendrome.ucdavis.edu/treegenes/protein/view_protein.php?id=254",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://dendrome.ucdavis.edu/treegenes/protein/view_protein.php?id=[example_id]"
}
],
"generic_urls": [
"http://dendrome.ucdavis.edu/treegenes/"
],
"name": "Forest Tree Genome Database"
},
"TreeGrafter": {
"database": "TreeGrafter",
"entity_types": [
{
"example_id": "PANTHER:PTHR11455",
"example_url": "http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR10000",
"id_syntax": "PTN[0-9]{9}|PTHR[0-9]{5}|PTHR[0-9]{5}:SF[0-9]+",
"type_id": "NCIT:C20130",
"type_name": "protein family",
"url_syntax": "http://www.pantherdb.org/panther/lookupId.jsp?id=[example_id]"
}
],
"generic_urls": [
"http://www.pantherdb.org/"
],
"name": "TreeGrafter-generated GO annotations",
"rdf_uri_prefix": "http://identifiers.org/panther.family/"
},
"TriTrypDB": {
"database": "TriTrypDB",
"entity_types": [
{
"example_id": "Tb927.1.630",
"example_url": "https://tritrypdb.org/tritrypdb/app/record/gene/Tb927.1.630",
"id_syntax": "((LmjF|LinJ|LmxM|LINF)\\.[0-9]{2}\\.[0-9]{4})|(Tb[0-9]+\\.[A-Za-z0-9]+\\.[0-9]+)|(Tb\\.[0-9]{6}\\.[0-9]+)|",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "https://tritrypdb.org/tritrypdb/app/record/gene/[example_id]"
}
],
"generic_urls": [
"https://tritrypdb.org/"
],
"name": "TriTrypDB",
"rdf_uri_prefix": "http://identifiers.org/tritrypdb/"
},
"UBERON": {
"database": "UBERON",
"description": "A multi-species anatomy ontology",
"entity_types": [
{
"example_id": "UBERON:0002398",
"example_url": "http://purl.obolibrary.org/obo/UBERON_0002398",
"id_syntax": "[0-9]{7}",
"type_id": "CARO:0000000",
"type_name": "anatomical entity",
"url_syntax": "http://purl.obolibrary.org/obo/UBERON_[example_id]"
},
{
"example_id": "UBERON:0000069",
"id_syntax": "[0-9]{7}",
"type_id": "UBERON:0000105",
"type_name": "life cycle stage",
"url_syntax": "http://purl.obolibrary.org/obo/UBERON_[example_id]"
}
],
"generic_urls": [
"http://uberon.org"
],
"name": "Uber-anatomy ontology",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/UBERON_"
},
"UM-BBD": {
"database": "UM-BBD",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://eawag-bbd.ethz.ch/"
],
"name": "EAWAG Biocatalysis/Biodegradation Database"
},
"UM-BBD_enzymeID": {
"database": "UM-BBD_enzymeID",
"entity_types": [
{
"example_id": "UM-BBD_enzymeID:e0413",
"example_url": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=e0230",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=[example_id]"
}
],
"generic_urls": [
"http://eawag-bbd.ethz.ch/"
],
"name": "EAWAG Biocatalysis/Biodegradation Database"
},
"UM-BBD_pathwayID": {
"database": "UM-BBD_pathwayID",
"entity_types": [
{
"example_id": "UM-BBD_pathwayID:acr",
"example_url": "http://eawag-bbd.ethz.ch/acr/acr_map.html",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://eawag-bbd.ethz.ch/[example_id]/[example_id]_map.html"
}
],
"generic_urls": [
"http://eawag-bbd.ethz.ch/"
],
"name": "EAWAG Biocatalysis/Biodegradation Database"
},
"UM-BBD_reactionID": {
"database": "UM-BBD_reactionID",
"entity_types": [
{
"example_id": "UM-BBD_reactionID:r0129",
"example_url": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=r0129",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=[example_id]"
}
],
"generic_urls": [
"http://eawag-bbd.ethz.ch/"
],
"name": "EAWAG Biocatalysis/Biodegradation Database"
},
"UM-BBD_ruleID": {
"database": "UM-BBD_ruleID",
"entity_types": [
{
"example_id": "UM-BBD_ruleID:bt0330",
"example_url": "http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=bt0330",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=[example_id]"
}
],
"generic_urls": [
"http://eawag-bbd.ethz.ch/"
],
"name": "EAWAG Biocatalysis/Biodegradation Database"
},
"UniParc": {
"database": "UniParc",
"description": "A non-redundant archive of protein sequences extracted from Swiss-Prot, TrEMBL, PIR-PSD, EMBL, Ensembl, IPI, PDB, RefSeq, FlyBase, WormBase, European Patent Office, United States Patent and Trademark Office, and Japanese Patent Office",
"entity_types": [
{
"example_id": "UniParc:UPI000000000A",
"example_url": "https://www.uniprot.org/uniparc/UPI000000000A",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.uniprot.org/uniparc/[example_id]"
}
],
"generic_urls": [
"https://www.uniprot.org/uniparc/"
],
"name": "UniProt Archive"
},
"UniPathway": {
"database": "UniPathway",
"description": "UniPathway is a a metabolic door to UniProtKB/Swiss-Prot, a curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase.",
"entity_types": [
{
"example_id": "UniPathway:UPA00155",
"example_url": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=UPA00155",
"type_id": "GO:0008150",
"type_name": "biological_process",
"url_syntax": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=[example_id]"
}
],
"generic_urls": [
"http://www.grenoble.prabi.fr/obiwarehouse/unipathway"
],
"name": "UniPathway"
},
"UniProt": {
"database": "UniProt",
"description": "A central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR database",
"generic_urls": [
"http://www.uniprot.org"
],
"name": "Universal Protein Knowledgebase",
"synonyms": [
"Swiss-Prot",
"SwissProt",
"TrEMBL",
"TR"
]
},
"UniProtKB": {
"database": "UniProtKB",
"description": "A central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR database",
"entity_types": [
{
"example_id": "UniProtKB:P51587",
"example_url": "https://www.uniprot.org/uniprot/",
"id_syntax": "([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z]([0-9][A-Z][A-Z0-9]{2}){1,2}[0-9])((-[0-9]+)|-PRO_[0-9]{10}|-VAR_[0-9]{6}){0,1}",
"type_id": "PR:000000001",
"type_name": "protein",
"url_syntax": "https://www.uniprot.org/uniprot/[example_id]"
}
],
"generic_urls": [
"http://www.uniprot.org"
],
"name": "Universal Protein Knowledgebase",
"rdf_uri_prefix": "http://identifiers.org/uniprot/"
},
"UniProtKB-KW": {
"database": "UniProtKB-KW",
"entity_types": [
{
"example_id": "UniProtKB-KW:KW-0812",
"example_url": "https://www.uniprot.org/keywords/KW-0812",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.uniprot.org/keywords/[example_id]"
}
],
"generic_urls": [
"http://www.uniprot.org/keywords/"
],
"name": "UniProt Knowledgebase keywords",
"synonyms": [
"SP_KW"
]
},
"UniProtKB-SubCell": {
"database": "UniProtKB-SubCell",
"entity_types": [
{
"example_id": "UniProtKB-SubCell:SL-0012",
"example_url": "http://www.uniprot.org/locations/SL-0012",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.uniprot.org/locations/[example_id]"
}
],
"generic_urls": [
"https://www.uniprot.org/locations/"
],
"name": "UniProt Knowledgebase Subcellular Location vocabulary",
"synonyms": [
"SP_SL"
]
},
"UniRule": {
"database": "UniRule",
"entity_types": [
{
"example_id": "UniRule:UR000107224",
"example_url": "https://www.uniprot.org/unirule/UR000107224",
"id_syntax": "UR[0-9]{9}|MF_[0-9]{5}|PIRNR[0-9]{6}|PRU[0-9]{5}|RU[0-9]{6}",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://www.uniprot.org/unirule/[example_id]"
}
],
"generic_urls": [
"https://www.uniprot.org/unirule/"
],
"name": "Manually curated rules for automatic annotation of UniProtKB unreviewed entries"
},
"VZ": {
"database": "VZ",
"entity_types": [
{
"example_id": "VZ:957",
"example_url": "http://viralzone.expasy.org/all_by_protein/957.html",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://viralzone.expasy.org/all_by_protein/[example_id].html"
}
],
"generic_urls": [
"http://viralzone.expasy.org/"
],
"name": "ViralZone"
},
"WB": {
"database": "WB",
"entity_types": [
{
"example_id": "WB:WBGene00003001",
"example_url": "http://www.wormbase.org/get?name=WBGene00003001",
"id_syntax": "(CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8})",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "http://www.wormbase.org/get?name=[example_id]"
},
{
"example_id": "WB:WBVar00089843",
"example_url": "http://www.wormbase.org/get?name=WBVar00089843",
"id_syntax": "(CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8})",
"type_id": "VariO:0001",
"type_name": "variation",
"url_syntax": "http://www.wormbase.org/get?name=[example_id]"
},
{
"example_id": "WB:WBRNAi00110325",
"example_url": "http://www.wormbase.org/get?name=WBRNAi00110325",
"id_syntax": "(CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8})",
"type_id": "topic:3523",
"type_name": "RNAi",
"url_syntax": "http://www.wormbase.org/get?name=[example_id]"
},
{
"example_id": "WB:WBTransgene00000059",
"example_url": "http://www.wormbase.org/get?name=WBTransgene00000059",
"id_syntax": "(CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8})",
"type_id": "SO:0000902",
"type_name": "Transgene",
"url_syntax": "http://www.wormbase.org/get?name=[example_id]"
},
{
"example_id": "WB:CE00274",
"example_url": "http://www.wormbase.org/get?name=CE00274",
"id_syntax": "(CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8})",
"type_id": "PR:000000001",
"type_name": "protein",
"url_syntax": "http://www.wormbase.org/get?name=[example_id]"
}
],
"generic_urls": [
"http://www.wormbase.org/"
],
"name": "WormBase database of nematode biology",
"rdf_uri_prefix": "http://identifiers.org/wormbase/",
"synonyms": [
"WormBase"
]
},
"WBPhenotype": {
"database": "WBPhenotype",
"entity_types": [
{
"example_id": "WBPhenotype:0002117",
"example_url": "http://www.wormbase.org/get?name=WBPhenotype:0002117",
"id_syntax": "[0-9]{7}",
"type_id": "PATO:0000001",
"type_name": "quality",
"url_syntax": "http://www.wormbase.org/get?name=[example_id]"
}
],
"generic_urls": [
"http://www.wormbase.org/"
],
"name": "WormBase phenotype ontology",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/WBPhenotype_"
},
"WB_REF": {
"database": "WB_REF",
"entity_types": [
{
"example_id": "WB_REF:WBPaper00004823",
"example_url": "http://www.wormbase.org/get?name=WBPaper00004823",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.wormbase.org/get?name=[example_id]"
}
],
"generic_urls": [
"http://www.wormbase.org/"
],
"name": "WormBase database of nematode biology"
},
"WBbt": {
"database": "WBbt",
"entity_types": [
{
"example_id": "WBbt:0005792",
"example_url": "http://www.wormbase.org/get?name=WBbt:0005792",
"id_syntax": "[0-9]{7}",
"type_id": "GO:0005623",
"type_name": "cell",
"url_syntax": "http://www.wormbase.org/get?name=[example_id]"
},
{
"example_id": "WBbt:0005733",
"example_url": "http://www.wormbase.org/get?name=WBbt:0005733",
"id_syntax": "[0-9]{7}",
"type_id": "UBERON:0001062",
"type_name": "anatomical entity",
"url_syntax": "http://www.wormbase.org/get?name=[example_id]"
}
],
"generic_urls": [
"http://www.wormbase.org/"
],
"name": "C. elegans gross anatomy"
},
"WBls": {
"database": "WBls",
"entity_types": [
{
"example_id": "WBls:0000010",
"example_url": "http://www.wormbase.org/get?name=WBls:0000010",
"id_syntax": "[0-9]{7}",
"type_id": "WBls:0000075",
"type_name": "nematoda life stage",
"url_syntax": "http://www.wormbase.org/get?name=[example_id]"
}
],
"generic_urls": [
"http://www.wormbase.org/"
],
"name": "C. elegans development",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/WBls_"
},
"Wikipedia": {
"database": "Wikipedia",
"entity_types": [
{
"example_id": "Wikipedia:Endoplasmic_reticulum",
"example_url": "http://en.wikipedia.org/wiki/Endoplasmic_reticulum",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://en.wikipedia.org/wiki/[example_id]"
}
],
"generic_urls": [
"http://en.wikipedia.org/"
],
"name": "Wikipedia"
},
"WikipediaVersioned": {
"database": "WikipediaVersioned",
"entity_types": [
{
"example_id": "WikipediaVersioned:Fallopian_tube&oldid=998395727",
"example_url": "https://en.wikipedia.org/w/index.php?title=Fallopian_tube&oldid=998395727",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://en.wikipedia.org/w/index.php?title=[example_id]"
}
],
"generic_urls": [
"http://en.wikipedia.org/"
],
"name": "WikipediaVersioned"
},
"Xenbase": {
"database": "Xenbase",
"entity_types": [
{
"example_id": "Xenbase:XB-GENE-6255962",
"example_url": "http://www.xenbase.org/entry/XB-GENE-6255962",
"id_syntax": "XB-(GENE|LINE|TRANSGENE|MORPHOLINO)-[0-9]+",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "http://www.xenbase.org/entry/[example_id]"
},
{
"example_id": "Xenbase:XB-MORPHOLINO-17250301",
"example_url": "http://www.xenbase.org/entry/XB-MORPHOLINO-17250301",
"id_syntax": "XB-(GENE|LINE|TRANSGENE|MORPHOLINO)-[0-9]+",
"type_id": "SO:0000034",
"type_name": "morpholino oligo",
"url_syntax": "http://www.xenbase.org/entry/[example_id]"
},
{
"example_id": "Xenbase:XB-TRANSGENE-17326811",
"example_url": "http://www.xenbase.org/entry/XB-TRANSGENE-17326811",
"id_syntax": "XB-(GENE|LINE|TRANSGENE|MORPHOLINO)-[0-9]+",
"type_id": "SO:0000902",
"type_name": "transgene",
"url_syntax": "http://www.xenbase.org/entry/[example_id]"
},
{
"example_id": "Xenbase:XB-LINE-1248",
"example_url": "http://www.xenbase.org/entry/XB-LINE-1248",
"id_syntax": "XB-(GENE|LINE|TRANSGENE|MORPHOLINO)-[0-9]+",
"type_id": "EFO:0005135",
"type_name": "strain",
"url_syntax": "http://www.xenbase.org/entry/[example_id]"
}
],
"generic_urls": [
"http://www.xenbase.org/"
],
"name": "Xenbase",
"rdf_uri_prefix": "http://identifiers.org/xenbase/"
},
"YeastFunc": {
"database": "YeastFunc",
"entity_types": [
{
"type_id": "BET:0000000",
"type_name": "entity"
}
],
"generic_urls": [
"http://func.med.harvard.edu/yeast/"
],
"name": "Yeast Function"
},
"YuBioLab": {
"database": "YuBioLab",
"description": "CITGeneDB is a comprehensive database of human and mouse genes enhancing or suppressing Cold-Induced Thermogenesis (CIT).",
"generic_urls": [
"http://citgenedb.yubiolab.org"
],
"name": "CITGeneDB"
},
"ZFIN": {
"database": "ZFIN",
"entity_types": [
{
"example_id": "ZDB-GENE-990415-103",
"example_url": "http://zfin.org/ZDB-GENE-990415-103",
"id_syntax": "ZDB-(TRNAG|LINCRNAG|MIRNAG|NCRNAG|SNORNAG|GENE|GENO|MRPHLNO)-[0-9]{6}-[0-9]+",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "http://zfin.org/[example_id]"
},
{
"example_id": "ZDB-GENE-990415-103",
"example_url": "http://zfin.org/ZDB-GENE-990415-103",
"id_syntax": "ZDB-(TRNAG|LINCRNAG|MIRNAG|NCRNAG|SNORNAG|GENE|GENO|MRPHLNO)-[0-9]{6}-[0-9]+",
"type_id": "VariO:0001",
"type_name": "variation",
"url_syntax": "http://zfin.org/[example_id]"
}
],
"generic_urls": [
"http://zfin.org/"
],
"name": "Zebrafish Information Network",
"rdf_uri_prefix": "http://identifiers.org/zfin/"
},
"cribi_vitis": {
"database": "cribi_vitis",
"entity_types": [
{
"example_id": "VIT_00s0173g00270",
"example_url": "http://genomes.cribi.unipd.it/cgi-bin/pqs2/report.pl?gene_name=VIT_00s0173g00270&release=v1",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://genomes.cribi.unipd.it/cgi-bin/pqs2/report.pl?gene_name=[example_id]&release=v1"
}
],
"generic_urls": [
"http://genomes.cribi.unipd.it"
],
"name": "Vitis CRIBI database"
},
"dbSNP": {
"database": "dbSNP",
"entity_types": [
{
"example_id": "dbSNP:rs3131969",
"example_url": "http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs3131969",
"id_syntax": "\\d+",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=[example_id]"
}
],
"generic_urls": [
"http://www.ncbi.nlm.nih.gov/projects/SNP"
],
"name": "NCBI dbSNP",
"rdf_uri_prefix": "http://identifiers.org/dbsnp/"
},
"dictyBase": {
"database": "dictyBase",
"entity_types": [
{
"example_id": "dictyBase:DDB_G0277859",
"example_url": "http://dictybase.org/gene/DDB_G0277859",
"id_syntax": "DDB_G[0-9]{7}",
"type_id": "SO:0000704",
"type_name": "gene",
"url_syntax": "http://dictybase.org/gene/[example_id]"
}
],
"generic_urls": [
"http://dictybase.org"
],
"name": "dictyBase",
"rdf_uri_prefix": "http://identifiers.org/dictybase.gene/",
"synonyms": [
"DDB",
"DictyBase"
]
},
"dictyBase_REF": {
"database": "dictyBase_REF",
"entity_types": [
{
"example_id": "dictyBase_REF:10157",
"example_url": "http://dictybase.org/publication/10157",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://dictybase.org/publication/[example_id]"
}
],
"generic_urls": [
"http://dictybase.org"
],
"name": "dictyBase literature references",
"synonyms": [
"DDB_REF"
]
},
"dictyBase_gene_name": {
"database": "dictyBase_gene_name",
"entity_types": [
{
"example_id": "dictyBase_gene_name:mlcE",
"example_url": "http://dictybase.org/gene/mlcE",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "http://dictybase.org/gene/[example_id]"
}
],
"generic_urls": [
"http://dictybase.org"
],
"name": "dictyBase"
},
"gomodel": {
"database": "gomodel",
"entity_types": [
{
"example_id": "gomodel:5ae3b0f600001522",
"example_url": "http://www.geneontology.org/gocam/gomodel:5ae3b0f600001522",
"type_id": "BET:0000000",
"type_name": "model",
"url_syntax": "http://www.geneontology.org/gocam/[example_id]"
}
],
"generic_urls": [
"http://www.geneontology.org/gocam"
],
"name": "Gene Ontology Causal Activity Model Database",
"rdf_uri_prefix": "http://model.geneontology.org/"
},
"iBB": {
"database": "iBB",
"description": "RNAi phenotypes for beetle (Tribolium) genes",
"entity_types": [
{
"example_id": "TC006055",
"example_url": "https://ibeetle-base.uni-goettingen.de/details/TC006055",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://ibeetle-base.uni-goettingen.de/details|[example_id]"
}
],
"generic_urls": [
"https://ibeetle-base.uni-goettingen.de/"
],
"name": "iBeetleBase"
},
"iPTMnet": {
"database": "iPTMnet",
"entity_types": [
{
"example_id": "iPTM:P06493",
"example_url": "https://research.bioinformatics.udel.edu/iptmnet/entry/P06493/",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://research.bioinformatics.udel.edu/iptmnet/entry/[example_id]/"
}
],
"generic_urls": [
"https://research.bioinformatics.udel.edu/iptmnet/"
],
"name": "iPTMnet protein post-translational modification database"
},
"orcid": {
"database": "orcid",
"description": "ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers.",
"entity_types": [
{
"example_id": "orcid:0000-0003-4423-4370",
"example_url": "https://orcid.org/0000-0003-4423-4370",
"id_syntax": "^\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$",
"type_id": "BET:0000000",
"type_name": "entity",
"url_syntax": "https://orcid.org/[example_id]"
}
],
"generic_urls": [
"https://orcid.org/"
],
"name": "Open Researcher and Contributor"
},
"protein_id": {
"database": "protein_id",
"description": "protein identifier shared by DDBJ/EMBL-bank/GenBank nucleotide sequence databases",
"entity_types": [
{
"example_id": "protein_id:CAA71991",
"id_syntax": "[A-Z]{3}[0-9]{5}(\\.[0-9]+)?",
"type_id": "PR:000000001",
"type_name": "protein"
}
],
"generic_urls": [
"http://www.ddbj.nig.ac.jp/",
"http://www.ebi.ac.uk/ena/",
"http://www.ncbi.nlm.nih.gov/Genbank/"
],
"name": "DDBJ / ENA / GenBank"
}
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bioregistry-0.11.12/src/bioregistry/external/hl7/OID_Report.csv 0000644 0001751 0000177 00001160750 14655542206 023776 0 ustar 00runner docker Comp_OID,Symbolic_name,CodingSystemName,SubmitterFirst,SubmitterLast,Submitter_Email,Submitter2,Contact_person_desc,Contact_person_address,Contact_person_phone,Contact_person_email,Contact_person_info,Resp_body_name,Resp_body_address,Resp_body_phone,Resp_body_email,Resp_body_URL,Resp_body_Type,Resp_body_oid,External_OID_flag,externalOIDsubType,replacedBy,Oid_Type,assignment_status,AA_OID,AA_description,Object_description,Date_begun,Date_finalized,Entry_Timestamp,T396mnemonic,Preferred_Realm
2.16.840.1.113883.6,externalCodeSystems,HL7 Registered External Coding Systems,,,masked,,,,,masked,,,,,,,,,Int,14,,6,Complete,,,External coding systems registered in HL7 with an HL7 OID, , , ,,UV
2.16.840.1.113883.6.1,loinc,Logical Observation Identifier Names and Codes,Clement J.,McDonald,masked,,Daniel Vreeman,"410 West 10th StreetSuite 2000Indianapolis, IN 46202",317-274-9229,masked,Associate Director for Terminology Services,Regenstrief Institute,"410 West 10th StreetSuite 2000Indianapolis, IN 46202",317-423-5500 ,loinc@regenstrief.org,http://www.regenstrief.org,Academic,,Int,,,6,Complete,,HL7,"Logical Observation Identifiers Names and Codes (LOINC®) provides a set of universal codes and names for identifying laboratory and other clinical observations. One of the main goals of LOINC is to facilitate the exchange and pooling of results for clinical care, outcomes management, and research. LOINC was initiated by Regenstrief Institute research scientists who continue to develop it with the collaboration of the LOINC Committee. The LOINC table, LOINC codes, and LOINC panels and forms file are copyright © 1995-2010, Regenstrief Institute, Inc. and the LOINC Committee and available at no cost (http://loinc.org) under the license at http://loinc.org/terms-of-use.The laboratory portion of the LOINC database contains the usual clinical laboratory categories of chemistry, hematology, serology, microbiology (including parasitology and virology), toxicology; as well as categories for drugs and the cell counts, antibiotic susceptibilities, and more. The clinical portion of the LOINC database includes entries for vital signs, hemodynamics, intake/output, EKG, obstetric ultrasound, cardiac echo, radiology report titles, pulmonary ventilator management, document and section titles, patient assessment instruments (e.g. Glascow Coma Score, PHQ-9 depression scale, CMS-required patient assessment instruments), and other clinical observations.LOINC may be accessed at http://loinc.org",2007/07/18 12:00:00,2009/10/14 12:00:00,2013/11/21 03:13:27,LN,UV
2.16.840.1.113883.6.2,icd9cm,National Center for Health Statistics,Michelle,Williamson,masked,,Donna Pickett,"OCD/Classifications and Public Health Data Standards; National Center for Health StatisticsCenters for Disease Control and Prevention3311 Toledo RoadHyattsville, MD 20782","(301) 458-4434, 1.2.4. Fax (301) 458-4022",masked,,National Center for Health Statistics,"OCD/Classifications and Public Health Data Standards; National Center for Health StatisticsCenters for Disease Control and Prevention3311 Toledo RoadHyattsville, MD 20782",,,http://www.cdc.gov/nchs/icd9.htm.,Govt body,2.16.840.1.114222,Int,,"2.16.840.113883.6.103, 2.16.840.113883.6.104",6,Retired,,,"The International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM), Volumes I, II (diagnoses) and III (procedures) describes the classification of morbidity and mortality information for statistical purposes and for the indexing of healthcare records by diseases and procedures. The ICD-9-CM codes can be used as the value of the Act.cd attribute.Note that this has been retired in favor of an explicit split between the diagnosis codes and the procedures codes as per the Vocablary TC decision on Wednesday Q4, January 21, 2004. Replaced by 2.16.840.1.113883.6.103 and 2.16.840.1.113883.6.104 as voted by committee. -T. Klein", ,2009/10/07 12:00:00, ,I9C,UV
2.16.840.1.113883.6.3,icd10,ICD10,Ted,Klein,masked,,Nenad Kostanjsek,Avenue Appia 201211 Geneva 27Switzerland,+41794755474,masked,Technical Officer for Classifications and Terminologies,World Health Organization,Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,https://who.int,SDO,,Int,,,6,Complete,,HL7 International,"International Classification of Diseases revision 10 (ICD 10)Note this does NOT have the CM changes, and is specifically for international use.This node is the ontological branch in the HL7 OID tree. The actual ICD10 code systems (the various national and international versions) are defined below this node.", ,2009/10/07 12:00:00,2009/10/06 12:00:00,,UV
2.16.840.1.113883.6.4,icd10PCS,"International Classification of Diseases, 10th Revision, Procedure Coding System (ICD-10-PCS)",Michelle,Williamson,masked,,Pat Brooks,"CMM, HAPG, Division of Acute Care, Centers for Medicare and Medicaid Services, 7500 Security Boulevard; C4-08-06 Baltimore, MD 21244-1850","(410) 786-5318, 1.2.4. Fax (410) - 786-0169",masked,,Centers for Medicare and Medicaid Services,"7500 Security Boulevard; C4-08-06 Baltimore, MD 21244-1850",,,http://cms.hhs.gov/paymentsystems/icd9/icd10.asp,Govt body,,Int,,,6,Complete,,,"The International Classification of Diseases, 10th Revision, Procedure Coding System (ICD-10-PCS), describes the classification of inpatient procedures for statistical purposes and for the indexing of healthcare records by procedures. The ICD-10-PCS codes can be used as the value of the Act.cd attribute", ,2009/10/14 12:00:00,2009/10/14 12:00:00,,UV
2.16.840.1.113883.6.5,snm,SNOMED,,,masked,,,,,masked,,College of American Pathologists,,,,,,,Int,,,6,Complete,,,Systemized Nomenclature in Medicine Reference Terminology (SNOMED RT), ,2009/10/14 12:00:00,2009/10/14 12:00:00,SNM,UV
2.16.840.1.113883.6.6,read-Codes,CTV3,David,Robinson,masked,,"Paul Frosdick, NHS Information Authority","Aqueous 2, Rocky lane, Aston cross, Birmingham, UK",+44 (0)121 333 0331,masked,,National Health Service (UK),Aqueous IIAston CrossRocky LaneBirminghamB6 5RQUK,+44 (0)121 333 0333,information@nhsia.nhs.uk,http://www.nhsia.nhs.uk/def/home.asp,Provider,,Int,,,6,Complete,,National Health Service (UK),"Clinical Terms Version 3 - The Read Codes - contains over 200,000 coded concepts arranged in a sub-type hierarchical structure. Top level hierarchy sections: DisordersFindings MorphologySurgical proceduresRegimes & therapiesInvestigationsStages & scalesOccupationsOrganismsUnitsDrugsAppliances & equipment", ,2009/10/14 12:00:00,2009/10/14 12:00:00,,UV
2.16.840.1.113883.6.7,naaccrCodes,NAACCR,Ted,Klein,masked,,Lori Havener,"North American Association ofCentral Cancer Registries, Inc.2121 West White Oaks DriveSuite BSpringfield, IL 62704-6495",(217) 698-0800 Ext. 3,masked,,"North American Association ofCentral Cancer Registries, Inc.","2121 West White Oaks DriveSuite BSpringfield, IL 62704-6495",(217) 698-0800,,http://www.naaccr.org/,,,Int,14,,6,Complete,,,"NAACCR Cancer Registry code lists. This branch node has the short code list vocabularies used in NAACCR Cancer Registries, as defined in the NAACCR standards.", ,2009/10/14 12:00:00,2009/10/24 12:00:00,,UV
2.16.840.1.113883.6.8,ucum,Unified Code for Units of Measure,Harold,Solbrig,masked,,Gunther Schadow,"410 West 10th StreetSuite 2000Indianapolis, IN 46202",,masked,,Regenstrief Institute,"410 West 10th StreetSuite 2000Indianapolis, IN 46202",,loinc@regenstrief.iupui.edu,http://www.regenstrief.org,Academic,,Int,,,6,Complete,,,"Unified Code for Units of Measure. The Unified Code for Units of Measure is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business. The purpose is to facilitate unambiguous electronic communication of quantities together with their units. The focus is on electronic communication, as opposed to communication between humans. A typical application of The Unified Code for Units of Measure are electronic data interchange (EDI) protocols, but there is nothing that prevents it from being used in other types of machine communication.http://unitsofmeasure.org/", ,2009/10/14 12:00:00,2009/10/14 12:00:00,UCUM,UV
2.16.840.1.113883.6.9,iso4217-HL7,ISO 4217 currency code,,,masked,,,,,masked,,,,,,,SDO,,Int,,1.0.4217,6,Deprecated,,,ISO 4217 currency code, ,2009/10/14 12:00:00, ,,UV
2.16.840.1.113883.6.10,mime,IETF MIME,,,masked,,,,,masked,,,,,,,,,Int,,,6,Complete,,,IETF MIME media types, , , ,,UV
2.16.840.1.113883.6.11,url,URL,,,masked,,,,,masked,,,,,,,,,Int,,,6,Complete,,,Universal Resource Locator (URL) schemes. Currently there is no single authority for URL schemes. The authority for URL scheme assignments clearly lies within IANA or W3C and it is likely that a formal URL/URI assigning authority will be formed soon., , , ,,UV
2.16.840.1.113883.6.12,cpt-4,Current Procedure Terminology 4 (CPT-4),Harold,Solbrig,masked,,Dorith Brown,"American Medical Association515 N. State StreetChicago, IL 60610United States",1-312-464-5762,masked,CPT Intellectual Property Services,American Medical Association,"515 N. State StreetChicago, IL 60610United States",1-800-621-8335,,http://www.ama-assn.org/ama/pub/category/3113.html,Prof Soc,,Pxy,,,6,Complete,,HL7,American Medical Associationβs Current Procedure Terminology 4 (CPT-4) codes., ,2010/01/26 12:00:00, ,C4,UV
2.16.840.1.113883.6.13,cdt-ADAcodes,Code on Dental Procedures and Nomenclature,,,masked,,"Center for Dental Benefits, Coding and Quality","American Dental Association211 East ChicagoChicago, IL 60611Att. Practice Institute Center for Dental Benefits, Coding and Quality",312-440-2327,masked,CDT Code Maintenance and Development,American Dental Association,,,dentalcode@ada.org,http://www.ada.org/cdt,Prof Soc,,Int,,,6,Complete,,,"The CDT Code (Code on Dental Procedures and Nomenclature) is the dental procedure code set owned and maintained by the American Dental Association. It is under copyright and may be licensed for use. Licensing information is available on line at http://www.ada.org/en/publications/ada-catalog/cdt-products/licensing-for-commercial-users The CDT Code's purpose is to achieve uniformity, consistency and specificity in accurately documenting dental treatment and services. One use of the CDT Code is to provide for the efficient processing of dental claims, and another is to populate an Electronic Health Record.On August 17, 2000 the CDT Code was named as a HIPAA standard code set.", ,2009/10/14 12:00:00,2017/06/22 12:21:59,,UV
2.16.840.1.113883.6.14,HPC,HCPCS,,,masked,,,,,masked,,,,,,,,,Int,,,6,Complete,,,"Healthcare Financing Administration (HCFA) Common Procedure Coding System (HCPCS). Is composed of three βlevelsβ. Level I is CPT-4, level II is CDT-2, and level 3 are the HCPCS modifiers. Only the HCPCS modifiers are maintained by the Alpha-Numeric Editorial Panel, consisting of the Health Insurance Association of America and the Blue Cross and Blue Shield Association.", , , ,,UV
2.16.840.1.113883.6.15,nic,Nursing Intervention Classification,Suzanne,Bakken,masked,,Joanne McCloskey Dochterman and Gloria Bulechek,"Center for Nursing ClassificationCollege of NursingThe University of IowaIowa City, IA 52242",319-335-7051/319-335-7120/319-335-7115,masked,,Center for Nursing Classification,"College of NursingThe University of IowaIowa City, IA 52242",319-335-7051/319-335-7120/319-335-7115,joanne-dochterman@uiowa.edu,,,,Int,,,6,Complete,,,"NIC provides names and values for procedures/orders/service intent related to the treatment activities of nurses and other providers who may perform the same treatment activities. Names, definitions, and associated codes are attached for 486 interventions. Defining activities (anywhere from ten to several dozen) are listed for each of the interventions in the NIC classification book but are not attached to this document.", ,2009/10/14 12:00:00, ,,UV
2.16.840.1.113883.6.16,noc,NOC - Nursing Outcome Classification,Suzanne,Bakken,masked,,"Sue Moorhead, PhD","College of NursingUniversity of Iowa458 Nursing Building50 Newton RoadIowa City, IA 52242-1121",319-335-7110,masked,,University of Iowa College of Nursing,"College of NursingUniversity of Iowa101 Nursing Building50 Newton RoadIowa City, IA 52242-1121",,leslie-gannon@uiowa.edu,http://www.nursing.uiowa.edu/excellence/nursing_knowledge/clinical_effectiveness/noc.htm,,,Int,,,6,Complete,,,"The ANA's Congress of Nursing Practice Steering Committee on Databases to Support Clinical Nursing Practice has recognized Nursing Outcomes Classification (NOC) as a classification system useful for clinical nursing practice.The NOC 3rd edition includes 330 outcomes including 76 new outcomes and a revised measurement scale. Core outcomes are identified for 41 specialties, linkages with NANDA diagnoses and with Gordon's functional health patterns have been updated, and the outcomes are organized in both the NOC taxonomy and the Taxonomy of Nursing Practice. This edition of NOC also reports the research results form 10 clinical testing sites.", ,2009/10/14 12:00:00, ,,UV
2.16.840.1.113883.6.17,hhcc,Home HealthCare Classification System,Suzanne,Bakken,masked,,,,,masked,,,,,,,Academic,,Int,,2.16.840.1.113883.6.236,6,Complete,,,"Home HealthCare Classification System codes.Note that this code system has been retired, and has been replaced by 2.16.840.1.113883.6.236 CCC.", , , ,,UV
2.16.840.1.113883.6.18,ib,ISBT 128,Edwin A,Steane,masked,,Erwin Cabana,"PO Box 11309, San Bernardino, CA 92423",9097936516,masked,Technical Manager,ICCBBA,"PO Box 11309, San Bernardino, CA 92423",9097936516,iccbba@iccbba.org,https://www.iccbba.org,SDO,,Int,,,6,Complete,,,"ISBT 128 is the global standard for the terminology, identification, coding and labeling of medical products of human origin (including blood, cell, tissue, milk, and organ products). It is comprised of the ISBT 128 Technical Specification, ISBT 128 Standard Terminology, databases, reference tables, and product-specific labeling and coding documents. ISBT 128 coding is designed as a series of data structures that are technology-independent and can be used for bar coding, radio frequency tag encoding, and electronic data interchange. No changes are needed to use ISBT 128 in HL7 messages. ISBT 128 OIDs are documented in the ISBT 128 Technical Specification.", ,2001/05/10 12:00:00,2015/09/24 03:45:39,IB,UV
2.16.840.1.113883.6.19,camncvs,CAMNCVS,Melinna,Giannini,masked,,,,,masked,,,,,,,,,Int,,,6,Complete,,,CAM & Nursing Coding Vocabulary Set,2001/05/10 12:00:00, ,2001/05/10 04:05:00,,UV
2.16.840.1.113883.6.20,nanda,NANDA,Melinna,Giannini,masked,,"Kay C. Avant, RN, PhD, FAAN","7601 Tallahassee, Waco, Tx 76712",254 772 5572,masked,,North American Nursing Diagnosis Association,"1211Locust St., Philadelphia, PA19107",215 545 7222,www.NANDA@rmpinc.com,www.NANDA.org,,,Int,,,6,Complete,,,"The terminology consists of standardized terms and codes for patient problems or life processes expressed as nursing diagnoses. These data elements would be classified by HL7 as βobservationsβ. The taxonomy is multi-axial. It consists of 12 domains and 36 classes. All domains and classes are defined. There are 7 axes with definitions for each. Each nursing diagnosis consists of: a concept label or term expressed as a noun or a noun phrase; a definition of the term; a set of defining characteristics (signs and symptoms) of the diagnostic term; an approved list of modifiers of the term; a set of risk factors with definitions; and a set of related factors (or etiologies) for the term. The system preserves semantics by having robust review procedures and policies to ensure against semantic drift in the meanings of the encoded terms over time. NANDA as an organization is committed to updating the terminology on a regular biannual basis. NANDA has been in existence since 1973 and is thus the oldest developer of standardized language in nursing. Most other nursing language systems use many of the older NANDA terms in their vocabularies. The express purpose of the organization is to develop a comprehensive standardized nursing language that captures the conclusions that nurses make based on observations β in effect, the nursing diagnoses. The work is a continuing effort and diagnoses are revised, retired or added bi-annually. The codes are simple integers and are not linked to each other. If a diagnostic term is retired, the code is also retired. If a new diagnosis is added a new code is given to that term. If a diagnostic term is revised, the code is kept intact but the date of the revision is published alongside the term. Domains and classes are not coded.",2001/05/10 12:00:00,2001/05/10 12:00:00,2001/05/10 04:05:00,,UV
2.16.840.1.113883.6.21,nubc-UB92,NUBC UB92,Melinna,Giannini,masked,,,,,masked,,National Uniform Billing Committee (NUBC),,,tomundson@aha.org,http://www.nubc.org/,,,Int,,,6,Complete,,,"National Uniform Billing Council, UB 92",2001/05/10 12:00:00,2001/05/10 12:00:00,2001/05/10 04:05:00,,UV
2.16.840.1.113883.6.22,pnds,Perioperative Nursing Data Set,Suzanne,Bakken,masked,,Denise Downing,"2170 South Parker Road, Suite 300Denver, Colorado 80013",800-755-2676 ext. 216,masked,Perioperative Informatics Specialist,AORN,"2170 South Parker Road, Suite 300Denver, Colorado 80013",800-755-2676 X 216,ddowning@aorn.org,,Prof Soc,,Int,,,6,Complete,,,"The PNDS provides standardized terms and codes for patient problems/nursing diagnoses, nursing interventions including actual or expected (goal) outcomes. The PNDS provides standardized terms and codes for nursing interventions and outcome, as well as incorporating a subset of NANDA Nursing Diagnoses. The NANDA diagnoses in the PNDS have already been registered by HL7. The PNDS intervention and outcome statements have recently undergone a revision and update for integration into AORN˜s standardized perioperative documentation framework. While the PNDS model remains the same, the interventions have been subdivided to demonstrate the nursing process and perioperative plan of care. A conversion table is provided with the updated PNDS codes to the previous version of PNDS. For more information go to www.aorn.org or pnds@aorn.org ",2002/05/02 12:00:00,2002/10/09 12:00:00,2012/05/14 05:15:26,,UV
2.16.840.1.113883.6.23,nmmds,Nursing Management Minimum Data Set,Suzanne,Bakken,masked,,"Connie Delaney, PhD, RN, FAAN and Diane Huber, PhD, RN, FAAN","464 Nursing Building, Iowa City, Iowa 52242",319-335-7113 or 319-335-7110,masked,,"The University of Iowa, College of Nursing","464 Nursing Building, Iowa City, Iowa 52242",319-335-7113 or 319-335-7110,connie-delaney@uiowa.edu or diane-huber@uiowa.edu,,,,Int,,,6,Complete,,,"The NMMDS is the minimum set of items of information with uniform definitions and categories concerning the specific dimension of the context of patient care delivery. It represents the minimum data used to support the management and administration of patient/nursing care delivery across all types of settings. The NMMDS is composed of seventeen (17) data elements organized into three categories: environment, nurse resources, and financial resources. See Tables 1-3 for the elements and related definitions organized by each categories. The NMMDS most appropriately focuses at the first level of accountability for patient/client/family/community nursing care: this may be the delivery unit, service, or center of excellence level. The NMMDS supports numerous constructed variables as well as aggregation of data at the unit, institution, network, and system, etc levels. This minimum data set provides the structure for the collection of uniform information that influences quality of patient care, directly and indirectly.", ,2009/09/11 12:00:00, ,,UV
2.16.840.1.113883.6.24,mdc,ISO 11073-10101 Health informatics Point-of-care medical device communication - Nomenclature,Todd,Cooper,masked,,Melvin Reynolds,"AMS Consulting, Ashcote, Walford Road, Ross-on-Wye, Herefordshire, HR9 5PQ, UK",+44 1989 763120,masked,ISO TC215 WG2 SG1 Chair,IEEE 1073 General Committee,"12127 Ragweed StreetSan Diego, CA 92129-4103",858.484.8231,t.cooper@ieee.org,http://www.hl7.org,,,Int,,,6,Complete,,,"The nomenclature relates primarily to vital signs monitoring, but also includes semantics of other medical devices that are commonly used in acute care settings. There are multiple coding partitions each of which has a systematic name consisting of a set of base concepts and differentiating criteria.",2002/10/09 12:00:00,2002/10/10 12:00:00,2002/10/10 12:00:00,,UV
2.16.840.1.113883.6.25,abcCodes,ABCcodes,Melinna,Giannini,masked,,Melinna Giannini,"1065 S. Main, Building C, Las Cruces, NM 88005",505-527-0636,masked,,"Alternative Link Systems, Inc.","1065 S. Main, Building C, Las Cruces, NM 88005",505-527-0636,mg@alternativelink.com,http://www.alternativelink.com/ali/home/default.asp,,,Int,,,6,Complete,,,"These codes fit into standard message formats for HCPCS codes that are a named standard.ABC codes represent over 4,500 healthcare products and services. They fill gaps in older medical code sets such as CPT Β and HCPCS II and the retirement of state-specific HCPCS III codes. ABCcodes are a shorthand means of documenting healthcare procedures and treatments. Codes are an essential tool when computers are used to reduce paperwork and costs. Codes are also essential for managing the healthcare supply chain. The codes reflect care that is not described by conventional or allopathic centric code sets. ABC codes describe nursing, behavioral health, alternative medicine, ethnic and minority care, midwifery and spiritual care.",2002/10/10 12:00:00,2002/10/10 12:00:00,2002/10/10 12:00:00,,UV
2.16.840.1.113883.6.26,medcin,MEDCIN,David,Lareau,masked,,David Lareau,"14500 Avion Parkway, Suite 175Chantilly, VA 20151",703-803-8080,masked,,Medicomp Systems,"14500 Avion Parkway, Suite 175Chantilly, VA 20151",703-803-8080,info@medicomp.com,http://www.medicomp.com,,,Int,,,6,Complete,,,"MEDCIN contains more than 175,000 clinical data elements arranged in a hierarchy, with each item having weighted links to relevant diagnoses. The clinical data elements are organized into six basic termtypes designed to accommodate information relevant to a clinical encounter. The basic termtypes in MEDCINβs terminological hierarchy are as follows:SymptomsHistoryPhysical ExaminationTestsDiagnosesTherapyWithin this basic structure, MEDCIN terms are further organized in a ten level terminological hierarchy, supplemented by an optional, multi-hierarchical diagnostic index. For example, the symptom of βdifficulty breathingβ is placed in the terminological hierarchy as a subsidiary (or βchildβ) finding of βpulmonary symptoms,β although the presence (or absence) of difficulty breathing can related to conditions as diverse as myocardial infarction, bronchitis, pharyngeal foreign bodies, asthma, pulmonary embolism, etc. MEDCINβs diagnostic index provides more than 800 such links for difficulty breathing.",2002/10/10 12:00:00,2002/10/10 12:00:00,2002/10/10 12:00:00,,UV
2.16.840.1.113883.6.27,multum,Multum Lexicon,Tim,McNamara,masked,,,,,masked,,Multum Information Services,"3200 Cherry Creek South Drive Suite 300 Denver, CO 80209",(303) 733-4447,info@multum.com,http://www.multum.com,Vendor,,Int,,,6,Complete,,,"Broadly, the fields and values in the Multum Lexicon and the VantageRx Database are intended to be available for use in any HL7 message that includes a reference to non-veterinary drug products or active ingredients that are either approved for sale by the FDA or readily available in the United States. The following inter-related definitions recently circulated by us to the HL7 Vocabulary Technical Committee explain the scope of what we mean by βdrug productβ and βactive ingredientβ. (A definition for βdrug ingredientβ is also provided here because the definition of βactive ingredientβ is reliant on this term.)Drug ProductA drug product is a manufactured or extemporaneously-compounded physiologically-active material intended by the preparer to achieve therapeutic, diagnostic, or preventative effects via biochemical mechanisms when applied to an epithelial surface or placed in an internal body space of a targeted organism.Drug IngredientA drug ingredient is a chemical compound or biologic agent that occurs in a drug product.Active IngredientAn active ingredient is a drug ingredient that mediates one or more of the intended therapeutic, diagnostic, or preventative effects of a drug product and is present in sufficient quantities to achieve such effects according to the allopathic tradition of healthcare practice.",2002/10/10 12:00:00,2002/10/10 12:00:00,2002/10/10 12:00:00,,UV
2.16.840.1.113883.6.28,rcFB,The Read Codes Four Byte Set:,David,Robinson,masked,,"Paul Frosdick, NHS Information Authority","Aqueous 2, Rocky lane, Aston cross, Birmingham, UK",+44 (0)121 333 0331,masked,,National Health Service (UK),Aqueous IIAston CrossRocky LaneBirminghamB6 5RQUK,+44 (0)121 333 0333,information@nhsia.nhs.uk,http://www.nhsia.nhs.uk/def/home.asp,Provider,,Int,,,6,Complete,,National Health Service (UK),"The Read Codes Four Byte Set consists of 4 alphanumeric characters. This version contains approximately 40,000 codes arranged in a hierarchical structure. Top level hierarchy sections: DisordersFindings Surgical proceduresInvestigationsOccupationsDrugs",2002/10/10 12:00:00,2002/10/10 12:00:00,2002/10/10 12:00:00,,UV
2.16.840.1.113883.6.29,rcV2,The Read Codes Version 2,David,Robinson,masked,,"Paul Frosdick, NHS Information Authority","Aqueous 2, Rocky lane, Aston cross, Birmingham, UK",+44 (0)121 333 0331,masked,,National Health Service (UK),Aqueous IIAston CrossRocky LaneBirminghamB6 5RQUK,+44 (0)121 333 0333,information@nhsia.nhs.uk,http://www.nhsia.nhs.uk/def/home.asp,Provider,,Int,,,6,Complete,,National Health Service (UK),"The Read Codes Version 2 contains over 70,000 coded concepts arranged in a hierarchical structure. Top level hierarchy sections: DisordersFindings Surgical proceduresInvestigationsOccupationsDrugs",2002/10/10 12:00:00,2002/10/10 12:00:00,2002/10/10 12:00:00,,UV
2.16.840.1.113883.6.30,as4,ASTM E1238-E1467,,,masked,,,"ASTM International100 Barr Harbor Drive, PO Box C700West Conshohocken, PA 19428-2959 USA",,masked,,American Society for Testing & Materials,"ASTM International100 Barr Harbor Drive, PO Box C700West Conshohocken, PA 19428-2959 USA",,,http://www.astm.org/Standards/E1238.htm,Prof Soc,,Int,,,6,Obsolete,,HL7,"ASTM E1238/ E1467 UniversalAmerican Society for Testing & Materials and CPT4 (see Appendix X1 of Specification E1238 and Appendix X2 of Specification E1467).ASTM E1238-97 Standard Specification for Transferring Clinical Observations Between Independent Computer Systems (Withdrawn 2002). Has been replaced by ANSI NCCLS, available from http://www.clsi.org/",1999/12/30 12:00:00,2010/01/26 12:00:00,2010/01/26 11:34:56,AS4,UV
2.16.840.1.113883.6.76,ACR,ACR,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,American College of Radiology finding codes,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.77,ATC,ATC,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,American Type Culture Collection,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.78,as4e,AS4E,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,AS4 Neurophysiology Codes,1999/12/30 12:00:00, , ,,UV
2.16.840.1.113883.6.79,CDS,CDS,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,CDC Surveillance,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.80,CE,CE,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,CEN ECG diagnostic codes,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.81,CLP,CLP,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,CLIP,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.82,C5,C5,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,CPT-5,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.83,DCL,DCL,,,masked,,,,,masked,,,,,,,,,Int,,,6,Deprecated,,,DICOM Class Label; note these are now deprecated and are superceded by 1.2.840.10008.2.16.4,1899/12/30 12:00:27, ,2003/06/09 12:00:00,,UV
2.16.840.1.113883.6.31,dicomMDLTY,DICOM modality codes,,,masked,,,,,masked,,,,,,,,,Int,,1.2.840.10008.2.16.4,6,Deprecated,,,DICOM modality codes; note these are now deprecated and are superceded by 1.2.840.10008.2.16.4,1899/12/30 12:00:27,2009/10/14 12:00:00, ,,UV
2.16.840.1.113883.6.32,dicomqry,DICOM Query Label,,,masked,,,,,masked,,,,,,,,,Int,,1.2.840.10008.2.16.4,6,Deprecated,,,DICOM Query Label; note these are now deprecated and are superceded by 1.2.840.10008.2.16.4,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.33,ENZC,ENZC,,,masked,,,,,masked,,,,,,,,,Int,,,6,Rejected,,,"Enzyme CodesEntry rejected 1/26/2010. No information about the entry, code system cannot be located on the Web, no entries in the UMLS for this acronym, no reference information available, no names or company identification associated with entry.",1999/12/30 12:00:00,2010/01/26 12:00:00,2010/01/26 12:31:25,,UV
2.16.840.1.113883.6.34,euclides,EUCLIDES,,,masked,,,,,masked,,Euclides Foundation International,,,,,,,Int,,,6,Complete,,,EUCLIDES,1899/12/30 12:00:27,2009/10/14 12:00:00,2009/10/14 12:00:00,E,UV
2.16.840.1.113883.6.35,e5,Euclides quantity codes,,,masked,,,,,masked,,,,,,,,,Int,,,6,Complete,,,Euclides quantity codes,1899/12/30 12:00:27,2009/10/14 12:00:00,2009/10/14 12:00:00,E5,UV
2.16.840.1.113883.6.36,e6,Euclides Lab method codes,,,masked,,,,,masked,,,,,,,,,Int,,,6,Complete,,,Euclides Lab method codes,1899/12/30 12:00:27,2009/10/14 12:00:00,2009/10/14 12:00:00,E6,UV
2.16.840.1.113883.6.37,e7,Euclides Lab equipment codes,,,masked,,,,,masked,,,,,,,,,Int,,,6,Complete,,,Euclides Lab equipment codes,1899/12/30 12:00:27,2009/10/14 12:00:00,2009/10/14 12:00:00,E7,UV
2.16.840.1.113883.6.38,fdk,FDA K10,,,masked,,,,,masked,,,,,,,Govt body,,Int,,,6,Complete,,,FDA K10 device & analyte process codes,1899/12/30 12:00:27,2009/10/14 12:00:00,2009/10/14 12:00:00,FDK,UV
2.16.840.1.113883.6.39,hi,Health Outcomes Institute codes for outcome variables,,,masked,,,,,masked,,Stratis Health (formerly Foundation for Health Care Evaluation and Health Outcomes Institute),"2901 Metro Drive, Suite 400Bloomington, MN, 55425-1525",,,,,,Int,,,6,Complete,,,"Health Outcomes Institute codes for outcome variables available (with responses) from Stratis Health (formerly Foundation for Health Care Evaluation and Health Outcomes Institute), 2901 Metro Drive, Suite 400, Bloomington, MN, 55425-1525; (612) 854-3306 (voice); (612) 853-8503 (fax); dziegen@winternet.com. See examples in the Implementation Guide.",1899/12/30 12:00:27,2009/10/14 12:00:00,2009/10/14 12:00:00,HI,UV
2.16.840.1.113883.6.40,hibccHIN,HIBCC,,,masked,,,,,masked,,Health Industry Business Communications Council,"5110 N. 40th St., Ste 120Phoenix, AZ 85018",602.381.1091,info@hibcc.org,http://www.hibcc.org/,,,Int,,,6,Complete,,,"Health Industry Number (HIN) is a unique identifier for enumerating locations and providers of services and activities throughout the health industry. The HIN enumerates provider establishments and all other entities in the health industrysupply chain, as well as prescribers by location. The HIN is physically represented as a nine-character alphanumeric string comprising six randomly-assigned characters followed by a modulus-based check character in the seventh position, followed by a two-character suffix that identifies all known practice locations of prescribers, or the various services, activities or even administrative programs associated with health care establishments.",1899/12/30 12:00:27,2009/10/14 12:00:00,2009/10/14 12:00:00,HB,UV
2.16.840.1.113883.6.41,ics,International Classification of Clinical Services,,,masked,,,,,masked,,Commission on Professional and Hospital Activities (CPHA),,,,,,,Int,,,6,Complete,,,International Classification of Clinical Services.,1899/12/30 12:00:27,2009/10/14 12:00:00, ,ICS,UV
2.16.840.1.113883.6.42,icd9,"International Classification of Diseases, Version 9",Nenad,Kostanjsek,masked,,Nenad Kostanjsek,Avenue Appia 20 1211 Geneva 27 Switzerland,+41794755474,masked,Technical Officer for Classifications and Terminologies,World Health Organization,Avenue Appia 20 1211 Geneva 27 Switzerland,+ 41 22 791 21 11,info@who.int,https://who.int,SDO,,Int,,,6,Complete,,HL7 International,"International Classification of Diseases, Version 9 (ICD9)",1999/12/30 12:00:00,2009/10/14 12:00:00, ,,UV
2.16.840.1.113883.6.43,icd-o,International Classification of Diseases for Oncology: ICD-O,Ted,Klein,masked,,,,,masked,,World Health Organization (WHO),,,,http://www.who.int/en/,SDO,,Int,,,6,Complete,,,"This branch node heads up the different versions of the International Classification of Diseases for Oncology, which must be identified as different coding systems under HL7 terminology rules.",1899/12/30 12:00:27,2009/09/11 12:00:00, ,,UV
2.16.840.1.113883.6.44,ichppc-2,ICHPPC-2,Harold,Solbrig,masked,,,,,masked,,,,,,,,,Int,,,6,Complete,,HL7,"International Classification of Health Problems in Primary Care, Classification Committee of World Organization of National Colleges, Academies and Academic Associations of General Practitioners (WONCA), 3rd edition. An adaptation of ICD9 intended for use in General Medicine, Oxford University Press.http://www.annals.org/content/93/2/386.3.extractThere does not seem to be an authoritative source to access this material as a code system.",1999/12/30 12:00:00,2010/01/26 12:00:00,2010/01/26 12:40:40,IC2,UV
2.16.840.1.113883.6.45,icsd,International Classification of Sleep Disorders,,,masked,,JosΓ© Vis,Slaapcentrum SEIN Zwolle (SSZ)Dr. Denekampweg 208025 BV ZwolleThe Netherlands,+31-038 - 455 7185,masked,Secretary,European Society of Sleep Technologists,,,,http://www.esst.org/,SDO,,Int,,,6,Complete,,,International Classification of Sleep Disorders,1999/12/30 12:00:00,2010/01/26 12:00:00,2010/01/26 04:47:05,,UV
2.16.840.1.113883.6.46,iupp,IUPP,,,masked,,Dr. John W. Jost,"IUPAC Secretariat104 T.W. Alexander Drive, Building 19Research Triangle Park, NC 27709, USA",+1 919 485 8700,masked,Executive Director,International Union of Pure and Applied Chemistry,"IUPAC Secretariat104 T.W. Alexander Drive, Building 19Research Triangle Park, NC 27709, USA",+1 919 485 8700,secretariat@iupac.org,http://www.iupac.org,Prof Soc,,Int,,,6,Complete,,,IUPAC/IFCC Property Codeshttp://old.iupac.org/publications/epub/index.htmlhttp://www.iupac.org/web/ins/2001-068-1-700,1999/12/30 12:00:00,2010/01/26 12:00:00,2010/01/26 05:01:49,,UV
2.16.840.1.113883.6.47,iupc,IUPAC/IFCC Component Codes,,,masked,,Dr. John W. Jost,"IUPAC Secretariat104 T.W. Alexander Drive, Building 19Research Triangle Park, NC 27709, USA",+1 919 485 8700,masked,Executive Director,International Union of Pure and Applied Chemistry,"IUPAC Secretariat104 T.W. Alexander Drive, Building 19Research Triangle Park, NC 27709, USA",+1 919 485 8700,secretariat@iupac.org,http://www.iupac.org,Prof Soc,,Int,,,6,Complete,,HL7,IUPAC/IFCC Component Codeshttp://www.iupac.org/web/ins/2004-023-1-700,1999/12/30 12:00:00,2010/01/26 12:00:00,2010/01/26 05:07:56,,UV
2.16.840.1.113883.6.48,JC8,JC8,,,masked,,,,,masked,,,,,,,Govt body,,Int,,,6,Pending,,,Japanese Chemistry,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.49,OHA,OHA,,,masked,,,,,masked,,,,,,,,,Int,,2.16.840.1.113883.6.98,6,Rejected,,,"Omaha SystemDuplicate entry, request for OID assignment rejected. See replacedBy for the correct OID.",1899/12/30 12:00:27,2009/09/11 12:00:00, ,,UV
2.16.840.1.113883.6.50,POS,POS,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,POS Codes,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.51,SNM3,SNM3,,,masked,,,,,masked,,,,,,,SDO,,Int,,,6,Pending,,,SNOMED International,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.52,SNT,SNT,,,masked,,,,,masked,,,,,,,SDO,,Int,,,6,Pending,,,SNOMED topology codes (anatomic sites),1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.53,SDM,SDM,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,SNOMED- DICOM Microglossary,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.54,UC,UC,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,UCDS,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.55,UPC,UPC,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,Universal Product Code,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.56,UML,UML,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,Unified Medical Language,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.57,CDCA,CDCA,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,CDC Analyte Codes,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.58,CDCM,CDCM,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,CDC Methods/Instruments Codes,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.59,cvx,CVX,,,masked,,,,,masked,,,,,hq@hl7.org,,Govt body,,Int,,,6,Retired,,HL7,CDC Vaccine Codes used in the 1999 RRF research project at HL7.DO NOT USEThis OID has been retired as it only identifies the set of codes used in the RRF research project.,1999/12/30 12:00:00,2013/01/22 12:00:00,2013/01/22 09:28:18,,UV
2.16.840.1.113883.6.60,mvx,MVX,,,masked,,,,,masked,,,,,hq@hl7.org,,,,Int,,,6,Retired,,,CDC Vaccine Manufacturer CodesDO NOT USEThis OID was setup solely for use in the RRF research project in 1999. The correct OID for mvx is 2.16.840.1.113883.12.227,1999/12/30 12:00:00,2013/01/22 12:00:00,2013/01/22 11:00:53,,UV
2.16.840.1.113883.6.61,CAS,CAS,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,Chemical abstract codes,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.62,CST,CST,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,COSTART,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.63,FDDX,FDDX,,,masked,,,,,masked,,,,,,,Vendor,,Int,,,6,Pending,,,First DataBank Diagnostic Codes,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.64,FDDC,FDDC,,,masked,,,,,masked,,,,,,,Vendor,,Int,,,6,Pending,,,First DataBank Drug Codes,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.65,medispanMedicalConditions,Medi-Span Medical Conditions,,,masked,,Howard Strasberg,"Wolters Kluwer Health -- Medi-Span8425 Woodfield Crossing Blvd.Suite 490Indianapolis, IN 46240",858-481-4249,masked,VP Medical Informatics,Wolters Kluwer Health -- Medi-Span,,,howard.strasberg@wolterskluwer.com,http://www.medispan.com/,Vendor,,Int,,,6,Complete,,HL7 International,Medi-Span Medical Condition codes.,1999/12/30 12:00:00,2013/10/21 12:00:00,2013/10/21 03:33:00,,UV
2.16.840.1.113883.6.66,MEDX,MEDX,,,masked,,,,,masked,,,,,,,Vendor,,Int,,,6,Pending,,,Medical Economics Diagnostic Codes,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.67,MEDC,MEDC,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,Medical Economics Drug Codes,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.68,medispanGPI,Medi-Span GPI,,,masked,,Howard Strasberg,"Wolters Kluwer Health -- Medi-Span8425 Woodfield Crossing Blvd.Suite 490Indianapolis, IN 46240",858-481-4249,masked,VP Medical Informatics,Wolters Kluwer Health -- Medi-Span,,,howard.strasberg@wolterskluwer.com,http://www.medispan.com/,Vendor,,Int,,,6,Complete,,HL7 International,Medi-Span Generic Product Identifier.,1999/12/30 12:00:00,2013/10/21 12:00:00,2013/10/21 03:31:15,,UV
2.16.840.1.113883.6.69,ndc,National Drug Codes System,CAPT William A.,Hess,masked,,William A. Hess,Food and Drug Administration10903 New Hampshire AveWO32-Room 4152Silver Spring MD 20993-0002,301-796-8494,masked,Pharmacist,FDA Data Standards Council,Food and Drug Administration10903 New Hampshire AveWO32-Room 4152Silver Spring MD 20993-0002,301-796-8494,william.hess@fda.hhs.gov,http://www.fda.gov/ForIndustry/DataStandards/default.htm,,,Int,,,6,Complete,,,National Drug Codes System (which includes both the National Drug Codes (NDC) and the National Health Related Item Codes (NHRIC)).,1899/12/30 12:00:27,2009/10/14 12:00:00,2011/11/21 01:58:55,,UV
2.16.840.1.113883.6.70,MEDR,MEDR,,,masked,,,,,masked,,,,,,,,,Int,,2.16.840.1.113883.6.163,6,Rejected,,,"Medical Dictionary for Drug Regulatory Affairs (MEDuplicate entry, request for OID assignment rejected. See replacedBy for the correct OID.",1899/12/30 12:00:27,2009/09/11 12:00:00, ,,UV
2.16.840.1.113883.6.71,whoDDDrugCode,WHO Drug Dictionary Drug Code,,,masked,,Magnus Wallberg,Box 1051 SE-751 40 UPPSALA SWEDEN ,+46 18 65 60 60,masked,Technology Evangelist,Uppsala Monitoring Centre,Uppsala Monitoring CentreBox 1051 SE-751 40 UPPSALA SWEDEN ,+46 18 65 60 60,info@who-umc.org,http://www.who-umc.org/,SDO,,Int,,,6,Pending,,,"The Drug Code is the unique identifier of an entry in the B-format of the WHO Drug Dictionary. It consists of the 6 digit Drug Record Number identifying the base substance, the 2 digit Sequence 1 identifying the Salt/Esther form and the 3 digit Sequence 2 that identifies trade names or synonym names for a generic name.",1899/12/30 12:00:27, ,2016/12/14 07:28:27,,UV
2.16.840.1.113883.6.72,W4,W4,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,WHO rec# code with ASTM extension,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.73,whoATC,WHO Anatomical Therapeutic Chemical classification,Harold,Solbrig,masked,,Ola Strandberg,Box 1051SE-751 40 UppsalaSweden,+46 18 65 60 60,masked,Vendor Liaison Officer,World Health Organization,,,ola.strandberg@umc-products.com,http://www.who-umc.org/,SDO,,Int,14,,6,Complete,,,"WHO ATC, Anatomical Therapeutic Chemical classification. The classification system divides drugs into different groups according to the organ or system on which they act and/or their therapeutic and chemical characteristics. It contains several subsets.",1999/12/30 12:00:00,2011/02/23 12:00:00,2011/02/23 09:58:51,,UV
2.16.840.1.113883.6.74,art,ART,,,masked,,,,,masked,,,,,,http://www.who-umc.org/,,,Pxy,,,6,Complete,,,"WHO Adverse Reaction Terms, English language. http://www.umc-products.com/graphics/3149.pdf",1899/12/30 12:00:27,2009/09/11 12:00:00, ,,UV
2.16.840.1.113883.6.75,UMD,UMD,,,masked,,,,,masked,,,,,,,,,Int,,,6,Pending,,,MDNS,1899/12/30 12:00:27, , ,,UV
2.16.840.1.113883.6.84,IETF1766,IETF1766,HRS,,masked,,,,,masked,,,,,,,SDO,,Ext,,,6,Pending,,,Tags for the identification of languages, , ,2003/01/29 12:00:00,,UV
2.16.840.1.113883.6.85,naics,North American Industry Classification System,,HRS,masked,,,,,masked,,US Census Bureau,"U.S. Census Bureau4600 Silver Hill RoadWashington, DC 20233",301-763-INFO (4636),,http://www.census.gov,,,Int,,,6,Complete,,,"The North American Industry Classification System (NAICS) consists of a set of six digit codes that classify and categorize industries. It also organizes the categories on a production/process-oriented basis. This new, uniform, industry-wide classification system has been designed as the index for statistical reporting of all economic activities of the U.S., Canada, and Mexico.North American Industry Classification System(NAICS) for the United States, a new economic classification system that replaces the 1987 Standard Industrial Classification (SIC) for statistical purposes. NAICS is a system for classifying establishments by type of economic activity. Its purposes are: (1) to facilitate the collection, tabulation, presentation, and analysis of data relating to establishments, and (2) to promote uniformity and comparability in the presentation of statistical data describing the economy. NAICS will be used by Federal statistical agencies that collect or publish data by industry.More information may be found at http://www.census.gov/epcd/www/naicsusr.html", ,2009/10/14 12:00:00,2003/01/29 12:00:00,,UV
2.16.1,ISO3166-1,ISO3166-1,Ted,Klein,masked,,,,,masked,,,,,,,,,Ext,,1.0.3166.1,6,Retired,,,"Former OID for ISO 3166-1 Country codes; now is retired because it was entered in error. This should not be used. Note that ISO 3166-1 has numeric. 2-character, and 3-characters codes (synonyms), but HL7 has agreed that only the 2-character form is to be used (In v3 this will be done using value set machinery). ", , ,2005/09/16 12:00:00,,UV
2.16.2,ISO3166-2,ISO 3166 3 Character country codes,HRS,Klein,masked,Sundak Ganesan,,,,masked,,,,,,,SDO,,Ext,,,6,Deprecated,,,ISO 3166-2 Country subdivision codes; now is deprecated because it was entered in error., , ,2005/09/16 12:00:00,,UV
2.16.3,ISO3166-3,ISO 3166 Numeric Character country codes,HRS,Klein,masked,Sundak Ganesan,,,,masked,,,,,,,SDO,,Ext,,,6,Deprecated,,,ISO 3166-3 Obsolete country codes; now is deprecated because it was entered in error. Note that this may be used when a country that no longer has a code in 3166-1 must be transmitted (historical records)., , ,2005/09/16 12:00:00,,UV
2.16.840.1.113883.6.86,umls,Unified Medical Language System,HRS,,masked,,,,,masked,,National Library of Medicine,"National Library of Medicine8600 Rockville PikeBethesda, MD 20894",,custserv@nlm.nih.gov,http://www.nlm.nih.gov,Govt body,,Pxy,,,6,Complete,,,UMLS codes as CUIs making up the values in a coding system. More information may be found at http://www.nlm.nih.gov/research/umls/, ,2009/10/14 12:00:00,2003/01/29 12:00:00,,UV
2.16.840.1.113883.12.227,mvx,Vaccine Manufacturer,W. Ted,Klein,masked,,Rob Savage,"10 Calumet CirMadison, WI 53705",608 233 6129,masked,,Centers for Disease Control and Prevention,,,rbsavage@cdc.gov,http://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=mvx,HL7 body,2.16.840.1.114222,Int,,,6,Complete,2.16.840.1.113883,Health Level Seven International,"HL7 version 2.x Manufacturers of vaccines (code=MVX) used in chapter(s) 4; HL7 table 0227. The most current version of this code system, which is considered the source of truth, may be found at: http://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=mvxFor convenience of access, the content may also be accessed through the CDC PHINVADS system at https://phinvads.cdc.gov/vads/ViewCodeSystem.action?id=2.16.840.1.113883.12.227", ,2016/03/02 12:00:00,2013/01/22 11:05:20,"MVX, HL70227",US
2.16.840.1.113883.12.292,cvx,Vaccine Administered,W. Ted,Klein,masked,,Rob Savage,"10 Calumet CirMadison, WI 53705",608-233-6129,masked,,Centers for Disease Control and Prevention,,,rbsavage@cdc.gov,http://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx,HL7 body,2.16.840.1.114222,Int,,,6,Complete,2.16.840.1.113883,HL7,"HL7 version 2.x Vaccines administered (code = CVX)(parenteral, unless oral is noted) used in chapter(s) 4; HL7 table 0292. The most current code system and source of truth may be found at http://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx. The code system may also be access and downloaded fro convenience from PHINVADS at https://phinvads.cdc.gov/vads/ViewCodeSystem.action?id=2.16.840.1.113883.12.292Codes are never removed, but may be set to inactive when no longer available as a product. Note that in the case of historical immunization, the specific formulation may not be known. In this case, the vaccine is recorded using a code for the appropriate ""unspecified formulation"" of the vaccine.", ,2013/01/22 12:00:00,2013/01/22 11:03:38,"CVX, HL70292",US
2.16.840.1.113883.6.87,nmds,Nursing Minimum Data Set,Suzanne,Bakken,masked,,"Connie Delaney, PhD, RN, FAAN and Diane Huber, PhD, RN, FAAN","464 Nursing Building, Iowa City, Iowa 52242",319-335-7113 or 319-335-7110,masked,,"The University of Iowa, College of Nursing","464 Nursing Building, Iowa City, Iowa 52242",319-335-7113 or 319-335-7110,connie-delaney@uiowa.edu or diane-huber@uiowa.edu,,,,Int,,,6,Complete,,,The NMDS is the minimum set of items of information with uniform definitions and categories concerning the specific dimension of the context of patient care delivery. It represents the minimum data used to support the management and administration of patient/nursing care delivery across all types of settings., ,2009/09/11 12:00:00,2003/04/28 12:00:00,,UV
2.16.840.1.113883.6.88,rxNorm,RxNorm,Stuart,Nelson,masked,,,,,masked,,National Library of Medicine,"8600 Rockville Pike, Bethesda, MD 20894 ",(888) 346-3656,,http://www.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,,"RxNorm provides standard names for clinical drugs (active ingredient + strength + dose form) and for dose forms as administered to a patient. It provides links from clinical drugs, both branded and generic, to their active ingredients, drug components (active ingredient + strength), and related brand names. NDCs (National Drug Codes) for specific drug products (where there are often many NDC codes for a single product) are linked to that product in RxNorm. RxNorm links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, MediSpan, and Multum. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary.RxNorm is one of a suite of designated standards for use in U.S. Federal Government systems for the electronic exchange of clinical health information.", ,2009/10/14 12:00:00,2003/04/28 12:00:00,,UV
2.16.840.1.113883.6.89,deeds(old),DEEDS(old),,,masked,,Dan Pollock,,404-639-7715,masked,,Centers for Disease Control and Prevention,,,,http://www.cdc.gov,,2.16.840.1.114222,Int,,2.16.840.1.113883.6.102,6,retired,,,retired root for DEEDs from earlier work. Superceded., , ,2003/04/28 12:00:00,,UV
2.16.840.1.113883.6.90,icd10CM,"International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM)",Michelle,Williamson,masked,,Donna Pickett,,"(301) 458-4434, 1.2.4. Fax (301) 458-4022",masked,,National Center for Health Statistics/Centers for Disease Control and Prevention,"3311 Toledo Road; Hyattsville, MD 20782",,,http://www.cdc.gov/nchs/about/otheract/icd9/icd10cm.htm,Govt body,2.16.840.1.114222,Int,,,6,Complete,,,"The International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM), describes the classification of morbidity and mortality information for statistical purposes and for the indexing of healthcare records by diseases. The ICD-10-CM codes can be used as the value of the Act.cd attribute.", , ,2003/04/29 12:00:00,,UV
2.16.840.1.113883.6.91,fipspub92,FIPS_SOC,Ted,Klein,masked,,Elizabeth Lennon,"Stop 8901, Gaithersburg, MD 20899-8901",(301) 975-2832,masked,,"National Institute of Standards and Technology, Information Technology Laboratory","Stop 8901, Gaithersburg, MD 20899-8901",,,http://www.itl.nist.gov/,Govt body,,Int,,2.16.840.1.113883.6.243,6,Obsolete,,,"FIPSPUB92 - GUIDELINE FOR STANDARD OCCUPATIONAL CLASSIFICATION (SOC) CODES, version 1983 February 24. This entry is now obsolete, as FIPS92 was withdrawn from use in February 2005 by the US Government. It has been replaced by 2.16.840.1.113883.6.243; please use that OID instead.",2003/06/02 12:00:00,2009/09/15 12:00:00,2003/06/02 12:00:00,,UV
2.16.840.1.113883.6.92,fipsPUB2,FIPS PUB2 - STATE CODES,Ted,Klein,masked,,Elizabeth Lennon,"Stop 8901Gaithersburg, MD 20899-8901",(301) 975-2832,masked,,"National Institute of Standards and Technology, Information Technology Laboratory","Stop 8901Gaithersburg, MD 20899-8901",,,http://www.itl.nist.gov/,Govt body,,Int,,,6,Complete,,HL7,"FIPSPUB-2 - CODES FOR THE IDENTIFICATION OF THE STATES, THE DISTRICT OF COLUMBIA AND THE OUTLYING AREAS OF THE UNITED STATES, AND ASSOCIATED AREAS, version 1987 May 28",2003/06/02 12:00:00,2009/12/28 12:00:00,2009/12/28 06:00:13,,UV
2.16.840.1.113883.6.93,fipsPUB6-4,FIPS PUB 6-4 COUNTY CODES,Ted,Klein,masked,,Elizabeth Lennon,"Stop 8901Gaithersburg, MD 20899-8901",(301) 975-2832,masked,,"National Institute of Standards and Technology, Information Technology Laboratory","Stop 8901Gaithersburg, MD 20899-8901",(301) 975-NIST(6478),inquiries@nist.gov,http://www.itl.nist.gov/,Govt body,,Int,,,6,Complete,,,"FIPSPUB6-4 - Counties and Equivalent Entities of the United States, Its Possessions, and Associated Areas, version 1990 August 31",2003/06/02 12:00:00,2009/12/28 12:00:00,2009/12/28 05:59:42,,UV
1.2.840.10008.2.16.4,DCM,DICOM Controlled Terminology,Harry,Solomon,masked,,Harry Solomon,,,masked,,DICOM Standards Committee,,,,http://medical.nema.org/,SDO,,Ext,,,6,Complete,,,"Coded concepts defined in PS 3.16 Digital Imaging andCommunications in Medicine (DICOM): Part 16: Content Mapping Resource,Annex D: DICOM Controlled Terminology Definition",2003/06/09 12:00:00, ,2003/06/09 12:00:00,,UV
2.16.840.1.113883.6.94,icd10-CA,ICD10 CA,Gavin,Tong,masked,,Canadian Institute for Health Information,"4110 Yonge Street, Suite 300Toronto, ON M2P 2B7Canada",416-481-2002,masked,,Canadian Institute for Health Information,"495 Richmond Road, Suite 600Ottawa, ON K2A 4H6Canada",613-241-7860 ,ccicd-10@cihi.ca,www.cihi.ca,HL7 body,,Int,,,6,Complete,,HL7,ICD10 with Canadian modifications,2003/06/11 12:00:00,2009/12/23 12:00:00,2009/12/23 09:21:32,,UV
2.16.840.1.113883.6.95,cci,Canadian Classification of Health Interventions,Gavin,Tong,masked,Donald Kroetsch,Canadian Institute for Health Information,"4110 Yonge Street, Suite 300Toronto, ON M2P 2B7Canada",416-481-2002,masked,,CIHI (Canadian Institute for Health Information),"495 Richmond Road, Suite 600Ottawa, ON K2A 4H6Canada",613-241-7860 ,ccicd-10@cihi.ca,http://www.cihi.ca,SDO,,Int,,,6,Complete,,HL7,"CCI - Canadian Classification of Health Interventions, developed to accompany ICD-10-CA, maintained by CIHI (Canadian Institute for Health Information).For example: sections 3.AA-3.BZ Diagnostic Imaging Interventions on the Nervous System 3.AN.^ ^.^ ^ Diagnostic Imaging Interventions on the Brain 3.AN.40. ^ ^ Magnetic Resonance Imaging, Brain Incudes: That for meninges, ventricles, cerebellum, brain stem, cisterna [of brain], posterior fossa MRI, brain 3.AN.40.VA without contrast 3.AN.40.VC following intravenous injection of contrast 3.AN.40.VZ following percutaneous injection of contrastCIHI Toronto Attn: Director of Standards 4110 Yonge Street, Suite 300Toronto, ON M2P 2B7CanadaPhone: (416) 481.2002 Fax: (416) 481-2950www.cihi.ca",2003/06/11 12:00:00,2009/11/03 12:00:00,2009/12/22 11:08:11,,UV
2.16.840.1.113883.6.96,snomed-CT,SNOMED Clinical Terms,Ellen,Ryske,masked,,John Gutai,"International Health Terminology Standards Development Organisation Rued Langgaards Vej 7, 5te – 5A, 562300 Copenhagen SDenmark",+45 36448736,masked,Chief Technical Officer,International Health Terminology Standards Development Organisation ,"International Health Terminology Standards Development Organisation Rued Langgaards Vej 7, 5te – 5A, 562300 Copenhagen SDenmark",+45 36448736,jgu@ihtsdo.org,http://www.ihtsdo.org,Prof Soc,,Int,,,6,Complete,,,"SNOMED CT is a concept-based, scientifically validated terminology that provides a unique and permanent concept identifier that can be included in multiple HL7 data types including CD and CE. The concepts are managed to avoid ""semantic drift"" so the meaning remains constant. If the concept is found to be ambiguous or the meaning changes, the concept is inactivated but still retained and the identifier is never reused. SNOMED CT's concepts are interrelated hierarchically and using description logic. SNOMED CT concepts have a unique ""fully-specified name"", a preferred term, and, optionally, synonyms. The description languages include English and Spanish. ",2003/09/07 12:00:00,2009/10/14 12:00:00,2012/02/07 10:16:32,,UV
2.16.840.1.113883.6.97,icnp,International Classification for Nursing Practice,Amy,Amherdt,masked,,"Amy Coenen, Director - ICNPΒ Programme","University of Wisconsin-Milwaukee, College of NursingP.O. Box 413Milwaukee, Wisconsin, USA 53201-041",414 229-5146,masked,,International Council of Nurses (ICN),"3 place Jean-Marteau, CH-1201 Geneva, Switzerland",41 (22) 908 0100,icn@icn.ch,http://www.icn.ch/,Prof Soc,,Int,,,6,Complete,,,"ICNPΒ is a combinatorial terminology, using a multi-axial structure. ICNPΒ provides standardized terms and codes for terms in two classifications that can be used to compose or create pre-coordinated concepts to represent observations and procedures, specifically, patient problems/nursing diagnoses, nursing interventions including those focused on assessment and actual or expected (goal) outcomes.The ICNPΒ Classification for Nursing Phenomena is used to compose concepts or statements to represent observations (nursing diagnoses, patient problems, patient status, patient outcomes).The ICNPΒ Nursing Actions Classification is used to compose concepts or statements to represent procedures (nursing interventions)",2003/09/07 12:00:00,2009/10/14 12:00:00,2003/09/07 12:00:00,,UV
2.16.840.1.113883.6.98,oms,Omaha System,Karen S.,Martin,masked,,"Karen S. Martin, RN, MSN, FAAN","2115 S. 130th St., Omaha NE 68144",(402) 333-1962,masked,,"Karen S. Martin, RN, MSN, FAAN","2115 S. 130th St., Omaha NE 68144",(402) 333-1962,martinks@tconl.com,,Academic,,Int,,,6,Complete,,,"The Omaha System provides standardized terms, definitions, and codes for observations and procedures, specifically for client problems, multidisciplinary interventions including those focusing on assessment and care, and problem-specific client outcomes.",2003/09/09 12:00:00, ,2003/09/09 12:00:00,,UV
2.16.840.1.113883.6.99,ISO639-1,ISO 639-1 Alpha-2 Language Codes,Harold,Solbrig,masked,,Harold Solbrig,"200 First Street SW, Rocheseter, MN",507 284-0753,masked,,International Information Centre for Terminology (Infoterm),"Aichholzgasse 6/12A-1120 Vienna, Austria",+43/1/817 44 88,infopoint@infoterm.org,http://linux.infoterm.org/,SDO,,Pxy,,,6,Deprecated,,HL7,Codes for the Representation of Names of Languages Part 1: Alpha-2 Code. Used as part of the IETF 3066 specification for languages throughout the HL7 specification.This OID has been retired. Use the correct ISO identifier for this ISO standard 1.0.639.1 in the future.,2003/10/31 12:00:00,2009/12/23 12:00:00,2009/12/23 04:19:36,,UV
2.16.840.1.113883.6.100,ISO639-2,ISO 639-2 Alpha-3 Language Codes,Harold,Solbrig,masked,,Harold Solbrig,"200 First Street SW, Rocheseter, MN",507 284-0753,masked,,The Library of Congress Network Development & MARC Standards Office,"Washington, DC 20540-4402",1 202 707 6237,Iso639-2@loc.gov,,Govt body,,Pxy,,,6,Deprecated,,,Codes for the Representation of Names of Languages Part 2: Alpha-3 Code. Used as part of the IETF 3066 specification for languages throughout the HL7 specification.This OID is being retired; use the correct ISO identifier 1.0.639.2 for this vocabulary in the future.,2003/10/31 12:00:00,2009/12/23 12:00:00,2009/12/23 04:21:08,,UV
2.16.840.1.113883.6.101,providertaxonomy,Health Care Provider Taxonomy,Harold,Solbrig,masked,,Nancy Spector,"American Medical Association25 Massachusetts Ave, NWWashington, DC 20001",202-789-4586,masked,"Chair, National Uniform Claim Committee",National Uniform Claim Committee (NUCC),"American Medical Association25 Massachusetts Ave, NWWashington, DC 20001",202-789-4586,nancy.spector@ama-assn.org,http://www.nucc.org/,Prof Soc,,Pxy,,,6,Complete,,,"The Health Care Provider Taxonomy code set, as maintained by the National Uniform Claim Committee (NUCC), can be accessed at www.nucc.org/index.php?option=com_content&view=article&id=14&Itemid=125 The Health Care Provider Taxonomy code set is a nonmedical data code set designed for use in an electronic environment, specifically within the ASC X12N Health Care transactions. This includes the transactions mandated under HIPAA.The Health Care Provider Taxonomy code is a unique alphanumeric code, ten characters in length. The code set is structured into three distinct ""Levels"" including Provider Type, Classification, and Area of Specialization.In 2001, the NUCC took over the maintenance of the code set. Ongoing duties, including processing taxonomy code requests and maintenance of the code set, fall under the NUCC's Code Subcommittee.The NUCC is a voluntary organization of health care industry stakeholders representing providers, payers, designated standards maintenance organizations, public health organizations, and vendors. Additional information about the NUCC is available at: www.nucc.org. ",2003/10/31 12:00:00,2003/10/31 12:00:00,2014/01/24 09:44:04,HCPT,US
2.16.840.1.113883.6.102,DEEDS,DEEDS vocabularies,Wes,Rishel,masked,,Wes Rishel,,,masked,,Network Development & MARC Standards Office,,,,,SDO,,Pxy,,,6,Complete,,,root for the DEEDS code sets,2003/12/05 12:00:00,2003/12/05 12:00:00,2003/12/05 12:00:00,,UV
2.16.840.1.113883.6.102.2.10,DEEDS2.10,DEEDS2.10,Wes,Rishel,masked,,Wes Rishel,,,masked,,Network Development & MARC Standards Office,,,,,SDO,,Pxy,,,6,Complete,,,Code for ED Practitioner Role,2003/12/05 12:00:00,2003/12/05 12:00:00,2003/12/05 12:00:00,,UV
2.16.840.1.113883.6.102.4.2,DEEDS4.02,DEEDS4.02,Wes,Rishel,masked,,Wes Rishel,,,masked,,Network Development & MARC Standards Office,,,,,SDO,,Pxy,,,6,Complete,,,Mode of transport to ED,2003/12/05 12:00:00,2003/12/05 12:00:00,2003/12/05 12:00:00,,UV
2.16.840.1.113883.6.102.4.5,DEEDS4.05,DEEDS4.05,Wes,Rishel,masked,,Wes Rishel,,,masked,,Network Development & MARC Standards Office,,,,,SDO,,Pxy,,,6,Complete,,,ED Source of Referral,2003/12/05 12:00:00,2003/12/05 12:00:00,2003/12/05 12:00:00,,UV
2.16.840.1.113883.6.102.4.7,DEEDS4.07,DEEDS4.07,Wes,Rishel,masked,,Wes Rishel,,,masked,,Network Development & MARC Standards Office,,,,,SDO,,Pxy,,,6,Complete,,,Code for Initial Healthcare Encounter for Chief Complaint,2003/12/05 12:00:00,2003/12/05 12:00:00,2003/12/05 12:00:00,,UV
2.16.840.1.113883.6.102.4.8,DEEDS4.08,DEEDS4.08,Wes,Rishel,masked,,Wes Rishel,,,masked,,Network Development & MARC Standards Office,,,,,SDO,,Pxy,,,6,Complete,,,Code for Acuity Assessment,2003/12/05 12:00:00,2003/12/05 12:00:00,2003/12/05 12:00:00,,UV
2.16.840.1.113883.6.102.4.14,DEEDS4.14,DEEDS4.14,Wes,Rishel,masked,,Wes Rishel,,,masked,,Network Development & MARC Standards Office,,,,,SDO,,Pxy,,,6,Complete,,,Glasgow eye opening assessment,2003/12/05 12:00:00,2003/12/05 12:00:00,2003/12/05 12:00:00,,UV
2.16.840.1.113883.6.102.4.15,DEEDS4.15,DEEDS4.15,Wes,Rishel,masked,,Wes Rishel,,,masked,,Network Development & MARC Standards Office,,,,,SDO,,Pxy,,,6,Complete,,,Glasgow verbal component assessment,2003/12/05 12:00:00,2003/12/05 12:00:00,2003/12/05 12:00:00,,UV
2.16.840.1.113883.6.102.4.16,DEEDS4.16,DEEDS4.16,Wes,Rishel,masked,,Wes Rishel,,,masked,,Network Development & MARC Standards Office,,,,,SDO,,Pxy,,,6,Complete,,,Glasgow motor component assessment,2003/12/05 12:00:00,2003/12/05 12:00:00,2003/12/05 12:00:00,,UV
2.16.840.1.113883.6.102.4.18,DEEDS4.18,DEEDS4.18,Wes,Rishel,masked,,Wes Rishel,,,masked,,Network Development & MARC Standards Office,,,,,SDO,,Pxy,,,6,Complete,,,Systolic blood pressure special situation,2003/12/05 12:00:00,2003/12/05 12:00:00,2003/12/05 12:00:00,,UV
2.16.840.1.113883.6.102.4.22,DEEDS4.22,DEEDS4.22,Wes,Rishel,masked,,Wes Rishel,,,masked,,Network Development & MARC Standards Office,,,,,SDO,,Pxy,,,6,Complete,,,Heart rate method,2003/12/05 12:00:00,2003/12/05 12:00:00,2003/12/05 12:00:00,,UV
2.16.840.1.113883.6.102.4.24,DEEDS4.24,DEEDS4.24,Wes,Rishel,masked,,Wes Rishel,,,masked,,Network Development & MARC Standards Office,,,,,SDO,,Pxy,,,6,Complete,,,Respiratory rate special circumstances codes,2003/12/05 12:00:00,2003/12/05 12:00:00,2003/12/05 12:00:00,,UV
2.16.840.1.113883.6.102.4.27,DEEDS4.27,DEEDS4.27,Wes,Rishel,masked,,Wes Rishel,,,masked,,Network Development & MARC Standards Office,,,,,SDO,,Pxy,,,6,Complete,,,Patient temperature route,2003/12/05 12:00:00,2003/12/05 12:00:00,2003/12/05 12:00:00,,UV
2.16.840.1.113883.6.102.5.6,DEEDS5.06,DEEDS5.06,Wes,Rishel,masked,,Wes Rishel,,,masked,,Network Development & MARC Standards Office,,,,,SDO,,Pxy,,,6,Complete,,,Injury Activity,2003/12/05 12:00:00,2003/12/05 12:00:00,2003/12/05 12:00:00,,UV
2.16.840.1.113883.6.102.5.8,DEEDS5.08,DEEDS5.08,Wes,Rishel,masked,,Wes Rishel,,,masked,,Network Development & MARC Standards Office,,,,,SDO,,Pxy,,,6,Complete,,,Safety Equipment Use,2003/12/05 12:00:00,2003/12/05 12:00:00,2003/12/05 12:00:00,,UV
2.16.840.1.113883.6.102.5.19,DEEDS5.19,DEEDS5.19,Wes,Rishel,masked,,Wes Rishel,,,masked,,Network Development & MARC Standards Office,,,,,SDO,,Pxy,,,6,Complete,,,Clinical Finding Data Source,2003/12/05 12:00:00,2003/12/05 12:00:00,2003/12/05 12:00:00,,UV
2.16.840.1.113883.6.102.4.12,DEEDS4.12,DEEDS4.12,Wes,Rishel,masked,,Wes Rishel,,,masked,,Network Development & MARC Standards Office,,,,,SDO,,Pxy,,,6,Complete,,,ED Responsiveness Assessment,2003/12/05 12:00:00,2003/12/05 12:00:00,2003/12/05 12:00:00,,UV
2.16.840.1.113883.6.103,icd-9CM-diagnosiscodes,ICD-9-CM,Nenad,Kostanjsek,masked,,Nenad Kostanjsek,Avenue Appia 20 1211 Geneva 27 Switzerland,+41794755474,masked,Technical Officer for Classifications and Terminologies,World Health Organization,Avenue Appia 20 1211 Geneva 27 Switzerland,+ 41 22 791 21 11,info@who.int,https://who.int,SDO,,Int,,,6,Complete,,HL7 International,"The International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM), Volumes I, II (diagnoses) and III (procedures) describes the classification of morbidity and mortality information for statistical purposes and for the indexing of healthcare records by diseases and procedures. The ICD-9-CM codes can be used as the value of the Act.cd attribute.",2005/12/21 12:00:00,2005/12/21 12:00:00,2005/12/21 12:00:00,,UV
2.16.840.1.113883.6.104,ICD-9CM (procedure codes),National Center for Health Statistics,Michelle,Williamson,masked,,Donna Pickett,"OCD/Classifications and Public Health Data Standards; National Center for Health StatisticsCenters for Disease Control and Prevention3311 Toledo RoadHyattsville, MD 20782","(301) 458-4434, 1.2.4. Fax (301) 458-4022",masked,,National Center for Health Statistics,"OCD/Classifications and Public Health Data Standards; National Center for Health StatisticsCenters for Disease Control and Prevention3311 Toledo RoadHyattsville, MD 20782",,,http://www.cdc.gov/nchs/icd9.htm.,Govt body,2.16.840.1.114222,Int,,,6,Complete,,,"The International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM), Volumes I, II (diagnoses) and III (procedures) describes the classification of morbidity and mortality information for statistical purposes and for the indexing of healthcare records by diseases and procedures. The ICD-9-CM codes can be used as the value of the Act.cd attribute.",2005/12/21 12:00:00,2005/12/21 12:00:00,2005/12/21 12:00:00,,UV
2.16.840.1.113883.6.111,alt,Alternative Billing Concepts,Harold,Solbrig,masked,,Bernd G. Lucks,"6121 Indian School Road NE, Suite 131Albuquerque, NM 87110United States",+1-877-621-5465,masked,Chief Operating Officer,ABC Coding Solutions - Alternative Link,"6121 Indian School Road NE, Suite 131Albuquerque, NM 87110United States",+1-505-875-0002 ext,Legal@ABCcodes.com,http://www.abccodes.com,,,Pxy,,,6,Complete,,,"Alternative Billing Concepts (Altlink). Version 2004, sixth edition. Contact: Alternative Link LLC; 1065 Main St., Bldg. C, Las Cruces, NM 88005; phone: (505) 527-0636; http://www.alternativelink.com; mail@alternativelink.com.",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 05:22:59,,UV
2.16.840.1.113883.6.112,aod,Alcohol and Other Drug Thesaurus,Harold,Solbrig,masked,,Nancy Winstanley,"NIAAA Libraryc/o CSR Incorporated2107 Wilson Blvd., Suite 1000Arlington, VA 22201",+1 703-741-7147,masked,,NIAAA Library,"c/o CSR Incorporated2107 Wilson Blvd., Suite 1000Arlington, VA 22201",+1 703-741-7147,,,Prof Soc,,Pxy,,,6,Complete,,,"Alcohol and Other Drug Thesaurus: A Guide to Concepts and Terminology in Substance Abuse and Addiction. 3rd. ed. [4 Volumes.] Bethesda, MD: National Institute on Alcohol Abuse and Alcoholism (NIAAA) and Center for Substance Abuse Prevention (CSAP), 2000",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 05:16:17,,UV
2.16.840.1.113883.6.113,bi,Beth Israel Problem List Vocabulary,Harold,Solbrig,masked,,"Howard Goldberg, MD.","330 Brookline AvenueBoston, MA 02215",,masked,,Beth Israel Deaconess Medical Center,"330 Brookline AvenueBoston, MA 02215",+1 617-667-7000,,http://www.bidmc.org/,Provider,,Pxy,,,6,Complete,,HL7,"Beth Israel OMR Clinical Problem List Vocabulary. Version 1.0. Boston (MA): Beth Israel Deaconess Medical Center, 1999. Contact: Howard Goldberg, MD.; http://clinquery.bidmc.harvard.edu.",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 05:27:58,,UV
2.16.840.1.113883.6.114,ccpss,Clinical Problem Statements,Harold,Solbrig,masked,,"Steven Brown, M.D.",Room 442Eskind Biomedical LibraryVanderbilt University Medical Center2209 Garland AveNashville TN 37232-8340USA,+1 615-321-6335,masked,"Associate Professor, Biomedical Informatics",Vanderbilt University Medical Center,Eskind Biomedical LibraryVanderbilt University Medical Center2209 Garland AveNashville TN 37232-8340USA,,,,,,Pxy,,,6,Complete,,HL7,"Canonical Clincial Problem Statement System, Version 1.0 June 23, 1999. Contact: sbrown@vumclib.mc.vanderbilt.eduFrom UMLS",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 05:55:51,,UV
2.16.840.1.113883.6.115,ccs,Clinical Classifications Categories,Harold,Solbrig,masked,,"Anne Elixhauser, Ph.D.","AHRQ540 Gaither RoadRockville, MD 20850USA",+1 301-594-1430,masked,Senior Research Scientist,Agency for Healthcare Research and Quality,"540 Gaither RoadRockville, MD 20850USA",+1 301-427-1364,,http://www.ahrq.gov,Govt body,,Pxy,,,6,Complete,,HL7,"Clinical Classifications Software (CCS). Agency for Healthcare Research and Quality (AHRQ), Rockville, MD. Release Date: April 2003. URL: http://www.ahcpr.gov/data/hcup/ccsfact.htm Phone: 301-594-1364.",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 06:00:52,,UV
2.16.840.1.113883.6.116,CDT,Current Dental Terminology,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Rejected,,,"Version of Current Dental Terminology (CDT) version 4, included in the Healthcare Common Procedure Coding System (HCPCS).Request rejected. This is a duplicate of OID 2.16.840.1.113883.6.13",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.117,costar,Computer-Stored Ambulatory Records (COSTAR),Harold,Solbrig,masked,,"G.Octo Barnett, M.D.","Laboratory of Computer Science Massachusetts General Hospital50 Staniford Street, 5th FloorBoston, MA 02114USA",+1 617-726-3939,masked,,Laboratory of Computer Science Massachusetts General Hospital,"50 Staniford Street, 5th FloorBoston, MA 02114USA",,,http://www.lcs.mgh.harvard.edu/,Provider,,Pxy,,,6,Complete,,HL7,"Computer-Stored Ambulatory Records (COSTAR). Boston (MA): Massachusetts General Hospital, 1989-1995.",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 06:08:44,,UV
2.16.840.1.113883.6.118,CPM,Medical Entities Dictionary,Harold,Solbrig,masked,,"George Hripcsak, M.D.","Department of Biomedical InformaticsVanderbilt Clinic VC-5Columbia University622 W. 168th StreetNew York, New York 10032USA",+1 212-305-5780,masked,Professor and Chair,Columbia University DBMI,"Department of Biomedical InformaticsVanderbilt Clinic VC-5Columbia University622 W. 168th StreetNew York, New York 10032USA",+1 212-305-3302,,http://www.dbmi.columbia.edu,Academic,,Pxy,,,6,Complete,,,"Medical Entities Dictionary (CPM), Columbia Presbyterian Medical Center Medical Entities Dictionary. New York (NY): Columbia Presbyterian Medical Center, 2003",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 06:14:27,,UV
2.16.840.1.113883.6.119,fma,Foundational Model of Anatomy Ontology,Harold,Solbrig,masked,,Gail Dykstra,"UW Tech Transfer Digital VenturesUniversity of WashingtonSeattle, WA 98195USA",+ 1 206-543-4611,masked,curator,"Jose Leonardo V Mejino Jr. MD, Structural Informatics Group","Box 345420HSB BiostructureUniversity of Washington School of MedicineSeattle, WA 98195USA",206-543-7118,mejino@u.washington.edu,http://depts.washington.edu/ventures/UW_Technology/,Academic,,Pxy,,,6,Complete,,,Digital Anatomist Foundational Model of Anatomy (FMA)http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/FMA.php,2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 06:25:00,,UV
2.16.840.1.113883.6.12.1,cptSP,CPT Spanish,Harold,Solbrig,masked,,Dorith Brown,"American Medical Association515 N. State StreetChicago, IL 60610United States",1-312-464-5762,masked,CPT Intellectual Property Services,American Medical Association,"515 N. State StreetChicago, IL 60610United States",1-800-621-8335,,http://www.ama-assn.org,Prof Soc,,Pxy,,,6,Complete,,HL7,"Current Procedural Terminology (CPT), Spanish Translation. 4th ed. Chicago (IL): American Medical Association, 2000. http://www.ama-assn.org.",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 11:24:52,,UV
2.16.840.1.113883.6.120,csp,CRISP Thesaurus,Harold,Solbrig,masked,,Dorrette Finch,"6701 Rockledge DriveBethesda, MD 20892-7983USA",,masked,"Director, Division of Research Documentation",National Institutes of Health,"Anita Ghebeles, NIH/OD/OER/ORA6705 Rockledge Drive, Room 4162, MSC 7983Bethesda, MD 20892-7983USA",+1 301-435-0653,,http://www.nih.gov/,Govt body,,Pxy,,,6,Complete,,,"Computer Retrieval of Information on Scientific Projects (CRISP). Bethesda (MD): National Institutes of Health, Division of Research Grants, Research Documentation Section, 2004. http://crisp.cit.nih.gov/The CRISP system has been replaced by the RePORT Expenditures and Results (RePORTER) query tool.",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 06:51:16,,UV
2.16.840.1.113883.6.122,ddb,Diseases Database,Harold,Solbrig,masked,,Malcolm Duncan,"Medical Object Oriented Software Enterprises Ltd.Unit 36c Marryat SquareFulham, London SW6 6UA, UK",+44 (0)20 7381 4220,masked,,Medical Object Oriented Software Enterprises Ltd.,"Unit 36c Marryat SquareFulham, London SW6 6UA, UK",+44 (0)20 7381 4220,100416.1761@compuserve.com,http://www.diseasesdatabase.com,,,Pxy,,,6,Complete,,HL7,"Diseases Database 2000. May, 2000. London (England): Medical Object Oriented Software Enterprises Ltd., 2000. Contact: Malcolm Duncan ; http://www.diseasesdatabase.com/.",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 09:43:34,,UV
2.16.840.1.113883.6.125,dsm3r,DSM-III-R,Harold,Solbrig,masked,,--Needs CP data--,American Psychiatric Press Inc.1400 K Street N.W.Washington DC 20005USA,,masked,,American Psychiatric Press Inc.,1400 K Street N.W.Washington DC 20005USA,,csdept@appi.org,,Prof Soc,,Pxy,,,6,Complete,,HL7,"Diagnostic and Statistical Manual of Mental Disorders (DSM-III-R). 3rd ed. rev. Washington (DC): American Psychiatric Association, 1987.",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 09:47:19,,UV
2.16.840.1.113883.6.126,dsm4,DSM-IV,Harold,Solbrig,masked,,APA Answer Center,"1000 Wilson BoulevardSuite 1825Arlington, VA 22209USA",+1-703-907-7300,masked,,American Psychiatric Association,"1000 Wilson BoulevardSuite 1825Arlington, VA 22209USA",+1-703-907-7300,apa@psych.org,http://www.psych.org,Prof Soc,,Pxy,,,6,Complete,,,"Diagnostic and Statistical Manual of Mental Disorders (DSM-IV). 4th ed. Washington (DC): American Psychiatric Association, 1994.",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 09:51:56,,UV
2.16.840.1.113883.6.127,dxp,DXplain,Harold,Solbrig,masked,,"G. Octo Barnett, M.D.","Laboratory of Computer Science, Massachusetts General Hospital50 Staniford Street, 5th FloorBoston, MA 02114USA",+1 617-726-3939,masked,,"Laboratory of Computer Science, Massachusetts General Hospital","50 Staniford Street, 5th FloorBoston, MA 02114USA",+1 617-726-3939,Barnett.Octo@mgh.harvard.edu,http://www.lcs.mgh.harvard.edu/,Academic,,Pxy,,,6,Complete,,HL7,"DXplain (An expert diagnosis program). Boston (MA): Massachusetts General Hospital, 1994. http://dxplain.org/dxp/dxp.pl",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 09:55:31,,UV
2.16.840.1.113883.6.128,go,Gene Ontology,Harold,Solbrig,masked,,,,,masked,,The Gene Ontology Consortium,,,gohelp@geneontology.org,http://www.geneontology.org/,Prof Soc,,Pxy,,,6,Complete,,,"Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium (2000) Nature Genet. 25: 25-29, http://www.geneontology.org/#cite_go.ftp://ftp.geneontology.org/pub/go/ontology-archive/",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 09:59:32,,UV
2.16.840.1.113883.6.129,HCDT,Current Dental Terminology in HCPCS,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Rejected,,,"Version of Current Dental Terminology (CDT) version 4, included in the Healthcare Common Procedure Coding System (HCPCS).Request rejected. Appears to be a duplicate of 2.16.840.1.113883.6.13",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.130,HCPT,CPT in HCPCS,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Rejected,,,"Version of Physicians' Current Procedural Terminology (CPT) included in the Healthcare Common Procedure Coding System (HCPCS), 2004.Request rejected. Appears to be a duplicate of 2.16.840.1.113883.6.12",2005/01/25 12:00:00,2009/10/14 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.132,hlrel,ICPC2E ICD10 Relationships,Harold,Solbrig,masked,,Henk Lamberts,,,masked,,University of Amsterdam,,,H.Lamberts@AMC.UVA.NL,,Academic,,Pxy,,,6,Complete,,HL7,"ICPC2E-ICD10 relationships from Dr. Henk Lamberts (HLREL), 1998. University of Amsterdam. Contact: H.Lamberts@AMC.UVA.NL.",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 10:03:06,,UV
2.16.840.1.113883.6.133,HUGO,"HUGO, 2004",Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,2.16.840.1.113883.6.281,6,Rejected,,,"HUGO Gene Nomenclature, HUGO Gene Nomenclature Committee, Department of Biology, University College London, Wolfson House, 4 Stephenson Way, London NW1 2HE, UK. Tel: 44-20-7679-5027 Fax: 44-20-7387-3496 e-mail: nome@galton.ucl.ac.uk",2005/01/25 12:00:00,2005/01/25 12:00:00,2009/05/21 01:21:00,,UV
2.16.840.1.113883.6.135,icd10am,ICD-10 Austral Mod,Harold,Solbrig,masked,,--Needs CP data--,"University of SydneyFaculty of Health SciencesPO Box 170Lidcombe, NSW, Australia 1825",+61 2 9351 9461,masked,,"National Centre for Classification in Health, University of Sydney","University of SydneyFaculty of Health SciencesPO Box 170Lidcombe, NSW, Australia 1825",+61 2 9351 9461,D.Truran@cchs.usyd.edu.au,,Academic,,Pxy,,,6,Complete,,,"International Statistical Classification of Diseases and Related Health Problems, 10th Revision, Australian Modification; 2nd Edition, published January 2000. Developed and Maintained by the National Centre for Classification in Health, University of Sydn",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 10:06:23,,UV
2.16.840.1.113883.6.135.1,icd10AMAE,ICD-10 Austral Mod Am Engl,Harold,Solbrig,masked,,,"University of SydneyFaculty of Health SciencesPO Box 170Lidcombe, NSW, Australia 1825",+61 2 9351 9461,masked,,National Centre for Classification in Health,"University of SydneyFaculty of Health SciencesPO Box 170Lidcombe, NSW, Australia 1825",+61 2 9351 9461,D.Truran@cchs.usyd.edu.au,,SDO,,Pxy,,,6,Complete,,HL7,"International Statistical Classification of Diseases and Related Health Problems, Australian Modification (ICD-10-AM), Americanized English Equivalents, produced by NLM. Bethesda (MD): National Library of Medicine, UMLS project, 2000",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/07/07 04:21:03,,UV
2.16.840.1.113883.6.138,icpc,"International Classification of Primary Care, 1993 edition",Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,Prof Soc,,Pxy,14,,6,Complete,,,"The International Classification of Primary Care (ICPC). Denmark: World Organisation of Family Doctors, 1993. Various language translations are identified beneath this OID.",2005/01/25 12:00:00,2009/10/06 12:00:00,2009/10/06 09:58:39,,UV
2.16.840.1.113883.6.138.1,icpc-BAQ,International Classification of Primary Care 1993 Basque,Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,,,Pxy,,,6,Complete,,,"The International Classification of Primary Care (ICPC). Basque Translation. Denmark: World Organisation of Family Doctors, 1993.",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.138.10,icpc-NOR,International Classification of Primary Care 1993 Norwegian,Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,,,Pxy,,,6,Complete,,,"The International Classification of Primary Care (ICPC). Norwegian Translation. Denmark: World Organisation of Family Doctors, 1993.",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.138.11,icpc-POR,International Classification of Primary Care 1993 Portuguese,Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,,,Pxy,,,6,Complete,,,"The International Classification of Primary Care (ICPC). Portuguese Translation. Denmark: World Organisation of Family Doctors, 1993.",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.138.12,icpc-SPA,International Classification of Primary Care 1993 Spanish,Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,,,Pxy,,,6,Complete,,,"The International Classification of Primary Care (ICPC). Spanish Translation. Denmark: World Organisation of Family Doctors, 1993.",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.138.13,icpc-SWE,International Classification of Primary Care 1993 Swedish,Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,,,Pxy,,,6,Complete,,,"The International Classification of Primary Care (ICPC). Swedish Translation. Denmark: World Organisation of Family Doctors, 1993.",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.138.2,icpc-DAN,International Classification of Primary Care 1993 Danish,Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,,,Pxy,,,6,Complete,,,"The International Classification of Primary Care (ICPC). Danish Translation. Denmark: World Organisation of Family Doctors, 1993.",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.138.3,icpc-DUT,International Classification of Primary Care 1993 Dutch,Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,,,Pxy,,,6,Complete,,,"The International Classification of Primary Care (ICPC). Dutch Translation. Denmark: World Organisation of Family Doctors, 1993.",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.138.4,icpc-FIN,International Classification of Primary Care 1993 Finnish,Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,,,Pxy,,,6,Complete,,,"The International Classification of Primary Care (ICPC). Finnish Translation. Denmark: World Organisation of Family Doctors, 1993.",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.138.5,icpc-FRE,International Classification of Primary Care 1993 French,Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,,,Pxy,,,6,Complete,,,"The International Classification of Primary Care (ICPC). French Translation. Denmark: World Organisation of Family Doctors, 1993.",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.138.6,icpc-GER,International Classification of Primary Care 1993 German,Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,,,Pxy,,,6,Complete,,,"The International Classification of Primary Care (ICPC). German Translation. Denmark: World Organisation of Family Doctors, 1993.",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.138.7,icpc-HEB,International Classification of Primary Care 1993 Hebrew,Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,,,Pxy,,,6,Complete,,,"The International Classification of Primary Care (ICPC). Hebrew Translation, Denmark: World Organisation of Family Doctors, 1993",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.138.8,icpc-HUN,International Classification of Primary Care 1993 Hungarian,Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,,,Pxy,,,6,Complete,,,"The International Classification of Primary Care (ICPC). Hungarian Translation. Denmark: World Organisation of Family Doctors, 1993.",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.138.9,icpc-ITA,International Classification of Primary Care 1993 Italian,Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,SDO,,Pxy,,,6,Complete,,,"The International Classification of Primary Care (ICPC). Italian Translation. Denmark: World Organisation of Family Doctors, 1993.",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.139.1,icpc2E-ENG,"International Classification of Primary Care, second edition, English",Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,SDO,,Pxy,14,,6,Complete,,,"International Classification of Primary Care / prepared by the Classification Committee of the World Organization of National Colleges, Academies and Academic Associations of General Practitioners/Family Physicians (WONCA), known more briefly as the World",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.139.2,icpc2E-DUT,"ICPC2E, Dutch Translation",Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,,,Pxy,,,6,Complete,,,"Hirs, W., H.W. Becker, C. van Boven, S.K. Oskam, I.M. Okkes, H. Lamberts. International Classification of Primary Care 2E: 2nd ed. electronic. Dutch Translation. Amsterdam: Department of General Practice, Academic Medical Center/University of Amsterdam, D",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.139.3,mthicpc2E-AE,ICPC2E Am Engl (Metathesaurus),Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,,,Pxy,,,6,Complete,,,"Henk Lamberts and Inge Hofmans-Okkes. International Classification of Primary Care 2nd Edition, Electronic, 2E, American English Equivalents. Amsterdam: International Classification of Primary Care / prepared by the Classification Committee of the World Health Organization. Entry derived from the UMLS Metathesaurus.",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.140.1,icpc2E-P-AE,ICPC2E 1998 Plus Am Engl,Harold,Solbrig,masked,,--Needs CP data--,"8600 Rockville PikeBethesda, MD 20894",,masked,,National Library of Medicine,"8600 Rockville PikeBethesda, MD 20894",(301) 496-6308,,http://www.nlm.nih.gov/research/umls/,SDO,,Pxy,,,6,Complete,,,"International Classification of Primary Care, Version 2-Plus, Australian Modification. Americanized English Equivalents, January, 2000. Produced by NLM. Bethesda (MD): National Library of Medicine, UMLS project",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.140.2,icpc2E-P-AUS,ICPC2P 1998 Plus Austral Mod,Harold,Solbrig,masked,,--Needs CP data--,"8600 Rockville PikeBethesda, MD 20894",,masked,,National Library of Medicine,"8600 Rockville PikeBethesda, MD 20894",(301) 496-6308,,http://www.nlm.nih.gov/research/umls/,SDO,,Pxy,,,6,Complete,,,"International Classification of Primary Care, Version 2-Plus, Australian Modification. January, 2000",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.142.4,icpc2-icd10-ENG,ICPC2-ICD10 Thesaurus (English),Harold,Solbrig,masked,,Dr. Inge M. Okkes,Veemkade 12081019 BZ AMSTERDAMThe Netherlands,,masked,,WHO Collaborating Centre for the FIC in The Netherlands,Veemkade 12081019 BZ AMSTERDAMThe Netherlands,,,http://www.rivm.nl/who-fic/thesauruseng.htm,SDO,,Pxy,,,6,Complete,,,"Becker, H.W., C. van Boven, S.K. Oskam, I.M. Okkes, W. Hirs, H. Lamberts. ICPC2 - ICD10 Thesaurus, Version March, 2004. Amsterdam: Project ""Adaptation ICPC, integration and implementation of ICPC2 and ICD10(-CM)."" Department of General Practice, Academic ",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.142.1,icpc2-icd10-DUT,"ICPC2-ICD10ENG Thesaurus, Dutch Translation",Harold,Solbrig,masked,,Dr. Inge M. Okkes,Veemkade 12081019 BZ AMSTERDAMThe Netherlands,,masked,,WHO Collaborating Centre for the FIC in The Netherlands,Veemkade 12081019 BZ AMSTERDAMThe Netherlands,,,http://www.rivm.nl/who-fic/thesauruseng.htm,SDO,,Pxy,,,6,Complete,,,"International Classification of Primary Care / prepared by the Classification Committee of the World Organization of National Colleges, Academies and Academic Associations of General Practitioners/Family Physicians (WONCA), known more briefly as the World",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.142.2,mth-icpc2-icd10-7B,"ICPC2-ICD10 Thesaurus, 7-bit",Harold,Solbrig,masked,,Dr. Inge M. Okkes,Veemkade 12081019 BZ AMSTERDAMThe Netherlands,,masked,,WHO Collaborating Centre for the FIC in The Netherlands,Veemkade 12081019 BZ AMSTERDAMThe Netherlands,,,http://www.rivm.nl/who-fic/thesauruseng.htm,SDO,,Pxy,,,6,Complete,,,"International Classification of Primary Care / prepared by the Classification Committee of the World Organization of National Colleges, Academies and Academic Associations of General Practitioners/Family Physicians (WONCA), known more briefly as the World",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.142.3,mth-icpc2-icd10-AE,"ICPC2-ICD10 Thesaurus, Am Engl",Harold,Solbrig,masked,,Dr. Inge M. Okkes,Veemkade 12081019 BZ AMSTERDAMThe Netherlands,,masked,,WHO Collaborating Centre for the FIC in The Netherlands,Veemkade 12081019 BZ AMSTERDAMThe Netherlands,,,http://www.rivm.nl/who-fic/thesauruseng.htm,SDO,,Pxy,,,6,Complete,,,"International Classification of Primary Care / prepared by the Classification Committee of the World Organization of National Colleges, Academies and Academic Associations of General Practitioners/Family Physicians (WONCA), known more briefly as the World",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.158,jabl,Congenital Mental Retardation Syndromes,Harold,Solbrig,masked,,Stanley Jablonski,National Library of Medicine8600 Rockville PikeBethesda MD 20894USA,,masked,,National Library of Medicine,8600 Rockville PikeBethesda MD 20894USA,,stanley_jablonski@nlm.nih.gov,http://www.nlm.nih.gov/,Govt body,,Pxy,,,6,Complete,,HL7,"Online Congenital Multiple Anomaly/Mental Retardation Syndromes, 1999.",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 10:11:29,,UV
2.16.840.1.113883.6.159,LCH,Library of Congress Subject Headings,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,Govt body,,Pxy,,,6,Pending,,,"Library of Congress Subject Headings. 12th ed. Washington (DC): Library of Congress, 1989.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.160,MBD,MEDLINE Backfile,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,MEDLINE Backfiles (1994-1998). Bethesda (MD): National Library of Medicine. Contact: http://www.nlm.nih.gov.,2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.161,mcm,Glossary of Clinical Epidemiologic Terms,Harold,Solbrig,masked,,"R. Brian Haynes, M.D., Ph.D.","Clinical Epidemiology & Biostatistics and Medicine, Faculty of Health SciencesMcMaster UniversityRoom 2C10B1200 Main StreetWest Hamilton Ontario, Canada L8N 3Z5",(905) 525-9140,masked,,McMaster University,"Clinical Epidemiology & Biostatistics and Medicine, Faculty of Health SciencesMcMaster UniversityRoom 2C10B1200 Main StreetWest Hamilton Ontario, Canada L8N 3Z5",(905) 525-9140,,,Academic,,Pxy,,,6,Complete,,,"Glossary of Methodologic Terms for Clinical Epidemiologic Studies of Human Disorders. Canada: McMaster University, 1992.",2005/01/25 12:00:00,2010/01/26 12:00:00,2010/01/26 10:15:32,,UV
2.16.840.1.113883.6.162,MDDB,Master Drug Data Base,Harold,Solbrig,masked,,Howard Strasberg,"Wolters Kluwer Health8425 Woodfield Crossing Blvd, Suite 490Indianapolis, IN 46240",858.481.4249,masked,,Wolters Kluwer Health -- Medi-Span,"8425 Woodfield Crossing Blvd, Suite 490Indianapolis, IN 46240",,howard.strasberg@wolterskluwer.com,,Vendor,,Pxy,,,6,Retired,,HL7 International,"Master Drug Data Base, 2003",2005/01/25 12:00:00,2005/01/25 12:00:00,2013/10/22 03:48:02,,UV
2.16.840.1.113883.6.163,mdr,MedDRA,Elizabeth A.,d'Alelio,masked,,Patrick Revelle,"12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,masked,,"MedDRA MSSO/ Northrop Grumman,MedDRA MSSO/ Northrop Grumman","12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,Patrick.Revelle@ngc.com,www.meddramsso.com,,,Pxy,,,6,Complete,,,"MedDRA is a five-level hierarchy of terms. MedDRA was developed as an ICH initiative and is maintained and distributed by the MedDRA Maintenance and Support Services Organization (MSSO). Versions Versions are released twice per year and are identified by 2 numbers separated by a decimal point (e.g., 7.0, 7.1, 8.0, and 8.1). .0 releases may contain changes to the hierarchy. .1 releases will only contain additions, moves, and modifications of medical concept terms (Preferred Terms) and coding level terms (Lowest Level Terms). Concepts Concepts are represented by a MedDRA code and a MedDRA term name. The MedDRA code is an eight digit numeric code. MedDRA codes are unique and are never reused. The MedDRA term name is a 100 character alphanumeric field used to describe the concept or term. Hierarchies MedDRA is structured as a five level hierarchy. System Organ Classes (SOCs) are the broadest terms (e.g., Cardiac disorders, Investigations). The lowest level of the terminology is the Lowest Level Term (LLT) level. There are 26 SOCs and over 60,000 LLTs",2005/01/25 12:00:00,2005/08/23 12:00:00,2005/08/23 12:00:00,,UV
2.16.840.1.113883.6.163.1,MDRAE,MedDRA Am Engl,Elizabeth A.,d'Alelio,masked,,Patrick Revelle,"12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722v,masked,,"MedDRA MSSO/ Northrop Grumman,MedDRA MSSO/ Northrop Grumman","12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,Patrick.Revelle@ngc.com,www.meddramsso.com,,,Pxy,,,6,Complete,,,"Medical Dictionary for Regulatory Activities Terminology (MedDRA), American English Equivalents, Version 7.0. Bethesda, MD: National Library of Medicine, March 1, 2004 This is the English language version as encapsulated in the UMLS..",2005/01/25 12:00:00,2005/08/23 12:00:00,2005/08/23 12:00:00,,UV
2.16.840.1.113883.6.163.2,MDRDUT,MedDRA Dutch,Elizabeth A.,d'Alelio,masked,,Patrick Revelle,"12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,masked,,"MedDRA MSSO/ Northrop Grumman,MedDRA MSSO/ Northrop Grumman","12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,Patrick.Revelle@ngc.com,www.meddramsso.com,,,Pxy,,,6,Complete,,,"Medical Dictionary for Regulatory Activities Terminology (MedDRA) Version 7.0, Dutch Edition. International conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH). Reston, VA: MedDRA MSSO, March 1, 2004 This is the Dutch language version as encapsulated in the UMLS..",2005/01/25 12:00:00,2005/08/23 12:00:00,2005/08/23 12:00:00,,UV
2.16.840.1.113883.6.163.3,MDRFRE,MedDRA French,Elizabeth A.,d'Alelio,masked,,Patrick Revelle,"12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,masked,,"MedDRA MSSO/ Northrop Grumman,MedDRA MSSO/ Northrop Grumman","12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,Patrick.Revelle@ngc.com,www.meddramsso.com,,,Pxy,,,6,Complete,,,"Medical Dictionary for Regulatory Activities Terminology (MedDRA) Version 7.0, French Edition. International conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH). Reston, VA: MedDRA MSSO, March 1, 2004 This is the French language version as encapsulated in the UMLS..",2005/01/25 12:00:00,2005/08/23 12:00:00,2005/08/23 12:00:00,,UV
2.16.840.1.113883.6.163.4,MDRGER,MedDRA German,Elizabeth A.,d'Alelio,masked,,Patrick Revelle,"12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,masked,,"MedDRA MSSO/ Northrop Grumman,MedDRA MSSO/ Northrop Grumman","12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,Patrick.Revelle@ngc.com,www.meddramsso.com,,,Pxy,,,6,Complete,,,"Medical Dictionary for Regulatory Activities Terminology (MedDRA) Version 7.0, German Edition. International conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH). Reston, VA: MedDRA MSSO, March 1, 2004 This is the German language version as encapsulated in the UMLS..",2005/01/25 12:00:00,2005/08/23 12:00:00,2005/08/23 12:00:00,,UV
2.16.840.1.113883.6.163.5,MDRPOR,MedDRA Portuguese,Elizabeth A.,d'Alelio,masked,,Patrick Revelle,"12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,masked,,"MedDRA MSSO/ Northrop Grumman,MedDRA MSSO/ Northrop Grumman","12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,Patrick.Revelle@ngc.com,www.meddramsso.com,,,Pxy,,,6,Complete,,,"Medical Dictionary for Regulatory Activities Terminology (MedDRA) Version 7.0, Portuguese Edition. International conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH). Reston, VA: MedDRA MSSO, March 1, 2004. This is the Portuguese language version as encapsulated in the UMLS..",2005/01/25 12:00:00,2005/08/23 12:00:00,2005/08/23 12:00:00,,UV
2.16.840.1.113883.6.163.6,MDRSPA,MedDRA Spanish,Elizabeth A.,d'Alelio,masked,,Patrick Revelle,"12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,masked,,"MedDRA MSSO/ Northrop Grumman,MedDRA MSSO/ Northrop Grumman","12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,Patrick.Revelle@ngc.com,www.meddramsso.com,,,Pxy,,,6,Complete,,,"Medical Dictionary for Regulatory Activities Terminology (MedDRA) Version 7.0, Spanish Edition. International conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH). Reston, VA: MedDRA MSSO, March 1, 2004. This is the Spanish language version as encapsulated in the UMLS..",2005/01/25 12:00:00,2005/08/23 12:00:00,2005/08/23 12:00:00,,UV
2.16.840.1.113883.6.164,MDREX,MedDRA expanded,Elizabeth A.,d'Alelio,masked,,Patrick Revelle,"12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,masked,,"MedDRA MSSO/ Northrop Grumman,MedDRA MSSO/ Northrop Grumman","12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,Patrick.Revelle@ngc.com,www.meddramsso.com,,,Pxy,,,6,Complete,,,"Medical Dictionary for Regulatory Activities Terminology (MedDRA), with expanded abbreviations, Version 7.0. Bethesda, MD: National Library of Medicine, March 1, 2004.",2005/01/25 12:00:00,2005/08/23 12:00:00,2005/08/23 12:00:00,,UV
2.16.840.1.113883.6.164.1,MDREA,MedDRA Am Engl expanded,Elizabeth A.,d'Alelio,masked,,Patrick Revelle,"12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,masked,,"MedDRA MSSO/ Northrop Grumman,MedDRA MSSO/ Northrop Grumman","12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,Patrick.Revelle@ngc.com,www.meddramsso.com,,,Pxy,,,6,Complete,,,"Medical Dictionary for Regulatory Activities Terminology (MedDRA), American English Equivalents with expanded abbreviations, Version 7.0. Bethesda, MD: National Library of Medicine, March 1, 2004.",2005/01/25 12:00:00,2005/08/23 12:00:00,2005/08/23 12:00:00,,UV
2.16.840.1.113883.6.165,MTHMDRSPA,MTH MedDRA Spanish,Elizabeth A.,d'Alelio,masked,,Patrick Revelle,"12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,masked,,"MedDRA MSSO/ Northrop Grumman,MedDRA MSSO/ Northrop Grumman","12011 Sunset Hills Rd, VAR1 7B52, Reston, VA 20190",703-345-7722,Patrick.Revelle@ngc.com,www.meddramsso.com,,,Pxy,,,6,Complete,,,"Metathesaurus Forms of Medical Dictionary for Regulatory Activities Terminology (MedDRA) Version 7.0, Spanish Edition. Bethesda, MD: National Library of Medicine, March 2004.",2005/01/25 12:00:00,2005/08/23 12:00:00,2005/08/23 12:00:00,,UV
2.16.840.1.113883.6.172,MED,MEDLINE,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,MEDLINE Current Files (1999-2004). Bethesda (MD): National Library of Medicine. Contact: http://www.nlm.nih.gov.,2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.173,MEDLINEPLUS,MedlinePlus,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"MedlinePlus Health Topics. Bethesda (MD): National Library of Medicine, August 14, 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.174,MIM,Online Mendelian Inheritance in Man 1993,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Online Mendelian Inheritance in Man (OMIM). Baltimore (MD): Johns Hopkins University, Center for Biotechnology Information, 1994.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.175,mmsl,Multum,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,"Multum Information Services, Inc.","Colorado Center Tower One2000 South Colorado BoulevardSuite 11000Denver, Colorado 80222",888-633-4772 x1420,info@multum.com,http://www.multum.com/,,,Pxy,,,6,Complete,,HL7,"Medisource Lexicon. Multum Information Services, Inc., Denver, CO. Release Date: March 1, 2004. URL: http://www.multum.com/ Phone: 888-633-4772 x1420.http://www.multum.com/Lexicon.htm",2005/01/25 12:00:00,2005/01/25 12:00:00,2009/12/30 03:15:07,,UV
2.16.840.1.113883.6.176,mmx,Micromedex,Harold,Solbrig,masked,,,,,masked,,Thomson Reuters,"4301 Connecticut Avenue, NWSuite 330Washington, D.C. 20008",+1(877) 843-6796,,http://www.thomsonreuters.com/healthcare,Vendor,,Pxy,,,6,Complete,,,"Micromedex DRUGDEX, 2001. URL: http://www.micromedex.com/ Phone: 800-525-9083.http://www.micromedex.com/products/drugdex/Using a standardized outline format, the DRUGDEXΒ System harnesses this information and gives you easy access to current, accurate drug knowledge you can use with confidence. Reviewed by international experts, DRUGDEX evidence-based documents cover FDA-approved and investigational prescription and nonprescription drugs, as well as non-U.S. preparations. Areas discussed include dosage, pharmacokinetics, cautions, interactions, clinical applications, adverse effects, comparative efficacy, drug of choice information, and orphan drug status.Features * Provides evidence-based, unbiased, fully referenced information * Contains independently reviewed data from major drug centers and pharmacology services worldwide * Decreases risk of adverse drug events and saves valuable time by delivering data at the point of care * Helps determine off-label uses * Designated an official compendium for drug utilization review and screeningIntended Users * Healthcare professionals who prescribe, order, dispense, administer, or research drugs * Drug safety and information professionals * Research and development * Medical affairs professionals * Medical and pharmacy school faculty and studentsFor more details about the DRUGDEX System, see the Detailed Brochure.",2005/01/25 12:00:00,2009/12/30 12:00:00,2009/12/30 03:23:47,,UV
2.16.840.1.113883.6.177,MSH,MeSH,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Medical Subject Headings (MeSH). Bethesda (MD): National Library of Medicine, 2004",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.177.1,MSHCZE,MeSH Czech,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Czech translation of Medical Subject Headings (MeSH) 2003. Prague: Dept. of Bibliography, National Library of Medicine, 2003.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.177.10,MSHSPA,MeSH Spanish,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Descriptores en Ciencias de la Salud [Spanish translation of Medical Subject Headings (MeSH)], 2004. Sao Paulo: Latin American and Caribbean Center on Health Sciences Information. BIREME/PAHO/WHO, 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.177.11,MSHSWE,MeSH Swedish,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Swedish translation of Medical Subject Headings (MeSH), 2004. Stockholm: Karolinska Institutet, 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.177.2,MSHDUT,MeSH Dutch,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,Govt body,,Pxy,,,6,Pending,,,"Nederlandse vertaling van MeSH [Dutch translation of MeSH), 2004. Amsterdam: Nederlands Tijdschrift voor Geneeskunde [Dutch Journal of Medicine], 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.177.3,MSHFIN,MeSH Finnish,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Finnish translations of Medical Subject Headings (MeSH), 2004. Helsinki: Finnish Medical Society Duodecim, 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.177.4,MSHFRE,MeSH French,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,Govt body,,Pxy,,,6,Pending,,,"Thesaurus Biomedical Francais/Anglais [French translation of MeSH], 2004. Paris: Institut National de la Sante et Recherche Medicale, 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.177.5,MSHGER,MeSH German,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"German translation of Medical Subject Headings (MeSH), 2004. Cologne: Deutsches Institut fur Medizinische Dokumentation und Information, 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.177.6,MSHITA,MeSH Italian,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,Govt body,,Pxy,,,6,Pending,,,"Italian translation of Medical Subject Headings (MeSH), 2004. Rome: Istituto Superiore di Sanita, Settore Documentazione, 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.177.7,MSHJPN,MeSH Japanese,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"JAMAS Japanese Medical Thesaurus (JJMT). Tokyo: Japan Medical Abstracts Society; Igaku-Chuo-Zasshi, 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.177.8,MSHPOR,MeSH Portuguese,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Descritores em Ciencias da Saude [Portuguese translation of Medical Subject Headings (MeSH)], 2004. Sao Paulo (Brazil): Latin American and Caribbean Center on Health Sciences Information. BIREME/PAHO/WHO, 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.177.9,MSHRUS,MeSH Russian,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Russian Translation of Medical Subject Headings (MeSH). Moscow: State Central Scientific Medical Library, 2004",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.189,MTH,Metathesaurus Names,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,Govt body,,Pxy,,,6,Pending,,,"UMLS Metathesaurus. Bethesda, MD: National Library of Medicine.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.190,MTHCH,UMLS Hierarchical Terms CPT,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,Govt body,,Pxy,,,6,Pending,,,"Metathesaurus Hierarchical CPT Terms. Bethesda, MD: National Library of Medicine, 2004",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.191,MTHFDA,FDA National Drug Code Directory,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,Govt body,,Pxy,,,6,Pending,,,"Metathesaurus Forms of FDA National Drug Code Directory, 2004_01. Bethesda, MD: National Library of Medicine, 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.192,MTHHH,UMLS Hierarchical Terms HCPCS,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,Govt body,,Pxy,,,6,Pending,,,"Metathesaurus Hierarchical HCPCS Terms (These terms were created by the NLM to provide contextual information for HCPCS). Bethesda, MD: National Library of Medicine, 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.193,MTHICD9,UMLS ICD-9-CM Terms,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,Govt body,,Pxy,,,6,Pending,,,"Metathesaurus additional entry terms for ICD-9-CM [computer file]: international classification of diseases, ninth revision, clinical modification. Version 22. Bethesda, MD: U.S. Dept. of Health and Human Services, Public Health Service, National Institut",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.198,MTHMST,UMLS Minimal Standard Terms Intl,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy. Bethesda, MD: National Library of Medicine, 2001.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.198.1,MTHMSTFRE,UMLS Minimal Standard Terms French,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,Govt body,,Pxy,,,6,Pending,,,"Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy, French Translation. Bethesda, MD: National Library of Medicine, 2001.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.198.2,MTHMSTITA,UMLS Minimal Standard Terms Italian,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,Govt body,,Pxy,,,6,Pending,,,"Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy, Italian Translation. Bethesda, MD: National Library of Medicine, 2001.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.201,MTHPDQ,MTHPDQ,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Metathesaurus Forms of Physician Data Query (PDQ), 2004. Bethesda, MD: National Library of Medicine, 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.202,MTHSCT,Metathesaurus forms of SNOMED Clinical Terms,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Metathesaurus forms of SNOMED Clinical Terms. Bethesda (MD): National Library of Medicine, July 31, 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.202.1,MTHSCTSPA,Metathesaurus forms of Spanish SNOMED Clinical Terms,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Metathesaurus forms of Spanish SNOMED Clinical Terms. Bethesda (MD): National Library of Medicine, April 30, 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.204,NAN,Classification of Nursing Diagnoses,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Sparks Ralph, Sheila, Craft-Rosenberg, Martha, Herdman, T. Heather, Lavin, Mary Ann, editors. NANDA nursing diagnoses: definitions and classification 2003-2004. Philadelphia: NANDA International, 2003.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.205,NCBI,Taxonomy from NCBI,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,Govt body,,Pxy,,,6,Pending,,,"NCBI Taxonomy. National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 2001. http://www.ncbi.nlm.nih.gov/Taxonomy/",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.206,NCI,NCI Thesaurus,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,2.16.840.1.113883.3.26.1.1,6,Rejected,,,"NCI Thesaurus, 2004. Bethesda, MD: National Cancer Institute, National Institutes of Health, July 2004.This OID entry has been rejected upon review, as the object has already been registered by the NCI (owners).",2005/01/25 12:00:00,2005/01/25 12:00:00,2009/09/11 12:00:00,,UV
2.16.840.1.113883.6.207,NCISEER,NCI SEER ICD Mappings,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"NCI Surveillance, Epidemiology, and End Results (SEER) conversions between ICD-9-CM and ICD-10 neoplasm codes. National Cancer Institute, Bethesda, MD. Release Date: June 1999. URL: http://www-seer.ims.nci.nih.gov/Admin/ConvProgs/ Phone: 301-496-8510.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.208,nddf,National Drug Data File,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Complete,,,"National Drug Data File Plus Source Vocabulary 2004. San Bruno, CA: First DataBank, March 11, 2004.This entry was generated to support the Sources in the UMLS. Additional metadata is still missing.",2005/01/25 12:00:00,2009/09/11 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.209,NDFRT,National Drug File - Reference Terminology,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"National Drug File - Reference Terminology, 2004_01. Washington, DC: U.S. Department of Veterans Affairs, Veterans Health Administration, January 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.210,NEU,Neuronames Brain Hierarchy,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Bowden, Douglas M., Martin, Richard F., Dubach, Joev G. Neuronames Brain Hierarchy. Seattle (WA): University of Washington, Primate Information Center, 1999. http://rprcsgi.rprc.washington.edu/neuronames/",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.211,NLM-MED,Medline Data,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,National Library of Medicine (NLM) Medline Data. Bethesda (MD): National Library of Medicine. Contact: http://www.nlm.nih.gov.,2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.212,PCDS,Patient Care Data Set,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Ozbolt, Judy Grace. Patient Data Care Set (PCDS), Version 4.0, 1998.Contact: judy.ozbolt@mcmail.vanderbilt.edu; Vanderbilt University School of Nursing; 400-C Godchaux Hall; Nashville, TN 37240-0008; Telephone 615-343-3291",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.213,PDQ,Physician Data Query,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Physician Data Query (PDQ). Bethesda, MD: National Cancer Institute, 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.214,PPAC,Pharmacy Practice Activity Classification,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Pharmacy Practice Activity Classification (PPAC). Version 1. Washington (DC): American Pharmaceutical Association, 1998.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.215,PSY,Psychological Index Terms,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Thesaurus of Psychological Index Terms, Ninth Edition. Washington (DC): American Psychological Association, 2001.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.216,QMR,Quick Medical Reference,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Quick Medical Reference (QMR). San Bruno (CA): First DataBank, 1997.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.217,RAM,Clinical Concepts by R A Miller,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"QMR clinically related terms from Randolf A. Miller, 1999.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.220,RCDSY,Read Codes Synth,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Synthesized Read terms (without initial bracketed letters) of the Clinical Terms Version 3 (Q1, 1999), produced by NLM. Bethesda (MD): National Library of Medicine, UMLS project, 1999.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.220.1,RCDSA,Read Codes Am Synth,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,SDO,,Pxy,,,6,Pending,,,"American English equivalent of synthesized terms from the Clinical Terms Version 3 (Q1, 1999), produced by NLM. Bethesda (MD): National Library of Medicine, UMLS project, 1999.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.220.2,RCDAE,Read Codes Am Engl,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,SDO,,Pxy,,,6,Pending,,,"American English equivalent of the Clinical Terms Version 3 (Q1, 1999), produced by NLM. Bethesda (MD): National Library of Medicine, UMLS project, 1999.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.224,SPN,Standard Product Nomenclature,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Standard Product Nomenclature (SPN). Rockville, (MD); U.S. Food and Drug Administration, 2003",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.226,ULT,UltraSTAR,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Bell, Douglas. Ultrasound Structured Attribute Reporting (UltraSTAR). Boston (MA): Brigham & Womens Hospital, 1993.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.227,UMD,Universal Medical Devices Nomenclature,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"UniversalMedical Device Nomenclature System: Product Category Thesaurus. Plymouth Meeting (PA): ECRI, 2004.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.227.1,DMDUMD,Universal Medical Devices Nomenclature German,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"Die Nomenklatur fuer Medizinprodukte UMDNS [German translation of UMDNS]. Germany: Deutsches Institut fuer Medizinische Dokumentation und Information, 1996.",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.228,UWDA,Digital Anatomist,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,Academic,,Pxy,,,6,Pending,,,"University of Washington Digital Anatomist, (UWDA). Seattle (WA): University of Washinton, Version 1.7.3, March, 2003. Jose Mejino, M.D.; email: onard@biostr.washington.edu",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.229,VANDF,National Drug File,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"U.S. Department of Veterns Affairs, Veterans Health Administration National Drug File. Department of Veterans Affairs, Washington, DC. URL: http://www.vapbm.org/PBM/natform.htm",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.230,whoARTfl,WHO Adverse Reaction Terms foreign language translations,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,http://www.who-umc.org/,,,Pxy,,,6,Complete,,,"WHO Adverse Drug Reaction Terminology (WHOART). Uppsala (Sweden): WHO Collaborating Centre for International Drug Monitoring, 1997. This branch node OID contains identifiers for the different foreign language versions of this terminology. For more information, see http://www.umc-products.com/graphics/3149.pdf",2005/01/25 12:00:00,2009/09/11 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.230.1,whoFRE,WHO Adverse Reaction Terms French,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,http://www.who-umc.org/,,,Pxy,,,6,Complete,,,"WHO Adverse Drug Reaction Terminology (WHOART). French Translation. Uppsala (Sweden): WHO Collaborating Centre for International Drug Monitoring, 1997. For more information, see http://www.umc-products.com/graphics/3149.pdf",2005/01/25 12:00:00,2009/09/11 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.230.2,whoGER,WHO Adverse Reaction Terms German,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,http://www.who-umc.org/,,,Pxy,,,6,Complete,,,"WHO Adverse Drug Reaction Terminology (WHOART). German Translation. Uppsala (Sweden): WHO Collaborating Centre for International Drug Monitoring, 1997. For more information, see http://www.umc-products.com/graphics/3149.pdf",2005/01/25 12:00:00,2009/09/11 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.230.3,whoPOR,WHO Adverse Reaction Terms Portuguese,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,http://www.who-umc.org/,,,Pxy,,,6,Complete,,,"WHO Adverse Drug Reaction Terminology (WHOART). Portuguese Translation. Uppsala (Sweden): WHO Collaborating Centre for International Drug Monitoring, 1997. For more information, see http://www.umc-products.com/graphics/3149.pdf",2005/01/25 12:00:00,2009/09/11 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.230.4,whoSPA,WHO Adverse Reaction Terms Spanish,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,http://www.who-umc.org/,,,Pxy,,,6,Complete,,,"WHO Adverse Drug Reaction Terminology (WHOART). Spanish Translation. Uppsala (Sweden): WHO Collaborating Centre for International Drug Monitoring, 1997. For more information, see http://www.umc-products.com/graphics/3149.pdf",2005/01/25 12:00:00,2009/09/11 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.3.1,icd10ae,ICD-10 American English,Harold,Solbrig,masked,,Nenad Kostanjsek,Avenue Appia 201211 Geneva 27Switzerland,+41794755474,masked,Technical Officer for Classifications and Terminologies,World Health Organization,Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,https://who.int,SDO,,Int,,,6,Complete,,HL7 International,"International Statistical Classification of Diseases and Related Health Problems (ICD-10): Americanized Version. 10th rev. Geneva (Switzerland): World Health Organization, 1998.",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.3.2,icd10dut,"ICD10, Dutch Translation",Harold,Solbrig,masked,,Nenad Kostanjsek,Avenue Appia 201211 Geneva 27Switzerland,+41794755474,masked,Technical Officer for Classifications and Terminologies,World Health Organization,Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,https://who.int,SDO,,Int,,,6,Complete,,HL7 International,"Hirs, W., H.W. Becker, C. van Boven, S.K. Oskam, I.M. Okkes, H. Lamberts. ICD-10, Dutch Translation, 200403. Amsterdam: Department of General Practice, Academic Medical Center/University of Amsterdam, Dutch College of General Practitioners (NHG), March 20",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.3.3,dmdICD10,ICD-10 German,Harold,Solbrig,masked,,Nenad Kostanjsek,Avenue Appia 201211 Geneva 27Switzerland,+41794755474,masked,Technical Officer for Classifications and Terminologies,World Health Organization,Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,https://who.int,SDO,,Int,,,6,Complete,,HL7 International,"Internationale Klassifikation der Krankheiten 10 [German translation of ICD10]. Germany: Deutsches Institut fuer Medizinische Dokumentation und Information, 1998.",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.96.1,sctSPA,"SNOMED Clinical Terms, Spanish Language Edition",Harold,Solbrig,masked,,--Needs CP data--,,,masked,,,,,,,,,Pxy,,,6,Pending,,,"College of American Pathologists, SNOMED Clinical Terms, Spanish Language Edition, April 30, 2004. SNOMED International, 325 Waukegan Road, Northfield, IL 60093-2750. Phone: 800-323-4040 ext. 7700. Email: snomed@cap.org. URL: http://www.snomed.org",2005/01/25 12:00:00,2005/01/25 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.121,ietf3066,Tags for the Identification of Languages,Harold,Solbrig,masked,,--Needs CP data--,,,masked,,The Internet Engineering Task Force (IETF),"IETF Secretariatc/o Association Management Solutions, LLC (AMS)48377 Fremont Blvd., Suite 117Fremont, California 94538USA",+1-510-492-4080,iad@ietf.org,http://www.ietf.org,Prof Soc,,Pxy,,,6,Complete,,HL7,"IETF Network Working Group RFC 3066 - Tags for the Identification of Langugages, Alverstrand, 2001. (Obsoletes IETF 1766) http://www.ietf.org/rfc/rfc3066.txt",2005/01/25 12:00:00,2009/12/23 12:00:00,2009/12/23 10:40:58,,UV
2.16.840.1.113883.6.231,uspostalcodes,US Postal Codes,Ted,Klein,masked,,Robert McClure,,3039266771,masked,,United States Postal Service,,800-275-8777,unknown@us.gov,http://www.usps.com/,Govt body,,INT,,,6,Complete,,,Coding system of defined postal (ZIP) codes for the United States of America. This includes both the standard 5 digit codes and the ""ZIP+4"" codes that add a hyphen and 4 additional digits. Both the standard code and the extension can have leading zeros.,2005/03/03 12:00:00, ,2015/12/31 01:21:55,,UV
2.16.840.1.113883.6.232,sic,US Census Bureau,Ted,Klein,masked,,Ted Klein,"47 Old Saddle Rd. Ridge, NY 11961",631-924-6922,masked,"President, KCI",US Census Bureau,,,,http://www.census.gov/epcd/www/sic.html,Govt body,,INT,,,6,Complete,,,"The Standard Industrial Classification Codes that appear in a company's disseminated EDGAR filings indicate the company's type of business. These codes are also used in the Division of Corporation Finance as a basis for assigning review responsibility for the company's filings. For example, a company whose business was Metal Mining (SIC 1000) would have its filings reviewed by staffers in A/D Office 4.Note that this code system is published both by the US Bureau of Labor Statistics (BLS) at http://www.sec.gov/info/edgar/siccodes.htm, and by the US Occupational & Safety Health Administration (OSHA) at http://www.osha.gov/pls/imis/sic_manual.html.",2005/05/19 12:00:00,2009/09/11 12:00:00,2005/05/19 12:00:00,,UV
2.16.840.1.113883.6.233,VHA,US Department of Veterans Affairs,Omar,Bouhaddou,masked,,"Sarah Maulden, MD","Salt Lake OI Field Office, 550 Foothill Drive, Suite 400, Salt Lake City, UT 84113",801-588-5242,masked,,US Department of Veterans Affairs,"Salt Lake OI Field Office, 550 Foothill Drive, Suite 400, Salt Lake City, UT 84113",801-588-5242,Sarah.Maulden@med.va.gov,,Govt body,,INT,,,6,Complete,,,"VHA Enterprise Reference Terminology is based on CHI standard terminologies (e.g., SNOMED-CT, LOINC, HL7, NDF-RT, etc.) when available and on VHA own code sets when necessary (e.g., allergens). All concepts used within the VHA clinical environment receive a VHA Unique IDentifier or VUID.VHA Enterprise Reference Terminology complies with the semantics of the HL7 message structure",2005/05/19 12:00:00, ,2005/05/19 12:00:00,,UV
2.16.840.1.113883.6.234,ahfs,American Society of Health-System Pharmacists,Jeff,Shick,masked,,"Gerald K. McEvoy, Pharm.D.","7272 Wisconsin Avenue, Bethesda, Maryland, USA 20814",+1 (301) 657-3000,masked,,American Society of Health-System Pharmacists,"7272 Wisconsin Avenue, Bethesda, Maryland, USA 20814",+1 (301) 657-3000,ahfs@ashp.org,http://www.ahfsdruginformation.com/class,Prof Soc,,INT,,,6,Complete,,,"AHFS Pharmacologic-Therapeutic Classification System, a coding system of classifier for various pharmologic substances. For more information, see http://www.ahfsdruginformation.com/class",2005/06/06 12:00:00,2005/06/06 12:00:00,2009/08/10 03:02:31,,UV
2.16.840.1.113883.3.26.1.1,ncit,NCI Thesaurus,Frank,Hartel,masked,,Gilberto Fragoso,9609 Medical Center Dr1W102Rockville MD,240-276-5129,masked,Biomedical Informatics Program Manager,National Cancer Institute,9609 Medical Center DrRockville MD,240-276-5129,NCIAppSupport@nih.gov,https://datascience.cancer.gov,Govt body,2.16.840.1.113883.3.26,Ext,,,6,Complete,2.16.840.1.113883.3.26.1.1,,"NCI ThesaurusNCI Thesaurus is a biomedical thesaurus created specifically to meet the needs of the cancer research community, especially those engaged in translational research NCI Thesaurus is produced by the NCI Enterprise Vocabulary Services project. The NCI Thesaurus is open content provided under the CCBY 4.0 international license.",2005/07/14 12:00:00, ,2020/11/11 12:25:23,,UV
2.16.840.1.113883.6.235,csaid,CSAID,Donald,Kroetsch,masked,,,,,masked,,Canadian Standards Association (CSA),"5060 Spectrum WayMississauga, Ontario Canada L4W 5N6",(416) 747-4000,,,Govt body,,Int,,,6,Complete,,HL7,"Nature of injury (NOI) codes, which are part of the Work Injury or Disease Information coding system (CAN/CSA-Z795-96 - R2003).The CSA code set includes 3 parts: Nature of injury (NOI), body part (BP), side of body (SB). For example: NOI - Cut or laceration Injury = 03400BP - Upper Arm body part = 31100SOB - Left Side of Body = LThe Body Part codes are qualified by the Side of Body codes code system, to be more precise in specifying the location of the injury being coded.Code set is maintained by the Canadian Standards Association (CSA).Phone: (416) 747-4000 1-800-463-6727 Fax: (416) 747-2473",2002/03/12 12:00:00,2009/11/03 12:00:00, ,,UV
2.16.840.1.113883.6.238,PH_RaceAndEthnicity_CDC,PH_RaceAndEthnicity_CDC,Sundak,Ganesan,masked,,,,,masked,,"CDC,CDC",,,,http://www.cdc.gov/phin,Govt body,2.16.840.1.114222.4,Pxy,,,6,Complete,2.16.840.1.114222,,"Codes for Race, authored and maintained by the CDC",2005/08/15 12:00:00,2005/10/12 12:00:00,2005/10/13 12:00:00,,UV
2.16.840.1.113883.6.236,ccc,Clinical Care Classification System,Suzanne,Bakken,masked,,Virginia K. Saba,"2332 South Queen StreetArlington, VA 22202",703-521-6132,masked,Presodent & CEO SabaCare Inc.,Virginia K. Saba,,,vsaba@att.net,http://www.sabacare.com/,Academic,,Int,,,6,Complete,,,"Clinical Care Classification System Version 2.5 release is an updated version of version 20. published in 2004 when the system name(formerly Home Health Care Classification system) codes was change. The CCC System consists of two interrelated terminologies: CCC of 176 Nursing Diagnoses( which includes 528 CCC Nursing Outcomes from each nursing diagnoses combined with one of three qualifiers (Improved, stanbilized, or deteriorated) to document the expected or actual outcomes). The second terminology is the CCC of 804 Nursing Interventions which represents 201 Core Nursing Interventions each of which has to be combined with one of four Action Type Qualifiers (Assess/Monitor; Perform/Care. Teach/Instruct, or Manage/Refer). Both of the terminologies are classified by 21 Care Components to form a single system. The CCC System consists of a four level structure designed to document nursing practice following the six steps of the nursing process as recommended by the American Nurses Assocation (ANA) as professional nursing practice and for documenting the 'essence of care'. The ANA recognized the CCC System as early as 1992 and was one of the four earliest nursing terminologies designed to document nursing practice electronically in any healthcare setting where nurses function e.g. hospitals, outpatient departments, home health agencies, ambulatory care clinics, and other health care settings. The CCC System was the first nursing terminology to be recognized by the Secretary of HHS as interoperable and usable for documenting in the electronic health record systems. It is available as a free terminology with Permission -- fomr found on its web Site. For further information do visit its web site: http:www.Sabacare.com orhttp:www.clinicalcareclassification.comir contact Dr. Virginia K. Saba at vsaba@att.net",2005/07/15 12:00:00,2005/11/20 12:00:00,2011/09/30 02:01:44,,UV
2.16.840.1.113883.6.239,CDA_RUS,CDA_RUS,Emelin,,masked,,Emelin,,+7(495)202-2630,masked,,General Research Computer Center,,,,,,,INT,,,6,Complete,,,Coding system intended for use in the Russian clinical documents,2005/12/28 12:00:00, ,2005/12/28 12:00:00,,UV
2.16.840.1.113883.6.240,US_COC,US Census Occupation Code,Ted,Klein,masked,,,,,masked,,US Census Bureau,U.S. Census Bureau# 4700 Silver Hill Road# Washington DC 20233-0001,240-420-6020,,http://www.census.gov,Govt body,,Pxy,,,6,Complete,,,"Coding system of United States Census Occupation Codes, published by the US Governmetn Bureau of the Census. Doucmentation and Crosswalk mapping between the COC and the SOC and NAICS code systems available at http://www.census.gov/hhes/www/ioindex/view.html",2005/01/26 12:00:00, ,2005/01/26 12:00:00,,UV
2.16.840.1.113883.3.26.1.5,nciVersionOfNDF-RT,NCI Version of NDF-RT,Frank,Hartel,masked,Margaret Haber,Margaret Haber,"6116 Executive Blvd, Room 3111, Rockville, MD 20852",301 595 9185,masked,Assoc Dir Voc Services,National Cancer Institute,"6116 Executive Blvd, Room 3111, Rockville, MD 20852",301 595 9185,mhaber@mail.nih.gov,http://ncicb.nci.nih.gov/core/EVS,Govt body,2.16.840.1.113883.3.26.1.5,Ext,,,6,Complete,2.16.840.1.113883.3.26.1.5,,"The National Drug File RT (NDF-RT) is published by the US Veterans' Administration (VA). NDF-RT covers clinical drugs used at the VA. The NCI version of NDF-RT is used by NCI to provide automated terminology access to the Food and Drug Administration (FDA) Structured Product Label (SPL) initiative. NCI makes its version of NDF-RT available publicly thru the Web, download via FTP and via open APIs for Java, SOAP and HTTP.",2006/02/06 12:00:00,2009/10/14 12:00:00,2006/02/06 12:00:00,,UV
2.16.840.1.113883.5.1103,hc-AIC,Active Ingredient Code,Russell,Hamm,masked,Lloyd McKenzie,Infoway Standards Collaborative - SCWG 6,"150 King Street West, Suite 1300Toronto, Ontario M5H 1J9",1-877-595-3417,masked,SCWG 6 is responsible for registration and maintenance of code system OIDs used in Canada,Health Canada,"Therapeutic Products DirectorateHealth Products and Food BranchAddress Locator: 3106BOttawa, Ontario K1A 0K9",(613) 957-0368; Fax: (613) 952-7756,hc.DIN.sc@canada.ca,http://www.hc-sc.gc.ca/index-eng.php,Govt body,,Int,,,6,Complete,,,Foreign key for the Active Ingredient Table that relates active ingredients to specific products. More information can be found here: https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/drug-product-database/read-file-drug-product-database-data-extract.html,2006/03/25 12:00:00,2008/12/15 12:00:00,2020/11/17 09:28:20,,UV
2.16.840.1.113883.5.1104,hc-AIGC,Active Ingredient Group Code,Russell,Hamm,masked,Lloyd McKenzie,Infoway Standards Collaborative - SCWG 6,"150 King Street West, Suite 1300Toronto, Ontario M5H 1J9",1-877-595-3417,masked,SCWG 6 is responsible for registration and maintenance of code system OIDs used in Canada,Health Canada,"Therapeutic Products DirectorateHealth Products and Food BranchAddress Locator: 3106BOttawa, Ontario K1A 0K9",(613) 957-0368; Fax: (613) 952-7756,hc.DIN.sc@canada.ca,http://www.hc-sc.gc.ca/index-eng.php,Govt body,,Int,,,6,Complete,,,Codes for a particular grouping of active ingredients. This is the 5 characters of the active ingredient group number starting at position 3 and ending at position 7. https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/drug-product-database/terminology.html,2006/03/25 12:00:00,2008/12/15 12:00:00,2020/11/17 09:29:56,,UV
2.16.840.1.113883.5.1106,hc-AIGN,Active Ingredient Group Number,Russell,Hamm,masked,Lloyd McKenzie,Infoway Standards Collaborative - SCWG 6,"150 King Street West, Suite 1300Toronto, Ontario M5H 1J9",1-877-595-3417,masked,SCWG 6 is responsible for registration and maintenance of code system OIDs used in Canada,Health Canada,"Therapeutic Products DirectorateHealth Products and Food BranchAddress Locator: 3106BOttawa, Ontario K1A 0K9",(613) 957-0368; Fax: (613) 952-7756,hc.DIN.sc@canada.ca,http://www.hc-sc.gc.ca/index-eng.php,Govt body,,Int,,,6,Complete,,,The AIG number is a 10 digit number that identifies products that have the same active ingredient(s) and ingredient strength(s). The AIGn is comprised of three portions:• the first portion (2 digits) identifies the number of active ingredients• the second portion(5 digits) identifies the unique groups of active ingredients(s);• the last portion (3 digits) identifies the active ingredient group strength. The strength group has a tolerance of -2% to +10%.More information can be found here: https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/drug-product-database/terminology.html,2006/03/25 12:00:00,2008/12/15 12:00:00,2020/11/17 09:32:37,,UV
2.16.840.1.113883.5.1108,encode-FM,Electronic Nomenclature and Classification Of Disorders and Encounters for Family Medicine,Russell,Hamm,masked,Lloyd McKenzie,Russell Hamm,,,masked,,INSITE Family Medicine Inc.,,,insite@insite-fm.com,http://www.insite-fm.com/,Vendor,,Int,,,6,Complete,,,"ENCODE-FM is a systematic and hierarchical controlled clinical terminology for family medicine, intended for use in electronic medical records incorporated into the software of any vendor. It was derived from our knowledge of ICPC, ICD-10, and our aggregate 60-year clinical family medicine experience. Development occurred over a period of approximately ten years and was initially presented internationally at the Symposium on Computer Applications in Medical Care (SCAMC) 1991 under its original name SIN-FM. The product was subsequently enhanced in order to be the standard terminology for the national database of the College of Family Physicians of Canada ""Clinical Practice Management Network"".ENCODE-FM has been designed expressly for use at point of service in primary care. It addresses the issues of ease of data entry and accuracy of aggregate data retrieval in its design, the mapping to other classifications, and choice of words and terms. Published research (use links)(J. Amer. Medical Informatics Assoc. 3(3): 224-233, 1996; J. Amer. Medical Informatics Assoc., Symposium Supplement 1995, Vol 20: 135-139. 1996.) has shown that none of the large nomenclatures (each over 100,000 terms) intended to cover the whole health care system, describe all clinical content or even all diseases. Alternatively, ENCODE-FM was designed to do one part of that task well - namely to be a CLINICAL terminology of ONLY symptoms, complaints, diagnoses, disorders and reasons for encounter for use in primary care electronic records. It is intended to facilitate data entry by the caregiver, and to allow data aggregation by the 3 internationally recognized classifications of disease used most commonly in primary care ICPC, ICD-10, and ICD09CM.It was also designed to be an evolving terminology, so that as the terminology and usage of medical terms changes, ENCODE can be readily updated with the changes. ENCODE-FM currently contains 9378 terms.http://www.insite-fm.com/Products/ENCODE-FM",2006/03/25 12:00:00,2009/12/28 12:00:00,2009/12/28 06:47:12,,UV
2.16.840.1.113883.2.13,standardBillingUnit,Standard Billing Unit,Lynne,Gilbertson,masked,,Lynne Gilbertson,,615-754-0445,masked,"VP, Standards Development","National Council for Prescription Drug Programs (NCPDP),National Council for Prescription Drug Progr","9240 E. Raintree Drive, Scottsdale, AZ 85260",480-477-1000,ncpdp@ncpdp.org,,SDO,2.16.840.1.113883.3.79,INT,,,6,Complete,,,"NCPDP standard product billing codes of NCPDP field Unit of Measure (600-28). This billing code is assigned per product, placed in the Structured Product Label, and used in the pharmacy billing processing for consistent billing unit.",2006/06/07 12:00:00,2009/10/14 12:00:00,2008/11/21 01:00:36,,UV
2.16.840.1.113883.6.241,scdHECGISSpatialAccuracyTiers,SCDHEC GIS Spatial Accuracy Tiers,Cecil,Lynch,masked,,James T. Case,,(530) 752-4408,masked,,South Carolina Department of Health and Environmental Control,,,jtcase@ucdavis.edu,,Govt body,,Ext,,,6,Complete,,HL7 International,"The South Carolina Department of Health and Environmental Control GIS Spatial Data Accuracy Tiers have been derived from the National Standard for Spatial Data Accuracy as a means to categorize the accuracy of spatial data assignment utilizing a variety of tools for capturing coordinates including digitizers, geocoding software and global positioning system devices.",2006/06/25 12:00:00,2015/06/30 12:00:00,2015/06/30 08:21:14,,UV
2.16.840.1.113883.6.242,epsg-GeodeticParameterDataset,EPSG Geodetic parameter dataset,Cecil,Lynch,masked,,Abby Findlay,,,masked,,OGP Surveying and Positioning Committee,OGP209-215 Blackfriars RoadLondon SE1 8NLUK,,richard.j.wylde@exxonmobil.com,http://www.epsg.org/,Prof Soc,,Ext,,,6,Complete,,HL7,"The EPSG (European Petroleum Survey Group) dataset represents all Datums, coordinate references (projected and 2D geographic) and coordinate systems (including Cartesian coordinate systems) used in surveying worldwide. Each record includes a 4-8 digit unique identifier. The current version is available from http://www.epsg.org/. The database contains over 4000 records covering spatial data applications worldwide.",2006/06/25 12:00:00,2009/12/30 12:00:00,2009/12/30 03:31:07,,UV
2.16.840.1.113883.3.84,FDB HIC Code,FDB HIC Code,Peter,Scott,masked,,Peter Scott,"Suite 300, University Ave, PE Canada, C1A4K9",902 628 4592,masked,,"Deltaware Systems,Deltaware Systems","Suite 300, University Ave, PE Canada, C1A4K9",(902) 368-8122,dsi@deltaware.com,http://www.deltaware.com,Vendor,,INT,,,6,Complete,,,The FDB Hierarchical Ingredient Code is a six character identifier that represents an active ingredient and its specific therapeutic classification.,2006/07/05 12:00:00, ,2006/07/05 12:00:00,,UV
2.16.840.1.113883.6.243,soc,Standard Occupation Code,Cecil,Lynch,masked,,Cecil O Lynch,,916-412-5504,masked,,U.S. Bureau of Labor Statistics,"Division of Occupational Employment Statistics,Suite 2135,2 Massachusetts Ave., NE,Washington, DC 20212-0001",202-691-6500,soc@bls.gov,http://www.bls.gov/soc/,Govt body,,Pxy,,,6,Complete,,,"The Standard Occupational Classification (SOC) system is used by Federal statistical agencies to classify workers into occupational categories for the purpose of collecting, calculating, or disseminating data. All workers are classified into one of over 820 occupations according to their occupational definition. To facilitate classification, occupations are combined to form 23 major groups, 96 minor groups, and 449 broad occupations. Each broad occupation includes detailed occupation(s) requiring similar job duties, skills, education, or experience. This code system replaced the older FIPSPUB92, which was withdrawn in February 2005.",2006/07/30 12:00:00,2009/09/15 12:00:00,2006/07/30 12:00:00,,UV
2.16.840.1.113883.6.244,d1cs,DiagnosisONE Coding System,Ahmad,Kasmieh,masked,,Ahmad Kasmieh,,603 897-1884,masked,Chief Technology Officer,"DiagnosisONE, Inc.","61 Spit Brook RoadNashua, NH 03060 ",+1 603.897.1884 x5,inquiry@DiagnosisONE.com,http://www.diagnosisone.com,Vendor,,Int,,,6,Complete,,HL7 International,DiagnosisONE Coding System.,2006/09/07 12:00:00,2009/12/30 12:00:00,2010/11/16 04:40:29,,UV
2.16.840.1.113883.6.245,usBoardonGeographicNames ,U.S. Board on Geographic Names,Sundak,Ganesan,masked,byy4@cdc.gov,Roger L. Payne,,703-648-4544,masked,Manager,U.S. Geological Survey,"12201 Sunrise Valley Drive, MS 523, Reston, Virginia 20192-0523",1-888-275-8747,BGNEXEC@usgs.gov,http://geonames.usgs.gov/index.html,Govt body,,Int,,,6,Complete,,HL7 International,"The U.S. Board on Geographic Names is a Federal body created in 1890 and established in its present form by Public Law in 1947 to maintain uniform geographic name usage throughout the Federal Government. The Board comprises representatives of Federal agencies concerned with geographic information, population, ecology, and management of public lands. Sharing its responsibilities with the Secretary of the Interior, the Board promulgates official geographic feature names with locative attributes as well as principles, policies, and procedures governing the use of domestic names, foreign names, Antarctic names, and undersea feature names.",2006/09/07 12:00:00,2015/06/30 12:00:00,2015/06/30 09:11:05,,UV
2.16.840.1.113883.6.246,Telin,Telin,garry,Lee,masked,,Garry Lee,205 1040 7 Ave SW,1 (403) 616-0270,masked,Managing Partner,,,,,,Vendor,,INT,,,6,Pending,,,CDM messaging,2006/09/23 12:00:00, ,2006/09/23 12:00:00,,UV
2.16.840.1.113883.6.247,ethNICITY,ETHNICITY,Fred ,Agyepong,masked,,Health Information Standards,"13th Floor, ATB Place, 10025 Jasper Ave, Edmonton, Alberta, T5J 1S6Canada",780 427-4734,masked,,WHIC,"2nd Floor, 10025 Jasper Ave, Telus Plaza North Tower, Edmonton, Alberta, T5J 2N3",780 427 5135,whic.sec@whic.org,,Govt body,,Int,,,6,Complete,,HL7 International,"Relating to large groups of people classed according to common racial, national, tribal, religious, or cultural origin or background.",2006/09/27 12:00:00,2010/11/16 12:00:00,2018/10/19 11:21:41,,UV
2.16.840.1.113883.6.248,firSTNATIONSSTATUS,FIRST NATIONS STATUS,Fred,Agyepong,masked,,Health Information Standards,"13th Floor, ATB Place, 10025 Jasper Ave, Edmonton, Alberta, T5J 1S6Canada",780 427-4734,masked,,WHIC,"2nd Floor, 10025 Jasper Ave, Telus Plaza North Tower, Edmonton, Alberta, T5J 2N3",780 427 5135,whic.sec@whic.org,,Govt body,,Int,,,6,Complete,,HL7 International,Status indicator used to determine whether the individual lives or does not live on an Indian Reserve.,2006/09/27 12:00:00,2010/11/16 12:00:00,2018/10/19 11:34:39,,UV
2.16.840.1.113883.6.249,metabolicSyndrome,METABOLIC SYNDROME,Fred,Agyepong,masked,,Health Information Standards,"13th Floor, ATB Place, 10025 Jasper Ave, Edmonton, Alberta, T5J 1S6Canada",780 427-4734,masked,,WHIC,"2nd Floor, 10025 Jasper, Telus Plaza North Tower, Edmonton, Alberta, T5J 2N3",780 427-5135,whic.sec@whic.org,,Govt body,,Int,,,6,Complete,,,"A collection of metabolic risk factors in one individual. The root causes of metabolic syndrome are overweight / obesity, physical inactivity, and genetic factors. Various risk factors have been included in metabolic syndrome. Factors generally accepted as being characteristic of this syndrome include abdominal obesity, atherogenic dyslipidemia, raised blood pressure, insulin resistence with or without glucose intolerance, prothrombotic state, and proinflammatory state.",2006/09/27 12:00:00,2009/12/22 12:00:00,2018/10/19 12:02:58,,UV
2.16.840.1.113883.6.250,retINOPATHYINTERPRETATION,RETINOPATHY INTERPRETATION,Fred,Agyepong,masked,,Health Information Standards,"13th Floor, ATB Place, 10025 Jasper Ave, Edmonton, Alberta, T5J 1S6Canada",780 427-4734,masked,,WHIC,"2nd Floor, 10025 Jasper Ave, Telus Plaza North Tower, Edmonton, Alberta, T5J 2N3",780 427-5135,whic.sec@whic.org,,Govt body,,Int,,,6,Complete,,HL7 International,"Many times in addition to (or possibly instead of) reporting a physical measurement, a laboratory will indicate that the reported value is 'high', 'low', 'normal', or some other coded interpretation. Even when there is a value, interpretation is often offered to help convey the significance of a particular result.",2006/09/27 12:00:00,2010/11/16 12:00:00,2018/10/19 12:05:07,,UV
2.16.840.1.113883.6.251,smoKER,SMOKER,Fred,Agyepong,masked,,Health Information Standards,"13th Floor, ATB Place, 10025 Jasper Ave, Edmonton, Alberta, T5J 1S6Canada",780 427-4734,masked,,WHIC,"2nd Floor, 10025 Jasper Ave, Telus Plaza North Tower, Edmonton, Alberta, T5J 2N3",780 427-5135,whic.sec@whic.org,,Govt body,,Int,,,6,Complete,,HL7 International,"The person's use of and exposure to tobacco both in the past and currently. Questions to be answered include: Are they currently smoking (""current""), have they never smoked (""never""), have they smoked in the past but now stopped (""past""), or are they living with someone who smokes or being exposed to cigarette smoke frequently at home or in the work place (""passive"").",2006/09/27 12:00:00,2010/11/16 12:00:00,2018/10/19 12:06:12,,UV
2.16.840.1.113883.6.252,diaGNOSTICIMAGEMETHODCODE,DIAGNOSTIC IMAGE METHOD CODE,Fred,Agyepong,masked,,Health Information Standards,"13th Floor, ATB Place, 10025 Jasper Ave, Edmonton, Alberta, T5J 1S6Canada",780 427-4734,masked,,WHIC,"2nd Floor, 10025 Jasper Ave, Telus Plaza North Tower, Edmonton, Alberta, T5J 2N3",780 427-5135,whic.sec@whic.org,,Govt body,,Int,,,6,Complete,,,Indicates the means or technique used to perform the imaging.,2006/09/27 12:00:00,2010/11/16 12:00:00,2018/10/19 12:07:14,,UV
2.16.840.1.113883.4.64,gcn-seqno,Clinical Formulation ID,George,Robinson,masked,tom_bizzaro@firstdatabank.com,George Robinson,"First DataBank, Inc., 500 East 96th Street, Suite 500, Indianapolis, IN 46240",317-571-7248,masked,VP Knowledge Base Development,"First DataBank, Inc.,First DataBank, Inc.,First DataBank, Inc.,First DataBank, Inc.","500 East 96th Street, Suite 500, Indianapolis, IN 46240",317-571-7200,george_robinson@firstdatabank.com,http://www.firstdatabank.com,Vendor,2.16.840.1.113883.3.567,Int,,,6,Complete,,,"Clinical Formulation IDa six-character numeric column that represents a clinical drug formulation identifier that groups together drug products by the following criteria and is stored in the following columns:Ingredient List Identifier (HICL_SEQNO)-(formerly called the Hierarchical Ingredient Code List Sequence Number) represents the list or set of ingredients in a drug formulation. The HICL_SEQNO includes only active ingredients. Route of Administration (GCRT - The Route of Administration Code provides the normal site or method by which the drug is administered, such as oral, injection, or topical. Dosage Form (GCDF) - The Dosage Form Code represents a dosage form of the clinical formulation, such as tablet or capsule. Strength of Drug (STR) - The Drug Strength Description describes the drug potency in metric units. A unique GCN_SEQNO is assigned to each different combination of ingredient(s), strength, dosage form, and route of administration for a generic drug formulation. The GCN_SEQNO aggregates drug products that share like ingredient sets, route of administration, dosage form, and strength of drug but are marketed by multiple manufacturers.The GCN_SEQNO is included within the National Library of Medicine's RxNorm database. Within the Concept Names and Sources file it can be identified with a Source Abbreviation of ""NDDF"" and a Term Type value of ""CDC"".",2006/11/29 12:00:00,2010/03/10 12:00:00,2012/07/12 01:14:37,,UV
2.16.840.1.113883.4.65,hic-SEQN,Hierarchical Ingredient Code Sequence Number (HIC_SEQN),George,Robinson,masked,tom_bizzaro@firstdatabank.com,George Robinson,"First DataBank, Inc., 500 East 96th Street, Suite 500, Indianapolis, IN 46240",317-571-7248,masked,VP Knowledge Base Development,"First DataBank, Inc.","500 East 96th Street, Suite 500, Indianapolis, IN 46240",317-571-7200,george_robinson@firstdatabank.com,http://www.firstdatabank.com,Vendor,,Int,,,6,Complete,,HL7,Hierarchical Ingredient Code Sequence Number (HIC_SEQN)a six-character numeric column that represents a distinct active or inactive ingredient within the First DataBank database. The HIC_SEQN is a dumb number attached to the ingredient and will never change. A HIC_SEQN is associated to a Clinical Formulation Identifier (GCN_SEQNO) in the context of an active ingredient or to a packaged product in the context of an inactive (excipient) ingredient. It is listed in the National Library of Medicine's RxNorm Concept Names and Sources file with a Source Abbreviation of ""NDDF"" and a Term Type of ""IN"".,2006/11/29 12:00:00,2010/01/28 12:00:00,2010/01/28 12:08:03,,UV
2.16.840.1.113883.4.66,hic,Hierarchical Ingredient Code (HIC),George,Robinson,masked,tom_bizzaro@firstdatabank.com,George Robinson,"First DataBank, Inc., 500 East 96th Street, Suite 500, Indianapolis, IN 46240",317-571-7248,masked,VP Knowledge Base Development,"First DataBank, Inc.","500 East 96th Street, Suite 500, Indianapolis, IN 46240",317-571-7200,george_robinson@firstdatabank.com,http://www.firstdatabank.com,Vendor,,Int,,,6,Complete,,HL7,"Hierarchical Ingredient Code (HIC)a six-character alphanumeric column that represents the active ingredient and salt esters of a particular drug product (identified by NDC) within the First DataBank database. It also identifies the therapeutic class, pharmacological class, and organ system to which the drug is targeted. The HIC will only change for an ingredient if the ingredient is moved to a new therapeutic classification. ",2006/11/29 12:00:00,2010/01/28 12:00:00,2010/01/28 12:07:29,,UV
2.16.840.1.113883.6.253,mddid,MDDID,Sagara,Wickramasekara,masked,,Sagara Wickramasekara,,386-418-7193,masked,,,,,,,,,INT,,,6,Complete,,,Medispan Drug Descriptor IDEntry autogenerated to support Sources from the UMLS. Full metadata set still incomplete.,2006/11/30 12:00:00,2009/09/11 12:00:00,2006/11/30 12:00:00,,UV
2.16.840.1.113883.6.254,icf,International Classification of Function,William,Goossen,masked,,T. B. ΓstΓΌn,"20, Avenue Appia, 1211 Geneva, Switzerland",999-999-9999,masked,"Coordinator Classification, Assessment, Surveys and Terminology Unit.",World Health Organisation,"20, Avenue Appia, 1211 Geneva, Switzerland",999-999-9999,ustunb@who.int,http://www.who.int/classifications/icf/en/,SDO,,Int,,,6,Complete,,HL7 International,"ICF describes how people live with their health condition. ICF is a classification of health and health related domains that describe body functions and structures, activities and participation. The domains are classified from body, individual and societal perspectives. Since an individual's functioning and disability occurs in a context, ICF also includes a list of environmental factors. ICF is useful to understand and measure health outcomes. It can be used in clinical settings, health services or surveys at the individual or population level. Thus ICF complements ICD-10 , The International Statistical Classification of Diseases and Related Health Problems and therefore is looking beyond mortality and disease.",2007/02/20 12:00:00,2010/11/16 12:00:00,2010/11/16 09:45:22,,UV
2.16.840.1.113883.6.255,x12.3,X12.3 Data Elementary Dictionary,Keith,Boone,masked,,Stuart Beaton,,615.376.2483,masked,Co-Chair X12N/TG2/WG1 - Health Care Eligibility,X12N,,,StuartBeaton@aol.com,,SDO,,Int,,,6,Complete,,HL7 International,"X12.3 Data Elementary DictionaryThis is the root OID for vocabulary defined internally by X12N. OIDs for each vocabulary will be assigned underneath this OID by appending the X12N data element id to the root OID. Data Element 1336 is Insurance Type Code, so the OID for the X12N Insurance Type Code vocabulary will be 2.16.840.1.113883.6.255.1336",2007/02/23 12:00:00,2015/06/29 12:00:00,2015/06/29 03:22:43,,UV
2.16.840.1.113883.6.255.1336,x12N-1336,Insurance Type Code,Keith,Boone,masked,,Stuart Beaton,,615.376.2483,masked,Co-Chair X12N/TG2/WG1 Health Care Eligibility Work Group,X12N,,,StuartBeaton@aol.com,,SDO,,Ext,,,6,Complete,2.16.840.1.113883.6.255.1336,X12N,Insurance Type Code ,2007/02/23 12:00:00,2015/06/29 12:00:00,2015/06/29 03:25:38,,UV
2.16.840.1.113883.6.256,radLex,RadLex,Cecil,Lynch,masked,Fred Behlen,Chris Carr,"820 Jorie BoulevardOak Brook, IL 60523",1-630-368-3739,masked,Director of Informatics,Radiological Society of North America,"820 Jorie BoulevardOak Brook, IL 60523",1-630-368-3739,ccarr@rsna.org,http://www.radlex.org,Prof Soc,,Ext,,,6,Complete,,,"RadLex terminology comprises coded terms used in the acquisition and management of diagnostic images and related data, and in the representation of imaging-related findings and results. RadLex terms would be used in both Orders and Observations, appearing in HL7 V2 OBX segments and in HL7 V3 Acts describing both imaging procedures and the observations derived therefrom. RadLex codes will also be used in HL7 CDA documents, as they will be in related DICOM Structured Reporting (SR) objects used in imaging applications.",2007/04/18 12:00:00,2009/12/30 12:00:00,2009/12/30 03:42:20,,UV
2.16.840.1.113883.6.257,mds,Minimum Data Set for Long Term Care,Keith,Boone,masked,,Keith W. Boone,,617-519-2076,masked,,Centers for Medicare and Medicaid Services,,,keith.boone@ge.com,,,,Int,,,6,Complete,,HL7 International,"The Minimum Data Set for Long Term Care Version 2.0 (MDS 2.0) is a federally mandated (in the United States) standard assessment form. This instrument is specified by the Centers for Medicare and Medicaid Services, and requires nursing facilities to conduct a comprehensive, accurate, standardized, reproducible assessment of each resident˜s functional capacity.The MDS specifies a number of answer lists used in the responses to the questions posed. Each answer list has been assigned a number. This OID is the root OID for assigning OIDs to the MDS answer lists.",2007/06/14 12:00:00,2015/06/30 12:00:00,2015/06/30 09:21:23,,UV
2.16.840.1.113883.4.79,GCDF,GCDF,George,Robinson,masked,,George Robinson,"500 E 96th St., Suite 500, Indianapolis, IN 46240",317-571-7248,masked,VP Knowledge Base Development,"First DataBank, Inc,First DataBank, Inc,First DataBank, Inc,First DataBank, Inc,First DataBank, Inc,","500 East 96th Street, Suite 500",317-571-7248,george_robinson@firstdatabank.com,http://www.firstdatabank.com,Vendor,,INT,,,6,Complete,,,"GCDFDosage Form Code (2-character)a two-character alphanumeric column that represents a dosage form. The dosage form of a generic drug formulation describes the physical presentation of a drug, such as tablet, capsule, or liquid. It may also incorporate the delivery and release mechanism of the drug. A GCDF is associated to each GCN_SEQNO to identify that component of the generic drug formulation. ",2007/06/20 12:00:00, ,2007/06/20 12:00:00,,UV
2.16.840.1.113883.4.80,GCRT,GCRT,George,Robinson,masked,,George Robinson,"500 E 96th St, Suite 500, Indianapolis, IN 46240",317-571-7248,masked,VP Knowledge Base Dev,"First DataBank, Inc,First DataBank, Inc,First DataBank, Inc,First DataBank, Inc,First DataBank, Inc,","500 E 96th St., Suite 500, Indianapolis, IN 46240",317-571-7248,george_robinson@firstdatabank.com,http://www.firstdatabank.com,Vendor,,INT,,,6,Complete,,,"GCRTRoute of Administration Code (1-character)a one-character alphanumeric column that provides the normal site or method by which a drug is administered, such as oral, injection, or topical. A GCRT is associated to each GCN_SEQNO to identify that component of the generic drug formulation.",2007/06/20 12:00:00, ,2007/06/20 12:00:00,,UV
2.16.840.1.113883.6.258,caefi-rcco,Canadian Adverse Event Following Immunization reporting criteria and concurrent observations ,Wendy,Huang,masked,,Helen Anyoti,"100 promenade Eglantine Driveway Bldg # 6, Room 2437 Tunney's Pasture, Al 0602C Ottawa, Ontario Canada K1R 0K9",1-613-941-9132,masked,,Public Health Agency of Canada,"Vaccine Safety Unit, Bldg #6, Tunney's Pasture 0602C, Ottawa, Ontario K1Y 0L9",1-613-954-5590,CAEFI@phac-aspc.gc.ca,http://www.phac-aspc.gc.ca/im/aefi-form_e.html,Govt body,,Ext,,,6,Complete,,HL7 International,A set of codes describing the minimum data set for reporting adverse event information to Public Health Agency of Canada (PHAC) using the Canadian Adverse Event Following Immunization (CAEFI) and Health Canada paper forms currently in place for adverse event reporting. ,2007/06/20 12:00:00,2010/11/16 12:00:00,2010/11/16 09:57:36,,UV
2.16.840.1.113883.4.81,cpnum,Gold Standard's Clinical Pharmacology Monograph Number,Wuhong,Li,masked,,Wuhong Li,,813-579-3873,masked,,Gold Standard Inc.,"302 Knights Run Ave, Suite 800",,li.w@goldstandard.com,http://www.goldstandard.com,Vendor,2.16.840.1.113883.3.145,INT,,,6,Complete,,,Gold Standard's Clinical Pharmacology Monograph Number ,2007/12/27 12:00:00,2009/09/15 12:00:00,2007/12/27 12:00:00,,UV
2.16.840.1.113883.6.259,hsloc,Healthcare Service Location,Robert,Hausam,masked,Cecil Lynch,Dan Pollock,"1600 Clifton Road NEMail Stop A24Atlanta, GA 30333",1-404-639-4237,masked,,"Center's for Disease Control and Prevention,Center's for Disease Control and Prevention,Center's for","1600 Clifton Road NEMail Stop A24Atlanta, GA 30333",1-404-639-4237,dap1@cdc.gov,http://www.cdc.gov/phin/,Govt body,,Int,,,6,Complete,,HL7,"A comprehensive classification of locations and settings where healthcare services are provided. This code system is based on the NHSN location code system that has been developed over a number of years through CDC's interaction with a variety of healthcare facilities and is intended to serve a variety of reporting needs where coding of healthcare service locations is required.The content, including relationships, can be acced at the following location: http://www.cdc.gov/phin/activities/standards/vocabulary/index.html",2008/02/14 12:00:00,2009/10/20 12:00:00,2009/10/20 09:42:11,,UV
2.16.840.1.113883.6.260,icd-10-dualCoding,ICD-10 Dual Coding,Grahame,Grieve,masked,,Nenad Kostanjsek,Avenue Appia 201211 Geneva 27Switzerland,+41794755474,masked,Technical Officer for Classifications and Terminologies,World Health Organization,Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/en/,SDO,,Pxy,,,6,Complete,,HL7 International,"ICD-10 allows dual coding. Refer to Section 3.1.3 of the ICD-10 Instruction Manual (2nd Edition, http://www.who.int/entity/classifications/icd/ICD-10_2nd_ed_volume2.pdf). This OID identifies the code system that describes how to encode Dual Coding in a CD compatible expression (for Datatypes R2 CD only).An ICD-10 dual code expression SHALL consist of two ICD-10 codes separated by space. This code system SHALL NOT be used for single ICD-10 codes; the normal ICD-10 code system oid which is 2.16.840.1.113883.6.3 should be used in this case.Dual code expressions SHALL only be used per the rules described in the ICD-10 instruction manual.An example CD: J21.8 is: Acute bronchiolitis due to other specified organismsB95.6 is: Staphylococcus aureus as the cause of diseases classified to other chapters",2008/02/16 12:00:00,2022/02/10 12:00:00,2022/02/10 09:49:02,,UV
2.16.840.1.113883.6.261,ICD-9 Dual Coding,ICD-9 Dual Coding,Grahame,Grieve,masked,,Vocab co-chairs or Grahame,,+61394502230,masked,,"HL7,HL7,HL7,HL7",c/o HQ, (+1) 734-677-7777,hq@hl7.org,http://www.hl7.org,SDO,2.16.840.1.113883,Pxy,,,6,Edited,,,"ICD-9 Dual Coding Expression Syntax"", description: ICD-9 allows dual coding. Refer to Section ?? of the ICD-9 Instruction Manual (ref?). This OID identifies the code system that describes how to encode Dual Coding in a CD compatible expression (for Datatypes R2 CD only).An ICD-9 dual code expression SHALL consist of two ICD-9 codes separated by space. This code system SHALL NOT be used for single ICD-9 codes; the normal ICD-9 code system oid which is 2.16.840.1.113883.6.3 should be used in this case. DisplayName SHALL not be used.Dual code expressions SHALL only be used per the rules described in the ICD-9 instruction manual.An example CD: 989.5 is: Toxic effect of venomE905.9 is: Bite or string",2008/02/16 12:00:00, ,2008/03/02 07:07:05,,UV
2.16.840.1.113883.6.273,NHSNOccasionOfDetection,NHSN Occasion Of Detection,Sundak,Ganesan,masked,MAlbitz@cdc.gov,Daniel Pollock,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",404-639-4237,masked,"Surveillance Branch Chief, Division of Healthcare Quality Promotion",Centers for Disease Control and Prevention,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",(800) 311-3435 ,DPollock@cdc.gov,http://www.cdc.gov,Govt body,2.16.840.1.114222.4,Ext,,,6,Retired,,,"NHSN Occasion Of DetectionThis was created erroneously back in 2008, it is not a code system. This is (or was) intended to be a value set used at NHSN. More information may be found at https://www.cdc.gov/nhsn/cdaportal/index.html ",2008/02/17 12:00:00,2018/09/14 12:00:00,2018/09/14 11:26:02,,US
2.16.840.1.113883.6.263,NHSNHipReplacement ,NHSN Hip Replacement,Sundak,Ganesan,masked,MAlbitz@cdc.gov,Daniel Pollock,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",404-639-4237,masked,"Surveillance Branch Chief, Division of Healthcare Quality Promotion",Centers for Disease Control and Prevention,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",(800) 311-3435 ,DPollock@cdc.gov,http://www.cdc.gov,Govt body,2.16.840.1.114222.4,Int,,,6,Retired,,,"NHSN Hip Replacement This was created erroneously back in 2008, it is not a code system. This is intended to be a value set used at NHSN. More information may be found at https://www.cdc.gov/nhsn/cdaportal/index.html ",2008/02/17 12:00:00,2018/09/14 12:00:00,2018/09/14 11:17:23,,UV
2.16.840.1.113883.6.262,NHSNSpinalFusionApproach,NHSN Spinal Fusion Approach,Sundak,Ganesan,masked,MAlbitz@cdc.gov,Daniel Pollock,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",404-639-4237,masked,"Surveillance Branch Chief, Division of Healthcare Quality Promotion",Centers for Disease Control and Prevention,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",(800) 311-3435 ,DPollock@cdc.gov,http://www.cdc.gov,Govt body,2.16.840.1.114222.4,Int,,,6,Retired,,,"NHSN Spinal Fusion ApproachThis was created erroneously back in 2008, it is not a code system. This is intended to be a value set used at NHSN. More information may be found at https://www.cdc.gov/nhsn/cdaportal/index.html ",2008/02/17 12:00:00,2018/09/14 12:00:00,2018/09/14 11:16:28,,US
2.16.840.1.113883.6.264,NHSNKneeReplacement,NHSN KneeR eplacement,Sundak,Ganesan,masked,MAlbitz@cdc.gov,Daniel Pollock,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",404-639-4237,masked,"Surveillance Branch Chief, Division of Healthcare Quality Promotion",Centers for Disease Control and Prevention,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",(800) 311-3435 ,DPollock@cdc.gov,http://www.cdc.gov,Govt body,2.16.840.1.114222.4,Int,,,6,Retired,,,"NHSN Knee ReplacementThis was created erroneously back in 2008, it is not a code system. This is intended to be a value set used at NHSN. More information may be found at https://www.cdc.gov/nhsn/cdaportal/index.html ",2008/02/17 12:00:00,2018/09/14 12:00:00,2018/09/14 11:18:17,,UV
2.16.840.1.113883.6.265,NHSNSSILocationType,NHSN SSI Location Type,Sundak,Ganesan,masked,MAlbitz@cdc.gov,Daniel Pollock,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",404-639-4237,masked,"Surveillance Branch Chief, Division of Healthcare Quality Promotion",Centers for Disease Control and Prevention,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",(800) 311-3435 ,DPollock@cdc.gov,http://www.cdc.gov,Govt body,2.16.840.1.114222.4,Int,,,6,Retired,,,"NHSN SSI LocationTypeThis was created erroneously back in 2008, it is not a code system. This is intended to be a value set used at NHSN. More information may be found at https://www.cdc.gov/nhsn/cdaportal/index.html ",2008/02/17 12:00:00,2018/09/14 12:00:00,2018/09/14 11:18:55,,UV
2.16.840.1.113883.6.266,NHSNBSIRiskFactors,NHSN BSI Risk Factors,Sundak,Ganesan,masked,MAlbitz@cdc.gov,Daniel Pollock,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",404-639-4237,masked,"Surveillance Branch Chief, Division of Healthcare Quality Promotion",Centers for Disease Control and Prevention,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",(800) 311-3435 ,DPollock@cdc.gov,http://www.cdc.gov,Govt body,2.16.840.1.114222.4,Int,,,6,Retired,,,"NHSN Blood Stream Infection Risk FactorsThis was created erroneously back in 2008, it is not a code system. This is (or was) intended to be a value set used at NHSN. More information may be found at https://www.cdc.gov/nhsn/cdaportal/index.html ",2008/02/17 12:00:00,2018/09/14 12:00:00,2018/09/14 11:20:02,,UV
2.16.840.1.113883.6.267,NHSNLCBIPathways,NHSN LCBI Pathways,Sundak,Ganesan,masked,MAlbitz@cdc.gov,Daniel Pollock,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",404-639-4237,masked,"Surveillance Branch Chief, Division of Healthcare Quality Promotion",Centers for Disease Control and Prevention,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",(800) 311-3435 ,DPollock@cdc.gov,http://www.cdc.gov,Govt body,2.16.840.1.114222.4,Int,,,6,Retired,,,"NHSN Laboratory Confirmed Bloodstream Infection PathwaysThis was created erroneously back in 2008, it is not a code system. This is (or was) intended to be a value set used at NHSN. More information may be found at https://www.cdc.gov/nhsn/cdaportal/index.html ",2008/02/17 12:00:00,2018/09/14 12:00:00,2018/09/14 11:20:29,,UV
2.16.840.1.113883.6.268,NHSNInfectionType,NHSN Infection Type,Sundak,Ganesan,masked,MAlbitz@cdc.gov,Daniel Pollock,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",404-639-4237,masked,"Surveillance Branch Chief, Division of Healthcare Quality Promotion",Centers for Disease Control and Prevention,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",(800) 311-3435 ,DPollock@cdc.gov,http://www.cdc.gov,Govt body,2.16.840.1.114222.4,Int,,,6,Retired,,,"NHSN Infection Type This was created erroneously back in 2008, it is not a code system. This is (or was) intended to be a value set used at NHSN. More information may be found at https://www.cdc.gov/nhsn/cdaportal/index.html ",2008/02/17 12:00:00,2018/09/14 12:00:00,2018/09/14 11:20:55,,UV
2.16.840.1.113883.6.269,NHSNSpinalFusionLevel,NHSN Spinal Fusion Level,Sundak,Ganesan,masked,MAlbitz@cdc.gov,Daniel Pollock,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",404-639-4237,masked,"Surveillance Branch Chief, Division of Healthcare Quality Promotion",Centers for Disease Control and Prevention,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",(800) 311-3435 ,DPollock@cdc.gov,http://www.cdc.gov,Govt body,2.16.840.1.114222.4,Int,,,6,Retired,,,"NHSN Spinal Fusion LevelThis was created erroneously back in 2008, it is not a code system. This is (or was) intended to be a value set used at NHSN. More information may be found at https://www.cdc.gov/nhsn/cdaportal/index.html ",2008/02/17 12:00:00,2018/09/14 12:00:00,2018/09/14 11:21:25,,UV
2.16.840.1.113883.6.270,NHSNSummaryData,NHSN Summary Data,Sundak,Ganesan,masked,MAlbitz@cdc.gov,Daniel Pollock,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",404-639-4237,masked,"Surveillance Branch Chief, Division of Healthcare Quality Promotion",Centers for Disease Control and Prevention,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",(800) 311-3435 ,DPollock@cdc.gov,http://www.cdc.gov,Govt body,2.16.840.1.114222.4,Int,,,6,Retired,,,"NHSN Summary DataThis was created erroneously back in 2008, it is not a code system. This is (or was) intended to be a value set used at NHSN. More information may be found at https://www.cdc.gov/nhsn/cdaportal/index.html ",2008/02/17 12:00:00,2018/09/14 12:00:00,2018/09/14 11:21:56,,UV
2.16.840.1.113883.6.272,NHSNSSIAnatomicSite,NHSN SSI Anatomic Site,Sundak,Ganesan,masked,MAlbitz@cdc.gov,Daniel Pollock,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",404-639-4237,masked,"Surveillance Branch Chief, Division of Healthcare Quality Promotion",Centers for Disease Control and Prevention,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",(800) 311-3435 ,DPollock@cdc.gov,http://www.cdc.gov,Govt body,2.16.840.1.114222.4,Int,,,6,Retired,,,"NHSN Surgical Site Infection Anatomic Site This was created erroneously back in 2008, it is not a code system. This is (or was) intended to be a value set used at NHSN. More information may be found at https://www.cdc.gov/nhsn/cdaportal/index.html ",2008/02/17 12:00:00,2018/09/14 12:00:00,2018/09/14 11:22:46,,UV
2.16.840.1.113883.6.271,NHSNProcedureCategory,NHSN Procedure Category,Sundak,Ganesan,masked,MAlbitz@cdc.gov,Daniel Pollock,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",404-639-4237,masked,"Surveillance Branch Chief, Division of Healthcare Quality Promotion",Centers for Disease Control and Prevention,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333 ",(800) 311-3435 ,DPollock@cdc.gov,http://www.cdc.gov,Govt body,2.16.840.1.114222.4,Int,,,6,Retired,,,"NHSN Procedure CategoryThis was created erroneously back in 2008, it is not a code system. This is (or was) intended to be a value set used at NHSN. More information may be found at https://www.cdc.gov/nhsn/cdaportal/index.html ",2008/02/17 12:00:00,2018/09/14 12:00:00,2018/09/14 11:25:26,,UV
2.16.840.1.113883.6.274,NHSNVocabulary,NHSN HAI Vocabulary,Sundak,Ganesan,masked,MAlbitz@cdc.gov,Daniel Pollock,"1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333",404-639-4237,masked,"Surveillance Branch Chief, Division of Healthcare Quality Promotion","Centers for Disease Control and Prevention,Centers for Disease Control and Prevention","1600 Clifton Road,NE, Mail Stop A24,Atlanta, GA 30333",(800) 311-3435,DPollock@cdc.gov,http://www.cdc.gov,Govt body,2.16.840.1.114222.4,Int,,,6,Retired,,,"NHSN HAI Vocabulary used for Single Value bindings to Observation IdentifierThis was created erroneously back in 2008, it is not a code system. This is (or was) intended to be a value set used at NHSN. More information may be found at https://www.cdc.gov/nhsn/cdaportal/index.html ",2008/02/25 12:00:00,2018/09/14 12:00:00,2018/09/14 11:24:21,,US
1.0.3166.1,iso3166-1,ISO 3166 Part 1 Country Codes,Ted,Klein,masked,,Dr. Mary Lou Pelaprat,"Standards Department, ISO Central Secretariat, 1, chemin de la Voie Creuse, P.O. Box 56, CH-1211 Geneva 20 Switzerland",+41 22 749 73 66,masked,Secretary of ISO 3166/MA,International Standards Organization (ISO),"1 ch. de la Voie-Creuse, Case postale 56, CH-1211 Geneva 20, Switzerland",+41 22 749 01 11,central@iso.org,http://www.iso.org,SDO,1,Ext,,,6,Complete,,,"This OID identifies the coding system published in the ISO 3166-1 Standard for Country codes. This standard is released periodically, and a new OID will be assigned by ISO for new editions.Note that this is the overall root, and may be used to identify the code system without being edition-specific.",2008/03/31 12:00:00,2008/03/31 12:00:00,2008/03/31 12:00:00,,UV
1.0.3166.1.2,iso3166-1edition2,"ISO 3166 Part 1 Country Codes, 2nd Edition",Ted,Klein,masked,,Dr. Mary Lou Pelaprat,"Standards Department, ISO Central Secretariat, 1, chemin de la Voie Creuse, P.O. Box 56, CH-1211 Geneva 20 Switzerland",+41 22 749 73 66,masked,Secretary of ISO 3166/MA,International Standards Organization (ISO),"1 ch. de la Voie-Creuse, Case postale 56, CH-1211 Geneva 20, Switzerland",+41 22 749 01 11,,http://www.iso.org,SDO,1,EXT,,,6,Complete,,,"This OID identifies the coding system published in the ISO 3166-1 Standard for Country codes. It contains 3 sets of synonyms for the country codes: 2-character alphabetic, 3-character alphabetic, and numeric. Note that this is the 2nd edition of the standard.",2008/03/31 12:00:00,2008/03/31 12:00:00,2008/03/31 12:00:00,,UV
1.0.3166.1.2.2,iso3166-1edition2alpha2,"ISO 3166 Part 1 Country Codes, 2nd Edition, Alpha-2",Ted,Klein,masked,,Dr. Mary Lou Pelaprat,"Standards Department, ISO Central Secretariat, 1, chemin de la Voie Creuse, P.O. Box 56, CH-1211 Geneva 20 Switzerland",+41 22 749 73 66,masked,Secretary of ISO 3166/MA,International Standards Organization (ISO),"1 ch. de la Voie-Creuse, Case postale 56, CH-1211 Geneva 20, Switzerland",+41 22 749 01 11,,http://www.iso.org,SDO,1,EXT,,,6,Complete,,,"This OID identifies the coding system published in the ISO 3166-1 Standard for Country codes, 2nd edition, 2-character alphabetic codes.",2008/03/31 12:00:00,2008/03/31 12:00:00,2008/03/31 12:00:00,,UV
2.16.840.1.113883.6.275,usEPAsrs,US EPA Substance Registry System,John,Harman,masked,,John Harman,"1200 Pennsylvania Ave NW; Washington, DC 20460 MC: 2823T",202 566 0748,masked,Environmental Protection Specialist,US Environmental Protection Agency,"1200 Pennsylvania Ave NW; Washington, DC 20460; MC 2323T",202 566 0748,harman.john@epa.gov,,Govt body,,INT,,,6,Complete,,,"The United States Environmental Protection Agency's (US EPA) Substance Registry System (SRS) provides information on substances and how they are represented in US environmental statutes, in US EPA information systems, and in information systems owned by other organizations. The SRS provides standardized identification for each substance to improve data quality in US EPA systems and elsewhere.",2008/06/26 12:00:00, ,2008/06/26 12:00:00,,UV
1.0.3166.2,iso3166-2,ISO 3166 Part 2 Country Subdivision Codes,Ted,Klein,masked,,Dr. Mary Lou Pelaprat,"Standards Department, ISO Central Secretariat, 1, chemin de la Voie Creuse, P.O. Box 56, CH-1211 Geneva 20 Switzerland",+41 22 749 73 66,masked,Secretary of ISO 3166/MA,"International Standards Organization (ISO),International Standards Organization (ISO)","1 ch. de la Voie-Creuse, Case postale 56, CH-1211 Geneva 20, Switzerland",+41 22 749 01 11,,http://www.iso.org,SDO,1,EXT,,,6,Edited,,,"This OID identifies the coding system published in the ISO 3166-2 Standard for Country Subdivision codes. This standard is released periodically, and a new OID will be assigned by ISO for new editions.",2008/03/31 12:00:00,2008/06/22 12:00:00,2008/07/23 05:15:16,,UV
2.16.840.1.113883.13.26,pARClass,PAR Class,Laura,Gibson,masked,Karen Eckert,Laura Gibson,"8425 Woodfield Crossing Blvd Suite 490 Indianapolis, IN 46240",317-705-7616,masked,Product Manager,Medi-Span/Wolters Kluwer Health,"8425 Woodfield Crossing Blvd Suite 490 Indianapolis, IN 46240",317-735-5300,laura.gibson@wolterskluwer.com,http://www.medispan.com,Vendor,,Int,,,6,Complete,,,Medi-Span Prior Adverse Reaction (PAR) Class that identifies allergen classes used in drug-allergy screening.,2008/08/14 12:00:00,2010/11/18 12:00:00,2010/11/18 04:54:35,,UV
1.0.3166.1.2.3,iso3166-1edition2alpha3,"ISO 3166 Part 1 Country Codes, 2nd Edition, Alpha-3",Ted,Klein,masked,,Dr. Mary Lou Pelaprat,"Standards Department, ISO Central Secretariat, 1, chemin de la Voie Creuse, P.O. Box 56, CH-1211 Geneva 20 Switzerland",+41 22 749 73 66,masked,Secretary of ISO 3166/MA,International Standards Organization (ISO),"1 ch. de la Voie-Creuse, Case postale 56, CH-1211 Geneva 20, Switzerland",+41 22 749 01 11,,http://www.iso.org,SDO,1,EXT,,,6,Complete,,,"This OID identifies the coding system published in the ISO 3166-1 Standard for Country codes, 2nd edition, 3-character alphabetic codes.",2008/03/31 12:00:00,2008/03/31 12:00:00,2008/03/31 12:00:00,,UV
1.0.3166.1.2.1,iso3166-1edition2numeric,"ISO 3166 Part 1 Country Codes, 2nd Edition, Numeric",Ted,Klein,masked,,Dr. Mary Lou Pelaprat,"Standards Department, ISO Central Secretariat, 1, chemin de la Voie Creuse, P.O. Box 56, CH-1211 Geneva 20 Switzerland",+41 22 749 73 66,masked,Secretary of ISO 3166/MA,International Standards Organization (ISO),"1 ch. de la Voie-Creuse, Case postale 56, CH-1211 Geneva 20, Switzerland",+41 22 749 01 11,,http://www.iso.org,SDO,1,EXT,,,6,Complete,,,"This OID identifies the coding system published in the ISO 3166-1 Standard for Country codes, 2nd edition, numeric codes.",2008/03/31 12:00:00,2008/03/31 12:00:00,2008/03/31 12:00:00,,UV
2.16.840.1.113883.5.1105,hc-DIN,Health Canada Drug Id Number,Ted,Klein,masked,Lloyd McKenzie,Infoway Standards Collaborative - SCWG 6,"150 King Street West, Suite 1300 Toronto, Ontario M5H 1J9",1-877-595-3417,masked,,"Health Canada,Health Canada","Therapeutic Products Directorate Health Products and Food Branch Address Locator: 3106B Ottawa, Ontario K1A 0K9",(613) 957-0368; Fax: (613) 952-7756,hc.DIN.sc@canada.ca,http://www.hc-sc.gc.ca/index-eng.php,Govt body,,Int,,,6,Complete,,HL7,A Drug Identification Number (DIN) is a computer-generated eight digit number assigned by Health Canada to a drug product prior to being marketed in Canada. It uniquely identifies all drug products sold in a dosage form in Canada and is located on the label of prescription and over-the-counter drug products that have been evaluated and authorized for sale in Canada.A DIN uniquely identifies the following product characteristics:manufacturer;product name;active ingredient(s);strength(s) of active ingredient(s);pharmaceutical form; androute of administration.Note: The number has a leading zeroMore information can be found here: https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/applications-submissions/guidance-documents/regulatory-requirements-drug-identification-numbers/document.html,2006/03/25 12:00:00,2008/12/15 12:00:00,2020/11/17 09:31:03,,UV
2.16.840.1.113883.5.1107,hc-NPN,Health Canada Natural Product Number,Ted,Klein,masked,Lloyd McKenzie,Infoway Standards Collaborative - SCWG 6,"150 King Street West, Suite 1300 Toronto, Ontario M5H 1J9",1-877-595-3417,masked,,"Health Canada,Health Canada","Therapeutic Products Directorate Health Products and Food Branch Address Locator: 3106B Ottawa, Ontario K1A 0K9",(613) 957-0368; Fax: (613) 952-7756,hc.nnhpd-dpsnso.sc@canada.ca,http://www.hc-sc.gc.ca/index-eng.php,Govt body,,Int,,,6,Complete,,HL7,Natural Product Number (NPN) is an eight digit numerical code assigned to each natural health product approved to be marketed under the Natural Health Products Regulations. A Homeopathic Medicine Number (DIN-HM) is an eight digit numerical code assigned to each homeopathic medicine approved to be marketed under the Natural Health Products Regulations. More information can be found here: https://www.canada.ca/en/health-canada/services/drugs-health-products/natural-non-prescription/applications-submissions/product-licensing/licensed-natural-health-products-database.html,2006/03/25 12:00:00, ,2020/11/17 09:34:20,,UV
2.16.840.1.113883.6.276,GMDN,Global Medical Device Nomenclature,Ted,Klein,masked,Bob Dolin,Rick Geimer,"PO Box 3557, Federal Way, WA 98063",650-209-4839,masked,Chief Architect,GMDN Agency Ltd.,"The Stables, Sugworth Lane, Radley, Oxford, OX14 2HX, UK",+44 (0) 1865 735840 ,gmdn_agency@btinternet.com,http://www.gmdnagency.com,SDO,,INT,,,6,Complete,,,http://www.gmdnagency.com/,2008/10/24 12:00:00,2008/10/24 12:00:00,2008/10/24 12:00:00,,UV
1.0.4217,iso4217,ISO 4217 Currency Codes,Ted,Klein,masked,,Dr. Mary Lou Pelaprat,"Standards Department, ISO Central Secretariat, 1, chemin de la Voie Creuse, P.O. Box 56, CH-1211 Geneva 20 Switzerland",+41 22 749 73 66,masked,Secretary of ISO 3166/MA,"International Standards Organization (ISO),International Standards Organization (ISO)","1 ch. de la Voie-Creuse, Case postale 56, CH-1211 Geneva 20, Switzerland",+41 22 749 01 11,,http://www.iso.org,SDO,1,EXT,,,6,Complete,,,ISO 4217 Currency Codes,2008/03/31 12:00:00,2008/10/24 12:00:00,2008/10/24 09:36:00,,UV
2.16.840.1.113883.6.277,cdcNHSN,CDC - National Healthcare Safety Network (NHSN) code system,Sundak,Ganesan,masked,Ted Klein,Daniel Pollock,"1600 Clifton Road, NE, Mail Stop A24 Atlanta, GA 30333",404-639-4237,masked,,"Centers for Disease Control and Prevention - National Healthcare Safety Networ,Centers for Disease C","Centers for Disease Control and Prevention - National Healthcare Safety Network 1600 Clifton Road, NE, Mail Stop A24 Atlanta, GA 30333",404-639-4237,DPollock@cdc.gov,http://www.cdc.gov/ncidod/dhqp/nhsn.html,Govt body,2.16.840.1.114222,Ext,,,6,Complete,,HL7,"CDC - National Healthcare Safety Network (NHSN) code system - A set of patient safety and healthcare personnel safety vocabulary concepts and associated identifiers maintained as a code system by the CDC's National Healthcare Safety Network. CDC NHSN is planning to use these code system concepts in the HAI implementation guide. These concepts would be submitted for the HL7 Ballot (Dec 2008). CDC NHSN can provide complete list of concepts, identifiers and extended attributes for this code system.",2008/10/24 12:00:00,2008/10/24 12:00:00,2010/07/16 05:25:28,,UV
2.16.840.1.113883.2.20.5.1,pclocd,pan-Canadian LOINC ® Observation Code Database,Wendy,Huang,masked,,Clinical Systems Interoperability,Same as below,1-877-595-3417,masked,,Clinical Systems Interoperability,"Canada Health Infoway Inc.150 King St. West, Suite 1300Toronto, Ontario Canada M5H 1J9",1-877-595-3417,standards@infoway-inforoute.ca,http://www.infoway-inforoute.ca,Govt body,2.16.840.1.113883.2.20,Ext,,,6,Complete,2.16.840.1.113883.2.20.5.1,HL7,The pan Canadian LOINC Observation Code Database (pCLOCD) is the Canadian version of the LOINC® database. It was created using the LOINC® records and attributes that were constrained for Canadian use and supplemented to specifically meet Canadian requirements. It contains the core LOINC® attributes as required by Regenstrief copyright rules. The LOINC® Component has been customized to meet Canadian requirements and is displayed as the pan Canadian Component Name. This component name is the basis for the pan Canadian Display Name. Core attributes are include both English and Canadian French.This code system contains supplemental ""X"" codes defined in the pCLOCD that do not yet exist in the LOINC code system.,2008/12/02 12:00:00,2009/12/22 12:00:00,2016/03/09 09:29:47,,UV
2.16.840.1.113883.2.20.5.2,sctemp,pan-Canadian Temporary Codes,Wendy,Huang,masked,,Clinical Systems Interoperability,Same as below,1-877-595-3417,masked,,Clinical Systems Interoperability,"Canada Health Infoway Inc.150 King St. West Suite 1300, Toronto, Ontario Canada M5H 1J9",1-877-595-3417,standards@infoway-inforoute.ca,http://www.infoway-inforoute.ca,Govt body,2.16.840.1.113883.2.20,Ext,,,6,Complete,2.16.840.1.113883.2.20.5.2,HL7,"These pan-Canadian codes are maintained in circumstances where the desired code is not yet available in another code system (HL7 code systems, LOINC, SNOMED, etc.) In general, the codes will be deprecated once an equivalent code is available in the preferred code system.",2008/12/09 12:00:00,2009/12/22 12:00:00,2016/03/09 09:30:59,,UV
2.16.840.1.113883.2.20.5.3,scptype,pan-Canadian Provider Types,Wendy,Huang,masked,,Clinical Systems Interoperability,Same as below,1-877-595-3417,masked,,Clinical Systems Interoperability,"Canada Health Infoway150 King St. West Suite 1300, Toronto, OntarioCanada M5H 1J9",1-877-595-3417,standards@infoway-inforoute.ca,http://www.infoway-inforoute.ca,Govt body,2.16.840.1.113883.2.20,Ext,,,6,Complete,2.16.840.1.113883.2.20.5.3,HL7 Canada,This code system contains the list of provider types used in the pan-Canadian specifications.,2008/12/09 12:00:00,2009/12/28 12:00:00,2016/03/09 09:31:56,,UV
2.16.840.1.113883.2.20.5.4,scpqual,pan-Canadian Provider Qualification,Wendy,Huang,masked,,Clinical Systems Interoperability,Same as below,1-877-595-3417,masked,,Clinical Systems Interoperability,"Canada Health Infoway150 King St. West Suite 1300, Toronto, OntarioCanada M5H 1J9",1-877-595-3417,standards@infoway-inforoute.ca,http://www.infoway-inforoute.ca,Govt body,2.16.840.1.113883.2.20,Ext,,,6,Complete,2.16.840.1.113883.2.20.5.4,,This code system ocntains the list of provider qualifications used in the pan-Canadian specifications.,2008/12/09 12:00:00,2009/12/22 12:00:00,2016/03/09 09:32:50,,UV
2.16.840.1.113883.6.278,epsg-crs,European Petroleum Survey Group Geodetic Parameter Dataset Coordinate Reference System,Ted,Klein,masked,Lloyd McKenzie,Jack Verouden ,"Shell International E&P BV, Kesslerpark 1, 2288 GS Rijswijk (ZH), The Netherlands ",,masked,"Chair, OGP Surveying and Positioning Committee",International Association of Oil & Gas Producers,"209-215 Blackfriars Road, London SE1 8NL, United Kingdom",+44 (0)20 7633 0272,,http://www.epsg.org/Geodetic.html,Prof Soc,,Ext,,,6,Complete,,HL7,"The set of values found in the βCode β CRSβ column of the βCoordinate Reference Systemβ table as maintained in the EPSG geodetic parameter dataset. These define coordinate systems for geographic coordinates, including allowed axis, projection, datum and measurement units.",2008/12/16 12:00:00,2008/12/16 12:00:00,2008/12/16 12:00:00,,UV
2.16.840.1.113883.6.279,epsg-ca,European Petroleum Survey Group Geodetic Parameter Dataset Coordinate Axis,Ted,Klein,masked,Lloyd McKenzie,Jack Verouden ,"Shell International E&P BV, Kesslerpark 1, 2288 GS Rijswijk (ZH), The Netherlands ",,masked,"Chair, OGP Surveying and Positioning Committee",International Association of Oil & Gas Producers,"209-215 Blackfriars Road, London SE1 8NL, United Kingdom",+44 (0)20 7633 0272,,http://www.epsg.org/Geodetic.html,Prof Soc,,Ext,,,6,Complete,,HL7,The set of values found in the βCoord Axis Codeβ column of the βCoordinate Axisβ table as maintained in the EPSG geodetic parameter dataset. These define the axis for coordinate systems for geographic coordinates.,2008/12/16 12:00:00,2008/12/16 12:00:00,2008/12/16 12:00:00,,UV
2.16.840.1.113883.4.340,cmsLocalCodes,Centers for Medicare & Medicaid Services (CMS) Local Codes,Bob,Dolin,masked,,Bob Dolin,,949 466 4035,masked,,SDWG,NA,NA,,,HL7 body,,Int,,,6,Complete,,,Local codes assigned by Centers for Medicare & Medicaid Services (CMS).,2009/03/06 12:00:00,2010/01/29 12:00:00,2010/01/29 01:13:04,,UV
2.16.840.1.113883.3.24.6.1,fda-FFRN,Food and Drug Administration Food Facility Registration Numbers,William,Hess,masked,Ted Klein,CAPT William A. Hess,"HF-18, Pkln Bldg Rm 12-81, 5600 Fishers Lane, Rockville, MD 20857",301-827-7865,masked,,FDA Data Standards Council,"HF-18, Pkln Bldg Rm 12-81, 5600 Fishers Lane, Rockville, MD 20857",301-827-7865,William.hess@fda.hhs.gov,http://www.fda.gov/,Govt body,,INT,,2.16.840.1.113883.4.344,6,Retired,,,Entered in error originally - do not use. Correct OID for this item is 2.16.840.1.113883.4.344.,2009/03/08 12:00:00,2009/09/11 12:00:00,2009/03/08 06:08:00,,UV
2.16.840.1.113883.3.24.6.2,fda-FCE,Food and Drug Administration Food Canning Establishments,William,Hess,masked,Ted Klein,CAPT William A. Hess,"HF-18, Pkln Bldg Rm 12-81, 5600 Fishers Lane, Rockville, MD 20857",301-827-7865,masked,,FDA Data Standards Council,"HF-18, Pkln Bldg Rm 12-81, 5600 Fishers Lane, Rockville, MD 20857",301-827-7865,William.hess@fda.hhs.gov,http://www.fda.gov/,Govt body,,INT,,2.16.840.1.113883.4.345,6,Retired,,,Entered erroneously - do not use. The correct OID for this identifier system is 2.16.840.1.113883.4.345.,2009/03/08 12:00:00,2009/09/11 12:00:00,2009/03/08 06:08:00,,UV
2.16.840.1.113883.4.342,vich-AnimalBreed,VICH Animal Breed,Lise,Stevens,masked,Glenn Peterson,Glenn Peterson,"7519 Standish Place Rockville, MD 20855",240-453-6876,masked,MATHEMATICAL STATISTICIAN,Veterinary International Conference on Harmonisation (VICH),"c/o IFAH, International Federation for Animal Health Rue Defacqz 1-1000 Brussels, Belgium",+32-2-5437572,sec@vichsec.org,http://www.vichsec.org/,SDO,,Int,,,6,Complete,,,"VICH has created their own reference list to describe animal breeds. This list will be used for Individual Case Safety Reports (ICSR)involving animals. The list will be a valid vocabulary binding to the new Individual Case Safety Report Related Observation vocabulary concept domain. Since the list does not conform to standard naming or scientific conventions, the use of this list is restricted to reporting between VICH parties.",2009/03/18 12:00:00,2010/01/29 12:00:00,2010/01/29 01:14:26,,UV
2.16.840.1.113883.2.21.10,brazilianProcedureCodesSUS,Brazilian Procedure Codes SUS,Beatriz,Leao,masked,Marivan Santiago Abrahao,Beatriz de Faria Leao,Av. MAcuco 550 apto 72 Sao Paulo SP Brazil,+55-11-81141617,masked,,HL7 Brazil,"Rua Afonso Braz 644 sala 14,04511-001, SΓ£o Paulo, SP, Brasil",+55-11-3045-3045,chair@hl7brasil.org.br,,HL7 body,2.16.840.1.113883.2.21,Ext,,,6,Complete,2.16.840.1.113883.2.21.10,,Brazilian Procedure Codes used in the National Health System,2009/03/20 12:00:00,2009/09/15 12:00:00,2009/03/20 12:00:00,,UV
2.16.840.1.113883.6.280,refSeq,,Yan,Heras,masked,Ted Klein,,"National Center for Biotechnology Information National Library of MedicineBuilding 38ABethesda, MD 20894",(301) 496-2475,masked,,"National Center for Biotechnology Information,National Center for Biotechnology Information","National Center for Biotechnology Information National Library of MedicineBuilding 38ABethesda, MD 20894",(301) 496-2475,info@ncbi.nlm.nih.gov,http://www.ncbi.nlm.nih.gov,Govt body,,INT,,,6,Complete,,,"The Reference Sequence (RefSeq) is one of the NCBI projects, the RefSeq collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. ReqSeq is accessible via BLAST, Entrez, and the NCBI FTP site. Information is also available in Entrez Genomes and Entrez Gene, and for some genomes additional information is available in the Map Viewer. RefSeq entries can be used with the HL7 coded data type. For example, in the HL7 messages specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model, RefSeq entries can be used to as the observation values for genomic reference sequence identifiers (LOINC #: 48013-7). More information may be found at: http://www.ncbi.nlm.nih.gov/RefSeqVersioning informaiton:The latest release of RefSeq was released on May 13, 2009 with the release number of 35.RefSeq generates new releases roughly every two months. The dates of the three previous releases were:Release 34, March 12, 2009Release 33, January 20, 2009Release 32, November 17, 2008RefSeq is a free database for the public.",2009/05/21 12:00:00,2009/05/27 12:00:00,2009/05/22 12:09:15,,UV
2.16.840.1.113883.6.281,hgnc,HUGO Gene Nomenclature,Yan,Heras,masked,Ted Klein,"Dr. Elspeth Bruford, Coordinator of HGNC","Gene Nomenclature Committee (HGNC)EMBL Outstation - HinxtonEuropean Bioinformatics Institute Wellcome Trust Genome CampusHinxton, Cambridge, CB10 1SDUnited Kingdom",+ 44 (0) 01223492624,masked,,"HUGO Gene Nomenclature Committee,HUGO Gene Nomenclature Committee","Gene Nomenclature Committee (HGNC)EMBL Outstation - HinxtonEuropean Bioinformatics Institute Wellcome Trust Genome CampusHinxton, Cambridge, CB10 1SDUnited Kingdom",+ 44 (0) 01223492624,elspeth@ebi.ac.uk,http://www.genenames.org/,Prof Soc,,INT,,,6,Complete,,,"HUGO Gene Nomenclature Committee (HGNC) is committee jointly funded by the US National Human Genome Research Institute and the Wellcome Trust (UK). It operates under the auspices of HUGO, with key policy advice from an International Advisory Committee, and is responsible for approving gene names and symbols. All approved symbols are stored in the HGNC database. Each symbol is unique and each gene is only given one approved gene symbol. More than 28,000 human gene symbols and names have been approved so far. The vast majority of these is for protein-coding genes, but also includes symbols for peudogenes, non-coding RNAs, phenotypes and genomic features. HGNC gene symbols can be used with the HL7 coded data type. For example, in the HL7 messages specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model Implementation Guide, HGNC gene symbols can be used to as the observation values for gene identifiers. For example, OBX|1|CWE|48018-6^Gene identifier^||BRCA1^HGNC|Versioning Information:The version of the HGNC database is reported using the last updated date and timestamp. The last updated date and timestamp is posted on the main HGNC Search screen in the format like ""Monday March 30 23:00:56 2009"".HGNC is updated daily.HGNC is a free database for the public.",2009/05/21 12:00:00,2009/05/27 12:00:00,2009/05/22 12:10:03,,UV
2.16.840.1.113883.6.282,hgvs,,Yan,Heras,masked,Ted Klein,"Ms. Rania Horaitis, Executive Secretary","Gene Nomenclature Committee (HGNC)EMBL Outstation - HinxtonEuropean Bioinformatics Institute Wellcome Trust Genome CampusHinxton, Cambridge, CB10 1SDUnited Kingdom",+ 61-3-8344-1831,masked,,"HUGO Gene Nomenclature Committee,HUGO Gene Nomenclature Committee","Gene Nomenclature Committee (HGNC)EMBL Outstation - HinxtonEuropean Bioinformatics Institute Wellcome Trust Genome CampusHinxton, Cambridge, CB10 1SDUnited Kingdom",+ 61-3-8344-1831,rania@variome.org,http://www.hgvs.org/,Prof Soc,,INT,,,6,Complete,,,"HGVS nomenclatures are the guidelines for mutation nomenclature made by the Human Genome Variation Society. HGVS nomenclature can be used with the HL7 coded data type (code data type that accepts expression data, or a coded expression data type). This coded data type should be able to distinguish expressions in HGVS nomenclature from coded concepts. For example, in the HL7 messages specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model, HGVS nomenclature can be used to as the observation values for DNA sequence variations. For example, OBX|1|CWE|48004-6^DNA Sequence Variation^LN||c.1129C>T^^HGVS|Versioning information:The HGVS nomenclature for the description of sequence variants was last modified Feb 20, 2008.The HGVS nomenclature for the description of protein sequence variants was last modified May 12, 2007. The HGVS nomenclature for the description of DNA sequence variants was last modified June 15, 2007The HGVS nomenclature for the description of RNA sequence variants was last modified May 12, 2007HGVS nomenclatures can be used freely by the public.",2009/05/21 12:00:00,2009/05/27 12:00:00,2009/05/22 12:10:57,,UV
2.16.840.1.113883.6.283,lrg,Locus Reference Genomic Sequences (LRG),Yan,Heras,masked,Ted Klein,Paul Flicek,"Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK",+44(0)1223492581,masked,Team Leader Vetebrate Genomics,Wellcome Trust,"Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK",+44(0)1223 494 444,missingdata@gmail.com,http://ebi.ac.uk,Academic,,Int,,,6,Complete,,HL7,"In collaboration with NCBI, the European Bioinformatics Institute (EBI) is developing the Locus Reference Genomic Sequences (LRG) database, which is a database of reference sequences. LRG is a system for providing a genomic DNA sequence representation of a single gene that is idealized, has a permanent ID (with no versioning), and core content that never changes. LRG is not a nomenclature system. More than one LRG could be created for a region of interest, should that need arise. Additional annotations will be present that may change with time (each item carrying its own date stamp), so that the latest ancillary knowledge about a gene is directly available. In other words, an LRG sequence and its core annotation are not meant to represent current biology knowledge, but to provide a standard for reporting variation in a stable coordinate system. The combination of the LRG plus the updatable-annotation layer will be used to support the biological interpretation of variants.LRG identifiers can be used with the HL7 coded data type (code data type that accepts expression data, or a coded expression data type). This coded data type will be gene symbols can be used with the HL7 coded data type. For example, in the HL7 messages specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model, LRG identifiers can be used to as the observation values for Genomic Reference Sequence Identifier (LOINC code: 48013-7). LRG is a database that can be used freely by the public.",2009/05/21 12:00:00,2009/09/15 12:00:00,2009/06/05 12:09:59,,UV
2.16.840.1.113883.6.284,dbSNP,The Short Genetic Variations database,Yan,Heras,masked,Ted Klein,"Clem McDonald, MD","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",+1 301-496-4441,masked,,"National Center for Biotechnology Information,National Center for Biotechnology Information","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-2475,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,,"In collaboration with the National Human Genome Research Institute, The National Center for Biotechnology Information has established the dbSNP database to serve as a central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. The entries in the dbSNP database can be used with the HL7 coded data type. For example, in the HL7 messages specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model, dbSNP entries can be used to as the observation values for DNA sequence variation identifiers. For example, OBX|1|CWE|48004-6^DNA Sequence Variation Identifier^LN||rs55538123^^dbSNPVersioning is identified by the build id. A new build is released approximately every six months or every year. The latest build id is 130, and the dbSNP web query for built 130 was available on Apr 30, 2009.dbSNP is a database that can be used freely by the public.More information may be fouond at: http://www.ncbi.nlm.nih.gov/projects/SNP/",2009/05/21 12:00:00,2009/05/27 12:00:00,2009/05/22 12:12:32,dbSNP,UV
2.16.840.1.113883.4.358,veddra,Veterinary Dictionary for Drug Regulatory Activities (VEDDRA),Lise,Stevens,masked,William Hess,Glenn Peterson,"7500 Standish Place Rockville, MD 20855",240-453-6876,masked,Mathmatical Statistician,European Medicines Agency,7 Westferry Circus Canary Wharf London,44 2074188581,vet-phv@emea.europa.eu,http://www.emea.europa.eu/htms/aboutus/emeainfopoint.htm#pharmacovigilanceandPDR,Govt body,,Int,,,6,Complete,,,The Veterinary Dictionary for Drug Regulatory Activities (VEDDRA) is used for pharmacovigilence reporting between regulatory authorities and pharmaceutical companies for adverse events associated with the use of animal drug products.,2009/07/22 12:00:00,2010/03/09 12:00:00,2010/03/11 07:01:36,,UV
2.16.840.1.113883.13.51,vichOff-LabelUseCodes,VICH Off-Label Use Codes,Lise,Stevens,masked,William Hess,Glenn Peterson,7500 Standish Place,240-453-6876,masked,Mathematical Statistician,Veterinary Conference on Harrmonisation,"c/o IFAH, International Federation for Animal HealthRue Defacqz, 1 - 1000 Brussels (Belgium) ",32-2-5437572,sec@vichsec.org,http://www.vichsec.org/en/moreinfos.htm,SDO,,Int,,,6,Complete,,,The code system will be used to explain off label use of an animal drug product in the ICSR.,2009/07/22 12:00:00,2010/03/09 12:00:00,2010/03/09 01:48:15,,UV
2.16.840.1.113883.6.43.1,icd-o-3,"International Classification of Diseases for Oncology, version 3.",Ted,Klein,masked,,,,,masked,,World Health Organization (WHO),,,,http://www.who.int/en/,SDO,,Int,,,6,Complete,,,"International Classification of Diseases for Oncology, version 3. For more information see http://www.who.int/classifications/icd/adaptations/oncology/en/.",1899/12/30 12:00:27,2009/09/11 12:00:00,2009/09/11 05:00:00,,UV
2.16.840.1.113883.6.139,icpc2E,"International Classification of Primary Care, second edition (1998)",Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,SDO,,Pxy,14,,6,Complete,,,"International Classification of Primary Care / prepared by the Classification Committee of the World Organization of National Colleges, Academies and Academic Associations of General Practitioners/Family Physicians (WONCA), known more briefly as the World",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.142,icpc2-icd10-THSRS,ICPC2-ICD10 Thesaurus,Harold,Solbrig,masked,,Dr. Inge M. Okkes,Veemkade 12081019 BZ AMSTERDAMThe Netherlands,,masked,,WHO Collaborating Centre for the FIC in The Netherlands,Veemkade 12081019 BZ AMSTERDAMThe Netherlands,,,http://www.rivm.nl/who-fic/thesauruseng.htm,SDO,,Pxy,14,,6,Complete,,,"A diagnostic Terminology for semi-automatic Double Coding in Electronic Patient RecordsThe thesaurus is a part of the CD Rom: ""ICPC in the Amsterdam Transition Project. Extended Version. IM Okkes, SK Oskam, H. Lamberts. Amsterdam: Academic Medical Center/University of Amsterdam. Department of Family Medicine"", see also the web sitehttp://www.transitieproject.nl for this application of the thesaurus.This bilingual (English/Dutch) ICPC2-ICD10 thesaurus is derived from an extended version of the CD-Rom ICPC in the Amsterdam Transition Project, that was published as a companion to ICPC-2-R by Oxford University Press (2005). As was the case with the former thesaurus (published in Dutch in 2003), the content of this new thesaurus may be copied for academic purposes, and be used for teaching and research under the usual referencing conditions. Any other and/or commercial use requires prior permission from the authors, represented by Dr. Inge Okkes (see below).It is strongly recommended that you first go through the ICPC Tutorial, the Manual and the Glossary, and consider printing them. Becker, H.W., C. van Boven, S.K. Oskam, I.M. Okkes, W. Hirs, H. Lamberts. ICPC2 - ICD10 Thesaurus, Version March, 2004. Amsterdam: Project ""Adaptation ICPC, integration and implementation of ICPC2 and ICD10(-CM)."" Department of General Practice, Academic",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.140,icpc2E-P,ICPC2E 1998 Plus,Harold,Solbrig,masked,,,"8600 Rockville PikeBethesda, MD 20894",,masked,,National Library of Medicine,"8600 Rockville PikeBethesda, MD 20894",(301) 496-6308,,http://www.nlm.nih.gov/research/umls/,SDO,,Pxy,14,,6,Complete,,,"International Classification of Primary Care, Version 2-Plus. Produced by NLM. Bethesda (MD): National Library of Medicine, UMLS project. This node has the various modifications and translations produced under it.",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.138.14,icpc-ENG,International Classification of Primary Care 1993 (English),Harold,Solbrig,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201211 Geneva 27Switzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,,,Pxy,,,6,Complete,,,"The International Classification of Primary Care (ICPC). Swedish Translation. Denmark: World Organisation of Family Doctors, 1993.",2005/01/25 12:00:00,2009/10/07 12:00:00,2005/01/25 12:00:00,,UV
2.16.840.1.113883.6.285,hcpcs-Level-II,HCPCS Level II Alphanumeric Codes,Ted,Klein,masked,,Tom Oniki,GE Healthcare,410-786-3000,masked,,Centers for Medicare and Medicaid Services,"U.S. Centers for Medicare & Medicaid Services7500 Security BoulevardBaltimore, MD 21244",877-267-2323,hcpcs@cms.hhs.gov,https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo/index.html,Govt body,,Int,,,6,Complete,,CMS,"Level II of the HCPCS is a standardized coding system that is used primarily to identify products, supplies, and services not included in the CPT codes, such as ambulance services and durable medical equipment, prosthetics, orthotics, and supplies (DMEPOS) when used outside a physician's office. Because Medicare and other insurers cover a variety of services, supplies, and equipment that are not identified by CPT codes, the level II HCPCS codes were established for submitting claims for these items. The development and use of level II of the HCPCS began in the 1980's. Level II codes are also referred to as alpha-numeric codes because they consist of a single alphabetical letter followed by 4 numeric digits, while CPT codes are identified using 5 numeric digits.",2009/10/13 12:00:00,2010/11/22 12:00:00,2018/02/06 02:09:48,,UV
2.16.840.1.114222.4.1.181960.2.3,txdshslabNBSLocCod,Texas Department of State Health Services Laboratory Serivices Section Newborn Screening Newborn Local Code,Joshua,Escalante,masked,,Willis Gibson,"P.O. Box 149347Austin, TX 78714-9347",512 458 7111 ext 2879,masked,System Administrator,Texas Deparment of State Health Services,"P.O. Box 149347Austin, TX 78714-9347",512 458 7111,labappsupport@dshs.state.tx.us,www.dshs.state.tx.us/lab,Govt body,,Ext,,,6,Complete,2.16.840.1.114222.4.1.181960.2.3,Texas Department of State Health Services Laboratory Services Section ,"Texas Department of State Health Services Laboratory Services Section (Texas DSHS) will be creating an OID for defining the Newborn Local Code within the HL7 message created for health care facilities (hospitals, medical clinics, etc.) sending its Newborn Local Code to Texas DSHS. Newborn Screening Laboratory Information Management System (LIMS) is not currently capturing the health care facilities' Local Codes. ",2009/11/17 12:00:00,2009/12/30 12:00:00,2009/12/30 12:38:24,,UV
2.16.840.1.114222.4.1.181960.2.5,txdshslabNBSAutResInt,Texas Department of State Health Services Laboratory Serivices Section Newborn Screening Newborn Interpretation Code,Joshua,Escalante,masked,,Willis Gibson,"P.O. Box 149347Austin, TX 78714-9347",512 458 7111 ext 2879,masked,System Administrator,Texas Deparment of State Health Services,"P.O. Box 149347Austin, TX 78714-9347",512 458 7111,labappsupport@dshs.state.tx.us,www.dshs.state.tx.us/lab,Govt body,,Ext,,,6,Complete,2.16.840.1.114222.4.1.181960.2.5,Texas Department of State Health Services Laboratory Services Section ,"Texas Department of State Health Services Laboratory Services Section will be creating an OID for defining a Newborn Interpetation Code within the Newborn Screening Laboratory Information System (LIMS) for HL7 message purposes. The Interpretaion Code within the Newborn Screening defines a patient interpretation or result record as being 'Normal', 'Abnormal' or 'Unsatisfactory'. A result within a defined reference range is considered 'Normal'. A result outside the defined reference range is considered 'Abnormal'. A specimen or laboratory test not suitable for testing will be assigned an 'Unsatisfactory' result with further follow-up from the ordering facility required.",2009/11/17 12:00:00,2009/12/30 12:00:00,2009/12/30 12:41:59,,UV
2.16.840.1.113883.6.286,fdbHIC3,First DataBank Hierarchical Specific Therapeutic Class Code,Lloyd,McKenzie,masked,,Thomas R. Bizzaro,"First DataBank, Inc.500 East 96th Street, Suite 500Indianapolis, IN 46240USA",(317) 571-7247,masked,"Vice President, Health Policy and Industry Relations",First DataBanc Inc.,"First DataBank, Inc.South San Francisco, CA Corporate Headquarters701 Gateway Blvd., Suite 600So. San Francisco, CA 94080",317-571-7247,tom_bizzaro@firstdatabank.com,http://www.firstdatabank.com/,Vendor,,Int,,,6,Complete,,,"HIC3HIERARCHICAL SPECIFIC THERAPEUTIC CLASS CODEThe HIC3 (Hierarchical Specific Therapeutic Class Code) is a three-character alphanumeric identifier that, depending on its context, identifies the specific therapeutic class of a First DataBank identifier for an ingredient (HIC_SEQN), a Clinical Formulation ID (GCN_SEQNO), or each ingredient in an Ingredient List (HICL_SEQNO). Note: The HIC3 is now deprecated and is superceded by the HIC3_SEQN: a dumb number and a stable identifier that represents a Hierarchical Specific Therapeutic Class Code. First DataBank also offers the First DataBank Enhanced Therapeutic Classification System as an alternative to the First DataBank's Specific Therapeutic Classification.",2009/12/04 12:00:00,2009/12/30 12:00:00,2010/11/23 05:46:51,,UV
1.0.21000.6,iso21000-6-2004E-RDD,ISO/IEC 21000-6:2004(E) Rights Data Dictionary,Russell,Hamm,masked,,Russell Hamm,"6326 Fairway DR NWRochester MN, 55901",507-271-0227,masked,Informatics Architect,ISO/IEC,"International Organization for Standardization (ISO)1, ch. de la Voie-Creuse,Case postale 56CH-1211 Geneva 20, Switzerland",41 22 749 01 11,info@iso21000-6.net,http://iso21000-6.net/,SDO,,Ext,,,6,Complete,1.0.21000.6,ISO/IEC 21000-6 Registration Authority,"ISO/IEC 21000-6:2004 describes a Rights Data Dictionary which comprises a set of clear, consistent, structured, integrated and uniquely identified terms to support the MPEG-21 Rights Expression Language (REL), ISO/IEC 21000-5. Annex A specifies the methodology for and structure of the RDD Dictionary, and specifies how further Terms may be defined under the governance of a Registration Authority, requirements for which are described in Annex C.Taken together, these specifications and the RDD Dictionary and Database make up the RDD System. Use of the RDD System will facilitate the accurate exchange and processing of information between interested parties involved in the administration of rights in, and use of, Digital Items, and in particular it is intended to support ISO/IEC 21000-5 (REL). Clause 6 describes how ISO/IEC 21000-6:2004 relates to ISO/IEC 21000-5.As well as providing definitions of terms for use in ISO/IEC 21000-5, the RDD System is designed to support the mapping of terms from different namespaces. Such mapping will enable the transformation of metadata from the terminology of one namespace (or Authority) into that of another namespace. Mapping, to ensure minimum ambiguity or loss of semantic integrity, will be the responsibility of the Registration Authority. Provision of automated trm look-up is also a requirement.The RDD Dictionary is a prescriptive dctionary, in the sense that it defines a single meaning for a trm represented by a particular RddAuthorized TermName, but it is also inclusive in that it can recognize the prescription of other Headwords and definitions by other Authorities and incorporates them through mappings. The RDD Dictionary also supports the circumstance that the same name may have different meanings under different Authorities. ISO/IEC 21000-6:2004describes audit provisions so that additions, amendments and deletions to Terms and their attributes can be tracked.ISO/IEC 21000-6:2004 recognizes legal definitions as and only as Terms from other Authorities that can be mapped into the RDD Dictionary. Therefore Terms that are directly authorized by the RDD Registration Authority neither define nor prescribe intellectual property rights or other legal entities.",2009/12/15 12:00:00,2009/12/16 12:00:00,2009/12/16 05:30:01,,UV
1.0.639.3,iso639-3,ISO 639-3 Language Codes Alpha 3,William Ted,Klein,masked,,SIL International,"SIL InternationalISO 639-3 Registrar7500 W. Camp Wisdom Rd.Dallas, TX 75236","+1 972 708 7400, ext. 229",masked,ISO 639-3 Registrar,SIL International,"SIL InternationalISO 639-3 Registrar7500 W. Camp Wisdom Rd.Dallas, TX 75236","+1 972 708 7400, ext",iso639-3@sil.org,http://www.sil.org/ISO639-3/,Prof Soc,,Ext,,,6,Complete,1.0.639.3,ISO,"ISO 639-3 is a code that aims to define three-letter identifiers for all known human languages. At the core of ISO 639-3 are the individual languages already accounted for in ISO 639-2. The large number of living languages in the initial inventory of ISO 639-3 beyond those already included in ISO 639-2 was derived primarily from Ethnologue (15th edition). Additional extinct, ancient, historic, and constructed languages have been obtained from Linguist List.SIL International has been designated as the ISO 639-3/RA for the purpose of processing requests for alpha-3 language codes comprising the International Standard, Codes for the representation of names of languages - Part 3: Alpha-3 code for comprehensive coverage of languages. The ISO 639-3/RA receives and reviews applications for requesting new language codes and for the change of existing ones according to criteria indicated in the standard. It maintains an accurate list of information associated with registered language codes which can be viewed on or downloaded from this website, and processes updates of registered language codes. Notification of pending and adopted updates are also distributed on a regular basis to subscribers and other parties.",2009/12/23 12:00:00,2009/12/23 12:00:00,2009/12/23 02:00:20,,UV
1.0.639.1,iso639-1,ISO 639-1: Codes for the representation of names of languages -- Part 1: Alpha-2 code,William Ted,Klein,masked,,International Organization for Standardization (ISO),"ISO Central SecretariatInternational Organization for Standardization (ISO)1, ch. de la Voie-CreuseCase postale 56CH-1211 Geneva 20Switzerland ",+41 22 749 01 11,masked,ISO Central Secretariat,International Organization for Standardization (ISO),"ISO Central SecretariatInternational Organization for Standardization (ISO)1, ch. de la Voie-CreuseCase postale 56CH-1211 Geneva 20Switzerland ",+41 22 749 01 11,noone@noemail.org,http://www.iso.org/iso/home.htm,SDO,,Ext,,,6,Complete,1.0.639.1,ISO,"This part of ISO 639 provides a code consisting of language code elements comprising two-letter language identifiers for the representation of names of languages. The language identifiers according to this part of ISO 639 were devised originally for use in terminology, lexicography and linguistics, but may be adopted for any application requiring the expression of language in two-letter coded form, especially in computerized systems. The alpha-2 code was devised for practical use for most of the major languages of the world that are not only most frequently represented in the total body of the world's literature, but which also comprise a considerable volume of specialized languages and terminologies. Additional language identifiers are created when it becomes apparent that a significant body of documentation written in specialized languages and terminologies exists. Languages designed exclusively for machine use, such as computer-programming languages, are not included in this code.The code set is available from http://www.iso.org/iso/iso_catalogue/catalogue_ics/catalogue_detail_ics.htm?csnumber=22109&ICS1=1&ICS2=140&ICS3=20",2009/12/23 12:00:00,2009/12/23 12:00:00,2009/12/23 04:12:57,,UV
1.0.639.2,iso639-2,ISO 639-2: Codes for the representation of names of languages -- Part 2: Alpha-3 code,William Ted,Klein,masked,,International Organization for Standardization (ISO),"ISO Central SecretariatInternational Organization for Standardization (ISO)1, ch. de la Voie-CreuseCase postale 56CH-1211 Geneva 20Switzerland ",+41 22 749 01 11,masked,ISO Central Secretariat,International Organization for Standardization (ISO),"ISO Central SecretariatInternational Organization for Standardization (ISO)1, ch. de la Voie-CreuseCase postale 56CH-1211 Geneva 20Switzerland ",+41 22 749 01 11,noone@noemail.org,http://www.iso.org/iso/home.htm,SDO,,Ext,,,6,Complete,1.0.639.2,ISO,"Codes for the representation of names of languages, 3 character alphabetic codes. This has been superceded by ISO 639-3 for many purposes. ISO 639-2 was released in 1998. The code set is available from http://www.iso.org/iso/iso_catalogue/catalogue_tc/catalogue_detail.htm?csnumber=4767",2009/12/23 12:00:00,2009/12/23 12:00:00,2009/12/23 04:14:32,,UV
2.16.840.1.113883.6.287,rxTerms,RxTerms,William Ted,Klein,masked,Kin Wah Fung,Kin Wah Fung,"National Library of Medicine8600 Rockville PikeBethesda, MD 20894",301-435-3151,masked,Staff Scientist,National Library of Medicine,"8600 Rockville PikeBethesda, MD 20894",301-435-3151,custserv@nlm.nih.gov,http://wwwcf.nlm.nih.gov/umlslicense/rxtermApp/rxTerm.cfm,Govt body,,Int,,,6,Complete,,HL7,"RxTerms is a drug interface terminology derived from RxNorm for prescription writing or medication history recording (e.g. in e-prescribing systems, PHRs). The advantages of RxTerms are:"" Free to use."" Directly links to RxNorm, the U.S. drug terminology standard, and facilitates inclusion of RxNorm identifiers in electronic health records."" Efficient data entry - RxTerms separates the full names in RxNorm into two parts: drug name + route (e.g. INDERAL (Oral-pill)) and strength + dose form (e.g. 80 MG Tabs) to avoid big picklists with excessively long names. It excludes drugs from RxNorm that are obsolete or unavailable in the U.S."" User-friendly features - commonly used synonyms and abbreviations (e.g. HCTZ for hydrochlorothiazide), ""tall man"" lettering recommended by FDA to avoid medication errors (e.g. ChlorproMAZINE and ChlorproPAMIDE)."" Good coverage - retains the broad coverage of RxNorm for U.S. prescribable drugs - 99% coverage of both generic and brand names of U.S. most commonly prescribed drugs. RxTerms is tailored for U.S. prescribing and it might not be the right choice for many non-U.S. countries.RxNorm is the designated US Federal drug terminology standard. RxTerms provides an easy way to facilitate the generation of RxNorm codes by the efficient capture of prescription information. Version reporting method YYYYMM e.g. RxTerms-200911 RxTerms is updated monthly, in synch with the monthly full release of RxNorm",2010/01/11 12:00:00,2010/01/11 12:00:00,2010/01/11 02:30:17,,UV
2.16.840.1.113883.4.341,vichAnimalType,VICH Animal Type,Ted,Klein,masked,,"Yiying (CoCo) Tsai, PharmD, MPH ","U.S. Food and Drug Administration 5600 Fishers Lane, Rm 12-81 Rockville, MD 20857 ",+1 301-827-2297,masked,"LT, U.S. Public Health Service ",Veterinary International Conference on Harmonisation (VICH),"c/o IFAHInternational Federation for Animal HealthRue Defacqz 1-1000Brussels, Belgium",+32-2-5437572,sec@vichsec.org,http://www.vichsec.org/,Govt body,,Ext,,,6,Complete,2.16.840.1.113883.4.341,HL7 International,"VICH has created their own reference list for animal types. This list will be used to identify their animal species in Individual Case Safety Reports (ICSR). This list will be used for valid vocabulary bindings for the new ICSR Animal Type vocabulary concept domain. Since this list does not follow a standard naming or scientific convention, the list is expected to be used only for regulated reporting between VICH parties.",2010/03/19 12:00:00,2010/10/01 12:00:00,2010/10/01 05:19:12,,UV
2.16.840.1.113883.6.288,fdbHICL-SEQNO,First DataBank Ingredient List Identifier,Mili,Gera,masked,Thomas R. Bizzaro,Thomas R. Bizzaro,"First DataBank, Inc.500 East 96th Street, Suite 500Indianapolis, IN 46240USA",+1 317-571-7247,masked,"Vice President, Health Policy and Industry Relations","First DataBank, Inc.","First DataBank, Inc.South San Francisco, CA Corporate Headquarters701 Gateway Blvd., Suite 600So. San Francisco, CA 94080USA",+1 317-571-7247,tom_bizzaro@firstdatabank.com,http://www.firstdatabank.com/,Vendor,,Int,,,6,Complete,,,"The Ingredient List Identifier (Formerly called The Hierarchical Ingredient Code List Sequence Number) is a six character numeric identifier that represents a unique combination of active ingredients, irrespective of the manufacturer, package size, dosage form, route of administration, or strength.",2010/04/04 12:00:00,2010/04/04 12:00:00,2010/04/04 12:05:05,,UV
2.16.840.1.113883.6.289,fdbHIC4,Hierarchical Base Ingredient Code,Mili,Gera,masked,Thomas R. Bizzaro,Thomas R. Bizzaro,"First DataBank, Inc.500 East 96th Street, Suite 500Indianapolis, IN 46240USA",+1 317-571-7247,masked,"Vice President, Health Policy and Industry Relations","First DataBank, Inc.","South San Francisco, CA Corporate Headquarters701 Gateway Blvd., Suite 600So. San Francisco, CA 94080",+1 317-571-7247,tom_bizzaro@firstdatabank.com,http://www.firstdatabank.com/,Vendor,,Int,,,6,Complete,,HL7,The HIC4 (Hierarchical Base Ingredient Code) is a four-character alphanumeric column that represents the base active ingredient without salt ester. The HIC4 uses the active ingredients HIC3 as its base value then adds a unique fourth character to complete the Base Ingredient Code. Note: The HIC4 is now deprecated and is superceded by the HIC4_SEQN: a dumb number and a stable identifier that represents a Hierarchical Base Ingredient Code.,2010/05/05 12:00:00,2010/05/05 12:00:00,2010/05/05 12:30:19,,UV
2.16.840.1.113883.6.290,abcCodabar,ABC Codabar,Robert,Hausam MD,masked,Dan Pollock,"Daniel A. Pollock, M.D.","Daniel A. Pollock, M.D.Surveillance Branch ChiefDivision of Healthcare Quality PromotionNational Center for Preparedness, Detection, and Control of Infectious DiseasesCenters for Disease Control and PreventionMail Stop A24 Atlanta, GA 30333",(404) 639-4237,masked,"Surveillance Branch Chief, DHQP",AABB,"AABB8101 Glenbrook RoadBethesda, MD 20814-2749",(301) 907-6977,aabb@aabb.org,http://www.aabb.org,Prof Soc,,Int,,,6,Complete,,HL7 International,"ABC Codabar is a coding system for blood products (components). It was originally created by the American Blood Commission (ABC) (now defunct). The current list of ABC Codabar blood product codes is published by AABB (formerly American Association of Blood Banks). This list of blood product codes is no longer regularly maintained, and is incomplete according to current blood banking practice standards. It is intended to be replaced throughout the blood banking industry by the newer coding system ISBT 128. In some cases, however, the older ABC Codabar identifiers may still be issued and therefore may be required to be used in blood bank messaging (V2, V3) or hemovigilance reporting (CDA).",2010/06/28 12:00:00,2010/10/08 12:00:00,2010/10/08 03:08:36,,UV
2.16.840.1.113883.13.80,mDNID,Medi-Span Drug Name Identifier,Laura,Gibson,masked,Karen Eckert,Laura Gibson,"Wolters Kluwer Health -- Medi-Span8425 Woodfield Crossing Blvd.Suite 490Indianapolis, IN 46240",317-705-7616,masked,Product Manager,Wolters Kluwer Health -- Medi-Span,"Wolters Kluwer Health -- Medi-Span8425 Woodfield Crossing Blvd.Suite 490Indianapolis, IN 46240",317-705-7616,laura.gibson@wolterskluwer.com,http://www.medispan.com,Vendor,,Int,,,6,Complete,,,"Medi-Span Drug Name Identifier (DNID) that represents the drug name. The description that is represented by the DNID is the same as the name portion of the Medi-Span Drug Descriptor ID (DDID). Can be used in CPOE, e-prescribing, or other applications where a drug name is needed, but other attributes such as the dosage form, route of administration, or strength are not required.",2010/08/26 12:00:00,2010/11/04 12:00:00,2010/11/04 02:05:54,,UV
2.16.840.1.113883.13.81,mRDID,Medi-Span Routed Drug Identifier,Laura,Gibson,masked,Karen Eckert,Laura Gibson,"Wolters Kluwer Health -- Medi-Span8425 Woodfield Crossing BlvdSuite 490Indianapolis, IN 46240",317-705-7616,masked,Product Manager,Wolters Kluwer Health -- Medi-Span,"Wolters Kluwer Health -- Medi-Span8425 Woodfield Crossing BlvdSuite 490Indianapolis, IN 46240",317-705-7616,laura.gibson@wolterskluwer.com,http://www.medispan.com,Vendor,,Int,,,6,Complete,,,"Medi-Span Routed Drug Identifier (RDID) represents the routed drug. The description that is represented by the RDID includes the drug name and the route of administration. It is the same as the name and route portion of the Medi-Span Drug Descriptor ID (DDID). Can be used in CPOE, e-prescribing, or other applications where a routed drug is needed, but other attributes such as the dosage form or strength are not required.",2010/08/26 12:00:00,2010/11/04 12:00:00,2010/11/04 02:09:04,,UV
1.3.6.1.4.1.19376.1.8.2.1,pathLex,PathLex Anatomic Pathology Lexicon,William Ted,Klein,masked,Christel Daniel,Christel Daniel,,+33 60 484133,masked,Professor Associate,IHE Anatomic Pathology,15 Rue de l'ecole du Medicine75006 Paris France,+33 60 484133,christel.daniel@crc.jussieu.fr,,Academic,,Ext,6,,6,Complete,1.3.6.1.4.1.19376.1.8.2.1,HL7,"The PathLex project is launched by IHE and HL7 Anatomic Pathology, with the collaboration of other Anatomic Pathology organizations, including the College of American Pathologists, the French Society of Pathologists and the SEAP (Spanish Society of Pathology). The purpose and scope of the PathLex project is very similar to those of the RadLex project in the radiology domain. The Pathlex project has been designed to satisfy the needs of Anatomic Pathology information system vendors and users by adopting the best features of existing terminology systems, while producing new terms to fill critical gaps. Rather than re-inventing the wheel , PathLex unifies and supplements other terminology systems , such as SNOMED-CT, CIM-O or various vocablary tables defined by DICOM and HL7.",2010/10/04 12:00:00,2010/10/04 12:00:00,2010/10/04 05:16:53,na,UV
2.16.840.1.113883.3.26.1.6.1,caCISTerminologyCodes,caCISTerminologyCodes codeSystem,Cecil,Lynch,masked,,Cecil Lynch,"6500 Countrywoods LaneGranite Bay, CA 95746",916-412-5504,masked,NCI Chief Semantic Architect,NCI,"2115 E Jefferson St. Suite 6000 Rockville, MD 20852",301-451-4384,ncicb@pop.nci.nih.gov,http://ncicb.nci.nih.gov,Govt body,,Ext,,,6,Complete,2.16.840.1.113883.3.26.1.6.1,US National Cancer Institute,A codeSystem under the NCI CBIIT root used to define concepts for the NCI Cancer Clinical Information Suite (caCIS). The purpose of the codeSystem is to derive valueSets that have no concepts found in any other formal coding system.,2010/11/10 12:00:00,2010/11/12 12:00:00,2010/11/12 10:17:52,,UV
2.16.840.1.113883.6.291,cLIAInVitroDiagnosticsDatabase,Clinical Laboratory Improvement Amendments (CLIA) InVitro Diagnostics Database,Cecil,Lynch,masked,,Cecil Lynch,"6500 Countrywoods LaneGranite Bay, CA 95746",916-412-5504,masked,NCI Chief Semantic Architect,NCI,"2115 E Jefferson St. Suite 6000 Rockville, MD 20852",301-451-4384,ncicb@pop.nci.nih.gov,http://ncicb.nci.nih.gov,Govt body,,Int,,,6,Complete,,HL7 International,"This database contains the commercially marketed in vitro test systems categorized by the FDA since January 31, 2000 and tests categorized by the Centers for Disease Control and Prevention (CDC) prior to that date. The code value is the Test_System_ID which is a unique identifier for a test based on the test system, analyte and categorization. The database is updated monthly.",2010/12/15 12:00:00,2010/12/30 12:00:00,2010/12/30 08:40:51,,UV
2.16.840.1.113883.6.292,whoDDType,WHO Drug Dictionary Type,Ola,Strandberg,masked,,Ola Strandberg,Uppsala Monitoring CentreBox 1051SE-751 40 UppsalaSweden,+46 18 65 60 60,masked,Vendor Liaison Officer,Uppsala Monitoring Centre,Box 1051SE-751 40 UppsalaSweden,,info@umc-products.com,http://www.umc-products.com/,SDO,,Int,,,6,Complete,,,"The type of drug dictionary (e.g. WHO Drug Dictionary Enhanced, WHO Herbal Dictionary).",2011/02/23 12:00:00,2011/03/31 12:00:00,2011/03/31 08:53:55,,UV
2.16.840.1.113883.6.293,whoDDEdition,WHO Drug Dictionary Edition,Ola,Strandberg,masked,,Ola Strandberg,Uppsala Monitoring CentreBox 1051SE-751 40 UppsalaSweden,+46 18 65 60 60,masked,Vendor Liaison Officer,Uppsala Monitoring Centre,Box 1051SE-751 40 UppsalaSweden,,ola.strandberg@umc-products.com,http://www.umc-products.com/,SDO,,Int,,,6,Complete,,,The edition of the WHO Drug Dictionary (e.g. 201101).,2011/02/23 12:00:00,2011/03/31 12:00:00,2011/03/31 08:55:18,,UV
2.16.840.1.113883.6.294,whoDDMedProdId,WHO Drug Dictionary Medicinal Product ID,Ola,Strandberg,masked,,Magnus Wallberg,Uppsala Monitoring CentreBox 1051SE-751 40 UppsalaSweden,+46 18 65 60 60,masked,,Uppsala Monitoring Centre,Box 1051SE-751 40 UppsalaSweden,,info@who-umc.org,http://www.who-umc.org/,SDO,,Int,,,6,Complete,,,A unique identifier for a detailed entry in the WHO Drug Dictionary.,2011/02/23 12:00:00,2011/03/31 12:00:00,2016/12/14 07:23:14,,UV
2.16.840.1.113883.6.295,whoDDPharmForm,WHO Drug Dictionary Pharmaceutical Form,Ola,Strandberg,masked,,Ola Strandberg,Uppsala Monitoring CentreBox 1051SE-751 40 UppsalaSweden,+46 18 65 60 60,masked,Vendor Liaison Officer,Uppsala Monitoring Centre,Box 1051SE-751 40 UppsalaSweden,,info@umc-products.com,http://www.umc-products.com/,SDO,,Int,,,6,Complete,,,List of pharmaceutical forms for the WHO Drug Dictionary.,2011/02/23 12:00:00,2011/03/31 12:00:00,2011/03/31 09:01:05,,UV
2.16.840.1.113883.6.296,whoDDReference,WHO Drug Dictionary Validation Reference,Ola,Strandberg,masked,,Ola Strandberg,Uppsala Monitoring CentreBox 1051SE-751 40 UppsalaSweden,+46 18 65 60 60,masked,,Uppsala Monitoring Centre,Box 1051SE-751 40 UppsalaSweden,,info@umc-products.com,http://www.umc-products.com/,SDO,,Int,,,6,Complete,,,The reference used to validate the information about an entry in the WHO Drug Dictionary.,2011/02/23 12:00:00,2011/03/31 12:00:00,2011/03/31 09:03:26,,UV
2.16.840.1.113883.6.297,whoDDSDG,WHO Drug Dictionary Standard Drug Grouping,Ola,Strandberg,masked,,Ola Strandberg,Uppsala Monitoring CentreBox 1051SE-751 40 UppsalaSweden,+46 18 65 60 60,masked,,Uppsala Monitoring Centre,Box 1051SE-751 40 UppsalaSweden,,info@umc-products.com,http://www.umc-products.com/,SDO,,Int,,,6,Complete,,,A Standard Drug Grouping in the WHO Drug Dictionary Enhanced.,2011/02/23 12:00:00,2011/03/31 12:00:00,2011/03/31 09:04:38,,UV
2.16.840.1.113883.6.298,whoDDSDGScope,WHO Drug Dictionary Standard Drug Grouping Scope,Ola,Strandberg,masked,,Ola Strandberg,Uppsala Monitoring CentreBox 1051SE-751 40 UppsalaSweden,+46 18 65 60 60,masked,,Uppsala Monitoring Centre,Box 1051SE-751 40 UppsalaSweden,,info@umc-products.com,http://www.umc-products.com/,SDO,,Int,,,6,Complete,,,List of scopes for SDGs in the WHO Drug Dictionary.,2011/02/23 12:00:00,2011/03/31 12:00:00,2011/03/31 09:05:48,,UV
2.16.840.1.113883.6.73.1,whoATCLevel1,WHO Anatomical Therapeutic Chemical Classification Level 1 Code ,Ola,Strandberg,masked,,Ola Strandberg,Uppsala Monitoring CentreBox 1051SE-751 40 UppsalaSweden,+46 18 65 60 60,masked,,Uppsala Monitoring Centre,Box 1051SE-751 40 UppsalaSweden,,info@umc-products.com,http://www.umc-products.com/,SDO,,Ext,,,6,Complete,2.16.840.1.113883.6.73.1,HL7 International,WHO Anatomical Therapeutic Chemical Classification Level 1 Code. ,2011/02/23 12:00:00,2011/03/31 12:00:00,2011/03/31 09:08:55,,UV
2.16.840.1.113883.6.73.2,whoATCLevel2,WHO Anatomical Therapeutic Chemical Classification Level 2 Code,Ola,Strandberg,masked,,Ola Strandberg,Uppsala Monitoring CentreBox 1051SE-751 40 UppsalaSweden,+46 18 65 60 60,masked,,Uppsala Monitoring Centre,Box 1051SE-751 40 UppsalaSweden,,info@umc-products.com,http://www.umc-products.com/,SDO,,Ext,,,6,Complete,2.16.840.1.113883.6.73.2,HL7 International,WHO Anatomical Therapeutic Chemical Classification Level 2 Code.,2011/02/23 12:00:00,2011/03/31 12:00:00,2011/03/31 09:10:26,,UV
2.16.840.1.113883.6.73.3,whoATCLevel3,WHO Anatomical Therapeutic Chemical Classification Level 3 Code ,Ola,Strandberg,masked,,Ola Strandberg,Uppsala Monitoring CentreBox 1051SE-751 40 UppsalaSweden,+46 18 65 60 60,masked,,Uppsala Monitoring Centre,Box 1051SE-751 40 UppsalaSweden,,info@umc-products.com,http://www.umc-products.com/,SDO,,Ext,,,6,Complete,2.16.840.1.113883.6.73.3,HL7 International,WHO Anatomical Therapeutic Chemical Classification Level 3 Code ,2011/02/23 12:00:00,2011/03/31 12:00:00,2011/03/31 09:11:21,,UV
2.16.840.1.113883.6.73.4,whoATCLevel4,WHO Anatomical Therapeutic Chemical Classification Level 4 Code ,Ola,Strandberg,masked,,Ola Strandberg,Uppsala Monitoring CentreBox 1051SE-751 40 UppsalaSweden,+46 18 65 60 60,masked,,Uppsala Monitoring Centre,Box 1051SE-751 40 UppsalaSweden,,info@umc-products.com,http://www.umc-products.com/,SDO,,Ext,,,6,Complete,2.16.840.1.113883.6.73.4,HL7 International,WHO Anatomical Therapeutic Chemical Classification Level 4 Code. ,2011/02/23 12:00:00,2011/03/31 12:00:00,2011/03/31 09:13:42,,UV
2.16.840.1.113883.6.73.5,whoATCLevel5,WHO Anatomical Therapeutic Chemical Classification Level 5 Code ,Ola,Strandberg,masked,,Malin Jakobsson,Uppsala Monitoring CentreBox 1051SE-751 40 UppsalaSweden,+46 18 65 60 60,masked,,Uppsala Monitoring Centre,Box 1051SE-751 40 UppsalaSweden,,info@who-umc.org,http://www.who-umc.org/,SDO,,Ext,,,6,Complete,2.16.840.1.113883.6.73.5,HL7 International,WHO Anatomical Therapeutic Chemical Classification Level 5 Code. ,2011/02/23 12:00:00,2011/03/31 12:00:00,2016/05/17 03:33:20,,UV
2.16.840.1.113883.6.299,iscn,The International System for Human Cytogenetic Nomenclature ,Yan,Heras,masked,,Yan Heras,"PO Box 177, 3611 Route 5East Thetford, VT 05043",801-663-9209,masked,,International Standing Committee on Human Cytogenetic Nomenclature,"Current Chair the International Standing Committee on Human Cytogenetic Nomenclature (publisched ISCN 2009)Lisa G. ShafferSignature Genomic LaboratoriesSpokane, Washington, USA.",,info@signaturegenomics.com,,Prof Soc,,Int,,,6,Complete,,HL7 International,"The International System for Human Cytogenetic Nomenclature (ISCN) was created by the International Standing committee on Human Cytogenetic Nomenclature to represent the outcome of cytogenetic tests. ISCN specifies the nomenclature to describe karyotypes, chromosome abnormalities, in situ hybridization, etc. ISCN provides a list of symbols and abbreviated terms in adjunction with a set of rules, which can be used in the description of chromosomes and chromosome abnormalities, such as p for short arm of chromosome, q for long arm of chromosome, cen for centromere, del for deletion, ish for in situ hybridization, and plus sign (+) for gain, etc. A LOINC code is created to represent ""chromosome analysis results in ISCN expression"". In HL7 v2 messages, this LOINC code is used in OBX-3 with a coded result (CWE data type) that will be sent in OBX-5. The value of the coded result is an ISCN expression, and ISCN will be the code system for the coded result. Versioning is identified by the year of publication of the ISCN. The latest version is ISCN 2009. Previous publications include ISCN 2005, ISCN 1995, and ISCN 1985, etc.",2011/03/14 12:00:00,2011/04/15 12:00:00,2011/04/15 06:51:51,,UV
2.16.840.1.113883.6.300,naic-CoCode-cs,NAIC Company Code-code set,Durwin,Day,masked,,Durwin Day,,312-653-5948,masked,,William Todd Sells,"William Todd Sells National Association of Insurance Commissioners2301 McGee St., Ste. 800Kansas City, MO 64108",816-783-8403,tsells@naic.org,https://eapps.naic.org/cis/,Govt body,,Int,,,6,Complete,,HL7 International,The National Association of Insurance Commissioners issues the NAIC Company code (sometimes called ""NAIC Number"" or ""cocode"") for payers. Health plans obtain number by completing the Company Code Application. The NAIC Company Codes can be found by a company and state look-up at https://eapps.naic.org/cis/. For questions regarding cocodes please call NAIC at: 816-783-8600,2011/03/14 12:00:00,2011/04/15 12:00:00,2011/04/15 06:54:09,,US
2.16.840.1.113883.6.301,nubc-UB-04-Manual-cs,nubc-UB-04-Manual-code set,Durwin,Day,masked,"Lenel James, BCBSA",Durwin Day,,312-653-5948,masked,HL7 P2PPHR CCD IG co-lead,George Arges,"George ArgesChair, National Uniform Billing CommitteeSenior Director - Health Data Management GroupAmerican Hospital Association155 N. Wacker Drive, Suite 400Chicago, IL 60606-1725",312-422-3398,garges@aha.org,http://www.nubc.org/become.html,SDO,,Int,14,,6,Complete,,HL7,"The National Uniform Billing Committee (NUBC) is a voluntary committee whose work is coordinated through the offices of the American Hospital Association (AHA). The AHA's Health Data Management Group serves as chair and secretary to the NUBC. NUBC includes the participation of all the major national provider and payer organizations. The NUBC was formed to develop a single billing form and standard data set that could be used nationwide by institutional providers and payers for handling health care claims, the current UB-04 manual.In determining the data to be included, the NUBC strives to balance the need for the information against the burden of providing that information. In essence it applies the administrative simplification principles mentioned in the recently enacted Health Insurance Portability and Accountability Act of 1996 (HIPAA). Data elements identified as necessary for claims processing are, in most cases, assigned designated spaces on the form. The designated spaces are referred to as Form Locators and each one has a unique number. The current UB-04 data specifications manual seeks to identify the national requirements for preparing Medicare, Medicaid, OCHAMPUS, BCBS, and commercial insurance claims. The UB-04 manual with the codes is available by subscriptionfrom NUBC at http://www.nubc.org/become.html",2011/03/15 12:00:00,2011/03/23 12:00:00,2011/03/23 08:57:52,,US
2.16.840.1.113883.6.301.1,nubc-TypeOfBill-cs,NUBC Type Of Bill-value set-code set,Durwin,Day,masked,"Lenel James, BCBSA",Durwin Day,,312-653-5948,masked,HL7 P2PPHR CCD IG co-lead,George Arges,"George ArgesChair, National Uniform Billing CommitteeSenior Director - Health Data Management GroupAmerican Hospital Association155 N. Wacker Drive, Suite 400Chicago, IL 60606-1725",312-422-3398,garges@aha.org,http://www.nubc.org/become.html,SDO,,Ext,,,6,Complete,2.16.840.1.113883.6.301.1,HL7 International,"National Uniform Billing Committee (NUBC) UB-04 manual, UB form locator 04, thetype of bill code - claim code indicating the type of facility where services wereperformed. The UB-04 manual with the codes is available by subscriptionfrom NUBC at http://www.nubc.org/become.html",2011/03/15 12:00:00,2011/04/19 12:00:00,2011/04/19 12:41:46,,US
2.16.840.1.113883.6.301.2,nubc-TypeOfBillFrequency-cs,NUBC Type Of Bill Frequency-code set,Durwin,Day,masked,"Lenel James, BCBSA",Durwin Day,,312-653-5948,masked,HL7 P2PPHR CCD IG co-lead,George Arges,"George ArgesChair, National Uniform Billing CommitteeSenior Director - Health Data Management GroupAmerican Hospital Association155 N. Wacker Drive, Suite 400Chicago, IL 60606-1725",312-422-3398,garges@aha.org,http://www.nubc.org/become.html,SDO,,Ext,,,6,Complete,2.16.840.1.113883.6.301.2,HL7 International,"National Uniform Billing Committee (NUBC) UB-04 manual, UB form locator 04, thetype of bill frequency code - claim code specifying the frequency of the claim. The UB-04 manual with the codes is available by subscription from NUBC athttp://www.nubc.org/become.html",2011/03/15 12:00:00,2011/04/19 12:00:00,2011/04/19 12:44:53,,US
2.16.840.1.113883.6.301.3,nubc-ServiceLineRevenue-cs,NUBC Service Line Revenue-cs,Durwin,Day,masked,"Lenel James, BCBSA",Durwin Day,,312-653-5948,masked,HL7 P2PPHR CCD IG co-lead,George Arges,"George ArgesChair, National Uniform Billing CommitteeSenior Director - Health Data Management GroupAmerican Hospital Association155 N. Wacker Drive, Suite 400Chicago, IL 60606-1725",312-422-3398,garges@aha.org,http://www.nubc.org/become.html,SDO,,Ext,,,6,Complete,2.16.840.1.113883.6.301.3,HL7 International,"Code system of concepts specifying a revenue code as specified in the National Uniform Billing Committee (NUBC) UB-04 manual, UB form locator 42, the service line revenue code. These are claim codes indicating the identifying number for the product or service provided. The UB-04 Data Specifications Manual with the codes is available by subscription from NUBC at http://www.nubc.org/become.html. Used in HL7 Version 2.x messaging in the Revenue Code (GP1) value. Updated by NUBC annually; see the coding instructions for more detail.",2011/03/15 12:00:00,2011/04/19 12:00:00,2011/04/19 12:47:50,HL70456,US
2.16.840.1.113883.6.301.4,nubc-AdmissionSource-cs,NUBC Admission Source-code set,Durwin,Day,masked,"Lenel James, BCBSA",Durwin Day,,312-653-5948,masked,HL7 P2PPHR CCD IG co-leadOKEN=53,George Arges,"George ArgesChair, National Uniform Billing CommitteeSenior Director - Health Data Management GroupAmerican Hospital Association155 N. Wacker Drive, Suite 400Chicago, IL 60606-1725",312-422-3398,garges@aha.org,http://www.nubc.org/become.html,SDO,,Ext,,,6,Complete,2.16.840.1.113883.6.301.4,HL7 International,"National Uniform Billing Committee (NUBC) UB-04 manual, UB form locator 15, theadmission source code - claim code indicating the source of the admission. The UB-04manual with the codes is available by subscription from NUBC at http://www.nubc.org/become.html",2011/03/15 12:00:00,2011/04/19 12:00:00,2011/04/19 12:48:44,,US
2.16.840.1.114222.4.5.305,orgUnit-PHLIP,Organization Unit codes PHLIP,Riki,Merrick,masked,Sundak Ganesan,Riki Merrick,P.O. Box 2541CarmichaelCA 95609-2541,916.216.0052,masked,PH information specialist - contractor to APHL,Association of Public Health Laboratories,"8515 Georgia Avenue, Suite 700Silver SpringMD 20910",240.485.2745,phlip@aphl.org,http://www.aphl.org,Prof Soc,2.16.840.1.114222.4.1.213475,Ext,,,6,Complete,2.16.840.1.114222.4.5.305,Association of Public Health Laboratories,"An external code system, which is an extension of the Organization unit table HL70406.",2011/05/12 12:00:00,2011/05/30 12:00:00,2011/05/30 10:46:33,,US
2.16.840.1.114222.4.5.304,role-PHLIP,Role codes for PHLIP,Riki,Merrick,masked,Sundak Ganesan,Riki Merrick,P.O. Box 2541CarmichaelCA 95609-2541,916.216.0052,masked,PH information specialist - contractor to APHL,Association of Public Health Laboratories,"8515 Georgia Avenue, Suite 700Silver SpringMD 20910",240.485.2745,phlip@aphl.org,http://aphl.org,Prof Soc,2.16.840.1.114222.4.1.213475,Ext,,,6,Complete,2.16.840.1.114222.4.5.304,Association of Public Health Laboratories,"An external code system, which is an extension of the Organization Unit table HL7043.",2011/05/12 12:00:00,2011/05/30 12:00:00,2011/05/30 10:51:54,,US
2.16.840.1.114222.4.5.306,salmSerovar-CDC,Salmonella codes for serovar and formula CDC,Riki,Merrick,masked,Sundak Ganesan,Riki Merrick,P.O. Box 2541CarmichaelCA 95609-2541,916.216.0052,masked,PH information specialist - contractor to APHL,Association of Public Health Laboratories,"8515 Georgia Avenue, Suite 700Silver SpringMD 20910",240.485.2745,phlip@aphl.org,http://www.aphl.org,Prof Soc,2.16.840.1.114222.4.1.213475,Ext,,,6,Complete,2.16.840.1.114222.4.5.306,Association of Public Health Laboratories,"Will contain the Formula codes identifying the serovar formula for a specific Salmonella isolate and serovar codes, identifying the respective serovar names. CDC Salmonella lab is working with IHTSDO to find a more proper way of representing the formulas and serovars in SNOMED. This coding system is being used until that task has been accomplished. Formula codes are prefaced with an F and up to 19 numbers. Serovar codes are prefaced with an S and up to 19 numbers.",2011/05/12 12:00:00,2011/05/30 12:00:00,2011/05/30 10:54:18,,US
2.16.840.1.113883.6.302,un-sp-sc,United Nations Standard Products and Services Code,Jane,Daus,masked,,Jane Daus,"1400 S Wolf RoadWheeling, IL 60090",8474951289,masked,Business Functional Analyst,UNSPSC,,,info@unspsc.org,http://www.unspsc.org/Defaults.asp,Prof Soc,,Int,6,,6,Complete,,HL7 International,"The United Nations Standard Products and Services Code® (UNSPSC®) provides an open, global multi-sector standard for efficient, accurate classification of products and services. ",2011/07/25 12:00:00,2011/07/26 12:00:00,2011/07/26 07:47:34,UNSPSC,UV
2.16.840.1.113883.3.567.12.1,fdbMEDID,fdb Medication ID,George,Robinson,masked,Mili Gera,George Robinson,"First Databankc, Inc500 East 96th Street, Suite 500Indianapolis, IN 46240",317.571.7390,masked,Product Manager,"First Databank, Inc","701 Gateway Boulevard, Suite 400South San Francisco, CA 94080",800.633.3453,cc@firstdatabank.com,http://www.firstdatabank.com/,Vendor,2.16.840.1.113883.3.567,Ext,15,,6,Complete,2.16.840.1.113883.3.567.12.1,firstDataBank,"An eight-character numeric column that identifies the unique combination of product or generic name, route of administration, dosage form, strength, and strength unit-of-measure. It is the most specific name concept in NDDF Plus. This number is a stable identifier.Examples of its use include outpatient prescribing and patient medication profiling. In contrast to the inpatient setting, outpatient prescribing must be specific as to dosage form and strength. Attributes of the MEDID provide drug information and access to clinical and patient education modules within NDDF Plus.The fdbMEDID is the primary clinical drug concept distributed by FDB that is used to represent the clinical drug when prescribing, ordering or when generating a list of active patient medications. It spans both generically named and branded concepts and is very analogous to the RxNorm ""Semantic Brand Drug"" (SBD) and the RxNorm ""Semantic Clinical Drug"". In the context of HL7, the fdbMEDID would most likely be used when compiling a structured medication component for the CCD record. For stage 1 Meaningful Use, the fdbMEDID may be used to report the coded medication in the absence of an RxNorm code; for stage 2, it is likely that the fdbMEDID will be sent as a ""translation Code"" to represent the code associated to the value selected by the end user in the application as a companion to the ""interoperable Code"" which most likely will be RxNorm based.Within the HL7 CDA Medications Section, the fdbMEDID may be used to identify the enterprise coded medication value used in the context of a ""history of medication use,"" ""medications administered,"" or ""active medications"" (e.g., ""coded product name,"" ""coded brand name"").Within the HL7 CDA Allergy/Drug-Sensitivity Section, may be used to identify the enterprise coded medication value when used in the context of a ""product coded"".",2011/11/21 12:00:00,2011/11/21 12:00:00,2011/11/22 09:31:40,,US
2.16.840.1.113883.6.303,fdaProductClassificationSystem,FDA Product Classification System,William,Hess,masked,,William A. Hess,Food and Drug Administration10903 New Hampshire AveWO32-Room 4152Silver Spring MD 20993-0002,3017968494,masked,Pharmacist,Food and Drug Administration Data Standards Council,Food and Drug Administration10903 New Hampshire AveWO32-Room 4152Silver Spring MD 20993-0002,3017968494,william.hess@fda.hhs.gov,http://www.fda.gov/ForIndustry/DataStandards/default.htm,Govt body,,Int,,,6,Complete,,HL7 International,The Food and Drug Administration's Product Classification System is responsible for assigning classification concepts to regulated products.,2011/11/22 12:00:00,2011/11/29 12:00:00,2011/11/29 08:46:01,,UV
2.16.840.1.113883.6.304,vis-doc-type,Vaccine Information Sheet document type,Rob,Savage,masked,,Rob,"10 CalumetMadison, WI 53705",Savage,masked,,CDC/IISSB,tbd,tbd,iisinfo@cdc.gov,,Govt body,,Int,6,,6,Complete,,,"Clinicians are required to track the Vaccine Information Sheet (VIS) that was shared with the recipient of a vaccination. There are 3 attributes that must be tracked. 1. VIS type2. VIS version date3. Presentation dateCurrently there are LOINC, which support messaging the version date and presentation date. The CDC has worked with GS1 to develop a Global Document Type Identifier (GDTI) for the purpose of identifying the specific VIS document type. This GDTI will be captured in a bar code. It is composed of the code for the business that owns the document (0886983 for CDC), an application identifier, a document type identifier and a check digit. For our purposes we are only interested in the code for the owner and the document type identifier.",2011/12/28 12:00:00,2011/12/29 12:00:00,2011/12/28 11:14:40,VIS,US
2.16.840.1.113883.6.305,fhir-special-values,FHIR Special Values,Grahame,Grieve,masked,,Grahame Grieve,108 Loughnan RoadRingwood 3134Australia,+61411867065,masked,,Health Intersections Pty/Ltd,,,grahame@healthintersections.com.au,http://www.healthintersections.com.au/fhir/introduction.htm,Vendor,1.2.36.146595217,Int,6,,6,Complete,,HL7 International,The list of special codes defined for use through out FHIR instances.,2012/01/13 12:00:00,2012/02/28 12:00:00,2012/02/28 10:11:03,,UV
2.16.840.1.113883.6.306,fhir-resource-types,FHIR Resource Types,Grahame,Grieve,masked,,Grahame Grieve,108 Loughnan RoadRingwood 3134Australia,+61411867065,masked,,Health Intersections Pty/Ltd,,,grahame@healthintersections.com.au,http://www.healthintersections.com.au/fhir/introduction.htm,Vendor,1.2.36.146595217,Int,,,6,Complete,,HL7 International,The resource types that are defined by the FHIR project.,2012/01/13 12:00:00,2012/02/28 12:00:00,2012/02/28 10:19:23,,UV
2.16.840.1.113883.6.307,fhir-message-events,FHIR Message Events,Grahame,Grieve,masked,,Grahame Grieve,108 Loughnan RoadRingwood 3134Australia,+61411867065,masked,,Health Intersections Pty/Ltd,,,grahame@healthintersections.com.au,http://www.healthintersections.com.au/fhir/introduction.htm,Vendor,1.2.36.146595217,Int,,,6,Complete,,HL7 International,Message events defined by the FHIR project.,2012/01/13 12:00:00,2012/02/28 12:00:00,2012/02/28 10:20:10,,UV
2.16.840.1.113883.6.308,fhir-logical-interactions,FHIR Logical Interactions (REST),Grahame,Grieve,masked,,Grahame Grieve,108 Loughnan RoadRingwood 3134Australia,+61411867065,masked,,Health Intersections Pty/Ltd,,,grahame@healthintersections.com.au,http://www.healthintersections.com.au/fhir/introduction.htm,Vendor,1.2.36.146595217,Int,,,6,Complete,,HL7 International,The logical interactions defined for the RESTful framework in FHIR.,2012/01/13 12:00:00,2012/02/28 12:00:00,2012/02/28 10:21:08,,UV
2.16.840.1.113883.6.309,fhir-data-absent-reason,Data Absent Reason,Grahame,Grieve,masked,,Grahame Grieve,108 Loughnan RoadRingwood 3134Australia,+61411867065,masked,,Health Intersections Pty/Ltd,,,grahame@healthintersections.com.au,http://www.healthintersections.com.au/fhir/introduction.htm,Vendor,1.2.36.146595217,Int,,,6,Complete,,HL7 International,The codes for data absent reason as defined by FHIR.,2012/01/13 12:00:00,2012/02/28 12:00:00,2012/02/28 10:22:03,,UV
2.16.840.1.113883.3.567.12.2,fdbMedNameID,fdb Medication Name ID,George,Robinson,masked,Mili Gera,George Robinson,"First Databankc, Inc500 East 96th Street, Suite 500Indianapolis, IN 46240",317.571.7390,masked,Product Manager,"First DataBank, Inc","701 Gateway Boulevard, Suite 400South San Francisco, CA 94080",800.633.3453,cc@fdbhealth.com,http://www.firstdatabank.com/,Vendor,2.16.840.1.113883.3.567,Ext,15,,6,Complete,2.16.840.1.113883.3.567.12.2,firstDataBank,"An eight-character numeric that identifies a unique product or generic name, primarily used for navigational purposes when presenting name concepts to the end user. This number is a stable identifier. It is the most specific name concept in FDB MedKnowledge (NDDF Plus). This number is a stable identifier.Expamples of its use primary use include end user navigation from a text string to orderable or dispensable medication selection targets. Secondly, the fdbMedNameID may be used within proprietary allergy or drug-sensitivity documentation applications in the context of a medication ""allergen."" For example,the term ""Bactrim"" (fdb MedNameID = 5086) may be selected as a patient medication allergen. When screening prospective medications for potential allergies, ingredients associated to the fdb MedNameID are fetched in support of allergy detection algorithms. In the case of ""Bactrim,"" the ingredients ""trimethoprim"" and ""sulfamethoxazole"" would be fetched as related ingredient allergens.For interoperable medication allergen exchange, branded fdbMedNameID values will be cross-referenced to RxNorm Brand Names (example, ""Bactrim"" = RXCUI 151399, Terminology Type = BN); generically named fdbMedNameID values will be linked to RxNorm ingredients (e.g., Ingredient [IN], Precise Ingrdient [PIN] or Multiple Ingredient {MIN]). In the context of HL7, the fdbMedNameID would most likely be used when compiling a structured medication allergen within the Allergy Observation for a CDA document. Within the United States, it is expected that for brand-name based medication allergens, the RxNorm Brand Name would be exchanged as the interoperable code and the fdbMedNameID would be included as the ""translation Code"" to represent the code associated to term selected by the end user within FDB supported systems. For example:",2012/04/30 12:00:00,2012/05/22 12:00:00,2012/05/22 10:32:56,,UV
2.16.840.1.113883.3.221.5,payer-typology,Source of Payment Typology,Sundak,Ganesan,masked,Hetty Khan,Anna Orlova,"624 N. Broadway Room 382, Baltimore MD 21205",410-614-3463,masked,Executive Director,Public Health Data Standards Consortium,"624 N. Broadway Room 382, Baltimore MD 21205",410-614-3463,aorlova@jhsph.edu,http://phdsc.org/standards/payer-typology.asp,SDO,2.16.840.1.113883.3.221,Ext,6,,6,Complete,2.16.840.1.113883.3.221.5,Public Health Data Standards Consortium,The Source of Payment Typology was developed and is maintained by the Public Health Data Standards Consortium's Payer Type Subcommittee. The purpose of the Payer Typology Subcommittee is to create and refine a standard to allow consistent reporting of payer data to public health agencies for health care services and research.,2012/07/06 12:00:00,2012/07/12 12:00:00,2012/07/12 05:21:52,PHDSCPT,US
2.16.840.1.113883.3.567.12.3,fdbRoutedMedID,fdb Routed Medication ID,George,Robinson,masked,Milli Gera,George Robinson,"First Databankc, Inc500 East 96th Street, Suite 500Indianapolis, IN 46240",317.571.7390,masked,Product Manager,"First DataBank, Inc.","701 Gateway Boulevard, Suite 400South San Francisco, CA 94080",800.633.3453,cc@fdbhealth.com,http://www.fdbhealth.com/,Vendor,2.16.840.1.113883.3.567,Ext,15,,6,Complete,2.16.840.1.113883.3.567.12.3,firstDataBank,An eight-character numeric concept that identifies the product or generic name and route of administration. It is used for navigational purposes or to profile patient medications when the dosage form is unknown or not required. It is also used for entry into some clinical modules. This number is a stable identifier.,2012/07/10 12:00:00,2012/07/12 12:00:00,2012/07/12 06:23:33,,UV
2.16.840.1.113883.6.310,uscic,US Census Industry Code,Sundak,Ganesan,masked,Genny Luensman (CDC NIOSH),Sundak Ganesan,Centers for Disease Control and Prevention2500 Century Parkway Blvd NEAtlantaGA 30329,404-498-6685,masked,Health Scientist / Lead CDC Vocabulary Specialist,U.S. Census Bureau," U.S. Census Bureau Industry and Occupation Statistics Branch 4600 Silver Hill Road Washington, DC 20233",301-763-3239,NAICS@census.gov,http://www.census.gov/hhes/www/ioindex/,Govt body,,Int,6,,6,Complete,,HL7 International,"Alphabetical Indexes of Industries and Occupations were developed primarily for use in classifying a respondent's industry (employer's type of business) and occupation (employee's type of work) as reported in the Census 2000, the Current Population Survey, the American Community Survey, and other demographic surveys conducted by the Census Bureau. They list over 21,000 industry and 31,000 occupation titles in alphabetical order. They are comprehensive lists of specific industries and occupations developed over time and continuously updated through review of census and survey responses.For technical questions related to the Industry and Occupation Classification System, contact the Industry and Occupation Statistics Branch at 301-763-3239.",2012/07/12 12:00:00,2012/07/12 12:00:00,2012/07/12 08:48:07,uscic,US
2.16.840.1.113883.6.311,multum-main-drug-code,Multum Main Drug Code,Hugh,Glover,masked,Terri Meredith,Terri Meredith,"2000 S. Colorado Blvd #11000Denver, CO 80022USA",303-733-4447,masked,Senior Research Project Leader,Cerner Multum,"2000 S. Colorado Blvd #11000Denver, CO 80022USA",303-733-4447,tmeredith@cerner.com,http://www.multum.com,Vendor,2.16.840.1.113883.6.27,Int,6,,6,Complete,,HL7 International,"The Multum Main Drug Code, ""MMDC"", is the long integer identifier for drugs that share the same formulation. The formulation consists of a generic drug name, the strength of the drug product, the route of administration, and the dose form. It is meant to serve as the Multum identifier for a generic drug formulation in HL7 messages.",2012/07/13 12:00:00,2012/07/13 12:00:00,2012/07/13 08:42:36,,UV
2.16.840.1.113883.6.312,multum-drug-synonym-id,Multum Drug Synonym Identifier,Hugh,Glover,masked,Terri Meredith,Terri Meredith,"2000 S. Colorado Blvd #11000Denver, CO 80022USA",303-733-4447,masked,Senior Research Project Leader,Cerner Multum,"2000 S. Colorado Blvd #11000Denver, CO 80022USA",303-733-4447,tmeredith@cerner.com,http://www.multum.com,Vendor,2.16.840.1.113883.6.27,Int,6,,6,Complete,,HL7 International,"This long integer represents a drug name in the Multum data. The drug name can be a generic drug name, a branded drug name, a generic product name, a branded drug name, or other descriptive name. It is meant to serve as a Multum identifier in HL7 messages.",2012/07/13 12:00:00,2012/07/13 12:00:00,2012/07/13 08:43:29,,UV
2.16.840.1.113883.6.313,multum-allergy-category-id,Multum Drug Allergy Category,Hugh,Glover,masked,Terri Meredith,Terri Meredith,"2000 S. Colorado Blvd #11000Denver, CO 80022USA",303-733-4447,masked,Senior Research Project Leader,Cerner Multum,"2000 S. Colorado Blvd #11000Denver, CO 80022USA",303-733-4447,tmeredith@cerner.com,http://www.multum.com,Vendor,2.16.840.1.113883.6.27,Int,6,,6,Complete,,HL7 International,"The Multum Drug Allergy Category Identifier, alr_category_id, is a long integer that represents a group of drugs that share allergic cross reactivity and can be used in HL7 messaging to represent an allergy to multiple generic drug products, such as ""penicillins"".",2012/07/13 12:00:00,2012/07/13 12:00:00,2012/07/13 08:44:29,,UV
2.16.840.1.113883.6.314,multum-drug-id,Multum Generic Drug Identifier,Hugh ,Glover,masked,Terri Meredith,Terri Meredith,"2000 S. Colorado Blvd #11000Denver, CO 80022United States of America",303-733-4447,masked,Senior Research Project Leader,Cerner Multum,"2000 S. Colorado Blvd #11000Denver, CO 80022United States of America",303-733-4447,tmeredith@cerner.com,http://www.multum.com,Vendor,2.16.840.1.113883.6.27,Int,6,,6,Complete,,HL7 International,This is the 6 character identifier that represents a generic drug in the Multum data. It is formatted as ""d#####"". It is meant to serve as the Multum identifier for a generic drug in HL7 messages.,2012/07/13 12:00:00,2012/07/13 12:00:00,2012/07/13 08:45:20,,UV
1.2.36.104808988.1,best-practice-drug,BPDrug ,Grahame,Grieve,masked,,Frank Pyefinch,"PO Box 1911, Bundaberg. 4670 Australia",07 4155 8800,masked,,Best Practice,"PO Box 1911, Bundaberg. 4670 Australia",07 4155 8800,support@bpsoftware.com.au,http://www.bpsoftware.com.au,Vendor,,Ext,6,,6,Complete,1.2.36.104808988.1,Best Practice,This is the coded table of drug names/strengths/forms/pack sizes/PBS information used within the prescribing module of Best Practice.,2012/08/09 12:00:00,2012/08/09 12:00:00,2012/08/09 10:56:16,,AU
1.2.36.104808988.2,best-practice-term,BPTerm,Grahame,Grieve,masked,,Frank Pyefinch,"PO Box 1911, Bundaberg. 4670 Australia",07 4155 8800,masked,,Best Practice,"PO Box 1911, Bundaberg. 4670 Australia",07 4155 8800,support@bpsoftware.com.au,http://www.bpsoftware.com.au,Vendor,,Ext,6,,6,Complete,1.2.36.104808988.2,Best Practice,This is the coded table of clinical terms used for the Diagnosis/Procedure/Reason for Visit/Reason for Prescription lists within the Best Practice clinical modules.,2012/08/09 12:00:00,2012/08/09 12:00:00,2012/08/09 10:57:51,,AU
1.2.36.104808988.3,best-practice-immunisation,BPImmunisation,Grahame,Grieve,masked,,Frank Pyefinch,"PO Box 1911, Bundaberg. 4670 Australia",07 4155 8800,masked,,Best Practice,"PO Box 1911, Bundaberg. 4670 Australia",07 4155 8800,support@bpsoftware.com.au,http://www.bpsoftware.com.au,Vendor,,Ext,6,,6,Complete,1.2.36.104808988.3,Best Practice,This is the coded table of vaccines used within the Immunisation module of Best Practice.,2012/08/09 12:00:00,2012/08/09 12:00:00,2012/08/09 11:08:31,,AU
1.2.36.104808988.4,best-practice-substance,BPSubstance,Grahame,Grieve,masked,,Frank Pyefinch,"PO Box 1911, Bundaberg. 4670 Australia",07 4155 8800,masked,,Best Practice,"PO Box 1911, Bundaberg. 4670 Australia",07 4155 8800,support@bpsoftware.com.au,http://www.bpsoftware.com.au,Vendor,,Ext,6,,6,Complete,1.2.36.104808988.4,Best Practice,This is the coded table of generic ingredients used for allergy and drug interaction checking within Best Practice.,2012/08/09 12:00:00,2012/08/09 12:00:00,2012/08/09 11:10:59,,AU
1.2.36.104808988.5,best-practice-reaction,BPReaction,Grahame,Grieve,masked,,Frank Pyefinch,"PO Box 1911, Bundaberg. 4670 Australia",07 4155 8800,masked,,Best Practice,"PO Box 1911, Bundaberg. 4670 Australia",07 4155 8800,support@bpsoftware.com.au,http://www.bpsoftware.com.au,Vendor,,Ext,6,,6,Complete,1.2.36.104808988.5,Best Practice,This is the coded table of Allergy/Adverse drug reactions used for recording allergies and adverse drug reactions within Best Practice.,2012/08/09 12:00:00,2012/08/09 12:00:00,2012/08/09 11:12:44,,AU
2.16.840.1.113883.6.139.4,icpc2E-GER,"ICPC2E, German Translation",Tony,Schaller,masked,,World Health Organization (WHO),Avenue Appia 201202 GenevaSwitzerland,+ 41 22 791 21 11,masked,,World Health Organization (WHO),Avenue Appia 201202 GenevaSwitzerland,+ 41 22 791 21 11,info@who.int,http://www.who.int/classifications/icd/adaptations/icpc2/en/,SDO,,Ext,6,,6,Complete,2.16.840.1.113883.6.139.4,World Health Organization (WHO),"International Classification of Primary Care, Second edition (ICPC-2). German Translation.",2012/10/05 12:00:00,2012/10/06 12:00:00,2012/10/06 03:32:27,,UV
2.16.840.1.113883.6.301.5,nubc-patDiscStatus-cs,NUBC Patient Discharge Status-value set-code set,Brett,Marquard,masked,,Brett Marquard,,413-549-6886,masked,HL7 SDWG Co-Chair,George Arges,"Chair, National Uniform Billing CommitteeSenior Director - Health Data Management GroupAmerican Hospital Association155 N. Wacker Drive, Suite 400Chicago, IL 60606-1725",312-422-3398,garges@aha.org,http://www.nubc.org/become.html,SDO,,Ext,,,6,Complete,2.16.840.1.113883.6.301.5,HL7 International,"National Uniform Billing Committee (NUBC) UB-04 manual, UB form locator 17, thePatient Discharge Status - a code indicating the disposition or discharge status of the patient at the end service for the period covered on a bill, as reported in FL6, Statement Covers Period.The UB-04 manual with the codes is available by subscriptionfrom NUBC at http://www.nubc.org/become.html",2013/04/09 12:00:00,2013/04/10 12:00:00,2013/04/10 01:49:44,,US
2.16.840.1.113883.3.3150,ada-snodent,Systematized Nomenclature of Dentistry ,Jean ,Narcisi,masked,David Preble,Jean Narcisi,"American Dental Association 211 East ChicagoChicago, IL 60654Att. Department of Dental Informatics",312-440-2750,masked,Dental Informatics Director,American Dental Association,"American Dental Association 211 East ChicagoChicago, IL 60654Att. Department of Dental Informatics",312-440-2500,SNODENT@ada.org,http://www.ada.org/snodent.aspx,Prof Soc,2.16.840.1.113883.6.13,Int,,,6,Complete,,,"Systematized Nomenclature of Dentistry (SNODENT) is owned, maintained and distributed by the American Dental Association (ADA).SNODENT is a vocabulary designed for use in the electronic environment — for electronic health and dental records. The intended purpose is to: • Provide standardized terms for describing dental disease • Capture clinical detail and patient characteristics • Permit analysis of patient care services and outcomes • To be interoperable with Electronic Health Records (EHR) and Electronic Dental Records (EDR) SNODENT licensing information can be found at: http://www.ada.org/8466.aspx",2013/05/10 12:00:00,2013/05/10 12:00:00,2013/05/10 06:49:57,,UV
2.16.840.1.113883.3.1780.1.12.1.3,ca-CPDC,Canada Post Street Direction Code System,Wendy,Huang,masked,,Finnie Flores,"4110 Yonge St., Suite 300Toronto, ONM2P 2B7Canada",416-529-5201,masked,,Canada Post Corporation,Canada PostAttn: Customer Service35 Hughes St.Fredericton NB E3A 2W2Canada,1-866-607-6301,noemail@email.com,http://www.canadapost.ca/cpo/mc/default.jsf,Vendor,,Ext,6,,6,Complete,2.16.840.1.113883.3.1780.1.12.1.3,Canadian Institute for Health Information,A set of codes identifying Canada Post Street Direction code for the directional reference used to qualify the street name.The set of codes in English and French can be found here: http://www.canadapost.ca/tools/pg/manual/PGaddress-e.asp#1403220.,2013/07/04 12:00:00,2013/07/05 12:00:00,2013/07/05 04:31:55,,UV
2.16.840.1.113883.3.1780.1.12.1.4,ca-CPST,Canada Post Street Type,Wendy,Huang,masked,,Finnie Flores,"4110 Yonge St., Suite 300Toronto, ONM2P 2B7Canada",416-529-5201,masked,,Canada Post Corporation,Canada PostAttn: Customer Service35 Hughes St.Fredericton NB E3A 2W2Canada,1-866-607-6301,noemail@email.com,http://www.canadapost.ca/cpo/mc/default.jsf,Vendor,,Ext,6,,6,Complete,2.16.840.1.113883.3.1780.1.12.1.4,Canadian Institute for Health Information,A set of codes identifying Canada Post Street Type code that identifies the type of public thoroughfare in Canada.The set of codes in English can be found here: http://www.canadapost.ca/tools/pg/manual/PGaddress-e.asp#1423617.The set of codes in French can be found here: http://www.canadapost.ca/tools/pg/manual/PGaddress-f.asp#1435705.,2013/07/04 12:00:00,2013/07/05 12:00:00,2013/07/05 04:32:49,,UV
1.3.6.1.4.1.19376.1.3.5,ihelaw,IHE Laboratory Analytical Workflow (LAW) Analyzer result types,Riki,Merrick,masked,Mary Kennedy,Mary Kennedy,"College of American Pathologists325 Waukegan RoadNorthfield, IL 60093-2750",+001 847-832-7000,masked,IHE Lab Technical Committee Secretary,IHE International Laboratory Committee,,,lab@ihe.net,http://wiki.ihe.net/index.php?title=Laboratory_Analytical_Workflow_Profile,SDO,,Ext,,,6,Complete,1.3.6.1.4.1.19376.1.3.5,IHE International Laboratory Committee,The new IHELAW coding scheme will be set up for the purpose of classifying supplemental results sent by an Analyzer to an Analyzer Manager.,2013/07/08 12:00:00,2013/07/11 12:00:00,2013/07/11 02:36:46,IHELAW,UV
1.2.36.1.2001.1004.100,amt-v2,Australian Medicines Terminology (AMT) v2,Grahame,Grieve,masked,,Grahame Grieve,,+61411867065,masked,,NEHTA,"Level 25, 56 Pitt StreetSydney NSW 2000 Australia",61411867065,enquiries@nehta.gov.au,http://www.nehta.gov.au/,Govt body,,Ext,6,,6,Complete,1.2.36.1.2001.1004.100,NEHTA,"The Australian Medicines Terminology (AMT) is the national terminology to identify medicines used in Australia, using unique codes to deliver unambiguous, accurate and standardised names for both branded (trade) and generic (medicinal) products.This OID is used when exchanging AMT v2 Concept Identifiers in CDA documents.Note: AMT v2 uses the SNOMED CT infrastructure, but is not fully aligned with the underlying SNOMED CT infrastructure, so it has it's own OID. AMT v3 is fully aligned, and the standard SNOMED CT OID is used instead.",2013/10/29 12:00:00,2013/12/09 12:00:00,2013/12/09 07:39:20,,AU
2.16.840.1.113883.6.315,lexiglobalid,Lexicomp Global Identifer,Howard,Strasberg,masked,,Howard Strasberg,"Lexi-Comp, Inc.1100 Terex RoadHudson, Ohio, USA 44236 ",858-481-4249,masked,VP Medical Informatics,"Lexi-Comp, Inc.","Lexi-Comp, Inc.1100 Terex RoadHudson, Ohio, USA 44236 ",330-650-6506,howard.strasberg@wolterskluwer.com,http://www.lexi.com,Vendor,,Int,,,6,Complete,,HL7 International,Lexicomp Global Identifier,2014/02/19 12:00:00,2014/12/15 12:00:00,2014/12/15 12:22:02,,UV
2.16.840.1.113883.6.316,rfc5646,Tags for Identifying Languages - RFC5646,Robert,McClure,masked,,Addison Phillips,,3039266771,masked,"Globalization Architect (Amazon Lab126), Chair (W3C I18N WG)",The Internet Engineering Task Force (IETFΒ),,,addison@inter-locale.com,http://www.w3.org/International/articles/language-tags/Overview.en.php,SDO,,Int,6,,6,Complete,,,The code system used to uniquely identify a language as described in the RFC5646 (http://www.rfc-editor.org/rfc/rfc5646.txt) as defined in the ""current"" specification of BCP47 (http://tools.ietf.org/html/bcp47). The elements needed for the code system are provided by the IANA Language Subtag Registry (http://www.iana.org/assignments/language-subtag-registry) Usage of the code system is best explained by http://www.w3.org/International/articles/language-tags/Overview.en.php and http://www.w3.org/International/questions/qa-choosing-language-tags. The CLDR - Unicode Common Locale Data Repository project is a source for application libraries to support implementing this code system.,2014/11/10 12:00:00,2014/11/12 12:00:00,2014/11/12 02:03:18,,UV
2.16.840.1.113883.4.642.1.222,observationCategory,Observation Category,William Ted,Klein,masked,Rob Hausam,Grahame Grieve,,+1 734-677-7777,masked,FHIR Chief,HL7 International FHIR WG,"3300 Washtenaw Avenue, Suite 227Ann Arbor, MI 48104USA",+1 (734) 677-7777,hq@HL7.org,http://www.hl7.org,HL7 body,2.16.840.1.113883,Ext,,,6,Complete,2.16.840.1.113883.4.642.1.222,HL7 International,High level observation categories for the general type of observation being made. ,2015/11/13 12:00:00,2015/11/24 12:00:00,2015/11/24 06:12:46,,UV
2.16.840.1.113883.6.301.6,nubc-ValueCode-cs,NUBC Value Codes and Amounts for UB-04,William Ted,Klein,masked,Mary Kay McDaniel,Mary Kay McDaniel,"8200 Greensboro DriveSuite 1200McLean, VA 22102",+1 602 300 4246,masked,HL7 FM Vocabulary Facilitator,National Uniform Billing Committee (NUBC),"George ArgesChair, National Uniform Billing CommitteeSenior Director - Health Data Management GroupAmerican Hospital Association155 N. Wacker Drive, Suite 400Chicago, IL 60606-1725",+1 312 422 3398,garges@aha.org,http://www.nubc.org/become.html,Prof Soc,,Ext,,,6,Complete,2.16.840.1.113883.6.301.6,Health Level Seven International,"National Uniform Billing Committee (NUBC) UB-04 Data Specifications Manual, UB form locator 39 - 41, the Value Codes and Amounts - claim code indicating the value code (and amount) needed to process the claim. The UB-04 Data Specifications Manual with the codes is available by subscription from NUBC at http://www.nubc.org/become.html",2016/02/23 12:00:00,2016/02/23 12:00:00,2016/02/23 12:08:18,HL70153,US
2.16.840.1.113883.6.301.7,nubc-OccurrenceCode-cs,NUBC Occurrence Codes and Amounts for UB-04,William Ted,Klein,masked,Mary Kay McDaniel,Mary Kay McDaniel,"8200 Greensboro DriveSuite 1200McLean, VA 22102",+1 602 300 4246,masked,HL7 FM Vocabulary Facilitator,National Uniform Billing Committee (NUBC),"George ArgesChair, National Uniform Billing CommitteeSenior Director - Health Data Management GroupAmerican Hospital Association155 N. Wacker Drive, Suite 400Chicago, IL 60606-1725",+1 312 422 3398,garges@aha.org,http://www.nubc.org/become.html,Prof Soc,,Ext,,,6,Complete,2.16.840.1.113883.6.301.7,Health Level Seven International,"National Uniform Billing Committee (NUBC) UB-04 Data Specifications Manual, UB form locator 31 - 34, Occurrence Codes and Amounts - code and associated date defining a significant event relating to the bill that may affect payer processing the claim. The UB-04 Data Specifications Manual with the codes is available by subscription from NUBC at http://www.nubc.org/become.html ",2016/03/02 12:00:00,2018/10/02 12:00:00,2018/10/02 11:59:55,,UV
2.16.840.1.113883.6.301.8,nubc-OccurrenceSpan-cs,NUBC Occurrence Span Codes for UB-04,William Ted,Klein,masked,Mary Kay McDaniel,Mary Kay McDaniel,"8200 Greensboro DriveSuite 1200McLean, VA 22102",+1 602 300 4246,masked,HL7 FM Vocabulary Facilitator,National Uniform Billing Committee (NUBC),"George ArgesChair, National Uniform Billing CommitteeSenior Director - Health Data Management GroupAmerican Hospital Association155 N. Wacker Drive, Suite 400Chicago, IL 60606-1725",+1 312 422 3398,garges@aha.org,http://www.nubc.org/become.html,Prof Soc,,Ext,,,6,Complete,2.16.840.1.113883.6.301.8,Health Level Seven International,"National Uniform Billing Committee (NUBC) UB-04 Data Specifications Manual, UB form locator 35 - 36, Occurrence Span Codes and Dates - code and related dates that identify an event that relates to payment of the claim. The UB-04 Data Specifications Manual with the codes is available by subscription from NUBC at http://www.nubc.org/become.html",2016/03/02 12:00:00,2018/10/02 12:00:00,2018/10/02 12:00:38,,US
2.16.840.1.113883.6.301.9,cms-OCEEditCode-cs,CMS OCE Edit Codes,William Ted,Klein,masked,Mary Kay McDaniel,Mary Kay McDaniel,"8200 Greensboro DriveSuite 1200McLean, VA 22102",+1 602 300 4246,masked,HL7 FM Vocabulary Facilitator,National Uniform Billing Committee (NUBC),"US Department of Health and Human Services, Center for Medicare and Medicaid Services Centers for Medicare & Medicaid Services7500 Security Boulevard, Baltimore, MD 21244",,info@cms.gov,https://www.cms.gov/Medicare/Coding/OutpatientCodeEdit/index.html,Govt body,,Ext,,,6,Complete,2.16.840.1.113883.6.301.9,Health Level Seven International,"The OPPS functionality of the Integrated Outpatient Code Editor (I/OCE) software was developed for the implementation of the Medicare outpatient prospective payment system mandated by the 1997 Balanced Budget Act. CMS released the proposed OPPS rules using the Ambulatory Payment Classification (APC) system in the September 8, 1998 Federal Register. Final regulations were published in the April 7, 2000 Federal Register and the system became effective for Medicare on August 1, 2000.The APC-based OPPS developed by CMS is the outpatient equivalent of the inpatient, DRG-based PPS. The APC system establishes groups of covered services so that the services within each group are comparable clinically and with respect to the use of resources.Hospitals are required to use HCPCS when billing for outpatient services.The OCE not only identifies individual errors but also indicates what actions should be taken and the reasons why these actions are necessary. In order to accommodate this functionality, the OCE is structured to return lists of edit numbers. This structure facilitates the linkage between the actions being taken, the reasons for the actions and the information on the claim (e.g., a specific diagnosis) that caused the action. In general, the OCE performs all functions that require specific reference to HCPCS codes, HCPCS modifiers and ICD-10-CM diagnosis codes (ICD-9-CM diagnosis codes for historical claims with From Dates prior to 10/1/2015). Since these coding systems are complex and annually updated, the centralization of the direct reference to these codes and modifiers in a single program reduces effort and reduces the chance of inconsistent processing.This is a CMS maintained list of edits: Please see the following for additional information: • https://www.cms.gov/Medicare/Coding/OutpatientCodeEdit/index.html• https://www.cms.gov/Medicare/Coding/OutpatientCodeEdit/Background.htmlC• https://www.cms.gov/Medicare/Coding/OutpatientCodeEdit/OCEQtrReleaseSpecs.htmlThese fields are used in grouping and reimbursement for CMS APCs. Please refer to the ""Outpatient Prospective Payment System Final Rule"" (""OPPS Final Rule"") issued by CMS",2016/03/02 12:00:00,2018/10/02 12:00:00,2018/10/02 12:02:15,,UV
2.16.840.1.113883.6.301.11,presentOnAdmission,Present on Admission (POA) Indicator,William Ted,Klein,masked,Mary Kay McDaniel,Robert McClure,"MD Partners, Inc.511 S Miller AveLafayette, CO 80026-1545",+13039266771,masked,Vocabulary co-chair,Centers for Medicare and Medicaid Services,"Marilu HueCenters for Medicare & Medicaid Services7500 Security BoulevardBaltimore, MD 21244",,marilu.hue@cms.hhs.gov,https://www.cms.gov/Medicare/Medicare-Fee-for-Service-Payment/HospitalAcqCond/Coding,Govt body,,Ext,,,6,Complete,2.16.840.1.113883.6.301.11,Health Level Seven International,"Official short description:This code system consists of Present on Admission (POA) indicators which are assigned to the principal and secondary diagnoses (as defined in Section II of the Official Guidelines for Coding and Reporting) and the external cause of injury codes to indicate the presence or absence of the diagnosis at the time of inpatient admission.These codes are primarily used within the National Uniform Billing Committee (NUBC) UB-04 Data Specifications Manual, UB form locator 67, as the Present on Admission (POA) Indicator. Previous version of this OID had Full name: NUB Present On Admission Codes for UB04Symbolic name: nubc-PresentOnAdmissionUsed in HL7 Version 2.x messaging in the DG1 segment.",2016/03/02 12:00:00,2018/10/02 12:00:00,2021/01/06 05:17:42,HL70895,US
2.16.840.1.113883.6.317,populatedPlacesGNIS,Populated Places (GNIS) ,Hetty,Khan,masked,Mead Walker,Kryn Krautheim,CDC/National Center for Health StatisticsPO Box 12214Research Triangle Park NC 27709,919.541.0197,masked,Survey Statistician,"Centers for Disease Control and Prevention, National Center for Health Statistics","2500 Century Center ParkwayAtlanta, GA 30329",404-498-6685,dsq3@cdc.gov,http://phinvads.cdc.gov,Govt body,2.16.840.1.114222.4,Int,,,6,Complete,,HL7 International,"Codes for Named Populated Places, Primary County Divisions, and Other Locational Entities of the United States, Puerto Rico, and the Outlying Areas (without codes). This code system in a combination of GNIS and FIPS 55-3 codes that have been mapped. The former FIPS 55-3 standard was superseded by ANSI standard INCITS 446-2008. Former FIPS 55 data have been incorporated into the GNIS. The GNIS Feature ID superseded the FIPS55 Place Code (now the Census Code) as the Federal and national standard geographic feature record identifier. The Census Bureau continues to assign five digit Census Codes for internal purposes. http://geonames.usgs.gov/domestic/download_data.htm",2016/05/09 12:00:00,2016/06/14 12:00:00,2016/12/07 10:48:46,NCHSGNIS,UV
2.16.840.1.113883.6.318,clinVar-A,ClinVar Allele ID,Clement,McDonald,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 2089",(301 ) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","National Lister Hill Center of Biomedical Communications, National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",301-496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,"ClinVar table with Allele ID as the code, which is an identifier for an individual change. e.g. for a haplotype of five SNPs, each individual SNP has its own Allele ID.",2016/07/19 12:00:00,2016/07/19 12:00:00,2016/07/19 11:31:30,,UV
2.16.840.1.113883.6.319,clinVar-V,ClinVar Variant ID,Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","National Lister Hill Center of Biomedical Communications, National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",301-496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,"ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. The ClinVar records have a field for Allele ID and for Variant ID. All simple variants have an Allele ID. At present, all complex and most simple variants also have a Variant ID, and by the end of 2016, all variants will have a variant ID. This coding system uses the variant ID as the code and the variant name ( field TBD) from the ""variant_summary"" file as the code print string. The ""variant_summary"" file caries more than 20 fields , including the seperate components of the variant nane, the cytogenomic locatiaon, the genomic reference etc. Many of these attributes have been indexed to assist users and applications that need to find the ID for a particular variant. ",2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 03:32:56,,UV
2.16.840.1.113883.6.320,cosmic-Smpl,COSMIC - Simple Variants,Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","National Lister Hill Center of Biomedical Communications, National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",301-496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,"This table includes only simple somatic (cancer) mutations, one per unique mutation ID. The codes is the COSMIC mutation ID, and the name is ____. It carries fields analogous to most of the the key fields in ClinVar, but its reference sequences are Ensembl transcript reference sequences with prefixes of ENST; it specifies amino acid changes with the older, HGVS, single letter codes and it carries examples of primary cancers and primary tissues, fields that are not in ClinVar. COSMIC's source table includes multiple records per mutation - one per submission. The COSMIC-Simple Variants table carries only includes one record per unique mutation- more than 3 million of them.This coding system can be explored via the LHC table look up service (https://lforms-service.nlm.nih.gov/apidoc/cosmic/v1/doc.html)These contents are copyright COSMIC (http://cancer.sanger.ac.uk/cosmic/license) LHC has produced a look up table for these records, and for users to look up particular mutation IDs with permission from COSMIC. However, interested parties must contact COSMIC for permission to download these records. ",2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 03:51:16,,UV
2.16.840.1.113883.6.321,cosmic-Strc,COSMIC-Structural variants,Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications",Lister Hill National Center for Biomedical Communications,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",301-496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,COSMIC has divided structural variants into two tables: one called structural variants and one called copy number variants both kinds of which are carried in NCBIs dbVar table.The table for this coding system derives from COMIC's structural variation tables. The identifiers for these are pure numbers with no prefix and the name is __. These use Ensemble genomic Reference sequences (those whose codes begin with ENSG).,2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 03:53:44,,UV
2.16.840.1.113883.6.322,dbVar-GL,dbVar-Germline,Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,"dbVar is NCBI's database of genomic structural variations (including copy number variants) that are larger than 50 contiguous base pairs. It is the complement of dbSNP, which only contains variants occurring in 50 or fewer contiguous base pairs. It contains insertions, deletions, duplications, inversions, multinucleotide substitutions, mobile element insertions, translocations, and complex chromosomal rearrangements. Germline and Somatic variants are presented in separate files. Accordingly we have divided the coding system for dbVar the same way. This coding system represents the Germ line DbVar variants. The records it carries have IDs with prefixes of RSV , RSSV , ESV and ESSV. Those beginning with E represent submission from the European Bioinformatics Institute (EBI) those beginning with R were submitted through NCBI. In this case we include submitted records (ESSV or RSSV) and the summary records (RSV, ESV) that identify many similar submitted records in the one file.",2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 04:38:49,,UV
2.16.840.1.113883.6.323,dbVar-Som,dbVar-Somatic,Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301 ) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301 ) 496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,"dbVar is NCBI's database of genomic structural variations (including copy number variants) that are larger than 50 contiguous base pairs. It is the complement of dbSNP, which only contains variants occurring in 50 or fewer contiguous base pairs. It contains insertions, deletions, duplications, inversions, multinucleotide substitutions, mobile element insertions, translocations, and complex chromosomal rearrangements. Germline and Somatic variants are presented in seperate files. Accordingly we have divided the coding systemd for dbVar the same way. This coding system represents the Somatic (mostly cancer) variants in dbVar. As is true for the Germline half of dbVAR, the record IDs for the somatic dbVars have prefixes of RSV, RSSV, ESV and ESSV with the leading E and R having the meaning as from germline structural variant and we also include both the submitter records and the summary records in the same filed.",2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 04:45:17,,UV
2.16.840.1.113883.6.324,ensembl-G,Ensembl genomic reference sequence,Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,"Set of Ensembl genomic reference sequences whose identifiers have a prefix of ""ENSG."" It only includes genomic sequences associated with genes and uses the whole build plus the chromosome number to identify chromosome reference sequences, rather than a separate set of reference sequence identifier as NCBI does. ",2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 04:48:55,,UV
2.16.840.1.113883.6.325,ensembl-P,Ensembl protein reference sequence,Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,"Set of Ensembl protein reference sequences. Their identifiers are distinguished by the prefix of ""ENSP,"" and correspond to NCBI's ""NP_"" identifiers. ",2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 04:54:00,,UV
2.16.840.1.113883.6.326,ensembl-T,Ensembl transcript reference sequence,Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,"Set of reference sequences for transcripts of coding regions. Their identifiers all have a prefix of ""ENST."" There are parallels for most (if not all) of what is in Ensemble within NCBI. ""ENST"" parallels NCBI's ""NM_"" identifiers. In general, Ensembl takes its reference sequences directly from the build. NCBI adjusts its reference sequences by replacing known ""mutations"" with sequences that better reflect the population ""normal"". ",2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 05:00:00,,UV
2.16.840.1.113883.6.327,gHGVS,HGVS- Genomic syntax,Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,Syntax that describes the variations (mutations) at the genome level (the DNA before it is spliced to remove introns). The genomic syntax statements are distinguished by a leading ""g."",2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 05:12:11,,UV
2.16.840.1.113883.6.328,cHGVS,HGVS- Transcript syntax,Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,"Syntax that describes variations (mutations) at the transcript (messenger RNA) level. The transcript syntax statements, which can describe simple and complex variants, are distinguished by a leading ""c."" ",2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 05:14:21,,UV
2.16.840.1.113883.6.329,pHGVS,HGVS-Protein syntax,Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications"," Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,"Syntax that specifies the variations (mutations) at the amino acid level, which is induced by underlying DNA variants. The protein change statements are distinguished by a leading ""p."" ",2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 05:17:34,,UV
2.16.840.1.113883.6.330,refSeq-G,NCBI - genomic and chromosome reference sequences ,Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,Subset of NLM Human RefSeqs with prefix of ""NG_ or NC_"". Those prefixed with ""NC_"" represent the whole genomic RefSeq for individual chromosomes. Those prefixed with ""NG_"" represent genes with all of their introns and flanking regions and other larger or smaller genomic sequences. These are available separately in Gene reports all human RefSeqs: ftp://ftp.ncbi.nih.gov/gene/DATA/gene2refseq.gz,2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 05:24:09,,UV
2.16.840.1.113883.6.331,refSeq-P,NCBI - protein reference sequence,Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,"Reference sequences for proteins. Not commonly reported because Amino acid changes can be computed directly from DNA changes based on transcript reference sequence. However, some fields are interested only in the protein sequence change, and proteins can be sequenced independently of DNA sequencing. ",2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 05:26:15,,UV
2.16.840.1.113883.6.332,refSeq-T,NCBI-transcript reference sequences (RefSeq),Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,Subset of NLM RefSeq records whose with prefix of ""NM_"" are reference sequences that represents messenger RNA.,2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 05:30:30,,UV
2.16.840.1.113883.6.333,medgen-dis,NCBI MedGen disease subset ,Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,"MedGen-disease is a subset disease concepts (about 20,000 as of January 2016)taken from the MedGEN table. It includes most known genetic and clinical diseases. It was derived from the NIH Genetic Testing Registry (GTR), UMLS, HPO, Orphanet, ClinVar and other sources, and is probably the most complete compendium of genetic diseases, though it also includes most common clinical diseases. It uses UMLS IDs when they exist and its own ID when not, and links to SNOMED CT and other identifiers. The MedGen data base includes the inheritance and clinical features of each disease, as well as the map location of underlying genetic basis.",2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 05:32:22,,UV
2.16.840.1.113883.6.334,rxT-ingrd,RxTerms-Ingredients Subset,Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,"rxT-ingrd is a specialization of the RxNorm database that includes the ingredients in RxTerms except allergens (used for allergy testing), combination ingredients, and inactive ingredients. The subset is designed for identifying drugs that might be the focus of pharmacogenetic testing.",2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 05:34:55,,UV
2.16.840.1.113883.6.335,chrom-loc,Cytogenetic (chromosome) location,Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,"Chromosome location (AKA chromosome locus or cytogenetic location), is the standardized syntax for recording the position of genes and large mutations. It consists of three parts: the Chromosome number (e 1-22, X, Y), an indicator of which arm – either ""p"" for the short or ""q"" for the long, and then a series of numbers separated by dots that indicate the band, sub band and sub-sub band of the locus - e.g. 2p16.3 . There are other conventions for reporting ranges and locations at the end of the chromosomes. The table of these chromosome locations was loaded initially with the all of the locations found in NCBI's ClinVar variation tables. It will expand as additional sources become available.",2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 05:39:09,,UV
2.16.840.1.113883.6.336,hgnc-symb,HUGO Gene Nomenclature Committee Gene Code and Symbol,Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,"The HGNC gene table carries the GENE ID, gene symbol and full gene name. The GENE ID is specific to the species. The gene symbol and name will be shared by all species with the same gene. The HGNC-symb table carries only human genes. The code for this coding system is the HGNC gene code, the ""name"" or print string is the HGNC gene symbol. More than 28,000 human gene symbols and names have been assigned so far, but some human genes lack an HCGN code and symbol. These are mostly non protein coding genes.",2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 05:52:53,,UV
2.16.840.1.113883.6.337,lrg-refseq,Locus Reference Genomic Sequences (LRG),Clement,McDonald MD,masked,Shennon Lu,Clement McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications","Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",(301) 496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,HL7 International,"LRG is a manually curated record that contains stable and thus, un-versioned reference sequences designed specifically for reporting sequence variants with clinical implications. It provides a genomic DNA sequence representation of a single gene that is idealized, has a permanent ID (with no versioning), and core content that never changes. Their database includes maps to NCBI, Ensemble and USCS reference sequences. It has a total of 1073 sequences, as of April 2016 with identifiers of the form: ""LRG_####"", where #### can be from 1 to N, and N is the last gene processed. See PMIDs: 24285302, 20398331, 20428090 for more information.",2016/07/19 12:00:00,2016/07/20 12:00:00,2016/07/20 05:55:45,,UV
2.16.840.1.113883.6.338,hl-pft,Health Language Provider Friendly Terminology,Brian,Levy,masked,,Brian Levy,"4600 S. Syracuse St.Suite 1200Denver, CO 80237",7209402940,masked,,Wolters Kluwer Health Language,"4600 S. Syracuse St.Suite 1200Denver, CO 80237",7209402940,brian.levy@wolterskluwer.com,http://www.healthlanguage.com,Vendor,,Int,,,6,Complete,,HL7 International,The Health Language Provider Friendly Terminology represents an interface terminology used to capture Problem Lists and other structured data elements within an EMR. ,2017/03/01 12:00:00,2017/03/02 12:00:00,2017/03/02 04:26:09,,UV
2.16.840.1.113883.6.339,hpo,Human Phenotype Ontology,Clem,McDonald,masked,Shennon Lu,Clem McDona,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",+1 301-496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications",Lister Hill National Center for Biomedical Communications,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",+1 301-496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,Health Level Seven International,"The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect.",2017/07/28 12:00:00,2017/07/28 12:00:00,2017/07/28 03:43:09,HPO,UV
2.16.840.1.113883.6.340,geneCodeNCBI,NCBI Gene Code,Clem,McDonald,masked,Shennon Lu,Clem McDonald,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",+1 301-496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications",Lister Hill National Center for Biomedical Communications,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",+1 301-496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,Health Level Seven International,"Because not all genes have HGNC names and codes, NCBI has created gene IDs that cover the genes that are not registered by HGNC. When applicable, this variable identifies the gene on which the variant is located. The gene identifier is also carried in the transcript reference sequence database, and is part of a full HGVS expression.",2017/07/28 12:00:00,2017/07/28 12:00:00,2017/07/28 03:43:35,NCBI-GeneCode,UV
2.16.840.1.113883.6.341,hlaAllele,Human leukocyte antigen nomenclature,Clem,McDonald,masked,Shennon Lu,"Clem McDonald, MD","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",+1 301-496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications",Lister Hill National Center for Biomedical Communications,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",+1 301-496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,Health Level Seven International,"Human leukocyte antigen (HLA) complex contains more than 220 genes that encode for the proteins of the immune system. HLA alleles are most commonly used for histocompatibility testing for stem cell and solid organ transplantation. The WHO Nomenclature Committee for Factors of the HLA System is responsible for a common nomenclature of HLA alleles, allele sequences, and quality control, to communicate histocompatibility typing information to match donors and recipients. For the full specification, please go to this website: http://hla.alleles.org/nomenclature/naming.html .HLA nomenclature can also be used to represent sets of alleles that share sequence identity in the Antigen Recognition Site (ARS). G-groups are alleles that have identical DNA sequences in the ARS, while P-groups are alleles that have identical protein sequences in the ARS. These are described, respectively, in http://hla.alleles.org/alleles/g_groups.html and http://hla.alleles.org/alleles/p_groups.html.",2017/07/28 12:00:00,2017/07/28 12:00:00,2017/07/28 03:43:52,HLA-Allele,UV
2.16.840.1.113883.6.342,starAllele,Pharmacogenomics star allele nomenclature,Clem,McDonald,masked,Shennon Lu,"Clem McDonald, MD","Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",+1 301-496-4441,masked,"Director, Lister Hill National Center for Biomedical Communications",Lister Hill National Center for Biomedical Communications,"Lister Hill National Center for Biomedical CommunicationsU.S. National Library of Medicine8600 Rockville Pike, Bethesda, MD 20894",+1 301-496-4441,nlmlhclhcques@mail.nih.gov,https://lhncbc.nlm.nih.gov/,Govt body,,Int,,,6,Complete,,Health Level Seven International,"The star allele nomenclature is commonly used in pharmacogenomics as shorthand to specify one or more specific variants in a gene that is known to impact drug metabolism or response. A star allele can identify either a single variant or a group of variants found in cis, and therefore it usually represents a haplotype. A star allele name is composed of the gene symbol and an allele number, separated by an asterisk, e.g. TPMT*2. By convention, the *1 allele represents the allele that contains the ""reference"" sequence, although that is not true in all cases. Closely related alleles may be assigned a common number and be differentiated by a unique letter that specifies the suballele (e.g., TPMT*3A, TPMT*3B). Pharmacogenomics tests commonly report patient phenotypes as diplotypes, i.e. *1/*3A.",2017/07/28 12:00:00,2017/07/28 12:00:00,2017/07/28 03:44:15,Star-Allele,UV
2.16.840.1.113883.2.20.6.1,hc-CCDD,Canadian Clinical Drug Data Set,Attila,Farkas,masked,standards@infoway-inforoute.ca,Health Products and Food Branch,"A/L 2004, 250 Lanark AvenueOttawa, ON, K1A 0K9",613-291-3787,masked,"Manager, Data Science, Health Products and Food Branch",Health Products and Food Branch,"A/L 2004, 250 Lanark AvenueOttawa, ON, K1A 0K9",416-5953449,HPR-RPS@hc-sc.gc.ca,https://www.canada.ca/en/health-canada/corporate/about-health-canada/branches-agencies/health-products-food-branch.html,Govt body,2.16.840.1.113883.2.20.6,Ext,,,6,Complete,2.16.840.1.113883.2.20.6.1,HL7 Canada,The Canadian Clinical Drug Data Set provides codes for identification and a consistent approach to naming of medications and some medical devices in Canada. It has been designed and developed to reflect current clinical practice and safety advice and is freely available for use in digital health solutions and design applications. More information can be found here: https://infocentral.infoway-inforoute.ca/en/standards/canadian/ccdd,2017/09/06 12:00:00,2017/09/07 12:00:00,2020/11/13 03:36:30,,UV
2.16.840.1.113883.6.343,issue-details,SharedIssueDetails,Attila,Farkas,masked,,Lorie Carey,"150 King St. WestToronto, ONM5H 1J9",416 595 3400,masked,,Canada Health Infoway,"150 King St. WestToronto, ONM5H 1J9",416 595 3400,standards@infoway-inforoute.ca,,SDO,,Int,6,,6,Complete,,HL7 International,Provides codes to identify the issues that are returned as errors in response to messages received in the Canada Health Infoway PrescribeIT solution. Codes are a combination of alpha and numeric character with no spaces.,2017/10/17 12:00:00,2021/08/31 12:00:00,2021/08/31 11:24:25,,CA
2.16.840.1.113883.6.344,dsm5,DSM-5,Alexander,Henket,masked,,APA Answer Center,"800 Maine Ave. S.W., Suite 900, Washington D.C.",+1202-559-3900,masked,,American Psychiatry Association,"800 Maine Ave. S.W., Suite 900, Washington D.C.",+1202-559-3900,apa@psych.org,https://www.psychiatry.org,Prof Soc,,Int,,,6,Complete,,HL7 International,"The Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) is the 2013 update to the Diagnostic and Statistical Manual of Mental Disorders, the taxonomic and diagnostic tool published by the American Psychiatric Association (APA). In the United States, the DSM serves as a universal authority for psychiatric diagnoses. Treatment recommendations, as well as payment by health care providers, are often determined by DSM classifications, so the appearance of a new version has significant practical importance.The DSM-5 was published on May 18, 2013, superseding the DSM-IV-TR, which was published in 2000.",2018/01/31 12:00:00,2018/03/30 12:00:00,2018/03/30 09:26:36,,UV
2.16.840.1.113883.6.345,medrt,Medication Reference Terminology,Caroline,Macumber,masked,"Michael J. Lincoln MD, FACMI","Michael J. Lincoln MD, FACMI",,801-588-5200,masked,Chief Terminologist,US Department of Veterans Affairs,"550 Foothill BoulevardSalt Lake City, UT 84113",,michael.lincoln@va.gov,,Govt body,,Int,,,6,Complete,,HL7 International,"Medication Reference Terminology (MED-RT™) is the evolutionary successor to the Veterans Health Administration National Drug File – Reference Terminology (VHA NDF-RT™). Both are formal ontology representations of medication terminology, pharmacologic classifications, and asserted authoritative relationships between them.",2018/03/01 12:00:00,2018/03/30 12:00:00,2018/03/30 09:30:09,,UV
2.16.840.1.113883.6.346,medispanKDC,Medi-Span KDC,Howard,Strasberg,masked,,Howard Strasberg,"Wolters Kluwer8425 Woodfield Crossing Blvd.Suite 490Indianapolis, IN 46240",858-481-4249,masked,VP Medical Informatics,Wolters Kluwer,"8425 Woodfield Crossing Blvd.Suite 490Indianapolis, IN 46240",855-633-0577,howard.strasberg@wolterskluwer.com,https://www.wolterskluwercdi.com/,Vendor,,Int,,,6,Complete,,HL7 International,Medi-Span Knowledge Base Drug Code,2019/03/25 12:00:00,2019/03/30 12:00:00,2019/03/30 03:53:47,,UV
2.16.840.1.113883.6.347,icd11,ICD-11,Nenad,Kostanjsek,masked,,Nenad Kostanjsek,Avenue Appia 20 1211 Geneva 27 Switzerland,+41794755474,masked,Technical Officer for Classifications and Terminologies,World Health Organization,Avenue Appia 20 1211 Geneva 27 Switzerland,+ 41 22 791 21 11,info@who.int,https://who.int,SDO,,Int,,,6,Complete,,HL7 International,International Classification of Diseases 11th RevisionThe global standard for diagnostic health information,2019/05/10 12:00:00,2022/02/10 12:00:00,2022/02/10 10:18:30,,UV
2.16.840.1.113883.6.348,icaoSex,nternational Civil Aviation Organization Sex,William Ted,Klein,masked,Rob McClure,Rob McClure,TBD,3039266771,masked,TBD,International Civil Aviation Organization (ICAO),"International Civil Aviation Organization (ICAO)999 Robert-Bourassa Boulevard, Montréal, Québec H3C 5H7, Canada",+1 514-954-8219,icaohq@icao.int,https://www.icao.int/Pages/default.aspx,Prof Soc,,Int,,,6,Pending,,,Concepts representing recorded sex or gender values for international exchange as defined in the Gender Harmony project as specified by the International civil aviation organization.,2022/07/19 12:00:00, ,2022/08/04 11:54:17,,UV ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/hl7/__init__.py 0000644 0001751 0000177 00000003762 14655542206 023422 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Utilities for getting HL7 OIDs.
1. Navigate to https://www.hl7.org/oid/index.cfm?Comp_OID=2.16.840.1.113883.6.9
2. In ``OID_Type``, select 6) for external code system
3. Download CSV and copy in this directory (this might be automatable)
"""
import csv
from pathlib import Path
from typing import Mapping
__all__ = [
"get_hl7",
"HL7Aligner",
]
from bioregistry.external.alignment_utils import Aligner
HERE = Path(__file__).parent.resolve()
DATA = HERE.joinpath("OID_Report.csv")
COLUMNS = {
"Comp_OID": "prefix",
"Symbolic_name": "preferred_prefix",
"CodingSystemName": "name",
"assignment_status": "status",
"Resp_body_URL": "homepage",
"Resp_body_name": "organization",
"Object_description": "description",
}
def get_hl7(force_download: bool = False) -> Mapping[str, Mapping[str, str]]:
"""Get HL7 OIDs."""
rv = {}
with DATA.open() as file:
reader = csv.reader(file)
header = next(reader)
for row in reader:
row_dict = dict(zip(header, row))
record = {COLUMNS[k]: v for k, v in row_dict.items() if k in COLUMNS and v}
rv[record.pop("prefix")] = record
return rv
class HL7Aligner(Aligner):
"""Aligner for HL7 External Code Systems."""
# corresponds to the metaprefix in metaregistry.json
key = "hl7"
# This key tells the aligner that the prefix might not be super informative for
# lexical matching (in this case, they're OIDs, so definitely not helpful)
# and that there's another key inside each record that might be better
alt_key_match = "preferred_prefix"
# This function gets the dictionary of prefix -> record. Note that it's not
# called but only passed by reference.
getter = get_hl7
# This lists all of the keys inside each record to be displayed in the curation
# sheet. Below, the
curation_header = ("status", "preferred_prefix", "name", "homepage", "description")
if __name__ == "__main__":
HL7Aligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9619668
bioregistry-0.11.12/src/bioregistry/external/integbio/ 0000755 0001751 0000177 00000000000 14655546227 022416 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/integbio/__init__.py 0000644 0001751 0000177 00000011336 14655542206 024524 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download the Integbio registry."""
import json
import logging
from pathlib import Path
import pandas as pd
import requests
from bs4 import BeautifulSoup
__all__ = [
"get_integbio",
"IntegbioAligner",
]
from bioregistry.external.alignment_utils import Aligner
logger = logging.getLogger(__name__)
DIRECTORY = Path(__file__).parent.resolve()
PROCESSED_PATH = DIRECTORY / "processed.json"
SKIP = [
"Link(s) to Downloadable data",
"Link(s) to Metadata of downloadable data",
"Link(s) to Terms of use",
"Link(s) to How to use",
"Link(s) to API / SPARQL endopoint",
"Link to LSDB Archive",
"Link to MEDALS Database list",
"Link to TogoTV",
"Similar databases",
"Record maintainer",
"Record source",
"Acquisition date",
"Organism(s) covered",
"Date of creation of this record",
"Last update date of this record",
"Country/Region",
"J-GLOBAL ID", # about institutions?
"Contact information of database", # nice idea, but curation is bad so effectively unusable
]
def get_url() -> str:
"""Scrape the current download URL for Integbio.
:returns: The URL of the Integbio data download.
:raises ValueError: if the URL can't be found
.. warning::
Integbio deletes its old files, so it's impossible to download an old version of the
database
"""
base = "https://integbio.jp/dbcatalog/en/download"
res = requests.get(base)
soup = BeautifulSoup(res.text, "html.parser")
for anchor in soup.find_all("a"):
href = anchor.attrs["href"]
if href.startswith(
"https://integbio.jp/dbcatalog/files/zip/en_integbio_dbcatalog_ccbysa_"
) and href.endswith("_utf8.csv.zip"):
return href
raise ValueError(f"unable to find Integbio download link on {base}")
def _parse_references(s):
rv = []
for part in s.strip().split("||"):
ref = _parse_reference(part.strip())
if ref:
rv.append(ref)
return rv
def _parse_reference(part: str):
if "\\" in part: # it's pubmed followed by equvalent DOI
pubmed, _doi = part.split("\\")
return pubmed
if part.isnumeric(): # it's pubmed
return part
if part == "etc.":
return None
logger.debug(f"IntegBio unhandled reference part: {part}")
def _strip_split(s):
if pd.isna(s):
return None
return [k.strip() for k in s.strip().split("||")]
def _parse_fairsharing(s):
if s.startswith("https://fairsharing.org/10.25504/"):
return s.removeprefix("https://fairsharing.org/10.25504/")
elif s.startswith("https://fairsharing.org/"):
return s.removeprefix("https://fairsharing.org/")
logger.debug(f"unhandled FAIRsharing: {s}")
return None
def get_integbio(*, force_download: bool = False):
"""Get the integbio resource."""
url = get_url()
df = pd.read_csv(url)
df.rename(
columns={
"Database ID": "prefix",
"Database name": "name",
"Alternative name": "alt_name",
"Database description": "description",
"URL": "homepage",
"Link to FAIRsharing": "fairsharing",
"Reference(s) - PubMed ID/DOI": "references",
"Language(s)": "languages",
"Database maintenance site": "maintainer",
"Tag - Target": "target_keywords",
"Tag - Information type": "information_keywords",
"Operational status": "status",
},
inplace=True,
)
for key in SKIP:
del df[key]
df["fairsharing"] = df["fairsharing"].map(_parse_fairsharing, na_action="ignore")
df = df[df["languages"] != "ja"] # skip only japanese language database for now
del df["languages"]
# df["languages"] = df["languages"].map(_strip_split, na_action="ignore")
df["target_keywords"] = df["target_keywords"].map(_strip_split, na_action="ignore")
df["information_keywords"] = df["information_keywords"].map(_strip_split, na_action="ignore")
df["pubmeds"] = df["references"].map(_parse_references, na_action="ignore")
df["description"] = df["description"].map(lambda s: s.replace("\r\n", "\n"), na_action="ignore")
del df["references"]
# TODO ground database maintenance with ROR?
rv = {}
for _, row in df.iterrows():
rv[row["prefix"].lower()] = {k: v for k, v in row.items() if isinstance(v, (str, list))}
PROCESSED_PATH.write_text(json.dumps(rv, indent=True, ensure_ascii=False, sort_keys=True))
return rv
class IntegbioAligner(Aligner):
"""Aligner for the Integbio."""
key = "integbio"
alt_key_match = "name"
getter = get_integbio
curation_header = ("name", "alt_name", "homepage")
if __name__ == "__main__":
IntegbioAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723255221.0
bioregistry-0.11.12/src/bioregistry/external/integbio/processed.json 0000644 0001751 0000177 00006641056 14655544665 025326 0 ustar 00runner docker {
"nbdc00001": {
"description": "This database collects URL information from international life science databases and the associated basic metadata, including descriptions of the database and information about the species. Databases include those independently operated by the Ministry of Education, Culture, Sports, Science and Technology, the Ministry of Health, Labour and Welfare, the Ministry of Agriculture, Forestry and Fisheries, and the Ministry of Economy, Trade and Industry. Since the catalog began in October 2012, the respective ministries have continued to accumulate information for the database, adding to and updating the catalog, which includes:\n\n- Database Catalog\n- WINGpro\n- MEDALS Database Catalog\n- AgrID Database Catalog\n- National Institute of Biomedical Innovation database list",
"fairsharing": "4032",
"homepage": "https://integbio.jp/dbcatalog/?lang=en",
"information_keywords": [
"Bibliography/Documents",
"Portal"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "Integbio Database Catalog",
"prefix": "NBDC00001",
"status": "Active"
},
"nbdc00002": {
"description": "3DinSight is a database that helps users explore the relationship between the structure, function, and properties of biomolecules. Structural data are derived from the Protein Data Bank (PDB) and displayed as real-time 3D images by RasMol and Virtual Reality Modeling Language (VRML). Functional domains and mutations are identified by PROSITE and Protein Mutant Database, respectively.",
"homepage": "http://gibk26.bio.kyutech.ac.jp/jouhou/3dinsight/3DinSight.html",
"information_keywords": [
"3D structure"
],
"maintainer": "Kyushu Institute of Technology",
"name": "3DinSight",
"prefix": "NBDC00002",
"pubmeds": [
"9545451"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00003": {
"alt_name": "5'-end serial analysis of gene expression database",
"homepage": "http://5sage.gi.k.u-tokyo.ac.jp/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "The University of Tokyo Graduate School of Frontier Sciences",
"name": "5'SAGE",
"prefix": "NBDC00003",
"pubmeds": [
"15300261",
"15608259"
],
"status": "Inactive"
},
"nbdc00004": {
"alt_name": "Amino acid indices, substitution matrices and pair-wise contact potentials",
"description": "The AAindex database collects and organizes amino acid properties. Users can search from dozens of studies summarizing multiple biophysical parameters for three types of information:\n- AAindex1: Biophysical properties of individual amino acids. All indexed studies have been compared to other studies in the database and pairwise correlation coefficients between related studies are provided. \n- AAindex2: Substitution indices indicating amino acid similarity.\n- AAindex3: Pairwise contact potentials between amino acids in various contexts.\nAll three databases can be searched either by study or keyword using DBGET.",
"homepage": "http://www.genome.jp/aaindex/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "AAindex",
"prefix": "NBDC00004",
"pubmeds": [
"17998252",
"9847231",
"10592278",
"3244698",
"9053899"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00005": {
"description": "Animal Search System allows keyword searches to be performed on more than 2000 strains of mice available from the RIKEN BRC, including transgenic, knockout, inbred, wild-derived, ENU mutant and congenic strains. Although the top page is written in Japanese, each search result has a link to the English page. The system also provides detailed information that capture the characteristics of the strain, such as the strain name, description, gene details, references, availability status, images and so on.",
"homepage": "http://www2.brc.riken.jp/lab/animal/search.php",
"information_keywords": [
"Bioresource",
"Method",
"Image/Movie"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "Animal Search System",
"prefix": "NBDC00005",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Health/Disease"
]
},
"nbdc00006": {
"alt_name": "Archaeal Gene Network",
"description": "Arch genet is a database providing summaries of the expression of individual genes of Thermoplasma volcanium GSS1, a thermophilic archaeon, during adaptation to various environments, as identified experimentally. \nAll the genes in a given genome are not used simultaneously at any given time in vivo, and organisms adapt to various environments by the process of re-selecting concerned populations of genes although the genomic information remains the same. Arch genet provides visual data to contribute to a better understanding of gene networks as applicable to environmental adaptation.",
"homepage": "http://riodb.ibase.aist.go.jp/db067/",
"information_keywords": [
"Environment",
"Expression",
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "Arch GeNet",
"prefix": "NBDC00006",
"status": "Closed",
"target_keywords": [
"cDNA/EST",
"Protein"
]
},
"nbdc00007": {
"alt_name": "Archaebacterial Information Collection",
"description": "ARCHAIC stands for 'ARCHAebacterial Information Collection' is a database of analyzed archaebacterial genomic DNA sequences. Determinations follow a consistent method so that the overall organization of the genomes can be understood better and different species can be compared based on genomic DNA sequences. Information on the identification of genes, pseudo-genes, and operons, derived by original methods, is available. The complete genomic DNA sequences of Pyrococcus sp. OT3 and Thermoplasma volcanium GSS1, an aero/anaero-facultative archaebacterium, respectively, can also be found here.",
"homepage": "http://riodb.ibase.aist.go.jp/archaic/ARCHAIC.html",
"information_keywords": [
"Sequence"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "ARCHAIC",
"prefix": "NBDC00007",
"pubmeds": [
"9598984",
"11121031"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00008": {
"description": "ArkDB is a database that contains extensive mapping information of the genomes of farm animals and other animal species.\nThis repository records the maps in detail as well as their markers with some marker-marker relationships.\nA species table provides data on specific chromosomes.\nThe Maps menu leads to the results of mapping analyses.\nA keyword search is available.\nGFF files may be downloaded and displayed in the Ensembl genome browser.",
"homepage": "http://www.thearkdb.org/arkdb/",
"information_keywords": [
"Sequence"
],
"maintainer": "The Roslin Institute (University of Edinburgh)",
"name": "ArkDB",
"prefix": "NBDC00008",
"pubmeds": [
"11125062",
"19682365"
],
"status": "Closed",
"target_keywords": [
"Genetic variation"
]
},
"nbdc00009": {
"alt_name": "ArrayExpress Archive",
"description": "ArrayExpress is a database of experiments related to the structure, function, evolution, and mapping of genomes.\nIt contains information on gene expression obtained from microarray and sequencing studies.\nAltogether 36,292 experiments are listed. Each experiment is described and reported in detail.\nAltogether 13,748 arrays are listed and described.\nKeyword and advanced search options are available.\nThe data may also be downloaded.",
"fairsharing": "biodbcore-000305",
"homepage": "https://www.ebi.ac.uk/biostudies/arrayexpress",
"information_keywords": [
"Expression",
"Repository"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "ArrayExpress",
"prefix": "NBDC00009",
"pubmeds": [
"12519949",
"14744115",
"15608260",
"16939801",
"17132828",
"19015125",
"21071405"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"RNA",
"Protein"
]
},
"nbdc00010": {
"alt_name": "ARabidopsis Tiling-Array-based Detection of Exons",
"homepage": "http://omicspace.riken.jp/ARTADE/",
"information_keywords": [
"Expression"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "ARTADE",
"prefix": "NBDC00010",
"pubmeds": [
"16098113"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc00011": {
"description": "This database allows users to explore the gene expression of Aspergillus oryzae with different environmental stimuli from 21,368 EST clones.",
"homepage": "http://nribf21.nrib.go.jp/EST2/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "National Research Institute of Brewing",
"name": "Aspergillus oryzae EST DataBase",
"prefix": "NBDC00011",
"pubmeds": [
"18448366",
"17540709"
],
"status": "Suspended",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00012": {
"description": "The Atlas of genetics and Cytogenetics in Oncology and Haematology is a database for genes, cytogenetics and clinical entities in cancer, and cancer-prone diseases. It provides concise and updated reviews (cards) or longer texts (deep insights), a huge portal towards genetics and/or cancer databases and journals, teaching items in genetics for students in Medicine and in Sciences, and a case report section. Users are able to search data using gene name, solid tumors name, chromosomal number, or cancer-prone diseases.",
"homepage": "http://atlasgeneticsoncology.org/",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "ATLAS",
"name": "Atlas of Genetics and Cytogenetics in Oncology and Haematology",
"prefix": "NBDC00012",
"pubmeds": [
"10592271",
"9847226",
"11125120",
"12520000",
"10942808"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Health/Disease",
"Cell/Organelle"
]
},
"nbdc00013": {
"alt_name": "Barley Bioresource Database",
"description": "National BioResource Project (NBRP) BarleyDB includes information about the barley germplasm preserved in the Institute of Plant Science and Resources, Okayama University. Users can search and browse information of barley germplasm (spike/seed images, collection sites map) and full length cDNA clones and ESTs of barley. These barley resources are available for research purpose.",
"homepage": "http://earth.lab.nig.ac.jp/~dclust/cgi-bin/index.cgi?lang=en",
"information_keywords": [
"Bioresource",
"Sequence",
"Bibliography/Documents",
"Phenotype"
],
"maintainer": "National Institute of Genetics",
"name": "Barley DB",
"prefix": "NBDC00013",
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Organism",
"Genetic variation"
]
},
"nbdc00014": {
"alt_name": "Berkeley Drosophila Genome Project",
"description": "This is the website for the Berkeley Drosophila Genome Project, and has information about genomic sequencing, sequence annotations, as well as data on EST, cDNA, and gene expression patterns. It also distributes genomic or cDNA clones, library filters or fly stocks and vector maps.",
"homepage": "http://www.fruitfly.org/",
"information_keywords": [
"Bioresource",
"Sequence",
"Expression",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "The Berkeley Drosophila Genome Project",
"name": "BDGP",
"prefix": "NBDC00014",
"pubmeds": [
"10471706"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"Protein"
]
},
"nbdc00015": {
"description": "This gallery uses high quality images of spatial models of nucleic acids, proteins and their complexes. In this database, users can visualize basic biomolecules (nucleic acids and amino acid) and complex motifs (nucleic acid base-pairing, protein secondary structures and functional domains).",
"homepage": "http://dna00.bio.kyutech.ac.jp/image/gallery.html",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie",
"3D structure"
],
"maintainer": "Kyushu Institute of Technology",
"name": "Biomolecules Gallery",
"prefix": "NBDC00015",
"status": "Inactive",
"target_keywords": [
"DNA",
"RNA",
"Protein"
]
},
"nbdc00016": {
"description": "Users can use the BioTermNet database to explore relationships between proteins, DNA, gene expression, and drug compounds: 1. Related concepts from a single concept; 2. A single concept to a single concept; 3. Multiple concepts to a single concept; 4. Common concepts among multiple concepts; and 5. gene clustering. Key examples of these relationships are: the identification of interactions between drugs and biomolecules, linkage analyses of cancer-related genes, and interpretation of DNA/protein analyses. The output data is expressed as protein-protein/gene/family/compound (drug) interactions (PRIME), statistical relatedness, or protein-biological process function (PRIME-GO).",
"homepage": "http://btn.ontology.hgc.jp/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "The University of Tokyo The Institute of Medical Science Human Genome Center",
"name": "BioTermNet",
"prefix": "NBDC00016",
"status": "Inactive"
},
"nbdc00017": {
"description": "This photographic database contains images of mutant Bombyx mori larvae along with changes in larvae length. Currently, the database comprises more than 40 mutants that map to multiple chromosomes.",
"homepage": "http://papilio.ab.a.u-tokyo.ac.jp/bioresource/shimada/mutant_photo.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "The University of Tokyo",
"name": "Photographs of mutants in Bombyx mori",
"prefix": "NBDC00017",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc00018": {
"homepage": "http://riodb.ibase.aist.go.jp/brain/index.php",
"information_keywords": [
"Image/Movie"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "Brain Atlas Database of Japanese Monkey for WWW.",
"prefix": "NBDC00018",
"status": "Closed",
"target_keywords": [
"Organism"
]
},
"nbdc00019": {
"description": "BRENDA is an extensive database of enzymes, which came online in January 2013.\nAs many as 5858 various enzymes are listed and a comprehensive amount of information about each of these is available, for example enzyme structure, reaction and specificity, disease-related information, stability and functional parameters.\nThe search option EC Explorer gives entry to a page where the enzymes are grouped under oxidoreductases (of 6,523 organisms), transferases (of 4,594 organisms), hydrolases (of 7,847 organisms), lyases (of 3,498 organisms), isomerases (of 1,329 organisms) and ligases (of 1,100 organisms).\nA Quick search option (enter name or ID number) is offered, as well as a Full Text and an Advanced search option, where a combination of criteria can be entered to narrow down the search results.",
"fairsharing": "biodbcore-000249",
"homepage": "http://www.brenda-enzymes.info/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Technische Universitat Braunschweig",
"name": "The Comprehensive Enzyme Information System (BRENDA)",
"prefix": "NBDC00019",
"pubmeds": [
"11752250",
"14681450",
"11796225",
"12850129",
"17202167",
"18984617",
"21030441",
"21062828",
"21827651"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein",
"Health/Disease"
]
},
"nbdc00020": {
"alt_name": "Bacillus subtilis Genome Database",
"description": "BSORF is a repository for Bacillus subtilis genomic information from researchers in multiple countries. Detailed information regarding B. subtilis mutants is listed, as well as DNA array data and links to the KEGG Expression Database. In addition, users can search for nucleotide and amino acid sequence homology against B. subtilis genomic sequences or coding sequences.",
"homepage": "http://bacillus.genome.jp/",
"information_keywords": [
"Bioresource",
"Sequence",
"Expression"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "BSORF",
"prefix": "NBDC00020",
"pubmeds": [
"12682299"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein",
"Organism"
]
},
"nbdc00021": {
"fairsharing": "biodbcore-000431",
"homepage": "http://www.ncbi.nlm.nih.gov/cancerchromosomes",
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "Cancer Chromosomes",
"prefix": "NBDC00021",
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Cell/Organelle"
]
},
"nbdc00022": {
"alt_name": "Center for Animal Resources and Development Database",
"description": "CARD (Center for Animal Resources and Development) R-BASE (Resource Database) is the database for cryopreserved embryos of genetically engineered mice. CARD have over 1,500 mouse strains, 842,000 frozen embryos and 26,000 straws containing frozen sperm, and disclose information about 1,300 deposited strains. Over 400 strains of frozen embryos or mice produced from frozen embryos and sperm are available on request both domestically and internationally.",
"homepage": "http://cardb.cc.kumamoto-u.ac.jp/transgenic/index.jsp",
"information_keywords": [
"Bioresource",
"Ontology/Terminology/Nomenclature",
"Bibliography/Documents"
],
"maintainer": "Kumamoto University Institute of Resource Development and Analysis",
"name": "CARD R-BASE",
"prefix": "NBDC00022",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Organism",
"Health/Disease"
]
},
"nbdc00023": {
"alt_name": "Consensus CDS",
"description": "This database seeks to identify a core set of human and mouse protein coding regions of high quality that are consistently annotated.",
"fairsharing": "biodbcore-000432",
"homepage": "http://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi",
"information_keywords": [
"Sequence"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "CCDS",
"prefix": "NBDC00023",
"pubmeds": [
"19498102"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00025": {
"alt_name": "Cancer Gene Expression Database",
"description": "The CGED database comprises gene expression profile data and related clinical information for breast (prognosis and docetaxel treatment), colorectal, hepatocellular, esophageal, thyroid, and gastric cancers, collected through a collaboration between four medical centers in Japan. The data is searchable by type of cancer, gene name/symbol, Swiss-Prot functional annotation, GenBank accession number, RefSeq, or p-values/q-values for differential gene expression and results are displayed as graphical representations of expression and clinical data.",
"homepage": "http://lifesciencedb.jp/cged/",
"information_keywords": [
"Expression"
],
"maintainer": "DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "CGED",
"prefix": "NBDC00025",
"pubmeds": [
"15608255"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST",
"Health/Disease"
]
},
"nbdc00026": {
"alt_name": "Comparative Genomic Hybridization Database",
"description": "The CGH Database is a portal of databases with thorough data on human genome aberrations and variations. These have been detected by bacterial artificial chromosome (BAC) clones-based array comparative genomic hybridization (aCGH). There is a link to the CGH (Comparative Genomic Hybridization) Database with genomic aberrations that have been detected by conventional CGH and aCGH in more than a dozen different cancer cell lines. There is also a link to the MCG CNV Database, which provides genomic copy number variants that were detected by array-CGH analyses of healthy Japanese parent and child trios. These databases are partly supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), the Japan Science and Technology Corporation (JST) and the Industrial Technology Development Organization (NEDO).",
"homepage": "http://www.cghtmd.jp/CGHDatabase/index_e.jsp",
"information_keywords": [
"Expression"
],
"maintainer": "Tokyo Medical and Dental University Medical Research Institute",
"name": "CGH Data Base",
"prefix": "NBDC00026",
"status": "Active",
"target_keywords": [
"Genetic variation",
"Health/Disease"
]
},
"nbdc00027": {
"alt_name": "Chemical Entities of Biological Interest",
"description": "ChEBI is a collection of data on entities of biological interest.\nThis database concentrates on assembling data on smaller chemical compounds, such as atoms, molecules, ions, radicals etc. These should be produced in nature or be synthetic molecules affecting biological processes in living organisms.\nChEBI does not generally include molecules directly encoded by the genome.\nThe database contains 31,651 entries with annotations.\nA keyword search option is available.\nIn addition to this an advanced search option, which includes a structure drawing tool, is provided.\nThe ChEBI database can be searched individually or in combination with other databases.",
"homepage": "http://www.ebi.ac.uk/chebi/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "ChEBI",
"prefix": "NBDC00027",
"pubmeds": [
"17932057",
"19496059",
"19854951"
],
"status": "Active",
"target_keywords": [
"Carbohydrate",
"Lipid",
"Metabolite",
"Chemical compound"
]
},
"nbdc00028": {
"description": "This database collects EST for Chlamydomonas reinhardtii, each with blastx analysis against the non-redundant protein database results.",
"homepage": "https://www.kazusa.or.jp/e/plant/chlamy/EST/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Chlamydomonas reinhardtii EST index",
"prefix": "NBDC00028",
"pubmeds": [
"11089912",
"10691129"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00029": {
"alt_name": "Center for Information Biology gene Expression database",
"description": "CIBEX is a repository of gene expression data from microarray-based experiments measuring mRNA, SAGE tags, and proteomic data from mass spectrometry. All included data meet MIAME standards.",
"homepage": "http://cibex.nig.ac.jp/data/index.html",
"information_keywords": [
"Expression",
"Repository"
],
"maintainer": "Bioinformation and DDBJ Center, National Institute of Genetics, Research Organization of Information and Systems",
"name": "CIBEX",
"prefix": "NBDC00029",
"pubmeds": [
"14744116",
"15669238"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00030": {
"alt_name": "Clusters of SWISS-PROT and TrEMBL proteins database",
"homepage": "http://www.ebi.ac.uk/clustr/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "CluSTr",
"prefix": "NBDC00030",
"pubmeds": [
"11125042",
"15961444",
"12520029",
"11125045"
],
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc00031": {
"alt_name": "Comparative Regulatory Genomics",
"homepage": "http://corg.eb.tuebingen.mpg.de/cgi-bin/index.pl",
"information_keywords": [
"Sequence"
],
"maintainer": "Max-Planck-Institut fur Entwicklungsbiologie",
"name": "CORG",
"prefix": "NBDC00031",
"pubmeds": [
"12519946",
"16888353",
"17135197",
"15723697",
"12385988"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"DNA"
]
},
"nbdc00032": {
"alt_name": "Mechanism and Catalytic Site Atlas",
"description": "M-CSA is a database about enzyme reaction. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of enzymes. Each record contains references about protein and structure (sequence, biological species, PDB, Catalytic CATH Domains), enzyme reaction and enzyme mechanisms. This database represents a unified resource that combines the data in both MACiE (http://www.ebi.ac.uk/thornton-srv/databases/MACiE/) and the CSA (http://www.ebi.ac.uk/thornton-srv/databases/CSA/).",
"fairsharing": "biodbcore-001078/",
"homepage": "https://www.ebi.ac.uk/thornton-srv/m-csa/",
"information_keywords": [
"Sequence",
"3D structure",
"Interaction/Pathway"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "M-CSA",
"prefix": "NBDC00032",
"pubmeds": [
"29106569"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00033": {
"description": "The Codon Usage Database is an extended web-based version of CUTG (Codon Usage Tabulated from GenBank) and is used for exploration of codon usage within various organisms, chloroplast, and mitochondria. The database captures data from the NCBI-GenBank for 3,027,973 complete protein coding genes from 35,799 organisms. Users can search the database by organism with data expressed in tabular form: codon, frequency per 1000, number. In addition, the table can be modified to include the amino acid encoded by the codon.",
"homepage": "http://www.kazusa.or.jp/codon/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Codon Usage Database",
"prefix": "NBDC00033",
"pubmeds": [
"10592250"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc00034": {
"alt_name": "Genome database for Cyanobacteria",
"description": "CyanoBase combines sequence data, NCBI taxonomy and KEGG genome information with social genome annotation and features derived from UniProt for 39 species of Cyanobacteria. Links to BLAST and KazusaMart allow users to search for related genes and genomes. Users can also explore curated Cyanobacteria mutant information, as well as global proteome, interactome, and transcriptome relationships.",
"homepage": "http://genome.microbedb.jp/cyanobase",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "CyanoBase",
"prefix": "NBDC00034",
"pubmeds": [
"19880388",
"9399802",
"10592184",
"9847144",
"24275496",
"27899668"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00035": {
"alt_name": "Cyanobacteria Gene Annotation Database",
"description": "CYORF is an interactive community database that allows registered users to both access and annotate available cyanobacteria genome data. The database provides reliable information regarding experimental data, sequences, and gene functions with corresponding citations.",
"homepage": "http://cyano.genome.jp/",
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "CYORF",
"prefix": "NBDC00035",
"pubmeds": [
"17211581"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00036": {
"alt_name": "Definitive Haplotype Database",
"description": "D-HaploDB is a database of genome-wide definitive haplotypes that allows users to view SNP alleles, LD bins, and CNVs by sequence name, gene name, locus, or other landmark search query, with 1.7 million SNPs and 2,339 CNVRs determined with high-throughput array-based oligonucleotide hybridization techniques. The advantages of this technique include:\n1. Haplotypes can be read directly from genotyping\n2. CNVSs can be detected with higher signal-to-noise ratio\n3. Heterozygous sites of overlapping CNVSs do not need to be resolved.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/dhaplodb/desc.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Kyushu University Medical Institute of Bioregulation",
"name": "D-HaploDB (Archive)",
"prefix": "NBDC00036",
"pubmeds": [
"17166862",
"16251461",
"19424418",
"20537301"
],
"status": "Active",
"target_keywords": [
"Genetic variation"
]
},
"nbdc00037": {
"alt_name": "A curated catalogue of structural variation in the human genome",
"description": "Database of Genomic Variants is a repository that provides information about variations in structure in the human genome.\nThe database offers information on genomic changes in DNA segments larger than 1kb as well as annotated insertion/deletion variations in a range of 100bp to 1kb. Only healthy samples were studied, which makes the results very useful to apply as controls in future related studies.\nThe collection contains 101,923 entries. \nThe number of CNVs identified is 6,6741 and inversions are 953.\nThere were 34,229 InDels in the 100bp to 1kb range.\nData concerning whole chromosomes can be retrieved.\nKeyword and Blast search options are also provided.",
"homepage": "http://dgv.tcag.ca/",
"information_keywords": [
"Sequence"
],
"maintainer": "The Centre for Applied Genomics",
"name": "Database of Genomic Variants",
"prefix": "NBDC00037",
"pubmeds": [
"15286789",
"17124402"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Health/Disease"
]
},
"nbdc00038": {
"description": "This database comprises 168 Caenorhabditis elegans genes compiled to help users identify phenotypes affecting germline development. Each gene displayed a significantly stronger signal by differential hybridization than a forward-substracted cDNA pool enriched for cDNA derived from meiotic nuclei. Several clones have shown sterility phenotypes as assessed by RNAi analysis.",
"homepage": "http://park.itc.u-tokyo.ac.jp/mgrl/germline/",
"information_keywords": [
"Phenotype",
"Expression",
"Image/Movie"
],
"maintainer": "The University of Tokyo",
"name": "Database of the RNAi phenotypes for the 168 genes analyzed",
"prefix": "NBDC00038",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc00039": {
"description": "PRINTS Version 42.0 is a collection of motifs called 'fingerprints', because they are applied to define the character of protein families. To obtain these protein fingerprints the SWISS-PROT and TrEMBL databases were scanned repetitively. The motifs are usually located on the protein sequence as separate, but consecutive units with no overlaps. They are more effective in encoding protein folds and determining their function than are single motifs. The database contains 2,156 fingerprints and 12,444 single motifs.\nThis repository can be search by means of entering an accession number, a PRINTS code, a database code, a sequence or by making use of the provided keyword search option. A Blast sequence search option as well as a BLOCKS search option is provided. This database was created on 2 February 2012.",
"fairsharing": "biodbcore-000568",
"homepage": "http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/index.php",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Manchester",
"name": "PRINTS",
"prefix": "NBDC00039",
"pubmeds": [
"7937065",
"7971946",
"2330366"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00040": {
"description": "DBGET is an integrated system to help users search across an assemblage of major biological databases. The biological databases included are classified into five categories:\n1. KEGG databases \n2. Other DBGET databases\n3. Searchable databases\n4. Link-only databases\n5. PubMed databases\nSearches can encompass a specific database, database category, or include all available databases.",
"homepage": "http://www.genome.jp/dbget/",
"information_keywords": [
"Portal"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "DBGET Search",
"prefix": "NBDC00040",
"pubmeds": [
"9697222"
],
"status": "Active"
},
"nbdc00041": {
"alt_name": "a Protein Polymorphism database",
"description": "dbProP is a database for supporting research on protein polymophisms. It provides information on amino acid polymorphisms and splicing variants found in protein coding region. dbProP has collected all kind of polymorphisms that cause amino acid substitution thoroughly. It also contains data for SNPs candidates and splicing variants predicted from transcription sequence clusters. It allows to retrieve data with a variety of criteria such as gene name, protein motif, Unigene ID, gene database registration number, position on chromosome, absolute base range from a marker and source tissue.",
"homepage": "http://dbprop.nirs.qst.go.jp/Prop/index_e.html",
"information_keywords": [
"Sequence"
],
"maintainer": "National Institute of Radiological Sciences",
"name": "dbProP",
"prefix": "NBDC00041",
"status": "Inactive",
"target_keywords": [
"Genetic variation",
"Protein"
]
},
"nbdc00042": {
"alt_name": "SNPs in the transcriptional promoter regions in human",
"description": "dbQSNP is a database of SNPs to help users characterize regulatory mechanisms of genes with medical importance. The database collects and presents experimental data of SNP sequences and allele frequencies in the promoter regions by SSCP analysis. dbQSNP records can be easily searched by a BLAST-search against STS sequences found in the database or by keyword or chromosomal location.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/dbqsnp/desc.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Kyushu University Medical Institute of Bioregulation",
"name": "dbQSNP (Archive)",
"prefix": "NBDC00042",
"pubmeds": [
"15977179",
"12449392",
"12491901",
"11083945",
"11242937",
"9371745",
"2687159"
],
"status": "Active",
"target_keywords": [
"Genetic variation"
]
},
"nbdc00043": {
"alt_name": "A database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information",
"description": "The DBTBS database consists of experimentally validated data for Bacillus subtilis regulated genes and transcription factors to help users elucidate complete gene regulatory networks. Search tools allow exploration of intergenic conservation with homologous genes from Gram-positive bacteria and locations of specific motif sequences within the B. subtilis genome.",
"homepage": "http://dbtbs.hgc.jp/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "The University of Tokyo The Institute of Medical Science Human Genome Center",
"name": "DBTBS",
"prefix": "NBDC00043",
"pubmeds": [
"14681362",
"17962296"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00044": {
"alt_name": "Database of Tunicate Gene Regulation",
"description": "DBTGR collects information on tunicate gene regulation, including experimental data, reported gene activities, and identified regulatory elements present in promoter sequences. Users can search by organism name, tissue type, specific transcription factor, identified gene, or a genome region, to build an understanding of the regulatory systems underlying the developmental and physiological processes of vertebrates.",
"homepage": "http://dbtgr.hgc.jp/",
"information_keywords": [
"Sequence",
"Expression",
"Bibliography/Documents"
],
"maintainer": "The University of Tokyo The Institute of Medical Science Human Genome Center",
"name": "DBTGR",
"prefix": "NBDC00044",
"pubmeds": [
"16381930"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00045": {
"alt_name": "Database of Transcriptional Start Sites",
"description": "DBTSS provides precise positional information for transcription start sites (TSSs) of eukaryotic mRNAs. One characteristic of DBTSS is coverage of TSS information on a major part of human adult and embryonic tissues. To identify single nucleotide variations (SNVs) in the regulatory regions, TSS information are associated with public and original SNVs data. For example, this database includes RNA-seq data of subcellular-fractionated RNAs, ChIP Seq data of histone modifications and binding sites of RNA polymerase II / several transcription factors in cultured cell lines.",
"fairsharing": "biodbcore-000024",
"homepage": "http://dbtss.hgc.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tokyo The Institute of Medical Science Human Genome Center",
"name": "DBTSS",
"prefix": "NBDC00045",
"pubmeds": [
"19910371",
"11752328",
"17942421",
"21372179",
"19237398"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"DNA"
]
},
"nbdc00046": {
"alt_name": "DNA Data Bank of Japan",
"description": "DDBJ, which is organized by NIG (National Institute of genetics), is one of the three databanks that constitute International Nucleotide Sequence Database (INSD). DDBJ shares new and updated data with EMBL and GenBank at any given moment, and Japanese researchers submit 99% of INSD data through DDBJ. It privides sequence data search systems such as getentry, ARSA, TXSearch and BLAST. Phylogenetic analysis is also available on the web by using sequence alignment program; ClustalW.",
"fairsharing": "biodbcore-000027",
"homepage": "https://www.ddbj.nig.ac.jp/index-e.html",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "Bioinformation and DDBJ Center, National Institute of Genetics, Research Organization of Information and Systems",
"name": "DDBJ",
"prefix": "NBDC00046",
"pubmeds": [
"18927114",
"21062814",
"24194602"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"DNA",
"RNA"
]
},
"nbdc00047": {
"alt_name": "Deinococci Genome Database",
"description": "The DeinoBase database annotates open reading frames within the Deinococcus radiodurans genome to help users discover new DNA repair genes and gain a better understanding of the molecular basis for resistance to DNA damage. An additional goal of DeinoBase is to sequence whole genomes of other Deinococcus bacterial species for comparative genomics analyses.",
"homepage": "http://yayoi.kansai.jaea.go.jp/php/DeinoBase/index.php",
"information_keywords": [
"Sequence"
],
"maintainer": "Japan Atomic Energy Agency",
"name": "DeinoBase",
"prefix": "NBDC00047",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00048": {
"alt_name": "Drosophila Genetic Resource Center",
"description": "DGRC is the integrated retrieval system for Drosophila strains collected and maintained by NBRP 'Drosophila'. DGRC provides strain search system to input information such as genotypes, cytolocations, names of a species and phenotypes. This database also supplies chromosome maps that strains are mapped. Requests for Drosophila strains are available by using online contact form.",
"homepage": "http://fruitfly.jp/flystock/index_e.html",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "Kyoto Institute of Technology Drosophila Genetic Resource Center",
"name": "DGRC",
"prefix": "NBDC00048",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc00049": {
"alt_name": "Database of Interacting Proteins",
"description": "The DIP is a database of experimentally determined interactions between proteins. It contains protein pairs that are known to bind with each other at two amino acid chains. Each entry is curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Each protein participating in a DIP interaction cross-references to, at least, one of the major protein databases - PIR, SWISSPROT and/or GENBANK. This database can be searched with node, BLAST, or text searches.",
"fairsharing": "biodbcore-000558",
"homepage": "http://dip.doe-mbi.ucla.edu/dip/Main.cgi",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Repository"
],
"maintainer": "University of California",
"name": "DIP",
"prefix": "NBDC00049",
"pubmeds": [
"14681454",
"1175232",
"11125102",
"10592249"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00050": {
"alt_name": "a genome database of microorganisms sequenced at NITE",
"description": "This is a database containing genomic information of 29 microorganisms.\nSequencing of these microorganisms (2 Eukaryota, 4 Archaea and 23 Bacteria) was done by the National Institute of Technology and Evaluation (NITE)\nFull text, Advanced, Blast and Sequence searches are enabled.\nGenome data may be downloaded via FTP, but the site administrators request feedback outlining the work the information was used for in order for them to improve the database.\nAll relevant posters, publications and patents acquired using information from this site have to clearly state that NITE is the source of information displayed.",
"homepage": "http://www.bio.nite.go.jp/dogan/Top",
"information_keywords": [
"Bioresource",
"Method",
"Sequence",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "NITE (National Institute of Technology and Evaluation)",
"name": "DOGAN",
"prefix": "NBDC00050",
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Protein",
"Organism"
]
},
"nbdc00051": {
"alt_name": "electrostatic surface of Functional-site",
"description": "eF-site is a database of molecular surfaces and electrostatic potentials for structures in the PDB that allows users to identify active sites and predict molecular recognition mechanisms to infer protein function. The molecular surfaces, with both electrostatic and hydrophobic properties, can be calculated for individual protein subunits, protein complexes, and/or dsDNA in protein-DNA complexes.",
"homepage": "https://pdbj.org/eF-site/",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "eF-site",
"prefix": "NBDC00051",
"pubmeds": [
"12836670",
"14871866",
"15689509",
"12876308",
"12831893",
"12876312",
"12836670",
"6879170"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00052": {
"alt_name": "Database for the Exchangeable Gene Trap Clones",
"description": "EGTC is a mouse gene trap resource which allows users to find information on cell lines and mice with targeted genetic exchanges of over 1000 genes. Analysis is either via gene replacement or knockout techniques, and is geared toward developmentally relevant genes.",
"homepage": "http://egtc.jp/action/main/index",
"information_keywords": [
"Bioresource",
"Sequence",
"Image/Movie"
],
"maintainer": "Kumamoto University Institute of Resource Development and Analysis",
"name": "EGTC",
"prefix": "NBDC00052",
"pubmeds": [
"19199955"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"DNA",
"Organism",
"Cell/Organelle"
]
},
"nbdc00053": {
"alt_name": "EMBL Nucleotide Sequence Database",
"description": "The European Nucleotide Archive (ENA) is a database that contains information about the structure and layout of nucleotide sequencing experiments.\nThe content of such a workflow covers the input data, the data the machine delivers and the interpreted results.\nText search and sequence search option are provided.\nENA data can be downloaded through the ENA Browser in a variety of data formats.",
"homepage": "http://www.ebi.ac.uk/embl/",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "EMBL-Bank",
"prefix": "NBDC00053",
"pubmeds": [
"18978013"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"DNA",
"RNA"
]
},
"nbdc00054": {
"description": "ENSEMBL is a collection of automatically annotated genome databases for vertebrates and a number of eukaryotes, integrated with all other relevant biological data available.\nThe repository covers data on gene annotation, microarray probeset mapping and comparative genomics among many other topics.\nInformation may be downloaded by a variety of means: \nFor small amounts of data, an export option is suggested.\nFor larger amounts of data, an FTP site is provided from where a complete database may be downloaded in one of various formats, from flat files to MySQL dumps.",
"fairsharing": "biodbcore-000330",
"homepage": "http://uswest.ensembl.org/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Wellcome Sanger Institute",
"name": "Ensembl",
"prefix": "NBDC00054",
"pubmeds": [
"11752248",
"28365736"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00055": {
"description": "This search engine combs for information from over 30 major databases at NCBI, including PubMed, nucleic acids, amino acid sequences, expression data, PubChem (small molecules with biochemical functions), protein structure, sequenced genomes, and taxonomy. The search engine provides links to the search results, as well as to other related databases.",
"homepage": "https://www.ncbi.nlm.nih.gov/search/",
"information_keywords": [
"Portal",
"Bibliography/Documents",
"Taxonomy"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "Search NCBI databases",
"prefix": "NBDC00055",
"status": "Active",
"target_keywords": [
"Health/Disease",
"Genome/Gene",
"Protein",
"Chemical compound"
]
},
"nbdc00056": {
"description": "The ENU mutants allows users to find mutant mouse lines. The program has performed a large-scale mutagenesis and screened several mice, categorized by morphological and behavioral phenotypes. Phenotypes can be searched by experiment or keyword and mutants can be ordered. An Oracle-based mutagenesis database is also available.",
"homepage": "http://www.brc.riken.jp/lab/gsc/mouse/",
"information_keywords": [
"Bioresource",
"Method",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "ENU Mutants (A large Scale Mutagenesis Project in Riken GSC)",
"prefix": "NBDC00056",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc00057": {
"alt_name": "Encyclopedia of Protein Structures",
"description": "eProtS is a dictionary about protein molecules that are particularly important for biology with images of the protein three-dimensional structures. eProtS aims to support understanding the structures and the biological functions of proteins for non-specialists of protein structures. Proteins are classified according to the original (old version) eProtS, biological (cellular) functions or biochemical functions. This website also provides information about species, biological context, structure description, links to PDB entries and links to references.",
"homepage": "https://pdbj.org/info/eprots",
"information_keywords": [
"Bibliography/Documents",
"3D structure"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "eProtS",
"prefix": "NBDC00057",
"status": "Suspended",
"target_keywords": [
"Protein"
]
},
"nbdc00058": {
"description": "This database provides a comprehensive resource about the E. coli O157:H7 Sakai genome, including a species-specific BLAST function, ORF, gene, rRNA, and tRNA location lists, O157:H7 Sakai plasmid sequences, comparative genomics, and an FTP system for bulk data download.",
"homepage": "http://genome.bio.titech.ac.jp/bacteria/o157/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Tokyo Institute of Technology Graduate School of Bioscience and Biotechnology",
"name": "Escherichia coli O157:H7 Sakai",
"prefix": "NBDC00058",
"pubmeds": [
"12481030",
"11597449",
"11111050",
"11108008",
"10691128",
"10734605",
"9628576",
"11258796"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"DNA",
"RNA",
"Protein"
]
},
"nbdc00059": {
"alt_name": "Eukaryotic Comparative Genome Browser",
"homepage": "http://www-btls.jst.go.jp/ComparativeGenomics/index_j.html",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "JST (Japan Science and Technology Agency)",
"name": "ECGB",
"prefix": "NBDC00059",
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00060": {
"description": "Extremobase is a database of genome sequences from various extremophiles. Complete genome sequences are available for seven species, and metagenome sequences are available for three additional conditions. For each sample, descriptive statistics are presented and users can search for ORFs or criteria such as molecular weight or length. Sequence comparison by BLAST is also supported.",
"homepage": "http://www.jamstec.go.jp/gbrowser/cgi-bin/top.cgi",
"information_keywords": [
"Environment",
"Sequence"
],
"maintainer": "Japan Agency for Marine-Earth Science and Technology",
"name": "Extremobase",
"prefix": "NBDC00060",
"status": "Suspended",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc00061": {
"alt_name": "A Database of Enzyme Catalytic Mechanisms",
"description": "The EzCatDB database contains enzyme catalytic mechanisms.\nData in the Protein Data Bank (PDB) are analyzed and classified in reference to the literature. Data are then organized and sets of data with enzyme information like E.C. number, information on the annotated ligand and active residues of PDB proteins, and catalytic mechanisms can be searched. There are also links to other databases such as, \nCATH, KEGG, PubMed, PDBsum, and Swiss-prot.",
"homepage": "https://ezcatdb.cbrc.pj.aist.go.jp/EzCatDB",
"information_keywords": [
"3D structure"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "EzCatDB",
"prefix": "NBDC00061",
"pubmeds": [
"17039546",
"15608227"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc00062": {
"alt_name": "Protein Structure Model Database",
"description": "RIKEN FAMSBASE is a genome-wide protein structure model database that contains a large number of protein models from many organisms, including databases human, rat, mouse, and also novel influenza (swine-origin influenza A/H1N1) proteins. It allows searches using gene(ORF) Name, PDB ID, Motif Name or Keywords.",
"homepage": "http://fams.bio.chuo-u.ac.jp/RIKEN/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Department of Biological Sciences, Chuo University",
"name": "FAMSBASE",
"prefix": "NBDC00062",
"pubmeds": [
"12520053",
"18428727",
"11021542"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00064": {
"alt_name": "A Database of Drosophila Genes & Genomes",
"description": "This database contains genetic information on Drosophila. It allows users to search using BLAST, GenomeBrowser or QuickSearch tool with taxonomical information and image-based data on the life-cycle stages of Drosophila. The information of Drosophila material resources are also provided.",
"fairsharing": "biodbcore-000037",
"homepage": "http://flybase.org/",
"information_keywords": [
"Bioresource",
"Ontology/Terminology/Nomenclature",
"Sequence",
"Expression",
"Interaction/Pathway",
"Image/Movie",
"Bibliography/Documents",
"Taxonomy",
"Repository"
],
"maintainer": "Genetics Society of America",
"name": "FlyBase",
"prefix": "NBDC00064",
"pubmeds": [
"7925011",
"7937045",
"27799470"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"RNA",
"Protein",
"Organism",
"Health/Disease"
]
},
"nbdc00065": {
"alt_name": "A Drosophila Image Database",
"description": "FlyView is an image database of the development and genetics of Drosophila.\nIt specializes in the expression patterns of cloned genes and enhancer trap lines.\nAll images are annotated and these annotations may be entered into a search option to receive additional information.\nMore than 3,700 pictures from 796 enhancer-trap lines are available.\nOptions to search for pattern elements or stocks are present.\nA complete list of all lines available may also be retrieved.\nThe creators of the database ask for as many contributions as possible to enhance the contents. \nThis site is compatible with the main Drosophila database FlyBase.",
"homepage": "http://flyview.uni-muenster.de/",
"information_keywords": [
"Bioresource",
"Expression",
"Image/Movie",
"Repository"
],
"maintainer": "University of Munster",
"name": "FlyView",
"prefix": "NBDC00065",
"pubmeds": [
"9441952"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle"
]
},
"nbdc00066": {
"description": "This database of cDNA sequences allows users to download human sequences, with different compressed packages of full length or 5'-end single read sequences available.",
"homepage": "http://cdna.hgc.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tokyo The Institute of Medical Science",
"name": "Full Length cDNA",
"prefix": "NBDC00066",
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00067": {
"alt_name": "Malaria Full-Length cDNA Database (Plasmodium falciparum)",
"description": "FULL-malaria collects sequence and expression information on the major malaria strain Plasmodia falciparum as well as P. vivax and the murine viruses P. yoelii and P. berghei. Users can search sequences and chromosomes, and data can be downloaded. The site also has a phylogenetic comparison tool for various Plasmodia species and next-generation RNA-sequencing data from field samples, including both viral and human patient expression profiles.",
"homepage": "http://fullmal.hgc.jp/index_ajax.html",
"information_keywords": [
"Sequence",
"Expression",
"Taxonomy"
],
"maintainer": "The University of Tokyo The Institute of Medical Science",
"name": "Full-Malaria",
"prefix": "NBDC00067",
"pubmeds": [
"18987005",
"14681428",
"11125052",
"16005745",
"8125298",
"9373149"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00068": {
"alt_name": "Toxoplasma Full-Length cDNA Database",
"description": "This database features a genome browser for transcriptome analysis of Toxoplasma gondii, with original data produced by the oligo-capping method, namely, full-length cDNA clones and TSS sequences. Also, background information on toxoplasma, the construction of the toxoplasma full-length cDNA library and a BLAST search function are available. \nThe database contains links to other full-length cDNA databases for parasites and anthropods.",
"homepage": "http://fullmal.hgc.jp/index_tg_ajax.html",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tokyo The Institute of Medical Science",
"name": "Full-Toxoplasma",
"prefix": "NBDC00068",
"pubmeds": [
"14987357"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00069": {
"alt_name": "Global Biodiversity Information Facility free and open access to biodiversity data",
"description": "GBIF (Global Biodiversity Information Facility) is a database of information on Biodiversity and its global effect.\nA network of countries across the globe has access to, and participates in supplying, information to the database. \nThere are 38 countries that support the facility financially and are therefore members of the voting governing board.\nThe database contains 396,026,747 indexed records and 10,004 sets of data provided by 464 publishers.\nIt is imperative that the users of any data obtained by means of the GBIF Portal will always give credit to the original data publishers. \nA keyword search option is provided whereby the facility can be searched for information on a specific group of organisms of a specific country or as displayed in a specific set of data.",
"fairsharing": "biodbcore-000635",
"homepage": "http://www.gbif.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Repository"
],
"maintainer": "GBIF Secretariat",
"name": "GBIF",
"prefix": "NBDC00069",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00071": {
"alt_name": "Genome Medicine Database of Japan",
"description": "The Genome Medicine Database of Japan (GeMDBJ) is an integrated database developed by the Study Groups of Millennium Genome Project (MGP), focusing on Alzheimer's disease, Cancer, Diabetes mellitus, Hypertension, Bronchial asthma and Pharmacogenetics (SGMGP). The database provides selected clinical and demographic data, SNPs (including those from JSNP and MGP) and expression profiles analyzed by Affymetrix geneChip. Much of the data is mapped to the human genome and can be visualized using a custom Genome Viewer.\nThe GeMDBJ has now been closed. The main data are available in the Integrative Disease Omics DatabaseοΌiDOx DBοΌ( http://gemdbj.ncc.go.jp/omics/index.html ).",
"homepage": "https://gemdbj.nibio.go.jp/dgdb/index.do",
"information_keywords": [
"Sequence",
"Expression",
"Image/Movie"
],
"maintainer": "National Institutes of Biomedical Innovation, Health and Nutrition",
"name": "GeMDBJ",
"prefix": "NBDC00071",
"pubmeds": [
"19507519",
"20507324",
"20121473"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"Protein",
"Health/Disease"
]
},
"nbdc00072": {
"alt_name": "Gene Name Dictionary",
"description": "This site contains a dictionary of gene names (GENA). The dictionary can be searched for a gene, family or compound in the genome of one of 7 species, of which Homo sapiens is one.",
"homepage": "http://gena.ontology.hgc.jp:8081/search/servlet/gena",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "The University of Tokyo The Institute of Medical Science Human Genome Center",
"name": "GENA",
"prefix": "NBDC00072",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00073": {
"description": "The gene database provides information on gene sequence, structure, location, and function for annotated genes from the NCBI database. Users can search by accession ID or keyword, compare and identify sequences using BLAST, or submit references into function (RIFs) based on experimental results. Bulk download and an update mailing list are available.",
"fairsharing": "biodbcore-000449",
"homepage": "http://www.ncbi.nlm.nih.gov/gene",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "NCBI Gene",
"prefix": "NBDC00073",
"pubmeds": [
"21115458"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00074": {
"alt_name": "Gene Ontology",
"description": "GO is a database which provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data. It contains data of terms, definitions and ontology structure. The most recent version of the ontology and the annotation files contributed by members of the GO Consortium are available for download. The GO provides the AmiGO browser and search engine which are web browser-based access to the GO database.",
"homepage": "http://www.geneontology.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "GO (Gene Ontology) Consortium",
"name": "GO",
"prefix": "NBDC00074",
"pubmeds": [
"22102568",
"19578431"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein"
]
},
"nbdc00075": {
"alt_name": "Microarray Gene Annotation",
"description": "geneAnnot Version 2.2 is a database of probe-sets and genes and their relationship to each other.\nThe content of this repository is collected by comparing individual probe sequences with available cDNAs and genes obtained from Ensembl, RefSeq and GenBank.\nThe sequences of transcripts and their positions in the genome are identified with the help of the geneLoc system.\nSearch options by probe-set, gene Symbol or geneCards ID are available.",
"homepage": "http://genecards.weizmann.ac.il/geneannot/index.shtml",
"information_keywords": [
"Sequence"
],
"maintainer": "Weizmann Institute of Science/Department of Biological",
"name": "GeneAnnot",
"prefix": "NBDC00075",
"pubmeds": [
"14725348",
"14962929",
"18005434"
],
"status": "Inactive",
"target_keywords": [
"DNA"
]
},
"nbdc00076": {
"alt_name": "Gene Network Inference Engine based on Supervised Analysis",
"description": "GENIES is used to predict functional associations between genes. The system can be used in a simple mode (default method and parameters) or an advanced mode (selected parameters). After specifying the organism, users can upload data files (tab-delimited text files of 'profile' for each dataset, or a pre-computed 'kernel matrix'). GENIES allows four different outputs: a pathway list, inferred list, search, and details.",
"homepage": "http://www.genome.jp/tools/genies/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "GENIES",
"prefix": "NBDC00076",
"pubmeds": [
"11472995"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00077": {
"alt_name": "Integrated database of E.coli K-12 (W3110)",
"description": "GenoBase is a database on the complete system involving the living conditions of Escherichia coli K-12 (W3110). This public repository provides sequence information compiled in ORFs, as well as functions, DNA and amino acid sequences. Proteome and transcriptome information include 2-D protein maps, bioinformatics based on gene-clustering analysis, multivariate analysis of gene functions and gene networks help to infer the function of ORFs and their interrelationships. All available literature on E.coli K-12 has been incorporated here. Keyword Search quickly searches all fields while Search/Clip provides information on gene, position and DNA sequence.",
"homepage": "http://ecoli.naist.jp/GB/",
"information_keywords": [
"Bioresource",
"Sequence",
"Expression",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Nara Institute of Science and Technology",
"name": "GenoBase",
"prefix": "NBDC00077",
"pubmeds": [
"16738554",
"16606699"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein"
]
},
"nbdc00078": {
"description": "This is the complete genome sequence of the industrial microorganism Streptomyces avermitilis known for producing avermectins, a group of antiparasitic agents, and also called Streptomyces avermectinius MA-4680T(= NBRC 14893T). Physical maps, KEGG pathway analyses, lineage trees based on 16S rRNA, etc. are also available.",
"homepage": "http://avermitilis.ls.kitasato-u.ac.jp/",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "Kitasato University Kitasato Institute for Life Sciences",
"name": "Genome Project of Streptomyces avermitilis",
"prefix": "NBDC00078",
"pubmeds": [
"12692562",
"11572948",
"12893267"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein"
]
},
"nbdc00079": {
"alt_name": "Genomic Object Net Pathway Database",
"description": "GON is a software platform for biological pathway modeling and simulation. It is based on two architectures, hybrid functional Petri net (HFPN) and XML technology. Pathway models of HFPN are also explained in detail. Petri nets provide a method of describing concurrent systems for manufacturing systems and communication protocols and representing biological pathways graphically. Petri Net Pathways includes IL-1,G-protein and TPO signaling pathways as well as a new pathway model of p53 and related genes.",
"homepage": "http://genome.ib.sci.yamaguchi-u.ac.jp/~gon/index.html",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Yamaguchi University Faculty of Science",
"name": "GON",
"prefix": "NBDC00079",
"status": "Inactive",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc00080": {
"alt_name": "Gene Expression Omnibus",
"description": "This is a public data repository of functional genomics data obtained through microarrays and sequencing. Records are carefully examined by experts and standardized to comply with Minimum Information About a Microarray Experiment (MIAME) standards. The data can be searched by sample name, analysis platform, organism, assay details, and keywords. Raw data can also be downloaded from the database.",
"fairsharing": "biodbcore-000441",
"homepage": "http://www.ncbi.nlm.nih.gov/geo/",
"information_keywords": [
"Sequence",
"Expression",
"Image/Movie",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "GEO",
"prefix": "NBDC00080",
"pubmeds": [
"21097893",
"18940857",
"17160034",
"17099226",
"16939800",
"16888359",
"15608262",
"11752295"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00081": {
"description": "GermOnline 4 is a unique microarray expression database across various species.\nIt focusses on gametogenesis, mitosis, meiosis and germline development.\nIt contains information on high-throughput expression data collected with geneChips as well as protein-protein interaction data and protein-DNA binding data obtained from in vivo experiments. \nSample annotations and genome annotation information are provided.\nData on orthologs is also available.\nThe species covered are, among others, Homo sapiens, Mus musculus, Rattus norvegicus and Saccharomyces cereviciae.\nA keyword search option is offered by entering a gene symbol, a database identification number or the Ensembl identifier into the search field.",
"fairsharing": "biodbcore-000378",
"homepage": "http://www.germonline.org/index.html",
"information_keywords": [
"Expression",
"Interaction/Pathway",
"Classification"
],
"maintainer": "Universite de Rennes",
"name": "GermOnline",
"prefix": "NBDC00081",
"pubmeds": [
"14681481",
"17145711",
"21149299",
"19450266"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein"
]
},
"nbdc00082": {
"alt_name": "Ciona intestinalis genomic and cDNA resources",
"description": "The Ghost database provides genomic DNA and cDNA resources for Ciona intestinalis. genes encoding transcription factors that regulate processes like development can be identified to provide molecular information on complex developmental processes and insight into chordate evolution. Genome Browser and BLAST search for genomes, EST and shotgun reads are provided.",
"homepage": "http://ghost.zool.kyoto-u.ac.jp/SearchGenomekh.html",
"information_keywords": [
"Sequence",
"Expression",
"Image/Movie"
],
"maintainer": "Kyoto University Graduate School of Science",
"name": "Ghost Database",
"prefix": "NBDC00082",
"pubmeds": [
"16141696",
"16252120"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Organism"
]
},
"nbdc00083": {
"alt_name": "Genome Information Broker",
"homepage": "http://gib.genes.nig.ac.jp",
"information_keywords": [
"Sequence"
],
"maintainer": "National Institute of Genetics",
"name": "GIB",
"prefix": "NBDC00083",
"pubmeds": [
"11752256"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00084": {
"alt_name": "Human Mitochondrial Genome Polymorphism Database",
"description": "GiiB was a research and development core institute of biotechnology in Gifu prefecture, and it was closed down in 2012. GiiB-JST mtSNP contains the entire mitochondrial DNA sequences of human and mitochondrial SNPs (mtSNPs) data associated with age-related conditions and energy metabolism. The main content of GiiB-JST mtSNP is information about mtSNPs of individuals belonging to 7 different groups; centenarians, patients with Parkinson's disease, patients with Alzheimer's disease, young obese males, young non-obese males, and type-2 diabetes patients with or without severe vascular involvement. This database provides mtSNP search systems such as alignment programs and secondary-structure prediction data to evaluate the functional differences among sets of mtSNPs.",
"homepage": "http://mtsnp.tmig.or.jp/mtsnp/index_e.shtml",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "Gifu International Institute of Biotechnology",
"name": "GiiB-JST mtSNP",
"prefix": "NBDC00084",
"pubmeds": [
"15466285",
"16318308"
],
"status": "Inactive",
"target_keywords": [
"Genetic variation",
"RNA",
"Health/Disease",
"Cell/Organelle"
]
},
"nbdc00085": {
"alt_name": "GPCR-Ligand Database",
"description": "GLIDA is a GPCR-Ligand Database. The superfamily of G-protein coupled receptors (GPCRs) is a large class of cell surface receptors that regulate various cellular functions and are important targets for modern drugs. The functions of some GPCRs have not been identified, and this database is useful in GPCR-related drug discovery. The GLIDA web interface has a GPCR search page and a ligand search page, each with a classification menu and a keyword search. Starting either from a GPCR or a ligand, biological and chemical information can be searched as well as crossover between them.",
"homepage": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "Kyoto University Graduate School of Pharmaceutical Sciences",
"name": "GLIDA",
"prefix": "NBDC00085",
"pubmeds": [
"16381956",
"17986454"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Metabolite",
"Drug"
]
},
"nbdc00086": {
"description": "This database contains experimental data on mammalian Ξ²-globin gene clusters and sequences. Users can find information on the effects of spontaneous mutations of the human hemoglobin gene as well as experimental data on the regulation of Ξ²-globin gene clusters. Additionally, users can use online tools to compare sequences.",
"homepage": "http://globin.cse.psu.edu/",
"information_keywords": [
"Sequence"
],
"maintainer": "Pennsylvania State University",
"name": "Globin Gene Server",
"prefix": "NBDC00086",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00087": {
"description": "Glyco epitopes are carbohydrate antigens involved in various physiological functions such as cell to cell recognition, fertilization, and blood hormone regulation. This database provides information on the glyco epitopes and antibodies that have been used to analyze their expression. The glycol epitopes are linked to their antibodies, as well as to the original manuscripts on the internet.",
"homepage": "http://www.glycoepitope.jp/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Ritsumeikan University",
"name": "GlycoEpitope",
"prefix": "NBDC00087",
"status": "Active",
"target_keywords": [
"Protein",
"Carbohydrate",
"Lipid"
]
},
"nbdc00088": {
"alt_name": "A Database for Triticeae and Avena",
"description": "Graingenes provides information on wheat and barley research. Users can browse through class data such as references, authors, genes, polymorphisms, proteins, and sequences. Each record is linked to associated databases and web resources. Users can also use BLAST, CMap, and GenomeBrowser.",
"homepage": "https://wheat.pw.usda.gov/GG3/",
"information_keywords": [
"Sequence",
"Image/Movie"
],
"maintainer": "USDA-ARS (Agricultural Research Service of the US Department of Agriculture)",
"name": "GrainGenes",
"prefix": "NBDC00088",
"pubmeds": [
"16219925",
"12519977"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Protein"
]
},
"nbdc00089": {
"alt_name": "Genomes TO Protein structures and functions",
"description": "GTOP is a integrated database of information on structures and functions of proteins identified by various genome projects. This database, which mainly uses sequence homology analyses, features information on 3D structure of proteins predicted by Reverse PSI-BLAST against PDB. Functional prediction is mainly performed by BLAST search against Swissprot. Results of analysis contains information on protein motifs, family classification, prediction of domains (transmembrane helix and coiled-coil) and repetitive sequences.",
"homepage": "http://spock.genes.nig.ac.jp/~genome/gtop.html",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "National Institute of Genetics",
"name": "GTOP",
"prefix": "NBDC00089",
"pubmeds": [
"18987007",
"11752318"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00090": {
"alt_name": "Genomes to protein structures and functions",
"homepage": "http://structure.rice.dna.affrc.go.jp/gtop/gtop.html",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "GTOP (Rice version)",
"prefix": "NBDC00090",
"pubmeds": [
"11752318",
"11802435",
"12598694",
"12628242",
"12761299",
"12234664",
"11163980"
],
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc00091": {
"alt_name": "The Human Anatomical Gene Expression Library",
"description": "The Human Anatomical gene Expression Library, H-ANGEL database, is a resource with information on human gene expressions. The human gene expression data can be displayed across 40 distinct tissues and different platforms. Two query interfaces are available: With ' H-Inv Locus Search for gene Expression ', gene expression patterns associated with a particular locus can be retrieved across different tissues and platforms using related identifiers e.g. HIX (H-Inv locus ID), ACC_NO (Genbank ID), Unigene ID, LocusLink ID, OMIM ID, Definition (Genbank), and Product (Genbank).\nWith Expression Pattern Search, a specific expression pattern can be identified across ten tissue categories, and all loci within H-Angel that match the pattern defined by the user can be retrieved.",
"homepage": "http://h-invitational.jp/hinv/h-angel/",
"information_keywords": [
"Expression",
"Localization"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "H-ANGEL",
"prefix": "NBDC00091",
"pubmeds": [
"15608263",
"15103394",
"18089548"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00092": {
"alt_name": "H-Invitational Database",
"description": "H-InvDB is the H-Invitational Database, which integrates human DNA sequences and the proteins for which they carry the production code. Detailed structures of these genes, as well as variations are provided. Indications of where they are located, grouped together and expressed physiologically are also given.\nAn extensive array of views, listing the content under a variety of headings is present.\nVarious search methods are offered e.g. by entering a keyword (simple) or a sequence (Blast). An advanced (more specific) search option is also available. The site can be utilised with the REST application (send request, receive response) as well as the SOAP (send message with search parameters, receive an XML-formatted document) method.",
"fairsharing": "biodbcore-000682",
"homepage": "http://www.h-invitational.jp/hinv/ahg-db/index.jsp",
"information_keywords": [
"Sequence",
"Expression",
"Classification"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "H-InvDB",
"prefix": "NBDC00092",
"pubmeds": [
"19933760",
"18089548",
"15103394",
"18852891",
"16845023",
"16185827"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"RNA",
"Protein",
"Health/Disease"
]
},
"nbdc00094": {
"description": "HarvEST is a database and viewing tools for EST in the following organisms: Barley, Brachypodium, Cassava, Citrus, Coffee, Cowpea, Musa (banana/plantain), Soybean, Rice, Wheat. This database contains all EST sequences which have been quality trimmed, cleaned of vector, and assembled using CAP3 with quality values. It includes an ACE file viewer that allows the user to examine the sequence alignment and readily determine where individual sequences reliably deviate from a consensus sequence, including SNPs. Key features of HarvEST include: a choice of assemblies, sequence alignment viewing, synteny displays (available only in Windows versions), archived BLAST hit information, unigene export, Boolean searching with user-defined quantitative settings, and various other searching, reporting and export functions. The unigene export feature is able to be applied to entire assemblies, individual libraries, or any combination of libraries.",
"homepage": "http://harvest.ucr.edu/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "University of California",
"name": "HarvEST",
"prefix": "NBDC00094",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00095": {
"description": "The Hepatitis Virus Database includes all HCV/HBV/HEV/HAV/HAD entries from the latest release of the DNA Data Bank of Japan, arranged both from genomic location and phylogenetic relation. Map information and a reference map can be accessed from individual virus databases, and data sets consisting of full annotated data, nucleic acid sequences or amino acid sequences can be obtained. The 'account mode' can be used to make private divisions of obtained data.",
"homepage": "http://s2as02.genes.nig.ac.jp/",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "National Institute of Genetics",
"name": "Hepatitis Virus Database",
"prefix": "NBDC00095",
"pubmeds": [
"17877727"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00096": {
"alt_name": "A navigator of small molecules in Protein Data Bank which is called heterogen atoms or in short hetatoms",
"description": "Het-PDB Navi is a database of heterogen molecules in the Protein Data Bank (PDB), which act as cofactors for enzymes or stabilizers of proteins. Entries can be surveyed to study their interactions statistically. Searches can be performed based on PDB code, hetero-atom code, protein name or hetero-atom name. Help with the use of the RasMol application is also provided.",
"homepage": "http://hetpdbnavi.nagahama-i-bio.ac.jp/index.php?mode=0",
"information_keywords": [
"Interaction/Pathway",
"3D structure"
],
"maintainer": "Nagahama Institute of Bio-Science and Technology",
"name": "Het-PDB Navi",
"prefix": "NBDC00096",
"pubmeds": [
"14999012"
],
"status": "Active",
"target_keywords": [
"Protein",
"Carbohydrate",
"Lipid",
"Metabolite",
"Chemical compound"
]
},
"nbdc00097": {
"alt_name": "The Human Gene Mutation Database",
"description": "HGMD is a integrated database of germ-line mutations which are underlying or associated with human inherited disease in nuclear genes. This database contains all germ-line disease-causing mutations and disease-associated/functional polymorphisms reported in the literature. Furthermore, it includes the data about single base-pair substitutions in coding (e.g. missense and nonsense), regulatory and splicing-relevant regions of human nuclear genes, micro-deletions and micro-insertions, indels, repeat expansions, as well as gross gene lesions (deletions, insertions and duplications) and complex gene rearrangements. These data are provided in a readily accessible format to all interested parties, whether they are from an academic, clinical or commercial background.",
"homepage": "http://www.hgmd.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "Institute of Medical Genetics in Cardiff",
"name": "HGMD",
"prefix": "NBDC00097",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Health/Disease"
]
},
"nbdc00099": {
"alt_name": "Homologous Interactions Database",
"description": "HINTdb contains protein-protein interactions experimentally determined by IntAct, BioGRID and HPRD. Homologous interactions are identified by PSI-Blast and orthologous and paralogous interactions by KEGG Orthology. The InterPro database is used for domain information on the proteins, and gene ontology terms are those of the GO database. The user can select interactions of a particular protein and view homologs of the interaction.",
"homepage": "http://hintdb.hgc.jp/hint/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "The University of Tokyo The Institute of Medical Science",
"name": "HINTdb",
"prefix": "NBDC00099",
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc00100": {
"description": "This database contains information on human immunodeficiency virus (HIV) genetic sequences, epitopes, drug resistance-associated mutations, and clinical trials data for vaccines.",
"homepage": "http://www.hiv.lanl.gov/content/index",
"information_keywords": [
"Sequence"
],
"maintainer": "Los Alamos National Secutiry, LLC",
"name": "HIV DATABASES",
"prefix": "NBDC00100",
"status": "Active",
"target_keywords": [
"RNA",
"Protein",
"Health/Disease"
]
},
"nbdc00101": {
"description": "In Homologenes, users can find automatically constructed homologous gene sets from the full-length genome sequences of a wide range of eukaryotic species, as well as mRNA and protein sequences.",
"fairsharing": "biodbcore-000443",
"homepage": "http://www.ncbi.nlm.nih.gov/homologene",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "HomoloGene",
"prefix": "NBDC00101",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00102": {
"alt_name": "Human Organized Whole genome Database Powered by RDF",
"description": "HOWDY-R (Human Organized Whole genome Database Powered by RDF) is a database for retrieve human genome information in different data sources that are available to public. The information you could find here is automatically extracted from the genetic databases and shown with all data having the identifiers in common and linking to one another. HOWDY-R facilitates obtaining information of human genes by using official symbols and aliases.",
"homepage": "https://howdy.biosciencedbc.jp/HOWDY-R/",
"information_keywords": [
"Sequence"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "HOWDY-R",
"prefix": "NBDC00102",
"pubmeds": [
"11752279",
"20058496"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"Protein",
"Health/Disease"
]
},
"nbdc00103": {
"alt_name": "Human Protein Reference Database",
"description": "HPRD (Human Protein Reference Database) version 9 is a manually curated, fully GO compliant protein database.\nThe repository contains 30,047 protein entries, 41,327 protein-protein interactions and 93,710 posttranslational modifications. There are 112,158 occurrences of protein expression, 22,490 of subcellular positioning and 470 domains are identified. \nAll the information in HPRD, including features of proteins such as post-translational modifications, tissue expression, subcellular localization and protein-protein interactions, may be downloaded as XML and FLAT files. Permission is, however, necessary before this may be done.\nThe database can be browsed by selecting a protein, domain, motif, PTM or localization class of interest from a list that is provided. \nA Blast search option is available by entering a nucleotide or protein sequence.",
"fairsharing": "biodbcore-000395",
"homepage": "http://www.hprd.org",
"information_keywords": [
"Sequence"
],
"maintainer": "Institute of Bioinformatics",
"name": "HPRD",
"prefix": "NBDC00103",
"pubmeds": [
"18988627"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST",
"Protein",
"Health/Disease"
]
},
"nbdc00104": {
"alt_name": "A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project",
"description": "The HUGE database is published by the Kazusa DNA Research Institute based on the results of its Kazusa Human cDNA Project to sequence and analyze long (>4 kb) human cDNAs and establish methods to predict the primary structure of proteins with various biological activities. Information on the predicted primary structure of newly identified human proteins that may be involved in cellular structure/motility, gene expression and nucleic acid metabolism, cell signaling/communication, etc. is available.",
"fairsharing": "biodbcore-000407",
"homepage": "http://www.kazusa.or.jp/huge/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "HUGE",
"prefix": "NBDC00104",
"pubmeds": [
"9847221",
"10592264",
"11752282",
"14681467"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein"
]
},
"nbdc00105": {
"alt_name": "IMGT, the international ImMunoGeneTics information system",
"description": "IMGT is a database that offers information on immunogenetics and immunoinformatics.\nThis repository focuses on T cell receptors, immunoglobulins and major histocompatibility of humans and other vertebrates.\nInformation on vertebrate and invertebrate proteins related to the immune system are also covered.\nThe IMGT repository contains a series of databases namely for genome, structure, monoclonal antibodies and sequence.\nA number of interactive tools like IMGT/V-QUEST, IMGT/Phylogene and IMGT/Allele-Align are available.\nAccess is also provided to 10 IMGT Web resources, of which a few are The IMGT Medical page, The IMGT Biotechnology page, IMGT Scientific chart and The IMGT Immunoinformatics page.\nA keyword search option is available.",
"fairsharing": "biodbcore-000363",
"homepage": "https://www.imgt.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Sequence",
"3D structure"
],
"maintainer": "CNRS (The National Centre for Scientific Research)||Montpellier University, Montpellier",
"name": "IMGT",
"prefix": "NBDC00105",
"pubmeds": [
"12818634",
"9847182",
"10592230",
"11125093",
"12520009",
"15972004",
"15608269",
"18978023"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"Protein",
"Cell/Organelle"
]
},
"nbdc00106": {
"description": "IMGT/HLA is a database that specializes in the human major histocompatibility complex and its sequences.\nThere are 8,949 allele sequences that are available, and of them, 6919 are HLA Class I Alleles, 1,875 are HLA Class II Alleles and 155 are other non-HLA Alleles.\nInformation about the source material, from which the sequences were obtained, is provided in detail.\nAuthors of publications regularly check their data against IMGT/HLA first to ascertain the official name of their sequence to avoid confusion due to multiple names for the same product.\nAn IMGT/HLA Alignment Tool is provided as well as protein and nucleotide Blast search options.",
"fairsharing": "biodbcore-000171",
"homepage": "http://www.ebi.ac.uk/imgt/hla/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Sequence"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "IPD-IMGT/HLA",
"prefix": "NBDC00106",
"pubmeds": [
"31667505",
"26826444",
"25048120"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle"
]
},
"nbdc00107": {
"alt_name": "Integrating Network Objects with Hierarchies Pathway Database",
"description": "INOH provides information on the molecular pathways in humans, mice, rats and other organisms. This data is collected from literature and the pathway describing terms used are also linked to at least two additional databases, namely SWISS-PROT and gene Ontology (GO). Both these links were tested and found to work well.\nThe data (new as well as archived) and pathways themselves can be downloaded to personal computers for later use.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/inoh/desc.html",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Interaction/Pathway"
],
"maintainer": "The University of Tokyo Graduate School of Medicine",
"name": "INOH Pathway Database (Archive)",
"prefix": "NBDC00107",
"pubmeds": [
"22120663",
"17094236",
"18629146",
"15089754",
"11590099"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00108": {
"alt_name": "Integrated documentation resource for protein families, domains and functional sites",
"description": "InterPro is a database that analyses proteins functionally and classifies them into families as well as predicts their domain and sites in the genome.\nThis repository harvests its content from a large number of related databases and consolidates its findings into a single searchable resource avoiding the occurrence of redundant entries.\nInterPro aims to update their content every 8 weeks.\nA keyword search is available and an option is provided where a protein sequence can be entered for analysis.",
"fairsharing": "biodbcore-000315",
"homepage": "http://www.ebi.ac.uk/interpro/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "InterPro",
"prefix": "NBDC00108",
"pubmeds": [
"22096229",
"22301074",
"15980438",
"21785143",
"18836194"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00109": {
"alt_name": "Integrated Protein Knowledgebase",
"description": "The iProClass database integrates protein information from a variety of sources. The database connects information from several different common web databases and provides users a report including ontology, sequence, structure, gene family, and literature links. Users can search using keywords or IDs from any of the linked databases.",
"homepage": "https://proteininformationresource.org/pirwww/dbinfo/iproclass.shtml",
"maintainer": "Georgetown University Medical Center",
"name": "iProClass",
"prefix": "NBDC00109",
"pubmeds": [
"11125047",
"12520030",
"15022647"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00110": {
"alt_name": "data depository for Drosophila researchers",
"description": "Jfly consists of following 3 contents to support Drosophila researchers.\n1. Jfly mailing list seivice is the membership system to exchange information on Drosophila research, and it forwards the mail magazine of bionet.drosophila newsgroup to Jfly members.\n2. Jfly homepage is a database that stores back issues of mail magazine, protocols, the address book of researchers and information on stock lists of Drosophila strains. Some contents are only available in Japanese.\n3. FlyBrain is atlas and database for anatomical images of the Drosophila central nervous system.",
"homepage": "http://jfly.iam.u-tokyo.ac.jp/index.html",
"information_keywords": [
"Bioresource",
"Image/Movie",
"Bibliography/Documents",
"Portal"
],
"maintainer": "The University of Tokyo Institute of Molecular and Cellular Biosciences",
"name": "J*FLY",
"prefix": "NBDC00110",
"status": "Inactive"
},
"nbdc00111": {
"alt_name": "Japan Drosophila Database",
"description": "JDD is an introductory database on genetics and taxonomy of Drosophila. JDD stores images of wild-types and mutants, cytological maps, information on taxonomy of Drosophilidae and proteome atlas with search function. This database provides search systems of gene symbols, species name and taxonomic references. English page of each content is not constructed, and the home page of JDD provides only links to the Japanese pages.",
"homepage": "http://www.dgrc.kit.ac.jp/~jdd/index_en.html",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents",
"Taxonomy"
],
"maintainer": "Kyoto Institute of Technology Drosophila Genetic Resource Center",
"name": "JDD",
"prefix": "NBDC00111",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Organism",
"Cell/Organelle"
]
},
"nbdc00112": {
"alt_name": "A Database of Japanese Single Nucleotide Polymorphism for Geriatric Research",
"description": "JG-SNP is a database for accurate medical information and SNPs associated with geriatric diseases. This database contains information on clinical and pathological diagnoses, autopsy findings and SNPs kept by Tokyo Metropolitan Geriatric Hospital. Correlation between genetic polymorphisms and geriatric diseases can be searched by SNPs data and diagnoses, respectively.",
"homepage": "http://www.tmghig.jp/jg-snp/english/E_top.html",
"maintainer": "Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology",
"name": "JG-SNP",
"prefix": "NBDC00112",
"pubmeds": [
"15336912"
],
"status": "Inactive",
"target_keywords": [
"Genetic variation",
"Health/Disease"
]
},
"nbdc00113": {
"alt_name": "Japan Mouse/Rat Strain Resources Database",
"description": "JMSR is constructed by the genetic Informatics Laboratory, National Institute of genetics (NIG) as a database of mouse and rat strains stocked in Japan. JMSR covers almost all the bioresources of mice and rats available in Japan including frozen embryos, frozen sperm, organs and ES cells. This database provides a query form to cross-search databases of 10 stock centers for the strains. A link in each search result shows detailed information on a request for the bioresource.",
"homepage": "http://www.shigen.nig.ac.jp/mouse/jmsr/top.jsp",
"information_keywords": [
"Bioresource"
],
"maintainer": "National Institute of Genetics",
"name": "JMSR",
"prefix": "NBDC00113",
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease"
]
},
"nbdc00114": {
"alt_name": "Japanese Single Nucleotide Polymorphisms",
"description": "JSNP is a database consisting of common gene variations found in the Japanese population. In 2002, it was released information related to 190,562 genetic variations.\nThe original database has been retired. The Genotype frequency data are available in NBDC Human Database (http://humandbs.biosciencedbc.jp/en/), and the JSNP original SNP data in 'JSNP data FASTA files' are available in Life Science Database Archive (https://dbarchive.biosciencedbc.jp/index-e.html).",
"homepage": "https://dbarchive.biosciencedbc.jp/en/jsnp/desc.html",
"information_keywords": [
"Sequence"
],
"maintainer": "The institute of medical science, The University of Tokyo",
"name": "JSNP (Archive)",
"prefix": "NBDC00114",
"pubmeds": [
"12436197",
"11752280",
"12426569"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc00115": {
"alt_name": "Functional hierarchies and binary relationships of biological entities",
"description": "The KEGG BRITE database contains functional hierarchies and binary relationships of biological entities, and includes many types of relationships. KEGG BRITE maps large-scale molecular datasets in genomics, transcriptomics, proteomics, and metabolomics to BRITE functional hierarchies, and allows biological interpretation of higher-level systemic functions.",
"homepage": "http://www.genome.jp/kegg/brite.html",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Classification"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG BRITE",
"prefix": "NBDC00115",
"status": "Active"
},
"nbdc00116": {
"description": "The KEGG EXPRESSION database provides microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species from the Japanese research community.",
"homepage": "http://www.genome.jp/kegg/expression/",
"information_keywords": [
"Expression"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG EXPRESSION Database",
"prefix": "NBDC00116",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00117": {
"alt_name": "Molecular building blocks of life in the chemical space",
"description": "The KEGG LIGAND database is a composite consisting of COMPOUND, GLYCAN, REACTION, RPAIR, RCLASS, and ENZYME databases. The primary database is relational, and the KegDraw interface is used to generate the secondary DBGET database. Chemical structure search includes SIMCOMP and SUBCOMP with which the query compound is partially or fully matched, respectively, and a similar glycan structure search. Reaction search and prediction is also available.",
"homepage": "http://www.genome.jp/kegg/ligand.html",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG LIGAND Database",
"prefix": "NBDC00117",
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc00118": {
"alt_name": "Wiring diagrams of molecular interactions, reactions, and relations",
"description": "The KEGG PATHWAY database has manually drawn pathway maps that represent molecular interaction and reaction networks for the following: Global Map, Metabolism, genetic Information Processing, Cellular Processes, Organismal Systems, Human Diseases and also structure relationships in Drug Development. By using KEGG PATHWAY mapping, molecular datasets can be mapped for the biological interpretation of higher-level systemic functions.",
"homepage": "http://www.genome.jp/kegg/pathway.html",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG PATHWAY Database",
"prefix": "NBDC00118",
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease",
"Carbohydrate",
"Lipid",
"Metabolite",
"Cell/Organelle"
]
},
"nbdc00119": {
"alt_name": "Sequence Similarity Database (Orthologs/paralogs, conserved gene clusters, and sequence motifs)",
"description": "The KEGG SSDB (Sequence Similarity DataBase) organizes amino acid sequence similarities among all protein-coding genes in complete genomes computationally generated from the geneS database in KEGG. Using the SSEARCH program, all possible pairwise genomes are compared and gene pairs with a Smith-Waterman similarity score of 100 or more are entered into SSDB together with the information on best hits and bidirectional best hits (best-best hits). \nSSDB is a weighted and directed graph that can be used to search orthologs and paralogs, and conserved gene clusters, taking positional correlations on the chromosome into consideration.",
"homepage": "http://www.kegg.jp/kegg/ssdb/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG SSDB Database",
"prefix": "NBDC00119",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00120": {
"alt_name": "Knowledge-Oriented Molecular Biological Encyclopedia",
"description": "This site contains information on full-length cDNA from rice, classified into approximately 28,000 groups of clones, and part of the 'rice full-length cDNA' project to construct a full-length cDNA library from stressed tissues. It includes not only the nucleotide sequence and encoded amino acid sequence information, but also the results of the homology search with public databases, mapping information, pattern of alternative splicing, protein domain information, transmembrane structure, cellular localization, and gene function by gene Ontology. \nThe original site (http: //cdna01.dna.affrc.go.jp/cDNA/) has been closed. KOME is available from LSDB archive site.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/kome/desc.html",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "KOME (Archive)",
"prefix": "NBDC00120",
"pubmeds": [
"12869764",
"18043742"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Protein"
]
},
"nbdc00121": {
"description": "KONCHU is an entomology database of Japanese, East Asian and Pacific insect species with spiders and mites. KONCHU contains following seven main contents; KONCHUR (a entomology reference database), MOKUROKU (a checklist treating all the insect species or subspecies recorded from Japan), DJI (a dictionary of Japanese insect names), ELKUType (the type collection of the Entomological Laboratory of Kyushu University), TABR (Tropical bee reference database), HANABACHI and TOBIKOBACHI (image databases on useful Japanese insects).",
"homepage": "http://konchudb.agr.agr.kyushu-u.ac.jp/index-e.html",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie",
"Bibliography/Documents",
"Portal"
],
"maintainer": "Kyushu University Faculty of Agriculture",
"name": "KONCHU",
"prefix": "NBDC00121",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc00122": {
"description": "KONCHUR is a reference database of the main Japanese entomological and zoological journals associated with Japanese, East Asian and Pacific insects. A taxon is treated as one record in this database, and each record is composed of 13 items of data and tags including taxon names (scientific name and Japanese name), order, family, synonymy and distribution. This database allows to search records by keywords from these items. Search results show additional useful information such as type locality of new recorded species, type depository and host records of parasitic insects.",
"homepage": "http://konchudb.agr.agr.kyushu-u.ac.jp/konchur/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Kyushu University Faculty of Agriculture",
"name": "KONCHUR",
"prefix": "NBDC00122",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc00124": {
"alt_name": "NBRP Lotus / Glycine",
"description": "NBRP Legume Base is a database for offering research materials of two legume species; Lotus japonicus and Glycine max (soybean). Legume Base provides a query form to search resources of each species and check availability. In addition, this database contains two databases; 'Legume Base - Lotus japonicus' and 'Glycine max Database'. Both of them cover detailed information on the two species including lists of strains, phenotypes and genotypes.",
"homepage": "https://legumebase.nbrp.jp/legumebase/top.jsp",
"information_keywords": [
"Phenotype",
"Bioresource"
],
"maintainer": "University of Miyazaki, Faculty of Agriculture",
"name": "Legume Base",
"prefix": "NBDC00124",
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Organism",
"Cell/Organelle"
]
},
"nbdc00125": {
"description": "The LinkDB database links information between hundreds of molecular biology databases. The database consists of the following three sections: (1) 'Original' links are information extracted from the database entries provided by the GenomeNet DBGET system. (2) 'Reverse' links are information derived from the original links by exchanging a source entry and its target entry. (3) 'Equivalent' links indicate equivalent contents between KEGG geneS, COMPOUND, DRUG, REACTION databases and other databases other than KEGG. Users can search the link information by entry and also download equivalent link information for a selected organism, or for compound drug and reaction.",
"homepage": "http://www.genome.jp/linkdb/",
"information_keywords": [
"Portal"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "LinkDB Search",
"prefix": "NBDC00125",
"status": "Active"
},
"nbdc00126": {
"description": "Lipidbank is the official database of the Japanese Conference on the Biochemistry of Lipids (JCBL). Natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins can be freely searched. It also provides more than 6000 unique molecular structures (ChemDraw cdx format, MDL MOL format) with their lipid names (common name, IUPAC), spectral information (mass, UV, IR, NMR and others), and links to published information.",
"fairsharing": "biodbcore-000581",
"homepage": "http://lipidbank.jp/",
"information_keywords": [
"Image/Movie",
"Chemical structure"
],
"maintainer": "The Japanese Conference on the Biochemistry of Lipids",
"name": "LipidBank",
"prefix": "NBDC00126",
"pubmeds": [
"12058481"
],
"status": "Active",
"target_keywords": [
"Lipid"
]
},
"nbdc00127": {
"description": "LSD Project is a database of life science terms with free online devices for dictionaries and translation. The English version of LSD Project site is composed of following 4 online services.\n1. English-Japanese and Japanese-English dictionaries (WebLSD, WebLSD mini)\n2. To make an English-Japanese vocabulary list on a web browser (EtoJ Vocabulary)\n3. English-Japanese translation of life science terms (EtoJ)\n4. English spell checker of life science and general terms (WebSpell)\nWebLSD mini is available on iPhone and Android smartphones.",
"homepage": "https://lsd-project.jp/cgi-bin/lsdproj/ejlookup04.pl",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Life Science Dictionary Project",
"name": "LIFE SCIENCE DICTIONARY",
"prefix": "NBDC00127",
"status": "Active"
},
"nbdc00128": {
"alt_name": "MAboya ( the ascidian, Halocynthia roretzi ) Gene Expression patterns and Sequence Tags",
"description": "MAGEST is a database of newly identified maternal cDNAs of the ascidian Halocynthia roretzi to examine the mRNA population. Collected 3' and 5' tag sequences of mRNAs and their expression data from whole-mount in situ hybridization in early embryos, as well as additional information are available through this public database.",
"homepage": "http://magest.hgc.jp/",
"information_keywords": [
"Sequence",
"Expression",
"Image/Movie"
],
"maintainer": "The University of Tokyo The Institute of Medical Science",
"name": "MAGEST",
"prefix": "NBDC00128",
"pubmeds": [
"10592202",
"11752271"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00129": {
"alt_name": "Maize Genetics and Genomics Database",
"description": "MaizeGDB is a integrated database of the crop plant and model organism Zea mays. It contains maps, gene product information, loci and their various alleles, phenotypes (both naturally occurring and as a result of directed mutagenesis), stocks, sequences, molecular markers, references and contact information for maize researchers on worldwide. Moreover, users are able to obtain various community support service bulletin boards including the Editorial Board's list of high-impact papers, information about the Annual Maize genetics Conference and the Jobs board where employment opportunities are posted.",
"fairsharing": "biodbcore-000414",
"homepage": "http://www.maizegdb.org/",
"information_keywords": [
"Bioresource",
"Sequence",
"Expression",
"Interaction/Pathway",
"Image/Movie",
"Portal"
],
"maintainer": "MaizeGDB (Maize Genetics and Genomoics Database) Working Group",
"name": "MaizeGDB",
"prefix": "NBDC00129",
"pubmeds": [
"17202174",
"14681441",
"21565781"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"Protein",
"Organism"
]
},
"nbdc00130": {
"alt_name": "Microbial Genome Database for Comparative Analysis",
"description": "MBGD is a database with a workbench system for comparative analysis of completely sequenced microbial genomes, mainly for creating orthologous or homologous gene cluster tables. MBGD classifies genomes by the hierarchical clustering method known as UPGMA, using precomputed similarity relationships identified by all-against-all BLAST search. Users can change the set of organisms or cutoff parameters to create their own orthologous groupings. Thus comparative genomics is facilitated from various points of view such as ortholog identification, paralog clustering, motif analysis and gene order comparison.",
"homepage": "http://mbgd.genome.ad.jp/",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "National Institute for Basic Biology",
"name": "MBGD",
"prefix": "NBDC00130",
"pubmeds": [
"12519947",
"17135196",
"19906735",
"23118485"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc00131": {
"alt_name": "Medaka Expression Pattern Database",
"description": "This database includes information regarding gene expression patterns in medaka (Oryzias latipes), confirmed by in situ hybridization. It also contains expression data of regulatory sequences. Each data entry has information on the gene name, Ensembl ID, images of the expression pattern, and developmental stage. The database can be searched by gene ID, Ensembl ID, tissue name, and developmental stage. Users can also find organized Medaka anatomical terms (Medaka Fish Ontology; MFO), and the explanatory informations of Medaka developmental stages.",
"fairsharing": "biodbcore-000695",
"homepage": "http://mepd.cos.uni-heidelberg.de/mepd/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Expression"
],
"maintainer": "EMBL (European Molecular Biology Laboratory)",
"name": "MEPD",
"prefix": "NBDC00131",
"pubmeds": [
"12519950"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00132": {
"alt_name": "Medical Subject Headings",
"description": "This is a database of keywords representing the content of articles and biological information. The keywords are structured in layers to allow users to find more detailed information or perform abstract searches.",
"homepage": "https://www.nlm.nih.gov/mesh/meshhome.html",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "MeSH",
"prefix": "NBDC00132",
"pubmeds": [
"20623263",
"15360776",
"15360776"
],
"status": "Active"
},
"nbdc00133": {
"alt_name": "Microbial Genome Workbench",
"description": "The Microbial Genome Workbench (MG Workbench) is a database that enables research into the genomes of Archaea and Bacteria. This repository is specifically focused on information gathered by comparing proteins and genes inter-genomically as well as intra-genomically.\nA gene may be located by entering its name, synonyms, PID, Swiss-Prot ID or PDB ID and a keyword in a blast search application.\nA specific microbial genome may also be searched for a short sequence pattern, although this route is stated to be very slow in providing results.\nDirect access to the genome map of an organism of choice is also given.\nInformation on restriction digestion of DNA and simulated protein digestion by a chosen enzyme is retrievable.",
"homepage": "http://www.bioscinet.org/cgi-bin/mgw.pl",
"information_keywords": [
"Sequence"
],
"maintainer": "National Institute of Genetics",
"name": "MG Workbench",
"prefix": "NBDC00133",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00134": {
"alt_name": "Mammalian Gene Collection",
"description": "MGC is a full-length cDNA clone database for mammalian genes. It contains information such as gene names, GenBank records, and a link to GenBank. Users can search using gene names or keywords for human, mouse, rat, and bovine genes. Additionally, users can find distributor information for cDNA clones as well as information on vectors.",
"homepage": "http://mgc.nci.nih.gov/",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "MGC",
"prefix": "NBDC00134",
"pubmeds": [
"19767417",
"15489334",
"15489330",
"15088387",
"12477932"
],
"status": "Closed",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00135": {
"alt_name": "Mouse Genome Informatics",
"description": "This is a comprehensive site for mouse research. The site contains detailed information on mouse genes, gene expression data, polymorphisms and mutations, pathways, data on model rats for hereditary cancers, and phenotypes of each mouse model system. They have developed and provided The Human - Mouse: Disease Connection (HMDC) and Mammalian Phenotype Ontology.",
"fairsharing": "biodbcore-000421",
"homepage": "http://www.informatics.jax.org/",
"information_keywords": [
"Phenotype",
"Bioresource",
"Ontology/Terminology/Nomenclature",
"Sequence",
"Expression",
"Interaction/Pathway",
"Image/Movie",
"Bibliography/Documents",
"Classification",
"Repository"
],
"maintainer": "The Jackson Laboratory",
"name": "MGI",
"prefix": "NBDC00135",
"pubmeds": [
"19274630",
"10592195",
"21062809",
"21282667"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"Organism",
"Health/Disease"
]
},
"nbdc00136": {
"alt_name": "microRNA database",
"description": "miRBase is a database for published microRNA sequences and annotations, which include mature miRNA sequences (indicated by miR), and hairpin structures predicted by sequences that are precursors for miRNA (indicated by mir). A variety of search methods can be used, including by keyword, genomic position, cluster, expression data, and user-provided sequences. Furthermore, these sequences and annotations can be downloaded.",
"fairsharing": "biodbcore-000569",
"homepage": "http://mirbase.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "Faculty of Life Sciences, The University of Manchester",
"name": "miRBase",
"prefix": "NBDC00136",
"status": "Active",
"target_keywords": [
"RNA"
]
},
"nbdc00137": {
"alt_name": "Mitochondrial Genome Database of Fish",
"description": "MitoFish is a database for the fish mitochondrial genome, which allows users to find data from complete nucleotide sequences of the mitochondrial genomes of fish. Based on the nucleotide sequence data from a fish mitochondrial genome, BLAST homology search (sequence similarity search) of the nucleotide sequence can be conducted against fish complete or complete + partial mitochondrial genome databases.",
"homepage": "http://mitofish.aori.u-tokyo.ac.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tokyo Atmosphere and Ocean Research Institute",
"name": "MitoFish",
"prefix": "NBDC00137",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle"
]
},
"nbdc00138": {
"description": "This database provides all information and resources involved in the sequencing of Lotus japonicus (Miyakogusa), the first sequenced legume, by The Kazusa DNA Research Institute. Clone list, Genomic map and Insertion tag lines are provided.",
"homepage": "http://www.kazusa.or.jp/lotus/index.html",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "miyakogusa.jp",
"prefix": "NBDC00138",
"pubmeds": [
"18511435"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00139": {
"alt_name": "Mouse Microsatellite Data Base of Japan",
"description": "MMDBJ is a database of mouse microsatellite loci to provide information about simple sequence length polymorphisms (SSLPs) among different strains. MMDBJ features SSLP loci obtained from strains derived from Mus musculus molossinus (Japanese wild mouse). Each record contains polymorphism data, PCR condition and a link to Ensembl Genome Browser web page to view primer sequences. This database also provides a search engine and a linkage map of mouse microsatellite loci.",
"homepage": "http://www.shigen.nig.ac.jp/mouse/mmdbj/top.jsp",
"information_keywords": [
"Sequence",
"Image/Movie"
],
"maintainer": "National Institute of Genetics",
"name": "MMDBJ",
"prefix": "NBDC00139",
"pubmeds": [
"15153678"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Genetic variation"
]
},
"nbdc00140": {
"description": "MOKUROKU is a checklist of all the insect species or subspecies recorded from Japan. MOKUROKU was constructed as an online database based on a book written in Japanese; ' A Check List of Japanese Insects '. A species or subspecies is treated as one record in this database, and each record consists of following 5 items; scientific names of family, genus, species (or subspecies), Japanese name (taxon name) and distribution. Users can search insects by keywords from these 5 items.",
"homepage": "http://konchudb.agr.agr.kyushu-u.ac.jp/mokuroku/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Kyushu University",
"name": "MOKUROKU",
"prefix": "NBDC00140",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc00141": {
"alt_name": "National BioResource Project Morning glory",
"description": "National BioResource Project Morning glory collects resources of the Japanese morning glory (Ipomoea nil or Pharbitis nil). Requests for the resources are available by email. genetic data of mutant strains and Ipomoea related species are recorded in a database, and it allows to search strains, gene classes and gene symbols. Users can browse tables of phenotype class, images (seeds, leafs and flower organs), and linkage maps of the Japanese morning glory.",
"homepage": "http://www.shigen.nig.ac.jp/asagao/index.jsp",
"information_keywords": [
"Bioresource",
"Ontology/Terminology/Nomenclature",
"Sequence",
"Image/Movie"
],
"maintainer": "Kyushu University",
"name": "NBRP Morning glory",
"prefix": "NBDC00141",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc00143": {
"description": "This is the database of the Mycoplasma penetrans genome project. Complete nucleotide sequence, protein sequences and annotation table are available to investigate the pathogenicity of this relatively new pathogen, characterized by the ability to penetrate human cells. Often associated with HIV carriers or infection and possibly involved in the development of immunodeficiency, it can cause urethritis and respiratory disease in humans by itself.",
"homepage": "http://mollicutes.nih.go.jp/Mypet/",
"information_keywords": [
"Sequence"
],
"maintainer": "National Institute of Infectious Diseases",
"name": "Mycoplasma penetrans Genome",
"prefix": "NBDC00143",
"pubmeds": [
"12466555",
"12486060"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00144": {
"description": "This is a site by which the culture catalogue of the Biological Resource Center of the National Institute of Technology and Evaluation (NITE) may be searched for information.\nA comprehensive amount of data is provided on each of a list of 59 phages. \nA Sequence search option as well as a Homology search option is available.\nIt is also possible to order cultures from this site.",
"homepage": "https://www.nite.go.jp/nbrc/catalogue/?lang=en",
"information_keywords": [
"Bioresource"
],
"maintainer": "NITE (National Institute of Technology and Evaluation)",
"name": "NBRC Culture Catalogue Search",
"prefix": "NBDC00144",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00145": {
"description": "NBRP Chrysanthemum provides resources of plants belonging to the genus Chrysanthemum and closely related genera; the tribe Anthemideae. The resource list consists of wild strains, garden species and experimental strains including interspecific hybrids, intergeneric hybrids and artificial polyploids. Users can search strains by keywords such as a species name, Japanese name, phenotype and karyotype. Search results show information on stock availability and resource types (plant stock, seed stock and culture stock).",
"homepage": "http://www.shigen.nig.ac.jp/chrysanthemum/",
"information_keywords": [
"Bioresource",
"Image/Movie"
],
"maintainer": "National Institute of Genetics",
"name": "National BioResource Project Chrysanthemum",
"prefix": "NBDC00145",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00146": {
"description": "NBRP E.coli Strain stocks mutants and clones of Escherichia coli to distribute to academic researchers and non-academia research users. These resources have been mainly collected and maintained by National Institute of genetics (NIG). The resource list consists of gene mutants (ME Collection, JE Collection and IH E.coli Mutant Collection), clones (ASKA Clone, plasmid and cosmid), genomewide mutants, phage and cloning vector. Users can search available resources using the Resource Type table on the home page and Quick Search at the top of the page.",
"homepage": "https://shigen.nig.ac.jp/ecoli/strain/locale/change?lang=en",
"information_keywords": [
"Bioresource"
],
"maintainer": "National Institute of Genetics",
"name": "NBRP E.coli Strain",
"prefix": "NBDC00146",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"Organism"
]
},
"nbdc00147": {
"description": "NBRP Medaka is a database for offering resources of Medaka (Oryzias latipes) maintained by National Institute for Basic Biology and Niigata University. Medaka resources consist of live-resources (wild populations, related species, inbred strains, mutants and transgenics) and clone libraries (cDNA, BAC and Fosmid). Users can search available resources using the βOverview for strainsβ page, keyword search and Blast search. This database also provides research tools including atlas (Medaka Atlas), phylogenetic trees (Medaka Tree), genome browser (Medaka Map) and laboratory manuals.",
"homepage": "http://www.shigen.nig.ac.jp/medaka/",
"information_keywords": [
"Bioresource",
"Sequence",
"Image/Movie"
],
"maintainer": "National Institute of Genetics",
"name": "NBRP Medaka",
"prefix": "NBDC00147",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"Organism"
]
},
"nbdc00148": {
"description": "Oryzabase is an integrated database that collects information and resources related to rice strains. This database provides following 7 contents; strain stock information, mutants information, chromosome maps, gene dictionary, reference list, fundamental knowledge of rice science and featured links. Users can search available strains from each link of 'Strains' category, and order seeds, plant bodies (only users in Japan) or DNA resources. Oryzabase will receive registration of newly identified rice genes and mutants.",
"fairsharing": "biodbcore-000494",
"homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/locale/change?lang=en",
"information_keywords": [
"Bioresource",
"Sequence",
"Expression",
"Image/Movie",
"Bibliography/Documents",
"Portal"
],
"maintainer": "National Institute of Genetics",
"name": "Oryzabase",
"prefix": "NBDC00148",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Cell/Organelle"
]
},
"nbdc00149": {
"description": "KOMUGI is an integrated database of wheat managed by the National BioResource Project (NBRP)-Wheat. This database mainly collects strain information on wheat (the genus Triticum) and related species (the genus Aegilops) including experimental lines. It also contains some accessions of other related species (rye; the genus Secale and oats; the genus Avena), the list of gene symbols, gene sequence data and chromosome maps. Available resources are listed as 'NBRP Strains' and 'NBRP cDNA', then users can order them by using query forms in 'Strains' category and 'cDNA' category, respectively.",
"homepage": "http://www.shigen.nig.ac.jp/wheat/komugi/",
"information_keywords": [
"Phenotype",
"Bioresource",
"Sequence",
"Expression"
],
"maintainer": "National Institute of Genetics",
"name": "KOMUGI",
"prefix": "NBDC00149",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Organism",
"Cell/Organelle"
]
},
"nbdc00150": {
"alt_name": "Nucleic Acid Database",
"description": "The Nucleic Acid Database Project (NDB) aims to collect and distribute information on nucleic acid structures. Each entry contains information on nucleic acid sequences, its structure and the characteristics, the primary citation, experimental information, as well as a link to PDB. Furthermore, structure coordinates and structure factors can be downloaded from the site.",
"fairsharing": "biodbcore-000513",
"homepage": "http://ndbserver.rutgers.edu",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "The State University of New Jersey",
"name": "NDB",
"prefix": "NBDC00150",
"pubmeds": [
"1384741"
],
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Protein"
]
},
"nbdc00151": {
"alt_name": "Non-Redundant B.subtilis database",
"description": "NRsub is a database that contains information covering the whole genome of Bacillus subtilis.\nThis site also provides knowledge of codon usage and gene mapping. \nInformation available has been cross-referenced with the SWISS-PROT, ENZYME and HOBACGEN databases.\nSearch can be done by keyword, sequence name, gene accession number, www-query or a full text search.",
"fairsharing": "biodbcore-000217",
"homepage": "http://pbil.univ-lyon1.fr/nrsub/nrsub.html",
"maintainer": "Pole Bioinformatique Lyonnais",
"name": "NRSub",
"prefix": "NBDC00151",
"pubmeds": [
"8594597",
"9399801"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00152": {
"alt_name": "Operon DataBase",
"description": "All known operons from numerous species have been collected from literature and other public databases in this database, which also includes a system to predict operons by user definitions. Operon candidates are provided based on logic operations of the following parameters: intergenic distance, intergenic step, pathway, co-expression, and ortholog. Prediction accuracy can also be obtained.",
"homepage": "http://operondb.jp/",
"information_keywords": [
"Expression",
"Interaction/Pathway",
"Classification"
],
"maintainer": "Niigata University Graduate School of Medical and Dental Sciences",
"name": "ODB",
"prefix": "NBDC00152",
"pubmeds": [
"16381886",
"21051344"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00153": {
"alt_name": "Online Mendelian Inheritance in Animals",
"description": "OMIA is a database of inherited disorders, other (single-locus) traits, and genes in animals which is not include human, mouse and rat because of presence of their own resources. The records contain basical textual information, references, and links to OMIM, PubMed, and gene. The content on the site is manually curated.",
"fairsharing": "biodbcore-000579",
"homepage": "https://omia.org/home/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "University of Sydney",
"name": "OMIA",
"prefix": "NBDC00153",
"pubmeds": [
"12520001",
"33156546"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00154": {
"alt_name": "Online Mendelian Inheritance in Man",
"description": "OMIM is a database of human disease and genetic information and the online representation of Mendelian Inheritance in Man, a project initiated in the 1960s. The database summarizes heritable traits and provides information on both the trait and experimentally determined genetic causes. The database is manually curated by experts and can be searched by OMIM ID, gene, disease, or phenotype.",
"fairsharing": "biodbcore-000761",
"homepage": "http://www.ncbi.nlm.nih.gov/omim",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "OMIM",
"prefix": "NBDC00154",
"pubmeds": [
"18842627"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc00155": {
"description": "National Bioresource Project - 'Pathogenic microbes' collects reliable strains of pathogenic microorganisms (fungi, actinomycetes, bacteria and protozoa) to support education and research in infectious diseases. Contents of 'Database' category including keyword search and 'Animation' category are only available in Japanese, and some resources restrict database access. This database also provides the picture lists of pathogenic fungi and actinomycetes. Requests for distribution and deposition of resources are available by email.\n\nThis site has been moved to the following URLs (2018.4.1).\nPathogenic bacteria: https://pathogenic-bacteria.nbrp.jp/\nPathogenic eukaryotic microorganisms: https://pathogenic-microbes.nbrp.jp/",
"homepage": "http://pathogenic.lab.nig.ac.jp/",
"information_keywords": [
"Bioresource",
"Image/Movie"
],
"maintainer": "National Institute of Genetics",
"name": "National Bioresource Project - Pathogenic microbes",
"prefix": "NBDC00155",
"status": "Closed",
"target_keywords": [
"Organism",
"Health/Disease"
]
},
"nbdc00156": {
"alt_name": "worldwide Protein Data Bank",
"description": "This is an international public repository for three-dimensional structures and structure coordinates (conformations) of proteins and nucleic acids, and the central database for biological structural data. Data obtained through X-ray crystallography and NMR experiments are stored in PDB. In addition to three-dimensional information of proteins, users can find amino acid sequences, protein-related information on GO, and other compounds bound to the protein.",
"homepage": "https://www.wwpdb.org",
"information_keywords": [
"Image/Movie",
"3D structure",
"Repository"
],
"maintainer": "wwPDB consortium",
"name": "wwPDB",
"prefix": "NBDC00156",
"pubmeds": [
"14634627",
"30357364"
],
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Protein"
]
},
"nbdc00157": {
"alt_name": "Protein Data Bank Japan",
"description": "PDBj in Japan maintains a single PDB archive of macromolecular structural data in conjunction with the RCSB, the BMRB in USA and the PDBe in EU as a member of the Worldwide Protein Data Bank. PDBj provides entry search with sequence homology and structure similarity, structural bioinformatics web services such as a molecular visualizing software and tutorials of them. From this website, users can deposit protein structural information solved by X-ray crystallography or NMR spectroscopy in the PDB. For the structure search, you can use PDBj Mine (http://pdbj.org/mine) . The PDBj data are updated on every Wednesday 9 a.m. (Japan time).",
"fairsharing": "biodbcore-000498",
"homepage": "http://pdbj.org",
"information_keywords": [
"Image/Movie",
"3D structure",
"Repository"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "PDBj",
"prefix": "NBDC00157",
"pubmeds": [
"14634627",
"27789697"
],
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Protein"
]
},
"nbdc00158": {
"description": "This database was reorganized the data of PDB (Protein Data Bank) to suit sequence analysis by the Institute for Chemical Research, Kyoto University. In PDB, there are a number of polypeptide chains per an entry. In this database, it have been separated out into another entries, and added additional information.",
"homepage": "http://www.genome.jp/dbget-bin/www_bfind?pdbstr",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "PDBSTR",
"prefix": "NBDC00158",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00159": {
"alt_name": "Profiling of Escherichia coli chromosome",
"description": "PEC is a database for characterization of the E. coli genome and each gene's function. This database features gene classification based on essentiality for cell growth of E. coli using information from research reports and mutation studies. Users can search genes or deletion mutations by a keyword, genomic location, length and the classification. Search results show information on strains related to each gene or deletion, and online requests for them are available via links to the NBRP E.coli Strain web pages.",
"homepage": "http://www.shigen.nig.ac.jp/ecoli/pec/index.jsp",
"information_keywords": [
"Sequence"
],
"maintainer": "National Institute of Genetics",
"name": "PEC",
"prefix": "NBDC00159",
"pubmeds": [
"18392982"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00160": {
"alt_name": "a Protein Extraction, Description and Analysis Tool",
"description": "PEDANT 3 is a database of information regarding the extraction, description and analysis of proteins.\nIt contains this information for a variety of Archaeal, Bacterial, Eukaryotic, Fungal, Metazoan, Viral and Plant species.\nAvailable data on protein function includes the results of Blast similarity searches against known non-redundant protein sequences and searches for motif similarities in the Pfam, BLOCKS and PROSITE databases.\nThe cellular roles and functions are predicted by means of BLAST searches against protein sequences of which the function is known.\nA keyword search option is also available.",
"homepage": "http://pedant.gsf.de/",
"information_keywords": [
"Sequence"
],
"maintainer": "German Research Center for Environmental Health",
"name": "PEDANT3 database",
"prefix": "NBDC00160",
"pubmeds": [
"11222261",
"12519983",
"15608204",
"17148486",
"18940859"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00161": {
"alt_name": "Pig Expression Data Explorer",
"description": "This database provides sequencing information for genome (contigs), cDNAs and cSNPs (SNPs on cDNAs) on pig. It allows users to search with filters for comparing sequences or annotations (for example, similarity searches between different species). Sequences can be downloaded and similarity searches (BLAST) can be performed with user-provided sequences.",
"homepage": "http://pede.dna.affrc.go.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "PEDE",
"prefix": "NBDC00161",
"pubmeds": [
"17145712",
"14681463"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Genetic variation"
]
},
"nbdc00162": {
"description": "PEPTIDOME is a database for endogenous peptides in cells, tissues and body. PEPTIDOME contains molecular and physiological information of the peptides obtained from brains of mouse, pig and rat. This database provides search engines of endogenous peptides and literatures. Users can search peptides by amino acid sequences or keywords such as names, physicochemical properties, natural abundance and biological activities.",
"homepage": "http://www.peptidome.jp/index.html",
"information_keywords": [
"Method",
"Chemical structure"
],
"maintainer": "National Cardiovascular Center Research Institute",
"name": "PEPTIDOME",
"prefix": "NBDC00162",
"status": "Inactive",
"target_keywords": [
"Metabolite"
]
},
"nbdc00163": {
"description": "Pfam Version 26.0 is a comprehensive database of protein families containing multiple sequence alignments and HMMs.\nThis repository provides data on 13,672 protein families.\nThe site can be searched with a known protein sequence for matching families. \nOptions to search for a Pfam family, clan, sequence or structure are available.\nA keyword search option is also provided.",
"fairsharing": "biodbcore-000081",
"homepage": "http://pfam.xfam.org",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "Pfam",
"prefix": "NBDC00163",
"pubmeds": [
"16381856",
"22127870",
"26673716"
],
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc00164": {
"alt_name": "Pharmacogenomics Knowledge Base",
"description": "PharmGKB is a database of genotype-drug response knowledge. The database contains information about genes, diseases, and drugs independently and information on how the three factors interact. PharmGKB is curated by scientists and engineers with expertise in pharmacogenomics. Bulk data is available for download.",
"fairsharing": "biodbcore-000525",
"homepage": "http://www.pharmgkb.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Interaction/Pathway"
],
"maintainer": "Stanford University",
"name": "PharmGKB",
"prefix": "NBDC00164",
"pubmeds": [
"11752281",
"18949600",
"22103613"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Chemical compound",
"Drug"
]
},
"nbdc00165": {
"description": "PHYSCObase is a database for sharing information on the moss Physcomitrella patens, which provides a simple system for studying many traits shared with flowering plants. All Physcomitrella DNA sequences in public databases as well as expressed sequence tags (EST) are available. Searches are conducted by EST, genomic sequence, or full-length cDNA with BLAST. The default dataset is PHYSCObase contigs, which contains all assembled sequences and exhibits high sensitivity. PHYSCObase clones and PHYSCObase contigs new datasets are also available.",
"homepage": "http://moss.nibb.ac.jp/",
"information_keywords": [
"Method",
"Sequence",
"Bibliography/Documents"
],
"maintainer": "National Institute for Basic Biology",
"name": "PHYSCObase",
"prefix": "NBDC00165",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00166": {
"description": "This RIKEN BioResource Center database is called Physcomitrella patens (moss) full-length cDNA clones, is closely related to the PHYSCObase database, and provides Physcomitrella DNA sequences. A total of 149,363 clones have been deposited, and are available for search by keyword or BLAST.",
"homepage": "http://www.brc.riken.jp/lab/epd/catalog/p_patens.html",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "Physcomitrella patens Full-Length cDNA Clone Database Search",
"prefix": "NBDC00166",
"pubmeds": [
"12808149",
"18079367"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00167": {
"alt_name": "Protein Information Resource",
"description": "PIR is an integrated public bioinformatics resource that supports proteomic and genomic research. Users can find information such as protein names, gene names, protein function, subunits, as well as links to citations, DNA sequences, ontology, pathways, and other related data.",
"homepage": "https://proteininformationresource.org",
"information_keywords": [
"Sequence"
],
"maintainer": "Georgetown University Medical Center",
"name": "PIR",
"prefix": "NBDC00167",
"pubmeds": [
"10592177",
"11125041",
"10869023",
"11752247",
"12520019",
"17569631"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00168": {
"alt_name": "A Database of Plant Cis-acting Regulatory DNA Elements",
"description": "This database is a collection of nucleotide sequence motifs related to the regulations of gene expressions, such as promoters, in higher plants. The data are annotated and the database provides users with information of publications, links to PubMed and DDBJ/EMBL/GenBank accession numbers. Users can search this database for possible motifs in their own sequence data.",
"homepage": "https://www.dna.affrc.go.jp/PLACE/",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "New PLACE",
"prefix": "NBDC00168",
"pubmeds": [
"9847208"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00169": {
"description": "Plant snoRNA Version 1.2 is a database that combines information of the Arabidopsis genome gathered during 3 separate computerbased searches for box C/D snoRNA genes with the results from ncRNA studies added.\nThis list of snoRNAs were applied to the genomes of a variety of non-Arabidopsis plant species and thus assisted in the identification of more or less 250 genes from these species.\nThe database includes the alignment sequences of these 250 genes.\nThe content of the database is presented in a series of tables.\nThe sequences can be downloaded in FASTA file format.",
"homepage": "https://bioinf.hutton.ac.uk/cgi-bin/plant_snorna/home",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "James Hutton Institute",
"name": "Plant snoRNA Database",
"prefix": "NBDC00169",
"pubmeds": [
"12520043",
"10829025",
"11469857",
"11780637",
"11266566",
"10380797",
"9312032",
"9578473",
"9596627",
"12136108",
"11706161",
"223845",
"4447901",
"8799814",
"9664033"
],
"status": "Inactive",
"target_keywords": [
"RNA"
]
},
"nbdc00170": {
"alt_name": "Protein Mutant Database",
"description": "PMD is a collections of literature data related to natural and artificial mutants for all kinds of proteins except members of the globin and immunoglobulin families. PMD treats an article as one entry, and each entry contains data about one or more protein mutants. This database allows users to search articles by keywords or amino acid sequences using BLAST. Each entry in search results shows details of the article (authors, journal, MEDLINE link, etc) and mutation (the position of amino acid substitution, insertion or deletion, kind of mutations, functional or structural features, etc). The authors of articles in academic journals can submit protein mutant data to PMD.",
"homepage": "http://pmd.ddbj.nig.ac.jp/~pmd/pmd.html",
"information_keywords": [
"Sequence"
],
"maintainer": "National Institute of Genetics",
"name": "PMD",
"prefix": "NBDC00170",
"pubmeds": [
"9847227",
"8073043"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00171": {
"description": "Polymorphism of Microsatellite Markers is a database of genotypic information on microsatellite loci in the Japanese population. This database contains data on location, heterozygosity, the number of alleles and repeat unit for each locus. It treats 4868 microsatellite markers of 64 normal Japanese individuals. The website summarized the datasets in a table representing the number of microsatellite loci, the average number of alleles per locus and average of heterozygosity per locus on each chromosome.",
"homepage": "http://www002.upp.so-net.ne.jp/kyama-Q/MS.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Kyushu University Medical Institute of Bioregulation",
"name": "Polymorphism of Microsatellite Markers",
"prefix": "NBDC00171",
"status": "Inactive",
"target_keywords": [
"cDNA/EST",
"Genetic variation"
]
},
"nbdc00172": {
"alt_name": "Protein Research Foundation",
"description": "PRF is a collection of the information related to amino acids, peptides and proteins and making databases. It consists of there databases; Literature Database (PRF/LITDB), Peptide/Protein Sequence Database (PRF/SEQDB) and Synthetic Compounds Database (PRF/SYNDB). PRF/LITDB contains information of articles dealing with peptides from scientific journals accessible in Japan. PRF/SEQDB contains amino acid sequences of peptides and proteins, including sequences predicted from genes. Users are also search literature in which the sequence is presented. In PRF/SYNDB, unnatural amino acids, amino acid derivatives and chemically synthesized peptides are registered.",
"homepage": "http://www.prf.or.jp/index-e.html",
"information_keywords": [
"Method",
"Sequence",
"Bibliography/Documents",
"Portal"
],
"maintainer": "Protein Research Foundation",
"name": "PRF",
"prefix": "NBDC00172",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00174": {
"description": "ProDom is an extensive database providing information on protein domain families.\nIt was created automatically by performing a global comparison of all the protein sequences that could be found.\nThe database can be searched by means of accession number, SWISS-PROT/TrEMBL identifier, or keywords.\nThe site also provides access to related databases namely InterPro, PROSITE, PFAM and PDB.\nThe ProDom domains may also be viewed on 3D structures created by the graphical interface.",
"fairsharing": "biodbcore-000375",
"homepage": "http://prodom.prabi.fr/prodom/current/html/home.php",
"information_keywords": [
"Classification"
],
"maintainer": "Rhone-Alpes Bioinformatics Center",
"name": "ProDom",
"prefix": "NBDC00174",
"pubmeds": [
"9009835",
"9399865",
"9847197",
"10592243",
"12230033",
"15608179"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00175": {
"description": "ProMode-Elastic is a database of normal mode analysis of PDB data using elastic network model in torsional angle space. Normal mode analysis are performed by unique developed program, PDBETA.\nIt provides the following information;\n1) Fluctuation of atoms and Fluctuation of dihedral angles. Time average and data for the 3 lowest-frequency normal modes are given by graphs.\n2) Correlation between fluctuating atoms. Time average and data for the 10 lowest-frequency normal modes are given by a triangle map. Furthermore, a distance map between residues are given by a triangle map. \n3) Animation of fluctuating molecules displayed on the viewers, jV (PDBj) and Jmol, for the 10 lowest-frequency normal modes. GIF animation is also available.\n4) Displacement vectors exhibited on the viewers, jV (PDBj) and Jmol, for the 10 lowest-frequency normal modes. Moreover, static images for displacement vectors are presented.\nIn this database, some numerical data are downloadable.",
"homepage": "http://pdbj.org/promode-elastic",
"information_keywords": [
"3D structure"
],
"maintainer": "Waseda University",
"name": "ProMode-Elastic",
"prefix": "NBDC00175",
"pubmeds": [
"15059828"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00176": {
"alt_name": "Thermodynamic Database for Protein-Nucleic Acid Interactions",
"description": "The ProNIT database provides data on experimentally determined thermodynamic interactions between proteins and nucleic acids. The properties of the interacting protein and nucleic acid, reference materials, and thermodynamic parameters like binding constants, changes in free energy, enthalpy and heat capacity are available. Thermodynamic knowledge of proteins is as fundamental as sequence and structural information, because proteins behave according to the law of thermodynamics. Biological function of proteins can thus be studied.",
"homepage": "http://gibk26.bio.kyutech.ac.jp/jouhou/pronit/pronit.html",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Kyushu Institute of Technology",
"name": "ProNIT",
"prefix": "NBDC00176",
"pubmeds": [
"16381846",
"11724731",
"11987161"
],
"status": "Inactive",
"target_keywords": [
"DNA",
"Protein"
]
},
"nbdc00177": {
"alt_name": "Thermodynamic Database for Protein and Mutants",
"description": "The data in the ProTherm database include thermodynamic parameters such as Gibbs free energy change, enthalpy change, heat capacity change, transition temperature etc., for wild type and mutant proteins that are important for understanding the structure and stability of proteins. There is also information about the secondary structure and accessibility of wild type residues, experimental conditions (pH, temperature, buffer, ion and protein concentration), measurements and methods used for each data, and activity information (Km and Kcat).",
"homepage": "http://gibk26.bio.kyutech.ac.jp/jouhou/Protherm/protherm.html",
"information_keywords": [
"Method",
"Chemical structure"
],
"maintainer": "Kyushu Institute of Technology",
"name": "ProTherm",
"prefix": "NBDC00177",
"pubmeds": [
"14681373",
"16381846",
"11752320",
"11987161",
"10592247",
"9847203"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00178": {
"description": "Pseudogene.org is a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase. It contains annotations, nucleotide sequences, amino acid sequence, individual sequence alignment about Eukaryote and Prokaryote pseudogenes and pseudomotifs.\nPseudogenes are analyzed using sequence alignment programs (such as FASTA or BLAST) to detect matching regions in the nucleotide sequence.",
"homepage": "http://www.pseudogene.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "Yale University",
"name": "Pseudogene.org",
"prefix": "NBDC00178",
"pubmeds": [
"17099229"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00179": {
"description": "This database contains bibliographic information from journal articles in the field of life science as well as MEDLINE (title, authors, journal name, abstracts). Links are provided for articles with free access to the full article.",
"fairsharing": "biodbcore-000456",
"homepage": "http://www.ncbi.nlm.nih.gov/pubmed",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "PubMed",
"prefix": "NBDC00179",
"status": "Active"
},
"nbdc00180": {
"alt_name": "Macaca fascicularis cDNA database",
"description": "QFbase is a cDNA database of the crab-eating macaque (Macaca fascicularis). QFbase contains EST and full-length sequences of macaque cDNAs obtained from brain, testis, bone marrow, liver, pancreas, thymus, heart, spleen, and kidney. The clones can be searched by keywords or cDNA sequences using BLAST, and requests for some clones are available through the HSRRB (Human Science Research Resource Bank) website. This database also provides human-macaque alignments of coding sequences and genome browser (QFbase-GBrowse) mapping the cDNA clones on the rhesus macaque genome.",
"homepage": "http://gene.nibiohn.go.jp/qfbase/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "National Institutes of Biomedical Innovation, Health and Nutrition",
"name": "QFbase",
"prefix": "NBDC00180",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00181": {
"alt_name": "Rice Annotation Database",
"homepage": "http://golgi.gs.dna.affrc.go.jp/SY-1102/rad/",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "RAD",
"prefix": "NBDC00181",
"pubmeds": [
"15608281"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc00182": {
"alt_name": "Rice Annotation Project DataBase",
"description": "This database contains highly accurate annotations on the rice genome provided by the rice annotation project (RAP). Literature-based annotation data will be updated a few times a year. Information can be viewed graphically using GBrowse/JBrowse. Additionally, similarity searches (BLAST, BLAT) can be performed with user-provided sequences against the rice genome. Furthermore, Genome-wide variation data among >500 rice accessions are visualized by the multiple genome browser TASUKE+.",
"homepage": "http://rapdb.dna.affrc.go.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "RAP-DB",
"prefix": "NBDC00182",
"pubmeds": [
"23299411",
"24280374"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00183": {
"alt_name": "RIKEN Arabidopsis Genome Encyclopedia",
"description": "The RARGE database was created to enhance the RIKEN Arabidopsis resource, which provides full-length cDNAs, transposon mutants and microarray experiments. Users can search BLAST for homogeneous comparison of a queried sequence with Arabidopsis Full-length cDNAs and the Ac/Ds Transposon Tagging Lines, as well as full-length DNAs, transposon mutants, microarray, genome map, alternative splicing and transcription factor (RARTF) and the phenotypic information of transposon mutants (RAPID) and nuclear-encoded chloroplast proteins.",
"homepage": "http://rarge-v2.psc.riken.jp",
"information_keywords": [
"Sequence",
"Expression",
"Portal"
],
"maintainer": "RIKEN CSRS (RIKEN Center for Sustainable Resource Science)",
"name": "RARGE",
"prefix": "NBDC00183",
"pubmeds": [
"15608280",
"24272250"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Organism"
]
},
"nbdc00184": {
"alt_name": "The Ribosomal Database Project",
"description": "This database is a collection of rRNA sequences for fungai, bacteria and archaea. The site provides a variety of analytical tools, including rRNA sequence alignments, similarity search tools, and classification of species from rRNA sequences.",
"homepage": "http://rdp.cme.msu.edu/",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "Michigan State University",
"name": "RDP",
"prefix": "NBDC00184",
"pubmeds": [
"1598241",
"8332524",
"7524021",
"8594608",
"9016515",
"9847171",
"10592216",
"11125082",
"12520046",
"15608200",
"17090583",
"19004872",
"24288368"
],
"status": "Inactive",
"target_keywords": [
"RNA"
]
},
"nbdc00185": {
"description": "REACTOME is a database of human pathways for basic research, genome analysis, pathway modeling, systems biology and education. It contains manually curated and peer-reviewed pathway data which are annotated by expert biologists, in collaboration with Reactome editorial staff and cross-referenced to many bioinformatics databases. This database provides an intuitive website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. The curated human pathway data are available to infer orthologous events in 20 non-human species including mouse, rat, chicken, worm, fly, yeast, plant and bacteria. Using species comparison tool, users are able to compare predicted pathways with those of human to find reactions and pathways common to a selected species and human.",
"fairsharing": "biodbcore-000329",
"homepage": "https://reactome.org",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Reactome team",
"name": "REACTOME",
"prefix": "NBDC00185",
"pubmeds": [
"15608231",
"29145629"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00186": {
"alt_name": "Riken Expression Array Database",
"description": "READ is a database of mouse expression studies that allows users to explore gene expression patterns in up to 49 mouse tissues. In addition to gene data, users can also use READ to find other genes with similar expression patterns in a selected range of tissues. A BLAST function is also provided so that a sequence can be searched to find matching genes, which then will be linked to relevant expression information.\nREAD service were terminated in 2013, and users can download the raw data of this service from ' http://read.gsc.riken.jp/dist '.",
"homepage": "http://read.gsc.riken.jp",
"information_keywords": [
"Expression"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "READ",
"prefix": "NBDC00186",
"pubmeds": [
"11752296",
"11226216"
],
"status": "Closed",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00187": {
"alt_name": "Reference Sequence",
"description": "RefSeq is a database of standard reference genomic, transcript, and protein sequences. The database contains consensus sequence data for over 20,000 organisms and over 27 million proteins and is designed to provide a common basis for experimental studies that can be searched using accession ID, keyword, or BLAST. Bulk data is available for FTP download.",
"fairsharing": "biodbcore-000457",
"homepage": "https://www.ncbi.nlm.nih.gov/refseq/",
"information_keywords": [
"Sequence"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "RefSeq",
"prefix": "NBDC00187",
"pubmeds": [
"22121212",
"18927115",
"10592200"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"RNA",
"Protein",
"Cell/Organelle"
]
},
"nbdc00188": {
"alt_name": "The Rat Genome Database",
"description": "This is a comprehensive site for rat genome researches. In addition to information on rat genes, the site contains information on rat strains, data on rat models for disease, and publications.",
"fairsharing": "biodbcore-000417",
"homepage": "http://rgd.mcw.edu",
"information_keywords": [
"Bioresource",
"Ontology/Terminology/Nomenclature",
"Sequence",
"Interaction/Pathway",
"Repository"
],
"maintainer": "Medical College of Wisconsin/Bioinformatics Research Center",
"name": "RGD",
"prefix": "NBDC00188",
"pubmeds": [
"21478484",
"17151068"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"DNA",
"Organism",
"Health/Disease"
]
},
"nbdc00189": {
"alt_name": "Genome database for Rhizobia with annotation",
"description": "RhizoBase is a database of rhizobia sequence resources for users to obtain genomic information and perform searches. There are 22 currently available species, and in addition to gene and sequence searches, users can download raw sequence data as well functional annotation information.",
"homepage": "http://genome.microbedb.jp/rhizobase",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "RhizoBase",
"prefix": "NBDC00189",
"pubmeds": [
"24275496"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00191": {
"alt_name": "Rice Proteome Database",
"description": "This database is a collection of two-dimensional electrophoretic gel spots obtained using various tissues of rice and subcellular organelles. A variety of protocols related to proteomic analysis are also provided on the site.\nThe original site (http: //gene64.dna.affrc.go.jp/RPD/) has been closed. RPD is available from LSDB archive site.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/rpd/desc.html",
"information_keywords": [
"Method",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "RPD (Archive)",
"prefix": "NBDC00191",
"pubmeds": [
"16217611",
"14681440"
],
"status": "Active",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc00192": {
"description": "This database contains Arabidopsis thaliana cDNA sequences that users can query to obtain full clone sequences, particularly from AGI-coded data. The sequence coverage is selectable (full clone, 5' only, or 3' only) and each clone is linked to A. thaliana and NCBI Nucleotide records.",
"homepage": "http://www.brc.riken.jp/lab/epd/catalog/cdnaclone.html",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "RIKEN Arabidopsis Full-Length Clone Database Search",
"prefix": "NBDC00192",
"pubmeds": [
"9778851",
"11910074",
"15608280",
"16769687"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00193": {
"alt_name": "Rice Mitochondrial Genome",
"description": "This site contains information on the mitochondrial genome of rice, including sequences and physical maps.\nThe original site (http: //rmg.rice.dna.affrc.go.jp/) has been closed. The RMG is available from LSDB archive site.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/rmg/desc.html",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "RMG (Archive)",
"prefix": "NBDC00193",
"pubmeds": [
"12471441"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Cell/Organelle"
]
},
"nbdc00194": {
"alt_name": "Rice Microarray Opening Site",
"description": "RMOS is a database of comprehensive information for Rice Microarray Project (April 1999 - March 2003). In addition to microarray data, users can also find information of the general background for Microarray techniques and the research data related to the custom microarray developed in the project.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/rmos/desc.html",
"information_keywords": [
"Method",
"Expression",
"Bibliography/Documents"
],
"maintainer": "National Institute of Agrobiological Sciences",
"name": "RMOS (Archive)",
"prefix": "NBDC00194",
"pubmeds": [
"14681439",
"14982972",
"15029956",
"12956525",
"12728997",
"12438691",
"11967095",
"17448460",
"11214972"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00195": {
"alt_name": "Ribosomal Protein Gene Database",
"description": "The original site was retired, and it is available in NBDC Life Science Database Archive.",
"homepage": "http://ribosome.med.miyazaki-u.ac.jp/",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "University of Miyazaki Frontier Science Research Center",
"name": "RPG",
"prefix": "NBDC00195",
"pubmeds": [
"14681386"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein",
"Cell/Organelle"
]
},
"nbdc00196": {
"alt_name": "The Sendai Arabidopsis Seed Stock Center",
"description": "SASSC is a search tool for finding Arabidopsis mutant seed lines. The site consists of a search box that can be used to locate genes of interest, retrieve information on mutant phenotypes, and request seeds.",
"homepage": "http://sassc.epd.brc.riken.jp/sassc/create_search_panel2.php?mode=general",
"information_keywords": [
"Bioresource",
"Image/Movie"
],
"maintainer": "RIKEN Tsukuba Institute",
"name": "SASSC Quick search",
"prefix": "NBDC00196",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc00198": {
"alt_name": "Systems Biology and Medicine Database",
"description": "SBM DB is comprehensive database of gene expression profiles. This database is constructed with three databases; 1) RefExA is a comprehensive gene expression database of Human normal tissues, normal cultured cells and cancer cell lines with geneChip HG-U133A, can help investigation of human disease. 2) HUVEC DB is a database for HUVEC (Human Umbilical Vein Endothelial Cells) gene expression with stimuli by TNF&alpha etc.. 3) IHC DB is a database for nuclear receptor protein expression and localization in each normal organ (rat tissues) using antibody and immunohistochemical staining. These databases enable to compare the transcriptome of various tissues, organs and experiments. mRNA expression levels of genes are measured with oligo-nucleotide DNA microarray geneChip.",
"homepage": "http://www.lsbm.org/site_e/database/index.html",
"information_keywords": [
"Expression",
"Image/Movie"
],
"maintainer": "The University of Tokyo Research Center for Advanced Science and Technology",
"name": "SBM DB",
"prefix": "NBDC00198",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein",
"Health/Disease",
"Cell/Organelle"
]
},
"nbdc00199": {
"alt_name": "Saccharomyces cerevisiae Morphological Database 2",
"description": "SCMD is a database of micrographs of budding yeast with thousands of images of mutant strains and results from automated data mining analysis of several parameters of these mutants. genes and phenotypes can be searched and extensive phenotype statistics are provided.",
"homepage": "http://www.yeast.ib.k.u-tokyo.ac.jp/SCMD/datasheet.php",
"information_keywords": [
"Image/Movie"
],
"maintainer": "The University of Tokyo Graduate School of Frontier Sciences",
"name": "SCMD 2",
"prefix": "NBDC00199",
"pubmeds": [
"15980577",
"14681423"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc00200": {
"alt_name": "Structural Classification of Proteins 2",
"description": "SCOP2 is a database for organizing structurally characterized proteins according to their structural and evolutionary relationships. In this database, proteins are organized according to their structural and evolutionary relationships, but instead of a simple tree-like hierarchy these relationships form a complex network of nodes. Then, the classification of proteins is described in terms of a directed acyclic graph in which each node defines a relationship of particular type and is exemplified by a region of protein structure and sequence.",
"fairsharing": "biodbcore-000423",
"homepage": "http://scop2.mrc-lmb.cam.ac.uk",
"information_keywords": [
"3D structure",
"Classification"
],
"maintainer": "MRC (The Medical Research Council) Laboratory of Molecular Biology",
"name": "SCOP2",
"prefix": "NBDC00200",
"pubmeds": [
"24293656",
"7723011",
"11752311",
"14681400",
"18000004"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00201": {
"alt_name": "Sugi Genome Database",
"description": "Sugi Genome Database is a database for genome of sugi (Cryptomeria japonica) and a Japanese conifer (Chamaecyparis obtusa). It provides information about EST, DNA markers, a linkage map, and genetic diversity in these species.",
"homepage": "http://www.ffpri.affrc.go.jp/labs/cjgenome/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Forestry and Forest Products Research Institute",
"name": "SGD",
"prefix": "NBDC00201",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc00202": {
"alt_name": "Saccharomyces Genome Database",
"description": "This is an integrated database for budding yeast Saccharomyces cerevisiae. It contains search and analysis tools based on genes, sequences, and functions, as well as information related to citations, and the community. The information is updated and maintained by curators. It enables users to find functional relationships to sequences and gene products of fungi and higher organisms can also be verified. The SGD also maintains all gene names for budding yeast through the gene Name Registry.",
"fairsharing": "biodbcore-000100",
"homepage": "http://www.yeastgenome.org/",
"information_keywords": [
"Bioresource",
"Ontology/Terminology/Nomenclature",
"Sequence",
"Expression",
"Interaction/Pathway",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Stanford University",
"name": "SGD",
"prefix": "NBDC00202",
"pubmeds": [
"9399804",
"22110037"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein",
"Organism"
]
},
"nbdc00203": {
"alt_name": "EST analysis of silkworm gene expression",
"description": "SilkBase is a database of expressed genes from Bombyx mori and the related species Samia cynthia ricini and Mandarina fosimid. The database contains thousands of EST reads from randomly selected cDNAs from each species. Users can perform keyword or BLAST searches for each against cDNAs. Links for requesting resources are also provided.",
"homepage": "http://silkbase.ab.a.u-tokyo.ac.jp/cgi-bin/index.cgi",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tokyo",
"name": "SilkBase",
"prefix": "NBDC00203",
"pubmeds": [
"14614147"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00204": {
"alt_name": "Silkworm Genetic Resource Database",
"description": "Silkworm Base is a database of silkworm resources including eggs, larvae, pupas, cocoons and cloned DNA established by Kyushu University and National Institute of genetics. Silkworm Base consists of information on genetic resource stocks, mutant strains, references, distribution requests and related sites. Each entry contains a strain name, phenotype data, genetic background (gene symbol, allele, etc), origin, references, images and feeding ability. Users can search available resources by keywords from those items.",
"homepage": "http://www.shigen.nig.ac.jp/silkwormbase/index.jsp",
"information_keywords": [
"Bioresource",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "National Institute of Genetics",
"name": "Silkworm Base",
"prefix": "NBDC00204",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc00205": {
"description": "Silver Project: Ape Genome Sequencing is a repository of ape nucleotide sequences maintained by Division of Population genetics, National Institute of genetics (NIG). This database contains comparative data of human and ape sequences including those determined under Silver Project, chimpanzee and gorilla sequences retrieved from DDBJ/EMBL/GenBank International Nucleotide Sequence Database. Users can browse phylogenetic trees based on coding regions, noncoding regions or mitochondrial DNA, as well as alignments of human and ape sequences.",
"homepage": "http://sayer.lab.nig.ac.jp/~silver/index.html",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "National Institute of Genetics",
"name": "Silver Project: Ape Genome Sequencing",
"prefix": "NBDC00205",
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00206": {
"alt_name": "The Single Nucleotide Polymorphism Database (dbSNP)",
"description": "dbSNP collects information on polymorphisms based on single and small-scale multi-base substitutions, including insertions and deletions, microsatelites, and non-polymorphic variants. Differences in the frequency of polymorphisms in a population can be visually compared for each SNP.",
"fairsharing": "biodbcore-000438",
"homepage": "http://www.ncbi.nlm.nih.gov/snp/",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "dbSNP",
"prefix": "NBDC00206",
"pubmeds": [
"11125122",
"10592272"
],
"status": "Active",
"target_keywords": [
"Genetic variation"
]
},
"nbdc00207": {
"alt_name": "Signaling Pathway Database",
"description": "SPAD is a database of protein signaling cascades with pathway diagrams for a limited number of extracellular signaling pathways in three broad areas: growth factors, cytokines, and hormones. Each component of a pathway is hyperlinked to a page containing further details.",
"homepage": "http://www.grt.kyushu-u.ac.jp/spad/",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences",
"name": "SPAD",
"prefix": "NBDC00207",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00208": {
"description": "Species 2000 is a collection of all the species in the world (microbes, fungi, plants and animals).\nThe data is obtained, and made available by combining a comprehensive number of species databases from all over the world. This enables the database developers to cover all the major organism groups.\nThis checklist contains information on more than 1,3M species from 115 databases.\nIt incorporates the Catalogue of Life, which contains a taxonomic tree of organisms and a nine-tiered taxonomic classification system that can be browsed and searched.",
"homepage": "http://www.sp2000.org",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "University of Reading",
"name": "Species 2000",
"prefix": "NBDC00208",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00209": {
"description": "NAISTrap is a database of gene-trapped ES cell lines generated by a gene trapping method termed UPATrap. Each entry consists of following 7 items; the clone number, name of the trapped gene, expression pattern in ES cells, identity, coding sequence in mRNA, deleted region and trapped sequence. NAISTrap provides a tutorial for the UPATrap and other gene trapping methods. Users can order available resources by e-mail.",
"homepage": "http://bsw3.aist-nara.ac.jp/kawaichi/naistrap-e.html",
"information_keywords": [
"Bioresource",
"Expression"
],
"maintainer": "Nara Institute of Science and Technology Graduate School of Biological Sciences",
"name": "The NAISTrap Project",
"prefix": "NBDC00209",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle"
]
},
"nbdc00210": {
"alt_name": "The National BioResource Project for the Rat in Japan",
"description": "NBRP-Rat is a database for collection, preservation and supply of rat strains with phenotypic and genotypic profiles. NBRP-Rat contains standardized strains as well as many mutant lines (spontaneous mutants, congenic and recombinant strains, transgenic and mutagenized rats, etc) from Japan and abroad. This database provides a query form to order or deposit strains and research tools such as the phenome database, phylogenetic trees and a genetic chart. Users can search available strains by keywords, preservation status, genetic categories and research categories.",
"homepage": "http://www.anim.med.kyoto-u.ac.jp/NBR/strains/Strains_list.aspx",
"information_keywords": [
"Bioresource",
"Expression"
],
"maintainer": "Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University",
"name": "NBRP-Rat",
"prefix": "NBDC00210",
"pubmeds": [
"19654430",
"15129252",
"16584579",
"15591307"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Organism"
]
},
"nbdc00211": {
"description": "TMIG-2DPAGE Database is a database of aging-related proteome of human cells. This database contains information for investigating molecular mechanisms involved in cellular aging, aging-related diseases, and oxidative stress-induced cell damages. Each entry is linked to the standard spot protein map of the two-dimensional gel image of SDS-PAGE in order to be accessible by clicking the mouse on it. 2D gel images of TIG-3 (for profiling in-vitro aging of nornal human diploid fibroblasts), SH-SY5Y (human neuroblastoma-derived dopaminergic cell line), HUVEC (human umbilical vein endothelial cells) and Werner's syndrome skin fibroblasts (under construction) are included.",
"homepage": "http://www.proteome.jp/2D/",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology",
"name": "TMIG-2DPAGE Database",
"prefix": "NBDC00211",
"pubmeds": [
"9548301"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00212": {
"description": "This database of tobacco cDNA clones contains 5' and 3' sequence information for each clone, generated from BY-2 cells. Users can search by gene or clone information, or locate clones by BLAST search.",
"homepage": "http://www.brc.riken.jp/lab/epd/catalog/n_tabacum.html",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "Tobacco EST clones from BY-2 cells Database Search",
"prefix": "NBDC00212",
"pubmeds": [
"15509851"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00213": {
"description": "TP-Search is an integrated database on drug transporters, which are thought to play an important role in the pharmacokinetics of drugs. This database contains information extracted from a large number of published papers. It includes information related to drug transporters, tissue, compounds name, drug-drug interaction, gender difference, KO mice and rats, \npathophysiology and genetic diseases. Users are able to search by tissue name, genetic polymorphisms or genetic diseases. It's necessary to registrate with your e-mail address.",
"homepage": "http://togodb.dbcls.jp/tpsearch",
"maintainer": "The University of Tokyo Graduate School of Pharmaceutical Sciences",
"name": "TP-Search",
"prefix": "NBDC00213",
"pubmeds": [
"15587938"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Protein",
"Health/Disease"
]
},
"nbdc00214": {
"description": "This database contains three working data tables displaying the effect of genes from a particular category on organismal characteristics, based on transcriptome analysis of the two-component system in E.coli. HTML and PDF formats are available.",
"homepage": "http://ecoli.aist-nara.ac.jp/xp_analysis/2_components/",
"information_keywords": [
"Expression"
],
"maintainer": "Nara Institute of Science and Technology",
"name": "Transcriptome analysis of 2 component system in Eschericia coli",
"prefix": "NBDC00214",
"pubmeds": [
"12366850"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc00215": {
"alt_name": "The influence of Transposed Elements (TEs) on the transcriptome of 7 species",
"description": "Transpogene is a database that focusses on how the transcriptome of 7 species are influenced by transposed elements (TEs).\nIt consists of a collection of TEs, which are located in the protein-coding genes of these organisms.\nThe genomes represented are human, mouse, chicken, Zebrafish, fruit fly, nematode and sea squirt, evidently stretching widely across the animal kingdom.\nExamples of effects these TEs may have on their hosting genes include the creation of new exons, insertion of TEs into introns, exons, and promoters and involvement in the cause and development of diseases.\nA search option is available where a keyword e.g. the Swissprot entry name or a number of other identifying codes can be entered and various criteria can be selected to narrow down the search results.\nThe Transpogene database is also downloadable in its entirety.",
"homepage": "http://transpogene.tau.ac.il/",
"information_keywords": [
"Sequence"
],
"maintainer": "Tel Aviv University",
"name": "TranspoGene",
"prefix": "NBDC00215",
"pubmeds": [
"17986453"
],
"status": "Inactive",
"target_keywords": [
"DNA"
]
},
"nbdc00216": {
"description": "This database of Arabidopsis transposon mutants can be searched by line ID or gene model ID to locate available mutants, which can be ordered for further study.",
"homepage": "http://www.brc.riken.jp/lab/epd/catalog/transposon.html",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "Transposon tag line Database Search",
"prefix": "NBDC00216",
"pubmeds": [
"8220445",
"8893547",
"12177482",
"14996221",
"15840642"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc00217": {
"alt_name": "Transcription Product Database",
"description": "This database compares a number of metabolic pathways in a group of seven single-celled microorganisms (also called archaea) namely the citric acid cycle, the energy producing glycolytic pathway and the processes by which amino acids and nucleic acids are synthesized.\nLinks to two related databases, namely Archaic (ARCHAebacterial Information Collection) and Arch genet (Archaeal gene Network) are available. These were tested and found functional.",
"homepage": "http://riodb.ibase.aist.go.jp/trap/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "TraP",
"prefix": "NBDC00217",
"pubmeds": [
"9598984",
"11121031"
],
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc00218": {
"alt_name": "Database on Translational Signals",
"description": "TRSIG is a database of mRNA sequence elements that influence translation events. The database contains signals such as regulatory elements and caps. The database can be searched by BLAST, or annotated signals can be browsed.",
"homepage": "http://gibk26.bio.kyutech.ac.jp/jouhou/trsig/blast.html",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "Kyushu Institute of Technology",
"name": "TRSIG",
"prefix": "NBDC00218",
"status": "Inactive",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc00219": {
"description": "UCSC Genome Browser is a database which contains the reference sequence and working draft assemblies for a large collection of genomes. It is also a portal site to the ENCODE and Neandertal projects.\nThis database provides following tools;\n1) The Genome Browser zooms and scrolls over chromosomes, showing the work of annotators worldwide. \n2) The gene Sorter shows expression, homology and other information on groups of genes that can be related in many ways.\n3) Blat quickly maps your sequence to the genome. \n4) The Table Browser provides convenient access to the underlying database.\n5) Visigene lets you browse through a large collection of in situ mouse and frog images to examine expression patterns.\n6) Genome Graphs allows you to upload and display genome-wide data sets.",
"fairsharing": "biodbcore-000107",
"homepage": "http://genome.ucsc.edu/",
"information_keywords": [
"Sequence",
"Expression",
"Image/Movie"
],
"maintainer": "University California Santa Cruz",
"name": "UCSC Genome Browser",
"prefix": "NBDC00219",
"pubmeds": [
"17993665"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Protein"
]
},
"nbdc00220": {
"description": "This database contains sets of transcriptional sequences obtained from the same locus. It includes information such as the homology between transcripts and the reference protein, expression pattern, cDNA clones, and genomic position.",
"fairsharing": "biodbcore-000459",
"homepage": "http://www.ncbi.nlm.nih.gov/unigene",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "UniGene",
"prefix": "NBDC00220",
"pubmeds": [
"8849440",
"7670480"
],
"status": "Closed",
"target_keywords": [
"cDNA/EST",
"Protein"
]
},
"nbdc00221": {
"alt_name": "The Universal Protein Resource",
"description": "This database contains information on amino acid sequences and their functions. It is composed of four core databases, UniProtKB, UniRef, UniParc, and Proteomes. UniProtKB contains two types of data, which are manually curated high quality SwissProt annotations based on literature information, and automatically annotated TrEMBL. \nUniRef provides results of sequence similarity searches. \nUniParc integrates information such as ID for other databases per sequence ID.\nProteomes provides proteome data of each organism with completely sequenced genomes.",
"homepage": "http://www.uniprot.org/",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "UniProt Consortium",
"name": "UniProt",
"prefix": "NBDC00221",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00222": {
"fairsharing": "biodbcore-000437",
"homepage": "http://www.ncbi.nlm.nih.gov/probe",
"information_keywords": [
"Method",
"Sequence",
"Expression",
"Bibliography/Documents",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "Probe",
"prefix": "NBDC00222",
"status": "Closed",
"target_keywords": [
"Genetic variation"
]
},
"nbdc00223": {
"alt_name": "University of Tokyo Genome Browser",
"description": "This is a browser for the Medaka (Oryzias latipes) genome. The site allows users to perform BLAST searches or query by ID. Data is also available for download.",
"homepage": "http://utgenome.org/medaka/",
"information_keywords": [
"Expression"
],
"maintainer": "The University of Tokyo Graduate School of Frontier Sciences",
"name": "UTGB Medaka Genome Browser",
"prefix": "NBDC00223",
"pubmeds": [
"17932069",
"17554307"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation"
]
},
"nbdc00224": {
"description": "VPARA is a database of Vibrio parahaemolyticus genome sequence data. The database features BLAST and keyword searching and provides data for download in several formats.",
"homepage": "http://genome.bio.titech.ac.jp/bacteria/vpara/",
"information_keywords": [
"Sequence"
],
"maintainer": "Tokyo Institute of Technology Graduate School of Bioscience and Biotechnology",
"name": "V. parahaemolyticus Genome Information",
"prefix": "NBDC00224",
"pubmeds": [
"6756788",
"12620739",
"12169621",
"12142404",
"10834969"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"DNA",
"RNA",
"Protein"
]
},
"nbdc00225": {
"alt_name": "Xenopus laevis Database",
"description": "XDB is a database of Xenopus laevis EST sequences. The database contains over 250,000 ESTs that can be searched by BLAST, keyword, or domain. A spatial expression browser is also available.",
"homepage": "http://xenopus.nibb.ac.jp/",
"information_keywords": [
"Expression",
"Image/Movie"
],
"maintainer": "National Institute for Basic Biology",
"name": "XDB",
"prefix": "NBDC00225",
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Cell/Organelle"
]
},
"nbdc00227": {
"alt_name": "National BioResource Project - Yeast",
"description": "National BioResource Project - Yeast is a database of the budding yeast (Saccharomyces cerevisiae) and the fission yeast (Schizosaccharomyces pombe) resources. This database contains strains, plasmids, genomic DNA and cDNA clones of yeast strains. Users can search available resources by keywords such as loci, genes and depositor's name.",
"homepage": "https://yeast.nig.ac.jp/yeast/top.xhtml",
"information_keywords": [
"Bioresource"
],
"maintainer": "Osaka City University Graduate School of Medicine",
"name": "NBRP Yeast",
"prefix": "NBDC00227",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"DNA",
"Organism"
]
},
"nbdc00228": {
"description": "Bombyx mori EST Sequences in Full-length cDNA Libraries is a database of silkworm (Bombyx mori) EST sequences maintained by Graduate School of Agricultural and Life Sciences, The University of Tokyo. Each enrtry contains a clone name and full-length sequence. Users can perform BLAST search against EST sequences, and retrieve the sequences from this database and SilkBase; another database of silkworm ESTs.",
"homepage": "http://papilio.ab.a.u-tokyo.ac.jp/Bombyx_EST/",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tokyo Graduate School of Agricultural and Life Sciences",
"name": "Bombyx mori EST Sequences in Full-length cDNA Libraries",
"prefix": "NBDC00228",
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00229": {
"alt_name": "Rice Tos17 Insertion Mutant Database",
"description": "The Functional Genomics Research Team at the National Institute of Agricultural Sciences is creating a gene disruption system in rice using the endogenous transposon, Tos17. This database allows users to search sequences adjacent to the transposon, as well as strain names from the results of PCR screening using a three-dimensional DNA pool.",
"homepage": "https://tos.nias.affrc.go.jp/index.html.en",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "Mutant Panel",
"prefix": "NBDC00229",
"pubmeds": [
"12897251",
"17180734",
"8755553",
"16100779",
"8755553",
"16100779",
"15284490",
"11228433",
"9291976"
],
"status": "Active",
"target_keywords": [
"DNA",
"Organism"
]
},
"nbdc00236": {
"alt_name": "Gal4 Enhancer Trap Insertion Database",
"description": "GETDB is a collection of information of Gal4 enhancer trap lines in D. melanogaster. The database contains insertion site, expression pattern, and mutant phenotype information on nearly 7000 gene trap fly lines. Users can search or browse by gene, location, chromosome position, and strain ID. Insertions were mapped using 5' end mapping of the Gal4 promoter. Stocks of the insertion mutants are also available.",
"homepage": "http://kyotofly.kit.jp/stocks/GETDB/getdb.html",
"information_keywords": [
"Bioresource",
"Sequence",
"Image/Movie"
],
"maintainer": "Kyoto Institute of Technology Drosophila Genetic Resource Center",
"name": "GETDB",
"prefix": "NBDC00236",
"pubmeds": [
"12324948"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc00237": {
"alt_name": "Tropical bee reference database",
"description": "TABR is a reference database of tropical asian bees. A taxon is treated as one record in this database, and each record is composed of 11 items including taxonomical information (sex, locality and depository of the type, source of the original description), distributional data and references. Users can search records by keywords from these items.",
"homepage": "http://konchudb.agr.agr.kyushu-u.ac.jp/tabr/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Kyushu University Faculty of Agriculture",
"name": "TABR",
"prefix": "NBDC00237",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc00238": {
"description": "This is a database of soybean proteins. The database contains comparative information on the proteomes of several tissues in various environmental conditions. The proteomes of leaf, hypocotyl, and root were determined by 2D-PAGE and can be comparatively analyzed.",
"homepage": "http://proteome.dc.affrc.go.jp/Soybean/",
"information_keywords": [
"Expression",
"Localization"
],
"maintainer": "National Agriculture and Food Research Organization,National Institute of Crop Science",
"name": "Soybean Proteome Database",
"prefix": "NBDC00238",
"pubmeds": [
"19489578",
"22661982"
],
"status": "Inactive"
},
"nbdc00239": {
"alt_name": "The Data Base of Ethno-medicines in the world",
"description": "ETHMEDmmm is a database of collections which stored in The Museum of Materia Medica. It contains both general and scientific information of the samples; traditional Japanese & Chinese crude drug, Unani crude drug, Thai crude drug, Ayurvedic crude drugs and Indonesian (JAMU) crude drugs. Each entry includes common name, English name, function, properties, common uses, etc..",
"homepage": "http://ethmed.toyama-wakan.net/SearchEn/",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "University of Toyama Institute of Natural Medicine",
"name": "ETHMEDmmm",
"prefix": "NBDC00239",
"status": "Active",
"target_keywords": [
"Drug"
]
},
"nbdc00241": {
"alt_name": "Database of protein domains, families and functional sites",
"description": "ExPASy PROSITE is a database of protein domains, protein families and their functional sites.\nThis repository also provides profiles and associated patterns, which can be used to identify the above.\nThis version (20.91) was made available on 4 March 2013.\nIt contains 1,661 documentation entries, 1,053 profiles and 1,308 patterns.\nThe database can be searched by entering a document number, a ProRule description, a taxonomic series or by calling up a page, whereupon the proteins are listed according to the number of positive UniProtKB hits, from most to least.\nThe option is also provided to have a sequence scanned against PROSITE patterns and profiles.\nIn the Advanced search option that is available, additional criteria may be added when a scan request is entered to specify the results more accurately.",
"fairsharing": "biodbcore-000527",
"homepage": "http://prosite.expasy.org/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "PROSITE",
"prefix": "NBDC00241",
"pubmeds": [
"12230035",
"19858104",
"12230035",
"16845026",
"16091411"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00242": {
"description": "geneCards Version 3 is a database of human genes that provides brief but comprehensive genomic related data, on all known human genes.\nThe information consists of data on transcriptomes, proteomes, functions and disease involvement of human genes.\nThis content was obtained from a large number of relevant sources.\nApproved gene symbols and standard nomenclature is used.\nThe site provides information on a total of 122,413 genes, which include 21660 protein-coding genes, 79,344 RNA genes, 16,763 pseudogenes, 767 genetic loci, 146 gene clusters and 3,733 genes that cannot be placed in any of these categories.\nA simple keyword search option and an advanced search option are available.",
"fairsharing": "biodbcore-000593",
"homepage": "http://www.genecards.org/",
"information_keywords": [
"Expression"
],
"maintainer": "Weizmann Institute of Science",
"name": "GeneCards",
"prefix": "NBDC00242",
"pubmeds": [
"9097728",
"9789091",
"12424129",
"20689021"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"RNA",
"Protein",
"Health/Disease"
]
},
"nbdc00243": {
"description": "This site is a comprehensive collection of research results on chromatin modifications (histone modifications, DNA methylation, DNase footprinting) in genomes. Each record contains sample information, assay type, source data, and citations. Additionally, experimental data can be visualized on genomic sequences using the NCBI sequence viewer.",
"homepage": "http://www.ncbi.nlm.nih.gov/epigenomics",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "Epigenomics",
"prefix": "NBDC00243",
"pubmeds": [
"21075792"
],
"status": "Closed",
"target_keywords": [
"DNA",
"Protein",
"Cell/Organelle"
]
},
"nbdc00244": {
"alt_name": "Database of Genomic Structural Variation",
"description": "This database contains information on large-scale variations in genomic structure (insertions, deletions, translocations, and inversions, etc.). Information can be searched by keyword, a research browse list, or the genome browser.",
"fairsharing": "biodbcore-000463",
"homepage": "http://www.ncbi.nlm.nih.gov/dbvar/",
"information_keywords": [
"Sequence",
"Bibliography/Documents",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "dbVar",
"prefix": "NBDC00244",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc00245": {
"description": "This database is a comprehensive resource on proteins and their isoforms contained in human blood plasma and serum. It contains information on isoform-specific expression, associated disease, localization, post-translational modifications, and single nucleotide polymorphisms. All of the information is manually annotated after a thorough review and investigation of the literature. Each protein can be searched and browsed by keywords, molecular function, domains, motifs, PTM, and cellular constituents.",
"homepage": "http://www.plasmaproteomedatabase.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "Johns Hopkins University",
"name": "Plasma Proteome Database",
"prefix": "NBDC00245",
"pubmeds": [
"16041672"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Protein",
"Health/Disease"
]
},
"nbdc00246": {
"description": "This is a database of amphibian species in the World, with stratified biological classification. It contains information on synonyms, English name, habitat (distribution), subclassification, comments, and literature for each classification (class, order, family, subfamily, genus, and species).",
"homepage": "https://amphibiansoftheworld.amnh.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Taxonomy"
],
"maintainer": "American Museum of Natural History",
"name": "Amphibian Species of the World",
"prefix": "NBDC00246",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00247": {
"alt_name": "The Anopheles Database",
"description": "This is a database on mosquitoes that are vectors for malaria such as Anopheles gambiae and Aedes aegypti, as well as their genomes. It contains information related to research on drug resistance, species name, and vectors. The database can be filtered by species name or source region of infestation",
"homepage": "http://anobase.vectorbase.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "NIAID (The National Institute of Allergy and Infectious Diseases)",
"name": "AnoBase",
"prefix": "NBDC00247",
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00248": {
"alt_name": "The World Bird Database",
"description": "This is a database of birds. It contains information on distribution, classification, and synonyms in a variety of languages. The distribution can be viewed as a world map. It also contains records from world-wide investigations of birds.",
"homepage": "http://avibase.bsc-eoc.org/avibase.jsp",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Bird Studies Canada",
"name": "Avibase",
"prefix": "NBDC00248",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00249": {
"alt_name": "Barcode of Life Data Systems",
"description": "BOLD is a portal database for the acquisition, storage, analysis, and publication of DNA barcode records. It's constructed with four databases; \n1) Public Data Portal is a data retrieval interface that allows for searching all 1.3M public records in BOLD using multiple search criteria including geography, taxonomy, and depository. Search results can be summarized, plotted on high-res maps, and downloaded.\n2) BIN database is a searchable database of Barcode Index Numbers (BINs), sequence clusters that closely approximate species.\n3) Publication is a collection of barcode publications and publications that have utilized barcode records.\n4) Primer database is a comprehensive registry of primers used in the generation of barcode sequences.",
"fairsharing": "biodbcore-000231",
"homepage": "http://v4.boldsystems.org",
"information_keywords": [
"Taxonomy"
],
"maintainer": "CBOL (The Consortium for the Barcode of Life)",
"name": "BOLD",
"prefix": "NBDC00249",
"pubmeds": [
"18784790"
],
"status": "Active",
"target_keywords": [
"DNA",
"Organism"
]
},
"nbdc00251": {
"homepage": "http://bio.tokyo.jst.go.jp/biores/index.htm",
"maintainer": "JST (Japan Science and Technology Agency)",
"name": "Bio-Resourse Network",
"prefix": "NBDC00251",
"status": "Closed",
"target_keywords": [
"Organism"
]
},
"nbdc00252": {
"description": "This is a collection of metabolic pathways and their genomes for each species. It contains predictions of metabolic pathways, genome regions of unidentified enzymes, and operons for species, about organisms which sequence analysis is completed. Furthermore, the site has the information on metabolic pathway collected from journal articles, a genome browser, visualization tools, and a search tool.",
"homepage": "http://biocyc.org/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "SRI International",
"name": "BioCyc",
"prefix": "NBDC00252",
"pubmeds": [
"22102576",
"16246909"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"RNA",
"Protein"
]
},
"nbdc00253": {
"description": "This is a database of automatically extracted motifs from multiple amino acid sequence alignments of similar proteins.",
"homepage": "http://blocks.fhcrc.org/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "Fred Hutchinson Cancer Research Center",
"name": "Blocks",
"prefix": "NBDC00253",
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc00254": {
"description": "CAGE Viewer is a database of mouse CAGE sequencing information. The database contains sequences and statistics on data obtained from Cap-Analysis gene expression experiments by the FANTOM consortium. Users can access data by library, tissue, developmental stage, or chromosome. Several search functions are supported.",
"homepage": "https://fantom.gsc.riken.jp/3/cage/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research) Wako Institute",
"name": "CAGE Basic Viewer",
"prefix": "NBDC00254",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00255": {
"alt_name": "A Comprehensive Database on the Genetics of Epilepsy",
"description": "CarpeDB is a portal database of epilepsy genetics. It contains information of epilepsy genes and associated publications. Researchers are able to submit new epilepsy genes and/or candidates, or scientific papers and/or abstracts. This database is available as a novel source for epilepsy researchers by featuring scores of epilepsy genes and associated publications in one locus.",
"fairsharing": "biodbcore-000551",
"homepage": "http://carpedb.ua.edu/",
"information_keywords": [
"Bibliography/Documents",
"Repository"
],
"maintainer": "The University of Alabama",
"name": "CarpeDB",
"prefix": "NBDC00255",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00256": {
"alt_name": "The Cancer Genome Anatomy Project",
"description": "This database is a collection of gene expression profiles of normal, precancer, and cancer cells. It is a project of the National Cancer Institute in the US, with the objective of improving detection, diagnosis, and treatment of cancer. Resources for this project can be obtained through cancer-related communities.",
"homepage": "http://cgap.nci.nih.gov/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "CGAP",
"prefix": "NBDC00256",
"pubmeds": [
"10889913",
"10933042",
"11269648",
"11568889",
"11684445",
"12082587",
"12119410",
"12449737",
"12618197",
"12743998"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"RNA",
"Protein",
"Health/Disease"
]
},
"nbdc00257": {
"description": "Codon Table is a database of mRNA codon interpretations and statistics, such as frequency of use in the genome. The database contains cytoplasmic and mitochondrial genetic code information for several species, including animals, plants, and bacteria.",
"homepage": "http://www.kazusa.or.jp/java/codon_table_java/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Codon Table",
"prefix": "NBDC00257",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc00258": {
"description": "This site contains annotations and tools for protein domain structures. It is comprised of: \n(1) Conserved Domain Database (CDD), which contains information on well-annotated multiple sequence alignment models for ancient domains and full-length proteins,\n(2) CD-Search and Batch CD-Search for search domains in the Conserved Domain Database (CDD) and conserved domains on multiple protein sequences respectively,\n(3) Subfamily Protein Architecture Labeling Engine (SPARCLE), which is a resource of the functional characterization of protein sequences,\n(4) Conserved Domain Architecture Retrieval Tool (CDART) for search protein similarities based on domain architecture,r and\n(5) CDTree for a helper application.",
"fairsharing": "biodbcore-000433",
"homepage": "http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml",
"information_keywords": [
"Image/Movie",
"Classification"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "Conserved Domains and Protein Classification",
"prefix": "NBDC00258",
"pubmeds": [
"21109532",
"15215404",
"17135202",
"12368255"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00259": {
"description": "This is a database of target genes for the transcription factor CREB (cyclic AMP response element-binding protein). The following information is included for each target gene:\n1. CREB binding site on the promoter\n2. Promoter localization due to CREB\n3. gene activation by cAMP in cellular tissues",
"homepage": "http://natural.salk.edu/CREB/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Salk Institute",
"name": "CREB Target Gene Database",
"prefix": "NBDC00259",
"pubmeds": [
"15753290"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00260": {
"alt_name": "Database of Genomic Variants Archive",
"description": "DGVa (Database of Genomic Variants archive) is a repository that offers the storage of, access to and sharing of available genomic structural variants, in all species.\nThis repository receives information from, and supplies data to, a number of resources.\nThe database contains information on variations at the single nucleotide level as well as on variations ranging from tens to thousands of base pairs and more in size. \nData on deletions, insertions, translocations and inversions are supplied.\nThese variations are important in the medical field since they probably play a major role in the development of disease.\nIt is also becoming evident that genomic structural variations have an important effect on an individual's characteristics and is therefore of significant value to study and understand, as is the role it has played in the evolution of species.\nData can be downloaded as DVF files, searched for in the Ensembl Genome Browser or found in the Database of Genomic Variants.",
"fairsharing": "biodbcore-000628",
"homepage": "http://www.ebi.ac.uk/dgva/",
"information_keywords": [
"Phenotype",
"Sequence",
"Bibliography/Documents"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "DGVa",
"prefix": "NBDC00260",
"status": "Active",
"target_keywords": [
"Genetic variation",
"Health/Disease"
]
},
"nbdc00261": {
"alt_name": "Disease Ontology",
"description": "This site provides a Disease Ontology, which is a standardized ontology organized by human disease terms and related medical concepts. The DO terms are associated with MeSH, ICD, NCI's thesaurus, SNOMED and OMIM to integrate disease and medical vocabularies.",
"fairsharing": "FAIRsharing.8b6wfq",
"homepage": "https://disease-ontology.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Institute of Genome Sciences, University of Maryland School of Medicine",
"name": "DO",
"prefix": "NBDC00261",
"pubmeds": [
"30407550"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00262": {
"description": "This is a database provides information on genes, metabolites, reactions, operons and metabolic pathway of Escherichia coli. The data were curated based on literature. It is a member of the BioCyc database collections.",
"fairsharing": "biodbcore-000521",
"homepage": "http://ecocyc.org/",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "SRI International",
"name": "EcoCyc",
"prefix": "NBDC00262",
"pubmeds": [
"21097882"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein",
"Metabolite"
]
},
"nbdc00263": {
"alt_name": "Eukaryotic Gene Orthologues",
"homepage": "http://compbio.dfci.harvard.edu/tgi/ego/",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "Dana-Farber Cancer Institute",
"name": "EGO",
"prefix": "NBDC00263",
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00264": {
"alt_name": "Enzyme nomenclature database",
"description": "ExPASy ENZYME is a database of the classified naming system of enzymes and information related to their names.\nThis database contains 5,096 active entries and was last updated on 6 March 2013.\nThe repository can be searched by entering an EC number, enzyme class, description (official or alternative name), chemical compound or cofactor or by entering one or more words found in the comments attached to the entries.",
"homepage": "http://enzyme.expasy.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Classification"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "ENZYME",
"prefix": "NBDC00264",
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc00265": {
"alt_name": "Endogenous Regulatory OligoPeptide knowledgebase",
"description": "EROP(Endogenous Regulatory OligoPeptide)-Moscow is a database that provides information on a collection of oligopeptide sequences. \nThese sequences contain any number of amino acid residues, from 2 to 50.\nAnnotations of a high level of accuracy, such as an oligopeptide's source, function, structure and post-translational modifications are provided.\nThis database contains information on 10,229 sequences. \nInformation can be retrieved by entering the EROP-accession ID, the name of the oligopeptide, its function, the family name and/or the biological classification (oligopeptide source). \nThe database may also be searched by entering physicochemical features, for instance, the amino acid number, its sequence or molecular mass.\nThis version was released on 21 August 2010.",
"homepage": "http://erop.inbi.ras.ru/",
"information_keywords": [
"Sequence"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "EROP-Moscow",
"prefix": "NBDC00265",
"pubmeds": [
"16381860"
],
"status": "Active",
"target_keywords": [
"Protein",
"Carbohydrate"
]
},
"nbdc00267": {
"alt_name": "Four-dimensional Ascidian Body Atlas",
"description": "FABA is a database of the developmental stages of Ciona intestinalis, with 3D images taken at critical time points, as well as movies of the development process, for standardization of C. intestinalis studies. Images were acquired at zygote, cleavage, gastrula, neurula, tailbud, and larva stages. Downloads are available, as is a companion site (FABA2) with images of organisms post-hatching.",
"homepage": "https://www.bpni.bio.keio.ac.jp/chordate/faba/1.4/top.html",
"information_keywords": [
"Image/Movie",
"3D structure"
],
"maintainer": "Keio University",
"name": "FABA",
"prefix": "NBDC00267",
"pubmeds": [
"17557317"
],
"status": "Active",
"target_keywords": [
"Protein",
"Organism"
]
},
"nbdc00269": {
"alt_name": "The Frequency of Inherited Disorders Database",
"description": "FIDD (Frequency of Inherited Disorders Database) belongs to the Institute of Medical genetics at the Cardiff University School of Medicine.\nThis database provides information about the frequency of human Mendelian disorders and how widespread these diseases occur.\nThe site was created for the purpose of use in medical research and the study of epidemiological occurrences in order to establish genetic service delivery.\nFIDD contains a total of 1580 records of human genetic disorders listed in 14 groups related to the organ, body system or biological function affected.\nThere are 280 disorders that are covered, and of them 109 are autosomal dominant, 136 are autosomal recessive and 35 are X-linked.\nThere are 969 articles, which have been published in 215 journals, a variety of 119 books, 9 doctoral theses and 22 reports that were scrutinized to obtain the information available in this repository.\nThe results reveal 24 cardiac disorders, 34 endocrine disorders and 44 disorders of the eye. It also contains information on 31 disorders of the gastrointestinal system, 353 hematological anomalies and 22 disorders causing mental handicaps. A total of 234 disorders of the metabolic system and 588 affecting the neurological and neuromuscular systems are described, and 3 psychiatric disorders, 35 of the renal system and 25 respiratory disorders are also covered. The information content also include 72 disorders of the skeletal and craniofacial group, 46 skin anomalies and 69 disorders that could not be allocated to a specific body system.\nA keyword search option is available whereby information can be retrieved by entering the body system, disease, population or OMIM number in question.",
"homepage": "https://medicapps.cardiff.ac.uk/fidd/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Cardiff University School of Medicine",
"name": "FIDD",
"prefix": "NBDC00269",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00270": {
"description": "FishBase is a relational database containing information about fish around the world to cater to different professionals such as research scientists, fisheries managers, zoologists and many more. Each entry contains scientific names, common names , pictures, links to other tables, links to internet sources, etc. Moreover, various genetic data are available for many species. All items are referenced, with full citation. Scientific names are verified against Eschmeyer's Catalog of Fishes. Users enter FishBase through common names which classified by country and language. Full academic course with exercises in Ichthyology is available in Fish-On-Line.",
"homepage": "http://www.fishbase.org/search.php?lang=English",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie"
],
"maintainer": "FishBase Consortium",
"name": "FishBase",
"prefix": "NBDC00270",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00271": {
"description": "Flytrap is an HTML-based repository on gene expression.\nThis database provides information on gene expression patterns in the brain of the fruit fly Drosophila.\nThe P-element transposon of Drosophila makes it possible to develop enhancer-trap elements containing minimal promoter regions, which induce transcription.\nThe data is displayed as a list of all the lines studied. This list still needs to be completed and many images have not been annotated or mapped yet.\nThe final list will, after completion, contain 300 lines.\nA basic keyword search option is available.",
"homepage": "http://www.fly-trap.org/",
"information_keywords": [
"Expression",
"Image/Movie"
],
"maintainer": "The University of Edinburgh",
"name": "Flytrap",
"prefix": "NBDC00271",
"status": "Inactive",
"target_keywords": [
"Protein",
"Organism"
]
},
"nbdc00272": {
"alt_name": "The fMRI Data Center",
"homepage": "http://www.fmridc.org/f/fmridc",
"maintainer": "University of California",
"name": "FMRIDC",
"prefix": "NBDC00272",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc00273": {
"alt_name": "Foundational Model Anatomy",
"description": "FMA is a computer-based knowledge source for biomedical informatics. This site is open source and available for general use. It contains a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. Its ontological framework can be applied and extended to all other species.",
"homepage": "http://si.washington.edu/projects/fma",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "University of Washington",
"name": "FMA",
"prefix": "NBDC00273",
"pubmeds": [
"14759820",
"14759821"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00274": {
"alt_name": "Genetic Modification Clinical Research Information System",
"description": "The GeMCRIS is a resource that provides information of human gene transfer research registred with the NIH, which contains medical onditions under study, gene products used study, information of delivery of gene products, and summary of protocols.\nSearches are possible by protocol, researcher, or keywords.",
"homepage": "http://www.gemcris.od.nih.gov/Contents/GC_HOME.asp",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Office of Biotechnology Activities",
"name": "GeMCRIS",
"prefix": "NBDC00274",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00275": {
"description": "Genatlas is a collection of information on gene mapping and the diseases they are genetically related to. \nThe data is obtained by scanning available literature on a regular basis.\nThis database contains information on 22,723 genes, 5,065 phenotypes and 113,755 citations.\nNew information is available immediately after the site is updated and this is done daily.\nSeveral search options are available. \nA search for all genes involved with one disease, called a phenotype search, reveals information pertaining to chromosomal diseases.\nA full search of the gene Database, on the basis of DNA characteristics, RNA characteristics, protein characteristics, expression, and/or pathology gives information about all diseases related to one gene.\nA search of the Citation Database leads to a list of all citations about a particular gene or disease.",
"fairsharing": "biodbcore-000377",
"homepage": "http://genatlas.medecine.univ-paris5.fr/",
"information_keywords": [
"Phenotype",
"Sequence",
"Expression",
"Bibliography/Documents"
],
"maintainer": "Universite Rene Descartes",
"name": "GENATLAS",
"prefix": "NBDC00275",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein",
"Health/Disease"
]
},
"nbdc00276": {
"description": "This is a public database of DNA sequences with annotations. It is a part of the International Nucleotide Sequence Database Collaboration, and cooperates with the DNA DataBank of Japan (DDBJ) as well as the European Molecular Biology Laboratory (EMBL).",
"fairsharing": "biodbcore-000001",
"homepage": "http://www.ncbi.nlm.nih.gov/genbank/",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "GenBank",
"prefix": "NBDC00276",
"pubmeds": [
"22144687",
"21071399"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"DNA",
"RNA"
]
},
"nbdc00277": {
"description": "This site collects information of genes, and has customizability and extensibility features.The data can be searched by gene symbol, gene ID, gene ontology, Affymetrix IDs, Interpro, and genomic intervals. It contains information of tissue-specific expression levels, many kinds of accessions, functional annotations, links to information of transcripts and proteins, and citations.",
"homepage": "http://biogps.org/",
"information_keywords": [
"Expression"
],
"maintainer": "Genomics Institute of the Novartis Research Foundation",
"name": "BioGPS",
"prefix": "NBDC00277",
"pubmeds": [
"19919682"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Health/Disease"
]
},
"nbdc00278": {
"description": "geneLoc Version 3.09 is a database consisting of integrated maps for all human chromosomes.\nEach gene is assigned a geneCards ID indicating its location in the human genome.\nThe database takes into account every exon and classifies DNA segments, among other criteria, according to sequence tagged sites and expressed sequence tag clusters.\nLinks to relevant databases are provided.\nThis repository contains a total of 543,907 entries of which 115,002 are gene symbols, 23,768 are EST clusters and 405,137 are markers.\nA keyword search option is available.",
"homepage": "http://genecards.weizmann.ac.il/geneloc/index.shtml",
"maintainer": "Weizmann Institute of Science",
"name": "GeneLoc",
"prefix": "NBDC00278",
"pubmeds": [
"12855462"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00279": {
"description": "GenomeNet is a Japanese network of database resources and bioinformatics tools constructed by Kyoto University Bioinformatics Center. GenomeNet provides following resources and services.\n1. Integrated database retrieval system (DBGET)\n2. Databases for genome research and biomedical science (KEGG, varDB, community databases of collaborators, etc)\n3. Bioinformatics tools for sequence, genome and chemical analysis (BLAST / FASTA, OC Viewer, SIMCOMP / SUBCOMP, etc)",
"homepage": "http://www.genome.jp/en/",
"information_keywords": [
"Portal"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "GenomeNet",
"prefix": "NBDC00279",
"status": "Active"
},
"nbdc00280": {
"alt_name": "Global Invasive Species Database",
"description": "The GISD is a database of information about species that negatively impact biodiversity. It contains information of invasive alien species which covers all taxonomic groups from micro-organisms to animals and plants in all ecosystems and is supplied by or reviewed by expert contributors from around the world. Each entry contains taxonomic name, organism type, habitat description, general impacts, introduction pathways to new locations, etc.. Users are able to search with species name, location, habitat type, organism type or taxonomic name.",
"homepage": "http://www.iucngisd.org/gisd/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "The Invasive Species Specialist Group",
"name": "GISD",
"prefix": "NBDC00280",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00281": {
"description": "GOALL is a tool for visualization of interrelated data. The viewer graphically plots data, which can then be searched within the browser window to obtain further information. Several datasets are already plotted in the tool and can be searched and examined in detail.",
"homepage": "http://www.shigen.nig.ac.jp/ontology/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "National Institute of Genetics",
"name": "GOALL",
"prefix": "NBDC00281",
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00282": {
"homepage": "http://omicspace.riken.jp/",
"information_keywords": [
"Expression"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "RIKEN Hub Database Project",
"prefix": "NBDC00282",
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc00283": {
"description": "Chem-BLAST provides information of similar chemicals in terms of structure, using data of PDB and PubCHEM. A taxonomy of structural fragments is used for annotating, querying and analyzing chemical compounds.",
"homepage": "http://xpdb.nist.gov/hivsdb/hivsdb.html",
"information_keywords": [
"3D structure",
"Chemical structure"
],
"maintainer": "National Institute of Standards and Technology",
"name": "HIV Structural Database and Chem-BLAST",
"prefix": "NBDC00283",
"pubmeds": [
"15861385",
"16508960"
],
"status": "Active",
"target_keywords": [
"Protein",
"Chemical compound",
"Drug"
]
},
"nbdc00284": {
"alt_name": "Homologous Vertebrate Genes Database",
"description": "HOVERGEN is a database of homologous vertebrate genes using the ACNUC sequence database. It contains all of vertebrate protein sequences from the UniProt Knowledgebase and all the corresponding nucleotide sequences in EMBL, and those information were structured in the ACNUC database.",
"fairsharing": "biodbcore-000501",
"homepage": "http://pbil.univ-lyon1.fr/databases/hovergen.php",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "Pole Bioinformatique Lyonnais",
"name": "HOVERGEN",
"prefix": "NBDC00284",
"pubmeds": [
"8036164",
"15713731"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00285": {
"alt_name": "Homologous Processed Pseudogenes database",
"description": "Hoppsigen is a nucleic database.\nIt provides information on homologous retroelements (like SINE and LINE).\nThere are 5,823 human retroelements and 3,934 mouse retroelements that have been identified and are contained in the repository.\nThe non-functional sequences were given the name pseudogenes.\nThe database, however, also contains functional genes obtained from ENSEMBL.\nA multiple alignment was calculated between the functional genes and their homologous retroelements. This was done for each family.\nA phylogenetic tree was also determined for each alignment and is available in the database.\nA www-query search option is provided.",
"homepage": "http://pbil.univ-lyon1.fr/databases/hoppsigen.html",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "Pole Bioinformatique Lyonnais",
"name": "Hoppsigen",
"prefix": "NBDC00285",
"pubmeds": [
"15608268"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00286": {
"alt_name": "A Database of the World's Lepidopteran Hostplants",
"description": "HOSTS is a database that provides information on the host plants for Lepidoptera, an order of insects that comprises the butterflies and moths of the world.\nThis repository contains data obtained from 180,000 records about 22,000 Lepidoptera species.\nAlthough there is still much to be discovered out there, this may be considered the most extensive collection of data on this topic available at present.\nText Search and Drill-down Search options are provided. In the Drill-down search mode, the Lepidoptera or the plant family name is entered. The family group, genus and species are then selected, the one after the other, as the drop-down boxes appear.",
"homepage": "http://www.nhm.ac.uk/research-curation/research/projects/hostplants/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Natural History Museum",
"name": "HOSTS",
"prefix": "NBDC00286",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00287": {
"alt_name": "Homo Sapiens Splice Sites Dataset",
"description": "HS3D (Homo Sapiens Splice Sites Dataset) version 1.2 is a database that contains information on human exon, intron and splice regions.\nData on 4,523 exons and 3,802 introns is provided.\nThe format of the data is explained.\nThe database may be downloaded entirely in a series of 12 files provided for this purpose.",
"homepage": "http://www.sci.unisannio.it/docenti/rampone/",
"information_keywords": [
"Sequence"
],
"maintainer": "Universita degli Studi del Sannio di Benevento",
"name": "HS3D",
"prefix": "NBDC00287",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00288": {
"homepage": "http://projects.tcag.ca/humandup/",
"information_keywords": [
"Sequence"
],
"maintainer": "The Centre for Applied Genomics",
"name": "Human Genome Segmental Duplication Database",
"prefix": "NBDC00288",
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00289": {
"description": "IARC TP53 Database is a database about mutations, genetic diseases and anotations on human p53. It contains information such as gene variations, somatic mutations, germline mutations, status in cell lines, mouse models, exon/intron distributions, codons, and mutation type. Datasets such as the functional activity of somatic and missense mutations within cancer tissue are also available. The data are collected from peer-reviewed literature and mutation data repositories.",
"homepage": "http://p53.iarc.fr/",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "International Agency for Research on Cancer",
"name": "IARC TP53 Database",
"prefix": "NBDC00289",
"pubmeds": [
"17311302",
"12007217",
"10084119",
"10447253",
"9399837",
"9016527",
"8594564",
"7937055"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Protein",
"Organism",
"Health/Disease",
"Cell/Organelle"
]
},
"nbdc00290": {
"alt_name": "IMGT, the international ImMunoGeneTics information system/LIGM-DB",
"description": "This is a sequence database with annotations on immunoglobulins and T-cell receptors of humans and other vertebrates. Each record includes sequences, details of identification and classification of the sequence, source citation, and level of annotation (manual or not). Searches can be performed by species, gene type or gene function.",
"homepage": "https://www.imgt.org/ligmdb/",
"information_keywords": [
"Sequence"
],
"maintainer": "CNRS (The National Centre for Scientific Research)||Montpellier University, Montpellier",
"name": "IMGT/LIGM-DB",
"prefix": "NBDC00290",
"pubmeds": [
"16381979",
"18978023"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00291": {
"alt_name": "INtegrated Rice Genome Explorer : INE",
"homepage": "http://ine.dna.affrc.go.jp/giot/",
"information_keywords": [
"Sequence"
],
"maintainer": "National Institute of Agrobiological Sciences",
"name": "INE",
"prefix": "NBDC00291",
"pubmeds": [
"10592192"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc00296": {
"alt_name": "subcellular localization database",
"description": "LOCATE is a database containing information on how and where in the cell and its membrane proteins are located and on the organization of the cell membrane. \nThis information can reveal the functional role a specific protein fulfills in a cell.\nThe content of this database was collected by computational methods, immunofluorescence-based assays and by manually screening more than 1,700 publications.\nThe proteins studied were obtained from the RIKEN FANTOM4 mouse and human protein sequence set.\nThis database contains information on 58,128 mouse proteins and 64,637 human proteins.\nA keyword search is available whereby data can be retrieved by entering a protein's ID, description, domain ID, domain name or location.\nAn Advanced search option is also provided where a combination of search criteria may be entered.",
"fairsharing": "biodbcore-000212",
"homepage": "http://locate.imb.uq.edu.au/",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Queensland",
"name": "LOCATE",
"prefix": "NBDC00296",
"pubmeds": [
"17986452",
"16381849"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc00297": {
"alt_name": "Micro Array Expression DAta search",
"description": "MAEDA is a database of Arabidopsis gene expression profiles that can be searched by gene ID. Expression in normal and stress conditions was measured by cDNA microarrays.",
"homepage": "http://rarge.psc.riken.jp/microarray/microarray.pl",
"information_keywords": [
"Expression"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "MAEDA",
"prefix": "NBDC00297",
"pubmeds": [
"12164808",
"12444421"
],
"status": "Closed",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00298": {
"alt_name": "High Resolution Mass Spectral Database",
"description": "MassBank is a high-resolution mass spectral database that involves the JST-BIRD project, and was developed by the Institute for Advanced Biosciences, Keio University (IAB) Analytical Chemistry Group, and the RIKEN Plant Science Center (PSC) Metabolomics Research Group. MassBank is used to search chemical compounds that have been detected by mass spectrometry for chemical identification, structure detail, similar spectrum search, etc. MassBank was recognized as the official mass spectral database of the Mass Spectrometry Society of Japan in 2008. It also contains the results of the NEDO project.",
"homepage": "http://www.massbank.jp/Index",
"information_keywords": [
"Method",
"Chemical structure"
],
"maintainer": "The Mass Spectrometry Society of Japan",
"name": "MassBank",
"prefix": "NBDC00298",
"pubmeds": [
"20623627"
],
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc00299": {
"alt_name": "Minimotif Miner (Application to search for short sequence motifs in proteins)",
"description": "MnM is a database for short sequence motifs in protein. It provides information of short contiguous peptide motifs that have a known function in at least one other protein (Minimotifs). Minimotif functions include posttranslational modification of the minimotifs, binding to a target protein or molecule, and protein trafficking. Users can search motifs by protein names, sequences and various IDs.",
"fairsharing": "biodbcore-000064",
"homepage": "http://cse-mnm.engr.uconn.edu:8080/MNM/SMSSearchServlet",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "University of Connecticut||University of Nevada",
"name": "MnM",
"prefix": "NBDC00299",
"pubmeds": [
"22146221",
"18978024",
"16489333"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00300": {
"description": "Mouse genetic Resources is a database of available mouse strains established in the Mammalian genetics Laboratory, National Institute of genetics (NIG). This database stocks information on resources of laboratory strains, congenic strains, recombinant strains, mutant stocks, wild mouse-derived strains and consomic strains. Each entry contains strain information (a strain name, gene, etc), history of a strain, stock condition and a type of a resource (frozen or live). Some entries include images of adult mice. Users can search available strains by keywords from those items.",
"homepage": "http://www.shigen.nig.ac.jp/mouse/nig/locale/change/?lang=en",
"information_keywords": [
"Bioresource"
],
"maintainer": "Mammalian Genetics Laboratory, National Institute of Genetics",
"name": "Mouse Genetic Resources",
"prefix": "NBDC00300",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00302": {
"homepage": "http://www.myccancergene.org/",
"maintainer": "Johns Hopkins University",
"name": "Myc Cancer Gene",
"prefix": "NBDC00302",
"pubmeds": [
"14519204"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00303": {
"description": "NONCODE is a comprehensive database of noncoding RNAs, excluding tRNAs and rRNAs, from an extensive number of biological organisms, from eukaryotes to viroids.\nThis repository contains 411,554 sequences from 1,239 organisms of which 73,372 are lncRNAs.\nAnnotated information on the expression profiles of 27,408 lncRNAs and the potential functions of 1,635 lncRNAs is included.\nWhen the database was created, the references were all manually consulted to confirm the sequences.\nA new classification system is introduced, based on the cellular process in which the sequence takes part.\nA keyword search option and Blast search option is available.",
"fairsharing": "biodbcore-000076",
"homepage": "http://www.noncode.org",
"information_keywords": [
"Sequence",
"3D structure",
"Expression"
],
"maintainer": "Bioinformatics Research Group, Institute of Computing Technology, Chinese Academy of Sciences.",
"name": "NONCODE",
"prefix": "NBDC00303",
"pubmeds": [
"22135294",
"18000000",
"15608158"
],
"status": "Active",
"target_keywords": [
"RNA",
"Health/Disease"
]
},
"nbdc00304": {
"alt_name": "The Ocean Biogeographic information System",
"description": "OBIS is a integrated database of marine biogeographic data from all over the world. It contains information on where and when marine species have been recorded. Users are able to search the datasets by species name, higher taxonomic level, geographic area, depth and time; and then map and find environmental data related to the locations. Furthermore, users can choose data type and data format to download data.",
"fairsharing": "biodbcore-000768",
"homepage": "http://www.iobis.org",
"information_keywords": [
"Repository"
],
"maintainer": "Census of Marine Life",
"name": "OBIS",
"prefix": "NBDC00304",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00305": {
"alt_name": "Open Biomedical Ontologies",
"description": "The OBO Foundry provides a catalog of ontologies used in medicine or life sciences. Users can find details of each ontology in the list. Each ontology and the list are downloadable as owl file, and as YAML, JSON-LD and RDF/Turtle, respectively.",
"homepage": "http://www.obofoundry.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "BBOP οΌBerkeley Bioinformatics Open-source ProjectοΌ",
"name": "OBO",
"prefix": "NBDC00305",
"pubmeds": [
"16564748",
"17321117",
"16549013",
"16964349",
"16442850",
"16964349",
"16435295",
"16360342"
],
"status": "Active"
},
"nbdc00306": {
"alt_name": "Ovarian Kaleidoscope Database",
"description": "Okdb is a database of genes related to the biological function, expression patterns, and regulation of genes expressed in the ovaries. Information such as gene function, expression pattern, mutations, and phenotype can be found for humans, mouse, rat, bovine, ovine, porcine, D. melanogaster, and C. elegans. Searches can be performed by species, expression site, or function, etc.",
"homepage": "http://okdb.appliedbioinfo.net",
"information_keywords": [
"Expression",
"Repository"
],
"maintainer": "Stanford University",
"name": "Okdb",
"prefix": "NBDC00306",
"pubmeds": [
"22441797",
"12021167",
"10965872"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00307": {
"description": "OWL Version 31.1 is a database comprised of the results of a comparative study of 4 sources of sequence information.\nThese sources are SWISS-PROT, PIR, GenBank and NRL-3D.\nRedundancies of sequences have been avoided at all cost, even by eliminating sequences that display trivial differences from other sequences that are already present.\nOWL is therefore a comparatively small repository, simplifying the process of similarity checks.\nThis version of the repository contains 279,796 entries and 89,624,288 residues.\nThe database can be searched by means of entering an accession number, a database code, a sequence or by making use of the provided keyword search option.",
"homepage": "http://www.bioinf.manchester.ac.uk/dbbrowser/OWL/index.php",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Manchester Bioinformatics Education and Research",
"name": "OWL",
"prefix": "NBDC00307",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00308": {
"description": "PDBsum is a database that contains the annotated 3-dimensional structures of all the proteins in the Protein Data Bank (PDB).\nThe diagrams indicate the protein chains, ligands, DNA and the metal ions present in the protein structures and also how these molecules interact with each other.\nThis database contains 92,037 ProteinDataBase entries.\nPDB code, text and sequence search options are available.\nData files can also be downloaded from the site.",
"fairsharing": "biodbcore-000323",
"homepage": "http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/",
"information_keywords": [
"Image/Movie",
"3D structure"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "PDBsum",
"prefix": "NBDC00308",
"pubmeds": [
"18996896",
"15608193",
"11125097",
"9433130",
"17384425"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00309": {
"alt_name": "Functional Genomics of Plant Transporters",
"description": "This database contains information on plant transporters. It provides information about proteins (name, synonyms, keywords, description, sequence, length, mass, features, etc.), RNA and DNA sequences, citations.",
"homepage": "http://plantst.genomics.purdue.edu/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "Purdue University",
"name": "PlantsT",
"prefix": "NBDC00309",
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00312": {
"alt_name": "PRoteomics IDEntifications database",
"description": "This is a public repository for proteomics data, containing identification data on mass spectrometric peptides and proteins, and post-translational modifications, in which data are supported by spectral evidence. PRIDE is a core member of the ProteomeXchange (PX) consortium.",
"fairsharing": "biodbcore-000325",
"homepage": "http://www.ebi.ac.uk/pride/",
"information_keywords": [
"Repository"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "PRIDE",
"prefix": "NBDC00312",
"pubmeds": [
"19906717"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00313": {
"alt_name": "Protein Kinase Resource",
"description": "This system integrates information on protein kinases (sequences, conformations, annotations) and allows users to browse and analyze the data through a web interface. Searches can be performed by structure, BLAST motif, or citation. Kinome trees can also be viewed here.",
"homepage": "http://www0.nih.go.jp/mirror/Kinases/pk_home.html",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "San Diego Supercomputer Center",
"name": "PKR",
"prefix": "NBDC00313",
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00314": {
"alt_name": "RIKEN Arabidopsis Full-length cDNA",
"description": "This is a database of Arabidopsis cDNA sequence information that can be searched by gene description, locus, or cDNA clone and contains available mutant information for each gene, in addition to sequence information.",
"homepage": "http://rarge-v2.psc.riken.jp/cdna",
"information_keywords": [
"Sequence"
],
"maintainer": "RIKEN CSRS (RIKEN Center for Sustainable Resource Science)",
"name": "RAFL cDNAs",
"prefix": "NBDC00314",
"pubmeds": [
"11910074"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00315": {
"alt_name": "Rice Expression Database",
"description": "The Rice Expression Database (RED) is a database that aggregates the gene expression data that has been analyzed using 8987EST array in the Microarray Project that was underway as part of the Rice Genome Project. RED holds raw and normalized data from expression profiles obtained by the Rice Microarray Project and other research groups.\nThe original site (http: //red.dna.affrc.go.jp/cgi-bin/sogo.cgi?sid=&pj=0&lang=ja&class=852) has been closed. The Rice Expression Database is available from LSDB archive site.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/red/desc.html",
"information_keywords": [
"Expression"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "RED (Archive)",
"prefix": "NBDC00315",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00316": {
"alt_name": "The World Biodiversity Information Network (REMIB)",
"description": "REMIB (The World Biodiversity Information Network) is a database that contains and shares information on biological diversity from more of 200 countries, with 5,763,632 records. To browse the database, a set of regulations need to be read and agreed to, then a key search option is made available.",
"homepage": "http://www.conabio.gob.mx/remib_ingles/doctos/remib_ing.html",
"information_keywords": [
"Taxonomy",
"Portal"
],
"maintainer": "Mexican National Commission on Biodiversity",
"name": "REMIB",
"prefix": "NBDC00316",
"status": "Active"
},
"nbdc00317": {
"description": "This is a database for repetitive DNA. It is comprised of databases of model sequences for the repetitive DNA (Repbase Update, RU) and electronic journals (Repbase Reports, RR). RU is a collection of sequences for repetitive DNA obtained from different eukaryotes, and users can search by the type of repetitive DNA, internal elements, and species. RR contains literature used to present the sequences collected in RU. (Paid subscription required)",
"homepage": "http://www.girinst.org/repbase/",
"information_keywords": [
"Sequence",
"Bibliography/Documents",
"Repository"
],
"maintainer": "Genetic Information Research Institute",
"name": "Repbase",
"prefix": "NBDC00317",
"pubmeds": [
"16093699",
"10973072",
"9666329"
],
"status": "Active",
"target_keywords": [
"DNA"
]
},
"nbdc00318": {
"alt_name": "The Rice Genome Research Program",
"description": "This is a web site of Rice Genome Research Program in Japan. It contains high-density molecular genetic maps, yeast artificial chromosome (YAC) sequence maps, 65000 EST base sequence information, and gene expression maps annotated onto YAC sequence maps.",
"homepage": "http://rgp.dna.affrc.go.jp/E/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "RGP",
"prefix": "NBDC00318",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc00319": {
"description": "RIKEN BioResource Center Experimental Animal Division is a repository of information on mouse resources maintained by RIKEN BioResource Center (RIKEN BRC). This repository contains genetically-engineered strains, ENU mutants, inbred and wild-derived strains developed mainly in Japan. This repository provides a database of mouse phenotypes; Pheno-Pub, and protocols used in mouse experiments such as genotyping PCR, FACS analysis, etc. Users can search available resources from Pheno-Pub, as well as by keywords.",
"homepage": "http://www.brc.riken.jp/lab/animal/en/",
"information_keywords": [
"Bioresource",
"Portal"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "RIKEN BioResource Center Experimental Animal Division",
"prefix": "NBDC00319",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00320": {
"description": "This site is about The Council for SAM Research. It supplies senescence-accelerated mouse (SAM) for members of this council. The information of SAM microsatellite marker is also supplied in this site.",
"homepage": "http://www.samrc.jp/firste.html",
"information_keywords": [
"Bioresource",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "The Council for SAM Research",
"name": "The Council for SAM Research",
"prefix": "NBDC00320",
"status": "Active",
"target_keywords": [
"Genetic variation",
"Organism"
]
},
"nbdc00321": {
"alt_name": "Surveillance Epidemiology and End Results",
"description": "This site collects data of cancers, such as morbidity and survival rate, for over 30 types of cancer in the US since 1973. It includes statistics data and tools to visualize those statistic data, and research data of incidence and population related to age, sex, race, year of diagnosis, and geographic areas. A signature on Research Data Agreement is necessary for use research data.",
"homepage": "http://seer.cancer.gov/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NCI (National Cancer Institute, National Institutes of Health)",
"name": "SEER",
"prefix": "NBDC00321",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00322": {
"alt_name": "SHared Information of GENetic resources",
"description": "SHIGEN is a portal site of bioresource information in Japan maintained by National Institute of genetics (NIG). SHIGEN provides the list of databases constructed at NIG, information sites for bioresources (NBRP; National BioResource Project, WGR; Worldwide genetic Resources and JGR; Japan genetic Resources), monthly newsletters (BioResource now!) and bioinformatics tools. Users can search resource information by keywords through those 3 information sites.",
"homepage": "http://www.shigen.nig.ac.jp/index.htm",
"information_keywords": [
"Bioresource",
"Portal"
],
"maintainer": "National Institute of Genetics",
"name": "SHIGEN",
"prefix": "NBDC00322",
"status": "Active"
},
"nbdc00323": {
"description": "SnoRNABase is an extensive database of human small nucleolar RNAs (snoRNAs) constructed with the invaluable assistance of Laboratoire de Biologie Mol?culaire Eucaryote (LBME) and Jean-Pierre Bachellerie in particular. \nThis repository provides the sequences of both snoRNA classes, namely C/D box snoRNAs and H/ACA box snoRNAs.\nIn version 2 of the database each class contains information on a set of four proteins.\nIn the updated version 3 of the database different sequences are used and the nucleotides are numbered differently.\nKeyword search and Blast search options are available.",
"homepage": "http://www-snorna.biotoul.fr/",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "Laboratoire de Biologie Moleculaire des Eucaryotes",
"name": "snoRNABase",
"prefix": "NBDC00323",
"pubmeds": [
"16381836"
],
"status": "Active",
"target_keywords": [
"RNA"
]
},
"nbdc00324": {
"description": "This is a database of protocols, including experimental procedures and important points, used primarily in the life sciences and medical sciences. Protocols can be searched by text or field of research. Video-based protocols can also be found.",
"homepage": "https://experiments.springernature.com",
"information_keywords": [
"Method",
"Bibliography/Documents"
],
"maintainer": "Springer Nature",
"name": "Springer Nature Experiments",
"prefix": "NBDC00324",
"status": "Active"
},
"nbdc00325": {
"alt_name": "Sequence Retrieval System",
"description": "SRS is a vast collection of linked genomic databases covering a wide variety of biological topics. \nThese databanks can be searched individually or in combination to obtain specific information needed. A number of analysis tools are available e.g. alignment, display, edit, nucleic, protein and phylogeny tools, allowing the researcher access to a vast amount of genomic information.\nText and List search options are provided wherein the data sought can be requested as a single ID or as a list of sequence IDs.",
"homepage": "http://srs.ebi.ac.uk/",
"information_keywords": [
"Portal"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "SRS",
"prefix": "NBDC00325",
"pubmeds": [
"12176845",
"11847095",
"15215339",
"8435768",
"8743681"
],
"status": "Closed"
},
"nbdc00326": {
"alt_name": "Stanford Microarray database",
"fairsharing": "biodbcore-000524",
"homepage": "http://smd.stanford.edu/",
"information_keywords": [
"Expression"
],
"maintainer": "Stanford University",
"name": "SMD",
"prefix": "NBDC00326",
"pubmeds": [
"18953035",
"17182626",
"15608265",
"12519956",
"11125075"
],
"status": "Closed",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00327": {
"description": "This database contains molecular sequence information on papillomaviruses and related cellular proteins. Maintenance on the original database has stopped and the data can be viewed as an archive.",
"homepage": "http://pave.niaid.nih.gov/lanl-archives/",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "LANL (Los Alamos National Laboratory)",
"name": "HPV Sequence Database",
"prefix": "NBDC00327",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein"
]
},
"nbdc00328": {
"alt_name": "Orthoptera Species File Online",
"description": "The Orthoptera Species File is a database that provides information on the classification of living and fossilized Orthoptera (grass-hoppers etc.)\nThis database contains 43,070 scientific names, 25,920 valid species, 196,300 quotations from 15,000 references, 480 sound recordings, 76,700 images and 88,500 specimen records.\nA simple name search and an advanced search option are available.",
"homepage": "http://orthoptera.speciesfile.org/HomePage.aspx",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Illinois Natural History Survey||Museum of Comparative Zoology",
"name": "OSF online",
"prefix": "NBDC00328",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00329": {
"description": "The Chromosome 7 Annotation Project is a database that contains descriptive information of human chromosome 7. It is fully sequenced and annotated with medically relevant data. Chromosome 7 houses genes related to more than 360 diseases and disorders e.g. cystic fibrosis, Russell-Silver syndrome and Williams-Beuren syndrome. It is also believed that chromosome 7 carries loci for a number of neuropsychiatric diseases e.g. autism, alcoholism, bipolar affective disorder, panic disorder and schizophrenia. Although it has not yet been identified, cytogenetic evidence suggests that chromosome 7 carries a gene that causes cancer. The database provides access to a table of clinical breakpoints in chromosome 7 as well as a comprehensive list of other tables containing genetic information about this chromosome. Keyword and Blast search options are available. Even the families of diseased patients may search the database for information by selecting a link called 'Family Village'.",
"fairsharing": "biodbcore-000263",
"homepage": "http://www.chr7.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "The Centre for Applied Genomics",
"name": "The Chromosome 7 Annotation Project",
"prefix": "NBDC00329",
"pubmeds": [
"12690205"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00330": {
"description": "FUGU GENOME ASSEMBLY is a repository that offers genomic data of the Fugu, a puffer fish that is eaten as a Japanese delicacy.\nThe database contains information on BACs, cosmids, ESTs and contigs arranged in four separate releases. \nThe total size of the Fugu genome, including repeats, is around 365 Mbases.\nA keyword search is available.\nAdditionally, a Blast search option is provided by which a known sequence can be compared to the Fugu Genome sequence.\nDatasets can be downloaded.",
"homepage": "https://fugu.crick.ac.uk/News/FuguWebsite_02_04_03.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Queen Mary, University of London",
"name": "DRAFT SEQUENCE OF FUGU GENOME ASSEMBLY RELEASE 1, 2, 3 and 4",
"prefix": "NBDC00330",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc00331": {
"description": "This is a homepage of The New York Botanical Garden that is engaged in plant research and conservation. It provides data of books and articles about plants in the world, and information of plants with photos and commentaries, etc.",
"homepage": "https://www.nybg.org/plant-research-and-conservation/collections-resources/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "The New York Botanical Garden",
"name": "The New York Botanical Garden",
"prefix": "NBDC00331",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00332": {
"description": "PomBase is a scientific resource for genomic information on the fission yeast Schizosaccharomyces pombe. \nThis database offers extensive information on the structural and functional aspects of the yeast genome.\nThe sequenced size of the genome, not including rRNA is 12.57Mbp.\nThe nucleus of the yeast cell contains 3 chromosomes of which the size ranges from 2.45Mbp to 5.58Mbp\nThere are 5124 protein coding genes that have been counted and they are packed on the DNA molecules at a density of 554.49 genes per Mb. \nA comprehensive number of datasets are available for download.\nSearch options available are a Simple keyword search, an Advanced search, a gene list search, a Blast search and a Genome Browser.",
"fairsharing": "biodbcore-000139",
"homepage": "http://www.pombase.org/",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "Wellcome Sanger Institute",
"name": "PomBase",
"prefix": "NBDC00332",
"pubmeds": [
"22039153"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00333": {
"homepage": "http://www.nbii.gov/termination/index.html",
"maintainer": "National Biological Information Infrastructure",
"name": "United States Regulatory Agencies Unified Biotechnology Website",
"prefix": "NBDC00333",
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc00334": {
"alt_name": "World Biodiversity Database",
"description": "WBD (World Biodiversity Database) contains 21 separate projects.\nThe repository covers a total of 25,493 unique taxonomic groups as well as an additional 4,149 closely related groups.\nInformation can be retrieved with a keyword search by entering the scientific name of a species, its common name, or the name of a project.\nThe database also provides a list of the projects involved and gives a short description of each.",
"homepage": "http://wbd.etibioinformatics.nl/bis/index.php",
"information_keywords": [
"Image/Movie",
"Taxonomy"
],
"maintainer": "ETI BioInformatics",
"name": "WBD",
"prefix": "NBDC00334",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc00338": {
"description": "This is a database of genomic research associated with pigs. It includes DNA markers such as microsatellite markers for pigs, a swine linkage map viewer (ToNMaP), and the Sus scrofa radiation hybrid (SSRH), developed by the Animal Genome Research Program (AGP). Information of full-length cDNA clones and ESTs can also be accessed through this site, as well as those sequences, SNP mapping information, and BLAST results.",
"homepage": "http://animal.dna.affrc.go.jp/agp/database.html",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "Animal Genome Research Program",
"prefix": "NBDC00338",
"pubmeds": [
"8138161",
"10612229",
"11167524",
"12648097",
"12873213",
"12755823",
"17145712",
"14681463",
"10612229",
"11167524",
"10690355",
"10947985",
"12648097",
"12755823",
"12871218",
"12873213",
"15777643",
"16189668",
"16441290",
"16263171",
"16712934",
"17112699"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Genetic variation"
]
},
"nbdc00339": {
"description": "Database of animal specimens from polar regions is a specimen database of animals in Antarctic regions maintained by the National Institute of Polar Research (NIPR). Each entry contains a specimen picture, sample number, photo number, scientific names and inforamation on habitat(s). Users can search specimens by classification based on table data in the site, scientific names, English names and sample numbers.",
"homepage": "http://animal.nipr.ac.jp/index_e.html",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie",
"Taxonomy"
],
"maintainer": "National Institute of Polar Research",
"name": "Database of animal specimens from polar regions",
"prefix": "NBDC00339",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc00340": {
"description": "Plant Heredity Resource Search is a database of plant species belonging to the mandarin orange family, particularly to the mandarin orange subfamily in the Saga University Digital Library. Each entry includes the Japanese names (family, subfamily, genus and species), scientific names, distribution data and others. These items except for scientific names are only available in Japanese. Some entries contain images of flowers, fruits, leaves, etc.",
"homepage": "http://www.dl.saga-u.ac.jp/z3950/plant/search_e.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Saga University",
"name": "Plant Heredity Resource Search",
"prefix": "NBDC00340",
"status": "Closed",
"target_keywords": [
"Organism"
]
},
"nbdc00343": {
"description": "Movie Archives of Animal Behavior is a repository of published movie data on animal behaviors. This repository contains QuickTime (.mov) or mpeg (.mpg, mp4) movies and detailed information including author(s), shot day, name of species, keyword, explanation text, references, etc. Users can search movies by level of hierarchy, as well as keywords.",
"homepage": "http://www.momo-p.com/index-e.html",
"information_keywords": [
"Image/Movie",
"Repository"
],
"maintainer": "Teikyo University of Science & Technology Faculty Life & Environmental Sciences Department of Animal Sciences",
"name": "Movie Archives of Animal Behavior",
"prefix": "NBDC00343",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00344": {
"description": "This is a database of specimen of Lepidoptera in Tomakomai Experimental Forest (Forest Research Station) of Hokkaido University.",
"homepage": "https://bioinfo.museum.hokudai.ac.jp/db/?ml_lang=en",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie"
],
"maintainer": "Hokkaido University The Hokkaido University Museum",
"name": "TOEFbioinfo",
"prefix": "NBDC00344",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00345": {
"description": "Handbook of Antarctic Mosses is a database of the bryophytes around Syowa Station, East Antarctica maintained by National Institute of Polar Research (NIPR). Each entry contains the scientific name, description with sketches, toxonomic and ecological information, distribution data with maps and photographs. Users can search bryophyte species from the taxonomical list, indexes of photographs or habitats.",
"homepage": "http://polaris.nipr.ac.jp/~antmoss/ham/index_e.html",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie"
],
"maintainer": "National Institute of Polar Research",
"name": "Handbook of Antarctic Mosses",
"prefix": "NBDC00345",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc00350": {
"description": "Wood database is a portal database about wood specimens housed in the xylarium of the Forestry and Forest Products Research Institute (TWTw). It's constructed with three databases;\n1) Database of Japanese Woods\nThis database contains surface views of wood specimens, optical microscopic images of preparations, and images of voucher herbarium specimens.\n2) Database of Wood Specimens\nThis database contains specimen no. (TWTw No.), family name, species name, original wood specimen no., collection\ndate, collector(s), herbarium no. of the voucher specimen, herbarium housing the voucher specimen, provenance, country, altitude, latitude, longitude, habit, habitat, various notes, and note on collection or accession.\n3) Microscopic Identification of Japanese Woods \nThis database is an identification system of Japanese woods based on the IAWA List of Hardwood Identification (IAWA Committee 1989).",
"homepage": "http://db.ffpri.affrc.go.jp/WoodDB/index-E.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Forestry and Forest Products Research Institute",
"name": "Wood Database",
"prefix": "NBDC00350",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00351": {
"alt_name": "A three-dimensional-structure database of natural metabolites",
"description": "This database is composed of three-dimensional structures and physical properties of natural metabolites, mainly those useful in agriculture (design of chemicals used in agriculture, compositional analysis of food). Compounds with similar structures and physical properties can be searched through an easy interface.",
"fairsharing": "biodbcore-000465",
"homepage": "http://www.3dmet.dna.affrc.go.jp/",
"information_keywords": [
"3D structure"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "3DMET",
"prefix": "NBDC00351",
"status": "Inactive",
"target_keywords": [
"Metabolite",
"Chemical compound"
]
},
"nbdc00352": {
"description": "5S ribosomal RNA database contains information on nucleotide sequences of 5S rRNAs and their genes.\nDiagrams of the secondary structure of 5S rRNAs are provided, indicating the positions of deletion and insertion of nucleotides as they were observed in the corresponding alignments.\nA taxonomic browser is available as well as a search option for sequence alignments.",
"homepage": "http://combio.pl/rrna/",
"information_keywords": [
"Sequence"
],
"maintainer": "Department of Computational Biology, Adam Mickiewicz University",
"name": "5S Ribosomal RNA Database",
"prefix": "NBDC00352",
"pubmeds": [
"10592212",
"26490961"
],
"status": "Active",
"target_keywords": [
"RNA"
]
},
"nbdc00353": {
"description": "This database contains all available information on variants in the collagen gene, that may lead to the development of the genetic disorder osteogenesis imperfecta. \nThe genes in which these variations were found to appear are COL1A1, COL1A2, BMP1, CRTAP, FKBP10, IFITM5, LEPRE1, PLOD2, PPIB, SERPINF1, SERPINH1, SP7, TMEM38B and WNT1.\nWhen variations take place in the type III collagen gene, COL3A1, Ehlers-Danlos syndrome type IV is usually the outcome.\nClassical Ehlers-Danlos syndrome is most often caused by variations in the type V collagen genes, COL5A1 and COL5A2 .\nCopies of the two papers that describe the database are available for download in Adobe Acrobat format.",
"homepage": "http://www.le.ac.uk/genetics/collagen",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "University of Leicester Department of Genetics",
"name": "ostogenesis imperfecta & Ehlers-Danlos syndrome variant databases",
"prefix": "NBDC00353",
"pubmeds": [
"9016532",
"9399846"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc00354": {
"description": "A List of Biodiversity Websites in Japan is a portal site about catalog databases related to biodiversity in Japan. This database collects only the web site that includes images clearly indicating characteristic of each species or specimen with their photography information (place and date), Japanese name, a scientific name, etc.",
"homepage": "http://protist.i.hosei.ac.jp/gbif/DB_list/indexE.html",
"information_keywords": [
"Bibliography/Documents",
"Portal"
],
"maintainer": "Hosei University",
"name": "A List of Biodiversity Websites in Japan",
"prefix": "NBDC00354",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00355": {
"alt_name": "A CLAssification of Mobile genetic Elements",
"description": "ACLAME Version 4 is a database of the mobile genetic elements (MGEs) as found in the genomes of all phages, plasmids and transposons known at present - 811 hosts in total.\nInformation on 122,154 proteins, discovered to be present in 2,326 MGEs, is provided.\nThe proteins were grouped in families as follows:\nThe prophages contained 6,822 clusters, the plasmids 18,228 groups, the viruses and prophages 16,057 groups and the viruses 11,503 clusters.\nThe database is in the process of developing a classification system of the functional modules of these MGEs at the protein level, gene level, and higher.\nKeyword and Blast search options are available.\nAn option is also offered whereby host-specific groups of MGEs can be viewed.",
"fairsharing": "biodbcore-000549",
"homepage": "http://aclame.ulb.ac.be/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Universite Libre de Bruxelles",
"name": "ACLAME",
"prefix": "NBDC00355",
"pubmeds": [
"19933762",
"18238785",
"18234706",
"17614261",
"17482656",
"17064288",
"14681355"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"DNA",
"Protein"
]
},
"nbdc00356": {
"description": "Addgene is a non-profit organization providing plasmids to researchers. It is a collaboration with several hundred research teams, creating a high quality plasmid library and repository used for publications. By linking the plasmid to its publications, researchers always have access to necessary plasmid and associated data. The site contains links to deposit plasmids, request plasmids, access sequence information on plasmids, as well as links to a vector database and associated protocols. They provide Viral service, CRISPR tools, Fluorescent proteins, Cancer resources as special colections.",
"fairsharing": "biodbcore-000196",
"homepage": "http://www.addgene.org/",
"information_keywords": [
"Bioresource",
"Method",
"Sequence",
"Repository"
],
"maintainer": "Addgene",
"name": "addgene",
"prefix": "NBDC00356",
"status": "Active",
"target_keywords": [
"DNA"
]
},
"nbdc00357": {
"description": "Algae Resource Database is a database of micro and macro algae culture collections established by National Institute for Environmental Studies (NIES) and collaborative institutes. Each entry contains information on the stock center, scientific names, locality, habit, cell size, organization (unicellular, multicellular, colonia, flagellate, filamentous, coccoid or branched), gene, etc, and some entries include images. Users can search available algal resources by keywords from those items. This database also provides phylogenetic trees, an image list and a search engine of references related to algal research.",
"homepage": "http://www.shigen.nig.ac.jp/algae/",
"information_keywords": [
"Bioresource",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "National Institute of Genetics",
"name": "Algae Resource Database",
"prefix": "NBDC00357",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Organism"
]
},
"nbdc00358": {
"alt_name": "A Search Service for Abbreviation / Long Form",
"description": "Allie is a database and an online search service for abbreviations and long forms used in life science. Allie contains an abbreviation list and its corresponding bibliographic data. Users can search for the long forms of abbreviations or the abbreviations of long forms from titles and abstracts of papers in the entire MEDLINE. Search results show abbreviations or long forms, research areas, co-occurring abbreviations and PubMed/MEDLINE information related to the inquired item.",
"homepage": "http://allie.dbcls.jp/en",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "Allie",
"prefix": "NBDC00358",
"pubmeds": [
"21498548"
],
"status": "Active"
},
"nbdc00359": {
"description": "AARS is a database of Aminoacyl-tRNA synthetases in a number of microbial organisms. This repository provides a link 'Amino acid sequences', which opens up a list of amino acids for Class I Aminoacyl-tRNA synthetases and for Class II Aminoacyl-tRNA synthetases. Selecting any one of these amino acids provides entry to a page containing detailed information on the organism as well as the sequence of nucleotide bases of the amino acid. An option to download batches of Fasta files of the sequences is available. The 3D X-ray diffraction structures and the NMR structures of the aminoacyl-tRNA synthetases are also accessible.",
"homepage": "http://rose.man.poznan.pl/aars",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "Poznan Supercomputing and Networking Center",
"name": "Aminoacyl-tRNA synthetases database",
"prefix": "NBDC00359",
"pubmeds": [
"11125115"
],
"status": "Inactive",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc00360": {
"description": "Analysis of CASP8 targets and predictions is a database about the analysis of CASP8 targets and predictions. This database provides 3D models (TS: Tertiary structure prediction) which were evaluated using LGA GDT-TS scores and several other methods. Server models superimposed with target structures are downloadable and can be visualized as PyMOL scripts. Structure images including mostly animated GIFs on target pages are prepared in PyMOL.",
"homepage": "http://prodata.swmed.edu/CASP8/evaluation/CASP8Home.htm",
"information_keywords": [
"3D structure"
],
"maintainer": "University of Texas Southwestern Medical Center",
"name": "Analysis of CASP8 targets and predictions",
"prefix": "NBDC00360",
"pubmeds": [
"20157476"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00361": {
"description": "Androgen Database is a repository that provides information about mutations of the Androgen Receptor gene.\nThese mutations may have an effect on the development and progress of prostate cancer.\nMutations which inactivate androgen receptor genes, thereby creating severe androgen insensitivity, may result in a full or partial external female phenotype.\nThe mutations contained in this database are listed in a simple 5' - 3' sequence.\nThe complete Database of Androgen Receptor gene Mutations is available for download in PDF format, Excel format and as FileMakerPro.",
"homepage": "http://androgendb.mcgill.ca/",
"information_keywords": [
"Sequence"
],
"maintainer": "Lady Davis Institute for Medical Research",
"name": "The Androgen Receptor Gene Mutations Database World Wide Web Server",
"prefix": "NBDC00361",
"pubmeds": [
"10727996",
"15146455",
"15242343",
"15705293",
"9399843",
"22334387"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00362": {
"alt_name": "The Aphid Genome Database",
"description": "Aphidbase 2.1 is a database containing information collected in a study of the genomes of aphids.\nAn aphidbase blast server is available, as well as GBrowse, from which information on the assembly of the genome of A. pisum may be collected.\nThe apollo-aphidbase2.gnlp may also be accessed and downloaded.\nSeveral links lead to associated databases as follows:\nPhylomeDB opens up a database of collections of gene phylogenies (phylomes).\nAcypiCyc leads to a database of the metabolic pathways of A. pisum.\nGO gives access to the Chado Term Hierarchy Report.\nGalaxy leads to a database, which can be accessed only by logging in with a registered e-mail address and password.",
"fairsharing": "biodbcore-000374",
"homepage": "http://bipaa.genouest.org/is/aphidbase/",
"information_keywords": [
"Sequence"
],
"maintainer": "INRAE (National Research Institute for Agriculture, Food and Environment)",
"name": "AphidBase",
"prefix": "NBDC00362",
"pubmeds": [
"20482635",
"17237053"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein"
]
},
"nbdc00363": {
"homepage": "http://gerg03.gsc.riken.jp/DNABook_DB/VIEW/Book_Top.php?BOOK_ID=BOOK_3",
"information_keywords": [
"Bioresource"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "AQUA DNABook",
"prefix": "NBDC00363",
"status": "Closed",
"target_keywords": [
"cDNA/EST",
"DNA",
"Health/Disease"
]
},
"nbdc00364": {
"description": "This is a database of Arabidopsis thaliana expressed sequences. The database contains consensus gene sequences and EST reads and allows for BLAST and keyword search. Data are available for download.",
"homepage": "https://www.kazusa.or.jp/e/plant/arabi/EST/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Arabidopsis thaliana EST Index",
"prefix": "NBDC00364",
"pubmeds": [
"10907847"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00365": {
"description": "This database contains information on the complete sequenced genome of the Arabidopsis thaliana.\nThe Arabidopsis thaliana genome project aims to decode this information and to connect it to an array of biological data in order to discover the functions and interactions of these sequences and genes. \nHeatmaps of the Arabidopsis thaliana chromosomes, graphically indicating the position and density of sequence features, may be viewed.\nLists that are available are a clone list, chromosome list, genetic element list and a list of sequenced contigs.\nArabidopsis thaliana genome sequence data may be downloaded for private use.",
"homepage": "http://pgsb.helmholtz-muenchen.de/plant/athal/",
"information_keywords": [
"Sequence"
],
"maintainer": "Helmholtz Zentrum Munchen",
"name": "Arabidopsis thaliana project",
"prefix": "NBDC00365",
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00366": {
"description": "Ares lab Yeast Intron Database is a database for information about the spliceosomal introns of the yeast Saccharomyces cerevisiae. It contains known spliceosomal introns in the yeast genome and documented the splice sites actually used. Through the use of microarrays designed to monitor splicing, splice site contexts are identified and analyzed in terms of the nature and activities of the trans-acting factors that mediate splice site recognition. This database also includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page for browsing and can be downloaded for other types of analysis.",
"homepage": "http://intron.ucsc.edu/yeast4.3/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "University California Santa Cruz",
"name": "Ares lab Yeast Intron Database",
"prefix": "NBDC00366",
"pubmeds": [
"10734188",
"12073325",
"11988574",
"10496214",
"10024174"
],
"status": "Active",
"target_keywords": [
"RNA"
]
},
"nbdc00367": {
"alt_name": "All-round Retrieval of Sequence and Annotation",
"description": "ARSA is a database with a high-speed retrieval system of sequence and annotation data maintained by DNA Data Bank of Japan (DDBJ). ARSA covers amino acid sequence data derived from patents and various databases including DDBJ, UniProt, PDB, etc. Users can search for sequences and annotations using Boolean operators, and download the search results in Flat File, XML, or fasta format.",
"homepage": "http://ddbj.nig.ac.jp/arsa/",
"information_keywords": [
"Sequence"
],
"maintainer": "Bioinformation and DDBJ Center, National Institute of Genetics, Research Organization of Information and Systems",
"name": "ARSA",
"prefix": "NBDC00367",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation"
]
},
"nbdc00368": {
"alt_name": "Alternative splicing-induced ALteration of Protein Structure",
"description": "AS-ALPS is a database of alternative splicing products. The database contains information on how splice isoforms impact protein structures and protein-protein interactions. When investigating a gene, information on all isoforms can be obtained and domains affected by each isoform are highlighted.",
"homepage": "http://as-alps.nagahama-i-bio.ac.jp/",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "Nagahama Institute of Bio-Science and Technology",
"name": "AS-ALPS",
"prefix": "NBDC00368",
"pubmeds": [
"19015123",
"16872759"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein"
]
},
"nbdc00369": {
"alt_name": "Comprehensive Aspergillus oryzae Genome Database",
"description": "This is a genome sequence database for Aspergillus oryzae, determined using the RIB40 strain from the National Research Institute of Brewing. Users can perform keyword searches of gene annotations in the genome, BLAST searches of genomic sequences, and download data.",
"homepage": "https://nribf21.nrib.go.jp/CAoGD/",
"information_keywords": [
"Sequence"
],
"maintainer": "National Research Institute of Brewing",
"name": "CAoGD",
"prefix": "NBDC00369",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00370": {
"alt_name": "Alternative Splicing Sequence Enriched Tags",
"description": "ASSETs is a resource for alternate splicing information, containing data tables from a study of mouse alternate splicing that developed a library of expressed alternate splicing tags. Data is available for download.",
"homepage": "http://genome.gsc.riken.jp/splicing/",
"information_keywords": [
"Sequence"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "ASSETs",
"prefix": "NBDC00370",
"pubmeds": [
"15782199"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00371": {
"alt_name": "Alternative Splicing and Transcription Archives",
"description": "This is a database of alternative splice variants and their transcripts. The database is named ASTRA, an anagram for 'Alternative Splicing and TRanscription Archives'. Information was gathered by studying the patterns by which alternative splicing of DNA sequences take place and how transcription of these sequences are initiated. This study involved the human genome and that of five additional species namely the mouse, D. melanogaster, C. elegans, A. thaliana and O.sativa.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/astra/desc.html",
"information_keywords": [
"Sequence"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "ASTRA (Archive)",
"prefix": "NBDC00371",
"pubmeds": [
"16500940",
"16219431"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc00372": {
"description": "Atgenexpress is a database of Arabidopsis gene expression. The main tool available at this site is an applet that makes connections between gene expression in various stress and environmental conditions. Users can explore expression by any of several experimental parameters, including tissues, conditions, and genotypes. Data is available for download.",
"homepage": "http://atpbsmd.yokohama-cu.ac.jp/",
"information_keywords": [
"Environment",
"Expression"
],
"maintainer": "KIHARA Institute for Biological Research : Plant Biotechnology Division",
"name": "AtGenExpress",
"prefix": "NBDC00372",
"pubmeds": [
"15086809",
"15806101",
"17376166",
"18419781"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00374": {
"alt_name": "Arabidopsis thaliana trans-factor and cis-element prediction database",
"description": "ATTED-II is a coexpression database for Arabidopsis and other plant species. It stores calculated coexpression data based on microarray data and RNAseq data from AtGenExpress (TAIR), ArrayExpress and DDBJ. Mutual rank (MR) index is used as a coexpression measure, shows a higher predictive power for gene function than the Pearsonβs correlation coefficient (PCC). ATTED-II provides a list of coexpressed genes and their orthologous for a query gene. NetworkDrawer tool provides drawing of gene networks in multiple query genes. The coexpression data are downloadable from Bulk download page.",
"fairsharing": "biodbcore-000211",
"homepage": "http://atted.jp/",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Tohoku University||The University of Tokyo The Institute of Medical Science Human Genome Center",
"name": "ATTED-II",
"prefix": "NBDC00374",
"pubmeds": [
"29216398",
"26546318",
"24334350",
"21217125",
"18953027",
"17130150"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc00375": {
"alt_name": "Beta Cell Biology Consortium",
"description": "The Beta Cell Biology Consortium was to advance understanding associated with the development and function of the islets of Langerhans through functional genomics research data and distribution of resources; however, they have stopped operations as of August 1, 2015. The database contains information about antibodies, genomics study, mouse ECS lines, and mouse strains as screenshots.",
"homepage": "http://www.betacell.org/",
"information_keywords": [
"Bioresource",
"Method"
],
"maintainer": "Beta Cell Biology Consortium",
"name": "BCBC",
"prefix": "NBDC00375",
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc00376": {
"description": "This is a database for gene and genome information of beans. \nMost of the pages are not accessible to view (Feb., 2017).",
"homepage": "http://beangenes.cws.ndsu.nodak.edu",
"information_keywords": [
"Sequence"
],
"maintainer": "North Dakota State University",
"name": "BeanGenes (A Phaseolus/Vigna sp. Database)",
"prefix": "NBDC00376",
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00377": {
"homepage": "http://mcb.harvard.edu/BioLinks.html",
"information_keywords": [
"Portal"
],
"maintainer": "Harvard University Department of Molecular and Cellular Biology",
"name": "Biology Links",
"prefix": "NBDC00377",
"status": "Inactive"
},
"nbdc00378": {
"description": "This is a database of new biomarker candidates based on relationships between biomarker candidates and clinical disorders. The database integrates information related to biomarkers from literature databases, such as MEDLINE, OMIM and PPI. Keyword search is available.",
"homepage": "http://omicspace.riken.jp/Biomarker/",
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "Biomarker Candidates (Inferences of Novel Biomarker Candidate Functions)",
"prefix": "NBDC00378",
"status": "Inactive",
"target_keywords": [
"Health/Disease",
"Drug"
]
},
"nbdc00379": {
"description": "This database is a collection of metabolic and signaling pathways in organisms, as well as interaction sets between biological molecules associated with disease and other biological processes. Each entry contains information including pathway maps, relevant citations, genes, proteins sequences, and data on compounds.",
"fairsharing": "biodbcore-000430",
"homepage": "http://www.ncbi.nlm.nih.gov/biosystems/",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "BioSystems",
"prefix": "NBDC00379",
"pubmeds": [
"19854944"
],
"status": "Closed",
"target_keywords": [
"Protein",
"Health/Disease",
"Metabolite",
"Cell/Organelle"
]
},
"nbdc00380": {
"alt_name": "Biological Magnetic Resonance Data Bank",
"description": "BMRB is a database of biomolecular magnetic resonance data. Proteins, peptides, and nucleic acids, and other molecules are represented in NMR and PDB data form. Several search functions are supported and users can upload or download data.",
"fairsharing": "biodbcore-000584",
"homepage": "http://www.bmrb.wisc.edu/",
"information_keywords": [
"3D structure",
"Repository"
],
"maintainer": "University of Wisconsin System Board of Regents",
"name": "BMRB",
"prefix": "NBDC00380",
"pubmeds": [
"17984079"
],
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Protein"
]
},
"nbdc00381": {
"alt_name": "Bombyx mori genome Map information system",
"description": "This database integrates genetic maps and molecular linkage map information on the silkworm genome. The association between the genetic and physical maps, as well as marker information, can be easily viewed through the graphical interface.",
"homepage": "http://sgp.dna.affrc.go.jp/BombMap/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "BombMap",
"prefix": "NBDC00381",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc00382": {
"description": "This database contains information on silkworm mutant lines generated through the enhancer trap method, including GFP reporter expression sites and images, and genomic insertion sites. In collaboration with the silkworm genome database (KAIKObase), transposon vector insertion sites can be mapped on to a chromosomal map.",
"homepage": "http://sgp.dna.affrc.go.jp/ETDB/",
"information_keywords": [
"Sequence",
"Expression",
"Image/Movie"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "Bombyx Trap DataBase",
"prefix": "NBDC00382",
"pubmeds": [
"19843344"
],
"status": "Active",
"target_keywords": [
"DNA",
"Organism"
]
},
"nbdc00383": {
"description": "This is a collection of books and documents in the biology and biomedical field that can be accessed online for free. References within the text are linked to PubMed.",
"homepage": "http://www.ncbi.nlm.nih.gov/books",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "Bookshelf",
"prefix": "NBDC00383",
"status": "Active"
},
"nbdc00384": {
"description": "Breast Tumor Image Database is an image database of breast tumors constructed by National Kyusyu Cancer Center. This database contains mammograms, ultrasound images, MRI data sets, cytology and histological images. Each entry includes a disorder name, basic and detailed data such as location and size of the tumor, as well as images with inspection data. Users can search medical cases or images by keywords, histological classification, kinds of cases, age and inspection methods.",
"homepage": "http://breast-tumor.midb.jp/lib/chlang.php?lang=en",
"information_keywords": [
"Image/Movie"
],
"maintainer": "National Hospital Organization Kyushu Cancer Center",
"name": "Breast Tumor Image Database",
"prefix": "NBDC00384",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00385": {
"description": "The Broad Institute is a research institute established in 2004 between the Whitehead Institute at Massachusetts Institute of Technology (MIT) and the Harvard Institute of Chemistry and Cell Biology (ICCB) at Harvard University. Users can download software developed by the institute or browse research data. It contains 'Integrative genomics viewer', 'Genome Analsis Toolkit', and 'TumorPortal', etc.",
"homepage": "http://www.broadinstitute.org/",
"information_keywords": [
"Portal"
],
"maintainer": "Broad Institute of Harvard and MIT",
"name": "Broad Institute of MIT and Harvard",
"prefix": "NBDC00385",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00387": {
"homepage": "http://elegans.som.vcu.edu/",
"information_keywords": [
"Portal"
],
"maintainer": "Virginia Commonwealth University",
"name": "Caenorhabditis elegans WWW Server",
"prefix": "NBDC00387",
"status": "Closed"
},
"nbdc00388": {
"alt_name": "Cancer Image Reference Database",
"description": "NCC-CIR is a database of cancer images for physicians. It contains medical images such as radiographs, MR, endoscopic images, ultrasonographs, pathological images, etc. which associated with diagnostic information. This database allows to search by case title, anatomical code, imaging modality and image findings through an easy-to-use interface.",
"homepage": "http://cir.ncc.go.jp/en/index.html",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "National Cancer Center",
"name": "NCC-CIR",
"prefix": "NBDC00388",
"status": "Closed",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00389": {
"homepage": "http://amber.gsc.riken.jp/cassava/",
"information_keywords": [
"Sequence"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "Cassava Full-Length cDNA Database",
"prefix": "NBDC00389",
"pubmeds": [
"18096061"
],
"status": "Closed",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00390": {
"alt_name": "Brain Transcriptome Database",
"description": "BrainTx is a neuroinformatics database that contains gene expression information related to various stages and states of the brain. The database contains transcriptome information that can be explored in several ways. Users can search for genes of interest alone or in combination with stratifications for expression patterns, regions, brain specificity, and peak expression time. Data were collected from developing mouse brains.",
"homepage": "http://www.cdtdb.neuroinf.jp/CDT/Top.jsp",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Sequence",
"Expression",
"Image/Movie"
],
"maintainer": "BrainTx platform committee",
"name": "BrainTx",
"prefix": "NBDC00390",
"pubmeds": [
"18603407",
"15018818",
"21243430"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc00391": {
"alt_name": "Candida Genome Database",
"description": "This database is a genome database for Candida. It contains manually curated annotations on genes and proteins, as well as genomic sequences of the human pathogen Candida. Users can view the information of four strains of Candida, including C. albicans, C. dubliniensis, C. glabrata, and C. parapsilosis, which are metabolic pathways, experimental data, and full text of publications as well as genomic information.",
"fairsharing": "biodbcore-000276",
"homepage": "http://www.candidagenome.org",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Bibliography/Documents",
"Repository"
],
"maintainer": "Stanford University",
"name": "CGD",
"prefix": "NBDC00391",
"pubmeds": [
"19808938",
"19577928",
"19465905",
"17090582",
"16879419",
"15608216",
"22064862"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"Protein",
"Health/Disease"
]
},
"nbdc00392": {
"description": "ChimerDB is a comprehensive database of fusion genes. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data.\nUsers can search database by genes, gene pairs and diseases. The whole content of database can be downloaded as database schema, MySQL database dumpfiles and excel format data files.",
"homepage": "http://203.255.191.229:8080/chimerdbv31/mindex.cdb",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "Ewha Womans University",
"name": "ChimerDB",
"prefix": "NBDC00392",
"pubmeds": [
"27899563",
"19906715",
"16381848"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"RNA"
]
},
"nbdc00393": {
"alt_name": "A database of mutant phenotypes of nuclear-encoded chloroplast proteins",
"description": "This is a database of Arabidopsis proteins targeted to chloroplasts initially identified by in silico prediction and confirmed using mutant strains. Users can search for genes or keywords of interest. Results include mutant phenotypes and, in many cases, TEM images. Data tables are available for download.",
"homepage": "http://rarge-v2.psc.riken.jp/chloroplast/",
"information_keywords": [
"Phenotype",
"Image/Movie"
],
"maintainer": "RIKEN PSC (RIKEN Plant Science Center)",
"name": "Chloroplast Function Database II",
"prefix": "NBDC00393",
"pubmeds": [
"23230006",
"19912565"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc00394": {
"alt_name": "National BioResource Project Ciona Intestinalis",
"description": "NBRP Ciona Intestinalis collects, maintains and distributes wild type and transgenic lines of C. intestinalis.\n1. Wild type (closed colony) of C. intestinalis are bred and distributed by Kyoto University and The University of Tokyo.\n2. The transgenic lines and mutants of C. intestinalis are produced and distributed by University of Tsukuba.\nCITRES (Ciona Intestinalis Transgenic line RESources) is a database of C. intestinalis resources maintained by University of Tsukuba. This database contains GFP expressed images of transgenic Ciona and lists of strains, DNA constructs, corresponding references and protocols. Users can search resources by expression stages, as well as keywords including vector names, created methods and expression patterns.",
"homepage": "http://marinebio.nbrp.jp",
"information_keywords": [
"Bioresource",
"Method",
"Expression",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "University of Tsukuba Shimoda Marine Research Center",
"name": "NBRP Ciona Intestinalis",
"prefix": "NBDC00394",
"status": "Active",
"target_keywords": [
"DNA",
"Organism"
]
},
"nbdc00395": {
"description": "CleanEx is a database of gene expression related information in humans and in mice.\nSearch options can be accessed directly by entering the gene ID/symbol, or the Target ID. A complete list of expression datasets, classified according to the organism, may also be retrieved.Datasets can be compared for common trends, genes and numerical results.\nThis site was last updated on 11 Jun 2008.",
"fairsharing": "biodbcore-000291",
"homepage": "http://cleanex.vital-it.ch/",
"information_keywords": [
"Expression"
],
"maintainer": "Under survey",
"name": "CleanEx",
"prefix": "NBDC00395",
"pubmeds": [
"14681477"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00396": {
"description": "This is an integrated database of libraries and clones. Information such as clone names, library information, nucleotide sequence information, and contact information of the clone distributer can be accessed here. The information can be browsed through the genome or the cell-based library. Clone DB was formerly known as NCBI Clone Registry.",
"homepage": "http://www.ncbi.nlm.nih.gov/clone/",
"information_keywords": [
"Bioresource",
"Sequence",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "Clone DB",
"prefix": "NBDC00396",
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00397": {
"alt_name": "Clusters of Orthologous Groups of proteins",
"description": "This database defines all orthologs of protein sequences coded by known genomes. The species name, protein name, and phylogenetic tree of orthologous clusters can be viewed through this site. Each cluster is comprised of individual proteins and its paralogs, matched to evolutionarily conserved molecular domains.",
"fairsharing": "biodbcore-000434",
"homepage": "http://www.ncbi.nlm.nih.gov/COG",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "COGs",
"prefix": "NBDC00397",
"pubmeds": [
"9381173",
"12969510"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00398": {
"alt_name": "Full-length cDNA Database",
"description": "Comparasite is a database of cDNA sequence information for seven parasitic species. In addition to sequences from individual species, the database contains homology information on genes from the seven species or subsets thereof. Bulk data is available for download.",
"homepage": "http://comparasite.hgc.jp/",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "The University of Tokyo The Institute of Medical Science",
"name": "Comparasite",
"prefix": "NBDC00398",
"pubmeds": [
"17151081",
"16902086",
"14681428",
"12703735"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00399": {
"description": "The EMBL Database is a repository of entirely sequenced genomes.\nThe database contains complete genome sequences of 146 archaea, 2,204 bacteria and 166 eukaryotic organisms.\nThe repository also gives access to the DNA sequences of 57 archaeal viruses, 3,900 organellae, 1,178 phages, 1,018 plasmids, 56 viroids and 3,176 viruses.\nText, advanced and sequence search options are available.",
"homepage": "http://www.ebi.ac.uk/genomes",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "EBI Genomes Pages",
"prefix": "NBDC00399",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00400": {
"alt_name": "Database of conformation changes in protein structures",
"description": "ConfC is a database of the structure of protein and how its conformation changes for various reasons.\nThree sub-databases are offered. The first contains changes in protein structure which took place over many years (evolution). The second describes changes that take place when proteins bind with one another. The third contains data on small fluctuations in the structure of different molecules in a sample of a protein.\nThe purpose of this collection is to determine the effect mutations, deletions and insertions in the RNA sequence coding for the production of various proteins have upon the stability of its structure and how these affect its function. It also aims to determine whether structural changes may lead to the development of disease and to suggest ways in which these can be prevented or treated. \nA simple search function, where search parameters are entered, is available.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/confc/desc.html",
"information_keywords": [
"3D structure"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "ConfC (Archive)",
"prefix": "NBDC00400",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00401": {
"alt_name": "Conserved Domain Database",
"description": "This is a collection of muliple sequence alignment models for ancient domains and full-length proteins, for the purpose of giving annotations for proteins. This database includes domain information curated by NCBI as well as those imported from the external sources; Pfam, SMART, COG, PRK, and TIGRFAM.",
"homepage": "http://www.ncbi.nlm.nih.gov/cdd",
"information_keywords": [
"Sequence",
"Image/Movie",
"Classification"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "CDD",
"prefix": "NBDC00401",
"pubmeds": [
"18984618",
"17135202",
"15215404",
"12368255"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00402": {
"alt_name": "Cytokines & Cells Online Pathfinder Encyclopedia",
"description": "COPE (Cytokines & Cells Online Pathfinder Encyclopedia) version 31.4 is a comprehensive database of cytokine-related information.\nThe repository contains more than 31400 pages, upwards of 84890 cited references and 1137890+ internal hyperlinks.\nIt contains 19 subgroups, from Angiogenesis, through Chemokines and Modulins to Virulence Factors, which were created in order to organize the vast amount of information in a searchable format.\nInformation obtained from this database is free for use by academic institutions and non-profit organizations and it is wholly dependent on donations for its growth and maintenance.",
"homepage": "http://www.cells-talk.com",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Under survey",
"name": "COPE",
"prefix": "NBDC00402",
"status": "Active",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc00403": {
"alt_name": "Collaboration of Regional Entities for the Advancement of Technological Excellence",
"description": "CREATE is a database of sequence information for long cDNA clones from humans and mice, selected specifically because they were particularly large. This site serves as a portal to two other database functionalities (InGaP, for expression profiles, and InCeP, for pathway information), and two search functions, one for protein solubility and the other for subcellular localization as determined by transfected GFP-fusion proteins.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/create-portal/desc.html",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "CREATE portal (Archive)",
"prefix": "NBDC00403",
"pubmeds": [
"15500254",
"16769695"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Protein"
]
},
"nbdc00404": {
"alt_name": "Cell System Markup Language",
"description": "CSML is a resource for the annotation of biological pathways. The database focuses on a standardized system for denoting biological processes across several types of experiments. Several models are provided, as well as tools such as Cell Illustrator for annotating and representing original data.",
"homepage": "http://www.csml.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Interaction/Pathway"
],
"maintainer": "The University of Tokyo The Institute of Medical Science",
"name": "CSML",
"prefix": "NBDC00404",
"status": "Inactive",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc00405": {
"alt_name": "Database of homologous proteins in cyanobacteria and plastids",
"description": "CyanoClust is a database of homologous proteins in cyanobacteria, plastids, and bacteria. The database contains clustered homology groups with an emphasis on domain conservation across species. A phylogeny based on these groups is also provided.",
"homepage": "http://gclust.c.u-tokyo.ac.jp/CyanoClust/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "The University of Tokyo",
"name": "CyanoClust database",
"prefix": "NBDC00405",
"pubmeds": [
"20428314"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00406": {
"description": "The Cystic Fibrosis Mutation Database (CFTR1) is a collection of mutations and sequence variants in the CFTR gene, which is related to the development and progress of the genetic disease Cystic Fibrosis.\nCurrently the CFTR mutation database contains 1,935 listed mutations. \nGraphic, basic text and advanced text search options are available.\nA number of linked sites are available for more information on Cystic Fibrosis in general.",
"homepage": "http://www.genet.sickkids.on.ca/cftr/app",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "SickKids (The Hospital for Sick Children)",
"name": "Cystic Fibrosis Mutation Database",
"prefix": "NBDC00406",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein",
"Health/Disease"
]
},
"nbdc00407": {
"description": "DaphniaBASE is a database of water flea sequence data with clone and contig mapping information and a BLAST browser for searching sequences. gene homology tables and bulk data download are also available.",
"homepage": "http://daphnia.nibb.ac.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "National Institute for Basic Biology",
"name": "DaphniaBASE",
"prefix": "NBDC00407",
"pubmeds": [
"16094427"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00408": {
"description": "The Journal of Biological Databases and Curation is a database that provides information on database development. \nThis repository gives guidance on methods of selecting, preserving and maintaining vast amounts of biological data in order to enable effective use of these archives at present and in the future.\nDirection is provided on how to apply the information found in this journal when new research projects are planned.\nGuidance is also given on organizing research results in an accessible format, for instance as a database, to make it available to other scientists for use in their research and to enable computational analysis of such results.\nNew ideas on database development and user tutorials for database tools are welcomed.\nKeyword and Advanced search options are available.",
"homepage": "http://database.oxfordjournals.org/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Oxford University Press",
"name": "The Journal of Biological Databases and Curation",
"prefix": "NBDC00408",
"status": "Active"
},
"nbdc00410": {
"description": "This database aims to provide the fermentation industry (and namely that of sake production) with applicable information about the filamentous fungus Aspergillus oryzae.\nIt consists of sequenced cDNA clones of the Aspergillus oryzae.\nA FastA search function is available.\nThe owners of the database are looking into building it out further by adding information about transcripts of the above fungus.",
"homepage": "http://riodb.ibase.aist.go.jp/ffdb/",
"information_keywords": [
"Sequence"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "Database of genomes and transcriptional regulations for filamentous fungi",
"prefix": "NBDC00410",
"status": "Closed",
"target_keywords": [
"cDNA/EST",
"DNA"
]
},
"nbdc00411": {
"alt_name": "Database for Structure-based Protein Interaction Research",
"description": "This database indicates the interaction sites on proteins and shows how the structures of these sites change when the proteins interact with other substances. This information enables the researcher to determine how these structural changes affect its function.\nThe search function offers direct access to the Protein Data Bank and also to the PROSITE database of proteins. It used to offer access to the BLOCKS database of protein and nucleotide sequence classification, but this last database is no longer updated and may prove unreliable.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/dbspire/desc.html",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "DB-SPIRE (Archive)",
"prefix": "NBDC00411",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00412": {
"alt_name": "Cytokine Family Database",
"description": "This database contains a collection of expressed sequence tag (EST) sequences of human cytokines from GenBank's database at the National Center for Biotechnology Information (NCBI). EST sequences are grouped by cytokine family and by gene, and links to various open databases are provided for each gene, cDNA sequence, or protein. This site is currently closed.",
"homepage": "http://cytokine.medic.kumamoto-u.ac.jp",
"information_keywords": [
"Sequence"
],
"maintainer": "Kumamoto University Graduate School of Medical Sciences",
"name": "dbCFC",
"prefix": "NBDC00412",
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein"
]
},
"nbdc00413": {
"alt_name": "Expressed Sequence Tags database",
"description": "This is one of the world's largest repository for EST with information on multiple species. Users can also submit their own data.",
"fairsharing": "biodbcore-000435",
"homepage": "https://www.ncbi.nlm.nih.gov/genbank/dbest/",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "dbEST",
"prefix": "NBDC00413",
"pubmeds": [
"8401577"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00414": {
"alt_name": "Genotypes and Phenotypes",
"description": "This is a database for research on genotypes and phenotypes in humans, including genome-wide association studies (GWAS), medical sequencing, and molecular diagnostic assays. The dataset is classified into public data and controlled-access data, and an application procedure is required for access to controlled-access data.",
"fairsharing": "biodbcore-000462",
"homepage": "http://www.ncbi.nlm.nih.gov/gap",
"information_keywords": [
"Phenotype",
"Bibliography/Documents",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "dbGaP",
"prefix": "NBDC00414",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00415": {
"alt_name": "Head-to-head Gene Database",
"description": "DBH2H is a database of head-to-head oriented genes across multiple species, with information on all genes transcribed in opposing directions with start sites within 1kb of each other in several eukaryotes. Users can browse, search, and BLAST the database. Data is available for download.",
"homepage": "http://lifecenter.sgst.cn/h2h/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Shanghai Center for Bioinformation Technology",
"name": "DBH2H",
"prefix": "NBDC00415",
"pubmeds": [
"16839196"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc00416": {
"alt_name": "DataBase for Systems Biology",
"description": "DBSB is a listing of systems biology studies. Users can browse links to papers, figures, and data tables of several systems-level projects, with a focus on circadian rhythm and DNA methylation.",
"homepage": "http://sirius.cdb.riken.jp/",
"maintainer": "RIKEN (The Institute of Physical and Chemical Research) Kobe Institute",
"name": "DBSB",
"prefix": "NBDC00416",
"pubmeds": [
"12152080",
"15665827",
"11854264",
"11403560",
"12151263"
],
"status": "Inactive",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc00417": {
"alt_name": "database of Sequence Tagged Sites",
"description": "This is a database of sequence tagged sites those are sequence data for short genomic sequences used as a landmark in the genome. This database was already retired, and in this page, users can find the information about how to search and use those sequences.",
"fairsharing": "biodbcore-000439",
"homepage": "http://www.ncbi.nlm.nih.gov/projects/dbSTS/",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "dbSTS",
"prefix": "NBDC00417",
"pubmeds": [
"2781285"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00418": {
"alt_name": "DROSOPHILA GENE SEARCH PROJECT",
"description": "DGSP is a database of Drosophila insertion mutant lines. The database contains information on over 20,000 insertion strains that were used to map genes. A genome browser and search function are provided, and strains can be requested.",
"homepage": "http://gsdb.biol.se.tmu.ac.jp/~dclust/",
"information_keywords": [
"Phenotype",
"Bioresource",
"Sequence",
"Expression",
"Image/Movie"
],
"maintainer": "Tokyo Metropolitan University",
"name": "DGSP",
"prefix": "NBDC00418",
"pubmeds": [
"9927464"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"DNA",
"Organism"
]
},
"nbdc00419": {
"alt_name": "Dictyostelium cDNA Database",
"description": "Dicty_cDB is a database of Dictyostelium discoideum sequencing data. The database contains information on sequenced clones and contigs obtained by EST analysis. Keyword, pattern, homology, and BLAST searches are supported. \nThe original site was retired, and it is available in NBDC Life Science Database Archive.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/dicty-cdb/desc.html",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Tsukuba Graduate School of Life and Environmental Sciences",
"name": "Dicty_cDB (Archive)",
"prefix": "NBDC00419",
"pubmeds": [
"11911458"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Protein"
]
},
"nbdc00420": {
"description": "This site contains information related to the ameboid protozoan Dictyostelium discoideum, including information of genomes and genes, conferences, experimental protocols, tools for analysis, and distribution of strains.",
"fairsharing": "biodbcore-000767",
"homepage": "http://dictybase.org/",
"information_keywords": [
"Bioresource",
"Method",
"Ontology/Terminology/Nomenclature",
"Sequence",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Northwestern University",
"name": "dictyBase",
"prefix": "NBDC00420",
"pubmeds": [
"21087999",
"18974179",
"16381903",
"16957284",
"14681427"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"Protein",
"Organism"
]
},
"nbdc00421": {
"alt_name": "Dinucleotide Property Database",
"description": "This database is a collection of thermodynamic properties and structural characteristics of DNA and RNA dinucleotide. It contains 125 published properties, such as twists, bends, rolls (in DNA-protein complex), and slides (in DNA-protein complex).",
"homepage": "http://diprodb.fli-leibniz.de",
"information_keywords": [
"Sequence"
],
"maintainer": "FLI (Fritz Lipmann Institute)",
"name": "DiProDB",
"prefix": "NBDC00421",
"pubmeds": [
"18805906"
],
"status": "Active",
"target_keywords": [
"DNA",
"RNA"
]
},
"nbdc00422": {
"description": "Human cDNA Clones is a database of human cDNA clones for which a copy can be distributed by Biological Resource Center (NBRC), NITE. This database contains Human cDNA clones from Human Gateway? Entry Clones, Full-length Human cDNA Clones and Splicing-Variant Human cDNA Clones. Users are able to search clones using sequence ID, keywords and sequence. NBRC is distributing copies of the human cDNA clones to both academia and industries under their distribution policy.",
"homepage": "https://www.nite.go.jp/nbrc/hflcdna/cgi-bin/e/Clone_Search.cgi",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "NITE (National Institute of Technology and Evaluation)",
"name": "Distribution of Human cDNA Clones",
"prefix": "NBDC00422",
"status": "Closed",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00423": {
"alt_name": "Dictionary of Japanese Insect Names",
"description": "DJI is a database of Japanese insects names treating all the insect species or subspecies recorded from Japan. DJI provides two methods of searching. First, users can search Japanese names from scientific ones, then search results show the Japanese names and scientific names (family only, or genus and species). Second, users can search scientific names from Japanese ones, then search results show scientific names (family, genus and species) and the Japanese names.",
"homepage": "http://konchudb.agr.agr.kyushu-u.ac.jp/dji/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Kyushu University Faculty of Agriculture",
"name": "DJI",
"prefix": "NBDC00423",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc00424": {
"homepage": "http://gerg03.gsc.riken.jp/DNABook_DB/VIEW/Book_Top.php?BOOK_ID=BOOK_6",
"information_keywords": [
"Bioresource"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "Pyrococcus DNABook",
"prefix": "NBDC00424",
"status": "Closed",
"target_keywords": [
"DNA"
]
},
"nbdc00425": {
"description": "This is a database for DNA-protein interactions in E.coli. It collects sequence-specific DNA-binding proteins and sequences of the binding sites. They compiled DNA-binding site matrices and predict binding sites in the genome using the matrices.",
"homepage": "http://arep.med.harvard.edu/dpinteract",
"information_keywords": [
"Sequence"
],
"maintainer": "Harvard University",
"name": "DPInteract",
"prefix": "NBDC00425",
"status": "Active",
"target_keywords": [
"DNA",
"Protein"
]
},
"nbdc00426": {
"description": "This is a database of EST sequences for two species of seaweed, the Mediterranean Posidonia and the Zostera. Each entry contains information on Swiss-Prot homology search results, gene Ontology and Pfam, KEGG search results, and sequence information.",
"homepage": "http://drzompo.uni-muenster.de/",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Munster",
"name": "Dr. Zompo (Data Repository for Seagrass ESTs including: Posidonia oceanica, Zostera marina)",
"prefix": "NBDC00426",
"pubmeds": [
"20157482",
"18239962",
"21226908"
],
"status": "Suspended",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00427": {
"alt_name": "DDBJ Trace Archive",
"description": "DTA is a repository of single-pass reads obtained from large-scale sequencing projects using capillary sequencers. DTA contains trace data, which consists of DNA sequence chromatograms (sequence data), base calls, and quality estimates for single-pass reads. DTA is maintained by DDBJ (DNA Data Bank of Japan), the member of INSDC in Japan, and DDBJ collects trace data in cooperation with the other members of INSDC. Users can search trace data at the DTA Search or NCBI Trace Archive, and download them from the DTA FTP site.",
"fairsharing": "biodbcore-001699/",
"homepage": "https://www.ddbj.nig.ac.jp/dta/index-e.html",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "Bioinformation and DDBJ Center, National Institute of Genetics, Research Organization of Information and Systems",
"name": "DTA",
"prefix": "NBDC00427",
"pubmeds": [
"22110025"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"DNA",
"RNA"
]
},
"nbdc00428": {
"alt_name": "European Bioinformatics Institute",
"description": "EBI is the website of the European Bioinformatics Institute. The site contains data from EBI experiments and basic research programs as well as information on training and links to resources affiliated with the Institute. News releases and links to upcoming conferences are also provided.",
"homepage": "http://www.ebi.ac.uk",
"information_keywords": [
"Portal",
"Interaction/Pathway",
"Expression",
"3D structure",
"Repository"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "EBI",
"prefix": "NBDC00428",
"pubmeds": [
"19934258"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Chemical compound"
]
},
"nbdc00429": {
"alt_name": "Genome Annotation for Alternative Splicing",
"description": "ECgene is a database that provides annotation for alternative splicing of the genome.\nStatistics on total gene number (spliced and unspliced), number of transcripts, AS genes and isoforms are displayed in a searchable format for the human genome and that of 8 other animal species. Tables with information for each species can be browsed and downloaded.",
"homepage": "http://genome.ewha.ac.kr/ECgene/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Ewha Womans University",
"name": "Ecgene",
"prefix": "NBDC00429",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc00430": {
"description": "ECRbase is a database of regulatory conserved sequences. The database contains sections on conserved regions across multiple genome comparisons, computationally and experimentally determined promoter locations, chromosome synteny maps, and transcription factor binding sequences. Data are available for download as gzip'd text tables.",
"homepage": "http://ecrbase.dcode.org/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "ECRbase",
"prefix": "NBDC00430",
"pubmeds": [
"17090579"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00431": {
"alt_name": "Enhanced Microbial Genomes Library",
"description": "EMBGLib is a database of completely sequenced microbial genomes. The database contains genomes from the NCBI GenBank which have been further processed and annotated. The database can be searched by keyword, sequence name, or accession number, or by more advanced web server query. Sequences of interest can also be downloaded by HTTP or FTP.",
"homepage": "http://pbil.univ-lyon1.fr/emglib/emglib.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Universite Claude Bernard Lyon 1",
"name": "EMGLib",
"prefix": "NBDC00431",
"pubmeds": [
"10592183"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein"
]
},
"nbdc00432": {
"alt_name": "European Nucleotide Archive",
"description": "ENA is a database of data from global nucleotide sequencing projects. The database contains information on projects from raw phases trhough complete functional annotation. Users can search by keyword or DNA sequence. Bulk data is available for download.",
"fairsharing": "biodbcore-000310",
"homepage": "https://www.ebi.ac.uk/ena/browser/home",
"information_keywords": [
"Method",
"Sequence",
"Repository"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "ENA",
"prefix": "NBDC00432",
"pubmeds": [
"20972220"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"DNA"
]
},
"nbdc00433": {
"description": "EnsemblBacteria is a database of thousands of bacterial genomes. The database can be searched by gene, genome, or BLAST, and several tools are available. Data and ensembl software can also be downloaded.",
"homepage": "http://bacteria.ensembl.org/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Ensembl Project",
"name": "EnsemblBacteria",
"prefix": "NBDC00433",
"pubmeds": [
"19884133"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00434": {
"description": "EnsemblFungi is a database of fungal genomes. The database contains sequences from dozens of fungal species which can be searched by gene, genome, or BLAST. Tools for processing data are also available, as are bulk data downloads.",
"homepage": "http://fungi.ensembl.org/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Ensembl Project",
"name": "EnsemblFungi",
"prefix": "NBDC00434",
"pubmeds": [
"19884133"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00435": {
"description": "EnsemblMetazoa is a database of metazoan genomes. The database contains sequences from dozens of metazoa which can be searched by gene, genome, or BLAST. Tools for processing data are also available, as are bulk data downloads.",
"homepage": "http://metazoa.ensembl.org/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Ensembl Project",
"name": "EnsemblMetazoa",
"prefix": "NBDC00435",
"pubmeds": [
"19884133"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00436": {
"description": "EnsemblPlants is a database of plant genomes. The database contains sequences from dozens of plants which can be searched by gene, genome, or BLAST. Tools for processing data are also available, as are bulk data downloads.",
"homepage": "http://plants.ensembl.org/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Ensembl Project",
"name": "EnsemblPlants",
"prefix": "NBDC00436",
"pubmeds": [
"19884133"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00437": {
"description": "EnsemblProtists is a database of protist genomes. The database contains sequences from dozens of protists which can be searched by gene, genome, or BLAST. Tools for processing data are also available, as are bulk data downloads.",
"homepage": "http://protists.ensembl.org/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Ensembl Project",
"name": "EnsemblProtists",
"prefix": "NBDC00437",
"pubmeds": [
"19884133"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00438": {
"alt_name": "The Eukaryotic Promoter Database",
"description": "EPD is a satabase of unique gene promoters. The database contains non-redundant sequences of promoters for genes transcribed by RNA polymerase II. Users can search the database, browse promoter elements, or download sequences via HTTP or FTP.",
"fairsharing": "biodbcore-000653",
"homepage": "https://epd.expasy.org/epd/",
"information_keywords": [
"Sequence"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "EPD",
"prefix": "NBDC00438",
"pubmeds": [
"16381980",
"14681364",
"11752326",
"10592254",
"9847211",
"9399872"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00439": {
"alt_name": "Erythropoiesis database",
"description": "EpoDB is a database about genes which relate to vertebrate red blood cells. It contains DNA sequence, structural features, protein information, gene expression information and transcription factor binding sites. Information about genes is brought together from different sources. This database is able to return the same specific region of sequence from a number of related genes for further analysis. Moreover, it provides visualization tools that makes it easy and efficient to interpret the information in EpoDB or from the analyses.",
"fairsharing": "biodbcore-000258",
"homepage": "http://www.cbil.upenn.edu/EpoDB/release/version_2.2/epodb.html",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "University of Pennsylvania",
"name": "EpoDB",
"prefix": "NBDC00439",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00440": {
"alt_name": "Solubility database of all E.coli proteins",
"description": "eSOL is a database about the solubility of entire ensemble proteins of E.coli individually synthesized by PURE system that is chaperon free. This database provides the solubility of proteins which synthesized from ASKA library (A complete Set of E.coli K-12 ORF Archive). Entries can be searched on keywords containing JW ID, ECK number, B number, gene name, Locus name, Synonyms of locus, gene product description, SCOP assignment or browsed on gene name. Users can download expression data, un-expression data, and chaperone data.",
"homepage": "http://www.tanpaku.org/tp-esol/index.php?lang=en",
"information_keywords": [
"Expression"
],
"maintainer": "National Institute of Genetics",
"name": "eSOL",
"prefix": "NBDC00440",
"pubmeds": [
"19251648",
"22615364",
"11479568"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00441": {
"description": "EST is a database of short single-read transcript sequences. The database contains thousands of sequences determined by traditional sequencing of gene transcripts in dozens of organisms. The database can be searched by keyword or BLAST. Users can submit sequences or download data via FTP.",
"homepage": "http://www.ncbi.nlm.nih.gov/nucest",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "EST (A collection of short single-read transcript sequences from GenBank)",
"prefix": "NBDC00441",
"status": "Closed",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00442": {
"alt_name": "ESTerases and alpha/beta Hydrolase Enzymes and Relatives",
"description": "ESTHER is a database of hydrolase family enzymes. The database contains information on hydrolases and related enzymes from over 5000 species including sequences, structures, mutations, and disease associations. Users can search the database or use various tools to compare and analyze hydrolases.",
"homepage": "http://bioweb.supagro.inra.fr/ESTHER/general?what=index",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Bibliography/Documents",
"3D structure",
"Chemical structure",
"Classification"
],
"maintainer": "INRAE (National Research Institute for Agriculture, Food and Environment)",
"name": "ESTHER",
"prefix": "NBDC00442",
"pubmeds": [
"14681380",
"21933125"
],
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease"
]
},
"nbdc00443": {
"alt_name": "Evolutionary annotation database",
"description": "This is a database of corresponding genes (orthologs) linking humans with fourteen other vertebrates.\nSimilarities in sequence of the corresponding genomes and in the amino acids these sequences facilitated production of were compared. \nDifferent splicing variants were also included in the comparison.\nOutcomes of these comparisons were analyzed to predict evolutionary links between the species and is displayed in a tree format.\nSearch by keyword, accession number or gene symbol is possible.",
"fairsharing": "biodbcore-000206",
"homepage": "http://www.h-invitational.jp/evola/search.html",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "Evola",
"prefix": "NBDC00443",
"pubmeds": [
"17982176"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00444": {
"homepage": "http://pdbjets.protein.osaka-u.ac.jp/",
"information_keywords": [
"Sequence",
"3D structure",
"Classification"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "Evolutionary Trace Server",
"prefix": "NBDC00444",
"pubmeds": [
"16809388"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00446": {
"alt_name": "Four-dimensional Ascidian Body Atlas 2",
"description": "FABA2 is a database of ascidian's three-dimensional (3D) and cross-sectional images in late developmental stages. It contains the images which were acquired by visualizing F-actin of ascidian, C. intestinalis from 17.5hpf hatching larva to 7dpf juvenile, stained with alexa fluor phalloidin by confocal laser scanning microscope (CLSM) and reconstructed from more than 3,000 high-resolution real images. Time-lapse images by stereo microscope were obtained and matched with images by CLSM which correspond to 31 different stages.",
"homepage": "https://www.bpni.bio.keio.ac.jp/chordate/faba2/top.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Keio University",
"name": "FABA2",
"prefix": "NBDC00446",
"pubmeds": [
"17557317"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Organism"
]
},
"nbdc00447": {
"alt_name": "Functional Annotation of Mouse 3",
"description": "FANTOM3 is a database of the mouse transcriptome, with comprehensive information on expressed mouse genes assembled using technologies developed by the FANTOM consortium. Several sets of data are available for bulk FTP download, and links to cDNA annotation browsers are provided.",
"homepage": "http://fantom3.gsc.riken.jp",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Genome Exploration Research Group, RIKEN Genomic Sciences Center",
"name": "FANTOM3",
"prefix": "NBDC00447",
"pubmeds": [
"16645617",
"16141072",
"16141073"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00448": {
"alt_name": "Functional Annotation of the Mammalian Genome 4",
"description": "FANTOM is a database about functional annotations of the Mammalian genomes. It contains experimental data of the FANTOM consortium which is an international collaborative research project initiated and organized by the RIKEN Omics Science Center. This database includes CAGE tags, mapping, and promoters (clusters or aggregations of CAGE tags as units of promoter) for human and mouse, and information about the experiments and data processing. Users are able to use genome browser or EDGE express DB which is designed for integrating and interpreting large high-throughput expression datasets in the context of biological networks.",
"homepage": "http://fantom.gsc.riken.jp/4/index.php?lang=en",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "RIKEN Omics Science Center",
"name": "FANTOM4",
"prefix": "NBDC00448",
"pubmeds": [
"20211142",
"19377474",
"19377478",
"19377475"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"DNA",
"RNA",
"Protein"
]
},
"nbdc00449": {
"description": "Flavonoid Database is a wiki-based database of flavonoids maintained by Arita Laboratory, the University of Tokyo. This database includes indexes for flavonoids, authors of journal papers and journal titles, and information on food containing flavonoids. Users can search flavonoids from backbone structures, hydroxylation and methylation patterns, glycosylation patterns and other modifications.",
"homepage": "http://metabolomics.jp/wiki/Category:FL",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents",
"Chemical structure"
],
"maintainer": "The University of Tokyo Graduate School of Science Department of Biophysics and Biochemistry",
"name": "Flavonoid Database",
"prefix": "NBDC00449",
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc00450": {
"description": "FLJ is a sequence analysis database that is focused on mRNA variations of human genome and cDNA sequences. There are about 20 to 25 thousand human genes and 100 thousand mRNA varieties, which are apparently caused by transcription start site (TSS) variations and splicing. \nIn the previous human cDNA project, approximately 30 thousand FLJ human full-length sequenced cDNAs were deposited in DDBJ/GenBank/EMBL, and approximately 1.4 million of 5'-end sequences (5'-EST) of FLJ full-length cDNAs from approximately 100 kinds of cDNA libraries of human tissues and cells that were constructed by the oligo-capping method were obtained. These FLJ cDNAs included approximately 80% of all human genes. In the project we developed an efficient splicing variant cDNA cloning and evaluation system, obtaining more than a thousand full-length sequenced cDNAs, which we used with the human genome to construct a sequence analysis database focused on mRNA variations.",
"homepage": "http://flj.lifesciencedb.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "Molecular Profiling Research Center for Drug Discovery, AIST",
"name": "FLJ Human cDNA Database",
"prefix": "NBDC00450",
"pubmeds": [
"20728443",
"22140100",
"20728443",
"19880432",
"19073703",
"19054851",
"16344560",
"16303743",
"14702039",
"11808872",
"11853313",
"11375929",
"11337467",
"11700583",
"10756096"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Genetic variation"
]
},
"nbdc00451": {
"alt_name": "The Cyanobacterial Chlorophyll Fluorescence Database",
"description": "Fluorome is a database of cyanobacterial chlorophyll fluorescence information, with information on the kinetic responses of hundreds of gene deletion mutants. Users can search by ORF, gene, or mutation and obtain information on phenotype and mutations that result in similar kinetic response.",
"homepage": "http://www.photosynthesis.jp/fluorome/",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Waseda University School of Education",
"name": "Fluorome",
"prefix": "NBDC00451",
"pubmeds": [
"17284470"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Metabolite"
]
},
"nbdc00452": {
"alt_name": "Functional RNA Database",
"description": "fRNAdb is a sequence database hosting a large collection of non-coding RNA sequence data that were obtained from public non-coding databases. Users of the fRNAdb database can search the sequences by inputting associated keywords, e.g., miRNA or snoRNA. By adding the name of the disease or the tissue, the search will be more specific.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/frnadb/desc.html",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "fRNAdb (Archive)",
"prefix": "NBDC00452",
"pubmeds": [
"17099231",
"16683036",
"16185827",
"16381832",
"15608158",
"12520045",
"17145715",
"16381836",
"17099226",
"18948287"
],
"status": "Active",
"target_keywords": [
"RNA"
]
},
"nbdc00453": {
"description": "Fugu Genome Project is a database of the pufferfish (Takifugu rubripes) genome. The database contains a genome browser with BLAST search, genetic linkage maps, and functional annotations of transscription factor genes. Genome data is available for download.",
"homepage": "http://www.fugu-sg.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "Institute of Molecular and Cell Biology",
"name": "FUGU GENOME PROJECT",
"prefix": "NBDC00453",
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00454": {
"alt_name": "Anopheles Full-length cDNA database",
"description": "This database of the Anopheles genome allows for browsing cDNA clones mapped to the genome, keyword search, BLAST search, or bulk data download, and provides links to other genome databases.",
"homepage": "http://fullmal.hgc.jp/index_ag_ajax.html",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tokyo The Institute of Medical Science Human Genome Center",
"name": "Full-Anopheles",
"prefix": "NBDC00454",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00455": {
"alt_name": "Babesia Full-length cDNA database",
"description": "This is a database of the Babesia genomes, and allows for browsing of the cDNA clones mapped to the genomes, keyword search, or bulk data download and provides links to other genome databases.",
"homepage": "http://fullmal.hgc.jp/index_bb_ajax.html",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tokyo The Institute of Medical Science Human Genome Center",
"name": "Full-Babesia",
"prefix": "NBDC00455",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00456": {
"alt_name": "Cryptosporidium Full-Length cDNA Database",
"description": "This is a database of the Cryptosporidium genome to browse the cDNA clones mapped to the genome, keyword search, BLAST search, or bulk data download and provides links to other genome databases.",
"homepage": "http://fullmal.hgc.jp/index_cp_ajax.html",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tokyo The Institute of Medical Science Human Genome Center",
"name": "Full-Cryptosporidium",
"prefix": "NBDC00456",
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Protein"
]
},
"nbdc00457": {
"alt_name": "Echinococcosis Full-length cDNA database",
"description": "This database of the Ecchinococcus multilocularis genome allows browsing cDNA clone sequences and BLAST search. Data is available for download.",
"homepage": "http://fullmal.hgc.jp/index_em_ajax.html",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tokyo The Institute of Medical Science Human Genome Center",
"name": "Full-Echinococcosis",
"prefix": "NBDC00457",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00458": {
"alt_name": "Tsetse Full-length cDNA database",
"description": "This is a database of the Tsetse fly genome. The database allows for browsing of the cDNA clones mapped to the genome, keyword search, BLAST search, or bulk data download and provides links to other genome databases.",
"homepage": "http://fullmal.hgc.jp/index_arth.html",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tokyo The Institute of Medical Science Human Genome Center",
"name": "Full-Tsetse",
"prefix": "NBDC00458",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00460": {
"description": "Fungus and Actinomycetes Gallery is an image database of pathogenic fungi (fungi, yeasts and mushrooms) and actinomycetes maintained by Medical Mycology Research Center (MMRC), Chiba University. Each entry contains the Jananese and scientific names, an image of a pathogenic fungus or actinomycete, diversity and culture condition. Users can use the data and images only for educational and research purposes.",
"homepage": "http://www.pf.chiba-u.ac.jp/english/gallery.html",
"information_keywords": [
"Bioresource",
"Image/Movie"
],
"maintainer": "Chiba University Research Center for Pathogenic Fungi and Microbial Toxicoses",
"name": "Fungus and Actinomycetes Gallery",
"prefix": "NBDC00460",
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease"
]
},
"nbdc00461": {
"description": "G-compass is a browser intended for searching comparative genomes.\nConserved genomic regions between humans and another 12 vertebrates (chicken, chimpanzee, cow, dog, horse, medaka, mouse, opossum, rat, rhesus monkey, tetradon and zebrafish) can be visualized based on the original genome alignments. Annotations of human genes/transcripts originally come from H-InvDB, while the ortholog information come from the Evola sub-database. Use of the G-compass database is free of charge.",
"homepage": "http://www.h-invitational.jp/g-compass/",
"information_keywords": [
"Sequence"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "G-compass",
"prefix": "NBDC00461",
"pubmeds": [
"19846439",
"16169162"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc00462": {
"alt_name": "Glycoanalysis by the three axes of MS and chromatography",
"description": "GALAXY is a database about mapping of carbohydrate chains for structural determination and prediction. It contains data on approximately 500 different PA-glycans that were analyzed using original 2-D/3-D mapping method. Data in this site includes the structures, HPLC elution positions expressed in glucose units (GU) on ODS and amide-silica columns, relative molecular mass, code numbers, sources of samples, and references.",
"homepage": "http://www.glycoanalysis.info/galaxy2/ENG/index.jsp",
"information_keywords": [
"Chemical structure"
],
"maintainer": "Nagoya City University Graduate School of Pharmaceutical Sciences",
"name": "GALAXY",
"prefix": "NBDC00462",
"status": "Inactive",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc00463": {
"alt_name": "Gastrointestinal Medical Image Database",
"description": "MIDB is a database about medical images of gastrointestinal tumors. It contains images obtained by ultrasonography, endoscopy, X-ray, CT, MRI, macroview or histology and results of blood test. This database allows to search using a list of disease. Moreover, it allows to search cases or images using keywords, histopathological classfications, locations, technique, methods, etc..",
"homepage": "http://www.midb.jp/db/en/",
"information_keywords": [
"Image/Movie"
],
"maintainer": "National Hospital Organization Kyushu Cancer Center",
"name": "MIDB",
"prefix": "NBDC00463",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00464": {
"description": "Gclust is a database of homologous proteins across organisms. It contains protein homology information for bacteria, cyanobacteria, algae, and plants. All homologous genes for any given species are represented. Proteins can be searched by keyword or BLAST. Bulk data is available for download.",
"homepage": "http://gclust.c.u-tokyo.ac.jp/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "The University of Tokyo Graduate School of Arts and Sciences",
"name": "Gclust Server",
"prefix": "NBDC00464",
"pubmeds": [
"19158159",
"16901089",
"14571386"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00465": {
"alt_name": "Genotyping Microarray based CNV Analysis",
"description": "It appears this site concerns a research project where the comprehensive amount of information created by the Human Genome Project is studied in terms of the way human genes are expressed, proteins are produced and how different proteins react with one another, in order to understand the complex biological systems that take place in the human body. \nThe aim of the study is to eventually be able to apply what they learn to better diagnose and/or treat human disease.\nStudying the changes that develop in the human genome when a cancerous growth develops in the liver or pancreas, led to the deduction that these genomic changes activate oncogenes and inactive tumor suppressor genes.\nHow the genome is interpreted and packaged is of vital importance to normal cell development and differentiation and mistakes taking place during these processes have an important effect on the development and outcome of disease.",
"homepage": "http://www.genome.rcast.u-tokyo.ac.jp/CNV/gemca_details.html",
"information_keywords": [
"Expression"
],
"maintainer": "The University of Tokyo Research Center for Advanced Science and Technology",
"name": "GEMCA",
"prefix": "NBDC00465",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc00466": {
"description": "gene Expression in Tooth Database contains a wide variety of information characterizing the underlying biology of teeth. gene expression can be browsed by gene family, visualized in several experiments, and broken down by tooth tissue component.",
"homepage": "http://bite-it.helsinki.fi",
"information_keywords": [
"Expression"
],
"maintainer": "University of Helsinki",
"name": "Gene Expression in Tooth Database",
"prefix": "NBDC00466",
"status": "Inactive",
"target_keywords": [
"cDNA/EST",
"Protein"
]
},
"nbdc00467": {
"alt_name": "All Of gene Expression",
"description": "This is an interface to search/view gene expression data in EBI ArrayExpress. The statistical value from metadata in ArrayExpress are shown as interactive graphs and users can select data by organisms and experiment types. Each data are linked to EBI ArrayExpress.",
"homepage": "https://aoe.dbcls.jp/en",
"information_keywords": [
"Expression"
],
"maintainer": "DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "AOE",
"prefix": "NBDC00467",
"pubmeds": [
"31978081"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"RNA",
"Protein"
]
},
"nbdc00468": {
"alt_name": "Gene Ontology Annotation Database",
"description": "GOA is a database of gene function and interaction information. The database contains manual and automated annotations of gene ontology. Users can download current and previous versions of the database including gene annotations, gene interactions, and ontology mapping files.",
"fairsharing": "biodbcore-000313",
"homepage": "https://www.ebi.ac.uk/GOA",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "GOA",
"prefix": "NBDC00468",
"pubmeds": [
"18957448",
"22123736",
"19744993"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc00469": {
"description": "geneDB is a database of genomic and proteomic data of several species generally regarded as pests or parasites. The database contains information pages for dozens of species across six large classes including viruses, protozoa, helminths, bacteria, and vectors. Users can search by sequence feature or ID or browse the database.",
"fairsharing": "biodbcore-000044",
"homepage": "http://www.genedb.org",
"information_keywords": [
"Sequence"
],
"maintainer": "Wellcome Sanger Institute",
"name": "GeneDB",
"prefix": "NBDC00469",
"pubmeds": [
"22116062"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00470": {
"description": "GENIA is a database of computationally mined information regarding genes, molecules, and pathways. The site explains data mining procedures in detail and provides corpuses for several pathways. Data can be downloaded in BioNLP Shared Task-flavored standoff format.",
"homepage": "http://www.geniaproject.org",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "The University of Tokyo The Graduate School of Information Science and Technology",
"name": "GENIA Project",
"prefix": "NBDC00470",
"status": "Active"
},
"nbdc00471": {
"description": "GENIUS II is a database system in which all protein-cording regions of organisms are assigned to the published three-dimensional structures. It uses the multiple intermediate sequence search method.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/genius/desc.html",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "GENIUS II (Archive)",
"prefix": "NBDC00471",
"pubmeds": [
"10195280",
"10211823",
"14751990"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00472": {
"alt_name": "Genomic Exploration of the Hemiascomycete Yeasts",
"description": "This database contains sequence data with annotations and classifications of 18 species of Hemiascomycete Yeast. Each record includes details on the gene, position, protein family name, and links to other databases.",
"homepage": "http://www.genolevures.org/",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "Bordeaux Bioinformatics Center",
"name": "Genolevures",
"prefix": "NBDC00472",
"status": "Suspended",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00473": {
"description": "Genome is a database of sequences and information on completed genome projects. The database contains complete sequences for dozens of organisms from microbes to mammals, as well as the genomes of organelles and viruses. Several sequence exploration tools (including map viewer and protein clusters) are available. Users can submit genomes or download data via FTP.",
"homepage": "http://www.ncbi.nlm.nih.gov/genome",
"information_keywords": [
"Sequence",
"Bibliography/Documents",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "Genome",
"prefix": "NBDC00473",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Cell/Organelle"
]
},
"nbdc00474": {
"description": "This site is a portal site by EMBL-EBI. The site contains easy links to several free-access database systems and tools coordinate and hosted by EMBL-EBI, including topics ranging from chemical biology to molecular and cellular structures. Within each of nine categories, links to dozens of other resources are provided from which users can access online data or download software and bulk data.",
"homepage": "https://www.ebi.ac.uk/services",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Sequence",
"3D structure",
"Chemical structure",
"Expression",
"Interaction/Pathway",
"Bibliography/Documents",
"Portal",
"Repository"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "EMBL-EBI > Services",
"prefix": "NBDC00474",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"RNA",
"Protein",
"Chemical compound"
]
},
"nbdc00475": {
"description": "Genome network platform is an integrated database and web viewers for the Genome Network Project. It integrates experimental data, which generated from the project in association with the public databases, relating to the following information: 1) transcription starting position of human genes in the human genome, 2) conjunction to control region on transcriptional factors and the human genome, 3) protein-protein interaction with a central focus on transcription factors. This database provides the following functions: a) 'Genome Explorer' for annotation of landmarks (genes, transcription start sites, etc.) aligned in accordance with their genome locations. b) 'PPI Network' for a graphical view of protein-protein interaction (PPI) network from the experimental data generated under the project and the public datasets. c) 'Expression Profile' to cluster genes by expression pattern and display the result with heatmap, and for genes which have relation of coregulation and anti-coregulation. d) 'Comparison Viewer' for comparison the genomic region of Human/Mouse. Users are able to obtain the distributed clones.",
"homepage": "http://genomenetwork.nig.ac.jp/index_e.html",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "National Institute of Genetics",
"name": "Genome Network Platform",
"prefix": "NBDC00475",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00476": {
"description": "BioProject is a database which collects the results of research projects under the umbrella of the project or initiative. The database consists of tables of projects, which users can search or browse to find all data outputs related to that project. Users can submit projects or download data via FTP.",
"fairsharing": "biodbcore-000684",
"homepage": "http://www.ncbi.nlm.nih.gov/bioproject",
"information_keywords": [
"Sequence",
"Bibliography/Documents",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "BioProject (Formerly Genome Project)",
"prefix": "NBDC00476",
"pubmeds": [
"22139929"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00477": {
"description": "This is a database of the Symbiobacterium thermophilum genome, with an annotation table, the complete sequence, and images of S. thermophilum. Information about the organism is also provided.",
"homepage": "http://hp.brs.nihon-u.ac.jp/~projects/genome/STH/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "Nihon University Advanced Research Institute for the Sciences and Humanities",
"name": "Genome Project of Symbiobacterium thermophilum",
"prefix": "NBDC00477",
"pubmeds": [
"15383646"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00478": {
"description": "Genome Atlas Database is a resource for bacterial and archael genome resources. The database contains the most recent genome sequences of simple single-celled organisms. Users can browse by bacterial and archeal taxa organized in descriptive tables or search by organism, taxa group, or NCBI project ID.",
"homepage": "http://www.cbs.dtu.dk/services/GenomeAtlas/",
"information_keywords": [
"Sequence"
],
"maintainer": "DTU Health Tech",
"name": "GenomeAtlasDatabase",
"prefix": "NBDC00478",
"pubmeds": [
"15256401"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein"
]
},
"nbdc00480": {
"homepage": "http://www.genpac-nalapro.com/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "NalaPro Technologies, Inc.",
"name": "Genpac",
"prefix": "NBDC00480",
"status": "Inactive"
},
"nbdc00481": {
"alt_name": "Gene Expression Nervous System Atlas",
"description": "GENSAT is a database of gene expression in the central nervious system. The database contains expression data from experiments in several genetically engineered mouse lines presented in the form of images of nervous system tissue. Brightfield and confocal images are available for hundreds of genes expressed in the nervous system. Users can browse by structure or search by gene, order mouse lines, and download data.",
"homepage": "http://www.gensat.org/about.jsp",
"information_keywords": [
"Expression",
"Image/Movie"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "GENSAT",
"prefix": "NBDC00481",
"pubmeds": [
"14586460"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00482": {
"alt_name": "Gene Expression Omnibus Data Sets",
"description": "GEO DataSets is a database of gene expression experiments, which is a part of GEO repository ( http://integbio.jp/dbcatalog/en/record/nbdc00080 ). The database contains summary information on thousands of published experiments studying gene expression. Users can search data sets by organism, gene, or keyword, and obtain expression profiles for a single gene across many studies in the dataset or compare expression profiles between data sets. Experimental datasets are also available to download via FTP.",
"homepage": "http://www.ncbi.nlm.nih.gov/gds",
"information_keywords": [
"Expression",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "GEO Data Sets",
"prefix": "NBDC00482",
"pubmeds": [
"11752295",
"21097893"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00483": {
"alt_name": "Genomes Online Database",
"description": "GOLD is a data management system that catalogs genome and metagenome sequencing projects with associated metadata from around the world. GOLD (v.6) provides information for 28,744 Studies, 272,234 Organisms, 21,910 Biosamples, 134,884 Sequencing Projects and 111,625 Analysis Projects. Advanced Search feature allow users to explore GOLD's different project levels above.",
"fairsharing": "biodbcore-000117",
"homepage": "https://gold.jgi.doe.gov/index",
"information_keywords": [
"Bibliography/Documents",
"Portal",
"Repository"
],
"maintainer": "DOE Joint Genome Institute",
"name": "GOLD",
"prefix": "NBDC00483",
"pubmeds": [
"27794040"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00484": {
"description": "GPCRdb is a database of G-coupled protein receptor information. The database contains gene and protein sequence information as well as protein structure, binding site, and conservation data. Users can search by protein ID or keyword, browse by family, structure, model, or oligomers, or utilize several GPCR-specific tools.",
"fairsharing": "biodbcore-000292",
"homepage": "http://gpcrdb.org",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "CMBI (Centre for Molecular and Biomolecular Informatics)",
"name": "GPCRdb",
"prefix": "NBDC00484",
"pubmeds": [
"21045054"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00485": {
"description": "GRAMENE is a database of comparative sequence information in grass plants. The database has sections for genomes, genes, genetic diversity, metabolic pathways, ontologies, markers, QTLs, and BLAST search. A news feed for the latest database updates is also provided. Users can search all sections by keyword, and data is available to download.",
"fairsharing": "biodbcore-000297",
"homepage": "http://www.gramene.org",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Sequence",
"Bibliography/Documents",
"Taxonomy"
],
"maintainer": "Cold Spring Harbor Laboratory",
"name": "GRAMENE",
"prefix": "NBDC00485",
"pubmeds": [
"21076153"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Protein"
]
},
"nbdc00486": {
"description": "GSS is a database of collected, unannotated sequences. The database contains sequences from a variety of projects, including random surveys, exon-traps, and clone-end sequencing, primarily of genomic origin. Users can submit sequences or download via FTP.",
"homepage": "https://www.ncbi.nlm.nih.gov/genbank/dbgss/",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "GSS",
"prefix": "NBDC00486",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00487": {
"alt_name": "Genome wide association database",
"description": "GWAS DB is a database of gene-disease associations from published studies. The database contains a wealth of information about the studies and links to results and genes associated with several diseases. Diseases, genes, studies, and SNPs can be searched and results provide links and plots to association information. Please refer to the Sharing Policy (http://gwas.biosciencedbc.jp/gwasdb/db_policy_en.html) to use the data.",
"homepage": "http://gwas.biosciencedbc.jp/cgi-bin/gwasdb/gwas_top.cgi",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "GWAS DB",
"prefix": "NBDC00487",
"pubmeds": [
"19629137"
],
"status": "Closed",
"target_keywords": [
"Genetic variation",
"Health/Disease"
]
},
"nbdc00488": {
"alt_name": "Gypsy Database 2.0",
"description": "GyDb is a database of mobile genetic elements. The database contains information on several mobile element families and mobility systems, as well as tools for searching via BLAST or analyzing using HMM. Mobile elements can be submitted to the database. Phylogenetic trees and an alignment tool are also available.",
"homepage": "http://gydb.org/index.php/Main_Page",
"information_keywords": [
"Sequence",
"Image/Movie",
"Bibliography/Documents",
"Classification"
],
"maintainer": "La Universitat de Valencia, Universidad Politecnica de Valencia",
"name": "GyDB",
"prefix": "NBDC00488",
"pubmeds": [
"21036865"
],
"status": "Active",
"target_keywords": [
"DNA",
"Protein"
]
},
"nbdc00489": {
"alt_name": "Human-transcriptome DataBase for Alternative Splicing",
"description": "H-DBAS is the Human-transcriptome DataBase for Alternative Splicing, and is based on H-InvDB. Features of H-DBAS include annotated information of genome-wide human AS variants. Representative AS variants (RASVs) were identified from data of 6 model mammals, namely, human, mouse, rat, chimpanzee, macaque and dog, and are provided as full-length cDNA data sets, mRNA data sets and RNA data sets. Equally-spliced variants between these mammals were identified and compared sets are available. Splice sites and motifs that affect SNPs in humans, RASVs that affect protein function in humans and AS junctions tedetced by RNA-Sez tags are provided.",
"fairsharing": "biodbcore-000241",
"homepage": "http://www.h-invitational.jp/h-dbas/?lang=en",
"information_keywords": [
"Sequence"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "H-DBAS",
"prefix": "NBDC00489",
"pubmeds": [
"20433709",
"19969536",
"18838389",
"17130147",
"16914452",
"15103394"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST",
"RNA"
]
},
"nbdc00491": {
"description": "Database for hematological malignancy is an image database of hematological malignancies constructed by National Kyusyu Cancer Center. Each entry consists of a disorder name, histological images and detailed data on a medical case. Users can search medical cases by keywords, WHO Classification of tumours, FAB Classification, cell staining methods and detailed data (gender, age and others).",
"homepage": "http://www.midb.jp/blood_db/db.php?lang=en",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "National Hospital Organization Kyushu Cancer Center",
"name": "Database for hematological malignancy",
"prefix": "NBDC00491",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00492": {
"alt_name": "Human Endogenous Retrovirus Database",
"description": "HERVd is a database of retroviruses endogenous to the human genome. Sequences were collected by computational search of published genome data covering greater than 90% of the human genome. Users can search by several parameters including family and chromosome, as well as perform BLAT and FASTA searches.",
"fairsharing": "biodbcore-000193",
"homepage": "http://herv.img.cas.cz",
"information_keywords": [
"Sequence"
],
"maintainer": "Academy of Sciences of the Czech Republic",
"name": "HERVd",
"prefix": "NBDC00492",
"pubmeds": [
"11752294",
"14681356"
],
"status": "Active"
},
"nbdc00493": {
"alt_name": "Human Gene and Protein Database",
"description": "The Human gene and Protein Database (HGPD) provides SDS-PAGE patterns of human genes and proteins.\nNow that the human genome sequence has been elucidated, the functional and structural analysis of genes has become important. Many Japanese and other cDNA projects have supplied high quality data on full-length cDNAs. Using the Gateway cloning system (Invitrogen, CA, USA) to construct human Gateway entry clones from full-length cDNAs, systematic and comprehensive expression of human proteins can be achieved. In the 'GW: Gateway Summary' window, amino acid and nucleotide sequences of open reading frame (ORF) regions for each cDNA and sequence differences are presented. Proteins are shown in the 'PE: Protein Expression' window and image data in the 'SL: Subcellular Localization' window. Most cDNA sequence analysis data in HGPD are also shared with the FLJ Human cDNA Database. Search can be conducted for ID, Keyword, BLAST and Category",
"fairsharing": "biodbcore-000047",
"homepage": "http://hgpd.lifesciencedb.jp/cgi/index.cgi",
"information_keywords": [
"Bioresource",
"Sequence",
"Expression",
"Image/Movie"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "HGPD",
"prefix": "NBDC00493",
"pubmeds": [
"19073703",
"22140100"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Protein"
]
},
"nbdc00494": {
"description": "GWAS Central is a database of summary findings from published GWAS. The database contains entries for phenotypes or diseases, genes, and markers used in the studies. Users can search or browse by gene, genomic region, or study.",
"fairsharing": "biodbcore-000566",
"homepage": "http://www.gwascentral.org/",
"information_keywords": [
"Phenotype",
"Sequence",
"Bibliography/Documents",
"Repository"
],
"maintainer": "University of Leicester",
"name": "GWAS Central",
"prefix": "NBDC00494",
"pubmeds": [
"18948288",
"11752345",
"10592273"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc00495": {
"alt_name": "Hydrogen and Hydration Database",
"description": "HHDB is a database of hydrogen atoms in 3D structures. The database contains images and statistics of localized hydrogens and water atoms in PDB structures. The database will calculate and provide plots of bond angles in a selected set of structures.",
"homepage": "http://hhdb.taka.qst.go.jp/hx3/",
"information_keywords": [
"Image/Movie",
"3D structure"
],
"maintainer": "National Institutes for Quantum and Radiological Science and Technology",
"name": "HHDB",
"prefix": "NBDC00495",
"status": "Suspended",
"target_keywords": [
"Protein"
]
},
"nbdc00496": {
"description": "Histone Database is a resource for sequences and properties of histones and related proteins. The database contains sequences for histones across eukaryotic species, including alignments across species and the sequences of all human histones. Structures of histones in complex with DNA are also available.",
"homepage": "https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/browse/",
"information_keywords": [
"Sequence",
"3D structure",
"Classification"
],
"maintainer": "National Human Genome Research Institute, National Institute of Health",
"name": "HistoneDB",
"prefix": "NBDC00496",
"pubmeds": [
"22025671"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Protein",
"Organism"
]
},
"nbdc00497": {
"alt_name": "A database of high confidence protein-protein interactions",
"description": "HitPredict is a database of protein-protein interactions. The database contains thousands of high-confidence interactions that can be searched by name, ID, or publication. The database is a non-redundant compilation of three high-quality sources, and each protein is notated with several identifiers.",
"homepage": "http://www.hitpredict.org",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "The University of Tokyo The Institute of Medical Science Human Genome Center",
"name": "HitPredict",
"prefix": "NBDC00497",
"pubmeds": [
"26708988",
"20947562",
"15833142"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00498": {
"description": "Homeodomain Resource is a resource for sequences and properties of homeodomain proteins. The database contains sequences of proteins containing homeodomains and solved structures of homeodomains in complex with other proteins or nucleic acids. The database also includes information on diseases associated with homeodomain protein mutations.",
"homepage": "http://research.nhgri.nih.gov/homeodomain/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"3D structure"
],
"maintainer": "National Human Genome Research Institute, National Institute of Health",
"name": "Homeodomain Resource",
"prefix": "NBDC00498",
"pubmeds": [
"20157477"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"DNA",
"Protein",
"Health/Disease"
]
},
"nbdc00500": {
"alt_name": "Human Meiotic Recombination Hot Spots",
"description": "HUMHOT is a database of human recombination hot spots. The database collects information where meiotic recombination occurs frequently into different categories. Hot spots can be searched by position or locus name, and general features of hotspots are provided.",
"homepage": "http://www.jncasr.ac.in/humhot/menuframe.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Jawaharlal Nehru Centre for Advanced Scientific Research",
"name": "HUMHOT",
"prefix": "NBDC00500",
"pubmeds": [
"16381857"
],
"status": "Inactive",
"target_keywords": [
"DNA"
]
},
"nbdc00501": {
"alt_name": "integrated Clinical Omics Database",
"description": "iCOD is an integrated database of medical cases and clinical omics data maintained by Tokyo Medical and Dental University Hospital Faculty of Medicine. The English version of this database contains case information of hepatic carcinoma based on clinical, pathological, and environmental data. This database provides the 2-dimensional-3-layered (2D-3L) map to analyze the correlation between pathology and genes. Users can search cases and disease genes by keywords, and restrict search results of cases by selecting categories of metadata.",
"homepage": "http://omics.tmd.ac.jp/icod_pub_eng/portal/top.do",
"information_keywords": [
"Expression",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Tokyo Medical and Dental University",
"name": "iCOD",
"prefix": "NBDC00501",
"pubmeds": [
"21143802"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Cell/Organelle"
]
},
"nbdc00502": {
"description": "IES MDS Database is a database which characterizes sequence dynamics in Spirotrichea. The database contains information on the sequences that are eliminated and rearranged during the process of genetic rearrangement in the lifecycle of these ciliates. Users can search by organism or gene name to retreive dynamic sequences.",
"homepage": "https://knot.math.usf.edu/mds_ies_db/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Princeton University",
"name": "IES MDS Database",
"prefix": "NBDC00502",
"pubmeds": [
"14751966",
"15552058",
"15258807"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00503": {
"alt_name": "International Gene Trap Consortium",
"description": "IGTC is a public library of gene trap insertions that can be used to analyse gene function in mice. It contains gene trap cell lines which are distributed on a non-collaborative basis for nominal handling fees. Users are able to determine if the IGTC has trapped your gene or locus of interest using the BLAST search function to align your sequence to our database of trapped genes and cell line sequences. This database allows to search based on keywords or expression profile.",
"homepage": "http://www.genetrap.org/",
"information_keywords": [
"Bioresource",
"Sequence",
"Expression",
"Image/Movie"
],
"maintainer": "International Gene Trap Consortium",
"name": "IGTC",
"prefix": "NBDC00503",
"pubmeds": [
"16381950"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Cell/Organelle"
]
},
"nbdc00504": {
"alt_name": "the Internatinal Mouse Strain Resource",
"description": "IMSR is a database of mouse strains. The database contains information on available mutant and wild type strains, stocks, and ES cell lines. Users can search available resources by strain state and type, repository, and filter by mutation type. Results indicate specifics of strains, references to primary literature, and provide contact information which can be used to obtain the strain or line.",
"homepage": "http://www.findmice.org/",
"information_keywords": [
"Bioresource"
],
"maintainer": "The Jackson Laboratory, Medical Research Council",
"name": "IMSR",
"prefix": "NBDC00504",
"pubmeds": [
"15619965",
"10098412"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc00505": {
"alt_name": "The Intein Database and Registry",
"description": "InBase is a database of spliced proteins. The database contains sequences of proteins which are cleaved and bonded after being translated. The database consists of a registry of 'inteins' across several species and extensive information about the features of spliced proteins and process of protein splicing.",
"homepage": "http://www.inteins.com",
"information_keywords": [
"Sequence"
],
"maintainer": "New England Biolabs Inc.",
"name": "InBase",
"prefix": "NBDC00505",
"pubmeds": [
"11752343"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00506": {
"description": "Info-PubMed is a tool for searching the MEDLINE literature database. The site provides a Java applet with several windows for searching, examining, and organizing the literature. Requires Java, so may not work with some browsers.",
"homepage": "http://www-tsujii.is.s.u-tokyo.ac.jp/info-pubmed/",
"information_keywords": [
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "The University of Tokyo The Graduate School of Information Science and Technology",
"name": "Info-PubMed",
"prefix": "NBDC00506",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein",
"Health/Disease"
]
},
"nbdc00507": {
"description": "IntAct is a database of molecular interactions. The database contains information on more than 400,000 interactions gathered from primary literature. Users can search by gene, protein, or publication, among others, and the database includes manually annotated data from several other interaction databases. Software and bulk data, updoated weekly, are also available for download.",
"fairsharing": "biodbcore-000054",
"homepage": "http://www.ebi.ac.uk/intact/main.xhtml",
"information_keywords": [
"Interaction/Pathway",
"Repository"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "IntAct",
"prefix": "NBDC00507",
"pubmeds": [
"19850723",
"22121220"
],
"status": "Active",
"target_keywords": [
"Protein",
"Metabolite"
]
},
"nbdc00508": {
"alt_name": "Integrated relational Enzyme database",
"description": "IntEnz is a resource for enzymatic nomenclature. The site contains information on naming conventions based on the interantional standards for enzyme classification. Users can browse classifications by type, access standard definitions, submit entries, and download entry data in several formats.",
"fairsharing": "biodbcore-000314",
"homepage": "http://www.ebi.ac.uk/intenz/index.jsp",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Repository"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "IntEnz",
"prefix": "NBDC00508",
"pubmeds": [
"14681451"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc00509": {
"description": "International HapMap Project is a database of genes associated with human disease and response to pharmaceuticals. It contains genotypes, frequencies, linkage disequilibrium properties, phasing data, allocated SNPs, recombination rates and hotspot, SNP assays, perlegen amplicons, raw data, inferred genotypes and haplogroups of mitochondrial and chrY. Users are able to use the generic Genome Browser to view HapMap Project data in the context of other genomic features, as well as retrieve genotypes and frequencies for specific genomic regions. In this database, many data, software, and documentation have been made publicly available.",
"homepage": "http://hapmap.ncbi.nlm.nih.gov/",
"information_keywords": [
"Sequence"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "International HapMap Project",
"prefix": "NBDC00509",
"status": "Closed",
"target_keywords": [
"Genetic variation",
"Health/Disease"
]
},
"nbdc00510": {
"description": "IS FINDER is a database of bacterial and archaeal insertion sequences. The database contains sequence and position information on insertion elements. Links to external databases are provided for each entry.",
"fairsharing": "biodbcore-000296",
"homepage": "http://www-is.biotoul.fr/",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "Laboratoire de Microbiologie et Genetique Moleculaire",
"name": "IS FINDER",
"prefix": "NBDC00510",
"pubmeds": [
"16381877"
],
"status": "Active",
"target_keywords": [
"DNA"
]
},
"nbdc00511": {
"alt_name": "INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY",
"description": "IUBMB Nomenclature is a database of enzyme nomenclature standards. The site contains specific information on standard naming and classification of enzymes based on internationally recognized standards. Classifications for other (non-enzymatic) proteins are also indicated.",
"homepage": "https://www.qmul.ac.uk/sbcs/iubmb/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "University of London",
"name": "IUBMB Nomenclature",
"prefix": "NBDC00511",
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Protein"
]
},
"nbdc00513": {
"description": "J. Craig Venter Institute is the website of a major genome biology laboratory. The site contains informaton about the Institute and projects being conducted there, inculding programs focused on mammalian genomics, microbial and environmental genomics, infectious disease, synthetic biology, and informatics. News about and results of several projects are provided. It contains following databases:\n1) Castor Bean Database (http://castorbean.jcvi.org/index.php)\n2) Medicago truncatula Genome Database (https://www.jcvi.org/medicago-truncatula-genome-database) \n3) Forensics Microbiome Database (http://fmd.jcvi.org)",
"homepage": "http://www.jcvi.org/",
"information_keywords": [
"Portal"
],
"maintainer": "JCVI (J. Craig Venter Institute)",
"name": "J. Craig Venter Institute",
"prefix": "NBDC00513",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc00516": {
"description": "Japanese Ant Image Database is an image database of ant species recorded in Japan. Each entry contains images with scale bars, the scientific and Japanese names, description, a distribution map, remarks and references. Users can search ant genera and species from distribution regions in Japan, regional commonness and rarity, or name indexes. This database also provides the menu for beginners, such as Gakken's Photo Encyclopedia 'Ants', terminology for myrmecology and information on type specimens of Japanese ants.",
"homepage": "http://ant.miyakyo-u.ac.jp/E/index.html",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie",
"Taxonomy"
],
"maintainer": "Miyagi University of Education",
"name": "Japanese Ant Image Database",
"prefix": "NBDC00516",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00517": {
"alt_name": "Japan Consortium for Glycobiology and Glycotechnology Database",
"description": "JCGGDB is a portal database of all glycan-related data in Japan. It contains information of large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals. It allows to search by keywords, glycan structure, cheminformatics, infection, disease or experimental protocols.",
"homepage": "https://jcggdb.jp/index_en.html",
"information_keywords": [
"Chemical structure"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "JCGGDB",
"prefix": "NBDC00517",
"status": "Active",
"target_keywords": [
"Health/Disease",
"Carbohydrate",
"Chemical compound"
]
},
"nbdc00518": {
"description": "The JCRB Cell Bank database organizes information for distribution of cell cultures. Information is available on how to order, culture, and preserve cells.",
"homepage": "http://cellbank.nibiohn.go.jp/english/",
"information_keywords": [
"Bioresource"
],
"maintainer": "National Institutes of Biomedical Innovation, Health and Nutrition",
"name": "JCRB Cell Bank",
"prefix": "NBDC00518",
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc00519": {
"alt_name": "Jena Library of Biological Macromolecules",
"description": "JenaLib is a database of molecular structures. The database contains solved structures biopolymers, including homogenous and heterogenous entities. The database contains several subsections based on constituent molecules, with links to PDB structures for each biopolymer. The database also contains tools for domain classification and structural analysis.",
"homepage": "http://jenalib.fli-leibniz.de",
"information_keywords": [
"Image/Movie",
"3D structure"
],
"maintainer": "FLI (Fritz Lipmann Institute)",
"name": "JenaLib",
"prefix": "NBDC00519",
"pubmeds": [
"8872391",
"10592237",
"11752308",
"9154005"
],
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Protein"
]
},
"nbdc00520": {
"alt_name": "Kazusa Full-length Tomato cDNA Database",
"description": "KaFTom is a database of tomato expressed sequences. The database contains EST reads from several different tissues of the MicroTom cultivar. Data were obtained by sequencing cDNA clones and are available for browsing, BLAST search, and bulk download.",
"homepage": "http://www.pgb.kazusa.or.jp/kaftom/",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "KaFTom",
"prefix": "NBDC00520",
"pubmeds": [
"20350329",
"15975739",
"15975739"
],
"status": "Closed",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00521": {
"description": "This database contains two-dimensional electrophoretic (proteome) information for the silkworm. Spot information depending on tissues or developmental stage can be searched by keywords and image selections.",
"homepage": "http://kaiko2ddb.dna.affrc.go.jp/cgi-bin/search_2DDB.cgi",
"information_keywords": [
"Image/Movie"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "KAIKO Proteome Database",
"prefix": "NBDC00521",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00522": {
"description": "This database contains both the genetic and physical map information for the silkworm genome. A variety of viewers are available to graphically view markers, genes, and genomic positions of traits, as well as annotation information. Additionally, BLAST searches can be performed with user-provided sequences against the silkworm genome sequence. This is a part of SILKWORM GENOME RESEARCH PROGRAM (http://integbio.jp/dbcatalog/en/record/nbdc00950).",
"homepage": "http://sgp.dna.affrc.go.jp/KAIKObase/",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "KAIKObase",
"prefix": "NBDC00522",
"pubmeds": [
"19843344"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00523": {
"description": "This is a system to allow BLAST searches of silkworm DNA and amino acid sequences. The BLAST searches can be performed with user-provided sequences against silkworm sequences. This is a part of SILKWORM GENOME RESEARCH PROGRAM (http://integbio.jp/dbcatalog/en/record/nbdc00950).",
"homepage": "http://kaikoblast.dna.affrc.go.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "KAIKOBLAST",
"prefix": "NBDC00523",
"status": "Suspended",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00524": {
"alt_name": "KAIKO Genome Automated Annotation System",
"description": "This is a system that automatically predicts gene structures coding for proteins using existing silkworm genomic sequences. The predictions are made by combining the analytical results of several tools (geneScan, FgeneSH, HMMER). Users can browse previous predictions and input their own sequences for new predictions. This is a part of SILKWORM GENOME RESEARCH PROGRAM (http://integbio.jp/dbcatalog/en/record/nbdc00950).",
"homepage": "http://kaikogaas.dna.affrc.go.jp",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "KAIKOGAAS",
"prefix": "NBDC00524",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00525": {
"alt_name": "Kazusa Plant Pathway Viewer",
"description": "This web-based tool, KaPPA-View4, represents -omics data on plant metabolic pathway maps that users upload. Differences in gene expressions and metabolite accumulation between samples are visually represented as hue of the gene and metabolite symbols. gene-to-gene and metabolite-to-metabolite relationships, including correlation coefficients of gene co-expressions can be overlayed on the pathway maps. This helps to better understand transcripts and metabolites when examining the roles of genes in the metabolic pathway. The system has been revised, and the processing speed was improved compared to previous versions. Both Windows and Mac OS X are fully supported now and all features of the database are available. Users can use their own metabolic pathway maps for analyses. After uploading DNA microarray or metabolite data, fitting data for each gene or compound is displayed on a metabolic pathway map.",
"homepage": "http://kpv.kazusa.or.jp/en/",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "KaPPA-View 4",
"prefix": "NBDC00525",
"pubmeds": [
"16010003",
"21097783"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Protein",
"Metabolite"
]
},
"nbdc00526": {
"alt_name": "Kazusa Arabidopsis thaliana Annotation Abstract",
"description": "KATANA (Kazusa Arabidopsis thaliana Annotation Abstract) is a guide to help in the search of Arabidopsis genomic information in concerned public databases, because naming conventions and gene annotations may be different between different databases. It can be searched by annotation ('ANNOME'), metabolic pathway or gene ontology and is linked to detailed information at the original sites. It is part of the 'Green Biotechnology Program' supported by New Energy and Industrial Technology Development (NEDO).",
"homepage": "http://www.kazusa.or.jp/katana/index.html",
"maintainer": "Kazusa DNA Research Institute",
"name": "KATANA",
"prefix": "NBDC00526",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00528": {
"description": "KazusaMart is a data integration system of plant and microbial genomic data and was developed using BioMart.",
"homepage": "http://mart.kazusa.or.jp/biomart/martview",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "KazusaMart1.0",
"prefix": "NBDC00528",
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00529": {
"alt_name": "Kyoto Chlamydomonas Genome Database",
"description": "This is a genome database for the green algae Chlamydomonas. Users are required to contact the database maintainer. Chlorophyll DNA was first discovered in Chlamydomonas, and is used worldwide as a model organism for genetic research on photosynthesis, reproduction, and flagellar motors, because it allows DNA transformation between chlorophyll, mitochondrial, and nuclear genomes.",
"homepage": "http://www.molecule.lif.kyoto-u.ac.jp/kcgd.html",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Kyoto University Graduate School of Biostudies",
"name": "KCGD",
"prefix": "NBDC00529",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc00530": {
"alt_name": "Kyoto Encyclopedia of Genes and Genomes",
"description": "KEGG is an integrated database for interpretation of biological systems from genomic and molecular-level information. KEGG consists of 16 main databases categorized into systems information, genomic information and chemical information. This database features to map elementary datasets (genes, small molecules, etc) in each KEGG database to network datasets (pathway maps, hierarchical lists, etc). Users can perform keyword search against the entire KEGG database, as well as BLAST/FASTA search and SIMCOMP search.",
"fairsharing": "biodbcore-000663",
"homepage": "http://www.kegg.jp/kegg/",
"information_keywords": [
"Portal"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG",
"prefix": "NBDC00530",
"pubmeds": [
"9287494",
"16381885",
"14681412",
"24214961"
],
"status": "Active"
},
"nbdc00531": {
"alt_name": "KEGG Distributed Annotation System",
"homepage": "http://keggdas.hgc.jp",
"maintainer": "The University of Tokyo The Institute of Medical Science Human Genome Center",
"name": "KEGG DAS",
"prefix": "NBDC00531",
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00532": {
"alt_name": "Molecular building blocks of life in the genomic space",
"description": "KEGG geneS is a catalog of gene information for multiple species with species-specified gene information for all species with complete genome sequences. The database references primary sources and provides pathway, ortholog, paralog, and motif searching functions. Results of gene searches include nucleotide and protein information.",
"homepage": "http://www.genome.jp/kegg/genes.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG GENES Database",
"prefix": "NBDC00532",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00533": {
"alt_name": "Glycome informatics resource integrating genomics and chemistry",
"description": "KEGG GLYCAN is a database of glycan structures. The database contains structures of glycans involved in KEGG reactions and specifies several parameters of the glycans, as well as collecting links to other glycan-relevant databases. The database is searchable by KEGG G-index ID.",
"homepage": "http://www.genome.jp/kegg/glycan/",
"information_keywords": [
"Interaction/Pathway",
"Chemical structure"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG GLYCAN",
"prefix": "NBDC00533",
"pubmeds": [
"16014746",
"16362924",
"19327755",
"15215393",
"16159923",
"18546491"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein",
"Carbohydrate"
]
},
"nbdc00534": {
"alt_name": "Biochemical Compounds Declarative Database",
"homepage": "http://www.biocheminfo.org/klotho",
"information_keywords": [
"Chemical structure"
],
"maintainer": "University of Missouri Bioinformatics Consortium",
"name": "Klotho",
"prefix": "NBDC00534",
"status": "Active"
},
"nbdc00535": {
"alt_name": "Keio Mutation autoimmune database",
"description": "KMaiDB is a database of mutations involved in autoimmune disorders, assembled by manual curation of OMIM. A Java browser of mutations known to be involved in disease can be used to browse chromosomes to find disease-associated genes or genes to find causative mutations.",
"homepage": "http://www.mutationview.jp/MutationView/jsp/mutview/index.jsp?db=ai",
"information_keywords": [
"Sequence"
],
"maintainer": "Keio University School of Medicine",
"name": "KMaiDB",
"prefix": "NBDC00535",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00536": {
"alt_name": "Keio Mutation blood database",
"description": "KMbloodDB is a database of mutations involved in blood disorders. The database contains a Java browser of mutations known to be involved in disease and was assembled by manual curation of OMIM. Users can browse chromosomes to find disease-associated genes or genes to find causative mutations.",
"homepage": "http://www.mutationview.jp/MutationView/jsp/mutview/index.jsp?db=blood",
"information_keywords": [
"Sequence"
],
"maintainer": "Keio University School of Medicine",
"name": "KMbloodDB",
"prefix": "NBDC00536",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00537": {
"alt_name": "Keio Mutation brain database",
"description": "KMbrainDB is a database of mutations involved in neurological disease with a Java browser of mutations known to be involved in disease. It was assembled by manual curation of OMIM. Users can browse chromosomes to find disease-associated genes or genes to find causative mutations.",
"homepage": "http://www.mutationview.jp/MutationView/jsp/mutview/index.jsp?db=brain",
"information_keywords": [
"Sequence"
],
"maintainer": "Keio University School of Medicine",
"name": "KMbrainDB",
"prefix": "NBDC00537",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00538": {
"alt_name": "Keio Mutation cancer database",
"description": "KMcancerDB is a database of mutations involved in various cancers. The database contains a Java browser of mutations known to be involved in disease and was assembled by manual curation of OMIM. Users can browse chromosomes to find disease-associated genes or genes to find causative mutations.",
"homepage": "http://www.mutationview.jp/MutationView/jsp/mutview/index.jsp?db=cancer",
"information_keywords": [
"Sequence"
],
"maintainer": "Keio University School of Medicine",
"name": "KMcancerDB",
"prefix": "NBDC00538",
"pubmeds": [
"17233812"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00539": {
"alt_name": "Keio Mutation Databases",
"description": "KMDB is a database of human mutations. The site has html and java functionalities to explore mutations affecting several anatomical systems as well as sub-databases for each anatomical system. The Java functionality is extensively linked such that users can choose organ, disease, or gene and obtain information on published connections between genes and diseases. Causative mutations and gene structures are also available. MutationView software can also be downloaded. For academic use only.",
"homepage": "http://www.mutationview.jp/MutationView/jsp/index.jsp",
"information_keywords": [
"Sequence"
],
"maintainer": "Keio University",
"name": "KMDB/MutationView",
"prefix": "NBDC00539",
"pubmeds": [
"12762231",
"11125127",
"10592275"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00540": {
"alt_name": "Keio Mutation ear database",
"description": "KMearDB is a database of mutations involved in auditory disorders. It contains a Java browser of mutations known to be involved in disease and was assembled by manual curation of OMIM. Users can browse chromosomes to find disease-associated genes or genes to find causative mutations.",
"homepage": "http://www.mutationview.jp/MutationView/jsp/mutview/index.jsp?db=ear",
"information_keywords": [
"Sequence"
],
"maintainer": "Keio University School of Medicine",
"name": "KMearDB",
"prefix": "NBDC00540",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00541": {
"alt_name": "Keio Mutation eye database",
"description": "KMeyeDB is a database of mutations involved in vision disorders and contains a Java browser of mutations known to be involved in disease. It was assembled by manual curation of OMIM. Users can browse chromosomes to find disease-associated genes or genes to find causative mutations.",
"homepage": "http://www.mutationview.jp/MutationView/jsp/mutview/index.jsp?db=eye",
"information_keywords": [
"Sequence"
],
"maintainer": "Keio University School of Medicine",
"name": "KMeyeDB",
"prefix": "NBDC00541",
"pubmeds": [
"20232414",
"10612828",
"9847228"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00542": {
"alt_name": "Keio Mutation heart database",
"description": "KMheartDB is a database of mutations involved in heart disease assembled by manual curation of OMIM. The database contains a Java browser of mutations known to be involved in disease. Users can browse chromosomes to find disease-associated genes or genes to find causative mutations.",
"homepage": "http://www.mutationview.jp/MutationView/jsp/mutview/index.jsp?db=heart",
"information_keywords": [
"Sequence"
],
"maintainer": "Keio University School of Medicine",
"name": "KMheartDB",
"prefix": "NBDC00542",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00543": {
"alt_name": "Keio Mutation muscle database",
"description": "KMmuscleDB is a database of mutations involved in muscular disorders, with a Java browser of mutations known to be involved in disease. The database was assembled by manual curation of OMIM. Users can browse chromosomes to find disease-associated genes or genes to find causative mutations.",
"homepage": "http://www.mutationview.jp/MutationView/jsp/mutview/index.jsp?db=muscle",
"information_keywords": [
"Sequence"
],
"maintainer": "Keio University School of Medicine",
"name": "KMmuscleDB",
"prefix": "NBDC00543",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00544": {
"alt_name": "Keio Mutation syndrome database",
"description": "KMsyndromeDB is a database of mutations involved in syndromic diseases. The database contains a Java browser of mutations known to be involved in disease. It was assembled by manual curation of OMIM. Users can browse chromosomes to find disease-associated genes or genes to find causative mutations.",
"homepage": "http://www.mutationview.jp/MutationView/jsp/mutview/index.jsp?db=syndrome",
"information_keywords": [
"Sequence"
],
"maintainer": "Keio University School of Medicine",
"name": "KMsyndromeDB",
"prefix": "NBDC00544",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00545": {
"alt_name": "A Comprehensive Species-Metabolite Relationship Database",
"description": "This database provides information on how species and metabolites relate to each other.\nSearches can be done on the Web by entering the organism's name or that of the metabolite or its molecular weight or formula.\nThe site also offers the option to download the database and work offline.",
"homepage": "http://www.knapsackfamily.com/KNApSAcK/",
"information_keywords": [
"Bibliography/Documents",
"Chemical structure"
],
"maintainer": "Nara Institute of Science and Technology",
"name": "KNApSAcK",
"prefix": "NBDC00545",
"pubmeds": [
"22123792"
],
"status": "Active",
"target_keywords": [
"Metabolite",
"Chemical compound"
]
},
"nbdc00546": {
"alt_name": "Kazusa ORFeome Project",
"description": "KOP is a database of human ORF clones data with two collections of clones that can be used for functional studies and a list of genes grouped by function. Clones are chosen based on the KIAA human ORF set and are available for order.",
"homepage": "http://www.kazusa.or.jp/kop/",
"information_keywords": [
"Bioresource",
"Sequence",
"Image/Movie"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "KOP",
"prefix": "NBDC00546",
"pubmeds": [
"16769670",
"18316326",
"16769688"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Protein",
"Health/Disease"
]
},
"nbdc00547": {
"alt_name": "Annotation of Full-Length, Intact L1 Element",
"description": "L1Base is a database of mobile elements in the human genome. The database contains position and activity information on L1 elements annotated from human genome sequences. T",
"homepage": "http://l1base.charite.de/l1base.php",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Wurzburg",
"name": "L1Base",
"prefix": "NBDC00547",
"pubmeds": [
"15608246",
"17963496"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00548": {
"description": "Labome.Org is a database organizing biomedical knowledge. It contains information of grants, publications, and patents around research topics, genomes and genes, scientific experts, and species for easy browsing and searching.",
"homepage": "http://www.labome.org/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "National Center for Biotechnology Information, Computer Retrieval of Information on Scientific Projects, United States Patent and Trademark Office",
"name": "Labome.Org",
"prefix": "NBDC00548",
"status": "Inactive"
},
"nbdc00550": {
"alt_name": "Life Science Database Archive",
"description": "Life Science Database Archive is an archive of databases generated by life scientists in Japan as national public goods. This archive contains databases deposited from research institutions with metadata in a unified format to search datasets easily. Users can search for datasets across metadata and databases and perform BLAST search, as well as download the whole datasets with clear terms of use.",
"fairsharing": "biodbcore-000801",
"homepage": "https://dbarchive.biosciencedbc.jp/index-e.html",
"information_keywords": [
"Portal",
"Repository"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "LSDB Archive",
"prefix": "NBDC00550",
"status": "Active"
},
"nbdc00551": {
"alt_name": "LIGANDs Data Base Open and eXtensible",
"description": "LigandBox is a database of small chemical compounds for drug screening on computer docking studies. This database contains 3D molecular structures produced by calculation based on 2D structural data of chemicals those are provided by companies and KEGG databases. Users can search chemical compounds by structural information, physical quantity, as well as keywords.",
"homepage": "http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en",
"information_keywords": [
"3D structure"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "LigandBox",
"prefix": "NBDC00551",
"pubmeds": [
"27493549"
],
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc00552": {
"description": "This database of Lotus japonicus expressed sequences contains consensus gene sequences and EST reads, and allows for BLAST and keyword search. Data are available for download.",
"homepage": "https://www.kazusa.or.jp/e/plant/lotus/EST/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Lotus japonicus (miyakogusa) EST dataset",
"prefix": "NBDC00552",
"pubmeds": [
"15915647",
"11089912",
"15284495",
"10819328",
"10907852"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Protein"
]
},
"nbdc00553": {
"description": "This is a database specifically for mutations in the OCRL1 gene, known to cause Lowe syndrome with primary symptoms such as congenital cataracts, mental retardation, and renal tubular acidosis. \nThis site was retired, and all data were transfered to the ClinVar (http://integbio.jp/dbcatalog/en/record/nbdc01514).",
"homepage": "http://research.nhgri.nih.gov/lowe/",
"information_keywords": [
"Sequence"
],
"maintainer": "National Human Genome Research Institute, National Institute of Health",
"name": "Lowe Syndrome Mutation Database",
"prefix": "NBDC00553",
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein",
"Health/Disease"
]
},
"nbdc00554": {
"alt_name": "Life Science DataBase",
"description": "LSDB is a portal site for the 'Integrated Database Project', which aims to improve usability and integration of Japan's life science databases. This portal site contains database portals, research tools, resources and databases for life science research. Users can search for appropriate databases using database portals ('Life science projects in Japan' and 'Database Catalog'), as well as browse protocols and video tutorials of these contents.",
"homepage": "http://lifesciencedb.jp/?lng=en",
"information_keywords": [
"Portal"
],
"maintainer": "DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "LSDB",
"prefix": "NBDC00554",
"status": "Active"
},
"nbdc00555": {
"alt_name": "Medaka Genome Database",
"description": "M Base is a database of Medaka genome resources. It contains links to EST sequence data, a linkage map, and BAC clones. Users can BLAST search the EST and BAC databases, and determine linkage from a variety of crosses.",
"homepage": "http://mbase.nig.ac.jp/mbase/medaka_top.html",
"information_keywords": [
"Sequence"
],
"maintainer": "National Institute of Genetics",
"name": "M Base",
"prefix": "NBDC00555",
"status": "Active",
"target_keywords": [
"cDNA/EST",
"DNA"
]
},
"nbdc00556": {
"alt_name": "A Drosophila Melanogaster 5'-end mRNA Transcription Database",
"description": "MachiBase is a browser for the Drosophila genome. Users can search by location or keyword, and a highly customizable display is provided. Sequences were collected by 5' SAGE analysis. Bulk data is available for download.",
"homepage": "http://machibase.gi.k.u-tokyo.ac.jp/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "The University of Tokyo Graduate School of Frontier Sciences",
"name": "MachiBase",
"prefix": "NBDC00556",
"pubmeds": [
"18842623"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00557": {
"description": "This is a database of expression analysis for Bradyrhizobium japonicum, containing gene expression data in response to various treatment conditions. A link to the original publication is also available.",
"homepage": "http://orca10.bio.sci.osaka-u.ac.jp/array02/",
"information_keywords": [
"Expression"
],
"maintainer": "Osaka University Graduate School of Science",
"name": "MacroArray Analysis Page of Bradyrhizobium japonicum",
"prefix": "NBDC00557",
"pubmeds": [
"18511436"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00558": {
"description": "The Macrophage Curated Database Index is a database of primary literature pertaining to macrophage functionality. It is a searchable list of macrophage papers and provides links to the original publications and contains links to several studies of macrophages and features images for relevant pathways from each paper.",
"homepage": "http://gnp.hgc.jp/macrophage/",
"information_keywords": [
"Expression",
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "The University of Tokyo The Institute of Medical Science",
"name": "Macrophage Curated Database Index",
"prefix": "NBDC00558",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle"
]
},
"nbdc00559": {
"description": "Makino Herbarium Type Specimen Image Database is a database of plant type specimens based on the collection preserved at the Makino Herbarium in Tokyo Metropolitan University. Each record consists of digital images of type specimens and 13 items including scientific names, location data, type status, etc. Users can search type specimens by family names, type names, current scientific names, specimen IDs and locations. This database also provides the thumbnail list of type specimens sorted by family names.",
"homepage": "http://ameba.i.hosei.ac.jp/BIDP/MakinoCD/makino/html_e/index0.html",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie",
"Taxonomy"
],
"maintainer": "Tokyo Metropolitan University",
"name": "Makino Herbarium Type Specimen Image Database",
"prefix": "NBDC00559",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00560": {
"alt_name": "Mammalian Crania Photographic Archive Second Edition",
"description": "MCPA2 is a collection of 10,956 photographs of mammalian crania, which have been taken with a high-resolution digital camera. Each entry contains photographs from six different angles (anterior, posterior, left, right, superior, and inferior) with caliper measurements and information (taxonomy, sex, and age). Some entries also contains photographs of crania with the mandible (only Primates) or pictures of living mammals. This database allows to browse data using phylogenetic table, Japanese name, English name, scientific name, or the order and genus lists. It provides pictures via FTP, specimens' text information and measurements, and current HTML data for this site except image files for downloads.",
"homepage": "https://dept.dokkyomed.ac.jp/dep-m/macro/mammal/en/mammal.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Dokkyo Medical University",
"name": "MCPA2",
"prefix": "NBDC00560",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00561": {
"alt_name": "Multi-document Clustering System for Biomedicine",
"description": "McSyBi is a site for searching related literature. The site consists of a search function that queries a database of clustered literature references. Users can query by PMID. Not all papers are represented.",
"homepage": "http://textlens.hgc.jp/McSyBi/index.html",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "The University of Tokyo The Institute of Medical Science Human Genome Center",
"name": "McSyBi",
"prefix": "NBDC00561",
"pubmeds": [
"16996316"
],
"status": "Inactive",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00562": {
"alt_name": "Metalloprotein Database and Browser",
"homepage": "http://metallo.scripps.edu",
"information_keywords": [
"Image/Movie",
"3D structure"
],
"maintainer": "The Scripps Research Institute",
"name": "MDB",
"prefix": "NBDC00562",
"pubmeds": [
"11752342"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00564": {
"alt_name": "METI database portal for life science",
"description": "This site is a portal providing access to a large number of integrated Life Science databases.\nIts construction and maintenance is made possible by the financial support from the Ministry of Economy, Trade and Industry (METI), JAPAN.\nAn advanced search option is provided.\nTwo manuals and fourteen project reports are available for download.\nMEDALS (the name of the site) is an anagram for MEti DAtabase portal for Life Science.",
"homepage": "http://medals.jp/etop",
"information_keywords": [
"Bibliography/Documents",
"Portal"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "MEDALS",
"prefix": "NBDC00564",
"status": "Active"
},
"nbdc00565": {
"description": "MEDIE is a tool for data mining published literature. The site provides search prompts and examples for users to obtain experimentally validated connections from the MEDLINE literature database. Users provide simple semantic search terms and MEDIE provides references regarding the search.",
"homepage": "http://www.nactem.ac.uk/medie/index.cgi",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Bibliography/Documents"
],
"maintainer": "The University of Tokyo The Graduate School of Information Science and Technology",
"name": "MEDIE",
"prefix": "NBDC00565",
"status": "Inactive"
},
"nbdc00566": {
"alt_name": "the Peptidase Database",
"description": "MEROPS is a database of peptidases. The database contains peptidases from multiple species grouped by sequence-similarity families. The database also contains information on proteins known to inhibit peptidases. Users can search by protein or gene name, identifier, organism, substrate, or sequence by BLAST. The database is also available for download.",
"fairsharing": "biodbcore-000514",
"homepage": "http://merops.sanger.ac.uk",
"information_keywords": [
"Sequence",
"3D structure",
"Classification"
],
"maintainer": "Wellcome Sanger Institute",
"name": "MEROPS",
"prefix": "NBDC00566",
"pubmeds": [
"17991683",
"22086950"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00567": {
"alt_name": "the database for DNA methylation and environmental epigenetic effects",
"description": "MethDB is a database providing a resource to store DNA methylation data and to make these data readily available to the public. It contains information about the occurrence of methylated cytosines in the DNA and as much background information which includes the origin of the sample, phenotype, expression of the related gene, etc.. Analysis tools are not included, but external tools are available and users are invited to develop further software for the analysis of methylation patterns.",
"homepage": "http://www.methdb.de/",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "MethDB team",
"name": "MethDB",
"prefix": "NBDC00567",
"status": "Active",
"target_keywords": [
"DNA"
]
},
"nbdc00568": {
"alt_name": "Medaka Genome Initiative",
"description": "MGI is a website of Medaka genome studies. The site has links to various projects, some of which are published papers and some of which can be searched and browsed further to obtain sequence and genome mapping information.",
"homepage": "http://park.itc.u-tokyo.ac.jp/K-medaka/MGI2/MGI.html",
"maintainer": "The University of Tokyo Graduate School of Frontier Sciences",
"name": "MGI",
"prefix": "NBDC00568",
"pubmeds": [
"15602912"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00570": {
"alt_name": "Micro-Tom Database",
"description": "MiBASE is a database of sequence and expression information for the tomato cultivar Micro-Tom. The database contains cDNA clone sequences, gene pathway information, gene expression profiles, and Unigene and BLAST search tools for genes and sequences, respectively. The database consists of separate modules for each means of exploring Micro-Tom data. Bulk data is also available for download.",
"homepage": "http://www.pgb.kazusa.or.jp/mibase/",
"information_keywords": [
"Bioresource",
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "MiBASE",
"prefix": "NBDC00570",
"pubmeds": [
"20350329",
"15975739"
],
"status": "Closed",
"target_keywords": [
"cDNA/EST",
"Genetic variation"
]
},
"nbdc00571": {
"alt_name": "The miR-Ontology Knowledgebase",
"description": "miRO is a database of microRNA information. The database contains entries for miRNAs, target genes, tissue expression, and other functional information. Users can search or use several miRNA tools inculding reverse translation of proteins to gene sequences and miRNA network targets.",
"homepage": "http://microrna.osumc.edu/miro/",
"information_keywords": [
"Phenotype"
],
"maintainer": "The Ohio State University Wexner Medical Center",
"name": "miRo2",
"prefix": "NBDC00571",
"pubmeds": [
"20157481"
],
"status": "Inactive",
"target_keywords": [
"RNA",
"Health/Disease"
]
},
"nbdc00572": {
"alt_name": "Mendelian Inheritance and the Mitochondrion",
"homepage": "http://www.ccrnp.ncifcrf.gov/mitoDat/",
"maintainer": "Center for Cancer Research Nanobiology Program",
"name": "MitoDat",
"prefix": "NBDC00572",
"pubmeds": [
"8740181"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein",
"Health/Disease",
"Cell/Organelle"
]
},
"nbdc00573": {
"alt_name": "The database of molecular motions",
"description": "MolMovDB is a database of the motions that occur in proteins and other macromolecules, particularly using movies. This database classifies macromolecular motions into a limited number of categories, first on the basis of size (distinguishing between fragment, domain and subunit motions) and then on the basis of packing. Moreover, it contains tools to interpolate between two conformations (the Morph Server) and predict possible motions in a single structure and an interface to a hinge prediction service, which acts on single structures and predicts likely residue points for flexibility.",
"homepage": "http://molmovdb.org/",
"information_keywords": [
"Image/Movie",
"3D structure"
],
"maintainer": "Yale University",
"name": "MolMovDB",
"prefix": "NBDC00573",
"pubmeds": [
"9722650"
],
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Protein"
]
},
"nbdc00574": {
"description": "The Mouse Basement Membrane Bodymap is a visual database of extracellular protein localization. The database consists of high-resolution images of hundreds of mouse embryos showing the localization of dozens of extracellular matrix and basement membrane proteins. Images were obtained by IHC and users can zoom and display images using the built-in Bodymap applet.",
"homepage": "http://dbarchive.biosciencedbc.jp/archive/matrixome/bm/home.html",
"information_keywords": [
"Expression",
"Image/Movie"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "Mouse Basement Membrane Bodymap",
"prefix": "NBDC00574",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00575": {
"description": "The Mouse DNA Microarray database is a resource of gene expression data for C57BL/J6 and 129 mouse strains. The database contains gene expression profiles from brain, liver, and spleen from these two lines that are presented as lists of differentially expressed genes. The stated intention is for use as a background for transgenic mouse experiments to dissect strain-specific expression differences from changes due to transgene expression.",
"homepage": "http://www.kazusa.or.jp/DNA_Microarray/mouse/2003-B6vs129/",
"information_keywords": [
"Expression"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Mouse DNA Microarray",
"prefix": "NBDC00575",
"pubmeds": [
"15029957"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00576": {
"description": "Mouse Genome Databases is a resource for genetic and genomic mouse data. The database contains collected data files from several genome mapping projects. The available files include resources from many different mouse strains as well as tools for mapping QTLs. Users can download files in Excel and FileMaker Pro formats.",
"homepage": "http://www.nervenet.org/main/dictionary.html",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "Neurogenetics at University of Tennessee Health Science Center",
"name": "Mouse Genome Databases",
"prefix": "NBDC00576",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Organism"
]
},
"nbdc00577": {
"alt_name": "Mouse Tumor Biology Database",
"description": "MTB Database is a database of tumor biology in mice. The database contains information on experimentally induced and characterized tumors sorted by mouse strain and genetics. Users can search by tumor type and affected tissue. gene expression data sets are avaiable for download.",
"homepage": "http://tumor.informatics.jax.org/mtbwi/index.do",
"information_keywords": [
"Image/Movie"
],
"maintainer": "The Jackson Laboratory",
"name": "MTB Database",
"prefix": "NBDC00577",
"pubmeds": [
"11888882"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00578": {
"alt_name": "A portal to worldwide mutant databases",
"homepage": "http://omicspace.riken.jp/MusBanks/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "MusBanks",
"prefix": "NBDC00578",
"status": "Closed",
"target_keywords": [
"Organism"
]
},
"nbdc00579": {
"description": "MutationView is a database of mutations known to cause disease. The database contains a browser to inspect mutation loci and allows searches by gene, disease, or protein domain. The database is compiled from OMIM mutation entries.",
"homepage": "http://mutationview.jp/MutationViewV2Server/top",
"information_keywords": [
"Sequence"
],
"maintainer": "Keio University School of Medicine",
"name": "MutationView",
"prefix": "NBDC00579",
"pubmeds": [
"12762231",
"11125127",
"10592275"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00581": {
"alt_name": "National BioResource Project Bacillus subtilis",
"description": "National BioResource Project Bacillus subtilis is a database of B. subtilis knockout strains mainly established by the Ogasawara Laboratory at the Nara Institute of Science and Technology (NAIST). This database contains gene disrupted strains, strains with genomic deletion or single region deletion, genome reduced mutants and a wild strain. Users can search available resources by keywords such as strain names and related genes, as well as search B. subtilis genes using BLAST. This database provides lists of strains, the genome viewer and protocols to create mutant strains.",
"homepage": "https://shigen.nig.ac.jp/bsub/locale/change?lang=en",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "National Institute of Genetics",
"name": "NBRP Bacillus subtilis",
"prefix": "NBDC00581",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc00582": {
"description": "NBRP is a portal site of the National BioResource Project (NBRP), which aims to collect, preserve, and provide bioresources for life sciences research. Bioresources associated with NBRP consist of experimental animals, plants, microbes, cells and DNA materials. This portal site provides introduction pages of individual projects, newsletters (BioResource now!) and information on stock centers maintaining bioresources and corresponding databases. Users can search bioresources from categories of species and materials (strains or DNA clones), as well as by keywords.",
"homepage": "http://www.nbrp.jp/localeAction.do?lang=en",
"information_keywords": [
"Bioresource",
"Portal"
],
"maintainer": "National Institute of Genetics",
"name": "NBRP Information Site",
"prefix": "NBDC00582",
"status": "Active"
},
"nbdc00583": {
"alt_name": "National BioResource Project Cellular slime molds",
"description": "National BioResource Project Cellular slime molds is a database of the social amoebae (cellular slime molds, Dictyostelium discoideum) resources collected mainly from Japanese laboratories. Each entry in the strain list contains the strain name, parental strain, associated gene, mutagenesis method, use conditions and request availability. Each entry in the gene list includes the clone name, gene name, remark, use conditions and request availability. Users can search available strains or cDNA clones by keywords from those items.",
"homepage": "http://nenkin.nbrp.jp/locale/change?lang=en",
"information_keywords": [
"Bioresource"
],
"maintainer": "National Institute of Genetics",
"name": "NBRP Nenkin",
"prefix": "NBDC00583",
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Organism"
]
},
"nbdc00584": {
"alt_name": "National Center for Biotechnology Information",
"description": "NCBI is a portal site for US biological study data. The site contains links to several NIH research resources, most of which are repositories for submission of data from government-funded and/or published projects. Users can search the entire NCBI collection or perform keyword searches of a specific database from the NCBI search bar. Constituent databases contain a wealth of data for download.",
"homepage": "http://www.ncbi.nlm.nih.gov",
"information_keywords": [
"Portal",
"Bibliography/Documents",
"Taxonomy",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "NCBI",
"prefix": "NBDC00584",
"pubmeds": [
"22140104"
],
"status": "Active",
"target_keywords": [
"Health/Disease",
"Genome/Gene",
"Protein",
"Chemical compound"
]
},
"nbdc00585": {
"description": "The Rice Genome page contains information on the full genetic code for Oryza sativa. The database contains sequences from five completed and several other initiated (sequence read- or trace-only) projects. Chromosome browser, BLAST, and other related projects are also available from this genome information page.",
"homepage": "https://www.ncbi.nlm.nih.gov/genome/10",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NIH (National Institutes of Health)",
"name": "Genome - Genome information for rice",
"prefix": "NBDC00585",
"pubmeds": [
"20487381"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00586": {
"description": "NCP Mutation and Patient Database contains information on mutations which cause neuronal ceroid lipofuscinoses. The database contains information about several genes which are causative of NCL as well as resources such as lists of clinicians, researchers, and meetings regarding NCL.",
"homepage": "https://www.ucl.ac.uk/ncl-disease/mutation-and-patient-database",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "University College London",
"name": "NCL Mutation and Patient Database",
"prefix": "NBDC00586",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00587": {
"description": "RNA Bibliography is a searchable database of over 30,000 articles pertaining to RNA.",
"homepage": "http://www.ncrna.org/rna-bibliography",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "RNA Bibliography - ncRNA.org",
"prefix": "NBDC00587",
"status": "Inactive",
"target_keywords": [
"RNA"
]
},
"nbdc00588": {
"description": "This is a database of genome browser tracks relevant to RNA. The database consists of a list of RNA tracks that can be accessed by the UCSC genome browser and provides statistics and details for each track in human, mouse, rat, and Drosophila genomes.",
"homepage": "http://www.ncrna.org/custom-tracks",
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "Project Specific Custom Tracks - ncRNA.org",
"prefix": "NBDC00588",
"pubmeds": [
"18440970"
],
"status": "Inactive",
"target_keywords": [
"RNA"
]
},
"nbdc00589": {
"description": "Neal's DNA Mutation site is a resource for mutations in a select number of genes. The database contains information on characterized mutations of the human HPRT and p53 genes as well as bacterial lacZ and lacI genes. Software for mutation spectra analysis and a relational database are also available.",
"homepage": "http://www.ibiblio.org/dnam/mainpage.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Glaxo Wellcome, Inc.",
"name": "Neal's DNA Mutation Site",
"prefix": "NBDC00589",
"pubmeds": [
"9399835"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00590": {
"description": "Neuraminidase Structure DB is a database of the predicted three-dimensional structures of neuraminidase which is a target protein for the development of anti-influenza drugs. This database contains information on predicted three-dimensional structures of neuraminidase, which are predicted with homology modeling method of Full Automatic Modeling System (FAM; a system developed by Dr. Umeyama, Senior Visiting Scientist at RIKEN/Professor at Kitasato University). Neuraminidases are classified into 9 subtypes (N1 to N9). The database provides 1603 three-dimensional models of all subtypes of the protein.",
"homepage": "http://protein.gsc.riken.jp/Research/index_na.html",
"information_keywords": [
"3D structure"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "Neuraminidase Structure DB",
"prefix": "NBDC00590",
"pubmeds": [
"16187353"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Health/Disease"
]
},
"nbdc00591": {
"description": "INCF Japan Node is a repository for neuroinformatics; neuroscience and information science maintained by RIKEN Brain Science Institute (RIKEN BSI). This repository consists of documents and links related to neuroinformatics. Some documents are only available in Japanese. Users can search within the website by keywords, and download document flies.",
"homepage": "https://www.neuroinf.jp/?ml_lang=en",
"information_keywords": [
"Portal"
],
"maintainer": "Neuroinformatics Unit, RIKEN Center for Brain Science",
"name": "INCF Japan Node",
"prefix": "NBDC00591",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00592": {
"description": "New Natural Compounds purified in RIKEN is a database of new compounds isolated from microorganisms in the Antibiotics Laboratory and Chemical Biology Research Group, RIKEN. Each entry contains a name, chemical formula, producing organism (the scientific name), biological activity, abstract and references of a new compound. Users can search compounds by keywords from those items.",
"homepage": "http://www.cbrg.riken.jp/csrs/en/compounds.html",
"information_keywords": [
"Chemical structure",
"Bibliography/Documents"
],
"maintainer": "RIKEN CSRS (RIKEN Center for Sustainable Resource Science)",
"name": "New Natural Compounds purified in RIKEN (Antibiotics Lab and Chemical Biology Research Group)",
"prefix": "NBDC00592",
"pubmeds": [
"22595423",
"22052940",
"22406264",
"22186593",
"22360440",
"22506091"
],
"status": "Active",
"target_keywords": [
"Chemical compound",
"Drug",
"Metabolite"
]
},
"nbdc00594": {
"alt_name": "The Nematode Expression Pattern DataBase",
"description": "NEXTDB is a database of nematode expression data. The database contains EST information as well as images from in situ hybridization. Maps of genetic entities, images of hybridizations, sequences, and homology search are available, as is a list of RNAi phenotypes.",
"fairsharing": "biodbcore-000466",
"homepage": "http://nematode.nig.ac.jp",
"information_keywords": [
"Expression",
"Image/Movie"
],
"maintainer": "National Institute of Genetics",
"name": "NEXTDB",
"prefix": "NBDC00594",
"pubmeds": [
"11231151"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Organism"
]
},
"nbdc00595": {
"description": "This mouse genome database contains a browser that allows users to investigate the mouse genome chromosome by chromosome, and further links to the genes on each chromosome. gene details and BAC mapping tools are also available. Bulk data is available for download.",
"homepage": "http://molossinus.nig.ac.jp/mog2/",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "National Institute of Genetics",
"name": "NIG Mouse Genome Database",
"prefix": "NBDC00595",
"pubmeds": [
"23604024",
"26013919"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00596": {
"description": "This is a database of mouse phenotypes with phenotype information of mutants from a Mus molossinus cross. Physiological and behavior phenotypes have been evaluated in different crosses and can be browsed and downloaded.",
"homepage": "http://molossinus.lab.nig.ac.jp/phenotype/index.html",
"maintainer": "National Institute of Genetics",
"name": "NIG Mouse Phenotype Database",
"prefix": "NBDC00596",
"pubmeds": [
"19448335",
"18256237",
"15574823"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc00597": {
"description": "This is the genome database for Nocardia species, which can cause nocardosis in humans. The database contains browsable genome content of several Nocardia strains and related species, a genome browser, and lists of genes in several functional categories. The process of sequencing is also detailed. External links to related resources are provided.",
"homepage": "http://nocardia.nih.go.jp",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "National Institute of Infectious Diseases",
"name": "Nocardia farcinica Genome Project Page",
"prefix": "NBDC00597",
"pubmeds": [
"21097631",
"19942945",
"17314425",
"16569850",
"15466710"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00598": {
"description": "This database is a collection of information associated with the sequence and function of non-coding RNA. There are over 30,000 sequences spanning a total of 99 species from Bacteria, Archaea, and Eukaryota. Sequence information is obtained from GenBank, annotations are obtained from FANTOM3 (mouse) and H-invitational Integrated Database (humans), while the genome mapping information uses the UCSC genome browser. The sequences and annotations of small cytoplasmic RNAs from bacteria is obtained from the Rfam database. This database does not include microRNA, snoRNA, and housekeeping RNAs such as rRNA, tRNA, snRNA, and SPR RNA.",
"homepage": "http://biobases.ibch.poznan.pl/ncRNA",
"information_keywords": [
"Sequence"
],
"maintainer": "Poznan University",
"name": "Noncoding RNA database",
"prefix": "NBDC00598",
"status": "Active",
"target_keywords": [
"RNA"
]
},
"nbdc00599": {
"alt_name": "information system for Nuclear Receptors",
"description": "NucleaRDB is a database of nuclear hormone receptors. The database contains gene and protein sequence, mutation, and ligand binding information. Users can search or browse receptors by family or structure. BLAST search and an alignment builidng tool are also available.",
"fairsharing": "biodbcore-000077",
"homepage": "http://www.receptors.org/nucleardb/",
"information_keywords": [
"Sequence"
],
"maintainer": "University of California, San Francisco, Centre for Molecular and Biomolecular Informatics",
"name": "NucleaRDB",
"prefix": "NBDC00599",
"pubmeds": [
"11125133"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00600": {
"description": "Nucleotide is a database of nucleic acid sequences. The database contains sequence entities from a variety of sources covering hundreds of organisms. The major resources GenBank and RefSeq repositories are both available through Nucleotide. Users can submit nucleotide sequences and data is available for download.",
"homepage": "http://www.ncbi.nlm.nih.gov/nuccore",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "Nucleotide",
"prefix": "NBDC00600",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation"
]
},
"nbdc00601": {
"alt_name": "O- and C-glycosylated proteins database",
"description": "O-GlycBase is a database of glycosylated proteins. The database contains over two hundred entries of known O- and C-glycosylated proteins. Users can download redundant or unique files of glycosylated proteins.",
"homepage": "https://services.healthtech.dtu.dk/datasets/OglycBase/",
"information_keywords": [
"Sequence"
],
"maintainer": "Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark",
"name": "O-GlycBase",
"prefix": "NBDC00601",
"pubmeds": [
"9847232"
],
"status": "Active",
"target_keywords": [
"Protein",
"Carbohydrate"
]
},
"nbdc00602": {
"alt_name": "Oligomer Architecture and Molecular Interface",
"description": "OLIGAMI is a database of protein structure information emphasizing quaternary structure. The database contains curated structure entries that can be browsed by SCOP hierarchy. Searches are also available by PDB or keyword. Results are visualized in a 3D Jmol applet and coordinates can be downloaded.",
"homepage": "http://protein.t.soka.ac.jp/oligami/",
"information_keywords": [
"3D structure"
],
"maintainer": "Soka University",
"name": "OLIGAMI",
"prefix": "NBDC00602",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00603": {
"homepage": "http://omicspace.riken.jp/db/genome.html",
"information_keywords": [
"Sequence"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "OmicBrowse",
"prefix": "NBDC00603",
"pubmeds": [
"15262794",
"17077097"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00605": {
"homepage": "http://omicspace.riken.jp/OmicScan/",
"maintainer": "RIKEN Yokohama Institute",
"name": "OmicScan (Integrating MEDLINE and Omics Database)",
"prefix": "NBDC00605",
"status": "Closed",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00606": {
"alt_name": "DNA Replication Origin Database",
"description": "OriDB is a database of budding yeast origins of replication. The database contains validated origins and links to studies predicting and confirming the sites. The sites are listed by location, and maps and other site-specific information are available.",
"homepage": "http://www.oridb.org/index.php",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "University of Aberdeen Foresterhill",
"name": "OriDB",
"prefix": "NBDC00606",
"pubmeds": [
"17065467"
],
"status": "Closed",
"target_keywords": [
"DNA"
]
},
"nbdc00607": {
"alt_name": "Protein and Associated Nucleotide Domains with Inferred Trees",
"description": "PANDIT is a database of protein domain conservation and relationship information. The database contains phylogenic trees of proteins indicating the degree of similarity between domains of evolutionarily related proteins represented in the Pfam database. Raw data for all phylogenies can be downloaded.",
"homepage": "http://www.ebi.ac.uk/research/goldman/software/pandit",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "PANDIT",
"prefix": "NBDC00607",
"pubmeds": [
"16381879"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00608": {
"alt_name": "Pathway resource list",
"description": "Pathguide is a database of biological pathways. The database contains information on hundreds of pathways including metabolic and signaling pathways as well as protein-protein and gene regulatory networks. The website collects information from several other web resources and formats. Users can search by organism, availability, and data standard, and links are provided to the constituent databases.",
"homepage": "http://www.pathguide.org/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Memorial Sloan-Kettering Cancer Center, the University of Toronto",
"name": "Pathguide",
"prefix": "NBDC00608",
"pubmeds": [
"16381921"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Metabolite"
]
},
"nbdc00611": {
"alt_name": "A Public Database of Transcription Factor and Regulatory Sequence Annotation",
"description": "PAZAR is a database of regulatory sequence information, including information about transcription factors. The database contains information collected from dozens of published studies of gene regulatory information. Users can search by transcription factor, target gene, or regulatory sequence of interest as well as browse by gene or study.",
"fairsharing": "biodbcore-000499",
"homepage": "http://www.pazar.info",
"information_keywords": [
"Sequence"
],
"maintainer": "Centre for Molecular Medicine and Therapeutic",
"name": "PAZAR",
"prefix": "NBDC00611",
"pubmeds": [
"17916232",
"18971253"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00612": {
"alt_name": "Representative protein chains from PDB",
"description": "The site contains the same data as the Protein Data Bank (PDB). The information has however been reorganized to form two lists, one of 1746 membrane protein chains and another containing the full complement (145181) of protein chains, including those on the first list.\nThe links to both these lists were tested and found functional.",
"fairsharing": "biodbcore-000299",
"homepage": "http://mbs.cbrc.jp/pdbreprdb-cgi/reprdb_menu.pl",
"information_keywords": [
"Classification"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "PDB-REPRDB",
"prefix": "NBDC00612",
"pubmeds": [
"12520060",
"11125096",
"9322039"
],
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc00613": {
"alt_name": "Protein Data Bank Europe",
"description": "PDBe is a database of protein structures. The database is the European resource for the Protein Databank and contains molecular structure coordinates and visualizations of thousands of proteins. Users can search for entries, browse by several curated categories, submit structures, and download coordinate data.",
"fairsharing": "biodbcore-000322",
"homepage": "http://www.ebi.ac.uk/pdbe/",
"information_keywords": [
"Image/Movie",
"3D structure",
"Repository"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "PDBe",
"prefix": "NBDC00613",
"pubmeds": [
"22110033"
],
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Protein"
]
},
"nbdc00614": {
"alt_name": "Prion Disease Database",
"description": "PDDB is a database of prion disease research. The database contains a variety of information pertaining to understanding prion diseases, from histological images of prion disease-affected brains to gene expresion and networks. gene expression data are available for download.",
"homepage": "http://prion.systemsbiology.net/cgi-bin/dispatcher.cgi/Welcome/display",
"information_keywords": [
"Sequence",
"Expression",
"Image/Movie"
],
"maintainer": "Institute for Systems Biology, University of Cambridge",
"name": "PDDB",
"prefix": "NBDC00614",
"pubmeds": [
"20157484"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Health/Disease"
]
},
"nbdc00615": {
"alt_name": "Mammalian Promoter/Enhancer Database",
"description": "PEDB is a database of mammalian promoters and enhancers. The database contains information regarding the sequence and location of transcriptional regulatory elements as determined by conservation and other computational analysis in humans, mice, and rats. Users can search for genes or gene functions.",
"homepage": "http://promoter.cdb.riken.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research) Kobe Institute",
"name": "PEDB",
"prefix": "NBDC00615",
"pubmeds": [
"18815372"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00616": {
"alt_name": "Prostate Expression Database",
"description": "PEDB is a database of gene expression and related information specific to prostate cells. The database contains several prostate tissue data sets in both humans and mice. Users can search by gene, experiment, or BLAST search and explore expression with several other tools.",
"homepage": "http://www.pedb.org",
"information_keywords": [
"Expression"
],
"maintainer": "Fred Hutchinson Cancer Research Center",
"name": "PEDB",
"prefix": "NBDC00616",
"pubmeds": [
"11752298",
"10592228",
"9847181"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00617": {
"homepage": "http://www.ncbi.nlm.nih.gov/peptidome",
"information_keywords": [
"Repository"
],
"maintainer": "NIH (National Institutes of Health)",
"name": "Peptidome - NCBI",
"prefix": "NBDC00617",
"pubmeds": [
"19942688"
],
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc00618": {
"description": "Petri Net Pathways is a database containing models of animated biological pathways.\nThey are also explained in detail.\nThe pathways available are EGFR, GPCR, PIP, Ca-signaling, MAPK, transcriptional reactions, GTPase, PKA and endocytosis.\nThe pathways are accessible from the main body of the homepage and they can be downloaded from there.",
"homepage": "http://genome.ib.sci.yamaguchi-u.ac.jp/pnp/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Yamaguchi University Faculty of Science",
"name": "Petri Net Pathways",
"prefix": "NBDC00618",
"pubmeds": [
"21685573"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00619": {
"alt_name": "Pathogenic Fungi Database",
"description": "PFDB is a database of research and educational resources related to pathogenic fungi. This database contains lists of pathogenic fungi (yeasts and molds), mycoses and media. Users need a password to read detailed disease pages.",
"homepage": "http://www.pfdb.net/myhtml/database_eng.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Teikyo University Institute of Medical Mycology",
"name": "PFDB",
"prefix": "NBDC00619",
"status": "Inactive",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00620": {
"alt_name": "A Catalog of Non-Synonymous SNP",
"description": "PicSNP is a database of single nucleotide mutations in the human genome that collects non-synonymous mutations from draft versions of the genome on GenBank. Users can locate SNPs by gene or by annotation.",
"homepage": "http://plaza.umin.ac.jp/~hchang/picsnp/",
"information_keywords": [
"Sequence"
],
"maintainer": "University hospital Medical Information Network",
"name": "PicSNP",
"prefix": "NBDC00620",
"pubmeds": [
"11549289"
],
"status": "Inactive",
"target_keywords": [
"Genetic variation",
"Protein"
]
},
"nbdc00621": {
"alt_name": "Pig Genomics Informatics System",
"description": "PigGIS is a database of the pig genome that allows users to browse and search the genome, providing several browsing options as well as search functions, including BLAST. Data are also available for download.",
"fairsharing": "biodbcore-000224",
"homepage": "http://pig.genomics.org.cn/",
"information_keywords": [
"Sequence"
],
"maintainer": "BGI (Beijing Genomics Institute)",
"name": "PigGIS",
"prefix": "NBDC00621",
"pubmeds": [
"17090590"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation"
]
},
"nbdc00622": {
"alt_name": "Database of Protein interaction SITEs",
"description": "PiSITE is a database of protein interaction domain information containing protein structures annotated with known and predicted protein interaction sites, determined by interaction sites in PDB structures. In addition to interaction sites, users can also obtain interaction information on interaction partners. Java is required to view structures.",
"homepage": "http://pisite.hgc.jp/",
"information_keywords": [
"Interaction/Pathway",
"3D structure"
],
"maintainer": "The University of Tokyo The Institute of Medical Science",
"name": "PiSITE",
"prefix": "NBDC00622",
"pubmeds": [
"18836195"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00623": {
"description": "Plant Repeat Databases is a collection of DNA sequence repeats found in plants. The database consists of annotated repeat sequences determined by sequence analysis of completed plant genome projects. Repeats are separated into classes and given a unique code. Users can search sequences or download repeat subsets.",
"homepage": "http://plantrepeats.plantbiology.msu.edu/index.html",
"information_keywords": [
"Sequence",
"Chemical structure"
],
"maintainer": "Michigan State University",
"name": "Plant Repeat Databases",
"prefix": "NBDC00623",
"pubmeds": [
"14681434"
],
"status": "Closed",
"target_keywords": [
"DNA"
]
},
"nbdc00624": {
"alt_name": "Polymorphism in microRNA Target Site",
"description": "PolymiRTS is a database of DNA variations which occur naturally in predicted and experimentally identified microRNA (miRNA) target sites. It provides links between SNPs in miRNA target sites, cis-acting expression quantitative trait loci (eQTLs), and the results of genome-wide association studies (GWAS) of human diseases. Data are created by scanning 3'UTRs of mRNAs in human and mouse for SNPs in miRNA target sites, and identifying the potential downstream effects of these polymorphisms on gene expression and complex traits. This database also includes polymorphisms in target sites that have been supported by a variety of experimental methods and polymorphisms in miRNA seed regions.",
"fairsharing": "biodbcore-000089",
"homepage": "http://compbio.uthsc.edu/miRSNP/",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tennessee Health Science Center",
"name": "PolymiRTS",
"prefix": "NBDC00624",
"pubmeds": [
"22080514",
"17099235"
],
"status": "Inactive",
"target_keywords": [
"Genetic variation",
"RNA"
]
},
"nbdc00625": {
"description": "This is a database of Poplar cDNA clones with 5' and 3' sequence information for each clone. Users can search by gene or clone information, or locate clones by BLAST search.",
"homepage": "http://www.brc.riken.jp/lab/epd/catalog/poplarclone.html",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "Poplar Full-Length Clone Database Search",
"prefix": "NBDC00625",
"pubmeds": [
"18053163",
"15653793"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00626": {
"description": "Popset is a database of collected sequences which have been used to determine phylogenetic relation amongst individuals in a sample. Data sets can include individuals of any relation, from the same species to millions of years of evolutionary separation. Users can submit datasets and download via FTP.",
"homepage": "http://www.ncbi.nlm.nih.gov/popset",
"information_keywords": [
"Taxonomy",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "Popset",
"prefix": "NBDC00626",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00627": {
"description": "This is a database of Porphyra yezoensis expressed sequences containing consensus gene sequences and EST reads that allows for BLAST and keyword search. Data are available for download.",
"homepage": "https://www.kazusa.or.jp/e/plant/porphyra/EST/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Porphyra yezoensis (susabinori) EST dataset",
"prefix": "NBDC00627",
"pubmeds": [
"22013916",
"10907854"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Protein"
]
},
"nbdc00628": {
"alt_name": "Positional MEDLINE",
"description": "PosMed is a database connecting data of several types, with information about associations between genes, metabolites, diseases, and other biological categories. Users can search for any category type to explore connections. Data is collected from literature and web resources and semantically connected.",
"homepage": "http://omicspace.riken.jp/PosMed/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "PosMed",
"prefix": "NBDC00628",
"pubmeds": [
"19468046"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00629": {
"alt_name": "Protein-Protein Interaction viewer",
"description": "This website shows how different human proteins interact with one another.\nInformation on 32,198 human protein interactions is available.\nA search function, where keywords, H-InvDB IDs, or accession numbers of the researched proteins need to be entered, is provided.",
"homepage": "http://www.h-invitational.jp/hinv/ppi/index.html",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "PPI view",
"prefix": "NBDC00629",
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00630": {
"alt_name": "PSC-RIKEN Database of EST/Gene Expression",
"description": "This database contains information on the way genes are expressed in plants like Zinnia elegans and also its EST's. This information was collected by applying a tool called Silicon genetics (genet).\nIt is planned to add the same data for other organisms, for instance Arabidopsis, Lotus japonica and BY-2 in the future. \nA Blast search option is provided.",
"homepage": "http://mrg.psc.riken.go.jp/PRIDE/index.html",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "PRIDE",
"prefix": "NBDC00630",
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00631": {
"alt_name": "PRImate GENes",
"description": "PRIGEN is a database of chimpanzee cDNA sequences. The database contains sequences from several tissues annotated by comparison to human transcripts. Users can search by keyword or BLAST, and bulk download is available.",
"homepage": "http://www.prigen.org",
"information_keywords": [
"Sequence"
],
"maintainer": "National Institutes of Biomedical Innovation, Health and Nutrition",
"name": "PRIGEN",
"prefix": "NBDC00631",
"pubmeds": [
"17574350",
"15677748",
"12727913"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00632": {
"alt_name": "Platform for RIKEN Metabolomics",
"description": "PRIMe is a database of metabolomics and transcriptomics with several tools for metabolomic research, primarily centered around MS measurements. Metabolic profiles are also correlated with gene expression profiles, and data is available for download.",
"homepage": "http://prime.psc.riken.jp/",
"information_keywords": [
"Portal"
],
"maintainer": "RIKEN CSRS (RIKEN Center for Sustainable Resource Science)",
"name": "PRIMe",
"prefix": "NBDC00632",
"pubmeds": [
"23292601",
"19032166"
],
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc00633": {
"alt_name": "Platform for RIKEN Metabolomics - SpinAssign",
"description": "SpinAssign is a tool for annotating 2D 13C-HSQC NMR peaks. The site allows users to input peaks that are then interpreted and identified to their originating metabolite. The annotations are based on previous standardized spectroscopic measurements. Users can specify tolerances for the identification algorithm.",
"homepage": "http://dmar.riken.jp/spinassign/",
"information_keywords": [
"Method"
],
"maintainer": "RIKEN CSRS (RIKEN Center for Sustainable Resource Science)",
"name": "PRIMe - SpinAssign",
"prefix": "NBDC00633",
"pubmeds": [
"19032166",
"20121204",
"19030231",
"17035691",
"15356336"
],
"status": "Inactive",
"target_keywords": [
"Metabolite"
]
},
"nbdc00634": {
"alt_name": "Platform for RIKEN Metabolomics - Standard Spectrum Search",
"description": "Standard Spectrum Search is a database of metabolite NMR spectra. The database consists of dozens of spectra and is designed to aid users in metabolomic experiments. Users can search for compound name, KEGG ID, PubChem ID, or formula, and retrieve spectral peaks under various conditions.",
"homepage": "http://prime.psc.riken.jp/menta.cgi/prime/standard_index",
"maintainer": "RIKEN CSRS (RIKEN Center for Sustainable Resource Science)",
"name": "PRIMe - Standard Spectrum Search",
"prefix": "NBDC00634",
"pubmeds": [
"19032166"
],
"status": "Closed",
"target_keywords": [
"Metabolite"
]
},
"nbdc00635": {
"alt_name": "PROfiling of PHEnotypic Characteristics in Yeast",
"description": "PROPHECY is a database of mutant yeast phenotypes. The database contains information on the growth rate of hundreds of mutants including several different growth metrics in multiple environmental conditions. Users can query by experiment or perform searches for genes of interest.",
"homepage": "http://prophecy.lundberg.gu.se",
"information_keywords": [
"Phenotype"
],
"maintainer": "Goteborgs universitet",
"name": "PROPHECY",
"prefix": "NBDC00635",
"pubmeds": [
"12489126",
"14676322",
"17148481"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00636": {
"description": "NCBI Protein is a collection of amino acid sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. A record includes the amino acid sequence, organism information, literature, links to other NCBI databases such as BioProject, BioSample, etc.",
"fairsharing": "FAIRsharing.rtndct",
"homepage": "https://www.ncbi.nlm.nih.gov/protein",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "NCBI Protein",
"prefix": "NBDC00636",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00637": {
"description": "Protein Clusters is a database of related protein families. The database contains clustered protein families across all kingdoms of life, grouped by sequence and structural similarity. Clusters are determined by BLAST similarity of protein sequences in the Refseq genome database. Users can download via FTP.",
"fairsharing": "biodbcore-000454",
"homepage": "http://www.ncbi.nlm.nih.gov/proteinclusters",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "Protein Cluster",
"prefix": "NBDC00637",
"pubmeds": [
"18940865"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00638": {
"description": "Pseudomonas Genome Database is a resource for the completed genome projects of several Pseudomonas species. The database contains the complete genome sequence of dozens of strains. Users can search or use comparative tools, and sequences are available for download.",
"fairsharing": "biodbcore-000519",
"homepage": "http://www.pseudomonas.com",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway",
"Taxonomy"
],
"maintainer": "Simon Fraser University",
"name": "Pseudomonas Genome Database V2",
"prefix": "NBDC00638",
"pubmeds": [
"20929876",
"18978025",
"15608211"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"DNA",
"RNA",
"Protein"
]
},
"nbdc00639": {
"description": "PTM-Switchboard is a database of known cases of TF-PTMs affecting gene transcriptions. This database contains triplets of genes as a primary data type about the model organism S. cerevisiae (budding yeast). PTM-Switchboard stores triplets of genes as a primary data type such that the ability of one gene (the TF) to regulate a target gene is dependent on a third gene (the modifying enzyme). Currently, this database is populated with experimentally characterized examples of the Modifier-Transcription Factor-gene (MFG) triplets manually curated from the literature. Furthermore, it provides a framework for searching and analyzing the data, and also serve to benchmark computational methods for identifying novel MFG triplets. The entire 'Gold Set' of fully characterized and experimentally validated MFG triplets is available for download in a simple tab-delimited text format.",
"homepage": "http://cagr.pcbi.upenn.edu/PTMswitchboard",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "University of Pennsylvania",
"name": "PTM-Switchboard",
"prefix": "NBDC00639",
"pubmeds": [
"18927104"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00640": {
"description": "PubChem BioAssay is a database of the biological activity characteristics of various PubChem substances. The database contains readouts and descriptions of experiments analyzing a number of compounds. Users can submit results and download via FTP.",
"homepage": "http://www.ncbi.nlm.nih.gov/pcassay",
"information_keywords": [
"Method",
"Image/Movie",
"Bibliography/Documents",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "PubChem BioAssay",
"prefix": "NBDC00640",
"pubmeds": [
"22140110"
],
"status": "Active",
"target_keywords": [
"Metabolite",
"Chemical compound"
]
},
"nbdc00641": {
"description": "PubChem Compound is a database of chemical structrues of validated small molecules. The dataase contains entries for PubChem entities which are grouped by structural identity and similarity. Users can submit compounds and download via FTP.",
"homepage": "http://www.ncbi.nlm.nih.gov/pccompound",
"information_keywords": [
"Image/Movie",
"Chemical structure",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "PubChem Compound",
"prefix": "NBDC00641",
"pubmeds": [
"22140110"
],
"status": "Active",
"target_keywords": [
"Metabolite",
"Chemical compound"
]
},
"nbdc00642": {
"description": "PubChem Substance is a database of samples of chemical entities which links to the biological activity of those samples in PubChem BioAssay. The database contains structural information on substances with links to further information in cases where the substance has been more fully characterized. It consists of records of chemical entities deposited by various contributors, so a chemical entity may be described different records with different data in this database.",
"homepage": "http://www.ncbi.nlm.nih.gov/pcsubstance",
"information_keywords": [
"Bibliography/Documents",
"Chemical structure",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "PubChem Substance",
"prefix": "NBDC00642",
"pubmeds": [
"22140110"
],
"status": "Active",
"target_keywords": [
"Chemical compound",
"Drug",
"Metabolite"
]
},
"nbdc00643": {
"alt_name": "Database of genes transcriptionally modulated by ionizing radiation in mammalian cells",
"description": "Radiation genes is a database of genes whose transcription varies in response to ionizing radiation. The database contains gene expression microarray data from published papers wherein mammalian cells are exposed to radiation. Users can submit or search data by gene, organism, cell type, and several experimental parameters.",
"homepage": "http://bbcd.bio.uniroma1.it/radiationgenes/",
"information_keywords": [
"Expression",
"Bibliography/Documents"
],
"maintainer": "CASPUR (Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universita e Ricerca)",
"name": "Radiation Gene",
"prefix": "NBDC00643",
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00644": {
"alt_name": "RIKEN Arabidopsis Phenome Information Database",
"description": "RAPID is a database of Arabidopsis phenotypes resulting from transposition events. Users can search the database for phenotypes of interest, including images of mutant plants.",
"homepage": "http://rarge.psc.riken.jp/phenome/",
"information_keywords": [
"Phenotype",
"Image/Movie"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "RAPID",
"prefix": "NBDC00644",
"pubmeds": [
"16813574"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc00645": {
"alt_name": "Resource of Asian Primary Immunodeficiency Diseases",
"description": "RAPID is a database of mutations leading to immunodeficiency diseases. It has gene and protein information on causative mutations and associated information about gene expression, protein structure, and phenotypes relating to IDs. Tools are also available to predict how mutations affect protein structures, and to explore potentially causative mutations.",
"homepage": "http://web16.kazusa.or.jp/rapid/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "RAPID",
"prefix": "NBDC00645",
"pubmeds": [
"18842635"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein",
"Health/Disease"
]
},
"nbdc00646": {
"alt_name": "RIKEN Arabidopsis Transcription Factor database",
"description": "RARTF is a database of Arabidopsis transcription factors grouped into families listed on the front page. After selecting a family, users can then explore transcription factors in that group. Sequence, results of family-specific BLAST, and protein motif displays are available for each TF.",
"homepage": "http://rarge.psc.riken.jp/rartf/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "RARTF",
"prefix": "NBDC00646",
"pubmeds": [
"16769687",
"11118137"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00648": {
"alt_name": "The Restriction Enzyme Database",
"description": "REBASE is a database of restriction enzymes. The database contains entries by publication authors, and the database can be searched by identifiers such as name and number. Tools for digests and comparison of sequences are provided.",
"fairsharing": "biodbcore-000475",
"homepage": "http://rebase.neb.com/rebase/rebase.html",
"information_keywords": [
"Bioresource",
"Sequence",
"Repository"
],
"maintainer": "New England Biolabs Inc.",
"name": "REBASE",
"prefix": "NBDC00648",
"pubmeds": [
"19846593"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc00649": {
"alt_name": "Database of translational recoding events",
"description": "Recode2 is a database about genes which utilize non-standard translation for gene expression purposes. It contains information of recoding events such as programmed ribosomal frameshifting, translational bypassing (aka hopping) and mRNA specific codon redefinition. The sequences of the genes that use recoding for their expression are also included in this database. In this database, the recoding sites and the known stimulatory signals are annotated together with notes on factors that are known to affect recoding efficiencies. Each entry is downloadable in RecodeML format. The entire database is available in SQL format for an easy integration.",
"homepage": "https://recode.ucc.ie/",
"information_keywords": [
"Sequence"
],
"maintainer": "University College Cork",
"name": "Recode v. 2.0",
"prefix": "NBDC00649",
"pubmeds": [
"19783826"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc00650": {
"alt_name": "The Recombinant Virus Database",
"description": "RVD is a database of sequence and functional information about recombinant viruses generated, in part, to understand gene expression and function. Viruses are classified by type and all viruses in the database can be browsed and searched by sequence or keyword.",
"homepage": "https://dnaconda.riken.jp//rvd/index.html",
"information_keywords": [
"Bioresource",
"Method",
"Sequence"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "RVD",
"prefix": "NBDC00650",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc00651": {
"alt_name": "Rice Expression Database II",
"homepage": "http://cdna01.dna.affrc.go.jp/cDNA/EXPRESSION/description.html",
"information_keywords": [
"Expression"
],
"maintainer": "National Institute of Agrobiological Sciences",
"name": "RED II",
"prefix": "NBDC00651",
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00652": {
"alt_name": "Reference Database of Immune Cells",
"description": "RefDIC is a database of immune cell gene expression information with data from mRNA expression experiments on several cell types, and particular focus on immunologically relevant cells. In addition to expression profiles, several tools are available to aid in characterization and functional annotation.",
"homepage": "http://refdic.rcai.riken.jp/welcome.cgi",
"information_keywords": [
"Expression",
"Bibliography/Documents"
],
"maintainer": "RIKEN Research Center for Allergy and Immunology",
"name": "RefDIC",
"prefix": "NBDC00652",
"pubmeds": [
"17893089"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Protein",
"Cell/Organelle"
]
},
"nbdc00653": {
"alt_name": "A curated database of regulatory interactions in Prokaryotes",
"description": "RegTransBase is a database of regulatory regions in prokaryotes. The database contains two sets of data, one collected from the literature and one carefully manually currated. Users can browse by categories including taxa, phenotype, or technique, or search by gene, effector, or full text. Several annotation databases are available for download.",
"homepage": "http://regtransbase.lbl.gov/cgi-bin/regtransbase?page=main",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "LBNL (Lawrence Berkeley National Laboratory)",
"name": "RegTransBase",
"prefix": "NBDC00653",
"pubmeds": [
"17142223"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00654": {
"alt_name": "RNA family database",
"description": "Rfam is a database of RNA sequence and structure families. The database contains information on families and sequences of constituent members which can be searched by keyword or taxonomy. Data can also be downloaded via FTP.",
"homepage": "http://rfam.xfam.org",
"information_keywords": [
"Sequence",
"Bibliography/Documents",
"Classification"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "Rfam",
"prefix": "NBDC00654",
"pubmeds": [
"12520045",
"15608160",
"18945806",
"18953034",
"21062808",
"25392425"
],
"status": "Active",
"target_keywords": [
"RNA"
]
},
"nbdc00655": {
"description": "RIKEN ENU-based gene-driven mutagenesis is a collection of information on the ENU-based gene-driven mutagenesis system and ENU mutant mice resources. This site contains the target gene list of the ENU-based gene-driven mutagenesis. The list includes gene names, locations of target genes and availability of mutant strains. Users can request resources to send the applicaition form by courier.",
"homepage": "http://www.brc.riken.go.jp/lab/mutants/genedriven_name.htm",
"information_keywords": [
"Bioresource"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "RIKEN ENU-based gene-driven mutagenesis",
"prefix": "NBDC00655",
"pubmeds": [
"18781157",
"19558788",
"16139793",
"17584492"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc00656": {
"description": "Rhodococcus Genome Project is the genome database for a bacteria which can break down polychlorinated biphenyls. The site includes a genome browser, BLAST search, and sequence retreival tools. Genome and other sequence data is available for download.",
"homepage": "http://www.rhodococcus.ca/index.jsp",
"information_keywords": [
"Sequence"
],
"maintainer": "Rhodococcus Genome Project",
"name": "Rhodococcus genome Project",
"prefix": "NBDC00656",
"pubmeds": [
"17030794",
"15516593"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"DNA",
"Protein"
]
},
"nbdc00657": {
"homepage": "http://gerg03.gsc.riken.jp/DNABook_DB/VIEW/Book_Top.php?BOOK_ID=BOOK_5",
"information_keywords": [
"Bioresource"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "Rice Full-Length cDNA Encyclopedia DNABook",
"prefix": "NBDC00657",
"status": "Closed",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00659": {
"description": "This database of Arabidopsis mutant lines contains several hundred mutant T1 lines with visible phenotypes produced by activation tagging. Users can order seeds of interest.",
"homepage": "https://metadb.riken.jp/metadb/db/SciNetS_ria37i",
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "RIKEN Arabidopsis Activation tagging line",
"prefix": "NBDC00659",
"pubmeds": [
"1455228",
"10069079"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc00660": {
"alt_name": "RIKEN BioResource Center",
"description": "RIKEN BRC is a portal site for biological resources and associated bioinformatics tools maintained by RIKEN. RIKEN BRC contains catalogs and search systems for experimental animals, plants, cultured cell lines and DNA materials. Users can search available resources from the website of each search system or catalog.",
"fairsharing": "biodbcore-000506",
"homepage": "http://www.brc.riken.jp/inf/en/index.shtml",
"information_keywords": [
"Bioresource"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "RIKEN BRC",
"prefix": "NBDC00660",
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Organism",
"Cell/Organelle"
]
},
"nbdc00661": {
"description": "Arabidopsis activation (T-DNA)-tagged lines is a database of T-DNA-tagged Arabidopsis plants maintained by RIKEN BioResource Center (RIKEN BRC). This database includes information on activation-tagged line resources such as the style of distribution, background ecotype, the vector for transformation, the selection marker, etc, and the list of lines with dominant or recessive phenotypes. Each record in the list contains a picture and phenotype data on plant growth (the dwarf phenotype), leaves and others. Users can order a seed pool set for screening or mutant lines in the list by e-mail.",
"homepage": "http://epd.brc.riken.jp/en/seed/activ",
"information_keywords": [
"Bioresource"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "Arabidopsis activation (T-DNA)-tagged lines",
"prefix": "NBDC00661",
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Organism",
"Cell/Organelle"
]
},
"nbdc00662": {
"description": "Cell Search System is a database of cultured cell lines derived from animal and human tissues maintained by RIKEN BioResource Center (RIKEN BRC). Although a home page of the site is written in Japanese, the keyword search system is available in English. Records are written in both Japanese and English, and each record contains a general character, animal common name (the species a cell line is derived from), tissue, photo, etc. Users can search available cell lines by keywords, and order them by e-mail.",
"homepage": "http://cellbank.brc.riken.jp/cell_bank/WebSearch/?lang=En",
"information_keywords": [
"Bioresource"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "Cell Search System - RIKEN BRC CELL BANK",
"prefix": "NBDC00662",
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc00663": {
"description": "RIKEN BRC DNA BANK is a database of cloned DNA, vector and recombinant adenovirus resources maintained by RIKEN BioResource Center (RIKEN BRC). Each record contains the type (DNA, vector, shuttle vector or virus), classification (plasmid, cosmid, phage, recombinant adenovirus, etc), the organism of inserted DNA, description, gene name and others. Users can search available resources by keywords from those items. This database also provides laboratory manuals, supplemental data and publication lists about the resources.",
"homepage": "http://dna.brc.riken.jp/en/",
"information_keywords": [
"Bioresource"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "RIKEN BRC DNA BANK",
"prefix": "NBDC00663",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc00664": {
"description": "JCM is a database of cultured microbial strains and their genomic DNA samples maintained by RIKEN BioResource Center (RIKEN BRC). JCM stocks strains of aerobic and anaerobic bacteria including actinomycetes, archaea and fungi including yeasts. Each entry contains the scientific name, accession numbers, culture medium data and reference information. Users can search available resources by keywords from those items, and order them by FAX or e-mail.",
"fairsharing": "biodbcore-000505",
"homepage": "https://metadb.riken.jp/metadb/db/rikenbrc_jcm_microbe",
"information_keywords": [
"Phenotype",
"Bioresource"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "Metadata of JCM resources",
"prefix": "NBDC00664",
"pubmeds": [
"22339691",
"21378133",
"22105532",
"21724957",
"21724955",
"21764984"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00665": {
"description": "This is a tool for BLAST searching multiple plant species. The website contains a sequence input window and allows users to specify the search parameters. Multiple species can be searched at the same time.",
"homepage": "http://www.brc.riken.jp/lab/epd/blast/",
"information_keywords": [
"Sequence"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "RIKEN BRC PLANT DATABASE SERCH - BLAST Search",
"prefix": "NBDC00665",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00666": {
"description": "RIKEN Hub Database is an integrated database of data resources published by RIKEN. Thid database contains entries of databases, researchers, literature, omics annotations and biomedical resources (PosMed). This database provides search engines, genome browsers, tutorials and various other research tools. Users can search remarkable targets and recent published report trends for recent 5 years by keywords.",
"homepage": "http://omicspace.riken.jp/db/index.html.en",
"information_keywords": [
"Sequence"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "RIKEN Hub Database",
"prefix": "NBDC00666",
"pubmeds": [
"18263641"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00668": {
"homepage": "http://gerg03.gsc.riken.jp/DNABook_DB/VIEW/Book_Top.php?BOOK_ID=BOOK_1",
"information_keywords": [
"Bioresource"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "RIKEN Mouse Genome Encyclopedia DNABook",
"prefix": "NBDC00668",
"status": "Closed",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00670": {
"alt_name": "RIKEN Structural Genomics/Proteomics Initiative",
"description": "This site is a database of structures, functions and functional networks of proteins researched by RIKEN Structural Genomics/Proteomics Initiative. It contains three-dimensional (3D) folded structures, annotations and PDB list of proteins which are important of a life activity or valuable for drug designs.",
"homepage": "http://www.rsgi.riken.jp/rsgi_e/index.html",
"information_keywords": [
"3D structure",
"Portal"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "RSGI",
"prefix": "NBDC00670",
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00671": {
"description": "This is a database of cassava cDNA clones with 5' and 3' sequence information for each clone. Users can search by gene or clone information, or locate clones by BLAST search.",
"homepage": "http://www.brc.riken.go.jp/lab/epd/catalog/cassavaclone.html",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "RIKEN-CIAT Cassava Full-Length Clone Database Search",
"prefix": "NBDC00671",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00672": {
"alt_name": "A Database of Rodent Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Mouse cDNA Project",
"description": "ROUGE is a database of long rodent cDNA clones designed to compliment the HUGE database of long human cDNA clones. The database contains sequence information for mouse clones from the mKIAA sequencing project, which can be browsed or searched. ROUGE was conducted as part of the CREATE program.",
"fairsharing": "biodbcore-000408",
"homepage": "http://www.kazusa.or.jp/rouge/index.html",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "ROUGE",
"prefix": "NBDC00672",
"pubmeds": [
"15368895",
"15449545",
"15188409",
"14621295",
"12693553",
"12465718"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"RNA",
"Protein"
]
},
"nbdc00673": {
"alt_name": "RIKEN Populus Database",
"description": "RPOPDB is a Populus genome sequence resource with genome browser and search functions to explore the sequence of Populus. Keyword and BLAST search are available, and the BLAST search can be configured to include other plant species.",
"homepage": "http://rpop.psc.riken.jp/index.pl",
"information_keywords": [
"Sequence"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "RPOPDB",
"prefix": "NBDC00673",
"pubmeds": [
"18053163",
"15653793"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00674": {
"alt_name": "The S/MAR transaction DataBase",
"description": "S/MARt DB is a database of cellular scaffolds and matrix data. The database contains scaffold, matrix, and nuclear matrix information from species ranging from yeast to humans. genes with experimentally identified interactions with scaffold and matrix components are available in tabular or searchable formats.",
"homepage": "http://smartdb.bioinf.med.uni-goettingen.de/",
"information_keywords": [
"Sequence"
],
"maintainer": "Gesellschaft fur Biotechnologische Forschung",
"name": "S/MARt DB",
"prefix": "NBDC00674",
"pubmeds": [
"11752340"
],
"status": "Active",
"target_keywords": [
"DNA",
"Protein"
]
},
"nbdc00675": {
"alt_name": "Systematic consolidation of Arabidopsis and other Botanical REsource",
"description": "SABRE is a database of plant resources. The database contains collected information about Arabidopsis and other plants, particularly cDNA sequences and clones. All clones in the database can be requested and acquired.",
"homepage": "http://saber.epd.brc.riken.jp/sabre/SABRE0101.cgi",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "RIKEN Tsukuba Institute",
"name": "SABRE",
"prefix": "NBDC00675",
"pubmeds": [
"24323624"
],
"status": "Closed",
"target_keywords": [
"cDNA/EST",
"Protein"
]
},
"nbdc00676": {
"alt_name": "Surveyed conserved motif ALignment diagram and the Associating Dendrogram",
"description": "The SALAD database supports the construction of dendrograms from amino acid sequence similarities in plants, clustering them into proteins with similar functions. This database has following functions; \n1) Conserved domains (motifs) can be displayed graphically,\n2) annotations between plant species can be compared easily\n3) similar annotations can be clustered\n4) molecular evolutionary trees can be constructed easily per conserved motif. \nThe database uses non-redundant complete genomic information for the analysis, and an amino acid displacement matrix for clustering. The most current version supports comparisons of up to 10 plant species.",
"homepage": "http://salad.dna.affrc.go.jp/salad/en/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "SALAD Database",
"prefix": "NBDC00676",
"pubmeds": [
"19854933"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00677": {
"description": "Wellcome Trust Sanger Institute is a major European research program. The website contains information on the faculty and research projects at Sanger Institute as well as links to data sets available for download focused largely on genome sequencing projects.",
"homepage": "http://www.sanger.ac.uk",
"information_keywords": [
"Portal"
],
"maintainer": "Wellcome Sanger Institute",
"name": "Wellcome Trust Sanger Institute",
"prefix": "NBDC00677",
"status": "Active"
},
"nbdc00678": {
"description": "This is a database of gene information in Schizosaccharomyces pombe. The database contains information on the cloning of genes, intracellular location of proteins, and images. Data were attained by the Chemical genetics Laboratory of RIKEN and are available for browsing in this database. The Wellcome Trust geneDB is linked with this database. Expression vectors and strains are available for distribution.",
"homepage": "http://www.riken.jp/SPD/index.html",
"information_keywords": [
"Bioresource",
"Sequence",
"Expression",
"Localization",
"Image/Movie"
],
"maintainer": "RIKEN CSRS (RIKEN Center for Sustainable Resource Science)",
"name": "Schizosaccharomyces pombe Postgenome Database",
"prefix": "NBDC00678",
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00681": {
"description": "This site offers the tabulated information of the GPCR (G-protein coupled receptor) genes of 56 eukaryotic species, from humans right down to budding yeast cells. For each of these species a detailed karyotype is offered indicating the position of each of the sequences identified. The list contains genes that are expressed in vivo as well as those that are lying dormant.\nThe processes by which the sequences were found and screened include a gene finder, sequence alignment, domain and motif assignment and a predictor of transmembrane helixes.",
"homepage": "http://sevens.cbrc.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "SEVENS",
"prefix": "NBDC00681",
"pubmeds": [
"16126348",
"19718507"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00682": {
"alt_name": "Simple Modular Architecture Research Tool",
"description": "SMART is a database of protein domains found in several different protein classes. The database contains classification information for domains and the proteins they can be found in. Users can search by sequence or domain information. The database can also be requested for local installation.",
"fairsharing": "FAIRsharing.hsbpq3",
"homepage": "http://smart.embl-heidelberg.de",
"information_keywords": [
"3D structure",
"Chemical structure",
"Classification"
],
"maintainer": "EMBL (European Molecular Biology Laboratory)",
"name": "SMART",
"prefix": "NBDC00682",
"pubmeds": [
"22053084",
"18978020",
"16381859",
"9600884"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00683": {
"alt_name": "snoRNA Orthological Gene Database",
"description": "snOPY is a database of small nucleolar RNA orthology. The database contains snoRNA sequences for several model organisms and related species. In addition to snoRNA sequences the database provides information on target sequences and gene loci. BLAST search and annotations of snoRNA targeted sites are available.",
"homepage": "http://snoopy.med.miyazaki-u.ac.jp",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "University of Miyazaki Frontier Science Research Center",
"name": "snOPY",
"prefix": "NBDC00683",
"status": "Active",
"target_keywords": [
"RNA"
]
},
"nbdc00684": {
"description": "SNPedia is a database of human genetic variation. The database contains entries on DNA variations collected from primary literature. A for-payment tool is also available which helps users annotate genotype information. Users can access SNPs by rs number to explore established functions in disease.",
"fairsharing": "biodbcore-000145",
"homepage": "http://www.snpedia.com/",
"information_keywords": [
"Bibliography/Documents",
"Repository"
],
"maintainer": "River Road Bio",
"name": "SNPedia",
"prefix": "NBDC00684",
"pubmeds": [
"22140107"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Health/Disease"
]
},
"nbdc00685": {
"alt_name": "RIKEN Soybean Full-Length cDNA Database",
"description": "This is a database of soybean cDNA sequences. In addition to soybean sequence information, it contains collected sequence information for several species, which can be searched by keyword or BLAST, such that users can compare soybean sequences to those of other plants.",
"homepage": "http://spectra.psc.riken.jp/menta.cgi/rsoy/index",
"information_keywords": [
"Sequence"
],
"maintainer": "RIKEN CSRS (RIKEN Center for Sustainable Resource Science)",
"name": "rsoy",
"prefix": "NBDC00685",
"pubmeds": [
"18927222"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00686": {
"alt_name": "Strongylocentrotus purpuratus database",
"description": "SpBase is a database of the sea urchin genome. In addition to a genome browser, the database contains several types of sequence and gene expression information as well as links to external resources. Bulk data is available for download.",
"homepage": "http://www.spbase.org/SpBase/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "California Institute of Technology",
"name": "SpBase",
"prefix": "NBDC00686",
"pubmeds": [
"19010966"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc00687": {
"alt_name": "Sequence Read Archive",
"description": "SRA is a database of raw sequence reads from next-generation sequencing systems. The database contains millions of unannotated raw reads generated from a variety of projects. Data can be submitted to the archive or downloaded via FTP.",
"fairsharing": "biodbcore-000444",
"homepage": "http://www.ncbi.nlm.nih.gov/sra",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "SRA",
"prefix": "NBDC00687",
"pubmeds": [
"22009675"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"RNA"
]
},
"nbdc00688": {
"alt_name": "Signal Recognition Particle Database",
"description": "SRPDB is a database of signal recognition particle sequences in bacteria, archaea, fungi, and plants. The database contains background information on SRPs and SRP proteins, and sequence alignment as well as 3D structure information for SRP RNAs.",
"homepage": "https://rth.dk/resources/rnp/SRPDB/SRPDB.html",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "Department of Biochemistry, University of Texas Health Science Center",
"name": "SRPDB",
"prefix": "NBDC00688",
"pubmeds": [
"16381838"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc00689": {
"alt_name": "Short Tandem Repeat DNA Internet Database",
"description": "STRBase is a database of markers for human identification. The database contains information on the use of genetic markers, particularly short tandem (microsatellite) repeats for forensic purposes. Lists of commonly used STRs are available as well as methodologies, and other marker types, species, and resources are also provided.",
"homepage": "http://www.cstl.nist.gov/div831/strbase/",
"information_keywords": [
"Sequence",
"Bibliography/Documents",
"Portal"
],
"maintainer": "National Institute of Standards and Technology",
"name": "STRBase",
"prefix": "NBDC00689",
"pubmeds": [
"11125125"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"DNA"
]
},
"nbdc00690": {
"alt_name": "Search Tool for the Retrieval of Interacting Genes/Proteins",
"description": "STRING is a database of known and predicted protein interactions, including both physical and functional interactions. It contains data which derived from four sources: genomic context, high-throughput experiments, coexpression and previous knowledge. This database quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable. It performs iterative searches and visualizes the results in their genomic context. Many data including protein sequences, protein network, interaction types for protein links, orthologous groups or full database dumps (license required) are downloadable.",
"fairsharing": "biodbcore-000340",
"homepage": "http://string-db.org/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Classification"
],
"maintainer": "STRING Consortium",
"name": "STRING",
"prefix": "NBDC00690",
"pubmeds": [
"18940858",
"17098935",
"15608232",
"12519996",
"10982861"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00691": {
"description": "Structure is a database of three-dimensional structures of biological molecules. The database contains entries for individual molecules as well as multi-component complexes. Several tools are available to examine macromolecular structures, and users can submit and download data via FTP.",
"fairsharing": "biodbcore-000447",
"homepage": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure",
"information_keywords": [
"Image/Movie",
"3D structure"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "Structure",
"prefix": "NBDC00691",
"pubmeds": [
"17135201",
"125200",
"22135289",
"10838572",
"22102591",
"8804824"
],
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Protein"
]
},
"nbdc00692": {
"description": "SubtiList is a database of the Bacillus subtilis genome. The database contains sequence and positional information for all genes mapped in the reference strain collected from the sequencing project and other databases. The genome can be searched by gene or region, and an interactive map tool is available. Users can also join a mailing list for updates.",
"fairsharing": "biodbcore-000389",
"homepage": "http://genolist.pasteur.fr/SubtiList/",
"information_keywords": [
"Sequence"
],
"maintainer": "Institut Pasteur",
"name": "SubtiList World-Wide Web Server",
"prefix": "NBDC00692",
"pubmeds": [
"7704253",
"9678589"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00693": {
"description": "SubtiWiki is a collaborative user database for the bacterium Bacillus subtilis. The database contains user annotations of genes, annotations, pathways, and interactions. Users can contribute and download several different summary information tables.",
"fairsharing": "biodbcore-000146",
"homepage": "http://subtiwiki.uni-goettingen.de/",
"information_keywords": [
"Bibliography/Documents",
"Method",
"Expression",
"Interaction/Pathway"
],
"maintainer": "Georg-August-Universitat Gottingen",
"name": "SubtiWiki",
"prefix": "NBDC00693",
"pubmeds": [
"26433225",
"20157485",
"19959575",
"22096228"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Metabolite"
]
},
"nbdc00694": {
"description": "This is a viewer of Swine DNA marker. It provides information of the primers, results of linkage map analysis and RH analysis. This site is a part of 'Animal Genome Research Program' (http://integbio.jp/dbcatalog/en/record/nbdc00338).",
"homepage": "http://agp.dna.affrc.go.jp/agp/db/marker/marker.html",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "Swine Marker Viewer",
"prefix": "NBDC00694",
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Genetic variation"
]
},
"nbdc00695": {
"alt_name": "SWISS-Two-dimensional polyacrylamide gel electrophoresis database",
"description": "SWISS-2DPAGE is a database of proteomic information. The database contains images and identified proteins in species from E. coli to human from a series of 2D-PAGE experiments used to identify proteins by size and charge. The database can be searched by several identifiers or accessed by viwing gel images. Data is available for download via FTP.",
"homepage": "http://world-2dpage.expasy.org/swiss-2dpage/",
"information_keywords": [
"Image/Movie"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "SWISS-2DPAGE",
"prefix": "NBDC00695",
"pubmeds": [
"9399867",
"9847204",
"10592248",
"15274128"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00696": {
"alt_name": "Transcription Analysis of BY-2",
"description": "This site provides information about the results found in a collaborative project of the Laboratories for Structural Construction and for gene Regulation, both housed in the Plant Science Center, RIKEN. Tobacco BY-2 cells were researched and resulted in the collection of EST and microarray information.\nA Blast search option is available. The FASTA format of the sequence researched is required.",
"homepage": "http://mrg.psc.riken.go.jp/strc/index.htm",
"information_keywords": [
"Sequence"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "TAB project",
"prefix": "NBDC00696",
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00697": {
"alt_name": "The Arabidopsis Information Resource",
"description": "TAIR is a database of Arabidopsis thaliana information. The database contains genetic and molecular information for the plant, including several browseable data formats including seed stocks, gene names, and mutant collections. Users can download data from several categories, from images to gene expression microarrays.",
"fairsharing": "biodbcore-000105",
"homepage": "http://www.arabidopsis.org",
"information_keywords": [
"Bioresource",
"Ontology/Terminology/Nomenclature",
"Sequence",
"Expression",
"Interaction/Pathway",
"Bibliography/Documents",
"Repository"
],
"maintainer": "Ohio State University",
"name": "TAIR",
"prefix": "NBDC00697",
"pubmeds": [
"26201819",
"17986450",
"22140109",
"12519987",
"12444417",
"11125061"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"Protein",
"Organism"
]
},
"nbdc00698": {
"description": "TRDB is a database of repeated genetic sequences. Users can query repeat sequences, use an analysis tool to find repeats in a query sequence, design primers, analyze mutations and origins of repeated sequences, and download several data types. Login required.",
"fairsharing": "biodbcore-000246",
"homepage": "http://tandem.bu.edu/cgi-bin/trdb/trdb.exe?taskid=7",
"information_keywords": [
"Sequence"
],
"maintainer": "Boston University",
"name": "Tandem Repeats Database",
"prefix": "NBDC00698",
"pubmeds": [
"17175540"
],
"status": "Inactive",
"target_keywords": [
"Genetic variation"
]
},
"nbdc00699": {
"alt_name": "Tandem Splice Site DataBase",
"description": "TassDB is a database of alternative gene splicing information. The database contains three different resources describing experimentally validated (GYNGYN and NAGNAG or GYN(0-10)GYN and NAGN(0-10)AG) or computationally predicted splicing donor and acceptor sites using different sequence specificity criteria. Users can search for genes or splice site types, and data is available for download.",
"homepage": "http://tassdb2.leibniz-fli.de",
"information_keywords": [
"Sequence"
],
"maintainer": "FLI (Leibniz Institute on Aging - Fritz Lipmann Institute)",
"name": "TassDB2",
"prefix": "NBDC00699",
"pubmeds": [
"17142241",
"20429909"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00700": {
"description": "Taxonomy is a database of systematic classifications of organisms repesented in public sequencing databases. The database contains phylogenetic relatonships and nomenclature for an estimated 10% of all living species. Tools include a browser, genetic codes, and a common evolutionary tree. Taxonomic classificatinos can be downloaded via FTP.",
"homepage": "http://www.ncbi.nlm.nih.gov/taxonomy",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Taxonomy"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "Taxonomy - NCBI",
"prefix": "NBDC00700",
"pubmeds": [
"18940862"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00701": {
"alt_name": "Riken Transcription Factor Database",
"description": "TFdb is a database of mouse transcription factors. The database contains information on known transcription factors, which are collated and annotated from several independent sources. Users can browse or search the database and retrieve ontology and sequence information.",
"homepage": "http://genome.gsc.riken.jp/TFdb/",
"maintainer": "RIKEN Yokohama Institute",
"name": "TFdb",
"prefix": "NBDC00701",
"pubmeds": [
"15336533"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00702": {
"description": "The Candida Albicans Physical Map Website is a portal site about Candida albicans genome and its annotation. It contains a physical map, based on a fosmid library, which was used in conjunction with a new assembly, Assembly 20, based on bioinformatics, to provide completed sequence for most chromosomes. This database contains also Single Nucleotide Polymorphism (SNP) map, based on Assembly 19 of the genome. Users are able to use the Assembly 20 contigs at the Candida Genome Database (CGD).",
"homepage": "http://cbs.umn.edu/candida-albicans/home",
"maintainer": "University of Minnesota",
"name": "The Candida Albicans Physical Map Website",
"prefix": "NBDC00702",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc00704": {
"description": "The Kidney Development Database is a resource of experimental information collected from multiple species. The database contains information on markers, mutations, genes, and critical stages in kidney development.",
"homepage": "http://golgi.ana.ed.ac.uk/kidhome.html",
"information_keywords": [
"Expression"
],
"maintainer": "University of Edinburgh",
"name": "The Kidney Development Database",
"prefix": "NBDC00704",
"pubmeds": [
"10322627"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00707": {
"description": "The RNA modification database is a integrated database of posttranscriptionally modified nucleosides from RNA. This database contains all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. The information in this database permits access to the modified nucleoside literature through provision of both computer-searchable Chemical Abstracts registry numbers and key literature citations. Moreover, this database provides an historical record of the initial reports of occurrence, characterization and chemical synthesis of modified nucleosides from RNA.",
"homepage": "http://mods.rna.albany.edu/",
"information_keywords": [
"Image/Movie"
],
"maintainer": "University at Albany",
"name": "The RNA modification database",
"prefix": "NBDC00707",
"pubmeds": [
"9399834",
"9016519",
"7518580"
],
"status": "Inactive",
"target_keywords": [
"RNA"
]
},
"nbdc00708": {
"description": "This is a database of bacterial RNA molecules with properties of both tRNA and mRNA, which described as tmRNA. The site includes information of tmRNA sequences, two-dimensional structures, proteolytic tags added by tmRNA, and relevant publications.",
"homepage": "http://bioinformatics.sandia.gov/tmrna/",
"information_keywords": [
"Sequence",
"Chemical structure"
],
"maintainer": "Indiana University",
"name": "The tmRNA Website",
"prefix": "NBDC00708",
"pubmeds": [
"9399824",
"9847167",
"10592213",
"11752287",
"14681369"
],
"status": "Suspended",
"target_keywords": [
"RNA"
]
},
"nbdc00709": {
"description": "The Wnt Homepage is a database of wnt pathway information. The database contains information on wnt genes and proteins and related components of its associated signaling pathways, including sequences, structures, and pathway maps. The database also contains information on wnt pathway involvement in diseases.",
"homepage": "http://www.stanford.edu/group/nusselab/cgi-bin/wnt/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "Stanford University",
"name": "The Wnt Homepage",
"prefix": "NBDC00709",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00710": {
"description": "This database of THz spectroscopic measurements of several biologically relevant compounds contains spectra for dozens of compounds, which can be browsed by name. Compound structures and transmittance spectra are available for each entry and results can be downloaded in .txt or .pdf format.",
"homepage": "http://www.riken.jp/THzdatabase/index.html",
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "THz spectral database",
"prefix": "NBDC00710",
"status": "Inactive",
"target_keywords": [
"Metabolite",
"Chemical compound",
"Drug"
]
},
"nbdc00711": {
"description": "TIGRFAMs is a database of sequence alignments of protein coding sequences in multiple species. The database contains protein families annotated by sequence similarity using an HMM algorithm. Users can search the database and download released data via FTP.",
"fairsharing": "biodbcore-000403",
"homepage": "http://www.jcvi.org/cgi-bin/tigrfams/index.cgi",
"information_keywords": [
"Classification"
],
"maintainer": "JCVI (J. Craig Venter Institute)",
"name": "TIGRFAMs",
"prefix": "NBDC00711",
"pubmeds": [
"12520025",
"11125044"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00712": {
"description": "TIGR Plant Transcript Assemblies is a database of transcript assemblies produced from EST projects. The database includes information on transcripts compiled from NCBI and UniProt databases which can be queried by identifier, accession, or BLAST. Transcript assemblies are available for download.",
"homepage": "http://plantta.jcvi.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "JCVI (J. Craig Venter Institute)",
"name": "TIGR Plant Transcript Assemblies",
"prefix": "NBDC00712",
"pubmeds": [
"17088284"
],
"status": "Closed",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00713": {
"alt_name": "Annotation of Beta-Barrel Membrane Proteins in Genomic Sequences",
"description": "This site contains a database of a comprehensive number of bacterial and eukaryotic TMBs (trans beta-barrel membrane proteins) furnished with descriptive and explanatory commentary and including their amino acid sequences.\nSix ways to locate the appropriate TMB are provided, of which the 'New Approach' appears to be the preferred method.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/tmbeta-genome/desc.html",
"information_keywords": [
"Sequence"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "TMBETA-GENOME (Archive)",
"prefix": "NBDC00713",
"pubmeds": [
"17088282",
"15531602",
"15833441",
"15980447",
"16204348"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00714": {
"alt_name": "Functional Database of Membrane Proteins",
"homepage": "https://dbarchive.biosciencedbc.jp/en/tmfunction/desc.html",
"information_keywords": [
"Sequence"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "TMFunction (Archive)",
"prefix": "NBDC00714",
"pubmeds": [
"18842639"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00715": {
"description": "The tmRDB is a database of the structures and functions of the tmRNA (earlier called \"10S RNA\"). This database provides aligned, annotated and phylogenetically ordered tmRNA sequences. It also provides sequences of tag peptide and tmRNA-associated proteins. The alignments of the tmRNA sequences represent conserved secondary structure elements where each base pair is proven by comparative sequence analysis. Whole sequences are downloadable.",
"homepage": "http://rth.dk/resources/rnp/tmRDB/tmRDB.html",
"information_keywords": [
"Sequence",
"3D structure",
"Chemical structure"
],
"maintainer": "UTHealth (University of Texas Health Science Center at Houston)",
"name": "tmRDB",
"prefix": "NBDC00715",
"pubmeds": [
"12520048"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc00716": {
"description": "National BioResource Project Tomato is a database of tomato resources. This database contains a tomato photo gallery and information on EMS mutagenesis lines, gamma irradiation-induced mutant lines, EMS and gamma irradiation-induced mutants and wild type cultivars. Users can search available strains by keywords, growth stages and phenotypes through the TOMATOMA (tomato mutants archive) website.",
"homepage": "http://tomato.nbrp.jp/indexEn.html",
"information_keywords": [
"Phenotype",
"Bioresource"
],
"maintainer": "University of Tsukuba Gene Research Center",
"name": "TOMATO (National BioResource Project)",
"prefix": "NBDC00716",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00717": {
"description": "This is a viewer of Swine Linkage Map. \nTwo linkage map, from NIAI and USDA, were used for the analysis. This site is a part of \"Animal Genome Research Program\" (http://integbio.jp/dbcatalog/en/record/nbdc00338).",
"homepage": "http://agp.dna.affrc.go.jp/agp/db/linkage/linkage.html",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "Swine Linkage Map Viewer",
"prefix": "NBDC00717",
"pubmeds": [
"12873213",
"12648097",
"11167524",
"10612229",
"8138161"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Genetic variation"
]
},
"nbdc00718": {
"description": "Germline Mutagenesis Database - SB transposon is a database of mutant mice. The database contains information on transposon insertion sites which have been experimentally verified in a mouse line. A database of mutants is available.",
"homepage": "http://variation.osu.edu/germline/SB_transposon/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Ohio State University",
"name": "Germline Mutagenesis Database - SB transposon",
"prefix": "NBDC00718",
"pubmeds": [
"16179923"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"DNA"
]
},
"nbdc00719": {
"description": "Transterm is a database of gene transcripts and their regulatory elements. The database contains thousands of gene sequences which can be analyzed to understand general properties of transcription and translation, or to search for regulatory sequences.",
"homepage": "http://crispr.otago.ac.nz/TT/index.php",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "University of Otago",
"name": "Transterm",
"prefix": "NBDC00719",
"pubmeds": [
"18984623",
"9399869"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00720": {
"alt_name": "tRNA gene database curated manually by experts",
"description": "tRNADB-CE is a database of manually curated tRNA gene information. It contains tRNA sequences that have been evaluated experimentally after initial identification by computational algorithms. Entries can be searched by keyword, and a BLAST search tool is available. Bulk download is also available.",
"homepage": "http://trna.ie.niigata-u.ac.jp",
"information_keywords": [
"Sequence"
],
"maintainer": "Niigata University Faculty of Engineering Department of Information Engineering",
"name": "tRNADB-CE",
"prefix": "NBDC00720",
"pubmeds": [
"21071414",
"18842632"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc00721": {
"description": "Tropical Medicine and Health is a database of journals published by Japanese Society of Tropical Medicine. This database allows to search journals which about a tropical disease and tropical medicine as an opinion journal of the medical treatment, research, and educational activities at overseas. Abstracts and full text of articles are distributed on PDF.",
"homepage": "https://www.jstage.jst.go.jp/browse/tmh",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "JST (Japan Science and Technology Agency)",
"name": "Tropical Medicine and Health",
"prefix": "NBDC00721",
"status": "Inactive",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00722": {
"alt_name": "Two-Dimensional Electrophoresis Database of HSG cells proteins",
"description": "The HSG Database is a resource of information on human salivary gland proteins. The site contains data generated from studies of an irradiated human salivary intercalated duct cell line. The proteins represented in the database have been characterized by 2D gel electrophoresis and further identified by MALDI-TOF. Images of the analyzed 2D gels and the annotated spots are available.",
"homepage": "http://cellbiosignal.jp/biochem/kamo/",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Iwate Medical University School of Dentistry",
"name": "HSG Database",
"prefix": "NBDC00722",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00723": {
"alt_name": "Unigene MicroSatellite database",
"description": "UgMicroSatdb is a database of DNA microsatellites. The database contains entries for dozens of species from bacteria to mammals, categorized by Linnean classification. Users can select the species of interest then explore microsatellites in that species using several different search options and parameters. A tutorial introducing site use is also available.",
"homepage": "http://www.veenuash.info/veenu/index.asp",
"information_keywords": [
"Sequence"
],
"maintainer": "Guru Gobind Singh Indraprastha University/University School of Biotechnology",
"name": "UgMicroSatdb",
"prefix": "NBDC00723",
"status": "Inactive",
"target_keywords": [
"Genetic variation"
]
},
"nbdc00724": {
"alt_name": "UK Crop Plant Bioinformatics Network",
"homepage": "http://ukcrop.net/",
"information_keywords": [
"Portal"
],
"maintainer": "UK CropNet Consortium",
"name": "UK CROPNET",
"prefix": "NBDC00724",
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00725": {
"alt_name": "University of Minnesota Biocatalysis/Biodegradation Database",
"description": "EAWAG-BBD is a database about information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. Each entry is presented with information on the starting and intermediate chemical compounds, the organisms that transform the compounds, the enzymes, and the genes. Users are able to search this database for compound, enzyme, microorganism, pathway, or BT rule name; chemical formula; chemical structure; CAS Registry Number; or EC code. This database is being expanded primarily with the help of advanced undergraduate and graduate students.",
"homepage": "http://eawag-bbd.ethz.ch/",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie",
"Chemical structure"
],
"maintainer": "University of Minnesota",
"name": "EAWAG-BBD",
"prefix": "NBDC00725",
"pubmeds": [
"19767608"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein",
"Metabolite"
]
},
"nbdc00726": {
"description": "UniVec is a database for the identification of vector contamination in sequencing projects. The database contains common vector sequences as well as tools for recognizing and purifying sequence reads of vector contamination. Information is represented in a drastically reduced non-redundant format to minimize computational intensity and complexity. UniVec can be downloaded via FTP.",
"fairsharing": "biodbcore-000461",
"homepage": "http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html#Overview",
"information_keywords": [
"Sequence"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "UniVec",
"prefix": "NBDC00726",
"status": "Active",
"target_keywords": [
"DNA"
]
},
"nbdc00727": {
"description": "This database contains cDNA (EST) information for the brown planthopper (BPH, Nilaparvata lugens). EST annotations and clustering information can be viewed through keyword searches.",
"homepage": "http://bphest.dna.affrc.go.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "UNKA (BPH) EST",
"prefix": "NBDC00727",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00729": {
"description": "This site provides access to the Saccharomyces database. Users can browse or search by chromosome, gene, and ORF. Results can be obtained in FASTA format. The original site has been closed. The raw data can be downloaded from LSDB Archive site ( https://dbarchive.biosciencedbc.jp/en/yeast-cdna/desc.html ).",
"homepage": "http://yeast.utgenome.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tokyo Graduate School of Science",
"name": "UTGB",
"prefix": "NBDC00729",
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00730": {
"description": "UTRdb is a database of untranslated region sequences and other information related to the regulation of genes by way of 5' and 3' UTRs. The database contains sequence information for hundreds of thousands of genes in dozens of species, and a second, more comprehensive resource specifically dedicated to human UTRs. Tools for analyzing UTRs and bulk data downloads are available.",
"homepage": "http://utrdb.ba.itb.cnr.it/",
"information_keywords": [
"Sequence"
],
"maintainer": "Institute for Biomedical Technologies",
"name": "UTRdb",
"prefix": "NBDC00730",
"pubmeds": [
"19880380",
"15608165",
"11752330",
"11897027",
"11591473",
"10592223"
],
"status": "Active",
"target_keywords": [
"RNA"
]
},
"nbdc00731": {
"description": "This site contains three systems that can be searched.\nThe Genome Browser combines a database of available genome annotations with an interactive web page.\nThe LD Search System facilitates searches for bins of alleles of linked loci showing a tendency to co-occur nonrandomly on chromosomal haplotypes.\nVarygene 2 contains a list of various types of polymorphisms, repeats, variations in structure and how these findings relate to the genome, its transcripts and function.",
"homepage": "http://h-invitational.jp/varygene/home.htm",
"information_keywords": [
"Sequence"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "VarySysDB",
"prefix": "NBDC00731",
"pubmeds": [
"18953038"
],
"status": "Inactive",
"target_keywords": [
"Genetic variation"
]
},
"nbdc00732": {
"description": "Vector DB is a database of genetic constructs used in molecular biology. The database contains sequences of hundreds of vectors which can be browsed by type. Search function is currently unavailable.",
"homepage": "http://genome-www.stanford.edu/vectordb//",
"information_keywords": [
"Sequence"
],
"maintainer": "Stanford University",
"name": "VectorDB",
"prefix": "NBDC00732",
"status": "Closed",
"target_keywords": [
"DNA"
]
},
"nbdc00733": {
"description": "Viral Probe is a list that contains a vast number of viral probes identified experimentally in the sequences of a comprehensive number of viruses. The sequences of each probe identified in each species of each genus of the virus families studied are available for browsing and download.\nA search option does not appear to be available, other than browsing the list and searching for the necessary species and/or probe identification name or number.",
"homepage": "http://genestamp.sinica.edu.tw/virus/viralProbe.htm",
"information_keywords": [
"Method",
"Sequence",
"Taxonomy"
],
"maintainer": "Academia Sinica",
"name": "Viral Probe Database",
"prefix": "NBDC00733",
"status": "Inactive",
"target_keywords": [
"DNA",
"RNA"
]
},
"nbdc00734": {
"description": "VISTA Enhancer Browser is a database of mammalian gene enhancers. The database contains information on human and mouse enhancer elements validated in transgenic mice. Data can be can be browsed by element and location, or searched by expression pattern or gene region. Enhancer sequences are available for download.",
"homepage": "http://enhancer.lbl.gov/",
"information_keywords": [
"Sequence",
"Expression",
"Image/Movie"
],
"maintainer": "LBNL (Lawrence Berkeley National Laboratory)",
"name": "VISTA Enhancer Browser",
"prefix": "NBDC00734",
"pubmeds": [
"17130149"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"DNA"
]
},
"nbdc00735": {
"homepage": "http://www.wehi.edu.au/other_domains/MalDB/who.html",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "Walter and Eliza Hall Institute of Medical Research",
"name": "WHO/TDR MALARIA Database",
"prefix": "NBDC00735",
"status": "Inactive",
"target_keywords": [
"cDNA/EST",
"RNA",
"Protein",
"Organism"
]
},
"nbdc00736": {
"alt_name": "Whole Genome Annotation",
"homepage": "http://rgp.dna.affrc.go.jp/whoga/",
"information_keywords": [
"Sequence"
],
"maintainer": "National Institute of Agrobiological Sciences",
"name": "WhoGA",
"prefix": "NBDC00736",
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc00738": {
"alt_name": "Worm ORFeome Database",
"description": "WORFDB is a database of C. elegans open reading frame information. The database contains data from ORF projects, which can be searched by keyword or BLAST, as well as data from RACE experiments to verify predicted genes. A database of promoters is also available.",
"homepage": "http://worfdb.dfci.harvard.edu",
"information_keywords": [
"Sequence"
],
"maintainer": "Harvard Medical School",
"name": "WORFDB",
"prefix": "NBDC00738",
"pubmeds": [
"15489327",
"12679813",
"12519990",
"11242119"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00739": {
"alt_name": "World-Two-dimensional polyacrylamide gel electrophoresis database",
"description": "World-2DPAGE is a database of proteomic reference resources. The database collects information on 2D-PAGE studies from published literature. Users can access a list of included databases or search by several identifiers.",
"fairsharing": "biodbcore-000530",
"homepage": "http://world-2dpage.expasy.org/repository/",
"information_keywords": [
"Image/Movie"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "World-2DPAGE Repository",
"prefix": "NBDC00739",
"pubmeds": [
"18617148"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00740": {
"description": "WormBase is a database of information on nematodes and other worms. The database contains extensive information on a number of species including genome sequences, genes, gene expression, proteins, and phenotypes. Users can search by keyword, BLAST, or BLAT, and create user accounts to save searches and other useful information.",
"fairsharing": "biodbcore-000156",
"homepage": "http://www.wormbase.org",
"information_keywords": [
"Bioresource",
"Ontology/Terminology/Nomenclature",
"Sequence",
"Expression",
"Image/Movie",
"Bibliography/Documents",
"Repository"
],
"maintainer": "Ontario Institute For Cancer Research",
"name": "WormBase",
"prefix": "NBDC00740",
"pubmeds": [
"29069413",
"27899279",
"26578572",
"24194605",
"23160413",
"24058818",
"22067452",
"21543339",
"19910365",
"17991679",
"17099234",
"16988424",
"16381915",
"15608221",
"15489338",
"14681445",
"12519966",
"11125056"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"Protein",
"Organism",
"Health/Disease"
]
},
"nbdc00741": {
"alt_name": "Xanthomonas oryzae pv. oryzae genome database",
"homepage": "http://microbe.dna.affrc.go.jp/Xanthomonas/",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "Xanthobase",
"prefix": "NBDC00741",
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Protein",
"Health/Disease"
]
},
"nbdc00742": {
"description": "The Yeast Interacting Proteins Database is a database of binary protein interactions detected by a yeast two-hybrid screen. The database contains downloadable data for all interactions or a subset of repeatedly observed interactions.",
"homepage": "http://itolab.med.kyushu-u.ac.jp//Y2H/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "The University of Tokyo Graduate School of Science Department of Biophysics and Biochemistry",
"name": "Yeast Interacting Proteins Database",
"prefix": "NBDC00742",
"pubmeds": [
"10655498",
"11283351"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00743": {
"description": "The yeast snoRNA database is a comprehensive database for small nucleolar RNAs (snoRNAs) from the yeast Saccharomyces cerevisiae. It allows to visualize the positions of pseudouridines, 2'-O-methylations, and base methylations in three-dimensional space in the ribosome and also in linear and secondary structure formats of ribosomal RNA. It provides additional perspective on where the modifications occur relative to functional regions within the rRNA and relative to other nearby modifications.\nThe database also includes details of the base pairing of snoRNAs with target RNAs, genomic organization of the yeast snoRNA genes, and information on corresponding snoRNAs and modifications in other model organisms.",
"homepage": "http://people.biochem.umass.edu/fournierlab/snornadb/main.php",
"information_keywords": [
"Phenotype",
"Sequence",
"Classification"
],
"maintainer": "University of Massachusetts Amherst",
"name": "UMASS Amherst Yeast snoRNA Database",
"prefix": "NBDC00743",
"pubmeds": [
"17283215"
],
"status": "Active",
"target_keywords": [
"RNA"
]
},
"nbdc00744": {
"alt_name": "Yeast Microarray Global Viewer",
"description": "yMGV is a database of yeast gene expression information collected by microarray. The database contains information from hundreds of experiments collected from published literature. Users can browse and analyze datasets by single gene, a gene list, common response, or compendia of related studies. Several additional tools are also provided to explore the data.",
"homepage": "http://www.transcriptome.ens.fr/ymgv",
"information_keywords": [
"Expression"
],
"maintainer": "Ecole normale superieure",
"name": "yMGV",
"prefix": "NBDC00744",
"pubmeds": [
"11752259",
"11433039"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00745": {
"alt_name": "National BioResource Project Zebrafish",
"description": "National BioResource Project Zebrafish is a database for preservation and distribution of zebrafish strains. The resource list consists of transgenic, mutant and wild strains maintained by RIKEN Brain Science Institute, National Institute of genetics and National Institutes of Natural Sciences. Each entry consists of 12 items such as the allele, the strain name and genotype. Some entries contain photo data. Users can search available resources by strain types and facilities, as well as keywords from these items.",
"homepage": "http://www.shigen.nig.ac.jp/zebra/index_en.html",
"information_keywords": [
"Bioresource"
],
"maintainer": "National Institute of Genetics",
"name": "NBRP Zebrafish",
"prefix": "NBDC00745",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00746": {
"alt_name": "The Zebrafish Model Organism Database",
"description": "ZFIN is a central repository and web-based resource for zebrafish genetics and development. This database contains manually curated data for zebrafish genes, phenotypes, genotypes, gene expression, antibodies, anatomical structures and publications from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. The database also contains a wide-ranging collection of web-based search forms and tools facilitates access to integrated views of these data promoting analysis and scientific discovery. ZFIN works closely with ZIRC to connect their genetic data with available probes and fish lines.",
"fairsharing": "biodbcore-000575",
"homepage": "http://zfin.org/",
"information_keywords": [
"Bioresource",
"Ontology/Terminology/Nomenclature",
"Sequence",
"Expression",
"Bibliography/Documents",
"Repository"
],
"maintainer": "University of Oregon/Zebrafish Information Network",
"name": "ZFIN",
"prefix": "NBDC00746",
"pubmeds": [
"21036866",
"17991680",
"11125057",
"10354586",
"9891346",
"9441953"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"Protein",
"Organism"
]
},
"nbdc00747": {
"alt_name": "Zebrafish Gene Trap and Enhancer Trap Database",
"description": "This is a database of the Koichi Kawakami Laboratory of the National Institute of genetics (NIG). It contains information of the Zebrafish. The data is gathered by use of the method of gene trapping, which involves inserting mutations into the genome, and by the application of an enhancer trap, a transgenic construction for the identification of enhancers. Enhancers are produced by the fusing of two proteins, for which genes are then inserted into the genome. \nAn advanced search option is available.",
"homepage": "http://kawakami.lab.nig.ac.jp/ztrap/",
"information_keywords": [
"Expression",
"Localization",
"Image/Movie"
],
"maintainer": "National Institute of Genetics",
"name": "zTRAP",
"prefix": "NBDC00747",
"pubmeds": [
"15693946"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"Organism"
]
},
"nbdc00761": {
"description": "The Japanese Fungi on Plants is an illustrated Encyclopedia of Japanese Filamentous Fungi, which collects and displays photos and information of fungi, such as scientific name, classification, conditions for growth, images of the asexual and sexual stages, images of symptoms, and index numbers for up to 100,000 species of fungi are also available.",
"homepage": "http://www.naro.affrc.go.jp/archive/niaes/inventory/microorg/eng/zukan-e.html",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents",
"Classification"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "Japanese Fungi on Plants",
"prefix": "NBDC00761",
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease"
]
},
"nbdc00766": {
"description": "Digital Atlas of Actinomycetes is a collection of micrographs and annotations about Actinomycetes. Data are collected from the 'Atlas of Actinomycetes' (Asakura Publishing Co., Tokyo, Japan; 1997) published by the Society for Actinomycetes Japan. This database allows to browse using section, genus and alphabetical index.",
"homepage": "http://www.actino.jp/DigitalAtlas1/index.htm",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Society for Actinomycetes Japan",
"name": "Digital Atlas of Actinomycetes",
"prefix": "NBDC00766",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc00767": {
"alt_name": "3D Electron Microscopy (3D-EM) Data Navigator",
"description": "EM Navigator is a web site to browse 3D electron microscopy (3D-EM) data of biological molecules and assemblies, based on EMDB and PDB data for beginners, non-specialists, and experts in 3D-EM or structural/molecular biology. Each entry contains interactive 3D images and associated information such as a summary, literature, experiment methods, slice data, etc.",
"homepage": "http://pdbj.org/emnavi/?&lang=en",
"information_keywords": [
"Image/Movie",
"3D structure"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "EM Navigator",
"prefix": "NBDC00767",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00769": {
"description": "Yorodumi is a database of 3D structures of biological molecules. This database contains 3D structure images of biological molecules from the Protein Data Bank (PDB) and EM Data Bank (EMDB) to easily watch, move and rotate. Jmol and jV (PDBj Viewer) are used as 3D molecular structure viewer applets.",
"homepage": "https://pdbj.org/emnavi/quick.php?lang=en",
"information_keywords": [
"3D structure"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "Yorodumi",
"prefix": "NBDC00769",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc00770": {
"description": "Protein Globe is a visual database of protein structures. The database consists of a spherical representation of protein fold structures (the globe) that users can navigate to select structures of interest. The globe is designed such that similar structures are close together. Users can then select structures and use other PDBj functionalities to explore further.",
"homepage": "http://www.pdbj.org/globe/",
"information_keywords": [
"3D structure"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "Protein Globe",
"prefix": "NBDC00770",
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc00771": {
"alt_name": "a DNA marker database for vegitables",
"description": "This database contains DNA marker and linkage map information for a variety of garden crops. For each crop, information such as the linkage map, DNA marker sequences, conditions for detection, data on polymorphisms between cultivars, and relevant publications can be accessed.",
"homepage": "https://vegmarks.nivot.affrc.go.jp/VegMarks/app/page/home",
"information_keywords": [
"Sequence"
],
"maintainer": "National Agriculture and Food Research Organization,National Institute of Vegetable and Tea Science",
"name": "VegMarks",
"prefix": "NBDC00771",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc00776": {
"description": "This encyclopedia describes forage crop diseases in Japan, including causal agents and photographs of the symptoms about forage crop diseases, in support of investigations and experiments conducted at the Institute of Livestock and Grassland Science. Users can perform searches by host plant name, pathogen, or pathogenic features, which lead to detailed information on the disease, photographs of the pathogen, and other relevant literatures.",
"homepage": "http://www.naro.affrc.go.jp/org/nilgs/diseases/detitle.html",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science",
"name": "Illustrated Encyclopedia of Forage Crop Diseases",
"prefix": "NBDC00776",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00781": {
"alt_name": "Medical Information Network Distribution Service",
"description": "This service provides information to medical professionals and patients on relevant treatment therapy options that are sufficiently supported by scientific evidence so the best possible treatment can be chosen and agreed upon by both parties, in accordance with patients' wishes, beliefs, medical ethics, and social restrictions. Medical consultation guidelines and literature references available from this service are prepared by experts based on scientific evidence. Recommendations in the guidelines are based on scientific judgments supported by the accumulated findings of medical research and therefore can support decision making in clinical settings. Guidelines and literature references can be found using the complete viewing and search function. A table of contents (for viewing), keyword search function, and question-based viewing (clinical questions) are available.",
"homepage": "https://minds.jcqhc.or.jp/english/english.php",
"information_keywords": [
"Bibliography/Documents",
"Phenotype"
],
"maintainer": "Japan Council for Quality Health Care",
"name": "MINDS",
"prefix": "NBDC00781",
"status": "Active",
"target_keywords": [
"Health/Disease",
"Organism"
]
},
"nbdc00782": {
"description": "This is a database of red clover expressed sequences. The database contains consensus gene sequences and EST reads and allows for BLAST and keyword search. Data are available for download.",
"homepage": "https://www.kazusa.or.jp/e/plant/red_clover/EST/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Trifolium pratense EST Index",
"prefix": "NBDC00782",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00783": {
"alt_name": "A comprehensive mass spectral tags archive for plant metabolomics",
"description": "MassBase is a fundamental archive of mass spectral tags (MST) for metabolomics. It includes both known and unknown assigned (or predicted) peaks that are found in biological samples (mainly plants) and standard chemical reagents for peak annotation. It provides raw mass chromatograms from various biological samples as well as text-file data of these raw chromatograms. It is expected to contribute to an understanding of the metabolism of organisms together with MassBank and KNApSAcK databases, and that it will help with the development of pipeline software to extract metabolite peaks from annotated metabolites in the process of linking DNA information to metabolism.",
"homepage": "http://webs2.kazusa.or.jp/massbase/index.php/",
"information_keywords": [
"Method"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "MassBase",
"prefix": "NBDC00783",
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc00784": {
"alt_name": "Regulatory-network Research in Arabidopsis T87 cultured cells",
"description": "This is a database of over-expression experiments in Arabidopsis T87 cultured cells. Approximately 185 constructs were selected as relating to metabolism and used for DNA microarray, GC-MS, and UPLC-MS assays. \nThe results of these analyses can be accessed to understand large-scale regulatory relationships involving gene expression and metabolite formation in plants.",
"homepage": "http://webs2.kazusa.or.jp/kagiana/rnr/",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "RnR",
"prefix": "NBDC00784",
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Metabolite"
]
},
"nbdc00785": {
"alt_name": "New Energy and Industrial Technology Development Organization Database",
"description": "NEDO database is a database of human spleen cDNA clones with sequence information for spleen clones listed by several indices and sequencing information and plots for each clone. In addition to browsing clones, users can search by FLJ ID, accession, or clone name.",
"homepage": "http://www.kazusa.or.jp/NEDO/",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "NEDO database",
"prefix": "NBDC00785",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00787": {
"description": "This is a database of the Streptococcus pyogenes genome. The database contains a genome browser, lists of ORFs and other functional elements, and BLAST search. Data is available for download.",
"homepage": "http://genome.bio.titech.ac.jp/bacteria/spyo/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Tokyo Institute of Technology",
"name": "Streptococcus pyogenes",
"prefix": "NBDC00787",
"pubmeds": [
"12799345"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein"
]
},
"nbdc00792": {
"alt_name": "Asian-Pacific Alien Species Database",
"homepage": "http://www.naro.affrc.go.jp/archive/niaes/techdoc/apasd/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "APASD",
"prefix": "NBDC00792",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00793": {
"alt_name": "Japan Existing Chemical Data Base",
"description": "JECDB is a database of toxicity testing reports for existing chemicals maintained by National Institute of Health Sciences (NIHS). JECDB contains reports on Japan's own existing chemicals safety program and the OECD HPV (high production volume) chemicals program. Each report consists of the nomenclature of the chemical, an abstract with summarized data from several studies in English and test results in Japanese. Users can search reports by CAS Registry Numbers, names of chemical substances, and toxicity tests.",
"homepage": "http://dra4.nihs.go.jp/mhlw_data/jsp/SearchPageENG.jsp",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NIHS (National Institute of Health Sciences)",
"name": "JECDB",
"prefix": "NBDC00793",
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc00795": {
"description": "NBRC is a database about bioresources collected by Biological Resource Center (NBRC), NITE. It includes collection of microbial resources and taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algae, bacteriophages and DNA resources for academic research and industrial applications. For users, it is able to distribute microorganism cultures, microbial genomic DNA clones, human cDNA clones, etc.",
"fairsharing": "biodbcore-000467",
"homepage": "http://www.nite.go.jp/en/nbrc/cultures/index.html",
"information_keywords": [
"Bioresource"
],
"maintainer": "NITE (National Institute of Technology and Evaluation)",
"name": "NBRC (Biological Resource Center, NITE)",
"prefix": "NBDC00795",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Organism"
]
},
"nbdc00796": {
"alt_name": "GlycoGene Database",
"description": "This database provides information on the 180 human glycogenes discovered up to the time it was created. A glycogene is a DNA sequence associated with glycan synthesis. Examples of glycogenes are glycosyltransferase, sugar-nucleotide synthases, sugar-nucleotide transporters and sulfotransferases.\nThe site contains important detail needed to study glycogenes. The information is presented as XML documents and include graphs. A simple keyword search is used to retrieve lists of glycogenes and their characteristics. Information can also be retrieved by means of the REST application (send request, receive response) as well as with the SOAP (send message with search parameters, receive an XML-formatted document) method.",
"homepage": "https://acgg.asia/ggdb2/",
"information_keywords": [
"Expression"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "GGDB",
"prefix": "NBDC00796",
"pubmeds": [
"15467393"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein",
"Carbohydrate"
]
},
"nbdc00798": {
"alt_name": "Lectin Frontier Database",
"description": "This database contains information about the quantity of interactions noted among a series of lectins and a panel of pyridylaminated (PA) glycans when exposed to an automated frontal affinity chromatography with fluorescence detection (FAC-FD) system. The data is presented in a bar graph format containing the affinity constants (Ka) of the lectins towards the glycans or, alternatively, an actual measurement (V-V0). It also provides the absolute values of sugar-protein interactions.\nThe information provided can be relied upon to be accurate and therefore this database is a valuable resource in biological studies of glycans.\nKeyword and advanced search options are provided.",
"homepage": "https://acgg.asia/lfdb2",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie",
"Chemical structure"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "LfDB",
"prefix": "NBDC00798",
"pubmeds": [
"17947995",
"15943812",
"12968376",
"12223272",
"805787"
],
"status": "Active",
"target_keywords": [
"Protein",
"Carbohydrate"
]
},
"nbdc00799": {
"alt_name": "Glycan Mass Spectral DataBase",
"description": "GMDB is a database of glycan mass spectral data. It provides a novel tool for use in glycomics research. Glycans can be identified easily and quickly through spectral matching. \nThe glycan structure of analytes can be estimated through comparison of the MSn spectra of analytes and MSn spectral images of glycans. Relevant spectral images can be searched based on a search of glycan composition or of m/z value.",
"homepage": "https://jcggdb.jp/rcmg/glycodb/Ms_ResultSearch",
"information_keywords": [
"Chemical structure"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "GMDB",
"prefix": "NBDC00799",
"pubmeds": [
"16053281"
],
"status": "Active",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc00801": {
"description": "This website was created to investigate whether it would be possible to share biological sample images with other interested Internet users. Feedback was requested in order to enable the site designers to further develop the concept.\nSection images of a rat brain are available. Lack of finance limited the number of images to only 7. \nActivity on this site ended in 2006. An e-mail address is however provided, should questions arise.",
"homepage": "http://riodb.ibase.aist.go.jp/rio-archive/frame.cgi?EDB055",
"information_keywords": [
"Image/Movie"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "Rat Brain Sections: Super-fine images",
"prefix": "NBDC00801",
"status": "Closed",
"target_keywords": [
"Organism"
]
},
"nbdc00802": {
"alt_name": "A database of local structures of protein segments",
"description": "This site contains a comprehensive collection of protein segments that were grouped according to similarities in their three-dimensional structure. These groups, called clusters, can be searched by entering a description of the backbone structure of the segment in question. Three possible methods of identification are provided, namely by input of the PDB ID and specific Chain ID of the segment, by direct input of the dihedral angles of the segment or by entering the appropriate DSSP (Define Secondary Structure of Proteins) symbols of the segment to be placed.",
"homepage": "http://riodb.ibase.aist.go.jp/proseg/",
"information_keywords": [
"3D structure",
"Classification"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "ProSeg",
"prefix": "NBDC00802",
"pubmeds": [
"18931918"
],
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc00803": {
"description": "Invasive Species of Japan is a integrated database of invasive and alien species in Japan. Each entry contains basic and invasion information, such as range, route, impact, etc. The database allows to search with keywords or browse by taxon. Moreover, it provides links to online resources.",
"homepage": "http://www.nies.go.jp/biodiversity/invasive/index_en.html",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "NIES (National Institute for Environmental Studies)",
"name": "Invasive Species of Japan",
"prefix": "NBDC00803",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00805": {
"description": "Taxonomy icon is a collection of icon materials illustrating biological species including Bacteria, Fungi, Protista, Plantae and Animalia. Taxonomy icon contains image icons of species and related information including common names, icon URLs, taxonomy IDs and the binomial names. Users can search, download, distribute and transmit icons under a Creative Commons license (Attribution 2.1 Japan).",
"homepage": "http://togodb.biosciencedbc.jp/togodb/view/taxonomy_icon_en",
"information_keywords": [
"Image/Movie"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "Taxonomy icon",
"prefix": "NBDC00805",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00806": {
"description": "TogoTV international is a repository of educational and tutorial videos demonstrating how to use biological databases and web tools such as NCBI, UCSC Genome Browser, etc. Each entry contains a title and a short explanation of a video, as well as an embedded video file. Users can search videos by keywords, tags and categories.",
"homepage": "https://togotv.dbcls.jp/en",
"information_keywords": [
"Image/Movie"
],
"maintainer": "DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "TogoTV",
"prefix": "NBDC00806",
"pubmeds": [
"21803786"
],
"status": "Active"
},
"nbdc00807": {
"alt_name": "Plant Organelles Database 3",
"description": "PODB3 is a collection of databases describing organelles and their behavior in plants. The site contains visualizations and movies of organelles, protocols for studying plant organelles, and links to external sites. It is made up of of 6 individual parts: 'The Electron Micrograph Database', 'The Perceptive Organelles Database', 'The Organelles Movie Database', 'The Organellome Database', 'The Functional Analysis Database', and 'External Links to other databases and Web pages'. All the data and protocols in this database are populated by direct submission of experimentally determined data from plant researchers.",
"homepage": "http://podb.nibb.ac.jp/Organellome",
"information_keywords": [
"Image/Movie",
"3D structure",
"Repository"
],
"maintainer": "National Institute for Basic Biology",
"name": "PODB3",
"prefix": "NBDC00807",
"pubmeds": [
"17932059",
"21115470",
"24092884"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc00808": {
"description": "Glycoforum is a portal site for glycoscience research. This portal site contains a search engine of literatures, newsletters, articles and information on forums related to glycoscience. Users can search within the website by keywords, and see the number of papers registered in Pubmed by categories.",
"homepage": "http://www.glycoforum.gr.jp/index.html",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Seikagaku Corporation",
"name": "Glycoforum",
"prefix": "NBDC00808",
"status": "Active",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc00812": {
"alt_name": "Drugs viewed as perturbants to the molecular system",
"description": "KEGG DRUG is a comprehensive database of drug information about all marketed drugs in Japan, as well as many prescription drugs in USA and Europe. KEGG DRUG is based on chemical structure or component, and each entry contains information about drug targets (pathways), metabolizing enzymes and other interacting molecules. This database also includes crude drugs and TCM (Tradictional Chinese Medicine). Users can check for drug-drug interaction, view structure maps representing the history of drug development and search drugs by generic names, trade names, and components.",
"homepage": "http://www.genome.jp/kegg/drug/",
"information_keywords": [
"Interaction/Pathway",
"Chemical structure"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG DRUG",
"prefix": "NBDC00812",
"status": "Active",
"target_keywords": [
"Drug"
]
},
"nbdc00813": {
"alt_name": "Diseases viewed as perturbed states of the molecular system",
"description": "KEGG DISEASE is a database of human diseases with information on perturbed molecular networks. Each disease entry contains a list of known disease genes, environmental factors (carcinogens, pathogens, etc), diagnostic markers and therapeutic drugs with reference information. This database provides maps of molecular networks associated with diseases through links to the KEGG PATHWAY database. Users can search human diseases by names, description, categories, pathways, and known causative genes.",
"homepage": "http://www.genome.jp/kegg/disease/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG DISEASE",
"prefix": "NBDC00813",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Drug"
]
},
"nbdc00814": {
"alt_name": "Metabolome informatics resource integrating genomics and chemistry",
"description": "KEGG COMPOUND is a database of biologically relevant compounds, including chemical structures and associated information for compounds in the KEGG database such as small molecules, biopolymers, and other related substances. The site also has a collection of links to other relevant KEGG resources such as GLYCAN.",
"homepage": "http://www.genome.jp/kegg/compound/",
"information_keywords": [
"Interaction/Pathway",
"Chemical structure"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG COMPOUND",
"prefix": "NBDC00814",
"pubmeds": [
"19327755",
"17921532",
"17400247",
"14505407",
"20460463"
],
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Protein",
"Chemical compound"
]
},
"nbdc00815": {
"description": "KEGG ENZYME is a database of enzymes involved in recognized KEGG biochemical reactions, and can be searched by KEGG enzyme ID or by name. Results include enzyme class, reaction, pathway, and gene information.",
"homepage": "http://www.genome.jp/dbget-bin/www_bfind?enzyme",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Interaction/Pathway"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "DBGET Search - ENZYME",
"prefix": "NBDC00815",
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc00816": {
"alt_name": "Organisms and ecosystems with genome sequence information",
"description": "KEGG GENOME is a database of full genome sequence information for multiple species. The database is a collection of references to descriptive genome literature and has links to reaction pathways in each organism, comparative tools, and taxonomy based on KEGG information and provides KEGG pathway information and links to outside resources including primary literature.",
"homepage": "http://www.genome.jp/kegg/genome.html",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG GENOME",
"prefix": "NBDC00816",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00817": {
"alt_name": "Linking genomes to pathways by ortholog annotation",
"description": "KEGG ORTHOLOGY is a database of KEGG pathway ortholog groups, and contains the pathways at the core of the KEGG representation system. Users can search for ortholog groups and explore members across species.",
"homepage": "http://www.genome.jp/kegg/ko.html",
"information_keywords": [
"Interaction/Pathway",
"Classification"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG ORTHOLOGY (KO) Database",
"prefix": "NBDC00817",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00818": {
"alt_name": "Knowledge base for predicting biodegradation and biosynthesis",
"description": "KEGG REACTION is a database of enzymatic reactions. The database contains all KEGG enzyme interactions and KEGG pathway metabolic reactions, including related pathways, and uses IUBMB nomenclature. Users can also find the reaction pathway of individual enzymes.",
"homepage": "http://www.genome.jp/kegg/reaction/",
"information_keywords": [
"Interaction/Pathway",
"Chemical structure",
"Classification"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG REACTION",
"prefix": "NBDC00818",
"pubmeds": [
"14505407",
"15600352",
"19477985",
"17516640",
"20435670"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc00819": {
"description": "KEGG RPAIR is a database of substrate-product reaction pairs. The database contains the main chemical reactants from KEGG REACTION events. Users can search for substrates or products by their KEGG compound ID to obtain all reaction pairs of that chemical, related reactions, and enzymes that catalyze the reaction.",
"homepage": "http://www.genome.jp/dbget-bin/www_bfind?rpair",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "DBGET Search - RPAIR",
"prefix": "NBDC00819",
"status": "Closed",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc00820": {
"description": "The KEGG VgeneS database contains gene and protein sequence information from sequenced viral genomes that can be searched by gene name or ID. Data is from and provides links to NCBI resources.",
"homepage": "http://www.genome.jp/dbget-bin/www_bfind?vgenes",
"information_keywords": [
"Sequence"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "DBGET Search - VGENES",
"prefix": "NBDC00820",
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00821": {
"description": "KEGG VGENOME is a database of viral genomes with sequence, and taxonomy information for sequenced viruses. The entry for each virus provides references to primary literature.",
"homepage": "http://www.genome.jp/dbget-bin/www_bfind?vgenome",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "DBGET Search - VGENOME",
"prefix": "NBDC00821",
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00822": {
"description": "This database is a collection of human embryo images. The images were collected by sagittal plane MR microscopy of embryos from the Kyoto Collection. Images can be browsed by developmental stage.",
"homepage": "http://www.bk.tsukuba.ac.jp/~mrlab/human_embryos/index.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "University of Tsukuba",
"name": "3D MR Microscopy of Human Development by Kyoto & Tsukuba Universities",
"prefix": "NBDC00822",
"pubmeds": [
"7114091",
"594909",
"5759548"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00831": {
"description": "Proteopedia is an interactive database of 3D structures of biological molecules. The database contains high-quality structures as well as explanatory articles for all proteins in PDB, as well as articles about several diseases and classes of proteins. The database is in wiki form and supports community editing.",
"homepage": "http://www.proteopedia.org/",
"information_keywords": [
"3D structure"
],
"maintainer": "Weizmann Institute of Science",
"name": "Proteopedia",
"prefix": "NBDC00831",
"pubmeds": [
"18673581"
],
"status": "Active",
"target_keywords": [
"DNA",
"Protein"
]
},
"nbdc00832": {
"homepage": "http://www.ebi.ac.uk/pdbe/pqs/",
"information_keywords": [
"3D structure"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "Protein Quaternary Structure",
"prefix": "NBDC00832",
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc00834": {
"description": "geneWiki is a database of gene and protein function. The database contains articles for all human genes featuring links to and from Wikipedia. Users can search, browse, and participate in editing of articles.",
"fairsharing": "biodbcore-000133",
"homepage": "https://en.wikipedia.org/wiki/Wikipedia:WikiProject_Genetics/Gene_Wiki",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Wikimedia Foundation Inc.",
"name": "Gene Wiki",
"prefix": "NBDC00834",
"pubmeds": [
"18613750",
"19755503",
"22075991",
"22165947"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00835": {
"description": "VIPERdb is a database of viral capsid structures. The database contains structural x-ray crystallographic and cryo-EM data on the structures of 350 icosahedral viruses. Structures are interactive and available for download, and can be searched by PDB ID or virus name.",
"homepage": "http://viperdb.scripps.edu/",
"information_keywords": [
"Sequence",
"Image/Movie",
"3D structure"
],
"maintainer": "The Scripps Research Institute",
"name": "VIPERdb",
"prefix": "NBDC00835",
"pubmeds": [
"18981051"
],
"status": "Inactive",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc00836": {
"description": "MedlinePlus is the patient-forward site of the US NIH National Library of Medicine. The database contains information on a variety of health topics, from diseases to drugs, presented for the general public. The database is curated and updated by NLM staff and seeks to provide users with straightforward, unbiased explanations and information.",
"homepage": "http://www.nlm.nih.gov/medlineplus/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NLM (National Library of Medicine)",
"name": "MedlinePlus",
"prefix": "NBDC00836",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00837": {
"description": "BodyParts3D is a database for anatomy representing shapes and positions of human body parts by 3D models. BodyParts3D contains 3D models of an adult human male labeled with anatomical terms. This database features a web based tool; Anatomography, which enables a user to create an anatomical image of human body parts and save it as a URL. A user can also redistribute a part or whole of the data from this database.",
"homepage": "http://lifesciencedb.jp/bp3d/?lng=en",
"information_keywords": [
"Image/Movie",
"3D structure"
],
"maintainer": "DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "BodyParts3D",
"prefix": "NBDC00837",
"pubmeds": [
"18835852"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00838": {
"description": "This database contains DNA sequence information for S. cereviseae. Sequences were obtained from a vector-capped cDNA library. The sequence data is available for download.",
"homepage": "http://itolab.med.kyushu-u.ac.jp//GCap/",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tokyo Graduate School of Science Department of Biophysics and Biochemistry",
"name": "Budding yeast cDNA sequencing project",
"prefix": "NBDC00838",
"pubmeds": [
"17101987"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00839": {
"alt_name": "Adiantum capillus-veneris EST",
"description": "AcEST is a database of fern EST data. The database contains sequences expressed in Adiantum capillus-veneris that have been collected from four different sequence libraries. Orthology to A. thaliana is predicted, BLAST searches can be performed, and data is available for download.",
"homepage": "http://togodb.dbcls.jp/acest",
"information_keywords": [
"Sequence"
],
"maintainer": "Tokyo Metropolitan University",
"name": "AcEST",
"prefix": "NBDC00839",
"pubmeds": [
"15940394"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00840": {
"alt_name": "Carbohydrate Structure Database",
"description": "This is a regularly updated manually curated database for natural carbohydrates. It aims at high-quality content and provides structural, bibliographic, taxonomic, NMR-spectroscopic and other related information on prokaryotic, plant and fungal glycans, glycopolymers, and glycoconjugates. The coverage in bacterial domain (and soon expected in fungal domain) is about 90% of all published structures. As of 2017, the database contains ~19000 structures from ~9000 organisms published in ~7000 papers, and ~8000 NMR spectra. Besides data, CSDB serves as a platform for numerous glyco-services, such as glycosyltransferase subdatabase, 1D and 2D NMR simulation, automated NMR-based structure elucidation, carbohydrate-based taxon clustering, distribution of structural fragments against taxa, and other. All data can be exported as RDF feeds.",
"fairsharing": "biodbcore-000187",
"homepage": "http://csdb.glycoscience.ru",
"information_keywords": [
"Bibliography/Documents",
"Taxonomy",
"Chemical structure"
],
"maintainer": "Russian Academy of Sciences",
"name": "CSDB",
"prefix": "NBDC00840",
"pubmeds": [
"29786940",
"26337239",
"24680503",
"21155523",
"26087011",
"27227420",
"29092007",
"28011601"
],
"status": "Active",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc00841": {
"alt_name": "Reviewed methylation database in cancer",
"description": "This is a database of DNA methylation in cancer. The data were collected from literature by automated textmining, and then, manually curated and annotated. Users can find methylation frequency of each gene in various type of cancer. It is allowed users to search the data by gene and by cancer type.",
"homepage": "http://www.pubmeth.org/",
"maintainer": "Ghent University",
"name": "PubMeth",
"prefix": "NBDC00841",
"pubmeds": [
"17932060"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00842": {
"description": "Lectin 3D is a database of lectin crystal structures. The database contains PDB structures of lectins from all kingdoms of life as solved by x-ray crystallography. Users can browse by kingdom and protein class using comprehensive drop-down lists. Advanced search is also available.",
"homepage": "http://lectin3d.cermav.cnrs.fr/search.php",
"information_keywords": [
"3D structure",
"Chemical structure"
],
"maintainer": "Centre de Recherches sur les Macromolecules Vegetales",
"name": "3D Lectin Database",
"prefix": "NBDC00842",
"status": "Inactive",
"target_keywords": [
"Protein",
"Carbohydrate",
"Metabolite"
]
},
"nbdc00843": {
"alt_name": "Yeast Mitochondrial Proteome 2-D database",
"description": "YMP is a database of yeast mitochondria proteins. The database contains information on proteins determined and confirmed using several different proteomic methods, as well as experimental datasets following environmental manipulation. Several 2D-PAGE experiments are represented.",
"homepage": "http://www.biochem.oulu.fi/proteomics/ymp.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "University of Oulu",
"name": "YMP",
"prefix": "NBDC00843",
"pubmeds": [
"14597615"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc00847": {
"description": "Morning Glories Database is a collection about the mutants of the morning glory (Ipomoea nil), closely related species and interspecific hybrids. It also includes cultivars of Convolvulaceae. Each entry contains image, relative description and references. It also provides lists of related books and articles in various fields, along with lists of older literature and Web links concerning the morning glory.",
"homepage": "http://mg.biology.kyushu-u.ac.jp/Yoneda_DB/E/menu.html",
"information_keywords": [
"Phenotype",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Hosei University",
"name": "Morning Glories Database",
"prefix": "NBDC00847",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00849": {
"description": "TOBIKOBACHI is the image database of Japanese encyrtid wasps based on the collection of Dr. Tetsusaburo Tachikawa. Each record consists of 16 items including images (general habitus and various parts of the body), scientific names (family, genus and species), the Japanese name, distribution data and so on. Users can search species by keywords from these items. Search results show scientific names, the Japanese names and links to display retrieved records.",
"homepage": "http://konchudb.agr.agr.kyushu-u.ac.jp/tobikobachi/index-e.html",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie"
],
"maintainer": "Kyushu University Faculty of Agriculture",
"name": "TOBIKOBACHI",
"prefix": "NBDC00849",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc00850": {
"description": "HANABACHI is an image database covering all the species of the Japanese bees. The data on family Andrenidae, the genera Nomada and Lasioglossum are now opened to the public. This website explains keys to identify families and genera of the Japanese bees. Each record consists of 18 items including scientific names, the Japanese name, taxonomical information (sex, locality and depository of the type, etc) and total/partial images. Users can search species by keywords from these items.",
"homepage": "http://konchudb.agr.agr.kyushu-u.ac.jp/hanabachi/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie"
],
"maintainer": "Kyushu University Faculty of Agriculture",
"name": "HANABACHI",
"prefix": "NBDC00850",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc00851": {
"description": "ELKUType is a database of information on type specimens preserved in the Entomological Laboratory, Kyushu University (ELKU). ELKUType is based on the holotypes, which are used in the original description for establishment of a new taxon. Each record consists of 17 items including a image of the holotype, scientific names (family, genus and species), the Japanese name and distribution data. Users can search records by keywords from these items.",
"homepage": "http://elkutype.aiic.jp",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie"
],
"maintainer": "Kyushu University Faculty of Agriculture",
"name": "ELKUType",
"prefix": "NBDC00851",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00856": {
"description": "DgeneS is a database of genes from draft genome sequences, including genes from sequencing projects not yet completed. The database can be searched by gene name, ID, or keyword and returns information on taxonomy, protein and nucleic acid sequence, and links to related databases.",
"homepage": "http://www.genome.jp/dbget-bin/www_bfind?dgenes",
"information_keywords": [
"Sequence"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "DBGET Search - DGENES",
"prefix": "NBDC00856",
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00857": {
"description": "EgeneS is a database of EST sequences and genes identified by sequencing expressed genes. The database can be searched by gene name, ID, or keyword and returns information on taxonomy, protein and nucleic acid sequence, and links to related databases.",
"homepage": "http://www.genome.jp/dbget-bin/www_bfind?egenes",
"information_keywords": [
"Sequence"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "DBGET Search - EGENES",
"prefix": "NBDC00857",
"status": "Closed",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00858": {
"description": "MGENES is a database of genes characterized by metagenomic sequencing and environmental sources. The database can be searched by gene name, ID, or keyword and returns information on taxonomy, protein and nucleic acid sequence, and links to related databases.",
"homepage": "https://www.genome.jp/mgenes/",
"information_keywords": [
"Environment",
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG MGENES",
"prefix": "NBDC00858",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00860": {
"alt_name": "KEGG Reaction Class",
"description": "KEGG RCLASS is a database of enzymatic reactions as organized by the KEGG system and contains an expandable list of all reaction types organized hierarchically. A search function for reaction class is also available. Users can obtain the compounds and enzymes involved for each specified reaction pathway.",
"homepage": "http://www.genome.jp/kegg-bin/get_htext?br08204.keg",
"information_keywords": [
"Interaction/Pathway",
"Chemical structure"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG RCLASS",
"prefix": "NBDC00860",
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc00866": {
"description": "This database is a collection of illustrations and information about Marine mammals. It contains an illustration of body, photographs of head bone, scientific name, classification, feature and habit, etc. Each record also links to Stranding Record(s) in Japan. The skull image database of marine mammals is incorporated into the Illustrated Guide of Marine Mammals.",
"homepage": "http://www.kahaku.go.jp/english/research/db/zoology/marmam/pictorial_book/index.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "National Museum of Nature and Science",
"name": "Illustrated Guide of Marine Mammals",
"prefix": "NBDC00866",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00867": {
"alt_name": "Embryonic Gene Expression Database for Biomedical Research Source",
"description": "EMBRYS is a database of mouse in situ hybridizations. The database contains images of gene expression at three time points in embryonic development, annotated by organ, which can be explored using an image viewer. Data are available for download.",
"homepage": "https://www.embrys.jp/embrys/html/MainMenu.html",
"information_keywords": [
"Expression",
"Image/Movie"
],
"maintainer": "Department of Systems BioMedicine, Tokyo Medical and Dental University (TMDU)",
"name": "EMBRYS",
"prefix": "NBDC00867",
"pubmeds": [
"20059953"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Organism"
]
},
"nbdc00870": {
"alt_name": "Entomopathogenic Fungi Database",
"description": "This is a database for entomopathogenic fungi, which attack healthy insects and ultimately lead to their death. Users can view photos of the pathogen after parasitizing the host, as well as images of proliferation in media and microscopic images. Searches can be performed by genus name, Japanese common name, and species list, as well as host species. Synonyms for the pathogen are also shown. All rights for data and photos in this site are reserved.",
"homepage": "http://www.naro.affrc.go.jp/org/fruit/epfdb/Ebun/Eindex.htm",
"information_keywords": [
"Image/Movie"
],
"maintainer": "National Agriculture and Food Research Organization,National Institute of Fruit Tree Science",
"name": "EPFDB",
"prefix": "NBDC00870",
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease"
]
},
"nbdc00875": {
"alt_name": "Rice Research Database",
"description": "RRDB is a database of cultivated rice constructed by Plant Genome Center (PGC). RRDB contains 1000 cultivated rice varieties in the world with 110000 entries of information on their characteristics. Users can search cultivars, traits and genetic relationships by keywords.",
"homepage": "http://www.pgcdna.co.jp/igs_system/abstract_e.html",
"maintainer": "Plant Genome Center Co.,Ltd.",
"name": "RRDB",
"prefix": "NBDC00875",
"status": "Closed",
"target_keywords": [
"Organism"
]
},
"nbdc00881": {
"alt_name": "University hospital Medical Information Network",
"description": "UMIN is a repository of medical data and hospital statistics for healthcare professionals. UMIN contains databases of clinical practice, research related information, medical education / clinical training and university hospital management. Databases except for those of research related information are only available in Japanese. Users can search clinical trials and Japanese academic societies in medicine and related fields by keywords.",
"homepage": "http://www.umin.ac.jp/english/",
"maintainer": "University hospital Medical Information Network",
"name": "UMIN",
"prefix": "NBDC00881",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00883": {
"description": "The TMIG-2DPAGE Proteome Database is clickable image maps for looking up the 2D gel proteome databases on human cell lines in XML. It contains information for proteomic approach to molecular mechanisms of cellular aging and oxidative stress-induced cell damages. 2D gel images of TIG-3 (human diploid fibroblast cell strain),HUVEC (human umbilical vein endothelial cells), SH-SY5Y (human neuroblastoma cell line) and \nEBV-transformed human B-lymphoblastoid cell line are included. This database also links to tools for proteomics in the web.",
"homepage": "http://www.proteome.jp/2D/",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology",
"name": "TMIG-2DPAGE Proteome Database",
"prefix": "NBDC00883",
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease"
]
},
"nbdc00892": {
"description": "This is a database of plant diseases created on the basis of a catalog, \"Common names of plant diseases in Japan\", which compiled by The Phytopathological Society of Japan. Searches can be performed by host species, disease name, pathogen name and host, and type of pathogen, as well as via host plant family list.",
"homepage": "http://www.gene.affrc.go.jp/databases-micro_pl_diseases_en.php",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "Database of Plant Diseases in Japan",
"prefix": "NBDC00892",
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease"
]
},
"nbdc00893": {
"description": "This site provides images and characteristics of Rice, Legume, Vegetables, Flower&Ornamental Plants, Millet and Forage Crops, which includes information of their distribution in the field and their morphology etc.",
"homepage": "http://www.gene.affrc.go.jp/databases-plant_images_en.php",
"information_keywords": [
"Image/Movie"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "NIAS Genebank : Illustrations of Plant",
"prefix": "NBDC00893",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc00894": {
"description": "This site provides images and characteristics, such as their appearance, of a large number of breeds and strains of chickens and silkworms in Japan.",
"homepage": "http://www.gene.affrc.go.jp/databases-animal_images_en.php",
"information_keywords": [
"Image/Movie"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "NIAS Genebank : Illustrations of animal / insects",
"prefix": "NBDC00894",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc00895": {
"description": "genetic resources center in NARO (National Agriculture and Food Research Organization) provides information on a range of genetic resources. It includes genetic informaton about plants, animal, microbial, and DNA (NIAS DNA bank) . It also includes information about distribution of those genetic resources.",
"homepage": "http://www.gene.affrc.go.jp/databases_en.php",
"information_keywords": [
"Bioresource"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "NIAS Genebank : Databases",
"prefix": "NBDC00895",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00896": {
"alt_name": "Magnaporthe grisea EST Database",
"homepage": "http://mg.dna.affrc.go.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "National Institute of Agrobiological Sciences",
"name": "MgNEST-DB",
"prefix": "NBDC00896",
"pubmeds": [
"19186180"
],
"status": "Closed",
"target_keywords": [
"cDNA/EST",
"Health/Disease"
]
},
"nbdc00899": {
"alt_name": "The carbohydrate structures metadatabase",
"description": "GlycomeDB is a database of carbohydrate structural information. The database contains structural information collected from other sites and studies which can be searched, accessed, and compared using several tools. Users can search by ID, structure, similarity, or species. Data is available for download. GlycomeDB is now closed, please use GlyTouCan (http://glytoucan.org/).",
"fairsharing": "biodbcore-000353",
"homepage": "http://www.glycome-db.org/",
"information_keywords": [
"Sequence",
"Chemical structure"
],
"maintainer": "German Cancer Research Center",
"name": "GlycomeDB",
"prefix": "NBDC00899",
"pubmeds": [
"25753706",
"21045056",
"19759275",
"18803830"
],
"status": "Active",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc00900": {
"description": "Glycoscience.de is a database of glycosylation and glycoproteins. The database contains experiment, sequence, and study information which can be browsed or searched. Tools for modeling carbohydrate chains and glycoproteins are available, as are tools for notating, visualizing, and analyzing glycoproteins.",
"fairsharing": "biodbcore-000190",
"homepage": "http://www.glycosciences.de/index.php",
"information_keywords": [
"Bibliography/Documents",
"3D structure",
"Chemical structure"
],
"maintainer": "Justus-Liebig University Giessen",
"name": "GLYCOSCIENCES.de",
"prefix": "NBDC00900",
"pubmeds": [
"30357361",
"16239495",
"20364395",
"19277543",
"19171971",
"17202175",
"17202164",
"16845109",
"15980456",
"15608187",
"15260896",
"15180909",
"15010309",
"15215392",
"12908101",
"11752350",
"11675023",
"10498779"
],
"status": "Inactive",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc00901": {
"alt_name": "Affynity Database For Protein-Ligand Complexes",
"description": "AffinDB is a database of protein-ligand complexes. The database contains affinity data and structures (in the form of PDB files) for hundreds of complexes. Users can browse by several ligand features including exact or a range of values, or browse interactions.",
"homepage": "http://pc1664.pharmazie.uni-marburg.de/affinity/index.php",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie",
"3D structure",
"Chemical structure"
],
"maintainer": "Department of Pharmaceutical Chemistry, Philipps-University Marburg",
"name": "AffinDB",
"prefix": "NBDC00901",
"pubmeds": [
"16381925"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00902": {
"alt_name": "Transfer RNA Database",
"description": "tRNAdb is a database of transfer RNAs from hundreds of species. The database is divided into nuclear and mitochondrial subsections, each of which includes complete tRNA gene compliments for the appropriate subcellular component. genes have been computationally detected and in many cases experimentally verified. Users can search and download tRNA sequences.",
"homepage": "http://trna.bioinf.uni-leipzig.de/DataOutput/",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Leipzig",
"name": "tRNAdb",
"prefix": "NBDC00902",
"pubmeds": [
"18957446"
],
"status": "Inactive",
"target_keywords": [
"RNA"
]
},
"nbdc00904": {
"description": "JASPAR is a database of transcription factor binding sites. The database contains experimentally verified promoter and other gene expression regulation sites represented as sequence logos indicating critical nucleotides for recognition and binding by a given factor. Dozens of species are represented, and users can search by protein, motif, species, or protein structure family.",
"homepage": "http://jaspar.genereg.net/",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Copenhagen",
"name": "JASPAR",
"prefix": "NBDC00904",
"pubmeds": [
"18006571"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00905": {
"description": "Human Protein Atlas is a database of protein expression and localization. The database contains information on where proteins localize within cells and lists antibodies for the detection of human proteins. Information on expression in cancer lines as well as RNA transcript expression is also represented. Elements can be searched by several positional characteristics.",
"fairsharing": "biodbcore-000411",
"homepage": "https://www.proteinatlas.org",
"information_keywords": [
"Expression",
"Image/Movie",
"Localization"
],
"maintainer": "Uppsala University",
"name": "Human Protein Atlas",
"prefix": "NBDC00905",
"pubmeds": [
"18853439",
"16127175",
"16237735",
"18853439"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Cell/Organelle",
"Organism"
]
},
"nbdc00906": {
"description": "This database has been retired. The data are available in UniCarbDB (http://integbio.jp/dbcatalog/en/record/nbdc01525).",
"homepage": "http://glycosuitedb.expasy.org/glycosuite/glycodb",
"information_keywords": [
"Chemical structure"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "GlycoSuite",
"prefix": "NBDC00906",
"status": "Closed",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc00907": {
"description": "MetaCyc is a database of metabolic pathways. The database contains hundreds of curated pathways from hundreds of organisms acorss all kingdoms of life. Users can search by gene, protein, enzyme, or keyword, and explore pathways across related species.",
"fairsharing": "biodbcore-000136",
"homepage": "http://metacyc.org/",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "SRI International",
"name": "MetaCyc",
"prefix": "NBDC00907",
"pubmeds": [
"17965431",
"16381923",
"14681452",
"11752254",
"10592180"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein",
"Metabolite"
]
},
"nbdc00908": {
"alt_name": "Small Molecule Pathway Database",
"description": "SMPDB is a database of the biological pathways of small molecules. The database contains pathway information on hundreds of small molecules, many unique to SMPDB. Users can browse pathways by category, search the database, or use structure, sequence, and small molecule tools to explore pathways.",
"fairsharing": "biodbcore-000352",
"homepage": "http://www.smpdb.ca/",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "University of Alberta",
"name": "SMPDB",
"prefix": "NBDC00908",
"pubmeds": [
"19948758"
],
"status": "Active",
"target_keywords": [
"Protein",
"Metabolite"
]
},
"nbdc00909": {
"alt_name": "Human Metabolome Database",
"description": "HUMDB is a database of human metabolites. The database contains information on thousands of metabolites produced by and found in the human body as a result of metabolic processes. genes and proteins related to the metabolites are also affiliated with records, where appropriate. Data on metabolites and the associated genes and proteins are available for download.",
"fairsharing": "biodbcore-000552",
"homepage": "http://www.hmdb.ca/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Classification"
],
"maintainer": "University of Alberta",
"name": "HMDB",
"prefix": "NBDC00909",
"pubmeds": [
"18953024"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein",
"Health/Disease",
"Metabolite"
]
},
"nbdc00910": {
"description": "Animal Genome Size Database contains information on the genomes of hundreds of species. For each species, the database reports the C value, information on the number of chromosomes, and details of the experimental methods used to determine genome size.",
"fairsharing": "biodbcore-000203",
"homepage": "http://www.genomesize.com/search.php",
"maintainer": "University of Guelph",
"name": "Animal Genome Size Database",
"prefix": "NBDC00910",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00911": {
"alt_name": "International Protein Index",
"homepage": "http://www.ebi.ac.uk/IPI/",
"information_keywords": [
"Sequence"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "IPI",
"prefix": "NBDC00911",
"pubmeds": [
"15221759"
],
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc00912": {
"description": "Plant DNA C-value Database is a resource for the nuclear genetic content of plants. The database contains values determined experimentally for a large range of plants covering thousands of species. Users can submit values and register to receive updates.",
"fairsharing": "biodbcore-000612",
"homepage": "http://data.kew.org/cvalues/",
"maintainer": "Royal Botanic Gardens, Kew",
"name": "Plant DNA C-value Database",
"prefix": "NBDC00912",
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00913": {
"alt_name": "Charting Pathways of Life",
"description": "BioCarta is a database of gene interaction models. The database contains high-quality images of several cellular signaling and interaction pathways, and each diagram is fully hyperlinked to products and information pages about individual genes. Users can access product sales pages for selected elements of each pathway.",
"homepage": "http://www.genecarta.com",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "BioCarta LLC",
"name": "BioCarta",
"prefix": "NBDC00913",
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc00914": {
"alt_name": "Plant Metabolic Network",
"description": "PMN is a database of plant metabolic pathways. The database contains information on metabolic pathways in over a dozen plant species which users can search by gene, protein, reactions, compounds, or pathways. Users can download pathway and enzyme data as well as pathway software.",
"homepage": "http://www.plantcyc.org/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Carnegie Institution for Science/Department of Plant Biology",
"name": "PMN",
"prefix": "NBDC00914",
"pubmeds": [
"22280840",
"20522724"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc00915": {
"description": "geneimprint is a database of epigenetics in mammals. The database contains general information, articles and news about genomic imprinting, and lists of mammalian genes which are known or suspected to be imprinted.",
"homepage": "http://www.geneimprint.com/",
"information_keywords": [
"Bibliography/Documents",
"Portal"
],
"maintainer": "Duke University",
"name": "Geneimprint",
"prefix": "NBDC00915",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00916": {
"description": "ITIS is a database of taxonomic nomenclature and information used in biodiversity and ecosystem preservation programs. The database contains information on species and serves as a respository for biodiversity information for US government programs. The database can be searched by taxon or hierarchically, and taxonomic data can be downloaded.",
"fairsharing": "biodbcore-000597",
"homepage": "http://www.itis.gov",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Bibliography/Documents",
"Taxonomy",
"Repository"
],
"maintainer": "Integrated Taxonomic Information System",
"name": "ITIS",
"prefix": "NBDC00916",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00917": {
"description": "GenProtEC is a database of the E. coli genome and proteome. The database contains related sequence information which can be searched by sequence or keyword, as well as several comparative and classification resources for functional characterization and exploration.",
"homepage": "http://genprotec.mbl.edu/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "Marine Biological Laboratory",
"name": "GenProtEC (E. Coli genome and proteome database)",
"prefix": "NBDC00917",
"pubmeds": [
"14681418",
"11948287",
"11677689",
"11574054",
"11471834",
"9399799"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc00918": {
"homepage": "http://cbio.mskcc.org/CancerGenes/Select.action",
"maintainer": "MSKCC (Memorial Sloan-Kettering Cancer Center)",
"name": "Cancer Genes",
"prefix": "NBDC00918",
"pubmeds": [
"17088289"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00919": {
"description": "Pathway Interaction Database is a database of interactions between biological molecules. The database consists of data on molecular interactions as well as functional networks and pathways. Pathways and molecules can be browsed or searched individually or in batch format. A variety of datasets are available for download.",
"fairsharing": "biodbcore-000425",
"homepage": "http://pid.nci.nih.gov/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "NCI (National Cancer Institute, National Institutes of Health)",
"name": "Pathway Interaction Database",
"prefix": "NBDC00919",
"pubmeds": [
"18832364"
],
"status": "Active",
"target_keywords": [
"Protein",
"Metabolite"
]
},
"nbdc00920": {
"alt_name": "Genomic Data Commons Data Portal",
"description": "GDC Data Portal is an interactive data system for researchers to search, download, upload, and analyze harmonized cancer genomic data sets, including TCGA (The Cancer Genome Atlas: https://cancergenome.nih.gov) and Therapeutically Applicable Research to Generate Effective Therapies (TARGET). It contains information about projects, primary sites, cases, files, genes and mutations. This database allows to browse using Projects, Exploration, Analysis or Repository lists. It also allows to search using primary sites, programs, disease types, data category or experimental strategies.",
"fairsharing": "biodbcore-000730",
"homepage": "https://portal.gdc.cancer.gov",
"information_keywords": [
"Sequence",
"Bibliography/Documents",
"Portal",
"Repository"
],
"maintainer": "NCI (National Cancer Institute, National Institutes of Health)",
"name": "GDC Data Portal",
"prefix": "NBDC00920",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00922": {
"description": "This site provides information about cancer types studied for the role of common and uncommon inherited variations in the genetic code associated with risk of cancer in DCEG. Each study is carried out using biological samples from study participant and techniques like genome-wide association studies (GWAS), whole genome scans, and new and emerging technologies and methods.",
"homepage": "https://dceg.cancer.gov/research/cancer-types",
"maintainer": "NCI (National Cancer Institute, National Institutes of Health)",
"name": "Cancer Types Studied in DCEG",
"prefix": "NBDC00922",
"pubmeds": [
"17529973",
"19330030",
"19330027",
"20237344"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc00923": {
"description": "HIV-1, Human Protein Interaction Database catalogs the interactions between the virus that causes AIDS and human proteins. The database contains information on HIV-1 proteins and datasets characterizing virus-human protein interactions. Reports are available for each HIV-1 protein individually and links are provided to external databases with related information.",
"fairsharing": "biodbcore-000442",
"homepage": "http://www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "HIV-1, Human Protein Interaction Database",
"prefix": "NBDC00923",
"pubmeds": [
"18927109",
"19025396",
"19262354"
],
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease"
]
},
"nbdc00924": {
"alt_name": "Immune Epitope Database",
"description": "IEDB is a database of immunological molecules. The database contains entries on epitopes, MHC alleles and assays measuring immunological entities gathered from the literature. Users can search by epitope structure, epitope source, recognition context, or disease associations. Epitope prediction tools are available online, and some tools are available for local download and operation.",
"homepage": "http://www.immuneepitope.org/",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "NIAID (The National Institute of Allergy and Infectious Diseases)",
"name": "IEDB",
"prefix": "NBDC00924",
"pubmeds": [
"19906713"
],
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease"
]
},
"nbdc00925": {
"description": "Health Information is a database of health and disease information for the general public. The database contains descriptions and explanations of medically relevant topics ranging from nutrition to concussions. Links are provided to related resources.",
"homepage": "http://health.nih.gov/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NIH (National Institutes of Health)",
"name": "Health Information",
"prefix": "NBDC00925",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00926": {
"alt_name": "Genetic Association Database",
"description": "GAD is a database of human genetic associations. The database contains entries collected from published association and genome-wide association studies which connect genes to diseases or other phenotypes. Users can browse by disease or gene, or perform single or batch searches. The database can be downloaded by request.",
"homepage": "http://geneticassociationdb.nih.gov/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NIH (National Institutes of Health)",
"name": "GAD",
"prefix": "NBDC00926",
"pubmeds": [
"20092628"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00927": {
"alt_name": "Biological Biochemical Image Database",
"description": "BBID is a database of biological images. The database contains images of all sorts including pathways, structures, gene famies, and cellular structures. Users can search keyword or browse by represented genes or the entire list of available keywords.",
"homepage": "http://bbid.grc.nia.nih.gov/",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "National Institute on Aging",
"name": "BBID",
"prefix": "NBDC00927",
"status": "Inactive",
"target_keywords": [
"Organism",
"Health/Disease",
"Cell/Organelle"
]
},
"nbdc00928": {
"alt_name": "Drugs and Lactation Database",
"description": "LactMed is a database of toxins and metabolites which may be found in breast milk. The database contains manually curated entries on compounds in milk as reported in primary literature. Users can search compounds or chemicals by name or CAS. Additional support, including an app, are also available.",
"homepage": "https://www.ncbi.nlm.nih.gov/books/NBK501922/?report=classic",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NLM (National Library of Medicine)",
"name": "LactMed",
"prefix": "NBDC00928",
"pubmeds": [
"17210549"
],
"status": "Active",
"target_keywords": [
"Chemical compound",
"Drug"
]
},
"nbdc00929": {
"alt_name": "Toxicology Data Network",
"description": "TOXNET is a database of toxins and hazardous chemicals. The database contains entries on environmental health issues and related conditions. Users can search the database by keyword, use various support features, or access sub-databases related to toxicity and specific products or biological processes.",
"homepage": "http://toxnet.nlm.nih.gov/",
"information_keywords": [
"Environment",
"Portal"
],
"maintainer": "NLM (National Library of Medicine)",
"name": "TOXNET",
"prefix": "NBDC00929",
"pubmeds": [
"11164971"
],
"status": "Closed",
"target_keywords": [
"Health/Disease",
"Chemical compound"
]
},
"nbdc00930": {
"alt_name": "Hazardous Substances Data Bank",
"description": "HSDB is a database of hazardous substances. The database contains information on toxic compounds gathered from primary, peer-reviewed literature. Users can search by compound, CAS, or symptom. Fact sheets and other support are also available.",
"homepage": "http://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?HSDB",
"information_keywords": [
"Bibliography/Documents",
"Chemical structure"
],
"maintainer": "NLM (National Library of Medicine)",
"name": "HSDB",
"prefix": "NBDC00930",
"pubmeds": [
"14728459",
"8545846"
],
"status": "Inactive",
"target_keywords": [
"Chemical compound"
]
},
"nbdc00931": {
"alt_name": "Integrated Risk Information System",
"description": "IRIS is a database of hazardous substance identification and response information. The database contains response information for over 500 chemicals. Users can search by keyword, compound, CAS number, or symptom, or browse the database.",
"homepage": "https://www.epa.gov/iris",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "U.S. Environmental Protection Agency",
"name": "IRIS",
"prefix": "NBDC00931",
"pubmeds": [
"10111413"
],
"status": "Active",
"target_keywords": [
"Health/Disease",
"Chemical compound"
]
},
"nbdc00932": {
"alt_name": "Chemical Carcinogenesis Research Information System",
"description": "CCRIS is a database of carcinogenic information. The database contains information related to the cancer-causing potential of over 8,000 compounds. Users can search by keyword, chemical, or CAS number.",
"homepage": "http://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?CCRIS",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NLM (National Library of Medicine)",
"name": "CCRIS",
"prefix": "NBDC00932",
"status": "Inactive",
"target_keywords": [
"Chemical compound"
]
},
"nbdc00933": {
"alt_name": "Toxicology Literature Online",
"description": "TOXLINE is a database of toxicology literature. The database contains links to primary literature on the toxicity of chemical substances, which can be searched by name, keyword, or CAS number.",
"homepage": "http://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?TOXLINE",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NLM (National Library of Medicine)",
"name": "TOXLINE",
"prefix": "NBDC00933",
"pubmeds": [
"10298318"
],
"status": "Inactive",
"target_keywords": [
"Chemical compound"
]
},
"nbdc00934": {
"alt_name": "Developmental and Reproductive Toxicology Database",
"description": "DART is a database of toxicity pertaining to development and reproduction. The database contains information on compounds which have been shown to have an impact on the earliest stages of life, from conception through early development. Users can search by keyword, chemical, or CAS number. The database returns primary research articles about the search term",
"homepage": "http://toxnet.nlm.nih.gov/newtoxnet/dart.htm",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NLM (National Library of Medicine)",
"name": "DART",
"prefix": "NBDC00934",
"status": "Inactive",
"target_keywords": [
"Chemical compound"
]
},
"nbdc00935": {
"alt_name": "Genetic Toxicology Data Bank",
"description": "gene-TOX is a database of toxic effects of chemical compounds on genetic material. The database contains entries on compounds and their potential negative effects on DNA. Users can search by compound and CAS.",
"homepage": "http://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?GENETOX",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NLM (National Library of Medicine)",
"name": "GENE-TOX",
"prefix": "NBDC00935",
"status": "Inactive",
"target_keywords": [
"Chemical compound"
]
},
"nbdc00936": {
"alt_name": "International Toxicity Estimates for Risk",
"description": "ITER is a database of risk information on chemical compounds. The database contains information on official statements about the harmful risks of hundreds of compounds. The database can be searched by affected tissue or system, chemical, or CAS number.",
"homepage": "http://www.iter.tera.org",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Toxicology Excellence for Risk Assessment",
"name": "ITER",
"prefix": "NBDC00936",
"pubmeds": [
"18655804"
],
"status": "Inactive",
"target_keywords": [
"Chemical compound"
]
},
"nbdc00937": {
"alt_name": "Genomic tRNA Database",
"description": "GtRNAdb is a database of tRNA gene predictions made by an original program (tRNAscan-SE) on complete or nearly complete genomes. It contains automated annotation for genomes of Eukarya, Archaea and Bacteria. With automated sequence analysis, exceptions to general identification rules, isoacceptor type predictions (esp. due to variable post-transcriptional anticodon modification), and questionable tRNA identifications (due to pseudogenes, SINES, or other tRNA-derived elements) are found.",
"homepage": "http://gtrnadb.ucsc.edu/",
"information_keywords": [
"Sequence"
],
"maintainer": "University of California",
"name": "GtRNAdb",
"prefix": "NBDC00937",
"pubmeds": [
"18984615",
"9023104"
],
"status": "Active",
"target_keywords": [
"RNA"
]
},
"nbdc00938": {
"description": "The Multi-Dimensional Human Embryo is a database for three-dimensional image reference of the human embryo based on magnetic resonance imaging. It contains images of embryo which is assigned a Carnegie stage (numbered from 1 to 23) based on its external features. This database also contains several major organs which were isolated from each T1-weighted embryo data set using image segmentation methods, then represented. Moreover, each embryo is optically photographed under a low-power microscope.",
"homepage": "https://embryo.stamps.umich.edu/index.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "University of Michigan",
"name": "The Multi-Dimensional Human Embryo",
"prefix": "NBDC00938",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00939": {
"description": "ChromatinDB is a database including genome-wide microarray data mapping patterns of histone modifications and other chromatin features for the model organism Saccharomyces cerevisiae. It provides the following features to enable exploration of chromatin regulatory mechanisms of yeast gene control.\n(1) The visualization tool of histone modification patterns and other chromatin features of selected genes.\n(2) The statistical analysis tool which allows the user to search for statistically significant patterns of enrichment in the histone modifications present in the genes that they have selected. \n(3) The data download tool which provides the user with easy access to the histone modification ChIP-microarray data sets that are stored in ChromatinDB.",
"homepage": "http://www.bioinformatics2.wsu.edu/cgi-bin/ChromatinDB/cgi/visualize_select.pl",
"information_keywords": [
"Expression"
],
"maintainer": "Washington State University",
"name": "ChromatinDB",
"prefix": "NBDC00939",
"pubmeds": [
"17485428"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein"
]
},
"nbdc00940": {
"alt_name": "International Mouse Phenotyping Consortium",
"description": "IMPC is a database about phenotyping of mouse mutants at protein-coding genes in the mouse using a combination of gene trapping and gene targeting in C57BL/6 mouse embryonic stem (ES) cells. It provides genotype-phenotype annotation, standard operating protocols, and the development of open source data analysis tools. Users are able to order the targeting vectors and mutant ES cells. Moreover, users are able to obtain mice, embryos, or sperm from mutant ES cells.",
"homepage": "http://www.mousephenotype.org",
"information_keywords": [
"Bioresource"
],
"maintainer": "International Mouse Phenotyping Consortium",
"name": "IMPC",
"prefix": "NBDC00940",
"pubmeds": [
"19525957",
"17448981",
"17218247"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"DNA",
"Organism",
"Cell/Organelle"
]
},
"nbdc00943": {
"alt_name": "Rice Genome Resource Center",
"description": "This is the home page for the Rice Genome Resource Center. It provides information regarding the distribution of full length rice cDNA clones (from NIAS DNA Bank) and of the Tos17 rice mutant strain.",
"homepage": "http://www.rgrc.dna.affrc.go.jp/",
"information_keywords": [
"Bioresource"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "RGRC",
"prefix": "NBDC00943",
"status": "Closed",
"target_keywords": [
"cDNA/EST",
"Organism"
]
},
"nbdc00945": {
"description": "This is a database of comprehensive analytical results derived from continuous monitoring of rice growth from sprouting to flowering, with images taken at intervals lasting from minutes to hours.\nThe original site (http: //www.gs.dna.affrc.go.jp/SY-1108/) has been closed. The Rice Growth Monitoring System is available from LSDB archive site.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/agritogo-rice-phenome/desc.html",
"information_keywords": [
"Phenotype",
"Image/Movie"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "The Rice Growth Monitoring System (Archive)",
"prefix": "NBDC00945",
"pubmeds": [
"14523250"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc00946": {
"homepage": "http://lyso.gs.dna.affrc.go.jp/",
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "Genome Methylation Database",
"prefix": "NBDC00946",
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00947": {
"homepage": "http://oryza-snp.dna.affrc.go.jp/en/index_en.html",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "NIAS Oryza SNP Database",
"prefix": "NBDC00947",
"status": "Closed",
"target_keywords": [
"Genetic variation"
]
},
"nbdc00948": {
"alt_name": "Rice Expression Profile Database",
"description": "This is a database of gene expression profiles for rice. gene expression profiles were obtained through microarray analysis of naturally grown rice tissues and organs, hormone-processed rice plants, and cells and tissues isolated by laser microdissection. Chromosomal locations, expression levels at each developmental stage, and probe sequences can be viewed on this site. Data can be searched by keywords, chromosome number, or by BLAST.",
"homepage": "http://ricexpro.dna.affrc.go.jp/",
"information_keywords": [
"Expression"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "RiceXPro",
"prefix": "NBDC00948",
"pubmeds": [
"21045061",
"21226959"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00949": {
"homepage": "http://koshigenome.dna.affrc.go.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "Koshihikari vs Nipponbare SNP Database",
"prefix": "NBDC00949",
"pubmeds": [
"20423466"
],
"status": "Closed",
"target_keywords": [
"Genetic variation"
]
},
"nbdc00950": {
"alt_name": "SILKWORM GENOME RESEARCH PROGRAM",
"description": "This is the site of the Silkworm Genome Research Program, which provides genome information of silkworm in KAIKObase, and tools such as KAIKOBLAST for the Blast search, and KAIKOGASS for visualization of integrated annotation of genome scaffolds.",
"homepage": "http://sgp.dna.affrc.go.jp/",
"information_keywords": [
"Portal"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "SGP",
"prefix": "NBDC00950",
"pubmeds": [
"19836396",
"19793867",
"19883703",
"20130748",
"20060470",
"19996320",
"20077574",
"20053988",
"20388903",
"20458474"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein"
]
},
"nbdc00951": {
"description": "This is a silkworm EST (cDNA) sequence database. Searches can be performed by clone name, gene ontology, or homology score.",
"homepage": "http://sgp.dna.affrc.go.jp/EST/",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "KAIKOcDNA",
"prefix": "NBDC00951",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00953": {
"alt_name": "Database for Gene function and expression of Baker's Yeast",
"description": "This database contains information on gene expression and function for baker's yeast. Using methods such as a comprehensive gene expression profile via a DNA microarray (transcriptomics) and comprehensive phenotypic profile via a yeast gene deletion strain library (phenomics), the database contains information on stress resistance-associated genes activated during breadmaking.",
"homepage": "http://www.naro.affrc.go.jp/org/nfri/english/Useful/yeast/index.html",
"information_keywords": [
"Phenotype",
"Expression"
],
"maintainer": "National Agriculture and Food Research Organization,National Food Research Institute",
"name": "DGBY",
"prefix": "NBDC00953",
"pubmeds": [
"16943074",
"17724779",
"19000619",
"16487347",
"16989656",
"18224659"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00954": {
"description": "Open TG-GATES is a toxicogenomics database. It stores gene expression data from rat liver and kidney samples (in vivo) and from primary rat and human hepatocytes (in vitro), after treatment with 170 drugs and chemical compounds. The database also contains associated toxicological data such as biochemical, blood and histopathological data.",
"homepage": "http://toxico.nibiohn.go.jp/english/index.html",
"information_keywords": [
"Expression",
"Image/Movie"
],
"maintainer": "National Institutes of Biomedical Innovation, Health and Nutrition",
"name": "Open TG-GATEs",
"prefix": "NBDC00954",
"status": "Inactive",
"target_keywords": [
"cDNA/EST",
"Health/Disease",
"Drug"
]
},
"nbdc00958": {
"description": "The Animal Resource Bank collects and provides mouse models of human disease (lysosomal disease models, model lifestyle-related diseases, nephrosis model, and cardiomyopathy model). Information is available for 144 strains of mice linked to 25 disease assays. The bank also supports researchers who use the experimental animals with services such as custody by frozen sperm, frozen embryos, and mouse.",
"homepage": "https://animal.nibiohn.go.jp/index.html.en",
"information_keywords": [
"Bioresource"
],
"maintainer": "National Institutes of Biomedical Innovation, Health and Nutrition",
"name": "Laboratory Animal Resource Bank",
"prefix": "NBDC00958",
"pubmeds": [
"22436580",
"22022544",
"21986317"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc00959": {
"description": "This site is a browser for finding available BAC clones of the genome of the B6N mouse strain and of the MSM mouse strain, a wild-derived inbred strain that originated from Japanese wild mice. Clicking on a specific chromosome in the provided diagram opens up a detailed chromosome map showing the locations of the clones and where contiguous DNA segments overlap. The number of available mapped BAC clones are 119,451 in B6N and 133,915 in MSM. A keyword search option is provided, whereby the database can be searched for a specific clone by entering the number of the chromosome on which it is located and/or its ID name or number.",
"homepage": "http://analysis2.lab.nig.ac.jp/mouseBrowser/cgi-bin/index.cgi?org=mm",
"information_keywords": [
"Sequence"
],
"maintainer": "NBRP Mouse Genome Information Upgrading Program (RIKEN BRC, RIKEN Genomic Sciences Center,\r\nand Comparative Genomics Laboratory, National Institute of Genetics)",
"name": "Mouse BAC browser",
"prefix": "NBDC00959",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc00960": {
"description": "This site provides information on certain target genes of Ciona intestinalis, and specifically the target gene for retinoic acid, an important metabolic substance in the growth and development of the embryo.\nCiona intestinalis, a mollusk-like invertebrate chordate, has often been used as a model in developmental biology and genomics, which is a branch of molecular biology involving the structure, function, evolution, and mapping of genomes.\nThrough microarray analysis, information is made available in four subsets: \n- Table S1 ranking the reproducibility of the clones from most to least.\n- The sequences of the clones.\n- In situ photos of selected cDNA clones.\n- The raw data obtained from four hybridization experiments, in the form of fluorescent images.",
"homepage": "http://www.cc.kochi-u.ac.jp/~tatataa/RA/RA-targets.html",
"information_keywords": [
"Expression",
"Image/Movie"
],
"maintainer": "Kochi University Faculty of Science",
"name": "RA target genes in the Ciona embryo",
"prefix": "NBDC00960",
"pubmeds": [
"12828686"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00961": {
"description": "NAISTrap is a database of clones listed in a table.\nEach clone is identified by its clone number (starting with 02e; 03e; 04e; 00v; 01v; 02v; 03v; 04v; 05v; 06v; 07v; 08v; 09v; 13v; 15v; 16v; 17v; 18v; 19v; 21v; 23v; 24v; 25v; 26v; 27v; 29v; 30v; 33v; 36v and 37v) and any number of the following qualities:\n- Trapped gene \n- Expression in ES cells (+ or -)\n- gene identity\n- CDS in mRNA\n- Deleted region\n- Trapped sequence\n- Nbspseq (?NBP sequence)\n- Symbol \n- GenBank Acc. \nThe \"Trapped sequence\" column provides a direct link to the sequence ONLY for the clones on page 1 and page 2 of the list (clone numbers starting with 02e to clone numbers starting with 16v)\nThe link provided in the \"Trapped sequence\" columns on page 3 and page 4 of the list (clone numbers starting with 17v to clone numbers starting with 37v), when selected, opens up the homepage of theNara Institute of Science and Technology (NAIST) Graduate School of Biological Sciences.",
"homepage": "http://bsw3.aist-nara.ac.jp/kawaichi/3kenfile/index.html",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "Nara Institute of Science and Technology Graduate School of Biological Sciences",
"name": "The NAISTrap database",
"prefix": "NBDC00961",
"pubmeds": [
"15010531"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle"
]
},
"nbdc00963": {
"description": "Society Catalog is a collection of information on Japanese academic societies in life science and related fields developed by the National Bioscience Database Center (NBDC) at the Japan Science Technology Agency (JST). Each record contains an academic overview (name, abbreviation, category class, etc), a contact address, free or paid public site URL(s) and details of academic journal(s). Users can search academic societies from hierarchical trees and lists, as well as by keywords from those items.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/lsdb-academycatalog/desc.html",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "Society Catalog (Archive)",
"prefix": "NBDC00963",
"status": "Active"
},
"nbdc00964": {
"description": "This is a catalog-format database containing information associated with projects in Japan: status, budget, summary, database site, download site, and links to press releases or publications.",
"homepage": "http://togodb.biosciencedbc.jp/togodb/view/lsdb_project_en",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "Life Science Projects in Japan",
"prefix": "NBDC00964",
"status": "Active"
},
"nbdc00967": {
"alt_name": "Ancient Genome Encyclopedia",
"homepage": "http://www.ddbj.nig.ac.jp/aDNA",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "National Institute of Genetics",
"name": "AGE",
"prefix": "NBDC00967",
"status": "Inactive"
},
"nbdc00968": {
"alt_name": "Human and mouse gene expression database",
"description": "The BodyMap is a database of gene expression in human and mouse tissues and cells based on analysis of 3' ESTs.",
"homepage": "http://bodymap.ims.u-tokyo.ac.jp",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "The University of Tokyo The Institute of Medical Science",
"name": "BodyMap",
"prefix": "NBDC00968",
"pubmeds": [
"11076866",
"10592203"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00969": {
"alt_name": "anatomical and taxonomical breakdown of animal EST",
"homepage": "http://bodymap.genes.nig.ac.jp/",
"information_keywords": [
"Sequence",
"Expression",
"Classification"
],
"maintainer": "National Institute of Genetics",
"name": "BodyMap-Xs",
"prefix": "NBDC00969",
"pubmeds": [
"16381946"
],
"status": "Closed",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc00970": {
"alt_name": "Human Disease to Drosophila Gene Database",
"homepage": "http://superfly.ucsd.edu/homophila",
"information_keywords": [
"Sequence"
],
"maintainer": "UCSD (University of California San Diego)",
"name": "HOMOPHILA",
"prefix": "NBDC00970",
"pubmeds": [
"11381037",
"11752278"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc00971": {
"alt_name": "Protein interaction and Molecular information database",
"description": "This database contains information on the protein kinases in the major eukaryotic species for which sequences have been determined. It includes data on classification of protein kinases, protein interaction data, domain information, structural information and ontology information. The data can be searched by pathway, type of protein or orthologs. It is an evolution of the Kinase Pathway Database (http://integbio.jp/dbcatalog/record/nbdc01037).",
"homepage": "http://prime.ontology.hgc.jp:8081/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "The University of Tokyo The Institute of Medical Science",
"name": "PRIME",
"prefix": "NBDC00971",
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00972": {
"alt_name": "Database for Protein-Ligand Interactions",
"homepage": "http://dna01.bse.kyutech.ac.jp/jouhou/prolint/prolint.html",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Kyushu Institute of Technology",
"name": "ProLINT",
"prefix": "NBDC00972",
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc00998": {
"alt_name": "Infrared and Raman Spectroscopy Literature Data Base",
"description": "This database contains information on Molecular Structure collected by the study of literature about Raman and Infrared Spectroscopy.\nA search option is available whereby information can be retrieved by entering a term or a description of the topic of interest.\nThe database coveres literature since 1982 to the present time.",
"homepage": "http://irsldb.pu-toyama.ac.jp/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Japan Society of Information and Knowledge",
"name": "IRSLDB",
"prefix": "NBDC00998",
"status": "Inactive",
"target_keywords": [
"DNA",
"RNA",
"Protein"
]
},
"nbdc01007": {
"alt_name": "Protein-protein Interactions Thermodynamic Database",
"description": "PINT is an anagram for Protein-protein INteractions Thermodynamic database.\nThis database contains concentrated experimental information on the thermodynamics that occur when proteins react with other proteins as found published in many different scientific journals and articles.\nResearchers can therefore save precious time by using this database as opposed to finding and reading all the separate contributing articles and journals themselves.\nLinks to other similar databases e.g. PDB, PUBMED, SWISS-PROT and PIR are provided.\nA text search and an advanced search options are available.",
"homepage": "http://www.bioinfodatabase.com/pint/index.html",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Under survey",
"name": "PINT",
"prefix": "NBDC01007",
"pubmeds": [
"16381844"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01009": {
"alt_name": "Serical Analysis of Gene Expression Tag to Gene Mapping",
"homepage": "http://www.ncbi.nlm.nih.gov/SAGE/",
"information_keywords": [
"Expression",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "SAGEmap",
"prefix": "NBDC01009",
"pubmeds": [
"10899154"
],
"status": "Closed"
},
"nbdc01020": {
"alt_name": "the Alternative Splicing Annotation Project II",
"description": "ASAP II is a database of alternative splicing information coming from genomics and proteomics. It provides precise gene exon-intron structure, alternative splicing, tissue specificity of alternative splice forms, and protein isoform sequences resulting from alternative splicing. As for human, EST libraries are classified and included into tissue and cancer classification, and lists of tissue & cancer (normal) specific alternatively spliced genes are calculated. ASAP II can be easily integrated with pygr (the Python Graph Database Framework for Bioinformatics) and its powerful features such as graph query, multi-genome alignment query and etc. Furthermore, it can help biologists design probe sequences for distinguishing specific mRNA isoforms. This database can be searched by several different criteria such as gene symbol, gene name and ID (Unigene, GenBank etc.).",
"homepage": "http://fold.doe-mbi.ucla.edu/ASAP2/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "University of California Los Angeles",
"name": "ASAP II",
"prefix": "NBDC01020",
"pubmeds": [
"17108355",
"12519958"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01021": {
"alt_name": "Base-Amino Acid Interactions Database",
"description": "This is a database showing the interactions among base-amino acids when searched for atom pairs of bases and amino acids that are closely related in structure.\nUpon entry of search parameters the search is linked to an additional database, called 3DinSight, which seeks information about the properties, structure and function of the biomolecules in question. This may help researchers to understand how they are related. \nIn addition to this, a molecular graphic (RasMol) image is provided, visually highlighting the specific atom pairs in the complex structure.",
"homepage": "http://gibk26.bio.kyutech.ac.jp/jouhou/baint/baint.html",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Kyushu Institute of Technology",
"name": "BAInt",
"prefix": "NBDC01021",
"status": "Inactive",
"target_keywords": [
"DNA",
"Protein"
]
},
"nbdc01022": {
"alt_name": "The Biological Information System for Marine Life",
"description": "BISMaL is a integrated database for biodiversity information, particularly in biogeographic data of marine organisms. It mainly collects information of marine organisms around Japan, and provides photographs, movies, distribution records, references and brief descriptions of morphology/ecology of each species or its higher taxon. Users are able to search and browse species by scientific names and/or keywords, or also search external databases (e.g. Google Scholar) by using the scientific name, which is indicated on the page top, as a search key.",
"homepage": "https://www.godac.jamstec.go.jp/bismal/e/",
"information_keywords": [
"Image/Movie",
"Taxonomy"
],
"maintainer": "Japan Agency for Marine-Earth Science and Technology",
"name": "BISMaL",
"prefix": "NBDC01022",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01023": {
"homepage": "http://bloodsage.gi.k.u-tokyo.ac.jp",
"information_keywords": [
"Expression"
],
"maintainer": "The University of Tokyo Graduate School of Frontier Sciences",
"name": "Blood SAGE",
"prefix": "NBDC01023",
"status": "Inactive",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01024": {
"homepage": "http://omicspace.riken.jp/Ce/rnai/jsp/index.jsp",
"information_keywords": [
"Phenotype"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research) Kobe Institute",
"name": "C. elegans RNAi Phenome Database",
"prefix": "NBDC01024",
"pubmeds": [
"11231151"
],
"status": "Closed",
"target_keywords": [
"Organism"
]
},
"nbdc01025": {
"description": "CELLPEDIA is a repository database providing current information on human cells. Cell morphology, gene expression, etc. of various cells, as well as literature references are available. CELLPEDIA is primarily a digital dictionary of human cells as applicable in biomedicine. It is categorized into differentiated and stem cells, and each category provides data on human cell taxonomy, cell images, journal articles and gene expressions, while the integrated page contains information on morphology, ontology and differentiation neighborhood links. Original cell analysis tools are also provided.\nNow, this database was closed, and a successor site is available; SHOGoiN (http://integbio.jp/dbcatalog/record/nbdc01430).",
"homepage": "http://cellpedia.cbrc.jp/cgi-bin/index.cgi",
"information_keywords": [
"Expression",
"Image/Movie"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "CELLPEDIA",
"prefix": "NBDC01025",
"status": "Closed",
"target_keywords": [
"cDNA/EST",
"Cell/Organelle"
]
},
"nbdc01026": {
"alt_name": "Ciona intestinalis Protein Database",
"description": "CiPro is a database of Ciona intestinalis proteins. The database contains several experimental and bioinformatic tools for characterizing proteins and expression of their related genes. Users can search the database using several criteria and data is available for download.",
"fairsharing": "biodbcore-000236",
"homepage": "http://cipro.ibio.jp/current/",
"information_keywords": [
"Sequence",
"Expression",
"Image/Movie",
"3D structure"
],
"maintainer": "University of Tsukuba Shimoda Marine Research Center",
"name": "CIPRO",
"prefix": "NBDC01026",
"pubmeds": [
"21071393"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc01027": {
"description": "DART is a integrated database about genome sequence and microarrays of Arabidops. It provides following functions;\n1) analysis of gene expression by microarrays,\n2) search and analysis for genes,\n3) useful tools for research.\nThis database allows to search genes using a number of gene or keywords. And it allows search microarrays for analysis using text or list of research results.",
"homepage": "http://dandelion.liveholonics.com/dart/index.php",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Nagoya University Graduate School of Bioagricultural Sciences",
"name": "DART",
"prefix": "NBDC01027",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc01028": {
"homepage": "http://p3krs.protein.osaka-u.ac.jp/p3kdb/v_menu.php",
"information_keywords": [
"3D structure"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "Database for Protein-3000 Project",
"prefix": "NBDC01028",
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc01029": {
"description": "DNA database (DDBJ/EMBL/GenBank=INSD) overview and search is a database of nucleotide sequences categorized by taxonomic groups, project types and countries of registration. This database contains all the nucleotide sequence data in INSD. Research project types consist of molecular types (transcriptome, functional RNA, immune gene, etc) and INSD (DDBJ) division (EST, GSS, patent data, etc). Users can search for research projects or INSD records using BLAST, as well as by keywords such as names of species, research institutes and countries.",
"homepage": "http://lifesciencedb.jp/ddbj-e/",
"information_keywords": [
"Sequence"
],
"maintainer": "DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "DNA database (DDBJ/EMBL/GenBank=INSD) overview and search",
"prefix": "NBDC01029",
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"DNA",
"RNA"
]
},
"nbdc01030": {
"alt_name": "House Dust Mite Full-Length cDNA Database (Dermatophagoides farinae)",
"description": "This database is a searchable directory of full-length dust mite (Dermatophagoides farinae) cDNA sequences. BLAST searches against the full-length mite cDNA database are possible by setting the search database to Organism Specific and the sub category as \"Full-Mite Dermatophagoides farinae (dust mite)\".",
"homepage": "http://fullmite.hgc.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tokyo The Institute of Medical Science",
"name": "Full-Mite",
"prefix": "NBDC01030",
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01031": {
"alt_name": "Group I Intron Sequence and Structure Database",
"description": "GISSD is a database of group I type introns with thousands of intron sequences from a wide range of species, providing phylogeny and structural information on the introns. Introns have been classified into several groups. Data is available for download.",
"homepage": "http://www.rna.whu.edu.cn/gissd/",
"information_keywords": [
"Sequence"
],
"maintainer": "RNA Research Group at Wuhan University/College of Life Sciences/Wuhan University",
"name": "GISSD",
"prefix": "NBDC01031",
"status": "Inactive",
"target_keywords": [
"DNA"
]
},
"nbdc01032": {
"description": "The Glycoconjugate Data Bank provides information about functions and roles of glycans. The site has two main domains, Glyco-net, which provides functional and network interaction information about glycans and related enzymes, and Structures, which links to 3D structures of glycans in PDB. Annotations of glycans are provided in text and a user-specified network of interactions and pathways can be constructed.",
"homepage": "http://bibi.sci.hokudai.ac.jp/",
"information_keywords": [
"Phenotype",
"Interaction/Pathway",
"3D structure",
"Chemical structure"
],
"maintainer": "Hokkaido University",
"name": "Glycoconjugate Data Bank",
"prefix": "NBDC01032",
"pubmeds": [
"17933765",
"17138593"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Health/Disease",
"Carbohydrate"
]
},
"nbdc01034": {
"alt_name": "Image Bioinformatics Research Group",
"homepage": "http://www.bioimage.org/ibrg/index.php/Image_Bioinformatics_Research_Group",
"information_keywords": [
"Expression",
"Image/Movie"
],
"maintainer": "Fred Hutchinson Cancer Research Center",
"name": "IBRG",
"prefix": "NBDC01034",
"status": "Inactive"
},
"nbdc01035": {
"alt_name": "Insect Microsatellite Database",
"description": "InSatDb is a database of insect microsatellite sequence and characteristic information. The database contains categorized information regarding fundamental characteristics of microsatellites such as location, size, and GC composition. Batch download and query access are available.",
"fairsharing": "biodbcore-000274",
"homepage": "http://cdfd.org.in/INSATDB/home.php",
"information_keywords": [
"Sequence"
],
"maintainer": "Centre for DNA Fingerprinting and Diagnostics",
"name": "InSatDb",
"prefix": "NBDC01035",
"pubmeds": [
"17082205"
],
"status": "Active",
"target_keywords": [
"Genetic variation"
]
},
"nbdc01036": {
"alt_name": "Database of Genomic Islands",
"description": "Islander is a database of information on genomic islands-short sequences found to have integrated into the DNA of a cell by means of an integrase-obtained from sequenced bacterial genomes.\nInformation can be retrieved using the scrollbar at the top of the page, by island, integration site or bacterial/archaeal host on either an A to Z list or a phylogenetic list (ordered by evolutionary similarity). All the available data on the chosen island, integration site or host will be displayed.",
"homepage": "https://bioinformatics.sandia.gov/islander/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Sandia National Laboratories",
"name": "Islander",
"prefix": "NBDC01036",
"pubmeds": [
"14681358"
],
"status": "Suspended",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01037": {
"description": "Kinase Pathway Database is an integrated database of classification of protein kinases in the major eukaryotic species (human, mouse, rat, yeast, nematode, fruit fly) for which genomic sequences have been determined. It includes information about functional conservation, interspecies orthologs, protein-protein interactions, domains, structure, and pathway information. Information of protein-protein interactions were extracted from the summary of publications using natural language processing (NLP). Interspecies comparison of pathways can also be performed.",
"homepage": "http://kinasedb.ontology.hgc.jp:8081/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "The University of Tokyo The Institute of Medical Science",
"name": "Kinase Pathway Database",
"prefix": "NBDC01037",
"pubmeds": [
"12799355"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01039": {
"alt_name": "Microsatellite Analysis Server 3.0",
"description": "MICAS is a tool that searches non-redundant microsatellites of a selected bacterial or archaeal genome sequence. It has been connected to the database, MICdb3.0, with accumulated information on microsatellites extracted from more than 5,000 published prokaryotic genome sequences, which is searcheable by keywords.",
"homepage": "http://www.mcr.org.in/micas/",
"information_keywords": [
"Sequence"
],
"maintainer": "Centre for DNA Fingerprinting and Diagnostics",
"name": "MICAS",
"prefix": "NBDC01039",
"status": "Active",
"target_keywords": [
"Genetic variation"
]
},
"nbdc01040": {
"description": "This is a database to visualize data provided in PDB format. Three-dimensional structures can be visualized using each type of viewer. Images can be automatically rotated to view the molecule as a whole.",
"homepage": "http://helixweb.nih.gov/cgi-bin/pdb",
"information_keywords": [
"3D structure"
],
"maintainer": "NIH (National Institutes of Health)",
"name": "Molecules To Go",
"prefix": "NBDC01040",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01041": {
"alt_name": "PlantPromoterDB",
"description": "PPDB is a database of plant promoter elements. This database contains position, motif, and sequence information for promoters from four major plant species. The promoters can be searched by gene name, ID, or model ID, and cross-species homology analyses can be performed.",
"fairsharing": "biodbcore-000603",
"homepage": "http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/index.cgi",
"information_keywords": [
"Sequence"
],
"maintainer": "Gifu University",
"name": "PPDB",
"prefix": "NBDC01041",
"pubmeds": [
"17947329",
"24194597"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01042": {
"alt_name": "A new database for meta-analysis of the prognostic value of genes",
"description": "This database offers information applicable to researchers who are studying and attempting to predict how gene expression affects the chances of survival and cure of a patient with cancer, by integrating the results of several related studies (called meta-analysis). It consists of a comprehensive library of publicly available cancer microarray datasets (each containing thousands of sequences) with clinical annotations. Such search may make it possible to link gene expression to prognosis.",
"homepage": "http://dna00.bio.kyutech.ac.jp/PrognoScan/",
"information_keywords": [
"Expression"
],
"maintainer": "Kyushu Institute of Technology",
"name": "PrognoScan",
"prefix": "NBDC01042",
"pubmeds": [
"19393097"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST",
"Health/Disease"
]
},
"nbdc01043": {
"alt_name": "Protein-Nucleic Acid Complex Database",
"description": "ProNuC is a database of interactions between proteins and nucleic acids, with 3D structural information on interaction between proteins and specific DNA motifs. It can be searched by protein name, motif type, and nucleic acid type and form. Structures are visualized in mono or stereo vision, or using the interactive 3DinSight application.",
"homepage": "http://gibk26.bio.kyutech.ac.jp/jouhou/pronuc/pronuc.html",
"information_keywords": [
"3D structure"
],
"maintainer": "Kyushu Institute of Technology",
"name": "ProNuc",
"prefix": "NBDC01043",
"status": "Inactive",
"target_keywords": [
"DNA",
"Protein"
]
},
"nbdc01044": {
"homepage": "http://219.121.17.221/DNABook_DB/VIEW/Book_Top.php?BOOK_ID=BOOK_4",
"information_keywords": [
"Bioresource"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "RIKEN Arabidopsis cDNA Encyclopedia DNABook",
"prefix": "NBDC01044",
"status": "Closed",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01045": {
"alt_name": "A database of compound microsatellite-SNP markers",
"description": "SNPSTR is a database of STR elements with nearby SNPs. The database seeks to use coupled structural and variation data to capture genetic information about population history. Users can search regions, accessions, or repeats for identified SNPSTR in human, mouse, rat, dog, and chicken,, or request access to download bulk data.",
"homepage": "http://www.sbg.bio.ic.ac.uk/~ino/SNPSTRdatabase.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Imperial College London",
"name": "SNPSTR",
"prefix": "NBDC01045",
"pubmeds": [
"17202172"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Genetic variation"
]
},
"nbdc01046": {
"description": "This database consists of the mapped genome of the soil bacterium, Streptomyces griseus IFO 13350. This organism produces the aminoglycoside antibiotic Streptomycin, which has been used, since its discovery more than 60 years ago, for the treatment of tuberculosis. Streptomyces griseus IFO 13350 has one chromosome, containing 8,545,929 base pairs and an average content of 72.2% GC.\nThis information suggests some 7138 open reading frames, 66 tRNA genes and six rRNA operons. \nA blast search option is available.",
"homepage": "http://park.itc.u-tokyo.ac.jp/hakko/genome.html",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tokyo",
"name": "Streptomyces griseus IFO 13350 Genome",
"prefix": "NBDC01046",
"pubmeds": [
"18375553"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01047": {
"alt_name": "Triticeae Full-Length CDS Database",
"description": "This database offers access to an annotated list of full-length coding DNA sequences of barley and wheat. It contains information on 8530 wheat sequences and 7341 barley sequences. The BarleyDB of Research Institute for Bioresources, Okayama University, contributed 5006 barley full-length cDNA sequences to the collection in this site.\n6162 of the wheat examples were recently sequenced in RIKEN and at the Kihara Institute for Biological Research, Yokohama City University. The National Bio Resource Project in Japan supported this project.\nA search option based on keywords is provided.\nAdditional information on gene function, GO terms, homologous DNA sequences and the related amino acid sequence of each cDNA sequence is given as well as the results of a search for homologous sequences in the genomes rice and sorghum.",
"homepage": "http://trifldb.psc.riken.jp/v3/index.pl",
"information_keywords": [
"Sequence"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "TriFLDB",
"prefix": "NBDC01047",
"pubmeds": [
"19448038"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01048": {
"alt_name": "Triticeae Mapped EST Database",
"description": "This database provides information on the EST's of Triticeae, a subfamily of grasses to which the domesticated species of wheat, barley and rye belong. Annotations on the position of these EST's on the genomic map of wheat and barley were obtained from three other related linkage maps that were already published.\nThe database can be searched by entering the chromosome names and markers.\nThe search results include annotated links to comparison maps for the rice genome.",
"homepage": "http://trimedb.psc.riken.jp/index.pl",
"information_keywords": [
"Sequence"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "TriMEDB",
"prefix": "NBDC01048",
"pubmeds": [
"18590523"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc01049": {
"alt_name": "C.elegans 3'UTR Database",
"description": "UTRome is a database of 3' UTRs in C. elegans. The database contains entries for all 3' UTRs in the genome. Users can search by gene and functional elements residing within 3' UTRs of those genes. The site includes protocols describing how sequences were determined and several files available for download.",
"homepage": "http://tomato.biodesign.asu.edu/cgi-bin/UTRome/utrome.cgi",
"information_keywords": [
"Sequence"
],
"maintainer": "Arizona State University",
"name": "worm UTRome",
"prefix": "NBDC01049",
"pubmeds": [
"25601023",
"20522740",
"17986455",
"19536255"
],
"status": "Active",
"target_keywords": [
"RNA"
]
},
"nbdc01050": {
"alt_name": "World Federation for Culture Collections",
"description": "The WFCC is a international database for the collection, authentication, maintenance and distribution of cultures of microorganisms and cultured cells. It contains data on the organisation, management, services and scientific interests of the culture collections. Each entry is linked to a second record containing the list of species held.",
"homepage": "http://www.wfcc.info/",
"information_keywords": [
"Bioresource"
],
"maintainer": "World Federation for Culture Collections",
"name": "WFCC",
"prefix": "NBDC01050",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01052": {
"description": "The database of AQUATIC ORGANISMS is for collating information on aquatic organisms. It contains information about species classification, biological details, scientific literature and genetics.",
"homepage": "http://aquadb.fra.affrc.go.jp/~aquadb/index_e.html",
"information_keywords": [
"Bioresource",
"Ontology/Terminology/Nomenclature",
"Bibliography/Documents"
],
"maintainer": "The National Research and Development Agency, Japan Fisheries Research and Education Agency (FRA)",
"name": "Database of AQUATIC ORGANISUMS",
"prefix": "NBDC01052",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc01054": {
"description": "COXPRESdb is a database of gene coexpression information. COXPRESdb features two major functions: a search capability for locating genes of interest and identifying coexpressed genes, and a visualization capability for representing the relationships in the database. gene expression data is collected from the NCBI GEO database and normalized. Users can query genes to find orthologs and co-expressed genes across multiple species and data is available for download.",
"homepage": "http://coxpresdb.jp/",
"information_keywords": [
"Expression",
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "The University of Tokyo The Institute of Medical Science Human Genome Center",
"name": "COXPRESdb",
"prefix": "NBDC01054",
"pubmeds": [
"17932064",
"19767600",
"19620096",
"18953027"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01056": {
"description": "The European Ribosomal RNA Database is a database of the RNA subunits critical to translation of RNA into proteins. The database currently contains only information on secondary structures of rRNA molecules.",
"homepage": "http://bioinformatics.psb.ugent.be/webtools/rRNA/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Gent/Department of Plant System Biology",
"name": "The European ribosomal RNA Database",
"prefix": "NBDC01056",
"pubmeds": [
"14681368"
],
"status": "Inactive",
"target_keywords": [
"RNA"
]
},
"nbdc01058": {
"alt_name": "Pathogenic Bacteria Data Base",
"homepage": "http://bac.hs.med.kyoto-u.ac.jp/PBDB-J.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Kyoto University Graduate School of Medicine",
"name": "PBDB",
"prefix": "NBDC01058",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc01059": {
"description": "KEGG ENVIRON is a database of crude drugs, essential oils, and medicinal harbs, all of which are mostly natural products of plants. Each entry is associated with the chemical component, efficacy information, and source species information whenever applicable.",
"homepage": "http://www.genome.jp/kegg/drug/environ.html",
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG ENVIRON",
"prefix": "NBDC01059",
"status": "Closed",
"target_keywords": [
"Health/Disease",
"Chemical compound",
"Drug"
]
},
"nbdc01060": {
"homepage": "http://snpnet.jst.go.jp/top.html",
"maintainer": "JST (Japan Science and Technology Agency)",
"name": "SNP Database Network in Japan",
"prefix": "NBDC01060",
"status": "Closed",
"target_keywords": [
"Genetic variation"
]
},
"nbdc01061": {
"alt_name": "JAMSTEC E-library of Deep-sea Images",
"homepage": "https://www.godac.jamstec.go.jp/jedi/e/index.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Japan Agency for Marine-Earth Science and Technology",
"name": "J-EDI",
"prefix": "NBDC01061",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01063": {
"description": "JAMSTEC E-library of Deep-sea Images is a database of valuable deep sea research videos and photos which were obtained by JAMSTEC submersibles. It provides videos and photos associated with detailed information including research location and context (ex. living organism or phenomena). Users are able to search for these data by content or dive information and browse them. Users are available to access videos and photos in low resolution on this site, and also high resolution data on request.",
"homepage": "http://www.godac.jamstec.go.jp/dsidb/e/",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Japan Agency for Marine-Earth Science and Technology",
"name": "Deep Sea Image Database",
"prefix": "NBDC01063",
"status": "Closed",
"target_keywords": [
"Organism"
]
},
"nbdc01065": {
"description": "Marine Biological Sample Database is a database of marine biological samples collected during the scientific missions of JAMSTEC vessels (NATSUSHIMA, KAIYO, YOKOSUKA, KAIREI and MIRAI) or submersibles. Each entry contains various sample information such as sample names, fixation and preservation methods, localities, related cruise and dive information, etc. This database allows to search by any keywords or specific data items and/or taxon trees. Moreover, it's available to search from a map.",
"homepage": "http://www.godac.jamstec.go.jp/bio-sample/index_e.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Japan Agency for Marine-Earth Science and Technology",
"name": "Marine Biological Sample Database",
"prefix": "NBDC01065",
"status": "Suspended",
"target_keywords": [
"Organism"
]
},
"nbdc01069": {
"alt_name": "Japan Fisheries Oceanography Database",
"homepage": "http://jfodb.dc.affrc.go.jp/",
"information_keywords": [
"Environment"
],
"maintainer": "The National Research and Development Agency, Japan Fisheries Research and Education Agency (FRA)",
"name": "JFODB",
"prefix": "NBDC01069",
"status": "Suspended",
"target_keywords": [
"Organism"
]
},
"nbdc01070": {
"description": "ExPASy is a database of bioinformatics resources. The database contains links to tools and other resources for several bioinformatics purposes including proteomics, genomics, systems biology, evolution, population genetics, and biophysics. Users can search for resources in all databases or within a specific category.",
"homepage": "http://www.expasy.org/",
"information_keywords": [
"Portal"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "ExPASy (Bioinformatics Resource Portal)",
"prefix": "NBDC01070",
"pubmeds": [
"12824418"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01071": {
"description": "DrugBank is a database of detailed informatics resources on approved and experimental drugs. The database contains informaiton on drug targets as well as the results of experiments resulting in extensive bioinformatics and chemoinformatics data. Users can browse or search by drug or target. Data is available for download.",
"fairsharing": "biodbcore-000304",
"homepage": "http://www.drugbank.ca/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Chemical structure"
],
"maintainer": "University of Alberta/Department of Computing Science",
"name": "DrugBank",
"prefix": "NBDC01071",
"pubmeds": [
"18048412",
"16381955"
],
"status": "Active",
"target_keywords": [
"Protein",
"Drug"
]
},
"nbdc01072": {
"information_keywords": [
"Expression",
"Bibliography/Documents"
],
"name": "The Stem Cell Community",
"prefix": "NBDC01072",
"status": "Closed",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc01073": {
"homepage": "http://riodb.ibase.aist.go.jp/liverproteindb1/index.html",
"information_keywords": [
"Expression"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "ARMLiPDB",
"prefix": "NBDC01073",
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc01074": {
"alt_name": "Co-expressed Biological Processes",
"description": "CoP is an integrated database consisting of multiple databases with information on co-expressed genes and biological processes in plants based on gene Ontology. The omics data in this database, originate from NCBI, TAIR and GRAMENE databases. For co-expression analyses in this database, the Confeito algorithm is used. The revised version, an upgrade from the CoexProcess database, was released on March 12, 2009. More than ten thousand probes and hundred chips are included and assembled Affymetrix geneChip microarrays include thale cress (Arabidopsis thaliana), soy beans (Glycine max), barley (Hordeum vulgare), rice (Oryza sativa), poplar (Populus trichocarpa), wheat (Triticum aestivum), grapes (Vitis vinifera), and maize (Zea mays), and other microarrays will be added in the future.",
"homepage": "http://webs2.kazusa.or.jp/kagiana/cop/",
"information_keywords": [
"Expression"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "CoP",
"prefix": "NBDC01074",
"status": "Closed",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01075": {
"alt_name": "Directed Acyclic Graphs Viewer",
"description": "DAGViz indicates the nature of this database, which is a Directed Acyclic Graphs Viewer.This site offers access to two databases namely KEGG (Kyoto Encyclopaedia of genes and Genomes) and GOA (gene Ontology Annotation). KEGG supplies information on complete genomes of 180 eukaryotes, 2139 bacteria and 147 Archaea. A search option is available by means of entering one of four possible descriptions namely, gene Ontology ID (GO ID), Exact GO term, Keyword GO term or gene Product. \nA limited list of organisms is also offered from which a name can be selected to have information retrieved from the above two databases.",
"homepage": "http://www.pgb.kazusa.or.jp/dagviz/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "DAGViz",
"prefix": "NBDC01075",
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01078": {
"homepage": "http://hinv.jp/H-ExP/",
"information_keywords": [
"Expression"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "H-Exp",
"prefix": "NBDC01078",
"status": "Closed"
},
"nbdc01079": {
"alt_name": "Kazusa Omics Data Market",
"description": "KomicMarket (Kazusa Omics Data Market) is a database that contains annotations of metabolite peaks that have been detected with mass spectrometry (MS) in studies of metabolomics. Data were mostly obtained with high-resolution MSs liquid chromatography.",
"homepage": "http://webs2.kazusa.or.jp/komicmarket/",
"information_keywords": [
"Method"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "KomicMarket",
"prefix": "NBDC01079",
"pubmeds": [
"18266924",
"24949426"
],
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc01080": {
"description": "MS-MS Fragment Viewer is a metabolomics database of the LC-FT/ICR-MS measurements of authentic compounds. It contains FT-MS, IT- and FT-MS/MS spectral data with chemical information such as accurate mass, molecular formula and predicted structure of each fragment ion. This database also includes PDA spectra of these compounds with additional structural information. With the system compounds observed in mass spectra can be assigned and structures of unknown compounds can be annotated.",
"homepage": "http://webs2.kazusa.or.jp/msmsfragmentviewer/",
"information_keywords": [
"Chemical structure"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "MS-MS Fragment Viewer",
"prefix": "NBDC01080",
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc01081": {
"alt_name": "EST Database of Trees for Sustainable Humanosphere",
"description": "RISH Database is an EST database of trees for sustainable humanosphere. This database has a BLAST search function and contains 6253 EST sequences of Acacia mangium unigene, an economic plant. Thujopsis dolabrata var. hondai unigene will also be available in the future.",
"homepage": "http://database.rish.kyoto-u.ac.jp/arch/acacia-est/data/blast_search.htm",
"information_keywords": [
"Sequence"
],
"maintainer": "Kyoto University",
"name": "RISH Database",
"prefix": "NBDC01081",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01083": {
"alt_name": "NITE Chemical Risk Information Platform",
"description": "NITE Chemical Risk Information Platform (NITE-CHRIP) is a database provided free of charge\nover the Internet, and shows comprehensive information on Risk Assessments and Laws &\nRegulations, etc., of chemical substances that can be searched by entering the number, name,\netc., or provided in list format for each category.",
"homepage": "https://www.nite.go.jp/chem/chrip/chrip_search/systemTop",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Bibliography/Documents"
],
"maintainer": "NITE (National Institute of Technology and Evaluation)",
"name": "NITE-CHRIP",
"prefix": "NBDC01083",
"status": "Inactive",
"target_keywords": [
"Chemical compound"
]
},
"nbdc01084": {
"alt_name": "Reference database for gene Expression Analysis",
"description": "RefExA is a reference database for gene expression analysis. Search terms include Genbank accession, Unigene cluster ID, gene symbol, and gene name and tissues consist of normal human tissues, normal cells and cancer cells.",
"homepage": "http://sbmdb.genome.rcast.u-tokyo.ac.jp/refexa/main_search.jsp",
"information_keywords": [
"Expression"
],
"maintainer": "The University of Tokyo Research Center for Advanced Science and Technology",
"name": "RefExA",
"prefix": "NBDC01084",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc01085": {
"description": "This database contains multi-omics data of Escherichia coli, a model organism. Data was gathered under the auspices of the Institute for Advanced Biosciences, Keio University, which is located in Tsuruoka city, Japan. The database is meant to contribute quantitative information about the inner molecular components of cells to the comprehensive knowledge of the highly complex nature of living systems, for a better understanding. CE-MS metabolome data, obtained by CE-MS analysis, RT-PCR transciptome data (quantitative measurements of intracellular mRNAs), proteome data (quantitative measurement of proteins) and fluxome data (GC-MS measurement of 13C-labeled compounds to measure metabolic flux) are also available.",
"homepage": "http://ecoli.iab.keio.ac.jp/",
"information_keywords": [
"Expression",
"Image/Movie"
],
"maintainer": "Keio University",
"name": "Escherichia coil Multi-omics Database",
"prefix": "NBDC01085",
"pubmeds": [
"17379776"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Protein",
"Metabolite"
]
},
"nbdc01086": {
"description": "This database provides information on how species and metabolites relate to each other as does the site above.\nThis page, however, offers the database in an attractive and user-friendly format, which the whole family should be able to understand and utilize.\nIt appears in the shape of a colorful graph with pictures and descriptive names indicating the topics the information is arranged by.\nOptimal use of the database requires for it to be downloaded to the user's personal computer.\nA manual on how to use the database is provided.",
"homepage": "http://www.knapsackfamily.com/KNApSAcK_Family/",
"information_keywords": [
"Bibliography/Documents",
"Portal"
],
"maintainer": "Nara Institute of Science and Technology",
"name": "KNApSAck Family",
"prefix": "NBDC01086",
"pubmeds": [
"22123792",
"23292603"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Metabolite"
]
},
"nbdc01087": {
"homepage": "http://www.ncrna.org/glocal/cgi-bin/hgGateway",
"information_keywords": [
"Sequence"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "UCSC GenomeBrowser for Functional RNA",
"prefix": "NBDC01087",
"status": "Closed",
"target_keywords": [
"RNA"
]
},
"nbdc01088": {
"alt_name": "NBDC",
"description": "NBDC Portal is a portal site for databases and web tools in life science, developed by Department of NBDC Program (NBDC) at the Japan Science Technology Agency (JST). The site contains the Database Catalog, Life Science Database Cross Search, Life Science Database Archive, etc. Users can access a variety of life science databases from this website.",
"homepage": "https://biosciencedbc.jp/en/",
"information_keywords": [
"Portal"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "Department of NBDC Program",
"prefix": "NBDC01088",
"status": "Active"
},
"nbdc01089": {
"description": "Life Science Database Cross Search is a data set collection and a cross search system for life science databases developed by the Department of NBDC Program (NBDC) at the Japan Science Technology Agency (JST). This cross search system includes entries of literature and patents, as well as various molecular data. Users can perform a keyword search across scattered databases in life science at once, and refine search results by selecting a category of databases, a database name or a gene name.",
"homepage": "https://dbsearch.biosciencedbc.jp/index.php?lang=en",
"information_keywords": [
"Bibliography/Documents",
"Portal"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "Life Science Database Cross Search",
"prefix": "NBDC01089",
"status": "Active"
},
"nbdc01095": {
"description": "TogoProt is a comprehensive protein-related database search system. A keyword search displays a list of protein families in the menu bar. When selecting the protein or protein family of interest, links will be displayed to relevant database entries.",
"homepage": "https://togoprot.biosciencedbc.jp/R/",
"information_keywords": [
"Portal"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "TogoProt",
"prefix": "NBDC01095",
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc01096": {
"alt_name": "Online Resource Finder for Lifesciences",
"description": "OReFiL is a database and a search system for online life science resources (databases, tools and web-services) mentioned in peer-reviewed papers. OReFiL covers MEDLINE entries and BioMed Central full-text papers to extract URLs of online resources. Users can search resources by free words, MeSH (Medical Subject Headings) terms and author names. Search results show titles of the hit resources with URLs, MeSH terms and links to corresponding PubMed entries, web pages and papers.",
"homepage": "http://orefil.dbcls.jp/en/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "OReFiL",
"prefix": "NBDC01096",
"pubmeds": [
"17683589"
],
"status": "Active"
},
"nbdc01098": {
"alt_name": "DDBJ Sequence Read Archive",
"description": "DRA is a repository for raw output data from next-generation sequencers maintained by DDBJ (DNA Data Bank of Japan) in cooperation with the other members of INSDC. DRA includes raw sequencing data with following 6 metadata objects; Submission (information on the submitter and data release), Study (study details), Sample (taxonomic information), Experiment (experimental setup details), Run (data files and run details) and Analysis (processed data and ancillary data). This repository provides manuals and video tutorials for data submission. Users can search archive data by keywords, organisms, study types, etc, and download metadata XML, FASTQ and SRA Lite files at the DRA Search or the FTP site.",
"homepage": "https://www.ddbj.nig.ac.jp/dra/index-e.html",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "Bioinformation and DDBJ Center, National Institute of Genetics, Research Organization of Information and Systems",
"name": "DRA",
"prefix": "NBDC01098",
"pubmeds": [
"21062823",
"21062814",
"20865494",
"19850725",
"19965774"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"RNA"
]
},
"nbdc01099": {
"alt_name": "Reference Expression dataset",
"description": "RefEx is a reference database of gene expression profiles in normal mammalian tissues. RefEx contains comparative expression data obtained from ESTs, microarray (geneChip), CAGE (Cap Analysis gene Expression) tags and RNA-seq for human, mouse and rat. Users can search for tissue-specific genes from a list of 40 organs, as well as gene names and symbols from lists of gene ontology, gene families and chromosomal regions or by keywords. Search results show gene names, heatmaps on 3D human body images visualizing the relative gene expression values, and corresponding reference datasets.",
"homepage": "http://refex.dbcls.jp/index.php?lang=en",
"information_keywords": [
"Expression"
],
"maintainer": "DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "RefEx",
"prefix": "NBDC01099",
"status": "Active",
"target_keywords": [
"cDNA/EST",
"RNA"
]
},
"nbdc01100": {
"alt_name": "Gene, Disease Features Ontology-based Overview System",
"description": "Gendoo is a database and a search system for diseases, drugs, biological phenomena and anatomy associated with genes and diseases. Gendoo contains MeSH (Medical Subject Headings) terms and OMIM (Online Mendelian Inheritance in Man) entries. Users can search related terms and entries by Entrez gene IDs / gene names, OMIM IDs / disease names and MeSH terms. Users can also input multiple IDs to show differences and similarities among them, such as type 1 and type 2 diabetes, by high-scoring lists or hierarchical-tree views.",
"homepage": "http://gendoo.dbcls.jp/",
"maintainer": "DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "Gendoo",
"prefix": "NBDC01100",
"pubmeds": [
"18430990",
"19498079"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc01102": {
"description": "GGRNA is a database and a Google-like full text search engine for genes and transcripts of 13 species (human, mouse, rat, chicken, etc). GGRNA contains mRNA and noncoding RNA entries archived in NCBI RefSeq. Users can search for words and phrases (gene names, IDs, gene descriptions, etc), as well as nucleotide and amino-acid sequences. This search engine provides various search operators. For example, users can also search for nucleotide sequences containing degenerate nucleotides or mismatches.",
"homepage": "http://ggrna.dbcls.jp/en/",
"information_keywords": [
"Sequence"
],
"maintainer": "DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "GGRNA",
"prefix": "NBDC01102",
"pubmeds": [
"22641850"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01104": {
"alt_name": "Search SRA Entries with PubMed Article",
"description": "Kusarinoko is a database of sequencing metadata. The database contains publicly available data for next-generation sequencing Sequence Read Archive (SRA) data. The database is constructed by mining SRA information from published literature. Study IDs and keywords are queried by simple search.",
"homepage": "http://g86.dbcls.jp/kusarinoko",
"information_keywords": [
"Method",
"Sequence",
"Bibliography/Documents"
],
"maintainer": "DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "kusarinoko",
"prefix": "NBDC01104",
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"DNA",
"RNA"
]
},
"nbdc01106": {
"description": "TargetMine is a data warehouse system for assisting drug discovery. It integrates biological data for human, mouse and rat from more than 16 public databases, allowing for the integrated analysis of protein structures, transcription factors, drugs and many other data types. The system has been applied to prioritizing target candidates and has led to experimentally verified potential new targets.",
"homepage": "http://targetmine.mizuguchilab.org/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"3D structure"
],
"maintainer": "National Institutes of Biomedical Innovation, Health and Nutrition",
"name": "TargetMine",
"prefix": "NBDC01106",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Health/Disease",
"Drug"
]
},
"nbdc01107": {
"alt_name": "Tomato selected BAC clone mixture Database",
"description": "This is a database for 5β- and 3β-terminal sequences of clones those constitutes a BAC clone library for Solanum lycopersicum. In order to provide enriched annotation for the clones, those sequences are linked to information in other databases, such as predicted protein family. Sequences of markers, including EST-SNP, EST-SSR and Intron-SNP, are supplied in the marker database.",
"homepage": "http://www.kazusa.or.jp/tomato_sbm/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Tomato SBM Database",
"prefix": "NBDC01107",
"pubmeds": [
"21044984",
"20431859"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01108": {
"alt_name": "Planarian Brain Database",
"description": "Plabrain DB is a database for analysis of planarian nervous system archived in Life Science Database Archive. Plabrain DB includes FACS-based single-cell PCR data and images of the gene expression analysis by whole-mount in situ hybridization and Immunohistochemical staining. Users can search images and PCR data of planarians by keywords, and download selected data as a CSV file.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/plabrain-db/desc.html",
"information_keywords": [
"Expression",
"Image/Movie"
],
"maintainer": "Kyoto University Graduate School of Science",
"name": "Plabrain DB",
"prefix": "NBDC01108",
"pubmeds": [
"20078655",
"20338223",
"19968467",
"20078655",
"17624455",
"17565705"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Cell/Organelle"
]
},
"nbdc01109": {
"homepage": "http://genebrainsystems.nimh.nih.gov/",
"information_keywords": [
"Expression",
"Image/Movie"
],
"maintainer": "NIMH (National Institute of Mental Health)",
"name": "Gene Brain Systems.nimh",
"prefix": "NBDC01109",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc01136": {
"alt_name": "Allergen Database for Food Safety",
"description": "It provides information of allergenic proteins and low-molecular weight allergenic compounds. \nThe allergenic proteins have been collected from literature sources and AllergenOnline ( http://www.allergenonline.org/ ), and low-molecular weight allergenic compounds were extracted from general allergen information provided in AllAllergy ( http://www.allallergy.net/allergenfind.cfm ) through the careful review.\nIt also provides homology search with known allergenic proteins and function to determine whether epitope sequences are present or not in query sequences.",
"homepage": "https://allergen.nihs.go.jp/ADFS/",
"information_keywords": [
"Sequence"
],
"maintainer": "NIHS (National Institute of Health Sciences)",
"name": "ADFS",
"prefix": "NBDC01136",
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease"
]
},
"nbdc01137": {
"alt_name": "Cimex lectularius EST",
"description": "ClEST is a database of bedbug (Cimex lectularius) ESTs and clusters archived in Life Science Database Archive. This database includes transcriptomes extracted from unique organs of the bedbug. Each entry of clusters contains description, category, length, sequence and the number of clones. Each entry of EST clones contains library data, category, cluster, the accession number, length and sequence. Users can search clusters and EST clones by keywords from those items.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/clest/desc.html",
"information_keywords": [
"Sequence"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "ClEST",
"prefix": "NBDC01137",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01138": {
"alt_name": "Systems and Structural Biology Center",
"description": "SSBC is a database about structures and functions of proteins elucidated at \"National Project on Protein Structural and Functional Analyses\" (the \"Protein 3000\" Project, 2002-2006). It contains images of x-ray diffraction and crystallization, and related experimental information, such as expression, purification, etc.",
"homepage": "https://metadb.riken.jp/metadb/db/SciNetS_ria46i",
"information_keywords": [
"Expression",
"Image/Movie",
"3D structure"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "SSBC",
"prefix": "NBDC01138",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01140": {
"alt_name": "Lotus japonicus Full-length cDNA Databases",
"description": "FuLoJa stands for Lotus japonicus Full-length cDNA Databases and includes full-length cDNA sequences of lotus japonicus that have been analysed with InterPro. Blast search is available.",
"homepage": "http://webs2.kazusa.or.jp/IntegrationDBRS/FuLoja/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "FuLoJa",
"prefix": "NBDC01140",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01141": {
"description": "This database is called MCG CNV and provides copy number variant (CNV) and loss of heterozygosity (LOH) data. These have been detected by microarray analyses using MCG arrays and SNP arrays. The incidence of CNV and LOH in healthy Japanese is available. This is essential to assess the pathogenicity of CNV or LOH, and to differentiate between \"pathogenic\" and \"benign\" CNV, which is useful in patients with pathology due to cryptic genomic aberrations.",
"homepage": "http://www.cghtmd.jp/CNVDatabase/top!changeEngLocale",
"information_keywords": [
"Expression"
],
"maintainer": "Tokyo Medical and Dental University",
"name": "MCG CNV Database",
"prefix": "NBDC01141",
"pubmeds": [
"15245590"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Health/Disease"
]
},
"nbdc01142": {
"description": "This is a database of nucleotide sequences of ESTs, cDNAs and oligo DNA microarray probes for Lotus japonicus andArabidopsis thaliana which were obtained from PMPj.",
"homepage": "http://webs2.kazusa.or.jp/IntegrationDBRS/pmpj-blast/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "PMPj-Blast",
"prefix": "NBDC01142",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01143": {
"alt_name": "Kazusa Molecular Formula Searcher",
"description": "Kazusa Molecular Formula Searcher (MFSearcher) is a RESTful Web service that provides researchers with high-throughput elemental composition prediction based on accurate mass values obtained by high-resolution mass spectrometers. It is also possible to immediately search major compound databases like KEGG, PubChem, KNApSAcK LIPID MAPS and Flavonoid Viewer.",
"homepage": "http://webs2.kazusa.or.jp/mfsearcher/",
"information_keywords": [
"Chemical structure"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "MFSearcher",
"prefix": "NBDC01143",
"pubmeds": [
"23162084"
],
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc01144": {
"alt_name": "Pocket Similarity Search using Multiple-Sketches",
"description": "This site contains a database of protein-ligand binding sites that have been compared and numbered according to resemblance in structure.\nComparing the huge amounts of small molecule binding sites of proteins available in the PDB (Protein Data Bank) is important in order to determine anticipated protein functions, the knowledge of which may then be applied in the research and discovery of new drugs. \nThe software program used, \"SketchSort\", proved to be an extremely fast method. All-pair similarity searches were done for 3.4 million binding sites and over 24 million analogous pairs were found.\nThe results, presented as a PoSSuM (Pocket Similarity Search using Multiple-Sketches) database contain all pairs identified and include commentary notes of various types, namely CATH (protein structure classification according to Class, Architecture, Topology and Homologous superfamily), SCOP (Structural Classification of Proteins), EC number (Enzyme Commission number) and gene ontology.\nTwo search modes are provided: \nSearch K, to find analogous binding sites to a familiar ligand-binding site entered and Search P, to predict ligands that show potential to bind to a protein structure entered.",
"fairsharing": "biodbcore-000127",
"homepage": "http://possum.cbrc.jp/PoSSuM/",
"information_keywords": [
"Image/Movie"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "PoSSuM",
"prefix": "NBDC01144",
"pubmeds": [
"22135290"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01145": {
"alt_name": "Database Of BIoSynthesis clusters CUrated and InTegrated",
"description": "Successful development of new drugs often relies on information about secondary metabolites produced by actinomycetes.\nThis is a database constructed from literature about recognized gene clusters of NRPSs (Non-Ribosomal Peptide Synthetases) and PKSs (Polyketide Synthases).\nData about these secondary metabolite biosynthesis gene clusters is herewith offered in a comprehensively descriptive manner. This saves the researcher the laborious task of gathering the information often dispersed in many references.\nText search, Module search and Blast search options for information retrieval are provided as is a menu allowing access to KS/A domain sequences.",
"homepage": "https://www.nite.go.jp/nbrc/pks/",
"information_keywords": [
"Sequence"
],
"maintainer": "NITE (National Institute of Technology and Evaluation)",
"name": "DoBISCUIT",
"prefix": "NBDC01145",
"pubmeds": [
"23185043"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Metabolite"
]
},
"nbdc01146": {
"alt_name": "Gene Trek in Prokaryote Space",
"description": "GTPS is a database of prokaryotic genome sequences performed re-annotation. This database contains chromosomal and plasmid sequences including re-annotated ORFs and RNAs of Bacteria and Archaea. Users can search organism and corresponding sequence data by species names, strain names, phrases, DDBJ accession number, grade classification by BLAST, etc. This database also provides browser tools of the whole genome or genes to view newly found ORFs.",
"homepage": "http://gtps.ddbj.nig.ac.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "Bioinformation and DDBJ Center, National Institute of Genetics, Research Organization of Information and Systems",
"name": "GTPS",
"prefix": "NBDC01146",
"pubmeds": [
"17166861"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01147": {
"alt_name": "BioSimulated DataBase",
"homepage": "http://bsd.genes.nig.ac.jp/bsd_web/Top.jsp",
"information_keywords": [
"Expression"
],
"maintainer": "National Institute of Genetics",
"name": "BSD",
"prefix": "NBDC01147",
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01148": {
"alt_name": "Genome Information Broker for Insertion sequence",
"description": "GIB-IS is a database of bacterial insertion sequences. It contains annotated IS determined from DDBJ. Users can search by organism, keyword, or IS ID, and data is available for download.",
"homepage": "http://gib-is.genes.nig.ac.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "Bioinformation and DDBJ Center, National Institute of Genetics, Research Organization of Information and Systems",
"name": "GIB-IS",
"prefix": "NBDC01148",
"status": "Closed",
"target_keywords": [
"DNA"
]
},
"nbdc01153": {
"description": "Sequence Navigator is a portal site to PDBj that uses BLAST to search for protein structures. The database contains 3D PDB structural representations of proteins and returns results homologous to the search sequence or PDB ID. Users can then cluster results and obtain superpositions of homologous structures.",
"homepage": "http://pdbj.org/seq-navi",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "Sequence Navigator",
"prefix": "NBDC01153",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01154": {
"alt_name": "Database of Aligned Structural Homologs",
"description": "DASH is a database of structural alignments for all known structurally homologous protein domains and chains in the PDB. This database allows to search using PDB ID or single sequence. Search results reveal a list about chains and representative domains. Each entry contains chain description, cluster representative, length, PDB data, canonical sequence, PDP domains and chain alignments, etc..",
"homepage": "https://sysimm.org/dash/",
"information_keywords": [
"Image/Movie",
"3D structure"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "DASH",
"prefix": "NBDC01154",
"pubmeds": [
"31062021"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01155": {
"alt_name": "Ciona intestinalis Adult In situ hybridization Database (ver.2 beta)",
"description": "CiAID is a database of RNA expression profiles of Ciona intestinalis. It contains in situ hybridization profiles for hundreds of genes profiled across many Ciona developmental stages. In addition to in situ data, 3D reconstructions are presented and technical advice is available.",
"homepage": "http://bioinfo.s.chiba-u.jp/ciaid/",
"information_keywords": [
"Expression",
"Image/Movie"
],
"maintainer": "Chiba University Graduate School of Advanced Integration Science Nanoscience",
"name": "CiAID",
"prefix": "NBDC01155",
"pubmeds": [
"15056923"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST",
"Organism"
]
},
"nbdc01156": {
"alt_name": "3-Dimensional Protein Localization",
"description": "3DPL is a database of the spatial and temporal localization of proteins in Ciona intestinalis. The database consists of z-stacked images of GFP-fusion proteins in C. intestinalis and can be used in conjunction with the FABA and FABA2 databases. Users can query genes, tissues, or developmental stages and view protein localization in a Java environment.",
"homepage": "https://www.bpni.bio.keio.ac.jp/chordate/3dpl/top.html",
"information_keywords": [
"Expression",
"Image/Movie"
],
"maintainer": "Keio University Faculty of Science and Technology",
"name": "3DPL",
"prefix": "NBDC01156",
"status": "Inactive",
"target_keywords": [
"Protein",
"Organism"
]
},
"nbdc01157": {
"alt_name": "Ascidians Chemical Biological Database",
"description": "ACBD is a database of compounds and small molecules that have been shown to affect Ciona intestinalis. It consists of entries for hundreds of compounds and contains descriptions of the chemicals and their effect on C. intestinalis systems.",
"homepage": "https://www.bpni.bio.keio.ac.jp/chordate/acbd/top.html",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Keio University Faculty of Science and Technology",
"name": "ACBD",
"prefix": "NBDC01157",
"status": "Inactive",
"target_keywords": [
"Chemical compound"
]
},
"nbdc01158": {
"description": "Kyoto Human Embryo Visualization Project is a database collecting 2D and reconstructed 3D images of human embryos. The embryos including anomalies were mainly derived from therapeutic abortions based on the Maternity Protection Law of Japan. The image gallery consists of gross pictures, MR microscopic images, EFIC data and histological sections, but this database restricts public access to some contents. Each entry is identified by the specimen number, and users can search images by developmental stages, specimen numbers and anomalies.",
"homepage": "http://bird.cac.med.kyoto-u.ac.jp/index_e.html",
"information_keywords": [
"Image/Movie",
"3D structure"
],
"maintainer": "Kyoto University Graduate School of Medicine Congenital Anomaly Research Center",
"name": "Kyoto Human Embryo Visualization Project",
"prefix": "NBDC01158",
"pubmeds": [
"17963260",
"20503356",
"18037794"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01159": {
"description": "List of TP Press Release on Research is a portal list of press releases and literature information about studies at the Targeted Proteins Research Program (TPRP) that is a national project promoted by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan. This list provides abstracts of researches and links to press releases or the full text and the abstract of published papers. It also contains press records and information of protein conformations which were registered in PDBj.",
"homepage": "http://www.tanpaku.org/e_news_release/",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Targeted Proteins Research Program",
"name": "List of TP Press Release on Research",
"prefix": "NBDC01159",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01160": {
"description": "TP Structure Gallery is a list of three-dimensional structures of proteins which were analyzed in the Targeted Proteins Research Program (TPRP) that is a national project promoted by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan. This database allows to search with keywords or categories, such as \"species\",\"X ray diffraction\" etc.\nEach entry is linked to PDBj database.",
"homepage": "http://www.tanpaku.org/tp_gallery/e_index.php",
"information_keywords": [
"Image/Movie",
"3D structure"
],
"maintainer": "Targeted Proteins Research Program",
"name": "TP Structure Gallery",
"prefix": "NBDC01160",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01161": {
"alt_name": "Targeted Proteins Atlas",
"description": "TP Atlas is a comprehensive database for achievements of Targeted Proteins Research Program which includes 35 TP projects ranging from signal transduction networks to enzymatic reaction pathways in the three fields of fundamental biology, medicine/pharmacology and food/environment. The database contains information on the target proteins, their structures, published papers and press release by navigating the network diagram drawn with a pathway drawing software, Cell Illustrator. Users are able to download files of the network illustrations for further editing and updating.",
"homepage": "http://www.tanpaku.org/tpatlas/index_e.html",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie",
"Bibliography/Documents",
"3D structure"
],
"maintainer": "National Institute of Genetics",
"name": "TP Atlas",
"prefix": "NBDC01161",
"pubmeds": [
"22644393"
],
"status": "Closed",
"target_keywords": [
"Protein",
"Metabolite",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc01162": {
"alt_name": "Advanced Technologies Atlas",
"description": "AT Atlas is a comprehensive database for achievements by research groups of \"Protein Production\", \"Structural Analysis\" and \"Chemical Regulation\"of Targeted Proteins Research Program. This database is composed of graphical abstract (flow chart) , information in text including actual application of the method and link to Protein Experimental Information Management System (PREIMS). It allows to find experimental methods used to elucidate the structure and/or functions of proteins that you are interested in. Further, users are able to reproduce the experimental process to study corresponding entries of PREIMS.",
"homepage": "http://www.tanpaku.org/atatlas/index_e.html",
"information_keywords": [
"Method",
"Interaction/Pathway",
"Image/Movie",
"Bibliography/Documents",
"3D structure"
],
"maintainer": "National Institute of Genetics",
"name": "AT Atlas",
"prefix": "NBDC01162",
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc01163": {
"alt_name": "PRotein Experimental Information Management System",
"description": "PREIMS is a database containing various experimental protocols, which have been developed during the Target Proteins Research Project (TPRP) promoted by the Ministry of education, Culture, Sports, Science and Technology (MEXT) of Japan. The experimental protocols are described by a normal flat text or by ontology constructed with the ontology editor, \"Hozo\".\nUsers can search with the keyword and the original ID that is identified at registration. The list of the experimental protocols in PREIMS is also usable to browse and access to each protocol. Protocols which are accessed directly from the protocol list are publicly available.",
"homepage": "http://preims.pdbj.org/preims/index_e.jsp",
"information_keywords": [
"Method",
"Ontology/Terminology/Nomenclature",
"Bibliography/Documents"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "PREIMS",
"prefix": "NBDC01163",
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01164": {
"description": "This site is a search tool of JCGGDB which is a database of glycan-related data in Japan. It allows to search glycan structures using the monosaccharide symbol defined by the Consortium for Functional Glycomics (CFG) in U.S.A.",
"homepage": "https://jcggdb.jp/idb/flash/GlycoEditor.jsp",
"information_keywords": [
"Image/Movie",
"Chemical structure"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "JCGGDB",
"prefix": "NBDC01164",
"status": "Active",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc01166": {
"description": "This is a database of detailed information about sugar chains, with structure information cross-linked from several databases. Various search functions are available.",
"homepage": "https://jcggdb.jp/idb/indexList.do?id=inchikey",
"information_keywords": [
"Image/Movie",
"Chemical structure"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "Glycan Structure (detail page)",
"prefix": "NBDC01166",
"status": "Active",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc01167": {
"alt_name": "Pathogen Adherence to Carbohydrate Database",
"description": "PACDB is a curated database of pathogens (e.g. bacteria, fungus, toxin and virus) adhering to carbohydrates expressed on the cell surface of host animals or plants. It provides many information of pathogens which reported to recognize the sugar moieties of host cells as a first step of bacterial adhesion and infection. It also includes the data of diseases caused by bacterial infections to host tissues. This database allows to easily access to entries using disease or species names.",
"homepage": "https://jcggdb.jp/search/PACDB.cgi?lang=en",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "PACDB",
"prefix": "NBDC01167",
"status": "Active",
"target_keywords": [
"Health/Disease",
"Carbohydrate"
]
},
"nbdc01168": {
"alt_name": "GlycoScience Protocol Online Database",
"description": "GlycoPOD is a collection of protocols for performing experiments on glycans. The database contains protocols for isolating glycans, analyses for specific types of glycans, and information on several other glycan-related systems. The database is presented as a list of protocols, each of which contains a step-by-step paradigm and example results.",
"homepage": "https://jcggdb.jp/GlycoPOD/protocolListShow",
"information_keywords": [
"Method",
"Bibliography/Documents"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "GlycoPOD",
"prefix": "NBDC01168",
"status": "Active",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc01169": {
"alt_name": "Tumor Markers Reference Databse",
"description": "TuMaRdb is a database of tumor biomarkers: molecular entities and diseases they have been linked to. Users can select by marker or disease and view particulars of published relationships. Diagnostic criteria and primary references are also provided.",
"homepage": "https://jcggdb.jp/search/TuMaRdb.cgi",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "TuMaRDB",
"prefix": "NBDC01169",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Health/Disease",
"Carbohydrate"
]
},
"nbdc01170": {
"alt_name": "Japan Monosacchairde Database",
"description": "JMSDB is a database of monosaccharide structures. The database contains the formula, name, and several standard nomenclatures for a variety of monosaccharides and provides structures for the molecules in a Java applet. The database is constructed as a list from which users can select an entry for more information.",
"homepage": "http://jcggdb.jp/search/ChemGlycan.cgi",
"information_keywords": [
"Chemical structure"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "JMSDB",
"prefix": "NBDC01170",
"status": "Active",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc01171": {
"alt_name": "Glyco-Disease Genes Database",
"description": "GDGDB is a database of the disease caused by mutations of glycan-related genes (glycosyltransferases, glycosidase, donor substrate synthesis enzymes, etc.). Each entry contains disease name, OMIM link, and the related-genes information. It also contains pathosis which obtained by pathologists. Users are able to browse entries in a disease name list.",
"homepage": "https://jcggdb.jp/doc/ProjectTop.action?langType=2&projectId=2",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "GDGDB",
"prefix": "NBDC01171",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc01172": {
"alt_name": "Functional Glycomics with KO mice database",
"description": "KOmouseDB is a collection of phenotype information of mice which have knockouts in genes relevant for glycan-related or glycoprotein. Each entry contains the method of KO, genes information, and the analysis result of glycan and phenotype. Moreover, it contains information of published papers. Users are able to browse entries in a genes name list.",
"homepage": "https://jcggdb.jp/doc/Project.action?projectId=1&langType=2",
"information_keywords": [
"Phenotype",
"Bibliography/Documents"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "KOmouseDB",
"prefix": "NBDC01172",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Organism",
"Carbohydrate"
]
},
"nbdc01173": {
"description": "JCGGDB Report is a collection of minireviews about the latest information for passways and the glycoscience of the carbohydrate chain and its related genes. It contains reports which associated with fundamental or functional researches (including the control of a gene, a passway, the synthetic resolution course, the substrate specificity). It contains also reports about the successful business or study which utilize a carbohydrate chain technology.",
"homepage": "https://jcggdb.jp/doc/ProjectTop.action?langType=2&projectId=3",
"information_keywords": [
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "JCGGDB Reports",
"prefix": "NBDC01173",
"status": "Inactive",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc01174": {
"description": "GlycoNAVI is a web site for carbohydrate research. It consist of the 'GlycoNAVI DataBase' for molecular information of carbohydrates, and chemical reactions of carbohydrate synthesis, the 'Route Searching System for Glycan Synthesis', and 'GlycoNAVI Tools' for editing two-dimensional molecular structure of carbohydrates.",
"fairsharing": "biodbcore-000002",
"homepage": "https://glyconavi.org",
"information_keywords": [
"3D structure",
"Chemical structure"
],
"maintainer": "The Noguchi Institute",
"name": "GlycoNAVI",
"prefix": "NBDC01174",
"status": "Active",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc01175": {
"description": "The Metabolite Activity database collects information on how metabolites affect various organisms. The database connects compound IDs, names, which organisms they effect, how the organism is affected, and provides primary research articles describing the activity. The database can be searched for any of these categories.",
"homepage": "http://www.knapsackfamily.com/MetaboliteActivity/top.jsp",
"information_keywords": [
"Image/Movie",
"Chemical structure"
],
"maintainer": "Nara Institute of Science and Technology Graduate School of Information Science",
"name": "KNApSAcK Biological Activity (Metabolite Activity)",
"prefix": "NBDC01175",
"pubmeds": [
"22123792",
"23509110"
],
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc01177": {
"description": "Metabolomics.JP is a portal site for metabolomics information maintained by Arita Laboratory, National Institute of Genetics. This portal site contains wiki-based databases with indexes of flavonoids, basic metabolites, crude drugs and plant taxa. Users can search flavonoids from backbone structures, hydroxylation and methylation patterns, glycosylation patterns and other modifications.",
"homepage": "http://metabolomics.jp/wiki/Main_Page",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie",
"Bibliography/Documents",
"Taxonomy",
"Portal"
],
"maintainer": "National Institute of Genetics",
"name": "Metabolomics.JP",
"prefix": "NBDC01177",
"pubmeds": [
"18822113",
"22230935"
],
"status": "Active",
"target_keywords": [
"Metabolite",
"Drug"
]
},
"nbdc01178": {
"description": "Mouse strain in RIKEN BioResource Center is a database of resource information maintained by RIKEN BioResource Center (RIKEN BRC) and collaborative institutes. Each entry contains a strain name, nomenclature, taxon, institute depositor, strain status and availability. Users can search available resources by keywords, and order them through the RIKEN BRC website.",
"homepage": "https://metadb.riken.jp/metadb/db/rikenbrc_mouse",
"information_keywords": [
"Bioresource"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "Metadata of BRC mouse resources and phenotypes",
"prefix": "NBDC01178",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01179": {
"description": "Cell lines in RIKEN BioResource Center is a database of resource information maintained by RIKEN BRC (RIKEN BioResource Center) and collaborative institutes. Each entry contains a cell line name, cell category, common name, quality data and attribution. Users can search available resources by keywords, and order them through the CELL BANK website.",
"homepage": "https://metadb.riken.jp/metadb/db/rikenbrc_cell",
"information_keywords": [
"Bioresource"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "Metadata of BRC cell resources",
"prefix": "NBDC01179",
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc01180": {
"alt_name": "Biophenome Linked Open Databases",
"description": "BioLOD.org is an integrated database of biological open data based on semantic web technology standards and maintained by RIKEN BASE (Bioinformatics And Systems Engineering Division). BioLOD.org contains open (browsable and downloadable) and not open (browsable, but not downloadable) data in various fields such as mouse strains, cell lines and plant abnormality. This database also provides tutorials for BioLOD.org and usecases of application for bioinformatics. Users can search available data and databases by keywords, and download them using various standard file formats like RDF and GFF.",
"homepage": "http://biolod.jp/",
"information_keywords": [
"Portal"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "BioLOD.org",
"prefix": "NBDC01180",
"status": "Closed"
},
"nbdc01181": {
"description": "This is a database of gene, strain, and environmental interaction in microorganisms. Users can search these data from a single search window based on semantic web technologies.",
"homepage": "https://microbedb.jp/",
"information_keywords": [
"Environment"
],
"maintainer": "National Institute of Genetics",
"name": "MicrobeDB.jp",
"prefix": "NBDC01181",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc01182": {
"alt_name": "Metagenome/Microbes Environmental Ontology",
"description": "MEO is a repository of ontology describing microbial habitats maintained by Tokyo Institute of Technology, Department of Biological Information. This repository consists of the OWL file of MEO, sample ttl and RDF/XML files. Sample files are linked between metagenomic data and environmental information by mapping metadata related to microbial habitats. Users can download those files and corresponding OWL files. The MEO data by Tokyo Institute of Technology was transferred form their original site (http: //mdb.bio.titech.ac.jp/meo) to BioPortal.\n\nγγγ",
"homepage": "https://bioportal.bioontology.org/ontologies/MEO",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Environment"
],
"maintainer": "Stanford Center for Biomedical Informatics Research",
"name": "MEO",
"prefix": "NBDC01182",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01183": {
"description": "The Metagenome Database is a database of sequence information from microbial sequencing projects. The database contains raw sequences and alignments from human metagenome projects that can be sorted and accessed by organ, microbe, or study. Data are available for download.",
"homepage": "http://www.metagenomics.jp/mg/",
"information_keywords": [
"Sequence"
],
"maintainer": "Tokyo Institute of Technology",
"name": "Metagenome.jp (Human Meta BodyMap)",
"prefix": "NBDC01183",
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01185": {
"description": "KEGG MEDICUS is an integrated database of diseases, drugs and other health-related substances. KEGG MEDICUS contains resources of KEGG DISEASE (diseases and genes), KEGG DRUG (drugs and components), KEGG PATHWAY (molecular pathways) and FDA drug labels. Users can search information on diseases and drugs against these KEGG databases and the DailyMed database in USA.",
"homepage": "http://www.kegg.jp/kegg/medicus.html",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Environment",
"Bibliography/Documents",
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG MEDICUS",
"prefix": "NBDC01185",
"pubmeds": [
"21942936"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Drug"
]
},
"nbdc01187": {
"description": "The SNP Control database is a collection of data from a large number of individuals. The data can be used as sample control data to determine statistical parameters in determining quality controls and designing case-control studies. The site has data from over 700 individuals organized by platform and can be searched by any commonly used identifier. Users can also search genes to find data on SNPs within the gene, or obtain information about genes containing a SNP of interest.",
"homepage": "https://gwas.biosciencedbc.jp/snpdb/snp_top.php",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "SNP control database",
"prefix": "NBDC01187",
"status": "Closed",
"target_keywords": [
"Genetic variation",
"Health/Disease"
]
},
"nbdc01188": {
"alt_name": "copy number variation database",
"description": "The CNV Control database hosts copy number data deposited and collected from published studies. The database contains CNV data from 160 Japanese individuals obtained on Affymetrix6.0 CNV technology in addition to deposited data from other platforms. Users can search by ID or locate variants associated with a given gene.",
"homepage": "http://gwas.biosciencedbc.jp/cgi-bin/cnvdb/cnv_top.cgi",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "CNV control DB",
"prefix": "NBDC01188",
"status": "Closed",
"target_keywords": [
"Genetic variation",
"Health/Disease"
]
},
"nbdc01189": {
"alt_name": "copy number variation association database",
"description": "The CNV Association database is a portal site for exploring associations between CNVs and disease. Currently, the database hosts disease-CNV association data for panic disorder. The database consists of CNV calls from 160 Japanese cases and is searchable by ID or gene.",
"homepage": "http://gwas.biosciencedbc.jp/cgi-bin/cccdb/ccc_top.cgi",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "CNV association DB",
"prefix": "NBDC01189",
"status": "Closed",
"target_keywords": [
"Genetic variation",
"Health/Disease"
]
},
"nbdc01190": {
"alt_name": "human genome variation database",
"description": "Human Variation Database is a collection of data regarding genomic variation. It contains variation information from a variety of published sources and captures all manner of genomic variation including nucleotide, indel, copy number, microsatellite, and structural types. The collected data come from all available methods of uncovering variation, up to and including NGS. Users can search or browse by gene, disease, position, or SNP identifier.",
"homepage": "http://gwas.biosciencedbc.jp/cgi-bin/hvdb/hv_top.cgi",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "Human Variation DB",
"prefix": "NBDC01190",
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc01191": {
"alt_name": "HLA database",
"description": "HLA DB is a database of disease and haplotype information for the human HLA region. The database consists of HLA haplotype sequences that can be searched and aligned against each other at each of several HLA loci. The database consists of sequence data, and in addition to alignments users can download FASTA versions of haplotypes of interest.",
"homepage": "https://gwas.biosciencedbc.jp/cgi-bin/hladb/hla_top.cgi",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "HLA DB",
"prefix": "NBDC01191",
"status": "Closed",
"target_keywords": [
"Genetic variation",
"Health/Disease"
]
},
"nbdc01192": {
"description": "Allie Portal is a portal site of Allie; an online search service for abbreviations and long forms in life science. Allie Portal consists of following 3 contents.\n1. Allie; an online search service.\n2. Interfaces to access the RDFized Allie database (SPARQL endpoint, Faceted Search and Allie Vocabulary).\n3. A download site for the tab-delimited files or RDF files used for Allie.",
"homepage": "http://data.allie.dbcls.jp/index_en.html",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "Allie RDF Data Portal",
"prefix": "NBDC01192",
"status": "Active"
},
"nbdc01193": {
"alt_name": "Structure Atlas of Human Genome",
"description": "SAHG is a database of protein structure predictions. The database contains predictions for proteins from every ORF found in the human genome based on RefSeq sequences and was constructed using complimentary structural and sequence homology-based approaches. Users can search for proteins (by keyword or BLAST) or browse by chromosome. Entries for each protein provide protein structure and domain information, 3D structure in a Java applet, and links to external databases. The original site ( http:// bird.cbrc.jp/sahg ) has been closed. Now, SAHG is available from LSDB archive site.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/sahg/desc.html",
"information_keywords": [
"3D structure"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "SAHG (Archive)",
"prefix": "NBDC01193",
"pubmeds": [
"21051360"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01194": {
"alt_name": "Plant Genome DataBase Japan",
"description": "The PGDBj database is for integrated searches of plant genome-related information (genome analysis, DNA markers, QTLs, Orthologs, etc.) and plant resource information provided in Japan. Basic information is also provided about plants that have been subjected to genome analysis.",
"homepage": "http://pgdbj.jp/index.html?ln=en",
"information_keywords": [
"Bioresource",
"Sequence",
"Bibliography/Documents",
"Classification",
"Portal"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "PGDBj",
"prefix": "NBDC01194",
"pubmeds": [
"24363285"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01196": {
"description": "The Autophagy Database aims to provide researchers with new information about autophagy-related proteins and their structure and also to make this data freely available to the wider interested public in a user-friendly format.\nAutophagy is a process of self-digestion that occurs in eukaryotic cells, by which starving cells degrade their materials in order to make the nutrients available for other important metabolic processes within the same organism. This process also serves to protect the organism against harmful antigens that may cause infection or disease. Autophagy may also be involved in developmental and anti-aging processes.\nThe study of autophagy is therefore of value in the academic arena as well as the medical field.\nA list of autophagy-related proteins is provided, including their three-dimensional structures as well as a search option for their homologs and orthologs.\nThe Targeted Proteins Research Program of the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan supports this database.",
"homepage": "http://www.tanpaku.org/autophagy/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Bibliography/Documents",
"3D structure",
"Classification"
],
"maintainer": "National Institute of Genetics",
"name": "Autophagy Database",
"prefix": "NBDC01196",
"pubmeds": [
"20972215"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01197": {
"description": "Naturalized Plants in Japan ~Seed-Image database~ is an image database of naturalized alien plant seeds recorded in Japan. This database contains plant images, information on morphological features of seeds and the name list of naturalized alien plants, as well as seed images. Seeds are categorized into 5 groups based on morphological features such as reticulation (wrinkles or projections), ridges, edges and achene fruit. Users can search seed images by family names, species names and those features.",
"homepage": "http://www.rib.okayama-u.ac.jp/wild/okayama_kika_v2/Seed-image-database.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Okayama University Institute of Plant Science and Resources",
"name": "Naturalized Plants in Japan ~Seed-Image database~",
"prefix": "NBDC01197",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01199": {
"alt_name": "Rheumatoid Arthritis variome",
"description": "RAvariome is a human genetic variant database for the autoimmune inflammatory disease, Rheumatoid Arthritis (RA). This database provides reproducible associations between genetic variants and RA for each geographical ancestry population. A validated list of risk variants is available for use in clinical research, preliminary RA-associated variants can be explored for detailed investigation, and new drug target genes for RA can be discovered. Services provided by this database include an overview of RA with genetic and environmental information, hot variants with RA-associated risk, all previously published association signals and individual genetic RA risk prediction.",
"homepage": "http://www.h-invitational.jp/hinv/rav/",
"information_keywords": [
"Sequence"
],
"maintainer": "National Institute of Advanced Industrial Science and Technology, Biomedicinal Information Research Center",
"name": "RAvariome",
"prefix": "NBDC01199",
"pubmeds": [
"24158836"
],
"status": "Inactive",
"target_keywords": [
"Genetic variation",
"Health/Disease"
]
},
"nbdc01200": {
"alt_name": "Protein Complex Database with complex quality index",
"description": "PCDq is a human protein complex database with quality index. The protein complex quality index (CQI) describes evidence levels of the protein members of protein complexes. Human protein complexes were predicted based on densely connected regions with cluster properties found in the integrated PPI network. Data entities that were integrated include protein function, localization, structure, expression profile, gene locus, as well as binary interactions between complex member proteins and complex outside adjacent proteins.",
"homepage": "http://www.h-invitational.jp/hinv/pcdq/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "National Institute of Advanced Industrial Science and Technology, Biomedicinal Information Research Center",
"name": "PCDq",
"prefix": "NBDC01200",
"pubmeds": [
"23282181"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01201": {
"description": "Quarterly journal \"Biohistory\" is a repository of a quarterly magazine; \"Biohistory\" published by JT Biohistory Research Hall. Biohistory has an annual theme, and each issue contains reports on latest biological research, interviews and biographies of Japanese scientists in biology based on the theme. Back issues of Biohistory publilshed in 2002-2007 are available in English.",
"homepage": "https://www.brh.co.jp/en/seimeishi/backnumber/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "JT Biohistory Research Hall",
"name": "Quarterly journal \"Biohistory\"",
"prefix": "NBDC01201",
"status": "Active"
},
"nbdc01203": {
"homepage": "http://psfs.cbrc.jp/tmbetadisc/",
"information_keywords": [
"Method",
"Sequence"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "TMBETA-DISC",
"prefix": "NBDC01203",
"pubmeds": [
"18434251",
"16204348",
"15980447",
"15833441",
"15531602"
],
"status": "Closed",
"target_keywords": [
"Protein"
]
},
"nbdc01205": {
"description": "The Mutation Database is a repository for information about genes that are causative for or implicated in ALS, PD, ALD, and HSP. A list of genes is provided for each disease and further information is provided for the gene including known mutations and functional domains. The database consists of primary data and results collected from publications.",
"homepage": "https://reseq.biosciencedbc.jp/resequence/",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "Mutation Database",
"prefix": "NBDC01205",
"pubmeds": [
"20556799"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc01206": {
"description": "CellMontage is a system to search and analyze microarray data. The system enables users to compare gene expression profiles with different platforms, and to find gene expressions in cells or organs similar to the query profile.",
"homepage": "http://cellmontage.cbrc.jp/cgi-bin/index.cgi",
"information_keywords": [
"Expression"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "CellMontage",
"prefix": "NBDC01206",
"pubmeds": [
"17895274"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle"
]
},
"nbdc01207": {
"description": "This is an database of genomes and results of functional genomic analysis of parasitic amoeba such as Entamoeba histolytica and Acanthamoeba, which is a family database of the EuPathDB. It includes the full genome sequence data and microarray expression data. A wide variety of search and download functions, as well as bioinformatics tools are supported for genes, genomes, motifs, SNPs, ESTs, and ORFs.",
"fairsharing": "biodbcore-000564",
"homepage": "http://amoebadb.org/amoeba/",
"information_keywords": [
"Sequence",
"Expression",
"Repository"
],
"maintainer": "EuPathDB Bioinformatics Resource Center",
"name": "AmoebaDB",
"prefix": "NBDC01207",
"pubmeds": [
"20974635",
"19914931"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"Protein"
]
},
"nbdc01208": {
"description": "AREsite is a database of the investigation of AU-rich elements (ARE) in vertebrate mRNA UTR sequences. Thisdatabase allows detailed investigation of functional elements by analysis of the phylogentic conservation and the structural context these motifs are embedded in. Furthermore, AREsite provides information about experimentally validated targets from extensive literature search.",
"homepage": "http://rna.tbi.univie.ac.at/AREsite",
"information_keywords": [
"Sequence",
"Bibliography/Documents",
"Classification"
],
"maintainer": "Institute of Theoretical Chemistry, University of Vienna",
"name": "AREsite",
"prefix": "NBDC01208",
"pubmeds": [
"21071424"
],
"status": "Active",
"target_keywords": [
"RNA"
]
},
"nbdc01209": {
"alt_name": "Allosteric Database",
"description": "The AlloSteric Database (ASD) provides a central resource for the display, search and analysis of structure, function and related annotation for allosteric molecules, which are annotated with a detailed description of allostery, biological process and related diseases, and modulators with binding affinity, physicochemical properties and therapeutic area. Modulators curated in ASD can be used to investigate potent allosteric targets for the query compound, and also help chemists to implement structure modifications for novel allosteric drug design.",
"homepage": "http://mdl.shsmu.edu.cn/ASD/",
"information_keywords": [
"Sequence",
"Image/Movie",
"3D structure",
"Chemical structure"
],
"maintainer": "Shanghai Jiao Tong University",
"name": "ASD",
"prefix": "NBDC01209",
"pubmeds": [
"21051350"
],
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Protein",
"Metabolite"
]
},
"nbdc01210": {
"homepage": "http://brix.switchlab.org/",
"information_keywords": [
"Sequence",
"Image/Movie"
],
"maintainer": "Flanders Institute of Biotechnology, Free University of Brussels",
"name": "BriX",
"prefix": "NBDC01210",
"pubmeds": [
"20972210",
"19880386"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01211": {
"alt_name": "Bio-molecule Stretching Database",
"description": "BSDB is a database that houses information about the mechanical stretching of proteins.\nBoth ends of a protein molecule are attached to a spring, and the free end of one spring is anchored. The force of resistance when the free end of the other spring is pulled at a constant speed is then measured for all the tested protein molecules.\nThe Database lists results for 17,134 protein structures with 250 amino acids or less.\nA search option by PDB ID input as well as an advanced search options are available.",
"homepage": "http://www.ifpan.edu.pl/BSDB/",
"information_keywords": [
"Chemical structure"
],
"maintainer": "Institute of Physics, Polish Academy of Sciences",
"name": "BSDB",
"prefix": "NBDC01211",
"pubmeds": [
"20929872"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01212": {
"alt_name": "Worm Developmental Dynamics Database",
"description": "WDDD is a database of C. elegans development. The database contains images and quantitative cell division data. Data were collected from RNAi screens of developing worms to describe the effect of genes on development. Data are available for download.",
"fairsharing": "biodbcore-000167",
"homepage": "http://so.qbic.riken.jp/wddd/index.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "RIKEN Quantitative Biology Center",
"name": "WDDD",
"prefix": "NBDC01212",
"pubmeds": [
"23172286"
],
"status": "Active",
"target_keywords": [
"Organism",
"Cell/Organelle"
]
},
"nbdc01213": {
"alt_name": "COMputational BRidge to Experiments",
"description": "COMBREX is a database of experimentally determined and computationally predicted functions for bacterial and archaeal genomes. This database presently consists of genes from over 1000 completely sequenced bacterial and archaeal genomes, supplemented with a number of individual genes whose biochemical function has been experimentally determined. The genes are organized into sequence-similar and likely isofunctional groups determined by NCBI, referred to as Protein Clusters.",
"homepage": "http://combrex.bu.edu/",
"information_keywords": [
"Phenotype",
"Taxonomy"
],
"maintainer": "Boston University",
"name": "COMBREX",
"prefix": "NBDC01213",
"pubmeds": [
"21097892"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01214": {
"alt_name": "Cervical Cancer Gene Database",
"description": "CCGD is a manually curated collection of experimenatlly validated genes which are thought to be involved in the different stages of cervical carcinogenesis. Each entry contains information relating to the gene and protein sequences, its location, architecture, function, chromosomal positions, accession numbers, gene, CDS sizes, gene ontology and homology to other eukaryotic genomes. CCDB provides rich cross reference to other web resources like Unigene, HPRD, HGNC, Ensemble and OMIM augmenting CCDB-specific information with external data. It also provides relevant literature references of genes included in the database.",
"homepage": "https://webs.iiitd.edu.in/raghava/ccdb/",
"information_keywords": [
"Sequence"
],
"maintainer": "Institute of Cytology and Preventive Oncology",
"name": "CCDB",
"prefix": "NBDC01214",
"pubmeds": [
"21045064"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein",
"Health/Disease"
]
},
"nbdc01215": {
"alt_name": "Long Non-Coding RNA Database",
"description": "lncRNAdb is a database providing comprehensive annotations of long non-coding RNAs (lncRNAs) in eukaryotes. Each record contains referenced information about the RNA, including sequences, structural information, genomic context, expression, subcellular localization, conservation, functional evidence and other relevant information. lncRNAdb allows to search by querying published RNA names and aliases, sequences, species and associated protein-coding genes, as well as terms contained in the annotations, such as the tissues in which the transcripts are expressed and associated diseases. Moreover, lncRNAdb is linked to the UCSC Genome Browser for visualization and Noncoding RNA Expression Database (NRED) for expression information from a variety of sources.",
"homepage": "http://www.lncrnadb.com",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "Institute for Molecular Bioscience, The University of Queensland",
"name": "lncRNAdb",
"prefix": "NBDC01215",
"pubmeds": [
"21112873"
],
"status": "Closed",
"target_keywords": [
"RNA"
]
},
"nbdc01217": {
"description": "miRTarBase Version 3.5 is a database that contains information about miRNA-target interactions (MTIs) obtained by manual search of scientific literature with data on 4867 miRNA-target interactions, 726 miRNAs and 2789 target genes from 17 species. The database can be browsed or searched by keyword, as well as downloaded.",
"fairsharing": "biodbcore-000615",
"homepage": "http://mirtarbase.cuhk.edu.cn/php/index.php",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "Institute of Bioinformatics and Systems Biology, National Chiao Tung University",
"name": "miRTarBase",
"prefix": "NBDC01217",
"pubmeds": [
"21071411"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc01218": {
"alt_name": "Plant microRNA Knowledge Base",
"description": "PmiRKB (Plant microRNA Knowledge Base) is a database collecting information on miRNAs from Arabidopsis thaliana and Oryza sativa.The functional modules that are provided are MiR-Tar, SNPs, Self-reg and Pri-miRNAs. The MiR module contains miRNA sequences and information on pre-miRNA clusters. Target regions of SNPs-from 7 Arabidopsis and of 21 Oryza subspecies-found in miRNAs and pre-miRNAs are provided. Scenes of transcription surrounding the pre-miRNAs are made available with the Pri-miR module, and cleavage signals in target recognition sites of miRNA are revealed by the MiR-Tar module. The Self-reg module makes it possible to infer signals of remnants produced in the process of miRNA-mediated self-regulation and miRNA precursor processing. A keyword search option is provided.",
"homepage": "http://bis.zju.edu.cn/pmirkb",
"information_keywords": [
"Sequence"
],
"maintainer": "Zhejiang University",
"name": "PmiRKB",
"prefix": "NBDC01218",
"pubmeds": [
"20719744"
],
"status": "Inactive",
"target_keywords": [
"Genetic variation",
"RNA"
]
},
"nbdc01219": {
"alt_name": "TransMembrane Protein Helix-Packing Database",
"description": "The TMPad database contains information on the structural folds in alpha-helical membrane proteins obtained from observing helix-helix interactions experimentally. Additionally, information is provided on the geometric descriptors of these interactions, the accessibility of lipids, topology, ligand and on the observed binding sites. The structures of TM helix-packing and their functions are also organized according to a classification system. This database contains 1107 transmembrane alpha-helical protein entries, 4061 protein chains, 17413 helix-helix interactions and 954 Pubmed links. Search options provided are by PDB identifier, by keyword or by multiple identifiers (advanced).",
"homepage": "http://bio-cluster.iis.sinica.edu.tw/TMPad/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Image/Movie",
"3D structure",
"Chemical structure"
],
"maintainer": "Bioinformatics Lab., Institute of Information Science, Academia Sinica",
"name": "TMPad",
"prefix": "NBDC01219",
"pubmeds": [
"21177659"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01220": {
"alt_name": "Polymorphic Simple Sequence Repeats Database",
"description": "PSSRdb is a relational database of polymorphic simple sequence repeats (PSSRs) extracted from 85 different species of prokaryotes. It contains the data of perfect SSRs which are the tandem repeats of nucleotide motifs of the sizes 1-6 bp and exhibit intra-species polymorphism. PSSRs found in coding and non-coding regions were separately stored in two different logically connected databases. Both the databases contain 357 tables each of which contains an useful information pertaining to PSSRs viz., motif types, repeat copy numbers of SSRs, genomic location of SSRs, and information pertaining to the coding regions harboring or flanking the PSSRs.",
"homepage": "http://pssrdb.cdfd.org.in/project1.php",
"information_keywords": [
"Sequence"
],
"maintainer": "Centre for DNA Fingerprinting and Diagnostics",
"name": "PSSRdb",
"prefix": "NBDC01220",
"pubmeds": [
"21112874"
],
"status": "Inactive",
"target_keywords": [
"Genetic variation",
"DNA"
]
},
"nbdc01221": {
"description": "ArachnoServer is a manually curated database which contains information on the sequence, three-dimensional structure, and biological activity of protein toxins derived from spider venom. All spider toxin entries are sourced from UniProtKB/Swiss-Prot, then manually curated using available literature and patent information. Spider taxonomy is based on the latest version of the authoritative World Spider Catalog. A key property of ArachnoServer is the use of a molecular target ontology based on the channel and receptor subtype definitions recommended by IUPHAR. Furthermore, in addition to any legacy synonyms, all peptide toxins in the database have been assigned names according to the recently described rational nomenclature for spider toxins (King et al., 2008).\nThis database allows advanced searches of toxin information, browsing, as well as similarity searches using BLAST. Each toxin record is displayed in a single page and a toxin's structure can be dynamically visualised.",
"fairsharing": "biodbcore-000504",
"homepage": "http://www.arachnoserver.org/mainMenu.html",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "QFAB (Queensland Facility for Advanced Bioinformatics)",
"name": "ArachnoServer",
"prefix": "NBDC01221",
"pubmeds": [
"19674480",
"19674480"
],
"status": "Suspended",
"target_keywords": [
"Protein"
]
},
"nbdc01222": {
"alt_name": "Extracellular Matrix interactions DataBase",
"description": "MatrixDB is a database focused on interactions established by extracellular proteins and polysaccharides. This database takes into account the multimeric nature of the extracellular proteins, for example, collagens, laminins and thrombospondins which are multimers.This database includes interaction data extracted from the literature by manual curation, and this database offers access to relevant data involving extracellular proteins provided by thier IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database.\nMatrixDB is an active member of the International Molecular Exchange (IMEx) consortium.",
"homepage": "http://matrixdb.univ-lyon1.fr",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "ICBMS (Institute for Molecular and Supramolecular Chemistry and Biochemistry, University of Lyon 1)",
"name": "MatrixDB",
"prefix": "NBDC01222",
"pubmeds": [
"20852260",
"20213321",
"19147664"
],
"status": "Active",
"target_keywords": [
"Protein",
"Carbohydrate",
"Metabolite"
]
},
"nbdc01224": {
"description": "CancerResource is a database for drug-target relationships related to cancer as well as for supporting information or experimental data. Drug-target relationships are determined by a manually curated text-mining of publicly available literature. A couple of resources that provide similar data with slightly different background and intention are mined for comparison with the CancerResource text-mining and integrated into this knowledgebase. Moreover, to strengthen the literature mining, which is in its result a compilation of direct knowledge of drug-target relationships, interactions that are known in the PDB is added to that part.",
"homepage": "http://data-analysis.charite.de/care/",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Charite - University Medicine Berlin, Institute for Physiology, Structural Bioinformatics Group",
"name": "CancerResource",
"prefix": "NBDC01224",
"pubmeds": [
"20952398",
"26590406"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease",
"Drug"
]
},
"nbdc01225": {
"alt_name": "Hymenoptera Genome Database",
"description": "The Hymenoptera Genome Database (HGD) is a comprehensive database providing access to curated data contributed by an extensive, active research community working on insect species of the order Hymenoptera. HGD contains data from 9 different species in the phylogeny of Hymenoptera, allowing researchers to leverage genetic, genome sequence and gene expression data, as well as the biological knowledge of related model organisms. Curated data at HGD contains predicted and annotated gene sets supported with evidence tracks such as ESTs/cDNAs, small RNA sequences and GC composition domains. Data can be queried using genome browsers and/or BLAST/PSI-BLAST servers, and it may also be downloaded to perform local searches.",
"fairsharing": "biodbcore-000358",
"homepage": "http://HymenopteraGenome.org",
"information_keywords": [
"Sequence"
],
"maintainer": "Georgetown University",
"name": "HGD",
"prefix": "NBDC01225",
"pubmeds": [
"21071397"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01226": {
"description": "This is a project for users to submit structural annotations for proteins using PDB data and to build a community of information exchange. As of 2011, approximately 75,000 PDB entries were submitted, classified according to categories (enzyme classification, experimental method, alphabetization, publication date, species, type of structure). Additionally, users can create Structure Reports using a template for PDB entries.",
"homepage": "http://pdbwiki.org/wiki/Main_Page",
"information_keywords": [
"3D structure"
],
"name": "PDBWiki",
"prefix": "NBDC01226",
"status": "Inactive",
"target_keywords": [
"DNA",
"Protein"
]
},
"nbdc01230": {
"alt_name": "Great Ape Information Network",
"description": "This is a page of informational network related to superfamily hominoidea in Japan (chimpanzee, bonobo, gorilla, orangutan, gibbon). Information such as distribution charts, maternal pedigrees, and individual records in the Japanese islands are managed as part of a database. In addition to supporting the development of academic research, the Network is also involved in the well-being and preservation efforts of similar apes. In order to accomplish this, the Network gathers information regarding apes in Japan (photographs and resources). The National Institute of genetics and Kyoto University (Primate Research Institute and Wildlife Research Center) collaborate as a part of this network, with the Primate Research Institute implementing GAIN activities as a Joint Usage/Research Center as of 2010.",
"homepage": "http://www.shigen.nig.ac.jp/gain/top.jsp",
"maintainer": "National Institute of Genetics",
"name": "GAIN",
"prefix": "NBDC01230",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01231": {
"description": "Fragment Store is a database, that provides access to information about fragments of compounds with their properties (e.g. charge, hydrophobicity, binding site preferences). It allows the user to do statistical analysis of the fragments properties and binding site preferences. And furthermore, the database supports to build an adequate fragment library for fragment based drug design.",
"homepage": "http://bioinf-applied.charite.de/fragment_store/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Image/Movie",
"Chemical structure"
],
"maintainer": "Charite - University Medicine Berlin, Institute for Physiology, Structural Bioinformatics Group",
"name": "FragmentStore",
"prefix": "NBDC01231",
"pubmeds": [
"20965964"
],
"status": "Inactive",
"target_keywords": [
"Metabolite",
"Chemical compound",
"Drug"
]
},
"nbdc01233": {
"homepage": "http://rgm2.lab.nig.ac.jp/taxonomy/NCBI_taxonomy/browse.php",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Taxonomy"
],
"maintainer": "National Institute of Genetics",
"name": "Species Dictionary",
"prefix": "NBDC01233",
"status": "Closed",
"target_keywords": [
"Organism"
]
},
"nbdc01234": {
"alt_name": "QTL Annotation Rice Online database",
"description": "Q-TARO is a database of Rice QTLs from published research papers. By screening for redundancy of traits at the same physical positions, as of March 31 of 2008, 1051 QTLs extracted from 463 reports were selected as representative QTLs. Currently, QTL information is not updated.",
"homepage": "http://qtaro.abr.affrc.go.jp/",
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "Q-TARO",
"prefix": "NBDC01234",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc01235": {
"alt_name": "Overview of functionally characterized Genes in Rice Online database",
"description": "This database is comprised of gene loci whose function has been linked to a phenotype in published papers in the Web of Science. The information, such as phenotype, method of functional analysis, and genomic position, are shown on the same platform (table and genome browser) as the QTL database, Q-TARO (http://integbio.jp/dbcatalog/record/nbdc01234). As such, comparisons between genomic distribution and the QTL region registered in Q-TARO can be compared.",
"homepage": "http://qtaro.abr.affrc.go.jp/ogro/table",
"information_keywords": [
"Phenotype"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "OGRO",
"prefix": "NBDC01235",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc01236": {
"alt_name": "Alternative Splicing Prediction Data Base",
"description": "ASPicDB is a database which provided access to reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano' et al. 2006), and to the functional annotation of predicted isoforms. It allows users to select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. Furthermore, ASPicDB includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST data and their library source annotation.",
"homepage": "http://srv00.recas.ba.infn.it/ASPicDB/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "CASPUR (Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universita e Ricerca)",
"name": "ASPicDB",
"prefix": "NBDC01236",
"pubmeds": [
"21051348",
"18388144",
"16845044"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein",
"Health/Disease"
]
},
"nbdc01237": {
"alt_name": "Signaling Pathway Integrated Knowledge Engine",
"description": "SPIKE is a knowledge-base of highly curated human signaling pathways. SPIKE contains three main software parts:\n1) A database of biological signaling pathways. It's constructed of carefully curated information from the literature and data from large public sources.\n2) A visualization package that allows interactive graphic representations of regulatory interactions stored in the DB and superposition of functional genomic and proteomic data on the maps. \n3) An algorithmic inference engine for analyzation of the networks for novel functional interplays between network components.",
"fairsharing": "biodbcore-000531",
"homepage": "http://www.cs.tau.ac.il/~spike/",
"information_keywords": [
"Interaction/Pathway",
"Repository"
],
"maintainer": "Tel Aviv University",
"name": "SPIKE",
"prefix": "NBDC01237",
"pubmeds": [
"21097778",
"18289391"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01238": {
"description": "UCSC Xena is a suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. The database provides whole-genome to base-pair level views of several different types of genomics data, including some next-generation sequencing platforms.",
"homepage": "http://xena.ucsc.edu",
"information_keywords": [
"Expression"
],
"maintainer": "University California Santa Cruz",
"name": "UCSC Xena",
"prefix": "NBDC01238",
"pubmeds": [
"21059681",
"20529912",
"23109555"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc01240": {
"alt_name": "Comprehensive Amino Acids Sequences Annotated database",
"description": "This is a database of amino acid sequences, which integrates various protein related informations. It includes sequences of amino acids come from many species and cross-reference IDs from DDBJ DAD in Japan, NCBI NR in USA and UniRef in Europe.",
"homepage": "http://www.tanpaku.org/casadb/index.html.en",
"information_keywords": [
"Sequence"
],
"maintainer": "National Institute of Genetics",
"name": "CASA db",
"prefix": "NBDC01240",
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01241": {
"alt_name": "Functionally Annotated Japanese Protein Structural Information",
"description": "This is an on-demand analysis database performing functional predictions for amino acid sequences designated within a protein. The functional predictions are made by analysis using feature of each sequence, the three-dimensional structures, predictions on regions of disorder, as well as sequence and conformational similarities to published proteins or domains.\nThis project was developed as a part of the Targeted Proteins Research Program (TPRP) from the Ministry of Education, Culture, Sports, Science and Technology, Japan.",
"homepage": "http://www.tanpaku.org/fujidb/index.php?lang=en",
"information_keywords": [
"Sequence",
"Image/Movie",
"3D structure"
],
"maintainer": "National Institute of Genetics",
"name": "FUJI DB",
"prefix": "NBDC01241",
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01242": {
"alt_name": "Protein-Compound Interaction Database",
"description": "This is a database of collected and merged information on protein-compound interactions throughout the world. The data are obtained from ChEMBL, DrugBank, CTD, and PubChem BioAssay. Users can search by interactions information for each protein and compound or protein-compound/compound-protein interactions. PCI DB was developed as a project of the Ministry of Education, Culture, Sports, Science and Technology Target Protein Research Program.",
"homepage": "http://www.tanpaku.org/pci/pci_home_en.html",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "National Institute of Genetics",
"name": "PCI DB",
"prefix": "NBDC01242",
"status": "Inactive",
"target_keywords": [
"Protein",
"Chemical compound"
]
},
"nbdc01243": {
"description": "This is a comprehensive database for enzymes, which catalyze pyrimidine biosynthesis or oxidation-reduction reactions, and are candidates of the effective target in regard to drug development for trypanosomiasis (such as African sleeping sickness, South American Chagas disease). Links to PDB, OMIM, NCBI, as well as mRNA and protein sequence information are included. The list can be filtered by category or motif, and searched by keywords. This database was developed as a project of the Targeted Proteins Research Program (TPRP) from the Ministry of Education, Culture, Sports, Science and Technology, Japan.",
"homepage": "http://www.tanpaku.org/tdb/",
"maintainer": "National Institute of Genetics",
"name": "Trypanosomes Database",
"prefix": "NBDC01243",
"status": "Closed",
"target_keywords": [
"Protein",
"Health/Disease",
"Drug"
]
},
"nbdc01244": {
"alt_name": "BInary SubComplex Database",
"description": "BISC is a protein-protein interaction (PPI) database intending to bridge between the two communities most active in their characterisation: structural biology and functional genomics researchers. The database offers users access to binary subcomplexes, (i.e. physical direct interactions between proteins) that are either structurally characterised or modellable entries in the main functional genomics PPI databases BioGRID, IntAct and HPRD. Provided web services are available to further investigate the validity of postulated PPI by inspection of their hypothetical modelled interfaces.",
"homepage": "http://bisc.soe.ucsc.edu",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Image/Movie",
"3D structure"
],
"maintainer": "University of California at Santa Cruz",
"name": "BISC",
"prefix": "NBDC01244",
"pubmeds": [
"21081561"
],
"status": "Suspended",
"target_keywords": [
"Protein"
]
},
"nbdc01245": {
"alt_name": "Catfish Genome Database",
"description": "cBARBEL (abbreviated from catfish Breeder And Researcher Bioinformatics Entry Location) is an online open-access database for genome biology of ictalurid catfish (Ictalurus spp.). It serves as a comprehensive, integrative platform for all aspects of catfish genetics, genomics and related data resources. cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with SNP information overlay, and GBrowse-based organization of catfish genomic data based on sequence similarity with zebrafish chromosomes. Subsections of the database are tightly related, allowing a user with a sequence or search string of interest to navigate seamlessly from one area to another.",
"homepage": "https://www.animalgenome.org/catfish/cbarbel/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Department of Fisheries and Allied Aquacultures, Auburn University",
"name": "cBARBEL",
"prefix": "NBDC01245",
"pubmeds": [
"20935046"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc01246": {
"alt_name": "Coronary Artery Disease Gene Database",
"description": "CADgene is a comprehensive database for Coronary Artery Disease (CAD) genes. It consists of manually extracted information of the CAD related genes from literature. Currently, this database contains more than 300 CAD related genes and their detailed information associated with CAD from about 2000 publications. These genes have been classified into 12 functional categories based on their roles in CAD. Each gene is given extracted information from related studies (e.g. the size of case-control, population, SNP, odds ratio, P-value, etc.) for useful annotations, which include general gene information, gene Ontology annotations, KEGG pathways, protein-protein interactions and others.",
"homepage": "http://www.bioguo.org/CADgene/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Huazhong University of Science and Technology",
"name": "CADgene",
"prefix": "NBDC01246",
"pubmeds": [
"21045063"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc01247": {
"description": "ChemProt is a disease chemical biology database, which is based on a compilation of multiple chemical-protein-disease annotation resources. The database includes over 1,700,000 unique chemicals with biological activity for more than 19,000 proteins. ChemProt is able to assist in the in silico evaluation of environmental chemicals, natural products and approved drugs, as well as the selection of new compounds based on their activity profile against most known biological targets, including those related to adverse drug events.\nResults from the disease chemical biology database associate citalopram, an antidepressant, with osteogenesis imperfect and leukemia and bisphenol A with certain types of cancer, respectively.",
"homepage": "http://potentia.cbs.dtu.dk/ChemProt/",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie",
"Chemical structure"
],
"maintainer": "DTU Health Tech",
"name": "ChemProt",
"prefix": "NBDC01247",
"pubmeds": [
"20935044",
"23185041",
"26876982"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Chemical compound",
"Health/Disease"
]
},
"nbdc01248": {
"description": "Clover Garden is a database that provides easy access to clover (Trifolium species) genome information. The database contains marker information including gel image, linkage map and reference list.",
"homepage": "http://clovergarden.jp/",
"information_keywords": [
"Sequence",
"Image/Movie"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Clover Garden",
"prefix": "NBDC01248",
"pubmeds": [
"16769692",
"13679984"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01250": {
"description": "This is a database for the Jatropha genome. It contains the complete genome sequence, amino acid sequences, and motif predictions via InterPro. BLAST homology searches, keywords searches, as well as data download is possible from this site.",
"homepage": "http://www.kazusa.or.jp/jatropha/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Jatropha Genome Database",
"prefix": "NBDC01250",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01251": {
"description": "This database provides comprehensive annotation and genes predicted to be transcription factors from genome sequences of primary legume model plants: soybean (Glycine max), Lotus japonicus and Medicago truncatula. The database also has a good search function, allowing searches by transcription factor family name, keywords, gene ID, GO terms, and cis-motifs. Homology searches by BLAST as well as display and download of information through the genome browser is also possible.",
"homepage": "http://legumetfdb.psc.riken.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "LegumeTFDB",
"prefix": "NBDC01251",
"pubmeds": [
"19933159"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01252": {
"description": "This database contains information of genes predicted to be transcription factors from the complete soybean genome sequences (Glyma1.0 model) and the comprehensive annotation. Currently, the database contains 4,342 records of gene loci encoding 5,035 transcription factor models in 61 families. The database also has a good search function, allowing searches by transcription factor family name, keywords, gene ID, GO terms, and cis motifs. Homology searches by BLAST as well as display and download of information through the genome browser is also possible.",
"homepage": "http://soybeantfdb.psc.riken.jp/index.pl",
"information_keywords": [
"Sequence"
],
"maintainer": "RIKEN Yokohama Institute",
"name": "SoybeanTFDB",
"prefix": "NBDC01252",
"pubmeds": [
"19884168"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01253": {
"alt_name": "A peptide database with MS/MS spectra",
"description": "PepBase is a peptide database which consists of experimental data of Arabidopsis phosphopeptide measured by a single analytical platform at the proteomics laboratory of IAB, Keio Univ.",
"homepage": "http://pepbase.iab.keio.ac.jp/phospho/msb/",
"information_keywords": [
"Sequence"
],
"maintainer": "Keio University",
"name": "PepBase",
"prefix": "NBDC01253",
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01254": {
"description": "This database provides marker information for soybean. Each marker has information on EST-SSR, including primer sequences and links to corresponding EST sequences. Marker information can be easily obtained from the linkage maps. Site-wide searches using keywords is also possible.",
"homepage": "http://marker.kazusa.or.jp/Soybean/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Soybean Marker Database",
"prefix": "NBDC01254",
"pubmeds": [
"18192281"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Genetic variation"
]
},
"nbdc01255": {
"description": "This is the genome database for tomato, a model organism for the Solanum family. Information such as DNA markers in tomatoes, SNP annotations (functional markers), and contigs, scaffolds, and predicted genes and their annotations obtained through selected BAC clone mixture (SBM) can be accessed through the site. The DNA marker database contains EST-SNP, EST-SSR, Genome-SSR, and Intron-SNP, as well as linkage maps for three strains of tomatoes.",
"homepage": "http://www.kazusa.or.jp/tomato/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "KaTomicsDB",
"prefix": "NBDC01255",
"pubmeds": [
"21044984",
"20431859",
"23641178"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation"
]
},
"nbdc01256": {
"description": "The gene Research Center at the University of Tsukuba, as a core research institute for NBRP (the National BioResource Project) tomato, possesses many varieties of tomato cultivars and seeds of wild relatives. Additionally, it is involved in the large-scale production of EMS and gamma ray mutant lines of the dwarf tomato variety micro-tom. TOMATOMA serves as a resource supply of cultivars, wild relatives, and micro-tom mutants (for a fee) to promote research on tomatoes worldwide. Searches can be performed by strain or trait. This page is linked from each record in NBRP TOMATO (http://integbio.jp/dbcatalog/record/nbdc00716).",
"homepage": "http://tomatoma.nbrp.jp/index.jsp",
"information_keywords": [
"Bioresource"
],
"maintainer": "University of Tsukuba",
"name": "TOMATOMA (Tomato Mutants Archive)",
"prefix": "NBDC01256",
"pubmeds": [
"21258066"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01257": {
"homepage": "http://umdb.um.u-tokyo.ac.jp/DShokubu/nepal/Seedplants/specimen_dic/findrecords.php?",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "The University of Tokyo The University Museum",
"name": "Flora of Nepal Database (Seed plants)",
"prefix": "NBDC01257",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01258": {
"alt_name": "Leaf Senescence Database",
"description": "LSD is a database of published senescence-associated genes (SAGs) and mutants. Each entry in the LSD represents a gene or mutant obtained from the research paper, with information of GO annotation, PPI and interaction with microRNA. Both genes and mutant phenotypes are obtained by searching and browsing and entries can also be retrieved by name, keyword, references and annotation. All gene sequence and annotation data are available for download.",
"homepage": "https://bigd.big.ac.cn/lsd/",
"information_keywords": [
"Phenotype",
"Sequence",
"Expression",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "National Genomics Data Center, China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences",
"name": "LSD",
"prefix": "NBDC01258",
"pubmeds": [
"31599330",
"21097471"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc01259": {
"description": "RIKEN Plant Hormone Research Network consists of six research groups related to plant hormone study. This site provides data and information on hormone metabolic pathways and genes in Arabidopsis and our hormone analysis platform. Our publications are also available.",
"homepage": "http://hormones.psc.riken.jp/",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie",
"Portal"
],
"maintainer": "RIKEN CSRS (RIKEN Center for Sustainable Resource Science)",
"name": "RIKEN Plant Hormone Research Network",
"prefix": "NBDC01259",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Metabolite"
]
},
"nbdc01260": {
"alt_name": "Live Images of Plant Stomata Database",
"description": "This database was constructed with the objective of promoting research on intracellular structures in the guard cells of plants. The database contains 11,160 optically sliced images of guard cells. These microscopic images were obtained by creating A. thaliana transgenic plants expressing fluorescent marker proteins for each organelle. Each image contains information on the target construction, marker protein, promoters, and related publications.",
"homepage": "https://www.higaki-lab.net/lips/",
"information_keywords": [
"Expression",
"Image/Movie",
"3D structure"
],
"maintainer": "Kumamoto University",
"name": "LIPS",
"prefix": "NBDC01260",
"pubmeds": [
"22582142"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc01261": {
"description": "Tohoku Univ. Brassica Seed Bank includes germplasm of genus Brassica and its allies collected from Mediterranean area and obtained by seed exchange with universities and institutes in many countries. The germplasm is freely available to researchers for academic purpose.",
"homepage": "http://www.agri.tohoku.ac.jp/pbreed/Seed_Stock_DB/Stock_English_top.html",
"information_keywords": [
"Bioresource"
],
"maintainer": "Tohoku University Graduate School of Agricultural Science",
"name": "Tohoku Univ. Brassica Seed Bank",
"prefix": "NBDC01261",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01262": {
"alt_name": "The Kazusa Arabidopsis data opening site",
"description": "This database provides the sequencing data for Arabidopsis determined by the Kazusa DNA Laboratory, as a part of the international collaborative project for the Arabidopsis genome sequence spearheaded by the Arabidopsis Genome Initiatives (AGI). This page collects sequences determined by other research groups participating in the project, and displays the analyzed results by the Kazusa Lab using the Arabidopsis Genome Displayer. Data can be accessed by chromosome, BLAST, and keyword searches.",
"homepage": "http://www.kazusa.or.jp/kaos/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "KAOS",
"prefix": "NBDC01262",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01264": {
"description": "The Microbial Culture Collection at the National Institute for Environmental Studies collects and distributes culture strains of cyanobacteria, eukaryotic microalgae, protozoa, and endangered algae. It also accepts deposition of culture strains important for research or environmental issues. The stock strains can be searched by keywords or the classification list, which leads to detailed information including photos. The desired strains and some kinds of culture media can be ordered online. Users can also search references.",
"homepage": "http://mcc.nies.go.jp/localeAction.do?lang=en",
"information_keywords": [
"Bioresource",
"Environment",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "NIES (National Institute for Environmental Studies)",
"name": "MICROBIAL CULTURE COLLECTION",
"prefix": "NBDC01264",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01265": {
"alt_name": "The Kobe University Macro-Algal Culture Collection",
"description": "KU-MACC accepts for deposit strains and distributes Algal culture strains. It provides inrformation about stock strain lists, culturing and submission methods, ways to purchase, and documents related to sending and receiving strains.",
"homepage": "http://ku-macc.nbrp.jp/locale/change?lang=en",
"information_keywords": [
"Bioresource",
"Image/Movie"
],
"maintainer": "Kobe University Research Center for Inland Seas",
"name": "KU-MACC",
"prefix": "NBDC01265",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01266": {
"description": "This database provides access to data on oceanic islands plant specimens of the herbarium of the University Tokyo. The records include data and images of specimens in the Angiosperm, the Gymnosperm and the Fern and its allies of the Bonin Islands.",
"homepage": "http://umdb.um.u-tokyo.ac.jp/DShokubu/spm/English/top.htm",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Herbarium, University of Tokyo",
"name": "Oceanic Islands Plant Specimen Database",
"prefix": "NBDC01266",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01267": {
"description": "This is a database of bacteria and filamentous fungi living in agricultural environment. Databases such as the Index of Parasitic and Symbiotic Microbes on Wild Plants in Japan, 2,4-D-degrading microorganism database, microorganism museum specimen databases, Burkholderia cepacia complex bacterial database, and the Biosafety Level in Japan can be browsed. Cross-sectional searches of these databases is also possible.",
"homepage": "http://www.niaes.affrc.go.jp/inventory/microorg_e/index.html",
"information_keywords": [
"Environment",
"Portal"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "microForce",
"prefix": "NBDC01267",
"status": "Inactive"
},
"nbdc01268": {
"description": "researchmap is a platform for managing, publishing, and sharing information on researchers in Japan. Over 300,000 researchers have registered their profiles and research outputs on researchmap. researchmap has been integrated into the systems of universities and provides features to help users find researchers for industry-academia collaboration and joint research.",
"homepage": "https://researchmap.jp/?lang=en",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "JST (Japan Science and Technology Agency)",
"name": "researchmap",
"prefix": "NBDC01268",
"status": "Inactive"
},
"nbdc01270": {
"alt_name": "HiCEP Peak Database",
"description": "The PeakDB provides the expression profiles of peak signals in mouse ES cells detected by HiCEP.",
"homepage": "http://hicepweb.nirs.go.jp/peakdb/query?request=dbmain&lang=ja",
"information_keywords": [
"Expression"
],
"maintainer": "National Institute of Radiological Sciences",
"name": "PeakDB",
"prefix": "NBDC01270",
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01271": {
"description": "MOLECULAR PROBE LIBRARY is a database of PET probes which are manufactured with NIRS technology. It is one of the world's largest molecular probe library.",
"homepage": "http://www.nirs.qst.go.jp/research/division/mic/db/eng/index.html",
"information_keywords": [
"Method",
"Bibliography/Documents",
"Chemical structure"
],
"maintainer": "National Institute of Radiological Sciences",
"name": "MOLECULAR PROBE LIBRARY",
"prefix": "NBDC01271",
"status": "Suspended",
"target_keywords": [
"Chemical compound"
]
},
"nbdc01272": {
"alt_name": "Radiosynthesis Database of PET Probes",
"description": "RaDaP is an online database for radiosynthesis of PET probes (total about 3,000 compounds). Detailed data can be obtained by simply clicking the link.",
"homepage": "http://www.nirs.qst.go.jp/research/division/mic/db2/",
"information_keywords": [
"Bibliography/Documents",
"Chemical structure"
],
"maintainer": "National Institute of Radiological Sciences",
"name": "RaDaP",
"prefix": "NBDC01272",
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc01274": {
"description": "Sagace is a web-based search engine to retrieve information from biomedical databases in Japan. It aims primarily to assist biomedical research and drug development, and offers features including a faceted navigation and rich snippets to show informative metadata.",
"homepage": "http://sagace.nibiohn.go.jp/en/index.html",
"information_keywords": [
"Method",
"Bibliography/Documents"
],
"maintainer": "National Institutes of Biomedical Innovation, Health and Nutrition",
"name": "Sagace (Search for Biomedical Data & Resources in Japan)",
"prefix": "NBDC01274",
"pubmeds": [
"23110816"
],
"status": "Active",
"target_keywords": [
"Health/Disease",
"Drug"
]
},
"nbdc01276": {
"description": "Gray's Anatomy of the Human Body is an online resource for human anatomy. This page contains reproductions of the original plates from the landmark Gray's Anatomy atlas. Users can search for anatomical structures or browse by structure.",
"homepage": "https://www.bartleby.com/107/",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Bartleby.com, Inc.",
"name": "Gray's Anatomy of the Human Body",
"prefix": "NBDC01276",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01277": {
"description": "WikiProject Molecular and Cellular Biology is a resource for molecular biology information. The site contains summary pages and links to primary research on a variety of molecular biology topics. Users can edit and add information pages and search to find articles on a particular topic. The site also categorizes pages by quality and development of the information.",
"homepage": "http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Molecular_and_Cellular_Biology",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Wikimedia Foundation Inc.",
"name": "WikiProject Molecular and Cellular Biology",
"prefix": "NBDC01277",
"status": "Active"
},
"nbdc01278": {
"description": "Information on local vegetables of Thailand is collected, managed, and recorded in this database. It was discovered that these vegetables have useful physiological functions.",
"homepage": "http://www.jircas.affrc.go.jp/project/value_addition/Local_Vegetables_of_Thailand_home.html",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "JIRCAS (Japan International Research Center for Agricultural Sciences)",
"name": "Local Vegetables of Thailand",
"prefix": "NBDC01278",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01282": {
"alt_name": "A database of the plants of the Sahel",
"description": "This database contains information of plants distribution in Sahel. Most of the information in this database, such as photos, local name (Zarma), and use of plants, were collected in Fakara, which is in the southeast of Republic of Niger. The wide variety of plants includes those from croplands, fallows, pastureland, roadside, and tiger bush (vegetation growing from shrubs in barren land).",
"homepage": "http://www.jircas.affrc.go.jp/project/africa_dojo/FakaraPlants/Fakara_Plants_home.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "JIRCAS (Japan International Research Center for Agricultural Sciences)",
"name": "Fakara Plants",
"prefix": "NBDC01282",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01283": {
"description": "This is a database of images of wild plants in the lowland savanna of West Africa. Weed species primarily include those identified in the lowland savanna of the Tamale region in northern Ghana. The database was constructed as a central source of information for the development of weed suppressing technologies.",
"homepage": "https://www.jircas.go.jp/en/database/db06",
"information_keywords": [
"Image/Movie"
],
"maintainer": "JIRCAS (Japan International Research Center for Agricultural Sciences)",
"name": "Plants in lowland savanna of west Afric",
"prefix": "NBDC01283",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01285": {
"description": "This database contains pathological data from animal experiments on the biological effects of internal exposure to plutonium.",
"homepage": "http://www.nirs.qst.go.jp/db/anzendb/PuDB/PuDB_Eng.html",
"information_keywords": [
"Method",
"Image/Movie"
],
"maintainer": "National Institute of Radiological Sciences",
"name": "Internal Pu Exposure Animal Pathology Studies Database",
"prefix": "NBDC01285",
"status": "Suspended",
"target_keywords": [
"Organism",
"Health/Disease",
"Chemical compound"
]
},
"nbdc01288": {
"alt_name": "Graphs of Predicted Monitoring Data",
"description": "This database helps to estimate the intake and the effective dose from bioassay measurements. The results are shown in graphical form",
"homepage": "http://www.nirs.qst.go.jp/db/anzendb/RPD/gpmd.php",
"information_keywords": [
"Method"
],
"maintainer": "National Institute of Radiological Sciences",
"name": "MDAID",
"prefix": "NBDC01288",
"status": "Active",
"target_keywords": [
"Health/Disease",
"Chemical compound"
]
},
"nbdc01291": {
"description": "FFPRI FluxNet Database is a database of observational research focused on measuring carbon dioxide flux using micrometeorological techniques at five research sites in Japan. It provides information of meteorological conditions, photosynthetically active radiation, heat fluxes, CO2 flux, ecosystem respiration, etc. Users need to obtain assent for data download.",
"homepage": "https://www2.ffpri.go.jp/labs/flux/data_e.html",
"information_keywords": [
"Environment"
],
"maintainer": "Forestry and Forest Products Research Institute",
"name": "FFPRI FluxNet Database",
"prefix": "NBDC01291",
"status": "Active"
},
"nbdc01292": {
"alt_name": "Forest EST and Genome database",
"description": "ForestGEN is a database that provides EST (Expressed Sequenced Tag) and genome information on forest organisms, including trees, microbes such as fungi and nematodes, insects, and mushrooms. This database contributes to advances in forest sciences in areas such as Genomics, Population genetics, Plant pathology, Tree breeding and Ecology.",
"homepage": "https://forestgen.ffpri.go.jp/en/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Forestry and Forest Products Research Institute",
"name": "ForestGEN",
"prefix": "NBDC01292",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01293": {
"alt_name": "Phytosociological Releve' Database",
"description": "Phytosociological RelevΓ© Database (PRDB) is composed of many plot (relevΓ©) data on vegetation collected throughout Japan with the phytosociological method. A relevΓ© datum comprises the ID no., survey date, surveyor name, references, surveyed area, location, environmental data, community structure, species name and their dominance, etc. The PRDB provides information on distribution of a variety of species.",
"homepage": "http://www.ffpri.affrc.go.jp/labs/prdb/EnglishVer/index-e.html",
"maintainer": "Forestry and Forest Products Research Institute",
"name": "PRDB",
"prefix": "NBDC01293",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01294": {
"description": "This database is an image database of longicorn beetles of Bukit Bangkirai. Data in this database were collected in a small part (300 ha) of Bukit Bangkirai (about 1,500ha) in east Kalimantan only in a short period between 1999 and 2001.\nEach entry contains images, species name, size, sex, distribution, published literature, etc. This database allows to search data using thumbnail images, species name list, or genus name.",
"homepage": "https://db.ffpri.go.jp/longicorn_id/index-E.html",
"information_keywords": [
"Environment",
"Image/Movie"
],
"maintainer": "Forestry and Forest Products Research Institute",
"name": "Image database of longicorn beetles of Bukit Bangkirai",
"prefix": "NBDC01294",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01298": {
"description": "This is the database of the herbarium of plants specimen maintained by the Forestry and Forest Products Research Institution. These databases have been collected by generations of employees, with some dating back to 1920. The locality of collections range from Hokkaido to Okinawa and also include foreign countries.",
"homepage": "http://www2.ffpri.affrc.go.jp/labs/herbariumdb/en",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Forestry and Forest Products Research Institute",
"name": "F.F.P.R.I. Herbarium DataBase",
"prefix": "NBDC01298",
"status": "Suspended",
"target_keywords": [
"Organism"
]
},
"nbdc01299": {
"alt_name": "Forest Dynamics Database",
"description": "This is a collection of data on tree survival and growth, which measured over the long term in large natural forest test plots located throughout Japan by the Forestry and Forest Products Research Institute. It contains detailed information on mature trees, saplings, seedlings, seeds, litter, forest floor vegetation, terrain, and environment which can be browsed and downloaded. Users must be registered to download data.",
"homepage": "http://fddb.ffpri-108.affrc.go.jp/en/index.html",
"information_keywords": [
"Environment",
"Bibliography/Documents"
],
"maintainer": "Forestry and Forest Products Research Institute",
"name": "FDDB",
"prefix": "NBDC01299",
"status": "Suspended",
"target_keywords": [
"Organism"
]
},
"nbdc01300": {
"description": "This is a database of long-term data on coniferous and deciduous trees. It includes data about 68 genuses and 93 species of coniferous and deciduous trees in 11 regions of South East Asia, and 2 regions of Papua New Guinea, collected by the Forestry and Forest Products Research Institute. The accumulated data include physical characteristics such as volume density, percentage of contraction, and water absorption, processing suitability such as drying and cutting, strength properties such as bending strength, and chemical properties such as pulp properties. Furthermore, the site contains slice photos of timber viewed as a cross-sectional surface, straight grain surface, and cross grain surface by light microscopy, as well as color photos of timber surfaces. This database can be used as a basic resource for selecting appropriate woods when creating timber for building, furniture, or plywoods and laminated lumber.",
"homepage": "https://www2.ffpri.go.jp/fdb/esawoodq/wood.html",
"maintainer": "Forestry and Forest Products Research Institute",
"name": "The Database of Properties of South-east Asian Timbers",
"prefix": "NBDC01300",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01307": {
"alt_name": "Minimum Requirements for Biological Products",
"description": "MRBP was developed to specify the manufacturing methods, descriptive definitions, quality, storage, test methods, etc. of vaccines, antitoxins, blood products and other biological products for human use, according to Article 42(1) of the Pharmaceutical Affairs Law. This English version (PDF file) is not based on the current Japanese version of the MRBP.",
"homepage": "http://www.niid.go.jp/niid/en/mrbp-e.html",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "National Institute of Infectious Diseases",
"name": "MRBP",
"prefix": "NBDC01307",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01312": {
"alt_name": "Infectious Agents Surveillance Report",
"description": "This surveillance report contains data concerning patients and laboratory findings obtained by the National Epidemiological Surveillance of Infectious Diseases and other data covering various aspects of infectious diseases. The prefectural and municipal health centers and public health institutes (PHIs), the Department of Food Sanitation, the Ministry of Health, Labour and Welfare, and quarantine stations, have provided the above data.",
"homepage": "https://www.niid.go.jp/niid/en/iasr.html",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "National Institute of Infectious Diseases",
"name": "IASR",
"prefix": "NBDC01312",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01319": {
"alt_name": "Hazard Evaluation Support System Integrated Platform",
"description": "HESS has two databases. One is a toxicity knowledge database, which contains information on repeated dose toxicity and toxicity mechanisms. The other is a metabolism knowledge database containing rat metabolism maps and information on absorption, distribution, metabolism and excretion (ADME) in rats and humans. HESS allows chemicals to be categorized on the basis of structural, physicochemical and mechanistic similarities and helps to predict the repeated dose toxicity of untested chemicals by means of category approach. HESS is downloadable after registration (free).",
"homepage": "https://www.nite.go.jp/en/chem/qsar/hess-e.html",
"information_keywords": [
"Bibliography/Documents",
"Chemical structure"
],
"maintainer": "NITE (National Institute of Technology and Evaluation)",
"name": "HESS",
"prefix": "NBDC01319",
"status": "Active",
"target_keywords": [
"Health/Disease",
"Chemical compound"
]
},
"nbdc01320": {
"description": "GlycosideDB is a database of glycoside provided by Japan Consortium for Glycobiology and Glycotechnology database (JCGGDB) and other organizations in Japan. Each entry contains IUPAC, structure, the composition of glycoside, SMILES, etc.. Glycoside entries are categorized based on the connection between Glycan and Aglycon. This database allows to search by the categories, names, structures, glycan or aglicon list.",
"homepage": "https://jcggdb.jp/search/GlycosideDB.cgi",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Sequence",
"Chemical structure"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "GlycosideDB",
"prefix": "NBDC01320",
"status": "Active",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc01321": {
"description": "This web cite is a search tool for Japan Consortium for Glycobiology and Glycotechnology database (JCGGDB). It allows to search by keywords in many databases about glycan-related data in Japan (glycoprotein, glycolipid, glycosaminoglycans, polysaccharides ,etc.)",
"homepage": "https://jcggdb.jp/search/search.cgi?keyword=&lang=en",
"information_keywords": [
"Chemical structure",
"Portal"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "Search Across Glycoscience DBs - JCGGDB",
"prefix": "NBDC01321",
"status": "Active",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc01322": {
"alt_name": "Biological Magnetic Resonance Data Bank Japan",
"description": "This is a portal site with manuals, tools, and search functions for data registration to BMRB that is a database of biomolecular magnetic resonance data (http://integbio.jp/dbcatalog/en/record/nbdc00380).",
"homepage": "https://bmrbdep.pdbj.org",
"information_keywords": [
"Portal",
"3D structure",
"Bibliography/Documents",
"Repository"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "BMRBj",
"prefix": "NBDC01322",
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Protein",
"Metabolite"
]
},
"nbdc01323": {
"alt_name": "Kazusa Metabolomics Portal",
"description": "Komics is a portal database of databases, tools and other information about metabolomics studies which were developed and produced in Kazusa DNA Research Institute. It's constructed with many databases for metabolome \"raw\" data, metabolite annotations of the peaks, metabolic pathway data of transcriptome and metabolome analysis, etc..",
"homepage": "http://www.kazusa.or.jp/komics/en/",
"information_keywords": [
"Portal"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "KOMICS",
"prefix": "NBDC01323",
"status": "Inactive",
"target_keywords": [
"Metabolite"
]
},
"nbdc01324": {
"description": "Metabolonote is a specialized database system which manages \"metadata\" accompanied with the experimental data of Metabolomics studies. This database manages metadata by separating it mainly into four layers, namely information about sample sets (SE), samples (S), analytical methods (M), and data analysis procedures (D). It allows users to easily publish and utilize Metabolomics data by simplifying the metadata record process.",
"homepage": "http://metabolonote.kazusa.or.jp/",
"information_keywords": [
"Method",
"Bibliography/Documents"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Metabolonote",
"prefix": "NBDC01324",
"pubmeds": [
"25905099"
],
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc01325": {
"alt_name": "The Theileria orientalis Genome Annotation Database",
"description": "TOT-DB is a database covering the whole genome of the parasitic intracellular protozoan, Theileria orientalis, sequenced with a whole genome shotgun sequence method, combined with manual gap closing followed by automated/manual annotation. Using G-integra genome browser, users are able to browse physical maps of the T. orientalis genome and their gene structures. This database is available for comparative genome analysis between highly pathogenic species, T. parva or T. annulata, and non-transforming species, T. orientalis. It also allows searches for homology by BLAST. The genome sequences and gene annotation of T. orientalis is downloadable.",
"homepage": "http://totdb.czc.hokudai.ac.jp/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Hokkaido University Research Center for Zoonosis Control",
"name": "TOT-DB",
"prefix": "NBDC01325",
"pubmeds": [
"22951932"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01331": {
"description": "This database is based on the book \"Glossary of Korean, Chinese and Japanese Fishery Terminology\" published under the cooperation of three fisheries research organizations belonging to China, Korea, and Japan. Search and browsing of terms are possible on this database in Japanese, Chinese, Korean and English.",
"homepage": "https://www.fishery-terminology.jp/index_e.html",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "The National Research and Development Agency, Japan Fisheries Research and Education Agency (FRA)",
"name": "Database of Japanese, Chinese, And Korean Fishery Terminology",
"prefix": "NBDC01331",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc01333": {
"description": "This database consists of a dataset on the A-line monitoring surveys carried out in Kuroshio-Oyashio region by Fisheries Research Agency since 1988. Vertical profiles of chlorophyll a and nutrients, and standing stock of netplankton are included.",
"homepage": "http://tnfri.fra.affrc.go.jp/seika/a-line/a-line_index2.html",
"information_keywords": [
"Environment"
],
"maintainer": "The National Research and Development Agency, Japan Fisheries Research and Education Agency (FRA)",
"name": "A-line Database",
"prefix": "NBDC01333",
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc01334": {
"description": "This database collects the N-line monitoring surveys carried out in the coastal and offshore Okhotsk Sea along Hokkaido, Japan, by Hokkaido National Fisheries Research Institute, Fisheries Research Agency since 2000. Vertical profiles of chlorophyll a and nutrients, and standing stock of netplankton are contained.",
"homepage": "http://hnf.fra.affrc.go.jp/n-line/index_e.html",
"information_keywords": [
"Environment"
],
"maintainer": "The National Research and Development Agency, Japan Fisheries Research and Education Agency (FRA)",
"name": "N-line Database",
"prefix": "NBDC01334",
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc01338": {
"description": "WorldMap is a database of world-wide utilization of plant species sorted by individual countries. Each entry contains species name, purpose, and references. Users are able to search by \nclicking flags of countries or typing in a scientific name.",
"homepage": "http://www.knapsackfamily.com/KNApSAcK_World/top.jsp",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Nara Institute of Science and Technology",
"name": "KNApSAcK World Map",
"prefix": "NBDC01338",
"pubmeds": [
"22123792"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01340": {
"description": "Biological Activity (Natural Activity) is a database about relationships between medicinal plants and their biological activities. Each entry contains a species name, biological activities and links to KNApSAcK Core System. It allows to search with species or browse with all data list.",
"homepage": "http://www.knapsackfamily.com/BiologicalActivity/top.jsp",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Nara Institute of Science and Technology",
"name": "KNApSAcK Biological Activity (Natural Activity)",
"prefix": "NBDC01340",
"pubmeds": [
"22123792"
],
"status": "Active",
"target_keywords": [
"Health/Disease",
"Metabolite"
]
},
"nbdc01341": {
"alt_name": "Motorcycle Metabolic Pathway",
"description": "Motorcycle is a database for enzyme-enzyme reaction of metabolism in medicinal plants. It contains manually curated information about amino acid sequence, metabolic enzyme reaction, plants names and references. It allows to search using KRID, enzyme, species or gene names. Moreover, it allows to search with BLASTP.",
"homepage": "http://www.knapsackfamily.com/motorcycle/top.php",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Nara Institute of Science and Technology",
"name": "KNApSAcK Motorcycle",
"prefix": "NBDC01341",
"pubmeds": [
"22123792",
"23509110"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01342": {
"description": "MetalMine is a database for metal ion binding proteins in medicinal plants. It contains manually curated information about metal ions, amino acid residues, and hetero molecules included in the metal binding site. Moreover, it displays metal binding site structures by clicking on PDB id. This database allows to browse by metal and keyword lists. It also allows to search with metal-binding residues in sequence or PDB ID.",
"homepage": "http://metalmine.mydns.jp/metalmine/index.html",
"information_keywords": [
"Image/Movie",
"Chemical structure"
],
"maintainer": "Nara Institute of Science and Technology",
"name": "KNApSAcK MetalMine",
"prefix": "NBDC01342",
"pubmeds": [
"22123792"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01343": {
"description": "KAMPO is a database for formulae of Japanese traditional medicine (Kampo) and medicinal plants. It provides scientific names, efficacy, a list of Kampo formulae and detailed information about blends of medicinal plant. It allows searches by lists of medicinal plants (for Kampo formula) or Kampo formulae (for medicinal plants).",
"homepage": "http://www.knapsackfamily.com/kampo/top.jsp",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Nara Institute of Science and Technology",
"name": "KNApSAcK KAMPO",
"prefix": "NBDC01343",
"pubmeds": [
"22123792"
],
"status": "Active",
"target_keywords": [
"Health/Disease",
"Drug"
]
},
"nbdc01344": {
"description": "JAMU DB is a database of medicinal plants often included in Jamu, a herbal medicine, in Indonesia. It contains information about Jamu name, effect, ingredient herbs, etc. In this database, users are able to retrieve formulae from the names of medicinal plants, and also the names of medicinal plants from formula names.",
"homepage": "http://www.knapsackfamily.com/jamu/top.jsp",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Nara Institute of Science and Technology",
"name": "KNApSAcK JAMU DB",
"prefix": "NBDC01344",
"pubmeds": [
"22123792"
],
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease",
"Metabolite",
"Drug"
]
},
"nbdc01345": {
"description": "Lunch Box is a database covering food history or medical effects of edible plants. Each entry contains scientific name, introduction into Japan, edibility, health care/ medicinal usage, related literature, processed food, etc. All information is curated from published literature.",
"homepage": "http://www.knapsackfamily.com/LunchBox/top.jsp",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Nara Institute of Science and Technology",
"name": "KNApSAcK Lunch Box",
"prefix": "NBDC01345",
"pubmeds": [
"22123792"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01346": {
"alt_name": "H-Inv Extended Protein Database",
"description": "H-EPD provides comprehensive, non-redundant human protein sequences, including both curated and predicted human proteins, and made by merging H-Inv proteins (predicted from transcriptome) with UniProtKB/Swiss-Prot and RefSeq proteins (curated). H-EPD was designed as a reference database for human proteome research.",
"homepage": "http://hinv.jp/hinv/h-epd/",
"information_keywords": [
"Sequence"
],
"maintainer": "Molecular Profiling Research Center for Drug Discovery, AIST",
"name": "H-EPD",
"prefix": "NBDC01346",
"pubmeds": [
"23245335"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01347": {
"homepage": "http://recountdb.cbrc.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "Recount DB",
"prefix": "NBDC01347",
"pubmeds": [
"22139942"
],
"status": "Closed",
"target_keywords": [
"RNA"
]
},
"nbdc01348": {
"description": "This site is a platform for sharing data from studies in humans, providing rules and frameworks for promoting the utilization and sharing of the enormous amount of human data while considering protection of personal information. The site was established by the JST NBDC and cooperates with the DNA Data Bank of Japan (DDBJ) to publish data. This site can provide data related to humans as well as guidelines for the use of such information.",
"homepage": "https://humandbs.dbcls.jp/en/",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "Database Center for Life Science (DBCLS)",
"name": "NBDC Human Database",
"prefix": "NBDC01348",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc01349": {
"alt_name": "Systems Science of Biological Dynamics database",
"description": "SSBD is a database which provides a rich set of resources for analyzing quantitative biological data, such as single-molecule, cell, and gene expression nuclei. It contains quantitative biological data collected from a variety of species, sources and methods. These data are obtained from both experiment and computational simulation and are represented in a new Biological Dynamics Markup Language (BDML). Users are able to exchange, store, compare and analyze data with this new data format through the database. It also allows users to download quantitative biological dynamics data directly.",
"fairsharing": "biodbcore-000786",
"homepage": "https://ssbd.riken.jp/",
"information_keywords": [
"Image/Movie",
"Repository"
],
"maintainer": "RIKEN BDR (RIKEN Center for Biosystems Dynamics Research)",
"name": "SSBD:database",
"prefix": "NBDC01349",
"pubmeds": [
"27412095",
"25414366"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc01350": {
"description": "KONAGAbase is a genomic database of the diamondback moth (Plutella xylostella) (KONAGA is the Japanese word for the diamondback moth). The database currently provides the following sequence data with useful annotation information by BLAST, HMMER3, and Blast2GO: genome sequence data, transcriptome sequence data and putative gene set.",
"homepage": "http://dbm.dna.affrc.go.jp/px/",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "KONAGAbase",
"prefix": "NBDC01350",
"pubmeds": [
"23837716"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"RNA"
]
},
"nbdc01351": {
"description": "This is the first version of genetic linkage map of the brown planthopper (BPH). The consensus map consists of 474 SSR, 43 SNPs and 1 STS totaling 518 markers with 472 unique positions. The map would provide initial information for BPH genomics studies, and particularly for identifying a genetic basis of the virulence, and to facilitate QTL analysis of other important traits.",
"homepage": "https://sogo.dna.affrc.go.jp/cgi-bin/sogo.cgi?class=unka",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "Brown planthopper Maps & Markers Database",
"prefix": "NBDC01351",
"pubmeds": [
"23204257"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc01357": {
"description": "These pages offer research data and descriptions about radiation and associated diseases.",
"homepage": "https://www.rerf.or.jp/en/library/data-en/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Radiation Effects Research Foundation",
"name": "Downlodable Data (Radiation Effects Research Foundation)",
"prefix": "NBDC01357",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01362": {
"alt_name": "acupuncture and moxibustion medical care general bibliographic-data-base",
"description": "This database provides bibliographic information about acupuncture and moxibustion medical care (such as: article title, authors, journal title, year, volume and pages). The full text is available for articles with no copyright restrictions.",
"homepage": "http://jaclid.jsam.jp/dspace/index.jsp?locale=en",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "The Japan Society of Acupuncture and Moxibustion",
"name": "JACLiD",
"prefix": "NBDC01362",
"status": "Suspended",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01379": {
"alt_name": "Integrated Neglected TROpical disease DataBase",
"description": "iNTRODB is an integrated database for searching drug-target proteins from parasitic protozoa genomes that cause neglected tropical disease (NTD) including leishmaniasis, Chagas' disease and Human African trypanosomiasis. It provides structural information of the proteins mainly obtained from the PDB as well as chemical information from ChEMBL. It also contains genome information from gene DB. This database allows user to set search conditions such as e-values of homology or phenotypes (RIT-seq).",
"homepage": "http://www.bi.cs.titech.ac.jp/introdb/about.html",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"3D structure"
],
"maintainer": "Tokyo Institute of Technology",
"name": "iNTRODB",
"prefix": "NBDC01379",
"status": "Inactive",
"target_keywords": [
"Protein",
"Health/Disease",
"Metabolite"
]
},
"nbdc01380": {
"description": "Coelacanth Genome Project is a database for whole genome sequencing of extant coelacanth species and comparative genomic analyses. It provides Gbrowse, BLAST and keyword search. Genome sequence, gene sequences, protein sequences, non-cording RNA, and fosmid end sequences are available through the website.This database also contains CT-scan images and three-dimensional images of coelacanths.",
"homepage": "http://coelacanth.nig.ac.jp/",
"information_keywords": [
"Sequence",
"Image/Movie"
],
"maintainer": "National Institute of Genetics",
"name": "Coelacanth Genome Project",
"prefix": "NBDC01380",
"pubmeds": [
"23878157"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc01381": {
"alt_name": "Strawberry Genome And Resource Entry",
"description": "Strawberry GARDEN is a database about genome of cultivated strawberry (F. x ananassa). It contains gene sequences and annotations, which obtained through comparison with its wild relatives, and mapped onto the reference genome, along with the previously published F. vesca genome sequence. Users are able to search by BLSAT or keywords. \nThis database also contains strawberry marker database.",
"homepage": "http://strawberry-garden.kazusa.or.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Strawberry GARDEN",
"prefix": "NBDC01381",
"pubmeds": [
"24282021"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc01382": {
"alt_name": "Arabidopsis DNA Microarray probe information",
"description": "ARTRA is an Arabidopsis transcriptome and microarray database developed by Takara Bio inc. that contains transcriptome sequences and gene-specific sequences for a DNA microarray and RNAi knockdown triggers.",
"homepage": "http://artra.kazusa.or.jp/artra/ARI3_101/index.html",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "ARTRA",
"prefix": "NBDC01382",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01383": {
"alt_name": "Japan chemical collaborative knowledge database",
"description": "J-CHECK is a database developed to provide the information regarding \"Act on the Evaluation of Chemical Substances and Regulation of Their Manufacture, etc. \"(CSCL) by the authorities of the law, Ministry of Health, Labour and Welfare, Ministry of Economy, Trade and Industry, and Ministry of the Environment. J-CHECK provides the information regarding CSCL, such as the list of CSCL, chemical safety information obtained in the existing chemicals survey program, risk assessment, etc. in cooperation with eChemPortal by OECD.",
"homepage": "https://www.nite.go.jp/chem/jcheck/top.action?request_locale=en",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Bibliography/Documents"
],
"maintainer": "NITE (National Institute of Technology and Evaluation)",
"name": "J-CHECK",
"prefix": "NBDC01383",
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc01384": {
"alt_name": "KAMEMUSHI (PS: oriental stink bug) EST",
"description": "PcsEST is a database about ESTs of an oriental stink bug (PS, Plautia crossota stali), called \"CYABANE-AO-KAMEMUSHI\" in Japanese. Each entry contains sequences, gene ontology, and homology values for NCBI-NR, Drosophila and C. elegans. This database allows searches using key words, clone names, gene ontology terms or homology values.",
"homepage": "http://pcsest.dna.affrc.go.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "PcsEST",
"prefix": "NBDC01384",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01385": {
"alt_name": "YUSURIKA cDNA",
"description": "This database provides ESTs about the Sleeping Chironomid, Polypedilum vanderplanki (Diptera, Chironomidae). The cDNAs are derived from various cDNA libraries constructed from larval whole bodies 0h, 12 h and 36 h after desiccation treatment. Each entry contains sequences, gene ontology, and homology values for NCBI-NR, Drosophila, or C. elegans. This database allows searches using keywords, clone names, gene ontology terms or homology values.",
"homepage": "http://pvcdna.dna.affrc.go.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "PVcDNA",
"prefix": "NBDC01385",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01386": {
"description": "This database provides ESTs of the green rice leafhopper (NC, Nephotettix cincticeps), called \"TSUMAGURO-YOKOBAI\" in Japanese. Each entry contains sequences, gene ontology, and homology values for NCBI-NR, Drosophila, or C. elegans. This database allows searches using key words, clone names, gene ontology terms or homology values.",
"homepage": "http://ncest.dna.affrc.go.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "YOKOBAI (NC: green rice leafhopper) EST",
"prefix": "NBDC01386",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01387": {
"description": "\"Comprehensive Medicinal Plant Database\" is an encyclopaedia of medicinal plants and provides a user-friendly interface for searching and viewing information about medicinal plants used for Kampo and herbal medicines. Available information includes medicinal plants, herbal medicines, their components and relevant genes and cultivation methods, as well as a list of herbal medicines widely available in Japan (labeled \"model herbal medicines\") with their measured components. It also provides other data such as methods of cultivation and propagation and the interior morphology of herbal medicines.",
"homepage": "http://mpdb.nibiohn.go.jp/index(EN).html",
"information_keywords": [
"Sequence",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "National Institutes of Biomedical Innovation, Health and Nutrition",
"name": "Comprehensive Medical Plant Database",
"prefix": "NBDC01387",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Health/Disease",
"Drug"
]
},
"nbdc01389": {
"alt_name": "Functional Annotation of the Mammalian Genome",
"description": "FANTOM5 is a database about comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes. It contains experimental data of the FANTOM consortium, an international collaborative research project initiated and organized by the RIKEN. This database contains mapped data using Cap Analysis of gene Expression (CAGE), which are the sets of transcripts, transcription factors, promoters and enhancers active in the majority of mammalian primary cell types. These data is furthermore complemented with profiles from cancer cell lines, and tissues.",
"homepage": "https://fantom.gsc.riken.jp/5/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "FANTOM5",
"prefix": "NBDC01389",
"pubmeds": [
"24670763",
"24670764"
],
"status": "Active",
"target_keywords": [
"DNA",
"RNA"
]
},
"nbdc01391": {
"alt_name": "Microbial Functional Potential",
"description": "MiFuP is a database of functional potentials deduced from microbial genomes. Users can easily search for microbes with potential functions of interest or for functional potentials from your microbial genome sequences or cds sequences. Associated MiFuP wiki is an information web site about microbial functions (e.g., detailed description of each function, underlying mechanisms, representative microbes, industrial use). MiFuP wiki is in Japanese only.",
"homepage": "https://www.nite.go.jp/nbrc/mifup/",
"maintainer": "NITE (National Institute of Technology and Evaluation)",
"name": "MiFuP",
"prefix": "NBDC01391",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01392": {
"alt_name": "Human Genetic Variation Database",
"description": "HGVD is a database providing a central resource to archive and display Japanese genetic variation and association between the variation and transcription level of genes. It contains genetic variations determined by exome sequencing of 1,208 individuals and genotyping data of common variations obtained from a cohort of 3,248 individuals. This database includes information such as alleles, genotype frequencies, number of samples, coverages, and expression QTL (eQTL) significances. The HGVD browser allows to search using gene name / ID, rsID of dbSNP, pathogenic variation, or chromosome numbers.",
"homepage": "http://www.genome.med.kyoto-u.ac.jp/SnpDB/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Kyoto University",
"name": "HGVD",
"prefix": "NBDC01392",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc01395": {
"alt_name": "Traditional Medical & Pharmaceutical Database",
"description": "TradMPD is a database of traditional medical and pharmaceutical drugs. It collects information on crude drugs, Kampo formulas, and related experimental materials such as, crude drug name, botanical source, pharmacological effects, gene information of related plants, chemical-analysis information, literature, etc.",
"homepage": "http://dentomed.toyama-wakan.net/index_en",
"information_keywords": [
"Sequence",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "University of Toyama Institute of Natural Medicine",
"name": "TradMPD",
"prefix": "NBDC01395",
"status": "Active",
"target_keywords": [
"Metabolite",
"Chemical compound",
"Drug"
]
},
"nbdc01396": {
"alt_name": "KNApSAcK Bicycle Algae Metabolic Pathway",
"description": "KNApSAcK Bicycle is a database on proteins and metabolism reaction of algae. It contains information about proteins that existed in algae, and reaction mechanism or pathway in which such proteins participate. It allows to compare amino-acid sequences or DNA sequences swith the database using BLASTP Search, BLASTX Search or BLASTN Search.",
"homepage": "http://www.knapsackfamily.com/bicycle/top.html",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Nara Institute of Science and Technology",
"name": "KNApSAcK Bicycle",
"prefix": "NBDC01396",
"status": "Inactive",
"target_keywords": [
"Protein",
"Metabolite"
]
},
"nbdc01399": {
"description": "This is a database for the Dianthus caryophyllus (carnation) genome information. The sequence data for each gene, annotations such as GO, and results of BLASTP analysis against databases such as UniProt can be found here. BLAST searches using own sequence data and data downloads are also possible.",
"homepage": "http://carnation.kazusa.or.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Carnation DB",
"prefix": "NBDC01399",
"pubmeds": [
"24344172"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01400": {
"description": "Raphanus sativus Genome DataBase is a database of DNA markers of Raphanus sativus. It contains information on sequences including markers of EST-SSR, isozyme, R-EST, RAPD, RFLP, SSR, STS, and linkage maps. This database allows to search using SNP tables or BLAST search.",
"homepage": "http://radish.kazusa.or.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Raphanus sativus Genome DataBase",
"prefix": "NBDC01400",
"pubmeds": [
"24848699"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation"
]
},
"nbdc01401": {
"description": "DAIZUbase is an integrated soybean genome database and data mining tools; 2 map browsers (GBrowse, UnifiedMap), a gene viewer, and BLAST search system. This database provides three data mining approaches.\n1) Narrowing the range of a scaffold (chromosome) by GBrowse or UnifiedMap\n2) Keyword search\n3) Sequence homology search by BLAST",
"homepage": "https://daizubase.daizu.dna.affrc.go.jp",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "DAIZUbase",
"prefix": "NBDC01401",
"pubmeds": [
"23136506"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01402": {
"alt_name": "Flowering Plant Gene Picker",
"description": "This database is an annotation pipeline for flowering plant genomes. If users submit a DNA sequence, fpgp predicts exon-intron structures on the basis of full-length cDNA (FLcDNA) evidence, and simultaneously finds protein-coding regions in the predicted transcripts. For the prediction, 10 published plant genome sets are used, and users can download the gene prediction data in those genomes.",
"homepage": "http://fpgp.dna.affrc.go.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "fpgp",
"prefix": "NBDC01402",
"pubmeds": [
"20668003"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST",
"Protein"
]
},
"nbdc01403": {
"alt_name": "Komugi Genome Sequence Program",
"description": "Komugi GSP is a genome analysis program for wheat in Japan. This database includes the data of genome sequences, transcriptomes, and gene annotations. Some data are downloadable, including the genome sequencing data of wheat chromosome 6B, in collaboration with the members of IWGSC (International Wheat Genome Sequencing Consortium), and RNA-Seq data.",
"homepage": "http://komugigsp.dna.affrc.go.jp/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "Komugi GSP",
"prefix": "NBDC01403",
"pubmeds": [
"24086083"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc01404": {
"alt_name": "Plant Gene Family Database",
"description": "PGF-DB is a database for analysis of gene families from Oryza sativa, Sorghum bicolor, Zea mays, and Arabidopsis thaliana. It contains more than ten thousands gene families constructed by the Markov clustering (MCL) method and the complete linkage method of BLASTP. The names of gene families are assigned based on the InterPro domains to associate the gene family names to their related gene functions.",
"homepage": "http://green.dna.affrc.go.jp/PGF-DB/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "PGF-DB",
"prefix": "NBDC01404",
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01405": {
"alt_name": "African Rice Annotation DataBase",
"description": "AfRicA DB is a database for genome annotation of O. glaberrima. It provides various kinds of information such as genome annotations, insertion/deletion, single nucleotide polymorphism (SNP), and simple sequence repeat (SSR). Users are able to compare their sequences with the genomic sequences of O. glaberrima by BLAST search.",
"homepage": "http://green.dna.affrc.go.jp/Og/",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "AfRicA DB",
"prefix": "NBDC01405",
"pubmeds": [
"21323774"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc01406": {
"alt_name": "Barley Gene Expression Database",
"description": "Bex-db is a database of a malting barley (Haruna Nijo, two-rowed) transcriptome data. It includes sequences of barley full-length DNAs and expression profiles resulting from microarray analysis. It also contains partial sequences of more than 309,000 novel expressed sequence tags (ESTs) for analysis. Users are able to browse the data via keyword, sequence homology and expression profile search options.",
"homepage": "https://barleyflc.dna.affrc.go.jp/bexdb/index.html",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "bex-db",
"prefix": "NBDC01406",
"pubmeds": [
"24399916"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01407": {
"alt_name": "Field transcriptome database",
"description": "FiT-DB is a database for gene expression and statistical modeling of transcriptomic dynamics in field conditions. It contains 461 microarray data of Oryza sativa and the best-fit model and parameters for each gene in the statistical modeling. Users are able to find what and how factor(s) affect gene expressions in the field. They are also able to search genes affected by any given factors.",
"homepage": "http://fitdb.dna.affrc.go.jp/",
"information_keywords": [
"Expression"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "FiT-DB",
"prefix": "NBDC01407",
"pubmeds": [
"23217716"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01408": {
"description": "The DDIDA database provides mechanism-based information about drugs, micromolecules and body phenotypic response (disease/symptom) relationships. The data are derived from DailyMed drug labels, DrugBank, KEGG, GenBank, OMIM, MeSH, AERS, International Classification of Diseases (ICD). It integrates drug information, micromolecular information, phenotypic response (symptom/disease), drug-adverse event information, drug-target interaction data, and micromolecule-disease relationships. The data quality is checked by experts and will be continuously updated.",
"homepage": "http://cgs.pharm.kyoto-u.ac.jp/ddida/",
"information_keywords": [
"Phenotype",
"Interaction/Pathway"
],
"maintainer": "Kyoto University",
"name": "DDIDA",
"prefix": "NBDC01408",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Chemical compound",
"Drug"
]
},
"nbdc01411": {
"description": "This site is a database for the morbidity and the mortality of VLBW infants in Japan. It provides data about infants who were born in the participating hospitals with birth weight at or less than 1500 g or who were admitted to these facilities within 28 days of birth.",
"homepage": "http://plaza.umin.ac.jp/nrndata/indexe.htm",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Tokyo Women's Medical University, Maternal and Perinatal Center",
"name": "Neonatal Research Network Database in Japan",
"prefix": "NBDC01411",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01412": {
"description": "This database provides gene information and literature information about GatVirus. Users can specify an option such as gene sequence and kind of virus.",
"homepage": "http://teine.cc.sapmed.ac.jp/~gatvirus/ddbj2/",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "National Institute of Infectious Diseases",
"name": "GatVirus Database",
"prefix": "NBDC01412",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc01413": {
"description": "Percellome Database is a toxic genomics database that provides experimental data on gene expression and toxicity in mouse, rat, and human cells following exposure to more than 100 chemical compounds. This databases is accessible using the RESTful WebAPI.",
"homepage": "http://www.nihs.go.jp/tox/percellome_e.html",
"information_keywords": [
"Expression"
],
"maintainer": "NIHS (National Institute of Health Sciences)",
"name": "PercellomeDB",
"prefix": "NBDC01413",
"pubmeds": [
"16571132"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Chemical compound"
]
},
"nbdc01418": {
"description": "This database provides evidence reports by publications about Kampo Treatment, Japanese Acupuncture and Moxibustion, Anma-Massage-Shiatsu, and Korean Medicine Treatment.",
"homepage": "http://jhes.umin.ac.jp/team.html",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Japan Hand Search & Electronic Search Society",
"name": "Evidence Reports of Traditional East Asian Medicine (ETEAM)",
"prefix": "NBDC01418",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01422": {
"description": "Orphanet is a portal site for rare diseases and orphan drugs. It provides inventory of rare diseases and classification, inventory of orphan drugs, clinical trials, etc.",
"fairsharing": "biodbcore-000497",
"homepage": "http://www.orpha.net/consor/cgi-bin/Disease_Search_List.php?lng=EN",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Orphanet",
"name": "Orphanet",
"prefix": "NBDC01422",
"pubmeds": [
"12655825"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01423": {
"description": "ClinicalTrials.gov is a results database of publicly and privately supported clinical studies of human participants conducted around the world. It provides a registry to submit studies and is maintained by the National Library of Medicine (NLM) at the National Institutes of Health (NIH).",
"fairsharing": "biodbcore-000470",
"homepage": "https://clinicaltrials.gov/",
"information_keywords": [
"Bibliography/Documents",
"Repository"
],
"maintainer": "NLM (National Library of Medicine)",
"name": "ClinicalTrials.gov",
"prefix": "NBDC01423",
"pubmeds": [
"11033590"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01424": {
"description": "GGGenome is an ultrafast search engine for nucleotide sequences. It allows searches for sequences containing mismatches, gaps or inserts. GGGenome shows the first 50 results for each strand of the query sequence. A maximum of 10000 results can be retrieved in various formats.",
"homepage": "https://gggenome.dbcls.jp/en/",
"information_keywords": [
"Sequence"
],
"maintainer": "DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "Ultrafast sequence search GGGenome",
"prefix": "NBDC01424",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01425": {
"description": "WormTSS is a comprehensive collection of transcription start sites (TSSs) for trans-spliced genes in C. elegans. It consists of a genome browser and a TSS list. The list contains information about outron and exon TSSs, such as TSS ID, gene name, common gene name, position, and Gaussian distribution. Users are able to search genes from the list or by keywords, or browse using the genome browser. This database allows download of embryo TSS list, adult TSS list, 5'SAGE Illumina single-end reads and 5'SAGE Illumina paired-end reads.",
"homepage": "http://wormtss.utgenome.org/browser/",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tokyo",
"name": "WormTSS",
"prefix": "NBDC01425",
"pubmeds": [
"23636945"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01426": {
"description": "The Medaka Methylome Browser database gathers kowledge about methylomes of medaka genomes with Illumina sequencing at single-base resolution using genomic DNA from three libraries (liver, blastulae, and testes) of the two strains, Hd-rR and HNI.",
"homepage": "https://utgenome.org/medaka_v2/#!Methylation.md",
"information_keywords": [
"Sequence"
],
"maintainer": "The University of Tokyo",
"name": "Medaka Methylome Browser",
"prefix": "NBDC01426",
"pubmeds": [
"22689467"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01427": {
"description": "The Mouse Phenotype Database is for raw data of behavioral tests from mouse strains. Data were collected from published articles. It comprises three parts; Mouse Phenotype Database, C57BL6 Substrain Behavior Database, and Software for behavioral analysis.",
"homepage": "http://www.mouse-phenotype.org/",
"information_keywords": [
"Phenotype",
"Method",
"Bibliography/Documents"
],
"maintainer": "Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University",
"name": "Mouse Phenotype Database",
"prefix": "NBDC01427",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01428": {
"description": "KEGG MODULE is a database of manually defined functional units called KEGG modules identified by M numbers, used for annotation and biological interpretation of sequenced genomes. It contains four types of KEGG modules;\n1) pathway modules - representing tight functional units in KEGG metabolic pathway maps\n2) structural complexes - often forming molecular machineries\n3) functional sets - for other types of essential sets, such as Aminoacyl-tRNA synthases, prokaryotes, etc.\n4) signature modules - as markers of phenotypes, such as EHEC pathogenicity signature, Shiga toxin, etc.",
"homepage": "http://www.genome.jp/kegg/module.html",
"information_keywords": [
"Phenotype",
"Interaction/Pathway"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG MODULE",
"prefix": "NBDC01428",
"pubmeds": [
"23384306"
],
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc01429": {
"description": "KEGG Metagenomes is a database about environmental samples with which metagenome sequences are determined.",
"homepage": "http://www.genome.jp/kegg/catalog/org_list3.html",
"information_keywords": [
"Environment",
"Sequence",
"Bibliography/Documents"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG Metagenomes",
"prefix": "NBDC01429",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01430": {
"alt_name": "Human Omics database for the Generation of iPS and Normal Cells",
"description": "SHOGoin is a database about differentiated and stem cells in humans. Each entry contains information about morphologic features, related articles, OBO cell type ontology, cell neighborhood, gene expression and cell images. This database succeeds CELLPEDIA database (http://integbio.jp/dbcatalog/en/record/nbdc01025).",
"homepage": "http://shogoin.stemcellinformatics.org/",
"information_keywords": [
"Expression",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Center for iPS Cell Research and Application, Kyoto University",
"name": "SHOGoiN",
"prefix": "NBDC01430",
"status": "Inactive",
"target_keywords": [
"cDNA/EST",
"Cell/Organelle"
]
},
"nbdc01431": {
"alt_name": "Asian Insect Information Center",
"description": "AIIC is a portal site of databases about types and normal specimens collected in Asia and the Pacific Area. It is composed of insect databases, mainly based on the Kyushu University Collection. Each record contains scientific names (family, genus and species), locality, collecting date, collector, etc, according to a format of the Darwin Core of the Global Biodiversity Information Facility (GBIF).",
"homepage": "http://aiic.jp/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie",
"Portal"
],
"maintainer": "Kyushu University Faculty of Agriculture",
"name": "AIIC",
"prefix": "NBDC01431",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01432": {
"alt_name": "Ascidian Network of In Situ Expression and Embryological Data",
"description": "ANISEED is a database about gene expression in Ascidian embryos. It contains detailed anatomical ontologies for Ascidian embryos, and quantitative geometrical descriptions of developing cells obtained from reconstructed three-dimensional (3D) embryos up to the gastrula stages. In this database, fully annotated gene model sets are linked to high-resolution spatial gene expression patterns in wild-type and experimentally manipulated conditions and to experimentally validated cis-regulatory regions imported from specialized databases or extracted from literature articles. This database allows searches using following categories:\n1) Genome Annotations (genes, cDNA clones, cis-regulatory regions)\n2) Anatomy (anatomical ontology, embryo scheme)\n3) gene Expression & Function (expression data, phenotypes)\n4) Literature. \nIt also allows exploration by BLAST or genome browser.",
"fairsharing": "biodbcore-000752",
"homepage": "http://www.aniseed.cnrs.fr/aniseed/",
"information_keywords": [
"Sequence",
"Expression",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Institut de Biologie du DΓ©veloppement de Marseille",
"name": "ANISEED",
"prefix": "NBDC01432",
"pubmeds": [
"20647237"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01433": {
"alt_name": "Cancer related Gene/Protein and Disease Pathway Database",
"description": "CancerProView is an image database for cancer-associated protein (domains) and their interaction pathways. It contains information of transcripts and protein sequences about cancer genes/proteins.\nThis database allows searches by keyword, gene name, protein name, or cancer type. A disease name list is also available.",
"homepage": "http://cancerproview.dmb.med.keio.ac.jp/php/cpv.html",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "Keio University",
"name": "CancerProView",
"prefix": "NBDC01433",
"pubmeds": [
"22659240"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein",
"Health/Disease"
]
},
"nbdc01435": {
"description": "The Cassava Online Archive is a database about cassava mRNA sequences and ESTs currently available from NCBI (Genbank/EMBL/DDBJ) and their annotations. This database contains annotations based on the similarity search results collated from several protein databases and the similarity map results from the cassava (Manihot esculenta, Euphorbiaceae), castor bean (Ricinus communis, Euphorbiaceae), poplar (Populus trichocarpa, Salicaceae), grape (Vitis vinifera, Vitaceae), and Arabidopsis thaliana (Brassicaceae) genome sequences. It also contains domain organization as predicted by InterProScan and gene Ontology (GO) terms for improving the annotations. \nThis database allows to search with gene function, accession number, and sequence similarity (BLAST).",
"homepage": "http://cassava.psc.riken.jp/ver.1/",
"information_keywords": [
"Sequence"
],
"maintainer": "RIKEN CSRS (RIKEN Center for Sustainable Resource Science)",
"name": "Cassava Online Archive",
"prefix": "NBDC01435",
"pubmeds": [
"24040164"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation"
]
},
"nbdc01436": {
"alt_name": "CTRS",
"description": "CTRS is a portal site for the archiving hydrometeorological data observed by the multiple institutes and university in Tsukuba Science City, Japan. It contains observed data such as surface meteorological measurements, radiation measurements, flux data, soil temperature, soil moisture data, meteorological tower data, lidar data and sonde data. Data are obtained from the following institutes and university: Meteorological Research Institute (MRI), Terrestrial Environment Research Center (TERC) and Mt. Tsukuba Station (MtTSUKUBA) of the University of Tsukuba (UT). National Research Institute for Earth Science and Disaster Prevention (NIED), National Institute for Agro-Environmental Sciences (NIAES), National Institute for Environmental Studies (NIES), and National Institute of Fruit Tree Science (NIFTS).",
"homepage": "http://www.geoenv.tsukuba.ac.jp/~ceoptsukuba/index.html",
"information_keywords": [
"Environment",
"Portal"
],
"maintainer": "CEOP Tsukuba Reference Site Project",
"name": "CEOP Tsukuba Reference Site",
"prefix": "NBDC01436",
"status": "Active"
},
"nbdc01437": {
"description": "Cerebellar Platform is an integrated database for cerebellar research. This database contains mini-reviews of contemporary cerebellar research, list of papers and mathematical models for cerebellar operation. It allows users to browse by an index tree or data types (model, paper, picture, etc.).",
"homepage": "https://cerebellum.neuroinf.jp",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "Cerebellar Platform",
"prefix": "NBDC01437",
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc01439": {
"description": "This site is a database about synaptic connectivity of C. elegans. It contains figures and tables about the synaptic connectivity among neurons in the pharynx and the somatic nervous system except the pharynx. Users are able to choose some neuron classes and obtain their wiring data and diagram. The archive files in this database are downloadable.",
"homepage": "http://ims.dse.ibaraki.ac.jp/ccep/",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "Keio University",
"name": "Database of Synaptic Connectivity of C. elegans\r\nfor Computation",
"prefix": "NBDC01439",
"pubmeds": [
"8805",
"22462104"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc01440": {
"alt_name": "Database of transcriptional regulation in Streptomyces coelicolor and its closest relatives",
"description": "DBSCR is a database for transcriptional regulation events in Streptomyces coelicolor A3(2) and its closest relatives, such as S. griseus, S. peucetius, S. albogriseolus, S. vinezuelae, and S. cacaoi. It contains published information about a compilation of transcription factors with their regulated genes as well as their recognition sequences, which was experimentally characterized and reported in the literature. This database has lists of \"Transcription factor\", \"Regulated genes\" and \"Revised translation start sites (TLSs)\" and allows users to browse data using the lists. It also allows searches using keywords, sequence or weight matrix.",
"homepage": "http://dbscr.hgc.jp/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "DBSCR",
"prefix": "NBDC01440",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01441": {
"alt_name": "Dihedral Transition Analysis database",
"description": "DTA DATABASE collects results of DTA (Dihedral Transition Analysis) from comprehensive and non-redundant dataset of high-resolution protein structures. DTA is the method for characterizing protein motion from one given 3D protein structure to another, based on large changes of main chain dihedral angles. It allows to sort and search functions from different aspects. It also provides a list of protein pairs.",
"homepage": "http://kitao02.bio.titech.ac.jp/DTA/top.php",
"information_keywords": [
"3D structure"
],
"maintainer": "Tokyo Institute of Technology School of Life Science and Technology",
"name": "DTA DATABASE",
"prefix": "NBDC01441",
"pubmeds": [
"19147660"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01442": {
"description": "Dynamic Brain Platform is an integrated site which provides scientists, academics and other practitioners with current information about neural dynamics in the brain. This site provides various services such as data sets, models, popular research findings and articles and current developments in the field.",
"homepage": "https://dynamicbrain.neuroinf.jp/index.php?ml_lang=en",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "The Dynamic Brain Platform committee",
"name": "Dynamic Brain Platform",
"prefix": "NBDC01442",
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc01443": {
"alt_name": "Database for Endocrine disrupter-sensitive Genes in reproductive system",
"description": "ED-genes is a database for endocrine disrupter-sensitive genes in reproductive system. It contains information about sensitive genes to endocrine disrupters expressed in mammalian reproductive system which are identified by subtraction cloning (Representational Difference Analysis) and DNA microarray technologies.",
"homepage": "http://www.med.u-fukui.ac.jp/SEIKA2/ED-Genes.html",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "University of Fukui, Faculty of Medical Sciences",
"name": "ED-Genes",
"prefix": "NBDC01443",
"pubmeds": [
"15746888",
"15746888",
"15644576"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01444": {
"description": "This is a database of structural changes on alpha-galactosidase A (GLA) responsible for Fabry disease. It contains clinical phenotypes, genotypes, and structures of mutant GLAs. This database is freely accessible.",
"homepage": "http://fabry-database.org/",
"information_keywords": [
"Sequence",
"Image/Movie",
"Bibliography/Documents",
"3D structure"
],
"maintainer": "Meiji pharmaceutical university",
"name": "fabry-database.org",
"prefix": "NBDC01444",
"pubmeds": [
"21412250"
],
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease"
]
},
"nbdc01445": {
"alt_name": "An Online Atlas and Database of the Drosophila Nervous System",
"description": "Flybrain is an anatomical database of the central and peripheral nervous system of Drosophila melanogaster. It contains basic structure of the nervous system and more specific information concerning different anatomical structures, developmental stages, and visualization techniques. Image data and related information are searched by keyword or accession number.",
"homepage": "http://flybrain.neurobio.arizona.edu/",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Flybrain Database consortium",
"name": "FLY BRAIN",
"prefix": "NBDC01445",
"pubmeds": [
"7619521"
],
"status": "Inactive",
"target_keywords": [
"Organism",
"Cell/Organelle"
]
},
"nbdc01446": {
"alt_name": "FLYBRAIN Neuron Database",
"description": "FLYBRAIN Neuron Database is a integrated database about a central brain of Drosophila melanogaster. It's constructed with three databases and a tool; \n1) Neuron Data provides projection patterns of the identified neurons in diverse areas of the brain which were recorded in a unified format, with text-based descriptions as well as images and movies.\n2) Strain/Antibody Data contains information about the labeling patterns of various antibodies and expression driver strains to visualize identified neurons.\n3) Brain Region Data provides the nomenclature system of the neuropils.\n4) Brain Explorer is a visualization tool with which users can interactively examine three-dimensional reconstruction of the confocal serial section images with desired viewing angles and cross sections. Furthermore, comprehensive collection and versatile search function of the anatomical information reported in diverse publications make it possible to analyze possible connectivity between different brain regions.",
"homepage": "https://flybrain-ndb.virtualflybrain.org",
"information_keywords": [
"Expression",
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "The University of Tokyo",
"name": "Flybrain NDB",
"prefix": "NBDC01446",
"pubmeds": [
"21280038",
"16802334"
],
"status": "Active",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc01447": {
"alt_name": "Database of Apicomplexa Transcriptomes",
"description": "The DB-AT is a database composed of full-length cDNA datasets and RNA-seq datasets of several Parasites; malaria, Anopheles, Toxoplasma, Tsetse, Cryptosporidium, Babesia, Neospora, Eimeria, Theileria and Echinococcus. The database allows users to search by BLAST, dynamic RNA-Seq, phylogenetic tree, gene symbol, or chromosomal position.",
"homepage": "http://fullmal.hgc.jp/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Hokkaido University",
"name": "DB-AT",
"prefix": "NBDC01447",
"pubmeds": [
"25414358"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Health/Disease"
]
},
"nbdc01453": {
"alt_name": "Calpain for Modulatory Proteolysis Database",
"description": "CaMPDB is a database of calpain, a calcium-dependent protease as well as one of the most typical enzymes of modulatory proteolysis. This database consists of three parts: calpain, its substrates and calpastatin (endogenous inhibitor protein specific to calpain). It contains information about one or more proteolytic sites of each substrate collected from literature. Moreover, systematic experiments on proteolysis of peptide fragments including these sites were conducted, and resulting real values are stored in the substates part.",
"homepage": "http://www.calpain.org/",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "Bioinformatics Center, Kyoto University",
"name": "CaMPDB",
"prefix": "NBDC01453",
"pubmeds": [
"20238430"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01455": {
"alt_name": "Human Kidney and Urine Proteome Project",
"description": "This database is a portal site about an international project, Human Kidney and Urine Proteome Project. It contains databases for kidney and urine which were obtained by proteomics analysis. The databases deal with 2DGE-LC-Based Proteomics in Glomerulus, Rat IMCD Phosphoprotein, etc..",
"homepage": "http://www.hkupp.org",
"information_keywords": [
"Expression"
],
"maintainer": "HUPO (Human Proteom Organization)",
"name": "HKUPP",
"prefix": "NBDC01455",
"pubmeds": [
"17711322"
],
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease"
]
},
"nbdc01456": {
"alt_name": "Intrinsically Disordered proteins with Exten sive Annotations and Literatures",
"description": "This is a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references, and structural domain assignment. This database allows to browse by a list or search using keywords or BLAST. Data are downloadable with a XML file.",
"fairsharing": "biodbcore-000052",
"homepage": "https://www.ideal-db.org",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie",
"3D structure"
],
"maintainer": "IDEAL Development Team",
"name": "IDEAL",
"prefix": "NBDC01456",
"pubmeds": [
"22067451"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01457": {
"alt_name": "Immunoglobulin structure database",
"description": "Ig-Base is a collection of antibody data compiled from Protein Data Bank with associated annotations by manual inspection. Each entry contains PBD ID, antibody name, length and sequence of parts, etc. It allows searches using PDB ID, antibody names, length of CDRs, sequence or canonical structures.",
"homepage": "http://sysimm.ifrec.osaka-u.ac.jp/igBase/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"3D structure",
"Chemical structure"
],
"maintainer": "Osaka University",
"name": "Ig-Base",
"prefix": "NBDC01457",
"pubmeds": [
"18798566",
"18473362"
],
"status": "Suspended",
"target_keywords": [
"Protein"
]
},
"nbdc01458": {
"description": "IRView is a database and viewer of interacting regions (IRs) in protein sequences. It contains 3,417 IRs of human and mouse proteins obtained from several sources, together with other functional region data, such as InterPro regions, non-synonymous (missense) single nucleotide polymorphisms (SNPs) and variant regions. Since all region data in the IRView are stored and displayed as standardized positions on reference sequences, this database allows to intuitively comprehend positional relations of each region to others via the web interface.",
"homepage": "http://ir.hgc.jp/",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "The University of Tokyo The Institute of Medical Science",
"name": "IRView",
"prefix": "NBDC01458",
"pubmeds": [
"22592381"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Protein"
]
},
"nbdc01460": {
"description": "This database is a catalog of Striga hermonthica ESTs. It contains EST information which annotated using a free EST analysis tool, EST2uni. \nThis database provides the following features;\n1) Summary of S. hermonthica EST analysis,\n2) Keyword search of S. hermonthica ESTs,\n3) Blast search of S. hermonthica unigene database,\n4) putative SSRs and SNPs search,\n5) Analysis results of gene Ontology (GO).",
"homepage": "http://striga.psc.riken.jp/est2uni/index.php",
"information_keywords": [
"Sequence"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "Striga hermonthica EST Database",
"prefix": "NBDC01460",
"pubmeds": [
"20353604"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation"
]
},
"nbdc01462": {
"description": "SCCmec is a database of staphylococcal cassette chromosome mec (SCCmec) elements that encode methicillin-resistance, which are the most representative staphylococcal cassette chromosome elements (SCCs). This database contains information of stranis and sequences, and it provides three functions to understand SCCmec elements.\n1) \"Overview\" illustrate structures of SCCmec elements.\n2) \"Search\" provides convenient tools to compare new data to extant SCCmec elements by searching SCCmec database, and to ccr genes and Ccr proteins by searching ccr database. The comparison of two SCCmec sequences can be visualized by creating a dot plot. Phylogenetic relations of ccr genes or Ccr proteins can be visualized by creating a phylogenetic tree. \n3) \"Identification\" lists typing schemes and PCR methods to assign SCCmec elements.",
"homepage": "http://www.staphylococcus.net/index.php/en",
"information_keywords": [
"Sequence"
],
"maintainer": "Juntendo University",
"name": "SCCmec",
"prefix": "NBDC01462",
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01463": {
"alt_name": "SYMPtomics Hamamatsu Ontology for new Investigative Etiology",
"description": "SYMPHONIE is a database for disease caused by a genetic factor. It contains patient condition, diagnosis, and inspection data with the disease name, the causative gene, and the related gene. \nThis database allows searches by symptoms, disease names or gene names.",
"homepage": "http://symphonie.mpb.hama-med.ac.jp/Symphonie/jsp/index.jsp",
"maintainer": "Hamamatsu University School of Medicine",
"name": "SYMPHONIE",
"prefix": "NBDC01463",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc01464": {
"description": "The RAS/MAPK Syndromes Homepage includes a database about RAS/MAPK pathways implicated in growth-factor mediated cell proliferation, differentiation and cell death. It contains information about mutations related to RAS/MAPK syndromes, such as Costello syndrome, CFC (cardio-facio-cutaneous) syndrome and Noonan syndrome.",
"homepage": "http://www.medgen.med.tohoku.ac.jp/ras_mapk/index.html",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Tohoku University School of Medicine",
"name": "The RAS/MAPK syndromes Homepage",
"prefix": "NBDC01464",
"pubmeds": [
"18470943",
"12778136"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc01465": {
"alt_name": "A database for voucher specimens",
"description": "VSPECIMENS is a database about specimens referred in various researches (voucher specimens) . It provides digitized specimen information, such as label texts, images and bibliographic information from following datasets; \n1) Fern voucher specimen collection of the National Museum of Nature and Science\n2) Beetle voucher specimen collection of the National Institute for Agro-Environmental Sciences\n3) Hypenoptera voucher specimen collection of Kyushu University\n4) Coleoptera voucher specimen collection of Hokkaido University.\nThis database allows to search using a family name list or keywords.\nThe products are open to the public via VSpecimens website, GBIF Data Portal, GBIF Japan National Node.",
"homepage": "http://www.vspecimens.net/?locale=en",
"information_keywords": [
"Image/Movie",
"Taxonomy",
"Portal"
],
"maintainer": "Voucher Specimen Database Executive Committee",
"name": "VSPECIMENS",
"prefix": "NBDC01465",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc01466": {
"alt_name": "Retrovirous and Transposon tagged Cancer Gene Database",
"description": "RTCGD is a database of retrovirus and transposon tagged cancer gene in mouse. It contains information about clones, such as ID, tumor ID, strain, publication, etc.\nIt allows users to search by gene symbol, gene name, tumor models and/or tumor types, or gene-to-gene interaction.",
"homepage": "http://variation.osu.edu/rtcgd/index.html",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "The Ohio State University",
"name": "RTCGD",
"prefix": "NBDC01466",
"pubmeds": [
"14681473"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc01467": {
"description": "This database is a portal site for seven life science journals published from Japan. It includes descriptions and site links for \"Current Herpetology\", \"Journal of Mammalian Ova Research\", \"Mammal Study\", \"Ornithological Science\", \"Paleonotological Research\", \"Species Diversity\" and \"Zoological Science\".",
"homepage": "http://www.unibiopress.org/package/index.html",
"information_keywords": [
"Bibliography/Documents",
"Portal"
],
"maintainer": "UniBio Press",
"name": "UniBio Press Packages",
"prefix": "NBDC01467",
"status": "Active"
},
"nbdc01468": {
"description": "This is a database of THz spectroscopic measurements of several organic or inorganic materials. The database contains spectra and information of conditions for dozens of compounds. It allows browsing by compound name.",
"homepage": "http://thzdb.org/",
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)||NICT (National Institute of Information and Communications Technology)",
"name": "THz database",
"prefix": "NBDC01468",
"status": "Active",
"target_keywords": [
"Metabolite",
"Chemical compound",
"Drug"
]
},
"nbdc01469": {
"description": "This database is an on-line catalog of fungi cultures (TUFC strains) stored by Fungus/Mushroom Resource and Research Center (FMRC) in Tottori University. Each record contains taxonomy, species name, Japanese name, strain history, sequence data, etc. It allows searches using species name, Japanese name, keywords, or sequence. It is also able to search by a genus name list. The strains are distributable.",
"homepage": "http://muses.muses.tottori-u.ac.jp/facilities/FMRC/english/distribution.html",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "Tottori University Faculty of Agriculture Fungus/Mushroom Resource and Research Center",
"name": "TUFC Culture Online Catalogue",
"prefix": "NBDC01469",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01470": {
"alt_name": "UMIN Clinical Trials Registry",
"description": "UMIN-CTR is a registration database for clinical trials. Each entry contains title of the study, condition, objectives, assessment, study design, intervention, public contact, etc. It requires a UMIN ID and password in order to register clinical trials, but not to browse and search data.",
"homepage": "http://www.umin.ac.jp/ctr/index.htm",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "UMIN (University Hospital Medical Information Network Center)",
"name": "UMIN-CTR",
"prefix": "NBDC01470",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01472": {
"description": "SHELLS DATABASE is a database of shellfish. Each entry contains photographs of shellfish (mainly shells), Japanese name, species name, locality, distribution, references, etc.. This database allows to search by shape of shells, species name or Japanese name.",
"homepage": "https://bishogai.com/index.html",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents",
"Taxonomy"
],
"name": "SHELLS DATABASE",
"prefix": "NBDC01472",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01473": {
"alt_name": "Rangelands Atmosphere-Hydrosphere-Biosphere Interaction Study Experiment in Northeastern Asia Database",
"description": "RAISE Database is a database about the natural environments in northeastern Asia, with particular focus on Mongolia. It contains various data sets related to Hydrometeorology, aircraft observation, ground water, vegetation, etc.. It also includes maps, atlas and the other relevant data sets obtained by the RAISE project. The data are downloadable.",
"homepage": "http://raise.suiri.tsukuba.ac.jp/DVD/top/home.htm",
"information_keywords": [
"Environment"
],
"maintainer": "University of Tsukuba",
"name": "RAISE Database",
"prefix": "NBDC01473",
"status": "Inactive"
},
"nbdc01475": {
"description": "Visual Archive of Natural History Bibliotheca is a database of drawings and writings on natural history in Japan which has been retained at Tokyo National Museum. The drawings and writings are mainly created or collected in Edo and Meiji periods.",
"homepage": "http://webarchives.tnm.jp/infolib/meta_pub/G0000002070723ZF",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Tokyo National Museum",
"name": "Visual Archive of Natural History Bibliotheca",
"prefix": "NBDC01475",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01476": {
"alt_name": "NeuroImaging-platform",
"description": "NIMG-PF is a database about brain imaging. This database provides useful experimental data, analytical methods of brain imaging, and/or mathematical modeling as well as tutorial information. It allows users to browse by an index tree or data types (model, paper, picture, etc.).",
"homepage": "https://nimg.neuroinf.jp/?ml_lang=en",
"information_keywords": [
"Image/Movie"
],
"maintainer": "NIMG-PF committee||RIKEN CBS (RIKEN Center for Brain Science)",
"name": "NIMG-PF",
"prefix": "NBDC01476",
"status": "Active"
},
"nbdc01480": {
"alt_name": "Database of Parasites in Fish and Shellfish",
"description": "Database of Parasites in Fish and Shellfish (D-PAF) is a database of parasitic organisms in fishes, shellfishes and others which are usually made into seafood. Each entry contains concise pieces of clinical sign, parasitology, pathology, health hazard (risk assessment to public health), diagnosis and some clear photographs showing typical disease signs and parasite itself.",
"homepage": "http://fishparasite.fs.a.u-tokyo.ac.jp/index-eng.html",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Committee of D-PAF office",
"name": "D-PAF",
"prefix": "NBDC01480",
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease"
]
},
"nbdc01481": {
"description": "Experimental Techniques for Physiological Sciences is a database about summary of experimental protocols and techniques through a variety of physiological research activities. It contains variable information on experimental animal models, microscopic images, experimental protocols, tools, software and other experimental techniques. This database allows to browse using categories such as animal name, sample images, protocols, lecture videos, practice textbook etc..",
"homepage": "http://www.nips.ac.jp/tech/ipr/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "National Institute for Physiological Sciences",
"name": "Experimental Techniques for Physiological Sciences",
"prefix": "NBDC01481",
"status": "Active"
},
"nbdc01483": {
"description": "Annals of Nuclear Medicine is a portal site for two journals published by the Japanese Society of Nuclear Medicine. It includes archives of the 'Japanese journal of Nuclear Medicine' (in Japanese) and the \"Annals of Nuclear Medicine\" (in English). The \"Annals of Nuclear Medicine\" allows browsing of all abstracts and full text.",
"homepage": "http://www.jsnm.org/english/publications/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "The Japanese Society of Nuclear Medicine",
"name": "Annals of Nuclear Medicine",
"prefix": "NBDC01483",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01488": {
"description": "This database is a database of macroarray analysis data of Mesorhizobium loti MAFF303099. It contains average data about genome-wide expression difference between two conditions; free_living and bacteroid, free_living and starved or aero and microaero. It also provides lists of up and down-regulated genes, comparison of gene expression for amino acid metabolism between bacteroids and free-living cells, and list of primers used in RT-PCR experimetns.",
"homepage": "http://orca10.bio.sci.osaka-u.ac.jp/array01/",
"information_keywords": [
"Expression"
],
"maintainer": "Osaka University",
"name": "MacroArray Analysis Page of Mesorhizobium loti MAFF303099",
"prefix": "NBDC01488",
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01489": {
"description": "Neuropathology database is a database about fundamental knowledge on anatomy and pathology of the central nervous system. It provides images and information about normal anatomy, normal histology and cellular pathology on human brains. It also contains high resolution images of pathology specimens named \"Virtual Slide Contents\" which are available to e-learning.",
"homepage": "http://pathologycenter.jp/english/en_index.html",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Tokyo Metropolitan Institute of Medical Science",
"name": "Neuropathology Database",
"prefix": "NBDC01489",
"status": "Active",
"target_keywords": [
"Health/Disease",
"Cell/Organelle"
]
},
"nbdc01492": {
"description": "GFP-fusion library of Schizosaccharomyces pombe' is a database about intracellular localization of GFP-fusion proteins using genomic DNA library of Schizosaccharomyces pombe. It contains picture of the product and the DNA information using transformation. It allows to search from the list of localization patterns.",
"homepage": "https://www2.nict.go.jp/bio/seibutsu/CellMagic/english/gfp_fusionlibrary.html",
"information_keywords": [
"Expression",
"Image/Movie"
],
"maintainer": "NICT (National Institute of Information and Communications Technology)",
"name": "GFP-fusion library of Schizosaccharomyces pombe",
"prefix": "NBDC01492",
"pubmeds": [
"10759889"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle"
]
},
"nbdc01494": {
"alt_name": "Rice Proteogenomics Database",
"description": "OryzaPG-DB is a database for rice proteogenomics. It contains proteomic data such as the proteome of the rice undifferentiated cultured cells, and information on the corresponding cDNA, transcript and Genome sequences. This database allows browsing data per each chromosome or searching with keywords.",
"homepage": "https://github.com/MoHelmy/oryza-PG/",
"information_keywords": [
"Sequence"
],
"maintainer": "Keio University",
"name": "OryzaPG-DB",
"prefix": "NBDC01494",
"pubmeds": [
"21486466",
"22639657"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"RNA",
"Protein"
]
},
"nbdc01495": {
"alt_name": "PH Database",
"description": "PHDB is an integrated database for human physiome and systems biology researches. It contains three databases:\n1) PHML Model Database, which stores a number of modules representing biological/physiological functions which are formulated by mathematical equations to describe dynamic changes of states. The models in the database are written in an XML format called \"\"Physiological Hierachy ML (PHML)\"\"\n2) Morphology Database, which provides datasets representing morphometric models of biological organs. \n3) Timeseries database, which includes dynamic data obtained from physiological and numerical experiments.",
"homepage": "http://www.physiome.jp/phdb/index.html",
"information_keywords": [
"Image/Movie",
"Portal"
],
"maintainer": "physiome.jp",
"name": "PHDB",
"prefix": "NBDC01495",
"status": "Inactive",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01496": {
"description": "Epigenome project portal site is a portal database for epigenome project about human genome. \nThis database is constructed with databases about epigenome project-specific data, Cancer specific aberrant methylation data, original epigenome data by CREST IHEC Team, etc... \nThe epigenome project-specific data are able to browse with UCSC Genome Browser.",
"homepage": "http://epigenome.cbrc.jp/index.html",
"information_keywords": [
"Sequence",
"Portal"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "Epigenome project portal site",
"prefix": "NBDC01496",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Epigenetics",
"Health/Disease"
]
},
"nbdc01498": {
"description": "This site is a portal site about databases of sensory systems, brains, and behaviour of invertebrates, especially insects. The databases in this site contain photographs and movies, data acquisition equipment and other instrumentation, software, material for eduction, and bibliography.",
"homepage": "https://invbrain.neuroinf.jp/modules/htmldocs/IVBPF/Database/ivbpf.html?ml_lang=en",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents",
"Portal"
],
"maintainer": "RIKEN CBS (RIKEN Center for Brain Science)",
"name": "Database of Sensors, Brains, and Behaviors in Invertebrates",
"prefix": "NBDC01498",
"status": "Active",
"target_keywords": [
"Organism",
"Cell/Organelle"
]
},
"nbdc01501": {
"alt_name": "Galapagos Islands Image Database",
"description": "Galapagos Islands Image Database is a collection of photographic images about Galapagos Islands. It contains about 1,300 photographic images that Shuzo Ito (also spelt as Syuzo Itow) took in 16 field investigations of plants and vegetation in the Galapagos archipelago over 38 years since 1964. It also contains images of birds, other animals or cultural landscapes. This database allows to search by island and year, or keywords.",
"homepage": "http://gallery.lb.nagasaki-u.ac.jp/galapagos/index.html",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie",
"Bibliography/Documents",
"Taxonomy"
],
"maintainer": "Nagasaki University Library",
"name": "Galapagos Islands featuring the transition of plant life",
"prefix": "NBDC01501",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01502": {
"description": "Zoological Collection @ Stazione Zoologica 'Anton Dohrn' di Napoli (SZN) is a database about zoological collections owned by the Stazione Zoologica Anton Dohrn in Naples since 1910. It contains 4,373 VR object movies, 18,212 static images and 7,771 label information (about 2,722 species). It also contains 38 (total 8,406 pages) digitized documents, in which taxonomical, ecological and phylogenical information have been stored by their successive curators. Users are able to browse data by image lists or a taxon index.",
"homepage": "http://szn.i.hosei.ac.jp/HTML/index.php",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie",
"Bibliography/Documents",
"Taxonomy"
],
"maintainer": "Hosei Science Center, Italian-Japanese Biological Society and Stazione Zoologica di Napoli",
"name": "Zoological Collection Database @ Stazione Zoologica 'Anton Dohrn' di Napoli",
"prefix": "NBDC01502",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01503": {
"description": "TRP is a portal collecting databases and analysis tools related to transcriptional regulation research and includes brief descriptions about the databases or tools. This database allows searches by keywords or browsing by category, species and alphabetical order.",
"homepage": "http://www.abren.net/tfportal/new/",
"information_keywords": [
"Bibliography/Documents",
"Portal"
],
"maintainer": "Kyushu Institute of Technology",
"name": "Transcriptional Regulation Portal",
"prefix": "NBDC01503",
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01506": {
"description": "S. cerevisiae OriDB is a database providing a catalogue of confirmed and predicted DNA replication origin sites in fission yeast (Saccharomyces cerevisiae). Each record contains the following information: genomic location and chromosome context of the origin site; time of origin replication; and phylogenetic conservation of sequence elements.",
"fairsharing": "biodbcore-000080",
"homepage": "http://cerevisiae.oridb.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "OriDB.org",
"name": "S. cerevisiae OriDB",
"prefix": "NBDC01506",
"pubmeds": [
"17065467",
"22121216"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01507": {
"description": "S. pombe OriDB is a database providing a catalogue of confirmed and predicted DNA replication origin sites in budding yeast (S. pombe). Each record contains the following information: genomic location and chromosome context of the origin site; and time of origin replication.",
"homepage": "http://pombe.oridb.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "OriDB.org",
"name": "S. pombe OriDB",
"prefix": "NBDC01507",
"pubmeds": [
"17065467",
"22121216"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01508": {
"description": "The Integrative Disease Omics Database has been constructed through a project named \"Comprehensive exploration of drug targets based on integrative disease multi-omics analyses\" funded by National Institute of Biomedical Innovation.\nThe research team, which consists of six National Highly-Specialized Medical Research Centers (National Centers) and other research institutes, has collected highly qualified clinical samples with detailed clinical information and subjected them to multi-omics analyses (genomics, epigenomics, transcriptomics, proteomics, and metabolomics). In this database, the research team has released some data after careful consideration of patients' privacy and the ethical, legal and social implications (ELSI). Target diseases are: epilepsy, cancers (lung, kidney, breast, gastric), adiposity, non-alcoholic steatohepatitis, dilated cardiomyopathy, aortic aneurysm, allergic disease, childhood leukemia, Alzheimer's disease, and spinal canal stenosis.",
"homepage": "https://gemdbj.ncc.go.jp/omics/index_en.html",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "National Cancer Center",
"name": "Integrative Disease Omics Database (iDOx DB)",
"prefix": "NBDC01508",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Epigenetics",
"RNA",
"Protein",
"Health/Disease"
]
},
"nbdc01510": {
"alt_name": "A portal of phenotype data analyzed in Japan",
"description": "J-phenome is a portal for phenotype databases of model organisms, in cooperation with various Japanese projects to reveal the relation between phenotypes and gene functions. It contains phenotype data standardized across species using RDF, and is open to the public in the biomedical studies and innovations. This database was developed as a project of Database Integration Coordination Program in NBDC.",
"homepage": "http://jphenome.info/en/",
"information_keywords": [
"Phenotype",
"Bioresource",
"Image/Movie",
"Bibliography/Documents",
"Portal"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "J-phenome",
"prefix": "NBDC01510",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Organism"
]
},
"nbdc01512": {
"description": "Echinobase is a comparative genomics platform for the echinoderm clade. It contains information on genomes of Strongylocentrotus purpuratus, Lytechinus variegatus, Patiria miniata, Parastichopus parvamensis and Ophiothrix spiculata. It also contains transcriptomes for these and other echinoderms. This database allows to browsing or searching using JBrowse (Genome Browser), BLAST tools, BAC Table, etc.",
"homepage": "https://www.echinobase.org/entry/",
"information_keywords": [
"Sequence",
"Expression",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Center for Computational Regulatory Genomics, Beckman Institute",
"name": "Echinobase",
"prefix": "NBDC01512",
"pubmeds": [
"29761464"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc01513": {
"alt_name": "WCPDB - Thermus thermophilus HB8 Whole Cell Project Database -",
"description": "WCPDB is a database of functional proteins from an extremely thermophilic bacterium, Thermus thermophilus HB8. The database contains information derived from structural, functional, genomic and biological analyses.",
"homepage": "http://www.tanpaku.org/ThermusDB/index.html",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"3D structure"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research) Harima Institute",
"name": "WCPDB",
"prefix": "NBDC01513",
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01514": {
"description": "ClinVar is a freely available archive describing relationships between medically important variants and phenotypes. Submissions report human variation, interpretations of the relationship of that variation to human health, and the evidence supporting each interpretation. ClinVar is tightly coupled with dbSNP and dbVar, which maintain information about locations of variations on human assemblies, and also based on the phenotypic descriptions maintained in MedGen (http://www.ncbi.nlm.nih.gov/medgen). Each record contains the submitter, the variation and the phenotype. Furthermore, to facilitate evaluation of the medical importance of each variant, ClinVar aggregates submissions with the same variation/phenotype combination, adds value from other NCBI databases, and reports if there are conflicting clinical interpretations. Data in ClinVar are available in multiple formats, including html, download as XML, VCF or tab-delimited subsets.",
"fairsharing": "biodbcore-000739",
"homepage": "http://www.ncbi.nlm.nih.gov/clinvar/",
"information_keywords": [
"Phenotype",
"Bibliography/Documents",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "ClinVar",
"prefix": "NBDC01514",
"pubmeds": [
"24234437"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc01515": {
"alt_name": "RCSB PDB Molecule of the Month",
"description": "The RCSB PDB Molecule of the Month is a database of short accounts on selected molecules from the Protein Data Bank by David S. Goodsell (The Scripps Research Institute and the RCSB PDB). Each record includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details.",
"homepage": "http://pdb101.rcsb.org/motm/",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents",
"3D structure"
],
"maintainer": "RCSB PDB",
"name": "Molecule of the Month Archive",
"prefix": "NBDC01515",
"pubmeds": [
"25942442"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01517": {
"alt_name": "Genome-based Endogenous Viral Element Database",
"description": "gEVE database provides comprehensive datasets of sequences, genomic loci and functional annotations of endogenous viral elements (EVE), including endogenous retroviruses (ERV) among mammalian genomes. It contains datasets about 19 species, including humans and annotation lists of EVE sequences for each genome, with tables or sequences downloadable in CSV or FASTA format, respectively.",
"homepage": "http://geve.med.u-tokai.ac.jp",
"information_keywords": [
"Sequence"
],
"maintainer": "Tokai University School of Medicine",
"name": "gEVE database",
"prefix": "NBDC01517",
"pubmeds": [
"23335121",
"23864631",
"22674983"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01518": {
"alt_name": "Japanese Multi Omics Reference Panel",
"description": "jMorp is a database of metabolome and proteome data in plasma obtained from about 500 healthy volunteers in Tohoku University Tohoku Medical Megabank Organization (ToMMo). It contains metabolome data measured by proton NMR and LC-MS, and proteome data obtained by nanoLC-MS. This database allows browsing using 3 categories of analysis: Metabolites [NMR], Metabolites [MS], Proteins and search by keywords.",
"homepage": "https://jmorp.megabank.tohoku.ac.jp",
"maintainer": "Tohoku Medical Megabank Organization,Tohoku University",
"name": "jMorp",
"prefix": "NBDC01518",
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease",
"Metabolite"
]
},
"nbdc01519": {
"alt_name": "ARabidopsis Tiling-Array-based Detection of Exons version 2",
"description": "ARTADE2DB is a database that integrates not only the information predicted by Dynamic-Structure-based Dynamic Expression (DSDE) analysis, but also annotations and other functional information, such as phenotypes and literature citations, and is expected to contribute to the study of the functional genomics of A. thaliana.",
"homepage": "https://metadb.riken.jp/metadb/db/SciNetS_ria227i",
"information_keywords": [
"Expression"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "ARTADE2 predicted gene model database",
"prefix": "NBDC01519",
"pubmeds": [
"21227933"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01520": {
"alt_name": "Spectral Database for Organic Compounds",
"description": "The SDBS database consists of of sensory characteristics of vision, hearing, and touch measured by National Institute of Advanced Industrial Science and Technology. To allow searches for conditions such as age and types of disability, target people with disabilities and/or older people, totaling more than 3,000, were subjected to measurement. Their characteristics data were adopted as Japanese Industrial Standards (JISs) \"Guidelines for older persons and persons with disabilities\".",
"homepage": "http://sdbs.db.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi",
"information_keywords": [
"Chemical structure"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "SDBS",
"prefix": "NBDC01520",
"status": "Inactive",
"target_keywords": [
"Chemical compound"
]
},
"nbdc01521": {
"description": "This is a database collecting sensory characteristics of vision, hearing, and touch measured by National Institute of Advanced Industrial Science and Technology. To allow searches for conditions such as age and types of disability, target people with disabilities and/or older people, totaling more than 3,000, were subjected to measurement. Their characteristics data were adopted as Japanese Industrial Standards (JISs) \"Guidelines for older persons and persons with disabilities\".",
"homepage": "http://scdb.db.aist.go.jp/?lng=en",
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "Database of sensory characteristics of older persons and persons with disabilities",
"prefix": "NBDC01521",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01522": {
"description": "Digital Atlas of Actinomycetes 2 is a collection of micrographs and annotations about Actinomycetes. Data are collected from the 'Atlas of Actinomycetes' (Asakura Publishing Co., Tokyo, Japan; 1997) published by the Society for Actinomycetes Japan. This database allows browsing using section, taxonomy, genus and metabolite.",
"homepage": "http://www.actino.jp/DigitalAtlas/",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Society for Actinomycetes Japan",
"name": "Digital Atlas of Actinomycetes Ver. 2",
"prefix": "NBDC01522",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc01523": {
"alt_name": "RIKEN Brachypodium FLcDNA database",
"description": "RBFL BD is a comprehensive collection of full-length cDNAs from Brachypodium distachyon. It provides gene structural annotations of Brachypodium genes based on full-length cDNA sequences, in comparison with the latest publicly available annotations and allows searches using BLAST or keywords. Additional information on gene function, GO terms, homologous DNA sequences and the related amino acid sequence of each cDNA sequence is given, as well as the results of a search for homologous sequences in the genomes of rice and sorghum.",
"homepage": "http://brachy.bmep.riken.jp/ver.1/index.pl",
"information_keywords": [
"Sequence"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "RBFL DB",
"prefix": "NBDC01523",
"pubmeds": [
"24130698"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01524": {
"description": "SKIP is operated by Keio University of School of Medicine as an embodiment of the Human Stem Cells Informatization Project of the Ministry of Health, Labour and Welfare, Japan.\n\nSKIP aims to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine using stem cells and enhance social understanding by providing information on stem cells.",
"homepage": "https://skip.stemcellinformatics.org/SKIPSearch/search?lang=en",
"information_keywords": [
"Bioresource"
],
"maintainer": "Keio University School of Medicine",
"name": "SKIP Stemcell DATABASE",
"prefix": "NBDC01524",
"status": "Active",
"target_keywords": [
"Health/Disease",
"Cell/Organelle"
]
},
"nbdc01525": {
"description": "UniCarbKB is a knowledge database of glycan structures of glycoproteins. It provides comprehensive information concerning glycan structures and published glycoprotein information, including global and site-specific attachment information. \nThis database mainly searches records from three databases:\n(1) GlycosuiteDB, a glycan structure database;\n(2) EUROCarbDB, an informatic standards database;\n(3) GlycoBase, which contains elution positions (expressed as glucose unit values) for more than 650 2AB-labeled N-linked and O-linked glycan structures determined by a combination of HPLC, UPLC, exoglycosidase sequencing and mass spectrometry (MALDI-MS, ESI-MS, ESI-MS/MS, LC-MS, LC-ESI-MS/MS).\nThis database allows searches by names of taxonomy, tissue, protein name, protein accession or composition.",
"fairsharing": "biodbcore-000692",
"homepage": "http://www.unicarbkb.org",
"information_keywords": [
"Chemical structure"
],
"maintainer": "Macquarie University",
"name": "UniCarbKB",
"prefix": "NBDC01525",
"pubmeds": [
"24234447"
],
"status": "Active",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc01529": {
"description": "BRACHYPEDIA is a photo library about growth stages of Brachypodium distachyon. Each entry contains photographs and information such as Zadoks Decimal Code, numbers of leaves, tillers and node, or growth days.",
"homepage": "http://brachypedia.bmep.riken.jp/wiki/index.php/Main_Page",
"information_keywords": [
"Image/Movie"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "BRACHYPEDIA",
"prefix": "NBDC01529",
"pubmeds": [
"26156770"
],
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc01530": {
"alt_name": "Japan Chemical Substance Dictionary Web",
"description": "NikkajiWeb is a search service of the \"Japan Chemical Substance Dictionary (Nikkaji)\", an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST). It contains information about organic compounds and their mixtures such as Japanese name, English name, law regulation number, CAS registry number, chemical structure information, etc. This database allows searches with \"Advanced Textual Search\" or \"Chemical Structure Search\".",
"homepage": "http://doi.org/10.15079/NIKKAJI",
"information_keywords": [
"Chemical structure"
],
"maintainer": "JST (Japan Science and Technology Agency)",
"name": "NikkajiWeb",
"prefix": "NBDC01530",
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc01532": {
"alt_name": "Integrative Japanese Genome Variation Database",
"description": "iJGVD is a database about genome variation in the Japanese population. This database provides data of genomic variations obtained by whole-genome sequencing of Japanese individuals participating in the genome cohort study by ToMMo (Tohoku University Tohoku Medical Megabank Organization). It contains data on single nucleotide variations (SNVs) and their frequencies among the 1070 Japanese individuals from the cohort. SNVs and their information, such as allele frequency, can be retrieved with a genome browser that provides an intuitive view of SNV information, along with the reference human genome sequence using hg19/GRCh37 coordinate system.",
"homepage": "https://ijgvd.megabank.tohoku.ac.jp",
"information_keywords": [
"Sequence"
],
"maintainer": "Tohoku Medical Megabank Organization,Tohoku University",
"name": "iJGVD",
"prefix": "NBDC01532",
"pubmeds": [
"26292667"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc01533": {
"alt_name": "Caenorhabditis elegans GlycoGene DataBase",
"description": "CGGDB is a database of glycogenes of C. elegans. It consists of gene list, Expression and Phenotype of RNAi line and provides additional information on the roles of glycoconjugates in cell cycle progression mechanisms of germline and embryonic cells.",
"homepage": "https://jcggdb.jp/cggdb/",
"information_keywords": [
"Phenotype",
"Sequence",
"Expression"
],
"maintainer": "Kyushu University||AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "CGGDB",
"prefix": "NBDC01533",
"pubmeds": [
"25091817"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Carbohydrate"
]
},
"nbdc01534": {
"description": "GlycoNMR is a database of NMR analysis of glycan. Each record contains information about structure, glycan type, chemical name, coupling constant, chemical shift, etc. It allows searches using keywords, or browsing.",
"homepage": "https://glycoinfolab.jp/GlycoNMR/",
"information_keywords": [
"Method",
"3D structure",
"Chemical structure"
],
"maintainer": "The Noguchi Institute||RIKEN (The Institute of Physical and Chemical Research)||AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "GlycoNMR Database",
"prefix": "NBDC01534",
"status": "Inactive",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc01535": {
"description": "GlyTouCan is an international repository of glycan structures. This database contains uncurated glycan structures ranging in resolution from monosaccharide composition to fully defined structures, as long as there are no inconsistencies in the structure. The database allows users to search by text, graphic input or motif, and browse using motif-list or glycan-list.",
"homepage": "http://glytoucan.org/",
"information_keywords": [
"Method",
"Chemical structure",
"Repository"
],
"maintainer": "GlyTouCan Project Team",
"name": "GlyTouCan",
"prefix": "NBDC01535",
"pubmeds": [
"26476458",
"28922742"
],
"status": "Active",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc01536": {
"alt_name": "Microbial Culture Collection Vocabulary",
"description": "MCCV collects structured controlled vocabulary for describing meta information of microbial culture collection maintained in biological research centers.",
"homepage": "http://bioportal.bioontology.org/ontologies/MCCV",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "NCBO (The National Center for Biomedical Ontology)",
"name": "MCCV",
"prefix": "NBDC01536",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01537": {
"description": "PDB/RDF is a collection of PDB data in the Resource Description Framework (RDF) format. Users can search RDF entries by specifying PDB ID, properties (predicates) or keywords, and can see the RDF/XML files rendered in HTML. The ontology of wwPDB/RDF is semi-automatically generated. All RDF files are downloadable.",
"homepage": "http://rdf.wwpdb.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "wwPDB/RDF",
"prefix": "NBDC01537",
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Protein"
]
},
"nbdc01538": {
"description": "MBGD SPARQL Search is a search tool for the Microbial Genome Database for Comparative Analysis (MBGD) in the form of Resource Description Framework (RDF) made available through the SPARQL endpoint. MBGD RDF is based on the Ortholog Ontology (OrthO), a compact ontology for formalizing the structure of the ortholog information in the Semantic Web.",
"homepage": "http://mbgd.genome.ad.jp/sparql/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Sequence",
"Classification"
],
"maintainer": "National Institute for Basic Biology",
"name": "MBGD SPARQL Search",
"prefix": "NBDC01538",
"pubmeds": [
"25875762"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01539": {
"alt_name": "Environmental Specimen Bank",
"description": "es-BANK is a collection of environmental specimens collected from all over the world and stored at Ehime University Center for Marine Environmental Studies. They are provided to researchers for improving the scope of monitoring studies on environmental toxic substances.",
"homepage": "http://esbank-ehime.com/dnn/",
"information_keywords": [
"Bioresource",
"Environment"
],
"maintainer": "Ehime University Center for Marine Environmental Studies",
"name": "es-BANK",
"prefix": "NBDC01539",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01540": {
"alt_name": "VarySysDB Disease Edition",
"description": "VaDE is a database of human genome polymorphisms involved in traits such as various disease susceptibilities or drug responses, collected from a number of academic papers. This database provides a wealth of information about these genome polymorphisms, such as odds ratio, Ξ² value, sample population, p value and so on. Moreover, it evaluates reproducibility of associations in multiple independent studies.",
"homepage": "http://bmi-tokai.jp/VaDE/#en",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Tokai University School of Medicine",
"name": "VaDE",
"prefix": "NBDC01540",
"status": "Active",
"target_keywords": [
"Genetic variation",
"Health/Disease"
]
},
"nbdc01541": {
"description": "This is a portal site that integrates life science databases in RDF format. The portal is a data portal developed and operated by DBCLS with the aim of comprehensively collecting RDF datasets provided by a diverse range of life science databases and supported by Life Science Database Integration Project (the Project) of Japan Science and Technology Agency. The DBCLS formulated guidelines for the construction of high quality RDF data (https://github.com/dbcls/rdfizing-db-guidelines), and publishes only those data that meet a minimum level of quality for a highly reliable database. Users can browse the summaries of the data for the various databases. Data downloads and SPARQL (standard query language for RDF format data) searches are also possible.",
"fairsharing": "biodbcore-000803",
"homepage": "https://rdfportal.org/",
"information_keywords": [
"Portal",
"Repository"
],
"maintainer": "DBCLS(Database Center for Life Science)",
"name": "RDF Portal",
"prefix": "NBDC01541",
"status": "Active"
},
"nbdc01542": {
"description": "Pheno-Pub provides information of mouse phenotyping analysis. It contains results of the mouse phenotyping analysis operated based on \"Standard Operating Procedures; SOPs\"by Japan Mouse Clinic.",
"homepage": "http://ja.brc.riken.jp/lab/jmc/mouse_clinic/m-strain/phenopub_top.html",
"information_keywords": [
"Phenotype"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "Pheno-Pub",
"prefix": "NBDC01542",
"pubmeds": [
"24220852"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc01543": {
"alt_name": "a database for international sharing of mouse phenotyping protocols",
"description": "SDOP-DB is a comparative standardised-protocol database for the integration and sharing of mouse phenotyping protocols. The protocols are described using SDOP data fomat which enables direct and detailed comparison of procedural parameters.",
"homepage": "http://www.brc.riken.go.jp/lab/bpmp/SDOP/index.html",
"information_keywords": [
"Phenotype",
"Method",
"Repository"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "SDOP-DB",
"prefix": "NBDC01543",
"pubmeds": [
"20194625"
],
"status": "Active"
},
"nbdc01544": {
"description": "This Plant gene Database contains plant gene information focusing on the secondary metabolism and the transport mechanism of plants. The data was obtained by analyzing EST information from S. flavescensplant and L. erythrorhizon cells which were cultured in the selected cell-suspension culture systems where photosynthetic genes and those for morphogenesis are strongly suppressed. The database provides keyword search and BLAST search services useful for homology-based cloning of genes, identification of conserved amino acid domains and motif and phylogenetic analyses.",
"homepage": "http://database.rish.kyoto-u.ac.jp/arch/plantdb2/index_e.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Research Institute for Sustainable Humanosphere, Kyoto University",
"name": "EST Database for Useful Plants",
"prefix": "NBDC01544",
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01545": {
"description": "This database is a collection of section images from the brain and spinal cord of the common marmoset at age 0. It additionally contains images from Petaurus breviceps, Macaca mulatta and Macaca fuscata. Users need to register for access to full content.",
"homepage": "https://neuropathology.jp/marmoset_login/",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Tokyo Metropolitan Institute of Medical Science",
"name": "Digital Brain Atlas of the Common Marmoset (Callithrix jacchus)",
"prefix": "NBDC01545",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01546": {
"alt_name": "Mouse Multiple tissue Metabolome Database",
"description": "MMMDB is a freely available database containing a collection of metabolites measured from multiple tissues from single mice. It provides not only quantified concentration but also processed raw data such as electropherogram, mass spectrometry, and annotation (such as isotope and fragment). Datasets are collected from cerebra, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, and plasma, using a single instrument, not integrated from literature. Non-targeted analyses were performed by capillary electropherograms time-of-flight mass spectrometry (CE-TOFMS).",
"homepage": "http://mmmdb.iab.keio.ac.jp",
"maintainer": "Keio University",
"name": "MMMDB",
"prefix": "NBDC01546",
"pubmeds": [
"14582645",
"16608839"
],
"status": "Inactive",
"target_keywords": [
"Organism",
"Metabolite"
]
},
"nbdc01547": {
"description": "Pt_spiderBASE is a database for ESTs of the spider Parasteatoda tepidariorum, a model arthropod to study developmental biology, comparative embryology and evolutionary development.",
"homepage": "http://www.e-celldev.jp/pt_spiderbase/",
"information_keywords": [
"Sequence"
],
"maintainer": "JT Biohistory Research Hall",
"name": "Pt_spiderBASE",
"prefix": "NBDC01547",
"pubmeds": [
"17507394",
"20332148",
"21988916"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01548": {
"alt_name": "Database of Captive Primate Collection",
"description": "CaPriCo is a database of specimens in the captive Primate collection at Japan Monkey Centre. It contains information of skeletal specimens, including photographs.",
"homepage": "http://www.j-monkey.jp/caprico/index_e.php",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Japan Monkey Centre",
"name": "CaPriCo",
"prefix": "NBDC01548",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01549": {
"description": "Wood Diversity HSDB network is a collection of Wood Diversity databases maintained by universities in Japan.",
"homepage": "http://database.rish.kyoto-u.ac.jp/arch/bmi/index_e.html",
"information_keywords": [
"Image/Movie",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Research Institute for Sustainable Humanosphere, Kyoto University",
"name": "Wood Diversity HSDB network",
"prefix": "NBDC01549",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01552": {
"description": "E-Foram Stock is a database of planktonic foraminifera e-specimens (digital data), stored in the Tohoku university museum. It provides detailed information on real specimens corresponding to individual e-specimens. The e-Specimen is a virtual specimen system working on computers and can be viewed with 'Molcer', a freely downloadable software for PC provided by White Rabbit Corporation.",
"homepage": "http://webdb2.museum.tohoku.ac.jp/e-foram/index.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Tohoku University museum",
"name": "e-Foram Stock",
"prefix": "NBDC01552",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01554": {
"alt_name": "Open Teratoma Investigation",
"description": "OpenTein (Open Teratoma Investigation) is a database and repository for the digital images of stem cell-derived teratomas. It provides whole-slide images, which are searchable, zoomable, with annotations. Images are high-resolution and downloadable.",
"homepage": "http://opentein.hgc.jp/",
"information_keywords": [
"Image/Movie",
"Repository"
],
"maintainer": "The institute of medical science, The University of Tokyo",
"name": "OpenTein",
"prefix": "NBDC01554",
"pubmeds": [
"26496950"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc01555": {
"description": "The NIPH Clinical Trials Search is a portal site to cross-search the content of three national clinical research information registries in Japan: The University Hospital Medical Information Network Center (UMIN-CTR), The Japan Medical Association Center (JMACCT), The Japan Pharmaceutical Information Center (JAPIC). It also contains data of international clinical trials registry platform, ICTRP, in WHO, so users can also find clinical trials in other countries. The contents in this site are also accessible through the ICTRP.",
"homepage": "https://rctportal.niph.go.jp/en/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "National Institute of Public Health",
"name": "NIPH Clinical Trials Search",
"prefix": "NBDC01555",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01557": {
"alt_name": "Rice Expression Database II INAHO",
"description": "The original site (http: //red.dna.affrc.go.jp/INAHO/) has been closed. The RED II INAHO is available from LSDB archive.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/redii-inaho/desc.html",
"information_keywords": [
"Expression"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "RED II INAHO (Archive)",
"prefix": "NBDC01557",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01558": {
"description": "ChIP-Atlas is an integrative database for visualizing and exploiting public ChIP-seq data. This database covers almost all public ChIP-seq data submitted to the SRA (Sequence Read Archives) in NCBI, DDBJ or ENA. ChIP-Atlas is composed of 4 main features;\n1) Peak Browser\nIt graphically visualizes protein bindings on given genomic loci with genome browser (IGV).\n2) Target genes\nIt predicts target genes bound by given transcription factors.\n3) Colocalization\nIt predicts partner proteins colocalizing with given transcription factors.\n4) Enrichment Analysis\nIt predicts proteins bound to given genomic loci and genes.",
"homepage": "https://chip-atlas.org/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Kyushu University Graduate School of Medical Sciences||DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "ChIP-Atlas",
"prefix": "NBDC01558",
"pubmeds": [
"30413482"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc01560": {
"alt_name": "Protein Co-Migration Database for photosynthetic organisms",
"description": "PCoM is a database of protein complexes for photosynthetic organisms. This database stores the data obtained by LC-MS/MS analysis of the protein complexes after Blue-Native Page. Each part of chloroplast from Arabidopsis thaliana and whole cells of photosynthetic micro-organisms were used for the analysis.",
"homepage": "http://pcomdb.lowtem.hokudai.ac.jp/proteins/top",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Hokkaido University",
"name": "PCoM",
"prefix": "NBDC01560",
"pubmeds": [
"23667806"
],
"status": "Active",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc01561": {
"alt_name": "Census of Marine Zooplankton-Asia Database",
"homepage": "http://miwe9.aori.u-tokyo.ac.jp/db/index.html",
"information_keywords": [
"Environment",
"Geographic Distribution",
"Bibliography/Documents"
],
"maintainer": "Atmosphere and Ocean Research Institute, University of Tokyo",
"name": "CMarZ-Asia Database",
"prefix": "NBDC01561",
"status": "Inactive",
"target_keywords": [
"Organism",
"Genome/Gene"
]
},
"nbdc01562": {
"description": "TOMATOMICS is an integrated omics database of Solanum lycopersicum. It contains sequences of all Solanum lycopersicum ESTs, Micro-Tom full-length cDNAs, ITAG2.4 gene models, and SNPs. Sequences are assigned annotation based on the manual curation of published papers and the BLAST search. Users can search genes by keywords, browse data with a genome browser, and use BLAST. It also contains information about gene expression and coexpression.",
"homepage": "http://bioinf.mind.meiji.ac.jp/tomatomics/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Bioinformatics Laboratory of Meiji University",
"name": "TOMATOMICS",
"prefix": "NBDC01562",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation"
]
},
"nbdc01566": {
"alt_name": "Japanese DNA Barcode Database",
"description": "JBOL-DB is a database of voucher specimen combined with their sequences for DNA barcoding. It contains information about specimen with photographs and DNA sequences.",
"homepage": "http://db.jboli.org",
"information_keywords": [
"Sequence",
"Image/Movie",
"Taxonomy"
],
"maintainer": "Japanese DNA Barcode Database Committee",
"name": "JBOL-DB",
"prefix": "NBDC01566",
"status": "Inactive",
"target_keywords": [
"DNA",
"Organism"
]
},
"nbdc01567": {
"alt_name": "Virtual Brain with 3D-IDM Database",
"description": "ViBrism Database is a 3D-map database of endogenous gene expression in a virtual whole mouse brain. The data are produced by an original mapping framework Transcriptome Tomography. It contains over 36, 000 expression maps of the adult mouse brain (C57BL6/J 8-wk male). Users can search with gene symbols (\"Search by gene Name\") or expression similarity (\"Similarly Expressed gene Search\"), and browse the data on 2D/3D expression maps. Data files of the maps are downloadable.",
"homepage": "http://vibrism.neuroinf.jp",
"information_keywords": [
"Expression",
"Localization",
"Image/Movie"
],
"maintainer": "ViBrism Database Committee",
"name": "ViBrism Database",
"prefix": "NBDC01567",
"pubmeds": [
"23028969"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01568": {
"alt_name": "Navigating a Potential Metabolic Pathway",
"description": "M-path DB is a database of metabolic pathways calculated sets of compounds from the PubChem and ChEBI databases. It contains putative metabolic pathways for a series of chemical species, and produces networks including some interesting pathways.",
"homepage": "http://bp.scitec.kobe-u.ac.jp/m-path/db/",
"information_keywords": [
"Interaction/Pathway",
"Chemical structure"
],
"maintainer": "Kobe University",
"name": "M-path",
"prefix": "NBDC01568",
"pubmeds": [
"25398612"
],
"status": "Inactive",
"target_keywords": [
"Metabolite"
]
},
"nbdc01569": {
"description": "This database provides paleontology collections in the University Museum, the University of Tokyo. Each data contains photographs and references about specimen. This database also contains archival gallery of photoplates.",
"homepage": "http://umdb.um.u-tokyo.ac.jp/DKoseibu/en/index.html",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "The University Museum, The University of Tokyo",
"name": "Paleontology Collections Database",
"prefix": "NBDC01569",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01570": {
"description": "This site is an online catalog of zoological collections of The University Museum, The University of Tokyo (UMUT).",
"homepage": "http://umdb.um.u-tokyo.ac.jp/DDoubutu/TDoubutu.php",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "The University Museum, The University of Tokyo",
"name": "Tokyo University Museum, The University of Tokyo Zoology",
"prefix": "NBDC01570",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01571": {
"alt_name": "The genome database for Marchantia polymorpha",
"description": "MarpolBase is a genome database for Marchantia polymorpha, which includes complete genome sequence (JGI Ver. 3.1). It consists of following tools and a database; \n1) Genome browser\n2) Gene Nomenclature database\n3) Analytical Tools (BLAST, cDNA mapping/alignment, sgRNA designing for the CRISPR/Cas9 system etc)\n4) Sequence retrieval utilities\nIt allows to download Marchantia genome resources.",
"homepage": "http://marchantia.info",
"information_keywords": [
"Sequence",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "National Institute of Genetics",
"name": "MarpolBase",
"prefix": "NBDC01571",
"pubmeds": [
"28985561"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01573": {
"description": "Fermented foods in Thailand are classified by ingredients and described with pictures. Scientific names of organisms and microorganisms, which constitute the fermented foods, are appeared.",
"homepage": "http://www.jircas.affrc.go.jp/DB/DB11/",
"maintainer": "JIRCAS (Japan International Research Center for Agricultural Sciences)",
"name": "The traditional fermented foods of Thiland",
"prefix": "NBDC01573",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01574": {
"description": "This is a Web based pictorial database for common underwater plants in Thailand. \nThe international collaborative research group between Kasetsart University (KU), King Mongkut's Institute of Technology Ladkrabang (KMITL) and the Japan International Research Center for Agricultural Sciences (JIRCAS) contributed to collection of these data.",
"homepage": "https://www.jircas.affrc.go.jp/project/aquacult_Thailand/index.html",
"information_keywords": [
"Image/Movie",
"Environment"
],
"maintainer": "JIRCAS (Japan International Research Center for Agricultural Sciences)",
"name": "Common underwater plants in coastal areas of Thailand",
"prefix": "NBDC01574",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01577": {
"alt_name": "Plant Omics Data Center",
"description": "This database is a next-generation sequencing (NGS)-derived gene expression network (GEN) repository for a broad range of plant species. It contains transcript information (transcript variant, similarly expressed genes, transcription factor & cis-element, predicted ortholog and paralogs, and gene expression network, etc.), expression profiles of various tissues and various treated samples, and knowledge-based functional descriptions. Users can search those information by keyword search and blast search.",
"homepage": "http://plantomics.mind.meiji.ac.jp/podc/",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Meiji University",
"name": "PODC",
"prefix": "NBDC01577",
"pubmeds": [
"25505034"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01578": {
"description": "This is the ICGC, International Cancer Genome Consortium, Data Portal, which provides tools for visualizing, querying and downloading ICGC data released quarterly by the consortium's member projects. It includes various types of data, such as genes, donors, mutations, projects, genesets, files, compounds. Clinical Data are also included.",
"homepage": "https://dcc.icgc.org/",
"information_keywords": [
"Bibliography/Documents",
"Sequence"
],
"maintainer": "ICGC (International Cancer Genome Consortium)",
"name": "ICGC Data Portal",
"prefix": "NBDC01578",
"status": "Active",
"target_keywords": [
"Health/Disease",
"Genome/Gene"
]
},
"nbdc01580": {
"alt_name": "Human Brain Transcriptome",
"description": "HBT is a database of transcriptome data and associated metadata for the developing and adult human brain. It contains transcriptome data from experiments using the Affymetrix geneChip Human Exon 1.0 ST Arrays from over 1, 340 tissue samples obtained from both hemispheres of postmortem human brains. Samples are those from embryonic development to adulthood one, and are representative of both males and females from multiple ethnicities. Genome-wide genotyping data for 2.5 million markers (Illumina Human Omni 2.5-Quad Bead Chips) is available for all specimens upon request.",
"homepage": "http://hbatlas.org",
"information_keywords": [
"Expression"
],
"maintainer": "Yale University School of Medicine",
"name": "HBT",
"prefix": "NBDC01580",
"pubmeds": [
"24373884",
"22031440",
"19477152"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01581": {
"description": "This database is a sexualized planarian expressed sequence tag database. It contains sequence, classification, clustering, and annotation data about ESTs and clusters. Moreover, it provides results of EST microarray test.",
"homepage": "http://planarian.bio.keio.ac.jp/EST.html",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Keio University",
"name": "Planarian EST Database",
"prefix": "NBDC01581",
"pubmeds": [
"17409714"
],
"status": "Active",
"target_keywords": [
"cDNA/EST"
]
},
"nbdc01582": {
"alt_name": "Gene Signature DataBase",
"description": "geneSigDB is a database of fully traceable, standardized, annotated gene signatures which have been manually curated from published literatures. Data were collected from published articles which largely focused on gene expression in cancer, stem cells, immune cells, development and lung disease. Users can analyze geneSigDB gene signatures, or upload their own gene list and results can be viewed on a dynamic editable heatmap. All data can be downloaded in numerous formats including .gmt file format for gene set enrichment analysis or as a R/Bioconductor data file.",
"fairsharing": "biodbcore-000045",
"homepage": "http://genesigdb.org/genesigdb/",
"information_keywords": [
"Expression",
"Ontology/Terminology/Nomenclature",
"Bibliography/Documents"
],
"maintainer": "Dana-Farber Cancer Institute",
"name": "GeneSigDB",
"prefix": "NBDC01582",
"pubmeds": [
"22110038"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc01583": {
"alt_name": "Center for iPS Cell Research and Application (CiRA)",
"description": "CiRA Research Activities is a portal site for introducing research activities of CiRA, Center for iPS Cell Research and Application of Kyoto University. It contains bioresource information (Material Distribution page) related to iPS cells, and protocols of using iPS cells, and so on.",
"homepage": "http://www.cira.kyoto-u.ac.jp/e/research/",
"information_keywords": [
"Bioresource",
"Portal"
],
"maintainer": "Center for iPS Cell Research and Application, Kyoto University",
"name": "CiRA Research Activities",
"prefix": "NBDC01583",
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc01584": {
"homepage": "https://github.com/nhcollier/biocaster-ontology/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Nigel Collier",
"name": "biocaster-ontology",
"prefix": "NBDC01584",
"pubmeds": [
"18922806"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01585": {
"description": "This site provides a comprehensive resource of microRNA target predictions and expression profiles. \nThe target predictions of microRNAs are performed by a development of the miRanda algorithm, and microRNA expression profiles are derived from a comprehensive sequencing project of a large set of mammalian tissues and cell lines of normal and disease origin. \nUsers are able to explore (i) the set of genes that are potentially regulated by a particular microRNA, (ii) the implied cooperativity of multiple microRNAs on a particular mRNA and (iii) microRNA expression profiles in various tissues, with an improved graphical interface.\nThis resource provides functional information about the growing number of microRNAs, the interaction of microRNAs and those targets in many species, and novel discoveries in microRNA gene regulation.",
"homepage": "http://www.microrna.org/microrna/home.do",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "MSKCC (Memorial Sloan-Kettering Cancer Center)",
"name": "microRNA.org",
"prefix": "NBDC01585",
"pubmeds": [
"18158296"
],
"status": "Inactive",
"target_keywords": [
"RNA",
"Genome/Gene"
]
},
"nbdc01586": {
"description": "This is a search tool for compounds in RIKEN Natural products depository (RIKEN NPdepo). Each entry contains Compound name, CAS No., molecular weight, structure, InChI key, biological activity, sourse organisms, etc.. This database allows to search using compound ID, compound name, InChIKey or chemical structure.",
"homepage": "http://www.cbrg.riken.jp/npedia/?LANG=en",
"information_keywords": [
"Chemical structure"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "NPEdia Compounds Search",
"prefix": "NBDC01586",
"status": "Active",
"target_keywords": [
"Metabolite",
"Chemical compound"
]
},
"nbdc01587": {
"description": "This site provides gene expression profiles and related analytical tools to evaluate potential of chemical compounds as anticancer agents. The anticancer drug gene expression database contains information of gene expression profiles obtained from Human colon adenocarcinoma HT-29 cells which treated with anticancer compounds.",
"homepage": "http://scads.jfcr.or.jp/db/cs/",
"information_keywords": [
"Expression"
],
"maintainer": "SCADS (Screening Committee of Anticancer Drugs)",
"name": "Comprehensive transcriptomic analysis of molecularly targeted drugs in cancer for target pathway evaluation",
"prefix": "NBDC01587",
"pubmeds": [
"23176546"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Drug",
"Health/Disease"
]
},
"nbdc01588": {
"alt_name": "Human-Earth Microbes and Microbiomes",
"description": "HEMM is a database about microbial genomes and virtual metagenomes reconstructed from 16S rRNAs in microbial communities in every biosphere on a human body and various environment. It contains samples of 16S rRNA sequences which obtained from public databases, and the metagenomic contents virtually reconstructed from them. Users are able to observe functional and taxonomic distributions of metagenomes about a wide-range environments.",
"homepage": "http://hemm.org/",
"information_keywords": [
"Expression",
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Shujiro Okuda laboratory",
"name": "HEMM",
"prefix": "NBDC01588",
"pubmeds": [
"23149747"
],
"status": "Suspended",
"target_keywords": [
"Genome/Gene",
"RNA",
"Organism"
]
},
"nbdc01589": {
"alt_name": "mitochondrial tranfer RNA database",
"description": "mitotRNAdb is a database of mitochondrial tRNA genes. \nIt collects more than 30000 tRNA genes from metazoan mitochondrial RefSeq genomes. Users can search by DNA or RNA sequences, amino acid family, anticodon, references, Pubmed-ID of the reference, gene ID. In addition, searches concerning sequence or structure characteristics are possible. BLAST search is also available.",
"homepage": "http://mttrna.bioinf.uni-leipzig.de/mtDataOutput/",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Leipzig, University of Strasbourg",
"name": "mitotRNAdb",
"prefix": "NBDC01589",
"pubmeds": [
"18957446"
],
"status": "Inactive",
"target_keywords": [
"RNA",
"Genome/Gene",
"Organism"
]
},
"nbdc01591": {
"description": "This database provides information on a set of full-length, high quality human clones ORF (Open Reading Frame = the protein-coding sequence of genes) in the Gateway cloning system ready to use for recombinant protein expression. All clones are fully sequenced and annotated. Users are able to search this collection with term(s) and/or number range(s) and use the international distributor network to obtain clones of interest.",
"homepage": "http://www.orfeomecollaboration.org",
"information_keywords": [
"Sequence",
"Bioresource"
],
"maintainer": "ORFeome Collaboration",
"name": "ORFeome Collaboration",
"prefix": "NBDC01591",
"pubmeds": [
"26914201"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01594": {
"alt_name": "Japan ProteOme STandard Repository/Database",
"description": "This is a proteomic database named jPOST to integrate proteome information including post-translational modifications and absolute protein abundance, acquired by multiple projects and institutions. Currently, the jPOST repository part is open for researchers to deposit their proteome datasets, and the jPOST database part allows to search information about datasets and proteins (March, 2018).",
"fairsharing": "biodbcore-000941",
"homepage": "https://jpostdb.org",
"information_keywords": [
"Localization",
"Expression",
"Repository"
],
"maintainer": "jPOST project",
"name": "jPOST",
"prefix": "NBDC01594",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01595": {
"description": "This database is a collection of Repetitive DNA element sequence alignments, hidden Markov models (HMMs) and match lists for complete Eukaryotic genomes. It provides information about each model, and genome annotations for a collection of core genomes. Sequence alignments, profile HMMs, hit lists, and other underlying data are available for download.",
"fairsharing": "biodbcore-000165",
"homepage": "http://dfam.org",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Montana",
"name": "Dfam",
"prefix": "NBDC01595",
"pubmeds": [
"26612867",
"23203985"
],
"status": "Active",
"target_keywords": [
"DNA"
]
},
"nbdc01596": {
"description": "TreeFam is a database of phylogenetic trees inferred from animal genomes. It provides the following information about the TreeFam gene family:\n1) Summary page\nTextual background information on the TreeFam gene family\n2) Trees\nReconciled gene tree \n3) Alignment\nAn alignment of all homologous sequences in the TreeFam family\n4) Sequences\nInformation about sequences in the TreeFam family, including e-values, Pfam domains, sequence description, and the species name\n5) Species\nInteractive tree graphic displaying species distribution for the full alignment.",
"homepage": "http://www.treefam.org",
"information_keywords": [
"Sequence",
"Taxonomy",
"Classification"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "TreeFam",
"prefix": "NBDC01596",
"pubmeds": [
"16381935",
"18056084"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc01597": {
"description": "iPfam is a database about physical interactions of proteins that have a known structure reported in the Protein DataBank (PDB). It provides information about interactions between protein domains and protein-ligand interactions.",
"homepage": "http://ipfam.org",
"information_keywords": [
"3D structure",
"Interaction/Pathway"
],
"maintainer": "Howard Hughes Medical Institute",
"name": "iPfam",
"prefix": "NBDC01597",
"pubmeds": [
"24297255"
],
"status": "Closed",
"target_keywords": [
"Protein",
"Metabolite"
]
},
"nbdc01606": {
"description": "The Metabolite Ecology DB is a collection of information on the distribution of metabolites in various organisms. The database connects compounds, based on their IDs (KEGG) and names, with their distribution in the organism, as well as primary research articles describing the distribution. The database is searchable by compound ID (KEGG) or name and organism.",
"homepage": "http://www.knapsackfamily.com/MetaboliteEcology/top.jsp",
"information_keywords": [
"Chemical structure",
"Localization",
"Bibliography/Documents"
],
"maintainer": "Nara Institute of Science and Technology",
"name": "Metabolite Ecology DB",
"prefix": "NBDC01606",
"status": "Active",
"target_keywords": [
"Metabolite",
"Carbohydrate",
"Lipid",
"Chemical compound",
"Organism"
]
},
"nbdc01611": {
"description": "This site contains educational resources about PDBj. It is written to help a lay audience understand protein conformation.",
"homepage": "https://numon.pdbj.org/index.php?l=en",
"information_keywords": [
"3D structure",
"Image/Movie",
"Bibliography/Documents",
"Portal"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "PDBj numon",
"prefix": "NBDC01611",
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01615": {
"description": "KERO is a database that integrates single nucleotide variations, epigenomic data (histone modifications and methylation patterns of DNA) and transcriptomic information (expression levels and patterns of splicing) with human genomic information. This is a fellow site of DBTSS (http://integbio.jp/dbcatalog/en/record/nbdc00045), and the multi-omics data of cultured cells and model organisms are further connected in KERO.",
"homepage": "http://kero.hgc.jp",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "The University of Tokyo",
"name": "DBKERO",
"prefix": "NBDC01615",
"pubmeds": [
"25378318",
"24069199",
"21372179",
"19237398"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Epigenetics",
"RNA",
"Health/Disease",
"Cell/Organelle"
]
},
"nbdc01616": {
"description": "DBASS is a comprehensive repository of new exon boundaries that were induced by pathogenic mutations in human disease genes. This database consists of two databases, DBASS3 and DBASS5. They provide aberrant 5'- and 3'-splice sites that were activated either by mutations in the consensus sequences of natural exon-intron junctions (cryptic sites) or elsewhere ('de novo' sites). Data in DBASS3 and DBASS5 can be searched by disease phenotype, gene, mutation, location of aberrant splice sites in introns and exons and their distance from authentic counterparts, by bibliographic references and by the splice-site strength estimated with several prediction algorithms. The user is also able to retrieve reference sequences of both aberrant and authentic splice sites with the underlying mutation.",
"homepage": "http://www.dbass.org.uk",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Southampton",
"name": "DBASS",
"prefix": "NBDC01616",
"pubmeds": [
"20929868"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc01617": {
"alt_name": "Disease Annotated Chromatin Epigenetics Resource",
"description": "DAnCER is a database which integrates information on genes with chromatin modification (CM) function from five model organisms, including human. Currently integrated information on this database are gene functional annotations, Pfam domain architecture, protein interaction networks and associated human diseases. Additional supporting evidence includes orthology relationships across organisms, membership in protein complexes, and information on protein 3D structure. These data are available for 962 CM genes which are experimentally confirmed and manually curated and for over 5000 genes with predicted CM function on the basis of orthology and domain composition. DAnCER provides visual explorations of the integrated data and flexible query capabilities using a variety of data filters. Particularly, disease information and functional annotations are mapped onto the protein interaction networks, enabling the user to formulate new hypotheses on the function and disease associations of a given gene based on those of its interaction partners.",
"homepage": "http://wodaklab.org/dancer/",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "SickKids (The Hospital for Sick Children)",
"name": "DAnCER",
"prefix": "NBDC01617",
"pubmeds": [
"20876685"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Epigenetics",
"Health/Disease"
]
},
"nbdc01618": {
"description": "MicrosporidiaDB is a functional genomic database serving the microsporidia research communities. MicrosporidiaDB contains the genomes of Encephalitozoon cuniculi, E. intestinalis and E. bieneusi. Genomic scale data can be serched based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs, protein characteristics, phylogenetic relationships and functional data such as transcript (microarray and EST evidence) and protein expression data. This database belongs to the EuPathDB family of databases.",
"fairsharing": "biodbcore-000346",
"homepage": "https://microsporidiadb.org/micro/app",
"information_keywords": [
"Sequence",
"Expression",
"Ontology/Terminology/Nomenclature",
"Repository"
],
"maintainer": "EuPathDB Project Team",
"name": "MicrosporidiaDB",
"prefix": "NBDC01618",
"pubmeds": [
"20974635"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"DNA",
"Organism"
]
},
"nbdc01619": {
"description": "The RIKEN integrated database of mammals collects data from large-scale programs using mammals in RIKEN, such as FANTOM, ENU mutagenesis program and RIKEN Cerebellar Development Transcriptome Database (CDT-DB). In this database, original data are connected with public information such as genes and ontologies using the semantic-web technology.",
"homepage": "https://metadb.riken.jp/metadb/db/SciNetS_ria254i",
"information_keywords": [
"Taxonomy",
"Bibliography/Documents"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "The RIKEN integrated database of mammals",
"prefix": "NBDC01619",
"pubmeds": [
"21076152"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Cell/Organelle",
"Organism",
"Health/Disease"
]
},
"nbdc01620": {
"alt_name": "Compendium of Protein Lysine Modifications",
"description": "CPLA is a compendium database for lysine acetylated substrates. It contains 3,311 unique protein entries with 7,151 experimentally identified lysine acetylation sites, that were manually collected from the scientific literature. The regulatory roles of lysine acetylation were statistically analyzed with the gene Ontology (GO) and InterPro annotations.\n\nCombinations with protein-protein interaction information are systematically discovered a potential human lysine acetylation network (HLAN) among histone acetyltransferases (HATs), substrates and histone deacetylases (HDACs). There are 1862 triplet relationships of HAT-substrate-HDAC retrieved from the HLAN, at least 13 of which were previously experimentally verified.",
"fairsharing": "biodbcore-000577",
"homepage": "http://cplm.biocuckoo.org",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "The CUCKOO Workgroup",
"name": "CPLM",
"prefix": "NBDC01620",
"pubmeds": [
"24214993"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01624": {
"alt_name": "Allele Frequency Net Database",
"description": "AFND is a public database containing frequency information of several immune genes such as Human Leukocyte Antigens (HLA), Killer-cell Immunoglobulin-like Receptors (KIR), Major histocompatibility complex class I chain-related (MIC) genes, and a number of cytokine gene polymorphisms. It contains information at allele, haplotype and genotype level depending on the polymorphism. Users can navigate in a number of different options to search population frequencies, and also some other tools that can be useful for the community.",
"homepage": "http://www.allelefrequencies.net/",
"information_keywords": [
"Expression",
"Repository"
],
"maintainer": "The Royal Liverpool and NHS Broadgreen Hospitals||University of Liverpool",
"name": "AFND",
"prefix": "NBDC01624",
"pubmeds": [
"21062830",
"12753660",
"25414323"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc01625": {
"alt_name": "RNA Editing Sites to Protein 3D Structure",
"description": "RESOPS is a database for analyzing the correspondence of RNA editing sites to protein 3D structures. RNA editing data mapped onto amino acid sequence data can be downloaded. The database contains information on amino acid conversion pattern and correspondence to the protein 3D structure data auto-calculated based on these data.",
"homepage": "http://cib.cf.ocha.ac.jp/RNAEDITING/index.html",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "Center for Informational Biology, Ochanomizu University",
"name": "RESOPS",
"prefix": "NBDC01625",
"pubmeds": [
"19808808",
"18631376"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein",
"Cell/Organelle"
]
},
"nbdc01626": {
"description": "The Effective is a database for bioinformatic identification of eukaryotic-like domains that is performed by evaluating the taxonomic distributions of protein domains in a representative number of genomes of pathogens, symbionts, non-pathogens and eukaryotes (classification of bacteria according to the organism info in the microbial genome projects list of the NCBI). All protein domains that occur in eukaryotes and pathogens or eukaryotes and symbionts, but not or only rarely in non-pathogens, are detected.",
"fairsharing": "biodbcore-000707",
"homepage": "http://effectivedb.org",
"information_keywords": [
"Localization",
"Interaction/Pathway"
],
"maintainer": "Division of Computational Systems Biology, University of Vienna",
"name": "EffectiveDB",
"prefix": "NBDC01626",
"pubmeds": [
"21071416",
"26590402"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01627": {
"alt_name": "Genetic Variation and Drug",
"description": "VnD is a integrated database of the trilateral relationship among genomic variations, human diseases, and drugs. This database provides information about conformational changes and mutant proteins from drug-related genes, and structural and biochemical properties relevant to drug binding.\n\nVnD includes:\n\n(1) disease-related gene records and genetic variation records, which systematically integrated various resources\n\n(2) conformational changes in wild-type and mutant proteins from drug-related genes\n\n(3) the structural and biochemical properties relevant to drug binding such as the distribution of SNPs in proximal protein pockets, thermo-chemical stability, interactions with drugs and physico-chemical properties",
"homepage": "http://vnd.kobic.re.kr",
"information_keywords": [
"3D structure",
"Interaction/Pathway"
],
"maintainer": "Korean BioInformation Center",
"name": "VnD",
"prefix": "NBDC01627",
"pubmeds": [
"21051351"
],
"status": "Active",
"target_keywords": [
"Protein",
"Genetic variation",
"Drug",
"Health/Disease"
]
},
"nbdc01628": {
"description": "WebGeSTer DB is a database of intrinsic transcription terminators, and comprises of >2,200,000 terminators identified from a total of 2036 chromosomes and 1508 plasmids. This database contains information about structural parameters of individual terminators such as sequence, length of stem and loop, mismatches and gaps, U-trail, genomic coordinates and gene name and accession number in both tabular form and as a composite figure.",
"homepage": "http://pallab.serc.iisc.ernet.in/gester/",
"information_keywords": [
"Sequence",
"3D structure",
"Image/Movie"
],
"maintainer": "Department of Computational and Data Science, Indian Institute of Science",
"name": "WebGeSTer DB - A Transcription Terminator Database",
"prefix": "NBDC01628",
"pubmeds": [
"20972211"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"DNA",
"Organism"
]
},
"nbdc01630": {
"alt_name": "Protein Ontology",
"description": "PRO provides an ontological representation of protein-related entities by unambiguously defining them and showing the relationships between them. Each PRO term describes a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific.",
"homepage": "https://proconsortium.org/pro.shtml",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "University of Delaware||Georgetown University Medical Center",
"name": "PRO",
"prefix": "NBDC01630",
"pubmeds": [
"20935045"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01631": {
"alt_name": "The database of RNA-binding protein specificities",
"description": "RBPDB is a collection of RNA-binding proteins linked to a curated database of published observations of RNA binding. RBPDB can be searched in gene symbol, name or description, and experiments by experiment type, sequence or PubMed ID through the search boxes at the top of every page.",
"homepage": "http://rbpdb.ccbr.utoronto.ca/",
"information_keywords": [
"Classification",
"Interaction/Pathway"
],
"maintainer": "Department of Molecular Genetics, University of Toronto",
"name": "RBPDB",
"prefix": "NBDC01631",
"pubmeds": [
"21036867"
],
"status": "Active",
"target_keywords": [
"Protein",
"RNA"
]
},
"nbdc01632": {
"description": "ChemTHEATRE is a database to deposit and visualize monitoring data of environmental contaminants, especially chemicals in organisms. The data were collected from published articles and reports by public institutions.\nEach dataset comprises measurement data, experimental methods (Instrument information, Extraction method, Clean-up method, etc.), and biological specimens (Instrument group, Name of instrument, Extraction method, Clean-up method, etc.).",
"homepage": "https://chem-theatre.com",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Ehime University",
"name": "ChemTHEATRE",
"prefix": "NBDC01632",
"status": "Active",
"target_keywords": [
"Chemical compound",
"Organism"
]
},
"nbdc01633": {
"description": "Flora of Nepal Database (Ferns and its allies) is a database of specimens of pteridophytes in Nepal that are reserved in the University Museum at the University of Tokyo. Each entry includes primary collection data and images. This database is searchable by species, intraspecific taxa, locality, and primary collection data.",
"homepage": "http://umdb.um.u-tokyo.ac.jp/DShokubu/nepal/Ferns/specimen_dic/findrecords.php",
"information_keywords": [
"Geographic Distribution",
"Image/Movie",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "The University of Tokyo The University Museum",
"name": "Flora of Nepal Database (Ferns and its allies)",
"prefix": "NBDC01633",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01636": {
"alt_name": "Protein Structural Change DataBase",
"description": "The PSCDB contains information on the relationship between protein structural changes and ligand binding. Structural changes are classified into seven distinct classes based on the location of the ligand binding site and the mechanism underlying the structural change.",
"homepage": "https://www.ideal-db.org/pscdb/",
"information_keywords": [
"3D structure",
"Interaction/Pathway"
],
"maintainer": "Nagoya University, Graduate School of Information Science",
"name": "PSCDB",
"prefix": "NBDC01636",
"pubmeds": [
"22080505",
"21376729"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01637": {
"alt_name": "Kinase-Associated Neural Phospho-Signaling",
"description": "KANPHOS is a database for proteins that related to kinase-associated phospho-signaling systems in neural cells. It provides information on proteins that are activated (or inhibited) by kinases in response to extracellular stimuli. \nThis database supports three search modes: \n1) Search for substrates phosphorylated by a specific kinase. \n2) Search for kinases that phosphorylate a specific substrate. \n3) Search for kinases and their target substrates by a specific signaling pathway.\nRegistration is required for full access.",
"homepage": "https://kanphos.neuroinf.jp",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "KANPHOS Platform Committee",
"name": "KANPHOS",
"prefix": "NBDC01637",
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease"
]
},
"nbdc01638": {
"description": "The TF clone database provides the information of ORF clones (without STOP codons) of Arabidopsis transcription factors in the Gateway vector system. Also included in the database are RIKEN Arabidopsis Transcription Factor (RARTF) clones, based on TAIR10 gene annotation data, and other TF genes. Each entry contains the AGI code, Clone ID, ORF sequence, and gene annotation data.\nUsers can search the TF clone database using keywords from TAIR10 annotations and the family name of the RARTF database, as well as the distribution information in the \"Contact\" tab.",
"homepage": "https://plant.rtc.riken.jp/resource/tfclone/tfclone_information.html",
"information_keywords": [
"Bioresource"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "TF clone",
"prefix": "NBDC01638",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01640": {
"description": "HealthData.gov is a repository of health data. It contains information about clinical care provider quality, nationwide health service provider directories, databases of the latest medical and scientific knowledge, consumer product data, community health performance data, government spending data, and much more.",
"homepage": "https://www.healthdata.gov",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "U.S. Department of Health & Human Services",
"name": "HealthData.gov",
"prefix": "NBDC01640",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01641": {
"description": "This site for FAIRsharing.org is a registry site intended to promote data-sharing in the sciences, such as life, environmental, and biomedical sciences. It consists of \"Standards\", \"Databases\", \"Policies\", and \"Collections\" sections that catalog both in-house and crowd-sourced curated descriptions. The Biosharing.org (https: //biosharing.org) has been developed into the FAIRsharing.org in July, 2017.",
"homepage": "https://fairsharing.org",
"information_keywords": [
"Portal",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "FAIRsharing",
"name": "FAIRsharing.org",
"prefix": "NBDC01641",
"status": "Active"
},
"nbdc01642": {
"alt_name": "Dryad Digital Repository",
"description": "Dryad is a repository for data files associated with published scientific and medical literature. Users can examine the cited publication, its keywords, and a description of the data. All data submitted to Dryad are provided with the Creative Commons Zero (CC0) license.",
"homepage": "http://datadryad.org",
"information_keywords": [
"Bibliography/Documents",
"Portal",
"Repository"
],
"maintainer": "North Carolina State University",
"name": "Dryad",
"prefix": "NBDC01642",
"status": "Active"
},
"nbdc01646": {
"alt_name": "Tropical Coastal Ecosystems Portal",
"description": "TroCEP provides information on tropical coastal ecosystems; world distribution maps, plant species lists and ecosystem functions. Lists of Mangrove Flora are downloadable and are sorted by country/territory or species.",
"homepage": "http://www.nies.go.jp/TroCEP/index.html",
"information_keywords": [
"Bibliography/Documents",
"Environment",
"Geographic Distribution"
],
"maintainer": "NIES (National Institute for Environmental Studies)",
"name": "TroCEP",
"prefix": "NBDC01646",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01647": {
"description": "JaLTER Data Catalog Search is a search system for ecological observation database managed by JaLTER in order to facilitate long-term ecological researches. It provides metadata of each dataset, and simply browse datasets by category such as JaLTER sites, ecosystem types, projects and targets for measurement.",
"homepage": "http://db.cger.nies.go.jp/JaLTER/metacat/style/skins/jalter-en/index.jsp",
"information_keywords": [
"Environment",
"Bibliography/Documents"
],
"maintainer": "NIES (National Institute for Environmental Studies)",
"name": "JaLTER Data Catalog Search",
"prefix": "NBDC01647",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01648": {
"description": "Chironomid DNA Barcode Database is a search system for DNA barcoding information on chironomid specimens. It provides information for DNA sequence, taxonomic classifications, and collection places of samples. DNA barcoding has been used to identify species, along with morphological and ecological observations. The data in this database were published on GBIF (http://integbio.jp/dbcatalog/en/record/nbdc00069).",
"homepage": "http://www.nies.go.jp/yusurika/en/index.html",
"information_keywords": [
"Sequence",
"Taxonomy",
"Image/Movie"
],
"maintainer": "NIES (National Institute for Environmental Studies)",
"name": "Chironomid DNA Barcode Database",
"prefix": "NBDC01648",
"status": "Active",
"target_keywords": [
"DNA",
"Genome/Gene",
"Organism"
]
},
"nbdc01649": {
"description": "REFOLDdb is a database for the protein refolding methods, which based on published papers written about the refolding of recombinant proteins. A combined search (Article and Protein and Experiment), Blast search and statistics of REFOLDdb are available. All REFOLDdb data is freely downloadable.\nAll data in the other REFOLD databaseοΌhttp ://refold.med.monash.edu.auοΌ managed by Monash University (Australia) have been integrated with this database.",
"homepage": "http://pford.info/refolddb/",
"information_keywords": [
"Method",
"Sequence",
"3D structure",
"Bibliography/Documents"
],
"maintainer": "National Institute of Genetics",
"name": "REFOLDdb",
"prefix": "NBDC01649",
"pubmeds": [
"28438161"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01652": {
"description": "This is a portal site of Roadmap Epigenomics Project. The NIH Roadmap Epigenomics Mapping Consortium has generated high-quality, genome-wide maps of histone modifications, chromatin accessibility, DNA methylation and mRNA expression across 100s of human cell types and tissues. Users can browse available data and view data tracks on a USCS Genome Browser. Protocols and Tools are also available.",
"homepage": "http://www.roadmapepigenomics.org",
"information_keywords": [
"Sequence",
"Portal",
"Method",
"Localization"
],
"maintainer": "NIH Roadmap Epigenomics Mapping Consortium",
"name": "Roadmap Epigenomics Project",
"prefix": "NBDC01652",
"pubmeds": [
"25693563",
"20944595"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Epigenetics",
"DNA",
"Organism"
]
},
"nbdc01653": {
"alt_name": "Duplicated-gene Nucleotide Variants",
"description": "The dbDNV is a database about duplicated gene nucleotide variants (DNVs), which assist users to distinguish DNVs from single nucleotide polymorphisms (SNPs). It allows users obtain duplicated gene loci (DGL) by querying via the NCBI accession number of a reference transcript. Users can also browse the identified DNVs in the genomic order by clicking the chromosome name, and also get a list of DNVs after specifying a chromosome or a genomic region. By using IDs of the existing SNP records in dbSNP, users can find the DNVs located on the same genomic position of the SNPs.",
"homepage": "http://goods.ibms.sinica.edu.tw/DNVs/",
"information_keywords": [
"Sequence"
],
"maintainer": "Academia Sinica",
"name": "dbDNV",
"prefix": "NBDC01653",
"pubmeds": [
"21097891"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Organism"
]
},
"nbdc01654": {
"alt_name": "Dragon Database of Genes Implicated in Prostate Cancer",
"description": "DDPC is an integrated knowledgebase of genes experimentally verified to be involved in prostate cancer (PC). The database provides gene-associated data such as protein annotation, molecular pathways, ontologies and transcription regulation. This database contains information on pre-compiled literature based text-mining report. Moreover, it contains DrugBank data on drugs associated with prostate cancer.",
"homepage": "http://www.cbrc.kaust.edu.sa/ddpc/",
"information_keywords": [
"Interaction/Pathway",
"Ontology/Terminology/Nomenclature",
"Bibliography/Documents"
],
"maintainer": "KAUST (King Abdullah University of Science and Technology)",
"name": "DDPC",
"prefix": "NBDC01654",
"pubmeds": [
"20880996"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Drug"
]
},
"nbdc01655": {
"alt_name": "The International Human Epigenome Consortium Data Portal",
"description": "The IHEC Data Portal is a web resource to view, search and download epigenomics data released by the IHEC-associated projects such as ENCODE, NIH Roadmap, CEEHRC, Blueprint, DEEP, AMED-CREST, and KNIH. The International Human Epigenome Consortium (IHEC) coordinates the production of human reference epigenome maps relevant to health and disease. Users can select the datasets to view them in the grid, download or display them in a UCSC Genome Browser.",
"homepage": "http://epigenomesportal.ca/ihec/",
"information_keywords": [
"Sequence",
"Expression",
"Localization"
],
"maintainer": "McGill Epigenomics Data Coordination Centre||McGill Epigenomics Mapping Centre",
"name": "IHEC Data Portal",
"prefix": "NBDC01655",
"pubmeds": [
"27984737",
"27863956"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Epigenetics",
"DNA",
"Protein",
"Cell/Organelle",
"Organism"
]
},
"nbdc01656": {
"alt_name": "Yeast Promoter Atlas",
"description": "YPA is a database which collected comprehensive promoter features in Saccharomyces cerevisiae. The database intergrates various resources including promoter sequences, TSSs, 5'- and 3'UTRs, TATA boxes, TFBSs, nucleosome occupancy, DNA bendability, TF-TF interaction, and gene expression data. It provides a comprehensive view of the promoter regions.",
"homepage": "http://ypa.csbb.ntu.edu.tw/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "Department of Electrical Engineering, National Cheng Kung University",
"name": "YPA",
"prefix": "NBDC01656",
"pubmeds": [
"21045055"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc01657": {
"alt_name": "Canadian Epigenetics, Environment and Health Research Consortium Network",
"description": "CEEHRC is a Canadian member of IHEC (http://integbio.jp/dbcatalog/en/record/nbdc01655), which aims to produce reference human epigenome maps relevant to health and disease. The data produced by two epigenome mapping centres, Centre for Epigenome Mapping Technologies and McGill Epigenomics Mapping Centre can be accessed. Epigenetic and epigenomics tools, software and protocols are available.",
"homepage": "http://www.epigenomes.ca/",
"information_keywords": [
"Sequence",
"Expression",
"Localization",
"Portal"
],
"maintainer": "BC Cancer Agency's Genome Sciences Centre||McGill University",
"name": "CEEHRC NETWORK",
"prefix": "NBDC01657",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Epigenetics",
"DNA",
"Protein"
]
},
"nbdc01661": {
"alt_name": "The Bovine Genome Database",
"description": "The Bovine Genome Database is a database that integrates bovine genome sequence with annotations of genes and other genomics data. It provides several tools, which are the Blast, annotation tool, and data mining tool etc. The data mining tool, BovineMine, integrates the bovine genome, annotation, QTL, SNP and expression data with external sources of orthology, gene ontology, gene interaction and pathway information.",
"homepage": "http://BovineGenome.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Missouri",
"name": "BGD",
"prefix": "NBDC01661",
"pubmeds": [
"26481361",
"21123190",
"21092105"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc01662": {
"description": "EMDB is a unified data resource for 3-Dimensional electron microscopy. It's a portal for deposition and retrieval of 3DEM density maps, atomic models, and associated metadata, as well as a resource for news, events, software tools, data standards, validation methods for the 3DEM community.",
"fairsharing": "biodbcore-000596",
"homepage": "https://www.emdataresource.org",
"information_keywords": [
"3D structure",
"Image/Movie",
"Portal",
"Repository"
],
"maintainer": "EMDataResource",
"name": "EMDataResource",
"prefix": "NBDC01662",
"pubmeds": [
"26578576",
"20935055"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01663": {
"description": "This database contains information of approximately 69,000 bird specimens (skins, spread wings, skeletal specimens, spirit specimens, eggs, and nests) that Yamashina Institute for Ornithology possesses. The database shows almost all of the specimen labels those are extremely important for scientific studies. Users can search by keyword, taxonomy and geographical map.",
"homepage": "http://decochan.net/index.php?p=1&lang=e",
"information_keywords": [
"Taxonomy",
"Image/Movie",
"Geographic Distribution"
],
"maintainer": "Yamashina Institute for Ornithology",
"name": "Yamashina Institute for Ornithology Specimen Database",
"prefix": "NBDC01663",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01665": {
"alt_name": "GPCRs Interaction Partners Database",
"description": "GRIPDB is a database of G protein Coupled Receptor (GPCR) oligomerization. It provides information of the partner and the interfaces for oligomerization. Experimentally based data and computationally predicted data are included. The original site ( http ://grip.cbrc.jp/GDB/index.html ) has been closed. Now, GRIPDB is available from LSDB archive site.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/gripdb/desc.html",
"information_keywords": [
"Interaction/Pathway",
"Sequence"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "GRIPDB (Archive)",
"prefix": "NBDC01665",
"pubmeds": [
"21410407"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01666": {
"description": "FlyFactorSurvey is a database of DNA binding specificities for Drosophila transcription factors (TFs). The TFs were primarily determined using the bacterial one-hybrid system. It provides motifs and position weight matrices for over 200 TFs, including many unpublished motifs. Search tools and flat file downloads are available.",
"homepage": "http://mccb.umassmed.edu/ffs/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "University of Massachusetts Medical School",
"name": "FlyFactorSurvey",
"prefix": "NBDC01666",
"pubmeds": [
"21097781"
],
"status": "Active",
"target_keywords": [
"DNA",
"Protein"
]
},
"nbdc01667": {
"alt_name": "Tomato Functional Genomics Database",
"description": "TFGD is a comprehensive database of tomato functional genomics data. It contains gene expression data by the RNA-seq and microarrays, metabolite profiles and information of small RNAs and miRNAs. The tomato ESTs and BAC clones are distributed.",
"fairsharing": "biodbcore-000302",
"homepage": "http://ted.bti.cornell.edu",
"information_keywords": [
"Sequence",
"Expression",
"Bioresource",
"Interaction/Pathway"
],
"maintainer": "Cornell University",
"name": "TFGD",
"prefix": "NBDC01667",
"pubmeds": [
"20965973"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"RNA",
"Metabolite"
]
},
"nbdc01668": {
"description": "This database is a genome information database of a cellular slime mold, Acytostelium subglobosum. It contains gene information, such as a position obtained from EST analysis, structural predictions, and functions. This database allows to search by selecting a contig, gene ID, or selecting a gene of related species, Dictyostelium. The Ortholog/palalog information is also available.",
"fairsharing": "biodbcore-000775",
"homepage": "http://cosmos.bot.kyoto-u.ac.jp/acytodb/cgi-bin/index.cgi?org=as",
"information_keywords": [
"Sequence"
],
"maintainer": "Kyoto University",
"name": "Acytostelium Gene Database",
"prefix": "NBDC01668",
"pubmeds": [
"25758444"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01669": {
"alt_name": "Totally Integrated high-resolution Array cgh data and high-throughput sequencing Read data Archive human genome database",
"description": "TIARA is a database containing personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. The database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).",
"homepage": "http://tiara.gmi.ac.kr/",
"information_keywords": [
"Expression",
"Sequence"
],
"maintainer": "Genomic Medicine Institute, Seoul National University College of Medicine",
"name": "TIARA",
"prefix": "NBDC01669",
"pubmeds": [
"21051338",
"23515433"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc01670": {
"description": "TRIP Database is a manually curated database of protein-protein interactions (PPI) for mammalian transient receptor potential (TRP) channels. It provides 4 categories of PPI data, which are screening, validation, characterization, and functional consequence. There are many links to useful external databases for the purpose of providing information of sequence data, related diseases, etc.",
"homepage": "http://www.trpchannel.org",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "Department of Physiology, Seoul National University College of Medicine & Department of Computer Engineering, College of Engineering, Myongji University",
"name": "TRIP Database",
"prefix": "NBDC01670",
"pubmeds": [
"20851834",
"23071747"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Health/Disease"
]
},
"nbdc01671": {
"description": "Isobase is a database of functionally related orthologs, which are termed \"isologs\", developed from the multiple alignment of five major eukaryotic PPI networks, as computed by the global network alignment tools IsoRank and IsoRankN. Users can search high-confidence isologs between commonly studied organisms those are human, yeast, fly, worm, and mouse.",
"homepage": "http://groups.csail.mit.edu/cb/mna/isobase/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "MIT (Massachusetts Institute of Technology)",
"name": "Isobase",
"prefix": "NBDC01671",
"pubmeds": [
"21177658"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01672": {
"alt_name": "Mitochondrial Spatio-Temporal Expression Database",
"description": "MitoGenesisDB is a database focused on the dynamic of mitochondrial protein formation through global mRNA analyses on Saccharomyces cerevisiae. It provides time-course data of mRNA production, localization of mRNA that defines translation sites, and transcription rate and mRNA stability. Users can also search orthologous relationships between Saccharomyces cerevisiae and other model organisms those are human, mouse, Arabidopsis thaliana, and C.elegans, to apply the data of Saccharomyces cerevisiae to the other model organisms.",
"homepage": "http://www.dsimb.inserm.fr/dsimb_tools/mitgene/",
"information_keywords": [
"Expression",
"Localization"
],
"maintainer": "Dynamique des Structures et Interactions des Macromolecules Biologiques, INSERM",
"name": "MitoGenesisDB",
"prefix": "NBDC01672",
"pubmeds": [
"20833631"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01673": {
"description": "OMICtools is a database that provides an overview of more than 20,000 software tools and databases related to genomics, transcriptomics, proteomics and metabolomics. All of the information of tools and databases are manually curated. The tools have been classified by omic technologies associated with published evaluations of tool performance. Users can search and browse tools by more than 1,300 categories. Any developers and users can submit their tools to OMICtools.",
"homepage": "https://omictools.com",
"information_keywords": [
"Phenotype",
"Method",
"Sequence",
"3D structure",
"Chemical structure",
"Expression",
"Localization",
"Interaction/Pathway",
"Image/Movie",
"Bibliography/Documents",
"Repository"
],
"maintainer": "omicX",
"name": "OMICtools",
"prefix": "NBDC01673",
"pubmeds": [
"25024350"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Epigenetics",
"DNA",
"RNA",
"Protein",
"Metabolite",
"Drug",
"Cell/Organelle",
"Organism",
"Health/Disease"
]
},
"nbdc01674": {
"alt_name": "Multi-purpose Ecological Risk Assessment and Management Tool",
"description": "MeRAM is a free, user-friendly software for ecological risk assessment/management of chemicals substances. By installing MeRAM on a computer, users can perform assessment with only a few mouse clicks β ranging from initial risk assessment to high level risk assessment using species sensitivity distribution and population-level effect models. MeRAM contains not only the assessment methodologies, but also the necessary toxicity test data on approximately 3900 substances (190,000 data). In addition, the sample dataset for exposure assessment and toxicity assessment is included thereby users can thus use the tool even if users donβt have data at hand or expertise in ecological risk assessment and statistical analysis. Users can use it on Windows PC (Windows 7, Windows 8, Windows 10).",
"homepage": "https://en-meram.aist-riss.jp",
"information_keywords": [
"Environment",
"Method",
"Bibliography/Documents"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "AIST-MeRAM",
"prefix": "NBDC01674",
"status": "Active",
"target_keywords": [
"Chemical compound",
"Organism",
"Health/Disease"
]
},
"nbdc01675": {
"alt_name": "Thioester-active Enzymes",
"description": "ThYme is a database constructed to bring together amino acid sequences and 3D (tertiary) structures of the enzymes acting on thioester-containing substrates. These enzymes have been classified into families, members of which are similar in sequences, tertiary structures and catalytic mechanisms, implying common protein ancestry. If users take contact to the database mainteiner, the ThYme is available for download.",
"homepage": "https://thyme.engr.unr.edu/v2.0/",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "Iowa State University",
"name": "ThYme",
"prefix": "NBDC01675",
"pubmeds": [
"21045059"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01676": {
"alt_name": "Protein Circular Dichroism Data Base",
"description": "PCDDB is a public repository that archives circular dichroism (CD) and synchrotron radiation CD (SRCD) spectral data of proteins. It also provides associated experimental metadata and validation data. The entries are linked to the UniProt for sequences, the PDB for structures, the Enzyme Commission functional classification database and the CATH fold classification database.",
"fairsharing": "biodbcore-000613",
"homepage": "https://pcddb.cryst.bbk.ac.uk",
"information_keywords": [
"3D structure",
"Method",
"Repository"
],
"maintainer": "Birkbeck College, University of London||Queen Mary University of London",
"name": "PCDDB",
"prefix": "NBDC01676",
"pubmeds": [
"28580679",
"27613420",
"21071417"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01677": {
"alt_name": "Protein Localization Database for Human and Arabidopsis",
"description": "LocDB is a database that collects experimental annotations for the subcellular localization of proteins in Human (Homo sapiens) and Weed (Arabidopsis thaliana). In addition to the information experimentally proved, the database contains results of predictions by various subcellular localization prediction methods, which for providing a better platform for development of new prediction methods.",
"homepage": "http://www.rostlab.org/services/locDB/",
"information_keywords": [
"Localization",
"Bibliography/Documents"
],
"maintainer": "RostLab, Technische UniversitΓ€t MΓΌnchen",
"name": "LocDB",
"prefix": "NBDC01677",
"pubmeds": [
"21071420"
],
"status": "Active",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc01678": {
"description": "SuperSweet is a database for existing natural and artificial sweeteners, and also includes a homology modelled sweet taste receptor and docked binders. A graphical user-interface allows similarity searching, visualization of docked sweeteners into the modelled receptor etc. A carbohydrate classification tree and browsing features allow quick requests through the database.",
"homepage": "http://bioinformatics.charite.de/sweet/",
"information_keywords": [
"3D structure",
"Chemical structure",
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "CharitΓ© - UniversitΓ€tsmedizin Berlin",
"name": "SuperSweet",
"prefix": "NBDC01678",
"pubmeds": [
"20952410"
],
"status": "Active",
"target_keywords": [
"Carbohydrate",
"Chemical compound",
"Health/Disease",
"Protein"
]
},
"nbdc01679": {
"description": "This database is a collection about images based on specimens of Japanese longicorn beetles deposited at FFPRI, Forestry and Forest Products Research Institute. It contains images of specimens and data including scientific names, body length, sex, collection date, collection locality, etc. This database allows users to search with genus, specific name, families, subfamilies or prefecture names.",
"homepage": "https://db.ffpri.go.jp/longicorn_jp/index-E.html",
"information_keywords": [
"Image/Movie",
"Geographic Distribution",
"Taxonomy"
],
"maintainer": "Forestry and Forest Products Research Institute",
"name": "Image database of Longicorn Beetles of Japan",
"prefix": "NBDC01679",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01680": {
"alt_name": "an updated database of bacterial type II toxin-antitoxin loci",
"description": "TADB is a database for Type 2 Toxin-antitoxin (TA) loci in Bacteria and Archaea. Sequence information of nucleic acids and amino acids, loci in the genome, and information of the Replicons are provided.",
"homepage": "https://bioinfo-mml.sjtu.edu.cn/TADB2/index.php",
"information_keywords": [
"Sequence"
],
"maintainer": "Shanghai Jiao Tong University",
"name": "TADB 2.0",
"prefix": "NBDC01680",
"pubmeds": [
"20929871",
"29106666"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Metabolite"
]
},
"nbdc01681": {
"alt_name": "Regulatory Network in Protein Phosphorylation",
"description": "RegPhos is a database for kinases and their substrates. It provides the information that basic description for proteins, gene expression data in each type of cancers, gene name of substrates for kinases and phosphorylated sites in substrates. Users can search data by name of kinases or substrates, and explore phosphorylation network concerning protein-protein interaction, subcellular localization and metabolic pathways by a set of name of genes.",
"homepage": "http://140.138.144.141/~RegPhos/index.php",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Department of Computer Science and Engineering, Yuan Ze University",
"name": "RegPhos",
"prefix": "NBDC01681",
"pubmeds": [
"21037261",
"24771658"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01682": {
"description": "BioModels Database is a repository of mathematical models relate to biological and biomedical field. It covers a wide range of processes, such as metabolic pathways, protein-drug interactions, etc. Usually, the models described in peer-reviewed scientific literatures are collected, and then, they are manually curated and semantically enriched with cross-references to external data resources. All models are downloadable and available with the CC0 license (freely for use, modification and distribution).",
"fairsharing": "biodbcore-000306",
"homepage": "https://www.ebi.ac.uk/biomodels/",
"information_keywords": [
"Method",
"Interaction/Pathway",
"Bibliography/Documents",
"Repository"
],
"maintainer": "BioModels.net Team, EMBL-EBI",
"name": "BioModels",
"prefix": "NBDC01682",
"pubmeds": [
"25414348",
"26225232",
"20587024",
"16381960"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Epigenetics",
"Protein",
"Metabolite",
"Drug",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc01683": {
"description": "The BMRBj Data Server provides NMR-STAR data in BMRB (http://integbio.jp/dbcatalog/record/nbdc00380 ) in various formats. Users can select data format from XML, RDF, and JSON.",
"homepage": "https://bmrbpub.pdbj.org",
"information_keywords": [
"3D structure",
"Method"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "BMRBj Data Server",
"prefix": "NBDC01683",
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Protein",
"Metabolite"
]
},
"nbdc01684": {
"description": "Oncomineβ’ is a database for cancer microarray and a web application to integrate profiling-data of cancer genes in various types of cancers. They provide two types of platforms, Oncomine Research Edition for the academic and nonprofit cancer research communities (free) and Oncomine Research Premium Edition as a subscription version that includes multi-gene search, expanded analyses, custom concept upload, export capability and enhanced support, etc.",
"homepage": "https://www.oncomine.org",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "Thermo Fisher Scientific Inc.",
"name": "Oncomine",
"prefix": "NBDC01684",
"pubmeds": [
"15068665",
"17356713"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc01685": {
"description": "This database provides gene expression data after a drug administration and their analysis results using mouse. It offers comprehensive datasets representing drug-induced gene expression patterns in 24 organs of mouse. Drugs used in the analyses are popular in treating cancer, diabetes, neurological diseases, high cholesterol, metabolic diseases, etc. worldwide.",
"homepage": "https://www.d-iorgans.karydo-tx.com/en",
"information_keywords": [
"Expression",
"Localization",
"Interaction/Pathway"
],
"maintainer": "Karydo TherapeutiX, Inc.",
"name": "D-iOrgansAtlas",
"prefix": "NBDC01685",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Drug",
"Organism",
"Health/Disease"
]
},
"nbdc01689": {
"description": "Melonet DB is a database about whole gene expression in muskmelon (Cucumis melo L.). It contains expression patterns of whole gene in 30 different tissues of \"Earl's favorite Harukei-3 (Harukei-3)\" melon, and provides following tools: (1) Gene expression map viewer is designed to analyze tissue-specific gene expression pattern in 30 different tissues. (2) Coexpression viewer is designed to analyze coexpression relationship between genes. (3) Mutation analysis tools are aimed at to analyze whether nucleotide change(s) cause amino acid substitution, frame shift, or splicing variation within gene. (4) Sequence analysis tools are designed to analyze DNA sequence. Blast or \"oligo DNA mapper\" identify homologous genes or genomic positions, respectively, based on query sequence. (5) Primer design tools are designed to analyze primer sequence and find the best possible unique PCR primer pair based on target query sequence.",
"homepage": "https://melonet-db.dna.affrc.go.jp/ap/top",
"information_keywords": [
"Expression",
"Sequence",
"Localization"
],
"maintainer": "University of Tsukuba Graduate School of Life and Environmental Sciences",
"name": "Melonet DB",
"prefix": "NBDC01689",
"pubmeds": [
"29216378",
"22753475"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc01690": {
"alt_name": "HOCOMOCO",
"description": "HOmo sapiens COmprehensive MOdel COllection (HOCOMOCO) v10 provides transcription factor (TF) binding models for 601 human and 396 mouse TFs.\nIn addition to basic mononucleotide position weight matrices (PWMs), HOCOMOCO provides a set of dinucleotide position weight matrices based on ChIP-Seq data.\nAll the models were produced by the ChIPMunk motif discovery tool. Models are manually curated with assigning model quality ratings based upon benchmark studies or inherited from HOCOMOCO v9.\nChIP-Seq data for motif discovery was extracted from GTRD database of BioUML platform, that also provides an interface for motif finding (sequence scanning) with HOCOMOCO models. Other sequences of TF binding DNA regions were collected from existing databases and other public data. An appropriate TFBS model was selected for each TF, with similar models selected for related TFs.\nAll TFBS models and initial binding segments data used for motif discovery were mapped to UniPROT IDs. TF coding genes are linked with GeneCards entries. DNA binding domains are linked with TF class database.",
"fairsharing": "FAIRsharing.c1bjep",
"homepage": "http://hocomoco.autosome.ru/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Institute of Systems Biology Ltd||KAUST (King Abdullah University of Science and Technology)||Vavilov Institute of General Genetics, Russian Academy of Sciences",
"name": "HOmo sapiens transcription factor COmprehensive MOdel COllection (HOCOMOCO)",
"prefix": "NBDC01690",
"pubmeds": [
"23175603",
"26586801",
"20736340",
"23427986",
"24074225"
],
"status": "Active",
"target_keywords": [
"Protein",
"Genome/Gene"
]
},
"nbdc01691": {
"description": "MetalPDB is a resource aimed at conveying the information available on the three-dimensional structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are three-dimensional templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure embedding the site(s), and are the central objects of MetalPDB design. MFSs are grouped into equistructural (broadly defined as sites found in corresponding positions in similar structures) and equivalent sites (equistructural sites that contain the same metals), allowing users to easily analyze similarities and variations in metal-macromolecule interactions, and to link them to functional information.",
"fairsharing": "FAIRsharing.g646hq",
"homepage": "http://metalweb.cerm.unifi.it/",
"information_keywords": [
"3D structure",
"Interaction/Pathway"
],
"maintainer": "CERM, University of Florence, Florence",
"name": "MetalPDB",
"prefix": "NBDC01691",
"pubmeds": [
"23155064"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc01692": {
"alt_name": "Plant Resistance Gene Database",
"description": "PRGdb is an open and daily updated space about plant resistance genes, in which all information about this family is stored, curated and discussed. This resource encourages research community curation of plant resistance genes.",
"fairsharing": "FAIRsharing.ysp7ke",
"homepage": "http://www.prgdb.org",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "CRG (Comparative Genomics Group)",
"name": "PRGdb",
"prefix": "NBDC01692",
"pubmeds": [
"19906694",
"23161682"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Organism",
"Health/Disease"
]
},
"nbdc01693": {
"description": "BloodSpot is a database of mRNA expression in healthy and malignant haematopoiesis and includes data from both humans and mice. The core function of BloodSpot is to provide an expression plot of genes in healthy and cancerous haematopoietic cells at specific differentiation stages. In addition to the default plot, that displays an integrated expression plot, two additional levels of visualization are available; an interactive tree showing the hierarchical relationship between the samples, and a Kaplan-Meier survival plot. Prior to BloodSpot, this service was provided by an earlier project, HemaExplorer, also by the same research group. HemaExplorer was updated to the BloodSpot platform, which all users are encouraged to use instead.",
"fairsharing": "FAIRsharing.f5xs6m",
"homepage": "http://www.bloodspot.eu",
"information_keywords": [
"Expression"
],
"maintainer": "Bioinformatics Centre, University of Copenhagen||BRIC (Biotech Research and Innovation Centre, University of Copenhagen)||Danish State Hospital||Finsen Laboratory",
"name": "BloodSpot",
"prefix": "NBDC01693",
"pubmeds": [
"22745298",
"26507857",
"23143109"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle",
"Health/Disease",
"RNA"
]
},
"nbdc01694": {
"description": "This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The purpose of this database is to advance research on cellular activity, with the ultimate goal of improving human health.\nIt is a repository for images, movies, and animations of cells from a variety of organisms that demonstrate cellular architecture and functions. This comprehensive library is designed as a public resource first and foremost for research, and secondarily as a tool for education. The long-term goal is the construction of a library of images that will serve as primary data for research.",
"fairsharing": "FAIRsharing.8t18te",
"homepage": "http://www.cellimagelibrary.org",
"information_keywords": [
"Image/Movie"
],
"maintainer": "ASCB (American Society for Cell Biology)",
"name": "The Cell: An Image Library",
"prefix": "NBDC01694",
"pubmeds": [
"23203874"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc01695": {
"description": "mycoCLAP is a searchable resource for the knowledge and annotation of Characterized Lignocellulose-Active Proteins of fungal origin.",
"fairsharing": "FAIRsharing.ezp87",
"homepage": "http://mycoCLAP.fungalgenomics.ca",
"information_keywords": [
"Sequence"
],
"maintainer": "Centre for Structural and Functional Genomics, Concordia University",
"name": "mycoCLAP",
"prefix": "NBDC01695",
"pubmeds": [
"21622642"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Genome/Gene"
]
},
"nbdc01696": {
"description": "The Antibody Registry exists to give researchers a way to universally identify antibodies used in publications. The registry lists many commercial antibodies from about 200 vendors which have each been assigned a unique identifier. If the antibody that you are using does not appear in the list, an entry can be made by filling in as little as 2 pieces of information: the catalog number and the url of the vendor where our curators can find information and material data sheets. Many optional fields can also be filled in that will help curators identify the reagent. After submitting an antibody, you are given a permanent identifier that can be used in publications. This identifier even if it is later found to be a duplicate, can be quickly traced back in the antibody registry. We never delete records, but we collapse duplicate entries on a regular basis (the old identifiers are kept to help with search).",
"fairsharing": "FAIRsharing.3wdd17",
"homepage": "http://antibodyregistry.org",
"information_keywords": [
"Interaction/Pathway",
"Method"
],
"maintainer": "NIF (Neuroscience Information Framework)",
"name": "antibodyregistry.org",
"prefix": "NBDC01696",
"pubmeds": [
"24032093"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01697": {
"alt_name": "IRD",
"description": "The Influenza Research Database (IRD) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user-friendly interfaces for data retrieval, visualization, and comparative genomics analysis, together with personal login- protected 'workbench' spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature.",
"fairsharing": "FAIRsharing.ws7cgw",
"homepage": "http://www.fludb.org",
"information_keywords": [
"Expression",
"Sequence",
"3D structure"
],
"maintainer": "JCVI (J. Craig Venter Institute)||Northrop Grumman Health IT||Vecna Technologies",
"name": "Influenza Research Database",
"prefix": "NBDC01697",
"pubmeds": [
"22260278",
"22398283",
"24210098",
"24936976",
"25977790",
"25064525",
"25741011",
"25861210"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Health/Disease"
]
},
"nbdc01698": {
"description": "FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. Data are generally associated with peer reviewed manuscripts.",
"fairsharing": "FAIRsharing.veg2d6",
"homepage": "http://www.flowrepository.org",
"information_keywords": [
"Method",
"Bibliography/Documents"
],
"name": "FlowRepository",
"prefix": "NBDC01698",
"pubmeds": [
"22887982",
"22752950"
],
"status": "Active"
},
"nbdc01699": {
"alt_name": "GMD",
"description": "The Golm Metabolome Database (GMD) provides gas chromatography (GC) mass spectrometry (MS) reference spectra, reference metabolite profiles and tools for one of the most widespread routine technologies applied to the large scale screening and discovery of novel metabolic biomarkers.",
"fairsharing": "FAIRsharing.jykmkw",
"homepage": "http://gmd.mpimp-golm.mpg.de/",
"information_keywords": [
"Chemical structure",
"Method"
],
"maintainer": "Max Planck Institute of Molecular Plant Physiology (MPIMP)",
"name": "Golm Metabolome Database",
"prefix": "NBDC01699",
"pubmeds": [
"20526350"
],
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc01700": {
"description": "CellFinder maps validated gene and protein expression, phenotype and images related to cell types.The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells are related to more complex systems such as tissues, organs and organisms and arranged according to their position in development.\nCellFinder provides long-term data storage for validated and curated primary research data and provides additional expert-validation through relevant information extracted from text.",
"fairsharing": "FAIRsharing.mt6057",
"homepage": "http://cellfinder.org/",
"information_keywords": [
"Expression",
"Image/Movie",
"Phenotype",
"Method",
"Ontology/Terminology/Nomenclature"
],
"name": "CellFinder",
"prefix": "NBDC01700",
"pubmeds": [
"23599415",
"24304896",
"25344497"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle"
]
},
"nbdc01701": {
"alt_name": "MonosaccharideDB",
"description": "Database on carbohydrate building blocks / residues (monosaccharides). Provides various kinds of residue data, especially notation information.",
"fairsharing": "FAIRsharing.fgj73t",
"homepage": "http://www.monosaccharidedb.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "EuroCarbDB||Justus-Liebig University Giessen||Justus-Liebig University Giessen",
"name": "Monosaccharide Database",
"prefix": "NBDC01701",
"status": "Inactive",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc01702": {
"description": "Implemented the SNP discovery software autoSNP within a relational database to enable the efficient mining of the identified polymorphisms and the detailed interrogation of the data. AutoSNP was selected because it does not require sequence trace files and is thus applicable to a broader range of species and datasets.",
"fairsharing": "FAIRsharing.2h8cxh",
"homepage": "http://autosnpdb.appliedbioinformatics.com.au",
"information_keywords": [
"Sequence"
],
"maintainer": "ACPFG (Australian Centre For Plant Functional Genomics)",
"name": "autoSNPdb",
"prefix": "NBDC01702",
"pubmeds": [
"18854357"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc01703": {
"description": "miRNEST is an integrative collection of animal, plant and virus microRNA data. miRNEST is being gradually developed to create an integrative resource of miRNA-associated data. The data comes from our computational predictions (new miRNAs, targets, mirtrons, miRNA gene structures) as well as from other databases and publications.",
"fairsharing": "FAIRsharing.5pfx4r",
"homepage": "http://mirnest.amu.edu.pl",
"information_keywords": [
"Expression",
"Sequence",
"3D structure",
"Interaction/Pathway"
],
"maintainer": "Laboratory of Bioinformatics, Faculty of Biology, Adam Mickiewicz University",
"name": "miRNEST",
"prefix": "NBDC01703",
"pubmeds": [
"22135287",
"24243848"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"RNA"
]
},
"nbdc01704": {
"alt_name": "RNAJunction",
"description": "Within this database you will to able to find more than 12,000 extracted three-dimensional junction and kissing loop structures as well as detailed annotations for each.",
"fairsharing": "FAIRsharing.zzgvrv",
"homepage": "http://rnajunction.abcc.ncifcrf.gov",
"information_keywords": [
"3D structure",
"Interaction/Pathway"
],
"maintainer": "Advance Biomedical Computing Center||NCI (National Cancer Institute, National Institutes of Health)",
"name": "RNAJunction: A Database of RNA Junction and Kissing loop Structure",
"prefix": "NBDC01704",
"pubmeds": [
"17947325"
],
"status": "Inactive",
"target_keywords": [
"RNA"
]
},
"nbdc01705": {
"alt_name": "NASC",
"description": "The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.",
"fairsharing": "FAIRsharing.2sqcxs",
"homepage": "http://arabidopsis.info",
"information_keywords": [
"Bioresource"
],
"maintainer": "NASC (Nottingham Arabidopsis Stock Centre)",
"name": "Nottingham Arabidopsis Stock Centre Seeds Database",
"prefix": "NBDC01705",
"pubmeds": [
"14681484"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01706": {
"alt_name": "AFTOL",
"description": "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life.",
"fairsharing": "FAIRsharing.w2cepp",
"homepage": "http://aftol.org",
"information_keywords": [
"Taxonomy"
],
"maintainer": "AFTOL Team||Oregon State University",
"name": "Assembling the Fungal Tree of Life",
"prefix": "NBDC01706",
"pubmeds": [
"17486962"
],
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc01707": {
"alt_name": "AGRIS",
"description": "The Arabidopsis Gene Regulatory Information Server (AGRIS) is a new information resource of Arabidopsis promoter sequences, transcription factors and their target genes. AGRIS currently contains two databases, AtcisDB (Arabidopsis thaliana cis-regulatory database) and AtTFDB (Arabidopsis thaliana transcription factor database). The two databases, used in tandem, provide a powerful tool for use in continuous research.",
"fairsharing": "FAIRsharing.6v2d2h",
"homepage": "http://arabidopsis.med.ohio-state.edu",
"information_keywords": [
"Interaction/Pathway",
"Sequence"
],
"maintainer": "AGRIS Administrators||Ohio State University",
"name": "The Arabidopsis Gene Regulatory Information Server",
"prefix": "NBDC01707",
"pubmeds": [
"21059685"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01708": {
"description": "Allergome aims to supply information on Allergenic Molecules (Allergens) causing an IgE-mediated (allergic, atopic) disease (anaphylaxis, asthma, atopic dermatitis, conjunctivitis, rhinitis, urticaria). The resource is funded through the Allergen Data Laboratories via unrestricted grants from companies and institutions.",
"fairsharing": "FAIRsharing.w6cxgb",
"homepage": "http://www.allergome.org/",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "Allergy Data Laboratories s.c.||IFARAI (International Fund for Advanced Research in Allergy and Immunology)",
"name": "Allergome",
"prefix": "NBDC01708",
"pubmeds": [
"17393720",
"17434469"
],
"status": "Active",
"target_keywords": [
"Metabolite",
"Health/Disease"
]
},
"nbdc01709": {
"alt_name": "CAS Registry",
"description": "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and contains databases of chemical information. CAS Registry Numbers (often referred to as CAS RNs or CAS Numbers) are universally used to provide a unique, unmistakable identifier for chemical substances. A CAS Registry Number itself has no inherent chemical significance but provides an unambiguous way to identify a chemical substance or molecular structure when there are many possible systematic, generic, proprietary or trivial names.",
"fairsharing": "FAIRsharing.5gjjsg",
"homepage": "http://www.cas.org/content/chemical-substances",
"information_keywords": [
"Chemical structure",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "American Chemical Society",
"name": "Chemical Abstracts Service Registry",
"prefix": "NBDC01709",
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc01710": {
"description": "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures.",
"fairsharing": "FAIRsharing.yk38tw",
"homepage": "http://www.antweb.org",
"information_keywords": [
"Classification",
"Image/Movie"
],
"maintainer": "California Academy of Sciences",
"name": "AntWeb",
"prefix": "NBDC01710",
"pubmeds": [
"12867945"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01711": {
"description": "DNASU is a central repository for plasmid clones and collections. Currently we store and distribute over 197,000 plasmids including 75,000 human and mouse plasmids, full genome collections, the protein expression plasmids from the Protein Structure Initiative as the PSI: Biology Material Repository (PSI : Biology-MR), and both small and large collections from individual researchers. We are also a founding member and distributor of the ORFeome Collaboration plasmid collection.",
"fairsharing": "FAIRsharing.qqc7zw",
"homepage": "http://dnasu.org/DNASU/Home.do",
"information_keywords": [
"Bioresource"
],
"maintainer": "Arizona State University||NIH (National Institutes of Health)",
"name": "DNASU Plasmid Repository",
"prefix": "NBDC01711",
"pubmeds": [
"21360289",
"19906724"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"DNA",
"Genome/Gene"
]
},
"nbdc01712": {
"description": "The Telomerase Database is a Web-based tool for the study of structure, function, and evolution of the telomerase ribonucleoprotein. The objective of this database is to serve the research community by providing a comprehensive compilation of information known about telomerase enzyme and its substrate, telomeres.",
"fairsharing": "FAIRsharing.fqcrpt",
"homepage": "http://telomerase.asu.edu",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "Arizona State University",
"name": "Telomerase Database",
"prefix": "NBDC01712",
"pubmeds": [
"18073191"
],
"status": "Active",
"target_keywords": [
"Protein",
"DNA",
"Health/Disease",
"RNA"
]
},
"nbdc01713": {
"alt_name": "ATCC",
"description": "ATCC authenticates microorganisms and cell lines and manages logistics of long-term preservation and distribution of cultures for the scientific community. ATCC supports the cultures it acquires and authenticates with expert technical support, intellectual property management and characterization data.",
"fairsharing": "FAIRsharing.j0ezpm",
"homepage": "http://www.atcc.org/",
"information_keywords": [
"Bioresource"
],
"maintainer": "ATCC Standards Development Organisation",
"name": "American Type Culture Collection database",
"prefix": "NBDC01713",
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc01714": {
"alt_name": "DPD",
"description": "Drosophila Polymorphism Database, is a secondary database designed to provide a collection of all the existing polymorphic sequences in the Drosophila genus. It allows, for the first time, the search for any polymorphic set according to different parameter values of nucleotide diversity.",
"fairsharing": "FAIRsharing.ff7n4h",
"homepage": "http://dpdb.uab.es/dpdb/dpdb.asp",
"information_keywords": [
"Sequence"
],
"maintainer": "Barcelona University",
"name": "Drosophila polymorphism database",
"prefix": "NBDC01714",
"pubmeds": [
"16204116",
"18820438"
],
"status": "Inactive",
"target_keywords": [
"Genetic variation",
"Genome/Gene",
"DNA",
"Organism"
]
},
"nbdc01715": {
"alt_name": "GDP Database",
"description": "The GDP Database provides a public resource of gene disruptions of Drosophila genes using a single transposable element.",
"fairsharing": "FAIRsharing.6e05x2",
"homepage": "http://flypush.imgen.bcm.tmc.edu/pscreen/",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "Baylor College of Medicine",
"name": "Gene Disruption Project Database",
"prefix": "NBDC01715",
"pubmeds": [
"15238527",
"21515576",
"21985007",
"25824290",
"26102525"
],
"status": "Active",
"target_keywords": [
"Organism",
"Genome/Gene"
]
},
"nbdc01716": {
"alt_name": "PHI-base",
"description": "PHI-Base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions. PHI-base catalogues experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts.",
"fairsharing": "FAIRsharing.73cqdk",
"homepage": "http://www.phi-base.org/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Rothamsted Research",
"name": "Pathogen Host Interactions",
"prefix": "NBDC01716",
"pubmeds": [
"17942425",
"16381911",
"25414340",
"27915230"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Organism"
]
},
"nbdc01717": {
"alt_name": "UKSCB",
"description": "The UK Stem Cell Bank (UKSCB) hosted at the National Institute for Biological Standards and Control (NIBSC) is committed to working closely with the clinical and research communities to provide qualified stocks of human stem cell lines of adult, foetal and embryonic origin for both research use and for use in emerging human therapy.",
"fairsharing": "FAIRsharing.efwq12",
"homepage": "http://www.nibsc.org/science_and_research/advanced_therapies/uk_stem_cell_bank.aspx",
"information_keywords": [
"Bioresource"
],
"maintainer": "NIBSC (National Institute for Biological Standards and Control)",
"name": "UK Stem Cell Bank",
"prefix": "NBDC01717",
"pubmeds": [
"16290151"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc01718": {
"alt_name": "cisRED",
"description": "The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data.",
"fairsharing": "FAIRsharing.rwd4wq",
"homepage": "http://www.cisred.org/",
"information_keywords": [
"Sequence",
"Classification",
"Interaction/Pathway"
],
"maintainer": "BC Cancer Agency",
"name": "cis-Regulatory Element Database",
"prefix": "NBDC01718",
"pubmeds": [
"16381958"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01719": {
"alt_name": "BGI-RIS",
"description": "In BGI-RIS, sequence contigs of Beijing indica and Syngenta japonica have been further assembled and anchored onto the rice chromosomes. The database has annotated the rice genomes for gene content, repetitive elements, and SNPs. Sequence polymorphisms between different rice subspecies have also been identified.",
"fairsharing": "FAIRsharing.gk7nfn",
"homepage": "http://rise.genomics.org.cn/",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"name": "Beijing Genomics Institute Rice Information System",
"prefix": "NBDC01719",
"pubmeds": [
"14681438"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"DNA"
]
},
"nbdc01720": {
"alt_name": "ChickVD",
"description": "The chicken Variation Database (ChickVD) is an integrated information system for storage, retrieval, visualization and analysis of chicken variation data.",
"fairsharing": "FAIRsharing.d4q4g2",
"homepage": "http://chicken.genomics.org.cn",
"information_keywords": [
"Sequence"
],
"maintainer": "BGI (Beijing Genomics Institute)",
"name": "Chicken Variation Database",
"prefix": "NBDC01720",
"pubmeds": [
"15608233"
],
"status": "Inactive",
"target_keywords": [
"Genetic variation",
"Genome/Gene",
"DNA"
]
},
"nbdc01721": {
"alt_name": "IVDB",
"description": "IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively.",
"fairsharing": "FAIRsharing.nmavtd",
"homepage": "http://influenza.psych.ac.cn/",
"information_keywords": [
"Sequence"
],
"maintainer": "BGI (Beijing Genomics Institute)",
"name": "Influenza Virus Database",
"prefix": "NBDC01721",
"pubmeds": [
"17065465"
],
"status": "Active",
"target_keywords": [
"DNA",
"Genome/Gene"
]
},
"nbdc01722": {
"alt_name": "YH1",
"description": "The YH database presents the entire DNA sequence of a Han Chinese individual, as a representative of Asian population. This genome, named as YH, is the start of YanHuang Project, which aims to sequence 100 Chinese individuals in 3 years.assembled based on 3.3 billion reads (117.7Gbp raw data) generated by Illumina Genome Analyzer. In total of 102.9Gbp nucleotides were mapped onto the NCBI human reference genome (Build 36) by self-developed software SOAP (Short Oligonucleotide Alignment Program), and 3.07 million SNPs were identified.",
"fairsharing": "FAIRsharing.6cnw23",
"homepage": "http://yh.genomics.org.cn",
"information_keywords": [
"Sequence"
],
"name": "YanHuang - YH1 Genome Database",
"prefix": "NBDC01722",
"status": "Inactive",
"target_keywords": [
"DNA",
"Genome/Gene"
]
},
"nbdc01723": {
"alt_name": "Bgee",
"description": "Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from\nmultiple data types (bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data). Bgee is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Bgee produces calls of presence/absence of expression, and of differential over-/under-expression, integrated along with information of gene orthology, and of homology between organs. This allows comparisons of expression patterns between species.",
"fairsharing": "FAIRsharing.x6d6sx",
"homepage": "https://bgee.org",
"information_keywords": [
"Expression",
"Localization",
"Classification"
],
"maintainer": "BGEE administrators",
"name": "Bgee DataBase for Gene Expression Evolution",
"prefix": "NBDC01723",
"pubmeds": [
"23487185",
"25009735",
"22285560"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc01724": {
"alt_name": "BindingDB",
"description": "BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.",
"fairsharing": "FAIRsharing.3b36hk",
"homepage": "http://www.bindingdb.org",
"information_keywords": [
"Interaction/Pathway",
"Sequence",
"3D structure"
],
"maintainer": "BindingDB",
"name": "BindingDB database of measured binding affinities",
"prefix": "NBDC01724",
"pubmeds": [
"17145705"
],
"status": "Active",
"target_keywords": [
"Drug",
"Protein"
]
},
"nbdc01725": {
"alt_name": "NORINE",
"description": "Norine is a platform that includes a database of nonribosomal peptides together with tools for their analysis. Norine currently contains more than 1000 peptides.",
"fairsharing": "FAIRsharing.gf8yhy",
"homepage": "http://bioinfo.lifl.fr/norine/",
"information_keywords": [
"Sequence",
"Chemical structure"
],
"maintainer": "Bonsai Bioinformatics",
"name": "Non-Ribosomal Peptides Database",
"prefix": "NBDC01725",
"pubmeds": [
"17913739"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01726": {
"alt_name": "TRMP",
"description": "The Therapeutically Relevant Multiple Pathways Database is designed to provide information about such multiple pathways and related therapeutic targets described in the literatures, the targeted disease conditions, and the corresponding drugs/ligands directed at each of these targets.",
"fairsharing": "FAIRsharing.hm0s3e",
"homepage": "http://bidd.nus.edu.sg/group/trmp/trmp_ns.asp",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore",
"name": "Therapeutically Relevant Multiple Pathways Database",
"prefix": "NBDC01726",
"pubmeds": [
"15059817"
],
"status": "Inactive",
"target_keywords": [
"Health/Disease",
"Drug"
]
},
"nbdc01727": {
"alt_name": "APID Interactomes",
"description": "APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.",
"fairsharing": "FAIRsharing.8ye60e",
"homepage": "http://apid.dep.usal.es/",
"information_keywords": [
"3D structure",
"Interaction/Pathway"
],
"name": "Agile Protein Interactomes Dataserver",
"prefix": "NBDC01727",
"pubmeds": [
"27131791",
"16845013",
"17644818"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01728": {
"alt_name": "PRODORIC",
"description": "PRODORIC is a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites.",
"fairsharing": "FAIRsharing.2c45na",
"homepage": "http://prodoric.tu-bs.de/",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Department of Bioinformatics and Biochemistry, Institute for Biochemistry and Biotechnology, Technical University Braunschweig||NGFN (National Genome Research Network)||Project Management Julich",
"name": "PROkariotIC Database Of Gene-Regulation",
"prefix": "NBDC01728",
"pubmeds": [
"18974177",
"12519998"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"DNA",
"Protein"
]
},
"nbdc01729": {
"alt_name": "NMPDR",
"description": "The NMPDR provided curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma.",
"fairsharing": "FAIRsharing.9k5mbg",
"homepage": "http://www.nmpdr.org",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "Bioinformatics Resource Center, University of Wisconsin Biotechnology Center",
"name": "National Microbial Pathogen Data Resource",
"prefix": "NBDC01729",
"pubmeds": [
"17145713"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Organism"
]
},
"nbdc01730": {
"description": "siRecords is a collection of a diverse range of mammalian RNAi experiments . After choosing a gene, researchers can find all siRNA records targeting the gene, design a new siRNA targeting it, or submit siRNAs that have been tested. The resource also helps experimental RNAi researchers by providing them with the efficacy and other information about the siRNAs experiments designed and conducted previously against the genes of their interest.",
"fairsharing": "FAIRsharing.n2xy00",
"homepage": "http://c1.accurascience.com/siRecords/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "Biolead||NCI (National Cancer Institute, National Institutes of Health)",
"name": "siRecords",
"prefix": "NBDC01730",
"pubmeds": [
"18996894"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc01731": {
"alt_name": "SNAPPI-DB",
"description": "SNAPPI-DB is an object-oriented database of domain-domain interactions observed in structural data. The structural data is obtained from the MSD data warehouse as the MSD provides consistent data with links to many types of data about proteins and nucleic acids.",
"fairsharing": "FAIRsharing.zjcys8",
"homepage": "http://www.compbio.dundee.ac.uk/SNAPPI/index.jsp",
"information_keywords": [
"Interaction/Pathway",
"3D structure"
],
"maintainer": "University of Dundee",
"name": "Structure, Interfaces and Alignments for Protein-Protein Interactions Database",
"prefix": "NBDC01731",
"pubmeds": [
"17202171"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01732": {
"alt_name": "SYFPEITHI",
"description": "SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules.",
"fairsharing": "FAIRsharing.k6vsdr",
"homepage": "http://www.syfpeithi.de/",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Department of Medical Informatics, Institute of Medical Biometry und Informatics, Heidelberg University||University of TΓΌbingen",
"name": "Database of MHC Ligands and Peptide Motifs",
"prefix": "NBDC01732",
"pubmeds": [
"10602881"
],
"status": "Active",
"target_keywords": [
"Protein",
"Carbohydrate",
"Health/Disease"
]
},
"nbdc01734": {
"alt_name": "ORegAnno",
"description": "The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, the eVOC: Cell type ontology, and the Taxonomy database.",
"fairsharing": "FAIRsharing.8dak0r",
"homepage": "http://www.oreganno.org/",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "BC Cancer Agency",
"name": "Open Regulatory Annotation",
"prefix": "NBDC01734",
"pubmeds": [
"18006570",
"16397004"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01735": {
"alt_name": "MGG",
"description": "The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. The project is a partnership between the International Rice Blast Genome Consortium, and the Broad Institute. The project is facilitated by an Advisory Board made up of members of the rice blast research community.",
"fairsharing": "FAIRsharing.fj1d4d",
"homepage": "http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/Home.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Human Microbiome Project, Broad Institute",
"name": "Magnaporthe grisea Database",
"prefix": "NBDC01735",
"pubmeds": [
"26416668",
"15846337"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01736": {
"description": "The goal of MutDB is to annotate human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene. Click on the alphabet below to go alphabetically through the list of genes.",
"fairsharing": "FAIRsharing.pxm2h8",
"homepage": "http://mutdb.org/",
"information_keywords": [
"Expression",
"Sequence",
"3D structure"
],
"maintainer": "Buck Institute for Research on Aging||NLM (National Library of Medicine)",
"name": "MutDB",
"prefix": "NBDC01736",
"pubmeds": [
"15980479",
"17827212"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Protein"
]
},
"nbdc01737": {
"alt_name": "UniPROBE",
"description": "The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA binding specificities of proteins.",
"fairsharing": "FAIRsharing.8zf3ny",
"homepage": "http://the_brain.bwh.harvard.edu/uniprobe/",
"information_keywords": [
"Interaction/Pathway",
"Sequence"
],
"maintainer": "Bulyk Laboratory, Brigham and Women's Hospital/ Harvard Medical School",
"name": "Universal PBM Resource for Oligonucleotide Binding Evaluation",
"prefix": "NBDC01737",
"pubmeds": [
"18842628",
"21037262"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01738": {
"description": "CutDB is one of the first systematic efforts to build an easily accessible collection of documented proteolytic events for natural proteins in vivo or in vitro. A CutDB entry is defined by a unique combination of these three attributes: protease, protein substrate, and cleavage site. Currently, CutDB integrates 3,070 proteolytic events for 470 different proteases captured from public archives (such as MEROPS and HPRD) and publications.",
"fairsharing": "FAIRsharing.er98b1",
"homepage": "http://cutdb.burnham.org",
"name": "CutDB",
"prefix": "NBDC01738",
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01740": {
"alt_name": "CSD",
"description": "Established in 1965, the CSD is the world's repository for small-molecule organic and metal-organic crystal structures. Containing over 800,000 entries from x-ray and neutron diffraction analyses, this unique database of accurate 3D structures has become an essential resource to scientists around the world.",
"fairsharing": "FAIRsharing.vs7865",
"homepage": "http://www.ccdc.cam.ac.uk/solutions/csd-system/components/csd/",
"information_keywords": [
"3D structure",
"Chemical structure"
],
"maintainer": "CCDC (Cambridge Crystallographic Data Centre)",
"name": "The Cambridge Structural Database",
"prefix": "NBDC01740",
"pubmeds": [
"12037359"
],
"status": "Active",
"target_keywords": [
"Metabolite",
"Chemical compound"
]
},
"nbdc01741": {
"alt_name": "InteroPorc",
"description": "InteroPorc is an automatic prediction tool to infer protein-protein interaction networks. It is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8.",
"fairsharing": "FAIRsharing.3hrbfr",
"homepage": "http://biodev.extra.cea.fr/interoporc/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "LBI Team (CEA)",
"name": "Automatic molecular interaction predictions",
"prefix": "NBDC01741",
"pubmeds": [
"18508856"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01742": {
"alt_name": "CST",
"description": "A small pathway portal for showcasing Cell Signaling Technology phospho-antibody products. Contains pathway diagrams that are clickable and link to more information about each protein and the commercial products that are available for that protein.",
"fairsharing": "FAIRsharing.n8pxvx",
"homepage": "http://www.cellsignal.com/",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"name": "Cell Signaling Technology Pathway Database",
"prefix": "NBDC01742",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc01743": {
"alt_name": "PSP",
"description": "PhosphoSite Plus provides extensive information on mammalian post-translational modifications (PTMs). The resource supersedes PhosphoSite a mammalian protein database that provides information about in vivo phosphorylation sites.",
"fairsharing": "FAIRsharing.x8xt3k",
"homepage": "http://www.phosphosite.org",
"information_keywords": [
"Sequence",
"3D structure",
"Localization",
"Bibliography/Documents"
],
"maintainer": "Icahn School of Medicine at Mount Sinai||NCI (National Cancer Institute, National Institutes of Health)",
"name": "PhosphoSite Plus",
"prefix": "NBDC01743",
"pubmeds": [
"12478304",
"15174125",
"25514926"
],
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease"
]
},
"nbdc01744": {
"description": "The Autism Chromosome Rearrangement Database is a collection of hand curated breakpoints and other genomic features, related to autism, taken from publicly available literature, databases and unpublished data.",
"fairsharing": "FAIRsharing.ac329k",
"homepage": "http://projects.tcag.ca/autism",
"information_keywords": [
"Expression",
"Sequence",
"Phenotype"
],
"maintainer": "Center for Applied Genomics",
"name": "The Autism Chromosome Rearrangement Database",
"prefix": "NBDC01744",
"pubmeds": [
"18252227"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease",
"Organism"
]
},
"nbdc01746": {
"alt_name": "PlantTFDB",
"description": "Plant Transcription Factor Database (PlantTFDB) provides a comprehensive, high-quality resource of plant transcription factors (TFs), regulatory elements and interactions between them. In the latest version, It contains 320 370 TFs, classified into 58 families, from 165 species. Abundant functional and evolutionary annotations (e.g., GO, functional description, binding motifs, cis-element, regulation, references, orthologous groups and phylogenetic tree, etc.) are provided for identified TFs. In addition, multiple online tools are set up for TF identification, regulation prediction and functional enrichment analyses.",
"fairsharing": "FAIRsharing.ex3fqk",
"homepage": "http://planttfdb.cbi.pku.edu.cn",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "CBI (Center for Bioinformatics, Peking University)",
"name": "Plant Transcription Factor Database",
"prefix": "NBDC01746",
"pubmeds": [
"25750178",
"24174544"
],
"status": "Active",
"target_keywords": [
"Protein",
"Genome/Gene"
]
},
"nbdc01748": {
"alt_name": "KNOTTIN",
"description": "The KNOTTIN database provides standardized data on the knottin structural family (also referred to as the \"Inhibitor Cystine Knot (ICK) motif/family/fold\"). (Since it falls outside the scope of FAIRsharing, the record does not exist.)",
"information_keywords": [
"3D structure",
"Chemical structure"
],
"maintainer": "CBS (Centre de Biochimie Structurale)",
"name": "Knottin database",
"prefix": "NBDC01748",
"pubmeds": [
"18025039"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01749": {
"alt_name": "CTGA",
"description": "The Centre for Arab Genomic Studies (CAGS) initiated the ambitious project to establish the CTGA (Catalogue of Transmission Genetics in Arabs) database for genetic disorders in Arabs with the aim to enlighten the scientific community and the public on the occurrence of inherited disorders in Arabs and to suggest future investigation strategies.",
"fairsharing": "FAIRsharing.etp65g",
"homepage": "http://www.cags.org.ae/ctga/",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "Centre for Arab Genomic Studies",
"name": "Catalogue of Transmission Genetics in Arabs",
"prefix": "NBDC01749",
"pubmeds": [
"16381941"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc01750": {
"alt_name": "CABRI",
"description": "CABRI will refine tools and test the formation of an integrated resource centre service linking catalogue databases of different organism types, genetic materials and other \"biologicals\" in Europe so that the user world-wide can access these relevant catalogues during one searching session through a common entry point and request/order products to be delivered to their place of work.",
"fairsharing": "FAIRsharing.qx2rvz",
"homepage": "http://www.cabri.org",
"information_keywords": [
"Bioresource"
],
"maintainer": "Centro Biotecnologie Avanzate",
"name": "Common Access to Biological Resources and Information",
"prefix": "NBDC01750",
"pubmeds": [
"18629057"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc01751": {
"alt_name": "CGSC",
"description": "The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature.",
"fairsharing": "FAIRsharing.1tbrdz",
"homepage": "http://cgsc.biology.yale.edu/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Sequence"
],
"maintainer": "CGSC (Coli Genetic Stock Center, Yale University)",
"name": "The Coli Genetic Stock Center",
"prefix": "NBDC01751",
"pubmeds": [
"17352909"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01752": {
"description": "The IRESite database presents information about experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract the eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure.",
"fairsharing": "FAIRsharing.kd39j4",
"homepage": "http://www.iresite.org",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Charles University",
"name": "IRESite",
"prefix": "NBDC01752",
"pubmeds": [
"16381829",
"19917642"
],
"status": "Active",
"target_keywords": [
"DNA",
"Protein",
"RNA"
]
},
"nbdc01754": {
"description": "This resource is a collection of all proteins identified to be localized on kinetochore, centrosome, midbody, telomere and spindle from two fungi (S. cerevisiae and S. pombe) and five animals, including C. elegans, D. melanogaster, X. laevis, M. musculus and H. sapiens based on the rationale of \"Seeing is believing\" (Bloom K et al., 2005). Through ortholog searches, the proteins potentially localized at these sub-cellular regions were detected in 144 eukaryotes. Then the integrated and searchable database MiCroKiTS - Midbody, Centrosome, Kinetochore, Telomere and Spindle has been established. Currently, the MiCroKiTS 4.0 database was updated on Sep. 6, 2014, containing 87,983 unique protein entries.",
"fairsharing": "FAIRsharing.3cswbc",
"homepage": "http://microkit.biocuckoo.org/",
"information_keywords": [
"Sequence",
"Localization"
],
"maintainer": "The CUCKOO Workgroup",
"name": "MiCroKiTS",
"prefix": "NBDC01754",
"pubmeds": [
"19783819",
"25392421"
],
"status": "Active",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc01755": {
"description": "GenomeTraFaC is a database of conserved regulatory elements obtained by systematically analyzing the orthologous set of human and mouse genes. It mainly focuses on all of the high-quality mRNA entries of mouse and human genes in the Reference Sequence (RefSeq) database of the NCBI.",
"fairsharing": "FAIRsharing.f8pqxt",
"homepage": "http://genometrafac.cchmc.org",
"information_keywords": [
"Interaction/Pathway",
"Sequence"
],
"maintainer": "Cincinnati Children's Hospital Medical Center||NIH (National Institutes of Health)",
"name": "GenomeTraFaC",
"prefix": "NBDC01755",
"pubmeds": [
"17178752"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01756": {
"description": "An integrated database of human coding single nucleotide polymorphisms (SNPs) and their annotations.",
"fairsharing": "FAIRsharing.c1rep3",
"homepage": "http://polydoms.cchmc.org",
"information_keywords": [
"Sequence",
"3D structure",
"Ontology/Terminology/Nomenclature",
"Interaction/Pathway",
"Phenotype"
],
"maintainer": "Cincinnati Children's Hospital Medical Center",
"name": "PolyDoms",
"prefix": "NBDC01756",
"pubmeds": [
"17142238"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Protein",
"Health/Disease",
"Genome/Gene"
]
},
"nbdc01757": {
"alt_name": "GreenPhyl",
"description": "GreenPhylDB comprises 37 full genomes from the major phylum of plant evolution. Clustering of these genomes was performed to define a consistent and extensive set of homeomorphic plant families.",
"fairsharing": "FAIRsharing.j98570",
"homepage": "http://www.greenphyl.org",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "CIRAD (International Cooperation Center for Agricultural Research for Development)||Bioversity International||Generation Challenge Programme||South Green",
"name": "GreenPhylDB: A phylogenomic database for plant comparative genomics",
"prefix": "NBDC01757",
"pubmeds": [
"20864446"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc01759": {
"alt_name": "OTL",
"description": "Oryza Tag Line consists in a searchable database developed under the Oracle management system integrating phenotypic data resulting from the evaluation of the Genoplante rice insertion line library.",
"fairsharing": "FAIRsharing.61c2x6",
"homepage": "http://oryzatagline.cirad.fr/",
"information_keywords": [
"Sequence",
"Expression",
"Phenotype",
"Method"
],
"maintainer": "Bioversity International",
"name": "Oryza Tag Line",
"prefix": "NBDC01759",
"pubmeds": [
"17947330"
],
"status": "Active",
"target_keywords": [
"DNA",
"Genome/Gene",
"RNA"
]
},
"nbdc01761": {
"description": "fireDB is a database of Protein Data Bank structures, ligands and annotated functional site residues. The database can be accessed by PDB codes or UniProt accession numbers as well as keywords.",
"fairsharing": "FAIRsharing.5125qd",
"homepage": "http://firedb.bioinfo.cnio.es/",
"information_keywords": [
"3D structure",
"Chemical structure"
],
"name": "FireDB",
"prefix": "NBDC01761",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01762": {
"alt_name": "CAZy",
"description": "The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.",
"fairsharing": "FAIRsharing.ntyq70",
"homepage": "http://www.cazy.org/",
"information_keywords": [
"Classification"
],
"maintainer": "AFMB (Laboratoire Architecture et Fonction des Macromolecules Biologiques)||UniversitΓ© d'Aix-Marseille",
"name": "The Carbohydrate-Active enZYmes Database",
"prefix": "NBDC01762",
"pubmeds": [
"18838391",
"24270786"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01763": {
"description": "Diatoms are photosynthetic unicellular eukaryotes that play an essential role in marine ecosystems. On a global scale, they generate around one fifth of the oxygen we breathe. On this web site we present searchable databases of diatom ESTs (expressed sequence tags) that can be used to explore diatom biology.",
"fairsharing": "FAIRsharing.csbxzs",
"homepage": "http://www.biologie.ens.fr/diatomics/EST3",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "LMGM (Laboratoire de Microbiologie et Genetique Moleculaires)",
"name": "The Diatom EST Database",
"prefix": "NBDC01763",
"pubmeds": [
"19029140",
"15608213"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"DNA",
"RNA"
]
},
"nbdc01764": {
"description": "PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes). Researchers are able to use this resource to visualise the history of genes with the available phylogentic trees and multiple sequence alignments.",
"fairsharing": "FAIRsharing.7hxxc4",
"homepage": "http://phylomedb.org",
"information_keywords": [
"Classification",
"Sequence"
],
"maintainer": "CRG (Comparative Genomics Group)",
"name": "PhylomeDB",
"prefix": "NBDC01764",
"pubmeds": [
"17962297",
"21075798",
"24275491"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01765": {
"description": "figshare is a repository where users can make all of their research outputs available in a citable, shareable and discoverable manner.",
"fairsharing": "FAIRsharing.drtwnh",
"homepage": "http://figshare.com/",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents",
"Portal",
"Repository"
],
"maintainer": "Digital Science, Macmillan Publishers||Datacite",
"name": "figshare",
"prefix": "NBDC01765",
"pubmeds": [
"21772785"
],
"status": "Active"
},
"nbdc01766": {
"alt_name": "CCD",
"description": "The Chemical Component Dictionary is an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names.",
"fairsharing": "FAIRsharing.e58gcm",
"homepage": "http://www.ebi.ac.uk/pdbe-srv/pdbechem/",
"information_keywords": [
"3D structure",
"Image/Movie",
"Classification"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)||wwPDB||EMBL (European Molecular Biology Laboratory)",
"name": "Chemical Component Dictionary",
"prefix": "NBDC01766",
"pubmeds": [
"14681397"
],
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc01773": {
"alt_name": "EGA",
"description": "The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).",
"fairsharing": "FAIRsharing.mya1ff",
"homepage": "https://ega-archive.org/",
"information_keywords": [
"Sequence",
"Phenotype",
"Bibliography/Documents"
],
"maintainer": "CRG (Comparative Genomics Group)||ELIXIR, Wellcome Genome Campus||LMB (MRC Laboratory of Molecular Biology)||EMBL-EBI (European Bioinformatics Institute)",
"name": "The European Genome-phenome Archive",
"prefix": "NBDC01773",
"pubmeds": [
"20972220",
"26111507"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Genome/Gene",
"Organism"
]
},
"nbdc01774": {
"alt_name": "HGNC",
"description": "The HUGO Gene Nomenclature Committee (HGNC) aims to assign a unique and ideally meaningful name and symbol to every human gene. The HGNC database currently comprises over 40,000 public records containing approved human gene nomenclature and associated gene information. The website enables direct links to the searchable HGNC database and other related database resources, such as the HCOP orthology search tool and manually curated gene family webpages.",
"fairsharing": "FAIRsharing.29we0s",
"homepage": "http://www.genenames.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "HUGO (Human Genome Organisation)||Transforming Genetic Medicine Initiative",
"name": "HUGO Gene Nomenclature Committee",
"prefix": "NBDC01774",
"pubmeds": [
"27799471",
"25361968",
"23161694",
"20929869",
"17984084"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01775": {
"alt_name": "EcoGene",
"description": "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites.",
"fairsharing": "FAIRsharing.3q3kvn",
"homepage": "http://ecogene.org/",
"information_keywords": [
"Sequence"
],
"name": "Escherichia coli strain K12 genome database",
"prefix": "NBDC01775",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc01778": {
"alt_name": "SIDER",
"description": "SIDER contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect frequency, drug and side effect classifications as well as links to further information, for example drug_target relations.",
"fairsharing": "FAIRsharing.zzaykv",
"homepage": "http://sideeffects.embl.de",
"information_keywords": [
"Interaction/Pathway",
"Bibliography/Documents"
],
"name": "Side Effect Resource",
"prefix": "NBDC01778",
"pubmeds": [
"20087340"
],
"status": "Active",
"target_keywords": [
"Drug",
"Health/Disease"
]
},
"nbdc01779": {
"description": "The Blue Star STING database stores information on the interactions between proteins and other bio macromolecules. Structure descriptors used in the analysis of these interactions are stored in STING DB to aid research primarily into the problems challenging Brazilian agriculture, livestock and medicine.",
"fairsharing": "FAIRsharing.q7bkqr",
"homepage": "http://sms.cbi.cnptia.embrapa.br/SMS/index_s.html",
"information_keywords": [
"Interaction/Pathway",
"3D structure"
],
"maintainer": "Computational Biology Research Group , Embrapa/Informatica Agropecuaria",
"name": "STING",
"prefix": "NBDC01779",
"pubmeds": [
"15608194"
],
"status": "Active",
"target_keywords": [
"Protein",
"Metabolite"
]
},
"nbdc01780": {
"description": "CryptoDB serves as the functional genomics database for Cryptosporidium and related species. CryptoDB is a free, online resource for accessing and exploring genome sequence and annotation, functional genomics data, isolate sequences, and orthology profiles across organisms. It also includes supplemental bioinformatics analyses and a web interface for data-mining.",
"fairsharing": "FAIRsharing.t3nprm",
"homepage": "https://cryptodb.org/cryptodb/app",
"information_keywords": [
"Sequence",
"Expression",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "CBIL (Computational Biology and Informatics Laboratory, University of Pennsylvania)||Center for Tropical & Emerging Global Diseases, University of Georgia",
"name": "CryptoDB",
"prefix": "NBDC01780",
"pubmeds": [
"16381902"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"DNA",
"Organism"
]
},
"nbdc01781": {
"alt_name": "VEuPathDB",
"description": "The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB) focuses on eukaryotic pathogens and invertebrate vectors of infectious diseases, , encompassing data from prior resources devoted to parasitic species (EuPathDB), fungi (FungiDB) and vector species (VectorBase). While each of the taxonomic groups within this resource is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all of these resources, and the opportunity to leverage orthology for searches across genera.",
"fairsharing": "FAIRsharing.f94905",
"homepage": "https://veupathdb.org/veupathdb/app/",
"information_keywords": [
"Phenotype",
"Sequence",
"Portal"
],
"maintainer": "Institute of Integrative Biology, University of Liverpool||The Wellcome Trust Centre for Molecular Parasitology||Wellcome Sanger Institute ||Bioinformatics Resource Centers, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH)",
"name": "Eukaryotic Pathogen, Vector and Host Informatics Resource",
"prefix": "NBDC01781",
"pubmeds": [
"19914931",
"17098930",
"24936976",
"25388105",
"23161692"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation",
"Health/Disease",
"Organism"
]
},
"nbdc01782": {
"description": "A detailed study of Giardia lamblia's genome will provide insights into an early evolutionary stage of eukaryotic chromosome organization as well as other aspects of the prokaryotic / eukaryotic divergence.",
"fairsharing": "FAIRsharing.e7skwg",
"homepage": "http://giardiadb.org",
"information_keywords": [
"Sequence",
"Expression",
"Ontology/Terminology/Nomenclature"
],
"name": "GiardiaDB",
"prefix": "NBDC01782",
"pubmeds": [
"18824479"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"Genome/Gene",
"cDNA/EST",
"Organism"
]
},
"nbdc01783": {
"description": "PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.",
"fairsharing": "FAIRsharing.g4n8sw",
"homepage": "http://PlasmoDB.org",
"information_keywords": [
"Sequence",
"Expression",
"Ontology/Terminology/Nomenclature"
],
"name": "PlasmoDB",
"prefix": "NBDC01783",
"pubmeds": [
"18957442"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Organism",
"cDNA/EST"
]
},
"nbdc01784": {
"alt_name": "ToxoDB",
"description": "ToxoDB is a genome database for the genus Toxoplasma, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including toxoplasmosis.",
"fairsharing": "FAIRsharing.a08mtc",
"homepage": "https://toxodb.org",
"information_keywords": [
"Sequence",
"Expression",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Bioinformatics Resource Centers, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH)",
"name": "Toxoplasma Genomics Resource",
"prefix": "NBDC01784",
"pubmeds": [
"18003657"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Organism",
"cDNA/EST"
]
},
"nbdc01785": {
"description": "TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"fairsharing": "FAIRsharing.pv0ezt",
"homepage": "http://trichdb.org/trichdb/",
"information_keywords": [
"Sequence",
"Expression",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "CBIL (Computational Biology and Informatics Laboratory, University of Pennsylvania)||Center for Tropical & Emerging Global Diseases, University of Georgia",
"name": "TrichDB",
"prefix": "NBDC01785",
"pubmeds": [
"18824479"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Organism",
"cDNA/EST"
]
},
"nbdc01786": {
"description": "TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"fairsharing": "FAIRsharing.fs1z27",
"homepage": "http://tritrypdb.org/tritrypdb/",
"information_keywords": [
"Sequence",
"Expression",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "CBIL (Computational Biology and Informatics Laboratory, University of Pennsylvania)||Center for Tropical & Emerging Global Diseases, University of Georgia||Wellcome Sanger Institute",
"name": "TriTrypDB",
"prefix": "NBDC01786",
"pubmeds": [
"19843604"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Organism",
"cDNA/EST"
]
},
"nbdc01787": {
"alt_name": "HOMD",
"description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information.",
"fairsharing": "FAIRsharing.v3jf2q",
"homepage": "http://www.homd.org/",
"information_keywords": [
"Environment",
"Sequence",
"Expression",
"Localization",
"Taxonomy"
],
"maintainer": "Forsyth Institute",
"name": "Human Oral Microbiome Database",
"prefix": "NBDC01787",
"pubmeds": [
"20624719"
],
"status": "Active",
"target_keywords": [
"Organism",
"Genome/Gene"
]
},
"nbdc01788": {
"alt_name": "TIGR_TGI",
"description": "The goal of The Gene Index Project is to use the available EST and gene sequences, along with the reference genomes wherever available, to provide an inventory of likely genes and their variants and to annotate these with information regarding the functional roles played by these genes and their products.",
"fairsharing": "FAIRsharing.aftff2",
"homepage": "http://compbio.dfci.harvard.edu/tgi/",
"information_keywords": [
"Sequence"
],
"maintainer": "Harvard University||Dana-Farber Cancer Institute",
"name": "The Gene Index Project",
"prefix": "NBDC01788",
"pubmeds": [
"15608288",
"10592205"
],
"status": "Closed",
"target_keywords": [
"DNA",
"Genome/Gene"
]
},
"nbdc01789": {
"alt_name": "HC DPD",
"description": "The Health Canada Drug Product Database contains product specific information on drugs approved for use in Canada. The database is managed by Health Canada and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. It contains approximately 15,000 products which companies have notified Health Canada as being marketed.",
"fairsharing": "FAIRsharing.tyyn81",
"homepage": "http://www.hc-sc.gc.ca/dhp-mps/prodpharma/databasdon/index-eng.php",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Health Canada",
"name": "Health Canada Drug Product Database",
"prefix": "NBDC01789",
"status": "Active",
"target_keywords": [
"Drug"
]
},
"nbdc01790": {
"alt_name": "SABIO-RK",
"description": "SABIO-RK is a database for biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.",
"fairsharing": "FAIRsharing.cwx04e",
"homepage": "http://sabiork.h-its.org/",
"information_keywords": [
"Method"
],
"maintainer": "FAIRDOM||HITS (Heidelberg Institute for Theoretical Studies)",
"name": "SABIO-RK Biochemical Reaction Kinetics Database",
"prefix": "NBDC01790",
"pubmeds": [
"22102587"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01791": {
"alt_name": "euHCVdb",
"description": "The euHCVdb is mainly oriented towards protein sequence, structure and function analyses and structural biology of Hepatitis C Virus.",
"fairsharing": "FAIRsharing.bwctv",
"homepage": "https://euhcvdb.lyon.inserm.fr/euHCVdb/",
"information_keywords": [
"3D structure",
"Chemical structure"
],
"maintainer": "CNRS (The National Centre for Scientific Research)||IBCP (Institut de Biologie et Chimie des Proteines, Centre National de la Recherche Scientifique)||LMGM (Laboratoire de Microbiologie et Genetique Moleculaires)",
"name": "European Hepatitis C Virus database",
"prefix": "NBDC01791",
"pubmeds": [
"17142229",
"19519481"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01792": {
"description": "The Protein Classification Benchmark Collection was created in order to create standard datasets on which the performance of machine learning methods can be compared.",
"fairsharing": "FAIRsharing.88b6b5",
"homepage": "http://net.icgeb.org/benchmark/",
"information_keywords": [
"3D structure",
"Sequence"
],
"maintainer": "ICGEB (International Centre Genetic Engineering and Biotechnology)||Jedlik Laboratories: Bioinformatics, Faculty of Information Technology, PΓ‘zmΓ‘ny PΓ©ter Catholic University",
"name": "Protein Classification Benchmark Collection",
"prefix": "NBDC01792",
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01793": {
"description": "BAliBASE; a benchmark alignment database, including enhancements for repeats, transmembrane sequences and circular permutations.",
"fairsharing": "FAIRsharing.sed5tq",
"homepage": "http://www.lbgi.fr/balibase/",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "IGBMC (Institut de Genetique et de Biologie Moleculaire et Cellulaire)||LMGM (Laboratoire de Microbiologie et Genetique Moleculaires)",
"name": "BAliBASE",
"prefix": "NBDC01793",
"pubmeds": [
"11125126",
"16044462"
],
"status": "Active",
"target_keywords": [
"Protein",
"DNA"
]
},
"nbdc01794": {
"alt_name": "ABS",
"description": "ABS: A database of Annotated regulatory Binding Sites from known binding sites identified in promoters of orthologous vertebrate genes.",
"fairsharing": "FAIRsharing.7mnebr",
"homepage": "http://genome.imim.es/datasets/abs2005/",
"information_keywords": [
"Interaction/Pathway",
"Sequence"
],
"maintainer": "LMGM (Laboratoire de Microbiologie et Genetique Moleculaires)||SBI (The Structural Bioinformatics Laboratory)",
"name": "Annotated regulatory Binding Sites from Orthologous Promoters",
"prefix": "NBDC01794",
"pubmeds": [
"16381947"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01795": {
"description": "ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al.",
"fairsharing": "FAIRsharing.tp9z4q",
"homepage": "http://sbi.imim.es/archdb",
"information_keywords": [
"Classification",
"Sequence",
"3D structure"
],
"maintainer": "LMGM (Laboratoire de Microbiologie et Genetique Moleculaires)||SBI (The Structural Bioinformatics Laboratory)||bioinsilico.org",
"name": "ArchDB",
"prefix": "NBDC01795",
"pubmeds": [
"14681390",
"24265221"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01796": {
"description": "KinMutBase is a comprehensive database of disease-causing mutations in protein kinase domains. This resources provides plenty of information, namely mutation statistics and display, clickable sequences with mutations and changes to restriction enzyme patterns.",
"fairsharing": "FAIRsharing.q2ntvx",
"homepage": "http://structure.bmc.lu.se/idbase/KinMutBase/",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "University of Tampere",
"name": "KinMutBase",
"prefix": "NBDC01796",
"pubmeds": [
"10592276",
"15832311"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Genetic variation",
"Health/Disease",
"Genome/Gene"
]
},
"nbdc01797": {
"alt_name": "CADB",
"description": "Conformation Angles DataBase [ CADB-3.0 ] is a comprehensive, authoritative and timely knowledge base developed to facilitate retrieval of information related to the conformational angles (main-chain and side-chain) of the amino acid residues present in the non-redundant (both 25% and 90%) data set.",
"fairsharing": "FAIRsharing.wyz5he",
"homepage": "http://cluster.physics.iisc.ernet.in/cadb/",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "Indian Institute of Science",
"name": "Conformation Angles Database",
"prefix": "NBDC01797",
"pubmeds": [
"12520049",
"15858276"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01798": {
"alt_name": "DisProt",
"description": "The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part.",
"fairsharing": "FAIRsharing.dt9z89",
"homepage": "http://www.disprot.org/",
"information_keywords": [
"Sequence",
"3D structure",
"Chemical structure",
"Interaction/Pathway"
],
"maintainer": "BioComputing laboratory, University of Padua",
"name": "Database of Protein Disorder",
"prefix": "NBDC01798",
"pubmeds": [
"17145717"
],
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease"
]
},
"nbdc01799": {
"alt_name": "euGenes",
"description": "euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information.",
"fairsharing": "FAIRsharing.7fc5y6",
"homepage": "http://eugenes.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "BioComputing laboratory, University of Padua",
"name": "Eukaryotic Genes",
"prefix": "NBDC01799",
"pubmeds": [
"11752277"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01800": {
"alt_name": "wFleaBase",
"description": "wFleaBase includes data from all species of the genus, yet the primary species are Daphnia pulex and Daphnia magna, because of the broad set of genomic tools that have already been developed for these animals.",
"fairsharing": "FAIRsharing.h5epxm",
"homepage": "http://wfleabase.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "BioComputing laboratory, University of Padua",
"name": "Daphnia Water Flea Genome Database",
"prefix": "NBDC01800",
"pubmeds": [
"15752432"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation"
]
},
"nbdc01801": {
"description": "SpodoBase is an integrated database for the genomics of the Lepidoptera Spodoptera frugiperda. It is a publicly available structured database with insect pest sequences which will allow identification of a number of genes and comprehensive cloning of gene families of interest for the scientific community.",
"fairsharing": "FAIRsharing.c3kchy",
"homepage": "http://bioweb.ensam.inra.fr/spodobase/",
"information_keywords": [
"Sequence"
],
"maintainer": "National Institute of Agrobiological Sciences||ProDom Team",
"name": "SpodoBase",
"prefix": "NBDC01801",
"pubmeds": [
"16796757"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01802": {
"alt_name": "VirHostNet",
"description": "VirHostNet 2.0 integrates an extensive and original literature-curated dataset of virus/virus and virus/host protein-protein interactions complemented with publicly available data.",
"fairsharing": "FAIRsharing.m3316t",
"homepage": "http://virhostnet.prabi.fr",
"information_keywords": [
"Bibliography/Documents",
"Interaction/Pathway"
],
"maintainer": "INSERM (Institut National de la Sante et de la Recherche Medicale)",
"name": "VirHostNet 2.0",
"prefix": "NBDC01802",
"pubmeds": [
"18984613",
"25392406"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01803": {
"alt_name": "BuruList",
"description": "A database dedicated to the analysis of the genome of Mycobacterium ulcerans, the Buruli ulcer bacillus. It provides a complete dataset of DNA and protein sequences derived from the epidemic strain Agy99, linked to the relevant annotations and functional assignments.",
"fairsharing": "FAIRsharing.jrjqc7",
"homepage": "http://genolist.pasteur.fr/BuruList/",
"information_keywords": [
"Sequence"
],
"name": "Buruli ulcer bacillus Database",
"prefix": "NBDC01803",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc01804": {
"description": "Its purpose is to collate and integrate various aspects of the genomic information from E. coli, the paradigm of Gram-negative bacteria. Colibri provides a complete dataset of DNA and protein sequences derived from the paradigm strain E. coli K-12, linked to the relevant annotations and functional assignments. It allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.).",
"fairsharing": "FAIRsharing.hbbtbj",
"homepage": "http://genolist.pasteur.fr/Colibri/",
"information_keywords": [
"Sequence"
],
"name": "Colibri",
"prefix": "NBDC01804",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc01805": {
"alt_name": "LegioList",
"description": "LegioList is a database dedicated to the analysis of the genomes of Legionella pneumophila strain Paris (endemic in France), strain Lens (epidemic isolate), strain Phildelphia 1, and strain Corby. It also includes the genome of Legionella longbeachae strain NSW150.",
"fairsharing": "FAIRsharing.dntrmf",
"homepage": "http://genolist.pasteur.fr/LegioList/",
"information_keywords": [
"Sequence"
],
"name": "Legionella pneumophila genome database",
"prefix": "NBDC01805",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc01806": {
"alt_name": "ListiList",
"description": "ListiList is a database dedicated to the analysis of the genomes of the food-borne pathogen, Listeria monocytogenes, and its non-pathogenic relative, Listeria innocua. Its purpose is to collate and integrate various aspects of the genomic information from L. monocytogenes, a paradigm for bacterial-host interactions.",
"fairsharing": "FAIRsharing.93gy4v",
"homepage": "http://genolist.pasteur.fr/ListiList/",
"information_keywords": [
"Sequence"
],
"name": "Listeria innocua and Listeria monocytogenes genomes database",
"prefix": "NBDC01806",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc01807": {
"alt_name": "MypuList",
"description": "Its purpose is to collate and integrate various aspects of the genomic information from M. pulmonis, a mollicute causal agent of murine respiratory mycoplasmosis. MypuList provides a complete dataset of DNA and protein sequences derived from the strain M. pulmonis UAB CTIP, linked to the relevant annotations and functional assignments.",
"fairsharing": "FAIRsharing.pmz447",
"homepage": "http://genolist.pasteur.fr/MypuList/",
"information_keywords": [
"Sequence"
],
"name": "Mycoplasma pulmonis genome database",
"prefix": "NBDC01807",
"status": "Active",
"target_keywords": [
"DNA",
"Genome/Gene",
"Protein"
]
},
"nbdc01808": {
"alt_name": "PhotoList",
"description": "PhotoList, contains a database dedicated to the analysis of the genome of Photorhabdus luminescens. This analysis has been described in: \"The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens\"",
"fairsharing": "FAIRsharing.9ppftz",
"homepage": "http://genolist.pasteur.fr/PhotoList/",
"information_keywords": [
"Sequence"
],
"name": "Photorhabdus luminescens genome database",
"prefix": "NBDC01808",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc01809": {
"alt_name": "SagaList",
"description": "SagaList contains a database dedicated to the analysis of the genomes of the food-borne pathogen, Streptococcus agalactiae.",
"fairsharing": "FAIRsharing.x54ymh",
"homepage": "http://genolist.pasteur.fr/SagaList/",
"information_keywords": [
"Sequence"
],
"name": "Streptococcus agalactiae NEM316 / Serotype III genome database",
"prefix": "NBDC01809",
"status": "Active",
"target_keywords": [
"DNA",
"Genome/Gene",
"Protein"
]
},
"nbdc01812": {
"description": "The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools.",
"fairsharing": "FAIRsharing.dvyrsz",
"homepage": "http://www.peptideatlas.org",
"information_keywords": [
"Sequence"
],
"maintainer": "ISB (Institute for Systems Biology)||Seattle Proteome Center",
"name": "PeptideAtlas",
"prefix": "NBDC01812",
"pubmeds": [
"18451766",
"16381952"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01813": {
"alt_name": "BACTIBASE",
"description": "BACTIBASE contains calculated or predicted physicochemical properties of bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships structure/function and target organisms of these peptides and therefore better exploitation of their biological activity in both the medical and food sectors.",
"fairsharing": "FAIRsharing.5f5mfm",
"homepage": "http://bactibase.hammamilab.org/main.php",
"information_keywords": [
"Sequence",
"3D structure",
"Interaction/Pathway"
],
"maintainer": "ISSBAT (Higher Institute of Applied Biological Sciences of Tunis)||Laval University",
"name": "Bactibase: database dedicated to bacteriocins",
"prefix": "NBDC01813",
"pubmeds": [
"20105292",
"17941971"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01814": {
"description": "Human Proteinpedia is a community portal for sharing and integration of human protein data. It allows research laboratories to contribute and maintain protein annotations.",
"fairsharing": "FAIRsharing.xxdxtv",
"homepage": "http://www.humanproteinpedia.org/",
"information_keywords": [
"Expression",
"Localization",
"Method"
],
"maintainer": "Institute of Bioinformatics",
"name": "Human Proteinpedia",
"prefix": "NBDC01814",
"pubmeds": [
"18948298"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01815": {
"alt_name": "MycoBank",
"description": "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.",
"fairsharing": "FAIRsharing.v8se8r",
"homepage": "http://www.mycobank.org",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Sequence"
],
"maintainer": "IMA (International Mycological Association)||NLM (National Library of Medicine)",
"name": "Fungal Nomenclature and Species Bank",
"prefix": "NBDC01815",
"pubmeds": [
"24563843"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01816": {
"description": "The information in the database is presented at two levels: the initial view or landing pages for each target family provide expert-curated overviews of the key properties and selective ligands and tool compounds available. For selected targets more detailed introductory chapters for each family are available along with curated information on the pharmacological, physiological, structural, genetic and pathophysiogical properties of each target. The database is enhanced with hyperlinks to additional information in other databases including Ensembl, UniProt, PubChem, ChEMBL and DrugBank, as well as curated chemical information and literature citations in PubMed.",
"fairsharing": "FAIRsharing.f1dv0",
"homepage": "http://www.guidetopharmacology.org",
"information_keywords": [
"Sequence",
"Chemical structure",
"Interaction/Pathway"
],
"maintainer": "International Union of Basic and Clinical Pharmacology",
"name": "Guide to Pharmacology",
"prefix": "NBDC01816",
"pubmeds": [
"26464438",
"24234439"
],
"status": "Active",
"target_keywords": [
"Protein",
"Drug"
]
},
"nbdc01817": {
"description": "SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. The quantitative trait loci (QTL) represent more than 18 years of QTL mapping of more than 90 unique traits. SoyBase also contains the well-annotated 'Williams 82' genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. SoyBase is the repository for controlled vocabularies for soybean growth, development and trait terms, which are also linked to the more general plant ontologies.",
"fairsharing": "FAIRsharing.z4agsr",
"homepage": "https://soybase.org",
"information_keywords": [
"Phenotype",
"Ontology/Terminology/Nomenclature",
"Expression",
"Image/Movie",
"Interaction/Pathway",
"Sequence",
"Method"
],
"maintainer": "Iowa State University",
"name": "SoyBase",
"prefix": "NBDC01817",
"pubmeds": [
"20008513"
],
"status": "Active",
"target_keywords": [
"Organism",
"Genome/Gene",
"Genetic variation",
"DNA",
"Protein"
]
},
"nbdc01818": {
"alt_name": "EMMA",
"description": "The European Mouse Mutant Archive (EMMA) is a non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. The laboratory mouse is the most important mammalian model for studying genetic and multi-factorial diseases in man. Thus the work of EMMA will play a crucial role in exploiting the tremendous potential benefits to human health presented by the current research in mammalian genetics.",
"fairsharing": "FAIRsharing.g2fjt2",
"homepage": "https://www.infrafrontier.eu/",
"information_keywords": [
"Bioresource"
],
"maintainer": "Infrafrontier Research Infrastructure, Infrafrontier Gmbh",
"name": "European Mouse Mutant Archive",
"prefix": "NBDC01818",
"pubmeds": [
"19783817"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"DNA",
"Protein"
]
},
"nbdc01819": {
"alt_name": "IMG",
"description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. Currently, this site is being operated as IMG/M (NBDC02309).",
"fairsharing": "FAIRsharing.10bk29",
"homepage": "http://img.jgi.doe.gov/m",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "DOE JGI (Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory)",
"name": "Integrated Microbial Genomes",
"prefix": "NBDC01819",
"pubmeds": [
"17932063",
"22086953",
"24165883",
"24136997"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"DNA"
]
},
"nbdc01820": {
"description": "BeetleBase is a community resource for Tribolium genetics, genomics and developmental biology. The database is built on the Chado generic data model, and is able to store various types of data, ranging from genome sequences to mutant phenotypes.",
"fairsharing": "FAIRsharing.h5f091",
"homepage": "http://www.beetlebase.org/",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Kansas State University",
"name": "BeetleBase",
"prefix": "NBDC01820",
"pubmeds": [
"19820115"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein"
]
},
"nbdc01821": {
"alt_name": "YEASTRACT",
"description": "YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references.",
"fairsharing": "FAIRsharing.mphj4z",
"homepage": "http://www.yeastract.com",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Biological Sciences Research Group, Instituto Superior TΓ©cnico||Knowledge Discovery & Bioinformatics Research Group, Instituto Superior TΓ©cnico",
"name": "Yeast Searching for Transcriptional Regulators and Consensus Tracking",
"prefix": "NBDC01821",
"pubmeds": [
"20972212",
"24170807",
"18032429",
"16381908"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"DNA",
"RNA"
]
},
"nbdc01822": {
"description": "NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons. The goal of NeuroMorpho.Org is to provide dense coverage of available reconstruction data for the neuroscience community. The database currently holds over 37,500 neurons.",
"fairsharing": "FAIRsharing.drcy7r",
"homepage": "http://neuromorpho.org/",
"information_keywords": [
"Method",
"3D structure",
"Image/Movie"
],
"maintainer": "Krasnow Institute for Advanced Study||The National Academies of Sciences, Engineering, and Medicine",
"name": "NeuroMorpho.Org",
"prefix": "NBDC01822",
"pubmeds": [
"25653123",
"16552417",
"24972604",
"23522039",
"22536169",
"25576225",
"18949582"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc01823": {
"alt_name": "PMDB",
"description": "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques.",
"fairsharing": "FAIRsharing.wkaakq",
"homepage": "http://srv00.recas.ba.infn.it/PMDB/main.php",
"information_keywords": [
"3D structure"
],
"name": "Protein Model Database",
"prefix": "NBDC01823",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01824": {
"description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.",
"fairsharing": "FAIRsharing.bpxgb6",
"homepage": "http://greengenes.lbl.gov",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "LBNL (Lawrence Berkeley National Laboratory)",
"name": "Greengenes",
"prefix": "NBDC01824",
"pubmeds": [
"16820507"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc01825": {
"alt_name": "GPM",
"description": "Rather than being a complete record of a proteomics experiment, this database holds the minimum amount of information necessary for certain bioinformatics-related tasks, such as sequence assignment validation. Most of the data is held in a set of XML files.",
"fairsharing": "FAIRsharing.fhcmwq",
"homepage": "http://www.thegpm.org/GPMDB/index.html",
"information_keywords": [
"Chemical structure",
"Method"
],
"maintainer": "MCPSB (Manitoba Centre for Proteomics and Systems Biology)",
"name": "The Global Proteome Machine Database",
"prefix": "NBDC01825",
"pubmeds": [
"15595733"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01826": {
"description": "SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.",
"fairsharing": "FAIRsharing.frryvx",
"homepage": "http://supfam.org",
"information_keywords": [
"Classification",
"Chemical structure"
],
"name": "SUPERFAMILY",
"prefix": "NBDC01826",
"pubmeds": [
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"19036790",
"21062816",
"11697912"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01827": {
"alt_name": "MMMP",
"description": "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.",
"fairsharing": "FAIRsharing.xxtmjs",
"homepage": "http://www.mmmp.org/MMMP/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "MMMP (Melanoma Molecular Map Project)",
"name": "Melanoma Molecular Map Project",
"prefix": "NBDC01827",
"pubmeds": [
"18477889"
],
"status": "Inactive",
"target_keywords": [
"Health/Disease",
"Drug"
]
},
"nbdc01828": {
"description": "caNanoLab is a data sharing portal designed to facilitate information sharing across the international biomedical nanotechnology research community to expedite and validate the use of nanotechnology in biomedicine. caNanoLab provides support for the annotation of nanomaterials with characterizations resulting from physico-chemical, in vitro and in vivo assays and the sharing of these characterizations and associated nanotechnology protocols in a secure fashion.",
"fairsharing": "FAIRsharing.y1qpdm",
"homepage": "http://cananolab.nci.nih.gov/caNanoLab/",
"information_keywords": [
"Method",
"Portal",
"Bibliography/Documents"
],
"maintainer": "CBIIT (Center for Biomedical Informatics and Information Technology)||CCNEs (Centers of Cancer Nanotechnology Excellence)||NLC (Nanotechnology Characterization Laboratory)||NIH (National Institutes of Health)",
"name": "caNanoLab",
"prefix": "NBDC01828",
"pubmeds": [
"25364375"
],
"status": "Active",
"target_keywords": [
"Chemical compound",
"Health/Disease"
]
},
"nbdc01829": {
"alt_name": "SSToSS",
"description": "SSToSS is a database which provides sequence-structural templates of single member protein domain superfamilies like PASS2. Sequence-structural templates are recognized by considering the content and overlap of sequence similarity and structural parameters like, solvent inaccessibility, secondary structural content, hydrogen bonding and spatial packing of the residues among the protein of single member superfamilies.",
"fairsharing": "FAIRsharing.cwn40y",
"homepage": "http://caps.ncbs.res.in/SSTOSS/index.htm",
"information_keywords": [
"Classification",
"Sequence",
"3D structure"
],
"maintainer": "NCBS (National Center for Biological Sciences)",
"name": "Sequence-Structural Templates of Single-member Superfamilies",
"prefix": "NBDC01829",
"pubmeds": [
"16922694"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01830": {
"description": "AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes.",
"fairsharing": "FAIRsharing.vwmc9h",
"homepage": "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "AceView Worm Genome",
"prefix": "NBDC01830",
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Genome/Gene",
"RNA"
]
},
"nbdc01831": {
"description": "dbMHC provides access to HLA sequences, tools to support genetic testing of HLA loci, HLA allele and haplotype frequencies of over 90 populations worldwide, as well as clinical datasets on nematopoietic stem cell transplantation, and insulin dependant diabetes mellitus (IDDM), Rheumatoid Arthritis (RA), Narcolepsy and Spondyloarthropathy. All clinical datasets housed at the dbMHC provide access to genotypic and phenotypic data on anonimyzed samples with aggregate query functions, and complete download capability.",
"fairsharing": "FAIRsharing.r90425",
"homepage": "http://www.ncbi.nlm.nih.gov/mhc/",
"information_keywords": [
"Sequence",
"Expression"
],
"name": "dbMHC",
"prefix": "NBDC01831",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Protein"
]
},
"nbdc01832": {
"description": "NCBI takes great care to ensure that the translation for each coding sequence (CDS) present in GenBank records is correct. Central to this effort is careful checking on the taxonomy of each record and assignment of the correct genetic code for each organism and record. (Since it falls outside the scope of FAIRsharing, the record does not exist.)",
"homepage": "https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi",
"information_keywords": [
"Sequence"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "Genetic Codes",
"prefix": "NBDC01832",
"pubmeds": [
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"8281749"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01833": {
"description": "Influenza Virus Resource presents data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis, annotation and submission to GenBank. In addition, it provides links to other resources that contain flu sequences, publications and general information about flu viruses.",
"fairsharing": "FAIRsharing.13cdzp",
"homepage": "https://www.ncbi.nlm.nih.gov/genomes/FLU/Database/nph-select.cgi?go=database",
"information_keywords": [
"Sequence"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "Influenza Virus Resource",
"prefix": "NBDC01833",
"pubmeds": [
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],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Organism",
"Health/Disease"
]
},
"nbdc01834": {
"alt_name": "NCBI Virus",
"description": "NCBI Virus is an integrative, value-added resource designed to support retrieval, display and analysis of a curated collection of virus sequences and large sequence datasets. We are a community portal for viral sequence data, and our goal is to increase the usability of data archived in GenBank and other NCBI repositories. NCBI Viral Genomes Resource is a collection of virus genomic sequences that provides curated sequence data, related information and tools. It includes all complete viral genome sequences deposited in the International Nucleotide Sequence Database Collaboration (INSDC) databases, i.e. DDBJ, EMBL, and GenBank. Data are organized by viral taxonomy, and reference sequence records (RefSeqs) from one or more genome sequences for each viral species. After a RefSeq has been created for a species, other complete genomes from that same species are indexed as neighbors to the RefSeq.",
"fairsharing": "FAIRsharing.qt5ky7",
"homepage": "https://www.ncbi.nlm.nih.gov/genome/viruses/",
"information_keywords": [
"Sequence"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "NCBI Virus Sequences for Discovery",
"prefix": "NBDC01834",
"pubmeds": [
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],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Organism"
]
},
"nbdc01835": {
"description": "The organelle genomes are part of the NCBI Reference Sequence (RefSeq) project that provides curated sequence data and related information for the community to use as a standard.",
"fairsharing": "FAIRsharing.99sey6",
"homepage": "http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=2759&hopt=html",
"information_keywords": [
"Sequence"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "Organelle Genome Resource",
"prefix": "NBDC01835",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Cell/Organelle"
]
},
"nbdc01836": {
"alt_name": "PMC",
"description": "PubMed Central (PMC) is the U.S. National Institutes of Health (NIH) digital archive of biomedical and life sciences journal literature.",
"fairsharing": "FAIRsharing.wpt5mp",
"homepage": "http://www.ncbi.nlm.nih.gov/pmc/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "PubMed Central",
"prefix": "NBDC01836",
"pubmeds": [
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"22140104"
],
"status": "Active"
},
"nbdc01837": {
"description": "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.",
"fairsharing": "FAIRsharing.5949vn",
"homepage": "https://chem.nlm.nih.gov/chemidplus/",
"information_keywords": [
"3D structure",
"Image/Movie",
"Chemical structure"
],
"maintainer": "NLM (National Library of Medicine)",
"name": "ChemIDplus",
"prefix": "NBDC01837",
"pubmeds": [
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],
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc01838": {
"description": "This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and the Genome Browser that provides an integrated display of annotation data.",
"fairsharing": "FAIRsharing.qrw6b7",
"homepage": "http://rice.plantbiology.msu.edu/",
"information_keywords": [
"Sequence",
"Expression"
],
"name": "Rice Genome Annotation Project",
"prefix": "NBDC01838",
"pubmeds": [
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],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Cell/Organelle",
"Organism"
]
},
"nbdc01839": {
"alt_name": "DART",
"description": "A database for facilitating the search for drug adverse reaction target. DART contains information about known drug adverse reaction targets, functions and properties.",
"fairsharing": "FAIRsharing.v2f7t2",
"homepage": "http://bidd.nus.edu.sg/group/drt/dart.asp",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "National University of Singapore",
"name": "Drug Adverse Reaction Target",
"prefix": "NBDC01839",
"pubmeds": [
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],
"status": "Inactive",
"target_keywords": [
"Drug",
"DNA",
"Health/Disease",
"Protein"
]
},
"nbdc01840": {
"alt_name": "TAG",
"description": "The tumor-associated gene (TAG) database was designed to utilize information from well-characterized oncogenes and tumor suppressor genes to facilitate cancer research. All target genes were identified through text-mining approach from the PubMed database.",
"fairsharing": "FAIRsharing.znjr4p",
"homepage": "http://www.binfo.ncku.edu.tw/TAG/GeneDoc.php",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "NCKU (National Cheng Kung University) Bioinformatics Center",
"name": "Tumor Associated Gene database",
"prefix": "NBDC01840",
"pubmeds": [
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],
"status": "Active",
"target_keywords": [
"Health/Disease",
"Genome/Gene"
]
},
"nbdc01841": {
"description": "The database provides a means of investigating alternative splicing and can be used for identifying alternative splicing - related motifs, such as the exonic splicing enhancer (ESE), the exonic splicing silencer (ESS) and other intronic splicing motifs.",
"fairsharing": "FAIRsharing.anxkvb",
"homepage": "http://spliceinfo.mbc.nctu.edu.tw/",
"information_keywords": [
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"Interaction/Pathway"
],
"name": "SpliceInfo",
"prefix": "NBDC01841",
"status": "Inactive",
"target_keywords": [
"RNA"
]
},
"nbdc01842": {
"alt_name": "BioLINCC",
"description": "The goal of BioLINCC is to facilitate and coordinate the existing activities of the NHLBI Biorepository and the Data Repository and to expand their scope and usability to the scientific community through a single web-based user interface.",
"fairsharing": "FAIRsharing.a46gtf",
"homepage": "https://biolincc.nhlbi.nih.gov/home/",
"information_keywords": [
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],
"name": "Biologic Specimen and Data Repository Information Coordinating Center",
"prefix": "NBDC01842",
"pubmeds": [
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],
"status": "Active"
},
"nbdc01843": {
"alt_name": "CVRG",
"description": "The CardioVascular Research Grid (CVRG) project is creating an infrastructure for sharing cardiovascular data and data analysis tools. CVRG tools are developed using the Software as a Service model, allowing users to access tools through their browser, thus eliminating the need to install and maintain complex software.",
"fairsharing": "FAIRsharing.x80z26",
"homepage": "https://www.cvrgrid.org/",
"information_keywords": [
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],
"name": "The Cardiovascular Research Grid",
"prefix": "NBDC01843",
"status": "Inactive",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01844": {
"alt_name": "WebQTL",
"description": "GeneNetwork is a group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. GeneNetwork combines more than 25 years of legacy data generated by hundreds of scientists together with sequence data (SNPs) and massive transcriptome data sets (expression genetic or eQTL data sets).",
"fairsharing": "FAIRsharing.dt71b7",
"homepage": "http://www.genenetwork.org/",
"information_keywords": [
"Expression",
"Phenotype",
"Method",
"Interaction/Pathway"
],
"maintainer": "The UT Center for Integrative and Translational Genomics||NIMH (National Institute of Mental Health)",
"name": "GeneNetwork",
"prefix": "NBDC01844",
"pubmeds": [
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],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01845": {
"alt_name": "BEI",
"description": "BEI Resources provides reagents, tools and information for studying Category A, B, and C priority pathogens, emerging infectious disease agents, non-pathogenic microbes and other microbiological materials of relevance to the research community.",
"fairsharing": "FAIRsharing.gcxmpf",
"homepage": "http://www.beiresources.org/",
"information_keywords": [
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"Environment",
"Bioresource"
],
"maintainer": "ATCC Standards Development Organisation",
"name": "BEI Resource Repository",
"prefix": "NBDC01845",
"pubmeds": [
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],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Organism"
]
},
"nbdc01846": {
"alt_name": "NITRC",
"description": "Neuroimaging Informatics Tools and Resources Collaboratory (NITRC) facilitates finding and comparing neuroimaging resources for functional and structural neuroimaging analyses including popular tools as well as those that once might have been hidden in another researcher's laboratory or some obscure corner of cyberspace.",
"fairsharing": "FAIRsharing.6b9re3",
"homepage": "http://www.nitrc.org/",
"information_keywords": [
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"Image/Movie",
"Portal"
],
"name": "Neuroimaging Informatics Tools and Resources Collaboratory",
"prefix": "NBDC01846",
"pubmeds": [
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"26044860"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc01847": {
"alt_name": "NAHDAP",
"description": "NAHDAP acquires, preserves and disseminates data relevant to drug addiction and HIV research. The scope of the data housed at NAHDAP covers a wide range of legal and illicit drugs (alcohol, tobacco, marijuana, cocaine, synthetic drugs, and others) and the trajectories, patterns, and consequences of drug use as well as related predictors and outcomes.",
"fairsharing": "FAIRsharing.k34tv5",
"homepage": "http://www.icpsr.umich.edu/icpsrweb/NAHDAP/index.jsp",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "ICPSR (Inter-university Consortium for Political and Social Research)",
"name": "National Addiction & HIV Data Archive Program (NAHDAP)",
"prefix": "NBDC01847",
"status": "Inactive",
"target_keywords": [
"Health/Disease",
"Drug"
]
},
"nbdc01848": {
"alt_name": "NIDA",
"description": "The NIDA Data Share web site is an electronic environment that allows data from completed clinical trials to be distributed to investigators and the public in order to promote new research, encourage further analyses, and disseminate information to the community. Secondary analyses produced from data sharing multiply the scientific contribution of the original research.",
"fairsharing": "FAIRsharing.a7p1zt",
"homepage": "https://datashare.nida.nih.gov",
"information_keywords": [
"Bibliography/Documents"
],
"name": "NIDA Data Share",
"prefix": "NBDC01848",
"pubmeds": [
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],
"status": "Active",
"target_keywords": [
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"Drug"
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},
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"alt_name": "NIDA CGS",
"description": "This resource stores and distributes clinical data and biomaterials (DNA samples and cell lines) available in the NIDA Genetics Initiative. This includes blood and other biospecimens along with phenotypic data.",
"fairsharing": "FAIRsharing.hn4mwm",
"homepage": "https://nidagenetics.org/",
"information_keywords": [
"Bioresource",
"Phenotype",
"Sequence"
],
"maintainer": "RUCDR Infinite Biologics||Washington University in St Louis School of Medicine",
"name": "NIDA Center on Genetics Studies",
"prefix": "NBDC01849",
"status": "Active",
"target_keywords": [
"DNA",
"cDNA/EST",
"Cell/Organelle",
"Organism",
"Health/Disease"
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},
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"alt_name": "NIF",
"description": "NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web.",
"fairsharing": "FAIRsharing.v11s0z",
"homepage": "http://www.neuinfo.org/",
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"Phenotype",
"Sequence",
"Bibliography/Documents",
"Ontology/Terminology/Nomenclature",
"Method",
"Interaction/Pathway",
"Image/Movie",
"Portal"
],
"name": "Neuroscience Information Framework",
"prefix": "NBDC01850",
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"Genome/Gene",
"Protein"
]
},
"nbdc01851": {
"description": "The PhysioNet Resource is intended to stimulate current research and new investigations in the study of complex biomedical and physiologic signals. It offers free web access to large collections of recorded physiologic signals (PhysioBank) and related open-source software (PhysioToolkit).",
"fairsharing": "FAIRsharing.bemzxg",
"homepage": "http://www.physionet.org/",
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"Interaction/Pathway",
"Portal"
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"name": "PhysioNet",
"prefix": "NBDC01851",
"pubmeds": [
"14716615"
],
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease"
]
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"nbdc01852": {
"alt_name": "TCDB",
"description": "The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information. Descriptions, TC numbers, and examples of over 600 families of transport proteins are provided. Transport systems are classified on the basis of five criteria, and each of these criteria corresponds to one of the five numbers or letters within the TC# for a particular type of transporter.",
"fairsharing": "FAIRsharing.p3bzqb",
"homepage": "http://www.tcdb.org/",
"information_keywords": [
"Classification"
],
"maintainer": "UCSD (University of California San Diego)",
"name": "Transporter Classification Database",
"prefix": "NBDC01852",
"pubmeds": [
"16381841",
"19022853"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01853": {
"alt_name": "QTL Archive",
"description": "This site provides access to raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results are posted to accompany the data.",
"fairsharing": "FAIRsharing.2g4cfa",
"homepage": "http://phenome.jax.org/db/q?rtn=qtl/home",
"information_keywords": [
"Phenotype",
"Method"
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"maintainer": "Churchill Group, The Jackson Laboratory",
"name": "Quantitative Trait Loci Archive",
"prefix": "NBDC01853",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc01854": {
"alt_name": "NDAR",
"description": "National Database for Autism Research (NDAR) is an extensible, scalable informatics platform for austism spectrum disorder-relevant data at all levels of biological and behavioral organization (molecules, genes, neural tissue, behavioral, social and environmental interactions) and for all data types (text, numeric, image, time series, etc.). NDAR was developed to share data across the entire ASD field and to facilitate collaboration across laboratories, as well as interconnectivity with other informatics platforms.",
"fairsharing": "FAIRsharing.hsyjka",
"homepage": "http://ndar.nih.gov/",
"information_keywords": [
"Bibliography/Documents"
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"maintainer": "NIMH (National Institute of Mental Health)",
"name": "National Database for Autism Research (NDAR)",
"prefix": "NBDC01854",
"pubmeds": [
"22622767"
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"status": "Active",
"target_keywords": [
"Health/Disease",
"Organism"
]
},
"nbdc01855": {
"alt_name": "FITBIR",
"description": "The Federal Interagency Traumatic Brain Injury Research (FITBIR) informatics system is an extensible, scalable informatics platform for TBI relevant imaging, assessment, genomics, and other data types. It was developed to share data across the entire TBI research field and to facilitate collaboration between laboratories, as well as interconnectivity with other informatics platforms.",
"fairsharing": "FAIRsharing.rz7h29",
"homepage": "https://fitbir.nih.gov/",
"information_keywords": [
"Portal"
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"maintainer": "CDC (Centers for Disease Control and Prevention)||NINDS (National Institute of Neurological Disorders & Stroke)",
"name": "Federal Interagency Traumatic Brain Injury Research (FITBIR) Informatics System",
"prefix": "NBDC01855",
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease"
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},
"nbdc01856": {
"alt_name": "PDBP DMR",
"description": "The NINDS Parkinson's Disease (PD) Biomarkers Program Data Management Resource enables web-based data entry for clinical studies supporting PD biomarker development, as well as broad data sharing (imaging, clinical, genetic, and biospecimen analysis) across the entire PD research community. The PDBP DMR coordinates information and access to PD biospecimens distributed through the NINDS Human Genetics, DNA, iPSC , Cell Line and Biospecimen Repository and the Harvard Neurodiscovery Initiative.",
"fairsharing": "FAIRsharing.72j8ph",
"homepage": "https://pdbp.ninds.nih.gov/",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "NINDS (National Institute of Neurological Disorders & Stroke)",
"name": "Parkinson's Disease Biomarkers Program Data Management Resource",
"prefix": "NBDC01856",
"status": "Active",
"target_keywords": [
"Health/Disease",
"Genome/Gene"
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"alt_name": "BioGRID",
"description": "BioGRID is an interaction repository with data compiled through comprehensive curation efforts. BioGRID currently holds over 980,000 interactions curated from both high-throughput datasets and individual focused studies, as derived from over 55,000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding year (S. cerevisiae), fission yeast (S. pome), and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway. All data are freely provided via the search index and available for download in standardized formats.",
"fairsharing": "FAIRsharing.9d5f5r",
"homepage": "http://www.thebiogrid.org",
"information_keywords": [
"Interaction/Pathway",
"Repository"
],
"maintainer": "Princeton University||Samuel Lunenfeld Research Institute, Mount Sinai Hospital||University of Edinburgh||University of Montreal",
"name": "Biological General Repository for Interaction Datasets",
"prefix": "NBDC01857",
"pubmeds": [
"16381927",
"12620108"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
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"description": "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.",
"fairsharing": "FAIRsharing.qe8tz8",
"homepage": "http://hogenom.univ-lyon1.fr/",
"information_keywords": [
"Classification",
"Sequence",
"Taxonomy"
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"maintainer": "PBIL",
"name": "HOGENOM",
"prefix": "NBDC01858",
"pubmeds": [
"19534752"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc01859": {
"alt_name": "PIRSF",
"description": "The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.",
"fairsharing": "FAIRsharing.vssch2",
"homepage": "https://proteininformationresource.org/pirwww/dbinfo/pirsf.shtml",
"information_keywords": [
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"Sequence",
"3D structure",
"Interaction/Pathway",
"Classification"
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"maintainer": "Georgetown University Medical Center||PIR||University of Delaware||EMBL-EBI (European Bioinformatics Institute)",
"name": "PIR SuperFamily",
"prefix": "NBDC01859",
"pubmeds": [
"14681371"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01860": {
"alt_name": "PRIAM",
"description": "In English, PRIAM stands for enzyme-specific profiles for metabolic pathway prediction. PRIAM is a method for automated enzyme detection in a fully sequenced genome, based on all sequences available in the ENZYME database.",
"fairsharing": "FAIRsharing.bdv7z3",
"homepage": "http://priam.prabi.fr/",
"information_keywords": [
"Sequence",
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"maintainer": "PRABI, Rhone-Alpes Bioinformatics Center",
"name": "PRofils pour l'Identification Automatique du Metabolisme",
"prefix": "NBDC01860",
"pubmeds": [
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],
"status": "Inactive",
"target_keywords": [
"Protein",
"Genome/Gene"
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"nbdc01861": {
"alt_name": "DPVweb",
"description": "DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. The database will not be updated with sequence or taxonomic data from Aug 2013.",
"fairsharing": "FAIRsharing.52qw6p",
"homepage": "http://www.dpvweb.net",
"information_keywords": [
"Taxonomy",
"Sequence"
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"maintainer": "Rothamsted Research",
"name": "Description of Plant Viruses",
"prefix": "NBDC01861",
"pubmeds": [
"16381892"
],
"status": "Active",
"target_keywords": [
"Organism",
"Genome/Gene"
]
},
"nbdc01862": {
"description": "NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases.",
"fairsharing": "FAIRsharing.f63h4k",
"homepage": "http://www.narcis.nl/?Language=en",
"information_keywords": [
"Bibliography/Documents",
"Repository"
],
"maintainer": "VSNU (Association of Universities in the Netherlands)||DANS(Data Archiving and Networked Services)",
"name": "NARCIS",
"prefix": "NBDC01862",
"status": "Active"
},
"nbdc01863": {
"description": "ChemSpider is a freely available collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources.",
"fairsharing": "FAIRsharing.96f3gm",
"homepage": "http://www.chemspider.com/",
"information_keywords": [
"3D structure",
"Image/Movie"
],
"maintainer": "Royal Society of Chemistry",
"name": "ChemSpider",
"prefix": "NBDC01863",
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc01864": {
"description": "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry.",
"fairsharing": "FAIRsharing.2ma4gq",
"homepage": "http://ligand-depot.rutgers.edu/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"3D structure"
],
"maintainer": "Rutgers, The State University of New Jersey",
"name": "Ligand Expo",
"prefix": "NBDC01864",
"pubmeds": [
"15059838"
],
"status": "Active",
"target_keywords": [
"DNA",
"Protein",
"Chemical compound"
]
},
"nbdc01865": {
"alt_name": "RCSB PDB",
"description": "The Protein Data Bank archives information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. As a member of the wwPDB, the RCSB PDB provides simple and advanced searching for macromolecules and ligands, tabular reports, specialized visualization tools, sequence-structure comparisons, Molecule of the Month and other educational resources at PDB-101, and more.",
"fairsharing": "FAIRsharing.2t35ja",
"homepage": "https://www.rcsb.org/",
"information_keywords": [
"Image/Movie",
"3D structure"
],
"name": "RCSB Protein Data Bank",
"prefix": "NBDC01865",
"status": "Active",
"target_keywords": [
"DNA",
"Protein",
"RNA"
]
},
"nbdc01866": {
"description": "TargetTrack, a target registration database, provides information on the experimental progress and status of targets selected for structure determination.",
"fairsharing": "FAIRsharing.2p1gn5",
"homepage": "http://sbkb.org/tt/",
"information_keywords": [
"Sequence",
"3D structure"
],
"name": "TargetTrack",
"prefix": "NBDC01866",
"status": "Inactive"
},
"nbdc01867": {
"alt_name": "VEGA",
"description": "The Vertebrate Genome Annotation (VEGA) database is a central repository for high quality manual annotation of vertebrate finished genome sequence.",
"fairsharing": "FAIRsharing.mr293q",
"homepage": "http://vega.sanger.ac.uk/",
"information_keywords": [
"Sequence"
],
"maintainer": "Wellcome Sanger Institute",
"name": "The Vertebrate Genome Annotation Database",
"prefix": "NBDC01867",
"pubmeds": [
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"24316575"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01868": {
"alt_name": "3DID",
"description": "The database of 3D Interaction Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details necessary for understanding how interactions occur.",
"fairsharing": "FAIRsharing.jptb1m",
"homepage": "http://3did.irbbarcelona.org/",
"information_keywords": [
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"3D structure"
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"maintainer": "Structural Bioinformatics and Network Biology Group",
"name": "3D interacting domains",
"prefix": "NBDC01868",
"pubmeds": [
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"24081580"
],
"status": "Active",
"target_keywords": [
"Protein"
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"nbdc01869": {
"description": "Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences.",
"fairsharing": "FAIRsharing.z1czxj",
"homepage": "http://peroxibase.toulouse.inra.fr/",
"information_keywords": [
"Sequence",
"Classification"
],
"name": "PeroxiBase",
"prefix": "NBDC01869",
"pubmeds": [
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"23180785"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01870": {
"description": "InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactions and signaling responses involved in mammalian innate immunity. InnateDB incorporates information of the whole human, mouse and bovine interactomes by integrating interaction and pathway information from several of the major publicly available databases but aims to capture an improved coverage of the innate immunity interactome through manual curation.",
"fairsharing": "FAIRsharing.rb2drw",
"homepage": "http://www.innatedb.com/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Brinkman Laboratory, Simon Fraser University",
"name": "InnateDB",
"prefix": "NBDC01870",
"pubmeds": [
"23180781"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Organism",
"Health/Disease"
]
},
"nbdc01871": {
"description": "HumanCyc is a bioinformatics database that describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional analysis of Homo sapiens at the genomic level.",
"fairsharing": "FAIRsharing.zaa7w",
"homepage": "http://www.humancyc.org/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "SRI International",
"name": "HumanCyc",
"prefix": "NBDC01871",
"pubmeds": [
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],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Metabolite"
]
},
"nbdc01872": {
"alt_name": "PANTHER",
"description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.",
"fairsharing": "FAIRsharing.ty3dqs",
"homepage": "http://www.pantherdb.org",
"information_keywords": [
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"Classification",
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Thomas lab, University of Southern California",
"name": "Protein ANalysis THrough Evolutionary Relationships: Classification of Genes and Proteins",
"prefix": "NBDC01872",
"pubmeds": [
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"27899595",
"23868073",
"19597783"
],
"status": "Active",
"target_keywords": [
"Organism",
"Protein",
"Genome/Gene"
]
},
"nbdc01873": {
"alt_name": "HAMAP",
"description": "HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.",
"fairsharing": "FAIRsharing.63m4ss",
"homepage": "http://us.expasy.org/sprot/hamap/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "HAMAP database of microbial protein families",
"prefix": "NBDC01873",
"pubmeds": [
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"25348399"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01874": {
"alt_name": "SWISS-MODEL",
"description": "The SWISS-MODEL Repository is a database of annotated 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for protein sequences of selected model organisms.",
"fairsharing": "FAIRsharing.vxz9pn",
"homepage": "https://swissmodel.expasy.org/repository/",
"information_keywords": [
"Sequence",
"3D structure",
"Method"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "SWISS-MODEL Repository of 3D protein structure models",
"prefix": "NBDC01874",
"pubmeds": [
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"24782522"
],
"status": "Active",
"target_keywords": [
"Protein"
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},
"nbdc01875": {
"alt_name": "TCIA",
"description": "The Cancer Imaging Archive (TCIA) is a large archive of medical images of cancer accessible for public download. All images are stored in DICOM file format. The images are organized as \"Collections\", typically patients related by a common disease (e.g. lung cancer), image modality (MRI, CT, etc) or research focus.",
"fairsharing": "FAIRsharing.jrfd8y",
"homepage": "http://cancerimagingarchive.net/",
"information_keywords": [
"Image/Movie",
"Method",
"Repository"
],
"maintainer": "Frederick National Laboratory for Cancer Research||University of Arkansas for Medical Sciences",
"name": "The Cancer Imaging Archive",
"prefix": "NBDC01875",
"pubmeds": [
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"24772218",
"25414001",
"28925987",
"29871933",
"29934058"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01877": {
"alt_name": "JAX",
"description": "JAX Mice are the industry standard for animal model research, using precise genome solutions to better understand human disease. Our rigorous Animal Health Programs and stringent genetic quality standards ensure the reproducibility and validity of your experimental data.",
"fairsharing": "FAIRsharing.5701h1",
"homepage": "http://jaxmice.jax.org/",
"information_keywords": [
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"Sequence"
],
"maintainer": "The Jackson Laboratory",
"name": "JAX Mice Database",
"prefix": "NBDC01877",
"status": "Active",
"target_keywords": [
"Genetic variation",
"Genome/Gene",
"Health/Disease"
]
},
"nbdc01878": {
"alt_name": "MMRRC",
"description": "The MMRRC distributes and cryopreserves scientifically valuable, genetically engineered mouse strains and mouse ES cell lines with potential value for the genetics and biomedical research community.",
"fairsharing": "FAIRsharing.9dpd18",
"homepage": "http://www.mmrrc.org/",
"information_keywords": [
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"Sequence",
"Repository"
],
"maintainer": "University of California Los Angeles||University of Missouri||University of North Carolina||The Jackson Laboratory",
"name": "Mutant Mouse Regional Resource Centers",
"prefix": "NBDC01878",
"pubmeds": [
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],
"status": "Active",
"target_keywords": [
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"Genome/Gene"
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},
"nbdc01879": {
"alt_name": "CEBS",
"description": "CEBS (Chemical Effects in Biological Systems) is an integrated public repository for toxicogenomics data, including the study design and timeline, clinical chemistry and histopathology findings and microarray and proteomics data. CEBS contains data derived from studies of chemicals and of genetic alterations, and is compatible with clinical and environmental studies. CEBS is designed to permit the user to query the data using the study conditions, the subject responses and then, having identified an appropriate set of subjects, to move to the microarray module of CEBS to carry out gene signature and pathway analysis.",
"fairsharing": "FAIRsharing.ntv8pe",
"homepage": "https://cebs.niehs.nih.gov/cebs/",
"information_keywords": [
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"Bibliography/Documents",
"Repository"
],
"maintainer": "NTP (National Toxicology Program, NIEHS, NIH)",
"name": "Chemical Effects in Biological Systems",
"prefix": "NBDC01879",
"pubmeds": [
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"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Cell/Organelle",
"Chemical compound"
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"nbdc01880": {
"description": "Aspergillus Genomes is a resource for viewing annotated genes arising from various Aspergillus sequencing and annotation projects.",
"fairsharing": "FAIRsharing.pdx9yt",
"homepage": "http://www.aspergillus-genomes.org.uk/",
"information_keywords": [
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],
"name": "Aspergillus Genomes",
"prefix": "NBDC01880",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc01881": {
"alt_name": "iRefWeb",
"description": "iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID.",
"fairsharing": "FAIRsharing.t31wcb",
"homepage": "http://wodaklab.org/iRefWeb/",
"information_keywords": [
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],
"maintainer": "Toronto Hospital for Sick Children",
"name": "Interaction Reference Index Web Interface",
"prefix": "NBDC01881",
"pubmeds": [
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],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01882": {
"description": "TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa.",
"fairsharing": "FAIRsharing.zcn4w4",
"homepage": "http://www.treebase.org/",
"information_keywords": [
"Taxonomy",
"Sequence"
],
"maintainer": "Naturalis Biodiversity Center",
"name": "TreeBase",
"prefix": "NBDC01882",
"pubmeds": [
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],
"status": "Active",
"target_keywords": [
"Organism"
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"nbdc01883": {
"description": "The Enzyme Database was developed as a new way to access the data of the IUBMB Enzyme Nomenclature List. The data, which are stored in a MySQL database, preserve the formatting of chemical names according to IUPAC standards.",
"fairsharing": "FAIRsharing.da6cny",
"homepage": "http://www.enzyme-database.org",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Classification"
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"maintainer": "Trinity College Dublin",
"name": "ExplorEnz",
"prefix": "NBDC01883",
"pubmeds": [
"18776214"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01885": {
"alt_name": "DMDM",
"description": "Domain mapping of disease mutations (DMDM) is a database in which each disease mutation can be displayed by its gene, protein or domain location.",
"fairsharing": "FAIRsharing.kz6vpp",
"homepage": "http://bioinf.umbc.edu/dmdm/",
"information_keywords": [
"Phenotype",
"Sequence"
],
"maintainer": "University of Maryland",
"name": "Domain mapping of disease mutations",
"prefix": "NBDC01885",
"pubmeds": [
"20685956"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Health/Disease"
]
},
"nbdc01887": {
"alt_name": "OrthoDB",
"description": "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny.",
"fairsharing": "FAIRsharing.x989d5",
"homepage": "http://www.orthodb.org/v9/",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "Universite de Geneve",
"name": "Database of Orthologous Groups",
"prefix": "NBDC01887",
"pubmeds": [
"20972218",
"25428351"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc01888": {
"alt_name": "CATH domain",
"description": "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This collection is concerned with superfamily classification.",
"fairsharing": "FAIRsharing.xgcyyn",
"homepage": "http://www.cathdb.info/",
"information_keywords": [
"Sequence",
"3D structure",
"Classification"
],
"maintainer": "University College London",
"name": "CATH Protein Structure Classification",
"prefix": "NBDC01888",
"pubmeds": [
"9309224",
"27477482",
"26253692",
"25348408",
"11788987",
"27899584",
"29112716"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01889": {
"alt_name": "T3DB",
"description": "Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.",
"fairsharing": "FAIRsharing.psn0h2",
"homepage": "http://www.t3db.org/",
"information_keywords": [
"Chemical structure",
"Interaction/Pathway"
],
"maintainer": "Wishart Lab, University of Alberta",
"name": "Toxin and Toxin Target Database",
"prefix": "NBDC01889",
"pubmeds": [
"19897546",
"25378312"
],
"status": "Active",
"target_keywords": [
"Chemical compound",
"Metabolite",
"Protein",
"Health/Disease"
]
},
"nbdc01890": {
"description": "GpDB is a publicly accessible, relational database of G-proteins and their interactions with GPCRs and effector molecules. The sequences are classified according to a hierarchy of different classes, families and sub-families, based on extensive literature search.",
"fairsharing": "FAIRsharing.wfrsvq",
"homepage": "http://bioinformatics.biol.uoa.gr/gpDB",
"information_keywords": [
"Interaction/Pathway",
"Classification"
],
"maintainer": "University of Athens",
"name": "gpDB",
"prefix": "NBDC01890",
"pubmeds": [
"18441001",
"15619328"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01892": {
"alt_name": "Xenbase",
"description": "Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. It includes gene expression patterns that incorporate image data from the literature, large scale screens and community submissions.",
"fairsharing": "FAIRsharing.jrv6wj",
"homepage": "http://www.xenbase.org",
"information_keywords": [
"Expression",
"Phenotype",
"Method",
"Bibliography/Documents"
],
"maintainer": "Cincinnati Children's Hospital Medical Center||University of Calgary",
"name": "Xenopus laevis and tropicalis biology and genomics resource",
"prefix": "NBDC01892",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc01893": {
"alt_name": "ChemDB",
"description": "ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds.",
"fairsharing": "FAIRsharing.dstf7h",
"homepage": "http://cdb.ics.uci.edu",
"information_keywords": [
"3D structure",
"Chemical structure",
"Interaction/Pathway"
],
"maintainer": "Institute for Genomics and Bioinformatics, University of California, Irvine||University of California Los Angeles",
"name": "The UC Irvine ChemDB",
"prefix": "NBDC01893",
"pubmeds": [
"17599932",
"16174682"
],
"status": "Active",
"target_keywords": [
"Drug",
"Chemical compound"
]
},
"nbdc01895": {
"alt_name": "KOMP",
"description": "Knockout mutant mice strains. The KOMP repository is a resource of mouse embryonic stem (ES) cells containing a null mutation in every gene in the mouse genome. The KOMP collection of mice, ES Cells, and vectors are now distributed through the Mutant Mouse Resource and Research Center at UC Davis.",
"fairsharing": "FAIRsharing.an4drj",
"homepage": "https://www.mmrrc.org/catalog/StrainCatalogSearchForm.php?search_query=KOMP%20Repository",
"information_keywords": [
"Bioresource"
],
"maintainer": "University of California Los Angeles",
"name": "Knockout Mouse Project",
"prefix": "NBDC01895",
"pubmeds": [
"15340423"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01896": {
"alt_name": "PaleoBioDB",
"description": "The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data.",
"fairsharing": "FAIRsharing.r1k8kz",
"homepage": "https://paleobiodb.org/#/",
"information_keywords": [
"Taxonomy",
"Environment"
],
"maintainer": "University of California Santa Barbara",
"name": "Paleobiology Database",
"prefix": "NBDC01896",
"pubmeds": [
"18599780"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01897": {
"description": "VBASE2 is an integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank.",
"fairsharing": "FAIRsharing.qvxhb1",
"homepage": "http://www.vbase2.org",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Cologne",
"name": "VBASE2",
"prefix": "NBDC01897",
"pubmeds": [
"15608286"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Protein"
]
},
"nbdc01898": {
"alt_name": "RESID",
"description": "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.",
"fairsharing": "FAIRsharing.qaszjp",
"homepage": "http://pir.georgetown.edu/resid/",
"information_keywords": [
"Sequence",
"3D structure",
"Interaction/Pathway"
],
"maintainer": "Georgetown University||Protein Information Resource Consortium||University of Delaware",
"name": "RESID Database of Protein Modifications",
"prefix": "NBDC01898",
"pubmeds": [
"12520062",
"15174122"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01899": {
"alt_name": "CanGEM",
"description": "Clinical information about tumor samples and microarray data, with emphasis on array comparative genomic hybridization (aCGH) and data mining of gene copy number changes.",
"fairsharing": "FAIRsharing.ptsckv",
"homepage": "http://www.cangem.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Helsinki",
"name": "Cancer Genome Mine",
"prefix": "NBDC01899",
"pubmeds": [
"17932056"
],
"status": "Inactive",
"target_keywords": [
"Genetic variation",
"Health/Disease",
"Genome/Gene"
]
},
"nbdc01900": {
"description": "PseudoBase is a collection of RNA pseudoknots that have been made available for retrieval to the scientific community.",
"fairsharing": "FAIRsharing.5ey5w6",
"homepage": "http://www.ekevanbatenburg.nl/pb",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Leiden",
"name": "PseudoBase",
"prefix": "NBDC01900",
"pubmeds": [
"10592225",
"11125088",
"18988624"
],
"status": "Active",
"target_keywords": [
"Health/Disease",
"Organism",
"RNA"
]
},
"nbdc01901": {
"description": "This is a portal to the consensus yeast metabolic network as reconstructed from the genome sequence and literature. It is a highly annotated metabolic map of Saccharomyces cerevisiae S288c that is periodically updated by a team of collaborators from various research groups.",
"fairsharing": "FAIRsharing.cm6j6r",
"homepage": "http://yeast.sourceforge.net/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Manchester Center for Integrative Systems Biology",
"name": "YEASTNET: A consensus reconstruction of yeast metabolism",
"prefix": "NBDC01901",
"pubmeds": [
"18846089",
"24678285"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Metabolite"
]
},
"nbdc01902": {
"description": "RegulonDB is a model of the complex regulation of transcription initiation or regulatory network of the cell. On the other hand, it is also a model of the organization of the genes in transcription units, operons and simple and complex regulons. In this regard, RegulonDB is a computational model of mechanisms of transcriptional regulation.",
"fairsharing": "FAIRsharing.f0awr5",
"homepage": "http://regulondb.ccg.unam.mx/",
"information_keywords": [
"Expression",
"Interaction/Pathway",
"Classification"
],
"maintainer": "The National Autonomous University of Mexico at the Center for Genomic Sciences||University of Mexico",
"name": "RegulonDB",
"prefix": "NBDC01902",
"pubmeds": [
"21051347",
"23203884",
"26527724"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01903": {
"alt_name": "APD",
"description": "The data stored in the APD are gleaned from the Protein Data Bank (PDB), Swiss-Prot Protein Knowledgebase and PubMed National Library of Medicine. The antimicrobial peptides in this database contain less than 100 amino acid residues, are in the mature and active form, and primarily from natural sources, ranging from bacteria, fungi, plants, to animals.",
"fairsharing": "FAIRsharing.ctwd7b",
"homepage": "http://aps.unmc.edu/AP/main.php",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "University of Nebraska Medical Center",
"name": "Antimicrobial Peptide Database",
"prefix": "NBDC01903",
"pubmeds": [
"14681488",
"26602694",
"18957441"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Organism",
"Health/Disease"
]
},
"nbdc01904": {
"description": "eCrystals is the archive for Crystal Structures generated by the Southampton Chemical Crystallography Group and the EPSRC UK National Crystallography Service.\nIt contains all the fundamental and derived data resulting from a single crystal X-ray structure determination, but excluding the raw images.",
"fairsharing": "FAIRsharing.v448pt",
"homepage": "http://ecrystals.chem.soton.ac.uk/",
"information_keywords": [
"Method",
"3D structure"
],
"maintainer": "NCS (United Kingdom National Crystallography Service)||University of Southampton",
"name": "eCrystals",
"prefix": "NBDC01904",
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc01905": {
"alt_name": "UNITE",
"description": "UNITE is primarily a fungal rDNA internal transcribed spacer (ITS) sequence database, although they also welcome additional genes and genetic markers. UNITE focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria.",
"fairsharing": "FAIRsharing.cnwx8c",
"homepage": "http://unite.ut.ee/index.php",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "University of Tartu",
"name": "Molecular database for the identification of fungi",
"prefix": "NBDC01905",
"pubmeds": [
"30371820"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc01906": {
"alt_name": "Bacteriome.org",
"description": "Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase.",
"fairsharing": "FAIRsharing.mx5cxe",
"homepage": "https://www.compsysbio.org/bacteriome/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "University of Toronto",
"name": "Bacterial Protein Interaction Database",
"prefix": "NBDC01906",
"pubmeds": [
"17942431"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01907": {
"alt_name": "I2D",
"description": "Experimentally-determined interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection",
"fairsharing": "FAIRsharing.k56rjs",
"homepage": "http://ophid.utoronto.ca/ophidv2.204/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Jurisica Lab, Ontario Cancer Institute",
"name": "Interologous Interaction Database",
"prefix": "NBDC01907",
"pubmeds": [
"15657099",
"17535438"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01908": {
"alt_name": "ASAP",
"description": "ASAP is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data. It was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis.",
"fairsharing": "FAIRsharing.anpa6",
"homepage": "http://asap.genetics.wisc.edu/asap/home.php",
"information_keywords": [
"Expression",
"Classification",
"Interaction/Pathway"
],
"maintainer": "University of Wisconsin-Madison",
"name": "A Systematic Annotation Package",
"prefix": "NBDC01908",
"pubmeds": [
"12519969"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01909": {
"description": "VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes (as well as a number of non-vector genomes for comparative analysis) providing an integrated resource for the research community. VectorBase contains genome information for organisms such as Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever. Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes.",
"fairsharing": "FAIRsharing.3etvdn",
"homepage": "https://vectorbase.org/vectorbase/app",
"information_keywords": [
"Sequence",
"Expression",
"Localization",
"Environment"
],
"maintainer": "United States Department of Health and Human Services||VectorBase",
"name": "VectorBase",
"prefix": "NBDC01909",
"pubmeds": [
"19028744"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Organism"
]
},
"nbdc01910": {
"alt_name": "GDR",
"description": "The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database providing centralized access to Rosaceae genomics and genetics data and analysis tools to facilitate cross-species utilization of data.",
"fairsharing": "FAIRsharing.6v96ma",
"homepage": "http://www.rosaceae.org/",
"information_keywords": [
"Sequence",
"Expression",
"Phenotype",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Washington State University",
"name": "Genome Database for Rosaceae",
"prefix": "NBDC01910",
"pubmeds": [
"17932055",
"15357877"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Organism"
]
},
"nbdc01911": {
"alt_name": "Yeast Resource Center",
"description": "The National Center for Research Resources' Yeast Resource Center is located at the University of Washington in Seattle, Washington. The mission of the center is to facilitate the identification and characterization of protein complexes in the yeast Saccharomyces cerevisiae.",
"fairsharing": "FAIRsharing.karvzj",
"homepage": "http://www.yeastrc.org/pdr/",
"information_keywords": [
"Sequence",
"3D structure",
"Classification",
"Localization",
"Interaction/Pathway"
],
"maintainer": "Department of Molecular Biology, The Scripps Research Institute||Washington State University",
"name": "Yeast Resource Center Public Data Repository",
"prefix": "NBDC01911",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01912": {
"alt_name": "ScerTF",
"description": "ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor.",
"fairsharing": "FAIRsharing.qrv60a",
"homepage": "http://stormo.wustl.edu/ScerTF/",
"information_keywords": [
"Expression",
"Classification",
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Washington University in St Louis School of Medicine",
"name": "Saccharomyces cerevisiae Transcription Factor Database",
"prefix": "NBDC01912",
"pubmeds": [
"22140105"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Genome/Gene"
]
},
"nbdc01913": {
"alt_name": "ORDB",
"description": "ORDB began as a database of vertebrate OR genes and proteins and continues to support sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family.",
"fairsharing": "FAIRsharing.6375zh",
"homepage": "http://senselab.med.yale.edu/OrDB/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Sequence"
],
"maintainer": "Yale University School of Medicine",
"name": "Olfactory Receptor Database",
"prefix": "NBDC01913",
"pubmeds": [
"11752336",
"10592268",
"27694208"
],
"status": "Active",
"target_keywords": [
"Protein",
"Genome/Gene"
]
},
"nbdc01914": {
"alt_name": "GigaDB",
"description": "GigaDB primarily serves as a repository to host data and tools associated with articles in GigaScience; however, it also includes a subset of datasets that are not associated with GigaScience articles. GigaDB defines a dataset as a group of files (e.g., sequencing data, analyses, imaging files, software programs) that are related to and support an article or study.",
"fairsharing": "FAIRsharing.rcbwsf",
"homepage": "http://gigadb.org/",
"information_keywords": [
"Expression",
"Image/Movie",
"Method",
"Sequence",
"Repository"
],
"maintainer": "GigaScience/BGI HK Ltd",
"name": "Giga Science Database",
"prefix": "NBDC01914",
"pubmeds": [
"23587345"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01915": {
"description": "The ProteomeXchange consortium has been set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination.",
"fairsharing": "FAIRsharing.92dt9d",
"homepage": "http://www.proteomexchange.org/",
"information_keywords": [
"Expression",
"Localization",
"Portal"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)||ISB (Institute for Systems Biology)||UCSD (University of California San Diego)||National Center for Protein Sciences||University of Washington",
"name": "ProteomeXchange",
"prefix": "NBDC01915",
"pubmeds": [
"24727771",
"27924013"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01916": {
"description": "EBI Metagenomics has changed its name to MGnify to reflect a change in scope. This is a free-to-use resource aiming at supporting all metagenomics researchers. The service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. You can freely browse all the public data in the repository.",
"fairsharing": "FAIRsharing.dxj07r",
"homepage": "https://www.ebi.ac.uk/metagenomics/",
"information_keywords": [
"Expression",
"Method",
"Environment",
"Sequence",
"Repository"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "MGnify",
"prefix": "NBDC01916",
"pubmeds": [
"24165880",
"29069476"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc01917": {
"alt_name": "SoyKB",
"description": "Soybean Knowledge Base (SoyKB), is a comprehensive all-inclusive web resource developed for soybean translational genomics and molecular breeding. SoyKB stores information about genes/proteins, miRNAs/sRNAs, metabolites, SNPs, plant introduction (PI lines) and traits. It handles the management and integration of soybean genomics and multi-omics data along with gene function annotations, biological pathway and trait information. It has many useful tools including gene family search, multiple gene/metabolite analysis, motif analysis tool, protein 3D structure viewer and data download and upload capacity. It has a user-friendly web interface together with genome browser and pathway viewer, which displays data in an intuitive manner to the soybean researchers, breeders and consumers.\nThe QTLs, SNP, GWAS and traits information is seamlessly integrated in our newly developed suite of tools for the In Silico Breeding Program. It allows integration and extraction of the data in a tabular format as well as graphical visualization in our in-house Chromosome Visualizer. It also supports integration and visualization of Genotype by Sequencing (GBS) data for molecular breeding and phenotypic inferences. In addition, SoyKB now has capacity for incorporation of DNA methylation data and fast neutron mutation datasets. It is also linked seamlessly with P3DB for phosphorylation data. We have also incorporated suite of tools for differential expression analysis for microarray, transcriptomics RNA-seq, proteomics and metabolomics datasets. It includes access to gene lists, Venn diagrams, Volcano plots, functional annotations and pathway analysis. SoyKB is now powered by the iPlant Cyber-Infrastructure. The website is hosted on the iPlant's advanced computing infrastructure established to leverage the data analysis capabilities.",
"fairsharing": "FAIRsharing.cr410r",
"homepage": "http://soykb.org/",
"information_keywords": [
"Interaction/Pathway",
"Expression",
"Sequence",
"Phenotype",
"Method"
],
"maintainer": "University of Missouri",
"name": "Soybean Knowledge Base (SoyKB)",
"prefix": "NBDC01917",
"pubmeds": [
"22369646"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Epigenetics",
"RNA",
"Protein",
"Cell/Organelle"
]
},
"nbdc01918": {
"alt_name": "MitoBreak",
"description": "A comprehensive on-line resource with curated datasets of mitochondrial DNA (mtDNA) rearrangements.",
"fairsharing": "FAIRsharing.8fy3bn",
"homepage": "http://mitobreak.portugene.com",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Porto",
"name": "The mitochondrial DNA breakpoints database",
"prefix": "NBDC01918",
"pubmeds": [
"24170808"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc01919": {
"description": "The JCB DataViewer is an image hosting and visualization platform for original microscopy image datasets associated with articles published in The Journal of Cell Biology, a peer-reviewed journal published by The Rockefeller University Press. The JCB DataViewer can host multidimensional fluorescence microscopy images, 3D tomogram data, very large (gigapixel) images, and high content imaging screens. Images are presented in an interactive viewer, and the \"scores\" from high content screens are presented in interactive graphs with data points linked to the relevant images. The JCB DataViewer uses the Bio-Formats library to read over 120 different imaging file formats and convert them to the OME-TIFF image data standard.",
"fairsharing": "FAIRsharing.9vyk3d",
"homepage": "http://jcb-dataviewer.rupress.org",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"name": "JCB DataViewer",
"prefix": "NBDC01919",
"status": "Inactive",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc01920": {
"alt_name": "Progenetix",
"description": "The Progenetix database provides an overview of copy number abnormalities in human cancer from Comparative Genomic Hybridization (CGH) experiments. With 30817 cases from 1016 publications (Oct 2013), Progenetix is the largest curated database for whole genome CGH profiles. The current dataset contains 20621 chromosomal CGH and 10302 profiles from genomic array experiments. This data covers 365 diagnostic entities according to the International Classification of Disease in Oncology (ICD-O 3).\nAdditionally, the website attempts to lists all publications referring to cancer genome profiling experiments.",
"fairsharing": "FAIRsharing.65tdnz",
"homepage": "http://www.progenetix.org",
"information_keywords": [
"Expression",
"Bibliography/Documents"
],
"maintainer": "Michael Baudis Group, Institute of Molecular Life Sciences",
"name": "Progenetix - genomic copy number aberrations in cancer",
"prefix": "NBDC01920",
"pubmeds": [
"18088415",
"16568815",
"11751233",
"24225322"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc01921": {
"alt_name": "arrayMap",
"description": "The arrayMap database and bioinformatics resource facilitates the study of the genetics of human cancer. The Progenetix project provides the data customisation and visualization tools to mine the available data. The arrayMap database is developed by the group \"Theoretical Cytogenetics and Oncogenomics\" at the Institute of Molecular Life Sciences of the University of Zurich.",
"fairsharing": "FAIRsharing.1fbc5y",
"homepage": "http://www.arraymap.org",
"information_keywords": [
"Expression"
],
"maintainer": "Michael Baudis Group, Institute of Molecular Life Sciences||SIB (Swiss Institute of Bioinformatics)",
"name": "arrayMap - Genome Profiles in Cancer",
"prefix": "NBDC01921",
"pubmeds": [
"22629346",
"26615188",
"25428357",
"24476156"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc01922": {
"description": "GeneProf Data is an open web resource for analysed functional genomics experiments. We have built up a large collection of completely processed RNA-seq and ChIP-seq studies by carefully and transparently reanalysing and annotating high-profile public data sets. GeneProf makes these data instantly accessible in an easily interpretable, searchable and reusable manner and thus opens up the path to the advantages and insights gained from genome-scale experiments to a broader scientific audience. Moreover, GeneProf supports programmatic access to these data via web services to further facilitate the reuse of experimental data across tools and laboratories.",
"fairsharing": "FAIRsharing.qmygaa",
"homepage": "http://www.geneprof.org",
"information_keywords": [
"Interaction/Pathway",
"Expression"
],
"name": "GeneProf",
"prefix": "NBDC01922",
"status": "Inactive",
"target_keywords": [
"Protein",
"Genome/Gene",
"RNA"
]
},
"nbdc01923": {
"description": "CiteAb is the largest citation-ranked antibody search engine and provides a simple way to find antibodies that work.\nWe use the number of citations as a transparent method to rank antibodies.\nPowerful filters allow a user to further hone a search based on application, species reactivity, clonality and clone.",
"fairsharing": "FAIRsharing.d404th",
"homepage": "http://www.citeab.com",
"information_keywords": [
"Method"
],
"maintainer": "CiteAB||STORM Consultancy",
"name": "CiteAb",
"prefix": "NBDC01923",
"pubmeds": [
"24528853"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01924": {
"alt_name": "ModBase",
"description": "ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building, and model assessment (http://salilab.org/modeller/). ModBase currently contains almost 30 million reliable models for domains in 4.7 million unique protein sequences. ModBase allows users to compute or update comparative models on demand, through an interface to the ModWeb modeling server (http://salilab.org/modweb). ModBase models are also available through the Protein Model Portal (http://www.proteinmodelportal.org/).",
"fairsharing": "FAIRsharing.jwhdyr",
"homepage": "http://salilab.org/modbase",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "UCSF (Laboratory of Andrej Sali, University of California at San Francisco)",
"name": "ModBase database of comparative protein structure models",
"prefix": "NBDC01924",
"pubmeds": [
"21097780"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01925": {
"description": "CentrosomeDB is a collection of human and drosophila centrosomal genes that were reported in the literature and other sources. The database offers the possibility to study the evolution, function, and structure of the centrosome. They have compiled information from many sources, including Gene Ontology, disease-association, single nucleotide polymorphisms, and associated gene expression experiments.",
"fairsharing": "FAIRsharing.34pfmc",
"homepage": "http://centrosome.cnb.csic.es",
"maintainer": "CNB (National Centre for Biotechnolgy)",
"name": "CentrosomeDB",
"prefix": "NBDC01925",
"pubmeds": [
"24270791"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc01926": {
"description": "The discovery of broadly neutralizing antibodies (bNAbs) has provided an enormous impetus to the HIV vaccine research and to entire immunology. The bNAber database provides open, user friendly access to detailed data on the rapidly growing list of HIV bNAbs, including neutralization profiles, sequences, and three-dimensional structures (when available). It also provides an extensive list of visualization and analysis tools, such as heatmaps to analyze neutralization data as well as structure and sequence viewers to correlate bNAbs properties with structural and sequence features of individual antibodies. The goal of the bNAber database is to enable researchers in this field to easily compare and analyze available information on bNAbs thereby supporting efforts to design an effective vaccine for HIV/AIDS. The bNAber database not only provides easy access to data that currently is scattered in the supplementary materials sections of individual papers, but also contributes to the development of general standards of data that have to be presented with the discovery of new bNAbs and a universal mechanism of how such data can be shared.",
"fairsharing": "FAIRsharing.tgjsm4",
"homepage": "http://bnaber.org/",
"information_keywords": [
"Method",
"Sequence",
"3D structure"
],
"maintainer": "Ragon Institute||SBMRI||Sanford-Burnham Prebys Medical Discovery Institute||TSRI",
"name": "bNAber",
"prefix": "NBDC01926",
"pubmeds": [
"24214957"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01927": {
"description": "OMERO is client-server software for visualization, management and analysis of biological microscope images.",
"fairsharing": "FAIRsharing.t6srmn",
"homepage": "http://www.openmicroscopy.org/info/omero",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Open Microscopy Environment",
"name": "OMERO",
"prefix": "NBDC01927",
"pubmeds": [
"26476368",
"26223880",
"22373911"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc01928": {
"description": "CollecTF is a database of transcription factor binding sites (TFBS) in the Bacteria domain. It aims at becoming a reference, highly-accessed database by relying on its ability to customize navigation and data extraction, its relevance to the community, the quality and detail of the stored data and the up-to-date nature of the stored information.",
"fairsharing": "FAIRsharing.g2cf4x",
"homepage": "http://collectf.umbc.edu",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "University of Maryland",
"name": "CollecTF",
"prefix": "NBDC01928",
"pubmeds": [
"24234444"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc01929": {
"description": "DisGeNET is a discovery platform containing one of the largest collections available of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models, and the scientific literature, and covers the whole landscape of human diseases. The current version (v4.0) contains 429,036 associations, between 17,381 genes and 15,093 diseases, disorders and clinical or abnormal human phenotypes, and 72,870 variant-disease associations between 46,589 SNPs and 6,356 diseases and phenotypes. The data are homogeneously annotated with controlled vocabularies and community-driven ontologies. Additionally, several original metrics are provided to assist the prioritization of genotype-phenotype relationships. The information is accessible through a web interface, a Cytoscape App, an RDF SPARQL endpoint, scripts in several programming languages, and an R package.",
"fairsharing": "FAIRsharing.fssydn",
"homepage": "http://www.disgenet.org",
"information_keywords": [
"Phenotype",
"Sequence"
],
"maintainer": "IBI (Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics (GRIB) IMIM-UPF)",
"name": "DisGeNET: a database of gene-disease associations",
"prefix": "NBDC01929",
"pubmeds": [
"20861032",
"21695124",
"25877637"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Health/Disease",
"Genome/Gene"
]
},
"nbdc01930": {
"alt_name": "MCDRP",
"description": "'Manually Curated Database of Rice Proteins' (MCDRP) is a unique manually curated database based on published experimental data. Currently, the database has data for over 1800 rice proteins curated from > 4000 different experiments of over 400 research articles. Since every aspect of the experiment such as gene name, plant type, tissue and developmental stage has been digitized, experimental data can be rapidly accessed and integrated.",
"fairsharing": "FAIRsharing.qv0f6x",
"homepage": "http://www.genomeindia.org/biocuration",
"information_keywords": [
"Sequence",
"Expression",
"Localization",
"Interaction/Pathway",
"Phenotype",
"Environment",
"Bibliography/Documents"
],
"maintainer": "University of Delhi",
"name": "Manually Curated Database of Rice Proteins",
"prefix": "NBDC01930",
"pubmeds": [
"24214963"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein",
"Genetic variation"
]
},
"nbdc01931": {
"description": "The OpenNeuro project (formerly known as the OpenfMRI project) was established in 2010 to provide a resource for researchers interested in making their neuroimaging data openly available to the research community. It is managed by Russ Poldrack and Chris Gorgolewski of the Center for Reproducible Neuroscience at Stanford University. The project has been developed with funding from the National Science Foundation, National Institute of Drug Abuse, and the Laura and John Arnold Foundation.",
"fairsharing": "FAIRsharing.s1r9bw",
"homepage": "https://openneuro.org",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents",
"Repository"
],
"maintainer": "Laura and John Arnold Foundation||Stanford University||NIH (National Institutes of Health)",
"name": "OpenNeuro",
"prefix": "NBDC01931",
"pubmeds": [
"23847528",
"26048618"
],
"status": "Active"
},
"nbdc01932": {
"alt_name": "MONOCLdb",
"description": "MONOCLdb is an integrative and interactive database designed to retrieve and visualize annotations and expression profiles of long-non coding RNAs (lncRNAs) expressed in Collaborative Cross (http://compgen.unc.edu/) founder mice in response to respiratory influenza and SARS infections.",
"fairsharing": "FAIRsharing.qw7qtk",
"homepage": "http://www.monocldb.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Sequence",
"Interaction/Pathway"
],
"name": "The MOuse NOnCode Lung database",
"prefix": "NBDC01932",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc01933": {
"description": "iSpyBio is an intelligent and unbiased search engine for Life scientists. It ranks reagents by the number of data such as publications, reviews, characterization images and tested applications. It displays over 500,000 reagents such as antibodies, proteins, ELISA kits and biomolecules. iSpyBio's proprietary search algorithm is unique and rapidly analyzes the end-users search query against its large database. Powerful filters allow the user to enhance the search results, for example if they want a protein expressed in yeast or an antibody that only works in mouse. As iSpyBio syncs with supplier and other public databases, it is always up-to-date. This allows iSpyBio to exclude out of stock items but show the most recent testing results and peer-reviewed publications.",
"fairsharing": "FAIRsharing.17z0yf",
"homepage": "http://www.ispybio.com/",
"information_keywords": [
"Method",
"Image/Movie"
],
"name": "iSpyBio",
"prefix": "NBDC01933",
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Protein",
"Metabolite"
]
},
"nbdc01934": {
"description": "The purpose of this database is to collect and distribute statistical maps of the human brain. Such maps are acquired by scientist all around the world using brain imaging techniques such as MRI or PET in a combined effort to map the functions and structures of the brain.",
"fairsharing": "FAIRsharing.rm14bx",
"homepage": "http://neurovault.org",
"information_keywords": [
"Image/Movie"
],
"maintainer": "INCF (International Neuroinformatics Coordinating Facility )||Max Planck Institute for Human Cognitive and Brain Sciences||Stanford Digital Library||Stanford University",
"name": "NeuroVault",
"prefix": "NBDC01934",
"pubmeds": [
"25914639",
"25869863"
],
"status": "Active",
"target_keywords": [
"Organism",
"Cell/Organelle"
]
},
"nbdc01935": {
"alt_name": "CXIDB",
"description": "The Coherent X-ray Imaging Data Bank (CXIDB) offers scientists from all over the world a unique opportunity to access data from Coherent X-ray Imaging (CXI) experiments. It arose from the need to share the terabytes of data generated from X-ray free-electron laser experiments although it caters to all light sources. Accessibility is crucial not only to make efficient use of experimental facilities, but also to improve the reproducibility of results and enable new research based on previous experiments.",
"fairsharing": "FAIRsharing.y6w78m",
"homepage": "http://cxidb.org/",
"information_keywords": [
"3D structure",
"Image/Movie",
"Method",
"Repository"
],
"maintainer": "NERSC (National Energy Research Scientific Computing Center)||Uppsala University",
"name": "Coherent X-ray Imaging Data Bank",
"prefix": "NBDC01935",
"pubmeds": [
"22936162"
],
"status": "Active"
},
"nbdc01936": {
"alt_name": "INDI",
"description": "Database for open data sharing of resting-state fMRI and DTI images collected from over 50 sites around the world. These data collections now contain comprehensive phentoypic information, openly available via data usage agreements.",
"fairsharing": "FAIRsharing.ajpk6x",
"homepage": "http://fcon_1000.projects.nitrc.org/",
"information_keywords": [
"Image/Movie",
"Phenotype",
"Method"
],
"maintainer": "NIH Blueprint (National Institutes of Health Blueprint for Neuroscience Research)||NKI (Nathan S. Kline Institute for Psychiatric Research)",
"name": "International Neuroimaging Data-Sharing Initiative",
"prefix": "NBDC01936",
"pubmeds": [
"23123682",
"22284177"
],
"status": "Active",
"target_keywords": [
"Organism",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc01937": {
"description": "SciCrunch resource registry is the new name of the NIF registry. SciCrunch is a data sharing and display platform. Anyone can create a custom portal where they can select searchable subsets of hundreds of data sources, brand their web pages and create their community. SciCrunch will push data updates automatically to all portals on a weekly basis.",
"fairsharing": "FAIRsharing.kj4pvk",
"homepage": "https://scicrunch.org",
"information_keywords": [
"Portal",
"Repository"
],
"name": "SciCrunch",
"prefix": "NBDC01937",
"pubmeds": [
"26599696"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc01938": {
"alt_name": "EVA",
"description": "The European Variation Archive is an open-access archive that accepts submission of, and provides access to, all types of genetic variation data from all species. All users are able to download any dataset, or query our study catalogue via our variation table. Access to EVA data is also provided by RESTful web services for a variety of applications, such as annotation pipelines.",
"fairsharing": "FAIRsharing.6824pv",
"homepage": "http://www.ebi.ac.uk/eva/",
"information_keywords": [
"3D structure",
"Sequence",
"Repository"
],
"maintainer": "GEUVADIS (Genetic European Variation in Disease)||CIPF (Principe Felipe Research Centre Computational Genomics Department)||EMBL-EBI (European Bioinformatics Institute)||EMBL (European Molecular Biology Laboratory)",
"name": "European Variation Archive",
"prefix": "NBDC01938",
"pubmeds": [
"24037378",
"26673705"
],
"status": "Active",
"target_keywords": [
"DNA",
"Genetic variation",
"Genome/Gene"
]
},
"nbdc01939": {
"alt_name": "KNB",
"description": "An international repository intended to facilitate ecological and environmental research.\nFor scientists, the KNB is an efficient way to share, discover, access and interpret complex ecological data. Due to rich contextual information provided with KNB data, scientists are able to integrate and analyze data with less effort. The data originate from a highly-distributed set of field stations, laboratories, research sites, and individual researchers. The foundation of the KNB is the rich, detailed metadata provided by researchers that collect data, which promotes both automated and manual integration of data into new projects.\nAs part of the KNB effort, data management software is developed in a free and open source manner, so other groups can build upon the tools. The KNB is powered by the Metacat data management system, and is optimized for handling data sets described using the Ecological Metadata Language, but can store any XML-based metadata document.",
"fairsharing": "FAIRsharing.jjka8c",
"homepage": "https://knb.ecoinformatics.org",
"information_keywords": [
"Environment",
"Bibliography/Documents",
"Repository"
],
"maintainer": "DataONE||NCEAS (National Center for Ecological Analysis and Synthesis)",
"name": "The Knowledge Network for Biocomplexity",
"prefix": "NBDC01939",
"status": "Active"
},
"nbdc01940": {
"alt_name": "ChiTaRS",
"description": "The ESTs and mRNAs from GenBank have been used to identify chimeric RNAs of two or more different genes. By analyzing thousands of chimeric ESTs by RNA sequencing, we found that the expression level of chimeric ESTs is generally low and they are highly tissue specific in normal cells. Here we present the improved version of the ChiTaRS database (ChiTaRS-3.1) of about 40,000 chimeric transcripts in humans, mice, fruit flies, zebrafishes, cows, rats, pig and yeast. In the current version we extended the experimental data evidence as well as included a novel type of the sense-antisense chimeric transcripts of the same gene confirmed experimentally by RT-PCR, qPCR, RNA-sequencing and mass-spec peptides. In addition, we collected about 11,700 human cancer breakpoints with the expression levels of chimeric RNAs confirmed by the paired-end RNA-sequencing experiments in different tissues in humans, mice and fruit flies.",
"fairsharing": "FAIRsharing.gg60g3",
"homepage": "http://chitars.md.biu.ac.il/",
"information_keywords": [
"Sequence",
"Expression"
],
"name": "The Improved Database Of Chimeric Transcripts and RNA-Seq Data",
"prefix": "NBDC01940",
"pubmeds": [
"23143107",
"25414346",
"27899596"
],
"status": "Inactive",
"target_keywords": [
"cDNA/EST",
"RNA",
"Health/Disease"
]
},
"nbdc01941": {
"alt_name": "KiMoSys",
"description": "KiMoSys is a user-friendly platform that includes a public data repository of relevant published measurements, including metabolite concentrations (time-series and steady-state), flux data, and enzyme measurements in order to build ODE-based kinetic model. It is designed to search, exchange and disseminate experimental data (and associated kinetic models) for the systems modeling community.",
"fairsharing": "FAIRsharing.6erywc",
"homepage": "http://www.kimosys.org",
"information_keywords": [
"Method",
"Image/Movie",
"Bibliography/Documents",
"Repository"
],
"name": "Experimental data repository for KInetic MOdels of biological SYStems",
"prefix": "NBDC01941",
"pubmeds": [
"25115331"
],
"status": "Active",
"target_keywords": [
"Protein",
"Metabolite"
]
},
"nbdc01942": {
"alt_name": "MGDD",
"description": "The Moroccan Genetic Disease Database (MGDD) collect and document mutations and frequencies of polymorphisms reported in the Moroccan population. The information in the MGDD allow researchers and clinicians to find mutations associated to a given disease or gene of interest, and they can also find polymorphisms associated with susceptibility to a genetic disease or individual responses to pharmaceutical drugs or environmental factors.",
"fairsharing": "FAIRsharing.fe48sc",
"homepage": "http://mgdd.pasteur.ma/index.php",
"information_keywords": [
"Phenotype",
"Sequence"
],
"maintainer": "Pasteur Institute of Morocco",
"name": "Moroccan Genetic Disease Database",
"prefix": "NBDC01942",
"pubmeds": [
"23860041"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Genome/Gene",
"Health/Disease",
"Organism"
]
},
"nbdc01943": {
"alt_name": "EDI",
"description": "The Environmental Data Initiative is an NSF-funded project meant to accelerate curation and archive of environmental data, emphasizing data from projects funded by the NSF DEB. Programs served include Long Term Research in Environmental Biology (LTREB), Organization for Biological Field Stations (OBFS), Macrosystems Biology (MSB), and Long Term Ecological Research (LTER).",
"fairsharing": "FAIRsharing.xd3wmy",
"homepage": "https://portal.edirepository.org/",
"information_keywords": [
"Environment",
"Bibliography/Documents"
],
"name": "Environmental Data Initiative Data Repository",
"prefix": "NBDC01943",
"status": "Active"
},
"nbdc01944": {
"description": "The Trace Archives includes the following archives:\nThe Sequence Read Archive (SRA) stores raw sequence data from \"next-generation\" sequencing technologies including 454, IonTorrent, Illumina, SOLiD, Helicos and Complete Genomics. In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence.\nThe Trace Archive serves as the repository of sequencing data from gel/capillary platforms such as Applied Biosystems ABI 3730.\nThe Trace Assembly Archive stores pairwise alignment and multiple alignment of sequencing reads, linking basic trace data with finished genomic sequence as found in GenBank.",
"fairsharing": "FAIRsharing.abwvhp",
"homepage": "http://www.ncbi.nlm.nih.gov/Traces/home/",
"information_keywords": [
"Sequence"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "NCBI Trace Archives",
"prefix": "NBDC01944",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01945": {
"alt_name": "CCGD",
"description": "The Candidate Cancer Gene Database (CCGD) was developed to disseminate the results of transposon-based forward genetic screens in mice that identify candidate cancer genes. The purpose of the database is to allow cancer researchers to quickly determine whether or not a gene, or list of genes, has been identified as a potential cancer driver in a forward genetic screen in mice.",
"fairsharing": "FAIRsharing.8njqwk",
"homepage": "http://ccgd-starrlab.oit.umn.edu/",
"information_keywords": [
"Sequence"
],
"maintainer": "NIH (National Institutes of Health)",
"name": "Candidate Cancer Gene Database",
"prefix": "NBDC01945",
"pubmeds": [
"25190456"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc01946": {
"description": "FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge.",
"fairsharing": "FAIRsharing.rhpjhv",
"homepage": "http://www.flymine.org",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Cambridge Systems Biology Centre, University of Cambridge",
"name": "FlyMine",
"prefix": "NBDC01946",
"pubmeds": [
"17615057"
],
"status": "Active",
"target_keywords": [
"Protein",
"Genome/Gene"
]
},
"nbdc01947": {
"alt_name": "MouseMine",
"description": "A database of integrated mouse data from MGI, powered by InterMine. MouseMine is member of InterMOD, a consortium of model organism databases dedicated to making cross-species data analysis easier through ongoing coordination and collaborative system development.",
"fairsharing": "FAIRsharing.22z3re",
"homepage": "https://www.mousemine.org/mousemine/begin.do",
"information_keywords": [
"Expression",
"Phenotype",
"Method",
"Interaction/Pathway"
],
"maintainer": "Cambridge Systems Biology Centre, University of Cambridge||MGI (Mouse Genome Informatics)",
"name": "MouseMine @ MGI",
"prefix": "NBDC01947",
"pubmeds": [
"26092688"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Health/Disease"
]
},
"nbdc01948": {
"alt_name": "OSB",
"description": "Open Source Brain is a resource for sharing and collaboratively developing computational models of neural systems.",
"fairsharing": "FAIRsharing.1nshwd",
"homepage": "http://www.opensourcebrain.org",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie",
"Method",
"3D structure"
],
"name": "Open Source Brain",
"prefix": "NBDC01948",
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc01949": {
"alt_name": "NURSA",
"description": "The mission of NURSA is to accrue, develop, and communicate information that advances our understanding of the roles of nuclear receptors (NRs) and coregulators in human physiology and disease.",
"fairsharing": "FAIRsharing.vszknv",
"homepage": "http://www.nursa.org",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Baylor College of Medicine",
"name": "Nuclear Receptor Signaling Atlas",
"prefix": "NBDC01949",
"pubmeds": [
"19423650",
"16381851"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc01950": {
"description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.",
"fairsharing": "FAIRsharing.6gz84c",
"homepage": "http://bio2rdf.org",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Portal"
],
"name": "Bio2RDF",
"prefix": "NBDC01950",
"pubmeds": [
"18472304"
],
"status": "Active"
},
"nbdc01952": {
"alt_name": "euL1db",
"description": "Retrotransposons, which comprises LINE, SINE and LTR-containing elements, accounts for almost half of our genome (Fig. 1). They are mobile genetics elements - also known as jumping genes - but only the L1-HS subfamily has retained the ability to jump autonomously in modern humans. Their mobilization in germline - but also some somatic tissues - contributes to human genetic diversity and to diseases, such as cancer. euL1db provides a curated and comprehensive summary of L1-HS insertion polymorphisms identified in healthy or pathological human samples and published in peer-reviewed journals. It will help understanding the link between L1 retrotransposon insertion polymorphisms and phenotype or disease.",
"fairsharing": "FAIRsharing.ekrvbq",
"homepage": "http://eul1db.unice.fr",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"name": "euL1db, the European database of L1-HS retrotransposon insertions in humans",
"prefix": "NBDC01952",
"pubmeds": [
"25352549"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Genome/Gene",
"Health/Disease"
]
},
"nbdc01953": {
"alt_name": "KnotProt",
"description": "KnotProt collects information about proteins with knots or slipknots. The knotting complexity of proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The database presents extensive information about the biological function of proteins with non-trivial knotting and enables users to analyze new structures.",
"fairsharing": "FAIRsharing.f5b5j1",
"homepage": "http://knotprot.cent.uw.edu.pl/",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "University of Warsaw",
"name": "KnotProt: A database of proteins with knots and slipknots",
"prefix": "NBDC01953",
"pubmeds": [
"22685208"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01954": {
"alt_name": "Platinum",
"description": "Platinum is a manually curated, literature-derived database comprising over 1,000 mutations which for the first time associates experimental information on changes in protein-ligand affinity with the three-dimensional structures of the complex.",
"fairsharing": "FAIRsharing.51r558",
"homepage": "https://biosig.lab.uq.edu.au/platinum/",
"information_keywords": [
"Interaction/Pathway",
"3D structure",
"Sequence"
],
"maintainer": "CPqRR (Fiocruz Minas Centro de Pesquisas Rene Rachou)||St Vincent's Institute||Department of Biochemistry, University of Cambridge",
"name": "Protein-ligand affinity change upon mutation",
"prefix": "NBDC01954",
"pubmeds": [
"25324307"
],
"status": "Active",
"target_keywords": [
"Protein",
"Genome/Gene"
]
},
"nbdc01955": {
"alt_name": "ComPPI",
"description": "The compartmentalized protein-protein interaction database (ComPPI), provides qualitative information on the interactions, proteins and their localizations integrated from multiple databases for protein-protein interaction network analysis.",
"fairsharing": "FAIRsharing.rt38zh",
"homepage": "http://comppi.linkgroup.hu/",
"information_keywords": [
"Interaction/Pathway",
"Localization"
],
"maintainer": "LINK-group||NetBiol||Semmelweis University",
"name": "Compartmentalized Protein-Protein Interaction",
"prefix": "NBDC01955",
"status": "Active",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc01956": {
"description": "A database of protein disorder and mobility annotations. MobiDB was designed to offer a centralized resource for annotations of intrinsic protein disorder. The database features three levels of annotation: manually curated, indirect and predicted. Manually curated data is extracted from the DisProt database. Indirect data is inferred from PDB structures that are considered an indication of intrinsic disorder. The 10 predictors currently included (three ESpritz flavors, two IUPred flavors, two DisEMBL flavors, GlobPlot, VSL2b and JRONN) enable MobiDB to provide disorder annotations for every protein in absence of more reliable data. The new version also features a consensus annotation and classification for long disordered regions. In order to complement the disorder annotations, MobiDB features additional annotations from external sources. Annotations from the UniProt database include post-translational modifications and linear motifs. Pfam annotations are displayed in graphical form and are link-enabled, allowing the user to visit the corresponding Pfam page for further information. Experimental proteinβprotein interactions are also classified for disorder content.",
"fairsharing": "FAIRsharing.jwra3e",
"homepage": "http://mobidb.bio.unipd.it/",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "University of Padova",
"name": "MobiDB",
"prefix": "NBDC01956",
"pubmeds": [
"22661649",
"25361972"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01957": {
"description": "RepeatsDB (http://repeatsdb.bio.unipd.it/) is a database of annotated tandem repeat protein structures. Tandem repeats pose a difficult problem for the analysis of protein structures, as the underlying sequence can be highly degenerate. Several repeat types haven been studied over the years, but their annotation was done in a case-by-case basis, thus making large-scale analysis difficult. We developed RepeatsDB to fill this gap. Using state-of-the-art repeat detection methods and manual curation, we systematically annotated the Protein Data Bank, predicting 10 745 repeat structures. In all, 2797 structures were classified according to a recently proposed classification schema, which was expanded to accommodate new findings. In addition, detailed annotations were performed in a subset of 321 proteins. These annotations feature information on start and end positions for the repeat regions and units. RepeatsDB is an ongoing effort to systematically classify and annotate structural protein repeats in a consistent way. It provides users with the possibility to access and download high-quality datasets either interactively or programmatically through web services.",
"fairsharing": "FAIRsharing.pxnqyt",
"homepage": "http://repeatsdb.bio.unipd.it/",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "BioComputing laboratory, University of Padua||Institue of Molecular Biology, gGmbH||Structural Bioinformatics and Molecular Modelling Group, CRBM",
"name": "RepeatsDB",
"prefix": "NBDC01957",
"pubmeds": [
"24311564"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01958": {
"alt_name": "DEPOD",
"description": "DEPOD - the human DEPhOsphorylation Database is a manually curated database collecting human active and inactive phosphatases, their experimentally verified protein and non-protein substrates, and dephosphorylation site information, and pathways in which they are involved. It also provides links to popular kinase databases and protein-protein interaction databases for these phosphatases and substrates.",
"fairsharing": "FAIRsharing.q9j2e3",
"homepage": "http://www.depod.org/",
"information_keywords": [
"Sequence",
"3D structure",
"Interaction/Pathway"
],
"name": "The human DEPhOsphorylation Database",
"prefix": "NBDC01958",
"pubmeds": [
"25332398",
"23674824"
],
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease"
]
},
"nbdc01959": {
"alt_name": "OSF",
"description": "The OSF supports the entire research lifecycle: planning, execution, reporting, archiving, and discovery. Features include: automated versioning, logging of all actions, collaboration support, free and unlimited file storage, registrations, and connections to other tools/services (ie. Dropbox, figshare, Amazon S3, Dataverse, GitHub).\nIt is 100% free, open source, and intended for use in all domain areas.",
"fairsharing": "FAIRsharing.g4z879",
"homepage": "http://osf.io",
"information_keywords": [
"Bibliography/Documents",
"Portal"
],
"maintainer": "COS (Center for Open Science)",
"name": "Open Science Framework",
"prefix": "NBDC01959",
"pubmeds": [
"28891143",
"30025068"
],
"status": "Active"
},
"nbdc01960": {
"alt_name": "rrnDB",
"description": "The ribosomal RNA operon copy number database is a publicly available, curated resource for ribosomal operon (rrn) copy number information for Bacteria and Archaea.",
"fairsharing": "FAIRsharing.2wb6fv",
"homepage": "http://rrndb.umms.med.umich.edu/",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "University of Michigan",
"name": "The ribosomal RNA operon copy number database",
"prefix": "NBDC01960",
"pubmeds": [
"25414355",
"11125085",
"18948294"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"RNA"
]
},
"nbdc01961": {
"alt_name": "OCP",
"description": "Open Connectome Project: Reverse Engineering the Brain One Synapse at a Time",
"fairsharing": "FAIRsharing.44wk5g",
"homepage": "http://openconnecto.me",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"name": "Open Connectome Project",
"prefix": "NBDC01961",
"pubmeds": [
"24401992"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc01962": {
"alt_name": "SMIR",
"description": "The Sicas Medical Image Repository is a centralized storage system where the data such as Images, Segmentations, SSM can be used to build and shared statistical shape models. Dicom, ITK based images and statistical models in the statismo format can be stored on SMIR.",
"fairsharing": "FAIRsharing.vcmz9h",
"homepage": "https://www.smir.ch",
"information_keywords": [
"Image/Movie",
"Repository"
],
"maintainer": "Swiss Institute for Computer Assisted Surgery",
"name": "SICAS medical image repository",
"prefix": "NBDC01962",
"pubmeds": [
"24220210"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc01963": {
"alt_name": "GXD",
"description": "The Gene Expression Database (GXD) is a community resource for gene expression information from the laboratory mouse. GXD stores and integrates different types of expression data and makes these data freely available in formats appropriate for comprehensive analysis. There is particular emphasis on endogenous gene expression during mouse development.",
"fairsharing": "FAIRsharing.q9neh8",
"homepage": "http://www.informatics.jax.org/expression.shtml",
"information_keywords": [
"Expression"
],
"maintainer": "MGI (Mouse Genome Informatics)",
"name": "MGI Mouse Gene Expression Database",
"prefix": "NBDC01963",
"pubmeds": [
"24958384",
"24163257",
"21062809",
"17130151",
"11125060"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01964": {
"alt_name": "ImmPort",
"description": "The ImmPort system serves as a long-term, sustainable archive of immunology research data generated by investigators mainly funded through the NIAID/DAIT. The core component of the ImmPort system is an extensive data warehouse containing an integration of experimental data and clinical trial data. The analytical tools created and integrated as part of the ImmPort system are available to any researcher within ImmPort after registration and approval by DAIT. Additionally, the data provided mainly by NIAID/DAIT funded researchers in ImmPort will be available to all registered users after the appropriate embargo time. ImmPort, is the data submission portal where researchers upload, QC, and curate their data prior to sharing in OpenImmPort.",
"fairsharing": "FAIRsharing.bpkzqp",
"homepage": "http://immport.org",
"information_keywords": [
"Method",
"Bibliography/Documents",
"Repository"
],
"maintainer": "CEDAR (Center for Expanded Data Annotation and Retrieval)||Human Immunology Project Consortium||ISA-Tools, University of Oxford||Northrop Grumman Health IT||Stanford University||Technion - Israel Institute of Technology||University at Buffalo||University of California San Francisco||AMP (Accelerating Medicines Partnership)",
"name": "Immunology Database and Analysis Portal",
"prefix": "NBDC01964",
"pubmeds": [
"24791905",
"20839340",
"22431383"
],
"status": "Active"
},
"nbdc01965": {
"alt_name": "TrialShare",
"description": "The immune tolerance data management and visualization portal for studies sponsored by the Immune Tolerance Network (ITN) and collaborating investigators. Data from published studies are accessible to any user; data from current in-progress studies are accessible to study investigators and collaborators. Includes links to published figures, tools for visualization and analysis of data, and ability to query study data by subject, group, or any other study parameter.",
"fairsharing": "FAIRsharing.xw1wj5",
"homepage": "https://www.itntrialshare.org/",
"information_keywords": [
"Expression",
"Method",
"Sequence",
"Bibliography/Documents",
"Repository"
],
"name": "Immune Tolerance Network TrialShare",
"prefix": "NBDC01965",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Protein"
]
},
"nbdc01966": {
"alt_name": "IDA",
"description": "The LONI Image Data Archive (IDA) is a user-friendly environment for archiving, searching, sharing, tracking and disseminating neuroimaging and related clinical data. The IDA is utilized for dozens of neuroimaging research projects across North America and Europe and accommodates MRI, PET, MRA, DTI and other imaging modalities. The Image & Data Archive (IDA) provides tools and resources for de-identifying, integrating, searching, visualizing and sharing a diverse range of neuroscience data, helping facilitate collaborations between scientists worldwide.",
"fairsharing": "FAIRsharing.r4ph5f",
"homepage": "https://ida.loni.usc.edu/",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents",
"Repository"
],
"maintainer": "INI (The USC Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California)",
"name": "LONI Image Data Archive",
"prefix": "NBDC01966",
"status": "Active",
"target_keywords": [
"Health/Disease",
"Cell/Organelle"
]
},
"nbdc01967": {
"description": "VertNet is a collaborative project funded by the National Science Foundation that aims to make biodiversity data free and openly accessible on the web from publishers worldwide. Their emphasis has been vertebrate data historically, but data sets can be stored on any biodiversity data. It is beneficial to have all biodiversity data available and discoverable online, so they work with vertebrates, invertebrates, plants, fungi, paleo, or any other biological and natural history collection interested in sharing their data with the world.",
"fairsharing": "FAIRsharing.ctdss6",
"homepage": "http://www.vertnet.org/",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "MVZ (Museum of Vertebrate Zoology at Berkeley)||University of Colorado Boulder",
"name": "VertNet",
"prefix": "NBDC01967",
"pubmeds": [
"20169109"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01968": {
"alt_name": "FLOW",
"description": "Fulgoromorpha Lists On the Web (FLOW) is an online database that aims to provide an easy-access summary of available biological published primary data on planthoppers (Hemiptera, Fulgoromorpha), a group of major economic importance. It includes information on taxonomy, nomenclature, bibliography, distribution and various associated biological information on host-plants and parasites (including fossils).",
"fairsharing": "FAIRsharing.8a0a61",
"homepage": "https://flow.hemiptera-databases.org/flow/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Taxonomy",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "MNHN (MusΓ©um National d'Histoire Naturelle)",
"name": "Fulgoromorpha Lists On the Web",
"prefix": "NBDC01968",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01969": {
"alt_name": "SHARK",
"description": "SHARK (\"Svenskt HavsARKiv\" / \"Swedish Ocean Archive\") contains marine environmental monitoring data from the seas surrounding Sweden. SHARK is accessed via SHARKweb (for human-readable content) and SHARKdata (for computational access). Content includes marine physical, chemical and biological data collected within Swedish environmental monitoring programs.",
"fairsharing": "FAIRsharing.npf403",
"homepage": "http://www.smhi.se/en/services/open-data/national-archive-for-oceanographic-data",
"information_keywords": [
"Environment"
],
"maintainer": "SMHI (Swedish Meterological and Hydrological Institute)",
"name": "Swedish Ocean Archive",
"prefix": "NBDC01969",
"status": "Active"
},
"nbdc01970": {
"description": "speciesLink (also known as the Distributed Information System for Biological Collections: Integrating Species Analyst and SinBiota (FAPESP)) implements a distributed information system to retrieve primary biodiversity data from collections within the state of SΓ£o Paulo (Brazil) as well as data integrated from other networks and observation data registered in the SinBiota database.",
"fairsharing": "FAIRsharing.pjmdrp",
"homepage": "http://www.splink.org.br/index?lang=en",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "CRIA (The Reference Center on Environmental Information)",
"name": "speciesLink",
"prefix": "NBDC01970",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01971": {
"description": "Biological collections are replete with taxonomic, geographic, temporal, numerical, and historical information. This information is crucial for understanding and properly managing biodiversity and ecosystems, but is often difficult to access. Data publication is the act of making that information available online, and is the core mission of Canadensys. Most of the datasets contain specimen data, but checklists and observation data are present as well.",
"fairsharing": "FAIRsharing.jr4y76",
"homepage": "https://data.canadensys.net/explorer/occurrences/search?q=#tab_mapView",
"information_keywords": [
"Environment",
"Geographic Distribution",
"Taxonomy"
],
"maintainer": "Centre sur la Biodiversite de l'Universite de Montreal",
"name": "Canadensys",
"prefix": "NBDC01971",
"pubmeds": [
"24198712"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01972": {
"alt_name": "PGP",
"description": "This repository provides several plant genomic and phenotypic datasets resulting from IPK and German Plant Phenotyping Network (DPPN) research activities. It was established in January 2015. The background of the study is in plant genetic resources, in particular the association of genotypes and phenotypes. This archive aims to provide data from the \"system plant\" - from the root to bloom and seed, as well from sequence analysis to systems biology.Ge",
"fairsharing": "FAIRsharing.rf3m4g",
"homepage": "http://edal-pgp.ipk-gatersleben.de",
"information_keywords": [
"Phenotype",
"Localization",
"Repository"
],
"maintainer": "transPLANT (trans-national infrastructure for plant genomic science)||IPK (Leibniz Institute of Plant Genetics and Crop Plant Research)",
"name": "Plant Genomics and Phenomics Research Data Repository",
"prefix": "NBDC01972",
"pubmeds": [
"24958009",
"27087305"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc01973": {
"alt_name": "SCC",
"description": "The Stem Cell Commons were initiated by the Harvard Stem Cell Institute to develop a community for stem cell bioinformatics. This open source environment for sharing, processing and analyzing stem cell data brings together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons.",
"fairsharing": "FAIRsharing.84ebcy",
"homepage": "http://stemcellcommons.org/",
"information_keywords": [
"Expression",
"Sequence"
],
"maintainer": "Harvard Stem Cell Institute||Oxford e-Research Centre, Department of Engineering Science, University of Oxford",
"name": "Stem Cell Commons",
"prefix": "NBDC01973",
"pubmeds": [
"24303302"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Cell/Organelle"
]
},
"nbdc01974": {
"alt_name": "MIMIC-III",
"description": "MIMIC-III (Medical Information Mart for Intensive Care III) is a large, freely-available database comprising deidentified health-related data associated with over forty thousand patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012. The database includes information such as demographics, vital sign measurements made at the bedside (~1 data point per hour), laboratory test results, procedures, medications, caregiver notes, imaging reports, and mortality (both in and out of hospital). MIMIC supports a diverse range of analytic studies spanning epidemiology, clinical decision-rule improvement, and electronic tool development.",
"fairsharing": "FAIRsharing.pqnhpj",
"homepage": "http://mimic.physionet.org/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Beth Israel Deaconess Medical Center||LCP (Laboratory for Computational Physiology, Massachusetts Institute of Technology)||Philips Healthcare",
"name": "Medical Information Mart for Intensive Care III",
"prefix": "NBDC01974",
"pubmeds": [
"21283005",
"27219127"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01976": {
"alt_name": "NIDDK",
"description": "The NIDDK Central Repository stores biosamples, genetic and other data collected in designated NIDDK-funded clinical studies. The purpose of the NIDDK Central Repository is to expand the usefulness of these studies by allowing a wider research community to access data and materials beyond the end of the study.",
"fairsharing": "FAIRsharing.pr47jw",
"homepage": "https://repository.niddk.nih.gov/home/",
"information_keywords": [
"Repository"
],
"name": "NIDDK Central Repository",
"prefix": "NBDC01976",
"pubmeds": [
"21959867"
],
"status": "Active",
"target_keywords": [
"Health/Disease",
"Genome/Gene"
]
},
"nbdc01977": {
"alt_name": "dkNET",
"description": "The NIDDK Information Network provides access to large pools of data relevant to the mission of NIDDK. The dkNET portal contains information about research resources such as antibodies, vectors and mouse strains, data, protocols, and literature.",
"fairsharing": "FAIRsharing.1mapgk",
"homepage": "http://www.dknet.org",
"information_keywords": [
"Phenotype",
"Expression",
"Interaction/Pathway",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "UCSD (University of California San Diego)",
"name": "NIDDK Information Network",
"prefix": "NBDC01977",
"pubmeds": [
"26978244",
"26730820",
"26393351"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Protein"
]
},
"nbdc01978": {
"alt_name": "HCP",
"description": "The HCP is mapping the human connectome as accurately as possible in a large number of normal adults and is making this data freely available to the scientific community using a powerful, user-friendly informatics platform.",
"fairsharing": "FAIRsharing.ejeqy",
"homepage": "http://www.humanconnectome.org",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie",
"Method"
],
"maintainer": "University of Oxford||University of Minnesota||Washington University in St Louis||Radboud University",
"name": "Human Connectome Project",
"prefix": "NBDC01978",
"pubmeds": [
"22366334",
"21743807",
"25934470"
],
"status": "Active",
"target_keywords": [
"Organism",
"Cell/Organelle"
]
},
"nbdc01979": {
"alt_name": "PPMI",
"description": "PPMI is an observational clinical study to verify progression markers in Parkinson's disease. The study is designed to establish a comprehensive set of clinical, imaging and biosample data that will be used to define biomarkers of PD progression. Once these biomarkers are defined, they can be used in therapeutic studies. The clinical, imaging and biologic data are accessible to researchers in real time through the website.",
"fairsharing": "FAIRsharing.tamp4p",
"homepage": "http://www.ppmi-info.org",
"information_keywords": [
"Image/Movie",
"Method",
"Bibliography/Documents"
],
"maintainer": "LONI (Laboratory of Neuro Imaging, University of Southern California)",
"name": "Parkinson's Progression Markers Initiative",
"prefix": "NBDC01979",
"pubmeds": [
"21930184",
"26268663"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc01980": {
"description": "MoonProt Database is a manually curated, searchable, internet-based resource with information about the over 200 proteins that have been experimentally verified to be moonlighting proteins. Moonlighting proteins comprise a class of multifunctional proteins in which a single polypeptide chain performs multiple biochemical functions that are not due to gene fusions, multiple RNA splice variants or pleiotropic effects. The availability of this organized information provides a more complete picture of what is currently known about moonlighting proteins. The database will also aid researchers in other fields, including determining the functions of genes identified in genome sequencing projects, interpreting data from proteomics projects and annotating protein sequence and structural databases. In addition, information about the structures and functions of moonlighting proteins can be helpful in understanding how novel protein functional sites evolved on an ancient protein scaffold, which can also help in the design of proteins with novel functions.",
"fairsharing": "FAIRsharing.djyk2c",
"homepage": "http://www.moonlightingproteins.org",
"information_keywords": [
"Sequence",
"3D structure",
"Classification"
],
"maintainer": "University of Illinois at Chicago",
"name": "MoonProt",
"prefix": "NBDC01980",
"pubmeds": [
"25324305"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01981": {
"alt_name": "MW",
"description": "Experimental data generated by NIH Metabolomics Regional Comprehensive Metabolomics Resource Cores (RCMRC)s * and other NIH-sponsored projects is available for searching and analysis, via online interfaces. Users may also search the Metabolomics Workbench Metabolite Database, which now contains over 60,000 entries.",
"fairsharing": "FAIRsharing.xfrgsf",
"homepage": "http://www.metabolomicsworkbench.org",
"information_keywords": [
"Method",
"Bibliography/Documents",
"Repository"
],
"name": "Metabolomics Workbench",
"prefix": "NBDC01981",
"pubmeds": [
"26467476"
],
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc01982": {
"alt_name": "SBGrid-DG",
"description": "This resource provides open access to the host laboratory as well as the inhouse collections of X-ray diffraction, MicroED, and LLSM datasets.",
"fairsharing": "FAIRsharing.1hqd55",
"homepage": "http://data.sbgrid.org",
"information_keywords": [
"3D structure",
"Image/Movie",
"Method",
"Repository"
],
"maintainer": "The Institute for Quantitative Social Service, Harvard University||Harvard Medical School||SBGrid Consortium",
"name": "Structural Biology Data Grid",
"prefix": "NBDC01982",
"pubmeds": [
"24040512"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01983": {
"alt_name": "BioSample",
"description": "The BioSample database stores submitter-supplied descriptive information, or metadata, about the biological materials used in experimental assays, from which data stored in NCBI's primary data archives are derived.",
"fairsharing": "FAIRsharing.qr6pqk",
"homepage": "http://www.ncbi.nlm.nih.gov/biosample/",
"information_keywords": [
"3D structure",
"Expression",
"Sequence",
"Method",
"Phenotype",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "NCBI BioSample",
"prefix": "NBDC01983",
"pubmeds": [
"22139929"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle"
]
},
"nbdc01984": {
"description": "A world bioinformatic public service for high-speed access to up-to-date DNA & protein biological sequence databanks.",
"fairsharing": "FAIRsharing.73reht",
"homepage": "http://www.bio-mirror.net/",
"information_keywords": [
"Sequence",
"Portal"
],
"maintainer": "University of Indiana",
"name": "Bio-Mirror",
"prefix": "NBDC01984",
"pubmeds": [
"15059839"
],
"status": "Active",
"target_keywords": [
"DNA",
"Protein"
]
},
"nbdc01985": {
"alt_name": "RDoCdb",
"description": "RDoCdb is an informatics platform for the sharing of human subjects data related to Mental Health research. This database may be used to plan for data submission, share your data, query data that is already shared, or to share your results related to a publication or finding. RDoCdb is is a part of the NIMH Data Archive (NDA), powered by the National Database for Autism Research (NDAR) infrastructure.",
"fairsharing": "FAIRsharing.af3j4h",
"homepage": "http://rdocdb.nimh.nih.gov",
"information_keywords": [
"Bibliography/Documents",
"Repository"
],
"maintainer": "NIMH (National Institute of Mental Health)",
"name": "Research Domain Criteria Database",
"prefix": "NBDC01985",
"status": "Closed",
"target_keywords": [
"Health/Disease",
"Organism"
]
},
"nbdc01986": {
"alt_name": "NDCT",
"description": "NDCT is an informatics platform for the sharing of clinical trial data funded by the National Institute of Mental Health. NDCT is a part of the NIMH Data Archive (NDA), powered by the NDAR (National Database for Autism Research) infrastructure.",
"fairsharing": "FAIRsharing.1h7t5t",
"homepage": "https://data-archive.nimh.nih.gov/ndct/",
"information_keywords": [
"Bibliography/Documents",
"Repository"
],
"maintainer": "NIMH (National Institute of Mental Health)",
"name": "National Database for Clinical Trials related to Mental Illness",
"prefix": "NBDC01986",
"status": "Active",
"target_keywords": [
"Health/Disease",
"Organism"
]
},
"nbdc01988": {
"description": "The PlasmID Repository provides researchers with inexpensive sequencing and plasmid services, holding ~350,000 plasmids, including most human cDNAs as well as shRNA libraries. PlasmID was added to the DNA Resource Core in the spring of 2004 to reduce the burden on individual labs to store, maintain and distribute plasmid clones and supporting information.",
"fairsharing": "FAIRsharing.k9ptv7",
"homepage": "http://plasmid.med.harvard.edu/PLASMID/Home.xhtml",
"information_keywords": [
"Sequence",
"Bioresource"
],
"maintainer": "Beth Israel Deaconess Medical Center||Boston Children's Hospital||Division of Sleep & Circadian Disorders, Brigham and Women's Hospital/Harvard Medical School||Dana-Farber Cancer Institute||Harvard Medical School||Massachusetts General Hospital||NCI (National Cancer Institute, National Institutes of Health)",
"name": "PlasmID",
"prefix": "NBDC01988",
"status": "Inactive",
"target_keywords": [
"RNA",
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc01989": {
"description": "A crowdsourced collection of personal genomics data. Includes SNP genotyping, exome sequencing data, phenotypic annotation and quantified self tracking data.",
"fairsharing": "FAIRsharing.wjhf24",
"homepage": "https://www.opensnp.org",
"information_keywords": [
"Sequence",
"Phenotype",
"Method"
],
"maintainer": "Seven Bridges||openSNP Administrators",
"name": "openSNP",
"prefix": "NBDC01989",
"pubmeds": [
"24647222"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Genome/Gene"
]
},
"nbdc01990": {
"description": "Carlos III Networked Proteomics Platform, ProteoRed-ISCIII is a National Network for the coordination, integration and development of the Spanish Proteomics Facilities providing proteomics services for supporting Spanish researchers in the field of proteomics.",
"fairsharing": "FAIRsharing.7v8q4h",
"homepage": "http://www.proteored.org",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "CIMA (Centro de Investigacion Medica Aplicada)",
"name": "ProteoRed",
"prefix": "NBDC01990",
"pubmeds": [
"17031803",
"21983993",
"20097317"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc01991": {
"description": "ReMap is an integrative analysis of transcription factor ChIP-seq experiments publicly available, merged with the Encode dataset. The resource is an extensive regulatory catalogue of transcription factor binding sites from transcription factors (TFs). The data is available to browse or download either for a given transcription factor or for the entire dataset.",
"fairsharing": "FAIRsharing.c8dxsv",
"homepage": "https://remap2022.univ-amu.fr/",
"information_keywords": [
"Interaction/Pathway"
],
"name": "ReMap",
"prefix": "NBDC01991",
"pubmeds": [
"25477382"
],
"status": "Active",
"target_keywords": [
"Protein",
"Genome/Gene",
"Health/Disease",
"Cell/Organelle"
]
},
"nbdc01992": {
"alt_name": "iDigBio",
"description": "iDigBio is the US national resource for digitized information about vouchered natural history collections within the context established by the NIBA community strategic plan and is supported through funds from the NSF's ADBC (Advancing Digitization of Biodiversity Collections) program. Through ADBC, data and images for millions of biological specimens are being made available in electronic format for the research community, government agencies, students, educators, and the general public.",
"fairsharing": "FAIRsharing.d21jc4",
"homepage": "https://www.idigbio.org/",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents",
"Repository"
],
"name": "Integrated Digitized Biocollections",
"prefix": "NBDC01992",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc01993": {
"description": "VirusMentha is a collection of viral interactions manually curated from protein-protein databases that adhere to the IMEx consortium. This resource offers a series of tools to analyse selected proteins in the context of a network of interactions.",
"fairsharing": "FAIRsharing.6w29qp",
"homepage": "http://virusmentha.uniroma2.it/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "University of Rome Tor Vergata",
"name": "VirusMentha",
"prefix": "NBDC01993",
"pubmeds": [
"25217587"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01994": {
"alt_name": "SIGNOR",
"description": "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The entire network can be freely downloaded and used to support logic modeling or to interpret high content datasets. The core of this project is a collection of more than 11000 manually-annotated causal relationships between proteins that participate in signal transduction. Each relationship is linked to the literature reporting the experimental evidence. In addition each node is annotated with the chemical inhibitors that modulate its activity. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms.",
"fairsharing": "FAIRsharing.ss78t4",
"homepage": "http://signor.uniroma2.it/",
"information_keywords": [
"Bibliography/Documents",
"Interaction/Pathway"
],
"maintainer": "Bioinformatics and Computational biology Unit, Molecular genetics Lab, University of Rome Tor Vergata",
"name": "SIGNOR, the SIGnaling Network Open Resource",
"prefix": "NBDC01994",
"pubmeds": [
"26467481"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc01995": {
"alt_name": "CRC Atlas",
"description": "Colorectral Cancer Atlas is an web-based resource which integrates genomic and proteomic pertaining to colorectal cancer cell lines and tissues.\nData catalogued includes, quantitative and non-quantitative protein expression, sequence variations, cellular signaling pathways, protein-protein interactions, Gene Ontology terms, protein domains and post-translational modifications (PTMs).",
"fairsharing": "FAIRsharing.5mf7bd",
"homepage": "http://colonatlas.org/",
"information_keywords": [
"Bibliography/Documents",
"Sequence",
"Ontology/Terminology/Nomenclature",
"Expression",
"Interaction/Pathway"
],
"name": "Colorectal Cancer Atlas",
"prefix": "NBDC01995",
"pubmeds": [
"26496946"
],
"status": "Active",
"target_keywords": [
"Drug",
"Health/Disease",
"Cell/Organelle",
"Genome/Gene",
"Protein"
]
},
"nbdc01996": {
"alt_name": "DIDA",
"description": "DIDA (DIgenic diseases DAtabase) is a novel database that provides for the first time detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance.",
"fairsharing": "FAIRsharing.v1dcm3",
"homepage": "http://dida.ibsquare.be",
"information_keywords": [
"Sequence",
"Expression"
],
"name": "Digenic diseases database",
"prefix": "NBDC01996",
"pubmeds": [
"26481352"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc01997": {
"description": "Scratchpads are an online virtual research environment for biodiversity scientists, allowing anyone to share their data and create their own research networks. Sites are hosted at the Natural History Museum London, and offered freely to any scientist that completes an online registration form.\nSites can focus on specific taxonomic groups, or the biodiversity of a biogeographic region, or indeed any aspect of natural history. Scratchpads are also suitable for societies or for managing and presenting projects. Key features of Scratchpads include: tools to manage biological classifications, bibliography management, media (images, video and audio), rich taxon pages (with structured descriptions, specimen records, and distribution data), and character matrices. Scratchpads support various ways of communicating with site members and visitors such as blogs, forums, newsletters and a commenting system. Translations of the Scratchpad software are available via our localisation server and site content can be created in multiple languages.",
"fairsharing": "FAIRsharing.62p8w",
"homepage": "http://scratchpads.org/",
"information_keywords": [
"Bibliography/Documents",
"Taxonomy",
"Portal"
],
"maintainer": "BioVeL||Encyclopedia of Life||Natural History Museum||Pensoft Publishers||BHL (The Biodiversity Heritage Library)||ViBRANT (Virtual Biodiversity Research and Access Network for Taxonomy)||Vizzuality||e-monocot project",
"name": "Scratchpads",
"prefix": "NBDC01997",
"pubmeds": [
"22207806"
],
"status": "Active"
},
"nbdc01998": {
"description": "WholeCellSimDB is a database of whole-cell model simulations designed to make it easy for researchers to explore and analyze whole-cell model predictions including predicted:\n- Metabolite concentrations,\n- DNA, RNA and protein expression,\n- DNA-bound protein positions,\n- DNA modification positions, and\n- Ribome positions.",
"fairsharing": "FAIRsharing.ew61fn",
"homepage": "http://www.wholecellsimdb.org",
"information_keywords": [
"Expression"
],
"maintainer": "Karr Lab, Institute for Multiscale Biology & Genomics",
"name": "WholeCellSimDB",
"prefix": "NBDC01998",
"pubmeds": [
"25231498"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Metabolite",
"Protein",
"Cell/Organelle"
]
},
"nbdc01999": {
"description": "This database enables the reliable identification of an individual Interferon Regulated Gene (IRG) or IRG signatures from high-throughput data sets (i.e. microarray, proteomic data etc.). It also assists in identifying regulatory elements, chromosomal location and tissue expression of IRGs in human and mouse. This upgraded version, Interferome v2.0 has quantitative data, more detailed annotation and search capabilities and can be queried for one to a thousand genes, such as from from a microarray experiment.",
"fairsharing": "FAIRsharing.pp67qc",
"homepage": "http://www.interferome.org",
"information_keywords": [
"Method",
"Expression",
"Localization",
"Bibliography/Documents"
],
"maintainer": "ANDS (Australian National Data Service)||eResearch Centre, Monash University",
"name": "Interferome",
"prefix": "NBDC01999",
"pubmeds": [
"23203888",
"18996892"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Health/Disease"
]
},
"nbdc02000": {
"alt_name": "sorfs.org",
"description": "sORFs.org is a database for sORFs identified using ribosome profiling. Starting from ribosome profiling, sORFs.org identifies sORFs, incorporates state-of-the-art tools and metrics and stores results in a public database. Two query interfaces are provided, a default one enabling quick lookup of sORFs and a BioMart interface providing advanced query and export possibilities. At present, sORFs.org harbors 263 354 sORFs that demonstrate ribosome occupancy, originating from three different cell lines: HCT116 (human), E14_mESC (mouse) and S2 (fruit fly).",
"fairsharing": "FAIRsharing.x7pwnw",
"homepage": "http://www.sorfs.org",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "BIOBIX (Lab of bioinformatics and computational genomics)",
"name": "short Open Reading Frame database",
"prefix": "NBDC02000",
"pubmeds": [
"26527729"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc02001": {
"description": "Seanoe (SEA scieNtific Open data Edition) is a publisher of scientific data in the field of marine sciences. It is operated by Sismer within the framework of the PΓ΄le OcΓ©an.\nData published by SEANOE are available free. They can be used in accordance with the terms of the Creative Commons license selected by the author of data. Seance contributes to Open Access / Open Science movement for a free access for everyone to all scientific data financed by public funds for the benefit of research.\nAn embargo limited to 2 years on a set of data is possible; for example to restrict access to data of a publication under scientific review.\nEach data set published by SEANOE has a DOI which enables it to be cited in a publication in a reliable and sustainable way.\nThe long-term preservation of data filed in SEANOE is ensured by Ifremer infrastructure.",
"fairsharing": "FAIRsharing.bb5rna",
"homepage": "http://www.seanoe.org",
"information_keywords": [
"Bibliography/Documents",
"Environment",
"Repository"
],
"maintainer": "Ifremer (Institut francais de recherche pour l'exploitation de la mer)",
"name": "Seanoe",
"prefix": "NBDC02001",
"status": "Active"
},
"nbdc02002": {
"description": "probeBase is a manually maintained and curated database of rRNA-targeted oligonucleotide probes and primers. Contextual information and multiple options for evaluating in silico hybridization performance against the most recent rRNA sequence databases are provided for each oligonucleotide entry, which makes probeBase an important and frequently used resource for microbiology research and diagnostics.\nThe major features of probeBase include a classification of probes and primers according to the NCBI taxonomy database, a powerful and customizable search function, which serves to query for target organisms, probe names, primers, target sites, and references. The probeBase match tool can be used to match near-full length rRNA sequences against probeBase and find all published probes targeting the query sequences. The new proxy match tool extends this analysis to partial rRNA sequences, which exploits full-length sequences in the rRNA sequence database SILVA to find published probes potentially targeting partial query sequences. A tool for submitting new or missing probe sequences or references helps to keep probeBase up-to-date.",
"fairsharing": "FAIRsharing.t6wjn7",
"homepage": "http://www.probebase.net",
"information_keywords": [
"Sequence",
"Method"
],
"maintainer": "University of Vienna, Department of Microbiology and Ecosystem Science",
"name": "probeBase",
"prefix": "NBDC02002",
"pubmeds": [
"12520066",
"17099228",
"26586809"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc02003": {
"alt_name": "EK3D",
"description": "EK3D - an E. coli K antigen 3-dimensional structure database is a repository of 72 E. coli K antigens that provides information about the sugar composition, epimeric & enantiomeric forms and linkages between the sugar monomers.",
"fairsharing": "FAIRsharing.syayhh",
"homepage": "http://www.iith.ac.in/EK3D/",
"information_keywords": [
"3D structure",
"Classification"
],
"maintainer": "IITH (Indian Institute of Technology Hyderabad)",
"name": "E. coli K antigen 3-dimensional structure database",
"prefix": "NBDC02003",
"pubmeds": [
"26615200"
],
"status": "Active",
"target_keywords": [
"Epigenetics",
"Protein"
]
},
"nbdc02004": {
"description": "We developed a pipeline to annotate lncRNAs (Long non-coding RNAs) and applied it to 37 plant species and six algae, resulting in the annotation of more than 120 000 lncRNAs. To facilitate the study of lncRNAs for the plant research community, the information gathered is organised in the Green Non-Coding Database.",
"fairsharing": "FAIRsharing.fe9kyy",
"homepage": "http://greenc.sciencedesigners.com/",
"information_keywords": [
"Sequence"
],
"maintainer": "Sequentia Biotech SL",
"name": "GREENC",
"prefix": "NBDC02004",
"pubmeds": [
"26578586"
],
"status": "Inactive",
"target_keywords": [
"RNA",
"Organism"
]
},
"nbdc02005": {
"description": "The GeneWeaver data and analytics website is a publically available resource for storing, curating and analyzing sets of genes from heterogeneous data sources. The system enables discovery of relationships among genes, variants, traits, drugs, environments, anatomical structures and diseases implicitly found through gene set intersections. By enumerating the common and distinct biological molecules associated with all subsets of curated or user submitted groups of gene sets and gene networks, GeneWeaver empowers users with the ability to construct data driven descriptions of shared and unique biological processes, diseases and traits within and across species.",
"fairsharing": "FAIRsharing.1y79y9",
"homepage": "http://www.geneweaver.org",
"information_keywords": [
"Expression",
"Bibliography/Documents"
],
"maintainer": "Baylor University||Churchill Group, The Jackson Laboratory||University of Tennessee",
"name": "GeneWeaver",
"prefix": "NBDC02005",
"pubmeds": [
"22080549",
"26092690",
"19733230"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Drug",
"Health/Disease"
]
},
"nbdc02006": {
"description": "The HGTree database provides putative genome-wide horizontal gene transfer (HGT) information for 2,472 completely sequenced prokaryotic genomes. HGT detection is based on an explicit evolutionary model of tree reconstruction and relies on evaluating the conflicts between phylogenetic tree of each orthologous gene set and corresponding 16S rRNA species tree. The database provides quick and easy access to HGT-related genes in hundreds of prokaryotic genomes and provides functionalities to detect HGT in user-customized datasets and gene and genome sequences. The database is freely available and can be easily scaled and updated to keep pace with the rapid rise in genomic information.",
"fairsharing": "FAIRsharing.q33qzy",
"homepage": "http://hgtree.snu.ac.kr",
"information_keywords": [
"Taxonomy"
],
"maintainer": "CIIT (Comsats Institute of Information Technology)||Seoul National University",
"name": "HGTree",
"prefix": "NBDC02006",
"pubmeds": [
"26578597"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Organism"
]
},
"nbdc02007": {
"description": "BioXpress is a curated gene expression and disease association database where the expression levels are mapped to genes.",
"fairsharing": "FAIRsharing.8bva0r",
"homepage": "https://hive.biochemistry.gwu.edu/tools/bioxpress/",
"information_keywords": [
"Expression",
"Sequence"
],
"maintainer": "George Washington University",
"name": "BioXpress",
"prefix": "NBDC02007",
"pubmeds": [
"25819073"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"RNA",
"Health/Disease"
]
},
"nbdc02008": {
"alt_name": "SEA",
"description": "SEA (Super-Enhancer Archive) is a web-based comprehensive resource focusing on the collection, storage and online analysis of super-enhancers. It focuses on integrating super-enhancers in multiple species and annotating their potential roles in the regulation of cell identity gene expression. To facilitate data extraction, SEA supports multiple search options, including species, genome location, gene name, cell type/tissue, and super-enhancer name.",
"fairsharing": "FAIRsharing.bya6z",
"homepage": "http://sea.edbc.org/",
"information_keywords": [
"Interaction/Pathway",
"Taxonomy",
"Sequence",
"Expression"
],
"maintainer": "College of Bioinformatics Science and Technology, Harbin Medical University||GCER (Group of Computational Epigenetic Research)||Lab of Developmental Biology, Harbin Institute of Technology",
"name": "Super-Enhancer Archive",
"prefix": "NBDC02008",
"pubmeds": [
"26578594"
],
"status": "Active",
"target_keywords": [
"Protein",
"Genome/Gene",
"Cell/Organelle"
]
},
"nbdc02009": {
"alt_name": "BIGNASim",
"description": "Atomistic Molecular Dynamics Simulation Trajectories and Analyses of Nucleic Acid Structures.\nBIGNASim is a complete platform to hold and analyse nucleic acids simulation data, based on two noSQL database engines: Cassandra to hold trajectory data and MongoDB for analyses and metadata. Most common analyses (helical parameters, NMR observables, sitffness, hydrogen bonding and stacking energies and geometries) are pre-calculated for the trajectories available and shown using the interactive visualization offered by NAFlex interface. Additionaly, whole trajectories, fragments or meta-trajectories can be analysed or downloaded for further in-house processing.",
"fairsharing": "FAIRsharing.k5a3yt",
"homepage": "http://mmb.irbbarcelona.org/BIGNASim",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "ICREA (Cataland Institution for Research and Advanced Studies)||BSC (Barcelona Supercomputing Center)||Barcelona University||Institute for Research in Biomedicine",
"name": "Big Data Nucleic Acid Simulations Database",
"prefix": "NBDC02009",
"pubmeds": [
"26612862"
],
"status": "Active",
"target_keywords": [
"DNA"
]
},
"nbdc02010": {
"description": "SigMol is a specialized repository of quorom sensing signaling molecules (QSSMs) in prokaryotes. SigMol harbors information on QSSMs pertaining to different quorum sensing signaling systems namely acylated homoserine lactones (AHLs), diketopiperazines (DKPs), 4- hydroxy-2-alkylquinolines (HAQs), diffusible signal factors (DSFs), autoinducer-2 (AI-2) and others. The database includes biological as well as chemical aspects of signaling molecules. Biological information includes genes, preliminary bioassays, identification assays and applications, while chemical detail comprises of IUPAC name, SMILES and structure.",
"fairsharing": "FAIRsharing.p7ev6e",
"homepage": "http://bioinfo.imtech.res.in/manojk/sigmol/",
"information_keywords": [
"Method",
"Interaction/Pathway",
"3D structure"
],
"maintainer": "Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR)",
"name": "SigMol",
"prefix": "NBDC02010",
"pubmeds": [
"26490957"
],
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc02011": {
"description": "enviPath is both a database and a prediction system, for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways, and supports the annotation of pathways with experimental and environmental conditions. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products.",
"fairsharing": "FAIRsharing.g0c5qn",
"homepage": "https://envipath.org",
"information_keywords": [
"Method",
"Environment",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "Eawag||Johannes Gutenberg University",
"name": "enviPath",
"prefix": "NBDC02011",
"pubmeds": [
"26582924"
],
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc02012": {
"alt_name": "PAIN",
"description": "The PAIN Repository is a brain imaging archive for structural and functional magnetic resonance scans (MRI, fMRI and DTI) hosted at UCLA and open to all pain investigators.",
"fairsharing": "FAIRsharing.9fmyc7",
"homepage": "https://www.painrepository.org/repositories/",
"information_keywords": [
"Image/Movie",
"Method",
"Repository"
],
"maintainer": "Gail and Gerald Oppenheimer Center for Neurobiology of Stress at UCLA ||University of California",
"name": "The Pain and Interoception Imaging Network",
"prefix": "NBDC02012",
"pubmeds": [
"25902408"
],
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease"
]
},
"nbdc02013": {
"alt_name": "ABIDE",
"description": "Autism spectrum disorders (ASD) are characterized by qualitative impairment in reciprocal social communication, as well as by repetitive, restricted, and stereotyped behaviors. Previously considered rare, ASD are now recognized to occur in more than 1% of children, causing immense suffering to individuals and their families. The complexity and heterogeneity of ASD make it necessary to obtain large-scale samples which are difficult to attain in any individual lab. In response, the Autism Brain Imaging Data Exchange (ABIDE) provides previously collected resting state functional magnetic resonance imaging (R-fMRI) datasets from 539 individuals with ASD and 573 typical controls for the purpose of data sharing in the broader scientific community. This grass-root initiative involved 16 international sites, sharing 20 samples yielding 1112 datasets composed of both MRI data and an extensive array of phenotypic information common across nearly all sites (see below). This unprecedented effort is expected to facilitate discovery science and comparisons across samples. In accordance with HIPAA guidelines and 1000 Functional Connectomes Project / INDI protocols, all datasets are anonymous, with no protected health information included.",
"fairsharing": "FAIRsharing.16v73e",
"homepage": "http://fcon_1000.projects.nitrc.org/indi/abide/",
"information_keywords": [
"Image/Movie",
"Phenotype",
"Bibliography/Documents"
],
"name": "Autism Brain Imaging Data Exchange",
"prefix": "NBDC02013",
"pubmeds": [
"23774715"
],
"status": "Active",
"target_keywords": [
"Health/Disease",
"Organism"
]
},
"nbdc02014": {
"alt_name": "eMERGE",
"description": "eMERGE is a national network organized and funded by the National Human Genome Research Institute (NHGRI) that combines DNA biorepositories with electronic medical record (EMR) systems for large scale, high-throughput genetic research in support of implementing genomic medicine.",
"fairsharing": "FAIRsharing.1jwkjn",
"homepage": "https://emerge.mc.vanderbilt.edu/",
"information_keywords": [
"Phenotype",
"Bibliography/Documents"
],
"name": "Electronic Medical Records and Genomics",
"prefix": "NBDC02014",
"pubmeds": [
"23743551",
"21269473"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc02015": {
"alt_name": "LINCS Data Portal",
"description": "The LINCS Data Portal provides a unified interface for searching LINCS dataset packages and reagents.\nLINCS data are being made openly available as a community resource through a series of data releases, so as to enable scientists to address a broad range of basic research questions and to facilitate the identification of biological targets for new disease therapies. LINCS datasets consist of assay results from cultured and primary human cells treated with bioactive small molecules, ligands such as growth factors and cytokines, or genetic perturbations. Many different assays are used to monitor cell responses, including assays measuring transcript and protein expression; cell phenotype data are captured by biochemical and imaging readouts. Assays are typically carried out on multiple cell types, and at multiple timepoints; perturbagen activity is monitored at multiple doses.",
"fairsharing": "FAIRsharing.fb0r2g",
"homepage": "http://lincsportal.ccs.miami.edu/dcic-portal/",
"information_keywords": [
"Expression",
"Interaction/Pathway",
"Phenotype",
"Method",
"Portal"
],
"maintainer": "CPGR (Centre for Proteomic and Genomic Research)",
"name": "Library of Integrated Network-Based Cellular Signatures Data Portal",
"prefix": "NBDC02015",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle"
]
},
"nbdc02016": {
"alt_name": "DASHR",
"description": "Integrated annotation and sequencing-based expression data for all major classes of human small non-coding RNAs (sncRNAs) for both full sncRNA transcripts and mature sncRNA products derived from these larger RNAs.",
"fairsharing": "FAIRsharing.ztvs34",
"homepage": "http://lisanwanglab.org/DASHR",
"information_keywords": [
"Expression",
"Sequence"
],
"maintainer": "University of Pennsylvania||IBI (Institute for Biomedical Informatics, University of Pennsylvania)",
"name": "Database of small human non-coding RNAs",
"prefix": "NBDC02016",
"pubmeds": [
"26553799"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc02017": {
"alt_name": "Model Archive",
"description": "The Model Archive provides a stable archive for computational macro-molecular models published in the scientific literature. The model archive provides a unique stable accession code (DOI) for each deposited model, which can be directly referenced in the corresponding manuscripts. Model Archive is part of the Protein Model Portal (http://www.proteinmodelportal.org).",
"fairsharing": "FAIRsharing.tpqndj",
"homepage": "http://www.modelarchive.org/",
"information_keywords": [
"3D structure",
"Repository"
],
"maintainer": "Biozentrum, University of Basel||SIB (Swiss Institute of Bioinformatics)",
"name": "Model Archive - theoretical models of macromolecular structures",
"prefix": "NBDC02017",
"pubmeds": [
"19217386",
"23624946"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02018": {
"alt_name": "MFMD",
"description": "A comprehensive database established to offer a web-based access to founder mutation data in Mediterranean population. The database provides an overview about the spectrum of founder mutations found in Mediterranean population to the scientific community. Furthermore, MFMD will help scientists to design more efficient diagnostic tests and provides beneficial information to understand the history and the migration events of the Mediterranean population.",
"fairsharing": "FAIRsharing.1d0vs7",
"homepage": "http://mfmd.pasteur.ma/",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "INSERM (Institut National de la Sante et de la Recherche Medicale)||Pasteur Institute of Morocco",
"name": "Mediterranean Founder Mutation Database",
"prefix": "NBDC02018",
"pubmeds": [
"26173767"
],
"status": "Active",
"target_keywords": [
"Organism",
"Genetic variation",
"Genome/Gene",
"Health/Disease"
]
},
"nbdc02019": {
"alt_name": "MHAS",
"description": "The MHAS study is a series of questionnaires distributed in waves, the fourth of which was fielded in the Fall of 2015. Research goals include, but are not limited to the following: examination of the aging processes and its disease and disability burden in a large representative panel of older Mexicans; evaluation of the effects of individual behaviors, early life circumstances, migration and economic history, community characteristics, and family transfer systems on multiple health outcomes; and comparison of the health dynamics of older Mexicans with comparably aged Mexican-born migrants in the U.S. and second generation Mexican-American using similar data from the U.S. population (for example the biennial Health and Retirement Study HRS) to assess the durability of the migrant health advantage.",
"fairsharing": "FAIRsharing.n8qft8",
"homepage": "http://www.mhasweb.org/",
"information_keywords": [
"Bibliography/Documents"
],
"name": "Mexican Health and Aging Study",
"prefix": "NBDC02019",
"pubmeds": [
"26172238"
],
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease"
]
},
"nbdc02021": {
"alt_name": "NSRR",
"description": "The National Sleep Research Resource (NSRR) offers free web access to large collections of de-identified physiological signals and clinical data elements collected in well-characterized research cohorts and clinical trials. Using the tools provided, the researcher can search across thousands of data elements, identify those data of most relevance for given needs, explore the statistical distributions of each, and download the data as CSV files. Data include demographic, physiological, clinical, and other data types collected by each study.\nPhysiologic signals from overnight polysomnograms (sleep studies) are available by downloading European Data Format (EDF) files. The researcher can load summary measures of standardly scored sleep data. Specific scored annotations can be accessed by downloading XML files and can be viewed offline using the EDF Viewer.",
"fairsharing": "FAIRsharing.crjxwd",
"homepage": "https://sleepdata.org/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Division of Sleep & Circadian Disorders, Brigham and Women's Hospital/Harvard Medical School",
"name": "National Sleep Research Resource",
"prefix": "NBDC02021",
"pubmeds": [
"27070134"
],
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease"
]
},
"nbdc02022": {
"description": "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.",
"fairsharing": "FAIRsharing.mqvqde",
"homepage": "https://www.facebase.org/",
"information_keywords": [
"Interaction/Pathway",
"Expression",
"Phenotype",
"Image/Movie",
"Method",
"Bibliography/Documents"
],
"maintainer": "USC (University of Southern California)",
"name": "FaceBase",
"prefix": "NBDC02022",
"status": "Active",
"target_keywords": [
"Protein",
"Genome/Gene",
"RNA",
"Health/Disease"
]
},
"nbdc02023": {
"alt_name": "HMP",
"description": "The NIH Common Fund Human Microbiome Project (HMP) was established in 2008, with the mission of generating resources that would enable the comprehensive characterization of the human microbiome and analysis of its role in human health and disease. The HMP has characterized the microbial communities found at several different sites on the human body: nasal passages, oral cavity, skin, gastrointestinal tract, and urogenital tract.",
"fairsharing": "FAIRsharing.q04phv",
"homepage": "http://hmpdacc.org/",
"information_keywords": [
"Environment",
"Method",
"Bibliography/Documents"
],
"maintainer": "Baylor College of Medicine||Human Microbiome Project, Broad Institute||JCVI (J. Craig Venter Institute)||DACC (NIH Data Analysis and Coordination Center)||Washington University in St Louis School of Medicine",
"name": "NIH Human Microbiome Project",
"prefix": "NBDC02023",
"pubmeds": [
"22699609",
"22699610"
],
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease"
]
},
"nbdc02024": {
"description": "A free and public archive of animal tracking datasets associated with peer-reviewed publications. The Repository is the long-term archive associated with Movebank (movebank.org), a free, online database created to help animal tracking researchers to manage, share, protect, analyze, and archive their data. Hosted by the Max Planck Institute for Ornithology and the University of Konstanz Library.",
"fairsharing": "FAIRsharing.httzv2",
"homepage": "https://www.datarepository.movebank.org/",
"information_keywords": [
"Bibliography/Documents",
"Repository"
],
"maintainer": "MPIO (Max Planck Institue for Ornithology)||University of Konstanz Library",
"name": "Movebank Data Repository",
"prefix": "NBDC02024",
"pubmeds": [
"26578793"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02025": {
"description": "RegenBase is a knowledge base of SCI biology. RegenBase integrates curated literature-sourced facts and experimental details from publications, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. RegenBase enables researchers to organize and interrogate experimental data generated by spinal cord injury (SCI) research, with the ultimate goal of translating SCI experimental findings in model organisms into human therapies.",
"fairsharing": "FAIRsharing.9nns5e",
"homepage": "http://regenbase.org",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Stanford University Center for Biomedical Informatics Research||University of Miami School of Medicine",
"name": "RegenBase",
"prefix": "NBDC02025",
"pubmeds": [
"27055827"
],
"status": "Active",
"target_keywords": [
"Health/Disease",
"Organism"
]
},
"nbdc02026": {
"description": "SwissLipids is an expert-curated resource that provides a framework for the integration of lipid and lipidomic data with biological knowledge and models. SwissLipids is updated daily.",
"fairsharing": "FAIRsharing.pxr7x2",
"homepage": "http://www.swisslipids.org/#/",
"information_keywords": [
"Chemical structure",
"Interaction/Pathway"
],
"maintainer": "Swiss-Prot group, SIB Swiss Institute of Bioinformatics||Vital-IT group, SIB Swiss Institute of Bioinformatics",
"name": "SwissLipids",
"prefix": "NBDC02026",
"pubmeds": [
"25943471"
],
"status": "Active",
"target_keywords": [
"Protein",
"Lipid"
]
},
"nbdc02027": {
"description": "The dataset was obtained from series of usability tests on a software tool for visualizing continuous health status of a modeled patient. The emphasis of this results are on the hFigures visualization llibrary.\nThe software is a dashboard for visualizing the health status of a modeled virtual patient improving the health condition over a coaching program.\nThe files are in machine-readable format saved as comma separated values.\nThe questionnaires applied were:\nAfter Scenario Questionnaire\nComputer System Usability Questionnaire\nNielsen's Heuristic Evaluation\nThe questionnaires were done using the web application by Gary Perlman available in the url: garyperlman.com/quest/\nthe file laboratory.csv contains the tasks and their time to completion along with the errors occurred.\nThe tasks, software tool and research context is available in the article submitted to BMC Medical Informatics & Decision Making.\nThe experiment included three usability experts and eleven non-expert users.\nThe file asq.csv contains the answers to the three questions of the After Scenario Questionnaire.\nThe file csuq.csv contains the answers to the 19 questions of the Computer System Usability Questionnaire.\nThe file heuristics.csv contains the answers to the 10 questions of the Nielsen's Heuristic Evaluation.\nThis datasets are available under the MIT license.",
"fairsharing": "FAIRsharing.bc3cnk",
"homepage": "http://www.tut.fi/phi/?p=319",
"information_keywords": [
"Bibliography/Documents",
"Repository"
],
"maintainer": "Personal Health Informatics - Tampere University",
"name": "Visualizing Continuous Health Usability Test Results Dataset",
"prefix": "NBDC02027",
"status": "Inactive"
},
"nbdc02028": {
"alt_name": "PMR",
"description": "The Physiome Model Repository (PMR) is the main online repository for the IUPS Physiome Project, providing version and access controlled repositories, called workspaces, for users to store their data. PMR also provides a mechanism to create persistent access to specific revisions of a workspace, termed exposures. Exposure plugins are available for specific types of data (e.g., CellML or FieldML documents) which enable customizable views of the data when browsing the repository via a web browser, or an application accessing the repository's content via web services.",
"fairsharing": "FAIRsharing.bcjrnq",
"homepage": "https://models.physiomeproject.org",
"information_keywords": [
"Bibliography/Documents",
"Repository"
],
"maintainer": "Auckland Bioengineering Institute",
"name": "Physiome Model Repository",
"prefix": "NBDC02028",
"pubmeds": [
"21216774",
"17947072",
"18658182",
"19380315",
"21235804",
"27051515"
],
"status": "Active"
},
"nbdc02029": {
"description": "The FAIRDOMHub is a publicly available resource build using the SEEK software, which enables collaborations within the scientific community. FAIRDOM will establish a support and service network for European Systems Biology. It will serve projects in standardizing, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable. FAIRDOM is an initiative to develop a community, and establish an internationally sustained Data and Model Management service to the European Systems Biology community. FAIRDOM is a joint action of ERA-Net EraSysAPP and European Research Infrastructure ISBE.",
"fairsharing": "FAIRsharing.nnvcr9",
"homepage": "https://fairdomhub.org/",
"information_keywords": [
"Bibliography/Documents",
"Repository"
],
"maintainer": "HITS (Heidelberg Institute for Theoretical Studies)||University of Manchester",
"name": "FAIRDOMHub",
"prefix": "NBDC02029",
"pubmeds": [
"26508761",
"27899646",
"26978244",
"26160520",
"21943917"
],
"status": "Active"
},
"nbdc02030": {
"alt_name": "GnpIS",
"description": "GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, markers, polymorphisms, germplasms, phenotypes and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Institute for Agricultural Research. It is regularly improved and released several times per year.\nGnpIS is accessible through a web portal and allows to browse different types of data either independently through dedicated interfaces or simultaneously using a quick search ('google like search') or advanced search (Biomart, Galaxy, Intermine) tools.",
"fairsharing": "FAIRsharing.dw22y3",
"homepage": "https://urgi.versailles.inra.fr/gnpis",
"information_keywords": [
"Sequence",
"Expression",
"Phenotype",
"Method"
],
"maintainer": "ELIXIR, Wellcome Genome Campus||URGI||transplant",
"name": "Genetic and Genomic Information System",
"prefix": "NBDC02030",
"pubmeds": [
"23959375"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02031": {
"alt_name": "VAD",
"description": "Labome organizes reagent information from high quality suppliers. The reagents include antibodies, siRNA/shRNA, ELISA kits, cDNA clones, proteins/peptides, and biochemicals. To help solve the antibody quality problem, Labome manually curates antibody information from formal publications and develops Validated Antibody Database (VAD).",
"fairsharing": "FAIRsharing.j97pjn",
"homepage": "http://www.labome.com",
"information_keywords": [
"Method",
"Interaction/Pathway"
],
"maintainer": "Labome",
"name": "Validated Antibody Database",
"prefix": "NBDC02031",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Protein",
"RNA",
"Metabolite"
]
},
"nbdc02032": {
"description": "JWS Online is a Systems Biology tool for the construction, modification and simulation of kinetic models and for the storage of curated models.",
"fairsharing": "FAIRsharing.r09jt6",
"homepage": "https://jws2.sysmo-db.org/",
"information_keywords": [
"Method",
"Interaction/Pathway"
],
"maintainer": "Universiteit Stellenbosch",
"name": "JWS Online",
"prefix": "NBDC02032",
"pubmeds": [
"15072998"
],
"status": "Active"
},
"nbdc02033": {
"alt_name": "HPIDB",
"description": "HPIDB 3.0 is a resource that helps annotate, predict and display host-pathogen interactions (HPI). HPI that underpin infectious diseases are critical for developing novel intervention strategies. HPIDB is a host-pathogen protein-protein interaction (PPI) database, which serves as a unified resource for host-pathogen interactions. HPIDB integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource.",
"fairsharing": "FAIRsharing.fk0z49",
"homepage": "https://hpidb.igbb.msstate.edu",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "AgBase, Mississippi State University",
"name": "Host Pathogen Interaction Database",
"prefix": "NBDC02033",
"pubmeds": [
"20946599",
"27374121"
],
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease",
"Organism"
]
},
"nbdc02034": {
"description": "BiGG is a freely compendium of published genome-scale metabolic networks, combined into a single database. NCBI genome annotations are used to map genes, and metabolites are linked to many external databases such as KEGG, PubChem as well as others..",
"fairsharing": "FAIRsharing.va62ke",
"homepage": "http://bigg.ucsd.edu",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "University of California",
"name": "BiGG Models",
"prefix": "NBDC02034",
"pubmeds": [
"26476456",
"20426874"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Metabolite"
]
},
"nbdc02035": {
"alt_name": "GESDB",
"description": "GESDB is a platform for sharing simulation data and discussion of simulation techniques for human genetic studies. The database contains simulation scripts, simulated data, and documentations from published manuscripts. The forum provides a platform for Q&A for the simulated data and exchanging simulation ideas. GESDB aims to promote transparency and efficiency in simulation studies for human genetic studies.",
"fairsharing": "FAIRsharing.rbba3x",
"homepage": "http://gesdb.nhri.org.tw/",
"name": "Genetic Epidemiology Simulation Database",
"prefix": "NBDC02035",
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02036": {
"alt_name": "ORCID",
"description": "ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. ORCID is unique in its ability to reach across disciplines, research sectors and national boundaries. It is a hub that connects researchers and research through the embedding of ORCID identifiers in key workflows, such as research profile maintenance, manuscript submissions, grant applications, and patent applications.\nORCID provides two core functions: (1) a registry to obtain a unique identifier and manage a record of activities, and (2) APIs that support system-to-system communication and authentication. ORCID makes its code available under an open source license, and will post an annual public data file under a CC0 waiver for free download.",
"fairsharing": "FAIRsharing.nx58jg",
"homepage": "http://orcid.org/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "ORCID (Open Research and Contributor ID Initiative)",
"name": "Open Researcher and Contributor ID",
"prefix": "NBDC02036",
"status": "Active"
},
"nbdc02037": {
"alt_name": "EUCTR",
"description": "The EU Clinical Trials Register contains information on interventional clinical trials on medicines conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.",
"fairsharing": "biodbcore-000745",
"homepage": "https://www.clinicaltrialsregister.eu/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "European Medicines Agency",
"name": "EU Clinical Trial Register",
"prefix": "NBDC02037",
"status": "Active",
"target_keywords": [
"Drug",
"Health/Disease"
]
},
"nbdc02038": {
"alt_name": "EudraCT",
"description": "EudraCT (European Union Drug Regulating Authorities Clinical Trials) is the European Clinical Trials Database of all interventional clinical trials of medicinal products commencing in the European Union from 1 May 2004 onwards. The EudraCT database has been established in accordance with Directive 2001/20/EC.",
"fairsharing": "FAIRsharing.w1y0c7",
"homepage": "https://eudract.ema.europa.eu/results-web/index.xhtml",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "European Medicines Agency",
"name": "European Union Drug Regulating Authorities Clinical Trials",
"prefix": "NBDC02038",
"pubmeds": [
"15830257"
],
"status": "Inactive",
"target_keywords": [
"Drug",
"Health/Disease"
]
},
"nbdc02039": {
"alt_name": "DBETH",
"description": "DBETH is the Database of Bacterial Exotoxins for Human. The aim of this database is to assemble information on the toxins responsible for causing bacterial pathogenesis in humans.",
"fairsharing": "FAIRsharing.z1ars2",
"homepage": "http://www.hpppi.iicb.res.in/btox/",
"information_keywords": [
"Sequence",
"3D structure",
"Interaction/Pathway"
],
"maintainer": "Structural Biology and Bioinformatics Division Indian Institute of Chemical Biology",
"name": "Database of Bacterial Exotoxins for Human",
"prefix": "NBDC02039",
"pubmeds": [
"17090593",
"17090593",
"15608208"
],
"status": "Active",
"target_keywords": [
"Protein",
"Organism",
"Health/Disease"
]
},
"nbdc02040": {
"alt_name": "DistiLD",
"description": "The DistiLD database aims to increase the usage of existing genome-wide association studies (GWAS) results by making it easy to query and visualize disease-associated SNPs and genes in their chromosomal context.",
"fairsharing": "FAIRsharing.c1q6jd",
"homepage": "http://distild.jensenlab.org",
"information_keywords": [
"Sequence"
],
"maintainer": "Disease Systems Biology Group, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen",
"name": "DistiLD Database: Diseases and Traits in Linkage Disequilibrium Blocks",
"prefix": "NBDC02040",
"pubmeds": [
"22058129"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc02041": {
"description": "EcoliWiki is a community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.",
"fairsharing": "FAIRsharing.tx95wa",
"homepage": "https://ecoliwiki.org/colipedia/index.php/Welcome_to_EcoliWiki",
"information_keywords": [
"Portal",
"Bibliography/Documents",
"Classification",
"Sequence",
"Ontology/Terminology/Nomenclature",
"Expression",
"Interaction/Pathway",
"Localization",
"Phenotype",
"Method",
"3D structure"
],
"maintainer": "Texas A&M University",
"name": "EcoliWiki",
"prefix": "NBDC02041",
"pubmeds": [
"19576778"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02042": {
"alt_name": "eggNOG",
"description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).",
"fairsharing": "FAIRsharing.j1wj7d",
"homepage": "http://eggnog.embl.de",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"name": "Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups",
"prefix": "NBDC02042",
"pubmeds": [
"19900971",
"17942413"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02043": {
"alt_name": "ELM",
"description": "This computational biology resource mainly focuses on annotation and detection of eukaryotic linear motifs (ELMs) by providing both a repository of annotated motif data and an exploratory tool for motif prediction. ELMs, or short linear motifs (SLiMs), are compact protein interaction sites composed of short stretches of adjacent amino acids.",
"fairsharing": "FAIRsharing.rj3kj5",
"homepage": "http://elm.eu.org",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Classification",
"Interaction/Pathway",
"Sequence"
],
"maintainer": "Universitetet i Bergen",
"name": "Eukaryotic Linear Motifs",
"prefix": "NBDC02043",
"pubmeds": [
"12824381",
"26615199",
"22110040"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc02044": {
"alt_name": "ENCODE",
"description": "Encyclopedia of DNA Elements (ENCODE) has created a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. UCSC coordinated data for the ENCODE Consortium from its inception in 2003 (Pilot phase) to the end of the first 5 year phase of whole-genome data production in 2012. All data produced by ENCODE investigators and the results of ENCODE analysis projects from this period are hosted in the UCSC Genome browser and database.",
"fairsharing": "FAIRsharing.v0hbjs",
"homepage": "http://genome.ucsc.edu/ENCODE/",
"information_keywords": [
"Expression",
"Interaction/Pathway",
"Method",
"Bibliography/Documents"
],
"maintainer": "Genomics Institute, University of California",
"name": "Encyclopedia of DNA Elements at UCSC",
"prefix": "NBDC02044",
"pubmeds": [
"23193274",
"22075998",
"21037257",
"19920125",
"17166863"
],
"status": "Active",
"target_keywords": [
"RNA",
"Genome/Gene",
"Protein",
"Epigenetics",
"Cell/Organelle"
]
},
"nbdc02045": {
"description": "Thermodynamics calculator for biochemical reactions. eQuilibrator is a simple web interface designed to enable easy thermodynamic analysis of biochemical systems. eQuilibrator enables free-text search for biochemical compounds and reactions and provides thermodynamic estimates for both in a variety of conditions.",
"fairsharing": "FAIRsharing.5q1k",
"homepage": "http://equilibrator.weizmann.ac.il",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Mayo Clinic, Scottsdale||MIT (Massachusetts Institute of Technology)",
"name": "eQuilibrator - the biochemical thermodynamics calculator",
"prefix": "NBDC02045",
"pubmeds": [
"18645197",
"16878778",
"860983",
"22645166"
],
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc02046": {
"alt_name": "DRSC-FGR",
"description": "DRSC Functional Genomics Resources (DRSC-FGR) began as the Drosophila RNAi Screening Center (DRSC), founded by Prof. Norbert Perrimon in 2003, and the Transgenic RNAi Project (TRiP), founded by Prof. Perrimon in 2008. DRSC-FGR has been previously known as flyRNAi.org.\nIt has since grown into a functional genomics platform meeting the needs of the Drosophila and broader community.",
"fairsharing": "FAIRsharing.sbnhkq",
"homepage": "http://www.flyrnai.org/",
"information_keywords": [
"Bioresource",
"Method",
"Sequence"
],
"maintainer": "Howard Hughes Medical Institute||Harvard Medical School",
"name": "DRSC Functional Genomics Resources",
"prefix": "NBDC02046",
"pubmeds": [
"21880147",
"21251254",
"20367032",
"19720858",
"19487563",
"18084299",
"17853882",
"16964256",
"16381918"
],
"status": "Active",
"target_keywords": [
"RNA",
"Genome/Gene",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc02047": {
"alt_name": "FunCoup",
"description": "FunCoup is a framework to infer genome-wide functional couplings in 11 model organisms. Functional coupling, or functional association, is an unspecific form of association that encompasses direct physical interaction but also more general types of direct or indirect interaction like regulatory interaction or participation the same process or pathway.",
"fairsharing": "FAIRsharing.qbwrtn",
"homepage": "http://funcoup.sbc.su.se/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Stockholm Bioinformatics Center",
"name": "Networks of Functional Coupling of proteins",
"prefix": "NBDC02047",
"pubmeds": [
"19246318",
"22110034",
"24185702"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"RNA"
]
},
"nbdc02048": {
"alt_name": "FungiDB",
"description": "FungiDB is an integrated genomic and functional genomic database for the kingdom Fungi. The database integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining.",
"fairsharing": "FAIRsharing.xf30yc",
"homepage": "http://fungidb.org",
"information_keywords": [
"Bibliography/Documents",
"Sequence",
"Ontology/Terminology/Nomenclature",
"Classification",
"Expression",
"Phenotype",
"Method",
"Localization",
"Interaction/Pathway"
],
"maintainer": "CBIL (Computational Biology and Informatics Laboratory, University of Pennsylvania)||Center for Tropical & Emerging Global Diseases, University of Georgia||United States Department of Health and Human Services",
"name": "Fungal and Oomycete genomics resource",
"prefix": "NBDC02048",
"pubmeds": [
"22064857",
"24813190",
"27259951"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"DNA",
"Organism"
]
},
"nbdc02049": {
"alt_name": "FunTree",
"description": "A resource for exploring the evolution of protein function through relationships in sequence, structure, phylogeny and function.",
"fairsharing": "FAIRsharing.556qpw",
"homepage": "http://www.funtree.info/FunTree/",
"information_keywords": [
"Phenotype",
"3D structure",
"Localization",
"Classification"
],
"name": "FunTree: A Resource For Exploring The Functional Evolution Of Structurally Defined Enzyme Superfamilies",
"prefix": "NBDC02049",
"pubmeds": [
"26590404",
"22006843"
],
"status": "Active",
"target_keywords": [
"Organism",
"Protein"
]
},
"nbdc02050": {
"description": "The Expression Atlas is a free resource providing information on gene expression patterns under different biological conditions. Gene expression data is re-analysed in-house to detect genes showing interesting baseline and differential expression patterns, allowing a user to ask questions such as \"what are the genes expressed in normal human liver\" and \"what genes are differentially expressed between water-stressed rice plants and controls with normal watering?\". The resource also features a few proteomics data sets provided by collaborators for corroboration between gene- and protein-level expression results.",
"fairsharing": "FAIRsharing.f5zx00",
"homepage": "http://www.ebi.ac.uk/gxa",
"information_keywords": [
"Expression",
"Method"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "Expression Atlas",
"prefix": "NBDC02050",
"pubmeds": [
"19906730",
"24304889",
"26481351",
"29165655"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Organism"
]
},
"nbdc02051": {
"description": "HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using LD information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with chromatin state and protein binding annotation from the Roadmap Epigenomics and ENCODE projects, sequence conservation across mammals, the effect of SNPs on regulatory motifs, and the effect of SNPs on expression from eQTL studies. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.",
"fairsharing": "FAIRsharing.x18jh7",
"homepage": "http://compbio.mit.edu/HaploReg",
"information_keywords": [
"Sequence",
"Expression"
],
"name": "HaploReg",
"prefix": "NBDC02051",
"pubmeds": [
"26657631",
"22064851"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc02052": {
"alt_name": "HIstome",
"description": "HIstome (Human histone database) is a freely available, specialist, electronic database dedicated to display information about human histone variants, sites of their post-translational modifications and about various histone modifying enzymes.",
"fairsharing": "FAIRsharing.g56qnp",
"homepage": "http://www.iiserpune.ac.in/~coee/histome/",
"information_keywords": [
"Bibliography/Documents",
"Sequence",
"Interaction/Pathway"
],
"maintainer": "ACTREC (Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre)",
"name": "Human Histone Database",
"prefix": "NBDC02052",
"pubmeds": [
"22140112"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Protein",
"Health/Disease"
]
},
"nbdc02053": {
"alt_name": "HmtDB",
"description": "HmtDB is an open resource created to support population genetics and mitochondrial disease studies. The database hosts human mitochondrial genome sequences annotated with population and variability data, the latter being estimated through the application of the SiteVar/MitVarProt programs, based on site-specific nucleotide and aminoacid variability calculations. The annotations are manually curated thus adding value to the quality of the information provided to the end-user.",
"fairsharing": "FAIRsharing.m90ne8",
"homepage": "http://www.hmtdb.uniba.it",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Bari",
"name": "Human Mitochondrial Database",
"prefix": "NBDC02053",
"pubmeds": [
"16351753",
"2012"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Cell/Organelle",
"Organism",
"Health/Disease"
]
},
"nbdc02054": {
"description": "Database of interaction Hotspots across the proteome. Hot spots are energetically important residues at protein interfaces and they are not randomly distributed across the interface but rather clustered. These clustered hot spots form hot regions. HotRegion, provides information of these interfaces by using predicted hot spot residues, and structural properties of these interface residues such as pair potentials of interface residues, accessible surface area (ASA) and relative ASA values of interface residues of both monomer and complex forms of proteins. Also, the 3D visualization of the interface and interactions among hot spot residues are provided.",
"fairsharing": "FAIRsharing.m4a6d3",
"homepage": "http://prism.ccbb.ku.edu.tr/hotregion",
"information_keywords": [
"Interaction/Pathway",
"3D structure"
],
"maintainer": "Center for Computational Biology and Bioinformatics and College of Engineering (CCBB), Koc University (KU)",
"name": "HotRegion",
"prefix": "NBDC02054",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02055": {
"alt_name": "ICEberg",
"description": "A web-based resource for integrative and conjugative elements (ICEs) found in bacteria. It collates available data from experimental and bioinformatics analyses, and literature, about known and putative ICEs in bacteria as a PostgreSQL-based database called ICEberg. This database contains detailed information on all archived ICEs and the genes carried by each entity, including unique identifiers, species details and hyperlink-paths to other public databases, like NCBI, UniprotKB and KEGG.",
"fairsharing": "FAIRsharing.dz1xxr",
"homepage": "http://db-mml.sjtu.edu.cn/ICEberg/",
"information_keywords": [
"Sequence"
],
"maintainer": "State Key Laboratory of Microbial Metabolism, Shanghai Jiaotong University",
"name": "Integrative and Conjugative Elements in Bacteria",
"prefix": "NBDC02055",
"pubmeds": [
"22009673"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02056": {
"description": "Evolution of protein-protein Interfaces InterEvol is a resource for researchers to investigate the structural interaction of protein molecules and sequences using a variety of tools and resources.",
"fairsharing": "FAIRsharing.smqf7y",
"homepage": "http://biodev.cea.fr/interevol/",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "CNRS (The National Centre for Scientific Research)",
"name": "InterEvol database : Diving into the structure and evolution of protein complex interfaces",
"prefix": "NBDC02056",
"pubmeds": [
"22053089"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02057": {
"description": "The LegumeIP 2.0 database hosts large-scale genomics and transcriptomics data and provides integrative bioinformatics tools for the study of gene function and evolution in legumes.",
"fairsharing": "FAIRsharing.44yp73",
"homepage": "http://plantgrn.noble.org/LegumeIP/",
"information_keywords": [
"Sequence",
"Ontology/Terminology/Nomenclature",
"Expression"
],
"maintainer": "Zhao Bioinformatics Laboratory",
"name": "LegumeIP",
"prefix": "NBDC02057",
"pubmeds": [
"22110036",
"26578557"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02058": {
"alt_name": "mapperdb",
"description": "This resource provides information primarily on the upstream non-coding sequence data of genes in 3 genomes which gives insight into the transcription factors binding sites (TFBSs). For each transcript, the region scanned extends from 10,000bp upstream of the transcript start to 50bp downstream of the coding sequence start. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons.\nInformation displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs.",
"fairsharing": "FAIRsharing.1ex4pm",
"homepage": "http://genome.ufl.edu/mapperdb",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "University of Florida",
"name": "MAPPER-2",
"prefix": "NBDC02058",
"pubmeds": [
"15799782",
"15608292"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc02059": {
"description": "The MetaCrop resource contains information on the major metabolic pathways mainly in crops of agricultural and economic importance. The database includes manually curated information on reactions and the kinetic data associated with these reactions. Ontology terms are used and publication identification available to ease mining the data.",
"fairsharing": "FAIRsharing.wdbd3r",
"homepage": "http://metacrop.ipk-gatersleben.de",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Interaction/Pathway"
],
"maintainer": "IPK (Leibniz Institute of Plant Genetics and Crop Plant Research)",
"name": "MetaCrop 2.0",
"prefix": "NBDC02059",
"pubmeds": [
"17059592",
"17933764",
"20375443",
"22086948"
],
"status": "Active",
"target_keywords": [
"Metabolite",
"Organism"
]
},
"nbdc02060": {
"alt_name": "MimoDB",
"description": "Mimotope database, active site-mimicking peptides selected from phage-display libraries. It is a database which stores information on peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues, organs, and even entire organisms through phage display technology. Besides the peptide sequences, other information such as the corresponding target, template, library, and structures are also stored. All entries are manually extracted from published peer review articles and other public data sources such as Uniprot, GenBank and PDBSum.",
"fairsharing": "FAIRsharing.bv0zjz",
"homepage": "http://immunet.cn/mimodb",
"information_keywords": [
"Interaction/Pathway",
"Classification"
],
"maintainer": "HLAB (Huang's Lab)",
"name": "Mimotope Database",
"prefix": "NBDC02060",
"pubmeds": [
"21079566",
"22053087",
"26503249"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc02061": {
"alt_name": "MINAS",
"description": "MINAS contains the exact geometric information on the first and second-shell coordinating ligands of every metal ion present in nucleic acid structures that are deposited in the PDB and NDB. Containing also the sequence information of the binding pocket-proximal nucleotides, this database allows for a detailed search of all combinations of potential ligands and of coordination environments of metal ions. MINAS is therefore a perfect new tool to classify metal ion binding pockets in nucleic acids by statistics and to draw general conclusions about the different coordination properties of these ions.",
"fairsharing": "FAIRsharing.wqtfkv",
"homepage": "http://www.minas.uzh.ch",
"maintainer": "UZH Chemistry (Department of Chemistry, University of Zurich)",
"name": "MINAS - A Database of Metal Ions in Nucleic AcidS",
"prefix": "NBDC02061",
"pubmeds": [
"20047851",
"10"
],
"status": "Active",
"target_keywords": [
"DNA"
]
},
"nbdc02062": {
"alt_name": "MINT",
"description": "MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. As of September 2013, This resource uses the IntAct database framework to help reduce the effort of scientists and improve on IT development. MINT is an ELIXIR Core Resource.",
"fairsharing": "FAIRsharing.2bdvmk",
"homepage": "http://mint.bio.uniroma2.it",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Department of Biology, University of Rome Tor Vergata",
"name": "Molecular INTeraction database",
"prefix": "NBDC02062",
"pubmeds": [
"11911893",
"17135203",
"19897547",
"22096227"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02063": {
"description": "This is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins. The nearly completed sets of MIPs have been identified from the completed genome sequence of organisms available at NCBI. The structural models of MIP proteins were created by defined protocol. The database aims to provide key information of MIPs in particular based on sequence as well as structures. This will further help to decipher the function of uncharacterized MIPs.",
"fairsharing": "FAIRsharing.yd76dk",
"homepage": "http://bioinfo.iitk.ac.in/MIPModDB/",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "IIT Kanpur (Indian Institute of Technology Kanpur)",
"name": "MIPModDB: A Central Resource for the Superfamily of Major Intrinsic Proteins",
"prefix": "NBDC02063",
"pubmeds": [
"19930558",
"17445256"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02064": {
"description": "mirEX2 is a comprehensive platform for comparative analysis of primary microRNA expression data. RTβqPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface.",
"fairsharing": "FAIRsharing.q3b39v",
"homepage": "http://www.comgen.pl/mirex/",
"information_keywords": [
"Expression",
"Sequence",
"Localization"
],
"maintainer": "Wellcome Sanger Institute",
"name": "mirEX",
"prefix": "NBDC02064",
"pubmeds": [
"22013167",
"26141515"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc02065": {
"alt_name": "Identifiers.org",
"description": "The core of the Registry is a catalogue of data collections (corresponding to e.g. controlled vocabularies, databases), their URIs and the corresponding physical URLs (or resources). These resources are monitored daily to ensure data accessibility and the validity of the resolution mechanism.",
"fairsharing": "FAIRsharing.n14rc8",
"homepage": "https://identifiers.org/",
"information_keywords": [
"Bibliography/Documents",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "ELIXIR, Wellcome Genome Campus||SIB (Swiss Institute of Bioinformatics)",
"name": "Identifiers.org Registry",
"prefix": "NBDC02065",
"pubmeds": [
"18078503",
"22140103"
],
"status": "Active"
},
"nbdc02066": {
"description": "MitoMiner is an integrated data warehouse of mammalian localisation evidence, phenotypes and diseases. This data has been integrated to allow the creation of sophisticated data mining queries spanning many different sources. It is primarily concerned with data for mammals, zebrafish and yeasts.",
"fairsharing": "FAIRsharing.wx1yak",
"homepage": "http://mitominer.mrc-mbu.cam.ac.uk",
"information_keywords": [
"Phenotype",
"Localization",
"Sequence"
],
"maintainer": "MBU (MRC Mitochondrial Biology Unit, Cambridge, UK)",
"name": "MitoMiner",
"prefix": "NBDC02066",
"pubmeds": [
"19208617",
"26432830"
],
"status": "Inactive",
"target_keywords": [
"Cell/Organelle",
"Protein",
"Organism",
"Health/Disease"
]
},
"nbdc02067": {
"description": "modMine is an integrated web resource of data and tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.",
"fairsharing": "FAIRsharing.ekzmjp",
"homepage": "http://intermine.modencode.org/",
"information_keywords": [
"Interaction/Pathway",
"Bibliography/Documents",
"Sequence",
"Ontology/Terminology/Nomenclature",
"Classification",
"Phenotype",
"Method"
],
"maintainer": "LBNL (Lawrence Berkeley National Laboratory)||InterMine, System Biology Centre",
"name": "modMine",
"prefix": "NBDC02067",
"pubmeds": [
"19536255",
"21177976",
"21177974",
"22080565"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Genome/Gene",
"Genetic variation",
"RNA"
]
},
"nbdc02068": {
"alt_name": "MPD",
"description": "Characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies. Data sets are voluntarily contributed by researchers or retrieved by us from public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys.",
"fairsharing": "FAIRsharing.h6enr1",
"homepage": "http://phenome.jax.org",
"information_keywords": [
"Sequence",
"Phenotype",
"Expression"
],
"maintainer": "The Jackson Laboratory, Bar Harbor",
"name": "Mouse Phenome Database",
"prefix": "NBDC02068",
"pubmeds": [
"18987003",
"15619963",
"15130929",
"10967127"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Organism"
]
},
"nbdc02069": {
"alt_name": "NAPP",
"description": "NAPP (Nucleic Acids Phylogenetic Profile) enables users to retrieve RNA-rich clusters from any genome in a list of 1000+ sequenced bacterial genomes. RNA-rich clusters can be viewed separately or, alternatively, all tiles from RNA-rich clusters can be contiged into larger elements and retrieved at once as a CSV or GFF file for use in a genome browser or comparison with other predictions/RNA-seq experiments.",
"fairsharing": "FAIRsharing.vr52p3",
"homepage": "http://napp.u-psud.fr",
"information_keywords": [
"Classification",
"Sequence"
],
"maintainer": "Gautheret Lab, Institute for Integrative Biology of the Cell",
"name": "Nucleic Acid Phylogenetic Profile",
"prefix": "NBDC02069",
"pubmeds": [
"19237465",
"21984475"
],
"status": "Active",
"target_keywords": [
"RNA"
]
},
"nbdc02071": {
"description": "A comprehensive repository for omics data from the red spotted newt Notophthalmus viridescens from high throughput experiments. Newt-Omics aims to provide a comprehensive platform of expressed genes during tissue regeneration, including extensive annotations, expression data and experimentally verified peptide sequences with yet no homology to other publically available gene sequences. The goal is to obtain a detailed understanding of the molecular processes underlying tissue regeneration in the newt,that may lead to the development of approaches, efficiently stimulating regenerative pathways in mammalians.",
"fairsharing": "FAIRsharing.k6a8e5",
"homepage": "http://newt-omics.mpi-bn.mpg.de",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Bioinformatics and ECCPS bioinformatics service group, Max Planck Institute for Heart and Lung Research",
"name": "Newt-omics",
"prefix": "NBDC02071",
"pubmeds": [
"20047682",
"20139370",
"23425577"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02072": {
"description": "GENI-ACT is a resource that allows the research community to collaboratively annotate bacterial genomes. Changes can be suggested to existing genomes and these alterations can be ported back to NCBI Genbank. GENI-ACT also has modules which can be used for educational purposes.",
"fairsharing": "FAIRsharing.mhqkc7",
"homepage": "http://geni-act.org/",
"maintainer": "MGAN (Microbial Genome Annotation Network)",
"name": "GENI-ACT",
"prefix": "NBDC02072",
"pubmeds": [
"22116063",
"17090585",
"20711478"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02073": {
"alt_name": "PhenoM",
"description": "PhenoM (Phenomics of yeast Mutants) stores, retrieves, visualises and data mines the quantitative single-cell measurements extracted from micrographs of temperature-sensitive mutant cells. PhenoM allows users to rapidly search and retrieve raw images and their quantified morphological data for genes of interest. The database also provides several data-mining tools, including a PhenoBlast module for phenotypic comparison between mutant strains and a Gene Ontology module for functional enrichment analysis of gene sets showing similar morphological alterations.",
"fairsharing": "FAIRsharing.bp5hpt",
"homepage": "http://phenom.ccbr.utoronto.ca/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Image/Movie",
"Sequence",
"Phenotype",
"Method"
],
"maintainer": "Banting and Best Department of Medical Research, The Donnelly Centre, University of Toronto",
"name": "Phenomics of yeast Mutants",
"prefix": "NBDC02073",
"pubmeds": [
"21441928",
"22009677"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02074": {
"alt_name": "PINA",
"description": "The Protein Interaction Network Analysis (PINA)- is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms.",
"fairsharing": "FAIRsharing.7q4gsz",
"homepage": "http://omics.bjcancer.org/pina/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Interaction/Pathway"
],
"name": "Protein Interaction Network Analysis",
"prefix": "NBDC02074",
"pubmeds": [
"19079255",
"22067443"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc02075": {
"description": "Arabidopsis metabolomics database which provides researchers with resources to investigate the function of genes and metabolites.",
"fairsharing": "FAIRsharing.jskz3k",
"homepage": "http://www.plantmetabolomics.org",
"information_keywords": [
"Image/Movie",
"Chemical structure"
],
"maintainer": "Bioinformatics and Computational Biology Program, Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology (BBMB), Iowa State University",
"name": "Plantmetabolomics.org",
"prefix": "NBDC02075",
"pubmeds": [
"20147492"
],
"status": "Inactive"
},
"nbdc02076": {
"alt_name": "PlantNATsDB",
"description": "Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. PlantNATsDB (Plant Natural Antisense Transcripts DataBase) is a platform for annotating and discovering NATs by integrating various data sources. PlantNATsDB also provides an integrative, interactive and information-rich web graphical interface to display multidimensional data, and facilitate plant research community and the discovery of functional NATs.",
"fairsharing": "FAIRsharing.rn1pxg",
"homepage": "http://bis.zju.edu.cn/pnatdb/",
"information_keywords": [
"Expression",
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Ming Chen's Lab, Zhejiang University",
"name": "Plant Natural Antisense Transcripts Database",
"prefix": "NBDC02076",
"pubmeds": [
"22058132"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Cell/Organelle",
"Organism"
]
},
"nbdc02077": {
"description": "PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data.",
"fairsharing": "FAIRsharing.8pjgwx",
"homepage": "http://www.plexdb.org/",
"information_keywords": [
"Expression"
],
"maintainer": "USDA-ARS (Agricultural Research Service of the US Department of Agriculture)||Iowa State University",
"name": "PLEXdb",
"prefix": "NBDC02077",
"pubmeds": [
"18287702",
"22084198"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"DNA"
]
},
"nbdc02078": {
"alt_name": "Pocketome",
"description": "The Pocketome is an encyclopedia of conformational ensembles of druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry describes a site on a protein surface that is involved in transient interactions with small molecules and peptides.",
"fairsharing": "FAIRsharing.tc6df8",
"homepage": "http://pocketome.org",
"information_keywords": [
"Interaction/Pathway",
"Sequence",
"3D structure"
],
"maintainer": "The Abagyan Lab UC San Diego||UCSD (University of California San Diego)",
"name": "Pocketome: an encyclopedia of small-molecule binding sites in 4D",
"prefix": "NBDC02078",
"pubmeds": [
"19727619",
"22080553"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Drug"
]
},
"nbdc02079": {
"description": "Polbase is an open and searchable database providing information from published and unpublished sources on the biochemical, genetic, and structural information of DNA polymerases.",
"fairsharing": "FAIRsharing.s9ztmd",
"homepage": "http://polbase.neb.com",
"information_keywords": [
"Sequence",
"3D structure",
"Repository"
],
"maintainer": "New England Biolabs",
"name": "Polbase",
"prefix": "NBDC02079",
"pubmeds": [
"21993301"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Protein"
]
},
"nbdc02081": {
"alt_name": "ProtChemSI",
"description": "Protein-Chemical Structural Interactions provides information on the 3-dimensional chemical structures of protein interactions with low molecular weight.",
"fairsharing": "FAIRsharing.6zk9ea",
"homepage": "http://pcidb.russelllab.org/",
"information_keywords": [
"3D structure",
"Image/Movie",
"Interaction/Pathway"
],
"maintainer": "Cell Networks, University of Heidelberg",
"name": "Protein-Chemical Structural Interactions",
"prefix": "NBDC02081",
"pubmeds": [
"21573205"
],
"status": "Active",
"target_keywords": [
"Chemical compound",
"Protein"
]
},
"nbdc02082": {
"description": "This resource is a hierarchical clustering of UniProt protein sequences into hierarchical trees. This resource allows for the study of sub-family and super-family of a protein, using UniRef50 clusters.",
"fairsharing": "FAIRsharing.wv5q9d",
"homepage": "http://www.protonet.cs.huji.ac.il/",
"information_keywords": [
"Sequence",
"Classification",
"3D structure"
],
"maintainer": "School of Computer Science and Engineering, The Hebrew University of Jerusalem",
"name": "ProtoNet",
"prefix": "NBDC02082",
"pubmeds": [
"12520020",
"15608180",
"18629007",
"18689824",
"18586742",
"16672244",
"15596019",
"15382232",
"22121228",
"23563419"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc02083": {
"description": "Rhea is a comprehensive and non-redundant resource of expert-curated biochemical reactions designed for the functional annotation of enzymes and the description of metabolic networks. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions, using entities from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules.",
"fairsharing": "FAIRsharing.pn1sr5",
"homepage": "http://www.rhea-db.org",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "Rhea",
"prefix": "NBDC02083",
"pubmeds": [
"25332395",
"22135291",
"27789701"
],
"status": "Active",
"target_keywords": [
"Protein",
"Metabolite"
]
},
"nbdc02084": {
"alt_name": "RNA CoSSMos",
"description": "RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) database allows the systematic searching of all catalogued three-dimensional nucleic acid PDB structures that contain secondary structure motifs such as mismatches, (a)symmetric internal loops, hairpin loops, and bulge loops.",
"fairsharing": "FAIRsharing.vebj4e",
"homepage": "http://cossmos.slu.edu",
"information_keywords": [
"Sequence",
"3D structure"
],
"name": "RNA Characterization of Secondary Structure Motifs",
"prefix": "NBDC02084",
"pubmeds": [
"22127861"
],
"status": "Active",
"target_keywords": [
"Protein",
"RNA"
]
},
"nbdc02085": {
"description": "ModelDB provides an accessible location for storing and efficiently retrieving computational neuroscience models. ModelDB is tightly coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models.",
"fairsharing": "FAIRsharing.5rb3fk",
"homepage": "http://senselab.med.yale.edu/modeldb",
"information_keywords": [
"Method",
"Bibliography/Documents"
],
"maintainer": "Yale University||Yale University School of Medicine",
"name": "ModelDB",
"prefix": "NBDC02085",
"pubmeds": [
"15218350",
"8930855",
"15055399"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc02086": {
"alt_name": "SCRIPDB",
"description": "SCRIPDB is a chemical structure database designed to make patent metadata accessible. We index public-domain chemical information contained in U.S. patents, and provide the full patent text, reactions, and relationships described within any individual patent, as well as the original CDX, MOL, and TIFF files.",
"fairsharing": "FAIRsharing.sncr74",
"homepage": "http://dcv.uhnres.utoronto.ca/SCRIPDB",
"information_keywords": [
"3D structure",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "Jurisica Lab, Ontario Cancer Institute",
"name": "SCRIPDB: A Portal for Easy Access to Syntheses, Chemicals, and Reactions In Patents",
"prefix": "NBDC02086",
"pubmeds": [
"22067445"
],
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc02087": {
"description": "SNPeffect is a database for phenotyping human single nucleotide polymorphisms (SNPs). SNPeffect primarily focuses on the molecular characterization and annotation of disease and polymorphism variants in the human proteome. Further, SNPeffect holds per-variant annotations on functional sites, structural features and post-translational modification.",
"fairsharing": "FAIRsharing.qbt1gh",
"homepage": "http://snpeffect.switchlab.org",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Phenotype",
"3D structure"
],
"maintainer": "Switch Laboratory",
"name": "SNPeffect",
"prefix": "NBDC02087",
"pubmeds": [
"15608254",
"16809394",
"18086700",
"22075996"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Genetic variation",
"Health/Disease"
]
},
"nbdc02088": {
"alt_name": "STAP",
"description": "The STAP database contains refined versions of the NMR structures deposited in PDB. These refinements have been performed using statistical torsion angle potential and structurally- or experimentally- derived distance potential. The refined structures have a significantly improved structural quality compared to their initial NMR structure.",
"fairsharing": "FAIRsharing.ja9cdq",
"homepage": "http://psb.kobic.re.kr/stap/refinement/",
"information_keywords": [
"3D structure"
],
"maintainer": "KOBIC(Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology)",
"name": "Statistical Torsional Angles Potentials of NMR Refinement Database",
"prefix": "NBDC02088",
"pubmeds": [
"22102572",
"23408564",
"25279564",
"26504145"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc02089": {
"alt_name": "STITCH",
"description": "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.",
"fairsharing": "FAIRsharing.zhwa8x",
"homepage": "http://stitch.embl.de",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "BIOTEC (The Biotechnology Center, Technische Universitat Dresden)||EMBO (European Molecular Biology Organization)||University of Copenhagen",
"name": "Search Tool for Interactions of Chemicals",
"prefix": "NBDC02089",
"pubmeds": [
"18084021",
"19897548",
"24293645",
"22075997"
],
"status": "Active",
"target_keywords": [
"Protein",
"Chemical compound"
]
},
"nbdc02090": {
"description": "Zfishbook is a real-time database of transposon-labeled mutants in zebrafish. This resource provides services for any size of GBT mutagenesis projects on zebrafish to encourage collaboration in the research community.",
"fairsharing": "FAIRsharing.ne6jza",
"homepage": "http://www.zfishbook.org",
"information_keywords": [
"Bioresource",
"Expression",
"Image/Movie"
],
"maintainer": "Mayo Clinic",
"name": "zfishbook",
"prefix": "NBDC02090",
"pubmeds": [
"21552255",
"20528262",
"19858493",
"16859902",
"22067444"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02092": {
"description": "BacMap is a picture atlas of annotated bacterial genomes. It is an interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes.",
"fairsharing": "FAIRsharing.z6rbe3",
"homepage": "http://bacmap.wishartlab.com",
"information_keywords": [
"Sequence",
"Image/Movie",
"Interaction/Pathway",
"Bibliography/Documents",
"Phenotype"
],
"maintainer": "Wishart Lab, University of Alberta",
"name": "BacMap",
"prefix": "NBDC02092",
"pubmeds": [
"15608206",
"22135301"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Organism",
"Health/Disease"
]
},
"nbdc02093": {
"alt_name": "ccPDB",
"description": "ccPDB (Compilation and Creation of datasets from PDB) is a collection of commonly used data sets for structural or functional annotation of proteins. There are numerous datasets from the literature and the Protein Data Bank (PDB), which were used for developing methods to annotate proteins at the sequence (or residue) level. A tool is available for creating a wide range of customized data sets from PDB.",
"fairsharing": "FAIRsharing.3vfc16",
"homepage": "http://crdd.osdd.net/raghava/ccpdb/",
"information_keywords": [
"Method",
"Sequence",
"3D structure"
],
"maintainer": "Institute for Microbial Technology",
"name": "Compilation and Creation of datasets from PDB",
"prefix": "NBDC02093",
"pubmeds": [
"22139939"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02094": {
"description": "Detection of functional divergence in human protein families. Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family classification follows (largely) the classification suggested by HUGO Gene Nomenclature Committee. Sets of orthologous protein sequences were generated by mutual-best-hit strategy using full vertebrate genomes available in Ensembl. The scores, described on documentation page, are assigned to each individual residue in a protein, and presented in the form of a table (html or downloadable xls formats) and mapped, when appropriate, onto the related structure (Jmol, Pymol, Chimera).",
"fairsharing": "FAIRsharing.aqb4ne",
"homepage": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Evolution of Protein Structure and Function Group, Biomolecular Modelling and Design Division, Bioinformatics Institute",
"name": "CUBE-DB",
"prefix": "NBDC02094",
"pubmeds": [
"21931701",
"22139934"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02096": {
"description": "GWASdb comprises of collections of traits/diseases associated SNP (TASs) from current GWAS and their comprehensive functional annotations, as well as disease classifications",
"fairsharing": "FAIRsharing.dvwz21",
"homepage": "http://jjwanglab.org/gwasdb",
"information_keywords": [
"Phenotype",
"Classification"
],
"maintainer": "University of Hong Kong",
"name": "GWASdb",
"prefix": "NBDC02096",
"pubmeds": [
"22139925",
"22801476"
],
"status": "Inactive",
"target_keywords": [
"Genetic variation",
"Health/Disease"
]
},
"nbdc02097": {
"alt_name": "IPAVS",
"description": "iPAVS provides a collection of highly-structured manually curated human pathway data, it also integrates biological pathway information from several public databases and provides several tools to manipulate, filter, browse, search, analyze, visualize and compare the integrated pathway resources.",
"fairsharing": "FAIRsharing.jhfs8q",
"homepage": "http://ipavs.cidms.org",
"information_keywords": [
"Method",
"Interaction/Pathway"
],
"maintainer": "Systems Biology Laboratory of Gwangju Institute of Science and Technology, Department of Life Sciences",
"name": "Integrated Pathway Analysis and Visualization System",
"prefix": "NBDC02097",
"pubmeds": [
"21071716",
"21423387",
"18261742"
],
"status": "Inactive",
"target_keywords": [
"Metabolite",
"Health/Disease"
]
},
"nbdc02098": {
"description": "This resource details DNA methylation profiles in human and mouse brain. This database includes genome-wide DNA methylation profiles for human and mouse brains. The DNA methylation profiles were generated by Methylation Mapping Analysis by Paired-end Sequencing (Methyl-MAPS) method and analyzed by Methyl-Analyzer software package. The methylation profiles cover over 80% CpG dinucleotides in human and mouse brains in single-CpG resolution. The integrated genome browser (modified from UCSC Genome Browser allows users to browse DNA methylation profiles in specific genomic loci, to search specific methylation patterns, and to compare methylation patterns between individual samples.",
"fairsharing": "FAIRsharing.yxrs8t",
"homepage": "http://habanero.mssm.edu/methylomedb/index.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Columbia University",
"name": "MethylomeDB",
"prefix": "NBDC02098",
"pubmeds": [
"22140101",
"21216877"
],
"status": "Inactive",
"target_keywords": [
"Epigenetics",
"DNA",
"Organism"
]
},
"nbdc02099": {
"description": "MitoZoa is a specialized database collecting complete and nearly-complete (longer than 7 kb) mtDNA entries of metazoan species, excluding Placozoa. MitoZoa contains curated entries, whose gene annotation has been significantly improved using a semi-automatic reannotation pipeline and by manual curation of mitogenomics experts.\nMitoZoa has been specifically designed to address comparative analyses of mitochondrial genomic features in a given metazoan group or in species belonging to the same genus (congeneric species). MitoZoa focuses on mitochondrial gene order, non-coding regions, gene content, and gene sequences.",
"fairsharing": "FAIRsharing.26pqv5",
"homepage": "http://srv00.recas.ba.infn.it/mitozoa/",
"information_keywords": [
"Sequence",
"Taxonomy",
"Bibliography/Documents"
],
"name": "MitoZoa",
"prefix": "NBDC02099",
"pubmeds": [
"20080208"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle",
"RNA"
]
},
"nbdc02100": {
"description": "Nematode.net is the home page of the parasitic nematode EST project at The Genome Institute at Washington University in St. Louis. The site was established in 2000 as a component of the NIH-NIAID grant \"A Genomic Approach to Parasites from the Phylum Nematoda\". While Nematode.net started as a project site, over the years it became a community resource dedicated to the study of parasitic nematodes.",
"fairsharing": "FAIRsharing.dyfcen",
"homepage": "http://nematode.net",
"information_keywords": [
"Bibliography/Documents",
"Sequence",
"Ontology/Terminology/Nomenclature",
"Expression",
"Interaction/Pathway"
],
"maintainer": "McDonnell Genome Institute at Washington University School of Medicine||Genome Technology Access Center, Department of Genetics, Washington University School of Medicine",
"name": "Nematode.net",
"prefix": "NBDC02100",
"pubmeds": [
"14681448",
"18940860",
"21760913",
"18983679"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc02101": {
"alt_name": "SitEx",
"description": "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.",
"fairsharing": "FAIRsharing.5mr9c5",
"homepage": "http://www-bionet.sscc.ru/sitex/",
"information_keywords": [
"Sequence",
"Classification",
"3D structure"
],
"maintainer": "The Federal Research Center Institute of Cytology and Genetics Lab||Novosibirsk State University",
"name": "SitEx database of eukaryotic protein functional sites",
"prefix": "NBDC02101",
"pubmeds": [
"22139920"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc02102": {
"description": "DIANA-TarBase was initially released in 2006 and it was the first database aiming to catalogue published experimentally validated miRNA:gene interactions. DIANA-TarBase (v7.0), provides hundreds of thousands of high quality manually curated experimentally validated miRNA:gene interactions, enhanced with detailed meta-data.",
"fairsharing": "FAIRsharing.a0k4cd",
"homepage": "http://www.microrna.gr/tarbase",
"information_keywords": [
"Bibliography/Documents",
"Method",
"Interaction/Pathway"
],
"maintainer": "IBI (Institute for Biomedical Informatics, University of Pennsylvania)||Diana Lab Group||BSRC (Biomedical Sciences Research Center Alexander Fleming)",
"name": "TarBase",
"prefix": "NBDC02102",
"pubmeds": [
"18957447",
"16373484",
"25416803"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc02103": {
"description": "VIRsiRNAdb contains information on experimentally validated Viral siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region.",
"fairsharing": "FAIRsharing.h4etg",
"homepage": "http://crdd.osdd.net/servers/virsirnadb",
"information_keywords": [
"Sequence",
"Method",
"Interaction/Pathway"
],
"maintainer": "Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR)",
"name": "VIRsiRNAdb",
"prefix": "NBDC02103",
"pubmeds": [
"22139916"
],
"status": "Active",
"target_keywords": [
"RNA",
"Genome/Gene"
]
},
"nbdc02104": {
"description": "BRCA Share is a novel gene datashare initiative that provides scientists and commercial laboratory organizations around the world with open access to BRCA Share (formerly UMD-BRCA1) contains BRCA1 and BRCA2 genetic data. The program's goal is to accelerate research on BRCA gene mutations, particularly variants of uncertain significance, to improve the ability of clinical laboratory diagnostics to predict which individuals are at risk of developing these cancers.",
"fairsharing": "FAIRsharing.w8wbyj",
"homepage": "http://www.umd.be/BRCA1/",
"maintainer": "UMD (Universal Mutations Database)",
"name": "BRCA Share",
"prefix": "NBDC02104",
"pubmeds": [
"19339519",
"10612827",
"16086365",
"22144684",
"19370756"
],
"status": "Inactive",
"target_keywords": [
"Health/Disease",
"Genome/Gene",
"Genetic variation",
"ε₯εΊ·/ηΎζ£"
]
},
"nbdc02105": {
"alt_name": "HFV Database",
"description": "The Ebola and Hemorrhagic Fever Virus Database stems from the Hemorrhagic Fever Viruses (HFV) Database Project founded by Dr. Carla Kuiken in 2009 at the Los Alamos National Laboratory (LANL). The HFV Database was modeled on the Los Alamos HIV Database, led by Dr. Bette Korber, and translated much of its tools, infrastructure and philosophy from HIV to HFV.",
"fairsharing": "FAIRsharing.dd4j8j",
"homepage": "http://hfv.lanl.gov/content/index",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Theoretical Biology and Biophysics, T-10, Los Alamos National Laboratory",
"name": "Ebola and Hemorrhagic Fever Virus Database",
"prefix": "NBDC02105",
"pubmeds": [
"22064861"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Health/Disease"
]
},
"nbdc02106": {
"alt_name": "hiPathDB",
"description": "Human Integrated Pathway Database (hiPathDB) provides two different types of integration. The pathway-level integration is a simple collection of individual pathways as described in the original database. The entity-level integration creates a super pathway that merged all pathways by unifying redundant components.",
"fairsharing": "FAIRsharing.tber4e",
"homepage": "http://hipathdb.kobic.re.kr",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "KOBIC(Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology)",
"name": "Human Integrated Pathway Database",
"prefix": "NBDC02106",
"pubmeds": [
"22123737"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc02107": {
"description": "neXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data.",
"fairsharing": "FAIRsharing.62evqh",
"homepage": "https://www.nextprot.org",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "CALIPHO (Computer and Laboratory Investigation of Proteins of Human Origin Group, Swiss Institute of Bioinformatics)||SIB (Swiss Institute of Bioinformatics)",
"name": "neXtProt",
"prefix": "NBDC02107",
"pubmeds": [
"22139911",
"25593349",
"23205526",
"27899619"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Protein",
"Cell/Organelle",
"Genome/Gene",
"Health/Disease"
]
},
"nbdc02108": {
"description": "PASS2 contains alignments of structural motifs of protein superfamilies. PASS2 is an automatic version of the original superfamily alignment database, CAMPASS (CAMbridge database of Protein Alignments organised as Structural Superfamilies). PASS2 contains alignments of protein structures at the superfamily level and is in direct correspondence with SCOPe 2.04 release.",
"fairsharing": "FAIRsharing.htzwqf",
"homepage": "http://caps.ncbs.res.in/pass2/",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "Department of Biochemistry, University of Cambridge||NCBS (National Center for Biological Sciences)||Department of Crystallography, Birkbeck College, University of London",
"name": "PASS2",
"prefix": "NBDC02108",
"pubmeds": [
"2181150",
"10089493",
"9730927",
"11752316",
"15059245",
"9753697"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02109": {
"alt_name": "PrimerBank",
"description": "PrimerBank is a public resource for PCR primers. These primers are designed for gene expression detection or quantification (real-time PCR). PrimerBank contains over 306,800 primers covering most known human and mouse genes. There are several ways to search for primers: GenBank Accession, NCBI protein accession, NCBI Gene ID, Gene Symbol, PrimerBank ID or Keyword (gene description) or you can blast your gene sequence against the primerbank Sequence DB.",
"fairsharing": "FAIRsharing.8bwhme",
"homepage": "http://pga.mgh.harvard.edu/primerbank/",
"information_keywords": [
"Sequence"
],
"maintainer": "Center for Computational and Integrative Biology",
"name": "PCR Primer Database for Gene Expression Detection and Quantification",
"prefix": "NBDC02109",
"pubmeds": [
"22086960",
"19906719",
"14654707"
],
"status": "Active",
"target_keywords": [
"DNA",
"Genetic variation"
]
},
"nbdc02110": {
"alt_name": "ProOpDB",
"description": "The Prokaryotic Operon DataBase (ProOpDB) constitutes one of the most precise and complete repository of operon predictions in our days. Using our novel and highly accurate operon algorithm, we have predicted the operon structures of more than 1,200 prokaryotic genomes.",
"fairsharing": "FAIRsharing.p6hdm8",
"homepage": "http://operons.ibt.unam.mx/OperonPredictor",
"information_keywords": [
"Sequence",
"Image/Movie",
"Classification"
],
"name": "Prokaryotic Operon DataBase",
"prefix": "NBDC02110",
"pubmeds": [
"20385580",
"22096236"
],
"status": "Active",
"target_keywords": [
"Protein",
"Genome/Gene",
"Organism"
]
},
"nbdc02111": {
"description": "ProPortal is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. They provide a source of cross-referenced data across multiple scales of biological organizationβfrom the genome to the ecosystemβembracing the full diversity of ecotypic variation within this microbial taxon, its sister group, Synechococcus and phages that infect them.",
"fairsharing": "FAIRsharing.spxmc4",
"homepage": "http://proportal.mit.edu/",
"information_keywords": [
"Sequence"
],
"name": "ProPortal",
"prefix": "NBDC02111",
"pubmeds": [
"22102570"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02112": {
"alt_name": "TopFIND",
"description": "The Termini-Oriented Protein Function INferred Database (TopFIND) is an integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing state of proteins and functional implications thereof derived from research literature, contributions by the scientific community and biological databases.",
"fairsharing": "FAIRsharing.rkpmhn",
"homepage": "https://topfind.clip.msl.ubc.ca/",
"information_keywords": [
"Sequence"
],
"name": "Termini-Oriented Protein Function INferred Database",
"prefix": "NBDC02112",
"pubmeds": [
"21822272",
"25332401",
"22102574"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02113": {
"description": "The Therapeutic Target Database provides information about therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets.\nAlso included in this database are links to relevant databases containing information about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, clinical development status. All information is fully referenced.",
"fairsharing": "FAIRsharing.fwzf0w",
"homepage": "http://bidd.nus.edu.sg/group/ttd/ttd.asp",
"information_keywords": [
"Interaction/Pathway",
"3D structure",
"Sequence",
"Ontology/Terminology/Nomenclature",
"Bibliography/Documents"
],
"maintainer": "National University of Singapore",
"name": "TTD, Therapeutic Target Database",
"prefix": "NBDC02113",
"pubmeds": [
"19933260",
"11752352",
"24265219",
"26578601"
],
"status": "Inactive",
"target_keywords": [
"Drug",
"DNA",
"Health/Disease",
"Protein"
]
},
"nbdc02114": {
"description": "The UCSC Archaeal Genome Browser is a window on the biology of more than 100 microbial species from the domain Archaea. Basic gene annotation is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, nucleotide and protein motifs, non-coding RNA predictions, operon predictions, and other types of bioinformatic analyses. In addition, we display available gene expression data (microarray or high-throughput RNA sequencing). Direct contributions or notices of publication of functional genomic data or bioinformatic analyses from archaeal research labs are very welcome.",
"fairsharing": "FAIRsharing.12yd2z",
"homepage": "http://archaea.ucsc.edu",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "Department of Biomolecular Engineering, University of California Santa Cruz||Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz||University of California",
"name": "The UCSC Archaeal Genome Browser",
"prefix": "NBDC02114",
"pubmeds": [
"16381898",
"14681465",
"11932250"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"RNA",
"Organism"
]
},
"nbdc02115": {
"alt_name": "ViPR",
"description": "The Virus Pathogen Database and Analysis Resource (ViPR) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR captures various types of information, including sequence records, gene and protein annotations, 3D protein structures, immune epitope locations, clinical and surveillance metadata and novel data derived from comparative genomics analysis. The database is available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens and other viruses.",
"fairsharing": "FAIRsharing.2qx8n8",
"homepage": "http://www.viprbrc.org",
"information_keywords": [
"Expression",
"Sequence",
"3D structure",
"Bibliography/Documents"
],
"maintainer": "JCVI (J. Craig Venter Institute)||Northrop Grumman Health IT||Vecna Technologies",
"name": "Virus Pathogen Database and Analysis Resource",
"prefix": "NBDC02115",
"pubmeds": [
"22006842"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02116": {
"description": "WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community.",
"fairsharing": "FAIRsharing.1x53qk",
"homepage": "http://wikipathways.org",
"information_keywords": [
"Image/Movie",
"Interaction/Pathway"
],
"maintainer": "Universiteit Maastricht||Gladstone Institutes",
"name": "WikiPathways",
"prefix": "NBDC02116",
"pubmeds": [
"18651794",
"19649250",
"26481357",
"22096230"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02117": {
"alt_name": "YMDB",
"description": "The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker's yeast and Brewer's yeast). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions and other electronic databases.",
"fairsharing": "FAIRsharing.tawpg2",
"homepage": "http://www.ymdb.ca",
"information_keywords": [
"Chemical structure",
"Image/Movie",
"Sequence",
"Ontology/Terminology/Nomenclature",
"Localization",
"Interaction/Pathway"
],
"name": "The Yeast Metabolome DataBase",
"prefix": "NBDC02117",
"pubmeds": [
"22064855"
],
"status": "Active",
"target_keywords": [
"Protein",
"Metabolite"
]
},
"nbdc02118": {
"alt_name": "WholeCellKB",
"description": "WholeCellKB is a collection of open-access model organism databases specifically designed to enable whole-cell models. Currently, WholeCellKB contains a database of Mycoplasma genitalium, a Gram-positive bacterium and common human pathogen. The M. genitalium database is the most comprehensive description of any single organism to date, and was used to develop the first whole-cell computational model. The M. genitalium database was curated from over 900 primary research articles, reviews, books, and databases. The M. genitalium database is extensively cross-referenced to external resources including BioCyc, KEGG, and UniProt.\nWholeCellKB is also an open-source web-based software program for constructing model organism databases. The WholeCellKB software provides an extensive and fully customizable data model that fully describes individual species including the structure and function of each gene, protein, reaction, and pathway. \nWholeCellKB is freely accessible via a web-based user interface as well as via a RESTful web service.",
"fairsharing": "FAIRsharing.4dfs3p",
"homepage": "http://www.wholecellkb.org",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "Karr Lab, Institute for Multiscale Biology & Genomics",
"name": "Whole-Cell Knowledge Base",
"prefix": "NBDC02118",
"pubmeds": [
"23175606"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Cell/Organelle",
"Organism",
"Health/Disease"
]
},
"nbdc02119": {
"alt_name": "HAGR",
"description": "The Human Ageing Genomic Resources (HAGR) is a collection of databases and tools for the biology and genetics of ageing. HAGR features several databases with high-quality, manually-curated data: 1) GenAge, a database of genes associated with ageing in humans and model organisms; 2) AnAge, an extensive collection of longevity records and complementary traits for over 4,000 vertebrate species; and 3) GenDR, a database containing both gene mutations that interfere with dietary restriction-mediated lifespan extension and consistent gene expression changes induced by dietary restriction.",
"fairsharing": "FAIRsharing.bw1e90",
"homepage": "http://genomics.senescence.info/",
"information_keywords": [
"Sequence",
"3D structure",
"Expression"
],
"maintainer": "Institute of Integrative Biology, University of Liverpool",
"name": "Human Ageing Genomic Resources",
"prefix": "NBDC02119",
"pubmeds": [
"18986374"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Organism",
"Health/Disease"
]
},
"nbdc02120": {
"description": "PTMCode is a resource of known and predicted functional associations between protein post-translational modifications (PTMs) within and between interacting proteins.",
"fairsharing": "FAIRsharing.96xqbf",
"homepage": "http://ptmcode.embl.de",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"name": "PTMcode",
"prefix": "NBDC02120",
"pubmeds": [
"23193284",
"22806145",
"25361965"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02121": {
"alt_name": "SecReT4",
"description": "A web-based bacterial type IV secretion system resource for type IV secretion systems (T4SSs) and cognate effectors in bacteria.",
"fairsharing": "FAIRsharing.x0dzdt",
"homepage": "https://bioinfo-mml.sjtu.edu.cn/SecReT4/",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "Shanghai Jiao Tong University",
"name": "Type IV Secretion system Resource",
"prefix": "NBDC02121",
"pubmeds": [
"23193298"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02122": {
"description": "OrtholugeDB contains Ortholuge-based orthology predictions for completely sequenced bacterial and archaeal genomes. It is also a resource for reciprocal best BLAST-based ortholog predictions, in-paralog predictions (recently duplicated genes) and ortholog groups in Bacteria and Archaea. The Ortholuge method improves the specificity of high-throughput orthology prediction.",
"fairsharing": "FAIRsharing.675y92",
"homepage": "http://www.pathogenomics.sfu.ca/ortholugedb",
"information_keywords": [
"Sequence",
"3D structure",
"Classification"
],
"maintainer": "Fiona Brinkman Laboratory, Simon Fraser University",
"name": "OrtholugeDB",
"prefix": "NBDC02122",
"pubmeds": [
"16729895",
"23203876"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02123": {
"description": "The GenomeRNAi database collects RNAi phenotypes recorded in the literature for Homo sapiens and Drosophila melanogaster, as well as details on RNAi reagents. The data is well integrated with information from other resources, allowing comparison within and across species. Download files are provided.",
"fairsharing": "FAIRsharing.f55jfq",
"homepage": "http://www.genomernai.org",
"information_keywords": [
"Method",
"Sequence",
"Expression"
],
"maintainer": "Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and University of Heidelberg",
"name": "GenomeRNAi",
"prefix": "NBDC02123",
"pubmeds": [
"17135194",
"19910367",
"23193271"
],
"status": "Active",
"target_keywords": [
"RNA",
"Genome/Gene",
"Organism"
]
},
"nbdc02124": {
"alt_name": "MTBLS",
"description": "MetaboLights is a database is a collection of metabolite structures. This resource provides information on the compound origins,the biological roles, locations and concentrations, as well as experimental data from metabolic experiments. The tools and capabilities of this database is firmly routed in collaborative working worldwie with the metabolomics community such as the Metabolomics Society and the associated Metabolomics Standards Initiative (MSI).",
"fairsharing": "FAIRsharing.kkdpxe",
"homepage": "https://www.ebi.ac.uk/metabolights/",
"information_keywords": [
"Method",
"Chemical structure",
"Bibliography/Documents"
],
"maintainer": "Cambridge Systems Biology Centre, University of Cambridge||EMBL (European Molecular Biology Laboratory)",
"name": "MetaboLights",
"prefix": "NBDC02124",
"pubmeds": [
"23109552",
"23630246",
"23060735",
"23683662",
"27010336",
"28830114"
],
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc02125": {
"description": "The PlantRNA database compiles tRNA gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. For each tRNA gene, the linear secondary structure is given as well as biological information. This includes 5'- and 3'- flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences, aminoacyl-tRNA synthetases and enzymes responsible for tRNA maturation and modification. Data on mitochondrial import of nuclear-encoded tRNAs as well as the bibliome for the respective tRNAs and tRNA binding proteins are also included.",
"fairsharing": "FAIRsharing.fy2ebk",
"homepage": "http://plantrna.ibmp.cnrs.fr/",
"information_keywords": [
"Sequence"
],
"maintainer": "IBMP (Plant Molecular Biology Institute)",
"name": "PlantRNA",
"prefix": "NBDC02125",
"pubmeds": [
"21443625",
"23066098"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"RNA"
]
},
"nbdc02126": {
"alt_name": "IPD",
"description": "The Immuno Polymorphism Database (IPD), was developed in 2003 to provide a centralised system for the study of polymorphism in genes of the immune system.",
"fairsharing": "FAIRsharing.c3v6e6",
"homepage": "http://www.ebi.ac.uk/ipd/",
"information_keywords": [
"Sequence"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)||HLA Informatics Group, Anthony Nolan Research Institute",
"name": "Immuno-Polymorphism Database",
"prefix": "NBDC02126",
"pubmeds": [
"19875415",
"19172270",
"18449992",
"16944494",
"23180793"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Genome/Gene",
"Organism",
"Health/Disease"
]
},
"nbdc02127": {
"alt_name": "CTD",
"description": "The Comparative Toxicogenomics Database (CTD) advances understanding of the effects of environmental chemicals on human health. Biocurators manually curate chemical-gene, chemical-disease, and gene-disease relationships from the scientific literature. This core data is then internally integrated to generate inferred chemical-gene-disease networks. Additionally, the core data is integrated with external data sets (such as Gene Ontology and pathway annotations) to predict many novel associations between different data types. A unique and powerful feature of CTD is the inferred relationships generated by data integration that helps turn knowledge into discoveries by identifying novel connections between chemicals, genes, diseases, pathways, and GO annotations that might not otherwise be apparent using other biological resources.",
"fairsharing": "FAIRsharing.h3tjtr",
"homepage": "http://ctdbase.org/",
"information_keywords": [
"Environment",
"Bibliography/Documents",
"Phenotype",
"Interaction/Pathway"
],
"maintainer": "North Carolina State University",
"name": "Comparative Toxicogenomics Database",
"prefix": "NBDC02127",
"status": "Active",
"target_keywords": [
"Health/Disease",
"Chemical compound"
]
},
"nbdc02128": {
"alt_name": "2P2Idb",
"description": "2P2Idb is a hand-curated structural database dedicated to the modulation of protein-protein interactions (PPIs). \nIt includes all interactions for which both the protein-protein and protein-modulator complexes have been structurally characterized by X-ray or NMR. The 2P2I database currently contains 14 protein-protein complexes, 16 free proteins, 56 protein-ligand complexes and 53 small molecule inhibitors. Only inhibitors found at the interface (orthosteric modulators) have been considered in this version of the database. The web server provides links to related sites of interest, binding affinity data, pre-calculated structural information about protein-protein interfaces and 3D interactive views through java applets.",
"fairsharing": "FAIRsharing.pfes4f",
"homepage": "https://2p2idb.marseille.inserm.fr/",
"information_keywords": [
"Interaction/Pathway",
"3D structure"
],
"maintainer": "iSCB (Laboratory of Integrative Structural & Chemical Biology)",
"name": "Protein Protein Interaction Inhibition Database",
"prefix": "NBDC02128",
"pubmeds": [
"23203891",
"20231898"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc02129": {
"description": "MODOMICS is the first comprehensive database system for biology of RNA modification. It integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that carry out the respective reactions (together with their protein cofactors). Also included are the protein sequences, the structure data (if available), selected references from scientific literature, and links to other databases allowing to obtain comprehensive information about individual modified residues and proteins involved in their biosynthesis.",
"fairsharing": "FAIRsharing.3qh2tg",
"homepage": "http://modomics.genesilico.pl/",
"information_keywords": [
"Sequence",
"Chemical structure",
"Localization",
"Interaction/Pathway"
],
"maintainer": "Bujnicki Lab, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw (IIMCB)",
"name": "MODOMICS",
"prefix": "NBDC02129",
"pubmeds": [
"16381833",
"18854352",
"23118484"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc02130": {
"alt_name": "GUDID",
"description": "The Global Unique Device Identification Database (GUDID - pronounced \"Good ID\") is a database administered by the FDA as part of the UDI system.\nThe GUDID contains device identification information submitted by device companies to the FDA. The GUDID contains ONLY the Device Identifier (DI), which serves as the primary key to obtain information in the database. Production Identifiers (PI) are not submitted to or stored in the GUDID, but GUDID data indicates which PIs are on the device label.\nMany data elements in the GUDID correspond to information on the medical device label. The figure below shows a fictitious medical device label and identifies the GUDID data elements that appear on the label. Please refer to the FDA UDI website for more information about GUDID data elements.",
"fairsharing": "FAIRsharing.ennep4",
"homepage": "https://accessgudid.nlm.nih.gov/",
"information_keywords": [
"Method",
"Bibliography/Documents"
],
"maintainer": "FDA (United States Food and Drug Administration)",
"name": "Global Unique Device Identification Database",
"prefix": "NBDC02130",
"pubmeds": [
"25262248",
"24066364"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc02131": {
"alt_name": "PanelApp",
"description": "Genomics England PanelApp is a publically-available knowledgebase that allows virtual gene panels related to human disorders to be created, stored and queried. It includes a crowdsourcing tool that allows genes to be added or reviewed by experts throughout the worldwide scientific community, providing an opportunity for the standardisation of gene panels, and a consensus on which genes have sufficient evidence for disease association.\nThe diagnostic grade 'Green' genes and their modes of inheritance in the Version 1+ PanelApp virtual gene panels are used to direct the variant tiering process for the interpretation of genomes in the 100,000 Genomes Project. As panels in PanelApp are publically available, they can also be utilised by others. Experts are asked to register (https://panelapp.genomicsengland.co.uk/accounts/registration/) in order to review and rate the genes on the panel to indicate whether there is a diagnostic-grade level of evidence for the gene to be implicated in a given disease. Bioinformaticians can access the data via the PanelApp webservices (https://panelapp.genomicsengland.co.uk/#!Webservices). More detailed background information, instructions and updates can be found on the PanelApp homepage tabs.",
"fairsharing": "FAIRsharing.yfk4w2",
"homepage": "https://panelapp.genomicsengland.co.uk/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "Genomics England",
"name": "Genomics England | PanelApp",
"prefix": "NBDC02131",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc02132": {
"alt_name": "miRandola",
"description": "The miRandola database is the first resource for extracellular circulating RNAs. The first version of the database has been published on Plos One in 2012. It mainly contains information on circulating microRNAs and other non-coding RNAs. It is manually curated and constantly updated by the authors (usually once a year). We have extracted data from PubMed papers and Exocarta (a database that collects data regarding exosomes). We report information on methods of RNA extraction and qualification, diseases, experimental description, expression data and the potential biomarker role. We are updating the database with other RNAs and the future direction is to have a portal for all the non invasive biomarkers such as cell free DNA and circulating tumor cells.",
"fairsharing": "FAIRsharing.hs4d6r",
"homepage": "http://mirandola.iit.cnr.it/",
"information_keywords": [
"Method",
"Bibliography/Documents"
],
"maintainer": "IFC-CNR (Institute of Clinical Physiology)||Icahn School of Medicine at Mount Sinai||ITT (Institute of Informatics and Telematics, National Research Council)||Ohio State University||University of Catania",
"name": "miRandola: extracellular circulating RNAs database",
"prefix": "NBDC02132",
"pubmeds": [
"23094086",
"25077952"
],
"status": "Active",
"target_keywords": [
"RNA",
"Health/Disease",
"Cell/Organelle"
]
},
"nbdc02133": {
"alt_name": "ENCODE",
"description": "The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. ENCODE results from 2007 and later are available from this project. This covers data generated during the two production phases 2007-2012 and 2013-present.",
"fairsharing": "FAIRsharing.7ykpy5",
"homepage": "https://www.encodeproject.org/",
"information_keywords": [
"Method",
"Sequence",
"Interaction/Pathway"
],
"name": "ENCODE Project",
"prefix": "NBDC02133",
"pubmeds": [
"25776021",
"26527727",
"26980513"
],
"status": "Active",
"target_keywords": [
"Protein",
"Genome/Gene",
"RNA",
"Genetic variation"
]
},
"nbdc02134": {
"alt_name": "T2D KP",
"description": "The Type 2 Diabetes Knowledge Portal is an open-access resource for human genetic information on type 2 diabetes (T2D). It is a central repository for data from large genomic studies that identify DNA variants whose presence is linked to altered risk of having T2D or related traits such as high body mass index. Pinpointing these DNA variants, and the genes they affect, will spur novel insights about how T2D develops and suggest new potential targets for drugs or other therapies to treat T2D.",
"fairsharing": "FAIRsharing.95wk6e",
"homepage": "http://www.type2diabetesgenetics.org/",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"name": "Type 2 Diabetes Knowledge Portal",
"prefix": "NBDC02134",
"status": "Active",
"target_keywords": [
"Genetic variation",
"Genome/Gene",
"Organism",
"Health/Disease"
]
},
"nbdc02135": {
"alt_name": "DMDD",
"description": "Initiated in 2013, DMDD has the ambitious goal of identifying all embryonic lethal knockout lines made at the Wellcome Trust Sanger institute, through their work as a major centre for creation of individual mouse gene knockouts. DMDD uses a combination of comprehensive 3D imaging, tissue histology, immunocytochemistry and transcriptomics to identify abnormalities in embryo and placental structure for each embryonic lethal line. All data is made freely available via this web site, enabling individual researchers to identify lines relevant to their own research. The DMDD programme is coordinating its work with similar international efforts through the umbrella of the International Mouse Phenotyping Consortium.",
"fairsharing": "FAIRsharing.p5f1j4",
"homepage": "https://dmdd.org.uk",
"information_keywords": [
"Phenotype",
"Image/Movie",
"Method",
"3D structure"
],
"maintainer": "Francis Crick Institute",
"name": "Deciphering the Mechanisms of Developmental Disorders",
"prefix": "NBDC02135",
"pubmeds": [
"26519470"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Organism"
]
},
"nbdc02136": {
"alt_name": "MNXref",
"description": "MetaNetX/MNXref is a database for reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. The tools developed at MetaNetX are useful for accessing, analysing and manipulating metabolic networks. MetaNetX goal is to automate model construction and genome annotation for large-scale metabolic networks.",
"fairsharing": "FAIRsharing.szs7pn",
"homepage": "https://www.metanetx.org/",
"information_keywords": [
"Interaction/Pathway",
"Repository"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "MetaNetX",
"prefix": "NBDC02136",
"pubmeds": [
"26527720",
"23172809",
"23357920"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Metabolite"
]
},
"nbdc02137": {
"description": "data.eNanoMapper.net is a public database hosting nanomaterials characterization data and biological and toxicological information. The database provides various possibilities to search and explore information, and to download data in various standard formats. The database supports data upload through configurable Excel templates.",
"fairsharing": "FAIRsharing.r18yt0",
"homepage": "https://data.enanomapper.net/",
"information_keywords": [
"Method",
"Bibliography/Documents"
],
"maintainer": "eNanoMapper",
"name": "data.eNanoMapper.net",
"prefix": "NBDC02137",
"pubmeds": [
"25815161",
"26425413",
"21991315"
],
"status": "Active",
"target_keywords": [
"Chemical compound",
"Health/Disease"
]
},
"nbdc02138": {
"description": "STRENDA DB is a storage and search platform supported by the Beilstein-Institut that incorporates the STRENDA Guidelines in a user-friendly, web-based system. If you are an author who is preparing a manuscript containing functional enzymology data, STRENDA DB provides you the means to ensure that your data sets are complete and valid before you submit them as part of a publication to a journal.\nData entered in the STRENDA DB submission form are automatically checked for compliance with the STRENDA Guidelines; users receive warnings informing them when necessary information is missing.\nA successful formal compliance is confirmed by the awarding of a STRENDA Registry Number (SRN) and documented in a fact sheet (PDF) containing all input data that can be submitted with the manuscript to the journal. In addition, each dataset is assigned a DOI that allows reference and tracking of the data. The data become publicly available in the database only after the corresponding article has been peer-reviewed and published in a journal.\nThe STRENDA Commission, comprising an international panel of highly-regarded scientists who have wide-ranging expertise in areas such as biochemistry, enzyme nomenclature, bioinformatics, systems biology, modelling, mechanistic enzymology and theoretical biology, has established standards for data reporting in enzymology research. The aim of these STRENDA Guidelines is to improve the quality of data published in the scientific literature and to enable researchers to compare, evaluate, interpret and reproduce experimental research results published in the literature and databases.",
"fairsharing": "FAIRsharing.ekj9zx",
"homepage": "https://www.beilstein-strenda-db.org/strenda/",
"information_keywords": [
"Method",
"Bibliography/Documents"
],
"maintainer": "STRENDA Commission",
"name": "STRENDA DB",
"prefix": "NBDC02138",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02139": {
"description": "Gemma is a database for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. Users can search, access and visualize co-expression and differential expression results.",
"fairsharing": "FAIRsharing.t98nav",
"homepage": "http://www.chibi.ubc.ca/Gemma",
"information_keywords": [
"Expression",
"Interaction/Pathway",
"Bibliography/Documents"
],
"name": "Gemma",
"prefix": "NBDC02139",
"pubmeds": [
"22782548"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02140": {
"alt_name": "EMA",
"description": "The e-Mouse Atlas (EMA) is a detailed model of the developing mouse. Its purpose is not only to provide information about the shape, gross anatomy and detailed histological structure of the mouse, but also to provide a framework into which information about gene function can be mapped. The spatial, temporal and anatomical integration achieved by mapping diverse data to the organism itself rather than simply to database tables, allows powerful computational analyses. The website presents 3D volumetric models of the embryo linked, in most cases, to comprehensive and detailed images of histological structure. The embryo models and anatomy in EMA are organized by standard developmental stage (TS. after Theiler, 1989) and age of the embryo in days post coitum (dpc.). Gene-expression and other image data is also available.",
"fairsharing": "FAIRsharing.xhxe2j",
"homepage": "http://www.emouseatlas.org/emap/ema/home.php",
"information_keywords": [
"Image/Movie",
"Expression",
"3D structure"
],
"maintainer": "Churchill Group, The Jackson Laboratory||IGMM (MRC Institute of Genetics & Molecular Medicine, University of Edinburgh)",
"name": "e-Mouse Atlas",
"prefix": "NBDC02140",
"pubmeds": [
"24265223"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02141": {
"alt_name": "EMAGE",
"description": "EMAGE is a database of in situ gene expression data in the mouse embryo. mRNA in situ hybridisation, protein immunohistochemistry, in situ transgenic reporter data, and in situ enhancer data is included. These are sourced from the community and curators take this data and describe it in a standardised way that allows data query and exchange. The description includes a text-based component but the unique aspect of EMAGE is its spatial annotation focus.",
"fairsharing": "FAIRsharing.6qr9jp",
"homepage": "http://www.emouseatlas.org/emage/home.php",
"information_keywords": [
"Expression",
"Localization",
"Interaction/Pathway",
"3D structure"
],
"maintainer": "Churchill Group, The Jackson Laboratory||IGMM (MRC Institute of Genetics & Molecular Medicine, University of Edinburgh)",
"name": "e-Mouse Atlas of Gene Expression",
"prefix": "NBDC02141",
"pubmeds": [
"24265223"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02142": {
"alt_name": "RBP-Var",
"description": "RBP-Var is a database of functional variants involved in regulation mediated by RNA-binding proteins. Human genome variants can change the RNA structure and affect RNA-protein interactions.",
"fairsharing": "FAIRsharing.tx8cgr",
"homepage": "http://www.rbp-var.biols.ac.cn/",
"information_keywords": [
"Interaction/Pathway",
"Sequence"
],
"name": "RNA Binding Protein Variant Database",
"prefix": "NBDC02142",
"pubmeds": [
"26635394"
],
"status": "Active",
"target_keywords": [
"Protein",
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02143": {
"description": "The Coral Trait Database is a growing compilation of scleractinian coral life history trait, phylogenetic and biogeographic data. As of today, there are 68247 coral observations with 105243 trait entries of 147 traits for 1548 coral species in the database. Most of these entries are for shallow-water, reef-building species.",
"fairsharing": "FAIRsharing.4vthvs",
"homepage": "https://coraltraits.org/",
"information_keywords": [
"Environment",
"Geographic Distribution"
],
"name": "Coral Trait Database",
"prefix": "NBDC02143",
"pubmeds": [
"27023900"
],
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc02144": {
"description": "BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in Web Ontology Language (OWL), Resource Description Framework (RDF)(S), Open Biological and Biomedical Ontologies (OBO) format, and ProtΓ©gΓ© frames and Rich Release Format. BioPortal has a service-oriented architecture; the NCBO Web services provide the functionality found in BioPortal and these Web services can be incorporated into other software applications to access and use ontology content. BioPortal groups ontologies by domain to ease finding relevant ontologies and allows users to browse, search and visualize the content of ontologies. BioPortal also provides value-added features like ontology recommendation, text annotation, ontology mapping, and a reference index to resources like PubMed.",
"fairsharing": "FAIRsharing.4m97ah",
"homepage": "http://bioportal.bioontology.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Bibliography/Documents",
"Portal"
],
"maintainer": "Stanford Center for Biomedical Informatics Research",
"name": "BioPortal",
"prefix": "NBDC02144",
"pubmeds": [
"21672956"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc02145": {
"description": "IDog is an integrated resource for domestic dog (Canis lupus familiaris) and wild canids that provides the worldwide dog research community a variety of data services. This includes Genes, Genomes, SNPs, Breed/Disease Traits, Gene Expressions, Single Cell, Dog-Human Homolog Diseases and Literatures. In addition, iDog provides Online tools for performing genomic data visualization and analyses.",
"fairsharing": "FAIRsharing.exc0vp",
"homepage": "https://ngdc.cncb.ac.cn/idog/",
"information_keywords": [
"Sequence"
],
"maintainer": "BIGD (Big Data Center, Beijing Institute of Genomics)",
"name": "iDog",
"prefix": "NBDC02145",
"pubmeds": [
"25404132"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02146": {
"alt_name": "ODB",
"description": "OmicsDB is a database for the storage and management of omics data and auxiliary information. The database contains cross-species, cross-technique and cross-types. It offers user-submission tools of which aim to reduce the work revolving adherence to standards. The resource homepage is currently unavailable. If you have any information on the current status of this resource, please contact us.",
"fairsharing": "FAIRsharing.1v4zw7",
"homepage": "https://github.com/KeironO/omicsdb",
"name": "OmicsDB",
"prefix": "NBDC02146",
"status": "Inactive"
},
"nbdc02147": {
"alt_name": "candat",
"description": "The CancerData site is an effort of the Medical Informatics and Knowledge Engineering team (MIKE for short) of Maastro Clinic, Maastricht, The Netherlands. It offers a central, online repository for the sustained storage of clinical protocols, publications and research datasets. The data that are offered can vary from documents, spreadsheets to (bio-)medical images and treatment simulations. CancerData is a registered member of DataCite, which is an international consortium and member of the International DOI Foundation. Via DataCite, we have the ability to offer persistent identifiers to the datasets via the registration of Digital Object Identifiers (DOI).",
"fairsharing": "FAIRsharing.s2txbp",
"homepage": "https://www.cancerdata.org",
"information_keywords": [
"Image/Movie",
"Ontology/Terminology/Nomenclature",
"Bibliography/Documents",
"Repository"
],
"maintainer": "MAASTRO Clinic",
"name": "CancerData",
"prefix": "NBDC02147",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc02148": {
"alt_name": "CLIMA",
"description": "CLIMA 2 is the result of an integration effort aimed at including all certified STR profiles of human cell lines in a unique database. The contents of the database are dynamically summarized (i.e., they are always up-to-date) in a table in the home page. CLIMA can be used to identify researcher's cell lines. Moreover, it can be searched either by name or by locus. The identification of a cell line is performed according to the standard ANSI/ATCC ASN-0002-2011 on \"Authentication of Human Cell Lines: Standardization of STR Profiling\".",
"fairsharing": "FAIRsharing.qq9jf4",
"homepage": "http://bioinformatics.hsanmartino.it/clima2/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico)",
"name": "Cell Line Integrated Molecular Authentication Database",
"prefix": "NBDC02148",
"status": "Inactive",
"target_keywords": [
"Cell/Organelle",
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02149": {
"alt_name": "MDM",
"description": "MDM-Portal (Medical Data-Models) is a meta-data registry for creating, analysing, sharing and reusing medical forms, developed by the Institute of Medical Informatics, University of Muenster in Germany.\nsee also http://www.ncbi.nlm.nih.gov/pubmed/26868052\nElectronic forms for documentation of patient data are an integral part within the workflow of physicians. A huge amount of data is collected either through routine documentation forms (EHRs) for electronic health records or as case report forms (CRFs) for clinical trials. This raises major scientific challenges for health care, since different health information systems are not necessarily compatible with each other and thus information exchange of structured data is hampered.\nSoftware vendors provide a variety of individual documentation forms according to their standard contracts, which function as isolated applications. Furthermore, free availability of those forms is rarely the case. Currently less than 5 % of medical forms are freely accessible.\nBased on this lack of transparency harmonization of data models in health care is extremely cumbersome, thus work and know-how of completed clinical trials and routine documentation in hospitals are hard to be re-used.\nThe MDM-Portal serves as an infrastructure for academic (non-commercial) medical research to contribute a solution to this problem. It already contains more than 6,000 system-independent forms (CDISC ODM Format, www.cdisc.org, Operational Data Model) with more than 470,000 data-elements. This enables researchers to view, discuss, download and export forms in most common technical formats such as PDF, CSV, Excel, SQL, SPSS, R, etc. A growing user community will lead to a growing database of medical forms. In this matter, we would like to encourage all medical researchers to register and add forms and discuss existing forms.",
"fairsharing": "FAIRsharing.wnk2eq",
"homepage": "https://medical-data-models.org",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "IMI (Institute of Medical Informatics, University of Muenster)",
"name": "Medical Data Models",
"prefix": "NBDC02149",
"pubmeds": [
"26868052"
],
"status": "Active",
"target_keywords": [
"Health/Disease",
"Organism"
]
},
"nbdc02150": {
"alt_name": "ProbOnto",
"description": "ProbOnto, is an ontology-based knowledge base of probability distributions, featuring more than 150 uni- and multivariate distributions with their defining functions, characteristics, relationships and re-parameterization formulas. It can be used for model annotation and facilitates the encoding of distribution-based models, related functions and quantities. ProbOnto is both an ontology and a knowledge base, however its primary focus is the knowledge base.",
"fairsharing": "FAIRsharing.8zqzm9",
"homepage": "http://www.probonto.org",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "DDMoRe (Drug Disease Model Resource)",
"name": "Ontology and Knowledge Base of Probability Distributions",
"prefix": "NBDC02150",
"pubmeds": [
"27153608"
],
"status": "Active"
},
"nbdc02151": {
"alt_name": "ITHANET",
"description": "The ITHANET Portal represents an expanding resource for clinicians and researchers dealing with haemoglobinopathies and a port of call for patients in search of professional advice. The ITHANET Portal integrates information on news, events, clinical trials and thalassaemia-related organisations, research projects and other scientific networks, wiki-based content of protocols, clinical guidelines and educational articles. Most importantly, disease-specific databases are developed and maintained on the ITHANET Portal, such as databases of haemoglobin variations (IthaGenes), epidemiology (IthaMaps) and HbF inducers (IthaDrugs).",
"fairsharing": "FAIRsharing.tje0nv",
"homepage": "http://www.ithanet.eu",
"information_keywords": [
"Sequence",
"Phenotype"
],
"name": "The ITHANET Portal",
"prefix": "NBDC02151",
"pubmeds": [
"25058394",
"19657830"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Genome/Gene",
"Health/Disease",
"Organism"
]
},
"nbdc02152": {
"alt_name": "JGA",
"description": "The Japanese Genotype-phenotype Archive (JGA) is a service for permanent archiving and sharing of all types of individual-level genetic and de-identified phenotypic data resulting from biomedical research projects.",
"fairsharing": "FAIRsharing.pwgf4p",
"homepage": "https://www.ddbj.nig.ac.jp/jga",
"information_keywords": [
"Expression",
"Sequence",
"Phenotype",
"Method",
"Repository"
],
"maintainer": "Bioinformation and DDBJ Center, National Institute of Genetics, Research Organization of Information and Systems",
"name": "Japanese Genotype-phenotype Archive",
"prefix": "NBDC02152",
"pubmeds": [
"25477381"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Organism"
]
},
"nbdc02153": {
"description": "MitoCheck aims to integrate information on cellular function of human genes while giving access to supporting information such as microscopy images of phenotypes",
"fairsharing": "FAIRsharing.j4ebq1",
"homepage": "http://www.mitocheck.org",
"information_keywords": [
"Expression",
"Image/Movie",
"Interaction/Pathway"
],
"name": "MitoCheck",
"prefix": "NBDC02153",
"pubmeds": [
"20360735",
"20360068"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc02154": {
"alt_name": "IDR",
"description": "IDR is a prototype platform for publishing, mining and integrating bioimaging data at scale, following the Euro-BioImaging/ELIXIR imaging strategy using the OMERO and Bio-Formats open source software built by the Open Microscopy Environment. Deployed on an OpenStack cloud running on the EMBL-EBI's Embassy resource, it includes image data linked to independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super-resolution microscopy, and digital pathology.",
"fairsharing": "FAIRsharing.6wf1zw",
"homepage": "https://idr.openmicroscopy.org",
"information_keywords": [
"Expression",
"Image/Movie",
"Repository"
],
"maintainer": "Cambridge Systems Biology Centre, University of Cambridge||European Commission FP7",
"name": "Image Data Resource",
"prefix": "NBDC02154",
"pubmeds": [
"28775673"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc02155": {
"alt_name": "VPR",
"description": "A repository of reusable, modular and composable models of biological parts.",
"fairsharing": "FAIRsharing.tf3mhc",
"homepage": "http://www.virtualparts.org",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Bibliography/Documents"
],
"name": "Virtual Parts Repository",
"prefix": "NBDC02155",
"status": "Active"
},
"nbdc02156": {
"alt_name": "JAX-CKB",
"description": "The Jackson Laboratory Clinical Knowledgebase (CKB) is a semi-automated/manually curated database of gene/variant annotations, therapy knowledge, diagnostic/prognostic information, and clinical trials related to oncology. CKB not only contains current information on the protein effect of somatic gene variants, but also connects the variant to targeted therapies through an efficacy evidence annotation. In addition, CKB captures clinical trial patient eligibility criteria that include genomic alterations (genotype-specific). The public access version of CKB encompasses 82 commonly known driver genes. Users can search CKB via gene, gene variants, drug, drug class, indication, and clinical trials. The web-based version of CKB is designed to interrogate the knowledgebase for specific data attributes while also enabling a robust browse like feature when the desired content is unknown.",
"fairsharing": "FAIRsharing.e5y0j0",
"homepage": "https://jax.org/ckb",
"information_keywords": [
"3D structure",
"Bibliography/Documents",
"Sequence"
],
"maintainer": "The Jackson Laboratory",
"name": "Clinical Knowledgebase",
"prefix": "NBDC02156",
"pubmeds": [
"26772741"
],
"status": "Active",
"target_keywords": [
"Drug",
"Genome/Gene",
"Health/Disease",
"Genetic variation"
]
},
"nbdc02157": {
"alt_name": "CID",
"description": "In addition to data used in on-going collaborations, this database host images from France Bio Imaging microscopy facility with public access either associated to publications, either that make interest from an image processing point of view (such as challenges for developpers or for use in metrology). This resource requires a log in account, however some projects are available with a guest account.",
"fairsharing": "FAIRsharing.g63c77",
"homepage": "https://cid.curie.fr",
"information_keywords": [
"Image/Movie"
],
"maintainer": "BioImage Informatics, IPDM, France Bio-Imaging||Institut Curie||Strand Avadis",
"name": "Curie Image Database",
"prefix": "NBDC02157",
"status": "Inactive"
},
"nbdc02158": {
"alt_name": "AEKOS",
"description": "The Advanced Ecological Knowledge and Observation System (ΓKOS) is a data and 'research methods' knowledge base of Australia's terrestrial plants, animals and their environments. Links are also provided to related data stored in other thematic repositories (e.g., soil metabarcoding data) where appropriate. It was built to meet the needs of the ecosystem science, tertiary education, natural resource management industry and government sectors. AEKOS has four key services: self-service data submission (SHaRED - http://www.shared.org.au/) with DOIs for provenance, versioning and citations for uploading scientific datasets, Integrated Site Data (ISD) upload, access and intelligible reuse via its portal (http://www.aekos.org.au/) and a visualisation of TERN AusPlots plant survey data (Soils-to-Satellites - http://www.soils2satellites.org.au/). ISD upload service involves specialist ecological knowledge modelling of data that's mapped to the AEKOS ontological, 'methods description' and trait information models. Unlike self-service data submission, this service enables users to view the actual observations and measurements contained within data files - it maximises transparency. AEKOS is in the pipeline for Thomson & Reuters Data Citation Index with expected release in August 2016. There are currently 96,657 sites for mostly plants and their environmental data observed using 233,556 'plots'. Animal site data is growing with a 20-year plus ongoing desert monitoring program on plants and animals (13 sites with 25 plots) and an inventory survey of the globally unique platypus (277 sites with 2,134 plots). Regular updates for ongoing datasets occur quarterly. Responsive user support for SHaRED and AEKOS data download is available.",
"fairsharing": "FAIRsharing.2y6rkq",
"homepage": "http://www.aekos.org.au/",
"information_keywords": [
"Environment",
"Method",
"Image/Movie",
"Repository"
],
"maintainer": "The University of Adelaide (TERN Eco-informatics)",
"name": "TERN AEKOS",
"prefix": "NBDC02158",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02159": {
"description": "Webservice for 3D+time in vivo, in toto imaging data storage and annotation. Direct access to image processing workflows on EGI and local computer clusters for cell detection, shape segmentation and kinematics analysis with custom designed algorithms. Registration required.",
"fairsharing": "FAIRsharing.b050yp",
"homepage": "http://www.bioemergences.eu",
"information_keywords": [
"Image/Movie"
],
"maintainer": "UNESCO UNITWIN CS-DC",
"name": "BioEmergences",
"prefix": "NBDC02159",
"pubmeds": [
"27088892"
],
"status": "Active"
},
"nbdc02160": {
"alt_name": "BBBC",
"description": "The Broad Bioimage Benchmark Collection (BBBC) is a collection of freely downloadable microscopy image sets. Researchers are encouraged to use these image sets as reference points when developing, testing, and publishing new image analysis algorithms for the life sciences. In addition to the images themselves, each set includes a description of the biological application and some type of \"ground truth\" (expected results).",
"fairsharing": "FAIRsharing.j766zb",
"homepage": "https://data.broadinstitute.org/bbbc/",
"information_keywords": [
"Method",
"Image/Movie",
"Bibliography/Documents"
],
"name": "Broad Bioimage Benchmark Collection",
"prefix": "NBDC02160",
"pubmeds": [
"22743765"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc02161": {
"description": "The Mammographic Image Analysis Society database of digital mammograms contains 322 images (161 pairs) at 50 micron resolution in \"Portable Gray Map\" (PGM) format and associated truth data.",
"homepage": "https://www.repository.cam.ac.uk/handle/1810/250394",
"information_keywords": [
"Image/Movie"
],
"maintainer": "School of Clinical Medicine, University of Cambridge",
"name": "Mammography Image Analysis Society Database",
"prefix": "NBDC02161",
"status": "Closed",
"target_keywords": [
"Health/Disease"
]
},
"nbdc02162": {
"description": "Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate. It provides infrastructure and hosting for datasets.",
"fairsharing": "FAIRsharing.dnxzmk",
"homepage": "https://www.synapse.org/",
"information_keywords": [
"Method",
"Bibliography/Documents",
"Repository"
],
"maintainer": "Sage Bionetworks",
"name": "Synapse",
"prefix": "NBDC02162",
"pubmeds": [
"24071850"
],
"status": "Active"
},
"nbdc02163": {
"description": "Haeckaliens is a collection of 3D datasets and reconstructions of embryos obtained with the open-source optical tomography scanner \"OPenT\" .",
"fairsharing": "FAIRsharing.mrfyxv",
"homepage": "http://www.gabygmartins.info/research/haeckaliens",
"information_keywords": [
"3D structure",
"Image/Movie"
],
"maintainer": "IGC (Instituto Gulbenkian de Ciencia)",
"name": "Haeckaliens",
"prefix": "NBDC02163",
"status": "Inactive",
"target_keywords": [
"Cell/Organelle",
"Organism"
]
},
"nbdc02164": {
"description": "A repository of image / SPM data to support users of the Centre for Cell Imaging, University of Liverpool.",
"fairsharing": "FAIRsharing.nv1n5s",
"homepage": "http://cci02.liv.ac.uk/gallery/",
"information_keywords": [
"Image/Movie",
"Repository"
],
"maintainer": "Centre for Cell Imaging, Institute of Integrative Biology, University of Liverpool",
"name": "Liverpool CCI OMERO",
"prefix": "NBDC02164",
"pubmeds": [
"27009190"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc02165": {
"description": "The core of the system is tailored PACS (Picture Archiving and Communication System). It forms the basis for educational and research applications such as the development of databases of case studies describing the treatment of real patients. Images appropriate for teaching or research purposes are made anonymous. This database is in Czech and has restricted access.",
"fairsharing": "FAIRsharing.yvhq61",
"homepage": "http://www.medimed.cz",
"information_keywords": [
"Image/Movie",
"Method",
"Bibliography/Documents",
"Repository"
],
"name": "Educational and Research Picture Archiving and Communication System",
"prefix": "NBDC02165",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc02166": {
"alt_name": "The Virtual Brain Explorer for Zebrafish",
"description": "ViBE-Z, the Virtual Brain Explorer for Zebrafish is an imaging and image analysis framework for virtual colocalization studies in larval zebrafish brains, currently available for 72hpf, 48hpf and 96hpf old larvae. ViBE-Z contains a database with precisely aligned gene expression patterns (1um 3 resolution), an anatomical atlas, and a software. This software creates high-quality data sets by fusing multiple confocal microscopic image stacks, and aligns these data sets to the standard larva.",
"fairsharing": "FAIRsharing.xypv6g",
"homepage": "http://vibez.informatik.uni-freiburg.de",
"information_keywords": [
"Expression",
"Localization",
"Image/Movie"
],
"maintainer": "LIC (Life Imaging Center, University of Freiburg)",
"name": "ViBE-Z",
"prefix": "NBDC02166",
"pubmeds": [
"22706672"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02167": {
"description": "CAMPSign is a tool for identification of antimicrobial peptides belonging to one of the 45 major AMP families present in CAMPR3. The peptides are identified based on family signatures such as patterns and HMMs generated for experimentally known AMPs. Users can submit sequences for screening the presence of these AMP signatures. Users can further BLAST the sequence/s of interest to find homologous sequences in popular AMP databases such as CAMP, APD, AVPdb, BACTIBASE etc.\nThis work has been funded by grants from Department of Science & Technology, India and Indian Council of Medical Research.",
"fairsharing": "FAIRsharing.7ynng",
"homepage": "http://campsign.bicnirrh.res.in/",
"information_keywords": [
"Method",
"Classification"
],
"maintainer": "NIRRH (National Institute for Research in Reproductive Health)",
"name": "CAMPSign",
"prefix": "NBDC02167",
"pubmeds": [
"27089856"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02168": {
"alt_name": "ORA",
"description": "The Oxford University Research Archive (ORA) serves as an institutional repository for the University of Oxford and is home to the scholarly research output of its members. ORA-Data is an extra function of ORA which is aimed at University of Oxford researchers who have either deposited data at external archives and want a centralised record of this, or who need a repository to deposit research data. Using the service will prevent loss of data and increase the impact of your research. It provides permanent links between publications and underlying data, and can be used as a repository for secure, long-term preservation of raw data and associated documentation. It helps Oxford researchers fulfil funding bodies' requirements to take active steps in preserving data and documentation. Digital object identifiers (DOIs) are assigned to each item in the resource for citation and attribution. Even though only Oxford researchers can upload their data in ORA, the search facility is publicly accessible.",
"fairsharing": "FAIRsharing.rkwr6y",
"homepage": "https://ora.ox.ac.uk/",
"information_keywords": [
"Portal",
"Bibliography/Documents"
],
"maintainer": "Bodleian Library, University of Oxford",
"name": "Oxford University Research Archive",
"prefix": "NBDC02168",
"status": "Active"
},
"nbdc02169": {
"alt_name": "Bioc",
"description": "Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development.",
"fairsharing": "FAIRsharing.81ettx",
"homepage": "https://bioconductor.org",
"information_keywords": [
"Sequence",
"Expression",
"Method",
"Repository"
],
"maintainer": "Bioconductor",
"name": "Bioconductor",
"prefix": "NBDC02169",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc02170": {
"description": "DataMed is a prototype biomedical data search engine. Its goal is to discover data sets across data repositories or data aggregators. In the future it will allow searching outside these boundaries. DataMed supports the NIH-endorsed FAIR principles of Findability, Accessibility, Interoperability and Reusability of datasets with current functionality assisting in finding datasets and providing access information about them.\nThe data repositories covered in this initial release have been selected by the bioCADDIE team and represent only a small sample of biomedical data. Many highly relevant data sets have not yet been indexed. Please provide suggestions on data repositories that DataMed should cover.\nThe translation of user queries into structured data used in the search is being refined. Advanced search allows users to structure their queries. Some DataMed search features are not yet available for all data. Please provide feedback about the quality of search results.\nDataMed indexes the core metadata available for most datasets, but it offers enhanced search functions when repositories provide additional metadata. The Data Tag Suite (DATS) metadata specification has evolved with input from the community and will include a schema.org annotated serialization.\nYou can use the web interface and provide us feedback here about your search experience. This is a prototype in development and your valuable suggestions and comments will help us to make the system better.",
"fairsharing": "FAIRsharing.v5q4zc",
"homepage": "https://datamed.org",
"information_keywords": [
"Bibliography/Documents",
"Portal"
],
"name": "DataMed",
"prefix": "NBDC02170",
"status": "Active"
},
"nbdc02171": {
"alt_name": "MultiCellDB",
"description": "A database for storing MultiCellDS files. In the future, MultiCellDB will include a curated library of quality-controlled digital cell lines, starting with digital representations of breast cancer (MCF7, MCF10A, MDA-MB-231), lung cancer (HCC827, H1975), and metastatic colon cancer (HCT-116 and patient-derived lines) cell lines.\nThe user interface and API are under active development.",
"fairsharing": "FAIRsharing.nm7mt",
"homepage": "http://multicellds.org/MultiCellDB.php",
"information_keywords": [
"Phenotype",
"Method",
"Bibliography/Documents"
],
"name": "MultiCellular DataBase",
"prefix": "NBDC02171",
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc02172": {
"description": "denovo-db is a collection of germline de novo variants identified in the human genome. de novo variants are those present in children but not their parents.",
"fairsharing": "FAIRsharing.8zz0xc",
"homepage": "http://denovo-db.gs.washington.edu/",
"information_keywords": [
"Phenotype",
"Sequence"
],
"name": "denovo-db",
"prefix": "NBDC02172",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02173": {
"description": "The Chemical Probes Portal is an online open access catalog of annotated small molecule inhibitors, agonists and other chemical tools for biological research and preclinical drug discovery. Annotations for are extensive and distinguish between activity in cells and model organisms. Probe records also include ratings and commentary from our Scientific Advisory Board, which consists of known experts in medicinal chemistry, chemical biology, pharmacology and related fields.",
"fairsharing": "FAIRsharing.yrkkbt",
"homepage": "http://www.chemicalprobes.org",
"information_keywords": [
"Chemical structure",
"Interaction/Pathway",
"Repository"
],
"maintainer": "The University of North Carolina, Chapel Hill Eshelman School of Pharmacy",
"name": "The Chemical Probes Portal",
"prefix": "NBDC02173",
"pubmeds": [
"26196764"
],
"status": "Active",
"target_keywords": [
"Chemical compound",
"Protein",
"Drug"
]
},
"nbdc02174": {
"description": "ValidatorDB is a collection of validation results for the entire Protein Data Bank. Annotation (3-letter code) of HET residues larger than 6 heavy atoms is inspected, i.e. if the residue has the same topology and stereochemistry as the model ligand or residue stored in the wwCCD. Validation reports for the entire database can be inspected as well as for the arbitrary set of PDB entries or PDB annotations (3-letter residue code). Results are available in graphical form via Web UI and can be downloaded in the form of CSV files for further inspection.",
"fairsharing": "FAIRsharing.c9psgb",
"homepage": "http://webchem.ncbr.muni.cz/Platform/ValidatorDB",
"information_keywords": [
"3D structure"
],
"maintainer": "Central European Institute of Technology",
"name": "ValidatorDB",
"prefix": "NBDC02174",
"pubmeds": [
"25392418"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02175": {
"alt_name": "TDH",
"description": "The Tropical Data Hub (TDH) is an open portal enabling researchers to submit information relating to the tropics in an open and collaborative way. The TDH complements existing data repositories and will come to be acknowledged as the definitive source of information relating to the tropics, both within Australia and internationally. The information available through within the TDH relates to the physical and natural environment, societies and communities (e.g. linguistic and cultural data), and economies. The use of metadata will ensure that the TDH is readily accessible to governments, researchers and the business sector.",
"fairsharing": "FAIRsharing.x6nr7d",
"homepage": "https://tropicaldatahub.org/",
"information_keywords": [
"Environment",
"Geographic Distribution",
"Taxonomy",
"Portal"
],
"maintainer": "ANDS (Australian National Data Service)||James Cook University",
"name": "Tropical Data Hub",
"prefix": "NBDC02175",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02176": {
"description": "The vast majority of the bananas currently grown and consumed were not conventionally bred but are selections made over probably thousands of years from naturally occurring hybrids. Cultivated bananas are very nearly sterile and as a consequence are not propagated from seed but rather through vegetative propagation, primarily suckers as well as more recently micropropagated or tissue cultured bananas. These factors, very old selections, near sterility and vegetative propagation, mean that these bananas have not been genetically improved either for resistance or improved quality and are becoming increasing in affected by serious pests and diseases.",
"fairsharing": "FAIRsharing.pt7qd6",
"homepage": "http://www.banana21.org/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "QUT (Queensland University of Technology)",
"name": "Banana21",
"prefix": "NBDC02176",
"pubmeds": [
"23555698"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02177": {
"description": "The compendium of crop Proteins with Annotated Locations (cropPAL) collates more than 550 data sets from previously published fluorescent tagging or mass spectrometry studies and eight pre-computed subcellular predictions for barley, wheat, rice and maize proteomes. The data collection including metadata for proteins and studies can be accessed through the search portal. The reciprocal blast and EnsemblPLants homology tree allows the search for location data across the four crop species as well as compares it to Arabidopsis data from SUBA.",
"fairsharing": "FAIRsharing.p7btsb",
"homepage": "http://crop-pal.org/",
"information_keywords": [
"Localization",
"Interaction/Pathway"
],
"maintainer": "ANDS (Australian National Data Service)||Edwards Group, University of Western Australia",
"name": "CropPAL",
"prefix": "NBDC02177",
"pubmeds": [
"26556651"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc02178": {
"description": "This resource contains genome and gene sequences, features and isolationed chromosome alignments, while functional annotation can be searched in GBrowse. Chickpea forms a critical component of the Australian and Indian farming system, offering offer a high value alternative to cereals, an important disease break, opportunities for grass weed control and respite from high nitrogen application.",
"fairsharing": "FAIRsharing.kvee9e",
"homepage": "http://www.cicer.info/databases.php",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Edwards Group, University of Western Australia||The University of Queensland",
"name": "Chickpea Portal",
"prefix": "NBDC02178",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02179": {
"alt_name": "GP Notebook",
"description": "GPnotebook is a concise synopsis of the entire field of clinical medicine focused on the needs of the General Practitioner with material organised systematically to ensure rapid retrieval of information.\nThe content of GPnotebook is based on clinical practice in the United Kingdom and provides a clinical reference for general practitioners and medical students; it may also be a useful reference resource for other health professionals. As well as being a clinical reference, GPnotebook also aims to be a tool for clinical education, clinical governance and continuing professional development.",
"fairsharing": "FAIRsharing.b6asc0",
"homepage": "http://www.gpnotebook.co.uk",
"information_keywords": [
"Bibliography/Documents"
],
"name": "General Practice Notebook",
"prefix": "NBDC02179",
"pubmeds": [
"24567602"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc02180": {
"description": "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research.\nIts scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.",
"fairsharing": "FAIRsharing.hkk309",
"homepage": "http://web.expasy.org/cellosaurus/",
"information_keywords": [
"Bioresource"
],
"maintainer": "CALIPHO (Computer and Laboratory Investigation of Proteins of Human Origin Group, Swiss Institute of Bioinformatics)",
"name": "Cellosaurus",
"prefix": "NBDC02180",
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"Organism"
]
},
"nbdc02181": {
"alt_name": "Dolce",
"description": "Dolce is a database of DNA structure motifs based on an automatic classification method consisting of the combination of supervised and unsupervised approaches. This workflow has been applied to analyze 816 X-ray and 664 NMR DNA structures released till February 2013. Dinucleotides with unassigned conformations are either classified into one of already known 24 classes or into one of six new classes among so far unclassifiable data, which were newly identified and annotated among X-ray structures by authors of this tool.",
"fairsharing": "FAIRsharing.jhjnp0",
"homepage": "http://ich.vscht.cz/projects/dolce/viewHome",
"information_keywords": [
"Method",
"3D structure",
"Classification",
"Bibliography/Documents"
],
"name": "Database of local DNA conformers",
"prefix": "NBDC02181",
"pubmeds": [
"23800225"
],
"status": "Active",
"target_keywords": [
"DNA"
]
},
"nbdc02182": {
"alt_name": "TissueNet",
"description": "Knowledge of the molecular interactions of human proteins within tissues is important for identifying their tissue-specific roles and for shedding light on tissue phenotypes. However, many protein-protein interactions (PPIs) have no tissue-contexts. The TissueNet database bridges this gap by associating experimentally-identified PPIs with human tissues that were shown to express both pair-mates. Users can select a protein and a tissue, and obtain a network view of the query protein and its tissue-associated PPIs. TissueNet v.2 is an updated version of the TissueNet database previously featured in NAR. It includes over 40 human tissues profiled via RNA-sequencing or protein-based assays. Users can select their preferred expression data source and interactively set the expression threshold for determining tissue-association. The output of TissueNet v.2 underlines qualitative and quantitative features of query proteins and their PPIs. The tissue-specificity view highlights tissue-specific and globally-expressed proteins, and the quantitative view highlights proteins that were differentially expressed in the selected tissue relative to all other tissues. Together, these views allow users to quickly assess the unique versus global functionality of query proteins. Thus, TissueNet v.2 offers an extensive, quantitative and user-friendly interface to study the roles of human proteins across tissues.",
"fairsharing": "FAIRsharing.sv2rm8",
"homepage": "https://netbio.bgu.ac.il/tissuenet",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Ben-Gurion University of the Negev",
"name": "TissueNet v.2",
"prefix": "NBDC02182",
"pubmeds": [
"23193266"
],
"status": "Active",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc02183": {
"description": "In 2010, Brazil published the Catalog of Plants and Fungi of Brazil and launched the first online version of the List of Species of the Brazilian Flora, meeting Target 1 of the Global Strategy for Plant Conservation (GSPC-CBD). This botanical milestone was only achieved due to the commitment of more than 400 Brazilians and foreign taxonomists who worked on a platform where information about our flora was included and disseminated in real time. The \"Brazilian List\", as it was popularly known, closed in November 2015 with the publication of five papers and their respective databases dealing with the different groups of fungi and plants. We enthusiastically present in 2016, the brand new system that houses the Brazilian Flora 2020 project, aiming to achieve Target 1 established for 2020 by the GSPC-CBD. This new project icludes provisions to include descriptions, identification keys and illustrations to all species of plants, algae and fungi known in the country. The Brazilian Flora 2020 project is part of the Reflora Programme and is being conducted with the support of the Sistema de Informação sobre a Biodiversidade Brasileira (SiBBr). At the moment has nearly 700 scientists working in a network to prepare the monographs. These researchers are also responsible for nomenclatural information and geographic distribution (coverage in Brazil, endemism and biomes), as well as valuable data regarding life forms, substrate and vegetation types for each species. The search results on this page include information on endangered species (thanks to the cooperation with the Centro Nacional de Conservação da Flora) and allow access to the Index Herbariorum (due to the collaboration of The New York Botanical Garden). Besides this information, users can also access images of herbarium specimens, including nomenclatural types, from both the Reflora Virtual Herbarium and INCT Virtual Herbarium of Flora and Fungi; as well as images of live plants and scientific illustrations with all images included by the experts in each group.",
"fairsharing": "FAIRsharing.p0rfm1",
"homepage": "http://floradobrasil.jbrj.gov.br/",
"information_keywords": [
"Image/Movie",
"Taxonomy"
],
"maintainer": "REFLORA Programme",
"name": "Brazilian Flora 2020",
"prefix": "NBDC02183",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02184": {
"alt_name": "Proteome-pI",
"description": "Proteome-pI is an online database containing information about predicted isoelectric points for 5,029 proteomes (21 million of sequences) calculated using 18 methods.\nThe isoelectric point, the pH at which a particular molecule carries no net electrical charge, is an important parameter for many analytical biochemistry and proteomics techniques, especially for 2D gel electrophoresis (2D-PAGE), capillary isoelectric focusing, liquid chromatographyβmass spectrometry and X-ray protein crystallography.\nThe database allows the retrieval of virtual 2D-PAGE plots and the development of customized fractions of proteome based on isoelectric point and molecular weight. Moreover, Proteome-pI facilitates statistical comparisons of the various prediction methods as well as biological investigation of protein isoelectric point space in all kingdoms of life (http://isoelectricpointdb.org/statistics.html).\nThe database includes various statistics and tools for interactive browsing, searching and sorting. It can be searched and browsed by organism name, average isoelectric point, molecular weight or amino acid frequencies. Proteins with extreme pI values are also available. For individual proteomes, users can retrieve proteins of interest given the method, isoelectric point and molecular weight ranges (this particular feature can be highly useful to limit potential targets in analysis of 2DPAGE gels or before conducting mass spectrometry). Finally, some general statistics (total number of proteins, amino acids, average sequence length, amino acid and di-amino acid frequencies) and datasets corresponding to major protein databases such as UniProtKB/TrEMBL and the NCBI non-redundant (nr) database have also been precalculated.",
"fairsharing": "FAIRsharing.yxkdpg",
"homepage": "http://isoelectricpointdb.org/",
"information_keywords": [
"Image/Movie",
"Chemical structure",
"Sequence",
"3D structure",
"Method"
],
"maintainer": "Quantitative and Computational Biology Group, Max Planck Institute for Biophysical Chemistry",
"name": "Proteome-pI : proteome isoelectric point database",
"prefix": "NBDC02184",
"pubmeds": [
"27789699"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02185": {
"alt_name": "REFLORA",
"description": "The mission of this project was to built a virtual herbarium to display the images of Brazilian plants that are housed in foreign herbaria and was presented by the Brazilian Research Council (CNPq) to the Rio de Janeiro Botanical Garden (JBRJ) in December 2010. The objective was to provide capacity to store and display high quality data regarding Brazil's Flora within a public institution. \nThe Reflora Virtual Herbarium is designed to allow taxonomists to perform similar procedures to the ones they are used to do within physical collections. In this site they will access, rather than physical specimens, high quality images that can be consulted, re-determined and typified, amongst other functionalities. In due course, the curators of partner institutes will receive periodic and on-demand system reports and will be able to update data in their own collections. \n There are currently (2016-10-30) 1922914 images of specimens available in the Reflora Virtual Herbarium. Amongst them, 116925 are nomenclatural types and 525348 are georeferenced records.\nIf you are a trained taxonomist and would like to collaborate in the Reflora Virtual Herbarium, contact us by e-mail at reflora@jbrj.gov.br.",
"fairsharing": "FAIRsharing.m03n8s",
"homepage": "http://floradobrasil.jbrj.gov.br/reflora/herbarioVirtual",
"information_keywords": [
"Image/Movie",
"Bioresource",
"Taxonomy"
],
"maintainer": "REFLORA Programme",
"name": "Reflora Virtual Herbarium",
"prefix": "NBDC02185",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02186": {
"alt_name": "LinkProt",
"description": "LinkProt collects information about protein chains and complexes that form links. LinkProt detects deterministic links (with loops closed by cysteine), and determines likelihood of formation of links in networks of protein chains called MacroLinks. Links are presented graphically in an intuitive way, using tools that involves surfaces of minimal area spanned on closed loops. The database presents extensive information about biological functions of proteins with links and enables users to analyze new structures.",
"fairsharing": "FAIRsharing.tw6ecm",
"homepage": "http://linkprot.cent.uw.edu.pl/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "CeNT (Interdisciplinary Laboratory of Biological Systems Modelling, Center of New Technology)",
"name": "LinkProt: A database of proteins with topological links",
"prefix": "NBDC02186",
"pubmeds": [
"27794552"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02187": {
"description": "Generalist research data repository built and developed by OpenAIRE and CERN, to ensure that everyone can join in Open Science.",
"fairsharing": "FAIRsharing.wy4egf",
"homepage": "https://www.zenodo.org",
"information_keywords": [
"Bibliography/Documents",
"Repository"
],
"maintainer": "CERN (European Organisation for Nuclear Research)",
"name": "Zenodo",
"prefix": "NBDC02187",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc02188": {
"description": "mirDNMR is a database for the collection of gene-centered background DNMRs obtained from different methods and population variation data. The database has the following functions: (i) browse and search the background DNMRs of each gene predicted by four different methods, including GC content (DNMR-GC), sequence context (DNMR-SC), multiple factors (DNMR-MF) and local DNA methylation level (DNMR-DM); (ii) search variant frequencies in publicly available databases, including ExAC, ESP6500, UK10K, 1000G and dbSNP and (iii) investigate the DNM burden to prioritize candidate genes based on the four background DNMRs using three statistical methods (TADA, Binomial and Poisson test). In conclusion, mirDNMR can be widely used to identify the genetic basis of sporadic genetic diseases.",
"fairsharing": "FAIRsharing.68f4xz",
"homepage": "https://www.wzgenomics.cn/mirdnmr/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Wenzhou Medical University",
"name": "mirDNMR",
"prefix": "NBDC02188",
"pubmeds": [
"27799474"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Organism"
]
},
"nbdc02189": {
"alt_name": "MGIS",
"description": "The Musa Germplasm Information System (MGIS) contains key information on Musa germplasm diversity, including passport data, botanical classification, morpho-taxonomic descriptors, molecular studies, plant photographs and GIS information on 4771 accessions managed in 24 collections around the world, making it the most extensive source of information on banana genetic resources.",
"fairsharing": "FAIRsharing.kthr0s",
"homepage": "https://www.crop-diversity.org/mgis/",
"information_keywords": [
"3D structure",
"Phenotype",
"Method",
"Bioresource",
"Image/Movie"
],
"maintainer": "Bioversity International",
"name": "Musa Germplasm Information System",
"prefix": "NBDC02189",
"pubmeds": [
"29220435"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02190": {
"alt_name": "BGH",
"description": "The Banana Genome Hub centralises databases of genetic and genomic data for the Musa acuminata crop, and is the official portal for the Musa genome resources.",
"fairsharing": "FAIRsharing.p90p8q",
"homepage": "http://banana-genome-hub.southgreen.fr/",
"information_keywords": [
"Sequence",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "CIRAD (International Cooperation Center for Agricultural Research for Development)||Bioversity International||South Green",
"name": "Banana Genome Hub",
"prefix": "NBDC02190",
"pubmeds": [
"23707967"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02191": {
"description": "STOREDB provides infrastructure for sharing data and resources in radiation biology and epidemiology. It is a platform for the archiving and sharing of primary data and outputs of all kinds, including epidemiological and experimental data, from research on the effects of radiation. It also provides a directory of bioresources and databases containing information and materials that investigators are willing to share. STORE supports the creation of a radiation research commons.",
"fairsharing": "FAIRsharing.6h8d2r",
"homepage": "https://www.storedb.org",
"information_keywords": [
"Expression",
"Method",
"Bibliography/Documents",
"Repository"
],
"maintainer": "CONCERT-European Joint Programme for the Integration of Radiation Protection Research",
"name": "STOREDB",
"prefix": "NBDC02191",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease",
"Organism"
]
},
"nbdc02192": {
"description": "DrugCentral is online drug information that provides information on active ingredients, chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic mode of action. DrugCentral monitors FDA, EMA, and PMDA for new drug approval on regular basis to ensure currency of the resource. This resource was created and is maintained by the Division of Translational Informatics at the University of New Mexico School of Medicine.",
"fairsharing": "FAIRsharing.3me82d",
"homepage": "http://drugcentral.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Chemical structure",
"Interaction/Pathway",
"Phenotype"
],
"maintainer": "UNM School of Medicine",
"name": "DrugCentral",
"prefix": "NBDC02192",
"pubmeds": [
"27789690"
],
"status": "Active",
"target_keywords": [
"Chemical compound",
"Drug"
]
},
"nbdc02193": {
"alt_name": "TCRD",
"description": "TCRD is the central resource behind the Illuminating the Druggable Genome Knowledge Management Center (IDG-KMC). TCRD contains information about human targets, with special emphasis on four families of targets that are central to the NIH IDG initiative: GPCRs, kinases, ion channels and nuclear receptors. Olfactory GPCRs (oGPCRs) are treated as a separate family. A key aim of the KMC is to classify the development/druggability level of targets. The official public portal for TCRD is Pharos (pharos.nih.gov). Based on modern web design principles the Pharos interface provides facile access to all data types collected by the KMC. Given the complexity of the data surrounding any target, efficient and intuitive visualization has been a high priority, to enable users to quickly navigate & summarize search results and rapidly identify patterns. A critical feature of the interface is the ability to perform flexible search and subsequent drill down of search results. Underlying the interface is a RESTful API that provides programmatic access to all KMC data, allowing for easy consumption in user applications.",
"fairsharing": "FAIRsharing.1gn47b",
"homepage": "http://juniper.health.unm.edu/tcrd/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "European Commission FP7||Icahn School of Medicine at Mount Sinai||UNM School of Medicine||University of Miami School of Medicine",
"name": "Target Central Resource Database",
"prefix": "NBDC02193",
"pubmeds": [
"27903890"
],
"status": "Active",
"target_keywords": [
"Drug",
"Protein"
]
},
"nbdc02194": {
"alt_name": "BEGDB",
"description": "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate QM calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods.",
"fairsharing": "FAIRsharing.nbe4fq",
"homepage": "http://www.begdb.org/",
"information_keywords": [
"Interaction/Pathway",
"3D structure",
"Chemical structure"
],
"maintainer": "IOCB (Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences)",
"name": "The Benchmark Energy & Geometry Database",
"prefix": "NBDC02194",
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc02195": {
"alt_name": "HCVIVdb",
"description": "HCVIVdb is a database of published variations observed within the internal ribosome entry site (IRES) of the hepatitis C Virus.",
"fairsharing": "FAIRsharing.pj6a0t",
"homepage": "http://www.hcvivdb.org/",
"information_keywords": [
"Expression",
"Bibliography/Documents"
],
"name": "Hepatitis C Virus Ires Variation Database",
"prefix": "NBDC02195",
"pubmeds": [
"27527702"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Organism",
"Health/Disease"
]
},
"nbdc02196": {
"alt_name": "SWICZ",
"description": "Proteomics database for streptomyces and caulobacter and neisseria. Unique database in the field, containing knowledge based data of time series of protein expression for various stages of development of the given species.",
"fairsharing": "FAIRsharing.1h7yt4",
"homepage": "http://proteom.biomed.cas.cz/",
"information_keywords": [
"Expression"
],
"maintainer": "Biozentrum, University of Basel",
"name": "Swiss-Czech Proteomics Server",
"prefix": "NBDC02196",
"pubmeds": [
"14625849",
"16400688",
"15378695",
"17133369"
],
"status": "Active",
"target_keywords": [
"Protein",
"Organism"
]
},
"nbdc02197": {
"alt_name": "FoF",
"description": "The Face Of Fungi database allows deposition of taxonomic data, phenotypic details and other useful data. Its aim is to enhance current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database allows access to comprehensive metadata including descriptions of voucher and type specimens.",
"fairsharing": "FAIRsharing.jr31ex",
"homepage": "http://www.facesoffungi.org/",
"information_keywords": [
"Taxonomy",
"Phenotype",
"Method",
"Image/Movie"
],
"name": "Face Of Fungi",
"prefix": "NBDC02197",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02198": {
"description": "Open Targets designed and developed an integration and visualization platform that provides evidence about the association of known and potential drug targets with diseases. The platform is designed to support identification and prioritization of biological targets for follow-up. Each drug target is linked to a disease using integrated genome-wide data from a broad range of data sources. The platform provides either a target-centric workflow to identify diseases that may be associated with a specific target, or a disease-centric workflow to identify targets that may be associated with a specific disease. Users can easily transition between these target- and disease-centric workflows.",
"fairsharing": "FAIRsharing.3f9n4y",
"homepage": "https://www.targetvalidation.org",
"information_keywords": [
"Bibliography/Documents",
"Phenotype",
"Interaction/Pathway",
"Method"
],
"maintainer": "BioGen||Wellcome Sanger Institute",
"name": "Open Targets",
"prefix": "NBDC02198",
"pubmeds": [
"27899665"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Drug"
]
},
"nbdc02199": {
"description": "The MalaCards human disease database (http://www.malacards.org/) is an integrated compendium of annotated diseases mined from 68 data sources. MalaCards has a web card for each of βΌ20 000 disease entries, in six global categories. It portrays a broad array of annotation topics in 15 sections, including Summaries, Symptoms, Anatomical Context, Drugs, Genetic Tests, Variations and Publications. The Aliases and Classifications section reflects an algorithm for disease name integration across often-conflicting sources, providing effective annotation consolidation. A central feature is a balanced Genes section, with scores reflecting the strength of disease-gene associations. This is accompanied by other gene-related disease information such as pathways, mouse phenotypes and GO-terms, stemming from MalaCards' affiliation with the GeneCards Suite of databases. MalaCards' capacity to inter-link information from complementary sources, along with its elaborate search function, relational database infrastructure and convenient data dumps, allows it to tackle its rich disease annotation landscape, and facilitates systems analyses and genome sequence interpretation. MalaCards adopts a 'flat' disease-card approach, but each card is mapped to popular hierarchical ontologies (e.g. International Classification of Diseases, Human Phenotype Ontology and Unified Medical Language System) and also contains information about multi-level relations among diseases, thereby providing an optimal tool for disease representation and scrutiny.",
"fairsharing": "FAIRsharing.e4r5nj",
"homepage": "http://www.malacards.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "Weizmann Institute of Science",
"name": "MalaCards",
"prefix": "NBDC02199",
"pubmeds": [
"27899610"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc02200": {
"description": "MorphoBank is a web application providing an online database and workspace for evolutionary research in systematics (the science of determining the evolutionary relationships among species). MorphoBank invites scientists producing peer-reviewed research to upload images and affiliate data with those images (labels, species names, etc.). MorphoBank also offers a platform for live collaboration on phylgoenetic matrices by teams in a private workspace where they can also affiliate images with phylogenetic matrices.\nMorphoBank stores digital versions of both text and image-based observations on phenotypes. Phylogenetic matrices (Nexus or TNT format), particularly phenotypical matrices, 2D (including JPEG, GIF, PNG, TIFF and Photoshop) and 3D (PLY, STL, ZIP, TIFF and DCM) image data and video (MPEG-4, QuickTime and WindowsMedia). MorphoBank also offer a Documents folder for additional files about their research such as pdfs, word documents, and text files (e.g., morphometric data, phylogenetic trees).",
"fairsharing": "FAIRsharing.1y63n8",
"homepage": "https://data-search.nerc.ac.uk/geonetwork/srv/eng/catalog.search#/home",
"information_keywords": [
"Phenotype",
"Taxonomy",
"Image/Movie",
"Repository"
],
"name": "MorphoBank",
"prefix": "NBDC02200",
"pubmeds": [
"24987572",
"25861210"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02201": {
"alt_name": "VFB",
"description": "VFB is an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of Drosophila melanogaster. Our goal is to make it easier for researchers to find relevant anatomical information and reagents.\nWe integrate the neuroanatomical and expression data from the published literature, as well as image datasets onto the same brain template, making it possible to run cross searches, find similar neurons and compare image data on our 3D Viewer.",
"fairsharing": "FAIRsharing.nzaz6z",
"homepage": "http://www.virtualflybrain.org/",
"information_keywords": [
"Expression",
"Image/Movie",
"Interaction/Pathway",
"3D structure"
],
"maintainer": "FlyBase administrators||MRC Human Genetics Unit, University of Edinburgh||LMB (MRC Laboratory of Molecular Biology)||University of Cambridge||University of Edinburgh",
"name": "Virtual Fly Brain",
"prefix": "NBDC02201",
"pubmeds": [
"22180411",
"22402613",
"22676296"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"Genome/Gene",
"Organism"
]
},
"nbdc02202": {
"description": "GBIF Spain maintains this data repository, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). Able to assign DOIs to datasets, it ensures the data is disseminated in standardized format in order to facilitate wider reuse and integration of the data, for example into GBIF.org. GBIF Spain supports researchers in Spain by providing them helpdesk assistance and by hosting their data for free in this repository. It has already been used to publish/host data in scientific publications, e.g. http://dx.doi.org/10.15470/qomfu6 which is the data this Scientific Data publication is based on: http://dx.doi.org/10.1038/sdata.2016.85",
"fairsharing": "FAIRsharing.bk3z3n",
"homepage": "http://www.gbif.es/ipt/",
"information_keywords": [
"Taxonomy",
"Bibliography/Documents"
],
"maintainer": "GBIF (Global Biodiversity Information Facility in Spain)||GBIF (Global Biodiversity Information Facility, Copenhagen, Denmark)",
"name": "GBIF Spain IPT - GBIF Spain Repository",
"prefix": "NBDC02202",
"pubmeds": [
"27676217"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02203": {
"description": "A linked data server designed for ontologies. Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis. Ontobee dynamically dereferences and presents individual ontology term URIs to (i) HTML web pages for user-friendly web browsing and navigation, and to (ii) RDF source code for Semantic Web applications. Ontobee is the default linked data server for most OBO Foundry library ontologies. Ontobee has also been used for many non-OBO ontologies.",
"fairsharing": "FAIRsharing.q8fx1b",
"homepage": "http://www.ontobee.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "He Group, University of Michigan Medical School",
"name": "Ontobee",
"prefix": "NBDC02203",
"pubmeds": [
"27733503"
],
"status": "Active"
},
"nbdc02204": {
"description": "The Atlas of Living Australia (GBIF Australia) maintains this data repository in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). Able to assign DOIs to datasets, it ensures the data is disseminated in standardized format in order to facilitate wider reuse and integration of the data, for example into GBIF.org. GBIF Australia supports researchers in Australia by providing them helpdesk assistance and by hosting their data for free in this repository.",
"fairsharing": "FAIRsharing.v1h8rk",
"homepage": "https://bie.ala.org.au/search?q=",
"information_keywords": [
"Taxonomy",
"Bibliography/Documents"
],
"maintainer": "GBIF (Global Biodiversity Information Facility)||Atlas of Living Australia",
"name": "Atlas of Living Australia IPT - GBIF Australia Repository",
"prefix": "NBDC02204",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02205": {
"description": "Canadensys maintains this data repository, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). Able to assign DOIs to datasets, it ensures the data is disseminated in standardized format in order to facilitate wider reuse and integration of the data, for example into GBIF.org. Canadensys supports researchers in Canada by providing them helpdesk assistance and by hosting their data for free in this repository.",
"fairsharing": "FAIRsharing.v2sjcy",
"homepage": "http://data.canadensys.net/ipt/",
"information_keywords": [
"Taxonomy",
"Bibliography/Documents"
],
"maintainer": "Canadensys, Universite de Montreal Biodiversity Centre||GBIF (Global Biodiversity Information Facility)",
"name": "Canadensys IPT - GBIF Canadensys Repository",
"prefix": "NBDC02205",
"pubmeds": [
"24198712"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02206": {
"description": "The Colombian Biodiversity Information System (SiB Colombia) maintains this data repository, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). Able to assign DOIs to datasets, it ensures the data is disseminated in standardized format in order to facilitate wider reuse and integration of the data, for example into GBIF.org. SiB Colombia supports researchers in Colombia by providing them helpdesk assistance and by hosting their data for free in this repository.",
"fairsharing": "FAIRsharing.t80940",
"homepage": "http://ipt.biodiversidad.co/sib/",
"information_keywords": [
"Taxonomy",
"Bibliography/Documents"
],
"maintainer": "GBIF (Global Biodiversity Information Facility)||SiB Colombia",
"name": "SiB Colombia IPT - GBIF Colombia Repository",
"prefix": "NBDC02206",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02207": {
"description": "SureChEMBL is a publicly available large-scale resource containing compounds extracted from the full text, images and attachments of patent documents. The data are extracted from the patent literature according to an automated text and image-mining pipeline on a daily basis. SureChEMBL provides access to a previously unavailable, open and timely set of annotated compound-patent associations, complemented with sophisticated combined structure and keyword-based search capabilities against the compound repository and patent document corpus. Currently, the database contains 17 million compounds extracted from 14 million patent documents.",
"fairsharing": "FAIRsharing.q2n5wk",
"homepage": "https://www.surechembl.org",
"information_keywords": [
"Chemical structure",
"3D structure",
"Image/Movie",
"Bibliography/Documents"
],
"name": "SureChEMBL",
"prefix": "NBDC02207",
"pubmeds": [
"26582922"
],
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc02208": {
"description": "REGULATOR is a metazoan transcription factor (TF) and maternal factor resource, specifically designed for developmental biology studies. Maternal factors were expressed in unfertilized eggs, and gradually reduced as time goes on. In order to reduce the search space of developmentally important genes, we only focused on those specifically expressed genes in egg stages, whose expression value β₯ 8 times than the mean value of others. There are ~77 metazoan species in the current database. The identification of TFs was based on statistical information similarity of protein features.",
"fairsharing": "FAIRsharing.ey49c6",
"homepage": "http://www.bioinformatics.org/regulator",
"information_keywords": [
"Sequence",
"Expression",
"Classification",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Laboratory of Developmental Biology, Graduate School of Science, Osaka University",
"name": "REGULATOR",
"prefix": "NBDC02208",
"pubmeds": [
"25880930"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Organism"
]
},
"nbdc02209": {
"alt_name": "BCCM/GeneCorner",
"description": "The BCCM/GeneCorner Plasmid Collection warrants the long-term storage and distribution of plasmids, microbial host strains and DNA libraries of fundamental, biotechnological, educational or general scientific importance.\nThe focus is on the collection of recombinant plasmids that can replicate in a microbial host strain.\nBCCM/GeneCorner also accepts natural and genetically modified animal or human cell lines, including hybridomas, as well as other genetic material, in the safe deposit and patent deposit collections.",
"fairsharing": "FAIRsharing.k4yzh",
"homepage": "http://www.genecorner.ugent.be/",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "VIB (Flanders Institute for Biotechnology)",
"name": "BCCM/GeneCorner Plasmid Collection",
"prefix": "NBDC02209",
"pubmeds": [
"27177818",
"25882545"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Cell/Organelle",
"DNA"
]
},
"nbdc02210": {
"alt_name": "KBase",
"description": "KBase is the first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase aims to provide a knowledgebase: an integrated environment where knowledge and insights are created and multiplied.",
"fairsharing": "FAIRsharing.jsxqrk",
"homepage": "https://www.kbase.us",
"information_keywords": [
"Method",
"Sequence",
"Expression",
"Interaction/Pathway",
"Repository"
],
"maintainer": "LBNL (Lawrence Berkeley National Laboratory)",
"name": "US Department of Energy Systems Biology Knowledgebase",
"prefix": "NBDC02210",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Metabolite"
]
},
"nbdc02211": {
"alt_name": "CAMEO",
"description": "Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB. Benchmarking results are made available as reference data for methods development.",
"fairsharing": "FAIRsharing.dq34p2",
"homepage": "http://cameo3d.org/",
"information_keywords": [
"3D structure"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)||Swiss Institute of Bioinformatics and the Biozentrum University of Basel",
"name": "Continuously Automated Model Evaluation",
"prefix": "NBDC02211",
"pubmeds": [
"23624946"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02212": {
"alt_name": "SISu",
"description": "The Sequencing Initiative Suomi (SISu) search engine offers a way to search for data on sequence variants in the Finnish population. It provides valuable summary data for researchers and clinicians as well as other researchers with an interest in genetics in Finland. With SISu, you can examine the attributes and appearance of different variants in Finnish cohorts and see their aggregate distribution in Finland visualized on a map. The SISu project is an international collaboration between multiple research groups aiming to build tools for genomic medicine.",
"fairsharing": "FAIRsharing.t1a232",
"homepage": "http://www.sisuproject.fi/",
"information_keywords": [
"Sequence",
"Geographic Distribution"
],
"maintainer": "University of Helsinki",
"name": "Sequencing Initiative Suomi",
"prefix": "NBDC02212",
"pubmeds": [
"26030606",
"25078778"
],
"status": "Inactive",
"target_keywords": [
"Genetic variation",
"Health/Disease",
"Genome/Gene",
"Organism"
]
},
"nbdc02213": {
"description": "CRISPRdb acts as a gateway to a publicly accessible database and software. It enables the easy detection of CRISPR sequences in locally-produced data and the consultation of CRISPR sequence data present in the database. It also gives information on the presence of CRISPR-associated (cas) genes when they have been annotated as such.",
"fairsharing": "FAIRsharing.7sfedh",
"homepage": "http://crispr.i2bc.paris-saclay.fr/",
"information_keywords": [
"Sequence"
],
"maintainer": "Universitè Paris-Sud 11, CNRS",
"name": "CRISPRdb",
"prefix": "NBDC02213",
"pubmeds": [
"17537822",
"17521438",
"18442988"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02214": {
"alt_name": "Dolbico",
"description": "Dolbico, the Database Of Local Biomolecular Conformers, stores DNA structural data including the information about DNA local spatial arrangement. The main aim of Dolbico is the exploration of DNA structure at a local level. The analysis of local DNA structure is based on a classification system that uses 9 torsional angles (7 backbone angles and two glycosidic torsions) to categorize dinucleotides into several distinct conformational families. The implemented classification workflow is able not only to classify dinucleotides into already existing classes, but is also able to discover new classes in new solved DNA structures.",
"fairsharing": "FAIRsharing.m58329",
"homepage": "http://dolbico.org/",
"information_keywords": [
"Classification",
"3D structure"
],
"maintainer": "Laboratory of Informatics and Chemistry",
"name": "Database Of Local Biomolecular Conformers",
"prefix": "NBDC02214",
"status": "Active",
"target_keywords": [
"DNA"
]
},
"nbdc02215": {
"description": "The Ensembl genome annotation system, developed jointly by the EBI and the Wellcome Trust Sanger Institute, has been used for the annotation, analysis and display of vertebrate genomes since 2000. Since 2009, the Ensembl site has been complemented by the creation of five new sites, for bacteria, protists, fungi, plants and invertebrate metazoa, enabling users to use a single collection of (interactive and programatic) interfaces for accessing and comparing genome-scale data from species of scientific interest from across the taxonomy.",
"fairsharing": "FAIRsharing.923a0p",
"homepage": "https://ensemblgenomes.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)||Wellcome Sanger Institute",
"name": "Ensembl Genomes",
"prefix": "NBDC02215",
"pubmeds": [
"26578574"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation"
]
},
"nbdc02216": {
"description": "The Enzyme Portal integrates publicly available information about enzymes, such as small-molecule chemistry, biochemical pathways and drug compounds.",
"fairsharing": "FAIRsharing.bcdtjc",
"homepage": "http://www.ebi.ac.uk/enzymeportal/",
"information_keywords": [
"Chemical structure",
"Interaction/Pathway",
"Classification",
"Portal"
],
"name": "Enzyme Portal",
"prefix": "NBDC02216",
"pubmeds": [
"23175605"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Health/Disease",
"Drug"
]
},
"nbdc02217": {
"description": "LiceBase is a database for sea lice genomics. LiceBase provides the genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, Blast functionality and access to related high-thoughput genomics data.",
"fairsharing": "FAIRsharing.c7w81a",
"homepage": "https://licebase.org/",
"information_keywords": [
"Sequence",
"Image/Movie"
],
"maintainer": "Sea Lice Research Centre",
"name": "LiceBase",
"prefix": "NBDC02217",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"RNA",
"Organism"
]
},
"nbdc02218": {
"alt_name": "MicroScope",
"description": "MicroScope is a web-based platform for microbial comparative genome analysis and manual functional annotation. Its relational database schema stores precalculated results of syntactic and functional annotation pipelines as well as Pathway Tools and metabolic analysis specific to each genome.",
"fairsharing": "FAIRsharing.3t5qc3",
"homepage": "http://www.genoscope.cns.fr/agc/microscope/home/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Classification",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "LABGeM (Laboratoire d'Analyses Bioinformatiques pour la Genomique et le Metabolisme)",
"name": "Microbial Genome Annotation & Analysis Platform",
"prefix": "NBDC02218",
"pubmeds": [
"23193269"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02219": {
"alt_name": "BCCM/LMG",
"description": "BCCM/LMG is a bacterial culture collection currently comprising over 25.000 well-characterized strains. The biological origin of our collection is very broad, including bacterial isolates from food, clinical, veterinary, agricultural, aquatic and other environmental sources. This way, the biological resources of BCCM/LMG may serve the needs of various R&D sectors, including green, red, blue and white biotechnology.",
"fairsharing": "FAIRsharing.zfdxet",
"homepage": "http://bccm.belspo.be/about-us/bccm-lmg",
"information_keywords": [
"Phenotype",
"Bioresource"
],
"maintainer": "LM-UGent (Laboratory of Microbiology, Ghent University, Faculty of Sciences)",
"name": "BCCM/LMG Bacteria Collection",
"prefix": "NBDC02219",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02220": {
"alt_name": "BCCM/ULC",
"description": "BCCM/ULC is a small and dedicated public collection, currently containing one of the largest collections of documented (sub)polar cyanobacteria worldwide. The BCCM/ULC collection is hosted by the Centre for Protein Engineering (the Unit) of the University of Liège. The host Unit is very active in research projects concerning the cyanobacterial diversity and biogeography, with a focus on polar biotopes. The approach used is polyphasic, including the isolation of strains and culture-independent methods (DGGE, clone libraries, pyrosequencing based on the ribosomal operon sequences). The participation to field expeditions in the Antarctic and Arctic has enabled to collect samples in many locations. Moreover, taxonomic research is carried out by the host Unit to improve the classification of the cyanobacterial phylum. It is based on a polyphasic approach combining the morphological and molecular characterizations of the strains.",
"fairsharing": "FAIRsharing.1z88ee",
"homepage": "http://bccm.belspo.be/about-us/bccm-ulc",
"information_keywords": [
"Bioresource"
],
"maintainer": "CIP (Centre for Protein Engineering, University of Liege)",
"name": "BCCM/ULC Cyanobacteria Collection",
"prefix": "NBDC02220",
"pubmeds": [
"21592144"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02221": {
"alt_name": "OMA",
"description": "The OMA (βOrthologous MAtrixβ) project is a method and database for the inference of orthologs among complete genomes. The distinctive features of OMA are its broad scope and size, high quality of inferences, feature-rich web interface, availability of data in a wide range of formats and interfaces, and frequent update schedule of two releases per year.",
"fairsharing": "FAIRsharing.g3j5qj",
"homepage": "http://omabrowser.org/oma/about/",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "Dessimoz Lab,Computational Evolutionary Biology and Genomics||SIB (Swiss Institute of Bioinformatics)",
"name": "Orthologous MAtrix",
"prefix": "NBDC02221",
"pubmeds": [
"25399418",
"21113020",
"17545180",
"19055798"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02222": {
"alt_name": "BCCM/ITM",
"description": "BCCM/ITM harbours one the largest and most diverse collections of well-documented mycobacteria worldwide, including the TDR TB-Strain bank. BCCM/ITM is hosted by and sharing its research interests with the Mycobacteriology Unit at the Institute of Tropcial Medicine in Antwerp, dedicated in research to combat tuberculosis, Buruli ulcer and other mycobacterial diseases.",
"fairsharing": "FAIRsharing.5ckyx7",
"homepage": "http://bccm.belspo.be/about-us/bccm-itm",
"information_keywords": [
"Bioresource"
],
"maintainer": "ITM (Institute of Tropcial Medicine)",
"name": "BCCM/ITM Mycobacteria Collection",
"prefix": "NBDC02222",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Health/Disease",
"Drug"
]
},
"nbdc02223": {
"alt_name": "BCCM/DCG",
"description": "The BCCM/DCG public collection is the only culture collection worldwide specialized in diatoms, the most species-rich and ecologically important algal group. Other microalgae interesting from an applied perspective are included in the collection as well. Strains are kept as safe deposits or are publicly available for the scientific community. These are distributed worldwide as research or reference material to scientific institutions and companies.",
"fairsharing": "FAIRsharing.yxs0d0",
"homepage": "http://bccm.belspo.be/about-us/bccm-dcg",
"information_keywords": [
"Bioresource"
],
"maintainer": "PAE (Laboratory for Protistology & Aquatic Ecology, Ghent University)",
"name": "BCCM/DCG Diatoms Collection",
"prefix": "NBDC02223",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02224": {
"description": "The SugarBind Database (SugarBindDB) was created in 2002 as part of an effort by the MITRE Corporation (http://www.mitre.org) to develop a pathogen-capture technology based on the binding of viral, bacterial and biotoxin lectins to specific glycans (aka, sugars, carbohydrates) displayed on glycoprotein films. The database content results from compiling publicly available information. In 2010, the 2008 version of the database was migrated from MITRE Corporation to the SIB Swiss Institute of Bioinformatics in Geneva, Switzerland. From then, substantial changes in the database design and usage were undertaken and previous content was significantly extended.",
"fairsharing": "FAIRsharing.d064y6",
"homepage": "http://sugarbind.expasy.org/",
"information_keywords": [
"Chemical structure",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "SugarBind",
"prefix": "NBDC02224",
"pubmeds": [
"26578555"
],
"status": "Active",
"target_keywords": [
"Carbohydrate",
"Health/Disease"
]
},
"nbdc02225": {
"description": "The Swissregulon Database contains genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including i) Experimentally determined binding sites reported in the literature, ii) Known sequence-specificities of transcription factors, iii) ChIP-chip and ChIP-seq data, iiii) Alignments of orthologous non-coding regions.",
"fairsharing": "biodbcore-000879",
"homepage": "http://swissregulon.unibas.ch/sr/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "SwissRegulon",
"prefix": "NBDC02225",
"pubmeds": [
"17130146",
"23180783"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Epigenetics"
]
},
"nbdc02226": {
"description": "ViralZone is a web resource for viral genes and families, providing detailed molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot viral protein entries.",
"fairsharing": "FAIRsharing.tppk10",
"homepage": "http://viralzone.expasy.org/",
"information_keywords": [
"Sequence",
"Expression",
"Taxonomy"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "ViralZone",
"prefix": "NBDC02226",
"pubmeds": [
"20947564",
"23193299"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Health/Disease"
]
},
"nbdc02227": {
"alt_name": "BCCM/IHEM",
"description": "BCCM/IHEM is a fungal culture collection specialising in medical and veterinary isolates. They have almost 15000 isolates available from all over the world: yeasts and filamentous fungi, pathogens and allergenic or toxic species, reference strains and teaching material. The BCCM/IHEM collection of biomedical fungi and yeasts makes strains publicly available for medical, pharmaceutical and biological research, as well as for method validation, testing or educational purposes.\nDeposits of strains for public access are without costs for the depositor.",
"fairsharing": "FAIRsharing.etwpd5",
"homepage": "http://bccm.belspo.be/about-us/bccm-ihem",
"information_keywords": [
"Bioresource"
],
"maintainer": "WIV-ISP (Section of Mycology and Aerobiology, Scientific Institute of Public Health)",
"name": "BCCM/IHEM Biomedical Fungi and Yeasts Collection",
"prefix": "NBDC02227",
"status": "Active",
"target_keywords": [
"Health/Disease",
"Metabolite",
"Organism"
]
},
"nbdc02228": {
"alt_name": "BCCM/MUCL",
"description": "BCCM/MUCL develops and preserves the collection of filamentous fungi, yeasts and arbuscular mycorrhizal fungi, as well as the associated information, facilitates its valorization and provides services to third parties. BCCM/MUCL research is mainly focused on the following areas: fungal diversity in natural and anthropological ecosystems, agro-food (food and feed transformation and spoilage), and fungal-plant interactions.",
"fairsharing": "FAIRsharing.4njvzy",
"homepage": "http://bccm.belspo.be/about-us/bccm-mucl",
"information_keywords": [
"Classification",
"Bioresource"
],
"maintainer": "UniversitΓ© catholique de Louvain",
"name": "BCCM/MUCL Environmental and Applied Mycology",
"prefix": "NBDC02228",
"pubmeds": [
"27882467",
"26467250",
"27474519",
"27616803",
"27322722",
"27144478"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02229": {
"alt_name": "GSA",
"description": "GSA is a data repository specialized for archiving raw sequence reads. It supports data generated from a variety of sequencing platforms ranging from Sanger sequencing machines to single-cell sequencing machines and provides data storing and sharing services free of charge for worldwide scientific communities. In addition to raw sequencing data, GSA also accommodates secondary analyzed files in acceptable formats (like BAM, VCF). Its user-friendly web interfaces simplify data entry and submitted data are roughly organized as two parts, viz., Metadata and File, where the former can be further assorted into BioProject, BioSample, Experiment and Run, and the latter contains raw sequence reads.",
"fairsharing": "FAIRsharing.tdhkc6",
"homepage": "https://bigd.big.ac.cn/gsa/",
"information_keywords": [
"Sequence",
"Portal"
],
"name": "Genome Sequence Archive",
"prefix": "NBDC02229",
"pubmeds": [
"27899658",
"28387199"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"RNA"
]
},
"nbdc02230": {
"alt_name": "PMutData",
"description": "PMut Data Repository collects predictions of the pathological effect of all possible single amino acid variants on Uniref Human protein sequences. Predictions were prepared using PMut 2017 predictor (2017 version).",
"fairsharing": "FAIRsharing.tv6fxt",
"homepage": "http://mmb.irbbarcelona.org/PMut/repository",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "BSC (Barcelona Supercomputing Center)||Institute for Research in Biomedicine",
"name": "PMut Data Repository",
"prefix": "NBDC02230",
"pubmeds": [
"28453649"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Genome/Gene"
]
},
"nbdc02231": {
"alt_name": "DataONE",
"description": "DataONE is a community driven project providing access to data across multiple member repositories, supporting enhanced search and discovery of Earth and environmental data.",
"fairsharing": "FAIRsharing.yyf78h",
"homepage": "https://www.dataone.org",
"information_keywords": [
"Environment",
"Geographic Distribution",
"Taxonomy",
"Bibliography/Documents",
"Portal"
],
"maintainer": "Oak Ridge National Laboratory||University of California Santa Barbara||University of New Mexico",
"name": "Data Observation Network for Earth",
"prefix": "NBDC02231",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02232": {
"description": "Earthref.org is a compilation of of databases, networks and repositories for data and models on Earth science. This internet resource supports the quantitative understanding of the Earth as a chemical, physical and biological system.",
"fairsharing": "FAIRsharing.6cdn9x",
"homepage": "https://earthref.org",
"information_keywords": [
"Environment"
],
"maintainer": "College of Earth, Ocean and Atmospheric Science, Oregon State University||San Diego Supercomputer Center||Scripps Institution of Oceanography, University of California",
"name": "Earthref.org",
"prefix": "NBDC02232",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02233": {
"description": "mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. The aggregated data forms an interactome which includes many organisms. mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions.",
"fairsharing": "FAIRsharing.j1eyq2",
"homepage": "http://mentha.uniroma2.it/",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie"
],
"name": "mentha",
"prefix": "NBDC02233",
"pubmeds": [
"23900247"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02234": {
"alt_name": "IEDA Data Collections",
"description": "IEDA systems serve as primary community data collections for global geochemistry and marine Geoscience research to support the preservation, discovery, retrieval, and analysis of a wide range of observational field and analytical data types, enabling these data to be discovered and reused by a diverse community now and in the future. IEDA provides free and open access to all data holdings.",
"fairsharing": "FAIRsharing.be9dj8",
"homepage": "http://www.iedadata.org",
"information_keywords": [
"Environment",
"Bibliography/Documents",
"Portal"
],
"maintainer": "EarthChem||LDEO (Lamont-Doherty Earth Observatory, Columbia University)||Marine Geoscience Data System",
"name": "Interdisciplinary Earth Data Alliance Data Collections",
"prefix": "NBDC02234",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02235": {
"alt_name": "ORNL DAAC",
"description": "The ORNL DAAC mission is to assemble, distribute, and provide data services for a comprehensive archive of terrestrial biogeochemistry and ecological dynamics observations and models to facilitate research, education, and decision-making in support of NASA's Earth science.",
"fairsharing": "FAIRsharing.a833sq",
"homepage": "https://daac.ornl.gov",
"information_keywords": [
"Environment",
"Bibliography/Documents",
"Portal"
],
"maintainer": "Oak Ridge National Laboratory",
"name": "Oak Ridge National Laboratory, Distributed Active Archive Centre for Biogeochemical Dynamics",
"prefix": "NBDC02235",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02236": {
"alt_name": "HWG",
"description": "The Hardwood Genomics Project is a databases for expressed genes, genetic markers, genetic linkage maps, and reference populations. It provides lasting genomic and biological resources for the discovery and conservation of genes in hardwood trees for growth, adaptation and responses to environmental stresses such as drought, heat, insect pests and disease. All original sequence data is being deposited in NCBI's Sequence Read Archive and the genetic linkage maps and associated marker data will be available at the Dendrome database.",
"fairsharing": "FAIRsharing.srgkaf",
"homepage": "http://www.hardwoodgenomics.org/",
"information_keywords": [
"Expression",
"Sequence",
"Environment",
"Image/Movie"
],
"maintainer": "University of Tennessee, Knoxville Department of Entomology and Plant Pathology",
"name": "Hardwood Genomics Project",
"prefix": "NBDC02236",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"DNA",
"Organism"
]
},
"nbdc02237": {
"alt_name": "EIDC",
"description": "The Environmental Information Data Centre (EIDC) is a NERC Data Centre hosted by the Centre for Ecology & Hydrology (CEH). They manage nationally-important datasets concerned with the terrestrial and freshwater sciences.",
"fairsharing": "FAIRsharing.f7hyf3",
"homepage": "http://eidc.ceh.ac.uk",
"information_keywords": [
"Environment",
"Geographic Distribution",
"Bibliography/Documents",
"Portal"
],
"maintainer": "CEH (Centre for Ecology and Hydrology)||NERC (Natural Environment Research Council)",
"name": "NERC Environmental Information Data Centre",
"prefix": "NBDC02237",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02238": {
"alt_name": "SESAR Catalog",
"description": "SESAR operates a registry that distributes the International Geo Sample Number IGSN. SESAR catalogs and preserves sample metadata profiles, and provides access to the sample catalog via the Global Sample Search.",
"fairsharing": "FAIRsharing.ys5ta3",
"homepage": "https://www.geosamples.org",
"information_keywords": [
"Taxonomy",
"Environment",
"Bibliography/Documents",
"Portal"
],
"maintainer": "IEDA (Interdisciplinary Earth Data Alliance)||LDEO (Lamont-Doherty Earth Observatory, Columbia University)",
"name": "System for Earth Sample Registration Catalog",
"prefix": "NBDC02238",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02239": {
"alt_name": "LOVD",
"description": "The Leiden Open Variation Database (LOVD) provides a flexible, freely available tool for gene-centered collection and display of DNA variations. LOVD also provides patient-centered data storage and storage of NGS data, also of variants outside of genes. LOVD is open source, released under the GPL license, and is actively being improved.",
"fairsharing": "FAIRsharing.21tjj7",
"homepage": "http://www.lovd.nl/",
"information_keywords": [
"Phenotype",
"Sequence",
"Expression"
],
"maintainer": "LUMC (Leiden University Medical Center)",
"name": "Leiden Open Variation Database",
"prefix": "NBDC02239",
"pubmeds": [
"21520333",
"15977173"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"DNA",
"Genome/Gene",
"Health/Disease"
]
},
"nbdc02240": {
"alt_name": "RDA",
"description": "Research Data Australia is the data discovery service of the Australian Research Data Commons (ARDC). Research Data Australia helps you find, access, and reuse data for research from over one hundred Australian research organisations, government agencies, and cultural institutions. This services indexes metadata about the data stored by their data publishing partners, providing links out to the primary data.",
"fairsharing": "FAIRsharing.2g5kcb",
"homepage": "https://researchdata.edu.au/",
"information_keywords": [
"Bibliography/Documents",
"Portal"
],
"maintainer": "Australian National University||CSIROοΌCommonwealth Scientific and Industrial Research Organisation)||Monash University",
"name": "Research Data Australia",
"prefix": "NBDC02240",
"status": "Active"
},
"nbdc02241": {
"description": "Harvard Dataverse is a research data repository running on the open source web application Dataverse. Harvard Dataverse is fully open to the public, and allows upload and browsing of data from all fields of research. Dataverse allows users to share, preserve, cite, explore, and analyze research data. It facilitates making data available to others, and allows you to replicate others' work more easily. Researchers, data authors, publishers, data distributors, and affiliated institutions all receive academic credit and web visibility.",
"fairsharing": "FAIRsharing.t2e1ss",
"homepage": "https://dataverse.harvard.edu",
"information_keywords": [
"Bibliography/Documents",
"Portal"
],
"maintainer": "Institute for Quantitative Social Science, Harvard University||The Dataverse Project||Henry A. Murray Research Archives",
"name": "Harvard Dataverse",
"prefix": "NBDC02241",
"status": "Active"
},
"nbdc02242": {
"description": "Mendeley Data is a multidisciplinary, free-to-use open research data repository, where you can upload and share data files up to 10GB so they are archived, preserved and findable for the long-term. To ensure that research data stands the test of time, each version of a dataset is given a unique DOI, and dark archived with DANS (Data archiving and Networking Services), ensuring that every dataset and citation will be valid in perpetuity.",
"fairsharing": "FAIRsharing.3epmpp",
"homepage": "https://data.mendeley.com",
"information_keywords": [
"Bibliography/Documents",
"Portal"
],
"maintainer": "Elsevier Inc||Mendeley",
"name": "Mendeley Data",
"prefix": "NBDC02242",
"status": "Active"
},
"nbdc02243": {
"alt_name": "T3",
"description": "The Triticeae Toolbox (T3) is a repository for public wheat data generated by the Wheat Coordinated Agricultural Project (Wheat CAP). Funding is provided by the National Institute for Food and Agriculture (NIFA) and the United States Department of Agriculture (USDA). The current project is funded through NIFA's International Wheat Yield Partnership (IWYP) and part of the Agriculture and Food Research Initiative (AFRI).",
"fairsharing": "FAIRsharing.55ev2y",
"homepage": "https://triticeaetoolbox.org/",
"information_keywords": [
"Phenotype",
"Portal"
],
"name": "The Triticeae Toolbox",
"prefix": "NBDC02243",
"pubmeds": [
"27898834"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Genetic variation",
"Metabolite",
"Organism"
]
},
"nbdc02244": {
"description": "The PhenX (consensus measures for Phenotypes and eXposures) Toolkit is a web-based catalog of recommended, standard measures of phenotypes and environmental exposures for use in biomedical research. The PhenX Toolkit offers well-established, broadly validated measures of phenotypes and exposures relevant to investigators in human genomics, epidemiology, and biomedical research. The measures in the Toolkit are selected by Working Groups of domain experts using a consensus process. The Toolkit provides detailed protocols, information about the measures, and tools to help investigators incorporate PhenX measures into their studies.",
"fairsharing": "FAIRsharing.2wa7v7",
"homepage": "https://www.phenxtoolkit.org",
"information_keywords": [
"Phenotype",
"Method",
"Bibliography/Documents"
],
"maintainer": "Pat West",
"name": "PhenX Toolkit",
"prefix": "NBDC02244",
"pubmeds": [
"26132000",
"22954959"
],
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease"
]
},
"nbdc02245": {
"alt_name": "Chile NHS 2009",
"description": "The Chile National Health Survey 2009-2010 includes health status questionnaires including the SF-12, mental health questionnaires, physical activity questionnaires, and biological measurements taken during a physical exam. When using the database, please report to: jpalegre@minsal.cl",
"fairsharing": "FAIRsharing.6hb7c1",
"homepage": "http://epi.minsal.cl/bases-de-datos/",
"information_keywords": [
"Phenotype"
],
"maintainer": "Ministerio de Salud de Chile",
"name": "Chile National Health Survey 2009-2010",
"prefix": "NBDC02245",
"status": "Inactive",
"target_keywords": [
"Organism",
"Health/Disease"
]
},
"nbdc02246": {
"alt_name": "VDOG",
"description": "VDOG, Visual Database for Organelle Genome is an innovative database of the genome information in the organelles. Most of the data in VDOG are originally extracted from GeneBank, re-organized and represented.",
"fairsharing": "FAIRsharing.c7c4h1",
"homepage": "http://bio.njfu.edu.cn/VDOG",
"information_keywords": [
"Sequence"
],
"maintainer": "Nanjing Forestry University",
"name": "Visual Database for Organelle Genome",
"prefix": "NBDC02246",
"status": "Inactive",
"target_keywords": [
"Cell/Organelle",
"Genome/Gene"
]
},
"nbdc02247": {
"description": "The Belgium Biodiversity Platform maintains this data repository in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). The Belgian Biodiversity Platform is a science-policy interface that offers a privileged access to primary biodiversity data and research information. The Platform encourages interdisciplinary cooperation among scientists and serves as an interface between researchers and science-policy organizations. It provides advice on the designation of biodiversity research priorities and promotes Belgian biodiversity research in international fora.",
"fairsharing": "FAIRsharing.yd91ak",
"homepage": "http://ipt.biodiversity.be/",
"information_keywords": [
"Taxonomy"
],
"maintainer": "Belgian Biodiversity Platform",
"name": "Belgian BIF IPT - GBIF Belgium Repository",
"prefix": "NBDC02247",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02248": {
"alt_name": "MrBIF IPT - GBIF Belgium",
"description": "The Belgium Biodiversity Platform hosts this data repository on behalf of GBIF Mauritania (MrBIF) in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). More specifically, MrBIF aims to promote, coordinate and facilitate data sharing and dissemination; undertake surveys of potential biodiversity data publishers and data users; promote publication and use of biodiversity data; formulate and implement policies on biodiversity conservation; train young scientists and decisions makers; and acquire IT materials, stable Internet access and reliable power supply.",
"fairsharing": "FAIRsharing.h2v2ye",
"homepage": "http://ipt-mrbif.bebif.be/",
"information_keywords": [
"Taxonomy"
],
"maintainer": "ENS (L'Ecole Normale Superieure de Nouakchott)||Belgian Biodiversity Platform",
"name": "GBIF Mauritania IPT - GBIF Belgium",
"prefix": "NBDC02248",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02249": {
"description": "The Belgium Biodiversity Platform hosts this data repository on behalf of the SCAR Antarctic Biodiversity Portal biodiversity.aq in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). This IPT publisher serves terrestrial and marine Biodiversity data to the relevant global networks. The marine component of AntOBIS is part of an international data sharing network (Ocean Biogeographic Information System, OBIS) coordinated by the Intergovernmental Oceanographic Commission of UNESCO (United Nations Educational, Science and Cultural Organization) International Oceanographic Data and Information Exchange.",
"fairsharing": "FAIRsharing.ewyejx",
"homepage": "http://ipt.biodiversity.aq/",
"information_keywords": [
"Taxonomy"
],
"maintainer": "biodiversity.aq||Belgian Biodiversity Platform",
"name": "Antabif IPT - AntOBIS IPT - GBIF Belgium",
"prefix": "NBDC02249",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02250": {
"description": "The Belgium Biodiversity Platform hosts this data repository on behalf of BioFresh in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). Biofresh is an EU-funded international project that aims to build a global information platform for scientists and ecosystem managers with access to all available databases describing the distribution, status and trends of global freshwater biodiversity. BioFresh integrates the freshwater biodiversity competencies and expertise of 19 research institutions.",
"fairsharing": "FAIRsharing.9ff9zj",
"homepage": "http://data.freshwaterbiodiversity.eu/ipt/",
"information_keywords": [
"Taxonomy",
"Geographic Distribution",
"Environment"
],
"maintainer": "Belgian Biodiversity Platform||BioFresh",
"name": "Biofresh IPT - GBIF Belgium",
"prefix": "NBDC02250",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02251": {
"alt_name": "DanBIF IPT - GBIF Denmark",
"description": "DanBIF maintains this data repository in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). DanBIF carries out the work on making accessible the Danish, Faroese and Greenlandic resources of biodiversity data. DanBIF maintains the consensus checklist of all species known to occur in Denmark.",
"fairsharing": "FAIRsharing.p56z5r",
"homepage": "http://danbif.au.dk/ipt/",
"information_keywords": [
"Taxonomy"
],
"maintainer": "Danish Biodiversity Information Facility",
"name": "Danish Biodiversity Information Facility IPT - GBIF Denmark",
"prefix": "NBDC02251",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02252": {
"alt_name": "FinBIF Digitarium IPT - GBIF Finland",
"description": "Finnish Biodiversity Information Facility (FinBIF) maintains this data repository in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). FinBIF compiles Finnish biodiversity information to one single service for open access sharing and contains information on species, their occurrences, distribution and scientific collections.",
"fairsharing": "FAIRsharing.58bd67",
"homepage": "http://ipt.digitarium.fi/",
"information_keywords": [
"Taxonomy",
"Geographic Distribution",
"Environment"
],
"maintainer": "Digitarium - Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland||Finnish Museum of Natural History",
"name": "Finnish Biodiversity Information Facility Digitarium IPT - GBIF Finland",
"prefix": "NBDC02252",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02253": {
"description": "GBIF France aims to collect all primary biodiversity data hosted in France, regardless of whether they concern the biodiversity of French territory or the rest of the world. GBIF France also supports additional countries' nodes with the hosting of their IPTs.",
"fairsharing": "FAIRsharing.pq1njd",
"homepage": "http://ipt.gbif.fr/",
"information_keywords": [
"Taxonomy"
],
"maintainer": "GBIF France||ANR (The French National Research Agency)",
"name": "GBIF France IPT - GBIF France",
"prefix": "NBDC02253",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02254": {
"description": "GBIF France hosts this data repository on behalf of GBIF Benin in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT).",
"fairsharing": "FAIRsharing.ptp5tb",
"homepage": "http://ipt-benin.gbif.fr/",
"information_keywords": [
"Taxonomy"
],
"maintainer": "GBIF France",
"name": "GBIF Benin IPT - GBIF France",
"prefix": "NBDC02254",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02255": {
"description": "GBIF France hosts this data repository on behalf of GBIF Guinea in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). GBIF-GUINEE is established within the Centre d'Observation de Surveillance et d'Information Environnementales (COSIE) , the signatory of the GBIF Memorandum of Understanding, as a specialized team working on the collection of biodiversity occurrence data from data publishers to enable their publication on the Internet. The node of GBIF-GUINEE is mandated to collect species occurrence data on the national and international level in order to make these available to data users and decision makers. The data collected and disseminated by COSIE enable the generation of statistics to support decision making by authorities, in order to integrate ecological considerations into programmes and plans for the socio-economic development of Guniea. These ecological considerations have the goal of protection of the environment and biological diversity.",
"fairsharing": "FAIRsharing.hwx5xr",
"homepage": "http://ipt-guinee.gbif.fr/",
"information_keywords": [
"Taxonomy",
"Geographic Distribution",
"Environment"
],
"maintainer": "GBIF France",
"name": "GBIF Guinea IPT - GBIF France",
"prefix": "NBDC02255",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02256": {
"alt_name": "MadBIF IPT - GBIF France",
"description": "GBIF France hosts this data repository on behalf of Madagascar Biodiversity Information Facility (MadBIF) in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT). Most data collected within Madagascar is not documented and is only accessible to the person/team involved in the project for which the data has been collected. Moreover, there is a lack of data policy within the institutions of Madagascar. As a consequence, data knowledge is linked to individuals and disappears with them. The only public information that can be found is the information located in herbaria, museums, and various literature. MadBIF aims to promote and support publication of biodiversity data by data holders.",
"fairsharing": "FAIRsharing.gdj215",
"homepage": "http://ipt.madbif.mg/",
"information_keywords": [
"Taxonomy"
],
"maintainer": "CNRE (Centre National de Recherches sur l'Environnement)||GBIF France",
"name": "Madagascar Biodiversity Information Facility IPT - GBIF France",
"prefix": "NBDC02256",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02257": {
"description": "GBIF France hosts this data repository on behalf of GBIF Togo in collaboration with the GBIF Secretariat, built using an installation of the GBIF Integrated Publishing Toolkit (IPT).",
"fairsharing": "FAIRsharing.9ntzb2",
"homepage": "http://ipt-togo.gbif.fr/",
"information_keywords": [
"Taxonomy"
],
"maintainer": "GBIF France",
"name": "GBIF Togo IPT - GBIF France",
"prefix": "NBDC02257",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02258": {
"description": "GBIF Norway is the Norwegian participant node in the Global Biodiversity Information Facility, GBIF. They make primary data on biological diversity from the Norwegian collections and observation databases freely available and coordinate and support GBIF-related activities and data use in Norway.",
"fairsharing": "FAIRsharing.1gx1wq",
"homepage": "https://data.gbif.no/ipt/",
"information_keywords": [
"Taxonomy"
],
"maintainer": "Natural History Museum at the University of Oslo||GBIF Norway",
"name": "Norway IPT - GBIF Norway",
"prefix": "NBDC02258",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc02259": {
"description": "GBIF Portugal promotes the free and open sharing of primary biodiversity data and enriches knowledge of Portuguese and World biodiversity. It promotes the integration of Portuguese data publishers and resources of biodiversity information on the GBIF network, and the availability of biodiversity data for the scientific research and societal needs.",
"fairsharing": "FAIRsharing.gncawv",
"homepage": "http://ipt.gbif.pt/ipt/",
"information_keywords": [
"Taxonomy"
],
"maintainer": "Instituto Superior de Agronomia, University of Lisbon||GBIF Portugal",
"name": "Portugal IPT - GBIF Portugal",
"prefix": "NBDC02259",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02260": {
"alt_name": "SANBI IPT - GBIF South Africa",
"description": "The South African National Biodiversity Institute (SANBI) leads and coordinates research, and monitors and reports on the state of biodiversity in South Africa. The institute provides knowledge and information, gives planning and policy advice and pilots best-practice management models in partnership with stakeholders. SANBI engages in ecosystem restoration and rehabilitation, leads the human capital development strategy of the sector and manages the National Botanical Gardens as 'windows' to South Africa's biodiversity for enjoyment and education.",
"fairsharing": "FAIRsharing.ph9sby",
"homepage": "http://197.189.235.147:8080/iptsanbi/",
"information_keywords": [
"Taxonomy"
],
"maintainer": "SANBI (South African National Biodiversity Institute)",
"name": "South African National Biodiversity Institute IPT - GBIF South Africa",
"prefix": "NBDC02260",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02261": {
"description": "GBIF-Sweden serves researchers, public authorities and others interested in biodiversity as the Swedish hub for information and international exchange of data on the biological diversity of the world.\nThe ambition of GBIF-Sweden is to continuously harvest and publicly present up-to-date biodiversity data hosted by Swedish institutions and government authorities to stakeholders around the world through the international GBIF portal, in accordance with Swedish commitments under the international GBIF agreement. Where appropriate, GBIF-Sweden also aims to accumulate information about Swedish biodiversity kept elsewhere in the world and provide it to Swedish stakeholders in an appropriate form. Finally, GBIF-Sweden aims to play a leading role in stimulating digitization efforts aimed at increasing the quantity and quality of content provided to GBIF from Swedish institutions.",
"fairsharing": "FAIRsharing.7tx9zj",
"homepage": "http://www.gbif.se/ipt",
"information_keywords": [
"Taxonomy"
],
"maintainer": "GBIF Sweden",
"name": "Sweden IPT - GBIF Sweden",
"prefix": "NBDC02261",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02262": {
"alt_name": "TaiBIF IPT - GBIF Taiwan",
"description": "TaiBIF (Taiwan Biodiversity Information Facility) is the Taiwan portal of GBIF. Although Taiwan's land is not spacious, it possesses extraordinarily abundant biodiversity resources and many endemic species. TaiBIF is in charge of integrating Taiwan's biodiversity information, including lists of species and local experts, illustrations of species, introduction of endemic species and invasive species, Taiwan's terrestrial and marine organisms, biodiversity literature, geographical and environmental information, information about relevant institutions, organizations, projects, and observation spots, the Catalog of Life (a list of Taiwanese endemic species), and publications.",
"fairsharing": "FAIRsharing.y2vm4r",
"homepage": "http://ipt.taibif.tw/",
"information_keywords": [
"Taxonomy",
"Geographic Distribution",
"Environment"
],
"maintainer": "Taiwan Biodiversity Information Facility",
"name": "Taiwan Biodiversity Information Facility IPT - GBIF Taiwan",
"prefix": "NBDC02262",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02263": {
"alt_name": "OBIS-USA - USGS",
"description": "OBIS-USA brings together marine biological occurrence data - recorded observations of identifiable marine species at a known time and place, collected primarily from U.S. Waters or with U.S. funding. OBIS-USA is part of an international data sharing network (Ocean Biogeographic Information System, OBIS) coordinated by the Intergovernmental Oceanographic Commission, of UNESCO (United Nations Educational, Science and Cultural Organization International Oceanographic Data and Information Exchange.",
"fairsharing": "FAIRsharing.hvecpt",
"homepage": "https://www1.usgs.gov/obis-usa/ipt",
"information_keywords": [
"Taxonomy",
"Geographic Distribution",
"Environment"
],
"maintainer": "USGS (United States Geological Survey)",
"name": "Ocean Biogeographic Information System USA IPT - USGS",
"prefix": "NBDC02263",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02264": {
"alt_name": "NAS IPT - USGS",
"description": "The Nonindigenous Aquatic Species (NAS) information resource for the United States Geological Survey has been established as a central repository for spatially referenced biogeographic accounts of introduced aquatic species. The program provides scientific reports, online/realtime queries, spatial data sets, distribution maps, and general information. The data are made available for use by biologists, interagency groups, and the general public. The geographical coverage is the United States.",
"fairsharing": "FAIRsharing.7tz5g8",
"homepage": "https://nas.er.usgs.gov/ipt/",
"information_keywords": [
"Taxonomy",
"Geographic Distribution",
"Environment"
],
"maintainer": "USGS (United States Geological Survey)",
"name": "Nonindigenous Aquatic Species NAS IPT - USGS",
"prefix": "NBDC02264",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02265": {
"alt_name": "BISON IPT - USGS",
"description": "The U.S. node to GBIF represents an integral part of the U.S. Geological Survey's activities to collect, organize and share biological information. As with other initiatives, the U.S. GBIF node streamlines access to U.S. biodiversity information and links it with broader geoscience data to address critical societal issues. BISON is the primary project contributing to the node. It provides a specialized view of GBIF records for the U.S. and assists with provision of U.S. records to GBIF.",
"fairsharing": "FAIRsharing.w2vev5",
"homepage": "https://bison.usgs.gov/ipt/",
"information_keywords": [
"Taxonomy"
],
"maintainer": "USGS (United States Geological Survey)",
"name": "Biodiversity Information Serving Our Nation IPT - USGS",
"prefix": "NBDC02265",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02266": {
"description": "VertNet uses the Integrated Publishing Toolkit (IPT) to host published biodiversity data on the VertNet IPT for its participating institutions. The IPT is a free, open source web application designed to publish primary occurrence data, species checklists and taxonomies, and associated dataset metadata available for use on the Internet. Data are published as web-based Darwin Core Archives (simple ZIP files that contain tab-delimited or comma-separated text files organized using the Darwin Core Standard).",
"fairsharing": "FAIRsharing.x4zrrg",
"homepage": "http://ipt.vertnet.org:8080/ipt/",
"information_keywords": [
"Taxonomy"
],
"maintainer": "VertNet",
"name": "VertNet IPT",
"prefix": "NBDC02266",
"status": "Inactive",
"target_keywords": [
"Organism"
]
},
"nbdc02267": {
"description": "The foundation of chemical safety testing relies on chemistry information such as high-quality chemical structures and physical chemical properties. This information is used by scientists to predict the potential health risks of chemicals.\nThe Dashboard is part of a suite of dashboards developed by EPA to help evaluate the safety of chemicals. It provides access to a variety of information on over 700,000 chemicals currently in use.\nWithin the Dashboard, users can access chemical structures, experimental and predicted physicochemical and toxicity data, and additional links to relevant websites and applications. It maps curated physicochemical property data associated with chemical substances to their corresponding chemical structures.\nThese data are compiled from sources including the EPA's computational toxicology research databases, and public domain databases such as the National Center for Biotechnology Information's PubChem database.",
"fairsharing": "FAIRsharing.tfj7gt",
"homepage": "https://comptox.epa.gov/dashboard",
"information_keywords": [
"Chemical structure",
"Method"
],
"maintainer": "US Environmental Protection Agency",
"name": "EPA Comptox Chemicals Dashboard",
"prefix": "NBDC02267",
"pubmeds": [
"28475325",
"27367298",
"26812473",
"27885862",
"27987027"
],
"status": "Active",
"target_keywords": [
"Chemical compound",
"Health/Disease"
]
},
"nbdc02268": {
"description": "Built by recent PhD graduates, BenchSci is a free platform designed to help biomedical research scientists quickly and easily identify validated antibodies from publications. Using various filters including techniques, tissue, cell lines, and more, scientists can find out published data along with the antibody that match specific experimental contexts within seconds. Free registration & access for academic research scientists. Platform demo: https://youtu.be/VIS4CPnuQEw",
"fairsharing": "FAIRsharing.fwg0qf",
"homepage": "https://www.benchsci.com/",
"information_keywords": [
"Interaction/Pathway",
"Method",
"Bibliography/Documents"
],
"maintainer": "BenchSci",
"name": "BenchSci",
"prefix": "NBDC02268",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02269": {
"alt_name": "XMetDB",
"description": "XMetDB is an open access and open source database and web interface for the submission and retrieval of experimental metabolite data for drugs and other xenobiotics. It will also feature an open API for access to the database.",
"fairsharing": "FAIRsharing.bkxpmp",
"homepage": "http://www.xmetdb.org/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Department of Pharmaceutical Biosciences, Uppsala University||Department of Drug Design and Pharmacology, University of Copenhagen||Universiteit Maastricht||IDEAconsult",
"name": "Xenobiotics Metabolism Database",
"prefix": "NBDC02269",
"pubmeds": [
"27651835"
],
"status": "Active",
"target_keywords": [
"Drug"
]
},
"nbdc02270": {
"description": "The iDigBio IPT is a website that hosts biodiversity data and serves it in a standardised format, allowing aggregators such as iDigBio to index it into their portals whenever the data is applicable to that portal.",
"fairsharing": "FAIRsharing.ewh295",
"homepage": "http://ipt.idigbio.org",
"information_keywords": [
"Taxonomy"
],
"name": "iDigBio IPT",
"prefix": "NBDC02270",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02271": {
"alt_name": "HIPPIE",
"description": "HIPPIE integrates human protein-protein interactions from several manually curated source databases. It provides a web tool to query the interaction data, generate highly reliable, context-specific interaction networks and to make sense out of them.",
"fairsharing": "FAIRsharing.3pt56w",
"homepage": "http://cbdm.uni-mainz.de/hippie/",
"information_keywords": [
"Interaction/Pathway"
],
"name": "Human Protein-Protein Interaction rEference",
"prefix": "NBDC02271",
"pubmeds": [
"27794551",
"23300433",
"22348130"
],
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease"
]
},
"nbdc02272": {
"alt_name": "HMCA",
"description": "The Health and Medical Care Archive (HMCA) is the data archive of the Robert Wood Johnson Foundation (RWJF), the largest philanthropy devoted exclusively to health and health care in the United States. Operated by the Inter-university Consortium for Political and Social Research (ICPSR) at the University of Michigan, HMCA preserves and disseminates data collected by selected research projects funded by the Foundation and facilitates secondary analyses of the data. The data collections in HMCA include surveys of health care professionals and organizations, investigations of access to medical care, surveys on substance abuse, and evaluations of innovative programs for the delivery of health care. Our goal is to increase understanding of health and health care in the United States through secondary analysis of RWJF-supported data collections.",
"fairsharing": "FAIRsharing.szj2xw",
"homepage": "https://www.icpsr.umich.edu/web/pages/HMCA/index.html",
"information_keywords": [
"Bibliography/Documents",
"Portal"
],
"maintainer": "ICPSR (Inter-university Consortium for Political and Social Research)",
"name": "Health and Medical Care Archive",
"prefix": "NBDC02272",
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease"
]
},
"nbdc02273": {
"alt_name": "DSDR",
"description": "Data Sharing for Demographic Research (DSDR) supports the demographic community by disseminating, archiving, and preserving data relevant for population studies. The mission of DSDR is to serve as a locus of information for researchers who collect, analyze, and distribute primary data as well as researchers who analyze secondary data. DSDR aims to foster interdisciplinary collaborations between Demography and other disciplines.\nDSDR is located within ICPSR and supported by the Population Dynamics Branch (PDB) of the Eunice Kennedy Shriver National Institute of Child Health and Human Development (U24 HD048404).",
"fairsharing": "FAIRsharing.v4mara",
"homepage": "http://dsdr.icpsr.umich.edu/",
"information_keywords": [
"Environment",
"Repository"
],
"maintainer": "ICPSR (Inter-university Consortium for Political and Social Research)",
"name": "Data Sharing for Demographic Research",
"prefix": "NBDC02273",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Health/Disease"
]
},
"nbdc02274": {
"alt_name": "OBIS IPT",
"description": "OBIS provides data hosting and helpdesk support to publishers of marine data around the globe. EurOBIS/Flanders Marine Institute (VLIZ) hosts multiple IPT installations on behalf of various OBIS Nodes. Currently, there are more than 20 OBIS Nodes around the world connecting 500 institutions from 56 countries.",
"fairsharing": "FAIRsharing.k297hk",
"homepage": "http://ipt.vliz.be/",
"information_keywords": [
"Taxonomy",
"Environment",
"Portal"
],
"maintainer": "IOBIS",
"name": "Ocean Biogeographic Information System IPT",
"prefix": "NBDC02274",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02275": {
"alt_name": "eyeGENE",
"description": "The National Ophthalmic Disease Genotyping and Phenotyping Network (eyeGENE) is a genomic medicine initiative created by the National Eye Institute (NEI), part of the National Institutes of Health (NIH), in partnership with clinics and laboratories across the vision research community. The core mission of eyeGENE is to facilitate research into the causes and mechanisms of rare inherited eye diseases and accelerate pathways to treatments. eyeGENE was designed to achieve this goal through clinical and molecular diagnosis coupled with granting controlled access to clinical and genetic information in a data repository, to DNA in a biorepository, and to individuals consented to participate in research and clinical trials.\nThe eyeGENE Network currently includes a Coordinating Center at the NEI, CLIAβ -approved molecular genetic testing laboratories around the Nation, a patient registry, controlled-access centralized biorepository for DNA, and a curated de-identified genotype / phenotype database.\nThese components stimulate patient and eye health care provider interest in genetics-based clinical care and generate involvement in ophthalmic research, thereby accelerating vision research and treatment development for these diseases.",
"fairsharing": "FAIRsharing.5nnxqn",
"homepage": "https://eyegene.nih.gov",
"information_keywords": [
"Phenotype",
"Ontology/Terminology/Nomenclature",
"Bibliography/Documents"
],
"maintainer": "NEI NIH(National Eye Institute)",
"name": "eyeGENE: The National Ophthalmic Genotyping and Phenotyping Network",
"prefix": "NBDC02275",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc02276": {
"description": "GWIPS-viz is a freely available on-line genome browser which provides pre-populated ribosome profiling (Ribo-seq) and mRNA-seq tracks from published studies.",
"fairsharing": "FAIRsharing.ym3jjm",
"homepage": "http://gwips.ucc.ie/",
"information_keywords": [
"Expression",
"Interaction/Pathway",
"Method",
"Bibliography/Documents"
],
"name": "GWIPS-viz",
"prefix": "NBDC02276",
"pubmeds": [
"24185699"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein"
]
},
"nbdc02277": {
"alt_name": "qPrimerDB",
"description": "The qPrimerDB database stores information on qPCR primers. Accessible through a web front-end providing gene-specific and pre-computed primer pairs across 147 different organisms, including human, mouse, zebrafish, yeast, thale cress, rice, and maize. The qPrimerDB provides an interactive and information-rich web graphical interface to display search and BLAST results as table-based descriptions and associated links. In this database, we provide 3,331,426 of the best primer pairs for each gene based on primer pair coverage (PPC), as well as 47,726,569 alternative gene-specific primer pairs, which can be conveniently batch downloaded. We validated the specificity and efficiency of the qPCR primer pairs for 66 randomly selected genes in six different organisms through qPCR assays and gel electrophoresis. The qPrimerDB database represents a valuable, timesaving resource for gene expression analysis.",
"fairsharing": "FAIRsharing.qy4b7s",
"homepage": "http://biodb.swu.edu.cn/qprimerdb/",
"information_keywords": [
"Sequence",
"Method"
],
"maintainer": "Southwest University",
"name": "real-time quantitative PCR Primer Database",
"prefix": "NBDC02277",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"Organism"
]
},
"nbdc02278": {
"alt_name": "UKDS",
"description": "UK Data Service (UKDS) provides unified access to the UK's largest collection of social, economic and population data for research and teaching purposes covering a range of different disciplines. The majority of our data are fully anonymised, unless otherwise specified in the relevant online catalogue records, and are therefore not suitable for genealogical users or family historians. The UK Data Service is funded by the Economic and Social Research Council (ESRC) to meet the data needs of researchers, students and teachers from all sectors, including academia, central and local government, charities and foundations, independent research centres, think tanks, and business consultants and the commercial sector.",
"fairsharing": "FAIRsharing.1ky0cs",
"homepage": "https://www.ukdataservice.ac.uk/get-data",
"information_keywords": [
"Portal"
],
"maintainer": "University of Essex||University of Manchester",
"name": "UK Data Service",
"prefix": "NBDC02278",
"status": "Active"
},
"nbdc02279": {
"description": "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.",
"fairsharing": "FAIRsharing.mtjvme",
"homepage": "https://www.ebi.ac.uk/biostudies/",
"information_keywords": [
"Portal"
],
"maintainer": "European Commission FP7||EMBL (European Molecular Biology Laboratory)",
"name": "BioStudies",
"prefix": "NBDC02279",
"pubmeds": [
"26700850",
"29069414"
],
"status": "Active"
},
"nbdc02280": {
"alt_name": "CSIRO DAP",
"description": "The CSIRO Data Access Portal provides access to research data, software and other digital assets published by CSIRO across a range of disciplines.\nThe portal is maintained by CSIRO Information Management & Technology to facilitate sharing and reuse.",
"fairsharing": "FAIRsharing.fmc0g0",
"homepage": "https://data.csiro.au/collections",
"information_keywords": [
"Portal"
],
"maintainer": "CSIROοΌCommonwealth Scientific and Industrial Research Organisation)||ANDS (Australian National Data Service)",
"name": "CSIRO Data Access Portal",
"prefix": "NBDC02280",
"status": "Active"
},
"nbdc02281": {
"alt_name": "SND",
"description": "SND is a national resource that facilitates access to new and existing Swedish research data within and outside of Sweden. SND also provides support to researchers in Sweden throughout the process of data management.",
"fairsharing": "FAIRsharing.pn7yxf",
"homepage": "https://snd.gu.se/en",
"information_keywords": [
"Portal"
],
"maintainer": "Swedish National Data Service||University of Gothenburg",
"name": "Swedish National Data Service",
"prefix": "NBDC02281",
"status": "Active"
},
"nbdc02282": {
"alt_name": "DR",
"description": "The Donders Institute for Brain, Cognition and Behavior at the Radboud University created the Donders Repository for archiving, preserving and sharing the research data generated and processed at the institute.",
"fairsharing": "FAIRsharing.1sfhp3",
"homepage": "http://data.donders.ru.nl",
"information_keywords": [
"Bibliography/Documents",
"Repository"
],
"maintainer": "Radboud University||Donders Institute for Brain, Cognition and Behavior",
"name": "Donders Repository",
"prefix": "NBDC02282",
"status": "Active",
"target_keywords": [
"Organism",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc02283": {
"alt_name": "BCO-DMO",
"description": "The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is a publicly accessible earth science data repository created to curate, publicly serve (publish), and archive digital data and information from biological, chemical and biogeochemical research conducted in coastal, marine, great lakes and laboratory environments. The BCO-DMO repository works closely with investigators funded through the NSF OCE Division's Biological and Chemical Sections and the Division of Polar Programs Arctic Sciences and Antarctic Organisms & Ecosystems. The office provides services that span the full data life cycle, from data management planning support and DOI creation, to archive with appropriate national facilities.",
"fairsharing": "FAIRsharing.pjj4gd",
"homepage": "https://www.bco-dmo.org/",
"information_keywords": [
"Environment",
"Bibliography/Documents",
"Portal"
],
"name": "Biological and Chemical Oceanography Data Management Office",
"prefix": "NBDC02283",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02284": {
"description": "In 2013, we released the first version of Project Tycho containing weekly case counts for 50 notifiable conditions reported by health agencies in the United States for 50 states and 1284 cities between 1888 and 2014. Over the past four years, over 3700 users have registered to use Project Tycho data for a total of 40 creative works including peer-reviewed research papers, visualizations, online applications, and newspaper articles.\nProject Tycho 2.0 has expanded its scope to a global level and improved standardization, following FAIR (Findable, Accessible, Interoperable, and Reusable) Data Principles where possible. Project Tycho 2.0 includes case counts for 28 additional notifiable conditions for the US and includes data for dengue-related conditions for 99 countries between 1955 and 2010, obtained from the World Health Organization and Ministries of Health. Project Tycho 2.0 datasets are represented in a standard format and include standard SNOMED-CT codes for reported conditions, ISO 3166 codes for countries and first administrative level subdivisions, and NCBI TaxonID numbers for pathogens. Metadata for Project Tycho datasets are available on the website in human-readable format, but also in machine-interpretable DATS and DataCite metadata files.",
"fairsharing": "FAIRsharing.jnzrt",
"homepage": "https://www.tycho.pitt.edu/",
"information_keywords": [
"Phenotype"
],
"maintainer": "Project Tycho||University of Pittsburgh||University of Pittsburgh Medical Center||Public Health Dynamics Laboratory, University of Pittsburgh||Department of Epidemiology, University of Pittsburgh",
"name": "Project Tycho: Data for Health",
"prefix": "NBDC02284",
"pubmeds": [
"24283231"
],
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease"
]
},
"nbdc02285": {
"alt_name": "VDJdb",
"description": "The primary goal of VDJdb is to facilitate access to existing information on T-cell receptor antigen specificities, i.e. the ability to recognize certain epitopes in certain MHC contexts.\nOur mission is to both aggregate the scarce TCR specificity information available so far and to create a curated repository to store such data.\nIn addition to routine database updates providing the most up-to-date information, we make our best to ensure data consistency and fight irregularities in TCR specificity reporting with a complex database validation scheme.",
"fairsharing": "FAIRsharing.nwz68",
"homepage": "https://vdjdb.cdr3.net",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Portal"
],
"name": "VDJdb: a curated database of T-cell receptors with known antigen specificity",
"prefix": "NBDC02285",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Health/Disease"
]
},
"nbdc02286": {
"description": "The aim of e-ReColNat is to build a huge database consisting of species occurrence records through time, which will feed all kind of research and expertise in biodiversity survey, modelling global change, etc.",
"fairsharing": "FAIRsharing.anxqkv",
"homepage": "https://explore.recolnat.org",
"information_keywords": [
"Environment",
"Geographic Distribution",
"Taxonomy"
],
"maintainer": "RECOLNAT (RΓ©seau national des collections naturalistes )",
"name": "e-ReColNat",
"prefix": "NBDC02286",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02287": {
"alt_name": "IPA",
"description": "A data repository for the storage and sharing of Adaptive Immune Receptor Repertoire data. Primary public repository for the iReceptor Platform and Scientific Gateway.",
"fairsharing": "FAIRsharing.ekdqe5",
"homepage": "http://ireceptor.irmacs.sfu.ca/",
"information_keywords": [
"Repository"
],
"maintainer": "iReceptor, Simon Fraser University",
"name": "iReceptor Public Archive",
"prefix": "NBDC02287",
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease"
]
},
"nbdc02288": {
"alt_name": "EPD",
"description": "The EPD has been created and is maintained by the Lamond group in the University of Dundee. It combines a polyglot persistent database and web-application that provides open access to integrated proteomics data for >30 000 proteins from published studies on human cells and model organisms. It is designed to provide a user-friendly interface, featuring graphical navigation with interactive visualizations that facilitate powerful data exploration in an intuitive manner. The EPD offers a flexible and scalable ecosystem to integrate proteomics data with genomics information, RNA expression and other related, large-scale datasets",
"fairsharing": "FAIRsharing.sym4ne",
"homepage": "https://peptracker.com/epd",
"information_keywords": [
"Portal",
"Expression",
"Bibliography/Documents"
],
"maintainer": "Lamond Group||University of Dundee",
"name": "The Encyclopedia of Proteome Dynamics",
"prefix": "NBDC02288",
"pubmeds": [
"28981707"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc02290": {
"alt_name": "CSSI DCC",
"description": "The CSSI Data Coordinating Center (DCC) provides the greater Cancer Research and Biomedical Research communities access to the data from a myriad of projects that have been supported by CSSI -- serving as a permanent repository for these and related investigations. The DCC allows users in the community to download the metadata and data from these investigations in the ISA-TAB format. The DCC also allows any user to upload and download the metadata and data associated with investigations. The DCC has a graphical user interface allowing users to easily visualize the content within the data archives",
"fairsharing": "FAIRsharing.ccwcz6",
"homepage": "https://cssi-dcc.nci.nih.gov/cssiportal/",
"information_keywords": [
"Method",
"Bibliography/Documents",
"Repository"
],
"maintainer": "Frederick National Laboratory for Cancer Research",
"name": "NCI Center for Strategic Scientific Initiatives Data Coordinating Center",
"prefix": "NBDC02290",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc02291": {
"alt_name": "OmicsDI",
"description": "The Omics Discovery Index (OmicsDI) provides dataset discovery across a heterogeneous, distributed group of Transcriptomics, Genomics, Proteomics and Metabolomics data resources spanning eight repositories in three continents and six organisations, including both open and controlled access data resources. The resource provides a short description of every dataset: accession, description, sample/data protocols biological evidences, publication, etc. Based on these metadata, OmicsDI provides extensive search capabilities, as well as identification of related datasets by metadata and data content where possible. In particular, OmicsDI identifies groups of related, multi-omics datasets across repositories by shared identifiers.",
"fairsharing": "FAIRsharing.re1278",
"homepage": "http://www.omicsdi.org/home",
"information_keywords": [
"Expression",
"Localization",
"Portal"
],
"maintainer": "EMBL (European Molecular Biology Laboratory)||National Center for Protein Sciences",
"name": "Omics Discovery Index",
"prefix": "NBDC02291",
"pubmeds": [
"28486464"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Metabolite",
"Chemical compound",
"Health/Disease"
]
},
"nbdc02292": {
"alt_name": "MGA",
"description": "The Mass Genome Annotation (MGA) Data Repository stores published next generation sequencing data and other genome annotation data (such as gene start sites, SNPs, etc.) that, in conjunction with the ChIP-Seq and SSA servers, can be accessed and studied by scientists. The main characteristic of the MGA database is to store mapped data (in the form of genomic coordinates of mapped reads) and not sequence files. In this way, each sample present in the database has been pre-processed (for example sequence reads has been mapped to a genome) and presented in a standardized text format",
"fairsharing": "FAIRsharing.9997ek",
"homepage": "https://epd.expasy.org/mga/",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Ecole Polytechnique Federale de Lausanne||SIB (Swiss Institute of Bioinformatics)",
"name": "The MGA Data Repository",
"prefix": "NBDC02292",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02293": {
"alt_name": "GIN",
"description": "The German Neuroinformatics Node's data infrastructure (GIN) services provide a platform for comprehensive and reproducible management and sharing of neuroscience data. Building on well established versioning technology, GIN offers the power of a web based repository management service combined with a distributed file storage. The service addresses the range of research data workflows starting from data analysis on the local workstation to remote collaboration and data publication.",
"fairsharing": "FAIRsharing.nv6mrg",
"homepage": "http://gin.g-node.org",
"information_keywords": [
"Repository",
"Interaction/Pathway",
"Method",
"Bibliography/Documents"
],
"maintainer": "Ludwig-Maximilians-UniversitΓ€t MΓΌnchen, Department Biologie II, Division of Neurobiology||Leibniz Supercomputing Centre of the Bavarian Academy of Sciences and Humanities",
"name": "G-Node Data Infrastructure Services",
"prefix": "NBDC02293",
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc02294": {
"alt_name": "MFIB",
"description": "Mutual Folding Induced by Binding (MFIB) is a repository of protein complexes for which the folding of each constituent protein chain is coupled to the interaction forming the complex. This means that while the complexes are stable enough to have their structures solved by conventional structure determination methods (such as X-ray or NMR), the proteins or protein regions involved in the interaction do not have a stable structure in their free monomeric form (i.e. they are intrinsically disordered/unstructured).",
"fairsharing": "FAIRsharing.bwswdf",
"homepage": "http://mfib.enzim.ttk.mta.hu",
"information_keywords": [
"Method",
"Sequence",
"3D structure",
"Interaction/Pathway",
"Classification",
"Bibliography/Documents"
],
"maintainer": "Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences||MTA-ELTE Bioinformatics Research Group",
"name": "Mutual Folding Induced by Binding Database",
"prefix": "NBDC02294",
"pubmeds": [
"29036655"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02295": {
"alt_name": "DIBS",
"description": "Disordered Binding Sites (DIBS) is a repository of protein complexes that are formed by ordered and disordered proteins. Intrinsically disordered proteins (IDPs) do not have a stable 3D structure in isolation and therefore they defy structure determination by X-ray or NMR. However, many IDPs bind to ordered proteins and as a result of the interaction adopt a stable structure. In accord, complex structures involving binding sites in IDPs are available. DIBS offers a collection of these complexes where exactly one protein chain is disordered and all other proteins are ordered (i.e. are stable in their isolated form that is approved by available monomeric structures).",
"fairsharing": "FAIRsharing.rt4gyp",
"homepage": "http://dibs.enzim.ttk.mta.hu",
"information_keywords": [
"Method",
"Sequence",
"3D structure",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences||MTA-ELTE Momentum Bioinformatics Research Group",
"name": "Disordered Binding Sites Database",
"prefix": "NBDC02295",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02296": {
"alt_name": "FuzDB",
"description": "FuzDB compiles experimentally observed fuzzy protein complexes, where intrinsic disorder (ID) is maintained upon interacting with a partner (protein, nucleic acid or small molecule) and directly impacts biological function. Entries in the database have both (i) structural evidence demonstrating the structural multiplicity or dynamic disorder of the ID region(s) in the partner bound form of the protein and (ii) in vitro or in vivo biological evidence that indicates the significance of the fuzzy region(s) in the formation, function or regulation of the assembly. Unlike the other intrinsically disordered or unfolded protein databases, FuzDB focuses on ID regions within a biological context, including higher-order assemblies and presents a detailed analysis of the structural and functional data.",
"fairsharing": "FAIRsharing.d3bm3v",
"homepage": "http://protdyn-database.org/",
"information_keywords": [
"3D structure",
"Interaction/Pathway",
"Bibliography/Documents"
],
"name": "Database of fuzzy protein complexes",
"prefix": "NBDC02296",
"pubmeds": [
"27794553"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc02297": {
"alt_name": "genelab",
"description": "NASA GeneLab expands scientists' access to experiments that explore the molecular response of terrestrial biology to spaceflight environments. The vast amounts of raw data generated by experiments aboard the International Space Station are being made available to a worldwide community of scientists and computational researchers.",
"fairsharing": "FAIRsharing.64mr5a",
"homepage": "https://genelab.nasa.gov/",
"information_keywords": [
"Environment",
"Method",
"Expression",
"Bibliography/Documents"
],
"maintainer": "NASA Ames Research Center",
"name": "NASA GeneLab",
"prefix": "NBDC02297",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Metabolite"
]
},
"nbdc02298": {
"description": "Flavor is an expression of olfactory and gustatory sensations experienced through a multitude of chemical processes triggered by molecules. Beyond their key role in defining taste and smell, flavor molecules also regulate metabolic processes with consequences to health. Such molecules present in natural sources have been an integral part of human history with limited success in attempts to create synthetic alternatives. Given their utility in various spheres of life such as food and fragrances, it is valuable to have a repository of flavor molecules, their natural sources, physicochemical properties, and sensory responses. FlavorDB (http://cosylab.iiitd.edu.in/flavordb) comprises of 25,595 flavor molecules representing an array of tastes and odors. Among these 2254 molecules are associated with 936 natural ingredients belonging to 34 categories. The dynamic, user-friendly interface of the resource facilitates exploration of flavor molecules for divergent applications: finding molecules matching a desired flavor or structure; exploring molecules of an ingredient; discovering novel food pairings; finding the molecular essence of food ingredients; associating chemical features with a flavor and more. Data-driven studies based on FlavorDB can pave the way for an improved understanding of flavor mechanisms.",
"fairsharing": "FAIRsharing.7zfq1a",
"homepage": "http://cosylab.iiitd.edu.in/flavordb",
"information_keywords": [
"Chemical structure"
],
"maintainer": "IIIT-Delhi (Indraprastha Institute of Information Technology)",
"name": "FlavorDB",
"prefix": "NBDC02298",
"pubmeds": [
"29059383"
],
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc02299": {
"alt_name": "PrDB",
"description": "ProteomicsDB is a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data.\nProteomicsDB was first released in 2014 to enable the interactive exploration of the first draft of the human proteome. To date, it contains quantitative data from 78 projects totalling over 19k LC-MS/MS experiments. A standardized analysis pipeline enables comparisons between multiple datasets to facilitate the exploration of protein expression across hundreds of tissues, body fluids and cell lines.\nWe recently extended the data model to enable the storage and integrated visualization of other quantitative omics data. This includes transcriptomics data from e. g. NCBI GEO, protein-protein interaction information from STRING, functional annotations from KEGG, drug-sensitivity/selectivity\ndata from several public sources and reference mass spectra from the ProteomeTools project. The extended functionality transforms ProteomicsDB into a multi-purpose resource connecting quantification and meta-data for each protein. The rich user interface helps researchers to navigate all data sources in either a protein-centric or multi-protein-centric manner. Several options are available to download data manually, while our application programming interface enables accessing quantitative data systematically.",
"fairsharing": "FAIRsharing.6y9h91",
"homepage": "https://www.proteomicsdb.org/",
"information_keywords": [
"Sequence",
"Method",
"Expression",
"Localization",
"Interaction/Pathway"
],
"maintainer": "Technical University of Munich",
"name": "ProteomicsDB",
"prefix": "NBDC02299",
"pubmeds": [
"24870543"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02300": {
"description": "The Target-Pathogen database is a bioinformatic approach to prioritize drug targets in pathogens. Available genomic data for pathogens has created new opportunities for drug discovery and development, including new species, resistant and multiresistant ones. However, this data must be cohesively integrated to be fully exploited and be easy to interrogate. Target-Pathogen has been designed and developed as an online resource to allow genome wide based data consolidation from diverse sources focusing on structural druggability, essentiality and metabolic role of proteins. By allowing the integration and weighting of this information, this bioinformatic tool aims to facilitate the identification and prioritization of candidate drug targets for pathogens. With the structurome and drugome information Target-Pathogen is a unique resource to analyze whole genomes of relevants pathogens.",
"fairsharing": "FAIRsharing.dh32pc",
"homepage": "http://target.sbg.qb.fcen.uba.ar/patho/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Facultad de Ciencias Exactas y Naturales - Universidad de Buenos Aires",
"name": "Target Pathogen",
"prefix": "NBDC02300",
"pubmeds": [
"29106651"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Organism",
"Drug"
]
},
"nbdc02301": {
"alt_name": "BL",
"description": "An open, online platform that provides seamless access to cloud computing infrastructure and brain data and data derivatives. Brain Life addresses challenges to neuroscience open sharing and reproducibility by providing integrative mechanisms for publishing data, and algorithms while embedding them with computing resources to impact multiple scientific communities. This platform allows neuroscientists, computer scientists, statisticians, and engineers interested in brain data to use the data or develop and publish their analysis methods.",
"fairsharing": "FAIRsharing.by3p8p",
"homepage": "https://brainlife.io",
"information_keywords": [
"Repository",
"Image/Movie",
"Method"
],
"maintainer": "Indiana University",
"name": "Brain Life",
"prefix": "NBDC02301",
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc02302": {
"description": "A resource providing data on bioentities and their associated ontology terms for Plant Biology. The database provides access to ontology-based annotations of genes, phenotypes and germplasms from about 90 plant species. A number of internal and external ontologies are used to annotate the biological data available from this resource.",
"fairsharing": "FAIRsharing.k0kcjw",
"homepage": "http://www.planteome.org",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Phenotype",
"Method"
],
"maintainer": "Oregon State University||Bioversity International||New York Botanical Garden||LBNL (Lawrence Berkeley National Laboratory)",
"name": "Planteome",
"prefix": "NBDC02302",
"pubmeds": [
"26519402",
"25774204",
"25584184",
"25562316",
"23220694",
"22847540",
"18629207",
"18194960",
"17142475",
"16905665",
"15659431",
"29186578"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle"
]
},
"nbdc02303": {
"description": "The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease.",
"fairsharing": "FAIRsharing.6ba5fw",
"homepage": "http://alliancegenome.org",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Sequence",
"Portal"
],
"name": "Alliance of Genome Resources",
"prefix": "NBDC02303",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Organism"
]
},
"nbdc02304": {
"description": "Database of MacroMolecular INteractions",
"fairsharing": "FAIRsharing.hezt3h",
"homepage": "http://www.dommino.org",
"information_keywords": [
"Interaction/Pathway",
"3D structure"
],
"name": "DOMMINO: A comprehensive database of macromolecular interactions",
"prefix": "NBDC02304",
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc02305": {
"description": "A database for systems biology of DNA dynamics during the cell life.",
"fairsharing": "FAIRsharing.rq71dw",
"homepage": "http://dnatraffic.ibb.waw.pl/",
"information_keywords": [
"Bibliography/Documents",
"Ontology/Terminology/Nomenclature",
"Chemical structure",
"Image/Movie",
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Institute of Biochemistry and Biophysics Polish Academy of Sciences",
"name": "DNAtraffic",
"prefix": "NBDC02305",
"pubmeds": [
"22110027"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle"
]
},
"nbdc02306": {
"description": "Database of RNA interactions in post-transcriptional regulation.",
"fairsharing": "FAIRsharing.z0ea6a",
"homepage": "http://dorina.mdc-berlin.de",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Center for Comparative Functional Genomics, Department of Biology, New York University||MDC (Max Delbrueck Center for Molecular Medicine)||Max Planck Institute for Biology of Ageing||Howard Hughes Medical Institute",
"name": "doRiNA",
"prefix": "NBDC02306",
"pubmeds": [
"20371350",
"16458514",
"25416797"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc02307": {
"description": "A database of exosomes, membrane vesicles of endocytic origin released by diverse cell types.",
"fairsharing": "FAIRsharing.2z0e8b",
"homepage": "http://www.exocarta.org",
"information_keywords": [
"Method",
"Interaction/Pathway",
"Localization"
],
"maintainer": "Mathivanan Lab, La Trobe Institute for Molecular Science",
"name": "ExoCarta",
"prefix": "NBDC02307",
"pubmeds": [
"19810033"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"Protein",
"RNA",
"Lipid",
"Genome/Gene"
]
},
"nbdc02308": {
"alt_name": "GABI-Kat",
"description": "T-DNA insertions in Arabidopsis and their flanking sequence tags.",
"fairsharing": "FAIRsharing.hg2xzw",
"homepage": "http://www.gabi-kat.de/",
"information_keywords": [
"Sequence",
"Bioresource"
],
"name": "GABI-Kat SimpleSearch",
"prefix": "NBDC02308",
"pubmeds": [
"18758448",
"17062622",
"16488113",
"14756321",
"14682050",
"12874060",
"22080561"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02309": {
"description": "The Integrated Microbial Genomes (IMG) system serves as a community resource for analysis and annotation of genome and metagenome datasets in a comprehensive comparative context. The IMG data warehouse integrates genome and metagenome datasets provided by IMG users with a comprehensive set of publicly available genome and metagenome datasets.",
"fairsharing": "FAIRsharing.ae956n",
"homepage": "http://img.jgi.doe.gov/cgi-bin/m/main.cgi",
"information_keywords": [
"Bibliography/Documents",
"Sequence",
"Ontology/Terminology/Nomenclature",
"Classification",
"Expression",
"3D structure",
"Environment",
"Interaction/Pathway",
"Phenotype",
"Method"
],
"maintainer": "Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory",
"name": "IMG/M: the integrated metagenome data management and comparative analysis system",
"prefix": "NBDC02309",
"pubmeds": [
"16873494",
"17932063",
"24165883"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02311": {
"alt_name": "OGEE",
"description": "OGEE is an Online GEne Essentiality database. Gene essentiality is not a static and binary property, rather a context-dependent and evolvable property in all forms of life. In OGEE, we collect not only experimentally tested essential and non-essential genes, but also associated gene properties that contributes to gene essentiality.",
"fairsharing": "FAIRsharing.hsy066",
"homepage": "https://v3.ogee.info/#/home",
"information_keywords": [
"Phenotype",
"Sequence",
"Expression"
],
"name": "Online GEne Essentiality database",
"prefix": "NBDC02311",
"pubmeds": [
"27799467"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Cell/Organelle"
]
},
"nbdc02312": {
"description": "Oligonucleotides for targeted resequencing of the human genome",
"fairsharing": "FAIRsharing.qf46ys",
"homepage": "http://oligogenome.stanford.edu/",
"information_keywords": [
"Sequence"
],
"maintainer": "Stanford University School of Medicine",
"name": "The Human OligoGenome Resource: A Database for Customized Targeted Resequencing Covering the Human Genome",
"prefix": "NBDC02312",
"pubmeds": [
"21738606"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02313": {
"alt_name": "Autism KB",
"description": "Autism genetics KnowledgeBase, an evidence-based knowledgebase of autism genetics.",
"fairsharing": "FAIRsharing.990a1b",
"homepage": "http://autismkb.cbi.pku.edu.cn/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "CBI (Center for Bioinformatics, Peking University)",
"name": "Autism Knowledgebase",
"prefix": "NBDC02313",
"pubmeds": [
"22139918"
],
"status": "Inactive",
"target_keywords": [
"Genetic variation",
"Health/Disease",
"Genome/Gene"
]
},
"nbdc02314": {
"description": "Death Domain Database is a manually curated database of protein-protein interactions for Death Domain Superfamily.",
"fairsharing": "FAIRsharing.mw2ekr",
"homepage": "http://www.deathdomain.org",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Myongji University",
"name": "Death Domain Database",
"prefix": "NBDC02314",
"pubmeds": [
"22135292"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc02315": {
"description": "Gene3D takes CATH domain families (from PDB structures) and assigns them to the millions protein sequences (using Hidden Markov models generated from HMMER) with no PDB structures.",
"fairsharing": "FAIRsharing.fyqk5z",
"homepage": "http://gene3d.biochem.ucl.ac.uk",
"information_keywords": [
"Sequence",
"Classification",
"Interaction/Pathway"
],
"maintainer": "University College London||Research Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology, University College London",
"name": "Gene3D",
"prefix": "NBDC02315",
"pubmeds": [
"21646335",
"19906693",
"26139634",
"29112716"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Drug"
]
},
"nbdc02316": {
"alt_name": "IGDB.NSCLC",
"description": "Integrated Genomic Database of Non-Small Cell Lung Cancer.",
"fairsharing": "FAIRsharing.vm6g21",
"homepage": "http://igdb.nsclc.ibms.sinica.edu.tw",
"information_keywords": [
"Expression",
"Sequence",
"Method",
"Bibliography/Documents"
],
"maintainer": "IBMS (Institute of Biomedical Sciences, Academia Sinica)",
"name": "Integrated Genomic Database of Non-Small Cell Lung Cancer",
"prefix": "NBDC02316",
"pubmeds": [
"22139933"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"RNA"
]
},
"nbdc02318": {
"alt_name": "SCDE",
"description": "Comparison system for cancer stem cell analysis",
"fairsharing": "FAIRsharing.490xfb",
"homepage": "http://discovery.hsci.harvard.edu/",
"information_keywords": [
"Portal",
"Interaction/Pathway",
"Bibliography/Documents",
"Method",
"Phenotype",
"Expression"
],
"maintainer": "Dana-Farber Cancer Institute",
"name": "Stem Cell Discovery Engine",
"prefix": "NBDC02318",
"pubmeds": [
"22121217"
],
"status": "Closed",
"target_keywords": [
"Protein",
"Genome/Gene",
"Organism",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc02319": {
"description": "Drug-related information: medical indications, adverse drug effects, drug metabolism and Gene Ontology terms of the target proteins.",
"fairsharing": "FAIRsharing.se4zhk",
"homepage": "http://bioinformatics.charite.de/supertarget",
"information_keywords": [
"3D structure",
"Chemical structure",
"Ontology/Terminology/Nomenclature",
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Structural Bioinformatics Group, Institute of Molecular Biology and Bioinformatics, CharitΓ©-University Medicine Berlin",
"name": "SuperTarget",
"prefix": "NBDC02319",
"pubmeds": [
"17942422"
],
"status": "Inactive",
"target_keywords": [
"Drug",
"Chemical compound",
"Protein",
"Genome/Gene"
]
},
"nbdc02320": {
"description": "Identification and ranking of targets against neglected tropical diseases",
"fairsharing": "FAIRsharing.6c4fvf",
"homepage": "http://tdrtargets.org",
"information_keywords": [
"Interaction/Pathway",
"3D structure",
"Expression",
"Classification"
],
"maintainer": "University of Washington",
"name": "TDR Targets",
"prefix": "NBDC02320",
"pubmeds": [
"18927591",
"20808766",
"22116064"
],
"status": "Active",
"target_keywords": [
"Drug",
"Protein",
"Organism"
]
},
"nbdc02321": {
"alt_name": "VFDB",
"description": "VFDB is an integrated and comprehensive database of virulence factors for bacterial pathogens (also including Chlamydia and Mycoplasma).",
"fairsharing": "FAIRsharing.x2vch3",
"homepage": "http://www.mgc.ac.cn/VFs/",
"information_keywords": [
"Bibliography/Documents",
"Classification",
"Sequence",
"Phenotype"
],
"maintainer": "Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS&PUMC)",
"name": "Virulence Factor Database",
"prefix": "NBDC02321",
"pubmeds": [
"17984080",
"15608208"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Health/Disease"
]
},
"nbdc02322": {
"description": "A comprehensive online knowledgebase for the monkey research community.",
"fairsharing": "FAIRsharing.qkrmth",
"homepage": "http://www.rhesusbase.org",
"information_keywords": [
"Phenotype",
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "IMM (Institute of Molecular Medicine, Peking University)",
"name": "RhesusBase",
"prefix": "NBDC02322",
"pubmeds": [
"26882984",
"24577841",
"22965133"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc02323": {
"description": "AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products.",
"fairsharing": "FAIRsharing.kn4ycg",
"homepage": "http://www.agbase.msstate.edu/",
"information_keywords": [
"Sequence",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "AgBase, Mississippi State University",
"name": "AgBase",
"prefix": "NBDC02323",
"pubmeds": [
"21075795"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02324": {
"description": "Relative evolutionary importance of amino acids within a protein sequence.",
"fairsharing": "FAIRsharing.4eanvm",
"homepage": "http://mammoth.bcm.tmc.edu/ETserver.html",
"information_keywords": [
"Sequence",
"3D structure",
"Classification"
],
"maintainer": "Baylor College of Medicine",
"name": "Evolutionary Trace",
"prefix": "NBDC02324",
"pubmeds": [
"22183528"
],
"status": "Active",
"target_keywords": [
"Organism",
"Protein"
]
},
"nbdc02326": {
"alt_name": "CFGP",
"description": "The CFGP (Comparative Fungal Genomics Platform) was designed for comparative genomics projects with diverse fungal genomes.",
"fairsharing": "FAIRsharing.ssx7a2",
"homepage": "http://cfgp.snu.ac.kr",
"information_keywords": [
"Sequence"
],
"maintainer": "BPS (Bioinformatics Portal Site)",
"name": "Comparative Fungal Genomics Platform",
"prefix": "NBDC02326",
"pubmeds": [
"17947331"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02327": {
"description": "Patent data resources at the EBI contain patent abstracts, patent chemical compounds, patent sequences and patent equivalents. Multiple sets of patent sequences are available at EBI. Patent proteins cover sequences of EPO (European Patent Office) proteins, JPO (Japan Patent Office) proteins, KIPO (Korean Intellectual Property Office) proteins and USPTO (United States Patent and Trademark Office) proteins. Patent nucleotides contain the patent class data in the EMBL-Bank. Non-redundant patent sequences consist of 2 levels databases. Level-1 non-redundant patent sequences are 100% identical over the same length; Level-2 non-redundant patent sequences are identical and belong to a same patent family (a same invention).",
"fairsharing": "FAIRsharing.p3n3fn",
"homepage": "http://www.ebi.ac.uk/patentdata/proteins",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "SIB (Swiss Institute of Bioinformatics)",
"name": "Patent Data Resources",
"prefix": "NBDC02327",
"pubmeds": [
"19884134"
],
"status": "Active",
"target_keywords": [
"Protein",
"Genome/Gene"
]
},
"nbdc02328": {
"alt_name": "THGS",
"description": "A web based database of Transmembrane Helices in Genome Sequences.",
"fairsharing": "FAIRsharing.1nwy41",
"homepage": "http://pranag.physics.iisc.ernet.in/thgs/",
"information_keywords": [
"Sequence"
],
"maintainer": "Indian Institute of Science",
"name": "Transmembrane Helices in Genome Sequences",
"prefix": "NBDC02328",
"pubmeds": [
"14681375"
],
"status": "Inactive",
"target_keywords": [
"DNA",
"Genome/Gene"
]
},
"nbdc02329": {
"alt_name": "GenoList",
"description": "GenoList is an integrated environment for comparative exploration of microbial genomes. The current release integrates genome data for over 700 species (Genome Reviews). The query and navigation user interface includes specialized tools for subtractive genome analysis and dynamic synteny visualization.",
"fairsharing": "FAIRsharing.amxd1s",
"homepage": "http://genolist.pasteur.fr/",
"information_keywords": [
"Portal"
],
"maintainer": "Institut Pasteur",
"name": "GenoList Genome Browser",
"prefix": "NBDC02329",
"pubmeds": [
"18032431"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02330": {
"description": "A registry of Hereditary Auto-inflammatory Disorder Mutations.",
"fairsharing": "FAIRsharing.g6kz6h",
"homepage": "http://fmf.igh.cnrs.fr/ISSAID/infevers/",
"information_keywords": [
"Sequence",
"Phenotype"
],
"maintainer": "IGH (Institute of Human Genetics)",
"name": "Infevers",
"prefix": "NBDC02330",
"pubmeds": [
"18409191",
"12520003"
],
"status": "Inactive",
"target_keywords": [
"Genetic variation",
"Genome/Gene",
"Health/Disease",
"Organism"
]
},
"nbdc02331": {
"description": "The Cancer gene expression and microarray data of the National Cancer Institute",
"fairsharing": "FAIRsharing.gdqqm0",
"homepage": "https://array.nci.nih.gov/caarray/home.action",
"information_keywords": [
"Expression"
],
"maintainer": "NIH (National Institutes of Health)",
"name": "caArray",
"prefix": "NBDC02331",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02332": {
"description": "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.",
"fairsharing": "FAIRsharing.zf8s5t",
"homepage": "http://www.signaling-gateway.org",
"information_keywords": [
"Interaction/Pathway",
"Sequence"
],
"maintainer": "San Diego Supercomputer Center",
"name": "The Signaling Gateway",
"prefix": "NBDC02332",
"pubmeds": [
"17965093",
"21505029"
],
"status": "Inactive",
"target_keywords": [
"Protein"
]
},
"nbdc02333": {
"alt_name": "EORTC",
"description": "European Organisation for Research and Treatment of Cancer database of clinical trials.",
"fairsharing": "FAIRsharing.ja871b",
"homepage": "http://www.eortc.org/clinical-trials/",
"information_keywords": [
"Bibliography/Documents"
],
"name": "EORTC clinical trials",
"prefix": "NBDC02333",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc02334": {
"alt_name": "BDTNP",
"description": "A database containing the expression patterns of hundreds of Drosophila genes in 3D at cellular resolution.",
"fairsharing": "FAIRsharing.9jpd3v",
"homepage": "http://bdtnp.lbl.gov:8080/Fly-Net/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway",
"Image/Movie",
"Method"
],
"name": "Berkeley Drosophila Transcription Network Project",
"prefix": "NBDC02334",
"status": "Inactive",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02335": {
"description": "A collection of high resolution histological images from contributors across the Czech Republic.",
"fairsharing": "FAIRsharing.j9mm09",
"homepage": "http://atlases.muni.cz",
"information_keywords": [
"Phenotype",
"Image/Movie"
],
"maintainer": "MU (Masaryk University)",
"name": "Atlases - Pathology images",
"prefix": "NBDC02335",
"status": "Active",
"target_keywords": [
"Health/Disease",
"Organism"
]
},
"nbdc02336": {
"alt_name": "CeNDR",
"description": "Whole-genome sequence data, variant calls, and annotations of natural genetic variation in C. elegans species.",
"fairsharing": "FAIRsharing.ppdbrz",
"homepage": "http://www.elegansvariation.org",
"information_keywords": [
"Sequence",
"Environment",
"Bioresource"
],
"name": "C. elegans Natural Diversity Resource",
"prefix": "NBDC02336",
"status": "Active",
"target_keywords": [
"Genetic variation",
"Organism",
"Genome/Gene"
]
},
"nbdc02337": {
"description": "An integrated database and portal for wheat genome information.",
"fairsharing": "FAIRsharing.8yqqm4",
"homepage": "http://www.wheatgenome.info/wheat_genome_databases.php",
"information_keywords": [
"Sequence"
],
"maintainer": "Australian Research Council||Edwards Group, University of Western Australia||The University of Queensland",
"name": "WheatGenome.info",
"prefix": "NBDC02337",
"pubmeds": [
"22009731"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02338": {
"description": "This site hosts Brassica genome databases.",
"fairsharing": "FAIRsharing.mzk12n",
"homepage": "http://www.brassicagenome.net/details.php",
"information_keywords": [
"Sequence"
],
"maintainer": "Australian Research Council||The University of Queensland",
"name": "Brassica Genome",
"prefix": "NBDC02338",
"pubmeds": [
"21873998"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02339": {
"alt_name": "CARD",
"description": "A bioinformatic database of antimicrobial resistance genes, their products and associated phenotypes.",
"fairsharing": "FAIRsharing.9dbmwg",
"homepage": "http://arpcard.mcmaster.ca",
"information_keywords": [
"Sequence",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Department of Biochemistry and Biomedical Sciences, McMaster University",
"name": "Comprehensive Antibiotic Resistance Database",
"prefix": "NBDC02339",
"pubmeds": [
"23650175"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Health/Disease"
]
},
"nbdc02340": {
"description": "This database lists cell lines that are currently known to be cross-contaminated or otherwise misidentified.",
"fairsharing": "FAIRsharing.eyktqz",
"homepage": "http://iclac.org/databases/cross-contaminations/",
"information_keywords": [
"Bioresource",
"Environment"
],
"maintainer": "ATCC Standards Development Organisation||Cell Networks, University of Heidelberg||Genetica DNA Laboratories||JCRB Cell Bank (Japanese Collection of Research Bioresources Cell Bank)||RIKEN BRC (RIKEN BioResource Research Center)||SIB (Swiss Institute of Bioinformatics)||GBSI (UK Global Biological Standards Institute)",
"name": "ICLAC Database of Cross-Contaminated or Misidentified Cell Lines",
"prefix": "NBDC02340",
"pubmeds": [
"20143388"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle"
]
},
"nbdc02341": {
"alt_name": "NERC Data Catalogue Service",
"description": "A compendium of the United Kingdom's largest repository of Environmental and Earth Science data.",
"fairsharing": "FAIRsharing.xj7m8y",
"homepage": "https://csw-nerc.ceda.ac.uk",
"information_keywords": [
"Environment",
"Geographic Distribution",
"Interaction/Pathway",
"Portal"
],
"name": "Natural Environmental Research Council Data Catalogue Service",
"prefix": "NBDC02341",
"status": "Inactive",
"target_keywords": [
"Organism",
"Genome/Gene"
]
},
"nbdc02342": {
"alt_name": "GCMD",
"description": "This resource provides support to scientific community by providing access to Earth science data and services.",
"fairsharing": "FAIRsharing.3aabq1",
"homepage": "https://gcmd.gsfc.nasa.gov/index.html",
"information_keywords": [
"Environment",
"Geographic Distribution",
"Sequence",
"Expression",
"Interaction/Pathway",
"Portal"
],
"name": "NASA Global Change Master Directory",
"prefix": "NBDC02342",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Organism"
]
},
"nbdc02343": {
"description": "Oligonucleic Acid Drug Database is focused on nucleic acid drugs known as biopharmaceuticals and displayed approval drugs and information on three phases of clinical trial stage. It contains clinical information of nucleic acid drugs which based from pharmaceutical companies and clinical information sites (https://clinicaltrials.gov/, https://www.clinicaltrialsregister.eu/). This database also provides information on nucleic acid drugs that are being considered for future practical use (such as target diseases and related protein information).",
"homepage": "https://medals.jp/edrugnainfo.html",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "Nucleic Acid Drug Database",
"prefix": "NBDC02343",
"status": "Active",
"target_keywords": [
"DNA",
"RNA",
"Drug",
"Health/Disease"
]
},
"nbdc02344": {
"alt_name": "ASEAN-Japan Chemical Safety Database",
"description": "The ASEAN-Japan Chemical Safety Database (AJCSD) is a database co-developed by ASEAN countries and Japan based on an agreement reached at ASEAN Economic Ministers and METI Economic and Industrial Cooperation Committee (AMEICC) Working Group on Chemical Industry (WG-CI). The AJCSD contains regulatory information on chemical substances, hazardous information, GHS Classification results, sample SDS, etc.",
"homepage": "https://www.ajcsd.org/",
"information_keywords": [
"Chemical structure",
"Bibliography/Documents"
],
"maintainer": "NITE (National Institute of Technology and Evaluation)",
"name": "AJCSD",
"prefix": "NBDC02344",
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc02346": {
"description": "MiFuP Safety is a free web application that can assess whether a given microbe has any hazardous property based on its genome information. The system automatically identifies genes associated with potentially harmful functions, such as toxin production and antibiotic resistance, in given sequence(s), and quickly provides information on potential hazardous properties of the microbe.\nMiFuP Safety can take either nucleotide or protein sequence in FASTA format.",
"homepage": "https://www.nite.go.jp/nbrc/mrinda/mifup_safety/",
"information_keywords": [
"Phenotype",
"Sequence"
],
"maintainer": "NITE (National Institute of Technology and Evaluation)",
"name": "MiFuP Safety",
"prefix": "NBDC02346",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Metabolite",
"Health/Disease"
]
},
"nbdc02347": {
"description": "Rubber Genome & Transcriptome Database provides rubber tree genome sequence and multi-transcriptomics data. This database provides genome information including gene functional annotations and multi-transcriptome data of RNA-seq, full-length cDNAs including PacBio Isoform sequencing (Iso-Seq), ESTs and genome wide transcription start sites (TSSs) derived from CAGE technology. It also provides information about co-expressed genes for identifying functionally related gene sets and/or genes regulated by the same transcription factor (TF). Users are able to access multi-transcriptome data through both a gene-oriented web page and a genome browser. This database allows to keyword search, sequence homology search and gene expression search; users can also select their expression threshold easily.",
"homepage": "http://matsui-lab.riken.jp/rubber/home.html",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "Rubber Genome & Transcriptome Database",
"prefix": "NBDC02347",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc02348": {
"alt_name": "Agronomic Linked Data",
"description": "AgroLD is a RDF knowledge base that consists of data integrated from a variety of plant resources and ontologies. It provides a portal for bioinformatics and domain experts to exploit the homogenized data models towards efficiently generating research hypotheses.",
"homepage": "http://agrold.southgreen.fr/agrold/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Computational Biology Institute",
"name": "AgroLD",
"prefix": "NBDC02348",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Protein"
]
},
"nbdc02350": {
"description": "MeKO is a database of metabolomic data for Arabidopsis thaliana. It contains profiling data of metabolites in 50 Arabidopsis mutants, using gas chromatography/mass spectrometry (GC-MS). It allows to browse using a mutants list. Non-processed data, including chromatograms, mass spectra, and experimental metadata, follow the guidelines set by Metabolomics Standards Initiative (MSI) and are downloadable freely.",
"homepage": "http://prime.psc.riken.jp/meko/",
"information_keywords": [
"Phenotype",
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "RIKEN CSRS (RIKEN Center for Sustainable Resource Science)",
"name": "MeKO",
"prefix": "NBDC02350",
"pubmeds": [
"24828308"
],
"status": "Closed",
"target_keywords": [
"Genome/Gene",
"Metabolite"
]
},
"nbdc02351": {
"alt_name": "ReSpect for Phytochemicals",
"description": "ReSpect is a web-based database of MS/MS data pertaining to phytochemicals. It collects MSn spectra data from literature reports and authentic standards. It allows to using a fragment search which was established based on only the m/z values of query data and records. It also allows to search with spectra similarity or keywords.",
"homepage": "http://spectra.psc.riken.jp/",
"information_keywords": [
"Chemical structure"
],
"maintainer": "RIKEN CSRS (RIKEN Center for Sustainable Resource Science)",
"name": "ReSpect",
"prefix": "NBDC02351",
"pubmeds": [
"22867903"
],
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc02352": {
"alt_name": "RIKEN Heteroatom-containing Ion Finder",
"description": "RIKEN HIFI is a tool for Liquid Chromatography-Fourier transfer ion cyclotron resonance-mass spectrometry ( LC-FTICR-MS). This tool provides three features: (i) Element Search for searching heteroatom-containing ions can be with user's thresholds, (ii) List Search for searching data with uploaded datasets, and (iii) Compare Search for comparison of multiple datasets.",
"homepage": "http://spectra.psc.riken.jp/menta.cgi/hifi/index",
"information_keywords": [
"Chemical structure"
],
"maintainer": "RIKEN CSRS (RIKEN Center for Sustainable Resource Science)",
"name": "RIKEN HIFI",
"prefix": "NBDC02352",
"pubmeds": [
"23327693"
],
"status": "Closed",
"target_keywords": [
"Metabolite"
]
},
"nbdc02353": {
"description": "PubCaseFinder is a database of human disease-phenotype associations which employs a text mining-based approach to improve the coverage of Orphanet. It contains more than one million case reports from PubMed, and they were annotated for concepts of rare diseases and phenotypes.",
"homepage": "https://pubcasefinder.dbcls.jp",
"information_keywords": [
"Phenotype",
"Bibliography/Documents"
],
"maintainer": "DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "PubCaseFinder",
"prefix": "NBDC02353",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc02354": {
"description": "DropViz provides the Drop-seq data of single-cell RNA sequencing of 690,000 cells sampled from nine regions of the adult mouse brain. Users can visualize and re-analyze these gene-expression data with this interactive online software.",
"homepage": "http://dropviz.org",
"information_keywords": [
"Sequence",
"Expression",
"Localization"
],
"maintainer": "Harvard Medical School||Stanley Center for Psychiatric Research at Broad Institute",
"name": "DropViz",
"prefix": "NBDC02354",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Cell/Organelle"
]
},
"nbdc02355": {
"description": "Computational metabolomics is a collection about computational tools for metabolomics. It contains MS-DIAL, MS-FINDER, MRMPROBS, MRM-DIFF, SmetSearch, Cuated EI-MS and MS/MS databases, Aloutput, and Excel Macro applications.",
"homepage": "http://prime.psc.riken.jp/Metabolomics_Software/",
"information_keywords": [
"Method",
"Chemical structure",
"Portal"
],
"maintainer": "RIKEN CSRS (RIKEN Center for Sustainable Resource Science)",
"name": "Computational metabolomics",
"prefix": "NBDC02355",
"status": "Active",
"target_keywords": [
"Metabolite",
"Lipid"
]
},
"nbdc02356": {
"alt_name": "Medical genomics Japan Variant Database",
"description": "Medical Genomics Japan Variant Database (MGeND) provides the integrated information of genomic variations and clinical characteristics of Japanese. Gene and clinical information can be browsed from the sections below: \"Cancer\", \"Rare/Intractable disease\", \"Infectious Disease\", \"Dementia\" and \"Hearing loss\". Users can also search database by gene name or position in chromosome.",
"homepage": "https://mgend.ncgm.go.jp/",
"information_keywords": [
"Phenotype",
"Sequence",
"Repository"
],
"maintainer": "National Center for Global Health and Medicine",
"name": "MGeND",
"prefix": "NBDC02356",
"pubmeds": [
"31839973"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc02357": {
"description": "KEGG NETWORK accumulates variations of molecular interaction/reaction networks in Homo sapiens distinguishing gene variants and other perturbants. Each entry is called \"network elements\" and represented in KEGG pathway maps and perturbed network elements are caused by gene variants, viruses, drugs, etc.",
"homepage": "http://www.kegg.jp/kegg/network.html",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "KEGG NETWORK Database",
"prefix": "NBDC02357",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Drug",
"Health/Disease"
]
},
"nbdc02358": {
"description": "This is a collection of user dictionaries of Japanese technical terms in scientific field, which can be used for a morphological analysis engine, MeCab. It consists of the JST Thesaurus Headwords and Synonym Dictionary, J-GLOBAL MeSH Dictionary, and J-GLOBAL Nikkaji Dictionary. The dictionary items are based on IPA dictionary and encoded in UTF-8. Please note that these dictionaries cannot be used as a thesaurus because information on relations between words is not included in the dictionary.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/mecab/desc.html",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "MeCab user dictionary for science technology term",
"prefix": "NBDC02358",
"status": "Active"
},
"nbdc02359": {
"alt_name": "Integrated database of Japanese genomic variation",
"description": "TogoVar (NBDC's integrated database of Japanese genomic variation) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them. TogoVar provides variant frequencies in the Japanese population that have been aggregated across research projects. Two available datasets, JGA-NGS and JGA-SNP, are obtained by aggregating individual genomic data that have been registered in the NBDC Human Database / Japanese Genotype-phenotype Archive (JGA). In addition, TogoVar integrates information related to genotypes or phenotypes that has been compiled independently in a variety of different databases and provides information for interpreting variants in a one-stop, easy-to-understand manner.\nUsers can learn how to use it by a movie: https://togotv.dbcls.jp/en/20181012.html",
"fairsharing": "biodbcore-001182/",
"homepage": "https://togovar.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)||DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "TogoVar",
"prefix": "NBDC02359",
"pubmeds": [],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc02360": {
"description": "Rice SNP-Seek Database provides Genotype, Phenotype, and Variety Information for rice (Oryza sativa L.). The main functionalities are query for SNPs and Indels from the 3000 Genome Project including 5 reference rice genomes, query for phenotypes and passport data for the 3024 resequenced varieties, and genome browser to display sequence and features for the reference genomes. Bulk download is available. Users can order seeds from the IRRI Genebank Collection.",
"homepage": "http://snp-seek.irri.org/",
"information_keywords": [
"Phenotype",
"Bioresource",
"Sequence"
],
"maintainer": "IRRI (International Rice Research Institute)",
"name": "Rice SNP-Seek Database",
"prefix": "NBDC02360",
"pubmeds": [
"27899667",
"25429973"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Organism"
]
},
"nbdc02361": {
"description": "PED is a repository for pancreatic-derived -omics data. The database provides the research community with an open access tool to mine currently available pancreatic cancer experimental data sets generated by using large-scale transcriptomic, genomic, proteomic, miRNA and methylomic platforms. This database can be achieved using combined criteria from pancreatic (disease stages, regulation, differential expression, expression, platform technology, publication) and/or public data (antibodies, genomic region, gene-related accessions, ontology, expression patterns, multi-species comparisons, protein data, SNPs). Users are able to submit their own published dataset in this database.",
"fairsharing": "biodbcore-001125/",
"homepage": "http://www.pancreasexpression.org",
"information_keywords": [
"Expression",
"Bibliography/Documents"
],
"maintainer": "Barts Cancer Institute",
"name": "Pancreas Expression Database",
"prefix": "NBDC02361",
"pubmeds": [
"29059374",
"24163255",
"20959292",
"18045474"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Epigenetics",
"Health/Disease"
]
},
"nbdc02362": {
"alt_name": "Conformational diversity of Native State database",
"description": "CoDNaS is a database of redundant crystallographic structures for a given protein extensively linked with structural, biological and physicochemical information. For each protein as derived from PDB, the database contains the redundant collection of all corresponding different structures. As a measure of protein conformational diversity (PCD), the RMSD are obtained comparing all the structures deposited for each protein. \nThis database allows to browse by CATH hierarchy or search by PDB ID, Uniprot ID, CATH, conformational diversity, experimental method, etc..",
"homepage": "http://ufq.unq.edu.ar/codnas/index.php",
"information_keywords": [
"3D structure",
"Classification"
],
"maintainer": "Structural Bioinformatics Group, National University of Quilmes",
"name": "CoDNaS",
"prefix": "NBDC02362",
"pubmeds": [
"27022160",
"23846747"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02363": {
"alt_name": "Rice Variation Map v2.0",
"description": "RiceVarMap v2.0 is a comprehensive database for rice genomic variation and its functional annotation. It provides curated information of 17,397,026 genomic variations (including 14,541,446 SNPs and 2,855,580 small INDELs) from sequencing data of 4,726 rice accessions. Phenotype data and GWAS results for 13 agronomic traits and 840 metabolite traits are also provided. The database provides various variation query functions and many useful analysis tools. The query results are available for users to download through the website.",
"homepage": "http://ricevarmap.ncpgr.cn/v2/",
"information_keywords": [
"Phenotype",
"Sequence"
],
"maintainer": "National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University",
"name": "RiceVarMap v2.0",
"prefix": "NBDC02363",
"pubmeds": [
"25274737"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Organism"
]
},
"nbdc02364": {
"description": "\"Twins\" retrieves similar metabolites in chemical structure when user input KNApSAcK CID and Similarity (%). Resulting CID links to KNApSAcK Core database and KNApSAcK Metabolite Activity database.",
"homepage": "http://www.knapsackfamily.com/Twins/top.jsp",
"information_keywords": [
"Chemical structure"
],
"maintainer": "Nara Institute of Science and Technology",
"name": "KNApSAcK Twins",
"prefix": "NBDC02364",
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc02365": {
"description": "CobWeb is a database of alkaloid pathways. Users can browse pathways from the pathway map ID list. Pathway map ID(s) or object(s) in each map is/are highlighted when user input metabolite name(s) or species name. Each database object links to KNApSAcK Core metabolite information page.",
"homepage": "http://www.knapsackfamily.com/CobWeb/top.jsp",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Nara Institute of Science and Technology",
"name": "KNApSAcK CobWeb",
"prefix": "NBDC02365",
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc02366": {
"alt_name": "Medicago truncatula Genome Database",
"description": "This is the genome database for Medicago truncatula, a model legume. It currently hosts the latest version of the genome assembly and annotation. It provides keyword- and locus identifier-based searches, a BLAST search and bulk downloads of data sets. JBrowse-based genome browser interface exposes tracks for visualization. The site also implements MedicMine which provides a powerful query interface, integrates many types of data for Medicago truncatula.",
"fairsharing": "biodbcore-001063/",
"homepage": "http://www.medicagogenome.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "JCVI (J. Craig Venter Institute)",
"name": "MTGD",
"prefix": "NBDC02366",
"pubmeds": [
"25432968"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc02367": {
"alt_name": "Database for Flower Bio-engineering by CRES-T",
"description": "This database provides information of phenotype in transgenic plants created by CRES-T (Chimeric REpressor gene-Silencing Technology) system which is a novel gene silencing technology for genes encoding transcription factors. Users can search gene-constructs inducing preferable phenotype or browse list of gene-constructs. Almost all the transcription factors of Arabidopsis thaliana are applied to the strategy, and those constructs are used for creating transgenic plants which are not only Arabidopsis thaliana but also other economically important plants.",
"homepage": "http://www.cres-t.org/fiore/public_db/index.shtml",
"information_keywords": [
"Phenotype",
"Sequence",
"Expression",
"Image/Movie"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "FioreDB",
"prefix": "NBDC02367",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02368": {
"alt_name": "National Bioresource Project - Pathogenic bacteria",
"description": "National Bioresource Project - 'Pathogenic bacteria' collects reliable strains of pathogenic bacteria to support education and research in infectious diseases. Users can search resources by keywords. Requests for distribution of resources are available.",
"homepage": "http://pathogenic-bacteria.nbrp.jp/",
"information_keywords": [
"Bioresource"
],
"maintainer": "GCMR (Center for Conservation of Microbial Genetic Resource, Organization for Research and Community Development, Gifu University)",
"name": "NBRP - Pathogenic bacteria",
"prefix": "NBDC02368",
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease"
]
},
"nbdc02369": {
"alt_name": "National Bioresource Project - Pathogenic eukaryotic microorganisms",
"description": "National Bioresource Project - 'Pathogenic eukaryotic microorganisms' collects reliable strains of pathogenic microorganisms (fungi, actinomycetes and protozoa) to support education and research in infectious diseases. Users can search resources by keywords. Requests for distribution of resources are available. This database also provides a picture list of pathogenic fungi and actinomycetes (https://integbio.jp/dbcatalog/en/record/nbdc00460).",
"homepage": "https://pathogenic-microbes.nbrp.jp/",
"information_keywords": [
"Bioresource",
"Image/Movie"
],
"maintainer": "MMRC (Medical Mycology Research Center MMRC, Chiba University)",
"name": "NBRP - Pathogenic eukaryotic microorganisms",
"prefix": "NBDC02369",
"status": "Active",
"target_keywords": [
"Organism",
"Health/Disease"
]
},
"nbdc02371": {
"description": "PURL is a server for Persistent Uniform Resource Locators (URLs). On this site, users allows to create and register a persistent URL which is an address on the World Wide Web that points to other Web resources.",
"homepage": "https://purl.dbcls.jp/docs/index.html",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "DBCLS (Database Center for Life Science, Research Organization of Information and Systems)",
"name": "PURL",
"prefix": "NBDC02371",
"status": "Active"
},
"nbdc02372": {
"description": "This database provides metadata of the NBRP medaka database ( https://integbio.jp/dbcatalog/en/record/nbdc00147 ). Data on this site are available as downloadable RDF files and spreadsheets.",
"homepage": "https://metadb.riken.jp/metadb/db/NBRP_medaka",
"information_keywords": [
"Phenotype",
"Bioresource",
"Ontology/Terminology/Nomenclature",
"Taxonomy"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "NBRP Medaka Phenotype Metadata",
"prefix": "NBDC02372",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02373": {
"alt_name": "DeepBlue Epigenomic Data Server",
"description": "DeepBlue provides a programmatic interface for finding, selecting, filtering, summarizing and downloading epigenomic data from the main epigenome mapping projects: ENCODE, NIH Roadmap, BLUEPRINT and DEEP. A user manual, usage examples and a well-documented API are available. An optional web interface is available for non-programmers.",
"homepage": "http://deepblue.mpi-inf.mpg.de",
"information_keywords": [
"Sequence",
"Expression",
"Localization"
],
"maintainer": "Max Planck Institute for Informatics",
"name": "DeepBlue",
"prefix": "NBDC02373",
"pubmeds": [
"27084938"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Epigenetics",
"DNA",
"Protein",
"Cell/Organelle",
"Organism"
]
},
"nbdc02374": {
"description": "This is a database of type specimens of species and infraspecific taxa of the plant families preserved in the Herbarium, Department of Botany, the University Museum, the University of Tokyo (TI). Data are based on the Material Reports, The University Museum, University of Tokyo (1981- 2011), Catalogue of the Type specimens Preserved in the Herbarium, Department of Botany, The University Museum, The University of Tokyo Part 1-12.",
"homepage": "http://umdb.um.u-tokyo.ac.jp/DShokubu/herbarium/en_ver2/index.php",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "The University Museum, The University of Tokyo",
"name": "Type Collection Database",
"prefix": "NBDC02374",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02375": {
"description": "PlantExpress is a platform for gene expression network (GEN) analysis with the public microarray data of rice and Arabidopsis. For a single-species GEN analysis, PlantExpress provides functionalities specialized for each species, OryzaExpress and ArthaExpress. For a comparative (cross-species) GEN analysis, PlantExpress provides functions to compare GENs constructed with OryzaExpress and ArthaExpress on the basis of ortholog relationship.",
"homepage": "http://plantomics.mind.meiji.ac.jp/PlantExpress/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "Bioinformatics Laboratory of Meiji University",
"name": "PlantExpress",
"prefix": "NBDC02375",
"pubmeds": [
"28158643",
"21186175"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02376": {
"description": "NGSmethDB is a database for whole genome methylomes generated from short-read data sets obtained by bisulfite sequencing (WGBS) technology. Publicly available short-read data sets, mainly from NCBI GEO and the ROADMAP project, were used for the analysis by MethFlow that was an original pipeline for the integral analysis of bisulfite sequencing data. Selected data or dumps for entire methylomes can be downloaded on the web. Programmatic access to the database is also available.",
"homepage": "https://bioinfo2.ugr.es/NGSmethDB/",
"information_keywords": [
"Sequence",
"Localization"
],
"maintainer": "Computational Epigenomics Lab, Evolutionary Genomics and Bioinformatics Group, Dept. of Genetics, Inst. of Biotechnology, University of Granada",
"name": "NGSmethDB",
"prefix": "NBDC02376",
"pubmeds": [
"20965971",
"24271385",
"27794041"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Epigenetics"
]
},
"nbdc02377": {
"alt_name": "Web API for Biology",
"description": "WABI is a web API for using the search services of the DNA Data Bank of Japan (DDBJ) without needing to navigate the web front-end. WABI currently provides the following web APIs: BLAST, getentry, ARSA, ClustalW, VecScreen and MAFFT.",
"homepage": "https://www.ddbj.nig.ac.jp/wabi-e.html",
"information_keywords": [
"Method",
"Sequence"
],
"maintainer": "Bioinformation and DDBJ Center, National Institute of Genetics, Research Organization of Information and Systems",
"name": "WABI",
"prefix": "NBDC02377",
"pubmeds": [
"19417067"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02378": {
"alt_name": "Resource for Informatics of Glycomes at Soka",
"description": "RINGS is a freely available Web resource for academic glycobiologists to analyze their data using the latest data mining and algorithmic techniques. It provides a number of tools including a Glycan Miner Tool for mining alpha-closed frequent subtrees from a set of glycan structures, Glycan Pathway Predictor (GPP) tool for dynamically computing the N-glycan biosynthesis pathway from a given glycan structure and a glycan structure multiple alignment tool MCAW.",
"homepage": "https://rings.glycoinfo.org/",
"information_keywords": [
"Method",
"Chemical structure"
],
"maintainer": "Soka University Faculty of Science and Engineering",
"name": "RINGS",
"prefix": "NBDC02378",
"pubmeds": [
"20726803"
],
"status": "Active",
"target_keywords": [
"Carbohydrate"
]
},
"nbdc02379": {
"description": "This is a collection of miscellaneous plugins for ImageJ that is an open source image processing program designed for scientific multidimensional images.",
"homepage": "https://lpixel.net/en/products/lpixel-imagej-plugins/",
"information_keywords": [
"Method",
"Image/Movie"
],
"maintainer": "LPixel Inc.",
"name": "LPixel ImageJ Plugins",
"prefix": "NBDC02379",
"pubmeds": [
"24102769",
"20615231",
"20351265",
"19397744"
],
"status": "Active"
},
"nbdc02380": {
"alt_name": "PhytoChemical Interactions DB",
"description": "PCIDB is a database to elucidate therapeutic effect of plants on human. It provides integrated data from KNApSAcK, ChEMBL, CTD, OMIM and KEGG DISEASE. Users can search data by KNApSAcK Metabolite ID/NAME or KNApSAcK Species. Users can also browse data from KNApSAcK Metabolite Activity, KNApSAcK Natural Activity and 83 phytochemical clusters.",
"homepage": "https://www.genome.jp/db/pcidb",
"information_keywords": [
"Interaction/Pathway",
"Classification"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "PCIDB",
"prefix": "NBDC02380",
"status": "Active",
"target_keywords": [
"Metabolite",
"Health/Disease",
"Protein"
]
},
"nbdc02381": {
"description": "MCAW-DB is a database whereby users can view the multiple alignment analysis results obtained from the Multiple Carbohydrate Alignment with Weights (MCAW) tool.The database provides published analysis results of glycan array data from the Consortium for Functional Glycomics (CFG). Using MCAW-DB, the patterns of glycans found to bind to various GBP-glycan binding proteins are visualized.",
"homepage": "https://mcawdb.glycoinfo.org/",
"information_keywords": [
"Chemical structure",
"Interaction/Pathway"
],
"maintainer": "Soka University Faculty of Science and Engineering",
"name": "MCAW-DB",
"prefix": "NBDC02381",
"pubmeds": [
"29859376",
"28093404"
],
"status": "Active",
"target_keywords": [
"Protein",
"Carbohydrate"
]
},
"nbdc02382": {
"alt_name": "A database of DNA repair pathways",
"description": "REPAIRtoire is a database for DNA damage and repair. The database contains the following types of information: 1) DNA damage linked to environmental mutagenic and cytotoxic agents, 2) pathways comprising individual processes and enzymatic reactions involved in the removal of damage, 3) proteins participating in DNA repair, 4) diseases correlated with mutations in genes encoding DNA repair proteins. REPAIRtoire provides also links to publications and external databases.",
"homepage": "http://repairtoire.genesilico.pl",
"information_keywords": [
"Phenotype",
"Sequence",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "International Institute of Molecular and Cell Biology in Warsaw",
"name": "REPAIRtoire",
"prefix": "NBDC02382",
"pubmeds": [
"21051355"
],
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease"
]
},
"nbdc02383": {
"description": "This site provides pdbBAM files those are binary sequence alignment/mapping (BAM) formatted file, in which proteins in Protein Data Bank (PDB) are represented in their positions of the human genome. It can be visualized with genome browsers.",
"homepage": "http://aoba.hgc.jp/pdbbam/index.html",
"information_keywords": [
"Sequence",
"3D structure",
"Interaction/Pathway",
"Localization"
],
"maintainer": "United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine",
"name": "pdbBAM",
"prefix": "NBDC02383",
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc02384": {
"description": "This site is a portal site of data resources provided by the JT Biohistory Research Hall. It contains following databases: Pt_spiderBASE (a collection of nucleotide sequences from the common house spider Parasteatoda tepidariorum), Pt_spider Image/Movie Database (a collection of images and movies from the common house spider Parasteatoda tepidariorum and other spiders), Pt_spider Genome & Transcripts Data BASE, (genome sequence data produced by Baylor Colledge of Medicine Human Genome Sequencing Center, BCM-HGSC, and the spider genome research community), BLAST against arthropod genome/RNA databases (a collection includes NGS sequences of the isopod sea slater Ligia exotica and the decapoda freshwater shrimp Caridina multidentata) and InsectInDB (Insect Interaction Database for integrating chemical ecology and genomics).",
"homepage": "http://www.brh2.jp",
"information_keywords": [
"Interaction/Pathway",
"Image/Movie",
"Expression",
"Portal"
],
"maintainer": "JT Biohistory Research Hall",
"name": "JT Biohistory Research Hall : Data Resources",
"prefix": "NBDC02384",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Metabolite",
"Organism"
]
},
"nbdc02385": {
"description": "AtMetExpress LC-MS is a phytochemical atlas of Arabidopsis thaliana. Here, following two datasets are available; a dataset for phytochemical accumulation of many developmental stages and organs in Arabidopsis thaliana (AtMetExpress Development LC-MS) and a dataset of the composition of secondary metabolites among 20 Arabidopsis ecotypes (AtMetExpress 20 ecotypes LC-MS). Integrated clustering of transcriptome and metabolome data are also available.",
"homepage": "http://prime.psc.riken.jp/lcms/AtMetExpress/",
"information_keywords": [
"Localization"
],
"maintainer": "RIKEN CSRS (RIKEN Center for Sustainable Resource Science)",
"name": "AtMetExpress LC-MS",
"prefix": "NBDC02385",
"pubmeds": [
"20023150"
],
"status": "Closed",
"target_keywords": [
"Metabolite",
"Cell/Organelle",
"Organism"
]
},
"nbdc02387": {
"alt_name": "Research Environment for Comparative Genomics",
"description": "RECOG is a workbench software program using the MBGD (Microbial Genome Database for Comparative Analysis) data, which is used to conduct comparative genome analyses on a massive scale. RECOG is dedicated client software program that is available immediately after connecting to the MBGD server. Meanwhile, the analysis of newly determined microbial genomes, eukaryotic genomes, etc. that are not included in the MBGD can also be conducted in a local environment.",
"homepage": "http://mbgd.genome.ad.jp/RECOG/",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "National Institute for Basic Biology",
"name": "RECOG",
"prefix": "NBDC02387",
"pubmeds": [
"28451978"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02388": {
"description": "This is a catalog about strains of pathogenic fungi and actinomycetes isolated or stocked at the Medical Mycology Research Center, Chiba University. Each entry contains scientific name, isolated Date, Genotype, Serotype, DNA Sequence, etc. Users can search organisms by a list of Fungi, a list of Actinomycetes, DNA homology or strain names. Whole genome data of some organisms are downloadable, and users can order DNA samples on this website.",
"homepage": "https://daphne.pf.chiba-u.jp/distribution/catalog",
"information_keywords": [
"Sequence",
"Bioresource"
],
"maintainer": "Medical Mycology Research Center, Chiba University",
"name": "Pathogenic fungi/actinomycetes catalog",
"prefix": "NBDC02388",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Health/Disease"
]
},
"nbdc02389": {
"alt_name": "Buckwheat Genome DataBase",
"description": "BGDB is a genome database for Buckwheat. It provides a draft assembly sequence of the genome using short reads obtained by NGS, and information of predicted genes with annotation by BLAST analysis of the NCBI NR and/or TAIR 10 databases. The results of a domain search against InterPro are also available.",
"homepage": "http://buckwheat.kazusa.or.jp",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "BGDB",
"prefix": "NBDC02389",
"pubmeds": [
"27037832"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02390": {
"alt_name": "Fishes of Mainland Southeast Asia",
"description": "FiMSeA is a database about fishes of the mainland Southeast Asia. It contains information of fish specimens (Taxon, DNA information, Specimen preserved institute, Sampling location etc.) and digital-image photographs which obtained in Laos, Thailand, Cambodia, Vietnam, Malaysia and Japan. Users can search using a map, keywords or taxonomy trees.",
"homepage": "https://ffish.asia",
"information_keywords": [
"Environment",
"Geographic Distribution",
"Taxonomy",
"Image/Movie",
"Sequence"
],
"maintainer": "Nagao Natural Environment Foundation",
"name": "FiMSeA",
"prefix": "NBDC02390",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"Organism"
]
},
"nbdc02391": {
"description": "Mutation@A Glance is an integrated database for genetic variations including disease-causing mutations, cancer-related mutations and natural variants in human genes. It includes data in databases of Genetic variants (dbSNP, ClinVar, COSMIC, KGP3, ExAC), of Human diseases (OMIM, RAPID), and of Genes, transcripts and Proteins (NCBI Gene, RefSeq, Ensembl, UniProt, Protein Data Bank, HetPDB-Navi.).",
"homepage": "http://mutation.nagahama-i-bio.ac.jp",
"information_keywords": [
"Sequence",
"3D structure"
],
"maintainer": "Nagahama Institute of Bio-Science and Technology",
"name": "Mutation@A Glance",
"prefix": "NBDC02391",
"pubmeds": [
"20360267"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease",
"Protein"
]
},
"nbdc02393": {
"alt_name": "Algae Gene Coexpression Database",
"description": "ALCOdb is a gene coexpression database for microalgae. It provides gene coexpression data about two unicellular microalgae: a green alga Chlamydomonas reinhardtii and a red alga Cyanidioschyzon merolae. Original data were obtained from public databases such as Sequence Read Archive (http://integbio.jp/dbcatalog/record/nbdc01098) or Gene Expression Omnibus (http://integbio.jp/dbcatalog/record/nbdc00080), and analyzed. The information of orthologous genes in Arabidopsis thaliana and the other microalgae are provided, and users can check the coexpression genes in those organisms.",
"homepage": "http://alcodb.jp",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Tohoku University Graduate School of Information Sciences",
"name": "ALCOdb",
"prefix": "NBDC02393",
"pubmeds": [
"26644461"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02394": {
"description": "AlliumTDB is a database for transcriptomic data by RNA-Seq about Allium sp. Each entry contains sequence data, expression profile, BLAST annotations using TAIR, IRGSP or NCBI, and corresponding unigene data in each data set. BLAST search using own sequence data and keyword search are available.",
"homepage": "http://alliumtdb.kazusa.or.jp/index.html",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "AlliumTDB",
"prefix": "NBDC02394",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02395": {
"description": "Virus-Host DB is a database about the relationships between viruses and their hosts. It provides information of the relationships represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts. This database covers viruses with complete genomes stored in 1) NCBI/RefSeq and 2) GenBank whose accession numbers are listed in EBI Genomes. The host information is collected from RefSeq, GenBank (in free text format), UniProt, ViralZone, and manually curated with additional information obtained from literatures.",
"homepage": "http://www.genome.jp/virushostdb",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Kyoto University Institute for Chemical Research Bioinformatics Center",
"name": "Virus-Host DB",
"prefix": "NBDC02395",
"pubmeds": [
"26938550"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02399": {
"description": "This database provides the retinoid X receptor (RXR) binding sites in the human genome identified by a modified yeast one-hybrid system, and the experimentally validated regulatory SNPs (rSNPs) those affect the binding ability of RXR in the RXR binding sites.",
"homepage": "http://www.drkazu.com/TOHOrSNPdb.htm",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Department of Biomolecular Science, Faculty of Science, Toho University",
"name": "TOHO rSNP DB",
"prefix": "NBDC02399",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02400": {
"description": "This database provides the constitutive androstane receptor (CAR) binding sites in the human genome identified by a modified yeast one-hybrid system, and the experimentally validated regulatory SNPs (rSNPs) those affect the binding ability of CAR in the CAR binding sites.",
"homepage": "http://www.drkazu.com/TOHOrSNPdb2.html",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Department of Biomolecular Science, Faculty of Science, Toho University",
"name": "TOHO rSNP DB2",
"prefix": "NBDC02400",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02401": {
"description": "TodoFirGene is a transcriptome database for Abies sachalinensis. It provides gene expression data in the female flower, male flower, young leaf and inner bark, and gene annotations. It also provides links to the proteomes of 13 other species. The database can be queried by keywords, sequences or expression levels, and it has a bulk download page.",
"homepage": "http://plantomics.mind.meiji.ac.jp/todomatsu/",
"information_keywords": [
"Sequence",
"Expression",
"Localization"
],
"maintainer": "The University of Tokyo||Forestry and Forest Products Research Institute||Hokkaido Research Organization||Meiji University",
"name": "TodoFirGene",
"prefix": "NBDC02401",
"pubmeds": [
"29566239"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"RNA",
"Organism"
]
},
"nbdc02402": {
"alt_name": "Transcription Profile of Escherichia coli database",
"description": "TEC database provides the regulatory targets for all sigma factors and transcription factor (TF)s in E. coli identified by genomic SELEX screening. Users can search either TFs that may regulate specific genes or target genes regulated by TF(s) of specific interest. Then, the results can be filtered by binding intensity and/or location. Users can view both bar chart and heat map of TF binding, and can analyze consensus sequences and download raw data.",
"homepage": "https://shigen.nig.ac.jp/ecoli/tec/",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "National Institute of Genetics||TEC group",
"name": "TEC database",
"prefix": "NBDC02402",
"pubmeds": [
"26843427"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"Protein",
"Organism"
]
},
"nbdc02403": {
"description": "\"Global Red List of Japanese Threatened Plants\" provides information of threatened vascular plants from national or regional red lists of China, Japan, South Korea, East Russia and Taiwan. National or regional red lists were cited for determining status in each country or region. Users can browse Red list from Division and Family list.",
"homepage": "http://www.kahaku.go.jp/english/research/db/botany/redlist/index.html",
"information_keywords": [
"Geographic Distribution",
"Taxonomy"
],
"maintainer": "National Museum of Nature and Science",
"name": "Global Red List of Japanese Threatened Plants",
"prefix": "NBDC02403",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02404": {
"alt_name": "Neotoma Paleoecology Database",
"description": "The Neotoma Paleoecology Database is a community-curated data repository for paleoecological data spanning the last 5 million years. Data currently include fossil pollen, mammal, diatom, ostracode, and geochemical data. All data stored in Neotoma are free to use through a CC BY 4.0 license. Neotoma data can be accessed via the Neotoma Explorer interactive map-based interface, an API and also the neotoma R package.",
"homepage": "https://www.neotomadb.org",
"information_keywords": [
"Geographic Distribution",
"Taxonomy",
"Repository"
],
"maintainer": "Neotoma Leadership Council",
"name": "Neotoma",
"prefix": "NBDC02404",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02406": {
"alt_name": "Rare Disease Data Registry of Japan",
"description": "The RADDAR-J site was constructed for consolidating and supporting registry studies about intractable diseases covered by the Practical Research Project for Rare/Intractable Diseases of the Japan Agency for Medical Research and Development (AMED) and the Research Project on Rare/Intractable Disease of the Ministry of Health, Labour and Welfare (MHLW). It provides document templates required for the construction and operation of intractable disease registries.\nUsers can browse the list of intractable disease registries or search with keywords, and data collected by RADDAR-J may be available for secondary use for research.",
"homepage": "https://www.raddarj.org/en/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "RADDAR-J",
"name": "RADDAR-J",
"prefix": "NBDC02406",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc02407": {
"alt_name": "the MUTANTS",
"description": "The MUTANTS is a database of compounds (including natural substances) which have been tested for their mutagenicity (genotoxicity) by the systems of different genetic end-points. It provides CAS numbers, general uses and molecular weight as well as their chemical structures of compounds. It also provides test results of each compound for their mutagenicity (genotoxicity) and references from which data was cited. The test results are evaluated quantitatively rather than qualitatively, e. g. the minimum (Min.) or maximum (Max.) concentration for positive or negative results, respectively. Compounds are arranged alphabetically.",
"homepage": "http://www.j-ems.org/the-mutants/mo-ishidate/index.html",
"information_keywords": [
"Chemical structure",
"Bibliography/Documents"
],
"maintainer": "JEMS (The Japanese Environmental Mutagen Society)",
"name": "Database of Genotoxicity of Chemicals",
"prefix": "NBDC02407",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Chemical compound",
"Health/Disease"
]
},
"nbdc02410": {
"alt_name": "Database of Pathogenic Variants",
"description": "DPV provides information on germline pathogenic mutations in the Japanese population. The data of mutations were curated from published papers regarding Japanese patients with rare diseases and research activities in Japan. All registered variants can be downloaded as an aggregated single VCF file to use in laboratories.",
"homepage": "http://dpv.cmg.med.keio.ac.jp/dpv-pub/top",
"information_keywords": [
"Phenotype",
"Sequence",
"Bibliography/Documents"
],
"maintainer": "Center for Medical Genetics, Keio University School of Medicine",
"name": "DPV",
"prefix": "NBDC02410",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc02411": {
"alt_name": "Information site for evidence-based Japanese Integrative Medicine",
"description": "The site introduces evidence-based information on how to consider the relative advantages and disadvantages of complementary and alternative medicine including folk therapy. The investigation committee collects scientific knowledge on the safety and effectiveness of each therapy, and analyzes and formats the findings for publication to the website. Users can search across the website by keyword.",
"homepage": "http://www.ejim.ncgg.go.jp/en/index.html",
"information_keywords": [
"Bibliography/Documents",
"Portal"
],
"maintainer": "Osaka University",
"name": "eJIM",
"prefix": "NBDC02411",
"status": "Active",
"target_keywords": [
"Chemical compound",
"Drug",
"Health/Disease"
]
},
"nbdc02412": {
"alt_name": "Japanese Familial Alzheimer's Disease database",
"description": "JFADdb contains information about mutations in genes linked to dominantly inherited Alzheimer's disease (APP, PSEN1, and PSEN2) as well as FTDP-17 (MAPT and GRN) in the Japanese population. The database was created by literature search. Users can search for mutations and patients by gene, phenotype or keyword.",
"homepage": "http://www.alzdb.org/jfad/",
"information_keywords": [
"Phenotype",
"Sequence",
"Bibliography/Documents"
],
"maintainer": "Department of Molecular Genetics, Brain Research Institute, Niigata University",
"name": "JFADdb",
"prefix": "NBDC02412",
"pubmeds": [
"25694106"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc02414": {
"alt_name": "Sol Genomics Network",
"description": "SGN is a database of genome and phenotype data for species in the Solanaceae and their close relatives. It provides genome maps and sequences, QTLs, RNA-seq, and microarray data. Users can use tools, such as BLAST, Browse for browsing genomes, expression and map data viewers, a locus community annotation system and a QTL analysis tools.",
"fairsharing": "biodbcore-000301",
"homepage": "https://solgenomics.net",
"information_keywords": [
"Sequence",
"Expression",
"Phenotype",
"Method",
"Repository"
],
"maintainer": "Boyce Thompson Institute for Plant Research",
"name": "SGN",
"prefix": "NBDC02414",
"pubmeds": [
"25428362"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc02415": {
"description": "GlyCosmos Portal is a portal site of glycoscience-related web resources, which includes databases and repositories for glycogenes, glycoconjugates such as glycoproteins and glycolipids, molecular structures, and pathways, and which also includes standard notations for carbohydrate structures (WURCS) and ontologies for glycoscience.",
"homepage": "https://glycosmos.org/",
"information_keywords": [
"Chemical structure",
"Phenotype",
"Ontology/Terminology/Nomenclature",
"Sequence",
"Interaction/Pathway",
"Portal",
"Repository"
],
"maintainer": "GlyCosmos Portal",
"name": "GlyCosmos Portal",
"prefix": "NBDC02415",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Carbohydrate",
"Lipid",
"Health/Disease"
]
},
"nbdc02416": {
"alt_name": "Plant Genome And Resource Database ENtry",
"description": "Plant GARDEN is a portal site that curates genome and marker information of various plant species. It contains information about assembled genomes, markers (SSR, CAPS, SCAR), bio samples, gene annotation, amino acid, etc. It allows to browse using species, markers, traits (stress, fertility, yield, morphology, etc.), or search using BLAST, SNPs and Linkage Maps.",
"homepage": "https://plantgarden.jp/app_en/",
"information_keywords": [
"Sequence",
"Phenotype",
"Expression"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Plant GARDEN",
"prefix": "NBDC02416",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"cDNA/EST",
"Genetic variation",
"Organism"
]
},
"nbdc02418": {
"description": "Linnaeus NG is a data management system for species information developed and maintained by Naturalis Biodiversity Center. It contains a wide variety of information about taxa. This system allows users to create their own website for managing, organizing and publishing data about the taxonomy and species information such as the naming, synonyms, detailed species descriptions. Images and sounds can also be added with links to the relevant species.",
"homepage": "http://linnaeus.naturalis.nl",
"information_keywords": [
"Taxonomy",
"Bibliography/Documents"
],
"maintainer": "Naturalis Biodiversity Center",
"name": "Linnaeus NG",
"prefix": "NBDC02418",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02419": {
"alt_name": "Database of Pathogen Genomics and Epidemiology",
"description": "GenEpid-J is an integrated database of pathogen genomics and epidemiology focused on plasmids involving in the antimicrobial resistance.",
"homepage": "https://gph.niid.go.jp/genepid-j/",
"information_keywords": [
"Phenotype",
"Environment",
"Sequence",
"Geographic Distribution"
],
"maintainer": "National Institute of Infectious Diseases",
"name": "GenEpid-J",
"prefix": "NBDC02419",
"pubmeds": [
"26774245"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Drug",
"Genetic variation",
"Organism",
"Health/Disease"
]
},
"nbdc02420": {
"description": "GenomeSync is a large database of genome sequences mostly from NCBI Assembly. Once GenomeSync is downloaded using Syncthing software, a local copy of the database is continuously kept up-to-date automatically. For animals and plants, it includes one genome per species. A subset of NCBI taxonomy database is also included. Each genome is stored in single file, in NAF format which compresses from FASTA or FASTQ.",
"homepage": "http://genomesync.org/",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "Tokai University School of Medicine",
"name": "GenomeSync",
"prefix": "NBDC02420",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02421": {
"alt_name": "Brain Mapping by Integrated Neurotechnologies for Disease Studies Data Portal",
"description": "The Brain/MINDS Data Portal shares the data being produced in the Brain/MINDS project. The common marmoset (Callithrix jacchus) 3D reference brain atlas is available for download. It can be viewed by using a web viewer too. The portal also provides a dataset of human brain images obtained with 3T MRI (includes T1-weighted images of 57 patients with psychiatric disorders and 97 healthy controls) and images of transparent brains as technical innovations. Users can search for the datasets by keyword.",
"homepage": "https://www.brainminds.riken.jp/",
"information_keywords": [
"Phenotype",
"Expression",
"Method",
"Localization",
"Image/Movie",
"Portal"
],
"maintainer": "RIKEN CBS (RIKEN Center for Brain Science)||Brain/MINDS Database Council",
"name": "Brain/MINDS Data Portal",
"prefix": "NBDC02421",
"pubmeds": [
"25823872",
"27809998",
"29437168"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"Organism",
"Genome/Gene",
"Health/Disease"
]
},
"nbdc02422": {
"description": "The Marmoset Gene Atlas provides a whole brain, high-resolution gene expression atlas in the common marmoset (Callithrix jacchus). It provides in situ hybridization (ISH) data over the course of postnatal brain development to adult stage. Users can search for gene expression data by gene name or disease. This is a part of the Brain/MINDS project.",
"homepage": "https://gene-atlas.brainminds.riken.jp/",
"information_keywords": [
"Expression",
"Localization",
"Image/Movie",
"Sequence"
],
"maintainer": "RIKEN CBS (RIKEN Center for Brain Science)",
"name": "Marmoset Gene Atlas",
"prefix": "NBDC02422",
"pubmeds": [
"27809998",
"29111135"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle",
"Organism",
"Health/Disease"
]
},
"nbdc02425": {
"alt_name": "National BioResource Project Oxycomanthus Japonicus",
"description": "Misaki Marine Biological Station, University of Tokyo, participates in National Bio Resource Project for collection, maintenance and distribution of living juveniles and adults, fixed larvae, juveniles and adults, as well as cDNA libraries and arrayed BAC library of O. japonicus.",
"homepage": "http://marinebio.nbrp.jp/oxycomanthus/",
"information_keywords": [
"Bioresource"
],
"maintainer": "The University of Tokyo Graduate School of Science The Misaki Marine Biological Station",
"name": "OJRES (Oxycomanthus Japonicus RESources)",
"prefix": "NBDC02425",
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Cell/Organelle",
"Organism"
]
},
"nbdc02426": {
"alt_name": "integrative DNA methylation database",
"description": "iMETHYL is an integrative multi-omics (methylome, transcriptome, and genome) database. These data were obtained from WGBS, WGS, and RNA-Seq for CD4+ T-lymphocytes, monocytes, and neutrophils collected from approximately 100 subjects. From the genome browser, regions of interest can be specified using gene symbols, dbSNP ID and genomic positions. The genome browser provides graphical views of the methylation level, expression level and allele frequencies of each SNV in each of the three human cell types.",
"homepage": "http://imethyl.iwate-megabank.org/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Iwate Tohoku Medical Megabank Organization",
"name": "iMETHYL",
"prefix": "NBDC02426",
"pubmeds": [
"29263827",
"29619235"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Epigenetics",
"DNA",
"Cell/Organelle"
]
},
"nbdc02427": {
"alt_name": "VAriation effect on PROtein Structure and function",
"description": "VaProS is a new data cloud for Structural Life Science, integrates different databases/tools to provides protein/genome information for researchers. VaProS accepts keywords, DNA/protein sequence, EntrezGene ID and UniProtKB accession as a query. The search results are presented graphically as found in the protein-protein interactions, frequently used terms in literature, gene co-expression, the relationship between phenotype and protein 3D structure, structural effect of the gene mutation and so on.",
"homepage": "http://pford.info/vapros/",
"information_keywords": [
"3D structure",
"Expression",
"Interaction/Pathway",
"Phenotype",
"Bibliography/Documents",
"Portal"
],
"maintainer": "Waseda University",
"name": "VaProS",
"prefix": "NBDC02427",
"pubmeds": [
"28012137"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc02428": {
"alt_name": "H Genome TO Protein structures and functions",
"description": "hGTOP is a database of human, mouse, rat proteins identified in the genome, focuses on a structural annotation. The original GTOP (https://integbio.jp/dbcatalog/en/record/nbdc00089) includes proteins in over 1000 organisms. hGTOP provides protein annotation of 3D structures and functions based on similarity searches against PDB, SCOP, Pfam, and Swiss-Prot, 2D structure predictions, intrinsically disordered regions, functional motifs, and others. Users can select organism and search database by keyword. In addition, a number of homologs are shown in taxonomy tree.",
"homepage": "http://pford.info/hGTOP/",
"information_keywords": [
"Sequence",
"3D structure",
"Classification"
],
"maintainer": "National Institute of Genetics",
"name": "hGTOP",
"prefix": "NBDC02428",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02429": {
"alt_name": "Natural Ligand DataBase",
"description": "NLDB is a database of automatically collected and predicted 3D protein-ligand interactions in the enzymatic reactions of metabolic pathways registered in KEGG. NLDB provides three different types of data resources; the natural complexes are experimentally determined protein-ligand complex structures in PDB, the analog complexes are predicted based on known protein structures in a complex with a similar ligand, and the ab initio complexes are predicted by docking simulations. The database has a flexible search function based on various types of keywords, and an enrichment analysis function based on a set of KEGG compound IDs. In addition, NLDB shows the known polymorphisms found in human genome on protein structures.",
"homepage": "http://nldb.hgc.jp",
"information_keywords": [
"3D structure",
"Interaction/Pathway"
],
"maintainer": "Tohoku University Graduate School of Information Sciences",
"name": "NLDB",
"prefix": "NBDC02429",
"pubmeds": [
"27530928"
],
"status": "Active",
"target_keywords": [
"Protein",
"Metabolite",
"Chemical compound"
]
},
"nbdc02430": {
"alt_name": "National Bioresource Project C. elegans",
"description": "NBRP C. elegans is a National Bioresource Project for the experimental animal \"Nematode C. elegans\". Tokyo Women's Medical University is the core facility to collect, store and distribute deletion mutants, Cre recombinase transgenic and balancer strains of C. elegans.",
"homepage": "http://shigen.lab.nig.ac.jp/c.elegans/",
"information_keywords": [
"Phenotype",
"Bioresource"
],
"maintainer": "Tokyo Women's Medical University",
"name": "NBRP C. elegans",
"prefix": "NBDC02430",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Organism"
]
},
"nbdc02433": {
"alt_name": "Arabidopsis Information Portal",
"description": "Araport is an open-access online community resource for Arabidopsis research. It hosts the Araport11, updated Arabidopsis genome annotation from TAIR10. Araport offers two core web applications: ThaleMine for data mining and JBrowse for genome browsing. The site also hosts 'science apps,' that use dynamic web pages to present data obtained on-demand from third-party servers. The Araport11 data are also available by bulk download and web services.",
"fairsharing": "biodbcore-001076/",
"homepage": "https://www.araport.org/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway",
"Portal"
],
"maintainer": "JCVI (J. Craig Venter Institute)||Texas Advanced Computing Center, The University of Texas at Austin||University of Cambridge",
"name": "Araport",
"prefix": "NBDC02433",
"pubmeds": [
"28013278",
"27862469",
"25414324"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"RNA",
"Protein"
]
},
"nbdc02434": {
"description": "GlyGen is an integrated database for carbohydrate and glycoconjugate related data. It retrieves information from multiple international data sources and integrates and harmonizes this data including glycomics, genomics, proteomics (and glycoproteomics), cell biology, developmental biology and biochemistry. Users are able to seach data in three categories;\n1) Glyvcan: Search for glycan structures based on their chemical and structural properties.\n2) Protein: Search for proteins based on their sequences, accessions, and annotations.\n3) Glycoprotein: Search for glycoproteins based on the protein or glycan structures involved.",
"homepage": "https://www.glygen.org",
"information_keywords": [
"Sequence",
"Chemical structure",
"Expression",
"Interaction/Pathway",
"Portal"
],
"maintainer": "University of Georgia||George Washington University",
"name": "GlyGen",
"prefix": "NBDC02434",
"status": "Active",
"target_keywords": [
"Protein",
"Carbohydrate",
"Health/Disease"
]
},
"nbdc02435": {
"alt_name": "Drug Metabolism and pharmacokinetics Analysis Platform",
"description": "DruMAP is a database about drug metabolism and pharmacokinetics (PK) analysis. It consists of compound report database, PK search and PK prediction sites. Each compound report is curated from ChEMBL and collected all the relevant PK data on these compounds. In addition, it contains both in vitro and in vivo experimental data, chemical space of these compounds, physicochemical properties, efflux ratio of P-glycoprotein (P-gp), which is the major transporter in gut and brain. This database allows to search using Skecher or Keywords.",
"homepage": "https://drumap.nibiohn.go.jp/",
"information_keywords": [
"Chemical structure",
"Interaction/Pathway",
"Method"
],
"maintainer": "National Institutes of Biomedical Innovation, Health and Nutrition",
"name": "DruMAP",
"prefix": "NBDC02435",
"status": "Active",
"target_keywords": [
"Drug",
"Chemical compound"
]
},
"nbdc02440": {
"alt_name": "Phenotyping Hybrid Information System",
"description": "PHIS is an ontology-driven open source information system designed for plant phenomics. It allows assembling a number of datasets from different installations in controlled and field conditions (including phenotypic, environmental and contextual information), resulting in information that can be reused and reanalyzed. PHIS is accessed through an interactive web user interface after guest login, and also through a web service API.",
"homepage": "http://www.phis.inra.fr/",
"information_keywords": [
"Phenotype",
"Ontology/Terminology/Nomenclature",
"Environment",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "MISTEA / LEPSE, INRA (French National Institute for Agricultural Research)",
"name": "PHIS",
"prefix": "NBDC02440",
"pubmeds": [
"30152011"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02441": {
"description": "Eggplant Genome DataBase is a database about an eggplant (Solanum melongena L.)whole-genome dataset. Each entry contains nucleotide sequence, translated sequence, BLAST search data from other databases such as ITAG, TAIR, NR or Swissprot. It also contains GO annotation from InterProScan. This database allows to search using BLAST or keywords.",
"homepage": "http://eggplant.kazusa.or.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Eggplant Genome DataBase",
"prefix": "NBDC02441",
"pubmeds": [
"25233906"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02442": {
"description": "DBcherry is a database for cherry genomics. It contains information about Sweet cherry (Prunus avium), Satonishiki;\n1) whole genome sequences with gene annotation\n2) SNP, SSR, and indel molecular markers\n3) Genetic maps based on SNPs and SSRs\n4) Genome browser for genome, markers, and maps.\nIt also contains information about flowering cherry (Cerasus x yedoensis), Somei-Yoshino;\n1) whole genome sequences with gene annotation\n2) SNPs and indels.",
"homepage": "http://cherry.kazusa.or.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "DBcherry",
"prefix": "NBDC02442",
"pubmeds": [
"28541388"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02443": {
"description": "This is a collection of tissue specific transcriptomic data for Bombyx mori. RNAseq was applied for multiple tissues in Bombyx mori P50T strain using new reference genome data. Related SRA data were also included. The annotation of transcripts were created by Blast analysis against Human and Drosophila gene sets. The data were produced and organized by Institute of Agrobiological Sciences, National Agriculture and Food Research Organization /Research Center for Agricultural Information Technology , National Agriculture and Food Research Organization.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/kaiko/desc.html",
"information_keywords": [
"Expression",
"Sequence",
"Localization"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "Silkworm, Bombyx mori, reference transcriptome data",
"prefix": "NBDC02443",
"pubmeds": [],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02444": {
"alt_name": "Sweetpotato Genome And Resource Database Entry",
"description": "Sweetpotato GARDEN is a database for Sweetpotato (Ipomoea batatas) genomics. Each entry contains nucleotide sequence, BLAST search data from other databases such as TAIR and NR. It also contains GO annotation from InterProScan. Users can search genes by BLAST or genetic map. It also contains KEGG Map for metabolism.",
"homepage": "http://sweetpotato-garden.kazusa.or.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Sweetpotato GARDEN",
"prefix": "NBDC02444",
"pubmeds": [
"25805887",
"28281636"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02445": {
"description": "Zoysia Genome Database is a database for zoysiagrasses genomics. It contains sequencing and comparative analyses data about the genomes of zoysiagrasses; Z. japonica, Z. matrella, and Z. pacifica. Each entry has information about nucleotide sequence, BLAST search (TAIR, NR, IRGSP and Sbicolor), GO annotation, pseudomolecule and coding region. Users can search genes by BLAST or keywords.",
"homepage": "http://zoysia.kazusa.or.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Zoysia Genome Database",
"prefix": "NBDC02445",
"pubmeds": [
"26975196"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02446": {
"description": "Eucalyptus camaldulensis Genome Database contains genetic information of E. camaldulensis which was investigated by sequencing the genome and the cDNA using a combination of the conventional Sanger method and next-generation sequencing methods, followed by intensive bioinformatics analyses. Users can search by sequence similarity or keywords.",
"homepage": "http://www.kazusa.or.jp/eucaly/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Eucalyptus camaldulensis Genome Database",
"prefix": "NBDC02446",
"pubmeds": [],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02447": {
"alt_name": "Mum Genome And Resource Database Entry",
"description": "Mum GARDEN is a database for cultivated chrysanthemum genomics. Each entry contains sequences (genome, CDS, PEP), BLAST results from NR and Araport11, and InterProScan data. Additionally, this database provides information of SSR markers including motif, sequences of primers, number of repeats, scaffolds, etc. Users can search by keywords and BLAST. All data are downloadable.",
"homepage": "http://mum-garden.kazusa.or.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "Kazusa DNA Research Institute",
"name": "Mum GARDEN",
"prefix": "NBDC02447",
"pubmeds": [
"30689773"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02448": {
"alt_name": "Burkholderia Genome Database",
"description": "The Burkholderia Genome Database provides a resource for cystic fibrosis research community to perform multi-genome comparisons of strains within the Burkholderia cepacia complex and to other Burkholderia genomes. Users can search annotations/sequences and view multiple genomes with genome browser. It also collects additional information through other sites, such as subcellular localization predictions, and protein-protein interactions. All sequences and annotations can be downloaded.",
"homepage": "https://www.burkholderia.com/",
"information_keywords": [
"Sequence"
],
"maintainer": "Simon Fraser University",
"name": "Burkholderia Genome DB",
"prefix": "NBDC02448",
"pubmeds": [
"18842600"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02449": {
"alt_name": "Pig Genome Database",
"description": "Pig Genome Database (PGD) is a central pig genome information hub to support the community activities. The key functions of PDG include pig gene pages (a centralized gene search tool), a local copy of Biomart (for customizable genome information queries), genome feature alignment tools (Pig QTLdb and Gbrowse), integrated gene expression information (ANEXDB and ESTdb), a dedicated pig genome and gene set BLAST server, virtual comparative map database and tools (VCmap) and a livestock genetic/phenotypic trait correlation data (CorrDB).",
"homepage": "https://www.animalgenome.org/pig/genome/db/",
"information_keywords": [
"Sequence",
"Expression",
"Portal"
],
"maintainer": "Iowa State University",
"name": "PGD",
"prefix": "NBDC02449",
"pubmeds": [
"16261421"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02450": {
"alt_name": "sake yeast genome database",
"description": "SYGD contains the genome sequence of sake yeast strain, Kyokai no. 7 (K7). Users can search and browse the sequence and annotation information of the individual genes. It also provides Dot plot analysis and Differential analysis for comparison with the laboratory strain S288C genome.",
"homepage": "https://www.nrib.go.jp/English/researches/sygd_en.htm",
"information_keywords": [
"Sequence"
],
"maintainer": "National Research Institute of Brewing",
"name": "SYGD",
"prefix": "NBDC02450",
"pubmeds": [
"21900213"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02451": {
"alt_name": "Adaptive Laboratory Evolution database",
"description": "ALEdb is a database of mutations from adaptive laboratory evolution experimentation. The mutations stored at ALEdb are characterized by the genome position, the affected gene, the type of mutation, and the cell culture conditions used in the ALE experiment. Data from different studies can be exported and analyzed.",
"homepage": "https://aledb.org/",
"information_keywords": [
"Environment",
"Sequence",
"Bibliography/Documents"
],
"maintainer": "UCSD (University of California San Diego)",
"name": "ALEdb",
"prefix": "NBDC02451",
"pubmeds": [
"30357390"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02452": {
"alt_name": "Ancient mtDNA database",
"description": "AmtDB is a database of ancient human mitochondrial genomes. It provides both the mtDNA sequences (in FASTA format) and the metadata for the samples, freely accessible for download. All provided data are hand-curated. Users can search for and filter all samples according to IDs, dates, geolocation, site, culture, mtDNA haplogroup, etc. Visualization the search results on an interactive world map is also available.",
"homepage": "https://amtdb.org/",
"information_keywords": [
"Sequence",
"Geographic Distribution"
],
"maintainer": "Institute of Molecular Genetics of the ASCR",
"name": "AmtDB",
"prefix": "NBDC02452",
"pubmeds": [
"30247677"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"Cell/Organelle"
]
},
"nbdc02453": {
"alt_name": "Ancestral Genomes Resource",
"description": "Ancestral Genomes is a resource for the reconstructions of the protein-coding gene content of common ancestors of modern-day organisms. The reconstructed genes are based on the PANTHER database. All ancestral genes have information including stable identifier, protein name, reconstructed sequence, inferred GO functions and 'proxy genes' in extant species. Users can browse the Ancestral Genomes by selecting nodes in a species tree, and can compare an extant genome with any of its reconstructed ancestors. All data can be downloaded.",
"homepage": "http://ancestralgenomes.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Sequence",
"Taxonomy"
],
"maintainer": "USC (University of Southern California)",
"name": "Ancestral Genomes",
"prefix": "NBDC02453",
"pubmeds": [
"30371900"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Organism"
]
},
"nbdc02454": {
"alt_name": "A Website Exhibits SNP On Modification Event",
"description": "AWESOME is a comprehensive database to predict SNPs that may gain/loss protein post-translational modfication (PTM) sites. The PTM changes affected by SNPs were annotated by experimental data and prediction tools. Users can search SNPs, genes or position of interest, filter with specific modifications or prediction methods, to get a comprehensive PTM change induced by SNPs. AWESOME also supports a batch query and data download.",
"homepage": "http://www.awesome-hust.com/",
"information_keywords": [
"Sequence"
],
"maintainer": "Tongji Medical College Huazhong University of Sciences and Technology",
"name": "AWESOME",
"prefix": "NBDC02454",
"pubmeds": [
"30215764"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Protein"
]
},
"nbdc02455": {
"alt_name": "bacterial genome database",
"description": "BACTOME provides detailed information on a large collection of clinical Pseudomonas aeruginosa isolates. It includes gene sequence information, transcriptome profiles as well as phenotypic data. The phenotype section comprises hospital-derived data for each clinical isolate with phenotypes such as antibiotic resistance and virulence. The genome section comprises genomic data of all clinical isolates including pangenome and SNP information. The transcriptome section features an interactive gene browser containing the transcriptomes of all isolates.",
"homepage": "https://bactome.helmholtz-hzi.de/",
"information_keywords": [
"Phenotype",
"Sequence",
"Expression",
"Image/Movie"
],
"maintainer": "Helmholtz Centre for Infection Research",
"name": "Bactome",
"prefix": "NBDC02455",
"pubmeds": [
"30272193"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"DNA",
"RNA",
"Health/Disease"
]
},
"nbdc02456": {
"alt_name": "Comparative Analysis of Germline Microsatellites",
"description": "Comparative Analysis of Germline Microsatellites (CAGm) is a database of human germline microsatellites from 2529 individuals in the 1000 genomes project. Users can query genotypes, view multiple sequence alignments, and download data for further analysis.",
"homepage": "http://www.cagmdb.org/",
"information_keywords": [
"Sequence",
"Geographic Distribution",
"Classification"
],
"maintainer": "Edward Via College of Osteopathic Medicine",
"name": "CAGm",
"prefix": "NBDC02456",
"pubmeds": [
"30329086"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"DNA",
"Organism"
]
},
"nbdc02457": {
"alt_name": "Cancer Single-cell State Atlas",
"description": "CancerSEA provides an atlas of cancer single-cell functional states and associates protein-coding genes (PCGs) and lncRNAs with these functional states at single-cell level. Single-cell RNA-Seq datasets were manually curated with 14 cancer-related functional states. Users can search a gene (list) for the associated functional states or search functional state for the related PCG/lncRNA repertoires. All data in CancerSEA can be downloaded.",
"homepage": "http://biocc.hrbmu.edu.cn/CancerSEA/",
"information_keywords": [
"Phenotype",
"Sequence",
"Expression",
"Localization",
"Classification"
],
"maintainer": "Harbin Medical University",
"name": "CancerSEA",
"prefix": "NBDC02457",
"pubmeds": [
"30329142"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"RNA",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc02458": {
"description": "CancerSplicingQTL is a database to provide a comprehensive resource of splicing quantitative trait loci (sQTLs) across 33 human cancer types. Users can search, browse and download the three datasets; sQTLs, sQTLs associated with patient survival and sQTLs in GWAS linkage disequilibrium regions. Two query sections 'Single Search' and 'Batch Search' allow users to input cancer type(s), SNP(s), gene(s) or genomic region(s) to search sQTLs across all datasets.",
"homepage": "http://www.cancersplicingqtl-hust.com/",
"information_keywords": [
"Sequence",
"Phenotype"
],
"maintainer": "Huazhong University of Science and Technology",
"name": "CancerSplicingQTL",
"prefix": "NBDC02458",
"pubmeds": [
"30329095"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc02459": {
"description": "CellMarker database provides a manually curated, comprehensive and accurate resource of cell markers for various cell types in tissues of human and mouse. Users can search for cell markers by clicking on hyperlinks embedded in the web anatomical images, selecting tissue and cell type from the hierarchical trees, or entering gene symbol, gene ID or protein name. In addition, users can download all data and submit new data via the 'Download' and 'Submit' page, respectively.",
"homepage": "http://biocc.hrbmu.edu.cn/CellMarker/",
"information_keywords": [
"Method",
"Classification"
],
"maintainer": "Harbin Medical University",
"name": "CellMarker",
"prefix": "NBDC02459",
"pubmeds": [
"30289549"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc02460": {
"description": "The Cell Model Passports provides access to a cancer cell line and organoid model database containing curated patient, sample and model relationship information as well as genomic and functional datasets. The majority of models have associated datasets including somatic nucleotide variant, gene expression, copy number variation, methylation or drug sensitivity data. These large scale datasets can be available through the website as processed downloads and via the API.",
"homepage": "https://cellmodelpassports.sanger.ac.uk/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "Wellcome Sanger Institute",
"name": "Cell Model Passports",
"prefix": "NBDC02460",
"pubmeds": [
"30260411"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Epigenetics",
"Drug",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc02461": {
"description": "Tree Shrew Database is a knowledge base for Chinese tree shrew genome biology. It provides a comprehensive annotation for reference genome of the Chinese tree shrew, gene expression pattern in tissues, and mapping of single nucleotide polymorphisms (SNPs) from the result of sequencing the genomes of 6 wild tree shrews. It also integrated multiple common tools, such as Gbrowse, Blast, Genewise, Muscle.",
"homepage": "http://www.treeshrewdb.org",
"information_keywords": [
"Sequence",
"Expression",
"Localization"
],
"maintainer": "Kunming Institute of Zoology, Chinese Academy of Sciences",
"name": "Tree Shrew Database",
"prefix": "NBDC02461",
"pubmeds": [
"31418539"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Organism"
]
},
"nbdc02462": {
"description": "ChIPprimersDB is a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP). All primers listed are published in peer-reviewed manuscripts and a reported >5-fold change over a valid control. In addition to the primer sequences, the database includes their melting temperatures (Tm), information about the antibody, samples used in the experiment, the PubMed ID of the publication. The database can be searched by keyword, and all entries can be easily downloaded. Users can also submit their own published primer sequences.",
"homepage": "https://www.chipprimers.com/",
"information_keywords": [
"Method",
"Sequence",
"Bibliography/Documents",
"Repository"
],
"maintainer": "University of Miami Miller School of Medicine",
"name": "ChIPprimersDB",
"prefix": "NBDC02462",
"pubmeds": [
"30202990"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"Protein"
]
},
"nbdc02463": {
"alt_name": "Collective Molecular Activities of Useful Plants",
"description": "The CMAUP database provides collective molecular activities of useful plants (e.g. medicinal and food plants). Data are manually collected from literatures or from other related databases. Users can search plants by keywords, ingredient, plant usage classes, target proteins, KEGG pathways, gene ontologies, diseases and geographical locations. Each webpage of a specific plant shows general information, list of targeted human proteins, molecular activities and so on. The landscape of the target-ingredient activity profiles is further displayed by the 2D target-ingredient heatmap. All data can be freely downloaded.",
"homepage": "http://bidd.group/CMAUP/",
"information_keywords": [
"Interaction/Pathway",
"Geographic Distribution",
"Taxonomy"
],
"maintainer": "National University of Singapore",
"name": "CMAUP",
"prefix": "NBDC02463",
"pubmeds": [
"30357356"
],
"status": "Active",
"target_keywords": [
"Protein",
"Metabolite",
"Chemical compound",
"Drug",
"Organism",
"Health/Disease"
]
},
"nbdc02464": {
"description": "CoevDB is a database of intramolecular coevolution among over 8,000 protein-coding genes of the bony vertebrates (Euteleostomi clade). Prediction of coevolution can be obtained using the unique Coev software. Users can browse a list of genes, ranked by the number of unique pairs of sites having a medium or strong score of coevolution. Users can also query a gene of interest using the Ensembl identifier. The result page provides all the estimations of coevolution ranked by significance. These results can be visualized along the species tree. The full database is available to download (as MySQL dumps).",
"homepage": "http://phylodb.unil.ch/CoevDB/",
"information_keywords": [
"Sequence",
"Taxonomy",
"Classification"
],
"maintainer": "University of Lausanne",
"name": "CoevDB",
"prefix": "NBDC02464",
"pubmeds": [
"30357342"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02465": {
"description": "CRISPRlnc is a manually curated database of validated CRISPR/Cas9 sgRNAs for lncRNAs. The ID, position in the genome, sequence and functional description of these lncRNAs, as well as the sequence, protoacceptor-motif (PAM), CRISPR type and validity of their paired sgRNAs were handled. CRISPRlnc provides the tools for browsing, searching and downloading data, as well as online BLAST service and genome browse server.",
"homepage": "http://crisprlnc.xtbg.ac.cn/",
"information_keywords": [
"Method",
"Sequence",
"Bibliography/Documents"
],
"maintainer": "Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences",
"name": "CRISPRlnc",
"prefix": "NBDC02465",
"pubmeds": [
"30285246"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc02466": {
"alt_name": "Database of somatic mutations in normal cells",
"description": "DSMNC is a comprehensive catalogue of somatic single nucleotide variations (SNVs) occurring in a normal cell from various human and mouse normal tissues. Each entry contains chromosome position, reference allele, variant allele, VAF, gene name, amino acid substitution, species, gender, tissue/cell type, single-cell genomics biotechnology/method, control sample/tissue, etc. Users can browse using SNVs table or chromosome browsers.",
"homepage": "http://dsmnc.big.ac.cn",
"information_keywords": [
"Sequence",
"Method"
],
"maintainer": "BGI (Beijing Genomics Institute)",
"name": "DSMNC",
"prefix": "NBDC02466",
"pubmeds": [
"30380071"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Cell/Organelle"
]
},
"nbdc02467": {
"description": "dbAMP is a database of anti-microbial peptides (AMPs) which are naturally encoded by genes and generally containing 12-100 amino acids. It provides information of antibacterial activities, physical-chemical properties, target species, structures, interacting proteins, links to external databases etc. It includes two categories of AMPs: experimental AMPs from published articles or public databases and predicted AMPs from public databases. Users can browse using following keys; peptide sequences, organisms, structures, targets and references.",
"homepage": "http://140.138.77.240/~dbamp/index.php",
"information_keywords": [
"Sequence",
"3D structure",
"Interaction/Pathway"
],
"maintainer": "Arieh Warshel Institute of Computational Biology, The Chinese University of Hong Kong",
"name": "dbAMP",
"prefix": "NBDC02467",
"pubmeds": [
"30380085"
],
"status": "Inactive",
"target_keywords": [
"Protein",
"Drug",
"Health/Disease"
]
},
"nbdc02468": {
"alt_name": "Editome disease knowledgebase",
"description": "EDK is a curated knowledgebase of associations between abnormal RNA modifications and human diseases. It provides comprehensive integration of knowledge on abnormal RNA editing events occurred in mRNA, miRNA, lncRNA and viruses, and aberrant RNA editing enzyme activities, which are related to human diseases.",
"homepage": "https://bigd.big.ac.cn/edk",
"information_keywords": [
"Sequence"
],
"maintainer": "National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences",
"name": "EDK",
"prefix": "NBDC02468",
"pubmeds": [
"30357418",
"29036542"
],
"status": "Active",
"target_keywords": [
"RNA",
"Health/Disease"
]
},
"nbdc02469": {
"alt_name": "Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry",
"description": "EncoMPASS is a database for relating integral membrane proteins from the points of view of their sequence, structure, and quaternary and internal symmetries. Analysis was done for all membrane-spanning PDB entries and separately for all membrane-spanning chains found therein in terms of the relationships between integral membrane proteins using structural and sequence similarity, and the symmetry of integral membrane proteins structures. It contains;\n1) General information about the complete biological unit of each membrane protein structure. \n2) A list of chains contained in the biological unit and their relationships to other structures in the database. \n3) Raw output from two symmetry detection programs: CE-Symm and SymD. \n4) Consensus results from processing with SymD and CE-Symm with default and customized parameters.",
"homepage": "https://encompass.ninds.nih.gov",
"information_keywords": [
"Sequence",
"3D structure",
"Interaction/Pathway"
],
"maintainer": "NINDS (National Institute of Neurological Disorders & Stroke)",
"name": "EncoMPASS",
"prefix": "NBDC02469",
"pubmeds": [
"30357403"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02470": {
"alt_name": "Endothelial cell database",
"description": "EndoDB is an expert curated added-value database of publicly available endothelial (single) cell gene expression data. It collects endothelial transcriptomics datasets including single cell RNA-seq datasets from the Gene Expression Omnibus and ArrayExpress repositories. Each dataset is applied to principal component analysis, differential analysis, gene set enrichment analysis and metabolic gene expression analysis, and be visualized in publication-ready figures and tables. It is freely available.",
"homepage": "https://endotheliomics.shinyapps.io/endodb/",
"information_keywords": [
"Expression"
],
"maintainer": "CCB (VIB-KU Leuven Center for Cancer Biology)",
"name": "EndoDB",
"prefix": "NBDC02470",
"pubmeds": [
"30357379"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle"
]
},
"nbdc02471": {
"alt_name": "Eukaryotic Nucleic acid binding Protein Database",
"description": "ENPD is a database for nucleic acid binding proteins (NBPs) and their functional information. It contains information of NBPs (DNA binding proteins: DBPs, RNA-binding proteins: RBPs, DNA and RNA binding proteins: DRBPs) from various eukaryotic organisms, which were predicted by manual curation and analysis of transcriptomes and genomes. Each entry includes NBP name, symbol, gene description, species, coding sequence, domain Information, inferred DNA binding motifs and inferred RNA binding motifs.",
"homepage": "http://qinlab.sls.cuhk.edu.hk/ENPD",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway",
"Classification"
],
"maintainer": "School of Life Sciences, The Chinese University of Hong Kong",
"name": "ENPD",
"prefix": "NBDC02471",
"pubmeds": [
"30476229"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"RNA",
"Protein"
]
},
"nbdc02472": {
"alt_name": "Encyclopedia of Traditional Chinese Medicine",
"description": "ETCM is a comprehensive database for the commonly used herbs and traditional Chinese medicines (TCMs). It provides information of material plants, such as Chinese name, scientific name, and chemical ingredients, and also provides predicted target genes of those ingredients and related diseases of each TCM. Users can browse Herbs, Formulas, Ingredients, Targets, Diseases, and also can explore the relationships among TCM herbs, formula, and ingredients.",
"homepage": "http://www.tcmip.cn/ETCM/",
"information_keywords": [
"Phenotype",
"Chemical structure",
"Interaction/Pathway"
],
"maintainer": "The Encyclopedia of Traditional Chinese Medicine",
"name": "ETCM",
"prefix": "NBDC02472",
"pubmeds": [
"30365030"
],
"status": "Active",
"target_keywords": [
"Drug",
"Genome/Gene",
"Metabolite",
"Health/Disease"
]
},
"nbdc02473": {
"alt_name": "Extracellular vesicle miRNA database",
"description": "EVmiRNA is a comprehensive database of miRNA in extracellular vesicles. It provides miRNA expression profiles, miRNA related drug, miRNA regulated pathways, miRNA function and related publications. Those data originally come from NCBI SRA. This database allows users to browse data at three aspects; 1) Samples: Users can browse sample cancer types, heatmap, expressed miRNAs, SRA sample information. 2) miRNAs: This list contains miRNA basic information and the expression histogram. Click the miRNA ID link, users can browse comprehensive miRNA information, contain miRNA basic information, miRNA expression profiles, miRNA related drug, miRNA regulated pathways, miRNA function, and related publications. 3) Specific miRNA: specific miRNAs in each source and cancer.",
"homepage": "http://bioinfo.life.hust.edu.cn/EVmiRNA",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "College of Life Science and Technology, HUST",
"name": "EVmiRNA",
"prefix": "NBDC02473",
"pubmeds": [
"30335161"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc02474": {
"alt_name": "A knowledgebase of Epigenome-Wide Association Studies",
"description": "EWAS Atlas is an integrated database focusing on DNA methylation which is one of the key epigenetic marks. It contains manually curated data of EWAS knowledge from extensive publications, such as traits, types, publications, studies, associations, hypermethylation percentage, CpG Island etc. In addition, this database is equipped with a powerful trait enrichment analysis tool, which is capable of profiling trait-trait and trait-epigenome relationships.",
"homepage": "http://bigd.big.ac.cn/ewas",
"information_keywords": [
"Sequence",
"Expression",
"Phenotype",
"Interaction/Pathway"
],
"maintainer": "National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences",
"name": "EWAS Atlas",
"prefix": "NBDC02474",
"pubmeds": [
"30364969"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Epigenetics",
"DNA",
"Health/Disease"
]
},
"nbdc02475": {
"alt_name": "epigenome-wide association study database",
"description": "EWASdb is a comprehensive database for epigenome-wide association studies (EWAS). Users can search studies by information of single epi-marker used in studies, KEGG pathway and GO categories. It provides information of EWAS studies, such as related disease/phenotype, contributor, publication title, summary, PubMed ID, and link to significant markers, KEGG pathways and GO categories.",
"homepage": "http://www.bioapp.org/ewasdb/",
"information_keywords": [
"Phenotype",
"Method",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "Harbin Medical University",
"name": "EWASdb",
"prefix": "NBDC02475",
"pubmeds": [
"30321400",
"29566144",
"27760738"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"Epigenetics",
"Health/Disease"
]
},
"nbdc02476": {
"alt_name": "Fusion Gene annotation DataBase",
"description": "FusionGDB is a database about fusion gene annotation. This database collects data of clinically relevant fusion genomes from three representative fusion gene resources: the improved database of chimeric transcripts and RNA-seq data (ChiTaRS 3.1), an integrative resource for cancer-associated transcript fusions (TumorFusions), and The Cancer Genome Atlas (TCGA). Gene assessment across pan-cancer fusion genes, open reading frame (ORF) assignment, and protein domain retention search based on multiple isoform gene structure with multiple break points were performed for the collected fusion genomes. It also provides the fusion transcript and amino acid sequences for each break point and gene isoforms. Each entry contains multiple annotation such as gene summary, assessment scores of each gene in pan-cancer, biological process gene ontologies, functional description, retention information and protein-protein interaction (PPI), related drugs and diseases through six categories.",
"homepage": "https://compbio.uth.edu/FusionGDB2/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "UTHealth (University of Texas Health Science Center at Houston)",
"name": "FusionGDB2",
"prefix": "NBDC02476",
"pubmeds": [
"30407583",
"34755868"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"Health/Disease"
]
},
"nbdc02477": {
"description": "gcMeta is an integrated platform for microbiome research. It contains information and data about microbiome research studies, such as study name, project ID, descriptions, sample environment, experiment type, etc. This database allows users to browse using experiment type, sample environment or sources.",
"homepage": "https://gcmeta.wdcm.org",
"information_keywords": [
"Environment",
"Sequence",
"Bibliography/Documents"
],
"maintainer": "Chinese Academy of Sciences",
"name": "gcMeta",
"prefix": "NBDC02477",
"pubmeds": [
"30365027"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02478": {
"alt_name": "Human ACtive Enhancer to interpret Regulatory variants",
"description": "HACER is a database of human active enhancer to interpret regulatory variants, which includes active, transcribed enhancers derived from GRO-seq, PRO-seq and CAGE data. It provides not only information of cell-type-specific enhancers but also information of transcriptional regulatory network involved in enhancers. Each entry contains basic information of the enhancer, information of transcription factors bound to the enhancer, target genes, and GWAS SNPs and eQTLs in the enhancer.",
"homepage": "http://bioinfo.vanderbilt.edu/AE/HACER",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "Vanderbilt University Medical Center",
"name": "HACER",
"prefix": "NBDC02478",
"pubmeds": [
"30247654"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"Genetic variation",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc02479": {
"description": "HmtVar is a manually-curated database for variability and pathogenicity information about human mtDNA. It collects variation data from HmtDB (https://www.hmtdb.uniba.it), which originally from GenBank, and which are found in complete genome of human mitochondrion in individuals with apparently healthy phenotype and with disease phenotypes. The rCRS (revised Cambridge Reference Sequence) was used to determine those variants. Each entry contains basic information of variations, pathogenicity predictions and links to external resources. The raw data for each variant is downloadable.",
"homepage": "https://www.hmtvar.uniba.it",
"information_keywords": [
"Expression",
"Sequence",
"Phenotype",
"Interaction/Pathway"
],
"maintainer": "University of Bari",
"name": "HmtVar",
"prefix": "NBDC02479",
"pubmeds": [
"30371888"
],
"status": "Inactive",
"target_keywords": [
"DNA",
"Genetic variation",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc02480": {
"description": "iDog is an integrated resource for domestic dog (Canis lupus familiaris) and wild canids. It includes information about Genes, Genomes, SNPs, Breed/Disease Traits, Gene Expressions, GO Function Annotations, Dog-Human Homolog Diseases and Literatures. In addition, it provides online tools for performing genomic data visualization and analyses.",
"homepage": "https://bigd.big.ac.cn/idog/",
"information_keywords": [
"Sequence",
"Expression",
"Phenotype",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences",
"name": "iDog",
"prefix": "NBDC02480",
"pubmeds": [
"30371881"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Organism",
"Health/Disease"
]
},
"nbdc02481": {
"description": "KinaMetrix is a database to investigate kinase conformations and inhibitor space. It contains the geometric descriptors describing kinase conformation, and the information of ligands, in addition to the basic information such as PDB ID, UniProt ID, gene name, species and conformation classification. Users can upload a structure to classify it by the structure and find kinases with similar conformation.",
"homepage": "http://kinametrix.com",
"information_keywords": [
"3D structure",
"Interaction/Pathway",
"Classification"
],
"maintainer": "Icahn School of Medicine at Mount Sinai",
"name": "KinaMetrix",
"prefix": "NBDC02481",
"pubmeds": [
"30321373",
"29861272",
"25420233"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02482": {
"description": "LipDB is a database about small RNA sequencing profiles in liquid biopsy studies. All data in this database were acquired from SRA database, and users can browse a list of studies, search studies by attribution of samples, or search a miRNA by the number. Visualization of miRNA distribution in biofluid type, health state, gender, RNA extraction protocol, library preparation protocol, microvesicle extraction and study is provided.",
"homepage": "https://bioinfo5.ugr.es/liqdb",
"information_keywords": [
"Expression",
"Localization"
],
"maintainer": "Computational Epigenomics Lab, Evolutionary Genomics and Bioinformatics Group, Dept. of Genetics, Inst. of Biotechnology, University of Granada",
"name": "liqDB",
"prefix": "NBDC02482",
"pubmeds": [
"30357370"
],
"status": "Active",
"target_keywords": [
"RNA",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc02483": {
"description": "MemProtMD is a database about intrinsic membrane protein structures derived from Protein Data Bank, which inserted into simulated lipid bilayers using Coarse-Grained Self Assembly Molecular Dynamics simulations. Each entry contains the results of simulations and subsequent analysis providing interactive 3D visualizations of the assembled bilayer and 2D visualizations of lipid contact data and membrane protein topology. It allows users to search by keywords, PDB ID or Uniprot ID, or browsed using classification systems, such as Pfam, Gene Ontology annotation, mpstruc or the Transporter Classification Database. Data are provided to run further molecular simulations of proteins in the database.",
"homepage": "http://memprotmd.bioch.ox.ac.uk",
"information_keywords": [
"3D structure",
"Image/Movie"
],
"maintainer": "SBCB Unit, Department of Biochemistry, University of Oxford",
"name": "MemProtMD",
"prefix": "NBDC02483",
"pubmeds": [
"30418645"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02484": {
"description": "MethMotif is an integrative database of transcription factor binding motifs coupled with DNA methylation profiles using the results of ChIP-seq and Whole Genome Bisulfite Sequencing (WGBS). The data in this database were originally downloaded from ENCODE and GEO. It is constructed with following parts;\n1) Explore in Heatmap:\nDistribution of CG beta scores in factor peak regions\n2) MethMotif Database:\nA two-dimensional database\n3) MethMotif Batch Query:\nA tool implemented in MethMotif website, which allows users to study the occurrences of TFBSs and their respective DNA methylation states within a given list of genomic loci.",
"homepage": "https://bioinfo-csi.nus.edu.sg/methmotif",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Cancer Science Institute of Singapore",
"name": "MethMotif",
"prefix": "NBDC02484",
"pubmeds": [
"30380113"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Epigenetics",
"DNA",
"Protein",
"Cell/Organelle"
]
},
"nbdc02485": {
"description": "NucMap is a database about genome-wide nucleosome positioning map of organisms. The nucleosome positioning information is provided by a single nucleotide resolution in every organism. Users can browse the information on the genome, or search the information by a gene/transcript. In the result of Sample Search, each entry contains sample information such as organelles, experiment strategies, and references, and it also contains related omics data for the sample.",
"homepage": "https://bigd.big.ac.cn/nucmap/",
"information_keywords": [
"Sequence",
"Localization"
],
"maintainer": "BIGD (Big Data Center, Beijing Institute of Genomics)",
"name": "NucMap",
"prefix": "NBDC02485",
"pubmeds": [
"30335176"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"Protein"
]
},
"nbdc02486": {
"description": "OncoBase is an integrated database for annotating somatic mutations from more than 120 cancer projects. Data are collected from TCGA, ICGC, COSMIC and ClinVar.\nIt provides comprehensive annotation and prediction of regulatory somatic mutations. Each entry includes information about Mutation_Target_Pair, BioCircos_View, Regulatory_Elements, Regulatory_Network, TF_Binding, Motif_Break, Quantitative_Trait_Locus, Expression, and Co-Expression, etc.",
"homepage": "http://www.oncobase.biols.ac.cn",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "Peking University Cancer Hospital and Institute||Chinese Academy of Sciences||University of Michigan",
"name": "OncoBase",
"prefix": "NBDC02486",
"pubmeds": [
"30445567"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc02487": {
"description": "OpenProt is a database that enforces a polycistronic model of eukaryotic genome annotations. It annotates known proteins (RefProts), novel predicted isoforms (Isoforms) and novel predicted proteins from alternative ORFs (AltProts). It also provides supporting evidence for each protein, such as mass-spectrometry and ribosome profiling detection, protein homology and predictions of funtional domains. Ensembl, NCBI RefSeq and combined Ensembl+RefSeq annotations are available for all species.",
"homepage": "http://www.openprot.org",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "UniversitΓ© de Sherbrooke",
"name": "OpenProt",
"prefix": "NBDC02487",
"pubmeds": [
"30299502"
],
"status": "Active",
"target_keywords": [
"Protein",
"Genome/Gene"
]
},
"nbdc02489": {
"alt_name": "Methylation quantitative trait loci in cancer",
"description": "Pancan-meQTL is a database for systematically prediction about the effects of SNPs on methylation levels of human genome. It provides cis-meQTLs (SNPs affect local methylation levels of CpG sties) and trans-meQTLs (SNPs affect distant methylation levels of CpG sites) across cancer types by using thousands of genotype and methylation data from The Cancer Genome Atlas (TCGA). Users can browse or search following information;\n1) cis-meQTLs and trans-meQTLs across different cancer types\n2) meQTLs associated with patient overall survival across different cancer types\n3) meQTLs in GWAS linkage disequilibrium (LD) regions.",
"homepage": "http://bioinfo.life.hust.edu.cn/Pancan-meQTL",
"information_keywords": [
"Sequence",
"Phenotype",
"Expression"
],
"maintainer": "Huazhong University of Science and Technology||UTHealth (University of Texas Health Science Center at Houston)",
"name": "Pancan-meQTL",
"prefix": "NBDC02489",
"pubmeds": [
"30203047"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Epigenetics",
"Health/Disease"
]
},
"nbdc02490": {
"alt_name": "Plant Editosome Database",
"description": "PED is a curated database of RNA editosome in plants, which is focused on the curation, integration and standardization of plant RNA editing factors (editosome) and the related data. It provides detailed relevant information, including factor name, protein family, subclass, structure, species, associated plant phenotype(s), edited gene(s), organelle and PMID(s). Each entry also contains more details covering treatment, trait, phenotype, editing frequency, etc.",
"homepage": "https://bigd.big.ac.cn/ped/home",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences",
"name": "PED",
"prefix": "NBDC02490",
"pubmeds": [
"30364952",
"30365034"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Cell/Organelle"
]
},
"nbdc02491": {
"alt_name": "piRNA targeting sites",
"description": "piRTarBase is a database about PIWI-interacting RNAs (piRNAs) which are a class of small noncoding RNAs that guard animal genomes against mutation by silencing transposons. It provides both predicted and experimentally identified piRNA targeting sites in Caenorhabditis elegans and Caenorhabditis briggsae. User can search a list of piRNA targeting sites or mRNA targets by a gene or piRNA. The piRTarBase integrates published mRNA and small RNA sequencing data.",
"homepage": "http://cosbi6.ee.ncku.edu.tw/piRTarBase/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "Department of Electrical Engineering, National Cheng Kung University",
"name": "piRTarBase",
"prefix": "NBDC02491",
"pubmeds": [
"30357353"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc02494": {
"description": "DILI-TOOLBOX is a portal site for liver toxicity database and prediction systems developed in the AMED Liver Toxicity Informatics System Development programs. It by the National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), National Institute of Advanced Industrial Science and Technology (AIST), Meiji Pharmaceutical University (MPU) and Kumamoto University.",
"homepage": "https://dili-toolbox.nibiohn.go.jp",
"information_keywords": [
"Portal",
"Expression",
"Method",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "National Institutes of Biomedical Innovation, Health and Nutrition",
"name": "DILI-TOOLBOX",
"prefix": "NBDC02494",
"status": "Inactive",
"target_keywords": [
"Chemical compound",
"Genome/Gene",
"Health/Disease"
]
},
"nbdc02495": {
"description": "DILI-cSEARCH is a comprehensive database about liver toxicity caused by drugs and chemicals. It offers cross search access to information of Open TG-GATEs, DrugMatrix, LINKS and LTKB (Liver Toxicity Knowledge Base) including in vitro/in vivo experimental conditions, toxicological profiles, gene expression profiles, and much more.",
"homepage": "https://dili-csearch.nibiohn.go.jp/en",
"information_keywords": [
"Method",
"Expression"
],
"maintainer": "National Institutes of Biomedical Innovation, Health and Nutrition||Kumamoto University",
"name": "DILI-cSEARCH",
"prefix": "NBDC02495",
"status": "Inactive",
"target_keywords": [
"Chemical compound",
"Drug",
"Health/Disease"
]
},
"nbdc02496": {
"alt_name": "Toxic process interpretable knowledge system",
"description": "TOXPILOT is a system for visualization maps of toxic process ontology (TXPO) which systematizes terms involving toxicity courses and processes. It provides following search categories; \n1) Toxic course map visualized a toxic course as causal relationships between processes.\n2) Process Map visualized the selected process based on the systemic functioning decomposition approach.\n3) Ontology provides the definition and related information about each term based on the TXPO.\n4) Route search provides the upstream or downstream paths of the focused process.\n5) General course map visualizes common to multiple toxic courses.",
"homepage": "https://toxpilot.nibiohn.go.jp",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Interaction/Pathway"
],
"maintainer": "National Institutes of Biomedical Innovation, Health and Nutrition",
"name": "TOXPILOT",
"prefix": "NBDC02496",
"status": "Inactive",
"target_keywords": [
"Chemical compound",
"Drug",
"Health/Disease"
]
},
"nbdc02497": {
"description": "toxBridge is a database that stores statistical analysis results using differential gene expression when compounds are exposed. It is possible to display feasible bridging capabilities between rat in vivo/vitro and human in vitro based on signature genes and pathways.",
"homepage": "https://toxbridge.id3inst.org/top",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Molecular Profiling Research Center for Drug Discovery, AIST",
"name": "toxBridge",
"prefix": "NBDC02497",
"status": "Inactive",
"target_keywords": [
"Chemical compound",
"Genome/Gene",
"Health/Disease"
]
},
"nbdc02498": {
"description": "toxRank is an application that provides a list of compounds those exhibit an expression profile similar to that of the genes inputted by user. This tool visualizes the clustering of the compounds and relation of genes/pathways with flexible manner for the purpose of liver toxicity prediction.",
"homepage": "https://toxrank.id3inst.org/",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Molecular Profiling Research Center for Drug Discovery, AIST",
"name": "toxRank",
"prefix": "NBDC02498",
"status": "Inactive",
"target_keywords": [
"Chemical compound",
"Genome/Gene",
"Health/Disease"
]
},
"nbdc02502": {
"description": "FMODB is a database of quantum mechanical data based on the FMO method. It contains PDBID-Chain (detail data of the displayed structure), IFIE SUM (Summation of ES, EX, CT+mix, DI(MP2) etc.) , electrostatic interaction (ES), exchange-repulsion (ER), CT+mix, etc.. It allows to search by PDB ID, Keywords, and Blast. In \"BaseStructure\", there are 3 kinds of structural categories, X - ray, NMR and MD. IFIE data (PDB file, checkpoint file, IFIE data) is downloadable.",
"homepage": "https://drugdesign.riken.jp/FMODB/",
"information_keywords": [
"3D structure",
"Chemical structure",
"Interaction/Pathway"
],
"maintainer": "FMODD Consortium",
"name": "FMODB",
"prefix": "NBDC02502",
"pubmeds": [],
"status": "Active",
"target_keywords": [
"Protein",
"Drug",
"Chemical compound"
]
},
"nbdc02503": {
"description": "Food Metabolome Repository is a database for food metabolome data obtained using liquid chromatography-mass spectrometry (LC-MS). Each record contains a two-dimensional mass chromatogram, peak information (RT, m/z, int, adduct, DB search result, MSn, FSs) and sample details.",
"homepage": "http://metabolites.in/foods/",
"information_keywords": [
"Chemical structure",
"Image/Movie"
],
"maintainer": "Kazusa DNA Research Institute||National Institute of Genetics",
"name": "Food Metabolome Repository",
"prefix": "NBDC02503",
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc02504": {
"description": "Factorbook is a transcription factor (TF)-centric wiki-style repository of all ENCODE ChIP-seq datasets on TF-binding regions, as well as the rich analysis results of these data. That organizes all the information associated with each TF, including the ChIP-seq peaks, discovered motifs, TF-TF interactions, and the chromatin features (histone modification patterns, DNase I cleavage, and nucleosome positioning) around the ChIP-seq peaks. The main page displays an alphabetized matrix of TFs and cell lines. Clicking the TF name opens the individual page on the TF. Factorbook is planned to update whenever more ENCODE data are available.",
"homepage": "http://www.factorbook.org/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "University of Massachusetts Medical School",
"name": "Factorbook",
"prefix": "NBDC02504",
"pubmeds": [
"22955990",
"23203885"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Epigenetics",
"DNA",
"Protein"
]
},
"nbdc02505": {
"alt_name": "Next Generation Sequencing Quality Control Generator",
"description": "NGS-QC database is the first QC indicator database covering the largest collection of ChIP-seq and enrichment-related NGS datasets. Most of the current certified entries are part of the public repository GEO. Database can be searched based on Organism, Target Molecule, QC grade, etc. A scatter plot provides the user a summary and exact range of the quality descriptors of all the experiments that come under their searched queries.\nUsers can evaluate the quality of their own NGS dataset relative to the datasets present in the entire database through the Galaxy platform instance NGS-QC Generator.\nOther tools like LOGIQA hosting quality scores for long-range genome interaction assays (e.g. Hi-C), and QC Genomics providing a central access to the largest collection of genomic data are also available.",
"homepage": "http://www.ngs-qc.org/",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Institute of Genetics and Molecular and Cellular Biology",
"name": "NGS-QC",
"prefix": "NBDC02505",
"pubmeds": [
"24038469",
"26484107",
"27008019",
"27335635",
"27185059"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Epigenetics",
"DNA",
"RNA",
"Protein"
]
},
"nbdc02506": {
"alt_name": "Yeast GFP Fusion Localization Database",
"description": "YeastGFP is a database of yeast strains expressing full-length, chromosomally tagged green fluorescent protein (GFP) fusion proteins. It contains high-resolution, high-coverage localization dataset in the context of transcriptional, genetic, and protein-protein interaction data. It helps reveal the logic of transcriptional co-regulation, and provides a comprehensive view of interactions within and between organelles in eukaryotic cells.",
"homepage": "https://yeastgfp.yeastgenome.org/",
"information_keywords": [
"Expression",
"Image/Movie",
"Bioresource"
],
"maintainer": "Stanford University",
"name": "Yeast GFP",
"prefix": "NBDC02506",
"pubmeds": [
"14562095",
"14562106",
"18629296"
],
"status": "Active",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc02507": {
"alt_name": "Collection of Yeast Cell and Localization Patterns",
"description": "CYCLoPs is a comprehensive database of protein abundance and localization for budding yeast Saccharomyces cerevisiae. It contains high resolution images covering about 75% of the yeast proteome (~4144 proteins) under multiple chemical and genetic perturbations. Protein abundance and localization change of proteins after treatments are indicated by intensity of GFP. The treatment conditions are rapamycin, hydroxy-urea, rpd3 knockout and alpha-factor.",
"homepage": "https://thecellvision.org/cyclops/",
"information_keywords": [
"Expression",
"Localization",
"Image/Movie"
],
"maintainer": "University of Toronto",
"name": "CYCLoPs",
"prefix": "NBDC02507",
"pubmeds": [
"26048563",
"26046442"
],
"status": "Active",
"target_keywords": [
"Protein",
"Organism",
"Cell/Organelle"
]
},
"nbdc02508": {
"alt_name": "Cistrome Data Browser",
"description": "Cistrome DB is a portal site for public ChIP-seq and DNase-seq datasets. It provides a comprehensive knowledgebase of all of the publicly available ChIP-Seq and DNase-Seq data in mouse and human, which contains manually curated information for each ChIP-seq and DNase-seq data, analysis results processed with a uniform pipeline, and comprehensive quality control metrics for each dataset. It also provides functions to analysis and visualize these datasets.",
"homepage": "http://dc2.cistrome.org/#/",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Cistrome Project",
"name": "CistromeDB",
"prefix": "NBDC02508",
"pubmeds": [
"30462313",
"27789702"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein"
]
},
"nbdc02509": {
"description": "LncRRIsearch is a web server for comprehensive prediction of interactions between long non-coding RNA (lncRNA)-lncRNA and lncRNA-mRNA in human and mouse. Users can also search Tissue-specific RNA-RNA interactions and RNA-RNA interactions based on the subcellular localization.",
"homepage": "http://rtools.cbrc.jp/LncRRIsearch/",
"information_keywords": [
"Interaction/Pathway",
"Sequence",
"Expression",
"Localization"
],
"maintainer": "CBBD-OIL",
"name": "LncRRIsearch",
"prefix": "NBDC02509",
"pubmeds": [
"31191601"
],
"status": "Active",
"target_keywords": [
"RNA",
"Genome/Gene"
]
},
"nbdc02510": {
"alt_name": "Collagen reference database",
"description": "Collagenseq is a reference database about type I collagen. Each record obtained from various species contains academic name and English name of the organism, taxonomy ID, and the amino acid sequence.",
"homepage": "https://togodb.biosciencedbc.jp/db/collagenseq",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "NBDC (Japan Science and Technology Agency Department of NBDC Program)",
"name": "Collagenseq",
"prefix": "NBDC02510",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02511": {
"description": "JMC Primates Brain Imaging Repository is a collection of high-resolution MRI data of non-human primate brains stored in Japan Monkey Centre. Each record contains species information, individual information about the specimen, imaging conditions and brain MRI images (surface reconstructed images, T2-weighted images, diffusion weighted images, fractional anisotropy maps, etc.).",
"homepage": "http://www.j-monkey.jp/BIR/index_e.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Japan Monkey Centre",
"name": "Japan Monkey Centre (JMC) Primates Brain Imaging Repository",
"prefix": "NBDC02511",
"pubmeds": [
"30357587"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02512": {
"alt_name": "predicted endogenous viral elements in eukaryotic genomes",
"description": "pEVE is a database about predicted endogenous viral elements (EVEs) in eukaryotic genomes. It contains BLASTN search results of eukaryotic and viral genomes as target and query sequences to comprehensively identify EVEs in eukaryotic genomes. Each genomic sequence is obtained from GenomeSync database. Each record contains blast score, blast e-value, percent identity, aligned length of query, eukaryote organism name, and eukaryote genome accession. This database allows users to browse the results with Homology viewer using query taxon, genome, or sequence.",
"homepage": "http://peve.med.u-tokai.ac.jp/",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "Tokai University School of Medicine",
"name": "pEVE",
"prefix": "NBDC02512",
"pubmeds": [
"29425804"
],
"status": "Active",
"target_keywords": [
"DNA",
"RNA"
]
},
"nbdc02513": {
"alt_name": "Catalyst Acquisition by Data Science",
"description": "Catalyst Acquisition by Data Science (CADS) is an integrated visual platform for materials informatics. It provides three basic functions for users:Β \n1) Data Management: CADS provides data repository, allowing users to share data and analysis reports with collaborators of their choosing.\n2) Analysis: It provides data visualization tools (scatter plotting, histograms, etc.) and machine learning functions for catalyst data analysis and machine learning model selection.\n3) Prediction: It provides data prediction capabilities with the βAnalysisβ function, allowing users to apply learning models for predicting new output (e.g. predicting new catalysts).",
"homepage": "https://cads.eng.hokudai.ac.jp/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Catalyst Informatics Project",
"name": "CADS",
"prefix": "NBDC02513",
"status": "Active",
"target_keywords": [
"Chemical compound"
]
},
"nbdc02514": {
"alt_name": "Plasmid Atlas",
"description": "pATLAS is a database for searching plasmids with tools to visualize relationships between plasmids. Users can search plasmids by the name, taxa, antibiotic resistance and virulence genes, plasmid families, sequence length and sequence similarity. In the plasmid network, it is able to represent plasmids identified by external pipelines using mapping, mash screen or assembly from high-throughput sequencing data.",
"homepage": "http://www.patlas.site",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "Faculdade de Medicina, Universidade de Lisboa",
"name": "pATLAS",
"prefix": "NBDC02514",
"pubmeds": [
"30395323"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"DNA"
]
},
"nbdc02515": {
"description": "PLSDB is a database about bacterial plasmids retrieved from the NCBI nucleotide database. Users can select plasmids by various parameters such as the sequence length, topology, and taxonomic information. Users can also search nucleotide sequences by either using Mash for longer sequences (e.g. contigs or long reads), or by using BLASTn for shorter sequences (e.g. genes).",
"homepage": "https://ccb-microbe.cs.uni-saarland.de/plsdb",
"information_keywords": [
"Sequence",
"Bibliography/Documents"
],
"maintainer": "Saarland University",
"name": "PLSDB",
"prefix": "NBDC02515",
"pubmeds": [
"3038009"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"DNA"
]
},
"nbdc02516": {
"description": "PopHumanScan is a catalog about thousands of regions of the human genome showing evidences of selection along the human lineage. This database retrieved the population genomic data from PopHuman, which represents the most complete pipeline for population genomics analysis of the 1000 genome project data. To detect local adaptation, many methods and statistics were applied, which were selection tests based on the allele frequency spectrum and the levels of variability (Tajimaβs D, Fu and Liβs D and F, Fay and Wuβs H); selection tests based on comparisons of polymorphism and divergence and its derived estimators (MKT, Ξ±); selection tests based on the linkage disequilibrium (iHS and XP-EHH) and selection tests based on population differentiation (FST).",
"homepage": "https://pophumanscan.uab.cat",
"information_keywords": [
"Sequence",
"Environment",
"Geographic Distribution"
],
"maintainer": "Institut de Biotecnologia i de Biomedicina, Universitat AutΓ²noma de Barcelona",
"name": "PopHumanScan",
"prefix": "NBDC02516",
"pubmeds": [
"30335169"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Organism"
]
},
"nbdc02517": {
"description": "qPhos is a database for comprehensive resource of protein phosphorylation in human tissues and cell lines. The data were curated from published literatures to provide protein phosphorylation dynamics under various conditions. Quantified phosphorylation sites were annotated with the sequence and structure properties of the protein, candidate of upstream kinases and their inhibitors. Users can search data by UniProt accession, gene/protein name, and keyword of the function, sample or condition. Furthermore, users can submit own quantitative phosphoproteome data and analyze kinase activity profile using the submitted data by qKinAct service annotating the kinase activity-related phosphorylation sites.",
"homepage": "http://qphos.cancerbio.info",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "Sun Yat-sen University Cancer Center",
"name": "qPhos",
"prefix": "NBDC02517",
"pubmeds": [
"30380102"
],
"status": "Active",
"target_keywords": [
"Protein",
"Cell/Organelle",
"Organism"
]
},
"nbdc02518": {
"description": "RetroRules is a database of reaction rules for metabolic pathway. It provides a complete set of reaction rules, which were extracted from public databases and expressed in the community-standard SMARTS format, augmented by a rule representation at different levels of specificity (the atomic environment around the reaction center). Each record contains information such as EC Number, Penalty Score, Diameter, Direction, Has Stereo, Reaction rules, Related mono-component reaction(s), etc. Users can search records by EC number, reaction ID or substrate structure query.",
"homepage": "https://retrorules.org",
"information_keywords": [
"Chemical structure",
"Interaction/Pathway"
],
"maintainer": "INRAE (National Research Institute for Agriculture, Food and Environment)",
"name": "RetroRules",
"prefix": "NBDC02518",
"pubmeds": [
"30321422"
],
"status": "Active",
"target_keywords": [
"Metabolite",
"Protein"
]
},
"nbdc02519": {
"description": "RNAct is a database of the proteinβRNA interactome. RNA-binding proteins (RBPs) are collected from experimental interaction data or predicted from SONAR and catRAPID (proteinβRNA interaction prediction algorithm) signature. Users can search interaction data from both RBPs and RNAs by the name or IDs.",
"homepage": "http://rnact.crg.eu",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "CRG (Centre for Genomic Regulation)",
"name": "RNAct",
"prefix": "NBDC02519",
"pubmeds": [
"30445601"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein"
]
},
"nbdc02520": {
"alt_name": "The comprehensive human Super-Enhancer database",
"description": "SEdb is a database about super-enhancers in gene regulation. It collects detailed genetic and epigenetic annotation information on super-enhancers, including common SNPs, motif changes, expression quantitative trait locus (eQTL), risk SNPs, transcription factor binding sites (TFBSs), CRISPR/Cas9 target sites and DNase I hypersensitivity sites (DHSs). The data were collected from samples of NCBI GEO/SRA, ENCODE, Roadmap and GGR.",
"homepage": "http://www.licpathway.net/sedb",
"information_keywords": [
"Expression",
"Localization",
"Interaction/Pathway"
],
"maintainer": "Harbin Medical University",
"name": "SEdb",
"prefix": "NBDC02520",
"pubmeds": [
"30371817"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc02521": {
"description": "SSRome is an integrated database and pipelines for exploring microsatellites in a wide range of organisms. It contains microsatellite DNA motifs which were identified across Plants, Metazoa, Prokaryotes, Mitochondrial and Chloroplast sequenced genomes, in addition to all available NCBI ESTs till March 2017. All datasets of microsatellites motifs and markers are downloadable freely in very convenient way. Users can update a sequence and analyze it.",
"homepage": "http://mggm-lab.easyomics.org",
"information_keywords": [
"Sequence",
"Method"
],
"maintainer": "Agricultural Genetic Engineering Research Institute",
"name": "SSRome",
"prefix": "NBDC02521",
"pubmeds": [
"30365025"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Genome/Gene",
"DNA",
"Cell/Organelle",
"Organism"
]
},
"nbdc02522": {
"description": "SymMap is a database for integration with traditional Chinese medicine (TCM) and modern medicine (MM) through both internal molecular mechanism and external symptom mapping. It contains massive descriptive information on herbs, TCM symptoms, MM symptoms, ingredients, targets and diseases. It also provides pairwise relationships among all these six types of components through direct association or indirect statistical inference.",
"homepage": "http://www.symmap.org",
"information_keywords": [
"Phenotype",
"Interaction/Pathway"
],
"maintainer": "Beijing University of Chinese Medicine",
"name": "SymMap",
"prefix": "NBDC02522",
"pubmeds": [
"30380087"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Drug",
"Health/Disease"
]
},
"nbdc02523": {
"description": "Trips-viz is a database for Ribosome profiling (Ribo-seq) data that have been produced using publicly available ribosome profiling and corresponding RNA-seq datasets from SRA.\nTrip-Viz provides a set of graphical analysis tools to understand a Ribo-Seq result and to compare translated features across different samples of Ribo-Seq, which are able to use for;\n1) interactive visualization of an aggregate of ribosome profiling data at subcodon resolution in the context of single transcripts,\n2) plotting data obtained from multiple different samples on the same transcript,\n3) getting meta-information from an entire dataset, aggregating information from multiple transcripts to assess the quality of datasets,\n4) finding genes whose expression is significantly up/down-regulated relative to others.\nUsers can also upload and analyze their own data.",
"homepage": "http://trips.ucc.ie",
"information_keywords": [
"Expression"
],
"maintainer": "University College Cork",
"name": "Trips-Viz",
"prefix": "NBDC02523",
"pubmeds": [
"30239879"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA"
]
},
"nbdc02524": {
"description": "BioResource MetaDatabase is a data repository for metadata of bioresources in RIKEN. This database provides life-science data in the bases of standardized metadata techniques including semantic web and Resource Description Framework (RDF).",
"homepage": "https://knowledge.brc.riken.jp/",
"information_keywords": [
"Bioresource",
"Phenotype",
"Portal"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "BioResource MetaDatabase",
"prefix": "NBDC02524",
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"Organism",
"Genome/Gene"
]
},
"nbdc02525": {
"alt_name": "Mouse genome database with high added value",
"description": "MoG+ is a mouse genome database which shows mouse genomic variation visually to compare inbred mouse strains established in Japan (JF1/Ms etc.) to frequently used classical inbred strain such as C57BL/6J (whose genome is predominantly derived from the West European subspecies M. m. domesticus). It provides genome polymorphism information, such as single-nucleotide polymorphisms and short insertions and deletions in the genomes. This is a successor database of NIG_MoG2 (NIG Mouse Genome Database) that had been maintained by the Genetic Informatics Laboratory in the National Institute of Genetics.",
"homepage": "https://molossinus.brc.riken.jp/mogplus/",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "RIKEN BRC (RIKEN BioResource Research Center)",
"name": "MoG+",
"prefix": "NBDC02525",
"pubmeds": [
"23604024",
"26013919"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02526": {
"description": "UniLectin is a database for manually curated and predicted lectins. It provides information about the classification and curation of lectins (with UniLectin3D module), the prediction of Ξ²-propeller lectins (with PropLec module) and the prediction of all lectin classes (Available on demand).",
"homepage": "http://www.unilectin.eu",
"information_keywords": [
"Sequence",
"3D structure",
"Classification"
],
"maintainer": "UniLectin",
"name": "UniLectin",
"prefix": "NBDC02526",
"pubmeds": [
"30239928"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02527": {
"alt_name": "Virulence factors",
"description": "Victors is a database about virulence factors (VFs) collected by manual curation from peer-reviewed publications. Those VFs come from pathogenic organisms showed pathogenicity to animals and humans, such as bacteria, viruses, parasites and fungi. Each entry contains Gene Name, Sequence Strain (Species/Organism), NCBI Gene ID, Locus Tag, Protein Accession, etc.",
"homepage": "http://www.phidias.us/victors",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "University of Michigan Medical School",
"name": "Victors",
"prefix": "NBDC02527",
"pubmeds": [
"30365026"
],
"status": "Inactive",
"target_keywords": [
"Genome/Gene",
"Protein",
"Organism",
"Health/Disease"
]
},
"nbdc02528": {
"alt_name": "Virtual metabolic human",
"description": "VMH is an integrated database for human and gut microbial metabolisms linked to diseases and nutritional data. The core data are hundreds of genome-scale metabolic reconstructions by Recon3D that provides the underlying over 13,000 networks of metabolic reactions based on manually curation through literatures. It enables rapid analyses and interpretations of complex data by enabling complex queries of its content, by providing a detailed graphical representation of human metabolism, and by distributing computational models for simulating human and microbial metabolism.",
"homepage": "https://www.vmh.life",
"information_keywords": [
"Sequence",
"Chemical structure",
"Interaction/Pathway"
],
"maintainer": "LCSB (Luxembourg Centre for Systems Biomedicine of the University of Luxembourg)",
"name": "VMH",
"prefix": "NBDC02528",
"pubmeds": [
"30371894",
"29457794",
"29457794"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Metabolite",
"Cell/Organelle",
"Organism",
"Health/Disease"
]
},
"nbdc02529": {
"description": "YeastRGB is a database for abundance and localization of proteins in Saccharomyces cerevisiae. It provides fluorescence microscopy data of yeasts, which were introduced ORF libraries tagged with fluorescence proteins by SWAT technology at the N-terminus and C-terminus of the ORF, in addition to the classic C-terminus tagged GFP yeast library.",
"homepage": "http://www.yeastRGB.org",
"information_keywords": [
"Localization",
"Image/Movie"
],
"maintainer": "Weizmann Institute of Science",
"name": "YeastRGB",
"prefix": "NBDC02529",
"pubmeds": [
"30357397"
],
"status": "Active",
"target_keywords": [
"cDNA/EST",
"Protein",
"Cell/Organelle"
]
},
"nbdc02530": {
"alt_name": "Combined Annotation-Dependent Depletion",
"description": "It is a site for Combined Annotation-Dependent Depletion (CADD), which is a framework for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. The CADD objectively weights and integrates diverse annotations by contrasting variants survived natural selection with simulated mutations. The variants those are functional, deleterious and disease causal are quantitatively sorted out its priorities across a wide range of functional categories, effect sizes and genetic architectures.",
"homepage": "http://cadd.gs.washington.edu",
"information_keywords": [
"Sequence"
],
"maintainer": "University of Washington",
"name": "CADD",
"prefix": "NBDC02530",
"pubmeds": [
"30371827",
"24487276"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Organism",
"Health/Disease"
]
},
"nbdc02531": {
"description": "GENCODE is a database to identify and classify all gene features in the human and mouse genomes. It provides foundational reference genome annotation, and includes comprehensive gene sets those consist of protein coding and non-coding loci including alternatively spliced isoforms and pseudogenes. Manual annotations are conducted to the regions requiring expert investigation. It contains information such as chromosome name, annotation source, feature type, genomic location, genomic strand, genomic phase, etc. Users can access the data through genome browsers and download the data on the site or through APIs.",
"homepage": "http://www.gencodegenes.org",
"information_keywords": [
"Sequence"
],
"maintainer": "EMBL (European Molecular Biology Laboratory)",
"name": "GENCODE",
"prefix": "NBDC02531",
"pubmeds": [
"30357393"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02532": {
"description": "Haemosphere is a data portal for RNA-Seq datasets, including each celltype of the dataset, cell_lineage, tissue, treatment, immunophenotype, species, and strain, etc. It contains Haemopedia datasets providing from Walter and Eliza Hall Institute and some other key datasets of interest to the haematopoiesis community. Users can search for genes of interest, view their expression profiles across a range of cell types within a dataset, perform differential expression analyses and manage gene sets easily.",
"homepage": "http://haemosphere.org",
"information_keywords": [
"Expression",
"Localization",
"Interaction/Pathway"
],
"maintainer": "The Walter and Eliza Hall Institute of Medical Research",
"name": "Haemosphere",
"prefix": "NBDC02532",
"pubmeds": [
"30395284",
"27499199",
"29617932"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle"
]
},
"nbdc02533": {
"alt_name": "Human gene networks for disease research",
"description": "HumanNet is a database for human gene networks, which integrates diverse types of omics data and provides gene-disease associations by their own network inference algorithms. Users can predict and organize genes relevant to a specific disease. HumanNet v2 comprises a hierarchy of human gene networks, and performs well in ranking disease-linked gene sets with minimal literature-dependent biases. Integrated networks, component networks and protein-protein interaction networks derived from non-human organisms (interologs) are downloadable.",
"homepage": "https://www.inetbio.org/humannet/",
"information_keywords": [
"Sequence",
"Phenotype",
"Interaction/Pathway"
],
"maintainer": "Network Biomedicine Lab, Yonsei University||Marcotte Lab, University of Texas at Austin",
"name": "HumanNet",
"prefix": "NBDC02533",
"pubmeds": [
"30418591",
"21536720"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Health/Disease"
]
},
"nbdc02534": {
"description": "LncACTdb is a database for LncRNA-Associated Competing Triplets (LncACT). It provides manually curated and predicted ceRNA interactions. The class of ceRNAs in LncACTdb contains endogenously generated molecules (including lncRNAs, circular RNAs, coding genes, pseudogenes) and exogenously introduced molecules (including viral RNAs and artificially engineered RNAs). It includes information of the association between ceRNAs and miRNA, Species, Tissue/Cell line, Phenotype/Disease, Experimental methods, Reference and the Functional description. This database provides tools to find function of LncAct, survival of LncAct and network of LncActd, and functional ceRNAs using expression profiles inputted by user.",
"homepage": "http://bio-bigdata.hrbmu.edu.cn/LncACTdb/",
"information_keywords": [
"Phenotype",
"Sequence",
"Interaction/Pathway"
],
"maintainer": "College of Bioinformatics Science and Technology, Harbin Medical University",
"name": "LncACTdb 3.0",
"prefix": "NBDC02534",
"pubmeds": [
"30476305",
"25800746"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Health/Disease"
]
},
"nbdc02535": {
"description": "MoonDB is a database of predicted and manually curated extreme multifunctional (EMF) proteins and moonlighting proteins, which are proteins that perform multiple unrelated functions. This database provides information of protein functions based on knowledge of protein-protein interactions and GO term annotations. Each entry is cross-referenced in the UniProt Knowledgebase (UniProtKB).",
"homepage": "http://moondb.hb.univ-amu.fr",
"information_keywords": [
"Ontology/Terminology/Nomenclature",
"Interaction/Pathway"
],
"maintainer": "TAGC, Inserm U1090",
"name": "MoonDB",
"prefix": "NBDC02535",
"pubmeds": [
"30371819",
"26054620"
],
"status": "Active",
"target_keywords": [
"Protein",
"Health/Disease"
]
},
"nbdc02536": {
"description": "OrthoInspector is a catalog of orthologs predicted across three domains of life, Eukaryota, Bacteria, and Archaea. Each entry provides a fully searchable list of orthologs and inparalogs across multiple species, and tools to investigate function and evolutionary history of the protein. Users can query this site using a Uniprot identifier or access, or using a BLAST similarity search with a protein sequence.",
"homepage": "https://lbgi.fr/orthoinspectorv3/",
"information_keywords": [
"Sequence",
"Classification"
],
"maintainer": "ICube, UniversitΓ© de Strasbourg",
"name": "OrthoInspector",
"prefix": "NBDC02536",
"pubmeds": [
"30380106",
"25273105",
"21219603"
],
"status": "Active",
"target_keywords": [
"Protein",
"Organism"
]
},
"nbdc02537": {
"description": "Stemformatics is a web-based data platform to find interesting genes in gene expression datasets of stem cells. It contains public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. All of the data on this site has been hand-picked, curated and checked for experimental reproducibility and design quality, and normalized in-house. It contains information about genes in the public and private domains for stem cell datasets. Users can visualize data using Gene Expression Graph, Multiview, YuGene, KEGG pathways, etc.",
"homepage": "https://www.stemformatics.org",
"information_keywords": [
"Expression",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "University of Melbourne",
"name": "Stemformatics",
"prefix": "NBDC02537",
"pubmeds": [
"30407577",
"23466562"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Cell/Organelle"
]
},
"nbdc02538": {
"description": "Vesiclepedia is a manually curated compendium of molecular data (lipid, RNA and protein) identified in Extracellular vesicles. The Extracellular vesicles are classified into following three broad classes; (i) ectosomes or shedding microvesicles, (ii) exosomes, (iii) apoptotic bodies. Each record contains experiment ID, Identified molecule, Identification method, Pubmed ID, organism, authors, sample information, etc. Users can browse using lists of organisms, vesicle types, content types and sample materials.",
"homepage": "http://www.microvesicles.org",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "La Trobe Institute for Molecular Sciences",
"name": "Vesiclepedia",
"prefix": "NBDC02538",
"pubmeds": [
"30395310",
"23271954"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"RNA",
"Protein",
"Lipid",
"Metabolite",
"Genome/Gene"
]
},
"nbdc02539": {
"alt_name": "Precision medicine knowledgebase",
"description": "PreMedKB is a database for integrating information on diseases, genes, variants, drugs, and the relationships between any two or more of these four components. This database contains information of gene functions, involved pathways, disease categories, drug product status, variant types, etc. It also combines data from multiple sources and illustrates the confidence of the relationship using a semantic network.",
"homepage": "http://www.fudan-pgx.org/premedkb/index.html#/home",
"information_keywords": [
"Sequence",
"3D structure",
"Interaction/Pathway"
],
"maintainer": "Fudan University",
"name": "PreMedKB",
"prefix": "NBDC02539",
"pubmeds": [
"30407536"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Drug",
"Health/Disease"
]
},
"nbdc02540": {
"description": "iProX is a public platform for collecting and sharing raw data, analysis results and metadata obtained from proteomics experiments. The iProX repository employs a web-based proteome data submission process and open sharing of mass spectrometry-based proteomics datasets. iProX is a member of the ProteomeXchange (PX) consortium.",
"fairsharing": "biodbcore-001335/",
"homepage": "https://www.iprox.org/",
"information_keywords": [
"Bibliography/Documents",
"Repository"
],
"maintainer": "BPRC (Beijing Proteome Research Center)",
"name": "iProX",
"prefix": "NBDC02540",
"pubmeds": [
"30252093"
],
"status": "Active",
"target_keywords": [
"Protein",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc02541": {
"description": "LncBook is a curated knowledgebase of human lncRNAs that features a comprehensive collection of human lncRNAs and systematic curation of lncRNAs by multi-omics data integration, functional annotation and disease association. It integrates multi-omics data from expression, methylation, genome variation and lncRNA-miRNA interaction. A core component of LncBook is the community-curated LncRNAWiki portal, which a wiki-based, publicly editable and open-content platform for community curation of human long non-coding RNAs (lncRNAs).",
"fairsharing": "biodbcore-001262/",
"homepage": "https://ngdc.cncb.ac.cn/lncbook/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "BIGD (Big Data Center, Beijing Institute of Genomics)",
"name": "LncBook",
"prefix": "NBDC02541",
"pubmeds": [
"30329098"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"RNA",
"Health/Disease"
]
},
"nbdc02542": {
"alt_name": "Patients-Derived tumor Xenograft Finder",
"description": "PDX Finder is an open repository for the upload and storage of clinical, genomic and functional Patient-Derived Xenograph (PDX) data which provides a comprehensive global catalogue of PDX models available for researchers across distributed repository databases. Integrated views are provided for histopathological image data, molecular classification of tumors, host mouse strain metadata, tumor genomic data and metrics on tumor response to chemotherapeutics. The data model for PDX Finder is based on the minimal information standard for PDX models developed in collaboration with a broad range of stakeholders who create and/or use PDX models in basic and pre-clinical cancer research.",
"fairsharing": "FAIRsharing.j3y6a0",
"homepage": "http://www.pdxfinder.org",
"information_keywords": [
"Phenotype",
"Bibliography/Documents",
"Portal",
"Repository"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)||The Jackson Laboratory",
"name": "PDX Finder",
"prefix": "NBDC02542",
"pubmeds": [
"30535239"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc02543": {
"description": "piRBase stores information on piRNAs and piRNA-associated data to support piRNA functional analysis.",
"fairsharing": "biodbcore-001422/",
"homepage": "http://bigdata.ibp.ac.cn/piRBase/",
"information_keywords": [
"Sequence",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "Institute of Biophysics, Chinese Academy of Sciences",
"name": "piRBase",
"prefix": "NBDC02543",
"pubmeds": [
"30371818",
"25425034"
],
"status": "Active",
"target_keywords": [
"RNA",
"Genome/Gene",
"Epigenetics"
]
},
"nbdc02544": {
"description": "Development of a Drug Discovery Informatics System is a portal site containing databases and tools for predicting pharmacokinetics and toxicity (cardiotoxicity / hepatotoxicity). These databases and tools were constructed by \"Drug discovery support informatics system construction project at AMEDβ to support drug creation in all Japan.",
"homepage": "https://www.id3inst.org",
"information_keywords": [
"Method",
"Interaction/Pathway",
"Portal"
],
"maintainer": "Development of a Drug Discovery Informatics System",
"name": "Development of a Drug Discovery Informatics System",
"prefix": "NBDC02544",
"status": "Inactive",
"target_keywords": [
"Drug",
"Chemical compound",
"Health/Disease"
]
},
"nbdc02547": {
"description": "AMED Cardiotoxicity Database is a database about small molecules which bind to various ion channels and potentially cause cardiotoxic risk.\nIt compiles cardiotoxicity-related information of small molecules from publicly available databases and integrates them in standardized format. As an initial target, bioactivities for hERG potassium channel were collected from ChEMBL, NIH Chemical Genomics Center, and hERGCentral.",
"homepage": "https://drugdesign.riken.jp/hERGdb",
"information_keywords": [
"Chemical structure",
"Interaction/Pathway"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "AMED Cardiotoxicity Database",
"prefix": "NBDC02547",
"pubmeds": [
"29979714"
],
"status": "Active",
"target_keywords": [
"Chemical compound",
"Cell/Organelle",
"Health/Disease"
]
},
"nbdc02548": {
"alt_name": "Mikan Genome Database",
"description": "Mikan Genome Database (MiGD) is an integrated database for mandarin molecular breeding. It provides the following contents: (1) comparative genome browser which shows genome-wide variants and depth of coverage of re-sequencing data among nine citrus species, (2)genome sequence and annotation data of C. unshiu and P. trifoliata genomes which newly assembled by MiGD team, (3) CAPS maker database including 2,696 primer sets and restriction enzyme with electrophoresis photos, and (4) BLAST service against gene and genome sequences of four citrus species.",
"homepage": "https://mikan.dna.affrc.go.jp/",
"information_keywords": [
"Sequence"
],
"maintainer": "NARO (National Agriculture and Food Research Organization)",
"name": "MiGD",
"prefix": "NBDC02548",
"pubmeds": [],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"DNA"
]
},
"nbdc02549": {
"alt_name": "Crowd Extracted Expression of Differential Signatures",
"description": "CREEDS is a knowledgebase for associations between drugs, genes and diseases based on the data from a crowdsourcing microtask project implemented to annotate and reanalyze gene expression profiles from GEO. Signatures of these data are unique and are manually validated for quality. This database visualizes all of the signatures in a packed circles layout in which similar signatures are closer to each other. Furthermore, it has interactive heatmaps of hierarchically clustered matrices of all signatures.",
"homepage": "http://amp.pharm.mssm.edu/CREEDS/",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "Icahn School of Medicine at Mount Sinai",
"name": "CREEDS",
"prefix": "NBDC02549",
"pubmeds": [
"27667448"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc02550": {
"alt_name": "Molecular Signatures Database",
"description": "MSigDB is a collection of annotated gene sets for use with Enrichment Analysis (GSEA) software which is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. It contains 9 major collections of the gene sets;\nH: hallmark gene sets\nC1: positional gene sets\nC2: curated gene sets\nC3: regulatory target gene sets\nC4: computational gene sets\nC5: ontology gene sets\nC6: oncogenic signature gene sets\nC7: immunologic signature gene sets\nC8: cell type signature gene sets",
"homepage": "http://www.gsea-msigdb.org/gsea/msigdb/index.jsp",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "Broad Institute of Harvard and MIT||UCSD (University of California San Diego)",
"name": "MSigDB",
"prefix": "NBDC02550",
"pubmeds": [
"16199517"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc02552": {
"description": "MushPlant database is a database about toxic plants and mushrooms. It contains statistical data of food poisoning cases caused by toxic plants and mushrooms between 2000 and 2018, DNA-based identification methods based upon specific loci (eg, ITS, RPB2, matK), sequence data links, analytical methods and examples of molecular phylogenetic study.",
"homepage": "http://www.nihs.go.jp/dnfi/Mush-en.html",
"information_keywords": [
"Method",
"Sequence",
"Chemical structure",
"Bibliography/Documents"
],
"maintainer": "NIHS (National Institute of Health Sciences)",
"name": "MushPlant",
"prefix": "NBDC02552",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Metabolite",
"Organism",
"Health/Disease"
]
},
"nbdc02553": {
"alt_name": "High-quality INTeractomes",
"description": "HINT (High-quality INTeractomes) is a database of high-quality protein-protein interactions. The interactions are collected from 8 interactome resources (BioGRID, MINT, iRefWeb, DIP, IntAct, HPRD, MIPS and the PDB), and manually varidated.",
"homepage": "http://hint.yulab.org/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Cornell University",
"name": "HINT",
"prefix": "NBDC02553",
"pubmeds": [
"22846459"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02554": {
"description": "INstruct is a database of protein interactome networks in human and six model organisms. In this site, protein-protein interaction interfaces have been identified based on structural information derived from co-crystal evidence in PDB. A record shows the protein-protein interaction as domain interaction, and it also shows suggested proteins that interact via the same domain pairs as queried proteins.",
"homepage": "http://instruct.yulab.org/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "Cornell University",
"name": "INstruct",
"prefix": "NBDC02554",
"pubmeds": [
"23599502"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02555": {
"description": "ChEMBL is a database for bioactive molecules. It collects information of small molecules, such as calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data), and the target information. Metadata of assays for small molecule activities or assays for binding activities between small molecules and its targets are also provided.",
"fairsharing": "FAIRsharing.m3jtpg",
"homepage": "https://www.ebi.ac.uk/chembl/",
"information_keywords": [
"Chemical structure",
"Interaction/Pathway",
"Repository"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "ChEMBL",
"prefix": "NBDC02555",
"pubmeds": [
"33507738",
"30398643",
"25883136"
],
"status": "Active",
"target_keywords": [
"Chemical compound",
"Drug",
"Protein"
]
},
"nbdc02556": {
"alt_name": "International Classification of Diseases 11th Revision",
"description": "This is a website for ICD (International Statistical Classification of Diseases and Related Health Problems) -11, which is an organized collection of global standard terms for health data and clinical documentation. The ICD-11 has been developed by the World Health Organization (WHO). There is a link to ICD-10 (previous version) in this site.",
"fairsharing": "bsg-s001436/",
"homepage": "https://icd.who.int/en",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "World Health Organization",
"name": "ICD-11",
"prefix": "NBDC02556",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc02558": {
"alt_name": "Clinical Interpretation of Variants in Cancer",
"description": "CIViC is a knowledgebase for Clinical Interpretation of Variants in Cancer. It has collected knowledge of the therapeutic, prognostic, diagnostic and predisposing relevance of inherited and somatic variants in cancer based on expert-crowdsourcing.",
"fairsharing": "FAIRsharing.Yedluf",
"homepage": "https://civicdb.org/",
"information_keywords": [
"Bibliography/Documents",
"Repository"
],
"maintainer": "The McDonnell Genome Institute, Washington University School of Medicine",
"name": "CIVIC",
"prefix": "NBDC02558",
"pubmeds": [
"28138153"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease",
"Drug"
]
},
"nbdc02559": {
"alt_name": "Human Phenotype Ontology",
"description": "The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotype specialized in human disease. The medical literatures, Orphanet, DECIPHER, and OMIM are used for developing the HPO.",
"fairsharing": "FAIRsharing.kbtt7f",
"homepage": "https://hpo.jax.org",
"information_keywords": [
"Phenotype",
"Ontology/Terminology/Nomenclature"
],
"maintainer": "The Jackson Laboratory",
"name": "HPO",
"prefix": "NBDC02559",
"pubmeds": [
"33264411"
],
"status": "Active",
"target_keywords": [
"Health/Disease",
"Genome/Gene"
]
},
"nbdc02560": {
"description": "MedGen is a portal database about conditions and phenotypes related to Medical Genetics. It aggregates terms from the NIH Genetic Testing Registry (GTR), UMLS, HPO, Orphanet, ClinVar and other sources into concepts, and assigns a unique identifier and a preferred name and symbol. Each entry includes names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder. This database provides links to such resources as:\nGenetic tests registered in the NIH Genetic Testing Registry (GTR), GeneReviews, ClinVar, OMIM, Related genes, Disorders with similar clinical features, Medical and research literature, Practice guidelines, Consumer resources, Ontologies such as HPO and ORDO.",
"homepage": "https://www.ncbi.nlm.nih.gov/medgen/",
"information_keywords": [
"Phenotype",
"Ontology/Terminology/Nomenclature",
"Bibliography/Documents"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "MedGen",
"prefix": "NBDC02560",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc02561": {
"alt_name": "Genome Aggregation Database",
"description": "GnomAD is a resource for exome and genome sequencing data from a wide variety of large-scale sequencing projects. It contains following datasets; \nThe v2 data set (GRCh37/hg19) provided on this website spans 125,748 exome sequences and 15,708 whole-genome sequences from unrelated individuals sequenced as part of various disease-specific and population genetic studies. The v3.1 data set (GRCh38) spans 76,156 genomes, selected as in v2. Mitochondrial DNA (mtDNA) variants for gnomAD are also available.",
"homepage": "https://gnomad.broadinstitute.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "Genome Aggregation Database Consortium",
"name": "gnomAD",
"prefix": "NBDC02561",
"pubmeds": [
"32461654"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc02562": {
"alt_name": "Drug Gene Interaction database",
"description": "DGIdb is a database about drug-gene interactions and the druggable genome. It collects and integrates drug-gene interactions and gene druggability information from papers, databases and web resources, such as DrugBank, PharmGKB, ChEMBL, Drug Target Commons, TTD, and others, using a combination of expert curation and text-mining. It consists of gene records for gene details, drug records for drug details and Interaction records for interaction of the genes and drugs. Users can enter a list of genes to retrieve all known or potentially druggable genes in that list. Results can be filtered by source, interaction type, or gene category.",
"homepage": "https://www.dgidb.org/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "McDonnell Genome Institute at Washington University School of Medicine",
"name": "DGiDB",
"prefix": "NBDC02562",
"pubmeds": [
"33237278",
"29156001",
"26531824",
"24122041"
],
"status": "Active",
"target_keywords": [
"Drug",
"Health/Disease"
]
},
"nbdc02563": {
"alt_name": "Mondo Disease Ontology",
"description": "Mondo is an ontology for integrating disease definitions. It collects disease definitions and data models from numerous sources, which include HPO, OMIM, SNOMED CT, ICD, PhenoDB, MedDRA, MedGen, ORDO, DO, GARD, etc. It provides a hierarchical structure which can be used for classification or \"rolling up\" diseases to higher level groupings.",
"fairsharing": "FAIRsharing.b2979t",
"homepage": "https://mondo.monarchinitiative.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Monarch Initiative",
"name": "MONDO",
"prefix": "NBDC02563",
"pubmeds": [
"31701156"
],
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc02564": {
"alt_name": "Medical Dictionary for Regulatory Activities",
"description": "MedDRA is a standardized medical terminology for regulatory information of medical products. It is available for use in the registration, documentation and safety monitoring of medical products. It is provided in many languages, which are Chinese, Czech, Dutch, French, German, Hungarian, Italian, Japanese, Korean, Portuguese, Portuguese - Brazilian, Russian, and Spanish in addition to English Master.",
"fairsharing": "FAIRsharing.ad3137",
"homepage": "https://www.meddra.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "ICH (The International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use)",
"name": "MedDRA",
"prefix": "NBDC02564",
"status": "Active",
"target_keywords": [
"Drug",
"Health/Disease"
]
},
"nbdc02565": {
"description": "DDBJ BioSample is a database to store descriptive information about biological samples used to generate experimental data. The data are shared among DDBJ, EBI and NCBI BioSample databases. It includes information of species, details of experimental samples (e.g., organs, tissues, cell type, environment and phenotypes).",
"fairsharing": "biodbcore-001519/",
"homepage": "https://www.ddbj.nig.ac.jp/biosample/index-e.html",
"information_keywords": [
"Method",
"Classification",
"Bibliography/Documents",
"Repository"
],
"maintainer": "Bioinformation and DDBJ Center, National Institute of Genetics, Research Organization of Information and Systems",
"name": "DDBJ BioSample",
"prefix": "NBDC02565",
"status": "Active",
"target_keywords": [
"Organism",
"Cell/Organelle"
]
},
"nbdc02566": {
"alt_name": "Locus Reference Genomic",
"description": "LRG is a database of stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. NCBI (RefSeq) and EMBL-EBI (Ensembl/GENCODE) are working together to rationalise differences in their gene sets. Records contain information about genomic, transcript and protein sequences, annotations, maps about the genome assembly, etc. This database allows users to search using LRG identifier, HGNC gene name, NCBI and Ensembl accession numbers (gene or transcript), gene synonym or LRG status (public or pending). Genome browsers on Ensembl, NCBI and UCSC are available.",
"homepage": "http://www.lrg-sequence.org/",
"information_keywords": [
"Sequence"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)||NCBI (National Center for Biotechnology Information)",
"name": "LRG",
"prefix": "NBDC02566",
"pubmeds": [
"24285302"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Health/Disease"
]
},
"nbdc02567": {
"alt_name": "International Nucleotide Sequence Database Collaboration",
"description": "It is a portal site for the INSDC(International Nucleotide Sequence Database Collaboration), which is an initiative operated between DDBJ, EMBL-EBI and NCBI. Each organization operates DNA databases in close coordination and cooperation with each other to achieve common accession numbers, and standardize data format (INSD-XML). The databases are called the International Nucleotide Sequence Databases (INSD).",
"homepage": "http://www.insdc.org/",
"information_keywords": [
"Sequence",
"Portal"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)||NCBI (National Center for Biotechnology Information)||Bioinformation and DDBJ Center, National Institute of Genetics, Research Organization of Information and Systems",
"name": "INSDC",
"prefix": "NBDC02567",
"pubmeds": [],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02568": {
"alt_name": "Allosteric Mutation Analysis and Polymorphism of Signaling database",
"description": "The AlloMAPS database provides data on the energetics of communication in proteins with well-documented allosteric regulation, allosteric signalling in PDBselect chains, and allosteric effects of mutations. In addition to energetics of allosteric signaling between known functional and regulatory sites, allosteric modulation caused by the binding to these sites, by SNPs, and by mutations designated by the user can be explored. Allosteric Signaling Maps (ASMs), which are produced via the exhaustive computational scanning for stabilizing and destabilizing mutations and for the modulation range caused by the sequence position are available for each protein/protein chain in the database.",
"fairsharing": "FAIRsharing.aIe9SA",
"homepage": "http://allomaps.bii.a-star.edu.sg",
"information_keywords": [
"Sequence",
"3D structure",
"Interaction/Pathway"
],
"maintainer": "BII (Bioinformatics Institute, A*STAR)",
"name": "AlloMAPS",
"prefix": "NBDC02568",
"pubmeds": [
"30365033"
],
"status": "Active",
"target_keywords": [
"Genetic variation",
"Protein",
"Health/Disease"
]
},
"nbdc02569": {
"alt_name": "CuGenDB",
"description": "The recent genome sequence assemblies of major cucurbit crop species, including cucumber, melon, watermelon and pumpkin have made it feasible to use advanced genomic approaches in cucurbit breeding. Under the CucCAP project (http://cuccap.org), the Cucurbit Genomics Database (CuGenDB) aims to accelerate the breeding progress of cucurbit crops. Tripal was used to help manage, store, distribute and analyze the large amount of recently generated genotype and phenotype data. CuGenDB integrates genetic, genomics, transcriptomics and other biological data.",
"fairsharing": "FAIRsharing.PkY7Hl",
"homepage": "http://cucurbitgenomics.org",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "BTI (Boyce Thompson Institute, Cornell University)",
"name": "Cucurbit Genomics Database",
"prefix": "NBDC02569",
"pubmeds": [
"30321383"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Genetic variation"
]
},
"nbdc02570": {
"description": "Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome. This is a reimplementation at EMBL-EBI of a resource previously hosted at JCVI.",
"fairsharing": "FAIRsharing.A0ozDj",
"homepage": "https://www.ebi.ac.uk/interpro/genomeproperties",
"information_keywords": [
"Expression",
"Interaction/Pathway",
"Taxonomy"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "Genome Properties",
"prefix": "NBDC02570",
"pubmeds": [
"30364992"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc02571": {
"alt_name": "Sex-Associated Gene Database",
"description": "Many animal species present sex differences. Sex-associated genes (SAGs), which have female-biased or male-biased expression, have major influences on the remarkable sex differences in important traits such as growth, reproduction, disease resistance and behaviors. However, the SAGs resulting in the vast majority of phenotypic sex differences are still unknown. To provide a useful resource for the functional study of SAGs, we manually curated public RNA-seq datasets with paired female and male biological replicates from the same condition and systematically re-analyzed the datasets using standardized methods. We identified 27,793 female-biased SAGs and 64,043 male-biased SAGs from 2,828 samples of 21 species, including human, chimpanzee, macaque, mouse, rat, cow, horse, chicken, zebrafish, seven fly species and five worm species. All these data were cataloged into SAGD, a user-friendly database of SAGs where users can browse SAGs by gene, species, drug, and dataset. In SAGD, the expression, annotation, targeting drugs, homologs, ontology and related RNA-seq datasets of SAGs are provided to help researchers to explore their functions and potential applications in agriculture and human health.",
"fairsharing": "FAIRsharing.SFORSe",
"homepage": "http://bioinfo.life.hust.edu.cn/SAGD",
"information_keywords": [
"Expression",
"Localization"
],
"maintainer": "College of Life Science and Technology, Huazhong Agricultural University",
"name": "SAGD",
"prefix": "NBDC02571",
"pubmeds": [
"30380119"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02572": {
"description": "Translocatome is a database that collects and characterises manually curated and predicted translocating proteins from human cells. The prediction is made by a gradient boosting based machine learning algorithm (XGBoost), using highly curated positive and negative learning sets.",
"fairsharing": "FAIRsharing.FL1LNB",
"homepage": "http://translocatome.linkgroup.hu",
"information_keywords": [
"Localization",
"Interaction/Pathway"
],
"maintainer": "LINK-group",
"name": "Translocatome",
"prefix": "NBDC02572",
"pubmeds": [
"30380112"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02573": {
"alt_name": "Alzheimer's disease multi-omics database",
"description": "ADMIX database is an integrated database about Alzheimer's disease multi-omics data. It contains publicly available data in genomics, epigenomics, transcriptomics and proteomics (only transcriptomics data are available, July, 2021). It includes studies by microarray (gene, probe, tissue, comparison) and by RNA-seq (tissue, comparison, log2FC and study data link) and expression graph on entorhinal, hippocampus, temporal cortex and frontal cortex. Users can search expression data by gene name.",
"homepage": "http://www.alzdb.org/admix/gene_submit.html",
"information_keywords": [
"Expression"
],
"name": "ADMIX database",
"prefix": "NBDC02573",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease"
]
},
"nbdc02574": {
"alt_name": "Japanese aquatic macroinvertebrate reference",
"description": "J-amir is a collection of digital data about aquatic macroinvertebrates inhabiting Japan. It contains photo-images and analyzed DNA sequences (partial coding regions of 18S rRNA, histone H3, and mitochondrial cytochrome c oxidase subunit I genes) of each specimen.",
"homepage": "http://www.b.s.osakafu-u.ac.jp/~mkato/J-amir_home.htm",
"information_keywords": [
"Sequence",
"Taxonomy",
"Image/Movie"
],
"maintainer": "Osaka Prefecture University",
"name": "J-amir",
"prefix": "NBDC02574",
"pubmeds": [
"32995390"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02575": {
"description": "IMORI is a database of sequence resources about the Japanese fire bellied newt. It contains sequences from transcriptome data in various stages, such as development, regeneration and reproduction, and those annotations. Users are able to use their BLAST server to align a given sequence to transcripts. De novo assembled transcriptome data (fasta) and annotation (Blastx with NR data in NCBI) are downloadable.",
"homepage": "http://antler.is.utsunomiya-u.ac.jp/imori/",
"information_keywords": [
"Sequence",
"Expression"
],
"maintainer": "Japan Newt Research Community",
"name": "IMORI",
"prefix": "NBDC02575",
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02576": {
"description": "Phos-tag SDS-PAGE database is a collection about Phos-tag (a novel phosphate-binding tag) SDS-PAGE images for analyzing phosphorylated proteins. Each entry contains SDS-PAGE image, reference, composition of gel and detection. The data can be searched by protein names and browse proteins in the alphabetical list.",
"homepage": "http://phostag.hiroshima-u.ac.jp/index(E).html",
"information_keywords": [
"Method",
"Image/Movie",
"Interaction/Pathway"
],
"maintainer": "Hiroshima University Faculty of Pharmaceutical Sciences",
"name": "Phos-tag SDS-PAGE database",
"prefix": "NBDC02576",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02577": {
"description": "KNApSAcK Biomarker is a database for human biomarkers that provide indication of diseases. The biomarker information, which are biomarker name, related diseases, marker type (metabolite or protein), and references, is collected from reliable articles. The data can be searched by keywords.",
"homepage": "http://www.knapsackfamily.com/Biomarker/top.php",
"information_keywords": [
"Interaction/Pathway",
"Bibliography/Documents",
"Repository"
],
"maintainer": "Nara Institute of Science and Technology",
"name": "KNApSAcK Biomarker",
"prefix": "NBDC02577",
"pubmeds": [
"33705530"
],
"status": "Active",
"target_keywords": [
"Protein",
"Metabolite",
"Health/Disease"
]
},
"nbdc02578": {
"alt_name": "Proteomic profiling for classification of compounds",
"description": "ChemProteoBase is a database about proteomic profiling of cells treated with chemical drugs based on 2D-DIGE. Each entry contains protein name, position (x, y), Mascot Score, Uniprot ID, response to chemicals, and chemical information, etc.",
"homepage": "http://www.cbrg.riken.jp/csrs/xtra/ProteomePage/",
"information_keywords": [
"Expression",
"Interaction/Pathway"
],
"maintainer": "RIKEN (The Institute of Physical and Chemical Research)",
"name": "ChemProteoBase",
"prefix": "NBDC02578",
"pubmeds": [
"30519944",
"20534344"
],
"status": "Active",
"target_keywords": [
"Protein",
"Chemical compound",
"Drug",
"Health/Disease"
]
},
"nbdc02579": {
"description": "ncRNA-eQTL is a database of SNPs influencing ncRNA (non-coding RNA) expression. It provides information of ncRNA-related eQTLs (Expression quantitative trait locus) across 33 cancer types determined using data from The Cancer Genome Atlas (TCGA). eQTLs those are related with patient overall survival times by survival data and those are overlapped with known disease- and trait-associated loci by linking to GWAS (genome-wide association study) data are also provided. Users can search data by type of cancer, Gene ID and SNP ID, and download the results.",
"homepage": "http://ibi.hzau.edu.cn/ncRNA-eQTL",
"information_keywords": [
"Sequence",
"Expression",
"Phenotype",
"Interaction/Pathway"
],
"maintainer": "Huazhong Agricultural University, College of Informatics",
"name": "ncRNA-eQTL",
"prefix": "NBDC02579",
"pubmeds": [
"31410488"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Genetic variation",
"Health/Disease"
]
},
"nbdc02580": {
"alt_name": "Open Germline Receptor Database",
"description": "OGRDB is a database of the repertoires of human germline receptor alleles. Each data is submitted by researchers and reviewed and accepted by IARC (International Agency for Research on Cancer). This database mainly contains sequence names defined by IARC, sequences of full length and coding regions, functionality, and histories of the progress of the review by IARC. All the data can be downloaded at once.",
"homepage": "https://ogrdb.airr-community.org",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "Institute of Structural and Molecular Biology, Birkbeck College",
"name": "OGRDB",
"prefix": "NBDC02580",
"pubmeds": [
"31566225"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"DNA",
"Genetic variation"
]
},
"nbdc02581": {
"alt_name": "o RNA motifs enrichment in complete transcriptomes",
"description": "oRNAment is a database of putative RBP (RNA-binding-protein) binding site instances in coding and non-coding RNA in five species. For each RBP, this database mainly provides an organism it is derived from, the coding gene, the name and position on the genome of its motif, and similarity score to the canonical motif. Users can search from an organism, RBP name, attributes of gene and mRNA, and a region of a motif. Search results and all data are downloadable.",
"homepage": "https://rnabiology.ircm.qc.ca/oRNAment",
"information_keywords": [
"Sequence",
"Classification",
"Interaction/Pathway"
],
"maintainer": "LΓ©cuyer Lab, Institut de Recherches Cliniques de MontΓ©ral",
"name": "oRNAment",
"prefix": "NBDC02581",
"pubmeds": [
"31724725"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Protein"
]
},
"nbdc02582": {
"alt_name": "Prokaryotic Antiviral Defense System Arsenal",
"description": "PADS Arsenal is a database of genes associated with 18 categories of prokaryotic antiviral defense systems. This database mainly contains Assembly accessions, the number of genes related to each defense system, their Gene symbols, their positions, and Product accessions. The data can be searched from species, a system, an Assembly accession, and a gene. The search result is downloadable.",
"homepage": "http://bigd.big.ac.cn/padsarsenal/",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "China National Center for Bioinformation / Beijing Institute of Genomics, Chinese",
"name": "PADS Arsenal",
"prefix": "NBDC02582",
"pubmeds": [
"31620779"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02583": {
"description": "It is a set of 16S RNA sequences for metagenomic analysis using kraken2. Sequences with taxonomy ID, accession No. and definition are provided in fasta format.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/metagenomerefdb/desc.html",
"information_keywords": [
"Sequence"
],
"maintainer": "Graduate School of Integrated Sciences for Life, Hiroshima University",
"name": "16S RNA sequence set for metagenomic analysis",
"prefix": "NBDC02583",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02584": {
"alt_name": "AlphaFold Protein Structure Database",
"description": "AlphaFold DB is a database for protein structure predictions for human and 20 other key organisms. Each entry contains basic information about the protein and three separate outputs from AlphaFold, which are 3D coordinates (including side chains appeared when users click on the sequence in the viewer)β¨, a per-residue confidence metric called pLDDT, and predicted aligned error of the protein.",
"homepage": "https://alphafold.ebi.ac.uk",
"information_keywords": [
"3D structure"
],
"maintainer": "EMBL-EBI (European Bioinformatics Institute)",
"name": "AlphaFold DB",
"prefix": "NBDC02584",
"pubmeds": [
"34265844"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02585": {
"description": "KampoDB is an integrated database for natural medicines such as herbal medicines. It provides information of kampo formulas, including crude drugs, constituent natural compounds, and their target proteins those are known and predicted one.",
"homepage": "https://wakanmoview.inm.u-toyama.ac.jp/kampo/",
"information_keywords": [
"Chemical structure",
"Bibliography/Documents"
],
"maintainer": "University of Toyama Institute of Natural Medicine",
"name": "KampoDB",
"prefix": "NBDC02585",
"pubmeds": [
"30046160"
],
"status": "Active",
"target_keywords": [
"Metabolite",
"Chemical compound",
"Drug",
"Health/Disease"
]
},
"nbdc02586": {
"description": "PhaSepDB is a database of proteins related to phase separation (PS) and Membraneless organelles (MLOs) . This database mainly contains the protein names, links to Uniprot, coding gene symbols, organism information, location in a cell, PubMed ID of referenced publication, and experiment information. Users can browse proteins with gene symbols and Uniprot ID, and location in a cell. All data are downloadable.",
"homepage": "http://db.phasep.pro/",
"information_keywords": [
"Method",
"Localization",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "Peking University",
"name": "PhaSepDB",
"prefix": "NBDC02586",
"pubmeds": [
"31584089"
],
"status": "Active",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc02587": {
"description": "PhaSePro is a database of proteins driving LLPS (liquid-liquid phase separation) in cells. For each of them, this database mainly provides the protein information, the coding gene, the source species, the taxis of membraneless organelle formed, the types of molecular interactions related to LLPS, and supporting literature from PubMed. The data can be searched by gene and protein names, and the result and all data are downloadable.",
"homepage": "https://phasepro.elte.hu/",
"information_keywords": [
"Method",
"Sequence",
"3D structure",
"Interaction/Pathway",
"Bibliography/Documents"
],
"maintainer": "Department of Biochemistry, EΓΆtvΓΆs LorΓ‘nd University",
"name": "PhaSePro",
"prefix": "NBDC02587",
"pubmeds": [
"31612960"
],
"status": "Active",
"target_keywords": [
"Protein",
"Cell/Organelle",
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc02588": {
"description": "It is a database for non-B DNAs which do not fall into a right-handed Watson-Crick double-helix. This database provides information of genomic regions predicted to form non-B DNA forms, including Z-DNA motifs, quadruplex forming motifs, inverted repeats, mirror repeats and direct repeats and their associated subsets of cruciforms, triplex and slipped structures, etc.",
"homepage": "https://nonb-abcc.ncifcrf.gov/apps/site/default",
"information_keywords": [
"3D structure",
"Sequence"
],
"name": "non-B DB",
"prefix": "NBDC02588",
"pubmeds": [
"21097885",
"23125372"
],
"status": "Active",
"target_keywords": [
"DNA",
"Genome/Gene"
]
},
"nbdc02589": {
"description": "PhenoModifier is a database about genetic modifiers for elucidating the genetic basis of human phenotypic variation. It contains human genetic modifiers information, which manually curated from scientific literature, such as the modifier variants, the target disease or phenotype, modifier effects, etc. This database allows to search using human gene name, variant or disease name.",
"homepage": "https://www.biosino.org/PhenoModifier",
"information_keywords": [
"Phenotype"
],
"maintainer": "Shanghai Children's Hospital, Shanghai Jiao Tong University",
"name": "PhenoModifier",
"prefix": "NBDC02589",
"pubmeds": [
"31642469"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc02590": {
"alt_name": "Plant miRNA ENcyclopedia",
"description": "PmiREN is a comprehensive database for functional plant miRNA in about 180 species phylogenetically ranging from chlorophytes to angiosperms. Each record contains information about organism, miRNA loci (MIRs), secondary structure and sequence, miRNA cluster information, miRNA expression in various tissues, syntenic blocks, predicted target gene with its confidence. Users can browse data with species tree or search using miRNA identifier, keywords, sequences, genomic location, clusters, expression, syntenic blocks, target genes, etc.",
"homepage": "http://www.pmiren.com",
"information_keywords": [
"Sequence",
"Expression",
"Localization"
],
"maintainer": "Beijing Agro-Biotechnology Research Center, BAAFS",
"name": "PmiREN",
"prefix": "NBDC02590",
"pubmeds": [
"34554254",
"31602478",
"30521000"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Organism"
]
},
"nbdc02591": {
"description": "QTLbase is a database about genome-wide QTL summary statistics for many human molecular traits across over 70 tissue/cell types. It contains associations between genotypes and molecular traits such as gene and protein expression, DNA methylation, histone modification, splicing event, chromatin accessibility, RNA editing, etc. QTLbase allows users to query, compare, and visualize QTLs at tissue-wise, phenome-wise and variant-wise levels, and also incorporates large-scale tissue/cell typeβspecific genomic features and functional annotations to interpret the underlying QTL mechanisms.",
"homepage": "http://mulinlab.org/qtlbase",
"information_keywords": [
"Phenotype",
"Expression",
"Localization"
],
"maintainer": "Research Center of Basic Medical Sciences, Tianjin Medical University",
"name": "QTLbase",
"prefix": "NBDC02591",
"pubmeds": [
"31598699"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Epigenetics",
"RNA",
"Protein"
]
},
"nbdc02593": {
"alt_name": "Small RNA Expression Atlas",
"description": "SEA is a database for the expression of small RNA (miRNA, piRNA, snoRNA, snRNA, siRNA) and pathogens. It contains sRNA expression information from re-analyzed published samples, including many disease datasets and high quality predicted miRNAs. In addition, SEA also stores sRNA differential expression, sRNA based classification, pathogenic sRNA signatures from bacteria and viruses, and pathogen differential expression. It also contains gene targets and diseases associated with a miRNA.",
"homepage": "http://sea.ims.bio",
"information_keywords": [
"Sequence",
"Expression",
"Localization"
],
"maintainer": "ZMNH Institute of Medical Systems Biology",
"name": "SEAweb",
"prefix": "NBDC02593",
"pubmeds": [
"31598718"
],
"status": "Active",
"target_keywords": [
"RNA",
"Health/Disease"
]
},
"nbdc02594": {
"alt_name": "Global Genome Epidemiology Database",
"description": "gGENEPID is an integrated database for pathogen genome and epidemiological investigation. It contains genome information about 35 pathogens stipulated in the Infectious Diseases Control Law from NCBI public data and lists the analyzed data such as project name (NCBI link), region, species, host disease, and collection date for each organism. It summarizes regions and years of data with pie graphs on the global map.",
"homepage": "https://gph.niid.go.jp/ggenepid",
"information_keywords": [
"Sequence",
"Geographic Distribution",
"Bibliography/Documents"
],
"maintainer": "Pathogen Genomics Center, National Institute of Infectious Diseases",
"name": "gGENEPID",
"prefix": "NBDC02594",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Health/Disease"
]
},
"nbdc02598": {
"alt_name": "SARS (severe acute respiratory syndrome) -CoV2 Protein NMR Database",
"description": "SARS-CoV2-COV2-NMR DB is a 2D NMR spectra database about SARS-CoV-2 proteins. It retains 2D NMR spectra of 22 structural domains, including 3 non-canonical sequences, which ensure the structural homogeneity and quality of the purified proteins. It includes 2 sections; 13C Ile, Leu, Met, Val methyl TROSY spectra and 15N TROSY spectra.",
"homepage": "https://cov2nmr.aist.go.jp/",
"information_keywords": [
"3D structure",
"Image/Movie"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "SARS-Cov2NMR Protein DB",
"prefix": "NBDC02598",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02599": {
"description": "mFAERS is a search system about side effects reported in the FDA Adverse Event Reporting System (FAERS) public data. It provides information on intractable diseases designated by the Ministry of Health, Labor and Welfare in a coordination with the side effects. This system allows to search by drug name, disease name, and side effect name. It also scores the association between medications and side effects.",
"homepage": "https://mfaers.medals.jp/mfaers/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "mFAERS",
"prefix": "NBDC02599",
"status": "Active",
"target_keywords": [
"Drug",
"Health/Disease"
]
},
"nbdc02601": {
"description": "This is a database for all members in whole of Asterales. It includes taxon name, chromosome number (n and 2n), DNA contents, genbank accession numbers (for the nuclear or chloroplast DNA sequencesοΌYou can know that taxa used for molecular phylogenetic analyses), habit (life form) and size of plant, reproductive system, collection locality (Nation), Author (s) and the title of paper and published journal names.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/asteraceae-chr-index/desc.html",
"information_keywords": [
"Taxonomy",
"Bibliography/Documents"
],
"maintainer": "Kobe University",
"name": "Index to Chromosome numbers in Asteraceae",
"prefix": "NBDC02601",
"status": "Active",
"target_keywords": [
"Organism",
"Genome/Gene"
]
},
"nbdc02602": {
"description": "snoDB is a database of human snoRNA, which data are collected from other established databases, publications and experimental data generated by the group. Each entry contains information about synonym, box type, location, conservation, genomic sequence and expression data.",
"homepage": "https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/",
"information_keywords": [
"Sequence",
"Expression",
"Localization",
"Interaction/Pathway"
],
"maintainer": "Department of Biochemistry, University of Sherbrooke",
"name": "snoDB",
"prefix": "NBDC02602",
"pubmeds": [
"31598696"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"RNA",
"Health/Disease"
]
},
"nbdc02603": {
"description": "SNP2APA is a database for exploring the effects of single nucleotide polymorphisms (SNPs) on alternative polyadenylation (APA). SNP2APA allows users to :\n Browse or search cis-apaQTLs and trans-apaQTLs across different cancer types; \n Browse or search apaQTLs associated with patient overall survival across different cancer types; \n Browse or search apaQTLs in GWAS linkage disequilibrium (LD) regions; \n Predict the effects of SNP on PAS by submitting wild sequence and mutant sequence; \n Download figures and all apaQTL results.",
"homepage": "http://gong_lab.hzau.edu.cn/SNP2APA",
"information_keywords": [
"Sequence",
"Expression",
"Localization",
"Interaction/Pathway"
],
"maintainer": "College of informatics, HZAU",
"name": "SNP2APA",
"prefix": "NBDC02603",
"pubmeds": [
"31511885"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc02604": {
"description": "SyntDB is a database about human long non-coding RNAs conserved across primates. Each record contains Ensembl ID, reference alias, lncRNA, biotype of reference transcript, isoforms, lncRNA information, expression, sequence, disease and interactions, and conservation etc. This database allows users to search using alias, Ensembl Gene ID, Transcript ID or sequence.",
"homepage": "http://syntdb.amu.edu.pl",
"information_keywords": [
"Sequence",
"Expression",
"Interaction/Pathway"
],
"maintainer": "Faculty of Biology, Adam Mickiewicz University",
"name": "SyntDB",
"prefix": "NBDC02604",
"pubmeds": [
"31728519"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"RNA",
"Organism",
"Health/Disease"
]
},
"nbdc02605": {
"description": "TerrestrialMetagenomeDB is a repository of curated metadata for terrestrial metagenomes. Data are collected from MG-RAST and the Sequence Read Archive (SRA), the two main metagenome repositories, and includes two sections; βComplete datasetβ holds the full content of the databases' current version. On the other hand, the βInteractive mapβ provides a more intuitive way of selecting metagenomes directly from the world map, although being limited by the metagenomes with a pair of valid geographic coordinates available.",
"homepage": "https://webapp.ufz.de/tmdb",
"information_keywords": [
"Sequence",
"Environment"
],
"maintainer": "Helmholz-Zentrum for Environmental Research",
"name": "TerrestrialMetagenomeDB",
"prefix": "NBDC02605",
"pubmeds": [
"31728526"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02606": {
"description": "TSEA-DB is a database for trait-associated tissue specificity. This database contains trait collection decoded with tissue-specific enrichment analysis (TSEA) and their related genes which include (1) Genome-wide association studies (GWAS) by manual curation, and (2) UKBB GWAS data. This database allows users to search using Multi-Trait Collection (MTC), Expanded Trait Collection (ETC), UK Biobank Panel, Tissue Panel, etc.",
"homepage": "https://bioinfo.uth.edu/TSEADB",
"information_keywords": [
"Phenotype",
"Expression",
"Localization"
],
"maintainer": "UTHealth (University of Texas Health Science Center at Houston)",
"name": "TSEA-DB",
"prefix": "NBDC02606",
"pubmeds": [
"31680168"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Health/Disease"
]
},
"nbdc02608": {
"description": "MedDRA/J is a Japanese version of MedDRA (http://www.meddra.org) which is a pragmatic, medically valid terminology with an emphasis on ease of use for data entry, retrieval, analysis, and display, as well as a suitable balance between sensitivity and specificity within the regulatory environment.",
"homepage": "https://www.jmo.pmrj.jp/english",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Pharmaceutical and Medical Device Regulatory Science Society of Japan",
"name": "MedDRA/J",
"prefix": "NBDC02608",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc02610": {
"alt_name": "Material Management Center",
"description": "MMC is a database of tangible research materials (Materials) which are created or acquired through research activities. This database contains information about materials such as genes, cells, seeds, experimental animals, plants, microorganisms, compounds, etc.",
"homepage": "https://mmc-u.jp/en/",
"information_keywords": [
"Bioresource"
],
"maintainer": "Material Management Center, Kyushu University",
"name": "MMC",
"prefix": "NBDC02610",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism",
"Cell/Organelle",
"Chemical compound",
"Protein"
]
},
"nbdc02611": {
"alt_name": "Variability of Drug Transporter Database",
"description": "VARIDT is a database for drug transporters (DTs) confirmed by their corresponding drugs, which covers the comprehensive sets of DT variability data, and allows the interplay analysis among different aspects of DT variability. Each drug transporter (DT) entry contains gene name, protein name, 3D structure, synonyms, tissue specificity, function, disease(s) and endogenous metabolites (EMs) handled information.",
"homepage": "http://varidt.idrblab.net/",
"information_keywords": [
"Sequence",
"3D structure",
"Interaction/Pathway"
],
"maintainer": "College of Pharmaceutical Sciences, Zhejiang University",
"name": "VARIDT",
"prefix": "NBDC02611",
"pubmeds": [
"34747471",
"31495872"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Protein",
"Drug",
"Health/Disease"
]
},
"nbdc02612": {
"description": "VDJbase is a database of adaptive immune receptor genes, genotypes and haplotypes. In this database, collections are inferred from immune receptor repertoire sequences, and also added genomically derived material. This database allows users to browse the adaptive immune receptor repertoire (AIRR) datasets and alleles, browse the genomically-derived datasets and alleles, and view alignments in a genome browser.",
"homepage": "https://www.VDJbase.org",
"information_keywords": [
"Sequence"
],
"maintainer": "Faculty of Engineering, Bar Ilan University||Institute of Structural and Molecular Biology, Birkbeck College",
"name": "VDJbase",
"prefix": "NBDC02612",
"pubmeds": [
"31602484"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"Health/Disease"
]
},
"nbdc02613": {
"alt_name": "Viral Integration Site DataBase",
"description": "VISDB is a knowledgebase of site-related information about viruses integrated into human genome. It covers 9 main viruses, including 5 DNA oncoviruses (HBV, HPV, EBV, MCV, AAV2) and 4 RNA retroviruses (HIV, MLV, HTLV, XMRV). Each entry is carefully curated from publications and includes information for fusion event, validated (yes or no), detection method, sample type (tumor or nontumor), disease, quality evaluation, virus sequence, host sequence, miRNAs for regulate target gene, upstream and downstream sequences, etc.",
"homepage": "https://bioinfo.uth.edu/VISDB/index.php",
"information_keywords": [
"Sequence",
"Interaction/Pathway"
],
"maintainer": "UTHealth (University of Texas Health Science Center at Houston)",
"name": "VISDB",
"prefix": "NBDC02613",
"pubmeds": [
"31598702"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation",
"RNA",
"Health/Disease"
]
},
"nbdc02614": {
"description": "DNAproDB is a database for DNA-protein complexes. The site consists of a database, structure processing pipeline and web-based visualization tool. The database contains structural and biochemical features of DNA-protein complexes from the Protein Data Bank (3D structure, residue contact map, Helical contact map, protein chain information, DNA-protein interfaces, etc.). Users can search structures based on structural and bio-physical features of the protein, DNA, DNA-protein interactions in the structure.",
"homepage": "https://dnaprodb.usc.edu",
"information_keywords": [
"3D structure",
"Interaction/Pathway"
],
"maintainer": "USC (University of Southern California)",
"name": "DNAproDB",
"prefix": "NBDC02614",
"pubmeds": [
"31612957",
"28431131"
],
"status": "Active",
"target_keywords": [
"DNA",
"Protein"
]
},
"nbdc02615": {
"description": "EnhancerAtlas is a database providing enhancer annotation in nine species including human (hg19), mouse (mm9), fly (dm3), worm (ce10), zebrafish (danRer10), rat (rn5), yeast (sacCer3), chicken (galGal4) and boar (susScr3). It contains consensus enhancers which predicted based on multiple high throughput experimental datasets (e.g. histone modification, CAGE, GRO-seq, transcription factor binding and DHS). This database allows users to (1) examine the experimental evidence for the predicted enhancers in a given genomic region; (2) compare the enhancers across different cell/tissue types; (3) identify the enhancers associated with a particular gene; (4) predict the regulatory elements for a list of genomic regions.",
"homepage": "http://www.enhanceratlas.org/indexv2.php",
"information_keywords": [
"Expression",
"Localization"
],
"maintainer": "Johns Hopkins School of Medicine",
"name": "EnhancerAtlas 2.0",
"prefix": "NBDC02615",
"pubmeds": [
"31740966",
"27515742"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Genetic variation"
]
},
"nbdc02616": {
"description": "MatrisomeDB is a database of proteomic data for extracellular matrix (ECM). It provides hierarchically-clustered tissue distribution heatmap of proteins with confidence score, and link information of genes, proteins and raw data of experiments. Users can search data by gene symbols, proteins description or tissue types those are normal tissues and various cancers.",
"homepage": "https://matrisomedb.org",
"information_keywords": [
"Expression",
"Localization",
"Repository"
],
"maintainer": "Koch Institute for Integrative Cancer Research at MIT||University of Illinois at Chicago",
"name": "MatrisomeDB",
"prefix": "NBDC02616",
"pubmeds": [
"31586405",
"22159717",
"26163349",
"36399478"
],
"status": "Active",
"target_keywords": [
"Protein",
"Cell/Organelle"
]
},
"nbdc02617": {
"alt_name": "MicroSatellite DataBase",
"description": "MSDB is a database of simple sequence repeats (SSRs), also known as microsatellites. Each entry contains chromosome No., repeat class, repeat length, related gene name, annotations (exon, intron, intergenic or genic), and distance from TSS, etc. It allows users to browse using species list or species names. The data have been regularly updated by using UCSC, RefSeq and GenBank databases.",
"homepage": "http://data.ccmb.res.in/msdb",
"information_keywords": [
"Sequence"
],
"maintainer": "CCMB (CSIR-Centre for Cellular & Molecular Biology)",
"name": "MSDB",
"prefix": "NBDC02617",
"pubmeds": [
"31599331"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02618": {
"description": "OHNOLOGS is a repository of genes retained from whole genome duplications in the Vertebrate genomes. It contains ohnolog pairs and families in various vertebrate genomes computed with pre-defined or user-defined confidence levels (q-scores). These ohnolog pairs and families have been constructed using a quantitative multiple-genome comparative approach.",
"homepage": "http://ohnologs.curie.fr",
"information_keywords": [
"Sequence",
"Taxonomy"
],
"maintainer": "The Isambert Lab, Institute Curie",
"name": "OHNOLOGS",
"prefix": "NBDC02618",
"pubmeds": [
"31612943",
"26181593"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02619": {
"description": "BioHiKR is a database for bioluminescence. Each entry contains information of organism, protein, habitat, wave and ligand, which data links to Wikipedia and Uniprot and/or PDBj.",
"homepage": "http://www.biohikr.life",
"information_keywords": [
"Sequence",
"3D structure",
"Interaction/Pathway"
],
"maintainer": "Faculty of Science, Ochanomizu University||Faculty of Science and Engineering, Waseda University",
"name": "BioHiKR",
"prefix": "NBDC02619",
"status": "Active",
"target_keywords": [
"Protein",
"Organism"
]
},
"nbdc02620": {
"description": "MOROKOSHI Sorghum transcriptome database provides transcriptomic data in Sorghum bicolor. It contains information of ESTs from a normalized full-length cDNAs library of five growth stages of whole plant body and three growth stages of panicles. Additionally, it contains three tissue specific RNA-Seq analysis data (panicles, seeds and stems). Data of orthologs, similar expression genes and co-expression network are also provided.",
"homepage": "http://matsui-lab.riken.jp/morokoshi/Home.html",
"information_keywords": [
"Sequence",
"Expression",
"Localization",
"Interaction/Pathway"
],
"maintainer": "RIKEN CSRS (RIKEN Center for Sustainable Resource Science)",
"name": "MOROKOSHI Sorghum transcriptome database",
"prefix": "NBDC02620",
"pubmeds": [
"25505007"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST"
]
},
"nbdc02621": {
"description": "Flora of Myanmar Database is a database about flora specimens collected in Myanmar (Burma). It contains the records of specimens deposited in herbaria of National Museum of Nature and Science, Tokyo (TNS), the University of Tokyo (TI) and Forest Research Institute (RAF), Forest Department. Each entry contains taxon, collection data, locality and specimens image.",
"homepage": "https://www.kahaku.go.jp/research/db/botany/myanmarflora/",
"information_keywords": [
"Taxonomy",
"Geographic Distribution",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "National Museum of Nature and Science",
"name": "Flora of Myanmar Database",
"prefix": "NBDC02621",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02622": {
"alt_name": "AntiBodies Chemically Defined database",
"description": "The ABCD database is a repository of sequenced antibodies, integrating curated information about the antibody and its antigen with cross-links to standardized databases of chemical and protein entities. This database provides a comprehensive list of sequenced antibodies with their known targets, such as a common name, a list of synonyms, information about the target and the epitope, reference of at least one publication, applications, cross-references to original databases, etc. It also assigns a unique ID number for each antibody, that can be used in academic publications to increase reproducibility of experiments. This database allows to search using the name of an antibody, however, it recommends using the name of a target, UniProtKB ID, ChEBI ID or the name of an species.",
"fairsharing": "FAIRsharing.Z8OKi5",
"homepage": "https://web.expasy.org/abcd/",
"information_keywords": [
"Bibliography/Documents",
"Interaction/Pathway",
"Method",
"Repository"
],
"maintainer": "Geneva Antibody Facility",
"name": "ABCD database",
"prefix": "NBDC02622",
"pubmeds": [
"31410491"
],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02623": {
"description": "MetaboBank is an integrated metabolome data repository. It contains various metabolome data such as experimental raw data from mass spectrometry (MS), NMR analysis, imaging MS and those metadata. It allows to search using methods, data format, or organism. Metadata are described in the MAGE-TAB format, which is standard in functional genomics (GEA and EBI ArrayExpress) and proteomics (SDRF-Proteomics). It also compatible with ISA-TAB used by the MetaboLights at EBI. Each data is associated by Resource Description Framework (RDF), which enable to further expansion.",
"homepage": "https://www.ddbj.nig.ac.jp/metabobank/index-e.html",
"information_keywords": [
"Bibliography/Documents",
"Repository"
],
"maintainer": "Bioinformation and DDBJ Center, National Institute of Genetics, Research Organization of Information and Systems",
"name": "MetaboBank",
"prefix": "NBDC02623",
"status": "Active",
"target_keywords": [
"Metabolite"
]
},
"nbdc02624": {
"alt_name": "Vertebrate Gene Nomenclature Committee",
"description": "The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in selected vertebrate species that lack a nomenclature authority; currently these are chimpanzee, macaque, dog, cat, cattle, pig and horse. The VGNC also coordinates with the existing vertebrate nomenclature committees, MGNC (mouse), RGNC (rat), CGNC (chicken), XNC (Xenopus frog) and ZNC (zebrafish), to ensure genes are named in line with their human homologs.",
"fairsharing": "FAIRsharing.eBP3tb",
"homepage": "https://vertebrate.genenames.org/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "Vertebrate Gene Nomenclature Committee",
"name": "VGNC",
"prefix": "NBDC02624",
"pubmeds": [
"33152070"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein"
]
},
"nbdc02626": {
"description": "PubChem is the world's largest collection of freely accessible chemical information. Searches can be performed via a number of descriptors such as name, molecular formula and structure. Information is provided for chemical and physical properties, biological activities, safety and toxicity information, patents, literature citations and more. PubChem is organized as three linked databases within the NCBI's Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool.",
"fairsharing": "FAIRsharing.qt3w7z",
"homepage": "https://pubchem.ncbi.nlm.nih.gov",
"information_keywords": [
"Method",
"Chemical structure",
"Bibliography/Documents",
"Repository"
],
"maintainer": "NCBI (National Center for Biotechnology Information)",
"name": "PubChem",
"prefix": "NBDC02626",
"pubmeds": [
"33151290"
],
"status": "Active",
"target_keywords": [
"Protein",
"Metabolite",
"Chemical compound"
]
},
"nbdc02627": {
"alt_name": "Phosphorylation activity measurement-based pathway profiling database for drug-response",
"description": "Phosprof (phosphorylation profiling database) is a database to present cellular response to representative drugs as the significant pathways. It based on the original analysis of collected experimental data of phosphorylation activities using protein arrays. Phosphorylation activity measurement allows evaluation of signal transduction activity directly and provides direct estimation of responsible pathway of a cellular event. Comparison between various approved drugs, whose target phenotype is already known, can be helpful for drug development.",
"homepage": "https://phosprof.medals.jp/",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "phosprof",
"prefix": "NBDC02627",
"pubmeds": [
"35994309"
],
"status": "Active",
"target_keywords": [
"Protein",
"Drug"
]
},
"nbdc02628": {
"description": "RNAapt3D is a database of RNA aptamer which contains RNA sequences, their secondary/tertiary structural information, target proteins of RNA aptamers and network of RNA-protein interaction. The tertiary structures are predicted by a given RNA sequence considering a wide variety of secondary structures with a modelling tool, RASCAL, and molecular dynamics simulations. This database can be used to provide insights for tertiary structural analysis, motif search with base flip position and a starting point by RNA-protein complex molecular simulations. This database facilitates a study on the design of RNA aptamer for a target molecule and improves the efficiency and the productivity in candidate selection.",
"homepage": "https://rnaapt3d.medals.jp/",
"information_keywords": [
"Sequence",
"3D structure",
"Interaction/Pathway"
],
"maintainer": "AIST (National Institute of Advanced Industrial Science and Technology)",
"name": "RNAapt3D",
"prefix": "NBDC02628",
"pubmeds": [
"36146935"
],
"status": "Active",
"target_keywords": [
"RNA",
"Protein",
"Drug"
]
},
"nbdc02629": {
"alt_name": "Joint Environmental Data Integration System/Oshima Coastal Environmental data Acquisition Network System database",
"description": "JEDI System/OCEANS DB is a database containing images of marine plankton and environmental monitoring data. The physical, chemical, biological and engineering data observed by OCEANS (Oshima Coastal Environmental data Acquisition Network Sysmtem) of JEDI (Joint Environmental Data Integration) System at Habu port of Izu Oshima, Tokyo, Japan, from August 10, 2014 to August 10, 2018. See www2.kaiyodai.ac.jp/~hide/JEDI/ for more information.",
"homepage": "https://dbarchive.biosciencedbc.jp/en/jedisystem-oceansdb/desc.html",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Tokyo University of Marine Science and Technology",
"name": "JEDI System/OCEANS DB",
"prefix": "NBDC02629",
"pubmeds": [],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02630": {
"description": "EnteroBase is an online resource for analyzing and visualizing genomic variation within enteric bacteria strain. It contains metadata, genomic assemblies and deduced genotyping data about Salmonella, Escherichia/Shigella, Clostridioides, Vibrio, Yersinia, Helicobacter and Moraxella. Each entry is associated with metadata and genomic assemblies, as well as with deduced genotyping data.",
"homepage": "https://enterobase.warwick.ac.uk/",
"information_keywords": [
"Sequence",
"Repository"
],
"maintainer": "Warwick Medical School, University of Warwick",
"name": "EnteroBase",
"prefix": "NBDC02630",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02632": {
"alt_name": "RIKEN BRC Experimental Plant Web Catalog",
"description": "Exp-Plant Catalog is a database of plant bio-resource information in the stock of Experimental Plant Division of RIKEN BioResource Research Center (BRC). It contains seeds, DNA resources (RAFL clone, TF clone, TAC clone) and cell lines about model plants such as Arabidopsis thaliana, Brachypodium distachyon, Brassica rapa etc.. It allows to search using resource lists or keywords (BRC No, Cell Line, Plant Name, Culture type, origin).",
"homepage": "https://plant.rtc.riken.jp/resource/home/index.html",
"information_keywords": [
"Bioresource",
"Sequence"
],
"maintainer": "Experimental Plant Division, RIKEN BioResource Research Center",
"name": "Exp-Plant Catalog",
"prefix": "NBDC02632",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"cDNA/EST",
"Organism"
]
},
"nbdc02633": {
"description": "NeuroGT database is a brain atlas of neurogenic tagging mouse lines with CreER drivers for birthdate-based classification and manipulation of mouse neurons. It provides a catalog of image data of the neurons tagged by individual lines across the brain and information about birthdate tag driver line, reporter mouse line for visualization of neurogenic-tagged neurons, age of mouse, TM stage (embryonic day at which tamoxifen was administered), antibody (used for immunostaining against a reporter protein), etc..",
"homepage": "https://ssbd.riken.jp/neurogt/",
"information_keywords": [
"Image/Movie"
],
"maintainer": "RIKEN",
"name": "NeuroGT database",
"prefix": "NBDC02633",
"pubmeds": [
"35474959"
],
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02634": {
"alt_name": "Python-based database & analyzer for DIStortion of Heme porphyrin",
"description": "PyDISH is a database of heme porphyrin structures. Each entry is composed of one heme molecule liganded to a hemeprotein and includes information for the heme, axial ligands and information about them, protein function, orientation of propionate sidechains, structural resolution, and deposition date. It allows to search using browser with distortion of porphyrin and its axial ligands are displayed. PyDISH also provides several analytic tools for investigating the correlation between the distortion of heme and the axial ligands or protein function.",
"homepage": "https://pydish.bio.info.hiroshima-cu.ac.jp",
"information_keywords": [
"Chemical structure",
"3D structure",
"Image/Movie"
],
"maintainer": "Hiroshima City University",
"name": "PyDISH",
"prefix": "NBDC02634",
"pubmeds": [],
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02635": {
"alt_name": "Immune Cell Gene Expression Atlas from the University of Tokyo",
"description": "ImmuNexUT is a gene expression and eQTL atlas from 28 types of immune cells isolated from 10 distinct human immune mediated diseases (IMDs) and healthy donors. Each entry contains gene expression atlas for healthy individuals or normalized atlas of healthy individuals and patients with IMDs.This atlas links IMD GWAS variants to susceptible genes, cell types, and environment.\nIt allows to search using Gene Symbol or SNP ID.",
"homepage": "https://www.immunexut.org/",
"information_keywords": [
"Expression"
],
"maintainer": "The University of Tokyo",
"name": "ImmuNexUT",
"prefix": "NBDC02635",
"pubmeds": [
"33930287"
],
"status": "Active",
"target_keywords": [
"Genome/Gene"
]
},
"nbdc02636": {
"alt_name": "Open Oral Pathological Images Dataset",
"description": "The OOPID (Open Oral Pathological Images Dataset) project is developing open images dataset of human oral pathological image.",
"homepage": "https://oopid.jp",
"information_keywords": [
"Image/Movie"
],
"maintainer": "Nihon University School of Dentistry at Matsudo",
"name": "OOPID",
"prefix": "NBDC02636",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc02637": {
"description": "Kagoshima University Museum Vascular Plants Database is a database of vascular plant specimens collected in Kagoshima University Museum. Each entry contains taxon, collection data, name information, type information and specimens image. It allows to search using family/genus/epithet or Japanese name.",
"homepage": "https://dbs.kaum.kagoshima-u.ac.jp/musedb/s_plant/s_plant.php",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents",
"Taxonomy"
],
"maintainer": "Kagoshima University The Kagoshima University Museum",
"name": "Kagoshima University Museum Vascular_Plants Database",
"prefix": "NBDC02637",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02638": {
"alt_name": "Functional ANnoTation Of the Mammalian genome 6",
"description": "FANTOM6 is a database for function of long non-coding RNAs (lncRNAs) in the human genome. \nIt contains experimental data of the FANTOM project 6, such as mapped data using Cap Analysis of gene Expression (CAGE), microRNA atlas about chicken, rats, dogs and macaca and transcriptome and epigenome data in each cell type.",
"homepage": "https://fantom.gsc.riken.jp/6/",
"information_keywords": [
"Sequence",
"Expression",
"Image/Movie"
],
"maintainer": "RIKEN",
"name": "FANTOM6",
"prefix": "NBDC02638",
"pubmeds": [
"2718982"
],
"status": "Active",
"target_keywords": [
"RNA"
]
},
"nbdc02639": {
"description": "Genome sequencing of JCM strains under the NBRP program (Eukaryotic microbes) is a database about sequenced microbial strains and their genome DNAs. The determination about draft genome sequences are supported by National BioResource Project (NBRP). Each entry contains scientific name, JCM no., summary, BioProject ID, summary of assembly and annotation etc.. Each microbial strains and their genome DNAs are available from RIKEN BRC-JCM and RIKEN BRC-DNA Bank, respectively.",
"homepage": "https://www.jcm.riken.jp/cgi-bin/nbrp/nbrp_list.cgi",
"information_keywords": [
"Bioresource",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "RIKEN",
"name": "Genome sequencing of JCM strains under the NBRP program (Eukaryotic microbes)",
"prefix": "NBDC02639",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02640": {
"description": "Yeast strains with specific characteristics is a list of Yeast strains in JCM. This list is generated according to the requested one(s) presented below that were tested according to The Yeasts, a taxonomic study 5th edn (Elsevier). The results are scored as either positive (yellow-colored, including strongly, delayed, latent and slowly positive) or weakly positive (grey-colored).",
"homepage": "https://www.jcm.riken.jp/cgi-bin/jcm/function?KEY=YEAST",
"information_keywords": [
"Bioresource",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "RIKEN",
"name": "Yeast strains with specific characteristics",
"prefix": "NBDC02640",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Organism"
]
},
"nbdc02641": {
"alt_name": "BioBank Japan PheWeb",
"description": "PheWeb.jp is a database about genome-wide association study (GWAS) summary statistics of the BioBank Japan Project (BBJ). It provides GWAS results in the Japanese population (mainly from BBJ) using the PheWeb platform, with public access to the full summary statistics. This database allows to search using keywords or browse with lists of phenotypes, top hit about p-value, etc..",
"homepage": "https://pheweb.jp/",
"information_keywords": [
"Phenotype"
],
"maintainer": "BioBank Japan Project||Department of Statistical Genetics at Osaka University Graduate School of Medicine",
"name": "PheWeb.jp",
"prefix": "NBDC02641",
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Health/Disease",
"Genetic variation"
]
},
"nbdc02642": {
"description": "CUBIC-Cloud is a cloud-based framework for single-cell-resolution whole mouse brain analysis.\nBrain database: for upload and manage your brain data.\nNotebooks: for analyze your data and create graphs.\nStudio: for visualize the brain with an interactive 3D viewer.",
"homepage": "https://cubic-cloud.com",
"information_keywords": [
"Image/Movie",
"Repository"
],
"maintainer": "CUBIC Stars Co., Ltd.",
"name": "CUBIC-Cloud",
"prefix": "NBDC02642",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02645": {
"description": "Wild moths genetic resources is a resource database about wild moths. It contains ordering information and strain details, such as origin, hibernation, host plants, voltinism, images and movies. This database provides resources (egg, larva and cocoon) of Antheraea yamamai, Antheraea pernyi, Samia cynthia pryeri, Samia cynthia ricini, Rhodinia fugax, and Actias aliena.",
"homepage": "https://shigen.nig.ac.jp/wildmoth/index.jsp",
"information_keywords": [
"Bioresource",
"Image/Movie",
"Bibliography/Documents"
],
"maintainer": "National Institute of Genetics",
"name": "NBRP-Silkworm Collection, preservation, and distribution of Wild moths genetic resources",
"prefix": "NBDC02645",
"status": "Active",
"target_keywords": [
"Organism"
]
},
"nbdc02646": {
"description": "PreDom is a database and related prediction services about domain-domain interfaces. It consists of following sections:\nPreDom:DiD is a database of domain-domain interface which used information of structural domains defined in SCOP or CATH database. It contains amino acid sequence, domain-domain interaction residue and interactive 3D image with JSmol.\nPreDom:Interface predicts domain-domain interaction residues from the 3D structure of domain. Domain interface residues are predicted by two algorithm; KIP and IP.\nPreDom:Structure predicts 3D structure about multi-domain protein using 3D structure of each domain.\nPreDom:Evtrace predicts functional sites of a protein on the basis of phylogenetic and structural information.",
"homepage": "http://harrier.nagahama-i-bio.ac.jp/domain/",
"information_keywords": [
"Sequence",
"3D structure",
"Interaction/Pathway"
],
"maintainer": "Nagahama Institute of Bio-Science and Technology",
"name": "PreDom",
"prefix": "NBDC02646",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02647": {
"alt_name": "Electron Microscopy Public Image Archive PDBj",
"description": "EMPIAR-PDBj is a mirroring server of EMPIAR, which is a public resource for raw, 2D electron microscopy images. Each entry contains information about publication, related EMDB entry, experimental metadata and image files. This database allows to browse, upload, download and reprocess the thousands of raw, 2D images used to build a 3D structure. It also describes how to deposit big EM image data to EMPIAR.",
"homepage": "https://empiar.pdbj.org/en/",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents",
"Repository"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "EMPIAR-PDBj",
"prefix": "NBDC02647",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02648": {
"alt_name": "Biological Structure Model Archive",
"description": "BSM-Arc is an archive about protein/DNA/RNA structure obtained via in-silico methods. Each entry contains DOI of the corresponding paper, abstract, authors, PDB IDs, a graphical abstract and data files.",
"homepage": "https://bsma.pdbj.org",
"information_keywords": [
"Image/Movie",
"Bibliography/Documents",
"Repository"
],
"maintainer": "Osaka University Institute for Protein Research",
"name": "BSM-Arc",
"prefix": "NBDC02648",
"status": "Active",
"target_keywords": [
"Protein"
]
},
"nbdc02649": {
"alt_name": "Database of Drug Development for Rare Diseases",
"description": "DDrare is a database about clinical trials, drug target genes and pathways which related to mostly rare diseases designated by the Ministry of Health, Labour and Welfare (MHLW), Japan. It contains information about diseases, drugs, target genes, target pathways and clinical trials from world's four major registries of Japan, US, EU and China. This database allows to cross-reference and search using diseases, drugs, and target genes/pathways lists.",
"homepage": "https://ddrare.nibiohn.go.jp/index_e.html",
"information_keywords": [
"Interaction/Pathway"
],
"maintainer": "National Institutes of Biomedical Innovation, Health and Nutrition",
"name": "DDrare",
"prefix": "NBDC02649",
"status": "Active",
"target_keywords": [
"Health/Disease",
"Drug",
"Genome/Gene"
]
},
"nbdc02650": {
"description": "WHOCC ATC/DDD Index is a list of the complete anatomical therapeutic chemical index with drug therapies. It contains ATC codes and DDDs for substance name and/or ATC levels. It also shows the text from the Guidelines for ATC classification and DDD assignment linked to the ATC level. The text in the Guidelines gives information related to the background for the ATC and DDD assignment.",
"homepage": "https://atcddd.fhi.no/atc_ddd_index/",
"information_keywords": [
"Bibliography/Documents"
],
"maintainer": "WHO Collaborating Centre for Drug Statistics Methodology, Norwegian Institute of Public Health",
"name": "WHOCC ATC/DDD Index",
"prefix": "NBDC02650",
"status": "Active",
"target_keywords": [
"Chemical compound",
"Drug",
"Health/Disease"
]
},
"nbdc02651": {
"alt_name": "NCI Thesaurus",
"description": "NCI Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities. NCIt features: stable, unique codes for biomedical concepts; preferred terms, synonyms, research codes, external source codes, and other information; over 100,000 textual definitions; links to NCI Metathesaurus and other information sources; and over 400,000 cross-links between concepts, providing formal logic-based definition of many concepts. NCIt is a widely recognized standard for biomedical coding and reference, used by a broad variety of public and private partners both nationally and internationally including the Clinical Data Interchange Standards Consortium Terminology (CDISC), the U.S. Food and Drug Administration (FDA), the Federal Medication Terminologies (FMT), and the National Council for Prescription Drug Programs (NCPDP).",
"homepage": "https://ncithesaurus.nci.nih.gov/ncitbrowser/",
"information_keywords": [
"Ontology/Terminology/Nomenclature"
],
"maintainer": "National Cancer Institute at Frederick",
"name": "NCIt",
"prefix": "NBDC02651",
"status": "Active",
"target_keywords": [
"Health/Disease"
]
},
"nbdc02652": {
"description": "The information in the database is presented at two levels: the initial view or landing pages for each target family provide expert-curated overviews of the key properties and selective ligands and tool compounds available. For selected targets more detailed introductory chapters for each family are available along with curated information on the pharmacological, physiological, structural, genetic and pathophysiogical properties of each target. Recent extensions to the database provide specific portals for accessing data on immunopharmacology (IUPHAR Guide to IMMUNOPHARMACOLOGY; www.guidetoimmunopharmacology.org), and on malaria pharmacology (IUPHAR/MMV Guide to MALARIA PHARMACOLOGY; www.guidetomalariapharmacology.org). The database is enhanced with hyperlinks to additional information in other databases including Ensembl, UniProt, PubChem and ChEMBL, as well as curated chemical information and literature citations in PubMed.",
"fairsharing": "FAIRsharing.f1dv0",
"homepage": "https://www.guidetopharmacology.org/",
"information_keywords": [
"Sequence",
"Chemical structure",
"Bibliography/Documents"
],
"maintainer": "The International Union of Basic and Clinical Pharmacology (IUPHAR)||British Pharmacological Society (BPS)",
"name": "IUPHAR/BPS Guide to PHARMACOLOGY",
"prefix": "NBDC02652",
"pubmeds": [
"37897341"
],
"status": "Active",
"target_keywords": [
"Genome/Gene",
"Protein",
"Metabolite",
"Chemical compound",
"Drug",
"Health/Disease"
]
},
"nbdc02654": {
"description": "Marmoset PFC Connectome is a database about connectomics mapping of the marmoset prefrontal cortex (PFC) projections. Each entry contains region of injection, tracers, injection site, images of sections or layers.",
"homepage": "https://dataportal.brainminds.jp/marmoset-tracer-injection",
"information_keywords": [
"Localization",
"Interaction/Pathway",
"Image/Movie"
],
"maintainer": "RIKEN CBS (RIKEN Center for Brain Science)",
"name": "Marmoset PFC Connectome",
"prefix": "NBDC02654",
"pubmeds": [
"37196659"
],
"status": "Active",
"target_keywords": [
"Cell/Organelle",
"Organism"
]
}
} ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9659667
bioregistry-0.11.12/src/bioregistry/external/lov/ 0000755 0001751 0000177 00000000000 14655546227 021416 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/lov/__init__.py 0000644 0001751 0000177 00000004630 14655542206 023523 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download the LOV registry."""
import json
import tempfile
from collections import defaultdict
from pathlib import Path
from typing import Dict, List, Union
from pystow.utils import download, read_rdf
from bioregistry.external.alignment_utils import Aligner
__all__ = [
"get_lov",
"LOVAligner",
]
DIRECTORY = Path(__file__).parent.resolve()
PROCESSED_PATH = DIRECTORY / "processed.json"
URL = "https://lov.linkeddata.es/lov.n3.gz"
RECORD_SPARQL = """\
SELECT ?vocab ?name ?prefix ?uri_prefix ?description ?modified ?homepage
WHERE {
?vocab vann:preferredNamespacePrefix ?prefix .
?vocab dcterms:title ?name .
OPTIONAL { ?vocab vann:preferredNamespaceUri ?uri_prefix . }
OPTIONAL { ?vocab dcterms:description ?description . }
OPTIONAL { ?vocab dcterms:modified ?modified . }
OPTIONAL { ?vocab foaf:homepage ?homepage . }
}
ORDER BY ?vocab
"""
KEYWORD_SPARQL = """\
SELECT ?vocab ?keyword
WHERE { ?vocab dcat:keyword ?keyword . }
"""
columns = ["vocab", "name", "prefix", "uri_prefix", "description", "modified", "homepage"]
def get_lov(*, force_download: bool = False, force_refresh: bool = False):
"""Get the LOV data cloud registry."""
if PROCESSED_PATH.exists() and not force_download and not force_refresh:
return json.loads(PROCESSED_PATH.read_text())
with tempfile.TemporaryDirectory() as dir:
path = Path(dir).joinpath("lov.n3.gz")
download(url=URL, path=path)
graph = read_rdf(path)
keywords = defaultdict(set)
for vocab, keyword in graph.query(KEYWORD_SPARQL):
keywords[str(vocab)].add(str(keyword))
records = {}
for result in graph.query(RECORD_SPARQL):
d: Dict[str, Union[str, List[str]]] = {k: str(v) for k, v in zip(columns, result) if v}
if k := keywords.get(str(result[0])):
d["keywords"] = sorted(k)
if "uri_prefix" in d:
d["uri_prefix"] = d["uri_prefix"] + "$1" # type:ignore
if "homepage" in d:
del d["vocab"]
else:
d["homepage"] = d.pop("vocab")
records[d["prefix"]] = d
PROCESSED_PATH.write_text(json.dumps(records, indent=2))
return records
class LOVAligner(Aligner):
"""Aligner for LOV."""
key = "lov"
getter = get_lov
curation_header = ("name", "homepage", "uri_prefix")
if __name__ == "__main__":
LOVAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254811.0
bioregistry-0.11.12/src/bioregistry/external/lov/processed.json 0000644 0001751 0000177 00001574334 14655544033 024312 0 ustar 00runner docker {
"cl": {
"name": "Cinelab ontology",
"prefix": "cl",
"uri_prefix": "http://advene.org/ns/cinelab/ld#$1",
"description": "The Advene project aims at providing a model and various formats to share annotations about digital video documents (movies, courses, conferences...), as well as tools to edit and visualize the hypervideos generated from both the annotations and the audiovisual documents. Teachers, moviegoers, etc. can use them to exchange multimedia comments and analyses about video documents.\n\nThe Cinelab model allows not only to represent video annotations, but also an elicitation of their structure (through notions of schema and annotation type), as well as their presentations with views (templates applied on data to produce hypervideos) and queries.\n\nThis model has been developed by the partners of the Cinelab project (2007-2008, funded by the french national research agency), and used afterwards in a number of projects and applications, including Advene (LIRIS) and Ligne de temps (IRI).",
"modified": "2015-03-29",
"homepage": "http://advene.org/cinelab/",
"keywords": [
"Multimedia"
]
},
"geop": {
"name": "FAO Geopolitical Ontology",
"prefix": "geop",
"uri_prefix": "http://aims.fao.org/aos/geopolitical.owl#$1",
"description": "FAO's geopolitical ontology version 1.1 was populated with FAO, UN and internationally recognized data sources.",
"modified": "2011-01-18",
"keywords": [
"Geography"
],
"homepage": "http://aims.fao.org/aos/geopolitical.owl"
},
"eac-cpf": {
"name": "EAC-CPF Descriptions Ontology for Linked Archival Data:",
"prefix": "eac-cpf",
"uri_prefix": "http://archivi.ibc.regione.emilia-romagna.it/ontology/eac-cpf/$1",
"description": "Derive from the EAC-CPF original XML schema. Encoded Archival Context for Corporate Bodies, Persons, and Families provides a grammar for encoding names of creators of archival materials and related information.",
"modified": "2013-02-18",
"homepage": "http://archivi.ibc.regione.emilia-romagna.it/ontology/semanticEnvironment/index.html",
"keywords": [
"Catalogs"
]
},
"bag": {
"name": "Vocabulary for the Dutch base registration of buildings and addresses (BAG)",
"prefix": "bag",
"uri_prefix": "http://bag.basisregistraties.overheid.nl/def/bag#$1",
"description": "Basisregistraties Adressen en Gebouwen (BAG) vocabulaire",
"modified": "2018-05-02",
"keywords": [
"Geography"
],
"homepage": "http://bag.basisregistraties.overheid.nl/def/bag"
},
"awol": {
"name": "Atom Syndication Ontology",
"prefix": "awol",
"uri_prefix": "http://bblfish.net/work/atom-owl/2006-06-06/#$1",
"description": "The AtomOWL ontology is inspired from the work done by the atom working group. This ontology is working off the rfc 4287 published among othe places at http://www.atompub.org/rfc4287.html . The AtomOWL ontology uses as much as possible the same terms as the format there to make the relation easy to understand. The AtomOWL name space is slightly different from the atom namespace [see post http://www.imc.org/atom-syntax/mail-archive/msg16476.html]. But this is a good thing as it helps distinguish the ontology from the rfc 4287 serialisation.",
"modified": "2006-06-26",
"homepage": "http://bblfish.net/work/atom-owl/2006-06-06/AtomOwl.html",
"keywords": [
"API"
]
},
"cbs": {
"name": "De Centraal Bureau voor de Statistiek (CBS) ontologie",
"prefix": "cbs",
"uri_prefix": "http://betalinkeddata.cbs.nl/def/cbs#$1",
"description": "Ontologie voor datasets van het CBS",
"modified": "2018-05-02",
"keywords": [
"Geography",
"Government"
],
"homepage": "http://betalinkeddata.cbs.nl/def/cbs"
},
"bimerr-op": {
"name": "Occupancy Profile ontology",
"prefix": "bimerr-op",
"uri_prefix": "http://bimerr.iot.linkeddata.es/def/occupancy-profile#$1",
"description": "The Occupancy Profile ontology has been developed to represent people\u2019s behavior inside building spaces.",
"modified": "2020-06-25",
"keywords": [
"Environment",
"People"
],
"homepage": "http://bimerr.iot.linkeddata.es/def/occupancy-profile#"
},
"faldo": {
"name": "Feature Annotation Location Description Ontology",
"prefix": "faldo",
"uri_prefix": "http://biohackathon.org/resource/faldo#$1",
"description": "Used to describe a location that consists of a number of Regions but where the order is not known. e.g. the oddly named order() keyword in a INSDC file.",
"modified": "2012-09-07",
"keywords": [
"Geography"
],
"homepage": "http://biohackathon.org/resource/faldo"
},
"brk": {
"name": "Key Register Cadastre (BRK) vocabulary",
"prefix": "brk",
"uri_prefix": "http://brk.basisregistraties.overheid.nl/def/brk#$1",
"description": "Basisregistratie Kadaster (BRK) vocabulaire",
"modified": "2018-03-29",
"keywords": [
"Environment",
"Geography"
],
"homepage": "http://brk.basisregistraties.overheid.nl/def/brk"
},
"brt": {
"name": "Key Register Topography (BRT) vocabulary",
"prefix": "brt",
"uri_prefix": "http://brt.basisregistraties.overheid.nl/def/top10nl#$1",
"description": "Vocabulary for the Dutch key register of topography (BRT)",
"modified": "2018-03-29",
"keywords": [
"Environment",
"Geography"
],
"homepage": "http://brt.basisregistraties.overheid.nl/def/top10nl"
},
"caresses": {
"name": "CARESSES Ontology",
"prefix": "caresses",
"uri_prefix": "http://caressesrobot.org/ontology#$1",
"description": "The CARESSES Ontology encodes guidelines defined by experts in Transcultural Nursing, with the aim of offering a specific tool for endowing social assistive robots (assisting older adults) with cultural competence.",
"modified": "2019-06-17",
"keywords": [
"Health"
],
"homepage": "http://caressesrobot.org/ontology"
},
"plink": {
"name": "PersonLink Ontology",
"prefix": "plink",
"uri_prefix": "http://cedric.cnam.fr/isid/ontologies/PersonLink.owl#$1",
"description": "A Multilingual and Multicultural Ontology Representing Family Relationships.",
"modified": "2015-02-14",
"keywords": [
"People"
],
"homepage": "http://cedric.cnam.fr/isid/ontologies/PersonLink.owl"
},
"dtx_srti": {
"name": "LOD SRTI DATEX II",
"prefix": "dtx_srti",
"uri_prefix": "http://cef.uv.es/lodroadtran18/def/transporte/dtx_srti#$1",
"description": "An RDF/OWL vocabulary to represent SRTI DATEX II profile (according the Commission Delegated Regulation (EU) No 886/2013) within the European LOD-RoadTran18 action \"Supporting the cross-border use of Road Traffic Data with Linked Open Data based on DATEX II (LOD-RoadTran18)\" (Agreement No: INEA/CEF/ICT/A2018/1803421, Action No: 2018-EU-IA-0088). The vocabulary is used for mapping between DATEX II and LOD formats.",
"modified": "2022-03-03",
"keywords": [
"Transport"
],
"homepage": "http://cef.uv.es/lodroadtran18/def/transporte/dtx_srti"
},
"va": {
"name": "The Visual Analytics Vocabulary",
"prefix": "va",
"uri_prefix": "http://code-research.eu/ontology/visual-analytics#$1",
"description": "This vocabulary allows the semantic description of visual analytics applications. It is based on the RDF Data Cube Vocabulary and the Semanticscience Integrated Ontology.",
"modified": "2014-03-24",
"keywords": [
"Methods"
],
"homepage": "http://code-research.eu/ontology/visual-analytics"
},
"cbo": {
"name": "Comic Book Ontology",
"prefix": "cbo",
"uri_prefix": "http://comicmeta.org/cbo/$1",
"description": "A metadata vocabulary for describing comic books and comic book collections.",
"modified": "2015-12-05",
"homepage": "https://github.com/comicmeta/ComicBookOntology",
"keywords": [
"Image",
"Metadata"
]
},
"ctag": {
"name": "Common Tag Vocabulary",
"prefix": "ctag",
"uri_prefix": "http://commontag.org/ns#$1",
"description": "Common Tags are references to unique, well-defined concepts, complete with metadata and their own URLs.",
"modified": "2009-06-08",
"homepage": "http://commontag.org/Specification",
"keywords": [
"Tag"
]
},
"oc": {
"name": "OntoMedia Core",
"prefix": "oc",
"uri_prefix": "http://contextus.net/ontology/ontomedia/core/expression#$1",
"description": "OntoMedia (Ontology for Media) has been designed to describe the interactions occurring in multimedia.",
"modified": "2005-05-03",
"keywords": [
"Multimedia"
],
"homepage": "http://contextus.net/ontology/ontomedia/core/expression#"
},
"osr": {
"name": "OntoMedia Space Representation",
"prefix": "osr",
"uri_prefix": "http://contextus.net/ontology/ontomedia/core/space#$1",
"description": "The OntoMedia Space representation denotes areas of landscape. Expands on the AKT location ontology",
"modified": "2014-06-19",
"keywords": [
"Geography"
],
"homepage": "http://contextus.net/ontology/ontomedia/core/space#"
},
"being": {
"name": "OntoMedia Being Representation",
"prefix": "being",
"uri_prefix": "http://contextus.net/ontology/ontomedia/ext/common/being#$1",
"description": "A vocabulary to describe the interactions between persons and groups occurring in multimedia.",
"modified": "2013-09-19",
"keywords": [
"Multimedia"
],
"homepage": "http://contextus.net/ontology/ontomedia/ext/common/being#"
},
"trait": {
"name": "OntoMedia Trait Representation",
"prefix": "trait",
"uri_prefix": "http://contextus.net/ontology/ontomedia/ext/common/trait#$1",
"description": "OntoMedia (Ontology for Media) has been designed to describe the traits of entities.",
"modified": "2005-05-11",
"keywords": [
"Multimedia"
],
"homepage": "http://contextus.net/ontology/ontomedia/ext/common/trait#"
},
"date": {
"name": "OntoMedia Date Part Representation",
"prefix": "date",
"uri_prefix": "http://contextus.net/ontology/ontomedia/misc/date#$1",
"description": "OntoMedia (Ontology for Media) Date Component has been designed to describe the different ways of marking time in media.",
"modified": "2005-05-11",
"keywords": [
"Time"
],
"homepage": "http://contextus.net/ontology/ontomedia/misc/date#"
},
"pproc": {
"name": "PPROC ontology",
"prefix": "pproc",
"uri_prefix": "http://contsem.unizar.es/def/sector-publico/pproc#$1",
"description": "The PPROC ontology defines the necessary concepts to describe public procurement process and the contracts of public sector (public e-procurement). The ontology has been designed with the main purpose of publishing data about public contracts.",
"modified": "2015-01-11",
"homepage": "http://contsem.unizar.es/def/sector-publico/pproc.html",
"keywords": [
"Contracts"
]
},
"cci": {
"name": "Ontology for Cloud Computing instances",
"prefix": "cci",
"uri_prefix": "http://cookingbigdata.com/linkeddata/ccinstances#$1",
"description": "Ontology for Cloud Computing Instances. Instance are classes of VM that comprise varying combinations of CPU, memory, storage, and networking capacity. This ontology allows to define the instantiation model of MVs used in large cloud computing providers such as Amazon, Azure, etc.",
"modified": "2018-05-23",
"keywords": [
"Industry",
"Services"
],
"homepage": "http://cookingbigdata.com/linkeddata/ccinstances"
},
"ccp": {
"name": "Vocabulary for prices options in Cloud Computing Services",
"prefix": "ccp",
"uri_prefix": "http://cookingbigdata.com/linkeddata/ccpricing#$1",
"description": "Simple and direct pricing ontology for Cloud Computing Services. This ontology allows to define model of prices used in large cloud computing providers such as Amazon, Azure, etc., including options for regions, type of instances, prices specification, etc.",
"modified": "2018-05-23",
"keywords": [
"Industry",
"Support"
],
"homepage": "http://cookingbigdata.com/linkeddata/ccpricing"
},
"ccr": {
"name": "Vocabulary for Regions and Zones on Cloud Computing",
"prefix": "ccr",
"uri_prefix": "http://cookingbigdata.com/linkeddata/ccregions#$1",
"description": "Ontology for the definition of regions and zones of availability on CloudComputing platforms and services. This ontology allows to define model of regions used in large cloud computing providers such as Amazon, Azure, etc.",
"modified": "2018-05-23",
"keywords": [
"Geography",
"Industry",
"Services"
],
"homepage": "http://cookingbigdata.com/linkeddata/ccregions"
},
"ccsla": {
"name": "Service Level Agreement for Cloud Computing",
"prefix": "ccsla",
"uri_prefix": "http://cookingbigdata.com/linkeddata/ccsla#$1",
"description": "Service Level Agreement for Cloud Computing Services. This ontology allows to define model of SLA/SLO used in large cloud computing providers such as Amazon, Azure, etc., including terms, claims, credit, compensations, etc",
"modified": "2018-05-23",
"keywords": [
"Services",
"Support"
],
"homepage": "http://cookingbigdata.com/linkeddata/ccsla"
},
"crsw": {
"name": "ReSIST Courseware Ontology",
"prefix": "crsw",
"uri_prefix": "http://courseware.rkbexplorer.com/ontologies/courseware#$1",
"description": "The ReSIST Courseware Ontology represents the various educational courses and resources within the ReSIST project",
"modified": "2006-05-03",
"keywords": [
"Academy"
],
"homepage": "http://courseware.rkbexplorer.com/ontologies/courseware"
},
"cc": {
"name": "Creative Commons Rights Expression Language",
"prefix": "cc",
"uri_prefix": "http://creativecommons.org/ns#$1",
"description": "The Creative Commons Rights Expression Language (CC REL) lets you describe copyright licenses in RDF",
"modified": "2008-03-03",
"keywords": [
"Metadata"
],
"homepage": "http://creativecommons.org/ns"
},
"oad": {
"name": "Ontology for archival description",
"prefix": "oad",
"uri_prefix": "http://culturalis.org/oad#$1",
"description": "An ontology for the description of archival data (OAD, \u201cOntology of Archival Description\u201d) using the Web Ontology Language (OWL). This ontology represents the classes and properties needed to expose the archival resources as linked data.",
"modified": "2018-08-02",
"keywords": [
"Catalogs"
],
"homepage": "http://culturalis.org/oad#"
},
"agrelon": {
"name": "Agent Relationship Ontology",
"prefix": "agrelon",
"uri_prefix": "http://d-nb.info/standards/elementset/agrelon#$1",
"description": "The ontology of agent relationships, AgRelOn, defines relations of persons to other persons and to organisations",
"modified": "2019-06-13",
"keywords": [
"People"
],
"homepage": "http://d-nb.info/standards/elementset/agrelon"
},
"dnbt": {
"name": "DNB Metadata Terms",
"prefix": "dnbt",
"uri_prefix": "http://d-nb.info/standards/elementset/dnb#$1",
"description": "Das DNB RDF-Vokabular (dnb:) ist eine Sammlung von Klassen, Properties und Datentypen, die im Rahmen des LinkedData-Dienstes der DNB verwendung finden. Es ist ein Komplement zur GND-Ontologie (gndo:), die besonders f\u00fcr die Representation der Daten aus der Gemeinsamen Normdatei (GND) konstruiert wurde. Das DNB-Vokabular dagegen hat einen allgemeineren Scope.",
"modified": "2019-02-12",
"keywords": [
"Metadata"
],
"homepage": "http://d-nb.info/standards/elementset/dnb"
},
"gndo": {
"name": "GND-Ontologie",
"prefix": "gndo",
"uri_prefix": "http://d-nb.info/standards/elementset/gnd#$1",
"description": "GND stands for \"Gemeinsame Normdatei\" (Integrated Authority File) and offers a broad range of elements to describe authorities. The GND originates from the German library community and aims to solve the name ambiguity problem in the library world.",
"modified": "2019-02-12",
"keywords": [
"Catalogs"
],
"homepage": "http://d-nb.info/standards/elementset/gnd#"
},
"locah": {
"name": "The LOCAH RDF Vocabulary",
"prefix": "locah",
"uri_prefix": "http://data.archiveshub.ac.uk/def/$1",
"description": "This vocabulary derived from the Encoded Archival Description standard has been developed in 2010-2011 by the LOCAH project.",
"modified": "2015-01-11",
"homepage": "http://data.archiveshub.ac.uk/about.html",
"keywords": [
"Catalogs"
]
},
"ebg": {
"name": "euBusinessGraph ontology",
"prefix": "ebg",
"uri_prefix": "http://data.businessgraph.io/ontology#$1",
"description": "The euBusinessGraph (`ebg:`) ontology represents companies, type/status/economic classification, addresses, identifiers, company officers (e.g., directors and CEOs), and dataset offerings.\n\nIt uses `schema:domainIncludes/rangeIncludes` (which are polymorphic) to describe which properties are applicable to a class, \nrather than `rdfs:domain/range` (which are monomorphic) to prescribe what classes must be applied to each node using a property.\nWe find that this enables more flexible reuse and combination of different ontologies.\nWe reuse the following ontologies and nomenclatures, and extend them where appropriate with classes and properties:\n\n- W3C Org, W3C RegOrg (basic company data), \n\n- W3C Time (officer membership), \n\n- W3C Locn (addresses),\n\n- schema.org (domain/rangeIncludes and various properties)\n\n- DBpedia ontology (jurisdiction)\n\n- NGEO and Spatial (NUTS administrative divisions)\n\n- ADMS (identifiers), \n\n- FOAF, SIOC (blog posts),\n\n- RAMON, SKOS (NACE economic classifications and various nomenclatures),\n\n- VOID (dataset descriptions).\n\nThis is only a reference. See more detail in the [EBG Semantic Model](https://docs.google.com/document/d/1dhMOTlIOC6dOK_jksJRX0CB-GIRoiYY6fWtCnZArUhU/edit) google document, which includes an informative description of classes and properties, gives examples and data provider rules, and provides more schema and instance diagrams.",
"modified": "2020-02-11",
"keywords": [
"eBusiness"
],
"homepage": "http://data.businessgraph.io/ontology#"
},
"cochrane": {
"name": "Cochrane Core Vocabulary Ontology",
"prefix": "cochrane",
"uri_prefix": "http://data.cochrane.org/ontologies/core/$1",
"description": "The Cochrane Core ontology describes the entities and concepts that exist in the domain of evidence based healthcare. It is used for the construction of the Cochrane Linked Data Vocabulary containing some 400k terms including Interventions (Drugs, Procedures etc), Populations (Age, Sex, Condition), and clinical Outcomes.",
"modified": "2019-09-06",
"homepage": "https://data.cochrane.org/ontologies/core/index-en.html",
"keywords": [
"Health",
"Society"
]
},
"pico": {
"name": "Cochrane PICO Ontology",
"prefix": "pico",
"uri_prefix": "http://data.cochrane.org/ontologies/pico/$1",
"description": "The PICO ontology provides a machine accessible version of the PICO framework. It essentially provides a model for describing evidence in a consistent way. The model allows the specifying of complex populations, detailed interventions and their comparisons as well as the outcomes considered. The PICO ontology was originally designed to model the questions asked and answered in Cochrane's systematic reviews. As a leader in the field of evidence based healthcare Cochrane uses the PICO model when framing and publishing evidence based questions. The PICO model is widely adopted for describing healthcare evidence, furthermore is equally applicable in other evidence-based domains. It essentially provides a model for describing evidence in a consistent way.",
"modified": "2019-09-06",
"homepage": "https://data.cochrane.org/ontologies/pico/index-en.html",
"keywords": [
"Health",
"Society"
]
},
"mus": {
"name": "DOREMUS is an extension of the FRBRoo model for describing the music.",
"prefix": "mus",
"uri_prefix": "http://data.doremus.org/ontology#$1",
"description": "DOREMUS is an extension of the FRBRoo model for describing the music.",
"modified": "2017-06-05",
"homepage": "https://github.com/DOREMUS-ANR/doremus-ontology",
"keywords": [
"FRBR",
"Music"
]
},
"era": {
"name": "ERA vocabulary",
"prefix": "era",
"uri_prefix": "http://data.europa.eu/949/$1",
"description": "This is the human and machine readable Vocabulary/Ontology governed by the European Union Agency for Railways. It represents the concepts and relationships linked to the sectorial legal framework and the use cases under the Agency\u00b4s remit. Currently, this vocabulary covers the European railway infrastructure and the vehicles authorized to operate over it. It is a semantic/browsable representation of the RINF and ERATV application guides that were built by domain experts in the RINF and ERATV working parties.\nSince version 2.6.0, the ontology includes the routebook concepts described in appendix D2 \\\"Elements the infrastructure manager has to provide to the railway undertaking for the Route Book\\\" (https://eur-lex.europa.eu/eli/reg_impl/2019/773/oj) and the appendix D3 \\\"ERTMS trackside engineering information relevant to operation that the infrastructure manager shall provide to the railway undertaking\\\".",
"modified": "2023-03-29",
"keywords": [
"Transport",
"Travel"
],
"homepage": "http://data.europa.eu/949/"
},
"eli": {
"name": "The European Legislation Identifier",
"prefix": "eli",
"uri_prefix": "http://data.europa.eu/eli/ontology#$1",
"description": "Transposition of the ELI metadata fields into an OWL ontology",
"modified": "2018-05-23",
"keywords": [
"Contracts",
"FRBR"
],
"homepage": "http://data.europa.eu/eli/ontology"
},
"esco": {
"name": "The ESCO ontology",
"prefix": "esco",
"uri_prefix": "http://data.europa.eu/esco/model#$1",
"description": "The ontology of the taxonomy \"European Skills, Competences, qualifications and Occupations\".\n\nThe ontology considers three ESCO pillars (or taxonomy) and 2 registers.\nThe three pillars are:\n- Occupation\n- Skill (and competences)\n- Qualification\n\nFor the construction and use of the ESCO pillars, the following modelling artefacts are used:\n- Facetting support to specialize ESCO pillar concepts based on bussiness relevant Concept Groups (e.g. species, languages, ...)\n- Conept Groups, Thesaurus array and Compound terms (as detailed in ISO 25964) to organize faceted concepts\n- SKOS mapping properties to relate ESCO pillar concepts to concepts in other (external) taxonomies (e.g. FoET, ISCO88 and ISCO08. More mappings can be added in the future.)\n- Tagging ESCO pillar concepts by other (external) taxonomies (NUTS, EQF, NACE, ...)\n- Capture gender specifics on the labels of the ESCO pillar concepts\n- Rich ESCO concept relationships holding a description and other specific characteristics of the relation between two ESCO pillar concepts.\n\nESCO maintains two additional registers:\n- Awarding Body\n- Work Context\nAwarding Bodies typically are referenced by ESCO qualifications.\nOccupations can have one or more work context.",
"modified": "2014-10-23",
"keywords": [
"Services",
"Society"
],
"homepage": "http://data.europa.eu/esco/model"
},
"eurio": {
"name": "EURIO: EUropean Research Information Ontology",
"prefix": "eurio",
"uri_prefix": "http://data.europa.eu/s66#$1",
"description": "The EUropean Research Information Ontology (EURIO) conceptualises, formally encodes and makes available in an open, structured and machine-readable format data about resarch projects funded by the EU's framework programmes for research and innovation.",
"modified": "2021-08-20",
"keywords": [
"Academy",
"Metadata"
],
"homepage": "http://data.europa.eu/s66#"
},
"geofla": {
"name": "Ontologie des unit\u00e9s administratives de l'IGN",
"prefix": "geofla",
"uri_prefix": "http://data.ign.fr/def/geofla#$1",
"description": "Ontologie d\u00e9crivant le d\u00e9coupage administratif de la France m\u00e9tropolitaine, des d\u00e9partements d'outre mer, ou de la collectivit\u00e9 d\u00e9partementale de Mayotte, repr\u00e9sent\u00e9e comme une hi\u00e9rarchie de classes OWL",
"modified": "2015-01-11",
"keywords": [
"Geography"
],
"homepage": "http://data.ign.fr/def/geofla"
},
"geom": {
"name": "Ontologie des primitives g\u00e9om\u00e9triques",
"prefix": "geom",
"uri_prefix": "http://data.ign.fr/def/geometrie#$1",
"description": "An ontology for describing the shape and the location of topographic entities",
"modified": "2015-01-11",
"keywords": [
"Geometry"
],
"homepage": "http://data.ign.fr/def/geometrie"
},
"ignf": {
"name": "Ontologie des syst\u00e8mes de coordonn\u00e9es de r\u00e9f\u00e9rence",
"prefix": "ignf",
"uri_prefix": "http://data.ign.fr/def/ignf#$1",
"description": "Codes pour la description de syst\u00e8mes de coordonn\u00e9es de r\u00e9f\u00e9rence conforme ISO TC/211. Les traductions fran\u00e7aises des termes et leurs d\u00e9finitions sont pour la plupart issues du glossaire multilingue ISO/TC 211 disponible ici: http://www.isotc211.org/Terminology.htm",
"modified": "2016-06-28",
"keywords": [
"Geography"
],
"homepage": "http://data.ign.fr/def/ignf"
},
"topo": {
"name": "Ontologie des \u00e9l\u00e9ments du territoire et de ses infrastructures de l'IGN",
"prefix": "topo",
"uri_prefix": "http://data.ign.fr/def/topo#$1",
"description": "Ontologie d\u00e9crivant les \u00e9l\u00e9ments du territoire et ses infrastructures. Elle repend l'essentiel du vocabulaire de la BDTOPO(IGN) et vise \u00e0 couvrir l'ensemble des entit\u00e9s topographiques et administratives du territoire national. Les th\u00e8mes couverts sont: le r\u00e9seau routier, le r\u00e9seau ferroviaire, le r\u00e9seau de transport d'\u00e9nergie, le r\u00e9seau hydrographique, les b\u00e2timents, la v\u00e9g\u00e9tation arbor\u00e9e, l'orographie, les communes, les points d'activit\u00e9 ou d'int\u00e9r\u00eat.",
"modified": "2014-04-12",
"keywords": [
"Geography"
],
"homepage": "http://data.ign.fr/def/topo"
},
"food": {
"name": "Food Ontology",
"prefix": "food",
"uri_prefix": "http://data.lirmm.fr/ontologies/food#$1",
"description": "This ontology models the Food domain. It allows to describe ingredients and food products. Ontology used by the Open Food Facts dataset",
"modified": "2013-09-24",
"keywords": [
"Food"
],
"homepage": "http://data.lirmm.fr/ontologies/food"
},
"oan": {
"name": "Ontologie de l'Assembl\u00e9e Nationale",
"prefix": "oan",
"uri_prefix": "http://data.lirmm.fr/ontologies/oan/$1",
"description": "Cette ontologie repr\u00e9sente la description du fonctionnement de l'Assembl\u00e9e Nationale fran\u00e7aise.",
"modified": "2012-04-25",
"keywords": [
"Government"
],
"homepage": "http://data.lirmm.fr/ontologies/oan"
},
"osp": {
"name": "Ontologie du Service Public",
"prefix": "osp",
"uri_prefix": "http://data.lirmm.fr/ontologies/osp#$1",
"description": "Ontologie d'une organisation publique, plus particuli\u00e8rement d'un tribunal, d'une organisation internationale ou d'un pays.",
"modified": "2013-03-07",
"keywords": [
"Society"
],
"homepage": "http://data.lirmm.fr/ontologies/osp"
},
"passim": {
"name": "PASSIM ontology",
"prefix": "passim",
"uri_prefix": "http://data.lirmm.fr/ontologies/passim#$1",
"description": "Description of the operation of a transport information service",
"modified": "2014-07-22",
"keywords": [
"Travel"
],
"homepage": "http://data.lirmm.fr/ontologies/passim"
},
"poste": {
"name": "Ontologie de la Poste",
"prefix": "poste",
"uri_prefix": "http://data.lirmm.fr/ontologies/poste#$1",
"description": "Vocabulaire d\u00e9crivant la r\u00e9partition des points de contact du r\u00e9seau postal en France m\u00e9tropolitaine, Guadeloupe, Guyane, La R\u00e9union, Martinique, Mayotte, Monaco, Monte-Carlo et Saint-Pierre et Miquelon",
"modified": "2014-05-21",
"keywords": [
"Society"
],
"homepage": "http://data.lirmm.fr/ontologies/poste"
},
"vdpp": {
"name": "Vocabulary for Dataset Publication Projects",
"prefix": "vdpp",
"uri_prefix": "http://data.lirmm.fr/ontologies/vdpp#$1",
"description": "The Vocabulary of Dataset Publication Projects (VDPP) allows to represent the status of a dataset publication project. It is mainly based on the Provenance Vocabulary (PRV), the Dataset Provenance Vocabulary (VOIDP), the Vocabulary of Interlinked Datasets (VoID), and the Description of a Project (DOAP) vocabulary.",
"modified": "2011-03-27",
"homepage": "http://data.lirmm.fr/ontologies/vdpp.html",
"keywords": [
"Quality"
]
},
"lom": {
"name": "Learning Object Metadata Ontology",
"prefix": "lom",
"uri_prefix": "http://data.opendiscoveryspace.eu/lom_ontology_ods.owl#$1",
"description": "An ontology and vocabulary used for exposing IEEE LOM, a metadata standard for educational contents, as Linked Data. \nIt is intended as a bridge for linkage of educational metadata into Linked Open Data (LOD). In this ontology, we designed a mapping of IEEE LOM elements to RDF based on Linked Data principles.",
"modified": "2015-03-30",
"homepage": "http://data.opendiscoveryspace.eu/",
"keywords": [
"Metadata"
]
},
"g50k": {
"name": "50K Gazetteer Vocabulary",
"prefix": "g50k",
"uri_prefix": "http://data.ordnancesurvey.co.uk/ontology/50kGazetteer/$1",
"description": "A vocabulary developed to describe the Ordance Survey 50k Gazetteer linked data",
"modified": "2015-01-11",
"keywords": [
"Geography"
],
"homepage": "http://data.ordnancesurvey.co.uk/ontology/50kGazetteer/"
},
"osadm": {
"name": "The administrative geography and civil voting area ontology",
"prefix": "osadm",
"uri_prefix": "http://data.ordnancesurvey.co.uk/ontology/admingeo/$1",
"description": "An ontology describing the administrative and voting area geography of Great Britain",
"modified": "2013-09-04",
"keywords": [
"Geography"
],
"homepage": "http://data.ordnancesurvey.co.uk/ontology/admingeo/"
},
"osgeom": {
"name": "Ordnance Survey Geometry Ontology",
"prefix": "osgeom",
"uri_prefix": "http://data.ordnancesurvey.co.uk/ontology/geometry/$1",
"description": "A provisional small geometry vocabulary used by Ordnance Survey vocabularies and datasets. Likely to change when some standard way of representing geometries in RDF is agreed.",
"modified": "2012-10-08",
"keywords": [
"Geometry"
],
"homepage": "http://data.ordnancesurvey.co.uk/ontology/geometry/"
},
"postcode": {
"name": "Postcode Ontology",
"prefix": "postcode",
"uri_prefix": "http://data.ordnancesurvey.co.uk/ontology/postcode/$1",
"description": "An ontology describing the postcode geography in Great Britain.",
"modified": "2013-09-04",
"keywords": [
"Geography"
],
"homepage": "http://data.ordnancesurvey.co.uk/ontology/postcode/"
},
"osspr": {
"name": "Spatial Relations Ontology",
"prefix": "osspr",
"uri_prefix": "http://data.ordnancesurvey.co.uk/ontology/spatialrelations/$1",
"description": "An ontology describing basic spatial relations.",
"modified": "2013-09-04",
"keywords": [
"Geometry"
],
"homepage": "http://data.ordnancesurvey.co.uk/ontology/spatialrelations/"
},
"pna": {
"name": "Press.net Asset Ontology",
"prefix": "pna",
"uri_prefix": "http://data.press.net/ontology/asset/$1",
"description": "Press.net Asset Ontology describes news assets (text, images, video, data, etc), the relationships between them and how assets can be classified and semantically annotated.",
"modified": "2012-01-11",
"keywords": [
"Press"
],
"homepage": "http://data.press.net/ontology/asset/"
},
"pnc": {
"name": "Press.net Classification Ontology",
"prefix": "pnc",
"uri_prefix": "http://data.press.net/ontology/classification/$1",
"description": "The Press.net Classification Ontology allows assets to be holistically classified using a controlled vocabulary or taxonomy.",
"modified": "2012-09-25",
"keywords": [
"Catalogs"
],
"homepage": "http://data.press.net/ontology/classification/"
},
"pne": {
"name": "Press.net Event Ontology",
"prefix": "pne",
"uri_prefix": "http://data.press.net/ontology/event/$1",
"description": "Press.net Event Ontology models news-worthy events and their relationship to news assets and stuff (simple entities) in the world.",
"modified": "2012-04-20",
"keywords": [
"Press"
],
"homepage": "http://data.press.net/ontology/event/"
},
"pni": {
"name": "SNaP Identifier Ontology",
"prefix": "pni",
"uri_prefix": "http://data.press.net/ontology/identifier/$1",
"description": "The Identifier Ontology models non-RDF based Identifiers for resources. It is used to maintain a mapping between RDF resources identifiers and their equivalent IDs in an alternate, non-RDF based domain.",
"modified": "2012-03-21",
"homepage": "http://data.press.net/ontology/",
"keywords": [
"Support"
]
},
"pns": {
"name": "Press.net Stuff Ontology",
"prefix": "pns",
"uri_prefix": "http://data.press.net/ontology/stuff/$1",
"description": "Press.net Stuff Ontology models real world entities. There are two kinds of stuff: tangibles and intangibles. Tangible stuff includes persons, locations and organizations. Intangibles are abstract concepts such as smoking, feminism or love.",
"modified": "2012-06-18",
"keywords": [
"Press"
],
"homepage": "http://data.press.net/ontology/stuff/"
},
"pnt": {
"name": "Press.net Tag Ontology",
"prefix": "pnt",
"uri_prefix": "http://data.press.net/ontology/tag/$1",
"description": "Press.net Tag Ontology defines relationships for semantically annotating taggable things (for example news assets) with domain entities (stuff) and events.",
"modified": "2011-10-03",
"keywords": [
"Tag"
],
"homepage": "http://data.press.net/ontology/tag/"
},
"swc": {
"name": "Semantic Web Conference Ontology",
"prefix": "swc",
"uri_prefix": "http://data.semanticweb.org/ns/swc/ontology#$1",
"description": "The Semantic Web Conference ontology (SWC) is an ontology for describing academic conferences",
"modified": "2009-05-11",
"homepage": "http://data.semanticweb.org/ns/swc/swc_2009-05-09.html",
"keywords": [
"Academy",
"Society"
]
},
"game": {
"name": "TotL Game Ontology",
"prefix": "game",
"uri_prefix": "http://data.totl.net/game/$1",
"description": "This schema describes games with a known state, and few or no random elements.",
"modified": "2014-02-17",
"keywords": [
"Games"
],
"homepage": "http://data.totl.net/game/"
},
"bperson": {
"name": "Persoon",
"prefix": "bperson",
"uri_prefix": "http://data.vlaanderen.be/ns/persoon#$1",
"description": "Person ontology in Dutch",
"modified": "2017-03-31",
"homepage": "http://data.vlaanderen.be/ns/#Vocabularia",
"keywords": [
"People",
"Society"
]
},
"dataid": {
"name": "DataID",
"prefix": "dataid",
"uri_prefix": "http://dataid.dbpedia.org/ns/core#$1",
"description": "DBpedia Data ID is an ontology with the goal of describing LOD datasets via RDF files in a uniform way. Established vocabularies like DCAT, VoID, Prov-O and SPARQL Service Description are used for maximum compatibility.",
"modified": "2016-09-14",
"homepage": "http://wiki.dbpedia.org/projects/dbpedia-dataid",
"keywords": [
"Metadata"
]
},
"cis": {
"name": "Cultural-ON (Cultural ONtology): Ontologia dei Luoghi della Cultura e degli Eventi Culturali",
"prefix": "cis",
"uri_prefix": "http://dati.beniculturali.it/cis/$1",
"description": "The ontology aims at modelling the data on cultural institutes or sites such as data regarding the agents that play a specific role on cultural institutes or sites, the sites themselves, the contact points, all multimedia files which describe the cultural institute or site and any other information useful to the public in order to access the institute or site. Moreover, the ontology represents events that can take place in specific cultural institutes or sites.",
"modified": "2016-03-30",
"homepage": "http://dati.beniculturali.it/lodview/cis/.html",
"keywords": [
"Events",
"Government",
"Multimedia"
]
},
"ocd": {
"name": "Ontologia Camera dei Deputati",
"prefix": "ocd",
"uri_prefix": "http://dati.camera.it/ocd/$1",
"description": "Ontology of the Chamber of Deputies of the Italian Parliament.",
"modified": "2013-05-02",
"homepage": "http://dati.camera.it/ocd/reference_document/",
"keywords": [
"Government"
]
},
"shoah": {
"name": "Shoah Vocabulary Specification",
"prefix": "shoah",
"uri_prefix": "http://dati.cdec.it/lod/shoah/$1",
"description": "L'ontologia sul dominio \"Shoah\", proposta qui in versione beta, ha l'obiettivo di descrivere in maniera formale i concetti e le relazioni che caratterizzano e specificano il processo di persecuzione e deportazione degli ebrei dall'Italia fra il 1943 e il 1945.",
"modified": "2014-01-01",
"keywords": [
"People"
],
"homepage": "http://dati.cdec.it/lod/shoah/"
},
"ispra": {
"name": "Ispra Ontology",
"prefix": "ispra",
"uri_prefix": "http://dati.isprambiente.it/ontology/core#$1",
"description": "ISPRA ontology aims at the description of the processes and activities of the Institute in the areas circumscribed by the first published datasets.",
"modified": "2015-12-14",
"keywords": [
"Catalogs",
"Environment"
],
"homepage": "http://dati.isprambiente.it/ontology/core#"
},
"san-lod": {
"name": "SAN Ontologia",
"prefix": "san-lod",
"uri_prefix": "http://dati.san.beniculturali.it/SAN/$1",
"description": "SAN Ontology",
"modified": "2015-03-02",
"keywords": [
"Catalogs"
],
"homepage": "http://dati.san.beniculturali.it/SAN/"
},
"orges": {
"name": "Ontology about Spanish public organizations",
"prefix": "orges",
"uri_prefix": "http://datos.gob.es/def/sector-publico/organizacion#$1",
"description": "Extensi\u00f3n de la ontolog\u00eda de Organizaciones para adecuarla al Directorio Com\u00fan de entidades p\u00fablicas en Espa\u00f1a.",
"modified": "2015-02-19",
"keywords": [
"Government"
],
"homepage": "http://datos.gob.es/def/sector-publico/organizacion#"
},
"dbpedia-owl": {
"name": "The DBpedia Ontology",
"prefix": "dbpedia-owl",
"uri_prefix": "http://dbpedia.org/ontology/$1",
"description": "The DBpedia ontology provides the classes and properties used in the DBpedia data set.",
"modified": "2016-05-21",
"homepage": "http://wiki.dbpedia.org/Ontology",
"keywords": [
"General & Upper"
]
},
"basic": {
"name": "OWL representation of ISO 19103 (Basic types package)",
"prefix": "basic",
"uri_prefix": "http://def.seegrid.csiro.au/isotc211/iso19103/2005/basic#$1",
"description": "An OWL representation of (some of) the basic types described in ISO 19103:2005, required as primitives in other ontologies based on ISO 19100 series standards",
"modified": "2013-11-14",
"keywords": [
"Methods"
],
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19103/2005/basic"
},
"gm": {
"name": "OWL representation of ISO 19107 (Geographic Information)",
"prefix": "gm",
"uri_prefix": "http://def.seegrid.csiro.au/isotc211/iso19107/2003/geometry#$1",
"description": "An OWL representation of part of the model for geometry and space from ISO 19107:2003 Geographic Information - Spatial Schema",
"modified": "2013-11-14",
"keywords": [
"Geometry"
],
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19107/2003/geometry"
},
"tm": {
"name": "A vocabulary for temporal objects in Geographic Information",
"prefix": "tm",
"uri_prefix": "http://def.seegrid.csiro.au/isotc211/iso19108/2002/temporal#$1",
"description": "An OWL representation of part of the model for Temporal objects and reference systems from ISO 19108:2002 Geographic Information - Temporal Schema",
"modified": "2014-08-13",
"keywords": [
"Time"
],
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19108/2002/temporal"
},
"gf": {
"name": "OWL representation of ISO 19109 (General Feature Model)",
"prefix": "gf",
"uri_prefix": "http://def.seegrid.csiro.au/isotc211/iso19109/2005/feature#$1",
"description": "An OWL representation of part of the General Feature Model described in ISO 19109 and the General Feature Instance model described in Annex C of ISO 19156:2011.",
"modified": "2013-11-14",
"keywords": [
"Geography"
],
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19109/2005/feature"
},
"dq": {
"name": "OWL representation of ISO 19115 (Geographic Information - Metadata - Data quality package)",
"prefix": "dq",
"uri_prefix": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/dataquality#$1",
"description": "An OWL representation of parts of the Geographic Metadata model described in ISO 19115:2003 with Corrigendum 2006 - DQ Package",
"modified": "2014-08-28",
"keywords": [
"Quality"
],
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/dataquality"
},
"ext": {
"name": "OWL representation of ISO 19115 (Geographic Information - Metadata - Extent package)",
"prefix": "ext",
"uri_prefix": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/extent#$1",
"description": "An OWL representation of parts of the Geographic Metadata model described in ISO 19115:2003 with Corrigendum 2006 - EX Package",
"modified": "2014-08-28",
"keywords": [
"Geometry"
],
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/extent"
},
"li": {
"name": "OWL representation of ISO 19115 (Geographic Information - Metadata - Lineage package)",
"prefix": "li",
"uri_prefix": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/lineage#$1",
"description": "An OWL representation of parts of the Geographic Metadata model described in ISO 19115:2003 with Corrigendum 2006 - LI Package",
"modified": "2014-08-13",
"keywords": [
"Support"
],
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/lineage"
},
"md": {
"name": "OWL representation of ISO 19115",
"prefix": "md",
"uri_prefix": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/metadata#$1",
"description": "An OWL representation of parts of the Geographic Metadata model described in ISO 19115:2003 with Corrigendum 2006 - MD Package.",
"modified": "2014-08-28",
"keywords": [
"Geography"
],
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/metadata"
},
"h2o": {
"name": "Ontology for conversion of ISO/TC 211",
"prefix": "h2o",
"uri_prefix": "http://def.seegrid.csiro.au/isotc211/iso19150/-2/2012/basic#$1",
"description": "This ontology establishes classes corresponding to stereotypes used in ISO-conformant models, as used in the rules for conversion of the ISO TC 211 Harmonized Model from the UML to OWL representations",
"modified": "2014-01-07",
"keywords": [
"Methods"
],
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19150/-2/2012/basic"
},
"om": {
"name": "ISO 19156 Observation Model",
"prefix": "om",
"uri_prefix": "http://def.seegrid.csiro.au/isotc211/iso19156/2011/observation#$1",
"description": "An OWL representation of the Observation Schema described in clause 6 of ISO 19156:2011 Geographic Information - Observations and Measurements",
"modified": "2014-06-19",
"keywords": [
"Geography"
],
"homepage": "http://def.seegrid.csiro.au/isotc211/iso19156/2011/observation"
},
"sam": {
"name": "The Sampling Features Schema Vocabulary",
"prefix": "sam",
"uri_prefix": "http://def.seegrid.csiro.au/isotc211/iso19156/2011/sampling#$1",
"description": "An OWL representation of the Sampling Features Schema described in clauses 8-10 of ISO 19156:2011 Geographic Information - Observations and Measurements.",
"modified": "2014-08-28",
"homepage": "http://www.essepuntato.it/lode/owlapi/http://def.seegrid.csiro.au/isotc211/iso19156/2011/sampling",
"keywords": [
"Methods"
]
},
"oml": {
"name": "OWL for Observations",
"prefix": "oml",
"uri_prefix": "http://def.seegrid.csiro.au/ontology/om/om-lite#$1",
"description": "An OWL representation of the Observation Schema described in clauses 7-8 of ISO 19156:2011 Geographic Information - Observations and Measurements / OGC Abstract Specification - Topic 20.",
"modified": "2016-01-20",
"keywords": [
"Geography"
],
"homepage": "http://def.seegrid.csiro.au/ontology/om/om-lite"
},
"samfl": {
"name": "OWL for Sampling Features",
"prefix": "samfl",
"uri_prefix": "http://def.seegrid.csiro.au/ontology/om/sam-lite#$1",
"description": "A simple OWL representation of the Sampling Features Schema described in clauses 9-11 of ISO 19156:2011 Geographic Information - Observations and Measurements",
"modified": "2015-11-17",
"keywords": [
"Geography"
],
"homepage": "http://def.seegrid.csiro.au/ontology/om/sam-lite"
},
"obws": {
"name": "Object with states ontology",
"prefix": "obws",
"uri_prefix": "http://delicias.dia.fi.upm.es/ontologies/ObjectWithStates.owl#$1",
"description": "Ontology including the content ontology design pattern for modelling objects with states.",
"modified": "2016-04-15",
"keywords": [
"Methods"
],
"homepage": "http://delicias.dia.fi.upm.es/ontologies/ObjectWithStates.owl"
},
"poder": {
"name": "Poder Vocabulary",
"prefix": "poder",
"uri_prefix": "http://dev.poderopedia.com/vocab/$1",
"description": "Un vocabulario para expresar informaci\u00f3n acerca de personas, y sus relaciones con organizaciones y empresas",
"modified": "2012-05-17",
"homepage": "http://dev.poderopedia.com/documentation/index",
"keywords": [
"People"
]
},
"dogont": {
"name": "Ontology Modeling for Intelligent Domotic Environments",
"prefix": "dogont",
"uri_prefix": "http://elite.polito.it/ontologies/dogont$1",
"description": "The DogOnt ontology supports device/network independent description of houses, including both controllable and architectural elements.",
"modified": "2015-01-11",
"homepage": "http://iot-ontologies.github.io/dogont/",
"keywords": [
"Environment",
"IoT"
]
},
"eupont": {
"name": "EUPont: an ontology for End User Programming of the IoT",
"prefix": "eupont",
"uri_prefix": "http://elite.polito.it/ontologies/eupont.owl#$1",
"description": "EUPont is an ontology to model high level rules for Internet of Things End User Programming (IoT-EUP).",
"modified": "2018-02-09",
"keywords": [
"IoT"
],
"homepage": "http://elite.polito.it/ontologies/eupont.owl"
},
"op": {
"name": "Observable properties",
"prefix": "op",
"uri_prefix": "http://environment.data.gov.au/def/op#$1",
"description": "A general purpose ontology for observable properties. The ontology supports description of both qualitative and quantitative properties. The allowed scale or units of measure may be specified. A property may be linked to substances-or-taxa and to features or realms, if they play a role in the definition.",
"modified": "2016-02-28",
"keywords": [
"Methods"
],
"homepage": "http://environment.data.gov.au/def/op"
},
"ep": {
"name": "EPrints Ontology",
"prefix": "ep",
"uri_prefix": "http://eprints.org/ontology/$1",
"description": "Describes the main classes and properties which EPrints adds to voID, DC, BIBO and SKOS etc",
"modified": "2010-10-20",
"keywords": [
"Catalogs"
],
"homepage": "http://eprints.org/ontology/"
},
"ecrm": {
"name": "Erlangen CRM / OWL",
"prefix": "ecrm",
"uri_prefix": "http://erlangen-crm.org/current/$1",
"description": "Erlangen CRM / OWL - An OWL DL 1.0 implementation of the CIDOC Conceptual Reference Model, based on: Nick Crofts, Martin Doerr, Tony Gill, Stephen Stead, Matthew Stiff (eds.): Definition of the CIDOC Conceptual Reference Model (http://cidoc-crm.org/).\nThis implementation has been originally created by Bernhard Schiemann, Martin Oischinger and G\u00fcnther G\u00f6rz at the Friedrich-Alexander-University of Erlangen-Nuremberg, Department of Computer Science, Chair of Computer Science 8 (Artificial Intelligence) in cooperation with the Department of Museum Informatics of the Germanisches Nationalmuseum Nuremberg and the Department of Biodiversity Informatics of the Zoologisches Forschungsmuseum Alexander Koenig Bonn.\nThe Erlangen CRM / OWL implementation of the CIDOC Conceptual Reference Model is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License.",
"modified": "2017-01-03",
"keywords": [
"General & Upper"
],
"homepage": "http://erlangen-crm.org/current/"
},
"ngeo": {
"name": "NeoGeo Geometry Ontology",
"prefix": "ngeo",
"uri_prefix": "http://geovocab.org/geometry#$1",
"description": "A vocabulary for specifying geographical regions in RDF",
"modified": "2012-02-05",
"homepage": "http://geovocab.org/geometry.html",
"keywords": [
"Geometry"
]
},
"spatial": {
"name": "NeoGeo Spatial Ontology",
"prefix": "spatial",
"uri_prefix": "http://geovocab.org/spatial#$1",
"description": "A vocabulary for describing topological relations between features",
"modified": "2012-02-05",
"homepage": "http://geovocab.org/doc/neogeo/",
"keywords": [
"Geometry"
]
},
"gov": {
"name": "Ontologie zur Modellierung historischer Verwaltungsinformationen.",
"prefix": "gov",
"uri_prefix": "http://gov.genealogy.net/ontology.owl#$1",
"description": "The Genealogisches Orts-Verzeichnis (GOV) contains information about current and historical political, ecclesiastical and legal administrative affiliations of settlements and administrative units. In addition several time-dependent values (such as names, population numbers, postal codes etc.) are given.",
"modified": "2015-07-29",
"keywords": [
"Society",
"Time"
],
"homepage": "http://gov.genealogy.net/ontology.owl"
},
"r4r": {
"name": "Relations for Reusing (R4R) Ontology",
"prefix": "r4r",
"uri_prefix": "http://guava.iis.sinica.edu.tw/r4r/$1",
"description": "R4R is a light-weight ontology for representing general relationships of resource for publication and reusing. It asserts that a certain reusing context occurred and determined by its two basic relations, namely, isPackagedWith and isCitedBy. The isPackagedWith relation declares the resource is ready to be reused by incorporating License and Provenance information. The Cites relation is an exceptional to isCitedBy which occurs only two related objects cite each other at the same time. Five resource objects including article, data, code, provenance and license are major class concepts to represent in this ontology. \n\nThe namespace for all R4R terms is http://guava.iis.sinica.edu.tw/r4r/",
"modified": "2015-03-11",
"keywords": [
"Quality",
"Support"
],
"homepage": "http://guava.iis.sinica.edu.tw/r4r"
},
"mrel": {
"name": "MARC Code List for Relators",
"prefix": "mrel",
"uri_prefix": "http://id.loc.gov/vocabulary/relators/$1",
"description": "MARC relators are defined as both RDF properties and SKOS concepts",
"modified": "2014-06-03",
"keywords": [
"Vocabularies"
],
"homepage": "http://id.loc.gov/vocabulary/relators"
},
"turismo": {
"name": "Ontolog\u00eda de Turismo para el Ayuntamiento de Zaragoza",
"prefix": "turismo",
"uri_prefix": "http://idi.fundacionctic.org/cruzar/turismo#$1",
"description": "Esta ontolog\u00eda se ha construido dentro del proyecto financiado por el Ayuntamiento de Zaragoza: \"Un visitante, una ruta\", una aplicaci\u00f3n inform\u00e1tica para el c\u00e1lculo de rutas tur\u00edsticas en la ciudad de Zaragoza en base al perfil y contexto del usuario.",
"modified": "2007-11-02",
"keywords": [
"Travel"
],
"homepage": "http://idi.fundacionctic.org/cruzar/turismo"
},
"frad": {
"name": "FRAD model",
"prefix": "frad",
"uri_prefix": "http://iflastandards.info/ns/fr/frad/$1",
"description": "This is the element set of native RDF classes and properties described in the Functional Requirements for Authority Data model. The model also uses elements previously described in the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model.",
"modified": "2015-01-11",
"homepage": "http://metadataregistry.org/schema/show/id/24.html",
"keywords": [
"FRBR"
]
},
"frbrer": {
"name": "FRBRer model",
"prefix": "frbrer",
"uri_prefix": "http://iflastandards.info/ns/fr/frbr/frbrer/$1",
"description": "This is the element set of native RDF classes and properties described in the current text (Feb 2009) of the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model.",
"modified": "2015-07-14",
"keywords": [
"FRBR"
],
"homepage": "http://iflastandards.info/ns/fr/frbr/frbrer/"
},
"isbd": {
"name": "ISBD elements",
"prefix": "isbd",
"uri_prefix": "http://iflastandards.info/ns/isbd/elements/$1",
"description": "This is a registration of classes and properties from International Standard Bibliographic Description (ISBD), consolidated edition, published by De Gruyter Saur in July 2011 (ISBN 978-3-11-026379-4).",
"modified": "2015-03-11",
"keywords": [
"Catalogs",
"Metadata"
],
"homepage": "http://iflastandards.info/ns/isbd/elements/"
},
"imo": {
"name": "The IMGpedia Ontology",
"prefix": "imo",
"uri_prefix": "http://imgpedia.dcc.uchile.cl/ontology#$1",
"description": "La Ontologia de IMGpedia provee terminos para referirse a descriptores visuales y relaciones de similitud entre imagenes",
"modified": "2018-01-12",
"keywords": [
"Image"
],
"homepage": "http://imgpedia.dcc.uchile.cl/ontology"
},
"dso": {
"name": "Data Structure Ontology",
"prefix": "dso",
"uri_prefix": "http://inference-web.org/2.0/ds.owl#$1",
"description": "This ontology offers OWL-Lite definition for object list. It is a restricted version of OWL-S ObjectList",
"modified": "2009-06-28",
"keywords": [
"General & Upper"
],
"homepage": "http://inference-web.org/2.0/ds.owl"
},
"pmlp": {
"name": "PML2 provenance ontology",
"prefix": "pmlp",
"uri_prefix": "http://inference-web.org/2.0/pml-provenance.owl#$1",
"description": "The provenance part of PML2 ontology. It is a fundamental component of PML2 ontology.",
"modified": "2015-01-11",
"keywords": [
"Quality"
],
"homepage": "http://inference-web.org/2.0/pml-provenance.owl"
},
"hr": {
"name": "hRESTS Ontology",
"prefix": "hr",
"uri_prefix": "http://iserve.kmi.open.ac.uk/ns/hrests#$1",
"description": "hRESTS is a vocabulary for describing RESTful Web services",
"modified": "2013-10-23",
"keywords": [
"API"
],
"homepage": "http://iserve.kmi.open.ac.uk/ns/hrests"
},
"msm": {
"name": "Minimal Service Model",
"prefix": "msm",
"uri_prefix": "http://iserve.kmi.open.ac.uk/ns/msm#$1",
"description": "A simple RDF(S) ontology able to capture (part of) the semantics of both Web services and Web APIs",
"modified": "2014-09-03",
"keywords": [
"API"
],
"homepage": "http://iserve.kmi.open.ac.uk/ns/msm"
},
"kdo": {
"name": "The Knowledge Diversity Ontology",
"prefix": "kdo",
"uri_prefix": "http://kdo.render-project.eu/kdo#$1",
"description": "The Knowledge Diversity Ontology aims at providing a vocabulary that describes different dimensions of knowledge diversity of the Web. To support the representation of diversity information, the conceptual model of the Knowledge Diversity Ontology includes concepts and relations that were identified and modelled by focusing on real world scenarios in context of customer feedback, news, and Wikipedia opinion mining as well as content and sentiment analysis.",
"modified": "2014-06-07",
"keywords": [
"Quality"
],
"homepage": "http://kdo.render-project.eu/kdo#"
},
"kgc": {
"name": "KGRC Ontology",
"prefix": "kgc",
"uri_prefix": "http://kgc.knowledge-graph.jp/ontology/kgc.owl#$1",
"description": "This vocabulary set can represent 5W1H (Who, What, When, Where, Why, How) in event (scene) descriptions. This file is also provided in Knowledge Graph Reasoning Challenge.",
"modified": "2023-02-01",
"keywords": [
"Academy",
"Support"
],
"homepage": "http://kgc.knowledge-graph.jp/ontology/kgc.owl"
},
"spfood": {
"name": "SmartProducts Food Domain Model",
"prefix": "spfood",
"uri_prefix": "http://kmi.open.ac.uk/projects/smartproducts/ontologies/food.owl#$1",
"description": "Defines concepts and properties specific for the SmartProducts Philips use case (cooking domain).",
"modified": "2015-01-11",
"homepage": "http://projects.kmi.open.ac.uk/smartproducts/ontology.html",
"keywords": [
"Food"
]
},
"ends": {
"name": "Vocabulary of endpoint status (availability, responseTime)",
"prefix": "ends",
"uri_prefix": "http://labs.mondeca.com/vocab/endpointStatus#$1",
"description": "Endpoint Status vocabulary intends to describe endpoint availability",
"modified": "2011-02-24",
"homepage": "http://labs.mondeca.com/vocab/endpointStatus/index.html",
"keywords": [
"API"
]
},
"lawd": {
"name": "Linking Ancient World Data Ontology",
"prefix": "lawd",
"uri_prefix": "http://lawd.info/ontology/$1",
"description": "The goal of LAWD is to fill in the cracks between the data used and published by projects with a focus on the ancient world and the standard Linked Data vocablary schemes, like Dublin Core, the Open Annotation Collaboration, and CIDOC-CRM.",
"modified": "2014-09-03",
"homepage": "https://github.com/lawdi/LAWD",
"keywords": [
"Catalogs"
]
},
"lemon": {
"name": "LExicon Model for ONtologies",
"prefix": "lemon",
"uri_prefix": "http://lemon-model.net/lemon#$1",
"description": "Lemon: The lexicon model for ontologies is designed to allow for descriptions of lexical information regarding ontological elements and other RDF resources. Lemon covers mapping of lexical decomposition, phrase structure, syntax, variation, morphology, and lexicon-ontology mapping.",
"modified": "2016-07-13",
"homepage": "http://www.lemon-model.net/",
"keywords": [
"Vocabularies"
]
},
"lvont": {
"name": "Lexvo.org Ontology",
"prefix": "lvont",
"uri_prefix": "http://lexvo.org/ontology#$1",
"description": "An ontology for natural language terms description, including scripts, languages and meanings. The Lexvo.org ontology is still under development and may not be able to address all needs. Please also consider using the Lingvoj Ontology and the GOLD ontology, whereever appropriate.",
"modified": "2014-01-29",
"homepage": "http://www.lexvo.org/",
"keywords": [
"Vocabularies"
]
},
"earth": {
"name": "The Linked Earth Ontology",
"prefix": "earth",
"uri_prefix": "http://linked.earth/ontology#$1",
"description": "The Linked Earth Ontology aims to provide a common vocabulary for annotating paleoclimatology data",
"modified": "2016-06-13",
"keywords": [
"Environment",
"Society"
],
"homepage": "http://linked.earth/ontology#"
},
"ldvm": {
"name": "Vocabulary for Linked Data Visualization Model",
"prefix": "ldvm",
"uri_prefix": "http://linked.opendata.cz/ontology/ldvm/$1",
"description": "Vocabulary for Linked Data Visualization Model (LDVM) serves for description and configuration of components and pipelines according to LDVM",
"modified": "2015-04-02",
"keywords": [
"Methods"
],
"homepage": "http://linked.opendata.cz/ontology/ldvm/"
},
"kees": {
"name": "KEES Ontology",
"prefix": "kees",
"uri_prefix": "http://linkeddata.center/kees/v1#$1",
"description": "KEES (Knowledge Exchange Engine Schema ) ontology describes a knowledge base configuration in terms of ABox and TBox statements together with their accrual and reasoning policies. This vocabulary is designed to drive automatic data ingestion in a graph database according KEES and Linked (Open) Data principles.",
"modified": "2016-02-04",
"keywords": [
"Industry",
"Services"
],
"homepage": "http://linkeddata.center/kees/v1"
},
"cfrl": {
"name": "Corporate Financial Reports and Loans Ontology",
"prefix": "cfrl",
"uri_prefix": "http://linkeddata.finki.ukim.mk/lod/ontology/cfrl#$1",
"description": "The Corporate Financial Reports and Loans Ontology (CFRL).",
"modified": "2014-09-01",
"keywords": [
"eBusiness"
],
"homepage": "http://linkeddata.finki.ukim.mk/lod/ontology/cfrl#"
},
"trao": {
"name": "Transport Administration Ontology",
"prefix": "trao",
"uri_prefix": "http://linkeddata.finki.ukim.mk/lod/ontology/tao#$1",
"description": "Transport Administration Ontology (TAO) for describing data from Swedish Transport Administration Web site.",
"modified": "2015-06-17",
"keywords": [
"Services",
"Transport",
"Travel"
],
"homepage": "http://linkeddata.finki.ukim.mk/lod/ontology/tao#"
},
"veo": {
"name": "Vehicle Emissions Ontology",
"prefix": "veo",
"uri_prefix": "http://linkeddata.finki.ukim.mk/lod/ontology/veo#$1",
"description": "An ontology for describing vehicles and their emissions.",
"modified": "2014-09-01",
"keywords": [
"Environment",
"Industry"
],
"homepage": "http://linkeddata.finki.ukim.mk/lod/ontology/veo#"
},
"lode": {
"name": "Linking Open Descriptions of Events",
"prefix": "lode",
"uri_prefix": "http://linkedevents.org/ontology/$1",
"description": "An ontology for publishing descriptions of historical events as Linked Data, and for mapping between other event-related vocabularies and ontologies.",
"modified": "2010-10-07",
"keywords": [
"Events"
],
"homepage": "http://linkedevents.org/ontology/"
},
"lgdo": {
"name": "LinkedGeoData ontology",
"prefix": "lgdo",
"uri_prefix": "http://linkedgeodata.org/ontology/$1",
"description": "LinkedGeoData ontology has been derived from concepts defined by Open Street Map",
"modified": "2014-07-26",
"homepage": "http://linkedgeodata.org/Datasets",
"keywords": [
"Geography"
]
},
"lsc": {
"name": "Linked Science Core Vocabulary",
"prefix": "lsc",
"uri_prefix": "http://linkedscience.org/lsc/ns#$1",
"description": "LSC, the Linked Science Core Vocabulary, is a lightweight vocabulary providing terms to enable publishers and researchers to relate things in science to time, space, and themes.",
"modified": "2011-11-29",
"keywords": [
"Methods"
],
"homepage": "http://linkedscience.org/lsc/ns#"
},
"teach": {
"name": "Teaching Core Vocabulary Specification",
"prefix": "teach",
"uri_prefix": "http://linkedscience.org/teach/ns#$1",
"description": "TEACH, the Teaching Core Vocabulary, is a lightweight vocabulary providing terms to enable teachers to relate things in their courses together. The Teaching Core Vocabulary is based on practical requirements set by providing seminar and course descriptions as Linked Data.",
"modified": "2013-04-25",
"keywords": [
"Academy"
],
"homepage": "http://linkedscience.org/teach/ns#"
},
"nlon": {
"name": "National Library of Korea Ontology",
"prefix": "nlon",
"uri_prefix": "http://lod.nl.go.kr/ontology/$1",
"description": "This specification describes National Library of Korea Ontology vocaburaries using W3C's RDF and OWL technology.",
"modified": "2015-11-23",
"keywords": [
"Catalogs"
],
"homepage": "http://lod.nl.go.kr/ontology/"
},
"scip": {
"name": "Scientific People Ontology",
"prefix": "scip",
"uri_prefix": "http://lod.taxonconcept.org/ontology/sci_people.owl#$1",
"description": "A vocabulary for description of scientific people, focused on bio sciences",
"modified": "2012-07-03",
"keywords": [
"Academy"
],
"homepage": "http://lod.taxonconcept.org/ontology/sci_people.owl"
},
"txn": {
"name": "TaxonConcept Ontology",
"prefix": "txn",
"uri_prefix": "http://lod.taxonconcept.org/ontology/txn.owl#$1",
"description": "This ontology and the related TaxonConcept data set mints identifiers that are tied to a specific species concept which can have several names and classifications.",
"modified": "2013-05-20",
"keywords": [
"Biology"
],
"homepage": "http://lod.taxonconcept.org/ontology/txn.owl"
},
"loted": {
"name": "LOTED ontology",
"prefix": "loted",
"uri_prefix": "http://loted.eu/ontology#$1",
"description": "A vocabulary for European Calls for Tenders (in english, german, and french)",
"modified": "2012-07-03",
"homepage": "http://loted.eu/",
"keywords": [
"Contracts"
]
},
"opus": {
"name": "SwetoDblp Ontology of Computer Science Publications",
"prefix": "opus",
"uri_prefix": "http://lsdis.cs.uga.edu/projects/semdis/opus#$1",
"description": "This file specifies in RDF Schema format the classes and properties for SwetoDblp. These classes and properties are based on the internal LSDIS Library portal engine.",
"modified": "2007-05-01",
"homepage": "http://knoesis.wright.edu/library/ontologies/swetodblp/",
"keywords": [
"Catalogs"
]
},
"lsq": {
"name": "The Linked SPARQL Queries Vocabulary (LSQ(V))",
"prefix": "lsq",
"uri_prefix": "http://lsq.aksw.org/vocab#$1",
"description": "The Linked SPARQL Queries Vocabulary (LSQ(V)), defined using RDF(S) and OWL, provides a machine readable vocabulary to help describe queries in SPARQL logs and their statistics. The vocabulary builds upon the SPIN vocabulary and the Service Description vocabulary.",
"modified": "2015-09-07",
"homepage": "http://aksw.github.io/LSQ/",
"keywords": [
"Metadata",
"Support"
]
},
"cpmeta": {
"name": "Ontology of Integrated Carbon Observation System (ICOS)",
"prefix": "cpmeta",
"uri_prefix": "http://meta.icos-cp.eu/ontologies/cpmeta/$1",
"description": "OWL vocabulary describing metadata of two environmental research infrastructures: ICOS and SITES",
"modified": "2023-01-24",
"keywords": [
"Environment"
],
"homepage": "http://meta.icos-cp.eu/ontologies/cpmeta/"
},
"rdarel2": {
"name": "RDA Relationships GR2",
"prefix": "rdarel2",
"uri_prefix": "http://metadataregistry.org/uri/schema/RDARelationshipsGR2/$1",
"description": "RDA Relationships for Persons, Corporate Bodies, Families",
"modified": "2013-04-15",
"keywords": [
"People"
],
"homepage": "http://metadataregistry.org/uri/schema/RDARelationshipsGR2"
},
"mexalgo": {
"name": "MEX Algorithm Ontology",
"prefix": "mexalgo",
"uri_prefix": "http://mex.aksw.org/mex-algo#$1",
"description": "MEX is an RDF vocabulary designed to facilitate interoperability between published machine learning experiments results on the Web. The mex-algo layer represents the algorithm information existing into a basic machine learning experiment.",
"modified": "2014-04-05",
"keywords": [
"Methods"
],
"homepage": "http://mex.aksw.org/mex-algo"
},
"mexcore": {
"name": "MEX Core Vocabulary",
"prefix": "mexcore",
"uri_prefix": "http://mex.aksw.org/mex-core#$1",
"description": "MEX is an RDF vocabulary designed to facilitate interoperability between published machine learning experiments results on the Web. The mex-core layer represents the core information gathered from a basic machine learning experiment design.",
"modified": "2016-05-01",
"keywords": [
"Methods"
],
"homepage": "http://mex.aksw.org/mex-core"
},
"mexperf": {
"name": "MEX Performance Ontology",
"prefix": "mexperf",
"uri_prefix": "http://mex.aksw.org/mex-perf#$1",
"description": "MEX e um vocabulario modelado para facilitar a interoperabilidade entre resultados de experimentos de aprendizado de maquinas publicados na Web. A camada mex-perf e o 3o. nivel na abordagem MEX para representar performances de algoritmos de aprendizado de maquinas",
"modified": "2016-05-01",
"keywords": [
"Methods"
],
"homepage": "http://mex.aksw.org/mex-perf"
},
"moat": {
"name": "Meaning of a Tag Ontology",
"prefix": "moat",
"uri_prefix": "http://moat-project.org/ns#$1",
"description": "An ontology that let users define relationships between Tag objects and URIs of Semantic Web resources",
"modified": "2008-01-15",
"keywords": [
"Tag"
],
"homepage": "http://moat-project.org/ns#"
},
"nen3610": {
"name": "NEN 3610 - Basismodel geo-informatie",
"prefix": "nen3610",
"uri_prefix": "http://modellen.geostandaarden.nl/def/nen3610#$1",
"description": "NEN 3610 - base model geo-information \u2013 terms, definitions, relationships and general rules for the exchange of information about earth related spatial objects",
"modified": "2022-06-01",
"homepage": "https://geonovum.github.io/nen3610-werkomgeving",
"keywords": [
"Geography"
]
},
"dcndl": {
"name": "NDL Metadata Terms",
"prefix": "dcndl",
"uri_prefix": "http://ndl.go.jp/dcndl/terms/$1",
"description": "RDF Schema declaration for Japan NDL Metadata Terms",
"modified": "2011-12-01",
"keywords": [
"Metadata"
],
"homepage": "http://ndl.go.jp/dcndl/terms/"
},
"tac": {
"name": "TripleAccessControl Ontology",
"prefix": "tac",
"uri_prefix": "http://ns.bergnet.org/tac/0.1/triple-access-control#$1",
"description": "The TripleAccessControl Ontology is an extension to WebAccessControl Ontology to describe access control rules for RDF triples.",
"modified": "2011-09-15",
"keywords": [
"API"
],
"homepage": "http://ns.bergnet.org/tac/0.1/triple-access-control"
},
"smg": {
"name": "CERISE CIM Profile for Smart Grids",
"prefix": "smg",
"uri_prefix": "http://ns.cerise-project.nl/energy/def/cim-smartgrid#$1",
"description": "A Profile of the IEC Common Information Model for Smart Grids, developed by the Cerise-SG project.",
"modified": "2014-05-22",
"keywords": [
"Industry"
],
"homepage": "http://ns.cerise-project.nl/energy/def/cim-smartgrid"
},
"sql": {
"name": "SQL Abstract Syntax Trees Vocabulary",
"prefix": "sql",
"uri_prefix": "http://ns.inria.fr/ast/sql#$1",
"description": "The SQL AST Vocabulary allows SQL code abstract syntax trees to be published in RDF.",
"modified": "2014-07-31",
"keywords": [
"API"
],
"homepage": "http://ns.inria.fr/ast/sql#"
},
"emotion": {
"name": "Emotion Ontology for Context Awareness",
"prefix": "emotion",
"uri_prefix": "http://ns.inria.fr/emoca#$1",
"description": "EmOCA is used to contextualize dimensionnal emotion and to categorize it for human readability.",
"modified": "2013-11-26",
"homepage": "http://ns.inria.fr/emoca/",
"keywords": [
"People"
]
},
"ludo": {
"name": "Ludo Ontology",
"prefix": "ludo",
"uri_prefix": "http://ns.inria.fr/ludo$1",
"description": "Ludo is an ontology created to enable the description and representation of Serious Games that use structured data published on the Web through the Linked Data as a knowledge base. From the representation of the players\u2019 profile and their contextual information whithin the game, it is possible to generate personalized recommendations of related educational resources in order to stimulate the learning process while playing.",
"modified": "2016-05-10",
"keywords": [
"Games"
],
"homepage": "http://ns.inria.fr/ludo"
},
"ludo-gm": {
"name": "Ludo Game Model Ontology",
"prefix": "ludo-gm",
"uri_prefix": "http://ns.inria.fr/ludo/v1/gamemodel#$1",
"description": "Given the increasing amount of structured data published on the Web, many possibilities are open for creating new types of games that use resources from the Web of Data. In particular, if we consider the subcategory of Serious Games in which the object of the game is to educate the user through the interactive discovery of real-life concepts (associated to Semantic Web resources), the inclusion of a semantic representation of the user profile and his contextual information becomes an important element to recommend the user more accurate concepts. Ludo is an ontology that allows the creation of Serious Games with those characteristics.",
"modified": "2016-08-26",
"keywords": [
"Games"
],
"homepage": "http://ns.inria.fr/ludo/v1/gamemodel#"
},
"ludo-gp": {
"name": "Ludo - Game Presentation",
"prefix": "ludo-gp",
"uri_prefix": "http://ns.inria.fr/ludo/v1/gamepresentation#$1",
"description": "Given the increasing amount of structured data published on the Web, many possibilities are open for creating new types of games that use resources from the Web of Data. In particular, if we consider the subcategory of Serious Games in which the object of the game is to educate the user through the interactive discovery of real-life concepts (associated to Semantic Web resources), the inclusion of a semantic representation of the user profile and his contextual information becomes an important element to recommend the user more accurate concepts. Ludo is an ontology that allows the creation of Serious Games with those characteristics.",
"modified": "2016-08-26",
"keywords": [
"Games"
],
"homepage": "http://ns.inria.fr/ludo/v1/gamepresentation#"
},
"ludo-vc": {
"name": "Ludo - Virtual Context",
"prefix": "ludo-vc",
"uri_prefix": "http://ns.inria.fr/ludo/v1/virtualcontext#$1",
"description": "Given the increasing amount of structured data published on the Web, many possibilities are open for creating new types of games that use resources from the Web of Data. In particular, if we consider the subcategory of Serious Games in which the object of the game is to educate the user through the interactive discovery of real-life concepts (associated to Semantic Web resources), the inclusion of a semantic representation of the user profile and his contextual information becomes an important element to recommend the user more accurate concepts. Ludo is an ontology that allows the creation of Serious Games with those characteristics.",
"modified": "2016-08-26",
"keywords": [
"Games"
],
"homepage": "http://ns.inria.fr/ludo/v1/virtualcontext#"
},
"ludo-xapi": {
"name": "Experience API (xAPI)",
"prefix": "ludo-xapi",
"uri_prefix": "http://ns.inria.fr/ludo/v1/xapi#$1",
"description": "This is an OWL formalization of the statements defined in the Experience API (xAPI) specification. It is a module of the LUDO ontology.",
"modified": "2016-05-12",
"keywords": [
"API"
],
"homepage": "http://ns.inria.fr/ludo/v1/xapi"
},
"munc": {
"name": "Meta-Uncertainty",
"prefix": "munc",
"uri_prefix": "http://ns.inria.fr/munc#$1",
"description": "An OWL vocabulary for describing uncertainty metadata.",
"modified": "2019-02-01",
"keywords": [
"Metadata"
],
"homepage": "http://ns.inria.fr/munc/"
},
"ntag": {
"name": "Nice Tag Ontology",
"prefix": "ntag",
"uri_prefix": "http://ns.inria.fr/nicetag/2010/09/09/voc#$1",
"description": "NiceTag Ontology is an ontology which describes as generally as possible tags or rather tag actions understood as a speech acts occurring on the Web",
"modified": "2010-09-09",
"homepage": "http://ns.inria.fr/nicetag/2010/09/09/voc.html",
"keywords": [
"Tag"
]
},
"nrv": {
"name": "Normative Requirements Vocabulary",
"prefix": "nrv",
"uri_prefix": "http://ns.inria.fr/nrv#$1",
"description": "An OWL vocabulary for describing normative requirements.",
"modified": "2017-08-08",
"keywords": [
"Methods",
"Security"
],
"homepage": "http://ns.inria.fr/nrv"
},
"prissma": {
"name": "Presentation of Resources for Interoperable Semantic and Shareable Mobile Adaptability",
"prefix": "prissma",
"uri_prefix": "http://ns.inria.fr/prissma/v2#$1",
"description": "PRISSMA (Presentation of Resources for Interoperable Semantic and Shareable Mobile Adaptability) is a domain-independent vocabulary for displaying Web of Data resources in mobile environments.",
"modified": "2012-03-20",
"homepage": "http://ns.inria.fr/prissma/v1/prissma_v1.html",
"keywords": [
"API"
]
},
"psh": {
"name": "Probabilistic SHACL Validation",
"prefix": "psh",
"uri_prefix": "http://ns.inria.fr/probabilistic-shacl/$1",
"description": "An OWL vocabulary to include and exploit probabilistic information in SHACL validation reports",
"modified": "2023-03-16",
"homepage": "http://ns.inria.fr/probabilistic-shacl/psh.html",
"keywords": [
"Quality",
"RDF"
]
},
"provoc": {
"name": "Product Vocabulary",
"prefix": "provoc",
"uri_prefix": "http://ns.inria.fr/provoc#$1",
"description": "ProVoc (Product Vocabulary) est un vocabulaire qui peut \u00eatre utilis\u00e9 pour repr\u00e9senter des informations et les manipuler \u00e0 travers le Web. L'ontologie permet de repr\u00e9senter : 1) La hi\u00e9rarchie d'une soci\u00e9t\u00e9 : Groupe (Entreprise), Divisions d'un groupe, Marques d'une division ou d'un groupe, 2) La production d'une soci\u00e9t\u00e9 : Gammes de produits (attach\u00e9es \u00e0 une marque), produits d'une gamme, packages de produits (un panier alimentaire par exemple), composition des produits...",
"modified": "2016-02-18",
"keywords": [
"eBusiness"
],
"homepage": "http://ns.inria.fr/provoc"
},
"s4ac": {
"name": "Social Semantic SPARQL Security For Access Control Ontology",
"prefix": "s4ac",
"uri_prefix": "http://ns.inria.fr/s4ac/v2#$1",
"description": "Un vocabulaire permettant de cr\u00e9er des r\u00e8gles fines de contr\u00f4le d'acc\u00e8s pour les donn\u00e9es li\u00e9es",
"modified": "2011-10-06",
"homepage": "http://ns.inria.fr/s4ac/v2/s4ac_v2.html",
"keywords": [
"API"
]
},
"edupro": {
"name": "EduProgression Ontology",
"prefix": "edupro",
"uri_prefix": "http://ns.inria.fr/semed/eduprogression#$1",
"description": "The EduProgression ontology formalizes the educational progressions of the French educational system, making possible to represent the existing progressions in a standard formal model, searchable and understandable by machines (OWL).",
"modified": "2016-09-13",
"keywords": [
"Academy",
"Support"
],
"homepage": "http://ns.inria.fr/semed/eduprogression/"
},
"npg": {
"name": "Nature.com Core Ontology",
"prefix": "npg",
"uri_prefix": "http://ns.nature.com/terms/$1",
"description": "The Core Ontology is a formal model providing definitions for the key concepts of interest to content publishing at Macmillan Science and Education.",
"modified": "2015-04-30",
"homepage": "http://www.nature.com/ontologies/",
"keywords": [
"Press"
]
},
"og": {
"name": "Open Graph Protocol Vocabulary",
"prefix": "og",
"uri_prefix": "http://ogp.me/ns#$1",
"description": "The Open Graph protocol enables any web page to become a rich object in a social graph. For instance, this is used on Facebook to enable any web page to have the same functionality as a Facebook Page.",
"modified": "2013-02-16",
"homepage": "http://ogp.me/",
"keywords": [
"API"
]
},
"opo": {
"name": "Online Presence Ontology",
"prefix": "opo",
"uri_prefix": "http://online-presence.net/opo/ns#$1",
"description": "Ontology for representing Online Presence",
"modified": "2010-07-01",
"homepage": "http://online-presence.net/opo/spec/",
"keywords": [
"People"
]
},
"dm2e": {
"name": "DM2E model",
"prefix": "dm2e",
"uri_prefix": "http://onto.dm2e.eu/schemas/dm2e/$1",
"description": "The DM2E model is a specialisation of the Europeana Data Model (EDM) and can be used for the description of manuscripts in the cultural heritage domain.",
"modified": "2015-01-20",
"keywords": [
"Metadata"
],
"homepage": "http://onto.dm2e.eu/schemas/dm2e"
},
"dbug": {
"name": "DOAP Bugs",
"prefix": "dbug",
"uri_prefix": "http://ontologi.es/doap-bugs#$1",
"description": "An extension of DOAP for the description of bugs",
"modified": "2011-02-15",
"keywords": [
"Methods"
],
"homepage": "http://ontologi.es/doap-bugs#"
},
"deps": {
"name": "DOAP Dependencies",
"prefix": "deps",
"uri_prefix": "http://ontologi.es/doap-deps#$1",
"description": "An extension to DOAP for describing a project's requirements",
"modified": "2013-07-31",
"keywords": [
"Methods"
],
"homepage": "http://ontologi.es/doap-deps#"
},
"lsweb": {
"name": "ELSEWeb Data Ontology",
"prefix": "lsweb",
"uri_prefix": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-data.owl#$1",
"description": "The ELSEWeb Data ontology provides simple classes for describing datasets. This project provides foundational support for the ELSEWeb project(http://elseweb.cybershare.utep.edu/).\nwebsite: http://elseweb.cybershare.utep.edu/ontologies\nemail: nvillanuevarosales@utep.edu",
"modified": "2015-09-24",
"homepage": "http://elseweb.cybershare.utep.edu/ontologies",
"keywords": [
"Metadata"
]
},
"edac": {
"name": "ELSEWeb EDAC Ontology",
"prefix": "edac",
"uri_prefix": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-edac.owl#$1",
"description": "The ELSEWeb EDAC ontology describes datasets published by EDAC. This project provides foundational support for the ELSEWeb project(http://elseweb.cybershare.utep.edu/).\nwebsite: http://elseweb.cybershare.utep.edu/ontologies\nemail: nvillanuevarosales@utep.edu",
"modified": "2015-09-24",
"homepage": "http://elseweb.cybershare.utep.edu/ontologies",
"keywords": [
"Catalogs",
"Support"
]
},
"lswpm": {
"name": "ELSEWeb Lifemapper Parameters Ontology",
"prefix": "lswpm",
"uri_prefix": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-lifemapper-parameters.owl#$1",
"description": "The ELSEWeb Lifemapper parameters ontology provides auxiliary classes and instances that describe input parameters of Lifemapper modelling services. This ontology provides support for the ELSEWeb project(http://elseweb.cybershare.utep.edu/).\nwebsite: http://elseweb.cybershare.utep.edu/ontologies\nemail: nvillanuevarosales@utep.edu",
"modified": "2015-09-24",
"homepage": "http://elseweb.cybershare.utep.edu/ontologies",
"keywords": [
"Support"
]
},
"lslife": {
"name": "ELSEWeb Lifemapper Ontology",
"prefix": "lslife",
"uri_prefix": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-lifemapper.owl#$1",
"description": "The ELSEWeb Lifemapper ontology provides classes for describing biodiversity modelling services provided by Lifemapper. This project provides support for the ELSEWeb project(http://elseweb.cybershare.utep.edu/).\nwebsite: http://elseweb.cybershare.utep.edu/ontologies\nemail: nvillanuevarosales@utep.edu",
"modified": "2015-09-24",
"homepage": "http://elseweb.cybershare.utep.edu/ontologies",
"keywords": [
"Services",
"Support"
]
},
"lswmo": {
"name": "ELSEWeb Modelling Ontology",
"prefix": "lswmo",
"uri_prefix": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-modelling.owl#$1",
"description": "The ELSEWeb Modelling ontology provides simple classes for describing data models. This project provides foundational support for the ELSEWeb project(http://elseweb.cybershare.utep.edu/).\nwebsite: http://elseweb.cybershare.utep.edu/ontologies\nemail: nvillanuevarosales@utep.edu",
"modified": "2014-05-01",
"keywords": [
"Services",
"Support"
],
"homepage": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-modelling.owl"
},
"lsmap": {
"name": "ELSEWeb Mappings Ontology",
"prefix": "lsmap",
"uri_prefix": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-data.owl#$1",
"description": "The ELSEWeb mappings ontology imports related upper level ontologies and vocabularies and aligns ELSEWeb ontologies to importec classes. This ontology provides support for the ELSEWeb project(http://elseweb.cybershare.utep.edu/).\nwebsite: http://elseweb.cybershare.utep.edu/ontologies\nemail: nvillanuevarosales@utep.edu",
"modified": "2015-09-24",
"keywords": [
"Support"
],
"homepage": "http://ontology.cybershare.utep.edu/ELSEWeb/mappings/elseweb-mappings.owl"
},
"dbowl": {
"name": "Relational to Ontology Mapping Primitive",
"prefix": "dbowl",
"uri_prefix": "http://ontology.cybershare.utep.edu/dbowl/relational-to-ontology-mapping-primitive.owl#$1",
"description": "Primitive ontology for database to Semantic Web mapping which subsumes classes that represent mappings to explicit OWL constructs, such as OWL class, object property, data property, etc. Classes in this ontology are populated by individuals representing components of the database schema being mapped.",
"modified": "2016-03-01",
"keywords": [
"Methods"
],
"homepage": "http://ontology.cybershare.utep.edu/dbowl"
},
"gci": {
"name": "Global City Indicator Foundation Ontology",
"prefix": "gci",
"uri_prefix": "http://ontology.eil.utoronto.ca/GCI/Foundation/GCI-Foundation.owl#$1",
"description": "Global City Indicator Foundation Ontology developed by the Information Engineering Group, Mechanical & Industrial Engineering, University of Toronto. Contains the foundation ontologies required to represent ISO 37120 city indicators, including Placenames, Time, Measurement, Provenance, Statistics, Validity and Trust. See: Fox, M.S., (2013), \"A Foundation Ontology for Global City Indicators\", Global City Institute Working Paper, Vol. 1, No.4, pp. 1-45. Global Cities Institute, University of Toronto. Updated 24 June 2014: http://www.eil. Based on the Global City Indicators Facility, University of Toronto: http://www.cityindicators.org/Deliverables/Core%20and%20Supporting%20Indicators%20Table%20SEPTEMBER%202011.pdf.\n\nContact: Mark S. Fox, msf@eil.utoronto.ca",
"modified": "2015-04-15",
"keywords": [
"Society"
],
"homepage": "http://ontology.eil.utoronto.ca/GCI/Foundation/GCI-Foundation.owl"
},
"iso37120": {
"name": "ISO 37120 indicator URIs",
"prefix": "iso37120",
"uri_prefix": "http://ontology.eil.utoronto.ca/ISO37120.owl#$1",
"description": "ISO 37120 \u2013 Sustainable Development and Resilience of Communities \u2013 Indicators for City Services and Quality of Life (under TC268)\n\nhttp://ontology.eil.utoronto.ca/ISO37120.html\n\nThis OWL file defines a class for each indicator defined in the ISO 37120 standard. Names for each indicator are provided. Text definitions are provided only for Economy, Education and Energy indicators, due to copyright restrictions imposed by ISO. This file is meant to provide a single URI for each indicator.\n\nAn ontology for representing an indicator's supporting data plus meta information such as provenance, validity and trust can be found in:\nhttp://ontology.eil.utoronto.ca/GCI/Foundation/GCI-Foundation.owl\n\nDocumentation of the ontology can be found in:\nhttp://eil.utoronto.ca/smartcities/papers/GCI-Foundation-Ontology.pdf",
"modified": "2016-08-12",
"homepage": "http://ontology.eil.utoronto.ca/ISO37120.html",
"keywords": [
"General & Upper",
"Society"
]
},
"ic": {
"name": "International Contact Ontology: Addresses, phone numbers and emails.",
"prefix": "ic",
"uri_prefix": "http://ontology.eil.utoronto.ca/icontact.owl#$1",
"description": "This ontology provides basic classes and more detailed properties for representating international street addresses, phone numbers and emails. Rather than using existing ontologies, such as vcard, it was decided to create a new one as the vcard and foaf ignore the details of international addresses, phone numbers, etc.",
"modified": "2015-04-16",
"keywords": [
"People"
],
"homepage": "http://ontology.eil.utoronto.ca/icontact.owl"
},
"open311": {
"name": "Open 311 Ontology: An Ontology for publishing a city's non-emergency events.",
"prefix": "open311",
"uri_prefix": "http://ontology.eil.utoronto.ca/open311#$1",
"description": "Open 311 Ontology\n\nThis ontology generalizes the concepts that appear in 311 open data files published by several cities (Toronto, New York, Chicago, Vancouver) across North America. It provides a generis representation of 311 data that other cities can map their data onto and be used as a means of achieving interoperability.",
"keywords": [
"Events",
"Society"
],
"homepage": "http://ontology.eil.utoronto.ca/open311.owl"
},
"irao": {
"name": "Informatics Research Artifacts Ontology",
"prefix": "irao",
"uri_prefix": "http://ontology.ethereal.cz/irao/$1",
"description": "Informatics Research Artifacts Ontology, described using W3C RDF Schema and the Web Ontology Language OWL.",
"modified": "2021-05-27",
"keywords": [
"API",
"Catalogs"
],
"homepage": "http://ontology.ethereal.cz/irao"
},
"itsmo": {
"name": "IT Service Management Ontology",
"prefix": "itsmo",
"uri_prefix": "http://ontology.it/itsmo/v1#$1",
"description": "IT Service Management Ontology (ITSMO) provides the vocabulary for annotating resources related to IT Service Management. ITSMO tries to be consistent with 2011 ITIL glossary.",
"modified": "2012-11-04",
"homepage": "http://ontology.it/itsmo/v1/itsmo.html",
"keywords": [
"Services"
]
},
"omn": {
"name": "Open-Multinet Upper Ontology",
"prefix": "omn",
"uri_prefix": "http://open-multinet.info/ontology/omn#$1",
"description": "This ontology defines the most abstract concepts and properties that are needed to semantically manage resource within federated infrastructures",
"modified": "2015-04-04",
"keywords": [
"Services"
],
"homepage": "http://open-multinet.info/ontology/omn"
},
"omnfed": {
"name": "Open-Multinet Upper Federation Ontology",
"prefix": "omnfed",
"uri_prefix": "http://open-multinet.info/ontology/omn-federation#$1",
"description": "This ontology defines concepts related to federation of internet infrastructures.",
"modified": "2015-04-04",
"keywords": [
"Industry",
"Society"
],
"homepage": "http://open-multinet.info/ontology/omn-federation"
},
"omnlc": {
"name": "Open-Multinet Upper Lifecycle Ontology",
"prefix": "omnlc",
"uri_prefix": "http://open-multinet.info/ontology/omn-lifecycle#$1",
"description": "This ontology defines generic concepts related to the life cycle of resource or service.",
"modified": "2015-04-08",
"keywords": [
"PLM"
],
"homepage": "http://open-multinet.info/ontology/omn-lifecycle"
},
"am": {
"name": "OSLC Asset Management Vocabulary",
"prefix": "am",
"uri_prefix": "http://open-services.net/ns/asset#$1",
"description": "This specification builds on the Open Services for Lifecycle Collaboration (OSLC) Core v2.0 Specification to define the resources, properties and operations supported by an OSLC Asset Management (OSLC-Asset) provider. Asset Management resources include Assets, Artifacts and supporting resources defined in the OSLC Core specification.",
"modified": "2012-08-24",
"homepage": "http://open-services.net/wiki/asset-management/OSLC-Asset-Management-2.0-Specification/",
"keywords": [
"PLM"
]
},
"oslc": {
"name": "OSLC Core Vocabulary",
"prefix": "oslc",
"uri_prefix": "http://open-services.net/ns/core#$1",
"description": "The Open Services for Lifecycle Collaboration (OSLC) initiative is creating a family of web services specifications for products, services and other tools that support all phases of the software and product lifecycle. This OSLC Core Specification sets out the common features that every OSLC Service can be expected to support",
"modified": "2014-05-23",
"homepage": "http://open-services.net/bin/view/Main/OslcCoreSpecification",
"keywords": [
"PLM"
]
},
"ov": {
"name": "OpenVocab",
"prefix": "ov",
"uri_prefix": "http://open.vocab.org/terms/$1",
"description": "OpenVocab is a community maintained vocabulary intended for use on the Semantic Web, ideal for properties and classes that don't warrant the effort of creating or maintaining a full schema. OpenVocab allows anyone to create and modify vocabulary terms using their web browser.",
"modified": "2011-11-25",
"keywords": [
"General & Upper"
],
"homepage": "http://open.vocab.org/terms"
},
"opmo": {
"name": "Open Provenance Model",
"prefix": "opmo",
"uri_prefix": "http://openprovenance.org/model/opmo#$1",
"description": "The Open Provenance Model is a model of provenance that is designed to meet the following requirements: (1) To allow provenance information to be exchanged between systems, by means of a compatibility layer based on a shared provenance model. (2) To allow developers to build and share tools that operate on such a provenance model. (3) To define provenance in a precise, technology-agnostic manner. (4) To support a digital representation of provenance for any 'thing', whether produced by computer systems or not. (5) To allow multiple levels of description to coexist. (6) To define a core set of rules that identify the valid inferences that can be made on provenance representation.",
"modified": "2015-01-11",
"keywords": [
"Quality"
],
"homepage": "http://openprovenance.org/model/opmo"
},
"of": {
"name": "Open Fridge vocabulary",
"prefix": "of",
"uri_prefix": "http://owlrep.eu01.aws.af.cm/fridge#$1",
"description": "Ontology for Open Fridge project",
"modified": "2015-01-11",
"keywords": [
"Industry",
"IoT"
],
"homepage": "http://owlrep.eu01.aws.af.cm/fridge"
},
"shw": {
"name": "Smart Home Weather",
"prefix": "shw",
"uri_prefix": "http://paul.staroch.name/thesis/SmartHomeWeather.owl#$1",
"description": "An ontology defining weather-related concepts and properties being relevant to smart home systems that provide predictive control.",
"modified": "2014-03-23",
"homepage": "https://paul.staroch.name/thesis/thesis.pdf",
"keywords": [
"Environment",
"IoT"
]
},
"nif": {
"name": "NLP Interchange Format",
"prefix": "nif",
"uri_prefix": "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core#$1",
"description": "The NLP Interchange Format (NIF) is an RDF/OWL-based format that aims to achieve interoperability between Natural Language Processing (NLP) tools, language resources and annotations.",
"modified": "2015-01-11",
"keywords": [
"Vocabularies"
],
"homepage": "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core#"
},
"rlog": {
"name": "RDF Logging Ontology",
"prefix": "rlog",
"uri_prefix": "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/rlog#$1",
"description": "This is a helper ontology for NIF 2.0 to be able to log errors and warning messages.",
"modified": "2015-04-01",
"keywords": [
"API"
],
"homepage": "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/rlog#"
},
"pmofn": {
"name": "Predicate Model for Ontologies (PreMOn) - FrameNet ontology module",
"prefix": "pmofn",
"uri_prefix": "http://premon.fbk.eu/ontology/fn#$1",
"description": "The FrameNet module of the PreMOn ontology extends the core module for representing concepts specific to FrameNet. The modeling is based on the [FrameNet II: Extended Theory and Practice](https://framenet2.icsi.berkeley.edu/docs/r1.5/book.pdf) book.",
"modified": "2017-08-23",
"keywords": [
"Tag"
],
"homepage": "http://premon.fbk.eu/ontology/fn"
},
"pmonb": {
"name": "Predicate Model for Ontologies (PreMOn) - NomBank ontology module",
"prefix": "pmonb",
"uri_prefix": "http://premon.fbk.eu/ontology/nb#$1",
"description": "The NomBank module of the PreMOn ontology extends the core module for representing concepts specific to NomBank. The modelling is based on the NomBank Specifications.",
"modified": "2015-10-28",
"homepage": "http://premon.fbk.eu/ontology/nb",
"keywords": [
"Tag"
]
},
"pmopb": {
"name": "Predicate Model for Ontologies (PreMOn) - PropBank ontology module",
"prefix": "pmopb",
"uri_prefix": "http://premon.fbk.eu/ontology/pb#$1",
"description": "The PropBank module of the PreMOn ontology extends the core module for representing concepts specific to PropBank.",
"modified": "2015-10-28",
"homepage": "http://premon.fbk.eu/ontology/pb",
"keywords": [
"Tag"
]
},
"pmovn": {
"name": "Predicate Model for Ontologies (PreMOn) - VerbNet ontology module",
"prefix": "pmovn",
"uri_prefix": "http://premon.fbk.eu/ontology/vn#$1",
"description": "The VerbNet module of the PreMOn ontology extends the core module with classes and properties specific to the VerbNet predicate model. The modelling is based on the VerbNet Annotation Guidelines.",
"modified": "2015-10-28",
"homepage": "http://premon.fbk.eu/ontology/vn",
"keywords": [
"Tag"
]
},
"acrt": {
"name": "Agent Certification Ontology",
"prefix": "acrt",
"uri_prefix": "http://privatealpha.com/ontology/certification/1#$1",
"description": "This document specifies a vocabulary for asserting the existence of official endorsements or certifications of agents, such as people and organizations.",
"modified": "2014-01-23",
"keywords": [
"Quality"
],
"homepage": "http://privatealpha.com/ontology/certification/1#"
},
"agr": {
"name": "Agreements ontology",
"prefix": "agr",
"uri_prefix": "http://promsns.org/def/agr#$1",
"description": "This Agreements Ontology is designed to model 'agreements' which are social contracts that include licenses, laws, contracts, Memoranda of Understanding, standards and definitional metadata. Its purpose is to support data sharing by making explicit the relationships between agreements and data and agreements and Agents (people and organisations). Eventually it will also help with the interplay between different classes of agreements.",
"modified": "2017-10-09",
"homepage": "http://promsns.org/def/agr/agr.html",
"keywords": [
"Contracts",
"Government"
]
},
"dprov": {
"name": "Decision Provenance ontology (DecPROV)",
"prefix": "dprov",
"uri_prefix": "http://promsns.org/def/do#$1",
"description": "This ontology is a reduced-in-scope version of the [W3C Decisions and Decision-Making Incubator Group](https://www.w3.org/2005/Incubator/decision/)'s Decision Ontology (DO) which can be found at . It has been re-worked to align entirely with the W3C's [PROV ontology](https://www.w3.org/TR/prov-o/) since it is widely recognised that analysing the elements of decisions *post hoc* is an exercise in provenance.\n\nUnlike the original DO, this ontology cannot be used for *normative* scenarios: it is only capable of recording decisions that have already been made (so-called *data-driven* use in the DO). This is because PROV, to which this ontology is completely mapped, does not have a templating system which can indicate what *should* occur in future scenarios.\n\nThis ontology introduces only one new element for decision modelling over that which was present in the DO: an Agent which allows agency in decision making to be recorded.",
"modified": "2017-09-01",
"homepage": "http://promsns.org/def/decprov/",
"keywords": [
"Vocabularies"
]
},
"obo": {
"name": "Ontology for Biomedical Investigation",
"prefix": "obo",
"uri_prefix": "http://purl.obolibrary.org/obo/$1",
"description": "The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.",
"modified": "2019-08-06",
"keywords": [
"Biology",
"Health"
],
"homepage": "http://purl.obolibrary.org/obo/obi.owl"
},
"iot-lite": {
"name": "Iot-lite ontology",
"prefix": "iot-lite",
"uri_prefix": "http://purl.oclc.org/NET/UNIS/fiware/iot-lite#$1",
"description": "iot-lite is a lightweight ontology based on SSN to describe Internet of Things (IoT) concepts and relationships.",
"modified": "2015-06-01",
"keywords": [
"Environment",
"IoT"
],
"homepage": "http://purl.oclc.org/NET/UNIS/fiware/iot-lite#"
},
"ldr": {
"name": "Linked Data Rights (LDR)",
"prefix": "ldr",
"uri_prefix": "http://purl.oclc.org/NET/ldr/ns#$1",
"description": "The Linked Data Rights ontology provides the vocabulary for creating rights expressions for Linked Data resources.",
"modified": "2014-08-30",
"homepage": "http://oeg-dev.dia.fi.upm.es/licensius/static/ldr/",
"keywords": [
"Contracts"
]
},
"ucum": {
"name": "Units of measurement ontology",
"prefix": "ucum",
"uri_prefix": "http://purl.oclc.org/NET/muo/ucum/$1",
"description": "The instances of this ontology have been automatically\n generated from the UCUM (The Unified Code for Units of Measure).\n See http://aurora.rg.iupui.edu/UCUM/ for more details\n on UCUM. The members of the MyMobileWeb consortium\n explicitly acknowledge the copyright of the data from\n the UCUM ontology.",
"modified": "2008-01-01",
"keywords": [
"General & Upper"
],
"homepage": "http://purl.oclc.org/NET/muo/ucum/"
},
"mvco": {
"name": "Media Value Chain Ontology",
"prefix": "mvco",
"uri_prefix": "http://purl.oclc.org/NET/mvco.owl#$1",
"description": "The Media Value Chain Ontology (MVCO) is an ontology for formalizing the representation of the Media Value Chain. It couples naturally with the MPEG-21 multimedia framework, and its standardization as Part 19 of this ISO/IEC standard is underway (at the editing time of this document).",
"modified": "2010-05-07",
"homepage": "http://dmag.ac.upc.edu/ontologies/mvco/",
"keywords": [
"Multimedia"
]
},
"cff": {
"name": "Climate and Forecast (CF) features",
"prefix": "cff",
"uri_prefix": "http://purl.oclc.org/NET/ssnx/cf/cf-feature#$1",
"description": "This is an ontology representation of the generic features defined by Climate and Forecast (CF) standard names vocabulary (http://cf-pcmdi.llnl.gov/documents/cf-standard-names/), maintained by the Program for Climate Model Diagnosis and Intercomparison (http://cf-pcmdi.llnl.gov/ ) which is intended for use with climate and forecast data, in the atmosphere, surface and ocean domains.",
"modified": "2011-06-20",
"keywords": [
"Environment"
],
"homepage": "http://purl.oclc.org/NET/ssnx/cf/cf-feature"
},
"cfp": {
"name": "Climate and Forecast (CF) standard names parameter vocabulary",
"prefix": "cfp",
"uri_prefix": "http://purl.oclc.org/NET/ssnx/cf/cf-property#$1",
"description": "This is an ontology representation of the climatic data variables defined by Climate and Forecast (CF) standard names vocabulary (http://cf-pcmdi.llnl.gov/documents/cf-standard-names/), maintained by the Program for Climate Model Diagnosis and Intercomparison (http://cf-pcmdi.llnl.gov/ ) which is intended for use with climate and forecast data, in the atmosphere, surface and ocean domains.",
"modified": "2011-06-20",
"keywords": [
"Environment",
"IoT"
],
"homepage": "http://purl.oclc.org/NET/ssnx/cf/cf-property"
},
"aws": {
"name": "Ontology for Meteorological sensors",
"prefix": "aws",
"uri_prefix": "http://purl.oclc.org/NET/ssnx/meteo/aws#$1",
"description": "This ontology is part of the Agriculture Meteorology example showcasing the ontology developed by the W3C Semantic Sensor Networks incubator group (SSN-XG). It is published here in order to generalize the potential usage and the alignment with other standardization efforts of the SSN ontology.",
"modified": "2011-06-20",
"keywords": [
"Environment",
"IoT",
"Methods"
],
"homepage": "http://purl.oclc.org/NET/ssnx/meteo/aws"
},
"qu": {
"name": "Quantity Kinds and Units",
"prefix": "qu",
"uri_prefix": "http://purl.oclc.org/NET/ssnx/qu/qu#$1",
"description": "This ontology is partially based on the SysML QUDV (Quantities, Units, Dimensions and Values) proposed by a working group of the SysML 1.2 Revision Task Force (RTF), working in close coordination with the OMG MARTE specification group.\nIn order to generalize its potential usage and alignment with other standardization efforts concerning quantities and units, the QU ontology has been further developed as a complement to the Agriculture Meteorology example showcasing the ontology developed by the W3C Semantic Sensor Networks incubator group (SSN-XG).",
"modified": "2011-06-20",
"keywords": [
"Methods"
],
"homepage": "http://purl.oclc.org/NET/ssnx/qu/qu"
},
"limoo": {
"name": "License Model Ontology",
"prefix": "limoo",
"uri_prefix": "http://purl.org/LiMo/0.1#$1",
"description": "A vocabulary to describe licenses",
"modified": "2013-05-20",
"keywords": [
"Metadata"
],
"homepage": "http://purl.org/LiMo/0.1#"
},
"botany": {
"name": "Biological Taxonomy Vocabulary 0.2 (Botany)",
"prefix": "botany",
"uri_prefix": "http://purl.org/NET/biol/botany#$1",
"description": "This is a specialist botanical variant of the Biological Taxonomy Vocabulary.",
"modified": "2009-03-18",
"keywords": [
"Biology"
],
"homepage": "http://purl.org/NET/biol/botany#"
},
"biol": {
"name": "Biological Taxonomy Vocabulary 0.2 (Core)",
"prefix": "biol",
"uri_prefix": "http://purl.org/NET/biol/ns#$1",
"description": "An RDF vocabulary for the taxonomy of all forms of life",
"modified": "2008-10-06",
"keywords": [
"Biology"
],
"homepage": "http://purl.org/NET/biol/ns#"
},
"event": {
"name": "The Event Ontology",
"prefix": "event",
"uri_prefix": "http://purl.org/NET/c4dm/event.owl#$1",
"description": "This ontology deals with the notion of reified events - events seen as first-class objects.",
"modified": "2007-10-25",
"homepage": "http://motools.sourceforge.net/event/event.html",
"keywords": [
"Events"
]
},
"keys": {
"name": "Keys Ontology",
"prefix": "keys",
"uri_prefix": "http://purl.org/NET/c4dm/keys.owl#$1",
"description": "A vocabulary for musical keys and notes",
"modified": "2007-02-25",
"keywords": [
"Music"
],
"homepage": "http://purl.org/NET/c4dm/keys.owl"
},
"tl": {
"name": "The Timeline Ontology",
"prefix": "tl",
"uri_prefix": "http://purl.org/NET/c4dm/timeline.owl#$1",
"description": "Extends owl-time ontology with support for several timelines, acting as a backbone to adress time interval/instants. Mainly designed with a multimedia use-case in mind.",
"modified": "2007-10-29",
"homepage": "http://motools.sourceforge.net/timeline/timeline.html",
"keywords": [
"Time"
]
},
"semsur": {
"name": "The Semantic Survey Ontology (semsur)",
"prefix": "semsur",
"uri_prefix": "http://purl.org/SemSur/$1",
"description": "SemSur, the Semantic Survey Ontology, is a core ontology for describing individual research problems, approaches, implementations and evaluations in a structured, comparable way.",
"modified": "2018-04-20",
"homepage": "http://sda.tech/SemSur/Documentation/Semsur.html",
"keywords": [
"Methods"
]
},
"acco": {
"name": "Accomodation Ontology",
"prefix": "acco",
"uri_prefix": "http://purl.org/acco/ns#$1",
"description": "A vocabulary for the description of hotels, vacation homes, camping sites, and other accommodation offers for e-commerce",
"modified": "2013-03-25",
"keywords": [
"eBusiness"
],
"homepage": "http://purl.org/acco/ns"
},
"arch": {
"name": "Archival collections ontology",
"prefix": "arch",
"uri_prefix": "http://purl.org/archival/vocab/arch#$1",
"description": "An RDF vocabulary for describing archival collections and the names associated with them",
"modified": "2012-07-03",
"homepage": "http://gslis.simmons.edu/archival/arch/index.html",
"keywords": [
"Catalogs"
]
},
"taxon": {
"name": "TaxonMap Ontology",
"prefix": "taxon",
"uri_prefix": "http://purl.org/biodiversity/taxon/$1",
"description": "This is the initial vocabulary for mapping the various taxon classes on the Linked Open Data Cloud",
"modified": "2013-03-18",
"keywords": [
"Biology"
],
"homepage": "http://purl.org/biodiversity/taxon/"
},
"biotop": {
"name": "BioTop",
"prefix": "biotop",
"uri_prefix": "http://purl.org/biotop/biotop.owl#$1",
"description": "Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network",
"modified": "2012-04-24",
"homepage": "http://purl.org/biotop",
"keywords": [
"Biology"
]
},
"frapo": {
"name": "Funding, Research Administration and Projects Ontology",
"prefix": "frapo",
"uri_prefix": "http://purl.org/cerif/frapo/$1",
"description": "FRAPO, the Funding, Research Administration and Projects Ontology, is a CERIF-compliant ontology written in OWL 2 DL for describing research project administrative information.",
"modified": "2014-01-31",
"keywords": [
"Academy"
],
"homepage": "http://purl.org/cerif/frapo/"
},
"cdtype": {
"name": "The Collection Description Type Namespace",
"prefix": "cdtype",
"uri_prefix": "http://purl.org/cld/cdtype/$1",
"description": "Types defined by the Dublin Core Collections Application Profile",
"modified": "2013-08-20",
"homepage": "http://dublincore.org/groups/collections/collection-application-profile/",
"keywords": [
"Catalogs"
]
},
"cld": {
"name": "The Collection Description Terms",
"prefix": "cld",
"uri_prefix": "http://purl.org/cld/terms/$1",
"description": "An expression in RDF of the application profile for collection-level description developed by the Dublin Core Collection Description Task Group.",
"modified": "2013-08-20",
"homepage": "http://dublincore.org/groups/collections/collection-application-profile/",
"keywords": [
"Catalogs"
]
},
"coll": {
"name": "Collections Ontology",
"prefix": "coll",
"uri_prefix": "http://purl.org/co/$1",
"description": "The Collections Ontology (CO) defines unordered collections (Set and Bag) and ordered collections (or List). This ontology has been inspired by the work \"Putting OWL in Order: Patterns for Sequences in OWL\" by Drummond et al. (OWL-ED 2006).",
"modified": "2012-03-19",
"homepage": "http://code.google.com/p/collections-ontology/",
"keywords": [
"Support"
]
},
"cold": {
"name": "'Configuration as Linked Data' ontology",
"prefix": "cold",
"uri_prefix": "http://purl.org/configurationontology#$1",
"description": "Ontology for the description of customizable products. It models the configuration process as the traversal of a graph of partially defined products, or \"Configurations\"",
"modified": "2013-11-21",
"keywords": [
"eBusiness"
],
"homepage": "http://purl.org/configurationontology"
},
"coo": {
"name": "Car Options Ontology",
"prefix": "coo",
"uri_prefix": "http://purl.org/coo/ns#$1",
"description": "The COO provides a vocabulary for exposing available configuration options for car models. It allows indicating choices that can be made as well as compatibility, dependency, and inclusion information. The ontology imports and extends the GoodRelations ontology for e-commerce",
"modified": "2010-10-12",
"homepage": "http://purl.org/coo/ns.html",
"keywords": [
"Industry"
]
},
"coreo": {
"name": "Core-o: Competence Reference Ontology",
"prefix": "coreo",
"uri_prefix": "http://purl.org/coreo#$1",
"description": "An ontology to describe competences and human capabilities",
"modified": "2023-05-08",
"keywords": [
"Environment",
"Society"
],
"homepage": "http://purl.org/coreo"
},
"ds": {
"name": "Dataset Catalog Vocabulary",
"prefix": "ds",
"uri_prefix": "http://purl.org/ctic/dcat#$1",
"description": "This vocabulary is used for modelling catalogs of datasets and its relationships with the datasets",
"modified": "2013-03-22",
"homepage": "http://data.fundacionctic.org/vocab/catalog/datasets.html",
"keywords": [
"Catalogs"
]
},
"emp": {
"name": "Vocabulario de Ofertas de Empleo",
"prefix": "emp",
"uri_prefix": "http://purl.org/ctic/empleo/oferta#$1",
"description": "This is a vocabulary for modeling jobs offer in Spain.",
"modified": "2013-09-03",
"keywords": [
"Society"
],
"homepage": "http://purl.org/ctic/empleo/oferta"
},
"loc": {
"name": "Vocabulario de Localizaciones",
"prefix": "loc",
"uri_prefix": "http://purl.org/ctic/infraestructuras/localizacion#$1",
"description": "This vocabulary is used to describe the physical location of public places.",
"modified": "2011-11-05",
"keywords": [
"Geography"
],
"homepage": "http://purl.org/ctic/infraestructuras/localizacion"
},
"ctorg": {
"name": "Vocabulario de la estructura de organismos p\u00fablicos",
"prefix": "ctorg",
"uri_prefix": "http://purl.org/ctic/infraestructuras/organizacion#$1",
"description": "El objetivo de este vocabulario es la creaci\u00f3n de un esquema que permita definir los contenidos de la informaci\u00f3n relacionada con los \u00f3rganos de gobierno y los centros p\u00fablicos que ofrecen servicios. Se identifican ciertas variables en el dominio de los centros p\u00fablicos, que se modelan a trav\u00e9s de ciertos tipos de datos y de propiedades relacionadas entre los recursos. Se utiliza Ontologies for e-Government para modelar las principales caracter\u00edsticas.",
"modified": "2013-04-24",
"keywords": [
"Government"
],
"homepage": "http://purl.org/ctic/infraestructuras/organizacion"
},
"elec": {
"name": "Vocabulario de Resultados Electorales",
"prefix": "elec",
"uri_prefix": "http://purl.org/ctic/sector-publico/elecciones#$1",
"description": "El objetivo de este vocabulario es la creaci\u00f3n de un esquema que permita definir los contenidos de informaci\u00f3n relacionada con procesos electorales y sus resultados. \t\t\tSe identifican ciertas variables en el dominio de las elecciones, que se modelan a trav\u00e9s de ciertos tipos de datos y de propiedades relacionadas entre los recursos.",
"modified": "2013-01-17",
"keywords": [
"Government"
],
"homepage": "http://purl.org/ctic/sector-publico/elecciones"
},
"cwmo": {
"name": "Creative Workshop Management Ontology (CWMO)",
"prefix": "cwmo",
"uri_prefix": "http://purl.org/cwmo/#$1",
"description": "Creative Workshop Management Ontology (CWMO) - an ontology designed to describe the creative workshop domain, to permit reasoning on creative method and to describe resources gathered inside Creative Support System. The primary goal of the ontology is to cover all knowledge about creative workshop and creative method necessary for Creative support system. The second goal is to provide interoperability between distributed Creative Support System.",
"modified": "2017-02-16",
"keywords": [
"Image",
"Multimedia"
],
"homepage": "http://purl.org/cwmo/#"
},
"dcam": {
"name": "DCMI Abstract Model",
"prefix": "dcam",
"uri_prefix": "http://purl.org/dc/dcam/$1",
"description": "An abstract model for Dublin Core metadata",
"modified": "2012-06-14",
"homepage": "http://dublincore.org/documents/abstract-model/",
"keywords": [
"General & Upper"
]
},
"dctype": {
"name": "DCMI Type Vocabulary",
"prefix": "dctype",
"uri_prefix": "http://purl.org/dc/dcmitype/$1",
"description": "The DCMI Type Vocabulary provides a general, cross-domain list of approved terms that may be used as values for the Resource Type element to identify the genre of a resource.",
"modified": "2012-06-14",
"homepage": "http://dublincore.org/documents/dcmi-type-vocabulary",
"keywords": [
"General & Upper"
]
},
"dce": {
"name": "Dublin Core Metadata Element Set",
"prefix": "dce",
"uri_prefix": "http://purl.org/dc/elements/1.1/$1",
"description": "The Dublin Core Metadata Element Set is a vocabulary of fifteen properties for use in resource description. The name \"Dublin\" is due to its origin at a 1995 invitational workshop in Dublin, Ohio; \"core\" because its elements are broad and generic, usable for describing a wide range of resources.",
"modified": "2012-06-14",
"homepage": "http://dublincore.org/documents/dces",
"keywords": [
"Metadata"
]
},
"dcterms": {
"name": "DCMI Metadata Terms",
"prefix": "dcterms",
"uri_prefix": "http://purl.org/dc/terms/$1",
"description": "an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.",
"modified": "2012-06-14",
"homepage": "http://dublincore.org/documents/dcmi-terms",
"keywords": [
"Metadata"
]
},
"dita": {
"name": "DITA RDF ontology",
"prefix": "dita",
"uri_prefix": "http://purl.org/dita/ns#$1",
"description": "The DITA RDF ontology translates the semantics of a subset of the vocabulary described in the DITA 1.2 specification in a format that can be understood in the semantic Web of data. By Colin Maudry, licensed under the terms of the Unlicense (public domain).",
"modified": "2014-08-03",
"homepage": "https://github.com/ColinMaudry/dita-rdf",
"keywords": [
"RDF"
]
},
"dpn": {
"name": "Data Provider Node ontology",
"prefix": "dpn",
"uri_prefix": "http://purl.org/dpn#$1",
"description": "This ontology is being developed by CSIRO under the eReefs project for describing data provider nodes, web services available and datasets that are hosted by them. This ontology features a module for describing Datasets. It does not however describe geospatial, temporal, organisational or domain concepts as these are intended to be included from other ontologies via the imports statement. Other modules complementary to the DPN ontology are http://purl.org/dpn/dataset and http://purl.org/dpn/services. This version aligns DCAT and DC terms and imports DPN services.",
"modified": "2015-08-05",
"keywords": [
"Services",
"Support"
],
"homepage": "http://purl.org/dpn"
},
"dqm": {
"name": "The Data Quality Management Vocabulary",
"prefix": "dqm",
"uri_prefix": "http://purl.org/dqm-vocabulary/v1/dqm#$1",
"description": "The Data Quality Management Vocabulary - An Ontology for Data Requirements Management, Data Quality Monitoring, Data Quality Assessment, and Data Cleansing",
"modified": "2011-10-09",
"homepage": "http://purl.org/dqm-vocabulary",
"keywords": [
"Quality"
]
},
"dsn": {
"name": "DSNotify Eventsets: A vocabulary for change events in linked data sources",
"prefix": "dsn",
"uri_prefix": "http://purl.org/dsnotify/vocab/eventset/$1",
"description": "DSNotify Eventsets is a vocabulary for events that change resources in linked data sources.",
"modified": "2014-06-19",
"keywords": [
"RDF"
],
"homepage": "http://purl.org/dsnotify/vocab/eventset/"
},
"eem": {
"name": "The EPCIS Event Model",
"prefix": "eem",
"uri_prefix": "http://purl.org/eem#$1",
"description": "This vocabulary is based on the EPC Information Services Specification http://www.gs1.org/sites/default/files/docs/epc/epcis_1_0_1-standard-20070921.pdf",
"modified": "2013-07-16",
"keywords": [
"Events"
],
"homepage": "http://purl.org/eem"
},
"daq": {
"name": "Dataset Quality Vocabulary",
"prefix": "daq",
"uri_prefix": "http://purl.org/eis/vocab/daq#$1",
"description": "Quality metrics can be (in principle) calculated on various forms of data (such as datasets, graphs, set of triples etc...). This vocabulary allow the owner/user of such RDF data to calculate metrics on multiple (and different) resources.",
"modified": "2015-04-01",
"homepage": "http://butterbur04.iai.uni-bonn.de/ontologies/daq/daq#",
"keywords": [
"Quality"
]
},
"essglobal": {
"name": "ESSGlobal Vocabulary",
"prefix": "essglobal",
"uri_prefix": "http://purl.org/essglobal/vocab/$1",
"description": "Un vocabulario para la Economia Social y Solid\u00e1ria (ESS). Este vocabulario es concebido para ser conjugado con los esquemas de metadados/vocabularios/ontologias: dcterms, good relations, foaf, vcard, organization e schema.org - esto esta definido em el Perfil de Aplicaci\u00f3n Dublin Core de la ESS. Vocabulario desarollado por el grupo ESSGlobal de la Red Intercontinental para la promoci\u00f3n de Economia Social y Solidaria (RIPESS).",
"modified": "2015-05-04",
"keywords": [
"Society"
],
"homepage": "http://purl.org/essglobal/vocab/"
},
"gen": {
"name": "Vocabulary for Linked Genealogical Data",
"prefix": "gen",
"uri_prefix": "http://purl.org/gen/0.1#$1",
"description": "A simple RDF vocabulary containing terms to facilitate the linking of genealogical data.",
"modified": "2015-01-11",
"homepage": "https://github.com/joshhansen/vocab-gen",
"keywords": [
"People"
]
},
"gr": {
"name": "The GoodRelations Ontology for Semantic Web-based E-Commerce",
"prefix": "gr",
"uri_prefix": "http://purl.org/goodrelations/v1#$1",
"description": "The GoodRelations ontology provides the vocabulary for annotating e-commerce offerings (1) to sell, lease, repair, dispose, or maintain commodity products and (2) to provide commodity services.",
"modified": "2011-10-01",
"homepage": "http://www.heppnetz.de/ontologies/goodrelations/v1.html",
"keywords": [
"eBusiness"
]
},
"dicom": {
"name": "Healthcare metadata - DICOM ontology",
"prefix": "dicom",
"uri_prefix": "http://purl.org/healthcarevocab/v1#$1",
"description": "Ontology for healthcare metadata - especially metadata found in DICOM files (Digital Imaging and Communications in Medicine, see http://dicom.nema.org/). Author: Michael Brunnbauer, Bonubase GmbH (www.bonubase.com). The author's email address is brunni@netestate.de. See http://purl.org/healthcarevocab/v1help for explanations.",
"modified": "2015-01-11",
"keywords": [
"Health"
],
"homepage": "http://purl.org/healthcarevocab/v1"
},
"holy": {
"name": "Hydrogen Ontology",
"prefix": "holy",
"uri_prefix": "http://purl.org/holy/ns#$1",
"description": "This is the Hydrogen Ontology (HOLY). HOLY is a domain ontology for describing the complex structure of hydrogen-based markets. HOLY contributes to the systemic modeling of the hydrogen domain with a focus on its value chain. Hence, it provides a foundation for retrieval, storage, and delivery of market insights.",
"modified": "2023-06-14",
"keywords": [
"Environment"
],
"homepage": "http://purl.org/holy/ns#"
},
"pat": {
"name": "Patch Request Ontology",
"prefix": "pat",
"uri_prefix": "http://purl.org/hpi/patchr#$1",
"description": "The Patch Request Ontology provides a schema to describe desired changes in Linked Data. By wrapping the Graph Update Ontology (guo) patch requests can be formulated to add, modify or delete particular triples (or subgraphs) within a dataset.",
"modified": "2015-01-20",
"homepage": "http://patchr.s16a.org/ontologies/patchr.html",
"keywords": [
"RDF"
]
},
"ru": {
"name": "Representational Units Metadata Ontology",
"prefix": "ru",
"uri_prefix": "http://purl.org/imbi/ru-meta.owl#$1",
"description": "Draft for a recommendation for metadata on Representational Units (RU) which appear in ontologies. It is so far harmonized for implementation through owl annotation properties.",
"modified": "2009-04-08",
"keywords": [
"Metadata"
],
"homepage": "http://purl.org/imbi/ru-meta.owl"
},
"inno": {
"name": "Ontology for Innovation",
"prefix": "inno",
"uri_prefix": "http://purl.org/innovation/ns#$1",
"description": "One key use case for this ontology is to facilitate the matching of needs and innovations.",
"modified": "2011-05-08",
"keywords": [
"Industry"
],
"homepage": "http://purl.org/innovation/ns"
},
"fiesta-iot": {
"name": "FIESTA-IoT Ontology",
"prefix": "fiesta-iot",
"uri_prefix": "http://purl.org/iot/ontology/fiesta-iot#$1",
"description": "The FIESTA-IoT ontology takes inspiration from the well-known Noy et al. methodology for reusing and interconnecting existing ontologies. To build the ontology, we leverage a number of core concepts from various mainstream ontologies and taxonomies, such as Semantic Sensor Network (SSN), M3-lite (a lite version of M3 ontology), WGS84, IoT-lite, Time, and DUL ontology.",
"modified": "2017-02-09",
"keywords": [
"IoT"
],
"homepage": "http://purl.org/iot/ontology/fiesta-iot"
},
"fiesta-priv": {
"name": "FIESTA-Priv Ontology",
"prefix": "fiesta-priv",
"uri_prefix": "http://purl.org/iot/ontology/fiesta-iot#$1",
"description": "FIESTA-Priv Ontology",
"keywords": [
"IoT"
],
"homepage": "http://purl.org/iot/ontology/fiesta-priv#"
},
"iottaxolite": {
"name": "The IoTTaxonomy-lite Taxonomy",
"prefix": "iottaxolite",
"uri_prefix": "http://purl.org/iot/vocab/iot-taxonomy-lite#$1",
"description": "The IoT-Taxonomy-lite is adapted from M3-lite taxonomy. This taxonomy is refactored and defines many other concepts such as subclasses of Feature-of-Interest and Quality-of-Observation.",
"modified": "2019-09-07",
"keywords": [
"IoT"
],
"homepage": "http://purl.org/iot/vocab/iot-taxonomy-lite#"
},
"m3lite": {
"name": "The Machine-to-Machine Measurement (M3) Lite Ontology",
"prefix": "m3lite",
"uri_prefix": "http://purl.org/iot/vocab/m3-lite#$1",
"description": "M3 lite taxonomy is designed for the FIESTA-IOT H2020 EU project. We refactor, clean and simplify the M3 ontology designed by Eurecom (Amelie Gyrard). M3 ontology lite is currently aligned with the quantity taxonomy used by several testbeds: SmartSantander (Spain), University of Surrey (United Kingdom), KETI (Korea) and Com4Innov (France).",
"modified": "2017-07-29",
"keywords": [
"IoT",
"Services"
],
"homepage": "http://purl.org/iot/vocab/m3-lite#"
},
"ipo": {
"name": "IPO - Issue Procedure Ontology",
"prefix": "ipo",
"uri_prefix": "http://purl.org/ipo/core#$1",
"description": "Vocabulary for describing issues (or problems) and corresponding symptoms and solutions to a broad variety of contexts. It is intended to provide a generic, reusable core ontology that can be extended or specialized for use in domain-specific situations, aimed at supporting linked data publishing. The solutions are represented by procedures, which are possible workflows for solving corresponding issues.",
"modified": "2015-07-30",
"keywords": [
"Methods"
],
"homepage": "http://purl.org/ipo/core"
},
"iso-thes": {
"name": "ISO 25964 SKOS extension",
"prefix": "iso-thes",
"uri_prefix": "http://purl.org/iso25964/skos-thes#$1",
"description": "This vocabulary aims at providing interoperability between SKOS and ISO 25964 \u2010 1:2011, the new standard for thesauri",
"modified": "2015-03-17",
"keywords": [
"Vocabularies"
],
"homepage": "http://purl.org/iso25964/skos-thes"
},
"lib": {
"name": "Library extension of schema.org",
"prefix": "lib",
"uri_prefix": "http://purl.org/library/$1",
"description": "Experimental \"library\" extension vocabulary for use with Schema.org",
"modified": "2012-06-18",
"keywords": [
"Catalogs"
],
"homepage": "http://purl.org/library/"
},
"limo": {
"name": "Linked Statistical Models Vocabulary",
"prefix": "limo",
"uri_prefix": "http://purl.org/limo-ontology/limo#$1",
"description": "A Vocabulary for Incorporating Predictive Models into the Linked Data Web",
"modified": "2013-10-15",
"keywords": [
"Methods"
],
"homepage": "http://purl.org/limo-ontology/limo/"
},
"gold": {
"name": "General Ontology for Linguistic Description",
"prefix": "gold",
"uri_prefix": "http://purl.org/linguistics/gold/$1",
"description": "The General Ontology for Linguistic Description (GOLD) was created primarily for applications involving descriptive linguistics.",
"modified": "2010-01-01",
"keywords": [
"Vocabularies"
],
"homepage": "http://purl.org/linguistics/gold"
},
"api": {
"name": "Linked Data API Vocabulary",
"prefix": "api",
"uri_prefix": "http://purl.org/linked-data/api/vocab#$1",
"description": "Configuration vocabulary for the Linked Data API",
"modified": "2010-02-19",
"keywords": [
"RDF"
],
"homepage": "http://purl.org/linked-data/api/vocab#"
},
"qb": {
"name": "The data cube vocabulary",
"prefix": "qb",
"uri_prefix": "http://purl.org/linked-data/cube#$1",
"description": "This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF.",
"modified": "2014-07-31",
"homepage": "http://www.w3.org/TR/vocab-data-cube/",
"keywords": [
"Methods",
"W3C Rec"
]
},
"sdmx": {
"name": "SDMX-RDF vocabulary",
"prefix": "sdmx",
"uri_prefix": "http://purl.org/linked-data/sdmx#$1",
"description": "This vocabulary extends the data cube vocabulary to support publication of statistical data in RDF, using an information model based on SDMX",
"modified": "2010-07-22",
"homepage": "https://raw.githubusercontent.com/UKGovLD/publishing-statistical-data/master/specs/src/main/vocab/sdmx.ttl",
"keywords": [
"Methods"
]
},
"sdmx-code": {
"name": "SDMX Code",
"prefix": "sdmx-code",
"uri_prefix": "http://purl.org/linked-data/sdmx/2009/code#$1",
"description": "Defines subclasses and instances of codes used in SDMX, such as currencies, decimals, frequencies ...",
"modified": "2010-07-21",
"homepage": "https://code.google.com/p/publishing-statistical-data/",
"keywords": [
"Methods"
]
},
"sdmx-dimension": {
"name": "SDMX Dimension",
"prefix": "sdmx-dimension",
"uri_prefix": "http://purl.org/linked-data/sdmx/2009/dimension#$1",
"description": "Defines dimensions for the statistical \"cubes\" defined by SDMX",
"modified": "2010-07-22",
"keywords": [
"Methods"
],
"homepage": "http://purl.org/linked-data/sdmx/2009/dimension"
},
"lyou": {
"name": "Linking-you vocabulary",
"prefix": "lyou",
"uri_prefix": "http://purl.org/linkingyou/$1",
"description": "Vocabulary for describing common webpages provided by an organisation",
"modified": "2012-12-01",
"keywords": [
"Multimedia"
],
"homepage": "http://purl.org/linkingyou/"
},
"lv": {
"name": "lobid vocab",
"prefix": "lv",
"uri_prefix": "http://purl.org/lobid/lv#$1",
"description": "Under this name space new properties and classes needed for the lobid.org service are defined . Already existing properties and classes which are (re)used in lobid.org aren't documented here.",
"modified": "2015-02-09",
"keywords": [
"Catalogs"
],
"homepage": "http://purl.org/lobid/lv"
},
"media": {
"name": "The Media RDF Vocabulary",
"prefix": "media",
"uri_prefix": "http://purl.org/media#$1",
"description": "In order to enable and encourage the sharing, distribution, syndication, and aggregation of media content, the authors propose the Media RDF vocabulary, an open standard for distributed media metadata.",
"modified": "2008-07-09",
"keywords": [
"Multimedia"
],
"homepage": "http://purl.org/media"
},
"muto": {
"name": "Modular Unified Tagging Ontology (MUTO)",
"prefix": "muto",
"uri_prefix": "http://purl.org/muto/core#$1",
"description": "The Modular and Unified Tagging Ontology (MUTO) is an ontology for tagging and folksonomies. It is based on a thorough review of earlier tagging ontologies and unifies core concepts in one consistent schema. It supports different forms of tagging, such as common, semantic, group, private, and automatic tagging, and is easily extensible.",
"modified": "2011-11-16",
"homepage": "http://purl.org/muto",
"keywords": [
"Tag"
]
},
"gufo": {
"name": "gUFO: A Lightweight Implementation of the Unified Foundational Ontology (UFO)",
"prefix": "gufo",
"uri_prefix": "http://purl.org/nemo/gufo#$1",
"description": "The objective of gUFO is to provide a lightweight implementation of the Unified Foundational Ontology (UFO) [1-5] suitable for Semantic Web OWL 2 DL applications. \n\nIntended users are those implementing UFO-based lightweight ontologies that reuse gUFO by specializing and instantiating its elements.\n\nThere are three implications of the use of the term lightweight. First of all, we have employed little expressive means in an effort to retain computational properties for the resulting OWL ontology. Second, we have selected a subset of UFO-A [1, 2] and UFO-B [3] to include here. In particular, there is minimalistic support for UFO-B (only that which is necessary to establish the participation of objects in events and to capture historical dependence between events). Third, a lightweight ontology, differently from a reference ontology, is designed with the purpose of providing an implementation artifact to structure a knowledge base (or knowledge graph). This has driven a number of pragmatic implementation choices which are discussed in comments annotated to the various elements of this implementation. \n\nThe 'g' in gUFO stands for gentle. At the same time, \"gufo\" is the Italian word for \"owl\".\n\n\nFor the source repository, see: ",
"modified": "2019-11-11",
"homepage": "https://github.com/nemo-ufes/gufo",
"keywords": [
"Events",
"General & Upper"
]
},
"vgo": {
"name": "The Video Game Ontology",
"prefix": "vgo",
"uri_prefix": "http://purl.org/net/VideoGameOntology#$1",
"description": "The Video Game Ontology is an ontology designed for describing video games and all the resources related to their game plays.",
"modified": "2015-05-05",
"keywords": [
"Games"
],
"homepage": "http://purl.org/net/VideoGameOntology"
},
"cart": {
"name": "cartCoordOnt",
"prefix": "cart",
"uri_prefix": "http://purl.org/net/cartCoord#$1",
"description": "Ontology for representation of cartesian co-ordinates",
"modified": "2015-07-03",
"keywords": [
"Geography",
"Geometry"
],
"homepage": "http://purl.org/net/cartCoord#"
},
"dbm": {
"name": "DBM Ontology",
"prefix": "dbm",
"uri_prefix": "http://purl.org/net/dbm/ontology#$1",
"description": "An ontology for the Drug Bureau of Macedonia (DBM).",
"modified": "2014-09-01",
"keywords": [
"Health"
],
"homepage": "http://purl.org/net/dbm/ontology#"
},
"hifm": {
"name": "HIFM Ontology",
"prefix": "hifm",
"uri_prefix": "http://purl.org/net/hifm/ontology#$1",
"description": "An ontology for describing brand-name drugs.",
"modified": "2014-04-01",
"keywords": [
"Biology",
"Health"
],
"homepage": "http://purl.org/net/hifm/ontology#"
},
"lio": {
"name": "Lightweight Image Ontology",
"prefix": "lio",
"uri_prefix": "http://purl.org/net/lio#$1",
"description": "A Lightweight Ontology for Describing Images",
"modified": "2014-05-16",
"keywords": [
"Image"
],
"homepage": "http://purl.org/net/lio"
},
"bibtex": {
"name": "BibTeX ontology",
"prefix": "bibtex",
"uri_prefix": "http://purl.org/net/nknouf/ns/bibtex#$1",
"description": "Transformation of bibTeX into an OWL ontology",
"modified": "2003-12-29",
"keywords": [
"Catalogs"
],
"homepage": "http://purl.org/net/nknouf/ns/bibtex"
},
"ex": {
"name": "Example vocabulary",
"prefix": "ex",
"uri_prefix": "http://purl.org/net/ns/ex#$1",
"description": "Vocabulary to include sample codes in a schema. Can work with XSLT (http://purl.org/net/ns/ns-schema.xsl) to present schema as XHTML list with examples.",
"modified": "2007-12-13",
"keywords": [
"Metadata"
],
"homepage": "http://purl.org/net/ns/ex"
},
"ont": {
"name": "Ontology annotation DLiser vocabulary",
"prefix": "ont",
"uri_prefix": "http://purl.org/net/ns/ontology-annot#$1",
"description": "Vocabulary to define some annotation properties as subproperties of common Dublin Core terms",
"modified": "2007-11-07",
"keywords": [
"Metadata"
],
"homepage": "http://purl.org/net/ns/ontology-annot"
},
"opmv": {
"name": "Open Provenance Model Vocabulary",
"prefix": "opmv",
"uri_prefix": "http://purl.org/net/opmv/ns#$1",
"description": "OPMV, the Open Provenance Model Vocabulary, provides terms to enable practitioners of data publishing to publish their data responsibly.",
"modified": "2010-10-06",
"keywords": [
"Quality"
],
"homepage": "http://purl.org/net/opmv/ns#"
},
"p-plan": {
"name": "The P-PLAN Ontology",
"prefix": "p-plan",
"uri_prefix": "http://purl.org/net/p-plan#$1",
"description": "The Ontology for Provenance and Plans (P-Plan) is an extension of the PROV-O ontology [PROV-O] created to represent the plans that guided the execution of scientific processes. P-Plan describes how the plans are composed and their correspondence to provenance records that describe the execution itself.",
"modified": "2014-03-12",
"homepage": "http://www.opmw.org/model/p-plan/",
"keywords": [
"Methods"
]
},
"plo": {
"name": "Playlist Ontology",
"prefix": "plo",
"uri_prefix": "http://purl.org/net/po#$1",
"description": "An ontology for describing playlists, playlist entries and songs.",
"modified": "2014-08-26",
"keywords": [
"Music"
],
"homepage": "http://purl.org/net/po#"
},
"prv": {
"name": "Provenance Vocabulary Core Ontology",
"prefix": "prv",
"uri_prefix": "http://purl.org/net/provenance/ns#$1",
"description": "The Provenance Vocabulary Core Ontology provides the main classes and properties required to describe provenance of data on the Web.",
"modified": "2012-03-14",
"keywords": [
"Quality"
],
"homepage": "http://purl.org/net/provenance/ns#"
},
"prvt": {
"name": "Provenance Vocabulary types",
"prefix": "prvt",
"uri_prefix": "http://purl.org/net/provenance/types#$1",
"description": "Extends the Provenance Vocabulary by defining subclasses of the types of provenance elements introduced in the core ontology.",
"modified": "2012-03-14",
"keywords": [
"Quality"
],
"homepage": "http://purl.org/net/provenance/types#"
},
"sor": {
"name": "SORON: Social Relationships ONtology",
"prefix": "sor",
"uri_prefix": "http://purl.org/net/soron/$1",
"description": "The Social Relationships ONtology (SORON) attempts to describe the different types of social relationships in society (both objective and subjective). Current version focuses on inter-personal 1:1 relationships (except family relationships). Other types of relationships may be covered in later versions. It complements FOAF and RELATIONSHIP ontologies.",
"modified": "2015-05-12",
"keywords": [
"People"
],
"homepage": "http://purl.org/net/soron"
},
"step": {
"name": "Semantic Trajectory Episodes",
"prefix": "step",
"uri_prefix": "http://purl.org/net/step#$1",
"description": "A lightweight ontology for representing semantic trajectories and contextual elements in terms of features of interests and episodes.",
"modified": "2015-11-03",
"keywords": [
"Geography",
"Time"
],
"homepage": "http://purl.org/net/step"
},
"tsn": {
"name": "Territorial Statistical Nomenclature Ontology",
"prefix": "tsn",
"uri_prefix": "http://purl.org/net/tsn#$1",
"description": "This RDF ontology allows describing any Territorial Statistical Nomenclature (TSN) (i.e., partition of the territory) used as a support to socio-economic data (statistical data that describe territory in terms of population, unemployement rate, transport access, etc.).",
"modified": "2017-01-31",
"keywords": [
"Geography",
"Geometry",
"Government"
],
"homepage": "http://purl.org/net/tsn#"
},
"tsnc": {
"name": "Territorial Statistical Nomenclature Change Ontology",
"prefix": "tsnc",
"uri_prefix": "http://purl.org/net/tsnchange#$1",
"description": "The TSN-Change ontology aims at describing changes that occured from one version of a Territorial Statistical Nomenclature (TSN) (i.e., partition of the territory) and its subsequent (e.g., change in territorial units boundaries to reflect an administrative reorganisation).",
"modified": "2017-05-15",
"keywords": [
"Geography",
"Geometry",
"Government",
"Metadata"
],
"homepage": "http://purl.org/net/tsnchange#"
},
"label": {
"name": "label",
"prefix": "label",
"uri_prefix": "http://purl.org/net/vocab/2004/03/label#$1",
"description": "Term definitions for singular and plural label properties",
"modified": "2004-03-28",
"keywords": [
"Vocabularies"
],
"homepage": "http://purl.org/net/vocab/2004/03/label"
},
"wf-invoc": {
"name": "Workflow Invocation Ontology",
"prefix": "wf-invoc",
"uri_prefix": "http://purl.org/net/wf-invocation#$1",
"description": "Wf-invoc is a simple profile of the P-plan ontology to describe how workflow steps are invoked within a workflow execution.",
"modified": "2013-05-17",
"homepage": "http://www.opmw.org/model/wf-invocation/",
"keywords": [
"Methods"
]
},
"wfm": {
"name": "The Workflow Motif Ontology",
"prefix": "wfm",
"uri_prefix": "http://purl.org/net/wf-motifs#$1",
"description": "Ontology for describing Workflow Motifs. Workflow Motifs outline the kinds of data-intensive activities that are observed in workflows (data-operation motifs) and the different manners in which activities are implemented within workflows (workflow-oriented motifs).",
"modified": "2013-03-15",
"homepage": "http://vocab.linkeddata.es/motifs/",
"keywords": [
"Methods"
]
},
"uby": {
"name": "ubyCat.owl",
"prefix": "uby",
"uri_prefix": "http://purl.org/olia/ubyCat.owl#$1",
"description": "OLiA Annotation Model for Uby Parts of Speech (Gurevych et al, 2012)\nextracted from the Uby DTD (http://purl.org/olia/ubyCat.owl, version of Nov 21th, 2012).\n\nReferences\nIryna Gurevych, Judith Eckle-Kohler, Silvana Hartmann, Michael Matuschek, Christian M. Meyer and Christian Wirth, 2012, Uby - A Large-Scale Unified Lexical-Semantic Resource, Proceedings of the 13th Conference of the European Chapter of the Association for Computational Linguistics (EACL 2012), Avignon, France.\n\nThe DTD is made available under a Creative Commons Attribution-ShareAlike 3.0 Unported (CC BY-SA 3.0) license which is available at http://creativecommons.org/licenses/by-sa/3.0/\nYou are free to share (copy, distribute and transmit) the work, to develop your own extensions (adapt, remix) of the work, and to make commercial use of the work.",
"modified": "2015-10-04",
"homepage": "https://www.ukp.tu-darmstadt.de/data/lexical-resources/uby",
"keywords": [
"Support",
"Tag"
]
},
"ocds": {
"name": "Schema for an Open Contracting Release (OCDS)",
"prefix": "ocds",
"uri_prefix": "http://purl.org/onto-ocds/ocds#$1",
"description": "The OCDS is a data model that aims at structuring and publishing contracting data (tenders, procurements, awards, transactions, etc.). It got international adoption and is one of the leading models in this domain.",
"modified": "2018-07-03",
"homepage": "https://github.com/ColinMaudry/open-contracting-ld",
"keywords": [
"Contracts"
]
},
"af": {
"name": "Audio Features Ontology",
"prefix": "af",
"uri_prefix": "http://purl.org/ontology/af/$1",
"description": "This vocabulary expresses some common concepts to represent some features of audio signals.",
"modified": "2008-06-23",
"homepage": "http://motools.sourceforge.net/doc/audio_features.html",
"keywords": [
"Music"
]
},
"ao": {
"name": "Association Ontology",
"prefix": "ao",
"uri_prefix": "http://purl.org/ontology/ao/core#$1",
"description": "Provides basic concepts and properties for describing specific association statements to something, e.g. an occasion, a genre or a mood ...",
"modified": "2010-09-13",
"keywords": [
"Support"
],
"homepage": "http://purl.org/ontology/ao/core#"
},
"bibo": {
"name": "The Bibliographic Ontology",
"prefix": "bibo",
"uri_prefix": "http://purl.org/ontology/bibo/$1",
"description": "The Bibliographic Ontology Specification provides main concepts and properties for describing citations and bibliographic references (i.e. quotes, books, articles, etc) on the Semantic Web.",
"modified": "2009-11-04",
"keywords": [
"Catalogs"
],
"homepage": "http://purl.org/ontology/bibo/"
},
"cco": {
"name": "Cognitive Characteristics Ontology",
"prefix": "cco",
"uri_prefix": "http://purl.org/ontology/cco/core#$1",
"description": "The Cognitive Characteristics Ontology specification provides a vocabulary for describing cognitive pattern within contexts, their temporal dynamics and their origins, on/ for the Semantic Web.",
"modified": "2010-09-26",
"keywords": [
"People"
],
"homepage": "http://purl.org/ontology/cco/core#"
},
"chord": {
"name": "The OMRAS2 Chord Ontology",
"prefix": "chord",
"uri_prefix": "http://purl.org/ontology/chord/$1",
"description": "This document describes the first draft of a chord ontology based on work from the Centre for Digital Music, Queen Mary, University of London. It has been created as part of the OMRAS2 project and is intended to provide a common, versatile vocabulary for describing chords and chord sequences in RDF.",
"modified": "2007-10-25",
"keywords": [
"Music"
],
"homepage": "http://purl.org/ontology/chord/"
},
"co": {
"name": "Counter Ontology",
"prefix": "co",
"uri_prefix": "http://purl.org/ontology/co/core#$1",
"description": "The Counter Ontology specification provides basic concepts and properties for describing a general counter concept and some important sub counters",
"modified": "2010-09-13",
"keywords": [
"Methods"
],
"homepage": "http://purl.org/ontology/co/core#"
},
"daia": {
"name": "Document Availability Information Ontology",
"prefix": "daia",
"uri_prefix": "http://purl.org/ontology/daia/$1",
"description": "The Document Availability Information Ontology (DAIA) describes the current availability of documents in libraries and similar institutions. Availability can be expressed in terms of specific services.",
"modified": "2011-12-15",
"homepage": "https://github.com/gbv/daia/",
"keywords": [
"Catalogs"
]
},
"docso": {
"name": "Document Service Ontology",
"prefix": "docso",
"uri_prefix": "http://purl.org/ontology/dso#$1",
"description": "A micro-ontology that defines a set of typical document-related services such as provided by libraries, museums and archives.",
"modified": "2013-12-05",
"keywords": [
"Services"
],
"homepage": "http://purl.org/ontology/dso"
},
"dvia": {
"name": "The visualization vocabulary for LOD applications",
"prefix": "dvia",
"uri_prefix": "http://purl.org/ontology/dvia#$1",
"description": "dvia is an RDF vocabulary designed to facilitate interoperability between visualization applications published on the Web.",
"modified": "2013-10-09",
"homepage": "http://data.eurecom.fr/ontology/dvia/",
"keywords": [
"API"
]
},
"ecpo": {
"name": "Enumeration and Chronology of Periodicals Ontology",
"prefix": "ecpo",
"uri_prefix": "http://purl.org/ontology/ecpo#$1",
"description": "Defines the common bibliographic terms for the description of enumeration and chronology of periodicals",
"modified": "2014-08-07",
"keywords": [
"Press",
"Time"
],
"homepage": "http://purl.org/ontology/ecpo"
},
"holding": {
"name": "Holding Ontology",
"prefix": "holding",
"uri_prefix": "http://purl.org/ontology/holding#$1",
"description": "A vocabulary to express (library) holdings in RDF",
"modified": "2014-06-30",
"keywords": [
"Catalogs"
],
"homepage": "http://purl.org/ontology/holding"
},
"is": {
"name": "Info Service Ontology",
"prefix": "is",
"uri_prefix": "http://purl.org/ontology/is/core#$1",
"description": "The Information Service Ontology specification provides basic concepts and properties for describing different information services, e.g. Wikipedia, MusicBrainz, Freebase",
"modified": "2010-07-31",
"keywords": [
"Services"
],
"homepage": "http://purl.org/ontology/is/core#"
},
"mo": {
"name": "Music Ontology",
"prefix": "mo",
"uri_prefix": "http://purl.org/ontology/mo/$1",
"description": "The Music Ontology Specification provides main concepts and properties fo describing music (i.e. artists, albums and tracks) on the Semantic Web",
"modified": "2013-07-22",
"homepage": "http://musicontology.com/",
"keywords": [
"Music"
]
},
"olo": {
"name": "Ordered List Ontology",
"prefix": "olo",
"uri_prefix": "http://purl.org/ontology/olo/core#$1",
"description": "The Ordered List Ontology Specification provides basic concepts and properties for describing ordered lists as semantic graphs.",
"modified": "2010-07-23",
"homepage": "http://smiy.sourceforge.net/olo/spec/orderedlistontology.html",
"keywords": [
"Support"
]
},
"pbo": {
"name": "Play Back Ontology",
"prefix": "pbo",
"uri_prefix": "http://purl.org/ontology/pbo/core#$1",
"description": "The Play Back Ontology specification provides basic concepts and properties for describing concepts that are related to the play back domain.",
"modified": "2010-09-13",
"keywords": [
"Music"
],
"homepage": "http://purl.org/ontology/pbo/core#"
},
"place": {
"name": "The Places Ontology",
"prefix": "place",
"uri_prefix": "http://purl.org/ontology/places#$1",
"description": "The Places Ontology is a simple lightweight ontology for describing places of geographic interest.",
"modified": "2010-11-27",
"keywords": [
"Geography"
],
"homepage": "http://purl.org/ontology/places"
},
"po": {
"name": "Programmes ontology",
"prefix": "po",
"uri_prefix": "http://purl.org/ontology/po/$1",
"description": "This ontology aims at providing a simple vocabulary for describing programmes. It covers brands, series (seasons), episodes, broadcast events, broadcast services, etc.",
"modified": "2010-02-20",
"homepage": "http://www.bbc.co.uk/ontologies/programmes/2009-09-07.shtml",
"keywords": [
"Multimedia"
]
},
"pr": {
"name": "Property Reification Vocabulary",
"prefix": "pr",
"uri_prefix": "http://purl.org/ontology/prv/core#$1",
"description": "A vocabulary for describing the ontology design pattern of property reification.",
"modified": "2011-02-19",
"keywords": [
"RDF"
],
"homepage": "http://purl.org/ontology/prv/core#"
},
"rec": {
"name": "Recommendation Ontology",
"prefix": "rec",
"uri_prefix": "http://purl.org/ontology/rec/core#$1",
"description": "The Recommendation Ontology specification provides basic concepts and properties for describing recommendations on/ for the Semantic Web.",
"modified": "2010-08-02",
"keywords": [
"Rec"
],
"homepage": "http://purl.org/ontology/rec/core#"
},
"service": {
"name": "The Service Ontology",
"prefix": "service",
"uri_prefix": "http://purl.org/ontology/service#$1",
"description": "A micro-ontology that defines the general concept of a service.",
"modified": "2013-11-24",
"homepage": "https://github.com/dini-ag-kim/service-ontology/",
"keywords": [
"Services"
]
},
"sim": {
"name": "The Similarity Ontology",
"prefix": "sim",
"uri_prefix": "http://purl.org/ontology/similarity/$1",
"description": "An ontology to describe associations between things. Although this ontology was designed with music similarity in mind, it can readily be applied to other domains.",
"modified": "2010-03-10",
"keywords": [
"Support"
],
"homepage": "http://purl.org/ontology/similarity/"
},
"ssso": {
"name": "Simple Service Status Ontology",
"prefix": "ssso",
"uri_prefix": "http://purl.org/ontology/ssso#$1",
"description": "An event-based RDF ontology for typical status in fulfillment of a service",
"modified": "2014-07-02",
"homepage": "https://github.com/gbv/ssso/",
"keywords": [
"Services"
]
},
"stories": {
"name": "Stories Ontology",
"prefix": "stories",
"uri_prefix": "http://purl.org/ontology/stories/$1",
"description": "The Stories ontology was developed in collaboration with the BBC, with an aim to creating an ontology for narrative representation that could be applied across a diverse set of cases. These included accounts of events in Northern Ireland, the storylines of Doctor Who episodes, and key events of the Battle of Britain.",
"modified": "2013-05-16",
"homepage": "http://www.contextus.net/stories",
"keywords": [
"Events"
]
},
"nsl": {
"name": "A News Storyline Ontology",
"prefix": "nsl",
"uri_prefix": "http://purl.org/ontology/storyline/$1",
"description": "The News Storyline Ontology is a generic model for describing and organising the stories news organisations tell. The ontology is intended to be flexible to support any given news or media publisher's approach to handling news stories. At the heart of the ontology, is the concept of Storyline.",
"modified": "2013-05-01",
"homepage": "http://www.bbc.co.uk/ontologies/storyline/2013-05-01.html",
"keywords": [
"Press"
]
},
"wi": {
"name": "The Weighted Interests Vocabulary",
"prefix": "wi",
"uri_prefix": "http://purl.org/ontology/wi/core#$1",
"description": "The Weighted Interests Vocabulary specification provides basic concepts and properties for describing describing preferences (interests) within contexts, their temporal dynamics and their origin on/ for the Semantic Web.",
"modified": "2010-09-14",
"keywords": [
"People"
],
"homepage": "http://purl.org/ontology/wi/core#"
},
"wlo": {
"name": "BBC Wildlife Ontology",
"prefix": "wlo",
"uri_prefix": "http://purl.org/ontology/wo/$1",
"description": "A simple vocabulary for describing biological species and related taxa.",
"modified": "2013-12-18",
"homepage": "http://www.bbc.co.uk/ontologies/wildlife/2010-11-04.shtml",
"keywords": [
"Biology"
]
},
"wo": {
"name": "Weighting Ontology",
"prefix": "wo",
"uri_prefix": "http://purl.org/ontology/wo/core#$1",
"description": "The Weighting Ontology specification provides a vocabulary for describing weightings and their referenced scales, on/ for the Semantic Web.",
"modified": "2010-09-14",
"keywords": [
"Methods"
],
"homepage": "http://purl.org/ontology/wo/core#"
},
"ofrd": {
"name": "Fridge and Freezer Vocabulary",
"prefix": "ofrd",
"uri_prefix": "http://purl.org/opdm/refrigerator#$1",
"description": "Vocabulary to describe fridges and freezers",
"modified": "2014-08-18",
"keywords": [
"Industry"
],
"homepage": "http://purl.org/opdm/refrigerator#"
},
"oo": {
"name": "Open Organisations",
"prefix": "oo",
"uri_prefix": "http://purl.org/openorg/$1",
"description": "This vocabulary provides supplementary terms for organisations wishing to publish open data about themselves.",
"modified": "2013-04-17",
"homepage": "http://neologism.ecs.soton.ac.uk/oo",
"keywords": [
"Society"
]
},
"oslo": {
"name": "OSLO Exchange Standard",
"prefix": "oslo",
"uri_prefix": "http://purl.org/oslo/ns/localgov#$1",
"description": "This version of the OSLO Exchange Standard provides a minimum set of classes and properties for describing a natural person, i.e. the individual as opposed to any role they may play in society or the relationships they have to other people, organisations and property; all of which contribute significantly to the broader concept of identity. The vocabulary is closely integrated with the Person, Organisation and Location Vocabularies published by the W3C in the Gov Linked Data Project. The OSLO specification is the result of a public-private partnership initiated by V-ICT-OR, the Flemish Organization for ICT in Local Government.",
"modified": "2014-05-30",
"keywords": [
"Society"
],
"homepage": "http://purl.org/oslo/ns/localgov"
},
"pav": {
"name": "Provenance, Authoring and Versioning",
"prefix": "pav",
"uri_prefix": "http://purl.org/pav/$1",
"description": "PAV is a lightweight ontology for tracking Provenance, Authoring and Versioning. PAV specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources.",
"modified": "2014-08-28",
"homepage": "http://pav-ontology.github.io/pav/",
"keywords": [
"Quality"
]
},
"poso": {
"name": "Positioning System Ontology",
"prefix": "poso",
"uri_prefix": "http://purl.org/poso/$1",
"description": "This ontology provides the terminologies used for positioning systems.",
"modified": "2022-07-25",
"keywords": [
"Geography",
"Geometry"
],
"homepage": "http://purl.org/poso/"
},
"posocm": {
"name": "Positioning System Ontology Common Technologies, Algorithms and Systems",
"prefix": "posocm",
"uri_prefix": "http://purl.org/poso/common/$1",
"description": "This ontology provides the terminologies used for positioning systems.",
"modified": "2022-07-25",
"keywords": [
"Geometry",
"Services"
],
"homepage": "http://purl.org/poso/common/"
},
"pc": {
"name": "Public Contracts Ontology",
"prefix": "pc",
"uri_prefix": "http://purl.org/procurement/public-contracts#$1",
"description": "Public Contracts Ontology offers a means of expression for describing public contracts in the public sector",
"modified": "2012-10-10",
"keywords": [
"Contracts"
],
"homepage": "http://purl.org/procurement/public-contracts"
},
"prog": {
"name": "The Event Programme Vocabulary",
"prefix": "prog",
"uri_prefix": "http://purl.org/prog/$1",
"description": "This Vocabulary provides the means to create a document which describes a large event or other connected series of events. The primary purpose is to help humans comprehend the programme, not describe absolute truth. A single event (or even series) may have multiple programmes.",
"modified": "2009-11-01",
"keywords": [
"Events"
],
"homepage": "http://purl.org/prog/"
},
"qb4o": {
"name": "Vocabulary for publishing OLAP data cubes",
"prefix": "qb4o",
"uri_prefix": "http://purl.org/qb4olap/cubes#$1",
"description": "This vocabulary allows to publish and operate with OLAP cubes in RDF",
"modified": "2015-07-11",
"keywords": [
"Catalogs"
],
"homepage": "http://purl.org/qb4olap/cubes"
},
"voidext": {
"name": "Extended Vocabulary of Interlinked Datasets (VoIDext)",
"prefix": "voidext",
"uri_prefix": "http://purl.org/query/voidext#$1",
"description": "The Extension of the Vocabulary of Interlinked Datasets (VoID) RDF Schema that includes the concept of virtual links. This extension enhances interoperability among heterogeneous and distributed RDF data sets by bridging them through explicitly defined virtual links.",
"modified": "2019-01-30",
"keywords": [
"Metadata"
],
"homepage": "http://purl.org/query/voidext"
},
"reco": {
"name": "RECommendations Ontology",
"prefix": "reco",
"uri_prefix": "http://purl.org/reco#$1",
"description": "The RECO ontology defines the vocabulary for representing preferences-as-constraints and preferences-as-ratings as RDF graphs. This lightweight vocabulary provides domain-independent means to describe user profiles in a coherent and context-aware way. RECO has been designed as an extension of both Friend-Of-A-Friend (FOAF) and Who Am I! (WAI) ontologies.",
"modified": "2011-08-01",
"keywords": [
"Methods",
"RDF"
],
"homepage": "http://purl.org/reco#"
},
"rss": {
"name": "Vocabulary for Rich Site Summary (RSS) 1.0",
"prefix": "rss",
"uri_prefix": "http://purl.org/rss/1.0/$1",
"description": "RDF Schema declaration for Rich Site Summary (RSS) 1.0",
"modified": "2000-12-06",
"homepage": "http://web.resource.org/rss/1.0/",
"keywords": [
"API"
]
},
"saws": {
"name": "Sharing Ancient Wisdoms Ontology",
"prefix": "saws",
"uri_prefix": "http://purl.org/saws/ontology#$1",
"description": "Ontology for the Sharing Ancient Wisdoms (SAWS) project, to represent the information and knowledge available in medieval gnomologia (collections of wise sayings). SAWS concentrates mainly on Ancient Greek and Arabic manuscripts containing wisdom literature. All class descriptions are provided by domain experts and the ontology has been developed through collaboration between these experts and ontology developers.",
"modified": "2013-06-07",
"homepage": "http://www.ancientwisdoms.ac.uk/media/ontology/",
"keywords": [
"Catalogs"
]
},
"biro": {
"name": "The Bibliographic Reference Ontology",
"prefix": "biro",
"uri_prefix": "http://purl.org/spar/biro/$1",
"description": "BiRO, the Bibliographic Reference Ontology, is an ontology structured according to the FRBR model to define bibliographic records (as subclasses of frbr:Work) and bibliographic references (as subclasses of frbr:Expression), and their compilations into bibliographic collections such as library catalogues, and into bibliographic lists such as reference lists in journal articles, respectively.",
"modified": "2013-05-11",
"keywords": [
"SPAR"
],
"homepage": "http://purl.org/spar/biro"
},
"c4o": {
"name": "C4O, the Citation Counting and Context Characterization Ontology",
"prefix": "c4o",
"uri_prefix": "http://purl.org/spar/c4o/$1",
"description": "C4O allows the characterization of bibliographic citations in terms of their number and their context.",
"modified": "2013-05-11",
"keywords": [
"SPAR"
],
"homepage": "http://purl.org/spar/c4o"
},
"cito": {
"name": "CiTO, the Citation Typing Ontology",
"prefix": "cito",
"uri_prefix": "http://purl.org/spar/cito/$1",
"description": "The Citation Typing Ontology enables characterization of the nature or type of citations",
"modified": "2018-02-16",
"homepage": "http://www.sparontologies.net/ontologies/cito",
"keywords": [
"SPAR"
]
},
"dcite": {
"name": "The DataCite Ontology",
"prefix": "dcite",
"uri_prefix": "http://purl.org/spar/datacite/$1",
"description": "The DataCite Ontology is an ontology written in OWL 2 DL to enable certain metadata properties of the DataCite Metadata Specification version 2.0 (http://datacite.org/schema/DataCite-MetadataKernel_v2.0.pdf) to be described in RDF.",
"modified": "2014-05-21",
"keywords": [
"SPAR"
],
"homepage": "http://purl.org/spar/datacite"
},
"deo": {
"name": "The Discourse Elements Ontology",
"prefix": "deo",
"uri_prefix": "http://purl.org/spar/deo/$1",
"description": "The Discourse Elements Ontology is an ontology for describing the major rhetorical elements of a document such as a journal article. It is a subsidiary ontology that is imported into the Document Components Ontology, itself part of SPAR, the Semantic Publishing and Referencing Ontologies",
"modified": "2015-07-03",
"homepage": "http://www.essepuntato.it/lode/http://purl.org/spar/deo",
"keywords": [
"SPAR"
]
},
"doco": {
"name": "DoCO, the Document Components Ontology",
"prefix": "doco",
"uri_prefix": "http://purl.org/spar/doco/$1",
"description": "An ontology for describing the component parts of a bibliographic document",
"modified": "2015-07-03",
"homepage": "https://sparontologies.github.io/doco/current/doco.html",
"keywords": [
"SPAR"
]
},
"fabio": {
"name": "FRBR-aligned Bibliographic Ontology",
"prefix": "fabio",
"uri_prefix": "http://purl.org/spar/fabio/$1",
"description": "FaBiO, the FRBR-aligned Bibliographic Ontology, is an ontology for recording and publishing on the Semantic Web bibliographic records of scholarly endeavours. It forms part of SPAR, a suite of Semantic Publishing and Referencing Ontologies.",
"modified": "2019-02-19",
"homepage": "https://github.com/SPAROntologies/fabio",
"keywords": [
"SPAR"
]
},
"pro": {
"name": "The Publishing Roles Ontology",
"prefix": "pro",
"uri_prefix": "http://purl.org/spar/pro/$1",
"description": "PRO, the Publishing Roles Ontology, is an ontology for describing the role(s) in the publication process of a particular agent over a defined period of time. It forms part of SPAR, a suite of Semantic Publishing and Referencing Ontologies.",
"modified": "2013-12-18",
"keywords": [
"SPAR"
],
"homepage": "http://purl.org/spar/pro"
},
"pso": {
"name": "The Publishing Status Ontology",
"prefix": "pso",
"uri_prefix": "http://purl.org/spar/pso/$1",
"description": "an ontology for describing the status held by a bibliographic document or other publication entity at each of the various stages in the publishing process. It forms part of SPAR, a suite of Semantic Publishing and Referencing Ontologies",
"modified": "2014-02-01",
"keywords": [
"SPAR"
],
"homepage": "http://purl.org/spar/pso"
},
"pwo": {
"name": "The Publishing Workflow Ontology",
"prefix": "pwo",
"uri_prefix": "http://purl.org/spar/pwo/$1",
"description": "An ontology for describing the workflow associated with the publication of a document.",
"modified": "2015-06-18",
"keywords": [
"SPAR"
],
"homepage": "http://purl.org/spar/pwo"
},
"scoro": {
"name": "Scholarly Contributions and Roles Ontology",
"prefix": "scoro",
"uri_prefix": "http://purl.org/spar/scoro/$1",
"description": "SCoRO, the Scholarly Contributions and Roles Ontology, is an ontology for use by authors and publishers for describing the contributions that may be made and the roles that may be held by a person with respect to a journal article or other publication, and by research administrators and others for describing contributions and roles with respect to other aspects of scholarly research.",
"modified": "2017-09-04",
"homepage": "https://sparontologies.github.io/scoro/current/scoro.html",
"keywords": [
"Academy"
]
},
"rev": {
"name": "Review Vocabulary",
"prefix": "rev",
"uri_prefix": "http://purl.org/stuff/rev#$1",
"description": "Vocabulary for expressing reviews and ratings",
"modified": "2007-11-08",
"keywords": [
"Rec"
],
"homepage": "http://purl.org/stuff/rev#"
},
"dr": {
"name": "Discourse relationships vocabulary",
"prefix": "dr",
"uri_prefix": "http://purl.org/swan/2.0/discourse-relationships/$1",
"description": "Relationships without range and domains meant to be reused in different contexts",
"modified": "2010-10-12",
"keywords": [
"Support"
],
"homepage": "http://purl.org/swan/2.0/discourse-relationships/"
},
"tempo": {
"name": "TempO - Temporal Ontology",
"prefix": "tempo",
"uri_prefix": "http://purl.org/tempo/$1",
"description": "In a typical (uni)temporal data model every resource's appearance (and disappearance) is being tracked.\nNumerous systems accomplish unitemporal tracking, either externally by e.g. using git to record the insertion or deletion of a resource, or internally by e.g. using prov:generatedAtTime and prov:invalidatedAtTime.\nThis axis of time is known as *system time*, and none of TempO's concern because for one there is readily available support, and moreover because unitemporal tracking is used for principally true statements, i.e. those that have always been (considered) true or will always be (considered) true.\n\nTempO addresses bitemporal and tritemporal setups: Resources which are (known or believed to be) valid and efficacious for some time.\nA second time axis orthogonal to system time is introduced, that is a resource can be valid even though it is currently not in the system, or, conversely, can be already or still invalid by the time it enters the system.\n\nEfficacy, sometimes called decision time, is yet another concept orthogonal to validity, i.e. a resource that is no longer or not yet valid can be efficacious.\nThe converse, a valid but inefficacious resource in the system, is *usually* not encountered but TempO does not impose restrictions on the shape of the time area.\n\nIn general the necessity for tracking both validity and efficacy arises in areas where concepts are assigned a code or label that is subject to reuse following invalidation.\nTracking efficacy and validity concurrently then allows for fine-grained control over how much future knowledge or how much past knowledge we tolerate in a datset.\n\nExample:\n--------\nCzechoslovakia was founded in 1918 but became part of Germany, Hungary and Poland in 1938.\nIt was reestablished in 1945 but split into two sovereign states in 1993.\nThe ISO 3166 country code for Czechoslovakia used to be 'CS', assigned in 1974, published in February 1978, and invalidated with the country's split.\nIn 2003 ISO 3166 reassigned the country code 'CS' to Serbia and Montenegro.\nThe facts were assembled in 2018 and written down as follows:\n\n cc:CSHH\n a cc:ISO3166-CountryCode ;\n rdfs:label \"CS\" ;\n cc:refersTo \"Czechoslovakia\" ;\n prov:generatedAtTime \"2018-02-29T04:00:00Z\"^^xsd:dateTime .\n tempo:validFrom \"1978-02\"^^xsd:gYearMonth ;\n tempo:validTill \"1993-01-01\"^^xsd:date ;\n tempo:efficaciousFrom \"1918\"^^xsd:gYear , \"1945\"^^xsd:gYear ;\n tempo:efficaciousTill \"1938\"^^xsd:gYear , \"2003\"^^xsd:gYear .\n\nThe use of the country code 'CS' in a statement from 1988 can be resolved to cc:CSHH, as of today, free from ambiguity; it was valid back then after all and we know that today.\nThe same query in 2017 (point-in-time query) would have yielded no results because the information hadn't been in the system back then.\nPoint-in-time queries, however, are not TempO's major concern so only as-of-today queries are assumed from now on.\n\nFollowing the country's split it is highly likely that news reports from, say, 1994 highlighting the then-recent past would still have used 'CS' to refer to cc:CSHH.\nAccording to the resource this is possible, a query for 'CS' in 1994 would bring up cc:CSHH as it is efficacious but marked as invalidated.\n\nOn the other end of history, the use of the code 'CS' in, say, 1976 is plausible. The code was decided on but not yet formally published.\nA query for 'CS' as used in 1976 would bring up cc:CSHH, marked as anachronistic.\nGoing back further, a statement from, say 1942, using the code 'CS' must clearly refer to something else.\nA query for 'CS' as used in 1976 would yield not yield any results.\n\n--\n\nThe ontology IRI http://purl.org/tempo/ always resolve to the latest version of TempO. Particular versionIRIs such as http://purl.org/tempo/0.1/ can be used by clients to force the import of a particular version.\n\nThe goal of TempO is to allow for temporal constraints with control over how much future or past is permissible directly on the published resource, and as such, TempO does not restrict domain/ranges.",
"modified": "2022-08-20",
"keywords": [
"Time"
],
"homepage": "http://purl.org/tempo"
},
"theatre": {
"name": "Theatre Ontology",
"prefix": "theatre",
"uri_prefix": "http://purl.org/theatre#$1",
"description": "An ontology for organising theatrical data.",
"modified": "2013-04-18",
"keywords": [
"Events"
],
"homepage": "http://purl.org/theatre#"
},
"tio": {
"name": "The Tickets Ontology",
"prefix": "tio",
"uri_prefix": "http://purl.org/tio/ns#$1",
"description": "A vocabulary for describing tickets for events, transportation, or points of interest for e-commerce.",
"modified": "2010-11-17",
"keywords": [
"eBusiness"
],
"homepage": "http://purl.org/tio/ns#"
},
"toco": {
"name": "Toucan Ontology",
"prefix": "toco",
"uri_prefix": "http://purl.org/toco/$1",
"description": "A ontology developed for telecommunciation network systems with hybrid technologies, e.g., WiFi, LiFi, LTE, 2G/3G, optical, etc.",
"modified": "2019-03-29",
"keywords": [
"API"
],
"homepage": "http://purl.org/toco/"
},
"dpo": {
"name": "Diabetes Pharmacology Ontology",
"prefix": "dpo",
"uri_prefix": "http://purl.org/twc/dpo/ont/$1",
"description": "The Diabetes Pharmacology Ontology contains the classes needed to describe antihyperglycemic therapies.",
"modified": "2022-12-18",
"homepage": "https://tetherless-world.github.io/diabetes-pharmacology-ontology/",
"keywords": [
"Biology",
"Health"
]
},
"cmo": {
"name": "Conceptual Model Ontology",
"prefix": "cmo",
"uri_prefix": "http://purl.org/twc/ontologies/cmo.owl#$1",
"description": "An ontology to tie classes and properties to SKOS concepts",
"modified": "2006-06-30",
"keywords": [
"General & Upper"
],
"homepage": "http://purl.org/twc/ontologies/cmo.owl"
},
"cdm": {
"name": "Conceptual Depth and Momentum",
"prefix": "cdm",
"uri_prefix": "http://purl.org/twc/ontology/cdm.owl#$1",
"description": "An attempt to represent how universal/accepted/popular a URI is",
"modified": "2011-09-23",
"keywords": [
"RDF"
],
"homepage": "http://purl.org/twc/ontology/cdm.owl#"
},
"conversion": {
"name": "Conversion Ontology",
"prefix": "conversion",
"uri_prefix": "http://purl.org/twc/vocab/conversion/$1",
"description": "Ontology used to describe interpretations of tabular literals to produce RDF",
"modified": "2013-04-15",
"keywords": [
"RDF"
],
"homepage": "http://purl.org/twc/vocab/conversion/"
},
"uco": {
"name": "Used Cars Ontology",
"prefix": "uco",
"uri_prefix": "http://purl.org/uco/ns#$1",
"description": "A Web vocabulary for describing aspects of used cars for e-commerce.",
"modified": "2012-12-31",
"homepage": "http://ontologies.makolab.com/uco/ns.html#",
"keywords": [
"eBusiness"
]
},
"uneskos": {
"name": "UNESKOS Vocabulary",
"prefix": "uneskos",
"uri_prefix": "http://purl.org/umu/uneskos#$1",
"description": "An RDF vocabulary for extending some SKOS and ISO-THES functions in order to improve the linked data consumption of SKOS datasets",
"modified": "2015-09-10",
"keywords": [
"RDF"
],
"homepage": "http://purl.org/umu/uneskos"
},
"summa": {
"name": "SUMMA Vocabulary",
"prefix": "summa",
"uri_prefix": "http://purl.org/voc/summa/$1",
"description": "The SUMMA Vocabulary enables to request and represent summarized RDf resources. It should be used in context to the SUMMA API definition.",
"modified": "2015-04-11",
"keywords": [
"API"
],
"homepage": "http://purl.org/voc/summa/"
},
"aiiso": {
"name": "Academic Institution Internal Structure Ontology",
"prefix": "aiiso",
"uri_prefix": "http://purl.org/vocab/aiiso/schema#$1",
"description": "The Academic Institution Internal Structure Ontology (AIISO) provides classes and properties to describe the internal organizational structure of an academic institution. AIISO is designed to work in partnership with Participation (http://purl.org/vocab/participation/schema), FOAF (http://xmlns.com/foaf/0.1/) and aiiso-roles (http://purl.org/vocab/aiiso-roles/schema) to describe the roles that people play within an institution.",
"modified": "2008-09-25",
"homepage": "http://vocab.org/aiiso/schema-20080925.html",
"keywords": [
"Academy"
]
},
"bio": {
"name": "BIO: A vocabulary for biographical information",
"prefix": "bio",
"uri_prefix": "http://purl.org/vocab/bio/0.1/$1",
"description": "A vocabulary for describing biographical information about people, both living and dead.",
"modified": "2011-06-14",
"homepage": "http://vocab.org/bio/0.1/.html",
"keywords": [
"People"
]
},
"cs": {
"name": "Changeset",
"prefix": "cs",
"uri_prefix": "http://purl.org/vocab/changeset/schema#$1",
"description": "This vocabulary defines a set of terms for describing changes to resource descriptions.",
"modified": "2009-05-18",
"keywords": [
"Quality"
],
"homepage": "http://purl.org/vocab/changeset/schema"
},
"frbr": {
"name": "Expression of Core FRBR Concepts in RDF",
"prefix": "frbr",
"uri_prefix": "http://purl.org/vocab/frbr/core#$1",
"description": "An expression in RDF of the concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR)",
"modified": "2009-05-16",
"homepage": "http://vocab.org/frbr/core.html",
"keywords": [
"FRBR"
]
},
"frbre": {
"name": "Extended FRBR",
"prefix": "frbre",
"uri_prefix": "http://purl.org/vocab/frbr/extended#$1",
"description": "Expression of Extended FRBR Concepts in RDF",
"modified": "2005-08-10",
"keywords": [
"FRBR"
],
"homepage": "http://purl.org/vocab/frbr/extended"
},
"lcy": {
"name": "Lifecycle Schema",
"prefix": "lcy",
"uri_prefix": "http://purl.org/vocab/lifecycle/schema#$1",
"description": "The Lifecycle Schema provides classes and properties that allow the specification of a lifecycle that any resource may pass through.",
"modified": "2008-06-03",
"keywords": [
"PLM"
],
"homepage": "http://purl.org/vocab/lifecycle/schema"
},
"part": {
"name": "Participation Schema",
"prefix": "part",
"uri_prefix": "http://purl.org/vocab/participation/schema#$1",
"description": "The participation ontology is a simple model for describing the roles that people play within groups. It is intended that specific domains will create subclasses of roles within their own areas of expertise.",
"modified": "2008-09-25",
"keywords": [
"Society"
],
"homepage": "http://purl.org/vocab/participation/schema"
},
"rel": {
"name": "Relationship",
"prefix": "rel",
"uri_prefix": "http://purl.org/vocab/relationship/$1",
"description": "A vocabulary for describing relationships between people",
"modified": "2010-04-19",
"homepage": "http://vocab.org/relationship/.html",
"keywords": [
"People"
]
},
"vann": {
"name": "VANN: A vocabulary for annotating vocabulary descriptions",
"prefix": "vann",
"uri_prefix": "http://purl.org/vocab/vann/$1",
"description": "A vocabulary for annotating descriptions of vocabularies with examples and usage notes.",
"modified": "2010-06-07",
"keywords": [
"Metadata"
],
"homepage": "http://purl.org/vocab/vann/"
},
"voaf": {
"name": "Vocabulary of a Friend",
"prefix": "voaf",
"uri_prefix": "http://purl.org/vocommons/voaf#$1",
"description": "Un vocabulaire de description des vocabulaires RDF et de leurs relations mutuelles",
"modified": "2013-05-24",
"homepage": "http://purl.org/vocommons/voaf/index.html",
"keywords": [
"Metadata"
]
},
"vsearch": {
"name": "vSearch Vocabulary",
"prefix": "vsearch",
"uri_prefix": "http://purl.org/vsearch/$1",
"description": "The vSearch vocabulary facilitates the querying and retrieval of vocabulary terms from a vocabularies directory. It can be used to map keywords with mapped result terms accompanied with a ranking value.",
"modified": "2016-01-16",
"keywords": [
"Vocabularies"
],
"homepage": "http://purl.org/vsearch/"
},
"vso": {
"name": "Vehicle Sales Ontology",
"prefix": "vso",
"uri_prefix": "http://purl.org/vso/ns#$1",
"description": "The Vehicle Sales Ontology for Semantic Web-based E-Commerce",
"modified": "2010-10-02",
"keywords": [
"eBusiness"
],
"homepage": "http://purl.org/vso/ns"
},
"vvo": {
"name": "Volkswagen Vehicles Ontology",
"prefix": "vvo",
"uri_prefix": "http://purl.org/vvo/ns#$1",
"description": "A vocabulary for describing Volkswagen-specific features of automobiles and their components",
"modified": "2010-10-12",
"homepage": "http://purl.org/vvo/ns.html",
"keywords": [
"Industry",
"eBusiness"
]
},
"wai": {
"name": "Roles and Profiles Ontology",
"prefix": "wai",
"uri_prefix": "http://purl.org/wai#$1",
"description": "WAI vocabulary aims to extend the FOAF specification through introducing the concepts of roles and profiles. In society, people are more than just persons, they can be musicians, presidents of government, firemen, football players or car drivers in a traffic jam.",
"modified": "2010-10-11",
"homepage": "http://vocab.ctic.es/wai/wai.html",
"keywords": [
"People"
]
},
"ro": {
"name": "The Research Object Ontology",
"prefix": "ro",
"uri_prefix": "http://purl.org/wf4ever/ro#$1",
"description": "This ontology shows how AO and ORE ontologies can be used together to define a ResearchObject. This ontology is further customized by the wf4ever ontology.",
"modified": "2013-11-30",
"keywords": [
"Metadata"
],
"homepage": "http://purl.org/wf4ever/ro"
},
"wfdesc": {
"name": "The Wfdesc ontology",
"prefix": "wfdesc",
"uri_prefix": "http://purl.org/wf4ever/wfdesc#$1",
"description": "This ontology (\"wfdesc\") describes an abstract workflow description structure, allowing the description of a scientific workflow as a direct acyclic graph, or a dataflow. This ontology is meant as an upper ontology for more specific workflow definitions, and as a way to express abstract workflows. The wfprov ontology shows how to link these descriptions to a provenance trace of a workflow execution.",
"modified": "2016-01-28",
"keywords": [
"PLM"
],
"homepage": "http://purl.org/wf4ever/wfdesc"
},
"wfprov": {
"name": "The Wfprov Ontology",
"prefix": "wfprov",
"uri_prefix": "http://purl.org/wf4ever/wfprov#$1",
"description": "The wfprov ontology shows how to express minimal provenance information about the execution of a workflow described using the wfdesc ontology.",
"modified": "2015-03-23",
"keywords": [
"PLM"
],
"homepage": "http://purl.org/wf4ever/wfprov"
},
"xapi": {
"name": "xAPI Controlled Vocabulary Ontology",
"prefix": "xapi",
"uri_prefix": "http://purl.org/xapi/ontology#$1",
"description": "This ontology contains a list of the classes and properties that can be used when for creating and publishing a controlled vocabulary dataset for xAPI communities of practice.",
"modified": "2015-08-13",
"homepage": "https://github.com/adlnet/xAPI-Spec/blob/1.0.3/xAPI.md",
"keywords": [
"API"
]
},
"uniprot": {
"name": "Uniprot Core Ontology",
"prefix": "uniprot",
"uri_prefix": "http://purl.uniprot.org/core/$1",
"description": "Properties and classes used for protein annotation",
"modified": "2012-10-03",
"keywords": [
"Biology"
],
"homepage": "http://purl.uniprot.org/core/"
},
"sou": {
"name": "QUDT VOCAB Systems of Units Release 2.1.34",
"prefix": "sou",
"uri_prefix": "http://qudt.org/2.1/vocab/sou/$1",
"description": "QUDT VOCAB Systems of Units Release 2.1.34",
"modified": "2016-07-04",
"keywords": [
"Methods"
],
"homepage": "http://qudt.org/2.1/vocab/sou"
},
"qudt": {
"name": "Quantities, Units, Dimensions and Types",
"prefix": "qudt",
"uri_prefix": "http://qudt.org/schema/qudt/$1",
"description": "The QUDT, or 'Quantity, Unit, Dimension and Type' collection of ontologies define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems.",
"modified": "2020-04-20",
"homepage": "http://qudt.org",
"keywords": [
"Methods"
]
},
"rdaa": {
"name": "RDA Agent properties",
"prefix": "rdaa",
"uri_prefix": "http://rdaregistry.info/Elements/a/$1",
"description": "The Agent properties element set consists of properties representing the attributes and relationships of the RDA Agent, Person, Family, and Corporate Body entities. Each property in the element set has a domain of the class representing one of these entities.",
"modified": "2015-12-31",
"homepage": "https://github.com/RDARegistry/RDA-Vocabularies/",
"keywords": [
"FRBR"
]
},
"rdac": {
"name": "RDA Classes",
"prefix": "rdac",
"uri_prefix": "http://rdaregistry.info/Elements/c/$1",
"description": "The Classes element set consists of classes representing the RDA entities, including Work, Expression, Manifestation, Item, Person, Family, Corporate Body, and Agent.",
"modified": "2015-12-31",
"homepage": "https://github.com/RDARegistry/RDA-Vocabularies/blob/master/ttl/Elements/c.ttl",
"keywords": [
"FRBR"
]
},
"rdae": {
"name": "RDA Expression properties",
"prefix": "rdae",
"uri_prefix": "http://rdaregistry.info/Elements/e/$1",
"description": "The Expression properties element set consists of properties representing the attributes and relationships of the RDA Expression entity. Each property in the element set has a domain of the class representing this entity.",
"modified": "2014-07-30",
"keywords": [
"FRBR"
],
"homepage": "http://rdaregistry.info/Elements/e"
},
"rdai": {
"name": "RDA Item properties",
"prefix": "rdai",
"uri_prefix": "http://rdaregistry.info/Elements/i/$1",
"description": "The Item properties element set consists of properties representing the attributes and relationships of the RDA Item entity.",
"modified": "2015-12-31",
"homepage": "https://github.com/RDARegistry/RDA-Vocabularies/blob/master/ttl/Elements/i.ttl",
"keywords": [
"FRBR"
]
},
"rdam": {
"name": "RDA Manifestation properties",
"prefix": "rdam",
"uri_prefix": "http://rdaregistry.info/Elements/m/$1",
"description": "The Manifestation properties element set consists of properties representing the attributes and relationships of the RDA Manifestation entity.",
"modified": "2015-12-31",
"homepage": "https://github.com/RDARegistry/RDA-Vocabularies/",
"keywords": [
"FRBR"
]
},
"rdau": {
"name": "RDA Unconstrained properties",
"prefix": "rdau",
"uri_prefix": "http://rdaregistry.info/Elements/u/$1",
"description": "The Unconstrained properties element set consists of properties representing the attributes and relationships of the all RDA entities. Each property in the element set has semantics which are independent of the FRBR model and has no specified domain or range.",
"modified": "2015-12-30",
"keywords": [
"FRBR"
],
"homepage": "http://rdaregistry.info/Elements/u"
},
"rdaw": {
"name": "RDA Work properties",
"prefix": "rdaw",
"uri_prefix": "http://rdaregistry.info/Elements/w/$1",
"description": "The Work properties element set consists of properties representing the attributes and relationships of the RDA Work entity.",
"modified": "2015-12-31",
"homepage": "https://github.com/RDARegistry/RDA-Vocabularies/blob/master/ttl/Elements/w.ttl",
"keywords": [
"FRBR"
]
},
"disco": {
"name": "DDI-RDF Discovery Vocabulary",
"prefix": "disco",
"uri_prefix": "http://rdf-vocabulary.ddialliance.org/discovery#$1",
"description": "A metadata vocabulary for documenting research and survey data",
"modified": "2013-09-30",
"homepage": "http://rdf-vocabulary.ddialliance.org/discovery.html",
"keywords": [
"Methods"
]
},
"phdd": {
"name": "Physical Data Description",
"prefix": "phdd",
"uri_prefix": "http://rdf-vocabulary.ddialliance.org/phdd#$1",
"description": "Physical data description (PHDD) of existing or published data (tables) in a rectangular format. The data could be either represented in records with character-separated values (CSV) or in records with fixed length.",
"modified": "2014-05-25",
"homepage": "http://www.ddialliance.org/Specification/RDF/PHDD",
"keywords": [
"CSV"
]
},
"xkos": {
"name": "XKOS",
"prefix": "xkos",
"uri_prefix": "http://rdf-vocabulary.ddialliance.org/xkos#$1",
"description": "An extension of SKOS for representaion of nomenclatures",
"modified": "2016-03-20",
"keywords": [
"Vocabularies"
],
"homepage": "http://rdf-vocabulary.ddialliance.org/xkos"
},
"obsm": {
"name": "Observation Method Ontology",
"prefix": "obsm",
"uri_prefix": "http://rdf.geospecies.org/methods/observationMethod#$1",
"description": "This is a taxonomy of some observation methods. It is incomplete",
"modified": "2009-02-15",
"keywords": [
"Biology"
],
"homepage": "http://rdf.geospecies.org/methods/observationMethod.rdf"
},
"geosp": {
"name": "GeoSpecies Ontology",
"prefix": "geosp",
"uri_prefix": "http://rdf.geospecies.org/ont/geospecies#$1",
"description": "The GeoSpecies Ontology is used to describe geographical distribution of living species.",
"modified": "2012-10-02",
"keywords": [
"Environment"
],
"homepage": "http://rdf.geospecies.org/ont/geospecies"
},
"idemo": {
"name": "Ontologie d\u00e9mographique de l'INSEE",
"prefix": "idemo",
"uri_prefix": "http://rdf.insee.fr/def/demo#$1",
"description": "Ontologie des classes et propri\u00e9t\u00e9s utilis\u00e9es pour la d\u00e9mographie, notamment le recensement de la population",
"modified": "2012-12-26",
"keywords": [
"Methods"
],
"homepage": "http://rdf.insee.fr/def/demo"
},
"igeo": {
"name": "Ontologie g\u00e9ographique de l'INSEE",
"prefix": "igeo",
"uri_prefix": "http://rdf.insee.fr/def/geo#$1",
"description": "Ontology describing geographic entities as seen by the French Statistical Institute",
"modified": "2015-01-11",
"homepage": "http://rdf.insee.fr/geo/index.html",
"keywords": [
"Geography"
]
},
"aos": {
"name": "Appearances Ontology Specification",
"prefix": "aos",
"uri_prefix": "http://rdf.muninn-project.org/ontologies/appearances#$1",
"description": "Appearances is an ontology that grew out of the need to record personal appearance details about individuals while taking into account errors of perception and translation between various diffferent standards. Originally it was meant to record physical caracteristics of Great War soldiers from their medical files, but it became evident that the resource was also useful for other purposes.",
"modified": "2012-11-15",
"keywords": [
"People"
],
"homepage": "http://rdf.muninn-project.org/ontologies/appearances"
},
"mil": {
"name": "Military Ontology Specification",
"prefix": "mil",
"uri_prefix": "http://rdf.muninn-project.org/ontologies/military#$1",
"description": "The Muninn Military Ontology marks up information about military people, organizations and events.",
"modified": "2015-07-05",
"keywords": [
"Society"
],
"homepage": "http://rdf.muninn-project.org/ontologies/military"
},
"meb": {
"name": "The myExperiment Base Ontology",
"prefix": "meb",
"uri_prefix": "http://rdf.myexperiment.org/ontologies/base/$1",
"description": "This ontology provides the base elements required by myExperiment for content management, social networking and object annotation.",
"modified": "2013-03-26",
"keywords": [
"Academy"
],
"homepage": "http://rdf.myexperiment.org/ontologies/base/"
},
"snarm": {
"name": "Simple Network Access Rights Management Ontology",
"prefix": "snarm",
"uri_prefix": "http://rdf.myexperiment.org/ontologies/snarm/$1",
"description": "This ontology is designed for representing access rights within a simple network of associated users/groups",
"modified": "2011-09-02",
"keywords": [
"API"
],
"homepage": "http://rdf.myexperiment.org/ontologies/snarm/"
},
"bevon": {
"name": "BEVON: Beverage Ontology",
"prefix": "bevon",
"uri_prefix": "http://rdfs.co/bevon/$1",
"description": "Beverage Ontology is a Web vocabulary for describing beverages, mainly alcoholic.",
"modified": "2015-07-23",
"keywords": [
"Food"
],
"homepage": "http://rdfs.co/bevon/"
},
"juso": {
"name": "Juso Ontology",
"prefix": "juso",
"uri_prefix": "http://rdfs.co/juso/$1",
"description": "Juso Ontology is a Web vocabulary for describing geographical addresses and features.",
"modified": "2015-10-02",
"keywords": [
"Geography",
"Geometry"
],
"homepage": "http://rdfs.co/juso/"
},
"juso.kr": {
"name": "South Korea Extension to Juso Ontology",
"prefix": "juso.kr",
"uri_prefix": "http://rdfs.co/juso/kr/$1",
"description": "South Korea Extension to Juso Ontology is a Web vocabulary that extends Juso Ontology to describe geographical addresses and features in South Korea.",
"modified": "2015-10-07",
"keywords": [
"Geography",
"Geometry"
],
"homepage": "http://rdfs.co/juso/kr/"
},
"scot": {
"name": "Social Semantic Cloud of Tags",
"prefix": "scot",
"uri_prefix": "http://rdfs.org/scot/ns#$1",
"description": "SCOT is an ontology for describing the structure and the semantics for tagging data across heterogenous users, sources, and applications.",
"modified": "2012-08-13",
"homepage": "http://scot-project.net/scot/spec/scot.html",
"keywords": [
"Tag"
]
},
"sioc": {
"name": "Semantically-Interlinked Online Communities",
"prefix": "sioc",
"uri_prefix": "http://rdfs.org/sioc/ns#$1",
"description": "SIOC is an ontology for describing the information in online communities.",
"modified": "2010-03-25",
"homepage": "http://rdfs.org/sioc/spec/",
"keywords": [
"Society"
]
},
"tsioc": {
"name": "SIOC Types Ontology Module",
"prefix": "tsioc",
"uri_prefix": "http://rdfs.org/sioc/types#$1",
"description": "Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining subclasses and subproperties of SIOC terms.",
"modified": "2010-03-25",
"homepage": "http://rdfs.org/sioc/spec/#sec-modules",
"keywords": [
"Society"
]
},
"ruto": {
"name": "Test-Driven Data Debugging Ontology",
"prefix": "ruto",
"uri_prefix": "http://rdfunit.aksw.org/ns/core#$1",
"description": "The Databugger ontology describes concepts used in Databugger, a test driven data-debugging framework that can run automatically generated (based on a schema) and manually generated test cases against an endpoint.",
"modified": "2014-01-10",
"homepage": "http://aksw.org/Projects/RDFUnit.html",
"keywords": [
"Quality"
]
},
"rdag1": {
"name": "RDA Group 1 Elements",
"prefix": "rdag1",
"uri_prefix": "http://rdvocab.info/Elements/$1",
"description": "This is the provisional registration of the RDA Group 1 Element Vocabulary, managed by the DCMI/RDA Task Group.",
"modified": "2012-08-30",
"keywords": [
"Metadata"
],
"homepage": "http://rdvocab.info/Elements"
},
"rdag2": {
"name": "RDA Group 2 Elements",
"prefix": "rdag2",
"uri_prefix": "http://rdvocab.info/ElementsGr2/$1",
"description": "The second group of metadata elements defined by RDA",
"modified": "2011-10-13",
"keywords": [
"Metadata"
],
"homepage": "http://rdvocab.info/ElementsGr2"
},
"rdag3": {
"name": "RDA Group 3 Elements",
"prefix": "rdag3",
"uri_prefix": "http://rdvocab.info/ElementsGr3/$1",
"description": "This group of RDA elements defines preferred and variant names for concepts, places and events",
"modified": "2011-08-01",
"keywords": [
"Metadata"
],
"homepage": "http://rdvocab.info/ElementsGr3"
},
"rdarel": {
"name": "RDA Relationships for Works, Expressions, Manifestations, Items",
"prefix": "rdarel",
"uri_prefix": "http://rdvocab.info/RDARelationshipsWEMI/$1",
"description": "A vocabulary defining a large variety of specific relationships between the various levels of the FRBR pile.",
"modified": "2012-03-09",
"keywords": [
"Metadata"
],
"homepage": "http://rdvocab.info/RDARelationshipsWEMI"
},
"rdarole": {
"name": "RDA Roles",
"prefix": "rdarole",
"uri_prefix": "http://rdvocab.info/roles/$1",
"description": "Defines possible roles linking agents to FRBR objects (works, expressions, manifestations, items)",
"modified": "2015-01-11",
"homepage": "http://dublincore.org/dcmirdataskgroup",
"keywords": [
"FRBR"
]
},
"rdafrbr": {
"name": "FRBR Entities for RDA",
"prefix": "rdafrbr",
"uri_prefix": "http://rdvocab.info/uri/schema/FRBRentitiesRDA/$1",
"description": "Defines the core RDA classes, including FRBR levels Work, Expression, Manifestation and Item.",
"modified": "2012-03-26",
"keywords": [
"FRBR"
],
"homepage": "http://rdvocab.info/uri/schema/FRBRentitiesRDA"
},
"reegle": {
"name": "Renewable Energy and Energy Efficiency",
"prefix": "reegle",
"uri_prefix": "http://reegle.info/schema#$1",
"description": "Vocabulary used to describe clean energy actors, projects and technologies",
"modified": "2014-06-10",
"keywords": [
"Environment"
],
"homepage": "http://reegle.info/schema"
},
"donto": {
"name": "Dataset Ontology",
"prefix": "donto",
"uri_prefix": "http://reference.data.gov.au/def/ont/dataset#$1",
"description": "The data.gov.au Dataset Ontology is an OWL ontology designed to describe the characteristics of datasets published on data.gov.au.\n\nThe ontology contains elements which describe the publication, update, origin, governance, spatial and temporal coverage and other contextual information about the dataset. The ontology also covers aspects of organisational custodianship and governance.\n \nBy using this ontology to describe datasets on data.gov.au publishers increase discoverability and enable the consumption of this information in other applications/systems as Linked Data. It further enables decentralised publishing of catalogs and facilitates federated dataset search across sites, e.g. in datasets that are published by the States.\n \nOther publishers of Linked Data may make assertions about data published using this ontology, e.g. they may publish information about the use of the dataset in other applications.",
"modified": "2015-06-19",
"homepage": "https://github.com/AGLDWG/dataset-ont",
"keywords": [
"Government",
"Metadata"
]
},
"isoadr": {
"name": "ISO19160-1:2015 Address ontology",
"prefix": "isoadr",
"uri_prefix": "http://reference.data.gov.au/def/ont/iso19160-1-address#$1",
"description": "This ontology is a version of the ISO TC211, Group for Ontology Management (GOM)'s OWL ontology interpretation of the ISO19160-1:2015 \"Addressing -- Part 1: Conceptual model\" standard (see https://www.iso.org/standard/61710.html) taken from that ontology's source code, published at https://github.com/ISO-TC211/GOM/tree/master/isotc211_GOM_harmonizedOntology/19160-1/2015.",
"modified": "2017-11-27",
"homepage": "http://pid.data.gov.au/websrv/reference/def/ont/iso19160-1-address/ont.ttl",
"keywords": [
"Geography",
"Quality",
"Tag",
"Vocabularies"
]
},
"cgov": {
"name": "Central Government Ontology",
"prefix": "cgov",
"uri_prefix": "http://reference.data.gov.uk/def/central-government/$1",
"description": "An ontology of UK central government",
"modified": "2012-08-28",
"keywords": [
"Government"
],
"homepage": "http://reference.data.gov.uk/def/central-government"
},
"interval": {
"name": "Intervals Ontology",
"prefix": "interval",
"uri_prefix": "http://reference.data.gov.uk/def/intervals/$1",
"description": "An ontology for time intervals",
"modified": "2010-03-08",
"keywords": [
"Time"
],
"homepage": "http://reference.data.gov.uk/def/intervals"
},
"odv": {
"name": "Organogram Data Vocabulary",
"prefix": "odv",
"uri_prefix": "http://reference.data.gov.uk/def/organogram/$1",
"description": "Extension of data cube for civil service junior posts",
"modified": "2011-06-11",
"keywords": [
"Methods"
],
"homepage": "http://reference.data.gov.uk/def/organogram"
},
"parl": {
"name": "Parliament Ontology",
"prefix": "parl",
"uri_prefix": "http://reference.data.gov.uk/def/parliament/$1",
"description": "An ontology of UK Parliament",
"modified": "2010-06-17",
"keywords": [
"Government"
],
"homepage": "http://reference.data.gov.uk/def/parliament"
},
"pay": {
"name": "Payments ontology",
"prefix": "pay",
"uri_prefix": "http://reference.data.gov.uk/def/payment#$1",
"description": "Vocabulary for representing payments, such as government expenditures, using the data cube representation.",
"modified": "2010-11-16",
"homepage": "http://data.gov.uk/resources/payments",
"keywords": [
"Contracts"
]
},
"gts": {
"name": "Geologic Timescale model",
"prefix": "gts",
"uri_prefix": "http://resource.geosciml.org/ontology/timescale/gts#$1",
"description": "This is an RDF/OWL representation of the GeoSciML Geologic Timescale model, which has been adapted from the model described in Cox, S.J.D, & Richard, S.M. (2005) A formal model for the geologic timescale and GSSP, compatible with geospatial information transfer standards, Geosphere, Geological Society of America 1/3, 119\u2013137.",
"modified": "2017-04-28",
"keywords": [
"Time"
],
"homepage": "http://resource.geosciml.org/ontology/timescale/gts"
},
"thors": {
"name": "The Temporal Ordinal Reference Systems",
"prefix": "thors",
"uri_prefix": "http://resource.geosciml.org/ontology/timescale/thors#$1",
"description": "An OWL representation of the model for Temporal Ordinal Reference Systems defined in GeoSciML v3.",
"modified": "2017-04-28",
"keywords": [
"Time"
],
"homepage": "http://resource.geosciml.org/ontology/timescale/thors"
},
"cro": {
"name": "Copyright Ontology",
"prefix": "cro",
"uri_prefix": "http://rhizomik.net/ontologies/copyrightonto.owl#$1",
"description": "The Copyright Ontology is a contribution geared towards the development of copyright-aware Digital Rights Management (DRM) systems.",
"modified": "2019-09-02",
"homepage": "http://rhizomik.net/html/ontologies/copyrightonto/",
"keywords": [
"Multimedia"
]
},
"ac": {
"name": "Core terms defined by Audubon Core",
"prefix": "ac",
"uri_prefix": "http://rs.tdwg.org/ac/terms/$1",
"description": "This term list includes all currently valid terms that have been defined in the core Audubon Core namespace ac:.",
"modified": "2023-05-09",
"keywords": [
"Environment",
"Metadata"
],
"homepage": "http://rs.tdwg.org/ac/terms/"
},
"sao": {
"name": "SALT Annotation Ontology",
"prefix": "sao",
"uri_prefix": "http://salt.semanticauthoring.org/ontologies/sao#$1",
"description": "The SALT Annotation Ontology represents the connection layer between the rhetorical and argumentation and the document structure and content",
"modified": "2009-06-16",
"keywords": [
"Metadata"
],
"homepage": "http://salt.semanticauthoring.org/ontologies/sao"
},
"sdo": {
"name": "SALT Document Ontology",
"prefix": "sdo",
"uri_prefix": "http://salt.semanticauthoring.org/ontologies/sdo#$1",
"description": "The SALT Document Ontology captures the linear structure of the publication, in addition to the identification and revisioning information of the publication's content.",
"modified": "2009-06-16",
"keywords": [
"Catalogs"
],
"homepage": "http://salt.semanticauthoring.org/ontologies/sdo"
},
"mv": {
"name": "MobiVoc: Open Mobility Vocabulary",
"prefix": "mv",
"uri_prefix": "http://schema.mobivoc.org/$1",
"description": "Our goal is to significantly improve the data mobility between all stakeholders by providing a standardized vocabulary using Semantic Web technologies and ontologies. For the open vocabulary covering various mobility aspects we use RDF (Resource Description Framework) - a recommended specification of the World Wide Web Consortium (W3C) and the so-called lingua franca for the integration of data and web. We invite everyone who is interested to join our MobiVoc initiative and to participate in the development of the Open Mobility Vocabulary.",
"modified": "2018-01-18",
"keywords": [
"IoT",
"Services",
"Transport"
],
"homepage": "http://schema.mobivoc.org/"
},
"schema": {
"name": "Schema.org vocabulary",
"prefix": "schema",
"uri_prefix": "http://schema.org/$1",
"description": "Search engines including Bing, Google, Yahoo! and Yandex rely on schema.org markup to improve the display of search results, making it easier for people to find the right web pages.",
"modified": "2020-03-10",
"homepage": "https://schema.org/docs/about.html",
"keywords": [
"General & Upper"
]
},
"odrs": {
"name": "Open Data Rights Statement Vocabulary",
"prefix": "odrs",
"uri_prefix": "http://schema.theodi.org/odrs#$1",
"description": "A vocabulary that supports the publication of Open Data by providing the means to capture machine-readable \"rights statements\", e.g. the licensing information, copyright notices and attribution requirements that are associated with the publication and re-use of a dataset.",
"modified": "2013-07-29",
"keywords": [
"Quality"
],
"homepage": "http://schema.theodi.org/odrs"
},
"maso": {
"name": "S\u00e9curit\u00e9 Agents Mobiles",
"prefix": "maso",
"uri_prefix": "http://securitytoolbox.appspot.com/MASO#$1",
"description": "Ontology for security of mobile agents",
"modified": "2013-05-03",
"keywords": [
"Security"
],
"homepage": "http://securitytoolbox.appspot.com/MASO"
},
"algo": {
"name": "Algorithms Ontology",
"prefix": "algo",
"uri_prefix": "http://securitytoolbox.appspot.com/securityAlgorithms#$1",
"description": "An ontology describing cryptographic algorithms",
"modified": "2015-01-11",
"keywords": [
"Security"
],
"homepage": "http://securitytoolbox.appspot.com/securityAlgorithms#"
},
"security": {
"name": "Security Ontology",
"prefix": "security",
"uri_prefix": "http://securitytoolbox.appspot.com/securityMain#$1",
"description": "A security ontology to annotate resources with security-related information",
"modified": "2015-03-27",
"keywords": [
"Security"
],
"homepage": "http://securitytoolbox.appspot.com/securityMain"
},
"stac": {
"name": "Security Toolbox : Attacks and Countermeasures",
"prefix": "stac",
"uri_prefix": "http://securitytoolbox.appspot.com/stac#$1",
"description": "A vocabulary to describe main security and cryptographic concepts: attacks, security mechanisms, OSI model, security protocols, security tools in numerous technologies: Web applications, network management, Sensor networks, Cellular (2G, 3G, 4G) and Wireless (Wifi), etc.",
"modified": "2013-06-02",
"homepage": "http://securitytoolbox.appspot.com/",
"keywords": [
"Security"
]
},
"sio": {
"name": "Semanticscience Integrated Ontology",
"prefix": "sio",
"uri_prefix": "http://semanticscience.org/resource/$1",
"description": "The semanticscience integrated ontology (SIO) provides a simple, integrated ontology (types, relations) for objects, processes and their attributes. This project provides foundational support for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.",
"modified": "2016-09-27",
"homepage": "http://semanticscience.org",
"keywords": [
"Biology"
]
},
"mdr": {
"name": "The Semantic Turkey metadata registry ontology",
"prefix": "mdr",
"uri_prefix": "http://semanticturkey.uniroma2.it/ns/mdr#$1",
"description": "An application profile of DCAT combining it with other metadata vocabularies (e.g. VoID, DCTERMS, LIME)\n to meet requirements elicited in various use cases of the Semantic Web platform Semantic Turkey",
"modified": "2022-05-06",
"keywords": [
"Metadata"
],
"homepage": "http://semanticturkey.uniroma2.it/ns/mdr"
},
"sem": {
"name": "The SEM Ontology",
"prefix": "sem",
"uri_prefix": "http://semanticweb.cs.vu.nl/2009/11/sem/$1",
"description": "The SEM Ontology defines entities that make up the context of an event: Events, Actors, Places, Times.",
"modified": "2009-11-30",
"keywords": [
"Events"
],
"homepage": "http://semanticweb.cs.vu.nl/2009/11/sem/"
},
"apps4X": {
"name": "The vocabulary for Co-creation Events based on Open Data",
"prefix": "apps4X",
"uri_prefix": "http://semweb.mmlab.be/ns/apps4X#$1",
"description": "apps4X is an RDF vocabulary defined to facilitate the description of Open-Data-based Co-creation events",
"modified": "2014-06-19",
"keywords": [
"RDF"
],
"homepage": "http://semweb.mmlab.be/ns/apps4X"
},
"lc": {
"name": "The Linked Connections ontology",
"prefix": "lc",
"uri_prefix": "http://semweb.mmlab.be/ns/linkedconnections#$1",
"description": "This ontology provides the predicates necessary to describe a connection or hop from one transit stop to another.",
"modified": "2015-07-02",
"keywords": [
"Transport"
],
"homepage": "http://semweb.mmlab.be/ns/linkedconnections#Ontology"
},
"odapps": {
"name": "The vocabulary for (L)OD ideas and applications",
"prefix": "odapps",
"uri_prefix": "http://semweb.mmlab.be/ns/odapps#$1",
"description": "odapps is an RDF vocabulary defined to facilitate the description of Open-Data-based ideas and applications published on the Web.",
"modified": "2014-06-16",
"keywords": [
"RDF"
],
"homepage": "http://semweb.mmlab.be/ns/odapps"
},
"oh": {
"name": "The Opening Hours vocabulary",
"prefix": "oh",
"uri_prefix": "http://semweb.mmlab.be/ns/oh#$1",
"description": "A vocabulary to describe opening hours using calendars (recommended: iCal, RDFCal or schema.org) published on the Web.",
"modified": "2015-05-22",
"homepage": "https://github.com/pietercolpaert/openinghoursontology",
"keywords": [
"Time"
]
},
"st": {
"name": "The Stop Times ontology",
"prefix": "st",
"uri_prefix": "http://semweb.mmlab.be/ns/stoptimes#$1",
"description": "This ontology provides the predicates necessary to describe an arrival of a transit vehicle and its departure at a certain Stop.",
"modified": "2015-09-13",
"keywords": [
"Society",
"Travel"
],
"homepage": "http://semweb.mmlab.be/ns/stoptimes#Ontology"
},
"dqc": {
"name": "The Data Quality Constraints Library",
"prefix": "dqc",
"uri_prefix": "http://semwebquality.org/ontologies/dq-constraints#$1",
"description": "This RDF document contains a library of data quality constraints represented as SPARQL query templates based on the SPARQL Inferencing Framework (SPIN). The data quality constraint templates are especially useful for the identification of data quality problems during data entry and for periodic quality checks during data usage.",
"modified": "2011-03-28",
"keywords": [
"Quality",
"eBusiness"
],
"homepage": "http://semwebquality.org/ontologies/dq-constraints"
},
"ha": {
"name": "Home Activity",
"prefix": "ha",
"uri_prefix": "http://sensormeasurement.appspot.com/ont/home/homeActivity#$1",
"description": "An ontology to detect activity in a smart home",
"modified": "2014-05-12",
"keywords": [
"Environment"
],
"homepage": "http://sensormeasurement.appspot.com/ont/home/homeActivity#"
},
"vra": {
"name": "RDFS Ontology for VRA",
"prefix": "vra",
"uri_prefix": "http://simile.mit.edu/2003/10/ontologies/vraCore3#$1",
"description": "The VRA Core is a set of metadata elements to describe works of visual culture as well as the images that document them.",
"modified": "2003-10-14",
"keywords": [
"Image"
],
"homepage": "http://simile.mit.edu/2003/10/ontologies/vraCore3#"
},
"rsctx": {
"name": "Recommender System Context",
"prefix": "rsctx",
"uri_prefix": "http://softeng.polito.it/rsctx#$1",
"description": "This ontology represent context which may be interesting in providing recommendations to users.",
"modified": "2017-01-17",
"keywords": [
"API",
"Services"
],
"homepage": "http://softeng.polito.it/rsctx"
},
"cwrc": {
"name": "L'Ontologie CWRC",
"prefix": "cwrc",
"uri_prefix": "http://sparql.cwrc.ca/ontologies/cwrc#$1",
"description": "The CWRC Ontology is the ontology of the Canadian Writing Research Collaboratory.",
"modified": "2018-09-30",
"keywords": [
"People",
"Society"
],
"homepage": "http://sparql.cwrc.ca/ontologies/cwrc"
},
"losp": {
"name": "Linked open specialities RF",
"prefix": "losp",
"uri_prefix": "http://sparql.sstu.ru:3030/speciality/$1",
"description": "\u041e\u043d\u0442\u043e\u043b\u043e\u0433\u0438\u044f \"\u0421\u043f\u0435\u0446\u0438\u0430\u043b\u044c\u043d\u043e\u0441\u0442\u0438\" \u043e\u043f\u0438\u0441\u044b\u0432\u0430\u0435\u0442 \u0432\u0441\u0435 \u0432\u043e\u0437\u043c\u043e\u0436\u043d\u044b\u0435 \u0441\u043f\u0435\u0446\u0438\u0430\u043b\u044c\u043d\u043e\u0441\u0442\u0438(\u043d\u0430\u043f\u0440\u0430\u0432\u043b\u0435\u043d\u0438\u044f) \u0432 \u0420\u0424, \u0432 \u043a\u0430\u043a\u0438\u0445 \u0423\u0413\u041d\u0421 \u043e\u043d\u0438 \u0441\u043e\u0441\u0442\u043e\u044f\u0442, \u0430 \u0442\u0430\u043a\u0436\u0435 \u0438\u043d\u0444\u043e\u0440\u043c\u0430\u0446\u0438\u044f \u043e\u0431 \u0438\u0445 \u0441\u0442\u0430\u0440\u044b\u0445 \u043a\u043e\u0434\u0430\u0445/\u0433\u0440\u0443\u043f\u043f\u0430\u0445/\u043d\u0430\u0437\u0432\u0430\u043d\u0438\u044f\u0445.",
"modified": "2017-03-08",
"keywords": [
"Support",
"Tag"
],
"homepage": "http://sparql.sstu.ru:3030/speciality/"
},
"spcm": {
"name": "Software Process Control Model",
"prefix": "spcm",
"uri_prefix": "http://spi-fm.uca.es/spdef/models/deployment/spcm/1.0#$1",
"description": "Planning and monitoring the execution of software projects can be carried out with different supporting tools, from issue tracking systems to Gantt chart tools or even with using simple spreadsheets. This vocabulary includes the common elements for controlling software development or maintenance projects.",
"modified": "2014-01-09",
"homepage": "http://spi-fm.uca.es/spdef/models/deployment/spcm/1.0.html",
"keywords": [
"PLM"
]
},
"swpm": {
"name": "Software Work Product Model",
"prefix": "swpm",
"uri_prefix": "http://spi-fm.uca.es/spdef/models/deployment/swpm/1.0#$1",
"description": "During the modeling of software processes, work products are traditionally treated as atomic units, with names but no structure, and they are generated or changed during the course of the projects. In fact, the language SPEM does not offer mechanisms to detail the structure of work products, allowing only identify whether it is an artifact, a deliverable or an outcome of the project. The typical work products in the software processes are often documents or source code and they are managed from specialized or generic tools. For example, software modeling tools such as Rational Rose, or version control systems such as Git are examples of specialized tools that provide support to the management of certain types of work products. However, other generic tools such as content management systems, document management systems and collaborative editing systems or wikis can also be used to manage evidences of the processes. The design of models for certain types of work products has been an approach used in model-driven web methodologies. However, it is common the need for adapting and customizing well-known methodologies for their application in concrete situations and in specific organizations, a.k.a. process tailoring. Therefore, a vocabulary to define flexible work products in terms of structure and type of its artifacts is proposed here.",
"modified": "2013-12-15",
"keywords": [
"PLM"
],
"homepage": "http://spi-fm.uca.es/spdef/models/deployment/swpm/1.0"
},
"itm": {
"name": "Issue Tracking tool Model",
"prefix": "itm",
"uri_prefix": "http://spi-fm.uca.es/spdef/models/genericTools/itm/1.0#$1",
"description": "This vocabulary defines the common characteristics of task management tools or issue tracking systems, such as Jira, Redmine or Trac.",
"modified": "2014-06-19",
"keywords": [
"PLM"
],
"homepage": "http://spi-fm.uca.es/spdef/models/genericTools/itm/1.0"
},
"vmm": {
"name": "Visual Modeling tool Model",
"prefix": "vmm",
"uri_prefix": "http://spi-fm.uca.es/spdef/models/genericTools/vmm/1.0#$1",
"description": "In Software Engineering, as well as in other disciplines, it is common to use model-editing tools using a visual language. In particular, the editing tools allow you to design UML software models, so that let you manage much of the work products of a project. From the study of several UML tools, such as Enterprise Architect, Visual Paradigm for UML or Rational Rose, this vocabulary has been defined. This vocabulary represents the basic structure of these UML tools, but does not exclude others that allow you to use other visual languages for modeling software systems or other entities.",
"modified": "2013-12-15",
"keywords": [
"PLM"
],
"homepage": "http://spi-fm.uca.es/spdef/models/genericTools/vmm/1.0"
},
"wikim": {
"name": "WIKI tool Model",
"prefix": "wikim",
"uri_prefix": "http://spi-fm.uca.es/spdef/models/genericTools/wikim/1.0#$1",
"description": "From the study of different wiki systems, such as MediaWiki, Confluence or DokuWiki, this vocabulary has designed. Note that this vocabulary does not fully describe the conceptual model of all types of the wiki systems, but only their main elements.",
"modified": "2013-12-15",
"keywords": [
"PLM"
],
"homepage": "http://spi-fm.uca.es/spdef/models/genericTools/wikim/1.0"
},
"sp": {
"name": "SPIN SPARQL Syntax",
"prefix": "sp",
"uri_prefix": "http://spinrdf.org/sp#$1",
"description": "An RDF Schema to syntactically represent SPARQL queries (including SPARQL UPDATE) as RDF triples.",
"modified": "2013-09-13",
"keywords": [
"RDF"
],
"homepage": "http://spinrdf.org/sp"
},
"spin": {
"name": "SPIN Inferencing Vocabulary",
"prefix": "spin",
"uri_prefix": "http://spinrdf.org/spin#$1",
"description": "An RDF Schema that can be used to attach constraints and rules to RDFS classes, and to encapsulate reusable SPARQL queries into functions and templates.",
"modified": "2014-08-28",
"homepage": "http://spinrdf.org/spin.html",
"keywords": [
"RDF"
]
},
"spt": {
"name": "SPITFIRE Ontology",
"prefix": "spt",
"uri_prefix": "http://spitfire-project.eu/ontology/ns/$1",
"description": "TheSPITFIRE Ontology (spt) is based on the alignment among Dolce+DnS Ultralite(dul), the W3C Semantic Sensor Network ontology (ssn) and the Event Model-F ontology (event).",
"modified": "2014-01-14",
"homepage": "http://spitfire-project.eu/incontextsensing/ontology.php",
"keywords": [
"IoT",
"Methods"
]
},
"dfc-b": {
"name": "DFC Business Ontology",
"prefix": "dfc-b",
"uri_prefix": "http://static.datafoodconsortium.org/ontologies/DFC_BusinessOntology.owl#$1",
"description": "DFC Business Ontology",
"modified": "2019-10-21",
"keywords": [
"Food",
"eBusiness"
],
"homepage": "http://static.datafoodconsortium.org/ontologies/DFC_BusinessOntology.owl"
},
"dfc": {
"name": "Data Food Consortium Ontology",
"prefix": "dfc",
"uri_prefix": "http://static.datafoodconsortium.org/ontologies/DFC_FullModel.owl#$1",
"description": "A common vocabulary for digital food platforms",
"modified": "2019-10-21",
"keywords": [
"Food"
],
"homepage": "http://static.datafoodconsortium.org/ontologies/DFC_FullModel.owl"
},
"dfc-p": {
"name": "A common vocabulary for digital food platforms (Product Glossary Part)",
"prefix": "dfc-p",
"uri_prefix": "http://static.datafoodconsortium.org/ontologies/DFC_ProductGlossary.owl#$1",
"description": "A common vocabulary for digital food platforms (Product Glossary Part)",
"modified": "2019-10-21",
"keywords": [
"Food",
"Metadata"
],
"homepage": "http://static.datafoodconsortium.org/ontologies/DFC_ProductGlossary.owl"
},
"dfc-t": {
"name": "A common vocabulary for digital food platforms (Technical Part)",
"prefix": "dfc-t",
"uri_prefix": "http://static.datafoodconsortium.org/ontologies/DFC_TechnicalOntology.owl#$1",
"description": "A common vocabulary for digital food platforms (Technical Part)",
"modified": "2019-10-21",
"keywords": [
"Food",
"Support"
],
"homepage": "http://static.datafoodconsortium.org/ontologies/DFC_TechnicalOntology.owl"
},
"frappe": {
"name": "FraPPE: Frame, Pixel, Place, Event vocabulary",
"prefix": "frappe",
"uri_prefix": "http://streamreasoning.org/ontologies/frappe#$1",
"description": "FraPPE is a vocabulary to enable Visual Analytics operations on geo-spatial time varying data. By enabling Visual Analytics instruments FraPPE ease the capture, correlation and comparison operations on geo-spatial data from different sources evolving over time",
"modified": "2015-04-28",
"keywords": [
"Geography",
"Multimedia"
],
"homepage": "http://streamreasoning.org/ontologies/frappe#"
},
"swpo": {
"name": "Semantic Web Portal Ontology",
"prefix": "swpo",
"uri_prefix": "http://sw-portal.deri.org/ontologies/swportal#$1",
"description": "The aim of the Semantic Web Portal Ontology is to serve as the conceptual backbone for community portals driven by Semantic Web technologies.",
"modified": "2004-10-20",
"keywords": [
"Society"
],
"homepage": "http://sw-portal.deri.org/ontologies/swportal"
},
"bot": {
"name": "BotDCAT-AP - Data Catalogue vocabulary Application Profile for chatbots",
"prefix": "bot",
"uri_prefix": "http://swa.cefriel.it/ontologies/botdcat-ap#$1",
"description": "A vocabulary to describe data sources in a way they can be easily reused and accessed by chatbots.",
"modified": "2017-04-01",
"keywords": [
"Catalogs",
"Services"
],
"homepage": "http://swa.cefriel.it/ontologies/botdcat-ap"
},
"swrc": {
"name": "Semantic Web for Research Communities",
"prefix": "swrc",
"uri_prefix": "http://swrc.ontoware.org/ontology#$1",
"description": "An ontology for modeling entities of research communities such as persons, organisations, publications (bibliographic metadata) and their relationship",
"modified": "2007-06-22",
"homepage": "http://ontoware.org/swrc",
"keywords": [
"Academy"
]
},
"taxref-ld": {
"name": "TAXREF-LD Ontology",
"prefix": "taxref-ld",
"uri_prefix": "http://taxref.mnhn.fr/lod/$1",
"description": "Repr\u00e9sentation du r\u00e9f\u00e9rentiel taxonomique TAXREF comme un jeu de donn\u00e9es li\u00e9es. Cette ressource est \u00e0 la fois une ontologies des classes repr\u00e9sentant les taxons, et un th\u00e9saurus (SKOS concept scheme) des noms scientifiques d\u00e9signant ces taxons.",
"modified": "2022-07-29",
"keywords": [
"Biology",
"Environment"
],
"homepage": "http://taxref.mnhn.fr/lod/taxref-ld"
},
"dave": {
"name": "Data Value Vocabulary (DaVe)",
"prefix": "dave",
"uri_prefix": "http://theme-e.adaptcentre.ie/dave#$1",
"description": "The Data Value Vocabulary (DaVe) is an extensible core vocabulary that allows user to use custom data value dimensions and metrics to characterise data value in a specific context. This flexibility allows for the comprehensive modelling of data value. As a data value model, DaVe allows users to monitor data value as it occurs within a data exploitation or value creation process (data value chain)",
"modified": "2017-11-30",
"homepage": "http://theme-e.adaptcentre.ie/dave/",
"keywords": [
"General & Upper",
"Geometry",
"IoT"
]
},
"tp": {
"name": "Tourpedia Ontology",
"prefix": "tp",
"uri_prefix": "http://tour-pedia.org/download/tp.owl#$1",
"description": "A vocabulary to describe touristic places: accommodations, points of interest, restaurants and attractions.",
"modified": "2015-06-08",
"keywords": [
"Events",
"Travel"
],
"homepage": "http://tour-pedia.org/download/tp.owl"
},
"umbel": {
"name": "Upper Mapping and Binding Exchange Layer",
"prefix": "umbel",
"uri_prefix": "http://umbel.org/umbel#$1",
"description": "UMBEL provides a general vocabulary of classes and predicates for describing domain ontologies, with the specific aim of promoting interoperability with external datasets and domains.",
"modified": "2014-08-28",
"keywords": [
"General & Upper"
],
"homepage": "http://umbel.org/umbel"
},
"uri4uri": {
"name": "URI Vocabulary",
"prefix": "uri4uri",
"uri_prefix": "http://uri4uri.net/vocab#$1",
"description": "This vocabulary describes the entities which may be derived from a URI and the relationships between them, such as Internet Domains, prototcols, file suffixes etc. It was initially issued as part of an April 1st gag, but has utility beyond the initial joke.",
"modified": "2013-04-01",
"keywords": [
"API"
],
"homepage": "http://uri4uri.net/vocab"
},
"doap": {
"name": "Description of a Project vocabulary",
"prefix": "doap",
"uri_prefix": "http://usefulinc.com/ns/doap#$1",
"description": "The Description of a Project (DOAP) vocabulary, described using W3C RDF Schema and the Web Ontology Language.",
"modified": "2012-01-04",
"homepage": "https://github.com/edumbill/doap/wiki",
"keywords": [
"Society"
]
},
"hto": {
"name": "Haystack Tagging Ontology",
"prefix": "hto",
"uri_prefix": "http://vcharpenay.github.io/hto/hto.xml#$1",
"description": "The Haystack Tagging Ontology is an OWL ontology for Project Haystack, a domain vocabulary for Building Automation Systems.",
"modified": "2016-10-20",
"homepage": "http://project-haystack.org/",
"keywords": [
"Industry"
]
},
"vivo": {
"name": "VIVO Core Ontology",
"prefix": "vivo",
"uri_prefix": "http://vivoweb.org/ontology/core#$1",
"description": "An ontology of academic and research domain, developed in the framework of the VIVO project",
"modified": "2014-07-12",
"homepage": "http://www.vivoweb.org/download",
"keywords": [
"Academy"
]
},
"voag": {
"name": "Vocabulary Of Attribution and Governance",
"prefix": "voag",
"uri_prefix": "http://voag.linkedmodel.org/voag#$1",
"description": "VOAG is intended to specify licensing, attribution, provenance and governance of an ontology.",
"modified": "2012-11-01",
"keywords": [
"Quality"
],
"homepage": "http://voag.linkedmodel.org/schema/voag"
},
"drm": {
"name": "Data Reference Model",
"prefix": "drm",
"uri_prefix": "http://vocab.data.gov/def/drm#$1",
"description": "A metamodel for government data",
"modified": "2012-03-17",
"homepage": "http://vocab.data.gov/def/drm.html",
"keywords": [
"General & Upper"
]
},
"fea": {
"name": "Federal Enterprise Architecture Vocabulary",
"prefix": "fea",
"uri_prefix": "http://vocab.data.gov/def/fea#$1",
"description": "To facilitate efforts to transform the Federal Government to one that is citizen-centered, results-oriented, and market-based, the Office of Management and Budget (OMB) is developing the Federal Enterprise Architecture (FEA), a business-based framework for Governmentwide improvement.",
"modified": "2015-06-26",
"keywords": [
"Government"
],
"homepage": "http://vocab.data.gov/def/fea"
},
"gd": {
"name": "Government Data Vocabulary",
"prefix": "gd",
"uri_prefix": "http://reference.data.gov/def/govdata/$1",
"description": "A RDF Schema that defines concepts and relationships common to all Open Government Data",
"modified": "2011-11-21",
"homepage": "http://vocab.data.gov/gd.html",
"keywords": [
"Government"
]
},
"hosp": {
"name": "Hospital Vocabulary",
"prefix": "hosp",
"uri_prefix": "http://health.data.gov/def/hospital/$1",
"description": "A RDF Schema that defines concepts and relationships used for Hospital data.",
"modified": "2015-09-30",
"keywords": [
"Health"
],
"homepage": "http://vocab.data.gov/hosp"
},
"datex": {
"name": "Linked Datex II",
"prefix": "datex",
"uri_prefix": "http://vocab.datex.org/terms#$1",
"description": "This document gives URIs to all terms used within Datex II. the Datex standard was developed for information exchange between traffic management centres, traffic information centres and service providers in Europe",
"modified": "2016-06-13",
"keywords": [
"Government",
"Services",
"Travel"
],
"homepage": "http://vocab.datex.org/terms#"
},
"br": {
"name": "Brainstorm Ontology",
"prefix": "br",
"uri_prefix": "http://vocab.deri.ie/br#$1",
"description": "A lightweight ontology to structure e- brainstorming sessions",
"modified": "2011-07-09",
"keywords": [
"Society"
],
"homepage": "http://vocab.deri.ie/br"
},
"c4n": {
"name": "Call for Anything vocabulary",
"prefix": "c4n",
"uri_prefix": "http://vocab.deri.ie/c4n#$1",
"description": "A vocabulary to describe calls, such as call for tenders, call for proposals, call for papers, etc.",
"modified": "2010-02-04",
"keywords": [
"Contracts"
],
"homepage": "http://vocab.deri.ie/c4n"
},
"cogs": {
"name": "COGS Vocabulary",
"prefix": "cogs",
"uri_prefix": "http://vocab.deri.ie/cogs#$1",
"description": "Vocabulary for describing ETL and data transformation activities.",
"modified": "2014-03-10",
"homepage": "http://vocab.deri.ie/cogs.html",
"keywords": [
"RDF"
]
},
"csp": {
"name": "Constraint Satisfaction Problems Vocabulary",
"prefix": "csp",
"uri_prefix": "http://vocab.deri.ie/csp#$1",
"description": "A vocabulary to represent Constraint Satisfaction Problems (CSPs) in which constraints are expressed by Boolean expressions on fluents.",
"modified": "2011-06-29",
"keywords": [
"Industry"
],
"homepage": "http://vocab.deri.ie/csp"
},
"dady": {
"name": "Dataset Dynamics (dady) vocabulary",
"prefix": "dady",
"uri_prefix": "http://purl.org/NET/dady#$1",
"description": "A vocabulary that allows for coarse-grained descriptions of the data-source dynamics as well as the discovery of change notification mechanism(s).",
"modified": "2010-01-27",
"keywords": [
"RDF"
],
"homepage": "http://vocab.deri.ie/dady"
},
"odapp": {
"name": "Open Data Applications Vocabulary",
"prefix": "odapp",
"uri_prefix": "http://vocab.deri.ie/odapp#$1",
"description": "Un premier jet d'un vocabulaire pour d\u00e9crire les applications bas\u00e9es sur des donn\u00e9es open data. Ces applications sont typiquement list\u00e9es sur les catalogues d'open data gouvernementaux, ou dans les concours d'application open data.",
"modified": "2012-07-17",
"keywords": [
"API"
],
"homepage": "http://vocab.deri.ie/odapp"
},
"orca": {
"name": "orca, the Ontology of Reasoning, Certainty and Attribution",
"prefix": "orca",
"uri_prefix": "http://vocab.deri.ie/orca#$1",
"description": "orca, the Ontology of Reasoning, Certainty and Attribution, is an ontology for characterizing the certainty of information, how it is known, and its source",
"modified": "2012-11-09",
"homepage": "http://vocab.deri.ie/orca.html",
"keywords": [
"Metadata"
]
},
"pdo": {
"name": "Project Documents Ontology",
"prefix": "pdo",
"uri_prefix": "http://ontologies.smile.deri.ie/pdo#$1",
"description": "The Project Documents Ontology models the inherent structure and concepts of various documents in a project-specific setting, like meeting minutes, status reports etc.",
"modified": "2010-07-09",
"homepage": "http://vocab.deri.ie/pdo",
"keywords": [
"Society"
]
},
"ppo": {
"name": "Privacy Preference Ontology",
"prefix": "ppo",
"uri_prefix": "http://vocab.deri.ie/ppo#$1",
"description": "An ontology to create privacy preferences for Linked Data",
"modified": "2013-11-13",
"keywords": [
"API"
],
"homepage": "http://vocab.deri.ie/ppo"
},
"raul": {
"name": "RAUL Vocabulary",
"prefix": "raul",
"uri_prefix": "http://purl.org/NET/raul#$1",
"description": "A vocabulary to describe Web form widgets. Strongly aligned with the meta model of HTML Web forms. A RESTful service that can render HTML Web forms from RaUL models can be found at: http://w3c.org.au/raul",
"modified": "2013-02-22",
"homepage": "http://vocab.deri.ie/raul.html",
"keywords": [
"API"
]
},
"rooms": {
"name": "Buildings and Rooms Vocabulary",
"prefix": "rooms",
"uri_prefix": "http://vocab.deri.ie/rooms#$1",
"description": "A simple vocabulary for describing the rooms in a building.",
"modified": "2012-10-02",
"homepage": "http://vocab.deri.ie/rooms.html",
"keywords": [
"Environment",
"Geography"
]
},
"scovo": {
"name": "The Statistical Core Vocabulary",
"prefix": "scovo",
"uri_prefix": "http://purl.org/NET/scovo#$1",
"description": "A vocabulary for representing statistical data on the Web. Note :The SCOVO vocabulary is deprecated. We strongly advise to use the Data Cube Vocabulary instead.",
"modified": "2012-08-09",
"keywords": [
"Methods"
],
"homepage": "http://vocab.deri.ie/scovo"
},
"scsv": {
"name": "Schema.org CSV",
"prefix": "scsv",
"uri_prefix": "http://purl.org/NET/schema-org-csv#$1",
"description": "Mapping vocabulary for CSV files that use Schema.org terms in the header.",
"modified": "2012-05-22",
"keywords": [
"CSV"
],
"homepage": "http://vocab.deri.ie/scsv"
},
"search": {
"name": "Sindice Search Vocabulary",
"prefix": "search",
"uri_prefix": "http://sindice.com/vocab/search#$1",
"description": "A vocabulary for ranked search results, for use in the Sindice API.",
"modified": "2013-02-22",
"homepage": "http://vocab.deri.ie/search.html",
"keywords": [
"API"
]
},
"tao": {
"name": "Trust Assertion Ontology",
"prefix": "tao",
"uri_prefix": "http://vocab.deri.ie/tao#$1",
"description": "TAO is a light-weight vocabulary to describe asserted user\u2019s subjective trust values.",
"modified": "2013-02-22",
"homepage": "http://vocab.deri.ie/tao.html",
"keywords": [
"Quality"
]
},
"void": {
"name": "Vocabulary of Interlinked Datasets",
"prefix": "void",
"uri_prefix": "http://rdfs.org/ns/void#$1",
"description": "The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets.",
"modified": "2011-03-06",
"homepage": "http://www.w3.org/TR/void/",
"keywords": [
"Metadata"
]
},
"gvp": {
"name": "Getty Vocabulary Program ontology",
"prefix": "gvp",
"uri_prefix": "http://vocab.getty.edu/ontology#$1",
"description": "The GVP Ontology defines classes, properties and values (skos:Concepts) used in GVP LOD. It is complete regarding AAT and TGN (as of version 2.0), and will be extended in time with more elements needed for the other GVP vocabularies (ULAN, CONA).",
"modified": "2015-03-25",
"keywords": [
"Vocabularies"
],
"homepage": "http://vocab.getty.edu/ontology"
},
"gtfs": {
"name": "General Transit Feed Specification",
"prefix": "gtfs",
"uri_prefix": "http://vocab.gtfs.org/terms#$1",
"description": "This ontology is a translation of the General Transit Feed Specification towards URIs. Its intended use is creating an exchange platform where the Linked GTFS model can be used as a start to get the right data into the right format.",
"modified": "2014-10-27",
"homepage": "https://raw.githubusercontent.com/OpenTransport/vocabulary/master/gtfs/gtfs.ttl",
"keywords": [
"Travel"
]
},
"geod": {
"name": "Landinndelingen i Norge",
"prefix": "geod",
"uri_prefix": "http://vocab.lenka.no/geo-deling#$1",
"description": "Dette er et vokabular for administrativ inndeling av Norge, matrikkelen, steder og andre geografiske ting.",
"modified": "2012-10-11",
"keywords": [
"Geography"
],
"homepage": "http://vocab.lenka.no/geo-deling"
},
"transit": {
"name": "TRANSIT",
"prefix": "transit",
"uri_prefix": "http://vocab.org/transit/terms/$1",
"description": "A vocabulary for describing transit systems and routes",
"modified": "2011-03-28",
"keywords": [
"Travel"
],
"homepage": "http://vocab.org/transit/terms/"
},
"whisky": {
"name": "Whisky Ontology",
"prefix": "whisky",
"uri_prefix": "http://vocab.org/whisky/terms/$1",
"description": "A small vocabulary for describing whisky varieties",
"modified": "2008-09-25",
"keywords": [
"Food"
],
"homepage": "http://vocab.org/whisky/terms"
},
"comm": {
"name": "Vocabulary related to incident communication",
"prefix": "comm",
"uri_prefix": "http://vocab.resc.info/communication#$1",
"description": "This vocabulary is intended to describe all the aspects which are needed to communicate incident related information for fire department services",
"modified": "2014-09-12",
"keywords": [
"Society"
],
"homepage": "http://vocab.resc.info/communication"
},
"incident": {
"name": "Vocabulary to describe incident response by emergency services",
"prefix": "incident",
"uri_prefix": "http://vocab.resc.info/incident#$1",
"description": "Vocabulary to describe the response to a incident by emergency services.\nThis is NOT intended to describe the incident itself, it describes the response",
"modified": "2015-06-22",
"keywords": [
"Methods"
],
"homepage": "http://vocab.resc.info/incident"
},
"vrank": {
"name": "Vocabulary for Ranking",
"prefix": "vrank",
"uri_prefix": "http://purl.org/voc/vrank#$1",
"description": "The Vocabulary for Ranking (vRank) is an RDF Schema vocabulary for materializing ranking computations.",
"modified": "2014-06-10",
"keywords": [
"Methods"
],
"homepage": "http://vocab.sti2.at/vrank"
},
"amlo-core": {
"name": "AMLO-core vocabulary",
"prefix": "amlo-core",
"uri_prefix": "http://w3id.org/amlo/core#$1",
"description": "The AMLO-core is the main module of the AMLO projects that extends the Financial Industry Business Ontology (FIBO) with some concepts to describe the Anti Money Laundering (AML) knowledge and facts.",
"modified": "2020-01-01",
"keywords": [
"Industry",
"Services"
],
"homepage": "http://w3id.org/amlo/core"
},
"jup": {
"name": "Ontology of Building Accessibility",
"prefix": "jup",
"uri_prefix": "http://w3id.org/charta77/jup/$1",
"description": "Slovnik prisupnosti budov vznikl v ramci projektu Mapy bez barier, ktery realizuje Nadace Charty 77 - Konto Bariery. Vychazi z Metodiky kategorizace pristupnosti objektu, je vsak doplnen i o entity vyplyvajici z pozadavku projektu. Tento slovnik je i tematem diplomove prace Ontologie pristupnosti budov. Projekt je spolufinancovan z prostredku Evropske unie, Evropskeho fondu pro regionalni rozvoj.",
"modified": "2016-07-14",
"keywords": [
"Society"
],
"homepage": "http://w3id.org/charta77/jup"
},
"dstv": {
"name": "DSTV:Steel Construction Ontology",
"prefix": "dstv",
"uri_prefix": "http://w3id.org/dstv#$1",
"description": "DSTV ontology",
"modified": "2023-02-28",
"keywords": [
"Environment",
"Industry"
],
"homepage": "http://w3id.org/dstv"
},
"dt": {
"name": "Data Template (DT) Ontology",
"prefix": "dt",
"uri_prefix": "https://w3id.org/dt#$1",
"description": "The Data Template (DT) Ontology is based on concepts and principles for creating templates from ISO 23387 and the associated XML data schema, which is currently under development.",
"modified": "2024-06-11",
"keywords": [
"Metadata",
"Methods"
],
"homepage": "http://w3id.org/dt"
},
"bato": {
"name": "Battery Testing Ontology",
"prefix": "bato",
"uri_prefix": "http://w3id.org/emmo-bto/bto#$1",
"description": "The Battery Testing Ontology (BTO) is an application-level ontology belonging to EMMO's ecosystem, meant to model battery testing methodologies and techniques, like the partial discharge test. BTO is connected and aligned with a number of EMMO-based ontologies, including CHAMEO, Battery Domain Ontology and Electrochemistry.",
"modified": "2024-04-12",
"keywords": [
"Industry"
],
"homepage": "http://w3id.org/emmo-bto/bto"
},
"hpo": {
"name": "Hyperdimensional Polymer Ontology",
"prefix": "hpo",
"uri_prefix": "http://w3id.org/emmo-hpo/hpo#$1",
"description": "An ontology to capture the staggering diversity of polymeric materials and their applications.",
"modified": "2024-04-12",
"keywords": [
"Industry"
],
"homepage": "http://w3id.org/emmo-hpo/hpo"
},
"experts": {
"name": "MAEO - MarketPlace Agent and Expert Ontology",
"prefix": "experts",
"uri_prefix": "http://w3id.org/emmo-maeo/maeo#$1",
"description": "The MarketPlace Agent and Expert Ontology (MAEO) is an ontology for modeling experts, expertise, and more broadly, knowledge providers and knowledge seekers for the subject areas of Materials Modeling. MAEO is an EMMO-compliant application ontology, and has been loosely aligned with a number of existing ontologies, including Friend-Of-A-Friend (FOAF) and five recently-developed EMMO-based domain ontologies for the classification of materials, models, manufacturing processes, characterization methods and software products related to Materials Modeling.",
"modified": "2024-04-12",
"keywords": [
"Industry"
],
"homepage": "http://w3id.org/emmo-maeo/maeo"
},
"ioc": {
"name": "IOC: Internet of Construction Ontology",
"prefix": "ioc",
"uri_prefix": "http://w3id.org/ioc#$1",
"description": "The Internet of Construction Ontology (IoC) construction process ontology is intended to represent a comprehensive solution of how processes in the construction industry can be modelled. Due to the iterative nature of creating an ontology, the construction process ontology presented here can at best be considered a working state at the time of publication. Our approach emphasizes the simplest and most comprehensive mapping possible, which is only extended based on insights from practical use when otherwise compelling limitations in usability and applicability arise. Thus, the extension and refinement of the developed construction process ontology strongly depends on the integration of further areas of the construction value chain and the connection of further domain ontologies.",
"modified": "2024-01-30",
"keywords": [
"Industry",
"Methods"
],
"homepage": "http://w3id.org/ioc"
},
"medred": {
"name": "MedRed ontology: clinical data acquisition model",
"prefix": "medred",
"uri_prefix": "http://w3id.org/medred/medred#$1",
"description": "Cette ontologie a \u00e9t\u00e9 con\u00e7ue pour representer des Instruments pour l'aquisition de donn\u00e9es cliniques, dans le contexte du projet MedRed project (https://www.hevs.ch/en/rad-institutes/institute-of-information-systems/projects/medical-research-data-acquisition-platform-14092)",
"modified": "2017-05-08",
"keywords": [
"Biology",
"Health"
],
"homepage": "http://w3id.org/medred/medred#"
},
"m4i": {
"name": "Metadata4Ing: An ontology for describing the generation of research data within a scientific activity.",
"prefix": "m4i",
"uri_prefix": "http://w3id.org/nfdi4ing/metadata4ing#$1",
"description": "Metadata4Ing defines classes and properties or reuses such classes and properties from other ontologies to describe research processes and research data management in NFDI4Ing. \nNew concepts and properties are located in the namespace of Metadata4Ing.\nMetadata4Ing does not import complete ontologies for the sake of relevance, readability, understandability and usability by and for engineers.\nInstead, it tries to make re-use of existing identifiers for classes and properties by re-using all or a relevant subset of the axioms from the original ontology.\nThese statements have been extracted in different ways, e.g. by using Prot\u00e9g\u00e9 tools importing an ontology and copying axioms of relevant items to Metadata4Ing or by download from data services or raw files of ontologies and manual copypasting.\nIn some cases there was a need to extend or modify the original set of statements about an entity, e.g. because labels and definitions were expressed with a different owl:AnnotationProperty than the rest of Metadata4Ing, or because a skos:preflabel or a skos:definition in any of the languages we would like to support was missing.\nAny editorial changes on elements from external ontologies are declared in Metadata4Ing by an annotation with skos:editorialNote at item-level.\nTo get the original set of statements we encourage to visit the original namespace of the respective item.\nMetadata4Ing reuses elements from the following ontologies:\n- BIBO = Bibliographic Ontology \n- BIRO = Bibliographic Reference Ontology \n- DCAT = Data Catalog \n- DCTERMS = Dublin Core Terms \n- FOAF = Friend of a Friend \n- OWL = Web Ontology Language \n- PROV = Provenance Namespace \n- QUDT = Quantities, Units, Dimensions and Types \n- RDF = Resource Description Framework \n- RDFS = RDF Schema \n- SCHEMA = schema.org \n- SKOS = Simple Knowledge Organization System \n- SSN = Semantic Sensor Network Ontology \n- VANN = Vocabulary for Annotating vocabulary descriptions \n- XSD = XML Schema Definition \n- EMMO = European Materials and Modelling Ontology \n- BFO = Basic Formal Ontology \n- RO = Relation Ontology \n- PIMS-II = PIMS Interoperability Infrastructure \n- D-SI = Digital System of Units",
"modified": "2023-09-27",
"homepage": "https://nfdi4ing.pages.rwth-aachen.de/metadata4ing/metadata4ing/",
"keywords": [
"Academy",
"Metadata"
]
},
"rml-cc": {
"name": "RML-Containers",
"prefix": "rml-cc",
"uri_prefix": "http://w3id.org/rml/$1",
"description": "RML module to generate RDF collections and containers",
"modified": "2023-06-15",
"keywords": [
"RDF",
"W3C Rec"
],
"homepage": "http://w3id.org/rml/cc/"
},
"rml": {
"name": "RML: Generic Mapping Language for RDF",
"prefix": "rml",
"uri_prefix": "http://w3id.org/rml/$1",
"description": "Generic Mapping Language for RDF (RDB/CSV/TSV/XML/JSON/... to RDF) - Vocabulary description",
"modified": "2023-06-15",
"keywords": [
"RDF",
"W3C Rec"
],
"homepage": "http://w3id.org/rml/core"
},
"rml-fnml": {
"name": "RML-FNML",
"prefix": "rml-fnml",
"uri_prefix": "http://w3id.org/rml/$1",
"description": "RML-FNML provides data transformations for generating knowledge graphs from (semi-)structured data",
"modified": "2023-06-15",
"keywords": [
"RDF",
"W3C Rec"
],
"homepage": "http://w3id.org/rml/fnml/"
},
"rml-io": {
"name": "RML-IO: Source and Target",
"prefix": "rml-io",
"uri_prefix": "http://w3id.org/rml/$1",
"description": "RML-IO enables the description of input data sources and target output data serialization",
"modified": "2023-06-15",
"keywords": [
"RDF",
"W3C Rec"
],
"homepage": "http://w3id.org/rml/io/"
},
"rml-star": {
"name": "RML-star",
"prefix": "rml-star",
"uri_prefix": "http://w3id.org/rml/$1",
"description": "RML module for generating RDF-star graphs",
"modified": "2023-06-15",
"keywords": [
"RDF",
"W3C Rec"
],
"homepage": "http://w3id.org/rml/star/"
},
"roh": {
"name": "The ASIO ontology",
"prefix": "roh",
"uri_prefix": "http://w3id.org/roh#$1",
"description": "An ontology to address the Research Management of the CRUE's Spanish University System (Sistema Universitario Espa\u00f1ol) by applying an encompassing model not only capable of addressing the universities of the CRUE but also more belonging to the European Union.",
"modified": "2022-01-01",
"keywords": [
"Academy",
"Support"
],
"homepage": "http://w3id.org/roh"
},
"vocals": {
"name": "VoCaLS: A Vocabulary and Catalog for Linked Streams",
"prefix": "vocals",
"uri_prefix": "http://w3id.org/rsp/vocals#$1",
"description": "This ontology aims to model RDF streams, their metadata, and access endpoints for publishing and consuming these streams",
"modified": "2017-12-10",
"keywords": [
"IoT"
],
"homepage": "http://w3id.org/rsp/vocals#"
},
"cbcm": {
"name": "The European Union Company Mobility Ontology (EUCM ontology)",
"prefix": "cbcm",
"uri_prefix": "http://w3id.org/um/cbcm/eu-cm-ontology#$1",
"description": "This ontology describes terms concerning companies, their cross-border movements within the European Union (EU), and associated EU company legislation.",
"modified": "2021-12-10",
"keywords": [
"Society",
"eBusiness"
],
"homepage": "http://w3id.org/um/cbcm/eu-cm-ontology"
},
"fel": {
"name": "A Fine-grained Entity Linking vocabulary",
"prefix": "fel",
"uri_prefix": "http://w3id.org/vcb/fel#$1",
"description": "This RDF vocabulary can be use to describe and categorize annotations involving entity mentions (sub-strings of text) that link to knowledgebase identifiers",
"modified": "2019-10-24",
"keywords": [
"Vocabularies"
],
"homepage": "http://w3id.org/vcb/fel#"
},
"vir": {
"name": "VIR - Visual Representation ontology",
"prefix": "vir",
"uri_prefix": "http://w3id.org/vir#$1",
"description": "This ontology, called VIR, is an extension of CIDOC-CRM created to sustain propositions on the nature of visual elements and permit these descriptions to be published on the Web.\nWith the term visual element, we refer to those signs identified in the visual space as distinct and documentable units, and subject to an analytical interpretation.\nThe scope of this ontology is to s to provide a framework to support the identification, annotation and interconnections between diverse visual elements and presents and assist their documentation and retrieval. Specifically, the model aims to clarify the identity and the relation of these visual signs, providing the necessary classes to characterise their constituent elements, reference, symbolic content and source of interpretation.\nVIR expands on key entities and properties from CIDOC-CRM, introducing new classes and relationships responding to the visual and art historical community, specifically building up on the iconographical tradition. The result is a model which differentiates between interpretation and element identified, providing a clear distinction between denotation and signification of an element. As a consequence of such distinction, the ontology allows for the definition of diverse denotative criteria for the same representation, which could change based on traditions and perspective. Visual objects can be, in fact, polysemic and ambiguous, and it is not so easy to pin down a denotative or connotative meaning because they are very much context-dependent.",
"modified": "2019-02-26",
"keywords": [
"Multimedia"
],
"homepage": "http://w3id.org/vir#"
},
"wikibase": {
"name": "Wikibase system ontology",
"prefix": "wikibase",
"uri_prefix": "http://wikiba.se/ontology#$1",
"description": "The system ontology of Wikibase",
"modified": "2021-12-05",
"homepage": "shorturl.at/jkGVZ",
"keywords": [
"Metadata",
"Multimedia"
]
},
"agls": {
"name": "AGLS Metadata Terms",
"prefix": "agls",
"uri_prefix": "http://www.agls.gov.au/agls/terms/$1",
"description": "The AGLS Metadata Terms Namespace provides URIs for the AGLS Metadata Terms Vocabulary in the context of AGLS Metadata Standard, a set of metadata properties and associated usage guidelines to improve the visibility, manageability and interoperability of online information and services. Vocabulary terms are declared using RDF Schema language to support RDF applications. It will be updated according to AGLS Working Group decisions.",
"modified": "2010-06-30",
"homepage": "https://agls.gov.au/schemas/rdfs/",
"keywords": [
"Metadata"
]
},
"akt": {
"name": "AKT Reference Ontology",
"prefix": "akt",
"uri_prefix": "http://www.aktors.org/ontology/portal#$1",
"description": "The AKT Reference Ontology has been designed to support the AKT-2 demonstrator (\"AKTive Portal\"), and subsequent activities. The ontology, designed by the AKT-2 group and codified by Enrico Motta, extends Version 1.",
"modified": "2003-02-10",
"homepage": "http://d3e.open.ac.uk/akt/2002/ref-onto.html",
"keywords": [
"Society"
]
},
"akts": {
"name": "AKT Support Ontology",
"prefix": "akts",
"uri_prefix": "http://www.aktors.org/ontology/support#$1",
"description": "The AKT Reference Ontology has been designed to support the AKT-2 demonstrator (\"AKTive Portal\"), and subsequent activities",
"modified": "2003-02-10",
"keywords": [
"Support"
],
"homepage": "http://www.aktors.org/ontology/support"
},
"arp": {
"name": "Arpenteur Ontology",
"prefix": "arp",
"uri_prefix": "http://www.arpenteur.org/ontology/Arpenteur.owl#$1",
"description": "Arpenteur ontology is dedicated to photogrammetry, archeology and oceanology communities \n\t in order to perform tasks such as image processing, photogrammetry and modelling.",
"modified": "2018-01-15",
"keywords": [
"Geography",
"Geometry"
],
"homepage": "http://www.arpenteur.org/ontology/Arpenteur.owl"
},
"bbc": {
"name": "BBC Ontology",
"prefix": "bbc",
"uri_prefix": "http://www.bbc.co.uk/ontologies/bbc/$1",
"description": "The BBC ontology is used to describe BBC concepts in the store. For example, the BBC divisions (products) publishing linked data and interfacing with the triplestore, the platforms for which we produce content and the web documents that publish or are relevant to the BBC's content.",
"modified": "2015-03-19",
"keywords": [
"Press"
],
"homepage": "http://www.bbc.co.uk/ontologies/bbc"
},
"bbccms": {
"name": "BBC CMS Ontology",
"prefix": "bbccms",
"uri_prefix": "http://www.bbc.co.uk/ontologies/cms/$1",
"description": "An ontology to represent the content management systems and their interaction with the triplestore.",
"modified": "2016-02-01",
"keywords": [
"API"
],
"homepage": "http://www.bbc.co.uk/ontologies/cms"
},
"bbccore": {
"name": "BBC Core Concepts",
"prefix": "bbccore",
"uri_prefix": "http://www.bbc.co.uk/ontologies/coreconcepts/$1",
"description": "The generic BBC ontology for people, places,events, organisations, themes which represent things that make sense across the BBC. This model is meant to be generic enough, and allow clients (domain experts) link their own concepts",
"modified": "2016-05-10",
"keywords": [
"General & Upper"
],
"homepage": "http://www.bbc.co.uk/ontologies/coreconcepts"
},
"cwork": {
"name": "Creative Work Ontology",
"prefix": "cwork",
"uri_prefix": "http://www.bbc.co.uk/ontologies/creativework/$1",
"description": "This ontology defines the terms required to describe the creative works produced by the BBC and their associated metadata.",
"modified": "2016-02-01",
"keywords": [
"Catalogs"
],
"homepage": "http://www.bbc.co.uk/ontologies/creativework"
},
"bbcprov": {
"name": "BBC Provenance Ontology",
"prefix": "bbcprov",
"uri_prefix": "http://www.bbc.co.uk/ontologies/provenance/$1",
"description": "The provenance ontology supports data management and auditing tasks. It is used to define the different types of named graphs we used in the store (quad store) and enables their association with metadata that allow us to manage, validate and expose data to BBC services",
"modified": "2015-08-11",
"keywords": [
"Quality"
],
"homepage": "http://www.bbc.co.uk/ontologies/provenance"
},
"sport": {
"name": "BBC Sport Ontology",
"prefix": "sport",
"uri_prefix": "http://www.bbc.co.uk/ontologies/sport/$1",
"description": "A simple ontology for representing competitive sports events.",
"modified": "2016-01-01",
"keywords": [
"Events"
],
"homepage": "http://www.bbc.co.uk/ontologies/sport"
},
"biopax": {
"name": "BioPAX Level 3 ontology",
"prefix": "biopax",
"uri_prefix": "http://www.biopax.org/release/biopax-level3.owl#$1",
"description": "The goal of the BioPAX group is to develop a common exchange format for biological pathway data. More information is available at http://www.biopax.org. This ontology is freely available under the LGPL license",
"modified": "2010-07-20",
"keywords": [
"Biology"
],
"homepage": "http://www.biopax.org/release/biopax-level3.owl"
},
"blt": {
"name": "British Library Terms RDF schema",
"prefix": "blt",
"uri_prefix": "http://www.bl.uk/schemas/bibliographic/blterms#$1",
"description": "Some useful terms for describing bibliographic resources that other models did not include. Version 1.4: brings the description for this schema in line with \"Metadata recommendations for Linked Open Vocabulairies\", version 1.1.; dct:license replaced by cc:license and the value changed from http://www.opendatacommons.org/licenses/pddl/1.0/ to http://creativecommons.org/publicdomain/mark/1.0/; various typos corrected. Version 1.4.1: added links to previous schema versions",
"modified": "2013-10-03",
"keywords": [
"Catalogs"
],
"homepage": "http://www.bl.uk/schemas/bibliographic/blterms"
},
"crm": {
"name": "CIDOC Conceptual Reference Model",
"prefix": "crm",
"uri_prefix": "http://www.cidoc-crm.org/cidoc-crm/$1",
"description": "This is the encoding approved by CRM-SIG in the meeting 21/11/2012 as the official current version for the CIDOC CRM namespace. Note that this is NOT a definition of the CIDOC CRM, but an encoding derived from the authoritative release of the CIDOC CRM v5.0.4 on http://www.cidoc-crm.org/official_release_cidoc.html",
"modified": "2012-12-17",
"keywords": [
"General & Upper"
],
"homepage": "http://www.cidoc-crm.org/cidoc-crm/"
},
"coun": {
"name": "ISO 3166 Country Codes",
"prefix": "coun",
"uri_prefix": "http://www.daml.org/2001/09/countries/iso-3166-ont#$1",
"description": "Basic properties of a country as defined by ISO 3166 (code and name)",
"modified": "2003-08-11",
"homepage": "http://www.daml.org/ontologies/352",
"keywords": [
"Geography"
]
},
"dk": {
"name": "The Data Knowledge Vocabulary",
"prefix": "dk",
"uri_prefix": "http://www.data-knowledge.org/dk/$1",
"description": "The Data Knowledge Vocabulary allows for a comprehensive description of data assets and enterprise data management. It covers a business data dictionary, data quality management, data governance, the technical infrastructure and many other aspects of enterprise data management. The vocabulary represents a linked data implementation of the Data Knowledge Model which resulted from extensive applied research.",
"modified": "2018-02-14",
"keywords": [
"Industry",
"Methods",
"Vocabularies",
"eBusiness"
],
"homepage": "http://www.data-knowledge.org/dk/"
},
"ctxdesc": {
"name": "Context Descriptor Pattern",
"prefix": "ctxdesc",
"uri_prefix": "http://www.demcare.eu/ontologies/contextdescriptor.owl#$1",
"description": "OWL pattern for describing activity models as abstract dependencies among classes.",
"modified": "2015-09-17",
"homepage": "http://www.demcare.eu/ontologies/ctxdesc.html",
"keywords": [
"Metadata"
]
},
"demlab": {
"name": "Dem@Care Lab Ontology for Dementia Assessment",
"prefix": "demlab",
"uri_prefix": "http://www.demcare.eu/ontologies/demlab.owl#$1",
"description": "The ontology has been developed in the framework of the Dem@Care project for representing the experimentation protocol towards diagnostic support and assessment of Dementia in a controlled environment. The aim of the protocol is to provide a brief overview of their health status of the participants during consultation (cognition, behaviours and function), and to correlate the system (sensor) data with the data collected using typical dementia care assessment tools.",
"modified": "2014-09-02",
"homepage": "http://www.demcare.eu/ontologies/demlab.html",
"keywords": [
"Health"
]
},
"km4c": {
"name": "km4city, the DISIT Knowledge Model for City and Mobility",
"prefix": "km4c",
"uri_prefix": "http://www.disit.org/km4city/schema#$1",
"description": "A Knowledge Model to describe a smart city, that interconnect data from infomobility service, Open Data and other source",
"modified": "2015-07-28",
"keywords": [
"Environment",
"Services",
"Society"
],
"homepage": "http://www.disit.org/km4city/schema"
},
"ebucore": {
"name": "EBU Ontology",
"prefix": "ebucore",
"uri_prefix": "http://www.ebu.ch/metadata/ontologies/ebucore/ebucore#$1",
"description": "Combined with the EBU Class Conceptual Data Model (CCDM) of simple business objects, EBUCore provides the appropriate framework for descriptive and technical metadata for use in Service Oriented Architectures and also in audiovisual ontologies for semantic web and linked data developments.",
"modified": "2015-08-04",
"homepage": "http://tech.ebu.ch/lang/en/MetadataEbuCore",
"keywords": [
"Multimedia"
]
},
"ceo": {
"name": "Consumer Electronics Ontology",
"prefix": "ceo",
"uri_prefix": "http://www.ebusiness-unibw.org/ontologies/consumerelectronics/v1#$1",
"description": "An Ontology for Consumer Electronics Products and Services",
"modified": "2012-07-03",
"keywords": [
"Industry"
],
"homepage": "http://www.ebusiness-unibw.org/ontologies/consumerelectronics/v1"
},
"eclap": {
"name": "ECLAP, Performing Arts Vocabulary",
"prefix": "eclap",
"uri_prefix": "http://www.eclap.eu/schema/eclap/$1",
"description": "The ECLAP vocabulary provide classes and properties for the description of multimedia content related with performing arts.",
"modified": "2014-09-04",
"keywords": [
"Multimedia"
],
"homepage": "http://www.eclap.eu/schema/eclap/"
},
"pattern": {
"name": "The Pattern Ontology",
"prefix": "pattern",
"uri_prefix": "http://www.essepuntato.it/2008/12/pattern#$1",
"description": "An ontology defining formally patterns for segmenting a document into atomic components, in order to be manipulated independently and re-flowed in different contexts.",
"modified": "2013-07-16",
"keywords": [
"Catalogs"
],
"homepage": "http://www.essepuntato.it/2008/12/pattern"
},
"tvc": {
"name": "The Time-indexed Value in Context",
"prefix": "tvc",
"uri_prefix": "http://www.essepuntato.it/2012/04/tvc/$1",
"description": "A pattern for the description of scenarios that involve entities having some value during a particular time and within a particular context.",
"modified": "2012-06-08",
"keywords": [
"Time"
],
"homepage": "http://www.essepuntato.it/2012/04/tvc"
},
"citof": {
"name": "Functions of Citations",
"prefix": "citof",
"uri_prefix": "http://www.essepuntato.it/2013/03/cito-functions/$1",
"description": "CiTOFunctions is an ontology that provides a classification for citations. In particular, it classifies CiTO properties (each defining a particular citational act)",
"modified": "2013-05-20",
"keywords": [
"SPAR"
],
"homepage": "http://www.essepuntato.it/2013/03/cito-functions"
},
"vag": {
"name": "The Vagueness Ontology",
"prefix": "vag",
"uri_prefix": "http://www.essepuntato.it/2013/10/vagueness/$1",
"description": "The Vagueness Ontology (VO) allows one to specify vagueness characterisations of the TBox entities of an ontology.",
"modified": "2013-11-28",
"keywords": [
"Support"
],
"homepage": "http://www.essepuntato.it/2013/10/vagueness"
},
"cerif": {
"name": "CERIF Ontology 1.3",
"prefix": "cerif",
"uri_prefix": "http://www.eurocris.org/ontologies/cerif/1.3#$1",
"description": "The Common European Research Information Format (CERIF) Ontology Specification provides basic concepts and properties for describing research information as semantic data.",
"modified": "2013-04-23",
"keywords": [
"General & Upper"
],
"homepage": "http://www.eurocris.org/ontologies/cerif/1.3"
},
"edm": {
"name": "Europeana Data Model vocabulary",
"prefix": "edm",
"uri_prefix": "http://www.europeana.eu/schemas/edm/$1",
"description": "The Europeana Data Model (EDM) is aimed at being an integration medium for collecting, connecting and enriching the descriptions provided by Europeana data providers.",
"modified": "2013-05-20",
"keywords": [
"Catalogs"
],
"homepage": "http://www.europeana.eu/schemas/edm/"
},
"gn": {
"name": "The Geonames ontology",
"prefix": "gn",
"uri_prefix": "http://www.geonames.org/ontology#$1",
"description": "The Geonames ontology provides elements of description for geographical features defined in the geonames.org data base",
"modified": "2012-10-29",
"homepage": "http://www.geonames.org/ontology/documentation.html",
"keywords": [
"Geography"
]
},
"marl": {
"name": "Marl Ontology Specification",
"prefix": "marl",
"uri_prefix": "http://www.gsi.dit.upm.es/ontologies/marl/ns#$1",
"description": "Marl is a standardised data schema designed to annotate and describe subjective opinions expressed on the web or in particular Information Systems.",
"modified": "2013-05-10",
"homepage": "http://www.gsi.dit.upm.es/ontologies/marl/",
"keywords": [
"Support"
]
},
"onyx": {
"name": "Onyx Emotion Ontology",
"prefix": "onyx",
"uri_prefix": "http://www.gsi.dit.upm.es/ontologies/onyx/ns#$1",
"description": "Onyx is a vovabulary designed designed to annotate and describe the emotions expressed by user-generated content on the web or in particular Information Systems.",
"modified": "2015-01-11",
"homepage": "http://www.gsi.dit.upm.es/ontologies/onyx/",
"keywords": [
"Support"
]
},
"tag": {
"name": "Tag ontology",
"prefix": "tag",
"uri_prefix": "http://www.holygoat.co.uk/owl/redwood/0.1/tags/$1",
"description": "An ontology that let users define relationships between Tag objects and URIs of Semantic Web resources",
"modified": "2005-12-21",
"keywords": [
"Tag"
],
"homepage": "http://www.holygoat.co.uk/owl/redwood/0.1/tags/"
},
"mtlo": {
"name": "MarineTLO Ontology",
"prefix": "mtlo",
"uri_prefix": "http://www.ics.forth.gr/isl/MarineTLO/v4/marinetlo.owl#$1",
"description": "MarineTLO is a top-level ontology for the marine domain (also applicable to the terrestrial domain).",
"modified": "2014-08-02",
"homepage": "http://www.ics.forth.gr/isl/MarineTLO/",
"keywords": [
"Biology"
]
},
"voidwh": {
"name": "Void Warehouse Ontology",
"prefix": "voidwh",
"uri_prefix": "http://www.ics.forth.gr/isl/VoIDWarehouse/VoID_Extension_Schema.owl$1",
"description": "An extension of W3C VoID that is able to represent these metrics for expressing the Connectivity Metrics of a Semantic Warehouse.",
"modified": "2014-07-19",
"keywords": [
"Metadata"
],
"homepage": "http://www.ics.forth.gr/isl/VoIDWarehouse/VoID_Extension_Schema.owl"
},
"oae": {
"name": "Open NEE Model",
"prefix": "oae",
"uri_prefix": "http://www.ics.forth.gr/isl/oae/core#$1",
"description": "The Open NEE Model defines an extension of the Open Annotation Data Model (http://www.openannotation.org/spec/core) that allows describing in RDF the result of a Named Entity Extraction (NEE) process, enabling thereby an application to run advanced (SPARQL) queries over the annotated data. The model also exploits the Open NEE Configuration Model (http://www.ics.forth.gr/isl/oncm) for relating the output of a NEE process with an applied configuration (serving provenance information to the output of the entire NEE process).",
"modified": "2015-03-25",
"keywords": [
"Metadata"
],
"homepage": "http://www.ics.forth.gr/isl/oae/core"
},
"onc": {
"name": "Open NEE Configuration Model",
"prefix": "onc",
"uri_prefix": "http://www.ics.forth.gr/isl/oncm/core#$1",
"description": "The Open NEE Configuration Model defines a Linked Data-based model for describing a configuration supported by a Named Entity Extraction (NEE) service. It is based on the model proposed in \"Configuring Named Entity Extraction through Real-Time Exploitation of Linked Data\" (http://dl.acm.org/citation.cfm?doid=2611040.2611085) for configuring such services, and allows a NEE service to describe and publish as Linked Data its entity mining capabilities, but also to be dynamically configured.",
"modified": "2015-03-25",
"keywords": [
"Methods"
],
"homepage": "http://www.ics.forth.gr/isl/oncm/core"
},
"identity": {
"name": "Ontology of digital identity.",
"prefix": "identity",
"uri_prefix": "http://www.identity.org/ontologies/identity.owl#$1",
"description": "v.2.0 based on P3P1.0 Specification http://www.w3.org/TR/P3P/",
"modified": "2014-04-03",
"keywords": [
"Security"
],
"homepage": "http://www.identity.org/ontologies/identity.owl"
},
"lifecycle": {
"name": "IoT-Lifecycle",
"prefix": "lifecycle",
"uri_prefix": "http://purl.org/vocab/lifecycle/schema#$1",
"description": "This ontology is a specialization of the lifecycle vocabulary (http://purl.org/vocab/lifecycle/schema) meant to be used in the context of IoT. It is used as a module in the IoT core domain ontology IoT-O (www.irit.fr/recherches/MELODI/ontologies/IoT-O). \n\nIoT-Lifecycle adds a specific state definition (ParametrizedState) and a specific transition (Update) that is useful to model actuators.",
"modified": "2016-02-26",
"keywords": [
"Services"
],
"homepage": "http://www.irit.fr/recherches/MELODI/ontologies/IoT-Lifecycle"
},
"ioto": {
"name": "IoT-O",
"prefix": "ioto",
"uri_prefix": "http://www.irit.fr/recherches/MELODI/ontologies/IoT-O#$1",
"description": "IoT-O is a core domain Internet of Things ontology. It is intended to model horizontal knowledge about IoT systems and applications, and to be extended with vertical, application specific knowledge.\nIt is constituted of different modules : \n - A sensing module, based on W3C's SSN (http://purl.oclc.org/NET/ssnx/ssn)\n - An acting module, based on SAN (http://www.irit.fr/recherches/MELODI/ontologies/SAN)\n - A service module, based on MSM (http://iserve.kmi.open.ac.uk/ns/msm/msm-2014-09-03.rdf) and hRest (http://www.wsmo.org/ns/hrests)\n - A lifecycle module, based on a lifecycle vocabulary (http://vocab.org/lifecycle/schema-20080603.rdf) and an iot-specific extension (http://www.irit.fr/recherches/MELODI/ontologies/IoT-Lifecycle)\n - An energy module, based on powerOnt (ttp://elite.polito.it/ontologies/poweront.owl)\n\nIoT-O developping team also contributes to the oneM2M IoT interoperability standard.",
"modified": "2015-02-20",
"keywords": [
"IoT",
"Services"
],
"homepage": "http://www.irit.fr/recherches/MELODI/ontologies/IoT-O"
},
"SAN": {
"name": "SAN (Semantic Actuator Network)",
"prefix": "SAN",
"uri_prefix": "http://www.irit.fr/recherches/MELODI/ontologies/SAN#$1",
"description": "This ontology is intended to describe Semantic Actuator Networks, as a counterpoint to SSN definition of Semantic Sensor Networks. An actuator is a physical device having an effect on the world (see Actuator for more information).\n\nIt is worth noticing that some concepts are imported from SSN, but not SSN as a whole. This is a design choice intended to separate as much as possible the definition on actuator from the definition of sensor, which are completely different concept that can be used independantly from each other.\n\nThis ontology is used as a ontological module in IoT-O ontology.",
"modified": "2016-02-26",
"keywords": [
"IoT",
"Support"
],
"homepage": "http://www.irit.fr/recherches/MELODI/ontologies/SAN"
},
"mod": {
"name": "MOD: Metadata for Ontology Description and publication",
"prefix": "mod",
"uri_prefix": "http://www.isibang.ac.in/ns/mod#$1",
"description": "This specification describes MOD, a metadata vocabulary to describe and publish ontologies",
"modified": "2021-12-06",
"keywords": [
"Metadata"
],
"homepage": "http://www.isibang.ac.in/ns/mod"
},
"ivoam": {
"name": "Messengers",
"prefix": "ivoam",
"uri_prefix": "http://www.ivoa.net/rdf/messenger#$1",
"description": "A vocabulary of particles used for observations in astronomy.\nThis list started its existence as the controlled vocabulary for\nVODataService's vs:Waveband type; the machine-readable identifiers are in\nupper case for backwards compatibility.",
"modified": "2023-05-09",
"keywords": [
"Image",
"Industry"
],
"homepage": "http://www.ivoa.net/rdf/messenger"
},
"music": {
"name": "Music Vocabulary",
"prefix": "music",
"uri_prefix": "http://www.kanzaki.com/ns/music#$1",
"description": "\u97f3\u697d\u4f5c\u54c1\u3001\u697d\u5668\u3001\u6f14\u594f\u60c5\u5831\u3092\u8a18\u8ff0\u3059\u308b\u305f\u3081\u306e\u30dc\u30ad\u30e3\u30d6\u30e9\u30ea\u3002Opera_Event\uff08\u6f14\u594f\uff09\u3068Opera\uff08\u4f5c\u54c1\uff09\u3084\u3001String_Quartette\uff08\u4f5c\u54c1\uff09\u3068StringQuartetEnsemble\uff08\u56e3\u4f53\uff09\u306e\u3088\u3046\u306b\u3001\u65e5\u5e38\u8a9e\u3067\u306f\u4e21\u65b9\u306e\u610f\u5473\u306b\u4f7f\u308f\u308c\u308b\u30af\u30e9\u30b9\u306e\u533a\u5225\u306b\u6ce8\u610f\u3002\u3053\u306e\u30d0\u30fc\u30b8\u30e7\u30f3\u3067\u306f\u3001\u97f3\u697d\u4f5c\u54c1\u3001\u305d\u306e\u8868\u73fe\uff08\u6f14\u594f\u3001\u697d\u8b5c\u306a\u3069\uff09\u3068\u30a4\u30d9\u30f3\u30c8\uff08\u6f14\u594f\u4f1a\uff09\u3092\u3088\u308a\u7cbe\u5bc6\u306b\u30e2\u30c7\u30ea\u30f3\u30b0\u3059\u308b\u3079\u304f\u5b9f\u9a13\u4e2d\u3002",
"modified": "2007-10-31",
"keywords": [
"Events"
],
"homepage": "http://www.kanzaki.com/ns/music"
},
"whois": {
"name": "Who's who description vocabulary",
"prefix": "whois",
"uri_prefix": "http://www.kanzaki.com/ns/whois#$1",
"description": "A vocabulary to describe a person's profile and history",
"modified": "2012-09-16",
"keywords": [
"People"
],
"homepage": "http://www.kanzaki.com/ns/whois"
},
"lexinfo": {
"name": "LexInfo Ontology",
"prefix": "lexinfo",
"uri_prefix": "http://www.lexinfo.net/ontology/2.0/lexinfo#$1",
"description": "\u041e\u043d\u0442\u043e\u043b\u043e\u0433\u0438\u044f \u0442\u0438\u043f\u043e\u0432, \u0437\u043d\u0430\u0447\u0435\u043d\u0438\u0439 \u0438 \u0441\u0432\u043e\u0439\u0441\u0442\u0432, \u0438\u0441\u043f\u043e\u043b\u044c\u0437\u0443\u0435\u043c\u044b\u0445 \u0441\u043e\u0432\u043c\u0435\u0441\u0442\u043d\u043e \u0441 \u043e\u043d\u0442\u043e\u043b\u043e\u0433\u0438\u0435\u0439 lemon, \u0447\u0430\u0441\u0442\u0438\u0447\u043d\u043e \u044f\u0432\u043b\u044f\u0435\u0442\u0441\u044f \u043f\u0440\u043e\u0438\u0437\u0432\u043e\u0434\u043d\u043e\u0439 \u043e\u0442 ISOcat",
"modified": "2016-07-13",
"keywords": [
"Vocabularies"
],
"homepage": "http://www.lexinfo.net/ontology/2.0/lexinfo"
},
"semio": {
"name": "Semio, an ontology of signs",
"prefix": "semio",
"uri_prefix": "http://www.lingvoj.org/semio#$1",
"description": "A vocabulary to describe signs in a semiotic approach",
"modified": "2015-01-11",
"keywords": [
"Vocabularies"
],
"homepage": "http://www.lingvoj.org/semio.rdf"
},
"dtype": {
"name": "Datatype Ontology",
"prefix": "dtype",
"uri_prefix": "http://www.linkedmodel.org/schema/dtype#$1",
"description": "The ontology 'dtype' provides a specification of simple data types such as enumerations. These are needed in support of the conversion of XML Schemas and UML Models to OWL. Codelists are also defined in 'dtype'.",
"modified": "2014-06-28",
"keywords": [
"RDF"
],
"homepage": "http://www.linkedmodel.org/schema/dtype"
},
"vaem": {
"name": "Vocabulary for Attaching Essential Metadata",
"prefix": "vaem",
"uri_prefix": "http://www.linkedmodel.org/schema/vaem#$1",
"description": "The purpose of VAEM is to provide, by import, a foundation for commonly needed resources when building an ontology.",
"modified": "2014-08-11",
"homepage": "http://linkedmodel.org/doc/vaem/1.2/",
"keywords": [
"Metadata"
]
},
"llont": {
"name": "LinkLion - the Link Discovery Portal",
"prefix": "llont",
"uri_prefix": "http://www.linklion.org/ontology#$1",
"description": "LinkLion - the Link Discovery Portal",
"modified": "2015-03-25",
"keywords": [
"Services"
],
"homepage": "http://www.linklion.org/ontology"
},
"mads": {
"name": "Metadata Authority Description Schema",
"prefix": "mads",
"uri_prefix": "http://www.loc.gov/mads/rdf/v1#$1",
"description": "MADS/RDF (Metadata Authority Description Schema in RDF) is a knowledge organization system (KOS) designed for use with controlled values for names (personal, corporate, geographic, etc.), thesauri, taxonomies, subject heading systems, and other controlled value lists",
"modified": "2015-10-28",
"homepage": "http://www.loc.gov/standards/mads/rdf/",
"keywords": [
"Metadata"
]
},
"premis": {
"name": "PREMIS Ontology",
"prefix": "premis",
"uri_prefix": "http://www.loc.gov/premis/rdf/v1#$1",
"description": "This ontology identifies the classes and properties used to describe preservation metadata in RDF.",
"modified": "2018-10-12",
"homepage": "http://id.loc.gov/ontologies/premis.html",
"keywords": [
"Catalogs"
]
},
"geof": {
"name": "Geo Features",
"prefix": "geof",
"uri_prefix": "http://www.mindswap.org/2003/owl/geo/geoFeatures20040307.owl#$1",
"description": "This ontology contains geographic feature classes and associated properties including classes and properties for describing the spatial location of the geographic feature. The classes and properties have been defined based on an ESRI dataset.",
"modified": "2004-02-20",
"keywords": [
"Geography"
],
"homepage": "http://www.mindswap.org/2003/owl/geo/geoFeatures20040307.owl"
},
"pimsii": {
"name": "Physicalistic Interpretation of Modelling and Simulation - Interoperability Infrastructure (PIMS-II)",
"prefix": "pimsii",
"uri_prefix": "http://www.molmod.info/semantics/pims-ii.ttl#$1",
"description": "The Physicalistic Interpretation of Modelling and Simulation - Interoperability Infrastructure (PIMS-II) is a mid-level ontology with a focus on documenting cognitive processes and epistemic metadata",
"modified": "2023-05-09",
"keywords": [
"Metadata"
],
"homepage": "http://www.molmod.info/semantics/pims-ii.ttl"
},
"np": {
"name": "Nano publication ontology",
"prefix": "np",
"uri_prefix": "http://www.nanopub.org/nschema#$1",
"description": "The nanopub ontology",
"modified": "2022-05-19",
"homepage": "http://www.nanopub.org/2013/WD-guidelines-20131215/",
"keywords": [
"Metadata",
"Methods"
]
},
"moac": {
"name": "Management of a Crisis Vocabulary",
"prefix": "moac",
"uri_prefix": "http://observedchange.com/moac/ns#$1",
"description": "MOAC, the Management of a Crisis Vocabulary, is a lightweight vocabulary aiming to provide terms to enable practitioners to relate different \"things\" in crisis management activities together as Linked Data. The initial MOAC terms originated from the Inter Agency Standing Committee (IASC), Emergency Shelter Cluster in Haiti, UNOCHA 3W Who What Where Contact Database",
"modified": "2012-01-29",
"keywords": [
"Environment"
],
"homepage": "http://www.observedchange.com/moac/ns#"
},
"tisc": {
"name": "Open Time and Space Core Vocabulary",
"prefix": "tisc",
"uri_prefix": "http://observedchange.com/tisc/ns#$1",
"description": "TISC, the Open Time and Space Core Vocabulary, is a lightweight spatiotemporal vocabulary aiming to provide spatial and temporal terms such as \"happensAt\", \"locatedAt\", \"rightOf\" to enable practitioners to relate their data to time and space.",
"modified": "2014-07-11",
"keywords": [
"Events"
],
"homepage": "http://www.observedchange.com/tisc/ns#"
},
"oecc": {
"name": "Extended Creative Commons Ontology",
"prefix": "oecc",
"uri_prefix": "http://www.oegov.org/core/owl/cc#$1",
"description": "Creative Commons Ontology, extending RDF file at http://creativecommons.org/schema.rdf",
"modified": "2009-08-20",
"keywords": [
"Metadata"
],
"homepage": "http://www.oegov.org/core/owl/cc"
},
"gc": {
"name": "oeGOV Government Core Ontology",
"prefix": "gc",
"uri_prefix": "http://www.oegov.org/core/owl/gc#$1",
"description": "The Government Core Ontology establishes a foundation for all oegov ontologies.",
"modified": "2009-08-24",
"keywords": [
"Government"
],
"homepage": "http://www.oegov.org/core/owl/gc"
},
"oum": {
"name": "Ontology of units of Measure (OM)",
"prefix": "oum",
"uri_prefix": "http://www.ontology-of-units-of-measure.org/resource/om-2/$1",
"description": "The Ontology of units of Measure (OM) 2.0 models concepts and relations important to scientific research. It has a strong focus on units, quantities, measurements, and dimensions.",
"modified": "2020-06-06",
"keywords": [
"IoT",
"Services"
],
"homepage": "http://www.ontology-of-units-of-measure.org/resource/om-2/"
},
"infor": {
"name": "Information Realization",
"prefix": "infor",
"uri_prefix": "http://www.ontologydesignpatterns.org/cp/owl/informationrealization.owl#$1",
"description": "Allows designers to model information objects and their realizations. This allows to reason about physical objects and the information they realize, by keeping them distinguished.",
"modified": "2011-01-30",
"keywords": [
"Support"
],
"homepage": "http://www.ontologydesignpatterns.org/cp/owl/informationrealization.owl"
},
"odpart": {
"name": "Ontology Design Pattern Participation",
"prefix": "odpart",
"uri_prefix": "http://www.ontologydesignpatterns.org/cp/owl/participation.owl#$1",
"description": "The basic participation pattern, without temporal indexing. It clones equivalent elements from DOLCE-UltraLite.",
"modified": "2011-01-30",
"keywords": [
"Support"
],
"homepage": "http://www.ontologydesignpatterns.org/cp/owl/participation.owl"
},
"semiotics": {
"name": "A content ontology pattern that encodes a basic semiotic theory, by reusing the situation pattern.",
"prefix": "semiotics",
"uri_prefix": "http://www.ontologydesignpatterns.org/cp/owl/semiotics.owl#$1",
"description": "A content ontology pattern that encodes a basic semiotic theory, by reusing the situation pattern. The basic classes are: Expression, Meaning, Reference (the semiotic triangle), LinguisticAct (for the pragmatics), and Agent.\nA linguistic act is said to be context for expressions, with their meanings and references, and agents involved.\nBased on this pattern, several specific linguistic acts, such as 'tagging', 'translating', 'defining', 'formalizing', etc. can be defined, so constituting a formal vocabulary for a pragmatic web.",
"modified": "2007-01-01",
"keywords": [
"General & Upper",
"Metadata"
],
"homepage": "http://www.ontologydesignpatterns.org/cp/owl/semiotics.owl"
},
"seq": {
"name": "Sequence Pattern",
"prefix": "seq",
"uri_prefix": "http://www.ontologydesignpatterns.org/cp/owl/sequence.owl#$1",
"description": "Intended to represent sequence schemas. It defines the notion of transitive and intransitive precedence and their inverses. It can then be used between tasks, processes, time intervals, spatially locate objects, situations, etc.",
"modified": "2011-01-30",
"keywords": [
"Support"
],
"homepage": "http://www.ontologydesignpatterns.org/cp/owl/sequence.owl"
},
"situ": {
"name": "Situation Pattern",
"prefix": "situ",
"uri_prefix": "http://www.ontologydesignpatterns.org/cp/owl/situation.owl#$1",
"description": "A pattern to represent contexts or situations, and the things that are contextualized.",
"modified": "2015-01-11",
"keywords": [
"Events"
],
"homepage": "http://www.ontologydesignpatterns.org/cp/owl/situation.owl"
},
"tis": {
"name": "Time Indexed Situation",
"prefix": "tis",
"uri_prefix": "http://www.ontologydesignpatterns.org/cp/owl/timeindexedsituation.owl$1",
"description": "A generic pattern usable for all situations that require a temporal indexing.",
"modified": "2015-01-11",
"keywords": [
"Events"
],
"homepage": "http://www.ontologydesignpatterns.org/cp/owl/timeindexedsituation.owl"
},
"ti": {
"name": "The Time Interval Pattern",
"prefix": "ti",
"uri_prefix": "http://www.ontologydesignpatterns.org/cp/owl/timeinterval.owl#$1",
"description": "This pattern is extracted from DOLCE-UltraLite by partial clone of elements and expansion. Two datatype properties have been added which allow to express the boundaries of the time interval.",
"modified": "2015-01-11",
"keywords": [
"Time"
],
"homepage": "http://www.ontologydesignpatterns.org/cp/owl/timeinterval.owl"
},
"dul": {
"name": "DOLCE+DnS Ultralite",
"prefix": "dul",
"uri_prefix": "http://www.ontologydesignpatterns.org/ont/dul/DUL.owl#$1",
"description": "The DOLCE+DnS Ultralite ontology. It is a simplification of some parts of the DOLCE Lite-Plus library (cf. http://www.ontologydesignpatterns.org/ont/dul/DLP397.owl)",
"modified": "2017-04-10",
"homepage": "http://ontologydesignpatterns.org/wiki/Ontology:DOLCE+DnS_Ultralite",
"keywords": [
"General & Upper"
]
},
"iol": {
"name": "Information Objects ontology",
"prefix": "iol",
"uri_prefix": "http://www.ontologydesignpatterns.org/ont/dul/IOLite.owl#$1",
"description": "An ontology of information objects, encodings and realizations, as a plugin to DOLCE-Ultralite",
"modified": "2010-02-09",
"keywords": [
"General & Upper"
],
"homepage": "http://www.ontologydesignpatterns.org/ont/dul/IOLite.owl"
},
"ontopic": {
"name": "Ontopic Ontology",
"prefix": "ontopic",
"uri_prefix": "http://www.ontologydesignpatterns.org/ont/dul/ontopic.owl#$1",
"description": "An ontology of topics as used in thesauri, subject directories, etc.",
"modified": "2010-02-05",
"keywords": [
"Vocabularies"
],
"homepage": "http://www.ontologydesignpatterns.org/ont/dul/ontopic.owl"
},
"lmm1": {
"name": "Lexical MetaModel Level 1",
"prefix": "lmm1",
"uri_prefix": "http://www.ontologydesignpatterns.org/ont/lmm/LMM_L1.owl#$1",
"description": "This ontology is a composition of some content design patterns for the semiotic triangle. Its structure is extracted from DOLCE-Ultralite (DOLCE+c.DnS), but it uses a different terminology,",
"modified": "2010-02-09",
"keywords": [
"Vocabularies"
],
"homepage": "http://www.ontologydesignpatterns.org/ont/lmm/LMM_L1.owl"
},
"lmm2": {
"name": "Lexical MetaModel Level 2",
"prefix": "lmm2",
"uri_prefix": "http://www.ontologydesignpatterns.org/ont/lmm/LMM_L2.owl#$1",
"description": "An ontology for aligning existing linguistic ontologies, and for describing the research objects of NLP.",
"modified": "2010-02-09",
"keywords": [
"Vocabularies"
],
"homepage": "http://www.ontologydesignpatterns.org/ont/lmm/LMM_L2.owl"
},
"irw": {
"name": "The Identity of Resources on the Web ontology",
"prefix": "irw",
"uri_prefix": "http://www.ontologydesignpatterns.org/ont/web/irw.owl#$1",
"description": "This ontology is an evolution of IRE ontology. It describes identification of resources on the Web, through the definition of relationships between resources and their representations on the Web. The requirement is to describe what can be identified by URIs and how this is handled e.g. in form of HTTP requests and reponds.",
"modified": "2009-03-09",
"keywords": [
"Quality"
],
"homepage": "http://www.ontologydesignpatterns.org/ont/web/irw.owl"
},
"cpa": {
"name": "Content Pattern Annotations",
"prefix": "cpa",
"uri_prefix": "http://www.ontologydesignpatterns.org/schemas/cpannotationschema.owl#$1",
"description": "A set of annotation properties to be used for ontology design patterns",
"modified": "2009-06-02",
"keywords": [
"Metadata"
],
"homepage": "http://www.ontologydesignpatterns.org/schemas/cpannotationschema.owl"
},
"pext": {
"name": "PROTON Extent module",
"prefix": "pext",
"uri_prefix": "http://www.ontotext.com/proton/protonext#$1",
"description": "Upper-level ontology with extensions to handle Linked Open Data (LOD)",
"modified": "2014-01-28",
"homepage": "http://www.ontotext.com/proton-ontology",
"keywords": [
"PROTON"
]
},
"ptop": {
"name": "PROTON (Proto Ontology), Top Module",
"prefix": "ptop",
"uri_prefix": "http://www.ontotext.com/proton/protontop#$1",
"description": "The PROTON Top module represents the most general classes",
"modified": "2012-02-13",
"homepage": "http://www.ontotext.com/proton-ontology",
"keywords": [
"PROTON"
]
},
"ore": {
"name": "The OAI ORE terms vocabulary",
"prefix": "ore",
"uri_prefix": "http://www.openarchives.org/ore/terms/$1",
"description": "Open Archives Initiative Object Reuse and Exchange (OAI-ORE) defines standards for the description and exchange of aggregations of Web resources.",
"modified": "2008-10-17",
"homepage": "http://www.openarchives.org/ore/vocabulary",
"keywords": [
"Catalogs"
]
},
"gsp": {
"name": "OGC GeoSPARQL",
"prefix": "gsp",
"uri_prefix": "http://www.opengis.net/ont/geosparql#$1",
"description": "A Geographic Query Language for RDF Data OGC 11-052r5",
"modified": "2023-11-16",
"homepage": "https://opengeospatial.github.io/ogc-geosparql/",
"keywords": [
"Geometry"
]
},
"gml": {
"name": "OGC Geometry",
"prefix": "gml",
"uri_prefix": "http://www.opengis.net/ont/gml#$1",
"description": "A specialization of GeoSPARQL defining specific subtypes of Geometry",
"modified": "2012-09-11",
"keywords": [
"Geometry"
],
"homepage": "http://www.opengis.net/ont/gml"
},
"sf": {
"name": "Simplified Features Geometry",
"prefix": "sf",
"uri_prefix": "http://www.opengis.net/ont/sf#$1",
"description": "A specification of GeoSPARQL for simple features geometries (points, lines, polygons ...)",
"modified": "2012-09-11",
"keywords": [
"Geometry"
],
"homepage": "http://www.opengis.net/ont/sf"
},
"opmw": {
"name": "The OPMW Ontology",
"prefix": "opmw",
"uri_prefix": "http://www.opmw.org/ontology/$1",
"description": "OPMW is a OPMV profile to model the executions and definitions of scientific workflows.",
"modified": "2014-12-22",
"homepage": "http://www.opmw.org/ontology/",
"keywords": [
"Methods"
]
},
"ostop": {
"name": "Ordnance Survey Topography Ontology",
"prefix": "ostop",
"uri_prefix": "http://www.ordnancesurvey.co.uk/ontology/Topography/v0.1/Topography.owl#$1",
"description": "The general purpose of this ontology is to provide a library of high level concepts that are used by the other modules within the whole OS Topographic ontology. The ontology also describes the relationships and instances common to more than one module.",
"modified": "2008-02-24",
"keywords": [
"Geography"
],
"homepage": "http://www.ordnancesurvey.co.uk/ontology/Topography/v0.1/Topography.owl"
},
"drama": {
"name": "Drammar: a comprehensive ontology of drama",
"prefix": "drama",
"uri_prefix": "http://www.purl.org/drammar#$1",
"description": "Designed with the goals to describe and encode the core dramatic qualities and to serve as a knowledge base underlying a number of applications, Drammar is a comprehensive ontology of drama, realized through a collaboration of computer scientists and drama scholars. It makes the knowledge about drama available as a vocabulary for the linked interchange of drama encodings and readily usable by automatic reasoners.\nBy avoinding references to style and artistic qualities Drammar aims at representing the elements shared by different, cross-media manifestations of drama, the so\u2013called intangible elements of drama as an intangible cultural heritage form.",
"modified": "2018-06-11",
"keywords": [
"Multimedia"
],
"homepage": "http://www.purl.org/drammar"
},
"remetca": {
"name": "ReMetCa Ontology",
"prefix": "remetca",
"uri_prefix": "http://www.purl.org/net/remetca#$1",
"description": "Ontology for poetry description",
"modified": "2014-10-14",
"keywords": [
"SPAR"
],
"homepage": "http://www.purl.org/net/remetca#"
},
"acm": {
"name": "ACM Classification Ontology",
"prefix": "acm",
"uri_prefix": "http://acm.rkbexplorer.com/ontologies/acm#$1",
"description": "This ontology is a representation of The ACM Computing Classification System [1998]",
"modified": "2013-04-25",
"keywords": [
"Catalogs"
],
"homepage": "http://www.rkbexplorer.com/ontologies/acm"
},
"hdo": {
"name": "HelpDesk support Ontology",
"prefix": "hdo",
"uri_prefix": "http://www.samos.gr/ontologies/helpdeskOnto.owl#$1",
"description": "Simple ontology developed for integration purposes. Describe helpdesk entities used to record support tickets for diagnosis and resolve purpuses. The ontology re-uses a) W3C ORG and REGORG ontologies, b) DUL upper ontology, and c) GoodRelations ontology.",
"modified": "2013-04-25",
"homepage": "http://www.samos.gr/ontologies/helpdeskOnto.html",
"keywords": [
"Support"
]
},
"sealit": {
"name": "SeaLiT Ontology",
"prefix": "sealit",
"uri_prefix": "http://www.sealitproject.eu/ontology/$1",
"description": "The SeaLiT Ontology is a formal ontology intended to facilitate the integration, mediation and interchange of heterogeneous information related to maritime history. It aims at providing the semantic definitions needed to transform disparate, localised information sources of maritime history into a coherent global resource. It also serves as a common language for domain experts and IT developers to formulate requirements and to agree on system functionalities with respect to the correct handling of historical information. The ontology uses and extends the CIDOC Conceptual Reference Model (ISO 21127:2014), in particular version 7.1.1, as a general ontology of human activity, things and events happening in space and time.",
"modified": "2022-06-02",
"keywords": [
"Events",
"Travel"
],
"homepage": "http://www.sealitproject.eu/ontology/"
},
"nie": {
"name": "NEPOMUK Information Element Core Ontology",
"prefix": "nie",
"uri_prefix": "http://www.semanticdesktop.org/ontologies/2007/01/19/nie#$1",
"description": "The Core Ontology of the NEPOMUK suite defines basic elements such as Data Object, Information Element ...",
"modified": "2012-10-03",
"homepage": "http://www.semanticdesktop.org/ontologies/",
"keywords": [
"SSDesk"
]
},
"nco": {
"name": "NEPOMUK Contact Ontology",
"prefix": "nco",
"uri_prefix": "http://www.semanticdesktop.org/ontologies/2007/03/22/nco#$1",
"description": "NEPOMUK Contact Ontology describes contact information, common in many places on the desktop. It evolved from the VCARD specification (RFC 2426) and has been inspired by the Vcard Ontology by Renato Ianella. The scope of NCO is much broader though. This document gives an overview of the classes, properties and intended use cases of the NCO ontology.",
"modified": "2012-07-06",
"homepage": "http://www.semanticdesktop.org/ontologies/",
"keywords": [
"SSDesk"
]
},
"nfo": {
"name": "NEPOMUK File Ontology",
"prefix": "nfo",
"uri_prefix": "http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#$1",
"description": "Part of Nepomuk Information Element Ontology Framework",
"modified": "2012-06-10",
"homepage": "http://www.semanticdesktop.org/ontologies",
"keywords": [
"SSDesk"
]
},
"ncal": {
"name": "NEPOMUK Calendar Ontology",
"prefix": "ncal",
"uri_prefix": "http://www.semanticdesktop.org/ontologies/2007/04/02/ncal#$1",
"description": "The NEPOMUK Calendaring Ontology intends to provide vocabulary for describing calendaring data (events, tasks, journal entries) which is an important part of the body of information usually stored on a desktop. It is an adaptation of the ICALTZD ontology created by the W3C RDF Calendar Task Force of the Semantic Web Interest Group in the Semantic Web Activity.",
"modified": "2011-06-27",
"homepage": "http://www.semanticdesktop.org/ontologies/2007/04/02/ncal/",
"keywords": [
"Time"
]
},
"nao": {
"name": "NEPOMUK Annotation Ontology",
"prefix": "nao",
"uri_prefix": "http://www.semanticdesktop.org/ontologies/2007/08/15/nao#$1",
"description": "The NEPOMUK Annotation Ontology is an ontology for annotation, providing vocabulary which is commonly required to annotate resources on the semantic desktop.",
"modified": "2013-08-28",
"homepage": "http://www.semanticdesktop.org/ontologies/",
"keywords": [
"SSDesk"
]
},
"nrl": {
"name": "NEPOMUK Representational Language",
"prefix": "nrl",
"uri_prefix": "http://www.semanticdesktop.org/ontologies/2007/08/15/nrl#$1",
"description": "Designed on top of RDF, it addresses certain limitations on the part of RDF/S. In particular it includes support for Named Graphs",
"modified": "2012-08-25",
"homepage": "http://www.semanticdesktop.org/ontologies/",
"keywords": [
"SSDesk"
]
},
"ontosec": {
"name": "Ontology Security",
"prefix": "ontosec",
"uri_prefix": "http://www.semanticweb.org/ontologies/2008/11/OntologySecurity.owl#$1",
"description": "This ontology covers the domain of security in the field of mobile applications.",
"modified": "2013-05-22",
"keywords": [
"Security"
],
"homepage": "http://www.semanticweb.org/ontologies/2008/11/OntologySecurity.owl"
},
"traffic": {
"name": "Road Traffic Management",
"prefix": "traffic",
"uri_prefix": "http://www.sensormeasurement.appspot.com/ont/transport/traffic#$1",
"description": "An ontology that describes the management of the traffic in a straight road with two lanes, both in the same direction.",
"modified": "2014-05-16",
"homepage": "http://here.com/traffic",
"keywords": [
"Industry"
]
},
"ct": {
"name": "Connectivity types",
"prefix": "ct",
"uri_prefix": "http://www.tele.pw.edu.pl/~sims-onto/ConnectivityType.owl#$1",
"description": "Defines types of connectivity used in communication and bearer services accessible in certain connectivity.",
"modified": "2007-08-23",
"homepage": "http://www.tele.pw.edu.pl/~sims-onto/",
"keywords": [
"Security"
]
},
"msr": {
"name": "Measurement Ontology",
"prefix": "msr",
"uri_prefix": "http://www.telegraphis.net/ontology/measurement/measurement#$1",
"description": "The Measurement Ontology is an ontology in which measurements may be rendered",
"modified": "2009-06-06",
"keywords": [
"Methods"
],
"homepage": "http://www.telegraphis.net/ontology/measurement/measurement#"
},
"rdf": {
"name": "The RDF Concepts Vocabulary",
"prefix": "rdf",
"uri_prefix": "http://www.w3.org/1999/02/22-rdf-syntax-ns#$1",
"description": "This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts.",
"modified": "2019-12-16",
"homepage": "http://www.w3.org/TR/rdf11-concepts/",
"keywords": [
"W3C Rec"
]
},
"xhv": {
"name": "XHTML Vocabulary",
"prefix": "xhv",
"uri_prefix": "http://www.w3.org/1999/xhtml/vocab#$1",
"description": "This is a vocabulary collection utilized by XHTML Family modules and document types using XHTML Modularization, including XHTML Role and XHTML + RDFa as defined in rdfa-syntax.",
"modified": "2010-01-27",
"keywords": [
"API"
],
"homepage": "http://www.w3.org/1999/xhtml/vocab"
},
"rdfs": {
"name": "The RDF Schema vocabulary",
"prefix": "rdfs",
"uri_prefix": "http://www.w3.org/2000/01/rdf-schema#$1",
"description": "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary.",
"modified": "2014-02-25",
"homepage": "http://www.w3.org/TR/rdf-schema/",
"keywords": [
"W3C Rec"
]
},
"log": {
"name": "SWAP Logic Ontology",
"prefix": "log",
"uri_prefix": "http://www.w3.org/2000/10/swap/log#$1",
"description": "Une ontologie \"historique\" utilis\u00e9e par l'outil en ligne de commande cwm, au temps des balbutiements du web s\u00e9mantique (~ 2000 - 2003 ?)",
"modified": "2000-10-01",
"homepage": "http://www.w3.org/2000/10/swap/doc/CwmBuiltins",
"keywords": [
"RDF"
]
},
"con": {
"name": "Contact",
"prefix": "con",
"uri_prefix": "http://www.w3.org/2000/10/swap/pim/contact#$1",
"description": "Utility concepts for everyday life",
"modified": "2011-02-01",
"keywords": [
"People"
],
"homepage": "http://www.w3.org/2000/10/swap/pim/contact"
},
"doc": {
"name": "Works, licences, derivatives and dependencies",
"prefix": "doc",
"uri_prefix": "http://www.w3.org/2000/10/swap/pim/doc#$1",
"description": "Defines properties and relationships between works.",
"modified": "2006-07-29",
"keywords": [
"Catalogs"
],
"homepage": "http://www.w3.org/2000/10/swap/pim/doc"
},
"rec54": {
"name": "Model of the W3C Process",
"prefix": "rec54",
"uri_prefix": "http://www.w3.org/2001/02pd/rec54#$1",
"description": "This is (the start of) an event-based model of the W3C process; e.g. RECdd is the class of Recommendation Director's Decisions; \ti.e. messages to w3c-ac-members announcing a new W3C Recommendation.",
"modified": "2014-06-12",
"keywords": [
"Metadata"
],
"homepage": "http://www.w3.org/2001/02pd/rec54#"
},
"xsd": {
"name": "XML Schema",
"prefix": "xsd",
"uri_prefix": "http://www.w3.org/2001/XMLSchema#$1",
"description": "The XML Schema representation",
"keywords": [
"W3C Rec"
],
"homepage": "http://www.w3.org/2001/XMLSchema"
},
"tmo": {
"name": "Translational Medicine Ontology",
"prefix": "tmo",
"uri_prefix": "http://www.w3.org/2001/sw/hcls/ns/transmed/$1",
"description": "The Translational Medicine Ontology (TMO) is a high-level, patient-centric ontology that extends existing domain ontologies to integrate data across aspects of drug discovery and clinical practice. The ontology has been developed by participants in the World Wide Web Consortium's Semantic Web for Health Care and Life Sciences Interest Group",
"modified": "2012-07-03",
"keywords": [
"Health"
],
"homepage": "http://www.w3.org/2001/sw/hcls/ns/transmed/"
},
"owl": {
"name": "The OWL 2 Schema vocabulary",
"prefix": "owl",
"uri_prefix": "http://www.w3.org/2002/07/owl#$1",
"description": "This ontology partially describes the built-in classes and properties that together form the basis of the RDF/XML syntax of OWL 2.",
"modified": "2009-11-15",
"homepage": "http://www.w3.org/TR/owl2-rdf-based-semantics/",
"keywords": [
"W3C Rec"
]
},
"cal": {
"name": "Internet Calendaring and Scheduling Core Object Specification",
"prefix": "cal",
"uri_prefix": "http://www.w3.org/2002/12/cal/ical#$1",
"description": "A vocabulary for description of events and calendars",
"modified": "2015-01-11",
"homepage": "http://www.w3.org/TR/rdfcal/",
"keywords": [
"Time"
]
},
"geo": {
"name": "WGS84 Geo Positioning",
"prefix": "geo",
"uri_prefix": "http://www.w3.org/2003/01/geo/wgs84_pos#$1",
"description": "A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum.",
"modified": "2009-04-20",
"homepage": "http://www.w3.org/2003/01/geo/",
"keywords": [
"Geography"
]
},
"vs": {
"name": "SemWeb Vocab Status ontology",
"prefix": "vs",
"uri_prefix": "http://www.w3.org/2003/06/sw-vocab-status/ns#$1",
"description": "An RDF vocabulary for relating SW vocabulary terms to their status.",
"modified": "2011-12-12",
"keywords": [
"Metadata"
],
"homepage": "http://www.w3.org/2003/06/sw-vocab-status/ns"
},
"swrl": {
"name": "Semantic Web Rule Language",
"prefix": "swrl",
"uri_prefix": "http://www.w3.org/2003/11/swrl#$1",
"description": "OWL definition of the RDF Concrete Syntax for the Semantic Web Rule Language",
"modified": "2004-05-21",
"keywords": [
"Vocabularies"
],
"homepage": "http://www.w3.org/2003/11/swrl"
},
"exif": {
"name": "Exif data description vocabulary",
"prefix": "exif",
"uri_prefix": "http://www.w3.org/2003/12/exif/ns#$1",
"description": "Vocabulary to describe an Exif format picture data. All Exif 2.2 tags are defined as RDF properties, as well as several terms to help this schema.",
"modified": "2003-08-19",
"homepage": "http://www.w3.org/2003/12/exif/",
"keywords": [
"Image"
]
},
"grddl": {
"name": "Gleaning Resource Descriptions from Dialects of Languages Vocabulary",
"prefix": "grddl",
"uri_prefix": "http://www.w3.org/2003/g/data-view#$1",
"description": "Gleaning Resource Descriptions from Dialects of Languages Vocabulary",
"modified": "2007-10-31",
"keywords": [
"Vocabularies"
],
"homepage": "http://www.w3.org/2003/g/data-view"
},
"skos": {
"name": "Simple Knowledge Organization System",
"prefix": "skos",
"uri_prefix": "http://www.w3.org/2004/02/skos/core#$1",
"description": "The Simple Knowledge Organization System (SKOS) is a common data model for sharing and linking knowledge organization systems via the Semantic Web.",
"modified": "2009-08-18",
"homepage": "http://www.w3.org/2009/08/skos-reference/skos.html",
"keywords": [
"W3C Rec"
]
},
"rdfg": {
"name": "Graph",
"prefix": "rdfg",
"uri_prefix": "http://www.w3.org/2004/03/trix/rdfg-1/$1",
"description": "Properties allowing statement of intensional equivalence between RDF graphs",
"modified": "2004-12-31",
"homepage": "http://www.w3.org/2004/03/trix/",
"keywords": [
"RDF"
]
},
"swp": {
"name": "Graph Authority",
"prefix": "swp",
"uri_prefix": "http://www.w3.org/2004/03/trix/swp-1/$1",
"description": "This vocabulary allows to attach an authority to a named graph",
"modified": "2004-03-01",
"keywords": [
"RDF"
],
"homepage": "http://www.w3.org/2004/03/trix/swp-1"
},
"fresnel": {
"name": "Fresnel Lens and Format Core Vocabulary",
"prefix": "fresnel",
"uri_prefix": "http://www.w3.org/2004/09/fresnel#$1",
"description": "OWL Full vocabulary for defining lenses and formats on RDF models.",
"modified": "2015-01-11",
"keywords": [
"RDF"
],
"homepage": "http://www.w3.org/2004/09/fresnel"
},
"test": {
"name": "Test Metadata",
"prefix": "test",
"uri_prefix": "http://www.w3.org/2006/03/test-description#$1",
"description": "This ontology aims at defining the Quality Assurance Framework by collecting the test development experience of W3C Working Groups and summarizing the work done about tests and metadata.",
"modified": "2005-09-14",
"homepage": "http://www.w3.org/TR/test-metadata/",
"keywords": [
"Quality"
]
},
"gso": {
"name": "Generic Specific Ontology",
"prefix": "gso",
"uri_prefix": "http://www.w3.org/2006/gen/ont#$1",
"description": "Ontology for Relating Generic and Specific Information Resources",
"modified": "2009-04-20",
"keywords": [
"Support"
],
"homepage": "http://www.w3.org/2006/gen/ont"
},
"time": {
"name": "Time Ontology",
"prefix": "time",
"uri_prefix": "http://www.w3.org/2006/time#$1",
"description": "This vocabulary defines temporal entities such as time intervals, their properties and relationships.",
"modified": "2017-04-06",
"homepage": "http://www.w3.org/TR/owl-time",
"keywords": [
"Time"
]
},
"te": {
"name": "Time Entry",
"prefix": "te",
"uri_prefix": "http://www.w3.org/2006/time-entry#$1",
"description": "An entry sub-ontology of time (OWL-Time).",
"modified": "2012-08-31",
"keywords": [
"Time"
],
"homepage": "http://www.w3.org/2006/time-entry"
},
"tzont": {
"name": "Time Zone Ontology",
"prefix": "tzont",
"uri_prefix": "http://www.w3.org/2006/timezone#$1",
"description": "A vocabulary to describe time zones and their geographical coverage.",
"modified": "2006-12-31",
"keywords": [
"Time"
],
"homepage": "http://www.w3.org/2006/timezone"
},
"vcard": {
"name": "An Ontology for vCards",
"prefix": "vcard",
"uri_prefix": "http://www.w3.org/2006/vcard/ns#$1",
"description": "This ontology models and represents vCards in RDF using current best practices",
"modified": "2014-05-22",
"homepage": "http://www.w3.org/TR/vcard-rdf/",
"keywords": [
"People"
]
},
"wdrs": {
"name": "Protocol for Web Description Resources",
"prefix": "wdrs",
"uri_prefix": "http://www.w3.org/2007/05/powder-s#$1",
"description": "The Protocol for Web Description Resources (POWDER) allows metadata to be associated with groups of resources such as those found on a Web site.",
"modified": "2010-11-08",
"keywords": [
"API"
],
"homepage": "http://www.w3.org/2007/05/powder-s"
},
"common": {
"name": "The Delivery Context Ontology",
"prefix": "common",
"uri_prefix": "http://www.w3.org/2007/uwa/context/common.owl#$1",
"description": "The Delivery Context Ontology models the knowledge of the environment in which devices interact with the Web or other services",
"modified": "2019-10-23",
"keywords": [
"Multimedia",
"Support"
],
"homepage": "http://www.w3.org/2007/uwa/context/deliverycontext.owl"
},
"skosxl": {
"name": "SKOS eXtension for Labels",
"prefix": "skosxl",
"uri_prefix": "http://www.w3.org/2008/05/skos-xl#$1",
"description": "SKOS-XL defines an extension for the Simple Knowledge Organization System, providing additional support for describing and linking lexical entities.",
"modified": "2009-08-18",
"homepage": "http://www.w3.org/TR/skos-reference/skos-xl.html",
"keywords": [
"W3C Rec"
]
},
"cnt": {
"name": "Representing Content in RDF",
"prefix": "cnt",
"uri_prefix": "http://www.w3.org/2011/content#$1",
"description": "Representing Content in RDF as defined by http://www.w3.org/TR/Content-in-RDF/",
"modified": "2011-05-10",
"homepage": "http://www.w3.org/TR/Content-in-RDF10/",
"keywords": [
"RDF"
]
},
"http": {
"name": "HTTP in RDF",
"prefix": "http",
"uri_prefix": "http://www.w3.org/2011/http#$1",
"description": "A namespace for describing HTTP messages (http://www.w3.org/Protocols/rfc2616/rfc2616.html)",
"modified": "2011-04-29",
"keywords": [
"API"
],
"homepage": "http://www.w3.org/2011/http"
},
"vin": {
"name": "Wine Ontology",
"prefix": "vin",
"uri_prefix": "http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#$1",
"description": "This ontology was used as example in the first OWL Recommendation (February 2004)",
"modified": "2003-12-09",
"keywords": [
"Food"
],
"homepage": "http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine"
},
"fowl": {
"name": "Food Ontology in OWL",
"prefix": "fowl",
"uri_prefix": "http://www.w3.org/TR/2003/PR-owl-guide-20031209/food#$1",
"description": "Along with Wine Ontology, was used as example in the first OWL Recommendation (February 2004)",
"modified": "2013-02-23",
"keywords": [
"Food"
],
"homepage": "http://www.w3.org/TR/2003/PR-owl-guide-20031215/food"
},
"adms": {
"name": "Asset Description Metadata Schema",
"prefix": "adms",
"uri_prefix": "http://www.w3.org/ns/adms#$1",
"description": "ADMS is a profile of DCAT, used to describe semantic assets (or just 'Assets'), defined as highly reusable metadata (e.g. xml schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies) that are used for eGovernment system development.",
"modified": "2015-07-22",
"homepage": "http://www.w3.org/TR/vocab-adms/",
"keywords": [
"Metadata"
]
},
"acl": {
"name": "Basic Access Control ontology",
"prefix": "acl",
"uri_prefix": "http://www.w3.org/ns/auth/acl#$1",
"description": "Defines the element of Authorization and its essential properties, and also some classes of access such as read and write.",
"modified": "2012-12-18",
"homepage": "http://www.w3.org/wiki/WebAccessControl",
"keywords": [
"API"
]
},
"cert": {
"name": "The Cert Ontology",
"prefix": "cert",
"uri_prefix": "http://www.w3.org/ns/auth/cert#$1",
"description": "Ontology for Certificates and crypto stuff.",
"modified": "2008-11-13",
"keywords": [
"Quality"
],
"homepage": "http://www.w3.org/ns/auth/cert#"
},
"csvw": {
"name": "CSV on the Web Vocabulary",
"prefix": "csvw",
"uri_prefix": "http://www.w3.org/ns/csvw#$1",
"description": "This document describes the RDFS vocabulary description used in the Metadata Vocabulary for Tabular Data along with the default JSON-LD Context.",
"modified": "2015-12-17",
"keywords": [
"Vocabularies",
"W3C Rec"
],
"homepage": "http://www.w3.org/ns/csvw#"
},
"dcat": {
"name": "Data Catalog Vocabulary",
"prefix": "dcat",
"uri_prefix": "http://www.w3.org/ns/dcat#$1",
"description": "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web",
"modified": "2020-02-04",
"homepage": "http://www.w3.org/TR/vocab-dcat/",
"keywords": [
"W3C Rec"
]
},
"dqv": {
"name": "Data Quality Vocabulary",
"prefix": "dqv",
"uri_prefix": "http://www.w3.org/ns/dqv#$1",
"description": "The Data Quality Vocabulary (DQV) is seen as an extension to DCAT to cover the quality of the data, how frequently is it updated, whether it accepts user corrections, persistence commitments etc. When used by publishers, this vocabulary will foster trust in the data amongst developers.",
"modified": "2016-08-26",
"homepage": "https://www.w3.org/TR/vocab-dqv/",
"keywords": [
"Quality"
]
},
"duv": {
"name": "Dataset Usage Vocabulary",
"prefix": "duv",
"uri_prefix": "http://www.w3.org/ns/duv#$1",
"description": "The Dataset Usage Vocabulary (DUV) is used to describe consumer experiences, citations, and feedback about datasets from the human perspective.",
"modified": "2016-08-30",
"keywords": [
"People",
"Society"
],
"homepage": "http://www.w3.org/ns/duv"
},
"prof": {
"name": "Profiles Vocabulary",
"prefix": "prof",
"uri_prefix": "http://www.w3.org/ns/dx/prof/$1",
"description": "This vocabulary is for describing relationships between standards/specifications, profiles of them and supporting artifacts such as validating resources.\n\nThis model starts with [http://dublincore.org/2012/06/14/dcterms#Standard](dct:Standard) entities which can either be Base Specifications (a standard not profiling any other Standard) or Profiles (Standards which do profile others). Base Specifications or Profiles can have Resource Descriptors associated with them that defines implementing rules for the it. Resource Descriptors must indicate the role they play (to guide, to validate etc.) and the formalism they adhere to (dct:format) to allow for content negotiation. A vocabulary of Resource Roles are provided alongside this vocabulary but that list is extensible.",
"modified": "2018-02-16",
"keywords": [
"Metadata",
"RDF"
],
"homepage": "http://www.w3.org/ns/dx/prof"
},
"earl": {
"name": "Evaluation and Report Language",
"prefix": "earl",
"uri_prefix": "http://www.w3.org/ns/earl#$1",
"description": "EARL is a vocabulary, the terms of which are defined across a set of specifications and technical notes, and that is used to describe test results. The primary motivation for developing this vocabulary is to facilitate the exchange of test results between Web accessibility evaluation tools in a vendor-neutral and platform-independent format. It also provides reusable terms for generic quality assurance and validation purposes.",
"modified": "2011-05-10",
"homepage": "http://www.w3.org/TR/EARL10/",
"keywords": [
"Quality"
]
},
"hydra": {
"name": "The Hydra Core Vocabulary",
"prefix": "hydra",
"uri_prefix": "http://www.w3.org/ns/hydra/core#$1",
"description": "A lightweight vocabulary for hypermedia-driven Web APIs",
"modified": "2015-01-11",
"homepage": "http://www.w3.org/ns/hydra/spec/latest/core/",
"keywords": [
"RDF"
]
},
"ldp": {
"name": "Linked Data Platform",
"prefix": "ldp",
"uri_prefix": "http://www.w3.org/ns/ldp#$1",
"description": "A set of best practices and simple approach for a read-write Linked Data architecture, based on HTTP access to web resources that describe their state using the RDF data model.",
"modified": "2015-02-26",
"homepage": "http://www.w3.org/TR/ldp/",
"keywords": [
"API"
]
},
"lexdcp": {
"name": "Lexicon Model for Ontologies - Decomp",
"prefix": "lexdcp",
"uri_prefix": "http://www.w3.org/ns/lemon/decomp#$1",
"description": "A model for the representation of lexical information relative to ontologies. Decomposition module.",
"modified": "2016-01-10",
"keywords": [
"Support",
"Tag"
],
"homepage": "http://www.w3.org/ns/lemon/decomp"
},
"lime": {
"name": "Lexicon Model for Ontologies - LIngusitic MEtadata (LIME)",
"prefix": "lime",
"uri_prefix": "http://www.w3.org/ns/lemon/lime#$1",
"description": "LIME (LInguistic MEtadata) is a vocabulary for expressing linguistic metadata about linguistic resources and linguistically grounded datasets.",
"modified": "2016-01-10",
"keywords": [
"General & Upper",
"Support"
],
"homepage": "http://www.w3.org/ns/lemon/lime"
},
"ontolex": {
"name": "Lexicon Model for Ontologies - Core",
"prefix": "ontolex",
"uri_prefix": "http://www.w3.org/ns/lemon/ontolex#$1",
"description": "A model for the representation of lexical information relative to ontologies. Core module.",
"modified": "2016-01-10",
"homepage": "https://www.w3.org/2016/05/ontolex/",
"keywords": [
"Support",
"Tag"
]
},
"synsem": {
"name": "Lexicon Model for Ontologies - Synsem",
"prefix": "synsem",
"uri_prefix": "http://www.w3.org/ns/lemon/synsem#$1",
"description": "A model for the representation of lexical information relative to ontologies. Syntax and semantics module.",
"modified": "2016-01-10",
"keywords": [
"Support",
"Tag"
],
"homepage": "http://www.w3.org/ns/lemon/synsem"
},
"vartrans": {
"name": "Lexicon Model for Ontologies - Vartrans",
"prefix": "vartrans",
"uri_prefix": "http://www.w3.org/ns/lemon/vartrans#$1",
"description": "A model for the representation of lexical information relative to ontologies. Variation and translation module.",
"modified": "2016-01-10",
"keywords": [
"Support"
],
"homepage": "http://www.w3.org/ns/lemon/vartrans"
},
"locn": {
"name": "ISA Programme Location Core Vocabulary",
"prefix": "locn",
"uri_prefix": "http://www.w3.org/ns/locn#$1",
"description": "The ISA Programme Location Core Vocabulary provides a minimum set of classes and properties for describing any place in terms of its name, address or geometry. The vocabulary is specifically designed to aid the publication of data that is interoperable with EU INSPIRE Directive.",
"modified": "2015-03-23",
"keywords": [
"Geography",
"Geometry"
],
"homepage": "http://www.w3.org/ns/locn"
},
"ma-ont": {
"name": "Ontology for Media Resources",
"prefix": "ma-ont",
"uri_prefix": "http://www.w3.org/ns/ma-ont#$1",
"description": "The Ontology for Media Resources 1.0 describes a core vocabulary of properties and a set of mappings between different metadata formats of media resources hat describe media resources published on the Web (as opposed to local archives, museums, or other non-web related and non-shared collections of media resources).",
"modified": "2013-03-20",
"homepage": "http://www.w3.org/TR/mediaont-10/",
"keywords": [
"Multimedia"
]
},
"mls": {
"name": "Machine Learning Schema",
"prefix": "mls",
"uri_prefix": "http://www.w3.org/ns/mls#$1",
"description": "ML-Schema is a collaborative, community effort with a mission to develop, maintain, and promote standard schemas for data mining and machine learning algorithms, datasets, and experiments",
"modified": "2016-10-17",
"homepage": "http://ml-schema.github.io/documentation/",
"keywords": [
"Methods",
"Support"
]
},
"oa": {
"name": "Open Annotation Data Model",
"prefix": "oa",
"uri_prefix": "http://www.w3.org/ns/oa#$1",
"description": "The Open Annotation Core Data Model specifies an interoperable framework for creating associations between related resources, annotations, using a methodology that conforms to the Architecture of the World Wide Web. This ontology is a non-normative OWL formalization of the textual OA specification at http://www.openannotation.org/spec/core/20130208/index.html",
"modified": "2016-11-12",
"keywords": [
"Quality"
],
"homepage": "http://www.w3.org/ns/oa#"
},
"odrl": {
"name": "The Open Digital Rights Language (ODRL) Ontology",
"prefix": "odrl",
"uri_prefix": "http://www.w3.org/ns/odrl/2/$1",
"description": "The Open Digital Rights Language (ODRL) provides flexible and interoperable mechanisms to support transparent and innovative use of digital content in publishing, distribution, and consumption of of digital media across all sectors and communities. The ODRL Policy model is broad enough to support traditional rights expressions for commercial transaction, open access expressions for publicly distributed content, and privacy expressions for social media.",
"modified": "2017-09-16",
"homepage": "https://www.w3.org/TR/odrl-vocab/",
"keywords": [
"Metadata"
]
},
"org": {
"name": "Core organization ontology",
"prefix": "org",
"uri_prefix": "http://www.w3.org/ns/org#$1",
"description": "Vocabulary for describing organizational structures, specializable to a broad variety of types of organization.",
"modified": "2014-04-12",
"homepage": "http://www.w3.org/TR/vocab-org/",
"keywords": [
"W3C Rec"
]
},
"person": {
"name": "ISA Programme Person Core Vocabulary",
"prefix": "person",
"uri_prefix": "http://www.w3.org/ns/person#$1",
"description": "The Person Core Vocabulary provides a minimum set of classes and properties for describing a natural person",
"modified": "2014-06-19",
"keywords": [
"People"
],
"homepage": "http://www.w3.org/ns/person"
},
"prov": {
"name": "W3C PROVenance Interchange",
"prefix": "prov",
"uri_prefix": "http://www.w3.org/ns/prov#$1",
"description": "The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web.",
"modified": "2015-01-11",
"homepage": "http://www.w3.org/TR/prov-o/",
"keywords": [
"W3C Rec"
]
},
"rr": {
"name": "RDB to RDF Mapping Language Schema",
"prefix": "rr",
"uri_prefix": "http://www.w3.org/ns/r2rml#$1",
"description": "A vocabulary which can be used to specify a mapping of relational data to RDF.",
"modified": "2012-07-16",
"homepage": "http://www.w3.org/TR/r2rml/",
"keywords": [
"RDF"
]
},
"radion": {
"name": "Repository Asset Distribution",
"prefix": "radion",
"uri_prefix": "http://www.w3.org/ns/radion#$1",
"description": "RADion, and the higher level vocabularies that build upon it, are intended as a model that facilitates federation and co-operation. It is not the primary intention that repository owners redesign or convert their current systems and data to conform to RADion, but rather that it acts as a common layer among repositories that want to exchange data.",
"modified": "2012-10-11",
"keywords": [
"Metadata"
],
"homepage": "http://www.w3.org/ns/radion#"
},
"rdfa": {
"name": "RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting",
"prefix": "rdfa",
"uri_prefix": "http://www.w3.org/ns/rdfa#$1",
"description": "This document describes the RDFa Vocabulary for Term and Prefix Assignment. The Vocabulary is used to modify RDFa 1.1 processing behavior",
"modified": "2013-03-11",
"keywords": [
"RDF"
],
"homepage": "http://www.w3.org/ns/rdfa#"
},
"rdft": {
"name": "The RDF 1.1 Test Vocabulary",
"prefix": "rdft",
"uri_prefix": "http://www.w3.org/ns/rdftest#$1",
"description": "This is a vocabulary document and is used to define classes and properties used in\n RDF 1.1 Test Cases and associated test manifests.\n The URI of the vocabulary is http://www.w3.org/ns/rdftest# (abbreviated by rdft: in this document).\n Turtle and an JSON-LD versions of the vocabulary are also available.\n The vocabulary is published by W3C.",
"modified": "2014-02-25",
"keywords": [
"RDF",
"W3C Rec"
],
"homepage": "http://www.w3.org/ns/rdftest"
},
"rov": {
"name": "Registered Organization Vocabulary",
"prefix": "rov",
"uri_prefix": "http://www.w3.org/ns/regorg#$1",
"description": "The Registered Organization Vocabulary is a profile of the Organization Ontology for describing organizations that have gained legal entity status through a formal registration process, typically in a national or regional register.",
"modified": "2013-12-21",
"homepage": "http://www.w3.org/2011/gld/",
"keywords": [
"Society"
]
},
"sh": {
"name": "W3C Shapes Constraint Language (SHACL) Vocabulary",
"prefix": "sh",
"uri_prefix": "http://www.w3.org/ns/shacl#$1",
"description": "This vocabulary defines terms used in SHACL, the W3C Shapes Constraint Language.",
"modified": "2017-07-20",
"homepage": "https://www.w3.org/TR/shacl/",
"keywords": [
"Quality",
"W3C Rec"
]
},
"solid": {
"name": "Solid terms",
"prefix": "solid",
"uri_prefix": "http://www.w3.org/ns/solid/terms#$1",
"description": "Solid terms",
"modified": "2018-01-24",
"keywords": [
"General & Upper",
"Services"
],
"homepage": "http://www.w3.org/ns/solid/terms"
},
"sosa": {
"name": "Sensor, Observation, Sample, and Actuator (SOSA) Ontology",
"prefix": "sosa",
"uri_prefix": "http://www.w3.org/ns/sosa/$1",
"description": "This ontology is based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group.",
"modified": "2017-04-17",
"keywords": [
"Environment",
"IoT"
],
"homepage": "http://www.w3.org/ns/sosa/"
},
"sd": {
"name": "SPARQL 1.1 Service Description",
"prefix": "sd",
"uri_prefix": "http://www.w3.org/ns/sparql-service-description#$1",
"description": "Un vocabulaire pour d\u00e9crire des services SPARQL publi\u00e9s via le protocole SPARQL 1.1 pour RDF. Ces descriptions fournissent un m\u00e9canisme par lequel un client ou un utilisateur final peuvent obtenir des informations sur le service SPARQL, telles que les extensions de fonctions support\u00e9es ou les d\u00e9tails \u00e0 propos des jeux de donn\u00e9es disponibles.",
"modified": "2013-03-21",
"homepage": "http://www.w3.org/TR/sparql11-service-description/",
"keywords": [
"W3C Rec"
]
},
"ssno": {
"name": "Semantic Sensor Network Ontology",
"prefix": "ssno",
"uri_prefix": "http://www.w3.org/ns/ssn/$1",
"description": "This ontology describes sensors and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.",
"modified": "2017-04-17",
"keywords": [
"IoT",
"Methods",
"W3C Rec"
],
"homepage": "http://www.w3.org/ns/ssn/"
},
"ssn": {
"name": "Semantic Sensor Network Ontology",
"prefix": "ssn",
"uri_prefix": "http://www.w3.org/ns/ssn/$1",
"description": "This ontology describes sensors and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.",
"modified": "2017-04-17",
"keywords": [
"IoT",
"Methods",
"W3C Rec"
],
"homepage": "http://www.w3.org/ns/ssn/"
},
"ui": {
"name": "A user interface ontology",
"prefix": "ui",
"uri_prefix": "http://www.w3.org/ns/ui#$1",
"description": "An ontology suitable for describing forms, sequences in widgets",
"modified": "2020-03-22",
"keywords": [
"Support"
],
"homepage": "http://www.w3.org/ns/ui"
},
"caso": {
"name": "Context Aware System Observation Ontology",
"prefix": "caso",
"uri_prefix": "http://www.w3id.org/def/caso#$1",
"description": "CASO (Context Aware System Observation) is an ontology for context aware system and observation services. Its goal is to describe all the processing of the context.",
"modified": "2021-02-23",
"keywords": [
"IoT"
],
"homepage": "http://www.w3id.org/def/caso#"
},
"uiot": {
"name": "Urban IoT Ontologies - Core Module",
"prefix": "uiot",
"uri_prefix": "http://www.w3id.org/urban-iot/core#$1",
"description": "Modulo core delle ontologie per gli apparati IoT urbani.",
"modified": "2020-12-02",
"keywords": [
"IoT",
"Services"
],
"homepage": "http://www.w3id.org/urban-iot/core"
},
"uiote": {
"name": "Ontologie per gli Apparati IoT Urbani - Modulo Electric Mobility",
"prefix": "uiote",
"uri_prefix": "http://www.w3id.org/urban-iot/electric#$1",
"description": "Modulo Electric Mobility delle ontologie per gli apparati IoT urbani.",
"modified": "2020-01-01",
"keywords": [
"IoT",
"Transport"
],
"homepage": "http://www.w3id.org/urban-iot/electric"
},
"uiots": {
"name": "Ontologie per gli Apparati IoT Urbani - Modulo Sharing Mobility",
"prefix": "uiots",
"uri_prefix": "http://www.w3id.org/urban-iot/sharing#$1",
"description": "Sharing Mobility module of the suite of ontologies for urban IoT devices.",
"keywords": [
"Services",
"Transport"
],
"homepage": "http://www.w3id.org/urban-iot/sharing"
},
"d2rq": {
"name": "D2RQ - Language Specification",
"prefix": "d2rq",
"uri_prefix": "http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1#$1",
"description": "This document specifies the D2RQ mapping language. D2RQ is a declarative language to describe mappings between relational database schemata and OWL/RDFS ontologies.",
"modified": "2012-03-12",
"homepage": "http://d2rq.org/",
"keywords": [
"RDF"
]
},
"wl": {
"name": "WSMO-Lite Ontology",
"prefix": "wl",
"uri_prefix": "http://www.wsmo.org/ns/wsmo-lite#$1",
"description": "WSMO-Lite is a lightweight approach to the semantic annotation of Web service descriptions, defined by the STI2 working group Conceptual Models for Services",
"modified": "2013-05-30",
"homepage": "http://www.wsmo.org/ns/wsmo-lite/",
"keywords": [
"API"
]
},
"foaf": {
"name": "Friend of a Friend vocabulary",
"prefix": "foaf",
"uri_prefix": "http://xmlns.com/foaf/0.1/$1",
"description": "FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people's heads, in physical or digital documents, or in the form of factual data, it can be linked.",
"modified": "2014-01-14",
"homepage": "http://www.foaf-project.org/",
"keywords": [
"People"
]
},
"wot": {
"name": "Web Of Trust",
"prefix": "wot",
"uri_prefix": "http://xmlns.com/wot/0.1/$1",
"description": "Web Of Trust (wot) RDF vocabulary, described using W3C RDF Schema and the Web Ontology Language.",
"modified": "2004-02-23",
"keywords": [
"Quality",
"Security"
],
"homepage": "http://xmlns.com/wot/0.1/"
},
"zbwext": {
"name": "ZBW Extensions",
"prefix": "zbwext",
"uri_prefix": "http://zbw.eu/namespaces/zbw-extensions/$1",
"description": "Extensions to SKOS and other standard vocabularies used by the German National Library of Economics (ZBW)",
"modified": "2017-04-12",
"keywords": [
"Vocabularies"
],
"homepage": "http://zbw.eu/namespaces/zbw-extensions"
},
"spvqa": {
"name": "Scholarly Papers Vocabulary with Focus on Qualtitative Analysis",
"prefix": "spvqa",
"uri_prefix": "https://bmake.th-brandenburg.de/spv#$1",
"description": "The ontology is aimed at the support of research groups in the field of Business Modeling and Knowledge Engineering (BMaKE) in their collaborative work for qualitatively analyzing scholarly papers as well as sharing the results of that analyses and judgements.",
"modified": "2017-06-05",
"homepage": "https://bmake.th-brandenburg.de/spv",
"keywords": [
"Quality",
"Tag",
"Vocabularies"
]
},
"istex": {
"name": "Istex ontology for scholarly documents and extracted entities",
"prefix": "istex",
"uri_prefix": "https://data.istex.fr/ontology/istex#$1",
"description": "ISTEX est une plateforme qui a pour ambition d\u2019offrir, \u00e0 l\u2019ensemble de la communaut\u00e9 de l\u2019enseignement sup\u00e9rieur et de la recherche fran\u00e7aise qui le souhaite, un acc\u00e8s en ligne aux collections r\u00e9trospectives de la litt\u00e9rature scientifique dans toutes les disciplines. \u00c0 ce r\u00e9servoir in\u00e9gal\u00e9 en ressources multidisciplinaires s\u2019ajoute un nombre important de services \u00e0 valeur ajout\u00e9e permettant d\u2019en optimiser l\u2019exploitation gr\u00e2ce \u00e0 des outils de fouille de contenus (TDM) et de valorisation interactive.",
"modified": "2018-12-17",
"homepage": "https://data.istex.fr/ontology/istex/",
"keywords": [
"Academy",
"Metadata",
"Press"
]
},
"atm": {
"name": "Air Traffic Management (ATM) Vocabulary",
"prefix": "atm",
"uri_prefix": "https://data.nasa.gov/ontologies/atmonto/ATM#$1",
"description": "Defines specific air traffic management concepts used in aircraft navigation through the US National Airspace System",
"modified": "2018-03-28",
"keywords": [
"Transport",
"Travel"
],
"homepage": "https://data.nasa.gov/ontologies/atmonto/ATM#"
},
"nas": {
"name": "US National Airspace System (NAS) vocabulary",
"prefix": "nas",
"uri_prefix": "https://data.nasa.gov/ontologies/atmonto/NAS#$1",
"description": "Defines concepts related to the structure of the US National Airspace System (NAS)",
"modified": "2018-03-28",
"keywords": [
"Transport",
"Travel"
],
"homepage": "https://data.nasa.gov/ontologies/atmonto/NAS#"
},
"atd": {
"name": "Air Traffic Data",
"prefix": "atd",
"uri_prefix": "https://data.nasa.gov/ontologies/atmonto/data#$1",
"description": "Defines concepts related to airport status, including weather, forecasts, and airport operations",
"modified": "2018-03-28",
"keywords": [
"IoT",
"Transport"
],
"homepage": "https://data.nasa.gov/ontologies/atmonto/data#"
},
"eqp": {
"name": "Aircraft Equipment Vocabulary",
"prefix": "eqp",
"uri_prefix": "https://data.nasa.gov/ontologies/atmonto/equipment#$1",
"description": "Defines aircraft models, aircraft systems / subsystems, and aircraft characteristics",
"modified": "2018-03-28",
"keywords": [
"Industry",
"Transport",
"Travel"
],
"homepage": "https://data.nasa.gov/ontologies/atmonto/equipment#"
},
"atts": {
"name": "Air Traffic Temporal and Spacial Vocabulary",
"prefix": "atts",
"uri_prefix": "https://data.nasa.gov/ontologies/atmonto/general#$1",
"description": "Defines temporal / spatial concepts and general-purpose datastructures",
"modified": "2018-03-28",
"keywords": [
"Geography",
"Geometry",
"IoT",
"Time"
],
"homepage": "https://data.nasa.gov/ontologies/atmonto/general#"
},
"decision": {
"name": "Decision ontology",
"prefix": "decision",
"uri_prefix": "https://decision-ontology.googlecode.com/svn/trunk/decision.owl#$1",
"description": "Decision-making is a process that can result in some decision and decision is a situation of indicating one of the considered options. Decision Ontology provides means for precise distinguishing and distinct treatment of these two aspects.",
"modified": "2012-04-18",
"homepage": "http://code.google.com/p/decision-ontology/",
"keywords": [
"Support"
]
},
"tresiot": {
"name": "Ontology for Trust Recommendation in Social Internet of Things",
"prefix": "tresiot",
"uri_prefix": "https://liidr.org/trust-recommendation-in-social-internet-of-things/$1",
"description": "This ontology models trust recommendation concepts in SIoT to bridge the gap between abstract trust concepts and real-world device concepts.",
"modified": "2023-05-12",
"keywords": [
"IoT"
],
"homepage": "https://liidr.org/trust-recommendation-in-social-internet-of-things/"
},
"ei2a": {
"name": "Aragon Interoperable Information Structure Ontology\nEI2A",
"prefix": "ei2a",
"uri_prefix": "http://opendata.aragon.es/def/ei2a#$1",
"description": "The initiative Arag\u00f3n Open Data was initiated by agreement of 17 of July of 2012 of the Government of Aragon. Under the same was ordered the start of the project to open public data and on February 6, 2013 was implemented through the Portal opendata.aragon.es .\n\nThroughout this time there have been numerous works to achieve automation in the publication of information to ensure that third parties can reuse it in the best way. Given the volume of data that begins to exist, within the line of work of automation in information management, all those elements that help in the improvement of the structuring of information and the standardization of the data contained in the databases are beginning to have a special relevance.\n\nBased on this, within the General Directorate of Electronic Administration and Information Society, the idea arises of generating a set of technical and legal rules that allow to deepen in that standardization and that lead to think in the creation of the Interoperable Information Scheme Of Aragon (E2IA). The E2IA thus emerges as the framework in which the open data and in general the information of the Government of Aragon can begin to be automated in a much more profound way. The E2IA has to have a number of technical, organizational and legal elements that need to be developed.\n\nFor this reason, the Technological Institute of Aragon (ITAINNOVA) has been entrusted with carrying out actions consisting in identifying, studying and analyzing current research trends and technological development in relation to ontologies and dictionaries of data interoperability, defining the ontological proposal, performing The necessary tests to validate the ontological proposal and generate the text and web versions of the ontology.",
"modified": "2021-10-21",
"homepage": "https://opendata.aragon.es/def/ei2a/index.en.htm",
"keywords": [
"Government",
"Vocabularies"
]
},
"ci": {
"name": "A Content Inventory Vocabulary",
"prefix": "ci",
"uri_prefix": "https://privatealpha.com/ontology/content-inventory/1#$1",
"description": "This vocabulary defines a number of concepts peculiar to content strategy which are not accounted for by other vocabularies.",
"modified": "2018-10-06",
"keywords": [
"Metadata"
],
"homepage": "https://privatealpha.com/ontology/content-inventory/1#"
},
"ibis": {
"name": "IBIS Vocabulary",
"prefix": "ibis",
"uri_prefix": "https://privatealpha.com/ontology/ibis/1#$1",
"description": "This document specifies a vocabulary for describing an IBIS (issue-based information system).",
"modified": "2018-02-22",
"keywords": [
"People",
"Society"
],
"homepage": "https://privatealpha.com/ontology/ibis/1#"
},
"tfo": {
"name": "Transformation Functions Ontology",
"prefix": "tfo",
"uri_prefix": "https://privatealpha.com/ontology/transformation/1#$1",
"description": "This document describes functions which transform HTTP representations, i.e., the actual literal payloads of HTTP messages.",
"keywords": [
"Methods"
],
"homepage": "https://privatealpha.com/ontology/transformation/1#"
},
"apco": {
"name": "African Public Contract Ontology",
"prefix": "apco",
"uri_prefix": "https://purl.org/cm/onto/apco#$1",
"description": "APCO is an ontology that allows the description of public procurement terms",
"modified": "2022-08-31",
"keywords": [
"Government",
"Services"
],
"homepage": "https://purl.org/cm/onto/apco"
},
"edifact-o": {
"name": "EDIFACT Ontology",
"prefix": "edifact-o",
"uri_prefix": "https://purl.org/edifact/ontology#$1",
"description": "An Ontology for representing EDIFACT Messages.",
"modified": "2023-12-06",
"keywords": [
"Methods"
],
"homepage": "https://purl.org/edifact/ontology"
},
"airs": {
"name": "Alliance of Information and Referral Services (AIRS) Vocabulary",
"prefix": "airs",
"uri_prefix": "https://raw.githubusercontent.com/airs-linked-data/lov/latest/src/airs_vocabulary.ttl#$1",
"description": "The AIRS Linked Open Vocabulary is a way to describe human services information and referral (I&R) concepts. AIRS is the Alliance of Information and Referral Services (airs.org), which possesses over 1,000 member agencies primarily in the United States and Canada. The AIRS LOV is based on the AIRS XML Schema, available at: https://airs-xml.googlecode.com/hg/tags/3.1/airs.xsd",
"modified": "2015-02-15",
"homepage": "https://github.com/airs-linked-data/lov",
"keywords": [
"Services"
]
},
"saref": {
"name": "SAREF: the Smart Appliances REFerence ontology",
"prefix": "saref",
"uri_prefix": "https://saref.etsi.org/core/$1",
"description": "The Smart Appliances REFerence (SAREF) ontology is a shared model of consensus that facilitates the matching of existing assets (standards/protocols/datamodels/etc.) in the smart appliances domain. The SAREF ontology provides building blocks that allow separation and recombination of different parts of the ontology depending on specific needs.",
"modified": "2020-05-29",
"keywords": [
"Industry",
"IoT",
"Services"
],
"homepage": "https://saref.etsi.org/core/"
},
"s4agri": {
"name": "SAREF extension for Agriculture",
"prefix": "s4agri",
"uri_prefix": "https://saref.etsi.org/saref4agri/$1",
"description": "This ontology extends the SAREF ontology for the Agricultural domain. This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx), which was established with the goal to create three SAREF extensions, one of them for the Agricultural domain.",
"modified": "2020-06-05",
"keywords": [
"Food",
"IoT"
],
"homepage": "https://saref.etsi.org/saref4agri/"
},
"s4bldg": {
"name": "SAREF extension for building devices",
"prefix": "s4bldg",
"uri_prefix": "https://saref.etsi.org/saref4bldg/$1",
"description": "This ontology extends the SAREF ontology for the building domain by defining building devices and how they are located in a building. This extension is based on the ISO 16739:2013 Industry Foundation Classes (IFC) standard for data sharing in the construction and facility management industries. The descriptions of the classes and properties extracted from IFC have been taken from the IFC documentation.",
"modified": "2020-06-05",
"keywords": [
"IoT"
],
"homepage": "https://saref.etsi.org/saref4bldg/"
},
"s4city": {
"name": "SAREF extension for Smart City",
"prefix": "s4city",
"uri_prefix": "https://saref.etsi.org/saref4city/$1",
"description": "This ontology extends the SAREF ontology for the Smart City domain. This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx), which was established with the goal to create three SAREF extensions, one of them for the Smart City domain.",
"modified": "2020-06-05",
"keywords": [
"Government",
"IoT"
],
"homepage": "https://saref.etsi.org/saref4city/"
},
"s4ehaw": {
"name": "SAREF4EHAW: an extension of SAREF for eHealth Ageing Well domain",
"prefix": "s4ehaw",
"uri_prefix": "https://saref.etsi.org/saref4ehaw/$1",
"description": "The objective of SAREF4EHAW is to extend SAREF ontology for the eHealth/Ageing-well (EHAW) vertical. Clause 4.1 of the present document shortly introduces a high level view of the envisioned SAREF4EHAW semantic model and modular ontology, with the retained concepts (i.e. classes) and their relations. \nSAREF4EHAW extension has been specified and formalised by investigating EHAW domain related resources, as reported in ETSI TR 103 509, such as: potential stakeholders, standardization initiatives, alliances/associations, European projects, EC directives, existing ontologies, and data repositories. Therefore, SAREF4EHAW modular ontology shall both:\n - Allow the implementation of a limited set of typical EHAW related use cases already identified in ETSI TR 103 509, i.e.\n - Use case 1 ?elderly at home monitoring and support?,\n - Use case 2 ?monitoring and support of healthy lifestyles for citizens?,\n - Use case 3 ?Early Warning System (EWS) and Cardiovascular Accidents detection?.\n - Fulfil the eHealth Ageing Well related requirements provided in ETSI TR 103 509, mainly the ontological ones that were mostly taken as input for the ontology specification.\n\nSAREF4EHAW mainly reuses the following existing ontologies: SAREF, ETSI SmartBAN reference model, SAREF 4 Environment extension and W3C SSN System module. The following figure presents the high level view of SAREF4EHAW ontology.\n\nFor semantic interoperability handling purposes, an ontology based solution, combined with sensing-as-a-service and WoT strategies, is retained for SAREF4EHAW. Therefore, an upper level ontology, at service level, shall also behas been fully modelled (Service class and sub-classes depicted in the previous figure).\nFor embedded semantic analytics purposes, SAREF4EHAW shall behas been designed using the modularity principle (see ETSI TR 103 509) and can thus be mainly described by the following self-contained knowledge sub-ontologies (or modules): HealthActor, Ban, HealthDevice, Function (measured data related concepts included) and Service.",
"modified": "2020-05-01",
"keywords": [
"IoT"
],
"homepage": "https://saref.etsi.org/saref4ehaw/"
},
"s4ener": {
"name": "SAREF4EE: the EEbus/Energy@home extension of SAREF",
"prefix": "s4ener",
"uri_prefix": "https://saref.etsi.org/saref4ener/$1",
"description": "This is the extension of SAREF for the EEBus and Energy@Home project. The documentation of SAREF4EE is available at http://ontology.tno.nl/SAREF4EE_Documentation_v0.1.pdf. SAREF4EE represents 1) The configuration information exchanged in the use case 'Remote Network Management' according to the EEBus Technical Report, Protocol Specification- Remote Network Management, version 1.0.0.2, 2015-09-19; 2) The scheduling information about power sequences exchanged in the use cases Appliance scheduling through CEM and remote start' and 'Automatic cycle rescheduling', according to the message structures described in General Message Structures, version 0.1.1, 2015-10-07; 3) The monitor and control information exchanged in the use case 'Communicate appliance status and info on manually planned cycles', according to the monitoring and control part of the Energy@Home Data Model, version 1.0; and 4) the event-based data exchanged in the use case 'Demand Response', according to General Message Structures, version 0.1.1, 2015-10-07.",
"modified": "2020-06-04",
"keywords": [
"Environment",
"Services"
],
"homepage": "https://saref.etsi.org/saref4ener/"
},
"s4envi": {
"name": "SAREF extension for environment",
"prefix": "s4envi",
"uri_prefix": "https://saref.etsi.org/saref4envi/$1",
"description": "This ontology extends the SAREF ontology for the environment domain, specifically for the light pollution domain, including concepts like photometers, light, etc.",
"modified": "2021-02-25",
"keywords": [
"Environment",
"IoT"
],
"homepage": "https://saref.etsi.org/saref4envi/"
},
"s4inma": {
"name": "SAREF4INMA: an extension of SAREF for the industry and manufacturing domain",
"prefix": "s4inma",
"uri_prefix": "https://saref.etsi.org/saref4inma/$1",
"description": "SAREF4INMA is an extension of SAREF for the industry and manufacturing domain. SAREF4INMA focuses on extending SAREF for the industry and manufacturing domain to solve the lack of interoperability between various types of production equipment that produce items in a factory and, once outside the factory, between different organizations in the value chain to uniquely track back the produced items to the corresponding production equipment, batches, material and precise time in which they were manufactured. SAREF4INMA is specified and published by ETSI in the TS 103 410-5 associated to this ontology file. SAREF4INMA was created to be aligned with related initiatives in the smart industry and manufacturing domain in terms of modelling and standardization, such as the Reference Architecture Model for Industry 4.0 (RAMI), which combines several standards used by the various national initiatives in Europe that support digitalization in manufacturing. The full list of use cases, standards and requirements that guided the creation of SAREF4INMA are described in the associated ETSI TR 103 507.",
"modified": "2019-04-30",
"keywords": [
"Industry",
"IoT"
],
"homepage": "https://saref.etsi.org/saref4inma/"
},
"s4syst": {
"name": "SAREF4SYST: an extension of SAREF for typology of systems and their inter-connections",
"prefix": "s4syst",
"uri_prefix": "https://saref.etsi.org/saref4syst/$1",
"description": "The present document is the technical specification of SAREF4SYST, a generic extension of [ETSI TS 103 264 SAREF](https://www.etsi.org/deliver/etsi_ts/103200_103299/103264/02.01.01_60/ts_103264v020101p.pdf) that defines an ontology pattern which can be instantiated for different domains. SAREF4SYST defines Systems, Connections between systems, and Connection Points at which systems may be connected. These core concepts can be used generically to define the topology of features of interest, and can be specialized for multiple domains. The topology of features of interest is highly important in many use cases. If a room holds a lighting device, and if it is adjacent with an open window to a room whose luminosity is low, then by turning on the lighting device in the former room one may expect that the luminosity in the latter room will rise.\n\nThe SAREF4SYST ontology pattern can be instantiated for different domains. For example to describe zones inside a building (systems), that share a frontier (connections). Properties of systems are typically state variables (e.g. agent population, temperature), whereas properties of connections are typically flows (e.g. heat flow).\n\nSAREF4SYST has two main aims: on the one hand, to extend SAREF with the capability or representing general topology of systems and how they are connected or interact and, on the other hand, to exemplify how ontology patterns may help to ensure an homogeneous structure of the overall SAREF ontology and speed up the development of extensions.\n\nSAREF4SYST consists both of a core ontology, and guidelines to create ontologies following the SAREF4SYST ontology pattern. The core ontology is a lightweight OWL-DL ontology that defines 3 classes and 9 object properties.\n\nUse cases for ontology patterns are described extensively in [ETSI TR 103 549 Clauses 4.2 and 4.3](https://www.etsi.org/deliver/etsi_tr/103500_103599/103549/01.01.01_60/tr_103549v010101p.pdf).\n\nFor the Smart Energy domain:\n\n- Electric power systems can exchange electricity with other electric power systems. The electric energy can flow both ways in some cases (from the Public Grid to a Prosumer), or in only one way (from the Public Grid to a Load). Electric power systems can be made up of different sub-systems. Generic sub-types of electric power systems include producers, consumers, storage systems, transmission systems. \n- Electric power systems may be connected one to another through electrical connection points. An Electric power system may have multiple connection points (Multiple Winding Transformer generally have one single primary winding with two or more secondary windings). Generic sub-types of electrical connection points include plugs, sockets, direct-current, single-phase, three-phase, connection points. \n- An Electrical connection may exist between two Electric power systems at two of their respective connection points. Generic sub-types of electrical connections include Single-phase Buses, Three-phase Buses. A single-phase electric power system can be connected using different configurations at a three-phase bus (RN, SN, TN types).\n\nFor the Smart Building domain:\n\n- Buildings, Storeys, Spaces, are different sub-types of Zones. Zones can contain sub-zones. Zones can be adjacent or intersect with other zones. \n- Two zones may share one or more connections. For example some fresh air may be created inside a storey if it has two controllable openings to the exterior at different cardinal points. \n\nA graphical overview of the SAREF4SYST ontology is provided in Figure 1. In such figure:\n\n- Rectangles are used to denote Classes. The label of the rectangle is the identifier of the Class.\n- Plain arrows are used to represent Object Properties between Classes. The label of the arrow is the identifier of the Object Property. The origin of the arrow is the domain Class of the property, and the target of the arrow is the range Class of the property.\n- Dashed arrows with identifiers between stereotype signs (i.e. \"`<< >>`\") refer to OWL axioms that are applied to some property. Four pairs of properties are inverse one of the other; the property `s4syst:connectedTo` is symmetric, and properties `s4syst:hasSubSystem` and `s4syst:hasSubSystem` are transitive.\n- A symbol =1 near the target of an arrow denotes that the associated property is functional. A symbol ? denotes a local existential restriction.\n\n\n",
"modified": "2020-06-14",
"keywords": [
"IoT"
],
"homepage": "https://saref.etsi.org/saref4syst/"
},
"s4watr": {
"name": "SAREF extension for water",
"prefix": "s4watr",
"uri_prefix": "https://saref.etsi.org/saref4watr/$1",
"description": "This ontology extends the SAREF ontology for the water domain. This work has been developed in the context of the STF 566, which was established with the goal to create three SAREF extensions, one of them for the water domain.",
"modified": "2020-06-03",
"keywords": [
"Environment",
"IoT"
],
"homepage": "https://saref.etsi.org/saref4watr/"
},
"s4wear": {
"name": "SAREF4WEAR: an extension of SAREF for Wearables",
"prefix": "s4wear",
"uri_prefix": "https://saref.etsi.org/saref4wear/$1",
"description": "SAREF4WEAR is an extension of SAREF for Wearables",
"modified": "2020-02-01",
"keywords": [
"IoT"
],
"homepage": "https://saref.etsi.org/saref4wear/"
},
"edu": {
"name": "Education Ontology",
"prefix": "edu",
"uri_prefix": "https://schema.edu.ee/$1",
"description": "The ontology describes the main concepts in the field of education and the connections between them. The current version emphasizes the details of the study material, learning outcomes and the curriculum.",
"modified": "2020-02-14",
"keywords": [
"Academy"
],
"homepage": "https://schema.edu.ee/"
},
"pubsub": {
"name": "Eccenca Publish-Subscribe Vocabulary",
"prefix": "pubsub",
"uri_prefix": "https://vocab.eccenca.com/pubsub/$1",
"description": "The eccenca Publish-Subscribe Vocabulary defines concepts and relations to create statements about publishers, subscribers and their subscriptions in a Publish-Subscribe environment based on the PubSubHubbub Core 0.4 specification.",
"modified": "2016-07-12",
"keywords": [
"API",
"Services"
],
"homepage": "https://vocab.eccenca.com/pubsub/"
},
"eccrev": {
"name": "RDF changes and revisions vocabulary",
"prefix": "eccrev",
"uri_prefix": "https://vocab.eccenca.com/revision/$1",
"description": "A vocabulary & data model for describing RDF changes and revisions. It defines the Commit & Revision classes together with their expected properties.",
"modified": "2016-03-14",
"keywords": [
"RDF"
],
"homepage": "https://vocab.eccenca.com/revision/"
},
"bci": {
"name": "Brain Computing Interface (BCI) Ontology",
"prefix": "bci",
"uri_prefix": "https://w3id.org/BCI-ontology#$1",
"description": "The BCI ontology specifies a foundational metadata model set for real-world multimodal Brain Computing Interface (BCI) data capture activities. The ontology defines a minimalist and simple abstract metadata foundational model for real-world BCI applications that monitors human activity in any scenario. BCI multimodal domain applications are encouraged to extend and use this ontology in their implementations.",
"modified": "2016-10-13",
"keywords": [
"IoT"
],
"homepage": "https://w3id.org/BCI-ontology"
},
"cem": {
"name": "Crime Event Model (CEM)",
"prefix": "cem",
"uri_prefix": "https://w3id.org/CEMontology/$1",
"description": "The Crime Event Model is an ontology for the representation of crime events extracted from local newspapers. It could be employed for Crime Analysis purposes: extracting crime information from newspapers and enriching them with proper machine-readable semantics is a critical task to help law enforcement agencies at preventing crime, supporting criminal investigations and evaluating the action of law enforcement agencies themselves. The model is based on the fundamental 5W1H journalistic questions, that are Who?, What?, When?, Where?, Why? and How?. Another important requirement was the attempt to exploit existing knowledge graphs and ontologies such as the Simple Event Model (SEM) Ontology and the Schema.org data model for interoperability and interconnection.",
"modified": "2022-06-14",
"keywords": [
"Events",
"Methods"
],
"homepage": "https://w3id.org/CEMontology"
},
"CPSWatch": {
"name": "The Cyber Physical System Watch Ontology",
"prefix": "CPSWatch",
"uri_prefix": "https://w3id.org/CPSWatch#$1",
"description": "This ontology defines a vocabulary for describing cyber physical systems for monitoring purpose. It contains two main concepts: CPSWatch#MonitoredSystem that is a top level description of a System that is modeled and CPSWatch#MonitoringSensor that is a top level description of a sensor used to monitor the CPSWatch#MonitoredSystem.",
"modified": "2023-12-07",
"keywords": [
"IoT"
],
"homepage": "https://w3id.org/CPSWatch"
},
"tax": {
"name": "EUTaxO - EUdaphobase Taxonomy Ontology",
"prefix": "tax",
"uri_prefix": "https://w3id.org/EUTaxO#$1",
"description": "EUdaphobase Taxonomy Ontology for the European Soil-Biology Data Warehouse for Soil Protection",
"modified": "2022-09-29",
"keywords": [
"Biology"
],
"homepage": "https://w3id.org/EUTaxO"
},
"gcon": {
"name": "GConsent - a consent ontology based on the GDPR",
"prefix": "gcon",
"uri_prefix": "https://w3id.org/GConsent#$1",
"description": "GConsent provides concepts and relationships for defining consent and its associated information or metadata with a view towards GDPR compliance. It is the outcome of an analysis of consent and requirements associated with obtaining, using, and changes in consent as per the GDPR. The ontology also provides an approach to using its terms in various scenarios and use-cases (see more information in the documentation) which is intended to assist in its adoption.",
"modified": "2018-11-25",
"homepage": "http://openscience.adaptcentre.ie/ontologies/GConsent/docs/ontology",
"keywords": [
"People",
"Society"
]
},
"gdprov": {
"name": "The GDPR Provenance ontology",
"prefix": "gdprov",
"uri_prefix": "https://w3id.org/GDPRov#$1",
"description": "GDPRov is an OWL2 ontology to express provenance metadata of consent and data lifecycles towards documenting compliance for GDPR.",
"modified": "2018-04-06",
"homepage": "https://openscience.adaptcentre.ie/ontologies/GDPRov/docs/ontology",
"keywords": [
"People",
"Quality",
"Society"
]
},
"gdprt": {
"name": "GDPR text EXTensions",
"prefix": "gdprt",
"uri_prefix": "https://w3id.org/GDPRtEXT#$1",
"description": "The General Data Protection Regulation (GDPR) is comprised of several articles, each with points that refer to specific concepts. The general convention of referring to these points and concepts is to quote the specific article or point using a human-readable reference. This ontology provides a way to refer to the points within the GDPR using the EurLex ontology published by the European Publication Office. It also defines the concepts defined, mentioned, and requried by the GDPR using the Simple Knowledge Organization System (SKOS) ontology.",
"modified": "2018-07-03",
"homepage": "https://openscience.adaptcentre.ie/ontologies/GDPRtEXT/deliverables/docs/ontology",
"keywords": [
"Metadata",
"People",
"Society"
]
},
"hht": {
"name": "Historical Hierarchical Territories",
"prefix": "hht",
"uri_prefix": "https://w3id.org/HHT#$1",
"description": "The notion of territory plays a major role in human and social sciences. In an historical context, most approaches are irrelevant as they rely on geometric data, which is not available. In order to represent historical territories,we conceived the HHT ontology (Hierarchical Historical Territory) to represent hierarchical historical territorial divisions, without having to know their geometry. This approach relies on a notion of building blocks to replace polygonal geometry",
"modified": "2023-12-01",
"keywords": [
"Events",
"Geography"
],
"homepage": "https://w3id.org/HHT"
},
"tro": {
"name": "Transparent Relations Ontology",
"prefix": "tro",
"uri_prefix": "https://w3id.org/TRO#$1",
"description": "A vocabulary to represent relations that should be more transparent, usually between powerfull people or institutions",
"modified": "2022-04-01",
"keywords": [
"People",
"eBusiness"
],
"homepage": "https://w3id.org/TRO"
},
"airo": {
"name": "AI Risk Ontology",
"prefix": "airo",
"uri_prefix": "https://w3id.org/airo#$1",
"description": "AIRO represents AI risk concepts and relations based on the AI Act draft and ISO 31000 standard series.",
"modified": "2021-01-20",
"keywords": [
"Quality",
"Society"
],
"homepage": "https://w3id.org/airo"
},
"amv": {
"name": "AMV:Algorithm Metadata Vocabulary",
"prefix": "amv",
"uri_prefix": "https://w3id.org/amv#$1",
"description": "Metadata vocabularies are used in various domains of study. It provides an in-depth description of the resources. In this work, we develop Algorithm Metadata Vocabulary (AMV), a vocabulary for capturing and storing the metadata about the algorithms (a procedure or a set of rules that is followed step-by-step to solve a problem, especially by a computer). The snag faced by the researchers in the current time is the failure of getting relevant results when searching for algorithms in any search engine. AMV is represented as a semantic model and produced OWL file, which can be directly used by anyone interested to create and publish algorithm metadata as a knowledge graph, or to provide metadata service through SPARQL endpoint. To design the vocabulary, we propose a well-defined methodology, which considers real issues faced by the algorithm users and the practitioners. The evaluation shows a promising result.",
"modified": "2023-02-06",
"keywords": [
"Metadata"
],
"homepage": "https://w3id.org/amv"
},
"r-arco": {
"name": "ArCo Ontology (ArCo network)",
"prefix": "r-arco",
"uri_prefix": "https://w3id.org/arco/ontology/arco/$1",
"description": "The ArCo module is the root of the network ArCo - Architecture of Knowledge. It imports all the other modules and models top-level distinctions from the cultural heritage domain.",
"modified": "2019-10-24",
"keywords": [
"Catalogs"
],
"homepage": "https://w3id.org/arco/ontology/arco"
},
"ctlog": {
"name": "Catalogue Ontology (ArCo network)",
"prefix": "ctlog",
"uri_prefix": "https://w3id.org/arco/ontology/catalogue/$1",
"description": "The Catalogue module allows the description of concepts related to the Italian General Catalogue of Cultural Heritage (ICCD-MiBAC), and in particular catalogue records, that is XML files recording all data gathered by a cataloguer on a particular cultural property.",
"modified": "2019-10-23",
"keywords": [
"Catalogs"
],
"homepage": "https://w3id.org/arco/ontology/catalogue"
},
"cdesc": {
"name": "Context Description Ontology (ArCo network)",
"prefix": "cdesc",
"uri_prefix": "https://w3id.org/arco/ontology/context-description/$1",
"description": "The Context Description module includes models for the context of a cultural property, in a broad sense: agents (e.g.: author, collector, copyright holder), objects (e.g.: inventories, bibliography, protective measures, other cultural properties, collections etc.), activities (e.g.: surveys, conservation interventions), situations (e.g.: commission, coin issuance, estimate, legal situation) related, involved or involving the cultural property. Thus it represents attributes that do not result from a measurement of features in a cultural property, but are associated with it.",
"modified": "2019-10-23",
"keywords": [
"General & Upper",
"Society"
],
"homepage": "https://w3id.org/arco/ontology/context-description"
},
"arco": {
"name": "Core Ontology (ArCo network)",
"prefix": "arco",
"uri_prefix": "https://w3id.org/arco/ontology/core/$1",
"description": "The Core module represents general-purpose concepts orthogonal to the whole network, which are imported by all other ontology modules (e.g. part-whole relation, classification).",
"modified": "2019-06-01",
"keywords": [
"Services",
"Society"
],
"homepage": "https://w3id.org/arco/ontology/core"
},
"cevent": {
"name": "Cultural Event Ontology (ArCo network)",
"prefix": "cevent",
"uri_prefix": "https://w3id.org/arco/ontology/cultural-event/$1",
"description": "The Cultural Event module models cultural events, i.e. events involving cultural properties.",
"modified": "2019-10-23",
"keywords": [
"Events"
],
"homepage": "https://w3id.org/arco/ontology/cultural-event"
},
"ddesc": {
"name": "Denotative Description Ontology (ArCo network)",
"prefix": "ddesc",
"uri_prefix": "https://w3id.org/arco/ontology/denotative-description/$1",
"description": "The Denotative Description module encodes the characteristics of a cultural property, as detectable and/or detected during the cataloguing process and measurable according to a reference system. Examples include measurements e.g. length, constituting materials e.g. clay, employed techniques e.g. melting, conservation status e.g. good, decent, bad.\nIn this module are used as template the following Ontology Design Patterns:\n- http://www.ontologydesignpatterns.org/cp/owl/collectionentity.owl\n- http://www.ontologydesignpatterns.org/cp/owl/classification.owl\n- http://www.ontologydesignpatterns.org/cp/owl/descriptionandsituation.owl\n- http://www.ontologydesignpatterns.org/cp/owl/situation.owl",
"modified": "2019-10-23",
"keywords": [
"General & Upper",
"Society"
],
"homepage": "https://w3id.org/arco/ontology/denotative-description"
},
"a-loc": {
"name": "Location Ontology (ArCo network)",
"prefix": "a-loc",
"uri_prefix": "https://w3id.org/arco/ontology/location/$1",
"description": "The module Location models information related to the localization and georeferencing of a cultural property.\nIn this module are used as template the following Ontology Design Patterns:\n- http://www.ontologydesignpatterns.org/cp/owl/collectionentity.owl\n- http://www.ontologydesignpatterns.org/cp/owl/classification.owl\n- http://www.ontologydesignpatterns.org/cp/owl/place.owl\n- http://www.ontologydesignpatterns.org/cp/owl/timeindexedsituation.owl\n- http://www.ontologydesignpatterns.org/cp/owl/situation.owl",
"modified": "2020-03-27",
"keywords": [
"Geography"
],
"homepage": "https://w3id.org/arco/ontology/location"
},
"bcom": {
"name": "Building Concrete Monitoring Ontology (BCOM)",
"prefix": "bcom",
"uri_prefix": "https://w3id.org/bcom#$1",
"description": "The Building Concrete Monitoring Ontology (BCOM) is defined for capturing information of concrete work, concrete curing and testing of concrete properties. Further Information on the development and usage of the Ontology can be found in the following publication: Liu et al. (2021): An ontology integrating as-built information for infrastructure asset management using BIM and semantic web. In: Proceedings of 2021 European Conference on Computing in Construction, Online eConference, URL: https://ec-3.org/publications/conferences/2021/paper/?id=167",
"modified": "2021-07-26",
"keywords": [
"Industry"
],
"homepage": "https://w3id.org/bcom"
},
"bto": {
"name": "BOT: Building Topology Ontology",
"prefix": "bto",
"uri_prefix": "https://w3id.org/bot#$1",
"description": "The Building Topology Ontology (BOT) is a simple ontology defining the core concepts of a building.\n\nIt is a simple, easy to extend ontology for the construction industry to document and exchange building data on the web.\n\nChanges since version 0.2.0 of the ontology are documented in:\nhttps://w3id.org/bot/bot.html#changes\n\nThe version 0.2.0 of the ontology is documented in:\nMads Holten Rasmussen, Pieter Pauwels, Maxime Lefran\u00e7ois, Georg Ferdinand Schneider, Christian Anker Hviid and Jan Karlsh\u00f8j (2017) Recent changes in the Building Topology Ontology, 5th Linked Data in Architecture and Construction Workshop (LDAC2017), November 13-15, 2017, Dijon, France, https://www.researchgate.net/publication/320631574_Recent_changes_in_the_Building_Topology_Ontology\n\nThe initial version 0.1.0 of the ontology was documented in:\nMads Holten Rasmussen, Pieter Pauwels, Christian Anker Hviid and Jan Karlsh\u00f8j (2017) Proposing a Central AEC Ontology That Allows for Domain Specific Extensions, Lean and Computing in Construction Congress (LC3): Volume I \u2013 Proceedings of the Joint Conference on Computing in Construction (JC3), July 4-7, 2017, Heraklion, Greece, pp. 237-244 https://doi.org/10.24928/JC3-2017/0153",
"modified": "2020-07-31",
"homepage": "https://w3c-lbd-cg.github.io/bot/index.html",
"keywords": [
"Industry"
]
},
"cdc": {
"name": "CDC: Construction Dataset Context ontology",
"prefix": "cdc",
"uri_prefix": "https://w3id.org/cdc#$1",
"description": "The Construction Dataset Context (CDC) ontology is an extension of DCAT v2.0, a W3C Recommendation ontology for describing (RDF and non-RDF) datasets published on the Web. Using this extension, it becomes possible to describe a context for construction-related datasets that are being distributed using Web technology as well as datasets that are not shared outside an organization such as local copies, work in progress and other datasets that remain internal. This dataset metadata encompasses the temporal context (period or snapshot), the type of content of the dataset (as-built, design, etc.) and relations between contextualized datasets (previous as-built, requirements related to a design, etc.). In addition, this DCAT extension also provides terminology for managing dataset distributions that are scoped to a certain (named or default) graph of an RDF file or quadstore.",
"modified": "2021-02-26",
"keywords": [
"Industry"
],
"homepage": "https://w3id.org/cdc"
},
"citedcat": {
"name": "CiteDCAT-AP Vocabulary",
"prefix": "citedcat",
"uri_prefix": "https://w3id.org/citedcat-ap/$1",
"description": "CiteDCAT-AP is an extension of the DCAT application profile for data portals in Europe (DCAT-AP) for describing resources documented by using the DataCite metadata schema - the de facto standard for data citation, and used across scientific disciplines. Its basic use case is to make research data searchable on general data portals, thereby bridging the gap between scientific and public sector information. For this purpose, CiteDCAT-AP provides an RDF vocabulary and the corresponding RDF syntax binding for the metadata elements defined in DataCite.",
"modified": "2021-03-28",
"homepage": "https://ec-jrc.github.io/datacite-to-dcat-ap/",
"keywords": [
"Catalogs",
"Methods"
]
},
"cmd": {
"name": "Compound Measure Description",
"prefix": "cmd",
"uri_prefix": "https://w3id.org/cmd#$1",
"description": "This document is a vocabulary to describe compound measures, i.e. measures with several metric or item that are organized with serveral dimensions. The description of such a measure relies on a Tree-Structure of Requirement (TSoR): a set of requirements structured hierarchicaly with analysis element. A TSoR represents the main measure. Several information may be added to explicitely indicate how the overall score on the measure should be calculated based on the hierarchy, relative importance of the node of the hierarchy and an aggregation function. The measure can be described completely and unambiguously from the organisation to the requirements and the implementation.",
"modified": "2024-05-06",
"keywords": [
"Metadata",
"Methods"
],
"homepage": "https://w3id.org/cmd#"
},
"cocoon": {
"name": "Cloud Computing Services Ontology",
"prefix": "cocoon",
"uri_prefix": "https://w3id.org/cocoon/v1.0#$1",
"description": "Simple ontology for Cloud Computing Services. This ontology allows to define model of prices used in large cloud computing providers such as Google, Amazon, Azure, etc., including options for regions, type of instances, prices specification, etc.",
"modified": "2019-02-04",
"keywords": [
"Contracts",
"Services"
],
"homepage": "https://w3id.org/cocoon/v1.0"
},
"contax": {
"name": "ConTax ontology",
"prefix": "contax",
"uri_prefix": "https://w3id.org/con-tax#$1",
"description": "An ontology containing additional terminology for structuring and annotating RDFS/OWL taxonomies for describing constructions (components, materials, spatial zones, damages, construction tasks and properties). It also functions as an index for known taxonomies starting from root classes and properties.",
"modified": "2021-02-26",
"keywords": [
"Industry"
],
"homepage": "https://w3id.org/con-tax"
},
"cto": {
"name": "CTO: Construction Tasks Ontology",
"prefix": "cto",
"uri_prefix": "https://w3id.org/cto#$1",
"description": "The Construction Tasks Ontology (CTO) describes tasks operating on construction elements, spatial zones and/or damages. The tasks are either planned or executed depending on the dataset metadata context of the dataset its used in. Five different types of tasks are defined: instalment, removal, modification, repair and inspection. \nConsequences of tasks on the dataset, i.e. added and/or deleted triples, are modeled using reified statements. The tasks can link to a reified statement using the CTO relations.",
"modified": "2021-02-26",
"keywords": [
"Industry"
],
"homepage": "https://w3id.org/cto"
},
"dba": {
"name": "Description Banking Archives Ontology",
"prefix": "dba",
"uri_prefix": "https://w3id.org/dba/ontology/$1",
"description": "The ontology, presented here in a beta version, is based on the analysis of the documentation and descriptive requirements of the Intesa Sanpaolo Historical Archive and is intended to describe the content of historical banking documents and of some of the activities carried out by the bank, particularly in relation to third parties (loans, charity donations, seizures and confiscations, etc.), which involve the initiation of processes or the production of documents. The focal point of the descriptive model is the bank - an entity that initiates different types of processes, whose common feature is that they are structured into various stages/events - and the relationship between the documentation produced and the information it contains. In fact, this ontology is based on information collected from archived documents which describe various processes and activities carried out by banking institutions: the starting point for its construction were the inventories and databases of documentation stored in the Historical Archive which was produced by the various banks that over time were merged into Intesa Sanpaolo. The ontology was created to provide a sufficiently abstract representation and model for describing the processes of various banking activities from which the documentation was produced - from a company's request for financing and its outcome, to the preparation of seizure, confiscation and asset restitution filings, to charitable contributions, just to mention a few examples - reusing models that were already well established and widely used. The structure of the proposed ontology is in fact intended to adapt to the various activities, described in the archive files that a banking institution performs in relation to third parties. The proposed ontology is therefore not an ontology on banking activity in general, but on the relationship between this activity and the documents that are produced. Moreover, its objective is not to describe the documents in the strict sense of the term, for which reference is made to OAD ontology. The purpose of this project is to lay the initial, and fundamental, building blocks for describing the complexity, variety, and breadth of the domain of archiving bank records and the data they contain. Despite having data from different banks relating to different activities and having already made arrangements for the integration of third-party datasets and ontologies, before completing the project we will have to wait for the processing of representations based on other types of documents and banking institutions, including non-Italian ones.",
"modified": "2022-01-05",
"keywords": [
"Catalogs"
],
"homepage": "https://w3id.org/dba/ontology/"
},
"dco": {
"name": "domOS Common Ontology",
"prefix": "dco",
"uri_prefix": "https://w3id.org/dco#$1",
"description": "domOS Common Ontology (dCO) represents a common information model to share a unified understanding for humans and machines and to ensure semantic interoperability in a heterogeneous IoT infrastructure. This ontology allows the decoupling of the infrastructure from the software services and applications.",
"modified": "2021-09-30",
"keywords": [
"IoT"
],
"homepage": "https://w3id.org/dco"
},
"foo": {
"name": "Forest Observatory Ontology (FOO)",
"prefix": "foo",
"uri_prefix": "https://w3id.org/def/foo#$1",
"description": "This ontology describes wildlife observations generated by sensors.",
"modified": "2024-06-01",
"keywords": [
"Biology",
"Environment"
],
"homepage": "https://w3id.org/def/foo#"
},
"nyon": {
"name": "NyOn: A Multilingual Legal Ontology for Globalized Judicial System",
"prefix": "nyon",
"uri_prefix": "https://w3id.org/def/nyon#$1",
"description": "An ontology that represents concepts in the legal domain.",
"modified": "2020-04-04",
"keywords": [
"Metadata"
],
"homepage": "https://w3id.org/def/nyon#"
},
"dg": {
"name": "DINGO Ontology",
"prefix": "dg",
"uri_prefix": "https://w3id.org/dingo#$1",
"description": "The DINGO ontology (Data Integration for Grant Ontology) defines the terms of the DINGO vocabulary and provides a machine readable extensible framework to model data relative to projects, funding, project and funding actors, and, notably, funding policies. It is designed to yield high modeling power and elasticity to cope with the huge variety in funding and project practices, which makes it applicable to many areas where funding is an important aspect: first of all research, but also the arts, cultural conservation, and many others.",
"modified": "2020-01-10",
"keywords": [
"Services",
"Support"
],
"homepage": "https://w3id.org/dingo/"
},
"dio": {
"name": "The Design Intent Ontology",
"prefix": "dio",
"uri_prefix": "https://w3id.org/dio#$1",
"description": "The scope of the DIO is the domain of design intent or design rationale that needs to be documented while undertaking the design of any artifact",
"modified": "2016-01-04",
"keywords": [
"Methods",
"Services"
],
"homepage": "https://w3id.org/dio"
},
"dot": {
"name": "Damage Topology Ontology",
"prefix": "dot",
"uri_prefix": "https://w3id.org/dot#$1",
"description": "Ontology that defines the topology of damages in constructions.",
"modified": "2018-10-12",
"keywords": [
"Geography",
"Industry"
],
"homepage": "https://w3id.org/dot#"
},
"dpv": {
"name": "Data Privacy Vocabulary (DPV)",
"prefix": "dpv",
"uri_prefix": "https://w3id.org/dpv#$1",
"description": "The Data Privacy Vocabulary (DPV) provides terms (classes and properties) to represent information about processing of personal data, for example - purposes, processing operations, personal data, technical and organisational measures.",
"modified": "2022-08-18",
"homepage": "https://github.com/w3c/dpv/",
"keywords": [
"People",
"Security"
]
},
"pd": {
"name": "Personal Data Categories",
"prefix": "pd",
"uri_prefix": "https://w3id.org/dpv/pd#$1",
"description": "Extension to the Data Privacy Vocabulary (DPV) providing additional categories of personal data",
"modified": "2022-04-02",
"keywords": [
"People",
"Society"
],
"homepage": "https://w3id.org/dpv/pd"
},
"dsd": {
"name": "Description of a Data Source",
"prefix": "dsd",
"uri_prefix": "https://w3id.org/dsd#$1",
"description": "To ensure comparability between schemas from different data models, the Description of a Data Source (DSD) vocabulary has been developed.",
"modified": "2023-03-27",
"keywords": [
"API",
"Catalogs"
],
"homepage": "https://w3id.org/dsd"
},
"ecfo": {
"name": "The Emission Conversion Factor Ontology",
"prefix": "ecfo",
"uri_prefix": "https://w3id.org/ecfo#$1",
"description": "This ontology defines a vocabulary for describing carbon emission conversion factors (CF). These are values typically used to calculate carbon emissions where the CF multiplies a quantified estimate of the energy (e.g., kWh of electricity, litters of fuel, etc.) used by a particular activity.",
"modified": "2023-05-08",
"keywords": [
"Environment"
],
"homepage": "https://w3id.org/ecfo"
},
"eeo": {
"name": "Experimental Evaluation Ontology",
"prefix": "eeo",
"uri_prefix": "https://w3id.org/eeo#$1",
"description": "An ontology to describe experiments, evaluations and their relation.",
"modified": "2020-12-01",
"keywords": [
"Methods"
],
"homepage": "https://w3id.org/eeo"
},
"emmo": {
"name": "Elementary Multiperspective Material Ontology (EMMO)",
"prefix": "emmo",
"uri_prefix": "https://w3id.org/emmo#$1",
"description": "Elementary Multiperspective Material Ontology (EMMO)\n\nEMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) based on current materials modelling knowledge, including physical sciences, analytical philosophy and information and communication technologies.\n\nIt provides the connection between the physical world, materials characterisation world and materials modelling world.",
"modified": "2024-07-04",
"keywords": [
"Industry"
],
"homepage": "https://w3id.org/emmo"
},
"chameo": {
"name": "CHAracterisation MEthodology Ontology",
"prefix": "chameo",
"uri_prefix": "https://w3id.org/emmo/domain/characterisation-methodology/chameo#$1",
"description": "CHAMEO is a domain ontology designed to model the common aspects across the different characterisation techniques and methodologies.",
"modified": "2024-04-12",
"keywords": [
"Metadata",
"Methods"
],
"homepage": "https://w3id.org/emmo/domain/characterisation-methodology/chameo"
},
"puv": {
"name": "Parameter Usage Vocabulary ontology",
"prefix": "puv",
"uri_prefix": "https://w3id.org/env/puv#$1",
"description": "A simple ontology which implements the Parameter Usage Vocabulary semantic model, as described at https://github.com/nvs-vocabs/P01",
"modified": "2021-03-17",
"homepage": "https://github.com/nvs-vocabs/P01",
"keywords": [
"Environment",
"Methods"
]
},
"eppl": {
"name": "The EP-Plan ontology",
"prefix": "eppl",
"uri_prefix": "https://w3id.org/ep-plan#$1",
"description": "PROV extension for linking Plans and parts of plans to their respective executions.",
"modified": "2019-03-06",
"homepage": "https://github.com/TrustLens/EP-PLAN/tree/master/docs/ontologies",
"keywords": [
"IoT",
"Methods"
]
},
"fog": {
"name": "FOG: File Ontology for Geometry formats",
"prefix": "fog",
"uri_prefix": "https://w3id.org/fog#$1",
"description": "The File Ontology for Geometry formats (FOG) describes meaningful relations towards geometry snippets in RDF literals, geometry files on relative or absolute URLs and ontology-based geometry descriptions. The defined properties in this ontology are related towards each other and additional metadata is provided, such as file extension and related specifications/sources (incl. entries in dbpedia and Wikidata). \n\nThe initial version of the ontology (v0.0.1) was documented in:\n\nBonduel, Mathias, Wagner, Anna, Pauwels, Pieter, Vergauwen, Maarten, & Klein, Ralf (2019). Including Widespread Geometry Formats in Semantic Graphs Using RDF Literals. In Proceedings of the European Conference on Computing in Construction (EC3 2019). Chania, Greece.",
"modified": "2019-05-27",
"keywords": [
"Geometry"
],
"homepage": "https://w3id.org/fog"
},
"gom": {
"name": "GOM: Geometry Metadata Ontology",
"prefix": "gom",
"uri_prefix": "https://w3id.org/gom#$1",
"description": "- Version 0.0.1: initial version",
"modified": "2019-10-24",
"keywords": [
"Geometry",
"Metadata"
],
"homepage": "https://w3id.org/gom"
},
"hpont": {
"name": "The Heat Pump Ontology (HPOnt).",
"prefix": "hpont",
"uri_prefix": "https://w3id.org/hpont#$1",
"description": "The Heat Pump Ontology (HPOnt) aims to formalize and represent all the relevant information of Heat Pumps.\n\nThe HPOnt has been developed as part of the REACT project which has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement no. 824395.",
"modified": "2021-09-06",
"keywords": [
"IoT",
"Transport"
],
"homepage": "https://w3id.org/hpont"
},
"aml": {
"name": "AutomationML Ontology",
"prefix": "aml",
"uri_prefix": "https://w3id.org/i40/aml#$1",
"description": "A vocabulary to represent the AutomationML Standard - IEC 62714",
"modified": "2016-03-23",
"keywords": [
"Industry",
"Support"
],
"homepage": "https://w3id.org/i40/aml"
},
"rami": {
"name": "rami - Reference Architecture Model",
"prefix": "rami",
"uri_prefix": "http://iais.fraunhofer.de/vocabs/rami#$1",
"description": "A vocabulary which represents the Reference Architecture Model for Industry 4.0 (RAMI), including the concept of the Administration Shell I4.0 Component.",
"modified": "2015-11-30",
"keywords": [
"Industry"
],
"homepage": "https://w3id.org/i40/rami/"
},
"sto": {
"name": "i40 Standards Lanscape Vocabulary",
"prefix": "sto",
"uri_prefix": "https://w3id.org/i40/sto#$1",
"description": "A vocabulary to describe the relation between standards in use on the Industry 4.0, and related concepts",
"modified": "2017-01-25",
"homepage": "http://i40.semantic-interoperability.org/sto/index.html",
"keywords": [
"Industry"
]
},
"iadopt": {
"name": "I-ADOPT Framework ontology",
"prefix": "iadopt",
"uri_prefix": "https://w3id.org/iadopt/ont/$1",
"description": "The I-ADOPT Framework ontology",
"modified": "2021-10-15",
"keywords": [
"Biology",
"Environment"
],
"homepage": "https://w3id.org/iadopt/ont"
},
"ctrl": {
"name": "CTRLont - An ontology to formally specify the control domain",
"prefix": "ctrl",
"uri_prefix": "https://w3id.org/ibp/CTRLont#$1",
"description": "CTRLont specifies concepts and relationships of control actors on a high level",
"modified": "2019-04-29",
"keywords": [
"Services"
],
"homepage": "https://w3id.org/ibp/CTRLont"
},
"iddo": {
"name": "The Interconnected Data Dictionary Ontology (IDDO)",
"prefix": "iddo",
"uri_prefix": "https://w3id.org/iddo#$1",
"description": "The interconnected data dictionary ontology maps the data model of the ISO 23386 for the describing, creating, and maintenance of properties in interconnected data dictionaries.",
"modified": "2021-12-06",
"keywords": [
"Catalogs",
"Support"
],
"homepage": "https://w3id.org/iddo"
},
"ids": {
"name": "IDS Information Model",
"prefix": "ids",
"uri_prefix": "https://w3id.org/idsa/core/$1",
"description": "This ontology defines classes and properties for describing participants, infrastructure, data and services of the International Data Spaces (formerly known as Industrial Data Space).",
"modified": "2020-08-18",
"keywords": [
"API",
"Catalogs",
"Contracts",
"Services"
],
"homepage": "https://w3id.org/idsa/core"
},
"ifc": {
"name": "IFC4_ADD1",
"prefix": "ifc",
"uri_prefix": "https://w3id.org/ifc/IFC4_ADD1#$1",
"description": "OWL ontology for the IFC conceptual data schema and exchange file format for Building Information Model (BIM) data",
"modified": "2015-12-11",
"keywords": [
"Environment",
"IoT"
],
"homepage": "https://w3id.org/ifc/IFC4_ADD1"
},
"authn_provider": {
"name": "Authentication Provider",
"prefix": "authn_provider",
"uri_prefix": "https://w3id.org/inrupt/namespace/vocab/authn_provider/$1",
"description": "Information about authentication providers which might be identity providers or other services such as ones providing JSON Web Tokens.",
"modified": "2023-09-20",
"keywords": [
"API"
],
"homepage": "https://w3id.org/inrupt/namespace/vocab/authn_provider/"
},
"iot-tta": {
"name": "Ontology for Internet of Things Technologies, Tools, and Applications",
"prefix": "iot-tta",
"uri_prefix": "https://w3id.org/iot-tta#$1",
"description": "The Internet of Things taxonomy is extended with semantic ontologies for IoT layers, containing classes, properties, individuals, and rules specific to IoT technologies, tools, and applications",
"modified": "2022-08-27",
"homepage": "https://tudorliv.github.io/IoT-TTA/",
"keywords": [
"Industry",
"IoT"
]
},
"icb": {
"name": "isCharacterisedBy ontology design pattern",
"prefix": "icb",
"uri_prefix": "https://w3id.org/isCharacterisedBy#$1",
"description": "The goal of this ontology design pattern is to characterise a subject or group of subjects of interest by assigning qualifiable or quantifiable attributes or characteristics.",
"modified": "2023-05-30",
"keywords": [
"General & Upper"
],
"homepage": "https://w3id.org/isCharacterisedBy"
},
"isoprops": {
"name": "ISO 23386 Property Ontology (ISOProps)",
"prefix": "isoprops",
"uri_prefix": "https://w3id.org/isoprops#$1",
"description": "The ISO Property (ISOProps) ontology maps the data model of the ISO 23386 for the describing, creating, and maintenance of properties in interconnected data dictionaries.\n\nThe namespace for ISOProps terms is [https://w3id.org/isoprops](https://w3id.org/isoprops)\n\nThe preferred prefix for the ISOProps namespace is `isoprops`.\n\n## Ontology Overview \n![IDDO Ontology](Ontology_Overview.png \"Ontology\")\n\n## Assigning an ISOProps Property to a Feature of Interest\n![Property_Assignment](Property_Assignment.png \"Property_Assignment\")\n\n## Relation between DCAT vocabulary and the ISOProps ontology\n![DataCatalog_Overview](DataCatalog_Overview.png \"DataCatalog_Overview\")",
"modified": "2024-06-11",
"keywords": [
"Catalogs",
"Metadata"
],
"homepage": "https://w3id.org/isoprops"
},
"lh": {
"name": "LegalHTML Ontology",
"prefix": "lh",
"uri_prefix": "https://w3id.org/legalhtml/ov#$1",
"description": "An ontology for metadata about legal texts represented using the LegalHTML format",
"modified": "2023-05-08",
"keywords": [
"Metadata"
],
"homepage": "https://w3id.org/legalhtml/ov"
},
"loin": {
"name": "Level of Information Need (LOIN) Ontology",
"prefix": "loin",
"uri_prefix": "https://w3id.org/loin#$1",
"description": "The Level of Information Need (LOIN) Ontology is defined for specifying information requirements for delivery of data in a buildings' life cycle. The LOIN ontology is based on the standard BS EN 17412-1 (2020). Furthermore, it is extended with vocabulary for connecing Information Delivery Specifications (IDS) and Information containers for linked document delivery (ICDD) as per ISO 21597-1 (2020).",
"modified": "2024-06-11",
"keywords": [
"Metadata",
"Methods"
],
"homepage": "https://w3id.org/loin"
},
"mdo-calc": {
"name": "Materials Design Ontology - Calculation Module",
"prefix": "mdo-calc",
"uri_prefix": "https://w3id.org/mdo/calculation/$1",
"description": "This is the calculation module of Materials Design Ontology.",
"modified": "2019-11-07",
"keywords": [
"Biology",
"Support"
],
"homepage": "https://w3id.org/mdo/calculation/"
},
"core": {
"name": "Materials Design Ontology - Core Module",
"prefix": "core",
"uri_prefix": "https://w3id.org/mdo/core/$1",
"description": "This is the core module in Materials Design Ontology.",
"modified": "2019-11-07",
"keywords": [
"Industry"
],
"homepage": "https://w3id.org/mdo/core/"
},
"mdo": {
"name": "Materials Design Ontology - Full",
"prefix": "mdo",
"uri_prefix": "https://w3id.org/mdo/full/$1",
"description": "This is the Materials Design Ontology.",
"modified": "2019-11-07",
"keywords": [
"Biology",
"Support"
],
"homepage": "https://w3id.org/mdo/full/"
},
"mdoprov": {
"name": "Materials Design Ontology - Provenance Module",
"prefix": "mdoprov",
"uri_prefix": "https://w3id.org/mdo/provenance/$1",
"description": "This is the provenance module of Materials Design Ontology.",
"modified": "2020-04-02",
"keywords": [
"Metadata"
],
"homepage": "https://w3id.org/mdo/provenance/"
},
"mdo-struc": {
"name": "Materials Design Ontology - Structure Module",
"prefix": "mdo-struc",
"uri_prefix": "https://w3id.org/mdo/structure/$1",
"description": "This is the structure module in Materials Design Ontology.",
"modified": "2019-11-07",
"keywords": [
"Biology",
"Support"
],
"homepage": "https://w3id.org/mdo/structure/"
},
"modp": {
"name": "Metadata for Ontology Description and publication",
"prefix": "modp",
"uri_prefix": "https://w3id.org/mod#$1",
"description": "Metadata for Ontology Description and publication",
"modified": "2021-12-06",
"keywords": [
"Metadata",
"Vocabularies"
],
"homepage": "https://w3id.org/mod"
},
"mdi": {
"name": "RDF vocabulary to describe a Multidimensional Interface.",
"prefix": "mdi",
"uri_prefix": "https://w3id.org/multidimensional-interface/ontology#$1",
"description": "An RDF vocabulary to describe and facilitate the usage of a Multidimensional Interface.",
"modified": "2016-06-28",
"keywords": [
"Multimedia"
],
"homepage": "https://w3id.org/multidimensional-interface/ontology"
},
"nen2660": {
"name": "NEN 2660-2:2022 'Rules for information modelling of the built environment - Part 2: Practical configuration, extension and implementation of NEN 2660-1''",
"prefix": "nen2660",
"uri_prefix": "https://w3id.org/nen2660/def#$1",
"description": "Ontology which is a normative part of the Dutch NEN 2660-2 standard",
"modified": "2023-05-10",
"keywords": [
"Industry"
],
"homepage": "https://w3id.org/nen2660/"
},
"nno": {
"name": "The Neural Network Ontology",
"prefix": "nno",
"uri_prefix": "https://w3id.org/nno/ontology#$1",
"description": "This is the Neural Network Ontology. Designed by the AIFB (http://www.aifb.kit.edu/web/Web_Science)",
"modified": "2020-06-03",
"keywords": [
"Methods",
"Support"
],
"homepage": "https://w3id.org/nno/ontology"
},
"noria": {
"name": "The NORIA Ontology",
"prefix": "noria",
"uri_prefix": "https://w3id.org/noria/ontology/$1",
"description": "The NORIA-O project is a data model for IT networks, events and operations information.\nThe ontology is developed using web technologies (e.g. RDF, OWL, SKOS) and is intended as a structure for realizing an IT Service Management (ITSM) Knowledge Graph (KG) for Anomaly Detection (AD) and Risk Management applications.\nThe model has been developed in collaboration with operational teams, and in connection with third parties linked vocabularies.\n\nAlignment with third parties vocabularies is implemented on a per class or per property basis when relevant (e.g. with `rdfs:subClassOf`, `owl:equivalentClass`).\nDirections for direct instanciation of these vocabularies are provided for cases where implementing a class/property alignment is redundant.\nAlignment holds for the following vocabulary releases:\n- [BBO](https://hal.archives-ouvertes.fr/hal-02365012/) 1.0.0\n- [BOT](https://w3id.org/bot/) 0.3.2\n- [DevOps-Infra](https://oeg-upm.github.io/devops-infra/) 1.0.0\n- [FOLIO](https://github.com/IBCNServices/Folio-Ontology) 1.0.0\n- [ORG](https://www.w3.org/TR/vocab-org/) 0.8\n- [PEP](https://w3id.org/pep/) 1.1\n- [SEAS](https://w3id.org/seas/) 1.1\n- [SLOGERT](https://sepses.ifs.tuwien.ac.at/ns/log/index-en.html) 1.1.0\n- [UCO](https://github.com/ucoProject/uco) Release-0.8.0",
"modified": "2022-12-15",
"keywords": [
"API"
],
"homepage": "https://w3id.org/noria/ontology/"
},
"ofo": {
"name": "Occupant Feedback Ontology",
"prefix": "ofo",
"uri_prefix": "https://w3id.org/ofo#$1",
"description": "The aim of the Occupant Feedback Ontology is to semantically describe passive and active occupant feedback and to enable integration of this feedback with linked building data.",
"modified": "2022-02-01",
"keywords": [
"IoT",
"Services"
],
"homepage": "https://w3id.org/ofo#"
},
"sdont": {
"name": "The Software Description Ontology",
"prefix": "sdont",
"uri_prefix": "https://w3id.org/okn/o/sd#$1",
"description": "An ontology for describing software and their links to inputs, outputs and variables. The ontology extends schema.org and codemeta vocabularies",
"modified": "2021-05-23",
"keywords": [
"Metadata",
"Methods"
],
"homepage": "https://w3id.org/okn/o/sd"
},
"sdom": {
"name": "The Software Description Ontology for Models",
"prefix": "sdom",
"uri_prefix": "https://w3id.org/okn/o/sdm#$1",
"description": "The Software Description Ontology for Models (SDM) expands the software description ontology (SD) to add information about scientific software models. Examples of scientific software models are hydrology models, agriculture models or economy models.",
"modified": "2023-03-01",
"keywords": [
"Support"
],
"homepage": "https://w3id.org/okn/o/sdm"
},
"omg": {
"name": "OMG: Ontology for Managing Geometry",
"prefix": "omg",
"uri_prefix": "https://w3id.org/omg#$1",
"description": "The Ontology for Managing Geometry (OMG) is an ontology for describing geometry descriptions of objects. It provides means to support the application of multiple geometry descriptions of the same object as well as the description of the geometry evolution over time. The OMG is based the concepts introduced in the Ontology for Property Management (OPM) ontology. \n\nThis ontology was created within the research project SCOPE, funded by the German Federal Ministry for Economic Affairs and Energy (BMWi).\n\nThe initial version of the ontology (v0.0.1) is documented in:\nWagner, Anna, Bonduel, Mathias, Pauwels, Pieter & R\u00fcppel, Uwe(2019). Relating Geometry Descroptions to its Derivatives on the Web. In Proceedings of the European Conference on Computing in Construction (EC3 2019). Chania, Greece.",
"modified": "2018-11-28",
"keywords": [
"Geometry"
],
"homepage": "https://w3id.org/omg"
},
"ontouml": {
"name": "OntoUML Metamodel Vocabulary",
"prefix": "ontouml",
"uri_prefix": "https://w3id.org/ontouml#$1",
"description": "A reference implementation of the OntoUML metamodel in OWL.",
"modified": "2023-07-27",
"keywords": [
"Methods",
"RDF"
],
"homepage": "https://w3id.org/ontouml"
},
"ocmv": {
"name": "OntoUML/UFO Catalog Metadata Vocabulary",
"prefix": "ocmv",
"uri_prefix": "https://w3id.org/ontouml-models/vocabulary#$1",
"description": "Specification of the metadata used to describe models in the OntoUML/UFO Catalog.",
"modified": "2023-07-28",
"keywords": [
"General & Upper",
"Metadata"
],
"homepage": "https://w3id.org/ontouml-models/vocabulary"
},
"otl": {
"name": "The Open Traffic Lights ontology",
"prefix": "otl",
"uri_prefix": "https://w3id.org/opentrafficlights#$1",
"description": "This ontology provides the terms necessary to describe the status of traffic lights.",
"modified": "2018-10-31",
"keywords": [
"Services"
],
"homepage": "https://w3id.org/opentrafficlights"
},
"opm": {
"name": "OPM: Ontology for Property Management",
"prefix": "opm",
"uri_prefix": "https://w3id.org/opm#$1",
"description": "The Ontology for Property Management (OPM) extends the concepts introduced in the Smart Energy Aware Systems (SEAS) Evaluations ontology.",
"keywords": [
"Environment",
"IoT"
],
"homepage": "https://w3id.org/opm"
},
"okh": {
"name": "Open Know How (OKH) ontology",
"prefix": "okh",
"uri_prefix": "https://w3id.org/oseg/ont/okh#$1",
"description": "Used for indexing, searching and comparing Open Source Hardware projects",
"modified": "2022-02-22",
"keywords": [
"Methods"
],
"homepage": "https://w3id.org/oseg/ont/okh"
},
"peco": {
"name": "The Provenance of Emission Calculations Ontology",
"prefix": "peco",
"uri_prefix": "https://w3id.org/peco#$1",
"description": "This ontology defines a vocabulary for describing provenance traces of carbon emission calculations by capturing the quantifiable measurements of carbon emission sources used by some activities (e.g., electricity used by a machinery to produce a product, petrol used to make a car journey, etc.) and emission conversion factors used to estimate the carbon emissions produced by these. In addition, the ontology provides the ability to capture various data transformations that occurred before energy estimates may be used with relevant conversion factors. For example, sensors may provide raw readings about a water flow of an irrigation rig in an agri-food operation which is then used as a proxy to estimate the total volume of fertilisers used.",
"modified": "2023-05-08",
"keywords": [
"Environment"
],
"homepage": "https://w3id.org/peco"
},
"pep": {
"name": "Process Execution ontology.",
"prefix": "pep",
"uri_prefix": "https://w3id.org/pep/$1",
"description": "The process execution ontology is a proposal for a simple extension of both the [W3C Semantic Sensor Network](https://www.w3.org/TR/vocab-ssn/) and the [Semantic Actuator Network](https://www.irit.fr/recherches/MELODI/ontologies/SAN.owl) ontology cores.",
"modified": "2016-07-01",
"keywords": [
"Industry",
"Methods",
"Services"
],
"homepage": "https://w3id.org/pep/"
},
"rto": {
"name": "Rail Topology Ontology",
"prefix": "rto",
"uri_prefix": "https://w3id.org/rail/topo#$1",
"description": "The Rail Topology Ontology models foundational rail topology concepts..",
"modified": "2021-04-20",
"keywords": [
"Transport"
],
"homepage": "https://w3id.org/rail/topo#"
},
"rains": {
"name": "The RAInS Ontology",
"prefix": "rains",
"uri_prefix": "https://w3id.org/rains#$1",
"description": "An ontology to model accountability of AI systems which use machine learning.",
"modified": "2022-05-09",
"keywords": [
"API",
"Methods"
],
"homepage": "https://w3id.org/rains"
},
"rdfp": {
"name": "The RDF Presentation ontology",
"prefix": "rdfp",
"uri_prefix": "https://w3id.org/rdfp/$1",
"description": "## RDF Presentation and RDF Presentation Negotiation\n\nAn RDF graph can be presented in several ways, using different media types. Examples of RDF media types include `application/rdf+xml`, `text/turtle`, `application/json+ld`.\n\nToday, most of the content consumed/produced/published, on the Web is not presented in RDF. \n\nIn the Web of Things, HTTP servers and clients would rather exchange lightweight documents, potentially binary. \nCurrently, most existing RDF Presentations generically apply to any RDF graph, at the cost of being heavy text-based documents.\nYet, lightweight HTTP servers/clients could be better satisfied with consuming/producing/publishing lightweight documents, may its structure be application-specific.",
"modified": "2016-08-31",
"keywords": [
"API",
"RDF"
],
"homepage": "https://w3id.org/rdfp/"
},
"react": {
"name": "The REACT Ontology",
"prefix": "react",
"uri_prefix": "https://w3id.org/react#$1",
"description": "The REACT ontology aims to represent all the necessary knowledge to support the achievement of island energy independence through renewable energy generation and storage, a demand response platform, and promoting user engagement in a local energy community.\n\nThe REACT ontology has been developed as part of the REACT project which has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement no. 824395.",
"modified": "2021-06-01",
"keywords": [
"Environment",
"IoT"
],
"homepage": "https://w3id.org/react"
},
"rbdoc": {
"name": "RiverBench documentation ontology",
"prefix": "rbdoc",
"uri_prefix": "https://w3id.org/riverbench/schema/documentation#$1",
"description": "Ontology with metadata needed to generate documentation of datasets, distributions, profiles, etc. in RiverBench",
"modified": "2023-05-08",
"keywords": [
"Catalogs",
"Metadata"
],
"homepage": "https://w3id.org/riverbench/schema/documentation"
},
"rb": {
"name": "RiverBench metadata ontology",
"prefix": "rb",
"uri_prefix": "https://w3id.org/riverbench/schema/metadata#$1",
"description": "Ontology for describing datasets and profiles in the RiverBench benchmark suite.",
"modified": "2023-05-08",
"keywords": [
"Catalogs",
"Metadata"
],
"homepage": "https://w3id.org/riverbench/schema/metadata"
},
"saont": {
"name": "The System Accountability Ontology",
"prefix": "saont",
"uri_prefix": "https://w3id.org/sao#$1",
"description": "An ontology to model accountability of generic systems.",
"modified": "2022-05-09",
"keywords": [
"API",
"Support"
],
"homepage": "https://w3id.org/sao"
},
"sbeo": {
"name": "SBEO: Smart Building Evacuation Ontology",
"prefix": "sbeo",
"uri_prefix": "https://w3id.org/sbeo#$1",
"description": "Smart Building Evacuation Ontology (SBEO) is an ontology that couples the information about any building with its occupants such that it can be used in many useful ways. For example, indoor localization of people, detection of any hazard, a recommendation of normal routes such as shopping or stadium seating routes, or safe and feasible emergency evacuation routes or both of them all together. \n\nThe core SBEO covers the concepts related to the geometry of building, devices and components of the building, route graphs correspondent to the building topology, users' characteristics and preferences, situational awareness of both building (hazard detection, status of routes in terms of availability and occupancy) and users (tracking, management of groups, status in terms of fitness), and emergency evacuation.",
"modified": "2020-07-12",
"homepage": "https://qasimkhalid.github.io/SBEO/",
"keywords": [
"IoT",
"Services"
]
},
"seas": {
"name": "SEAS ontology",
"prefix": "seas",
"uri_prefix": "https://w3id.org/seas/$1",
"description": "This vocabulary is version v0.1 of the ITEA2 Smart Energy Aware Systems project vocabulary. It enables the description of electricity measurements of a site using the Data Cube W3C vocabulary.",
"modified": "2016-05-25",
"keywords": [
"Industry"
],
"homepage": "https://w3id.org/seas/"
},
"seasb": {
"name": "The SEAS Battery ontology.",
"prefix": "seasb",
"uri_prefix": "https://w3id.org/seas/$1",
"description": "This ontology defines batteries and their state of charge ratio property.",
"modified": "2016-10-30",
"homepage": "https://ci.mines-stetienne.fr/seas/index.html",
"keywords": [
"Environment",
"Industry",
"IoT"
]
},
"seasbo": {
"name": "The SEAS Building Ontology",
"prefix": "seasbo",
"uri_prefix": "https://w3id.org/seas/$1",
"description": "The SEAS Building ontology describes a taxonomy of buildings, building spaces, and rooms.\n\nSome categorizations are based on the energy efficiency related to their insulation etc., although the actual values for classes depend the country specific regulations and geographical locations.\n\nOther categorizations are based on occupancy and activities. There is no single accepted categorization available. This taxonomy uses some types selected from:\n\n- International building occupancy based categories (USA)\n- The Classification of Types of Constructions (EU)\n- Finnish building categorization VTJ2000 (Finland)\n- Wikipedia category page for Rooms: https://en.wikipedia.org/wiki/Category:Rooms",
"modified": "2016-01-26",
"keywords": [
"Environment",
"Society"
],
"homepage": "https://w3id.org/seas/BuildingOntology"
},
"seasd": {
"name": "The SEAS Device ontology",
"prefix": "seasd",
"uri_prefix": "https://w3id.org/seas/$1",
"description": "The SEAS Device ontology defines `seas:Device` as physical system that are designed to execute one or more procedures that involve the physical world.",
"modified": "2016-05-10",
"homepage": "https://ci.mines-stetienne.fr/seas/index.html",
"keywords": [
"Environment",
"Industry",
"IoT"
]
},
"seas-eval": {
"name": "The SEAS Evaluation ontology",
"prefix": "seas-eval",
"uri_prefix": "https://w3id.org/seas/$1",
"description": "The Evaluation ontology describes evaluation of [`seas:Property`ies](https://w3id.org/seas/Property). There may be:\n\n- direct evaluations, or\n- qualified evaluations.",
"modified": "2016-09-21",
"keywords": [
"Methods",
"Support"
],
"homepage": "https://w3id.org/seas/EvaluationOntology"
},
"foio": {
"name": "The SEAS Feature of Interest ontology.",
"prefix": "foio",
"uri_prefix": "https://w3id.org/seas/FeatureOfInterestOntology/$1",
"description": "This ontology defines feature of interest and their properties, as an extension of the core classes of the SSN ontology (https://www.w3.org/ns/ssn/).\n\nA feature of interest is an abstraction of a real world phenomena (thing, person, event, etc). A feature of interest is then defined in terms of its properties, which are qualifiable, quantifiable, observable or operable qualities of the feature of interest. \n\nAlignments to other ontologies are proposed in external documents: \n\n- [SSNAlignment](https://w3id.org/seas/SSNAlignment) proposes an alignment to the [SSN ontology](http://www.w3.org/ns/ssn/).\n- [QUDTAlignment](https://w3id.org/seas/QUDTAlignment) proposes an alignment to the [QUDT ontology](http://qudt.org/).",
"modified": "2016-07-01",
"keywords": [
"Events"
],
"homepage": "https://w3id.org/seas/FeatureOfInterestOntology"
},
"seasfo": {
"name": "The SEAS Forecasting ontology",
"prefix": "seasfo",
"uri_prefix": "https://w3id.org/seas/$1",
"description": "The SEAS Forecasting ontology extends the [Procedure Execution ontology (PEP)](https://w3id.org/pep/)",
"modified": "2017-08-29",
"keywords": [
"Environment",
"IoT"
],
"homepage": "https://w3id.org/seas/ForecastingOntology"
},
"seas-op": {
"name": "The SEAS Failable System ontology",
"prefix": "seas-op",
"uri_prefix": "https://w3id.org/seas/$1",
"description": "The SEAS Operating Ontology defines evaluations of operating features of interest.",
"modified": "2016-07-24",
"keywords": [
"Industry"
],
"homepage": "https://w3id.org/seas/OperatingOntology"
},
"seas-qudt": {
"name": "QUDT Alignment.",
"prefix": "seas-qudt",
"uri_prefix": "https://w3id.org/seas/$1",
"description": "This ontology defines proposed alignemnts with the QUDT ontology.",
"modified": "2016-09-19",
"keywords": [
"Industry"
],
"homepage": "https://w3id.org/seas/QUDTAlignment"
},
"seas-stats": {
"name": "The SEAS Statistics ontology.",
"prefix": "seas-stats",
"uri_prefix": "https://w3id.org/seas/$1",
"description": "This ontology defines common evaluation interpretation concepts for statistics.",
"modified": "2016-07-21",
"keywords": [
"Industry",
"Methods"
],
"homepage": "https://w3id.org/seas/StatisticsOntology"
},
"seas-sys": {
"name": "The SEAS System ontology",
"prefix": "seas-sys",
"uri_prefix": "https://w3id.org/seas/$1",
"description": "The System Ontology defines Systems, Connections between systems, and Connection Points at which systems may be connected. This ontology is then specialized for multiple domains. For example:\n\n- In electric energy: \n - power systems consume, produce, store, and exchange electricity;\n - power connections are where electricity flows between systems;\n - power connection points are plugs, sockets, or power busses.\n- In the electricity market:\n - players and markets are systems;\n - connections are contracts or transactions between two players, or between a player and a market;\n - connection points include offers and bids.",
"modified": "2016-12-09",
"keywords": [
"Industry"
],
"homepage": "https://w3id.org/seas/SystemOntology"
},
"seast": {
"name": "The SEAS Time Ontology.",
"prefix": "seast",
"uri_prefix": "https://w3id.org/seas/$1",
"description": "This ontology defines:\n- a set of subclasses of `seas:Evaluation` to better interpret evaluations of quantifiable properties.\n- a set of sub properties of `seas:hasProperty` to qualify time-related properties.",
"modified": "2016-07-05",
"homepage": "https://ci.mines-stetienne.fr/seas/index.html",
"keywords": [
"Environment",
"Industry",
"IoT",
"Time"
]
},
"seasto": {
"name": "The SEAS Trading ontology",
"prefix": "seasto",
"uri_prefix": "https://w3id.org/seas/$1",
"description": "The Seas Trading Ontology defines concepts and relations to describe ownership, trading, bilateral contracts and market licenses:\n\n- players own systems and trade commodities, which have a price;\n- bilateral electricity contracts are connections between electricity traders at which they exchange\nelectricity;\n- electricity markets are connections between electricity traders at which they exchange electricity,\nusing a market license;\n- electricity markets can be cleared, and balanced;\n- evaluations can have a traded volume validity context",
"modified": "2016-11-15",
"keywords": [
"Environment",
"Industry",
"Services"
],
"homepage": "https://w3id.org/seas/TradingOntology"
},
"swemls": {
"name": "Semantic-Web Machine Learning System (SWeMLS) Ontology",
"prefix": "swemls",
"uri_prefix": "https://w3id.org/semsys/ns/swemls#$1",
"description": "An ontology to describe a Semantic-Web Machine Learning System (SWeMLS)",
"modified": "2021-11-30",
"homepage": "https://semantic-systems.org/ns/swemls/index-en.html",
"keywords": [
"Metadata",
"Methods"
]
},
"seo": {
"name": "The Scientific Events Ontology",
"prefix": "seo",
"uri_prefix": "https://w3id.org/seo#$1",
"description": "The vocabulary allows for the description of data about scientific events such as conferences, symposiums and workshops.",
"modified": "2019-04-10",
"homepage": "https://saidfathalla.github.io/SEOontology/Documentation/SEO.html",
"keywords": [
"Academy",
"Events"
]
},
"modsci": {
"name": "ModSci, Modern Science Ontology.",
"prefix": "modsci",
"uri_prefix": "https://w3id.org/skgo/modsci#$1",
"description": "ModSci is a reference ontology for modelling different types of modern sciences and related entities, such as scientific discoveries, renowned scientists, instruments, phenomena ... etc.",
"modified": "2022-12-18",
"keywords": [
"Academy",
"Society"
],
"homepage": "https://w3id.org/skgo/modsci#"
},
"sw-quality": {
"name": "SQuAP Ontology",
"prefix": "sw-quality",
"uri_prefix": "https://w3id.org/squap/SoftwareQuality/$1",
"description": "Quality, architecture, and process are considered the keystones of software engineering. ISO defines them in three separate standards. However, their interaction has been poorly studied, so far. The SQuAP model (Software Quality, Architecture, Process) describes twenty-eight main factors that impact on software quality in banking systems, and each factor is described as a relation among some characteristics from the three ISO standards. Hence, SQuAP makes such relations emerge rigorously, although informally. SQaAP-Ont is an OWL ontology that formalises those relations in order to represent and reason via Linked Data about software engineering in a three-dimensional model consisting of quality, architecture, and process characteristics.",
"modified": "2019-07-16",
"keywords": [
"Industry",
"Quality"
],
"homepage": "https://w3id.org/squap/"
},
"sri": {
"name": "Smart Readiness Indicator Vocabulary",
"prefix": "sri",
"uri_prefix": "https://w3id.org/sri#$1",
"description": "A vocabulary specifying concepts and structures needed to represent different data cubes needed for the Smart Readiness Indicator.",
"modified": "2023-11-30",
"keywords": [
"IoT",
"Quality"
],
"homepage": "https://w3id.org/sri"
},
"stax": {
"name": "RDF Stream Taxonomy (RDF-STaX)",
"prefix": "stax",
"uri_prefix": "https://w3id.org/stax/ontology#$1",
"description": "RDF-STaX is an OWL 2 DL ontology that enables describing the types of RDF streams and defines relations between them.",
"modified": "2024-01-09",
"homepage": "https://w3id.org/stax/dev",
"keywords": [
"API",
"RDF"
]
},
"tb": {
"name": "Timebank Ontology",
"prefix": "tb",
"uri_prefix": "https://w3id.org/timebank#$1",
"description": "An ontology to describe people and requests for timebanks. This includes the poeple's skills, limitations, and environment.",
"modified": "2020-04-01",
"homepage": "https://tobiasgrubenmann.github.io/Ontologies/Timebank/0.2/index.html",
"keywords": [
"Services",
"eBusiness"
]
},
"todo": {
"name": "TODO: Task-Oriented Dialogue management Ontology",
"prefix": "todo",
"uri_prefix": "https://w3id.org/todo#$1",
"description": "With the aim of enhancing natural communication between workers in industrial environments and the systems to be used by them, TODO (Task-Oriented Dialogue management Ontology) has been developed to be the core of task-oriented dialogue systems. TODO is a core ontology that provides task-oriented dialogue systems with the necessary means to be capable of naturally interacting with workers (both at understanding and at ommunication levels) and that can be easily adapted to different industrial scenarios, reducing adaptation time and costs. Moreover, it allows to store and reproduce the dialogue process to be able to learn from new interactions.",
"modified": "2020-04-21",
"keywords": [
"Industry",
"Services"
],
"homepage": "https://w3id.org/todo"
},
"tddfa": {
"name": "TODODFA: Frame-Action Module for Task-Oriented Dialogue management Ontology (TODO)",
"prefix": "tddfa",
"uri_prefix": "https://w3id.org/todo/tododfa#$1",
"description": "Module for Action (and Frame) modelling inside domain.",
"modified": "2020-04-21",
"keywords": [
"Industry",
"Services"
],
"homepage": "https://w3id.org/todo/tododfa"
},
"tddial": {
"name": "TODODial: Dialogue Module for Task-Oriented Dialogue management Ontology (TODO)",
"prefix": "tddial",
"uri_prefix": "https://w3id.org/todo/tododial#$1",
"description": "Module for dialogue process and system output management.",
"modified": "2020-04-21",
"keywords": [
"Industry",
"Services"
],
"homepage": "https://w3id.org/todo/tododial"
},
"tddm": {
"name": "TODODM: Dialogue Management Module for Task-Oriented Dialogue management Ontology (TODO)",
"prefix": "tddm",
"uri_prefix": "https://w3id.org/todo/tododm#$1",
"description": "Module for dialogue process and system output management.",
"modified": "2020-04-21",
"keywords": [
"Industry",
"Services"
],
"homepage": "https://w3id.org/todo/tododm"
},
"tddom": {
"name": "TODODom: Domain Module for Task-Oriented Dialogue management Ontology (TODO)",
"prefix": "tddom",
"uri_prefix": "https://w3id.org/todo/tododom#$1",
"description": "Module for domain modelling.",
"modified": "2020-04-21",
"keywords": [
"Industry",
"Services"
],
"homepage": "https://w3id.org/todo/tododom"
},
"tddt": {
"name": "TODODT: Dialogue Tracing Module for Task-Oriented Dialogue management Ontology (TODO)",
"prefix": "tddt",
"uri_prefix": "https://w3id.org/todo/tododt#$1",
"description": "Module for dialogue tracing.",
"modified": "2020-04-21",
"keywords": [
"Industry",
"Services"
],
"homepage": "https://w3id.org/todo/tododt"
},
"tddw": {
"name": "TODODW: World Module for Task-Oriented Dialogue management Ontology (TODO)",
"prefix": "tddw",
"uri_prefix": "https://w3id.org/todo/tododw#$1",
"description": "Module for scenario modelling (world elements) of domain.",
"modified": "2020-06-20",
"keywords": [
"Industry",
"Services"
],
"homepage": "https://w3id.org/todo/tododw"
},
"tree": {
"name": "TREE",
"prefix": "tree",
"uri_prefix": "https://w3id.org/tree#$1",
"description": "A hypermedia specification for fragmenting collections.",
"modified": "2022-09-06",
"keywords": [
"Methods",
"Support"
],
"homepage": "https://w3id.org/tree"
},
"tribont": {
"name": "TribOnt ontology",
"prefix": "tribont",
"uri_prefix": "https://w3id.org/tribont#$1",
"description": "The goal is to represent the tribological experiments by relaying on the representation included in the core,, sample and equipment modules.",
"modified": "2023-06-02",
"keywords": [
"Methods"
],
"homepage": "https://w3id.org/tribont"
},
"tribont-core": {
"name": "Core module",
"prefix": "tribont-core",
"uri_prefix": "https://w3id.org/tribont/core#$1",
"description": "The goal of this module is to represent the common classes, and object and data properties included in two or more modules of the TribOnt ontology.",
"modified": "2023-05-30",
"keywords": [
"Methods"
],
"homepage": "https://w3id.org/tribont/core"
},
"tribont-equipment": {
"name": "Equipment module",
"prefix": "tribont-equipment",
"uri_prefix": "https://w3id.org/tribont/equipment#$1",
"description": "The goal of this module is to represent the equipment hierarchy model involved in the tribological experiments.",
"modified": "2023-06-02",
"keywords": [
"Methods"
],
"homepage": "https://w3id.org/tribont/equipment"
},
"tribont-material": {
"name": "Material module",
"prefix": "tribont-material",
"uri_prefix": "https://w3id.org/tribont/material#$1",
"description": "The goal of this module is to represent the materials that can be involved in the tribological experiments as part of the tested samples.",
"modified": "2023-06-02",
"keywords": [
"Methods"
],
"homepage": "https://w3id.org/tribont/material"
},
"tribont-sample": {
"name": "Sample module",
"prefix": "tribont-sample",
"uri_prefix": "https://w3id.org/tribont/sample#$1",
"description": "The goal of this module is to represent the sample systems , and the undelaying samples, involved in the tribological experiments.",
"modified": "2023-05-30",
"keywords": [
"Methods"
],
"homepage": "https://w3id.org/tribont/sample"
},
"usability": {
"name": "Usability",
"prefix": "usability",
"uri_prefix": "https://w3id.org/usability#$1",
"description": "\u041e\u043d\u0442\u043e\u043b\u043e\u0433\u0438\u044f \"\u0423\u0434\u043e\u0431\u0441\u0442\u0432\u043e \u0438\u0441\u043f\u043b\u044c\u0437\u043e\u0432\u0430\u043d\u0438\u044f\" \u043f\u0440\u0435\u0434\u043d\u0430\u0437\u043d\u0430\u0447\u0435\u043d\u0430 \u0434\u043b\u044f \u0444\u0438\u043a\u0441\u0430\u0446\u0438\u0438 \u0434\u0430\u043d\u043d\u044b\u0445 \u043e \u0432\u0437\u0430\u0438\u043c\u043e\u0434\u0435\u0439\u0441\u0442\u0432\u0438\u0438 \u043f\u043e\u043b\u044c\u0437\u043e\u0432\u0430\u0442\u0435\u043b\u044f \u0441 \u043f\u0440\u043e\u0433\u0440\u0430\u043c\u043c\u043d\u043e\u0439 \u0441\u0438\u0441\u0442\u0435\u043c\u043e\u0439 \u043f\u043e\u0441\u0440\u0435\u0434\u0441\u0442\u0432\u043e\u043c \u0433\u0440\u0430\u0444\u0438\u0447\u0435\u0441\u043a\u043e\u0433\u043e \u043f\u043e\u043b\u044c\u0437\u043e\u0432\u0430\u0442\u0435\u043b\u044c\u0441\u043a\u043e\u0433\u043e \u0438\u043d\u0442\u0435\u0440\u0444\u0435\u0439\u0441\u0430",
"modified": "2018-09-06",
"keywords": [
"Events",
"Support"
],
"homepage": "https://w3id.org/usability"
},
"lingvo": {
"name": "The Lingvoj Ontology",
"prefix": "lingvo",
"uri_prefix": "https://w3id.org/vocab/lingvoj#$1",
"description": "An ontology for using languages as resources",
"modified": "2020-05-31",
"homepage": "https://lingvoj.linkedvocabs.org/",
"keywords": [
"Vocabularies"
]
},
"olca": {
"name": "Ontology Loose Coupling Annotation",
"prefix": "olca",
"uri_prefix": "https://w3id.org/vocab/olca#$1",
"description": "A vocabulary defining annotations enabling loose coupling between classes and properties in ontologies. Those annotations define with some accuracy the expected use of properties, in particular across vocabularies, without the formal constraints entailed by the use of OWL or RDFS constructions",
"modified": "2020-05-31",
"keywords": [
"Metadata"
],
"homepage": "https://w3id.org/vocab/olca"
},
"sdm": {
"name": "SPARQL endpoint metadata",
"prefix": "sdm",
"uri_prefix": "https://w3id.org/vocab/sdm#$1",
"description": "A small vocabulary for representing SPARQL endpoint metadata on the web",
"modified": "2016-03-16",
"keywords": [
"Metadata"
],
"homepage": "https://w3id.org/vocab/sdm"
},
"xbrll": {
"name": "A lightweight XBRL vocabulary",
"prefix": "xbrll",
"uri_prefix": "https://w3id.org/vocab/xbrll#$1",
"description": "An attempt to publish XBRL standard following best practices on the Web. Not an official version from XBRL International and under development",
"modified": "2016-05-18",
"keywords": [
"Industry",
"Services"
],
"homepage": "https://w3id.org/vocab/xbrll"
},
"wfont": {
"name": "Wind Farm Ontology (wfont)",
"prefix": "wfont",
"uri_prefix": "https://w3id.org/wfont#$1",
"description": "The Wind Farm Ontology (wfont) describes wind farms and their components. It is inspired by the SANDIA Report SAND2009-1171 and DAEKIN project outcomes. It reuses the AffectedBy and EEP (Execution-Executor-Procedure) ontology design patterns to discover sensors or actuators that observe or act on a given quality or feature of interest.",
"modified": "2021-11-04",
"keywords": [
"Environment",
"IoT"
],
"homepage": "https://w3id.org/wfont"
},
"hw": {
"name": "Home Weather",
"prefix": "hw",
"uri_prefix": "https://www.auto.tuwien.ac.at/downloads/thinkhome/ontology/WeatherOntology.owl$1",
"description": "Smart home ontology for weather phenomena and exterior conditions",
"modified": "2014-05-12",
"homepage": "https://www.auto.tuwien.ac.at/projectsites/thinkhome/ontologies.html",
"keywords": [
"Environment",
"IoT"
]
},
"gleif-base": {
"name": "Global Legal Entity Identifier Foundation Base Ontology",
"prefix": "gleif-base",
"uri_prefix": "https://www.gleif.org/ontology/Base/$1",
"description": "Ontology defining generic concepts for reuse by other Global Legal Entity Identifier Foundation (GLEIF) ontologies. It defines generic classes for (legal) Entities and their relationships and statuses; and generic properties for different types of name and address. It makes use of the OMG Languages Countries and Codes (LCC) ontology (based on the ISO 3166 standard) for country and region information.",
"modified": "2019-07-11",
"keywords": [
"Geography",
"People"
],
"homepage": "https://www.gleif.org/ontology/Base/"
},
"gleif-elf": {
"name": "Entity Legal Form Ontology",
"prefix": "gleif-elf",
"uri_prefix": "https://www.gleif.org/ontology/EntityLegalForm/$1",
"description": "Ontology defining concepts for Entity Legal Forms and their abbreviations by jurisdiction, based on ISO 20275. Though used by Global Legal Entity Identifier Foundation (GLEIF) for Legal Entity Identifier registration, it is more broadly applicable.",
"modified": "2019-02-01",
"keywords": [
"Contracts",
"Industry"
],
"homepage": "https://www.gleif.org/ontology/EntityLegalForm/"
},
"gleif-geo": {
"name": "Global Legal Entity Identifier Foundation Geocoding Ontology",
"prefix": "gleif-geo",
"uri_prefix": "https://www.gleif.org/ontology/Geocoding/$1",
"description": "Ontology defining concepts for Geocoding of addresses. It is based on the geocoding used in the Global Legal Entity Identifier Foundation (GLEIF) Golden Copy Data, but is more broadly applicable.",
"modified": "2019-02-01",
"keywords": [
"Geography"
],
"homepage": "https://www.gleif.org/ontology/Geocoding/"
},
"gleif-L1": {
"name": "Global Legal Entity Identifier Foundation Level 1 Ontology - Who Is Who",
"prefix": "gleif-L1",
"uri_prefix": "https://www.gleif.org/ontology/L1/$1",
"description": "Ontology for legal entity identifier registration. It was designed for Global Legal Entity Identifier Foundation (GLEIF) Level 1 data corresponding to the Common Data Format version 2.1. It covers key reference data for a legal entity identifiable with an LEI. The ISO 17442 standard developed by the International Organization for Standardization defines a set of attributes or LEI reference data that comprises the most essential elements of identification. It specifies the minimum reference data, which must be supplied for each LEI: The official name of the legal entity as recorded in the official registers. The registered address of that legal entity. The country of formation. The codes for the representation of names of countries and their subdivisions. The date of the first LEI assignment; the date of last update of the LEI information; and the date of expiry, if applicable.",
"modified": "2019-02-01",
"keywords": [
"People"
],
"homepage": "https://www.gleif.org/ontology/L1/"
},
"gleif-L2": {
"name": "Global Legal Entity Identifier Foundation Level 2 Ontology - Who Owns Whom",
"prefix": "gleif-L2",
"uri_prefix": "https://www.gleif.org/ontology/L2/$1",
"description": "Ontology for legal entity parent relationships. It was designed for Global Legal Entity Identifier Foundation (GLEIF) Level 2 data corresponding to the Relationship Record format, version 1.1. Legal entities that have or acquire an LEI report their \u2018direct accounting consolidating parent\u2019 as well as their \u2018ultimate accounting consolidating parent\u2019, or for International Branches \u2018is an International Branch of'. Otherwise they must provide a Reporting Exception.",
"modified": "2019-02-01",
"keywords": [
"People"
],
"homepage": "https://www.gleif.org/ontology/L2/"
},
"gleif-ra": {
"name": "Global Legal Entity Identifier Foundation Registration Authority Ontology",
"prefix": "gleif-ra",
"uri_prefix": "https://www.gleif.org/ontology/RegistrationAuthority/$1",
"description": "Ontology defining concepts for Business Registries, including the jurisdictions served. This is based on the Registration Authority Code List (RAL) used for Global Legal Entity Identifier Foundation (GLEIF) registration, but is more broadly applicable.",
"modified": "2019-02-01",
"keywords": [
"Contracts"
],
"homepage": "https://www.gleif.org/ontology/RegistrationAuthority/"
},
"gleif-repex": {
"name": "Global Legal Entity Identifier Foundation Reporting Exception Ontology",
"prefix": "gleif-repex",
"uri_prefix": "https://www.gleif.org/ontology/ReportingException/$1",
"description": "Ontology for representing exceptions to reporting of parents, for entities registered with a Legal Entity Identifier. The Global Legal Identifier System (GLEIS) requires that legal entities with an LEI provide information on their ultimate and direct accounting consolidating parents. Relationship reporting is mandatory with exceptions allowed for certain well-defined reasons. This ontology provides a simple structure for recording reasons for each exception by LEI.",
"modified": "2019-02-01",
"keywords": [
"Events"
],
"homepage": "https://www.gleif.org/ontology/ReportingException/"
},
"rico": {
"name": "International Council on Archives Records in Contexts Ontology (ICA RiC-O)",
"prefix": "rico",
"uri_prefix": "https://www.ica.org/standards/RiC/ontology#$1",
"description": "RiC-O (Records in Contexts-Ontology) is an OWL ontology for describing\n archival record resources. As the second part of Records in Contexts standard,\n it is a formal representation of Records in Contexts Conceptual Model (RiC-CM). \t\t\n The current official version is v0.2; it is\n compliant with RiC-CM v0.2 full draft, that will be published in February or\n March 2021, and that is slightly different from RiC-CM\n v0.2 preview, that was published in December 2019.\n RiC-O provides a generic vocabulary and formal rules for creating RDF\n datasets (or generating them from existing archival metadata) that describe in a\n consistent way any kind of archival record resource. It can support publishing\n RDF datasets as Linked Data, querying them using SPARQL, and making inferences\n using the logic of the ontology.",
"modified": "2021-02-12",
"homepage": "https://www.ica.org/standards/RiC/RiC-O_v0-2.html",
"keywords": [
"Catalogs",
"Multimedia"
]
},
"mso-em": {
"name": "MSO-EM: Ontologies for modelling, simulation, optimization (MSO) and epistemic metadata (EM)",
"prefix": "mso-em",
"uri_prefix": "https://www.purl.org/mso-em#$1",
"description": "MSO-EM is a system of ontologies for documenting the knowledge status of models and data; the aim is to make models and data explainable-AI-ready (XAIR).",
"modified": "2024-07-10",
"keywords": [
"Environment",
"General & Upper"
],
"homepage": "https://www.purl.org/mso-em"
},
"hctl": {
"name": "Hypermedia Controls Ontology",
"prefix": "hctl",
"uri_prefix": "https://www.w3.org/2019/wot/hypermedia#$1",
"description": "Ontology designed to provide an RDF representation of Hypermedia Controls, in particular links and forms.",
"modified": "2020-06-01",
"keywords": [
"Multimedia"
],
"homepage": "https://www.w3.org/2019/wot/hypermedia#"
},
"jsonsc": {
"name": "JSON Schema in RDF",
"prefix": "jsonsc",
"uri_prefix": "https://www.w3.org/2019/wot/json-schema#$1",
"description": "Module for data schema specifications, part of the W3C Web of Things (WoT) Thing Description model",
"modified": "2020-06-01",
"keywords": [
"IoT",
"RDF"
],
"homepage": "https://www.w3.org/2019/wot/json-schema#"
},
"wotsec": {
"name": "Security mechanisms for the Web of Things",
"prefix": "wotsec",
"uri_prefix": "https://www.w3.org/2019/wot/security#$1",
"description": "Security mechanisms for the the Web of Thing",
"modified": "2020-06-01",
"keywords": [
"IoT",
"Security"
],
"homepage": "https://www.w3.org/2019/wot/security#"
},
"td": {
"name": "Thing Description Ontology",
"prefix": "td",
"uri_prefix": "https://www.w3.org/2019/wot/td#$1",
"description": "This ontology aims to model the Web of Things domain according to the W3C Interest Group (http://w3c.github.io/wot/)",
"modified": "2020-06-01",
"keywords": [
"IoT",
"Services"
],
"homepage": "https://www.w3.org/2019/wot/td"
},
"ws": {
"name": "An ontology for describing Workspaces.",
"prefix": "ws",
"uri_prefix": "http://www.w3.org/ns/pim/space#$1",
"description": "This ontology is for use in describing\nWorkspaces. Workspaces are places where data is stored and associated policies of privacy.\nA given application typically stores information in several different\nworkspaces, some being user private, some shared, and some public.\nit is crucial that the user has easy control over the destiny of information.",
"modified": "2021-10-01",
"keywords": [
"API"
],
"homepage": "https://www.w3.org/ns/pim/space"
},
"w3c-ssn": {
"name": "Semantic Sensor Network Ontology",
"prefix": "w3c-ssn",
"uri_prefix": "https://www.w3.org/ns/ssn/$1",
"description": "This ontology describes sensors and observations, and related concepts. It does not describe domain concepts, time, locations, etc. as these are intended to be included from other ontologies via OWL imports.",
"modified": "2016-12-07",
"keywords": [
"Environment",
"IoT"
],
"homepage": "https://www.w3.org/ns/ssn"
},
"simu": {
"name": "Simulation Ontology",
"prefix": "simu",
"uri_prefix": "https://www.w3id.org/simulation/ontology/$1",
"description": "This ontology was designed to conceptualize symbolic meanings following Baudrillard's Simulacra and Simulation theory. Symbols, their meaning, the context in which the symbolic meaning (or simulation) exists and the source of the simulation are linked to a N-ary Simulation Class.",
"modified": "2023-01-10",
"keywords": [
"General & Upper"
],
"homepage": "https://www.w3id.org/simulation/ontology/"
},
"sur": {
"name": "The Survey Ontology",
"prefix": "sur",
"uri_prefix": "https://w3id.org/survey-ontology#$1",
"description": "Ontology for surveys based on the Coney data model.",
"modified": "2020-07-23",
"keywords": [
"Methods"
],
"homepage": "https://www.w3id.org/survey-ontology"
},
"yoga": {
"name": "Yoga Ontology",
"prefix": "yoga",
"uri_prefix": "https://yogaontology.org/ontology/$1",
"description": "Yoga Ontology is the list of vocabularies that define the yogic practice. Where Yoga is the union of the mind and body.",
"modified": "2020-07-16",
"keywords": [
"Health",
"People"
],
"homepage": "https://yogaontology.org/ontology/"
}
} ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9659667
bioregistry-0.11.12/src/bioregistry/external/miriam/ 0000755 0001751 0000177 00000000000 14655546227 022074 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/miriam/__init__.py 0000644 0001751 0000177 00000010212 14655542206 024172 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download registry information from Identifiers.org/MIRIAMs."""
import json
from operator import itemgetter
from pathlib import Path
from pystow.utils import download
from bioregistry.constants import RAW_DIRECTORY, URI_FORMAT_KEY
from bioregistry.external.alignment_utils import Aligner
__all__ = [
"get_miriam",
"MiriamAligner",
]
DIRECTORY = Path(__file__).parent.resolve()
RAW_PATH = RAW_DIRECTORY / "miriam.json"
PROCESSED_PATH = DIRECTORY / "processed.json"
MIRIAM_URL = "https://registry.api.identifiers.org/resolutionApi/getResolverDataset"
SKIP = {
"merops",
"hgnc.family",
# Appear to be unreleased records
"f82a1a",
"4503",
"6vts",
}
SKIP_URI_FORMATS = {
"http://arabidopsis.org/servlets/TairObject?accession=$1",
}
def get_miriam(force_download: bool = False, force_process: bool = False):
"""Get the MIRIAM registry."""
if PROCESSED_PATH.exists() and not force_download and not force_process:
with PROCESSED_PATH.open() as file:
return json.load(file)
download(url=MIRIAM_URL, path=RAW_PATH, force=force_download)
with open(RAW_PATH) as file:
data = json.load(file)
data["payload"]["namespaces"] = sorted(data["payload"]["namespaces"], key=itemgetter("prefix"))
if force_download:
with open(RAW_PATH, "w") as file:
json.dump(data, file, indent=2, sort_keys=True, ensure_ascii=False)
rv = {
record["prefix"]: _process(record)
for record in data["payload"]["namespaces"]
# records whose prefixes start with `dg.` appear to be unreleased
if not record["prefix"].startswith("dg.") and record["prefix"] not in SKIP
}
with PROCESSED_PATH.open("w") as file:
json.dump(rv, file, indent=2, sort_keys=True)
return rv
#: Pairs of MIRIAM prefix and provider codes to skip
PROVIDER_BLACKLIST = {
("ega.study", "omicsdi"),
# see discussion at https://github.com/biopragmatics/bioregistry/pull/944
("bioproject", "ebi"),
("pmc", "ncbi"),
}
def _process(record):
prefix = record["prefix"]
rv = {
"prefix": prefix,
"id": record["mirId"][len("MIR:") :],
"name": record["name"],
"deprecated": record["deprecated"],
"namespaceEmbeddedInLui": record["namespaceEmbeddedInLui"],
"sampleId": record["sampleId"],
"description": record["description"],
"pattern": record["pattern"],
}
resources = [
_preprocess_resource(resource)
for resource in record.get("resources", [])
if not resource.get("deprecated")
]
if not resources:
return rv
has_official = any(resource["official"] for resource in resources)
if has_official:
primary = next(resource for resource in resources if resource["official"])
rest = [resource for resource in resources if not resource["official"]]
else:
primary, *rest = resources
rv["homepage"] = primary["homepage"]
if URI_FORMAT_KEY in primary:
rv[URI_FORMAT_KEY] = primary[URI_FORMAT_KEY]
extras = []
for provider in rest:
code = provider["code"]
if code in SKIP_PROVIDERS or (prefix, code) in PROVIDER_BLACKLIST:
continue
del provider["official"]
extras.append(provider)
if extras:
rv["providers"] = extras
return rv
SKIP_PROVIDERS = {
"ols", # handled by the Bioregistry's metaregistry
"bptl", # handled by the Bioregistry's metaregistry
"bioentitylink",
}
def _preprocess_resource(resource):
rv = {
"official": resource["official"],
"homepage": resource["resourceHomeUrl"],
"code": resource["providerCode"],
"name": resource["name"],
"description": resource["description"],
}
uri_format = resource["urlPattern"].replace("{$id}", "$1")
if uri_format not in SKIP_URI_FORMATS:
rv[URI_FORMAT_KEY] = uri_format
return rv
class MiriamAligner(Aligner):
"""Aligner for the MIRIAM registry."""
key = "miriam"
getter = get_miriam
curation_header = ("deprecated", "name", "description")
include_new = True
if __name__ == "__main__":
MiriamAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254533.0
bioregistry-0.11.12/src/bioregistry/external/miriam/processed.json 0000644 0001751 0000177 00002176517 14655543405 024774 0 ustar 00runner docker {
"3dmet": {
"deprecated": true,
"description": "3DMET is a database collecting three-dimensional structures of natural metabolites.",
"homepage": "http://www.3dmet.dna.affrc.go.jp/",
"id": "00000066",
"name": "3DMET",
"namespaceEmbeddedInLui": false,
"pattern": "^B\\d{5}$",
"prefix": "3dmet",
"sampleId": "B00162",
"uri_format": "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1"
},
"4dn": {
"deprecated": false,
"description": "The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases.",
"homepage": "https://data.4dnucleome.org/",
"id": "00000833",
"name": "4D Nucleome",
"namespaceEmbeddedInLui": false,
"pattern": "^4DN[A-Z]{2}[A-Z0-9]{7}$",
"prefix": "4dn",
"sampleId": "4DNES265ETYQ",
"uri_format": "https://data.4dnucleome.org/$1"
},
"abs": {
"deprecated": false,
"description": "The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography.",
"homepage": "http://genome.crg.es/datasets/abs2005/",
"id": "00000277",
"name": "ABS",
"namespaceEmbeddedInLui": false,
"pattern": "^A\\d+$",
"prefix": "abs",
"sampleId": "A0014",
"uri_format": "http://genome.crg.es/datasets/abs2005/entries/$1.html"
},
"aceview.worm": {
"deprecated": false,
"description": "AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression.",
"homepage": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm",
"id": "00000282",
"name": "Aceview Worm",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z0-9-]+$",
"prefix": "aceview.worm",
"sampleId": "aap-1",
"uri_format": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1"
},
"addgene": {
"deprecated": false,
"description": "Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world.",
"homepage": "http://addgene.org/",
"id": "00000675",
"name": "Addgene Plasmid Repository",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$",
"prefix": "addgene",
"sampleId": "50943",
"uri_format": "http://addgene.org/$1"
},
"adw": {
"deprecated": false,
"description": "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology.",
"homepage": "https://animaldiversity.org/",
"id": "00000492",
"name": "Animal Diversity Web",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z_a-z]+$",
"prefix": "adw",
"sampleId": "Lycalopex_vetulus",
"uri_format": "https://animaldiversity.org/accounts/$1/"
},
"affy.probeset": {
"deprecated": false,
"description": "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration.",
"homepage": "http://www.affymetrix.com/",
"id": "00000394",
"name": "Affymetrix Probeset",
"namespaceEmbeddedInLui": false,
"pattern": "\\d{4,}((_[asx])?_at)?",
"prefix": "affy.probeset",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "Bio2RDF",
"homepage": "http://cu.affymetrix.bio2rdf.org/fct/",
"name": "Bio2RDF",
"uri_format": "http://cu.affymetrix.bio2rdf.org/describe/?url=http://bio2rdf.org/affymetrix:$1"
}
],
"sampleId": "243002_at",
"uri_format": "https://www.affymetrix.com/LinkServlet?probeset=$1"
},
"aftol.taxonomy": {
"deprecated": false,
"description": "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species.",
"homepage": "http://aftol.org/data.php",
"id": "00000411",
"name": "AFTOL",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "aftol.taxonomy",
"sampleId": "959",
"uri_format": "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1"
},
"agricola": {
"deprecated": false,
"description": "AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century.",
"homepage": "http://agricola.nal.usda.gov/",
"id": "00000589",
"name": "AGRICOLA",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "agricola",
"sampleId": "50018",
"uri_format": "http://ddr.nal.usda.gov/dspace/handle/10113/$1"
},
"allergome": {
"deprecated": false,
"description": "Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources.",
"homepage": "http://www.allergome.org/",
"id": "00000334",
"name": "Allergome",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "allergome",
"sampleId": "1948",
"uri_format": "http://www.allergome.org/script/dettaglio.php?id_molecule=$1"
},
"amoebadb": {
"deprecated": false,
"description": "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"homepage": "http://amoebadb.org/amoeba/",
"id": "00000148",
"name": "AmoebaDB",
"namespaceEmbeddedInLui": false,
"pattern": "^EDI_\\d+$",
"prefix": "amoebadb",
"sampleId": "EDI_244000",
"uri_format": "https://amoebadb.org/amoeba/app/record/gene/$1"
},
"antibodyregistry": {
"deprecated": false,
"description": "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.",
"homepage": "http://antibodyregistry.org/",
"id": "00000516",
"name": "Antibody Registry",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{6}$",
"prefix": "antibodyregistry",
"sampleId": "493771",
"uri_format": "http://antibodyregistry.org/AB_$1"
},
"antweb": {
"deprecated": false,
"description": "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures.",
"homepage": "http://www.antweb.org/",
"id": "00000146",
"name": "AntWeb",
"namespaceEmbeddedInLui": false,
"pattern": "^casent\\d+(\\-D\\d+)?$",
"prefix": "antweb",
"sampleId": "casent0106247",
"uri_format": "http://www.antweb.org/specimen.do?name=$1"
},
"aop": {
"deprecated": false,
"description": "International repository of Adverse Outcome Pathways.",
"homepage": "https://aopwiki.org/",
"id": "00000617",
"name": "AOPWiki",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "aop",
"sampleId": "98",
"uri_format": "https://aopwiki.org/aops/$1"
},
"aop.events": {
"deprecated": false,
"description": "International repository of Adverse Outcome Pathways.",
"homepage": "https://aopwiki.org/",
"id": "00000652",
"name": "AOPWiki (Key Event)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "aop.events",
"sampleId": "3",
"uri_format": "https://aopwiki.org/events/$1"
},
"aop.relationships": {
"deprecated": false,
"description": "International repository of Adverse Outcome Pathways.",
"homepage": "https://aopwiki.org/",
"id": "00000653",
"name": "AOPWiki (Key Event Relationship)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "aop.relationships",
"sampleId": "5",
"uri_format": "https://aopwiki.org/relationships/$1"
},
"aop.stressor": {
"deprecated": false,
"description": "International repository of Adverse Outcome Pathways.",
"homepage": "https://aopwiki.org/",
"id": "00000654",
"name": "AOPWiki (Stressor)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "aop.stressor",
"sampleId": "9",
"uri_format": "https://aopwiki.org/stressors/$1"
},
"apd": {
"deprecated": false,
"description": "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides.",
"homepage": "http://aps.unmc.edu/AP/",
"id": "00000278",
"name": "APD",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{5}$",
"prefix": "apd",
"sampleId": "01001",
"uri_format": "http://aps.unmc.edu/AP/database/query_output.php?ID=$1"
},
"aphidbase.transcript": {
"deprecated": false,
"description": "AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information.",
"homepage": "http://www.aphidbase.com/aphidbase",
"id": "00000393",
"name": "AphidBase Transcript",
"namespaceEmbeddedInLui": false,
"pattern": "^ACYPI\\d{6}(-RA)?$",
"prefix": "aphidbase.transcript",
"sampleId": "ACYPI000159",
"uri_format": "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1"
},
"apid.interactions": {
"deprecated": false,
"description": "APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.",
"homepage": "http://cicblade.dep.usal.es:8080/APID/",
"id": "00000576",
"name": "APID Interactomes",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$",
"prefix": "apid.interactions",
"sampleId": "P01116",
"uri_format": "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1"
},
"arachnoserver": {
"deprecated": false,
"description": "ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information.",
"homepage": "http://www.arachnoserver.org/",
"id": "00000193",
"name": "ArachnoServer",
"namespaceEmbeddedInLui": false,
"pattern": "^AS\\d{6}$",
"prefix": "arachnoserver",
"sampleId": "AS000060",
"uri_format": "http://www.arachnoserver.org/toxincard.html?id=$1"
},
"ardb": {
"deprecated": false,
"description": "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes.",
"homepage": "http://ardb.cbcb.umd.edu/",
"id": "00000522",
"name": "Antibiotic Resistance Genes Database",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z_]{3}[0-9]{4,}$",
"prefix": "ardb",
"sampleId": "CAE46076",
"uri_format": "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1"
},
"ark": {
"deprecated": false,
"description": "Archival Resource Keys (ARKs) serve as persistent identifiers, or stable, trusted references for information objects. Among other things, they aim to be web addresses (URLs) that don\u2019t return 404 Page Not Found errors. The ARK Alliance is an open global community supporting the ARK infrastructure on behalf of research and scholarship. End users, especially researchers, rely on ARKs for long term access to the global scientific and cultural record. Since 2001 some 8.2 billion ARKs have been created by over 1000 organizations \u2014 libraries, data centers, archives, museums, publishers, government agencies, and vendors. They identify anything digital, physical, or abstract. ARKs are open, mainstream, non-paywalled, decentralized persistent identifiers that can be created by an organization as soon as it is registered with a NAAN (Name Assigning Authority Number). Once registered, an ARK organization can create unlimited numbers of ARKs and publicize them via the n2t.net global resolver or via their own local resolver.",
"homepage": "https://arks.org",
"id": "00000592",
"name": "Archival Resource Key (ARK)",
"namespaceEmbeddedInLui": true,
"pattern": "^(ark\\:)/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$",
"prefix": "ark",
"sampleId": "/53355/cl010066723",
"uri_format": "https://n2t.net/ark:$1"
},
"arrayexpress": {
"deprecated": false,
"description": "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.",
"homepage": "https://www.ebi.ac.uk/arrayexpress/",
"id": "00000036",
"name": "ArrayExpress",
"namespaceEmbeddedInLui": false,
"pattern": "^[AEP]-\\w{4}-\\d+$",
"prefix": "arrayexpress",
"providers": [
{
"code": "omicsdi",
"description": "ArrayExpress through OmicsDI",
"homepage": "https://www.omicsdi.org/",
"name": "ArrayExpress through OmicsDI",
"uri_format": "https://www.omicsdi.org/dataset/arrayexpress-repository/$1"
}
],
"sampleId": "E-MEXP-1712",
"uri_format": "https://www.ebi.ac.uk/arrayexpress/experiments/$1"
},
"arrayexpress.platform": {
"deprecated": false,
"description": "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results.",
"homepage": "https://www.ebi.ac.uk/arrayexpress/",
"id": "00000294",
"name": "ArrayExpress Platform",
"namespaceEmbeddedInLui": false,
"pattern": "^[AEP]-\\w{4}-\\d+$",
"prefix": "arrayexpress.platform",
"sampleId": "A-GEOD-50",
"uri_format": "https://www.ebi.ac.uk/arrayexpress/arrays/$1"
},
"arraymap": {
"deprecated": false,
"description": "arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome.",
"homepage": "https://www.arraymap.org",
"id": "00000621",
"name": "ArrayMap",
"namespaceEmbeddedInLui": false,
"pattern": "^[\\w\\-:,]{3,64}$",
"prefix": "arraymap",
"sampleId": "icdom:8500_3",
"uri_format": "https://www.arraymap.org/pgx:$1"
},
"arxiv": {
"deprecated": false,
"description": "arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology.",
"homepage": "https://arxiv.org/",
"id": "00000035",
"name": "arXiv",
"namespaceEmbeddedInLui": false,
"pattern": "^(\\w+(\\-\\w+)?(\\.\\w+)?)?\\d{4,7}(\\.\\d+(v\\d+)?)?$",
"prefix": "arxiv",
"sampleId": "0807.4956v1",
"uri_format": "https://arxiv.org/abs/$1"
},
"asap": {
"deprecated": false,
"description": "ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources.",
"homepage": "http://asap.ahabs.wisc.edu/asap/home.php",
"id": "00000283",
"name": "ASAP",
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"deprecated": false,
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"covid19": {
"deprecated": false,
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"homepage": "https://worldwide.espacenet.com/classification",
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"uri_format": "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1"
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"deprecated": false,
"description": "Repeated CRISPR (\"clustered regularly interspaced short palindromic repeats\") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data.",
"homepage": "http://crispr.i2bc.paris-saclay.fr/",
"id": "00000626",
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"uri_format": "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1"
},
"crop2ml": {
"deprecated": false,
"description": "CropMRespository is a database of soil and crop biophysical process models.",
"homepage": "http://www.crop2ml.org",
"id": "00001015",
"name": "CropMRepository",
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"sampleId": "000000001",
"uri_format": "http://www.crop2ml.org/cropmdb/$1"
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"cryptodb": {
"deprecated": false,
"description": "CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"homepage": "https://cryptodb.org/cryptodb/",
"id": "00000149",
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"pattern": "^\\w+",
"prefix": "cryptodb",
"sampleId": "cgd7_230",
"uri_format": "https://cryptodb.org/cryptodb/app/record/gene/$1"
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"csa": {
"deprecated": false,
"description": "The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme.",
"homepage": "https://www.ebi.ac.uk/thornton-srv/databases/CSA/",
"id": "00000144",
"name": "CSA",
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"pattern": "^[0-9][A-Za-z0-9]{3}$",
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"uri_format": "https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1"
},
"csd": {
"deprecated": false,
"description": "The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode.",
"homepage": "https://www.ccdc.cam.ac.uk/",
"id": "00000820",
"name": "Cambridge Structural Database",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]{6}(\\d{2})?$",
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"uri_format": "https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG"
},
"cst": {
"deprecated": false,
"description": "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways.",
"homepage": "http://www.cellsignal.com/pathways/index.html",
"id": "00000429",
"name": "Cell Signaling Technology Pathways",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9_-]+$",
"prefix": "cst",
"sampleId": "Akt_PKB",
"uri_format": "http://www.cellsignal.com/reference/pathway/$1.html"
},
"cst.ab": {
"deprecated": false,
"description": "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products.",
"homepage": "http://www.cellsignal.com/catalog/index.html",
"id": "00000430",
"name": "Cell Signaling Technology Antibody",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
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"sampleId": "3305",
"uri_format": "http://www.cellsignal.com/products/$1.html"
},
"cstr": {
"deprecated": false,
"description": "CSTR is an identifier for Common Science and Technology Resources, to provide persistent identification services for the positioning, traceability, citation, statistics and evaluation of science and technology resources. ",
"homepage": "https://www.cstr.cn/en/",
"id": "00000998",
"name": "CSTR",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{5}\\.\\d{2}\\..*$",
"prefix": "cstr",
"sampleId": "31253.11.sciencedb.j00001.00123",
"uri_format": "https://cstr.cn/$1"
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"ctd.chemical": {
"deprecated": false,
"description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.",
"homepage": "http://ctdbase.org/",
"id": "00000098",
"name": "CTD Chemical",
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"pattern": "^[CD]\\d+$",
"prefix": "ctd.chemical",
"sampleId": "D001151",
"uri_format": "http://ctdbase.org/detail.go?type=chem&acc=$1"
},
"ctd.disease": {
"deprecated": false,
"description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.",
"homepage": "http://ctdbase.org/",
"id": "00000099",
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"pattern": "^D\\d+$",
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"uri_format": "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1"
},
"ctd.gene": {
"deprecated": false,
"description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.",
"homepage": "http://ctdbase.org/",
"id": "00000100",
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"pattern": "^\\d+$",
"prefix": "ctd.gene",
"sampleId": "101",
"uri_format": "http://ctdbase.org/detail.go?type=gene&acc=$1"
},
"cubedb": {
"deprecated": false,
"description": "Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available.",
"homepage": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html",
"id": "00000397",
"name": "Cube db",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z_0-9]+$",
"prefix": "cubedb",
"sampleId": "AKR",
"uri_format": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/"
},
"d1id": {
"deprecated": false,
"description": "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences.",
"homepage": "https://www.dataone.org",
"id": "00000611",
"name": "DataONE",
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"pattern": "\\S+",
"prefix": "d1id",
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"uri_format": "https://cn.dataone.org/cn/v2/resolve/{$1}"
},
"dailymed": {
"deprecated": false,
"description": "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read.",
"homepage": "https://dailymed.nlm.nih.gov/dailymed/",
"id": "00000434",
"name": "DailyMed",
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"uri_format": "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1"
},
"dandi": {
"deprecated": false,
"description": "DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable).\nDANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data.\nThese data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.",
"homepage": "https://dandiarchive.org/",
"id": "00000786",
"name": "DANDI: Distributed Archives for Neurophysiology Data Integration",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{6}(\\/\\d+\\.\\d+\\.\\d+)?$",
"prefix": "dandi",
"sampleId": "000017",
"uri_format": "https://dandiarchive.org/dandiset/$1"
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"darc": {
"deprecated": false,
"description": "DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.",
"homepage": "http://darcsite.genzentrum.lmu.de/darc/index.php",
"id": "00000366",
"name": "DARC",
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"uri_format": "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1"
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"dashr": {
"deprecated": false,
"description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records.",
"homepage": "http://lisanwanglab.org/DASHR/",
"id": "00000564",
"name": "DASHR",
"namespaceEmbeddedInLui": false,
"pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$",
"prefix": "dashr",
"sampleId": "hsa-mir-200a",
"uri_format": "http://lisanwanglab.org/DASHR/entry/$1"
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"deprecated": false,
"description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression.",
"homepage": "https://dashr1.lisanwanglab.org/show-expression-table.php?start=0",
"id": "00000565",
"name": "DASHR expression",
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"prefix": "dashr.expression",
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"uri_format": "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable"
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"datanator.gene": {
"deprecated": false,
"description": "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.",
"homepage": "https://datanator.info/",
"id": "00000720",
"name": "Datanator Gene",
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"prefix": "exac.gene",
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"deprecated": false,
"description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information.",
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"name": "ExAC Transcript",
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"prefix": "exac.transcript",
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"uri_format": "http://exac.broadinstitute.org/transcript/$1"
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"deprecated": false,
"description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information.",
"homepage": "http://exac.broadinstitute.org/",
"id": "00000541",
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"deprecated": false,
"description": "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.",
"homepage": "https://www.facebase.org",
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"name": "FaceBase Data Repository",
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"prefix": "facebase",
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"uri_format": "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1"
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"fairsharing": {
"deprecated": false,
"description": "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies.",
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"id": "00000364",
"name": "FAIRsharing",
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"prefix": "fairsharing",
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"deprecated": false,
"description": "FlyBase is the database of the Drosophila Genome Projects and of associated literature.",
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"pattern": "^FB\\w{2}\\d{7}$",
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{
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"name": "FlyBase through the Alliance of Genome Resources",
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"sampleId": "FBgn0011293",
"uri_format": "http://flybase.org/reports/$1.html"
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"deprecated": false,
"description": "DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms.",
"homepage": "http://www.fungalbarcoding.org/",
"id": "00000410",
"name": "Fungal Barcode",
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"sampleId": "2224",
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"fcb": {
"deprecated": false,
"description": "Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR).\n\n",
"homepage": "https://w3id.org",
"id": "00000891",
"name": "the FAIR Cookbook",
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"pattern": "^FCB\\d{3}",
"prefix": "fcb",
"sampleId": "FCB005",
"uri_format": "https://w3id.org/faircookbook/$1"
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"deprecated": false,
"description": "FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field.",
"homepage": "https://flowrepository.org/",
"id": "00000672",
"name": "FlowRepository",
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"pattern": "^FR\\-FCM\\-\\w{4}$",
"prefix": "flowrepository",
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"description": "The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy.",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/fma/",
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"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/fma/terms?obo_id=FMA:$1"
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"foodb.compound": {
"deprecated": false,
"description": "FooDB is resource on food and its constituent compounds. It includes data on the compound\u2019s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds.",
"homepage": "http://foodb.ca/foods",
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"pattern": "^FDB\\d+$",
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"sampleId": "FDB002100",
"uri_format": "http://foodb.ca/compounds/$1"
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"deprecated": false,
"description": "FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies.",
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"id": "00000661",
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"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/foodon/terms?obo_id=FOODON:$1"
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"fplx": {
"deprecated": false,
"description": "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships.",
"homepage": "https://sorgerlab.github.io/famplex",
"id": "00000651",
"name": "FamPlex",
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"pattern": "^[a-zA-Z0-9][A-Za-z0-9_]+$",
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"sampleId": "RAS",
"uri_format": "https://sorgerlab.github.io/famplex/$1"
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"fsnp": {
"deprecated": false,
"description": "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.",
"homepage": "http://compbio.cs.queensu.ca/F-SNP/",
"id": "00000496",
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"pattern": "^rs\\d+$",
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"uri_format": "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1"
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"funcbase.fly": {
"deprecated": false,
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data.",
"homepage": "http://func.mshri.on.ca/fly",
"id": "00000461",
"name": "FuncBase Fly",
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"pattern": "^\\d+$",
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"sampleId": "10194",
"uri_format": "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1"
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"funcbase.human": {
"deprecated": false,
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data.",
"homepage": "http://func.mshri.on.ca/human/",
"id": "00000462",
"name": "FuncBase Human",
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"uri_format": "http://func.mshri.on.ca/human/genes/list_functional_scores/$1"
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"funcbase.mouse": {
"deprecated": false,
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse.",
"homepage": "http://func.mshri.on.ca/mouse/",
"id": "00000463",
"name": "FuncBase Mouse",
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"pattern": "^\\d+$",
"prefix": "funcbase.mouse",
"sampleId": "1351341",
"uri_format": "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1"
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"funcbase.yeast": {
"deprecated": false,
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast.",
"homepage": "http://func.mshri.on.ca/yeast",
"id": "00000464",
"name": "FuncBase Yeast",
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"pattern": "^\\d+$",
"prefix": "funcbase.yeast",
"sampleId": "2701",
"uri_format": "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1"
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"funderregistry": {
"deprecated": false,
"description": "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world.",
"homepage": "https://www.crossref.org/",
"id": "00000847",
"name": "FunderRegistry",
"namespaceEmbeddedInLui": false,
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"uri_format": "http://data.crossref.org/fundingdata/funder/10.13039/$1"
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"fungidb": {
"deprecated": false,
"description": "FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina.",
"homepage": "https://fungidb.org/fungidb",
"id": "00000365",
"name": "FungiDB",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z_0-9]+$",
"prefix": "fungidb",
"sampleId": "CNBG_0001",
"uri_format": "https://fungidb.org/fungidb/app/record/gene/$1"
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"ga4ghdos": {
"deprecated": false,
"description": "Assists in resolving data across cloud resources.",
"homepage": "http://github.com/ga4gh/data-object-service-schemas",
"id": "00000671",
"name": "Data Object Service",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-zA-Z0-9\\-:#/\\.]+$",
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"uri_format": "https://dataguids.org/ga4gh/dos/v1/dataobjects/$1"
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"gabi": {
"deprecated": false,
"description": "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'.",
"homepage": "http://www.gabipd.org/",
"id": "00000164",
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"pattern": "^\\w+$",
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"uri_format": "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject"
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"gateway": {
"deprecated": false,
"description": "The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access.",
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"prefix": "gateway",
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"uri_format": "https://web.www.healthdatagateway.org/dataset/$1"
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"gcst": {
"deprecated": false,
"description": "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide.",
"homepage": "https://www.ebi.ac.uk",
"id": "00000715",
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"uri_format": "https://www.ebi.ac.uk/gwas/studies/$1"
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"deprecated": false,
"description": "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis.",
"homepage": "https://gdc.cancer.gov",
"id": "00000604",
"name": "Genomic Data Commons Data Portal",
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"pattern": "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$",
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"uri_format": "https://portal.gdc.cancer.gov/cases/$1"
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"deprecated": false,
"description": "The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies.",
"homepage": "https://www.cancerrxgene.org",
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"name": "Genomics of Drug Sensitivity in Cancer",
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"pattern": "^[0-9]+$",
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"uri_format": "https://www.cancerrxgene.org/translation/Drug/$1"
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"deprecated": false,
"description": "GenAtlas is a database containing information on human genes, markers and phenotypes.",
"homepage": "http://genatlas.medecine.univ-paris5.fr/",
"id": "00000208",
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"deprecated": false,
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"homepage": "http://www.genecards.org/",
"id": "00000323",
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"pattern": "^[A-Za-z-0-9_]+(\\@)?$",
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"uri_format": "https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1"
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"genedb": {
"deprecated": true,
"description": "GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the \"Pathogen Genomics\" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed.",
"homepage": "https://www.genedb.org/",
"id": "00000106",
"name": "GeneDB",
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"homepage": "http://urgi.versailles.inra.fr/Genefarm/",
"id": "00000211",
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"genetree": {
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"homepage": "http://www.ensembl.org/",
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"name": "GeneTree",
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"homepage": "http://en.wikipedia.org/wiki/Gene_Wiki",
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"description": "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank.",
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"namespaceEmbeddedInLui": false,
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"description": "Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome.",
"homepage": "https://www.ebi.ac.uk/interpro/genomeproperties/",
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"uri_format": "https://www.ebi.ac.uk/interpro/genomeproperties/#$1"
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"description": "The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval.",
"homepage": "https://www.ncbi.nlm.nih.gov/geo/",
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"uri_format": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1"
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"description": "An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in \"The US declared war on Germany\" vs. the US in \"The plane entered US airspace\".",
"homepage": "https://github.com/ufbmi",
"id": "00000824",
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"deprecated": false,
"description": "GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"homepage": "https://giardiadb.org/giardiadb/",
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"uri_format": "https://giardiadb.org/giardiadb/app/record/gene/$1"
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"github": {
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"description": "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors.",
"homepage": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/",
"id": "00000493",
"name": "GLIDA GPCR",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z-_0-9]+$",
"prefix": "glida.gpcr",
"sampleId": "ACM1_HUMAN",
"uri_format": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1"
},
"glida.ligand": {
"deprecated": false,
"description": "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands.",
"homepage": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/",
"id": "00000494",
"name": "GLIDA Ligand",
"namespaceEmbeddedInLui": false,
"pattern": "^L\\d+$",
"prefix": "glida.ligand",
"sampleId": "L000001",
"uri_format": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1"
},
"glycoepitope": {
"deprecated": false,
"description": "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes.",
"homepage": "https://www.glycoepitope.jp/epitopes/",
"id": "00000478",
"name": "GlycoEpitope",
"namespaceEmbeddedInLui": false,
"pattern": "^EP\\d{4}$",
"prefix": "glycoepitope",
"sampleId": "EP0311",
"uri_format": "https://www.glycoepitope.jp/epitopes/$1"
},
"glycomedb": {
"deprecated": false,
"description": "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.",
"homepage": "https://glytoucan.org/",
"id": "00000114",
"name": "GlycomeDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "glycomedb",
"sampleId": "G77500AY",
"uri_format": "https://glytoucan.org/Structures/Glycans/$1"
},
"glyconavi": {
"deprecated": false,
"description": "GlycoNAVI is a website for carbohydrate research. It consists of the \"GlycoNAVI Database\" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the \"GlycoNAVI tools\" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools.",
"homepage": "https://www.noguchi.or.jp/",
"id": "00000830",
"name": "GlycoNAVI",
"namespaceEmbeddedInLui": false,
"pattern": "^GN_[A-Za-z]*[_]*[A-Za-z0-9-:_]+$",
"prefix": "glyconavi",
"sampleId": "GN_GlyTouCan_G03681DA",
"uri_format": "https://glyconavi.org/hub/?id=$1"
},
"glycopost": {
"deprecated": false,
"description": "GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their \"raw/processed\" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines.",
"homepage": "https://glycopost.glycosmos.org",
"id": "00000721",
"name": "GlycoPOST",
"namespaceEmbeddedInLui": false,
"pattern": "^GPST[0-9]{6}$",
"prefix": "glycopost",
"sampleId": "GPST000024",
"uri_format": "https://glycopost.glycosmos.org/entry/$1"
},
"glytoucan": {
"deprecated": false,
"description": "GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data.",
"homepage": "https://glytoucan.org",
"id": "00000608",
"name": "GlyTouCan",
"namespaceEmbeddedInLui": false,
"pattern": "^G[0-9]{5}[A-Z]{2}$",
"prefix": "glytoucan",
"sampleId": "G00054MO",
"uri_format": "https://glytoucan.org/Structures/Glycans/$1"
},
"gmd": {
"deprecated": false,
"description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena.",
"homepage": "http://gmd.mpimp-golm.mpg.de/",
"id": "00000274",
"name": "Golm Metabolome Database",
"namespaceEmbeddedInLui": false,
"pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$",
"prefix": "gmd",
"sampleId": "68513255-fc44-4041-bc4b-4fd2fae7541d",
"uri_format": "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx"
},
"gmd.analyte": {
"deprecated": false,
"description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes.",
"homepage": "http://gmd.mpimp-golm.mpg.de/",
"id": "00000426",
"name": "Golm Metabolome Database Analyte",
"namespaceEmbeddedInLui": false,
"pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$",
"prefix": "gmd.analyte",
"sampleId": "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80",
"uri_format": "http://gmd.mpimp-golm.mpg.de/Analytes/$1"
},
"gmd.gcms": {
"deprecated": false,
"description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra.",
"homepage": "http://gmd.mpimp-golm.mpg.de/",
"id": "00000424",
"name": "Golm Metabolome Database GC-MS spectra",
"namespaceEmbeddedInLui": false,
"pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$",
"prefix": "gmd.gcms",
"sampleId": "53d583d8-40c6-40e1-9296-23f821cd77a5",
"uri_format": "http://gmd.mpimp-golm.mpg.de/Spectrums/$1"
},
"gmd.profile": {
"deprecated": false,
"description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues.",
"homepage": "http://gmd.mpimp-golm.mpg.de/",
"id": "00000423",
"name": "Golm Metabolome Database Profile",
"namespaceEmbeddedInLui": false,
"pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$",
"prefix": "gmd.profile",
"sampleId": "10b38aaf-b977-4950-85b8-f4775f66658d",
"uri_format": "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1"
},
"gmd.ref": {
"deprecated": false,
"description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances.",
"homepage": "http://gmd.mpimp-golm.mpg.de/",
"id": "00000425",
"name": "Golm Metabolome Database Reference Substance",
"namespaceEmbeddedInLui": false,
"pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$",
"prefix": "gmd.ref",
"sampleId": "8cf84adb-b4db-4807-ac98-0004247c35df",
"uri_format": "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1"
},
"gnd": {
"deprecated": false,
"description": "The Gemeinsame Normdatei (Integrated Authority File) or GND is an international authority file for person names, subject headings and corporate bodies. It is used mainly for documentation in libraries and increasingly also by archives and museums. The GND is managed by the German National Library in cooperation with various regional library networks in German-speaking Europe and other partners.",
"homepage": "https://lobid.org/",
"id": "00001002",
"name": "Gemeinsame Normdatei",
"namespaceEmbeddedInLui": false,
"pattern": "[0-9X\\-]+",
"prefix": "gnd",
"sampleId": "117145750",
"uri_format": "https://lobid.org/gnd/$1"
},
"gnpis": {
"deprecated": false,
"description": "GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest.",
"homepage": "https://urgi.versailles.inra.fr/gnpis/",
"id": "00000627",
"name": "GnpIS",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9]+$",
"prefix": "gnpis",
"sampleId": "AY109603",
"uri_format": "https://urgi.versailles.inra.fr/gnpis/#result/term=$1"
},
"go": {
"deprecated": false,
"description": "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.",
"homepage": "http://amigo.geneontology.org/",
"id": "00000022",
"name": "Gene Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^GO:\\d{7}$",
"prefix": "go",
"providers": [
{
"code": "quickgo",
"description": "QuickGO (Gene Ontology browser)",
"homepage": "https://www.ebi.ac.uk/QuickGO/",
"name": "QuickGO (Gene Ontology browser)",
"uri_format": "https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:$1"
},
{
"code": "CURATOR_REVIEW",
"description": "GO Browser",
"homepage": "http://www.informatics.jax.org/searches/GO_form.shtml",
"name": "GO Browser",
"uri_format": "http://www.informatics.jax.org/searches/GO.cgi?id=GO:$1"
},
{
"code": "CURATOR_REVIEW",
"description": "GO through PANTHER",
"homepage": "http://www.pantherdb.org/",
"name": "GO through PANTHER",
"uri_format": "http://www.pantherdb.org/panther/category.do?categoryAcc=GO:$1"
}
],
"sampleId": "0006915",
"uri_format": "http://amigo.geneontology.org/amigo/term/GO:$1"
},
"go_ref": {
"deprecated": false,
"description": "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made.",
"homepage": "http://www.geneontology.org/cgi-bin/references.cgi",
"id": "00000450",
"name": "Gene Ontology Reference",
"namespaceEmbeddedInLui": true,
"pattern": "^GO_REF:\\d{7}$",
"prefix": "go_ref",
"sampleId": "0000041",
"uri_format": "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-$1.md"
},
"goa": {
"deprecated": false,
"description": "The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups.",
"homepage": "https://www.ebi.ac.uk/GOA/",
"id": "00000196",
"name": "GOA",
"namespaceEmbeddedInLui": false,
"pattern": "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$",
"prefix": "goa",
"sampleId": "P12345",
"uri_format": "https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1"
},
"gold": {
"deprecated": false,
"description": "The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.",
"homepage": "https://gold.jgi.doe.gov/",
"id": "00000733",
"name": "Genomes OnLine Database (GOLD)",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z][a-z][0-9]+$",
"prefix": "gold",
"sampleId": "Gs0000008",
"uri_format": "https://gold.jgi.doe.gov/resolver?id=$1"
},
"gold.genome": {
"deprecated": false,
"description": "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by \u2018gold\u2019 prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed \u2018gold\u2019 namespace.\n\nThe GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes.",
"homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi",
"id": "00000401",
"name": "GOLD genome",
"namespaceEmbeddedInLui": false,
"pattern": "^(Gi|Gc)\\d+$",
"prefix": "gold.genome",
"sampleId": "Gi07796",
"uri_format": "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1"
},
"gold.meta": {
"deprecated": false,
"description": "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by \u2018gold\u2019 prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed \u2018gold\u2019 namespace. \n\nThe GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples.",
"homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi",
"id": "00000402",
"name": "GOLD metadata",
"namespaceEmbeddedInLui": false,
"pattern": "^Gm\\d+$",
"prefix": "gold.meta",
"sampleId": "Gm00047",
"uri_format": "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1"
},
"google.patent": {
"deprecated": false,
"description": "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date.",
"homepage": "https://www.google.com/patents/",
"id": "00000537",
"name": "Google Patents",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]{2}\\d+([A-Z])?$",
"prefix": "google.patent",
"sampleId": "US4145692",
"uri_format": "https://www.google.com/patents/$1"
},
"gpcrdb": {
"deprecated": false,
"description": "The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models.",
"homepage": "http://www.gpcrdb.org/",
"id": "00000212",
"name": "GPCRDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "gpcrdb",
"sampleId": "RL3R1_HUMAN",
"uri_format": "http://www.gpcrdb.org/protein/$1/"
},
"gpmdb": {
"deprecated": false,
"description": "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns.",
"homepage": "http://gpmdb.thegpm.org/",
"id": "00000649",
"name": "GPMDB",
"namespaceEmbeddedInLui": false,
"pattern": "^GPM\\d+$",
"prefix": "gpmdb",
"providers": [
{
"code": "omicsdi",
"description": "GPMDB through OmicsDI",
"homepage": "https://www.omicsdi.org/",
"name": "GPMDB through OmicsDI",
"uri_format": "https://www.omicsdi.org/dataset/gpmdb/$1"
}
],
"sampleId": "GPM32310002988",
"uri_format": "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1"
},
"gramene.gene": {
"deprecated": false,
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene.",
"homepage": "http://www.gramene.org/",
"id": "00000182",
"name": "Gramene genes",
"namespaceEmbeddedInLui": false,
"pattern": "^GR\\:\\d+$",
"prefix": "gramene.gene",
"sampleId": "GR:0080039",
"uri_format": "http://www.gramene.org/db/genes/search_gene?acc=$1"
},
"gramene.protein": {
"deprecated": false,
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene.",
"homepage": "http://www.gramene.org/",
"id": "00000181",
"name": "Gramene protein",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "gramene.protein",
"sampleId": "78073",
"uri_format": "http://www.gramene.org/db/protein/protein_search?protein_id=$1"
},
"gramene.qtl": {
"deprecated": false,
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene.",
"homepage": "http://www.gramene.org/",
"id": "00000184",
"name": "Gramene QTL",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "gramene.qtl",
"sampleId": "CQG5",
"uri_format": "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1"
},
"gramene.taxonomy": {
"deprecated": false,
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene.",
"homepage": "http://www.gramene.org/",
"id": "00000183",
"name": "Gramene Taxonomy",
"namespaceEmbeddedInLui": false,
"pattern": "^GR\\_tax\\:\\d+$",
"prefix": "gramene.taxonomy",
"sampleId": "GR_tax:013681",
"uri_format": "http://www.gramene.org/db/ontology/search?id=$1"
},
"greengenes": {
"deprecated": false,
"description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.",
"homepage": "http://greengenes.lbl.gov/",
"id": "00000165",
"name": "GreenGenes",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "greengenes",
"sampleId": "100000",
"uri_format": "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1"
},
"grid": {
"deprecated": false,
"description": "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally.",
"homepage": "https://www.grid.ac/",
"id": "00000593",
"name": "GRID",
"namespaceEmbeddedInLui": false,
"pattern": "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$",
"prefix": "grid",
"sampleId": "grid.225360.0",
"uri_format": "https://www.grid.ac/institutes/$1"
},
"grin.taxonomy": {
"deprecated": false,
"description": "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact.",
"homepage": "http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en",
"id": "00000166",
"name": "GRIN Plant Taxonomy",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "grin.taxonomy",
"sampleId": "19333",
"uri_format": "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1"
},
"gro": {
"deprecated": false,
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.",
"homepage": "http://www.gramene.org/",
"id": "00000508",
"name": "Gramene Growth Stage Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^GRO:\\d+$",
"prefix": "gro",
"sampleId": "0007133",
"uri_format": "http://www.gramene.org/db/ontology/search?id=GRO:$1"
},
"grsdb": {
"deprecated": false,
"description": "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.",
"homepage": "http://bioinformatics.ramapo.edu/GRSDB2/",
"id": "00000495",
"name": "GRSDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "grsdb",
"sampleId": "10142",
"uri_format": "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1"
},
"gsso": {
"deprecated": false,
"description": "The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology.",
"homepage": "https://bioportal.bioontology.org/",
"id": "00000712",
"name": "Gender, Sex, and Sexual Orientation (GSSO) Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^GSSO:\\d{6}$",
"prefix": "gsso",
"sampleId": "002368",
"uri_format": "http://purl.obolibrary.org/obo/GSSO_$1"
},
"gtex": {
"deprecated": false,
"description": "The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation.",
"homepage": "https://www.gtexportal.org",
"id": "00000663",
"name": "GTEx",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w.+$",
"prefix": "gtex",
"sampleId": "BRIP1",
"uri_format": "https://www.gtexportal.org/home/gene/$1"
},
"gudmap": {
"deprecated": false,
"description": "The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract.",
"homepage": "http://www.gudmap.org/",
"id": "00000643",
"name": "GUDMAP",
"namespaceEmbeddedInLui": false,
"pattern": "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$",
"prefix": "gudmap",
"sampleId": "Q-2958",
"uri_format": "https://gudmap.org/id/$1"
},
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"deprecated": false,
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"id": "00000542",
"name": "GWAS Central Marker",
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"pattern": "^HGVM\\d+$",
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"sampleId": "HGVM15354",
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"deprecated": false,
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"homepage": "https://www.gwascentral.org/phenotypes",
"id": "00000543",
"name": "GWAS Central Phenotype",
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"pattern": "^HGVPM\\d+$",
"prefix": "gwascentral.phenotype",
"sampleId": "HGVPM623",
"uri_format": "https://www.gwascentral.org/phenotype/$1"
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"deprecated": false,
"description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study.",
"homepage": "https://www.gwascentral.org/studies",
"id": "00000540",
"name": "GWAS Central Study",
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"pattern": "^HGVST\\d+$",
"prefix": "gwascentral.study",
"sampleId": "HGVST1828",
"uri_format": "https://www.gwascentral.org/study/$1"
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"homepage": "https://www.ebi.ac.uk/gxa/",
"id": "00000379",
"name": "GXA Expt",
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"pattern": "^[AEP]-\\w{4}-\\d+$",
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{
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"homepage": "https://www.omicsdi.org/",
"name": "GXA Expt through OmicsDI",
"uri_format": "https://www.omicsdi.org/dataset/atlas-experiments/$1"
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"deprecated": false,
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"homepage": "https://www.ebi.ac.uk/gxa/",
"id": "00000378",
"name": "GXA Gene",
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"pattern": "^\\w+$",
"prefix": "gxa.gene",
"sampleId": "AT4G01080",
"uri_format": "https://www.ebi.ac.uk/gxa/genes/$1"
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"deprecated": false,
"description": "HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries.",
"homepage": "https://hamap.expasy.org/",
"id": "00000292",
"name": "HAMAP",
"namespaceEmbeddedInLui": false,
"pattern": "^MF_\\d+$",
"prefix": "hamap",
"sampleId": "MF_01400",
"uri_format": "https://hamap.expasy.org/unirule/$1"
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"deprecated": false,
"description": "The Human Chromosome Ontology (HCO) provides simple and stable URIs for human reference genome versions to semantically identify human chromosomes.",
"homepage": "https://dbcls.rois.ac.jp/",
"id": "00001040",
"name": "Human Chromosome Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^.+$",
"prefix": "hco",
"sampleId": "MT",
"uri_format": "http://biohackathon.org/resource/hco#$1"
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"deprecated": false,
"description": "the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses.",
"homepage": "http://euhcvdb.ibcp.fr/euHCVdb/",
"id": "00000207",
"name": "HCVDB",
"namespaceEmbeddedInLui": false,
"pattern": "^M\\d{5}$",
"prefix": "hcvdb",
"sampleId": "M58335",
"uri_format": "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1"
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"hdr": {
"deprecated": false,
"description": "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders.",
"homepage": "http://research.nhgri.nih.gov/apps/homeodomain/web/",
"id": "00000497",
"name": "Homeodomain Research",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
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"sampleId": "63",
"uri_format": "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1"
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"deprecated": false,
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"homepage": "http://www.hgmd.cf.ac.uk/ac/index.php",
"id": "00000392",
"name": "HGMD",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z_0-9]+$",
"prefix": "hgmd",
"sampleId": "CALM1",
"uri_format": "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1"
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"deprecated": false,
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"homepage": "https://www.genenames.org",
"id": "00000080",
"name": "HGNC",
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"pattern": "^((HGNC|hgnc):)?\\d{1,5}$",
"prefix": "hgnc",
"sampleId": "2674",
"uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1"
},
"hgnc.genefamily": {
"deprecated": false,
"description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.",
"homepage": "https://www.genenames.org/",
"id": "00000573",
"name": "HGNC gene family",
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"prefix": "hgnc.genefamily",
"sampleId": "141",
"uri_format": "https://www.genenames.org/cgi-bin/genefamilies/set/$1"
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"deprecated": false,
"description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.",
"homepage": "https://www.genenames.org",
"id": "00000709",
"name": "HGNC Gene Group",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "hgnc.genegroup",
"sampleId": "141",
"uri_format": "https://www.genenames.org/data/genegroup/#!/group/$1"
},
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"deprecated": false,
"description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol.",
"homepage": "https://www.genenames.org/",
"id": "00000362",
"name": "HGNC Symbol",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z-0-9_]+(\\@)?$",
"prefix": "hgnc.symbol",
"sampleId": "DAPK1",
"uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/symbol/$1"
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"deprecated": false,
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"homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp",
"id": "00000167",
"name": "H-InvDb Locus",
"namespaceEmbeddedInLui": false,
"pattern": "^HIX\\d{7}(\\.\\d+)?$",
"prefix": "hinv.locus",
"sampleId": "HIX0004394",
"uri_format": "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1"
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"deprecated": false,
"description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view.",
"homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp",
"id": "00000169",
"name": "H-InvDb Protein",
"namespaceEmbeddedInLui": false,
"pattern": "^HIP\\d{9}(\\.\\d+)?$",
"prefix": "hinv.protein",
"sampleId": "HIP000030660",
"uri_format": "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1"
},
"hinv.transcript": {
"deprecated": false,
"description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view.",
"homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp",
"id": "00000168",
"name": "H-InvDb Transcript",
"namespaceEmbeddedInLui": false,
"pattern": "^HIT\\d{9}(\\.\\d+)?$",
"prefix": "hinv.transcript",
"sampleId": "HIT000195363",
"uri_format": "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1"
},
"hmdb": {
"deprecated": false,
"description": "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.",
"homepage": "http://www.hmdb.ca/",
"id": "00000051",
"name": "HMDB",
"namespaceEmbeddedInLui": false,
"pattern": "^HMDB\\d+$",
"prefix": "hmdb",
"sampleId": "HMDB00001",
"uri_format": "http://www.hmdb.ca/metabolites/$1"
},
"hogenom": {
"deprecated": false,
"description": "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.",
"homepage": "http://pbil.univ-lyon1.fr/databases/hogenom/",
"id": "00000213",
"name": "HOGENOM",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "hogenom",
"sampleId": "HBG284870",
"uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1"
},
"homd.seq": {
"deprecated": false,
"description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.",
"homepage": "http://www.homd.org/index.php",
"id": "00000170",
"name": "HOMD Sequence Metainformation",
"namespaceEmbeddedInLui": false,
"pattern": "^SEQF\\d+$",
"prefix": "homd.seq",
"sampleId": "SEQF1003",
"uri_format": "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1"
},
"homd.taxon": {
"deprecated": false,
"description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.",
"homepage": "http://www.homd.org/index.php",
"id": "00000171",
"name": "HOMD Taxonomy",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "homd.taxon",
"sampleId": "811",
"uri_format": "http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$1&view=dynamic"
},
"homologene": {
"deprecated": false,
"description": "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.",
"homepage": "https://www.ncbi.nlm.nih.gov/homologene/",
"id": "00000275",
"name": "HomoloGene",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "homologene",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "Bio2RDF",
"homepage": "http://homologene.bio2rdf.org/fct",
"name": "Bio2RDF",
"uri_format": "http://homologene.bio2rdf.org/describe/?url=http://bio2rdf.org/homologene:$1"
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],
"sampleId": "1000",
"uri_format": "https://www.ncbi.nlm.nih.gov/homologene/$1"
},
"hovergen": {
"deprecated": false,
"description": "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.",
"homepage": "http://pbil.univ-lyon1.fr/databases/hovergen.php",
"id": "00000074",
"name": "HOVERGEN",
"namespaceEmbeddedInLui": false,
"pattern": "^HBG\\d+$",
"prefix": "hovergen",
"sampleId": "HBG004341",
"uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN"
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"hp": {
"deprecated": false,
"description": "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.",
"homepage": "http://human-phenotype-ontology.github.io/",
"id": "00000571",
"name": "Human Phenotype Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^HP:\\d{7}$",
"prefix": "hp",
"sampleId": "0000118",
"uri_format": "https://hpo.jax.org/app/browse/term/HP:$1"
},
"hpa": {
"deprecated": false,
"description": "The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers.",
"homepage": "http://www.proteinatlas.org/",
"id": "00000336",
"name": "HPA",
"namespaceEmbeddedInLui": false,
"pattern": "^ENSG\\d{11}$",
"prefix": "hpa",
"sampleId": "ENSG00000026508",
"uri_format": "http://www.proteinatlas.org/$1"
},
"hpm.peptide": {
"deprecated": false,
"description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra.",
"homepage": "http://www.humanproteomemap.org/index.php",
"id": "00000527",
"name": "Human Proteome Map Peptide",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "hpm.peptide",
"sampleId": "9606117",
"uri_format": "http://www.humanproteomemap.org/spectrum.php?pep_id=$1"
},
"hpm.protein": {
"deprecated": false,
"description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.",
"homepage": "http://www.humanproteomemap.org/index.php",
"id": "00000526",
"name": "Human Proteome Map Protein",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "hpm.protein",
"sampleId": "1968",
"uri_format": "http://www.humanproteomemap.org/protein.php?hpm_id=$1"
},
"hprd": {
"deprecated": false,
"description": "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.",
"homepage": "http://www.hprd.org/",
"id": "00000377",
"name": "HPRD",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "hprd",
"sampleId": "00001",
"uri_format": "http://www.hprd.org/protein/$1"
},
"hpscreg": {
"deprecated": false,
"description": "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines).",
"homepage": "https://hpscreg.eu/",
"id": "00000674",
"name": "Human Pluripotent Stem Cell Registry",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$",
"prefix": "hpscreg",
"sampleId": "BCRTi001-A",
"uri_format": "https://hpscreg.eu/cell-line/$1"
},
"hssp": {
"deprecated": false,
"description": "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.",
"homepage": "http://swift.cmbi.kun.nl/swift/hssp/",
"id": "00000215",
"name": "HSSP",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{4}$",
"prefix": "hssp",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "HSSP at CMBI",
"homepage": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/",
"name": "HSSP at CMBI",
"uri_format": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$1.hssp.bz2"
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],
"sampleId": "102l",
"uri_format": "ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2"
},
"huge": {
"deprecated": false,
"description": "The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.",
"homepage": "http://www.kazusa.or.jp/huge/",
"id": "00000263",
"name": "HUGE",
"namespaceEmbeddedInLui": false,
"pattern": "^KIAA\\d{4}$",
"prefix": "huge",
"sampleId": "KIAA0001",
"uri_format": "http://www.kazusa.or.jp/huge/gfpage/$1/"
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"iao": {
"deprecated": false,
"description": "An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch.",
"homepage": "http://www.ontobee.org/ontology/IAO",
"id": "00000603",
"name": "Information Artifact Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{7}$",
"prefix": "iao",
"sampleId": "0000030",
"uri_format": "http://purl.obolibrary.org/obo/IAO_$1"
},
"icd": {
"deprecated": false,
"description": "The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes.",
"homepage": "http://www.who.int/classifications/icd/en/",
"id": "00000009",
"name": "ICD",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]\\d+(\\.[-\\d+])?$",
"prefix": "icd",
"sampleId": "C34",
"uri_format": "https://icd.who.int/browse10/2019/en#/$1"
},
"icdc": {
"deprecated": false,
"description": "The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer.",
"homepage": "https://caninecommons.cancer.gov/#/",
"id": "00000812",
"name": "Integrated Canine Data Commons",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{6}$",
"prefix": "icdc",
"sampleId": "000009",
"uri_format": "https://caninecommons.cancer.gov/#/study/$1"
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"deprecated": false,
"description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements.",
"homepage": "http://db-mml.sjtu.edu.cn/ICEberg/",
"id": "00000469",
"name": "ICEberg element",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "iceberg.element",
"sampleId": "100",
"uri_format": "http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1"
},
"iceberg.family": {
"deprecated": false,
"description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families.",
"homepage": "http://db-mml.sjtu.edu.cn/ICEberg/",
"id": "00000470",
"name": "ICEberg family",
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"description": "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis.",
"homepage": "http://www.genoscope.cns.fr/agc/microscope",
"id": "00000631",
"name": "MicroScope",
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"pattern": "^\\d+$",
"prefix": "microscope",
"sampleId": "5601141",
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"microsporidia": {
"deprecated": false,
"description": "MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"homepage": "http://microsporidiadb.org/micro/",
"id": "00000152",
"name": "MicrosporidiaDB",
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"pattern": "^\\w+$",
"prefix": "microsporidia",
"sampleId": "ECU03_0820i",
"uri_format": "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"
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"deprecated": false,
"description": "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.",
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"name": "OMIM",
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"pattern": "^[*#+%^]?\\d{6}$",
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{
"code": "CURATOR_REVIEW",
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"name": "OMIM mirror at John Hopkins",
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"sampleId": "603903",
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"deprecated": false,
"description": "MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank.",
"homepage": "http://immunet.cn/bdb/",
"id": "00000251",
"name": "MimoDB",
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"pattern": "^\\d+$",
"prefix": "mimodb",
"sampleId": "1",
"uri_format": "http://immunet.cn/bdb/index.php/mimoset/$1"
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"deprecated": false,
"description": "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation.",
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"id": "00000645",
"name": "Minimal Viable Identifier",
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"pattern": "^[A-Za-z0-9]+$",
"prefix": "minid",
"sampleId": "b97957",
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"deprecated": false,
"description": "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. ",
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"id": "00000707",
"name": "MINID Test",
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"pattern": "[A-Za-z0-9]+$",
"prefix": "minid.test",
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"uri_format": "https://hdl.handle.net/hdl:20.500.12633/$1"
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"deprecated": false,
"description": "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals.",
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"name": "MINT",
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{
"code": "CURATOR_REVIEW",
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"name": "The Molecular INTeraction database (MINT)",
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"deprecated": false,
"description": "MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures.",
"homepage": "http://bioinfo.iitk.ac.in/MIPModDB",
"id": "00000256",
"name": "MIPModDB",
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"pattern": "^\\w+$",
"prefix": "mipmod",
"sampleId": "HOSAPI0399",
"uri_format": "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1"
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"deprecated": false,
"description": "The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form \u201cPREFIX:ACCESSION\u201d or \"PROVIDER/PREFIX:ACCESSION\u201d commonly used to specify bioinformatics and other data resources.",
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"id": "00000599",
"name": "Identifiers.org Registry",
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"pattern": "^MIR:\\d{8}$",
"prefix": "mir",
"sampleId": "00100037",
"uri_format": "https://resolver.api.identifiers.org/resolveMirId/MIR:$1"
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"mirbase": {
"deprecated": false,
"description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR).",
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"id": "00000078",
"name": "miRBase Sequence",
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"pattern": "MI\\d{7}",
"prefix": "mirbase",
"sampleId": "MI0000001",
"uri_format": "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1"
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"deprecated": false,
"description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence.",
"homepage": "http://www.mirbase.org/",
"id": "00000235",
"name": "miRBase mature sequence",
"namespaceEmbeddedInLui": false,
"pattern": "MIMAT\\d{7}",
"prefix": "mirbase.mature",
"sampleId": "MIMAT0000001",
"uri_format": "http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1"
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"deprecated": false,
"description": "mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT\u2013qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages.",
"homepage": "http://comgen.pl/mirex/?page=home",
"id": "00000329",
"name": "mirEX",
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"pattern": "^\\d+(\\w+)?$",
"prefix": "mirex",
"sampleId": "165a",
"uri_format": "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes"
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"deprecated": true,
"description": "MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections.",
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"name": "MIRIAM Registry collection",
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"pattern": "^MIR:000\\d{5}$",
"prefix": "miriam.collection",
"sampleId": "MIR:00000008"
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"deprecated": false,
"description": "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases.",
"homepage": "https://www.ebi.ac.uk/miriam/",
"id": "00000188",
"name": "MIRIAM Registry resource",
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"pattern": "^MIR:001\\d{5}$",
"prefix": "miriam.resource",
"sampleId": "MIR:00100005",
"uri_format": "https://www.ebi.ac.uk/miriam/main/resources/$1"
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"mirnest": {
"deprecated": false,
"description": "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species.",
"homepage": "http://rhesus.amu.edu.pl/mirnest/copy/",
"id": "00000246",
"name": "miRNEST",
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"prefix": "mirnest",
"sampleId": "MNEST029358",
"uri_format": "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1"
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"deprecated": false,
"description": "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments.",
"homepage": "http://mirtarbase.mbc.nctu.edu.tw/",
"id": "00000562",
"name": "miRTarBase",
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"pattern": "^MIRT\\d{6}$",
"prefix": "mirtarbase",
"sampleId": "MIRT000002",
"uri_format": "http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1"
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"mlc": {
"deprecated": false,
"description": "MLCommons Association artifacts, including benchmark results, datasets, and saved models.",
"homepage": "https://mlcommons.org/en/",
"id": "00000828",
"name": "MLCommons Association",
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"pattern": "^[0-9a-zA-Z\\.\\-\\_]+$",
"prefix": "mlc",
"sampleId": "0.7-123",
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"mmdb": {
"deprecated": false,
"description": "The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites.",
"homepage": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure",
"id": "00000121",
"name": "Molecular Modeling Database",
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"pattern": "^\\d{1,5}$",
"prefix": "mmdb",
"sampleId": "50885",
"uri_format": "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1"
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"deprecated": false,
"description": "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.",
"homepage": "http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp",
"id": "00000075",
"name": "Melanoma Molecular Map Project Biomaps",
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"pattern": "^\\d+$",
"prefix": "mmmp:biomaps",
"sampleId": "37",
"uri_format": "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1"
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"deprecated": false,
"description": "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples.",
"homepage": "https://mmp.sfb.uit.no/databases/marcat/",
"id": "00000615",
"name": "MarCat",
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"pattern": "^MMP\\d+.\\d+$",
"prefix": "mmp.cat",
"sampleId": "MMP743597.11",
"uri_format": "https://mmp.sfb.uit.no/databases/marcat/#/records/$1"
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"deprecated": false,
"description": "MarDB includes all sequenced marine microbial genomes regardless of level of completeness.",
"homepage": "https://mmp.sfb.uit.no/databases/mardb/",
"id": "00000614",
"name": "MarDB",
"namespaceEmbeddedInLui": false,
"pattern": "^MMP\\d+.\\d+$",
"prefix": "mmp.db",
"sampleId": "MMP02954345.1",
"uri_format": "https://mmp.sfb.uit.no/databases/mardb/#/records/$1"
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"mmp.fun": {
"deprecated": false,
"description": "MarFun is manually curated database for marine fungi which is a part of the MAR databases.",
"homepage": "https://mmp.sfb.uit.no/databases/marfun",
"id": "00000729",
"name": "MarFun",
"namespaceEmbeddedInLui": false,
"pattern": "^MMP\\d+.\\d+$",
"prefix": "mmp.fun",
"sampleId": "MMP3888430",
"uri_format": "https://mmp.sfb.uit.no/databases/marfun/#/records/$1"
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"mmp.ref": {
"deprecated": false,
"description": "MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes.",
"homepage": "https://mmp.sfb.uit.no/databases/marref/",
"id": "00000613",
"name": "MarRef",
"namespaceEmbeddedInLui": false,
"pattern": "^MMP\\d+.\\d+$",
"prefix": "mmp.ref",
"sampleId": "MMP3312982.2",
"uri_format": "https://mmp.sfb.uit.no/databases/marref/#/records/$1"
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"mmrrc": {
"deprecated": false,
"description": "The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections.",
"homepage": "http://www.mmrrc.org/",
"id": "00000324",
"name": "MMRRC",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "mmrrc",
"sampleId": "70",
"uri_format": "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1"
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"mo": {
"deprecated": false,
"description": "The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data.",
"homepage": "https://mged.sourceforge.net/ontologies/MGEDontology.php",
"id": "00000303",
"name": "MGED Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "mo",
"sampleId": "ArrayGroup",
"uri_format": "https://mged.sourceforge.net/ontologies/MGEDontology.php#$1"
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"mobidb": {
"deprecated": false,
"description": "MobiDB is a database of protein disorder and mobility annotations.",
"homepage": "https://mobidb.org/",
"id": "00000637",
"name": "MobiDB",
"namespaceEmbeddedInLui": false,
"pattern": "^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$",
"prefix": "mobidb",
"sampleId": "P10636",
"uri_format": "https://mobidb.org/$1"
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"mod": {
"deprecated": false,
"description": "The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications.",
"homepage": "http://bioportal.bioontology.org/ontologies/PSIMOD",
"id": "00000056",
"name": "Protein Modification Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^MOD:\\d{5}",
"prefix": "mod",
"sampleId": "00001",
"uri_format": "http://bioportal.bioontology.org/ontologies/1041?p=terms&conceptid=MOD:$1"
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"modeldb": {
"deprecated": false,
"description": "ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment.",
"homepage": "https://modeldb.science",
"id": "00000131",
"name": "ModelDB",
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"pattern": "^\\d+$",
"prefix": "modeldb",
"sampleId": "45539",
"uri_format": "https://modeldb.science/$1"
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"deprecated": false,
"description": "Concept used by ModelDB, an accessible location for storing and efficiently retrieving computational neuroscience models.",
"homepage": "https://www.yale.edu",
"id": "00000905",
"name": "ModelDB concept",
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"pattern": "\\d+",
"prefix": "modeldb.concept",
"sampleId": "3639",
"uri_format": "https://senselab.med.yale.edu/ModelDB/ModelList?id=$1"
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"moid": {
"deprecated": false,
"description": "M3G stands for \u201cMetadata Management and distribution system for Multiple GNSS Networks\u201d. M3G allows to upload, validate, and distribute GNSS station metadata such as IGS-style site logs, information about local networks, DOIs, nominal data provision, data licenses attached to the daily RINEX data, etc...",
"homepage": "https://www.astro.oma.be/en/",
"id": "00001068",
"name": "Metadata Management and distribution system for Multiple GNSS Networks",
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"pattern": "[a-zA-Z0-9]+\\.[a-f0-9]{24}",
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"sampleId": "station.6051b2f8b9142a5b8c676342",
"uri_format": "https://gnss-metadata.eu/MOID/$1"
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"molbase": {
"deprecated": false,
"description": "Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier.",
"homepage": "http://www.molbase.com/",
"id": "00000458",
"name": "Molbase",
"namespaceEmbeddedInLui": false,
"pattern": "^(\\d{1,7}\\-\\d{2}\\-\\d)|([A-Za-z0-9\\+\\-\\_]+)$",
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"sampleId": "128796-39-4",
"uri_format": "http://www.molbase.com/en/index.php?app=search&search_keyword=$1"
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"deprecated": false,
"description": "MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations. ",
"homepage": "http://www.upol.cz/en/",
"id": "00000768",
"name": "MolMeDB",
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"pattern": "^[m,M]{2}[0-9]{5}[0-9]*$",
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"sampleId": "MM00040",
"uri_format": "https://molmedb.upol.cz/mol/$1"
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"deprecated": false,
"description": "The Morpheus model repository is an open-access data resource to store, search and retrieve unpublished and published computational models of spatio-temporal and multicellular biological systems, encoded in the MorpheusML language and readily executable with the Morpheus software.\n",
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"id": "00000725",
"name": "Morpheus model repository",
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"pattern": "^M[0-9]{4,}$",
"prefix": "morpheus",
"sampleId": "M0001",
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"deprecated": false,
"description": "The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways.",
"homepage": "https://bioportal.bioontology.org/ontologies/MP",
"id": "00000580",
"name": "Mammalian Phenotype Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^MP:\\d{7}$",
"prefix": "mp",
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{
"code": "CURATOR_REVIEW",
"description": "Mammalian Phenotype Ontology at The Jackson Lab",
"homepage": "http://www.informatics.jax.org/",
"name": "Mammalian Phenotype Ontology at The Jackson Lab",
"uri_format": "http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1"
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],
"sampleId": "0005452",
"uri_format": "https://bioportal.bioontology.org/ontologies/MP/MP:$1"
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"mpid": {
"deprecated": false,
"description": "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts.",
"homepage": "http://www.jcvi.org/mpidb/about.php",
"id": "00000124",
"name": "Microbial Protein Interaction Database",
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"pattern": "^\\d+$",
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{
"code": "ebi",
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"homepage": "https://www.ebi.ac.uk/intact/",
"name": "Microbial Protein Interaction Database subset through IntAct",
"uri_format": "https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$1"
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],
"sampleId": "172",
"uri_format": "http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1"
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"ms": {
"deprecated": false,
"description": "The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance.",
"homepage": "https://bioportal.bioontology.org/ontologies/MS",
"id": "00000590",
"name": "Mass Spectrometry Controlled Vocabulary",
"namespaceEmbeddedInLui": true,
"pattern": "^MS:\\d{7}$",
"prefix": "ms",
"sampleId": "1000001",
"uri_format": "http://purl.bioontology.org/ontology/MS/MS:$1"
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"deprecated": false,
"description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.",
"homepage": "http://multicellds.org/MultiCellDB.php",
"id": "00000584",
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"homepage": "http://multicellds.org/MultiCellDB.php",
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"deprecated": false,
"description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data.",
"homepage": "http://multicellds.org/MultiCellDB.php",
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"deprecated": false,
"description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).",
"homepage": "http://www.metabolomicsworkbench.org/",
"id": "00000647",
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"pattern": "^PR[0-9]{6}$",
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"homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/",
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"name": "SABIO-RK Reaction",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "sabiork.reaction",
"sampleId": "75",
"uri_format": "http://sabiork.h-its.org/newSearch?q=sabioreactionid:$1"
},
"sasbdb": {
"deprecated": false,
"description": "Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data.",
"homepage": "http://www.sasbdb.org/",
"id": "00000572",
"name": "SASBDB",
"namespaceEmbeddedInLui": false,
"pattern": "^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$",
"prefix": "sasbdb",
"sampleId": "SASDAX8",
"uri_format": "http://www.sasbdb.org/data/$1"
},
"sbo": {
"deprecated": false,
"description": "The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort.",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/sbo",
"id": "00000024",
"name": "Systems Biology Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^SBO:\\d{7}$",
"prefix": "sbo",
"sampleId": "0000262",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/sbo/terms?obo_id=SBO:$1"
},
"sciflection": {
"deprecated": false,
"description": "Sciflection is a public repository for experiments and associated spectra, usually uploaded from Electronic Lab Notebooks, shared under FAIR conditions",
"homepage": "https://sciformation.com/sciflection.html",
"id": "00000973",
"name": "Sciflection",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$",
"prefix": "sciflection",
"sampleId": "5ede4273-b26c-4ea4-adb7-3ce294ab3397",
"uri_format": "https://sciflection.com/$1"
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"scop": {
"deprecated": false,
"description": "The SCOP (Structural Classification of Protein) database is a comprehensive ordering of all proteins of known structure according to their evolutionary, functional and structural relationships. The basic classification unit is the protein domain. Domains are hierarchically classified into species, proteins, families, superfamilies, folds, and classes.",
"homepage": "http://scop.mrc-lmb.cam.ac.uk/scop/",
"id": "00000371",
"name": "SCOP",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "scop",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "SCOP at Berkeley",
"homepage": "http://scop.berkeley.edu/",
"name": "SCOP at Berkeley",
"uri_format": "http://scop.berkeley.edu/sunid=$1"
}
],
"sampleId": "47419",
"uri_format": "http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=$1"
},
"scretf": {
"deprecated": false,
"description": "ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor.",
"homepage": "http://stormo.wustl.edu/ScerTF/",
"id": "00000244",
"name": "ScerTF",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "scretf",
"sampleId": "RSC3",
"uri_format": "http://stormo.wustl.edu/ScerTF/details/$1/"
},
"sdbs": {
"deprecated": false,
"description": "The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra.",
"homepage": "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi",
"id": "00000319",
"name": "Spectral Database for Organic Compounds",
"namespaceEmbeddedInLui": false,
"pattern": "\\d+$",
"prefix": "sdbs",
"sampleId": "4544",
"uri_format": "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1"
},
"sedml.format": {
"deprecated": false,
"description": "Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).",
"homepage": "http://sed-ml.org/",
"id": "00000841",
"name": "SED-ML data format",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z]+(\\..*?)?$",
"prefix": "sedml.format",
"sampleId": "csv",
"uri_format": "https://sed-ml.org/urns.html#format:$1"
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"sedml.language": {
"deprecated": false,
"description": "Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).",
"homepage": "http://sed-ml.org/",
"id": "00000843",
"name": "SED-ML model format",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z]+(\\..*?)?$",
"prefix": "sedml.language",
"sampleId": "sbml.level-3.version-2",
"uri_format": "https://sed-ml.org/urns.html#language:$1"
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"seed": {
"deprecated": false,
"description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.",
"id": "00000552",
"name": "SEED Subsystem",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"prefix": "seed",
"sampleId": "Biotin_biosynthesis"
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"deprecated": false,
"description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.",
"homepage": "http://modelseed.org/",
"id": "00000553",
"name": "SEED Compound",
"namespaceEmbeddedInLui": false,
"pattern": "^cpd\\d+$",
"prefix": "seed.compound",
"sampleId": "cpd15380",
"uri_format": "http://modelseed.org/biochem/compounds/$1"
},
"seed.reaction": {
"deprecated": false,
"description": "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions.",
"homepage": "http://modelseed.org/biochem/reactions/",
"id": "00000692",
"name": "SEED Reactions",
"namespaceEmbeddedInLui": false,
"pattern": "^rxn\\d+$",
"prefix": "seed.reaction",
"sampleId": "rxn00001",
"uri_format": "http://modelseed.org/biochem/reactions/$1"
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"sgd": {
"deprecated": false,
"description": "The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae.",
"homepage": "https://www.yeastgenome.org/",
"id": "00000023",
"name": "SGD",
"namespaceEmbeddedInLui": false,
"pattern": "^((S\\d+$)|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?))$",
"prefix": "sgd",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "Bio2RDF",
"homepage": "http://sgd.bio2rdf.org/fct",
"name": "Bio2RDF",
"uri_format": "http://sgd.bio2rdf.org/describe/?url=http://bio2rdf.org/sgd:$1"
},
{
"code": "agr",
"description": "SGD through the Alliance of Genome Resources",
"homepage": "https://www.alliancegenome.org",
"name": "SGD through the Alliance of Genome Resources",
"uri_format": "https://www.alliancegenome.org/gene/SGD:$1"
}
],
"sampleId": "S000003909",
"uri_format": "https://www.yeastgenome.org/locus/$1"
},
"sgd.pathways": {
"deprecated": false,
"description": "Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD).",
"homepage": "http://pathway.yeastgenome.org/",
"id": "00000057",
"name": "Saccharomyces genome database pathways",
"namespaceEmbeddedInLui": false,
"pattern": "^PWY\\w{2}\\-\\d{3}$",
"prefix": "sgd.pathways",
"sampleId": "PWY3O-214",
"uri_format": "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1"
},
"sgn": {
"deprecated": false,
"description": "The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant.",
"homepage": "http://solgenomics.net/",
"id": "00000185",
"name": "Sol Genomics Network",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "sgn",
"sampleId": "0001",
"uri_format": "http://solgenomics.net/phenome/locus_display.pl?locus_id=$1"
},
"sheepqtldb": {
"deprecated": false,
"description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs.",
"homepage": "https://www.animalgenome.org/QTLdb",
"id": "00000507",
"name": "Animal Genome Sheep QTL",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "sheepqtldb",
"sampleId": "19803",
"uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"
},
"sider.drug": {
"deprecated": false,
"description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER.",
"homepage": "http://sideeffects.embl.de/",
"id": "00000435",
"name": "SIDER Drug",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "sider.drug",
"sampleId": "2244",
"uri_format": "http://sideeffects.embl.de/drugs/$1/"
},
"sider.effect": {
"deprecated": false,
"description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER.",
"homepage": "http://sideeffects.embl.de/",
"id": "00000436",
"name": "SIDER Side Effect",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d+$",
"prefix": "sider.effect",
"sampleId": "C0017565",
"uri_format": "http://sideeffects.embl.de/se/$1/"
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"signaling-gateway": {
"deprecated": false,
"description": "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.",
"homepage": "http://www.signaling-gateway.org/molecule",
"id": "00000045",
"name": "Signaling Gateway",
"namespaceEmbeddedInLui": false,
"pattern": "A\\d{6}$",
"prefix": "signaling-gateway",
"sampleId": "A001094",
"uri_format": "http://www.signaling-gateway.org/molecule/query?afcsid=$1"
},
"signor": {
"deprecated": false,
"description": "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature.",
"homepage": "https://signor.uniroma2.it/",
"id": "00000808",
"name": "SIGNOR",
"namespaceEmbeddedInLui": false,
"pattern": "^SIGNOR\\-[A-Z]+\\d+$",
"prefix": "signor",
"sampleId": "SIGNOR-C2",
"uri_format": "https://signor.uniroma2.it/relation_result.php?id=$1"
},
"sio": {
"deprecated": false,
"description": "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities.",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/sio",
"id": "00000851",
"name": "Semanticscience Integrated Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^SIO_\\d{6,6}$",
"prefix": "sio",
"sampleId": "SIO_000276",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/sio/terms?short_form=$1"
},
"sisu": {
"deprecated": false,
"description": "The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies.",
"homepage": "http://www.sisuproject.fi/",
"id": "00000624",
"name": "SISu",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+:[0-9]+$",
"prefix": "sisu",
"sampleId": "17:41223048",
"uri_format": "http://search.sisuproject.fi/#/variant/$1"
},
"sitex": {
"deprecated": false,
"description": "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.",
"homepage": "http://www-bionet.sscc.ru/sitex/",
"id": "00000252",
"name": "SitEx",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "sitex",
"sampleId": "1000",
"uri_format": "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1"
},
"skm": {
"deprecated": false,
"description": "Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors. ",
"homepage": "http://www.nib.si/eng/",
"id": "00000968",
"name": "Stress Knowledge Map",
"namespaceEmbeddedInLui": false,
"pattern": "^rx[0-9]{5}$",
"prefix": "skm",
"sampleId": "rx00408",
"uri_format": "https://skm.nib.si/api/pss/reactions?reaction_id=$1&return_field=summary"
},
"slm": {
"deprecated": false,
"description": "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions.",
"homepage": "http://www.swisslipids.org/#/",
"id": "00000550",
"name": "SwissLipids",
"namespaceEmbeddedInLui": true,
"pattern": "^SLM:\\d+$",
"prefix": "slm",
"sampleId": "000048885",
"uri_format": "http://www.swisslipids.org/#/entity/SLM:$1/"
},
"smart": {
"deprecated": false,
"description": "The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures.",
"homepage": "http://smart.embl-heidelberg.de/",
"id": "00000118",
"name": "SMART",
"namespaceEmbeddedInLui": false,
"pattern": "^SM\\d{5}$",
"prefix": "smart",
"sampleId": "SM00015",
"uri_format": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1"
},
"smpdb": {
"deprecated": false,
"description": "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.",
"homepage": "https://smpdb.ca/",
"id": "00000104",
"name": "Small Molecule Pathway Database",
"namespaceEmbeddedInLui": false,
"pattern": "^SMP\\d+$",
"prefix": "smpdb",
"sampleId": "SMP00001",
"uri_format": "http://smpdb.ca/view/$1"
},
"snomedct": {
"deprecated": false,
"description": "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc.",
"homepage": "http://www.snomedbrowser.com/",
"id": "00000269",
"name": "SNOMED CT",
"namespaceEmbeddedInLui": false,
"pattern": "^(\\w+)?\\d+$",
"prefix": "snomedct",
"sampleId": "284196006",
"uri_format": "http://www.snomedbrowser.com/Codes/Details/$1"
},
"snp2tfbs": {
"deprecated": false,
"description": "SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome.",
"homepage": "https://ccg.epfl.ch/snp2tfbs/",
"id": "00000766",
"name": "SNP2TFBS",
"namespaceEmbeddedInLui": false,
"pattern": "^rs[0-9]+$",
"prefix": "snp2tfbs",
"sampleId": "rs11603840",
"uri_format": "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1"
},
"so": {
"deprecated": false,
"description": "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data.",
"homepage": "http://www.sequenceontology.org/",
"id": "00000081",
"name": "Sequence Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^SO:\\d{7}$",
"prefix": "so",
"sampleId": "0000704",
"uri_format": "http://www.sequenceontology.org/miso/current_release/term/SO:$1"
},
"soybase": {
"deprecated": false,
"description": "SoyBase is a repository for curated genetics, genomics and related data resources for soybean.",
"homepage": "http://soybase.org/",
"id": "00000291",
"name": "SoyBase",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\-)?\\w+(\\-)?\\w+$",
"prefix": "soybase",
"sampleId": "BARC-013845-01256",
"uri_format": "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1"
},
"spdx": {
"deprecated": false,
"description": "The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception.",
"homepage": "https://spdx.org",
"id": "00000687",
"name": "SPDX License List",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9A-Za-z\\-.]+$",
"prefix": "spdx",
"sampleId": "CC-BY-1.0",
"uri_format": "https://spdx.org/licenses/$1"
},
"spike.map": {
"deprecated": false,
"description": "SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps.",
"homepage": "http://www.cs.tau.ac.il/~spike/",
"id": "00000321",
"name": "SPIKE Map",
"namespaceEmbeddedInLui": false,
"pattern": "^spike\\d{5}$",
"prefix": "spike.map",
"sampleId": "spike00001",
"uri_format": "http://www.cs.tau.ac.il/~spike/maps/$1.html"
},
"splash": {
"deprecated": false,
"description": "The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance.",
"homepage": "http://mona.fiehnlab.ucdavis.edu/",
"id": "00000566",
"name": "SPLASH",
"namespaceEmbeddedInLui": false,
"pattern": "^splash\\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$",
"prefix": "splash",
"sampleId": "splash10-0zq2000000-77302b0326a418630a84",
"uri_format": "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1"
},
"spp": {
"deprecated": false,
"description": "The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways.",
"homepage": "https://www.signalingpathways.org/index.jsf",
"id": "00000726",
"name": "Signaling Pathways Project",
"namespaceEmbeddedInLui": false,
"pattern": "^10.\\w{4}/\\w{10}$",
"prefix": "spp",
"sampleId": "10.1621/vwN2g2HaX3",
"uri_format": "https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1"
},
"stap": {
"deprecated": false,
"description": "STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB).",
"homepage": "http://psb.kobic.re.kr/STAP/refinement/",
"id": "00000399",
"name": "STAP",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9][A-Za-z0-9]{3}$",
"prefix": "stap",
"sampleId": "1a24",
"uri_format": "http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1"
},
"stato": {
"deprecated": false,
"description": "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots.",
"homepage": "https://www.ebi.ac.uk",
"id": "00001051",
"name": "Statistical Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^STATO:\\d+$",
"prefix": "stato",
"sampleId": "0000138",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/stato/classes?obo_id=STATO:$1"
},
"stitch": {
"deprecated": false,
"description": "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.",
"homepage": "http://stitch.embl.de/",
"id": "00000266",
"name": "STITCH",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{14}$",
"prefix": "stitch",
"sampleId": "BQJCRHHNABKAKU",
"uri_format": "http://stitch.embl.de/interactions/$1"
},
"storedb": {
"deprecated": false,
"description": "STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons.",
"homepage": "https://www.storedb.org/",
"id": "00000577",
"name": "STOREDB",
"namespaceEmbeddedInLui": false,
"pattern": "^STOREDB:(STUDY|FILE|DATASET)\\d+$",
"prefix": "storedb",
"sampleId": "STOREDB:STUDY1040",
"uri_format": "https://www.storedb.org/?$1"
},
"string": {
"deprecated": false,
"description": "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions.\r\nThe interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.",
"homepage": "http://string.embl.de/",
"id": "00000265",
"name": "STRING",
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"deprecated": false,
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"code": "ncbi",
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"deprecated": false,
"description": "This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein.",
"homepage": "https://www.uniprot.org",
"id": "00000739",
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"namespaceEmbeddedInLui": false,
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"deprecated": false,
"description": "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information.",
"homepage": "http://www.uniprot.org/",
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{
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{
"code": "CURATOR_REVIEW",
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"homepage": "http://www.uniprot.org/uniparc/",
"name": "UniProt Isoform through UniParc",
"uri_format": "http://www.uniprot.org/uniparc/?query=$1"
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"sampleId": "Q5BJF6-3",
"uri_format": "http://www.uniprot.org/uniprot/$1"
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"uniref": {
"deprecated": false,
"description": "The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.",
"homepage": "https://www.uniprot.org/",
"id": "00000878",
"name": "UniRef",
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"prefix": "uniref",
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"uri_format": "https://www.uniprot.org/uniref/$1"
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"deprecated": false,
"description": "UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences.",
"homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists",
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"name": "UniSTS",
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"prefix": "unists",
"sampleId": "456789",
"uri_format": "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1"
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"unite": {
"deprecated": false,
"description": "UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa.",
"homepage": "http://unite.ut.ee/",
"id": "00000352",
"name": "Unite",
"namespaceEmbeddedInLui": false,
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"prefix": "unite",
"sampleId": "UDB000691",
"uri_format": "http://unite.ut.ee/bl_forw.php?nimi=$1"
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"uo": {
"deprecated": false,
"description": "Ontology of standardized units",
"homepage": "https://www.ebi.ac.uk/ols4/ontologies/uo",
"id": "00000136",
"name": "Unit Ontology",
"namespaceEmbeddedInLui": true,
"pattern": "^UO:\\d{7}?",
"prefix": "uo",
"sampleId": "0000080",
"uri_format": "https://www.ebi.ac.uk/ols4/ontologies/uo/terms?obo_id=UO:$1"
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"uspto": {
"deprecated": false,
"description": "The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement.",
"homepage": "http://patft.uspto.gov/netahtml/PTO/index.html",
"id": "00000538",
"name": "USPTO",
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"pattern": "^(D|PP|R|T|H|X|AI)?\\d+$",
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"utrdb": {
"deprecated": false,
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"homepage": "https://utrdb.cloud.ba.infn.it/utrdb/index_107.html",
"id": "00000993",
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"pattern": "([3-5][A-Z])\\w+[^A-Z][0-9]",
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"uri_format": "https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e=$1"
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"validatordb": {
"deprecated": false,
"description": "Database of validation results for ligands and non-standard residues in the Protein Data Bank.",
"homepage": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/",
"id": "00000633",
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"namespaceEmbeddedInLui": false,
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"uri_format": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/$1"
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"vario": {
"deprecated": false,
"description": "The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level.",
"homepage": "http://bioportal.bioontology.org/ontologies/VARIO",
"id": "00000406",
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{
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"uri_format": "http://www.ontobee.org/search?ontology=VariO&keywords=VariO_$1&submit=Search+terms"
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],
"sampleId": "0294",
"uri_format": "https://purl.bioontology.org/ontology/VARIO?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVariO_$1"
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"vbase2": {
"deprecated": false,
"description": "The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes.",
"homepage": "http://www.vbase2.org/vbase2.php",
"id": "00000320",
"name": "Vbase2",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
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"vbrc": {
"deprecated": false,
"description": "The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis.",
"homepage": "http://vbrc.org/",
"id": "00000448",
"name": "VBRC",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
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"sampleId": "35742",
"uri_format": "http://vbrc.org/gene_detail.asp?gene_id=$1"
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"vcell": {
"deprecated": false,
"description": "Models developed with the Virtual Cell (VCell) software prorgam.",
"homepage": "https://health.uconn.edu/",
"id": "00000893",
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"namespaceEmbeddedInLui": false,
"pattern": "^\\d{5,}$",
"prefix": "vcell",
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"uri_format": "https://vcell.org/biomodel-$1"
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"vectorbase": {
"deprecated": false,
"description": "VectorBase is part of the VEuPathDB, a NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens and related species of interest. Currently, VectorBase contains genome information for approximately 80 organisms: mosquitoes, bed bugs, biting midges, ticks, tsetse flies, mites, sand flies, house flies, body lice, stable flies, kissing bugs, and a snail which is an intermediate host.",
"homepage": "https://www.vectorbase.org/",
"id": "00000232",
"name": "VectorBase",
"namespaceEmbeddedInLui": false,
"pattern": "^\\D{4}\\d{6}(\\-\\D{2})?$",
"prefix": "vectorbase",
"sampleId": "ISCW007415",
"uri_format": "https://vectorbase.org/gene/$1"
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"vegbank": {
"deprecated": false,
"description": "VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. ",
"homepage": "http://vegbank.org/",
"id": "00000723",
"name": "VegBank",
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"pattern": "^VB\\.[A-Za-z][A-Za-z]\\..*$",
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"uri_format": "http://vegbank.org/cite/$1"
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"vfb": {
"deprecated": false,
"description": "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster.",
"homepage": "https://VirtualFlyBrain.org",
"id": "00000680",
"name": "Virtual Fly Brain",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9a-zA-Z]{8}$",
"prefix": "vfb",
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"uri_format": "http://virtualflybrain.org/reports/$1"
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"vfdb.gene": {
"deprecated": false,
"description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes.",
"homepage": "http://www.mgc.ac.cn/VFs/",
"id": "00000472",
"name": "VFDB Gene",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
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"uri_format": "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1"
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"vfdb.genus": {
"deprecated": false,
"description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus.",
"homepage": "http://www.mgc.ac.cn/VFs/",
"id": "00000471",
"name": "VFDB Genus",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
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"vgnc": {
"deprecated": false,
"description": "The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee.",
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"id": "00000765",
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"uri_format": "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1"
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"viaf": {
"deprecated": false,
"description": "The VIAF\u00ae (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web.",
"homepage": "http://viaf.org",
"id": "00000685",
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"description": "The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information.",
"homepage": "http://www.viprbrc.org/brc/home.do?decorator=vipr",
"id": "00000407",
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"viralzone": {
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"description": "ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.",
"homepage": "http://www.expasy.org/viralzone/",
"id": "00000449",
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"uri_format": "http://viralzone.expasy.org/all_by_protein/$1.html"
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"description": "The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region.",
"homepage": "http://crdd.osdd.net/servers/virsirnadb",
"id": "00000249",
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"description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.",
"homepage": "https://www.vmh.life/",
"id": "00000774",
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"uri_format": "https://www.vmh.life/#gene/$1"
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"description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.",
"homepage": "https://www.vmh.life/",
"id": "00000636",
"name": "VMH metabolite",
"namespaceEmbeddedInLui": false,
"pattern": "[a-zA-Z0-9_\\(\\_\\)\\[\\]]+",
"prefix": "vmhmetabolite",
"sampleId": "h2o",
"uri_format": "https://www.vmh.life/#metabolite/$1"
},
"vmhreaction": {
"deprecated": false,
"description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.",
"homepage": "https://www.vmh.life/",
"id": "00000640",
"name": "VMH reaction",
"namespaceEmbeddedInLui": false,
"pattern": "[a-zA-Z0-9_\\(\\_\\)\\[\\]]+",
"prefix": "vmhreaction",
"sampleId": "HEX1",
"uri_format": "https://www.vmh.life/#reaction/$1"
},
"wb": {
"deprecated": false,
"description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities.",
"homepage": "https://www.wormbase.org/",
"id": "00000027",
"name": "WormBase",
"namespaceEmbeddedInLui": false,
"pattern": "^WB[A-Z][a-z]+\\d+$",
"prefix": "wb",
"providers": [
{
"code": "agr",
"description": "WormBase through the Alliance of Genome Resources",
"homepage": "https://www.alliancegenome.org",
"name": "WormBase through the Alliance of Genome Resources",
"uri_format": "https://www.alliancegenome.org/gene/WB:$1"
}
],
"sampleId": "WBGene00000001",
"uri_format": "https://www.wormbase.org/get?name=$1"
},
"wb.rnai": {
"deprecated": false,
"description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes.",
"homepage": "https://www.wormbase.org/",
"id": "00000466",
"name": "WormBase RNAi",
"namespaceEmbeddedInLui": false,
"pattern": "^WBRNAi\\d{8}$",
"prefix": "wb.rnai",
"sampleId": "WBRNAi00086878",
"uri_format": "https://www.wormbase.org/species/c_elegans/rnai/$1"
},
"wikidata": {
"deprecated": false,
"description": "Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic.",
"homepage": "https://www.wikidata.org/",
"id": "00000549",
"name": "Wikidata",
"namespaceEmbeddedInLui": false,
"pattern": "^(Q|P)\\d+$",
"prefix": "wikidata",
"sampleId": "Q2207226",
"uri_format": "http://www.wikidata.org/entity/$1"
},
"wikigenes": {
"deprecated": false,
"description": "WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process.",
"homepage": "http://www.wikigenes.org/",
"id": "00000437",
"name": "WikiGenes",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "wikigenes",
"sampleId": "3771877",
"uri_format": "http://www.wikigenes.org/e/gene/e/$1.html"
},
"wikipathways": {
"deprecated": false,
"description": "WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki-like style.",
"homepage": "http://www.wikipathways.org/",
"id": "00000076",
"name": "WikiPathways",
"namespaceEmbeddedInLui": false,
"pattern": "WP\\d{1,5}(\\_r\\d+)?$",
"prefix": "wikipathways",
"providers": [
{
"code": "scholia",
"description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.\n",
"homepage": "https://scholia.toolforge.org/",
"name": "Scholia",
"uri_format": "https://scholia.toolforge.org/wikipathways/$1"
}
],
"sampleId": "WP100",
"uri_format": "http://www.wikipathways.org/instance/$1"
},
"wikipedia.en": {
"deprecated": false,
"description": "Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay.",
"homepage": "http://en.wikipedia.org/wiki/Main_Page",
"id": "00000384",
"name": "Wikipedia (En)",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z-0-9_]+$",
"prefix": "wikipedia.en",
"providers": [
{
"code": "CURATOR_REVIEW",
"description": "Wikipedia structured content through DBpedia",
"homepage": "http://wiki.dbpedia.org/",
"name": "Wikipedia structured content through DBpedia",
"uri_format": "http://dbpedia.org/page/$1"
}
],
"sampleId": "SM_UB-81",
"uri_format": "http://en.wikipedia.org/wiki/$1"
},
"worfdb": {
"deprecated": false,
"description": "WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends).",
"homepage": "http://worfdb.dfci.harvard.edu/",
"id": "00000288",
"name": "Worfdb",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\.\\d+)?",
"prefix": "worfdb",
"sampleId": "T01B6.1",
"uri_format": "http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1"
},
"wormpep": {
"deprecated": false,
"description": "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project.",
"homepage": "https://www.wormbase.org/db/seq/protein",
"id": "00000031",
"name": "Wormpep",
"namespaceEmbeddedInLui": false,
"pattern": "^CE\\d{5}$",
"prefix": "wormpep",
"sampleId": "CE28239",
"uri_format": "https://www.wormbase.org/db/seq/protein?name=$1"
},
"worms": {
"deprecated": false,
"description": "The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts.",
"homepage": "http://www.marinespecies.org/",
"id": "00000581",
"name": "World Register of Marine Species",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "worms",
"sampleId": "146421",
"uri_format": "http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1"
},
"xenbase": {
"deprecated": false,
"description": "Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions.",
"homepage": "https://www.xenbase.org/",
"id": "00000186",
"name": "Xenbase",
"namespaceEmbeddedInLui": false,
"pattern": "^XB\\-\\w+\\-\\d+$",
"prefix": "xenbase",
"sampleId": "XB-GENE-922462",
"uri_format": "https://www.xenbase.org/entry/$1"
},
"ydpm": {
"deprecated": false,
"description": "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition.",
"homepage": "http://www-deletion.stanford.edu/YDPM/",
"id": "00000465",
"name": "YDPM",
"namespaceEmbeddedInLui": false,
"pattern": "^Y[A-Z]{2}\\d+[CW]$",
"prefix": "ydpm",
"sampleId": "YAL001C",
"uri_format": "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1"
},
"yeastintron": {
"deprecated": false,
"description": "The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460].",
"homepage": "http://intron.ucsc.edu/yeast4.3/",
"id": "00000521",
"name": "Yeast Intron Database v4.3",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]+$",
"prefix": "yeastintron",
"sampleId": "SNR17A",
"uri_format": "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1"
},
"yetfasco": {
"deprecated": false,
"description": "The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats.",
"homepage": "http://yetfasco.ccbr.utoronto.ca/",
"id": "00000339",
"name": "YeTFasCo",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+\\_\\d+(\\.\\d+)?$",
"prefix": "yetfasco",
"sampleId": "YOR172W_571.0",
"uri_format": "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1"
},
"yid": {
"deprecated": false,
"description": "The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521].",
"homepage": "http://compbio.soe.ucsc.edu/yeast_introns.html",
"id": "00000460",
"name": "Yeast Intron Database v3",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]+$",
"prefix": "yid",
"sampleId": "SNR17A",
"uri_format": "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1"
},
"yrcpdr": {
"deprecated": false,
"description": "The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions.",
"homepage": "http://www.yeastrc.org/pdr/",
"id": "00000459",
"name": "YRC PDR",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"prefix": "yrcpdr",
"sampleId": "2673500",
"uri_format": "http://yeastrc.org/pdr/viewProtein.do?id=$1"
},
"zfin": {
"deprecated": false,
"description": "ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN.",
"homepage": "http://zfin.org",
"id": "00000079",
"name": "ZFIN Bioentity",
"namespaceEmbeddedInLui": false,
"pattern": "^ZDB\\-\\w+\\-\\d+\\-\\d+$",
"prefix": "zfin",
"providers": [
{
"code": "agr",
"description": "ZFIN through the Alliance of Genome Resources",
"homepage": "https://www.alliancegenome.org",
"name": "ZFIN through the Alliance of Genome Resources",
"uri_format": "https://test.alliancegenome.org/gene/ZFIN:$1"
}
],
"sampleId": "ZDB-GENE-041118-11",
"uri_format": "http://zfin.org/$1"
},
"zinc": {
"deprecated": false,
"description": "ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number.",
"homepage": "http://zinc15.docking.org/",
"id": "00000529",
"name": "ZINC",
"namespaceEmbeddedInLui": false,
"pattern": "^(ZINC)?\\d+$",
"prefix": "zinc",
"sampleId": "ZINC1084",
"uri_format": "http://zinc15.docking.org/substances/$1"
}
} ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9659667
bioregistry-0.11.12/src/bioregistry/external/n2t/ 0000755 0001751 0000177 00000000000 14655546227 021321 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/n2t/__init__.py 0000644 0001751 0000177 00000005253 14655542206 023430 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download registry information from N2T."""
import json
from pathlib import Path
from typing import Mapping
import yaml
from pystow.utils import download
from bioregistry.constants import RAW_DIRECTORY, URI_FORMAT_KEY
from bioregistry.external.alignment_utils import Aligner
__all__ = [
"get_n2t",
"N2TAligner",
]
URL = "https://n2t.net/e/n2t_full_prefixes.yaml"
DIRECTORY = Path(__file__).parent.resolve()
RAW_PATH = RAW_DIRECTORY / "n2t.yml"
PROCESSED_PATH = DIRECTORY / "processed.json"
SKIP = {
"zzztestprefix": "test prefix should not be considered",
"urn": "too meta",
"url": "too meta",
"purl": "too meta",
"lsid": "too meta",
"hdl": "paid service, too meta",
"repec": "irrelevant prefix from economics",
"merops": "issue with miriam having duplicate prefixes for this resource", # FIXME
"hgnc.family": "issue with miriam having duplicate prefixes for this resource", # FIXME
}
SKIP_URI_FORMATS = {
"http://arabidopsis.org/servlets/TairObject?accession=$1",
}
def get_n2t(force_download: bool = False):
"""Get the N2T registry."""
if PROCESSED_PATH.exists() and not force_download:
with PROCESSED_PATH.open() as file:
return json.load(file)
download(url=URL, path=RAW_PATH, force=True)
# they give malformed YAML so time to write a new parser
with RAW_PATH.open() as file:
data = yaml.safe_load(file)
rv = {
key: _process(record)
for key, record in data.items()
if record["type"] == "scheme" and "/" not in key and key not in SKIP
}
with PROCESSED_PATH.open("w") as file:
json.dump(rv, file, sort_keys=True, indent=2)
return rv
def _process(record):
rv = {
"name": record.get("name"),
URI_FORMAT_KEY: _get_uri_format(record),
"description": record.get("description"),
"homepage": record.get("more"),
"pattern": record.get("pattern"),
"example": record.get("test"),
"namespaceEmbeddedInLui": (record.get("prefixed") == "true"),
}
return {k: v for k, v in rv.items() if v is not None}
def _get_uri_format(record):
raw_redirect = record.get("redirect")
if raw_redirect is None:
return None
uri_format = raw_redirect.replace("$id", "$1")
if uri_format in SKIP_URI_FORMATS:
return None
return uri_format
class N2TAligner(Aligner):
"""Aligner for the N2T."""
key = "n2t"
getter = get_n2t
curation_header = ("name", "homepage", "description")
def get_skip(self) -> Mapping[str, str]:
"""Get the prefixes in N2T that should be skipped."""
return SKIP
if __name__ == "__main__":
N2TAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254390.0
bioregistry-0.11.12/src/bioregistry/external/n2t/processed.json 0000644 0001751 0000177 00001476401 14655543166 024217 0 ustar 00runner docker {
"3dmet": {
"description": "3DMET is a database collecting three-dimensional structures of natural metabolites.",
"example": "B00162",
"homepage": "http://www.3dmet.dna.affrc.go.jp/",
"name": "3DMET database",
"namespaceEmbeddedInLui": false,
"pattern": "^B\\d{5}$",
"uri_format": "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1"
},
"abs": {
"description": "The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography.",
"example": "A0014",
"homepage": "http://genome.crg.es/datasets/abs2005/",
"name": "ABS at IMIM",
"namespaceEmbeddedInLui": false,
"pattern": "^A\\d+$",
"uri_format": "http://genome.crg.es/datasets/abs2005/entries/$1.html"
},
"aceview.worm": {
"description": "AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression.",
"example": "aap-1",
"homepage": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm",
"name": "AceView Worm at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z0-9-]+$",
"uri_format": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1"
},
"addgene": {
"description": "Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world.",
"example": "50943",
"homepage": "http://addgene.org/",
"name": "Addgene Plasmid Repository",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$",
"uri_format": "http://addgene.org/$1"
},
"adw": {
"description": "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology.",
"example": "Lycalopex_vetulus",
"homepage": "https://animaldiversity.org/",
"name": "Animal Diversity Web at University of Michigan",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z_a-z]+$",
"uri_format": "https://animaldiversity.org/accounts/$1/"
},
"affy.probeset": {
"description": "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration.",
"example": "243002_at",
"homepage": "http://www.affymetrix.com/",
"name": "Affymetrix ProbeSet in Santa Clara",
"namespaceEmbeddedInLui": false,
"pattern": "\\d{4,}((_[asx])?_at)?",
"uri_format": "https://www.affymetrix.com/LinkServlet?probeset=$1"
},
"aftol.taxonomy": {
"description": "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species.",
"example": "959",
"homepage": "http://aftol.org/data.php",
"name": "AFTOL at University of Minnesota",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1"
},
"agricola": {
"description": "AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century.",
"example": "50018",
"homepage": "http://agricola.nal.usda.gov/",
"name": "AGRICOLA at National Agricultural Library",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://ddr.nal.usda.gov/dspace/handle/10113/$1"
},
"allergome": {
"description": "Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources.",
"example": "1948",
"homepage": "http://www.allergome.org/",
"name": "Allergome at Rome",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.allergome.org/script/dettaglio.php?id_molecule=$1"
},
"amoebadb": {
"description": "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"example": "EDI_244000",
"homepage": "http://amoebadb.org/amoeba/",
"name": "AmoebaDB at EuPathDB",
"namespaceEmbeddedInLui": false,
"pattern": "^EDI_\\d+$",
"uri_format": "https://amoebadb.org/amoeba/app/record/gene/$1"
},
"antibodyregistry": {
"description": "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.",
"example": "493771",
"homepage": "http://antibodyregistry.org/",
"name": "Antibody Registry at University of California",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{6}$",
"uri_format": "http://antibodyregistry.org/AB_$1"
},
"antweb": {
"description": "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures.",
"example": "casent0106247",
"homepage": "http://www.antweb.org/",
"name": "AntWeb at California Academy of Sciences",
"namespaceEmbeddedInLui": false,
"pattern": "^casent\\d+(\\-D\\d+)?$",
"uri_format": "http://www.antweb.org/specimen.do?name=$1"
},
"aop": {
"description": "International repository of Adverse Outcome Pathways.",
"example": "98",
"homepage": "https://aopwiki.org/",
"name": "AOPWiki",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://aopwiki.org/aops/$1"
},
"aop.events": {
"description": "International repository of Adverse Outcome Pathways.",
"example": "3",
"homepage": "https://aopwiki.org/",
"name": "AOPWiki (Key Event)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://aopwiki.org/events/$1"
},
"aop.relationships": {
"description": "International repository of Adverse Outcome Pathways.",
"example": "5",
"homepage": "https://aopwiki.org/",
"name": "AOPWiki (Key Event Relationship)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://aopwiki.org/relationships/$1"
},
"aop.stressor": {
"description": "International repository of Adverse Outcome Pathways.",
"example": "9",
"homepage": "https://aopwiki.org/",
"name": "AOPWiki (Stressor)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://aopwiki.org/stressors/$1"
},
"apd": {
"description": "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides.",
"example": "01001",
"homepage": "http://aps.unmc.edu/AP/",
"name": "APD at Nebraska",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{5}$",
"uri_format": "http://aps.unmc.edu/AP/database/query_output.php?ID=$1"
},
"aphidbase.transcript": {
"description": "AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information.",
"example": "ACYPI000159",
"homepage": "http://www.aphidbase.com/aphidbase",
"name": "AphidBase at INRA",
"namespaceEmbeddedInLui": false,
"pattern": "^ACYPI\\d{6}(-RA)?$",
"uri_format": "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1"
},
"apid.interactions": {
"description": "APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.",
"example": "P01116",
"homepage": "http://cicblade.dep.usal.es:8080/APID/",
"name": "APID at Salamanca",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$",
"uri_format": "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1"
},
"arachnoserver": {
"description": "ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information.",
"example": "AS000060",
"homepage": "http://www.arachnoserver.org/",
"name": "ArachnoServer at Brisbane",
"namespaceEmbeddedInLui": false,
"pattern": "^AS\\d{6}$",
"uri_format": "http://www.arachnoserver.org/toxincard.html?id=$1"
},
"ardb": {
"description": "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes.",
"example": "CAE46076",
"homepage": "http://ardb.cbcb.umd.edu/",
"name": "ARDB at University of Maryland",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z_]{3}[0-9]{4,}$",
"uri_format": "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1"
},
"ark": {
"example": "/88435/hq37vq534",
"homepage": "https://wiki.ucop.edu/display/Curation/ARK",
"name": "Archival Resource Key",
"namespaceEmbeddedInLui": false,
"uri_format": "n2t.net/ark:$1"
},
"arrayexpress": {
"description": "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.",
"example": "E-MEXP-1712",
"homepage": "https://www.ebi.ac.uk/arrayexpress/",
"name": "ArrayExpress",
"namespaceEmbeddedInLui": false,
"pattern": "^[AEP]-\\w{4}-\\d+$",
"uri_format": "https://www.ebi.ac.uk/arrayexpress/experiments/$1"
},
"arrayexpress.platform": {
"description": "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results.",
"example": "A-GEOD-50",
"homepage": "https://www.ebi.ac.uk/arrayexpress/",
"name": "ArrayExpress Platform at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^[AEP]-\\w{4}-\\d+$",
"uri_format": "https://www.ebi.ac.uk/arrayexpress/arrays/$1"
},
"arraymap": {
"description": "arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome.",
"example": "icdom:8500_3",
"homepage": "https://www.arraymap.org",
"name": "ArrayMap",
"namespaceEmbeddedInLui": false,
"pattern": "^[\\w\\-:,]{3,64}$",
"uri_format": "https://www.arraymap.org/pgx:$1"
},
"arxiv": {
"description": "arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology.",
"example": "0807.4956v1",
"homepage": "https://arxiv.org/",
"name": "Cornell University arXiv",
"namespaceEmbeddedInLui": false,
"pattern": "^(\\w+(\\-\\w+)?(\\.\\w+)?)?\\d{4,7}(\\.\\d+(v\\d+)?)?$",
"uri_format": "https://arxiv.org/abs/$1"
},
"asap": {
"description": "ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources.",
"example": "ABE-0009634",
"homepage": "http://asap.ahabs.wisc.edu/asap/home.php",
"name": "ASAP at University of Wisconsin",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9-]+$",
"uri_format": "http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1"
},
"ascl": {
"description": "The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001).",
"example": "1801.012",
"homepage": "http://ascl.net/",
"name": "Astrophysics Source Code Library",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9\\.]+$",
"uri_format": "http://ascl.net/$1"
},
"asin": {
"description": "Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue.",
"example": "0471491039",
"homepage": "https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182",
"name": "Amazon Standard Identification Number (ASIN)",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]{10}$",
"uri_format": "https://amzn.com/$1"
},
"aspgd.locus": {
"description": "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information.",
"example": "ASPL0000349247",
"homepage": "http://www.aspgd.org/",
"name": "AspGD at Stanford Medical School",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z_0-9]+$",
"uri_format": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1"
},
"aspgd.protein": {
"description": "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information.",
"example": "ASPL0000349247",
"homepage": "http://www.aspgd.org/",
"name": "AspGD Protein at Stanford Medical School",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z_0-9]+$",
"uri_format": "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1"
},
"atc": {
"description": "The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels.",
"example": "A10BA02",
"homepage": "http://www.whocc.no/atc_ddd_index/",
"name": "Anatomical Therapeutic Chemical Index at WHO",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z](\\d+([A-Z]{1,2}(\\d+)?)?)?$",
"uri_format": "http://www.whocc.no/atc_ddd_index/?code=$1"
},
"atcc": {
"description": "The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences.",
"example": "11303",
"homepage": "http://www.atcc.org/",
"name": "ATCC in Virginia",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.lgcstandards-atcc.org/Products/All/$1.aspx"
},
"atcvet": {
"description": "The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use.",
"example": "QJ51RV02",
"homepage": "http://www.whocc.no/atcvet/atcvet_index/",
"name": "Anatomical Therapeutic Chemical Vet Index at WHO",
"namespaceEmbeddedInLui": false,
"pattern": "^Q[A-Z0-9]+$",
"uri_format": "http://www.whocc.no/atcvet/atcvet_index/?code=$1"
},
"atfdb.family": {
"description": "The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found.",
"example": "CUT",
"homepage": "http://www.bioguo.org/AnimalTFDB/family_index.php",
"name": "Animal TFDB at Hubei Bioinformatics & Molecular Imaging Key Laboratory",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://www.bioguo.org/AnimalTFDB/family.php?fam=$1"
},
"autdb": {
"description": "AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder.",
"example": "ADA",
"homepage": "http://autism.mindspec.org/autdb/",
"name": "AutDB at MindSpec",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]+[A-Z-0-9]{2,}$",
"uri_format": "http://autism.mindspec.org/GeneDetail/$1"
},
"bacdive": {
"description": "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity.",
"example": "131392",
"homepage": "https://bacdive.dsmz.de/",
"name": "Bacterial Diversity Metadatabase",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"uri_format": "https://bacdive.dsmz.de/strain/$1"
},
"bacmap.biog": {
"description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information.",
"example": "1050",
"homepage": "http://bacmap.wishartlab.com/",
"name": "BacMap Biography at University of Alberta",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://bacmap.wishartlab.com/organisms/$1"
},
"bacmap.map": {
"description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information.",
"example": "AP011135",
"homepage": "http://bacmap.wishartlab.com/",
"name": "BacMap Genome Map at University of Alberta",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$",
"uri_format": "http://bacmap.wishartlab.com/maps/$1/index.html"
},
"bao": {
"description": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.",
"example": "0002989",
"homepage": "http://bioportal.bioontology.org/ontologies/BAO/",
"name": "BioAssay Ontology through BioPortal",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{7}$",
"uri_format": "http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1"
},
"bdgp.est": {
"description": "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI).",
"example": "EY223054.1",
"homepage": "https://www.ncbi.nlm.nih.gov/dbEST/index.html",
"name": "BDGP EST at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\.)?(\\d+)?$",
"uri_format": "https://www.ncbi.nlm.nih.gov/nucest/$1"
},
"bdgp.insertion": {
"description": "BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element.",
"example": "KG09531",
"homepage": "http://flypush.imgen.bcm.tmc.edu/pscreen/",
"name": "BDGP Gene Disruption Project",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1"
},
"bdsc": {
"description": "The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research.",
"example": "33607",
"homepage": "https://bdsc.indiana.edu/about/mission.html",
"name": "BDSC at Indiana University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://bdsc.indiana.edu/stocks/$1"
},
"beetlebase": {
"description": "BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications.",
"example": "TC010103",
"homepage": "http://beetlebase.org/",
"name": "BeetleBase at Kansas State University",
"namespaceEmbeddedInLui": false,
"pattern": "^TC\\d+$",
"uri_format": "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1"
},
"begdb": {
"description": "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods.",
"example": "4214",
"homepage": "http://www.begdb.com",
"name": "Benchmark Energy & Geometry Database",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"uri_format": "http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1"
},
"bgee.family": {
"description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species.",
"example": "ENSFM00500000270089",
"homepage": "http://bgee.unil.ch/bgee/bgee",
"name": "Bgee at Lausanne",
"namespaceEmbeddedInLui": false,
"pattern": "^(ENSFM|ENSGTV:)\\d+$",
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1"
},
"bgee.gene": {
"description": "Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee.",
"example": "FBgn0000015",
"homepage": "https://bgee.org/",
"name": "Bgee gene",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z]+\\d+$",
"uri_format": "https://bgee.org/?page=gene&gene_id=$1"
},
"bgee.organ": {
"description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures.",
"example": "EHDAA:2185",
"homepage": "http://bgee.unil.ch/bgee/bgee",
"name": "Bgee at Lausanne",
"namespaceEmbeddedInLui": false,
"pattern": "^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\\:\\d+$",
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_id=$1&organ_children=on"
},
"bgee.stage": {
"description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages.",
"example": "HsapDO:0000004",
"homepage": "http://bgee.unil.ch/bgee/bgee",
"name": "Bgee at Lausanne",
"namespaceEmbeddedInLui": false,
"pattern": "^(FBvd|XtroDO|HsapDO|MmusDO)\\:\\d+$",
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_id=$1&stage_children=on"
},
"bigg.compartment": {
"description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments.",
"example": "c",
"homepage": "http://bigg.ucsd.edu/compartments/",
"name": "BiGG Compartment at University of California",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z_A-Z]+$",
"uri_format": "http://bigg.ucsd.edu/compartments/$1"
},
"bigg.metabolite": {
"description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes.",
"example": "12dgr161",
"homepage": "http://bigg.ucsd.edu/universal/metabolites",
"name": "BiGG Metabolite at University of Cakifornia",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z_A-Z0-9]+$",
"uri_format": "http://bigg.ucsd.edu/models/universal/metabolites/$1"
},
"bigg.model": {
"description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models.",
"example": "iECABU_c1320",
"homepage": "http://bigg.ucsd.edu/models",
"name": "BiGG Model at University of California",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z_A-Z0-9]+$",
"uri_format": "http://bigg.ucsd.edu/models/$1"
},
"bigg.reaction": {
"description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions.",
"example": "13GS",
"homepage": "http://bigg.ucsd.edu/universal/reactions",
"name": "BiGG Reaction at University of California",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z_A-Z0-9]+$",
"uri_format": "http://bigg.ucsd.edu/models/universal/reactions/$1"
},
"bindingdb": {
"description": "BindingDB is the first public database of protein-small molecule affinity data.",
"example": "e999",
"homepage": "https://www.bindingdb.org",
"name": "BindingDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w\\d+$",
"uri_format": "http://www.bindingdb.org/compact/$1"
},
"biocarta.pathway": {
"description": "BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps.",
"example": "h_aktPathway",
"homepage": "https://www.biocarta.com/",
"name": "BioCarta Pathway at NCI",
"namespaceEmbeddedInLui": false,
"pattern": "^([hm]\\_)?\\w+Pathway$",
"uri_format": "https://cgap.nci.nih.gov/Pathways/BioCarta/$1"
},
"biocatalogue.service": {
"description": "The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all.",
"example": "614",
"homepage": "https://www.biocatalogue.org/",
"name": "BioCatalogue at EMBL-EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://www.biocatalogue.org/services/$1"
},
"biocyc": {
"description": "BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms.",
"example": "ECOLI:CYT-D-UBIOX-CPLX",
"homepage": "http://biocyc.org",
"name": "BioCyc at SRI International",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z-0-9]+(\\:)?[A-Za-z0-9+_.%-:]+$",
"uri_format": "http://biocyc.org/getid?id=$1"
},
"biogrid": {
"description": "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe.",
"example": "31623",
"homepage": "http://thebiogrid.org/",
"name": "BioGRID database of physical and genetic interactions",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://thebiogrid.org/$1"
},
"biomaps": {
"description": "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.",
"example": "37",
"homepage": "http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp",
"name": "main webpage",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1"
},
"biominder": {
"description": "Database of the dielectric properties of biological tissues.",
"example": "aef4c195-9cf9-46db-a12a-7cfd1ff3eec3",
"homepage": "https://datalab.rwth-aachen.de/MINDER",
"name": "Bio-MINDER Tissue Database",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z0-9\\-]+$",
"uri_format": "https://datalab.rwth-aachen.de/MINDER/resource/$1"
},
"biomodels.db": {
"description": "BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests.",
"example": "BIOMD0000000048",
"homepage": "https://www.ebi.ac.uk/biomodels/",
"name": "BioModels Database",
"namespaceEmbeddedInLui": false,
"pattern": "^((BIOMD|MODEL)\\d{10})|(BMID\\d{12})$",
"uri_format": "https://www.ebi.ac.uk/biomodels/$1"
},
"biomodels.kisao": {
"description": "The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment.",
"example": "KISAO_0000057",
"homepage": "http://bioportal.bioontology.org/ontologies/KISAO",
"name": "KiSAO via NCBO's Bioportal",
"namespaceEmbeddedInLui": false,
"pattern": "^KISAO_\\d+$",
"uri_format": "http://purl.bioontology.org/ontology/KISAO/kisao:$1"
},
"biomodels.teddy": {
"description": "The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.",
"example": "TEDDY_0000066",
"homepage": "http://teddyontology.sourceforge.net/",
"name": "TEDDY through BioPortal",
"namespaceEmbeddedInLui": false,
"pattern": "^TEDDY_\\d{7}$",
"uri_format": "http://purl.bioontology.org/ontology/TEDDY/$1"
},
"biomodels.vocabulary": {
"description": "Vocabulary used in the RDF representation of SBML models.",
"example": "rateRule",
"homepage": "http://biomodels.net/rdf/vocabulary.rdf",
"name": "Vocabulary via BioModels.net",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z]+$",
"uri_format": "http://biomodels.net/rdf/vocabulary.rdf#$1"
},
"bionumbers": {
"description": "BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data.",
"example": "104674",
"homepage": "https://bionumbers.hms.harvard.edu",
"name": "BioNumbers database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1"
},
"bioportal": {
"description": "BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies.",
"example": "1046",
"homepage": "http://bioportal.bioontology.org/",
"name": "BioPortal at National Center for Biomedical Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://bioportal.bioontology.org/ontologies/$1"
},
"bioproject": {
"description": "BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories.",
"example": "PRJDB3",
"homepage": "https://www.ncbi.nlm.nih.gov/bioproject",
"name": "BioProject at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^PRJ[DEN][A-Z]\\d+$",
"uri_format": "https://www.ncbi.nlm.nih.gov/bioproject?term=$1"
},
"biosample": {
"description": "The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation.",
"example": "SAMEA2397676",
"homepage": "https://www.ebi.ac.uk/biosamples/",
"name": "BioSamples Database at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^SAM[NED](\\w)?\\d+$",
"uri_format": "https://www.ebi.ac.uk/biosamples/sample/$1"
},
"biostudies": {
"description": "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.",
"example": "S-EPMC6266652",
"homepage": "https://www.ebi.ac.uk/biostudies/",
"name": "BioStudies database",
"namespaceEmbeddedInLui": false,
"pattern": "^S-[A-Z]{4}[A-Z\\d\\-]+$",
"uri_format": "https://www.ebi.ac.uk/biostudies/studies/$1"
},
"biosystems": {
"description": "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources.",
"example": "001",
"homepage": "https://www.ncbi.nlm.nih.gov/biosystems/",
"name": "BioSystems database at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://www.ncbi.nlm.nih.gov/biosystems/$1"
},
"biotools": {
"description": "Tool and data services registry.",
"example": "uniprotkb",
"homepage": "https://bio.tools/",
"name": "BioTools",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9\\_]*$",
"uri_format": "https://bio.tools/$1"
},
"bitterdb.cpd": {
"description": "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds.",
"example": "46",
"homepage": "http://bitterdb.agri.huji.ac.il/dbbitter.php",
"name": "BitterDB Compound at The Hebrew University of Jerusalem",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1"
},
"bitterdb.rec": {
"description": "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors.",
"example": "1",
"homepage": "http://bitterdb.agri.huji.ac.il/dbbitter.php",
"name": "BitterDB Receptor at The Hebrew University of Jerusalem",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1"
},
"bold.taxonomy": {
"description": "The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information.",
"example": "27267",
"homepage": "http://www.boldsystems.org/",
"name": "BOLD taxonomy browser",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1"
},
"brenda": {
"description": "BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data.",
"example": "1.1.1.1",
"homepage": "https://www.brenda-enzymes.org/",
"name": "Brenda enzyme database",
"namespaceEmbeddedInLui": false,
"pattern": "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$",
"uri_format": "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1"
},
"broad": {
"description": "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae.",
"example": "S7000002168151102",
"homepage": "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/",
"name": "Broad Fungal Genome Initiative at Broad Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^S\\d+$",
"uri_format": "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1"
},
"bto": {
"description": "The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.",
"example": "0000146",
"homepage": "http://bioportal.bioontology.org/ontologies/BTO",
"name": "Brenda Tissue Ontology through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^BTO:\\d{7}$",
"uri_format": "http://purl.bioontology.org/ontology/BTO/BTO:$1"
},
"bugbase.expt": {
"description": "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments.",
"example": "288",
"homepage": "http://bugs.sgul.ac.uk/E-BUGS",
"name": "BugBase Expt at University of London",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view"
},
"bugbase.protocol": {
"description": "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols.",
"example": "67",
"homepage": "http://bugs.sgul.ac.uk/E-BUGS",
"name": "BugBase Protocol at University of London",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$1&action=view"
},
"bykdb": {
"description": "The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information.",
"example": "A0A009E7X8",
"homepage": "https://bykdb.ibcp.fr/BYKdb/",
"name": "BYKdb at CNRS",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]+$",
"uri_format": "https://bykdb.ibcp.fr/data/html/annotated/$1.html"
},
"cabri": {
"description": "CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it.",
"example": "dsmz_mutz-id:ACC 291",
"homepage": "http://www.cabri.org/",
"name": "CABRI Cell Lines catalogue in Genova (SRS)",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-Za-z]+)?(\\_)?([A-Za-z-]+)\\:([A-Za-z0-9 ]+)$",
"uri_format": "http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]"
},
"cadsr": {
"description": "The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR.",
"example": "3771992",
"homepage": "https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki",
"name": "Cancer Data Standards Registry and Repository",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]*$",
"uri_format": "https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1]"
},
"cameo": {
"description": "The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB.",
"example": "2018-03-24_00000030_1",
"homepage": "https://cameo3d.org",
"name": "CAMEO",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9\\-_]+$",
"uri_format": "https://www.cameo3d.org/sp/targets/target/$1"
},
"caps": {
"description": "CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps.",
"example": "434",
"homepage": "http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home",
"name": "CAPS-DB at Leeds Institute of Molecular Medicine",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1"
},
"cas": {
"description": "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information.",
"example": "50-00-0",
"homepage": "http://commonchemistry.org",
"name": "CAS through Common Chemistry",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{1,7}\\-\\d{2}\\-\\d$",
"uri_format": "http://commonchemistry.org/ChemicalDetail.aspx?ref=$1"
},
"cath": {
"description": "CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence.",
"example": "1.10.8.10",
"homepage": "http://www.cathdb.info",
"name": "CATH Node through UCL",
"namespaceEmbeddedInLui": false,
"pattern": "^[1-4]\\.[0-9]+\\.[0-9]+\\.[0-9]+$",
"uri_format": "http://www.cathdb.info/cathnode/$1"
},
"cath.domain": {
"description": "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains.",
"example": "1cukA01",
"homepage": "http://www.cathdb.info/",
"name": "CATH domain at UCL",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://www.cathdb.info/domain/$1"
},
"cath.superfamily": {
"description": "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification.",
"example": "1.10.10.200",
"homepage": "http://www.cathdb.info/",
"name": "CATH superfamily at UCL",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+(\\.\\d+(\\.\\d+(\\.\\d+)?)?)?$",
"uri_format": "http://www.cathdb.info/cathnode/$1"
},
"cattleqtldb": {
"description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs.",
"example": "4685",
"homepage": "http://www.animalgenome.org/cgi-bin/QTLdb/BT/index",
"name": "Animal QTL Cattle at Iowa State University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_ID=$1"
},
"cazy": {
"description": "The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features.",
"example": "GT10",
"homepage": "http://www.cazy.org/",
"name": "CAZy at CNRS",
"namespaceEmbeddedInLui": false,
"pattern": "^(GT|GH|PL|CE|CBM)\\d+(\\_\\d+)?$",
"uri_format": "http://www.cazy.org/$1.html"
},
"cbioportal": {
"description": "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.",
"example": "laml_tcga_pub",
"homepage": "http://www.cbioportal.org",
"name": "The cBioPortal for Cancer Genomics",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z0-9\\_]+$",
"uri_format": "http://www.cbioportal.org/study?id=$1#summary"
},
"ccds": {
"description": "The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations.",
"example": "CCDS13573.1",
"homepage": "http://www.ncbi.nlm.nih.gov/CCDS/",
"name": "Consensus CDS at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^CCDS\\d+\\.\\d+$",
"uri_format": "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1"
},
"cco": {
"description": "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process.",
"example": "0000003",
"homepage": "https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CCO",
"name": "Cell Cycle Ontology through OLS",
"namespaceEmbeddedInLui": true,
"pattern": "^CCO\\:\\w+$",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1"
},
"cdd": {
"description": "The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution.",
"example": "cd00400",
"homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd",
"name": "Conserved Domain Database at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^(cd)?\\d{5}$",
"uri_format": "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"
},
"cdpd": {
"description": "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN).",
"example": "63250",
"homepage": "http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp",
"name": "Canadian Drug Identification Number at Health Canada",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1"
},
"cellimage": {
"description": "The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.",
"example": "24801",
"homepage": "http://cellimagelibrary.org/",
"name": "Cell Image Library at American Society for Cell Biology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://cellimagelibrary.org/images/$1"
},
"cellosaurus": {
"description": "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.",
"example": "CVCL_0030",
"homepage": "https://web.expasy.org/cellosaurus/",
"name": "Cellosaurus through SIB",
"namespaceEmbeddedInLui": false,
"pattern": "CVCL_[A-Z0-9]{4}",
"uri_format": "https://web.expasy.org/cellosaurus/$1"
},
"cgd": {
"description": "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.",
"example": "CAL0003079",
"homepage": "http://www.candidagenome.org/",
"name": "Candida Genome Database at Stanford University",
"namespaceEmbeddedInLui": false,
"pattern": "^CAL\\d{7}$",
"uri_format": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"
},
"cgsc": {
"description": "The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature.",
"example": "74",
"homepage": "http://cgsc.biology.yale.edu/index.php",
"name": "CGSC at Yale university",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://cgsc.biology.yale.edu/Site.php?ID=$1"
},
"charprot": {
"description": "CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession.",
"example": "CH_001923",
"homepage": "http://www.jcvi.org/charprotdb",
"name": "CharProt at JCVI",
"namespaceEmbeddedInLui": false,
"pattern": "^CH_\\d+$",
"uri_format": "http://www.jcvi.org/charprotdb/index.cgi/view/$1"
},
"chebi": {
"description": "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds.",
"example": "36927",
"homepage": "https://www.ebi.ac.uk/chebi/",
"name": "ChEBI (Chemical Entities of Biological Interest)",
"namespaceEmbeddedInLui": true,
"pattern": "^CHEBI:\\d+$",
"uri_format": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1"
},
"chembl.compound": {
"description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.",
"example": "CHEMBL308052",
"homepage": "https://www.ebi.ac.uk/chembldb/",
"name": "ChEMBL compound database at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^CHEMBL\\d+$",
"uri_format": "https://www.ebi.ac.uk/chembl/compound/inspect/$1"
},
"chembl.target": {
"description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.",
"example": "CHEMBL3467",
"homepage": "https://www.ebi.ac.uk/chembldb/",
"name": "ChEMBL targets database at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^CHEMBL\\d+$",
"uri_format": "https://www.ebi.ac.uk/chembl/target/inspect/$1"
},
"chemdb": {
"description": "ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds.",
"example": "3966782",
"homepage": "http://cdb.ics.uci.edu/",
"name": "ChemDB at UC Irvine",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1"
},
"chemidplus": {
"description": "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.",
"example": "57-27-2",
"homepage": "https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp",
"name": "ChemIDplus at National Library of Medicine",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+\\-\\d+\\-\\d+$",
"uri_format": "https://chem.nlm.nih.gov/chemidplus/rn/$1"
},
"chemspider": {
"description": "ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources.",
"example": "56586",
"homepage": "http://www.chemspider.com/",
"name": "ChemSpider at RSC",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.chemspider.com/Chemical-Structure.$1.html"
},
"chickenqtldb": {
"description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs.",
"example": "14362",
"homepage": "http://www.animalgenome.org/cgi-bin/QTLdb/GG/index",
"name": "Animal QTL Chicken at Iowa State University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.animalgenome.org/cgi-bin/QTLdb/GG/qdetails?QTL_ID=$1"
},
"cl": {
"description": "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.",
"example": "0000232",
"homepage": "http://bioportal.bioontology.org/ontologies/CL",
"name": "Cell Type Ontology through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^CL:\\d{7}$",
"uri_format": "http://purl.bioontology.org/ontology/CL/CL:$1"
},
"cldb": {
"description": "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories.",
"example": "cl3603",
"homepage": "http://bioinformatics.hsanmartino.it/hypercldb/indexes.html",
"name": "CLDB at Genova",
"namespaceEmbeddedInLui": false,
"pattern": "^(cl|tum)\\d+$",
"uri_format": "http://bioinformatics.hsanmartino.it/hypercldb/$1.html"
},
"clinicaltrials": {
"description": "ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries",
"example": "NCT00222573",
"homepage": "https://clinicaltrials.gov/",
"name": "ClinicalTrials.gov at NIH",
"namespaceEmbeddedInLui": false,
"pattern": "^NCT\\d{8}$",
"uri_format": "https://clinicaltrials.gov/ct2/show/$1"
},
"clinvar": {
"description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier.",
"example": "12345",
"homepage": "http://www.ncbi.nlm.nih.gov/clinvar/",
"name": "ClinVar Variant at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1"
},
"clinvar.record": {
"description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession.",
"example": "RCV000033555.3",
"homepage": "http://www.ncbi.nlm.nih.gov/clinvar/",
"name": "ClinVar Record at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^RCV\\d+(\\.\\d+)?$",
"uri_format": "http://www.ncbi.nlm.nih.gov/clinvar/$1/"
},
"clinvar.submission": {
"description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession.",
"example": "SCV000151292",
"homepage": "http://www.ncbi.nlm.nih.gov/clinvar/",
"name": "ClinVar Submission at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^SCV\\d+(\\.\\d+)?$",
"uri_format": "http://www.ncbi.nlm.nih.gov/clinvar?term=$1"
},
"combine.specifications": {
"description": "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network.",
"example": "sbgn.er.level-1.version-1.2",
"homepage": "https://co.mbine.org/standards/",
"name": "COMBINE at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\-|\\.|\\w)*$",
"uri_format": "https://co.mbine.org/specifications/$1"
},
"complexportal": {
"description": "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases.",
"example": "CPX-2158",
"homepage": "https://www.ebi.ac.uk/complexportal",
"name": "Complex Portal",
"namespaceEmbeddedInLui": false,
"pattern": "^CPX-[0-9]+$",
"uri_format": "https://www.ebi.ac.uk/complexportal/complex/$1"
},
"comptox": {
"description": "The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks.",
"example": "DTXSID2021028",
"homepage": "https://comptox.epa.gov/dashboard",
"name": "CompTox Chemistry Dashboard",
"namespaceEmbeddedInLui": false,
"pattern": "^DTXSID\\d+$",
"uri_format": "https://comptox.epa.gov/dashboard/$1"
},
"compulyeast": {
"description": "Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record.",
"example": "O08709",
"homepage": "http://compluyeast2dpage.dacya.ucm.es/",
"name": "Compluyeast database at Universidad Complutense Madrid",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$",
"uri_format": "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1"
},
"conoserver": {
"description": "ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails.",
"example": "2639",
"homepage": "http://www.conoserver.org/",
"name": "ConoServer at University of Queensland",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.conoserver.org/?page=card&table=protein&id=$1"
},
"coriell": {
"description": "The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world.",
"example": "GM17027",
"homepage": "http://ccr.coriell.org/",
"name": "Coriell Cell Repositories at Coriell Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]{2}\\d+$",
"uri_format": "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1"
},
"corum": {
"description": "The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded.",
"example": "100",
"homepage": "https://mips.helmholtz-muenchen.de/genre/proj/corum/",
"name": "CORUM at Institute for Bioinformatics and Systems Biology (Germany)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://mips.helmholtz-muenchen.de/corum/?id=$1"
},
"cosmic": {
"description": "COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes.",
"example": "BRAF",
"homepage": "http://cancer.sanger.ac.uk/cosmic/",
"name": "COSMIC Gene at Sanger",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]+$",
"uri_format": "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1"
},
"cpc": {
"description": "The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013.",
"example": "A01M1/026",
"homepage": "https://worldwide.espacenet.com/classification",
"name": "Cooperative Patent Classification at Espace",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-H,Y]|[A-H, Y]\\d{2}|[A-H, Y]\\d{2}[A-Z]|[A-H, Y]\\d{2}[A-Z]\\d{1,3}|[A-H, Y]\\d{2}[A-Z]\\d{1,3}(\\/)?\\d{2,})$",
"uri_format": "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1"
},
"crisprdb": {
"description": "Repeated CRISPR (\"clustered regularly interspaced short palindromic repeats\") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data.",
"example": "551115",
"homepage": "http://crispr.i2bc.paris-saclay.fr/",
"name": "CRISPRdb",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"uri_format": "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1"
},
"cryptodb": {
"description": "CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"example": "cgd7_230",
"homepage": "https://cryptodb.org/cryptodb/",
"name": "CryptoDB at EuPathDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+",
"uri_format": "https://cryptodb.org/cryptodb/app/record/gene/$1"
},
"csa": {
"description": "The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme.",
"example": "1a05",
"homepage": "https://www.ebi.ac.uk/thornton-srv/databases/CSA/",
"name": "CSA at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9][A-Za-z0-9]{3}$",
"uri_format": "https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1"
},
"cst": {
"description": "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways.",
"example": "Akt_PKB",
"homepage": "http://www.cellsignal.com/pathways/index.html",
"name": "CST Pathways at Cell Signaling Technology",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9_-]+$",
"uri_format": "http://www.cellsignal.com/reference/pathway/$1.html"
},
"cst.ab": {
"description": "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products.",
"example": "3305",
"homepage": "http://www.cellsignal.com/catalog/index.html",
"name": "CST Antibody at Cell Signaling Technology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.cellsignal.com/products/$1.html"
},
"ctd.chemical": {
"description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.",
"example": "D001151",
"homepage": "http://ctdbase.org/",
"name": "Comparative Toxicogenomics Database (Chemical)",
"namespaceEmbeddedInLui": false,
"pattern": "^[CD]\\d+$",
"uri_format": "http://ctdbase.org/detail.go?type=chem&acc=$1"
},
"ctd.disease": {
"description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.",
"example": "D053716",
"homepage": "http://ctdbase.org/",
"name": "Comparative Toxicogenomics Database (Disease)",
"namespaceEmbeddedInLui": false,
"pattern": "^D\\d+$",
"uri_format": "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1"
},
"ctd.gene": {
"description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.",
"example": "101",
"homepage": "http://ctdbase.org/",
"name": "Comparative Toxicogenomics Database (Gene)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://ctdbase.org/detail.go?type=gene&acc=$1"
},
"cubedb": {
"description": "Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available.",
"example": "AKR",
"homepage": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html",
"name": "Cube db at Bioinformatics Institute (Singapore)",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z_0-9]+$",
"uri_format": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/"
},
"d1id": {
"description": "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences.",
"example": "00030692-0FE1-4A1B-955E-A2E55D659267",
"homepage": "https://www.dataone.org",
"name": "DataONE",
"namespaceEmbeddedInLui": false,
"pattern": "\\S+",
"uri_format": "https://cn.dataone.org/cn/v2/resolve/{$1}"
},
"dailymed": {
"description": "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read.",
"example": "973a9333-fec7-46dd-8eb5-25738f06ee54",
"homepage": "https://dailymed.nlm.nih.gov/dailymed/",
"name": "DailyMed at NLM",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9-]+",
"uri_format": "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1"
},
"darc": {
"description": "DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.",
"example": "1250",
"homepage": "http://darcsite.genzentrum.lmu.de/darc/index.php",
"name": "DARC at University of Munich",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1"
},
"dashr": {
"description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records.",
"example": "hsa-mir-200a",
"homepage": "http://lisanwanglab.org/DASHR/",
"name": "DASHR at University of Pennsylvania",
"namespaceEmbeddedInLui": false,
"pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$",
"uri_format": "http://lisanwanglab.org/DASHR/entry/$1"
},
"dashr.expression": {
"description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression.",
"example": "hsa-mir-200a",
"homepage": "https://dashr1.lisanwanglab.org/show-expression-table.php?start=0",
"name": "DASHR expression at University of Pennsylvania",
"namespaceEmbeddedInLui": false,
"pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$",
"uri_format": "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable"
},
"datf": {
"description": "DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals.",
"example": "AT1G01030.1",
"homepage": "http://datf.cbi.pku.edu.cn/",
"name": "DATF through PlantTFDB",
"namespaceEmbeddedInLui": false,
"pattern": "^AT[1-5]G\\d{5}(\\.\\d+)?$",
"uri_format": "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1"
},
"dbd": {
"description": "The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins.",
"example": "0045310",
"homepage": "http://www.transcriptionfactor.org/",
"name": "DBD at MRC Laboratory of Molecular Biology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD"
},
"dbest": {
"description": "The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms.",
"example": "BP100000",
"homepage": "https://www.ncbi.nlm.nih.gov/nucest",
"name": "dbEST at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-Z]+)?\\d+(\\.\\d+)?$",
"uri_format": "https://www.ncbi.nlm.nih.gov/nucest/$1"
},
"dbg2introns": {
"description": "The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank.",
"example": "Cu.me.I1",
"homepage": "http://webapps2.ucalgary.ca/~groupii/",
"name": "Bacterial Group II Introns at University of Calgary",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$",
"uri_format": "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1"
},
"dbgap": {
"description": "The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype.",
"example": "phs000768.v2.p1",
"homepage": "https://www.ncbi.nlm.nih.gov/projects/gap",
"name": "dbGaP through NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^phs[0-9]{6}(.v\\d+.p\\d+)?$",
"uri_format": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1"
},
"dbprobe": {
"description": "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.",
"example": "1000000",
"homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe",
"name": "dbProbe at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://www.ncbi.nlm.nih.gov/probe/?term=$1"
},
"dbsnp": {
"description": "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.",
"example": "rs121909098",
"homepage": "https://www.ncbi.nlm.nih.gov/snp/",
"name": "dbSNP at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^rs\\d+$",
"uri_format": "https://www.ncbi.nlm.nih.gov/snp/$1"
},
"degradome": {
"description": "The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced.",
"example": "Ax1",
"homepage": "http://degradome.uniovi.es/",
"name": "Degradome Database at",
"namespaceEmbeddedInLui": false,
"pattern": "^[AMCST][0-9x][0-9]$",
"uri_format": "http://degradome.uniovi.es/cgi-bin/protease/$1"
},
"depod": {
"description": "The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources.",
"example": "PTPN1",
"homepage": "http://www.depod.bioss.uni-freiburg.de",
"name": "DEPOD at EMBL",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]+$",
"uri_format": "http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1"
},
"dev.ga4ghdos": {
"description": "Assists in resolving data across cloud resources.",
"example": "23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00",
"homepage": "http://github.com/ga4gh/data-object-service-schemas",
"name": "Data Object Service",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-zA-Z0-9\\-:#\\.]+$",
"uri_format": "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1"
},
"dictybase.est": {
"description": "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information.",
"example": "DDB0016567",
"homepage": "http://dictybase.org/",
"name": "Dictybase Gene at Northwestern University",
"namespaceEmbeddedInLui": false,
"pattern": "^DDB\\d+$",
"uri_format": "http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1"
},
"dictybase.gene": {
"description": "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information.",
"example": "DDB_G0267522",
"homepage": "http://dictybase.org/",
"name": "Dictybase Gene at Northwestern University",
"namespaceEmbeddedInLui": false,
"pattern": "^DDB_G\\d+$",
"uri_format": "http://dictybase.org/gene/$1"
},
"did": {
"description": "DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary.",
"example": "sov:WRfXPg8dantKVubE3HX8pw",
"homepage": "https://w3c-ccg.github.io/did-spec/",
"name": "Decentralized Identifiers (DIDs)",
"namespaceEmbeddedInLui": true,
"pattern": "^did:[a-z0-9]+:[A-Za-z0-9.\\-:]+$",
"uri_format": "https://uniresolver.io/#did:$1"
},
"dip": {
"description": "The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions",
"example": "DIP-743N",
"homepage": "https://dip.doe-mbi.ucla.edu/",
"name": "Database of interacting proteins",
"namespaceEmbeddedInLui": false,
"pattern": "^DIP(\\:)?\\-\\d{1,}[ENXS]$",
"uri_format": "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1"
},
"disprot": {
"description": "The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part.",
"example": "DP00003",
"homepage": "http://www.disprot.org/",
"name": "DisProt at Indiana University",
"namespaceEmbeddedInLui": false,
"pattern": "^DP\\d{5}$",
"uri_format": "http://www.disprot.org/$1"
},
"doi": {
"description": "The Digital Object Identifier System is for identifying content objects in the digital environment.",
"example": "10.1038/nbt1156",
"homepage": "https://www.doi.org/",
"name": "Digital Object Identifier",
"namespaceEmbeddedInLui": false,
"pattern": "^(doi\\:)?\\d{2}\\.\\d{4}.*$",
"uri_format": "https://doi.org/$1"
},
"doid": {
"description": "The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts.",
"example": "11337",
"homepage": "http://disease-ontology.org/",
"name": "Human Disease Ontology at Northwestern University",
"namespaceEmbeddedInLui": true,
"pattern": "^DOID\\:\\d+$",
"uri_format": "http://disease-ontology.org/term/DOID:$1"
},
"dommino": {
"description": "DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides.",
"example": "2GC4",
"homepage": "http://dommino.org/",
"name": "DOMMINO at University of Missouri",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9][A-Za-z0-9]{3}$",
"uri_format": "http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1"
},
"door": {
"description": "DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes.",
"example": "1398574",
"homepage": "http://csbl.bmb.uga.edu/DOOR/operon.php",
"name": "DOOR v1 at University of Georgia",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1"
},
"doqcs.model": {
"description": "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models.",
"example": "57",
"homepage": "http://doqcs.ncbs.res.in/",
"name": "Database of Quantitative Cellular Signaling (DOQCS) - Model Access",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1"
},
"doqcs.pathway": {
"description": "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways.",
"example": "131",
"homepage": "http://doqcs.ncbs.res.in/",
"name": "Database of Quantitative Cellular Signaling (DOQCS) - Pathway Access",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1"
},
"dpv": {
"description": "Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene.",
"example": "100",
"homepage": "http://www.dpvweb.net/",
"name": "DPV at Rothamsted",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1"
},
"dragondb.allele": {
"description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information.",
"example": "cho",
"homepage": "http://www.antirrhinum.net/",
"name": "DragonDB Allele at University of British Columbia",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele"
},
"dragondb.dna": {
"description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information.",
"example": "3hB06",
"homepage": "http://www.antirrhinum.net/",
"name": "DragonDB DNA at University of British Columbia",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d\\w+$",
"uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA"
},
"dragondb.locus": {
"description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information.",
"example": "DEF",
"homepage": "http://www.antirrhinum.net/",
"name": "DragonDB Locus at University of British Columbia",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus"
},
"dragondb.protein": {
"description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information.",
"example": "AMDEFA",
"homepage": "http://www.antirrhinum.net/",
"name": "DragonDB Protein at University of British Columbia",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide"
},
"drsc": {
"description": "The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene.",
"example": "DRSC05221",
"homepage": "http://flyrnai.org/",
"name": "DRSC at Harvard Medical School",
"namespaceEmbeddedInLui": false,
"pattern": "^DRSC\\d+$",
"uri_format": "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1"
},
"drugbank": {
"description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information.",
"example": "DB00001",
"homepage": "http://www.drugbank.ca/",
"name": "DrugBank drug information",
"namespaceEmbeddedInLui": false,
"pattern": "^DB\\d{5}$",
"uri_format": "http://www.drugbank.ca/drugs/$1"
},
"drugbankv4.target": {
"description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database.",
"example": "BE0000048",
"homepage": "http://www.drugbank.ca/targets",
"name": "DrugBank Target information version 4",
"namespaceEmbeddedInLui": false,
"pattern": "^BE\\d{7}$",
"uri_format": "http://www.drugbank.ca/biodb/bio_entities/$1"
},
"ec-code": {
"description": "The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions.",
"example": "1.1.1.1",
"homepage": "https://www.ebi.ac.uk/intenz/",
"name": "IntEnZ (Integrated relational Enzyme database)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+\\.-\\.-\\.-|\\d+\\.\\d+\\.-\\.-|\\d+\\.\\d+\\.\\d+\\.-|\\d+\\.\\d+\\.\\d+\\.(n)?\\d+$",
"uri_format": "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1"
},
"echobase": {
"description": "EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products.",
"example": "EB0170",
"homepage": "http://www.york.ac.uk/",
"name": "EchoBASE at the University of York",
"namespaceEmbeddedInLui": false,
"pattern": "^EB\\d+$",
"uri_format": "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1"
},
"eco": {
"description": "Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity.",
"example": "0000006",
"homepage": "http://bioportal.bioontology.org/ontologies/ECO",
"name": "Evidence Code Ontology through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "ECO:\\d{7}$",
"uri_format": "http://purl.bioontology.org/ontology/ECO/ECO:$1"
},
"ecogene": {
"description": "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites.",
"example": "EG10173",
"homepage": "http://ecogene.org/",
"name": "EcoGene at University of Miami",
"namespaceEmbeddedInLui": false,
"pattern": "^EG\\d+$",
"uri_format": "http://www.ecogene.org/gene/$1"
},
"ecoliwiki": {
"description": "EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes.",
"example": "aaeA",
"homepage": "http://ecoliwiki.net/colipedia/",
"name": "EcoliWiki at Texas Agrilife Research",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9-]+$",
"uri_format": "http://ecoliwiki.net/colipedia/index.php/$1:Gene"
},
"ecyano.entity": {
"description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities.",
"example": "23",
"homepage": "http://www.e-cyanobacterium.org/bcs/entity/",
"name": "e-cyanobacterium entity at Masaryk University Brno",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://e-cyanobacterium.org/bcs/entity/$1/"
},
"ecyano.model": {
"description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models.",
"example": "26",
"homepage": "http://e-cyanobacterium.org/models/",
"name": "e-cyanobacterium entity at Masaryk University Brno",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://e-cyanobacterium.org/models/model/$1/"
},
"ecyano.rule": {
"description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules.",
"example": "56",
"homepage": "http://www.e-cyanobacterium.org/bcs/rule/",
"name": "e-cyanobacterium entity at Masaryk University Brno",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://e-cyanobacterium.org/bcs/rule/$1/"
},
"edam": {
"description": "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).",
"example": "data_1664",
"homepage": "http://bioportal.bioontology.org/ontologies/EDAM",
"name": "EDAM through BioPortal",
"namespaceEmbeddedInLui": false,
"pattern": "^(data|topic|operation|format)\\_\\d{4}$",
"uri_format": "http://purl.bioontology.org/ontology/EDAM/$1"
},
"efo": {
"description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.",
"example": "0004859",
"homepage": "http://bioportal.bioontology.org/ontologies/EFO",
"name": "EFO through BioPortal",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{7}$",
"uri_format": "http://purl.bioontology.org/ontology/EFO/efo:EFO_$1"
},
"ega.dataset": {
"description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.",
"example": "EGAD00000000001",
"homepage": "https://www.ebi.ac.uk/ega/dataset",
"name": "EGA Dataset at European Bioinformatics Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^EGAD\\d{11}$",
"uri_format": "https://www.ebi.ac.uk/ega/datasets/$1"
},
"ega.study": {
"description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.",
"example": "EGAS00000000001",
"homepage": "https://www.ebi.ac.uk/ega/studies",
"name": "EGA Study at European Bioinformatics Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^EGAS\\d{11}$",
"uri_format": "https://www.ebi.ac.uk/ega/studies/$1"
},
"eggnog": {
"description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).",
"example": "veNOG12876",
"homepage": "http://eggnog.embl.de/version_3.0/",
"name": "eggNOG Version 3 at European Molecular Biology Laboratory",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1"
},
"elm": {
"description": "Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances.",
"example": "CLV_MEL_PAP_1",
"homepage": "http://elm.eu.org/",
"name": "ELM at EMBL (Germany)",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z_0-9]+$",
"uri_format": "http://elm.eu.org/elms/elmPages/$1.html"
},
"emdb": {
"description": "The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community.",
"example": "EMD-1001",
"homepage": "https://www.ebi.ac.uk/pdbe/emdb/",
"name": "EMDB at Protein Data Bank in Europe",
"namespaceEmbeddedInLui": false,
"pattern": "^EMD-\\d{4}$",
"uri_format": "https://www.ebi.ac.uk/pdbe/entry/emdb/$1"
},
"ena.embl": {
"description": "The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers.",
"example": "BN000065",
"homepage": "https://www.ncbi.nlm.nih.gov/Genbank/",
"name": "ENA through GenBank",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]+[0-9]+(\\.\\d+)?$",
"uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1"
},
"encode": {
"description": "The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns.",
"example": "ENCSR163RYW",
"homepage": "www.encodeproject.org",
"name": "ENCODE: Encyclopedia of DNA Elements",
"namespaceEmbeddedInLui": false,
"pattern": "^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$",
"uri_format": "https://www.encodeproject.org/$1"
},
"ensembl": {
"description": "Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms.",
"example": "ENSG00000139618",
"homepage": "https://www.ensembl.org/",
"name": "Ensembl at Sanger/EMBL-EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^((ENS[FPTG]\\\\d{11}(\\\\.\\\\d+)?)|(FB\\\\w{2}\\\\d{7})|(Y[A-Z]{2}\\\\d{3}[a-zA-Z](\\\\-[A-Z])?)|([A-Z_a-z0-9]+(\\\\.)?(t)?(\\\\d+)?([a-z])?))$",
"uri_format": "https://www.ensembl.org/id/$1"
},
"ensembl.bacteria": {
"description": "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes.",
"example": "MU9_3181",
"homepage": "https://bacteria.ensembl.org/",
"name": "Ensembl Bacteria at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^((EB\\w+)|([A-Z0-9]+\\_[A-Z0-9]+))$",
"uri_format": "https://bacteria.ensembl.org/id/$1"
},
"ensembl.fungi": {
"description": "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes.",
"example": "CADAFLAT00006211",
"homepage": "https://fungi.ensembl.org/",
"name": "Enzembl Fungi at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z-a-z0-9]+$",
"uri_format": "https://fungi.ensembl.org/id/$1"
},
"ensembl.metazoa": {
"description": "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes.",
"example": "FBtr0084214",
"homepage": "https://metazoa.ensembl.org/",
"name": "Enzembl Metazoa at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\.)?\\d+$",
"uri_format": "https://metazoa.ensembl.org/id/$1"
},
"ensembl.plant": {
"description": "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes.",
"example": "AT1G73965",
"homepage": "https://plants.ensembl.org/",
"name": "Enzembl Plants at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\.\\d+)?(\\.\\d+)?$",
"uri_format": "https://plants.ensembl.org/id/$1"
},
"ensembl.protist": {
"description": "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes.",
"example": "PF3D7_1328700",
"homepage": "https://protists.ensembl.org",
"name": "Ensembl Protists at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "https://protists.ensembl.org/id/$1"
},
"envo": {
"description": "The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations.",
"example": "09200010",
"homepage": "http://purl.bioontology.org/ontology/ENVO/",
"name": "The Environment Ontology through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^ENVO:\\d{8}$",
"uri_format": "http://purl.bioontology.org/ontology/ENVO/ENVO:$1"
},
"eo": {
"description": "The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.",
"example": "0007404",
"homepage": "http://bioportal.bioontology.org/ontologies/PECO",
"name": "Plant Environment Ontology through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^(P)?EO\\:\\d{7}$",
"uri_format": "http://purl.bioontology.org/ontology/PECO/EO:$1"
},
"epd": {
"description": "The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.",
"example": "TA_H3",
"homepage": "http://epd.vital-it.ch/",
"name": "EPD at Swiss Institute of Bioinformatics",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z-_0-9]+$",
"uri_format": "http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1"
},
"erm": {
"description": "The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project.",
"example": "ERM00000044",
"homepage": "https://nanocommons.github.io/identifiers/",
"name": "European Registry of Materials",
"namespaceEmbeddedInLui": false,
"pattern": "^ERM[0-9]{8}$",
"uri_format": "https://nanocommons.github.io/identifiers/registry#$1"
},
"erv": {
"description": "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features.",
"example": "THE1B",
"homepage": "https://herv.img.cas.cz/",
"name": "Human Endogenous Retrovirus Database",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9\\-\\_]+$",
"uri_format": "https://herv.img.cas.cz/s/$1"
},
"eu89h": {
"description": "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union.",
"example": "jrc-eurl-ecvam-chemagora",
"homepage": "http://data.jrc.ec.europa.eu/",
"name": "JRC Data Catalogue",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z0-9\\-_]+$",
"uri_format": "http://data.europa.eu/89h/$1"
},
"euclinicaltrials": {
"description": "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004. It also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.",
"example": "2008-005144-16",
"homepage": "https://www.clinicaltrialsregister.eu/",
"name": "EU Clinical Trials at European Medicines Agency",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{4}\\-\\d{6}\\-\\d{2}$",
"uri_format": "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1"
},
"exac.gene": {
"description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information.",
"example": "ENSG00000169174",
"homepage": "http://exac.broadinstitute.org/",
"name": "ExAC Gene at Exome Aggregation Consortium",
"namespaceEmbeddedInLui": false,
"pattern": "^ENSG\\d{11}$",
"uri_format": "http://exac.broadinstitute.org/gene/$1"
},
"exac.transcript": {
"description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information.",
"example": "ENST00000407236",
"homepage": "http://exac.broadinstitute.org/",
"name": "ExAC Transcript at Exome Aggregation Consortium",
"namespaceEmbeddedInLui": false,
"pattern": "^ENST\\d{11}$",
"uri_format": "http://exac.broadinstitute.org/transcript/$1"
},
"exac.variant": {
"description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information.",
"example": "22-46615880-T-C",
"homepage": "http://exac.broadinstitute.org/",
"name": "ExAC Variant at Exome Aggregation Consortium",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$",
"uri_format": "http://exac.broadinstitute.org/variant/$1"
},
"facebase": {
"description": "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.",
"example": "FB00000917",
"homepage": "https://www.facebase.org",
"name": "FaceBase Data Repository",
"namespaceEmbeddedInLui": false,
"pattern": "^FB\\d{8}$",
"uri_format": "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1"
},
"fairsharing": {
"description": "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies.",
"example": "bsg-000052",
"homepage": "https://fairsharing.org/",
"name": "FAIRSharing at University of Oxford",
"namespaceEmbeddedInLui": false,
"pattern": "^bsg-[dscp]?\\d{6}$",
"uri_format": "https://fairsharing.org/$1"
},
"fb": {
"description": "FlyBase is the database of the Drosophila Genome Projects and of associated literature.",
"example": "FBgn0011293",
"homepage": "https://www.alliancegenome.org",
"name": "FlyBase through the Alliance of Genome Resources",
"namespaceEmbeddedInLui": false,
"pattern": "^FB\\w{2}\\d{7}$",
"uri_format": "https://www.alliancegenome.org/gene/FB:$1"
},
"fbol": {
"description": "DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms.",
"example": "2224",
"homepage": "http://www.fungalbarcoding.org/",
"name": "Fungal Barcode at Fungal Biodiversity Centre",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T"
},
"flowrepository": {
"description": "FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field.",
"example": "FR-FCM-ZYGW",
"homepage": "https://flowrepository.org/",
"name": "FlowRepository",
"namespaceEmbeddedInLui": false,
"pattern": "^FR\\-FCM\\-\\w{4}$",
"uri_format": "https://flowrepository.org/id/$1"
},
"fma": {
"description": "The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy.",
"example": "67112",
"homepage": "http://bioportal.bioontology.org/ontologies/FMA",
"name": "Foundational Model of Anatomy through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^FMA:\\d+$",
"uri_format": "http://purl.bioontology.org/ontology/FMA_subset/FMA:$1"
},
"foodb.compound": {
"description": "FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds.",
"example": "FDB002100",
"homepage": "http://foodb.ca/foods",
"name": "FooDB database of food additives at University of Alberta",
"namespaceEmbeddedInLui": false,
"pattern": "^FDB\\d+$",
"uri_format": "http://foodb.ca/compounds/$1"
},
"foodon": {
"description": "FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies.",
"example": "03307879",
"homepage": "https://foodon.org",
"name": "FoodOn Food Ontology through OLS",
"namespaceEmbeddedInLui": true,
"pattern": "^FOODON:[0-9]{8}$",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1"
},
"fplx": {
"description": "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships.",
"example": "RAS",
"homepage": "http://bioportal.bioontology.org/ontologies/FPLX/",
"name": "FPLX through BioPortal",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-zA-Z0-9][A-Za-z0-9_]+$",
"uri_format": "http://bioportal.bioontology.org/ontologies/FPLX/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FFPLX%23_$1"
},
"fsnp": {
"description": "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.",
"example": "rs17852708",
"homepage": "http://compbio.cs.queensu.ca/F-SNP/",
"name": "F-SNP at Queen's University (Canada)",
"namespaceEmbeddedInLui": false,
"pattern": "^rs\\d+$",
"uri_format": "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1"
},
"funcbase.fly": {
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data.",
"example": "10194",
"homepage": "http://func.mshri.on.ca/fly",
"name": "FuncBase Fly at Harvard Medical School",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1"
},
"funcbase.human": {
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data.",
"example": "119514",
"homepage": "http://func.mshri.on.ca/human/",
"name": "FuncBase Human at Harvard Medical School",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://func.mshri.on.ca/human/genes/list_functional_scores/$1"
},
"funcbase.mouse": {
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse.",
"example": "1351341",
"homepage": "http://func.mshri.on.ca/mouse/",
"name": "FuncBase Mouse at Harvard Medical School",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1"
},
"funcbase.yeast": {
"description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast.",
"example": "2701",
"homepage": "http://func.mshri.on.ca/yeast",
"name": "FuncBase Yeast at Harvard Medical School",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1"
},
"fungidb": {
"description": "FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina.",
"example": "CNBG_0001",
"homepage": "https://fungidb.org/fungidb",
"name": "FungiDB at University of California",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z_0-9]+$",
"uri_format": "https://fungidb.org/fungidb/app/record/gene/$1"
},
"ga4ghdos": {
"description": "Assists in resolving data across cloud resources.",
"example": "dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d",
"homepage": "http://github.com/ga4gh/data-object-service-schemas",
"name": "Data Object Service",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-zA-Z0-9\\-:#/\\.]+$",
"uri_format": "https://dataguids.org/ga4gh/dos/v1/dataobjects/$1"
},
"gabi": {
"description": "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'.",
"example": "2679240",
"homepage": "http://www.gabipd.org/",
"name": "GABI at Max Planck",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject"
},
"gcst": {
"description": "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide.",
"example": "GCST000035",
"homepage": "https://www.ebi.ac.uk/gwas/studies",
"name": "GWAS Catalog",
"namespaceEmbeddedInLui": false,
"pattern": "^GCST\\d{6}$",
"uri_format": "https://www.ebi.ac.uk/gwas/studies/$1"
},
"gdc": {
"description": "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis.",
"example": "ae8c77fe-e6c8-44d5-8265-4a38c637bbef",
"homepage": "https://gdc.cancer.gov",
"name": "Genomic Data Commons",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$",
"uri_format": "https://portal.gdc.cancer.gov/cases/$1"
},
"gdsc": {
"description": "The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies.",
"example": "1242",
"homepage": "https://www.cancerrxgene.org",
"name": "Genomics of Drug Sensitivity in Cancer",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"uri_format": "https://www.cancerrxgene.org/translation/Drug/$1"
},
"genatlas": {
"description": "GenAtlas is a database containing information on human genes, markers and phenotypes.",
"example": "HBB",
"homepage": "http://genatlas.medecine.univ-paris5.fr/",
"name": "Genatlas at Paris Descartes University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1"
},
"genecards": {
"description": "The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene.",
"example": "ABL1",
"homepage": "http://www.genecards.org/",
"name": "GeneCards at Weizmann Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z-0-9_]+(\\@)?$",
"uri_format": "https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1"
},
"genedb": {
"description": "GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the \"Pathogen Genomics\" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed.",
"example": "LinJ.20.0070",
"homepage": "https://www.genedb.org/",
"name": "GeneDB at Sanger Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^[\\w\\d\\.-]*$",
"uri_format": "https://www.genedb.org/gene/$1"
},
"genefarm": {
"description": "GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products.",
"example": "4892",
"homepage": "http://urgi.versailles.inra.fr/Genefarm/",
"name": "GeneFarm at Unité de Recherche en Génomique Végétale",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1"
},
"genetree": {
"description": "Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl.",
"example": "ENSGT00550000074763",
"homepage": "http://www.ensembl.org/",
"name": "GeneTree at Ensembl",
"namespaceEmbeddedInLui": false,
"pattern": "^ENSGT\\d+$",
"uri_format": "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1"
},
"genewiki": {
"description": "The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI.",
"example": "1017",
"homepage": "http://en.wikipedia.org/wiki/Gene_Wiki",
"name": "Gene Wiki through BioGPS",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1"
},
"genpept": {
"description": "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank.",
"example": "CAA71118.1",
"homepage": "https://www.ncbi.nlm.nih.gov/protein",
"name": "GenPept at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{3}\\d{5}(\\.\\d+)?$",
"uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept"
},
"genprop": {
"description": "Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome.",
"example": "GenProp0699",
"homepage": "https://www.ebi.ac.uk/interpro/genomeproperties/",
"name": "Genome Properties",
"namespaceEmbeddedInLui": false,
"pattern": "^GenProp\\d+$",
"uri_format": "https://www.ebi.ac.uk/interpro/genomeproperties/#$1"
},
"geo": {
"description": "The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval.",
"example": "GDS1234",
"homepage": "https://www.ncbi.nlm.nih.gov/geo/",
"name": "Gene Expression Omnibus at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^G(PL|SM|SE|DS)\\d+$",
"uri_format": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1"
},
"giardiadb": {
"description": "GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"example": "GL50803_102438",
"homepage": "https://giardiadb.org/giardiadb/",
"name": "GiardiaDB at EuPathDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "https://giardiadb.org/giardiadb/app/record/gene/$1"
},
"glida.gpcr": {
"description": "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors.",
"example": "ACM1_HUMAN",
"homepage": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/",
"name": "GLIDA GPCR at Kyoto University",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z-_0-9]+$",
"uri_format": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1"
},
"glida.ligand": {
"description": "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands.",
"example": "L000001",
"homepage": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/",
"name": "GLIDA Ligand at Kyoto University",
"namespaceEmbeddedInLui": false,
"pattern": "^L\\d+$",
"uri_format": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1"
},
"glycoepitope": {
"description": "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes.",
"example": "EP0311",
"homepage": "https://www.glycoepitope.jp/epitopes/",
"name": "GlycoEpitope at Ritsumeikan University",
"namespaceEmbeddedInLui": false,
"pattern": "^EP\\d{4}$",
"uri_format": "https://www.glycoepitope.jp/epitopes/$1"
},
"glycomedb": {
"description": "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.",
"example": "G77500AY",
"homepage": "https://glytoucan.org/",
"name": "GlycomeDB carbohydrate structure database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "https://glytoucan.org/Structures/Glycans/$1"
},
"glytoucan": {
"description": "GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data.",
"example": "G00054MO",
"homepage": "https://glytoucan.org",
"name": "The Glycan Repository",
"namespaceEmbeddedInLui": false,
"pattern": "^G[0-9]{5}[A-Z]{2}$",
"uri_format": "https://glytoucan.org/Structures/Glycans/$1"
},
"gmd": {
"description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena.",
"example": "68513255-fc44-4041-bc4b-4fd2fae7541d",
"homepage": "http://gmd.mpimp-golm.mpg.de/",
"name": "Golm Metabolome Database at Max Planck Institute of Molecular Plant Physiology",
"namespaceEmbeddedInLui": false,
"pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$",
"uri_format": "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx"
},
"gmd.analyte": {
"description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes.",
"example": "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80",
"homepage": "http://gmd.mpimp-golm.mpg.de/",
"name": "Golm Metabolome Database (Analyte) at Max Planck Institute of Molecular Plant Physiology",
"namespaceEmbeddedInLui": false,
"pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$",
"uri_format": "http://gmd.mpimp-golm.mpg.de/Analytes/$1"
},
"gmd.gcms": {
"description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra.",
"example": "53d583d8-40c6-40e1-9296-23f821cd77a5",
"homepage": "http://gmd.mpimp-golm.mpg.de/",
"name": "Golm Metabolome Database (GC-MS Spectra) at Max Planck Institute of Molecular Plant Physiology",
"namespaceEmbeddedInLui": false,
"pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$",
"uri_format": "http://gmd.mpimp-golm.mpg.de/Spectrums/$1"
},
"gmd.profile": {
"description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues.",
"example": "10b38aaf-b977-4950-85b8-f4775f66658d",
"homepage": "http://gmd.mpimp-golm.mpg.de/",
"name": "Golm Metabolome Database (Profile) at Max Planck Institute of Molecular Plant Physiology",
"namespaceEmbeddedInLui": false,
"pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$",
"uri_format": "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1"
},
"gmd.ref": {
"description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances.",
"example": "8cf84adb-b4db-4807-ac98-0004247c35df",
"homepage": "http://gmd.mpimp-golm.mpg.de/",
"name": "Golm Metabolome Database (Reference Substance) at Max Planck Institute of Molecular Plant Physiology",
"namespaceEmbeddedInLui": false,
"pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$",
"uri_format": "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1"
},
"gnpis": {
"description": "GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest.",
"example": "AY109603",
"homepage": "https://urgi.versailles.inra.fr/gnpis/",
"name": "GnpIS",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9]+$",
"uri_format": "https://urgi.versailles.inra.fr/gnpis/#result/term=$1"
},
"go": {
"description": "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.",
"example": "0006915",
"homepage": "http://amigo.geneontology.org/",
"name": "AmiGO 2",
"namespaceEmbeddedInLui": true,
"pattern": "^GO:\\d{7}$",
"uri_format": "http://amigo.geneontology.org/amigo/term/GO:$1"
},
"go.ref": {
"description": "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made.",
"example": "GO_REF:0000041",
"homepage": "http://www.geneontology.org/cgi-bin/references.cgi",
"name": "Gene Ontology Reference at The Gene Ontology Consortium",
"namespaceEmbeddedInLui": false,
"pattern": "^GO_REF:\\d{7}$",
"uri_format": "http://www.geneontology.org/cgi-bin/references.cgi#$1"
},
"goa": {
"description": "The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups.",
"example": "P12345",
"homepage": "https://www.ebi.ac.uk/GOA/",
"name": "GOA through QuickGO",
"namespaceEmbeddedInLui": false,
"pattern": "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$",
"uri_format": "https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1"
},
"gold.genome": {
"description": "The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes.",
"example": "Gi07796",
"homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi",
"name": "GOLD genome at Department of Energy Joint Genome Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^[Gi|Gc]\\d+$",
"uri_format": "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1"
},
"gold.meta": {
"description": "The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples.",
"example": "Gm00047",
"homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi",
"name": "GOLD metadata at Department of Energy Joint Genome Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^Gm\\d+$",
"uri_format": "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1"
},
"google.patent": {
"description": "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date.",
"example": "US4145692",
"homepage": "https://www.google.com/patents/",
"name": "Google Patents at Google",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]{2}\\d+([A-Z])?$",
"uri_format": "https://www.google.com/patents/$1"
},
"gpcrdb": {
"description": "The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models.",
"example": "RL3R1_HUMAN",
"homepage": "http://www.gpcrdb.org/",
"name": "GPCRDB at Radboud University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://www.gpcrdb.org/protein/$1/"
},
"gpmdb": {
"description": "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns.",
"example": "GPM32310002988",
"homepage": "http://gpmdb.thegpm.org/",
"name": "GPMDB",
"namespaceEmbeddedInLui": false,
"pattern": "^GPM\\d+$",
"uri_format": "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1"
},
"gramene.gene": {
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene.",
"example": "GR:0080039",
"homepage": "http://www.gramene.org/",
"name": "Gramene Genes at Cold Spring Harbor",
"namespaceEmbeddedInLui": false,
"pattern": "^GR\\:\\d+$",
"uri_format": "http://www.gramene.org/db/genes/search_gene?acc=$1"
},
"gramene.growthstage": {
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.",
"example": "0007133",
"homepage": "http://www.gramene.org/",
"name": "Gramene Growth Stage Ontology at Cold Spring Harbor",
"namespaceEmbeddedInLui": true,
"pattern": "^GRO\\:\\d+$",
"uri_format": "http://www.gramene.org/db/ontology/search?id=GRO:$1"
},
"gramene.protein": {
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene.",
"example": "78073",
"homepage": "http://www.gramene.org/",
"name": "Gramene Protein at Cold Spring Harbor",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.gramene.org/db/protein/protein_search?protein_id=$1"
},
"gramene.qtl": {
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene.",
"example": "CQG5",
"homepage": "http://www.gramene.org/",
"name": "Gramene Quantitative Trait Loci at Cold Spring Harbor",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1"
},
"gramene.taxonomy": {
"description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene.",
"example": "GR_tax:013681",
"homepage": "http://www.gramene.org/",
"name": "Gramene Taxonomy at Cold Spring Harbor",
"namespaceEmbeddedInLui": false,
"pattern": "^GR\\_tax\\:\\d+$",
"uri_format": "http://www.gramene.org/db/ontology/search?id=$1"
},
"greengenes": {
"description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.",
"example": "100000",
"homepage": "http://greengenes.lbl.gov/",
"name": "GreenGenes at Lawrence Berkeley",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1"
},
"grid": {
"description": "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally.",
"example": "grid.225360.0",
"homepage": "https://www.grid.ac/",
"name": "GRID at Digital Science & Research Ltd.",
"namespaceEmbeddedInLui": false,
"pattern": "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$",
"uri_format": "https://www.grid.ac/institutes/$1"
},
"grin.taxonomy": {
"description": "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact.",
"example": "19333",
"homepage": "http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en",
"name": "GRIN at Maryland",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1"
},
"grsdb": {
"description": "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.",
"example": "10142",
"homepage": "http://bioinformatics.ramapo.edu/GRSDB2/",
"name": "GRSDB v2 at Ramapo College of New Jersey",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1"
},
"gtex": {
"description": "The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. ",
"example": "BRIP1",
"homepage": "https://www.gtexportal.org",
"name": "The GTEx Project",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w.+$",
"uri_format": "https://www.gtexportal.org/home/gene/$1"
},
"gudmap": {
"description": "The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract.",
"example": "Q-2958",
"homepage": "http://www.gudmap.org/",
"name": "GUDMAP",
"namespaceEmbeddedInLui": false,
"pattern": "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$",
"uri_format": "https://gudmap.org/id/$1"
},
"gwascentral.marker": {
"description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker.",
"example": "HGVM15354",
"homepage": "https://www.gwascentral.org/markers/",
"name": "GWAS Central Marker at University of Leicester",
"namespaceEmbeddedInLui": false,
"pattern": "^HGVM\\d+$",
"uri_format": "https://www.gwascentral.org/marker/$1"
},
"gwascentral.phenotype": {
"description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype.",
"example": "HGVPM623",
"homepage": "https://www.gwascentral.org/phenotypes",
"name": "GWAS Central Phenotype at University of Leicester",
"namespaceEmbeddedInLui": false,
"pattern": "^HGVP\\d+$",
"uri_format": "https://www.gwascentral.org/phenotype/$1"
},
"gwascentral.study": {
"description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study.",
"example": "HGVST1828",
"homepage": "https://www.gwascentral.org/studies",
"name": "GWAS Central Study at University of Leicester",
"namespaceEmbeddedInLui": false,
"pattern": "^HGVST\\d+$",
"uri_format": "https://www.gwascentral.org/study/$1"
},
"gxa.expt": {
"description": "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments.",
"example": "E-MTAB-2037",
"homepage": "https://www.ebi.ac.uk/gxa/",
"name": "GXA Expt at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^[AEP]-\\w{4}-\\d+$",
"uri_format": "https://www.ebi.ac.uk/gxa/experiments/$1"
},
"gxa.gene": {
"description": "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes.",
"example": "AT4G01080",
"homepage": "https://www.ebi.ac.uk/gxa/",
"name": "GXA Gene at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "https://www.ebi.ac.uk/gxa/genes/$1"
},
"hamap": {
"description": "HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries.",
"example": "MF_01400",
"homepage": "https://hamap.expasy.org/",
"name": "HAPMAP at Swiss Institute of Bioinformatics",
"namespaceEmbeddedInLui": false,
"pattern": "^MF_\\d+$",
"uri_format": "https://hamap.expasy.org/unirule/$1"
},
"hcvdb": {
"description": "the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses.",
"example": "M58335",
"homepage": "http://euhcvdb.ibcp.fr/euHCVdb/",
"name": "HCVDB at CNRS",
"namespaceEmbeddedInLui": false,
"pattern": "^M\\d{5}$",
"uri_format": "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1"
},
"hdr": {
"description": "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders.",
"example": "63",
"homepage": "http://research.nhgri.nih.gov/apps/homeodomain/web/",
"name": "Homeodomain Research at National Human Genome Research Institute (NIH)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1"
},
"hgmd": {
"description": "The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases.",
"example": "CALM1",
"homepage": "http://www.hgmd.cf.ac.uk/ac/index.php",
"name": "HGMD at Cardiff University",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z_0-9]+$",
"uri_format": "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1"
},
"hgnc": {
"description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database.",
"example": "2674",
"homepage": "https://www.genenames.org",
"name": "HUGO Genome Nomenclature Committee",
"namespaceEmbeddedInLui": false,
"pattern": "^((HGNC|hgnc):)?\\d{1,5}$",
"uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1"
},
"hgnc.genefamily": {
"description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.",
"example": "141",
"homepage": "https://www.genenames.org/",
"name": "HGNC gene family at HUGO Genome Nomenclature Committee",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://www.genenames.org/cgi-bin/genefamilies/set/$1"
},
"hgnc.symbol": {
"description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol.",
"example": "DAPK1",
"homepage": "https://www.genenames.org/",
"name": "HGNC Symbol at HUGO Genome Nomenclature Committee",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z-0-9_]+(\\@)?$",
"uri_format": "https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1"
},
"hinv.locus": {
"description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view.",
"example": "HIX0004394",
"homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp",
"name": "H-Invitational Locus View at BIRC",
"namespaceEmbeddedInLui": false,
"pattern": "^HIX\\d{7}(\\.\\d+)?$",
"uri_format": "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1"
},
"hinv.protein": {
"description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view.",
"example": "HIP000030660",
"homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp",
"name": "H-Invitational Protein View at BIRC",
"namespaceEmbeddedInLui": false,
"pattern": "^HIP\\d{9}(\\.\\d+)?$",
"uri_format": "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1"
},
"hinv.transcript": {
"description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view.",
"example": "HIT000195363",
"homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp",
"name": "H-Invitational Transcript View at BIRC",
"namespaceEmbeddedInLui": false,
"pattern": "^HIT\\d{9}(\\.\\d+)?$",
"uri_format": "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1"
},
"hmdb": {
"description": "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.",
"example": "HMDB00001",
"homepage": "http://www.hmdb.ca/",
"name": "The Human Metabolome Database",
"namespaceEmbeddedInLui": false,
"pattern": "^HMDB\\d+$",
"uri_format": "http://www.hmdb.ca/metabolites/$1"
},
"hogenom": {
"description": "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.",
"example": "HBG284870",
"homepage": "http://pbil.univ-lyon1.fr/databases/hogenom/",
"name": "HOGENOM at CNRS",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1"
},
"homd.seq": {
"description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.",
"example": "SEQF1003",
"homepage": "http://www.homd.org/index.php",
"name": "HOMD sequence metainformation at The Forsyth Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^SEQF\\d+$",
"uri_format": "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1"
},
"homd.taxon": {
"description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.",
"example": "811",
"homepage": "http://www.homd.org/index.php",
"name": "HOMD taxon information at The Forsyth Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$1&view=dynamic"
},
"homologene": {
"description": "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.",
"example": "1000",
"homepage": "https://www.ncbi.nlm.nih.gov/homologene/",
"name": "Homologene at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://www.ncbi.nlm.nih.gov/homologene/$1"
},
"hovergen": {
"description": "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.",
"example": "HBG004341",
"homepage": "http://pbil.univ-lyon1.fr/databases/hovergen.php",
"name": "Hovergen",
"namespaceEmbeddedInLui": false,
"pattern": "^HBG\\d+$",
"uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN"
},
"hp": {
"description": "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.",
"example": "0000118",
"homepage": "http://human-phenotype-ontology.github.io/",
"name": "Human Phenotype Ontology at Institute for Medical Genetics and Human Genetics",
"namespaceEmbeddedInLui": true,
"pattern": "^HP:\\d{7}$",
"uri_format": "http://compbio.charite.de/hpoweb/showterm?id=HP:$1"
},
"hpa": {
"description": "The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers.",
"example": "ENSG00000026508",
"homepage": "http://www.proteinatlas.org/",
"name": "Human Protein Atlas at AlbaNova University",
"namespaceEmbeddedInLui": false,
"pattern": "^ENSG\\d{11}$",
"uri_format": "http://www.proteinatlas.org/$1"
},
"hpm.peptide": {
"description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra.",
"example": "9606117",
"homepage": "http://www.humanproteomemap.org/index.php",
"name": "Human Proteome Map Peptide at Institute of Bioinformatics (Bangalore)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.humanproteomemap.org/spectrum.php?pep_id=$1"
},
"hpm.protein": {
"description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.",
"example": "1968",
"homepage": "http://www.humanproteomemap.org/index.php",
"name": "Human Proteome Map Protein at Institute of Bioinformatics (Bangalore)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.humanproteomemap.org/protein.php?hpm_id=$1"
},
"hprd": {
"description": "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.",
"example": "00001",
"homepage": "http://www.hprd.org/",
"name": "Human Protein Reference Database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.hprd.org/protein/$1"
},
"hpscreg": {
"description": "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines).",
"example": "BCRTi001-A",
"homepage": "https://hpscreg.eu/",
"name": "Human Pluripotent Stem Cell Registry",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$",
"uri_format": "https://hpscreg.eu/cell-line/$1"
},
"hssp": {
"description": "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.",
"example": "102l",
"homepage": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/",
"name": "HSSP at CMBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{4}$",
"uri_format": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$1.hssp.bz2"
},
"huge": {
"description": "The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.",
"example": "KIAA0001",
"homepage": "http://www.kazusa.or.jp/huge/",
"name": "HUGE at Kazusa DNA Research Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^KIAA\\d{4}$",
"uri_format": "http://www.kazusa.or.jp/huge/gfpage/$1/"
},
"iao": {
"description": "An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch.",
"example": "0000030",
"homepage": "http://www.ontobee.org/ontology/IAO",
"name": "IAO through Ontobee",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/IAO_$1"
},
"icd": {
"description": "The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes.",
"example": "C34",
"homepage": "http://www.who.int/classifications/icd/en/",
"name": "International Statistical Classification of Diseases and Related Health Problems",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]\\d+(\\.[-\\d+])?$",
"uri_format": "http://apps.who.int/classifications/icd10/browse/2010/en#/$1"
},
"iceberg.element": {
"description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements.",
"example": "100",
"homepage": "http://db-mml.sjtu.edu.cn/ICEberg/",
"name": "ICEberg element at Shanghai Jiaotong University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1"
},
"iceberg.family": {
"description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families.",
"example": "1",
"homepage": "http://db-mml.sjtu.edu.cn/ICEberg/",
"name": "ICEberg family at Shanghai Jiaotong University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$1"
},
"ideal": {
"description": "IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments.",
"example": "IID00001",
"homepage": "http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/",
"name": "IDEAL at Maebashi Institute of Technology",
"namespaceEmbeddedInLui": false,
"pattern": "^IID\\d+$",
"uri_format": "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/idealItem.php?id=$1"
},
"ido": {
"description": "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases.",
"example": "0000504",
"homepage": "https://www.ebi.ac.uk/ols/ontologies/ido",
"name": "IDO through OLS",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1"
},
"idoo": {
"description": "Identifiers.org Ontology",
"example": "DataCollection",
"homepage": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology",
"name": "Identifiers.org Ontology",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9a-zA-Z]+$",
"uri_format": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1"
},
"idot": {
"description": "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.",
"example": "identifierPattern",
"homepage": "https://identifiers.org/",
"name": "IdoT via biomodels.net",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z]+$",
"uri_format": "https://biomodels.net/vocab/idot.rdf#$1"
},
"igsn": {
"example": "SSH000SUA",
"homepage": "http://www.geosamples.org/",
"name": "International Geo Sample Number",
"namespaceEmbeddedInLui": false,
"uri_format": "hdl.handle.net/10273/$1"
},
"imex": {
"description": "The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources.",
"example": "IM-19210-3",
"homepage": "https://www.imexconsortium.org/",
"name": "IMEx Consortium running at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^IM-\\d+(-?)(\\d+?)$",
"uri_format": "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1"
},
"img.gene": {
"description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information.",
"example": "638309541",
"homepage": "http://img.jgi.doe.gov/",
"name": "Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1"
},
"img.taxon": {
"description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information.",
"example": "648028003",
"homepage": "http://img.jgi.doe.gov/",
"name": "Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1"
},
"imgt.hla": {
"description": "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature.",
"example": "A*01:01:01:01",
"homepage": "https://www.ebi.ac.uk/imgt/hla/allele.html",
"name": "IMGT HLA at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9*:]+$",
"uri_format": "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1"
},
"imgt.ligm": {
"description": "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates.",
"example": "M94112",
"homepage": "http://www.imgt.org/",
"name": "IMGT LIGM at CNRS",
"namespaceEmbeddedInLui": false,
"pattern": "^M\\d+$",
"uri_format": "http://www.imgt.org/ligmdb/view?id=$1"
},
"inchi": {
"description": "The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier.",
"example": "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3",
"homepage": "http://webbook.nist.gov/chemistry",
"name": "InChI through NIST",
"namespaceEmbeddedInLui": false,
"pattern": "^InChI\\=1S?\\/[A-Za-z0-9\\.]+(\\+[0-9]+)?(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,\\/\\?\\;\\.]+)*$",
"uri_format": "http://webbook.nist.gov/cgi/cbook.cgi?$1"
},
"inchikey": {
"description": "The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI.",
"example": "RYYVLZVUVIJVGH-UHFFFAOYSA-N",
"homepage": "http://cactus.nci.nih.gov/chemical/structure",
"name": "InChiKey resolver at NCI",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-Z])?",
"uri_format": "http://cactus.nci.nih.gov/chemical/structure/$1/names"
},
"insdc": {
"description": "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences.",
"example": "X58356",
"homepage": "https://www.ncbi.nlm.nih.gov/nuccore/",
"name": "INSDC through Nucleotide database at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$",
"uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1"
},
"insdc.cds": {
"description": "The coding sequence or protein identifiers as maintained in INSDC.",
"example": "AAA35559",
"homepage": "https://www.ncbi.nlm.nih.gov/protein/",
"name": "INSDC CDS through NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$",
"uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1"
},
"insdc.gca": {
"description": "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage.",
"example": "GCA_000155495.1",
"homepage": "https://www.ncbi.nlm.nih.gov/assembly/",
"name": "Genome assembly database NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^GCA_[0-9]{9}\\.[0-9]$",
"uri_format": "https://www.ncbi.nlm.nih.gov/assembly/$1"
},
"insdc.sra": {
"description": "The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.",
"example": "SRX000007",
"homepage": "https://www.ncbi.nlm.nih.gov/sra",
"name": "Sequence Read Archive at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^[SED]R[APRSXZ]\\d+$",
"uri_format": "https://www.ncbi.nlm.nih.gov/sra/$1"
},
"intact": {
"description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data.",
"example": "EBI-2307691",
"homepage": "https://www.ebi.ac.uk/intact/",
"name": "IntAct at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^EBI\\-[0-9]+$",
"uri_format": "https://www.ebi.ac.uk/intact/interaction/$1"
},
"intact.molecule": {
"description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules.",
"example": "EBI-366083",
"homepage": "https://www.ebi.ac.uk/intact/",
"name": "IntAct Molecule at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^EBI\\-[0-9]+$",
"uri_format": "https://www.ebi.ac.uk/intact/molecule/$1"
},
"interpro": {
"description": "InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.",
"example": "IPR000100",
"homepage": "https://www.ebi.ac.uk/interpro/",
"name": "InterPro",
"namespaceEmbeddedInLui": false,
"pattern": "^IPR\\d{6}$",
"uri_format": "https://www.ebi.ac.uk/interpro/entry/$1"
},
"ird.segment": {
"description": "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s).",
"example": "CY077097",
"homepage": "http://www.fludb.org/",
"name": "IRD at BioHealthBase",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$",
"uri_format": "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1"
},
"irefweb": {
"description": "iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.",
"example": "617102",
"homepage": "http://wodaklab.org/iRefWeb/",
"name": "iRefWeb Protein Interaction Reference Index",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://wodaklab.org/iRefWeb/interaction/show/$1"
},
"isbn": {
"description": "The International Standard Book Number (ISBN) is for identifying printed books.",
"example": "9781584885658",
"homepage": "http://isbndb.com/",
"name": "ISBNDB - ISBN Database",
"namespaceEmbeddedInLui": false,
"pattern": "^(ISBN)?(-13|-10)?[:]?[ ]?(\\d{2,3}[ -]?)?\\d{1,5}[ -]?\\d{1,7}[ -]?\\d{1,6}[ -]?(\\d|X)$",
"uri_format": "http://isbndb.com/search-all.html?kw=$1"
},
"isfinder": {
"description": "ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available.",
"example": "ISA1083-2",
"homepage": "http://www-is.biotoul.fr/i",
"name": "IS Finder at CNRS",
"namespaceEmbeddedInLui": false,
"pattern": "^IS\\w+(\\-\\d)?$",
"uri_format": "https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1"
},
"isni": {
"description": "ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC. The mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described.",
"example": "000000012281955X",
"homepage": "http://www.isni.org",
"name": "International Standard Name Identifier",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]{15}[0-9X]{1}$",
"uri_format": "http://www.isni.org/isni/$1"
},
"issn": {
"description": "The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books.",
"example": "1776-3045",
"homepage": "https://portal.issn.org",
"name": "ISSN Portal",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{4}-\\d{3}[\\dX]$",
"uri_format": "https://portal.issn.org/resource/ISSN/$1"
},
"iuphar.family": {
"description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits.",
"example": "78",
"homepage": "http://www.guidetopharmacology.org/",
"name": "The IUPHAR/BPS Guide to PHARMACOLOGY",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1"
},
"iuphar.ligand": {
"description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands.",
"example": "1755",
"homepage": "http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all",
"name": "IUPHAR ligand at University of Edinburgh",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1"
},
"iuphar.receptor": {
"description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits.",
"example": "101",
"homepage": "http://www.guidetopharmacology.org/targets.jsp",
"name": "IUPHAR Receptor at University of Edinburgh",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1"
},
"jaxmice": {
"description": "JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory.",
"example": "005012",
"homepage": "http://jaxmice.jax.org/",
"name": "JAX Mice at Jackson Laboratory",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://jaxmice.jax.org/strain/$1.html"
},
"jcggdb": {
"description": "JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc.",
"example": "JCGG-STR008690",
"homepage": "http://jcggdb.jp/index_en.html",
"name": "JCGGDB at Advanced Science Institute (Japan)",
"namespaceEmbeddedInLui": false,
"pattern": "^JCGG-STR\\d{6}$",
"uri_format": "http://jcggdb.jp/idb/jcggdb/$1"
},
"jcm": {
"description": "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2.",
"example": "17254",
"homepage": "http://www.jcm.riken.go.jp/",
"name": "JCM at RIKEN BioResource Center",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1"
},
"jcsd": {
"description": "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST).",
"example": "J55.713G",
"homepage": "http://jglobal.jst.go.jp/en/",
"name": "Japan Chemical Substance Dictionary",
"namespaceEmbeddedInLui": false,
"pattern": "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$",
"uri_format": "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1"
},
"jstor": {
"description": "JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration.",
"example": "3075966",
"homepage": "http://www.jstor.org/",
"name": "JSTOR Online",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.jstor.org/stable/$1"
},
"jws": {
"description": "JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser.",
"example": "curien",
"homepage": "http://jjj.mib.ac.uk/index.html",
"name": "JWS Online Model Repository at Manchester",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://jjj.mib.ac.uk/models/$1"
},
"kaggle": {
"description": "Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions.",
"example": "nasa/kepler-exoplanet-search-results",
"homepage": "https://kaggle.com",
"name": "Kaggle",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9a-zA-Z\\-]+\\/[0-9a-zA-Z\\-]+$",
"uri_format": "https://www.kaggle.com/$1"
},
"kegg": {
"description": "Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.",
"example": "hsa00190",
"homepage": "http://www.kegg.jp/",
"name": "KEGG at Kyoto University Bioinformatics Center",
"namespaceEmbeddedInLui": false,
"pattern": "^([CHDEGTMKR]\\d+)|(\\w+:[\\w\\d\\.-]*)|([a-z]{3,5})|(\\w{2,4}\\d{5})$",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"kegg.compound": {
"description": "KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life.",
"example": "C12345",
"homepage": "https://www.genome.jp/kegg/ligand.html",
"name": "KEGG LIGAND Database",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d+$",
"uri_format": "https://www.kegg.jp/entry/$1"
},
"kegg.disease": {
"description": "The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system.",
"example": "H00076",
"homepage": "http://www.genome.jp/kegg/disease/",
"name": "KEGG Disease at Kyoto University Bioinformatics Center",
"namespaceEmbeddedInLui": false,
"pattern": "^H\\d+$",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"kegg.drug": {
"description": "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules.",
"example": "D00123",
"homepage": "https://www.genome.jp/kegg/drug/",
"name": "KEGG DRUG Database",
"namespaceEmbeddedInLui": false,
"pattern": "^D\\d+$",
"uri_format": "https://www.kegg.jp/entry/$1"
},
"kegg.environ": {
"description": "KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable.",
"example": "ev:E00032",
"homepage": "http://www.genome.jp/kegg/drug/environ.html",
"name": "KEGG ENVIRON Database",
"namespaceEmbeddedInLui": false,
"pattern": "^(ev\\:)?E\\d+$",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"kegg.genes": {
"description": "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources.",
"example": "syn:ssr3451",
"homepage": "http://www.genome.jp/kegg/genes.html",
"name": "KEGG GENES Database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+:[\\w\\d\\.-]*$",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"kegg.genome": {
"description": "KEGG Genome is a collection of organisms whose genomes have been completely sequenced.",
"example": "eco",
"homepage": "http://www.genome.jp/kegg/catalog/org_list.html",
"name": "KEGG Genome Database",
"namespaceEmbeddedInLui": false,
"pattern": "^(T0\\d+|\\w{3,5})$",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"kegg.glycan": {
"description": "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways.",
"example": "G00123",
"homepage": "https://www.genome.jp/kegg/glycan/",
"name": "KEGG GLYCAN Database",
"namespaceEmbeddedInLui": false,
"pattern": "^G\\d+$",
"uri_format": "https://www.kegg.jp/entry/$1"
},
"kegg.metagenome": {
"description": "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species.",
"example": "T30002",
"homepage": "http://www.genome.jp/kegg/catalog/org_list3.html",
"name": "KEGG Metagenome Database",
"namespaceEmbeddedInLui": false,
"pattern": "^T3\\d+$",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"kegg.module": {
"description": "KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules.",
"example": "M00002",
"homepage": "http://www.kegg.jp/kegg/module.html",
"name": "KEGG Module at Kyoto University Bioinformatics Center",
"namespaceEmbeddedInLui": false,
"pattern": "^([a-z]{3,5}_)?M\\d{5}$",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"kegg.orthology": {
"description": "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms.",
"example": "K00001",
"homepage": "http://www.genome.jp/kegg/ko.html",
"name": "KEGG Orthology Database",
"namespaceEmbeddedInLui": false,
"pattern": "^K\\d+$",
"uri_format": "http://www.kegg.jp/entry/$1"
},
"kegg.pathway": {
"description": "KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.",
"example": "hsa00620",
"homepage": "https://www.genome.jp/kegg/pathway.html",
"name": "KEGG PATHWAY Database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{2,4}\\d{5}$",
"uri_format": "https://www.kegg.jp/entry/$1"
},
"kegg.reaction": {
"description": "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life.",
"example": "R00100",
"homepage": "https://www.genome.jp/kegg/reaction/",
"name": "KEGG Reaction Database",
"namespaceEmbeddedInLui": false,
"pattern": "^R\\d+$",
"uri_format": "https://www.kegg.jp/entry/$1"
},
"knapsack": {
"description": "Knapsack provides information on metabolites and the taxonomic class with which they are associated.",
"example": "C00000001",
"homepage": "http://kanaya.aist-nara.ac.jp/KNApSAcK/",
"name": "KnapSack at Nara Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d{8}",
"uri_format": "http://kanaya.naist.jp/knapsack_jsp/information.jsp?word=$1"
},
"lei": {
"description": "Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland.",
"example": "HWUPKR0MPOU8FGXBT394",
"homepage": "https://www.gleif.org/",
"name": "Global LEI Index",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$",
"uri_format": "https://www.gleif.org/lei/$1"
},
"lgic": {
"description": "The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available.",
"example": "5HT3Arano",
"homepage": "https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php",
"name": "Ligand-Gated Ion Channel database at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php"
},
"licebase": {
"description": "Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects.",
"example": "EMLSAT00000003403",
"homepage": "https://licebase.org",
"name": "LiceBase",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9\\-\\/]+$",
"uri_format": "https://licebase.org/?q=$1"
},
"ligandbook": {
"description": "Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community.",
"example": "785",
"homepage": "https://ligandbook.org/",
"name": "LigandBook",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"uri_format": "https://ligandbook.org/package/$1"
},
"ligandbox": {
"description": "LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds.",
"example": "D00001",
"homepage": "http://ligandbox.protein.osaka-u.ac.jp/ligandbox//cgi-bin/index.cgi?LANG=en",
"name": "LigandBox at",
"namespaceEmbeddedInLui": false,
"pattern": "^D\\d{5}",
"uri_format": "http://ligandbox.protein.osaka-u.ac.jp/ligandbox/cgi-bin/liginf.cgi?id=$1"
},
"ligandexpo": {
"description": "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.",
"example": "ABC",
"homepage": "http://ligand-expo.rcsb.org/",
"name": "Ligand Expo at Rutgers",
"namespaceEmbeddedInLui": false,
"pattern": "^(\\w){3}$",
"uri_format": "http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid"
},
"lincs.cell": {
"description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.",
"example": "LCL-2085",
"homepage": "http://lincsportal.ccs.miami.edu/cells/",
"name": "LINCS Portal",
"namespaceEmbeddedInLui": false,
"pattern": "(^LCL-\\d+$)|(^LDC-\\d+$)|(^ES-\\d+$)|(^LSC-\\d+$)|(^LPC-\\d+$)",
"uri_format": "http://lincsportal.ccs.miami.edu/cells/#/view/$1"
},
"lincs.data": {
"description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level).",
"example": "LDS-1110",
"homepage": "http://lincsportal.ccs.miami.edu/datasets/",
"name": "LINCS Data at University of Miami",
"namespaceEmbeddedInLui": false,
"pattern": "^[EL]D[SG]-\\d+$",
"uri_format": "http://lincsportal.ccs.miami.edu/datasets/#/view/$1"
},
"lincs.protein": {
"description": "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins.",
"example": "200282",
"homepage": "http://lincs.hms.harvard.edu/db/proteins/",
"name": "LINCS Protein at Harvard Medical School",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://lincs.hms.harvard.edu/db/proteins/$1/"
},
"lincs.smallmolecule": {
"description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC).",
"example": "LSM-6306",
"homepage": "http://lincsportal.ccs.miami.edu/SmallMolecules/",
"name": "LINCS Portal",
"namespaceEmbeddedInLui": false,
"pattern": "^LSM-\\d+$",
"uri_format": "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1"
},
"lipidbank": {
"description": "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.",
"example": "BBA0001",
"homepage": "http://lipidbank.jp/index.html",
"name": "LipidBank the Lipid database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+\\d+$",
"uri_format": "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1"
},
"lipidmaps": {
"description": "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.",
"example": "LMPR0102010012",
"homepage": "http://www.lipidmaps.org",
"name": "Department of Bioengineering and the San Diego Supercomputer Center",
"namespaceEmbeddedInLui": false,
"pattern": "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$",
"uri_format": "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1"
},
"lrg": {
"description": "Locus Reference Genomic (LRG) provides identifiers to stable genomic DNA sequences for regions of the human genome, providing a recognized reference-sequence standard for reporting sequence variants. LRG is maintained by the NCBI and the European Bioinformatics Institute (EBI).",
"example": "LRG_1",
"homepage": "http://uswest.ensembl.org/",
"name": "Locus Reference Genomic through Ensembl mirror (US west)",
"namespaceEmbeddedInLui": false,
"pattern": "^LRG_\\d+$",
"uri_format": "http://uswest.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1"
},
"ma": {
"description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)",
"example": "0002502",
"homepage": "http://www.informatics.jax.org/",
"name": "Mouse Adult Gross Anatomy at The Jackson Laboratory",
"namespaceEmbeddedInLui": true,
"pattern": "^MA:\\d+$",
"uri_format": "http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1"
},
"macie": {
"description": "MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved.",
"example": "M0001",
"homepage": "https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html",
"name": "MACiE database of mechanisms, annotation and classification in enzymes",
"namespaceEmbeddedInLui": false,
"pattern": "^M\\d{4}$",
"uri_format": "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1"
},
"maizegdb.locus": {
"description": "MaizeGDB is the maize research community's central repository for genetics and genomics information.",
"example": "25011",
"homepage": "http://www.maizegdb.org/",
"name": "MaizeGDB at Missouri",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1"
},
"mamo": {
"description": "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.",
"example": "MAMO_0000026",
"homepage": "http://bioportal.bioontology.org/ontologies/MAMO",
"name": "MAMO through BioPortal",
"namespaceEmbeddedInLui": false,
"pattern": "^MAMO_\\d{7}$",
"uri_format": "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/$1"
},
"massbank": {
"description": "MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da).",
"example": "PB000166",
"homepage": "http://www.massbank.jp",
"name": "MassBank in Japan",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]{2}[A-Z0-9][0-9]{5}$",
"uri_format": "http://www.massbank.jp/jsp/FwdRecord.jsp?id=$1"
},
"massive": {
"description": "MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data.",
"example": "MSV000082131",
"homepage": "https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp",
"name": "MassIVE",
"namespaceEmbeddedInLui": false,
"pattern": "^MSV\\d+$",
"uri_format": "https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1"
},
"matrixdb.association": {
"description": "MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations.",
"example": "P00747__P07355",
"homepage": "http://matrixdb.univ-lyon1.fr/",
"name": "MatrixDB Association",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$",
"uri_format": "http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association"
},
"mdm": {
"description": "The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems.",
"example": "4776",
"homepage": "https://medical-data-models.org/",
"name": "MDM at University of Muenster",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://medical-data-models.org/forms/$1"
},
"meddra": {
"description": "The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT).",
"example": "10015919",
"homepage": "http://bioportal.bioontology.org/ontologies/MEDDRA",
"name": "MedDRA through BioPortal",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://purl.bioontology.org/ontology/MEDDRA/$1"
},
"medgen": {
"description": "MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder.",
"example": "760050",
"homepage": "https://www.ncbi.nlm.nih.gov/medgen/",
"name": "MedGen at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^[CN]*\\d{4,7}$",
"uri_format": "https://www.ncbi.nlm.nih.gov/medgen/$1"
},
"medlineplus": {
"description": "MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language.",
"example": "002804",
"homepage": "http://www.nlm.nih.gov/medlineplus/",
"name": "MedlinePlus at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm"
},
"merops.family": {
"description": "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families.",
"example": "S1",
"homepage": "http://merops.sanger.ac.uk/index.htm",
"name": "Merops Family at Sanger Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^[SCTAGMNU]\\d+$",
"uri_format": "http://merops.sanger.ac.uk/cgi-bin/famsum?family=$1"
},
"merops.inhibitor": {
"description": "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors.",
"example": "I31.952",
"homepage": "http://merops.sanger.ac.uk/index.htm",
"name": "MEROPS Inhibitor at Sanger Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^I\\d{2}\\.\\d{3}$",
"uri_format": "http://merops.sanger.ac.uk/cgi-bin/pepsum?id=$1"
},
"mesh": {
"description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc.",
"example": "C000100",
"homepage": "http://id.nlm.nih.gov/mesh/",
"name": "MeSH Linked Data at National Library of Medicine",
"namespaceEmbeddedInLui": false,
"pattern": "^(C|D)\\d{6}$",
"uri_format": "http://id.nlm.nih.gov/mesh/$1"
},
"mesh.2012": {
"description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012.",
"example": "17186",
"homepage": "http://www.nlm.nih.gov/mesh/",
"name": "MeSH at National Library of Medicine",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9]+$",
"uri_format": "http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded"
},
"mesh.2013": {
"description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013.",
"example": "17165",
"homepage": "http://www.nlm.nih.gov/mesh/",
"name": "MeSH 2013 at National Library of Medicine",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9]+$",
"uri_format": "http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded"
},
"metabolights": {
"description": "MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies.",
"example": "MTBLS1",
"homepage": "https://www.ebi.ac.uk/metabolights/",
"name": "MetaboLights at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^MTBLS\\d+$",
"uri_format": "https://www.ebi.ac.uk/metabolights/$1"
},
"metacyc.compound": {
"description": "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.",
"example": "CPD-10330",
"homepage": "https://metacyc.org",
"name": "MetaCyc Metabolic Pathway Database",
"namespaceEmbeddedInLui": false,
"pattern": "^CPD-\\d{5}$",
"uri_format": "https://metacyc.org/compound?orgid=META&id=$1"
},
"metacyc.reaction": {
"description": "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.",
"example": "RXN-14904",
"homepage": "https://metacyc.org",
"name": "MetaCyc Metabolic Pathway Database - Reaction",
"namespaceEmbeddedInLui": false,
"pattern": "^RXN-\\d{5}$",
"uri_format": "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1"
},
"metanetx.chemical": {
"description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components.",
"example": "MNXM1723",
"homepage": "http://www.metanetx.org/",
"name": "MetaNetX chemical at SIB Swiss Institute of Bioinformatics",
"namespaceEmbeddedInLui": false,
"pattern": "^(MNXM\\d+|BIOMASS)$",
"uri_format": "https://www.metanetx.org/chem_info/$1"
},
"metanetx.compartment": {
"description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments.",
"example": "MNXC15",
"homepage": "http://www.metanetx.org/",
"name": "MetaNetX compartment at SIB Swiss Institute of Bioinformatics",
"namespaceEmbeddedInLui": false,
"pattern": "^(MNX[CD]\\d+|BOUNDARY)$",
"uri_format": "http://www.metanetx.org/comp_info/$1"
},
"metanetx.reaction": {
"description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions.",
"example": "MNXR101574",
"homepage": "http://www.metanetx.org/",
"name": "MetaNetX reaction at SIB Swiss Institute of Bioinformatics",
"namespaceEmbeddedInLui": false,
"pattern": "^MNXR\\d+$",
"uri_format": "http://www.metanetx.org/equa_info/$1"
},
"metlin": {
"description": "The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry.",
"example": "1455",
"homepage": "http://masspec.scripps.edu/",
"name": "METLIN at Scripps Center, Molecular Biology and Center for Mass Spectrometry, La Jolla",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{4}$",
"uri_format": "http://metlin.scripps.edu/metabo_info.php?molid=$1"
},
"mex": {
"description": "A public place to process, interpret and share GC/MS metabolomics datasets.",
"example": "36",
"homepage": "https://www.metabolome-express.org/",
"name": "Metabolome Express",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://www.metabolome-express.org/datasetview.php?datasetid=$1"
},
"mge": {
"description": "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.",
"example": "2",
"homepage": "http://aclame.ulb.ac.be/",
"name": "Aclame database of mobile genetic elements",
"namespaceEmbeddedInLui": true,
"pattern": "^mge:\\d+$",
"uri_format": "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1"
},
"mgi": {
"description": "The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.",
"example": "2442292",
"homepage": "http://www.informatics.jax.org/",
"name": "Mouse Genome Informatics Database",
"namespaceEmbeddedInLui": true,
"pattern": "^MGI:\\d+$",
"uri_format": "http://www.informatics.jax.org/accession/MGI:$1"
},
"mgnify.proj": {
"description": "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.",
"example": "ERP004492",
"homepage": "https://www.ebi.ac.uk/metagenomics",
"name": "MGnify Project",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]+[0-9]+$",
"uri_format": "https://www.ebi.ac.uk/metagenomics/projects/$1"
},
"mgnify.samp": {
"description": "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.",
"example": "SRS086444",
"homepage": "https://www.ebi.ac.uk/metagenomics",
"name": "MGnify Sample",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]+[0-9]+$",
"uri_format": "https://www.ebi.ac.uk/metagenomics/samples/$1"
},
"microscope": {
"description": "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis.",
"example": "5601141",
"homepage": "http://www.genoscope.cns.fr/agc/microscope",
"name": "MicroScope",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1"
},
"microsporidia": {
"description": "MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"example": "ECU03_0820i",
"homepage": "http://microsporidiadb.org/micro/",
"name": "MicrosporidiaDB at EuPathDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"
},
"mim": {
"description": "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.",
"example": "603903",
"homepage": "https://omim.org/",
"name": "OMIM at John Hopkins",
"namespaceEmbeddedInLui": false,
"pattern": "^[*#+%^]?\\d{6}$",
"uri_format": "https://omim.org/entry/$1"
},
"mimodb": {
"description": "MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank.",
"example": "1",
"homepage": "http://immunet.cn/bdb/",
"name": "BDB at University of Electronic Science and Technology of China",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://immunet.cn/bdb/index.php/mimoset/$1"
},
"minid": {
"description": "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation.",
"example": "b97957",
"homepage": "http://minid.bd2k.org",
"name": "Minimal Identifiers for Transient Data",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9]+$",
"uri_format": "http://n2t.net/ark:/57799/$1"
},
"mint": {
"description": "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals.",
"example": "MINT-7905142",
"homepage": "https://www.ebi.ac.uk/intact/",
"name": "MINT subset through IntAct",
"namespaceEmbeddedInLui": false,
"pattern": "^MINT\\-\\d{1,7}$",
"uri_format": "https://www.ebi.ac.uk/intact/query/interaction_id:$1"
},
"mipmod": {
"description": "MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures.",
"example": "HOSAPI0399",
"homepage": "http://bioinfo.iitk.ac.in/MIPModDB",
"name": "MIPModDB at Indian Institute of Technology Kanpur",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1"
},
"mir": {
"description": "The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or \"PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources.",
"example": "00100037",
"homepage": "https://identifiers.org/registry",
"name": "Identifiers.org Registry through EBI",
"namespaceEmbeddedInLui": true,
"pattern": "^MIR:\\d{8}$",
"uri_format": "https://identifiers.org/registry?query=\"MIR:$1\""
},
"mirbase": {
"description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR).",
"example": "MI0000001",
"homepage": "http://www.mirbase.org/",
"name": "miRBase Sequence Database",
"namespaceEmbeddedInLui": false,
"pattern": "MI\\d{7}",
"uri_format": "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1"
},
"mirbase.mature": {
"description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence.",
"example": "MIMAT0000001",
"homepage": "http://www.mirbase.org/",
"name": "miRBase",
"namespaceEmbeddedInLui": false,
"pattern": "MIMAT\\d{7}",
"uri_format": "http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1"
},
"mirex": {
"description": "mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages.",
"example": "165a",
"homepage": "http://comgen.pl/mirex/?page=home",
"name": "mirEX at Adam Mickiewicz University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+(\\w+)?$",
"uri_format": "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes"
},
"miriam.collection": {
"description": "MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections.",
"example": "MIR:00000008",
"homepage": "https://www.ebi.ac.uk/miriam/",
"name": "MIRIAM Resources (data collection)",
"namespaceEmbeddedInLui": false,
"pattern": "^MIR:000\\d{5}$",
"uri_format": "https://www.ebi.ac.uk/miriam/main/$1"
},
"miriam.resource": {
"description": "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases.",
"example": "MIR:00100005",
"homepage": "https://www.ebi.ac.uk/miriam/",
"name": "MIRIAM Registry (resources)",
"namespaceEmbeddedInLui": false,
"pattern": "^MIR:001\\d{5}$",
"uri_format": "https://www.ebi.ac.uk/miriam/main/resources/$1"
},
"mirnest": {
"description": "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species.",
"example": "MNEST029358",
"homepage": "http://rhesus.amu.edu.pl/mirnest/copy/",
"name": "miRNEST at Adam Mickiewicz University",
"namespaceEmbeddedInLui": false,
"pattern": "^MNEST\\d+$",
"uri_format": "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1"
},
"mirtarbase": {
"description": "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments.",
"example": "MIRT000002",
"homepage": "http://mirtarbase.mbc.nctu.edu.tw/",
"name": "miRTarBase at National Chiao Tung University",
"namespaceEmbeddedInLui": false,
"pattern": "^MIRT\\d{6}$",
"uri_format": "http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1"
},
"mmdb": {
"description": "The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites.",
"example": "50885",
"homepage": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure",
"name": "MMDB at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{1,5}$",
"uri_format": "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1"
},
"mmp.cat": {
"description": "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples.",
"example": "MMP743597.11",
"homepage": "https://mmp.sfb.uit.no/databases/marcat/",
"name": "MarCat through SfB",
"namespaceEmbeddedInLui": false,
"pattern": "^MMP\\d+.\\d+$",
"uri_format": "https://mmp.sfb.uit.no/databases/marcat/#/records/$1"
},
"mmp.db": {
"description": "MarDB includes all sequenced marine microbial genomes regardless of level of completeness.",
"example": "MMP02954345.1",
"homepage": "https://mmp.sfb.uit.no/databases/mardb/",
"name": "MarDB through SfB",
"namespaceEmbeddedInLui": false,
"pattern": "^MMP\\d+.\\d+$",
"uri_format": "https://mmp.sfb.uit.no/databases/mardb/#/records/$1"
},
"mmp.ref": {
"description": "MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes.",
"example": "MMP3312982.2",
"homepage": "https://mmp.sfb.uit.no/databases/marref/",
"name": "MarRef through SfB",
"namespaceEmbeddedInLui": false,
"pattern": "^MMP\\d+.\\d+$",
"uri_format": "https://mmp.sfb.uit.no/databases/marref/#/records/$1"
},
"mmrrc": {
"description": "The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections.",
"example": "70",
"homepage": "http://www.mmrrc.org/",
"name": "MMRRC at University of North Carolina",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1"
},
"mo": {
"description": "The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data.",
"example": "ArrayGroup",
"homepage": "http://bioportal.bioontology.org/",
"name": "MGED Ontology at BioPortal",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://purl.bioontology.org/ontology/MO/$1"
},
"mobidb": {
"description": "MobiDB is a database of protein disorder and mobility annotations.",
"example": "P10636",
"homepage": "http://mobidb.bio.unipd.it",
"name": "MobiDB",
"namespaceEmbeddedInLui": false,
"pattern": "^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$",
"uri_format": "http://mobidb.bio.unipd.it/$1"
},
"mod": {
"description": "The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications.",
"example": "00001",
"homepage": "http://bioportal.bioontology.org/ontologies/PSIMOD",
"name": "Protein modifications ontology through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^MOD:\\d{5}",
"uri_format": "http://bioportal.bioontology.org/ontologies/1041?p=terms&conceptid=MOD:$1"
},
"modeldb": {
"description": "ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment.",
"example": "45539",
"homepage": "http://senselab.med.yale.edu/ModelDB/",
"name": "ModelDB at SenseLab",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1"
},
"molbase": {
"description": "Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier.",
"example": "128796-39-4",
"homepage": "http://www.molbase.com/",
"name": "Molbase at Chinese Academy of Sciences",
"namespaceEmbeddedInLui": false,
"pattern": "^(\\d{1,7}\\-\\d{2}\\-\\d)|([A-Za-z0-9\\+\\-\\_]+)$",
"uri_format": "http://www.molbase.com/en/index.php?app=search&search_keyword=$1"
},
"mp": {
"description": "The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways.",
"example": "0005452",
"homepage": "https://bioportal.bioontology.org/ontologies/MP",
"name": "Mammalian Phenotype Ontology through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^MP:\\d{7}$",
"uri_format": "https://bioportal.bioontology.org/ontologies/MP/MP:$1"
},
"mpid": {
"description": "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts.",
"example": "172",
"homepage": "http://www.jcvi.org/mpidb/about.php",
"name": "Microbial Protein Interaction Database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1"
},
"ms": {
"description": "The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance.",
"example": "1000001",
"homepage": "https://bioportal.bioontology.org/ontologies/MS",
"name": "Mass Spectrometry Controlled Vocabulary through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^MS:\\d{7}$",
"uri_format": "http://purl.bioontology.org/ontology/MS/MS:$1"
},
"multicellds.cell_line": {
"description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.",
"example": "MCDS_L_0000000001",
"homepage": "http://multicellds.org/MultiCellDB.php",
"name": "MultiCellDS Digital Cell Line at Keck School of Medicine",
"namespaceEmbeddedInLui": false,
"pattern": "^MCDS_L_[a-zA-Z0-9]{1,10}$",
"uri_format": "http://multicellds.org/MultiCellDB/$1"
},
"multicellds.collection": {
"description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections).",
"example": "MCDS_C_0000000001",
"homepage": "http://multicellds.org/MultiCellDB.php",
"name": "MultiCellDScollection at Keck School of Medicine",
"namespaceEmbeddedInLui": false,
"pattern": "^MCDS_C_[a-zA-Z0-9]{1,10}$",
"uri_format": "http://multicellds.org/MultiCellDB/$1"
},
"multicellds.snapshot": {
"description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data.",
"example": "MCDS_S_0000000001",
"homepage": "http://multicellds.org/MultiCellDB.php",
"name": "MultiCellDS snapshot at Keck School of Medicine",
"namespaceEmbeddedInLui": false,
"pattern": "^MCDS_S_[a-zA-Z0-9]{1,10}$",
"uri_format": "http://multicellds.org/MultiCellDB/$1"
},
"mw.project": {
"description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).",
"example": "PR000001",
"homepage": "http://www.metabolomicsworkbench.org/",
"name": "Metabolomics Workbench Project",
"namespaceEmbeddedInLui": false,
"pattern": "^PR[0-9]{6}$",
"uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1"
},
"mw.study": {
"description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).",
"example": "ST000900",
"homepage": "http://www.metabolomicsworkbench.org/",
"name": "Metabolomics Workbench Study",
"namespaceEmbeddedInLui": false,
"pattern": "^ST[0-9]{6}$",
"uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1"
},
"myco.lepra": {
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.",
"example": "ML0224",
"homepage": "http://mycobrowser.epfl.ch/leprosy.html",
"name": "MycoBrowser leprae at Global Health Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^ML\\w+$",
"uri_format": "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1"
},
"myco.marinum": {
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information.",
"example": "MMAR_2462",
"homepage": "http://mycobrowser.epfl.ch/marinolist.html",
"name": "MycoBrowser marinum at Global Health Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^MMAR\\_\\d+$",
"uri_format": "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1"
},
"myco.smeg": {
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.",
"example": "MSMEG_3769",
"homepage": "http://mycobrowser.epfl.ch/smegmalist.html",
"name": "MycoBrowser smegmatis at Global Health Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^MSMEG\\w+$",
"uri_format": "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1"
},
"myco.tuber": {
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information.",
"example": "Rv1908c",
"homepage": "http://tuberculist.epfl.ch/",
"name": "MycoBrowser tuberculosis at Global Health Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^Rv\\d{4}(A|B|c)?$",
"uri_format": "http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1"
},
"mycobank": {
"description": "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.",
"example": "349124",
"homepage": "http://www.mycobank.org/",
"name": "MycoBank at Fungal Biodiversity Centre",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1"
},
"mzspec": {
"description": "The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it.",
"example": "PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2",
"homepage": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum",
"name": "Universal Spectrum Identifier through Peptide Atlas",
"namespaceEmbeddedInLui": true,
"pattern": "^mzspec:.+$",
"uri_format": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum?usi=mzspec:$1"
},
"napdi": {
"description": "The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs).",
"example": "28",
"homepage": "https://repo.napdi.org/",
"name": "Natural Product-Drug Interaction Research Data Repository",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"uri_format": "https://repo.napdi.org/study/$1"
},
"napp": {
"description": "NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters.",
"example": "351",
"homepage": "http://napp.u-psud.fr/",
"name": "NAPP at CNRS",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1"
},
"narcis": {
"description": "NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases.",
"example": "oai:cwi.nl:4725",
"homepage": "http://www.narcis.nl/?Language=en",
"name": "NARCIS at The Hague",
"namespaceEmbeddedInLui": false,
"pattern": "^oai\\:cwi\\.nl\\:\\d+$",
"uri_format": "http://www.narcis.nl/publication/RecordID/$1"
},
"nasc": {
"description": "The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.",
"example": "N1899",
"homepage": "http://arabidopsis.info/",
"name": "NASC at University of Nottingham",
"namespaceEmbeddedInLui": false,
"pattern": "^(\\w+)?\\d+$",
"uri_format": "http://arabidopsis.info/StockInfo?NASC_id=$1"
},
"nbn": {
"description": "The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier.",
"example": "urn:nbn:fi:tkk-004781",
"homepage": "http://nbn-resolving.org/resolve_urn.htm",
"name": "NBN through URN Resolver at German National Library",
"namespaceEmbeddedInLui": false,
"pattern": "^urn\\:nbn\\:[A-Za-z_0-9]+\\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$",
"uri_format": "http://nbn-resolving.org/resolver?identifier=urn:nbn:$1&verb=redirect"
},
"nbrc": {
"description": "NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information.",
"example": "00001234",
"homepage": "http://www.nbrc.nite.go.jp/e/index.html",
"name": "NBRC Catalogue at National Institute of Technology Evaluation",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1"
},
"ncbigene": {
"description": "Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis.",
"example": "100010",
"homepage": "https://www.ncbi.nlm.nih.gov/gene",
"name": "Entrez Gene (NCBI)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://www.ncbi.nlm.nih.gov/gene/$1"
},
"ncbiprotein": {
"description": "The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.",
"example": "CAA71118.1",
"homepage": "https://www.ncbi.nlm.nih.gov/protein",
"name": "NCBI Protein at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^(\\w+\\d+(\\.\\d+)?)|(NP_\\d+)$",
"uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1"
},
"ncim": {
"description": "NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical.",
"example": "C0026339",
"homepage": "http://ncim.nci.nih.gov/",
"name": "NCIm at National Cancer Institue",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d+$",
"uri_format": "http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1"
},
"ncit": {
"description": "NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code.",
"example": "C80519",
"homepage": "http://ncit.nci.nih.gov/",
"name": "NCIt at National Cancer Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d+$",
"uri_format": "http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1"
},
"ndc": {
"description": "The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily.",
"example": "0002-1975-61",
"homepage": "http://www.accessdata.fda.gov/scripts/cder/ndc/",
"name": "National Drug Code at Food and Drug Administration",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+\\-\\d+\\-\\d+",
"uri_format": "http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1"
},
"neurolex": {
"description": "The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex).",
"example": "Birnlex_721",
"homepage": "http://www.neurolex.org/wiki/Main_Page",
"name": "NeuroLex Neuroscience Lexicon",
"namespaceEmbeddedInLui": false,
"pattern": "^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO|nifext_)\\d+$",
"uri_format": "http://www.neurolex.org/wiki/$1"
},
"neuromorpho": {
"description": "NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons.",
"example": "Rosa2",
"homepage": "http://neuromorpho.org/index.jsp",
"name": "NeuroMorpho",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://neuromorpho.org/neuron_info.jsp?neuron_name=$1"
},
"neurondb": {
"description": "NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.",
"example": "265",
"homepage": "http://senselab.med.yale.edu/NeuronDB/",
"name": "NeuronDB at SenseLab",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1"
},
"neurovault.collection": {
"description": "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images.",
"example": "3304",
"homepage": "http://neurovault.org",
"name": "NeuroVault Collection",
"namespaceEmbeddedInLui": false,
"pattern": "^[1-9][0-9]*$",
"uri_format": "https://neurovault.org/collections/$1"
},
"neurovault.image": {
"description": "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images.",
"example": "58788",
"homepage": "http://neurovault.org",
"name": "NeuroVault",
"namespaceEmbeddedInLui": false,
"pattern": "^[1-9][0-9]*$",
"uri_format": "https://neurovault.org/images/$1"
},
"nextdb": {
"description": "NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones.",
"example": "6b1",
"homepage": "http://nematode.lab.nig.ac.jp/",
"name": "NEXTDB at Shizuoka",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9]+$",
"uri_format": "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1"
},
"nextprot": {
"description": "neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases.",
"example": "NX_O00165",
"homepage": "https://www.nextprot.org/",
"name": "nextProt at Swiss Institute of Bioinformatics",
"namespaceEmbeddedInLui": false,
"pattern": "^NX_\\w+",
"uri_format": "https://www.nextprot.org/db/entry/$1"
},
"ngl": {
"description": "NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA.",
"example": "GLDS-141",
"homepage": "https://genelab-data.ndc.nasa.gov/genelab/",
"name": "NASA GeneLab",
"namespaceEmbeddedInLui": false,
"pattern": "^GLDS-\\d+$",
"uri_format": "https://genelab-data.ndc.nasa.gov/genelab/accession/$1"
},
"niaest": {
"description": "A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones.",
"example": "J0705A10",
"homepage": "http://lgsun.grc.nia.nih.gov/cDNA/",
"name": "NIAEST at National Institute on Aging",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w\\d{4}\\w\\d{2}(\\-[35])?$",
"uri_format": "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1"
},
"nmr": {
"description": "nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi.",
"example": "1000003",
"homepage": "https://www.ebi.ac.uk/ols/ontologies/nmrcv",
"name": "NMR through OLS",
"namespaceEmbeddedInLui": true,
"pattern": "^NMR:\\d+$",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1"
},
"noncodev3": {
"description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4.",
"example": "377550",
"homepage": "http://www.noncode.org/",
"name": "NONCODE at Chinese Academy of Sciences",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1"
},
"noncodev4.gene": {
"description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions.",
"example": "NONHSAG00001",
"homepage": "http://www.bioinfo.org/NONCODEv4/",
"name": "NONCODE v4 Gene at Chinese Academy of Sciences",
"namespaceEmbeddedInLui": false,
"pattern": "^NONHSAG\\d{5}$",
"uri_format": "http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1"
},
"noncodev4.rna": {
"description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts.",
"example": "NONHSAT000001",
"homepage": "http://www.bioinfo.org/NONCODEv4/",
"name": "NONCODE v4 Transcript at Chinese Academy of Sciences",
"namespaceEmbeddedInLui": false,
"pattern": "^NONHSAT\\d{6}$",
"uri_format": "http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1"
},
"norine": {
"description": "Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings.",
"example": "NOR00681",
"homepage": "http://bioinfo.lifl.fr/norine/",
"name": "NORINE at Computer Science Laboratory of Lille",
"namespaceEmbeddedInLui": false,
"pattern": "^NOR\\d+$",
"uri_format": "http://bioinfo.lifl.fr/norine/result.jsp?ID=$1"
},
"nuclearbd": {
"description": "NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs.",
"example": "prgr_human",
"homepage": "http://www.receptors.org/nucleardb/",
"name": "NucleaRDB at Radboud University Nijmegen Medical Centre",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+\\_\\w+$",
"uri_format": "http://www.receptors.org/nucleardb/proteins/$1"
},
"obi": {
"description": "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).",
"example": "OBI_0000070",
"homepage": "http://www.ontobee.org/",
"name": "OBI through Ontobee",
"namespaceEmbeddedInLui": false,
"pattern": "(^OBI:\\d{7}$)|(^OBI_\\d{7}$)",
"uri_format": "http://purl.obolibrary.org/obo/$1"
},
"occ": {
"description": "The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law.",
"example": "br/1",
"homepage": "https://w3id.org/oc/corpus",
"name": "OpenCitations Corpus",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z][a-z]/[0-9]+$",
"uri_format": "https://w3id.org/oc/corpus/$1"
},
"oci": {
"description": "Each OCI (Open Citation Identifier) has a simple structure: oci:number-number, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/ for additional information. OCIs for citations stored within the OpenCitations Corpus are constructed by combining the OpenCitations Corpus local identifiers for the citing and cited bibliographic resources, separating them with a dash. For example, oci:2544384-7295288 is a valid OCI for the citation between two papers stored within the OpenCitations Corpus. OCIs can also be created for bibliographic resources described in an external bibliographic database, if they are similarly identified there by identifiers having a unique numerical part. For example, the OCI for the citation that exists between Wikidata resources Q27931310 and Q22252312 is oci:01027931310–01022252312. OCIs can also be created for bibliographic resources described in external bibliographic database such as Crossref or DataCite where they are identified by alphanumeric Digital Object Identifiers (DOIs), rather than purely numerical strings.",
"example": "1-18",
"homepage": "http://opencitations.net",
"name": "OpenCitations",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+-[0-9]+$",
"uri_format": "https://w3id.org/oc/oci/$1"
},
"oclc": {
"description": "The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information.",
"example": "634515043",
"homepage": "https://www.oclc.org/en/about.html",
"name": "Online Computer Library Center (OCLC) WorldCat",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+$",
"uri_format": "https://www.worldcat.org/oclc/$1"
},
"odor": {
"description": "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors",
"example": "74",
"homepage": "http://senselab.med.yale.edu/OdorDB",
"name": "Odor Molecules DataBase at Yale University School of Medicine",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5"
},
"oid": {
"description": "OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes.",
"example": "2.16.840",
"homepage": "http://www.oid-info.com/introduction.htm",
"name": "OID Repository",
"namespaceEmbeddedInLui": false,
"pattern": "^[\\d.]+$",
"uri_format": "http://www.oid-info.com/cgi-bin/display?oid=$1&submit=Display&action=display"
},
"oma.grp": {
"description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs.",
"example": "LCSCCPN",
"homepage": "https://omabrowser.org/cgi-bin/gateway.pl",
"name": "OMA Group through OMA browser at ETH Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]+$",
"uri_format": "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1"
},
"oma.protein": {
"description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records.",
"example": "HUMAN16963",
"homepage": "https://omabrowser.org/cgi-bin/gateway.pl",
"name": "OMA Protein through OMA browser at ETH Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]{5}\\d+$",
"uri_format": "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1"
},
"omia": {
"description": "Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse).",
"example": "1000",
"homepage": "http://omia.angis.org.au/",
"name": "OMIA at University of Sydney",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://omia.angis.org.au/$1/"
},
"omit": {
"description": "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes).",
"example": "0005506",
"homepage": "https://www.ebi.ac.uk/ols/ontologies/omit/",
"name": "Ontology for miRNA Target (OMIT) through OLS",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{7}$",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$1"
},
"opb": {
"description": "The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.",
"example": "OPB_00573",
"homepage": "http://bioportal.bioontology.org/ontologies/OPB",
"name": "Ontology of Physics for Biology through Bioportal",
"namespaceEmbeddedInLui": false,
"pattern": "^OPB_\\d+$",
"uri_format": "http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23$1"
},
"opm": {
"description": "The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization.",
"example": "1h68",
"homepage": "http://opm.phar.umich.edu/",
"name": "OPM at University of Michigan",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9][A-Za-z0-9]{3}$",
"uri_format": "http://opm.phar.umich.edu/protein.php?pdbid=$1"
},
"orcid": {
"description": "ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities.",
"example": "0000-0002-5355-2576",
"homepage": "https://orcid.org",
"name": "ORCID at Bethesda",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$",
"uri_format": "https://orcid.org/$1"
},
"ordb": {
"description": "The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs).",
"example": "8497",
"homepage": "http://senselab.med.yale.edu/OrDB/",
"name": "Olfactory Receptor Database at Yale University School of Medicine",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://senselab.med.yale.edu/ORDB/Data/$1"
},
"oridb.sacch": {
"description": "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae.",
"example": "1",
"homepage": "http://cerevisiae.oridb.org/index.php",
"name": "OriDB Saccharomyces at University of Nottingham",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://cerevisiae.oridb.org/details.php?id=$1"
},
"oridb.schizo": {
"description": "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe.",
"example": "1",
"homepage": "http://pombe.oridb.org/index.php",
"name": "OriDB Schizosaccharomyces at University of Nottingham",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://pombe.oridb.org/details.php?id=$1"
},
"orphanet": {
"description": "Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases.",
"example": "85163",
"homepage": "http://www.orpha.net/consor/",
"name": "Orphanet at Inserm",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1"
},
"orphanet.ordo": {
"description": "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).",
"example": "Orphanet_C023",
"homepage": "https://www.ebi.ac.uk/ols/ontologies/ordo",
"name": "ORDO via OLS",
"namespaceEmbeddedInLui": false,
"pattern": "^Orphanet(_|:)C?\\d+$",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/ordo/terms?short_form=$1"
},
"orthodb": {
"description": "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups",
"example": "Q9P0K8",
"homepage": "http://cegg.unige.ch/orthodb4",
"name": "OrthoDB at Swiss Institute of Bioinformatics",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://cegg.unige.ch/orthodb/results?searchtext=$1"
},
"oryzabase.gene": {
"description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information.",
"example": "117",
"homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/",
"name": "Oryzabase v4 Gene at National Institute of Genetics (Japan)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1"
},
"oryzabase.mutant": {
"description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information.",
"example": "21393",
"homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/",
"name": "Oryzabase v4 Mutant at National Institute of Genetics (Japan)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1"
},
"oryzabase.reference": {
"description": "The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan.",
"example": "42840",
"homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/",
"name": "Oryzabase",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1"
},
"oryzabase.stage": {
"description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information.",
"example": "34",
"homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/",
"name": "Oryzabase v4 Stage at National Institute of Genetics (Japan)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1"
},
"oryzabase.strain": {
"description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information.",
"example": "1",
"homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/",
"name": "Oryzabase v4 Strain at National Institute of Genetics (Japan)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1"
},
"otl": {
"description": "Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information.",
"example": "AADB12",
"homepage": "http://oryzatagline.cirad.fr/",
"name": "Oryza Tag Line at CIRAD-INRA-SUPAGRO-UMI",
"namespaceEmbeddedInLui": false,
"pattern": "^A[A-Z]+\\d+$",
"uri_format": "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1"
},
"p3db.protein": {
"description": "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites.",
"example": "70",
"homepage": "http://www.p3db.org/",
"name": "P3DB Protein at University of Missouri",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.p3db.org/protein.php?id=$1&ref=0"
},
"p3db.site": {
"description": "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins.",
"example": "65",
"homepage": "http://www.p3db.org/",
"name": "P3DB Site at University of Missouri",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.p3db.org/phosphosite.php?id=$1&ref=0"
},
"paleodb": {
"description": "The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data.",
"example": "83088",
"homepage": "http://paleodb.org/",
"name": "PaleoDB at Macquarie University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://fossilworks.org/?a=taxonInfo&taxon_no=$1"
},
"panther.family": {
"description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families.",
"example": "PTHR12345",
"homepage": "http://www.pantherdb.org/",
"name": "PANTHER Family at USC (Los Angeles)",
"namespaceEmbeddedInLui": false,
"pattern": "^PTHR\\d{5}(\\:SF\\d{1,3})?$",
"uri_format": "http://www.pantherdb.org/panther/family.do?clsAccession=$1"
},
"panther.node": {
"description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes.",
"example": "PTN000000026",
"homepage": "http://pantree.org/",
"name": "PANTHER Node at USC (Los Angeles)",
"namespaceEmbeddedInLui": false,
"pattern": "^PTN\\d{9}$",
"uri_format": "http://www.pantree.org/node/annotationNode.jsp?id=$1"
},
"panther.pathway": {
"description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components.",
"example": "P00024",
"homepage": "http://www.pantherdb.org/",
"name": "PANTHER Pathway at USC (Los Angeles)",
"namespaceEmbeddedInLui": false,
"pattern": "^P\\d{5}$",
"uri_format": "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1"
},
"panther.pthcmp": {
"description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway components may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation.",
"example": "P00266",
"homepage": "http://www.pantherdb.org/",
"name": "PANTHER Pathway Component at USC (Los Angeles)",
"namespaceEmbeddedInLui": false,
"pattern": "^G|P|U|C|S\\d{5}$",
"uri_format": "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1"
},
"pass2": {
"description": "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.",
"example": "46977",
"homepage": "http://caps.ncbs.res.in/pass2/",
"name": "PASS2 at National centre for Biological Sciences (India)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1"
},
"pathwaycommons": {
"description": "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.",
"example": "485991",
"homepage": "http://www.pathwaycommons.org/pc/",
"name": "Pathway Commons",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.pathwaycommons.org/pc/record2.do?id=$1"
},
"pato": {
"description": "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.",
"example": "0001998",
"homepage": "http://bioportal.bioontology.org/ontologies/PATO",
"name": "PATO through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^PATO:\\d{7}$",
"uri_format": "http://purl.bioontology.org/ontology/PATO/PATO:$1"
},
"paxdb.organism": {
"description": "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species.",
"example": "9606",
"homepage": "http://pax-db.org/",
"name": "PaxDb v3 at University of Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://pax-db.org/#!species/$1"
},
"paxdb.protein": {
"description": "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels.",
"example": "977869",
"homepage": "http://pax-db.org/",
"name": "PaxDb v3 at University of Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://pax-db.org/#!protein/$1"
},
"pazar": {
"description": "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors.",
"example": "TF0001053",
"homepage": "http://www.pazar.info/",
"name": "Pazar Transcription Factor at University of British Columbia",
"namespaceEmbeddedInLui": false,
"pattern": "^TF\\w+$",
"uri_format": "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1"
},
"pdb": {
"description": "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.",
"example": "2gc4",
"homepage": "https://www.pdb.org/",
"name": "RCSB PDB",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9][A-Za-z0-9]{3}$",
"uri_format": "https://www.rcsb.org/pdb/explore/explore.do?structureId=$1"
},
"pdb-ccd": {
"description": "The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names.",
"example": "AB0",
"homepage": "https://www.ebi.ac.uk/pdbe-srv/pdbechem/",
"name": "Protein Data Bank Chemical Component Dictionary at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{3}$",
"uri_format": "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1"
},
"pdb.ligand": {
"description": "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands.",
"example": "TRQ",
"homepage": "http://www.pdb.org/",
"name": "PDB Ligand at RCSB",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9]+$",
"uri_format": "http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$1"
},
"peptideatlas": {
"description": "The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools.",
"example": "PAp00000009",
"homepage": "http://www.peptideatlas.org/",
"name": "PeptideAtlas at ISB",
"namespaceEmbeddedInLui": false,
"pattern": "^PAp[0-9]{8}$",
"uri_format": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1"
},
"peptideatlas.dataset": {
"description": "Experiment details about PeptideAtlas entries. Each PASS entry provides direct access to the data files submitted to PeptideAtlas.",
"example": "PASS01237",
"homepage": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_Summary",
"name": "PeptideAtlas Dataset",
"namespaceEmbeddedInLui": false,
"pattern": "^PASS\\d{5}$",
"uri_format": "http://www.peptideatlas.org/PASS/$1"
},
"peroxibase": {
"description": "Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences.",
"example": "5282",
"homepage": "http://peroxibase.toulouse.inra.fr/",
"name": "Peroxibase at University of Geneva",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1"
},
"pfam": {
"description": "The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.",
"example": "PF01234",
"homepage": "https://pfam.xfam.org/",
"name": "Pfam at EMBL-EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^PF\\d{5}$",
"uri_format": "https://pfam.xfam.org/family/$1"
},
"pgx": {
"description": "The Progenetix database provides an overview of copy number abnormalities in human cancer from currently 32317 array and chromosomal Comparative Genomic Hybridization (CGH) experiments, as well as Whole Genome or Whole Exome Sequencing (WGS, WES) studies. The cancer profile data in Progenetix was curated from 1026 articles and represents 364 different cancer types, according to the International classification of Diseases in Oncology (ICD-O).",
"example": "icdom:8500_3",
"homepage": "http://progenetix.org/",
"name": "Progenetix",
"namespaceEmbeddedInLui": false,
"pattern": "^[\\w\\-:,]{3,64}$",
"uri_format": "http://progenetix.org/pgx:$1"
},
"pharmgkb.disease": {
"description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.",
"example": "PA447218",
"homepage": "http://www.pharmgkb.org/",
"name": "PharmGKB Disease at Stanford",
"namespaceEmbeddedInLui": false,
"pattern": "^PA\\d+$",
"uri_format": "http://www.pharmgkb.org/disease/$1"
},
"pharmgkb.drug": {
"description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.",
"example": "PA448710",
"homepage": "http://www.pharmgkb.org/",
"name": "PharmGKB Drug at Stanford",
"namespaceEmbeddedInLui": false,
"pattern": "^PA\\d+$",
"uri_format": "http://www.pharmgkb.org/drug/$1"
},
"pharmgkb.gene": {
"description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.",
"example": "PA131",
"homepage": "http://www.pharmgkb.org/",
"name": "PharmGKB Gene at Stanford",
"namespaceEmbeddedInLui": false,
"pattern": "^PA\\w+$",
"uri_format": "http://www.pharmgkb.org/gene/$1"
},
"pharmgkb.pathways": {
"description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies.",
"example": "PA146123006",
"homepage": "http://www.pharmgkb.org/",
"name": "PharmGKB at Stanford",
"namespaceEmbeddedInLui": false,
"pattern": "^PA\\d+$",
"uri_format": "http://www.pharmgkb.org/pathway/$1"
},
"phenolexplorer": {
"description": "Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis.",
"example": "75",
"homepage": "http://www.phenol-explorer.eu/foods/",
"name": "Phenol-Explorer Database on Phenol content of foods",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://phenol-explorer.eu/foods/$1"
},
"phosphopoint.kinase": {
"description": "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information.",
"example": "AURKA",
"homepage": "http://kinase.bioinformatics.tw/",
"name": "PhosphoPoint Kinase at National Taiwan University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1"
},
"phosphopoint.protein": {
"description": "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information.",
"example": "AURKA",
"homepage": "http://kinase.bioinformatics.tw/",
"name": "PhosphoPoint Phosphoprotein at National Taiwan University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0"
},
"phosphosite.protein": {
"description": "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database.",
"example": "12300",
"homepage": "http://www.phosphosite.org/homeAction.do",
"name": "PhosphoSite",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{5}$",
"uri_format": "http://www.phosphosite.org/proteinAction.do?id=$1"
},
"phosphosite.residue": {
"description": "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence.",
"example": "2842",
"homepage": "http://www.phosphosite.org/homeAction.do",
"name": "PhosphoSite Residue",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.phosphosite.org/siteAction.do?id=$1"
},
"phylomedb": {
"description": "PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins.",
"example": "Phy000CLXM_RAT",
"homepage": "http://phylomedb.org/",
"name": "PhylomeDB at Centro de Investigación Príncipe Felipe",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://phylomedb.org/?seqid=$1"
},
"phytozome.locus": {
"description": "Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information.",
"example": "Glyma0021s00410",
"homepage": "http://www.phytozome.net/",
"name": "Phytozome Locus at Joint Genome Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9]+$",
"uri_format": "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1"
},
"pid.pathway": {
"description": "The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information.",
"example": "pi3kcipathway",
"homepage": "http://pid.nci.nih.gov/",
"name": "NCI Pathway Interaction Database (Pathway)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1"
},
"pigqtldb": {
"description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs.",
"example": "14",
"homepage": "http://www.animalgenome.org/cgi-bin/QTLdb/SS/index",
"name": "Animal QTL Pig at Iowa State University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=$1"
},
"pina": {
"description": "Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms.",
"example": "Q13485",
"homepage": "http://cbg.garvan.unsw.edu.au/pina/",
"name": "Protein Interaction Network Analysis (PINA) at Garvan Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$",
"uri_format": "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?ac=$1&showExtend=null"
},
"piroplasma": {
"description": "PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"example": "TA14985",
"homepage": "http://piroplasmadb.org/",
"name": "PiroplasmaBD at EuPathDB",
"namespaceEmbeddedInLui": false,
"pattern": "^TA\\d+$",
"uri_format": "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"
},
"pirsf": {
"description": "The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.",
"example": "PIRSF000100",
"homepage": "https://pir.georgetown.edu/",
"name": "PIRSF",
"namespaceEmbeddedInLui": false,
"pattern": "^PIRSF\\d{6}$",
"uri_format": "https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1"
},
"planttfdb": {
"description": "The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors.",
"example": "Ath_AT1G01030.1",
"homepage": "http://planttfdb.cbi.pku.edu.cn",
"name": "PlantTFDB at Peking University",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\\._\\-#]*)$",
"uri_format": "http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1"
},
"plasmodb": {
"description": "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"example": "PF11_0344",
"homepage": "http://plasmodb.org/plasmo/",
"name": "PlasmoDB at EuPathDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"
},
"pmap.cutdb": {
"description": "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites).",
"example": "25782",
"homepage": "http://cutdb.burnham.org",
"name": "CutDB at The Burnham Institute for Medical Research",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://cutdb.burnham.org/relation/show/$1"
},
"pmap.substratedb": {
"description": "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates.",
"example": "1915",
"homepage": "http://substrate.burnham.org/",
"name": "SubstrateDB at The Burnham Institute for Medical Research",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://substrate.burnham.org/protein/annotation/$1/html"
},
"pmc": {
"description": "PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature.",
"example": "PMC3084216",
"homepage": "http://europepmc.org/",
"name": "Europe PMC",
"namespaceEmbeddedInLui": false,
"pattern": "PMC\\d+",
"uri_format": "http://europepmc.org/articles/$1"
},
"pmdb": {
"description": "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques.",
"example": "PM0012345",
"homepage": "https://bioinformatics.cineca.it/PMDB/",
"name": "Protein Model Database at University of Rome",
"namespaceEmbeddedInLui": false,
"pattern": "^PM\\d{7}",
"uri_format": "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1"
},
"pmp": {
"description": "The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers.",
"example": "Q0VCA6",
"homepage": "http://www.proteinmodelportal.org/",
"name": "PMP at University of Basel",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$",
"uri_format": "http://www.proteinmodelportal.org/query/uniprot/$1"
},
"po": {
"description": "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.",
"example": "0009089",
"homepage": "http://bioportal.bioontology.org/ontologies/PO",
"name": "Plant Ontology through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^PO:\\d+$",
"uri_format": "http://purl.bioontology.org/ontology/PO/PO:$1"
},
"pocketome": {
"description": "Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries.",
"example": "1433C_TOBAC_1_252",
"homepage": "http://www.pocketome.org/sfSearch.cgi?act=browseall",
"name": "Pocketome at UCSD Skaggs School",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z_0-9]+",
"uri_format": "http://www.pocketome.org/files/$1.html"
},
"polbase": {
"description": "Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity.",
"example": "19-T4",
"homepage": "http://polbase.neb.com/",
"name": "PolBase at New England BioLabs",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z-0-9]+$",
"uri_format": "https://polbase.neb.com/polymerases/$1#sequences"
},
"pombase": {
"description": "PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets.",
"example": "SPCC13B11.01",
"homepage": "http://www.pombase.org/",
"name": "PomBase at University of Cambridge",
"namespaceEmbeddedInLui": false,
"pattern": "^S\\w+(\\.)?\\w+(\\.)?$",
"uri_format": "http://www.pombase.org/spombe/result/$1"
},
"pr": {
"description": "The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies.",
"example": "000000024",
"homepage": "https://proconsortium.org/",
"name": "Protein Ontology at Georgetown",
"namespaceEmbeddedInLui": true,
"pattern": "^PR\\:P?\\d+$",
"uri_format": "https://proconsortium.org/app/entry/PR:$1"
},
"pride": {
"description": "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays.",
"example": "1",
"homepage": "https://www.ebi.ac.uk/pride/",
"name": "PRIDE at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://www.ebi.ac.uk/pride/archive/assays/$1"
},
"pride.project": {
"description": "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects.",
"example": "PXD000440",
"homepage": "https://www.ebi.ac.uk/pride/",
"name": "PRIDE Project at EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^P(X|R)D\\d{6}$",
"uri_format": "https://www.ebi.ac.uk/pride/archive/projects/$1"
},
"prints": {
"description": "PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours.",
"example": "PR00001",
"homepage": "http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/",
"name": "PRINTS through SPRINT",
"namespaceEmbeddedInLui": false,
"pattern": "^PR\\d{5}$",
"uri_format": "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off"
},
"probonto": {
"description": "ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities.",
"example": "PROB_c0000005",
"homepage": "https://www.ebi.ac.uk/ols/ontologies/probonto",
"name": "ProbOnto through OLS",
"namespaceEmbeddedInLui": false,
"pattern": "^PROB_c\\d+$",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=$1"
},
"prodom": {
"description": "ProDom is a database of protein domain families generated from the global comparison of all available protein sequences.",
"example": "PD10000",
"homepage": "http://prodom.prabi.fr/prodom/current/html/home.php",
"name": "ProDom Protein Domain Database",
"namespaceEmbeddedInLui": false,
"pattern": "^PD\\d+$",
"uri_format": "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1"
},
"proglyc": {
"description": "ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information.",
"example": "AC119",
"homepage": "http://www.proglycprot.org/",
"name": "ProGlycProt at IMT",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z]C\\d{1,3}$",
"uri_format": "http://www.proglycprot.org/detail.aspx?ProId=$1"
},
"prosite": {
"description": "PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.",
"example": "PS00001",
"homepage": "https://www.expasy.org/prosite/",
"name": "ExPASy PROSITE",
"namespaceEmbeddedInLui": false,
"pattern": "^PS\\d{5}$",
"uri_format": "https://prosite.expasy.org/$1"
},
"protclustdb": {
"description": "ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.",
"example": "O80725",
"homepage": "https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters",
"name": "ProtClustDB at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1"
},
"proteomicsdb.peptide": {
"description": "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein.",
"example": "53504",
"homepage": "https://www.proteomicsdb.org/#peptideSearch",
"name": "Proteomics DB Peptide at Center for Integrated Protein Science",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://www.proteomicsdb.org/#human/proteinDetails/$1/peptides/"
},
"proteomicsdb.protein": {
"description": "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins.",
"example": "53504",
"homepage": "https://www.proteomicsdb.org/#human",
"name": "Proteomics DB Protein at Center for Integrated Protein Science",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://www.proteomicsdb.org/#human/proteinDetails/$1/summary"
},
"protonet.cluster": {
"description": "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information.",
"example": "4349895",
"homepage": "http://www.protonet.cs.huji.ac.il/",
"name": "ProtoNet at Hebrew University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1"
},
"protonet.proteincard": {
"description": "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information.",
"example": "16941567",
"homepage": "http://www.protonet.cs.huji.ac.il/",
"name": "ProtoNet at Hebrew University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1"
},
"pscdb": {
"description": "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion.",
"example": "051",
"homepage": "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html",
"name": "PSCDB at Nagoya University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html"
},
"pseudomonas": {
"description": "The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.",
"example": "PSEEN0001",
"homepage": "http://www.pseudomonas.com/",
"name": "Pseudomonas Genome Database at Simon Fraser University",
"namespaceEmbeddedInLui": false,
"pattern": "^P\\w+$",
"uri_format": "http://www.pseudomonas.com/feature/show/?locus_tag=$1"
},
"psimi": {
"description": "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.",
"example": "0308",
"homepage": "https://www.ebi.ac.uk/ols/ontologies/mi",
"name": "Molecular Interactions Ontology through OLS",
"namespaceEmbeddedInLui": true,
"pattern": "^MI:\\d{4}$",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1"
},
"psipar": {
"description": "Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms.",
"example": "PAR:0116",
"homepage": "https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR",
"name": "Protein Affinity Reagents through OLS",
"namespaceEmbeddedInLui": false,
"pattern": "^PAR:\\d+$",
"uri_format": "https://www.ebi.ac.uk/ontology-lookup/?termId=$1"
},
"pubchem.bioassay": {
"description": "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results.",
"example": "1018",
"homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay ",
"name": "PubChem Bioassay at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=$1"
},
"pubchem.compound": {
"description": "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records.",
"example": "100101",
"homepage": "https://pubchem.ncbi.nlm.nih.gov/",
"name": "NCBI PubChem Compound",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=$1"
},
"pubchem.substance": {
"description": "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records.",
"example": "100101",
"homepage": "https://pubchem.ncbi.nlm.nih.gov/",
"name": "NCBI PubChem Substance",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=$1"
},
"pubmed": {
"description": "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.",
"example": "16333295",
"homepage": "https://www.ncbi.nlm.nih.gov/PubMed/",
"name": "NCBI PubMed",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://www.ncbi.nlm.nih.gov/pubmed/$1"
},
"pw": {
"description": "The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions.",
"example": "0000208",
"homepage": "http://bioportal.bioontology.org/ontologies/PW",
"name": "Pathway Ontology through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^PW:\\d{7}$",
"uri_format": "http://purl.bioontology.org/ontology/PW/PW:$1"
},
"px": {
"description": "The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination.",
"example": "PXD000500",
"homepage": "http://www.proteomexchange.org/",
"name": "ProteomeXchange at Seattle",
"namespaceEmbeddedInLui": false,
"pattern": "^(R)?PXD\\d{6}$",
"uri_format": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1"
},
"rbk": {
"description": "(Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function.",
"example": "Q-2958",
"homepage": "https://www.rebuildingakidney.org/",
"name": "Rebuilding a Kidney",
"namespaceEmbeddedInLui": false,
"pattern": "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$",
"uri_format": "https://www.rebuildingakidney.org/id/$1"
},
"reactome": {
"description": "The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.",
"example": "R-HSA-201451",
"homepage": "https://www.reactome.org/",
"name": "Reactome, a curated knowledgebase of biological pathways",
"namespaceEmbeddedInLui": false,
"pattern": "(^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$)|(^REACT_\\d+(\\.\\d+)?$)",
"uri_format": "https://reactome.org/content/detail/$1"
},
"rebase": {
"description": "REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.",
"example": "101",
"homepage": "http://rebase.neb.com/rebase/",
"name": "REBASE at New England Biolabs",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://rebase.neb.com/rebase/enz/$1.html"
},
"refseq": {
"description": "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.",
"example": "NP_012345",
"homepage": "https://www.ncbi.nlm.nih.gov/projects/RefSeq/",
"name": "The NCBI Reference Sequence database",
"namespaceEmbeddedInLui": false,
"pattern": "^((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\\d+|(NZ\\_[A-Z]{4}\\d+))(\\.\\d+)?$",
"uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1"
},
"resid": {
"description": "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.",
"example": "AA0001",
"homepage": "http://pir0.georgetown.edu/resid/",
"name": "RESID at Georgetown University",
"namespaceEmbeddedInLui": false,
"pattern": "^AA\\d{4}$",
"uri_format": "http://pir0.georgetown.edu/cgi-bin/resid?id=$1"
},
"rfam": {
"description": "The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion.",
"example": "RF00230",
"homepage": "https://rfam.xfam.org/",
"name": "Rfam at EMBL-EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^RF\\d{5}$",
"uri_format": "https://rfam.xfam.org/family/$1"
},
"rfc": {
"example": "5013",
"homepage": "https://www.ietf.org/",
"name": "Internet Standard -- IETF Request for Comments",
"namespaceEmbeddedInLui": false,
"uri_format": "https://tools.ietf.org/rfc/rfc$1"
},
"rgd": {
"description": "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes.",
"example": "2018",
"homepage": "http://rgd.mcw.edu/",
"name": "Rat Genome Database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{4,}$",
"uri_format": "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1"
},
"rgd.qtl": {
"description": "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes.",
"example": "1354581",
"homepage": "http://rgd.mcw.edu/",
"name": "Rat Genome Database qTL at Medical College of Wisconsin",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1"
},
"rgd.strain": {
"description": "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology.",
"example": "5688061",
"homepage": "http://rgd.mcw.edu/",
"name": "Rat Genome Database strain at Medical College of Wisconsin",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1"
},
"rhea": {
"description": "Rhea is a manually annotated reaction database, where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest), providing detailed information about structure, formulae and charge. It is populated with the reactions found in the EC list, IntEnz and ENZYME databases), as well as other biochemical reactions, including those that are often termed \"spontaneous\".",
"example": "12345",
"homepage": "https://www.rhea-db.org/",
"name": "Rhea",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{5}$",
"uri_format": "https://www.rhea-db.org/reaction?id=$1"
},
"ricegap": {
"description": "The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines.",
"example": "LOC_Os02g13300",
"homepage": "http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml",
"name": "Rice Genome Annotation Project at TIGR",
"namespaceEmbeddedInLui": false,
"pattern": "^LOC\\_Os\\d{1,2}g\\d{5}$",
"uri_format": "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1"
},
"ricenetdb.compound": {
"description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.",
"example": "OSC1416",
"homepage": "http://bis.zju.edu.cn/ricenetdb",
"name": "RiceNetDB Compound",
"namespaceEmbeddedInLui": false,
"pattern": "^OSC\\d{4}$",
"uri_format": "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1"
},
"ricenetdb.gene": {
"description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.",
"example": "LOC_Os01g49190.1",
"homepage": "http://bis.zju.edu.cn/ricenetdb/",
"name": "RiceNetDB",
"namespaceEmbeddedInLui": false,
"pattern": "^LOC\\_Os\\d{1,2}g\\d{5}\\.\\d$",
"uri_format": "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1"
},
"ricenetdb.mirna": {
"description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.",
"example": "osa-miR446",
"homepage": "http://bis.zju.edu.cn/ricenetdb",
"name": "RiceNetDB miRNA",
"namespaceEmbeddedInLui": false,
"pattern": "^osa-miR\\d{3,5}[a-z]{0,1}$",
"uri_format": "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1"
},
"ricenetdb.protein": {
"description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.",
"example": "LOC_Os01g49190",
"homepage": "http://bis.zju.edu.cn/ricenetdb/",
"name": "RiceNetDB",
"namespaceEmbeddedInLui": false,
"pattern": "^LOC\\_Os\\d{1,2}g\\d{5}$",
"uri_format": "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1"
},
"ricenetdb.reaction": {
"description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.",
"example": "OSR0818",
"homepage": "http://bis.zju.edu.cn/ricenetdb",
"name": "RiceNetDB Reaction",
"namespaceEmbeddedInLui": false,
"pattern": "^OSR\\d{4}$",
"uri_format": "http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1"
},
"rnacentral": {
"description": "RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases.",
"example": "URS0000759CF4",
"homepage": "https://rnacentral.org/",
"name": "RNAcentral through EMBL-EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^URS[0-9A-F]{10}(\\_\\d+)?$",
"uri_format": "https://rnacentral.org/rna/$1"
},
"rnamods": {
"description": "The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA.",
"example": "101",
"homepage": "http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm",
"name": "RNA Modification Database at University of Utah",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{3}$",
"uri_format": "http://mods.rna.albany.edu/mods/modifications/view/$1"
},
"ro": {
"description": "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies.",
"example": "RO_0002533",
"homepage": "http://obofoundry.org/ontology/ro.html",
"name": "OBO Relation Ontology through OntoBee",
"namespaceEmbeddedInLui": false,
"pattern": "^RO_\\d{7}$",
"uri_format": "http://purl.obolibrary.org/obo/$1"
},
"ror": {
"example": "03yrm5c26",
"homepage": "http://ror.org",
"name": "Research Organization Registry",
"namespaceEmbeddedInLui": false,
"uri_format": "https://ror.org/$1"
},
"rouge": {
"description": "The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.",
"example": "mKIAA4200",
"homepage": "http://www.kazusa.or.jp/rouge/",
"name": "Rouge at Kazusa DNA Research Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^m\\w+$",
"uri_format": "http://www.kazusa.or.jp/rouge/gfpage/$1/"
},
"rrid": {
"description": "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools. The initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch.",
"example": "AB_262044",
"homepage": "https://scicrunch.org/resolver",
"name": "RRID at SciCrunch",
"namespaceEmbeddedInLui": true,
"pattern": "^RRID:[A-Z_a-z-0-9]+$",
"uri_format": "https://scicrunch.org/resolver/RRID:$1"
},
"sabiork.compound": {
"description": "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information.",
"example": "75",
"homepage": "http://sabiork.h-its.org/",
"name": "SABIO-RK Compound",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://sabiork.h-its.org/newSearch?q=$1"
},
"sabiork.ec": {
"description": "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data.",
"example": "2.7.1.1",
"homepage": "http://sabiork.h-its.org/",
"name": "SABIO-RK Reaction Kinetics Database - Enzyme Classification (EC)",
"namespaceEmbeddedInLui": false,
"pattern": "^((\\d+)|(\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$",
"uri_format": "http://sabiork.h-its.org/newSearch?q=ecnumber:$1"
},
"sabiork.kineticrecord": {
"description": "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information.",
"example": "5046",
"homepage": "http://sabiork.h-its.org/",
"name": "SABIO-RK Reaction Kinetics Database - Kinetic Dataset",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1"
},
"sabiork.reaction": {
"description": "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information.",
"example": "75",
"homepage": "http://sabiork.h-its.org/",
"name": "SABIO-RK reaction",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://sabiork.h-its.org/newSearch?q=sabioreactionid:$1"
},
"sasbdb": {
"description": "Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data.",
"example": "SASDAX8",
"homepage": "http://www.sasbdb.org/",
"name": "SASBDB at European Molecular Biology Laboratory",
"namespaceEmbeddedInLui": false,
"pattern": "^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$",
"uri_format": "http://www.sasbdb.org/data/$1"
},
"sbo": {
"description": "The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort.",
"example": "0000262",
"homepage": "https://www.ebi.ac.uk/sbo/",
"name": "SBO",
"namespaceEmbeddedInLui": true,
"pattern": "^SBO:\\d{7}$",
"uri_format": "https://www.ebi.ac.uk/sbo/main/SBO:$1"
},
"scop": {
"description": "The SCOP (Structural Classification of Protein) database is a comprehensive ordering of all proteins of known structure according to their evolutionary, functional and structural relationships. The basic classification unit is the protein domain. Domains are hierarchically classified into species, proteins, families, superfamilies, folds, and classes.",
"example": "47419",
"homepage": "http://scop.berkeley.edu/",
"name": "SCOP at Berkeley",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://scop.berkeley.edu/sunid=$1"
},
"scretf": {
"description": "ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor.",
"example": "RSC3",
"homepage": "http://stormo.wustl.edu/ScerTF/",
"name": "ScerTF at Washington University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://stormo.wustl.edu/ScerTF/details/$1/"
},
"sdbs": {
"description": "The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra.",
"example": "4544",
"homepage": "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi",
"name": "SDBS at AIST",
"namespaceEmbeddedInLui": false,
"pattern": "\\d+$",
"uri_format": "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1"
},
"seed": {
"description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.",
"example": "Biotin_biosynthesis",
"homepage": "http://seed-viewer.theseed.org/seedviewer.cgi",
"name": "SEED Subsystem at Argonne National Laboratory",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1"
},
"seed.compound": {
"description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.",
"example": "cpd15380",
"homepage": "http://modelseed.org/",
"name": "SEED Compound at Argonne National Laboratory",
"namespaceEmbeddedInLui": false,
"pattern": "^cpd\\d+$",
"uri_format": "http://modelseed.org/biochem/compounds/$1"
},
"seed.reaction": {
"description": "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions.",
"example": "rxn00001",
"homepage": "http://modelseed.org/biochem/reactions/",
"name": "SEED Reactions",
"namespaceEmbeddedInLui": false,
"pattern": "^rxn\\d+$",
"uri_format": "http://modelseed.org/biochem/reactions/$1"
},
"sgd": {
"description": "The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae.",
"example": "S000003909",
"homepage": "https://www.yeastgenome.org/",
"name": "SGD",
"namespaceEmbeddedInLui": false,
"pattern": "^((S\\d+$)|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?))$",
"uri_format": "https://www.yeastgenome.org/locus/$1"
},
"sgd.pathways": {
"description": "Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD).",
"example": "PWY3O-214",
"homepage": "http://pathway.yeastgenome.org/",
"name": "Saccharomyces cerevisiae pathways at SGD.",
"namespaceEmbeddedInLui": false,
"pattern": "^PWY\\w{2}\\-\\d{3}$",
"uri_format": "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1"
},
"sgn": {
"description": "The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant.",
"example": "0001",
"homepage": "http://solgenomics.net/",
"name": "Sol Genomics Network at Boyce Thompson Institute for Plant Research",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://solgenomics.net/phenome/locus_display.pl?locus_id=$1"
},
"sheepqtldb": {
"description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs.",
"example": "19803",
"homepage": "http://www.animalgenome.org/cgi-bin/QTLdb/OA/index",
"name": "Animal QTL Sheep at Iowa State University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=$1"
},
"sider.drug": {
"description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER.",
"example": "2244",
"homepage": "http://sideeffects.embl.de/",
"name": "SIDER Drug v2 at EMBL (Heidelberg)",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://sideeffects.embl.de/drugs/$1/"
},
"sider.effect": {
"description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER.",
"example": "C0017565",
"homepage": "http://sideeffects.embl.de/",
"name": "SIDER Side Effect v2 at EMBL (Heidelberg)",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d+$",
"uri_format": "http://sideeffects.embl.de/se/$1/"
},
"signaling-gateway": {
"description": "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.",
"example": "A001094",
"homepage": "http://www.signaling-gateway.org/molecule",
"name": "Signaling Gateway Molecule Pages",
"namespaceEmbeddedInLui": false,
"pattern": "A\\d{6}$",
"uri_format": "http://www.signaling-gateway.org/molecule/query?afcsid=$1"
},
"sisu": {
"description": "The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies.",
"example": "17:41223048",
"homepage": "http://www.sisuproject.fi/",
"name": "SISu",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9]+:[0-9]+$",
"uri_format": "http://search.sisuproject.fi/#/variant/$1"
},
"sitex": {
"description": "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.",
"example": "1000",
"homepage": "http://www-bionet.sscc.ru/sitex/",
"name": "SitEx at Novosibirsk State University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1"
},
"smart": {
"description": "The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures.",
"example": "SM00015",
"homepage": "http://smart.embl-heidelberg.de/",
"name": "SMART (Simple Modular Architecture Research Tool)",
"namespaceEmbeddedInLui": false,
"pattern": "^SM\\d{5}$",
"uri_format": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1"
},
"smpdb": {
"description": "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.",
"example": "SMP00001",
"homepage": "http://www.smpdb.ca/pathways",
"name": "Small Molecule Pathway Database",
"namespaceEmbeddedInLui": false,
"pattern": "^SMP\\d+$",
"uri_format": "http://smpdb.ca/view/$1"
},
"snomedct": {
"description": "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc.",
"example": "284196006",
"homepage": "http://www.snomedbrowser.com/",
"name": "SNOMED-CT at The National Pathology Exchange",
"namespaceEmbeddedInLui": false,
"pattern": "^(\\w+)?\\d+$",
"uri_format": "http://www.snomedbrowser.com/Codes/Details/$1"
},
"so": {
"description": "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data.",
"example": "0000704",
"homepage": "http://bioportal.bioontology.org/ontologies/SO",
"name": "Sequence Ontology through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^SO:\\d{7}$",
"uri_format": "http://purl.bioontology.org/ontology/SO/SO:$1"
},
"soybase": {
"description": "SoyBase is a repository for curated genetics, genomics and related data resources for soybean.",
"example": "BARC-013845-01256",
"homepage": "http://soybase.org/",
"name": "SoyBase at Iowa State University",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\-)?\\w+(\\-)?\\w+$",
"uri_format": "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1"
},
"spdx": {
"description": "The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception.",
"example": "CC-BY-1.0",
"homepage": "https://spdx.org",
"name": "SPDX License List",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9A-Za-z\\-.]+$",
"uri_format": "https://spdx.org/licenses/$1"
},
"spike.map": {
"description": "SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps.",
"example": "spike00001",
"homepage": "http://www.cs.tau.ac.il/~spike/",
"name": "SPIKE database at Tel Aviv University",
"namespaceEmbeddedInLui": false,
"pattern": "^spike\\d{5}$",
"uri_format": "http://www.cs.tau.ac.il/~spike/maps/$1.html"
},
"splash": {
"description": "The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance.",
"example": "splash10-0zq2000000-77302b0326a418630a84",
"homepage": "http://mona.fiehnlab.ucdavis.edu/",
"name": "Mass Bank of North America (MoNA)",
"namespaceEmbeddedInLui": false,
"pattern": "^splash\\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$",
"uri_format": "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1"
},
"stap": {
"description": "STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB).",
"example": "1a24",
"homepage": "http://psb.kobic.re.kr/STAP/refinement/",
"name": "STAP at Korean Bioinformation Center",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9][A-Za-z0-9]{3}$",
"uri_format": "http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1"
},
"stitch": {
"description": "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.",
"example": "BQJCRHHNABKAKU",
"homepage": "http://stitch.embl.de/",
"name": "STITCH",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{14}$",
"uri_format": "http://stitch.embl.de/interactions/$1"
},
"storedb": {
"description": "STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons.",
"example": "STOREDB:STUDY1040",
"homepage": "https://www.storedb.org/",
"name": "STOREDB at University of Cambridge",
"namespaceEmbeddedInLui": false,
"pattern": "^STOREDB:(STUDY|FILE|DATASET)\\d+$",
"uri_format": "https://www.storedb.org/?$1"
},
"string": {
"description": "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.",
"example": "P53350",
"homepage": "http://string-db.org/",
"name": "STRING Mirror at Heidelberg",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$",
"uri_format": "http://string-db.org/interactions/$1"
},
"subtilist": {
"description": "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments.",
"example": "BG11523",
"homepage": "http://genolist.pasteur.fr/SubtiList/",
"name": "SubtiList at Pasteur Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^BG\\d+$",
"uri_format": "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1"
},
"subtiwiki": {
"description": "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. Note: Currently, direct access to RNA products is restricted. This is expected to be rectified soon.",
"example": "BSU29180",
"homepage": "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page",
"name": "SubtiWiki website",
"namespaceEmbeddedInLui": false,
"pattern": "^BSU\\d{5}$",
"uri_format": "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1"
},
"sugarbind": {
"description": "The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands.",
"example": "lectins/172",
"homepage": "http://sugarbind.expasy.org/",
"name": "SugarBind",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z]+\\/[0-9]+$",
"uri_format": "http://sugarbind.expasy.org/$1"
},
"supfam": {
"description": "SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt.",
"example": "SSF57615",
"homepage": "http://supfam.org/SUPERFAMILY/",
"name": "SUPFAM at MRC and University of Bristol",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1"
},
"swh": {
"description": "Software Heritage is the universal archive of software source code.",
"example": "1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d",
"homepage": "https://archive.softwareheritage.org",
"name": "Software Heritage",
"namespaceEmbeddedInLui": true,
"pattern": "^swh:[1-9]:[a-z][a-z][a-z]:[a-f0-9]+$",
"uri_format": "https://archive.softwareheritage.org/browse/swh:$1"
},
"swiss-model": {
"description": "The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences.",
"example": "P23298",
"homepage": "https://swissmodel.expasy.org",
"name": "SWISS-MODEL at SIB Swiss Institute of Bioinformatics",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "https://swissmodel.expasy.org/repository/uniprot/$1"
},
"swisslipid": {
"description": "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions.",
"example": "000048885",
"homepage": "http://www.swisslipids.org/#/",
"name": "SwissLipids at Swiss Institute of Bioinformatics",
"namespaceEmbeddedInLui": true,
"pattern": "^SLM:\\d+$",
"uri_format": "http://www.swisslipids.org/#/entity/SLM:$1/"
},
"swissregulon": {
"description": "A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form.",
"example": "AHR",
"homepage": "http://swissregulon.unibas.ch",
"name": "SwissRegulon",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9]+$",
"uri_format": "http://swissregulon.unibas.ch/query/$1"
},
"t3db": {
"description": "Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.",
"example": "T3D0001",
"homepage": "http://www.t3db.org/",
"name": "Toxin and Toxin Target Database",
"namespaceEmbeddedInLui": false,
"pattern": "^T3D\\d+$",
"uri_format": "http://www.t3db.org/toxins/$1"
},
"tair.gene": {
"description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus.",
"example": "Gene:2200934",
"homepage": "http://arabidopsis.org/index.jsp",
"name": "The Arabidopsis Information Resource (TAIR) Gene",
"namespaceEmbeddedInLui": false,
"pattern": "^Gene:\\d{7}$"
},
"tair.locus": {
"description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS.",
"example": "2200950",
"homepage": "http://arabidopsis.org/index.jsp",
"name": "The Arabidopsis Information Resource (TAIR) Locus",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d{7}$",
"uri_format": "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1"
},
"tair.protein": {
"description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept",
"example": "AASequence:1009107926",
"homepage": "http://arabidopsis.org/index.jsp",
"name": "The Arabidopsis Information Resource (TAIR) Protein",
"namespaceEmbeddedInLui": false,
"pattern": "^AASequence:\\d{10}$"
},
"tarbase": {
"description": "TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used.",
"example": "hsa-let-7a-2-3p",
"homepage": "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index",
"name": "TarBase v7 at University of Thessaly",
"namespaceEmbeddedInLui": false,
"pattern": "^[a-z]{3}\\-(mir|let|lin)\\-\\w+(\\-\\w+\\-\\w+)?",
"uri_format": "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1"
},
"taxonomy": {
"description": "The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.",
"example": "9606",
"homepage": "https://www.ncbi.nlm.nih.gov/Taxonomy/",
"name": "NCBI Taxonomy",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1"
},
"tcdb": {
"description": "The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally.",
"example": "5.A.1.1.1",
"homepage": "http://www.tcdb.org/",
"name": "TCDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+(\\.[A-Z])?(\\.\\d+)?(\\.\\d+)?(\\.\\d+)?$",
"uri_format": "http://www.tcdb.org/search/result.php?tc=$1"
},
"tgd": {
"description": "The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature.",
"example": "TTHERM_00648910",
"homepage": "http://ciliate.org/index.php/",
"name": "TGD at Stanford University",
"namespaceEmbeddedInLui": false,
"pattern": "^TTHERM\\_\\d+$",
"uri_format": "http://ciliate.org/index.php/feature/details/$1"
},
"tigrfam": {
"description": "TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins.",
"example": "TIGR00010",
"homepage": "http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi",
"name": "TIGRFAM at JCVI",
"namespaceEmbeddedInLui": false,
"pattern": "^TIGR\\d+$",
"uri_format": "http://www.jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=$1"
},
"tissuelist": {
"description": "The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified.",
"example": "TS-0285",
"homepage": "https://www.uniprot.org/docs/tisslist.txt",
"name": "Tissue List at Swiss Institute of Bioinformatics",
"namespaceEmbeddedInLui": false,
"pattern": "^TS-\\d{4}$",
"uri_format": "https://www.uniprot.org/tissues/$1"
},
"tol": {
"description": "The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). Each page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things.",
"example": "98034",
"homepage": "http://tolweb.org/tree/",
"name": "Tree of Life Web",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://tolweb.org/$1"
},
"topdb": {
"description": "The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases.",
"example": "AP00378",
"homepage": "http://topdb.enzim.hu/",
"name": "TOPDB at Hungarian Academy of Sciences",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]+$",
"uri_format": "http://topdb.enzim.hu/?m=show&id=$1"
},
"topfind": {
"description": "TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.",
"example": "Q9UKQ2",
"homepage": "http://clipserve.clip.ubc.ca/topfind",
"name": "TopFind at University of British Columbia",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$",
"uri_format": "http://clipserve.clip.ubc.ca/topfind/proteins/$1"
},
"toxoplasma": {
"description": "ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"example": "TGME49_053730",
"homepage": "http://toxodb.org/toxo/",
"name": "ToxoDB at EuPathDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"
},
"treebase": {
"description": "TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc.",
"example": "TB2:S1000",
"homepage": "http://treebase.org/",
"name": "TreeBASE (hosted at National Evolutionary Synthesis Center)",
"namespaceEmbeddedInLui": false,
"pattern": "^TB[1,2]?:[A-Z][a-z]?\\d+$",
"uri_format": "http://purl.org/phylo/treebase/phylows/study/$1?format=html"
},
"treefam": {
"description": "TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments.",
"example": "TF101014",
"homepage": "http://www.treefam.org/",
"name": "TreeFam database",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w{1,2}\\d+$",
"uri_format": "http://www.treefam.org/family/$1"
},
"trichdb": {
"description": "TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"example": "TVAG_386080",
"homepage": "http://trichdb.org/trichdb/",
"name": "TrichDB at EuPathDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"
},
"tritrypdb": {
"description": "TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"example": "Tb927.8.620",
"homepage": "http://tritrypdb.org/tritrypdb/",
"name": "TriTrypDB at EuPathDB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\.)?\\w+(\\.)?\\w+",
"uri_format": "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"
},
"ttd.drug": {
"description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.",
"example": "DAP000773",
"homepage": "http://bidd.nus.edu.sg/group/ttd/ttd.asp",
"name": "Therapeutic Target Database Drug",
"namespaceEmbeddedInLui": false,
"pattern": "^DAP\\d+$",
"uri_format": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1"
},
"ttd.target": {
"description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.",
"example": "TTDS00056",
"homepage": "http://bidd.nus.edu.sg/group/ttd/ttd.asp",
"name": "Therapeutic Target Database Target",
"namespaceEmbeddedInLui": false,
"pattern": "^TTDS\\d+$",
"uri_format": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1"
},
"uberon": {
"description": "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.",
"example": "0008203",
"homepage": "http://bioportal.bioontology.org/ontologies/UBERON",
"name": "UBERON through bioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^UBERON\\:\\d+$",
"uri_format": "http://purl.bioontology.org/ontology/UBERON/UBERON:$1"
},
"ubio.namebank": {
"description": "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context.",
"example": "2555646",
"homepage": "http://www.ubio.org",
"name": "uBio NameBank at The Marine Biological Laboratory",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.ubio.org/browser/details.php?namebankID=$1"
},
"umbbd.compound": {
"description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information.",
"example": "c0001",
"homepage": "http://umbbd.ethz.ch/",
"name": "Biocatalysis/Biodegradation Database Mirror (Compound) at ETH Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^c\\d+$",
"uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1"
},
"umbbd.enzyme": {
"description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information.",
"example": "e0333",
"homepage": "http://umbbd.ethz.ch/",
"name": "Biocatalysis/Biodegradation Database Mirror (Enzyme) at ETH Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^e\\d+$",
"uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1"
},
"umbbd.pathway": {
"description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information.",
"example": "ala",
"homepage": "http://umbbd.ethz.ch/",
"name": "Biocatalysis/Biodegradation Database Mirror (Pathway) at ETH Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1"
},
"umbbd.reaction": {
"description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information.",
"example": "r0001",
"homepage": "http://umbbd.ethz.ch/",
"name": "Biocatalysis/Biodegradation Database Mirror (Reaction) at ETH Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^r\\d+$",
"uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1"
},
"umbbd.rule": {
"description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules.",
"example": "bt0001",
"homepage": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules",
"name": "Biocatalysis/Biodegradation Database Mirror (Biotransformation Rule) at ETH Zurich",
"namespaceEmbeddedInLui": false,
"pattern": "^bt\\d+$",
"uri_format": "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1"
},
"umls": {
"description": "The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank.",
"example": "C0021390",
"homepage": "http://linkedlifedata.com/",
"name": "Unified Medical Language System at LinkedLifeData",
"namespaceEmbeddedInLui": false,
"pattern": "^C\\d+$",
"uri_format": "http://linkedlifedata.com/resource/umls/id/$1"
},
"unigene": {
"description": "A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.",
"example": "4900",
"homepage": "http://www.ncbi.nlm.nih.gov/unigene",
"name": "UniGene at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1"
},
"unii": {
"description": "The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information.",
"example": "3G6A5W338E",
"homepage": "http://fdasis.nlm.nih.gov/srs/",
"name": "UNII at U.S. Food and Drug Administration",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]+$",
"uri_format": "http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=$1"
},
"unimod": {
"description": "Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide).",
"example": "1200",
"homepage": "http://www.unimod.org/",
"name": "Unimod at Matrix Sciences Ltd.",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.unimod.org/modifications_view.php?editid1=$1"
},
"uniparc": {
"description": "The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases.",
"example": "UPI000000000A",
"homepage": "http://www.uniprot.org/uniparc/",
"name": "UniParc through UniProt",
"namespaceEmbeddedInLui": false,
"pattern": "^UPI[A-F0-9]{10}$",
"uri_format": "http://www.uniprot.org/uniparc/$1"
},
"unipathway.compound": {
"description": "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds.",
"example": "UPC04349",
"homepage": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway",
"name": "UniPathway Compound at Swiss Institute of Bioinformatics (SIB)",
"namespaceEmbeddedInLui": false,
"pattern": "^UPC\\d{5}$",
"uri_format": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1"
},
"unipathway.reaction": {
"description": "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions.",
"example": "UCR00226",
"homepage": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway",
"name": "UniPathway Reaction at Swiss Institute of Bioinformatics (SIB)",
"namespaceEmbeddedInLui": false,
"pattern": "^UCR\\d{5}$",
"uri_format": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1"
},
"uniprot": {
"description": "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information.",
"example": "P0DP23",
"homepage": "https://www.uniprot.org/",
"name": "Universal Protein Resource using Persistent URL system",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$",
"uri_format": "https://purl.uniprot.org/uniprot/$1"
},
"uniprot.isoform": {
"description": "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information.",
"example": "Q5BJF6-3",
"homepage": "http://www.uniprot.org/uniparc/",
"name": "UniProt Isoform through UniParc",
"namespaceEmbeddedInLui": false,
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\-\\d+)$",
"uri_format": "http://www.uniprot.org/uniparc/?query=$1"
},
"unists": {
"description": "UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences.",
"example": "456789",
"homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists",
"name": "UniSTS at NCBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1"
},
"unite": {
"description": "UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa.",
"example": "UDB000691",
"homepage": "http://unite.ut.ee/",
"name": "Unite at University of Tartu",
"namespaceEmbeddedInLui": false,
"pattern": "^UDB\\d{6}$",
"uri_format": "http://unite.ut.ee/bl_forw.php?nimi=$1"
},
"uo": {
"description": "Ontology of standardized units",
"example": "0000080",
"homepage": "http://bioportal.bioontology.org/ontologies/UO",
"name": "Unit Ontology through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^UO:\\d{7}?",
"uri_format": "http://purl.bioontology.org/ontology/UO/UO:$1"
},
"uspto": {
"description": "The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement.",
"example": "4145692",
"homepage": "http://patft.uspto.gov/netahtml/PTO/index.html",
"name": "USPTO patents at USPTO",
"namespaceEmbeddedInLui": false,
"pattern": "^(D|PP|R|T|H|X|AI)?\\d+$",
"uri_format": "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1"
},
"validatordb": {
"description": "Database of validation results for ligands and non-standard residues in the Protein Data Bank.",
"example": "ByStructure/2h6o",
"homepage": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/",
"name": "ValidatorDB",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z0-9\\/]+$",
"uri_format": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/$1"
},
"vario": {
"description": "The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level.",
"example": "0294",
"homepage": "http://bioportal.bioontology.org/ontologies/VARIO",
"name": "VariO through BioPortal",
"namespaceEmbeddedInLui": true,
"pattern": "^VariO:\\d+$",
"uri_format": "http://purl.bioontology.org/ontology/VARIO/VariO:$1"
},
"vbase2": {
"description": "The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes.",
"example": "humIGHV025",
"homepage": "http://www.vbase2.org/vbase2.php",
"name": "Vbase2 at German Research Centre for Biotechnology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://www.vbase2.org/vgene.php?id=$1"
},
"vbrc": {
"description": "The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis.",
"example": "35742",
"homepage": "http://vbrc.org/",
"name": "VBRC at University of Alabama",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://vbrc.org/gene_detail.asp?gene_id=$1"
},
"vectorbase": {
"description": "VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis.",
"example": "ISCW007415",
"homepage": "https://www.vectorbase.org/",
"name": "Vectorbase at EMBL-EBI",
"namespaceEmbeddedInLui": false,
"pattern": "^\\D{4}\\d{6}(\\-\\D{2})?$",
"uri_format": "https://www.vectorbase.org/search/site/$1?&site=\"Genome\""
},
"vfb": {
"description": "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster.",
"example": "00000001",
"homepage": "https://VirtualFlyBrain.org",
"name": "Virtual Fly Brain",
"namespaceEmbeddedInLui": false,
"pattern": "^[0-9a-zA-Z]{8}$",
"uri_format": "http://virtualflybrain.org/reports/$1"
},
"vfdb.gene": {
"description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes.",
"example": "VFG2154",
"homepage": "http://www.mgc.ac.cn/VFs/",
"name": "VFDB Gene at Institute of Pathogen Biology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1"
},
"vfdb.genus": {
"description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus.",
"example": "Chlamydia",
"homepage": "http://www.mgc.ac.cn/VFs/",
"name": "VFDB Genus at Institute of Pathogen Biology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+$",
"uri_format": "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1"
},
"viaf": {
"description": "The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web.",
"example": "75121530",
"homepage": "http://viaf.org",
"name": "Virtual International Authority File",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://viaf.org/viaf/$1"
},
"vipr": {
"description": "The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information.",
"example": "BeAn 70563",
"homepage": "http://www.viprbrc.org/brc/home.do?decorator=vipr",
"name": "ViPR Strain at J. Craig Venter Institute",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z 0-9]+$",
"uri_format": "http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena"
},
"viralzone": {
"description": "ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.",
"example": "992",
"homepage": "http://www.expasy.org/viralzone/",
"name": "ViralZone at SIB",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://viralzone.expasy.org/all_by_protein/$1.html"
},
"virsirna": {
"description": "The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region.",
"example": "virsi1909",
"homepage": "http://crdd.osdd.net/servers/virsirnadb",
"name": "VIRsiRNA at Institute of Microbial Technology",
"namespaceEmbeddedInLui": false,
"pattern": "^virsi\\d+$",
"uri_format": "http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1"
},
"vmhmetabolite": {
"description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.",
"example": "h2o",
"homepage": "http://vmh.uni.lu",
"name": "VMH metabolite",
"namespaceEmbeddedInLui": false,
"pattern": "[a-zA-Z0-9_\\(\\_\\)\\[\\]]+",
"uri_format": "http://vmh.uni.lu/#metabolite/$1"
},
"vmhreaction": {
"description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.",
"example": "HEX1",
"homepage": "https://vmh.uni.lu",
"name": "VMH reaction",
"namespaceEmbeddedInLui": false,
"pattern": "[a-zA-Z0-9_\\(\\_\\)\\[\\]]+",
"uri_format": "https://vmh.uni.lu/#reaction/$1"
},
"wb": {
"description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities.",
"example": "WBGene00000001",
"homepage": "https://www.wormbase.org/",
"name": "WormBase",
"namespaceEmbeddedInLui": false,
"pattern": "^WB[A-Z][a-z]+\\d+$",
"uri_format": "https://www.wormbase.org/get?name=$1"
},
"wb.rnai": {
"description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes.",
"example": "WBRNAi00086878",
"homepage": "https://www.wormbase.org/",
"name": "WormBase RNAi",
"namespaceEmbeddedInLui": false,
"pattern": "^WBRNAi\\d{8}$",
"uri_format": "https://www.wormbase.org/species/c_elegans/rnai/$1"
},
"wikidata": {
"description": "Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic.",
"example": "Q2207226",
"homepage": "https://www.wikidata.org/",
"name": "Wikidata at Wikimedia Foundation",
"namespaceEmbeddedInLui": false,
"pattern": "^Q\\d+$",
"uri_format": "https://www.wikidata.org/wiki/$1"
},
"wikigenes": {
"description": "WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process.",
"example": "3771877",
"homepage": "http://www.wikigenes.org/",
"name": "WikiGenes at Massachusetts Institute of Technology",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.wikigenes.org/e/gene/e/$1.html"
},
"wikipathways": {
"description": "WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style. All content is under the Creative Commons Attribution 3.0 Unported license.",
"example": "WP100",
"homepage": "http://www.wikipathways.org/",
"name": "Wikipathways",
"namespaceEmbeddedInLui": false,
"pattern": "WP\\d{1,5}(\\_r\\d+)?$",
"uri_format": "http://www.wikipathways.org/instance/$1"
},
"wikipedia.en": {
"description": "Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay.",
"example": "SM_UB-81",
"homepage": "http://wiki.dbpedia.org/",
"name": "Wikipedia structured content through DBpedia",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Za-z-0-9_]+$",
"uri_format": "http://dbpedia.org/page/$1"
},
"worfdb": {
"description": "WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends).",
"example": "T01B6.1",
"homepage": "http://worfdb.dfci.harvard.edu/",
"name": "Worm Orf DB at Harvard",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+(\\.\\d+)?",
"uri_format": "http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1"
},
"wormpep": {
"description": "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project.",
"example": "CE28239",
"homepage": "https://www.wormbase.org/db/seq/protein",
"name": "Wormpep (Master)",
"namespaceEmbeddedInLui": false,
"pattern": "^CE\\d{5}$",
"uri_format": "https://www.wormbase.org/db/seq/protein?name=WP:$1"
},
"worms": {
"description": "The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts.",
"example": "146421",
"homepage": "http://www.marinespecies.org/",
"name": "World Register of Marine Species",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1"
},
"xenbase": {
"description": "Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions.",
"example": "922462",
"homepage": "http://www.xenbase.org/",
"name": "Xenbase at University of Calgary",
"namespaceEmbeddedInLui": false,
"pattern": "^(XB-GENE-)?\\d+$",
"uri_format": "http://www.xenbase.org/gene/showgene.do?method=displayGeneSummary&geneId=$1"
},
"ydpm": {
"description": "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition.",
"example": "YAL001C",
"homepage": "http://www-deletion.stanford.edu/YDPM/",
"name": "YDPM at Stanford University School of Medicine",
"namespaceEmbeddedInLui": false,
"pattern": "^Y[A-Z]{2}\\d+[CW]$",
"uri_format": "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1"
},
"yeastintron": {
"description": "The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460].",
"example": "SNR17A",
"homepage": "http://intron.ucsc.edu/yeast4.3/",
"name": "Yeast Intron Database version 4.3 at Baskin School of Engineering",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]+$",
"uri_format": "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1"
},
"yetfasco": {
"description": "The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats.",
"example": "YOR172W_571.0",
"homepage": "http://yetfasco.ccbr.utoronto.ca/",
"name": "YeTFasCo at University of Toronto",
"namespaceEmbeddedInLui": false,
"pattern": "^\\w+\\_\\d+(\\.\\d+)?$",
"uri_format": "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1"
},
"yid": {
"description": "The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521].",
"example": "SNR17A",
"homepage": "http://compbio.soe.ucsc.edu/yeast_introns.html",
"name": "Yeast Intron Database version 3 at Baskin School of Engineering",
"namespaceEmbeddedInLui": false,
"pattern": "^[A-Z0-9]+$",
"uri_format": "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1"
},
"yrcpdr": {
"description": "The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions.",
"example": "2673500",
"homepage": "http://www.yeastrc.org/pdr/",
"name": "YRC PDR at University of Washington",
"namespaceEmbeddedInLui": false,
"pattern": "^\\d+$",
"uri_format": "http://yeastrc.org/pdr/viewProtein.do?id=$1"
},
"zfin": {
"description": "ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN.",
"example": "ZDB-GENE-041118-11",
"homepage": "http://zfin.org",
"name": "ZFIN at University of Oregon",
"namespaceEmbeddedInLui": false,
"pattern": "^ZDB\\-\\w+\\-\\d+\\-\\d+$",
"uri_format": "http://zfin.org/$1"
},
"zinc": {
"description": "ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number.",
"example": "ZINC1084",
"homepage": "http://zinc15.docking.org/",
"name": "ZINC at University of California (San Francisco)",
"namespaceEmbeddedInLui": false,
"pattern": "^(ZINC)?\\d+$",
"uri_format": "http://zinc15.docking.org/substances/$1"
}
} ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9659667
bioregistry-0.11.12/src/bioregistry/external/ncbi/ 0000755 0001751 0000177 00000000000 14655546227 021531 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/ncbi/__init__.py 0000644 0001751 0000177 00000012347 14655542206 023642 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download registry information from NCBI."""
import json
import logging
import re
import textwrap
from pathlib import Path
from typing import Dict, Sequence
from urllib.parse import urlsplit, urlunsplit
from bs4 import BeautifulSoup
from pystow.utils import download
from bioregistry.constants import RAW_DIRECTORY
from bioregistry.external.alignment_utils import Aligner
__all__ = [
"get_ncbi",
"NcbiAligner",
]
logger = logging.getLogger(__name__)
DIRECTORY = Path(__file__).parent.resolve()
RAW_PATH = RAW_DIRECTORY / "ncbi.html"
PROCESSED_PATH = DIRECTORY / "processed.json"
URL = "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/"
NCBI_URL_PARTS = urlsplit(URL)
DATA_TABLE_CAPTION_RE = re.compile(r"db_xref List")
MISSING = {
"EnsemblGenomes-Gn",
}
REWRITES = {
"JGI Phytozome": "Phytozome",
"UniProtKB/Swiss-Prot": "UniProt",
}
XREF_PREFIX = [
'/db_xref="', # standard
'db_xref="', # ERIC
'/dbxref="', # PDB
"/db_xref=", # Xenbase
]
REDUNDANT = {
"ATCC(dna)": "ATCC",
"ATCC(in host)": "ATCC",
"UniProtKB/TrEMBL": "UniProt",
"LocusID": "GeneID", # As of March 2005
}
OBSOLETE = {
"ERIC", # should be at http://www.ericbrc.org/portal/eric/, but gone.
"PBmice", # website down
}
def get_ncbi(force_download: bool = False) -> Dict[str, Dict[str, str]]:
"""Get the NCBI data."""
if PROCESSED_PATH.exists() and not force_download:
with PROCESSED_PATH.open() as file:
return json.load(file)
download(url=URL, path=RAW_PATH, force=True)
with RAW_PATH.open() as file:
soup = BeautifulSoup(file, "html.parser")
# find the data table based on its caption element
data_table = soup.find("caption", string=DATA_TABLE_CAPTION_RE).parent
rv = {}
for row in data_table.find_all("tr"):
cells = row.find_all("td")
if not cells:
continue
prefix = cells[0].text.strip()
prefix = REWRITES.get(prefix, prefix)
if prefix in REDUNDANT:
logger.warning(f"skipping {prefix}")
continue
name = cells[2].text.strip()
if not (prefix and name): # blank line
continue
item = {"name": name}
link = cells[0].find("a")
if link and "href" in link.attrs:
link_href = link.attrs["href"].strip()
if link_href:
url_parts = urlsplit(link_href)
if not url_parts.netloc: # handle relative links
if url_parts.path.startswith("/"): # relative to site root
url_parts = (
NCBI_URL_PARTS.scheme,
NCBI_URL_PARTS.netloc,
url_parts.path,
url_parts.query,
url_parts.fragment,
)
else: # relative to the page we got it from
url_parts = (
NCBI_URL_PARTS.scheme,
NCBI_URL_PARTS.netloc,
NCBI_URL_PARTS.path + url_parts.path,
url_parts.query,
url_parts.fragment,
)
item["homepage"] = urlunsplit(url_parts)
else: # absolute links can pass through unchanged
item["homepage"] = link_href
if prefix not in MISSING:
examples = cells[4].text.strip()
# only bother with the first line of examples
example = examples.split("\n")[0].strip()
for xref_prefix in XREF_PREFIX:
if example.startswith(xref_prefix):
stripped_example = example[len(xref_prefix) :].rstrip('"').lstrip()
break
else:
raise ValueError(f"[{prefix}] wrong xref prefix: {example}")
if ":" not in stripped_example:
raise ValueError(f"[{prefix}] not formatted as CURIE: {example}")
if not stripped_example.lower().startswith(prefix.lower()):
raise ValueError(f"[{prefix}] invalid prefix: {example}")
parsed_prefix, identifier = [x.strip() for x in stripped_example.split(":", 1)]
if prefix.casefold() != REWRITES.get(parsed_prefix, parsed_prefix).casefold():
raise ValueError(
f"example does not start with prefix {prefix} -> {identifier} from {example}"
)
item["example"] = identifier
rv[prefix] = item
with PROCESSED_PATH.open("w") as file:
json.dump(rv, file, indent=2, sort_keys=True)
return rv
class NcbiAligner(Aligner):
"""Aligner for NCBI xref registry."""
key = "ncbi"
getter = get_ncbi
getter_kwargs = dict(force_download=False)
curation_header = ("name", "example", "homepage")
def get_curation_row(self, external_id, external_entry) -> Sequence[str]:
"""Return the relevant fields from an NCBI entry for pretty-printing."""
return [
textwrap.shorten(external_entry["name"], 50),
external_entry.get("example"),
external_entry.get("homepage"),
]
if __name__ == "__main__":
NcbiAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254391.0
bioregistry-0.11.12/src/bioregistry/external/ncbi/processed.json 0000644 0001751 0000177 00000043230 14655543167 024415 0 ustar 00runner docker {
"AFTOL": {
"example": "959",
"name": "Assembling the Fungal Tree of Life"
},
"APHIDBASE": {
"example": "ACYPI007424",
"homepage": "http://www.aphidbase.com",
"name": "Aphid Genome Database"
},
"ASAP": {
"example": "ABE-0000006",
"homepage": "https://asap.genetics.wisc.edu/asap/logon.php",
"name": "A Systematic Annotation Package for Community Analysis of Genomes"
},
"ATCC": {
"example": "123456",
"homepage": "http://www.atcc.org/",
"name": "American Type Culture Collection database"
},
"AceView/WormGenes": {
"example": "vha-6",
"homepage": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/",
"name": "AceView Worm Genome"
},
"AntWeb": {
"example": "CASENT0058943-D01",
"homepage": "http://www.antweb.org",
"name": "Ant Database"
},
"ApiDB": {
"example": "cgd1_1090",
"homepage": "http://eupathdb.org/eupathdb/",
"name": "Apicomplexan Database Resources"
},
"ApiDB_CryptoDB": {
"example": "cgd7_20",
"homepage": "http://cryptodb.org/cryptodb/",
"name": "Cryptosporidium Genome Resources"
},
"ApiDB_PlasmoDB": {
"example": "PF11_0344",
"homepage": "http://www.plasmodb.org/plasmo/home.jsp",
"name": "Plasmodium Genome Resources"
},
"ApiDB_ToxoDB": {
"example": "49.m00014",
"homepage": "http://www.toxodb.org/toxo/home.jsp",
"name": "Toxoplasma Genome Resources"
},
"Araport": {
"example": "AT1G01010",
"homepage": "https://www.araport.org/",
"name": "Arabidopsis Information Portal"
},
"Axeldb": {
"example": "32B3.1",
"homepage": "http://www.dkfz-heidelberg.de/molecular_embryology/axeldb.htm",
"name": "A Xenopus laevis database"
},
"BDGP_EST": {
"example": "123456",
"homepage": "http://www.fruitfly.org/EST/index.shtml",
"name": "Berkeley Drosophila Genome Project EST database"
},
"BDGP_INS": {
"example": "123456",
"homepage": "http://www.fruitfly.org/",
"name": "Berkeley Drosophila Genome Project -- Insertion"
},
"BEEBASE": {
"example": "GB55480",
"homepage": "http://hymenopteragenome.org/beebase/?q=home",
"name": "BeeBase"
},
"BEETLEBASE": {
"example": "TC030551",
"homepage": "http://www.beetlebase.org/",
"name": "Tribolium Genome Database -- Insertion"
},
"BEI": {
"example": "NR-50065",
"homepage": "https://www.beiresources.org/",
"name": "BEI Resources"
},
"BGD": {
"example": "BT10004",
"homepage": "http://bovinegenome.org/genepages/btau40/",
"name": "Bovine Genome Database"
},
"BOLD": {
"example": "EPAF263",
"homepage": "http://www.barcodinglife.com",
"name": "Barcode of Life database"
},
"CABRI": {
"example": "ACC 424",
"name": "Common Access to Biological Resources and Information Project"
},
"CCAP": {
"example": "1460/15",
"homepage": "http://www.ccap.ac.uk/",
"name": "Culture Collection of Algae and Protozoa"
},
"CDD": {
"example": "02194",
"homepage": "https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml",
"name": "Conserved Domain Database"
},
"CGD": {
"example": "CAL0005934",
"homepage": "http://www.candidagenome.org/",
"name": "Candida Genome Database"
},
"ECOCYC": {
"example": "sroC",
"homepage": "https://ecocyc.org/",
"name": "E. coli database"
},
"ENSEMBL": {
"example": "HUMAN-Clone-AC005612",
"homepage": "http://useast.ensembl.org/index.html",
"name": "Database of automatically annotated genomic data"
},
"EPD": {
"example": "EP00576",
"homepage": "http://epd.vital-it.ch/",
"name": "Eukaryotic Promoter Database"
},
"ERIC": {
"example": "ABY-0246137",
"name": "Enteropathogen Resource Integration Center"
},
"ESTLIB": {
"example": "1200",
"name": "EBI's EST library identifier"
},
"EcoGene": {
"example": "EG11277",
"homepage": "http://ecogene.org",
"name": "Database of Escherichia coli Sequence and Function"
},
"EnsemblGenomes": {
"example": "AAC73116",
"homepage": "http://ensemblgenomes.org",
"name": "Extending Ensembl across taxonomic space"
},
"EnsemblGenomes-Gn": {
"homepage": "http://ensemblgenomes.org",
"name": "EnsemblGenomes Gene"
},
"EnsemblGenomes-Tr": {
"example": "MAPG_00606T0",
"homepage": "http://ensemblgenomes.org",
"name": "EnsemblGenomes Transcript"
},
"FANTOM_DB": {
"example": "0610005A07",
"homepage": "http://fantom.gsc.riken.go.jp/",
"name": "Database of Functional Annotation of Mouse"
},
"FBOL": {
"example": "2224",
"homepage": "http://www.fungalbarcoding.org/",
"name": "International Fungal Working Group Fungal Barcoding."
},
"FLYBASE": {
"example": "FBgn0000024",
"homepage": "http://www.flybase.org/",
"name": "Database of Genetic and molecular data of Drosophila."
},
"Fungorum": {
"example": "ID550186",
"homepage": "http://www.indexfungorum.org",
"name": "Index Fungorum"
},
"GABI": {
"example": "HA05J18",
"homepage": "http://www.gabipd.org/information/about.shtml",
"name": "Network of Different Plant Genomic Research Projects"
},
"GDB": {
"example": "G00-128-600",
"name": "Human Genome Database accession numbers"
},
"GI": {
"example": "1234567890",
"name": "GenInfo identifier, used as a unique sequence identifier for nucleotide and proteins"
},
"GO": {
"example": "123",
"homepage": "http://amigo.geneontology.org/",
"name": "Gene Ontology Database identifier"
},
"GOA": {
"example": "P01100",
"homepage": "http://www.ebi.ac.uk/GOA/",
"name": "Gene Ontology Annotation Database Identifier"
},
"GRIN": {
"example": "1005973",
"homepage": "http://www.ars-grin.gov/",
"name": "Germplasm Resources Information Network"
},
"GeneDB": {
"example": "SPCC285.16c",
"homepage": "http://www.genedb.org/",
"name": "Curated gene database for Leishmania major and Trypanosoma brucei"
},
"GeneID": {
"example": "3054987",
"homepage": "https://www.ncbi.nlm.nih.gov/gene",
"name": "Entrez Gene Database (replaces NCBI Locus Link)"
},
"Greengenes": {
"example": "269185",
"homepage": "http://greengenes.lbl.gov/",
"name": "16S rRNA gene database"
},
"H-InvDB": {
"example": "HIT000000001",
"homepage": "http://www.h-invitational.jp",
"name": "H-Invitational Database"
},
"HGNC": {
"example": "HGNC:2041",
"homepage": "http://www.genenames.org/cgi-bin/search",
"name": "Human Gene Nomenclature Database"
},
"HMP": {
"example": "0536",
"homepage": "http://www.hmpdacc.org/",
"name": "Human Microbiome Project"
},
"HOMD": {
"example": "tax_078",
"homepage": "http://www.homd.org/",
"name": "Human Oral Microbiome Database"
},
"HPM": {
"example": "8106",
"homepage": "http://www.humanproteomemap.org/",
"name": "Human Proteome Map"
},
"HSSP": {
"example": "12GS",
"name": "Database of homology-derived secondary structure of proteins"
},
"I5KNAL": {
"example": "OFAS008986",
"homepage": "https://i5k.nal.usda.gov/",
"name": "i5k Workspace"
},
"IKMC": {
"example": "66303",
"homepage": "http://www.knockoutmouse.org/",
"name": "International Knockout Mouse Consortium"
},
"IMGT/GENE-DB": {
"example": "IGKC",
"homepage": "http://www.imgt.org/genedb/",
"name": "Immunogenetics database, immunoglobulin and T-cell receptor genes"
},
"IMGT/HLA": {
"example": "HLA00031",
"homepage": "http://www.ebi.ac.uk/imgt/hla/",
"name": "Immunogenetics database, human MHC"
},
"IMGT/LIGM": {
"example": "U03895",
"homepage": "http://www.imgt.org/IMGTinformation/LIGM.html",
"name": "Immunogenetics database, immunoglobulins and T-cell receptors"
},
"IRD": {
"example": "CEIRS-CIP045-123456.2",
"homepage": "http://www.fludb.org/",
"name": "Influenza Research Database"
},
"ISFinder": {
"example": "ISA1083-2",
"homepage": "http://www-is.biotoul.fr/",
"name": "Insertion sequence elements database"
},
"ISHAM-ITS": {
"example": "MITS310",
"homepage": "http://its.mycologylab.org/DefaultSlideUD.aspx?Page=Home",
"name": "ITS reference database for pathogenic fungi"
},
"InterPro": {
"example": "IPR002928",
"homepage": "http://www.ebi.ac.uk/interpro/",
"name": "InterPro protein sequence database"
},
"IntrepidBio": {
"example": "5259707746",
"homepage": "http://server1.intrepidbio.com/",
"name": "Intrepid BioInformatics"
},
"JCM": {
"example": "1339",
"homepage": "http://www.jcm.riken.go.jp/",
"name": "Japan Collection of Microorganisms"
},
"JGIDB": {
"example": "Chluvu1_81011",
"homepage": "http://genome.jgi-psf.org/",
"name": "JGI Genome Portal"
},
"MGI": {
"example": "MGI:1894891",
"homepage": "http://www.informatics.jax.org/",
"name": "Mouse Genome Informatics"
},
"MIM": {
"example": "123456",
"homepage": "https://www.ncbi.nlm.nih.gov/omim",
"name": "Mendelian Inheritance in Man numbers"
},
"MaizeGDB": {
"example": "635633",
"homepage": "http://www.maizegdb.org/",
"name": "Maize Genome Database unique identifiers"
},
"MarpolBase": {
"example": "Mp1g00010.1",
"homepage": "http://marchantia.info/",
"name": "Genome Database for Marchantia polymorpha"
},
"MedGen": {
"example": "C0010674",
"homepage": "https://www.ncbi.nlm.nih.gov/medgen",
"name": "Human Medical Genetics"
},
"MycoBank": {
"example": "8284",
"homepage": "http://www.mycobank.org",
"name": "Fungal Nomenclature and Species Bank"
},
"NBRC": {
"example": "3189",
"homepage": "http://www.nbrc.nite.go.jp/e/catalog-e.html",
"name": "NITE Biological Resource Center"
},
"NMPDR": {
"example": "fig|306254.1.peg.183",
"homepage": "http://www.nmpdr.org",
"name": "National Microbial Pathogen Data Resource"
},
"NRESTdb": {
"example": "Y01A01",
"homepage": "http://www.mgi-nibm.my/nrestdb/",
"name": "Natural Rubber EST database"
},
"NextDB": {
"example": "CELK01662",
"homepage": "http://nematode.lab.nig.ac.jp/",
"name": "Nematode Expression Pattern DataBase"
},
"OrthoMCL": {
"example": "OG5_130679",
"homepage": "http://orthomcl.org/orthomcl",
"name": "Ortholog Groups of Protein Sequences"
},
"Osa1": {
"example": "LOC_Os01g12345",
"homepage": "http://rice.plantbiology.msu.edu/",
"name": "Rice Genome Annotation Project"
},
"PBmice": {
"example": "38",
"homepage": "http://www.idmshanghai.cn/PBmice/",
"name": "PiggyBac Mutagenesis Information Center"
},
"PDB": {
"example": "12GS",
"homepage": "http://www.rcsb.org/pdb/",
"name": "Biological macromolecule three dimensional structure database"
},
"PFAM": {
"example": "PF00003",
"homepage": "http://pfam.xfam.org/",
"name": "Collection of protein families"
},
"PGN": {
"example": "aam01-1ms3-a05",
"name": "Plant Genome Network"
},
"PIR": {
"example": "S12345",
"homepage": "http://pir.georgetown.edu/",
"name": "Protein Information Resource accession numbers"
},
"PSEUDO": {
"example": "CAC44644.1",
"name": "EMBL pseudo protein identifier"
},
"Pathema": {
"example": "BA_4405",
"homepage": "http://pathema.jcvi.org/",
"name": "Pathema Genome Resource"
},
"Phytozome": {
"example": "Glyma0021s00410",
"homepage": "http://phytozome.jgi.doe.gov/pz/portal.html",
"name": "Plant Genome Network"
},
"PomBase": {
"example": "SPBC11B10.09",
"homepage": "http://www.pombase.org/",
"name": "Database of Structural and Functional Data for Schizosaccaromyces pombe"
},
"PseudoCAP": {
"example": "PA0001",
"homepage": "http://www.pseudomonas.com/",
"name": "Pseudomonas Genome Database"
},
"RAP-DB": {
"example": "Os01g1234567",
"homepage": "http://rapdb.dna.affrc.go.jp/",
"name": "Rice Annotation Project Database"
},
"RATMAP": {
"example": "5",
"name": "Rat Genome Database"
},
"RBGE_garden": {
"example": "20021433",
"homepage": "http://elmer.rbge.org.uk/bgbase/livcol/bgbaselivcol.php",
"name": "Royal Botanic Garden Edinburgh Living Collections"
},
"RBGE_herbarium": {
"example": "E00217291",
"homepage": "http://elmer.rbge.org.uk/bgbase/vherb/bgbasevherb.php",
"name": "Royal Botanic Garden Edinburgh Herbarium"
},
"RFAM": {
"example": "RF00230",
"homepage": "http://www.sanger.ac.uk/Software/Rfam/",
"name": "RNA families database of alignments and CMs"
},
"RGD": {
"example": "620528",
"homepage": "http://rgd.mcw.edu/rgdweb/search/search.html",
"name": "Rat Genome Database"
},
"RNAcentral": {
"example": "URS00001B9622_9606",
"homepage": "http://rnacentral.org",
"name": "Noncoding RNA Sequence Database"
},
"RZPD": {
"example": "IMAGp998I142450Q6",
"homepage": "http://www.gate2biotech.com/rzpd-german-science-centre-for-genome/",
"name": "Resource Centre Primary Database Clone Identifiers"
},
"RiceGenes": {
"example": "AA231856",
"homepage": "http://www.gramene.org/",
"name": "Rice database accession numbers"
},
"SEED": {
"example": "fig|83331.1.peg.1",
"homepage": "http://www.theseed.org",
"name": "The SEED Database"
},
"SGD": {
"example": "L0000470",
"homepage": "http://www.yeastgenome.org/",
"name": "Saccharomyces Genome Database"
},
"SGN": {
"example": "E553090",
"homepage": "http://www.sgn.cornell.edu",
"name": "SOL Genomics Network"
},
"SK-FST": {
"example": "FST:SK32219",
"name": "Saskatoon Arabidopsis T-DNA mutant population - SK Collection"
},
"SRPDB": {
"example": "Arth.aure._CP000474",
"homepage": "http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html",
"name": "Signal Recognition Particle Database"
},
"SoyBase": {
"example": "Satt005",
"homepage": "http://soybase.org",
"name": "Glycine max Genome Database"
},
"SubtiList": {
"example": "BG10001",
"homepage": "http://genolist.pasteur.fr/SubtiList/",
"name": "Bacillus subtilis genome sequencing project"
},
"TAIR": {
"example": "AT1F51370",
"homepage": "http://www.arabidopsis.org/servlets/Search?type=gene&action=new_search",
"name": "Arabidopsis IR"
},
"TIGRFAM": {
"example": "TIGR00094",
"homepage": "http://www.tigr.org/TIGRFAMs/index.shtml",
"name": "TIGR protein families"
},
"TubercuList": {
"example": "Rv3322c",
"homepage": "http://tuberculist.epfl.ch/",
"name": "TubercuList knowledge base"
},
"UNILIB": {
"example": "1002",
"name": "Unified Library Database, a library-level view of the EST and SAGE libraries present in dbEST, UniGene and SAGEmap"
},
"UNITE": {
"example": "UDB000157",
"homepage": "http://unite.ut.ee/index.php",
"name": "Molecular database for the identification of fungi"
},
"UniProt": {
"example": "P12345",
"homepage": "http://www.uniprot.org",
"name": "section of the UniProt Knowledgebase, containing annotated records, which include curator-evaluated computational analysis, as well as, information extracted from the literature"
},
"UniSTS": {
"example": "486599",
"name": "Database of Sequence Tagged Sites"
},
"VBASE2": {
"example": "humIGKV165",
"homepage": "http://www.vbase2.org/",
"name": "Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse"
},
"VGNC": {
"example": "VGNC:4927",
"homepage": "http://vertebrate.genenames.org/data/gene-symbol-report/#!/",
"name": "Vertebrate Gene Nomenclature Committee"
},
"VISTA": {
"example": "hs123",
"homepage": "http://enhancer.lbl.gov/",
"name": "Vista Enhancer Browser"
},
"VectorBase": {
"example": "ENSANGG00000007825",
"homepage": "http://www.vectorbase.org/index.php",
"name": "Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens"
},
"ViPR": {
"example": "HRV-A34_p1058_sR263_2008",
"homepage": "http://www.viprbrc.org/brc/home.do?decorator=vipr",
"name": "Virus Pathogen Resource"
},
"WorfDB": {
"example": "pos-1",
"homepage": "http://worfdb.dfci.harvard.edu/",
"name": "C. elegans ORFeome cloning project"
},
"WormBase": {
"example": "R13H7",
"homepage": "http://www.wormbase.org/",
"name": "Caenorhabditis elegans Genome Database"
},
"Xenbase": {
"example": "XB-GENE-1019547",
"homepage": "http://www.xenbase.org/common/",
"name": "Xenopus laevis and tropicalis biology and genomics resource"
},
"ZFIN": {
"example": "ZDB-GENE-011205-17",
"homepage": "http://zfin.org",
"name": "Zebrafish Information Network"
},
"dbEST": {
"example": "123456",
"homepage": "https://www.ncbi.nlm.nih.gov/genbank/dbest",
"name": "EST database maintained at the NCBI."
},
"dbProbe": {
"example": "38",
"homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe",
"name": "NCBI Probe database Public registry of nucleic acid reagents"
},
"dbSNP": {
"example": "4647",
"homepage": "https://www.ncbi.nlm.nih.gov/snp",
"name": "Variation database maintained at the NCBI."
},
"dbSTS": {
"example": "456789",
"name": "STS database maintained at the NCBI."
},
"dictyBase": {
"example": "DDB0191090",
"homepage": "http://dictybase.org/",
"name": "Dictyostelium genome database"
},
"miRBase": {
"example": "MI0000681",
"homepage": "http://www.mirbase.org/",
"name": "miRNA Database"
},
"niaEST": {
"example": "L0304H12-3",
"homepage": "http://esbank.nia.nih.gov/",
"name": "NIA Mouse cDNA Project"
},
"taxon": {
"example": "4932",
"homepage": "https://www.ncbi.nlm.nih.gov/taxonomy",
"name": "NCBI's taxonomic identifier"
}
} ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9659667
bioregistry-0.11.12/src/bioregistry/external/obofoundry/ 0000755 0001751 0000177 00000000000 14655546227 023004 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/obofoundry/__init__.py 0000644 0001751 0000177 00000011605 14655542206 025111 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download registry information from the OBO Foundry."""
import json
import logging
from pathlib import Path
from typing import Mapping, Optional
import requests
import yaml
from pystow.utils import download
from bioregistry.constants import RAW_DIRECTORY
from bioregistry.external.alignment_utils import Aligner
__all__ = [
"get_obofoundry",
"get_obofoundry_example",
"OBOFoundryAligner",
]
logger = logging.getLogger(__name__)
DIRECTORY = Path(__file__).parent.resolve()
RAW_PATH = RAW_DIRECTORY / "obofoundry.yaml"
PROCESSED_PATH = DIRECTORY / "processed.json"
OBOFOUNDRY_URL = "https://raw.githubusercontent.com/OBOFoundry/OBOFoundry.github.io/master/registry/ontologies.yml"
SKIP = {
"obo_rel": "replaced",
}
def get_obofoundry(force_download: bool = False, force_process: bool = False):
"""Get the OBO Foundry registry."""
if PROCESSED_PATH.exists() and not force_download and not force_process:
with PROCESSED_PATH.open() as file:
return json.load(file)
download(url=OBOFOUNDRY_URL, path=RAW_PATH, force=force_download)
with RAW_PATH.open() as file:
data = yaml.full_load(file)
rv = {
record["id"]: _process(record) for record in data["ontologies"] if record["id"] not in SKIP
}
for key, record in rv.items():
for depends_on in record.get("depends_on", []):
if depends_on not in rv:
logger.warning("issue in %s: invalid dependency: %s", key, depends_on)
else:
rv[depends_on].setdefault("appears_in", []).append(key)
with PROCESSED_PATH.open("w") as file:
json.dump(rv, file, indent=2, sort_keys=True, ensure_ascii=False)
return rv
def _process(record):
for key in ("browsers", "usages", "build", "layout", "taxon"):
if key in record:
del record[key]
oid = record["id"].lower()
rv = {
"name": record["title"],
"description": record.get("description"),
"deprecated": record["activity_status"] != "active",
"homepage": record.get("homepage") or record.get("repository"),
"preferredPrefix": record.get("preferredPrefix"),
"license": record.get("license", {}).get("label"),
"license.url": record.get("license", {}).get("url"),
"contact": record.get("contact", {}).get("email"),
"contact.label": record.get("contact", {}).get("label"),
"contact.github": record.get("contact", {}).get("github"),
"contact.orcid": record.get("contact", {}).get("orcid"),
"repository": record.get("repository"),
"domain": record.get("domain"),
}
for key in ("publications", "twitter"):
value = record.get(key)
if value:
rv[key] = value
dependencies = record.get("dependencies")
if dependencies:
rv["depends_on"] = sorted(
dependency["id"]
for dependency in record.get("dependencies", [])
if dependency.get("type") not in {"BridgeOntology"}
)
for product in record.get("products", []):
if product["id"] == f"{oid}.obo":
rv["download.obo"] = product["ontology_purl"]
elif product["id"] == f"{oid}.json":
rv["download.json"] = product["ontology_purl"]
elif product["id"] == f"{oid}.owl":
rv["download.owl"] = product["ontology_purl"]
logo = record.get("depicted_by")
if logo:
if logo.startswith("/images/"):
logo = f"https://obofoundry.org{logo}"
rv["logo"] = logo
return {k: v for k, v in rv.items() if v is not None}
def get_obofoundry_example(prefix: str) -> Optional[str]:
"""Get an example identifier from the OBO Library PURL configuration."""
url = f"https://raw.githubusercontent.com/OBOFoundry/purl.obolibrary.org/master/config/{prefix}.yml"
data = yaml.safe_load(requests.get(url).content)
examples = data.get("example_terms")
if not examples:
return None
return examples[0].rsplit("_")[-1]
class OBOFoundryAligner(Aligner):
"""Aligner for the OBO Foundry."""
key = "obofoundry"
getter = get_obofoundry
curation_header = ("deprecated", "name", "description")
include_new = True
normalize_invmap = True
def get_skip(self) -> Mapping[str, str]:
"""Get the prefixes in the OBO Foundry that should be skipped."""
return SKIP
def _align_action(self, bioregistry_id, external_id, external_entry):
super()._align_action(bioregistry_id, external_id, external_entry)
if (
self.manager.get_example(bioregistry_id)
or self.manager.has_no_terms(bioregistry_id)
or self.manager.is_deprecated(bioregistry_id)
):
return
example = get_obofoundry_example(external_id)
if example:
self.internal_registry[bioregistry_id]["example"] = example
if __name__ == "__main__":
OBOFoundryAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723255145.0
bioregistry-0.11.12/src/bioregistry/external/obofoundry/processed.json 0000644 0001751 0000177 00000661541 14655544551 025701 0 ustar 00runner docker {
"aao": {
"contact": "david.c.blackburn@gmail.com",
"contact.label": "David Blackburn",
"contact.orcid": "0000-0002-1810-9886",
"deprecated": true,
"domain": "anatomy and development",
"homepage": "http://github.com/seger/aao",
"name": "Amphibian gross anatomy"
},
"ado": {
"contact": "alpha.tom.kodamullil@scai.fraunhofer.de",
"contact.github": "akodamullil",
"contact.label": "Alpha Tom Kodamullil",
"contact.orcid": "0000-0001-9896-3531",
"depends_on": [
"bfo"
],
"deprecated": false,
"description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/ado.owl",
"homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Alzheimer's Disease Ontology",
"preferredPrefix": "ADO",
"repository": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO"
},
"adw": {
"contact": "adw_geeks@umich.edu",
"contact.label": "Animal Diversity Web technical staff",
"deprecated": true,
"domain": "organisms",
"homepage": "http://www.animaldiversity.org",
"name": "Animal natural history and life history"
},
"aeo": {
"appears_in": [
"ehdaa2"
],
"contact": "J.Bard@ed.ac.uk",
"contact.label": "Jonathan Bard",
"deprecated": true,
"description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology",
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/aeo.owl",
"homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology/",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Anatomical Entity Ontology",
"preferredPrefix": "AEO",
"repository": "https://github.com/obophenotype/human-developmental-anatomy-ontology"
},
"aero": {
"contact": "mcourtot@gmail.com",
"contact.label": "Melanie Courtot",
"contact.orcid": "0000-0002-9551-6370",
"deprecated": true,
"description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/aero.owl",
"homepage": "http://purl.obolibrary.org/obo/aero",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Adverse Event Reporting Ontology"
},
"afpo": {
"contact": "mcmelek@msn.com",
"contact.github": "Melek-C",
"contact.label": "Melek Chaouch",
"contact.orcid": "0000-0001-5868-4204",
"deprecated": false,
"description": "AfPO is an ontology that can be used in the study of diverse populations across Africa. It brings together publicly available demographic, anthropological and genetic data relating to African people in a standardised and structured format. The AfPO can be employed to classify African study participants comprehensively in prospective research studies. It can also be used to classify past study participants by mapping them using a language or ethnicity identifier or synonyms.",
"domain": "organisms",
"download.json": "http://purl.obolibrary.org/obo/afpo.json",
"download.obo": "http://purl.obolibrary.org/obo/afpo.obo",
"download.owl": "http://purl.obolibrary.org/obo/afpo.owl",
"homepage": "https://github.com/h3abionet/afpo",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "African Population Ontology",
"preferredPrefix": "AfPO",
"repository": "https://github.com/h3abionet/afpo"
},
"agro": {
"contact": "m.a.laporte@cgiar.org",
"contact.github": "marieALaporte",
"contact.label": "Marie-AngΓ©lique Laporte",
"contact.orcid": "0000-0002-8461-9745",
"depends_on": [
"bfo",
"envo",
"foodon",
"go",
"iao",
"ncbitaxon",
"obi",
"pato",
"peco",
"po",
"ro",
"to",
"uo",
"xco"
],
"deprecated": false,
"description": "Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments",
"domain": "agriculture",
"download.owl": "http://purl.obolibrary.org/obo/agro.owl",
"homepage": "https://github.com/AgriculturalSemantics/agro",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Agronomy Ontology",
"preferredPrefix": "AGRO",
"publications": [
{
"id": "http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf",
"title": "Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics."
}
],
"repository": "https://github.com/AgriculturalSemantics/agro"
},
"aism": {
"appears_in": [
"colao",
"lepao"
],
"contact": "entiminae@gmail.com",
"contact.github": "JCGiron",
"contact.label": "Jennifer C. GirΓ³n",
"contact.orcid": "0000-0002-0851-6883",
"depends_on": [
"bfo",
"bspo",
"caro",
"pato",
"ro",
"uberon"
],
"deprecated": false,
"description": "The AISM contains terms used in insect biodiversity research for describing structures of the exoskeleton and the skeletomuscular system. It aims to serve as the basic backbone of generalized terms to be expanded with order-specific terminology.",
"domain": "anatomy and development",
"download.json": "http://purl.obolibrary.org/obo/aism.json",
"download.obo": "http://purl.obolibrary.org/obo/aism.obo",
"download.owl": "http://purl.obolibrary.org/obo/aism.owl",
"homepage": "https://github.com/insect-morphology/aism",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)",
"preferredPrefix": "AISM",
"repository": "https://github.com/insect-morphology/aism"
},
"amphx": {
"contact": "hescriva@obs-banyuls.fr",
"contact.github": "hescriva",
"contact.label": "Hector Escriva",
"contact.orcid": "0000-0001-7577-5028",
"depends_on": [
"uberon"
],
"deprecated": false,
"description": "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/amphx.obo",
"download.owl": "http://purl.obolibrary.org/obo/amphx.owl",
"homepage": "https://github.com/EBISPOT/amphx_ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "The Amphioxus Development and Anatomy Ontology",
"preferredPrefix": "AMPHX",
"repository": "https://github.com/EBISPOT/amphx_ontology"
},
"apo": {
"contact": "stacia@stanford.edu",
"contact.github": "srengel",
"contact.label": "Stacia R Engel",
"contact.orcid": "0000-0001-5472-917X",
"deprecated": false,
"description": "A structured controlled vocabulary for the phenotypes of Ascomycete fungi",
"domain": "phenotype",
"download.obo": "http://purl.obolibrary.org/obo/apo.obo",
"download.owl": "http://purl.obolibrary.org/obo/apo.owl",
"homepage": "http://www.yeastgenome.org/",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Ascomycete phenotype ontology",
"preferredPrefix": "APO",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/20157474",
"title": "New mutant phenotype data curation system in the Saccharomyces Genome Database"
}
],
"repository": "https://github.com/obophenotype/ascomycete-phenotype-ontology"
},
"apollo_sv": {
"appears_in": [
"scdo"
],
"contact": "hoganwr@gmail.com",
"contact.github": "hoganwr",
"contact.label": "William Hogan",
"contact.orcid": "0000-0002-9881-1017",
"deprecated": false,
"description": "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/apollo_sv.owl",
"homepage": "https://github.com/ApolloDev/apollo-sv",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Apollo Structured Vocabulary",
"preferredPrefix": "APOLLO_SV",
"publications": [
{
"id": "https://doi.org/10.1186/s13326-016-0092-y",
"title": "The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation"
}
],
"repository": "https://github.com/ApolloDev/apollo-sv"
},
"aro": {
"appears_in": [
"scdo"
],
"contact": "mcarthua@mcmaster.ca",
"contact.github": "agmcarthur",
"contact.label": "Andrew G. McArthur",
"contact.orcid": "0000-0002-1142-3063",
"deprecated": false,
"description": "Antibiotic resistance genes and mutations",
"domain": "microbiology",
"download.owl": "http://purl.obolibrary.org/obo/aro.owl",
"homepage": "https://github.com/arpcard/aro",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Antibiotic Resistance Ontology",
"preferredPrefix": "ARO",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/31665441",
"title": "CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database."
}
],
"repository": "https://github.com/arpcard/aro"
},
"ato": {
"contact": "david.c.blackburn@gmail.com",
"contact.label": "David Blackburn",
"contact.orcid": "0000-0002-1810-9886",
"deprecated": true,
"domain": "organisms",
"homepage": "http://www.amphibanat.org",
"name": "Amphibian taxonomy"
},
"bcgo": {
"contact": "jiezheng@pennmedicine.upenn.edu",
"contact.github": "zhengj2007",
"contact.label": "Jie Zheng",
"contact.orcid": "0000-0002-2999-0103",
"deprecated": true,
"description": "An application ontology built for beta cell genomics studies.",
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/bcgo.owl",
"homepage": "https://github.com/obi-bcgo/bcgo",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Beta Cell Genomics Ontology",
"repository": "https://github.com/obi-bcgo/bcgo"
},
"bco": {
"appears_in": [
"fovt"
],
"contact": "rlwalls2008@gmail.com",
"contact.github": "ramonawalls",
"contact.label": "Ramona Walls",
"contact.orcid": "0000-0001-8815-0078",
"deprecated": false,
"description": "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.",
"domain": "organisms",
"download.owl": "http://purl.obolibrary.org/obo/bco.owl",
"homepage": "https://github.com/BiodiversityOntologies/bco",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Biological Collections Ontology",
"preferredPrefix": "BCO",
"publications": [
{
"id": "https://doi.org/10.1371/journal.pone.0089606",
"title": "Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies"
}
],
"repository": "https://github.com/BiodiversityOntologies/bco"
},
"bfo": {
"appears_in": [
"ado",
"agro",
"aism",
"cdno",
"colao",
"duo",
"ecocore",
"epio",
"foodon",
"fovt",
"hso",
"lepao",
"mco",
"ons",
"pcl",
"pco",
"psdo",
"rbo",
"uberon",
"xpo",
"zp"
],
"contact": "phismith@buffalo.edu",
"contact.github": "phismith",
"contact.label": "Barry Smith",
"contact.orcid": "0000-0003-1384-116X",
"deprecated": false,
"description": "The upper level ontology upon which OBO Foundry ontologies are built.",
"domain": "upper",
"download.obo": "http://purl.obolibrary.org/obo/bfo.obo",
"download.owl": "http://purl.obolibrary.org/obo/bfo.owl",
"homepage": "http://ifomis.org/bfo/",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"logo": "https://avatars2.githubusercontent.com/u/12972134?v=3&s=200",
"name": "Basic Formal Ontology",
"preferredPrefix": "BFO",
"repository": "https://github.com/BFO-ontology/BFO"
},
"bila": {
"contact": "henrich@embl.de",
"contact.github": "ThorstenHen",
"contact.label": "Thorsten Henrich",
"contact.orcid": "0000-0002-1548-3290",
"deprecated": true,
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/bila.owl",
"homepage": "http://4dx.embl.de/4DXpress",
"name": "Bilateria anatomy"
},
"bootstrep": {
"contact": "vlee@ebi.ac.uk",
"contact.label": "Vivian Lee",
"deprecated": true,
"domain": "chemistry and biochemistry",
"homepage": "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html",
"name": "Gene Regulation Ontology"
},
"bspo": {
"appears_in": [
"aism",
"colao",
"fovt",
"lepao",
"uberon",
"zp"
],
"contact": "cjmungall@lbl.gov",
"contact.github": "cmungall",
"contact.label": "Chris Mungall",
"contact.orcid": "0000-0002-6601-2165",
"deprecated": false,
"description": "An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/bspo.obo",
"download.owl": "http://purl.obolibrary.org/obo/bspo.owl",
"homepage": "https://github.com/obophenotype/biological-spatial-ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Biological Spatial Ontology",
"preferredPrefix": "BSPO",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/25140222",
"title": "Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology."
}
],
"repository": "https://github.com/obophenotype/biological-spatial-ontology"
},
"bto": {
"contact": "c.dudek@tu-braunschweig.de",
"contact.github": "chdudek",
"contact.label": "Christian-Alexander Dudek",
"contact.orcid": "0000-0001-9117-7909",
"deprecated": false,
"description": "A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.",
"domain": "anatomy and development",
"download.json": "http://purl.obolibrary.org/obo/bto.json",
"download.obo": "http://purl.obolibrary.org/obo/bto.obo",
"download.owl": "http://purl.obolibrary.org/obo/bto.owl",
"homepage": "http://www.brenda-enzymes.org",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "BRENDA tissue / enzyme source",
"preferredPrefix": "BTO",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/21030441",
"title": "The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources"
}
],
"repository": "https://github.com/BRENDA-Enzymes/BTO"
},
"caro": {
"appears_in": [
"aism",
"colao",
"gallont",
"lepao",
"pco",
"ehdaa2"
],
"contact": "haendel@ohsu.edu",
"contact.github": "mellybelly",
"contact.label": "Melissa Haendel",
"contact.orcid": "0000-0001-9114-8737",
"deprecated": false,
"description": "An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species",
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/caro.owl",
"homepage": "https://github.com/obophenotype/caro/",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Common Anatomy Reference Ontology",
"preferredPrefix": "CARO",
"repository": "https://github.com/obophenotype/caro"
},
"cdao": {
"contact": "balhoff@renci.org",
"contact.github": "balhoff",
"contact.label": "Jim Balhoff",
"contact.orcid": "0000-0002-8688-6599",
"deprecated": false,
"description": "a formalization of concepts and relations relevant to evolutionary comparative analysis",
"domain": "organisms",
"download.owl": "http://purl.obolibrary.org/obo/cdao.owl",
"homepage": "https://github.com/evoinfo/cdao",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Comparative Data Analysis Ontology",
"preferredPrefix": "CDAO",
"publications": [
{
"id": "https://doi.org/10.4137/EBO.S2320",
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"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Drosophila development",
"preferredPrefix": "FBdv",
"repository": "https://github.com/FlyBase/drosophila-developmental-ontology"
},
"fbsp": {
"contact": "cp390@cam.ac.uk",
"contact.github": "Clare72",
"contact.label": "Clare Pilgrim",
"contact.orcid": "0000-0002-1373-1705",
"deprecated": true,
"description": "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.",
"domain": "organisms",
"download.owl": "http://purl.obolibrary.org/obo/fbsp.owl",
"homepage": "http://www.flybase.org/",
"name": "Fly taxonomy"
},
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"contact": "georgeta.bordea@u-bordeaux.fr",
"contact.github": "getbordea",
"contact.label": "Georgeta Bordea",
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"deprecated": false,
"description": "Food-Drug interactions automatically extracted from scientific literature",
"domain": "diet, metabolomics, and nutrition",
"download.owl": "http://purl.obolibrary.org/obo/fideo.owl",
"homepage": "https://gitub.u-bordeaux.fr/erias/fideo",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Food Interactions with Drugs Evidence Ontology",
"preferredPrefix": "FIDEO",
"repository": "https://gitub.u-bordeaux.fr/erias/fideo"
},
"fix": {
"contact.label": "chEBI",
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"description": "An ontology of physico-chemical methods and properties.",
"domain": "chemistry and biochemistry",
"download.obo": "http://purl.obolibrary.org/obo/fix.obo",
"download.owl": "http://purl.obolibrary.org/obo/fix.owl",
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"name": "Physico-chemical methods and properties"
},
"flopo": {
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],
"contact": "robert.hoehndorf@kaust.edu.sa",
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"contact.label": "Robert Hoehndorf",
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"deprecated": false,
"description": "Traits and phenotypes of flowering plants occurring in digitized Floras",
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"name": "Flora Phenotype Ontology",
"preferredPrefix": "FLOPO",
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}
],
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},
"flu": {
"contact": "burkesquires@gmail.com",
"contact.label": "Burke Squires",
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"download.owl": "http://purl.obolibrary.org/obo/flu.owl",
"homepage": "http://purl.obolibrary.org/obo/flu/",
"name": "Influenza Ontology"
},
"fma": {
"contact": "mejino@u.washington.edu",
"contact.label": "Onard Mejino",
"deprecated": true,
"description": "This is currently a slimmed down version of FMA",
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/fma.owl",
"homepage": "http://si.washington.edu/projects/fma",
"license": "CC BY 3.0",
"license.url": "https://creativecommons.org/licenses/by/3.0/",
"name": "Foundational Model of Anatomy Ontology (subset)",
"preferredPrefix": "FMA",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/18688289",
"title": "Translating the Foundational Model of Anatomy into OWL"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/18360535",
"title": "The foundational model of anatomy in OWL: Experience and perspectives"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/16779026",
"title": "Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study"
}
],
"repository": "https://bitbucket.org/uwsig/fma"
},
"fobi": {
"contact": "polcaes@gmail.com",
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"contact.label": "Pol Castellano Escuder",
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"depends_on": [
"chebi",
"foodon"
],
"deprecated": false,
"description": "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data",
"domain": "diet, metabolomics, and nutrition",
"download.owl": "http://purl.obolibrary.org/obo/fobi.owl",
"homepage": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Food-Biomarker Ontology",
"preferredPrefix": "FOBI",
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{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/32556148",
"title": "FOBI: an ontology to represent food intake data and associate it with metabolomic data"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/34601570",
"title": "The fobitools framework: the first steps towards food enrichment analysis"
}
],
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},
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"agro",
"envo",
"fobi",
"maxo",
"one",
"ons"
],
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"contact.orcid": "0000-0002-8844-9165",
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"bfo",
"chebi",
"envo",
"eo",
"ncbitaxon",
"obi",
"ro",
"uberon"
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"deprecated": false,
"description": "A broadly scoped ontology representing entities which bear a βfood roleβ. It encompasses materials in natural ecosystems and agriculture that are consumed by humans and domesticated animals. This includes any generic (unbranded) raw or processed food material found in processing plants, markets, stores or food distribution points. FoodOn also imports nutritional component and dietary pattern terms from other OBO Foundry ontologies to support interoperability in diet and nutrition research",
"domain": "diet, metabolomics, and nutrition",
"download.owl": "http://purl.obolibrary.org/obo/foodon.owl",
"homepage": "https://foodon.org/",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Food Ontology",
"preferredPrefix": "FOODON",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/31304272",
"title": "FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration"
}
],
"repository": "https://github.com/FoodOntology/foodon"
},
"fovt": {
"contact": "meghan.balk@gmail.com",
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"contact.label": "Meghan Balk",
"contact.orcid": "0000-0003-2699-3066",
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"bco",
"bfo",
"bspo",
"iao",
"oba",
"pato",
"ro",
"uberon"
],
"deprecated": false,
"description": "FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA).",
"domain": "phenotype",
"download.obo": "http://purl.obolibrary.org/obo/fovt.obo",
"download.owl": "http://purl.obolibrary.org/obo/fovt.owl",
"homepage": "https://github.com/futres/fovt",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "FuTRES Ontology of Vertebrate Traits",
"preferredPrefix": "FOVT",
"repository": "https://github.com/futres/fovt"
},
"fypo": {
"contact": "vw253@cam.ac.uk",
"contact.github": "ValWood",
"contact.label": "Val Wood",
"contact.orcid": "0000-0001-6330-7526",
"deprecated": false,
"description": "FYPO is a formal ontology of phenotypes observed in fission yeast.",
"domain": "phenotype",
"download.obo": "http://purl.obolibrary.org/obo/fypo.obo",
"download.owl": "http://purl.obolibrary.org/obo/fypo.owl",
"homepage": "https://github.com/pombase/fypo",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"logo": "https://github.com/pombase/website/blob/master/src/assets/FYPO_logo_tiny.png",
"name": "Fission Yeast Phenotype Ontology",
"preferredPrefix": "FYPO",
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{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/23658422",
"title": "FYPO: The Fission Yeast Phenotype Ontology."
}
],
"repository": "https://github.com/pombase/fypo"
},
"gallont": {
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"contact.label": "Andy Deans",
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"flopo",
"ncbitaxon",
"obi",
"pato",
"po",
"poro",
"ro"
],
"deprecated": false,
"description": "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls.",
"domain": "phenotype",
"download.json": "http://purl.obolibrary.org/obo/gallont.json",
"download.obo": "http://purl.obolibrary.org/obo/gallont.obo",
"download.owl": "http://purl.obolibrary.org/obo/gallont.owl",
"homepage": "https://adeans.github.io/gallont/",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Plant Gall Ontology",
"preferredPrefix": "GALLONT",
"repository": "https://github.com/adeans/gallont"
},
"gaz": {
"appears_in": [
"scdo"
],
"contact": "lschriml@som.umaryland.edu",
"contact.github": "lschriml",
"contact.label": "Lynn Schriml",
"contact.orcid": "0000-0001-8910-9851",
"deprecated": true,
"description": "A gazetteer constructed on ontological principles. The countries are actively maintained.",
"domain": "environment",
"download.obo": "http://purl.obolibrary.org/obo/gaz.obo",
"download.owl": "http://purl.obolibrary.org/obo/gaz.owl",
"homepage": "http://environmentontology.github.io/gaz/",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Gazetteer",
"repository": "https://github.com/EnvironmentOntology/gaz"
},
"gecko": {
"contact": "rbca.jackson@gmail.com",
"contact.github": "beckyjackson",
"contact.label": "Rebecca Jackson",
"contact.orcid": "0000-0003-4871-5569",
"deprecated": false,
"description": "An ontology to represent genomics cohort attributes",
"domain": "organisms",
"download.owl": "http://purl.obolibrary.org/obo/gecko.owl",
"homepage": "https://github.com/IHCC-cohorts/GECKO",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Genomics Cohorts Knowledge Ontology",
"preferredPrefix": "GECKO",
"repository": "https://github.com/IHCC-cohorts/GECKO"
},
"genepio": {
"contact": "damion_dooley@sfu.ca",
"contact.github": "ddooley",
"contact.label": "Damion Dooley",
"contact.orcid": "0000-0002-8844-9165",
"depends_on": [
"chebi",
"ncbitaxon",
"po",
"ro",
"uberon"
],
"deprecated": false,
"description": "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/genepio.owl",
"homepage": "http://genepio.org/",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Genomic Epidemiology Ontology",
"preferredPrefix": "GENEPIO",
"repository": "https://github.com/GenEpiO/genepio"
},
"geno": {
"contact": "mhb120@gmail.com",
"contact.github": "mbrush",
"contact.label": "Matthew Brush",
"contact.orcid": "0000-0002-1048-5019",
"deprecated": false,
"description": "An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases.",
"domain": "biological systems",
"download.owl": "http://purl.obolibrary.org/obo/geno.owl",
"homepage": "https://github.com/monarch-initiative/GENO-ontology/",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Genotype Ontology",
"preferredPrefix": "GENO",
"repository": "https://github.com/monarch-initiative/GENO-ontology"
},
"geo": {
"contact": "hoganwr@gmail.com",
"contact.github": "hoganwr",
"contact.label": "Bill Hogan",
"contact.orcid": "0000-0002-9881-1017",
"deprecated": false,
"description": "An ontology of geographical entities",
"domain": "environment",
"download.owl": "http://purl.obolibrary.org/obo/geo.owl",
"homepage": "https://github.com/ufbmi/geographical-entity-ontology/wiki",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Geographical Entity Ontology",
"preferredPrefix": "GEO",
"repository": "https://github.com/ufbmi/geographical-entity-ontology"
},
"gno": {
"contact": "nje5@georgetown.edu",
"contact.github": "edwardsnj",
"contact.label": "Nathan Edwards",
"contact.orcid": "0000-0001-5168-3196",
"deprecated": false,
"description": "GlyTouCan provides stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations). GNOme organizes these stable accessions for interative browsing, for text-based searching, and for automated reasoning with well-defined characterization levels.",
"domain": "chemistry and biochemistry",
"download.json": "http://purl.obolibrary.org/obo/gno.json",
"download.obo": "http://purl.obolibrary.org/obo/gno.obo",
"download.owl": "http://purl.obolibrary.org/obo/gno.owl",
"homepage": "https://gnome.glyomics.org/",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Glycan Naming and Subsumption Ontology (GNOme)",
"preferredPrefix": "GNO",
"publications": [
{
"id": "https://doi.org/10.5281/zenodo.6678278",
"title": "GNOme - Glycan Naming and Subsumption Ontology"
}
],
"repository": "https://github.com/glygen-glycan-data/GNOme"
},
"go": {
"appears_in": [
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"chiro",
"cl",
"ecocore",
"ecto",
"envo",
"maxo",
"pcl",
"pco",
"planp",
"uberon",
"xpo",
"zp"
],
"contact": "suzia@stanford.edu",
"contact.github": "suzialeksander",
"contact.label": "Suzi Aleksander",
"contact.orcid": "0000-0001-6787-2901",
"depends_on": [
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"ncbitaxon",
"ro",
"uberon"
],
"deprecated": false,
"description": "An ontology for describing the function of genes and gene products",
"domain": "biological systems",
"download.json": "http://purl.obolibrary.org/obo/go.json",
"download.obo": "http://purl.obolibrary.org/obo/go.obo",
"download.owl": "http://purl.obolibrary.org/obo/go.owl",
"homepage": "http://geneontology.org/",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"logo": "https://obofoundry.org/images/go_logo.png",
"name": "Gene Ontology",
"preferredPrefix": "GO",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/10802651",
"title": "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/33290552",
"title": "The Gene Ontology resource: enriching a GOld mine"
}
],
"repository": "https://github.com/geneontology/go-ontology",
"twitter": "news4go"
},
"gro": {
"contact": "po-discuss@plantontology.org",
"contact.label": "Plant Ontology Administrators",
"deprecated": true,
"domain": "anatomy and development",
"homepage": "http://www.gramene.org/plant_ontology/",
"name": "Cereal Plant Gross Anatomy"
},
"gsso": {
"appears_in": [
"ontoavida",
"scdo"
],
"contact": "kronkcj@mail.uc.edu",
"contact.github": "Superraptor",
"contact.label": "Clair Kronk",
"contact.orcid": "0000-0001-8397-8810",
"deprecated": false,
"description": "The Gender, Sex, and Sexual Orientation (GSSO) ontology has terms for annotating interdisciplinary information concerning gender, sex, and sexual orientation for primary usage in the biomedical and adjacent sciences.",
"domain": "organisms",
"download.json": "http://purl.obolibrary.org/obo/gsso.json",
"download.obo": "http://purl.obolibrary.org/obo/gsso.obo",
"download.owl": "http://purl.obolibrary.org/obo/gsso.owl",
"homepage": "https://gsso.research.cchmc.org/",
"license": "Apache 2.0 License",
"license.url": "http://www.apache.org/licenses/LICENSE-2.0",
"name": "Gender, Sex, and Sexual Orientation (GSSO) ontology",
"preferredPrefix": "GSSO",
"repository": "https://github.com/Superraptor/GSSO"
},
"habronattus": {
"contact": "peteremidford@yahoo.com",
"contact.label": "Peter Midford",
"contact.orcid": "0000-0001-6512-3296",
"deprecated": true,
"domain": "organisms",
"homepage": "http://www.mesquiteproject.org/ontology/Habronattus/index.html",
"name": "Habronattus courtship"
},
"hancestro": {
"contact": "dwelter.ontologist@gmail.com",
"contact.github": "daniwelter",
"contact.label": "Danielle Welter",
"contact.orcid": "0000-0003-1058-2668",
"deprecated": false,
"description": "The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies.",
"domain": "organisms",
"download.owl": "http://purl.obolibrary.org/obo/hancestro.owl",
"homepage": "https://ebispot.github.io/hancestro/",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Human Ancestry Ontology",
"preferredPrefix": "HANCESTRO",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/29448949",
"title": "A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog"
}
],
"repository": "https://github.com/EBISPOT/hancestro"
},
"hao": {
"contact": "diapriid@gmail.com",
"contact.github": "mjy",
"contact.label": "Matt Yoder",
"contact.orcid": "0000-0002-5640-5491",
"deprecated": false,
"description": "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/hao.obo",
"download.owl": "http://purl.obolibrary.org/obo/hao.owl",
"homepage": "http://hymao.org",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Hymenoptera Anatomy Ontology",
"preferredPrefix": "HAO",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/21209921",
"title": "A gross anatomy ontology for hymenoptera"
}
],
"repository": "https://github.com/hymao/hao"
},
"hom": {
"contact": "bgee@sib.swiss",
"contact.github": "fbastian",
"contact.label": "Frederic Bastian",
"contact.orcid": "0000-0002-9415-5104",
"deprecated": false,
"description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.",
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/hom.owl",
"homepage": "https://github.com/BgeeDB/homology-ontology",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"name": "Homology Ontology",
"preferredPrefix": "HOM",
"publications": [
{
"id": "https://doi.org/10.1016/j.tig.2009.12.012",
"title": "An ontology to clarify homology-related concepts"
}
],
"repository": "https://github.com/BgeeDB/homology-ontology"
},
"hp": {
"appears_in": [
"chiro",
"maxo",
"scdo"
],
"contact": "dr.sebastian.koehler@gmail.com",
"contact.github": "drseb",
"contact.label": "Sebastian Koehler",
"contact.orcid": "0000-0002-5316-1399",
"deprecated": false,
"description": "A structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease.",
"domain": "phenotype",
"download.json": "http://purl.obolibrary.org/obo/hp.json",
"download.obo": "http://purl.obolibrary.org/obo/hp.obo",
"download.owl": "http://purl.obolibrary.org/obo/hp.owl",
"homepage": "http://www.human-phenotype-ontology.org/",
"license": "hpo",
"license.url": "https://hpo.jax.org/app/license",
"logo": "https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/logo/HPO-logo-black_small.png",
"name": "Human Phenotype Ontology",
"preferredPrefix": "HP",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/18950739",
"title": "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease."
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/26119816",
"title": "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease."
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/24217912",
"title": "The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data."
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/30476213",
"title": "Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources."
}
],
"repository": "https://github.com/obophenotype/human-phenotype-ontology",
"twitter": "hp_ontology"
},
"hsapdv": {
"appears_in": [
"scdo"
],
"contact": "frederic.bastian@unil.ch",
"contact.github": "fbastian",
"contact.label": "FrΓ©dΓ©ric Bastian",
"contact.orcid": "0000-0002-9415-5104",
"deprecated": false,
"description": "Life cycle stages for Human",
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"scdo"
],
"contact": "yongqunh@med.umich.edu",
"contact.github": "yongqunh",
"contact.label": "Yongqunh He",
"contact.orcid": "0000-0001-9189-9661",
"deprecated": false,
"description": "VO is a biomedical ontology in the domain of vaccine and vaccination.",
"domain": "health",
"download.owl": "http://purl.obolibrary.org/obo/vo.owl",
"homepage": "https://violinet.org/vaccineontology",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "Vaccine Ontology",
"preferredPrefix": "VO",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/23256535",
"title": "Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses"
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/21624163",
"title": "Mining of vaccine-associated IFN-Ξ³ gene interaction networks using the Vaccine Ontology"
}
],
"repository": "https://github.com/vaccineontology/VO"
},
"vsao": {
"contact": "wasila.dahdul@usd.edu",
"contact.label": "Wasila Dahdul",
"contact.orcid": "0000-0003-3162-7490",
"deprecated": true,
"description": "Vertebrate skeletal anatomy ontology.",
"domain": "anatomy and development",
"download.owl": "http://purl.obolibrary.org/obo/vsao.owl",
"homepage": "https://www.nescent.org/phenoscape/Main_Page",
"name": "Vertebrate Skeletal Anatomy Ontology-"
},
"vt": {
"appears_in": [
"scdo"
],
"contact": "caripark@iastate.edu",
"contact.github": "caripark",
"contact.label": "Carissa Park",
"contact.orcid": "0000-0002-2346-5201",
"deprecated": false,
"description": "An ontology of traits covering vertebrates",
"domain": "phenotype",
"download.owl": "http://purl.obolibrary.org/obo/vt.owl",
"homepage": "https://github.com/AnimalGenome/vertebrate-trait-ontology",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "Vertebrate trait ontology",
"preferredPrefix": "VT",
"repository": "https://github.com/AnimalGenome/vertebrate-trait-ontology"
},
"vto": {
"contact": "balhoff@renci.org",
"contact.github": "balhoff",
"contact.label": "Jim Balhoff",
"contact.orcid": "0000-0002-8688-6599",
"deprecated": false,
"description": "Comprehensive hierarchy of extinct and extant vertebrate taxa.",
"domain": "organisms",
"download.obo": "http://purl.obolibrary.org/obo/vto.obo",
"download.owl": "http://purl.obolibrary.org/obo/vto.owl",
"homepage": "https://github.com/phenoscape/vertebrate-taxonomy-ontology",
"license": "CC0 1.0",
"license.url": "http://creativecommons.org/publicdomain/zero/1.0/",
"name": "Vertebrate Taxonomy Ontology",
"preferredPrefix": "VTO",
"publications": [
{
"id": "https://doi.org/10.1186/2041-1480-4-34",
"title": "The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes"
}
],
"repository": "https://github.com/phenoscape/vertebrate-taxonomy-ontology"
},
"wbbt": {
"contact": "raymond@caltech.edu",
"contact.github": "raymond91125",
"contact.label": "Raymond Lee",
"contact.orcid": "0000-0002-8151-7479",
"deprecated": false,
"description": "A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/wbbt.obo",
"download.owl": "http://purl.obolibrary.org/obo/wbbt.owl",
"homepage": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "C. elegans Gross Anatomy Ontology",
"preferredPrefix": "WBbt",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/18629098",
"title": "Building a cell and anatomy ontology of Caenorhabditis elegans"
}
],
"repository": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology"
},
"wbls": {
"contact": "cgrove@caltech.edu",
"contact.github": "chris-grove",
"contact.label": "Chris Grove",
"contact.orcid": "0000-0001-9076-6015",
"deprecated": false,
"description": "A structured controlled vocabulary of the development of Caenorhabditis elegans.",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/wbls.obo",
"download.owl": "http://purl.obolibrary.org/obo/wbls.owl",
"homepage": "https://github.com/obophenotype/c-elegans-development-ontology",
"license": "CC BY 4.0",
"license.url": "https://creativecommons.org/licenses/by/4.0/",
"name": "C. elegans development ontology",
"preferredPrefix": "WBls",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/31642470",
"title": "WormBase: a modern Model Organism Information Resource"
}
],
"repository": "https://github.com/obophenotype/c-elegans-development-ontology"
},
"wbphenotype": {
"contact": "cgrove@caltech.edu",
"contact.github": "chris-grove",
"contact.label": "Chris Grove",
"contact.orcid": "0000-0001-9076-6015",
"deprecated": false,
"description": "A structured controlled vocabulary of Caenorhabditis elegans phenotypes",
"domain": "phenotype",
"download.obo": "http://purl.obolibrary.org/obo/wbphenotype.obo",
"download.owl": "http://purl.obolibrary.org/obo/wbphenotype.owl",
"homepage": "https://github.com/obophenotype/c-elegans-phenotype-ontology",
"license": "CC BY 4.0",
"license.url": "http://creativecommons.org/licenses/by/4.0/",
"name": "C. elegans phenotype",
"preferredPrefix": "WBPhenotype",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/21261995",
"title": "Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community."
}
],
"repository": "https://github.com/obophenotype/c-elegans-phenotype-ontology"
},
"xao": {
"appears_in": [
"xpo"
],
"contact": "Erik.Segerdell@cchmc.org",
"contact.github": "seger",
"contact.label": "Erik Segerdell",
"contact.orcid": "0000-0002-9611-1279",
"deprecated": false,
"description": "XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis.",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/xao.obo",
"download.owl": "http://purl.obolibrary.org/obo/xao.owl",
"homepage": "http://www.xenbase.org/anatomy/xao.do?method=display",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Xenopus Anatomy Ontology",
"preferredPrefix": "XAO",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/18817563",
"title": "An ontology for Xenopus anatomy and development."
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/24139024",
"title": "Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase."
}
],
"repository": "https://github.com/xenopus-anatomy/xao"
},
"xco": {
"appears_in": [
"agro",
"ecto"
],
"contact": "jrsmith@mcw.edu",
"contact.github": "jrsjrs",
"contact.label": "Jennifer Smith",
"contact.orcid": "0000-0002-6443-9376",
"deprecated": false,
"description": "Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.",
"domain": "health",
"download.obo": "http://purl.obolibrary.org/obo/xco.obo",
"download.owl": "http://purl.obolibrary.org/obo/xco.owl",
"homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000",
"license": "CC0 1.0",
"license.url": "https://creativecommons.org/publicdomain/zero/1.0/",
"logo": "http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif",
"name": "Experimental condition ontology",
"preferredPrefix": "XCO",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/22654893",
"title": "Three ontologies to define phenotype measurement data."
},
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/24103152",
"title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications."
}
],
"repository": "https://github.com/rat-genome-database/XCO-experimental-condition-ontology"
},
"xlmod": {
"contact": "lutz.fischer@tu-berlin.de",
"contact.github": "lutzfischer",
"contact.label": "Lutz Fischer",
"contact.orcid": "0000-0003-4978-0864",
"deprecated": false,
"description": "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.",
"domain": "chemistry and biochemistry",
"download.obo": "http://purl.obolibrary.org/obo/xlmod.obo",
"download.owl": "http://purl.obolibrary.org/obo/xlmod.owl",
"homepage": "http://www.psidev.info/groups/controlled-vocabularies",
"license": "CC BY 3.0",
"license.url": "https://creativecommons.org/licenses/by/3.0/",
"name": "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary",
"preferredPrefix": "XLMOD",
"repository": "https://github.com/HUPO-PSI/xlmod-CV"
},
"xpo": {
"contact": "Erik.Segerdell@cchmc.org",
"contact.github": "seger",
"contact.label": "Erik Segerdell",
"contact.orcid": "0000-0002-9611-1279",
"depends_on": [
"bfo",
"chebi",
"cl",
"go",
"iao",
"pato",
"ro",
"xao"
],
"deprecated": false,
"description": "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis.",
"domain": "phenotype",
"download.obo": "http://purl.obolibrary.org/obo/xpo.obo",
"download.owl": "http://purl.obolibrary.org/obo/xpo.owl",
"homepage": "https://github.com/obophenotype/xenopus-phenotype-ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Xenopus Phenotype Ontology",
"preferredPrefix": "XPO",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/35317743",
"title": "The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development."
}
],
"repository": "https://github.com/obophenotype/xenopus-phenotype-ontology"
},
"ypo": {
"contact": "cherry@genome.stanford.edu",
"contact.label": "Mike Cherry",
"contact.orcid": "0000-0001-9163-5180",
"deprecated": true,
"domain": "phenotype",
"homepage": "http://www.yeastgenome.org/",
"name": "Yeast phenotypes"
},
"zea": {
"contact": "Leszek@missouri.edu",
"contact.label": "Leszek Vincent",
"contact.orcid": "0000-0002-9316-2919",
"deprecated": true,
"domain": "anatomy and development",
"homepage": "http://www.maizemap.org/",
"name": "Maize gross anatomy"
},
"zeco": {
"appears_in": [
"mco"
],
"contact": "ybradford@zfin.org",
"contact.github": "ybradford",
"contact.label": "Yvonne Bradford",
"contact.orcid": "0000-0002-9900-7880",
"deprecated": false,
"description": "Experimental conditions applied to zebrafish, developed to facilitate experiment condition annotation at ZFIN",
"domain": "environment",
"download.json": "http://purl.obolibrary.org/obo/zeco.json",
"download.obo": "http://purl.obolibrary.org/obo/zeco.obo",
"download.owl": "http://purl.obolibrary.org/obo/zeco.owl",
"homepage": "https://github.com/ybradford/zebrafish-experimental-conditions-ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Zebrafish Experimental Conditions Ontology",
"preferredPrefix": "ZECO",
"repository": "https://github.com/ybradford/zebrafish-experimental-conditions-ontology"
},
"zfa": {
"appears_in": [
"zp"
],
"contact": "van_slyke@zfin.org",
"contact.github": "cerivs",
"contact.label": "Ceri Van Slyke",
"contact.orcid": "0000-0002-2244-7917",
"deprecated": false,
"description": "A structured controlled vocabulary of the anatomy and development of the Zebrafish",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/zfa.obo",
"download.owl": "http://purl.obolibrary.org/obo/zfa.owl",
"homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Zebrafish anatomy and development ontology",
"preferredPrefix": "ZFA",
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/24568621",
"title": "The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio."
}
],
"repository": "https://github.com/cerivs/zebrafish-anatomical-ontology"
},
"zfs": {
"contact": "van_slyke@zfin.org",
"contact.github": "cerivs",
"contact.label": "Ceri Van Slyke",
"contact.orcid": "0000-0002-2244-7917",
"deprecated": false,
"description": "Developmental stages of the Zebrafish",
"domain": "anatomy and development",
"download.obo": "http://purl.obolibrary.org/obo/zfs.obo",
"download.owl": "http://purl.obolibrary.org/obo/zfs.owl",
"homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Zebrafish developmental stages ontology",
"preferredPrefix": "ZFS",
"repository": "https://github.com/cerivs/zebrafish-anatomical-ontology"
},
"zp": {
"contact": "ybradford@zfin.org",
"contact.github": "ybradford",
"contact.label": "Yvonne Bradford",
"contact.orcid": "0000-0002-9900-7880",
"depends_on": [
"bfo",
"bspo",
"go",
"pato",
"ro",
"uberon",
"zfa"
],
"deprecated": false,
"description": "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.",
"domain": "phenotype",
"download.obo": "http://purl.obolibrary.org/obo/zp.obo",
"download.owl": "http://purl.obolibrary.org/obo/zp.owl",
"homepage": "https://github.com/obophenotype/zebrafish-phenotype-ontology",
"license": "CC BY 3.0",
"license.url": "http://creativecommons.org/licenses/by/3.0/",
"name": "Zebrafish Phenotype Ontology",
"preferredPrefix": "ZP",
"repository": "https://github.com/obophenotype/zebrafish-phenotype-ontology"
}
} ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9699667
bioregistry-0.11.12/src/bioregistry/external/ols/ 0000755 0001751 0000177 00000000000 14655546227 021413 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/ols/__init__.py 0000644 0001751 0000177 00000021641 14655542206 023521 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download registry information from the OLS."""
import datetime
import enum
import json
import logging
from email.utils import parseaddr
from functools import lru_cache
from operator import itemgetter
from pathlib import Path
from textwrap import dedent
from typing import Any, Mapping, Optional
import requests
from pydantic import BaseModel
from bioregistry.constants import RAW_DIRECTORY
from bioregistry.external.alignment_utils import Aligner
from bioregistry.parse_version_iri import parse_obo_version_iri
from bioregistry.utils import OLSBroken
__all__ = [
"get_ols",
"OLSAligner",
]
logger = logging.getLogger(__name__)
DIRECTORY = Path(__file__).parent.resolve()
URL = "https://www.ebi.ac.uk/ols4/api/ontologies?size=1000"
RAW_PATH = RAW_DIRECTORY / "ols.json"
PROCESSED_PATH = DIRECTORY / "processed.json"
OLS_PROCESSING = DIRECTORY / "processing_ols.json"
OLS_SKIP = {
"co_321:root": "this is a mistake in the way OLS imports CO",
"phi": "this is low quality and has no associated metadata",
"epso": "can't figure out / not sure if still exists",
"epio": "can't figure out / not sure if still exists",
"cpont": "no own terms?",
"schemaorg_https": "duplicate of canonical HTTP version",
"hpi": "nonsensical duplication of HP",
}
def get_ols(force_download: bool = False):
"""Get the OLS registry."""
if PROCESSED_PATH.exists() and not force_download:
with PROCESSED_PATH.open() as file:
return json.load(file)
data = requests.get(URL).json()
if "_embedded" not in data:
raise OLSBroken
data["_embedded"]["ontologies"] = sorted(
data["_embedded"]["ontologies"],
key=itemgetter("ontologyId"),
)
if "next" in data["_links"]:
raise NotImplementedError(
"Need to implement paging since there are more entries than fit into one page"
)
RAW_PATH.write_text(json.dumps(data, indent=2, sort_keys=True))
processed = {}
for ontology in data["_embedded"]["ontologies"]:
ols_id = ontology["ontologyId"]
if ols_id in OLS_SKIP:
continue
# TODO better docs on how to maintain this file
config = get_ols_processing().get(ols_id)
if config is None:
if ols_id not in OLS_SKIP:
logger.warning("[%s] need to curate processing file", ols_id)
continue
processed[ols_id] = _process(ontology, config)
with PROCESSED_PATH.open("w") as file:
json.dump(processed, file, indent=2, sort_keys=True)
return processed
class VersionType(str, enum.Enum):
"""Types for OLS ontology versions."""
date = "date"
semver = "semver"
other = "other"
sequential = "sequential"
garbage = "garbage"
missing = "missing"
class OLSConfig(BaseModel):
"""Configuration for processing an OLS ontology."""
prefix: str
version_type: VersionType
version_date_format: Optional[str] = None
version_prefix: Optional[str] = None
version_suffix: Optional[str] = None
version_suffix_split: Optional[str] = None
version_iri_prefix: Optional[str] = None
version_iri_suffix: Optional[str] = None
def _get_email(ols_id, config) -> Optional[str]:
mailing_list = config.get("mailingList")
if not mailing_list:
return None
name, email = parseaddr(mailing_list)
if email.startswith("//"):
logger.debug("[%s] invalid email address: %s", ols_id, mailing_list)
return None
return email
def _get_license(ols_id, config) -> Optional[str]:
license_value = (config.get("annotations") or {}).get("license", [None])[0]
if license_value == "Unspecified":
logger.info("[%s] unspecified license in OLS. Contact: %s", ols_id, config["mailingList"])
return None
if not license_value:
logger.info("[%s] missing license in OLS. Contact: %s", ols_id, config["mailingList"])
return license_value
def _get_version(ols_id, config, processing: OLSConfig) -> Optional[str]:
version_iri = config.get("versionIri")
if version_iri:
_, _, version = parse_obo_version_iri(version_iri, ols_id)
if version:
return version
version = config.get("version")
if version is None and processing.version_iri_prefix:
if not version_iri.startswith(processing.version_iri_prefix):
logger.info("[%s] version IRI does not start with appropriate prefix", ols_id)
else:
version = version_iri[len(processing.version_iri_prefix) :]
if processing.version_iri_suffix:
version = version[: -len(processing.version_iri_suffix)]
if version is None:
logger.info(
"[%s] missing version in OLS. Contact: %s, consider version.iri %s",
ols_id,
config["mailingList"],
version_iri,
)
else:
if version != version.strip():
logger.info(
"[%s] extra whitespace in version: %s. Contact: %s",
ols_id,
version,
config["mailingList"],
)
version = version.strip()
version_prefix = processing.version_prefix
if version_prefix:
if not version.startswith(version_prefix):
raise ValueError(
dedent(
f"""\
[{ols_id}] version "{version}" does not start with prefix "{version_prefix}".
Update the ["{ols_id}"]["prefix"] entry in the OLS processing configuration.
"""
)
)
version = version[len(version_prefix) :]
if processing.version_suffix_split:
version = version.split()[0]
version_suffix = processing.version_suffix
if version_suffix:
if not version.endswith(version_suffix):
raise ValueError(
f"[{ols_id}] version {version} does not end with prefix {version_suffix}"
)
version = version[: -len(version_suffix)]
version_type = processing.version_type
version_date_fmt = processing.version_date_format
if version_date_fmt:
if version_date_fmt in {"%Y-%d-%m"}:
logger.info(
"[%s] confusing date format: %s. Contact: %s",
ols_id,
version_date_fmt,
config["mailingList"],
)
try:
version = datetime.datetime.strptime(version, version_date_fmt).strftime("%Y-%m-%d")
except ValueError:
logger.info("[%s] wrong format for version %s", ols_id, version)
elif not version_type:
logger.info("[%s] no type for version %s", ols_id, version)
return version
def _process( # noqa:C901
ols_entry: Mapping[str, Any], processing: OLSConfig
) -> Optional[Mapping[str, str]]:
ols_id = ols_entry["ontologyId"]
config = ols_entry["config"]
version_iri = config["versionIri"]
title = config.get("title") or config.get("localizedTitles", {}).get("en")
description = config.get("description") or config.get("localizedDescriptions", {}).get("en")
rv = {
"prefix": ols_id,
# "preferred_prefix": config["preferredPrefix"],
"name": title,
"version.iri": _clean_url(version_iri),
"version": _get_version(ols_id, config, processing),
"description": description,
"homepage": _clean_url(config["homepage"]),
# "tracker": _clean_url(config["tracker"]),
"contact": _get_email(ols_id, config),
"license": _get_license(ols_id, config),
}
download = _clean_url(config["fileLocation"])
if download is None:
pass
elif download.endswith(".obo"):
rv["download_obo"] = download
elif download.endswith(".owl"):
rv["download_owl"] = download
elif download.endswith(".rdf") or download.endswith(".ttl"):
rv["download_rdf"] = download
else:
logger.warning("[%s] unknown download type %s", ols_id, download)
rv = {k: v.strip() for k, v in rv.items() if v}
return rv
def _clean_url(url: Optional[str]) -> Optional[str]:
if url is None:
return url
if "CO_" in url and url.startswith("http://127.0.0.1:5900"):
return "https://cropontology.org" + url[len("http://127.0.0.1:5900") :]
return url
@lru_cache(maxsize=1)
def get_ols_processing() -> Mapping[str, OLSConfig]:
"""Get OLS processing configurations."""
with OLS_PROCESSING.open() as file:
data = json.load(file)
return {record["prefix"]: OLSConfig(**record) for record in data["configurations"]}
class OLSAligner(Aligner):
"""Aligner for the OLS."""
key = "ols"
getter = get_ols
curation_header = ("name",)
include_new = True
def get_skip(self) -> Mapping[str, str]:
"""Get skipped entries from OLS."""
return OLS_SKIP
if __name__ == "__main__":
OLSAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254394.0
bioregistry-0.11.12/src/bioregistry/external/ols/processed.json 0000644 0001751 0000177 00000403177 14655543172 024305 0 ustar 00runner docker {
"ado": {
"description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining.",
"download_owl": "http://purl.obolibrary.org/obo/ado.owl",
"homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO",
"name": "Alzheimer's Disease Ontology (ADO)",
"prefix": "ado",
"version": "2023-09-20",
"version.iri": "http://purl.obolibrary.org/obo/ado/releases/2023-09-20/ado.owl"
},
"aeo": {
"description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology",
"download_owl": "http://purl.obolibrary.org/obo/aeo.owl",
"homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology/",
"name": "Anatomical Entity Ontology",
"prefix": "aeo",
"version": "2014-12-05",
"version.iri": "http://purl.obolibrary.org/obo/aeo/releases/2014-12-05/aeo.owl"
},
"aero": {
"description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events",
"homepage": "http://purl.obolibrary.org/obo/aero",
"name": "Adverse Event Reporting Ontology",
"prefix": "aero"
},
"afo": {
"description": "Allotrope Merged Ontology Suite",
"name": "Allotrope Merged Ontology Suite",
"prefix": "afo",
"version": "2024/06",
"version.iri": "http://purl.allotrope.org/voc/afo/merged/REC/2024/06/merged-without-qudt-and-inferred"
},
"agro": {
"description": "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities",
"download_owl": "http://purl.obolibrary.org/obo/agro.owl",
"homepage": "https://github.com/AgriculturalSemantics/agro",
"name": "Agronomy Ontology",
"prefix": "agro",
"version": "2022-11-02",
"version.iri": "http://purl.obolibrary.org/obo/agro/releases/2022-11-02/agro.owl"
},
"aism": {
"description": "The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research.",
"download_owl": "http://purl.obolibrary.org/obo/aism.owl",
"homepage": "https://github.com/insect-morphology/aism",
"name": "Ontology for the Anatomy of the Insect SkeletoMuscular system",
"prefix": "aism",
"version": "2024-06-20",
"version.iri": "http://purl.obolibrary.org/obo/aism/releases/2024-06-20/aism.owl"
},
"amphx": {
"description": "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).",
"download_owl": "http://purl.obolibrary.org/obo/amphx.owl",
"homepage": "https://github.com/EBISPOT/amphx_ontology",
"name": "Amphioxus Development and Anatomy Ontology (AMPHX)",
"prefix": "amphx",
"version": "2020-12-18",
"version.iri": "http://purl.obolibrary.org/obo/amphx/releases/2020-12-18/amphx.owl"
},
"apo": {
"description": "A structured controlled vocabulary for the phenotypes of Ascomycete fungi.",
"download_owl": "http://purl.obolibrary.org/obo/apo.owl",
"homepage": "http://www.yeastgenome.org/",
"name": "Ascomycete Phenotype Ontology (APO)",
"prefix": "apo",
"version": "2024-08-03",
"version.iri": "http://purl.obolibrary.org/obo/apo/releases/2024-08-03/apo.owl"
},
"apollo_sv": {
"description": "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.",
"download_owl": "http://purl.obolibrary.org/obo/apollo_sv.owl",
"homepage": "https://github.com/ApolloDev/apollo-sv",
"name": "Apollo Structured Vocabulary (Apollo-SV)",
"prefix": "apollo_sv",
"version": "2024-04-19",
"version.iri": "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-04-19/apollo_sv.owl"
},
"aro": {
"description": "Antibiotic resistance genes and mutations",
"download_owl": "http://purl.obolibrary.org/obo/aro.owl",
"homepage": "https://github.com/arpcard/aro",
"name": "Antibiotic Resistance Ontology",
"prefix": "aro"
},
"bao": {
"description": "The BioAssay Ontology (BAO) describes biological screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 700 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation.",
"homepage": "http://bioassayontology.org",
"name": "BioAssay Ontology",
"prefix": "bao",
"version": "2.8.11",
"version.iri": "http://www.bioassayontology.org/bao/bao_complete.owl"
},
"bcgo": {
"description": "An application ontology built for beta cell genomics studies.",
"homepage": "https://github.com/obi-bcgo/bcgo",
"name": "Beta Cell Genomics Ontology",
"prefix": "bcgo",
"version": "2015-07-08",
"version.iri": "http://purl.obolibrary.org/obo/bcgo/2015-07-08/bcgo.owl"
},
"bcio": {
"description": "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation.",
"download_owl": "http://humanbehaviourchange.org/ontology/bcio.owl",
"homepage": "https://www.humanbehaviourchange.org/",
"name": "The Behaviour Change Intervention Ontology",
"prefix": "bcio",
"version": "2024-07-03",
"version.iri": "http://humanbehaviourchange.org/ontology/bcio.owl/2024-07-03"
},
"bco": {
"description": "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.",
"download_owl": "http://purl.obolibrary.org/obo/bco.owl",
"homepage": "https://github.com/BiodiversityOntologies/bco",
"name": "Biological Collections Ontology",
"prefix": "bco",
"version": "2021-11-14",
"version.iri": "http://purl.obolibrary.org/obo/bco/releases/2021-11-14/bco.owl"
},
"bfo": {
"description": "The upper level ontology upon which OBO Foundry ontologies are built.",
"download_owl": "http://purl.obolibrary.org/obo/bfo.owl",
"homepage": "http://ifomis.org/bfo/",
"name": "Basic Formal Ontology",
"prefix": "bfo",
"version": "2019-08-26",
"version.iri": "http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl"
},
"bila": {
"homepage": "http://4dx.embl.de/4DXpress",
"name": "Bilateria anatomy",
"prefix": "bila",
"version": "2019-06-12",
"version.iri": "http://purl.obolibrary.org/obo/bila/releases/2019-06-12/bila.owl"
},
"bspo": {
"description": "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies.",
"download_owl": "http://purl.obolibrary.org/obo/bspo.owl",
"homepage": "https://github.com/obophenotype/biological-spatial-ontology",
"name": "Biological Spatial Ontology",
"prefix": "bspo",
"version": "2023-05-27",
"version.iri": "http://purl.obolibrary.org/obo/bspo/releases/2023-05-27/bspo.owl"
},
"bto": {
"description": "A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.",
"download_owl": "http://purl.obolibrary.org/obo/bto.owl",
"homepage": "http://www.brenda-enzymes.org",
"name": "The BRENDA Tissue Ontology (BTO)",
"prefix": "bto",
"version": "2021-10-26",
"version.iri": "http://purl.obolibrary.org/obo/bto/releases/2021-10-26/bto.owl"
},
"cao": {
"contact": "schalk@unf.edu",
"description": "The Chemical Analysis Ontology (CAO) is an ontology developed as part of the Chemical Analaysis Metadata Project (ChAMP) as a resource to semantically annotate standards developed using the ChAMP platform. For more information go to http://champ-project.org.",
"download_owl": "https://champ.stuchalk.domains.unf.edu/images/ontology/cao.owl",
"homepage": "https://champ.stuchalk.domains.unf.edu/cao",
"name": "Chemical Analysis Metadata Platform (ChAMP) Ontology version 0.2",
"prefix": "cao",
"version": "0.2"
},
"caro": {
"description": "The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies.",
"download_owl": "http://purl.obolibrary.org/obo/caro.owl",
"homepage": "https://github.com/obophenotype/caro/",
"name": "Common Anatomy Reference Ontology",
"prefix": "caro",
"version": "2023-03-15",
"version.iri": "http://purl.obolibrary.org/obo/caro/releases/2023-03-15/caro.owl"
},
"ccf": {
"contact": "infoccf@indiana.edu",
"description": "The Common Coordinate Framework (CCF) Ontology is an application ontology built to support the development of the Human Reference Atlas (HRA). It unifies vocabulary for HRA construction and usage\u2014making it possible to ingest external data sources; supporting uniform tissue sample registration that includes the spatial positioning and semantic annotations within 3D reference organs; and supporting user-formulated cross-domain queries over tissue donor properties, anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology consists of three major ontologies. The Biological Structure Ontology records anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships between them. The ASCT+B tables are authored by human experts using templated Google Sheets. The biomarkers, cell types, and anatomical structures are mapped to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible. All relationships between anatomical structures and from cell types to anatomical structures are valid Uberon and CL relationships. The Spatial Ontology defines the shape, size, location, and rotation of experimental tissue and data major anatomical structures in the 3D Reference Object Library. The Specimen Ontology captures the sex, age, and other information on donors that provided tissue data used in the construction of the HRA.",
"download_owl": "https://purl.org/ccf/2.0/ccf.owl",
"homepage": "https://hubmapconsortium.github.io/ccf/pages/ccf-ontology.html",
"name": "Human Reference Atlas Common Coordinate Framework Ontology",
"prefix": "ccf",
"version": "2.3.0",
"version.iri": "http://purl.org/ccf/releases/2.3.0/ccf.owl"
},
"cco": {
"contact": "vladimir.n.mironov@gmail.com",
"description": "The Cell Cycle Ontology extends existing ontologies for cell cycle knowledge building a resource that integrates and manages knowledge about the cell cycle components and regulatory aspects.",
"download_owl": "http://www.bio.ntnu.no/ontology/CCO/cco.owl",
"homepage": "http://www.semantic-systems-biology.org/apo",
"name": "Cell Cycle Ontology",
"prefix": "cco"
},
"cdao": {
"description": "a formalization of concepts and relations relevant to evolutionary comparative analysis",
"download_owl": "http://purl.obolibrary.org/obo/cdao.owl",
"homepage": "https://github.com/evoinfo/cdao",
"name": "Comparative Data Analysis Ontology",
"prefix": "cdao",
"version": "2024-01-25",
"version.iri": "http://purl.obolibrary.org/obo/cdao/2024-01-25/cdao.owl"
},
"cdno": {
"description": "The CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. These terms are intended primarily to be associated with datasets that quantify concentration of chemical nutritional components derived from samples taken from any stage in the production of food raw materials (including from crops, livestock, fisheries) and through processing and supply chains. Additional knowledge associated with these dietary sources may be represented by terms that describe functional, physical and other attributes. Whilst recognising that dietary nutrients within food substrates may be present as complex and dynamic physical and chemical structures or mixtures, CDNO focuses on components typically quantified in an analytical chemistry laboratory. The primary CDNO class \u2018dietary nutritional component\u2019 contains hierarchical sets of terms organised to reflect commonly used classifications of chemical food composition. This class does not represent an exhaustive classification of chemical components, but focuses on structuring terms according to widely accepted categories. This class is independent of, but may be used in conjunction with, classes that describe \u2018analytical methods\u2019 for quantification, \u2018physical properties\u2019 or \u2018dietary function\u2019. Quantification data may be used and reported in research literature, to inform food composition tables and labelling, or for supply chain quality assurance and control. More specifically, terms within the \u2018nutritional component concentration\u2019 class may be used to represent quantification of components described in the \u2018dietary nutritional component\u2019 class. Concentration data are intended to be described in conjunction with post-composed metadata concepts, such as represented by the Food Ontology (FoodOn) \u2018Food product by organism\u2019, which derives from some food or anatomical entity and a NCBI organismal classification ontology (NCBITaxon) entity. The common vocabulary and relationships defined within CDNO should facilitate description, communication and exchange of material entity-derived nutritional composition datasets typically generated by analytical laboratories. The organisation of the vocabulary is structured to reflect common categories variously used by those involved in crop, livestock or other organismal production, associated R&D and breeding, as well as the food processing and supply sector, and nutritionists, inlcuding compilers and users of food composition databases. The CDNO therefore supports characterisation of genetic diversity and management of biodiversity collections, as well as sharing of knowledge relating to dietary composition between a wider set of researchers, breeders, farmers, processors and other stakeholders. Further development of the functional class should also assist in understanding how interactions between organismal genetic and environmental variation contribute to human diet and health in the farm to fork continuum.",
"download_owl": "http://purl.obolibrary.org/obo/cdno.owl",
"homepage": "https://cdno.info/",
"name": "Compositional Dietary Nutrition Ontology",
"prefix": "cdno",
"version": "2024-06-21",
"version.iri": "http://purl.obolibrary.org/obo/cdno/releases/2024-06-21/cdno.owl"
},
"ceph": {
"description": "An anatomical and developmental ontology for cephalopods",
"download_owl": "http://purl.obolibrary.org/obo/ceph.owl",
"homepage": "https://github.com/obophenotype/cephalopod-ontology",
"name": "Cephalopod Ontology",
"prefix": "ceph",
"version": "2016-01-12",
"version.iri": "http://purl.obolibrary.org/obo/ceph/releases/2016-01-12/ceph.owl"
},
"chebi": {
"description": "A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds.",
"download_owl": "http://purl.obolibrary.org/obo/chebi.owl",
"homepage": "http://www.ebi.ac.uk/chebi",
"name": "Chemical Entities of Biological Interest",
"prefix": "chebi",
"version": "236",
"version.iri": "http://purl.obolibrary.org/obo/chebi/236/chebi.owl"
},
"cheminf": {
"description": "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.",
"download_owl": "http://purl.obolibrary.org/obo/cheminf.owl",
"homepage": "https://github.com/semanticchemistry/semanticchemistry",
"name": "chemical information ontology (cheminf) - information entities about chemical entities",
"prefix": "cheminf",
"version": "2.1.0"
},
"chiro": {
"description": "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.",
"download_owl": "http://purl.obolibrary.org/obo/chiro.owl",
"homepage": "https://github.com/obophenotype/chiro",
"name": "CHEBI Integrated Role Ontology",
"prefix": "chiro",
"version": "2015-11-23",
"version.iri": "http://purl.obolibrary.org/obo/chiro/releases/2015-11-23/chiro.owl"
},
"chmo": {
"contact": "chemistry-ontologies@googlegroups.com",
"description": "CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI).",
"download_owl": "http://purl.obolibrary.org/obo/chmo.owl",
"homepage": "https://github.com/rsc-ontologies/rsc-cmo",
"name": "Chemical Methods Ontology",
"prefix": "chmo",
"version": "2022-04-19",
"version.iri": "http://purl.obolibrary.org/obo/chmo/releases/2022-04-19/chmo.owl"
},
"cido": {
"contact": "cido-discuss@googlegroups.com",
"description": "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.",
"download_owl": "http://purl.obolibrary.org/obo/cido.owl",
"homepage": "https://github.com/cido-ontology/cido",
"name": "CIDO: Ontology of Coronavirus Infectious Disease",
"prefix": "cido",
"version": "2024-02-16",
"version.iri": "http://purl.obolibrary.org/obo/cido/releases/2024-02-16/cido.owl"
},
"cio": {
"description": "An ontology to capture confidence information about annotations.",
"download_owl": "http://purl.obolibrary.org/obo/cio.owl",
"homepage": "https://github.com/BgeeDB/confidence-information-ontology",
"name": "Confidence Information Ontology",
"prefix": "cio",
"version": "2015-03-10",
"version.iri": "http://purl.obolibrary.org/obo/cio/releases/2015-03-10/cio.owl"
},
"cl": {
"description": "An ontology of cell types.",
"download_owl": "http://purl.obolibrary.org/obo/cl.owl",
"homepage": "https://obophenotype.github.io/cell-ontology/",
"name": "Cell Ontology",
"prefix": "cl",
"version": "2024-07-10",
"version.iri": "http://purl.obolibrary.org/obo/cl/releases/2024-07-10/cl.owl"
},
"clao": {
"description": "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).",
"download_owl": "http://purl.obolibrary.org/obo/clao.owl",
"homepage": "https://github.com/luis-gonzalez-m/Collembola",
"name": "Collembola Anatomy Ontology",
"prefix": "clao",
"version": "2021-09-27",
"version.iri": "http://purl.obolibrary.org/obo/clao/releases/2021-09-27/clao.owl"
},
"clo": {
"description": "The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.",
"download_owl": "http://purl.obolibrary.org/obo/clo.owl",
"homepage": "https://github.com/CLO-Ontology/CLO",
"name": "CLO: Cell Line Ontology",
"prefix": "clo",
"version": "2.1.188"
},
"clyh": {
"description": "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica.",
"download_owl": "http://purl.obolibrary.org/obo/clyh.owl",
"homepage": "https://github.com/EBISPOT/clyh_ontology",
"name": "Clytia hemisphaerica Development and Anatomy Ontology (CLYH)",
"prefix": "clyh",
"version": "2020-05-29",
"version.iri": "http://purl.obolibrary.org/obo/clyh/releases/2020-05-29/clyh.owl"
},
"cmo": {
"description": "Morphological and physiological measurement records generated from clinical and model organism research and health programs.",
"download_owl": "http://purl.obolibrary.org/obo/cmo.owl",
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
"name": "Clinical measurement ontology",
"prefix": "cmo",
"version": "2.221",
"version.iri": "http://purl.obolibrary.org/obo/cmo/2.221/cmo.owl"
},
"cmpo": {
"contact": "jupp@ebi.ac.uk",
"description": "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations.",
"download_owl": "http://www.ebi.ac.uk/cmpo/cmpo.owl",
"homepage": "http://www.ebi.ac.uk/cmpo",
"name": "Cellular Microscopy Phenotype Ontology",
"prefix": "cmpo",
"version": "2017-12-19",
"version.iri": "http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl"
},
"cob": {
"description": "COB brings together key terms from a wide range of OBO projects to improve interoperability.",
"download_owl": "http://purl.obolibrary.org/obo/cob.owl",
"homepage": "https://obofoundry.org/COB/",
"name": "Core Ontology for Biology and Biomedicine",
"prefix": "cob",
"version": "2023-11-16",
"version.iri": "http://purl.obolibrary.org/obo/cob/releases/2023-11-16/cob.owl"
},
"colao": {
"description": "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research.",
"download_owl": "http://purl.obolibrary.org/obo/colao.owl",
"homepage": "https://github.com/insect-morphology/colao",
"name": "Coleoptera Anatomy Ontology",
"prefix": "colao",
"version": "2024-06-21",
"version.iri": "http://purl.obolibrary.org/obo/colao/releases/2024-06-21/colao.owl"
},
"covoc": {
"description": "The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.",
"download_owl": "https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl",
"homepage": "https://github.com/EBISPOT/covoc",
"name": "CoVoc Coronavirus Vocabulary",
"prefix": "covoc",
"version": "2022-10-26",
"version.iri": "http://purl.obolibrary.org/obo/covoc/releases/2022-10-26/covoc.owl"
},
"cro": {
"description": "A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability.",
"download_owl": "http://purl.obolibrary.org/obo/cro.owl",
"homepage": "https://github.com/data2health/contributor-role-ontology",
"name": "Contributor Role Ontology",
"prefix": "cro",
"version": "2019-12-11",
"version.iri": "http://purl.obolibrary.org/obo/cro/releases/2019-12-11/cro.owl"
},
"cryoem": {
"contact": "isanchez@cnb.csic.es",
"description": "Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles",
"download_owl": "http://scipion.i2pc.es/ontology/cryoem.owl",
"homepage": "http://scipion.i2pc.es/ontology/cryoem",
"name": "Cryo Electron Microscopy ontology",
"prefix": "cryoem",
"version": "2021-03-09",
"version.iri": "http://scipion.i2pc.es/ontology/cryoem/releases/2021-03-09/cryoem.owl"
},
"cteno": {
"description": "An anatomical and developmental ontology for ctenophores (Comb Jellies)",
"download_owl": "http://purl.obolibrary.org/obo/cteno.owl",
"homepage": "https://github.com/obophenotype/ctenophore-ontology",
"name": "Ctenophore Ontology",
"prefix": "cteno",
"version": "2016-10-19",
"version.iri": "http://purl.obolibrary.org/obo/cteno/releases/2016-10-19/cteno.owl"
},
"cvdo": {
"description": "An ontology to describe entities related to cardiovascular diseases",
"download_owl": "http://purl.obolibrary.org/obo/cvdo.owl",
"homepage": "https://github.com/OpenLHS/CVDO",
"name": "Cardiovascular Disease Ontology",
"prefix": "cvdo",
"version": "2024-05-17",
"version.iri": "http://purl.obolibrary.org/obo/cvdo/2024-05-17/cvdo.owl"
},
"dc": {
"download_rdf": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_elements.rdf",
"prefix": "dc"
},
"dcterms": {
"download_rdf": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_terms.rdf",
"prefix": "dcterms"
},
"ddanat": {
"description": "A structured controlled vocabulary of anatomies of the slime-mold Dictyostelium discoideum.",
"download_owl": "http://purl.obolibrary.org/obo/ddanat.owl",
"homepage": "http://dictybase.org/",
"name": "Dicty Anatomy Ontology (DDANAT)",
"prefix": "ddanat"
},
"ddpheno": {
"description": "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum.",
"download_owl": "http://purl.obolibrary.org/obo/ddpheno.owl",
"homepage": "http://dictybase.org/",
"name": "Dicty Phenotype Ontology (DDPHENO)",
"prefix": "ddpheno",
"version": "2023-08-26",
"version.iri": "http://purl.obolibrary.org/obo/ddpheno/releases/2023-08-26/ddpheno.owl"
},
"dicom": {
"contact": "dclunie@dclunie.com",
"description": "DICOM Controlled Terminology",
"download_owl": "ftp://medical.nema.org/MEDICAL/Dicom/Resources/Ontology/DCM/dcm.owl",
"homepage": "http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html",
"name": "DICOM Controlled Terminology",
"prefix": "dicom",
"version": "2024c_20240617"
},
"dideo": {
"description": "The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology",
"download_owl": "http://purl.obolibrary.org/obo/dideo.owl",
"homepage": "https://github.com/DIDEO/DIDEO",
"name": "Drug-drug Interaction and Drug-drug Interaction Evidence Ontology",
"prefix": "dideo",
"version": "2023-10-16",
"version.iri": "http://purl.obolibrary.org/obo/dideo/release/2023-10-16/dideo.owl"
},
"disdriv": {
"description": "Drivers of human diseases including environmental, maternal and social exposures.",
"download_owl": "http://purl.obolibrary.org/obo/disdriv.owl",
"homepage": "http://www.disease-ontology.org",
"name": "Disease Drivers",
"prefix": "disdriv",
"version": "2023-12-15",
"version.iri": "http://purl.obolibrary.org/obo/disdriv/releases/2023-12-15/disdriv.owl"
},
"doid": {
"description": "The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts.",
"download_owl": "http://purl.obolibrary.org/obo/doid.owl",
"homepage": "http://www.disease-ontology.org",
"name": "Human Disease Ontology",
"prefix": "doid",
"version": "2024-07-31",
"version.iri": "http://purl.obolibrary.org/obo/doid/releases/2024-07-31/doid.owl"
},
"dpo": {
"description": "An ontology for the description of Drosophila melanogaster phenotypes.",
"download_owl": "http://purl.obolibrary.org/obo/dpo.owl",
"homepage": "http://purl.obolibrary.org/obo/fbcv",
"name": "Drosophila Phenotype Ontology (DPO)",
"prefix": "dpo",
"version": "2024-06-13",
"version.iri": "http://purl.obolibrary.org/obo/dpo/releases/2024-06-13/dpo.owl"
},
"dron": {
"description": "An ontology to support comparative effectiveness researchers studying claims data.",
"download_owl": "http://purl.obolibrary.org/obo/dron.owl",
"homepage": "https://github.com/ufbmi/dron",
"name": "The Drug Ontology",
"prefix": "dron",
"version": "2024-08-05",
"version.iri": "http://purl.obolibrary.org/obo/dron/releases/2024-08-05/dron.owl"
},
"duo": {
"description": "DUO is an ontology which represent data use conditions.",
"download_owl": "http://purl.obolibrary.org/obo/duo.owl",
"homepage": "https://github.com/EBISPOT/DUO",
"name": "Data Use Ontology",
"prefix": "duo",
"version": "2021-02-23",
"version.iri": "http://purl.obolibrary.org/obo/duo/releases/2021-02-23/duo.owl"
},
"ecao": {
"description": "None",
"download_owl": "http://purl.obolibrary.org/obo/ecao.owl",
"homepage": "https://github.com/echinoderm-ontology/ecao_ontology",
"name": "Echinoderm Anatomy and Development Ontology",
"prefix": "ecao",
"version.iri": "http://purl.obolibrary.org/obo/ecao/releases/2024-07-28/ecao-simple.owl"
},
"eco": {
"description": "The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the biological research domain that arise from laboratory experiments, computational methods, literature curation, or other means.",
"download_owl": "http://purl.obolibrary.org/obo/eco.owl",
"homepage": "https://www.evidenceontology.org",
"name": "Evidence & Conclusion Ontology (ECO)",
"prefix": "eco",
"version": "2024-07-19",
"version.iri": "http://purl.obolibrary.org/obo/eco/releases/2024-07-19/eco.owl"
},
"ecocore": {
"description": "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.",
"download_owl": "http://purl.obolibrary.org/obo/ecocore.owl",
"homepage": "https://github.com/EcologicalSemantics/ecocore",
"name": "An ontology of core ecological entities",
"prefix": "ecocore",
"version": "2022-03-09",
"version.iri": "http://purl.obolibrary.org/obo/ecocore/releases/2022-03-09/ecocore.owl"
},
"ecto": {
"description": "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology).",
"download_owl": "http://purl.obolibrary.org/obo/ecto.owl",
"homepage": "https://github.com/EnvironmentOntology/environmental-exposure-ontology",
"name": "Environment Exposure Ontology",
"prefix": "ecto",
"version": "2023-02-14",
"version.iri": "http://purl.obolibrary.org/obo/ecto/releases/2023-02-14/ecto.owl"
},
"edam": {
"contact": "edam@elixir-dk.org",
"description": "EDAM is a simple ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM provides a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use.",
"download_owl": "https://raw.githubusercontent.com/edamontology/edamontology/master/releases/EDAM.owl",
"homepage": "http://edamontology.org",
"name": "Bioinformatics operations, data types, formats, identifiers and topics",
"prefix": "edam"
},
"efo": {
"contact": "efo-users@lists.sourceforge.net",
"description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for OpenTargets.org",
"download_owl": "http://www.ebi.ac.uk/efo/efo.owl",
"homepage": "http://www.ebi.ac.uk/efo",
"name": "Experimental Factor Ontology",
"prefix": "efo",
"version": "3.68.0",
"version.iri": "http://www.ebi.ac.uk/efo/releases/v3.68.0/efo.owl"
},
"ehdaa2": {
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the developing human.",
"download_owl": "http://purl.obolibrary.org/obo/ehdaa2.owl",
"homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology",
"name": "Human developmental anatomy, abstract",
"prefix": "ehdaa2",
"version": "2013-07-04",
"version.iri": "http://purl.obolibrary.org/obo/ehdaa2/releases/2013-07-04/ehdaa2.owl"
},
"emap": {
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).",
"homepage": "http://emouseatlas.org",
"name": "Mouse gross anatomy and development, timed",
"prefix": "emap",
"version": "2020-04-13",
"version.iri": "http://purl.obolibrary.org/obo/emap/releases/2020-04-13/emap.owl"
},
"emapa": {
"description": "An ontology for mouse anatomy covering embryonic development and postnatal stages.",
"download_owl": "http://purl.obolibrary.org/obo/emapa.owl",
"homepage": "http://www.informatics.jax.org/expression.shtml",
"name": "Mouse Developmental Anatomy Ontology",
"prefix": "emapa",
"version": "2023-11-14",
"version.iri": "http://purl.obolibrary.org/obo/emapa/releases/2023-11-14/emapa.owl"
},
"enm": {
"description": "The eNanoMapper project (https://www.enanomapper.net/), NanoCommons project (https://www.nanocommons.eu/) and ACEnano project (http://acenano-project.eu/) are creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO.",
"download_owl": "http://enanomapper.github.io/ontologies/enanomapper.owl",
"homepage": "http://www.enanomapper.net/",
"name": "eNanoMapper ontology",
"prefix": "enm",
"version": "10.0",
"version.iri": "http://enanomapper.github.io/ontologies/releases/10.0/enanomapper.owl"
},
"ensemblglossary": {
"description": "The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used.",
"download_owl": "https://raw.githubusercontent.com/Ensembl/ensembl-glossary/master/ensembl-glossary.owl",
"homepage": "http://ensembl.org/glossary",
"name": "Ensembl Glossary",
"prefix": "ensemblglossary",
"version": "2023-01-04",
"version.iri": "http://ensembl.org/glossary/ensembl-glossary/releases/2023-01-04/ensembl-glossary.owl"
},
"envo": {
"description": "ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities",
"download_owl": "http://purl.obolibrary.org/obo/envo.owl",
"homepage": "http://environmentontology.org/",
"name": "The Environment Ontology",
"prefix": "envo",
"version": "2024-07-01",
"version.iri": "http://purl.obolibrary.org/obo/envo/releases/2024-07-01/envo.owl"
},
"eupath": {
"description": "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.",
"download_owl": "http://purl.obolibrary.org/obo/eupath.owl",
"homepage": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology",
"name": "VEuPathDB Ontology",
"prefix": "eupath",
"version": "2023-05-30",
"version.iri": "http://purl.obolibrary.org/obo/eupath/2023-05-30/eupath.owl"
},
"exo": {
"description": "ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics.",
"download_owl": "http://purl.obolibrary.org/obo/exo.owl",
"homepage": "https://github.com/CTDbase/exposure-ontology",
"name": "Exposure ontology (ExO)",
"prefix": "exo",
"version": "2022-06-29",
"version.iri": "http://purl.obolibrary.org/obo/exo/releases/2022-06-29/exo.owl"
},
"fao": {
"description": "A structured controlled vocabulary for the anatomy of fungi.",
"download_owl": "http://purl.obolibrary.org/obo/fao.owl",
"homepage": "https://github.com/obophenotype/fungal-anatomy-ontology/",
"name": "Fungal gross anatomy",
"prefix": "fao",
"version": "2020-05-07",
"version.iri": "http://purl.obolibrary.org/obo/fao/releases/2020-05-07/fao.owl"
},
"fbbi": {
"description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.",
"download_owl": "http://purl.obolibrary.org/obo/fbbi.owl",
"homepage": "http://cellimagelibrary.org/",
"name": "Biological Imaging Methods Ontology",
"prefix": "fbbi",
"version": "2020-11-06",
"version.iri": "http://purl.obolibrary.org/obo/fbbi/releases/2020-11-06/fbbi.owl"
},
"fbbt": {
"description": "An ontology representing the gross anatomy of Drosophila melanogaster.",
"download_owl": "http://purl.obolibrary.org/obo/fbbt.owl",
"homepage": "http://purl.obolibrary.org/obo/fbbt",
"name": "Drosophila gross anatomy",
"prefix": "fbbt",
"version": "2024-06-13",
"version.iri": "http://purl.obolibrary.org/obo/fbbt/releases/2024-06-13/fbbt.owl"
},
"fbcv": {
"description": "A miscellaneous ontology of terms used for curation in FlyBase, including the DPO.",
"download_owl": "http://purl.obolibrary.org/obo/fbcv.owl",
"homepage": "http://purl.obolibrary.org/obo/fbcv",
"name": "FlyBase Controlled Vocabulary (FBcv)",
"prefix": "fbcv",
"version": "2024-06-13",
"version.iri": "http://purl.obolibrary.org/obo/fbcv/releases/2024-06-13/fbcv.owl"
},
"fbdv": {
"description": "An ontology of Drosophila melanogaster developmental stages.",
"download_owl": "http://purl.obolibrary.org/obo/fbdv.owl",
"homepage": "http://purl.obolibrary.org/obo/fbdv",
"name": "Drosophila Developmental Ontology",
"prefix": "fbdv",
"version": "2024-06-13",
"version.iri": "http://purl.obolibrary.org/obo/fbdv/releases/2024-06-13/fbdv.owl"
},
"fbsp": {
"description": "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.",
"homepage": "http://www.flybase.org/",
"name": "Fly taxonomy",
"prefix": "fbsp",
"version": "2017-11-19",
"version.iri": "http://purl.obolibrary.org/obo/fbsp/releases/2017-11-19/fbsp.owl"
},
"fideo": {
"description": "Food-Drug interactions automatically extracted from scientific literature",
"download_owl": "http://purl.obolibrary.org/obo/fideo.owl",
"homepage": "https://gitub.u-bordeaux.fr/erias/fideo",
"name": "Food Interactions with Drugs Evidence Ontology",
"prefix": "fideo",
"version": "2023-12-18",
"version.iri": "http://purl.obolibrary.org/obo/fideo/releases/2023-12-18/fideo.owl"
},
"fix": {
"description": "An ontology of physico-chemical methods and properties.",
"download_owl": "http://purl.obolibrary.org/obo/fix.owl",
"homepage": "http://www.ebi.ac.uk/chebi",
"name": "Physico-chemical methods and properties",
"prefix": "fix",
"version": "2020-04-13",
"version.iri": "http://purl.obolibrary.org/obo/fix/releases/2020-04-13/fix.owl"
},
"flopo": {
"description": "Traits and phenotypes of flowering plants occurring in digitized Floras",
"download_owl": "http://purl.obolibrary.org/obo/flopo.owl",
"homepage": "https://github.com/flora-phenotype-ontology/flopoontology",
"name": "Flora Phenotype Ontology",
"prefix": "flopo"
},
"fma": {
"description": "This is currently a slimmed down version of FMA",
"download_owl": "http://purl.obolibrary.org/obo/fma.owl",
"homepage": "http://si.washington.edu/projects/fma",
"name": "Foundational Model of Anatomy Ontology (subset)",
"prefix": "fma",
"version": "2020-04-13",
"version.iri": "http://purl.obolibrary.org/obo/fma/releases/2020-04-13/fma.owl"
},
"fobi": {
"description": "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data",
"download_owl": "http://purl.obolibrary.org/obo/fobi.owl",
"homepage": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology",
"name": "Food-Biomarker Ontology",
"prefix": "fobi",
"version.iri": "http://purl.obolibrary.org/obo/fobi/fobi.owl"
},
"foodon": {
"description": "A broadly scoped ontology representing entities which bear a \u201cfood role\u201d. It encompasses materials in natural ecosystems and agriculture that are consumed by humans and domesticated animals. This includes any generic (unbranded) raw or processed food material found in processing plants, markets, stores or food distribution points. FoodOn also imports nutritional component and dietary pattern terms from other OBO Foundry ontologies to support interoperability in diet and nutrition research",
"download_owl": "http://purl.obolibrary.org/obo/foodon.owl",
"homepage": "https://foodon.org/",
"name": "Food Ontology",
"prefix": "foodon",
"version": "2024-07-12",
"version.iri": "https://github.com/FoodOntology/foodon/releases/download/v2024-07-12/foodon.owl"
},
"fovt": {
"description": "These are the terms that are improted for FOVT to describe vertebrate traits.",
"download_owl": "http://purl.obolibrary.org/obo/fovt.owl",
"homepage": "https://github.com/futres/fovt",
"name": "FuTRES Ontology of Vertebrate Traits",
"prefix": "fovt",
"version": "2023-05-31",
"version.iri": "http://purl.obolibrary.org/obo/fovt/releases/2023-05-31/fovt.owl"
},
"fypo": {
"description": "A formal ontology of phenotypes observed in fission yeast.",
"download_owl": "http://purl.obolibrary.org/obo/fypo.owl",
"homepage": "https://github.com/pombase/fypo",
"name": "Fission Yeast Phenotype Ontology (FYPO)",
"prefix": "fypo",
"version": "2024-08-01",
"version.iri": "http://purl.obolibrary.org/obo/fypo/releases/2024-08-01/fypo.owl"
},
"gaz": {
"description": "A gazetteer constructed on ontological principles. The countries are actively maintained.",
"download_owl": "http://purl.obolibrary.org/obo/gaz.owl",
"homepage": "http://environmentontology.github.io/gaz/",
"name": "Gazetteer",
"prefix": "gaz"
},
"gecko": {
"description": "An ontology to represent genomics cohort attributes.",
"download_owl": "http://purl.obolibrary.org/obo/gecko.owl",
"homepage": "https://github.com/IHCC-cohorts/GECKO",
"name": "Genomics Cohorts Knowledge Ontology",
"prefix": "gecko",
"version": "2021-01-18",
"version.iri": "http://purl.obolibrary.org/obo/gecko/releases/2021-01-18/gecko.owl"
},
"genepio": {
"description": "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.",
"download_owl": "http://purl.obolibrary.org/obo/genepio.owl",
"homepage": "http://genepio.org/",
"name": "Genomic Epidemiology Ontology",
"prefix": "genepio",
"version": "2023-08-19",
"version.iri": "http://purl.obolibrary.org/obo/genepio/releases/2023-08-19/genepio.owl"
},
"geno": {
"description": "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013",
"download_owl": "http://purl.obolibrary.org/obo/geno.owl",
"homepage": "https://github.com/monarch-initiative/GENO-ontology/",
"name": "GENO ontology",
"prefix": "geno",
"version": "2023-10-08",
"version.iri": "http://purl.obolibrary.org/obo/geno/releases/2023-10-08/geno.owl"
},
"geo": {
"description": "An ontology of geographical entities",
"download_owl": "http://purl.obolibrary.org/obo/geo.owl",
"homepage": "https://github.com/ufbmi/geographical-entity-ontology/wiki",
"name": "Geographical Entity Ontology",
"prefix": "geo",
"version": "2016-03-26"
},
"gexo": {
"contact": "vladimir.n.mironov@gmail.com",
"description": "Gene Expression Ontology",
"download_rdf": "http://www.bio.ntnu.no/ontology/GeXO/gexo.rdf",
"homepage": "http://www.semantic-systems-biology.org/apo",
"name": "Gene Expression Ontology",
"prefix": "gexo"
},
"gno": {
"description": "An ontology for glycans based on GlyTouCan, but organized by subsumption.",
"download_owl": "http://purl.obolibrary.org/obo/gno.owl",
"homepage": "https://gnome.glyomics.org/",
"name": "Glycan Naming Ontology",
"prefix": "gno",
"version": "2024-05-21",
"version.iri": "http://purl.obolibrary.org/obo/gno/2024-05-21/gno.owl"
},
"go": {
"description": "The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms.",
"download_owl": "http://purl.obolibrary.org/obo/go/extensions/go-plus.owl",
"homepage": "http://geneontology.org/",
"name": "Gene Ontology",
"prefix": "go",
"version": "2024-06-17",
"version.iri": "http://purl.obolibrary.org/obo/go/releases/2024-06-17/extensions/go-plus.owl"
},
"gsso": {
"description": "GSSO is the Gender, Sex, and Sex Orientation ontology, including terms related to gender identity and expression, sexual and romantic identity and orientation, and sexual and reproductive behavior.",
"download_owl": "http://purl.obolibrary.org/obo/gsso.owl",
"homepage": "https://gsso.research.cchmc.org/",
"name": "GSSO - the Gender, Sex, and Sexual Orientation ontology",
"prefix": "gsso",
"version": "2.0.5",
"version.iri": "http://purl.obolibrary.org/obo/gsso/releases/2.0.5/gsso.owl"
},
"hancestro": {
"description": "Human ancestry ontology for the NHGRI GWAS Catalog",
"download_owl": "http://purl.obolibrary.org/obo/hancestro.owl",
"homepage": "https://ebispot.github.io/hancestro/",
"name": "Human Ancestry Ontology",
"prefix": "hancestro",
"version": "2024-06-21",
"version.iri": "http://purl.obolibrary.org/obo/hancestro/releases/2024-06-21/hancestro.owl"
},
"hao": {
"description": "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)",
"download_owl": "http://purl.obolibrary.org/obo/hao.owl",
"homepage": "http://hymao.org",
"name": "Hymenoptera Anatomy Ontology",
"prefix": "hao",
"version": "2023-06-01",
"version.iri": "http://purl.obolibrary.org/obo/hao/2023-06-01/hao.owl"
},
"hcao": {
"description": "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas.",
"download_owl": "https://raw.githubusercontent.com/ebi-ait/ontology/master/hcao.owl",
"name": "Human Cell Atlas Ontology",
"prefix": "hcao",
"version.iri": "http://ontology.data.humancellatlas.org/ontologies/hcao/releases/2023-05-16/hcao.owl"
},
"hom": {
"description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.",
"download_owl": "http://purl.obolibrary.org/obo/hom.owl",
"homepage": "https://github.com/BgeeDB/homology-ontology",
"name": "Homology Ontology",
"prefix": "hom",
"version": "2015-01-07",
"version.iri": "http://purl.obolibrary.org/obo/hom/releases/2015-01-07/hom.owl"
},
"hp": {
"description": "The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities and clinical features encountered in human disease.",
"download_owl": "http://purl.obolibrary.org/obo/hp/hp-international.owl",
"homepage": "http://www.human-phenotype-ontology.org/",
"name": "Human Phenotype Ontology",
"prefix": "hp",
"version": "2024-07-01",
"version.iri": "http://purl.obolibrary.org/obo/hp/releases/2024-07-01/hp-international.owl"
},
"hsapdv": {
"description": "Life cycle stages for Human",
"download_owl": "http://purl.obolibrary.org/obo/hsapdv.owl",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv",
"name": "Human Developmental Stages",
"prefix": "hsapdv"
},
"hso": {
"description": "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance.",
"download_owl": "http://purl.obolibrary.org/obo/hso.owl",
"homepage": "https://w3id.org/hso",
"name": "Health Surveillance Ontology",
"prefix": "hso",
"version": "2021-12-13",
"version.iri": "http://purl.obolibrary.org/obo/hso/2021-12-13/hso.owl"
},
"htn": {
"description": "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines",
"download_owl": "http://purl.obolibrary.org/obo/htn.owl",
"homepage": "https://github.com/aellenhicks/htn_owl",
"name": "Hypertension Ontology For Clinical Data",
"prefix": "htn"
},
"iao": {
"description": "The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch.",
"download_owl": "http://purl.obolibrary.org/obo/iao.owl",
"homepage": "https://github.com/information-artifact-ontology/IAO/",
"name": "Information Artifact Ontology (IAO)",
"prefix": "iao",
"version": "2022-11-07",
"version.iri": "http://purl.obolibrary.org/obo/iao/2022-11-07/iao.owl"
},
"iceo": {
"description": "A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning.",
"download_owl": "http://purl.obolibrary.org/obo/iceo.owl",
"homepage": "https://github.com/ontoice/ICEO",
"name": "ICEO: Ontology of Integrative and Conjugative Elements",
"prefix": "iceo",
"version": "2.1"
},
"ico": {
"description": "The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field.",
"download_owl": "http://purl.obolibrary.org/obo/ico.owl",
"homepage": "https://github.com/ICO-ontology/ICO",
"name": "Informed Consent Ontology (ICO)",
"prefix": "ico",
"version": "1.0.187"
},
"ido": {
"description": "A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology that hosts terms of general relevance across the domain, while extension ontologies host terms to specific to a particular part of the domain.",
"download_owl": "http://purl.obolibrary.org/obo/ido.owl",
"homepage": "http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology",
"name": "Infectious Disease Ontology",
"prefix": "ido",
"version": "2017-11-03",
"version.iri": "http://purl.obolibrary.org/obo/ido/2017-11-03/ido.owl"
},
"idocovid19": {
"contact": "johnbeverley2021@u.northwestern.edu",
"description": "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease.",
"homepage": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19",
"name": "The COVID-19 Infectious Disease Ontology",
"prefix": "idocovid19",
"version": "2020-07-21",
"version.iri": "http://purl.obolibrary.org/obo/2020-21-07/ido-covid-19.owl"
},
"idomal": {
"description": "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.",
"download_owl": "http://purl.obolibrary.org/obo/idomal.owl",
"homepage": "https://www.vectorbase.org/ontology-browser",
"name": "Malaria Ontology",
"prefix": "idomal",
"version": "2015-03-16",
"version.iri": "http://purl.obolibrary.org/obo/idomal/2015-03-16/idomal.owl"
},
"ino": {
"description": "he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles.",
"download_owl": "http://purl.obolibrary.org/obo/ino.owl",
"homepage": "https://github.com/INO-ontology/ino",
"name": "INO: Interaction Network Ontology",
"prefix": "ino",
"version": "1.1.13"
},
"kisao": {
"description": "A classification of algorithms for simulating biology, their parameters, and their outputs",
"download_owl": "http://purl.obolibrary.org/obo/kisao.owl",
"homepage": "https://github.com/SED-ML/KiSAO",
"name": "Kinetic Simulation Algorithm Ontology",
"prefix": "kisao",
"version": "2.30"
},
"labo": {
"description": "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents.",
"download_owl": "http://purl.obolibrary.org/obo/labo.owl",
"homepage": "https://github.com/OpenLHS/LABO",
"name": "clinical LABoratory Ontology",
"prefix": "labo",
"version": "2021-06-08",
"version.iri": "http://purl.obolibrary.org/obo/labo/2021-06-08/labo.owl"
},
"lepao": {
"description": "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research.",
"download_owl": "http://purl.obolibrary.org/obo/lepao.owl",
"homepage": "https://github.com/insect-morphology/lepao",
"name": "Lepidoptera Anatomy Ontology",
"prefix": "lepao",
"version": "2023-02-18",
"version.iri": "http://purl.obolibrary.org/obo/lepao/releases/2023-02-18/lepao.owl"
},
"ma": {
"description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus).",
"download_owl": "http://purl.obolibrary.org/obo/ma.owl",
"homepage": "https://github.com/obophenotype/mouse-anatomy-ontology",
"name": "Mouse adult gross anatomy",
"prefix": "ma",
"version": "2017-02-07",
"version.iri": "http://purl.obolibrary.org/obo/ma/releases/2017-02-07/ma.owl"
},
"mamo": {
"description": "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.",
"download_rdf": "https://raw.githubusercontent.com/EBISPOT/mamo/main/mamo.rdf",
"homepage": "http://sourceforge.net/p/mamo-ontology/wiki/Home/",
"name": "Mathematical Modelling Ontology",
"prefix": "mamo",
"version": "2023-02-03"
},
"maxo": {
"description": "An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations.",
"download_owl": "http://purl.obolibrary.org/obo/maxo.owl",
"homepage": "https://github.com/monarch-initiative/MAxO",
"name": "Medical Action Ontology",
"prefix": "maxo",
"version": "2024-07-29",
"version.iri": "http://purl.obolibrary.org/obo/maxo/releases/2024-07-29/maxo.owl"
},
"mco": {
"description": "Microbial Conditions Ontology is an ontology...",
"download_owl": "http://purl.obolibrary.org/obo/mco.owl",
"homepage": "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology",
"name": "Microbial Conditions Ontology",
"prefix": "mco",
"version": "2019-05-15",
"version.iri": "http://purl.obolibrary.org/obo/mco/releases/2019-05-15/mco.owl"
},
"mf": {
"description": "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning.",
"download_owl": "http://purl.obolibrary.org/obo/mf.owl",
"homepage": "https://github.com/jannahastings/mental-functioning-ontology",
"name": "Mental Functioning Ontology",
"prefix": "mf",
"version": "2022-07-19",
"version.iri": "http://purl.obolibrary.org/obo/MF/2022-07-19/MF.owl"
},
"mfmo": {
"description": "The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors.",
"download_owl": "http://purl.obolibrary.org/obo/mfmo.owl",
"homepage": "https://github.com/rdruzinsky/feedontology",
"name": "Mammalian Feeding Muscle Ontology",
"prefix": "mfmo",
"version": "2013-11-16",
"version.iri": "http://purl.obolibrary.org/obo/mfmo/2013-11-16/mfmo.owl"
},
"mfoem": {
"description": "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings.",
"download_owl": "http://purl.obolibrary.org/obo/mfoem.owl",
"homepage": "https://github.com/jannahastings/emotion-ontology",
"name": "Emotion Ontology",
"prefix": "mfoem",
"version": "2022-07-19",
"version.iri": "http://purl.obolibrary.org/obo/MFOEM/2022-07-19/MFOEM.owl"
},
"mfomd": {
"description": "The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF).",
"download_owl": "http://purl.obolibrary.org/obo/mfomd.owl",
"homepage": "https://github.com/jannahastings/mental-functioning-ontology",
"name": "Mental Disease Ontology",
"prefix": "mfomd",
"version": "2020-04-26",
"version.iri": "http://purl.obolibrary.org/obo/MFOMD/2020-04-26/MFOMD.owl"
},
"mi": {
"description": "A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions.",
"download_owl": "http://purl.obolibrary.org/obo/mi.owl",
"homepage": "https://github.com/HUPO-PSI/psi-mi-CV",
"name": "Molecular Interactions Controlled Vocabulary",
"prefix": "mi"
},
"miapa": {
"description": "The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies.\n\nThis ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA.",
"download_owl": "http://purl.obolibrary.org/obo/miapa.owl",
"homepage": "http://www.evoio.org/wiki/MIAPA",
"name": "Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology",
"prefix": "miapa"
},
"micro": {
"description": "An ontology of prokaryotic phenotypic and metabolic characters",
"download_owl": "http://purl.obolibrary.org/obo/micro.owl",
"homepage": "https://github.com/carrineblank/MicrO",
"name": "Ontology of Prokaryotic Phenotypic and Metabolic Characters",
"prefix": "micro",
"version": "1.5.1"
},
"miro": {
"description": "Application ontology for entities related to insecticide resistance in mosquitos",
"download_owl": "http://purl.obolibrary.org/obo/miro.owl",
"name": "Mosquito insecticide resistance",
"prefix": "miro",
"version": "2014-05-14",
"version.iri": "http://purl.obolibrary.org/obo/miro/releases/2014-05-14/miro.owl"
},
"mmo": {
"description": "A representation of the variety of methods used to make clinical and phenotype measurements.",
"download_owl": "http://purl.obolibrary.org/obo/mmo.owl",
"homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000",
"name": "Measurement method ontology",
"prefix": "mmo",
"version": "2.136",
"version.iri": "http://purl.obolibrary.org/obo/mmo/2.136/mmo.owl"
},
"mmusdv": {
"description": "Life cycle stages for Mus Musculus",
"download_owl": "http://purl.obolibrary.org/obo/mmusdv.owl",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv",
"name": "Mouse Developmental Stages",
"prefix": "mmusdv"
},
"mod": {
"description": "PSI-MOD is an ontology consisting of terms that describe protein chemical modifications",
"download_owl": "http://purl.obolibrary.org/obo/mod.owl",
"homepage": "http://www.psidev.info/MOD",
"name": "Protein modification",
"prefix": "mod",
"version": "1.031.6",
"version.iri": "http://purl.obolibrary.org/obo/mod/1.031.6/mod.owl"
},
"mondo": {
"description": "A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.",
"download_owl": "http://purl.obolibrary.org/obo/mondo.owl",
"homepage": "https://monarch-initiative.github.io/mondo",
"name": "Mondo Disease Ontology",
"prefix": "mondo",
"version": "2024-08-06",
"version.iri": "http://purl.obolibrary.org/obo/mondo/releases/2024-08-06/mondo.owl"
},
"mop": {
"contact": "chemistry-ontologies@googlegroups.com",
"description": "MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation.",
"download_owl": "http://purl.obolibrary.org/obo/mop.owl",
"homepage": "https://github.com/rsc-ontologies/rxno",
"name": "MOP",
"prefix": "mop",
"version": "2022-05-11",
"version.iri": "http://purl.obolibrary.org/obo/mop/releases/2022-05-11/mop.owl"
},
"mp": {
"description": "The Mammalian Phenotype Ontology is being developed by Cynthia L. Smith, Susan M. Bello, Anna, Anagnostopoulos, Carroll W. Goldsmith and Janan T. Eppig, as part of the Mouse Genome Database (MGD) Project, Mouse Genome Informatics (MGI), The Jackson Laboratory, Bar Harbor, ME. This file contains pre-coordinated phenotype terms, definitions and synonyms that can be used to describe mammalian phenotypes. The ontology is represented as a directed acyclic graph (DAG). It organizes phenotype terms into major biological system headers such as nervous system and respiratory system. This ontology is currently under development. Weekly updates are available at the Mouse Genome Informatics (MGI) ftp site (ftp://ftp.informatics.jax.org/pub/reports/index.html#pheno) as well as the OBO Foundry site (http://obofoundry.org/). Japanese labels of MP were created by the MP Japanese Translation Project (https://github.com/dbcls/MP_Japanse). Questions, comments and suggestions are welcome, and should be directed to pheno@jax.org, Susan.Bello@jax.org or to GitHub tracker (https://github.com/mgijax/mammalian-phenotype-ontology/issues) MGD is funded by NIH/NHGRI grant HG000330.",
"download_owl": "http://purl.obolibrary.org/obo/mp/mp-international.owl",
"homepage": "https://www.informatics.jax.org/vocab/mp_ontology/",
"name": "The Mammalian Phenotype Ontology",
"prefix": "mp",
"version": "2024-07-02",
"version.iri": "http://purl.obolibrary.org/obo/mp/releases/2024-07-02/mp-international.owl"
},
"mpath": {
"description": "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes",
"download_owl": "http://purl.obolibrary.org/obo/mpath.owl",
"homepage": "http://www.pathbase.net",
"name": "Mouse pathology ontology",
"prefix": "mpath",
"version": "2020-05-19",
"version.iri": "http://purl.obolibrary.org/obo/mpath/2020-05-19/mpath.owl"
},
"mpio": {
"description": "An ontology of minimum information regarding potential drug-drug interaction information.",
"download_owl": "http://purl.obolibrary.org/obo/mpio.owl",
"homepage": "https://github.com/MPIO-Developers/MPIO",
"name": "Minimum PDDI Information Ontology",
"prefix": "mpio",
"version": "2023-10-17",
"version.iri": "http://purl.obolibrary.org/obo/mpio/release/2023-10-17/mpio.owl"
},
"mro": {
"description": "The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions.",
"download_owl": "http://purl.obolibrary.org/obo/mro.owl",
"homepage": "https://github.com/IEDB/MRO",
"name": "MHC Restriction Ontology",
"prefix": "mro",
"version": "2024-08-02",
"version.iri": "http://purl.obolibrary.org/obo/mro/2024-08-02/mro.owl"
},
"ms": {
"contact": "psidev-ms-vocab@lists.sourceforge.net",
"description": "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.",
"download_owl": "http://purl.obolibrary.org/obo/ms.owl",
"homepage": "http://www.psidev.info/groups/controlled-vocabularies",
"name": "Mass spectrometry ontology",
"prefix": "ms",
"version": "4.1.168",
"version.iri": "http://purl.obolibrary.org/obo/ms/4.1.168/ms.owl"
},
"msio": {
"description": "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.",
"download_owl": "https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl",
"homepage": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO",
"name": "Metabolomics Standards Initiative Ontology (MSIO)",
"prefix": "msio",
"version": "1.0.1"
},
"nbo": {
"description": "An ontology of human and animal behaviours and behavioural phenotypes",
"download_owl": "http://purl.obolibrary.org/obo/nbo.owl",
"homepage": "https://github.com/obo-behavior/behavior-ontology/",
"name": "Neuro Behavior Ontology",
"prefix": "nbo",
"version": "2023-07-04",
"version.iri": "http://purl.obolibrary.org/obo/nbo/releases/2023-07-04/nbo.owl"
},
"ncbitaxon": {
"description": "An ontology representation of the NCBI organismal taxonomy",
"download_owl": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
"homepage": "https://github.com/obophenotype/ncbitaxon",
"name": "NCBI organismal classification",
"prefix": "ncbitaxon",
"version": "2024-07-03",
"version.iri": "http://purl.obolibrary.org/obo/ncbitaxon/2024-07-03/ncbitaxon.owl"
},
"ncit": {
"description": "NCI Thesaurus (NCIt)is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities. The NCIt OBO Edition aims to increase integration of the NCIt with OBO Library ontologies. NCIt OBO Edition releases should be considered experimental.",
"download_owl": "http://purl.obolibrary.org/obo/ncit.owl",
"homepage": "https://github.com/NCI-Thesaurus/thesaurus-obo-edition",
"name": "NCI Thesaurus OBO Edition",
"prefix": "ncit",
"version": "2024-05-07",
"version.iri": "http://purl.obolibrary.org/obo/ncit/releases/2024-05-07/ncit.owl"
},
"ncro": {
"contact": "ncro-devel@googlegroups.com",
"description": "An ontology for non-coding RNA, both of biological origin, and engineered.",
"download_owl": "http://purl.obolibrary.org/obo/ncro.owl",
"homepage": "http://omnisearch.soc.southalabama.edu/w/index.php/Ontology",
"name": "Non-Coding RNA Ontology",
"prefix": "ncro",
"version.iri": "http://purl.obolibrary.org/obo/ncro/2015-12-10/ncro-combined.owl"
},
"ngbo": {
"description": "Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.",
"download_owl": "http://purl.obolibrary.org/obo/ngbo.owl",
"homepage": "https://github.com/Dalalghamdi/NGBO",
"name": "Next generation biobanking ontology(NGBO).",
"prefix": "ngbo",
"version": "2022-10-05",
"version.iri": "http://purl.obolibrary.org/obo/ngbo/2022-10-05/ngbo.owl"
},
"nmrcv": {
"description": "This artefact is an MSI-approved controlled vocabulary primarily developed under COSMOS EU and PhenoMeNal EU governance. The nmrCV is supporting the nmrML XML format with standardized terms. nmrML is a vendor agnostic open access NMR raw data standard. Its primaly role is analogous to the mzCV for the PSI-approved mzML XML format. It uses BFO2.0 as its Top level. This CV was derived from two predecessors (The NMR CV from the David Wishart Group, developed by Joseph Cruz) and the MSI nmr CV developed by Daniel Schober at the EBI. This simple taxonomy of terms (no DL semantics used) serves the nuclear magnetic resonance markup language (nmrML) with meaningful descriptors to amend the nmrML xml file with CV terms. Metabolomics scientists are encouraged to use this CV to annotrate their raw and experimental context data, i.e. within nmrML. The approach to have an exchange syntax mixed of an xsd and CV stems from the PSI mzML effort. The reason to branch out from an xsd into a CV is, that in areas where the terminology is likely to change faster than the nmrML xsd could be updated and aligned, an externally and decentrallised maintained CV can accompensate for such dynamics in a more flexible way. A second reason for this set-up is that semantic validity of CV terms used in an nmrML XML instance (allowed CV terms, position/relation to each other, cardinality) can be validated by rule-based proprietary validators: By means of cardinality specifications and XPath expressions defined in an XML mapping file (an instances of the CvMappingRules.xsd ), one can define what ontology terms are allowed in a specific location of the data model.",
"download_owl": "http://nmrml.org/cv/stable/nmrCV.owl",
"homepage": "http://nmrml.org/cv/",
"name": "nuclear magnetic resonance CV",
"prefix": "nmrcv",
"version": "1.1.0"
},
"nomen": {
"description": "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature.",
"download_owl": "http://purl.obolibrary.org/obo/nomen.owl",
"homepage": "https://github.com/SpeciesFileGroup/nomen",
"name": "NOMEN - A nomenclatural ontology for biological names",
"prefix": "nomen"
},
"oae": {
"description": "The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc.",
"download_owl": "http://purl.obolibrary.org/obo/oae.owl",
"homepage": "https://github.com/OAE-ontology/OAE/",
"name": "OAE: Ontology of Adverse Events",
"prefix": "oae",
"version": "1.2.47"
},
"oarcs": {
"description": "OArCS is an ontology describing the Arthropod ciruclatory system.",
"download_owl": "http://purl.obolibrary.org/obo/oarcs.owl",
"homepage": "https://github.com/aszool/oarcs",
"name": "Ontology of Arthropod Circulatory Systems",
"prefix": "oarcs",
"version": "2019-04-18",
"version.iri": "http://purl.obolibrary.org/obo/hao/2019-04-18/hao.owl"
},
"oba": {
"description": "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO.",
"download_owl": "http://purl.obolibrary.org/obo/oba.owl",
"homepage": "https://github.com/obophenotype/bio-attribute-ontology",
"name": "Ontology of Biological Attributes (OBA)",
"prefix": "oba",
"version": "2024-06-27",
"version.iri": "http://purl.obolibrary.org/obo/oba/releases/2024-06-27/oba.owl"
},
"obcs": {
"description": "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012.",
"download_owl": "http://purl.obolibrary.org/obo/obcs.owl",
"homepage": "https://github.com/obcs/obcs",
"name": "OBCS: Ontology of Biological and Clinical Statistics",
"prefix": "obcs",
"version": "2023-12-08",
"version.iri": "http://purl.obolibrary.org/obo/obcs/2023-12-08/obcs.owl"
},
"obi": {
"description": "An ontology for representing biomedical investigations, including study designs, the collection and preparation of the targets of investigation, assays, instrumentation and reagents used, as well as the data generated and the types of analysis performed on the data to reach conclusions, and their documentation.",
"download_owl": "http://purl.obolibrary.org/obo/obi.owl",
"homepage": "http://obi-ontology.org",
"name": "Ontology for Biomedical Investigations",
"prefix": "obi",
"version": "2024-06-10",
"version.iri": "http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl"
},
"obib": {
"description": "The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology.",
"download_owl": "http://purl.obolibrary.org/obo/obib.owl",
"homepage": "https://github.com/biobanking/biobanking",
"name": "Ontology for BIoBanking (OBIB)",
"prefix": "obib",
"version": "2023-04-05",
"version.iri": "http://purl.obolibrary.org/obo/obib/2023-04-05/obib.owl"
},
"ogg": {
"description": "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets.",
"download_owl": "http://purl.obolibrary.org/obo/ogg.owl",
"homepage": "https://bitbucket.org/hegroup/ogg",
"name": "OGG: Ontology of Genes and Genomes",
"prefix": "ogg",
"version": "1.0.59"
},
"ogms": {
"description": "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats.\n\nOGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.",
"download_owl": "http://purl.obolibrary.org/obo/ogms.owl",
"homepage": "https://github.com/OGMS/ogms",
"name": "Ontology for General Medical Science",
"prefix": "ogms",
"version": "2021-08-19",
"version.iri": "http://purl.obolibrary.org/obo/ogms/2021-08-19/ogms.owl"
},
"ogsf": {
"description": "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.",
"download_owl": "http://purl.obolibrary.org/obo/ogsf.owl",
"homepage": "https://github.com/linikujp/OGSF",
"name": "Ontology of Genetic Susceptibility Factor",
"prefix": "ogsf",
"version": "2.0"
},
"ohd": {
"description": "The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies.",
"download_owl": "http://purl.obolibrary.org/obo/ohd.owl",
"homepage": "https://purl.obolibrary.org/obo/ohd/home",
"name": "Oral Health and Disease Ontology",
"prefix": "ohd",
"version": "2024-06-21",
"version.iri": "http://purl.obolibrary.org/obo/ohd/releases/2024-06-21/ohd.owl"
},
"ohmi": {
"description": "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.",
"download_owl": "http://purl.obolibrary.org/obo/ohmi.owl",
"homepage": "https://github.com/ohmi-ontology/ohmi",
"name": "OHMI: Ontology of Host-Microbiome Interactions",
"prefix": "ohmi",
"version": "2019-09-17",
"version.iri": "http://purl.obolibrary.org/obo/ohmi/2019-09-17/ohmi.owl"
},
"ohpi": {
"description": "OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration).",
"download_owl": "http://purl.obolibrary.org/obo/ohpi.owl",
"homepage": "https://github.com/OHPI/ohpi",
"name": "OHPI: Ontology of Host-Pathogen Interactions",
"prefix": "ohpi",
"version": "2019-09-30",
"version.iri": "http://purl.obolibrary.org/obo/ohpi/releases/2019-09-30"
},
"olatdv": {
"description": "Life cycle stages for Medaka",
"download_owl": "http://purl.obolibrary.org/obo/olatdv.owl",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv",
"name": "Medaka Developmental Stages",
"prefix": "olatdv"
},
"om": {
"contact": "hajo.rijgersberg@wur.nl",
"description": "The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units meter and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant: km/s/Mpc, or the quantity vaselife. OM defines the complete set of concepts in the domain as distinguished in the textual standards. As a result the ontology can answer a wider range of competency questions than the existing approaches do. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology; Typography; Shipping; Food engineering; Post-harvest; technology; Dynamics of texture and taste; Packaging",
"download_rdf": "https://raw.githubusercontent.com/HajoRijgersberg/OM/master/om-2.0.rdf",
"homepage": "https://github.com/HajoRijgersberg/OM",
"name": "Ontology of units of Measure (OM)",
"prefix": "om",
"version": "2.0.57"
},
"omiabis": {
"description": "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)",
"homepage": "https://github.com/OMIABIS/omiabis-dev",
"name": "Ontologized MIABIS",
"prefix": "omiabis",
"version": "2014-05-28"
},
"omit": {
"description": "Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain",
"download_owl": "http://purl.obolibrary.org/obo/omit.owl",
"homepage": "http://omit.cis.usouthal.edu/",
"name": "Ontology for MIRNA Target",
"prefix": "omit",
"version": "dev",
"version.iri": "http://purl.obolibrary.org/obo/omit/dev/omit.owl"
},
"omo": {
"description": "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO).",
"download_owl": "http://purl.obolibrary.org/obo/omo.owl",
"homepage": "https://github.com/information-artifact-ontology/ontology-metadata",
"name": "OBO Metadata Ontology",
"prefix": "omo",
"version": "2023-11-02",
"version.iri": "http://purl.obolibrary.org/obo/omo/releases/2023-11-02/omo.owl"
},
"omp": {
"description": "An ontology of phenotypes covering microbes",
"download_owl": "http://purl.obolibrary.org/obo/omp.owl",
"homepage": "http://microbialphenotypes.org",
"name": "Ontology of Microbial Phenotypes",
"prefix": "omp",
"version": "2024-03-25",
"version.iri": "http://purl.obolibrary.org/obo/omp/releases/2024-03-25/omp.owl"
},
"omrse": {
"description": "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations.",
"download_owl": "http://purl.obolibrary.org/obo/omrse.owl",
"homepage": "https://github.com/mcwdsi/OMRSE/wiki/OMRSE-Overview",
"name": "Ontology for Modeling and Representation of Social Entities",
"prefix": "omrse",
"version": "2024-03-22",
"version.iri": "http://purl.obolibrary.org/obo/omrse/releases/2024-03-22/omrse.owl"
},
"one": {
"description": "An ontology to standardize research output of nutritional epidemiologic studies.",
"download_owl": "http://purl.obolibrary.org/obo/one.owl",
"homepage": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies",
"name": "Ontology for Nutritional Epidemiology",
"prefix": "one"
},
"ons": {
"description": "An ontology for description of concepts in the nutritional studies domain.",
"download_owl": "http://purl.obolibrary.org/obo/ons.owl",
"homepage": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies",
"name": "Ontology for Nutritional Studies",
"prefix": "ons",
"version": "2024-07-03",
"version.iri": "https://raw.githubusercontent.com/enpadasi/Ontology-for-Nutritional-Studies/releases/download/v2024-07-03/ons.owl"
},
"ontoavida": {
"description": "The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of the most widely used computational approach for performing experimental evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment).\n\nThe lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight.\n\nOntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Do\u00f1ana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA).\n\nMore information can be found at https://obofoundry.org/ontology/ontoavida.html",
"download_owl": "http://purl.obolibrary.org/obo/ontoavida.owl",
"homepage": "https://gitlab.com/fortunalab/ontoavida",
"name": "OntoAvida: ontology for Avida digital evolution platform.",
"prefix": "ontoavida",
"version": "2022-03-15",
"version.iri": "http://purl.obolibrary.org/obo/ontoavida/releases/2022-03-15/ontoavida.owl"
},
"ontoneo": {
"description": "The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby.",
"download_owl": "http://purl.obolibrary.org/obo/ontoneo.owl",
"homepage": "ontoneo.com",
"name": "Obstetric and Neonatal Ontology",
"prefix": "ontoneo",
"version": "2021-04-29",
"version.iri": "http://purl.obolibrary.org/obo/ontoneo/releases/2021-04-29/ontoneo.owl"
},
"oostt": {
"description": "The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2).",
"download_owl": "http://purl.obolibrary.org/obo/oostt.owl",
"homepage": "https://github.com/OOSTT/OOSTT",
"name": "Ontology of Organizational Structures of Trauma centers and Trauma Systems",
"prefix": "oostt",
"version": "2024-01-25",
"version.iri": "http://purl.obolibrary.org/obo/oostt/release/2024-01-25/oostt.owl"
},
"opl": {
"description": "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.",
"download_owl": "http://purl.obolibrary.org/obo/opl.owl",
"homepage": "https://github.com/OPL-ontology/OPL",
"name": "Ontology for Parasite Lifecycle",
"prefix": "opl",
"version": "2023-08-28",
"version.iri": "http://purl.obolibrary.org/obo/opl/2023-08-28/opl.owl"
},
"opmi": {
"description": "OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles.",
"download_owl": "http://purl.obolibrary.org/obo/opmi.owl",
"homepage": "https://github.com/OPMI/opmi",
"name": "OPMI: Ontology of Precision Medicine and Investigation",
"prefix": "opmi",
"version": "1.0.166"
},
"ordo": {
"description": "The Orphanet Rare Disease ontology (ORDO) is jointly developed by Orphanet and the EBI to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It derived from the Orphanet database (www.orpha.net ) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA),databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10).",
"download_owl": "http://www.orphadata.org/data/ORDO/ordo_orphanet.owl",
"name": "Orphanet Rare Disease Ontology",
"prefix": "ordo",
"version": "4.5",
"version.iri": "https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.5.owl"
},
"ornaseq": {
"description": "An application ontology designed to annotate next-generation sequencing experiments performed on RNA.",
"download_owl": "http://purl.obolibrary.org/obo/ornaseq.owl",
"homepage": "http://kim.bio.upenn.edu/software/ornaseq.shtml",
"name": "Ontology for RNA sequencing (ORNASEQ)",
"prefix": "ornaseq",
"version": "2019-07-08",
"version.iri": "http://purl.obolibrary.org/obo/ornaseq/2019-07-08/ornaseq.owl"
},
"orth": {
"description": "The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way.",
"homepage": "http://purl.org/net/orth",
"name": "Orthology Ontology",
"prefix": "orth",
"version": "2.0",
"version.iri": "http://purl.org/net/orth/2.0"
},
"ovae": {
"description": "OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE).",
"download_owl": "http://purl.obolibrary.org/obo/ovae.owl",
"homepage": "http://www.violinet.org/ovae/",
"name": "OVAE: Ontology of Vaccine Adverse Events",
"prefix": "ovae",
"version": "1.0.34"
},
"owl": {
"name": "The OWL 2 Schema vocabulary (OWL 2)",
"prefix": "owl",
"version": "$Date: 2009/11/15 10:54:12 $",
"version.iri": "http://www.w3.org/2002/07/owl"
},
"pato": {
"description": "An ontology of phenotypic qualities (properties, attributes or characteristics).",
"download_owl": "http://purl.obolibrary.org/obo/pato.owl",
"homepage": "https://github.com/pato-ontology/pato/",
"name": "PATO - the Phenotype And Trait Ontology",
"prefix": "pato",
"version": "2024-03-28",
"version.iri": "http://purl.obolibrary.org/obo/pato/releases/2024-03-28/pato.owl"
},
"pcl": {
"description": "Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties.",
"download_owl": "http://purl.obolibrary.org/obo/pcl.owl",
"homepage": "https://github.com/obophenotype/provisional_cell_ontology",
"name": "Provisional Cell Ontology",
"prefix": "pcl",
"version": "2024-07-11",
"version.iri": "http://purl.obolibrary.org/obo/pcl/releases/2024-07-11/pcl.owl"
},
"pco": {
"description": "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology.",
"download_owl": "http://purl.obolibrary.org/obo/pco.owl",
"homepage": "https://github.com/PopulationAndCommunityOntology/pco",
"name": "Population and Community Ontology",
"prefix": "pco",
"version": "2021-05-03",
"version.iri": "http://purl.obolibrary.org/obo/pco/releases/2021-05-03/pco.owl"
},
"pdro": {
"description": "An ontology to describe entities related to prescription of drugs",
"download_owl": "http://purl.obolibrary.org/obo/pdro.owl",
"homepage": "https://github.com/OpenLHS/PDRO",
"name": "The Prescription of Drugs Ontology",
"prefix": "pdro",
"version": "2021-06-08",
"version.iri": "http://purl.obolibrary.org/obo/pdro/2021-06-08/pdro.owl"
},
"pdumdv": {
"description": "Life cycle stages for Platynereis dumerilii",
"download_owl": "http://purl.obolibrary.org/obo/pdumdv.owl",
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv",
"name": "Platynereis Developmental Stages",
"prefix": "pdumdv"
},
"peco": {
"description": "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments.",
"download_owl": "http://purl.obolibrary.org/obo/peco.owl",
"homepage": "http://planteome.org/",
"name": "Plant Experimental Conditions Ontology",
"prefix": "peco",
"version": "2023-11-10",
"version.iri": "http://purl.obolibrary.org/obo/peco/releases/2023-11-10/peco.owl"
},
"phipo": {
"description": "Ontology of species-neutral phenotypes observed in pathogen-host interactions.",
"download_owl": "http://purl.obolibrary.org/obo/phipo.owl",
"homepage": "https://github.com/PHI-base/phipo",
"name": "Pathogen Host Interactions Phenotype Ontology",
"prefix": "phipo",
"version": "2024-04-04",
"version.iri": "http://purl.obolibrary.org/obo/phipo/releases/2024-04-04/phipo.owl"
},
"plana": {
"description": "PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea.",
"download_owl": "http://purl.obolibrary.org/obo/plana.owl",
"homepage": "https://github.com/obophenotype/planaria-ontology",
"name": "Planarian Anatomy Ontology (PLANA)",
"prefix": "plana",
"version": "2023-03-13",
"version.iri": "http://purl.obolibrary.org/obo/plana/releases/2023-03-13"
},
"planp": {
"description": "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea.",
"download_owl": "http://purl.obolibrary.org/obo/planp.owl",
"homepage": "https://github.com/obophenotype/planarian-phenotype-ontology",
"name": "Planarian Phenotype Ontology (PLANP)",
"prefix": "planp",
"version": "2020-03-28",
"version.iri": "http://purl.obolibrary.org/obo/planp/releases/2020-03-28/planp.owl"
},
"po": {
"description": "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.",
"download_owl": "http://purl.obolibrary.org/obo/po.owl",
"homepage": "http://browser.planteome.org/amigo",
"name": "Plant Ontology",
"prefix": "po",
"version": "2024-04-17",
"version.iri": "http://purl.obolibrary.org/obo/po/releases/2024-04-17/po.owl"
},
"poro": {
"description": "An ontology describing the anatomical structures and characteristics of Porifera (sponges)",
"download_owl": "http://purl.obolibrary.org/obo/poro.owl",
"homepage": "https://github.com/obophenotype/porifera-ontology",
"name": "Porifera (sponge) ontology",
"prefix": "poro",
"version": "2016-10-06",
"version.iri": "http://purl.obolibrary.org/obo/poro/releases/2016-10-06/poro.owl"
},
"ppo": {
"contact": "ppo-discuss@googlegroups.com",
"description": "An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales.",
"download_owl": "http://purl.obolibrary.org/obo/ppo.owl",
"homepage": "https://github.com/PlantPhenoOntology/PPO",
"name": "Plant Phenology Ontology",
"prefix": "ppo",
"version": "2018-10-26",
"version.iri": "https://raw.githubusercontent.com/PlantPhenoOntology/ppo/master/releases/2018-10-26/ppo.owl"
},
"pr": {
"description": "An ontological representation of protein-related entities",
"download_owl": "http://purl.obolibrary.org/obo/pr.owl",
"homepage": "http://proconsortium.org",
"name": "PRotein Ontology (PRO)",
"prefix": "pr",
"version": "69.0",
"version.iri": "http://purl.obolibrary.org/obo/pr/69.0/pr.owl"
},
"pride": {
"description": "The PRIDE PRoteomics IDEntifications (PRIDE) database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence.",
"download_owl": "https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/pride_cv.owl",
"homepage": "https://github.com/PRIDE-Utilities/pride-ontology",
"name": "PRIDE Controlled Vocabulary",
"prefix": "pride"
},
"probonto": {
"contact": "probonto.dev@gmail.com",
"description": "ProbOnto, is an ontology-based knowledge base of probability distributions, featuring more than eighty uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulas.",
"download_rdf": "file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/probonto.ttl",
"homepage": "http://probonto.org",
"name": "Probability Distribution Ontology",
"prefix": "probonto",
"version": "2.5.0"
},
"proco": {
"description": "PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry.",
"download_owl": "http://purl.obolibrary.org/obo/proco.owl",
"homepage": "https://github.com/proco-ontology/PROCO",
"name": "PROCO: PROcess Chemistry Ontology",
"prefix": "proco",
"version": "2022-04-11",
"version.iri": "http://purl.obolibrary.org/obo/proco/releases/2022-04-11/proco.owl"
},
"prov": {
"homepage": "https://www.w3.org/TR/prov-o/",
"name": "Provenance Ontology (PROV-O)",
"prefix": "prov"
},
"psdo": {
"description": "Performance Summary Display Ontology (PSDO) is an application ontology about motivating information in performance summaries and the visual and textual entities that are used to communicate about performance. Motivating information includes performance comparisons and changes that motivate improvement or sustainment, such as improvement towards a goal, loss of high performer status, or the presence of a performance gap. Visual and textual entities include charts, tables, and graphs that display performance information. PSDO's domain focus is healthcare organizations that use clinical quality dashboards and feedback interventions for healthcare professionals and teams. Performance information is commonly about the quality of care and health outcomes that have been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is supported by the NIH, National Library of Medicine (1K01LM012528-01, 1R01LM013894-01).\n\nLandis-Lewis Z, Stansbury C, Rinc\u00f3n J, Gross C. Performance Summary Display Ontology: Feedback intervention content, delivery, and interpreted information. International Conference on Biomedical Ontology 2022 (ICBO 2022). https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf",
"download_owl": "http://purl.obolibrary.org/obo/psdo.owl",
"homepage": "https://github.com/Display-Lab/psdo",
"name": "Performance Summary Display Ontology",
"prefix": "psdo",
"version": "1.0.1",
"version.iri": "http://purl.obolibrary.org/obo/2022-02-23/psdo.owl"
},
"pso": {
"description": "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter.",
"download_owl": "http://purl.obolibrary.org/obo/pso.owl",
"homepage": "https://github.com/Planteome/plant-stress-ontology",
"name": "Plant Stress Ontology",
"prefix": "pso",
"version": "2023-11-14",
"version.iri": "http://purl.obolibrary.org/obo/pso/releases/2023-11-14/pso.owl"
},
"pw": {
"description": "A controlled vocabulary for annotating gene products to pathways.",
"download_owl": "http://purl.obolibrary.org/obo/pw.owl",
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
"name": "Pathway ontology",
"prefix": "pw",
"version": "7.85",
"version.iri": "http://purl.obolibrary.org/obo/pw/7.85/pw.owl"
},
"rbo": {
"description": "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.",
"download_owl": "http://purl.obolibrary.org/obo/rbo.owl",
"homepage": "https://github.com/Radiobiology-Informatics-Consortium/RBO",
"name": "Radiation Biology Ontology",
"prefix": "rbo",
"version": "2024-05-31",
"version.iri": "http://purl.obolibrary.org/obo/rbo/releases/2024-05-31/rbo.owl"
},
"rdfs": {
"name": "The RDF Schema vocabulary (RDFS)",
"prefix": "rdfs"
},
"reproduceme": {
"contact": "sheeba.samuel@uni-jena.de",
"description": "The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility.",
"homepage": "https://w3id.org/reproduceme/research",
"name": "REPRODUCE-ME Ontology",
"prefix": "reproduceme",
"version": "1.1"
},
"reto": {
"contact": "vladimir.n.mironov@gmail.com",
"description": "Regulation of Transcription",
"download_rdf": "http://www.bio.ntnu.no/ontology/ReTO/reto.rdf",
"homepage": "http://www.semantic-systems-biology.org/apo",
"name": "Regulation of Transcription Ontology",
"prefix": "reto"
},
"rex": {
"description": "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time.",
"download_owl": "http://purl.obolibrary.org/obo/rex.owl",
"name": "Physico-chemical process",
"prefix": "rex",
"version": "2017-11-19",
"version.iri": "http://purl.obolibrary.org/obo/rex/releases/2017-11-19/rex.owl"
},
"rexo": {
"contact": "vladimir.n.mironov@gmail.com",
"description": "Regulation of Gene Expression",
"download_rdf": "http://www.bio.ntnu.no/ontology/ReXO/rexo.rdf",
"homepage": "http://www.semantic-systems-biology.org/apo",
"name": "Regulation of Gene Expression Ontology",
"prefix": "rexo"
},
"ro": {
"description": "Relationship types shared across multiple ontologies",
"download_owl": "http://purl.obolibrary.org/obo/ro.owl",
"homepage": "https://oborel.github.io/",
"name": "Relation Ontology",
"prefix": "ro",
"version": "2024-04-24",
"version.iri": "http://purl.obolibrary.org/obo/ro/releases/2024-04-24/ro.owl"
},
"rs": {
"description": "Ontology of rat strains",
"download_owl": "http://purl.obolibrary.org/obo/rs.owl",
"homepage": "http://rgd.mcw.edu/rgdweb/search/strains.html",
"name": "Rat Strain Ontology",
"prefix": "rs",
"version": "6.229",
"version.iri": "http://purl.obolibrary.org/obo/rs/6.229/rs.owl"
},
"rxno": {
"contact": "chemistry-ontologies@googlegroups.com",
"description": "RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels\u2013Alder cyclization.",
"download_owl": "http://purl.obolibrary.org/obo/rxno.owl",
"homepage": "https://github.com/rsc-ontologies/rxno",
"name": "RXNO",
"prefix": "rxno",
"version": "2021-12-16",
"version.iri": "http://purl.obolibrary.org/obo/rxno/releases/2021-12-16/rxno.owl"
},
"sbo": {
"description": "Terms commonly used in Systems Biology, and in particular in computational modeling.",
"download_owl": "http://purl.obolibrary.org/obo/sbo.owl",
"homepage": "http://www.ebi.ac.uk/sbo/",
"name": "Systems Biology Ontology",
"prefix": "sbo",
"version": "2021-08-28"
},
"scdo": {
"description": "An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease.",
"download_owl": "http://purl.obolibrary.org/obo/scdo.owl",
"homepage": "https://scdontology.h3abionet.org/",
"name": "Sickle Cell Disease Ontology",
"prefix": "scdo",
"version": "2021-04-15",
"version.iri": "http://purl.obolibrary.org/obo/scdo/releases/2021-04-15/scdo.owl"
},
"schemaorg_http": {
"download_rdf": "https://schema.org/version/latest/schemaorg-all-http.rdf",
"prefix": "schemaorg_http"
},
"sepio": {
"description": "An ontology for representing the provenance of scientific claims and the evidence that supports them.",
"download_owl": "http://purl.obolibrary.org/obo/sepio.owl",
"homepage": "https://github.com/monarch-initiative/SEPIO-ontology",
"name": "Ontology for Scientific Evidence and Provenance Information",
"prefix": "sepio",
"version": "2023-06-13",
"version.iri": "http://purl.obolibrary.org/obo/sepio/releases/2023-06-13/sepio.owl"
},
"shareloc": {
"description": "ShareLoc defines terms to annotate data sets from single molecule localization microscopy, including but not limited to: imaging technique, biological structures or molecules of interest, cell types, experimental condition, labeling method, fixation protocol, etc.",
"download_owl": "https://raw.githubusercontent.com/imodpasteur/ShareLoc.XYZ/ontology/shareloc.owl",
"name": "ShareLoc",
"prefix": "shareloc"
},
"sibo": {
"description": "Social Behavior in insects",
"download_owl": "http://purl.obolibrary.org/obo/sibo.owl",
"homepage": "https://github.com/obophenotype/sibo",
"name": "Social Insect Behavior Ontology",
"prefix": "sibo",
"version": "2015-06-15",
"version.iri": "http://purl.obolibrary.org/obo/sibo/releases/2015-06-15/sibo.owl"
},
"sio": {
"contact": "sio-ontology@googlegroups.com",
"description": "The Semanticscience Integrated Ontology (SIO) provides a simple, integrated ontology of types and relations for rich description of objects, processes and their attributes.",
"download_owl": "https://raw.githubusercontent.com/micheldumontier/semanticscience/master/ontology/sio/release/sio-release.owl",
"homepage": "https://github.com/micheldumontier/semanticscience",
"name": "Semanticscience Integrated Ontology",
"prefix": "sio",
"version": "1.59",
"version.iri": "http://semanticscience.org/ontology/sio/v1.59/sio-release.owl"
},
"skos": {
"download_rdf": "http://www.w3.org/TR/skos-reference/skos.rdf",
"prefix": "skos"
},
"slm": {
"description": "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions.",
"download_rdf": "file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/swisslipids.ttl",
"name": "SwissLipids",
"prefix": "slm"
},
"snomed": {
"description": "SNOMED CT or SNOMED Clinical Terms is a systematically organized computer processable collection of medical terms providing codes, terms, synonyms and definitions used in clinical documentation and reporting.",
"download_owl": "file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/snomed-inferred.owl",
"name": "SNOMED CT (International Edition)",
"prefix": "snomed",
"version": "2020-01-31",
"version.iri": "http://snomed.info/sct/900000000000207008/version/20200131"
},
"so": {
"description": "A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases.",
"download_owl": "http://purl.obolibrary.org/obo/so.owl",
"homepage": "http://www.sequenceontology.org/",
"name": "Sequence types and features ontology",
"prefix": "so",
"version": "2024-06-05",
"version.iri": "http://purl.obolibrary.org/obo/so/2024-06-05/so.owl"
},
"spd": {
"description": "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).",
"download_owl": "http://purl.obolibrary.org/obo/spd.owl",
"homepage": "http://research.amnh.org/atol/files/",
"name": "Spider Ontology",
"prefix": "spd"
},
"srao": {
"contact": "contact@fairsharing.org",
"description": "The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies.",
"download_owl": "https://github.com/FAIRsharing/subject-ontology/raw/master/SRAO.owl",
"homepage": "https://github.com/FAIRsharing/subject-ontology",
"name": "FAIRsharing Subject Ontology (SRAO)",
"prefix": "srao",
"version": "2023-10-10",
"version.iri": "http://www.fairsharing.org/ontology/subject/SRAO/releases/2023-10-10/SRAO.owl"
},
"stato": {
"description": "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots.",
"download_owl": "http://purl.obolibrary.org/obo/stato.owl",
"homepage": "http://stato-ontology.org/",
"name": "STATO: the statistical methods ontology",
"prefix": "stato",
"version": "2024-07-07",
"version.iri": "http://purl.obolibrary.org/stato.owl/1.5"
},
"swo": {
"description": "The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community.",
"download_owl": "http://purl.obolibrary.org/obo/swo.owl",
"homepage": "https://github.com/allysonlister/swo",
"name": "Software ontology",
"prefix": "swo",
"version": "2023-03-05",
"version.iri": "http://www.ebi.ac.uk/swo/swo/releases/2023-03-05/swo.owl"
},
"symp": {
"description": "The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases.",
"download_owl": "http://purl.obolibrary.org/obo/symp.owl",
"homepage": "http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page",
"name": "Symptom Ontology",
"prefix": "symp",
"version": "2024-05-17",
"version.iri": "http://purl.obolibrary.org/obo/symp/releases/2024-05-17/symp.owl"
},
"t4fs": {
"description": "A terminology for the skills necessary to make data FAIR and to keep it FAIR.",
"download_owl": "http://purl.obolibrary.org/obo/t4fs.owl",
"homepage": "https://github.com/terms4fairskills/FAIRterminology",
"name": "terms4FAIRskills",
"prefix": "t4fs",
"version": "2023-03-02",
"version.iri": "http://purl.obolibrary.org/obo/t4fs/releases/2023-03-02/t4fs.owl"
},
"tads": {
"description": "The anatomy of the Tick, Families: Ixodidae, Argassidae",
"download_owl": "http://purl.obolibrary.org/obo/tads.owl",
"homepage": "https://www.vectorbase.org/ontology-browser",
"name": "Tick Anatomy Ontology",
"prefix": "tads",
"version": "2015-08-20",
"version.iri": "http://purl.obolibrary.org/obo/tads/2015-08-20/tads.owl"
},
"tao": {
"description": "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa",
"homepage": "http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology",
"name": "Teleost Anatomy Ontology",
"prefix": "tao",
"version": "2012-08-10",
"version.iri": "http://purl.obolibrary.org/obo/tao/2012-08-10/tao.owl"
},
"taxrank": {
"description": "A vocabulary of taxonomic ranks (species, family, phylum, etc)",
"download_owl": "http://purl.obolibrary.org/obo/taxrank.owl",
"homepage": "https://github.com/phenoscape/taxrank",
"name": "Taxonomic rank vocabulary",
"prefix": "taxrank",
"version": "2016-04-15",
"version.iri": "http://purl.obolibrary.org/obo/taxrank/releases/2016-04-15/taxrank.owl"
},
"teddy": {
"description": "TEDDY is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems and Synthetic Biology.",
"download_owl": "file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/teddy-inferred-fixed.owl",
"name": "Terminology for Description of Dynamics",
"prefix": "teddy",
"version": "2014-04-24",
"version.iri": "http://identifiers.org/combine.specifications/teddy.rel-2014-04-24"
},
"tgma": {
"description": "A structured controlled vocabulary of the anatomy of mosquitoes.",
"download_owl": "http://purl.obolibrary.org/obo/tgma.owl",
"homepage": "https://www.vectorbase.org/ontology-browser",
"name": "Mosquito gross anatomy ontology",
"prefix": "tgma",
"version": "2013-06-03",
"version.iri": "http://purl.obolibrary.org/obo/tgma/releases/2013-06-03/tgma.owl"
},
"to": {
"description": "A controlled vocabulary to describe phenotypic traits in plants.",
"download_owl": "http://purl.obolibrary.org/obo/to.owl",
"homepage": "http://browser.planteome.org/amigo",
"name": "Plant Trait Ontology",
"prefix": "to",
"version": "2023-07-17",
"version.iri": "http://purl.obolibrary.org/obo/to/releases/2023-07-17/to.owl"
},
"trans": {
"description": "The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.",
"download_owl": "http://purl.obolibrary.org/obo/trans.owl",
"homepage": "https://github.com/DiseaseOntology/PathogenTransmissionOntology",
"name": "Pathogen Transmission Ontology",
"prefix": "trans",
"version": "2022-10-10",
"version.iri": "http://purl.obolibrary.org/obo/trans/releases/2022-10-10/trans.owl"
},
"tto": {
"description": "An ontology covering the taxonomy of teleosts (bony fish)",
"download_owl": "http://purl.obolibrary.org/obo/tto.owl",
"homepage": "https://github.com/phenoscape/teleost-taxonomy-ontology",
"name": "Teleost taxonomy ontology",
"prefix": "tto"
},
"txpo": {
"description": "Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.\n\nThe TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms.\n\nIn applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp",
"download_owl": "http://purl.obolibrary.org/obo/txpo.owl",
"homepage": "https://toxpilot.nibiohn.go.jp/",
"name": "TOXic Process Ontology (TXPO)",
"prefix": "txpo",
"version": "2022-12-07",
"version.iri": "http://purl.obolibrary.org/obo/txpo/releases/2022-12-07/txpo.owl"
},
"uberon": {
"description": "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.",
"download_owl": "http://purl.obolibrary.org/obo/uberon.owl",
"homepage": "http://uberon.org",
"name": "Uber-anatomy ontology",
"prefix": "uberon",
"version": "2024-08-07",
"version.iri": "http://purl.obolibrary.org/obo/uberon/releases/2024-08-07/uberon.owl"
},
"unimod": {
"contact": "psidev-ms-vocab@lists.sourceforge.net",
"description": "Unimod is a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, an d site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide).",
"download_owl": "https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/unimod.owl",
"homepage": "http://www.unimod.org/",
"name": "Unimod protein modification database for mass spectrometry",
"prefix": "unimod"
},
"uo": {
"description": "Metrical units for use in conjunction with PATO",
"download_owl": "http://purl.obolibrary.org/obo/uo.owl",
"homepage": "https://github.com/bio-ontology-research-group/unit-ontology",
"name": "Units of measurement ontology",
"prefix": "uo",
"version": "2023-05-25",
"version.iri": "http://purl.obolibrary.org/obo/uo/releases/2023-05-25/uo.owl"
},
"upa": {
"description": "A manually curated resource for the representation and annotation of metabolic pathways",
"download_owl": "http://purl.obolibrary.org/obo/upa.owl",
"homepage": "https://github.com/geneontology/unipathway",
"name": "Unipathway",
"prefix": "upa",
"version": "2024-03-06",
"version.iri": "http://purl.obolibrary.org/obo/upa/releases/2024-03-06/upa.owl"
},
"vbo": {
"description": "Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.",
"download_owl": "http://purl.obolibrary.org/obo/vbo.owl",
"homepage": "https://github.com/monarch-initiative/vertebrate-breed-ontology",
"name": "Vertebrate Breed Ontology",
"prefix": "vbo",
"version": "2024-05-22",
"version.iri": "http://purl.obolibrary.org/obo/vbo/releases/2024-05-22/vbo.owl"
},
"vo": {
"description": "The Vaccine Ontology (VO) is a community-based biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine types and annotations, integrate various vaccine data, and support computer-assisted reasoning. The VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities.",
"download_owl": "http://purl.obolibrary.org/obo/vo.owl",
"homepage": "https://violinet.org/vaccineontology",
"name": "Vaccine Ontology",
"prefix": "vo",
"version": "2024-07-13",
"version.iri": "http://purl.obolibrary.org/obo/vo/releases/2024-07-13/vo.owl"
},
"vsao": {
"description": "Vertebrate skeletal anatomy ontology.",
"homepage": "https://www.nescent.org/phenoscape/Main_Page",
"name": "Vertebrate Skeletal Anatomy Ontology-",
"prefix": "vsao",
"version": "2012-11-06",
"version.iri": "http://purl.obolibrary.org/obo/vsao/2012-11-06/vsao.owl"
},
"vt": {
"description": "The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.",
"download_owl": "http://purl.obolibrary.org/obo/vt.owl",
"homepage": "https://github.com/AnimalGenome/vertebrate-trait-ontology",
"name": "The Vertebrate Trait Ontology",
"prefix": "vt",
"version": "2024-07-22",
"version.iri": "http://purl.obolibrary.org/obo/vt/releases/2024-07-22/vt.owl"
},
"vto": {
"description": "Comprehensive hierarchy of extinct and extant vertebrate taxa.",
"download_owl": "http://purl.obolibrary.org/obo/vto.owl",
"homepage": "https://github.com/phenoscape/vertebrate-taxonomy-ontology",
"name": "Vertebrate Taxonomy Ontology",
"prefix": "vto",
"version": "2020-11-13",
"version.iri": "http://purl.obolibrary.org/obo/vto/2020-11-13/vto.owl"
},
"wbbt": {
"description": "Ontology about the gross anatomy of the C. elegans",
"download_owl": "http://purl.obolibrary.org/obo/wbbt.owl",
"homepage": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology",
"name": "C. elegans Gross Anatomy Ontology",
"prefix": "wbbt",
"version": "2024-07-01",
"version.iri": "http://purl.obolibrary.org/obo/wbbt/releases/2024-07-01/wbbt.owl"
},
"wbls": {
"description": "Ontology about the development and life stages of the C. elegans",
"download_owl": "http://purl.obolibrary.org/obo/wbls.owl",
"homepage": "https://github.com/obophenotype/c-elegans-development-ontology",
"name": "C. elegans Development Ontology",
"prefix": "wbls",
"version": "2024-04-09",
"version.iri": "http://purl.obolibrary.org/obo/wbls/releases/2024-04-09/wbls.owl"
},
"wbphenotype": {
"description": "Ontology about C. elegans and other nematode phenotypes",
"download_owl": "http://purl.obolibrary.org/obo/wbphenotype.owl",
"homepage": "https://github.com/obophenotype/c-elegans-phenotype-ontology",
"name": "C elegans Phenotype Ontology",
"prefix": "wbphenotype",
"version": "2024-06-05",
"version.iri": "http://purl.obolibrary.org/obo/wbphenotype/releases/2024-06-05/wbphenotype.owl"
},
"xao": {
"description": "XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis.",
"download_owl": "http://purl.obolibrary.org/obo/xao.owl",
"homepage": "http://www.xenbase.org/anatomy/xao.do?method=display",
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"version_date_format": "%Y-%m-%d"
},
{
"prefix": "mco",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "mf",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "mfmo",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "mfoem",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "mfomd",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "mi",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "miapa",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "micro",
"version_type": "semver",
"version_prefix": "MicrO (An Ontology of Prokaryotic Phenotypic and Metabolic Characters). Version ",
"version_suffix_split": "True"
},
{
"prefix": "miro",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "mmo",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "mmusdv",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "mod",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "mondo",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "mop",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "mp",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "mpath",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "mpio",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "mro",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "ms",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "msio",
"version_type": "semver"
},
{
"prefix": "nbo",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "ncbitaxon",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "ncit",
"version_type": "other"
},
{
"prefix": "ncro",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "nmrcv",
"version_type": "semver"
},
{
"prefix": "nomen",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "oae",
"version_type": "semver"
},
{
"prefix": "oarcs",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "oba",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "obcs",
"version_type": "sequential"
},
{
"prefix": "obi",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "obib",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "ogg",
"version_type": "semver",
"version_prefix": "Vision Release: "
},
{
"prefix": "ogi",
"version_type": "semver"
},
{
"prefix": "ogms",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "ogsf",
"version_type": "semver"
},
{
"prefix": "ohd",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "ohmi",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "ohpi",
"version_type": "date",
"version_date_format": "%d-%m-%Y",
"version_iri_prefix": "http://purl.obolibrary.org/obo/ohpi/releases/"
},
{
"prefix": "olatdv",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "om",
"version_type": "semver"
},
{
"prefix": "omiabis",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "omit",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "omo",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "omp",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "omrse",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "one",
"version_type": "missing"
},
{
"prefix": "ons",
"version_type": "date",
"version_date_format": "%B %Y"
},
{
"prefix": "ontoneo",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "oostt",
"version_type": "date",
"version_date_format": "%Y-%m-%d",
"version_prefix": "release version - "
},
{
"prefix": "opl",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "opmi",
"version_type": "semver",
"version_prefix": "Vision Release: "
},
{
"prefix": "ornaseq",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "ordo",
"version_type": "semver"
},
{
"prefix": "orth",
"version_type": "garbage"
},
{
"prefix": "ovae",
"version_type": "semver",
"version_prefix": "Vision Release: "
},
{
"prefix": "pato",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "pco",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "pdro",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "pdumdv",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "peco",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "phi",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "phipo",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "plana",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "planp",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "po",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "poro",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "ppo",
"version_type": "date",
"version_date_format": "%Y-%m-%d",
"version_iri_prefix": "https://raw.githubusercontent.com/PlantPhenoOntology/ppo/master/releases/",
"version_iri_suffix": "/ppo.owl"
},
{
"prefix": "pr",
"version_type": "date",
"version_date_format": "%d-%m-%Y",
"version_iri_prefix": "http://purl.obolibrary.org/obo/pr/",
"version_iri_suffix": "/pr.owl"
},
{
"prefix": "pride",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "probonto",
"version_type": "semver"
},
{
"prefix": "prov",
"version_type": "date",
"version_date_format": "%Y-%m-%d",
"version_prefix": "Recommendation version "
},
{
"prefix": "psdo",
"version_type": "semver"
},
{
"prefix": "pso",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "pw",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "rbo",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "reproduceme",
"version_type": "semver"
},
{
"prefix": "reto",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "rex",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "rexo",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "rnao",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "ro",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "rs",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "rxno",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "sbo",
"version_type": "date",
"version_date_format": "%d:%m:%Y %H:%M"
},
{
"prefix": "scdo",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "sdgio",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "sepio",
"version_type": "garbage"
},
{
"prefix": "sibo",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "sio",
"version_type": "semver"
},
{
"prefix": "so",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "spd",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "srao",
"version_type": "semver",
"version_iri_prefix": "http://www.fairsharing.org/ontology/subject/SRAO.owl/"
},
{
"prefix": "stato",
"version_type": "semver"
},
{
"prefix": "swo",
"version_type": "semver"
},
{
"prefix": "symp",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "tads",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "taxrank",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "tgma",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "to",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "trans",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "tto",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "txpo",
"version_type": "date",
"version_date_format": "%Y/%m/%d"
},
{
"prefix": "uberon",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "unimod",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "uo",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "upa",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "upheno",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "vario",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "vido",
"version_type": "date",
"version_date_format": "%Y-%d-%m"
},
{
"prefix": "vo",
"version_type": "semver"
},
{
"prefix": "vt",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "vto",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "wbbt",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "wbls",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "wbphenotype",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "xao",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "xco",
"version_type": "date",
"version_date_format": "%d-%m-%Y"
},
{
"prefix": "xl",
"version_type": "missing"
},
{
"prefix": "xlmod",
"version_type": "date",
"version_date_format": "%Y-%m-%d",
"version_iri_suffix": "/xlmod.owl",
"version_iri_prefix": "http://purl.obolibrary.org/obo/xlmod/release/"
},
{
"prefix": "t4fs",
"version_type": "date",
"version_date_format": "%Y-%m-%d",
"version_iri_suffix": "/t4fs.owl",
"version_iri_prefix": "http://purl.obolibrary.org/obo/t4fs/release/"
},
{
"prefix": "cpont",
"version_type": "date",
"version_date_format": "%Y-%m-%d",
"version_iri_suffix": "/cpont.owl",
"version_iri_prefix": "https://w3id.org/cpont/ontology/releases/"
},
{
"prefix": "vbo",
"version_type": "date",
"version_date_format": "%Y-%m-%d",
"version_iri_suffix": "/vbo.owl",
"version_iri_prefix": "http://purl.obolibrary.org/obo/vbo/release/"
},
{
"prefix": "xpo",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "zeco",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "zfa",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "zfs",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "zp",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "ontoavida",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "colao",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "lepao",
"version_type": "date",
"version_date_format": "%Y-%m-%d"
},
{
"prefix": "disdriv",
"version_type": "missing"
},
{
"prefix": "proco",
"version_type": "semver"
},
{
"prefix": "shareloc",
"version_type": "missing"
},
{
"prefix": "ado",
"version_type": "semver"
}
]
} ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9699667
bioregistry-0.11.12/src/bioregistry/external/ontobee/ 0000755 0001751 0000177 00000000000 14655546227 022251 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/ontobee/__init__.py 0000644 0001751 0000177 00000003606 14655542206 024360 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download registry information from OntoBee."""
import json
import textwrap
from pathlib import Path
from typing import Sequence
from bs4 import BeautifulSoup
from pystow.utils import download
from bioregistry.constants import RAW_DIRECTORY
from bioregistry.external.alignment_utils import Aligner
__all__ = [
"get_ontobee",
"OntobeeAligner",
]
DIRECTORY = Path(__file__).parent.resolve()
RAW_PATH = RAW_DIRECTORY / "ontobee.html"
PROCESSED_PATH = DIRECTORY / "processed.json"
URL = "http://www.ontobee.org/"
LEGEND = {
"F": "Foundry",
"L": "Library",
"N": "Not Specified/No",
}
def get_ontobee(force_download: bool = False):
"""Get the OntoBee registry."""
if PROCESSED_PATH.exists() and not force_download:
with PROCESSED_PATH.open() as file:
return json.load(file)
download(url=URL, path=RAW_PATH, force=True)
with RAW_PATH.open() as f:
soup = BeautifulSoup(f, "html.parser")
rv = {}
for row in soup.find(id="ontologyList").find("tbody").find_all("tr"):
cells = row.find_all("td")
prefix = cells[1].text
rv[prefix] = {
"name": cells[2].text,
"library": LEGEND[cells[3].text.upper()],
# "link": cells[1].find("a").attrs["href"],
}
with PROCESSED_PATH.open("w") as file:
json.dump(rv, file, indent=2, sort_keys=True)
return rv
class OntobeeAligner(Aligner):
"""Aligner for OntoBee xref registry."""
key = "ontobee"
getter = get_ontobee
curation_header = ("name", "url")
def get_curation_row(self, external_id, external_entry) -> Sequence[str]:
"""Return the relevant fields from an OntoBee entry for pretty-printing."""
return [
textwrap.shorten(external_entry["name"], 50),
external_entry.get("url"),
]
if __name__ == "__main__":
OntobeeAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254818.0
bioregistry-0.11.12/src/bioregistry/external/ontobee/processed.json 0000644 0001751 0000177 00000056546 14655544042 025144 0 ustar 00runner docker {
"ADO": {
"library": "Library",
"name": "Alzheimer's Disease Ontology"
},
"AEO": {
"library": "Library",
"name": "Anatomical Entity Ontology"
},
"AFO": {
"library": "Not Specified/No",
"name": "Allotrope Foundation Ontology"
},
"AGRO": {
"library": "Library",
"name": "Agronomy Ontology"
},
"AISM": {
"library": "Library",
"name": "Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)"
},
"AMPHX": {
"library": "Library",
"name": "The Amphioxus Development and Anatomy Ontology"
},
"APO": {
"library": "Library",
"name": "Ascomycete phenotype ontology"
},
"APOLLO_SV": {
"library": "Library",
"name": "Apollo Structured Vocabulary"
},
"ARO": {
"library": "Library",
"name": "Antibiotic Resistance Ontology"
},
"AfPO": {
"library": "Library",
"name": "African Population Ontology"
},
"BAO": {
"library": "Not Specified/No",
"name": "BioAssay Ontology"
},
"BCGO": {
"library": "Library",
"name": "Beta Cell Genomics Ontology"
},
"BCO": {
"library": "Library",
"name": "Biological Collections Ontology"
},
"BFO": {
"library": "Foundry",
"name": "Basic Formal Ontology"
},
"BFO11": {
"library": "Library",
"name": "Basic Formal Ontology (BFO) 1.1"
},
"BSPO": {
"library": "Library",
"name": "Biological Spatial Ontology"
},
"BTO": {
"library": "Library",
"name": "BRENDA tissue / enzyme source"
},
"CARO": {
"library": "Library",
"name": "Common Anatomy Reference Ontology"
},
"CCFO": {
"library": "Not Specified/No",
"name": "Common Coordinate Framework Ontology"
},
"CDAO": {
"library": "Library",
"name": "Comparative Data Analysis Ontology"
},
"CDNO": {
"library": "Library",
"name": "Compositional Dietary Nutrition Ontology"
},
"CEPH": {
"library": "Library",
"name": "Cephalopod Ontology"
},
"CHEBI": {
"library": "Foundry",
"name": "Chemical Entities of Biological Interest"
},
"CHEMINF": {
"library": "Library",
"name": "Chemical Information Ontology"
},
"CHIRO": {
"library": "Library",
"name": "CHEBI Integrated Role Ontology"
},
"CHMO": {
"library": "Library",
"name": "Chemical Methods Ontology"
},
"CIDO": {
"library": "Library",
"name": "Coronavirus Infectious Disease Ontology"
},
"CIO": {
"library": "Library",
"name": "Confidence Information Ontology"
},
"CL": {
"library": "Library",
"name": "Cell Ontology"
},
"CLAO": {
"library": "Library",
"name": "Collembola Anatomy Ontology"
},
"CLO": {
"library": "Library",
"name": "Cell Line Ontology"
},
"CLO-NICR": {
"library": "Not Specified/No",
"name": "Cell Line Ontology - Chinese National Infrastructure of Cell Line Resource"
},
"CLO-hPSCreg": {
"library": "Not Specified/No",
"name": "Cell Line Ontology - Human Pluripotent Stem Cell Registry"
},
"CLYH": {
"library": "Library",
"name": "Clytia hemisphaerica Development and Anatomy Ontology"
},
"CMF": {
"library": "Library",
"name": "CranioMaxilloFacial ontology"
},
"CMO": {
"library": "Library",
"name": "Clinical measurement ontology"
},
"COB": {
"library": "Library",
"name": "Core Ontology for Biology and Biomedicine"
},
"COLAO": {
"library": "Library",
"name": "Coleoptera Anatomy Ontology (COLAO)"
},
"CRO": {
"library": "Library",
"name": "Contributor Role Ontology"
},
"CTCAE-OAEview": {
"library": "Not Specified/No",
"name": "OAE CTCAE view"
},
"CTENO": {
"library": "Library",
"name": "Ctenophore Ontology"
},
"CTO": {
"library": "Library",
"name": "CTO: Core Ontology of Clinical Trials"
},
"CVDO": {
"library": "Library",
"name": "Cardiovascular Disease Ontology"
},
"DDANAT": {
"library": "Library",
"name": "Dictyostelium discoideum anatomy"
},
"DDPHENO": {
"library": "Library",
"name": "Dictyostelium discoideum phenotype ontology"
},
"DIDEO": {
"library": "Library",
"name": "Drug-drug Interaction and Drug-drug Interaction Evidence Ontology"
},
"DINTO": {
"library": "Library",
"name": "The Drug-Drug Interactions Ontology"
},
"DISDRIV": {
"library": "Library",
"name": "Disease Drivers Ontology"
},
"DOID": {
"library": "Foundry",
"name": "Human Disease Ontology"
},
"DRON": {
"library": "Library",
"name": "The Drug Ontology"
},
"DUO": {
"library": "Library",
"name": "Data Use Ontology"
},
"ECAO": {
"library": "Library",
"name": "The Echinoderm Anatomy and Development Ontology"
},
"ECO": {
"library": "Library",
"name": "Evidence and Conclusion Ontology"
},
"ECOCORE": {
"library": "Library",
"name": "An ontology of core ecological entities"
},
"ECTO": {
"library": "Library",
"name": "Environmental conditions, treatments and exposures ontology"
},
"EDAM": {
"library": "Not Specified/No",
"name": "EMBRACE Data and Methods"
},
"EFO": {
"library": "Not Specified/No",
"name": "Experimental Factor Ontology"
},
"EHDAA2": {
"library": "Library",
"name": "Human developmental anatomy, abstract"
},
"EMAPA": {
"library": "Library",
"name": "Mouse Developmental Anatomy Ontology"
},
"ENVO": {
"library": "Library",
"name": "Environment Ontology"
},
"EPIO": {
"library": "Library",
"name": "Epilepsy Ontology"
},
"EPO": {
"library": "Library",
"name": "Epidemiology Ontology"
},
"ERO": {
"library": "Library",
"name": "eagle-i resource ontology"
},
"EUPATH": {
"library": "Library",
"name": "VEuPathDB ontology"
},
"ExO": {
"library": "Library",
"name": "Exposure ontology"
},
"FAO": {
"library": "Library",
"name": "Fungal gross anatomy"
},
"FBbi": {
"library": "Library",
"name": "Biological Imaging Methods Ontology"
},
"FBbt": {
"library": "Library",
"name": "Drosophila gross anatomy"
},
"FBcv": {
"library": "Library",
"name": "Drosophila Phenotype Ontology"
},
"FBdv": {
"library": "Library",
"name": "Drosophila development"
},
"FIDEO": {
"library": "Library",
"name": "Food Interactions with Drugs Evidence Ontology"
},
"FIX": {
"library": "Library",
"name": "Physico-chemical methods and properties"
},
"FLOPO": {
"library": "Library",
"name": "Flora Phenotype Ontology"
},
"FMA": {
"library": "Library",
"name": "Foundational Model of Anatomy Ontology (subset)"
},
"FOBI": {
"library": "Library",
"name": "Food-Biomarker Ontology"
},
"FOODON": {
"library": "Library",
"name": "Food Ontology"
},
"FOVT": {
"library": "Library",
"name": "FuTRES Ontology of Vertebrate Traits"
},
"FYPO": {
"library": "Library",
"name": "Fission Yeast Phenotype Ontology"
},
"GALLONT": {
"library": "Library",
"name": "Plant Gall Ontology"
},
"GAZ": {
"library": "Library",
"name": "Gazetteer"
},
"GECKO": {
"library": "Library",
"name": "Genomics Cohorts Knowledge Ontology"
},
"GENEPIO": {
"library": "Library",
"name": "Genomic Epidemiology Ontology"
},
"GENO": {
"library": "Library",
"name": "Genotype Ontology"
},
"GEO": {
"library": "Library",
"name": "Geographical Entity Ontology"
},
"GNO": {
"library": "Library",
"name": "Glycan Naming and Subsumption Ontology (GNOme)"
},
"GO": {
"library": "Foundry",
"name": "Gene Ontology"
},
"GSSO": {
"library": "Library",
"name": "Gender, Sex, and Sexual Orientation (GSSO) ontology"
},
"HANCESTRO": {
"library": "Library",
"name": "Human Ancestry Ontology"
},
"HAO": {
"library": "Library",
"name": "Hymenoptera Anatomy Ontology"
},
"HINO": {
"library": "Not Specified/No",
"name": "Human Interaction Network Ontology"
},
"HOM": {
"library": "Library",
"name": "Homology Ontology"
},
"HP": {
"library": "Library",
"name": "Human Phenotype Ontology"
},
"HSO": {
"library": "Library",
"name": "Health Surveillance Ontology"
},
"HTN": {
"library": "Library",
"name": "Hypertension Ontology"
},
"HsapDv": {
"library": "Library",
"name": "Human Developmental Stages"
},
"IAO": {
"library": "Library",
"name": "Information Artifact Ontology"
},
"IAO-Onto-Meta": {
"library": "Not Specified/No",
"name": "IAO Ontology Metadata"
},
"ICDO": {
"library": "Not Specified/No",
"name": "International Classification of Disease Ontology"
},
"ICEO": {
"library": "Library",
"name": "Integrative and Conjugative Element Ontology"
},
"ICO": {
"library": "Library",
"name": "Informed Consent Ontology"
},
"IDO": {
"library": "Library",
"name": "Infectious Disease Ontology"
},
"IDOBRU": {
"library": "Not Specified/No",
"name": "Brucellosis Ontology"
},
"IDOMAL": {
"library": "Library",
"name": "Malaria Ontology"
},
"INO": {
"library": "Library",
"name": "Interaction Network Ontology"
},
"KISAO": {
"library": "Library",
"name": "Kinetic Simulation Algorithm Ontology"
},
"KTAO": {
"library": "Not Specified/No",
"name": "Kidney Tissue Atlas Ontology"
},
"LABO": {
"library": "Library",
"name": "clinical LABoratory Ontology"
},
"LEPAO": {
"library": "Library",
"name": "Lepidoptera Anatomy Ontology"
},
"LINCS-CLOview": {
"library": "Not Specified/No",
"name": "CLO LINCS view"
},
"LTHIDO": {
"library": "Not Specified/No",
"name": "LTHIDO"
},
"MA": {
"library": "Library",
"name": "Mouse adult gross anatomy"
},
"MAMO": {
"library": "Library",
"name": "Mathematical modeling ontology"
},
"MAXO": {
"library": "Library",
"name": "Medical Action Ontology"
},
"MCO": {
"library": "Library",
"name": "Microbial Conditions Ontology"
},
"MCRO": {
"library": "Library",
"name": "Model Card Report Ontology"
},
"MF": {
"library": "Library",
"name": "Mental Functioning Ontology"
},
"MFMO": {
"library": "Library",
"name": "Mammalian Feeding Muscle Ontology"
},
"MFOEM": {
"library": "Library",
"name": "Emotion Ontology"
},
"MFOMD": {
"library": "Library",
"name": "Mental Disease Ontology"
},
"MI": {
"library": "Library",
"name": "Molecular Interactions Controlled Vocabulary"
},
"MIAPA": {
"library": "Library",
"name": "MIAPA Ontology"
},
"MICRO": {
"library": "Library",
"name": "Ontology of Prokaryotic Phenotypic and Metabolic Characters"
},
"MIRO": {
"library": "Library",
"name": "Mosquito insecticide resistance"
},
"MMO": {
"library": "Library",
"name": "Measurement method ontology"
},
"MOD": {
"library": "Library",
"name": "Protein modification"
},
"MONDO": {
"library": "Library",
"name": "Mondo Disease Ontology"
},
"MOP": {
"library": "Library",
"name": "Molecular Process Ontology"
},
"MP": {
"library": "Library",
"name": "Mammalian Phenotype Ontology"
},
"MPATH": {
"library": "Not Specified/No",
"name": "Mouse pathology"
},
"MPIO": {
"library": "Library",
"name": "Minimum PDDI Information Ontology"
},
"MRO": {
"library": "Library",
"name": "MHC Restriction Ontology"
},
"MS": {
"library": "Library",
"name": "Mass spectrometry ontology"
},
"MmusDv": {
"library": "Library",
"name": "Mouse Developmental Stages"
},
"NBO": {
"library": "Library",
"name": "Neuro Behavior Ontology"
},
"NCBITaxon": {
"library": "Library",
"name": "NCBI organismal classification"
},
"NCIT": {
"library": "Library",
"name": "NCI Thesaurus OBO Edition"
},
"NCRO": {
"library": "Library",
"name": "Non-Coding RNA Ontology"
},
"NDF-RT": {
"library": "Not Specified/No",
"name": "National Drug File Reference Terminology"
},
"NFO": {
"library": "Not Specified/No",
"name": "NFO"
},
"NGBO": {
"library": "Library",
"name": "Next Generation Biobanking Ontology"
},
"NOMEN": {
"library": "Library",
"name": "NOMEN - A nomenclatural ontology for biological names"
},
"OAE": {
"library": "Library",
"name": "Ontology of Adverse Events"
},
"OARCS": {
"library": "Library",
"name": "Ontology of Arthropod Circulatory Systems"
},
"OBA": {
"library": "Library",
"name": "Ontology of Biological Attributes"
},
"OBCS": {
"library": "Library",
"name": "Ontology of Biological and Clinical Statistics"
},
"OBI": {
"library": "Foundry",
"name": "Ontology for Biomedical Investigations"
},
"OBI-NIAID-GSC-BRC-view": {
"library": "Not Specified/No",
"name": "OBI NIAID-GSC-BRC view"
},
"OBIB": {
"library": "Library",
"name": "Ontology for Biobanking"
},
"OBIws": {
"library": "Not Specified/No",
"name": "OBI web service, development version"
},
"OCCO": {
"library": "Library",
"name": "Occupation Ontology"
},
"OCE": {
"library": "Not Specified/No",
"name": "Ontology of Chemical Elements"
},
"OCMR": {
"library": "Not Specified/No",
"name": "Ontology of Chinese Medicine for Rheumatism"
},
"OCRe": {
"library": "Not Specified/No",
"name": "OCRe"
},
"OCVDAE": {
"library": "Not Specified/No",
"name": "Ontology of Cardiovascular Drug Adverse Events"
},
"ODAE": {
"library": "Not Specified/No",
"name": "Ontology of Drug Adverse Events"
},
"ODNAE": {
"library": "Not Specified/No",
"name": "Ontologyof Drug Neuropathy Adverse Events"
},
"OGG": {
"library": "Library",
"name": "The Ontology of Genes and Genomes"
},
"OGG-At": {
"library": "Not Specified/No",
"name": "Ontology of Genes and Genomes - Arabidopsis thaliana"
},
"OGG-Bru": {
"library": "Not Specified/No",
"name": "Ontology of Genes and Genomes - Brucella"
},
"OGG-Ce": {
"library": "Not Specified/No",
"name": "Ontology of Genes and Genomes - Caenorhabditis elegans"
},
"OGG-Dm": {
"library": "Not Specified/No",
"name": "Ontology of Genes and Genomes - Fruit Fly"
},
"OGG-Dr": {
"library": "Not Specified/No",
"name": "Ontology of Genes and Genomes - Zebrafish"
},
"OGG-Mm": {
"library": "Not Specified/No",
"name": "Ontology of Genes and Genomes - Mouse"
},
"OGG-Pf": {
"library": "Not Specified/No",
"name": "Ontology of Genes and Genomes - Plasmodium falciparum"
},
"OGG-Sc": {
"library": "Not Specified/No",
"name": "Ontology of Genes and Genomes - Yeast"
},
"OGI": {
"library": "Library",
"name": "Ontology for genetic interval"
},
"OGMS": {
"library": "Library",
"name": "Ontology for General Medical Science"
},
"OGSF": {
"library": "Library",
"name": "Ontology of Genetic Susceptibility Factor"
},
"OHD": {
"library": "Library",
"name": "Oral Health and Disease Ontology"
},
"OHMI": {
"library": "Library",
"name": "Ontology of Host-Microbiome Interactions"
},
"OHPI": {
"library": "Library",
"name": "Ontology of Host Pathogen Interactions"
},
"OLOBO": {
"library": "Not Specified/No",
"name": "Ontology for Linking Biological and Medical Ontologies"
},
"OMIABIS": {
"library": "Library",
"name": "Ontologized MIABIS"
},
"OMIT": {
"library": "Library",
"name": "Ontology for MIRNA Target"
},
"OMO": {
"library": "Library",
"name": "OBO Metadata Ontology"
},
"OMP": {
"library": "Library",
"name": "Ontology of Microbial Phenotypes"
},
"OMRSE": {
"library": "Library",
"name": "Ontology for Modeling and Representation of Social Entities"
},
"ONE": {
"library": "Library",
"name": "Ontology for Nutritional Epidemiology"
},
"ONS": {
"library": "Library",
"name": "Ontology for Nutritional Studies"
},
"ONTOAVIDA": {
"library": "Library",
"name": "OntoAvida: ontology for Avida digital evolution platform"
},
"ONTONEO": {
"library": "Library",
"name": "Obstetric and Neonatal Ontology"
},
"OOSTT": {
"library": "Library",
"name": "Ontology of Organizational Structures of Trauma centers and Trauma systems"
},
"OPL": {
"library": "Library",
"name": "Ontology for Parasite LifeCycle"
},
"OPMI": {
"library": "Library",
"name": "Ontology of Precision Medicine and Investigation"
},
"ORNASEQ": {
"library": "Library",
"name": "Ontology of RNA Sequencing"
},
"OSCI": {
"library": "Not Specified/No",
"name": "Ontology for Stem Cell Investigations"
},
"OVAE": {
"library": "Library",
"name": "Ontology of Vaccine Adverse Events"
},
"OlatDv": {
"library": "Library",
"name": "Medaka Developmental Stages"
},
"PATO": {
"library": "Foundry",
"name": "Phenotype And Trait Ontology"
},
"PCL": {
"library": "Library",
"name": "Provisional Cell Ontology"
},
"PCO": {
"library": "Library",
"name": "Population and Community Ontology"
},
"PDRO": {
"library": "Library",
"name": "The Prescription of Drugs Ontology"
},
"PECO": {
"library": "Library",
"name": "Plant Experimental Conditions Ontology"
},
"PHIPO": {
"library": "Library",
"name": "Pathogen Host Interaction Phenotype Ontology"
},
"PLANA": {
"library": "Library",
"name": "planaria-ontology"
},
"PLANP": {
"library": "Library",
"name": "Planarian Phenotype Ontology"
},
"PNO": {
"library": "Not Specified/No",
"name": "Proper Name Ontology"
},
"PO": {
"library": "Foundry",
"name": "Plant Ontology"
},
"PORO": {
"library": "Library",
"name": "Porifera Ontology"
},
"PPO": {
"library": "Library",
"name": "Plant Phenology Ontology"
},
"PR": {
"library": "Foundry",
"name": "PRotein Ontology (PRO)"
},
"PROCO": {
"library": "Library",
"name": "Process Chemistry Ontology"
},
"PSDO": {
"library": "Library",
"name": "Performance Summary Display Ontology"
},
"PSO": {
"library": "Library",
"name": "Plant Stress Ontology"
},
"PW": {
"library": "Library",
"name": "Pathway ontology"
},
"PdumDv": {
"library": "Library",
"name": "Platynereis Developmental Stages"
},
"RBO": {
"library": "Library",
"name": "Radiation Biology Ontology"
},
"REO": {
"library": "Not Specified/No",
"name": "Reagent Ontology"
},
"REX": {
"library": "Library",
"name": "Physico-chemical process"
},
"RNAO": {
"library": "Library",
"name": "RNA ontology"
},
"RO": {
"library": "Library",
"name": "Relation Ontology"
},
"RS": {
"library": "Library",
"name": "Rat Strain Ontology"
},
"RXNO": {
"library": "Library",
"name": "Name Reaction Ontology"
},
"SBO": {
"library": "Library",
"name": "Systems Biology Ontology"
},
"SCDO": {
"library": "Library",
"name": "Sickle Cell Disease Ontology"
},
"SDGIO": {
"library": "Not Specified/No",
"name": "Sustainable Development Goals Interface Ontology"
},
"SEP": {
"library": "Library",
"name": "Sample processing and separation techniques"
},
"SEPIO": {
"library": "Library",
"name": "Scientific Evidence and Provenance Information Ontology"
},
"SIBO": {
"library": "Library",
"name": "Social Insect Behavior Ontology"
},
"SIO": {
"library": "Not Specified/No",
"name": "Semanticscience Integrated Ontology"
},
"SLSO": {
"library": "Library",
"name": "Space Life Sciences Ontology"
},
"SO": {
"library": "Library",
"name": "Sequence types and features ontology"
},
"SPD": {
"library": "Library",
"name": "Spider Ontology"
},
"STATO": {
"library": "Library",
"name": "The Statistical Methods Ontology"
},
"SWO": {
"library": "Library",
"name": "Software ontology"
},
"SYMP": {
"library": "Library",
"name": "Symptom Ontology"
},
"T4FS": {
"library": "Library",
"name": "terms4FAIRskills"
},
"TADS": {
"library": "Library",
"name": "Tick Anatomy Ontology"
},
"TAXRANK": {
"library": "Library",
"name": "Taxonomic rank vocabulary"
},
"TGMA": {
"library": "Library",
"name": "Mosquito gross anatomy ontology"
},
"TO": {
"library": "Library",
"name": "Plant Trait Ontology"
},
"TRANS": {
"library": "Library",
"name": "Pathogen Transmission Ontology"
},
"TSO": {
"library": "Not Specified/No",
"name": "Transportation System Ontology"
},
"TTO": {
"library": "Library",
"name": "Teleost taxonomy ontology"
},
"TXPO": {
"library": "Library",
"name": "Toxic Process Ontology"
},
"UBERON": {
"library": "Library",
"name": "Uberon multi-species anatomy ontology"
},
"UO": {
"library": "Library",
"name": "Units of measurement ontology"
},
"UPA": {
"library": "Library",
"name": "Unipathway"
},
"UPHENO": {
"library": "Library",
"name": "Unified phenotype ontology (uPheno)"
},
"VBO": {
"library": "Library",
"name": "Vertebrate Breed Ontology"
},
"VICO": {
"library": "Not Specified/No",
"name": "Vaccination Informed Consent Ontology"
},
"VIDO": {
"library": "Not Specified/No",
"name": "Virus Infectious Disease Ontology"
},
"VIO": {
"library": "Not Specified/No",
"name": "Vaccine Investigation Ontology"
},
"VIVO-ISF": {
"library": "Not Specified/No",
"name": "VIVO-ISF"
},
"VO": {
"library": "Library",
"name": "Vaccine Ontology"
},
"VT": {
"library": "Library",
"name": "Vertebrate trait ontology"
},
"VTO": {
"library": "Library",
"name": "Vertebrate Taxonomy Ontology"
},
"VariO": {
"library": "Library",
"name": "Variation Ontology"
},
"WBPhenotype": {
"library": "Library",
"name": "C. elegans phenotype"
},
"WBbt": {
"library": "Library",
"name": "C. elegans Gross Anatomy Ontology"
},
"WBls": {
"library": "Library",
"name": "C. elegans development ontology"
},
"XAO": {
"library": "Foundry",
"name": "Xenopus Anatomy Ontology"
},
"XCO": {
"library": "Library",
"name": "Experimental condition ontology"
},
"XL": {
"library": "Library",
"name": "Cross-linker reagents ontology"
},
"XLMOD": {
"library": "Library",
"name": "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary"
},
"XPO": {
"library": "Library",
"name": "Xenopus Phenotype Ontology"
},
"ZECO": {
"library": "Library",
"name": "Zebrafish Experimental Conditions Ontology"
},
"ZFA": {
"library": "Foundry",
"name": "Zebrafish anatomy and development ontology"
},
"ZFS": {
"library": "Library",
"name": "Zebrafish developmental stages ontology"
},
"ZP": {
"library": "Library",
"name": "Zebrafish Phenotype Ontology"
},
"d-acts": {
"library": "Not Specified/No",
"name": "Ontology of Document Acts"
},
"miRNAO": {
"library": "Library",
"name": "microRNA Ontology"
},
"uberon-basic": {
"library": "Not Specified/No",
"name": "Uber anatomy ontology, basic version"
},
"uberon_collected_metazoa": {
"library": "Not Specified/No",
"name": "uberon_collected_metazoa"
},
"uberon_depictions": {
"library": "Not Specified/No",
"name": "uberon_depictions"
}
} ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9699667
bioregistry-0.11.12/src/bioregistry/external/pathguide/ 0000755 0001751 0000177 00000000000 14655546227 022570 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/pathguide/__init__.py 0000644 0001751 0000177 00000003012 14655542206 024666 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download registry information from Pathguide."""
import requests
from bs4 import BeautifulSoup
from bioregistry.external.alignment_utils import Aligner
__all__ = [
"get_pathguide",
"PathguideAligner",
]
def get_pathguide(*, force_download: bool = False):
"""Get the Pathguide metdata."""
res = requests.get("http://pathguide.org/")
soup = BeautifulSoup(res.text, "html.parser")
rv = {}
for tr in soup.find_all("tr"):
tr_id = tr.attrs.get("id")
if not tr_id or not tr_id.startswith("ResourceRow_"):
continue
pathguide_id = tr_id.removeprefix("ResourceRow_")
name_td, _, _availability_td, standards_td = list(tr)
name_a = name_td.find("a")
homepage = name_a.attrs["href"]
abbreviation, name = (s.strip() for s in name_a.text.split(" - ", 1))
standards = sorted(
{td.text for td in standards_td.find_all("td") if td.attrs.get("class") == ["Standard"]}
)
rv[pathguide_id] = {
"prefix": pathguide_id,
"abbreviation": abbreviation,
"name": name,
"homepage": homepage,
}
if standards:
rv[pathguide_id]["keywords"] = standards
return rv
class PathguideAligner(Aligner):
"""Aligner for the Pathguide."""
key = "pathguide"
alt_key_match = "abbreviation"
getter = get_pathguide
curation_header = ("abbreviation", "name", "homepage")
if __name__ == "__main__":
PathguideAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9699667
bioregistry-0.11.12/src/bioregistry/external/prefixcommons/ 0000755 0001751 0000177 00000000000 14655546227 023507 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/prefixcommons/__init__.py 0000644 0001751 0000177 00000021273 14655542206 025616 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download registry information from the Life Science Registry (LSR), which powers Prefix Commons.
.. seealso::
- http://tinyurl.com/lsregistry which should expand to
https://docs.google.com/spreadsheets/d/1cDGJcRteb9F5-jbw7Q7np0kk4hfWhdBHNYRIg3LXDrs/edit#gid=0
"""
import json
import logging
from pathlib import Path
from typing import Any, Dict, List, Mapping, Sequence
from pystow.utils import download
from bioregistry.constants import RAW_DIRECTORY
from bioregistry.external.alignment_utils import Aligner
from bioregistry.license_standardizer import standardize_license
__all__ = [
"get_prefixcommons",
"PrefixCommonsAligner",
]
logger = logging.getLogger(__name__)
DIRECTORY = Path(__file__).parent.resolve()
RAW_PATH = RAW_DIRECTORY / "prefixcommons.tsv"
PROCESSED_PATH = DIRECTORY / "processed.json"
GOOGLE_DOCUMENT_ID = "1c4DmQqTGS4ZvJU_Oq2MFnLk-3UUND6pWhuMoP8jgZhg"
URL = f"https://docs.google.com/spreadsheets/d/{GOOGLE_DOCUMENT_ID}/export?format=tsv&gid=0"
COLUMNS = [
"prefix", # "Preferred Prefix",
"synonyms",
"rdf_uri_prefix", # this is the RDF-useful version
"alternate_uri_formats", # these are alternative URI prefixes
"MIRIAM",
"BiodbcoreID",
"bioportal", # "BioPortal Ontology ID",
"miriam", # "identifiers.org",
"Abbreviation",
"name", # originally: Title,
"description", # "Description",
"pubmed_ids", # "PubMed ID"
"Organization",
"Type (warehouse, dataset or terminology)",
"keywords",
"homepage", # "Homepage",
"Functional?",
"part_of", # sub-namespace in dataset
"part of collection",
"license_url",
"License Text",
"Rights",
"pattern", # "ID regex",
"example", # "ExampleID",
"uri_format", # "Provider HTML URL",
"",
"MIRIAM checked",
"MIRIAM curator notes",
"MIRIAM coverage",
"updates",
"year last accessible",
"wayback url",
"last updated",
"last updated by",
"last updated by (orcid)",
]
KEEP = {
"prefix",
"synonyms",
"bioportal",
"miriam",
"name",
"description",
"pubmed_ids",
"keywords",
"homepage",
"pattern",
"example",
"uri_format",
"license_url",
"alternate_uri_formats",
"rdf_uri_prefix",
}
#: These contain synonyms with mismatches
DISCARD_SYNONYMS = {"biogrid", "cath", "zfa"}
SKIP_URI_FORMATS = {
"http://purl.obolibrary.org/obo/$1",
"http://www.ebi.ac.uk/ontology-lookup/?termId=$1",
"http://arabidopsis.org/servlets/TairObject?accession=$1",
}
def get_prefixcommons(force_download: bool = False, force_process: bool = False):
"""Get the Life Science Registry."""
if PROCESSED_PATH.exists() and not (force_download or force_process):
with PROCESSED_PATH.open() as file:
return json.load(file)
download(url=URL, path=RAW_PATH, force=force_download)
rows = {}
with RAW_PATH.open() as file:
lines = iter(file)
next(lines) # throw away header
for line in lines:
prefix, data = _process_row(line)
if prefix and data:
rows[prefix] = data
PROCESSED_PATH.write_text(json.dumps(rows, sort_keys=True, indent=2))
return rows
def _process_row(line: str):
cells = line.strip().split("\t")
prefix = cells[0]
cells_processed = [None if cell in {"N/A"} else cell for cell in cells]
rv: Dict[str, Any] = {
key: value.strip()
for key, value in zip(COLUMNS, cells_processed)
if key and value and key in KEEP
}
for key in ["name", "description", "example", "pattern"]:
if not rv.get(key):
return None, None
for key in ["keywords", "pubmed_ids"]:
values = rv.get(key)
if values:
rv[key] = [value.strip() for value in values.split(",")]
synonyms = rv.pop("synonyms", None)
if not synonyms:
pass
elif prefix in DISCARD_SYNONYMS:
pass
else:
synonyms_it = [s.strip() for s in synonyms.split(",")]
synonyms_it = [
synonym
for synonym in synonyms_it
if synonym.lower() != prefix.lower() and " " not in synonym
]
if synonyms_it:
rv["synonyms"] = synonyms_it
license_url = rv.pop("license_url", None)
if license_url:
rv["license"] = standardize_license(license_url)
uri_format = rv.pop("uri_format", None)
if uri_format:
uri_format = uri_format.replace("$id", "$1").replace("[?id]", "$1").replace("$d", "$1")
if uri_format not in SKIP_URI_FORMATS:
rv["uri_format"] = uri_format
uri_rdf_formats = _get_uri_formats(rv, "rdf_uri_prefix")
if uri_rdf_formats:
if len(uri_rdf_formats) > 1:
logger.warning("got multiple RDF formats for %s", prefix)
rv["rdf_uri_format"] = uri_rdf_formats[0]
alt_uri_formats_clean = _get_uri_formats(rv, "alternate_uri_formats")
if alt_uri_formats_clean:
rv["alt_uri_formats"] = alt_uri_formats_clean
pattern = rv.get("pattern")
if pattern:
if not pattern.startswith("^"):
pattern = f"^{pattern}"
if not pattern.endswith("$"):
pattern = f"{pattern}$"
rv["pattern"] = pattern
return prefix, rv
def _get_uri_formats(rv, key) -> List[str]:
uri_formats = rv.pop(key, None)
if not uri_formats:
return []
rv = []
for uri_format in uri_formats.split(","):
uri_format = uri_format.strip()
if not uri_format:
continue
if "identifiers.org" in uri_format: # FIXME some non-miriam resources might use this
continue
if "obofoundry.org" in uri_format: # FIXME some non-obo resources might use this
continue
if "obolibrary.org" in uri_format: # FIXME take this check out
continue
if "$1" in uri_format or "[?id]" in uri_format: # FIXME check if these come at the end
continue
uri_format = f"{uri_format}$1"
if uri_format in SKIP_URI_FORMATS:
continue
rv.append(uri_format)
return rv
SKIP = {
"redidb": "Website is dead",
"trnadbce": "Website is password protected",
"pogs_plantrbp": "Website is dead",
"smr": "no evidence of it existing",
}
PROVIDERS = {
"homeodomain_resource": "hdr",
"interpare": "pdb",
"consurfdb": "pdb",
"homstrad": "pdb",
"jail": "pdb",
"hotsprint": "pdb",
"lpfc": "pdb",
"pdbreprdb": "pdb",
"pdtd": "pdb",
"supersite": "pdb",
"pairsdb": "pdb",
"icbs": "pdb",
"pdbbind": "pdb",
"pdb.tm": "pdb",
"ligasite": "pdb",
"firedb": "pdb",
"dali": "pdb",
"pisite": "pdb",
"procognate": "pdb",
"binding_moad": "pdb",
"bhfucl": "uniprot",
"pdzbase": "uniprot",
"unisave": "uniprot",
"2dbaseecoli": "uniprot",
"swiss2dpage": "uniprot",
"siena2dpage": "uniprot",
"phci2dpage": "uniprot",
"reproduction2dpage": "uniprot",
"agbase": "uniprot",
"iproclass": "uniprot",
"asap_ii": "unigene",
"snp2nmd": "dbsnp",
"cangem": "ensembl",
"cisred": "ensembl",
"interferome": "ensembl",
"spliceinfo": "ensembl",
"piggis": "ensembl",
"corg": "ensembl",
"greglist": "ensembl",
"gxa": "ensembl",
"cyclebase": "ensembl",
"droid": "flybase",
"enzyme": "eccode",
"orenza": "eccode",
"explorenz": "eccode",
"fcp": "eccode",
"mousecyc": "mgi",
"imgt.3dstructuredb": "pdb",
"mapu": "ipi",
"sysbodyfluid": "ipi",
"uniprot.taxonomy": "ncbitaxon",
"domine": "pfam",
"dima": "pfam",
"interdom": "pfam",
"sdr": "pfam",
"ipfam": "pfam",
"hupi": "hgnc.symbol",
"chimerdb": "hgnc.symbol",
"po.psds": "po",
"cutdb": "pmap.cutdb",
"hubmed": "pubmed",
}
class PrefixCommonsAligner(Aligner):
"""Aligner for Prefix Commons."""
key = "prefixcommons"
getter = get_prefixcommons
curation_header = (
"name",
"synonyms",
"description",
"example",
"pattern",
"uri_format",
)
alt_keys_match = "synonyms"
include_new = False
def get_skip(self) -> Mapping[str, str]:
"""Get skip prefixes."""
return {**SKIP, **PROVIDERS}
def get_curation_row(self, external_id, external_entry) -> Sequence[str]:
"""Prepare curation rows for unaligned Prefix Commons registry entries."""
return [
external_entry["name"],
", ".join(external_entry.get("synonyms", [])),
external_entry.get("description", "").replace('"', ""),
external_entry.get("example", ""),
external_entry.get("pattern", ""),
external_entry.get("uri_format", ""),
]
if __name__ == "__main__":
PrefixCommonsAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723254379.0
bioregistry-0.11.12/src/bioregistry/external/prefixcommons/processed.json 0000644 0001751 0000177 00001755601 14655543153 026403 0 ustar 00runner docker {
"2dbaseecoli": {
"description": "2DBase of Escherichia coli stores 2D polyacrylamide gel electrophoresis and mass spectrometry proteome data for E. coli. This collection references a subset of Uniprot, and contains general information about the protein record.",
"example": "P39172",
"homepage": "http://2dbase.techfak.uni-bielefeld.de",
"keywords": [
"protein"
],
"name": "2D-PAGE Database of Escherichia coli",
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$",
"prefix": "2dbaseecoli",
"pubmed_ids": [
"17904107"
],
"synonyms": [
"2d-page.protein"
],
"uri_format": "http://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi?ac=$1"
},
"3dmet": {
"description": "3DMET is a database of three-dimensional structures of natural metabolites.",
"example": "B00162",
"homepage": "http://www.3dmet.dna.affrc.go.jp",
"keywords": [
"chemical",
"metabolite",
"structure"
],
"miriam": "3dmet",
"name": "Three-Dimensional Structure Database of Natural Metabolites",
"pattern": "^B\\d{5}$",
"prefix": "3dmet",
"pubmed_ids": [
"23293959",
"29892514"
]
},
"4dn": {
"description": "The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases.",
"example": "4DNESBOY2QLJ",
"homepage": "https://data.4dnucleome.org/",
"keywords": [
"DNA",
"protein"
],
"miriam": "4dn",
"name": "4D Nucleome",
"pattern": "^4DN[A-Z]{2}[A-Z0-9]{7}$",
"prefix": "4dn",
"pubmed_ids": [
"28905911"
],
"uri_format": "https://data.4dnucleome.org/$1"
},
"4dxpress": {
"description": "This database provides a platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments.",
"example": "98967",
"homepage": "http://4dx.embl.de/4DXpress",
"keywords": [
"gene expression"
],
"name": "4DXpress gene expression in major animals",
"pattern": "^\\d+$",
"prefix": "4dxpress",
"pubmed_ids": [
"17916571"
],
"uri_format": "http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID=$1"
},
"aaindex": {
"description": "AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. AAindex consists of three sections now: AAindex1 for the amino acid index of 20 numerical values, AAindex2 for the amino acid mutation matrix and AAindex3 for the statistical protein contact potentials.",
"example": "BUNA790102",
"homepage": "http://www.genome.ad.jp/aaindex/",
"keywords": [
"protein"
],
"name": "Amino acid indices, substitution matrices and pair-wise contact potentials",
"pattern": "^[A-Z]+\\d+$",
"prefix": "aaindex",
"pubmed_ids": [
"17998252"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?aaindex:$1"
},
"aao": {
"bioportal": "1090",
"description": "The Amphibian Anatomical Ontology (AmphibAnat) is an NSF-sponsored project dedicated to constructing semi-automatically a draft ontology of amphibian anatomy. In this project, small, subset ontologies are constructed manually, and data-mining software (that we develop) is used to mine electronic media for instances of concepts and properties to be added to the ontologies.",
"example": "ASD:0000138",
"homepage": "http://www.amphibanat.org",
"keywords": [
"obo",
"anatomy"
],
"name": "Amphibian Anatomical Ontology",
"pattern": "^[A-Z]+:\\d+$",
"prefix": "aao",
"pubmed_ids": [
"17992749"
]
},
"abs": {
"description": "ABS: A database of Annotated regulatory Binding Sites from known binding sites identified in promoters of orthologous vertebrate genes.",
"example": "A0014",
"homepage": "http://genome.imim.es/datasets/abs2005/",
"keywords": [
"interaction",
"gene",
"regulation"
],
"miriam": "abs",
"name": "ABS: a database of Annotated regulatory Binding Sites from Orthologous Promoters",
"pattern": "^A\\d+$",
"prefix": "abs",
"pubmed_ids": [
"16381947"
],
"uri_format": "http://genome.crg.es/datasets/abs2005/entries/$1.html"
},
"aceview.worm": {
"description": "AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes.",
"example": "AP2B1",
"homepage": "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/",
"keywords": [
"RNA",
"DNA",
"gene"
],
"miriam": "aceview.worm",
"name": "AceView Worm Genome",
"pattern": "^[a-z0-9-]+$",
"prefix": "aceview.worm",
"pubmed_ids": [
"16925834"
],
"synonyms": [
"aceview_wormgenes"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=[?species_database]&c=Gene&l=$1"
},
"aclame": {
"description": "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.",
"example": "mge:2",
"homepage": "http://aclame.ulb.ac.be",
"keywords": [
"genome",
"gene"
],
"miriam": "mge",
"name": "A CLAssification of Mobile genetic Elements",
"pattern": "^mge:\\d+$",
"prefix": "aclame",
"pubmed_ids": [
"14681355"
],
"uri_format": "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=$1"
},
"adda": {
"description": "ADDA, an automatic algorithm for domain decomposition and clustering of all protein domain families which uses alignments derived from an all-on-all sequence comparison to define domains within protein sequences based on a global maximum likelihood model.",
"example": "215451",
"homepage": "http://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb",
"keywords": [
"protein"
],
"name": "Automatic Domain Decomposition Algorithm",
"pattern": "^\\d+$",
"prefix": "adda",
"pubmed_ids": [
"12706730"
],
"uri_format": "http://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb/report_sequence?nid=$1"
},
"addgene": {
"description": "Addgene is a global, nonprofit repository that was created to help scientists share plasmids.",
"example": "41816",
"homepage": "http://www.addgene.org",
"keywords": [
"plasmid"
],
"miriam": "addgene",
"name": "Addgene",
"pattern": "^\\d+$",
"prefix": "addgene",
"pubmed_ids": [
"25392412"
],
"uri_format": "http://www.addgene.org/$1"
},
"affindb": {
"description": "The Affinity Database 'AffinDB' contains affinity data for protein-ligand complexes of the PDB. Its purpose is to provide direct and free access to the experimental affinity of a given complex structure.",
"example": "5",
"homepage": "http://www.agklebe.de/affinity",
"keywords": [
"protein",
"interaction"
],
"name": "Affinity Database for Protein-Ligand Complexes",
"pattern": "^\\d+$",
"prefix": "affindb"
},
"agbase": {
"description": "AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products.",
"example": "Q55FF3",
"homepage": "http://www.agbase.msstate.edu",
"keywords": [
"gene"
],
"name": "AgBase",
"pattern": "^[A-Z]\\d+$",
"prefix": "agbase",
"pubmed_ids": [
"21075795"
],
"uri_format": "http://www.agbase.msstate.edu/cgi-bin/getEntry.pl?db_pick=all&database=UniProtKB&gb_acc=$1"
},
"agd": {
"description": "The Ashbya Genome Database (AGD) 3.0 is a genome/transcriptome database containing gene annotation and high-density oligonucleotide microarray expression data for protein-coding genes from Ashbya gossypii and the model organism Saccharomyces cerevisiae.",
"example": "AGR144C",
"homepage": "http://agd.vital-it.ch",
"keywords": [
"expression",
"microarray",
"nucleotide"
],
"name": "Ashbya Genome Database",
"pattern": "^AGR\\w+$",
"prefix": "agd",
"pubmed_ids": [
"15001715"
],
"uri_format": "http://agd.vital-it.ch/Ashbya_gossypii/geneview?gene=$1"
},
"agsd": {
"description": "The Animal Genome Size Database (AGSD) is a comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources.",
"example": "4779",
"homepage": "http://www.genomesize.com",
"keywords": [
"DNA",
"genome"
],
"name": "Animal Genome Size Database",
"pattern": "^\\d+$",
"prefix": "agsd",
"uri_format": "http://www.genomesize.com/result_species.php?id=$1"
},
"alfred": {
"description": "ALFRED has been designed to make allele frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases.",
"example": "LO362836C",
"homepage": "http://alfred.med.yale.edu",
"keywords": [
"classification",
"genome"
],
"license": "http://alfred.med.yale.edu/alfred/fullcopyrightpage.asp",
"name": "The ALlele FREquency Database",
"pattern": "^[A-Z]+\\d+$",
"prefix": "alfred",
"pubmed_ids": [
"12519999"
],
"uri_format": "https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID=$1"
},
"allergome": {
"description": "Allergome aims to supply information on Allergenic Molecules (Allergens) causing an IgE-mediated (allergic, atopic) disease (anaphylaxis, asthma, atopic dermatitis, conjunctivitis, rhinitis, urticaria).",
"example": "1948",
"homepage": "http://www.allergome.org",
"keywords": [
"allergen"
],
"license": "CC BY-NC-SA 2.5",
"miriam": "allergome",
"name": "Allergome: a platform for allergen knowledge",
"pattern": "^\\d+$",
"prefix": "allergome",
"pubmed_ids": [
"17393720",
"17434469"
],
"uri_format": "http://www.allergome.org/script/refArray_view.php?idMol=$1"
},
"alterorf": {
"description": "AlterORF provides a database of such potentially mis-annotated ORFs. It has warehoused all alternate ORFs in fully sequenced microbial genomes that have significant hits with one or more of the protein features decribed in CDD, COG, KOG, PFAM, PRK and SMART in which the corresponding annotated genes that have been deposited in the databases have no such characteristics.",
"example": "NP_107992.1",
"homepage": "http://alterorf.cl/",
"keywords": [
"DNA",
"protein"
],
"name": "Alternate Open Reading Frame (ORF)",
"pattern": "^N[W/P]_\\d+$",
"prefix": "alterorf",
"pubmed_ids": [
"18096612"
],
"uri_format": "http://www.alterorf.cl/SearchResults/SearchResult.aspx?variable1=$1"
},
"alzgene": {
"description": "The AlzGene database provides a comprehensive, unbiased and regularly updated field synopsis of genetic association studies performed in Alzheimer\u2019s disease. In addition, hundreds of up-to-date meta-analyses are available for all eligible polymorphisms with sufficient data.",
"example": "88",
"homepage": "http://www.alzgene.org",
"keywords": [
"gene"
],
"name": "Alzheimer Gene Database",
"pattern": "^\\d+$",
"prefix": "alzgene",
"pubmed_ids": [
"17192785"
],
"uri_format": "http://www.alzgene.org/geneoverview.asp?geneid=$1"
},
"amoebadb": {
"description": "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"example": "EDI_244000",
"homepage": "http://amoebadb.org",
"keywords": [
"model organism"
],
"miriam": "amoebadb",
"name": "AmoebaDB",
"pattern": "^EDI_\\d+$",
"prefix": "amoebadb",
"pubmed_ids": [
"19914931"
],
"uri_format": "https://amoebadb.org/amoeba/app/record/gene/$1"
},
"anobase": {
"description": "AnoBase is a database containing genomic/biological information on anopheline mosquitoes, with an emphasis on Anopheles gambiae, the world's most important malaria vector.",
"example": "634",
"homepage": "http://www.anobase.org",
"keywords": [
"genome"
],
"name": "AnoBase: the Anopheles Database",
"pattern": "^\\d+$",
"prefix": "anobase",
"pubmed_ids": [
"16313559"
],
"uri_format": "http://www.anobase.org/genetool/v42/gene.php?id=$1"
},
"antijen": {
"description": "AntiJen v2.0, is a database containing quantitative binding data for peptides binding to MHC Ligand, TCR-MHC Complexes, T Cell Epitope, TAP , B Cell Epitope molecules and immunological Protein-Protein interactions. Most recently, AntiJen has included Peptide Library, Copy Numbers and Diffusion Coefficient data.",
"example": "KPVSQMRMATPLLM",
"homepage": "http://www.ddg-pharmfac.net/antijen/AntiJen/antijenhomepage.htm",
"keywords": [
"protein",
"interaction"
],
"name": "AntiJen: a kinetic, thermodynamic and cellular database v2.0",
"pattern": "^[A-Z]+$",
"prefix": "antijen",
"pubmed_ids": [
"16305757"
],
"uri_format": "http://www.darrenflower.info/scripts/aj_scripts/aj_mhccalc2.pl?epitope=$1&AL=%25&ST=%25&CAT=MHC&detailinfo=no&detailmin=&detailmax="
},
"antweb": {
"description": "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures.",
"example": "casent0106247",
"homepage": "https://www.antweb.org",
"keywords": [
"classification",
"anatomy"
],
"license": "CC BY-SA 3.0",
"miriam": "antweb",
"name": "AntWeb: Ant of the World",
"pattern": "^casent\\d+(\\-\\w+\\d+)?$",
"prefix": "antweb",
"pubmed_ids": [
"12867945"
],
"uri_format": "http://www.antweb.org/specimen.do?name=$1"
},
"apd": {
"description": "The Antimicrobial Peptide Database (APD) contains data from the Protein Data Bank (PDB), Swiss-Prot Protein Knowledgebase and PubMed National Library of Medicine. The antimicrobial peptides in this database contain less than 100 amino acid residues, are in the mature and active form, and primarily from natural sources, ranging from bacteria, fungi, plants, to animals.",
"example": "1228",
"homepage": "http://aps.unmc.edu/AP/",
"keywords": [
"protein"
],
"miriam": "apd",
"name": "Antimicrobial Peptide Database",
"pattern": "^\\d+$",
"prefix": "apd",
"pubmed_ids": [
"26602694"
],
"uri_format": "http://aps.unmc.edu/AP/database/query_output.php?ID=$1"
},
"aphidbase": {
"description": "The Aphid Genome Database's aim is to improve the current pea aphid genome assembly and annotation, and to provide new aphid genome sequences as well as tools for analysis of these genomes.",
"example": "ACYPI003698-RA",
"homepage": "http://www.aphidbase.com",
"keywords": [
"genome"
],
"miriam": "aphidbase.transcript",
"name": "Aphidbase: an aphid genomics database",
"pattern": "^ACYPI\\d+$",
"prefix": "aphidbase",
"pubmed_ids": [
"20482635"
]
},
"arachnoserver": {
"description": "ArachnoServer is a manually curated database containing information on the sequence, three-dimensional structure, and biological activity of protein toxins derived from spider venom.",
"example": "AS000060",
"homepage": "http://www.arachnoserver.org",
"keywords": [
"drug",
"protein"
],
"miriam": "arachnoserver",
"name": "ArachnoServer: Spider toxin database",
"pattern": "^AS\\d{6}$",
"prefix": "arachnoserver",
"pubmed_ids": [
"21036864",
"29069336"
],
"uri_format": "http://www.arachnoserver.org/toxincard.html?id=$1"
},
"aracxyls": {
"description": "A Database on a family of helix-turn-helix transcription factors from bacteria.",
"example": "102",
"homepage": "http://www.arac-xyls.org",
"keywords": [
"regulation"
],
"name": "AraC-XylS",
"pattern": "^\\d+$",
"prefix": "aracxyls",
"pubmed_ids": [
"11752325"
],
"uri_format": "http://www.eez.csic.es/arac-xyls/wfichas/$1rec.htm"
},
"archdb": {
"description": "ArchDB is a compilation of structural classifications of loops extracted from known protein structures. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al..",
"example": "39421",
"homepage": "http://sbi.imim.es/archdb",
"keywords": [
"classification",
"protein"
],
"name": "ArchDB",
"pattern": "^\\d+$",
"prefix": "archdb",
"pubmed_ids": [
"24265221"
],
"uri_format": "http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop=$1"
},
"arkdb": {
"description": "The ArkDB database system aims to provide a comprehensive public repository for genome mapping data from farmed and other animal Species",
"example": "ARKCHR00000087",
"homepage": "http://www.thearkdb.org",
"keywords": [
"genome"
],
"name": "ArkDB",
"pattern": "^ARKCHR\\d+$",
"prefix": "arkdb",
"uri_format": "http://www.thearkdb.org/arkdb/do/getMappableDetails?accession=$1"
},
"arrayexpress": {
"description": "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.",
"example": "E-MEXP-1712",
"homepage": "http://www.ebi.ac.uk/arrayexpress",
"keywords": [
"expression",
"microarray",
"nucleotide"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"miriam": "arrayexpress",
"name": "ArrayExpress",
"pattern": "^[AEP]-\\w{4}-\\d+$",
"prefix": "arrayexpress",
"pubmed_ids": [
"12519949"
],
"uri_format": "http://www.ebi.ac.uk/arrayexpress/experiments/$1"
},
"artadedb": {
"description": "ARTADE is a standard tool for the annotation of genome-wide tiling-array data in Arabidopsis.",
"example": "At4g09320",
"homepage": "http://omicspace.riken.jp/ARTADE/",
"keywords": [
"genome",
"gene expression"
],
"name": "ARabidopsis Tiling-Array-based Detection of Exons",
"pattern": "^At\\d[a-z]\\d+$",
"prefix": "artadedb",
"pubmed_ids": [
"16098113"
],
"uri_format": "http://omicspace.riken.jp/gps/index.html?url=/gps/LineMode/ArtadeSearch_Flower&hCheck=v200307&hHead=[?genomic_region]&highlight=$1"
},
"arxiv": {
"description": "arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology.",
"example": "0807.4956v1",
"homepage": "http://arxiv.org",
"keywords": [
"bibliography"
],
"name": "arXiv",
"pattern": "^(\\w+(\\-\\w+)?(\\.\\w+)?/)?\\d{4,7}(\\.\\d{4}(v\\d+)?)?$",
"prefix": "arxiv",
"uri_format": "http://arxiv.org/abs/$1"
},
"asap": {
"description": "ASAP is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data. It was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis.",
"example": "ABZ-0129277",
"homepage": "https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm",
"keywords": [
"genome",
"gene expression"
],
"name": "A Systematic Annotation Package",
"pattern": "^ABZ-\\d+$",
"prefix": "asap",
"pubmed_ids": [
"12519969",
"16381899"
],
"uri_format": "https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1"
},
"asap_ii": {
"description": "ASAP II supports 9 vertebrate species, 4 insects, and nematodes, and provides with extensive alternative splicing analysis and their splicing variants. As for human, newly added EST libraries were classified and included into previous tissue and cancer classification, and lists of tissue & cancer (normal) specific alternatively spliced genes are re-calculated and updated.",
"example": "Hs.463110",
"homepage": "http://bioinfo.mbi.ucla.edu/ASAP2/",
"keywords": [
"genome",
"gene expression"
],
"name": "ASAP II",
"pattern": "^UniGene ID$",
"prefix": "asap_ii",
"pubmed_ids": [
"17108355"
],
"synonyms": [
"asap2"
]
},
"aspd": {
"description": "ASPD (Artificial Selected Proteins/Peptides Database) is a curated database on selected from randomized pools proteins and peptides. Database access is realised by means of simple search system and SRS (Sequence Retrieval System). ASPD is integrated by means of hyperlinks with different databases (SWISS-PROT, PDB, PROSITE, ...).",
"example": "PH1AB123",
"homepage": "http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/",
"keywords": [
"protein"
],
"name": "Artificial Selected Proteins/Peptides Database",
"pattern": "^PH1[A-Z]+\\d+$",
"prefix": "aspd",
"pubmed_ids": [
"11752292"
]
},
"asrp": {
"description": "This project focuses on small RNAs. It involves function analysis, regulation, and the evolution of RNA silencing pathways at a genome-wide level. Technologies are being used in the sequence-based profiling of the genome of A. thaliana small RNAs and their classification associated with silencing effector proteins.",
"example": "365115",
"homepage": "http://asrp.cgrb.oregonstate.edu",
"keywords": [
"RNA",
"genome",
"regulation"
],
"name": "Arabidopsis Small RNA Project",
"pattern": "^\\d+$",
"prefix": "asrp",
"pubmed_ids": [
"15608278",
"17999994"
],
"uri_format": "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1"
},
"astd": {
"description": "The Alternative Splicing and Transcript Diversity (ASTD) database project is creating a database of alternative splice events and transcripts of genes from human, mouse and rat. Full length transcripts are generated with the aim of understanding the mechanism of alternative splicing on a genome-wide scale.",
"example": "ENSG00000136147",
"homepage": "http://www.ebi.ac.uk/astd/",
"keywords": [
"gene",
"transcript",
"alternative splicing"
],
"name": "Alternative Splicing and Transcript Diversity",
"pattern": "^ENSG\\d+$",
"prefix": "astd",
"pubmed_ids": [
"19059335"
],
"uri_format": "http://www.ebi.ac.uk/astd/geneview.html?acc=$1"
},
"atc": {
"alt_uri_formats": [
"http://purl.bioontology.org/ontology/UATC/$1"
],
"bioportal": "3021",
"description": "The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels.",
"example": "A10BA02",
"homepage": "http://www.whocc.no/atc_ddd_index/",
"keywords": [
"chemical"
],
"name": "Anatomical Therapeutic Chemical",
"pattern": "^\\w(\\d+)?(\\w{1,2})?(\\d+)?$",
"prefix": "atc",
"synonyms": [
"uatc"
],
"uri_format": "http://www.whocc.no/atc_ddd_index/?code=$1"
},
"atpid": {
"description": "The AtPID (Arabidopsis thaliana Protein Interactome Database) represents a centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome.The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier.",
"example": "AT2G36010",
"homepage": "http://atpid.biosino.org/",
"keywords": [
"protein",
"interaction"
],
"name": "Arabidopsis thaliana Protein Interactome Database",
"pattern": "^AT\\d+$",
"prefix": "atpid",
"uri_format": "http://atpid.biosino.org/simple_detail.php?pro=$1"
},
"attedii": {
"description": "ATTED-II provides co-regulated gene relationships in Arabidopsis thaliana to estimate gene functions.",
"example": "ATGGGCT",
"homepage": "http://atted.jp",
"keywords": [
"gene"
],
"name": "Arabidopsis thaliana trans-factor and cis-element prediction database",
"pattern": "^[A-Z]+$",
"prefix": "attedii",
"uri_format": "http://atted.jp/data/cis/$1.html"
},
"bacmap": {
"description": "BacMap is an interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes. BacMap allows you to manually explore genomic maps with rotation and zoom options where map gene labels are hyperlinked to detailed textual annotations. Several charts illustrating the proteomic and genomic characteristics of each chromosome are also available.",
"example": "NC_013356",
"homepage": "http://wishart.biology.ualberta.ca/BacMap",
"keywords": [
"genome"
],
"name": "BacMap: An Interactive Atlas for Exploring Bacterial Genomes",
"pattern": "^NC_\\d+$",
"prefix": "bacmap",
"uri_format": "http://wishart.biology.ualberta.ca/BacMap/cgview_linked_maps/$1/index.html"
},
"bactibase": {
"description": "BACTIBASE contains calculated or predicted physicochemical properties of 177 bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships structure/function and target organisms of these peptides and therefore better exploitation of their biological activity in both the medical and food sectors.",
"example": "BAC152",
"homepage": "http://bactibase.pfba-lab-tun.org/main.php",
"keywords": [
"protein"
],
"name": "Bactibase: database dedicated to bacteriocins",
"pattern": "^BA\\d+$",
"prefix": "bactibase",
"uri_format": "http://bactibase.pfba-lab-tun.org/$1"
},
"bcipep": {
"description": "BCIpep is collection of the peptides having the role in Humoral immunity. The peptides in the database has varying measure of immunogenicity.This database can assist in the development of method for predicting B cell epitopes, desigining synthetic vaccines and in disease diagnosis.",
"example": "10336",
"homepage": "http://bioinformatics.uams.edu/mirror/bcipep/",
"keywords": [
"protein"
],
"name": "A database of B cell Epitopes",
"pattern": "^\\d+$",
"prefix": "bcipep"
},
"bcsdb_glycoscience": {
"description": "This database is aimed at provision of structural, bibliographic, taxonomic and related information on bacterial carbohydrate structures.",
"example": "124",
"homepage": "http://www.glyco.ac.ru/bcsdb3/",
"keywords": [
"small molecule"
],
"name": "Bacterial Carbohydrates Structure Database",
"pattern": "^\\d+$",
"prefix": "bcsdb_glycoscience"
},
"bdgp": {
"description": "BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element.",
"example": "KG09531",
"keywords": [
"gene",
"sequence"
],
"name": "Drosphila Gene Disruption Database",
"pattern": "^\\w+$",
"prefix": "bdgp",
"pubmed_ids": [
"15238527"
],
"synonyms": [
"BDGP.insertion"
],
"uri_format": "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1"
},
"beetlebase": {
"description": "BeetleBase is being developed as an important community resource for Tribolium genetics, genomics and developmental biology.The database is built on the Chado generic data model, and is able to store various types of data, ranging from genome sequences to mutant phenotypes.",
"example": "TC010103",
"homepage": "http://www.beetlebase.org/",
"keywords": [
"genome"
],
"name": "BeetleBase",
"pattern": "^TC\\d+$",
"prefix": "beetlebase",
"pubmed_ids": [
"19820115"
],
"uri_format": "http://www.beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1"
},
"benchmark": {
"description": "The Protein Classification Benchmark Collection was created in order to create standard datasets on which the performance of machine learning methods can be compared.",
"example": "PCB00001",
"homepage": "http://net.icgeb.org/benchmark/",
"keywords": [
"protein",
"classification"
],
"name": "Protein Classification Benchmark Collection",
"pattern": "^PCB\\d+$",
"prefix": "benchmark",
"uri_format": "http://net.icgeb.org/benchmark/index.php?experiment=$1"
},
"bged": {
"description": "The database contains gene expression data for various physiological and pathological processes in mouse brain. All the data have been obtained by adaptor-tagged competitive PCR, an advanced version of quantitative PCR.",
"example": "[000000]1",
"homepage": "http://genome.mc.pref.osaka.jp/BGED/",
"keywords": [
"gene expression"
],
"name": "Brain Gene Expression Database",
"pattern": "^\\d+$",
"prefix": "bged",
"uri_format": "http://genome.mc.pref.osaka.jp/cgi-bin/BGED/Gene_info.pl?num=$1"
},
"bgee": {
"description": "Bgee is a database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently EST, Affymetrix, and in situ hybridization data) on anatomical and developmental ontologies. Then, in order to perform automated cross species comparisons, homology relationships across anatomical ontologies, and comparison criteria between developmental ontologies, are designed.",
"example": "FBgn0041195",
"homepage": "http://bgee.unil.ch",
"keywords": [
"gene expression"
],
"name": "Bgee DataBase for Gene Expression Evolution",
"pattern": "^[A-Z]+\\d+$",
"prefix": "bgee",
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=gene&action=expression&gene_id=$1"
},
"bgi.ris": {
"description": "In BGI-RIS, sequence contigs of Beijing indica and Syngenta japonica have been further assembled and anchored onto the rice chromosomes. The database has annotated the rice genomes for gene content, repetitive elements, and SNPs. Sequence polymorphisms between different rice subspecies have also been identified.",
"example": "BGIOSSBCE000001.1",
"homepage": "http://rice.genomics.org.cn/",
"keywords": [
"regulation",
"DNA"
],
"name": "Beijing Genomics Institute Rice Information System",
"pattern": "^BGI\\a+\\.\\d$",
"prefix": "bgi.ris",
"pubmed_ids": [
"14681438"
]
},
"bhfucl": {
"description": "Providing Full Gene Ontology Annotation To Genes Associated With Cardiovascular Processes",
"example": "P01023",
"homepage": "http://www.cardiovasculargeneontology.com",
"keywords": [
"ontology"
],
"name": "Cardiovascular Gene Ontology Annotation Initiative",
"pattern": "^[O/P/Q]\\d+$",
"prefix": "bhfucl"
},
"bid": {
"description": "The Binding Interface Database (BID) is structured to organize vast amounts of protein interaction information into tabular form, graphical contact maps, and descriptive functional profiles. Detailed protein descriptions, interaction descriptions, bond formation, and the strength of each amino acid's contribution to binding were systematically obtained by mining the primary literature containing alanine scanning and site-directed mutations.",
"example": "Collagen",
"homepage": "http://tsailab.org/wikiBID/index.php/Main_Page",
"keywords": [
"protein",
"interaction"
],
"name": "Binding Interface Database Wiki",
"pattern": "^[A-Z]+$",
"prefix": "bid",
"uri_format": "http://tsailab.org/wikiBID/index.php/$1"
},
"bind": {
"description": "BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways.",
"example": "98346",
"homepage": "http://bond.unleashedinformatics.com/",
"keywords": [
"interaction",
"small molecule",
"pathway"
],
"name": "Biomolecular Interaction Network Databank",
"pattern": "^\\d+$",
"prefix": "bind",
"uri_format": "http://www.bind.ca/Action?identifier=bindid&idsearch=$1"
},
"binding_moad": {
"description": "Binding MOAD's goal is to be the largest collection of well resolved protein crystal structures with clearly identified biologically relevant ligands annotated with experimentally determined binding data extracted from literature. It is a subset of PDB.",
"example": "1603",
"homepage": "http://www.BindingMOAD.org",
"keywords": [
"protein"
],
"name": "Binding Mother Of All Databases",
"pattern": "^\\d+$",
"prefix": "binding_moad",
"uri_format": "http://www.bindingmoad.org/moad/getMoadlet.do?id=$1"
},
"bindingdb": {
"description": "BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.",
"example": "22360",
"homepage": "http://www.bindingdb.org",
"keywords": [
"protein",
"interaction"
],
"name": "BindingDB database of measured binding affinities",
"pattern": "^\\d+$",
"prefix": "bindingdb",
"pubmed_ids": [
"17145705"
],
"uri_format": "http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=$1"
},
"biocatalogue": {
"description": "The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all.",
"example": "614",
"homepage": "http://www.biocatalogue.org/",
"keywords": [
"registry"
],
"name": "Curated catalogue of Life Science Web Services",
"pattern": "^\\d+$",
"prefix": "biocatalogue",
"pubmed_ids": [
"20484378"
],
"uri_format": "http://www.biocatalogue.org/services/$1"
},
"biocyc": {
"description": "The BioCyc collection of Pathway/Genome Databases (PGDBs) provides electronic reference sources on the pathways and genomes of different organisms.",
"example": "ECOLI:CYT-D-UBIOX-CPLX",
"homepage": "http://www.biocyc.org/",
"keywords": [
"genome",
"pathway",
"sequence"
],
"name": "BioCyc Database Collection",
"pattern": "^\\w+\\:[A-Za-z0-9-]+$",
"prefix": "biocyc",
"pubmed_ids": [
"16246909"
],
"uri_format": "http://biocyc.org/ECOLI/NEW-IMAGE?object=$1"
},
"biogrid": {
"description": "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe.",
"example": "31623",
"homepage": "http://www.thebiogrid.org",
"keywords": [
"protein",
"gene",
"interaction"
],
"name": "Biological General Repository for Interaction Datasets",
"pattern": "^\\d+$",
"prefix": "biogrid",
"pubmed_ids": [
"16381927"
],
"uri_format": "http://thebiogrid.org/$1"
},
"biomagresbank": {
"description": "A repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids.",
"example": "10046",
"homepage": "http://www.bmrb.wisc.edu/",
"keywords": [
"protein"
],
"name": "BioMagResBank",
"pattern": "^\\d+$",
"prefix": "biomagresbank",
"uri_format": "http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId=$1"
},
"biomodels": {
"alt_uri_formats": [
"http://biomodels.caltech.edu/$1"
],
"bioportal": "3022",
"description": "BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests.",
"example": "BIOMD0000000048",
"homepage": "http://www.ebi.ac.uk/biomodels/",
"keywords": [
"model"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "A Database of Annotated Published Models",
"pattern": "^((BIOMD|MODEL)\\d{10})|(BMID\\d{12})$",
"prefix": "biomodels",
"pubmed_ids": [
"16381960"
],
"synonyms": [
"biomodelsdatabase",
"biomodels.db"
],
"uri_format": "http://www.ebi.ac.uk/biomodels-main/$1"
},
"bionemo": {
"description": "Bionemo stores manually curated information about proteins and genes directly implicated in biodegradation metabolism. The database includes information on sequence, domains and structures for proteins; and sequence, regulatory elements and transcription units for genes.",
"example": "1092",
"homepage": "http://bionemo.bioinfo.cnio.es",
"keywords": [
"protein",
"gene",
"pathway",
"regulation"
],
"name": "Biodegradation Network Molecular Biology Database",
"pattern": "^\\d+$",
"prefix": "bionemo",
"uri_format": "http://bionemo.bioinfo.cnio.es/Run.cgi?rm=mode4&result=$1"
},
"bionumbers": {
"description": "BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data.",
"example": "104674",
"homepage": "http://www.bionumbers.hms.harvard.edu/search.aspx",
"name": "The Database of Useful Biological Numbers",
"pattern": "^\\d+$",
"prefix": "bionumbers",
"uri_format": "http://www.bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=$1&ver=1"
},
"biopixie": {
"description": "bioPIXIE is a novel system for biological data integration and visualization. It allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate.",
"example": "12",
"homepage": "http://pixie.princeton.edu/pixie/",
"keywords": [
"gene",
"interaction"
],
"name": "biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology",
"pattern": "^\\d+$",
"prefix": "biopixie",
"synonyms": [
"biopixie_mefit"
],
"uri_format": "http://avis.princeton.edu/pixie/viewgraph.php?graphID=$1"
},
"bioportal": {
"description": "BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protege frames. BioPortal functionality includes the ability to browse, search and visualize ontologies.",
"example": "1046",
"homepage": "http://bioportal.bioontology.org/",
"keywords": [
"ontology"
],
"name": "BioPortal",
"pattern": "^\\d+$",
"prefix": "bioportal",
"pubmed_ids": [
"19483092"
],
"uri_format": "http://bioportal.bioontology.org/ontologies/$1"
},
"biosystems": {
"description": "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources.",
"example": "1",
"homepage": "http://www.ncbi.nlm.nih.gov/biosystems/",
"keywords": [
"molecules",
"pathways"
],
"license": "http://www.nlm.nih.gov/copyright.html",
"name": "BioSystems",
"pattern": "^\\d+$",
"prefix": "biosystems",
"pubmed_ids": [
"19854944"
],
"synonyms": [
"bsid"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/biosystems/$1"
},
"biozon": {
"description": "The Biozon database relies on an extensive database schema that integrates information at the macro-molecular level as well as at the cellular level, from a variety of resources to create a unified biological knowledge resource with emphasis on protein and DNA characterization and classification. The database was designed so as to allow easy integration with other data types and existing and future databases.",
"example": "110194476",
"homepage": "http://biozon.org",
"keywords": [
"small molecule",
"protein",
"DNA"
],
"name": "Biozon",
"pattern": "^\\d+$",
"prefix": "biozon",
"uri_format": "http://biozon.org/Biozon/Profile/$1"
},
"bmph": {
"description": "Digitized access to the Roche Applied Science \"Biochemical Pathways\" Boehringer Mannheim wall chart of metabolism. Links are provided to the ENZYME database.",
"example": "C4",
"homepage": "http://www.expasy.org/cgi-bin/search-biochem-index",
"keywords": [
"pathway",
"enzyme"
],
"name": "Boehringer Mannheim Biochemical Pathways Wall Chart",
"pattern": "^[A-Z]\\d$",
"prefix": "bmph",
"uri_format": "http://www.expasy.org/cgi-bin/show_image?$1"
},
"bodymap": {
"description": "BodyMap is a data bank of exprsesion information of human and mouse genes, novel or known, in various tissues or cell types and various timings. The first generation map was created by random sequencing of clonse in 3'-directed cDNA libraries.",
"example": "GS05390",
"homepage": "http://bodymap.ims.u-tokyo.ac.jp/",
"keywords": [
"gene",
"DNA"
],
"name": "BodyMap; Human and Mouse gene expression database",
"pattern": "^GS\\d+$",
"prefix": "bodymap",
"uri_format": "http://bodymap.ims.u-tokyo.ac.jp/[?human/mouse]/gs_card.php?gs=$1"
},
"bodymapxs": {
"description": "BodyMap-Xs(cross species) is taxonomical and anatomical breakdown of latest animal EST data, clustered by UniGene and inter connected by Inparanoid.",
"example": "Hs.644639",
"homepage": "http://bodymap.jp/",
"keywords": [
"anatomy",
"DNA"
],
"name": "BodyMap Xs: Anatomical and Taxonomical Breakdown of Animal EST",
"pattern": "^[A-z]+.\\d+$",
"prefix": "bodymapxs"
},
"bold": {
"description": "The Barcode of Life Data Systems (BOLD) is an online workbench that aids collection, management, analysis, and use of DNA barcodes. It consists of 3 components (MAS, IDS, and ECS) that each address the needs of various groups in the barcoding community.",
"example": "27267",
"homepage": "http://www.barcodinglife.com",
"keywords": [
"DNA"
],
"name": "The Barcode of Life Data Systems",
"pattern": "^\\d+$",
"prefix": "bold",
"pubmed_ids": [
"18784790"
],
"synonyms": [
"bold.taxonomy"
],
"uri_format": "http://www.barcodinglife.com/views/taxbrowser.php?taxid=$1"
},
"bps": {
"description": "BPS is a database of RNA base pairs with quantitative information on the spatial arrangements of interacting bases, including higher-order base associations, and the context of these interactions in high-resolution crystal structures. The interactions are classified in terms of residue identities, base-pair positioning, and hydrogen-bonding patterns and related to the structural context in which they occur.",
"example": "AR0023_8",
"homepage": "http://bps.rutgers.edu",
"keywords": [
"DNA",
"interaction"
],
"name": "Database of RNA Base-pair Structures",
"pattern": "^[A-Z]+\\d+_\\d+$",
"prefix": "bps",
"uri_format": "http://bps.rutgers.edu/atlas/bp_record/$1"
},
"brenda": {
"description": "BRENDA is the main collection of enzyme functional data available to the scientific community.",
"example": "1.1.1.1",
"homepage": "http://www.brenda-enzymes.org",
"keywords": [
"enzyme"
],
"license": "http://www.brenda-enzymes.org",
"name": "The Comprehensive Enzyme Information System",
"pattern": "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$",
"prefix": "brenda",
"pubmed_ids": [
"18984617"
],
"uri_format": "http://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1"
},
"bto": {
"alt_uri_formats": [
"http://purl.org/obo/owl/BTO#$1"
],
"bioportal": "1005",
"description": "The Brenda tissue ontology is a structured controlled vocabulary established to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.",
"example": "BTO:0000146",
"homepage": "http://www.brenda-enzymes.info",
"keywords": [
"obo",
"tissue"
],
"name": "BRENDA Tissue Ontology",
"pattern": "^BTO:\\d{7}$",
"prefix": "bto",
"synonyms": [
"brendatissueontology",
"obo.bto"
]
},
"buchnerabase": {
"description": "BuchneraBase is a database designed to encapsulate and reference information obtained from the complete genome sequence of the gamma-proteobacterium Buchnera sp. APS.",
"example": "BB0299",
"homepage": "http://www.buchnera.org/",
"keywords": [
"genome"
],
"name": "BuchneraBase: An integrated post-genomic database for Buchnera sp. APS",
"pattern": "^BB\\d+$",
"prefix": "buchnerabase",
"uri_format": "http://www.york.ac.uk/res/thomas/Buchnerabase/resources/gene_page_aps.cfm?BBnum=$1"
},
"burulist": {
"description": "A database dedicated to the analysis of the genome of Mycobacterium ulcerans, the Buruli ulcer bacillus. It provides a complete dataset of DNA and protein sequences derived from the epidemic strain Agy99, linked to the relevant annotations and functional assignments.",
"example": "MUL_0018",
"homepage": "http://genolist.pasteur.fr/BuruList/",
"keywords": [
"genome",
"protein"
],
"name": "Buruli ulcer bacillus Database",
"pattern": "^MUL_\\d+$",
"prefix": "burulist"
},
"bykdb": {
"description": "The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information.",
"example": "A0AYT5",
"homepage": "http://bykdb.ibcp.fr/BYKdb/",
"keywords": [
"domain",
"microbial",
"sequence"
],
"name": "Bacterial Tyrosine Kinase Database",
"pattern": "^\\w+$",
"prefix": "bykdb",
"pubmed_ids": [
"22080550"
],
"uri_format": "http://bykdb.ibcp.fr/data/html/$1.html"
},
"cancergenes": {
"description": "The CancerGenes resource was designed to simplify the process of gene selection and prioritization in large collaborative projects. CancerGenes combines gene lists annotated by experts with information from key public databases.",
"example": "NP_114172.1",
"homepage": "http://cbio.mskcc.org/cancergenes",
"keywords": [
"gene"
],
"name": "CancerGenes",
"pattern": "^N[W/P]_\\d+$",
"prefix": "cancergenes",
"uri_format": "http://cbio.mskcc.org/Public/products/human_mapped/Mapback_html/$1.html"
},
"candidadb": {
"description": "A database dedicated to the analysis of the genome of the human fungal pathogen, Candida albicans. Its purpose is to collate and integrate various aspects of the genomic information from C. albicans, which is currently responsible for the vast majority of life-threatening fungal infections in immuno-compromized individuals. CandidaDB provides an almost complete dataset of DNA and protein sequences derived from C. albicans strain SC5314, linked to the relevant annotations and functional assignments.",
"example": "CA0205",
"homepage": "http://genolist.pasteur.fr/CandidaDB",
"keywords": [
"genome"
],
"name": "Candida albicans Database",
"pattern": "^CA\\d+$",
"prefix": "candidadb",
"synonyms": [
"candida"
]
},
"cangem": {
"description": "Cancer GEnome Mine is a public database for storing clinical information about tumor samples and microarray data, with emphasis on array comparative genomic hybridization (aCGH) and data mining of gene copy number changes.",
"example": "ENSG00000164794",
"homepage": "http://www.cangem.org/",
"keywords": [
"gene expression",
"genome"
],
"name": "Cancer GEnome Mine",
"pattern": "^ENSG\\d+$",
"prefix": "cangem",
"uri_format": "http://www.cangem.org/index.php?gene=$1"
},
"cas": {
"description": "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information.",
"example": "50-00-0",
"homepage": "http://www.cas.org/",
"keywords": [
"chemical",
"structure"
],
"name": "CAS: A Divison of the American Chemical Society",
"pattern": "^\\d{1,7}\\-\\d{2}\\-\\d$",
"prefix": "cas",
"synonyms": [
"chemicalabstractscas"
],
"uri_format": "http://commonchemistry.org/ChemicalDetail.aspx?ref=$1"
},
"catdb": {
"description": "CATdb collects together all the information on transcriptome experiments done at URGV with CATMA micro arrays",
"example": "6",
"homepage": "http://urgv.evry.inra.fr/CATdb",
"keywords": [
"gene expression"
],
"name": "A Complete Arabidopsis Transcriptome Database",
"pattern": "^\\d+$",
"prefix": "catdb",
"uri_format": "http://urgv.evry.inra.fr/cgi-bin/projects/CATdb/consult_project.pl?project_id=$1"
},
"cath": {
"description": "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This collection is concerned with superfamily classification.",
"example": "3.15",
"homepage": "http://www.cathdb.info/",
"keywords": [
"classification",
"protein",
"structure"
],
"name": "CATH Protein Structure Classification",
"pattern": "^\\d+(\\.\\d+(\\.\\d+(\\.\\d+)?)?)?$",
"prefix": "cath",
"pubmed_ids": [
"9309224"
],
"uri_format": "http://www.cathdb.info/cathnode/$1"
},
"catma": {
"description": "The aim of the Complete Arabidopsis Transcriptome MicroArray (CATMA) project was the design and production of high quality Gene-specific Sequence Tags (GSTs) covering most Arabidopsis genes. The GST repertoire is used by numerous groups for the production of DNA arrays for transcript profiling experiments.",
"example": "CATMA2a00190",
"homepage": "http://www.catma.org",
"keywords": [
"gene expression"
],
"name": "A Compelte Arabidopsis Transcriptome MicroArray Project",
"pattern": "^CATMA\\d[a-z]\\d+$",
"prefix": "catma"
},
"cattleqtldb": {
"description": "This Cattle Quantitative Trait Locus (QTL) database (Cattle QTLdb) has gathered all cattle QTL data published during the past 10+ years. The database and its peripheral tools make it possible to compare, confirm and locate on cattle chromosomes the most feasible location for genes responsible for quantitative trait important to cattle production.",
"example": "66",
"homepage": "http://www.animalgenome.org/cgi-bin/QTLdb/BT/index",
"keywords": [
"DNA",
"genome"
],
"name": "Cattle Quantitative Trait Locus database",
"pattern": "^\\d+$",
"prefix": "cattleqtldb",
"uri_format": "http://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_ID=$1"
},
"cazy": {
"description": "The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.",
"example": "GT10",
"homepage": "http://www.cazy.org/",
"keywords": [
"classification",
"polysaccharide"
],
"name": "The Carbohydrate-Active enZYmes Database",
"pattern": "^GT\\d+$",
"prefix": "cazy",
"pubmed_ids": [
"18838391"
],
"uri_format": "http://www.cazy.org/$1.html"
},
"ccd": {
"description": "The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names.",
"example": "AB0",
"homepage": "http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?APPLICATION=1",
"keywords": [
"chemical",
"classification"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Chemical Component Dictionary",
"pattern": "^\\w{3}$",
"prefix": "ccd",
"pubmed_ids": [
"14634627"
],
"synonyms": [
"het",
"pdb.het",
"pdb.ccd"
],
"uri_format": "http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?FUNCTION=record&ENTITY=CHEM_COMP&PRIMARYKEY=$1&APPLICATION=1"
},
"ccds": {
"description": "The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations.",
"example": "4824",
"homepage": "http://www.ncbi.nlm.nih.gov/CCDS/",
"keywords": [
"protein",
"gene"
],
"name": "The Consensus CDS",
"pattern": "^\\d+$",
"prefix": "ccds",
"pubmed_ids": [
"19498102"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1"
},
"ccm": {
"description": "The Cancer Cell Map is a selected set of human cancer focused pathways available for browsing adn searching.",
"example": "148",
"homepage": "http://cancer.cellmap.org",
"keywords": [
"pathway"
],
"name": "The Cancer Cell Map",
"pattern": "^\\d+$",
"prefix": "ccm",
"uri_format": "http://cancer.cellmap.org/cellmap/record.do?id=$1"
},
"cco": {
"alt_uri_formats": [
"http://purl.org/obo/owl/CCO#$1"
],
"bioportal": "1507",
"description": "An application ontology integrating knowledge about the eukaryotic cell cycle.",
"example": "CCO:P0000023",
"homepage": "http://www.semantic-systems-biology.org/cco/",
"keywords": [
"obo",
"cell cycle"
],
"name": "Cell Cycle Ontology",
"pattern": "^CCO\\:\\w+$",
"prefix": "cco",
"pubmed_ids": [
"19480664"
]
},
"cdd": {
"description": "The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, including NCBI-curated domains, which use 3D-structure information to explicitly to define domain boundaries and provide insights into sequence/structure/function relationships, as well as domain models imported from a number of external source databases (Pfam, SMART, COG, PRK, TIGRFAM).",
"example": "cd00400",
"homepage": "http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml",
"keywords": [
"protein",
"structure"
],
"license": "http://www.nlm.nih.gov/copyright.html",
"name": "Conserved Domain Database",
"pattern": "^cd\\d{5}$",
"prefix": "cdd",
"pubmed_ids": [
"18984618"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"
},
"cellimage": {
"description": "The Cell: An Image Library\u2122 is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.",
"example": "24801",
"keywords": [
"image"
],
"name": "The Cell: An Image Library",
"pattern": "^\\d+$",
"prefix": "cellimage",
"uri_format": "http://cellimagelibrary.org/images/$1"
},
"cgd": {
"description": "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.",
"example": "CAL0003079",
"homepage": "http://www.candidagenome.org/",
"keywords": [
"eukaryotic",
"genome",
"nucleotide"
],
"name": "Candida Genome Database",
"pattern": "^CAL\\d{7}$",
"prefix": "cgd",
"pubmed_ids": [
"15608216"
],
"uri_format": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"
},
"cged": {
"description": "CGED (Cancer Gene Expression Database) is a database of gene expression profile and accompanying clinical information.Genes in CGED can be searched by 1) gene names or identifiers, or 2) gene ontology terms or keywords in functional annotations in the SwissProt, or 3) cancer types and its clinical factors, or 4) gene expression differentials based on p value or q value.",
"example": "31424",
"homepage": "http://lifesciencedb.jp/cged/",
"keywords": [
"gene expression",
"ontology"
],
"name": "Cancer Gene Expression Database",
"pattern": "^\\d+$",
"prefix": "cged",
"uri_format": "http://lifesciencedb.jp/cgi-bin/cged/detail.cgi?ci=3&cg=$1"
},
"cgnc": {
"description": "The Chicken Gene Nomenclature Consortium (CGNC) provides standardized gene nomenclature for chicken genes.",
"example": "2218",
"homepage": "http://www.agnc.msstate.edu/",
"keywords": [
"gene"
],
"license": "http://www.agnc.msstate.edu/About.htm",
"name": "Chicken Gene Nomenclature Consortium",
"pattern": "^\\d+$",
"prefix": "cgnc",
"pubmed_ids": [
"19607656"
],
"uri_format": "http://www.agnc.msstate.edu/GeneReport.aspx?a=$1"
},
"cgsc": {
"description": "The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature.",
"example": "96846",
"homepage": "http://cgsc.biology.yale.edu/",
"keywords": [
"gene"
],
"name": "The Coli Genetic Stock Center",
"pattern": "^\\d+$",
"prefix": "cgsc",
"uri_format": "http://cgsc.biology.yale.edu/Site.php?ID=$1"
},
"chebi": {
"alt_uri_formats": [
"http://www.ebi.ac.uk/chebi/searchId.do;?chebiId=$1",
"http://www.loria.fr/~coulet/ontology/sopharm$1",
"http://www.ebi.ac.uk/ontology-lookup//version2.1/chebi.owl#$1",
"http://purl.org/obo/owl/CHEBI#$1",
"http://www.ebi.ac.uk/ontology-lookup/?termId=CHEBI:#$1"
],
"bioportal": "1007",
"description": "A structured classification of chemical compounds of biological relevance.",
"example": "17234",
"homepage": "http://www.ebi.ac.uk/chebi/",
"keywords": [
"obo",
"chemical"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Chemical Entities of Biological Interest",
"pattern": "^\\d+$",
"prefix": "chebi",
"pubmed_ids": [
"23180789"
],
"synonyms": [
"atp_chebi"
],
"uri_format": "http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$1"
},
"chembank": {
"description": "ChemBank is a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG).",
"example": "1000000",
"homepage": "http://chembank.broad.harvard.edu",
"keywords": [
"chemical",
"metabolite"
],
"name": "ChemBank",
"pattern": "^\\d+$",
"prefix": "chembank",
"pubmed_ids": [
"17947324"
],
"uri_format": "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$1"
},
"chembl": {
"description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.",
"example": "210313",
"homepage": "https://www.ebi.ac.uk/chembldb/",
"keywords": [
"molecules"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "chEMBL",
"pattern": "^\\d+$",
"prefix": "chembl",
"synonyms": [
"chembldb"
],
"uri_format": "https://www.ebi.ac.uk/chembldb/index.php/compound/inspect/$1"
},
"chemdb": {
"description": "ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds.",
"example": "3965223",
"homepage": "http://cdb.ics.uci.edu",
"keywords": [
"small molecule"
],
"name": "The UC Irvine ChemDB",
"pattern": "^\\d+$",
"prefix": "chemdb",
"pubmed_ids": [
"17599932"
],
"uri_format": "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1"
},
"chemidplus": {
"description": "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.",
"example": "000057272",
"homepage": "http://chem.sis.nlm.nih.gov/chemidplus/chemidheavy.jsp",
"keywords": [
"structure",
"molecules"
],
"license": "http://www.nlm.nih.gov/copyright.html",
"name": "ChemIDplus",
"pattern": "^\\d+$",
"prefix": "chemidplus",
"uri_format": "http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$1"
},
"chemspider": {
"description": "ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources.",
"example": "56586",
"homepage": "http://www.chemspider.com/",
"keywords": [
"structure",
"molecules"
],
"license": "http://www.rsc.org/Help/termsconditions.asp",
"name": "ChemSpider - Database of Chemical Structures and Property Predictions",
"pattern": "^\\d+$",
"prefix": "chemspider",
"uri_format": "http://www.chemspider.com/Chemical-Structure.$1.html"
},
"chickenqtldb": {
"description": "This Chicken Quantitative Trait Locus (QTL) database (Chicken QTLdb) has gathered all chicken QTL data published during the past 10+ years. The database and its peripheral tools make it possible to compare, confirm and locate on chicken chromosomes the most feasible location for genes responsible for quantitative trait important to chicken production.",
"example": "66",
"homepage": "http://www.animalgenome.org/cgi-bin/QTLdb/GG/index",
"keywords": [
"DNA",
"genome"
],
"name": "Chicken Quantitative Trait Locus database",
"pattern": "^\\d+$",
"prefix": "chickenqtldb",
"uri_format": "http://www.animalgenome.org/cgi-bin/QTLdb/GG/qdetails?QTL_ID=$1"
},
"chickvd": {
"description": "The chicken Variation Database (ChickVD) is an integrated information system for storage, retrieval, visualization and analysis of chicken variation data.",
"example": "443",
"homepage": "http://chicken.genomics.org.cn",
"name": "Chicken Variation Database",
"pattern": "^\\d+$",
"prefix": "chickvd",
"uri_format": "http://chicken.genomics.org.cn/chicken/jsp/gene_report.jsp?gene_id=$1"
},
"chimerdb": {
"description": "ChimerDB is the database of fusion sequences encompassing bioinformatics analysis of mRNA and EST sequences in the GenBank, manual collection of literature data, and integration with other known database such as OMIM",
"example": "ABL1",
"homepage": "http://genome.ewha.ac.kr/ChimerDB/",
"keywords": [
"RNA",
"DNA"
],
"name": "ChimerDB : A Knowledgebase for fusion sequences",
"pattern": "^[A-Z]+/\\d+$",
"prefix": "chimerdb"
},
"chromdb": {
"description": "The broad mission of ChromDB is display, annotate, and curate sequences of two broad functional classes of biologically important proteins: chromatin-associated proteins (CAPs) and RNA interference-associated proteins.",
"example": "8",
"homepage": "http://www.chromdb.org",
"keywords": [
"protein"
],
"name": "The Chromatin Database",
"pattern": "^\\d+$",
"prefix": "chromdb",
"uri_format": "http://www.chromdb.org/gene_record.html?g=$1"
},
"cipro": {
"description": "CIPRO is an integrated protein that has been developed to provide widespread information of the proteins expressed in the ascidian Ciona intestinalis, especially for the researcher who wants to get advance and useful information for starting biological and biomedical research. The protein information in CIPRO directly links to gene expression, a tool for peptide mass fingerprinting (PMF), intracellular localization, 3D image of early development, and transgenic resources.",
"example": "CIPRO82.31.5",
"homepage": "http://cipro.ibio.jp/2.0",
"keywords": [
"protein"
],
"name": "Ciona intestinalis Protein Database",
"pattern": "^CIPRO\\d+.\\d+.\\d+..$",
"prefix": "cipro"
},
"cisred": {
"description": "The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data.",
"example": "ENSG00000187919",
"homepage": "http://www.cisred.org/",
"keywords": [
"genome"
],
"name": "cis-Regulatory Element Database",
"pattern": "^ENSG\\d+$",
"prefix": "cisred",
"uri_format": "http://www.cisred.org/[?species]/gene_view?ensembl_id=$1"
},
"citexplore": {
"description": "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.",
"example": "16333295",
"homepage": "http://www.ebi.ac.uk/citexplore/",
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "CiteXplore",
"pattern": "^\\d+$",
"prefix": "citexplore",
"uri_format": "http://www.ebi.ac.uk/citexplore/citationDetails.do?dataSource=MED&externalId=$1"
},
"cl": {
"bioportal": "1006",
"description": "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.",
"example": "CL:0000232",
"homepage": "http://lists.sourceforge.net/lists/listinfo/obo-cell-type",
"keywords": [
"obo",
"cell"
],
"name": "Cell Ontology",
"pattern": "^CL:\\d+$",
"prefix": "cl"
},
"cleanest": {
"description": "CleanEST is a database to provide cleansed EST sequences of classified dbEST libraries. All dbEST libraries were classified according to organism, sequencing center, and eVOC ontologies (for human libraries). For each dbEST library, we provide three different EST sequences: \u2018raw\u2019, \u2018pre-cleansed\u2019, and \u2018user-cleansed\u2019",
"example": "21360",
"homepage": "http://cleanest.kobic.re.kr/",
"keywords": [
"DNA",
"ontology"
],
"name": "CleanEST",
"pattern": "^\\d+$",
"prefix": "cleanest",
"uri_format": "http://verdi.kobic.re.kr/cleanEST/library_view.jsp?libid=$1"
},
"clibe": {
"description": "A database for facilitating the analysis of Drug Binding Competitveness. It contains information about Computed Ligand-Receptor Interaction Energy and other attributes such as energy components; ligand classification, functions and properties. Ligand structure is also included.",
"example": "1e3z00103",
"homepage": "http://bidd.nus.edu.sg/group/CLiBE/",
"keywords": [
"interaction",
"small molecule"
],
"name": "Computed Ligand Binding Energy",
"pattern": "^\\d..[a-z]\\d..\\d+$",
"prefix": "clibe",
"uri_format": "http://bidd.nus.edu.sg/group/CLiBE/Detail.asp?ID=$1"
},
"clinicaltrials": {
"description": "ClinicalTrials.gov is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world.",
"example": "NCT00050895",
"homepage": "http://clinicaltrials.gov/",
"keywords": [
"disease",
"drug",
"human"
],
"license": "http://www.nlm.nih.gov/copyright.html",
"name": "ClinicalTrials.gov",
"pattern": "^NCT\\d{8}$",
"prefix": "clinicaltrials",
"uri_format": "http://clinicaltrials.gov/ct2/show/$1"
},
"clo": {
"alt_uri_formats": [
"http://purl.org/obo/owl/CL#$1",
"http://purl.org/obo/owl/CLO#$1"
],
"bioportal": "1314",
"description": "The Cell Line Ontology (CLO) is a community-based ontology in domain of biological cell lines with a focus on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications.",
"example": "CL:0000232",
"homepage": "http://sourceforge.net/projects/clo-ontology/",
"keywords": [
"ontology"
],
"name": "Cell Line Ontology",
"pattern": "^CL:\\d{7}$",
"prefix": "clo",
"pubmed_ids": [
"15693950"
],
"synonyms": [
"obo.clo"
]
},
"clustr": {
"description": "The CluSTr database offers an automatic classification of UniProt Knowledgebase and IPI proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences. The database provides links to InterPro, which integrates information on protein families, domains and functional sites from PROSITE, PRINTS, Pfam, ProDom, SMART, TIGRFAMs, Gene3D, SUPERFAMILY, PIR Superfamily and PANTHER.",
"example": "2978:40.1",
"homepage": "http://www.ebi.ac.uk/clustr/",
"keywords": [
"protein"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "CluSTr",
"pattern": "^[0-9A-Za-z]+:\\d+:\\d{1,5}(\\.\\d)?$",
"prefix": "clustr",
"pubmed_ids": [
"15961444"
]
},
"cmd": {
"description": "This database aims to record all published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP, FKBP10, LEPRE1 and PPIB genes.",
"example": "COL3A1",
"homepage": "http://www.le.ac.uk/genetics/collagen/",
"keywords": [
"gene"
],
"name": "Collagen Mutation Database",
"pattern": "^[A-Z,0-9]+$",
"prefix": "cmd",
"uri_format": "https://eds.gene.le.ac.uk/home.php?select_db=$1"
},
"cmr": {
"description": "The Comprehensive Microbial Resource (CMR) is a free website used to display information on all of the publicly available, complete prokaryotic genomes.",
"example": "NTL03BA0491",
"homepage": "http://cmr.jcvi.org/",
"keywords": [
"genome"
],
"name": "Comprehensive Microbial Resource at the J. Craig Venter Institute",
"pattern": "^$\\w+$",
"prefix": "cmr",
"uri_format": "http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=$1"
},
"cnidbase": {
"description": "CnidBase, the Cnidarian Evolutionary Genomics Database, is a tool for investigating the evolutionary, developmental and ecological factors that affect gene expression and gene function in cnidarians.",
"example": "CNS35",
"homepage": "http://cnidbase.com/index.cgi",
"keywords": [
"genome"
],
"name": "Cnidarian Evolutionary Genomics Database",
"pattern": "^CNS\\d+$",
"prefix": "cnidbase",
"uri_format": "http://cnidbase.com/index.cgi?cn_accession=$1"
},
"coc_central": {
"description": "CoC Central is a searchable database of residue conservation data covering the universe of known protein structures.",
"example": "1a65A",
"homepage": "http://kulibin.mit.edu/coc/",
"keywords": [
"protein"
],
"name": "Conservation of Conservation Central: A database of universally conserved residues in protein folds",
"pattern": "^[A-Z,0-9]+$",
"prefix": "coc_central",
"synonyms": [
"coc"
]
},
"cog": {
"description": "Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.",
"example": "145262",
"homepage": "http://www.ncbi.nlm.nih.gov/COG",
"keywords": [
"protein",
"genome"
],
"name": "Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes",
"pattern": "^\\d+$",
"prefix": "cog",
"uri_format": "http://www.ncbi.nlm.nih.gov/COG/grace/cogenome.cgi?g=$1"
},
"cogat": {
"bioportal": "1633",
"description": "The Cognitive Atlas is a collaborative knowledge building project that aims to develop a knowledge base (or ontology) that characterizes the state of current thought in cognitive science",
"example": "CAO_01019",
"homepage": "http://www.cognitiveatlas.org/",
"name": "Cognitive Atlas",
"pattern": "^CAO_\\d+$",
"prefix": "cogat",
"rdf_uri_format": "http://www.cognitiveatlas.org/ontology/cogat.owl#$1",
"uri_format": "http://www.cognitiveatlas.org/ontology/cogat.owl#$1"
},
"come": {
"description": "COMe is an attempt to classify metalloproteins and some other complex proteins using the concept of bioinorganic motif.",
"example": "BIM000347",
"homepage": "http://www.flymine.org/come/",
"keywords": [
"protein"
],
"name": "COMe",
"pattern": "^BIM\\d+$",
"prefix": "come",
"uri_format": "http://www.flymine.org/come/entry?gn=$1"
},
"comparasite": {
"description": "Comparasite, an integrated database of our original full-length cDNA sequence data, consists of seven sub-databases of apicomplexa protozoa, Plasmodium falciparum(12,484 cDNA sequences), Plasmodium yoelii (11,262 sequences), Plasmodium vivax (9,633 sequences), Plasmodium berghei (1,518 sequences), Toxoplasma gondii (7,400 sequences), Cryptosporidium parvum (5,921 sequences) and a tapeworm, Echinococcus multilocularis (10,966 sequences).",
"example": "1833",
"homepage": "http://comparasite.hgc.jp/",
"keywords": [
"DNA"
],
"name": "Comparasite: Full-length cDNA Database",
"pattern": "^\\d+$",
"prefix": "comparasite"
},
"comparative_genometrics": {
"description": "Devoted to the characterization of complete chromosome sequences by standardized genometric methods, the Comparative Genometrics website displays for sequenced genomes, three different genometric analyses: the DNA walk and the GC and TA skews during the initial phase. Although primarly focused on prokaryotic chromosomes, the CG website posts genometric information on paradigm plasmids, phages, viruses, and organelles.",
"example": "NC_013926",
"homepage": "http://www.unil.ch/comparativegenometrics/",
"keywords": [
"genome"
],
"name": "Comparative Genometrics",
"pattern": "^NC_\\d+$",
"prefix": "comparative_genometrics",
"uri_format": "http://www2.unil.ch/comparativegenometrics/$1.htm"
},
"compluyeast2dpage": {
"description": "Compluyeast-2D-DB is a Two-dimensional polyacrilamide gel electrophoresis federated database built with the Make2DDB package and integrated at the WORLD-2DPAGE of the ExPASy proteomics web server.",
"example": "P20029",
"homepage": "http://compluyeast2dpage.dacya.ucm.es/",
"keywords": [
"protein"
],
"name": "CompluYeast 2D-PAGE",
"pattern": "^P\\d+$",
"prefix": "compluyeast2dpage",
"uri_format": "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1"
},
"consurfdb": {
"description": "ConSurf-DB provides evolutionary conservation profiles for proteins of known structure in the PDB. Amino acid sequences similar to each sequence in the PDB were collected and multiply aligned using PSI-BLAST and MUSCLE, respectively.",
"example": "1d66",
"homepage": "http://consurfdb.tau.ac.il/",
"keywords": [
"protein"
],
"name": "The ConSurf Server Database: Server for the Identification of Functional Regions in Proteins",
"pattern": "^PDBID$",
"prefix": "consurfdb",
"uri_format": "http://consurfdb.tau.ac.il/consurf_db/$1/[?chain_id]/"
},
"corg": {
"description": "CORG stands for COmparative Regulatory Genomics. Non-coding DNA segments that are conserved across multiple homologous genomic sequences are good indicators of putative regulatory elements. We use a systematic approach to delineate such conserved non-coding blocks from a collection of vertebrate species.",
"example": "ENSG00000012048",
"homepage": "http://corg.molgen.mpg.de",
"keywords": [
"genome"
],
"name": "COmparative Regulatory Genomics",
"pattern": "^ENSG\\d+$",
"prefix": "corg",
"uri_format": "http://corg.eb.tuebingen.mpg.de/cgi-bin/get_gene_info_v38.pl?id=$1&species=[?species_name]&version=v38"
},
"corum": {
"description": "The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more.",
"example": "56",
"homepage": "http://mips.gsf.de/genre/proj/corum",
"keywords": [
"protein"
],
"name": "the Comprehensive Resource of Mammalian protein complexes",
"pattern": "^\\d+$",
"prefix": "corum",
"uri_format": "http://mips.helmholtz-muenchen.de/genre/proj/corum/complexdetails.html?id=$1"
},
"covdb": {
"description": "Coronavirus became a research hot spot after the outbreak of SARS in 2003. During two years study, our group identified three genotypes of CoV-HKU1 from patients and first documented recombination within human coronavirus (PubMed). At least eight bat coronaviruses were also identified by us (PubMed). This website intends to organize the genomic information and knowledge of known coronaviruses and provides some tools for sequence analysis.",
"example": "8088",
"homepage": "http://covdb.microbiology.hku.hk",
"name": "Coronavirus Database",
"pattern": "^\\d+$",
"prefix": "covdb"
},
"cpndb": {
"description": "cpnDB is a curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins.",
"example": "b10409",
"homepage": "http://cpndb.cbr.nrc.ca/",
"keywords": [
"protein"
],
"name": "A Chaperonin Database",
"pattern": "^b\\d+$",
"prefix": "cpndb",
"synonyms": [
"cpn"
],
"uri_format": "http://cpndb.cbr.nrc.ca/getRecord.php?id=$1"
},
"crest": {
"description": "The Crop EST Database (CR-EST) is a public available online resource providing access to sequence, classification, clustering, and annotation data of crop EST projects at the IPK.",
"example": "PSC04L10u",
"homepage": "http://pgrc.ipk-gatersleben.de/cr-est",
"keywords": [
"DNA"
],
"name": "CR-EST: The IPK Crop EST Database",
"pattern": "^PSC\\d+[a-z]$",
"prefix": "crest"
},
"cryptodb": {
"description": "CryptoDB is an integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers, it also includes supplemental bioinformatics analyses and a web interface for data-mining.",
"example": "cgd7_230",
"homepage": "http://cryptodb.org/cryptodb/",
"keywords": [
"genome"
],
"name": "Cryptosporidum Genomics Resource",
"pattern": "^\\w+$",
"prefix": "cryptodb",
"pubmed_ids": [
"16381902"
],
"uri_format": "http://cryptodb.org/cryptodb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"
},
"csa": {
"description": "The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme.",
"example": "1a05",
"homepage": "http://www.ebi.ac.uk/thornton-srv/databases/CSA/",
"keywords": [
"enzyme",
"structure"
],
"name": "Catalytic Site Atlas",
"pattern": "^[0-9][A-Za-z0-9]{3}$",
"prefix": "csa",
"pubmed_ids": [
"14681376"
],
"uri_format": "http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/CSA/CSA_Site_Wrapper.pl?pdb=$1"
},
"cst": {
"description": "A small pathway portal for showcasing Cell Signaling Technology phospho-antibody products. Contains pathway diagrams that are clickable and link to more information about each protein and the commercial products that are available for that protein.",
"example": "3762",
"homepage": "http://www.cellsignal.com/",
"keywords": [
"pathway"
],
"name": "Cell Signaling Technology Pathway Database",
"pattern": "^\\d+$",
"prefix": "cst",
"uri_format": "http://www.cellsignal.com/products/$1.html"
},
"ctad": {
"description": "Cancer-Testis Antigens database",
"example": "94",
"homepage": "http://www.cta.lncc.br/",
"name": "Cancer-Testis Antigens database",
"pattern": "^\\d+$",
"prefix": "ctad",
"uri_format": "http://www.cta.lncc.br/modelo.php?idgene=$1&idmeta=11"
},
"ctga": {
"description": "The Centre for Arab Genomic Studies (CAGS) initiated the ambitious project to establish the CTGA (Catalogue of Transmission Genetics in Arabs) database for genetic disorders in Arabs with the aim to enlighten the scientific community and the public on the occurrence of inherited disorders in Arabs and to suggest future investigation strategies.",
"example": "33771",
"homepage": "http://www.cags.org.ae",
"keywords": [
"genome"
],
"name": "Catalogue of Transmission Genetics in Arabs",
"pattern": "^\\d+$",
"prefix": "ctga",
"uri_format": "http://www.cags.org.ae/FMPro?-db=ctga.fp5&-format=/ctga/ctga_detail.html&-lay=main&Record_Category=Gene%20locus&-max=30&-recid=$1&-find="
},
"cutdb": {
"description": "CutDB is one of the first systematic efforts to build an easily accessible collection of documented proteolytic events for natural proteins in vivo or in vitro. A CutDB entry is defined by a unique combination of these three attributes: protease, protein substrate, and cleavage site. Currently, CutDB integrates 3,070 proteolytic events for 470 different proteases captured from public archives (such as MEROPS and HPRD) and publications.",
"example": "20153",
"homepage": "http://cutdb.burnham.org",
"keywords": [
"protein"
],
"name": "CutDB",
"pattern": "^\\d+$",
"prefix": "cutdb",
"uri_format": "http://cutdb.burnham.org/relation/show/$1"
},
"cutg": {
"description": "Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank.",
"example": "9606",
"homepage": "http://www.kazusa.or.jp/codon/",
"keywords": [
"gene",
"DNA"
],
"name": "Codon Usage Tabulated from GenBank",
"pattern": "^\\d+$",
"prefix": "cutg",
"uri_format": "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=$1"
},
"cyanobase": {
"description": "CyanoBase provides an easy way of accessing the sequences and all-inclusive annotation data on the structures of the cyanobacterial genomes.",
"example": "all3717",
"homepage": "http://genome.kazusa.or.jp/cyanobase",
"keywords": [
"genome"
],
"name": "CyanoBase",
"pattern": "^[a-z]+\\d+$",
"prefix": "cyanobase",
"uri_format": "http://genome.kazusa.or.jp/cyanobase/Synechocystis/genes/$1"
},
"cybase": {
"description": "CyBase is a curated database and information source for backbone-cyclised proteins. The database incorporates naturally occurring cyclic proteins as well as synthetic derivatives, grafted analogues and acyclic permutants. The database provides a centralized repository of information on all aspects of cyclic protein biology and addresses issues pertaining to the management and searching of topologically circular sequences.",
"example": "65",
"homepage": "http://research1t.imb.uq.edu.au/cybase/",
"keywords": [
"protein"
],
"name": "The Database of Cyclic Proteins",
"pattern": "^\\d+$",
"prefix": "cybase",
"uri_format": "http://research1t.imb.uq.edu.au/cybase/index.php?page=card&table=protein&id=$1"
},
"cyclebase": {
"description": "Cyclebase is centralized, standardized resource for researchers to inspect and download cell-cycle datasets. Results of our state-of-the-art analyses of individual experiments as well as combined datasets are also included. The database currently contains 4 organisms, 22 experiments, and 5,630,666 expression values.",
"example": "ENSG00000123485",
"homepage": "http://www.cyclebase.org",
"name": "CycleBase",
"pattern": "^ENSG\\d+$",
"prefix": "cyclebase",
"uri_format": "http://www.cyclebase.org/displaygene.action?geneName=$1&taxId=[$taxid]"
},
"cyclonet": {
"description": "Computational modelling of mammalian cell cycle regulation is a challenging task, which requires comprehensive knowledge on many interrelated processes in the cell. We have developed a web-based integrated database on cell cycle regulation in mammals in normal and pathological states (Cyclonet database)",
"example": "DGR0053",
"homepage": "http://cyclonet.biouml.org/",
"name": "Cyclonet",
"pattern": "^[A-Z]+\\d+$",
"prefix": "cyclonet"
},
"cygd": {
"description": "A major part of this information gets extracted by manual annotation from the yeast literature, and results of the systematic functional analysis projects as well as cross-references to other in-house or external databases (NCBI, PIR, PEDANT, EMBL] provide complementary material. In addition information and links to related ascomycetous species are added as far as genomic information is available.",
"example": "YFL039c",
"homepage": "http://mips.gsf.de/genre/proj/yeast/index.jsp",
"keywords": [
"genome"
],
"name": "Comprehensive Yeast Genome Database",
"pattern": "^\\w{2,3}\\d{2,4}(\\w)?$",
"prefix": "cygd",
"pubmed_ids": [
"15608217"
],
"synonyms": [
"mips_cygd"
],
"uri_format": "http://mips.helmholtz-muenchen.de/genre/proj/yeast/singleGeneReport.html?entry=$1"
},
"dailymed": {
"description": "DailyMed provides high quality information about marketed drugs including FDA labels (package inserts).",
"example": "3be94523-f6d6-4b25-82b0-3e0d021594c5",
"homepage": "http://dailymed.nlm.nih.gov/dailymed/",
"name": "Dailymed",
"pattern": "^[A-Za-z0-9]{8}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{12}$",
"prefix": "dailymed",
"uri_format": "http://dailymed.nlm.nih.gov/dailymed/lookup.cfm?setid=$1"
},
"dali": {
"description": "The Dali database is based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB). The classification and alignments are automatically maintained and continuously updated using the Dali search engine, http://www.ebi.ac.uk/~holm/DaliLite/ are provided.",
"example": "1tu9",
"homepage": "http://ekhidna.biocenter.helsinki.fi/dali/start",
"keywords": [
"protein",
"structure"
],
"name": "Dali database",
"pattern": "^PDBID$",
"prefix": "dali",
"uri_format": "http://ekhidna.biocenter.helsinki.fi/dali_server/results/$1/index.html"
},
"dart": {
"description": "A database for facilitating the search for drug adverse reaction target. It contains information about known drug adverse rection targets, functions and properties.",
"example": "DRT1TCCIBg",
"homepage": "http://xin.cz3.nus.edu.sg/group/drt/dart.asp",
"keywords": [
"DNA"
],
"name": "Drug Adverse Reaction Targets",
"pattern": "^Various$",
"prefix": "dart",
"uri_format": "http://xin.cz3.nus.edu.sg/group/DRT/Detail.asp?ID=$1"
},
"datf": {
"description": "The Database of Arabidopsis Transcription Factors (DATF) collects all Arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families.The Version 2 of DATF was updated at July 2006. It is based on the Arabidopsis Sequence of TAIR http://www.pdb.org, predicted Nuclear Location Signals, UniGene information, as well as links to literature reference.",
"example": "AT1G08970.3",
"homepage": "http://datf.cbi.pku.edu.cn",
"keywords": [
"regulation"
],
"name": "Database of Arabidopsis Transcription Factors",
"pattern": "^AT\\d[A-Z]\\d+$",
"prefix": "datf",
"uri_format": "http://datf.cbi.pku.edu.cn/entry-display.php?id=$1"
},
"dbd": {
"description": "DBD provides transcription factor predictions for more than 150 completely sequenced genomes available for browsing and download. Predictions are based on presence of sequence specific DNA binding domain assignments using hidden Markov models from the SUPERFAMILY and PFAM databases",
"example": "0035306",
"homepage": "http://www.transcriptionfactor.org",
"keywords": [
"regulation",
"genome"
],
"name": "DBD",
"pattern": "^\\d+$",
"prefix": "dbd",
"uri_format": "http://dbd.mrc-lmb.cam.ac.uk/DBD/index.cgi?Search/Domain+domain:$1"
},
"dbest": {
"description": "The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms.",
"example": "BP100000.1",
"homepage": "http://www.ncbi.nlm.nih.gov/dbEST/index.html",
"keywords": [
"DNA"
],
"name": "EST database maintained at the NCBI.",
"pattern": "^BP\\d+(\\.\\d+)?$",
"prefix": "dbest",
"uri_format": "http://www.ncbi.nlm.nih.gov/nucest/$1"
},
"dbpabp": {
"description": "DB-PABP is an attempt to document the publicly available experimentally determined PABPs. The purpose of the database is to provide life scientists who are interested in PA/PABP interactions with a comprehensive data repository, as well as computer scientists with a publicly available dataset to perform knowledge discovery and datamining studies.",
"example": "29",
"homepage": "http://ppa.bcf.ku.edu/DB_PABP/",
"keywords": [
"interaction"
],
"name": "DB-PABP: a Database of Polyanion Binding Proteins",
"pattern": "^\\d+$",
"prefix": "dbpabp",
"uri_format": "http://ppa.bcf.ku.edu/DB_PABP/protein_details.jsp?prot_id=$1"
},
"dbprobe": {
"description": "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.",
"example": "1000000",
"homepage": "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=probe",
"keywords": [
"nucleotide"
],
"name": "NCBI Probe database Public registry of nucleic acid reagents",
"pattern": "^\\d+$",
"prefix": "dbprobe",
"uri_format": "http://www.ncbi.nlm.nih.gov/genome/probe/reports/probereport.cgi?uid=$1"
},
"dbres": {
"description": "dbRES is a web-oriented comprehensive database for RNA Editing Site. dbRES contain only experimental validated RNA Editing Site. All the data in dbRES was manually collected from literatures reporting related experiment result or the GeneBank database.",
"example": "RESDB000000309",
"homepage": "http://bioinfo.au.tsinghua.edu.cn/dbRES/",
"keywords": [
"RNA"
],
"name": "dbRES: A web-oriented database for annotated RNA Editing Site",
"pattern": "^RESDB\\d+$",
"prefix": "dbres",
"uri_format": "http://bioinfo.au.tsinghua.edu.cn/dbRES/show_record.php?resid=$1"
},
"dbsnp": {
"description": "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.",
"example": "rs199422184",
"homepage": "http://www.ncbi.nlm.nih.gov/SNP/",
"keywords": [
"genome"
],
"name": "Database of single nucleotide polymorphism",
"pattern": "^rs\\d+$",
"prefix": "dbsnp",
"pubmed_ids": [
"11125122"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$1"
},
"dccp": {
"description": "The Database of Copper-Chelating Proteins (DCCP) is maintained by Shandong Provincial Research Center for Bioinformatic Engineering and Technique. DCCP currently contains two types of proteins, one with 3D structure, called DCCP_3D, which contains 500 entries of proteins, and the other without 3D structure, called DCCP_1D, which contains 5088 entries.",
"example": "49",
"homepage": "http://sdbi.sdut.edu.cn/DCCP/en/index.php",
"keywords": [
"protein",
"structure"
],
"name": "Database of Copper-Chelating Proteins",
"pattern": "^\\d+$",
"prefix": "dccp",
"uri_format": "http://sdbi.sdut.edu.cn/DCCP/en/Detail1D.php?id=$1"
},
"ddanat": {
"bioportal": "1008",
"description": "A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum.",
"example": "DDANAT_0010081",
"homepage": "http://dictybase.org/",
"keywords": [
"obo",
"anatomy",
"slime-mould"
],
"name": "Dictyostelium discoideum anatomy",
"pattern": "^DDANAT_\\d+$",
"prefix": "ddanat",
"synonyms": [
"ddana"
]
},
"ddbj": {
"description": "At present INSDC have released about 100 billion bases in total. This is the outcome of the collaboration among the three member banks for more than 20 years. However, this number will easily be surpassed when the 1000 human genomes project is completed and the result is submitted to INSDC in a few years, or even before that. DDBJ has also started to accept and release such mass sequence data.",
"example": "AJ457054",
"homepage": "http://www.ddbj.nig.ac.jp",
"keywords": [
"genome"
],
"name": "DNA Data Bank of Japan; a nucleotide sequence database",
"pattern": "^[A-Z]+\\d+$",
"prefix": "ddbj",
"synonyms": [
"dbj"
],
"uri_format": "http://xml.ddbj.nig.ac.jp/rest/Invoke?service=GetEntry&method=getDDBJEntry&accession=$1"
},
"ddoc": {
"description": "Many aspects of the information provided in the DDOC were curated by biologists, which emphasize its accuracy. DDOC provides details of the cell line, tissue or cell type, expression status, disease stage, tumour grade, OC type and laboratory method provided in the literature. The links to the relevant sources of data used to extract information related to genes are also included.",
"example": "42",
"homepage": "http://apps.sanbi.ac.za/ddoc/",
"keywords": [
"gene"
],
"name": "Dragon Database for Exploration of Ovarian Cancer Genes",
"pattern": "^\\d+$",
"prefix": "ddoc",
"uri_format": "http://apps.sanbi.ac.za/ddoc/details_general.php?geneID=$1"
},
"ded": {
"description": "Diatoms are photosynthetic unicellular eukaryotes that play an essential role in marine ecosystems. On a global scale, they generate around one fifth of the oxygen we breathe. On this web site we present searchable databases of diatom ESTs (expressed sequence tags) that can be used to explore diatom biology.",
"example": "PTMM00967",
"homepage": "http://www.biologie.ens.fr/diatomics/EST3",
"keywords": [
"DNA"
],
"name": "The Diatom EST Database",
"pattern": "^PT[A-Z]+\\d+$",
"prefix": "ded"
},
"defensins_knowledgebase": {
"description": "The defensins knowledgebase is a manually curated database and information source devoted to the defensin family of antimicrobial peptides. The current version of the database holds a comprehensive collection of over 350 defensin records each containing sequence, structure and activity information. A web-based interface provides access to the information and allows for text-based searching on various data fields. With the rapidly increasing interest in defensins, we hope that the knowledgebase will prove to be a valuable resource in the field of antimicrobial peptide research.",
"example": "177",
"homepage": "http://defensins.bii.a-star.edu.sg/",
"keywords": [
"protein"
],
"name": "Defensins Knowledgebase",
"pattern": "^\\d+$",
"prefix": "defensins_knowledgebase",
"uri_format": "http://defensins.bii.a-star.edu.sg/pops/pop_proteinDetails.php?id=$1"
},
"deg": {
"description": "DEG hosts records of currently available essential genes among a wide range of organisms. For prokaryotes, DEG contains essential genes in more than 10 bacteria, such as E. coli, B. subtilis, H. pylori, S. pneumoniae, M. genitalium and H. influenzae, whereas for eukaryotes, DEG contains those in yeast, humans, mice, worms, fruit flies, zebra fish and the plant A. thaliana.",
"example": "DEG10130001",
"homepage": "http://tubic.tju.edu.cn/deg",
"keywords": [
"gene"
],
"name": "Database of Essential Genes",
"pattern": "^DEG\\d+$",
"prefix": "deg"
},
"dictybase": {
"description": "Genome information, literature and experimental resources for Dictyostelium discoideum",
"example": "DBS0237308",
"homepage": "http://dictybase.org/",
"keywords": [
"genome"
],
"name": "Dictyostelium discoideum online informatics resource",
"pattern": "^DBS\\d{7}$",
"prefix": "dictybase"
},
"dima": {
"description": "DIMA is a Domain Interaction MAp and aims at becoming a comprehensive resource for functional and physical interactions among conserved protein-domains. The scope of the resource comprises both experimental data and computational predictions.",
"example": "PF00419",
"homepage": "http://mips.gsf.de/genre/proj/dima2",
"keywords": [
"interaction",
"protein"
],
"name": "Domain Interaction MAp Database",
"pattern": "^PF\\d+$",
"prefix": "dima",
"uri_format": "http://mips.helmholtz-muenchen.de/genre/proj/dima2/query/query.jsp?domain=$1"
},
"dip": {
"description": "The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions",
"example": "DIP-743N",
"homepage": "http://dip.doe-mbi.ucla.edu",
"keywords": [
"interaction",
"protein"
],
"license": "http://dip.doe-mbi.ucla.edu/dip/termsofuse.html",
"name": "Database of Interacting Proteins",
"pattern": "^DIP[\\:\\-]\\d{3}[EN]$",
"prefix": "dip",
"pubmed_ids": [
"14681454"
],
"uri_format": "http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1"
},
"diprodb": {
"description": "The Dinucleotide Property Database is designed to collect and analyse thermodynamic, structural and other dinucleotide properties. The table presenting all the dinucleotide properties can be pruned and rearranged by different criteria. The database contains different export and analysis functions.",
"example": "15",
"homepage": "http://diprodb.fli-leibniz.de",
"name": "Dinucleotide Property DataBase",
"pattern": "^\\d+$",
"prefix": "diprodb"
},
"disprot": {
"description": "The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part.",
"example": "DP00001",
"homepage": "http://www.disprot.org/",
"keywords": [
"protein",
"structure"
],
"name": "Database of protein disorder",
"pattern": "^DP\\d{5}$",
"prefix": "disprot",
"pubmed_ids": [
"17145717"
],
"uri_format": "http://www.disprot.org/protein.php?id=$1"
},
"do": {
"alt_uri_formats": [
"http://purl.org/obo/owl/DOID#$1",
"http://www.loria.fr/~coulet/ontology/sopharm/version2.1/disease_ontology.owl#$1",
"http://purl.org/obo/owl/DO#$1",
"http://www.owl-ontologies.com/NPOntology.owl#DOID_$1"
],
"bioportal": "1009",
"description": "The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts.",
"example": "DOID:11337",
"homepage": "http://diseaseontology.sourceforge.net/",
"keywords": [
"obo",
"disease",
"human",
"ontology"
],
"name": "Human disease ontology",
"pattern": "^DOID\\:\\d+$",
"prefix": "do",
"synonyms": [
"doid",
"diseaseontology",
"obo.do"
],
"uri_format": "http://disease-ontology.org/term/$1"
},
"doi": {
"alt_uri_formats": [
"http://hdl.handle.net/#$1"
],
"description": "The Digital Object Identifier System is for identifying content objects in the digital environment.",
"example": "10.1038/nbt1156",
"homepage": "http://www.doi.org/",
"keywords": [
"bibliography"
],
"name": "Digital Object Identifier",
"pattern": "^(doi\\:)?\\d{2}\\.\\d{4}.*$",
"prefix": "doi",
"uri_format": "http://dx.doi.org/$1"
},
"domine": {
"description": "DOMINE is a database of known and predicted protein domain (domain-domain) interactions. It contains interactions inferred from PDB entries, and those that are predicted by 8 different computational approaches using Pfam domain definitions.",
"example": "PF08521",
"homepage": "http://domine.utdallas.edu",
"keywords": [
"protein",
"interaction"
],
"name": "Database of Protein Domain Interactions",
"pattern": "^PF\\d+$",
"prefix": "domine",
"uri_format": "http://domine.utdallas.edu/cgi-bin/Domine?page=pfam&pfamid=$1"
},
"door": {
"description": "DOOR (Database of prOkaryotic OpeRons) is an operon database developed by Computational Systems Biology Lab (CSBL) at University of Georgia. The operons in the database are based on prediction.",
"example": "607986",
"homepage": "http://csbl1.bmb.uga.edu/OperonDB/",
"keywords": [
"DNA"
],
"name": "Database of prOkaryotic OpeRons",
"pattern": "^\\d+$",
"prefix": "door",
"uri_format": "http://csbl1.bmb.uga.edu/OperonDB/genedetail.php?id=$1"
},
"doqcs.model": {
"description": "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models.",
"example": "57",
"homepage": "http://doqcs.ncbs.res.in/",
"keywords": [
"model"
],
"license": "http://doqcs.ncbs.res.in/template.php?&y=faq#q2",
"name": "Database of Quantitative Cellular Signaling: Model",
"pattern": "^\\d+$",
"prefix": "doqcs.model",
"pubmed_ids": [
"12584128"
],
"uri_format": "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1"
},
"doqcs.pathway": {
"description": "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions.",
"example": "38",
"homepage": "http://doqcs.ncbs.res.in/",
"keywords": [
"pathway"
],
"license": "http://doqcs.ncbs.res.in/template.php?&y=faq#q2",
"name": "Database of Quantitative Cellular Signaling: Pathway",
"pattern": "^\\d+$",
"prefix": "doqcs.pathway",
"pubmed_ids": [
"12584128"
],
"uri_format": "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1"
},
"dpr": {
"description": "In order to simplify and streamline the transfer of plasmid materials to researchers, we have developed a novel strategy to avoid the most common concern encountered when distributing plasmids, namely the complexity of material transfer agreement (MTA) processing and the resulting delays this causes. The Expedited Process MTA, in which we created a network of institutions that agree to the terms of transfer in advance of a material request, eliminates these delays. By creating a repository of plasmids and expediting the process for receiving these plasmids, we strive to accelerate the accessibility and pace of scientific discovery.",
"example": "75687",
"homepage": "http://dnasu.asu.edu",
"keywords": [
"DNA"
],
"name": "DNASU Plasmid Repository",
"pattern": "^\\d+$",
"prefix": "dpr",
"uri_format": "http://dnasu.asu.edu/DNASU/GetCloneDetail.do?cloneid=$1"
},
"dpvweb": {
"description": "DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene (currently, n~9000).",
"example": "100",
"homepage": "http://www.dpvweb.net",
"keywords": [
"classification",
"gene"
],
"name": "Description of Plant Viruses",
"pattern": "^\\d+$",
"prefix": "dpvweb",
"pubmed_ids": [
"16381892"
],
"uri_format": "http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1"
},
"droid": {
"description": "DroID (Drosophila Interactions Database) is a comprehensive gene and protein interactions database designed specifically for the model organism Drosophila. The database includes published and unpublished low and high throughput data sets, genetic interactions, and computationally predicted interactions. The predicted interactions are generated based on interactions found in other organisms.",
"example": "FBgn0003145",
"homepage": "http://www.droidb.org",
"keywords": [
"gene",
"protein",
"interaction"
],
"name": "Drosophila Interactions Database",
"pattern": "^FB[a-z]+\\d+$",
"prefix": "droid"
},
"drugbank": {
"description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.",
"example": "DB00001",
"homepage": "http://www.drugbank.ca/",
"keywords": [
"drug",
"protein"
],
"license": "http://www.drugbank.ca/about",
"name": "DrugBank",
"pattern": "^DB\\d{5}$",
"prefix": "drugbank",
"pubmed_ids": [
"24203711",
"21059682",
"18048412",
"16381955"
],
"uri_format": "http://www.drugbank.ca/drugs/$1"
},
"dsmm": {
"description": "The purpose of this database is to provide an easily-searchable source of information about movies showing biomolecular motions that have been generated by computer simulation.",
"example": "115",
"homepage": "http://projects.villa-bosch.de/dbase/dsmm/",
"keywords": [
"small molecule"
],
"name": "Database of Simulated Molecular Motions",
"pattern": "^\\d+$",
"prefix": "dsmm"
},
"ebi.genomes": {
"description": "The Ensembl Genome Browser provides the best possible automatic annotation, graphical views and web-searchable datasets for a number of eukaryotic genomes including human, mouse, drosophila, anopheles, zebrafish with others to follow",
"example": "EF432053",
"homepage": "http://www.ebi.ac.uk/genomes",
"keywords": [
"genome"
],
"name": "EBI Genomes",
"pattern": "^[A-Z]+\\d+$",
"prefix": "ebi.genomes"
},
"echobase": {
"description": "EchoBase is a database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655.",
"example": "EB0170",
"homepage": "http://www.ecoli-york.org/",
"keywords": [
"gene",
"gene expression"
],
"name": "EchoBASE - an integrated post-genomic database for E. coli",
"pattern": "^EB\\d+$",
"prefix": "echobase",
"pubmed_ids": [
"15608209"
],
"uri_format": "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1"
},
"eco": {
"alt_uri_formats": [
"http://purl.org/obo/owl/ECO#$1"
],
"bioportal": "1012",
"description": "Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity.",
"example": "ECO:0000006",
"keywords": [
"obo",
"ontology"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Evidence Code Ontology",
"pattern": "^ECO:\\d{7}$",
"prefix": "eco",
"synonyms": [
"obo.eco"
]
},
"ecogene": {
"description": "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites.",
"example": "EG10173",
"homepage": "http://ecogene.org/",
"keywords": [
"genome",
"protein"
],
"name": "Escherichia coli strain K12 genome database",
"pattern": "^EG\\d+$",
"prefix": "ecogene",
"pubmed_ids": [
"10592181"
],
"uri_format": "http://ecogene.org/geneInfo.php?eg_id=$1"
},
"edam": {
"bioportal": "1498",
"description": "EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. The applications of EDAM are within organising tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web.",
"example": "EDAM_data:1664",
"homepage": "https://sourceforge.net/projects/edamontology/",
"keywords": [
"obo",
"ontology"
],
"name": "Bioinformatics operations, types of data, data formats and topics",
"pattern": "^EDAM_(data|topic)\\:\\d{4}$",
"prefix": "edam"
},
"egad": {
"description": "A database used to store gene, protein and TIGRFam/HMM information. Shows description of given EGAD, including name, nucleotide and protein information, and accession information used to derive EGAD term.",
"example": "10532",
"homepage": "http://cmr.jcvi.org/",
"keywords": [
"gene",
"protein"
],
"name": "EGAD database at the J. Craig Venter Institute",
"pattern": "^\\d+$",
"prefix": "egad",
"synonyms": [
"jcvi_egad"
]
},
"eggnog": {
"description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).",
"example": "NOG80852",
"homepage": "http://eggnog.embl.de",
"keywords": [
"gene"
],
"name": "Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups",
"pattern": "^\\w+$",
"prefix": "eggnog",
"pubmed_ids": [
"19900971"
],
"uri_format": "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1"
},
"ego": {
"description": "Eukaryotic Gene Orthologues (EGO) at DFGI are generated by pair-wise comparison between the Tentative Consensus (TC) sequences that comprise the Dana Farber Gene Indices from individual organisms. The reciprocal pairs of the best match were clustered into individual groups and multiple sequence alignments were displayed for each group. The EGO database can be accessed through the SEARCH function.",
"example": "971701",
"homepage": "http://compbio.dfci.harvard.edu/tgi/ego/",
"keywords": [
"gene"
],
"name": "Eukaryotic Gene Orthologs",
"pattern": "^\\d+$",
"prefix": "ego",
"uri_format": "http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/ego/ego_report.pl?ego=$1"
},
"ehda": {
"bioportal": "1022",
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20).",
"example": "EHDAA_1",
"homepage": "http://genex.hgu.mrc.ac.uk/",
"keywords": [
"obo",
"anatomy",
"development",
"human"
],
"name": "Human developmental anatomy, timed version",
"pattern": "^EHDA_\\d+$",
"prefix": "ehda"
},
"ehdaa": {
"bioportal": "1021",
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20).",
"example": "EHDAA_573",
"homepage": "http://genex.hgu.mrc.ac.uk/",
"keywords": [
"obo",
"anatomy",
"development",
"human"
],
"name": "Human developmental anatomy, abstract version",
"pattern": "^EHDAA_\\d+$",
"prefix": "ehdaa",
"synonyms": [
"hdaa"
]
},
"emap.ontology": {
"bioportal": "1010",
"description": "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).",
"example": "EMAP_3",
"homepage": "http://genex.hgu.mrc.ac.uk/",
"keywords": [
"obo",
"anatomy",
"development",
"mouse"
],
"name": "Mouse gross anatomy and development",
"pattern": "^EMAP_\\d+$",
"prefix": "emap.ontology"
},
"embl": {
"description": "International nucleotide sequence database collaboration, comprising EMBL-EBI nucleotide sequence data library (EMBL-Bank), DNA DataBank of Japan (DDBJ), and NCBI GenBank.",
"example": "AA816246",
"homepage": "http://www.ebi.ac.uk/embl/",
"keywords": [
"DNA"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "EMBL nucleotide sequence database",
"pattern": "^[A-Z]+\\d+$",
"prefix": "embl",
"synonyms": [
"emb",
"embl-cds",
"embl_con",
"embl_tpa",
"emblwgs"
],
"uri_format": "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+EntryPage+-e+[EMBL:$1]+-view+EmblEntry"
},
"emglib": {
"description": "The purpose of this database is to integrate various aspects on the genomic information of these organisms. It integrates completely sequenced genomes taken from the bacterial genome division of GenBank. Each genome is inserted in the database as a single entry. EMGLib allows one to easily browse through these data and retrieve information, using various criteria (keywords, sequence names, accession numbers, etc.)",
"example": "A00794",
"homepage": "http://pbil.univ-lyon1.fr/emglib/emglib.html",
"keywords": [
"genome"
],
"name": "Enhanced Microbial Genomes Library",
"pattern": "^[A-Z]+\\d+$",
"prefix": "emglib",
"uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/acnuc-search-id?query=$1&db=GenBank"
},
"ena": {
"description": "The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline.",
"example": "BN000065",
"homepage": "http://www.ebi.ac.uk/ena/",
"keywords": [
"DNA"
],
"name": "European Nucleotide Archive",
"pattern": "^[A-Z]+[0-9]+$",
"prefix": "ena",
"uri_format": "http://www.ebi.ac.uk/ena/data/view/$1"
},
"endonet": {
"description": "EndoNet is a database that provides information about endocrine networks. Using information about hormones' donor and acceptor cells a network is built that represents hormonal signaling pathways as a bipartite graph comprising hormones and tissues as node classes.",
"example": "290",
"homepage": "http://endonet.bioinf.med.uni-goettingen.de/",
"keywords": [
"pathway"
],
"name": "EndoNet",
"pattern": "^\\d+$",
"prefix": "endonet",
"uri_format": "http://endonet.bioinf.med.uni-goettingen.de/hormonedetail?id=$1"
},
"ensembl": {
"description": "Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes.",
"example": "ENSG00000139618",
"homepage": "http://www.ensembl.org/",
"keywords": [
"genome"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Ensembl",
"pattern": "^ENS[A-Z]*[FPTG]\\d{11}(\\.\\d+)?$",
"prefix": "ensembl",
"pubmed_ids": [
"16381931"
],
"uri_format": "http://www.ensembl.org/id/$1"
},
"ensembl.bacteria": {
"description": "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes.",
"example": "EBESCT00000015660",
"homepage": "http://bacteria.ensembl.org/",
"keywords": [
"genome"
],
"name": "Ensembl Bacteria",
"pattern": "^EB\\w+$",
"prefix": "ensembl.bacteria",
"pubmed_ids": [
"19884133"
],
"uri_format": "http://bacteria.ensembl.org/[?species_name]/Gene/Summary?g=$1"
},
"ensembl.fungi": {
"description": "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes.",
"example": "CADAFLAT00006211",
"homepage": "http://fungi.ensembl.org/",
"keywords": [
"genome"
],
"name": "Ensembl Fungi",
"pattern": "^\\w+$",
"prefix": "ensembl.fungi",
"uri_format": "http://fungi.ensembl.org/[?species_name]/Gene/Summary?g=$1"
},
"ensembl.metazoa": {
"description": "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes.",
"example": "AGAP006864",
"homepage": "http://metazoa.ensembl.org/",
"keywords": [
"genome"
],
"name": "Ensembl Metazoa",
"pattern": "^\\w+(\\.)?\\d+$",
"prefix": "ensembl.metazoa",
"uri_format": "http://metazoa.ensembl.org/[?species_name]/Gene/Summary?g=$1"
},
"ensembl.plant": {
"description": "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes.",
"example": "LOC_Os12g44300",
"homepage": "http://plants.ensembl.org/",
"keywords": [
"genome"
],
"name": "Ensembl Plants",
"pattern": "^\\w+$",
"prefix": "ensembl.plant",
"synonyms": [
"ensembl_plants"
],
"uri_format": "http://plants.ensembl.org/[?species_name]/Gene/Summary?g=$1"
},
"ensembl.protist": {
"description": "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes.",
"example": "PFC0120w",
"homepage": "http://protists.ensembl.org/",
"keywords": [
"genome"
],
"name": "Ensembl Protists",
"pattern": "^\\w+$",
"prefix": "ensembl.protist",
"synonyms": [
"ensembl_protists"
],
"uri_format": "http://protists.ensembl.org/[?species_name]/Gene/Summary?g=$1"
},
"enzyme": {
"description": "ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided",
"example": "1.2.7.6",
"homepage": "http://www.expasy.org/enzyme/",
"keywords": [
"enzyme"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Enzyme nomenclature database",
"pattern": "^\\d.\\d.\\d.\\d$",
"prefix": "enzyme",
"uri_format": "http://ca.expasy.org/enzyme/$1"
},
"eo": {
"bioportal": "1036",
"description": "A structured controlled vocabulary for the representation of plant environmental conditions.",
"example": "EO_0007191",
"homepage": "http://www.gramene.org/plant_ontology/ontology_browse.html#eo",
"keywords": [
"obo",
"plant"
],
"name": "Plant environmental conditions",
"pattern": "^EO_\\d+$",
"prefix": "eo"
},
"epcondb": {
"description": "EPConDB is a resource of the Beta Cell Biology Consortium which displays information about genes expressed in cells of the pancreas and their transcriptional regulation.",
"example": "110671376",
"homepage": "http://www.cbil.upenn.edu/EPConDB",
"keywords": [
"gene",
"regulation"
],
"name": "EPConDB: A resource of the Beta Cell Biology Consortinum",
"pattern": "^\\d+$",
"prefix": "epcondb",
"uri_format": "http://www.cbil.upenn.edu/epcondb42/showRecord.do?name=TranscriptRecordClasses.TranscriptRecordClass&project_id=GenomicsBC&primary_key=$1"
},
"epgd": {
"description": "The database is gene-centered and organized by paralog family. It focused on the paralogs and the duplication events in the evolution. The paralog families and paralogons can be searched by text or sequence, and are downloadable from the website in plain text files.",
"example": "3096",
"homepage": "http://epgd.biosino.org/EPGD/",
"keywords": [
"gene",
"DNA"
],
"name": "Eukaryotic Paralog Group Database",
"pattern": "^\\d+$",
"prefix": "epgd",
"uri_format": "http://epgd.biosino.org/EPGD/gene/geneinfor.jsp?geneID=$1"
},
"ergr": {
"description": "The aim of the Ethanol-Related Gene Resource (ERGR) database is to provide a comprehensive and useful gene resource to the Ethanol/Alcohol research community. Currently, the ERGR database contains more than 30 large datasets from literature and 21 mouse QTLs from public database.",
"example": "305351",
"homepage": "http://bioinfo.vipbg.vcu.edu/ERGR/",
"keywords": [
"gene"
],
"name": "Ethanol Related Gene Resource",
"pattern": "^\\d+$",
"prefix": "ergr",
"uri_format": "http://bioinfo.vipbg.vcu.edu/ERGR/geneinfo.php?id=$1"
},
"eropmoscow": {
"description": "EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence database which strives to provide a high level of annotations (such as descriptions of the structure of an oligopeptide, its source and function, post-translational modifications, etc.).",
"example": "E00002",
"homepage": "http://erop.inbi.ras.ru",
"keywords": [
"protein"
],
"name": "Endogenous Regulatory OligoPeptide knowledgebase-Moscow",
"pattern": "^E\\d+$",
"prefix": "eropmoscow",
"uri_format": "http://erop.inbi.ras.ru/result2.php?PepName=$1"
},
"esldb": {
"description": "eSLDB is a database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.",
"example": "HS000015122",
"homepage": "http://gpcr.biocomp.unibo.it/esldb",
"keywords": [
"protein"
],
"name": "eukaryotic Subcellular Localization database",
"pattern": "^[A-Z]+\\d+$",
"prefix": "esldb",
"uri_format": "http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice=$1"
},
"eugenes": {
"description": "euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information.",
"example": "MGgn0008978",
"homepage": "http://eugenes.org/",
"keywords": [
"genome",
"ontology"
],
"name": "Eukaryotic Genes",
"pattern": "^[A-Z]+\\d+$",
"prefix": "eugenes",
"synonyms": [
"eugenes:"
],
"uri_format": "http://eugenes.org:7072/.bin/fbidq.html?$1"
},
"euhcvdb": {
"description": "The euHCVdb is mainly oriented towards protein sequence, structure and function analyses and structural biology of Hepatitis C Virus.",
"example": "M58335",
"homepage": "http://euhcvdb.ibcp.fr/euHCVdb/",
"keywords": [
"protein"
],
"name": "European Hepatitis C Virus database",
"pattern": "^M\\d{5}$",
"prefix": "euhcvdb",
"pubmed_ids": [
"17142229"
],
"synonyms": [
"hcvdb"
],
"uri_format": "http://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1"
},
"everest": {
"description": "EVEREST combines methodologies from the fields of finite metric spaces, machine learning and statistical modeling and achieves state of the art results. Our process begins by constructing a database of protein segments that emerge in an all vs. all pairwise sequence comparison.",
"example": "P-11000522",
"homepage": "http://www.everest.cs.huji.ac.il",
"keywords": [
"protein"
],
"name": "EVolutionary Ensembles of REcurrent SegmenTs",
"pattern": "^[A-Z]+-\\d+$",
"prefix": "everest"
},
"evoc": {
"bioportal": "1013",
"description": "Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment.",
"example": "EV_0100011",
"homepage": "http://www.evocontology.org/",
"keywords": [
"obo",
"anatomy",
"cell",
"development",
"experiment"
],
"name": "eVOC (Expressed Sequence Annotation for Humans)",
"pattern": "^EV_\\d+$",
"prefix": "evoc",
"synonyms": [
"ev"
],
"uri_format": "http://www.evocontology.org/site/Main/BrowseEvoc?x_termid=$1"
},
"evola": {
"description": "Evola contains ortholog information of all human genes among vertebrates. Orthologs are a pair of genes in different species that evolved from a common ancestral gene by speciation. In Evola, orthologs were detected by comparative genomics and amino acid sequence analysis (Computational analysis).",
"example": "HIT000030236",
"homepage": "http://jbirc.jbic.or.jp/hinv/evola/",
"keywords": [
"genome"
],
"name": "Evolutionary Annotation Database",
"pattern": "^HIT\\d+$",
"prefix": "evola",
"uri_format": "http://www.h-invitational.jp/evola_main/annotation.cgi?hit=$1"
},
"explorenz": {
"description": "The Enzyme Database was developed as a new way to access the data of the IUBMB Enzyme Nomenclature List. The data, which are stored in a MySQL database, preserve the formatting of chemical names according to IUPAC standards.",
"example": "1.1.1.1",
"homepage": "http://www.enzyme-database.org",
"keywords": [
"enzyme",
"classification"
],
"name": "ExplorEnz - The Enzyme Database",
"pattern": "^EC Number$",
"prefix": "explorenz",
"uri_format": "http://www.enzyme-database.org/query.php?ec=$1"
},
"eyesite": {
"description": "The EyeSite database is an information and modelling resource for families of proteins that function in the eye. Homologues are collected from all species and clustered according to tissue type, function and sequence similarity. A principal feature of the site is structural annotations,which range from experimentally solved structures to close structural neighbours to distant structure predictions.",
"example": "341",
"homepage": "http://eyesite.cryst.bbk.ac.uk/",
"keywords": [
"protein"
],
"name": "EyeSite Database",
"pattern": "^\\d+$",
"prefix": "eyesite",
"uri_format": "http://eyesite.cryst.bbk.ac.uk/cgi-bin/get_family_page.cgi?FAMILY=$1"
},
"ezcatdb": {
"description": "The EzCatDB database analyzes and classifies enzyme catalytic mechanisms on the basis of information from literature and data that are derived from entries in the Protein Data Bank (PDB).",
"example": "T00024",
"homepage": "http://mbs.cbrc.jp/EzCatDB/",
"keywords": [
"enzyme",
"classification"
],
"name": "EzCatDB: A Database of Enzyme Catalytic Mechanisms",
"pattern": "^[A-Z]\\d+$",
"prefix": "ezcatdb",
"uri_format": "http://mbs.cbrc.jp/EzCatDB/search/get.do?dbcode=$1"
},
"fao": {
"bioportal": "1019",
"description": "The project aims to develop a controlled vocabulary to describe the 'anatomy' of fungi and other microbes, called the fungal anatomy ontology (FAO).",
"example": "FAO_0000001",
"homepage": "http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/",
"keywords": [
"obo",
"anatomy",
"fungi"
],
"name": "Fungal Anatomy Ontology",
"pattern": "^FAO_\\d+$",
"prefix": "fao"
},
"fbbi": {
"bioportal": "1023",
"description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.",
"example": "FBbi_00000222",
"homepage": "http://cellimagelibrary.org/",
"keywords": [
"obo",
"experiment",
"imaging"
],
"name": "Biological imaging methods",
"pattern": "^FBbi_\\d+$",
"prefix": "fbbi",
"synonyms": [
"fbbi.root"
]
},
"fbbt": {
"bioportal": "1015",
"description": "A structured controlled vocabulary of the anatomy of Drosophila melanogaster",
"example": "FBbt_00005835",
"homepage": "http://www.flybase.org/",
"keywords": [
"obo",
"anatomy",
"fly"
],
"name": "Drosophila gross anatomy",
"pattern": "^FBbt_\\d{8}$",
"prefix": "fbbt",
"synonyms": [
"fly_anatomy",
"fbbt_root"
]
},
"fbcv": {
"bioportal": "1017",
"description": "A structured controlled vocabulary used for various aspects of annotation by FlyBase. This ontology is maintained by FlyBase for various aspects of annotation not covered, or not yet covered, by other OBO ontologies. If and when community ontologies are available for the domains here covered FlyBase will use them.",
"example": "FBcv_0000013",
"homepage": "http://www.flybase.org/",
"keywords": [
"obo",
"descriptor",
"fly"
],
"name": "FlyBase Controlled Vocabulary",
"pattern": "^FBcv_\\d{7}$",
"prefix": "fbcv"
},
"fbdv": {
"alt_uri_formats": [
"http://purl.org/obo/owl/FBDV#$1"
],
"bioportal": "1016",
"description": "A structured controlled vocabulary of the development of Drosophila melanogaster.",
"example": "FBdv_00005291",
"homepage": "http://www.flybase.org/",
"keywords": [
"obo",
"development",
"fly"
],
"name": "Drosophila development",
"pattern": "^FBdv_\\d{8}$",
"prefix": "fbdv",
"synonyms": [
"fbdv.root"
]
},
"fcp": {
"description": "FCP is a publicly accessible web tool dedicated to analysing the current state and trends on the population of available structures along the classification schemes of enzymes and nuclear receptors, offering both graphical and quantitative data on the degree of functional coverage in that portion of the proteome by existing structures, as well as on the bias observed in the distribution of those structures among proteins.",
"example": "2.7.1.68",
"homepage": "http://cgl.imim.es/fcp/",
"name": "Functional Coverage of the Proteome",
"pattern": "^EC Number$",
"prefix": "fcp",
"uri_format": "http://cgl.imim.es/fcp/fcp.php?struct=1&compactId=EC.$1"
},
"fgdb": {
"description": "The MIPS Fusarium graminearum Genome Database aims to present information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Fusarium graminearum (Anamorph of Gibberella zeae).",
"example": "FGSG_14032",
"homepage": "http://mips.gsf.de/genre/proj/fusarium/",
"keywords": [
"genome"
],
"name": "Fusarium graminearum Genome Database",
"pattern": "^FGSG_\\d+$",
"prefix": "fgdb",
"uri_format": "http://mips.helmholtz-muenchen.de/genre/proj/FGDB/singleGeneReport.html?entry=$1"
},
"firedb": {
"description": "fireDB is a database of Protein Data Bank structures, ligands and annotated functional site residues. The database can be accessed by PDB codes or UniProt accession numbers as well as keywords.",
"example": "101mA",
"homepage": "http://firedb.bioinfo.cnio.es/",
"keywords": [
"protein"
],
"name": "fireDB: a database of annotated functionally important residues",
"pattern": "^PDBID$",
"prefix": "firedb",
"uri_format": "http://firedb.bioinfo.cnio.es/Php/FireDB.php?pdbcode=$1"
},
"fix": {
"bioportal": "1014",
"description": "FIX consists of two ontologies: methods and properties (but not objects, which are subject of the chemical ontology). The methods are applied to study the properties.",
"example": "FIX_0000000",
"keywords": [
"obo",
"property",
"experiment"
],
"name": "Physico-chemical methods and properties",
"pattern": "^FIX_\\d{7}$",
"prefix": "fix"
},
"flight": {
"description": "FLIGHT is an online resource compiling data from over 100 Drosophila in vivo and in vitro RNAi screens. FLIGHT includes details of RNAi reagents, and their predicted off-target effects, alongside RNAi screen hits, scores and phenotypes (including images and movies for high-content screens).",
"example": "3489915",
"homepage": "http://flight.licr.org/",
"keywords": [
"RNA"
],
"name": "FLIGHT",
"pattern": "^\\d+$",
"prefix": "flight",
"uri_format": "http://flight.licr.org/browse/view_rnai_hits.jsp?project_id=[$project_id]&screen_id=$1"
},
"flybase": {
"description": "FlyBase is an integrated resource for genetic, molecular, and descriptive data concerning the Drosophilidae, including interactive genomic maps, gene product descriptions, mutant allele phenotypes, genetic interactions, expression patterns, transgenic constructs and their insertions, anatomy and images, and genetic stock collections.",
"example": "FBgn0011293",
"homepage": "http://flybase.org/",
"keywords": [
"genome",
"interaction",
"anatomy",
"DNA"
],
"license": "http://flybase.org/static_pages/docs/copyright.html",
"name": "Drosophila genome database",
"pattern": "^FB\\w{2}\\d{7}$",
"prefix": "flybase",
"synonyms": [
"fb"
],
"uri_format": "http://flybase.org/reports/$1.html"
},
"flybase.est": {
"description": "The goals of the Drosophila Genome Center are to finish the sequence of the euchromatic genome of Drosophila melanogaster to high quality and to generate and maintain biological annotations of this sequence.",
"example": "123456",
"homepage": "http://www.fruitfly.org/EST/index.shtml",
"keywords": [
"genome"
],
"name": "Berkeley Drosophila Genome Project EST database",
"pattern": "^\\d+$",
"prefix": "flybase.est",
"synonyms": [
"bdgp_est"
]
},
"flymine": {
"description": "FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge.",
"example": "1047874",
"homepage": "http://www.flymine.org/",
"keywords": [
"genome",
"protein",
"gene expression"
],
"name": "FlyMine: An integrated database for Drosophila and Anopheles genomics",
"pattern": "^\\d+$",
"prefix": "flymine",
"uri_format": "http://www.flymine.org/release-25.0/objectDetails.do?id=$1"
},
"flytf": {
"description": "FlyTF is an integrated database of genomic and protein data for Drosophila site-specific transcription factors.",
"example": "122057953",
"homepage": "http://www.flytf.org",
"keywords": [
"genome",
"protein",
"regulation"
],
"name": "The Drosophila Transcription Factor Database",
"pattern": "^\\d+$",
"prefix": "flytf",
"uri_format": "http://www.flytf.org/flytfmine/objectDetails.do?id=$1"
},
"flytrap": {
"description": "This database presents the current results of large scale protein trapping screens that provide both information on which cells express each tagged gene, and subcellular localization of GFP-tagged proteins.",
"example": "BA00127",
"homepage": "http://flytrap.med.yale.edu/",
"keywords": [
"protein",
"gene"
],
"name": "FlyTrap: GFP Protein Trap Database",
"pattern": "^BA\\d+$",
"prefix": "flytrap",
"uri_format": "unavailable"
},
"flyview": {
"description": "FlyView is the beginning of an image database on Drosophila development and genetics, especially on expression patterns of genes (enhancer trap lines, cloned genes).The concept of FlyView includes compatibility to FlyBase, the main Drosophila database.",
"example": "P0160",
"homepage": "http://flyview.uni-muenster.de/",
"keywords": [
"gene expression"
],
"name": "FlyView: A Drosophila Image Database",
"pattern": "^P\\d+$",
"prefix": "flyview"
},
"fma": {
"alt_uri_formats": [
"http://purl.org/obo/owlapi/fma#$1",
"http://sig.uw.edu/fma#$1",
"http://purl.org/obo/owl/FMA#$1"
],
"bioportal": "1053",
"description": "FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy.",
"example": "FMA:67112",
"homepage": "http://sig.biostr.washington.edu/projects/fm/",
"keywords": [
"owl",
"anatomy",
"human"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "The Foundational Model of Anatomy Ontology",
"pattern": "^FMA:\\d+$",
"prefix": "fma",
"pubmed_ids": [
"17271570"
],
"synonyms": [
"obo.fma",
"fmaid"
]
},
"frnadb": {
"description": "fRNAdb is a database for comprehensive non-coding RNA sequences.",
"example": "FR021747",
"homepage": "http://www.ncrna.org/",
"keywords": [
"RNA"
],
"name": "fRNAdb: A comprehensive, non-coding RNA sequence database",
"pattern": "^FR\\d+$",
"prefix": "frnadb",
"uri_format": "http://www.ncrna.org/frnadb/detail.html?i_name=$1"
},
"fsnp": {
"description": "F-SNP database provides integrated information about the functional effects of SNPs obtained from 16 bioinformatics tools and databases. The functional effects are predicted and indicated at the splicing, transcriptional, translational, and post-translational level. As such, the F-SNP database helps identify and focus on SNPs with potential pathological effect to human health.",
"example": "rs36095613",
"homepage": "http://compbio.cs.queensu.ca/F-SNP/",
"keywords": [
"DNA",
"protein"
],
"name": "F-SNP: a collection of functional SNPs, specifically prioritized for disease association studies",
"pattern": "^rs\\d+$",
"prefix": "fsnp"
},
"fugoid": {
"description": "FUGOID collects and integrates various structural and functional data on organellar (mitochondrial and chloroplast) introns, particularly functional information about intron splicing and mobility. It is implemented in a relational database management system and can be searched either by intron information or by a major reference.",
"example": "14",
"homepage": "http://web.austin.utexas.edu/fugoid/introndata/main.htm",
"keywords": [
"DNA"
],
"name": "FUGOID: a Database for Functional Genomics of Organelle Introns",
"pattern": "^\\d+$",
"prefix": "fugoid",
"uri_format": "http://fugoid.webhost.utexas.edu/introndata/full_display.cfm?intronID=$1"
},
"g2cdb": {
"description": "Genes to Cognition (G2C) is a neuroscience research programme with the dual aim of discovering fundamental biological principles and important insights into brain disease.",
"example": "M00000026",
"homepage": "http://www.genes2cognition.org/",
"name": "Genes to Cognition Database",
"pattern": "^[A-Z]\\d+$",
"prefix": "g2cdb"
},
"gabi": {
"description": "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'.",
"example": "2679240",
"homepage": "http://www.gabi.de/",
"keywords": [
"gene",
"genome",
"plant"
],
"name": "Network of Different Plant Genomic Research Projects",
"pattern": "^\\w+$",
"prefix": "gabi",
"pubmed_ids": [
"18812395"
],
"uri_format": "http://gabi.rzpd.de/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject"
},
"gabikat": {
"description": "GABI-Kat SimpleSearch is a database of flanking sequence tags (FSTs) of T-DNA mutagenized Arabidopsis thaliana lines that were generated by the GABI-Kat project.",
"example": "048E04",
"homepage": "http://www.GABI-Kat.de",
"keywords": [
"DNA"
],
"name": "GABI-Kat: generation of flanking sequence tags (FSTs) from T-DNA mutagenised A. thaliana plants",
"pattern": "^\\d+[A-Z]\\d+$",
"prefix": "gabikat"
},
"geisha": {
"description": "GEISHA is the online repository of in situ hybridization and corresponding metadata for genes expressed in the chicken embryo during the first six days of development.",
"example": "2740",
"homepage": "http://geisha.arizona.edu",
"keywords": [
"gene expression"
],
"name": "Gallus Expression in situ Hybridization Analysis",
"pattern": "^\\d+$",
"prefix": "geisha",
"uri_format": "http://geisha.arizona.edu/geisha/search.jsp?gene=$1"
},
"genage": {
"description": "GenAge is a database of human and model organism genes related to longevity and aging, maintained by the Human Ageing Genomics Resources (HAGR) group.",
"example": "0001",
"homepage": "http://genomics.senescence.info/genes/",
"keywords": [
"aging",
"longevity",
"genes"
],
"license": "http://genomics.senescence.info/legal.html",
"name": "GenAge: The Ageing Gene Database",
"pattern": "^\\d+$",
"prefix": "genage",
"pubmed_ids": [
"23193293"
],
"uri_format": "http://genomics.senescence.info/genes/details.php?id=$1"
},
"genatlas": {
"description": "GenAtlas is a database containing information on human genes, markers and phenotypes.",
"example": "HBB",
"homepage": "http://www.genatlas.org/",
"keywords": [
"disorder",
"gene",
"human"
],
"name": "GenAtlas: human gene database",
"pattern": "^\\w+$",
"prefix": "genatlas",
"pubmed_ids": [
"9835018"
],
"uri_format": "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1"
},
"genbank": {
"description": "GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.",
"example": "AP008229",
"homepage": "http://www.ncbi.nlm.nih.gov/genbank/",
"keywords": [
"DNA"
],
"license": "http://www.nlm.nih.gov/copyright.html",
"name": "GenBank",
"pattern": "^\\w+$",
"prefix": "genbank",
"synonyms": [
"genbank_nucl_gi",
"genbank_protein_gi",
"gb",
"GenPept"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$1"
},
"gendis": {
"description": "Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases.",
"example": "46946",
"homepage": "http://caps.ncbs.res.in/gendis/home.html",
"keywords": [
"genome",
"classification"
],
"name": "Genomic Distribution of structural Superfamilies",
"pattern": "^\\d+$",
"prefix": "gendis",
"uri_format": "http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code=$1"
},
"gendr": {
"description": "GenDR is a database of genes associated with dietary restriction (DR). GenDR includes two datasets: 1) genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of DR; 2) genes robustly altered due to DR, derived from a meta-analysis of microarray DR studies in mammals",
"example": "2",
"homepage": "http://genomics.senescence.info/diet/",
"keywords": [
"dietary restriction",
"aging",
"longevity",
"genes"
],
"license": "http://genomics.senescence.info/legal.html",
"name": "GenDR: The Dietary Restriction Gene Database",
"pattern": "^\\d+$",
"prefix": "gendr",
"pubmed_ids": [
"22912585"
],
"uri_format": "http://genomics.senescence.info/diet/details.php?id=$1"
},
"geneannot": {
"description": "GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Probe-sets are related to GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq and Ensembl mRNA sequences, while assigning sensitivity and specificity scores to each probe-set to gene match.",
"example": "GSTA1",
"homepage": "http://genecards.weizmann.ac.il/geneannot/",
"keywords": [
"gene expression"
],
"name": "GeneAnnot: Microarray Gene Annotation",
"pattern": "^[A-Z]+/\\d+$",
"prefix": "geneannot"
},
"genecards": {
"description": "GeneCards is a searchable, integrated, database of human genes that provides concise genomic, transcriptomic, genetic, proteomic, functional and disease related information on all known and predicted human genes.",
"example": "ABL1",
"homepage": "http://bioinfo.weizmann.ac.il/genecards/",
"keywords": [
"genome"
],
"name": "GeneCards: human genes, protein and diseases",
"pattern": "^\\w+$",
"prefix": "genecards",
"pubmed_ids": [
"20689021"
],
"synonyms": [
"genecard"
],
"uri_format": "http://www.genecards.org/cgi-bin/carddisp.pl?gene=$1"
},
"genedb": {
"description": "GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the \"Pathogen Genomics\" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed.",
"example": "Cj1536c",
"homepage": "http://www.genedb.org/",
"keywords": [
"genome",
"sequence"
],
"license": "http://www.sanger.ac.uk/legal",
"name": "GeneDB",
"pattern": "^[\\w\\d\\.-]*$",
"prefix": "genedb",
"pubmed_ids": [
"14681429"
],
"uri_format": "http://www.genedb.org/gene/$1"
},
"genefarm": {
"description": "GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products.",
"example": "4892",
"homepage": "http://urgi.versailles.inra.fr/Genefarm/index.htpl",
"keywords": [
"expression",
"genome",
"nucleotide",
"sequence"
],
"name": "Structural and functional annotation of Arabidopsis thaliana gene and protein families.",
"pattern": "^\\d+$",
"prefix": "genefarm",
"pubmed_ids": [
"15608279"
],
"uri_format": "http://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1"
},
"geneloc": {
"description": "GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources",
"example": "17503",
"homepage": "http://genecards.weizmann.ac.il/geneloc/",
"keywords": [
"genome"
],
"name": "Gene Location",
"pattern": "^\\d+$",
"prefix": "geneloc",
"uri_format": "http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id=$1"
},
"genenote": {
"description": "GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E.",
"example": "GC06M052656",
"homepage": "http://genecards.weizmann.ac.il/genenote/",
"keywords": [
"gene expression"
],
"name": "Gene Normal Tissue Expression",
"pattern": "^GC\\d+$",
"prefix": "genenote",
"uri_format": "http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl?keyword_type=2_gc_id&keyword=$1&data_type=norm2&results=yes"
},
"genetree": {
"description": "Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl.",
"example": "ENSGT00550000074763",
"keywords": [
"classification",
"gene",
"protein"
],
"name": "Ensembl GeneTree",
"pattern": "^ENSGT\\d+$",
"prefix": "genetree",
"pubmed_ids": [
"16381931"
],
"uri_format": "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1"
},
"genetrees": {
"description": "This database provides an interface to databases and analysis methods designed to explore the global phylogenetic patterns of gene homology groups within and across species. GeneTrees consists of several databases of pre-compiled alignments and gene phylogenies for a variety of taxonomic groups.",
"example": "70552",
"homepage": "http://genetrees.vbi.vt.edu",
"keywords": [
"genome"
],
"name": "GeneTrees: A Phylogenomics Resource",
"pattern": "^\\d+$",
"prefix": "genetrees",
"uri_format": "http://genetrees.vbi.vt.edu/GetAlignment?al=$1"
},
"genomereviews": {
"description": "The Genome Reviews database provides an up-to-date, standardised and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes including the genomes of archaea, bacteria, bacteriophages and selected eukaryota",
"example": "34577",
"homepage": "http://www.ebi.ac.uk/GenomeReviews/",
"keywords": [
"genome"
],
"name": "Genome Reviews; an annotated view of completely sequenced genomes",
"pattern": "^\\d+$",
"prefix": "genomereviews",
"uri_format": "http://www.ebi.ac.uk/integr8/OrganismSelection.do?action=makeCurrent&proteomeId=$1"
},
"genomernai": {
"description": "The database contains phenotypes from cell-based RNA interference (RNAi) screens in Drosophila and Homo sapiens. In addition, the database provides an updated resource of RNAi reagents and their predicted quality that are available for the Drosophila and the human genome.",
"example": "394269",
"homepage": "http://rnai.dkfz.de",
"keywords": [
"RNA",
"genome"
],
"name": "GenomeRNAi",
"pattern": "^\\d+$",
"prefix": "genomernai",
"uri_format": "http://rnai.dkfz.de/GenomeRNAi/genedetails/$1"
},
"genprotec": {
"description": "GenProtEC is dedicated to the functions encoded by the Escherichia coli K-12 (strain MG1655) genome defined in the GenBank Accession No. NC_000913.2 deposit.",
"example": "b3128",
"homepage": "http://genprotec.mbl.edu",
"keywords": [
"genome"
],
"name": "GenProtEC",
"pattern": "^b\\d+$",
"prefix": "genprotec"
},
"gensat": {
"description": "The GENSAT project aims to map the expression of genes in the central nervous system of the mouse, using both in situ hybridization and transgenic mouse techniques.",
"example": "76681",
"homepage": "http://www.ncbi.nlm.nih.gov/projects/gensat/",
"keywords": [
"gene expression"
],
"name": "Gene Expression Nervous System Atlas",
"pattern": "^\\d+$",
"prefix": "gensat",
"uri_format": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gensat&cmd=retrieve&list_uids=$1"
},
"geo": {
"description": "The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval.",
"example": "GDS1234",
"homepage": "http://www.ncbi.nlm.nih.gov/geo/",
"keywords": [
"gene expression",
"genome"
],
"license": "http://www.nlm.nih.gov/copyright.html",
"name": "Gene Expression Omnibus",
"pattern": "^GDS\\d+$",
"prefix": "geo",
"pubmed_ids": [
"11752295"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=$1"
},
"giardiadb": {
"description": "A detailed study of Giardia lamblia's genome will provide insights into an early evolutionary stage of eukaryotic chromosome organization as well as other aspects of the prokaryotic / eukaryotic divergence.",
"example": "GL50803_102438",
"homepage": "http://giardiadb.org",
"keywords": [
"eukaryotic",
"genome"
],
"name": "GiardiaDB",
"pattern": "^GL\\d+_\\d+$",
"prefix": "giardiadb",
"pubmed_ids": [
"18824479"
],
"uri_format": "http://giardiadb.org/giardiadb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&primary_key=$1"
},
"gissd": {
"description": "Group I intron sequence and structure Database (GISSD) is a specialized and comprehensive database for group I introns, focusing on integrating useful group I intron information from all available databases. GISSD also wants to provide de novo data essential for understanding group I introns at a systematic level.",
"example": "319",
"homepage": "http://www.rna.whu.edu.cn/gissd",
"keywords": [
"DNA"
],
"name": "Group I intron sequence and structure Database",
"pattern": "^\\d+$",
"prefix": "gissd",
"uri_format": "http://www.rna.whu.edu.cn/perl/gissd/get_seq_exon.cgi?intron_id=$1"
},
"glycomapsdb": {
"description": "A database of GlycoMaps containing 2585 conformational maps.",
"example": "6819",
"homepage": "http://www.glycosciences.de/modeling/glycomapsdb/",
"keywords": [
"small molecule"
],
"name": "GlycoMapsDB",
"pattern": "^\\d+$",
"prefix": "glycomapsdb",
"synonyms": [
"glycomaps"
],
"uri_format": "http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=$1"
},
"glycomedb": {
"description": "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.",
"example": "1",
"homepage": "http://www.glycome-db.org/showMenu.action?major=database",
"keywords": [
"molecules",
"small molecules",
"structure"
],
"name": "GlycomeDB Carbohydrate Structure Database",
"pattern": "^\\d+$",
"prefix": "glycomedb",
"pubmed_ids": [
"19759275"
],
"uri_format": "http://www.glycome-db.org/database/showStructure.action?glycomeId=$1"
},
"gnd": {
"description": "The GPCR NaVa database describes sequence variants within the family of human G Protein-Coupled Receptors (GPCRs). GPCRs regulate many physiological functions and are the targets for most of today's medicines. The acronym NaVa stands for Natural Variant, which means any (non-artificial) variant that occurs in humans.",
"example": "1150",
"homepage": "http://nava.liacs.nl/",
"keywords": [
"protein",
"pathway"
],
"name": "GPCR Natural Variants database",
"pattern": "^\\d+$",
"prefix": "gnd",
"uri_format": "http://nava.liacs.nl/cgi-bin/nava.py?id=$1"
},
"go": {
"alt_uri_formats": [
"http://purl.org/obo/owl/GO#$1"
],
"bioportal": "1070",
"description": "The Gene Ontology project provides an ontology of defined terms representing gene product properties. The ontology covers three domains: cellular component, molecular function, and biological process.",
"example": "0006915",
"homepage": "http://www.geneontology.org/",
"keywords": [
"obo",
"gene",
"ontology"
],
"name": "The Gene Ontology",
"pattern": "^\\d{7}$",
"prefix": "go",
"pubmed_ids": [
"14681407",
"10802651"
],
"synonyms": [
"gene_ontology",
"obo.go"
],
"uri_format": "http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:$1"
},
"goa": {
"description": "The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups.",
"example": "go:0006915",
"homepage": "http://www.ebi.ac.uk/GOA",
"keywords": [
"gene",
"ontology",
"protein"
],
"name": "Gene Ontology Annotation",
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$",
"prefix": "goa",
"pubmed_ids": [
"18957448"
],
"synonyms": [
"goa-projects"
],
"uri_format": "http://www.ebi.ac.uk/QuickGO/GTerm?id=$1"
},
"gobase": {
"description": "GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts. GOBASE is currently expanding to include information on representative bacteria that are thought to be specifically related to the bacterial ancestors of mitochondria and chloroplasts",
"example": "11414850",
"homepage": "http://gobase.bcm.umontreal.ca/",
"keywords": [
"genome"
],
"name": "The Organelle Genome Database",
"pattern": "^\\d+$",
"prefix": "gobase"
},
"gold": {
"description": "GOLD: Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding complete and ongoing genome projects, as well as metagenomes and metadata, around the world.",
"example": "Gc01070",
"homepage": "http://www.genomesonline.org/",
"keywords": [
"genome"
],
"name": "Genomes Online Database",
"pattern": "^G[a-z]\\d+$",
"prefix": "gold",
"uri_format": "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1"
},
"gopad": {
"description": "The GO Partition Database was designed to feature ontology partitions with GO terms of similar specificity.The database, featuring GO partition sets for functional analysis of genes from human and ten other commonly-studied organisms with a total of 131,972 genes.",
"example": "166666",
"homepage": "http://bcl.med.harvard.edu/proj/gopart",
"keywords": [
"gene",
"ontology"
],
"name": "GO Partition Database",
"pattern": "^\\d+$",
"prefix": "gopad",
"uri_format": "http://bcl.med.harvard.edu/proteomics/proj/gopart/gopart_all_tbl_view_detail_list.php?masterkey=$1"
},
"gp": {
"description": "The NCBI Entrez Genome Project database is intended to be a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. The database is organized into organism-specific overviews that function as portals from which all projects in the database pertaining to that organism can be browsed and retrieved.",
"example": "31045",
"homepage": "http://www.ncbi.nlm.nih.gov/",
"keywords": [
"genome"
],
"name": "NCBI Genome Project Database",
"pattern": "^\\d+$",
"prefix": "gp",
"synonyms": [
"gpd"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=$1"
},
"gpcrdb": {
"description": "The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). The GPCRDB contains data on sequences, ligand binding constants and mutations. In addition, many different types of computationally derived data are stored such as multiple sequence alignments and homology models.",
"example": "RL3R1_HUMAN",
"homepage": "http://www.gpcr.org/7tm/",
"keywords": [
"small molecule",
"protein"
],
"name": "Information system for G protein-coupled receptors (GPCRs)",
"pattern": "^\\w+$",
"prefix": "gpcrdb",
"pubmed_ids": [
"21045054"
],
"uri_format": "http://www.gpcr.org/7tm/proteins/$1"
},
"gpdb": {
"description": "GpDB is a publicly accessible, relational database of G-proteins and their interactions with GPCRs and effector molecules. The sequences are classified according to a hierarchy of different classes, families and sub-families, based on extensive literature search.",
"example": "GPR0060",
"homepage": "http://bioinformatics.biol.uoa.gr/gpDB",
"keywords": [
"protein",
"small molecule"
],
"name": "gpDB: a database of GPCRs, G-proteins, Effectors and their interactions",
"pattern": "^GPR\\d+$",
"prefix": "gpdb"
},
"gpxmacrophage": {
"description": "Macrophage Expression Atlas is a database for expression profiles of macrophages challenged with a a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults.",
"example": "56",
"homepage": "http://ebola.gti.ed.ac.uk:8090/GPX/htdocs/index.html",
"keywords": [
"small molecule",
"pathway"
],
"name": "GPX-Macrophage Expression Atlas",
"pattern": "^\\d+$",
"prefix": "gpxmacrophage",
"synonyms": [
"gpxmacrophage:"
],
"uri_format": "http://gpxmea.gti.ed.ac.uk/GPX/cgi-bin/Scripts/showexperiment.cgi?HID=$1"
},
"gramene.po": {
"description": "A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part.",
"example": "GRO:0007143",
"homepage": "http://www.gramene.org/plant_ontology/",
"keywords": [
"obo",
"ontology",
"anatomy"
],
"name": "Plant Ontology",
"pattern": "^GRO:\\d+$",
"prefix": "gramene.po",
"uri_format": "http://www.gramene.org/db/ontology/search?id=$1"
},
"greengenes": {
"description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.",
"example": "100000",
"homepage": "http://greengenes.lbl.gov",
"keywords": [
"RNA"
],
"name": "Greengenes:16S rRNA gene database",
"pattern": "^\\d+$",
"prefix": "greengenes",
"pubmed_ids": [
"16820507"
],
"uri_format": "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1"
},
"greenphyldb": {
"description": "GreenPhylDB v2.0 comprises 16 full genomes from the major phylum of plant evolution. Clustering of these genomes was performed to define a consistent and extensive set of homeomorphic plant families.",
"example": "20939",
"homepage": "http://greenphyl.cirad.fr",
"keywords": [
"genome"
],
"name": "GreenPhylDB: A phylogenomic database for plant comparative genomics",
"pattern": "^\\d+$",
"prefix": "greenphyldb",
"uri_format": "http://greenphyl.cirad.fr/v2/cgi-bin/family.cgi?id=$1"
},
"greglist": {
"description": "Greglist is a database listing potential G-quadruplex regulated genes. G-rich DNA sequences can form G-quadruplexes motifs which are highly enriched in gene promoter regions in humans and other mammals. Greglist contains genes whose promoter regions have G-quadruplex motifs, and these genes are highly likely to be regulated by G-quadruplexes.",
"example": "ENSG00000166157",
"homepage": "http://tubic.tju.edu.cn/greglist/",
"keywords": [
"regulation",
"DNA"
],
"name": "Greglist",
"pattern": "^ENSG\\d+$",
"prefix": "greglist"
},
"grin": {
"description": "GRIN provides National Genetic Resources Program (NGRP) personnel and germplasm users continuous access to databases for the maintenance of passport, characterization, evaluation, inventory, and distribution data important for the effective management and utilization of national germplasm collections.",
"example": "159787",
"homepage": "http://www.ars-grin.gov/",
"name": "Germplasm Resources Information Network",
"pattern": "^\\d+$",
"prefix": "grin",
"uri_format": "http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=$1"
},
"grsdb": {
"description": "GRSDB2 is a second generation database of G-quadruplexes. Like its first version, GRSDB, it contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including that are alternatively processed (alternatively spliced or alternatively polyadenylated).",
"example": "3191",
"homepage": "http://bioinformatics.ramapo.edu/GRSDB2/",
"keywords": [
"DNA",
"RNA"
],
"name": "GRSDB",
"pattern": "^\\d+$",
"prefix": "grsdb",
"uri_format": "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1"
},
"gtop": {
"description": "GTOP is a database consisting of data analyses of proteins identified by various genome projects. This database mainly uses sequence homology analyses and features extensive utilization of information on three-dimensional structures.",
"example": "18063",
"homepage": "http://spock.genes.nig.ac.jp/~genome/gtop.html",
"keywords": [
"protein",
"structure"
],
"name": "Genomes TO Protein structures",
"pattern": "^\\d+$",
"prefix": "gtop",
"uri_format": "http://spock.genes.nig.ac.jp/~genome/cgi-bin/mas.pl.cgi?org=[?species]&gene=$1"
},
"gxa": {
"description": "The Gene Expression Atlas is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples.",
"example": "ENSMUSG00000030717",
"homepage": "http://www.ebi.ac.uk/gxa/",
"keywords": [
"gene expression"
],
"name": "Gene Expression Atlas",
"pattern": "^ENS[A-Z]+\\d+$",
"prefix": "gxa",
"uri_format": "http://www.ebi.ac.uk/gxa/gene/$1"
},
"hagr": {
"description": "The Human Ageing Genomic Resources (HAGR) is a collection of databases and tools designed to help researchers understand the genetics of human ageing through a combination of functional genomics and evolutionary biology.",
"example": "GSTA1",
"homepage": "http://genomics.senescence.info/",
"keywords": [
"genome"
],
"name": "Human Ageing Genomic Resources",
"pattern": "^[A-Z]+/\\d+$",
"prefix": "hagr",
"uri_format": "http://genomics.senescence.info/genes/entry.php?hgnc=$1"
},
"hamap": {
"description": "HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.",
"example": "MF_00323",
"homepage": "http://us.expasy.org/sprot/hamap/",
"keywords": [
"protein"
],
"name": "HAMAP database of microbial protein families",
"pattern": "^MF_\\d+$",
"prefix": "hamap",
"uri_format": "http://us.expasy.org/unirule/$1"
},
"hbvar": {
"description": "This is a relational database of information about hemoglobin variants and mutations that cause thalassemia.",
"example": "2526",
"homepage": "http://globin.cse.psu.edu/globin/hbvar",
"keywords": [
"protein"
],
"name": "A Database of Human Hemoglobin Variants and Thalassemias",
"pattern": "^\\d+$",
"prefix": "hbvar",
"uri_format": "http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=$1"
},
"hc": {
"bioportal": "1020",
"description": "An ontology for courtship behavior of the spider Habronattus californicus.",
"example": "Locomotion",
"homepage": "http://www.mesquiteproject.org/ontology/Habronattus/index.html",
"keywords": [
"anatomy",
"evidence",
"spider"
],
"name": "Habronattus courtship",
"pattern": "^\\w+$",
"prefix": "hc",
"uri_format": "http://www.mesquiteproject.org/ontology/Habronattus/$1.html"
},
"hcdpd": {
"description": "The Health Canada Drug Product Database contains product specific information on drugs approved for use in Canada. The database is managed by Health Canada and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. It contains approximately 15,000 products which companies have notified Health Canada as being marketed.",
"example": "63250",
"homepage": "http://www.hc-sc.gc.ca/dhp-mps/prodpharma/databasdon/index-eng.php",
"keywords": [
"drug"
],
"name": "Health Canada Drug Product Database",
"pattern": "^\\d+$",
"prefix": "hcdpd"
},
"hcnet": {
"description": "Heart and Calcium functional Network (HCNet) is a specialized database for mouse heart and calcium signaling toolkit genes. It contains the functional gene modules pre-calculated from the microarray data compendium using various algorithms for genetic network analyses.",
"example": "Mm.686",
"homepage": "http://sbrg2.gist.ac.kr/hcnet/",
"keywords": [
"gene expression"
],
"name": "Heart and Calcium Functional Network Database",
"pattern": "^Mm.\\d+$",
"prefix": "hcnet",
"uri_format": "http://sbrg2.gist.ac.kr/hcnet/ver1.1/php/showDetailGeneInfo.php?unigeneID=$1"
},
"hcpin": {
"description": "The HCPIN Website provides a comprehensive description of this biomedically important multipathway network together with experimental and homology models of HCPIN proteins useful for cancer biology research.",
"example": "132",
"homepage": "http://nesg.org:9090/HCPIN/",
"keywords": [
"pathway",
"protein"
],
"name": "Human Cancer Protein Interaction Network",
"pattern": "^\\d+$",
"prefix": "hcpin",
"uri_format": "http://nesg.org:9090/HCPIN/NShowProteinInfor.jsp?protein_id=$1"
},
"hcv": {
"description": "The HCV database group strives to present HCV-associated, hand-annotated genetic data in a userfriendly way, by providing access to the central database via web-accessible search interfaces and supplying a number of analysis tools.",
"example": "71867",
"homepage": "http://hcv.lanl.gov/",
"keywords": [
"gene"
],
"name": "Hepatitis C Virus (HCV) Database Project",
"pattern": "^\\d+$",
"prefix": "hcv",
"synonyms": [
"hcv_database"
],
"uri_format": "http://hcv.lanl.gov/components/sequence/HCV/asearch/query_one.comp?se_id=$1"
},
"hdbas": {
"description": "H-DBAS offers unique data and viewer for human Alternative Splicing (AS) analysis including genome-wide representative alternative splicing variants (RASVs), RASVs affecting protein functions, conserved RASVs compared with mouse genome (full length cDNAs).",
"example": "HIX0000013",
"homepage": "http://jbirc.jbic.or.jp/h-dbas/",
"keywords": [
"protein",
"genome"
],
"name": "Human-Transcriptome Database for Alternative Splicing",
"pattern": "^HIX\\d+$",
"prefix": "hdbas",
"uri_format": "http://jbirc.jbic.or.jp/h-dbas/locusOverview.do?db=all&hix=$1"
},
"hdbase": {
"description": "The purpose of HDBase is to collect and present information that wil assist Huntington's Disease researchers in their work including therapeutic studies (in mice), HD mouse models focussing on disease progression timelines, antibodies used, microarray gene expression studies, relevant genes and proteins, as well as molecular pathways thought to be involved in the disease process.",
"example": "5978",
"homepage": "http://hdbase.org/",
"name": "Huntington's Disease Database",
"pattern": "^\\d+$",
"prefix": "hdbase",
"uri_format": "http://hdbase.org/cgi-bin/jdrf_gene.cgi?ll_id=$1"
},
"hdr": {
"description": "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic, and functional information on the homeodomain family. A description of each of the major sections of the database can be found below, and users can navigate through the site using the links found in the menu that appears on the left-hand side of every page within the site.",
"example": "5978",
"homepage": "http://research.nhgri.nih.gov/homeodomain/",
"keywords": [
"genome"
],
"name": "Homeodomain Resource Database",
"pattern": "^\\d+$",
"prefix": "hdr",
"synonyms": [
"homeodb"
],
"uri_format": "http://research.nhgri.nih.gov/homeodomain/?mode=view&view=proteins&id=$1"
},
"hedgehog": {
"description": "This extensively annotated database collects information associated with the Hedgehog signaling pathway. Pathway model diagrams, lists of genes involved in the pathway, expression in tissues and mutations involved in disease. Listings of reagents and other community resources are available.",
"example": "79",
"homepage": "http://hedgehog.sfsu.edu/",
"keywords": [
"pathway",
"gene"
],
"name": "Hedgehog Signaling Pathway Database",
"pattern": "^\\d+$",
"prefix": "hedgehog",
"uri_format": "http://hedgehog.sfsu.edu/genes/$1.html"
},
"hembase": {
"description": "Based on the mapping of the human genome and the development of information databases, a broad description of genes transcribed in blood cells is now known. Hembase was developed to provide worldwide access to those genetic-based studies performed by scientists in the Molecular Biology and Genetics Section, Molecular Medicine Branch, Division of Intramural Research, National Institute of Diabetes and Digestive and Kidney Diseases",
"example": "8p21",
"homepage": "http://hembase.niddk.nih.gov/",
"keywords": [
"gene"
],
"name": "HemBase",
"pattern": "^\\dp\\d+$",
"prefix": "hembase",
"uri_format": "http://fmp-8.cit.nih.gov/hembase/detail.php?chrb=$1"
},
"hgnc": {
"bioportal": "1528",
"description": "The HGNC gives unique and meaningful names to every human gene. For each known human gene we approve a gene name and symbol (short-form abbreviation). All approved symbols are stored in the HGNC database.",
"example": "7",
"homepage": "http://www.genenames.org/",
"keywords": [
"classification",
"gene"
],
"name": "HUGO Gene Nomenclature Committee",
"pattern": "^\\d+$",
"prefix": "hgnc",
"synonyms": [
"hugo"
],
"uri_format": "http://www.genenames.org/data/hgnc_data.php?hgnc_id=$1"
},
"hgvbase": {
"description": "HGVbase was set up in an effort to improve analysis of common human genetic polymorphism by maintaining a high-quality database of all publicly available genomic variation data (primarily SNPs). Currently maintained by an academic European consortium it contains close to 2 million non-redundant entries. Data is harvested from three main areas, (i) collaboration with other variation databases, (ii) extraction from scientific literature and (iii) submissions from various research groups.",
"example": "HGVST315",
"homepage": "http://hgvbase.cgb.ki.se",
"keywords": [
"gene",
"genome"
],
"name": "Human Genome Variation Database: Genotype-to-Phenotype",
"pattern": "^HGVST\\d+$",
"prefix": "hgvbase",
"uri_format": "http://www.hgvbaseg2p.org/study/$1"
},
"histone_database": {
"description": "The Histone Database is a curated and searchable collection of full-length sequences and structures of histones and nonhistone proteins containing histone-like folds, compiled from major public databases.",
"example": "102146",
"homepage": "http://research.nhgri.nih.gov/histones/",
"keywords": [
"protein"
],
"name": "Histone Sequence Database: Histone Fold Proteins",
"pattern": "^\\d+$",
"prefix": "histone_database"
},
"hivmid": {
"description": "The HIV Molecular Immunology Database is an annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites.",
"example": "14",
"homepage": "http://hiv-web.lanl.gov/immunology/",
"keywords": [
"protein"
],
"name": "HIV Molecular Immunology Database",
"pattern": "^\\d+$",
"prefix": "hivmid"
},
"hmdb": {
"description": "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.",
"example": "HMDB00001",
"homepage": "http://www.hmdb.ca",
"keywords": [
"chemical",
"human",
"metabolite"
],
"license": "http://www.hmdb.ca/about#cite",
"name": "The Human Metabolome Database",
"pattern": "^HMDB\\d{5}$",
"prefix": "hmdb",
"pubmed_ids": [
"17202168"
],
"uri_format": "http://www.hmdb.ca/metabolites/$1"
},
"hmp": {
"description": "The HMP was launched by the National Institutes of Health Roadmap for Medical Research and is designed to fuel research into the multitude of microbes that live in the various environments of the human body.",
"example": "0010",
"homepage": "http://www.hmpdacc.org/",
"keywords": [
"small molecule"
],
"name": "Human Microbiome Project",
"pattern": "^\\d+$",
"prefix": "hmp",
"uri_format": "http://www.hmpdacc-resources.org/cgi-bin/hmp_catalog/main.cgi?section=HmpSummary&page=displayHmpProject&hmp_id=$1"
},
"hogenom": {
"description": "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.",
"example": "HBG284870",
"homepage": "http://pbil.univ-lyon1.fr/databases/hogenom.php",
"keywords": [
"classification",
"sequence"
],
"name": "The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms",
"pattern": "^\\w+$",
"prefix": "hogenom",
"pubmed_ids": [
"19534752"
],
"uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1"
},
"homd": {
"description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information.",
"example": "504",
"homepage": "http://www.homd.org/",
"keywords": [
"classification"
],
"name": "Human Oral Microbiome Database",
"pattern": "^\\d+$",
"prefix": "homd",
"uri_format": "http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$1&view=dynamic"
},
"homd.seq": {
"description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.",
"example": "SEQF1003",
"keywords": [
"genome",
"microbial"
],
"name": "HOMD Sequence Metainformation",
"pattern": "^SEQF\\d+$",
"prefix": "homd.seq",
"pubmed_ids": [
"20624719"
],
"uri_format": "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1"
},
"homd.taxon": {
"description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.",
"example": "811",
"keywords": [
"microbial",
"taxonomy"
],
"name": "HOMD Taxonomy",
"pattern": "^\\d+$",
"prefix": "homd.taxon",
"pubmed_ids": [
"20624719"
],
"uri_format": "http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$1&view=dynamic"
},
"homeodomain_resource": {
"description": "The Homeodomain Resource is an annotated collection of non-redundant protein sequences, three-dimensional structures, and genomic information for the homeodomain protein family. Release 3.0 contains 795 full-length homeodomain-containing sequences, 32 experimentally derived structures, and 143 homeobox loci implicated in human genetic disorders.",
"example": "479",
"homepage": "http://research.nhgri.nih.gov/homeodomain/",
"keywords": [
"protein",
"structure",
"genome"
],
"name": "Homeodomain Resource Database",
"pattern": "^\\d+$",
"prefix": "homeodomain_resource",
"uri_format": "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1"
},
"homologene": {
"description": "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.",
"example": "1000",
"homepage": "http://wwww.ncbi.nlm.nih.gov/homologene",
"keywords": [
"gene",
"genome"
],
"name": "NCBI Homologene",
"pattern": "^\\d+$",
"prefix": "homologene",
"pubmed_ids": [
"21097890"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/homologene/$1"
},
"homstrad": {
"description": "HOMSTRAD is a curated database of structure-based alignments for homologous protein families. All known protein structure are clustered into homologous families (i.e., common ancestry), and the sequences of representative members of each family are aligned on the basis of their 3D structures using the programs MNYFIT, STAMP and COMPARER.",
"example": "1bnca",
"homepage": "http://www-cryst.bioc.cam.ac.uk/homstrad",
"keywords": [
"protein",
"structure"
],
"name": "Homologous Structure Alignment Database",
"pattern": "^PDBID$",
"prefix": "homstrad",
"uri_format": "http://tardis.nibio.go.jp/cgi-bin/homstrad/getdata.cgi?id=$1"
},
"horde": {
"description": "HORDE (The Human Olfactory Data Explorer) is a database of human Olfactory Receptors (ORs), the largest multigene family in multicellular organisms. The database gives information on the OR proteins, their gene structure and their genomic organization. Also available are OR repertoires of other mammalian species.",
"example": "OR1E1",
"homepage": "http://bioportal.weizmann.ac.il/HORDE/",
"keywords": [
"gene",
"protein",
"structure"
],
"name": "Human Olfactory Receptor Data Exploratorium",
"pattern": "^[A-Z]+/\\d+$",
"prefix": "horde",
"uri_format": "http://genome.weizmann.ac.il/cgi-bin/horde/showGene.pl?symbol=$1"
},
"hotsprint": {
"description": "Hotsprint gives information about the evolutionary history of the residues on the interface and represents which residues are highly conserved on the interface. In this way, functionally and structurally important residues on the interface can be distinguished.",
"example": "1yp2A",
"homepage": "http://prism.ccbb.ku.edu.tr/hotsprint/",
"keywords": [
"protein"
],
"name": "Database of Computational Hot Spots in Protein Interfaces",
"pattern": "^PDBID$",
"prefix": "hotsprint",
"uri_format": "http://prism.ccbb.ku.edu.tr/hotsprint/result.php?queryId=$1"
},
"hovergen": {
"description": "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.",
"example": "HBG004341",
"homepage": "http://pbil.univ-lyon1.fr/databases/hovergen.html",
"keywords": [
"gene",
"DNA",
"protein"
],
"license": "http://pbil.univ-lyon1.fr/databases/hovergen.php",
"name": "HOVERGEN: Homologous Vertebrate Genes Database",
"pattern": "^HBG\\d+$",
"prefix": "hovergen",
"pubmed_ids": [
"15713731"
],
"uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN"
},
"howdy": {
"description": "HOWDY is an integrated database system for accessing and analyzing human genomic information. HOWDY stores information about relationships between genetic objects and the data extracted from a number of databases. Linear maps displaying markers and genes on contig sequences are available, from which an object can be chosen. Any search starting point identifies all the information matching the query.",
"example": "ab027466",
"homepage": "http://www-alis.tokyo.jst.go.jp/HOWDY/",
"keywords": [
"genome",
"gene"
],
"name": "Human Organized Whole Genome Database",
"pattern": "^[A-Z]+\\d+$",
"prefix": "howdy",
"uri_format": "http://howdy.jst.go.jp/HOWDYCL/HOWDY.pl?Cls=GenBank&Key=UKEY&Val=$1"
},
"hpa": {
"description": "The Human Protein Atlas (HPA) portal is a publicly available database with millions of high-resolution images showing the spatial distribution of proteins in 48 different normal tissues and 20 different cancer types as well as 47 different human cell lines.",
"example": "ENSG00000026508",
"homepage": "http://www.proteinatlas.org/",
"keywords": [
"protein",
"structure"
],
"name": "Human Protein Atlas",
"pattern": "^ENSG\\d{11}$",
"prefix": "hpa",
"pubmed_ids": [
"18669619"
],
"uri_format": "http://www.proteinatlas.org/gene_info.php?ensembl_gene_id=$1"
},
"hpmr": {
"description": "Plasma membrane protein sequences, literature, and expression database",
"example": "14",
"homepage": "http://www.receptome.org/HPMR/",
"keywords": [
"protein"
],
"name": "Human Plasma Membrane Receptome",
"pattern": "^\\d+$",
"prefix": "hpmr",
"uri_format": "http://www.receptome.org/HPMR/Families/Frameset_family.asp?FamId=$1"
},
"hprd": {
"description": "The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.",
"example": "00001",
"homepage": "http://www.hprd.org/",
"keywords": [
"protein",
"structure"
],
"name": "Human Protein Reference Database",
"pattern": "^\\d+$",
"prefix": "hprd",
"pubmed_ids": [
"18988627"
]
},
"hssp": {
"description": "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.",
"example": "102l",
"homepage": "http://www.cmbi.kun.nl/gv/hssp/",
"keywords": [
"clustering",
"protein",
"sequence"
],
"name": "Homology-derived secondary structure of proteins database",
"pattern": "^\\w{4}$",
"prefix": "hssp",
"pubmed_ids": [
"7937066",
"8594579"
]
},
"hubmed": {
"description": "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.",
"example": "16333295",
"homepage": "http://www.hubmed.org/",
"license": "http://www.nlm.nih.gov/copyright.html",
"name": "HubMed",
"pattern": "^\\d+$",
"prefix": "hubmed",
"uri_format": "http://www.hubmed.org/display.cgi?uids=$1"
},
"huge": {
"description": "HUGE is a database for human large proteins newly identified in the Kazusa cDNA project, the aim of which is to predict the primary structure of proteins from the sequences of human large cDNAs (>4 kb).",
"example": "KIAA0001",
"homepage": "http://www.kazusa.or.jp/huge/",
"keywords": [
"protein",
"DNA",
"structure"
],
"name": "Human Unidentified Gene-Encoded large proteins database",
"pattern": "^KIAA\\d{4}$",
"prefix": "huge",
"pubmed_ids": [
"14681467"
],
"uri_format": "http://www.kazusa.or.jp/huge/cgi/view_direct.cgi?id=$1"
},
"hupi": {
"description": "A survey of soluble human protein complexes containing components of the transcription and RNA processing machineries using protein affinity purification coupled to mass spectrometry.",
"example": "BRCA1",
"homepage": "http://hupi.ircm.qc.ca/hupi/index.jsp",
"keywords": [
"protein",
"RNA"
],
"name": "Database of the Human Proteotheque Initiative",
"pattern": "^[A-Z]+/\\d+$",
"prefix": "hupi",
"uri_format": "http://hupi.ircm.qc.ca/hupi/gene/$1"
},
"icbs": {
"description": "The Inter-Chain Beta-Sheet (ICBS) database identifies and characterizes all inter-chain beta-sheet interactions. The ICBS database is intended as a tool to further the study of \u00df-sheet protein-protein interactions, to identify new ICBS interactions as new structures are deposited and as old structures are revised in the Protein Data Bank, and to help select targets for drug design.",
"example": "1bdg",
"homepage": "http://www.igb.uci.edu/servers/icbs/",
"keywords": [
"protein",
"interaction",
"structure"
],
"name": "Inter-Chain Beta-Sheets",
"pattern": "^PDBID$",
"prefix": "icbs",
"uri_format": "http://contact14.ics.uci.edu/htmlfiles/$1.mmol.html"
},
"icd": {
"description": "The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes.",
"example": "C34",
"homepage": "http://www.who.int/classifications/icd/en/",
"keywords": [
"disease",
"taxonomy",
"classification"
],
"license": "http://www.who.int/about/copyright/en/index.html",
"name": "International Classification of Diseases",
"pattern": "^[A-Z]\\d+(\\.[-\\d+])?$",
"prefix": "icd",
"uri_format": "http://apps.who.int/classifications/icd10/browse/2010/en#/$1"
},
"icdo": {
"bioportal": "1670",
"description": "Ontology of Oncology as based on CDC SEER's ICDO-3 Code classification",
"example": "M-8272/O",
"name": "International Classification of Diseases for Oncology",
"pattern": "^[A-Z0-9]+\\/[0-9]+$",
"prefix": "icdo",
"synonyms": [
"icdo3",
"icd-o"
]
},
"icds": {
"description": "ICDS database is a database containing ICDS detected by a similarity-based approach. The definition of each interrupted gene is provided as well as the ICDS genomic localisation with the surrounding sequence.",
"example": "ICDS0023",
"homepage": "http://www-bio3d-igbmc.u-strasbg.fr/ICDS/",
"keywords": [
"gene"
],
"name": "Interrupted coding sequences",
"pattern": "^ICDS\\d+$",
"prefix": "icds",
"synonyms": [
"ics"
],
"uri_format": "http://www-bio3d-igbmc.u-strasbg.fr/ICDS/cgi-bin/gscope_html_server.tcsh?ICDS&PagesWeb&GvioManu&UnICDS&$1"
},
"idbd": {
"description": "IDBD provides links to global news, and life science journal search engines. The site also provides links to tool functions for gene sequence and protein structure analyses. It serves basic information on infection diseases and their causative agents.",
"example": "24",
"homepage": "http://biomarker.korea.ac.kr",
"keywords": [
"gene",
"DNA",
"protein",
"structure"
],
"name": "Infectious Disease Biomarker Database",
"pattern": "^\\d+$",
"prefix": "idbd",
"uri_format": "http://biomarker.korea.ac.kr/disease/disease_view_en.jsp?group=1&id=$1"
},
"iev": {
"bioportal": "1011",
"description": "The Event Ontology is an ontology of pathways. It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure.",
"example": "IEV_0000913",
"homepage": "http://www.inoh.org",
"keywords": [
"obo",
"pathway",
"structure"
],
"name": "Event (INOH pathway ontology)",
"pattern": "^IEV_\\d+$",
"prefix": "iev",
"uri_format": "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IEV&id=$1"
},
"igtcd": {
"description": "The International Gene Trap Consortium (IGTC) represents all publicly available gene trap cell lines, which are available on a non-collaborative basis for nominal handling fees. Researchers can search and browse the IGTC database for cell lines of interest using accession numbers or IDs, keywords, sequence data, tissue expression profiles and biological pathways.",
"example": "12056",
"homepage": "http://www.genetrap.org/",
"keywords": [
"gene"
],
"name": "International Gene Trap Consortium Database",
"pattern": "^\\d+$",
"prefix": "igtcd",
"uri_format": "http://www.genetrap.org/cgi-bin/annotation.py?gene_key=$1"
},
"ihop": {
"description": "By using genes and proteins as hyperlinks between sentences and abstracts, ihop converts the information in PubMed into one navigable resource and bring all the advantages of the internet to scientific literature investigation.",
"example": "32484",
"homepage": "http://www.ihop-net.org/UniPub/iHOP/",
"name": "Information Hyperlinked Over Proteins",
"pattern": "^\\d+$",
"prefix": "ihop",
"uri_format": "http://www.ihop-net.org/UniPub/iHOP/gs/$1.html"
},
"il2rgbase": {
"description": "X-linked severe combined immunodeficiency (XSCID or X-SCID) is an immune disorder caused by mutations in the X-linked gene IL2RG, which encodes the common gamma chain (c) of the lymphocyte receptors for interleukin-2 (IL-2) and many other cytokines. A database of human XSCID mutations (IL2RGbase) has been assembled. Information on new mutations may be submitted online.",
"example": "14",
"homepage": "http://research.nhgri.nih.gov/scid/",
"keywords": [
"gene",
"DNA",
"RNA"
],
"name": "X-linked SCID mutation database (IL2RGbase)",
"pattern": "^\\d+$",
"prefix": "il2rgbase",
"uri_format": "http://research.nhgri.nih.gov/apps/scid/scid_reference.html#$1"
},
"imex": {
"description": "The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources.",
"example": "IM-12080-80",
"homepage": "http://disber.net/imexdrupal/",
"keywords": [
"molecule",
"interaction"
],
"license": "http://disber.net/imexdrupal/node/5",
"name": "International Molecular Exchange",
"pattern": "^IM-\\d+(-?)(\\d+?)$",
"prefix": "imex",
"pubmed_ids": [
"17893861"
],
"uri_format": "http://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1"
},
"img.gene": {
"description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information.",
"example": "638309541",
"keywords": [
"gene",
"genome"
],
"name": "Integrated Microbial Genomes Gene",
"pattern": "^\\d+$",
"prefix": "img.gene",
"pubmed_ids": [
"17933782"
],
"uri_format": "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1"
},
"img.taxon": {
"description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information.",
"example": "648028003",
"keywords": [
"genome",
"taxonomy"
],
"name": "Integrated Microbial Genomes Taxon",
"pattern": "^\\d+$",
"prefix": "img.taxon",
"pubmed_ids": [
"17933782"
],
"uri_format": "http://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&taxon_oid=$1"
},
"imgt.3dstructuredb": {
"description": "IMGT/3Dstructure-DB and IMGT/Structural-Query are a novel 3D structure database and a new tool for immunological proteins.",
"example": "1UQS",
"homepage": "http://imgt.cines.fr/3Dstructure-DB/",
"keywords": [
"structure",
"protein"
],
"name": "IMGT/3Dstructure-DB",
"pattern": "^PDBID$",
"prefix": "imgt.3dstructuredb",
"uri_format": "http://imgt.cines.fr/3Dstructure-DB/cgi/details.cgi?pdbcode=$1"
},
"imgt.ligm": {
"description": "MGT/LIGM-DB is the IMGT comprehensive database of immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and other vertebrate species.",
"example": "A68511",
"homepage": "http://imgt.cines.fr/cgi-bin/IMGTlect.jv",
"keywords": [
"DNA"
],
"name": "IMGT/LIGM-DB",
"pattern": "^[A-Z]\\d+$",
"prefix": "imgt.ligm",
"pubmed_ids": [
"16381979"
],
"synonyms": [
"imgt_ligmdb"
]
},
"imgt.primerdb": {
"description": "The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR).",
"example": "IPP900099",
"homepage": "http://imgt.org/IMGTPrimerDB/",
"keywords": [
"DNA"
],
"name": "IMGT/PRIMER-DB",
"pattern": "^IPP\\d+$",
"prefix": "imgt.primerdb",
"uri_format": "http://imgt.org/IMGTPrimerDB/Check_PrDB.pl?numacc0=$1&origin=view&source=PrList"
},
"imgthla": {
"description": "The IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO Nomenclature Committee For Factors of the HLA System.",
"example": "A*01:01:01:01",
"homepage": "http://www.ebi.ac.uk/imgt/hla/",
"keywords": [
"DNA",
"RNA",
"protein"
],
"name": "IMGT/HLA",
"pattern": "^[A-Z0-9*:]+$",
"prefix": "imgthla",
"pubmed_ids": [
"16381979"
],
"uri_format": "http://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele.cgi?"
},
"imotdb": {
"description": "The interacting motif database or iMOTdb , lists interacting motifs thatare identified for all structural entries in the PDB. The conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting the common motifs shared among all superfamily members.",
"example": "53784",
"homepage": "http://caps.ncbs.res.in/imotdb/",
"keywords": [
"interaction",
"protein"
],
"name": "Database of Spatially Interacting Motifs in Proteins",
"pattern": "^\\d+$",
"prefix": "imotdb",
"uri_format": "http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode=$1"
},
"imr": {
"bioportal": "1029",
"description": "MoleculeRole Ontology is an ontology for proteins/chemicals. It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data.",
"example": "IMR_0800118",
"homepage": "http://www.inoh.org",
"keywords": [
"ontology",
"protein",
"small molecule"
],
"name": "MoleculeRole Ontology (INOH Protein name/family name ontology)",
"pattern": "^IMR_\\d+$",
"prefix": "imr",
"synonyms": [
"molecule_role"
],
"uri_format": "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id=$1"
},
"innatedb": {
"description": "InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans and mice to microbial infection. The database covers the innate immunity interactome by integrating known interactions and pathways from major public databases.",
"example": "20021",
"homepage": "http://www.innatedb.ca/",
"keywords": [
"gene",
"protein",
"interaction",
"pathway"
],
"name": "A Knowledge Resource for Innate Immunity Interactions and Pathways",
"pattern": "^\\d+$",
"prefix": "innatedb",
"uri_format": "http://www.innatedb.ca/getGeneCard.do?id=$1"
},
"insdc": {
"description": "The International Nucleotide Sequence Databases (INSD) have been developed and maintained collaboratively between DDBJ, EMBL, and GenBank for over 18 years.",
"example": "X58356",
"homepage": "http://www.insdc.org/",
"keywords": [
"DNA"
],
"name": "International Nucleotide Sequence Database Collaboration (GenBank, EMBL, DDBJ)",
"pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$",
"prefix": "insdc",
"pubmed_ids": [
"17148479",
"17202161",
"2326192",
"12436968"
],
"synonyms": [
"ddbj/embl/genbank",
"insd"
]
},
"insrd": {
"description": "insecticide resistance in mosquitos",
"example": "13890",
"homepage": "http://www.anobase.org/ir/",
"name": "Insecticide Resistance Database",
"pattern": "^\\d+$",
"prefix": "insrd",
"uri_format": "http://anobase.vectorbase.org/ir/assay.php?id=$1"
},
"intact": {
"description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.",
"example": "EBI-2307691",
"homepage": "http://www.ebi.ac.uk/intact",
"keywords": [
"protein",
"interaction"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "The IntAct molecular interaction database",
"pattern": "^EBI\\-\\d+$",
"prefix": "intact",
"pubmed_ids": [
"14681455"
],
"uri_format": "http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$1"
},
"integr8": {
"description": "The Integr8 web portal provides easy access to integrated information about deciphered genomes and their corresponding proteomes. Available data includes DNA sequences; protein sequences; statistical genome and proteome analysis; and information about orthology, paralogy, and synteny.",
"example": "30910",
"homepage": "http://www.ebi.ac.uk/integr8/",
"keywords": [
"genome",
"DNA",
"protein"
],
"name": "Integr8 (formerly Proteome Analysis Database)",
"pattern": "^\\d+$",
"prefix": "integr8",
"uri_format": "http://www.ebi.ac.uk/integr8/OrganismSelection.do?action=makeCurrent&proteomeId=$1"
},
"intenz": {
"description": "IntEnz is a freely available resource focused on enzyme nomenclature. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions.",
"example": "17854",
"homepage": "http://www.ebi.ac.uk/intenz",
"keywords": [
"classification",
"enzyme"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Integrated relational Enzyme database",
"pattern": "^\\d+$",
"prefix": "intenz",
"uri_format": "http://www.ebi.ac.uk/intenz/query?cmd=SearchID&id=$1"
},
"interdom": {
"description": "InterDom is a database of putative interacting protein domains derived from multiple sources, ranging from domain fusions (Rosetta Stone), protein interactions (DIP and BIND), protein complexes (PDB), to scientific literature (MEDLINE).",
"example": "PF00239",
"homepage": "http://interdom.i2r.a-star.edu.sg/",
"keywords": [
"protein",
"structure",
"interaction"
],
"name": "InterDom; protein domain interactions",
"pattern": "^PF\\d+$",
"prefix": "interdom"
},
"interferome": {
"description": "Interferome is a database of IFN regulated genes including Type I, II and III IFN regulated genes manually curated from more than 28 publicly available microarray datasets. Availability of sequence information from more than 37 species, together with comprehensive annotation will enable comparative genomics and phylogenetic analysis to be performed on these IRGs.",
"example": "ENSG00000187608",
"homepage": "http://www.interferome.org",
"keywords": [
"gene",
"regulation",
"gene expression",
"DNA",
"genome"
],
"name": "Interferome",
"pattern": "^ENSG\\d+$",
"prefix": "interferome"
},
"interfil": {
"description": "The Intermediate Filament Database functions as a continuously updated review of the intermediate filament field and it is hoped that users will contribute to the development and expansion of the database on a regular basis. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants.",
"example": "NM_006262",
"homepage": "http://www.interfil.org",
"keywords": [
"genome"
],
"name": "Human Intermediate Filament Database",
"pattern": "^N[A-Z]_\\d+$",
"prefix": "interfil",
"synonyms": [
"intermediate_filament_db"
],
"uri_format": "http://www.interfil.org/details.php?id=$1"
},
"interpare": {
"description": "InterPare is a database server for protein interaction interface information. It contains large-scale interface data of proteins whose 3D-structures are known. Protein interface information is derived from three different methods.",
"example": "1a9u",
"homepage": "http://interpare.kobic.re.kr/index.html",
"keywords": [
"interaction",
"protein",
"structure"
],
"name": "The Protein Interfaceome Database",
"pattern": "^PDBID$",
"prefix": "interpare",
"uri_format": "http://interpare.kobic.re.kr/cgi-bin/search_interface_from_interpare_new.cgi?pdb=$1"
},
"interpro": {
"description": "InterPro is an integrated database of predictive protein \"signatures\" used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites.",
"example": "IPR000100",
"homepage": "http://www.ebi.ac.uk/interpro",
"keywords": [
"domain",
"protein"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Integrated resource of protein families, domains and functional sites",
"pattern": "^IPR\\d{6}$",
"prefix": "interpro",
"pubmed_ids": [
"15608177"
],
"synonyms": [
"ipr"
],
"uri_format": "http://www.ebi.ac.uk/interpro/IEntry?ac=$1"
},
"ipath": {
"description": "LINNEA Pathways is based on a total of 248 signaling and metabolic human biological pathway maps created for Invitrogen\u2122 by GeneGo.",
"example": "408",
"homepage": "http://escience.invitrogen.com/ipath/",
"keywords": [
"pathway"
],
"name": "Linnea Pathways",
"pattern": "^\\d+$",
"prefix": "ipath",
"uri_format": "http://escience.invitrogen.com/ipath/iPath.jsp?cn=unknown&mapid=$1"
},
"ipdestdab": {
"description": "The European Searchable Tumour Line Database (ESTDAB) Database and Cell Bank provide a service enabling investigators to search online for HLA typed, immunologically characterised tumour cells.",
"example": "ESTDAB-136",
"homepage": "http://www.ebi.ac.uk/ipd/estdab/",
"keywords": [
"small molecule",
"gene",
"DNA"
],
"name": "The European Searchable Tumour Line Database",
"pattern": "^ESTDAB-\\d+$",
"prefix": "ipdestdab",
"uri_format": "http://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?$1"
},
"ipfam": {
"description": "iPfam is a resource that describes physical interactions between those Pfam domains that have a representative structure in the Protein DataBank (PDB).",
"example": "PF02749",
"homepage": "http://ipfam.sanger.ac.uk/",
"keywords": [
"interaction",
"protein",
"structure"
],
"name": "iPfam: the Protein Domain Interactions Database",
"pattern": "^[CL/PF]\\d+$",
"prefix": "ipfam",
"uri_format": "http://pfam.sanger.ac.uk/[family/clan]?acc=$1"
},
"ipi": {
"description": "IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI maintaisn a database of cross references between the primary data sources, it provides minimally redundant but complete sets of proteins for featured species, and it maintains stable and unique identifiers.",
"example": "IPI00000001",
"homepage": "http://www.ebi.ac.uk/IPI",
"keywords": [
"protein"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "International Protein Index",
"pattern": "^IPI\\d{8}$",
"prefix": "ipi",
"pubmed_ids": [
"15221759"
],
"uri_format": "http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$1&format=default"
},
"iproclass": {
"description": "The iProClass database provides value-added information reports for UniProtKB and unique UniParc proteins, with links to over 90 biological databases, including databases for protein families, functions and pathways, interactions, structures and structural classifications, genes and genomes, ontologies, literature, and taxonomy.",
"example": "P69380",
"homepage": "http://pir.georgetown.edu/iproclass/",
"keywords": [
"protein",
"pathway",
"interaction",
"structure",
"classification",
"gene",
"genome",
"ontology"
],
"name": "Integrated Protein Knowledgebase",
"pattern": "^[A-Z]\\d+$",
"prefix": "iproclass",
"uri_format": "http://pir.georgetown.edu/cgi-bin/ipcEntry?id=$1"
},
"ird.segment": {
"description": "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s).",
"example": "CY077097",
"keywords": [
"gene",
"protein"
],
"name": "IRD Segment Sequence",
"pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$",
"prefix": "ird.segment",
"pubmed_ids": [
"17965094"
],
"uri_format": "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1"
},
"irefweb": {
"description": "iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID.",
"example": "617102",
"homepage": "http://wodaklab.org/iRefWeb/",
"keywords": [
"interaction",
"protein"
],
"name": "Interaction Reference Index Web Interface",
"pattern": "^\\d+$",
"prefix": "irefweb",
"uri_format": "http://wodaklab.org/iRefWeb/interaction/show/$1"
},
"iresite": {
"description": "The IRESite database presents information about the experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure.",
"example": "322",
"homepage": "http://www.iresite.org",
"keywords": [
"RNA",
"regulation"
],
"name": "IRESite: The database of experimentally verified IRES structures",
"pattern": "^\\d+$",
"prefix": "iresite",
"uri_format": "http://www.iresite.org/IRESite_web.php?page=view&entry_id=$1"
},
"iris": {
"description": "IRIS is the rice implementation of the International Crop Information System (ICIS) which is a database system that provides integrated management of global information on genetic resources and crop cultivars. This includes germplasm pedigrees, field evaluations, structural and functional genomic data (including links to external plant databases) and environmental (GIS) data.",
"example": "597754",
"homepage": "http://www.iris.irri.org",
"keywords": [
"gene",
"structure",
"genome"
],
"name": "International Rice Information System",
"pattern": "^\\d+$",
"prefix": "iris"
},
"isbn": {
"description": "The International Standard Book Number (ISBN) is for identifying printed books.",
"example": "9781584885658",
"homepage": "http://isbndb.com/",
"keywords": [
"bibliography"
],
"name": "International Standard Book Number",
"pattern": "^\\d+$",
"prefix": "isbn",
"uri_format": "http://isbndb.com/search-all.html?kw=$1"
},
"ised": {
"description": "ISED catalogues the influenza sequence and epitope information obtained in countries worldwide and currently hosts a total of 49368 influenza A and 4761 influenza B virus sequence data including pandemic A/H1N1 2009 virus sequences collected in 42 countries, and a total of 545 amantadine-resistant influenza virus sequences collected in Korea.",
"example": "AY209920",
"homepage": "http://influenza.korea.ac.kr",
"keywords": [
"protein"
],
"name": "Influenza Sequence and Epitope Database",
"pattern": "^[A-Z]+\\d+$",
"prefix": "ised"
},
"isfinder": {
"description": "ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available.",
"example": "ISA1083-2",
"homepage": "http://www-is.biotoul.fr",
"keywords": [
"gene",
"sequence"
],
"name": "IS Finder",
"pattern": "^IS\\w+(\\-\\d)?$",
"prefix": "isfinder",
"pubmed_ids": [
"16381877"
],
"uri_format": "http://www-is.biotoul.fr/index.html?is_special_name=$1"
},
"its2": {
"description": "Optimal global pairwise alignments from about 270,000 ribosomal RNA (rRNA) internal transcribed spacer 2 (ITS2) sequences - all against all - have been generated in order to model ITS2 secondary structures based on sequences with known structures.",
"example": "133245",
"homepage": "http://its2.bioapps.biozentrum.uni-wuerzburg.de/cgi-bin/index.pl?about",
"keywords": [
"RNA",
"structure"
],
"name": "Internal Transcribed Spacer 2 Database",
"pattern": "^\\d+$",
"prefix": "its2",
"uri_format": "http://its2.bioapps.biozentrum.uni-wuerzburg.de/cgi-bin/its2.pl?Taxon_id=$1&method=All"
},
"iuphar.family": {
"description": "IUPHAR G protein-coupled receptors database",
"example": "78",
"homepage": "http://www.iuphar-db.org/DATABASE/ReceptorFamiliesForward?type=GPCR",
"keywords": [
"protein"
],
"name": "G protein-coupled receptors database",
"pattern": "^\\d+$",
"prefix": "iuphar.family",
"synonyms": [
"iuphar.gpcr"
],
"uri_format": "http://www.iuphar-db.org/DATABASE/FamilyIntroductionForward?familyId=$1"
},
"ivdb": {
"description": "IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively.",
"example": "E13035",
"homepage": "http://influenza.psych.ac.cn/",
"keywords": [
"genome",
"DNA",
"gene"
],
"name": "Influenza Virus Database",
"pattern": "^[A-Z]+\\d+$",
"prefix": "ivdb",
"uri_format": "http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id=$1"
},
"jail": {
"description": "Interfaces of macromolecules are a valuable basis to analyse the process of molecular recognition. JAIL classifies not only the interfaces between domain architectures but also those between protein chains and those between proteins and nucleic acids.",
"example": "2q9v",
"homepage": "http://bioinformatics.charite.de/jail",
"keywords": [
"small molecule",
"structure",
"protein"
],
"name": "JAIL",
"pattern": "^PDBID$",
"prefix": "jail",
"uri_format": "http://bioinf-apache.charite.de/jail/index.php?site=show_interfaces&pdb_id=$1"
},
"jaspar": {
"description": "The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes.",
"example": "MA1234",
"homepage": "http://jaspar.genereg.net",
"keywords": [
"small molecule",
"regulation"
],
"name": "JASPAR: The high-quality transcription factor binding profile database",
"pattern": "^MA\\d+$",
"prefix": "jaspar"
},
"jcm": {
"description": "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2.",
"example": "17254",
"homepage": "http://www.jcm.riken.go.jp/",
"keywords": [
"microbial",
"taxonomy"
],
"name": "Japan Collection of Microorganisms",
"pattern": "^\\d+$",
"prefix": "jcm",
"uri_format": "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1"
},
"jcsd": {
"description": "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST).",
"example": "J55.713G",
"keywords": [
"chemical",
"structure"
],
"name": "Japan Chemical Substance Dictionary",
"pattern": "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$",
"prefix": "jcsd",
"uri_format": "http://nikkajiweb.jst.go.jp/nikkaji_web/pages/top_e.jsp?CONTENT=syosai&SN=$1"
},
"jcvi.genprop": {
"description": "The Genome Properties system consists of a suite of \"Properties\" which are carefully defined attributes of prokaryotic organisms whose status can be described by numerical values or controlled vocabulary terms for individual completely sequenced genomes.",
"example": "GenProp0151",
"homepage": "http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenomePropertiesHomePage.cgi",
"keywords": [
"classification",
"genome"
],
"name": "Genome Properties database at the J. Craig Venter Institute",
"pattern": "^GenProp\\d+$",
"prefix": "jcvi.genprop",
"synonyms": [
"genprop"
],
"uri_format": "http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenomePropDefinition.cgi?prop_acc=$1"
},
"jws": {
"description": "JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser.",
"example": "curien",
"homepage": "http://jjj.mib.ac.uk/index.html",
"keywords": [
"model",
"pathway"
],
"name": "JWS Online Model Repository",
"pattern": "^\\w+$",
"prefix": "jws",
"pubmed_ids": [
"15072998"
],
"uri_format": "http://jjj.mib.ac.uk/cgi-bin/processModelSelection.py?keytype=modelname&keyword=$1"
},
"kdbi": {
"description": "Kinetic Data of Bio-molecular Interaction (KDBI) is a collection of experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligandbinding or reaction events described in the literature.",
"example": "5957",
"homepage": "http://bidd.nus.edu.sg/group/kdbi/kdbi.asp",
"keywords": [
"small molecule",
"protein",
"RNA",
"DNA",
"interaction"
],
"name": "Kinetic Data of Biomolecular Interactions",
"pattern": "^\\d+$",
"prefix": "kdbi",
"uri_format": "http://bidd.nus.edu.sg/group/KDBI/Detail-new.asp?ID=$1"
},
"kegg.brite": {
"description": "KEGG BRITE is a collection of hierarchical classifications (see new hierarchies and last updates) representing our knowledge on various aspects of biological systems. In contrast to KEGG PATHWAY, which is limited to molecular interactions and reactions, KEGG BRITE incorporates many different types of relationships.",
"example": "ko00071",
"homepage": "http://www.genome.jp/kegg/brite.html",
"keywords": [
"pathway",
"classification",
"ontology"
],
"name": "KEGG BRITE",
"pattern": "^[ko/br]\\d+$",
"prefix": "kegg.brite",
"synonyms": [
"br",
"brite"
],
"uri_format": "http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br$1"
},
"kegg.compound": {
"description": "KEGG COMPOUND is a chemical structure database for metabolic compounds and other chemical substances that are relevant to biological systems.",
"example": "C12345",
"homepage": "http://www.genome.jp/kegg/compound/",
"keywords": [
"small molecule"
],
"name": "KEGG Compound",
"pattern": "^C\\d+$",
"prefix": "kegg.compound",
"pubmed_ids": [
"22700311"
],
"synonyms": [
"cpd",
"kegg.compounds"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?cpd:$1"
},
"kegg.disease": {
"description": "The KEGG DISEASE database is a new collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry is identified by the H number and contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs.",
"example": "H00047",
"homepage": "http://www.genome.jp/kegg/disease/",
"keywords": [
"classification"
],
"name": "KEGG Disease",
"pattern": "^H\\d+$",
"prefix": "kegg.disease",
"synonyms": [
"ds",
"kegg.diseases"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?ds:$1"
},
"kegg.drug": {
"description": "KEGG DRUG is a unified drug information resource that contains chemical structures and/or chemical components of all prescription and OTC drugs in Japan, most prescription drugs in the USA, and many prescription drugs in Europe.",
"example": "D00123",
"homepage": "http://www.genome.jp/kegg/drug/",
"keywords": [
"small molecule"
],
"name": "KEGG Drug",
"pattern": "^D\\d+$",
"prefix": "kegg.drug",
"pubmed_ids": [
"16381885"
],
"synonyms": [
"dr",
"kegg.drugs"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?dr:$1"
},
"kegg.gene": {
"description": "KEGG GENES is a collection of gene catalogs for all complete genomes generated from publicly available resources, mostly NCBI RefSeq. They are subject to SSDB computation and KO assignment (gene annotation) by KOALA tool",
"example": "syn:ssr3451",
"homepage": "http://www.genome.jp/kegg/genes.html",
"keywords": [
"gene",
"DNA",
"protein"
],
"name": "KEGG Genes",
"pattern": "^\\w+:[\\w\\d\\.-]*$",
"prefix": "kegg.gene",
"pubmed_ids": [
"16381885"
],
"synonyms": [
"gene",
"kegg.genes"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?[?species]:$1"
},
"kegg.genome": {
"description": "Complete organism genomes",
"example": "T00047",
"homepage": "http://www.genome.jp/kegg/catalog/org_list.html",
"name": "KEGG Genome",
"pattern": "^T\\d+$",
"prefix": "kegg.genome",
"pubmed_ids": [
"22080510"
],
"synonyms": [
"gn",
"kegg.genomes"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?gn:$1"
},
"kegg.glycan": {
"description": "The KEGG GLYCAN structure database is a collection of experimentally determined glycan structures [1]. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways.",
"example": "G00123",
"homepage": "http://www.genome.jp/kegg/glycan/",
"keywords": [
"small molecule"
],
"name": "KEGG Glycan",
"pattern": "^G\\d+$",
"prefix": "kegg.glycan",
"pubmed_ids": [
"16014746"
],
"synonyms": [
"gl",
"kegg.glycans"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?gl:$1"
},
"kegg.metagenome": {
"description": "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species.",
"example": "T30002",
"keywords": [
"genome"
],
"name": "KEGG Metagenome",
"pattern": "^T3\\d+$",
"prefix": "kegg.metagenome",
"pubmed_ids": [
"22080510"
],
"synonyms": [
"kegg.metagenomes"
],
"uri_format": "http://www.genome.jp/kegg-bin/show_organism?org=$1"
},
"kegg.orthology": {
"description": "The KEGG reference pathway maps and BRITE functional hierarchies are represented in a general way to be applicable to all organisms. KEGG Orthology (KO) is the basis for this representation, consisting of manually defined ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes.",
"example": "K00001",
"homepage": "http://www.genome.jp/kegg/ko.html",
"keywords": [
"classification",
"pathway"
],
"name": "KEGG Orthology",
"pattern": "^K\\d+$",
"prefix": "kegg.orthology",
"synonyms": [
"ko"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?ko:$1"
},
"kegg.pathway": {
"alt_uri_formats": [
"http://www.genome.jp/kegg-bin/show_pathway?#$1"
],
"description": "KEGG PATHWAY is a collection of manually drawn pathway maps (see new maps, change history, and last updates) representing our knowledge on the molecular interaction and reaction networks",
"example": "map00071",
"homepage": "http://www.genome.jp/kegg/pathway.html",
"keywords": [
"pathway"
],
"name": "KEGG Pathway",
"pattern": "^map\\d+$",
"prefix": "kegg.pathway",
"pubmed_ids": [
"22700311"
],
"synonyms": [
"path",
"kegg.pathways"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?map$1"
},
"kegg.reaction": {
"description": "KEGG REACTION contains all reactions taken from KEGG ENZYME and additional reactions taken from the metabolic pathway maps in KEGG PATHWAY.",
"example": "R00047",
"homepage": "http://www.genome.jp/kegg/reaction/",
"keywords": [
"enzyme",
"pathway"
],
"name": "KEGG Reaction",
"pattern": "^R\\d+$",
"prefix": "kegg.reaction",
"pubmed_ids": [
"22700311"
],
"synonyms": [
"rn",
"kegg.reactions"
],
"uri_format": "http://www.genome.jp/dbget-bin/www_bget?rn:$1"
},
"kineticdb": {
"description": "KineticDB is the thoroughly curated database of protein folding kinetics which contains currently experiments on 87 unique proteins and about hundred of mutants. The main goal of KineticDB is to provide users with the diverse set of protein folding rates known from experiment.",
"example": "4",
"homepage": "http://KineticDB.protres.ru/db/index.pl",
"keywords": [
"protein",
"structure"
],
"name": "KineticDB - a Protein Folding Kinetics Database",
"pattern": "^\\d+$",
"prefix": "kineticdb",
"uri_format": "http://kineticdb.protres.ru/db/ind.pl?ind=$1"
},
"kinmutbase": {
"description": "KinMutBase is a comprehensive database of disease-causing mutations in protein kinase domains. This release of the database contains 582 mutations in 20 tyrosine kinase domains and 13 serine/threonine kinase domains. The database refers 1790 cases from 1322 families.",
"example": "K00046",
"homepage": "http://bioinf.uta.fi/KinMutBase/",
"keywords": [
"enzyme",
"protein"
],
"name": "KinMutBase: A registry of disease-causing mutations in protein kinase domains",
"pattern": "^K\\d+$",
"prefix": "kinmutbase"
},
"kisao": {
"bioportal": "1410",
"description": "The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment.",
"example": "KISAO_0000057",
"homepage": "http://biomodels.net/kisao/",
"keywords": [
"ontology"
],
"name": "Kinetic Simulation Algorithm Ontology",
"pattern": "^KISAO_\\d+$",
"prefix": "kisao",
"rdf_uri_format": "http://www.biomodels.net/kisao/KISAO#$1",
"synonyms": [
"biomodels.kisao"
]
},
"kznf": {
"description": "A database of Kr\u00fcppel-type zinc finger (ZNF) proteins",
"example": "2",
"homepage": "http://znf.igb.uiuc.edu/human/",
"name": "Human KZNF Gene Catalog",
"pattern": "^\\d+$",
"prefix": "kznf",
"pubmed_ids": [
"16606702"
],
"uri_format": "http://znf.igb.uiuc.edu/human/action/exploreView?type=locus&id=$1"
},
"l1base": {
"description": "L1Base is a dedicated database containing putatively active LINE-1 (L1) insertions residing in human and rodent genomes: a) intact in the two ORFs, full length L1s (FLI-L1s) and b) L1s with intact ORF2 but disrupted ORF1 (ORF2-L1s). In addition, due to their regulatory potential, the full length (>6000bp) non-intact L1s (FLnI-L1s) were also included in the database.",
"example": "11",
"homepage": "http://line1.molgen.mpg.de",
"keywords": [
"genome",
"DNA"
],
"name": "L1Base: Annotation of Full-Length, Intact L1 Elements",
"pattern": "^\\d+$",
"prefix": "l1base",
"uri_format": "http://line1.bioapps.biozentrum.uni-wuerzburg.de/details.php?DBN=[?family_name]&UID=$1"
},
"leger": {
"description": "The Proteome Database LEGER links (as an information warehouse) basic requirements of each listerial research project with state of the art knowledge that can be derived from functional genome studies. It provides information about gene functions, protein expression levels, subcellular localization of proteins, and the biological meaning of genes/proteins.",
"example": "Lmo0007",
"homepage": "http://leger2.gbf.de/cgi-bin/expLeger.pl",
"keywords": [
"protein",
"gene"
],
"name": "LEGER: Post-genome Database for Listeria Research",
"pattern": "^L[a-z]+\\d+$",
"prefix": "leger"
},
"legiolist": {
"description": "LegioList is a database dedicated to the analysis of the genomes of Legionella pneumophila strain Paris (endemic in France), strain Lens (epidemic isolate), strain Phildelphia 1, and strain Corby. It also includes the genome of Legionella longbeachae strain NSW150.",
"example": "baf",
"homepage": "http://genolist.pasteur.fr/LegioList/",
"keywords": [
"genome"
],
"name": "Legionella pneumophila genome database",
"pattern": "^[A-Z]+/\\d+$",
"prefix": "legiolist"
},
"leproma": {
"description": "The Leprosy knowledge base integrates genome details, protein information, drug and transcriptome data, mutant and operon annotation; structural views and comparative genomics, in a structured manner required for the rational development of new diagnostic, therapeutic and prophylactic measures against leprosy.",
"example": "pabB",
"homepage": "http://mycobrowser.epfl.ch/leprosy.html",
"keywords": [
"genome",
"protein",
"structure"
],
"name": "Mycobacterium leprae genome database",
"pattern": "^[A-Z]+/\\d+$",
"prefix": "leproma",
"uri_format": "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1&submit=Search"
},
"lgicdb": {
"description": "The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available.",
"example": "5HT3Arano",
"homepage": "http://www.ebi.ac.uk/compneur-srv/LGICdb/",
"keywords": [
"gene",
"protein",
"sequence"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Ligand-Gated Ion Channel database",
"pattern": "^\\w+$",
"prefix": "lgicdb",
"pubmed_ids": [
"9847222"
],
"synonyms": [
"lgic"
],
"uri_format": "http://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php"
},
"lhn": {
"bioportal": "1024",
"description": "An ontology for Loggerhead sea turtle (Caretta caretta) nesting behavior, based on the published ethogram of Hailman and Elowson.",
"example": "EKB_0000004",
"homepage": "http://www.mesquiteproject.org/ontology/Loggerhead/index.html",
"keywords": [
"obo",
"sea turtle",
"behavior"
],
"name": "Loggerhead nesting",
"pattern": "^EKB_\\d+$",
"prefix": "lhn"
},
"ligandexpo": {
"description": "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.",
"example": "ABC",
"homepage": "http://ligand-depot.rutgers.edu/",
"keywords": [
"interaction",
"structure",
"protein",
"chemical",
"nucleic acid"
],
"license": "http://ligand-depot.rutgers.edu/acknowledgements.html",
"name": "Ligand Expo",
"pattern": "^(\\w){3}$",
"prefix": "ligandexpo",
"pubmed_ids": [
"15059838"
],
"uri_format": "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid"
},
"ligasite": {
"description": "LigASite is a gold-standard dataset of biologically relevant binding sites in protein structures. It consists of proteins with one unbound structure and at least one structure of the protein-ligand complex. Both a redundant and a non-redundant (sequence identity lower than 25%) version is available. Quaternary structures proposed by PQS (2) are used for all structures in the dataset.",
"example": "1bkz",
"homepage": "http://www.bigre.ulb.ac.be/Users/benoit/LigASite/",
"keywords": [
"protein",
"structure",
"small molecule"
],
"name": "LigAsite",
"pattern": "^PDBID$",
"prefix": "ligasite",
"uri_format": "http://www.bigre.ulb.ac.be/Users/benoit/LigASite/index.php?apo=$1"
},
"lipidbank": {
"description": "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.",
"example": "BBA0001",
"homepage": "http://lipidbank.jp/index.html",
"keywords": [
"lipid",
"molecule",
"structure"
],
"name": "LipidBank",
"pattern": "^\\w+\\d+$",
"prefix": "lipidbank",
"pubmed_ids": [
"12058481"
],
"uri_format": "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1"
},
"lipidmaps": {
"description": "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.",
"example": "LMPR0102010012",
"homepage": "http://www.lipidmaps.org",
"keywords": [
"lipid",
"structure",
"taxonomy"
],
"license": "http://www.lipidmaps.org/about/terms_of_use.html",
"name": "LIPID MAPS",
"pattern": "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$",
"prefix": "lipidmaps",
"pubmed_ids": [
"17098933",
"15722563"
],
"uri_format": "http://www.lipidmaps.org/data/get_lm_lipids_dbgif.php?LM_ID=$1"
},
"listilist": {
"description": "ListiList is a database dedicated to the analysis of the genomes of the food-borne pathogen, Listeria monocytogenes, and its non-pathogenic relative, Listeria innocua. Its purpose is to collate and integrate various aspects of the genomic information from L. monocytogenes, a paradigm for bacterial-host interactions.",
"example": "LIN02037",
"homepage": "http://genolist.pasteur.fr/ListiList/",
"keywords": [
"genome"
],
"name": "Listeria innocua and Listeria monocytogenes genomes database",
"pattern": "^L[A-Z]+\\d+$",
"prefix": "listilist"
},
"locate": {
"description": "LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set.",
"example": "6000263",
"homepage": "http://locate.imb.uq.edu.au/",
"keywords": [
"protein"
],
"name": "Mammalian Protein Localization Database",
"pattern": "^\\d+$",
"prefix": "locate",
"uri_format": "http://locate.imb.uq.edu.au/cgi-bin/report.cgi?entry=$1"
},
"loqate": {
"description": "The data presented here is a result of systematically tracking the localization and abundance of 5330 yeast proteins at single-cell resolution under three different stress conditions (DTT, H2O2 and nitrogen starvation) using the GFP-tagged yeast library",
"example": "1001",
"homepage": "http://www.weizmann.ac.il/molgen/loqate/",
"license": "http://www.weizmann.ac.il/molgen/loqate/downloads",
"name": "The localization and quantitation atlas of the yeast proteome",
"pattern": "^\\d+$",
"prefix": "loqate",
"pubmed_ids": [
"24150937"
],
"uri_format": "http://www.weizmann.ac.il/molgen/loqate/gene/view/$1"
},
"lpfc": {
"description": "This library is useful for building models, threading, and exploratory analysis. It is also a useful mechanism for summarizing variability in NMR structures.",
"example": "1mba",
"homepage": "http://helix-web.stanford.edu/LPFC/",
"keywords": [
"structure",
"protein"
],
"name": "A Library of Protein Family Cores",
"pattern": "^PDBID$",
"prefix": "lpfc",
"uri_format": "http://helix-web.stanford.edu/cgi-bin/textsearch.cgi?key=$1"
},
"lsmd": {
"description": "Lowe oculocerebrorenal syndrome is an X-linked disorder caused by mutations in the OCRL1 gene, which encodes a 105-kDa Golgi protein with phosphatidylinositol (4,5) bisphosphate 5-phosphatase activity. This database of mutations causing Lowe syndrome has been established.",
"example": "15",
"homepage": "http://research.nhgri.nih.gov/lowe/",
"keywords": [
"DNA",
"gene",
"protein"
],
"name": "Lowe Syndrome Mutation Database",
"pattern": "^\\d+$",
"prefix": "lsmd",
"uri_format": "http://research.nhgri.nih.gov/lowe/db_retrieval.cgi?site_name=lowe&exon_intron_num=$1"
},
"ma": {
"alt_uri_formats": [
"http://purl.org/obo/owl/MA#$1"
],
"bioportal": "1000",
"description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus).",
"example": "MA:0000021",
"homepage": "http://www.informatics.jax.org/searches/AMA_form.shtml",
"keywords": [
"obo",
"anatomy",
"mouse"
],
"name": "Mouse adult gross anatomy",
"pattern": "^MA:\\d+$",
"prefix": "ma"
},
"macie": {
"description": "MACiE is an electronic database of well-characterised enzymatic reactions. MACiE is the result of more than three years' collaboration between the Mitchell and Murray-Rust groups in the Unilever Centre and Prof. Janet Thornton at the European Bioinformatics Institute. The database contains the reaction mechanisms for 100 individual enzymes; this includes the overall reactions and the multiple steps that constitute them.",
"example": "M0001",
"homepage": "http://www.ebi.ac.uk/thornton-srv/databases/MACiE/",
"keywords": [
"enzyme",
"pathway"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "MACiE",
"pattern": "^M\\d{4}$",
"prefix": "macie",
"pubmed_ids": [
"17082206"
],
"uri_format": "http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/getPage.pl?id=$1"
},
"magest": {
"description": "MAGEST is a database of maternal gene expression information for an Ascidian, Halocynthia roretzi. The ascidian has become an animal model in developmental biological research because it shows the simple developmental process and belongs to the one of chordate groups.",
"example": "11102",
"homepage": "http://magest.hgc.jp/",
"keywords": [
"gene expression"
],
"name": "MAboya Gene Expression patterns and Sequence Tags",
"pattern": "^\\d+$",
"prefix": "magest",
"uri_format": "http://magest.hgc.jp/db/show_contig_by_entry_id/$1"
},
"maizegdb": {
"description": "MaizeGDB is the maize research community's central repository for genetics and genomics information.",
"example": "25011",
"homepage": "http://www.maizegdb.org",
"keywords": [
"genome",
"DNA"
],
"name": "Maize Genetics and Genomics Database",
"pattern": "^\\d+$",
"prefix": "maizegdb",
"pubmed_ids": [
"18769488"
],
"synonyms": [
"maizegdb.locus",
"maizegdb_qtl"
],
"uri_format": "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1"
},
"malisam": {
"description": "MALISAM is a database of pairwise, structure-based alignments for structurally analogous motifs in proteins.",
"example": "d1a7j__d1kafa_",
"homepage": "http://prodata.swmed.edu/malisam",
"keywords": [
"protein"
],
"name": "MALISAM: Manual ALIgnments of Structurally Analogous Motifs",
"pattern": "^[a-z, 0-9]+_$",
"prefix": "malisam",
"uri_format": "http://prodata.swmed.edu/malisam/[$11][$12]/[$11][$12].html"
},
"mamit": {
"description": "Mamit-tRNA is a database for mammalian mitochondrial genomes, has been developed for deciphering structural features of mammalian mitochondrial tRNAs and as a helpful tool in the frame of human diseases linked to point mutations in mitochondrial tRNA genes",
"example": "7",
"homepage": "http://mamit-tRNA.u-strasbg.fr",
"keywords": [
"rna",
"trna"
],
"name": "Mamit-tRNA",
"pattern": "^\\d+$",
"prefix": "mamit",
"pubmed_ids": [
"17585048"
],
"synonyms": [
"mamit-trna"
],
"uri_format": "http://mamit-trna.u-strasbg.fr/mutations.asp?idAA=$1"
},
"mampol": {
"description": "The Mammalia Polymorphism Database is a secondary database designed to provide a collection of all the existing polymorphic sequences in the MammaliaOnline query interfaces facilitate data interrogation by different polymorphism parameter values and keyword queries (based on SQL searches).",
"example": "MAMpol005339",
"homepage": "http://mampol.uab.es",
"keywords": [
"DNA"
],
"name": "Mammalia Polymorphism Database",
"pattern": "^MAMpol\\d+$",
"prefix": "mampol",
"uri_format": "http://mampol.uab.es/cgi-bin/MamPol_s2.pl?Accession=$1"
},
"mao": {
"bioportal": "1026",
"description": "An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment.",
"example": "MAO:0000061",
"homepage": "http://bips.u-strasbg.fr/LBGI/MAO/mao.html",
"keywords": [
"obo",
"sequence",
"alignment"
],
"name": "Multiple Alignment Ontology",
"pattern": "^MAO_\\d+$",
"prefix": "mao"
},
"mapu": {
"description": "MAPU contains several body fluid proteomes; including plasma, urine, and cerebrospinal fluid. MAPU contains the peptides identifying each protein, measured masses, scores and intensities using a clickable interface of cell or body parts. Proteome data can be queried across proteomes by protein name, accession number, sequence similarity, peptide sequence and annotation information.",
"example": "IPI00377174",
"homepage": "http://www.mapuproteome.com",
"keywords": [
"protein"
],
"name": "Max-Planck Unified (MAPU) proteome database",
"pattern": "^IPI\\d+$",
"prefix": "mapu"
},
"mapviewer": {
"description": "The Map Viewer is a tool of Entrez Genomes that provides special browsing capabilities for eukaryotic chromosomes. It allows the user to view and search an organisms complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest.",
"example": "5061",
"homepage": "http://www.ncbi.nlm.nih.gov/mapview/",
"keywords": [
"genome"
],
"name": "MapViewer",
"pattern": "^\\d+$",
"prefix": "mapviewer",
"uri_format": "http://www.ncbi.nlm.nih.gov/projects/mapview/map_search.cgi?taxid=$1"
},
"matrixdb": {
"description": "MatrixDB is a database reporting mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. Full-length molecules, fragments and multimers present in the extracellular matrix are all included in the database.",
"example": "P00747_P07355",
"homepage": "http://matrixdb.ibcp.fr",
"keywords": [
"protein",
"small molecule",
"interaction"
],
"license": "http://dip.doe-mbi.ucla.edu/dip/termsofuse.html",
"name": "MatrixDB: Extracellular Matrix interactions database",
"pattern": "^[A-Z]\\d+_[A-Z]\\d+$",
"prefix": "matrixdb",
"pubmed_ids": [
"19147664"
],
"synonyms": [
"matrixdb.association"
],
"uri_format": "http://matrixdb.ibcp.fr/cgi-bin/model/report/default?name=$1&class=Association"
},
"mdpd": {
"description": "The Mutation Database for Parkinson.s Disease (MDPD) is designed to fulfill the need for information integration so that users can easily retrieve, inspect and enhance their knowledge on PD. The database contains 2391 entries on 202 genes extracted from 576 publications.",
"example": "A2M",
"homepage": "http://datam.i2r.a-star.edu.sg/mdpd/index.php",
"keywords": [
"gene",
"classification"
],
"name": "Mutation Database for Parkinson's Disease",
"pattern": "^[A-Z]+/\\d+$",
"prefix": "mdpd",
"uri_format": "http://datam.i2r.a-star.edu.sg/mdpd/detail.php?symbol=$1"
},
"medline": {
"description": "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.",
"example": "16333295",
"homepage": "http://www.ebi.ac.uk/Databases/MEDLINE/medline.html",
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Medline literature database",
"pattern": "^\\d+$",
"prefix": "medline",
"uri_format": "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-view+MedlineFull+[medline-PMID:$1]"
},
"mepd": {
"description": "The Medaka Expression Pattern Database (MEPD) stores and integrates information of gene expression during embryonic development of the small freshwater fish Medaka (Oryzias latipes).",
"example": "1468",
"homepage": "http://ani.embl.de:8080/mepd/",
"keywords": [
"gene expression"
],
"name": "MEPD: Medaka Expression Pattern Database",
"pattern": "^\\d+$",
"prefix": "mepd",
"uri_format": "http://ani.embl.de:8080/mepd/MdbShowClone01?cloneID=$1"
},
"merna": {
"description": "The RNA-metal binding database MERNA provides information that allows the classification of and search for specific metal binding motifs (e.g., tandem G-U pairs, loop E motif, A-platform motif). The RNA binding sites of 23 different metal ions are described, the most common of these being Mg2+, Na+, Ca2+, Cd2+ and K+.",
"example": "Mg",
"homepage": "http://merna.lbl.gov",
"keywords": [
"RNA",
"small molecule",
"regulation"
],
"name": "A Database of Metal Ion Binding Sites in RNA",
"pattern": "^Element Symbol$",
"prefix": "merna",
"uri_format": "http://merna.lbl.gov/search.php?type=simple&metal_ion=$1"
},
"merops": {
"description": "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.",
"example": "S01.001",
"homepage": "http://merops.sanger.ac.uk/",
"keywords": [
"protein",
"enzyme",
"structure"
],
"license": "http://merops.sanger.ac.uk/about/availability.shtml",
"name": "MEROPS - the Peptidase Database",
"pattern": "^S\\d{2}\\.\\d{3}$",
"prefix": "merops",
"pubmed_ids": [
"17991683"
],
"uri_format": "http://merops.sanger.ac.uk/cgi-bin/pepsum?id=$1"
},
"mesh": {
"alt_uri_formats": [
"http://bioonto.de/mesh.owl#$1"
],
"bioportal": "1351",
"description": "MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity",
"example": "D018377",
"homepage": "http://www.nlm.nih.gov/mesh/meshhome.html",
"keywords": [
"classification"
],
"name": "Medical Subject Headings",
"pattern": "^[A-Za-z0-9]+$",
"prefix": "mesh",
"rdf_uri_format": "http://purl.bioontology.org/ontology/MSH/$1",
"synonyms": [
"msh",
"bionto.mesh",
"mesh_cui"
]
},
"metagrowth": {
"description": "Metagrowth is a new type knowledge base aiming to guide the experimental studies on the culture conditions of obligate parasitic bacteria. The database entry is composed of the evidences and specific hypotheses derived from them. Currently 200 entries are available for Coxiella burnetii.",
"example": "E0241",
"homepage": "http://igs-server.cnrs-mrs.fr/axenic/",
"name": "Metagrowth",
"pattern": "^E\\d+$",
"prefix": "metagrowth",
"uri_format": "http://igs-server.cnrs-mrs.fr/axenic-cgi/www_get_evdb?evdb+$1"
},
"metatiger": {
"description": "metaTIGER is a collection of metabolic profiles and phylogenomic information on a taxonomically diverse range of eukaryotes. Phylogenomic information is provided by 2,257 large phylogenetic trees which can be interactively explored. High-throughput tree analysis can also be carried out to identify trees of interest.",
"example": "531",
"homepage": "http://www.bioinformatics.leeds.ac.uk/metatiger",
"keywords": [
"classification"
],
"name": "metaTIGER",
"pattern": "^\\d+$",
"prefix": "metatiger",
"uri_format": "http://www.bioinformatics.leeds.ac.uk/metatiger/cgi_bin/pathway.cgi?organism=[$11]&network=[$12]"
},
"methdb": {
"description": "MethDB is a public database for DNA methylation. The database contains currently methylation patterns, profiles and total methylation content data for 46 species, 160 tissues and 72 phenotypes coming from a total of 6667 experiments (as of 4/9/2002). These data can be conviniently searched and represented in different ways.",
"example": "759",
"homepage": "http://www.methdb.de",
"keywords": [
"DNA",
"small molecule"
],
"name": "MethDB - the database for DNA methylation and environmental epigenetic effects",
"pattern": "^\\d+$",
"prefix": "methdb"
},
"metnetdb": {
"description": "The MetNet database (MetNetDB) contains information on networks of metabolic and regulatory and interactions in Arabidopsis. Types of interactions in MetNetDB include transcription, translation, protein modification, assembly, allosteric regulation, translocation from one subcellular compartment to another.",
"example": "377369",
"homepage": "http://www.metnetdb.org/MetNet_db.htm",
"keywords": [
"pathway",
"interaction",
"regulation",
"protein",
"small molecule",
"DNA",
"RNA"
],
"name": "Metabolic Network Exchange",
"pattern": "^\\d+$",
"prefix": "metnetdb",
"uri_format": "http://metnetonline.org/browse_pathway2.php?pthID=$1"
},
"mfo": {
"bioportal": "1027",
"description": "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.",
"example": "MFO_0000001",
"homepage": "http://ani.embl.de:8080/mepd/",
"keywords": [
"obo",
"anatomy",
"development",
"fish"
],
"name": "Medaka fish anatomy and development",
"pattern": "^MFO_\\d+$",
"prefix": "mfo"
},
"mfungd": {
"description": "MfunGD provides a resource for annotated mouse proteins and their occurence in protein networks. Protein function annotation is performed using the Functional Catalogue annotation scheme, which is a hierarchically structured classification system.",
"example": "mc4002350",
"homepage": "http://mips.gsf.de/genre/proj/mfungd",
"keywords": [
"protein",
"pathway",
"classification"
],
"name": "MIPS Mouse Functional Genome Database",
"pattern": "^mc\\d+$",
"prefix": "mfungd",
"uri_format": "http://mips.helmholtz-muenchen.de/genre/proj/mfungd/singleGeneReport.html?entry=$1"
},
"mgc": {
"description": "The goal of the Mammalian Gene Collection (MGC), a trans-NIH initiative, is to provide researchers with unrestricted access to sequence-validated full-length protein-coding (FL-CDS) cDNA clones for human, mouse, and rat genes.",
"example": "23914",
"homepage": "http://mgc.nci.nih.gov/",
"keywords": [
"gene"
],
"name": "Mammalian Gene Collection",
"pattern": "^\\d+$",
"prefix": "mgc",
"uri_format": "http://mgc.nci.nih.gov/Tissues/LibInfo?LID=$1"
},
"mgg": {
"description": "The Magnaporthe grisea genome project is a partnership between the International Rice Blast Genome Consortium, and the Broad Institute. The project is facilitated by an Advisory Board made up of members of the rice blast research community.",
"example": "S7000002168104215",
"homepage": "http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/Home.html",
"keywords": [
"genome"
],
"name": "Magnaporthe grisea Database",
"pattern": "^[A-Z]\\d+$",
"prefix": "mgg",
"synonyms": [
"broadmgg"
],
"uri_format": "http://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1"
},
"mgi": {
"description": "The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.",
"example": "95484",
"homepage": "http://www.informatics.jax.org/",
"keywords": [
"expression",
"phenotype",
"sequence"
],
"name": "Mouse genome database (MGD) from Mouse Genome Informatics (MGI)",
"pattern": "^\\d+$",
"prefix": "mgi",
"pubmed_ids": [
"15608240"
],
"synonyms": [
"mgd"
],
"uri_format": "http://www.informatics.jax.org/searches/accession_report.cgi?id=mgi:$1"
},
"mgiid": {
"description": "Many newly sequenced bacterial group II introns are incorrectly identified or annotated. A major goal of this database is to be a resource in helping to identify and catalog group II introns in the databases.",
"example": "Cu.me.I1",
"homepage": "http://www.fp.ucalgary.ca/group2introns/",
"keywords": [
"DNA"
],
"name": "Mobile group II introns database",
"pattern": "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$",
"prefix": "mgiid",
"pubmed_ids": [
"22080509"
],
"synonyms": [
"dbg2introns"
],
"uri_format": "http://www.fp.ucalgary.ca/group2introns/$1.htm"
},
"mhcbn": {
"description": "The MHCBN is a curated database consisting of detailed information about Major Histocompatibility Complex (MHC) Binding,Non-binding peptides and T-cell epitopes. The database provides information about allele specific MHC binding peptides, MHC non-binding, TAP binding, TAP non-binding peptides and T-cell epitopes reported in literature.",
"example": "27940",
"homepage": "http://www.imtech.res.in/raghava/mhcbn/",
"keywords": [
"protein"
],
"name": "MHCBN: A comprehensive database of MHC binding and Non-binding peptides",
"pattern": "^\\d+$",
"prefix": "mhcbn",
"uri_format": "http://www.imtech.res.in/cgibin/mhcbn/display.pl?field=sno&value=$1"
},
"micado": {
"description": "Micado (MICrobial Advanced Database Organization) is a relational database dedicated to microbial genomes and functional analysis of Bacillus subtilis.",
"example": "AL009126",
"homepage": "http://genome.jouy.inra.fr/cgi-bin/micado/index.cgi",
"keywords": [
"genome"
],
"name": "MICrobial Advanced Database Organization",
"pattern": "^[A-Z,0-9]+$",
"prefix": "micado",
"uri_format": "http://genome.jouy.inra.fr/cgi-bin/micado/access.cgi?accessnumber=$1"
},
"microkit": {
"description": "The MiCroKit database is the first integrative resource to pin point most of identified components and related scientific information of midbody, centrosome and kinetochore.",
"example": "MCK-SC-00010",
"homepage": "http://microkit.biocuckoo.org/",
"keywords": [
"DNA",
"RNA",
"protein"
],
"name": "MiCroKit - An Integrated Database of Midbody, Centrosome, and Kinetochore",
"pattern": "^MCK-[A-Z]+-\\d+$",
"prefix": "microkit",
"uri_format": "http://microkit.biocuckoo.org/html/$1.html"
},
"microsporidia": {
"description": "MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.",
"example": "ECU03_0820i",
"homepage": "http://microsporidiadb.org/micro/",
"keywords": [
"eukaryotic",
"genome"
],
"name": "MicrosporidiaDB",
"pattern": "^\\w+$",
"prefix": "microsporidia",
"pubmed_ids": [
"19914931"
],
"uri_format": "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"
},
"mid": {
"description": "The MHC-Peptide Interaction Database version T (MPID-T) is a new generation database for sequence-structure-function information on T cell receptor/peptide/MHC interactions. It contains all structures of TcR/pMHC and pMHC complexes, with emphasis on the structural characterization of these complexes.",
"example": "MHCA0013",
"homepage": "http://surya.bic.nus.edu.sg/mpidt",
"keywords": [
"protein",
"interaction",
"structure"
],
"name": "MHC-Peptide Interaction Database version T",
"pattern": "^MHC[A/B]\\d+$",
"prefix": "mid"
},
"millipore_pathways": {
"description": "Cell signaling is part of a complex system of communication that regulates cellular activity and pathways are an essential tool for researchers to understand the mechanisms of cellular signaling. Millipore pathways provide the quickest way to visualize downstream and upstream protein activity. Pathway diagrams are obtained from GeneGO, with links to MilliPore products.",
"example": "219",
"homepage": "http://www.millipore.com/pathways/pw/pathways",
"keywords": [
"pathway"
],
"name": "Visualize metabolic and signaling pathways",
"pattern": "^\\d+$",
"prefix": "millipore_pathways",
"uri_format": "http://www.millipore.com/pathways/pathviewer.do?searchTerms=&diseaseAreaIds=&pathwayId=$1"
},
"mimi": {
"description": "MiMI provides a deeply merged view of several popular interaction databases including: BIND, HPRD, IntAct, GRID, and others. MiMI allows scientists to access one cohesive view of molecules found in these databases. Through a unique deep integration process, data that is complementary or conflicting among sites is highlighted.",
"example": "2873",
"homepage": "http://mimi.ncibi.org",
"keywords": [
"interaction",
"small molecule",
"protein"
],
"name": "Michigan Molecular Interactions",
"pattern": "^\\d+$",
"prefix": "mimi",
"uri_format": "http://mimi.ncibi.org/MimiWeb/gene-details-page-front.jsp?geneid=$1"
},
"mimodb": {
"description": "MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures.",
"example": "1",
"homepage": "http://immunet.cn/mimodb/",
"keywords": [
"interaction",
"protein"
],
"name": "MimoDB",
"pattern": "^\\d+$",
"prefix": "mimodb",
"pubmed_ids": [
"22053087"
],
"uri_format": "http://immunet.cn/mimodb/browse.php?table=mimoset&ID=$1"
},
"mint": {
"description": "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals.",
"example": "MINT-10000",
"homepage": "http://mint.bio.uniroma2.it/mint/",
"keywords": [
"protein",
"interaction"
],
"license": "http://dip.doe-mbi.ucla.edu/dip/termsofuse.html",
"name": "Molecular INTeraction Database",
"pattern": "^MINT\\-\\d{1,5}$",
"prefix": "mint",
"pubmed_ids": [
"17135203"
],
"uri_format": "http://mint.bio.uniroma2.it/mint/search/interactor.do?queryType=protein&interactorAc=$1"
},
"mipmod": {
"description": "MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures.",
"example": "HOSAPI0399",
"homepage": "http://bioinfo.iitk.ac.in/MIPModDB",
"keywords": [
"protein",
"structure"
],
"name": "MIPModDB",
"pattern": "^\\w+$",
"prefix": "mipmod",
"pubmed_ids": [
"22080560"
],
"uri_format": "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1"
},
"mips.plantsdb": {
"description": "The MIPS plant genomics group focuses on the analysis of plant genomes, using bioinformatic techniques. To store and manage the data, we developed a database, PlantsDB, that aims to provide a data and information resource for individual plant species. In addition PlantsDB provides a platform for integrative and comparative plant genome research.",
"example": "24980",
"homepage": "http://mips.helmholtz-muenchen.de/plant/genomes.jsp",
"keywords": [
"genome"
],
"name": "MIPS PlantsDB",
"pattern": "^\\d+$",
"prefix": "mips.plantsdb"
},
"mirbase": {
"description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. The miRBase Registry continues to provide gene hunters with unique names for novel miRNA genes prior to publication of results. The miRBase Targets database is a new resource of predicted miRNA targets in animals",
"example": "MI0000001",
"homepage": "http://www.mirbase.org/",
"keywords": [
"RNA",
"gene"
],
"name": "miRBase Sequence Database",
"pattern": "^MI\\d{7}$",
"prefix": "mirbase",
"pubmed_ids": [
"14681370"
],
"uri_format": "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1"
},
"mirbase.mature": {
"description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence.",
"example": "MIMAT0000001",
"keywords": [
"nucleotide",
"sequence"
],
"name": "miRBase mature sequence",
"pattern": "^MIMAT\\d{7}$",
"prefix": "mirbase.mature",
"uri_format": "http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1"
},
"mirgator": {
"description": "miRGator is a novel database and navigator tool for functional interpretation of miRNAs. Functional analyses and expression profiling are integrated with target gene prediction to infer biological function of miRNAs.",
"example": "hsa-mir-155",
"homepage": "http://genome.ewha.ac.kr/miRGator/miRGator.html",
"keywords": [
"RNA",
"gene"
],
"name": "miRGator: An integrated system for functional annotation of microRNAs",
"pattern": "^[a-z]+-[a-z]+-\\d+$",
"prefix": "mirgator"
},
"mirgen": {
"description": "miRGen is an integrated database of positional relationships between animal miRNAs and genomic annotation sets, and animal miRNA targets according to combinations of widely used target prediction programs.",
"example": "hsa-mir-155",
"homepage": "http://www.diana.pcbi.upenn.edu/miRGen",
"keywords": [
"RNA",
"genome",
"gene"
],
"name": "miRGen: microRNA Genomics Resource",
"pattern": "^[a-z]+-[a-z]+-\\d+$",
"prefix": "mirgen"
},
"miriam.resource": {
"description": "MIRIAM Resources is an online resource created to catalogue the data-types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding physical URLs, whether these are controlled vocabularies or databases.",
"example": "MIR:00100245",
"homepage": "http://www.ebi.ac.uk/miriam/",
"keywords": [
"registry"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "MIRIAM Resources",
"pattern": "^MIR:001\\d{5}$",
"prefix": "miriam.resource",
"pubmed_ids": [
"18078503"
],
"synonyms": [
"mir"
],
"uri_format": "http://www.ebi.ac.uk/miriam/main/resources/$1"
},
"mirnamap": {
"description": "miRNAMap was developed to collect experimental verified microRNAs and experimental verified miRNA target genes in human, mouse, rat, and other metazoan genomes. In addition to known miRNA targets, three computational tools previously developed, such as miRanda, RNAhybrid and TargetScan, were applied for identifying miRNA targets in 3' -UTR of genes.",
"example": "MI0003490",
"homepage": "http://mirnamap.mbc.nctu.edu.tw",
"keywords": [
"RNA",
"gene"
],
"name": "miRNAMap: genomic maps of studying gene regulation by metazoan microRNAs",
"pattern": "^MI\\d+$",
"prefix": "mirnamap",
"uri_format": "http://mirnamap.mbc.nctu.edu.tw/php/mirna_entry.php?acc=$1"
},
"mirnest": {
"description": "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species.",
"example": "MNEST029358",
"homepage": "http://lemur.amu.edu.pl/share/php/mirnest/",
"keywords": [
"expression",
"prediction"
],
"name": "miRNEST",
"pattern": "^MNEST\\d+$",
"prefix": "mirnest",
"pubmed_ids": [
"22135287"
],
"uri_format": "http://lemur.amu.edu.pl/share/php/mirnest/search.php?search_term=$1"
},
"mirortho": {
"description": "miROrtho contains predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine. It provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline.",
"example": "95423",
"homepage": "http://cegg.unige.ch/mirortho",
"keywords": [
"RNA",
"gene",
"genome"
],
"name": "miROrtho: the catalogue of animal microRNA genes",
"pattern": "^\\d+$",
"prefix": "mirortho",
"uri_format": "http://cegg.unige.ch/mirortho/entry_details/$1"
},
"mist": {
"description": "The Microbial Signal Transduction database contains the signal transduction proteins for 1017 complete bacterial and archaeal organisms. These are identified using various domain profiles that directly or indirectly implicate a particular protein in participating in signal transduction.",
"example": "624",
"homepage": "http://genomics.ornl.gov/mist",
"keywords": [
"regulation",
"protein",
"small molecule",
"pathway"
],
"name": "Microbial Signal Transduction database",
"pattern": "^\\d+$",
"prefix": "mist",
"uri_format": "http://genomics.ornl.gov/mist/view_organism.php?organism_id=$1"
},
"mitodat": {
"description": "This database is dedicated to the nuclear genes specifying the enzymes, structural proteins, and other proteins, many still not identified, involved in mitochondrial biogenesis and function. MitoDat highlights predominantly human nuclear-encoded mitochondrial proteins, although we are including proteins from other animals in addition to those currently known only from yeast and other fungal mitochondria, as well as from plant mitochondria.",
"example": "MD100041",
"homepage": "http://www-lecb.ncifcrf.gov/mitoDat/",
"keywords": [
"gene",
"enzyme",
"protein"
],
"name": "MitoDat: Mendelian Inheritance and the Mitochondrion",
"pattern": "^MD\\d+$",
"prefix": "mitodat",
"uri_format": "http://www-lecb.ncifcrf.gov/mitoDat/$1.html"
},
"mitoproteome": {
"description": "MitoProteome is an object-relational database of human mitochondrial protein sequences generated from information obtained from a comprehensive curation of public databases as well as from direct experimental evidence. MitoProteome contains both mitochondrial- and nuclear-encoded protein sequences.",
"example": "MP000776",
"homepage": "http://www.mitoproteome.org",
"keywords": [
"protein",
"structure"
],
"name": "MitoProteome",
"pattern": "^MP\\d+$",
"prefix": "mitoproteome",
"uri_format": "http://www.mitoproteome.org/data/proteome/index.cgi?db=mito&pid=L$1"
},
"mmcd": {
"description": "The goal of the Madison-Qingdao Metabolomics Consortium Database (MMCD) has been to support high-throughput NMR and MS approaches to the identification and quantification of metabolites present in biological samples. MMCD currently serves as a hub for information on small molecules of biological interest gathered from electronic databases and the scientific literature.",
"example": "cq_12198",
"homepage": "http://mmcd.nmrfam.wisc.edu/",
"keywords": [
"small molecule"
],
"name": "Madison Metabolomic Consortium Database",
"pattern": "^cq_\\d+$",
"prefix": "mmcd",
"uri_format": "http://mmcd.nmrfam.wisc.edu/test/cqsearch.py?cqid=$1"
},
"mmdb": {
"description": "The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more.",
"example": "50885",
"homepage": "http://www.ncbi.nlm.nih.gov/Structure/",
"keywords": [
"structure",
"protein",
"DNA",
"small molecule",
"interaction"
],
"name": "Molecular Modeling Database",
"pattern": "^\\d{1,5}$",
"prefix": "mmdb",
"pubmed_ids": [
"17135201"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1"
},
"mmmp": {
"description": "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma",
"example": "37",
"homepage": "http://www.mmmp.org/MMMP/",
"keywords": [
"interaction",
"pathway",
"molecule"
],
"name": "Melanoma Molecular Map Project",
"pattern": "^\\d+$",
"prefix": "mmmp",
"synonyms": [
"biomaps"
],
"uri_format": "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1"
},
"mmsinc": {
"description": "MMSsINC is a database of commercially-available compounds for virtual screening and chemoinformatic applications. MMsINC contains over 4 million non-redundant chemical compounds in 3D formats.",
"example": "MMs00000001",
"homepage": "http://mms.dsfarm.unipd.it/MMsINC",
"keywords": [
"small molecule",
"structure"
],
"name": "MMsINC",
"pattern": "^MMs\\d+$",
"prefix": "mmsinc",
"uri_format": "http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php?mmscode=$1"
},
"modeldb": {
"description": "ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment.",
"example": "45539",
"homepage": "http://senselab.med.yale.edu/ModelDB/",
"license": "http://senselab.med.yale.edu/ModelDB/HowToCite.html",
"name": "ModelDB",
"pattern": "^\\d+$",
"prefix": "modeldb",
"pubmed_ids": [
"15055399"
],
"uri_format": "http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1"
},
"modomics": {
"description": "MODOMICS integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that carry out the respective reactions. MODOMICS also provides literature information, and links to other databases, including the available protein sequence and structure data.",
"example": "ac4Cm",
"homepage": "http://genesilico.pl/modomics/",
"keywords": [
"small molecule",
"RNA",
"pathway",
"enzyme",
"structure",
"protein"
],
"name": "MODOMICS: A Database of RNA Modifications",
"pattern": "^[A-Z,0-9]+$",
"prefix": "modomics",
"uri_format": "http://modomics.genesilico.pl/modification?modification_id=$1"
},
"mokca": {
"description": "The MoKCa database has been developed to structurally and functionally annotate, and where possible predict, the phenotypic consequences of mutations in protein kinases implicated in cancer.",
"example": "47",
"homepage": "http://strubiol.icr.ac.uk/extra/mokca/",
"keywords": [
"protein",
"enzyme",
"gene expression"
],
"name": "Mutations of Kinases in Cancer",
"pattern": "^\\d+$",
"prefix": "mokca",
"uri_format": "http://strubiol.icr.ac.uk/extra/mokca/mut_by_prot.php?protein_q=$1"
},
"molmovdb": {
"description": "The Molecular Movements Database lists motions in proteins and other macromolecules. It is arranged around a multi-level classification scheme and includes motions of loops, domains, and subunits.",
"example": "f665230-5267",
"homepage": "http://bioinfo.mbb.yale.edu/MolMovDB/",
"keywords": [
"protein",
"small molecule",
"classification",
"structure"
],
"name": "Database of Macromolecular Movements",
"pattern": "^[A-Z,0-9]+$",
"prefix": "molmovdb",
"uri_format": "http://www.molmovdb.org/cgi-bin/morph.cgi?ID=$1"
},
"mosdb": {
"description": "The MOsDB is a resource for publicly available sequences of the rice (Oryza sativa L.) genome. The goal of MOsDB is to provide all available data about rice genes and genomics, including (in the future) mutant information and expression profiles. At this moment, the MOsDB database includes current (updated on daily basis) published sequences and gene annotation information of two Oryza sativa subspecies: japonica and indica.",
"example": "190",
"homepage": "http://mips.gsf.de/proj/plant/jsf/rice/index.jsp",
"keywords": [
"genome",
"gene"
],
"name": "The MIPS Oryza sativa database",
"pattern": "^\\d+$",
"prefix": "mosdb",
"uri_format": "http://mips.helmholtz-muenchen.de/plant/rice/reportsjsp/contigReport.jsp?contig_id=$1"
},
"motifmap": {
"description": "The MotifMap web interface allows users to filter motif sites using different threshold scores and conservation criteria, including Branch Length Score (BLS) and the Bayesian Branch Length Score (BBLS, see References). For a given motif and species, users can retrieve the genome-wide locations of the motif, and load them into the UCSC Genome Browser for visualization.",
"example": "M01082",
"homepage": "http://motifmap.ics.uci.edu/",
"keywords": [
"genome"
],
"name": "MotifMap",
"pattern": "^M\\d+$",
"prefix": "motifmap"
},
"mousecyc": {
"description": "MouseCyc is a new, manually curated database of both known and predicted metabolic pathways for the laboratory mouse. The database records for 1,060 genes in Mouse Genome Informatics (MGI) are linked directly to 347 pathways with 1,377 compounds and 2,018 enzymatic reactions in MouseCyc.",
"example": "MGI:1915391",
"homepage": "http://mousecyc.jax.org/",
"keywords": [
"pathway",
"gene",
"genome",
"enzyme"
],
"name": "Mouse Pathway Database",
"pattern": "^MGI:\\d+$",
"prefix": "mousecyc",
"uri_format": "http://mousecyc.jax.org/MOUSE/NEW-IMAGE?type=NIL&object=$1"
},
"mp": {
"alt_uri_formats": [
"http://purl.org/obo/owl/MP#$1"
],
"bioportal": "1025",
"description": "The Mammalian Phenotype Ontology is under development as a community effort to provide standard terms for annotating mammalian phenotypic data.",
"example": "MP:0000001",
"homepage": "http://www.informatics.jax.org/searches/MP_form.shtml",
"keywords": [
"obo",
"phenotype",
"mammalian"
],
"name": "Mammalian phenotype",
"pattern": "^MP:\\d+$",
"prefix": "mp",
"uri_format": "http://www.informatics.jax.org/searches/Phat.cgi?id=$1"
},
"mpath": {
"bioportal": "1031",
"description": "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes",
"example": "MPATH_606",
"homepage": "http://www.pathbase.net",
"keywords": [
"obo",
"phenotype",
"mouse"
],
"name": "Mouse pathology",
"pattern": "^MPATH_\\d+$",
"prefix": "mpath"
},
"mpd": {
"description": "The Mouse Phenome Database (MPD) is the database and web site of the Mouse Phenome Project. The MPD serves as a repository for protocols and raw data which are available for on-screen viewing and downloading.",
"example": "Csf1",
"homepage": "http://www.jax.org/phenome",
"name": "Mouse Phenome Database",
"pattern": "^[A-Z]+/\\d+$",
"prefix": "mpd",
"uri_format": "http://phenome.jax.org/db/q?rtn=markers/details&reqsym=$1"
},
"mpi": {
"description": "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts.",
"example": "172",
"homepage": "http://www.jcvi.org/mpidb/",
"keywords": [
"interaction",
"protein",
"small molecule"
],
"license": "http://www.jcvi.org/cms/legal/privacy-statement",
"name": "Microbial Protein Interaction Database",
"pattern": "^\\d+$",
"prefix": "mpi",
"pubmed_ids": [
"18556668"
],
"synonyms": [
"mpid",
"mpidb"
],
"uri_format": "http://www.jcvi.org/mpidb/interaction.php?pname=$1"
},
"mtbd": {
"description": "The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, and information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors.",
"example": "1374",
"homepage": "http://tumor.informatics.jax.org",
"keywords": [
"gene expression",
"DNA"
],
"name": "Mouse Tumor Biology Database",
"pattern": "^\\d+$",
"prefix": "mtbd",
"uri_format": "http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key=$1"
},
"mtbreglist": {
"description": "A database dedicated to the analysis of gene expression and regulation data in Mycobacterium tuberculosis. It is designed to contain most of the characterized transcription start sites and DNA binding sites cross-referenced with their respective transcription factor, along with some predicted regulatory motifs.",
"example": "51",
"homepage": "http://www.USherbrooke.ca/vers/MtbRegList",
"keywords": [
"gene expression",
"regulation",
"DNA",
"small molecule",
"protein"
],
"name": "MtbRegList",
"pattern": "^\\d+$",
"prefix": "mtbreglist",
"uri_format": "http://pages.usherbrooke.ca/gaudreau/MtbRegList/www/genome_ir_manip.php?id=$1"
},
"mutdb": {
"description": "The goal of MutDB is to annotate human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene. Click on the alphabet below to go alphabetically through the list of genes.",
"example": "8772",
"homepage": "http://mutdb.org/",
"keywords": [
"protein",
"structure",
"gene",
"gene expression"
],
"name": "MutDB",
"pattern": "^\\d+$",
"prefix": "mutdb",
"uri_format": "http://mutdb.org/cgi-bin/mutdb.pl?id=[?gene_symbol]&geneid=$1"
},
"myco.lepra": {
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.",
"example": "ML0224",
"homepage": "http://mycobrowser.epfl.ch/leprosy.html",
"keywords": [
"genome",
"sequence"
],
"name": "MycoBrowser leprae",
"pattern": "^ML\\w+$",
"prefix": "myco.lepra",
"uri_format": "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1"
},
"myco.marinum": {
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information.",
"example": "MMAR_2462",
"homepage": "http://mycobrowser.epfl.ch/marinolist.html",
"keywords": [
"genome",
"sequence"
],
"name": "MycoBrowser marinum",
"pattern": "^MMAR\\_\\d+$",
"prefix": "myco.marinum",
"uri_format": "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1"
},
"myco.smeg": {
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.",
"example": "MSMEG_3769",
"homepage": "http://mycobrowser.epfl.ch/smegmalist.html",
"keywords": [
"genome",
"sequence"
],
"name": "MycoBrowser smegmatis",
"pattern": "^MSMEG\\w+$",
"prefix": "myco.smeg",
"uri_format": "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1"
},
"myco.tuber": {
"description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information.",
"example": "Rv1908c",
"homepage": "http://tuberculist.epfl.ch/",
"keywords": [
"genome",
"sequence"
],
"name": "MycoBrowser tuberculosis",
"pattern": "^\\w+$",
"prefix": "myco.tuber",
"pubmed_ids": [
"20980200"
],
"uri_format": "http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1"
},
"mycobank": {
"description": "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.",
"example": "349124",
"homepage": "http://www.mycobank.org",
"keywords": [
"classification"
],
"name": "Fungal Nomenclature and Species Bank",
"pattern": "^\\d+$",
"prefix": "mycobank",
"uri_format": "http://www.mycobank.org/MycoTaxo.aspx?Link=T&Rec=$1"
},
"mypulist": {
"description": "Its purpose is to collate and integrate various aspects of the genomic information from M. pulmonis, a mollicute causal agent of murine respiratory mycoplasmosis. MypuList provides a complete dataset of DNA and protein sequences derived from the strain M. pulmonis UAB CTIP, linked to the relevant annotations and functional assignments.",
"example": "MYPU_0110",
"homepage": "http://genolist.pasteur.fr/MypuList/",
"keywords": [
"genome",
"DNA",
"protein",
"structure"
],
"name": "Mycoplasma pulmonis genome database",
"pattern": "^MYPU_\\d+$",
"prefix": "mypulist"
},
"napp": {
"description": "NAPP (Nucleic Acids Phylogenetic Profiling) is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters.",
"example": "351",
"homepage": "http://napp.u-psud.fr/",
"keywords": [
"clustering",
"nucleotide"
],
"name": "NAPP: Nucleic Acids Phylogenetic Profiling",
"pattern": "^\\d+$",
"prefix": "napp",
"uri_format": "http://napp.u-psud.fr/Niveau2.php?specie=$1"
},
"narcisse": {
"description": "Narcisse is a comparative genome browser. It is specifically dedicated to the comparative display and analysis of completely or partially sequenced genomes. The aim of this project is to provide an intuitive access to the results of whole genome comparison.",
"example": "A1C_06035",
"homepage": "http://narcisse.toulouse.inra.fr",
"keywords": [
"genome"
],
"name": "NARCISSE: a mirror view of conserved syntenies",
"pattern": "^[A-Z,0-9]+$",
"prefix": "narcisse"
},
"nasc": {
"description": "The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.",
"example": "57961",
"homepage": "http://arabidopsis.info",
"keywords": [
"genome"
],
"name": "Nottingham Arabidopsis Stock Centre Seeds Database",
"pattern": "^\\d+$",
"prefix": "nasc",
"uri_format": "http://arabidopsis.info/StockInfo?NASC_id=$1"
},
"nascarrays": {
"description": "NASCArrays is the Nottingham Arabidopsis Stock Centre's microarray database. Currently we hybridise over 1000 GeneChips per year mostly for Arabidopsis thaliana experiments which we make public, more than from any other GeneChip centre",
"example": "413",
"homepage": "http://affymetrix.arabidopsis.info/narrays/experimentbrowse.pl",
"keywords": [
"gene expression"
],
"name": "Nottingham Arabidopsis Stock Centre's microarray database",
"pattern": "^\\d+$",
"prefix": "nascarrays",
"uri_format": "http://affymetrix.arabidopsis.info/narrays/experimentpage.pl?experimentid=$1"
},
"natsdb": {
"description": "Natural Antisense Transcripts (NATs) are RNAs that are at least partially complementary to other endogenous RNAs. This database allows users to browse and search cis-NATs according to the species, gene name, accession number, description, chromosomal location and sequence.",
"example": "4921",
"homepage": "http://natsdb.cbi.pku.edu.cn/",
"keywords": [
"RNA",
"gene"
],
"name": "Natural Antisense Transcripts DataBase",
"pattern": "^\\d+$",
"prefix": "natsdb",
"uri_format": "http://natsdb.cbi.pku.edu.cn/nats_list.php?sa_type=SA_20&represent=1&keyword_term=&species=[?species_name]&id=$1"
},
"nbrc": {
"description": "To provide attractive biological resources with useful information attached, the NITE Biological Resource Center (NBRC) actively collects potentially useful biological resources (microorganisms and cloned genes) and distributes them to promote basic researches as well as industrial applications.",
"example": "00001234",
"homepage": "http://www.nbrc.nite.go.jp/e/index.html",
"keywords": [
"microbial",
"taxonomy"
],
"name": "NITE Biological Research Center Catalogue",
"pattern": "^\\d+$",
"prefix": "nbrc",
"uri_format": "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1"
},
"ncbi.protein": {
"description": "The Entrez Protein search and retrieval system contains protein entries that have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.",
"example": "CAA71118.1",
"homepage": "http://www.ncbi.nlm.nih.gov/protein",
"keywords": [
"protein"
],
"name": "NCBI Protein",
"pattern": "^\\w+\\d+(\\.\\d+)?$",
"prefix": "ncbi.protein",
"synonyms": [
"protein",
"ncbi-proteinid"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/protein/$1"
},
"ncbigene": {
"description": "NCBI Gene provides information for genes from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.",
"example": "1",
"homepage": "http://www.ncbi.nlm.nih.gov/gene",
"keywords": [
"genome",
"gene",
"DNA"
],
"name": "NCBI Gene",
"pattern": "^\\d+$",
"prefix": "ncbigene",
"pubmed_ids": [
"15608257"
],
"synonyms": [
"entrez.gene",
"entrezgene/locuslink",
"geneid"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/gene/$1"
},
"ncir": {
"description": "The primary objective of this database is to provide rapid access to all the RNA structures in which a particular rare base pair has been found. A secondary objective is to summarize the important properties that have been associated with each non-canonical base pair.",
"example": "1155",
"homepage": "http://prion.bchs.uh.edu/bp_type/",
"keywords": [
"RNA",
"structure",
"interaction"
],
"name": "Non-Canonical Interactions in RNA",
"pattern": "^\\d+$",
"prefix": "ncir",
"uri_format": "http://prion.bchs.uh.edu/bp_type/individual_record_page$1.html"
},
"ncit": {
"bioportal": "1032",
"description": "A vocabulary for clinical care, translational and basic research, and public information and administrative activities.",
"example": "C80519",
"homepage": "https://cabig.nci.nih.gov/community/concepts/EVS/",
"keywords": [
"thesaurus"
],
"name": "NCI Thesaurus",
"pattern": "^C\\d+$",
"prefix": "ncit",
"pubmed_ids": [
"19789731"
],
"rdf_uri_format": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#$1",
"synonyms": [
"ncithesaurus",
"nci",
"nci2009_04d",
"nci_thesaurus_code"
],
"uri_format": "http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1"
},
"ndfrt": {
"bioportal": "1352",
"description": "National Drug File - Reference Terminology Public Inferred Edition, 2008_03_11",
"example": "N0000175600",
"homepage": "http://www.va.gov",
"name": "National Drug File",
"pattern": "^N\\d+$",
"prefix": "ndfrt",
"rdf_uri_format": "http://purl.bioontology.org/ontology/NDFRT/$1"
},
"neibank": {
"description": "NEIBank is an integrated resource for genomics and bioinformatics in vision research. It includes expressed sequence tag (EST) data and sequence-verified cDNA clones for multiple eye tissues of several species, web-based access to human eye-specific SAGE data through EyeSAGE, and comprehensive, annotated databases of known human eye disease genes and candidate disease gene loci. All expression- and disease-related data are integrated in EyeBrowse, an eye-centric genome browser.",
"example": "NbLib0056",
"homepage": "http://neibank.nei.nih.gov",
"keywords": [
"genome",
"DNA",
"anatomy",
"gene"
],
"name": "NEIBank",
"pattern": "^NbLib\\d+$",
"prefix": "neibank",
"uri_format": "http://neibank.nei.nih.gov/cgi-bin/showDataTable.cgi?lib=$1"
},
"nembase": {
"description": "NEMBASE is a comprehensive Nematode Transcriptome Database. NEMBASE4 includes robust protein predictions (NemPep4), and protein families for 63 nematode species, over 600,000 ESTs and over 250,000 proteins.",
"example": "NBC00001",
"homepage": "http://www.nematodes.org",
"keywords": [
"RNA",
"protein",
"DNA"
],
"name": "Nematode & Neglected Genomics",
"pattern": "^NBC\\d+$",
"prefix": "nembase",
"uri_format": "http://www.nematodes.org/nembase4/cluster.php?cluster=$1"
},
"netpath": {
"description": "NetPath' is a curated resource of signal transduction pathways in humans. All 20 pathways are freely available in BioPAX, PSI-MI and SBML formats at this website. BioPAX is an emerging standard for pathway data exchange. The 10 cancer signaling pathways are also available for download and browsing from the Cancer Cell Map project website.",
"example": "NetPath_M6464",
"homepage": "http://www.netpath.org/",
"keywords": [
"pathway"
],
"name": "NetPath - Signal Transduction Pathways",
"pattern": "^NetPath_[A-Z]\\d+$",
"prefix": "netpath",
"uri_format": "http://www.netpath.org/molecule?molecule_id=$1"
},
"netpro": {
"description": "NetPro is a comprehensive database of Protein-Protein and Protein-Small molecules interaction, consisting of more than 320,000 interactions captured from more than 1500 abstracts, approximately 1600 published journals and more than 60,000 references.",
"example": "8851",
"homepage": "http://www.interactions.net.in/",
"keywords": [
"protein",
"small molecule",
"interaction"
],
"name": "Molecular Connections NetPro",
"pattern": "^\\d+$",
"prefix": "netpro",
"uri_format": "http://www.interactions.net.in/index_molreport.jsp?id=$1"
},
"neumore": {
"bioportal": "1521",
"description": "Neural Functional Motor Recovery Ontology",
"example": "Tissue",
"homepage": "http://cis.usouthal.edu/~huang/",
"name": "Neural Motor Recovery Ontology",
"pattern": "^\\w+$",
"prefix": "neumore",
"rdf_uri_format": "http://neumore.cis.usouthal.edu/ontologies/NeuMORE-v0.1.owl#$1",
"uri_format": "http://neumore.cis.usouthal.edu/ontologies/NeuMORE-v0.1.owl#$1"
},
"neurolex": {
"description": "The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex).",
"example": "Birnlex_721",
"homepage": "http://www.neurolex.org/wiki/Main_Page",
"keywords": [
"classification",
"neuroscience",
"ontology"
],
"name": "NeuroLex",
"pattern": "^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO)\\d+$",
"prefix": "neurolex",
"pubmed_ids": [
"18975148"
],
"uri_format": "http://www.neurolex.org/wiki/$1"
},
"neuromorpho": {
"description": "NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons.",
"example": "Rosa2",
"homepage": "http://neuromorpho.org/neuroMorpho/index.jsp",
"keywords": [
"anatomy",
"structure"
],
"license": "CC-BY-3.0",
"name": "NeuroMorpho",
"pattern": "^\\w+$",
"prefix": "neuromorpho",
"pubmed_ids": [
"16552417"
],
"uri_format": "http://neuromorpho.org/neuroMorpho/neuron_info.jsp?neuron_name=$1"
},
"neurondb": {
"description": "NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.",
"example": "265",
"homepage": "http://senselab.med.yale.edu/NeuronDB/",
"keywords": [
"anatomy",
"structure"
],
"license": "CC-BY-3.0",
"name": "NeuronDB",
"pattern": "^\\d+$",
"prefix": "neurondb",
"uri_format": "http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1"
},
"nextdb": {
"description": "The Kohara lab has been constructing an expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis and systematic whole mount in situ hybridization. NEXTDB is the database to integrate all information from the expression pattern project.",
"example": "C24A3",
"homepage": "http://nematode.lab.nig.ac.jp/",
"keywords": [
"gene expression",
"genome",
"DNA"
],
"name": "Nematode Expression Pattern DataBase",
"pattern": "^[A-Z]\\d+$",
"prefix": "nextdb",
"uri_format": "http://nematode.lab.nig.ac.jp/cgi-bin/dbest/SrchByCosmid.sh?csmd=$1"
},
"niaest": {
"description": "A searchable mouse cDNA library.",
"example": "J0705A10-3",
"homepage": "http://lgsun.grc.nia.nih.gov/cDNA/cDNA.html",
"keywords": [
"DNA"
],
"name": "NIA Mouse cDNA Project",
"pattern": "^[A-Z,0-9]+$",
"prefix": "niaest",
"uri_format": "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1"
},
"nikkaji": {
"description": "an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST).",
"example": "J818D",
"homepage": "http://nikkajiweb.jst.go.jp/nikkaji_web/pages/top_e.jsp",
"keywords": [
"drug"
],
"license": "http://nikkajiweb.jst.go.jp/nikkaji_web/pages/top_e.jsp",
"name": "Japan Chemical Substance Dictionary (Nikkaji)",
"pattern": "^J\\d+$",
"prefix": "nikkaji"
},
"nmpdr": {
"description": "The NMPDR provided curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma.",
"example": "fig|360108.3.peg.195",
"homepage": "http://www.nmpdr.org",
"keywords": [
"genome"
],
"name": "National Microbial Pathogen Data Resource",
"pattern": "^[A-Z,0-9]+$",
"prefix": "nmpdr",
"uri_format": "http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature=$1"
},
"nmr": {
"bioportal": "1033",
"description": "Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation.",
"example": "NMR_400113",
"homepage": "http://msi-ontology.sourceforge.net/",
"keywords": [
"owl",
"nmr"
],
"name": "NMR-instrument specific component of metabolomics investigations",
"pattern": "^NMR_\\d+$",
"prefix": "nmr",
"rdf_uri_format": "http://msi-ontology.sourceforge.net/ontology/NMR.owl#$1",
"synonyms": [
"msi.nmr"
]
},
"noncode": {
"description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics.",
"example": "377550",
"homepage": "http://www.noncode.org/",
"keywords": [
"expression",
"nucleotide"
],
"name": "NONCODE",
"pattern": "^\\d+$",
"prefix": "noncode",
"pubmed_ids": [
"22135294"
],
"uri_format": "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1"
},
"norine": {
"description": "Norine is a platform that includes a database of nonribosomal peptides together with tools for their analysis. Norine currently contains more than 1000 peptides.",
"example": "NOR00681",
"homepage": "http://bioinfo.lifl.fr/norine/",
"keywords": [
"protein"
],
"name": "Non-Ribosomal Peptides Database",
"pattern": "^NOR\\d+$",
"prefix": "norine",
"uri_format": "http://bioinfo.lifl.fr/norine/result.jsp?ID=$1"
},
"npd": {
"description": "The Nuclear Protein Database (NPD) is a searchable database of information on proteins that are localised to the nucleus of vertebrate cells.",
"example": "1NP00752",
"homepage": "http://npd.hgu.mrc.ac.uk",
"keywords": [
"protein"
],
"name": "Nuclear Protein Database",
"pattern": "^1NP\\d+$",
"prefix": "npd",
"uri_format": "http://npd.hgu.mrc.ac.uk/user/$1"
},
"nrestdb": {
"description": "The Natural Rubber EST database (NRESTdb) is an online resource which provides access to sequence, clustering, classification and annotation data of ESTs from rubber. The NRESTdb resources and facilities are aimed at providing a genomic data resource to facilitate rubber biotechnology research.",
"example": "A1012",
"homepage": "http://genome.ukm.my/nrestdb/",
"keywords": [
"DNA",
"classification"
],
"name": "The Natural Rubber EST Database",
"pattern": "^[A-Z]\\d+$",
"prefix": "nrestdb"
},
"ntdb": {
"description": "This database is a collection of thermodynamic and structural data, experimental methods, conditions and relevant literature citations on nucleic acids. The thermodynamic data of interest can be searched by structural features, thermodynamic parameters, experimental methods and the use of citation.",
"example": "BNA0002",
"homepage": "http://ntdb.chem.cuhk.edu.hk",
"keywords": [
"structure",
"DNA"
],
"name": "Thermodynamic Database for Nucleic Acids",
"pattern": "^BNA\\d+$",
"prefix": "ntdb",
"uri_format": "http://ntdb.chem.cuhk.edu.hk/data/$1.htm"
},
"nucleardb": {
"description": "The NucleaRDB is a part of a project devoted to build Molecular Class-Specific Information Systems (MCSIS) to provide, disseminate and harvest heterogeneous data. The NucleaRDB was built using the software developed for the GPCRDB.",
"example": "prgr_human",
"homepage": "http://www.receptors.org/NR/",
"keywords": [
"classification"
],
"name": "NucleaRDB: An Information System for Nuclear Receptors",
"pattern": "^\\w+\\_\\w+$",
"prefix": "nucleardb",
"pubmed_ids": [
"22064856"
],
"uri_format": "http://www.receptors.org/NR/seq/DR/$1.html"
},
"nursa": {
"description": "NURSA's mission is to further the objectives of the nuclear receptor and coregulation signaling scientific community in the key areas of research and education.",
"example": "5A1",
"homepage": "http://www.nursa.org",
"keywords": [
"protein",
"small molecule"
],
"name": "Nuclear Receptor Signalling Atlas",
"pattern": "^[A-Z,0-9]+$",
"prefix": "nursa",
"uri_format": "http://www.nursa.org/molecule.cfm?molType=[?molecule_type]&molId=$1"
},
"obi": {
"alt_uri_formats": [
"http://purl.org/obo/owl/OBI#$1"
],
"bioportal": "1123",
"description": "The Ontology for Biomedical Investigations (OBI) an ontology of investigations, the protocols and instrumentation used, the material used, the data generated and the types of analysis performed on it.",
"example": "OBI_0000011",
"homepage": "http://purl.obolibrary.org/obo/obi",
"keywords": [
"ontology"
],
"license": "CC-BY-3.0",
"name": "Ontology for Biomedical Investigations",
"pattern": "^OBI_\\d{7}$",
"prefix": "obi",
"synonyms": [
"obo.obi"
]
},
"odb": {
"description": "ODB (Operon DataBase) aims to collect known operons in multiple species and to offer a system to predict operons by user definitions. All the known operons are derived from the literature and from publicly available database including operon information.",
"example": "b2132",
"homepage": "http://www.genome.sk.ritsumei.ac.jp/odb/",
"keywords": [
"DNA",
"structure",
"regulation"
],
"name": "Operon database",
"pattern": "^[a-z]\\d+$",
"prefix": "odb",
"uri_format": "http://www.genome.sk.ritsumei.ac.jp/odb/odb2.rb?org=[?species]&genome_id=[?genome_id]&genes=$1"
},
"ogd": {
"description": "The Oomycete Genomics Database is a publicly accessible resource that includes functional assays and expression data, combined with transcript and genomic analysis and annotation. OGD builds upon data available from the Phytophthora Genome Consortium, Syngenta Phytophthora Consortium and the Phytophthora Functional Genomics Database.",
"example": "92",
"homepage": "http://www.oomycete.org/",
"keywords": [
"genome",
"gene expression",
"DNA",
"RNA"
],
"name": "Oomycete Genomics Database",
"pattern": "^\\d+$",
"prefix": "ogd",
"uri_format": "http://www.oomycete.org/ogd/sequence.html?sequence_id=$1"
},
"oglycbase": {
"description": "O-GLYCBASE is a database of O- and C-glycosylated proteins. It contains experimentally verified O- or C-glycosylation sites.",
"example": "002",
"homepage": "http://www.cbs.dtu.dk/databases/OGLYCBASE/",
"keywords": [
"small molecule",
"protein"
],
"name": "O-GLYCBASE",
"pattern": "^\\d+$",
"prefix": "oglycbase"
},
"okcam": {
"description": "OKCAM (Ontology-based Knowledgebase for Cell Adhesion Molecules) is an online resource for human genes known or predicted to be related to the processes of cell adhesion. These genes include members of the cadherin, immunoglobulin/FibronectinIII (IgFn), integrin, neurexin, neuroligin, and catenin families.",
"example": "23105",
"homepage": "http://okcam.cbi.pku.edu.cn",
"keywords": [
"ontology",
"small molecule",
"gene"
],
"name": "Ontology-based Knowledgebase for Cell Adhesion Molecules",
"pattern": "^\\d+$",
"prefix": "okcam",
"uri_format": "http://okcam.cbi.pku.edu.cn/entry-info.php?id=$1"
},
"oma": {
"description": "OMA offers a comprehensive search and numerous display options for 3.7 million proteins from 830 species. The main features are the orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed.",
"example": "ARATH2772",
"homepage": "http://www.omabrowser.org",
"keywords": [
"DNA",
"protein"
],
"name": "Identification of Orthologs from Complete Genome Data",
"pattern": "^[A-Z]+\\d+$",
"prefix": "oma",
"uri_format": "http://www.omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1"
},
"omia": {
"description": "Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse).",
"example": "1000",
"homepage": "http://omia.angis.org.au/",
"keywords": [
"gene",
"classification"
],
"name": "Online Mendelian Inheritance in Animals",
"pattern": "^\\d+$",
"prefix": "omia",
"uri_format": "http://omia.angis.org.au/retrieve.shtml?pid=$1"
},
"omim": {
"alt_uri_formats": [
"http://europe.omim.org/entry/#$1",
"http://us-east.omim.org/entry/#$1",
"http://omim.org/entry/#$1"
],
"description": "OMIM is a comprehensive, authoritative, and timely compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype.",
"example": "603903",
"homepage": "http://www.ncbi.nlm.nih.gov/omim/",
"keywords": [
"gene",
"gene expression"
],
"license": "http://www.nlm.nih.gov/copyright.html",
"name": "Online Mendelian Inheritance in Man",
"pattern": "^[*#+%^]?\\d{6}$",
"prefix": "omim",
"pubmed_ids": [
"15608251"
],
"synonyms": [
"mim"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/omim/$1"
},
"ootfd": {
"description": "ooTFD (object-oriented Transcription Factors Database) is a successor to TFD, the original Transcription Factors Database . ooTFD has been tested in a number of object-oriented database management systems, including ROL (Rule-based Object Language), and MOOD (Materials object-oriented database), and it is currently maintained using the pure java object database ozone .",
"example": "S05335",
"homepage": "http://www.ifti.org/ootfd",
"keywords": [
"regulation"
],
"name": "object-oriented Transcription Factors Database",
"pattern": "^S\\d+$",
"prefix": "ootfd"
},
"opb": {
"bioportal": "1141",
"description": "The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.",
"example": "OPB_00573",
"homepage": "https://sites.google.com/site/semanticsofbiologicalprocesses/projects/the-ontology-of-physics-for-biology-opb",
"keywords": [
"ontology",
"structure"
],
"name": "Ontology of Physics for Biology",
"pattern": "^OPB_\\d+$",
"prefix": "opb",
"rdf_uri_format": "http://bhi.washington.edu/OPB#$1",
"synonyms": [
"opb.properties"
]
},
"operondb": {
"description": "OperonDB is a database containing the results of a computational algorithm for locating operon structures in microbial genomes. OperonDB has grown from 34 genomes in its initial release to more than 500 genomes today.",
"example": "311402",
"homepage": "http://operondb.cbcb.umd.edu/cgi-bin/operondb/operons.cgi",
"keywords": [
"structure",
"DNA",
"protein",
"genome"
],
"name": "OperonDB: predicting operons in microbial genomes",
"pattern": "^\\d+$",
"prefix": "operondb",
"uri_format": "http://operondb.cbcb.umd.edu/cgi-bin/operondb/pairs.cgi?taxon_id=$1"
},
"ordb": {
"description": "ORDB began as a database of vertebrate OR genes and proteins and continues to support sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family.",
"example": "14673",
"homepage": "http://senselab.med.yale.edu/senselab/ordb/",
"keywords": [
"gene",
"protein"
],
"name": "Olfactory Receptor Database",
"pattern": "^\\d+$",
"prefix": "ordb",
"synonyms": [
"ord"
],
"uri_format": "http://senselab.med.yale.edu/ordb/eavdata.asp?o=$1"
},
"oreganno": {
"description": "The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, the eVOC: Cell type ontology, and the Taxonomy database",
"example": "OREG0005272",
"homepage": "http://www.oreganno.org/",
"keywords": [
"regulation",
"small molecule",
"protein",
"gene"
],
"name": "Open Regulatory Annotation",
"pattern": "^OREG\\d+$",
"prefix": "oreganno",
"uri_format": "http://www.oreganno.org/oregano/recordview.action?recid=$1"
},
"orenza": {
"description": "ORENZA provides an accurate and up to date list of Enzyme Activities for which no sequences are available in the main sequence protein databases.",
"example": "1.2.3.1",
"homepage": "http://www.orenza.u-psud.fr/",
"keywords": [
"enzyme",
"protein",
"structure"
],
"name": "ORENZA: a database of ORphan ENZyme Activities",
"pattern": "^EC Number$",
"prefix": "orenza",
"uri_format": "http://www.orenza.u-psud.fr/query_by_ec.php?EC_number=EC%20$1"
},
"orfdb": {
"description": "A collection of ORF clones available through Invitrogen.",
"example": "IOH36839",
"homepage": "http://orf.invitrogen.com/",
"keywords": [
"DNA"
],
"name": "ORFDB",
"pattern": "^[A-Z]+\\d+$",
"prefix": "orfdb",
"uri_format": "http://orf.invitrogen.com/cgi-bin/ORFCard?&ORF=$1&set=UltimateORFs&hboxPath=keyword"
},
"organelle_db": {
"description": "Organelle DB compiles protein localization data from organisms spanning the eukaryotic kingdom and presents an organized catalog of the known protein constituents of more than 50 organelles, subcellular structures, and protein complexes.",
"example": "1098025",
"homepage": "http://organelledb.lsi.umich.edu/",
"keywords": [
"protein",
"anatomy",
"structure"
],
"name": "Organelle DB",
"pattern": "^\\d+$",
"prefix": "organelle_db",
"uri_format": "http://organelledb.lsi.umich.edu/gene.php?id=$1"
},
"oridb": {
"description": "This database summarizes our knowledge of replication origins in the budding yeast Saccharomyces cerevisiae. Each proposed origin site has been assigned a Status (Confirmed, Likely, or Dubious) expressing the confidence that the site genuinely corresponds to an origin.",
"example": "16",
"homepage": "http://www.oridb.org/",
"keywords": [
"DNA",
"RNA"
],
"name": "The DNA Replication Origin Database",
"pattern": "^\\d+$",
"prefix": "oridb",
"uri_format": "http://www.oridb.org/details1.php?id=$1"
},
"orphanet": {
"description": "Orphanet is a database of information on rare diseases and orphan drugs for all publics. Its aim is to contribute to the improvement of the diagnosis, care and treatment of patients with rare diseases.",
"example": "85163",
"homepage": "http://www.orpha.net/consor/cgi-bin/home.php?Lng=GB",
"keywords": [
"disease",
"drug",
"human"
],
"license": "CC BY-ND 3.0",
"name": "Orphanet; a database dedicated to information on rare diseases and orphan drugs",
"pattern": "^\\d+$",
"prefix": "orphanet",
"pubmed_ids": [
"19058507"
],
"uri_format": "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=$1"
},
"orthodb": {
"description": "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny.",
"example": "EOG9VMFMQ",
"homepage": "http://cegg.unige.ch/orthodb/browse",
"keywords": [
"eukaryotic",
"protein",
"DNA"
],
"name": "Database of Orthologous Groups",
"pattern": "^EOG[A-Z,0-9]+$",
"prefix": "orthodb",
"pubmed_ids": [
"20972218"
],
"uri_format": "http://cegg.unige.ch/orthodb3/results?searchtext=$1"
},
"orthomcl": {
"description": "OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species/genomes, but also groups representing species-specific gene expansion families. So it serves as an important utility for automated eukaryotic genome annotation.",
"example": "OG4_11257",
"homepage": "http://orthomcl.cbil.upenn.edu",
"keywords": [
"genome",
"protein",
"structure",
"classification"
],
"name": "OrthoMCL: Ortholog Groups of Protein Sequences",
"pattern": "^OG4_\\d+$",
"prefix": "orthomcl",
"uri_format": "http://orthomcl.org/cgi-bin/OrthoMclWeb.cgi?rm=sequenceList&groupac=$1"
},
"otl": {
"description": "Oryza Tag Line consists in a searchable database developed under the Oracle management system integrating phenotypic data resulting from the evaluation of the G\u00e9noplante rice insertion line library.",
"example": "AGFC04",
"homepage": "http://urgi.versailles.inra.fr/OryzaTagLine/",
"keywords": [
"DNA"
],
"name": "Oryza Tag Line: An integrated database for the functional analysis of the rice genome",
"pattern": "^A[A-Z]+\\d+$",
"prefix": "otl",
"uri_format": "http://urgi.versailles.inra.fr/OryzaTagLine/cgi-bin/general_mutant.pl?line=$1"
},
"p3db": {
"description": "P3DB was established with an overall objective to provide a resource of protein phosphorylation data from multiple plants. P3DB uses MySQL database to store phosphorylation data.",
"example": "6401",
"homepage": "http://www.p3db.org",
"keywords": [
"protein",
"small molecule"
],
"name": "Plant Protein Phosphorylation Database",
"pattern": "^\\d+$",
"prefix": "p3db",
"uri_format": "http://digbio.missouri.edu/p3db/data/protein.php?id=$1"
},
"pairsdb": {
"description": "PairsDB is a collection of protein sequences and the BLAST and PSI-BLAST alignments between them. Instead of running BLAST or PSI-BLAST individually, results can be retrieved from a database of pre-computed alignments. PairsDB is continually updated and we aim to be as comprehensive as possible.",
"example": "1j3s-a",
"homepage": "http://pairsdb.csc.fi",
"keywords": [
"protein",
"structure"
],
"name": "PairsDB",
"pattern": "^PDBID$",
"prefix": "pairsdb",
"uri_format": "http://pairsdb.csc.fi/?query=seqinfo&accnum=$1"
},
"paleodb": {
"description": "The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data.",
"example": "83088",
"keywords": [
"taxonomy"
],
"name": "Paleobiology Database",
"pattern": "^\\d+$",
"prefix": "paleodb",
"uri_format": "http://paleodb.geology.wisc.edu/cgi-bin/bridge.pl?a=basicTaxonInfo&taxon_no=$1"
},
"pali": {
"description": "This database provides structure based sequence alignments for homologous proteins of known 3-D structure. The alignments available include those of pairwise (two proteins at a time) and multiple (simultaneous superposition of all the structures in a family).",
"example": "a.100.1.3",
"homepage": "http://pauling.mbu.iisc.ernet.in/~pali/",
"keywords": [
"protein",
"structure"
],
"name": "PALI: Phylogeny and ALIgnment of homologous protein structures",
"pattern": "^[A-Z.0-9]+$",
"prefix": "pali",
"uri_format": "http://pauling.mbu.iisc.ernet.in/~pali/cgi/members.cgi?famno=$1"
},
"pandit": {
"description": "PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains.",
"example": "PF00004",
"homepage": "http://www.ebi.ac.uk/goldman-srv/pandit",
"keywords": [
"DNA",
"protein",
"structure"
],
"name": "Protein and Associated NucleotideDomains with Inferred Trees",
"pattern": "^PF\\d+$",
"prefix": "pandit",
"uri_format": "http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam=$1"
},
"panther": {
"description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.",
"example": "PTHR12345",
"homepage": "http://www.pantherdb.org",
"keywords": [
"protein",
"classification",
"gene",
"pathway",
"ontology"
],
"license": "http://www.pantherdb.org/tou.jsp",
"name": "Protein ANalysis THrough Evolutionary Relationships: Classification of Genes and Proteins",
"pattern": "^PTHR\\d{5}(\\:SF{1,3})?$",
"prefix": "panther",
"pubmed_ids": [
"12952881"
],
"uri_format": "http://www.pantherdb.org/panther/family.do?clsAccession=$1"
},
"partigenedb": {
"description": "The PartiGene system provides an industry standard for these types of databases and has since been adopted by UK's Natural Environmental Research Council. This system has now been expanded into a fully automatable pipeline such that for the first time, a comprehensive database of ~250 sets of eukaryotic genes has been created.",
"example": "TFC0000035",
"homepage": "http://www.partigenedb.org/",
"keywords": [
"gene",
"DNA"
],
"name": "PartiGeneDB: A database of partial genomes",
"pattern": "^TFC\\d+$",
"prefix": "partigenedb",
"uri_format": "http://www.compsysbio.org/partigene/cluster.php?cluster=$1"
},
"pass2": {
"description": "PASS2 is an automatic version of the original superfamily alignment database, CAMPASS. The current version contains 628 multi member superfamilies and 566 structure based sequence annotated single member superfamilies. Sequence members for the superfamilies in different genomes have been listed and aligned.",
"example": "47391",
"homepage": "http://www.ncbs.res.in/~faculty/mini/campass/pass2.html",
"keywords": [
"structure",
"DNA",
"genome",
"classification"
],
"name": "Protein Alignments organised as Structural Superfamilies",
"pattern": "^\\d+$",
"prefix": "pass2",
"uri_format": "http://caps.ncbs.res.in/cgi-bin/mini/databases/campass/pass/pass.cgi?code=$1"
},
"pathguide": {
"description": "Pathguide contains information about 325 biological related resources and molecular interaction related resources.",
"example": "49",
"homepage": "http://pathguide.org",
"keywords": [
"pathway",
"interaction",
"small molecule",
"protein",
"gene"
],
"name": "Pathguide: The Pathway Resource List",
"pattern": "^\\d+$",
"prefix": "pathguide",
"uri_format": "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=$1"
},
"pathoplant": {
"description": "PathoPlant\u00ae is a database on plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. PathoPlant\u00ae also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon pathogen infection or elicitor treatment.",
"example": "MO000027",
"homepage": "http://www.pathoplant.de",
"keywords": [
"interaction",
"pathway",
"small molecule",
"gene expression",
"protein"
],
"name": "PathoPlant\u00ae",
"pattern": "^MO\\d+$",
"prefix": "pathoplant",
"uri_format": "http://www.pathoplant.de/detail.php?accNo=$1"
},
"pathwaycommons": {
"description": "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases",
"example": "485991",
"homepage": "http://www.pathwaycommons.org/pc/",
"keywords": [
"pathway"
],
"license": "http://www.pathwaycommons.org/pc/about.do",
"name": "Pathway Commons",
"pattern": "^\\d+$",
"prefix": "pathwaycommons",
"synonyms": [
"cpath"
],
"uri_format": "http://www.pathwaycommons.org/pc/record2.do?id=$1"
},
"pathwayontology": {
"description": "RGD uses four hierarchical, controlled vocabularies to annotate genes, QTLs, strains and homologs: Gene Ontology, Mammalian Phenotype Ontology, Disease Ontology and Pathway Ontology. The Ontology Browser allows you to retrieve all genes, QTLs, strains and homologs with similar annotations.",
"example": "281006",
"homepage": "http://rgd.mcw.edu/tools/ontology/ont_search.cgi",
"keywords": [
"gene",
"classification"
],
"name": "Pathway ontology",
"pattern": "^\\d+$",
"prefix": "pathwayontology",
"synonyms": [
"pw"
],
"uri_format": "http://rgd.mcw.edu/tools/ontology/ont_annot.cgi?term_key=$1&ontology=go"
},
"pato": {
"alt_uri_formats": [
"http://purl.org/obo/owl/PATO#$1"
],
"bioportal": "1107",
"description": "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.",
"example": "PATO:0001998",
"homepage": "http://obofoundry.org/wiki/index.php/PATO:Main_Page",
"keywords": [
"obo",
"ontology",
"quality",
"phenotype"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "PATO",
"pattern": "^PATO:\\d{7}$",
"prefix": "pato",
"synonyms": [
"obo.pato"
]
},
"patric": {
"description": "PATRIC, the PathoSystems Resource Integration Center, is a multi-faceted bioinformatic website containing genomic and associated information on the eight important human pathogens",
"example": "724",
"homepage": "http://patric.vbi.vt.edu/",
"keywords": [
"genome"
],
"name": "PATRIC: PathoSystems Resource Integration Center",
"pattern": "^\\d+$",
"prefix": "patric",
"uri_format": "http://patricbrc.vbi.vt.edu/portal/portal/patric/Taxon?cType=taxon&cId=$1"
},
"pazar": {
"description": "PAZAR is a software framework for the construction and maintenance of regulatory sequence data annotations; a framework which allows multiple boutique databases to function independently within a larger system (or information mall). The goal of PAZAR is to be the public repository for regulatory data.",
"example": "TF0000448",
"homepage": "http://www.pazar.info/",
"keywords": [
"regulation",
"DNA",
"RNA"
],
"name": "PAZAR",
"pattern": "^TF\\d+$",
"prefix": "pazar",
"uri_format": "http://www.pazar.info/cgi-bin/tf_search.cgi?searchtab=tfs&ID_list=PAZAR_TF&geneID=$1"
},
"pdb": {
"alt_uri_formats": [
"http://www.ebi.ac.uk/pdbsum/#$1",
"http://service.pdbj.org/mine/summary/#$1",
"http://proteopedia.org/wiki/index.php/#$1",
"http://www.pdbe.org/#$1"
],
"description": "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.",
"example": "2gc4",
"homepage": "http://www.pdb.org/",
"keywords": [
"protein",
"DNA",
"RNA",
"structure"
],
"name": "Protein Data Bank",
"pattern": "^\\d[A-Za-z0-9]{3}$",
"prefix": "pdb",
"pubmed_ids": [
"17142228"
],
"synonyms": [
"wwpdb",
"pdbe",
"proteindatabank",
"pdbj",
"pdbsumpdb"
],
"uri_format": "http://www.rcsb.org/pdb/explore/explore.do?structureId=$1"
},
"pdb.tm": {
"description": "PDBTM, the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank (PDB).",
"example": "1iij",
"homepage": "http://pdbtm.enzim.hu/",
"keywords": [
"protein",
"structure"
],
"name": "Protein Data Bank of Transmembrane Proteins",
"pattern": "^[A-Z,0-9]+$",
"prefix": "pdb.tm",
"uri_format": "http://pdbtm.enzim.hu/?m=show_entry&id=$1"
},
"pdbbind": {
"description": "The PDBbind database is designed to provide a collection of experimentally measured binding affinity data (Kd, Ki, and IC50) exclusively for the protein-ligand complexes available in the Protein Data Bank (PDB)",
"example": "1iij",
"homepage": "http://www.pdbbind.org/",
"keywords": [
"protein",
"interaction",
"small molecule"
],
"name": "PDBbind",
"pattern": "^[A-Z,0-9]+$",
"prefix": "pdbbind"
},
"pdbe": {
"description": "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.",
"example": "2OM1",
"homepage": "http://www.ebi.ac.uk/pdbe/",
"keywords": [
"protein",
"structure"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Protein Data Bank Europe",
"pattern": "^\\d+[A-Z]+$",
"prefix": "pdbe",
"uri_format": "http://www.pdbe.org/$1"
},
"pdbj": {
"description": "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.",
"example": "2OM1",
"homepage": "http://www.pdbj.org/",
"keywords": [
"protein",
"structure"
],
"name": "Protein Data Bank Japan",
"pattern": "^\\d+[A-Z]+$",
"prefix": "pdbj",
"uri_format": "http://service.pdbj.org/mine/Detail?PDBID=$1&PAGEID=Summary"
},
"pdbligand": {
"description": "PDB-Ligand is a three dimensional structure database of small molecular ligands that are bound to larger biolomocules deposited in the Protein Data Bank (PDB).",
"example": "1iij",
"homepage": "http://www.idrtech.com/PDB-Ligand/",
"keywords": [
"small molecule",
"protein",
"interaction",
"structure"
],
"name": "PDB-Ligand",
"pattern": "^[A-Z,0-9]+$",
"prefix": "pdbligand"
},
"pdbreprdb": {
"description": "PDB-REPRDB is a reorganized database of protein chains from PDB(Protein Data Bank), and provides 'the list of the representative protein chains' and 'the list of similar protein chain groups'.",
"example": "1IXBA",
"homepage": "http://mbs.cbrc.jp/pdbreprdb-cgi/reprdb_menu.pl",
"keywords": [
"protein",
"structure"
],
"name": "PDB-REPRDB: Representative Protein Chains from PDB",
"pattern": "^[A-Z,0-9]+$",
"prefix": "pdbreprdb"
},
"pdbsum": {
"description": "PDBsum provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.",
"example": "1kfv",
"homepage": "http://www.ebi.ac.uk/pdbsum",
"keywords": [
"protein",
"structure",
"interaction"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "PDBsum; at-a-glance overview of macromolecular structures",
"pattern": "^[A-Z,0-9]+$",
"prefix": "pdbsum",
"uri_format": "http://www.ebi.ac.uk/pdbsum/$1"
},
"pdtd": {
"description": "PDTD is a dual function database that associates an informatics database to a structural database of known and potential drug targets. PDTD is a comprehensive, web-accessible database of drug targets, and focuses on those drug targets with known 3D-structures. PDTD contains 1207 entries covering 841 known and potential drug targets with structures from the Protein Data Bank (PDB).",
"example": "1AJV",
"homepage": "http://www.dddc.ac.cn/pdtd/",
"keywords": [
"small molecule",
"structure",
"protein"
],
"name": "Potential Drug Target Database",
"pattern": "^[A-Z,0-9]+$",
"prefix": "pdtd",
"uri_format": "http://www.dddc.ac.cn/pdtd/detail.php?pdbId=$1"
},
"pdzbase": {
"description": "PDZBase is a manually curated protein-protein interaction database developed specifically for interactions involving PDZ domains. PDZBase currently contains 339 experimentally determined protein protein interactions.",
"example": "P31016",
"homepage": "http://icb.med.cornell.edu/services/pdz/start",
"keywords": [
"protein",
"interaction"
],
"name": "PDZBase",
"pattern": "^[A-Z]\\d+$",
"prefix": "pdzbase"
},
"pede": {
"description": "PEDE (Pig Expression Data Explorer) is a database of porcine EST collections derived from full-length cDNA libraries and full-length sequences of the cDNA clones picked from the EST collection.",
"example": "20060611C-000177",
"homepage": "http://pede.dna.affrc.go.jp/",
"keywords": [
"gene expression",
"DNA"
],
"name": "Pig Expression Data Explorer",
"pattern": "^[A-Z,0-9]+$",
"prefix": "pede",
"uri_format": "http://pede.dna.affrc.go.jp/seq_search/assembly_info.php?release=$1&name=$1"
},
"pepbank": {
"description": "PepBank is a database of peptides based on sequence text mining and public peptide data sources. Only peptides that are 20 amino acids or shorter are stored. Only peptides with available sequences are stored.",
"example": "21877",
"homepage": "http://pepbank.mgh.harvard.edu/",
"keywords": [
"protein",
"structure"
],
"name": "PepBank Peptide Database",
"pattern": "^\\d+$",
"prefix": "pepbank",
"uri_format": "http://pepbank.mgh.harvard.edu/interactions/details/$1"
},
"pepr": {
"description": "PEPR is an experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform. The primary goal of PEPR is to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets.",
"example": "3702",
"homepage": "http://pepr.cnmcresearch.org",
"keywords": [
"gene expression"
],
"name": "Public Expression Profiling Resource",
"pattern": "^\\d+$",
"prefix": "pepr",
"uri_format": "http://pepr.cnmcresearch.org/browse.do?action=list_[?exp/?prj_exp]&[?exp/?project]Id=$1"
},
"peptideatlas": {
"description": "The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools.",
"example": "PAp00000009",
"homepage": "http://www.peptideatlas.org",
"keywords": [
"mass spectrometry",
"protein",
"structure"
],
"license": "http://www.peptideatlas.org/publications.php",
"name": "PeptideAtlas",
"pattern": "^PAp[0-9]{8}$",
"prefix": "peptideatlas",
"pubmed_ids": [
"18451766"
],
"uri_format": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProtein?atlas_build_id=242&protein_name=$1&action=QUERY"
},
"peroxibase": {
"description": "Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences.",
"example": "5282",
"homepage": "http://peroxibase.toulouse.inra.fr/",
"keywords": [
"enzyme",
"protein",
"regulation"
],
"name": "PeroxiBase, a peroxidase database",
"pattern": "^\\d+$",
"prefix": "peroxibase",
"pubmed_ids": [
"19112168"
],
"uri_format": "http://peroxibase.toulouse.inra.fr/listing.php?action=view&id=$1"
},
"pfam": {
"alt_uri_formats": [
"http://pfam.sbc.su.se/family/#$1"
],
"description": "The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.",
"example": "PF01234",
"homepage": "http://pfam.sanger.ac.uk/",
"keywords": [
"domain",
"protein"
],
"license": "CC0-1.0",
"name": "Sanger Pfam Mirror",
"pattern": "^PF\\d{5}$",
"prefix": "pfam",
"pubmed_ids": [
"9847196",
"14681378",
"11752314",
"10592242",
"9399864",
"9223186"
],
"rdf_uri_format": "http://pfam.janelia.org/family/#$1",
"uri_format": "http://pfam.sanger.ac.uk/family?entry=$1"
},
"pgc": {
"description": "The list of plant sequencing projects in this page includes those that have reached the stage where active sequence determination is currently producing, or is expected to produce in the near future, GenBank accessions toward the goal of determining the sequence of that plant genome.",
"example": "4522",
"homepage": "http://www.ncbi.nlm.nih.gov/genomes/PLANTS/PlantList.html",
"keywords": [
"DNA",
"genome"
],
"name": "Plant Genome Central",
"pattern": "^\\d+$",
"prefix": "pgc"
},
"pgdb": {
"description": "PGDB is a curated and integrated database of human genes related to the prostate and prostatic diseases. Currently, PGDB covers genes that have been reported in the scientific literature to be involved in a number of molecular and genetic events occurred in the prostate such as gene mutation, gross deletion, methylation, polymorphism, over-expression and linkage (linkage disequilibrium).",
"example": "14",
"homepage": "http://www.ucsf.edu/pgdb/",
"keywords": [
"gene",
"gene expression",
"small molecule",
"DNA"
],
"name": "Human Prostate Gene DataBase",
"pattern": "^\\d+$",
"prefix": "pgdb",
"uri_format": "http://www.urogene.org/pgdb/gene/$1.html"
},
"pgn": {
"description": "PGN is a repository for plant EST sequence data located at Cornell. It comprises an analysis pipeline and a website, and presently contains mainly data from the Floral Genome Project.",
"example": "280859",
"homepage": "http://pgn.cornell.edu",
"keywords": [
"DNA"
],
"name": "Plant Genome Network",
"pattern": "^\\d+$",
"prefix": "pgn",
"uri_format": "http://pgn.cornell.edu/search/unigene_search_result.pl?unigene_id=$1"
},
"pharmgkb": {
"alt_uri_formats": [
"http://bioonto.de/pgkb.owl#$1"
],
"description": "PharmGKB curates primary genotype and phenotype data, annotates gene variants and gene-drug-disease relationships via literature review, and summarizes important PGx genes and drug pathways.",
"example": "PA445062",
"homepage": "http://www.pharmgkb.org/index.jsp",
"keywords": [
"gene",
"classification",
"gene expression",
"pathway"
],
"name": "Pharmacogenomics Knowledge Base",
"pattern": "^PA\\d+$",
"prefix": "pharmgkb",
"pubmed_ids": [
"11908751",
"22103613"
],
"uri_format": "http://www.pharmgkb.org/do/serve?objId=$1"
},
"pharmgkb.disease": {
"description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.",
"example": "PA447218",
"keywords": [
"pharmacogenomics"
],
"name": "PharmGKB Disease",
"pattern": "^PA\\d+$",
"prefix": "pharmgkb.disease",
"pubmed_ids": [
"11908751",
"22103613"
],
"uri_format": "http://www.pharmgkb.org/disease/$1"
},
"pharmgkb.drug": {
"description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.",
"example": "PA448710",
"keywords": [
"drug",
"pharmacogenomics"
],
"name": "PharmGKB Drug",
"pattern": "^PA\\d+$",
"prefix": "pharmgkb.drug",
"pubmed_ids": [
"11908751",
"22103613"
],
"uri_format": "http://www.pharmgkb.org/drug/$1"
},
"pharmgkb.gene": {
"description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.",
"example": "PA131",
"keywords": [
"gene",
"pharmacogenomics"
],
"name": "PharmGKB Gene",
"pattern": "^PA\\w+$",
"prefix": "pharmgkb.gene",
"pubmed_ids": [
"22103613"
],
"uri_format": "http://www.pharmgkb.org/gene/$1"
},
"pharmgkb.pathways": {
"description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies.",
"example": "PA146123006",
"keywords": [
"pathway",
"pharmacogenomics"
],
"name": "PharmGKB Pathways",
"pattern": "^PA\\d+$",
"prefix": "pharmgkb.pathways",
"pubmed_ids": [
"11908751",
"22103613"
],
"uri_format": "http://www.pharmgkb.org/pathway/$1"
},
"pharmvar": {
"description": "The Pharmacogene Variation (PharmVar) Consortium is the new home for PGx gene nomenclature serving as a centralized \u2018Next-Generation\u2019 Pharmacogene Variation data repository. The major focus of PharmVar is to catalogue allelic variation of genes impacting drug metabolism, disposition and response and provide a unifying designation system (nomenclature) for the global pharmacogenetic/genomic community. Efforts are synchronized between PharmVar, the Pharmacogenomic KnowledgeBase, and the Clinical Pharmacogenetic Implementation Consortium.",
"example": "CYP2A6",
"homepage": "https://www.pharmvar.org",
"keywords": [
"variant",
"gene",
"pharmacogenomics"
],
"name": "PharmVar",
"pattern": "^[A-z0-9]+$",
"prefix": "pharmvar",
"pubmed_ids": [
"29134625"
],
"synonyms": [
"pharmvar.gene"
],
"uri_format": "https://www.pharmvar.org/gene/$1"
},
"phci2dpage": {
"description": "Two-dimensional polyacrylamide gel electrophoresis database",
"example": "Q9Z8P2",
"homepage": "http://www.gram.au.dk/2d/2d.html",
"keywords": [
"protein"
],
"name": "Parasite host cell interaction 2D-PAGE database",
"pattern": "^[A-Z,0-9]+$",
"prefix": "phci2dpage",
"uri_format": "http://www.gram.au.dk/cgi-bin/get-2d-entry/def?$1"
},
"photolist": {
"description": "PhotoList, contains a database dedicated to the analysis of the genome of Photorhabdus luminescens. This analysis has been described in: \"The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens\"",
"example": "plu3909",
"homepage": "http://genolist.pasteur.fr/PhotoList/",
"keywords": [
"genome",
"DNA"
],
"name": "Photorhabdus luminescens genome database",
"pattern": "^plu\\d+$",
"prefix": "photolist"
},
"phylomedb": {
"description": "PhylomeDB is a public database for complete collections of gene phylogenies (phylomes). It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments.",
"example": "Phy000CLXM_RAT",
"homepage": "http://phylomedb.bioinfo.cipf.es",
"keywords": [
"genome",
"protein",
"taxonomy"
],
"name": "Database for complete collections of gene phylogenies",
"pattern": "^\\w+$",
"prefix": "phylomedb",
"pubmed_ids": [
"17962297"
],
"uri_format": "http://phylomedb.org/?seqid=$1"
},
"phytome": {
"description": "Phytome is an online comparative genomics resource that is built upon publicly available sequence and map information from a diverse set of plant species, with a focus on the angiosperms, or flowering plants. Phytome is designed to facilitate functional genomics, molecular breeding and evolutionary studies in model and non-model plant species.",
"example": "atha87460",
"homepage": "http://www.phytome.org",
"keywords": [
"genome"
],
"name": "Phytome: A Plant Comparative Genomics Resource",
"pattern": "^[a-z]+\\d+$",
"prefix": "phytome"
},
"pibase": {
"description": "PIBASE is a collection of all protein structural interfaces extracted from the Protein Data Bank and PQS structure databases. Both chain-chain and domain-domain (SCOP and CATH definitions) interfaces are detected.",
"example": "21692",
"homepage": "http://salilab.org/pibase",
"keywords": [
"protein",
"structure"
],
"name": "PIBASE: a database of structurally defined protein interfaces",
"pattern": "^\\d+$",
"prefix": "pibase",
"uri_format": "http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id=$1"
},
"pid": {
"description": "The Pathway Interaction Database is a highly-structured, curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways",
"example": "p38alphabetadownstreampathway",
"homepage": "http://pid.nci.nih.gov/",
"keywords": [
"pathway",
"small molecule",
"gene",
"protein"
],
"license": "http://www.cancer.gov/global/web/policies/allpages#5",
"name": "Pathway Interaction Database",
"pattern": "^\\w+$",
"prefix": "pid",
"pubmed_ids": [
"18832364"
],
"synonyms": [
"pid.pathway"
],
"uri_format": "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1"
},
"piggis": {
"description": "The Pig Genomic Informatics System (PigGIS) presents accurate pig gene annotations in all sequenced genomic regions. It integrates various available pig sequence data, including 3.84 million whole-genome-shortgun (WGS) reads and 0.7 million Expressed Sequence Tags (ESTs) generated by Sino-Danish Pig Genome Project, and 1 million miscellaneous GenBank records.",
"example": "ENST00000300175",
"homepage": "http://pig.genomics.org.cn/",
"keywords": [
"gene",
"genome",
"DNA",
"RNA",
"structure"
],
"name": "Pig Genomic Informatics System",
"pattern": "^ENS[A-Z]\\d+$",
"prefix": "piggis",
"uri_format": "http://pig.genomics.org.cn/transview.jsp?transcript=$1"
},
"pigqtldb": {
"description": "This Pig Quantitative Trait Locus (QTL) database (Pig QTLdb) has gathered all pig QTL data published during the past 10+ years. The database and its peripheral tools make it possible to compare, confirm and locate on pig chromosomes the most feasible location for genes responsible for quantitative trait important to pig production.",
"example": "66",
"homepage": "http://www.animalgenome.org/cgi-bin/QTLdb/SS/index",
"keywords": [
"DNA",
"genome"
],
"name": "Pig Quantitative Trait Locus database",
"pattern": "^\\d+$",
"prefix": "pigqtldb",
"uri_format": "http://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=$1"
},
"pint": {
"description": "PINT contains experimental data of several thermodynamic parameters along with literature, sequence and structural information and experimental conditions. Each entry contains the name and source of the proteins involved in binding, their PIR, SWISS-PROT and PDB codes, secondary structure and solvent accessibility of mutant positions and experimental conditions.",
"example": "PINT_CALM_MLCK",
"homepage": "http://www.bioinfodatabase.com/pint/",
"keywords": [
"DNA",
"RNA",
"protein",
"structure"
],
"name": "Protein-protein Interactions Thermodynamic Database",
"pattern": "^[A-Z]+$",
"prefix": "pint"
},
"pips": {
"description": "PIPs is a database of predicted human protein-protein interactions. The predictions have been made using a na\u00efve Bayesian classifier to calculate a Score of interaction. There are 37606 interactions with a Score \u22651 indicating that the interaction is more likely to occur than not to occur.",
"example": "5006",
"homepage": "http://www.compbio.dundee.ac.uk/www-pips",
"keywords": [
"protein",
"interaction"
],
"name": "Human Protein-Protein Interaction Prediction",
"pattern": "^\\d+$",
"prefix": "pips",
"uri_format": "http://www.compbio.dundee.ac.uk/www-pips/Identifier.jsp?ID=$1&Interactions=Prot&LR=1.0&modules=on"
},
"pirnabank": {
"description": "piRNABank is a web analysis system and resource, which provides comprehensive information on piRNAs in the widely studied mammals namely Human, Mouse, Rat, Zebrafish, Platypus and a fruit fly, Drosophila. It compiles all the possible clusters of piRNAs and also depicts piRNAs along with the associated genomic elements like genes and repeats on a genome wide map.",
"example": "mmu_piR_030801",
"homepage": "http://pirnabank.ibab.ac.in/",
"keywords": [
"RNA",
"gene",
"genome"
],
"name": "piRNA Database",
"pattern": "^[a-z]+_piR_\\d+$",
"prefix": "pirnabank"
},
"pirsf": {
"description": "The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.",
"example": "PIRSF000100",
"homepage": "http://pir.georgetown.edu/pirsf/",
"keywords": [
"protein",
"structure"
],
"name": "PIRSF; a whole-protein classification database",
"pattern": "^PIRSF\\d{6}$",
"prefix": "pirsf",
"pubmed_ids": [
"14681371"
],
"uri_format": "http://pir.georgetown.edu/cgi-bin/ipcSF?id=$1"
},
"pisite": {
"description": "The database PiSITE provides real interaction sites of proteins using the complex structures in PDB. According to the progress of several structural genomic projects, we have a large amount of structural data in PDB",
"example": "1byu",
"homepage": "http://pisite.hgc.jp/",
"keywords": [
"interaction",
"protein",
"structure",
"genome"
],
"name": "Database of Protein interaction SITEs",
"pattern": "^[A-Z.0-9]+$",
"prefix": "pisite",
"uri_format": "http://pisite.hgc.jp/cgi-bin/view.cgi?pdbid=$1&chain=[?chain]"
},
"place": {
"description": "PLACE is a database of motifs found in plant cis-acting regulatory DNA elements, all from previously published reports. It covers vascular plants only",
"example": "S000406",
"homepage": "http://www.dna.affrc.go.jp/PLACE/",
"keywords": [
"regulation",
"DNA",
"protein",
"small molecule"
],
"name": "A Database of Plant Cis-acting Regulatory DNA Elements",
"pattern": "^S\\d+$",
"prefix": "place"
},
"plantcyc": {
"description": "The Plant Metabolic Network (PMN) is a collaborative project among databases and biochemists with a common goal to build a broad network of plant metabolic pathway databases.",
"example": "JGI-262851",
"homepage": "http://www.plantcyc.org/",
"keywords": [
"pathway"
],
"name": "Plant Metabolic Network",
"pattern": "^JGI-\\d+$",
"prefix": "plantcyc",
"uri_format": "http://pmn.plantcyc.org/PLANT/NEW-IMAGE?type=GENE&object=$1"
},
"plantsp_plantst": {
"description": "PlantsT is part of the Plant Genome Program for the National Science Foundation and is a central site for the study of the uptake and translocation of mineral nutrients in plants. PlantsP is a central site for the study of phosphorylation and dephosphorylation sites.",
"example": "44367",
"homepage": "http://plantsp.sdsc.edu",
"keywords": [
"small molecule",
"regulation",
"DNA"
],
"name": "PlantsP/PlantsT",
"pattern": "^\\d+$",
"prefix": "plantsp_plantst",
"synonyms": [
"plantspst"
],
"uri_format": "http://plantst.genomics.purdue.edu/cgi-bin/detail.cgi?db=plants[?t/?p]&id=$1"
},
"planttfdb": {
"description": "Plant Transcription Factor Database collected 40976 transcription factors from 39 species, and they are classified into 58 families.",
"example": "Ath005712",
"homepage": "http://planttfdb.cbi.pku.edu.cn",
"keywords": [
"regulation",
"DNA",
"RNA",
"small molecule",
"protein",
"gene"
],
"name": "Plant Transcription Factor Database",
"pattern": "^[a-z]+\\d+$",
"prefix": "planttfdb",
"uri_format": "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=[?species_name]&did=$1"
},
"planttribes": {
"description": "PlantTribes is an objective classification system for plan proteins based on cluster analyses of the inferred proteomes of the sequenced angiospermsArabidopsis thaliana v Columbia, Oryza sativa v. japonica (Rice), and Populus trichocarpa (poplar).",
"example": "110807",
"homepage": "http://fgp.huck.psu.edu/tribedb/index.pl",
"keywords": [
"protein",
"classification",
"structure"
],
"name": "PlantTribes",
"pattern": "^\\d+$",
"prefix": "planttribes",
"uri_format": "http://fgp.huck.psu.edu/tribedb/gene.pl?action=view_gene&gene_id=$1"
},
"plasmodb": {
"description": "PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.",
"example": "PFA0765c",
"homepage": "http://PlasmoDB.org",
"keywords": [
"genome"
],
"name": "PlasmoDB",
"pattern": "^PF[A-Z,0-9]+$",
"prefix": "plasmodb",
"pubmed_ids": [
"18957442"
],
"uri_format": "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1&project_id=PlasmoDB"
},
"plpmdb": {
"description": "PLPMDB is a database for Pyridoxal-5'-phosphate dependent enzymes mutation information. All data have been extracted from publications and publicly available databases and organized to enable database searching.",
"example": "41",
"homepage": "http://www.studiofmp.com/plpmdb/",
"keywords": [
"enzyme",
"protein"
],
"name": "PLPMDB",
"pattern": "^\\d+$",
"prefix": "plpmdb",
"uri_format": "http://www.studiofmp.com/plpmdb/mutant.asp?Id=$1"
},
"plprot": {
"description": "Integrates data from large scale proteome analyses of different plastid types.These include etioplasts, chloroplasts, chromoplasts and the undifferentiated proplastid-like organelles of tobacco BY2 cells. This comparison allows establishing a core proteome that is common to all plastid types and provides furthermore information about plastid type-specific functions.",
"example": "plp_at_00098",
"homepage": "http://www.plprot.ethz.ch/",
"keywords": [
"protein"
],
"name": "PLprot: A Plastid Protein Database",
"pattern": "^plp_[a-z]+_\\d+$",
"prefix": "plprot",
"uri_format": "http://www.plprot.ethz.ch/index.php?page=ProteinDetails&plp_id=$1&organism=[?species_name]"
},
"pmap.cutdb": {
"description": "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites).",
"example": "pmap.21243",
"homepage": "http://www.proteolysis.org/",
"keywords": [
"pathway",
"protein",
"enzyme"
],
"name": "CutDB - Proteolytic event database",
"pattern": "^pmap.\\d+$",
"prefix": "pmap.cutdb",
"pubmed_ids": [
"17142225"
],
"uri_format": "http://www.proteolysis.org/proteases/m_summarypg/$1"
},
"pmap.substratedb": {
"description": "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates.",
"example": "1915",
"keywords": [
"domain",
"protein",
"reaction"
],
"name": "SubstrateDB - Protease substrates",
"pattern": "^\\w+$",
"prefix": "pmap.substratedb",
"pubmed_ids": [
"18842634"
],
"uri_format": "http://substrate.burnham.org/protein/annotation/$1/html"
},
"pmc": {
"description": "PubMed Central (PMC) is the U.S. National Institutes of Health (NIH) digital archive of biomedical and life sciences journal literature.",
"example": "PMC3084216",
"homepage": "http://www.pubmedcentral.nih.gov/",
"keywords": [
"bibliography"
],
"name": "Pubmed Central",
"pattern": "^PMC\\d+$",
"prefix": "pmc",
"synonyms": [
"pmcid"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/pmc/articles/$1/?tool=pmcentrez"
},
"pmd": {
"description": "The PMD is based on the literature, not on proteins. That is, each entry in the database corresponds to one article, which contains several or a number of protein mutants. Each database entry is identified by a serial number and is defined as either natur al or artificial, depending on the type of the mutation.",
"example": "A000170",
"homepage": "http://pmd.ddbj.nig.ac.jp/",
"keywords": [
"protein"
],
"name": "Protein Mutant Database",
"pattern": "^[A-Z]\\d+$",
"prefix": "pmd",
"uri_format": "http://spock.genes.nig.ac.jp/~pmd/cgi-bin/PMD/PMDentry.pl.cgi?$1"
},
"pmdb": {
"description": "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques.",
"example": "PM0012345",
"homepage": "http://www.caspur.it/PMDB/",
"keywords": [
"protein",
"structure"
],
"name": "Protein Model Database",
"pattern": "^PM\\d{7}$",
"prefix": "pmdb",
"uri_format": "http://mi.caspur.it/PMDB/user/search.php?idsearch=$1"
},
"pmp": {
"description": "The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models.",
"example": "Q0VCA6",
"homepage": "http://www.proteinmodelportal.org/",
"keywords": [
"prediction",
"protein",
"structure"
],
"name": "Protein Model Portal",
"pattern": "^\\d+$",
"prefix": "pmp",
"pubmed_ids": [
"19037750"
],
"synonyms": [
"proteinmodelportal"
],
"uri_format": "http://www.proteinmodelportal.org/query/uniprot/$1"
},
"pmrna": {
"description": "Identifier associated with affymetrix probesets.",
"example": "pmrna9933",
"keywords": [
"sequence"
],
"name": "PMRNA",
"pattern": "^pmrna\\d+$",
"prefix": "pmrna"
},
"po": {
"bioportal": "1587",
"description": "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plants.",
"example": "PO:0006220",
"homepage": "http://www.plantontology.org/",
"keywords": [
"ontology",
"structure",
"classification"
],
"name": "Plant Ontology",
"pattern": "^PO:\\d+$",
"prefix": "po",
"synonyms": [
"poc"
],
"uri_format": "http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=$1"
},
"po.psds": {
"bioportal": "1038",
"description": "A controlled vocabulary of growth and developmental stages in various plants. Note that this has been subsumed into the PO. This file is created by filtering plant_ontology_assert_basic.obo to contain only terms from the plant anatomical entity branch. For more information, please see: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/",
"example": "PO_0025338",
"homepage": "http://www.plantontology.org",
"keywords": [
"obo",
"development",
"plant"
],
"name": "Plant Structure Development Stage",
"pattern": "^PO_\\d{7}$",
"prefix": "po.psds"
},
"pod": {
"description": "The Plant Organelles Database Version 2 (PODB2) is a specialized database project to promote a comprehensive understanding of organelle dynamics, including organelle function, biogenesis, differentiation, movement, and interactions with other organelles.",
"example": "20060606182637",
"homepage": "http://podb.nibb.ac.jp/Organellome",
"keywords": [
"anatomy",
"interaction"
],
"name": "Plant Organelles Database",
"pattern": "^\\d+$",
"prefix": "pod",
"uri_format": "http://podb.nibb.ac.jp/Organellome/bin/browseImage.php?ID=Image-toshi_biochem.tohoku.ac.jp-$1"
},
"pogs_plantrbp": {
"description": "POGs is a relational database that integrates data from rice, maize, and Arabidopsis by placing the complete Arabidopsis and rice proteomes, and the available maize sequences into \"putative orthologous groups\" (POGs). POGs were assigned using InParanoid.",
"example": "7461",
"homepage": "http://plantrbp.uoregon.edu",
"keywords": [
"protein",
"classification"
],
"name": "POGs/PlantRBP",
"pattern": "^\\d+$",
"prefix": "pogs_plantrbp",
"uri_format": "http://plantrbp.uoregon.edu/pogView.php?id=$1"
},
"polydoms": {
"description": "An integrated database of human coding single nucleotide polymorphisms (SNPs) and their annotations.",
"example": "NP_955472",
"homepage": "http://polydoms.cchmc.org",
"keywords": [
"DNA"
],
"name": "PolyDoms: Mapping of Human Coding SNPs onto Protein Domains",
"pattern": "^[A-Z]+_\\d+$",
"prefix": "polydoms",
"uri_format": "http://polydoms.cchmc.org/polydoms/GD?DISP_OPTION=[?NonSynonymous/Synonymous]&field1=$1"
},
"polymorphix": {
"description": "This blast oriented interface allows you to retrieve families of polymorphic sequences. It is of special interest for molecular evolutionnary biologists and population geneticists",
"example": "HSN000159",
"homepage": "http://pbil.univ-lyon1.fr/polymorphix/query.php",
"keywords": [
"DNA",
"gene"
],
"name": "Polymorphix",
"pattern": "^[A-Z]+\\d+$",
"prefix": "polymorphix",
"uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/acnuc-dispfam?query=$1&db=Polymorphix"
},
"pomamo": {
"description": "GABI, acronym for \"Genomanalyse im biologischen System Pflanze\", is the name of a large collaborative network of different plant genomic research projects.",
"example": "1956",
"homepage": "https://gabi.rzpd.de/PoMaMo.html",
"keywords": [
"genome"
],
"name": "Potato Maps and More",
"pattern": "^\\d+$",
"prefix": "pomamo"
},
"pombase": {
"description": "PomBase is a model organism database for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation.",
"example": "SPCC13B11.01",
"homepage": "http://www.pombase.org",
"name": "Schizosaccharomyces pombe database",
"pattern": "^S\\w+(\\.)?\\w+(\\.)?$",
"prefix": "pombase",
"pubmed_ids": [
"22039153"
]
},
"pr": {
"alt_uri_formats": [
"http://purl.org/obo/owl/PR#$1"
],
"bioportal": "1062",
"description": "PRO provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp).",
"example": "PR:000000024",
"homepage": "http://pir.georgetown.edu/pro/",
"keywords": [
"obo",
"protein"
],
"name": "PRotein Ontology (PRO)",
"pattern": "^PR\\:\\d+$",
"prefix": "pr",
"pubmed_ids": [
"18047702"
],
"synonyms": [
"obo.pr",
"pro"
],
"uri_format": "http://pir.georgetown.edu/cgi-bin/pro/entry_pro?id=$1"
},
"precise": {
"description": "PRECISE (Predicted and Consensus Interaction Sites in Enzymes) is a database of interactions between the amino acid residues of an enzyme and its various ligands, i.e., substrate and transition state analogues, cofactors, inhibitors, and products.",
"example": "5",
"homepage": "http://precise.bu.edu/",
"keywords": [
"enzyme",
"protein",
"small molecule",
"structure"
],
"name": "PRedicted and Concensus Interaction Sites in Enzymes",
"pattern": "^\\d+$",
"prefix": "precise",
"uri_format": "http://precise.bu.edu/Output.aspx?UniqueID=$1"
},
"premod": {
"description": "The PReMod database describes more than 100,000 computational predicted transcriptional regulatory modules within the human genome1. These modules represent the regulatory potential for 229 transcription factors families and are the first genome-wide/transcription factor-wide collection of predicted regulatory modules for the human genome2.",
"example": "mod103457",
"homepage": "http://genomequebec.mcgill.ca/PReMod",
"keywords": [
"regulation",
"genome",
"gene",
"DNA",
"RNA",
"protein",
"small molecule"
],
"name": "Predicted Regulatory Modules",
"pattern": "^mod\\d+$",
"prefix": "premod",
"uri_format": "http://genomequebec.mcgill.ca/PReMod/show/module.do?method=showModule&moduleId=$1"
},
"priam": {
"description": "ENZYME-SPECIFIC PROFILES for metabolic pathway prediction. PRIAM is a method for automated enzyme detection in a fully sequenced genome, based on all sequences available in the ENZYME database.",
"example": "PRI002274",
"homepage": "http://priam.prabi.fr/",
"keywords": [
"enzyme",
"profile",
"pathway"
],
"name": "PRIAM: PRofils pour l'Identification Automatique du M\u00e9tabolisme",
"pattern": "^PRI\\d+$",
"prefix": "priam",
"pubmed_ids": [
"14602924"
],
"uri_format": "http://prodomweb.univ-lyon1.fr/priam/cgi-bin/ReqPRIAM_png.pl?priam_release=OCT11&priam_ac=$1"
},
"pride": {
"description": "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence.",
"example": "1",
"homepage": "http://www.ebi.ac.uk/pride/",
"keywords": [
"protein"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "PRoteomics IDEntifications database",
"pattern": "^\\d+$",
"prefix": "pride",
"pubmed_ids": [
"16381953",
"16041671",
"18033805",
"18428683"
],
"uri_format": "http://www.ebi.ac.uk/pride/experimentLink.do?experimentAccessionNumber=$1"
},
"probebase": {
"description": "probeBase is a comprehensive database containing published rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated information.",
"example": "pB-00049",
"homepage": "http://www.microbial-ecology.net/probebase/",
"keywords": [
"RNA",
"DNA",
"gene expression"
],
"name": "probeBase",
"pattern": "^pB-\\d+$",
"prefix": "probebase"
},
"procognate": {
"description": "PROCOGNATE is a database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam.",
"example": "1ldn",
"homepage": "http://www.ebi.ac.uk/thornton-srv/databases/procognate/index.html",
"keywords": [
"small molecule",
"protein",
"enzyme"
],
"name": "PROCOGNATE",
"pattern": "^[A-Z,0-9]+$",
"prefix": "procognate",
"uri_format": "http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/procognate/PDBquery.pl?PDBcode=$1&Classification=[?CATH/?SCOP/?Pfam]"
},
"prodom": {
"description": "ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database",
"example": "PD10000",
"homepage": "http://prodom.prabi.fr/",
"keywords": [
"protein",
"classification"
],
"name": "ProDom; a protein domain database",
"pattern": "^PD\\d+$",
"prefix": "prodom",
"pubmed_ids": [
"15608179"
],
"uri_format": "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1"
},
"promex": {
"description": "Promex is a mass spectral reference database. The database consists of tryptic peptide fragmentation mass spectra derived from Arabidopsis thaliana, Chlamydomonas reinhardii, Medicago truncatula and Solanum tuberosum.",
"example": "16356",
"homepage": "http://www.promexdb.org/",
"keywords": [
"protein"
],
"name": "Protein Mass spectra EXtraction",
"pattern": "^\\d+$",
"prefix": "promex",
"uri_format": "http://promex.pph.univie.ac.at/promex/?spec=$1"
},
"pronit": {
"description": "A database of thermodynamic data for protein-nucleic acids interactions",
"example": "7320",
"homepage": "http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html",
"keywords": [
"protein",
"DNA",
"interaction"
],
"name": "ProNIT",
"pattern": "^\\d+$",
"prefix": "pronit",
"uri_format": "http://gibk26.bse.kyutech.ac.jp/cgi-bin/jouhou/pronit/new/bind_entry.pl?ENTRY=$1"
},
"propreo": {
"bioportal": "1039",
"description": "A comprehensive proteomics data and process provenance ontology.",
"example": "protein",
"homepage": "http://knoesis.wright.edu/research/semsci/application_domain/sem_life_sci/glycomics/resources/ontologies/propreo/",
"keywords": [
"owl",
"proteomics"
],
"name": "Proteomics data and process provenance",
"pattern": "^\\w+$",
"prefix": "propreo",
"rdf_uri_format": "http://lsdis.cs.uga.edu/projects/glycomics/propreo#$1"
},
"prosite": {
"description": "PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them",
"example": "PS00001",
"homepage": "http://www.expasy.org/prosite",
"keywords": [
"protein",
"structure"
],
"license": "http://www.isb-sib.ch/disclaimer.html",
"name": "PROSITE; a protein domain and family database",
"pattern": "^PS\\d{5}$",
"prefix": "prosite",
"pubmed_ids": [
"16381852"
],
"synonyms": [
"prositedoc"
],
"uri_format": "http://www.expasy.org/cgi-bin/nicesite.pl?$1"
},
"protclustdb": {
"description": "ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.",
"example": "2728498",
"homepage": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=proteinclusters",
"keywords": [
"protein",
"structure"
],
"name": "ProtClustDB",
"pattern": "^\\d+$",
"prefix": "protclustdb",
"pubmed_ids": [
"18940865"
],
"synonyms": [
"protein_clusters"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=ShowDetailView&TermToSearch=$1"
},
"protcom": {
"description": "This database is a collection of protein-protein homo- and hetero-complexes as well as domain-domain structures. This issue of the database contains 17.024 entries (as of October 2007) of which 1350 are two-chain protein hetero-complexes, 7773 homodimers and 1589 are one-chain proteins parsed into two domains (domain structures).",
"example": "12e8LH",
"homepage": "http://www.ces.clemson.edu/compbio/protcom",
"keywords": [
"protein",
"structure"
],
"name": "Database of protein-protein complexes",
"pattern": "^[A-Z,0-9]+$",
"prefix": "protcom",
"uri_format": "http://www.ces.clemson.edu/compbio/protcom/print_file.cgi?pdbid=$1"
},
"proteus": {
"description": "ProTeus (PROtein TErminUS) is a tool for identification of short linear signatures in protein termini. It is based on a positional-based search method for revealing short significant signatures in termini of proteins.",
"example": "221800",
"homepage": "http://www.proteus.cs.huji.ac.il",
"keywords": [
"protein",
"structure"
],
"name": "Protein Terminus",
"pattern": "^\\d+$",
"prefix": "proteus"
},
"protherm": {
"description": "ProTherm is a collection of numerical data of thermodynamic parameters such as Gibbs free energy change, enthalpy change, heat capacity change, transition temperature etc. for wild type and mutant proteins, that are important for understanding the structure and stability of proteins.",
"example": "3115",
"homepage": "http://gibk26.bse.kyutech.ac.jp/jouhou/protherm/protherm.html",
"keywords": [
"protein",
"structure"
],
"name": "ProTherm",
"pattern": "^\\d+$",
"prefix": "protherm",
"uri_format": "http://gibk26.bse.kyutech.ac.jp/cgi-bin/jouhou/protherm/pp_entry.pl?ENTRY=$1"
},
"protonet.cluster": {
"description": "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information.",
"example": "4349895",
"keywords": [
"classification",
"clustering",
"protein"
],
"name": "ProtoNet Cluster",
"pattern": "^\\d+$",
"prefix": "protonet.cluster",
"pubmed_ids": [
"16672244"
],
"uri_format": "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1"
},
"protonet.proteincard": {
"description": "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information.",
"example": "16941567",
"keywords": [
"protein"
],
"name": "ProtoNet ProteinCard",
"pattern": "^\\d+$",
"prefix": "protonet.proteincard",
"pubmed_ids": [
"16672244"
],
"uri_format": "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1"
},
"pseudobase": {
"description": "PseudoBase is a collection of RNA pseudoknots that we make available for retrieval to the scientific community.",
"example": "PKB00322",
"homepage": "http://www.ekevanbatenburg.nl/pb",
"keywords": [
"RNA"
],
"name": "PseudoBase",
"pattern": "^PKB\\d+$",
"prefix": "pseudobase",
"uri_format": "http://www.ekevanbatenburg.nl/PKBASE/$1.HTML"
},
"pseudogene": {
"description": "Pseudogene is a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase.",
"example": "4",
"homepage": "http://www.pseudogene.org/",
"keywords": [
"gene"
],
"name": "PseudoGene",
"pattern": "^\\d+$",
"prefix": "pseudogene",
"uri_format": "http://tables.pseudogene.org/[?species_name]/$1"
},
"psi.mi": {
"alt_uri_formats": [
"http://purl.org/obo/owl/PSI-MI#$1"
],
"bioportal": "1040",
"description": "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.",
"example": "MI:0308",
"homepage": "http://psidev.sf.net",
"keywords": [
"obo",
"interaction",
"molecule"
],
"name": "Proteomic Standard Initiative for Molecular Interaction",
"pattern": "^MI:\\d{4}$",
"prefix": "psi.mi",
"pubmed_ids": [
"14755292"
],
"synonyms": [
"mi",
"obo.mi"
]
},
"psi.mod": {
"alt_uri_formats": [
"http://purl.org/obo/owl/PSI-MOD#$1"
],
"bioportal": "1041",
"description": "The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications.",
"example": "MOD:00001",
"homepage": "http://psidev.sourceforge.net/mod/",
"keywords": [
"ontology",
"protein",
"molecule",
"structure"
],
"name": "Protein Modification ontology",
"pattern": "^MOD:\\d{5}$",
"prefix": "psi.mod",
"synonyms": [
"mod",
"obo.psi-mod"
]
},
"pt": {
"bioportal": "1094",
"description": "This vocabulary describes a process that is the means of how a pathogen is transmitted from one host, reservoir, or source to another host. This transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.",
"example": "TRANS_0000001",
"homepage": "http://diseaseontology.sourceforge.net/",
"keywords": [
"obo",
"pathogen"
],
"name": "Pathogen transmission",
"pattern": "^TRANS_\\d{7}$",
"prefix": "pt",
"synonyms": [
"trans"
]
},
"ptmswitchboard": {
"description": "PTM-Switchboard is designed to catalog known cases of TF-PTMs affecting gene transcriptions.. PTM-Switchboard differs from existing molecular pathway databases in that, instead of using pairwise interactions as a primary data type, it stores triplets of genes such that the ability of one gene (the TF) to regulate a target gene is dependent on a third gene (the modifying enzyme).",
"example": "128",
"homepage": "http://cagr.pcbi.upenn.edu/PTMswitchboard/",
"keywords": [
"gene",
"regulation",
"DNA",
"pathway",
"small molecule",
"interaction",
"enzyme"
],
"name": "PTM-Switchboard",
"pattern": "^\\d+$",
"prefix": "ptmswitchboard",
"synonyms": [
"ptm"
],
"uri_format": "http://cagr.pcbi.upenn.edu/PTMswitchboard/jsp/detail.jsp?ID=$1"
},
"pto": {
"bioportal": "1037",
"description": "A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part.",
"example": "TO_0000017",
"homepage": "http://www.gramene.org/plant_ontology/",
"keywords": [
"obo",
"plant",
"trait"
],
"name": "Plant Trait Ontology",
"pattern": "^TO_\\d{7}$",
"prefix": "pto",
"synonyms": [
"to",
"gramene.po"
]
},
"pubchem.bioassay": {
"description": "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results.",
"example": "1018",
"homepage": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay",
"keywords": [
"small molecule"
],
"license": "http://www.nlm.nih.gov/copyright.html",
"name": "Pubchem: Bioassays",
"pattern": "^\\d+$",
"prefix": "pubchem.bioassay",
"pubmed_ids": [
"17170002"
],
"uri_format": "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=$1"
},
"pubchem.compound": {
"alt_uri_formats": [
"http://rdf.ncbi.nlm.nih.gov/pubchem/compound/$1"
],
"description": "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records.",
"example": "100101",
"keywords": [
"chemical",
"metabolite",
"structure"
],
"name": "Pubchem: Compounds",
"pattern": "^\\d+$",
"prefix": "pubchem.compound",
"synonyms": [
"pubchemcompound"
],
"uri_format": "http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?db=pccompound&term=$1"
},
"pubchem.substance": {
"alt_uri_formats": [
"http://rdf.ncbi.nlm.nih.gov/pubchem/substance/$1"
],
"description": "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records.",
"example": "100101",
"keywords": [
"small molecule",
"protein",
"structure"
],
"name": "Pubchem: Substances",
"pattern": "^\\d+$",
"prefix": "pubchem.substance",
"pubmed_ids": [
"17170002"
],
"synonyms": [
"pubchemsubstance"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pcsubstance&term=$1"
},
"pubmed": {
"alt_uri_formats": [
"http://europepmc.org/abstract/MED/#$1",
"http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-view+MedlineFull+[medline-PMID:#]$1",
"http://www.hubmed.org/display.cgi?uids=#$1"
],
"description": "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.",
"example": "23735196",
"homepage": "http://www.ncbi.nlm.nih.gov/pubmed/",
"keywords": [
"bibliography"
],
"name": "PubMed",
"pattern": "^\\d+$",
"prefix": "pubmed",
"pubmed_ids": [
"16381840"
],
"synonyms": [
"pmid",
"medline"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/pubmed/$1"
},
"pubmeth": {
"description": "Pubmeth is an annotated and reviewed database of methylation in cancer. It is based on automated textmining of literature and is afterwards manually curated and annotated.",
"example": "MGMT",
"homepage": "http://matrix.ugent.be/pubmeth/",
"keywords": [
"small molecule",
"structure"
],
"name": "Reviewed Methylation Database in Cancer",
"pattern": "^[A-Z,0-9]+$",
"prefix": "pubmeth",
"uri_format": "http://matrix.ugent.be/temp/static/$1.html"
},
"pw": {
"bioportal": "1035",
"description": "The goal of the Pathway Ontology is to capture the various kinds of biological networks, the relationships between them and the alterations or malfunctioning of such networks within a hierarchical structure. The five nodes are: classic metabolic pathways, regulatory pathways, signaling pathways, drug pathways and disease pathways for complex human conditions.",
"example": "PW_0000002",
"homepage": "ftp://rgd.mcw.edu/pub/data_release/ontology_obo_files/",
"keywords": [
"obo",
"pathway",
"human"
],
"name": "Pathway ontology",
"pattern": "^PW_\\d{7}$",
"prefix": "pw",
"pubmed_ids": [
"21478484"
],
"synonyms": [
"obo.pw"
],
"uri_format": "http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=$1"
},
"qppd": {
"description": "The Quantitative PCR Primer Database (QPPD) provides information about primers and probes that can be used to quantitate human and mouse mRNA by reverse transcription polymerase chain reaction (RT\u2013PCR) assays. All data has been gathered from published articles, cited in PubMed.",
"example": "NM_001982.2",
"homepage": "http://web.ncifcrf.gov/rtp/GEL/primerdb/default.asp",
"keywords": [
"gene",
"gene expression",
"RNA"
],
"name": "Quantitative PCR Primer Database",
"pattern": "^NM_\\d+$",
"prefix": "qppd",
"uri_format": "http://lpgws.nci.nih.gov/cgi-bin/PrimerViewer?acc=$1"
},
"rad": {
"description": "RAD is a contig-oriented database for high-quality manual annotation of RGP, which can present non-redundant contig analyses by merging the accumulated PAC/BAC clones.",
"example": "P0489E06",
"homepage": "http://golgi.gs.dna.affrc.go.jp/SY-1102/rad/index.html",
"keywords": [
"DNA"
],
"name": "Rice Annotation Database",
"pattern": "^[A-Z,0-9]+$",
"prefix": "rad",
"uri_format": "http://rad.dna.affrc.go.jp/SY-1102-cgi-bin/rad/PCA/ctl_frame.cgi?clone=$1"
},
"rapdb": {
"description": "The Rice Annotation Project (RAP) was conceptualized upon the completion of the rice genome sequencing in 2004 with the aim of providing the scientific community with an accurate and timely annotation of the rice genome sequence.",
"example": "Os01g0102600",
"homepage": "http://rapdb.dna.affrc.go.jp/",
"keywords": [
"genome",
"DNA"
],
"name": "The Rice Annotation Project Database",
"pattern": "^[A-Z,0-9]+$",
"prefix": "rapdb",
"uri_format": "http://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/build5?name=[$1"
},
"rapid": {
"description": "Resource of Asian Primary Immunodeficiency Diseases (RAPID) is a web-based compendium of molecular alterations in primary immunodeficiency diseases. Detailed information about genes and proteins that are affected in primary deficiency diseases is presented along with other pertinent information about protein-protein interactions, microarray gene expression profiles in various organs and cells of the immune system and mouse studies.",
"example": "AGID_26",
"homepage": "http://rapid.rcai.riken.jp/RAPID",
"keywords": [
"gene",
"protein",
"interaction",
"gene expression",
"anatomy"
],
"name": "Resource of Primary Immunodeficiency Diseases",
"pattern": "^AGID_\\d+$",
"prefix": "rapid",
"uri_format": "http://rapid.rcai.riken.jp/RAPID/diseasePhenotype?pid_id=$1"
},
"rarge": {
"description": "To enhance the utility of the RIKEN Arabidopsis resource (full-length cDNAs, transposon mutants and microarray experiments); the RARGE Database was constructed.",
"example": "52-0228-1",
"homepage": "http://rarge.gsc.riken.jp/",
"keywords": [
"DNA"
],
"name": "RIKEN Arabidopsis Genome Encyclopedia",
"pattern": "^\\d+$",
"prefix": "rarge",
"uri_format": "http://rarge.psc.riken.jp/dsmutant/detail.pl?keyword=$1"
},
"ratmap": {
"description": "The Rat Genome Database RatMap is focused on presenting rat genes, DNA-markers, QTL:s etc that is localized to chromosome. The database is dedicated to rat gene nomenclature and should be consulted for queries in such matters",
"example": "ENSRNOG00000008380",
"homepage": "http://ratmap.org",
"keywords": [
"genome",
"gene",
"DNA"
],
"name": "RatMap, the rat genome database",
"pattern": "^[A-Z]+\\d+$",
"prefix": "ratmap",
"uri_format": "http://ratmap.org/Showgene.php?gene_stable_id=$1"
},
"rcd": {
"bioportal": "1427",
"description": "Clinical Terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre",
"example": "X79tP",
"homepage": "http://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/RCD/",
"license": "https://uts.nlm.nih.gov/license.html",
"name": "Read Codes, Clinical Terms Version 3 (CTV3)",
"pattern": "^\\w+$",
"prefix": "rcd",
"rdf_uri_format": "http://purl.bioontology.org/ontology/RCD/$1",
"uri_format": "http://purl.bioontology.org/ontology/RCD/$1"
},
"reactome": {
"description": "The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.",
"example": "REACT_1590",
"homepage": "http://www.reactome.org",
"keywords": [
"human",
"pathway",
"reaction"
],
"name": "Reactome - a curated knowledgebase of biological pathways",
"pattern": "^REACT_\\d+(\\.\\d+)?$",
"prefix": "reactome",
"pubmed_ids": [
"15608231"
],
"synonyms": [
"identifier.reactome"
],
"uri_format": "http://www.reactome.org/cgi-bin/eventbrowser_st_id?FROM_REACTOME=1&ST_ID=$1"
},
"rebase": {
"description": "A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data.",
"example": "101",
"homepage": "http://rebase.neb.com",
"keywords": [
"enzyme",
"protein",
"structure",
"small molecule",
"genome",
"DNA",
"RNA"
],
"name": "Restriction enzymes and methylases database",
"pattern": "^\\d+$",
"prefix": "rebase",
"pubmed_ids": [
"19846593"
],
"uri_format": "http://rebase.neb.com/rebase/enz/$1.html"
},
"recode": {
"description": "Recode2 is a database of genes that utilize non-standard translation for gene expression purposes. Recoding events described in the database include programmed ribosomal frameshifting, translational bypassing (aka hopping) and mRNA specific codon redefinition.",
"example": "r200377",
"homepage": "http://recode.genetics.utah.edu",
"keywords": [
"gene expression",
"gene",
"DNA",
"RNA"
],
"name": "RECODE",
"pattern": "^r\\d+$",
"prefix": "recode",
"uri_format": "http://recode.ucc.ie/recode/$1/"
},
"redfly": {
"description": "REDflyis a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs).",
"example": "8",
"homepage": "http://redfly.ccr.buffalo.edu",
"keywords": [
"regulation"
],
"name": "Regulatory Elements Database for Drosophila",
"pattern": "^\\d+$",
"prefix": "redfly",
"uri_format": "http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id=$1"
},
"redidb": {
"description": "The REDIdb is a relational database in which all editing information such as substitutions, insertions and deletions occurring in a wide range of organisms is stored and maintained in ad hoc designed textual flat files (for details about REDIdb flat file structure see the \"structure\" page).",
"example": "EDI_000000081",
"homepage": "http://biologia.unical.it/py_script/search.html",
"keywords": [
"DNA",
"structure"
],
"name": "REDIdb",
"pattern": "^EDI_\\d+$",
"prefix": "redidb",
"uri_format": "http://biologia.unical.it/py_script/cgi-bin/retrieve.py?query=$1"
},
"refseq": {
"description": "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.",
"example": "NP_012345",
"homepage": "http://www.ncbi.nlm.nih.gov/RefSeq/",
"keywords": [
"protein",
"DNA",
"RNA"
],
"name": "Reference Sequence Database",
"pattern": "^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\\d+(\\.\\d+)?$",
"prefix": "refseq",
"pubmed_ids": [
"17130148"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/nuccore/$1"
},
"regtransbase": {
"description": "RegTransBase consists of two modules - a database of regulatory interactions based on literature and an expertly curated database of transcription factor binding sites.",
"example": "9368629",
"homepage": "http://regtransbase.lbl.gov",
"keywords": [
"regulation",
"interaction"
],
"name": "RegTransBase",
"pattern": "^\\d+$",
"prefix": "regtransbase",
"uri_format": "http://regtransbase.lbl.gov/cgi-bin/regtransbase?page=geneinfo&seqfeature_id=$1"
},
"regulondb": {
"description": "RegulonDB is a model of the complex regulation of transcription initiation or regulatory network of the cell. On the other hand, it is also a model of the organization of the genes in transcription units, operons and simple and complex regulons. In this regard, RegulonDB is a computational model of mechanisms of transcriptional regulation.",
"example": "ECK120000269",
"homepage": "http://regulondb.ccg.unam.mx/",
"keywords": [
"regulation",
"DNA",
"RNA"
],
"name": "RegulonDB",
"pattern": "^ECK\\d+$",
"prefix": "regulondb",
"uri_format": "http://regulondb.ccg.unam.mx/GeneController?key_id_org=ECK12&gene_id=$1&type=jsp"
},
"replicationdomain": {
"description": "ReplicationDomain is an online database resource for storing, sharing and visualizing DNA replication timing and transcription data, as well as other numerical epigenetic data types.",
"example": "349",
"homepage": "http://www.replicationdomain.org/",
"keywords": [
"DNA",
"RNA"
],
"name": "ReplicationDomain",
"pattern": "^\\d+$",
"prefix": "replicationdomain",
"uri_format": "http://www.replicationdomain.com/view-dataset.php?RecordID=$1"
},
"repo": {
"alt_uri_formats": [
"http://purl.bioontology.org/ontology/REPO.owl#$1"
],
"bioportal": "1552",
"description": "Ontology for livestock reproductive traits and phenotypes",
"example": "AbnormalParturition",
"name": "Reproductive trait and phenotype ontology",
"pattern": "^\\w+$",
"prefix": "repo",
"rdf_uri_format": "http://purl.bioontology.org/ontology/REPO$1",
"synonyms": [
"rtpo"
],
"uri_format": "http://purl.bioontology.org/ontology/REPO.owl#$1"
},
"reproduction2dpage": {
"description": "Two-dimensional polyacrylamide gel electrophoresis database",
"example": "Q9Z2X1",
"homepage": "http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi",
"keywords": [
"protein"
],
"name": "REPRODUCTION-2DPAGE",
"pattern": "^[A-Z,0-9]+$",
"prefix": "reproduction2dpage",
"uri_format": "http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi?ac=$1"
},
"resid": {
"description": "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.",
"example": "AA0001",
"homepage": "http://www.ebi.ac.uk/RESID/",
"keywords": [
"protein",
"small molecule",
"structure"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "RESID Database of Protein Modifications",
"pattern": "^AA\\d{4}$",
"prefix": "resid",
"pubmed_ids": [
"15174124"
],
"uri_format": "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$1']"
},
"rex": {
"bioportal": "1043",
"description": "REX is an ontology of physico-chemical processes and includes microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes.",
"example": "REX_0000517",
"homepage": "http://www.ebi.ac.uk/~kirill/REX/",
"keywords": [
"obo",
"biochemistry"
],
"name": "Physico-chemical process",
"pattern": "^REX_\\d{8}$",
"prefix": "rex"
},
"rgap": {
"description": "This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and the Genome Browser that provides an integrated display of annotation data.",
"example": "LOC_Os02g13300",
"homepage": "http://rice.plantbiology.msu.edu/",
"keywords": [
"genome",
"DNA"
],
"name": "Rice Genome Annotation Project",
"pattern": "^LOC\\_Os\\d{1,2}g\\d{5}$",
"prefix": "rgap",
"pubmed_ids": [
"17145706"
],
"synonyms": [
"rice"
],
"uri_format": "http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/?name=$1"
},
"rgd": {
"description": "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community.",
"example": "2018",
"homepage": "http://rgd.mcw.edu/genes/",
"keywords": [
"genome",
"gene",
"DNA"
],
"name": "Rat Genome Database",
"pattern": "^\\d{4,7}$",
"prefix": "rgd",
"pubmed_ids": [
"17151068"
],
"uri_format": "http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$1"
},
"rhea": {
"description": "Rhea is a manually annotated reaction database, where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest), providing detailed information about structure, formulae and charge. It is populated with the reactions found in the EC list, IntEnz and ENZYME databases), as well as other biochemical reactions, including those that are often termed \"spontaneous\".",
"example": "12345",
"homepage": "http://www.ebi.ac.uk/rhea/",
"keywords": [
"reaction",
"small molecule"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Reaction database",
"pattern": "^\\d{5}$",
"prefix": "rhea",
"uri_format": "http://www.ebi.ac.uk/rhea//reaction.xhtml?id=$1"
},
"ricecyc": {
"description": "RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project",
"example": "PWY-1042",
"homepage": "http://www.gramene.org/pathway/ricecyc.html",
"keywords": [
"pathway",
"gene"
],
"name": "Rice Metabolic Pathways",
"pattern": "^PWY-\\d+$",
"prefix": "ricecyc",
"uri_format": "http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object=$1"
},
"rissc": {
"description": "This is a database of ribosomal 16S-23S spacer sequences intended mainly for molecular biology studies in typing, phylogeny and population genetics.",
"example": "U07777",
"homepage": "http://egg.umh.es/rissc",
"keywords": [
"RNA"
],
"name": "Ribosomal Internal Spacer Sequence Collection",
"pattern": "^[A-Z]\\d+$",
"prefix": "rissc",
"uri_format": "http://egg.umh.es/rissc/fich.php?accession=$1"
},
"rmd": {
"description": "The database consists of 16S rRNA from Escherichia coli, 16S-like rRNA from other organisms, 23S rRNA from E. coli, and 23S-like from other organisms.",
"example": "65",
"homepage": "http://ribosome.fandm.edu/",
"keywords": [
"RNA"
],
"name": "Ribosomal Mutation Database",
"pattern": "^\\d+$",
"prefix": "rmd",
"synonyms": [
"16SMDB"
],
"uri_format": "http://ribosome.fandm.edu/node/$1"
},
"rna_sstrand": {
"description": "RNA STRAND contains known RNA secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known RNA secondary structures, and to provide the scientific community with simple yet powerful ways of analysing, searching and updating the proposed database.",
"example": "CRW_00469",
"homepage": "http://www.rnasoft.ca/sstrand",
"keywords": [
"RNA",
"structure"
],
"name": "RNA SSTRAND",
"pattern": "^[A-Z]_\\d+$",
"prefix": "rna_sstrand",
"uri_format": "http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID=$1"
},
"rnajunction": {
"description": "Within this database you will to able to find more than 12,000 extracted three-dimensional junction and kissing loop structures as well as detailed annotations for each.",
"example": "10387",
"homepage": "http://rnajunction.abcc.ncifcrf.gov",
"keywords": [
"structure",
"RNA"
],
"name": "RNAJunction: A Database of RNA Junction and Kissing loop Structure",
"pattern": "^\\d+$",
"prefix": "rnajunction",
"uri_format": "http://rnajunction.abcc.ncifcrf.gov/JunctionPage.php?jid=$1"
},
"rnamods": {
"description": "The RNA modification database provides a comprehensive listing of posttranscriptionally modified nucleosides from RNA and is maintained as an updated version of the initial printed report.",
"example": "080",
"homepage": "http://medlib.med.utah.edu/RNAmods/",
"keywords": [
"RNA",
"structure"
],
"name": "RNA Modification Database",
"pattern": "^\\d+$",
"prefix": "rnamods",
"synonyms": [
"rnamod"
],
"uri_format": "http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?$1"
},
"rnao": {
"bioportal": "1500",
"description": "The central aim of the RNA Ontology Consortium (ROC) is to develop an ontology to capture all aspects of RNA - from primary sequence to alignments, secondary and tertiary structure from base pairing and base stacking to sophisticated motifs.",
"example": "RNAO_0000112",
"homepage": "http://code.google.com/p/rnao/",
"keywords": [
"obo"
],
"name": "RNA ontology",
"pattern": "^RNAO_\\d{7}$",
"prefix": "rnao"
},
"rnrdb": {
"description": "The ribonucleotide reductase database (RNRdb) is a tool developed for RNR research that gives you the opportunity to retrieve RNR protein sequences from any organism that have been either experimentally characterised or predicted from genome sequence data.",
"example": "59843",
"homepage": "http://rnrdb.molbio.su.se/",
"keywords": [
"RNA",
"protein"
],
"name": "Ribonucleotide Reductase Database",
"pattern": "^\\d+$",
"prefix": "rnrdb",
"uri_format": "http://rnrdb.molbio.su.se/proteins_for_organism.html?organism_nr=$1"
},
"ro": {
"alt_uri_formats": [
"http://purl.org/obo/owl/RO_REL#$1",
"http://purl.org/obo/owlapi/relationship#$1"
],
"bioportal": "1042",
"description": "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies.",
"example": "part_of",
"homepage": "http://www.obofoundry.org/ro",
"keywords": [
"obo",
"relations"
],
"license": "CC-BY-3.0",
"name": "Relation Ontology",
"pattern": "^\\w+$",
"prefix": "ro",
"pubmed_ids": [
"15892874"
],
"synonyms": [
"obo_rel",
"obo.ro",
"ro_proposed_relation"
]
},
"roleo": {
"bioportal": "1538",
"description": "The Role Ontology (RoleO) is a ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles.",
"example": "RoleO_0000002",
"homepage": "http://sourceforge.net/projects/roleo",
"keywords": [
"obo"
],
"name": "Role Ontology",
"pattern": "^RoleO_\\d{7}$",
"prefix": "roleo"
},
"rouge": {
"description": "The ROUGE protein database is a sister database of HUGE protein database which has accumulated the results of comprehensive sequence analysis of human long cDNAs (KIAA cDNAs). The ROUGE protein database has been created to publicize the information obtained from mouse homologues of the KIAA cDNAs (mKIAA cDNAs).",
"example": "mKIAA0701",
"homepage": "http://www.kazusa.or.jp/rouge/",
"keywords": [
"protein",
"DNA"
],
"name": "A Database of Rodent Unidentified Gene-Encoded Large Proteins Analyzed",
"pattern": "^mKIAA\\d+$",
"prefix": "rouge",
"uri_format": "http://www.kazusa.or.jp/rouge/gfpage/$1/"
},
"rpg": {
"description": "A database that provides detailed information about ribosomal protein (RP) genes. It contains data from humans and other organisms, including Drosophila melanogaster, Caenorhabditis elegans, Saccharo myces cerevisiae, Methanococcus jannaschii and Escherichia coli.",
"example": "FUG10002",
"homepage": "http://ribosome.miyazaki-med.ac.jp/",
"keywords": [
"gene",
"protein"
],
"name": "Ribosomal Protein Gene database",
"pattern": "^[A-Z]+\\d+$",
"prefix": "rpg",
"uri_format": "http://ribosome.miyazaki-med.ac.jp/rpg.cgi?mode=gene&id=$1"
},
"rs": {
"bioportal": "1150",
"description": "This ontology defines the hierarchical display of the different rat strains as derived from the parental strains",
"example": "RS_0000271",
"homepage": "http://rgd.mcw.edu/",
"keywords": [
"obo"
],
"name": "Rat Strain Ontology",
"pattern": "^RS_\\d{7}$",
"prefix": "rs"
},
"rtprimerdb": {
"description": "RTPrimerDB is a public database for primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridisation Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimisation, and to introduce a certain level of uniformity and standardisation among different laboratories.",
"example": "4328",
"homepage": "http://medgen.ugent.be/rtprimerdb/",
"keywords": [
"gene expression"
],
"name": "RTPrimerDB",
"pattern": "^\\d+$",
"prefix": "rtprimerdb",
"uri_format": "http://medgen.ugent.be/rtprimerdb/assay_report.php?assay_id=$1"
},
"rvd": {
"description": "The RNA Virus Database is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments and contains translated genome sequences for all species.",
"example": "164750",
"homepage": "http://virus.zoo.ox.ac.uk/rnavirusdb/",
"keywords": [
"RNA",
"genome"
],
"name": "RNA Virus Database",
"pattern": "^\\d+$",
"prefix": "rvd",
"uri_format": "http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id=$1"
},
"s_mart_db": {
"description": "S/MARt DB collects information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix.",
"example": "SM0000020",
"homepage": "http://smartdb.bioinf.med.uni-goettingen.de/",
"keywords": [
"protein"
],
"name": "The S/MAR transaction DataBase",
"pattern": "^SM\\d$",
"prefix": "s_mart_db",
"synonyms": [
"smartdb"
],
"uri_format": "http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi?$1"
},
"sabiork.ec": {
"description": "The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data.",
"example": "2.7.1.1",
"keywords": [
"reaction"
],
"name": "SABIO-RK EC Record",
"pattern": "^((\\d+)|(\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$",
"prefix": "sabiork.ec",
"pubmed_ids": [
"17822389"
],
"uri_format": "http://sabiork.h-its.org/index2.jsp?EC=$1"
},
"sabiork.kinetic": {
"description": "The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information.",
"example": "5046",
"keywords": [
"classification",
"enzyme",
"kinetics"
],
"name": "SABIO-RK Kinetic Record",
"pattern": "^\\d+$",
"prefix": "sabiork.kinetic",
"pubmed_ids": [
"17822389"
],
"synonyms": [
"sabiok",
"sabio-kr",
"sabiork.kineticrecord"
],
"uri_format": "http://sabiork.h-its.org/kineticLawEntry.jsp?kinlawid=$1"
},
"sabiork.reaction": {
"description": "The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information.",
"example": "75",
"keywords": [
"kinetics",
"pathway",
"reaction"
],
"name": "SABIO-RK Reaction Record",
"pattern": "^\\d+$",
"prefix": "sabiork.reaction",
"synonyms": [
"sabior"
],
"uri_format": "http://sabiork.h-its.org/index2.jsp?reac=$1"
},
"sac": {
"description": "The goal of the SKY/M-FISH and CGH database is to provide a public platform for investigators to share and compare their molecular cytogenetic data.",
"example": "5608",
"homepage": "http://www.ncbi.nlm.nih.gov/sky/",
"keywords": [
"structure"
],
"name": "SKY/M-FISH and CGH",
"pattern": "^\\d+$",
"prefix": "sac"
},
"sagalist": {
"description": "SagaList contains a database dedicated to the analysis of the genomes of the food-borne pathogen, Streptococcus agalactiae.",
"example": "gbs1449",
"homepage": "http://genolist.pasteur.fr/SagaList/",
"keywords": [
"genome"
],
"name": "Streptococcus agalactiae NEM316 / Serotype III genome database",
"pattern": "^gbs\\d+$",
"prefix": "sagalist"
},
"salad": {
"description": "SALAD is a tool of systematic comparison of proteome data among the species. The database is termed SALAD (Surveyed conserved motif ALignment diagram and the Associating Dendrogram) database.",
"example": "AT1G12340",
"homepage": "http://salad.dna.affrc.go.jp/salad/",
"keywords": [
"protein"
],
"name": "Surveyed conserved motif ALignment diagram and teh Associating Dendrogram database",
"pattern": "^[A-Z,0-9]+$",
"prefix": "salad",
"uri_format": "http://salad.dna.affrc.go.jp/CGViewer/en/v3.0/cgv_clust_view.jsp?pfamid=$1"
},
"sao": {
"bioportal": "1068",
"description": "SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules.",
"example": "sao1289741256",
"homepage": "http://ccdb.ucsd.edu/SAO",
"keywords": [
"owl",
"biochemistry"
],
"name": "Subcellular Anatomy Ontology (SAO)",
"pattern": "^sao\\d+$",
"prefix": "sao",
"rdf_uri_format": "http://ccdb.ucsd.edu/SAO/1.2#$1",
"synonyms": [
"sao:"
]
},
"sbase": {
"description": "SBASE is a collection of protein domain sequences collected from the literature, from protein sequence databases and from genomic databases",
"example": "2017",
"homepage": "http://www.icgeb.org/sbase",
"keywords": [
"protein",
"structure"
],
"name": "Support Vector Machines Domain Prediction System",
"pattern": "^\\d+$",
"prefix": "sbase",
"uri_format": "http://hydra.icgeb.trieste.it/sbase/sbase.php?sec=search&sub=group&group_id=$1"
},
"sbo": {
"alt_uri_formats": [
"http://purl.org/obo/owl/SBO#$1"
],
"bioportal": "1046",
"description": "The Systems Biology Ontology is a set of controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modelling.",
"example": "SBO:0000262",
"homepage": "http://www.ebi.ac.uk/sbo/",
"keywords": [
"obo",
"systems biology"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Systems Biology Ontology",
"pattern": "^SBO:\\d{7}$",
"prefix": "sbo",
"pubmed_ids": [
"17118155"
],
"synonyms": [
"biomodels.sbo",
"Systems_Biology_Ontology"
],
"uri_format": "http://www.ebi.ac.uk/sbo/main/$1"
},
"sbro": {
"alt_uri_formats": [
"http://www.owl-ontologies.com/Ontology1171063716.owl#$1"
],
"bioportal": "1249",
"description": "An ontology representing a causal model of smoking behavior risk, including genetic and environmental components. It also includes concepts for describing smoking-related phenotypes.",
"example": "elimination_of_nicotine",
"keywords": [
"owl"
],
"miriam": "bioportal-sbro",
"name": "Smoking Behavior Risk Ontology",
"pattern": "^\\w$",
"prefix": "sbro",
"pubmed_ids": [
"19525886"
]
},
"scadb": {
"description": "The SCA database is a human spinocerebellar ataxia disease database designed to provide clinicians and researcher who study this disease the information of all possible short tandem repeats-containing genes within the disease-mapped chromosome regions, their genetic-links, priority selection tool, primer design tools and some of the experimental test results of these genes.",
"example": "16194389_1",
"homepage": "http://ymbc.ym.edu.tw/sca_ensembl/",
"keywords": [
"gene"
],
"name": "SCAdb: A Candidate Gene Database for Spinocerebellar ataxias",
"pattern": "^\\d+$",
"prefix": "scadb",
"uri_format": "http://ymbc.ym.edu.tw/cgi-bin/SCAdb_ensembl/aroundSTR.cgi?sca_type=SCA1&type=CAG&repeats_id=$1"
},
"schistodb": {
"description": "The Schistosoma Genome Resource",
"example": "SMP_043670.2",
"homepage": "http://SchistoDB.net",
"keywords": [
"genome"
],
"name": "SchistoDB; The Schistosoma Genome Resource",
"pattern": "^[A-Z,_,0-9]+$",
"prefix": "schistodb",
"uri_format": "http://schistocyc.schistodb.net/ptools/SM/NEW-IMAGE?type=GENE&object=$1"
},
"scmd": {
"description": "The Saccharomyces Cerevisiae Morphological Database(SCMD) is a collection of micrographs of budding yeast mutants.",
"example": "YER095w",
"homepage": "http://yeast.gi.k.u-tokyo.ac.jp/",
"keywords": [
"structure"
],
"name": "Saccharomyces cerevisiae Morphological Database",
"pattern": "^[A-Z,0-9]+$",
"prefix": "scmd",
"uri_format": "http://yeast.gi.k.u-tokyo.ac.jp/datamine/ViewStats.do?orf=$1"
},
"scop": {
"description": "The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known.",
"example": "47419",
"homepage": "http://scop.mrc-lmb.cam.ac.uk/scop",
"keywords": [
"protein",
"structure"
],
"name": "Structural Classification Of Proteins",
"pattern": "^\\d+$",
"prefix": "scop"
},
"scpd": {
"description": "Database containing promotor sequences found in Saccharomyces cerevisiae.",
"example": "CDC2",
"homepage": "http://rulai.cshl.edu/SCPD/",
"keywords": [
"DNA",
"RNA"
],
"name": "Saccharomyces cerevisiae promoter database",
"pattern": "^[A-Z.0-9]+$",
"prefix": "scpd",
"uri_format": "http://rulai.cshl.edu/cgi-bin/SCPD/getgene2?$1"
},
"sdap": {
"description": "SDAP is a Web server that integrates a database of allergenic proteins with various bioinformatics tools for performing structural studies related to allergens and characterization of their epitopes.",
"example": "610",
"homepage": "http://fermi.utmb.edu/SDAP",
"keywords": [
"protein",
"structure"
],
"name": "Structural Database of Allergenic Proteins",
"pattern": "^\\d+$",
"prefix": "sdap",
"uri_format": "http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid=$1"
},
"sdr": {
"description": "SDR is a database of predicted specificity-determining residues in protein families. Predicted positions may have been used during evolution to change the function of proteins within a protein family.",
"example": "PF00926.10",
"homepage": "http://paradox.harvard.edu/sdr",
"keywords": [
"protein",
"structure"
],
"name": "SDR",
"pattern": "^PF\\d+$",
"prefix": "sdr",
"uri_format": "http://paradox.harvard.edu/sdr/families/$1/$1_main.html"
},
"seedgenes": {
"description": "This project deals with genes that give a seed phenotype when disrupted by mutation. The long-term goal is to establish a comprehensive dataset of essential genes.",
"example": "TTN5",
"homepage": "http://www.seedgenes.org/",
"keywords": [
"gene"
],
"name": "SeedGenes",
"pattern": "^[A-Z,0-9]+$",
"prefix": "seedgenes",
"uri_format": "http://www.seedgenes.org/SeedGeneProfile?geneSymbol=$1"
},
"selectome": {
"description": "Selectome is a database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML on all branches of animal gene trees.",
"example": "TF101024",
"homepage": "http://bioinfo.unil.ch/selectome/",
"keywords": [
"gene"
],
"name": "Selectome: a Database of Positive Selection",
"pattern": "^[A-Z]+\\d+$",
"prefix": "selectome"
},
"selenodb": {
"description": "SelenoDB intends to be a comprehensive database for information on eukaryotic selenoproteins and related genes and proteins.",
"example": "SPG00000024",
"homepage": "http://www.selenodb.org/",
"keywords": [
"protein",
"gene"
],
"name": "SelenoDB",
"pattern": "^SPG\\d+$",
"prefix": "selenodb",
"uri_format": "http://www.selenodb.org/cgi-perl/feature_report.pl?feature=$1_1.0"
},
"sep": {
"bioportal": "1044",
"description": "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments, such as, and including, gel electrophoresis, column chromatography, capillary electrophoresis, centrifugation and so on. Developed jointly by the HUPO Proteomics Standards Initiative and The Metabolomics Standards Initiative.",
"example": "sep_00005",
"homepage": "http://psidev.info/index.php?q=node/312",
"keywords": [
"obo",
"protein"
],
"name": "Sample processing and separation techniques",
"pattern": "^sep_\\d+$",
"prefix": "sep"
},
"sgd": {
"description": "The Saccharomyces Genome Database (SGD) collects and organizes information about the molecular biology and genetics of the yeast Saccharomyces cerevisiae. SGD contains a variety of biological information and tools with which to search and analyze it.",
"example": "S000006169",
"homepage": "http://www.yeastgenome.org/",
"keywords": [
"eukaryotic",
"genome",
"nucleotide"
],
"name": "Saccharomyces Genome Database",
"pattern": "^S\\d+$",
"prefix": "sgd",
"pubmed_ids": [
"14681421"
],
"uri_format": "http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=$1"
},
"sgd.pathways": {
"description": "Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD).",
"example": "PWY3O-214",
"homepage": "http://www.yeastgenome.org/",
"keywords": [
"genome",
"pathway",
"sequence"
],
"name": "Saccharomyces genome database pathways",
"pattern": "^PWY\\w{2}\\-\\d{3}$",
"prefix": "sgd.pathways",
"pubmed_ids": [
"14681421"
],
"synonyms": [
"spt"
],
"uri_format": "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1"
},
"sgn": {
"description": "The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant.",
"example": "1",
"homepage": "http://www.sgn.cornell.edu",
"keywords": [
"pathway",
"small molecule",
"genome",
"plant"
],
"name": "Sol Genomics Network",
"pattern": "^\\d+$",
"prefix": "sgn",
"pubmed_ids": [
"20935049"
],
"uri_format": "http://solgenomics.net/phenome/locus_display.pl?locus_id=$1"
},
"sheepqtldb": {
"description": "This Sheep Quantitative Trait Locus (QTL) database (Sheep QTLdb) has gathered all sheep QTL data published during the past 10+ years. The database and its peripheral tools make it possible to compare, confirm and locate on sheep chromosomes the most feasible location for genes responsible for quantitative trait important to sheep production.",
"example": "66",
"homepage": "http://www.animalgenome.org/cgi-bin/QTLdb/OA/index",
"keywords": [
"DNA",
"genome"
],
"name": "Sheep Quantitative Trait Locus database",
"pattern": "^\\d+$",
"prefix": "sheepqtldb",
"uri_format": "http://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=$1"
},
"shibase": {
"description": "The database focuses on the comparative genomics of Shigella and provides a way to summarize large volumes of genomic and comparison data in a visually intuitive format.",
"example": "SDY2614",
"homepage": "http://www.mgc.ac.cn/ShiBASE/",
"keywords": [
"genome"
],
"name": "ShiBASE",
"pattern": "^[A-Z]+\\d+$",
"prefix": "shibase",
"uri_format": "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=$1"
},
"shr": {
"bioportal": "1665",
"description": "The goal of SHR project is to develop an ontology for the description of student health records. Student health records are created for entering college students in order to provide better health services will be formed. This file contains various sections such as history of disease, family history of disease, public examinations and ... .",
"example": "Family_Health_History",
"homepage": "http://www.shojaee.com/shr/",
"keywords": [
"owl",
"health"
],
"name": "Student Health Record",
"pattern": "^\\w$",
"prefix": "shr",
"rdf_uri_format": "http://www.shojaee.com/shr/shr.owl#$1",
"uri_format": "http://www.shojaee.com/shr/shr.owl#$1"
},
"siege": {
"description": "Smoking Induced Epithelial Gene Expression Database",
"example": "221577_x_at",
"homepage": "http://pulm.bumc.bu.edu/siegeDB",
"keywords": [
"gene expression"
],
"name": "Smoking Induced Epithelial Gene Expression Database",
"pattern": "^[A-Z,0-9]+$",
"prefix": "siege",
"uri_format": "http://pulm.bumc.bu.edu/cgi-bin/siegeDB/siege_html/compsearchgraph.cgi?$1"
},
"siena2dpage": {
"description": "Two-dimensional polyacrylamide gel electrophoresis database",
"example": "P00558",
"homepage": "http://www.bio-mol.unisi.it/2d/2d.html",
"keywords": [
"protein"
],
"name": "2D-PAGE database from the Department of Molecular Biology, University of Siena, Italy",
"pattern": "^[A-Z]\\d+$",
"prefix": "siena2dpage",
"uri_format": "http://www.bio-mol.unisi.it/cgi-bin/2d/2d.cgi?ac=$1"
},
"signaling-gateway": {
"description": "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.",
"example": "A001094",
"homepage": "http://www.signaling-gateway.org/molecule/",
"keywords": [
"pathway",
"protein",
"small molecule"
],
"license": "http://www.signaling-gateway.org/copyright/afcs.html",
"name": "The Signaling Gateway",
"pattern": "^A\\d{6}$",
"prefix": "signaling-gateway",
"pubmed_ids": [
"17965093",
"12478304",
"21505029"
],
"synonyms": [
"afcs",
"sgmp"
],
"uri_format": "http://www.signaling-gateway.org/molecule/query?afcsid=$1"
},
"silva": {
"description": "SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).",
"example": "AACY021460914",
"homepage": "http://www.arb-silva.de",
"keywords": [
"RNA"
],
"name": "SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data",
"pattern": "^[A-Z,0-9]+$",
"prefix": "silva",
"uri_format": "http://www.arb-silva.de/browser/ssu/$1/embl/?tx_pmtree_pi1[pid]=$1"
},
"sirnadb": {
"description": "A database of known siRNA molecules",
"example": "NM_005938",
"homepage": "http://sirna.cgb.ki.se",
"keywords": [
"RNA"
],
"name": "siRNAdb",
"pattern": "^NM_\\d+$",
"prefix": "sirnadb"
},
"sisyphus": {
"description": "The SISYPHUS database contains a collection of manually curated structural alignments and their interrelationships. Each multiple alignment within the SISYPHUS database consists of structurally similar regions common to a group of proteins.",
"example": "AL00048599",
"homepage": "http://sisyphus.mrc-cpe.cam.ac.uk",
"keywords": [
"structure",
"protein",
"interaction"
],
"name": "SISYPHUS",
"pattern": "^AL\\d+$",
"prefix": "sisyphus",
"uri_format": "http://sisyphus.mrc-cpe.cam.ac.uk/sisyphus/alignment.jsp?ac=$1"
},
"sitbac": {
"bioportal": "1237",
"description": "Context-based healthcare access-control policies",
"example": "EHR",
"homepage": "http://mis.hevra.haifa.ac.il/~morpeleg/",
"keywords": [
"owl",
"health"
],
"name": "Situation-Based Access Control",
"pattern": "^\\w$",
"prefix": "sitbac",
"rdf_uri_format": "http://www.semanticweb.org/ontologies/2008/1/Ontology1204037102846.owl#$1"
},
"sitex": {
"description": "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.",
"example": "1000",
"homepage": "http://www-bionet.sscc.ru/sitex/",
"keywords": [
"domain",
"eukaryotic",
"sequence",
"structure"
],
"name": "SitEx database of eukaryotic protein functional sites",
"pattern": "^\\d+$",
"prefix": "sitex",
"pubmed_ids": [
"22139920"
],
"uri_format": "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1"
},
"smart": {
"description": "The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures.",
"example": "SM00015",
"homepage": "http://smart.embl.de/",
"keywords": [
"domain",
"protein",
"structure"
],
"license": "CC BY-SA 3.0",
"name": "Simple Modular Architecture Research Tool; a protein domain database",
"pattern": "^SM\\d{5}$",
"prefix": "smart",
"pubmed_ids": [
"9847187"
],
"uri_format": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1"
},
"smpdb": {
"description": "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.",
"example": "SMP00001",
"homepage": "http://www.smpdb.ca/",
"keywords": [
"chemical",
"human",
"metabolite",
"pathway"
],
"license": "http://www.smpdb.ca/about#cite",
"name": "Small Molecule Pathway Database",
"pattern": "^SMP\\d{5}$",
"prefix": "smpdb",
"uri_format": "http://pathman.smpdb.ca/pathways/$1/pathway"
},
"smr": {
"description": "The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.",
"example": "smr03",
"homepage": "http://swissmodel.expasy.org/repository/",
"keywords": [
"protein",
"structure"
],
"name": "SWISS-MODEL Repository - a database of annotated 3D protein structure models",
"pattern": "^smr\\d+$",
"prefix": "smr",
"synonyms": [
"swissmodelrepository"
],
"uri_format": "http://swissmodel.expasy.org/repository/?pid=$1&uid=&token=&zid=async"
},
"snap": {
"description": "Snap is a sequence analysis tool providing a simple but detailed analysis of human genes and their variations. For each gene, a gene-gene relationship network can be generated based on protein-protein interaction data, metabolic pathway connections and extended through phylogenetic relations.",
"example": "ENSG00000187634",
"homepage": "http://snap.humgen.au.dk",
"keywords": [
"gene",
"protein",
"interaction",
"pathway"
],
"name": "SNAP: a SNP Annotation Platform",
"pattern": "^ENSG\\d+$",
"prefix": "snap",
"uri_format": "http://snap.humgen.au.dk/views/geneview.cgi?gene=$1"
},
"snomedct": {
"bioportal": "1353",
"description": "SNOMED Clinical Terms",
"example": "284196006",
"homepage": "http://ihtsdo.org",
"name": "Systematized Nomenclature of Medicine - Clinical Terms",
"pattern": "^(\\w+)?\\d+$",
"prefix": "snomedct",
"synonyms": [
"snomed",
"snomedct_2010_1_31",
"snomedct_2013_01_31"
]
},
"snornalbmedb": {
"description": "This is a database of human C/D box and H/ACA modification guide RNAs",
"example": "HBII-240",
"homepage": "http://www-snorna.biotoul.fr/",
"keywords": [
"RNA"
],
"name": "snoRNA-LBME-db",
"pattern": "^[A-Z,0-9]+$",
"prefix": "snornalbmedb",
"synonyms": [
"snornabase"
],
"uri_format": "http://www-snorna.biotoul.fr/plus.php?id=$1"
},
"snp2nmd": {
"description": "Elucidating the effects of genetic polymorphisms on genes and gene networks is an important step in disease association studies. We developed the SNP2NMD database for human SNPs (single nucleotide polymorphisms) that result in PTCs (premature termination codons) and trigger nonsense-mediated mRNA decay (NMD).",
"example": "rs10530",
"homepage": "http://variome.kobic.re.kr/SNP2NMD/",
"keywords": [
"gene",
"RNA",
"DNA"
],
"name": "SNP2NMD: A database of human SNPs (single nucleotide polymorphisms) causing NMD (nonsense-mediated mRNA decay)",
"pattern": "^[a-z]+\\d+$",
"prefix": "snp2nmd",
"uri_format": "http://variome.kobic.re.kr/SNP2NMD/snp2nmd.jsp?id=$1&rule=50"
},
"snp500cancer": {
"description": "The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer.",
"example": "TP53-47",
"homepage": "http://snp500cancer.nci.nih.gov",
"keywords": [
"DNA"
],
"name": "SNP500Cancer",
"pattern": "^TP\\d+-\\d+$",
"prefix": "snp500cancer",
"uri_format": "http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id=$1"
},
"snpeffect": {
"description": "The SNPeffect and PupaSuite databases are now synchronized to deliver annotations for both non-coding and coding SNP, as well as annotations for the SwissProt set of human disease mutations.",
"example": "23075009",
"homepage": "http://snpeffect.vib.be/",
"keywords": [
"DNA"
],
"name": "SNPeffect",
"pattern": "^\\d+$",
"prefix": "snpeffect",
"uri_format": "http://snpeffect.vib.be/snp_main.php?id=$1"
},
"so": {
"alt_uri_formats": [
"http://purl.org/obo/owl/SO#$1"
],
"bioportal": "1109",
"description": "The Sequence Ontology is a set of terms and relationships used to describe the features and attributes of biological sequence. SO includes different kinds of features which can be located on the sequence.",
"example": "SO:0000704",
"homepage": "http://www.sequenceontology.org/",
"keywords": [
"obo",
"ontology",
"DNA",
"RNA",
"structure"
],
"license": "http://www.sequenceontology.org/about/citing.html",
"name": "Sequence Ontology",
"pattern": "^SO:\\d{7}$",
"prefix": "so",
"pubmed_ids": [
"15892872"
],
"synonyms": [
"obo.so"
],
"uri_format": "http://www.sequenceontology.org/miso/current_release/term/$1"
},
"soy": {
"bioportal": "3028",
"description": "Growth, trait and development ontology for soybean",
"example": "SOY_0001650",
"homepage": "http://soybase.org",
"keywords": [
"obo",
"development",
"phenotype",
"spider"
],
"name": "SoyOntology",
"pattern": "^SOY_\\d{7}$",
"prefix": "soy"
},
"spbase": {
"description": "SpBase, is designed to present the results of the genome sequencing project for the purple sea urchin. THe sequences and annotations emerging from this effort are organized in a database that provides the research community access to those data not normally presented through NCBI and other large databases.",
"example": "SPU_000001",
"homepage": "http://spbase.org",
"keywords": [
"genome",
"DNA",
"RNA"
],
"name": "SpBase",
"pattern": "^SPU_\\d+$",
"prefix": "spbase",
"uri_format": "http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id=$1"
},
"spd": {
"description": "A collection of secreted proteins from Human, Mouse and Rat proteomes, which includes sequences from SwissProt, Trembl, Ensembl and Refseq.",
"example": "Q9UK53",
"homepage": "http://spd.cbi.pku.edu.cn",
"keywords": [
"protein",
"structure"
],
"name": "Secreted Protein Database",
"pattern": "^[A-Z]\\d+$",
"prefix": "spd",
"uri_format": "http://spd.cbi.pku.edu.cn/spd_pro.php?id=$1"
},
"spdo": {
"bioportal": "1091",
"description": "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).",
"example": "SPD_0000464",
"homepage": "http://research.amnh.org/atol/files/",
"keywords": [
"obo",
"anatomy",
"spider"
],
"name": "Spider Ontology",
"pattern": "^SPD_\\d{7}$",
"prefix": "spdo"
},
"spike": {
"description": "SPIKE (Signaling Pathway Integrated Knowledge Engine) is an interactive software environment that graphically displays biological signaling networks, allows dynamic layout and navigation through these networks, and enables the superposition of DNA microarray and other functional genomics data on interaction maps.",
"example": "spike00001",
"homepage": "http://www.cs.tau.ac.il/~spike/",
"keywords": [
"pathway",
"DNA",
"gene expression"
],
"name": "Signaling Pathway Integrated Knowledge Engine",
"pattern": "^spike\\d{5}$",
"prefix": "spike",
"pubmed_ids": [
"18289391",
"21097778"
],
"synonyms": [
"spike.map"
]
},
"spliceinfo": {
"description": "The database provides a means of investigating alternative splicing and can be used for identifying alternative splicing - related motifs, such as the exonic splicing enhancer (ESE), the exonic splicing silencer (ESS) and other intronic splicing motifs.",
"example": "ENSG00000012048",
"homepage": "http://spliceinfo.mbc.nctu.edu.tw/",
"keywords": [
"DNA",
"gene"
],
"name": "SpliceInfo",
"pattern": "^ENSG\\d+$",
"prefix": "spliceinfo",
"uri_format": "http://spliceinfo.mbc.nctu.edu.tw/info_show.php?gs_id=$1"
},
"splicenest": {
"description": "SpliceNest [1] is a web based graphical tool to explore gene structure, including alternative splicing, based on a mapping on the EST consensus sequences (contigs) from GeneNest [2] to the complete human genome.",
"example": "Hs635",
"homepage": "http://splicenest.molgen.mpg.de/",
"keywords": [
"gene",
"DNA",
"genome"
],
"name": "SpliceNest",
"pattern": "^[a-z]+\\d+$",
"prefix": "splicenest",
"uri_format": "http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster=$1"
},
"spodobase": {
"description": "An integrated database for the genomics of the Lepidoptera Spodoptera frugiperda",
"example": "Sf1F00061-3-1",
"homepage": "http://bioweb.ensam.inra.fr/spodobase/",
"keywords": [
"genome"
],
"name": "SpodoBase",
"pattern": "^Sf1F\\d+$",
"prefix": "spodobase",
"uri_format": "http://bioweb.ensam.inra.fr/Spodopterav3/sequence?name=$1&class=Sequence"
},
"sprint": {
"description": "SPRINT provides search access to the data bank of protein family fingerprints (PRINTS).",
"example": "PR00001",
"homepage": "http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/",
"keywords": [
"domain",
"protein"
],
"name": "SPRINT",
"pattern": "^PR\\d{5}$",
"prefix": "sprint",
"pubmed_ids": [
"10592232"
],
"uri_format": "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off"
},
"spto": {
"bioportal": "3029",
"description": "Solanaceae crop phenotypes and traits, developed in collaboration with the research community, especially for breeder traits of agronomic importance.",
"example": "SP_0000115",
"homepage": "http://solgenomics.net",
"keywords": [
"obo",
"phenotype",
"plant"
],
"name": "Solanaceae Phenotype Ontology",
"pattern": "^SP_\\d{7}$",
"prefix": "spto"
},
"sso": {
"bioportal": "1394",
"description": "The SSO encodes agreement among experts about how Emergency Department (ED) chief complaints are grouped into syndromes of public health importance (consensus definitions).",
"example": "Abdominal_pain",
"keywords": [
"owl",
"health"
],
"name": "Syndromic Surveillance Ontology",
"pattern": "^\\w$",
"prefix": "sso",
"rdf_uri_format": "http://surveillance.mcgill.ca/sso/syndromes.owl#$1"
},
"sstoss": {
"description": "SSToSS is a database which provides sequence-structural templates of single member protein domain superfamilies like PASS2. Sequence-structural templates are recognized by considering the content and overlap of sequence similarity and structural parameters like, solvent inaccessibility, secondary structural content, hydrogen bonding and spatial packing of the residues among the protein of single member superfamilies.",
"example": "01.01.005",
"homepage": "http://caps.ncbs.res.in/SSTOSS/index.htm",
"keywords": [
"protein",
"structure"
],
"name": "Sequence-Structural Templates of Single-member Superfamilies",
"pattern": "^\\d+.\\d+.\\d+$",
"prefix": "sstoss",
"uri_format": "http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code=$1"
},
"stitch": {
"description": "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.",
"example": "ICXJVZHDZFXYQC",
"homepage": "http://stitch.embl.de",
"keywords": [
"interaction",
"protein",
"small molecule"
],
"name": "STITCH: Chemical-Protein Interactions",
"pattern": "^\\w{14}$",
"prefix": "stitch",
"pubmed_ids": [
"18084021"
]
},
"straininfonet": {
"description": "You can use StrainInfo to search through the catalogs of over 60 BRCs",
"example": "182672",
"homepage": "http://www.StrainInfo.net",
"keywords": [
"DNA"
],
"name": "StrainInfo.net Bioportal",
"pattern": "^\\d+$",
"prefix": "straininfonet",
"uri_format": "http://www.straininfo.net/taxa/$1"
},
"strepto_db": {
"description": "Strepto-DB is a database for comparative genomics of group A and group B streptococci. It is based on OGeR (Open Genome Resource for comparative analysis of prokaryotic genomes) and includes all sequenced GAS and GBS strains and serovars available as EMBL genome review or NCBI GenBank files.",
"example": "9939",
"homepage": "http://oger.tu-bs.de/strepto_db",
"keywords": [
"genome"
],
"name": "Strepto-DB",
"pattern": "^\\d+$",
"prefix": "strepto_db",
"uri_format": "http://oger.tu-bs.de/websites/query_result.php?index=1&dbno=$1"
},
"string": {
"description": "STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations",
"example": "P53350",
"homepage": "http://string-db.org",
"keywords": [
"protein",
"interaction"
],
"name": "STRING: functional protein association networks",
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$",
"prefix": "string",
"pubmed_ids": [
"18940858"
]
},
"suba": {
"description": "SUBA provides a powerful tool to investigate subcellular localisation in Arabidopsis through the unification of disparate datasets and through the provision of a web accessible interface for the construction of powerful user based queries resulting in a one-stop-shop for protein localisation in this model plant.",
"example": "AT1G05560.1",
"homepage": "http://www.suba.bcs.uwa.edu.au/",
"keywords": [
"protein"
],
"name": "SUB-cellular location database for Arabidopsis proteins",
"pattern": "^[A-Z,0-9]+$",
"prefix": "suba",
"uri_format": "http://suba.plantenergy.uwa.edu.au/flatfile.php?id=$1"
},
"subtilist": {
"description": "Its purpose is to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments",
"example": "BG11523",
"homepage": "http://genolist.pasteur.fr/SubtiList/",
"keywords": [
"genome",
"DNA",
"protein"
],
"name": "Bacillus subtilis strain 168 genome database",
"pattern": "^BG\\d+$",
"prefix": "subtilist"
},
"subtiwiki": {
"description": "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. Note: Currently, direct access to RNA products is restricted. This is expected to be rectified soon.",
"example": "BSU29180",
"homepage": "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page",
"keywords": [
"gene",
"protein",
"RNA",
"DNA"
],
"name": "SubtiWiki",
"pattern": "^BSU\\d{5}$",
"prefix": "subtiwiki",
"pubmed_ids": [
"19959575",
"20157485"
],
"uri_format": "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1"
},
"sulfolobus": {
"description": "This database contains the three sequenced Sulfolobus genomes.",
"example": "10189",
"homepage": "http://www.sulfolobus.org",
"keywords": [
"genome"
],
"name": "Sulfolobus",
"pattern": "^\\d+$",
"prefix": "sulfolobus",
"uri_format": "http://www.sulfolobus.org/cbin/mutagen.pl?page=misc&gidinfo=$1"
},
"superfamily": {
"description": "SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.",
"example": "46556",
"homepage": "http://supfam.org",
"keywords": [
"protein",
"genome",
"structure",
"classification"
],
"name": "SUPERFAMILY database of structural and functional annotation",
"pattern": "^\\d+$",
"prefix": "superfamily",
"synonyms": [
"supfam"
],
"uri_format": "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?sunid=$1"
},
"superhapten": {
"description": "This database contains currently 7257 haptens, 453 commercially available related antibodies and 24 carriers",
"example": "2399",
"homepage": "http://bioinformatics.charite.de/superhapten",
"keywords": [
"small molecule"
],
"name": "SuperHapten",
"pattern": "^\\d+$",
"prefix": "superhapten",
"uri_format": "http://bioinformatics.charite.de/superhapten/fullinfo_hapten_chime.php?id=$1"
},
"supernatural": {
"description": "This database contains 45.917 compounds with 2.665.881 conformers available for purchase",
"example": "000068268",
"homepage": "http://bioinformatics.charite.de/supernatural",
"keywords": [
"small molecule"
],
"name": "SuperNatural",
"pattern": "^\\d+$",
"prefix": "supernatural",
"uri_format": "http://bioinformatics.charite.de/supernatural/marvin/fullinfo_roempp_marvin.php?cas=$1"
},
"supersite": {
"description": "The SuperSite is an encyclopedia that is dedicated to a ligand and binding site oriented view of the protein structural space. SuperSite integrates evolutionary information in the proteins as well as predicted binding sites from LigsiteCSC.",
"example": "1B89",
"homepage": "http://bioinf-tomcat.charite.de/supersite/",
"keywords": [
"small molecule",
"protein",
"structure"
],
"name": "SuperSite",
"pattern": "^[A-Z,0-9]+$",
"prefix": "supersite",
"uri_format": "http://bioinf-tomcat.charite.de/supersite/resultPDB.faces?pdbid=$1"
},
"supertoxic": {
"description": "A collection of toxic compounds from literature and web sources. The current version of this database compiles approx. 60,000 compounds with about 100,000 synonyms. These molecules are classified according to their toxicity based on more than 2,500,000 measurements.",
"example": "10276",
"homepage": "http://bioinformatics.charite.de/supertoxic",
"keywords": [
"small molecule"
],
"name": "SuperToxic",
"pattern": "^\\d+$",
"prefix": "supertoxic",
"uri_format": "http://bioinformatics.charite.de/supertoxic/index.php?site=detail_view&ids=($1)"
},
"swiss2dpage": {
"description": "SWISS-2DPAGE contains data on proteins identified on various 2-D PAGE and SDS-PAGE reference maps. You can locate these proteins on the 2-D PAGE maps or display the region of a 2-D PAGE map where one might expect to find a protein from UniProtKB/Swiss-Prot",
"example": "P00533",
"homepage": "http://www.expasy.org/ch2d/",
"keywords": [
"protein"
],
"name": "Two-dimensional polyacrylamide gel electrophoresis database from the Geneva University Hospital",
"pattern": "^[A-Z]\\d+$",
"prefix": "swiss2dpage",
"uri_format": "http://ca.expasy.org/swiss-2dpage/ac=$1"
},
"swissmodel": {
"description": "The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for sequences registered is SWISS-PROT.",
"example": "P23298",
"homepage": "http://swissmodel.expasy.org/",
"keywords": [
"protein",
"structure"
],
"name": "SWISS-MODEL repository of 3D protein structure models",
"pattern": "^\\w+$",
"prefix": "swissmodel",
"pubmed_ids": [
"18931379"
],
"uri_format": "http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$1"
},
"swo": {
"bioportal": "1413",
"description": "The Software Ontology (SWO) has the scope of describing types of software used in Bioinformatics. The SWO covers areas such as the software type, the manufacturer of the software, the input and output data types and the uses (i.e. objectives) the software can be put to. The SWO intends to use BFO as an upper level ontolgoy and subclasses types from the Ontology of Biomedical Investigations. Contact James Malone for info: malone@ebi.ac.uk",
"example": "SWO_0000396",
"homepage": "http://theswo.sourceforge.net",
"name": "Software Ontology",
"pattern": "^SWO_\\d{7}$",
"prefix": "swo",
"rdf_uri_format": "http://www.ebi.ac.uk/efo/swo/$1"
},
"syfpeithi": {
"description": "SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules.",
"example": "BC102564",
"homepage": "http://www.syfpeithi.de/",
"keywords": [
"protein",
"small molecule"
],
"name": "Database of MHC Ligands and Peptide Motifs",
"pattern": "^[A-Z]+\\d+$",
"prefix": "syfpeithi",
"uri_format": "http://www.ebi.ac.uk/cgi-bin/emblfetch?$1"
},
"symptom": {
"bioportal": "1224",
"description": "The symptom ontology was designed around the guiding concept of a symptom being: \"A perceived change in function, sensation or appearance reported by a patient indicative of a disease\"",
"example": "SYMP_0000461",
"homepage": "http://symptomontologywiki.igs.umaryland.edu/wiki/index.php/Main_Page",
"keywords": [
"obo",
"ontology"
],
"name": "Symptom Ontology",
"pattern": "^SYMP_\\d{7}$",
"prefix": "symptom",
"synonyms": [
"symptomontology",
"symp"
]
},
"sysbodyfluid": {
"description": "Sys-BodyFluid, contains 11 body fluid proteomes, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk, and amniotic fluid",
"example": "IPI00478115",
"homepage": "http://www.biosino.org/bodyfluid/",
"keywords": [
"protein"
],
"name": "Sys-BodyFluid",
"pattern": "^IPI\\d+$",
"prefix": "sysbodyfluid",
"uri_format": "http://www.biosino.org/bodyfluid/protein.jsp?proteinID=$1"
},
"systers": {
"description": "A collection of graph-based algorithms to hierarchically partition a large set of protein sequences into homologous families and superfamilies.",
"example": "1568",
"homepage": "http://systers.molgen.mpg.de/",
"keywords": [
"protein",
"structure",
"classification"
],
"name": "SYSTERS Protein Family Database",
"pattern": "^\\d+$",
"prefix": "systers",
"uri_format": "http://systers.molgen.mpg.de/cgi-bin/nph-fetchcluster.pl?CLNR=$1"
},
"t1dbase": {
"description": "T1DBase focuses on two research areas in type 1 diabetes (T1D): the genetics of T1D susceptibility and beta cell biology.",
"example": "7098",
"homepage": "http://t1dbase.org/",
"name": "Type 1 Diabetes Database",
"pattern": "^\\d+$",
"prefix": "t1dbase",
"uri_format": "http://t1dbase.org/page/Overview/display/gene_id/$1"
},
"t3db": {
"description": "Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.",
"example": "T3D0001",
"homepage": "http://www.t3db.org/",
"keywords": [
"protein",
"molecule"
],
"license": "http://www.t3db.org/about#cite",
"name": "Toxin and Toxin Target Database",
"pattern": "^T3D\\d+$",
"prefix": "t3db",
"uri_format": "http://www.t3db.org/toxins/$1"
},
"tair.gene": {
"description": "The reference gene model for a given locus",
"example": "Gene:2200934",
"keywords": [
"gene"
],
"name": "TAIR-Gene",
"pattern": "^Gene:\\d{7}$",
"prefix": "tair.gene",
"pubmed_ids": [
"12444417"
]
},
"tair.locus": {
"description": "The locus name",
"example": "AT1G01030",
"keywords": [
"genome"
],
"name": "TAIR-Locus",
"pattern": "^AT[1-5]G\\d{5}$",
"prefix": "tair.locus",
"pubmed_ids": [
"12444417"
],
"uri_format": "http://arabidopsis.org/servlets/TairObject?type=locus&name=$1"
},
"tair.protein": {
"description": "The protein entry",
"example": "AASequence:1009107926",
"keywords": [
"protein"
],
"name": "TAIR-Protein",
"pattern": "^AASequence:\\d{10}$",
"prefix": "tair.protein",
"pubmed_ids": [
"12444417"
]
},
"tao": {
"bioportal": "1110",
"description": "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa",
"example": "TAO_0000297",
"homepage": "https://www.nescent.org/phenoscape/Main_Page",
"keywords": [
"obo",
"classification",
"anatomy"
],
"name": "Teleost Anatomy Ontology",
"pattern": "^TAO_\\d{7}$",
"prefix": "tao",
"synonyms": [
"teleost_anatomy"
]
},
"targetdb": {
"description": "TargetDB, a target registration database, provides information on the experimental progress and status of targets selected for structure determination.",
"example": "BSGCAIR30339",
"homepage": "http://targetdb.pdb.org/",
"keywords": [
"structure"
],
"name": "TargetDB",
"pattern": "^BSGCAIR\\d+$",
"prefix": "targetdb"
},
"tassdb": {
"description": "TassDB stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors. Currently, 114,554 tandem splice sites of eight species are contained in the database, 5,209 of which have EST/mRNA evidence for alternative splicing.",
"example": "AVPI1",
"homepage": "http://helios.informatik.uni-freiburg.de/TassDB/",
"keywords": [
"RNA",
"DNA"
],
"name": "TAndem Splice Site DataBase",
"pattern": "^[A-Z.0-9]+$",
"prefix": "tassdb"
},
"taxonomy": {
"alt_uri_formats": [
"http://purl.org/obo/owl/NCBITaxon#$1",
"http://purl.org/obo/owl/TAXON#$1",
"http://bioportal.bioontology.org/ontologies/1132?p=terms&conceptid=obo:NCBITaxon_#$1"
],
"bioportal": "1132",
"description": "The NCBI taxonomy database contains the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence.",
"example": "9606",
"homepage": "http://www.ncbi.nlm.nih.gov/taxonomy",
"keywords": [
"DNA",
"protein",
"structure",
"classification"
],
"license": "http://www.nlm.nih.gov/copyright.html",
"name": "NCBI Taxonomy",
"pattern": "^\\d+$",
"prefix": "taxonomy",
"synonyms": [
"taxid",
"taxon",
"ncbitaxon",
"ncbitaxonomy",
"newt",
"taxman",
"ncbi_taxid",
"ncbi_taxon_id"
],
"uri_format": "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=$1"
},
"taxrank": {
"bioportal": "1419",
"description": "Taxonomic ranks drawn from both the NCBI taxonomy database and from a rank vocabulary developed for the TDWG biodiversity information standards group.",
"example": "TAXRANK:0000001",
"homepage": "https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary",
"keywords": [
"obo"
],
"name": "Taxonomic rank vocabulary",
"pattern": "^TAXRANK:\\d+$",
"prefix": "taxrank",
"synonyms": [
"taxonomic_rank"
]
},
"tbdb": {
"description": "TBDatabase (TBDB) makes available the tools and resources available at the Stanford Microarray Database and the Broad Institute.",
"example": "S7000000635247860",
"homepage": "http://tbdb.org",
"keywords": [
"gene expression"
],
"name": "Tuberculosis Database",
"pattern": "^[A-Z]\\d+$",
"prefix": "tbdb",
"uri_format": "http://genome.tbdb.org/annotation/genome/tbdb/GeneDetails.html?sp=$1"
},
"tbestdb": {
"description": "The taxonomically broad EST database TBestDB serves as a repository for EST data from a wide range of eukaryotes, many of which have previously not been thoroughly investigated.",
"example": "COL00000190",
"homepage": "http://tbestdb.bcm.umontreal.ca/searches/welcome.php",
"keywords": [
"DNA",
"RNA"
],
"name": "Taxonomically Broad EST Database",
"pattern": "^[A-Z]+\\d+$",
"prefix": "tbestdb",
"uri_format": "http://tbestdb.bcm.umontreal.ca/searches/contig.php?conDeID=$1"
},
"tc7ap": {
"description": "The objective of this project is to generate the most comprehensive description of human chromosome 7 to facilitate biological discovery, disease gene research and medical genetic applications.",
"example": "GA0008",
"homepage": "http://www.chr7.org",
"keywords": [
"genome"
],
"name": "The Chromosome 7 Annotation Project",
"pattern": "^GA\\d+$",
"prefix": "tc7ap",
"uri_format": "http://www.chr7.org/cgi-bin/geneview?id=$1"
},
"tccd": {
"description": "Cell Cycle Database is a collection of genes and proteins involved in human and yeast cell cycle",
"example": "TP53",
"homepage": "http://www.itb.cnr.it/cellcycle",
"keywords": [
"gene",
"protein",
"pathway"
],
"name": "The Cell Cycle DB",
"pattern": "^[A-Z,0-9]+$",
"prefix": "tccd",
"uri_format": "http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name=$1"
},
"tcdb": {
"description": "TCDB is a curated database of factual information from over 10,000 published references; it contains about 5,600 unique protein sequences that are classified into over 600 transporter families based on the TC-system.",
"example": "5.A.1.1.1",
"homepage": "http://www.tcdb.org/",
"keywords": [
"protein",
"structure"
],
"name": "Transport Classification Database",
"pattern": "^\\d+\\.[A-Z]\\.\\d+\\.\\d+\\.\\d+$",
"prefix": "tcdb",
"pubmed_ids": [
"16381841"
],
"synonyms": [
"tc"
],
"uri_format": "http://www.tcdb.org/search/result.php?tc=$1"
},
"tcruzidb": {
"description": "TcruziDB provides access to the published genome sequence data from strain (CL Brener), generated by TIGR, Karolinska & SBRI, functional genomics data and annotation generated by the Trypanosoma cruzi research community.",
"example": "Tc00.1047053508461.30",
"homepage": "http://tcruzidb.org/",
"keywords": [
"genome",
"DNA"
],
"name": "TcruziDB; An Integrated Trypanosoma cruzi Genome Resource",
"pattern": "^[a-z]+\\d+$",
"prefix": "tcruzidb",
"uri_format": "http://tcruzidb.org/tcruzidb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&project_id=&primary_key=$1"
},
"teddy": {
"alt_uri_formats": [
"http://purl.org/obo/owl/TEDDY#$1",
"http://biomodels.net/teddy/TEDDY#$1"
],
"bioportal": "1407",
"description": "The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.",
"example": "TEDDY_0000066",
"homepage": "http://teddyontology.sourceforge.net/",
"keywords": [
"ontology"
],
"license": "http://www.ebi.ac.uk/Information/termsofuse.html",
"name": "Terminology for the Description of Dynamics",
"pattern": "^TEDDY_\\d{7}$",
"prefix": "teddy",
"synonyms": [
"biomodels.teddy"
]
},
"tess": {
"description": "TESS is a web tool for predicting transcription factor binding sites in DNA sequences. It can identify binding sites using site or consensus strings and positional weight matrices from the TRANSFAC, JASPAR, IMD, and our CBIL-GibbsMat database.",
"example": "T00015",
"homepage": "http://www.cbil.upenn.edu/tess",
"keywords": [
"regulation",
"DNA"
],
"name": "Transcription Element Search System",
"pattern": "^[A-Z]\\d+$",
"prefix": "tess",
"uri_format": "http://www.cbil.upenn.edu/cgi-bin/tess/tess?request=FCT-DBRTRV-Accno&key=$1"
},
"tgd": {
"description": "Pages with links to phage information are also available, including a T4 genetic map reference figure, RB69, RB49, and Aeh1 Map figures, electron micrographs, annotation tables, sequence files, and links to NCBI T4 and Integrated Genomics RB69 annotation sites are available.",
"example": "RB51",
"homepage": "http://phage.bioc.tulane.edu",
"keywords": [
"genome"
],
"name": "T4-like genome database",
"pattern": "^[A-Z,0-9]+$",
"prefix": "tgd",
"uri_format": "http://phage.bioc.tulane.edu/cgi-bin/gbrowse/$1?name=$1"
},
"tgdb": {
"description": "The Tumor Gene Family of Databases contains information about genes which are targets for cancer-causing mutations; proto-oncogenes and tumor supressor genes. Its goal is to provide a standard set of facts (e.g. protein size, biochemical activity, chromosomal location, ...) about all known tumor genes. At present, the database contains over 2600 facts on over 300 genes.",
"example": "P53",
"homepage": "http://www.tumor-gene.org/tgdf.html",
"keywords": [
"gene"
],
"name": "Tumor Gene Family Databases (TGDBs)",
"pattern": "^[A-Z,0-9]+$",
"prefix": "tgdb",
"uri_format": "http://www.tumor-gene.org/cgi-bin/TGDB/tgdb_fetch_gene.cgi?gene=$1"
},
"tgma": {
"bioportal": "1030",
"description": "A structured controlled vocabulary of the anatomy of mosquitoes.",
"example": "TGMA_0001525",
"homepage": "http://www.anobase.org",
"keywords": [
"obo",
"anatomy",
"mosquito"
],
"name": "Mosquito gross anatomy",
"pattern": "^TGMA_\\d{7}$",
"prefix": "tgma"
},
"thealternativa": {
"bioportal": "3037",
"description": "A spanish thesaurus",
"example": "Areas",
"keywords": [
"owl",
"thesaurus",
"spanish"
],
"name": "thesaurus alternativa",
"pattern": "^\\w$",
"prefix": "thealternativa",
"rdf_uri_format": "http://www.owl-ontologies.com/thesaurus.owl#$1"
},
"thesaurus": {
"bioportal": "3034",
"description": "A spanish thesaurus",
"example": "Areas",
"keywords": [
"owl",
"thesaurus",
"spanish"
],
"name": "thesaurus",
"pattern": "^\\w$",
"prefix": "thesaurus",
"rdf_uri_format": "http://www.owl-ontologies.com/thesaurus.owl#$1"
},
"tied": {
"description": "The IEDB contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species.",
"example": "21",
"homepage": "http://www.iedb.org",
"keywords": [
"protein",
"small molecule"
],
"name": "The Immune Epitope Database (IEDB)",
"pattern": "^\\d+$",
"prefix": "tied",
"uri_format": "http://www.iedb.org/epId/$1"
},
"tigrfams": {
"description": "TIGRFAMs are protein families based on Hidden Markov Models or HMMs. This collection is used to see the curated seed alignmet for each TIGRFam, the full alignment of all family members and the cutoff scores for inclusion in each of the TIGRFAMs.",
"example": "TIGR00254",
"homepage": "http://www.jcvi.org/cms/research/projects/tigrfams/",
"keywords": [
"protein"
],
"name": "TIGRFAMs HMM collection at the J. Craig Venter Institute",
"pattern": "^TIGR\\d+$",
"prefix": "tigrfams",
"synonyms": [
"jcvi.tigrfams"
],
"uri_format": "http://cmr.jcvi.org/cgi-bin/CMR/HmmReport.cgi?hmm_acc=$1"
},
"tm-const": {
"bioportal": "1570",
"description": "The value set for the Constitution property of the International Classification of Traditional Medicine (ICTM).",
"example": "TM817079",
"homepage": "https://sites.google.com/site/whoictm/home",
"keywords": [
"owl",
"traditional medicine"
],
"name": "Traditional Medicine Constitution Value Set",
"pattern": "^TM\\d$",
"prefix": "tm-const",
"rdf_uri_format": "http://who.int/ictm/constitution#$1"
},
"tm-other-factors": {
"bioportal": "1571",
"description": "The value set for the Other Factors property of the International Classification of Traditional Medicine (ICTM).",
"example": "TM2302168",
"homepage": "https://sites.google.com/site/whoictm/home",
"keywords": [
"owl",
"traditional medicine"
],
"name": "Traditional Medicine Other Factors Value Set",
"pattern": "^TM\\d$",
"prefix": "tm-other-factors",
"rdf_uri_format": "http://who.int/ictm/otherFactors#$1"
},
"tm-signs-and-sympts": {
"bioportal": "1572",
"description": "The value set for the Signs and Symptoms property of the International Classification of Traditional Medicine (ICTM).",
"example": "TM529400",
"homepage": "https://sites.google.com/site/whoictm/home",
"keywords": [
"owl",
"traditional medicine"
],
"name": "Traditional Medicine Signs and Symptoms Value Set",
"pattern": "^TM\\d$",
"prefix": "tm-signs-and-sympts",
"rdf_uri_format": "http://who.int/ictm/signsAndSymptoms#$1"
},
"tomatest_db": {
"description": "This database has been designed to manage and to explore the huge amount of EST reads from 14 Solanaceae and 2 Rubiaceae species.",
"example": "SOLPN003470",
"homepage": "http://biosrv.cab.unina.it/tomatestdb",
"keywords": [
"DNA",
"RNA"
],
"name": "TomatEST DB",
"pattern": "^[A-Z]+\\d+$",
"prefix": "tomatest_db",
"uri_format": "http://biosrv.cab.unina.it/solestdb/clusterview.php?clid=$1"
},
"topdb": {
"description": "The Topology Data Bank of Transmembrane Proteins (TOPDB) is currently the most complete and comprehensive collection of transmembrane protein datasets containing experimentally derived topology information.",
"example": "AB00979",
"homepage": "http://topdb.enzim.hu",
"keywords": [
"protein"
],
"name": "The Topology Databank",
"pattern": "^[A-Z]+\\d+$",
"prefix": "topdb",
"uri_format": "http://topdb.enzim.hu/?m=show&id=$1"
},
"tpdb": {
"description": "This database is an attempt to catalog in a convenient, searchable fashion all publicly available information about the identities of mammalian proteins that become covalently adducted by chemically-reactive metabolites of xenobiotic agents including drugs.",
"example": "86",
"homepage": "http://tpdb.medchem.ku.edu:8080/protein_database/index.jsp",
"keywords": [
"protein",
"small molecule"
],
"name": "Target Protein Database",
"pattern": "^\\d+$",
"prefix": "tpdb",
"uri_format": "http://tpdb.medchem.ku.edu:8080/protein_database/protein_details.jsp?prot_id=$1"
},
"tpmd": {
"description": "The aims of TPMD are to share useful genotyping information including data of genotyped microsatellite markers, genotyping resources and laboratory supports for promoting genotyping and gene cloning of prevalent diseases.",
"example": "AFM234WG3",
"homepage": "http://tpmd.nhri.org.tw",
"keywords": [
"gene"
],
"name": "Taiwan polymorphic microsatellite marker database",
"pattern": "^[A-Z,0-9]+$",
"prefix": "tpmd",
"uri_format": "http://tpmd2.nhri.org.tw/tpmd/php-bin/filter.php?search=$1"
},
"tptad": {
"description": "The TIGR Plant Transcript Assemblies (TA) database uses expressed sequences collected from the NCBI GenBank Nucleotide database for the construction of transcript assemblies. The sequences collected include expressed sequence tags (ESTs) and full-length and partial cDNAs, but exclude computationally predicted gene sequences",
"example": "TA67744_4530",
"homepage": "http://plantta.tigr.org",
"keywords": [
"DNA"
],
"name": "TIGR Plant Transcript Assembly database",
"pattern": "^TA\\d+_\\d+$",
"prefix": "tptad",
"uri_format": "http://plantta.jcvi.org/cgi-bin/plantta_report.pl?ta=$1"
},
"transportdb": {
"description": "TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available.",
"example": "MMP0523",
"homepage": "http://www.membranetransport.org",
"keywords": [
"protein"
],
"name": "TransportDB",
"pattern": "^MMP\\d+$",
"prefix": "transportdb",
"uri_format": "http://www.membranetransport.org/protein.php?pOID=mmar1&pSynonym=$1"
},
"transterm": {
"description": "Transterm is a database providing access to mRNA sequences and associated regulatory elements.",
"example": "T0102",
"homepage": "http://mRNA.otago.ac.nz/Transterm.html",
"keywords": [
"RNA",
"regulation"
],
"name": "Transterm",
"pattern": "^T\\d+$",
"prefix": "transterm",
"uri_format": "http://mrna.otago.ac.nz/cgi-bin/tt_data_browse/RNAMotif?PatID=$1"
},
"tred": {
"description": "Transcriptional Regulatory Element Database (TRED) has been built in response to increasing needs of an integrated repository for both cis- and trans- regulatory elements in mammals, and the lack of such resources at present.",
"example": "21552",
"homepage": "http://rulai.cshl.edu/TRED",
"keywords": [
"DNA",
"regulation"
],
"name": "Transcriptional Regulatory Element Database",
"pattern": "^\\d+$",
"prefix": "tred",
"uri_format": "http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid=$1"
},
"treebase": {
"description": "TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa.",
"example": "1245",
"homepage": "http://www.treebase.org/",
"keywords": [
"classification"
],
"name": "TreeBase",
"pattern": "^\\d+$",
"prefix": "treebase",
"uri_format": "http://www.treebase.org/treebase-web/search/study/summary.html?id=$1"
},
"treefam": {
"description": "TreeFam (Tree families database) is a database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families.",
"example": "TF101142",
"homepage": "http://www.treefam.org",
"keywords": [
"gene",
"classification"
],
"name": "TreeFam",
"pattern": "^TF\\d+$",
"prefix": "treefam",
"uri_format": "http://www.treefam.org/cgi-bin/TFinfo.pl?ac=$1"
},
"trnadbce": {
"description": "The tRNA Gene DataBase Curated by Experts \"tRNADB-CE\" was constructed by analyzing 927 complete and 1301 draft genomes of Bacteria and Archaea, 171 complete virus genomes, 121 complete chloroplast genomes, 12 complete eukaryote (Plant and Fungi) genomes and approximately 230 million DNA sequence entries that originated from environmental metagenomic clones.",
"example": "265912",
"homepage": "http://trna.nagahama-i-bio.ac.jp",
"keywords": [
"RNA",
"gene",
"genome",
"DNA"
],
"name": "tRNA Gene Database",
"pattern": "^\\d+$",
"prefix": "trnadbce",
"uri_format": "http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID=$1"
},
"tropgene": {
"description": "TropGENE DB is a database that manages genetic and genomic information about tropical crops studied by Cirad. The database is organised into crop specific modules.",
"example": "ITC0084",
"homepage": "http://tropgenedb.cirad.fr/",
"keywords": [
"gene",
"genome"
],
"name": "TropGENE DB",
"pattern": "^[A-Z]+\\d+$",
"prefix": "tropgene"
},
"trrd": {
"description": "TRRD is a unique information resource, accumulating information on structural and functional organization of transcription regulatory regions of eukaryotic genes. Only experimentally confirmed information is included into TRRD.",
"example": "F186.1",
"homepage": "http://www.bionet.nsc.ru/trrd/",
"keywords": [
"regulation",
"structure",
"gene"
],
"name": "Transcription Regulatory Regions Database",
"pattern": "^[A-Z,0-9]+$",
"prefix": "trrd"
},
"tssrmd": {
"description": "The Small Subunit rRNA Modification Database provides a listing of reported post-transcriptionally modified nucleosides and sequence sites in small subunit rRNAs from bacteria, archaea and eukarya.",
"example": "2066",
"homepage": "http://library.med.utah.edu/SSUmods/",
"keywords": [
"RNA",
"structure"
],
"name": "The Small Subunit rRNA Modification Database",
"pattern": "^\\d+$",
"prefix": "tssrmd"
},
"tto": {
"bioportal": "1081",
"description": "The Teleost taxonomy ontology is being used to facilitate annotation of phenotypes, particularly for taxa that are not covered by NCBI because no submissions of molecular data have been made.",
"example": "TTO_2",
"homepage": "https://www.nescent.org/phenoscape/Main_Page",
"keywords": [
"obo",
"phenotype",
"fish"
],
"name": "Teleost taxonomy Ontology",
"pattern": "^TTO_\\d$",
"prefix": "tto",
"synonyms": [
"teleost_taxonomy"
]
},
"tuberculist": {
"description": "The TubercuList knowledge base integrates genome details, protein information, drug and transcriptome data, mutant and operon annotation, bibliography; structural views and comparative genomics, in a structured manner required for the rational development of new diagnostic, therapeutic and prophylactic measures against tuberculosis.",
"example": "Rv0115",
"homepage": "http://tuberculist.epfl.ch",
"keywords": [
"genome",
"protein",
"DNA"
],
"name": "Mycobacterium tuberculosis strain H37Rv genome database",
"pattern": "^Rv[0-9,a-z]+$",
"prefix": "tuberculist",
"uri_format": "http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1"
},
"u12db": {
"description": "the U12 Intron Database (U12DB), aims to catalog the U12 introns of completely sequenced eukaryotic genomes and associate orthologous introns with each other.",
"example": "24173",
"homepage": "http://genome.imim.es/cgi-bin/u12db/u12db.cgi",
"keywords": [
"genome",
"DNA"
],
"name": "U12 Intron Database",
"pattern": "^\\d+$",
"prefix": "u12db"
},
"ugmicrosatdb": {
"description": "UgMicroSatdb (Unigene MicroSatellite database), a web based relational database of microsatellites present in unigene sequences covering 80 genomes. UgMicroSatdb allows microsatellite search using multiple parameters like microsatellite type simple (perfect) and compound (perfect and imperfect), repeat unit length (mono- to hexa-nucleotide), repeat number, microsatellite length and repeat sequence class.",
"example": "UMD-10-1-1-4",
"homepage": "http://ipu.ac.in/usbt/UgMicroSatdb.htm",
"keywords": [
"DNA"
],
"name": "Unigene MicroSatellite Database",
"pattern": "^UGM-\\d+$",
"prefix": "ugmicrosatdb",
"uri_format": "http://www.veenuash.info/veenu/chromo.asp?ns=$1"
},
"uni-ece": {
"bioportal": "3048",
"description": "ECE college terminology",
"example": "Graduate",
"keywords": [
"owl",
"organization"
],
"name": "uni-ece",
"pattern": "^\\w$",
"prefix": "uni-ece",
"rdf_uri_format": "http://www.semanticweb.org/ontologies/2012/2/Ontology1331685116337.owl#$1"
},
"unigene": {
"description": "Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.",
"example": "4900",
"homepage": "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene",
"keywords": [
"DNA",
"gene",
"gene expression",
"protein"
],
"name": "UniGene gene-oriented nucleotide sequence clusters",
"pattern": "^\\d+$",
"prefix": "unigene",
"uri_format": "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1"
},
"uniparc": {
"description": "The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases.",
"example": "UPI000000000A",
"homepage": "http://www.ebi.ac.uk/uniparc/",
"keywords": [
"protein",
"structure"
],
"name": "UniProt Archive",
"pattern": "^UPI[A-F0-9]{10}$",
"prefix": "uniparc",
"pubmed_ids": [
"14681372"
],
"uri_format": "http://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$1"
},
"unipathway": {
"description": "UniPathway is a manually curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase. It provides a structured controlled vocabulary to describe the role of a protein in a metabolic pathway.",
"example": "UPA00206",
"homepage": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway",
"keywords": [
"pathway"
],
"name": "UniPathway, a metabolic door to UniProtKB/Swiss-Prot",
"pattern": "^UPA\\d{5}$",
"prefix": "unipathway",
"uri_format": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1"
},
"uniprot": {
"description": "UniProtKB consists of the manually annotated and reviewed Swiss-Prot, the automatically annotated TrEMBL, and the PIR protein databases.",
"example": "P62158",
"homepage": "http://www.uniprot.org/",
"keywords": [
"protein"
],
"name": "UniProt Knowledgebase",
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$",
"prefix": "uniprot",
"pubmed_ids": [
"16381842"
],
"rdf_uri_format": "http://purl.uniprot.org/uniprot/$1",
"synonyms": [
"uniprotkb",
"uniprotkb/trembl",
"swiss-prot",
"sp",
"UNIPROTKB/SWISSPROT"
],
"uri_format": "http://www.uniprot.org/uniprot/$1"
},
"uniprot.kw": {
"description": "UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries. There are 10 categories of keywords.",
"example": "KW-9998",
"homepage": "http://www.uniprot.org/keywords/",
"keywords": [
"classification"
],
"name": "UniProt Knowledgebase keywords",
"pattern": "^KW-\\d+$",
"prefix": "uniprot.kw",
"synonyms": [
"spkw",
"uniprotkb-kw"
],
"uri_format": "http://www.uniprot.org/keywords/$1"
},
"uniprot.taxonomy": {
"description": "The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.",
"example": "9606",
"homepage": "http://www.uniprot.org/taxonomy/",
"keywords": [
"DNA",
"protein",
"structure",
"classification"
],
"license": "CC BY-ND 3.0",
"name": "Uniprot Taxonomy",
"pattern": "^\\d+$",
"prefix": "uniprot.taxonomy",
"synonyms": [
"newt"
],
"uri_format": "http://www.uniprot.org/taxonomy/$1"
},
"unisave": {
"description": "The UniProtKB Sequence/Annotation Version Archive (UniSave) is a repository of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions.",
"example": "Q00001",
"homepage": "http://www.ebi.ac.uk/uniprot/unisave/",
"keywords": [
"protein"
],
"name": "UniSave",
"pattern": "^[A-Z]\\d+$",
"prefix": "unisave"
},
"unists": {
"description": "UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences.",
"example": "456789",
"homepage": "http://www.ncbi.nlm.nih.gov/unists",
"keywords": [
"gene",
"protein"
],
"name": "NCBI UniSTS",
"pattern": "^\\d+$",
"prefix": "unists",
"uri_format": "http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1"
},
"unite": {
"description": "The UNITE is primarily a fungal rDNA ITS sequence database, although we also welcome additional genes and genetic markers. UNITE focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria.",
"example": "UDB000691",
"homepage": "http://unite.ut.ee/index.php",
"keywords": [
"DNA"
],
"name": "Molecular database for the identification of fungi",
"pattern": "^UDB\\d{6}$",
"prefix": "unite",
"pubmed_ids": [
"20409185"
],
"uri_format": "http://unite.ut.ee/bl_forw.php?nimi=$1"
},
"uo": {
"alt_uri_formats": [
"http://purl.org/obo/owl/UO#$1",
"http://mimi.case.edu/ontologies/2009/1/UnitsOntology#$1"
],
"bioportal": "1112",
"description": "Ontology of standardized units in conjunction with PATO",
"example": "UO:0000080",
"homepage": "http://code.google.com/p/unit-ontology/",
"keywords": [
"obo",
"ontology"
],
"license": "CC-BY-3.0",
"name": "Unit Ontology",
"pattern": "^UO:\\d{7}?$",
"prefix": "uo",
"synonyms": [
"obo.unit",
"unit"
]
},
"utrome": {
"description": "The UTRome.org database is intended as a comprehensive resource for 3'UTR biology in C. elegans. The database provides detailed information on 3'UTR structures for all protein-coding mRNAs, and includes annotations extracted from other databases as well as new annotations generated as part of the NYU 3'UTRome project.",
"example": "2815",
"homepage": "http://www.utrome.org",
"keywords": [
"RNA"
],
"name": "UTRome",
"pattern": "^\\d+$",
"prefix": "utrome",
"uri_format": "http://128.122.61.5/cgi-bin/UTRome/utrome.cgi?action=gene&geneid=$1"
},
"vao": {
"bioportal": "1555",
"description": "Vertebrate anatomy ontology. Currently covers the skeletal system",
"example": "VSAO_0000183",
"homepage": "https://www.nescent.org/phenoscape/Main_Page",
"keywords": [
"obo",
"anatomy",
"vertebrate"
],
"name": "Vertebrate Anatomy Ontology",
"pattern": "^VSA_\\d{7}$",
"prefix": "vao",
"synonyms": [
"vsao"
]
},
"vbase2": {
"description": "VBASE2 is an integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank.",
"example": "humIGHV025",
"homepage": "http://www.vbase2.org",
"keywords": [
"gene"
],
"name": "VBASE2",
"pattern": "^\\w+$",
"prefix": "vbase2",
"pubmed_ids": [
"15608286"
],
"uri_format": "http://www.vbase2.org/vgene.php?id=$1"
},
"vbrc": {
"description": "The VBRC is one of eight NIH/NIAID-funded Bioinformatics Resource Centers nationwide providing a comprehensive web-based battery of informational and analytical tools and resources.",
"example": "VP0033331",
"homepage": "http://vbrc.org",
"name": "Viral Bioinformatics Resource Center",
"pattern": "^VP\\d+$",
"prefix": "vbrc"
},
"veb": {
"description": "The VISTA Enhancer Browser is a central resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice.",
"example": "1",
"homepage": "http://enhancer.lbl.gov/",
"keywords": [
"genome"
],
"name": "VISTA Enhancer Browser",
"pattern": "^\\d+$",
"prefix": "veb",
"synonyms": [
"veb:"
]
},
"vectorbase": {
"description": "VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for the research community. Currently, VectorBase contains genome information for two organisms: Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever.",
"example": "ISCW007415",
"homepage": "http://www.vectorbase.org/index.php",
"keywords": [
"gene",
"genome",
"protein"
],
"name": "Invertebrate Vectors of Human Pathogens",
"pattern": "^\\D{4}\\d{6}(\\-\\D{2})?$",
"prefix": "vectorbase",
"pubmed_ids": [
"19028744"
],
"uri_format": "http://www.vectorbase.org/[?species_name]/Gene/Summary?db=core;g=$1"
},
"vega": {
"description": "The Vertebrate Genome Annotation (VEGA) database is a central repository for high quality manual annotation of vertebrate finished genome sequence.",
"example": "OTTHUMG00000017411",
"homepage": "http://vega.sanger.ac.uk/",
"keywords": [
"genome"
],
"name": "The Vertebrate Genome Annotation Database",
"pattern": "^[A-Z]+\\d+$",
"prefix": "vega",
"uri_format": "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1"
},
"vhog": {
"bioportal": "1574",
"description": "vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 \"historical homology\". Each mapping has been manually reviewed, and we provide confidence codes and references when available.",
"example": "VHOG_0000555",
"homepage": "http://bgee.unil.ch",
"keywords": [
"obo",
"anatomy",
"development"
],
"name": "vertebrate Homologous Organ Groups",
"pattern": "^VHOG_\\d{7}$",
"prefix": "vhog"
},
"viperdb": {
"description": "VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration.",
"example": "2c6s",
"homepage": "http://viperdb.scripps.edu/",
"keywords": [
"structure",
"small molecule"
],
"name": "VIPERdb",
"pattern": "^[A-Z,0-9]+$",
"prefix": "viperdb",
"uri_format": "http://viperdb.scripps.edu/info_page.php?VDB=$1"
},
"virgen": {
"description": "VirGen a comprehensive viral genome resource, which organizes the \u2018sequence space\u2019 of viral genomes in a structured fashion. It has been developed with an objective to serve as an annotated and curated database for complete viral genome sequences.",
"example": "AY321118",
"homepage": "http://bioinfo.ernet.in/virgen/virgen.html",
"keywords": [
"genome"
],
"name": "VirGen",
"pattern": "^A[A-Z]\\d+$",
"prefix": "virgen"
},
"virmirdb": {
"description": "A database containing predicted viral miRNA candidate hairpins.",
"example": "11002",
"homepage": "http://alk.ibms.sinica.edu.tw",
"keywords": [
"RNA",
"structure"
],
"name": "Vir-Mir db",
"pattern": "^\\d+$",
"prefix": "virmirdb",
"uri_format": "http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id=$1"
},
"viroligo": {
"description": "The VirOligo database (1) is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place.",
"example": "BM0456",
"homepage": "http://viroligo.okstate.edu",
"keywords": [
"small molecule"
],
"name": "VirOligo",
"pattern": "^[A-Z]+\\d+$",
"prefix": "viroligo",
"uri_format": "http://viroligo.okstate.edu/main.php?vid=$1"
},
"virushostdb": {
"description": "Virus-Host DB organizes data about the relationships between viruses and their hosts, represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts. Virus-Host DB covers viruses with complete genomes stored in 1) NCBI/RefSeq and 2) GenBank whose accession numbers are listed in EBI Genomes. The host information is collected from RefSeq, GenBank (in free text format), UniProt, ViralZone, and manually curated with additional information obtained by literature surveys.",
"example": "438782",
"homepage": "https://www.genome.jp/virushostdb/",
"keywords": [
"virus"
],
"license": "CC BY-NC-SA 4.0",
"name": "Virus-HostDB",
"pattern": "^\\d+$",
"prefix": "virushostdb",
"pubmed_ids": [
"26938550"
],
"synonyms": [
"virus-hostdb"
],
"uri_format": "https://www.genome.jp/virushostdb/$1"
},
"vita": {
"description": "ViTa is a database which collects virus data from miRBase and ICTV, VirGne, VBRC.., etc, including known miRNAs on virus and supporting predicted host miRNA targets by miRanda and TargetScan. ViTa also rovide effective annotations, including human miRNA expression, virus infected tissues, annotation of virus and comparisons.",
"example": "AB016785",
"homepage": "http://vita.mbc.nctu.edu.tw/",
"keywords": [
"RNA",
"structure",
"gene expression"
],
"name": "ViTa: virus' miRNA target",
"pattern": "^[A-Z]+\\d+$",
"prefix": "vita",
"uri_format": "http://vita.mbc.nctu.edu.tw/search.php?acc=$1"
},
"vkcdb": {
"description": "Voltage-gated potassium channel database (VKCDB) is designed to serve as a resource for research on voltage-gated potassium channels. Protein sequences, references, functional data and many other relevant data are included in this database.",
"example": "VKC145",
"homepage": "http://vkcdb.biology.ualberta.ca/",
"keywords": [
"pathway",
"protein"
],
"name": "Voltage-gated K | Channel Database",
"pattern": "^VKC\\d+$",
"prefix": "vkcdb",
"uri_format": "http://vkcdb.biology.ualberta.ca/cgi-bin/vkcdb/vkcdb-scp/entry.cgi?vkcid=$1"
},
"vmd": {
"description": "VBI Microbial Database at VBI hosts data from a range of plant pathogenic oomycetes, fungi and bacteria primarily those under study at VBI.",
"example": "464033",
"homepage": "http://vmd.vbi.vt.edu/",
"keywords": [
"classification"
],
"name": "Virginia Bioinformatics Institute Microbial Database",
"pattern": "^\\d+$",
"prefix": "vmd",
"synonyms": [
"pamgovmd"
],
"uri_format": "http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi?ID=$1"
},
"vo": {
"bioportal": "1172",
"description": "A biomedical ontology in the vaccine domain",
"example": "VO_0000811",
"homepage": "http://www.violinet.org/vaccineontology",
"keywords": [
"obo",
"ontology",
"small molecule",
"vaccine"
],
"name": "Vaccine ontology",
"pattern": "^VO_\\d{7}$",
"prefix": "vo"
},
"vso": {
"bioportal": "3124",
"description": "The Vital Sign Ontology (VSO) covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.",
"example": "VSO_0000015",
"homepage": "http://code.google.com/p/vital-sign-ontology/",
"keywords": [
"owl",
"health"
],
"name": "Vital Sign Ontology",
"pattern": "^VSO_\\d{7}$",
"prefix": "vso"
},
"vt": {
"bioportal": "1659",
"description": "The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.",
"example": "VT_0015074",
"keywords": [
"obo",
"vertebrate",
"trait"
],
"name": "Vertebrate Trait Ontology",
"pattern": "^VT_\\d{7}$",
"prefix": "vt"
},
"vz": {
"description": "ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures",
"example": "886",
"homepage": "http://viralzone.expasy.org/",
"keywords": [
"virus"
],
"name": "ViralZone",
"pattern": "^\\d+$",
"prefix": "vz",
"uri_format": "http://viralzone.expasy.org/all_by_protein/$1.html"
},
"wbbt": {
"bioportal": "1048",
"description": "A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.",
"example": "WBbt_0005733",
"homepage": "http://www.wormbase.org/",
"keywords": [
"obo",
"anatomy",
"worm"
],
"name": "C. elegans gross anatomy",
"pattern": "^WBbt_\\d{7}$",
"prefix": "wbbt",
"synonyms": [
"worm_anatomy"
],
"uri_format": "http://wormbase.org/db/ontology/anatomy?name=$1"
},
"wbls": {
"bioportal": "1049",
"description": "A structured controlled vocabulary of the development of Caenorhabditis elegans.",
"example": "WBls_0000003",
"homepage": "http://www.wormbase.org/",
"keywords": [
"obo",
"development",
"worm"
],
"name": "C. elegans development",
"pattern": "^WBIs_\\d{7}$",
"prefix": "wbls",
"synonyms": [
"worm_development"
]
},
"wbphenotype": {
"bioportal": "1067",
"description": "A structured controlled vocabulary of Caenorhabditis elegans phenotypes",
"example": "WBPhenotype_0000517",
"homepage": "http://www.wormbase.org/",
"keywords": [
"obo",
"phenotype",
"worm"
],
"name": "C. elegans phenotype",
"pattern": "^WBPhenotype_\\d{7}$",
"prefix": "wbphenotype",
"synonyms": [
"worm_phenotype"
]
},
"wikipathways": {
"description": "WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style.",
"example": "WP100",
"homepage": "http://wikipathways.org/",
"keywords": [
"pathway"
],
"license": "CC0-1.0",
"name": "WikiPathways",
"pattern": "^P\\d{1,5}(\\_r\\d+)?$",
"prefix": "wikipathways",
"pubmed_ids": [
"18651794"
],
"uri_format": "http://www.wikipathways.org/index.php/Pathway:$1"
},
"wikipedia": {
"description": "Encyclopedia of Everything.",
"example": "SM_UB-81",
"homepage": "http://en.wikipedia.org/",
"name": "Wikipedia",
"pattern": "^[A-Za-z0-9_]+$",
"prefix": "wikipedia",
"synonyms": [
"wikipedia.en"
],
"uri_format": "http://en.wikipedia.org/wiki/$1"
},
"worfdb": {
"description": "In total, approximately 12,500 C. elegans ORFs are now available as Gateway Entry clones for various reverse proteomics (ORFeome v3.1). This work illustrates why the cloning of a complete C. elegans ORFeome, and likely the ORFeomes of other multicellular organisms, needs to be an iterative process that requires multiple rounds of experimental validation together with gradually improving gene predictions.",
"example": "R10E9.1",
"homepage": "http://worfdb.dfci.harvard.edu/",
"keywords": [
"DNA"
],
"name": "The C.elegans ORFeome cloning project",
"pattern": "^[A-Z,0-9]+$",
"prefix": "worfdb",
"uri_format": "http://worfdb.dfci.harvard.edu/searchallwormorfs.pl?sid=$1"
},
"world2dpage": {
"description": "A public repository, standards compliant, for proteomics image data published in the literature. This repository currently contains data from 16 published articles, putting together 22 reference maps for 15 species, totalizing nearly 4'400 identified spots.",
"example": "0020",
"homepage": "http://world-2dpage.expasy.org/repository/",
"keywords": [
"protein",
"structure",
"2d-page"
],
"name": "The World-2DPAGE database",
"pattern": "^\\d+$",
"prefix": "world2dpage",
"uri_format": "http://world-2dpage.expasy.org/repository/database=$1"
},
"wormbase": {
"description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results.",
"example": "WBGene00000001",
"homepage": "http://www.wormbase.org/",
"keywords": [
"genome",
"gene",
"anatomy"
],
"license": "http://wiki.wormbase.org/index.php/WormBaseWiki:Copyrights",
"name": "WormBase",
"pattern": "^WBGene\\d{8}$",
"prefix": "wormbase",
"pubmed_ids": [
"11125056"
],
"synonyms": [
"wb"
]
},
"wormpep": {
"description": "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project.",
"example": "CE28239",
"homepage": "http://www.wormbase.org/db/seq/protein",
"keywords": [
"protein",
"structure"
],
"name": "Caenorhabditis elegans genome sequencing project protein database",
"pattern": "^CE\\d{5}$",
"prefix": "wormpep",
"uri_format": "http://www.wormbase.org/db/seq/protein?name=$1"
},
"xco": {
"bioportal": "1585",
"description": "The Experimental Conditions Ontology is designed to represent the conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.",
"example": "XCO_0000001",
"homepage": "http://sourceforge.net/projects/phenoonto/",
"keywords": [
"obo",
"measurement"
],
"name": "Experimental Conditions Ontology",
"pattern": "^XCO_\\d{7}$",
"prefix": "xco"
},
"xenbase": {
"description": "Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions.",
"example": "6453898",
"homepage": "http://www.xenbase.org",
"keywords": [
"expression",
"genome"
],
"name": "Xenopus laevis and tropicalis biology and genomics resource",
"pattern": "^\\d+$",
"prefix": "xenbase",
"pubmed_ids": [
"19884130"
],
"uri_format": "http://www.xenbase.org/gene/showgene.do?method=display&geneId=$1"
},
"ydpm": {
"description": "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The database is hyperlinked with other public databases. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell",
"example": "YBL031W",
"homepage": "http://www-deletion.stanford.edu/YDPM/YDPM_index.html",
"keywords": [
"protein"
],
"name": "Yeast Deletion Project and Proteomics of Mitochondria Database",
"pattern": "^[A-Z,0-9]+$",
"prefix": "ydpm"
},
"yeastfunc": {
"description": "A website for the browsing of quantitative S. cerevisiae gene function predictions, gene function linkage predictions, and the evidence behind the predictions",
"example": "4306",
"homepage": "http://func.med.harvard.edu/yeast/",
"keywords": [
"gene",
"gene expression"
],
"name": "Yeast Function",
"pattern": "^\\d+$",
"prefix": "yeastfunc",
"uri_format": "http://func.med.harvard.edu/yeast/genes/list_functional_scores/$1"
},
"yeastract": {
"description": "YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references.",
"example": "YBR125c",
"homepage": "http://www.yeastract.com",
"keywords": [
"regulation",
"DNA",
"small molecule",
"gene"
],
"name": "Yeast Searching for Transcriptional Regulators and Consensus Tracking",
"pattern": "^[A-Z,0-9]+$",
"prefix": "yeastract",
"uri_format": "http://www.yeastract.com/view.php?existing=locus&orfname=$1"
},
"ygob": {
"description": "YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes.",
"example": "ADH1",
"homepage": "http://wolfe.gen.tcd.ie/ygob",
"keywords": [
"gene",
"genome"
],
"name": "Yeast Genome Order Browser",
"pattern": "^[A-Z,0-9]+$",
"prefix": "ygob",
"uri_format": "http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene=$1"
},
"yrc": {
"description": "The National Center for Research Resources' Yeast Resource Center is located at the University of Washington in Seattle, Washington. The mission of the center is to facilitate the identification and characterization of protein complexes in the yeast Saccharomyces cerevisiae.",
"example": "846763",
"homepage": "http://www.yeastrc.org/pdr/",
"keywords": [
"protein"
],
"name": "Yeast Resource Center Public Data Repository",
"pattern": "^\\d+$",
"prefix": "yrc",
"uri_format": "http://www.yeastrc.org/pdr/viewProtein.do?id=$1"
},
"zea": {
"bioportal": "1050",
"description": "Maize gross anatomy",
"example": "ZEA_0015177",
"homepage": "http://www.maizemap.org/",
"keywords": [
"obo",
"anatomy",
"maize"
],
"name": "Maize gross anatomy",
"pattern": "^ZEA_\\d{7}$",
"prefix": "zea"
},
"zfa": {
"bioportal": "1051",
"description": "A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio).",
"example": "ZFS_0000011",
"homepage": "http://zfin.org/zf_info/anatomy/dict/sum.html",
"keywords": [
"obo",
"anatomy",
"zebrafish"
],
"name": "Zebrafish anatomy and development Ontology",
"pattern": "^ZFS_\\d{7}$",
"prefix": "zfa"
},
"zfin": {
"description": "ZFIN serves as the zebrafish model organism database.",
"example": "ZDB-GENE-041118-11",
"homepage": "http://zfin.org/",
"keywords": [
"zebrafish",
"gene",
"genome"
],
"name": "Zebrafish Information Network genome database",
"pattern": "^ZDB\\-GENE\\-\\d+\\-\\d+$",
"prefix": "zfin",
"pubmed_ids": [
"17991680"
],
"uri_format": "http://zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID=$1"
},
"zifdb": {
"description": "ZiFDB organizes information on both individual zinc finger modules and engineered ZFAs; There are currently four sets of zinc finger modules available.",
"example": "1",
"homepage": "http://bindr.gdcb.iastate.edu:8080/ZiFDB/",
"keywords": [
"protein"
],
"name": "Zinc Finger Consortium Database",
"pattern": "^\\d+$",
"prefix": "zifdb",
"synonyms": [
"zif"
],
"uri_format": "http://bindr.gdcb.iastate.edu:8080/ZiFDB/controller/checkArticle?artId=$1"
}
} ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9699667
bioregistry-0.11.12/src/bioregistry/external/re3data/ 0000755 0001751 0000177 00000000000 14655546227 022141 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/re3data/__init__.py 0000644 0001751 0000177 00000014317 14655542206 024251 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Re3data is a registry of research data repositories.
Example API endpoint: https://www.re3data.org/api/v1/repository/r3d100010772
"""
import json
import logging
from pathlib import Path
from typing import Any, Mapping, Optional, Tuple
from xml.etree import ElementTree
import requests
from tqdm.contrib.concurrent import thread_map
from bioregistry.external.alignment_utils import Aligner
from bioregistry.utils import removeprefix
__all__ = [
"get_re3data",
"Re3dataAligner",
]
logger = logging.getLogger(__name__)
DIRECTORY = Path(__file__).parent.resolve()
PROCESSED_PATH = DIRECTORY / "processed.json"
BASE_URL = "https://www.re3data.org"
SCHEMA = "{http://www.re3data.org/schema/2-2}"
def get_re3data(force_download: bool = False):
"""Get the re3data registry.
This takes about 9 minutes since it has to look up each of the ~3K
records with their own API call.
:param force_download: If true, re-downloads the data
:returns: The re3data pre-processed data
"""
if PROCESSED_PATH.exists() and not force_download:
with PROCESSED_PATH.open() as file:
return json.load(file)
res = requests.get(f"{BASE_URL}/api/v1/repositories")
tree = ElementTree.fromstring(res.text)
identifier_to_doi = {}
for repository in tree.findall("repository"):
identifier_element = repository.find("id")
if identifier_element is None or identifier_element.text is None:
continue
doi_element = repository.find("doi")
doi = (
removeprefix(doi_element.text, "https://doi.org/")
if doi_element and doi_element.text
else None
)
identifier_to_doi[identifier_element.text.strip()] = doi
records = dict(
thread_map(
_get_record,
identifier_to_doi,
unit_scale=True,
unit="record",
desc="Getting re3data",
disable=True,
)
)
# backfill DOIs
for identifier, record in records.items():
doi = identifier_to_doi.get(identifier)
if doi:
record["doi"] = doi
with PROCESSED_PATH.open("w") as file:
json.dump(records, file, indent=2, sort_keys=True, ensure_ascii=False)
return records
def _get_record(identifier: str) -> Tuple[str, Mapping[str, Any]]:
res = requests.get(f"{BASE_URL}/api/v1/repository/{identifier}")
tree = ElementTree.fromstring(res.text)[0]
return identifier, _process_record(identifier, tree)
def _process_record(identifier: str, tree_inner):
xrefs = (
_clean_xref(element.text.strip())
for element in tree_inner.findall(f"{SCHEMA}repositoryIdentifier")
)
data = {
"prefix": identifier,
"name": tree_inner.find(f"{SCHEMA}repositoryName").text,
"description": tree_inner.find(f"{SCHEMA}description").text,
"homepage": tree_inner.find(f"{SCHEMA}repositoryURL").text,
"synonyms": [
element.text.strip() for element in tree_inner.findall(f"{SCHEMA}additionalName")
],
"xrefs": dict(tup for tup in xrefs if tup),
}
license_element = tree_inner.find(f"{SCHEMA}databaseLicense/{SCHEMA}databaseLicenseName")
if license_element:
data["license"] = license_element.text
return {k: v.strip() if isinstance(v, str) else v for k, v in data.items() if v}
def _clean_xref(xref: str) -> Optional[Tuple[str, str]]:
if (
xref.startswith("FAIRsharing_DOI:10.25504/")
or xref.startswith("FAIRsharing_doi:10.25504/")
or xref.startswith("FAIRsharing_dOI:10.25504/")
or xref.startswith("FAIRSharing_doi:10.25504/")
or xref.startswith("FAIRsharing_doi;10.25504/")
or xref.startswith("FAIRsharing_doi: 10.25504/")
or xref.startswith("fairsharing_DOI:10.25504/")
or xref.startswith("fairsharing_doi:10.25504/")
or xref.startswith("FAIRsharin_doi:10.25504/")
or xref.startswith("FAIRsharing_doi.:10.25504/")
or xref.startswith("FAIRsharing_DOI: 10.25504/")
or xref.startswith("FAIRsharing_doi::10.25504/")
or xref.startswith("FAIRsharing_doi:10.24404/")
):
return "fairsharing", xref[len("FAIRsharing_DOI:10.25504/") :]
for start, key in [
("biodbcore-", "biodbcore"),
("MIR:", "miriam"),
("ROR:", "ror"),
("OMICS_", "omics"),
("Omics_", "omics"),
("omics_", "omics"),
("ISSN ", "issn"),
("ISSN: ", "issn"),
("nif-", "nif"),
("ISNI:", "isni"),
("doi.org/", "doi"),
("doi:", "doi"),
("DOI:", "doi"),
("DOI: ", "doi"),
("RID:nlx_", "nlx"),
("PSSB-", "pssb"),
("OpenDOAR:", "opendoar"),
("openDOAR:", "opendoar"),
("ROAR:", "roar"), # e.g., see http://roar.eprints.org/14208/
("hdl:", "hdl"),
("https://fairsharing.org/", "fairsharing.legacy"),
("http://fairsharing.org/", "fairsharing.legacy"),
("Wikidata:", "wikidata"),
("https://doi.org/10.5281/zenodo.", "zenodo"),
("https://doi.org/", "doi"),
]:
if xref.startswith(start):
return key, xref[len(start) :]
if xref.startswith("RRID:"):
inner_xref = xref[len("RRID:") :]
if "_" in inner_xref:
prefix, identifier = inner_xref.split("_", 1)
return prefix.lower(), identifier
elif "-" in inner_xref:
try:
prefix, identifier = inner_xref.split("-", 1)
except ValueError:
logger.debug("can't parse RRID: %s", xref)
else:
return prefix.lower(), identifier
else:
logger.debug("unknown RRID: %s", xref)
return None
if "doi:" in xref:
for part in xref.split(" "):
if part.startswith("doi"):
return "doi", part[len("doi:") :]
logger.debug("re3data record had unparsable xref: %s", xref)
return None
class Re3dataAligner(Aligner):
"""Aligner for the Registry of Research Data Repositoris (r3data)."""
key = "re3data"
alt_key_match = "name"
getter = get_re3data
curation_header = ("name", "homepage", "description")
if __name__ == "__main__":
Re3dataAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723255135.0
bioregistry-0.11.12/src/bioregistry/external/re3data/processed.json 0000644 0001751 0000177 00011475125 14655544537 025045 0 ustar 00runner docker {
"r3d100000001": {
"description": "The Odum Institute Archive Dataverse contains social science data curated and archived by the Odum Institute Data Archive at the University of North Carolina at Chapel Hill. Some key collections include the primary holdings of the Louis Harris Data Center, the National Network of State Polls, and other Southern-focused public opinion data.\nPlease note that some datasets in this collection are restricted to University of North Carolina at Chapel Hill affiliates. Access to these datasets require UNC ONYEN institutional login to the Dataverse system.",
"homepage": "https://dataverse.unc.edu/dataverse/odum",
"name": "Odum Institute Archive Dataverse",
"prefix": "r3d100000001"
},
"r3d100000002": {
"description": "You will find in the Access to Archival Databases (AAD) resource online access to records in a small selection of historic databases preserved permanently in NARA. Out of the nearly 200,000 data files in its holdings, NARA has selected approximately 475 of them for public searching through AAD. We selected these data because the records identify specific persons, geographic areas, organizations, and dates. The records cover a wide variety of civilian and military functions and have many genealogical, social, political, and economic research uses. AAD provides: Access to over 85 million historic electronic records created by more than 30 agencies of the U.S. federal government and from collections of donated historical materials.\nBoth free-text and fielded searching options. The ability to retrieve, print, and download records with the specific information that you seek. Information to help you find and understand the records.",
"homepage": "https://aad.archives.gov/aad/",
"name": "Access to Archival Databases",
"prefix": "r3d100000002",
"synonyms": [
"AAD"
],
"xrefs": {
"nlx": "157752",
"scr": "010479"
}
},
"r3d100000004": {
"description": "The \"Database for Spoken German (DGD)\" is a corpus management system in the program area Oral Corpora of the Institute for German Language (IDS). It has been online since the beginning of 2012 and since mid-2014 replaces the spoken German database, which was developed in the \"Deutsches Spracharchiv (DSAv)\" of the IDS.\nAfter single registration, the DGD offers external users a web-based access to selected parts of the collection of the \"Archive Spoken German (AGD)\" for use in research and teaching. The selection of the data for external use depends on the consent of the respective data provider, who in turn must have the appropriate usage and exploitation rights. Also relevant to the selection are certain protection needs of the archive.\nThe Archive for Spoken German (AGD) collects and archives data of spoken German in interactions (conversation corpora) and data of domestic and non-domestic varieties of German (variation corpora). Currently, the AGD hosts around 50 corpora comprising more than 15000 audio and 500 video recordings amounting to around 5000 hours of recorded material with more than 7000 transcripts. With the Research and Teaching Corpus of Spoken German (FOLK) the AGD is also compiling an extensive German conversation corpus of its own.\n!!! Access to data of Datenbank Gesprochenes Deutsch (DGD) is also provided by: IDS Repository https://www.re3data.org/repository/r3d100010382 !!!",
"homepage": "https://dgd.ids-mannheim.de/DGD2Web/jsp/Welcome.jsp",
"name": "Datenbank Gesprochenes Deutsch",
"prefix": "r3d100000004",
"synonyms": [
"DGD",
"DGD2 (formerly)",
"Database for Spoken German",
"FDZ AGD",
"Forschungsdatenzentrum Archiv fΓΌr Gesprochenes Deutsch am Institut fΓΌr Deutsche Sprache"
]
},
"r3d100000005": {
"description": "UNC Dataverse is an open-source repository software application for archiving, sharing, and accessing research data of all kinds.\nEach dataverse within the larger repository contains a multitude of datasets, and each dataset contains descriptive metadata and data files.\nUNC Dataverse is hosted by Odum Institute for Research in Social Science.",
"homepage": "https://dataverse.unc.edu/",
"name": "UNC Dataverse",
"prefix": "r3d100000005",
"synonyms": [
"University of North Carolina Dataverse"
],
"xrefs": {
"fairsharing": "FAIRsharing.pS2p8c"
}
},
"r3d100000006": {
"description": "The ADS is an accredited digital repository for heritage data that supports research, learning and teaching with freely available, high quality and dependable digital resources by preserving and disseminating digital data in the long term. The ADS also promotes good practice in the use of digital data, provides technical advice to the heritage community, and supports the deployment of digital technologies.",
"homepage": "https://archaeologydataservice.ac.uk/",
"name": "Archaeology Data Service",
"prefix": "r3d100000006",
"synonyms": [
"ADS"
],
"xrefs": {
"fairsharing": "FAIRsharing.hm1mfg"
}
},
"r3d100000007": {
"description": "The ESO/ST-ECF science archive is a joint collaboration of the European Organisation for Astronomical Research in the Southern Hemisphere (ESO) and the Space Telescope - European Coordinating Facility (ST-ECF). ESO observational data can be requested after the proprietary period by the astronomical community.",
"homepage": "http://archive.eso.org/cms.html",
"name": "ESO Science Archive Facility",
"prefix": "r3d100000007",
"synonyms": [
"ESO/ST-ECF",
"European Southern Observatory Science Archive Facility"
]
},
"r3d100000011": {
"description": "The Natural Environment Research Council's Data Repository for Atmospheric Science and Earth Observation. The Centre for Environmental Data Analysis (CEDA) serves the environmental science community through three data centres, data analysis environments, and participation in a host of relevant research projects.\nWe aim to support environmental science, further environmental data archival practices, and develop and deploy new technologies to enhance access to data. Additionally we provide services to aid large scale data analysis.",
"homepage": "https://archive.ceda.ac.uk/",
"name": "The CEDA Archive",
"prefix": "r3d100000011",
"synonyms": [
"BADC (formerly)",
"British Atmospheric Data Centre (formerly)",
"NERC Earth Observation Data Centre (NEODC) is integrated in CEDA Archive",
"The Centre for Environmental Data Analysis Archive"
],
"xrefs": {
"fairsharing": "FAIRsharing.dbsEaD"
}
},
"r3d100000012": {
"description": "The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is a publicly accessible earth science data repository created to curate, publicly serve (publish), and archive digital data and information from biological, chemical and biogeochemical research conducted in coastal, marine, great lakes and laboratory environments. The BCO-DMO repository works closely with investigators funded through the NSF OCE Divisionβs Biological and Chemical Sections and the Division of Polar Programs Antarctic Organisms & Ecosystems. The office provides services that span the full data life cycle, from data management planning support and DOI creation, to archive with appropriate national facilities.",
"homepage": "https://www.bco-dmo.org/",
"name": "Biological and Chemical Oceanography Data Management Office",
"prefix": "r3d100000012",
"synonyms": [
"BCO-DMO"
],
"xrefs": {
"fairsharing": "FAIRsharing.pjj4gd"
}
},
"r3d100000013": {
"description": "The Blue Obelisk Data Repository lists many important chemoinformatics data such as element and isotope properties, atomic radii, etc. including references to original literature. Developers can use this repository to make their software interoperable.",
"homepage": "https://sourceforge.net/projects/blueobelisk/",
"name": "Blue Obelisk Data Repository",
"prefix": "r3d100000013",
"synonyms": [
"BODR"
]
},
"r3d100000015": {
"description": "<<>>!!!<<<",
"name": "California Water CyberInfrastructure",
"prefix": "r3d100000015"
},
"r3d100000016": {
"description": "The Canadian Astronomy Data Centre (CADC) was established in 1986 by the National Research Council of Canada (NRC), through a grant provided by the Canadian Space Agency (CSA). Over the past 30 years the CADC has evolved from an archiving centre---hosting data from Hubble Space Telescope, Canada-France-Hawaii Telescope, the Gemini observatories, and the James Clerk Maxwell Telescope---into a Science Platform for data-intensive astronomy. The CADC, in partnership with Shared Services Canada, Compute Canada, CANARIE and the university community (funded through the Canadian Foundation for Innovation), offers cloud computing, user-managed storage, group management, and data publication services, in addition to its ongoing mission to provide permanent storage for major data collections.\nLocated at NRC Herzberg Astronomy and Astrophysics Research Centre in Victoria, BC, the CADC staff consists of professional astronomers, software developers, and operations staff who work with the community to develop and deliver leading-edge services to advance Canadian research. The CADC plays a leading role in international efforts to improve the scientific/technical landscape that supports data intensive science. This includes leadership roles in the International Virtual Observatory Alliance and participation in organizations like the Research Data Alliance, CODATA, and the World Data Systems. CADC also contributes significantly to future Canadian projects like the Square Kilometre Array and TMT. \nIn 2019, the Canadian Astronomy Data Centre (CADC) delivered over 2 Petabytes of data (over 200 million individual files) to thousands of astronomers in Canada and in over 80 other countries. The cloud processing system completed over 6 million jobs (over 1100 core years) in 2019.",
"homepage": "https://www.cadc-ccda.hia-iha.nrc-cnrc.gc.ca/en/",
"name": "Canadian Astronomy Data Centre",
"prefix": "r3d100000016",
"synonyms": [
"CADC",
"CCDA",
"Centre canadien de donnΓ©es astronomiques"
]
},
"r3d100000017": {
"description": "=== !!!!! Due to changes in technology and funding, the RAD website is no longer available !!!!! ===",
"homepage": "https://www.cbil.upenn.edu/RAD",
"name": "RNA Abundance Database",
"prefix": "r3d100000017",
"synonyms": [
"RAD"
],
"xrefs": {
"nif": "0000-00133",
"omics": "00869",
"scr": "002771"
}
},
"r3d100000018": {
"description": ">>> !!!!! The Cell Centered Database is no longer on serice. It has been merged with \"Cell image library\": https://www.re3data.org/repository/r3d100000023 !!!!! <<<<",
"homepage": "https://library.ucsd.edu/dc/collection/bb5940732k",
"name": "Cell Centered Database",
"prefix": "r3d100000018",
"synonyms": [
"CCDB"
],
"xrefs": {
"nif": "0000-00007",
"scr": "002168"
}
},
"r3d100000019": {
"description": "The U.S. Department of Energyβs (DOE) Environmental Systems Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE) data archive serves Earth and environmental science data. ESS-DIVE is funded by the Data Management program within the Climate and Environmental Science Division under the DOEβs Office of Biological and Environmental Research program (BER), and is maintained by the Lawrence Berkeley National Laboratory.\n\nESS-DIVE will archive and publicly share data obtained from observational, experimental, and modeling research that is funded by the DOEβs Office of Science under its Subsurface Biogeochemical Research (SBR) and Terrestrial Ecosystem Science (TES) programs within the Environmental Systems Science (ESS) activity.\n\nESS-DIVE was launched in July 2017, and is designed to provide long-term stewardship and use of data from observational, experimental and modeling activities in the DOE in the Subsurface Biogeochemical Research (SBR) and Terrestrial Ecosystem Science (TES) Programs in the Environmental System Science (ESS) activity.",
"homepage": "https://ess-dive.lbl.gov/",
"name": "ESS-DIVE",
"prefix": "r3d100000019",
"synonyms": [
"Environmental System Science Data Infrastructure for a Virtual Ecosystem",
"formerly: CDIAC",
"formerly: Carbon Dioxide Information Analysis Center archive (1982 - Sept. 2017)"
],
"xrefs": {
"fairsharing": "fairsharing.d6pe1f"
}
},
"r3d100000020": {
"description": "The Coastal Data Information Program (CDIP) is an extensive network for monitoring waves and beaches along the coastlines of the United States. Since its inception in 1975, the program has produced a vast database of publicly-accessible environmental data for use by coastal engineers and planners, scientists, mariners, and marine enthusiasts. The program has also remained at the forefront of coastal monitoring, developing numerous innovations in instrumentation, system control and management, computer hardware and software, field equipment, and installation techniques.",
"homepage": "http://cdip.ucsd.edu/",
"name": "Coastal Data Information Program",
"prefix": "r3d100000020",
"synonyms": [
"CDIP"
]
},
"r3d100000021": {
"description": "Most or all of the features are no longer available via the CDS/DL website since provision of the EPSRC UK national Chemical Database Service has been taken over by the Royal Society of Chemistry from 1st January 2013. Daresbury now offers reduced database access, but CrystalWorks developments continue here. \nSome related features may be available via the RSC/CSD portal. For details of what is currently available on the CDS/DL website and also links to the RSC/CDS portal follow the link to the CDS/DL Homepage. // The service gives on-line access to a rich variety of quality databases in fields relating to chemistry. The CDS team also provides general support, training and advice.",
"homepage": "http://cds.dl.ac.uk/",
"name": "Chemical Database Service",
"prefix": "r3d100000021",
"synonyms": [
"CDS",
"CrystalWorks Server",
"STFC Chemical Database Service"
]
},
"r3d100000022": {
"description": "The Comprehensive Epidemiologic Data Resource (CEDR) is the U.S. Department of Energy (DOE) electronic database comprised of health studies of DOE contract workers and environmental studies of areas surrounding DOE facilities. DOE recognizes the benefits of data sharing and supports the public's right to know about worker and community health risks. CEDR provides independent researchers and educators with access to de-identified data collected since the Department's early production years. Current CEDR holdings include more than 76 studies of over 1 million workers at 31 DOE sites. Access to these data is at no cost to the user.",
"homepage": "https://oriseapps.orau.gov/cedr/",
"name": "Comprehensive Epidemiological Data Resource",
"prefix": "r3d100000022",
"synonyms": [
"CEDR",
"CEDR Epidemiologic Databases"
]
},
"r3d100000023": {
"description": "This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The Cell Image Library has been merged with \"Cell Centered Database\" in 2017. The purpose of the database is to advance research on cellular activity, with the ultimate goal of improving human health.",
"homepage": "http://www.cellimagelibrary.org/home",
"name": "The Cell Image Library",
"prefix": "r3d100000023",
"synonyms": [
"CIL",
"The Cell"
],
"xrefs": {
"fairsharing": "FAIRsharing.8t18te",
"nif": "0000-37639",
"scr": "003510"
}
},
"r3d100000027": {
"description": "CiteSeerx is an evolving scientific literature digital library and search engine that focuses primarily on the literature in computer and information science. CiteSeerx aims to improve the dissemination of scientific literature and to provide improvements in functionality, usability, availability, cost, comprehensiveness, efficiency, and timeliness in the access of scientific and scholarly knowledge. Rather than creating just another digital library, CiteSeerx attempts to provide resources such as algorithms, data, metadata, services, techniques, and software that can be used to promote other digital libraries. CiteSeerx has developed new methods and algorithms to index PostScript and PDF research articles on the Web.",
"homepage": "https://citeseerx.ist.psu.edu/",
"name": "CiteSeerX",
"prefix": "r3d100000027"
},
"r3d100000028": {
"description": "the Data Hub is a community-run catalogue of useful sets of data on the Internet. You can collect links here to data from around the web for yourself and others to use, or search for data that others have collected. Depending on the type of data (and its conditions of use), the Data Hub may also be able to store a copy of the data or host it in a database, and provide some basic visualisation tools.",
"homepage": "https://datahub.io/",
"name": "The Data Hub",
"prefix": "r3d100000028",
"synonyms": [
"datahub"
],
"xrefs": {
"nlx": "158409",
"scr": "003996"
}
},
"r3d100000031": {
"description": "The Google Code Archive contains the data found on the Google Code Project Hosting Service, which turned down in early 2016. This archive contains over 1.4 million projects, 1.5 million downloads, and 12.6 million issues.\nGoogle Project Hosting powers Project Hosting on Google Code and Eclipse Labs. Project Hosting on Google Code Eclipse Labs. It provides a fast, reliable, and easy open source hosting service with the following features: Instant project creation on any topic; Git, Mercurial and Subversion code hosting with 2 gigabyte of storage space and download hosting support with 2 gigabytes of storage space; Integrated source code browsing and code review tools to make it easy to view code, review contributions, and maintain a high quality code base; An issue tracker and project wiki that are simple, yet flexible and powerful, and can adapt to any development process; Starring and update streams that make it easy to keep track of projects and developers that you care about.",
"homepage": "https://code.google.com/archive/",
"name": "Google Code Project Hosting",
"prefix": "r3d100000031",
"synonyms": [
"Google Code",
"Google Code Archive",
"Google Project Hosting"
],
"xrefs": {
"scr": "000811"
}
},
"r3d100000032": {
"description": "<<>>!!!>>>",
"homepage": "http://forscenter.ch/en/data-and-research-information-services/2221-2/public-statistics/",
"name": "Communication Portal for Accessing Social Statistics",
"prefix": "r3d100000032",
"synonyms": [
"COMPASS"
]
},
"r3d100000033": {
"description": "The Center for Tropical Forest Science (CTFS) is a global network of forest research plots committed to the study of tropical and temperate forest function and diversity. The multi-institutional network comprises more than forty forest research plots across the Americas, Africa, Asia, and Europe, with a strong focus on tropical regions. CTFS monitors the growth and survival of about 6 million trees of approximately 10,000 species.",
"homepage": "https://forestgeo.si.edu/",
"name": "Forest Global Earth Observatory",
"prefix": "r3d100000033",
"synonyms": [
"CTFS-ForestGEO",
"ForestGEO",
"formerly: CTFS",
"formerly: Center for Tropical Forest Science"
]
},
"r3d100000034": {
"description": "CUGIR is an active online repository in the National Spatial Data Clearinghouse program. CUGIR provides geospatial data and metadata for New York State, with special emphasis on those natural features relevant to agriculture, ecology, natural resources, and human-environment interactions. In order to provide the best possible access to geospatial data for New York State, CUGIR coordinates its activities with those of the New York State GIS Clearinghouse",
"homepage": "https://cugir.library.cornell.edu/",
"name": "Cornell University Geospatial Information Repository",
"prefix": "r3d100000034",
"synonyms": [
"CUGIR"
],
"xrefs": {
"fairsharing": "FAIRsharing.b34ef7"
}
},
"r3d100000036": {
"description": "One of twelve NASA Science Mission Directorate (SMD) Data Centers that provide Earth science data, information, and services to research scientists, applications scientists, applications users, and students. The GES DISC is the home (archive) of NASA Precipitation and Hydrology, as well as Atmospheric Composition and Dynamics remote sensing data and information. The DISC also houses the Modern Era Retrospective-Analysis for Research and Applications (MERRA) data assimilation datasets (generated by GSFCβs Global Modeling and Assimilation Office), and the North American Land Data Assimilation System (NLDAS) and Global Land Data Assimilation System (GLDAS) data products (both generated by GSFC's Hydrological Sciences Branch).",
"homepage": "https://disc.gsfc.nasa.gov/",
"name": "Goddard Earth Sciences Data and Information Services Center",
"prefix": "r3d100000036",
"synonyms": [
"GES DISC"
],
"xrefs": {
"fairsharing": "FAIRsharing.7388wt"
}
},
"r3d100000037": {
"description": "The Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) for biogeochemical dynamics is one of the National Aeronautics and Space Administration (NASA) Earth Observing System Data and Information System (EOSDIS) data centers managed by the Earth Science Data and Information System (ESDIS) Project. The ORNL DAAC archives data produced by NASA's Terrestrial Ecology Program. The DAAC provides data and information relevant to biogeochemical dynamics, ecological data, and environmental processes, critical for understanding the dynamics relating to the biological, geological, and chemical components of Earth's environment.",
"homepage": "https://daac.ornl.gov/",
"name": "Oak Ridge National Laboratory Distributed Active Archive Center for Biogeochemical Dynamics",
"prefix": "r3d100000037",
"synonyms": [
"ORNL DAAC"
],
"xrefs": {
"fairsharing": "FAIRsharing.a833sq"
}
},
"r3d100000038": {
"description": "The Australian Antarctic Data Centre (AADC) provides data collection and data management services in Australia's Antarctic Science Program. The AADC manages science data from Australia's Antarctic research, maps Australia's areas of interest in the Antarctic region, manages Australia's Antarctic state of the environment reporting, and provides advice and education and a range of other products.",
"homepage": "https://data.aad.gov.au/",
"name": "Australian Antarctic Data Centre",
"prefix": "r3d100000038",
"synonyms": [
"AADC",
"Data management and spatial data services"
],
"xrefs": {
"fairsharing": "FAIRsharing.t1tvm9",
"nlx": "152019",
"scr": "006320"
}
},
"r3d100000039": {
"description": "GBIF is an international organisation that is working to make the world's biodiversity data accessible everywhere in the world. GBIF and its many partners work to mobilize the data, and to improve search mechanisms, data and metadata standards, web services, and the other components of an Internet-based information infrastructure for biodiversity.\nGBIF makes available data that are shared by hundreds of data publishers from around the world. These data are shared according to the GBIF Data Use Agreement, which includes the provision that users of any data accessed through or retrieved via the GBIF Portal will always give credit to the original data publishers.",
"homepage": "https://www.gbif.org/",
"name": "Global Biodiversity Information Facility",
"prefix": "r3d100000039",
"synonyms": [
"Data index of the Global Biodiversity Information Facility",
"GBIF.org"
],
"xrefs": {
"fairsharing": "FAIRsharing.zv11j3",
"nlx": "149475",
"ror": "05fjyn938",
"scr": "005904"
}
},
"r3d100000042": {
"description": "The World Bank recognizes that transparency and accountability are essential to the development process and central to achieving the Bankβs mission to alleviate poverty. The Bankβs commitment to openness is also driven by a desire to foster public ownership, partnership and participation in development from a wide range of stakeholders. As a knowledge institution, the World Bankβs first step is to share its knowledge freely and openly.",
"homepage": "https://data.worldbank.org/",
"name": "The World Bank Open Data",
"prefix": "r3d100000042",
"xrefs": {
"nlx": "156929",
"scr": "012767"
}
},
"r3d100000043": {
"description": "Data Basin is a science-based mapping and analysis platform that supports learning, research, and sustainable environmental stewardship.",
"homepage": "https://databasin.org/",
"name": "DataBasin",
"prefix": "r3d100000043",
"synonyms": [
"Data Basin"
],
"xrefs": {
"biodbcore": "001647"
}
},
"r3d100000044": {
"description": "Dryad is an open data publishing platform and a community committed to the open availability and routine re-use of all research data. We publish data in any format and any discipline. All Dryad data undergoes a curation process and is published under a CC0 waiver to promote reuse.",
"homepage": "https://datadryad.org/stash",
"name": "DRYAD",
"prefix": "r3d100000044",
"xrefs": {
"fairsharing": "FAIRsharing.wkggtx",
"nlx": "149486",
"omics": "20678",
"ror": "00x6h5n95",
"scr": "005910"
}
},
"r3d100000045": {
"description": "Data Observation Network for Earth (DataONE) is the foundation of new innovative environmental science through a distributed framework and sustainable cyberinfrastructure that meets the needs of science and society for open, persistent, robust, and secure access to well-described and easily discovered Earth observational data.\nSupported by the U.S. National Science Foundation (Grant #OCI-0830944) as one of the initial DataNets, DataONE will ensure the preservation, access, use and reuse of multi-scale, multi-discipline, and multi-national science data via three primary cyberinfrastucture elements and a broad education and outreach program.",
"homepage": "https://www.dataone.org/",
"name": "DataONE",
"prefix": "r3d100000045",
"synonyms": [
"Data Observation Network for Earth"
],
"xrefs": {
"fairsharing": "FAIRsharing.yyf78h",
"miriam": "00100815",
"nlx": "158410",
"ror": "00hr5y405",
"scr": "003999"
}
},
"r3d100000046": {
"description": "The European Environment Agency (EEA) is an agency of the European Union. Our task is to provide sound, independent information on the environment. We are a major information source for those involved in developing, adopting, implementing and evaluating environmental policy, and also the general public. Currently, the EEA has 33 member countries.\nEEA's mandate is: To help the Community and member countries make informed decisions about improving the environment, integrating environmental considerations into economic policies and moving towards sustainability\nTo coordinate the European environment information and observation network (Eionet)",
"homepage": "https://www.eea.europa.eu/en/analysis",
"name": "European Environment Agency, Datasets",
"prefix": "r3d100000046",
"synonyms": [
"EEA"
]
},
"r3d100000047": {
"description": "Edinburgh DataShare is a digital repository of research data produced at the University of Edinburgh, hosted by the Research Data Service in Information Services. Edinburgh University researchers who have produced research data associated with an existing or forthcoming publication, or which has potential use for other researchers, are invited to upload their dataset for sharing and safekeeping. A persistent identifier and suggested citation will be provided.",
"homepage": "https://datashare.ed.ac.uk/",
"name": "Edinburgh DataShare",
"prefix": "r3d100000047",
"synonyms": [
"DataShare"
],
"xrefs": {
"fairsharing.legacy": "4279",
"opendoar": "1176"
}
},
"r3d100000049": {
"description": "<<>>!!!>>>",
"homepage": "https://dc.zah.uni-heidelberg.de/potsdam/q/raw/info",
"name": "Potsdam Carte du Ciel Plates",
"prefix": "r3d100000049"
},
"r3d100010035": {
"description": "The Chandra Data Archive (CDA) plays a central role in the operation of the Chandra X-ray Center (CXC) by providing support to the astronomical community in accessing Chandra data. Its primary role is one of storage and distribution of all data products including those that users of the observatory need to perform their scientific studies using Chandra data.\nThe CDA offers access to digital archives through powerful query engines, including VO-compliant interfaces. The CDA also serves as a permanent storage repository of contributed data products by authors who have processed images or other pertinent and valuable datasets that are essential to their publications.",
"homepage": "https://cxc.cfa.harvard.edu/cda/",
"name": "The Chandra Data Archive",
"prefix": "r3d100010035",
"synonyms": [
"CDA"
]
},
"r3d100010050": {
"description": "The Research Data Archive (RDA) at NCAR contains a large and diverse collection of meteorological and oceanographic observations, operational and reanalysis model outputs, and remote sensing datasets to support atmospheric and geosciences research.",
"homepage": "https://rda.ucar.edu/",
"name": "Research Data Archive at NCAR",
"prefix": "r3d100010050",
"synonyms": [
"NCAR CISL RDA",
"National Center for Atmospheric Research Research Data Archive"
],
"xrefs": {
"fairsharing": "FAIRsharing.q31z3g"
}
},
"r3d100010051": {
"description": "The Harvard Dataverse is open to all scientific data from all disciplines worldwide. It includes the world's largest collection of social science research data. It is hosting data for projects, archives, researchers, journals, organizations, and institutions.",
"homepage": "https://dataverse.harvard.edu/",
"name": "Harvard Dataverse",
"prefix": "r3d100010051",
"synonyms": [
"The Dataverse Project"
],
"xrefs": {
"fairsharing": "fairsharing.t2e1ss",
"nif": "0000-00316",
"scr": "001997"
}
},
"r3d100010052": {
"description": "<<>>!!!>>> This unique resource covers the entire field of astronomy and astrophysics and this online version includes the full text of over 2,750 articles, plus sophisticated search and retrieval functionality, links to the primary literature, and is frequently updated with new material. An active editorial team, headed by the Encyclopedia's editor-in-chief, Paul Murdin, oversees the continual commissioning, reviewing and loading of new and revised content.In a unique collaboration, Nature Publishing Group and Institute of Physics Publishing published the most extensive and comprehensive reference work in astronomy and astrophysics in both print and online formats. First published as a four volume print edition in 2001, the initial Web version went live in 2002, and contained the original print material and was rapidly supplemented with numerous updates and newly commissioned material. Since July 2006 the Encyclopedia is published solely by Taylor & Francis.",
"homepage": "http://eaa.crcpress.com/",
"name": "Encyclopedia of Astronomy and Astrophysics",
"prefix": "r3d100010052",
"synonyms": [
"EAA"
]
},
"r3d100010054": {
"description": "USGS data and tools are the digital information in a format suitable for direct input to software that can analyze its meaning in the scientific, engineering, or business context for which the data were collected.",
"homepage": "https://www.usgs.gov/products/data",
"name": "U.S. Geological Survey",
"prefix": "r3d100010054",
"synonyms": [
"including: USGS Science Data Catalog"
]
},
"r3d100010055": {
"description": "Presented is information on changes in weather and climate extremes, as well as the daily dataset needed to monitor and analyse these extremes. map of participating countries.\nToday, ECA&D is receiving data from 59 participants for 62 countries and the ECA dataset contains 33265 series of observations for 12 elements at 7512 meteorological stations throughout Europe and the Mediterranean (see Daily data > Data dictionary). 51% of these series is public, which means downloadable from this website for non-commercial research. Participation to ECA&D is open to anyone maintaining daily station data",
"homepage": "https://www.ecad.eu/",
"name": "European Climate Assessment & Dataset project",
"prefix": "r3d100010055",
"synonyms": [
"ECA&D"
]
},
"r3d100010056": {
"description": "NOAA's Coral Reef Information System (CoRIS) is a web-based information portal that provides access to NOAA coral reef information and data products with emphasis on the U.S. states, territories and remote island areas. NOAA Coral Reef activities include coral reef mapping, monitoring and assessment; natural and socioeconomic research and modeling; outreach and education; and management and stewardship.",
"homepage": "https://www.coris.noaa.gov/",
"name": "CoRIS",
"prefix": "r3d100010056",
"synonyms": [
"Coral Reef Information System"
],
"xrefs": {
"fairsharing": "/FAIRsharing.ed5b45"
}
},
"r3d100010057": {
"description": "eCrystals - Southampton is the archive for Crystal Structures generated by the Southampton Chemical Crystallography Group and the EPSRC UK National Crystallography Service.",
"homepage": "http://ecrystals.chem.soton.ac.uk/",
"name": "eCrystals",
"prefix": "r3d100010057",
"synonyms": [
"eCrystals - Southampton"
],
"xrefs": {
"fairsharing": "fairsharing.v448pt"
}
},
"r3d100010059": {
"description": "ShareGeo Open was a repository of geospatial data, previously hosted by EDINA. ShareGeo Open has been discontinued, so its datasets have been migrated to this Edinburgh DataShare Collection, for preservation, in accordance with the agreement signed by all ShareGeo depositors.",
"homepage": "https://datashare.ed.ac.uk/handle/10283/2345",
"name": "ShareGeo Open",
"prefix": "r3d100010059",
"synonyms": [
"Edinburgh DataShare"
]
},
"r3d100010060": {
"description": "The Open Energy Information (OpenEI.org) initiative is a free, open source knowledge-sharing platform created to facilitate access to data, models, tools, and information that accelerate the transition to clean energy systems through informed decisions. Sponsored by the Department of Energy, and developed by the National Renewable Energy Lab, in support of the Open Government Initiative, OpenEI strives to make energy-related data and information searchable, accessible, and useful to both people and machines",
"homepage": "https://openei.org/wiki/Main_Page",
"name": "OpenEI",
"prefix": "r3d100010060",
"synonyms": [
"Open Energy Information",
"OpenEnergyInfo"
]
},
"r3d100010061": {
"description": "The Atmospheric Science Data Center (ASDC) at NASA Langley Research Center is responsible for processing, archiving, and distribution of NASA Earth science data in the areas of radiation budget, clouds, aerosols, and tropospheric chemistry.The ASDC specializes in atmospheric data important to understanding the causes and processes of global climate change and the consequences of human activities on the climate.",
"homepage": "https://eosweb.larc.nasa.gov/",
"name": "Atmospheric Science Data Center",
"prefix": "r3d100010061",
"synonyms": [
"ASDC",
"LaRC ASDC",
"NASA Langley Research Center, Atmospheric Science Data Center"
]
},
"r3d100010062": {
"description": "SAFER-Data is a web-based interface to the Environmental Data Archive maintained by the Environmental Research Centre (ERC) in the Environmental Protection Agency (EPA) of Ireland, who has responsibilities for a wide range of licensing, enforcement, monitoring and assessment activities associated with environmental protection.",
"homepage": "https://eparesearch.epa.ie/safer/",
"name": "SAFER-Data",
"prefix": "r3d100010062",
"synonyms": [
"EPA Secure Archive For Environmental Research Data"
]
},
"r3d100010063": {
"description": "Earth Resources Observation and Science (EROS) Center is a remotely sensed data management, systems development, and research field center for the U.S. Geological Survey's (USGS) Climate and Land Use Change Mission Area. The USGS is a bureau of the U.S. Department of the Interior. It currently houses one of the largest computer complexes in the Department of the Interior. EROS has approximately 600 government and contractor employees.",
"homepage": "https://www.usgs.gov/centers/eros",
"name": "Earth Resources Observation and Science Center",
"prefix": "r3d100010063",
"synonyms": [
"USGS EROS Archive",
"USGS EROS Center",
"WDC - Earth Resources Observation and Science EROS"
]
},
"r3d100010064": {
"description": ">>>!!!<<< Ecological Archives through the end of 2015 will be hosted on FigShare once the transition to publishing with Wiley is completed. Thereafter, supplemental material may be hosted on Wiley Online, and/or data deposited with FigShare, Dryad, and other repositories. >>>!!!<<< Ecological Archives publishes materials that are supplemental to articles that appear in the ESA journals (Ecology, Ecological Applications, Ecological Monographs, Ecosphere, Ecosystem Health and Sustainability and Bulletin of the Ecological Society of America), as well as peer-reviewed data papers with abstracts published in the printed journals. Three kinds of publications appear in Ecological Archives: appendices, supplements, and data papers.",
"homepage": "https://esapubs.org/archive/",
"name": "Ecological Archives",
"prefix": "r3d100010064",
"synonyms": [
"esa's ecological archives"
]
},
"r3d100010065": {
"description": "<<>>!!!>>> JEDI is an educational data archive service that collects, preserves, and distributes empirical data for academic, educational and governmental administrative purposes.",
"homepage": "https://www.hyogo-u.ac.jp/english/facilities/museum.html",
"name": "JEDI",
"prefix": "r3d100010065",
"synonyms": [
"JEDIγΈγγγγ"
]
},
"r3d100010066": {
"description": "figshare allows researchers to publish all of their research outputs in an easily citable, sharable and discoverable manner. All file formats can be published, including videos and datasets. Optional peer review process. figshare uses creative commons licensing.\nfigshare+ repository allows figshare users to share larger datasets, over 20GB up to many TBs, see: https://plus.figshare.com/",
"homepage": "https://figshare.com/",
"name": "figshare",
"prefix": "r3d100010066",
"xrefs": {
"fairsharing": "FAIRsharing.drtwnh",
"nlx": "34569",
"scr": "004328"
}
},
"r3d100010067": {
"description": "The Research Data Centre (FDZ-RV) was set-up in 2004 as an integral part of the German Federal Pension Insurance (Deutsche Rentenversicherung). Since then, the Research Data Centre produced several cross-sectional and longitudinal datasets, also called Scientific Use Files (SUF), available to researchers interested in issues of retirement, disability and rehabilitation. The datasets are released on an annual basis.\nThe Scientific Use Files are subsamples drawn from the pool of individuals who are insured in the Federal Pension Insurance. The information provided in the original datasets is necessary to administer the beneficiaries of the pension insurance.",
"homepage": "https://www.eservice-drv.de/FdzPortalWeb/",
"name": "Forschungsdatenzentrum der Rentenversicherung",
"prefix": "r3d100010067",
"synonyms": [
"Centre de donnΓ©es pour la recherche de lΒ΄assurance retraite allemande",
"Centro de Datos de InvestigaciΓ³n de la Seguridad Social Alemana de Pensiones",
"Centro di Dati per la Ricerca dellΒ΄Assicurazione Pensionistica Tedesca",
"FDZ-RV",
"Research Data Centre of the German Pension Insurance"
]
},
"r3d100010068": {
"description": "The WDCGG archives measurement data for greenhouse and related gases in the atmosphere and the ocean (58 gaseous species as of 24 May 2021). The data are classified into five categories according to the observation platforms or methods used.\nAir observation at stationary platform (surface)\nVertical profile observation of air (tower)\nAir observation by aircraft (aircraft)\nHydrographic sampling or observation of surface seawater and overlying air by ships (ship)\nSatellite observations (satellite)",
"homepage": "https://gaw.kishou.go.jp/",
"name": "World Data Centre for Greenhouse Gases",
"prefix": "r3d100010068",
"synonyms": [
"WDCGG",
"WMO World Data Centre for Greenhouse Gases"
],
"xrefs": {
"fairsharing": "FAIRsharing.71fae0"
}
},
"r3d100010069": {
"description": "The CEOS International Directory Network (IDN) home page and search portal serve as NASA's contribution to the Committee on Earth Observation Satellites (CEOS). IDN's mission is to assist researchers, policy makers, and the public in the discovery of and access to data relevant to global change and Earth science research. The Draft Metadata Management Tool (DMMT) is a metadata authoring tool that IDN contributors can use to propose new or modified CMR records.",
"homepage": "https://search.earthdata.nasa.gov/search?portal=idn",
"name": "International Directory Network",
"prefix": "r3d100010069",
"synonyms": [
"IDN",
"formerly: GCMD",
"formerly: Global Change Master Directory"
],
"xrefs": {
"fairsharing": "FAIRsharing.3aabq1"
}
},
"r3d100010070": {
"description": "The species Nothobranchius furzeri possesses several characteristics which make it a particularly attractive model system for age research: Inbred line GRZ shows a captive lifespan of only three months. There is large variation in life-history traits between different isolates. Lifespan can be prolonged by environmental manipulations and drugs. The aim of this website is to provide information on N. furzeri and to foster the development of a group of interest which aims at creating a consortium to establish this organism as a model for developmental and age research.",
"homepage": "https://www.nothobranchius.info//",
"name": "Nothobranchius furzeri Information Network",
"prefix": "r3d100010070",
"synonyms": [
"NFIN"
]
},
"r3d100010071": {
"description": "The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. The JGI Genome Portal provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms.\nDatabases: Genome Online Database (GOLD), Integrated Microbial Genomes (IGM), MycoCosm, Phytozome",
"homepage": "https://genome.jgi.doe.gov/portal/",
"name": "DOE Joint Genome Institute Genome Portal",
"prefix": "r3d100010071",
"synonyms": [
"JGI Genome Portal",
"US Department of Energy Joint Genome Institute Genome Web Portal"
],
"xrefs": {
"nif": "0000-21230",
"scr": "002383"
}
},
"r3d100010072": {
"description": "<<>>!!!>>>",
"homepage": "http://geodata.grid.unep.ch/",
"name": "Environmental data explorer",
"prefix": "r3d100010072",
"synonyms": [
"EDE",
"Explorateur de DonnΓ©es Environmentales"
],
"xrefs": {
"biodbcore": "001708"
}
},
"r3d100010073": {
"description": "GeoCommons is the public community of GeoIQ users who are building an open repository of data and maps for the world. The GeoIQ platform includes a large number of features that empower you to easily access, visualize and analyze your data. The GeoIQ platform powers the growing GeoCommons community of over 25,000 members actively creating and sharing hundreds of thousands of datasets and maps across the world. With GeoCommons, anyone can contribute and share open data, easily build shareable maps and collaborate with others.",
"homepage": "http://geocommons.com/",
"name": "GeoCommons Archive",
"prefix": "r3d100010073",
"synonyms": [
"gc"
]
},
"r3d100010074": {
"description": ">>>!!!<<>>!!!<<< \nInformation Archived on the Web\n\nInformation identified as archived on the Web is for reference, research or recordkeeping purposes. It has not been altered or updated after the date of archiving. Web pages that are archived on the Web are not subject to the Government of Canada Web Standards. As per the Communications Policy of the Government of Canada, you can request alternate formats. Please \"contact us\" to request a format other than those available.",
"homepage": "https://www.nrcan.gc.ca/evaluation/reports/2010/844",
"name": "GeoConnections - Discovery Portal",
"prefix": "r3d100010074",
"synonyms": [
"GDP",
"GΓ©oConnexions - Portail de dΓ©couverte"
]
},
"r3d100010075": {
"description": "GeoGratis is a portal provided by the Earth Sciences Sector (ESS) of Natural Resources Canada (NRCan) which provides geospatial data at no cost and without restrictions via your Web browser.\nThe data will be useful whether you are a novice who needs a geographic map for a presentation, or an expert who wants to overlay a vector layer of digital data on a classified multiband image, with a digital elevation model as a backdrop. The geospatial data are grouped in over 100 collections and are compatible with the most popular geographic information systems (GIS), with image analysis systems and the graphics applications of editing software.",
"homepage": "https://geogratis.gc.ca/",
"name": "GeoGratis",
"prefix": "r3d100010075",
"synonyms": [
"GΓ©ogratis"
]
},
"r3d100010076": {
"description": "The Chesapeake Bay Environmental Observatory (CBEO) is a prototype to demonstrate the utility of newly developed Cyberinfrastructure (CI) components for transforming environmental research, education, and management. The CBEO project uses a specific problem of water quality (hypoxia) as means of directly involving users and demonstrating the prototypeβs utility. \nData from the Test Bed are being brought into a CBEO Portal on a National Geoinformatics Grid developed by the NSF funded GEON. This is a cyberinfrastructure netwrok that allows users access to datasets as well as the tools with which to analyze the data.\nCurrently, Test Bed data avaialble on the CBEO Portal includes Water Quality Model output and water quality monitorig data from the Chesapeake Bay Program's CIMS database. This data is also available as aggregated \"data cubes\". Avaialble tools include the Data Access System for Hydrology (DASH), Hydroseek and an online R-based interpolator.",
"homepage": "https://cbeo.communitymodeling.org/",
"name": "Chesapeake Bay Environmental Observatory",
"prefix": "r3d100010076",
"synonyms": [
"CBEO"
],
"xrefs": {
"fairsharing.legacy": "3001"
}
},
"r3d100010078": {
"description": "Data.gov increases the ability of the public to easily find, download, and use datasets that are generated and held by the Federal Government. Data.gov provides descriptions of the Federal datasets (metadata), information about how to access the datasets, and tools that leverage government datasets",
"homepage": "https://www.data.gov/",
"name": "Data.gov",
"prefix": "r3d100010078",
"xrefs": {
"fairsharing": "FAIRsharing.6069e1",
"nlx": "70953"
}
},
"r3d100010079": {
"description": "The HEASARC is a multi-mission astronomy archive for the EUV, X-ray, and Gamma ray wave bands. Because EUV, X and Gamma rays cannot reach the Earth's surface it is necessary to place the telescopes and sensors on spacecraft. The HEASARC now holds the data from 25 observatories covering over 30 years of X-ray, extreme-ultraviolet and gamma-ray astronomy. Data and software from many of the older missions were restored by the HEASARC staff. Examples of these archived missions include ASCA, BeppoSAX, Chandra, Compton GRO, HEAO 1, Einstein Observatory (HEAO 2), EUVE, EXOSAT, HETE-2, INTEGRAL, ROSAT, Rossi XTE, Suzaku, Swift, and XMM-Newton.",
"homepage": "https://heasarc.gsfc.nasa.gov/",
"name": "High Energy Astrophysics Science Archive Research Center",
"prefix": "r3d100010079",
"synonyms": [
"HEASARC",
"NASA's HEASARC"
]
},
"r3d100010080": {
"description": "The primary interaction of low-energy x rays within matter, viz. photoabsorption and coherent scattering, have been described for photon energies outside the absorption threshold regions. These tables are based on a compilation of the available experimental measurements and theoretical calculations. For many elements there is little or no published data and in such cases it was necessary to rely on theoretical calculations and interpolations across Z. In order to improve the accuracy in the future considerably more experimental measurements are needed.",
"homepage": "https://henke.lbl.gov/optical_constants/",
"name": "X-Ray Database",
"prefix": "r3d100010080",
"synonyms": [
"X-ray interactions with matter"
]
},
"r3d100010081": {
"description": "The Durham High Energy Physics Database (HEPData), formerly: the Durham HEPData Project, has been built up over the past four decades as a unique open-access repository for scattering data from experimental particle physics. It currently comprises the data points from plots and tables related to several thousand publications including those from the Large Hadron Collider (LHC).\nThe Durham HepData Project has for more than 25 years compiled the Reactions Database containing what can be loosly described as cross sections from HEP scattering experiments. The data comprise total and differential cross sections, structure functions, fragmentation functions, distributions of jet measures, polarisations, etc... from a wide range of interactions. \nIn the new HEPData site (hepdata.net), you can explore new functionalities for data providers and data consumers, as well as the submission interface. HEPData is operated by CERN and IPPP at Durham University and is based on the digital library framework Invenio.",
"homepage": "https://hepdata.net/",
"name": "HEPData",
"prefix": "r3d100010081",
"synonyms": [
"High Energy Physics Data Repository",
"formerly: Durham HEPData Project"
],
"xrefs": {
"fairsharing": "FAIRsharing.awgyhy"
}
},
"r3d100010082": {
"description": "CUAHSI's Hydrologic Information System (CUAHSI-HIS) provides web services, tools, standards and procedures that enhance access to more and better data for hydrologic analysis",
"homepage": "https://www.cuahsi.org/",
"name": "CUAHSI",
"prefix": "r3d100010082",
"synonyms": [
"Universities Allied for Water Research"
],
"xrefs": {
"nlx": "154706",
"scr": "002197"
}
},
"r3d100010083": {
"description": "STScI's innovative ways to share Hubble's remarkable discoveries with the public.HubbleSite prepares and disseminates the photographs and animations seen in the news... as well as posters, slide shows, exhibits, and educational products in print and electronic formats",
"homepage": "https://hubblesite.org/resource-gallery",
"name": "HubbleSite",
"prefix": "r3d100010083"
},
"r3d100010084": {
"description": "Thousands of Temperature and salinity profiles obtained by means of Nansen hydrographic casts and available earlier only as station sheets have been digitized at the German Maritime and Hydrographic Agency (BSH).\nIn a cooperative effort between the KlimaCampus of the University of Hamburg and the German Oceanographic Data Centre (DOD, Hamburg) about 7500 hydrographic profiles were checked and identified as missing in the international oceanographic databases. Since most of the profiles were obtained in the decades before the second World War they represent an important extension of the international historical database and a respective contribution to the IOC Global Oceanographic Data Archeology and Rescue Project (GODAR). Since 2009 our efforts resulted in locating about 7500 hydrographic profiles that are not yet available for the oceanographic community.",
"homepage": "https://www.cen.uni-hamburg.de/en/icdc/data/ocean/historical-hydrographic-bsh.html",
"name": "Historical hydrographic data from BSH",
"prefix": "r3d100010084",
"synonyms": [
"Historische hydrographische Daten des BSH"
]
},
"r3d100010085": {
"description": "The most comprehensive database on fully determined inorganic crystal structures\nβ’ Full structural data: cell parameters, atom positions for all entries, displacement parameters\nβ’ Full bibliographic data: publication title, journal reference(s), author names\nβ’ Full structure description: Structural formula, compositions, ANX formulae, structure types\nβ’ High-quality data: extensive data evaluation and correction by senior experts\nβ’ Web and PC based software solutions, data updated twice a year\nβ’ 25+ years of serving the scientific community",
"homepage": "https://icsd.products.fiz-karlsruhe.de/",
"name": "Inorganic Crystal Structure Database",
"prefix": "r3d100010085",
"synonyms": [
"ICSD",
"ICSD Web"
],
"xrefs": {
"biodbcore": "001709",
"fairsharing": "FAIRsharing.a95199"
}
},
"r3d100010086": {
"description": "<<>>!!!>>>",
"homepage": "http://www.mitime.org/mirage/",
"name": "MIRAGE",
"prefix": "r3d100010086",
"synonyms": [
"MIRAGE 2011: Repository Enrichment from Archiving to Creation",
"Middlesex medical Image Repository with a CBIR Archiving Environment"
]
},
"r3d100010087": {
"description": "<<>>!!!>>>\nDay averages, maximum, minimum and month sums of the precipitation of about 70 German stations with archive since 2008.",
"homepage": "http://imkhp2.physik.uni-karlsruhe.de/~muehr/wetterwerte.html",
"name": "Aktuelle Wetter- und Klimawerte deutscher Stationen",
"prefix": "r3d100010087",
"xrefs": {
"nlx": "157759",
"scr": "003611"
}
},
"r3d100010088": {
"description": "OBIS strives to document the ocean's diversity, distribution and abundance of life. Created by the Census of Marine Life, OBIS is now part of the Intergovernmental Oceanographic Commission (IOC) of UNESCO, under its International Oceanographic Data and Information Exchange (IODE) programme",
"homepage": "https://obis.org/",
"name": "Ocean Biodiversity Information System",
"prefix": "r3d100010088",
"synonyms": [
"OBIS",
"formerly: Ocean Biogeographic Information System"
],
"xrefs": {
"fairsharing": "FAIRsharing.3rv9m8",
"nlx": "154698",
"scr": "006933"
}
},
"r3d100010089": {
"description": "IRSA is chartered to curate the calibrated science products from NASAs infrared and sub-millimeter missions, including five major large-area/all-sky surveys. IRSA exploits a re-useable architecture to deploy cost-effective archives for customers, including: the Spitzer Space Telescope; the 2MASS and IRAS all-sky surveys; and multi-mission datasets such as COSMOS, WISE and Planck mission",
"homepage": "https://irsa.ipac.caltech.edu/frontpage/",
"name": "NASA/IPAC InfraRed Science Archive",
"prefix": "r3d100010089",
"synonyms": [
"IRSA"
]
},
"r3d100010090": {
"description": "IUBio Archive is an archive of biology data and software. The archive includes items to browse, search and fetch public software, molecular data, biology news and documents.",
"homepage": "http://iubioarchive.bio.net/",
"name": "IUBio-Archive",
"prefix": "r3d100010090",
"synonyms": [
"IUBio"
]
},
"r3d100010091": {
"description": "JASPAR is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors and other proteins interacting with DNA in a sequence-specific manner.",
"homepage": "https://jaspar.elixir.no/",
"name": "JASPAR",
"prefix": "r3d100010091",
"xrefs": {
"fairsharing": "FAIRsharing.6641f3",
"nif": "0000-03061",
"omics": "00538",
"scr": "003030"
}
},
"r3d100010092": {
"description": "The KNB Data Repository is an international repository intended to facilitate ecological, environmental and earth science research in the broadest senses. For scientists, the KNB Data Repository is an efficient way to share, discover, access and interpret complex ecological, environmental, earth science, and sociological data and the software used to create and manage those data. Due to rich contextual information provided with data in the KNB, scientists are able to integrate and analyze data with less effort. The data originate from a highly-distributed set of field stations, laboratories, research sites, and individual researchers. The KNB supports rich, detailed metadata to promote data discovery as well as automated and manual integration of data into new projects. The KNB supports a rich set of modern repository services, including the ability to assign Digital Object Identifiers (DOIs) so data sets can be confidently referenced in any publication, the ability to track the versions of datasets as they evolve through time, and metadata to establish the provenance relationships between source and derived data.",
"homepage": "https://knb.ecoinformatics.org/",
"name": "KNB Data Repository",
"prefix": "r3d100010092",
"synonyms": [
"KNB",
"Knowledge Network for Biocomplexity"
],
"xrefs": {
"fairsharing": "FAIRsharing.jjka8c"
}
},
"r3d100010093": {
"description": "The NCEAS Data Repository contains information about the research data sets collected and collated as part of NCEAS' funded activities. Information in the NCEAS Data Repository is concurrently available through the Knowledge Network for Biocomplexity (KNB), an international data repository. A number of the data sets were synthesized from multiple data sources that originated from the efforts of many contributors, while others originated from a single.\nDatasets can be found at KNB repository https://knb.ecoinformatics.org/data , creator=NCEAS",
"homepage": "https://www.nceas.ucsb.edu/",
"name": "National Center for Ecological Analysis and Synthesis Data Repository",
"prefix": "r3d100010093",
"synonyms": [
"NCEAS Data Repository"
]
},
"r3d100010094": {
"description": "The KPDL covers cultural heritage, scientific and regional collections β digital copies of different forms of publications: books, journals, graphics, articles, leaflets, posters, playbills, photographs, invitations, maps, exhibition catalogues and trade fairs of the region. The Kujawsko-Pomorska Digital Library is to serve scientists, students, schoolchildren and all the citizens of the region.",
"homepage": "https://kpbc.umk.pl/dlibra",
"name": "Kujawsko-Pomorska Digital Library",
"prefix": "r3d100010094",
"synonyms": [
"Kujawsko-Pomorska Biblioteka Cyfrowa",
"Kujawsko-Pomorska digitale Bibliothek"
],
"xrefs": {
"opendoar": "186144",
"roar": "778"
}
},
"r3d100010096": {
"description": "<<>>!!!>>>> \nMolTable: An Open Access (Molecule Table) Portal for \"Advanced Chemoinformatics Research, Training and Services\"",
"homepage": "http://moltable.ncl.res.in/web/guest",
"name": "MolTable",
"prefix": "r3d100010100",
"synonyms": [
"Molecule table"
]
},
"r3d100010101": {
"description": "MorphoBank is a web application with tools and archives for evolutionary research, specifically systematics (the science of determining the evolutionary relationships among species). Study of the phenotype, which is often visually-based, is central to contemporary systematics and taxonomic research. MorphoBank was developed specifically to provide much needed tools for the expansion and modernization of phylogenetic work on the phenotype",
"homepage": "https://morphobank.org/",
"name": "MorphoBank",
"prefix": "r3d100010101",
"synonyms": [
"Homology of phenotypes over the web",
"MorphoBank Project"
],
"xrefs": {
"fairsharing": "FAIRsharing.1y63n8",
"nlx": "156938",
"scr": "003213"
}
},
"r3d100010102": {
"description": "BioInvestigation Index database enables storing and querying functionalities of experimental biological and biomedical metadata of Leibniz Institute of Plant Biochemistry",
"homepage": "https://github.com/ISA-tools/BioInvIndex",
"name": "bii",
"prefix": "r3d100010102",
"synonyms": [
"BioInvIndex",
"BioInvestigationIndex"
]
},
"r3d100010103": {
"description": "MassBank is the first public repository of mass spectral data for sharing them among scientific research community. MassBank data are useful for the chemical identification and structure elucidation of chemical comounds detected by mass spectrometry.MassBank system is originally designed for public sharing of reference mass spectra for metabolite identification. It is also useful for their in-house or local sharing. Recently it finds another application; sharing mass spectra of unknown metabolites for metabolite profiling. The IPB is operating the first european MassBank site, that is part of the consortial MassBank Project. You can access both the set of IPB Tandem-MS and Ion Trap spectra, as well as the other massbank sites.",
"homepage": "https://msbi.ipb-halle.de/MassBank/",
"name": "IPB MassBank",
"prefix": "r3d100010103",
"synonyms": [
"High resolution mass spectral database",
"IPB MS Database",
"JST-BIRD MassBank"
]
},
"r3d100010104": {
"description": "<<>>!!!>>>\nOngoing NEBC activities, including the development of Bio-Linux, are being moved into the new EOS programme http://environmentalomics.org/portfolio/big-data-infrastructure/ . Once the current material from this website has been moved into EOS, this NEBC site will remain on-line as an archive. \nEnvBase is the searchable index to the data deposited through the NEBC, as well as related NERC experimental data. At present this is chiefly from the grants funded by the NERC Environmental Genomics Science Programme and the subsequent Post-genomics and Proteomics Science Programme, but more data from ongoing projects continues to be added",
"homepage": "http://nebc.nerc.ac.uk/nebc_website_frozen/nebc.nerc.ac.uk//data/envbase.html",
"name": "EnvBase",
"prefix": "r3d100010104",
"synonyms": [
"A searchable index to environmental 'omic' datasets.",
"EnvBase data catalogue"
]
},
"r3d100010105": {
"description": "<<>>!!!<<< NEES network features 14 geographically-distributed, shared-use laboratories that support several types of experimental work: geotechnical centrifuge research, shake table tests, large-scale structural testing, tsunami wave basin experiments, and field site research >>>!!!>>>",
"homepage": "http://nees.org/",
"name": "NEEShub",
"prefix": "r3d100010105",
"synonyms": [
"Network for Earthquake Engineering Simulations",
"The George E. Brown, Jr. Network for Earthquake Engineering Simulation",
"a platform for research, collaboration and education"
]
},
"r3d100010106": {
"description": "The Neuroscience Information Framework is a dynamic index of data, materials, and tools. Please note, we do not accept direct data deposits, but if you wish to make your data repository or database available through our search, please contact us. An initiative of the NIH Blueprint for Neuroscience Research, NIF advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment.",
"homepage": "https://neuinfo.org/",
"name": "Neuroscience Information Framework",
"prefix": "r3d100010106",
"synonyms": [
"NIF"
],
"xrefs": {
"fairsharing": "FAIRsharing.v11s0z",
"nif": "0000-25673",
"omics": "01190",
"scr": "002894"
}
},
"r3d100010107": {
"description": "NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications. It contains contributions from over 80 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. To date, NeuroMorpho.Org is the largest collection of publicly accessible 3D neuronal reconstructions and associated metadata which can be used for detailed single cell simulations.",
"homepage": "https://neuromorpho.org/",
"name": "NeuroMorpho.Org",
"prefix": "r3d100010107",
"synonyms": [
"NeuroMorpho"
],
"xrefs": {
"fairsharing": "FAIRsharing.drcy7r",
"nif": "0000-00006",
"omics": "06594",
"scr": "002145"
}
},
"r3d100010108": {
"description": "The National Forestry Database is used to compile national statistics. Most of the data are provided by the provincial or territorial resource management organizations. Federal land data are provided by the responsible federal departments and compiled by the CFS.",
"homepage": "http://nfdp.ccfm.org/",
"name": "National Forestry Database",
"prefix": "r3d100010108",
"synonyms": [
"BDNF",
"Base de donnΓ©es nationale sur les forets",
"NFD"
]
},
"r3d100010109": {
"description": "The NSIDC Distributed Active Archive Center (DAAC) processes, archives, documents, and distributes data from NASA's past and current Earth Observing System (EOS) satellites and field measurement programs. The NSIDC DAAC focuses on the study of the cryosphere.\nThe NSIDC DAAC is one of NASA's Earth Observing System Data and Information System (EOSDIS) Data Centers.",
"homepage": "https://nsidc.org/data/data-programs/nsidc-daac",
"name": "NASA Distributed Active Archive Center at National Snow & Ice Data Center",
"prefix": "r3d100010109",
"synonyms": [
"DAAC",
"NASA DAAC at NSIDC"
]
},
"r3d100010110": {
"description": "NSIDC offers hundreds of scientific data sets for research, focusing on the cryosphere and its interactions. Data are from satellites and field observations. All data are free of charge.",
"homepage": "https://nsidc.org/data/",
"name": "National Snow and Ice Data Center",
"prefix": "r3d100010110",
"synonyms": [
"NSIDC",
"WDC - CU",
"WDC for Glaciology",
"World Data Center for Glaciology"
],
"xrefs": {
"nlx": "154742",
"scr": "002220"
}
},
"r3d100010111": {
"description": "The NASA Space Science Data Coordinated Archive serves as the permanent archive for NASA space science mission data. \"Space science\" means astronomy and astrophysics, solar and space plasma physics, and planetary and lunar science. As permanent archive, NSSDCA teams with NASA's discipline-specific space science \"active archives\" which provide access to data to researchers and, in some cases, to the general public.\nNSSDCA also serves as NASA's permanent archive for space physics mission data. It provides access to several geophysical models and to data from some non-NASA mission data.\nIn addition to supporting active space physics and astrophysics researchers, NSSDCA also supports the general public both via several public-interest web-based services (e.g., the Photo Gallery) and via the offline mailing of CD-ROMs, photoprints, and other items.",
"homepage": "https://nssdc.gsfc.nasa.gov/",
"name": "NASA Space Science Data Coordinated Archive",
"prefix": "r3d100010111",
"synonyms": [
"NASA's archive for space science mission data",
"NSSDCA"
],
"xrefs": {
"pssb": "00666"
}
},
"r3d100010113": {
"description": "<<>>!!!>>> The ONS challenge contains open solubility data, experiments with raw data from different scientists and institutions. It is part of the The Open Notebook Science wiki community, ideally suited for community-wide collaborative research projects involving mathematical modeling and computer simulation work, as it allows researchers to document model development in a step-by-step fashion, then link model prediction to experiments that test the model, and in turn, use feeback from experiments to evolve the model. By making our laboratory notebooks public, the evolutionary process of a model can be followed in its totality by the interested reader. Researchers from laboratories around the world can now follow the progress of our research day-to-day, borrow models at various stages of development, comment or advice on model developments, discuss experiments, ask questions, provide feedback, or otherwise contribute to the progress of science in any manner possible.",
"homepage": "http://onschallenge.wikispaces.com/list+of+experiments",
"name": "ONSchallenge",
"prefix": "r3d100010113",
"synonyms": [
"ONS"
]
},
"r3d100010114": {
"description": "Attention!\nData sets are not updated anymore.\nPlease, visit the BonaRes Repositorβiumβ for new datasets.\nOpen Research Data provides quality assessed data and their metadata such as context information on measurement objectives, equipment, methods, testing and investigation areas. The purpose of the repository is to secure quality, integrity and long-term availability of landscape and ecosystem research data as well as to enhance accessibility of free data from ZALF long-term monitoring campaigns, landscape laboratories (Agro-ScapeLabs), field trials and experiments.\nThe Leibniz Centre for Agricultural Landscape Research (ZALF) explores ecosystems in agricultural landscapes and the development of ecologically and economically viable land use systems. ZALF combines scientific expertise from agricultural science, geosciences, biosciences and socio-economics.",
"homepage": "https://open-research-data.zalf.de/default.aspx",
"name": "Open Research Data",
"prefix": "r3d100010114",
"synonyms": [
"The platform for freely accessible landscape research data",
"ZALF. Open Research Data"
],
"xrefs": {
"fairsharing": "FAIRsharing.585e03"
}
},
"r3d100010115": {
"description": "Open Context is a free, open access resource for the electronic publication of primary field research from archaeology and related disciplines. It emerged as a means for scholars and students to easily find and reuse content created by others, which are key to advancing research and education. Open Context's technologies focus on ease of use, open licensing frameworks, informal data integration and, most importantly, data portability.Open Context currently publishes 132 projects.",
"homepage": "https://opencontext.org/",
"name": "Open Context",
"prefix": "r3d100010115"
},
"r3d100010116": {
"description": "The University of Oxford Text Archive develops, collects, catalogues and preserves electronic literary and linguistic resources for use in Higher Education, in research, teaching and learning. We also give advice on the creation and use of these resources, and are involved in the development of standards and infrastructure for electronic language resources.",
"homepage": "https://ota.bodleian.ox.ac.uk/repository/xmlui/",
"name": "The University of Oxford Text Archive",
"prefix": "r3d100010116",
"synonyms": [
"OTA"
]
},
"r3d100010117": {
"description": "Fossilworks is a web-based portal to the Paleobiology Database. Fossilworks is the original public interface to the PaleoDB and is housed at Macquarie. It is a non-governmental, non-profit public resource. Its purpose is to provide global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data. The project's wider, long-term goal is to encourage collaborative efforts to answer large-scale paleobiological questions by developing a useful database infrastructure and bringing together large data sets.",
"homepage": "http://www.fossilworks.org/",
"name": "fossilworks",
"prefix": "r3d100010117",
"synonyms": [
"PaleoDB",
"Paleobiology Database"
]
},
"r3d100010118": {
"description": "The German Socio-Economic Panel Study (SOEP) is a wide-ranging representative longitudinal study of private households, located at the German Institute for Economic Research, DIW Berlin. Every year, there were nearly 11,000 households, and more than 20,000 persons sampled by the fieldwork organization TNS Infratest Sozialforschung.\nThe data provide information on all household members, consisting of Germans living in the Old and New German States, Foreigners, and recent Immigrants to Germany. The Panel was started in 1984.\nSome of the many topics include household composition, occupational biographies, employment, earnings, health and satisfaction indicators.",
"homepage": "https://www.diw.de/en/diw_01.c.678568.en/research_data_center_soep.html",
"name": "Forschungsdatenzentrum des SOEP",
"prefix": "r3d100010118",
"synonyms": [
"Das Sozio-Oekonomische Panel",
"FDZ SOEP",
"Research Data Center of the SOEP",
"Research Data Center of the Socio-Economic Panel"
],
"xrefs": {
"nlx": "151827",
"scr": "013140"
}
},
"r3d100010119": {
"description": "Specification Patterns is an online repository for information about property specification for finite-state verification. The intent of this repository is to collect patterns that occur commonly in the specification of concurrent and reactive systems.",
"homepage": "https://matthewbdwyer.github.io/psp/",
"name": "Spec Patterns",
"prefix": "r3d100010119",
"synonyms": [
"Specification Patterns"
]
},
"r3d100010120": {
"description": "The UK Polar Data Centre (UK PDC) is the focal point for Arctic and Antarctic environmental data management in the UK. Part of the Natural Environmental Research Councilβs (NERC) network of environmental data centres and based at the British Antarctic Survey, it coordinates the management of polar data from UK-funded research and supports researchers in complying with national and international data legislation and policy.",
"homepage": "https://www.bas.ac.uk/data/uk-pdc/",
"name": "UK Polar Data Centre",
"prefix": "r3d100010120",
"synonyms": [
"UK PDC"
],
"xrefs": {
"fairsharing": "FAIRsharing.t43bf6"
}
},
"r3d100010121": {
"description": "The PDS archives and distributes scientific data from NASA planetary missions, astronomical observations, and laboratory measurements. The PDS is sponsored by NASA's Science Mission Directorate. Its purpose is to ensure the long-term usability of NASA data and to stimulate advanced research",
"homepage": "https://pds.nasa.gov/",
"name": "PDS",
"prefix": "r3d100010121",
"synonyms": [
"The Planetary Data System"
],
"xrefs": {
"fairsharing": "FAIRsharing.f85eb7",
"ror": "006ndaj41"
}
},
"r3d100010123": {
"description": "MetaCrop is a database that summarizes diverse information about metabolic pathways in crop plants and allows automatic export of information for the creation of detailed metabolic models. MetaCrop is a database that contains manually curated, highly detailed information about metabolic pathways in crop plants, including location information, transport processes and reaction kinetics.",
"homepage": "https://apex.ipk-gatersleben.de/apex/f?p=269:111:::NO:::",
"name": "MetaCrop",
"prefix": "r3d100010123",
"xrefs": {
"fairsharing": "FAIRsharing.wdbd3r",
"nif": "0000-03113",
"scr": "003100"
}
},
"r3d100010124": {
"description": "The Crop EST Database (CR-EST) is a public available online resource providing access to sequence, classification, clustering, and annotation data of crop EST projects at the IPK. A view of these information give the summarized numbers about genomic data of species listed in the adjacent table.",
"homepage": "https://apex.ipk-gatersleben.de/apex/f?p=116:1",
"name": "CR-EST",
"prefix": "r3d100010124",
"synonyms": [
"The IPK Crop EST Database"
],
"xrefs": {
"nif": "0000-02695",
"scr": "007612"
}
},
"r3d100010125": {
"description": "A web database is provided which can be used to calculate photon cross sections for scattering, photoelectric absorption and pair production, as well as total attenuation coefficients, for any element, compound or mixture (Z β€ 100), at energies from 1 keV to 100 GeV.",
"homepage": "https://www.nist.gov/pml/xcom-photon-cross-sections-database",
"name": "NIST XCOM",
"prefix": "r3d100010125",
"synonyms": [
"NIST Standard Reference Database 8 (XGAM)",
"Photon Cross Section Database",
"XCOM"
],
"xrefs": {
"doi": "10.18434/T48G6X"
}
},
"r3d100010126": {
"description": "The GISAID Initiative promotes the international sharing of all influenza virus sequences, related clinical and epidemiological data associated with human viruses, and geographical as well as species-specific data associated with avian and other animal viruses, to help researchers understand how the viruses evolve, spread and potentially become pandemics. \n*** GISAID does so by overcoming disincentives/hurdles or restrictions, which discourage or prevented sharing of influenza data prior to formal publication.\n*** The Initiative ensures that open access to data in GISAID is provided free-of-charge and to everyone, provided individuals identify themselves and agree to uphold the GISAID sharing mechanism governed through its Database Access Agreement. GISAID calls on all users to agree to the basic premise of upholding scientific etiquette, by acknowledging the originating laboratories providing the specimen and the submitting laboratories who generate the sequence data, ensuring fair exploitation of results derived from the data, and that all users agree that no restrictions shall be attached to data submitted to GISAID, to promote collaboration among researchers on the basis of open sharing of data and respect for all rights and interests.",
"homepage": "https://www.gisaid.org/",
"name": "GISAID",
"prefix": "r3d100010126",
"synonyms": [
"GISAID EpiFlu database",
"Global initiative on sharing all influenza data"
],
"xrefs": {
"fairsharing": "FAIRsharing.2f7f9f",
"scr": "018279"
}
},
"r3d100010129": {
"description": "Pubchem contains 3 databases. 1. PubChem BioAssay: The PubChem BioAssay Database contains bioactivity screens of chemical substances described in PubChem Substance. It provides searchable descriptions of each bioassay, including descriptions of the conditions and readouts specific to that screening procedure. 2. PubChem Compound: The PubChem Compound Database contains validated chemical depiction information provided to describe substances in PubChem Substance. Structures stored within PubChem Compounds are pre-clustered and cross-referenced by identity and similarity groups. 3. PubChem Substance. The PubChem Substance Database contains descriptions of samples, from a variety of sources, and links to biological screening results that are available in PubChem BioAssay. If the chemical contents of a sample are known, the description includes links to PubChem Compound.",
"homepage": "https://pubchem.ncbi.nlm.nih.gov/",
"name": "PubChem",
"prefix": "r3d100010129",
"xrefs": {
"fairsharing": "FAIRsharing.qt3w7z",
"nlx": "42691",
"omics": "02734",
"scr": "010578"
}
},
"r3d100010130": {
"description": "<<>>!!!>>>\nThe JAE Data Archive, which is hosted by a server belonging to the Economics Department of Queen's University, contains data for all papers accepted after January, 1994, unless the data are confidential. There are also data for a few papers accepted earlier. Volume 10, No. 1 (1995) is the first issue in which all papers were accepted subject to the proviso that data be provided.\nFor some papers, especially more recent ones, the Data Archive also contains programs and supplementary material, such as technical appendices and additional graphs.",
"homepage": "http://qed.econ.queensu.ca/jae/",
"name": "Journal of Applied Econometrics Data Archive",
"prefix": "r3d100010130",
"synonyms": [
"JAE Data Archive"
]
},
"r3d100010131": {
"description": "<<>>!!!>>>",
"homepage": "http://ccdb.wishartlab.com/",
"name": "CyberCell Database",
"prefix": "r3d100010131",
"synonyms": [
"CCDB",
"CCDB"
],
"xrefs": {
"nif": "0000-02644",
"scr": "013423"
}
},
"r3d100010132": {
"description": "<<>>!!!>>>",
"homepage": "http://lrl-diffusion.univ-bpclermont.fr/mulce2/accesCorpus/accesCorpusMulce.php",
"name": "Multimodal Learning Corpus Exchange",
"prefix": "r3d100010132",
"synonyms": [
"LETEC",
"MULCE",
"MUltimodal contextualized Learner Corpus Exchange",
"Multimodal Learning and Teaching Corpora"
],
"xrefs": {
"issn": "2425-3316"
}
},
"r3d100010133": {
"description": "Research data from University of Pretoria. This data repository facilitates data publishing, sharing and collaboration of academic research, allowing UP to manage and in some cases showcase its data to the wider research community.\nPreviously UPSpace (https://repository.up.ac.za/) was used for both datasets and research outputs. Now UP Research Data Repository is dedicated for datasets.",
"homepage": "https://researchdata.up.ac.za/",
"name": "UP Research Data Repository",
"prefix": "r3d100010133",
"synonyms": [
"UP Data Repository",
"University of Pretoria Research Data Repository",
"formerly: UPSpace"
]
},
"r3d100010134": {
"description": "PANGAEA - Data Publisher for Earth & Environmental Sciences has an almost 30-year history as an open-access library for archiving, publishing, and disseminating georeferenced data from the Earth, environmental, and biodiversity sciences. Originally evolving from a database for sediment cores, it is operated as a joint facility of the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI) and the Center for Marine Environmental Sciences (MARUM) at the University of Bremen. PANGAEA holds a mandate from the World Meteorological Organization (WMO) and is accredited as a World Radiation Monitoring Center (WRMC). It was further accredited as a World Data Center by the International Council for Science (ICS) in 2001 and has been certified with the Core Trust Seal since 2019. The successful cooperation between PANGAEA and the publishing industry along with the correspondent technical implementation enables the cross-referencing of scientific publications and datasets archived as supplements to these publications. PANGAEA is the recommended data repository of numerous international scientific journals.",
"homepage": "https://www.pangaea.de/",
"name": "PANGAEA",
"prefix": "r3d100010134",
"synonyms": [
"Data Publisher for Earth and Environmental Science"
],
"xrefs": {
"fairsharing": "FAIRsharing.6yw6cp"
}
},
"r3d100010135": {
"description": "KADoNiS-p database:\nThe KADoNiS project is an online database for cross sections relevant to the s-process and p-process (Ξ³-process). The present p-process library includes all available experimental data from (p,Ξ³), (p,n), (Ξ±,Ξ³), (Ξ±,n), and (Ξ±,p) reactions between 70Ge and 209Bi in or close to the respective Gamow window.",
"homepage": "https://kadonis.org/",
"name": "Karlsruhe Astrophysical Database of Nucleosynthesis in Stars",
"prefix": "r3d100010135",
"synonyms": [
"KADoNIS"
]
},
"r3d100010136": {
"description": "The Prototype Data Portal allows to retrieve Data from World Data System (WDS) members. WDS ensures the long-term stewardship and provision of quality-assessed data and data services to the international science community and other stakeholders",
"homepage": "https://www.worlddatasystem.org/",
"name": "World Data System",
"prefix": "r3d100010136",
"synonyms": [
"International Council for Science World Data System",
"formerly: ICSU World Data System"
]
},
"r3d100010137": {
"description": "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. PRIDE encourages and welcomes direct user submissions of mass spectrometry data to be published in peer-reviewed publications.",
"homepage": "https://www.ebi.ac.uk/pride/",
"name": "PRoteomics IDEntifications Database",
"prefix": "r3d100010137",
"synonyms": [
"PRIDE"
],
"xrefs": {
"fairsharing": "FAIRsharing.e1byny",
"miriam": "00100094",
"nif": "0000-03336",
"omics": "02456",
"scr": "003411"
}
},
"r3d100010138": {
"description": "The Australian Data Archive (ADA) provides a national service for the collection and preservation of digital research data and to make these data available for secondary analysis by academic researchers and other users. The archive is based in POLIS: the Social Policy Research Centre (formerly the ANU Centre for Social Research and Methods - CSRM) at the Australian National University (ANU). Along with Australian data, ADA is also a repository for studies conducted in other countries, particularly throughout the Asia-Pacific region. The ADA data catalogue includes studies from countries including New Zealand, Bangladesh, Cambodia, China and Indonesia.",
"homepage": "https://ada.edu.au/",
"name": "Australian Data Archive",
"prefix": "r3d100010138",
"synonyms": [
"ADA Dataverse"
],
"xrefs": {
"fairsharing": "FAIRsharing.sN8d9i",
"scr": "014706"
}
},
"r3d100010139": {
"description": "The repository of the Hamburg Centre for Speech Corpora is used for archiving, maintenance, distribution and development of spoken language corpora. These usually consist of audio and / or video recordings, transcriptions and other data and structured metadata.\nThe corpora treat the focus on multilingualism and are generally freely available for research and teaching. Most of the measures maintained by the HZSK corpora were created in the years 2000-2011 in the framework of the SFB 538 \"Multilingualism\" at the University of Hamburg. The HZSK however also strives to take linguistic data from other projects or contexts, and to provide also the scientific community for research and teaching are available, provided that they are compatible with the current focus of HZSK, ie especially spoken language and multilingualism.",
"homepage": "https://www.fdr.uni-hamburg.de/communities/hzsk/?page=1&size=20",
"name": "Hamburger Zentrum fΓΌr Sprachkorpora Korpus Repositorium",
"prefix": "r3d100010139",
"synonyms": [
"HZSK Repository",
"Hamburg Centre for Speech Corpora Digital Repository"
]
},
"r3d100010140": {
"description": "CLAPOP is the portal of the Dutch CLARIN community. It brings together all relevant resources that were created within the CLARIN NL project and that now are part of the CLARIN NL infrastructure or that were created by other projects but are essential for the functioning of the CLARIN (NL) infrastructure.\nCLARIN-NL has closely cooperated with CLARIN Flanders in a number of projects. The common results of this cooperation and the results of this cooperation created by CLARIN Flanders are included here as well.",
"homepage": "https://portal.clarin.nl/",
"name": "CLAPOP",
"prefix": "r3d100010140",
"synonyms": [
"The Dutch CLARIN Portal Pages"
]
},
"r3d100010141": {
"description": "GAWSIS is being developed and maintained by the Federal Office of Meteorology and Climatology MeteoSwiss in collaboration with the WMO GAW Secretariat, the GAW World Data Centres and other GAW representatives to improve the management of information about the GAW network of ground-based stations. The application is presently hosted by the Swiss Laboratories for Materials Testing and Research Empa.\nGAWSIS provides the GAW community and other interested people with an up-to-date, searchable data base of\nsite descriptions, measurements programs and data available, contact people, bibliographic references. Linked data collections are hosted at the World Data Centers of the WMO Global Atmosphere Watch.",
"homepage": "https://gawsis.meteoswiss.ch/GAWSIS//index.html#/",
"name": "GAWSIS",
"prefix": "r3d100010141",
"synonyms": [
"GAW Station Information System"
]
},
"r3d100010142": {
"description": "FAIRsharing is a web-based, searchable portal of three interlinked registries, containing both in-house and crowdsourced manually curated descriptions of standards, databases and data policies, combined with an integrated view across all three types of resource. By registering your resource on FAIRsharing, you not only gain credit for your work, but you increase its visibility outside of your direct domain, so reducing the potential for unnecessary reinvention and proliferation of standards and databases.",
"homepage": "https://fairsharing.org/",
"name": "FAIRsharing",
"prefix": "r3d100010142",
"synonyms": [
"formerly: biosharing"
],
"xrefs": {
"fairsharing": "FAIRsharing.2abjs5",
"miriam": "00100463",
"nlx": "143602",
"omics": "17902",
"scr": "004177"
}
},
"r3d100010143": {
"description": "NSSDC is the nation-level space science data center which recognized by the Ministry of Science and Technology of China. As a repository for space science data, NSSDC assumes the responsibility of the long-term stewardship and offering a reliable service of space science data in China. It also has been the Chinese center for space science of the World Data Center (WDC) since 1988. In 2013, NSSDC became a regular member of World Data System.\nData resources are concentrated in the following fields of space physics and space environment, space astronomy, lunar and planetary science, space application and engineering. In space physics, the NSSDC maintains space-based observation data and ground-based observation data of the middle and upper atmosphere, ionosphere and earth surface, from Geo-space Double Star Exploration Program and Meridian Project. In space astronomy, NSSDC archived pointed observation data of Hard X-ray Modulation Telescope. In lunar and planetary science, space application and engineering, NSSDC also collects detection data of ChangβE from Lunar Exploration Program and science products of BeiDou satellites.",
"homepage": "https://www.nssdc.ac.cn/eng/",
"name": "National Space Science Data Center",
"prefix": "r3d100010143",
"synonyms": [
"NSSDC",
"World Data Center for Space Science",
"ε½εΆη©Ίι΄η§ε¦ζ°ζδΈεΏ"
],
"xrefs": {
"fairsharing": "FAIRsharing.snAELz"
}
},
"r3d100010144": {
"description": "The World Data Centre for Meteorology is located in Obninsk in the All-Russian Research Institute of Hydrometeorological Information World Data Centre (RIHMI-WDC). The task of the Centre is to collect and disseminate meteorological data and products worldwide and especially in Russia. The information basis of the Centre is updated on regular basis from various sources including the bilateral data exchange with the World Data Centre for Meteorology in Ashville, North Carolina, USA. The data holdings of WDC β Rockets, Satellites and Earth Rotation (WDC RSER) have become, in December 2015, part of the collection of WDC β Meteorology, Obninsk",
"homepage": "http://meteo.ru/mcd/ewdcmet.html",
"name": "World Data Centre for Meteorology, Obninsk",
"prefix": "r3d100010144",
"synonyms": [
"WDC - Meteorology, Obninsk"
],
"xrefs": {
"biodbcore": "001630"
}
},
"r3d100010145": {
"description": "<<>>!!!>>>. However, the WDS-SC is extremely pleased to learn that the data holdings of WDC β RSER have now become part of the collection of WDC β Meteorology, Obninsk (WDS Regular Member). The World Data Centre for Rockets, Satellite and Rotation of the Earth is located in Obninsk in the All-Russian Research Institute of Hydrometeorological Information World Data Centre (RIHMI-WDC). The task of the Centre is to collect and disseminate meteorological data and products worldwide and especially in Russia. Data are available from RIHMI-WDC site",
"homepage": "http://meteo.ru/mcd/ewdcroc",
"name": "World Data Centre for Rockets, Satellite and Rotation of the Earth",
"prefix": "r3d100010145",
"synonyms": [
"WDC RSER",
"WDC Rockets"
]
},
"r3d100010146": {
"description": "Swedish National Data Service (SND) is a research data infrastructure designed to assist researchers in preserving, maintaining, and disseminating research data in a secure and sustainable manner. The SND Search function makes it easy to find, use, and cite research data from a variety of scientific disciplines. Together with an extensive network of almost 40 Swedish higher education institutions and other research organisations, SND works for increased access to research data, nationally as well as internationally.",
"homepage": "https://snd.se/en",
"name": "Swedish National Data Service",
"prefix": "r3d100010146",
"synonyms": [
"SND",
"Svensk Nationell DatatjΓ€nst"
],
"xrefs": {
"fairsharing": "FAIRsharing.pn7yxf"
}
},
"r3d100010147": {
"description": "The CLARINΒ/Text+ repository at the Saxon Academy of Sciences and Humanities in Leipzig offers longΒterm preservation of digital resources, along with their descriptive metadata. The mission of the repository is to ensure the availability and longΒterm preservation of resources, to preserve knowledge gained in research, to aid the transfer of knowledge into new contexts, and to integrate new methods and resources into university curricula. Among the resources currently available in the Leipzig repository are a set of corpora of the Leipzig Corpora Collection (LCC), based on newspaper, Wikipedia and Web text. Furthermore several REST-based webservices are provided for a variety of different NLP-relevant tasks\nThe repository is part of the CLARIN infrastructure and part of the NFDI consortium Text+. It is operated by the Saxon Academy of Sciences and Humanities in Leipzig.",
"homepage": "https://repo.data.saw-leipzig.de/en",
"name": "Repository CLARIN Centre Leipzig",
"prefix": "r3d100010147",
"synonyms": [
"CLARIN repository at the Saxon Academy of Sciences and Humanities",
"Leipzig Corpora Collection",
"Repositorium der SΓ€chsischen Akademie der Wissenschaften zu Leipzig",
"SAW",
"Text+ centre at the Saxon Academy of Sciences and Humanities"
]
},
"r3d100010148": {
"description": "The Digital Collections include digitized manuscripts, prints, music, maps, photographs, newspapers and magazines from the rich holdings of the Bayerische Staatsbibliothek. \nAlmost the entire content (>98%) is available for download for research purposes or via IIIF APIs, including all available OCR data.",
"homepage": "https://www.digitale-sammlungen.de/de/",
"name": "Digitale Sammlungen",
"prefix": "r3d100010148",
"synonyms": [
"Digital Collections",
"frΓΌher: BABS",
"frΓΌher: Bibliothekarisches Archivierungs- und Bereitstellungssystem"
]
},
"r3d100010149": {
"description": "The Longitudinal Aging Study Amsterdam (LASA) at the VU University and VU University Medical Centre is initiated by the Ministry of Health, Welfare and Sports in 1991 to determine predictors and consequences of ageing. LASA focuses on, physical, emotional, cognitive and social functioning in late life, the connections between these aspects, and the changes that occur in the course of time",
"homepage": "https://www.lasa-vu.nl/index.htm",
"name": "Longitudinal Aging Study Amsterdam",
"prefix": "r3d100010149",
"synonyms": [
"LASA"
]
},
"r3d100010150": {
"description": "The LISS panel (Longitudinal Internet Studies for the Social sciences) is the principal component of the MESS project. It consists of 5000 households, comprising approximately 7500 individuals. The panel is based on a true probability sample of households drawn from the population register by Statistics Netherlands. Households that could not otherwise participate are provided with a computer and Internet connection. In addition to the LISS panel an Immigrant panel was available from October 2010 up until December 2014. This Immigrant panel consisted of around 1,600 households (2,400 individuals) of which 1,100 households (1,700 individuals) were of non-Dutch origin. The data from this panel are still available through the LISS data archive (https://www.dataarchive.lissdata.nl/study_units/view/162). \nPanel members complete online questionnaires every month of about 15 to 30 minutes in total. They are paid for each completed questionnaire. One member in the household provides the household data and updates this information at regular time intervals.",
"homepage": "https://www.lissdata.nl/",
"name": "LISS Panel",
"prefix": "r3d100010150",
"synonyms": [
"Longitudinal Internet Studies for the Social sciences"
]
},
"r3d100010151": {
"description": "CINES is the French national long-term preservation service provider for Higher Education and Research: more than 20 institutions (universities, librairies, labs) archive their digital heritage at CINES so that it's preserved over time in a secure, dedicated environment. This includes documents such as PhD theses or publications, digitized ancient/rare books, satellite imagery, 3D/vidΓ©os/image galleries, datasets, etc.",
"homepage": "https://www.cines.fr/en/preservation/",
"name": "PAC - Archiving Platform CINES",
"prefix": "r3d100010151",
"synonyms": [
"Archivage numΓ©rique pΓ©renne CINES",
"CINES PAC",
"Centre Informatique National de lβEnseignement SupΓ©rieur Archivage NumΓ©rique PΓ©renne",
"PAC - Long-term Preservation Platform CINES",
"PAC - Plateforme d'Archivage au CINES"
],
"xrefs": {
"issn": "2425-8792"
}
},
"r3d100010152": {
"description": "The repository is part of the National Research Data Infrastructure initiative Text+, in which the University of TΓΌbingen is a partner. It is housed at the Department of General and Computational Linguistics. The infrastructure is maintained in close cooperation with the Digital Humanities Centre, which is a core facility of the university, colaborating with the library and computing center of the university.\nIntegration of the repository into the national CLARIN-D and international CLARIN infrastructures gives it wide exposure, increasing the likelihood that the resources will be used and further developed beyond the lifetime of the projects in which they were developed.\nAmong the resources currently available in the TΓΌbingen Center Repository, researchers can find widely used treebanks of German (e.g. TΓΌBa-D/Z), the German wordnet (GermaNet), the first manually annotated digital treebank (Index Thomisticus), as well as descriptions of the tools used by the WebLicht ecosystem for natural language processing.",
"homepage": "https://uni-tuebingen.de/en/134314",
"name": "CLARIN repository at the University of TΓΌbingen",
"prefix": "r3d100010152",
"synonyms": [
"CLARIN Center TΓΌbingen",
"CLARIN Repository TΓΌbingen",
"TALAR",
"TΓΌbingen Archive of Language Resources"
]
},
"r3d100010153": {
"description": "VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain the actual plot records, vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. VegBank receives its data from the VegBank community of users.",
"homepage": "http://vegbank.org/vegbank/index.jsp",
"name": "VegBank",
"prefix": "r3d100010153",
"synonyms": [
"The Vegetation Plot Archive Project"
]
},
"r3d100010154": {
"description": ">>>!!!<<>>!!!<<< VENUS is a cabled undersea laboratory for ocean researchers and explorers. VENUS delivers real time information from seafloor instruments via fibre optic cables to the University of Victoria, BC. You can see ocean data live, recent and archived as well as learn more about on-going research",
"homepage": "http://dmas.uvic.ca/home?TREETYPE=1&LOCATION=233&TIMECONFIG=0",
"name": "VENUS in the Salish Sea",
"prefix": "r3d100010154",
"synonyms": [
"VENUS",
"Victoria Experimental Network Under the Sea"
]
},
"r3d100010155": {
"description": "The World Atlas of Language Structures (WALS) is a large database of structural (phonological, grammatical, lexical) properties of languages gathered from descriptive materials (such as reference grammars) by a team of 55 authors (many of them the leading authorities on the subject).",
"homepage": "https://wals.info/",
"name": "The World Atlas of Language Structures",
"prefix": "r3d100010155",
"synonyms": [
"The World Atlas of Language Structures online",
"WALS",
"WALS online"
]
},
"r3d100010156": {
"description": "The World Data Center for Remote Sensing of the Atmosphere, WDC-RSAT, offers scientists and the general public free access (in the sense of a βone-stop shopβ) to a continuously growing collection of atmosphere-related satellite-based data sets (ranging from raw to value added data), information products and services. Focus is on atmospheric trace gases, aerosols, dynamics, radiation, and cloud physical parameters. Complementary information and data on surface parameters (e.g. vegetation index, surface temperatures) is also provided. This is achieved either by giving access to data stored at the data center or by acting as a portal containing links to other providers.",
"homepage": "https://wdc.dlr.de/data_products/VIEWER/",
"name": "The World Data Center for Remote Sensing of the Atmosphere",
"prefix": "r3d100010156",
"synonyms": [
"WDC - Remote Sensing of the Atmosphere",
"WDC-RSAT",
"Weltdatenzentrum fΓΌr die Fernerkundung der AtmosphΓ€re"
]
},
"r3d100010157": {
"description": "The USU-IR digital repository system captures, stores, indexes, preserves, and distributes digital research material.",
"homepage": "https://repositori.usu.ac.id/",
"name": "USU Institutional Repository",
"prefix": "r3d100010157",
"synonyms": [
"Repositori Institusi Universitas Sumatera Utara",
"USU-IR",
"University of Sumatera Utara Institutional Repository"
],
"xrefs": {
"opendoar": "1717",
"roar": "2371"
}
},
"r3d100010158": {
"description": "FRED is an online database consisting of hundreds of thousands of economic data time series from scores of national, international, public, and private sources. FRED, created and maintained by the Research Department at the Federal Reserve Bank of St. Louis, goes far beyond simply providing data: It combines data with a powerful mix of tools that help the user understand, interact with, display, and disseminate the data. In essence, FRED helps users tell their data stories.",
"homepage": "https://fred.stlouisfed.org/",
"name": "Federal Reserve Economic Data",
"prefix": "r3d100010158",
"synonyms": [
"FRED"
]
},
"r3d100010159": {
"description": "SEDAC, the Socioeconomic Data and Applications Center, is one of the Distributed Active Archive Centers (DAACs) in the Earth Observing System Data and Information System (EOSDIS) of the U.S. National Aeronautics and Space Administration. SEDAC is a regular member of the World Data System and focuses on human interactions in the environment. Its mission is to develop and operate applications that support the integration of socioeconomic and Earth science data and to serve as an \"Information Gateway\" between the Earth and social sciences.",
"homepage": "https://sedac.ciesin.columbia.edu/",
"name": "NASA Socioeconomic Data and Applications Center",
"prefix": "r3d100010159",
"synonyms": [
"SEDAC"
],
"xrefs": {
"fairsharing": "FAIRsharing.4ufVpm"
}
},
"r3d100010160": {
"description": "<<>>!!!>>> see https://www.re3data.org/repository/r3d100010159\nThis record is combined with 'NASA Socioeconomic Data and Applications Center'\nThe World Data Center for Human Interactions in the Environment has been superseded by the NASA Socioeconomic Data and Applications Center (SEDAC), which is a regular member of the World Data System (WDS). The International Council for Science (ICSU) replaced the World Data Centers (WDC) with the WDS, which supports the provision of trusted scientific data services by certifying its members to ensure that they maintain the organizational capabilities and infrastructure for managing the data products and services that they offer. SEDAC focuses on human interactions in the environment and is one of the Distributed Active Archive Centers (DAACs) in the NASA Earth Observing System Data and Information System (EOSDIS). The NASA Earth Science Data and Information System (ESDIS) Project, a WDS Network Member, manages the EOSDIS science systems.",
"homepage": "https://sedac.ciesin.columbia.edu/",
"name": "World Data Center for Human Interactions in the Environments",
"prefix": "r3d100010160",
"synonyms": [
"WDC for Human Interactions in the Environment"
]
},
"r3d100010161": {
"description": "SeSam is an outstanding international collection of recent and fossil animals and plants from all over the world. It also holds an important specialized library. The really substantial data of this collection constitute the basis of every taxonomic-systematical, ecological, biogeographical or biostratigraphical fundamental research as well as every practical environmental research. Because of its historical referencings this collection is also a precious cultural treasure that generates the often expensive heavy mission of its conservation. The new system is called AQUiLA.",
"homepage": "https://search.senckenberg.de/aquila-public-search/search",
"name": "AQUiLA",
"prefix": "r3d100010161",
"synonyms": [
"SeSam",
"Senckenberg Sammlungen",
"Senckenberg scientific collections"
]
},
"r3d100010163": {
"description": "SIMBAD astronomical database is the world reference database for the identification of astronomical objects and provides basic data, cross-identifications, bibliography and measurements for astronomical objects outside the solar system. Using VizieR, the catalogue service for the CDS reference collection of astronomical catalogues and tables published in academic journals and the Aladin interactive software sky atlas for access, visualization and analysis of astronomical images, surveys, catalogues, databases and related data. Simbad bibliographic survey began in 1950 for stars (at least bright stars) and in 1983 for all other objects (outside the solar system)",
"homepage": "https://simbad.u-strasbg.fr/simbad/",
"name": "SIMBAD Astronomical Database",
"prefix": "r3d100010163",
"synonyms": [
"Set of Identifications, Measurements, and Bibliography for Astronomical Data"
],
"xrefs": {
"fairsharing": "FAIRsharing.rd6gxr",
"issn": "2417-8667"
}
},
"r3d100010164": {
"description": "SkyView is a Virtual Observatory on the Net generating images of any part of the sky at wavelengths in all regimes from Radio to Gamma-Ray.",
"homepage": "https://skyview.gsfc.nasa.gov/current/cgi/titlepage.pl",
"name": "SkyView",
"prefix": "r3d100010164",
"synonyms": [
"SkyView Virtual Observatory",
"The Internet's Virtual Telescope"
]
},
"r3d100010165": {
"description": "SLGO is positioning itself as being the most complete and diversified source of scientific data regarding the St. Lawrence's ecosystem. It has done so by clustering and sharing information, data, and expertise from government, academic, and community agencies.\nSLGO offers a range of products such as data visualization applications, data management tools, and modeling products able to meet information needs for domains such as public safety, climate change, resource management, and biodiversity conservation.\nAvailable at SLGO.ca: observations, forecasts, predictions, and data archives",
"homepage": "https://catalogue.ogsl.ca/en/",
"name": "SLGO Data Catalog",
"prefix": "r3d100010165",
"synonyms": [
"Catalogue de donnΓ©es de l'OGSL",
"Observatoire global du Saint-Laurent",
"St. Lawrence Global Observatory"
],
"xrefs": {
"fairsharing": "FAIRsharing.b74129"
}
},
"r3d100010166": {
"description": "SMOKA provides public science data obtained at Subaru Telescope, 188cm telescope at Okayama Astrophysical Observatory, 105cm Schmidt telescope at Kiso Observatory (University of Tokyo), MITSuME, and KANATA Telescope at Higashi-Hiroshima Observatory. It is intended mainly for astronomical researchers.",
"homepage": "https://smoka.nao.ac.jp/index.jsp",
"name": "SMOKA Science Archive",
"prefix": "r3d100010166",
"synonyms": [
"SMOKA",
"SMOKAγζ¦θ¦",
"Subaru Mitaka Okayama Kiso Archive",
"γ― γγ°γ δΈι·Ή 岑山 ζ¨ζ½ γ’γΌγ«γ€γγ·γΉγγ "
]
},
"r3d100010167": {
"description": "SourceForge is dedicated to making open source projects successful.\nWe thrive on community collaboration to help us create the leading resource for open source software development and distribution. \nIT professionals come to Sourceforge to develop, download, review, and publish open source software. Sourceforge is the largest, most trusted destination for Open Source Software discovery and development on the web.",
"homepage": "https://sourceforge.net/",
"name": "SourceForge",
"prefix": "r3d100010167",
"synonyms": [
"Find, create and publish Open Source software for free"
],
"xrefs": {
"fairsharing": "FAIRsharing.b138b5"
}
},
"r3d100010168": {
"description": "The Space Physics Data Facility (SPDF) leads in the design and implementation of unique multi-mission and multi-disciplinary data services and software to strategically advance NASA's solar-terrestrial program, to extend our science understanding of the structure, physics and dynamics of the Heliosphere of our Sun and to support the science missions of NASA's Heliophysics Great Observatory.\nMajor SPDF efforts include multi-mission data services such as Heliophysics Data Portal (formerly VSPO), CDAWeb and CDAWeb Inside IDL,and OMNIWeb Plus (including COHOWeb, ATMOWeb, HelioWeb and CGM) , science planning and orbit services such as SSCWeb, data tools such as the CDF software and tools, and a range of other science and technology research efforts. The staff supporting SPDF includes scientists and information technology experts.",
"homepage": "https://spdf.gsfc.nasa.gov/",
"name": "Space Physics Data Facility",
"prefix": "r3d100010168",
"synonyms": [
"NASA's Space Physics Data Facility",
"SPDF"
]
},
"r3d100010169": {
"description": "<<>>!!!>>>\n SumsDB (the Surface Management System DataBase) is a repository of brain-mapping data (surfaces & volumes; structural & functional data) from many laboratories.",
"name": "SumsDB",
"prefix": "r3d100010169",
"synonyms": [
"Surface management system database"
],
"xrefs": {
"nif": "0000-00016",
"scr": "002759"
}
},
"r3d100010170": {
"description": "TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but are only available to the authors, publication editors, or reviewers using a special access code.",
"homepage": "https://www.treebase.org/treebase-web/home.html",
"name": "TreeBASE",
"prefix": "r3d100010170",
"synonyms": [
"a database of phylogenetic knowledge"
],
"xrefs": {
"fairsharing": "FAIRsharing.zcn4w4",
"nif": "0000-03587",
"scr": "005688"
}
},
"r3d100010171": {
"description": "The Solar Data Analysis Center serves data from recent and current space-based solar-physics missions, funds and hosts much of the SolarSoft library, and leads the Virtual Solar Observatory (VSO) effort. SDAC is the active archive, providing network access to data from such missions as SOHO, Yohkoh, and TRACE.",
"homepage": "https://umbra.nascom.nasa.gov/index.html/index.html",
"name": "SDAC",
"prefix": "r3d100010171",
"synonyms": [
"Solar Data Analysis Center"
]
},
"r3d100010172": {
"description": "The World Data Centre for Aerosols (WDCA) is the data repository and archive for microphysical, optical, and chemical properties of atmospheric aerosol of the World Meteorological Organisation's (WMO) Global Atmosphere Watch (GAW) programme. The goal of the Global Atmosphere Watch (GAW) programme is to ensure long-term measurements in order to detect trends in global distributions of chemical constituents in air and the reasons for them. With respect to aerosols, the objective of GAW is to determine the spatio-temporal distribution of aerosol properties related to climate forcing and air quality on multi-decadal time scales and on regional, hemispheric and global spatial scales.",
"homepage": "https://www.gaw-wdca.org/",
"name": "World Data Center for Aerosols",
"prefix": "r3d100010172",
"synonyms": [
"WDCA",
"ebas"
]
},
"r3d100010173": {
"description": "GeoWeb is the MIT Libraries instance of GeoBlacklight and primarily contains data purchased for use by MIT affiliates.",
"homepage": "https://geodata.mit.edu/",
"name": "MIT GeoWeb",
"prefix": "r3d100010173"
},
"r3d100010174": {
"description": "This is a database for vegetation data from West Africa, i.e. phytosociological and dendrometric relevΓ©s as well as floristic inventories. The West African Vegetation Database has been developed in the framework of the projects βSUN - Sustainable Use of Natural Vegetation in West Africaβ and βBiodiversity Transect Analysis in Africaβ (BIOTA, https://www.biota-africa.org/).",
"homepage": "http://www.westafricanvegetation.org/menu/home.aspx",
"name": "West African Vegetation",
"prefix": "r3d100010174",
"synonyms": [
"A vegetation data network for West Africa"
]
},
"r3d100010175": {
"description": "The website for West Nile Virus education, statistics, and dead bird reporting for California.",
"homepage": "https://westnile.ca.gov/",
"name": "WestNile.ca.gov",
"prefix": "r3d100010175",
"synonyms": [
"California West Nile Virus Website",
"Fight the bite"
]
},
"r3d100010177": {
"description": "The WRDC, located at the Main Geophysical Observatory in St. Petersburg, Russia, processes solar radiation data currently submitted from more than 500 stations located in 56 countries and operates an archive with more than 1200 stations listed in its catalogue. The WRDC is the central depository of the measured components such as: global, diffuse and direct solar radiation, downward atmospheric radiation, net total and terrestrial surface radiation (upward), spectral radiation components (instantaneous fluxes), and sunshine duration, on hourly, daily or monthly basis.",
"homepage": "http://wrdc.mgo.rssi.ru/wrdc_en.htm",
"name": "World Radiation Data Centre",
"prefix": "r3d100010177",
"synonyms": [
"WRDC"
],
"xrefs": {
"biodbcore": "001577"
}
},
"r3d100010178": {
"description": "<<>>!!!>>>",
"homepage": "http://wwmm.ch.cam.ac.uk/crystaleye/",
"name": "CrystalEye (beta)",
"prefix": "r3d100010178",
"synonyms": [
"CrystalEye"
]
},
"r3d100010180": {
"description": "The 1000 Genomes Project is an international collaboration to produce an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts. This resource will support genome-wide association studies and other medical research studies.\nThe genomes of about 2500 unidentified people from about 25 populations around the world will be sequenced using next-generation sequencing technologies. The results of the study will be freely and publicly accessible to researchers worldwide.\nThe International Genome Sample Resource (IGSR) has been established at EMBL-EBI to continue supporting data generated by the 1000 Genomes Project, supplemented with new data and new analysis.",
"homepage": "https://www.internationalgenome.org/",
"name": "1000 Genomes",
"prefix": "r3d100010180",
"synonyms": [
"IGSR - International Genome Sample Resource",
"Thousand Genomes"
],
"xrefs": {
"fairsharing": "FAIRsharing.4Vs9VM",
"nlx": "143819",
"omics": "00261",
"scr": "006828"
}
},
"r3d100010181": {
"description": "AGS delivers geoscience in several key areas, including surficial mapping, bedrock mapping, geological modelling, resource evaluation (hydrocarbons, minerals), groundwater, and geological hazards. We also are responsible for maintaining the Alberta Table of Formations and providing geoscience outreach to stakeholders ranging from professional colleagues and academia to the general public.",
"homepage": "https://ags.aer.ca/",
"name": "Alberta Geological Survey",
"prefix": "r3d100010181",
"synonyms": [
"AGS"
],
"xrefs": {
"nlx": "157758",
"scr": "003402"
}
},
"r3d100010182": {
"description": "A collection of data at Agency for Healthcare Research and Quality (AHRQ) supporting research that helps people make more informed decisions and improves the quality of health care services. The portal contains U.S.Health Information Knowledgebase (USHIK) and Systematic Review Data Repository (SRDR) and other sources concerning cost, quality, accesibility and evaluation of healthcare and medical insurance.",
"homepage": "https://www.ahrq.gov/data/index.html",
"name": "Agency for Healthcare Research and Quality, Data & Surveys",
"prefix": "r3d100010182",
"synonyms": [
"AHRQ data & surveys"
],
"xrefs": {
"nlx": "157753",
"scr": "003604"
}
},
"r3d100010183": {
"description": "These are the UK-AIR (Air Information Resource) webpages providing in-depth information on air quality and air pollution in the UK. A range of information is available, from the latest pollution levels, pollution forecast information, a data archive, and details of the various monitoring networks.",
"homepage": "https://uk-air.defra.gov.uk/data/",
"name": "UK-AIR",
"prefix": "r3d100010183",
"synonyms": [
"Air Information Resource",
"UK Air Information Resource"
],
"xrefs": {
"fairsharing": "FAIRsharing.54e74f"
}
},
"r3d100010184": {
"description": "Satellite-tracked drifting buoys (\"drifters\") collect measurements of upper ocean currents and sea surface temperatures (SST) around the world as part of the Global Drifter Program.\nDrifter locations are estimated from 16-20 satellite fixes per day, per drifter. The Drifter Data Assembly Center (DAC) at NOAA's Atlantic Oceanographic and Meteorological Laboratory (AOML) assembles these raw data, applies quality control procedures, and interpolates them via kriging to regular six-hour intervals. The raw observations and processed data are archived at AOML and at the Marine Environmental Data Services (MEDS) in Canada.\nTwo types of data are available: \"metadata\" contains deployment location and time, time of drogue (sea anchor) loss, date of final transmission, etc. for each drifter. \"Interpolated data\" contains the quality-controlled, interpolated drifter observations.",
"homepage": "https://www.aoml.noaa.gov/phod/gdp/data.php",
"name": "GDP Drifter Data",
"prefix": "r3d100010184",
"synonyms": [
"Data from Global Drifter Program (GDP)"
]
},
"r3d100010185": {
"description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from our data pages to other Arabidopsis resources.",
"homepage": "https://www.arabidopsis.org/",
"name": "The Arabidopsis Information Resource",
"prefix": "r3d100010185",
"synonyms": [
"TAIR"
],
"xrefs": {
"fairsharing": "FAIRsharing.4dqw0",
"nlx": "61477",
"omics": "01662",
"scr": "004618"
}
},
"r3d100010186": {
"description": "US Department of Energyβs Atmospheric Radiation Measurement (ARM) Data Center is a long-term archive and distribution facility for various ground-based, aerial and model data products in support of atmospheric and climate research. ARM facility currently operates over 400 instruments at various observatories (https://www.arm.gov/capabilities/observatories/). \nARM Data Center (ADC) Archive currently holds over 11,000 data products with a total holding of over 3 petabytes of data that dates back to 1993, these include data from instruments, value added products, model outputs, field campaign and PI contributed data. The data center archive also includes data collected by ARM from related program (e.g., external data such as NASA satellite).",
"homepage": "https://www.arm.gov/data",
"name": "ARM Data Center",
"prefix": "r3d100010186",
"synonyms": [
"Atmospheric Radiation Measurement Facility Data Center"
],
"xrefs": {
"fairsharing": "FAIRsharing.g84yb7"
}
},
"r3d100010187": {
"description": "BEA produces economic accounts statistics that enable government and business decision-makers, researchers, and the American public to follow and understand the performance of the Nation's economy. To do this, BEA collects source data, conducts research and analysis, develops and implements estimation methodologies, and disseminates statistics to the public.",
"homepage": "https://apps.bea.gov/itable/index.cfm",
"name": "US Department of Commerce, Bureau of Economic Analysis, Interactive Data",
"prefix": "r3d100010187",
"synonyms": [
"BEA Interactive Data"
]
},
"r3d100010188": {
"description": ">>>!!!<<< Sorry.we are no longer in operation >>>!!!<<< The Beta Cell Biology Consortium (BCBC) was a team science initiative that was established by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). It was initially funded in 2001 (RFA DK-01-014), and competitively continued both in 2005 (RFAs DK-01-17, DK-01-18) and in 2009 (RFA DK-09-011). Funding for the BCBC came to an end on August 1, 2015, and with it so did our ability to maintain active websites.!!!\nOne of the many goals of the BCBC was to develop and maintain databases of useful research resources. A total of 813 different scientific resources were generated and submitted by BCBC investigators over the 14 years it existed. Information pertaining to 495 selected resources, judged to be the most scientifically-useful, has been converted into a static catalog, as shown below. In addition, the metadata for these 495 resources have been transferred to dkNET in the form of RDF descriptors, and all genomics data have been deposited to either ArrayExpress or GEO.\nPlease direct questions or comments to the NIDDK Division of Diabetes, Endocrinology & Metabolic Diseases (DEM).",
"homepage": "http://www.betacell.org/resource/",
"name": "Beta Cell Biology Consortium Reagent and Data Resources",
"prefix": "r3d100010188",
"synonyms": [
"BCBC Reagent and Data Resources"
],
"xrefs": {
"nlx": "144143",
"scr": "005136"
}
},
"r3d100010189": {
"description": "The BGS is a data-rich organisation with over 400 datasets in its care; including environmental monitoring data, digital databases, physical collections (borehole core, rocks, minerals and fossils), records and archives. Our data is managed by the National Geoscience Data Centre.",
"homepage": "https://www.bgs.ac.uk/geological-data/national-geoscience-data-centre/",
"name": "National Geoscience Data Centre",
"prefix": "r3d100010189",
"synonyms": [
"NGDC"
],
"xrefs": {
"fairsharing": "fairsharing.drz6sx"
}
},
"r3d100010190": {
"description": "BIBB has a strong tradition of survey-based research. It initiates and realises the collection of individual and firm-level data on crucial positions and transitions in the education and labour market system. The BIBB-FDZ covers a variety of data deploying different units of analysis and temporal designs and focusing on various thematic issues. Standard access to well prepared firm- and individual-level data on the attainment and utilization of vocational education and training\nDocumentation of these data sets, i.e. a description of their central characteristics, main issues and variables, data collection, anonymisation, weighting and recoding etc.\nAdvisory service on data choice, data access and handling, research potential and scope and validity of the data.\nSupply of a range of data tools such as standard measures and classifications in the fields of education, occupations, industries and regions (if possible also including cross-national fields), formally anonymous data for remote data access, or references to publications with the data.",
"homepage": "https://www.bibb.de/de/53.php",
"name": "Forschungsdatenzentrum im Bundesinstitut fΓΌr Berufsbildung",
"prefix": "r3d100010190",
"synonyms": [
"Research Data Centre at BIBB",
"bibb fdz"
]
},
"r3d100010191": {
"description": "BioMagResBank (BMRB) is the publicly-accessible depository for NMR results from peptides, proteins, and nucleic acids recognized by the International Society of Magnetic Resonance and by the IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy. In addition, BMRB provides reference information and maintains a collection of NMR pulse sequences and computer software for biomolecular NMR",
"homepage": "https://bmrb.io/",
"name": "Biological Magnetic Resonance Data Bank",
"prefix": "r3d100010191",
"synonyms": [
"BMRB",
"BioMagResBank",
"Biological Magnetic Resonance Databank"
],
"xrefs": {
"fairsharing": "FAIRsharing.p06nme",
"nif": "0000-21058",
"omics": "02858",
"scr": "002296"
}
},
"r3d100010192": {
"description": "The British Oceanographic Data Centre (BODC) is a national facility for looking after and distributing data concerning the marine environmentWe deal with biological, chemical, physical and geophysical data, and our databases contain measurements of nearly 22,000 different variables. Many of our staff have direct experience of marine data collection and analysis. They work alongside information technology specialists to ensure that data are documented and stored for current and future use.",
"homepage": "https://www.bodc.ac.uk/",
"name": "British Oceanographic Data Centre",
"prefix": "r3d100010192",
"synonyms": [
"BODC"
],
"xrefs": {
"fairsharing": "FAIRsharing.tj9xv0",
"ror": "03102fn17"
}
},
"r3d100010193": {
"description": "The Biological Records Centre (BRC), established in 1964, is a national focus in the UK for terrestrial and freshwater species recording. BRC works closely with the voluntary recording community, principally through support of national recording schemes and societies. It provides an application, IRecord, for people to use to record and submit their own wildlife observations to the repository. Map and access datasets via the NBN Gateway, an Internet based data delivery service.",
"homepage": "https://www.brc.ac.uk/",
"name": "BRC",
"prefix": "r3d100010193",
"synonyms": [
"Biological Records Centre"
]
},
"r3d100010194": {
"description": "bugwood.org is the host website of the Center for Invasive Species and Ecosystem Health at the University of Georgia (Formerly: Bugwood Network). The Center aims to develop, consolidate and disseminate information and programmes focused on invasive species, forest health, natural resources and agricultural management through technology development, programmes implementation, training, applied research and public awareness at state, regional, national and international levels. The site gives details of its products (Bugwood Image Database; Early Detection and Distribution Mapping and Bugwoodwiki). Details of its projects, services and personnel are provided. Users can also access image databases on Forestry, Insects, IPM, Invasive Species, Forest Pests, weed and Bark Beetle.",
"homepage": "https://images.bugwood.org/",
"name": "Bugwood Image Database System",
"prefix": "r3d100010194"
},
"r3d100010195": {
"description": "The Cooperative Association for Internet Data Analysis (CAIDA) is a collaborative undertaking among organizations in the commercial, government, and research sectors aimed at promoting greater cooperation in the engineering and maintenance of a robust, scalable global Internet infrastructure.It is an independent analysis and research group with particular focus on: Collection, curation, analysis, visualization, dissemination of sets of the best available Internet data, providing macroscopic insight into the behavior of Internet infrastructure worldwide, improving the integrity of the field of Internet science, improving the integrity of operational Internet measurement and management, informing science, technology, and communications public policies.",
"homepage": "https://catalog.caida.org/",
"name": "CAIDA Data",
"prefix": "r3d100010195",
"synonyms": [
"The Cooperative Association for Internet Data Analysis"
]
},
"r3d100010196": {
"description": "CalSurv is a comprehensive information on West Nile virus, plague, malaria, Lyme disease, trench fever and other vectorborne diseases in California β where they are, where theyβve been, where they may be headed and what new diseases may be emerging.The CalSurv Web site serves as a portal or a single interface to all surveillance-related Web sites in California.",
"homepage": "https://vectorsurv.org/",
"name": "Vectorborne Disease Surveillance System",
"prefix": "r3d100010196",
"synonyms": [
"VectorSurv"
]
},
"r3d100010197": {
"description": "Established in 1965, the CSD is the worldβs repository for small-molecule organic and metal-organic crystal structures. Containing the results of over one million x-ray and neutron diffraction analyses this unique database of accurate 3D structures has become an essential resource to scientists around the world. The CSD records bibliographic, chemical and crystallographic information for:organic molecules, metal-organic compounds whose 3D structures have been determined using X-ray diffraction, neutron diffraction. The CSD records results of: single crystal studies, powder diffraction studies which yield 3D atomic coordinate data for at least all non-H atoms. In some cases the CCDC is unable to obtain coordinates, and incomplete entries are archived to the CSD. \nThe CSD includes crystal structure data arising from: publications in the open literature and Private Communications to the CSD (via direct data deposition). \nThe CSD contains directly deposited data that are not available anywhere else, known as CSD Communications.",
"homepage": "https://www.ccdc.cam.ac.uk/solutions/software/csd/",
"name": "The Cambridge Structural Database",
"prefix": "r3d100010197",
"synonyms": [
"CSD",
"Cambridge Crystallographic Data Centre"
],
"xrefs": {
"fairsharing": "FAIRsharing.vs7865",
"nif": "0000-00174",
"scr": "007310"
}
},
"r3d100010198": {
"description": "CDC.gov is the Centers for Disease Control and Prevention primary online communication channel. CDC.gov provides users with credible, reliable health information on Data and Statistics, Diseases and Conditions, Emergencies and Disasters, Environmental Health, Healthy Living, Injury, Violence and Safety,Life Stages and Populations, Travelers' Health, Workplace Safety and Health",
"homepage": "https://www.cdc.gov/DataStatistics/",
"name": "Centers for Disease Control and Prevention, Data & Statistics",
"prefix": "r3d100010198",
"synonyms": [
"CDC",
"Centros para el Control y la Prevencion de Enfermedades, Datos y estadΓsticas"
],
"xrefs": {
"nlx": "inv_1005036",
"scr": "012976"
}
},
"r3d100010199": {
"description": "The Environmental Information Data Centre (EIDC) is part of the Natural Environment Research Council's (NERC) Environmental Data Service and is hosted by the UK Centre for Ecology & Hydrology (UKCEH). We manage nationally-important datasets concerned with the terrestrial and freshwater sciences.",
"homepage": "https://eidc.ac.uk/",
"name": "Environmental Information Data Centre",
"prefix": "r3d100010199",
"synonyms": [
"EIDC"
],
"xrefs": {
"fairsharing": "FAIRsharing.f7hyf3"
}
},
"r3d100010200": {
"description": "The United States Census Bureau (officially the Bureau of the Census, as defined in Title 13 U.S.C. Β§ 11) is the government agency that is responsible for the United States Census. It also gathers other national demographic and economic data. As a part of the United States Department of Commerce, the Census Bureau serves as a leading source of data about America's people and economy. The most visible role of the Census Bureau is to perform the official decennial (every 10 years) count of people living in the U.S. The most important result is the reallocation of the number of seats each state is allowed in the House of Representatives, but the results also affect a range of government programs received by each state. The agency director is a political appointee selected by the President of the United States.",
"homepage": "https://www.census.gov/",
"name": "United States Census Bureau",
"prefix": "r3d100010200",
"synonyms": [
"U.S.Census Bureau"
],
"xrefs": {
"nlx": "151862",
"scr": "011587"
}
},
"r3d100010201": {
"description": "The Economics & Business Data Center (EBDC) is a combined platform for empirical research in business administration and economics of the LudwigβMaximilian University of Munich (LMU) and the Ifo Institute and aims at opening new fields for empirical research in business administration and economics.\nIn this regard, the EBDC provides innovative datasets of German companies, containing both survey data of the Ifo Institute as well as external balance sheet data. Therefore, the tasks of the EBDC also include the procurement and administration of data sources for research and teaching, the central provision, updating and documentation of external databases, as well as the acquisition of corresponding support tools.\nBeyond that, the EBDC serves as a contact and central coordinator on licensing economic firm-level datasets for LMUβs Munich School of Management and LMUβs Department of Economics and supports researchers and guests of the LMU and the Ifo Institute on site. In the future, it will also conduct academic conferences on research with company data.",
"homepage": "https://www.ifo.de/ebdc",
"name": "LMU-ifo Economics & Business Data Center",
"prefix": "r3d100010201",
"synonyms": [
"EBDC"
]
},
"r3d100010202": {
"description": "The CESSDA Data Catalogue contains the metadata of all data in the holdings of CESSDA service providers. It is a one-stop-shop for search and discovery, enabling effective access to European research data for researchers. Details of over 40, 000 data collections are listed. These are harvested from fifteen different CESSDA Service Providers.",
"homepage": "https://datacatalogue.cessda.eu/",
"name": "CESSDA Data Catalogue",
"prefix": "r3d100010202",
"synonyms": [
"CESSDA DC"
],
"xrefs": {
"fairsharing": "FAIRsharing.a12316"
}
},
"r3d100010203": {
"description": "The MPC is responsible for the designation of minor bodies in the solar system: minor planets; comets, in conjunction with the Central Bureau for Astronomical Telegrams (CBAT); and natural satellites (also in conjunction with CBAT). The MPC is also responsible for the efficient collection, computation, checking and dissemination of astrometric observations and orbits for minor planets and comets",
"homepage": "https://www.minorplanetcenter.net/",
"name": "IAU Minor Planet Center",
"prefix": "r3d100010203",
"synonyms": [
"MPC"
]
},
"r3d100010204": {
"description": "Chinaβs digital forestry information platform was constructed according to the criteria and index system of forest sustainable management. the relative social, economic, and politic data was considered and collected, the database represents not only the current forestry development, but also the social, politic, and economic situations.",
"homepage": "http://www.forestdata.cn/",
"name": "China Forestry Scientific Data Center",
"prefix": "r3d100010204",
"synonyms": [
"CFSDC"
]
},
"r3d100010205": {
"description": "ChemSpider is a free chemical structure database providing fast access to over 58 million structures, properties and associated information. By integrating and linking compounds from more than 400 data sources, ChemSpider enables researchers to discover the most comprehensive view of freely available chemical data from a single online search. It is owned by the Royal Society of Chemistry.\nChemSpider builds on the collected sources by adding additional properties, related information and links back to original data sources. ChemSpider offers text and structure searching to find compounds of interest and provides unique services to improve this data by curation and annotation and to integrate it with usersβ applications.",
"homepage": "https://www.chemspider.com/",
"name": "ChemSpider",
"prefix": "r3d100010205",
"synonyms": [
"Search and share chemistry"
],
"xrefs": {
"fairsharing": "FAIRsharing.96f3gm",
"nlx": "152101",
"scr": "006360"
}
},
"r3d100010206": {
"description": "ChemSynthesis is a freely accessible database of chemicals. This website contains substances with their synthesis references and physical properties such as melting point, boiling point and density. There are currently more than 40,000 compounds and more than 45,000 synthesis references in the database.",
"homepage": "https://www.chemsynthesis.com/",
"name": "ChemSynthesis",
"prefix": "r3d100010206",
"synonyms": [
"ChemSynthesis Chemical Database",
"Chemical Synthesis Database"
]
},
"r3d100010207": {
"description": "CIESIN is an interdisciplinary research and data center that provides access to a wide range of global data, associated documentation, and visualization and analysis tools to improve understanding of human interactions in the environment.",
"homepage": "https://www.ciesin.columbia.edu/data.html",
"name": "Center for International Earth Science Information Network",
"prefix": "r3d100010207",
"synonyms": [
"CIESIN"
]
},
"r3d100010208": {
"description": "The SuiteSparse Matrix Collection is a large and actively growing set of sparse matrices that arise in real applications. The Collection is widely used by the numerical linear algebra community for the development and performance evaluation of sparse matrix algorithms. It allows for robust and repeatable experiments. Its matrices cover a wide spectrum of domains, include those arising from problems with underlying 2D or 3D geometry (as structural engineering, computational fluid dynamics, model reduction, electromagnetics, semiconductor devices, thermodynamics, materials, acoustics, computer graphics/vision, robotics/kinematics, and other discretizations) and those that typically do not have such geometry (optimization, circuit simulation, economic and financial modeling, theoretical and quantum chemistry, chemical process simulation, mathematics and statistics, power networks, and other networks and graphs.",
"homepage": "https://sparse.tamu.edu",
"name": "The SuiteSparse Matrix Collection",
"prefix": "r3d100010208",
"synonyms": [
"The University of Florida Sparse Matrix Collection (formerly)",
"UFL, Sparse Matrix Collection"
]
},
"r3d100010209": {
"description": "CLARIN is a European Research Infrastructure for the Humanities and Social Sciences, focusing on language resources (data and tools). It is being implemented and constantly improved at leading institutions in a large and growing number of European countries, aiming at improving Europe's multi-linguality competence. CLARIN provides several services, such as access to language data and tools to analyze data, and offers to deposit research data, as well as direct access to knowledge about relevant topics in relation to (research on and with) language resources. The main tool is the 'Virtual Language Observatory' providing metadata and access to the different national CLARIN centers and their data.",
"homepage": "https://www.clarin.eu/",
"name": "CLARIN-ERIC",
"prefix": "r3d100010209",
"synonyms": [
"Common Language Resources and Technology Infrastructure - European Research Infrastructure Consortium",
"European Research Infrastructure for Language Resources and Technology"
]
},
"r3d100010210": {
"description": "Historical Climate Data (formerly: The National Climate Data and Information Archive - NCDC) is a web-based resource maintained by Environment and Climate Change Canada and the Meteorological Service of Canada. The site houses a number of statistical and data compilation and viewing tools. From the website, users can access historical climate data for Canadian locations and dates, view climate normals and averages, and climate summaries. A list of Canadian air stations and their meteorological reports and activities is also available, along with rainfall statistics for more than 500 locations across Canada. Users can also download the Canadian daily climate data for 2006/07. In addition, technical documentation is offered for data users to interpret the available data. Other documentation includes a catalogue of Canadian weather reporting stations, a glossary, and a calculation of the 1971 to 2000 climate normals for Canada. This resource carries authority and accuracy because it is maintained by a national government department and service. While the majority of the statistics are historical, the data is up-to-date and contains current and fairly recent climate data. This government resource is intended for an audience that has the ability and knowledge to interpret climatological data",
"homepage": "https://climate.weather.gc.ca/",
"name": "Historical Climate Data Canada",
"prefix": "r3d100010210",
"synonyms": [
"DonnΓ©es climatiques historiques",
"formerly: Archives nationales d'information et de donnΓ©es climatologiques",
"formerly: National Climate Data and Information Archive"
],
"xrefs": {
"fairsharing": "FAIRsharing.155022"
}
},
"r3d100010211": {
"description": "ClinicalTrials.gov is a website and online database of clinical research studies and information about their results. The purpose of ClinicalTrials.gov is to provide information about clinical research studies to the public, researchers, and health care professionals. The U.S. government does not review or approve the safety and science of all studies listed on this website.",
"homepage": "https://clinicaltrials.gov/",
"name": "ClinicalTrials.gov",
"prefix": "r3d100010211",
"synonyms": [
"A service of the U.S. National Institutes of Health"
],
"xrefs": {
"fairsharing": "FAIRsharing.mewhad",
"nif": "0000-21091",
"omics": "01792",
"scr": "002309"
}
},
"r3d100010212": {
"description": "The main goal of the CLUES-project is to provide constrained simulations of the local universe designed to be used as a numerical laboratory of the current paradigm. The simulations will be used for unprecedented analysis of the complex dark matter and gasdynamical processes which govern the formation of galaxies. The predictions of these experiments can be easily compared with the detailed observations of our galactic neighborhood.\nSome of the CLUES data is now publicly available via the CosmoSim database (https://www.cosmosim.org/). This includes AHF halo catalogues from the Box 64, WMAP3 resimulations of the Local Group with 40963 particle resolution.",
"homepage": "https://www.clues-project.org/cms/",
"name": "Constrained Local UniversE Simulations",
"prefix": "r3d100010212",
"synonyms": [
"CLUES"
]
},
"r3d100010213": {
"description": "Including data and software from CrystalEye is this a open-access collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers. At present, this is the most comprehensive open resource for small molecule structures, freely available to all scientists in Lithuania and worldwide. Including data and software from CrystalEye, developed by Nick Day at the department of Chemistry, the University of Cambridge under supervision of Peter Murray-Rust.",
"homepage": "https://www.crystallography.net/cod/",
"name": "Crystallography Open Database",
"prefix": "r3d100010213",
"synonyms": [
"COD"
],
"xrefs": {
"fairsharing": "FAIRsharing.7mm5g5",
"nlx": "149430",
"scr": "005874"
}
},
"r3d100010214": {
"description": "<<>>!!!>>>",
"homepage": "https://easy.dans.knaw.nl/ui/home",
"name": "EASY",
"prefix": "r3d100010214",
"synonyms": [
"DANS-EASY",
"Electronic Archiving System"
],
"xrefs": {
"fairsharing": "FAIRsharing.w55kwn"
}
},
"r3d100010215": {
"description": "The UK Data Archive, based at the University of Essex, is curator of the largest collection of digital data in the social sciences and humanities in the United Kingdom. With several thousand datasets relating to society, both historical and contemporary, our Archive is a vital resource for researchers, teachers and learners. We are an internationally acknowledged centre of expertise in the areas of acquiring, curating and providing access to data. \n\nWe are the lead partner in the UK Data Service (https://service.re3data.org/repository/r3d100010230) through which data users can browse collections online and register to analyse and download them. Open Data collections are available for anyone to use. The UK Data Archive is a Trusted Digital Repository (TDR) certified against the CoreTrustSeal (https://www.coretrustseal.org/) and certified against ISO27001 for Information Security (https://www.iso.org/isoiec-27001-information-security.html).",
"homepage": "https://www.data-archive.ac.uk/find",
"name": "UK Data Archive",
"prefix": "r3d100010215",
"synonyms": [
"SSRC Data Bank",
"Social Science Research Council Data Bank",
"The UK's largest collection of digital research data in the social sciences and humanities",
"UKDA"
],
"xrefs": {
"fairsharing": "FAIRsharing.qtm44s",
"ror": "03fknw408",
"scr": "014708"
}
},
"r3d100010216": {
"description": "4TU.ResearchData, previously known as 4TU.Centre for Research Data, is a research data repository dedicated to the science, engineering and design disciplines. It offers the knowledge, experience and the tools to manage, publish and find scientific research data in a standardized, secure and well-documented manner. 4TU.ResearchData provides the research community with:\nCustomised advice and support on research data management;\nA long-term repository for scientific research data;\nSupport for current research projects;\nTools to enhance reuse of research data.",
"homepage": "https://data.4tu.nl",
"name": "4TU.ResearchData | science.engineering.design",
"prefix": "r3d100010216",
"synonyms": [
"formerly: 4TU.Centre for Research Data"
],
"xrefs": {
"fairsharing": "FAIRsharing.zcveaz",
"nlx": "151952",
"ror": "02d887280",
"scr": "006295"
}
},
"r3d100010217": {
"description": "DataFirst's open research data repository, based at the University of Cape Town, gives open access to disaggregated administrative and survey data from African governments and research entities. DataFirst also operates a secure centre at the university to give researchers access to highly-disaggregated South African data.",
"homepage": "https://www.datafirst.uct.ac.za/",
"name": "DataFirst",
"prefix": "r3d100010217"
},
"r3d100010218": {
"description": "DDBJ; DNA Data Bank of Japan is the sole nucleotide sequence data bank in Asia, which is officially certified to collect nucleotide sequences from researchers and to issue the internationally recognized accession number to data submitters.Since we exchange the collected data with EMBL-Bank/EBI; European Bioinformatics Institute and GenBank/NCBI; National Center for Biotechnology Information on a daily basis, the three data banks share virtually the same data at any given time. The virtually unified database is called \"INSD; International Nucleotide Sequence Database DDBJ collects sequence data mainly from Japanese researchers, but of course accepts data and issue the accession number to researchers in any other countries.",
"homepage": "https://www.ddbj.nig.ac.jp/index-e.html",
"name": "DNA Data Bank of Japan",
"prefix": "r3d100010218",
"synonyms": [
"DDBJ"
],
"xrefs": {
"fairsharing": "FAIRsharing.k337f0",
"nif": "0000-02740",
"omics": "01644",
"scr": "002359"
}
},
"r3d100010219": {
"description": "The DSMZ is the most comprehensive biological resource center worldwide. Being one of the world's largest collections, the DSMZ currently comprises more than 73,700 items, including about 31,900 different bacterial and 6,600 fungal strains, 840 human and animal cell lines, 1,500 plant viruses and antisera, 700 bacteriophages and 19,000 different types of bacterial genomic DNA. All biological materials accepted in the DSMZ collection are subject to extensive quality control and physiological and molecular characterization by our central services. In addition, DSMZ provides an extensive documentation and detailed diagnostic information on the biological materials. The unprecedented diversity and quality management of its bioresources render the DSMZ an internationally renowned supplier for science, diagnostic laboratories, national reference centers, as well as industrial partners.",
"homepage": "https://www.dsmz.de/",
"name": "DSMZ",
"prefix": "r3d100010219",
"synonyms": [
"Deutsche Sammlung von Mikroorganismen und Zellkulturen",
"Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures",
"Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen"
],
"xrefs": {
"nif": "0000-10209",
"scr": "001711"
}
},
"r3d100010220": {
"description": "The World Wide Molecular Matrix (WWMM) is an electronic repository for unpublished chemical data. WWMM is an open collection of information of small molecules. The \"Matrix\" in WWMM is influenced by William Gibson's vision of a cyberinfrastructure where all knowledge is accessible. The WWMM is an experiment to see how far this can be taken for chemical compounds. Although much of the information for a given compound has been Openly published, very little is available in Open electronic collections. The WWMM is aimed at catalysing this approach for chemistry and the current collection is made available under the Budapest Open Archive Initiative (http://www.budapestopenaccessinitiative.org/read).",
"homepage": "https://www.dspace.cam.ac.uk/handle/1810/724",
"name": "WorldWideMolecularMatrix",
"prefix": "r3d100010220",
"synonyms": [
"Open collection of information on small molecules",
"WWMM"
]
},
"r3d100010221": {
"description": "The European Bioinformatics Institute (EBI) has a long-standing mission to collect, organise and make available databases for biomolecular science. It makes available a collection of databases along with tools to search, download and analyse their content. These databases include DNA and protein sequences and structures, genome annotation, gene expression information, molecular interactions and pathways. Connected to these are linking and descriptive data resources such as protein motifs, ontologies and many others. In many of these efforts, the EBI is a European node in global data-sharing agreements involving, for example, the USA and Japan.",
"homepage": "https://www.ebi.ac.uk/",
"name": "EMBL-EBI",
"prefix": "r3d100010221",
"synonyms": [
"EBI",
"European Molecular Biology Laboratory - European Bioinformatics Institute"
],
"xrefs": {
"nlx": "72386",
"scr": "004727"
}
},
"r3d100010222": {
"description": "ArrayExpress is one of the major international repositories for high-throughput functional genomics data from both microarray and high-throughput sequencing studies, many of which are supported by peer-reviewed publications. Data sets are submitted directly to ArrayExpress and curated by a team of specialist biological curators. In the past (until 2018) datasets from the NCBI Gene Expression Omnibus database were imported on a weekly basis. Data is collected to MIAME and MINSEQE standards.",
"homepage": "https://www.ebi.ac.uk/biostudies/arrayexpress",
"name": "Array Express",
"prefix": "r3d100010222",
"synonyms": [
"functional genomics data"
],
"xrefs": {
"fairsharing": "FAIRsharing.6k0kwd",
"miriam": "00000036",
"nif": "0000-30123",
"omics": "01023",
"scr": "002964"
}
},
"r3d100010223": {
"description": "The Expression Atlas provides information on gene expression patterns under different biological conditions such as a gene knock out, a plant treated with a compound, or in a particular organism part or cell. It includes both microarray and RNA-seq data. The data is re-analysed in-house to detect interesting expression patterns under the conditions of the original experiment. There are two components to the Expression Atlas, the Baseline Atlas and the Differential Atlas.\nThe Baseline Atlas displays information about which gene products are present (and at what abundance) in \"normal\" conditions (e.g. tissue, cell type). It aims to answer questions such as \"which genes are specifically expressed in human kidney?\". This component of the Expression Atlas consists of highly-curated and quality-checked RNA-seq experiments from ArrayExpress. It has data for many different animal and plant species. New experiments are added as they become available.\nThe Differential Atlas allows users to identify genes that are up- or down-regulated in a wide variety of different experimental conditions such as yeast mutants, cadmium treated plants, cystic fibrosis or the effect on gene expression of mind-body practice. Both microarray and RNA-seq experiments are included in the Differential Atlas. Experiments are selected from ArrayExpress and groups of samples are manually identified for comparison e.g. those with wild type genotype compared to those with a gene knock out. Each experiment is processed through our in-house differential expression statistical analysis pipeline to identify genes with a high probability of differential expression.",
"homepage": "https://www.ebi.ac.uk/gxa/home",
"name": "Expression Atlas",
"prefix": "r3d100010223",
"synonyms": [
"Gene Expression Atlas"
],
"xrefs": {
"fairsharing": "FAIRsharing.f5zx00",
"nif": "0000-06686",
"omics": "03311",
"scr": "007989"
}
},
"r3d100010224": {
"description": "The National Atmospheric Chemistry Database (NAtChem) is a data archival and analysis facility operated by the Science and Technology Branch of Environment and Climate Change Canada. The purpose of the NAtChem database is to enhance atmospheric research through the archival and analysis of North American air and precipitation chemistry data. Such research includes investigations into the chemical nature of the atmosphere, atmospheric processes, spatial and temporal patterns, source-receptor relationships and long range transport of air pollutants.\nThe NAtChem Database contains air and precipitation chemistry data from many major regional-scale networks in North America. To contribute to NAtChem, networks must operate for a period of at least two years, must have wide area coverage, and must have regionally-representative sites (rural and background).",
"homepage": "https://www.canada.ca/en/environment-climate-change/services/air-pollution/monitoring-networks-data/national-atmospheric-chemistry-database.html",
"name": "The Canadian National Atmospheric Chemistry Database",
"prefix": "r3d100010224",
"synonyms": [
"La base de donnΓ©es nationales sur la chimie atmosphΓ©rique",
"NAtChem",
"The Canadian National Atmospheric Chemistry Database and Analysis System"
]
},
"r3d100010225": {
"description": "HYDAT is the archival database that contains all water information collected through the National Hydrometric Program. These data include: daily and monthly mean flow, water level and sediment concentration for over 2500 active and 5500 discontinued hydrometric monitoring station across Canada. HYDEX is a relational database that contains inventory information on the various streamflow, water level, and sediment stations (both active and discontinued) in Canada. This database contains information about the stations themselves, such as location, equipment, and type(s) of data collected.",
"homepage": "https://www.canada.ca/en/environment-climate-change/services/water-overview/quantity/monitoring/survey/data-products-services/national-archive-hydat.html",
"name": "HYDAT",
"prefix": "r3d100010225",
"synonyms": [
"HYDEX",
"National Water Data Archive"
]
},
"r3d100010226": {
"description": "The Alternative Fuels Data Center (AFDC) is a comprehensive clearinghouse of information about advanced transportation technologies. The AFDC offers transportation decision makers unbiased information, data, and tools related to the deployment of alternative fuels and advanced vehicles.\nThe AFDC launched in 1991 in response to the Alternative Motor Fuels Act of 1988 and the Clean Air Act Amendments of 1990. It originally served as a repository for alternative fuel performance data. The AFDC has since evolved to offer a broad array of information resources that support efforts to reduce petroleum use in transportation.\nThe AFDC serves Clean Cities stakeholders, fleets regulated by the Energy Policy Act, businesses, policymakers, government agencies, and the general public.",
"homepage": "https://afdc.energy.gov/",
"name": "Alternative Fuels Data Center",
"prefix": "r3d100010226",
"synonyms": [
"AFDC",
"EERE Alternative Fuels Data Center"
],
"xrefs": {
"fairsharing": "FAIRsharing.eef384"
}
},
"r3d100010227": {
"description": "The U.S. Energy Information Administration (EIA) collects, analyzes, and disseminates independent and impartial energy information to promote sound policymaking, efficient markets, and public understanding of energy and its interaction with the economy and the environment.",
"homepage": "https://www.eia.gov/",
"name": "U.S. Energy Information Administration",
"prefix": "r3d100010227",
"synonyms": [
"EIA",
"Independent Statistics & Analysis"
],
"xrefs": {
"biodbcore": "001635",
"fairsharing.legacy": "3125"
}
},
"r3d100010228": {
"description": "The Ensembl project produces genome databases for vertebrates and other eukaryotic species. Ensembl is a joint project between the European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Institute (WTSI) to develop a software system that produces and maintains automatic annotation on selected genomes.The Ensembl project was started in 1999, some years before the draft human genome was completed. Even at that early stage it was clear that manual annotation of 3 billion base pairs of sequence would not be able to offer researchers timely access to the latest data. The goal of Ensembl was therefore to automatically annotate the genome, integrate this annotation with other available biological data and make all this publicly available via the web. Since the website's launch in July 2000, many more genomes have been added to Ensembl and the range of available data has also expanded to include comparative genomics, variation and regulatory data. Ensembl is a joint project between European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL), and the Wellcome Trust Sanger Institute (WTSI). Both institutes are located on the Wellcome Trust Genome Campus in Hinxton, south of the city of Cambridge, United Kingdom.",
"homepage": "https://www.ensembl.org/index.html",
"name": "Ensembl",
"prefix": "r3d100010228",
"synonyms": [
"e!"
],
"xrefs": {
"fairsharing": "FAIRsharing.fx0mw7",
"miriam": "00100011",
"nif": "0000-21145",
"omics": "01647",
"scr": "002344"
}
},
"r3d100010229": {
"description": "Our knowledge of the many life-forms on Earth - of animals, plants, fungi, protists and bacteria - is scattered around the world in books, journals, databases, websites, specimen collections, and in the minds of people everywhere. Imagine what it would mean if this information could be gathered together and made available to everyone β anywhere β at a momentβs notice. This dream is becoming a reality through the Encyclopedia of Life.",
"homepage": "https://eol.org/",
"name": "Encyclopedia of Life",
"prefix": "r3d100010229",
"synonyms": [
"Global access to knowledge about life on earth",
"eol"
],
"xrefs": {
"fairsharing": "FAIRsharing.3J6NYn",
"nlx": "149476",
"scr": "005905"
}
},
"r3d100010230": {
"description": "The UK Data Service is a national data service funded by the ESRC to provide research access to the UKβs largest collection of social, economic and population data including UK government-sponsored surveys, cross-national surveys, longitudinal studies, UK census data, international aggregate, business data, and qualitative data.\nDesigned to meet the data needs of researchers, students and teachers from all sectors, including academia, central and local government, charities and foundations, independent research centres, think tanks, business consultants and analysts, communities and the commercial sector, the UK Data Service provides access to high-quality social and economic data; support for policy-relevant research; guidance and training for the development of skills in data use, and the development of best practice in digital preservation and sharing.\nData users can browse collections online and register to analyse and download them. Open Data collections are available for anyone to use.\nKey partners include JISC, the University of Manchester, University of Southampton, University of Leeds, University of Edinburgh and University College London (UCL). The lead partner is the UK Data Archive (https://service.re3data.org/repository/r3d100010215) based at the University of Essex, a Trusted Digital Repository (TDR) certified against the CoreTrustSeal (https://www.coretrustseal.org/) and certified against ISO27001 for Information Security (https://www.iso.org/standard/27001).\nThe UK Data Service replaces the earlier ESRC investments of the Economic and Social Data Service (ESDS), the Secure Data Service (SDS), the Survey Question Bank and elements of the ESRC Census Programme.",
"homepage": "https://www.ukdataservice.ac.uk/",
"name": "UK Data Service",
"prefix": "r3d100010230",
"synonyms": [
"UKDS"
],
"xrefs": {
"fairsharing": "FAIRsharing.1ky0cs",
"ror": "0468x4e75"
}
},
"r3d100010232": {
"description": "EUMETSAT's primary objective is to establish, maintain and exploit European systems of operational meteorological satellites. EUMETSAT is responsible for the launch and operation of the satellites and for delivering satellite data to end-users as well as contributing to the operational monitoring of climate and the detection of global climate changes. The EUMETSAT Product Navigator is the catalogue for all EUMETSAT data and products.",
"homepage": "https://user.eumetsat.int/catalogue",
"name": "Eumetsat",
"prefix": "r3d100010232",
"synonyms": [
"EUMETSAT Product Navigator",
"European Organisation for the Exploitation of Meteorological Satellites",
"Monitoring weather and climate from space"
],
"xrefs": {
"fairsharing": "FAIRsharing.a2e209"
}
},
"r3d100010233": {
"description": "The European Social Survey (the ESS) is a biennial multi-country survey covering over 30 nations. The first round was fielded in 2002/2003, the fifth in 2010/2011. The questionnaire includes two main sections, each consisting of approximately 120 items; a 'core' module which remains relatively constant from round to round, plus two or more 'rotating' modules, repeated at intervals. The core module aims to monitor change and continuity in a wide range of social variables, including media use; social and public trust; political interest and participation; socio-political orientations; governance and efficacy; moral; political and social values; social exclusion, national, ethnic and religious allegiances; well-being; health and security; human values; demographics and socio-economics",
"homepage": "https://www.europeansocialsurvey.org/",
"name": "European Social Survey",
"prefix": "r3d100010233",
"synonyms": [
"ESS Data",
"ESS Data archive"
]
},
"r3d100010234": {
"description": ">>>!!!<<< eyemoviepedia.com was shut down in the course of 2021 https://www.zbmed.de/en/research/completed-projects/eyemoviepedia/ >>>!!!<<<\nThe eyeMoviePedia videos moved successively to be found on PUBLISSO-Repository for Life Sciences (FRL) in the future. https://www.re3data.org/repository/r3d100013523\nTo view the new eyeMoviePedia collection see: https://repository.publisso.de/resource?query[0][term]=%22https%3A%2F%2Fd-nb.info%2Fgnd%2F1223212661%22",
"homepage": "http://www.eyemoviepedia.com/",
"name": "eyeMoviePedia",
"prefix": "r3d100010234",
"xrefs": {
"nlx": "157655",
"scr": "003541"
}
},
"r3d100010235": {
"description": "Research Data Centre Education is a service offered by the German Institute for International Educational Research, for the purpose of a comprehensive and permanent documentation of empirical educational research studies. This service offers a central access point to describing information on studies, assessment instruments used and assessed research data, as well as publications.",
"homepage": "https://www.fachportal-paedagogik.de/",
"name": "FACHPORTALpΓ€dagogik.DE",
"prefix": "r3d100010235",
"synonyms": [
"the German Education Portal"
]
},
"r3d100010236": {
"description": "LIAG's Geophysics Information System (FIS GP) serves for the storage and supply of geophysical measurements and evaluations of LIAG and its partners. \nThe architecture of the overall system intends a subdivision into an universal part (superstructure) and into several subsystems dedicated to geophysical methods (borehole geophysics, gravimetry, magnetics, 1D/2D geoelectrics, underground temperatures, seismics, VSP, helicopter geophysics and rock physics. The building of more subsystems is planned.",
"homepage": "https://www.fis-geophysik.de/",
"name": "Fachinformationssystem Geophysik",
"prefix": "r3d100010236",
"synonyms": [
"FIS GP",
"Geophysics Information System"
]
},
"r3d100010237": {
"description": "More than 25 years ago FIZ Karlsruhe started depositing crystal structure data linked to publications in German journals. At that time it was irrelevant whether the deposited structures were organic or inorganic. Today FIZ Karlsruhe is responsible for storing the structure data of inorganic compounds. Organic structure data are stored by the Cambridge Crystallographic Data Center.\nNowadays many publishers inform their authors that in parallel to a publication in a scientific journal, crystal structure data should also be stored in the Crystal Structure Depot at FIZ Karlsruhe. A CSD number will be assigned to the data for later reference in the publication. The data can then be ordered from the Crystal Structure Depot at FIZ Karlsruhe.",
"homepage": "https://www.fiz-karlsruhe.de/en/produkte-und-dienstleistungen/das-kristallstrukturdepot",
"name": "Das Kristallstrukturdepot",
"prefix": "r3d100010237",
"synonyms": [
"CSD",
"Crystal Structure Depot",
"Kristallstrukturdepot"
]
},
"r3d100010238": {
"description": "Here you will find information about the diversity of plants, the distribution and ecology as well as the history of the plant species in Frankfurt.",
"homepage": "http://www.flora-frankfurt.de/",
"name": "Flora von Frankfurt am Main",
"prefix": "r3d100010238",
"synonyms": [
"Flora-Frankfurt"
]
},
"r3d100010239": {
"description": "Forestry Images provides an accessible and easy to use archive of high quality images related to forest health and silviculture",
"homepage": "https://www.forestryimages.org/",
"name": "Forestry Images",
"prefix": "r3d100010239",
"synonyms": [
"Forestryimages"
]
},
"r3d100010241": {
"description": "RESΒ³T is a digitized version of a thermodynamic sorption database as required for the parametrization of Surface Complexation Models (SCM). It is mineral-specific and can therefore also be used for additive models of more complex solid phases such as rocks or soils. A user interface helps to access selected mineral and sorption data, to convert parameter units, to extract internally consistent data sets for sorption modeling. Data records comprise of mineral properties, specific surface area values, characteristics of surface binding sites and their protolysis, sorption ligand information, and surface complexation reactions",
"homepage": "https://www.hzdr.de/db/res3t.login",
"name": "RESΒ³T",
"prefix": "r3d100010241",
"synonyms": [
"RES[drei]T",
"RES[three]T",
"Rossendorf Expert System for Surface and Sorption Thermodynamics"
]
},
"r3d100010243": {
"description": "It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. The Browser is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of the data at many levels.",
"homepage": "https://genome.ucsc.edu/",
"name": "UCSC Genome Browser",
"prefix": "r3d100010243",
"synonyms": [
"UCSC Genome Bioinformatics",
"University of California Santa Cruz Genome Bioinformatics"
],
"xrefs": {
"fairsharing": "FAIRsharing.s22qdj",
"nif": "0000-03603",
"omics": "00926",
"scr": "005780"
}
},
"r3d100010245": {
"description": "The GeoNames geographical database covers all countries and contains over eight million placenames that are available for download free of charge.",
"homepage": "https://www.geonames.org/",
"name": "GeoNames",
"prefix": "r3d100010245",
"xrefs": {
"fairsharing": "FAIRsharing.56a0Uj"
}
},
"r3d100010246": {
"description": "<<>>!!!>>>- GEON is an open collaborative project that is developing cyberinfrastructure for integration of 3 and 4 dimensional earth science data. GEON will develop services for data integration and model integration, and associated model execution and visualization. Mid-Atlantic test bed will focus on tectonothermal, paleogeographic, and biotic history from the late-Proterozoicto mid-Paleozoic. Rockies test bed will focus on integration of data with dynamic models, to better understand deformation history. GEON will develop the most comprehensive regional datasets in test bed areas.",
"homepage": "http://www.geongrid.org/",
"name": "GEON",
"prefix": "r3d100010246",
"synonyms": [
"GEONGRID",
"Global Earth Observation Network"
]
},
"r3d100010247": {
"description": "The GSA Data Repository is an open file in which authors of articles in our journals can place information that supplements and expands on their article. These supplements will not appear in print but may be obtained from GSA.",
"homepage": "https://gsapubs.figshare.com/",
"name": "GSA Data Repository",
"prefix": "r3d100010247",
"synonyms": [
"Geological Society of America Data Repository"
]
},
"r3d100010248": {
"description": "GermOnline 4.0 is a cross-species database gateway focusing on high-throughput expression data relevant for germline development, the meiotic cell cycle and mitosis in healthy versus malignant cells. The portal provides access to the Saccharomyces Genomics Viewer (SGV) which facilitates online interpretation of complex data from experiments with high-density oligonucleotide tiling microarrays that cover the entire yeast genome.",
"homepage": "http://www.germonline.org/index.html",
"name": "GermOnline",
"prefix": "r3d100010248",
"xrefs": {
"fairsharing": "FAIRsharing.vk3v6s",
"issn": "2427-1748",
"nif": "0000-02906",
"omics": "02892",
"scr": "002807"
}
},
"r3d100010249": {
"description": "The German General Social Survey (ALLBUS) collects up-to-date data on attitudes, behavior, and social structure in Germany. Every two years since 1980 a representative cross section of the population is surveyed using both constant and variable questions. The ALLBUS data become available to interested parties for research and teaching as soon as they are processed and documented.",
"homepage": "https://www.gesis.org/en/allbus/allbus-home",
"name": "ALLBUS",
"prefix": "r3d100010249",
"synonyms": [
"Die Allgemeine BevΓΆlkerungsumfrage der Sozialwissenschaften",
"FDZ ALLBUS",
"German General Social Survey"
],
"xrefs": {
"nlx": "157750",
"scr": "003588"
}
},
"r3d100010250": {
"description": "HISTAT (Historical Statistics)provides data from studies of population, economic and social history as well as the historical Statistics under a single user interface to be made available online. HISTAT offers a variety of time series, Historical Statistics primarily from Germany, partly down to the 16 . century; the database is structured theme-and study-oriented. Studies are listed by subject area and can be individually selected. using an alphabetical list of authors of individual studies can also be selected. Moreover, a study on cross Keyword is offered. HISTAT provides information and research opportunities to both study level as well as at time series level. It offered a thesaurus-based meta-search for words, authors and studies in the study descriptions, the data (time series definitions) and the sources.",
"homepage": "https://histat.safe-frankfurt.de/index.php/en/index",
"name": "HISTAT",
"prefix": "r3d100010250",
"synonyms": [
"Historical Time Series",
"Zeitreihen zur Historischen Statistik"
]
},
"r3d100010251": {
"description": "<<>>!!!>>>",
"homepage": "https://search.gesis.org",
"name": "GESIS Suche",
"prefix": "r3d100010251",
"synonyms": [
"DBK",
"GESIS Data Catalogue DBK",
"GESIS Datenbestandskatalog DBK",
"GESIS search"
]
},
"r3d100010252": {
"description": "The GHDx is our user-friendly and searchable data catalog for global health, demographic, and other health-related datasets. It provides detailed information about datasets ranging from censuses and surveys to health records and vital statistics, globally. It also serves as a platform for data owners to share their data with the public. The GDB Compare visualization, which allows the user to see rate of change in disease incidence, globally or by country, by age or across all ages, is especially powerful as a tool. Be sure to try adding a bottom chart, like the map, to augment the treemap that loads by default in the top chart.",
"homepage": "https://ghdx.healthdata.org/",
"name": "Global Health Data Exchange",
"prefix": "r3d100010252",
"synonyms": [
"Discover the World's Health Data",
"GHDx"
]
},
"r3d100010253": {
"description": "<<>>!!!>>> Go-Geo is an online resource discovery tool which allows for the identification and retrieval of records describing the content, quality, condition and other characteristics of geospatial data that exist with UK tertiary education and beyond. The portal supports geospatial searching by interactive map, grid co-ordinates and place name, as well as the more traditional topic or keyword forms of searching. The portal is a key component of the UK academic Spatial Data Infrastructure.",
"homepage": "http://www.gogeo.ac.uk/gogeo/",
"name": "GO-GEO",
"prefix": "r3d100010253"
},
"r3d100010254": {
"description": "The global data compilation consisting of ca. 60,000 data points may be downloaded in csv/xml format. This compilation does not contain the descriptive codes relating to metadata that were included in the previous compilations. Users are advised to consult the references and make their own interpretations as to the quality of the data.",
"homepage": "https://www.ihfc-iugg.org/products/global-heat-flow-database",
"name": "The Global Heat Flow Database of the International Heat Flow Commission",
"prefix": "r3d100010254",
"synonyms": [
"International Heat-flow Database"
]
},
"r3d100010255": {
"description": "ICPSR maintains a data archive of more than 250,000 files of research in the social and behavioral sciences. It hosts 21 specialized collections of data in education, aging, criminal justice, substance abuse, terrorism, and other fields.\nICPSR advances and expands social and behavioral research, acting as a global leader in data stewardship and providing rich data resources and responsive educational opportunities for present and future generations.",
"homepage": "https://www.icpsr.umich.edu/web/pages/",
"name": "Inter-university Consortium for Political and Social Research",
"prefix": "r3d100010255",
"synonyms": [
"ICPSR data archive"
],
"xrefs": {
"fairsharing": "FAIRsharing.y0df7m",
"nif": "0000-00615",
"scr": "003194"
}
},
"r3d100010256": {
"description": "Data Sharing for Demographic Research (DSDR) aims to serve the demographic community by archiving, preserving, and and disseminating data relevant for population studies",
"homepage": "https://www.icpsr.umich.edu/web/pages/DSDR/index.html",
"name": "Data Sharing for Demographic Research",
"prefix": "r3d100010256",
"synonyms": [
"A data archive for demography and population sciences",
"DSDR"
],
"xrefs": {
"fairsharing": "FAIRsharing.v4mara",
"scr": "016310"
}
},
"r3d100010257": {
"description": "The Health and Medical Care Archive (HMCA) is the data archive of the Robert Wood Johnson Foundation (RWJF), the largest philanthropy devoted exclusively to health and health care in the United States. Operated by the Inter-university Consortium for Political and Social Research (ICPSR) at the University of Michigan, HMCA preserves and disseminates data collected by selected research projects funded by the Foundation and facilitates secondary analyses of the data. Our goal is to increase understanding of health and health care in the United States through secondary analysis of RWJF-supported data collections",
"homepage": "https://www.icpsr.umich.edu/web/pages/HMCA/index.html",
"name": "Health and Medical Care Archive",
"prefix": "r3d100010257",
"synonyms": [
"Data archive of the RWJF",
"Data archive of the Robert Wood Johnson Foundation",
"HMCA"
],
"xrefs": {
"fairsharing": "FAIRsharing.szj2xw"
}
},
"r3d100010259": {
"description": "NACDA acquires and preserves data relevant to gerontological research, processing as needed to promote effective research use, disseminates them to researchers, and facilitates their use. By preserving and making available the largest library of electronic data on aging in the United States, NACDA offers opportunities for secondary analysis on major issues of scientific and policy relevance",
"homepage": "https://www.icpsr.umich.edu/web/pages/NACDA/index.html",
"name": "National Archive of Computerized Data on Aging",
"prefix": "r3d100010259",
"synonyms": [
"NACDA"
],
"xrefs": {
"fairsharing": "FAIRsharing.xhzfk0",
"nlx": "149438",
"scr": "005876"
}
},
"r3d100010260": {
"description": "The central mission of the NACJD is to facilitate and encourage research in the criminal justice field by sharing data resources. Specific goals include providing computer-readable data for the quantitative study of crime and the criminal justice system through the development of a central data archive, supplying technical assistance in the selection of data collections and computer hardware and software for data analysis, and training in quantitative methods of social science research to facilitate secondary analysis of criminal justice data",
"homepage": "https://www.icpsr.umich.edu/web/pages/NACJD/index.html",
"name": "National Archive of Criminal Justice Data",
"prefix": "r3d100010260",
"synonyms": [
"NACJD",
"The source for data on crime and justice"
],
"xrefs": {
"fairsharing": "FAIRsharing.4wjhCf"
}
},
"r3d100010261": {
"description": "NAHDAP acquires, preserves and disseminates data relevant to drug addiction and HIV research. By preserving and making available an easily accessible library of electronic data on drug addiction and HIV infection in the United States, NAHDAP offers scholars the opportunity to conduct secondary analysis on major issues of social and behavioral sciences and public policy",
"homepage": "https://www.icpsr.umich.edu/web/pages/NAHDAP/index.html",
"name": "National Addiction & HIV Data Archive Program",
"prefix": "r3d100010261",
"synonyms": [
"NAHDAP"
],
"xrefs": {
"nif": "0000-06713",
"scr": "000636"
}
},
"r3d100010262": {
"description": "The changing demographic composition has expanded the scope of the U.S. racial and ethnic mosaic. As a result, interest and research on race and ethnicity has become more complex and expansive. RCMD seeks to assist in the public dissemination and preservation of quality data to generate more \"good science\" for years to come. Finally, RCMD wants to be part of an interactive community of persons interested and be involved in minority related issues/investigations in order to make possible the broadest scope of research endeavors and examinations.",
"homepage": "https://www.icpsr.umich.edu/web/pages/RCMD/index.html",
"name": "Resource Center for Minority Data",
"prefix": "r3d100010262",
"synonyms": [
"RCMD"
]
},
"r3d100010263": {
"description": "The Substance Abuse and Mental Health Data Archive (SAMHDA) is an initiative funded under contract HHSS283201500001C with the Center for Behavioral Health Statistics and Quality (CBHSQ), Substance Abuse and Mental Health Services Administration (SAMHSA), U.S. Department of Health and Human Services (HHS). CBHSQ has primary responsibility for the collection, analysis, and dissemination of SAMHSA's behavioral health data. Public use files and restricted use files are provided.\nCBHSQ promotes the access and use of the nation's substance abuse and mental health data through SAMHDA. SAMHDA provides public-use data files, file documentation, and access to restricted-use data files to support a better understanding of this critical area of public health.",
"homepage": "https://www.datafiles.samhsa.gov/",
"name": "Substance Abuse and Mental Health Data Archive",
"prefix": "r3d100010263",
"synonyms": [
"SAMHDA"
],
"xrefs": {
"nif": "0000-00618",
"scr": "007002"
}
},
"r3d100010264": {
"description": "The project is set up in order to improve the infrastructure for text-based linguistic research and development by building a huge, automatically annotated German text corpus and the corresponding tools for corpus annotation and exploitation. DeReKo constitutes the largest linguistically motivated collection of contemporary German texts, contains fictional, scientific and newspaper texts, as well as several other text types, contains only licenced texts, is encoded with rich meta-textual information, is fully annotated morphosyntactically (three concurrent annotations), is continually expanded, with a focus on size and stratification of data, may be analyzed free of charge via the query system COSMAS II, serves as a 'primordial sample' from which users may draw specialized sub-samples (socalled 'virtual corpora') to represent the language domain they wish to investigate.\n!!! Access to data of Das Deutsche Referenzkorpus is also provided by: IDS Repository https://www.re3data.org/repository/r3d100010382 !!!",
"homepage": "https://www.ids-mannheim.de/digspra/kl/projekte/korpora/",
"name": "Das Deutsche Referenzkorpus",
"prefix": "r3d100010264",
"synonyms": [
"Das Portal fΓΌr die Korpusrecherche in Textkorpora des Instituts fΓΌr Deutsche Sprache",
"DeReKo",
"The Mannheim German Reference Corpus"
]
},
"r3d100010266": {
"description": "MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. The projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, MouseMine Project, MouseCyc Project at MGI",
"homepage": "https://www.informatics.jax.org/",
"name": "Mouse Genome Informatics",
"prefix": "r3d100010266",
"synonyms": [
"MGI"
],
"xrefs": {
"fairsharing": "FAIRsharing.fcwyhz",
"nif": "0000-00096",
"omics": "01656",
"scr": "006460"
}
},
"r3d100010267": {
"description": "The International Ocean Discovery Program (IODP) is an international marine research collaboration that explores Earth's history and dynamics using ocean-going research platforms to recover data recorded in seafloor sediments and rocks and to monitor subseafloor environments. IODP depends on facilities funded by three platform providers with financial contributions from five additional partner agencies. Together, these entities represent 26 nations whose scientists are selected to staff IODP research expeditions conducted throughout the world's oceans.\nIODP expeditions are developed from hypothesis-driven science proposals aligned with the program's science plan Illuminating Earth's Past, Present, and Future. The science plan identifies 14 challenge questions in the four areas of climate change, deep life, planetary dynamics, and geohazards. Until 2013 under the name: International Ocean Drilling Program.",
"homepage": "https://www.iodp.org/",
"name": "International Ocean Discovery Program",
"prefix": "r3d100010267",
"synonyms": [
"Exploring the earth under the sea",
"IODP",
"Integrated Ocean Drilling Program"
]
},
"r3d100010268": {
"description": "IRIS offers free and open access to a comprehensive data store of raw geophysical time-series data collected from a large variety of sensors, courtesy of a vast array of US and International scientific networks, including seismometers (permanent and temporary), tilt and strain meters, infrasound, temperature, atmospheric pressure and gravimeters, to support basic research aimed at imaging the Earth's interior.",
"homepage": "https://www.iris.edu/hq/",
"name": "Incorporated Research Institutions for Seismology",
"prefix": "r3d100010268",
"synonyms": [
"IRIS"
],
"xrefs": {
"fairsharing": "FAIRsharing.x9rqf7",
"nlx": "154710",
"ror": "05xkn9s74",
"scr": "002201"
}
},
"r3d100010269": {
"description": "JCVI is a world leader in genomic research. The Institute studies the societal implications of genomics in addition to genomics itself. The Institute's research involves genomic medicine; environmental genomic analysis; clean energy; synthetic biology; and ethics, law, and economics.",
"homepage": "https://www.jcvi.org//",
"name": "J. Craig Venter Institute",
"prefix": "r3d100010269",
"synonyms": [
"JCVI"
],
"xrefs": {
"nlx": "42542",
"scr": "011269"
}
},
"r3d100010270": {
"description": "As cultural competence center for the region, the Landesarchiv serves as the repository for records of cultural and historical value and assures the access of archives in Baden-Wuerttemberg as part of the cultural heritage. It identifies, collects, and preserves state records and makes them available to all those who are interested in historical records.\nThe Landesarchiv houses archival collections ranging from deeds from the Middle Ages to digital sources of our time (databases, e-mails, internet pages). The Landesarchiv has already been providing diversified access to archival collections via internet and is actively working on research and presentation of the history of Southwest Germany.\nThe archival collections of the Landesarchiv convey the cultural and historical diversity in Southwest Germany. Each holding is unique and characterizes the distinctive history of the people and the region.\nThis makes the Landesarchiv an irreplaceable reservoir of knowledge and experience with remarkable quantitative dimensions: The Landesarchiv houses about 146 shelf kilometers of documents and books, 310 thousand charters as well as 350 thousand maps and plans completed with photographs and audio-visual records. Electronic data are stored in the digital stack of the Landesarchiv.",
"homepage": "https://www.landesarchiv-bw.de/",
"name": "State Archives of Baden-WΓΌrttemberg",
"prefix": "r3d100010270",
"synonyms": [
"Landesarchiv Baden-WΓΌrttemberg",
"la-bw"
]
},
"r3d100010271": {
"description": "OLAC, the Open Language Archives Community, is an international partnership of institutions and individuals who are creating a worldwide virtual library of language resources by: (i) developing consensus on best current practice for the digital archiving of language resources, and (ii) developing a network of interoperating repositories and services for housing and accessing such resources.\nThe OLAC system has 2016 been integrated with the Linguistic Linked Open Data Cloud.",
"homepage": "http://www.language-archives.org/",
"name": "OLAC",
"prefix": "r3d100010271",
"synonyms": [
"Open Language Archives Community"
]
},
"r3d100010272": {
"description": "We preserve environmental data for open and reproducible science, to promote synthesis across space and time, and to aid in the assessment of environmental change and its consequences.",
"homepage": "https://portal.edirepository.org/nis/home.jsp",
"name": "Environmental Data Initiative Repository",
"prefix": "r3d100010272",
"synonyms": [
"EDI Data Portal",
"formerly: The Long Term Ecological Research Repository"
],
"xrefs": {
"fairsharing": "FAIRsharing.xd3wmy"
}
},
"r3d100010273": {
"description": "The Marine Geoscience Data System (MGDS) is a trusted data repository that provides free public access to a curated collection of marine geophysical data products and complementary data related to understanding the formation and evolution of the seafloor and sub-seafloor. Developed and operated by domain scientists and technical specialists with deep knowledge about the creation, analysis and scientific interpretation of marine geoscience data, the system makes available a digital library of data files described by a rich curated metadata catalog. MGDS provides tools and services for the discovery and download of data collected throughout the global oceans. Primary data types are geophysical field data including active source seismic data, potential field, bathymetry, sidescan sonar, near-bottom imagery, other seafloor senor data as well as a diverse array of processed data and interpreted data products (e.g. seismic interpretations, microseismicity catalogs, geologic maps and interpretations, photomosaics and visualizations). Our data resources support scientists working broadly on solid earth science problems ranging from mid-ocean ridge, subduction zone and hotspot processes, to geohazards, continental margin evolution, sediment transport at glaciated and unglaciated margins.",
"homepage": "https://www.marine-geo.org/library/",
"name": "Marine Geoscience Data System",
"prefix": "r3d100010273",
"synonyms": [
"MGDS"
],
"xrefs": {
"fairsharing": "FAIRsharing.9enwm8"
}
},
"r3d100010274": {
"description": "This is an information resource for central nervous system imaging which integrates clinical information with magnetic resonance (MR), x-ray computed tomography (CT), and nuclear medicine images.",
"homepage": "https://www.med.harvard.edu/AANLIB/",
"name": "The whole brain Atlas",
"prefix": "r3d100010274",
"xrefs": {
"nif": "0000-00079",
"scr": "005390"
}
},
"r3d100010275": {
"description": "As the national oceanographic data centre for Canada, MEDS maintains centralized repositories of some oceanographic data types collected in Canada, and coordinates data exchanges between DFO and recognized intergovernmental organizations, as well as acts as a central point for oceanographic data requests. Real-time, near real-time (for operational oceanography) or historical data are made available as appropriate.",
"homepage": "https://meds-sdmm.dfo-mpo.gc.ca/isdm-gdsi/index-eng.html",
"name": "Marine Environmental Data Section",
"prefix": "r3d100010275",
"synonyms": [
"MEDS",
"SDMM",
"Section des donnΓ©es sur le milieu marin",
"formerly: Canadian Oceanographic Data Centre - CODC (1962-1971)",
"formerly: Integrated Science Data Management - ISDM (2005-2013)",
"formerly: Marine Environmental Data Service - MEDS (1971-2005)",
"formerly: Oceanography and Scientific Data - OSD (2013-2015)"
]
},
"r3d100010276": {
"description": "<<>>!!!>>>",
"homepage": "http://www.mmmp.org/MMMP/import.mmmp?page=aims_org.mmmp",
"name": "Melanoma Molecular Map Project",
"prefix": "r3d100010276",
"synonyms": [
"MMMP"
],
"xrefs": {
"fairsharing": "FAIRsharing.xxtmjs"
}
},
"r3d100010278": {
"description": "On June 1, 1990 the German X-ray observatory ROSAT started its mission to open a new era in X-ray astronomy. Doubtless, this is the most ambitious project realized up to now in the short history of this young astronomical discipline. Equipped with the largest imaging X-ray telescope ever inserted into an earth orbit ROSAT has provided a tremendous amount of new scientific data and insights.",
"homepage": "https://www.mpe.mpg.de/ROSAT",
"name": "The ROSAT Mission",
"prefix": "r3d100010278",
"synonyms": [
"RΓΆnten-Astronomie-Wave",
"x-ray satellite"
]
},
"r3d100010279": {
"description": "The Brain Biodiversity Bank refers to the repository of images of and information about brain specimens contained in the collections associated with the National Museum of Health and Medicine at the Armed Forces Institute of Pathology in Washington, DC. These collections include, besides the Michigan State University Collection, the Welker Collection from the University of Wisconsin, the Yakovlev-Haleem Collection from Harvard University, the Meyer Collection from the Johns Hopkins University, and the Huber-Crosby and Crosby-Lauer Collections from the University of Michigan and the C.U. AriΓ«ns Kappers brain collection from Amsterdam Netherlands.Introducing online atlases of the brains of humans, sheep, dolphins, and other animals. A world resource for illustrations of whole brains and stained sections from a great variety of mammals",
"homepage": "https://brains.anatomy.msu.edu/",
"name": "Brain Biodiversity Bank",
"prefix": "r3d100010279",
"synonyms": [
"BBBank",
"Michigan State University Brain Biodiversity Bank"
],
"xrefs": {
"nif": "0000-00059",
"scr": "003289"
}
},
"r3d100010280": {
"description": "The Henry A. Murray Research Archive is Harvard's endowed, permanent repository for quantitative and qualitative research data at the Institute for Quantitative Social Science, and provides physical storage for the entire IQSS Dataverse Network. Our collection comprises over 100 terabytes of data, audio, and video. We preserve in perpetuity all types of data of interest to the research community, including numerical, video, audio, interview notes, and other data. We accept data deposits through this web site, which is powered by our Dataverse Network software",
"homepage": "https://murray.harvard.edu/",
"name": "Henry A. Murray Research Archive at IQSS, Harvard University",
"prefix": "r3d100010280",
"synonyms": [
"Murray Archive"
]
},
"r3d100010281": {
"description": "NatureServe and its network of member programs are a leading source for reliable scientific information about species and ecosystems of the Western Hemisphere. This site serves as a portal for accessing several types of publicly available biodiversity data.",
"homepage": "https://www.natureserve.org/",
"name": "NatureServe",
"prefix": "r3d100010281",
"synonyms": [
"NatureServe network"
]
},
"r3d100010282": {
"description": "The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information",
"homepage": "https://www.ncbi.nlm.nih.gov/",
"name": "NCBI",
"prefix": "r3d100010282",
"synonyms": [
"National Center for Biotechnology Information"
],
"xrefs": {
"nif": "0000-00139",
"scr": "006472"
}
},
"r3d100010283": {
"description": "Gene Expression Omnibus: a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles.",
"homepage": "https://www.ncbi.nlm.nih.gov/geo/",
"name": "Gene Expression Omnibus",
"prefix": "r3d100010283",
"synonyms": [
"GEO"
],
"xrefs": {
"fairsharing": "FAIRsharing.5hc8vt",
"nif": "0000-00142",
"omics": "01030",
"scr": "007303"
}
},
"r3d100010284": {
"description": "Peptidome was a public repository that archived tandem mass spectrometry peptide and protein identification data generated by the scientific community. This repository is now offline and is in archival mode. All data may be obtained from the Peptidome FTP site. Due to budgetary constraints NCBI has discontinued the Peptidome Repository. All existing data and metadata files will continue to be made available from our ftp server a ftp://ftp.ncbi.nih.gov/pub/peptidome/ indefinitely. Those files are named according to their Peptidome accession number, allowing cited data to be identified and downloaded. All of the Peptidome studies have been made publicly available at the PRoteomics IDEntifications (PRIDE) database. A map of Peptidome to Pride accessions may be found at ftp://ftp.ncbi.nih.gov/pub/peptidome/peptidome-pride_map.txt.\n\nIf you have any specific questions, please feel free to contact us at info@ncbi.nlm.nih.gov.",
"homepage": "http://www.ncbi.nlm.nih.gov/peptidome/",
"name": "Peptidome",
"prefix": "r3d100010284"
},
"r3d100010285": {
"description": "The Reference Sequence (RefSeq) collection provides a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. RefSeq sequences form a foundation for medical, functional, and diversity studies. They provide a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis (especially RefSeqGene records), expression studies, and comparative analyses.",
"homepage": "https://www.ncbi.nlm.nih.gov/refseq/",
"name": "NCBI Reference Sequence Database",
"prefix": "r3d100010285",
"synonyms": [
"RefSeq"
],
"xrefs": {
"fairsharing": "FAIRsharing.4jg0qw",
"nif": "0000-03397",
"omics": "01659",
"scr": "003496"
}
},
"r3d100010286": {
"description": "<<>>!!!>>>\nNOAA's National Climatic Data Center (NCDC) is responsible for preserving, monitoring, assessing, and providing public access to the Nation's treasure of climate and historical weather data and information.",
"homepage": "http://www.ncdc.noaa.gov/",
"name": "NOAA National Centers for Environmental Information - formerly: National Climatic Data Center",
"prefix": "r3d100010286",
"synonyms": [
"NCEI",
"formerly: NCDC"
]
},
"r3d100010287": {
"description": "NC OneMap is a public service providing comprehensive discovery and access to North Carolina's geospatial data resources. NC OneMap, the State's Clearinghouse for geospatial information, relies on data sharing and partnerships.",
"homepage": "https://www.nconemap.gov/",
"name": "NC OneMap",
"prefix": "r3d100010287",
"xrefs": {
"fairsharing": "FAIRsharing.4f120c,"
}
},
"r3d100010288": {
"description": "The National Archives is home to millions of historical documents, known as records, which were created and collected by UK central government departments and major courts of law. Data of the fomer National Digital Archive of Datasets (NDAD) collection, which was active from 1997 to 2010 and preserves and provides online access to archived digital datasets and documents from UK central government departments, is integrated.\nAccess to records held by The National Archives and more than 2,500 other archives.",
"homepage": "https://discovery.nationalarchives.gov.uk/",
"name": "The National Archives",
"prefix": "r3d100010288",
"synonyms": [
"National Digital Archive of Datasets (NDAD)",
"The National Archives Discovery"
]
},
"r3d100010289": {
"description": "<<>>!!!>>>",
"homepage": "http://www.neodc.rl.ac.uk",
"name": "NERC Earth Observation Data Centre",
"prefix": "r3d100010289",
"synonyms": [
"NEODC"
],
"xrefs": {
"fairsharing": "FAIRsharing.7HtoZI"
}
},
"r3d100010290": {
"description": "Funded by the National Science Foundation (NSF) and proudly operated by Battelle, the National Ecological Observatory Network (NEON) program provides open, continental-scale data across the United States that characterize and quantify complex, rapidly changing ecological processes. The Observatoryβs comprehensive design supports greater understanding of ecological change and enables forecasting of future ecological conditions. NEON collects and processes data from field sites located across the continental U.S., Puerto Rico, and Hawaii over a 30-year timeframe. NEON provides free and open data that characterize plants, animals, soil, nutrients, freshwater, and the atmosphere. These data may be combined with external datasets or data collected by individual researchers to support the study of continental-scale ecological change.",
"homepage": "https://www.neonscience.org/",
"name": "National Ecological Observatory Network",
"prefix": "r3d100010290",
"synonyms": [
"NEON"
]
},
"r3d100010291": {
"description": "The Netlib repository contains freely available software, documents, and databases of interest to the numerical, scientific computing, and other communities.",
"homepage": "https://www.netlib.org/",
"name": "The Netlib",
"prefix": "r3d100010291"
},
"r3d100010292": {
"description": "<<>>!!!>>> \nThe NOAA National Centers for Environmental Information (formerly the National Geophysical Data Center) provide scientific stewardship, products and services for sea floor and lakebed data, including geophysics (gravity, magnetics, seismic reflection, bathymetry, water column sonar), and data derived from sediment and rock samples. \nNCEI compiles coastal and global digital elevation models, high-resolution models for tsunami inundation studies, provides stewardship for NOS data supporting charts and navigation, and is the US national long-term archive for MGG data",
"homepage": "https://www.ngdc.noaa.gov/mgg/mggd.html",
"name": "NOAA National Centers for Environmental Information - formerly: National Geophysical Data Center",
"prefix": "r3d100010292",
"synonyms": [
"World Data Service for Geophysics",
"formerly: NGDC"
]
},
"r3d100010293": {
"description": "The database includes world-wide cosmic-ray neutron observations (pressure-corrected 1 hour counts) since 1953. The date are opened in two formats; one is 4096-byte \"longformat\" data and the other one is 80-byte \"cardformat\" data. Since the \"cardformat\" data are prepared only for quick check of data, the \"longformat\" data, which include information for data usage (constant, factors, etc), should be used for research works. PS files (compressed) of yearly plots are also available.",
"homepage": "https://cidas.isee.nagoya-u.ac.jp/WDCCR/",
"name": "World Data Center for Cosmic Rays",
"prefix": "r3d100010293",
"synonyms": [
"WDCCR"
]
},
"r3d100010294": {
"description": "National Institute of Information and Communications Technology (NICT) has taken charge of the WDC for Ionosphere. WDC for Ionosphere archives ionospheric data and metadata from approximately 250 stations across the globe.",
"homepage": "https://wdc-c2.nict.go.jp/wdc_e.html",
"name": "WDC for Ionosphere and Space Weather",
"prefix": "r3d100010294"
},
"r3d100010295": {
"description": "Nobeyama Radio Polarimeters (NoRP) are observing the Sun with multiple frequencies in the microwave range. It is capable to obtain the total coming flux and the circular-polarization degree.",
"homepage": "https://solar.nro.nao.ac.jp/norp/",
"name": "Nobeyama Radio Polarimeters",
"prefix": "r3d100010295",
"synonyms": [
"NoRP",
"ιθΎΊε±±εΌ·εΊ¦εζ³’θ¨"
]
},
"r3d100010297": {
"description": "<<>>!!!>>>\n\nWorld Data System for Cold and Arid Regions(CARD) is a new scientific data sharing system which is established on the basis of the former World Data Center for Glaciology and Geocryology, Lanzhou and other data centers hosted by Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences. World Data System for Cold and Arid Regions is one of the constituents of World Data System. The data sharing system's main goals are to collect, manage and store the scientific data of Cold and Arid Regions area in China and provide the services for the scientific research of Cold and Arid Regions.",
"homepage": "http://card.westgis.ac.cn/",
"name": "Cold and Arid Regions Science Data Center at Lanzhou",
"prefix": "r3d100010297",
"synonyms": [
"CARD",
"WDC for Glaciology and Geocryology",
"World Data System for Cold and Arid Regions"
]
},
"r3d100010299": {
"description": "The mission of World Data Center for Climate (WDCC) is to provide central support for the German and European climate research community. The WDCC is member of the ISC's World Data System. Emphasis is on development and implementation of best practice methods for Earth System data management. Data for and from climate research are collected, stored and disseminated. The WDCC is restricted to data products. Cooperations exist with thematically corresponding data centres of, e.g., earth observation, meteorology, oceanography, paleo climate and environmental sciences. The services of WDCC are also available to external users at cost price. A special service for the direct integration of research data in scientific publications has been developed. The editorial process at WDCC ensures the quality of metadata and research data in collaboration with the data producers. A citation code and a digital identifier (DOI) are provided and registered together with citation information at the DOI registration agency DataCite.",
"homepage": "https://www.wdc-climate.de/ui/",
"name": "World Data Center for Climate",
"prefix": "r3d100010299",
"synonyms": [
"DKRZ long term archive"
],
"xrefs": {
"fairsharing": "FAIRsharing.x3hgaw"
}
},
"r3d100010300": {
"description": "IGETS is the International Geodynamics and Earth Tide Service of the International Association of Geodesy (IAG). The main objective of IGETS is to monitor temporal variations of the Earth gravity field through longβterm records from ground gravimeters, tiltmeters, strainmeters and other geodynamic sensors.\nIGETS continues the activities of the Global Geodynamics Project (GGP) to provide support to geodetic and geophysical research activities using superconducting gravimeter (SG) data within the context of an international network. Furthermore, IGETS continues the activities of the International Center for Earth Tides (ICET), in particular, in collecting, archiving and distributing Earth tide records from long series of gravimeters, tiltmeters, strainmeters and other geodynamic sensors.\nGFZ is the main Data Center and operates the IGETS data base of worldwide high precision SG records. EOST (Ecole et Observatoire des Sciences de la Terre, Strasbourg, France) is the secondary Data Center, The University of French Polynesia (Tahiti) and EOST (Strasbourg, France) are the two current Analysis Centers.",
"homepage": "https://isdc.gfz-potsdam.de/igets-data-base/",
"name": "International Geodynamics and Earth Tide Service",
"prefix": "r3d100010300",
"synonyms": [
"Global Geodynamic Project at GFZ Information System and Data Center (GGP ISDC) (formerly)",
"IGETS",
"IGETS Data Base at GFZ Potsdam"
]
},
"r3d100010301": {
"description": "The WDC has a FTP-server to distribute the PCN index derived from the geomagnetic observatory Qaanaaq (THL) and the Kp-index data products derived at the geomagnetic observatory Niemegk (NGK).\nThe WDC is also holding extensive archives of magnetograms and other geomagnetic observatory data products that predate the introduction of digital data recording. The material is in analogue form such as film or microfiche. \nThe Polar Cap index (abbreviation PC index) consists of the Polar Cap North (PCN) and the Polar Cap South (PCS) index, which are derived from magnetic measurements taken at the geomagnetic observatories Qaanaaq (THL, Greenland, +85o magnetic latitude) and Vostok (VOS, Antarctica, -83o magnetic latitude), respectively.\nThe idea behind these indices is to estimate the intensity of anti-sunward plasma convection in the polar caps. This convection is associated with electric Hall currents and consequent magnetic field variations perpendicular to the antisunward plasma flow (and related Hall current) which can be monitored at the Qaanaaq and Vostok magnetic observatories.\nPC aims at monitoring the energy input from solar wind to the magnetosphere (loading activity). The index is constructed in such a way that it has a linear relationship with the merging Electric Field at the magnetopause; consequently PC is given in units of mV/m as for the electric field.\nIn August 2013, the International Association of Geomagnetism and Aeronomy (IAGA) endorsed the PC index. The endorsed PC index is accessible at pcindex.org or through WDC Copenhagen.",
"homepage": "https://www.space.dtu.dk/english/research/scientific_data_and_models/world_data_center_for_geomagnetism",
"name": "World Data Centre for Geomagnetism, Copenhagen",
"prefix": "r3d100010301",
"synonyms": [
"WDC - Geomagnetism, Copenhagen"
]
},
"r3d100010303": {
"description": "ISRIC - World Soil Information is an independent foundation. As regular member of the ICS World Data System it is also known as World Data Centre for Soils (WDC-Soils). ISRIC was founded in 1966 through the International Soil Science Society (ISSS) and United Nations Educational, Scientific and Cultural Organization (UNESCO), with a mission to \"help to increase the availability and use of soil data, information and knowledge to enable better decision making for sustainable land management around the world\". Our work is organised according to four work streams: 1) Global soil information & standards, 2) Community of practice for soil information providers, 3) Products and services to support SLM (sustainable land management) decision making, and 4) Awareness, education and dialogues. \ndata.isric.org is our central location for searching and downloading soil data bases/maps from around the world. We support Open Data whenever possible, respecting inherited rights (licenses).",
"homepage": "https://www.isric.org/",
"name": "ISRIC - World Soil Information",
"prefix": "r3d100010303",
"synonyms": [
"WDC-Soils",
"World Data Centre for Soils"
]
},
"r3d100010304": {
"description": "BASS2000 archives ground-based solar survey data, and a long term data from France's observatories. The database contains spectroheliographs, radioheliographs, coronographs, and synoptic maps. BASS2000 provides data as GIF, PNG, JPEG, MPEG, PS, and Compressed Files.",
"homepage": "https://bass2000.obspm.fr/home.php",
"name": "BASS2000",
"prefix": "r3d100010304",
"synonyms": [
"BAse de donnΓ©es Solaire Sol",
"Solar Survey Archive",
"WDC - Solar Activity"
]
},
"r3d100010305": {
"description": "<<>>!!!>>>\nNCEI is responsible for hosting and providing access to one of the most significant archives on Earth, with comprehensive oceanic, atmospheric, and geophysical data. From the depths of the ocean to the surface of the sun and from million-year-old sediment records to near real-time satellite images, NCEI is the Nation's leading authority for environmental information.\nThe National Centers for Environmental Information (NCEI), which hosts the World Data Service for Oceanography is a national environmental data center operated by the National Oceanic and Atmospheric Administration (NOAA) of the U.S. Department of Commerce. NCEI are responsible for hosting and providing access to one of the most significant archives on earth, with comprehensive oceanic, atmospheric, and geophysical data. The primary mission of the World Data Service for Oceanography is to ensure that global oceanographic datasets collected at great cost are maintained in a permanent archive that is easily and openly accessible to the world science community and to other users.",
"homepage": "https://www.nodc.noaa.gov/index.html",
"name": "NOAA National Centers for Environmental Information - World Data Service for Oceanography",
"prefix": "r3d100010305",
"synonyms": [
"WDS for Oceanography",
"World Data Service for Oceanography",
"formerly: WDC - A",
"formerly: WDC - Oceanography, Silver Spring",
"formerly: World Data Center for Oceanography, Silver Spring"
]
},
"r3d100010309": {
"description": "The USGS currently houses the institute at the Center for Earth Resources Observation and Science (EROS) in Sioux Falls, South Dakota. The LCI will address land cover topics from local to global scales, and in both domestic and international settings. The USGS through the Land Cover Institute serves as a facilitator for land cover and land use science, applications, and production functions. The institute assists in the availability and technical support of land cover data sets through increasing public and scientific awareness of the importance of land cover science. LCI continues, after the reorganization of the World Data Centers in 2009, serving as the World Data Center (WDC) for land cover data for access to, or information about, land cover data of the world",
"homepage": "https://www.usgs.gov/search?keywords=Land+Cover+Institute",
"name": "The USGS Land Cover Institute",
"prefix": "r3d100010309",
"synonyms": [
"LCI",
"World Data Centre for Land Cover Data"
]
},
"r3d100010310": {
"description": "WDC for Meteorology, Asheville acquires, catalogues, and archives data and makes them available to requesters in the international scientific community. Data are exchanged with counterparts, WDC for Meteorology, Obninsk and WDC for Meteorology, Beijing as necessary to improve access. Special research data sets prepared under international programs such as the IGY, World Climate Program (WCP), Global Atmospheric Research Program (GARP), etc., are archived and made available to the research community. All data and special data sets contributed to the WDC are available to scientific investigators without restriction. Data are available from 1755 to 2015.",
"homepage": "https://www.ncdc.noaa.gov/wdcmet",
"name": "World Data Center for Meteorology, Asheville",
"prefix": "r3d100010310",
"synonyms": [
"WDC - Meteorology, Asheville"
]
},
"r3d100010311": {
"description": "Paleoclimatology data are derived from natural sources such as tree rings, ice cores, corals, and ocean and lake sediments. These proxy climate data extend the archive of weather and climate information hundreds to millions of years. The data include geophysical or biological measurement time series and some reconstructed climate variables such as temperature and precipitation.\nNCEI provides the paleoclimatology data and information scientists need to understand natural climate variability and future climate change. We also operate the World Data Center for Paleoclimatology, which archives and distributes data contributed by scientists around the world.",
"homepage": "https://www.ncei.noaa.gov/access/paleo-search/",
"name": "NOAA National Centers for Environmental Information - Paleoclimatology Data",
"prefix": "r3d100010311",
"synonyms": [
"Paleoclimatology Data",
"World Data Service for Paleoclimatology"
],
"xrefs": {
"rid": "000059",
"scr": "012149"
}
},
"r3d100010312": {
"description": "The IERS provides data on Earth orientation, on the International Celestial Reference System/Frame, on the International Terrestrial Reference System/Frame, and on geophysical fluids. It maintains also Conventions containing models, constants and standards.",
"homepage": "https://www.iers.org/IERS/EN/Home/home_node.html",
"name": "International Earth Rotation and Reference Systems Service",
"prefix": "r3d100010312",
"synonyms": [
"IERS",
"formerly: International Earth Rotation Service"
],
"xrefs": {
"fairsharing": "FAIRsharing.cbc5c8"
}
},
"r3d100010313": {
"description": "The mission of the National Earthquake Information Center (NEIC) is to determine rapidly the location and size of all destructive earthquakes worldwide and to immediately disseminate this information to concerned national and international agencies, scientists, and the general public. The NEIC compiles and maintains an extensive, global seismic database on earthquake parameters and their effects that serves as a solid foundation for basic and applied earth science research.\nThe NEIC maintained until 2012 the former 'World Data Center for Seismology'.",
"homepage": "https://www.usgs.gov/programs/earthquake-hazards/national-earthquake-information-center-neic",
"name": "National Earthquake Information Center",
"prefix": "r3d100010313",
"synonyms": [
"NEIC"
]
},
"r3d100010314": {
"description": "The CEBS database houses data of interest to environmental health scientists. CEBS is a public resource, and has received depositions of data from academic, industrial and governmental laboratories. CEBS is designed to display data in the context of biology and study design, and to permit data integration across studies for novel meta analysis.",
"homepage": "https://cebs-ext.niehs.nih.gov/cebs/",
"name": "Chemical Effects in Biological Systems",
"prefix": "r3d100010314",
"synonyms": [
"CEBS"
],
"xrefs": {
"fairsharing": "FAIRsharing.ntv8pe",
"nif": "0000-02649",
"omics": "06027",
"scr": "006778"
}
},
"r3d100010315": {
"description": "The Visible Human ProjectΒ is an outgrowth of the NLM's 1986 Long-Range Plan. It is the creation of complete, anatomically detailed, three-dimensional representations of the normal male and female human bodies. Acquisition of transverse CT, MR and cryosection images of representative male and female cadavers has been completed. The male was sectioned at one millimeter intervals, the female at one-third of a millimeter intervals.",
"homepage": "https://www.nlm.nih.gov/research/visible/visible_human.html",
"name": "Visible Human Project",
"prefix": "r3d100010315"
},
"r3d100010316": {
"description": "nmrshiftdb is a NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. Last not least, it features peer-reviewed submission of datasets by its users. The nmrshiftdb2 software is open source, the data is published under an open content license. Please consult the documentation for more detailed information. nmrshiftdb2 is the continuation of the NMRShiftDB project with additional data and bugfixes and changes in the software.",
"homepage": "https://nmrshiftdb.nmr.uni-koeln.de/",
"name": "NMRshiftDB",
"prefix": "r3d100010316",
"xrefs": {
"fairsharing": "FAIRsharing.nYaZ1N",
"omics": "18926"
}
},
"r3d100010318": {
"description": "The Nuclear Data Portal is a new generation of nuclear data services using modern and powerful DELL servers, Sybase relational database software, the Linux operating system with programming in Java. The Portal includes nuclear structure, decay and reaction data, as well as literature information. Data can be searched for using optimized query forms; results are presented in tables and interactive plots. Additionally, a number of nuclear science tools, codes, applications, and links are provided.\nThe databases includes are: CINDA - Computer Index of Nuclear Reaction Data, CSISRS alias EXFOR - Experimental nuclear reaction data, ENDF - Evaluated Nuclear Data File , ENSDF - Evaluated Nuclear Structure Data File, MIRD - Medical Internal Radiation Dose, NSR - Nuclear Science References, NuDat - Nuclear Structure & Decay Data, XUNDL - Experimental Unevaluated Nuclear Data List, Chart of Nuclides.\nNuclear Data Portal is a web service of National Nuclear Data Center.",
"homepage": "https://www.nndc.bnl.gov/content/NuclearPortal.html",
"name": "Nuclear Data Portal",
"prefix": "r3d100010318"
},
"r3d100010320": {
"description": "The Dynamic Maps, Geographic Information System (GIS) Data and Analysis Tools website provides maps, data and tools for renewable energy resources that determine which energy technologies are viable solutions in domestic and international regions.",
"homepage": "https://www.nrel.gov/gis/",
"name": "NREL Geospatial Data Science",
"prefix": "r3d100010320",
"synonyms": [
"NERL GIS",
"NREL Dynamic Maps, Geographic Information System (GIS) Data and Analysis Tools (formerly)",
"National Renewable Energy Laboratory Geospatial Data Science"
]
},
"r3d100010321": {
"description": "NREL advances critical science and technology through innovative research and development to improve the nation's electrical grid infrastructure, making it more flexible, reliable, resilient, secure, and sustainable.",
"homepage": "https://www.nrel.gov/grid/",
"name": "NREL Transforming energy - grid modernization",
"prefix": "r3d100010321",
"synonyms": [
"RReDC (formerly)",
"Renewable Resource Data Center (formerly)"
]
},
"r3d100010323": {
"description": "<<>>!!!>>>",
"homepage": "http://www.nsd.uib.no/european_election_database/",
"name": "European Election Database",
"prefix": "r3d100010323",
"synonyms": [
"EED"
]
},
"r3d100010324": {
"description": "OECD iLibrary is the online library of the Organisation for Economic Cooperation and Development (OECD) featuring its books, papers and statistics and is the gateway to OECDβs analysis and data. It replaced SourceOECD in July 2010.\nOECD iLibrary also contains content published by the International Energy Agency (IEA), the Nuclear Energy Agency (NEA), the OECD Development Centre, PISA (Programme for International Student Assessment), and the International Transport Forum (ITF).\nOECD iLibrary presents all content so users can find - and cite - tables and databases as easily as articles or chapters in any available format: PDF, WEB, XLS, DATA, ePUB, READ.",
"homepage": "https://www.oecd-ilibrary.org/statistics",
"name": "OECD iLibrary Statistics",
"prefix": "r3d100010324"
},
"r3d100010325": {
"description": "<<>>!!!>>>",
"homepage": "http://openlandscapes.zalf.de/default.aspx",
"name": "openLandscapes",
"prefix": "r3d100010325",
"synonyms": [
"The Knowledge Collection for Landscape Science"
]
},
"r3d100010326": {
"description": "OSTI is the DOE office that collects, preserves, and disseminates DOE-sponsored R&D results that are the outcomes of R&D projects or other funded activities at DOE labs and facilities nationwide and grantees at universities and other institutions. The information is typically in the form of technical documents, conference papers, articles, multimedia, and software, collectively referred to as scientific and technical information (STI).",
"homepage": "https://www.osti.gov/search-tools",
"name": "OSTI",
"prefix": "r3d100010326",
"synonyms": [
"DOE Data Centers",
"OSTI.GOV",
"Office of Scientific and Technical Information",
"Speeding access to science information from DOE and beyond",
"U.S. Department of Energy, Office of Scientific & Technical Information"
],
"xrefs": {
"nif": "0000-22793",
"scr": "002670"
}
},
"r3d100010327": {
"description": "The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. These are the molecules of life that are found in all organisms including bacteria, yeast, plants, flies, other animals, and humans. Understanding the shape of a molecule helps to understand how it works. This knowledge can be used to help deduce a structure's role in human health and disease, and in drug development. The structures in the archive range from tiny proteins and bits of DNA to complex molecular machines like the ribosome.",
"homepage": "https://www.rcsb.org/",
"name": "RCSB Protein Data Bank",
"prefix": "r3d100010327",
"synonyms": [
"RCSB PDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.2t35ja",
"miriam": "00100029",
"nif": "0000-00135",
"omics": "03036",
"scr": "012820"
}
},
"r3d100010328": {
"description": "Goal of the RDC at ZPID is the documentation and long-term archiving of research data from all areas of psychology and the social sciences in accordance with the FAIR principles, using specially created metadata and to provide use of the data for scientific purposes such as secondary analysis and reanalysis. The RDC at ZPID contains all areas of psychology, in particular data sets from clinical, developmental, educational, gero-, and work and organizational psychology stemming from longitudinal studies, major surveys, and test development.",
"homepage": "https://rdc-psychology.org/",
"name": "RDC at ZPID",
"prefix": "r3d100010328",
"synonyms": [
"FDZ am ZPID",
"Forschungsdatenzentrum am ZPID",
"Research Data Center at ZPID",
"formerly: PsychData"
],
"xrefs": {
"fairsharing": "FAIRsharing.a58029"
}
},
"r3d100010329": {
"description": "RAVE (RAdial Velocity Experiment) is a multi-fiber spectroscopic astronomical survey of stars in the Milky Way using the 1.2-m UK Schmidt Telescope of the Anglo-Australian Observatory (AAO). The RAVE collaboration consists of researchers from over 20 institutions around the world and is coordinated by the Leibniz-Institut fΓΌr Astrophysik Potsdam. As a southern hemisphere survey covering 20,000 square degrees of the sky, RAVE's primary aim is to derive the radial velocity of stars from the observed spectra. Additional information is also derived such as effective temperature, surface gravity, metallicity, photometric parallax and elemental abundance data for the stars. The survey represents a giant leap forward in our understanding of our own Milky Way galaxy; with RAVE's vast stellar kinematic database the structure, formation and evolution of our Galaxy can be studied.",
"homepage": "https://www.rave-survey.org/query/",
"name": "RAVE database",
"prefix": "r3d100010329",
"synonyms": [
"Radial Velocity Experiment Database"
]
},
"r3d100010330": {
"description": "Child Care & Early Education Research Connections promotes high quality research in child care and early education and the use of that research in policy making. Our vision is that children are well cared for and have rich learning experiences, and their families are supported and able to work. Through this Web site, we offer research and data resources for researchers, policy makers, practitioners, and others.",
"homepage": "https://www.researchconnections.org/childcare/welcome",
"name": "Child Care & Early Education Research Connections",
"prefix": "r3d100010330"
},
"r3d100010331": {
"description": "The Roper Center for Public Opinion Research is one of the world's leading archives of social science data, specializing in data from surveys of public opinion. The data held by the Roper Center range from the 1930s, when survey research was in its infancy, to the present. Most of the data are from the United States, but over 100 nations are represented.",
"homepage": "https://ropercenter.cornell.edu/",
"name": "Roper Center Public Opinion Archives",
"prefix": "r3d100010331"
},
"r3d100010333": {
"description": "The Roper Center has made available its entire collection of Primary exit polls. Primary exit polls datasets include standard demographic makeup of interviewee and questions pertinent to the issues of each state.",
"homepage": "https://ropercenter.cornell.edu/data-highlights/elections-and-presidents",
"name": "Roper Center for Public Opinion Research: Elections and Presidents",
"prefix": "r3d100010333"
},
"r3d100010335": {
"description": "The Wellcome Trust Sanger Institute is a charitably funded genomic research centre located in Hinxton, nine miles south of Cambridge in the UK. \nWe study diseases that have an impact on health globally by investigating genomes. Building on our past achievements and based on priorities that exploit the unique expertise of our Faculty of researchers, we will lead global efforts to understand the biology of genomes. We are convinced of the importance of making this research available and accessible for all audiences. reduce global health burdens.",
"homepage": "https://www.sanger.ac.uk/science/data/",
"name": "Wellcome Trust Sanger Institute, Scientific resources",
"prefix": "r3d100010335"
},
"r3d100010336": {
"description": "The Sloan Digital Sky Survey (SDSS) is one of the most ambitious and influential surveys in the history of astronomy. Over eight years of operations (SDSS-I, 2000-2005; SDSS-II, 2005-2008; SDSS-III 2008-2014; SDSS-IV 2013 ongoing), it obtained deep, multi-color images covering more than a quarter of the sky and created 3-dimensional maps containing more than 930,000 galaxies and more than 120,000 quasars. DSS-IV is managed by the Astrophysical Research Consortium for the Participating Institutions of the SDSS Collaboration including the Carnegie Institution for Science, Carnegie Mellon University, the Chilean Participation Group, Harvard-Smithsonian Center for Astrophysics, Instituto de AstrofΓsica de Canarias, The Johns Hopkins University, Kavli Institute for the Physics and Mathematics of the Universe (IPMU) / University of Tokyo, Lawrence Berkeley National Laboratory, Leibniz Institut fΓΌr Astrophysik Potsdam (AIP), Max-Planck-Institut fΓΌr Astrophysik (MPA Garching), Max-Planck-Institut fΓΌr Extraterrestrische Physik (MPE), Max-Planck-Institut fΓΌr Astronomie (MPIA Heidelberg), National Astronomical Observatory of China, New Mexico State University, New York University, The Ohio State University, Pennsylvania State University, Shanghai Astronomical Observatory, United Kingdom Participation Group, Universidad Nacional AutΓ³noma de MΓ©xico, University of Arizona, University of Colorado Boulder, University of Portsmouth, University of Utah, University of Washington, University of Wisconsin, Vanderbilt University, and Yale University.",
"homepage": "https://www.sdss.org/",
"name": "Sloan Digital Sky Survey",
"prefix": "r3d100010336",
"synonyms": [
"SDSS"
]
},
"r3d100010337": {
"description": "SeaDataNet is a standardized system for managing the large and diverse data sets collected by the oceanographic fleets and the automatic observation systems. The SeaDataNet infrastructure network and enhance the currently existing infrastructures, which are the national oceanographic data centres of 35 countries, active in data collection. The networking of these professional data centres, in a unique virtual data management system provide integrated data sets of standardized quality on-line. As a research infrastructure, SeaDataNet contributes to build research excellence in Europe.",
"homepage": "https://www.seadatanet.org/",
"name": "SeaDataNet",
"prefix": "r3d100010337",
"synonyms": [
"Pan-European Infrastructure for ocean & marine data management"
],
"xrefs": {
"fairsharing": "FAIRsharing.f82056",
"issn": "2427-383X"
}
},
"r3d100010338": {
"description": "The NBN Atlas is a collaborative project that aggregates biodiversity data from multiple sources and makes it available and usable online. It is the UKβs largest collection of freely available biodiversity data.",
"homepage": "https://nbnatlas.org/",
"name": "National Biodiversity Network Atlas",
"prefix": "r3d100010338",
"synonyms": [
"NBN Atlas",
"formerly: NBN Gateway",
"formerly: National Biodiversity Network Gateway"
],
"xrefs": {
"fairsharing": "FAIRsharing.p7YFEc"
}
},
"r3d100010339": {
"description": "Systema Dipterorum (and the former Biosystematic Database of World Diptera) is a source of names and information about those names and the taxa to which they apply. Systema Dipterorum is a set of tools to aid users in finding information about flies. The two main components of Systema Dipterorum are the Nomenclator and the Reference database.",
"homepage": "http://www.diptera.org/",
"name": "Systema Dipterorum",
"prefix": "r3d100010339",
"synonyms": [
"BDWD",
"The BioSystematic Database of World Diptera",
"The Diptera Site"
]
},
"r3d100010341": {
"description": "The ACE Science Center (ASC) serves to facilitate collaborative work on data from the Advanced Composition Explorer (ACE) spacecraft and to ensure that those data are properly archived and publicly available. The collaborators served are not limited to ACE project-funded investigators.",
"homepage": "https://izw1.caltech.edu/ACE/ASC/",
"name": "The ACE Science Center",
"prefix": "r3d100010341",
"synonyms": [
"ASC",
"The Advanced Composition Explorer Science Center"
]
},
"r3d100010342": {
"description": "The Data Center at the University of Wisconsin-Madison Space Science and Engineering Center (SSEC), is responsible for the access, maintenance and distribution of real-time and archive weather satellite data.",
"homepage": "https://www.ssec.wisc.edu/datacenter/",
"name": "Space Science and Engineering Center Satellite Data Services",
"prefix": "r3d100010342",
"synonyms": [
"SSEC Satellite Data Services"
]
},
"r3d100010344": {
"description": "The Global Terrorism Database (GTD) is an open-source database including information on terrorist events around the world from 1970 through 2020 (with annual updates planned for the future). Unlike many other event databases, the GTD includes systematic data on domestic as well as international terrorist incidents that have occurred during this time period and now includes more than 200,000 cases.",
"homepage": "http://www.start.umd.edu/gtd/",
"name": "Global Terrorism Database",
"prefix": "r3d100010344",
"synonyms": [
"GTD"
]
},
"r3d100010345": {
"description": "Stats NZ (Statistics New Zealand) collects data about New Zealandβs environment, economy and society. The information helps government, local councils, MΔori, businesses, communities, researchers and the public to measure, and make decisions about such things as: where we need roads, schools and hospitals, environmental progress, our quality of life, how families are doing, where to locate a business, and what products to sell.\nThe Statistics New Zealand Data Archive is a central repository for all the important statistical datasets and associated documentation, metadata and publications that Statistics New Zealand produces. It also acts as a safe repository for datasets produced by other government agencies and government funded statistical studies.\nThe key difference between the Statistics New Zealand Data Archive and other digital archives is that it contains primarily statistical data at unit record level. The unit record data is archived when it is no longer in regular use by its producer.",
"homepage": "https://www.stats.govt.nz/",
"name": "Statistics New Zealand",
"prefix": "r3d100010345",
"synonyms": [
"Stats NZ",
"Tatauranga Aotearoa"
]
},
"r3d100010346": {
"description": "The objective of the Database of Genomic Variants is to provide a comprehensive summary of structural variation in the human genome. We define structural variation as genomic alterations that involve segments of DNA that are larger than >1kb. Now we also annotate InDels in 100bp-1kb range. The content of the database is only representing structural variation identified in healthy control samples. The Database of Genomic Variants provides a useful catalog of control data for studies aiming to correlate genomic variation with phenotypic data. The database is continuously updated with new data from peer reviewed research studies. We always welcome suggestions and comments regarding the database from the research community.",
"homepage": "http://dgv.tcag.ca/dgv/app/home",
"name": "Database of Genomic Variants",
"prefix": "r3d100010346",
"synonyms": [
"A curated catalogue of human genomic structural variation",
"DGV"
],
"xrefs": {
"fairsharing": "FAIRsharing.76044b",
"nif": "0000-02721",
"scr": "007000"
}
},
"r3d100010347": {
"description": "The Digital Archaeological Record (tDAR) is an international digital repository for the digital records of archaeological investigations. tDARβs use, development, and maintenance are governed by Digital Antiquity, an organization dedicated to ensuring the long-term preservation of irreplaceable archaeological data and to broadening the access to these data.",
"homepage": "https://www.tdar.org/",
"name": "tDAR",
"prefix": "r3d100010347",
"synonyms": [
"The Digital Archaeological Record"
],
"xrefs": {
"fairsharing": "FAIRsharing.7fKiFY"
}
},
"r3d100010348": {
"description": "Time-sharing Experiments for the Social Sciences (TESS) offers researchers the opportunity to capture the internal validity of experiments while also realizing the benefits of working with a large, diverse population of research participants.",
"homepage": "https://www.tessexperiments.org/",
"name": "TESS",
"prefix": "r3d100010348",
"synonyms": [
"Time-sharing Experiments for the Social Sciences"
]
},
"r3d100010349": {
"description": "The Association of Religion Data Archives (ARDA) strives to democratize access to the best data on religion. Founded as the American Religion Data Archive in 1997 and going online in 1998, the initial archive was targeted at researchers interested in American religion. The targeted audience and the data collection have both greatly expanded since 1998, now including American and international collections and developing features for educators, journalists, religious congregations, and researchers. Data included in the ARDA are submitted by the foremost religion scholars and research centers in the world.",
"homepage": "https://www.thearda.com/",
"name": "Association of Religion Data Archives",
"prefix": "r3d100010349",
"synonyms": [
"ARDA"
]
},
"r3d100010350": {
"description": "The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans. BioGRID is an online interaction repository with data compiled through comprehensive curation efforts. All interaction data are freely provided through our search index and available via download in a wide variety of standardized formats.",
"homepage": "https://thebiogrid.org/",
"name": "BioGRID",
"prefix": "r3d100010350",
"synonyms": [
"Biological General Repository for Interaction Datasets"
],
"xrefs": {
"fairsharing": "fairsharing.9d5f5r",
"miriam": "00000058",
"nif": "0000-00432",
"omics": "01901",
"scr": "007393"
}
},
"r3d100010351": {
"description": "The Tree of Life Web Project is a collection of information about biodiversity compiled collaboratively by hundreds of expert and amateur contributors. Its goal is to contain a page with pictures, text, and other information for every species and for each group of organisms, living or extinct. Connections between Tree of Life web pages follow phylogenetic branching patterns between groups of organisms, so visitors can browse the hierarchy of life and learn about phylogeny and evolution as well as the characteristics of individual groups.",
"homepage": "http://www.tolweb.org/tree/phylogeny.html",
"name": "Tree of Life Web Project",
"prefix": "r3d100010351",
"synonyms": [
"ToL"
],
"xrefs": {
"nif": "0000-03586",
"scr": "005673"
}
},
"r3d100010352": {
"description": "<<>>!!!>>> CRYSTMET was previously included in the NCDS as part of CrystalWorks. Unfortunately we are no longer able to license the CRYSTMET database for access through the NCDS. Therefore the database will no longer be accessible from 1st July 2018. >>>> CRYSTMET contains chemical, crystallographic and bibliographic data together with associated comments regarding experimental details for each study. It is a database of critically evaluated crystallographic data for metals, including alloys, intermetallics and minerals.Using these data, a number of associated files are derived, a major one being a parallel file of calculated powder patterns. These derived data are included within the CRYSTMET product.",
"name": "CRYSTMET",
"prefix": "r3d100010352"
},
"r3d100010354": {
"description": "The THREDDS Data Server (TDS) is a web server that provides metadata and data access for scientific datasets, using OPeNDAP, OGC WMS and WCS, HTTP, and other remote data access protocols. Unidata is a diverse community of over 250 institutions vested in the common goal of sharing data, and tools to access and visualize that data. For more than 25 years Unidata has been providing data, tools, and support to enhance earth-system education and research. In an era of increasing data complexity, accessibility, and multidisciplinary integration, Unidata provides a rich set of services and tools.",
"homepage": "https://www.unidata.ucar.edu/software/tds/current/TDS.html",
"name": "THREDDS Data Server",
"prefix": "r3d100010354"
},
"r3d100010355": {
"description": "The Unidata community of over 260 universities is building a system for disseminating near real-time earth observations via the Internet. Unlike other systems, which are based on data centers where the information can be accessed, the Unidata IDD is designed so a university can request that certain data sets be delivered to computers at their site as soon as they are available from the observing system. The IDD system also allows any site with access to specialized observations to inject the dataset into the IDD for delivery to other interested sites.",
"homepage": "https://www.unidata.ucar.edu/projects/index.html#idd",
"name": "Unidata Internet Data Distribution",
"prefix": "r3d100010355",
"synonyms": [
"IDD"
]
},
"r3d100010356": {
"description": "Our mission is to provide the data services, tools, and cyberinfrastructure leadership that advance earth-system science, enhance educational opportunities, and broaden participation. Unidata's main RAMADDA server contains access to a variety of datasets including the full IDD feed, Case Studies and other project data. RAMADDA is a content management system for Earth Science data. More information is available here: https://ramadda.org/?",
"homepage": "https://ramadda.unidata.ucar.edu/repository",
"name": "Unidata's RAMADDA",
"prefix": "r3d100010356",
"synonyms": [
"Unidata's Motherlode Repository"
]
},
"r3d100010357": {
"description": "The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc).",
"homepage": "https://www.uniprot.org/",
"name": "The Universal Protein Resource",
"prefix": "r3d100010357",
"synonyms": [
"UniProt"
],
"xrefs": {
"nif": "0000-00377",
"scr": "002380"
}
},
"r3d100010358": {
"description": "<<>> NVO - National Virtual Observatory is closed now <<>> The National Virtual Observatory (NVO) was the predecessor of the VAO. It was a research project aimed at developing the technologies that would be used to build an operational Virtual Observatory. With the NVO era now over, a new organization has been funded in its place, with the explicit goal of creating useful tools for users to take advantage of the groundwork laid by the NVO. To carry on with the NVO's goals, we hereby introduce you to the Virtual Astronomical Observatory http://www.usvao.org/",
"homepage": "https://sites.google.com/site/usvirtualobservatory/",
"name": "National Virtual Observatory",
"prefix": "r3d100010358",
"synonyms": [
"NVO",
"US National Virtual Observatory"
]
},
"r3d100010359": {
"description": "The United States Naval Meteorology and Oceanography Command (NMOC) provides critical information from the ocean depths to the most distant reaches of space, meeting needs in the military, scientific, and civilian communities.\nThe following NMOC components make their products available to the public through this portal:\nThe Joint Typhoon Warning Center (JTWC) is the U.S. Department of Defense agency responsible for issuing tropical cyclone warnings for the Pacific and Indian Oceans.\nThe Fleet Numerical Meteorology and Oceanography Center (FNMOC) provides the highest quality, most relevant and timely worldwide meteorology and oceanography support to U.S. and coalition forces from its Operations Center in Monterey, California.\nThe Naval Oceanographic Office (NAVO) maximizes seapower by applying relevant oceanographic knowledge in support of U.S. National Security.",
"homepage": "https://www.metoc.navy.mil/index.html",
"name": "Naval Oceanography Portal",
"prefix": "r3d100010359",
"synonyms": [
"Naval Oceanography Portal - Data Services"
]
},
"r3d100010360": {
"description": "The Scientific Registry of Transplant Recipients (SRTR) is an ever-expanding national database of transplantation statistics. Founded in 1987, the registry exists to support the ongoing evaluation of the scientific and clinical status of solid organ transplantation, including kidney, heart, liver, lung, intestine, and pancreas. Data in the registry are collected by the Organ Procurement and Transplantation Network (OPTN) from hospitals and organ procurement organizations (OPOs) across the country. The SRTR contains current and past information about the full continuum of transplant activity, from organ donation and waiting list candidates to transplant recipients and survival statistics. This information is used to help develop evidence-based policy, to support analysis of transplant programs and OPOs, and to encourage research on issues of importance to the transplant community.",
"homepage": "https://www.srtr.org/",
"name": "Scientific Registry of Transplant Recipients",
"prefix": "r3d100010360",
"synonyms": [
"SRTR",
"US Transplant"
]
},
"r3d100010361": {
"description": "The United States Transuranium & Uranium Registries (USTUR) is a research program that studies actinide elements deposited within the human body β in persons with measurable, documented exposures to those elements.",
"homepage": "https://ustur.wsu.edu/",
"name": "United States Transuranium & Uranium Registries",
"prefix": "r3d100010361",
"synonyms": [
"USTUR"
]
},
"r3d100010362": {
"description": "The USA National Phenology Network serves science and society by promoting broad understanding of plant and animal phenology and its relationship with environmental change. The Network is a consortium of individuals and organizations that collect, share, and use phenology data, models, and related information.",
"homepage": "https://www.usanpn.org/home",
"name": "The USA National Phenology Network",
"prefix": "r3d100010362",
"synonyms": [
"USA-NPN"
]
},
"r3d100010363": {
"description": "VADS is the online resource for visual arts. It has provided services to the academic community for 12 years and has built up a considerable portfolio of visual art collections comprising over 100,000 images that are freely available and copyright cleared for use in learning, teaching and research in the UK. VADS provides: expert guidance and help for digital projects in art education; resource development and hosting for art education; project management and consultancy for art education; leadership in the innovative use of ICT in education through its research and development activities. VADS offers advice and guidance to the visual arts research, teaching and learning communities on all aspects of digital resource management from funding, through delivery and use, to preservation.",
"homepage": "https://vads.ac.uk/",
"name": "Visual Arts Data Service",
"prefix": "r3d100010363",
"synonyms": [
"VADS"
]
},
"r3d100010364": {
"description": "A collection of all 1.600 wall and ceiling paintings from 400 LΓΌbecker BΓΌrgerhΓ€usern",
"homepage": "https://www.wandmalerei-luebeck2020.uni-kiel.de/",
"name": "Wand- und Deckenmalerei in LΓΌbecker HΓ€usern 1300 bis 1800",
"prefix": "r3d100010364"
},
"r3d100010365": {
"description": "The database contains photographs of plants from West Africa in a broad geographical sense, mainly from the savanna regions.",
"homepage": "http://www.westafricanplants.senckenberg.de/root/index.php",
"name": "West African Plants",
"prefix": "r3d100010365",
"synonyms": [
"A Photo Guide"
]
},
"r3d100010366": {
"description": "WHOI is the world's leading non-profit oceanographic research organization. WHOI maintains unparalleled depth and breadth of expertise across a range of oceanographic research areas. Institution scientists and engineers work collaboratively within and across six research departments to advance knowledge of the global ocean and its fundamental importance to other planetary systems. At the same time, they also train future generations of ocean scientists and address problems that have a direct impact in efforts to understand and manage critical marine resources.",
"homepage": "https://www.whoi.edu/what-we-do/understand/data/",
"name": "Woods Hole Oceanographic Institution - Data & Repositories",
"prefix": "r3d100010366",
"synonyms": [
"WHOI"
]
},
"r3d100010367": {
"description": "The WOUDC processes, archives and publishes world ozone and UV data reported by over 400 stations comprising over 100 international agencies and universities. The World Ozone and Ultraviolet Radiation Data Centre (WOUDC) has the two component parts: the World Ozone Data Centre (WODC) and the World Ultraviolet Radiation Data Centre (WUDC). These data are available on-line with updates occuring every week and in addition to the on-line archive, data are published annually on CD-ROM, now DVD.",
"homepage": "https://woudc.org/",
"name": "World Ozone and Ultraviolet Radiation Data Centre",
"prefix": "r3d100010367",
"synonyms": [
"Centre Mondial des DonnΓ©es sur l'Ozone et le Rayonnment Ultraviolet",
"Centre mondial des donnΓ©es sur l'ozone et le rayonnement ultraviolet",
"WODC",
"WOUDC",
"WUDC"
]
},
"r3d100010368": {
"description": "FORS is the Swiss Centre of Expertise in the Social Sciences. FORS maintains a national digital archive for social science research data, implements large-scale national and international surveys, offers data and research information services to researchers and academic institutions, and conducts methodological and thematic research. FORS Data Service is FORSβ resource centre for research and teaching in the social sciences. It provides data management support and training, and it archives, disseminates and promotes quantitative and qualitative data. The Data Service maintains a comprehensive and up-to-date inventory of social science research projects in Switzerland, and makes available a wide range of datasets for secondary analysis. Databases at the FORS Data Service are: SWISSUbase and DeVisu (for variable level metadata for important surveys).",
"homepage": "https://forscenter.ch/data-services/",
"name": "FORS Data Service",
"prefix": "r3d100010368",
"synonyms": [
"FORS Data and Research Information Services for the Social Sciences",
"formerly: FORS DARIS"
]
},
"r3d100010370": {
"description": "Science Data Centre (SDC) is a service launched by Leibniz-Institute for Solarphysics (KIS). Its primary purpose is to provide a common platform for the solar community to store, access, analyse and archive solar data produced by a heterogeneous group of scientific instruments.\nChroTel is a telescope to observe the solar chromosphere across the full disk. ChroTel observes the Sun pseudo-simultaneously in three channels at Ca II K, H-alpha and Helium 1083.\nGRIS is the spectrograph developed by IAC, installed in the German solar telescope GREGOR of the Teide Observatory.\nLARS is an Absolute Reference Spectrograph. It performs fiber-coupled solar observations with the high-resolution Echelle Spectrograph of the Vacuum Tower Telescope (VTT) at the Observatorio del Teide on Tenerife.",
"homepage": "https://sdc.leibniz-kis.de/en/",
"name": "Science Data Centre Leibniz-Institute for Solarphysics",
"prefix": "r3d100010370",
"synonyms": [
"SDC KIS",
"formerly: ChroTel Data",
"formerly: Chromosphere Telescope"
]
},
"r3d100010371": {
"description": "<<>>!!!>>>",
"homepage": "https://zacat.gesis.org/webview/",
"name": "ZACAT",
"prefix": "r3d100010371",
"synonyms": [
"GESIS Online Study Catalogue"
]
},
"r3d100010372": {
"description": "The ZINC Database contains commercially available compounds for structure based virtual screening. It currently has compounds that can simply be purchased. It is provided in ready-to-dock, 3D formats with molecules represented in biologically relevant forms. It is available in subsets for general screening as well as target-, chemotype- and vendor-focused subsets. ZINC is free for everyone to use and download at the website zinc.docking.org.",
"homepage": "https://cartblanche22.docking.org/",
"name": "ZINC",
"prefix": "r3d100010372",
"synonyms": [
"CartBlanche"
],
"xrefs": {
"nif": "0000-31930",
"scr": "008596"
}
},
"r3d100010373": {
"description": "Launchpad is a software collaboration platform that provides: Bug tracking, Code hosting using Bazaar, Code reviews Ubuntu package building and hosting, Translations, Mailing lists, Answer tracking and FAQs, Specification tracking. Launchpad can host your projectβs source code using the Bazaar version control system",
"homepage": "https://code.launchpad.net",
"name": "Launchpad",
"prefix": "r3d100010373",
"xrefs": {
"nif": "0000-10278",
"scr": "006853"
}
},
"r3d100010374": {
"description": "The CSSDP project provides space scientists with access to a wide range of space data, observations, and investigative tools. It provides a seamless, single- point of access to these resources through a custom web portal. To date, more than 350 scientists are registered users of the CSSDP portal.\nThe project integrates data from sources such as the Canadian Geospace Monitoring Program and anticipates serving data from the NASA THEMIS satellite probes, the Canadian High-Artic Ionospheric Network (CHAIN), and the Alberta- based Enhanced Polar Outflow Probe (ePOP) satellite mission. This collection and presentation of space data is used to study the influence of the sun on near- Earth space environment, including phenomena such as geomagnetic storms, which cause the northern and southern lights. Geomagnetic storms are also known for often causing power outages, disturbances in polar communications, and the failure of satellites. The effects of space weather can also cause transpolar flight paths to be diverted, adding significant fuel costs to airlines and disruptions for travellers.",
"homepage": "https://cssdp.ca/",
"name": "Canadian Space Science Data Portal",
"prefix": "r3d100010374",
"synonyms": [
"CSSDP"
]
},
"r3d100010375": {
"description": "GitHub is the best place to share code with friends, co-workers, classmates, and complete strangers. Over three million people use GitHub to build amazing things together. With the collaborative features of GitHub.com, our desktop and mobile apps, and GitHub Enterprise, it has never been easier for individuals and teams to write better code, faster. Originally founded by Tom Preston-Werner, Chris Wanstrath, and PJ Hyett to simplify sharing code, GitHub has grown into the largest code host in the world.",
"homepage": "https://github.com",
"name": "GitHub",
"prefix": "r3d100010375",
"xrefs": {
"biodbcore": "001160",
"fairsharing": "FAIRsharing.c55d5e",
"nlx": "156051",
"scr": "002630"
}
},
"r3d100010376": {
"description": "The Land Processes Distributed Active Archive Center (LP DAAC) is a component of NASAs Earth Observing System (EOS) Data and Information System (EOSDIS). LP DAAC processes, archives, and distributes land data and products derived from the EOS sensors. Located just outside Sioux Falls, South Dakota, the LP DAAC handles data from three EOS instruments aboard two operational satellite platforms: ASTER and MODIS from Terra, and MODIS from Aqua. ASTER data are received, processed, distributed, and archived while MODIS land products are received, distributed, and archived.",
"homepage": "https://lpdaac.usgs.gov/",
"name": "Land Processes Distributed Active Archive Center",
"prefix": "r3d100010376",
"synonyms": [
"LP DAAC"
],
"xrefs": {
"fairsharing": "FAIRsharing.7dda2f"
}
},
"r3d100010377": {
"description": "In 2003, the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) at NIH established Data, Biosample, and Genetic Repositories to increase the impact of current and previously funded NIDDK studies by making their data and biospecimens available to the broader scientific community. These Repositories enable scientists not involved in the original study to test new hypotheses without any new data or biospecimen collection, and they provide the opportunity to pool data across several studies to increase the power of statistical analyses. In addition, most NIDDK-funded studies are collecting genetic biospecimens and carrying out high-throughput genotyping making it possible for other scientists to use Repository resources to match genotypes to phenotypes and to perform informative genetic analyses.",
"homepage": "https://repository.niddk.nih.gov/home/",
"name": "NIDDK Central Repository",
"prefix": "r3d100010377",
"synonyms": [
"NIDDK-CR",
"The National Institute of Diabetes and Digestive and Kidney Diseases"
],
"xrefs": {
"fairsharing": "FAIRsharing.pr47jw",
"nlx": "152673",
"scr": "006542"
}
},
"r3d100010379": {
"description": "The CCKP contains environmental, disaster risk, and socio-economic datasets, as well as synthesis products, such as the Climate Adaptation Country Profiles, which are built and packaged for specific user-focused functions such as climate change indices for a particular country. The portal also provides intelligent links to other resources and tools.",
"homepage": "https://climateknowledgeportal.worldbank.org/#",
"name": "Climate Change Knowledge Portal",
"prefix": "r3d100010379",
"synonyms": [
"CCKP"
]
},
"r3d100010381": {
"description": "The Bavarian Archive for Speech Signals (BAS) is a public institution hosted by the University of Munich. This institution was founded with the aim of making corpora of current spoken German available to both the basic research and the speech technology communities via a maximally comprehensive digital speech-signal database. The speech material will be structured in a manner allowing flexible and precise access, with acoustic-phonetic and linguistic-phonetic evaluation forming an integral part of it.",
"homepage": "https://clarin.phonetik.uni-muenchen.de/BASRepository/",
"name": "Bavarian Archive for Speech Signals",
"prefix": "r3d100010381",
"synonyms": [
"BAS CLARIN Repository",
"BAS Repository",
"Bayerisches Archiv fΓΌr Sprachsignale"
],
"xrefs": {
"hdl": "11858/00-1779-0000-000C-DAAF-B"
}
},
"r3d100010382": {
"description": "The domain of the IDS repository is the German language, mainly in its current form (contemporary New High German). Its designated community are national and international researchers in German and general linguistics. As an institutional repository, the repository provides long term archival of two important IDS projects: the Deutsches Referenzkorpus (βGerman Reference Corpusβ, DeReKo), which curates a large corpus of written German language, and the Archiv fΓΌr Gesprochenes Deutsch (βArchive of Spoken Germanβ, AGD), which curates several corpora of spoken German.\nIn addition, the repository enables germanistic researchers from IDS and from other research facilities and universities to deposit their research data for long term archival of data and metadata arising from research projects.",
"homepage": "http://repos.ids-mannheim.de/",
"name": "IDS Repository",
"prefix": "r3d100010382",
"synonyms": [
"IDS-Mannheim Repository",
"Institut fΓΌr Deutsche Sprache Repository"
]
},
"r3d100010383": {
"description": "The Language Archive at the Max Planck Institute in Nijmegen provides a unique record of how people around the world use language in everyday life. It focuses on collecting spoken and signed language materials in audio and video form along with transcriptions, analyses, annotations and other types of relevant material (e.g. photos, accompanying notes).",
"homepage": "https://archive.mpi.nl/tla/",
"name": "The Language Archive",
"prefix": "r3d100010383",
"synonyms": [
"TLA"
]
},
"r3d100010384": {
"description": "In collaboration with other centres in the Text+ consortium and in the CLARIN infrastructure, the CLARIND-UdS enables eHumanities by providing a service for hosting and processing language resources (notably corpora) for members of the research community. CLARIND-UdS centre thus contributes of lifting the fragmentation of language resources by assisting members of the research community in preparing language materials in such a way that easy discovery is ensured, interchange is facilitated and preservation is enabled by enriching such materials with meta-information, transforming them into sustainable formats and hosting them. We have an explicit mission to archive language resources especially multilingual corpora (parallel, comparable) and corpora including specific registers, both collected by associated researchers as well as researchers who are not affiliated with us.",
"homepage": "https://fedora.clarin-d.uni-saarland.de/index.en.html",
"name": "CLARIND-UdS: Language Resources Repository at UdS",
"prefix": "r3d100010384",
"synonyms": [
"CLARIND-UdS, Repositorium fΓΌr Sprachressourcen an der UniversitΓ€t des Saarlandes"
]
},
"r3d100010385": {
"description": "The German Text Archive (Deutsches Textarchiv, DTA) presents online a selection of key German-language works in various disciplines from the 17th to 19th centuries. The electronic full-texts are indexed linguistically and the search facilities tolerate a range of spelling variants. The DTA presents German-language printed works from around 1650 to 1900 as full text and as digital facsimile. The selection of texts was made on the basis of lexicographical criteria and includes scientific or scholarly texts, texts from everyday life, and literary works. The digitalisation was made from the first edition of each work. Using the digital images of these editions, the text was first typed up manually twice (βdouble keyingβ). To represent the structure of the text, the electronic full-text was encoded in conformity with the XML standard TEI P5. The next stages complete the linguistic analysis, i.e. the text is tokenised, lemmatised, and the parts of speech are annotated. The DTA thus presents a linguistically analysed, historical full-text corpus, available for a range of questions in corpus linguistics. Thanks to the interdisciplinary nature of the DTA Corpus, it also offers valuable source-texts for neighbouring disciplines in the humanities, and for scientists, legal scholars and economists.",
"homepage": "https://www.deutschestextarchiv.de/",
"name": "Deutsches Textarchiv",
"prefix": "r3d100010385",
"synonyms": [
"DTA"
]
},
"r3d100010386": {
"description": "LINDAT/CLARIN is designed as a Czech βnodeβ of Clarin ERIC (Common Language\nResources and Technology Infrastructure). It also supports the goals of the META-NET language technology network. Both networks aim at collection, annotation, development and free sharing of language data and basic technologies between institutions and individuals both in science and in all types of research. The Clarin ERIC infrastructural project is more focused on humanities, while META-NET aims at the development of language technologies and applications. The data stored in the repository are already being used in scientific publications in the Czech Republic.\nIn 2019 LINDAT/CLARIAH-CZ was established as a unification of two research infrastructures,\nLINDAT/CLARIN and DARIAH-CZ.",
"homepage": "https://lindat.mff.cuni.cz/repository/xmlui/",
"name": "LINDAT/CLARIAH-CZ repository",
"prefix": "r3d100010386",
"synonyms": [
"LINDAT/CLARIN repository"
]
},
"r3d100010387": {
"description": "The CLARIN Centre at the University of Copenhagen, Denmark, hosts and manages a data repository (CLARIN-DK-UCPH Repository), which is part of a research infrastructure for humanities and social sciences financed by the University of Copenhagen.\nThe CLARIN-DK-UCPH Repository provides easy and sustainable access for scholars in the humanities and social sciences to digital language data (in written, spoken, video or multimodal form) and provides advanced tools for discovering, exploring, exploiting, annotating, and analyzing data. CLARIN-DK also shares knowledge on Danish language technology and resources and is the Danish node in the European Research Infrastructure Consortium, CLARIN ERIC.",
"homepage": "https://repository.clarin.dk/repository/xmlui/",
"name": "CLARIN-DK-UCPH Repository",
"prefix": "r3d100010387",
"synonyms": [
"CLARIN-DK Datacenter",
"The CLARIN Centre at the University of Copenhagen"
]
},
"r3d100010390": {
"description": "The Research Data Centre Education is a focal point for empirical educational research regarding the archiving and retrieval of audiovisual research data (AV) data and survey instruments (questionnaires and tests). In Research Data Centre Education relevant for empirical educational research data sets and tools for secondary use are provided conform with data protection via a central data repository. Contextual information for each origin study and data and instruments as well as related publications complete the offer. Content of Research Data Centre Education formation (so far) focuses on instruments and data sets of SchulqualitΓ€ts- and teaching quality research. Observation and interview data in the form of (anonymous) transcripts and codes - be viewed freely accessible - if any. The release of the original AV data for a scientific re-use is linked to a registration by specifying a reasoned research interest in order to protect the privacy rights of the observed or interviewed people.",
"homepage": "https://www.fdz-bildung.de",
"name": "Forschungsdatenzentrum Bildung",
"prefix": "r3d100010390",
"synonyms": [
"FDZ Bildung",
"Research Data Centre for Education"
]
},
"r3d100010392": {
"description": "The geothermal information system (GeotIS) provides information and data compilations on deep aquifers in Germany relevant for geothermal exploitation. GeotIS is a public internet based information system and satisfies the demand for a comprehensive, largely scale-independent form of a geothermal atlas which can be continuously updated. GeotIS helps users identify geothermal potentials by visualizing temperature, hydraulic properties and depth levels of relevant stratigraphic units. A sophisticated map interface simplifies the navigation to all areas of interest. An additional component contains a catalogue of all geothermal installations in Germany. The primary objective of this project is to improve the quality of geothermal-plant project-planning and the estimation of the exploration risk for geothermal projects on selectable locations. However, concrete, location-specific analyses still remain the task of local feasibility studies.",
"homepage": "https://www.geotis.de/homepage/GeotIS-Startpage?loc=en",
"name": "Geothermal Information System",
"prefix": "r3d100010392",
"synonyms": [
"GeotIS",
"Geothermisches Informationssystem"
]
},
"r3d100010393": {
"description": "The IMSR is a searchable online database of mouse strains, stocks, and mutant ES cell lines available worldwide, including inbred, mutant, and genetically engineered strains. The goal of the IMSR is to assist the international scientific community in locating and obtaining mouse resources for research. Note that the data content found in the IMSR is as supplied by strain repository holders.\nFor each strain or cell line listed in the IMSR, users can obtain information about:\nWhere that resource is available (Repository Site); What state(s) the resource is available as (e.g. live, cryopreserved embryo or germplasm, ES cells); Links to descriptive information about a strain or ES cell line; Links to mutant alleles carried by a strain or ES cell line; Links for ordering a strain or ES cell line from a Repository; Links for contacting the Repository to send a query",
"homepage": "https://www.findmice.org/",
"name": "International Mouse Strain Resource",
"prefix": "r3d100010393",
"synonyms": [
"IMSR"
],
"xrefs": {
"nif": "0000-09876",
"scr": "001526"
}
},
"r3d100010395": {
"description": "LAUDATIO has developed an open access research data repository for historical corpora. For the access and (re-)use of historical corpora, the LAUDATIO repository uses a flexible and appropriate documentation schema with a subset of TEI customized by TEI ODD. The extensive metadata schema contains information about the preparation and checking methods applied to the data, tools, formats and annotation guidelines used in the project, as well as bibliographic metadata, and information on the research context (e.g. the research project). To provide complex and comprehensive search in the annotation data, the search and visualization tool ANNIS is integrated in the LAUDATIO-Repository.",
"homepage": "https://www.laudatio-repository.org/",
"name": "LAUDATIO",
"prefix": "r3d100010395",
"synonyms": [
"Long-term Access and Usage of Deeply Annotated Information"
]
},
"r3d100010398": {
"description": "With ARS - Antimicrobial Resistance Surveillance in Germany - the infrastructure for a nationwide surveillance of antimicrobial resistance has been established, which covers both the inpatient medical care and the ambulatory care sector. This is intended to reliable data on the epidemiology of antimicrobial resistance in Germany and differential statements provided by structural features of the health care and by region are possible. ARS is designed as a laboratory-based surveillance system for continuous collection of resistance data from routine for the full range of clinically relevant bacterial pathogens. Project participants and thus data suppliers are laboratories that analyze samples of medical facilities and doctors' offices microbiologically.",
"homepage": "https://ars.rki.de/",
"name": "ARS",
"prefix": "r3d100010398",
"synonyms": [
"Antibiotika-Resistenz-Surveillance"
]
},
"r3d100010399": {
"description": "The ZEW research data can be analysed here at ZEW in the ZEW-FDZ premises for research projects. The data provided is individual company data. Besides, the ZEW Financial Market Test provides data collected in the course of an expert survey. Furthermore, Scientific Use Files for eight data sets (three years after the implementation of the survey) and absolute anonymised Education Use Files for the Mannheim Innovation Panel can be used.",
"homepage": "https://kooperationen.zew.de/zew-fdz/startseite",
"name": "ZEW Forschungsdatenzentrum",
"prefix": "r3d100010399",
"synonyms": [
"ZEW research data for external researchers",
"ZEW-FDZ"
]
},
"r3d100010400": {
"description": "<<>>!!!>>>",
"homepage": "https://biiacs-dspace.cide.edu/",
"name": "Banco de InformaciΓ³n para la InvestigaciΓ³n Aplicada en Ciencias Sociales, Repositorio Institucional",
"prefix": "r3d100010400",
"synonyms": [
"BIIACS"
]
},
"r3d100010401": {
"description": "The aim of the project KCDC (KASCADE Cosmic Ray Data Centre) is the installation and establishment of a public data centre for high-energy astroparticle physics based on the data of the KASCADE experiment. KASCADE was a very successful large detector array which recorded data during more than 20 years on site of the KIT-Campus North, Karlsruhe, Germany (formerly Forschungszentrum, Karlsruhe) at 49,1Β°N, 8,4Β°O; 110m a.s.l. KASCADE collected within its lifetime more than 1.7 billion events of which some 433.000.000 survived all quality cuts. Initially about 160 million events are available here for public usage.",
"homepage": "https://kcdc.iap.kit.edu/",
"name": "KASCADE Cosmic Ray Data Centre",
"prefix": "r3d100010401",
"synonyms": [
"KCDC",
"Karlsruhe Shower Core and Array Detector"
]
},
"r3d100010402": {
"description": "The KNMI Climate Explorer is a web application to analysis climate data statistically.",
"homepage": "https://climexp.knmi.nl/start.cgi",
"name": "KNMI Climate Explorer",
"prefix": "r3d100010402",
"synonyms": [
"Climate Explorer"
]
},
"r3d100010403": {
"description": "The Mikulski Archive for Space Telescopes (MAST) is a NASA funded project to support and provide to the astronomical community a variety of astronomical data archives, with the primary focus on scientifically related data sets in the optical, ultraviolet, and near-infrared parts of the spectrum. MAST is located at the Space Telescope Science Institute (STScI).",
"homepage": "https://archive.stsci.edu/",
"name": "Barbara A. Mikulski Archive for Space Telescopes",
"prefix": "r3d100010403",
"synonyms": [
"MAST",
"Multimission Archive at STScI"
]
},
"r3d100010404": {
"description": "SACA&D is developed as part of the Digitisasi Data Historis (Didah) project. This project is focusing on the digitization and use of high-resolution historical climate data from Indonesia and other Southeast Asian countries",
"homepage": "http://sacad.database.bmkg.go.id/",
"name": "Southeast Asian Climate Assessment & Dataset",
"prefix": "r3d100010404",
"synonyms": [
"SACA&D"
]
},
"r3d100010405": {
"description": "The CliSAP-Integrated Climate Data Center (ICDC) allows easy access to climate relevant data from satellite remote sensing and in situ and other measurements in Earth System Sciences. These data are important to determine the status and the changes in the climate system. Additionally some relevant re-analysis data are included, which are modeled on the basis of observational data. ICDC cooperates with the \"Zentrum fΓΌr Nachhaltiges Forschungsdatenmanagement \"https://www.fdr.uni-hamburg.de/ to publish observational data with a doi.",
"homepage": "https://www.cen.uni-hamburg.de/en/icdc/data.html",
"name": "Integrated Climate Data Center",
"prefix": "r3d100010405",
"synonyms": [
"ICDC"
],
"xrefs": {
"fairsharing": "FAIRsharing.d95034"
}
},
"r3d100010406": {
"description": "<<>>!!!>>>\nWetter, Wolken, Klima is a collection of actual and archived climate dates of Germany since 2004. Based at KIT Meteorological Institute it includes special Cloud images from Karlsruhe, actual weather records based on 70 german stations, average snowfall and precipitation of Germany, weather warnings worldwide with archive, satellite images worldwide, actual weather radar worldwide, analyses and prognosis and precipitation rate of Baden-WΓΌrttemberg.",
"homepage": "http://imkhp2.physik.uni-karlsruhe.de/~muehr/wetter.html",
"name": "Wetter, Wolken, Klima",
"prefix": "r3d100010406"
},
"r3d100010407": {
"description": "The Karlsruher Wolkenatlas includes images of different cloud species and of some optical effects like circumzenithal arc, glories, and halos. Beside that phenomena like inversion or dust devil are shown. Another focus is on images of precipitation, different manifestations of precipation at earthground, rainbows and lightnings.",
"homepage": "https://www.wolkenatlas.de/",
"name": "Der Karlsruher Wolkenatlas",
"prefix": "r3d100010407",
"synonyms": [
"Wolken- und Wetterfotografie"
]
},
"r3d100010408": {
"description": "The Antibody Registry supports the RRID Initiative and exists to give researchers a way to universally identify antibodies used in publications. The registry lists many commercial antibodies from over 200 vendors, which have been assigned a unique identifier and over 2000 individual laboratories. If the antibody that you are using does not appear in the list, an entry can be made by filling in as little as 2 pieces of information: the catalog number and the url of the vendor where our curators can find information and material data sheets.",
"homepage": "https://antibodyregistry.org/",
"name": "The Antibody Registry",
"prefix": "r3d100010408",
"synonyms": [
"ABR"
],
"xrefs": {
"fairsharing": "FAIRsharing.3wdd17",
"nif": "0000-07730",
"scr": "006397"
}
},
"r3d100010409": {
"description": "ASTM International, formerly known as the American Society for Testing and Materials (ASTM), is a globally recognized leader in the development and delivery of international voluntary consensus standards. Today, some 12,000 ASTM standards are used around the world to improve product quality, enhance safety, facilitate market access and trade, and build consumer confidence.",
"homepage": "https://www.astm.org/Standard/index.html",
"name": "ASTM International",
"prefix": "r3d100010409",
"synonyms": [
"American Society for Testing and Materials"
],
"xrefs": {
"fairsharing": "FAIRsharing.hren8w"
}
},
"r3d100010410": {
"description": "GeoScenic offers access to images from the vast collections of geological photographs in BGS.",
"homepage": "http://geoscenic.bgs.ac.uk/asset-bank/action/viewHome",
"name": "BGS GeoScenic",
"prefix": "r3d100010410",
"synonyms": [
"British Geological Survey GeoScenic"
],
"xrefs": {
"fairsharing": "FAIRsharing.86302v"
}
},
"r3d100010411": {
"description": "CRAN is a network of ftp and web servers around the world that store identical, up-to-date, versions of code and documentation for R. R is βGNU Sβ, a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. Please consult the R project homepage for further information.",
"homepage": "https://cran.r-project.org/",
"name": "Comprehensive R Archive Network",
"prefix": "r3d100010411",
"synonyms": [
"CRAN"
],
"xrefs": {
"fairsharing": "FAIRsharing.1a283d",
"nif": "0000-30270",
"scr": "003005"
}
},
"r3d100010412": {
"description": ">>>!!!<<< duplicate >>>!!!<<< see https://www.re3data.org/repository/r3d100011538",
"homepage": "http://earthchem.org/library",
"name": "EarthChem Library",
"prefix": "r3d100010412",
"synonyms": [
"EarthChem"
],
"xrefs": {
"fairsharing": "FAIRsharing.ne5dn7",
"nlx": "154721",
"scr": "002207"
}
},
"r3d100010413": {
"description": "The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. The user can browse the ontologies through the website as well as programmatically via the OLS API.\nThe OLS provides a web service interface to query multiple ontologies from a single location with a unified output format.The OLS can integrate any ontology available in the Open Biomedical Ontology (OBO) format. The OLS is an open source project hosted on Google Code.",
"homepage": "https://www.ebi.ac.uk/ols/index",
"name": "Ontology Lookup Service",
"prefix": "r3d100010413",
"synonyms": [
"EMBL-EBI OLS",
"OLS"
],
"xrefs": {
"fairsharing": "FAIRsharing.Mkl9RR",
"nif": "0000-10390",
"omics": "02275",
"scr": "006596"
}
},
"r3d100010414": {
"description": "Starting September 2013, MINT uses the IntAct database infrastructure to limit the duplication of efforts and to optimise future software development. Data manually curated by the MINT curators can now be accessed from the IntAct homepage at the EBI. Data maintenance and release, MINT PSICQUIC and IMEx services are under the responsibility of the IntAct team, while curation effort will be carried by both groups.\nThe MINT development team now focuses on two new developments: mentha that integrates protein interaction information curated by IMEx databases and SIGNOR a database of logic relationships between human proteins. MINT is a public repository for molecular interactions reported in peer-reviewed journals.IT is a collection of molecular interaction databases that can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. A new component has been added called VirusMINT that explores the interactions of viral proteins with human proteins.",
"homepage": "https://mint.bio.uniroma2.it/",
"name": "Molecular INTeraction Database",
"prefix": "r3d100010414",
"synonyms": [
"MINT"
],
"xrefs": {
"fairsharing": "FAIRsharing.2bdvmk",
"nlx": "152821",
"omics": "02928",
"scr": "001523"
}
},
"r3d100010415": {
"description": "The NCBI Taxonomy database is a curated set of names and classifications for all of the organisms that are represented in GenBank. The EMBL and DDBJ databases, as well as GenBank, now use the NCBI Taxonomy as the standard classification for nucleotide sequences. Taxonomy Contains the names and phylogenetic lineages of more than 160,000 organisms that have molecular data in the NCBI databases. New taxa are added to the Taxonomy database as data are deposited for them. When new sequences are submitted to GenBank, the submission is checked for new organism names, which are then classified and added to the Taxonomy database.",
"homepage": "https://www.ncbi.nlm.nih.gov/taxonomy",
"name": "NCBI Taxonomy",
"prefix": "r3d100010415",
"synonyms": [
"Entrez Taxonomy"
],
"xrefs": {
"fairsharing": "FAIRsharing.fj07xj",
"nif": "0000-03179",
"scr": "003256"
}
},
"r3d100010416": {
"description": "OMIM is a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily. OMIM is authored and edited at the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, under the direction of Dr. Ada Hamosh. Its official home is omim.org.",
"homepage": "https://www.ncbi.nlm.nih.gov/omim",
"name": "Online Mendelian Inheritance in Man",
"prefix": "r3d100010416",
"synonyms": [
"OMIM"
],
"xrefs": {
"fairsharing": "FAIRsharing.9qkaz9",
"nif": "0000-03216",
"omics": "00278",
"scr": "006437"
}
},
"r3d100010417": {
"description": "The Rat Genome Database is a collaborative effort between leading research institutions involved in rat genetic and genomic research. Its goal, as stated in RFA: HL-99-013 is the establishment of a Rat Genome Database, to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community. A secondary, but critical goal is to provide curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data.",
"homepage": "https://rgd.mcw.edu",
"name": "Rat Genome Database",
"prefix": "r3d100010417",
"synonyms": [
"RGD"
],
"xrefs": {
"fairsharing": "FAIRsharing.pfg82t",
"nif": "0000-00134",
"omics": "01660",
"scr": "006444"
}
},
"r3d100010418": {
"description": "RunMyCode is a novel cloud-based platform that enables scientists to openly share the code and data that underlie their research publications. The web service only requires a web browser as all calculations are done on a dedicated cloud computer. Once the results are ready, they are automatically displayed to the user.",
"homepage": "http://www.runmycode.org/home",
"name": "RunMyCode",
"prefix": "r3d100010418",
"xrefs": {
"fairsharing": "FAIRsharing.f7p410",
"issn": "2427-3775",
"scr": "014011"
}
},
"r3d100010419": {
"description": "The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms.",
"homepage": "https://www.yeastgenome.org",
"name": "Saccharomyces Genome Database",
"prefix": "r3d100010419",
"synonyms": [
"SGD"
],
"xrefs": {
"fairsharing": "FAIRsharing.pzvw40",
"nif": "0000-03456",
"omics": "01661",
"scr": "004694"
}
},
"r3d100010420": {
"description": "SESAR, the System for Earth Sample Registration, is a global registry for specimens (rocks, sediments, minerals, fossils, fluids, gas) and related sampling features from our natural environment. SESAR's objective is to overcome the problem of ambiguous sample naming in the Earth Sciences.\nSESAR maintains a database of sample records that are contributed by its users. Each sample that is registered with SESAR is assigned an International Geo Sample Number IGSN to ensure its global unique identification.",
"homepage": "https://www.geosamples.org/",
"name": "System for Earth Sample Registration",
"prefix": "r3d100010420",
"synonyms": [
"SESAR"
],
"xrefs": {
"fairsharing": "FAIRsharing.ys5ta3",
"nlx": "154747",
"scr": "002222"
}
},
"r3d100010421": {
"description": "ZFIN serves as the zebrafish model organism database. The long term goals for ZFIN are a) to be the community database resource for the laboratory use of zebrafish, b) to develop and support integrated zebrafish genetic, genomic and developmental information, c) to maintain the definitive reference data sets of zebrafish research information, d) to link this information extensively to corresponding data in other model organism and human databases, e) to facilitate the use of zebrafish as a model for human biology and f) to serve the needs of the research community.\nZIRC is the Zebrafish International Resource Center, an independent NIH-funded facility providing a wide range of zebrafish lines, probes and health services. ZFIN works closely with ZIRC to connect our genetic data with available probes and fish lines.",
"homepage": "https://zfin.org/",
"name": "The Zebrafish Information Network",
"prefix": "r3d100010421",
"synonyms": [
"The zebrafish model organism database (formerly)",
"ZFIN"
],
"xrefs": {
"fairsharing": "FAIRsharing.ybxnhg",
"nif": "0000-21427",
"omics": "01666",
"scr": "002560"
}
},
"r3d100010422": {
"description": "ThermoML presents published experimental data extracted from 5 major journals in the field and links to ThermoML files, which represent experimental thermophysical and thermochemical property data reported in the corresponding articles. At the same time ThermoML is an XML-Based IUPAC Standard for Storage and Exchange of Experimental Thermophysical and Thermochemical Property Data.",
"homepage": "https://trc.nist.gov/ThermoML.html",
"name": "ThermoML",
"prefix": "r3d100010422",
"synonyms": [
"Representation of Published Experimental Data"
],
"xrefs": {
"fairsharing": "FAIRsharing.7b0fc3"
}
},
"r3d100010423": {
"description": "The Woods Hole Open Access Server, WHOAS, is an institutional repository that captures, stores, preserves, and redistributes the intellectual output of the Woods Hole scientific community in digital form. WHOAS is managed by the MBLWHOI Library as a service to the Woods Hole scientific community",
"homepage": "https://darchive.mblwhoilibrary.org/",
"name": "Woods Hole Open Access Server",
"prefix": "r3d100010423",
"synonyms": [
"WHOAS",
"a repository for the Woods Hole scientific community"
],
"xrefs": {
"fairsharing": "FAIRsharing.r3fzzc"
}
},
"r3d100010424": {
"description": "Launched in 2000, WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and some related nematodes. In addition to their curation work, all sites have ongoing programs in bioinformatics research to develop the next generations of WormBase structure, content and accessibility",
"homepage": "https://www.wormbase.org/",
"name": "WormBase",
"prefix": "r3d100010424",
"synonyms": [
"facilitating insights into nematode biology"
],
"xrefs": {
"fairsharing": "FAIRsharing.zx1td8",
"nif": "0000-00053",
"omics": "01664",
"scr": "003098"
}
},
"r3d100010425": {
"description": "The Research Data Centre (FDZ) of the German Federal Employment Agency (BA) at the Institute for Employment Research (IAB) is intended mainly to facilitate access to BA and IAB micro data for non-commercial empirical research using standardised and transparent access rules. The FDZ mediates between data producers and external users. We also control for compliance with data protection regulations.",
"homepage": "https://fdz.iab.de/",
"name": "Forschungsdatenzentrum der Bundesagentur fΓΌr Arbeit im Institut fΓΌr Arbeitsmarkt und Berufsforschung",
"prefix": "r3d100010425",
"synonyms": [
"Forschungsdatenzentrum der BA im IAB",
"Research Data Centre (FDZ) of the German Federal Employment Agency (BA) at the Institute for Employment Research (IAB)"
]
},
"r3d100010426": {
"description": "The basic goal of the research data centres of the statistical offices of the Federation and the LΓ€nder is to improve the accessibility and usability of microdata of official statistics by setting up various ways of using the data.\nResearch data centres of the Federal Statistical Office (FDZ-Bund) and the statistical offices of the LΓ€nder (FDZ-LΓ€nder) provide collectively access to selected microdata of official statistics to researchers for scientific purposes.",
"homepage": "https://www.forschungsdatenzentrum.de/en",
"name": "Forschungsdatenzentren der Statistischen Γmter des Bundes und der LΓ€nder",
"prefix": "r3d100010426",
"synonyms": [
"FDZ Bund",
"FDZ Land",
"FDZ LΓ€nder",
"Forschungsdatenzentrum der Statistischen Γmter der LΓ€nder",
"Forschungsdatenzentrum des Statistischen Bundesamts",
"Research Data Centres of the Federal Statistical Offices and of the Statistical Offices of the Federal States"
]
},
"r3d100010427": {
"description": "The Research Data Centre (Forschungsdatenzentrum, FDZ) at the Institute for Educational Quality Improvement (Institut zur QualitΓ€tsentwicklung im Bildungswesen, IQB) archives and documents data sets resulting from national and international assessment studies (such as DESI, PIRLS, PISA, IQB-Bildungstrends). Moreover, the FDZ makes these data sets available for re- and secondary analysis. Members of the scientific community can apply for access to the data sets archived at the FDZ.",
"homepage": "https://www.iqb.hu-berlin.de/fdz",
"name": "Forschungsdatenzentrum am IQB",
"prefix": "r3d100010427",
"synonyms": [
"FDZ am IQB",
"FDZ at IQB",
"Forschungsdatenzentrum am Institut zur QualitΓ€tsentwicklung",
"Research Data Centre at the Institute for Educational Quality Improvement"
],
"xrefs": {
"fairsharing": "FAIRsharing.43493f"
}
},
"r3d100010429": {
"description": "The FDZ-DZA (Forschungsdatenzentrum DZA) is a facility of the German Centre of Gerontology (Deutsches Zentrum fΓΌr Altersfragen, DZA) and has received accreditation as research data center DZA by the German Data Forum (RatSWD). Its main task is to make data of the German Ageing Survey DEAS and the German Survey on Volunteering (FWS) accessible to researchers by providing user-friendly Scientific Use Files (SUF), documentation of the contents and instruments as well support for scholars using the data.",
"homepage": "https://www.dza.de/en/research/fdz",
"name": "Forschungsdatenzentrum des Deutschen Zentrum fΓΌr Altersfragen",
"prefix": "r3d100010429",
"synonyms": [
"FDZ-DZA",
"Research Data Centre of the DZA"
]
},
"r3d100010430": {
"description": "The Survey of Health, Ageing and Retirement in Europe (SHARE) is a multidisciplinary and cross-national panel database of micro data on health, socio-economic status and social and family networks of more than 140,000 individuals (approximately 530,000 interviews) aged 50 or over from 28 European countries and Israel.",
"homepage": "https://share-eric.eu",
"name": "Survey of Health, Ageing and Retirement in Europe",
"prefix": "r3d100010430",
"synonyms": [
"SHARE"
],
"xrefs": {
"fairsharing.legacy": "4839"
}
},
"r3d100010431": {
"description": "The 2008-launched German Family Panel pairfam (βPanel Analysis of Intimate Relationships and Family Dynamicsβ) is a multi-disciplinary, longitudinal study for researching partnership and family dynamics in Germany. The annually collected survey data from a nationwide random sample of more than 12,000 persons of the three birth cohorts 1971-73, 1981-83, 1991-93 and their partners, parents and children offers unique opportunities for the analysis of partner and generational relationships as they develop over the course of multiple life phases.",
"homepage": "https://www.pairfam.de/en/",
"name": "Pairfam",
"prefix": "r3d100010431",
"synonyms": [
"FDZ pairfam",
"Forschungsdatenzentrum pairfam",
"Panel Analysis of Intimate Relationships and Family Dynamics"
]
},
"r3d100010432": {
"description": "The Research Data Center (RDC) βInternational Survey Programsβ provides researchers with data, services, and consultation on a number of important international study series which are under intensive curation by GESIS. They all cover numerous countries and, quite often, substantial time spans. The RDC provides optimal data preparation and access to a wide scope of data and topics for comparative analysis.",
"homepage": "https://www.gesis.org/en/institute/research-data-centers/rdc-international-survey-programs",
"name": "Forschungsdatenzentrum Internationale Umfrageprogramme",
"prefix": "r3d100010432",
"synonyms": [
"FDZ Internationale Umfrageprogramme",
"RDC International Survey Programmes",
"Research Data Center International Survey Programs"
]
},
"r3d100010433": {
"description": "The Research Data Center Elections is part of GESIS and provides access to a number of national survey datasets, e.g. the German Longitudinal Election Study (GLES). The RDC provides intensive data preparation and access to a wide scope of data and topics. Furthermore, the RDC offers consultation and creation of value-added services like data handbooks, cumulations, and training.",
"homepage": "https://www.gesis.org/wahlen/wahlen-home",
"name": "Forschungsdatenzentrum Wahlen",
"prefix": "r3d100010433",
"synonyms": [
"FDZ Wahlen",
"RDC Elections",
"Research Data Center Elections"
]
},
"r3d100010434": {
"description": "The GML contributes to the continual improvement of access to and information about official microdata; provides a service and research infrastructure for these data; adopts the function of an intermediary between the Federal Statistical Office and empirical research; conducts exemplary research based upon official data. The GML is an integral part of the German data infrastructure and features as one of six institutions funded by the German Council of Social and Economic Data.",
"homepage": "https://www.gesis.org/en/institute/research-data-centers/rdc-german-microdata-lab/",
"name": "FDZ German Microdata Lab",
"prefix": "r3d100010434",
"synonyms": [
"Forschungsdatenzentrum German Microdata Lab",
"GML",
"RDC German Microdata Lab"
]
},
"r3d100010435": {
"description": "As a center for scientific research and evidence-based policy advice, RWI requires an effective econometric infrastructure. The increased use of individual and firm data also requires effective regulations and tools for data protection. The research divisionβs objectives are to advise RWI researchers in methodical questions, to develop new econometric approaches to solve concrete research questions, and to ensure data protection.",
"homepage": "https://www.rwi-essen.de/forschung-beratung/weitere/forschungsdatenzentrum-ruhr",
"name": "Forschungsdatenzentrum Ruhr am RWI",
"prefix": "r3d100010435",
"synonyms": [
"FDZ Ruhr",
"Research Data Centre Ruhr at the RWI"
]
},
"r3d100010436": {
"description": "The Research Data Centre of the Robert Koch Institute (FDZ RKI) publishes the data of population-representative health surveys in the form of public use files (PUFs).The main purpose of health surveys is to generate a maximum amount of information on the state of health and health-related behaviour of Germany's resident population while ensuring an optimum use of funds. The methodology - i.e. the sample design, the principles on operationalization and measurement, and data-collection techniques - is largely modelled on the tried-and-tested methods of empirical social research. Health interview surveys (HIS) use established survey techniques such as filling out questionnaires, computer-assisted telephone interviews (CATI), computer-assisted personal interviews (CAPI), and online polling via the internet or email. The main difference compared to purely sociological surveys lies in the additional biomedical examinations, tests and medical-biochemical measurements, which generate significant added value in addition to the results of the surveys; this part is referred to internationally as the health examination survey (HES).",
"homepage": "https://www.rki.de/DE/Content/Forsch/FDZ/FDZ_node.html",
"name": "Forschungsdatenzentrum am Robert Koch Institut",
"prefix": "r3d100010436",
"synonyms": [
"FDZ RKI",
"Research Data Centre of the Robert Koch Institute"
]
},
"r3d100010437": {
"description": "Health education and health promotion are important elements of the health system in Germany. The Federal Centre for Health Education (BZgA) has been pursuing the goal of preventing health risks and encouraging health-promoting lifestyles since its establishment in 1967.\nIn addition, the understanding of health and prevention is changing. Against this backdrop, health education is - as a constant communication process - dedicated to the goal of enabling self-responsible action in relation to health.\nThe data sets can be requested from GESIS via the data archive for social sciences (DAS): https://www.gesis.org/institut/abteilungen/datenarchiv-fuer-sozialwissenschaften",
"homepage": "https://www.bzga.de/forschung/studien/",
"name": "Bundeszentrale fΓΌr Gesundheitliche AufklΓ€rung Studien",
"prefix": "r3d100010437",
"synonyms": [
"BZgA Studien",
"Federal Centre for Health Education (BZgA) studies",
"Forschungsdatenzentrum der Bundeszentrale fΓΌr gesundheitliche AufklΓ€rung"
]
},
"r3d100010438": {
"description": "The Research Data Center Wissenschaftsstatistik provides the scientific community with data on economics and innovation in Germany. Data on research and development (R&D) in Germany (collected on behalf of the Federal Ministry of Education and Research) and on the development and startup culture of universities are made available via scientific use files and campus use files. Most studies and data are in German.",
"homepage": "https://www.fdz-wissenschaftsstatistik.de/",
"name": "Forschungsdatenzentrum Wissenschaftsstatistik",
"prefix": "r3d100010438",
"synonyms": [
"FDZ Wissenschaftsstatistik",
"RDC Wissenschaftsstatistik",
"Research Data Centre Wissenschaftsstatistik of Stifterverband"
]
},
"r3d100010439": {
"description": "The FDZ-BO at DIW Berlin is a central archive for quantitative and qualitative operational and organizational data. It archives these, informs about their existence and provides datasets for secondary analytical purposes. The archiving of studies and datasets ensures long-term security and long-term availability of the data. In consultation with the responsible scientists, access to individual datasets is made possible as scientific use files, via remote data processing or as part of guest stays. The FDZ-BO offers detailed information on current research projects and develops concepts for research data management of organizational data.\nThe study portal (public in March 2019) provides an overview of existing studies in the field of business and organizational research: content, methodology, information on data and data availability information on how to gain access to the data.",
"homepage": "https://portal.fdz-bo.diw.de/",
"name": "FDZ-BO",
"prefix": "r3d100010439",
"synonyms": [
"FDZ-BO am Deutschen Institut fΓΌr Wirtschaftsforschung",
"Forschungsdatenzentrum Betriebs- und Organisationsdaten",
"Research Data Center for Business and Organizational Data"
]
},
"r3d100010440": {
"description": "IDSC is IZA's organizational unit whose purpose is to serve the scientific and infrastructural computing needs of IZA and its affiliated communities.\nIDSC is dedicated to supporting all users of data from the novice researcher to the experienced data analyst.\nIDSC aims at becoming the place for economically minded technologists and technologically savvy economists looking for data support, data access support and data services about labor economics.\nIDSC is actively involved in organizing events (see our next Red Cube Seminar Talk) for data professionals, data analysts, and scientific data users and young researchers to discuss and share findings and to establish contacts for future cooperation.\nAll data collected are accessible to the scientific community as scientific use files for scholarly analyses free of charge.\nThe Data Repository is available at https://datasets.iza.org/",
"homepage": "https://www.iza.org/en/research/idsc",
"name": "International Data Service Center of the Institute of Labor Economics",
"prefix": "r3d100010440",
"synonyms": [
"Forschungsdatenzentrum IDSC",
"IDSC IZA",
"Internationales Datenservicezentrum des Forschungsinstituts zur Zukunft der Arbeit"
]
},
"r3d100010441": {
"description": "The Measures of Effective Teaching(MET) project is the largest study of classroom teaching ever conducted in the United States. The University of Michigan compiled the MET data and video files into a rich research collection called the MET Longitudinal Database. Approved researchers can access the restricted MET quantitative and video data using secure online technical systems. The MET Longitudinal Database consists of a Web-based application for searching the collection and viewing the videos with accompanying metadata, and a Virtual Data Enclave that provides secure remote access to the quantitative data and documentation files.",
"homepage": "https://www.icpsr.umich.edu/web/pages/about/metldb.html",
"name": "Measures of Effective Teaching - Longitudinal Database",
"prefix": "r3d100010441",
"synonyms": [
"MET LDB",
"MET Longitudinal Database"
]
},
"r3d100010442": {
"description": "Data Center of Geography was created in 2011 in the framework of the interdisciplinary structure β world data systems β to ensure gathering, processing and conversion of data and to solve fundamental and applied problems in the sphere of geographical sciences.",
"homepage": "http://eng.geogr.msu.ru/structure/labs/WDC/",
"name": "World Data Center for Geography",
"prefix": "r3d100010442",
"synonyms": [
"Center of World Data System of Geography"
]
},
"r3d100010443": {
"description": "The department specializes on developing complex distributed systems for satellite data processing.\nThe main task given to the department is development, validation and implementation of different satellite data processing methods in the form of information services and certain systems",
"homepage": "http://inform.ikd.kiev.ua/en/",
"name": "Ukrainian Geospatial Data Center",
"prefix": "r3d100010443"
},
"r3d100010444": {
"description": "World Data Center for Oceanography serves to store and provide to users data on physical, chemical and dynamical parameters of the global ocean as well as oceanography-related papers and publications, which are either came from other countries through the international exchange or provided to the international exchange by organizations of the Russian Federation",
"homepage": "http://meteo.ru/mcd/ewdcoce.html",
"name": "World Data Center for Oceanography, Obninsk",
"prefix": "r3d100010444",
"synonyms": [
"WDC - B1",
"WDC - Oceanography, Obninsk",
"World Data Center - B"
]
},
"r3d100010446": {
"description": "WDC for STP, Moscow collects, stores, exchanges with other WDCs, disseminates the publications, sends upon requests data on the following Solar-Terrestrial Physics disciplines: Solar Activity and Interplanetary Medium, Cosmic Rays, Ionospheric Phenomena, Geomagnetic Variations.",
"homepage": "http://www.wdcb.ru/stp/index.en.html",
"name": "World Data Center for Solar-Terrestrial Physics, Moscow",
"prefix": "r3d100010446",
"synonyms": [
"WDC - Solar-Terrestrial Physics, Moscow",
"WDC for STP, Moscow",
"WDC for Solar-Earth Physics",
"ΠΠΈΡΠΎΠ²ΠΎΠΉ Π¦Π΅Π½ΡΡ ΠΠ°Π½Π½ΡΡ
ΠΏΠΎ ΠΠΌΠ±Π»Π΅ΠΌΠ° ΠΠ¦Π ΠΏΠΎ Π‘ΠΠ€ Π‘ΠΎΠ»Π½Π΅ΡΠ½ΠΎ-ΠΠ΅ΠΌΠ½ΠΎΠΉ Π€ΠΈΠ·ΠΈΠΊΠ΅"
]
},
"r3d100010447": {
"description": "World Data Center for Solid Earth Physics collects, stores, and disseminates a wide range of data on solid Earth physics disciplines: Seismology, Gravimetry, Heat Flow, Magnetic Measurements (main magnetic field), Archeo- & Paleomagnetism, Recent Movements.\nThese data are used as the basis for fundamental and applied scientific researches and education. The WDC for SEP invites scientists, institutions and other authors and data generators to contribute data to our Center in order to make data more widely available to the scientific community and to safe them.",
"homepage": "http://www.wdcb.ru/sep/",
"name": "World Data Center for Solid Earth Physics",
"prefix": "r3d100010447",
"synonyms": [
"WDC - Solid Earth Physics, Moscow",
"WDC for SEP"
]
},
"r3d100010448": {
"description": "WFCC-MIRCEN World Data Centre for Microorganisms (WDCM) provides a comprehensive directory of culture collections, databases on microbes and cell lines, and the gateway to biodiversity, molecular biology and genome projects.The WFCC is a Multidisciplinary Commission of the International Union of Biological Sciences (IUBS) and a Federation within the International Union of Microbiological Societies (IUMS). The WFCC is concerned with the collection, authentication, maintenance and distribution of cultures of microorganisms and cultured cells. Its aim is to promote and support the establishment of culture collections and related services, to provide liaison and set up an information network between the collections and their users, to organise workshops and conferences, publications and newsletters and work to ensure the long term perpetuation of important collections.",
"homepage": "https://www.wdcm.org/",
"name": "World Data Center of Microorganisms",
"prefix": "r3d100010448",
"synonyms": [
"WDCM",
"WFCC - MIRCEN World Data Centre for Microorganisms"
]
},
"r3d100010449": {
"description": "We are a leading international centre for genomics and bioinformatics research. Our mandate is to advance knowledge about cancer and other diseases, to improve human health through disease prevention, diagnosis and therapeutic approaches, and to realize the social and economic benefits of genomics research.",
"homepage": "https://www.bcgsc.ca/",
"name": "Canada's Michael Smith Genome Sciences Centre",
"prefix": "r3d100010449",
"synonyms": [
"GSC"
]
},
"r3d100010450": {
"description": "EDINA delivers online services and tools to benefit students, teachers and researchers in UK Higher and Further Education and beyond.",
"homepage": "https://edina.ac.uk/",
"name": "EDINA",
"prefix": "r3d100010450"
},
"r3d100010451": {
"description": "PARADISEC (the Pacific And Regional Archive for Digital Sources in Endangered Cultures) offers a facility for digital conservation and access to endangered materials from all over the world. Our research group has developed models to ensure that the archive can provide access to interested communities, and conforms with emerging international standards for digital archiving. We have established a framework for accessioning, cataloguing and digitising audio, text and visual material, and preserving digital copies. The primary focus of this initial stage is safe preservation of material that would otherwise be lost, especially field tapes from the 1950s and 1960s.",
"homepage": "https://www.paradisec.org.au/",
"name": "Pacific and Regional Archive for Digital Sources in Endangered Cultures",
"prefix": "r3d100010451",
"synonyms": [
"PARADISEC"
]
},
"r3d100010454": {
"description": "The Data Center for Aurora in NIPR is responsible for data archiving and dissemination of all-sky camera observations, visual observations, other optical observations (such as TV and photometric observations), auroral image and particle observations from satellites, geomagnetic observations, and observations of upper atmosphere phenomena associated with aurora such as ULF, VLF and CNA activities.\nThis Data Catalogue summarizes the collection of data sets, data books, related publications and facilities available in the WDC for Aurora as of December 2003.\nThe WDC for Aurora changed its name as \"Data Center for Aurora in NIPR\" in 2008 due to the disappearance of the WDC panel in ICSU.",
"homepage": "http://polaris.nipr.ac.jp/~aurora/",
"name": "Data Center for Aurora in NIPR",
"prefix": "r3d100010454",
"synonyms": [
"Polar Data Center",
"WDC for Aurora",
"World Data Center for Aurora"
],
"xrefs": {
"biodbcore": "001628"
}
},
"r3d100010455": {
"description": "<<>>!!!>>> The ICET Data Bank contains results from 360 tidal gravity stations: hourly values, main tidal waves obtained by least squares analyses, residual vectors, oceanic attraction and loading vectors. The Data Bank contains also data from tiltmeters and extensometers. ICET is responsible for the Information System and Data Center of the Global Geodynamic Project (GGP). The tasks ascribed to ICET are : to collect all available measurements of Earth tides (which is its task as World Data Centre C), to evaluate these data by convenient methods of analysis in order to reduce the very large amount of measurements to a limited number of parameters which should contain all the desired and needed geophysical information, to compare the data from different instruments and different stations distributed all over the world, evaluate their precision and accuracy from the point of view of internal errors as well as external errors, to help to solve the basic problem of calibrations and to organize reference stations or build reference calibration devices, to fill gaps in information or data as far as feasible, to build a data bank allowing immediate and easy comparison of Earth tide parameters with different Earth models and other geodetical and geophysical parameters like geographical position, Bouguer anomaly, crustal thickness and age, heat flow, ... to ensure a broad diffusion of the results and information to all interested laboratories and individual scientists.",
"homepage": "http://www.upf.pf/ICET/",
"name": "ICET",
"prefix": "r3d100010455",
"synonyms": [
"International Center for Earth Tides",
"formerly: World Data Center C For Earth Tides",
"formerly: World Data Centre for Earth Tides"
],
"xrefs": {
"issn": "2428-4556"
}
},
"r3d100010457": {
"description": "Until 2014 housed in the library of the Scott Polar Research Institute, the WDC for Glaciology, Cambridge, maintains a particularly comprehensive collection of publications covering all aspects of snow and ice worldwide. Glaciological literature has been systematically collected and catalogued at the Scott Polar Research Institute since 1920. The SPRI Picture Library houses one of the world's most comprehensive collections of historical photographs of the Polar Regions",
"homepage": "https://www.spri.cam.ac.uk/library/catalogue/sprilib/icesnow/",
"name": "World Data Centre for Glaciology, Cambridge",
"prefix": "r3d100010457",
"synonyms": [
"SPRILIB Ice and Snow",
"WDC-C for Glaciology",
"WDCGC"
]
},
"r3d100010463": {
"description": "DARTS primarily archives high-level data products obtained by JAXA's space science missions in astrophysics (X-rays, radio, infrared), solar physics, solar-terrestrial physics, and lunar and planetary science. In addition, we archive related space science data products obtained by other domestic or foreign institutes, and provide data services to facilitate use of these data.",
"homepage": "https://darts.isas.jaxa.jp/",
"name": "DARTS",
"prefix": "r3d100010463",
"synonyms": [
"ISAS Data Archive and Transmission System",
"World Data Center for Space Science Satellites"
]
},
"r3d100010464": {
"description": "Research Data Australia is the data discovery service of the Australian Research Data Commons (ARDC). The ARDC is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy Program.\nResearch Data Australia helps you find, access, and reuse data for research from over one hundred Australian research organisations, government agencies, and cultural institutions. We do not store the data itself here but provide descriptions of, and links to, the data from our data publishing partners.",
"homepage": "https://researchdata.edu.au/",
"name": "Research Data Australia",
"prefix": "r3d100010464",
"xrefs": {
"fairsharing": "FAIRsharing.2g5kcb"
}
},
"r3d100010465": {
"description": "<<>>!!!>>>",
"homepage": "http://www.march.es/ceacs/biblioteca/datalib/",
"name": "CEACS Data Library",
"prefix": "r3d100010465",
"synonyms": [
"Biblioteca de Datos de CEACS",
"Instituto Juan March - Center for Advanced Study in the Social Sciences (CEACS) Dataverse"
]
},
"r3d100010467": {
"description": "Scans of plates obtained at Landessternwarte Heidelberg-KΓΆnigstuhl and German-Spanish Astronomical Center (Calar Alto Observatory), Spain, 1900 through 1999.",
"homepage": "https://dc.zah.uni-heidelberg.de/lswscans/res/positions/q/form",
"name": "HDAP",
"prefix": "r3d100010467",
"synonyms": [
"Heidelberg Digitized Astronomical Plates"
]
},
"r3d100010468": {
"description": "ZENODO builds and operates a simple and innovative service that enables researchers, scientists, EU projects and institutions to share and showcase multidisciplinary research results (data and publications) that are not part of the existing institutional or subject-based repositories of the research communities.\nZENODO enables researchers, scientists, EU projects and institutions to:\neasily share the long tail of small research results in a wide variety of formats including text, spreadsheets, audio, video, and images across all fields of science.\ndisplay their research results and get credited by making the research results citable and integrate them into existing reporting lines to funding agencies like the European Commission.\neasily access and reuse shared research results.",
"homepage": "https://zenodo.org/",
"name": "Zenodo",
"prefix": "r3d100010468",
"xrefs": {
"fairsharing": "FAIRsharing.wy4egf",
"nlx": "158614",
"scr": "004129"
}
},
"r3d100010469": {
"description": "This data repository allows users to publish animal tracking datasets that have been uploaded to Movebank (https://www.movebank.org/ ). Published datasets have gone through a submission and review process, and are typically associated with a written study published in an academic journal. All animal tracking data in this repository are available to the public.",
"homepage": "https://www.datarepository.movebank.org/",
"name": "Movebank Data Repository",
"prefix": "r3d100010469",
"xrefs": {
"fairsharing": "FAIRsharing.httzv2"
}
},
"r3d100010472": {
"description": "Phaidra UniversitΓ€t Wien, is the innovative whole-university digital asset management system with long-term archiving functions, offers the possibility to archive valuable data university-wide with permanent security and systematic input, offering multilingual access using metadata (data about data), thus providing worldwide availability around the clock. As a constant data pool for administration, research and teaching, resources can be used flexibly, where continual citability allows the exact location and retrieval of prepared digital objects.",
"homepage": "https://phaidra.univie.ac.at/",
"name": "Phaidra UniversitΓ€t Wien",
"prefix": "r3d100010472",
"synonyms": [
"Permanent Hosting, Archiving and Indexing of Digital Resources and Assets"
],
"xrefs": {
"fairsharing": "FAIRsharing.6a56fd",
"opendoar": "1726",
"roar": "2475"
}
},
"r3d100010473": {
"description": "myExperiment is a collaborative environment where scientists can safely publish their workflows and in silico experiments, share them with groups and find those of others. Workflows, other digital objects and bundles (called Packs) can now be swapped, sorted and searched like photos and videos on the Web. Unlike Facebook or MySpace, myExperiment fully understands the needs of the researcher and makes it really easy for the next generation of scientists to contribute to a pool of scientific methods, build communities and form relationships β reducing time-to-experiment, sharing expertise and avoiding reinvention. myExperiment is now the largest public repository of scientific workflows.",
"homepage": "https://www.myexperiment.org/home",
"name": "myExperiment",
"prefix": "r3d100010473",
"xrefs": {
"fairsharing": "FAIRsharing.a971f7",
"nif": "0000-10309",
"scr": "001795"
}
},
"r3d100010474": {
"description": "The International Food Policy Research Institute (IFPRI) seeks sustainable solutions for ending hunger and poverty. In collaboration with institutions throughout the world, IFPRI is often involved in the collection of primary data and the compilation and processing of secondary data. The resulting datasets provide a wealth of information at the local (household and community), national, and global levels. IFPRI freely distributes as many of these datasets as possible and encourages their use in research and policy analysis. IFPRI Dataverse contains following dataverses: Agricultural Science and Knowledge Indicators - ASTI, HarvestChoice, Statistics on Public Expenditures for Economic Development - SPEED, International Model for Policy Analysis of Agricultural Commodities and Trade - IMPACT, Africa RISING Dataverse and Food Security Portal Dataverse.",
"homepage": "https://dataverse.harvard.edu/dataverse/IFPRI",
"name": "International Food Policy Research Institute Dataverse",
"prefix": "r3d100010474",
"synonyms": [
"IFPRI Dataverse"
]
},
"r3d100010475": {
"description": "<<>>!!!>>>\n DataFed is a web services-based software that non-intrusively mediates between autonomous, distributed data providers and users. The main goals of DataFed are: Aid air quality management and science by effective use of relevant data - Facilitate the access and flow of atmospheric data from provider to users - Support the development of user-driven data processing value chains. DataFed Catalog links searchable Datafed applications worldwide.",
"name": "DataFed",
"prefix": "r3d100010475",
"synonyms": [
"Data Federation"
]
},
"r3d100010477": {
"description": "The Australian National University undertake work to collect and publish metadata about research data held by ANU, and in the case of four discipline areas, Earth Sciences, Astronomy, Phenomics and Digital Humanities to develop pipelines and tools to enable the publication of research data using a common and repeatable approach. Aims and outcomes: To identify and describe research data held at ANU, to develop a consistent approach to the publication of metadata on the University's data holdings: Identification and curation of significant orphan data sets that might otherwise be lost or inadvertently destroyed, to develop a culture of data data sharing and data re-use.",
"homepage": "https://datacommons.anu.edu.au/DataCommons/",
"name": "ANU Data Commons",
"prefix": "r3d100010477",
"synonyms": [
"Australian National University Data Commons"
]
},
"r3d100010478": {
"description": "GigaDB primarily serves as a repository to host data and tools associated with articles published by GigaScience Press; GigaScience and GigaByte (both are online, open-access journals). GigaDB defines a dataset as a group of files (e.g., sequencing data, analyses, imaging files, software programs) that are related to and support a unit-of-work (article or study). GigaDB allows the integration of manuscript publication with supporting data and tools.",
"homepage": "http://gigadb.org/",
"name": "GigaDB",
"prefix": "r3d100010478",
"synonyms": [
"GigaScience Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.rcbwsf",
"nlx": "158413",
"scr": "004002"
}
},
"r3d100010479": {
"description": "<<>>!!!>>>, archived site: https://archive.is/6UyFH/image!!!",
"name": "DataBox",
"prefix": "r3d100010479",
"synonyms": [
"DataBox Dataverse Network"
]
},
"r3d100010480": {
"description": "The COSYNA observatory measures key physical, sedimentary, geochemical and biological parameters at high temporal resolution in the water column and at the sediment and atmospheric boundaries.\nCOSYNA delivers spatial representation through a set of fixed and moving platforms, like tidal flats poles, FerryBoxes, gliders, ship surveys, towed devices, remote sensing, etc..\nNew technologies like underwater nodes, benthic landers and automated sensors for water biogeochemical parameters are further developed and tested.\nA great variety of parameters is measured and processed, stored, analyzed, assimilated into models and visualized.",
"homepage": "https://codm.hzg.de/codm/",
"name": "COSYNA Data web portal",
"prefix": "r3d100010480",
"synonyms": [
"CODM"
],
"xrefs": {
"fairsharing": "FAIRsharing.f7e006"
}
},
"r3d100010482": {
"description": "The GAVO data centre at Zentrum fΓΌr Astronomie Heidelberg publishes astronomical data of all kinds β e.g., catalogues, images, spectra, time series, simulation results β in accordance with Virtual Observatory standards, making them findable and immediately usable through popular clients like TOPCAT, Aladin, or programatically through the astropy-affiliated package pyVO or the Java library STIL. We pay particular attention to providing thorough metadata to the VO Registry in order to facilitate discovery and reuse.\nWhile we have a clear focus on data produced with German contributions, we will usually publish data of other provenance, too. See https://docs.g-vo.org/DaCHS/data_checklist.html for an overview of what resource-level metadata we ask for; contact us for further information on how to publish through the German Astronomical Virtual Observatory.",
"homepage": "https://dc.zah.uni-heidelberg.de/",
"name": "GAVO Data Centre",
"prefix": "r3d100010482",
"synonyms": [
"GAVO Data Center",
"German Astrophysical Virtual Observatory Data Centre"
]
},
"r3d100010483": {
"description": "AUSSDA - The Austrian Social Science Data Archive is a certified, national research infrastructure for the social science community. We offer sustainable and easy-to-use services in the field of digital archiving and preservation. The main beneficiaries are researchers, students, educational institutions and media professionals.\nWe implement international standards to make research data findable, accessible, interoperable and reusable according to the FAIR principles. AUSSDA supports the open science movement to maximize the potential for data reuse. We stand for integrity in archiving and advocate for compliance with data protection and ethical principles in research data management.\nAUSSDA represents Austria as a national service provider in CESSDA ERIC, has locations at the universities of Vienna, Graz, Linz, Innsbruck, Krems and at the OeAW (Austrian Academy of Sciences) and works within a network of national and international partners.",
"homepage": "https://data.aussda.at/",
"name": "AUSSDA - Austrian Social Science Data Archive",
"prefix": "r3d100010483",
"xrefs": {
"fairsharing": "FAIRsharing.RJ3PDJ"
}
},
"r3d100010484": {
"description": "The Czech Social Science Data Archive (CSDA) of the Institute of Sociology of the Academy of Sciences of the Czech Republic accesses, processes, documents and stores data files from social science research projects and promotes their dissemination to make them widely available for secondary use in academic research and for educational purposes.",
"homepage": "https://archiv.soc.cas.cz/en/pristup-k-datum-2/nase-data",
"name": "Czech Social Science Data Archive",
"prefix": "r3d100010484",
"synonyms": [
"CSDA"
]
},
"r3d100010485": {
"description": "The Estonian Social Science Data Archive (ESSDA) contains Estonian Social science data and survey data, as well as university publications and Estonian radio archival materials.",
"homepage": "https://sisu.ut.ee/esta?lang=en",
"name": "Eesti Sotsiaalteaduslik Andmearhiiv",
"prefix": "r3d100010485",
"synonyms": [
"ESSDA",
"ESTA",
"Estonian Social Science Data Archive"
]
},
"r3d100010486": {
"description": "The National Archives makes Denmark's largest collection of questionnaire-based research data available to researchers and students. Order quantitative research data, conduct analyzes online and access register data and international survey data. Formerly known as the Danish Data Archive (DDA), it was the national social science data archive.",
"homepage": "https://www.rigsarkivet.dk/udforsk/survey-data/",
"name": "Rigsarkivets surveydata",
"prefix": "r3d100010486",
"synonyms": [
"National Archives' survey data",
"formerly: DDA",
"formerly: Danish Data Archive",
"formerly: Dansk Data Arkiv"
]
},
"r3d100010487": {
"description": "The Slovenian Social Science Data Archives (Slovenski Arhiv DruΕΎboslovnih podatkov - ADP) were established in 1997 as an organizational unit within the Institute of Social Sciences at the Faculty of Social Sciences, University of Ljubljana. Its tasks are to acquire significant data sources within a wide range of social science disciplines of interest to Slovenian social scientists, review and prepare them for digital preservation, and to disseminate them for further scientific, educational and other purposes.",
"homepage": "https://www.adp.fdv.uni-lj.si/eng/",
"name": "Slovenian Social Science Data Archives",
"prefix": "r3d100010487",
"synonyms": [
"ADP",
"Arhiv druzboslovnih podatkov"
]
},
"r3d100010488": {
"description": "Initiated in 1989 and established in 2014, the Luxembourg Institute of Socio-Economic Research (LISER) is a public research institute located in Luxembourg under the supervision of the Ministry of Higher Education and Research. Integrated into a unified legal framework (law of 3 December 2014) LISERβs missions are to undertake both fundamental and applied research in social sciences that aim to advance knowledge, support public policy both at the national and European level and inform society.\n\nLISER contributes to the advancement of scientific knowledge in social and economic matters across the activities of its three research departments \"Living Conditions\", \"Labour Market\" and \"Urban Development and Mobility\".\n\nIn parallel, the institute aligns itself with national and European priorities and fosters interdisciplinarity by focusing its research work on three priority research programmes: βCrossing Bordersβ, \"Health and Health Systems\" and \"Digital Transformation\".\n\nLISER hosts two complementary infrastructures, key drivers of its research development and excellence.\n- The Data Centre, which consists of two pillars, the data collection capability (direct and indirect data collection), and the data archiving and data management capability.\n- The Behavioural and Experimental Economics dedicated to investigating human decision-making by means of experiments performed in controlled environments. Its experimental approach contributes to improving the understanding of human behaviour in a large variety of socioeconomic contexts.\nLISER aims to be an internationally recognized socio-economic research institute specializing in the analysis of societal changes. Through its inter-and-multidisciplinary research, it makes a proactive and targeted contribution to the sustainable and inclusive development of societies at the national and international levels.",
"homepage": "https://www.liser.lu",
"name": "LISER",
"prefix": "r3d100010488",
"synonyms": [
"Luxembourg Institute of Socio-Economic Research",
"formerly: CEPS/INSTEAD Surveys"
]
},
"r3d100010489": {
"description": "The majority of the CIS research activity focuses on carrying out public opinion surveys. These surveys include electoral studies, its monthly public opinion barometers, monographic studies on different aspects of Spanish society and the surveys resulting from CIS involvement in international projects.\nAll the surveys the CIS takes are deposited in its Data Bank, and they are available to the public once the quality control, verification, anonymisation, codification and information uploading tasks have been concluded.\nIn addition to its surveys, the CIS also collects information about Spanish society through qualitative research studies: Fundamentally, discussion groups and in-depth interviews.",
"homepage": "https://www.cis.es/estudios/catalogo-estudios",
"name": "Centro de Investigaciones Sociologicas Data Bank y Estudios",
"prefix": "r3d100010489",
"synonyms": [
"Banco de Datos EspecΓfico de Estudios Sociales - ARCES del CIS",
"CIS Data Bank"
]
},
"r3d100010490": {
"description": "The Finnish Social Science Data Archive (FSD) is a national resource centre for research and education. FSD's mission is to preserve data collected to study Finnish society, people and cultural phenomena in the long term. FSD archives, promotes and disseminates digital research data for research, teaching and learning purposes. Data descriptions are published in Finnish and English on FSDβs service portal Aila, through which users also download data. Quantitative datasets are translated from Finnish into English on request, and a large number of datasets are available in English. All services are free of charge. FSD promotes transparency, accumulation and efficient reuse of scientific research as well as open access to research data. FSD is the Finnish Service Provider for CESSDA ERIC.",
"homepage": "https://www.fsd.tuni.fi/en/",
"name": "Finnish Social Science Data Archive",
"prefix": "r3d100010490",
"synonyms": [
"FSD",
"Finlands samhΓ€llsvetenskapliga dataarkiv",
"Yhteiskuntatieteellinen tietoarkisto"
],
"xrefs": {
"fairsharing": "FAIRsharing.2okP6D",
"isni": "0000 0004 7448 6517",
"ror": " 05wmhj005",
"wikidata": " Q11902697"
}
},
"r3d100010491": {
"description": "So.Da.Net network, following the Social Data Bank (SDB) of the National Centre for Social Research (EKKE) that pre-existed, in a time frame of five years has been linked and closely collaborated with the european data archives. EKKE through SDB has participated to the European Consortium of Social Science Data Archives (CESSDA ERIC) since 2000. The national research network Sodanet_GR has been formed in 2012 and is consisted of the following 7 organisations: \n1) National Centre for Social Research (EKKE) β Social Data Bank\n2) University of the Aegean β Department of Sociology\n3) National & Kapodistrian University of Athens β Department of Political Science & Public Administration\n4) Panteion University β Department of Political Science & History\n5) University of Peloponnese β Department of Social & Educational Policy\n6) Democritus University of Trace β Department of Social Administration & Political Science\n7) University of Crete β Department of Sociology .\n The So.Da.Net network is the Greek research infrastructure for the social sciences. \nSo.Da.Net supports multidisciplinary research and promotes the acquisition, exchange, processing as well as dissemination of data deriving from and related to social science research.",
"homepage": "https://sodanet.gr/",
"name": "Social Data Network",
"prefix": "r3d100010491",
"synonyms": [
"Greek Social Data Bank (earlier name)",
"SO.DA.NET",
"SoDaNet",
"The Greek research infrastructure for social sciences"
]
},
"r3d100010492": {
"description": "Lithuanian Data Archive for Social Sciences and Humanities (LiDA) is a virtual digital infrastructure for SSH data and research resources acquisition, long-term preservation and dissemination. All the data and research resources are documented in both English and Lithuanian according to international standards. Access to the resources is provided via Dataverse repository. LiDA curates different types of resources and they are published into catalogues according to the type: Survey Data, Aggregated Data (including Historical Statistics), Encoded Data (including News Media Studies), and Textual Data. Also, LiDA holds collections of social sciences and humanities data deposited by Lithuanian science and higher education institutions and Lithuanian state institutions (Data of Other Institutions).\n\nLiDA is hosted by the Centre for Data Analysis and Archiving of Kaunas University of Technology (data.ktu.edu).",
"homepage": "https://lida.dataverse.lt",
"name": "LiDA",
"prefix": "r3d100010492",
"synonyms": [
"Lietuvos humanitariniΕ³ ir socialiniΕ³ mokslΕ³ duomenΕ³ archyvas",
"Lithuanian Data Archive for Social Sciences and Humanities"
]
},
"r3d100010493": {
"description": "Sikt archives research data on people and society to make sure the data can be shared and is made available for reuse. We continuously enrich our data collections to provide a richer basis for research.\n\nSiktβs main focus is quantitative data matrices on individuals, organisations, administrative, political, and geographical actors. The archive specialise in survey data, which undergoes extensive curation at the variable level and detailed metadata is produced and published in Norwegian and English.",
"homepage": "https://sikt.no/en/find-data",
"name": "Sikt Research Data Archive",
"prefix": "r3d100010493",
"synonyms": [
"Sikt forskningsdataarkiv",
"formerly: Norsk senter for forskningsdata / Norwegian Centre for Research Data"
]
},
"r3d100010494": {
"description": "Quetelet-Progedo-Diffusion allows searching and accessing data from national public statistics (major surveys, censuses, databases) and large surveys from French research.\n- Major data, censuses and other databases of French National Statistics\n- Major French research data\n- Privileged access to international data",
"homepage": "https://data.progedo.fr/",
"name": "Quetelet-Progedo-Diffusion",
"prefix": "r3d100010494",
"synonyms": [
"French data archives for social sciences",
"Réseau français des centres de données pour les sciences sociales"
],
"xrefs": {
"issn": "2427-1683"
}
},
"r3d100010495": {
"description": "Unidata β Bicocca Data Archive is an interdepartmental center of the University of Milan-Bicocca, born in 2015. The center is the Italian point of reference for the research data archiving and dissemination, based on the example of the National Archives located in major European countries and beyond.\nUniData inherits the long work from the ADPSS-Sociodata Data Archive, born in 1999 in the Department of Sociology and Social Research at the same University.\nHere you can find only individual data from 2010.\nFor older surveys please visit ADPSS Sociodata, Data Archive for Social Sciences - Archivio Dati e Programmi Per le Scienze Soziali: https://www.unidata.unimib.it/old/ and\nADPSS-SOCIODATA Archivio Dati e Programmi per le Scienze Sociali Dataverse : https://dataverse.harvard.edu/dataverse/adpss",
"homepage": "https://www.unidata.unimib.it/?lang=en",
"name": "UNIDATA - Bicocca Data Archive",
"prefix": "r3d100010495",
"synonyms": [
"ADPSS Sociodata",
"ADPSS-SOCIODATA Archivio Dati e Programmi per le Scienze Sociali Dataverse",
"Archivio Dati e Programmi per le Scienze Sociali",
"Data Archive for Social Sciences"
]
},
"r3d100010496": {
"description": "TΓRKI Social Research Institute is an independent, employee-owned research organisation that specialises in policy research in the fields of social policy and the social consequences of economic policies. This includes related data-collection, archiving and statistical activities. We recently increased our involvement in the areas of strategic market research and health policy analysis. In addition, we regularly contribute to basic research, in the areas of social stratification and inequality, and to the methodology of empirical social research.",
"homepage": "https://adatbank.tarki.hu/en/",
"name": "TARKI Data Archive",
"prefix": "r3d100010496",
"synonyms": [
"TΓRKI"
],
"xrefs": {
"fairsharing": "FAIRsharing.d14d9f"
}
},
"r3d100010497": {
"description": "The Irish Social Science Data Archive (ISSDA) is Irelandβs leading centre for quantitative data acquisition, preservation, and dissemination. Its mission is to ensure wide access to quantitative datasets in the social sciences, and to advance the promotion of international comparative studies of the Irish economy and Irish society.",
"homepage": "https://www.ucd.ie/issda/",
"name": "Irish Social Science Data Archive",
"prefix": "r3d100010497",
"synonyms": [
"ISSDA"
]
},
"r3d100010498": {
"description": "RODA is the national Romanian institution specialised in archiving electronic data collections obtained by social research.\nThe archive contains data collections accessible for the academic community and the interested public, for secondary and comparative analysis, under certain access conditions ranging from free access to some level of restriction imposed by owners. The archive serves as an intermediary between the data owners and data users.",
"homepage": "http://www.roda.ro/en/home",
"name": "Romanian Social Data Archive",
"prefix": "r3d100010498",
"synonyms": [
"Arhiva RomΓ’nΔ de Date Sociale",
"RODA"
]
},
"r3d100010499": {
"description": "NAGRP Blast Center aggregates various sequence databases and makes them accessible via its website.",
"homepage": "https://www.animalgenome.org/blast/",
"name": "NAGRP Blast Center",
"prefix": "r3d100010499",
"synonyms": [
"National Animal Genome Research Program Blast Center"
]
},
"r3d100010501": {
"description": "The Crustal Dynamics Data Information System (CDDIS) was initially developed to provide a central data bank for NASA's Crustal Dynamics Project (CDP). The Crustal Dynamics Data Information System (CDDIS) supports data archiving and distribution activities for the space geodesy and geodynamics community. The main objectives of the system are to store space geodesy and geodynamics related data products in a central data bank, to maintain information about the archival of these data, and to disseminate these data and information in a timely manner to NASA investigators and cooperating institutions.",
"homepage": "https://cddis.nasa.gov/",
"name": "Crustal Dynamics Data Information System",
"prefix": "r3d100010501",
"synonyms": [
"CDDIS",
"NASA's archive of space geodesy data"
],
"xrefs": {
"fairsharing": "FAIRsharing.afa06f"
}
},
"r3d100010502": {
"description": "The Global Hydrology Resource Center (GHRC) provides both historical and current Earth science data, information, and products from satellite, airborne, and surface-based instruments. GHRC acquires basic data streams and produces derived products from many instruments spread across a variety of instrument platforms.",
"homepage": "https://ghrc.nsstc.nasa.gov/home/",
"name": "GHRC",
"prefix": "r3d100010502",
"synonyms": [
"Global Hydrology Resource Center",
"Marshall Distributed Active Archive Center (formerly)",
"NASA Earth Science Data Center"
]
},
"r3d100010503": {
"description": "LAADS DAAC is the web interface to the Level 1 and Atmosphere Archive and Distribution System (LAADS). The mission of LAADS is to provide quick and easy access to MODIS Level 1, Atmosphere and Land data products, VIIRS Level 1 and Land data products MAS and MERIS data products. MODIS (or Moderate Resolution Imaging Spectroradiometer) is a key instrument aboard the Terra (EOS AM) and Aqua (EOS PM) satellites.",
"homepage": "https://ladsweb.modaps.eosdis.nasa.gov/",
"name": "LAADS DAAC",
"prefix": "r3d100010503",
"synonyms": [
"LAADS web",
"Level 1 and Atmosphere Archive and Distribution System - Distributed Active Archive Center"
]
},
"r3d100010504": {
"description": "The Ocean Biology Processing Group (OBPG) serves as the Distributed Active Archive Center (DAAC) for all Ocean Biology (OB) data produced or collected under NASAβs Earth Observing System Data and Information System (EOSDIS). This website thus serves as the primary data access portal to the NASA OB.DAAC. The links below provide a variety of methods to access the holdings of the OB.DAAC, including visual browsers that enable point-and-click access by data levels and direct access for bulk download. In agreement with partner organizations, some data access requires user registration to enable better tracking of usage metrics.",
"homepage": "https://oceancolor.gsfc.nasa.gov/",
"name": "OceanColor web",
"prefix": "r3d100010504",
"synonyms": [
"OB.DAAC",
"Ocean Biology DAAC",
"Ocean Biology Data Active Archive Center"
]
},
"r3d100010505": {
"description": "The Physical Oceanography Distributed Active Archive Center (PO.DAAC) is an element of the Earth Observing System Data and Information System (EOSDIS). The EOSDIS provides science data to a wide community of users for NASA's Science Mission Directorate. \nSince the launch of NASA's first ocean-observing satellite, Seasat, in 1978, PO.DAAC has become the premier data center for measurements focused on ocean surface topography (OST), sea surface temperature (SST), ocean winds, sea surface salinity (SSS), gravity, ocean circulation and sea ice.In addition to providing access to its data holdings, PO.DAAC acts as a gateway to data stored at other ocean and climate archives. This and other tools and services enable PO.DAAC to support a wide user community working in areas such as ocean and climate research, applied science and industry, natural resource management, policy making, and general public consumption.",
"homepage": "https://podaac.jpl.nasa.gov/",
"name": "Physical Oceanography Distributed Active Archive Center",
"prefix": "r3d100010505",
"synonyms": [
"PO.DAAC"
],
"xrefs": {
"biodbcore": "001567",
"fairsharing": "FAIRsharing.6bb22f"
}
},
"r3d100010506": {
"description": "The SAR Data Center has a large data archive of Synthetic Aperture Radar (SAR) from a variety of sensors available at no cost. Much of the SAR data in the ASF SDC archive is limited in distribution to the scientific research community and U.S. Government Agencies. In accordance with the Memoranda of Understanding (MOU) between the relevant flight agencies (CSA, ESA, JAXA) and the U.S. State Department, the ASF SDC does not distribute SAR data for commercial use.\nThe research community can access the data (ERS-1, ERS-2, JERS-1, RADARSAT-1, and ALOS PALSAR) via a brief proposal process.",
"homepage": "https://www.asf.alaska.edu/",
"name": "Alaska Satellite Facility SAR Data Center",
"prefix": "r3d100010506",
"synonyms": [
"ASF SDC"
],
"xrefs": {
"nlx": "157757",
"scr": "003610"
}
},
"r3d100010508": {
"description": "The International Laser Ranging Service (ILRS) provides global satellite and lunar laser ranging data and their related products to support geodetic and geophysical research activities as well as IERS products important to the maintenance of an accurate International Terrestrial Reference Frame (ITRF). The service develops the necessary global standards/specifications and encourages international adherence to its conventions. The ILRS is one of the space geodetic services of the International Association of Geodesy (IAG).\n\nThe ILRS collects, merges, archives and distributes Satellite Laser Ranging (SLR) and Lunar Laser Ranging (LLR) observation data sets of sufficient accuracy to satisfy the objectives of a wide range of scientific, engineering, and operational applications and experimentation.",
"homepage": "https://ilrs.cddis.eosdis.nasa.gov/",
"name": "International Laser Ranging Service",
"prefix": "r3d100010508",
"synonyms": [
"ILRS"
]
},
"r3d100010509": {
"description": "The Alvin Frame-Grabber system provides the NDSF community on-line access to Alvin's video imagery co-registered with vehicle navigation and attitude data for shipboard analysis, planning deep submergence research cruises, and synoptic review of data post-cruise. The system is built upon the methodology and technology developed for the JasonII Virtual Control Van and a prototype system that was deployed on 13 Alvin dives in the East Pacific Rise and the Galapagos (AT7-12, AT7-13). The deployed prototype system was extremely valuable in facilitating real-time dive planning, review, and shipboard analysis.",
"homepage": "http://4dgeo.whoi.edu/alvin",
"name": "Alvin Frame-Grabber System",
"prefix": "r3d100010509",
"synonyms": [
"AlvinFG System"
]
},
"r3d100010510": {
"description": "Jason is a remote-controlled deep-diving vessel that gives shipboard scientists immediate, real-time access to the sea floor. Instead of making short, expensive dives in a submarine, scientists can stay on deck and guide Jason as deep as 6,500 meters (4 miles) to explore for days on end.\nJason is a type of remotely operated vehicle (ROV), a free-swimming vessel connected by a long fiberoptic tether to its research ship. The 10-km (6 mile) tether delivers power and instructions to Jason and fetches data from it.",
"homepage": "http://4dgeo.whoi.edu/jason",
"name": "Jason Virtual Van",
"prefix": "r3d100010510",
"xrefs": {
"biodbcore": "001491",
"fairsharing": "FAIRsharing.1ab6fc"
}
},
"r3d100010511": {
"description": "The WHOI Ship DataGrabber system provides the oceanographic community on-line access to underway ship data collected on the R/V Atlantis, Knorr, Oceanus, and Tioga (TBD). All the shipboard data is co-registered with the ship's GPS time and navigation systems.",
"homepage": "http://4dgeo.whoi.edu/shipdata/index.html",
"name": "WHOI Ship Data-Grabber System",
"prefix": "r3d100010511",
"xrefs": {
"fairsharing": "FAIRsharing.134085"
}
},
"r3d100010512": {
"description": "The Argo observational network consists of a fleet of 3000+ profiling autonomous floats deployed by about a dozen teams worldwide. WHOI has built about 10% of the global fleet. The mission lifetime of each float is about 4 years. During a typical mission, each float reports a profile of the upper ocean every 10 days. The sensors onboard record fundamental physical properties of the ocean: temperature and conductivity (a measure of salinity) as a function of pressure. The depth range of the observed profile depends on the local stratification and the float's mechanical ability to adjust it's buoyancy. The majority of Argo floats report profiles between 1-2 km depth. At each surfacing, measurements of temperature and salinity are relayed back to shore via satellite. Telemetry is usually received every 10 days, but floats at high-latitudes which are iced-over accumulate their data and transmit the entire record the next time satellite contact is established. With current battery technology, the best performing floats last 6+ years and record over 200 profiles.",
"homepage": "https://argo.whoi.edu/",
"name": "WHOI Argo Program",
"prefix": "r3d100010512",
"synonyms": [
"A Robotic Survey of Global Ocean Temperature & Salinity",
"Woods Hole Oceanographic Institution Argo Program"
]
},
"r3d100010514": {
"description": "The Data Library and Archives (DLA) is part of the joint library system supported by the Marine Biological Laboratory and the Woods Hole Oceanographic Institution. The DLA holds collections of administrative records, photographs, scientists' data and papers, film and video, historical instruments, as well as books, journals and technical reports.",
"homepage": "https://www.dla.whoi.edu/dla/",
"name": "Woods Hole Oceanographic Institution Data Library and Archives",
"prefix": "r3d100010514",
"synonyms": [
"WHOI DLA"
]
},
"r3d100010515": {
"description": "<<>>!!!>>>",
"homepage": "http://gis1server.whoi.edu/website/EPR_9N/viewer.htm",
"name": "WHOI Seafloor Data and Observation Visualization Environment",
"prefix": "r3d100010515",
"synonyms": [
"EPR Data Browser",
"SeaDOVE",
"Seafloor Data and Oberservation Visualization Environment"
]
},
"r3d100010516": {
"description": "Seafloor Sediments Data Collection is a collection of more than 14,000 archived marine geological samples recovered from the seafloor. The inventory includes long, stratified sediment cores, as well as rock dredges, surface grabs, and samples collected by the submersible Alvin.",
"homepage": "http://gis1server.whoi.edu/website/SC2k/viewer.htm",
"name": "Seafloor Sediments Data Collection",
"prefix": "r3d100010516",
"synonyms": [
"SEDCORE 2000"
]
},
"r3d100010517": {
"description": "Global Ocean Ecosystem Dynamics (GLOBEC) is the International Geosphere-Biosphere Programme (IGBP) core project responsible for understanding how global change will affect the abundance, diversity and productivity of marine populations. The programme was initiated by SCOR and the IOC of UNESCO in 1991, to understand how global change will affect the abundance, diversity and productivity of marine populations comprising a major component of oceanic ecosystems.\nThe aim of GLOBEC is to advance our understanding of the structure and functioning of the global ocean ecosystem, its major subsystems, and its response to physical forcing so that a capability can be developed to forecast the responses of the marine ecosystem to global change. \nU.S. GLOBEC Programm includes the Georges Bank / NW Atlantic Programm, the Northeast Pacific Programm and the Southern Ocean Program.",
"homepage": "https://www.usglobec.org/gaag/glance.php",
"name": "U.S. GLOBal Ocean ECosystems Dynamics",
"prefix": "r3d100010517",
"synonyms": [
"U.S. Globec"
]
},
"r3d100010519": {
"description": "The Objectively Analyzed air-sea Fluxes (OAFlux) project is a research and development project focusing on global air-sea heat, moisture, and momentum fluxes. The project is committed to produce high-quality, long-term, global ocean surface forcing datasets from the late 1950s to the present to serve the needs of the ocean and climate communities on the characterization, attribution, modeling, and understanding of variability and long-term change in the atmosphere and the oceans.",
"homepage": "https://oaflux.whoi.edu/",
"name": "OAFlux",
"prefix": "r3d100010519",
"synonyms": [
"Objectively Analyzed air-sea Fluxes for the Global Oceans",
"WHOI OAFlux Project"
],
"xrefs": {
"fairsharing": "FAIRsharing.db1dae"
}
},
"r3d100010520": {
"description": "The primary focus of the Upper Ocean Processes Group is the study of physical processes in the upper ocean and at the air-sea interface using moored surface buoys equipped with meteorological and oceanographic sensors.\nUOP Project Map The Upper Ocean Processes Group provides technical support to upper ocean and air-sea interface science programs. Deep-ocean and shallow-water moored surface buoy arrays are designed, fabricated, instrumented, tested, and deployed at sea for periods of up to one year",
"homepage": "https://uop.whoi.edu/",
"name": "Upper Ocean Processes Group",
"prefix": "r3d100010520",
"synonyms": [
"UOP"
],
"xrefs": {
"fairsharing": "FAIRsharing.73479c"
}
},
"r3d100010521": {
"description": "The U.S. launched the Joint Global Ocean Flux Study (JGOFS) in the late 1980s to study the ocean carbon cycle. An ambitious goal was set to understand the controls on the concentrations and fluxes of carbon and associated nutrients in the ocean. A new field of ocean biogeochemistry emerged with an emphasis on quality measurements of carbon system parameters and interdisciplinary field studies of the biological, chemical and physical process which control the ocean carbon cycle. As we studied ocean biogeochemistry, we learned that our simple views of carbon uptake and transport were severely limited, and a new \"wave\" of ocean science was born. U.S. JGOFS has been supported primarily by the U.S. National Science Foundation in collaboration with the National Oceanic and Atmospheric Administration, the National Aeronautics and Space Administration, the Department of Energy and the Office of Naval Research. U.S. JGOFS, ended in 2005 with the conclusion of the Synthesis and Modeling Project (SMP).",
"homepage": "https://usjgofs.whoi.edu/jg/dir/jgofs/",
"name": "US JGOFS Data System",
"prefix": "r3d100010521",
"synonyms": [
"US Joint Global Ocean Flux Study"
]
},
"r3d100010522": {
"description": "The Martha's Vineyard Coastal Observatory (MVCO) is a leading research and engineering facility operated by Woods Hole Oceanographic Institution. The observatory is located at South Beach and in the ocean a mile off the south shore of Martha's Vineyard where it provides real time and archived coastal oceanographic and meteorological data for researchers, students and the general public.",
"homepage": "https://mvco.whoi.edu/",
"name": "Martha's Vineyard Coastal Observatory",
"prefix": "r3d100010522",
"synonyms": [
"MVCO"
]
},
"r3d100010524": {
"description": "The NASA Exoplanet Archive collects and serves public data to support the search for and characterization of extra-solar planets (exoplanets) and their host stars. The data include published light curves, images, spectra and parameters, and time-series data from surveys that aim to discover transiting exoplanets. Tools are provided to work with the data, particularly the display and analysis of transit data sets from Kepler and CoRoT. All data are validated by the Exoplanet Archive science staff and traced to their sources. The Exoplanet Archive is the U.S. data portal for the CoRoT mission.",
"homepage": "https://exoplanetarchive.ipac.caltech.edu/",
"name": "NASA Exoplanet Archive",
"prefix": "r3d100010524"
},
"r3d100010525": {
"description": "NED is a comprehensive database of multiwavelength data for extragalactic objects, providing a systematic, ongoing fusion of information integrated from hundreds of large sky surveys and tens of thousands of research publications. The contents and services span the entire observed spectrum from gamma rays through radio frequencies. As new observations are published, they are cross- identified or statistically associated with previous data and integrated into a unified database to simplify queries and retrieval. Seamless connectivity is also provided to data in NASA astrophysics mission archives (IRSA, HEASARC, MAST), to the astrophysics literature via ADS, and to other data centers around the world.",
"homepage": "https://ned.ipac.caltech.edu/",
"name": "NASA/IPAC Extragalactic Database",
"prefix": "r3d100010525",
"synonyms": [
"NED"
],
"xrefs": {
"fairsharing": "FAIRsharing.b952rv"
}
},
"r3d100010526": {
"description": "The Keck Observatory Archive (KOA)is a collaboration between the NASA Exoplanet Science Institute (NExScI) and the W. M. Keck Observatory (WMKO). This collaboration is founded by the NASA. KOA has been archiving data from the High Resolution Echelle Spectrograph (HIRES) since August 2004 and data acquired with the Near InfraRed echelle SPECtrograph (NIRSPEC) since May 2010. The archived data extend back to 1994 for HIRES and 1999 for NIRSPEC. The W. M. Keck Observatory Archive (KOA) ingests and curates data from the following instruments: DEIMOS, ESI, HIRES, KI, LRIS, MOSFIRE, NIRC2, and NIRSPEC.",
"homepage": "https://nexsci.caltech.edu/archives/koa/",
"name": "Keck Observatory Archive",
"prefix": "r3d100010526",
"synonyms": [
"KOA"
],
"xrefs": {
"biodbcore": "001643",
"fairsharing": "FAIRsharing.a7abca"
}
},
"r3d100010527": {
"description": "The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). \nData arrive at ENA from a variety of sources. These include submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centres and routine and comprehensive exchange with our partners in the International Nucleotide Sequence Database Collaboration (INSDC).\nProvision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature.",
"homepage": "https://www.ebi.ac.uk/ena/browser/home",
"name": "European Nucleotide Archive",
"prefix": "r3d100010527",
"synonyms": [
"ENA"
],
"xrefs": {
"fairsharing": "FAIRsharing.dj8nt8",
"miriam": "00000372",
"nif": "0000-32981",
"omics": "01029",
"scr": "006515"
}
},
"r3d100010528": {
"description": "GenBankΒ is a comprehensive database that contains publicly available nucleotide sequences for almost 260 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP.",
"homepage": "https://www.ncbi.nlm.nih.gov/genbank/",
"name": "GenBank",
"prefix": "r3d100010528",
"xrefs": {
"fairsharing": "fairsharing.9kahy4",
"nif": "0000-02873",
"omics": "01650",
"scr": "002760"
}
},
"r3d100010529": {
"description": "ILTER is a 'network of networks', a global network of research sites located in a wide array of ecosystems that can help understand environmental change across the globe. ILTER's focus is on long-term, site-based research and monitoring.",
"homepage": "https://www.ilter.network/",
"name": "International Long Term Ecological Research",
"prefix": "r3d100010529",
"synonyms": [
"ILTER"
]
},
"r3d100010530": {
"description": "Earthdata powered by EOSDIS (Earth Observing System Data and Information System) is a key core capability in NASAβs Earth Science Data Systems Program. It provides end-to-end capabilities for managing NASAβs Earth science data from various sources β satellites, aircraft, field measurements, and various other programs. EOSDIS uses the metadata and service discovery tool Earthdata Search https://search.earthdata.nasa.gov/search. \nThe capabilities of EOSDIS constituting the EOSDIS Science Operations are managed by NASA's Earth Science Data and Information System (ESDIS) Project. The capabilities include: generation of higher level (Level 1-4) science data products for several satellite missions; archiving and distribution of data products from Earth observation satellite missions, as well as aircraft and field measurement campaigns. The EOSDIS science operations are performed within a distributed system of many interconnected nodes - Science Investigator-led Processing Systems (SIPS), and distributed, discipline-specific, Earth science Distributed Active Archive Centers (DAACs) with specific responsibilities for production, archiving, and distribution of Earth science data products. The DAACs serve a large and diverse user community by providing capabilities to search and access science data products and specialized services.",
"homepage": "https://www.earthdata.nasa.gov/",
"name": "Earthdata powered by EOSDIS",
"prefix": "r3d100010530",
"synonyms": [
"Earth Observing System Data and Information System",
"Earthdata"
],
"xrefs": {
"fairsharing": "FAIRsharing.OXUGmN"
}
},
"r3d100010531": {
"description": "IVS is an international collaboration of organizations which operate or support Very Long Baseline Interferometry (VLB I) components. The service aspect of IVS is meant to serve both outside users and the geodetic and astrometric community itself. Both the contributors and users of data will be served.",
"homepage": "https://ivscc.gsfc.nasa.gov/",
"name": "International VLBI Service for Geodesy and Astrometry of NASA",
"prefix": "r3d100010531",
"synonyms": [
"IVS",
"International Very Long Baseline Interferometry Service for Geodesy and Astrometry of NASA"
]
},
"r3d100010532": {
"description": "<<>>!!!>>>\nThe programme \"International Oceanographic Data and Information Exchange\" (IODE) of the \"Intergovernmental Oceanographic Commission\" (IOC) of UNESCO was established in 1961. Its purpose is to enhance marine research, exploitation and development, by facilitating the exchange of oceanographic data and information between participating Member States, and by meeting the needs of users for data and information products.",
"homepage": "http://www.oceandataportal.net/portal/portal/odp-theme/home",
"name": "OceanDataPortal",
"prefix": "r3d100010532",
"synonyms": [
"IODE Ocean Data Portal",
"ODP"
],
"xrefs": {
"fairsharing.legacy": "2992"
}
},
"r3d100010533": {
"description": "The International Space Environment Service (ISES) is a collaborative network of space weather service-providing organizations around the globe. Our mission is to improve, to coordinate, and to deliver operational space weather services. ISES is organized and operated for the benefit of the international space weather user community.",
"homepage": "http://www.spaceweather.org/",
"name": "International Space Environment Service",
"prefix": "r3d100010533",
"synonyms": [
"ISES"
]
},
"r3d100010537": {
"description": "The \"Subaru Observatory Project\" was originally planned for producing very important output to astronomical society by systematic time allocation and using characteristic functions of Subaru Telescope. The observation time for this project consists of guaranteed time both for telescope builders and for people responsible for telescope operation. 3 proposals were selected for execution during 2002 and 2003 fiscal years. They are Subaru Deep Field (SDF) (PI is Dr. Kashikawa at Mitaka, NAOJ), Subaru XMM-Newton Deep Survey (SXDS) (PI is Dr. Sekiguchi at Hilo, Subaru Telescope), and Disk and Planet Searches (SDPS) (PI is Dr. Hayashi at Hilo, Subaru Telescope). SOAPs web server provide the data (fully reduced images and catalogs) download obtained from SDF and SXDS projects. Raw Data are available at the SMOKA Science Archive: https://smoka.nao.ac.jp/",
"homepage": "http://soaps.nao.ac.jp/index.html",
"name": "SOAP",
"prefix": "r3d100010537",
"synonyms": [
"Subaru Observatory Astronomical Projects"
]
},
"r3d100010538": {
"description": "PDBe is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - we work to collate, maintain and provide access to the global repository of macromolecular structure data. We develop tools, services and resources to make structure-related data more accessible to the biomedical community.",
"homepage": "https://www.ebi.ac.uk/pdbe/",
"name": "Protein Data Bank in Europe",
"prefix": "r3d100010538",
"synonyms": [
"PDBe"
],
"xrefs": {
"fairsharing": "FAIRsharing.26ek1v",
"miriam": "00100037",
"nlx": "32372",
"scr": "004312"
}
},
"r3d100010539": {
"description": "ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data).\nThe data is abstracted and curated from the primary scientific literature, and cover a significant fraction of the SAR and discovery of modern drugs\nWe attempt to normalise the bioactivities into a uniform set of end-points and units where possible, and also to tag the links between a molecular target and a published assay with a set of varying confidence levels. Additional data on clinical progress of compounds is being integrated into ChEMBL at the current time.",
"homepage": "https://www.ebi.ac.uk/chembl/",
"name": "ChEMBL",
"prefix": "r3d100010539",
"xrefs": {
"fairsharing": "fairsharing.m3jtpg",
"omics": "02731",
"scr": "014042"
}
},
"r3d100010541": {
"description": "The National Archives and Records Administration (NARA) is the nation's record keeper. Of all documents and materials created in the course of business conducted by the United States Federal government, only 1%-3% are so important for legal or historical reasons that they are kept by us forever.\nThose valuable records are preserved and are available to you, whether you want to see if they contain clues about your familyβs history, need to prove a veteranβs military service, or are researching an historical topic that interests you.",
"homepage": "https://www.archives.gov/",
"name": "National Archives",
"prefix": "r3d100010541",
"synonyms": [
"NARA"
]
},
"r3d100010542": {
"description": "The server ESTHER (ESTerases and alpha/beta-Hydrolase Enzymes and Relatives) is dedicated to the analysis of proteins or protein domains belonging to the superfamily of alpha/beta-hydrolases, exemplified by the cholinesterases.",
"homepage": "https://bioweb.supagro.inrae.fr/ESTHER/general?what=index",
"name": "ESTHER database",
"prefix": "r3d100010542",
"synonyms": [
"ESTerases and alpha/beta-Hydrolase Enzymes and Relatives"
],
"xrefs": {
"nif": "0000-02817",
"scr": "008479"
}
},
"r3d100010543": {
"description": "PLMD (Protein Lysine Modifications Database) is an online data resource specifically designed for protein lysine modifications (PLMs). The PLMD 3.0 database was extended and adapted from CPLA 1.0 (Compendium of Protein Lysine Acetylation) database and CPLM 2.0 (Compendium of Protein Lysine Modifications) database",
"homepage": "http://plmd.biocuckoo.org/",
"name": "Protein Lysine Modification Database",
"prefix": "r3d100010543",
"synonyms": [
"PLMD"
],
"xrefs": {
"fairsharing": "fairsharing.se7ewy"
}
},
"r3d100010544": {
"description": "The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The latest release of DrugBank (version 5.1.1, released 2018-07-03) contains 11,881 drug entries including 2,526 approved small molecule drugs, 1,184 approved biotech (protein/peptide) drugs, 129 nutraceuticals and over 5,751 experimental drugs. Additionally, 5,132 non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences are linked to these drug entries. Each DrugCard entry contains more than 200 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data.",
"homepage": "https://go.drugbank.com/",
"name": "DrugBank",
"prefix": "r3d100010544",
"synonyms": [
"DrugBank Online",
"Open Data Drug & Drug Target Database"
],
"xrefs": {
"fairsharing": "fairsharing.353yat",
"miriam": "00000102",
"nif": "0000-00417",
"scr": "002700"
}
},
"r3d100010545": {
"description": "<<>>!!!>>>",
"homepage": "https://dataverse.harvard.edu/dataverse/census",
"name": "The Dataweb Dataverse",
"prefix": "r3d100010545",
"synonyms": [
"DataFerrett",
"TheDataWeb"
]
},
"r3d100010546": {
"description": "<<>>!!!<<<",
"homepage": "http://ecogene.org/",
"name": "EcoGene",
"prefix": "r3d100010546",
"synonyms": [
"Escherichia coli strain K12 genome database"
],
"xrefs": {
"fairsharing": "FAIRsharing.3q3kvn",
"miriam": "00000163",
"nif": "0000-02784",
"omics": "03184",
"scr": "002437"
}
},
"r3d100010547": {
"description": "Eurostat is the statistical office of the European Union situated in Luxembourg. Its task is to provide the European Union with statistics at European level that enable comparisons between countries and regions. Eurostat offers a whole range of important and interesting data that governments, businesses, the education sector, journalists and the public can use for their work and daily life.",
"homepage": "https://ec.europa.eu/eurostat/",
"name": "Eurostat",
"prefix": "r3d100010547"
},
"r3d100010548": {
"description": "The ISSAID website gathers resources related to the systemic autoinflammatory diseases in order to facilitate contacts between interested physicians and researchers.\nThe website provides support to share and rapidly disseminate information, thoughts, feelings and experiences to improve the quality of life of patients and families affected by systemic autoinflammatory diseases, and promote advances in the search for causes and cures.",
"homepage": "https://infevers.umai-montpellier.fr/web/",
"name": "Infevers",
"prefix": "r3d100010548",
"synonyms": [
"The registry of Auto-Inflammatory Disease mutations"
],
"xrefs": {
"fairsharing": "FAIRsharing.g6kz6h",
"issn": "2427-3902",
"nif": "0000-03022",
"scr": "007738"
}
},
"r3d100010549": {
"description": "Greengenes is an Earth Sciences website that assists clinical and environmental microbiologists from around the globe in classifying microorganisms from their local environments. A 16S rRNA gene database addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.",
"homepage": "https://greengenes.secondgenome.com/",
"name": "Greengenes",
"prefix": "r3d100010549",
"synonyms": [
"The Greengenes Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.bpxgb6",
"miriam": "00000165",
"nif": "0000-02927",
"scr": "002830"
}
},
"r3d100010550": {
"description": "During cell cycle, numerous proteins temporally and spatially localized in distinct sub-cellular regions including centrosome (spindle pole in budding yeast), kinetochore/centromere, cleavage furrow/midbody (related or homolog structures in plants and budding yeast called as phragmoplast and bud neck, respectively), telomere and spindle spatially and temporally. These sub-cellular regions play important roles in various biological processes. In this work, we have collected all proteins identified to be localized on kinetochore, centrosome, midbody, telomere and spindle from two fungi (S. cerevisiae and S. pombe) and five animals, including C. elegans, D. melanogaster, X. laevis, M. musculus and H. sapiens based on the rationale of \"Seeing is believing\" (Bloom K et al., 2005). Through ortholog searches, the proteins potentially localized at these sub-cellular regions were detected in 144 eukaryotes. Then the integrated and searchable database MiCroKiTS - Midbody, Centrosome, Kinetochore, Telomere and Spindle has been established.",
"homepage": "http://microkit.biocuckoo.org/index.php",
"name": "MiCroKitS",
"prefix": "r3d100010550",
"synonyms": [
"Midbody, Centrosome, Kinetochore and Spindle",
"formerly: MiCroKit"
],
"xrefs": {
"fairsharing": "fairsharing.3cswbc",
"nif": "0000-03126",
"scr": "007052"
}
},
"r3d100010551": {
"description": "The NDB is a resource for nucleic acid research and education. The NDB assembles and distributes information about the three-dimensional structures of nucleic acids through a variety of resources, including a searchable database, Atlas, and software",
"homepage": "http://ndbserver.rutgers.edu/",
"name": "Nucleic Acid Database",
"prefix": "r3d100010551",
"synonyms": [
"A Portal for Three-dimensional Structural Information about Nucleic Acids",
"NDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.bh0k78",
"nif": "0000-03184",
"scr": "003255"
}
},
"r3d100010552": {
"description": "The Mouse Phenome Database (MPD; phenome.jax.org) has characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies.",
"homepage": "https://phenome.jax.org/",
"name": "Mouse Phenome Database",
"prefix": "r3d100010552",
"synonyms": [
"MPD"
],
"xrefs": {
"fairsharing": "FAIRsharing.h6enr1",
"nif": "0000-03160",
"scr": "003212"
}
},
"r3d100010553": {
"description": "REFOLD has merged to REFOLDdb. \nREFOLDdb is a unique database for the life sciences research community, providing annotated information for designing new refolding protocols and customizing existing methodologies. We envisage that this resource will find wide utility across broad disciplines that rely on the production of pure, active, recombinant proteins. Furthermore, the database also provides a useful overview of the recent trends and statistics in refolding technology development.We based our resource on the existing REFOLD database, which has not been updated since 2009. We redesigned the data format to be more concise, allowing consistent representations among data entries compared with the original REFOLD database. The remodeled data architecture enhances the search efficiency and improves the sustainability of the database. After an exhaustive literature search we added experimental refolding protocols from reports published 2009 to early 2017. In addition to this new data, we fully converted and integrated existing REFOLD data into our new resource.",
"homepage": "http://p4d-info.nig.ac.jp/refolddatabase/",
"name": "REFOLDdb",
"prefix": "r3d100010553",
"synonyms": [
"including: REFOLD"
],
"xrefs": {
"fairsharing": "FAIRsharing.2srshy",
"nif": "0000-03396",
"scr": "007889"
}
},
"r3d100010554": {
"description": "<<>>!!!>>> The South African Data Archive promotes and facilitates the sharing of research data and related documentation of computerised raw quantitative data of large scale regional, national and international research projects mainly in the humanities and social sciences. It makes these datasets available to the research community for further analysis, comparative studies, longitudinal studies, teaching and decision-making purposes.",
"homepage": "http://sada.nrf.ac.za",
"name": "South African Data Archive",
"prefix": "r3d100010554",
"synonyms": [
"SADA"
]
},
"r3d100010555": {
"description": ">>>!!!<<< SMD has been retired.\nAfter approximately fifteen years of microarray-centric research service, the Stanford Microarray Database has been retired. We apologize for any inconvenience; please read below for possible resolutions to your queries.\nIf you are looking for any raw data that was directly linked to SMD from a manuscript, please search one of the public repositories.\n NCBI Gene Expression Omnibus\n EBI ArrayExpress\nAll published data were previously communicated to one (or both) of the public repositories.\nAlternatively, data for publications between 1997 and 2004 were likely migrated to the Princeton University MicroArray Database, and are accessible there.\nIf you are looking for a manuscript supplement (i.e. from a domain other than smd.stanford.edu), perhaps try searching the Internet Archive: Wayback Machine https://archive.org/web/ . >>>!!!<<<\nThe Stanford Microarray Database (SMD) is a DNA microarray research database that provides a large amount of data for public use.",
"homepage": "http://smd.princeton.edu/",
"name": "Stanford Microarray Database",
"prefix": "r3d100010555",
"synonyms": [
"SMD"
],
"xrefs": {
"fairsharing": "FAIRsharing.x93ckv",
"nlx": "94141",
"omics": "00870",
"scr": "004987"
}
},
"r3d100010556": {
"description": "MyTardis began at Monash University to solve the problem of users needing to store large datasets and share them with collaborators online. Its particular focus is on integration with scientific instruments, instrument facilities and research lab file storage. Our belief is that the less effort a researcher has to expend safely storing data, the more likely they are to do so.\nThis approach has flourished with MyTardis capturing data from areas such as protein crystallography, electron microscopy, medical imaging and proteomics and with deployments at Australian institutions such as University of Queensland, RMIT, University of Sydney and the Australian Synchrotron. Data access via https://www.massive.org.au/ and https://store.erc.monash.edu.au/experiment/view/104/ and see 'remarks'.",
"homepage": "https://www.mytardis.org/",
"name": "MyTardis",
"prefix": "r3d100010556",
"synonyms": [
"Tardis"
]
},
"r3d100010557": {
"description": "The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA binding specificities of proteins. This initial release of the UniPROBE database provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible sequence variants ('words') of length k ('k-mers'), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In total, the database currently hosts DNA binding data for 406 nonredundant proteins from a diverse collection of organisms, including the prokaryote Vibrio harveyi, the eukaryotic malarial parasite Plasmodium falciparum, the parasitic Apicomplexan Cryptosporidium parvum, the yeast Saccharomyces cerevisiae, the worm Caenorhabditis elegans, mouse, and human. The database's web tools (on the right) include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences",
"homepage": "http://thebrain.bwh.harvard.edu/uniprobe/",
"name": "Universal PBM Resource for Oligonucleotide Binding Evaluation",
"prefix": "r3d100010557",
"synonyms": [
"UniPROBE"
],
"xrefs": {
"nif": "0000-03611",
"omics": "00546",
"scr": "005803"
}
},
"r3d100010558": {
"description": "The DCS allows you to search a catalogue of metadata (information describing data) to discover and gain access to NERC's data holdings and information products. The metadata are prepared to a common NERC Metadata Standard and are provided to the catalogue by the NERC Data Centres.",
"homepage": "https://data-search.nerc.ac.uk/geonetwork/srv/ger/catalog.search#/home",
"name": "NERC Data Catalogue Service",
"prefix": "r3d100010558",
"synonyms": [
"NERC DCS",
"Natural Environment Research Council DCS",
"Natural Environmental Research Council Data Catalogue Service"
],
"xrefs": {
"fairsharing": "FAIRsharing.xj7m8y"
}
},
"r3d100010559": {
"description": ">>>!!!<<>>!!!<<< Cancer GEnome Mine is a public database for storing clinical information about tumor samples and microarray data, with emphasis on array comparative genomic hybridization (aCGH) and data mining of gene copy number changes.",
"homepage": "http://www.cangem.org/",
"name": "CanGEM",
"prefix": "r3d100010559",
"synonyms": [
"Cancer GEnome Mine"
],
"xrefs": {
"nif": "0000-02636",
"scr": "000728"
}
},
"r3d100010560": {
"description": "Codex Sinaiticus is one of the most important books in the world. Handwritten well over 1600 years ago, the manuscript contains the Christian Bible in Greek, including the oldest complete copy of the New Testament.\nThe Codex Sinaiticus Project is an international collaboration to reunite the entire manuscript in digital form and make it accessible to a global audience for the first time. Drawing on the expertise of leading scholars, conservators and curators, the Project gives everyone the opportunity to connect directly with this famous manuscript.",
"homepage": "https://codexsinaiticus.org/en/",
"name": "Codex Sinaiticus",
"prefix": "r3d100010560",
"synonyms": [
"Experience the oldest Bible"
]
},
"r3d100010561": {
"description": "The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. DisProt is a community resource annotating protein sequences for intrinsically disorder regions from the literature.\nIt classifies intrinsic disorder based on experimental methods and three ontologies for molecular function, transition and binding partner.",
"homepage": "https://www.disprot.org/",
"name": "DisProt",
"prefix": "r3d100010561",
"synonyms": [
"Database of Protein Disorder"
],
"xrefs": {
"fairsharing": "FAIRsharing.dt9z89",
"nif": "0000-02754",
"scr": "007097"
}
},
"r3d100010562": {
"description": "The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.",
"homepage": "https://www.ebi.ac.uk/emdb/",
"name": "Electron Microscopy Data Bank",
"prefix": "r3d100010562",
"synonyms": [
"EMDB",
"EMDB at PDBe",
"The Electron Microscopy Data Bank at Protein Data Bank in Europe"
],
"xrefs": {
"fairsharing": "FAIRsharing.651n9j",
"miriam": "00100738",
"nlx": "149453",
"scr": "006506"
}
},
"r3d100010563": {
"description": "Since the first discovery of RNA pseudoknots more and many more pseudoknots have been found. However, not all of those pseudoknot data are easy to trace. Sometimes the information is hidden in a publication where the title gives no hint that pseudoknot information is there. This was the first reason that we thought that a general accessible information source for pseudoknots would be handy.",
"homepage": "https://www.ekevanbatenburg.nl/PKBASE/PKB.HTML",
"name": "Pseudobase",
"prefix": "r3d100010563",
"synonyms": [
"A Pseudoknot Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.5ey5w6"
}
},
"r3d100010564": {
"description": "EMAGE (e-Mouse Atlas of Gene Expression) is an online biological database of gene expression data in the developing mouse (Mus musculus) embryo. The data held in EMAGE is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO) term. EMAGE is a freely available web-based resource funded by the Medical Research Council (UK) and based at the MRC Human Genetics Unit in the Institute of Genetics and Molecular Medicine, Edinburgh, UK.",
"homepage": "https://www.emouseatlas.org/emage/",
"name": "Emage",
"prefix": "r3d100010564",
"synonyms": [
"e-Mouse Atlas of Gene Expression"
],
"xrefs": {
"fairsharing": "FAIRsharing.6qr9jp",
"nif": "0000-00080",
"scr": "005391"
}
},
"r3d100010565": {
"description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. We actively gather datasets from public domain projects, and encourage direct data submission from the community.",
"homepage": "https://www.gwascentral.org/index",
"name": "GWAS Central",
"prefix": "r3d100010565",
"xrefs": {
"fairsharing": "FAIRsharing.vkr57k",
"nlx": "151672",
"scr": "006170"
}
},
"r3d100010566": {
"description": "The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download. The miRBase Registry provides miRNA gene hunters with unique names for novel miRNA genes prior to publication of results.",
"homepage": "https://www.mirbase.org/",
"name": "miRBase",
"prefix": "r3d100010566",
"xrefs": {
"fairsharing": "FAIRsharing.hmgte8",
"nif": "0000-03134",
"scr": "003152"
}
},
"r3d100010567": {
"description": "The Old Bailey Proceedings Online makes available a fully searchable, digitised collection of all surviving editions of the Old Bailey Proceedings from 1674 to 1913, and of the Ordinary of Newgate's Accounts between 1676 and 1772. It allows access to over 197,000 trials and biographical details of approximately 2,500 men and women executed at Tyburn, free of charge for non-commercial use.\nIn addition to the text, accessible through both keyword and structured searching, this website provides digital images of all 190,000 original pages of the Proceedings, 4,000 pages of Ordinary's Accounts, advice on methods of searching this resource, information on the historical and legal background to the Old Bailey court and its Proceedings, and descriptions of published and manuscript materials relating to the trials covered. Contemporary maps, and images have also been provided.",
"homepage": "https://www.oldbaileyonline.org/index.jsp",
"name": "Old Bailey Proceedings Online",
"prefix": "r3d100010567"
},
"r3d100010568": {
"description": "The Office for National Statistics (ONS) is the UKβs largest independent producer of official statistics and is the recognised national statistical institute for the UK. It is responsible for collecting and publishing statistics related to the economy, population and society at national, regional and local levels. It also conducts the census in England and Wales every ten years. The ONS plays a leading role in national and international good practice in the production of official statistics. It is the executive office of the UK Statistics Authority and although they are separate, they are still closely related.",
"homepage": "https://www.ons.gov.uk/",
"name": "Office for National Statistics",
"prefix": "r3d100010568",
"synonyms": [
"ONS",
"SYG",
"Swyddfa Ystadegau Gwladol"
]
},
"r3d100010569": {
"description": "UK RED is a database documenting the history of reading in Britain from 1450 to 1945. Reading experiences of British subjects, both at home and abroad presented in UK RED are drawn from published and unpublished sources as diverse as diaries, commonplace books, memoirs, sociological surveys, and criminal court and prison records.",
"homepage": "https://www.open.ac.uk/Arts/reading/UK/",
"name": "UK Reading Experience Database",
"prefix": "r3d100010569",
"synonyms": [
"UK RED"
]
},
"r3d100010570": {
"description": "PHI-base is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. PHI-base is therfore an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, PHI-base also includes antifungal compounds and their target genes.",
"homepage": "http://www.phi-base.org/",
"name": "PHI-base",
"prefix": "r3d100010570",
"synonyms": [
"Pathogen Host Interactions"
],
"xrefs": {
"fairsharing": "FAIRsharing.73cqdk",
"nif": "0000-03276",
"scr": "003331"
}
},
"r3d100010571": {
"description": "This site provides access to raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results are posted to accompany the data.",
"homepage": "https://phenome.jax.org/centers/QTLA",
"name": "QTL Archive",
"prefix": "r3d100010571",
"xrefs": {
"fairsharing": "FAIRsharing.2g4cfa",
"nlx": "151757",
"scr": "006213"
}
},
"r3d100010572": {
"description": "The World Values Survey (WVS) is a worldwide network of social scientists studying changing values and their impact on social and political life. The WVS in collaboration with EVS (European Values Study) carried out representative national surveys in more than 100 countries containing almost 90 percent of the world's population. These surveys show pervasive changes in what people want out of life and what they believe. In order to monitor these changes, the EVS/WVS has executed six waves of surveys, from 1981 to 2013.",
"homepage": "https://www.worldvaluessurvey.org/wvs.jsp",
"name": "World Values Survey",
"prefix": "r3d100010572",
"synonyms": [
"WVS"
]
},
"r3d100010573": {
"description": ">>>!!!<<< caArray Retirement Announcement >>>!!!<<< The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) instance of the caArray database was retired on March 31st, 2015. All publicly-accessible caArray data and annotations will be archived and will remain available via FTP download https://wiki.nci.nih.gov/x/UYHeDQ and is also available at GEO http://www.ncbi.nlm.nih.gov/geo/ . >>>!!!<<< While NCI will not be able to provide technical support for the caArray software after the retirement, the source code is available on GitHub https://github.com/NCIP/caarray , and we encourage continued community development. Molecular Analysis of Brain Neoplasia (Rembrandt fine-00037) gene expression data has been loaded into ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3073 >>>!!!<<< caArray is an open-source, web and programmatically accessible microarray data management system that supports the annotation of microarray data using MAGE-TAB and web-based forms. Data and annotations may be kept private to the owner, shared with user-defined collaboration groups, or made public. The NCI instance of caArray hosts many cancer-related public datasets available for download.",
"homepage": "https://wiki.nci.nih.gov/display/caArray2/caArray+Retirement+Announcement",
"name": "caArray",
"prefix": "r3d100010573",
"synonyms": [
"Array Data Management System"
],
"xrefs": {
"fairsharing": "FAIRsharing.gdqqm0",
"nlx": "151452",
"omics": "00864",
"scr": "006053"
}
},
"r3d100010574": {
"description": "caNanoLab is a data sharing portal designed to facilitate information sharing in the biomedical nanotechnology research community to expedite and validate the use of nanotechnology in biomedicine. caNanoLab provides support for the annotation of nanomaterials with characterizations resulting from physico-chemical and in vitro assays and the sharing of these characterizations and associated nanotechnology protocols in a secure fashion.",
"homepage": "https://cananolab.cancer.gov/#/",
"name": "caNanoLab",
"prefix": "r3d100010574",
"synonyms": [
"cancer Nanotechnology Laboratory"
],
"xrefs": {
"fairsharing": "FAIRsharing.y1qpdm",
"scr": "013717"
}
},
"r3d100010575": {
"description": "MICASE provides a collection of transcripts of academic speech events recorded at the University of Michigan. The original DAT audiotapes are held in the English Language Institute and may be consulted by bona fide researchers under special arrangements. Additional access: https://lsa.umich.edu/eli/language-resources/micase-micusp.html",
"homepage": "https://quod.lib.umich.edu/m/micase/",
"name": "Michigan Corpus of Academic Spoken English",
"prefix": "r3d100010575",
"synonyms": [
"MICASE"
]
},
"r3d100010578": {
"description": "IEDA2 is currently undergoing a website reconstruction and will be back soon. \nIEDA is a community-based facility that serves to support, sustain, and advance the geosciences by providing data services for observational Geoscience data from the Ocean, Earth, and Polar Sciences. IEDA welcomes and encourages investigators to contribute their data to the IEDA collections so that the data can be discovered and reused by a diverse community now and in the future. The IEDA collections are: EarthChem, Geochron, System for Earth Sample Registration (SESAR), Marine Geoscience Data System (MGDS), and USAP Data Center. Meta-Search provided on the portal through IEDA Data Browser http://www.iedadata.org/databrowser .",
"homepage": "https://www.iedadata.org/",
"name": "IEDA",
"prefix": "r3d100010578",
"synonyms": [
"IEDA Data Browser",
"Interdisciplinary Earth Data Alliance"
],
"xrefs": {
"fairsharing": "/FAIRsharing.be9dj8"
}
},
"r3d100010579": {
"description": "The Government is releasing public data to help people understand how government works and how policies are made. Some of this data is already available, but data.gov.uk brings it together in one searchable website. Making this data easily available means it will be easier for people to make decisions and suggestions about government policies based on detailed information.",
"homepage": "https://data.gov.uk/",
"name": "DATA.GOV.UK",
"prefix": "r3d100010579",
"synonyms": [
"Opening up Government"
]
},
"r3d100010580": {
"description": "The IGS global system of satellite tracking stations, Data Centers, and Analysis Centers puts high-quality GPS data and data products on line in near real time to meet the objectives of a wide range of scientific and engineering applications and studies.\nThe IGS collects, archives, and distributes GPS observation data sets of sufficient accuracy to satisfy the objectives of a wide range of applications and experimentation. These data sets are used by the IGS to generate the data products mentioned above which are made available to interested users through the Internet. In particular, the accuracies of IGS products are sufficient for the improvement and extension of the International Terrestrial Reference Frame (ITRF), the monitoring of solid Earth deformations, the monitoring of Earth rotation and variations in the liquid Earth (sea level, ice-sheets, etc.), for scientific satellite orbit determinations, ionosphere monitoring, and recovery of precipitable water vapor measurements.",
"homepage": "https://igs.org/",
"name": "International GNSS Service",
"prefix": "r3d100010580",
"synonyms": [
"IGS",
"International GPS Service"
]
},
"r3d100010582": {
"description": "Chinese Astronomical Data Center (CAsDC) is the scientific data service and infrastructure of National Astronomical Observatories, Chinese Academy of Sciences (NAOC), which is a key service from the China-VO. We are aiming to meet user requirements for astronomical research and education.\nThe CAsDC is based on World Data Center (WDC) for Astronomy, which is hosted at NAOC and has been providing data services to users since its initiation in 1980s. In 2012, the CAsDC became a regular member of the new created World Data System.",
"homepage": "https://nadc.china-vo.org/data/?locale=en",
"name": "Chinese Astronomical Data Center",
"prefix": "r3d100010582",
"synonyms": [
"CAsDC",
"China-VO",
"National Astronomical Data Center - NADC",
"World Data Center for Astronomy",
"δΈε½ε€©ζζ°ζδΈεΏ"
]
},
"r3d100010583": {
"description": "The CDPP is the French national data centre for natural plasmas of the solar system. The CDPP assures the long term preservation of data obtained primarily from instruments built using French resources, and renders them readily accessible and exploitable by the international community. The CDPP also provides services to enable on-line data analysis (AMDA), 3D data visualization in context (3DView), and a propagation tool which bridges solar perturbations to in-situ measurements. The CDPP is involved in the development of interoperability, participates in several Virtual Observatory projects, and supports data distribution for scientific missions (Solar Orbiter, JUICE).",
"homepage": "http://www.cdpp.eu/",
"name": "Plasma Physics Data Center",
"prefix": "r3d100010583",
"synonyms": [
"CDPP",
"Centre de DonnΓ©es de la Physique de Plasma"
],
"xrefs": {
"issn": "2417-8756"
}
},
"r3d100010584": {
"description": "Strasbourg astronomical Data Center (CDS) is dedicated to the collection and worldwide distribution of astronomical data and related information.\nAlongside data curation and service maintenance responsibilities, the CDS undertakes R&D activities that are fundamental to ensure the long term sustainability in a domain in which technology evolves very quickly. R&D areas include informatics, big data, and development of the astronomical Virtual Observatory (VO). CDS is a major actor in the VO with leading roles in European VO projects, the French Virtual Observatory and the International Virtual Observatory Alliance (IVOA). \nThe CDS hosts the SIMBAD astronomical database, the world reference database for the identification of astronomical objects; VizieR, the catalogue service for the CDS reference collection of astronomical catalogues and tables published in academic journals; and the Aladin interactive software sky atlas for access, visualization and analysis of astronomical images, surveys, catalogues, databases and related data.",
"homepage": "http://cdsweb.u-strasbg.fr/",
"name": "Strasbourg Astronomical Data Center",
"prefix": "r3d100010584",
"synonyms": [
"CDS",
"Centre de DonnΓ©es astronomiques de Strasbourg"
]
},
"r3d100010585": {
"description": "The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. The public version of the database includes this information and can be queried directly via this CGSC DB WebServer",
"homepage": "https://cgsc2.biology.yale.edu/",
"name": "E. coli Genetic Resources at Yale",
"prefix": "r3d100010585",
"synonyms": [
"CGSC",
"The Coli Genetic Stock Center"
],
"xrefs": {
"fairsharing": "FAIRsharing.1tbrdz",
"miriam": "00100377",
"nif": "0000-21083",
"scr": "002303"
}
},
"r3d100010586": {
"description": "dictyBase is an integrated genetic and literature database that contains published Dictyostelium discoideum literature, genes, expressed sequence tags (ESTs), as well as the chromosomal and mitochondrial genome sequences. Direct access to the genome browser, a Blast search tool, the Dictyostelium Stock Center, research tools, colleague databases, and much much more are just a mouse click away. Dictybase is a genome portal for the Amoebozoa. dictyBase is funded by a grant from the National Institute for General Medical Sciences.",
"homepage": "http://dictybase.org/",
"name": "dictybase",
"prefix": "r3d100010586",
"synonyms": [
"Dictyostelium discoideum"
],
"xrefs": {
"fairsharing": "FAIRsharing.4shj9c",
"miriam": "00100367",
"nif": "0000-02751",
"omics": "03158",
"scr": "006643"
}
},
"r3d100010587": {
"description": "EarthScope was a program of the National Science Foundation (NSF) that has deployed thousands of seismic, GPS, and other geophysical instruments to study the structure and evolution of the North American continent and the processes that cause earthquakes and volcanic eruptions.\nEarthScope was an Earth science program to explore the 4-dimensional structure of the North American continent. The EarthScope Program provides a framework for broad, integrated studies across the Earth sciences, including research on fault properties and the earthquake process, strain transfer, magmatic and hydrous fluids in the crust and mantle, plate boundary processes, large-scale continental deformation, continental structure and evolution, and composition and structure of the deep Earth. In addition, EarthScope offers a centralized forum for Earth science education at all levels and an excellent opportunity to develop cyberinfrastructure to integrate, distribute, and analyze diverse data set.",
"homepage": "https://www.earthscope.org/",
"name": "EarthScope",
"prefix": "r3d100010587"
},
"r3d100010588": {
"description": "The WDC is concerned with the collection, management, distribution and utilization of data from Chinese provinces, autonomous regions and counties,including:\nResource data:management,distribution and utlilzation of land, water, climate, forest, grassland, minerals, energy, etc.\nEnvironmental data:pollution,environmental quality, change, natural disasters,soli erosion, etc.\nBiological resources:animals, plants,wildlife\nSocial economy:agriculture, industry, transport, commerce,infrastructure,etc.\nPopulation and labor\nGeographic background data on scales of 1:4M,1:1M, 1:(1/2)M, 1:2500, etc.",
"homepage": "http://wdcrre.data.ac.cn/",
"name": "World Data Center for Renewable Resources and Environment",
"prefix": "r3d100010588",
"synonyms": [
"WDC - Renewable Resources and Environment",
"WDC-RRE"
]
},
"r3d100010589": {
"description": "FANTOM stands for 'Functional Annotation of the Mammalian Genome' and is the name of an international research consortium organized by the RIKEN Omics Science Center. The FANTOM5 project aims to build a full understanding of transcriptional regulation in a human system by generating transcriptional regulatory networks that define every human cell type.",
"homepage": "https://fantom.gsc.riken.jp/",
"name": "FANTOM",
"prefix": "r3d100010589",
"synonyms": [
"FANTOM DB",
"FANTOM5",
"Functional ANnotation Of the Mammalian genome",
"SSTAR"
],
"xrefs": {
"fairsharing": "FAIRsharing.99c9b0",
"nif": "0000-02833",
"scr": "002678"
}
},
"r3d100010590": {
"description": "The Fish Database of Taiwan is a complex of research data for about 25 years to the Lab of Fish Ecology and Evolution, which is situated in Biodiversity Research Center of Academia Sinica.",
"homepage": "https://fishdb.sinica.edu.tw/",
"name": "The Fish Database of Taiwan",
"prefix": "r3d100010590"
},
"r3d100010591": {
"description": "FlyBase is a database of genetic, genomic and functional data for Drosophila species, with a focus on the model organism Drosophila melanogaster.FlyBase contains a complete annotation of the Drosophila melanogaster genome that is updated several times per year.It also includes a searchable bibliography of research on Drosophila genetics in the last century. The site also provides a large database of images illustrating the full genome, and several movies detailing embryogenesis.",
"homepage": "https://flybase.org/",
"name": "FlyBase",
"prefix": "r3d100010591",
"synonyms": [
"A Database of Drosophila Genes and Genomes"
],
"xrefs": {
"fairsharing": "FAIRsharing.wrvze3",
"miriam": "00000030",
"nif": "0000-00558",
"omics": "01649",
"scr": "006549"
}
},
"r3d100010593": {
"description": "This site is dedicated to making high value health data more accessible to entrepreneurs, researchers, and policy makers in the hopes of better health outcomes for all. In a recent article, Todd Park, United States Chief Technology Officer, captured the essence of what the Health Data Initiative is all about and why our efforts here are so important.",
"homepage": "https://healthdata.gov/",
"name": "HealthData.gov",
"prefix": "r3d100010593",
"xrefs": {
"fairsharing": "FAIRsharing.kcpnmb",
"nlx": "143714",
"scr": "004386"
}
},
"r3d100010594": {
"description": "Herschel has been designed to observe the `cool universe'; it is observing the structure formation in the early universe, resolving the far infrared cosmic background, revealing cosmologically evolving AGN/starburst symbiosis and galaxy evolution at the epochs when most stars in the universe were formed, unveiling the physics and chemistry of the interstellar medium and its molecular clouds, the wombs of the stars, and unravelling the mechanisms governing the formation of and evolution of stars and their planetary systems, including our own solar system, putting it into context. In short, Herschel is opening a new window to study how the universe has evolved to become the universe we see today, and how our star the sun, our planet the earth, and we ourselves fit in.",
"homepage": "http://archives.esac.esa.int/hsa/aio/doc/",
"name": "Herschel Science Archive",
"prefix": "r3d100010594",
"synonyms": [
"HSA"
]
},
"r3d100010596": {
"description": "The International Service of Geomagnetic Indices (ISGI) is in charge of the elaboration and dissemination of geomagnetic indices, and of tables of remarkable magnetic events, based on the report of magnetic observatories distributed all over the planet, with the help of ISGI Collaborating Institutes.\nThe interaction between the solar wind, including plasma and interplanetary magnetic field, and the Earth's magnetosphere results in a transfer of energy and particles inside the magnetosphere. Solar wind characteristics are highly variable, and they have actually a direct influence on the shape and size of the magnetosphere, on the amount of transferred energy, and on the way this energy is dissipated. It is clear that the great diversity of sources of magnetic variations give rise to a great complexity in ground magnetic signatures.\nGeomagnetic indices aim at describing the geomagnetic activity or some of its components. Each geomagnetic index is related to different phenomena occurring in the magnetosphere, ionosphere and deep in the Earth in its own unique way. The location of a measurement, the timing of the measurement and the way the index is calculated all affect the type of phenomenon the index relates to.\nThe IAGA endorsed geomagnetic indices and lists of remarkable geomagnetic events constitute unique temporal and spatial coverage data series homogeneous since middle of 19th century.",
"homepage": "https://isgi.unistra.fr/",
"name": "International Service of Geomagnetic Indices",
"prefix": "r3d100010596",
"synonyms": [
"ISGI",
"SIIG",
"Service International des Indices GΓ©omagnΓ©tiques"
],
"xrefs": {
"fairsharing": "FAIRsharing.5Sfaz2"
}
},
"r3d100010597": {
"description": "The Infrared Space Observatory (ISO) is designed to provide detailed infrared properties of selected Galactic and extragalactic sources. The sensitivity of the telescopic system is about one thousand times superior to that of the Infrared Astronomical Satellite (IRAS), since the ISO telescope enables integration of infrared flux from a source for several hours. Density waves in the interstellar medium, its role in star formation, the giant planets, asteroids, and comets of the solar system are among the objects of investigation.\nISO was operated as an observatory with the majority of its observing time being distributed to the general astronomical community. One of the consequences of this is that the data set is not homogeneous, as would be expected from a survey. The observational data underwent sophisticated data processing, including validation and accuracy analysis. In total, the ISO Data Archive contains about 30,000 standard observations, 120,000 parallel, serendipity and calibration observations and 17,000 engineering measurements. In addition to the observational data products, the archive also contains satellite data, documentation, data of historic aspects and externally derived products, for a total of more than 400 GBytes stored on magnetic disks. The ISO Data Archive is constantly being improved both in contents and functionality throughout the Active Archive Phase, ending in December 2006.",
"homepage": "https://nida.esac.esa.int/nida-cl-web/",
"name": "The Infrared Space Observatory data archive",
"prefix": "r3d100010597",
"synonyms": [
"IDA",
"ISO Data Archive"
]
},
"r3d100010598": {
"description": "LAMBDA is a part of NASA's High Energy Astrophysics Science Archive Research Center (HEASARC). LAMBDA is a multi-mission NASA center of expertise for cosmic microwave background radiation research. LAMBDA exists to serve the CMB research community, and the greater cosmological research community.",
"homepage": "https://lambda.gsfc.nasa.gov/",
"name": "Legacy Archive for Microwave Background Data Analysis",
"prefix": "r3d100010598",
"synonyms": [
"High Energy Astrophysics Science Archive Research Center",
"LAMBDA"
]
},
"r3d100010599": {
"description": "DSpace@MIT is a service of the MIT Libraries to provide MIT faculty, researchers and their supporting communities stable, long-term storage for their digital research and teaching output and to maximize exposure of their content to a world audience.\nDSpace@MIT content includes conference papers, images, peer-reviewed scholarly articles, preprints, technical reports, theses, working papers, research datasets and more. This collection of more than 60,000 high-quality works is recognized as among the world's premier scholarly repositories and receives, on average, more than 1 million downloads per month.",
"homepage": "https://dspace.mit.edu/",
"name": "DSpace@MIT",
"prefix": "r3d100010599"
},
"r3d100010600": {
"description": "The Macaulay Library is the world's largest and oldest scientific archive of biodiversity audio and video recordings. The library collects and preserves recordings of each species' behavior and natural history, to facilitate the ability of others to collect and preserve such recordings, and to actively promote the use of these recordings for diverse purposes spanning scientific research, education, conservation, and the arts. All archived analog recordings in the collection, going back to 1929.",
"homepage": "https://www.macaulaylibrary.org/",
"name": "Macaulay Library",
"prefix": "r3d100010600",
"synonyms": [
"LNS",
"Library of Natural Sounds"
]
},
"r3d100010601": {
"description": "SILSO is the World Data Center for the production, preservation and dissemination of the international sunspot number.",
"homepage": "https://www.sidc.be/SILSO/home",
"name": "WDC Sunspot Index and Long-term Solar Observations",
"prefix": "r3d100010601",
"synonyms": [
"SILSO"
],
"xrefs": {
"fairsharing": "FAIRsharing.d6423b"
}
},
"r3d100010602": {
"description": "<<>>!!!>>> The Space Physics Interactive Data Resource from NOAA's National Geophysical Data Center allows solar terrestrial physics customers to intelligently access and manage historical space physics data for integration with environment models and space weather forecasts.",
"name": "Space Physics Interactive Data Resource",
"prefix": "r3d100010602",
"synonyms": [
"SPIDR"
]
},
"r3d100010603": {
"description": "Spitzer is the final mission in NASA's Great Observatories Program - a family of four orbiting observatories, each observing the Universe in a different kind of light (visible, gamma rays, X-rays, and infrared). Spitzer is also a part of NASA's Astronomical Search for Origins Program, designed to provide information which will help us understand our cosmic roots, and how galaxies, stars and planets develop and form.",
"homepage": "https://sha.ipac.caltech.edu/applications/Spitzer/SHA/",
"name": "Spitzer Heritage Archive",
"prefix": "r3d100010603",
"synonyms": [
"SHA"
]
},
"r3d100010604": {
"description": "STRING is a database of known and predicted protein interactions.\nThe interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:\n- Genomic Context\n- High-throughput Experiments\n- (Conserved) Coexpression\n- Previous Knowledge\nSTRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.",
"homepage": "https://string-db.org/",
"name": "STRING",
"prefix": "r3d100010604",
"synonyms": [
"Known and Predicted Protein-Protein Interactions"
],
"xrefs": {
"fairsharing": "FAIRsharing.9b7wvk",
"miriam": "00000265",
"nif": "0000-03503",
"omics": "29032",
"scr": "005223"
}
},
"r3d100010605": {
"description": "The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.",
"homepage": "https://swissmodel.expasy.org/repository/",
"name": "SWISS-MODEL Repository",
"prefix": "r3d100010605",
"synonyms": [
"SMR"
],
"xrefs": {
"fairsharing": "FAIRsharing.vxz9pn",
"nif": "0000-03522",
"scr": "013032"
}
},
"r3d100010606": {
"description": "<<>>!!!>>>",
"homepage": "http://www.teamnetwork.org/",
"name": "Tropical Ecology Assessment and Monitoring Network",
"prefix": "r3d100010606",
"synonyms": [
"Early Warning System for Nature",
"TEAM"
]
},
"r3d100010607": {
"description": "<<>>!!!>>>",
"homepage": "https://ushik.ahrq.gov/mdr/portals",
"name": "United States Health Information Knowledgebase",
"prefix": "r3d100010607",
"synonyms": [
"USHIK"
]
},
"r3d100010608": {
"description": "The task of WDC geomagnetism is to collect geomagnetic data from all over the globe and distribute those data to researchers and data users, as a World Data Center for Geomagnetism.",
"homepage": "https://wdc.kugi.kyoto-u.ac.jp/",
"name": "World Data Center for Geomagnetism, Kyoto",
"prefix": "r3d100010608",
"synonyms": [
"WDC - Geomagnetism, Kyoto",
"WDC for Geomag"
],
"xrefs": {
"fairsharing": "FAIRsharing.16e3f7"
}
},
"r3d100010609": {
"description": "Among the basic tasks of WDC-Ukraine there is collection, handling and storage of science data and giving access to it for usage both in science research and study process. That include contemporary tutoring technologies and resources of e-libraries and archives; remote access to own information resources for the wide circle of scientists from the universities and science institutions of Ukraine",
"homepage": "http://wdc.org.ua/",
"name": "World Data Center for Geoinformatics and Sustainable Development",
"prefix": "r3d100010609",
"synonyms": [
"WDC - Geoinformatics and Sustainable Development",
"WDC-Ukraine"
]
},
"r3d100010610": {
"description": "ALEXA is a microarray design platform for 'alternative expression analysis'. This platform facilitates the design of expression arrays for analysis of mRNA isoforms generated from a single locus by the use of alternative transcription initiation, splicing and polyadenylation sites. We use the term 'ALEXA' to describe a collection of novel genomic methods for 'alternative expression' analysis. 'Alternative expression' refers to the identification and quantification of alternative mRNA transcripts produced by alternative transcript initiation, alternative splicing and alternative polyadenylation. This website provides supplementary materials, source code and other downloads for recent publications describing our studies of alternative expression (AE). Most recently we have developed a method, 'ALEXA-Seq' and associated resources for alternative expression analysis by massively parallel RNA sequencing.",
"homepage": "http://www.alexaplatform.org/",
"name": "ALEXA",
"prefix": "r3d100010610",
"synonyms": [
"ALEXA-A",
"ALEXA-Seq",
"Alternative expression analysis"
],
"xrefs": {
"omics": "01328",
"scr": "006700"
}
},
"r3d100010611": {
"description": "!!! <<< Genome data generated by BC Genome Sciences Centre is no longer available through this site as it is regularly deposited into controlled data repositories such as the European Genome Phenome Archive (EGA); ICGC (International Cancer Genome Consortium) and the Genome Data Commons (GDC) <<< !!! Using serial analysis of gene expression (SAGE) and microarrays, we are examining total mRNA populations in all developmental stages, both in whole worms and in specific cells and tissues. In addition, we are building promoter::GFP constructs to monitor gene expression in transgenic worms, focusing on C. elegans genes that have human orthologues. Also available are web-based PCR primer design tools, and access to information about our C. elegans Fosmid library.",
"name": "C. Elegans Gene Expression",
"prefix": "r3d100010611"
},
"r3d100010612": {
"description": "We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo. We used ChIP-seq to map STAT1 targets in interferon-gamma (IFN-gamma)-stimulated and unstimulated human HeLa S3 cells, and compared the method's performance to ChIP-PCR and to ChIP-chip for four chromosomes.For both Chromatin- immunoprecipation Transcription Factors and Histone modifications. Sequence files and the associated probability files are also provided.",
"homepage": "http://www.bcgsc.ca/data/chipseq/chip-seq-data",
"name": "ChIP-Seq Transcription Factor Data",
"prefix": "r3d100010612",
"synonyms": [
"ChIP-Seq"
]
},
"r3d100010613": {
"description": "FPC Mapping data files from species that have been fingerprinted at Canada's Michael Smith Genome Sciences Centre (BCGSC).",
"homepage": "https://plone.bcgsc.ca/data/data",
"name": "Physical mapping data at Canada's Michael Smith Genome Sciences Centre - Data",
"prefix": "r3d100010613",
"synonyms": [
"BCGSC",
"FPC Database mapping files",
"Physical Mapping Data Access"
]
},
"r3d100010614": {
"description": "<<>>!!!>>>\n\nMapping, copy number analysis, sequence and gene expression data generated by the High Resolution Analysis of Follicular Lymphoma Genomes project. The data will be available for 24 patients with follicular lymphoma. All data will be made as widely and freely available as possible while safeguarding the privacy of participants, and protecting confidential and proprietary data.The data from this project will be submitted to public genomic data sources. These sources will be listed on this web site as the data becomes available in these external data sources.",
"homepage": "http://www.bcgsc.ca/data/hra-follicular-lymphoma",
"name": "Follicular Lymphoma Genome Data at Canada's Michael Smith Genome Sciences Centre (BCGSC)",
"prefix": "r3d100010614"
},
"r3d100010615": {
"description": "The Comparative Mammalian Brain Collection web site provides site visitors with images and information from several of the world's largest collections of well-preserved, sectioned and stained brains of mammals, principally those at the University of Wisconsin-Madison and Michigan State University. These collections are currently being consolidated into a central repository at the National Museum of Health and Medicine at the Armed Forces Institute of Pathology in Washington, DC. The collections have been a century in the making and represent the efforts of dozens of skilled scientists. Their colocation at a single facility will represent a national and international center for comparative brain study of the actual specimens. The centralized web site offers many kinds of access to the information contained in the specimens, for use by students and researchers worldwide.",
"homepage": "https://brainmuseum.org/",
"name": "Comparative Mammalian Brain Collections",
"prefix": "r3d100010615",
"synonyms": [
"brainmuseum"
],
"xrefs": {
"nif": "0000-00013",
"scr": "007273"
}
},
"r3d100010616": {
"description": "BRENDA is the main collection of enzyme functional data available to the scientific community worldwide. The enzymes are classified according to the Enzyme Commission list of enzymes. It is available free of charge for via the internet (http://www.brenda-enzymes.org/) and as an in-house database for commercial users (requests to our distributor Biobase). The enzymes are classified according to the Enzyme Commission list of enzymes. Some 5000 \"different\" enzymes are covered. Frequently enzymes with very different properties are included under the same EC number. BRENDA includes biochemical and molecular information on classification, nomenclature, reaction, specificity, functional parameters, occurrence, enzyme structure, application, engineering, stability, disease, isolation, and preparation. The database also provides additional information on ligands, which function as natural or in vitro substrates/products, inhibitors, activating compounds, cofactors, bound metals, and other attributes.",
"homepage": "https://www.brenda-enzymes.org",
"name": "BRENDA",
"prefix": "r3d100010616",
"synonyms": [
"BRENDA Enzyme Database",
"BRaunschweig ENzyme DAtabase"
],
"xrefs": {
"fairsharing": "FAIRsharing.etp533",
"nif": "0000-30222",
"omics": "02681",
"scr": "002997"
}
},
"r3d100010617": {
"description": "Candida Genome Database, a resource for genomic sequence data and gene and protein information for Candida albicans and related species. CGD is based on the Saccharomyces Genome Database. The Candida Genome Database (CGD) provides online access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans and related species. C. albicans is the best studied of the human fungal pathogens. It is a common commensal organism of healthy individuals, but can cause debilitating mucosal infections and life-threatening systemic infections, especially in immunocompromised patients. C. albicans also serves as a model organism for the study of other fungal pathogens.",
"homepage": "http://www.candidagenome.org/",
"name": "Candida Genome Database",
"prefix": "r3d100010617",
"synonyms": [
"CGD"
],
"xrefs": {
"fairsharing": "FAIRsharing.j7j53",
"nif": "0000-02634",
"omics": "03098",
"scr": "002036"
}
},
"r3d100010618": {
"description": "<<>>!!!>>>",
"homepage": "http://www.bioinformatics.dtu.dk",
"name": "DTU Bioinformatics",
"prefix": "r3d100010618",
"synonyms": [
"CBS (formerly)",
"Center for Biological Sequence Analysis (formerly)"
],
"xrefs": {
"nlx": "12329",
"scr": "003590"
}
},
"r3d100010619": {
"description": "<<>>!!!>>>",
"homepage": "http://www.cisred.org/",
"name": "cisRED",
"prefix": "r3d100010619",
"synonyms": [
"Databases of genome-wide regulatory module and element predictions",
"cis - Regulatory element database"
],
"xrefs": {
"fairsharing": "FAIRsharing.rwd4wq",
"nif": "0000-02665",
"omics": "01857",
"scr": "002098"
}
},
"r3d100010620": {
"description": "Apollo (previously DSpace@Cambridge) is the University of Cambridgeβs Institutional Repository (IR), preserving and providing access to content created by members of the University. The repository stores a range of content and provides different levels of access, but its primary focus is on providing open access to the Universityβs research publications.",
"homepage": "https://www.repository.cam.ac.uk/home",
"name": "Apollo",
"prefix": "r3d100010620",
"synonyms": [
"DSpace@Cambridge"
],
"xrefs": {
"opendoar": "109",
"roar": "390"
}
},
"r3d100010621": {
"description": "The CDC Data Catalogue describes the Climate Data of the DWD and provides access to data, descriptions and access methods. Climate Data refers to observations, statistical indices and spatial analyses. CDC comprises Climate Data for Germany, but also global Climate Data, which were collected and processed in the framework of international co-operation. The CDC Data Catalogue is under construction and not yet complete. The purposes of the CDC Data Catalogue are:\nto provide uniform access to climate data centres and climate datasets of the DWD\nto describe the climate data according to international metadata standards\nto make the catalogue information available on the Internet\nto support the search for climate data\nto facilitate the access to climate data and climate data descriptions",
"homepage": "https://cdc.dwd.de/portal/",
"name": "CDC - Climate Data Center",
"prefix": "r3d100010621",
"synonyms": [
"Deutscher Wetterdienst - DWD"
]
},
"r3d100010622": {
"description": "<<>>!!!>>> Environment and Climate Change Canada collects biological samples from a number of lakes and rivers across Canada in support of federally mandated programs. Environment and Climate Change Canada has collected fish and invertebrates from the Great Lakes since 1977 in support of the Great Lakes Water Quality Agreement (GLWQA). More recently, samples have been collected nationally to support Canada's Chemicals Management Plan and the Clean Air Regulatory Agenda. Environment and Climate Change Canada also maintains a specimen bank of frozen tissues which is a requirement of the GLWQA and is an integral part of departmental monitoring and research programs. The National Aquatic Biological Specimen Bank (NABSB) is located in a dedicated facility at the Canada Centre for Inland Waters in Burlington, Ontario. The NABSB holds more than 37,000 samples of fish and invertebrates collected over the last 30+ years of environmental monitoring in Canada. Research conducted using samples from the NABSB has produced more than 60 scientific publications, reports and book chapters",
"homepage": "https://www.ec.gc.ca/inre-nwri/default.asp?lang=En&n=D488F7DE-1",
"name": "Canadas National Aquatic Biological Specimen Bank and Database",
"prefix": "r3d100010622",
"synonyms": [
"BNSBA",
"Base de donnΓ©es et Banque nationale de spΓ©cimens biologiques aquatiques du Canada",
"NABSB"
]
},
"r3d100010623": {
"description": "The National Pollutant Release Inventory (NPRI) is Canada's legislated, publicly accessible inventory of pollutant releases (to air, water and land), disposals and transfers for recycling. It is a key resource for:\nidentifying pollution prevention priorities;\nsupporting the assessment and risk management of chemicals, and air quality modelling;\nhelping develop targeted regulations for reducing releases of toxic substances and air pollutants;\nencouraging actions to reduce the release of pollutants into the environment; and improving public understanding.\nThe NPRI comprises:\nInformation reported by facilities and published by Environment and Climate Change Canada under the authority of Sections 46 β 50 of the Canadian Environmental Protection Act, 1999 (CEPA 1999); and\nComprehensive emission summaries and trends for key air pollutants, based on facility-reported data and emission estimates for other sources such as motor vehicles, residential heating, forest fires and agriculture.\nFor the latest reporting year, 7,708 facilities reported to the NPRI on more than 300 listed substances. Comprehensive air pollutant emission summaries and trends were compiled by Environment and Climate Change Canada for criteria air contaminants (the main pollutants contributing to smog, acid rain and/or poor air quality), selected heavy metals and persistent organic pollutants.",
"homepage": "https://www.canada.ca/en/services/environment/pollution-waste-management/national-pollutant-release-inventory.html",
"name": "National Pollutant Release Inventory",
"prefix": "r3d100010623",
"synonyms": [
"Inventaire national des rejets de pollutants",
"NPRI",
"Surveillance de la pollution au Canada",
"Tracking Pollution in Canada"
],
"xrefs": {
"biodbcore": "001476",
"fairsharing": "FAIRsharing.f14e0b"
}
},
"r3d100010624": {
"description": "The goals of the Drosophila Genome Center are to finish the sequence of the euchromatic genome of Drosophila melanogaster to high quality and to generate and maintain biological annotations of this sequence. In addition to genomic sequencing, the BDGP is \n1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; \n2) characterizing the sequence and expression of cDNAs; and \n3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community.",
"homepage": "https://www.fruitfly.org/index.html",
"name": "Berkeley Drosophila Genome Project",
"prefix": "r3d100010624",
"synonyms": [
"BDGP"
],
"xrefs": {
"fairsharing": "FAIRsharing.kap6gp",
"nif": "0000-02867",
"omics": "22557",
"scr": "013094"
}
},
"r3d100010625": {
"description": "The main goal of the ECCAD project is to provide scientific and policy users with datasets of surface emissions of atmospheric compounds, and ancillary data, i.e. data required to estimate or quantify surface emissions.\nThe supply of ancillary data - such as maps of population density, maps of fires spots, burnt areas, land cover - could help improve and encourage the development of new emissions datasets.\nECCAD offers:\nAccess to global and regional emission inventories and ancillary data, in a standardized format\nQuick visualization of emission and ancillary data\nRationalization of the use of input data in algorithms or emission models\nAnalysis and comparison of emissions datasets and ancillary data\nTools for the evaluation of emissions and ancillary data\nECCAD is a dynamical and interactive database, providing the most up to date datasets including data used within ongoing projects. Users are welcome to add their own datasets, or have their regional masks included in order to use ECCAD tools.",
"homepage": "http://eccad.aeris-data.fr/",
"name": "ECCAD - the GEIA database",
"prefix": "r3d100010625",
"synonyms": [
"Emissions of atmospheric Compounds & Compilation of Ancillary Data",
"Global Emission Inventories Activity"
],
"xrefs": {
"fairsharing": "FAIRsharing.7f04e5"
}
},
"r3d100010626": {
"description": "<<>>!!!<<<",
"homepage": "https://www.genedb.org/",
"name": "GeneDB",
"prefix": "r3d100010626",
"xrefs": {
"fairsharing": "FAIRsharing.j7esqq",
"miriam": "00100139",
"nif": "0000-02880",
"scr": "002774"
}
},
"r3d100010627": {
"description": "The World Glacier Monitoring Service (WGMS) collects standardized observations on changes in mass, volume, area and length of glaciers with time (glacier fluctuations), as well as statistical information on the distribution of perennial surface ice in space (glacier inventories). Such glacier fluctuation and inventory data are high priority key variables in climate system monitoring; they form a basis for hydrological modelling with respect to possible effects of atmospheric warming, and provide fundamental information in glaciology, glacial geomorphology and quaternary geology. The highest information density is found for the Alps and Scandinavia, where long and uninterrupted records are available. As a contribution to the Global Terrestrial/Climate Observing System (GTOS, GCOS), the Division of Early Warning and Assessment and the Global Environment Outlook of UNEP, and the International Hydrological Programme of UNESCO, the WGMS collects and publishes worldwide standardized glacier data.",
"homepage": "https://wgms.ch/",
"name": "World Glacier Monitoring Service",
"prefix": "r3d100010627",
"synonyms": [
"WGMS"
],
"xrefs": {
"doi": "10.5904/wgms-fog-2018-11"
}
},
"r3d100010628": {
"description": "<<>>!!!>>>",
"homepage": "http://www.airc.aist.go.jp/gsrt/open-top.html",
"name": "Global Earth Observation Grid",
"prefix": "r3d100010628",
"synonyms": [
"GeoGrid"
]
},
"r3d100010629": {
"description": ">>>!!!<<< The repository is no longer available. >>>!!!<<< 2018-08-29: no more access to Geophyscial Multilingual Internet-Driven Information Service >>>!!!<<<",
"homepage": "http://www.geomind.eu/",
"name": "GEOMIND",
"prefix": "r3d100010629",
"synonyms": [
"Geophyscial Multilingual Internet-Driven Information Service"
]
},
"r3d100010630": {
"description": "GovData the data portal for Germany offers consistent and central access to administrative data at the federal, state, and local level. Objective is to make data more available and easier to use at a single location. As set out in the concept of \"open data\", we attempt to facilitate the use of open licenses and to increase the supply of machine-readable raw data.",
"homepage": "https://www.govdata.de/",
"name": "GOVDATA",
"prefix": "r3d100010630",
"synonyms": [
"Das Datenportal fΓΌr Deutschland"
]
},
"r3d100010631": {
"description": ">>>!!!<<< On June 1, 2020, the Academic Seismic Portal repositories at UTIG were merged into a single collection hosted at Lamont-Doherty Earth Observatory. Content here was removed July 1, 2020. Visit the Academic Seismic Portal @LDEO! https://www.marine-geo.org/collections/#!/collection/Seismic#summary (https://www.re3data.org/repository/r3d100010644) >>>!!!<<<",
"homepage": "http://www-udc.ig.utexas.edu/sdc/",
"name": "Academic Seismic Portal at UTIG",
"prefix": "r3d100010631",
"synonyms": [
"ASP"
],
"xrefs": {
"fairsharing": "FAIRsharing.ph8fx9",
"nlx": "154745",
"scr": "000403"
}
},
"r3d100010632": {
"description": "Insect Images is part of the Center for Invasive Species and Ecosystem Healthβs BugwoodImages. It provides an easily accessible archive of high quality images for use in educational applications. The focus of InsectImages is images related to entomology.\nInsect Images hosts Archives from the Ohio State University (OARDC), Southern Forest Insect Work Conference (SFIWC), Florida Department of Agriculture & Consumer Services, United States National Collection of Scale Insects Photographs (ScaleNet), Mactode Publications, The University of Georgia Museum of Natural History, the United States Geological Surveys Nonindigenous Aquatic Speies (NAS)and the collaborative survey 'Viruses in Imported and Domestically Produced Ornamentals'. In most cases, the images found in this system were taken by and loaned to us by photographers other than ourselves. Most are in the realm of public sector images. The photographs are in this system to be used",
"homepage": "https://www.insectimages.org/",
"name": "Insect Images",
"prefix": "r3d100010632",
"synonyms": [
"InsectImages"
]
},
"r3d100010633": {
"description": "invasive.org is a project of the University of Georgiaβs Center for Invasive Species and Ecosystem Health and one of the four major parts of BugwoodImages. The Focus is on invasive and exotic species of North America. This can be animals, plants, insects, and pathogens. It provides an easily accessible archive of high quality images for use in educational applications. In most cases, the images found in this system were taken by and loaned to us by photographers other than ourselves. Most are in the realm of public sector images. The photographs are in this system to be used.",
"homepage": "https://www.invasive.org/",
"name": "Invasive.org",
"prefix": "r3d100010633",
"synonyms": [
"Invasive and Exotic Species of North America"
]
},
"r3d100010634": {
"description": "IPM Images is a project of the University of Georgiaβs Center for Invasive Species and Ecosystem Health and one of the four major parts of BugwoodImages. The Focus is on Integrated Pest Management. It provides an easily accessible archive of high quality images for use in educational applications. In most cases, the images found in this system were taken by and loaned to us by photographers other than ourselves. Most are in the realm of public sector images. The photographs are in this system to be used",
"homepage": "https://www.ipmimages.org/",
"name": "IPM Images",
"prefix": "r3d100010634"
},
"r3d100010635": {
"description": "The World Data Centre section provides software and data catalogue information and data produced by IPS Radio and Space Services over the past few past decades. You can download data files, plot graphs from data files, check data availability, retrieve data sets and station information.",
"homepage": "https://www.sws.bom.gov.au/World_Data_Centre",
"name": "World Data Centre for Space Weather",
"prefix": "r3d100010635",
"synonyms": [
"SWS",
"Space Weather Services",
"WDC - Space Weather, Australia",
"formerly: WDC STS",
"formerly: World Data Centre for Solar-Terrestrial Science"
],
"xrefs": {
"fairsharing": "FAIRsharing.cc3QN9"
}
},
"r3d100010636": {
"description": "The IMPC is a confederation of international mouse phenotyping projects working towards the agreed goals of the consortium: To undertake the phenotyping of 20,000 mouse mutants over a ten year period, providing the first functional annotation of a mammalian genome. Maintain and expand a world-wide consortium of institutions with capacity and expertise to produce germ line transmission of targeted knockout mutations in embryonic stem cells for 20,000 known and predicted mouse genes.\nTest each mutant mouse line through a broad based primary phenotyping pipeline in all the major adult organ systems and most areas of major human disease.\nThrough this activity and employing data annotation tools, systematically aim to discover and ascribe biological function to each gene, driving new ideas and underpinning future research into biological systems;\nMaintain and expand collaborative βnetworksβ with specialist phenotyping consortia or laboratories, providing standardized secondary level phenotyping that enriches the primary dataset, and end-user, project specific tertiary level phenotyping that adds value to the mammalian gene functional annotation and fosters hypothesis driven research; and\nProvide a centralized data centre and portal for free, unrestricted access to primary and secondary data by the scientific community, promoting sharing of data, genotype-phenotype annotation, standard operating protocols, and the development of open source data analysis tools.\nMembers of the IMPC may include research centers, funding organizations and corporations.",
"homepage": "https://www.mousephenotype.org/",
"name": "International Mouse Phenotyping Consortium",
"prefix": "r3d100010636",
"synonyms": [
"IKMC",
"IMPC",
"Intgernational Mouse Phenotyping Consortium",
"The International Knockout Mouse Consortium"
],
"xrefs": {
"fairsharing": "FAIRsharing.LdoU1I",
"nlx": "151660",
"scr": "006158"
}
},
"r3d100010637": {
"description": "While focused on supporting the scientific community, ATCC activities range widely, from repository-related operations to providing specialized services, conducting in-house R&D and intellectual property management.\nATCC serves U.S. and international researchers by characterizing cell lines, bacteria, viruses, fungi and protozoa, as well as developing and evaluating assays and techniques for validating research resources and preserving and distributing biological materials to the public and private sector research communities. Our management philosophy emphasizes customer satisfaction, value addition, cost-effective operations and competitive benchmarking for all areas of our enterprise.",
"homepage": "https://www.atcc.org/",
"name": "American Type Culture Collection",
"prefix": "r3d100010637",
"synonyms": [
"ATCC"
],
"xrefs": {
"fairsharing": "fairsharing.j0ezpm",
"nif": "0000-10159",
"scr": "001672"
}
},
"r3d100010638": {
"description": "The Antarctic and Southern Ocean Data Portal, part of the US Antarctic Data Consortium, provides access to geoscience data, primarily marine, from the Antarctic region. The synthesis began in 2003 as the Antarctic Multibeam Bathymetry and Geophysical Data Synthesis (AMBS) with a focus on multibeam bathymetry field data and other geophysical data from the Southern Ocean collected with the R/V N. B. Palmer. In 2005, the effort was expanded to include all routine underway geophysical and oceanographic data collected with both the R/V N. B. Palmer and R/V L. Gould, the two primary research vessels serving the US Antarctic Program.",
"homepage": "https://www.marine-geo.org/collections/#!/collection/USAP#summary",
"name": "Antarctic & Southern Ocean Data Portal",
"prefix": "r3d100010638",
"synonyms": [
"ASODS"
],
"xrefs": {
"nlx": "154703",
"scr": "002193"
}
},
"r3d100010639": {
"description": "The GeoPRISMS Data Portal was established in early 2011 to serve the NSF-funded GeoPRISMS program as a dedicated data system to facilitate open and timely exchange of data in support of the interdisciplinary science goals of the program. GeoPrisms Data Portal focuses upon the coordinated, interdisciplinary investigation of the continental margins through two initiatives: the Subduction Cycles and Deformation (SCD) and Rift Initiation and Evolution (RIE). In order to address the fundamental scientific questions, each initiative is associated with Primary Sites to address a wide range of field, experimental and theoretical studies spanning broad spatial and temporal scales.",
"homepage": "https://www.marine-geo.org/collections/#!/collection/GeoPRISMS#summary",
"name": "GeoPRISMS Data Portal",
"prefix": "r3d100010639",
"synonyms": [
"Geodyanmic Processes at Rifting and Subducting Margins"
]
},
"r3d100010640": {
"description": "The Global Multi-Resolution Topography (GMRT) Synthesis is a dynamically maintained global multi-resolution synthesis of terrestrial and seafloor elevation data available as images & gridded data values.",
"homepage": "https://www.gmrt.org/",
"name": "Global Multi-Resolution Topography Data Portal",
"prefix": "r3d100010640",
"synonyms": [
"GMRT"
]
},
"r3d100010641": {
"description": "<<>>!!!>>>",
"homepage": "https://www.marine-geo.org/collections/#!/collection/MARGINS#summary",
"name": "MARGINS Data Portal",
"prefix": "r3d100010641"
},
"r3d100010642": {
"description": "The National Deep Submergence Facility (NDSF) operates the Human Occupied Vehicle (HOV) Alvin, the Remote Operated Vehicle (ROV) Jason 2, and the Autonomous Underwater Vehicle (AUV) Sentry. Data acquired with these platforms is provided both to the science party on each expedition, and to the Woods Hole Oceanographic Institution (WHOI) Data Library.",
"homepage": "https://ndsf.whoi.edu/data/",
"name": "NDSF Data Portal",
"prefix": "r3d100010642",
"synonyms": [
"National Deep Submergence Facility"
]
},
"r3d100010643": {
"description": "Ridge 2000 is a multidisciplinary science research program focused on integrated geological and biological studies of the Earth-encircling oceanic spreading center system.",
"homepage": "https://www.marine-geo.org/collections/#!/collection/Ridge2000#summary",
"name": "Ridge 2000 Data Portal",
"prefix": "r3d100010643",
"synonyms": [
"R2K Data Portal",
"Ridge Interdisciplinary Global Experiments"
]
},
"r3d100010644": {
"description": "The MGDS Academic Seismic Portal at Lamont-Doherty Earth Observatory (ASP-LDEO), now part of the IEDA Data Facility, was initiated in 2003 to preserve and provide open access to multi-channel seismic (MCS) and single channel seismic (SCS) field data collected for academic research supported by the US National Science Foundation. Multi-channel data are primarily from the marine seismic vessels operated by Lamont-Doherty Earth Observatory of Columbia University. Modern single channel seismic data from other vessels including the R/V Palmer and USCG Healy, as well as data from portable seismic systems, are also served. \nThe development of the Academic Seismic Portal has focused on the need to recover high value MCS data from older surveys as well as to establish sustainable procedures for preservation of data from modern programs. During the final two years of R/V Ewing operations, procedures were established for routine transfer of MCS data along with navigation and acquisition parameters, and other needed documentation to the ASP. Transfer of seismic data and acquisition information is now routine for the National Marine Seismic Facility, the R/V Marcus G. Langseth, which began science operations in February 2008. Data are documented and incorporated into the data system with full access restrictions protecting the scientists' rights to exclusive access during the proprietary hold period. Submission of data to the ASP helps ensure that NSF requirements for data sharing as outlined in the NSF OCE Data Policy are satisfied.\nData from the Academic Seismic Portal at UTIG has been migrated to LDEO. As we continue to verify the accuracy and completeness of this data, there may be temporary issues with some seismic metadata and web services.",
"homepage": "https://www.marine-geo.org/collections/#!/collection/Seismic#summary",
"name": "Academic Seismic Portal at LDEO",
"prefix": "r3d100010644",
"synonyms": [
"ASP at LDEO",
"Academic Seismic Portal at Lamont-Doherty Earth Observatory"
],
"xrefs": {
"nlx": "154704",
"scr": "002194"
}
},
"r3d100010645": {
"description": "<<>>!!!>>>",
"homepage": "http://www.mouseatlas.org/mouseatlas_index_html",
"name": "Mouse Atlas of Gene Expression",
"prefix": "r3d100010645"
},
"r3d100010646": {
"description": "When published in 2005, the Millennium Run was the largest ever simulation of the formation of structure within the ΞCDM cosmology. It uses 10(10) particles to follow the dark matter distribution in a cubic region 500h(β1)Mpc on a side, and has a spatial resolution of 5hβ1kpc. Application of simplified modelling techniques to the stored output of this calculation allows the formation and evolution of the ~10(7) galaxies more luminous than the Small Magellanic Cloud to be simulated for a variety of assumptions about the detailed physics involved. As part of the activities of the German Astrophysical Virtual Observatory we have created relational databases to store the detailed assembly histories both of all the haloes and subhaloes resolved by the simulation, and of all the galaxies that form within these structures for two independent models of the galaxy formation physics. We have implemented a Structured Query Language (SQL) server on these databases. This allows easy access to many properties of the galaxies and halos, as well as to the spatial and temporal relations between them. Information is output in table format compatible with standard Virtual Observatory tools. With this announcement (from 1/8/2006) we are making these structures fully accessible to all users. Interested scientists can learn SQL and test queries on a small, openly accessible version of the Millennium Run (with volume 1/512 that of the full simulation). They can then request accounts to run similar queries on the databases for the full simulations. In 2008 and 2012 the simulations were repeated.",
"homepage": "https://wwwmpa.mpa-garching.mpg.de/millennium/",
"name": "Virgo Millenium Database",
"prefix": "r3d100010646"
},
"r3d100010648": {
"description": "dbEST is a division of GenBank that contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms. Expressed Sequence Tags (ESTs) are short (usually about 300-500 bp), single-pass sequence reads from mRNA (cDNA). Typically they are produced in large batches. They represent a snapshot of genes expressed in a given tissue and/or at a given developmental stage. They are tags (some coding, others not) of expression for a given cDNA library.\nMost EST projects develop large numbers of sequences. These are commonly submitted to GenBank and dbEST as batches of dozens to thousands of entries, with a great deal of redundancy in the citation, submitter and library information. To improve the efficiency of the submission process for this type of data, we have designed a special streamlined submission process and data format.\ndbEST also includes sequences that are longer than the traditional ESTs, or are produced as single sequences or in small batches. Among these sequences are products of differential display experiments and RACE experiments. The thing that these sequences have in common with traditional ESTs, regardless of length, quality, or quantity, is that there is little information that can be annotated in the record.\nIf a sequence is later characterized and annotated with biological features such as a coding region, 5'UTR, or 3'UTR, it should be submitted through the regular GenBank submissions procedure (via BankIt or Sequin), even if part of the sequence is already in dbEST.\ndbEST is reserved for single-pass reads. Assembled sequences should not be submitted to dbEST. GenBank will accept assembled EST submissions for the forthcoming TSA (Transcriptome Shotgun Assembly) division. The individual reads which make up the assembly should be submitted to dbEST, the Trace archive or the Short Read Archive (SRA) prior to the submission of the assemblies.",
"homepage": "https://www.ncbi.nlm.nih.gov/genbank/dbest/",
"name": "Expressed Sequence Tags database",
"prefix": "r3d100010648",
"synonyms": [
"NCBI EST",
"dbEST"
],
"xrefs": {
"fairsharing": "FAIRsharing.v9fya8",
"miriam": "00000159",
"scr": "016578"
}
},
"r3d100010649": {
"description": "<<>>!!!>>>",
"homepage": "http://www.ncbi.nlm.nih.gov/dbSTS/",
"name": "database of Sequence Tagged Sites",
"prefix": "r3d100010649",
"synonyms": [
"dbSTS"
],
"xrefs": {
"fairsharing": "FAIRsharing.wk5azf",
"nif": "0000-20939",
"scr": "000400"
}
},
"r3d100010650": {
"description": "The Gene database provides detailed information for known and predicted genes defined by nucleotide sequence or map position. Gene supplies gene-specific connections in the nexus of map, sequence, expression, structure, function, citation, and homology data. Unique identifiers are assigned to genes with defining sequences, genes with known map positions, and genes inferred from phenotypic information. These gene identifiers are used throughout NCBI's databases and tracked through updates of annotation. Gene includes genomes represented by NCBI Reference Sequences (or RefSeqs) and is integrated for indexing and query and retrieval from NCBI's Entrez and E-Utilities systems.",
"homepage": "https://www.ncbi.nlm.nih.gov/gene?db=gene",
"name": "NCBI Gene",
"prefix": "r3d100010650",
"synonyms": [
"Entrez Gene",
"Gene"
],
"xrefs": {
"fairsharing": "FAIRsharing.5h3maw",
"nif": "0000-02801",
"omics": "01651",
"scr": "002473"
}
},
"r3d100010651": {
"description": "AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammalsβ transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release.\nAlternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm.\nIn this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated.",
"homepage": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/",
"name": "AceView",
"prefix": "r3d100010651",
"synonyms": [
"AceView genes"
],
"xrefs": {
"fairsharing": "FAIRsharing.vwmc9h",
"nif": "0000-21007",
"scr": "002277"
}
},
"r3d100010652": {
"description": "The NCBI Short Genetic Variations database, commonly known as dbSNP, catalogs short variations in nucleotide sequences from a wide range of organisms. These variations include single nucleotide variations, short nucleotide insertions and deletions, short tandem repeats and microsatellites. Short Genetic Variations may be common, thus representing true polymorphisms, or they may be rare. Some rare human entries have additional information associated withthem, including disease associations, genotype information and allele origin, as some variations are somatic rather than germline events.\n***NCBI will phase out support for non-human organism data in dbSNP and dbVar beginning on September 1, 2017***",
"homepage": "https://www.ncbi.nlm.nih.gov/snp/",
"name": "dbSNP",
"prefix": "r3d100010652",
"synonyms": [
"Database for short genetic variations",
"SNV"
],
"xrefs": {
"fairsharing": "FAIRsharing.edxb58",
"nif": "0000-02734",
"omics": "00264",
"scr": "002338"
}
},
"r3d100010653": {
"description": "The Conserved Domain Database is a resource for the annotation of functional units in proteins. Its collection of domain models includes a set curated by NCBI, which utilizes 3D structure to provide insights into sequence/structure/function relationships",
"homepage": "https://www.ncbi.nlm.nih.gov/cdd/",
"name": "Conserved Domain database",
"prefix": "r3d100010653",
"synonyms": [
"CDD",
"formerly: Conserved Domains and Protein Classification"
],
"xrefs": {
"nif": "0000-02647",
"scr": "002077"
}
},
"r3d100010654": {
"description": "As the third center for oceanography of the World Data Center following WDC-A of the United States and WDC-B of Russia, WDC-D for oceanography boasts long-term and stable sources of domestic marine basic data. The State Oceanic Administration now has long-term observations obtained from the fixed coastal ocean stations, offshore and oceanic research vessels, moored and drifting buoys. More and more marine data have been available from the Chinese-foreign marine cooperative surveys, analysis and measurement of laboratory samples, reception by the satellite ground station, aerial telemeter and remote sensing, the GOOS program and global ships of opportunity reports, etc; More marine data are being and will be obtained from the ongoing β863β program, one of the state key projects during the Ninth Five-year plan and the seasat No 1 which is scheduled to be launched next year. Through many yearsβ effort, the WDC-D for oceanography has established formal relationship of marine data exchange with over 130 marine institutions in more than 60 countries in the world and is maintaining a close relationship of data exchange with over 30 major national oceanographic data centers. The established China Oceanic Information Network has joined the international marine data exchange system via Internet. Through these channels, a large amount data have been acquired of through international exchange, which, plus the marine data collected at home for many years, has brought the WDC-D for Oceanography over 100 yearsβ global marine data with a total data amounting to more than 10 billion bytes. In the meantime, a vast amount of work has been done in the standardized and normalized processing and management of the data, and a series of national and professional standards have been formulated and implemented successively. Moreover, appropriate standards and norms are being formulated as required.",
"homepage": "http://www.nmdis.org.cn/",
"name": "National Marine Data and Information Service",
"prefix": "r3d100010654",
"synonyms": [
"China Oceanic Information Network",
"NMDIS"
]
},
"r3d100010655": {
"description": "OpenTopography facilitates community access to high-resolution, Earth science-oriented, topography data, and related tools and resources.\nThe OpenTopography Facility is based at the San Diego Supercomputer Center at the University of California, San Diego and is operated in collaboration with colleagues in the School of Earth and Space Exploration at Arizona State University and Earthscope Consortium. Core operational support for OpenTopography comes from the National Science Foundation Earth Sciences.",
"homepage": "https://opentopography.org/",
"name": "OpenTopography",
"prefix": "r3d100010655",
"synonyms": [
"A Portal to High-Resolution Topography Data and Tools"
],
"xrefs": {
"fairsharing": "FAIRsharing.88wme4",
"nlx": "154717",
"scr": "002204"
}
},
"r3d100010656": {
"description": "<< Regulation -> ORegAnno) https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=686342163_2it3aVMQVoXWn0wuCjkNOVX39wxy&c=chr1&g=oreganno >>>!!!>>> The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, the eVOC: Cell type ontology, and the Taxonomy database, where appropriate, with information regarding the original experimentation performed (evidence). ORegAnno further provides an open validation process for all regulatory annotation in the public domain. Assigned validators receive notification of new records in the database and are able to cross-reference the citation to ensure record integrity. Validators have the ability to modify any record (deprecating the old record and creating a new one) if an error is found. Further, any contributor to the database can comment on any annotation by marking errors, or adding special reports into function as they see fit. These features of ORegAnno ensure that the collection is of the highest quality and uniquely provides a dynamic view of our changing understanding of gene regulation in the various genomes.",
"homepage": "http://www.oreganno.org/",
"name": "ORegAnno",
"prefix": "r3d100010656",
"synonyms": [
"Open regulatory annotation database"
],
"xrefs": {
"nif": "0000-03223",
"scr": "007835"
}
},
"r3d100010657": {
"description": "This website aggregates several services that provide access to data of the INTEGRAL Mission.\nESA's INTErnational Gamma-Ray Astrophysics Laboratory is detecting some of the most energetic radiation that comes from space. It is the most sensitive gamma-ray observatory ever launched. INTEGRAL is an ESA mission in cooperation with Russia and the United States",
"homepage": "https://www.cosmos.esa.int/web/integral/home",
"name": "INTEGRAL data archives",
"prefix": "r3d100010657",
"synonyms": [
"International Gamma-Ray Astrophysics Laboratory data Archives"
]
},
"r3d100010659": {
"description": "Projects in the International Scientific Continental Drilling Program (ICDP) produce large amounts of data. Since the start of ICDP, data sharing has played an important part in ICDP projects, and the ICDP Operational Support Group, which provides the infrastructure for data capturing for many ICDP projects, has facilitated dissemination of data within project groups. With the online Scientific Drilling Database (SDDB; http://www.scientificdrilling.org), ICDP and GeoForschungsZentrum Potsdam (GFZ), Germany created a platform for the public dissemination of drilling data",
"homepage": "https://dataservices.gfz-potsdam.de/portal/?fq=datacentre_symbol:DOIDB.SDDB",
"name": "Scientific Drilling Database",
"prefix": "r3d100010659",
"synonyms": [
"SDDB"
]
},
"r3d100010660": {
"description": "The U.S. Antarctic Program Data Center (USAP-DC) provides the central Project Catalog for projects funded by the NSF for the U.S. Antarctic Program and Data Repository for multi-disciplinary investigator research datasets derived from these projects. Services provided support investigators in documenting, preserving, and disseminating their research results. All data are openly accessible to the international community for browse, search, and data download. Datasets are registered in the Antarctic Master Directory to comply with the Antarctic Treaty.",
"homepage": "https://www.usap-dc.org/",
"name": "U.S. Antarctic Program Data Center",
"prefix": "r3d100010660",
"synonyms": [
"USAP-DC"
],
"xrefs": {
"fairsharing": "FAIRsharing.XIxciC",
"nlx": "154744",
"scr": "002221"
}
},
"r3d100010661": {
"description": "The Flanders Marine Institute (VLIZ) is a centre for marine and coastal research. As a partner in various projects and networks it promotes and supports the international image of Flemish marine scientific research and international marine education.\nIn its capacity as a coordination and information platform, the Flanders Marine Institute (VLIZ) supports some thousand marine scientists in Flanders by disseminating their knowledge to policymakers, educators, the general public and scientists.",
"homepage": "http://www.vliz.be/en",
"name": "Flanders Marine Institute",
"prefix": "r3d100010661",
"synonyms": [
"VLIZ",
"Vlaams Instituut voor de Zee"
]
},
"r3d100010662": {
"description": "The WDC Geomagnetism, Edinburgh has a comprehensive set of digital geomagnetic data as well as indices of geomagnetic activity supplied from a worldwide network of magnetic observatories. The data and services at the WDC are available for scientific use without restrictions.",
"homepage": "https://wdc.bgs.ac.uk/",
"name": "World Data Centre for Geomagnetism, Edinburgh",
"prefix": "r3d100010662",
"synonyms": [
"WDC - Geomagnetism, Edinburgh",
"WDC for Geomag"
]
},
"r3d100010664": {
"description": "The World Stress Map (WSM) is a global compilation of information on the crustal present-day stress field maintained since 2009 at the Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences. It is a collaborative project between academia and industry that aims to characterize the crustal stress pattern and to understand the stress sources. All stress information is analysed and compiled in a standardized format and quality-ranked for reliability and comparability on a global scale. \nThe WSM is an open-access public database and is used by various academic and industrial institutions working in a wide range of Earth science disciplines such as geodynamics, hazard assessment, hydrocarbon exploitations and engineering.",
"homepage": "https://www.world-stress-map.org/",
"name": "World Stress Map",
"prefix": "r3d100010664",
"synonyms": [
"WSM",
"Weltkarte der tektonischen Spannungen"
],
"xrefs": {
"doi": "10.5880/WSM.2016.001"
}
},
"r3d100010665": {
"description": "The European Space Agency's (ESA) X-ray Multi-Mirror Mission (XMM-Newton) was launched by an Ariane 504 on December 10th 1999. XMM-Newton is ESA's second cornerstone of the Horizon 2000 Science Programme. It carries 3 high throughput X-ray telescopes with an unprecedented effective area, and an optical monitor, the first flown on a X-ray observatory. The large collecting area and ability to make long uninterrupted exposures provide highly sensitive observations.",
"homepage": "https://nxsa.esac.esa.int/nxsa-web/#home",
"name": "XMM-Newton Science Archive",
"prefix": "r3d100010665",
"synonyms": [
"X-ray Multi-Mirror Mission",
"XSA"
],
"xrefs": {
"issn": "2495-9332"
}
},
"r3d100010666": {
"description": "ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data collected by or in collaboration with researchers at the University of Wisconsin - Madison.\nASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments.",
"homepage": "https://asap.ahabs.wisc.edu/asap/home.php",
"name": "ASAP",
"prefix": "r3d100010666",
"synonyms": [
"A systematic annotation package for community analysis of genomes"
],
"xrefs": {
"fairsharing": "FAIRsharing.anpa6",
"nif": "0000-02571",
"scr": "001849"
}
},
"r3d100010667": {
"description": "The National Air Pollution Surveillance (NAPS) Program provides accurate and long-term air quality data of a uniform standard across Canada. The NAPS Network has a Canada-Wide database of criteria air contaminants from the early 1970s to the present for designated NAPS sites, as well as provincial, territorial and other sites. Trace contaminants are also monitored at several stations in the network and analyzed by the laboratory at River Road.",
"homepage": "https://www.canada.ca/en/environment-climate-change/services/air-pollution/monitoring-networks-data/national-air-pollution-program.html",
"name": "National Air Pollution Surveillance",
"prefix": "r3d100010667",
"synonyms": [
"NAPS",
"RNSPA",
"RΓ©seau national de surveillance de la pollution atmosphΓ©rique"
]
},
"r3d100010668": {
"description": "The Met Office is the UK's National Weather Service.\nWe have a long history of weather forecasting and have been working in the area of climate change for more than two decades.\nAs a world leader in providing weather and climate services, we employ more than 1,800 at 60 locations throughout the world. We are recognised as one of the world's most accurate forecasters, using more than 10 million weather observations a day, an advanced atmospheric model and a high performance supercomputer to create 3,000 tailored forecasts and briefings a day. These are delivered to a huge range of customers from the Government, to businesses, the general public, armed forces, and other organisations.",
"homepage": "https://www.metoffice.gov.uk/research/approach/overview",
"name": "Met office",
"prefix": "r3d100010668"
},
"r3d100010669": {
"description": "The IMEx consortium is an international collaboration between a group of major public interaction data providers who have agreed to share curation effort and develop and work to a single set of curation rules when capturing data from both directly deposited interaction data or from publications in peer-reviewed journals, capture full details of an interaction in a βdeepβ curation model, perform a complete curation of all protein-protein interactions experimentally demonstrated within a publication, make these interaction available in a single search interface on a common website, provide the data in standards compliant download formats, make all IMEx records freely accessible under the Creative Commons Attribution License",
"homepage": "https://www.imexconsortium.org/",
"name": "IMEx",
"prefix": "r3d100010669",
"synonyms": [
"The International Molecular Exchange Consortium"
],
"xrefs": {
"fairsharing.legacy": "3507",
"nif": "0000-00447",
"scr": "002805"
}
},
"r3d100010670": {
"description": "The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Please, check the reference page to find articles describing the DIP database in greater detail. The Database of Ligand-Receptor Partners (DLRP) is a subset of DIP (Database of Interacting Proteins). The DLRP is a database of protein ligand and protein receptor pairs that are known to interact with each other. By interact we mean that the ligand and receptor are members of a ligand-receptor complex and, unless otherwise noted, transduce a signal. In some instances the ligand and/or receptor may form a heterocomplex with other ligands/receptors in order to be functional. We have entered the majority of interactions in DLRP as full DIP entries, with links to references and additional information",
"homepage": "https://dip.doe-mbi.ucla.edu/dip/Main.cgi",
"name": "Database of Interacting Proteins",
"prefix": "r3d100010670",
"synonyms": [
"DIP"
],
"xrefs": {
"fairsharing": "FAIRsharing.qje0v8",
"nif": "0000-00569",
"omics": "01905",
"scr": "003167"
}
},
"r3d100010671": {
"description": "IntAct provides a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.",
"homepage": "https://www.ebi.ac.uk/intact/home",
"name": "IntAct",
"prefix": "r3d100010671",
"synonyms": [
"IntAct Molecular Interaction Database"
],
"xrefs": {
"nif": "0000-03026",
"omics": "01918",
"scr": "006944"
}
},
"r3d100010672": {
"description": "MatrixDB is a freely available database focused on interactions established by extracellular proteins and polysaccharides.\nMatrixDB takes into account the multimetric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB includes interaction data extracted from the literature by manual curation in our lab, and offers access to relevant data involving extracellular proteins provided by our IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. MatrixDB is in charge of the curation of papers published in Matrix Biology since January 2009",
"homepage": "http://matrixdb.univ-lyon1.fr/",
"name": "MatrixDB",
"prefix": "r3d100010672",
"synonyms": [
"Extracellular Matrix interactions DataBase"
],
"xrefs": {
"issn": "2426-6949",
"nif": "0000-10226",
"omics": "01918",
"scr": "001727"
}
},
"r3d100010673": {
"description": ">>>!!!<<< as stated 2017-06-09 MPIDB is no longer available under URL http://www.jcvi.org/mpidb/about.php >>>!!!<<< The microbial protein interaction database (MPIDB) aims to collect and provide all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, protein complex membership, and 3D domain contacts (iPfam, 3did). We do not include (spoke/matrix) binary interactions infered from pull-down experiments.",
"homepage": "http://www.jcvi.org/cms/home/",
"name": "The Microbial Protein Interaction Database",
"prefix": "r3d100010673",
"synonyms": [
"MPIDB"
],
"xrefs": {
"nif": "0000-10467",
"scr": "001898"
}
},
"r3d100010675": {
"description": "I2D (Interologous Interaction Database) is an on-line database of known and predicted mammalian and eukaryotic protein-protein interactions. It has been built by mapping high-throughput (HTP) data between species. Thus, until experimentally verified, these interactions should be considered \"predictions\". It remains one of the most comprehensive sources of known and predicted eukaryotic PPI. I2D includes data for S. cerevisiae, C. elegans, D. melonogaster, R. norvegicus, M. musculus, and H. sapiens.",
"homepage": "http://ophid.utoronto.ca/ophidv2.204/index.jsp",
"name": "Interologous Interaction Database",
"prefix": "r3d100010675",
"synonyms": [
"I2D"
],
"xrefs": {
"fairsharing": "FAIRsharing.k56rjs",
"nif": "0000-03005",
"scr": "002957"
}
},
"r3d100010676": {
"description": "InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures an improved coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralised resource. The database can be mined as a knowledgebase or used with our integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response.",
"homepage": "https://www.innatedb.com/",
"name": "InnateDB",
"prefix": "r3d100010676",
"synonyms": [
"A Knowlede Resource for Innate Immunity Interactions & Pathways"
],
"xrefs": {
"fairsharing": "FAIRsharing.rb2drw",
"nif": "0000-20808",
"scr": "006714"
}
},
"r3d100010677": {
"description": "<<>>!!!>>> \nUniProtKB/Swiss-Prot is the manually annotated and reviewed section of the UniProt Knowledgebase (UniProtKB).\nIt is a high quality annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions.\nSince 2002, it is maintained by the UniProt consortium and is accessible via the UniProt website.",
"homepage": "https://web.expasy.org/docs/swiss-prot_guideline.html",
"name": "UniProtKB/Swiss-Prot",
"prefix": "r3d100010677",
"synonyms": [
"UniProt Knowledgebase"
]
},
"r3d100010680": {
"description": "<< >>!!!<<< \nData is archived at ChemSpider https://www.chemspider.com/Search.aspx?dsn=UsefulChem and https://www.chemspider.com/Search.aspx?dsn=Usefulchem Group Bradley Lab \nsee more information at the Standards tab at 'Remarks'",
"homepage": "https://www.chemspider.com/Search.aspx?dsn=UsefulChem",
"name": "UsefulChem",
"prefix": "r3d100010680"
},
"r3d100010681": {
"description": "The long-term goal of this project is to implement a new strategy for preserving and providing access to the Astrophysical data heritage.\nIA2 is an ambitious Italian Astrophysical research infrastructure project that aims at co-ordinating different national initiatives to improve the quality of astrophysical data services. It aims at co-ordinating these developments and facilitating access to this data for research purposes.\nThe first working target, is the implementation of the TNG Long-Term Archive (LTA). Its feasibility was demonstrated by the LTA pilot project prototype, funded by CNAA in 2001 and completed successfully in July 2002. The implementation of the TNG archive implies:\nβ interfacing with the Centro \"Galileo Galilei\" (CGG) for the acquisition of TNG data;\nβ long-term storage of scientific, technical and auxiliary data from the TNG;\nβ providing accessibility by the CGG staff and by the scientific community to original and derived data;\nβ providing tools to support the life cycle of observing proposals.\nThe second target of the proposal aims at ensuring harmonization with other projects related to archiving of data of astrophysical interest, with particular reference to projects involving the Italian astronomical community (LBT, VST, GSC-II, DPOSS, β¦), to the Italian Solar and Solar System Physics community (SOLAR, SOLRA, ARTHEMIS which form SOLARNET β a future node of EGSO) and to the national and international coordination efforts fostering the idea of a multiwavelength Virtual Astronomical Observatory, and the use of the archived data through the Italian Astronomical Grid.",
"homepage": "https://www.ia2.inaf.it/",
"name": "Italian Centre for Astronomical Archive",
"prefix": "r3d100010681",
"synonyms": [
"Centro Italiano Archivi Astronomici",
"IA2"
]
},
"r3d100010683": {
"description": "<<>>!!!>>>",
"homepage": "http://mint.bio.uniroma2.it/HomoMINT/Welcome.do",
"name": "HomoMINT",
"prefix": "r3d100010683"
},
"r3d100010684": {
"description": "<<>>!!!>>>",
"homepage": "http://mint.bio.uniroma2.it/domino/",
"name": "domino",
"prefix": "r3d100010684",
"synonyms": [
"domaine peptide interactions"
]
},
"r3d100010685": {
"description": "virus mentha archives evidence about viral interactions collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. virus mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions. Protein interaction databases archive protein-protein interaction (PPI) information from published articles. However, no database alone has sufficient literature coverage to offer a complete resource to investigate \"the interactome\".\nvirus mentha's approach generates every week a consistent interactome (graph). Most importantly, the procedure assigns to each interaction a reliability score that takes into account all the supporting evidence. virus mentha offers direct access to viral families such as: Orthomyxoviridae, Orthoretrovirinae and Herpesviridae plus, it offers the unique possibility of searching by host organism. The website and the graphical application are designed to make the data stored in virus mentha accessible and analysable to all users.virus mentha superseeds VirusMINT. The Source databases are: MINT, DIP, IntAct, MatrixDB, BioGRID.",
"homepage": "https://virusmentha.uniroma2.it/",
"name": "virus mentha",
"prefix": "r3d100010685",
"synonyms": [
"VirusMINT",
"the interactome browser"
],
"xrefs": {
"fairsharing": "FAIRsharing.6w29qp",
"nif": "0000-03636",
"omics": "01909",
"scr": "005987"
}
},
"r3d100010689": {
"description": "Welcome to the digital flora of Panama. You may access the taxonomic list of lianas, common trees, shrubs and palms by species name, family, or by their common names in Panama. There are for each species: a botanical description, photos, scans, drawings, and a distribution map showing its presence or absence in a series of floristic inventories and plots established by the Center for Tropical Forest Science in the Panama Canal watershed. A map of its distribution in the countries of Panama and its neighbor Costa Rica includes data from the Global Biodiversity Information Facility (GBIF) network (https://www.gbif.org/). Some families include descriptions.",
"homepage": "http://ctfs.si.edu/PanamaAtlas/datasets/",
"name": "Smithsonian Tropical Research Institute Logo - Panama",
"prefix": "r3d100010689",
"synonyms": [
"CTFS-Panama"
]
},
"r3d100010690": {
"description": "The Khazar University Institutional Repository (KUIR), a suite of services offered by the Library Information Center, is an institutional repository maintained to support the university's researchers, collaborators, and students. Repository content consists of collections of research materials in digital format produced and selected by Khazar University faculty and their collaborators.",
"homepage": "http://dspace.khazar.org/jspui/",
"name": "Khazar University Institutional Repository",
"prefix": "r3d100010690",
"synonyms": [
"KUIR"
],
"xrefs": {
"opendoar": "1330",
"roar": "5487"
}
},
"r3d100010691": {
"description": "Borealis, the Canadian Dataverse Repository, is a bilingual, multidisciplinary, secure, Canadian research data repository, supported by academic libraries and research institutions across Canada. Borealis supports open discovery, management, sharing, and preservation of Canadian research data.\nBorealis is available to researchers who are affiliated with a participating Canadian university or research organization and their collaborators. Borealis is a shared service provided in partnership with Canadian regional academic library consortia, institutions, research organizations, and the Digital Research Alliance of Canada, with technical infrastructure hosted by Scholars Portal and the University of Toronto Libraries.",
"homepage": "https://borealisdata.ca/dataverse.xhtml",
"name": "Borealis",
"prefix": "r3d100010691",
"synonyms": [
"Borealis, le dΓ©pΓ΄t Dataverse canadien",
"Borealis, the Canadian Dataverse Repository",
"formerly: Scholars Portal Dataverse"
],
"xrefs": {
"fairsharing": "FAIRsharing.kwzydf"
}
},
"r3d100010692": {
"description": "The ProteomeXchange consortium has been set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination.\nCurrent members accepting submissions are:\nThe PRIDE PRoteomics IDEntifications database at the European Bioinformatics Institute focusing mainly on shotgun mass spectrometry proteomics data\nPeptideAtlas/PASSEL focusing on SRM/MRM datasets.",
"homepage": "https://www.proteomexchange.org/",
"name": "ProteomeXchange",
"prefix": "r3d100010692",
"synonyms": [
"PX"
],
"xrefs": {
"fairsharing": "FAIRsharing.92dt9d",
"miriam": "00000513",
"nlx": "158620",
"omics": "02458",
"scr": "004055"
}
},
"r3d100010693": {
"description": ">>>>!!!<<< NEPTUNE Canada is now part of Ocean Networks Canada and this website is being phased out. Please visit us on our new website at oceannetworks.ca >>>!!!<<< NEPTUNE Canada, the North-East Pacific Time-series Undersea Networked Experiments, is the world's first regional scale cabled deep ocean observing network. It consists of an 800km network of electroβoptic cable laid on the seabed over the northern Juan de Fuca tectonic plate, off the coast of British Columbia. This tectonic plate serves as an exceptional natural laboratory for ocean observation and experiments.\nNEPTUNE Canada instruments yield continuous realβtime data and imagery from the ocean surface to beneath the seafloor, and from the coast to the deep sea. They respond to events such as earthquakes, tsunamis, fish migrations, plankton blooms, storms and volcanic eruptions. NEPTUNE Canada offers a unique and exciting approach to ocean science.",
"homepage": "http://www.neptunecanada.ca/",
"name": "NEPTUNE Canada",
"prefix": "r3d100010693",
"synonyms": [
"NEPTUNE Canada regional network",
"Neptune in the NE Pacific",
"North-East Pacific Time-series Undersea Networked Experiments"
]
},
"r3d100010694": {
"description": " is a digital repository for social science data, including polling data. Data collections are: Statistics Canada, Canadian Gallup Polls, CORA - Canadian Opinion Research Archive, ICPSR - Interuniversity Consortium for Political and Social Research.",
"homepage": "https://odesi.ca/en",
"name": "",
"prefix": "r3d100010694",
"synonyms": [
"Initiative ontarienne en matière de documentation des données, de service d'extraction et d'infrastructure",
"Ontario Data Documentation, Extraction Service and Infrastructure"
]
},
"r3d100010696": {
"description": "WFCC Global Catalogue of Microorganisms (GCM) is expected to be a robust, reliable and user-friendly system to help culture collections to manage, disseminate and share the information related to their holdings. It also provides a uniform interface for the scientific and industrial communities to access the comprehensive microbial resource information.",
"homepage": "https://gcm.wdcm.org/",
"name": "Global Catalogue of Microorganisms",
"prefix": "r3d100010696",
"synonyms": [
"GCM"
],
"xrefs": {
"fairsharing": "FAIRsharing.81e8a7",
"scr": "016460"
}
},
"r3d100010699": {
"description": "ICRISAT performs crop improvement research, using conventional as well as methods derived from biotechnology, on the following crops: Chickpea, Pigeonpea, Groundnut, Pearl millet,Sorghum and Small millets. ICRISAT's data repository collects, preserves and facilitates access to the datasets produced by ICRISAT researchers to all users who are interested in. Data includes Phenotypic, Genotypic, Social Science, and Spatial data, Soil and Weather.",
"homepage": "https://dataverse.icrisat.org/",
"name": "ICRISAT Dataverse",
"prefix": "r3d100010699",
"synonyms": [
"ICRISAT Research Data",
"International Crops Research Institute for the Semi-Arid Tropics Dataverse Network"
],
"xrefs": {
"fairsharing": "FAIRsharing.a9c734"
}
},
"r3d100010700": {
"description": "The population-based cancer registries in each German federal state transfer data to the German Centre for Cancer Registry Data, as required by the Federal Cancer Registry Data Act. These data are combined, quality-checked, analysed and evaluated, and the results published in collaboration with the public health institutions of the federal states.",
"homepage": "https://www.krebsdaten.de/Krebs/DE/Home/homepage_node.html",
"name": "German Centre for Cancer Registry Data",
"prefix": "r3d100010700",
"synonyms": [
"Zentrum fΓΌr Krebsregisterdaten",
"ZfKD"
]
},
"r3d100010701": {
"description": "ScholarSphere is an institutional repository managed by Penn State University Libraries. Anyone with a Penn State Access ID can deposit materials relating to the Universityβs teaching, learning, and research mission to ScholarSphere. All types of scholarly materials, including publications, instructional materials, creative works, and research data are accepted.\nScholarSphere supports Penn Stateβs commitment to open access and open science. Researchers at Penn State can use ScholarSphere to satisfy open access and data availability requirements from funding agencies and publishers.",
"homepage": "https://scholarsphere.psu.edu/",
"name": "ScholarSphere",
"prefix": "r3d100010701",
"synonyms": [
"PennState ScholarSphere"
]
},
"r3d100010703": {
"description": "UCLA Library is adopting Dataverse, the open source web application designed for sharing, preserving and using research data. UCLA Dataverse will allow data, text, software, scripts, data visualizations, etc., created from research projects at UCLA to be made publicly available, widely discoverable, linkable, and ultimately, reusable",
"homepage": "https://dataverse.ucla.edu/",
"name": "UCLA Dataverse",
"prefix": "r3d100010703"
},
"r3d100010708": {
"description": "<<>>!!!>>> The Clean Energy Project Database (CEPDB) is a massive reference database for organic semiconductors with a particular emphasis on photovoltaic applications. It was created to store and provide access to data from computational as well as experimental studies, on both known and virtual compounds. It is a free and open resource designed to support researchers in the field of organic electronics in their scientific pursuits.\nThe CEPDB was established as part of the Harvard Clean Energy Project (CEP), a virtual high-throughput screening initiative to identify promising new candidates for the next generation of carbon-based solar cell materials.",
"homepage": "https://www.matter.toronto.edu/basic-content-page/open-software-data",
"name": "CEPDB",
"prefix": "r3d100010708",
"synonyms": [
"The Harvard Clean Energy Project Database"
]
},
"r3d100010710": {
"description": "The Stanford Digital Repository (SDR) is Stanford Libraries' digital preservation system. The core repository provides βback-officeβ preservation services β data replication, auditing, media migration, and retrieval -- in a secure, sustainable, scalable stewardship environment. Scholars and researchers across disciplines at Stanford use SDR repository services to provide ongoing, persistent, reliable access to their research outputs.",
"homepage": "https://searchworks.stanford.edu/?f%5Bbuilding_facet%5D%5B0%5D=Stanford%20Digital%20Repository",
"name": "Stanford Digital Repository",
"prefix": "r3d100010710",
"synonyms": [
"SDR"
]
},
"r3d100010712": {
"description": "N U C A S T R O D A T A . O R G is your WWW resource for utilizing nuclear information in studies of astrophysical systems. This site hyperlinks all online nuclear astrophysics datasets, hosts the Computational Infrastructure for Nuclear Astrophysics, and provides a mechnanism for researchers to share files online. We created the first online \"cloud computing\" system for nuclear astrophysics, a virtual pipeline that enables results from the nuclear laboratory to be rapidly incorporated into astrophysical simulations. This system, the Computational Infrastructure for Nuclear Astrophysics or CINA, came online at nucastrodata.org",
"homepage": "https://www.nucastrodata.org/",
"name": "Nucastrodata.org",
"prefix": "r3d100010712",
"synonyms": [
"CINA",
"Computational Infrastructure for Nuclear Astrophysics"
]
},
"r3d100010713": {
"description": "This Dataverse will contain data generated by ADS team members using ADS data.",
"homepage": "https://dataverse.harvard.edu/dataverse/ADS",
"name": "SAO/NASA Astrophysics Data System Dataverse",
"prefix": "r3d100010713",
"synonyms": [
"ADS Dataverse"
]
},
"r3d100010714": {
"description": "The UK Solar System Data Centre (UKSSDC) provides a STFC and NERC jointly funded central archive and data centre facility for Solar System science in the UK. The facilities include the World Data Centre for Solar-Terrestrial Physics, Chilton and the Cluster Ground-Based Data Centre.\nThe UKSSDC supports data archives for the whole UK solar system community encompassing solar, inter-planetary, magnetospheric, ionospheric and geomagnetic science.\nThe UKSSDC is part of RAL Space based at the STFC run Rutherford Appleton Laboratory in Oxfordshire.",
"homepage": "https://www.ukssdc.ac.uk/",
"name": "UK Solar System Data Centre",
"prefix": "r3d100010714",
"synonyms": [
"UKSSDC"
],
"xrefs": {
"fairsharing": "FAIRsharing.1frnts"
}
},
"r3d100010716": {
"description": "<<>>!!!>>>",
"homepage": "https://crawdad.org",
"name": "CRAWDAD",
"prefix": "r3d100010716",
"synonyms": [
"Community Resource for Archiving Wireless Data At Dartmouth (US site)",
"Mirror provided by the School of Computer Science at St Andrews (UK mirror)"
]
},
"r3d100010717": {
"description": "<<>>!!!>>>",
"homepage": "https://ndar.nih.gov/",
"name": "NDAR",
"prefix": "r3d100010717",
"synonyms": [
"National Database for Autism Research",
"Serving the autism research community"
],
"xrefs": {
"nlx": "143735",
"scr": "004434"
}
},
"r3d100010718": {
"description": "heidICON is provided by Heidelberg University Library and is the \"Virtual Slide Collection\" in progress of organization of Heidelberg University. In addition to record graphic material on current interest for research and teaching, the University departments and institutes can digitize and transfer their already existing slide collections.",
"homepage": "https://heidicon.ub.uni-heidelberg.de/search",
"name": "heidICON",
"prefix": "r3d100010718",
"synonyms": [
"Die Heidelberger Bilddatenbank",
"The image and multimedia database"
]
},
"r3d100010719": {
"description": "<<>>!!!>>>",
"homepage": "https://spectradspace.lib.imperial.ac.uk:8443/handle/10042/13",
"name": "SPECTRa Project",
"prefix": "r3d100010719",
"synonyms": [
"Submission, Preservation and Exposure of Chemistry Teaching and Research Data"
],
"xrefs": {
"hdl": "10042/13"
}
},
"r3d100010720": {
"description": "The scores and libretti in this Virtual Collection include first and early editions and manuscript copies of music from the eighteenth and early nineteenth centuries by J.S. Bach and Bach family members, Mozart, Schubert and other composers, as well as multiple versions of nineteenth century opera scores, seminal works of musical modernism, and music of the Second Viennese School. Many, such as variant editions of nineteenth century operas and related libretti, fall into intellectually related sets that are meant to be seen and used together. As a group, they give scholars a window into the study of historical performance practice that cannot be duplicated using the holdings of any one other library.",
"homepage": "https://library.harvard.edu/collections/digital-scores-and-libretti?_collection=scores",
"name": "Loeb Music Library",
"prefix": "r3d100010720",
"synonyms": [
"Digital Scores and Libretti Collection",
"Eda Kuhn Loeb Music Library"
]
},
"r3d100010721": {
"description": "Chempound is a new generation repository architecture based on RDF, semantic dictionaries and linked data. It has been developed to hold any type of chemical object expressible in CML and is exemplified by crystallographic experiments and computational chemistry calculations. In both examples, the repository can hold >50k entries which can be searched by SPARQL endpoints and pre-indexing of key fields. The Chempound architecture is general and adaptable to other fields of data-rich science.\nThe Chempound software is hosted at http://bitbucket.org/chempound and is available under the Apache License, Version 2.0",
"homepage": "https://journals.tdl.org/jodi/index.php/jodi/article/view/5873/5879",
"name": "Chempound",
"prefix": "r3d100010721",
"synonyms": [
"a Web2.0-inspired repository for physical science data"
]
},
"r3d100010724": {
"description": ">>> --- !!!! Attention: Obviously the institute does not exist any more. The links do not work anymore. !!!! --- <<< Our center is devoted to: Collection, compilation, evaluation, and dissemination of scientific information required for fusion research, and Investigation of problems arising in the course of development of fusion research. There are atomic and molecular (A & M) numerical databases and bibliographic databases on plasma physics and atomic physics.",
"homepage": "https://amdata.nifs.ac.jp/amdrc/",
"name": "Atomic and Molecular Data Research Center",
"prefix": "r3d100010724",
"synonyms": [
"AMDRC"
]
},
"r3d100010725": {
"description": "The Atomic and Molecular Data Unit operates within the Nuclear Data Section of the International Atomic Energy Agency, Vienna, Austria.The primary objective of the Atomic and Molecular Data Unit is to establish and maintain internationally recommended numerical databases on atomic and molecular collision and radiative processes, atomic and molecular structure characteristics, particle-solid surface interaction processes and physico-chemical and thermo-mechanical material properties for use in fusion energy research and other plasma science and technology applications.",
"homepage": "https://amdis.iaea.org/",
"name": "Atomic and Molecular Data Information System",
"prefix": "r3d100010725",
"synonyms": [
"AMDIS",
"provided by the Nuclear Data Section"
]
},
"r3d100010726": {
"description": "Numerical database of atomic and molecular processes and particle-surface interactions. ALADDIN has formatted data on atomic structure and spectra (energy levels,wave lengths, and transition probabilities); electron and heavy particle collisions with atoms, ions, and molecules (cross sections and/or rate coefficients, including, in most cases, analytic fit to the data); sputtering of surfaces by impact of main plasma constituents and self sputtering; particle reflection from surfaces; thermophysical and thermomechanical properties of beryllium and pyrolytic graphites.",
"homepage": "https://www-amdis.iaea.org/ALADDIN/",
"name": "ALADDIN",
"prefix": "r3d100010726",
"synonyms": [
"A Labelled Atomic Data INterface"
],
"xrefs": {
"nlx": "157749",
"scr": "010476"
}
},
"r3d100010727": {
"description": "The ADAS Project is a self-funding (i.e. funded by participants) project consisting of most major fusion laboratories along with other astrophysical and university groups. As an implementation, it is an interconnected set of computer codes and data collections for modelling the radiating properties of ions and atoms in plasmas. It can address plasmas ranging from the interstellar medium through the solar atmosphere and laboratory thermonuclear fusion devices to technological plasmas. ADAS assists in the analysis and interpretation of spectral emission and supports detailed plasma models.",
"homepage": "https://open.adas.ac.uk/",
"name": "OPEN-ADAS",
"prefix": "r3d100010727",
"synonyms": [
"Atomic data and analysis structure"
]
},
"r3d100010728": {
"description": "The EUROLAS Data Center (EDC) is one of the two data centers of the International Laser Ranging Service (ILRS). It collects, archives and distributes tracking data, predictions and other tracking relevant information from the global SLR network. Additionally EDC holds a mirror of the official Web-Pages of the ILRS at Goddard Space Flight Center (GSFC). And as result of the activities of the Analysis Working Group (AWG) of the ILRS, DGFI has been selected as analysis centers (AC) and as backup combination center (CC). This task includes weekly processing of SLR observations to LAGEOS-1/2 and ETALON-1/2 to compute station coordinates and earth orientation parameters. Additionally the combination of SLR solutions from the various analysis centres to a combinerd ILRS SLR solution.",
"homepage": "https://edc.dgfi.tum.de/en/",
"name": "EUROLAS Data Center",
"prefix": "r3d100010728",
"synonyms": [
"EDC"
],
"xrefs": {
"fairsharing": "FAIRsharing.4e7190,"
}
},
"r3d100010729": {
"description": "<<>>!!!>>>\nImportant note:\nThe database was no longer feeded with data or updated in the years 2005-2007. The financial support of the project had been stopped a few yers ahead that time.\nThe maintainance of the IT system couldn't be ensured anymore and system was shutdown in 2015.\nPlease see the other databases in the field.",
"homepage": "http://gaphyor.lpgp.u-psud.fr/",
"name": "GAPHYOR",
"prefix": "r3d100010729",
"synonyms": [
"GAz-PHYsics-ORsay"
],
"xrefs": {
"issn": "2425-0678"
}
},
"r3d100010730": {
"description": "Biological collections are replete with taxonomic, geographic, temporal, numerical, and historical information. This information is crucial for understanding and properly managing biodiversity and ecosystems, but is often difficult to access. Canadensys, operated from the UniversitΓ© de MontrΓ©al Biodiversity Centre, is a Canada-wide effort to unlock the biodiversity information held in biological collections.",
"homepage": "https://data.canadensys.net/ipt/",
"name": "Canadensys repository",
"prefix": "r3d100010730",
"synonyms": [
"Database of Vascular Plants of Canada",
"VASCAN"
],
"xrefs": {
"fairsharing": "FAIRsharing.v2sjcy"
}
},
"r3d100010731": {
"description": "On this server you'll find 127 items of primary data of the University of Munich. Scientists / students of all faculties of LMU and of institutions that cooperate with the LMU are invited to deposit their research data on this platform.",
"homepage": "https://data.ub.uni-muenchen.de/",
"name": "Open Data LMU",
"prefix": "r3d100010731"
},
"r3d100010732": {
"description": "***<<>> *** Stated 2017-08-28: To accommodate a wider scope of ophthalmic data, we launched our new Rotterdam Ophthalmic Data Repository.\nPlease visit http://www.rodrep.com/ for all data sets.\n*** The ORGIDS site will no longer be updated! ***<<>>***Through this portal, we will make data sets available that result from our glaucoma research. This includes visual fields, various imaging modalities and other data from both glaucomatous and normal subjects.The data was acquired during more than a decade.",
"homepage": "http://www.orgids.com/",
"name": "Open Rotterdam Glaucoma Imaging Data Sets",
"prefix": "r3d100010732",
"synonyms": [
"ORGIDS"
],
"xrefs": {
"nlx": "157652",
"scr": "003540"
}
},
"r3d100010734": {
"description": "The CSIRO Data Access Portal provides access to data published by CSIRO across a range of disciplines to facilitate sharing and reuse of data held by CSIRO.",
"homepage": "https://data.csiro.au/",
"name": "CSIRO Data Access Portal",
"prefix": "r3d100010734",
"synonyms": [
"CSIRO DAP"
],
"xrefs": {
"fairsharing": "FAIRsharing.fmc0g0"
}
},
"r3d100010735": {
"description": "The Rolling Deck to Repository (R2R) Program provides a comprehensive shore-side data management program for a suite of routine underway geophysical, water column, and atmospheric sensor data collected on vessels of the academic research fleet. R2R also ensures data are submitted to the NOAA National Centers for Environmental Information for long-term preservation.",
"homepage": "https://www.rvdata.us/",
"name": "Rolling Deck to Repository",
"prefix": "r3d100010735",
"synonyms": [
"R2R"
],
"xrefs": {
"fairsharing": "FAIRsharing.ZEbjok"
}
},
"r3d100010736": {
"description": "<<>>!!!>>>\nThe project analyzes educational processes in Germany from early childhood to late adulthood. The National Educational Panel Study (NEPS) has been set up to find out more about the acquisition of education in Germany, to plot the consequences of education for individual biographies, and to describe central educational processes and trajectories across the entire life span.\nSuch an interdisciplinary consortium of research institutes, researcher groups, and research.\npersonalities has been assembled in Bamberg. In addition, the competencies and experiences with longitudinal research available at numerous other locations have been networked to form a cluster of excellence.",
"homepage": "https://www.neps-data.de/Mainpage",
"name": "Nationales Bildungspanel",
"prefix": "r3d100010736",
"synonyms": [
"BildungsverlΓ€ufe in Deutschland",
"Educational trajectories in Germany",
"NEPS",
"National Educational Panel Study"
]
},
"r3d100010739": {
"description": "Sandrart.net: A net-based research platform on the history of art and culture in the 17th century. The projectβs main goal was an annotated, enriched and web-based edition of Joachim von Sandrartβs Teutscher Academie der Edlen Bau, Bild- und Mahlerey-KΓΌnste (1675β80), one of the most important source texts of the early modern period. Having lived and worked in a number of places throughout Europe, Sandrartβs biographical background makes his writings (with first-hand narrations on art, artists and art collections) a work of European dimension.",
"homepage": "http://ta.sandrart.net/en/",
"name": "Sandrart.net",
"prefix": "r3d100010739"
},
"r3d100010741": {
"description": "Addgene archives and distributes plasmids for researchers around the globe. They are working with thousands of laboratories to assemble a high-quality library of published plasmids for use in research and discovery. By linking plasmids with articles, scientists can always find data related to the materials they request.",
"homepage": "https://www.addgene.org/",
"name": "Addgene",
"prefix": "r3d100010741",
"xrefs": {
"fairsharing": "FAIRsharing.8hcczk",
"miriam": "00000675",
"nif": "0000-11872",
"scr": "002037"
}
},
"r3d100010742": {
"description": "The UCD Digital Library is a platform for exploring cultural heritage, engaging with digital scholarship, and accessing research data. The UCD Digital Library allows you to search, browse and explore a growing collection of historical materials, photographs, art, interviews, letters, and other exciting content, that have been digitised and made freely available.",
"homepage": "https://digital.ucd.ie/",
"name": "UCD Digital Library",
"prefix": "r3d100010742",
"synonyms": [
"An Leabharlann, An ColΓ‘iste Ollscoile, Baile Γtha Cliath",
"University College Dublin Digital Library"
]
},
"r3d100010743": {
"description": "The WURM project is a database of computed Raman and infrared spectra and other physical properties for minerals. The calculations are performed within the framework of the density-functional theory and the density-functional perturbation theory. The database is freely available for teaching and research purposes and is presented in a web-based format, hosted on the https://www.wurm.info/ web site. It provides the crystal structure, the parameters of the calculations, the dielectric properties, the Raman spectra with both peak positions and intensities and the infrared spectra with peak positions for minerals. It shows the atomic displacement patterns for all the zone-center vibrational modes and the associated Raman tensors. The web presentation is user friendly and highly oriented toward the end user, with a strong educational component in mind. A set of visualization tools ensures the observation of the crystal structure, the vibrational pattern, and the different spectra. Further developments include elastic and optical properties of minerals.",
"homepage": "https://www.wurm.info/",
"name": "WURM Project",
"prefix": "r3d100010743",
"synonyms": [
"a database of computed physical properties of minerals"
],
"xrefs": {
"issn": "2425-0287"
}
},
"r3d100010744": {
"description": "This Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house all publicly available QTL and trait mapping data (i.e. trait and genome location association data; collectively called \"QTL data\" on this site) on livestock animal species for easily locating and making comparisons within and between species. New database tools are continuely added to align the QTL and association data to other types of genome information, such as annotated genes, RH / SNP markers, and human genome maps. Besides the QTL data from species listed below, the QTLdb is open to house QTL/association date from other animal species where feasible. Note that the JAS along with other journals, now require that new QTL/association data be entered into a QTL database as part of their publication requirements.",
"homepage": "https://www.animalgenome.org/cgi-bin/QTLdb/index",
"name": "Animal QTLdb",
"prefix": "r3d100010744",
"synonyms": [
"Animal Quantitative Trait Loci"
],
"xrefs": {
"fairsharing": "FAIRsharing.HO0DyR",
"nif": "0000-02550",
"omics": "04527",
"scr": "001748"
}
},
"r3d100010745": {
"description": "Enlighten: research data is the institutional repository for research data of the University of Glasgow. As part of the CERIF 4 Datasets (C4D) project the University is exploring an extension of the CERIF standard. We have trialled methods of recording information about datasets to make them more visible, retrievable and usable.",
"homepage": "https://researchdata.gla.ac.uk/",
"name": "Enlighten",
"prefix": "r3d100010745",
"synonyms": [
"Research Data",
"Researchdata Glasgow"
]
},
"r3d100010746": {
"description": "The Plant Metabolic Network (PMN) provides a broad network of plant metabolic pathway databases that contain curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism in plants. The PMN currently houses one multi-species reference database called PlantCyc and 22 species/taxon-specific databases.",
"homepage": "https://plantcyc.org/",
"name": "PMN",
"prefix": "r3d100010746",
"synonyms": [
"Plant Metabolic Network"
],
"xrefs": {
"nlx": "15806",
"omics": "02764",
"scr": "003778"
}
},
"r3d100010747": {
"description": "Merritt is a curation repository for the preservation of and access to the digital research data of the ten campus University of California system and external project collaborators.\nMerritt is supported by the University of California Curation Center (UC3) at the California Digital Library (CDL).\nWhile Merritt itself is content agnostic, accepting digital content regardless of domain, format, or structure, it is being used for management of research data, and it forms the basis for a number of domain-specific repositories, such as the ONEShare repository for earth and environmental science and the DataShare repository for life sciences.\nMerritt provides persistent identifiers, storage replication, fixity audit, complete version history, REST API, a comprehensive metadata catalog for discovery, ATOM-based syndication, and curatorially-defined collections, access control rules, and data use agreements (DUAs).\nMerritt content upload and download may each be curatorially-designated as public or restricted.\nMerritt DOIs are provided by UC3's EZID service, which is integrated with DataCite.\nAll DOIs and associated metadata are automatically registered with DataCite and are harvested by Ex Libris PRIMO and Thomson Reuters Data Citation Index (DCI) for high-level discovery.\nMerritt is also a member node in the DataONE network; curatorially-designated data submitted to Merritt are automatically registered with DataONE for additional replication and federated discovery through the ONEMercury search/browse interface.",
"homepage": "https://merritt.cdlib.org/",
"name": "Merritt",
"prefix": "r3d100010747",
"synonyms": [
"UC3Merritt"
],
"xrefs": {
"fairsharing": "FAIRsharing.pkm8j3",
"nlx": "152126",
"scr": "000642"
}
},
"r3d100010748": {
"description": "Chemotion-repository is a repository for the publication, re-use and archiving of research data in the domain of chemistry. It is suitable for molecules, reactions, and associated data. It stores original data in diverse file-formats including standard file types and as well as descriptions, metadata, and ontologies. The repository is open to all researchers worldwide.",
"homepage": "https://www.chemotion-repository.net/welcome",
"name": "chemotion",
"prefix": "r3d100010748",
"synonyms": [
"Repository for molecules and research data"
],
"xrefs": {
"fairsharing": "FAIRsharing.iagXcR"
}
},
"r3d100010749": {
"description": "<<>>!!!>>>",
"homepage": "https://www.akka-technologies.com/en/innovation/projects/ingeoclouds",
"name": "InGeoCloudS",
"prefix": "r3d100010749",
"synonyms": [
"Inspired GEOdata CLOUD Services"
]
},
"r3d100010750": {
"description": "PUB represents the central publication data service of Bielefeld University. It serves Bielefeld academics to easily create and administer their personal publication lists and make them available on the web. The University Bielefeld encourages scientists to publish their research data on research data archives. The publications are intended to take account into personal and business related interests and carried out unter mandatory license conditions. The Bielefeld University supports faculties and scientific institutions to link their offerings with global data archives. The university-wide service \" PUB - Publications at Bielefeld University \" allows the primary publication of research data.",
"homepage": "https://pub.uni-bielefeld.de/record?cql=type%3Dresearch_data",
"name": "PUB Data Publications",
"prefix": "r3d100010750",
"synonyms": [
"PUB Datenpublikationen",
"Publications at Bielefeld University",
"Publikationen an der UniversitΓ€t Bielefeld"
],
"xrefs": {
"fairsharing": "FAIRsharing.x68mjp"
}
},
"r3d100010751": {
"description": "The Institutional repository collects, disseminates and preserves in digital form, the intellectual output that results from the academic and research activity of the Universitat Pompeu Fabra (UPF). Its Purpose is to Increase the impact of research done at the UPF and STIs intellectual memory.",
"homepage": "https://repositori.upf.edu/",
"name": "UPF Digital Repository",
"prefix": "r3d100010751",
"synonyms": [
"e-Repositori upf"
]
},
"r3d100010752": {
"description": "Research Data Finder is QUTβs discovery service for research data created or collected by QUT researchers. Designed to promote the visibility of QUT research datasets, Research Data Finder provides descriptions about shareable, reusable datasets available via open or mediated access.",
"homepage": "https://researchdatafinder.qut.edu.au/",
"name": "QUT Research Data Finder",
"prefix": "r3d100010752",
"synonyms": [
"Queensland University of Technology - Research Data Finder"
]
},
"r3d100010753": {
"description": "The Joint Evaluated Fission and Fusion File (JEFF) project is a collaboration between NEA Data Bank member countries. The JEFF library combines the efforts of the JEFF and EFF/EAF Working Groups to produce a common sets of evaluated nuclear data, mainly for fission and fusion applications. It contains a number of different data types, including neutron and proton interaction data, radioactive decay data, fission yields, and thermal scattering law data",
"homepage": "https://www.oecd-nea.org/dbdata/jeff/",
"name": "Joint Evaluated Fission and Fusion File",
"prefix": "r3d100010753",
"synonyms": [
"JEFF",
"JEFF Nuclear Data Library"
],
"xrefs": {
"fairsharing": "FAIRsharing.4ed3fb"
}
},
"r3d100010754": {
"description": "The TDB project aims to produce a database that:\ncontains data for all the elements of interest in radioactive waste disposal systems;\ndocuments why and how the data were selected;\ngives recommendations based on original experimental data, rather than compilations and estimates;\ndocuments the sources of experimental data used;\nis internally consistent; and\ntreats all solids and aqueous species of the elements of interest for nuclear waste storage performance assessment calculations.\nThe database compiles formation data (Gibbs energies, enthalpies, entropies and heat capacities) for each aqueous species and solid phase of interest, as well as chemical reactions and their corresponding thermodynamic data. Non thermodynamic data (diffusion or kinetics) and sorption data are not considered in the TDB project.",
"homepage": "https://www.oecd-nea.org/jcms/pl_22166/thermochemical-database-tdb-project",
"name": "Thermochemical Database",
"prefix": "r3d100010754",
"synonyms": [
"TDB Project"
]
},
"r3d100010755": {
"description": "The Data Bank operates a computer program service related to nuclear energy applications. The software library collects programs, compiles and verifies them in an appropriate computer environment, ensuring that the computer program package is complete and adequately documented.\nThis collection of material contains more than 2000 documented packages and group cross-section data sets. We distribute these codes on CD-ROM, DVD and via electronic transfer to about 900 nominated NEA Data Bank establishments (see the rules for requesters).\nStandard software verification procedures are used following an ANSI/ANS standard.",
"homepage": "https://www.oecd-nea.org/dbcps/",
"name": "NEA Data Bank Computer Program Services",
"prefix": "r3d100010755"
},
"r3d100010756": {
"description": "CEEHRC represents a multi-stage funding commitment by the Canadian Institutes of Health Research (CIHR) and multiple Canadian and international partners. The overall aim is to position Canada at the forefront of international efforts to translate new discoveries in the field of epigenetics into improved human health. The two sites will focus on sequencing human reference epigenomes and developing new technologies and protocols; they will also serve as platforms for other CEEHRC funding initiatives, such as catalyst and team grants.\n The complementary reference epigenome mapping efforts of the two sites will focus on a range of common human diseases. The Vancouver group will focus on the role of epigenetics in the development of cancer, including lymphoma and cancers of the ovary, colon, breast, and thyroid. The Montreal team will focus on autoimmune / inflammatory, cardio-metabolic, and neuropsychiatric diseases, using studies of identical twins as well as animal models of human disease.",
"homepage": "https://thisisepigenetics.ca/",
"name": "Canadian Epigenetics, Environment and Health Research Consortium Network",
"prefix": "r3d100010756",
"synonyms": [
"CEEHRC Network"
],
"xrefs": {
"scr": "017491"
}
},
"r3d100010757": {
"description": "Weed Images is a project of the University of Georgiaβs Center for Invasive Species and Ecosystem Health and one of the four major parts of BugwoodImages. The Focus is on damages of weed. It provides an easily accessible archive of high quality images for use in educational applications. In most cases, the images found in this system were taken by and loaned to us by photographers other than ourselves. Most are in the realm of public sector images. The photographs are in this system to be used.",
"homepage": "https://www.weedimages.org/",
"name": "Weed Images",
"prefix": "r3d100010757"
},
"r3d100010758": {
"description": "<<>>!!!>>> The ResearchCompendia platform is an attempt to use the web to enhance the reproducibility and verifiabilityβand thus the reliabilityβof scientific research. we provide the tools to publish the \"actual scholarship\" by hosting data, code, and methods in a form that is accessible, trackable, and persistent. Some of our short term goals include:\nTo expand and enhance the platform including adding executability for a greater variety of coding languages and frameworks, and enhancing output presentation.\nTo expand usership and to test the ResearchCompendia model in a number of additional fields, including computational mathematics, statistics, and biostatistics.\nTo pilot integration with existing scholarly platforms, enabling researchers to discover relevant Research Compendia websites when looking at online articles, code repositories, or data archives.",
"homepage": "https://researchcompendia.readthedocs.io/en/latest/index.html",
"name": "Research Compendia",
"prefix": "r3d100010758",
"synonyms": [
"Researchcompendia"
],
"xrefs": {
"nlx": "157262",
"scr": "003223"
}
},
"r3d100010759": {
"description": "The US Virtual Astronomical Observatory (VAO) is the VO effort based in the US, and it is one of many VO projects currently underway worldwide. The primary emphasis of the VAO is to provide new scientific research capabilities to the astronomy community. Thus an essential component of the VAO activity is obtaining input from US astronomers about the research tools that are most urgently needed in their work, and this information will guide the development efforts of the VAO.\n>>>!!!<<< Funding discontinued in 2014 and all software, documentation, and other digital assets developed under the VAO are stored in the VAO Project Repository https://sites.google.com/site/usvirtualobservatory/ . Code is archived on Github https://github.com/TomMcGlynn/usvirtualobservatory . >>>!!!<<<",
"homepage": "https://usvao.org/",
"name": "US Virtual Astronomical Observatory",
"prefix": "r3d100010759",
"synonyms": [
"VAO"
]
},
"r3d100010760": {
"description": "The Paleobiology Database (PaleoBioDB) is a non-governmental, non-profit public resource for paleontological data. It has been organized and operated by a multi-disciplinary, multi-institutional, international group of paleobiological researchers. Its purpose is to provide global, collection-based occurrence and taxonomic data for organisms of all geological ages, as well data services to allow easy access to data for independent development of analytical tools, visualization software, and applications of all types. The Databaseβs broader goal is to encourage and enable data-driven collaborative efforts that address large-scale paleobiological questions.",
"homepage": "https://paleobiodb.org/#/",
"name": "The Paleobiology Database",
"prefix": "r3d100010760",
"synonyms": [
"PBDB",
"PaleoBioDB",
"PaleoDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.r1k8kz",
"scr": "003798"
}
},
"r3d100010761": {
"description": "AmericasBarometer surveys are multi-country, regularly conducted surveys of democratic values and behaviors in the Americas. The raw data are available for free at all LAPOP consortium member institutions, and at all other users worldwide. Besides this a permanent ownership of the data, in becoming a 'repository', is possible for a fee.",
"homepage": "https://www.vanderbilt.edu/lapop/about-americasbarometer.php",
"name": "AmericasBarometer",
"prefix": "r3d100010761",
"synonyms": [
"BarΓ³metro de las AmΓ©ricas"
]
},
"r3d100010762": {
"description": "The United Nations Data (UND) site provides access to 32 databases and over 60million records. UN Statistical Databases include datasets on Energy Statistics, International Finances, The State of the Worldβs Children, and World Contraceptive Use; among many other global social, environmental and economic subjects.",
"homepage": "http://data.un.org/",
"name": "UNdata",
"prefix": "r3d100010762",
"synonyms": [
"United Nations Data",
"a world of information"
],
"xrefs": {
"biodbcore": "001678"
}
},
"r3d100010764": {
"description": "SCEC's mission includes gathering data on earthquakes, both in Southern California and other locales; integrate the information into a comprehensive understanding of earthquake phenomena; and communicate useful knowledge for reducing earthquake risk to society at large. The SCEC community consists of more than 600 scientists from 16 core institutions and 47 additional participating institutions. SCEC is funded by the National Science Foundation and the U.S. Geological Survey.",
"homepage": "https://www.scec.org/",
"name": "Southern California Earthquake Center",
"prefix": "r3d100010764",
"synonyms": [
"SCEC"
]
},
"r3d100010765": {
"description": "AMCSD is an interface to a crystal structure database that includes every structure published in the American Mineralogist, The Canadian Mineralogist, European Journal of Mineralogy and Physics and Chemistry of Minerals, as well as selected datasets from other journals. The database is maintained under the care of the Mineralogical Society of America and the Mineralogical Association of Canada, and financed by the National Science Foundation. You may search by a mineral of your choice, or choose a mineral from a complete list to help aid your research.",
"homepage": "http://rruff.geo.arizona.edu/AMS/amcsd.php",
"name": "American Mineralogist Crystal Structure Database",
"prefix": "r3d100010765",
"synonyms": [
"AMCSD"
],
"xrefs": {
"biodbcore": "001200",
"fairsharing": "FAIRsharing.6bfdfc"
}
},
"r3d100010766": {
"description": "The RRUFF Project is creating a complete set of high quality spectral data from well characterized minerals and is developing the technology to share this information with the world. The collected data provides a standard for mineralogists, geoscientists, gemologists and the general public for the identification of minerals both on earth and for planetary exploration.Electron microprobe analysis is used to determine the chemistry of each mineral.",
"homepage": "https://rruff.info/",
"name": "RRUFF Project",
"prefix": "r3d100010766",
"synonyms": [
"Database of Raman spectra, X-ray diffraction and chemistry data for minerals"
]
},
"r3d100010767": {
"description": "The Reciprocal Net is a distributed database used by research crystallographers to store information about molecular structures; much of the data is available to the general public. The Reciprocal Net project is still under development. Currently, there are 18 participating crystallography laboratories online. The project is funded by the National Science Foundation (NSF) and part of the National Science Digital Library. The contents of this collection will come principally from structures contributed by participating crystallography laboratories, thus providing a means for teachers, students, and the general public to connect better with current chemistry research. The Reciprocal Net's emphasis is on obtaining structures of general interest and usefulness to those several classes of digital library users.",
"homepage": "http://www.reciprocalnet.org/",
"name": "Reciprocal Net",
"prefix": "r3d100010767",
"xrefs": {
"nif": "0000-21353",
"scr": "008238"
}
},
"r3d100010768": {
"description": "<<>>!!!>>>",
"homepage": "http://factfinder2.census.gov/",
"name": "American FactFinder",
"prefix": "r3d100010768",
"xrefs": {
"nif": "0000-30094",
"scr": "002932"
}
},
"r3d100010769": {
"description": "OSGeo's mission is to support the collaborative development of open source geospatial software, in part by providing resources for projects and promoting freely available geodata. The Public Geodata Repository is a distributed repository and registry of data sources free to access, reuse, and re-distribute.",
"homepage": "https://www.osgeo.org/projects/geonetwork/",
"name": "Public Geodata Repository",
"prefix": "r3d100010769",
"synonyms": [
"OSGeo Public Geodata Repository"
]
},
"r3d100010770": {
"description": ">>>!!!<<< As stated 2017-05-16 The BIRN project was finished a few years ago. The web portal is no longer live.>>>!!!<<< BIRN is a national initiative to advance biomedical research through data sharing and online collaboration. It supports multi-site, and/or multi-institutional, teams by enabling researchers to share significant quantities of data across geographic distance and/or incompatible computing systems. BIRN offers a library of data-sharing software tools specific to biomedical research, best practice references, expert advice and other resources.",
"homepage": "https://neuroscienceblueprint.nih.gov/factSheet/birn.htm",
"name": "Biomedical Informatics Research Network",
"prefix": "r3d100010770",
"synonyms": [
"BIRN"
],
"xrefs": {
"nif": "0000-00027",
"scr": "005163"
}
},
"r3d100010772": {
"description": "Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and genes in 218 animal species (other than human and mouse and rats, which have their own resources) authored by Professor Frank Nicholas of the University of Sydney, Australia, with help from many people over the years. OMIA information is stored in a database that contains textual information and references, as well as links to relevant PubMed and Gene records at the NCBI, and to OMIM and Ensembl.",
"homepage": "https://www.omia.org/home/",
"name": "Online Mendelian Inheritance in Animals",
"prefix": "r3d100010772",
"synonyms": [
"OMIA"
],
"xrefs": {
"fairsharing": "FAIRsharing.tpey2t",
"nif": "0000-03215",
"scr": "006436"
}
},
"r3d100010773": {
"description": "The AOML Environmental Data Server (ENVIDS) provides interactive, on-line access to various oceanographic and atmospheric datasets residing at AOML. The in-house datasets include Atlantic Expendable Bathythermograph (XBT), Global Lagrangian Drifting Buoy, Hurricane Flight Level, and Atlantic Hurricane Tracks (North Atlantic Best Track and Synoptic). Other available datasets include Pacific Conductivitiy/Temperature/Depth Recorder (CTD) and World Ocean Atlas 1998.",
"homepage": "https://www.aoml.noaa.gov/",
"name": "Atlantic Oceanographic and Meteorological Laboratory",
"prefix": "r3d100010773",
"synonyms": [
"AOML"
]
},
"r3d100010774": {
"description": "<<>>!!!>>>. Although the web pages are no longer available, you will still be able to download the final UniGene builds as static content from the FTP site https://ftp.ncbi.nlm.nih.gov/repository/UniGene/. You will also be able to match UniGene cluster numbers to Gene records by searching Gene with UniGene cluster numbers. For best results, restrict to the βUniGene Cluster Numberβ field rather than all fields in Gene. For example, a search with Mm.2108[UniGene Cluster Number] finds the mouse transthyretin Gene record (Ttr). You can use the advanced search page https://www.ncbi.nlm.nih.gov/gene/advanced to help construct these searches. Keep in mind that the Gene record contains selected Reference Sequences and GenBank mRNA sequences rather than the larger set of expressed sequences in the UniGene cluster.",
"homepage": "https://www.ncbi.nlm.nih.gov/unigene",
"name": "UniGene",
"prefix": "r3d100010774",
"xrefs": {
"nlx": "41571",
"scr": "004405"
}
},
"r3d100010775": {
"description": "The Sequence Read Archive stores the raw sequencing data from such sequencing platforms as the Roche 454 GS System, the Illumina Genome Analyzer, the Applied Biosystems SOLiD System, the Helicos Heliscope, and the Complete Genomics. It archives the sequencing data associated with RNA-Seq, ChIP-Seq, Genomic and Transcriptomic assemblies, and 16S ribosomal RNA data.",
"homepage": "https://www.ncbi.nlm.nih.gov/sra",
"name": "Sequence Read Archive",
"prefix": "r3d100010775",
"synonyms": [
"SRA"
],
"xrefs": {
"fairsharing": "FAIRsharing.g7t2hv",
"nlx": "86174",
"omics": "01031",
"scr": "004891"
}
},
"r3d100010776": {
"description": "The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. Protein sequences are the fundamental determinants of biological structure and function.",
"homepage": "https://www.ncbi.nlm.nih.gov/protein",
"name": "NCBI Protein",
"prefix": "r3d100010776",
"xrefs": {
"nif": "0000-03178",
"scr": "003257"
}
},
"r3d100010777": {
"description": "NCBI PopSet collects DNA sequences to analyze the ways that populations are related by evolution. Such sequences indicate if populations originate from different members of the same species or from organisms of different species entirely.",
"homepage": "https://www.ncbi.nlm.nih.gov/popset",
"name": "NCBI PopSet",
"prefix": "r3d100010777",
"xrefs": {
"nlx": "99613",
"scr": "005049"
}
},
"r3d100010778": {
"description": "The NCBI Nucleotide database collects sequences from such sources as GenBank, RefSeq, TPA, and PDB. Sequences collected relate to genome, gene, and transcript sequence data, and provide a foundation for research related to the biomedical field.",
"homepage": "https://www.ncbi.nlm.nih.gov/nucleotide",
"name": "NCBI Nucleotide",
"prefix": "r3d100010778",
"xrefs": {
"nlx": "84100",
"scr": "004860"
}
},
"r3d100010779": {
"description": "The Structure database provides three-dimensional structures of macromolecules for a variety of research purposes and allows the user to retrieve structures for specific molecule types as well as structures for genes and proteins of interest. Three main databases comprise Structure-The Molecular Modeling Database; Conserved Domains and Protein Classification; and the BioSystems Database. Structure also links to the PubChem databases to connect biological activity data to the macromolecular structures. Users can locate structural templates for proteins and interactively view structures and sequence data to closely examine sequence-structure relationships.",
"homepage": "https://www.ncbi.nlm.nih.gov/structure",
"name": "NCBI Structure",
"prefix": "r3d100010779",
"xrefs": {
"nlx": "23947",
"scr": "004218"
}
},
"r3d100010780": {
"description": "<<>>!!!>>>",
"homepage": "http://www.ncbi.nlm.nih.gov/probe",
"name": "NCBI Probe",
"prefix": "r3d100010780",
"synonyms": [
"Probe"
],
"xrefs": {
"nlx": "80513",
"scr": "004816"
}
},
"r3d100010781": {
"description": "The HomoloGene database provides a system for the automated detection of homologs among annotated genes of genomes across multiple species. These homologs are fully documented and organized by homology group. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences.",
"homepage": "https://www.ncbi.nlm.nih.gov/homologene",
"name": "NCBI HomoloGene",
"prefix": "r3d100010781",
"xrefs": {
"nif": "0000-02975",
"omics": "01544",
"scr": "002924"
}
},
"r3d100010782": {
"description": ">>>!!! <<< The Epigenomics database was retired on June 1, 2016.\n\nAll epigenomics data are available in our GEO resource https://www.ncbi.nlm.nih.gov/geo >>> !!! <<< The Epigenomics database provides genomics maps of stable and reprogrammable nuclear changes that control gene expression and influence health. Users can browse current epigenomic experiments as well as search, compare and browse samples from multiple biological sources in gene-specific contexts. Many epigenomes contain modifications with histone marks, DNA methylation and chromatin structure activity. NCBI Epigenomics database contains datasets from the NIH Roadmap Epigenomics Project.",
"homepage": "http://www.ncbi.nlm.nih.gov/epigenomics",
"name": "NCBI Epigenomics",
"prefix": "r3d100010782",
"xrefs": {
"nlx": "151643"
}
},
"r3d100010783": {
"description": "<<>>!!!>>>",
"homepage": "http://www.ncbi.nlm.nih.gov/nucgss",
"name": "NCBI GSS",
"prefix": "r3d100010783",
"synonyms": [
"dbGSS"
],
"xrefs": {
"nif": "0000-20938",
"scr": "002146"
}
},
"r3d100010784": {
"description": "The Entrez Protein Clusters database contains annotation information, publications, structures and analysis tools for related protein sequences encoded by complete genomes. The data available in the Protein Clusters Database is generated from prokaryotic genomic studies and is intended to assist researchers studying micro-organism evolution as well as other biological sciences. Available genomes include plants and viruses as well as organelles and microbial genomes.",
"homepage": "https://www.ncbi.nlm.nih.gov/proteinclusters",
"name": "NCBI Protein Clusters",
"prefix": "r3d100010784",
"xrefs": {
"fairsharing": "FAIRsharing.da493y",
"nif": "0000-03354",
"scr": "003459"
}
},
"r3d100010785": {
"description": "<<>>!!!>>>\n\n\nThe Genome database contains annotations and analysis of eukaryotic and prokaryotic genomes, as well as tools that allow users to compare genomes and gene sequences from humans, microbes, plants, viruses and organelles. Users can browse by organism, and view genome maps and protein clusters.",
"homepage": "https://www.ncbi.nlm.nih.gov/genome",
"name": "NCBI Genome",
"prefix": "r3d100010785",
"xrefs": {
"nif": "0000-02802",
"scr": "002474"
}
},
"r3d100010786": {
"description": "The dbVar is a database of genomic structural variation containing data from multiple gene studies. Users can browse data containing the number of variant cells from each study, and filter studies by organism, study type, method and genomic variant. Organisms include human, mouse, cattle and several additional animals.\n***NCBI will phase out support for non-human organism data in dbSNP and dbVar beginning on September 1, 2017 ***",
"homepage": "https://www.ncbi.nlm.nih.gov/dbvar/",
"name": "NCBI dbVar",
"prefix": "r3d100010786",
"synonyms": [
"Database of genomic structural VARiation"
],
"xrefs": {
"nlx": "157217",
"scr": "003219"
}
},
"r3d100010788": {
"description": "The NCBI database of Genotypes and Phenotypes archives and distributes the results of studies that have investigated the interaction of genotype and phenotype, including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits. The database provides summaries of studies, the contents of measured variables, and original study document text. dbGaP provides two types of access for users, open and controlled. Through the controlled access, users may access individual-level data such as phenotypic data tables and genotypes.",
"homepage": "https://www.ncbi.nlm.nih.gov/gap/",
"name": "NCBI dbGaP",
"prefix": "r3d100010788",
"synonyms": [
"DataBase of Genotypes And Phenotypes",
"genotypes and phenotypes"
],
"xrefs": {
"fairsharing": "FAIRsharing.88v2k0",
"nif": "0000-23342",
"omics": "00263",
"scr": "002709"
}
},
"r3d100010789": {
"description": "BioModels is a repository of mathematical models of biological and biomedical systems. It hosts a vast selection of existing literature-based physiologically and pharmaceutically relevant mechanistic models in standard formats. Our mission is to provide the systems modelling community with reproducible, high-quality, freely-accessible models published in the scientific literature.",
"homepage": "https://www.ebi.ac.uk/biomodels/",
"name": "BioModels",
"prefix": "r3d100010789",
"xrefs": {
"fairsharing": "FAIRsharing.paz6mh",
"miriam": "00000007",
"nif": "0000-02609",
"omics": "02677",
"scr": "001993"
}
},
"r3d100010790": {
"description": "The National Center for Education Statistics (NCES) is responsible for collecting and analyzing data related to education, including assessing the performance of students from early childhood through secondary education as well as the literacy level of adults and post-secondary education surveys. Users can access data on public and private schools as well as public libraries and a college navigator tool containing information on over 7,000 post-secondary institutions.",
"homepage": "https://nces.ed.gov/",
"name": "National Center for Education Statistics",
"prefix": "r3d100010790",
"synonyms": [
"NCES"
]
},
"r3d100010791": {
"description": "The NCAR is a federally funded research and development center committed to research and education in atmospheric science and related scientific fields. NCAR seeks to support and enhance the scientific community nationally and globally by monitoring and researching the atmosphere and related physical and biological systems. Users can access climate and earth models created to better understand the atmosphere, the Earth and the Sun; as well as data from various NCAR research programs and projects. NCAR is sponsored by the National Science Foundation in addition to various other U.S. agencies.",
"homepage": "https://ncar.ucar.edu/",
"name": "National Center for Atmospheric Research",
"prefix": "r3d100010791",
"synonyms": [
"NCAR UCAR"
]
},
"r3d100010794": {
"description": "The Minnesota Population Center (MPC) is a University-wide interdisciplinary cooperative for demographic research. The MPC serves more than 80 faculty members and research scientists from eight colleges and institutes at the University of Minnesota. As a leading developer and disseminator of demographic data, we also serve a broader audience of some 50,000 demographic researchers worldwide.\nMPC is a DataONE member node: https://search.dataone.org/#profile/US_MPC",
"homepage": "https://pop.umn.edu/",
"name": "Minnesota Population Center",
"prefix": "r3d100010794",
"synonyms": [
"MPC"
]
},
"r3d100010795": {
"description": "The Maize Genetics and Genomics Database focuses on collecting data related to the crop plant and model organism Zea mays. The project's goals are to synthesize, display, and provide access to maize genomics and genetics data, prioritizing mutant and phenotype data and tools, structural and genetic map sets, and gene models. MaizeGDB also aims to make the Maize Newsletter available, and provide support services to the community of maize researchers.\nMaizeGDB is working with the Schnable lab, the Panzea project, The Genome Reference Consortium, and iPlant Collaborative to create a plan for archiving, dessiminating, visualizing, and analyzing diversity data.\nMMaizeGDB is short for Maize Genetics/Genomics Database. It is a USDA/ARS funded project to integrate the data found in MaizeDB and ZmDB into a single schema, develop an effective interface to access this data, and develop additional tools to make data analysis easier. Our goal in the long term is a true next-generation online maize database.aize genetics and genomics database.",
"homepage": "https://www.maizegdb.org/",
"name": "MaizeGDB",
"prefix": "r3d100010795",
"synonyms": [
"Maize Genetics and Genomics Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.aq280w",
"nif": "0000-03096",
"scr": "006600"
}
},
"r3d100010796": {
"description": "The Ligand-Gated Ion Channel database provides access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamate activated cationic channels superfamily. The development of the Ligand-Gated Ion Channel database was started in 1994, as part of Le Novère's work on the phylogeny of those receptors' subunits. It grew into a serious data resource, that served the community at large. However, it is not actively maintained anymore. In addition, bioinformatics technology evolved a lot over the last two decades, so that scientists can now generate quickly customised databases from trustworthy primary data resources. Therefore, we decided to officialy freeze the data resource. The resource will not disappear, and all the information and links will stay there. But people should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc.",
"homepage": "https://lenoverelab.org/lgicdb-lgicdb-php/",
"name": "Ligand-Gated Ion Channel Database",
"prefix": "r3d100010796",
"synonyms": [
"LGIC",
"LGICdb"
],
"xrefs": {
"fairsharing": "FAIRsharing.hjybww",
"nif": "0000-00037",
"scr": "002418"
}
},
"r3d100010797": {
"description": "Established by the HLA Informatics Group of the Anthony Nolan Research Institute, IPD provides a centralized system for studying the immune system's polymorphism in genes. The IPD maintains databases concerning the sequences of human Killer-cell Immunoglobulin-like Receptors (KIR), sequences of the major histocompatibility complex in a number of species, human platelet antigens (HPA), and tumor cell lines. Each subject has related, credible news, current research and publications, and a searchable database for highly specific, research grade genetic information.",
"homepage": "https://www.ebi.ac.uk/ipd/",
"name": "Immuno Polymorphism Database",
"prefix": "r3d100010797",
"synonyms": [
"IPD"
],
"xrefs": {
"fairsharing": "FAIRsharing.c3v6e6",
"nif": "0000-03038",
"omics": "03057",
"scr": "003004"
}
},
"r3d100010798": {
"description": "InterPro collects information about protein sequence analysis and classification, providing access to a database of predictive protein signatures used for the classification and automatic annotation of proteins and genomes. Sequences in InterPro are classified at superfamily, family, and subfamily. InterPro predicts the occurrence of functional domains, repeats, and important sites, and adds in-depth annotation such as GO terms to the protein signatures.",
"homepage": "https://www.ebi.ac.uk/interpro/",
"name": "InterPro",
"prefix": "r3d100010798",
"synonyms": [
"protein sequence analysis & classification"
],
"xrefs": {
"fairsharing": "FAIRsharing.pda11d",
"miriam": "00000011",
"nif": "0000-03035",
"omics": "01694",
"scr": "006695"
}
},
"r3d100010799": {
"description": "ICD serves as the international standard for diagnostic classification for all general epidemiological, many health management purposes and clinical use. The ICD's resources include the analysis of different population groups' general health situations, monitoring of the incidence and prevalence of diseases in relation to the characteristics of the individuals affected, reimbursement, resource allocation, quality, and guidelines. The records provide the basis for the compilation of national mortality and morbidity statistics, and enable the storage and retrieval of diagnostic information for clinical epidemiological and quality purposes.",
"homepage": "https://www.who.int/classifications/classification-of-diseases",
"name": "International Classification of Diseases",
"prefix": "r3d100010799",
"synonyms": [
"ICD"
],
"xrefs": {
"fairsharing": "FAIRsharing.97805c"
}
},
"r3d100010800": {
"description": "This site provides a central location for integrated near real-time or recent data relating to coral reefs, and also provides ecological forecasts (through artificial intelligence technology) as to the occurrence of specified environmental conditions, as prescribed by modelers, oceanographers and marine biologists.",
"homepage": "https://www.coral.noaa.gov/images/research/icon-2-pager-v7.pdf",
"name": "NOAA's Integrated Coral Observing Network",
"prefix": "r3d100010800",
"synonyms": [
"ICON"
]
},
"r3d100010801": {
"description": "The National Science Digital Library provides high quality online educational resources for teaching and learning, with current emphasis on the sciences, technology, engineering, and mathematics (STEM) disciplinesβboth formal and informal, institutional and individual, in local, state, national, and international educational settings. The NSDL collection contains structured descriptive information (metadata) about web-based educational resources held on other sites by their providers. These providers have contribute this metadata to NSDL for organized search and open access to educational resources via this website and its services.",
"homepage": "https://oercommons.org/hubs/NSDL",
"name": "National Science Digital Library",
"prefix": "r3d100010801",
"synonyms": [
"NSDL"
],
"xrefs": {
"fairsharing": "FAIRsharing.73afbf",
"nif": "0000-21294",
"scr": "008215"
}
},
"r3d100010803": {
"description": "IntEnz contains the recommendation of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalyzed reactions. Users can browse by enzyme classification or use advanced search options to search enzymes by class, subclass and sub-subclass information.",
"homepage": "https://www.ebi.ac.uk/intenz/",
"name": "Integrated Relational Enzyme database",
"prefix": "r3d100010803",
"synonyms": [
"IntEnz"
],
"xrefs": {
"fairsharing": "FAIRsharing.q1fdkc",
"nif": "0000-03028",
"omics": "02684",
"scr": "002992"
}
},
"r3d100010804": {
"description": "The IPD-IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (MHC) and includes the official sequences named by the WHO Nomenclature Committee For Factors of the HLA System. The IPD-IMGT/HLA Database is part of the international ImMunoGeneTics project (IMGT).\nThe database uses the 2010 naming convention for HLA alleles in all tools herein. To aid in the adoption of the new nomenclature, all search tools can be used with both the current and pre-2010 allele designations. The pre-2010 nomenclature designations are only used where older reports or outputs have been made available for download.",
"homepage": "https://www.ebi.ac.uk/ipd/imgt/hla/",
"name": "IMGT/HLA Database",
"prefix": "r3d100010804",
"synonyms": [
"IPD-IMGT/HLA",
"ImMunoGeneTics/HLA Database",
"International ImMunoGeneTics information system/Humane Leukozyten Antigene Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.e28v7g",
"nif": "0000-03014",
"scr": "002971"
}
},
"r3d100010805": {
"description": "The National Practitioner Data Bank (NPDB), or \"the Data Bank,\" is a confidential information clearinghouse created by Congress with the primary goals of improving health care quality, protecting the public, and reducing health care fraud and abuse in the U.S.",
"homepage": "https://www.npdb.hrsa.gov/",
"name": "The National Practitioner Data Bank",
"prefix": "r3d100010805",
"synonyms": [
"NPDB",
"The Data Bank"
]
},
"r3d100010806": {
"description": "<<>>!!!>>>",
"homepage": "http://www.dlese.org/lib/index.html",
"name": "Digital Library for Earth System Education",
"prefix": "r3d100010806",
"synonyms": [
"DLESE"
]
},
"r3d100010807": {
"description": "The DOE Data Explorer (DDE) is an information tool to help you locate DOE's collections of data and non-text information and, at the same time, retrieve individual datasets within some of those collections. It includes collection citations prepared by the Office of Scientific and Technical Information, as well as citations for individual datasets submitted from DOE Data Centers and other organizations.",
"homepage": "https://www.osti.gov/dataexplorer/",
"name": "DOE Data Explorer",
"prefix": "r3d100010807",
"synonyms": [
"DDE"
]
},
"r3d100010808": {
"description": "GOLD is currently the largest repository for genome project information world-wide. The accurate and efficient genome project tracking is a vital criterion for launching new genome sequencing projects, and for avoiding significant overlap between various sequencing efforts and centers.",
"homepage": "https://gold.jgi.doe.gov/index",
"name": "Genomes OnLine Database",
"prefix": "r3d100010808",
"synonyms": [
"GOLD"
],
"xrefs": {
"fairsharing": "FAIRsharing.5q1p14",
"nif": "0000-02918",
"omics": "06148",
"scr": "002817"
}
},
"r3d100010809": {
"description": "GRID-Geneva is a unique platform providing analyses and solutions for a wide range of environmental issues. GRID-Geneva serves primarily the needs of its three institutional partners - UNEP, the Swiss Federal Office for the Environment (FOEN) and the University of Geneva (UniGe) - which are linked by an ongoing, multi-year βPartnership Agreementβ, along with other local-to-global stakeholders. GRID-Geneva is also a bilingual English and French centre and the key francophone link within the global GRID network of centres. GRID-Geneva is a key centre of geo-spatial know-how, with strengths in GIS, IP/remote sensing and statistical analyses, integrated through modern spatial data infrastructures and web applications. Working at the interface between scientific information and policy/decision-making, GRID-Geneva also helps to develop capacities in these fields of expertise among target audiences, countries and other groups.",
"homepage": "https://unepgrid.ch/en/",
"name": "DEWA/GRID-Geneva",
"prefix": "r3d100010809",
"synonyms": [
"GRID-Geneva",
"Global Resource Information Database Geneva"
]
},
"r3d100010810": {
"description": "The OFA databases are core to the organizationβs objective of establishing control programs to lower the incidence of inherited disease. Responsible breeders have an inherent responsibility to breed healthy dogs. The OFA databases serve all breeds of dogs and cats, and provide breeders a means to respond to the challenge of improving the genetic health of their breed through better breeding practices. The testing methodology and the criteria for evaluating the test results for each database were independently established by veterinary scientists from their respective specialty areas, and the standards used are generally accepted throughout the world.",
"homepage": "https://ofa.org/advanced-search/",
"name": "OFA Records",
"prefix": "r3d100010810",
"synonyms": [
"OFA databases and DNA repository",
"Orthopedic Foundation for Animals"
]
},
"r3d100010811": {
"description": "<<>>!!!>>>\nCPANDA, the Cultural Policy & the Arts National Data Archive, was the world's first interactive digital archive of policy-relevant data on the arts and cultural policy in the United States. It was founded in 2001. It was a collaborative effort of Princeton University's Firestone Library and the Princeton Center for Arts and Cultural Policy Studies. The Pew Charitable Trusts underwrote the original development of the archive. The National Endowment for the Arts completed transferring all data content in January 2016. Check at ICPSR https://www.icpsr.umich.edu/web/ICPSR/search/studies?q=cpanda, the National Archive of Data on Arts and Culture (NADAC) https://www.icpsr.umich.edu/web/NADAC/search/studies?q=cpanda.\nThe old Cpanda URL http://www.cpanda.princeton.edu/ can be redirected to the zotero bibliography the data was moved to, https://www.zotero.org/bordelon/collections/3Q6Y9R6N. Confirm this is okay with Bobray Bordelon before implementing.",
"homepage": "http://www.cpanda.org/cpanda/",
"name": "Cultural Policy and the Arts National Data Archive",
"prefix": "r3d100010811",
"synonyms": [
"CPANDA"
]
},
"r3d100010812": {
"description": "The GHO data repository is WHO's gateway to health-related statistics for its 194 Member States. It provides access to over 1000 indicators on priority health topics including mortality and burden of diseases, the Millennium Development Goals (child nutrition, child health, maternal and reproductive health, immunization, HIV/AIDS, tuberculosis, malaria, neglected diseases, water and sanitation), non communicable diseases and risk factors, epidemic-prone diseases, health systems, environmental health, violence and injuries, equity among others. In addition, the GHO provides on-line access to WHO's annual summary of health-related data for its Member states: the World Health Statistics.",
"homepage": "https://apps.who.int/gho/data/?theme=main",
"name": "Global Health Observatory Data Repository",
"prefix": "r3d100010812",
"synonyms": [
"GHO Data Repository"
]
},
"r3d100010813": {
"description": "Wharton Research Data Services (WRDS) is a web-based business data research service from The Wharton School at the University of Pennsylvania. Developed in 1993 to support faculty research at Wharton, the service has evolved to become a common tool for research for over 290 institutions around the world. WRDS is the de facto standard for business data, providing researchers worldwide with instant access to financial, economic, and marketing data through a uniform, web-based interface. This hosted data service has become the locus for quantitative data research and is recognized by the academic and financial research community around the world as the leading business intelligence tool. WRDS provides access to COMPUSTAT, CRSP, IBES, NYSE-TAQ, Bureau van Dijk, Global Insight, OptionMetrics and other important business research databases.",
"homepage": "https://wrds-www.wharton.upenn.edu/",
"name": "Wharton Research Data Services",
"prefix": "r3d100010813",
"synonyms": [
"WRDS"
]
},
"r3d100010814": {
"description": "<<>>!!!>>>",
"homepage": "https://www.ebi.ac.uk/dgva/",
"name": "Database of Genomic Variants Archive",
"prefix": "r3d100010814",
"synonyms": [
"DGVa",
"DGVarchive"
],
"xrefs": {
"fairsharing": "FAIRsharing.txkh36",
"nlx": "86626",
"omics": "05335",
"scr": "004896"
}
},
"r3d100010815": {
"description": "M-CSA is a database of enzyme reaction mechanisms. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes. There are two kinds of entries in M-CSA. 'Detailed mechanism' entries are more complete and show the individual chemical steps of the mechanism as schemes with electron flow arrows. 'Catalytic Site' entries annotate the catalytic residues necessary for the reaction, but do not show the mechanism. The M-CSA (Mechanism and Catalytic Site Atlas) represents a unified resource that combines the data in both MACiE and the CSA",
"homepage": "https://www.ebi.ac.uk/thornton-srv/m-csa/search/",
"name": "Mechanism and Catalytic Site Atlas",
"prefix": "r3d100010815",
"synonyms": [
"CSA (formerly)",
"M-CSA",
"formerly: Catalytic Site Atlas"
],
"xrefs": {
"fairsharing": "FAIRsharing.BrubDI",
"nif": "0000-02699",
"omics": "23276",
"scr": "013099"
}
},
"r3d100010818": {
"description": "The majority of digital content in the ISPS Data Archive currently consists of social science research data from experiments, program files with the code for analyzing these data, requisite documentation to use and understand the data, and associated files. Access to the ISPS Data Archive is provided at no cost and is granted for scholarship and research purposes only.",
"homepage": "https://isps.yale.edu/research/data/",
"name": "ISPS Data Archive",
"prefix": "r3d100010818",
"synonyms": [
"Institution for Social and Policy Studies Data Archive",
"Yale ISPS"
],
"xrefs": {
"nlx": "156779",
"scr": "003127"
}
},
"r3d100010819": {
"description": "The General Social Survey (GSS) conducts basic scientific research on the structure and development of American society with a data-collection program designed to both monitor societal change within the United States and to compare the United States to other nations.",
"homepage": "https://gss.norc.org/",
"name": "General Social Survey",
"prefix": "r3d100010819",
"synonyms": [
"GSS"
]
},
"r3d100010820": {
"description": "The Population Research in Sexual Minority Health (PRISM) Data Archive is a collaborative project of the Center for Population Research in LGBT Health and the Inter-university Consortium for Political and Social Research (ICPSR). The PRISM data archive project is a primary initiative of the Center. PRISM makes high quality datasets useful for analysis of issues affecting sexual and gender minority populations in the United States available researchers, scholars, educators and practitioners.",
"homepage": "https://www.icpsr.umich.edu/icpsrweb/content/ICPSR/fenway.html",
"name": "The Population Research in Sexual Minority Health Data Archive",
"prefix": "r3d100010820",
"synonyms": [
"PRISM"
]
},
"r3d100010821": {
"description": "<<>>!!!>>>\nTeachingWithData.org is a portal where faculty can find resources and ideas to reduce the challenges of bringing real data into post-secondary classes. It allows faculty to introduce and build students' quantitative reasoning abilities with readily available, user-friendly, data-driven teaching materials.",
"homepage": "http://www.teachingwithdata.org/",
"name": "TeachingWithData.org",
"prefix": "r3d100010821",
"synonyms": [
"Pathway to Quantitative Literacy in the Social Sciences",
"TwD"
]
},
"r3d100010822": {
"description": "SDBS is an integrated spectral database system for organic compounds, which includes 6 different types of spectra under a directory of the compounds. The six spectra are as follows, an electron impact Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), a 1H nuclear magnetic resonance (NMR) spectrum, a 13C NMR spectrum, a laser Raman spectrum, and an electron spin resonance (ESR) spectrum.",
"homepage": "https://sdbs.db.aist.go.jp/sdbs/cgi-bin/cre_index.cgi",
"name": "Spectral Database for Organic Compounds",
"prefix": "r3d100010822",
"synonyms": [
"SDBS",
"ζζ©εεη©γγΉγγ―γγ«γγΌγΏγγΌγΉ"
],
"xrefs": {
"scr": "014671"
}
},
"r3d100010823": {
"description": "!!!This site has been decomissioned!!!!\nThe Geographic Information Support Team (GIST) Repository at the University of Georgia is a USAID-funded global archive of spatial data collected and distributed for the greater humanitarian community. If you want to search for data, you will need a valid email address to create an account.",
"homepage": "https://gistdata.itos.uga.edu/",
"name": "NEW GIST Data Repository",
"prefix": "r3d100010823",
"synonyms": [
"GIST"
]
},
"r3d100010824": {
"description": "<<>>!!!>>>",
"homepage": "https://www.icpsr.umich.edu/icpsrweb/NCAA/",
"name": "NCAA Student-Athlete Experiences Data Archive",
"prefix": "r3d100010824"
},
"r3d100010825": {
"description": "CPES provides access to information that relates to mental disorders among the general population. Its primary goal is to collect data about the prevalence of mental disorders and their treatments in adult populations in the United States. It also allows for research related to cultural and ethnic influences on mental health. CPES combines the data collected in three different nationally representative surveys (National Comorbidity Survey Replication, National Survey of American Life, National Latino and Asian American Study).",
"homepage": "https://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/20240",
"name": "Collaborative Psychiatric Epidemiology Surveys 2001 - 2003",
"prefix": "r3d100010825",
"synonyms": [
"CPES",
"ICPSR 20240"
]
},
"r3d100010826": {
"description": "The Berman Jewish Databank @ The Jewish Federations of North America is the central online address for quantitative studies of North American Jews and Jewish communities. Archives and makes available electronically questionnaires, reports and data files from the National Jewish Population Surveys (NJPS) of 1971, 1990 and 2000-01. It provides access to other national Jewish population reports, Jewish population statistics and approximately 200 local Jewish community studies from the major Jewish communities in North America.",
"homepage": "https://www.jewishdatabank.org/databank",
"name": "Berman Jewish Data Bank",
"prefix": "r3d100010826"
},
"r3d100010827": {
"description": "This database is a global archive and describes plant traits from throughout the globe. TRY is a network of vegetation scientists headed by DIVERSITAS, IGBP, iDiv, the Max Planck Institute for Biogeochemistry and an international Advisory Board. About half of the data are geo-referenced, providing a global coverage of more than 8000 measurement sites.",
"homepage": "https://www.try-db.org/TryWeb/Home.php",
"name": "TRY",
"prefix": "r3d100010827",
"synonyms": [
"Plant Trait Database"
]
},
"r3d100010828": {
"description": ">>>>>!!!<<<<< As of 01/12/2015, deposit of data on SLDR website will be suspended to allow the public opening of Ortolang platform https://www.ortolang.fr/#/market/home .>>>>>!!!<<<<<",
"homepage": "https://portal.issn.org/resource/ISSN/2429-6252",
"name": "Speech and Language Data Repository",
"prefix": "r3d100010828",
"synonyms": [
"Banco de datos de habla y lenguaje",
"Banque de donnΓ©es parole et langage",
"CRDO-Aix",
"Centre de ressources pour la description de l'oral",
"ORTOLANG Deposit and sharing",
"SLDR"
],
"xrefs": {
"issn": "2429-6252"
}
},
"r3d100010829": {
"description": "The India Water Portal is a web-based platform for sharing water management knowledge in India amongst practitioners and the general public. The included datasets can be browsed by data type, location, time, and other metadata. Data include rainfall, watersheds, groundwater, water quality, and irrigation.",
"homepage": "https://www.indiawaterportal.org/",
"name": "India Water Portal",
"prefix": "r3d100010829",
"synonyms": [
"IWP"
]
},
"r3d100010831": {
"description": "The CCHDO provides access to standard, well-described datasets from reference-quality repeat hydrography expeditions. It curates high quality full water column Conductivity-Temperature-Depth (CTD), hydrographic, carbon and tracer data from over 2,500 cruises from ~30 countries. It is the official data center for CTD and water sample profile data from the Global Ocean Ship-Based Hydrographic Investigations Program (GO-SHIP), as well as for WOCE, US Hydro, and other high quality repeat hydrography lines (e.g. SOCCOM, HOT, BATS, WOCE, CARINA.)",
"homepage": "https://cchdo.ucsd.edu/",
"name": "CCHDO",
"prefix": "r3d100010831",
"synonyms": [
"CLIVAR and Carbon Hydrographic Data Office"
],
"xrefs": {
"fairsharing": "FAIRsharing.b9775c",
"nlx": "154728",
"scr": "007093"
}
},
"r3d100010832": {
"description": "The Spatial Data Repository provides geographically-linked health and demographic data from the MEASURE Demographic and Health Surveys (DHS) project and the U.S. Census Bureau for mapping in a geographic information system (GIS).",
"homepage": "https://spatialdata.dhsprogram.com/home/",
"name": "Spatial Data Repository",
"prefix": "r3d100010832",
"synonyms": [
"The DHS Program",
"The Demographic and Health Surveys Program"
]
},
"r3d100010833": {
"description": "Morphbank :: Biological Imaging is a continuously growing database of images that scientists use for international collaboration, research and education. Images deposited in Morphbank :: Biological Imaging document a wide variety of research including: specimen-based research in comparative anatomy, morphological phylogenetics, taxonomy and related fields focused on increasing our knowledge about biodiversity.",
"homepage": "https://www.morphbank.net/",
"name": "Morphbank",
"prefix": "r3d100010833",
"synonyms": [
"Morphbank :: Biological Imaging"
],
"xrefs": {
"nlx": "156841",
"scr": "003147"
}
},
"r3d100010834": {
"description": "BioLINCC is the Biologic Specimen and Data Repository Coordinating Center. The center coordinates data and biospecimens from NHLBI-funded studies that are available for use in other approved studies. The center also creates teaching data sets from NHLBI-funded studies for use in training future biostatisticians.",
"homepage": "https://biolincc.nhlbi.nih.gov/home/",
"name": "Biologic Specimen and Data Repository Information Coordinating Center",
"prefix": "r3d100010834",
"synonyms": [
"BioLINCC"
],
"xrefs": {
"fairsharing": "FAIRsharing.a46gtf",
"nlx": "151758",
"scr": "013142"
}
},
"r3d100010835": {
"description": "The LRIS portal is the first element of scinfo.org.nz, a new repository of authoritative New Zealand science datasets and information. It is has been created in response to a growing expectation that government and publicly funded science data should be readily available in authoritative human and machine readable forms.",
"homepage": "https://lris.scinfo.org.nz/",
"name": "Land Resource Information Systems Portal",
"prefix": "r3d100010835",
"synonyms": [
"LRIS Portal"
]
},
"r3d100010836": {
"description": "The National Historical Geographic Information System (NHGIS) provides free online access to summary statistics and GIS boundary files for U.S. censuses and other nationwide surveys from 1790 through the present.",
"homepage": "https://www.nhgis.org/",
"name": "National Historical Geographic Information System",
"prefix": "r3d100010836",
"synonyms": [
"IPUMS NHGIS",
"NHGIS"
]
},
"r3d100010837": {
"description": "The Scholarly Database (SDB) at Indiana University aims to serve researchers and practitioners interested in the analysis, modeling, and visualization of large-scale scholarly datasets. The online interface provides access to six datasets: MEDLINE papers, registered Clinical Trials, U.S. Patent and Trademark Office patents (USPTO), National Science Foundation (NSF) funding, National Institutes of Health (NIH) funding, and National Endowment for the Humanities funding β over 26 million records in total.",
"homepage": "https://wiki.cns.iu.edu/display/SDBDOC/Scholarly-Database-at-Indiana-University_1246324.html",
"name": "Scholarly Database at Indiana University",
"prefix": "r3d100010837",
"synonyms": [
"SDB"
]
},
"r3d100010838": {
"description": "The Human Mortality Database (HMD) was created to provide detailed mortality and population data to researchers, students, journalists, policy analysts, and others interested in the history of human longevity. The Human Mortality Database (HMD) contains original calculations of death rates and life tables for national populations (countries or areas), as well as the input data used in constructing those tables. The input data consist of death counts from vital statistics, plus census counts, birth counts, and population estimates from various sources.",
"homepage": "https://www.mortality.org/",
"name": "Human Mortality Database",
"prefix": "r3d100010838",
"synonyms": [
"HMD"
],
"xrefs": {
"nif": "0000-21197",
"scr": "002370"
}
},
"r3d100010839": {
"description": "The Comparative Agendas Project (CAP) assembles and codes information on the policy processes of governments from around the world. CAP enables scholars, students, policy-makers and the media to investigate trends in policy-making across time and between countries. It classifies policy activities into a single, universal and consistent coding scheme.",
"homepage": "https://www.comparativeagendas.net/",
"name": "Comparative Agendas Project",
"prefix": "r3d100010839",
"synonyms": [
"CAP"
]
},
"r3d100010840": {
"description": "Nuclear Data Services contains atomic, molecular and nuclear data sets for the development and maintenance of nuclear technologies. It includes energy-dependent reaction probabilities (cross sections), the energy and angular distributions of reaction products for many combinations of target and projectile, and the atomic and nuclear properties of excited states, and their radioactive decay data. Their main concern is providing data required to design a modern nuclear reactor for electricity production. Approximately 11.5 million nuclear data points have been measured and compiled into computerized form.",
"homepage": "https://www-nds.iaea.org/",
"name": "Nuclear Data Services",
"prefix": "r3d100010840",
"synonyms": [
"NDS"
]
},
"r3d100010841": {
"description": "AidData contains information about international economic development assistance, dating back to 1947. AidData provides a searchable database of nearly one million past and present aid activities around the world, aid information management services and tools, data visualization technologies, and research designed to increase understanding of development finance. AidData is searchable by topic such as disaster prevention, energy supply, water supply or reconstruction relief. You may also search by specific regions including Africa, Europe, America, Asia, or Oceania.",
"homepage": "https://www.aiddata.org/",
"name": "AidData",
"prefix": "r3d100010841",
"synonyms": [
"Open Data for International Development"
],
"xrefs": {
"nlx": "157754",
"scr": "010480"
}
},
"r3d100010842": {
"description": "<<>>!!!>>>",
"homepage": "http://www.dna.affrc.go.jp/database/microbe.html",
"name": "Xanthobase",
"prefix": "r3d100010842",
"synonyms": [
"Xanthomonas oryzae pv. oryzae genome database"
]
},
"r3d100010843": {
"description": "Scripps Institute of Oceanography (SIO) Explorer includes five federated collections: SIO Cruises, SIO Historic Photographs, the Seamounts, Marine Geological Samples, and the Educatorβs Collection, all part of the US National Science Digital Library (NSDL). Each collection represents a unique resource of irreplaceable scientific research. The effort is collaboration among researchers at Scripps, computer scientists from the San Diego Supercomputer Center (SDSC), and archivists and librarians from the UCSD Libraries. In 2005 SIOExplorer was extended to the Woods Hole Oceanographic Institution with the Multi-Institution Scalable Digital Archiving project, funded through the joint NSF/Library of Congress digital archiving and preservation program, creating a harvesting methodology and a prototype collection of cruises, Alvin submersible dives and Jason ROV lowerings.",
"homepage": "https://siox.sdsc.edu/",
"name": "Scripps Institute of Oceanography Explorer",
"prefix": "r3d100010843",
"synonyms": [
"SIOExplorer",
"Scripps Explorer"
],
"xrefs": {
"fairsharing": "FAIRsharing.de9d18"
}
},
"r3d100010844": {
"description": "ABLES provides data on lead exposure of adults in the United States. The data comes from laboratory-reported elevated blood lead levels.",
"homepage": "https://www.cdc.gov/niosh/topics/lead/ables.html",
"name": "Adult Blood Lead Epidemiology and Surveillance Interactive Database",
"prefix": "r3d100010844",
"synonyms": [
"ABLES"
],
"xrefs": {
"nlx": "152003",
"scr": "006915"
}
},
"r3d100010845": {
"description": "The Census of Agriculture provides extensive data about U.S. agriculture at the country, state and county level. The census is conducted every 5 years, and it gathers uniform, detailed data about U.S. farms and ranches and their operators. Data from recent censuses are available in different formats, but historical censuses (back to 1840) are available in pdf format.",
"homepage": "https://www.nass.usda.gov/AgCensus/",
"name": "Census of Agriculture",
"prefix": "r3d100010845",
"synonyms": [
"United States Department of Agriculture Census of Agriculture"
]
},
"r3d100010846": {
"description": "SoyBase is a professionally curated repository for genetics, genomics and related data resources for soybean. It contains current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. SoyBase includes annotated \"Williams 82\" genomic sequence and associated data mining tools. The repository maintains controlled vocabularies for soybean growth, development, and traits that are linked to more general plant ontologies.",
"homepage": "https://soybase.org/",
"name": "SoyBase",
"prefix": "r3d100010846",
"synonyms": [
"SoyBase and the Soybean Breeder's Toolbox"
],
"xrefs": {
"fairsharing": "FAIRsharing.z4agsr",
"miriam": "00000291",
"nif": "0000-03483",
"omics": "02778",
"scr": "005096"
}
},
"r3d100010847": {
"description": "FAOSTAT provides time-series data about agriculture, nutrition, fisheries, forestry and food aid by country and region from 1961 to present. FAOSTAT is a multilingual database. Data can be searched, browsed, and downloaded.",
"homepage": "https://www.fao.org/faostat/en/#home",
"name": "FAOSTAT",
"prefix": "r3d100010847",
"xrefs": {
"fairsharing": "FAIRsharing.z0rqUk",
"nif": "0000-30554",
"scr": "006914"
}
},
"r3d100010848": {
"description": "The National Mine Map Repository (NMMR) collects, maintains, and provides U.S. coal and non-coal mine maps to individuals, public and private sectors. NMMR mine maps and data are searchable and indexed by state, county, company name, and mine name. Accessing NMMR mine maps and data requires contacting NMMR. NMMR has a diverse customer population and has provided data to efforts supporting industrial and commercial development, highway construction, and the preservation of public health, safety and welfare.",
"homepage": "https://www.osmre.gov/programs/national-mine-map-repository",
"name": "National Mine Map Repository",
"prefix": "r3d100010848",
"synonyms": [
"NMMR"
]
},
"r3d100010849": {
"description": "The NADP monitors precipitation chemistry from numerous sites around the United States. The NADP consists of 5 networks: National Trends Network, Mercury Deposition Network, Atmospheric Integrated Research Monitoring Network, Atmospheric Mercury Network, and Ammonia Monitoring Network. Data is provided by each network.",
"homepage": "https://nadp.slh.wisc.edu/",
"name": "National Atmospheric Deposition Program",
"prefix": "r3d100010849",
"synonyms": [
"NADP"
]
},
"r3d100010850": {
"description": "Phytozome is the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute. Families of related genes representing the modern descendants of ancestral genes are constructed at key phylogenetic nodes. These families allow easy access to clade-specific orthology/paralogy relationships as well as insights into clade-specific novelties and expansions.",
"homepage": "https://phytozome-next.jgi.doe.gov/",
"name": "Phytozome",
"prefix": "r3d100010850",
"synonyms": [
"The JGI Comparative Plant Genomics Portal"
],
"xrefs": {
"fairsharing": "FAIRsharing.83d06b",
"miriam": "00100556",
"nlx": "151490",
"omics": "03242",
"scr": "006507"
}
},
"r3d100010851": {
"description": "The American National Election Studies (ANES) conducts national surveys and pilot studies and provides large, multifaceted datasets.\nTime Series Studies are conducted during years of national elections, with pre-election and post-election surveys conducted in presidential election years and post-election surveys conducted during congressional election years. Pilot Studies are normally conducted in years when there is no national election and are designed to test new, or to refine existing, instrumentation and study designs. Other Major Data Collections includes panel studies and other special studies.",
"homepage": "https://electionstudies.org/",
"name": "American National Election Studies",
"prefix": "r3d100010851",
"synonyms": [
"ANES"
]
},
"r3d100010852": {
"description": "The Solar Dynamics Observatory (SDO) studies the solar atmosphere on small scales of space and time, in multiple wavelengths. This is a searchable database of all SDO data, including citizen scientist images, space weather and near real time data, and helioseismology data.",
"homepage": "https://sdo.gsfc.nasa.gov/",
"name": "Solar Dynamics Observatory",
"prefix": "r3d100010852",
"synonyms": [
"SDO Data"
]
},
"r3d100010853": {
"description": "The Pig Expression Data Explorer (PEDE) database system stores full-length cDNA libraries of swine data accesible via keyword and ID searches. Data is publically available, and may specifically interest genetic researchers interested in disease sucsceptibly, and major and minor porcine specific antigens.",
"homepage": "https://pede.dna.affrc.go.jp/",
"name": "Pig Expression Data Explorer",
"prefix": "r3d100010853",
"synonyms": [
"PEDE"
]
},
"r3d100010854": {
"description": "International Research Institute for Climate and Society (IRI) research focuses on climate, environmental monitoring, agriculture, health, water, and economic sectors in Africa, Asia and Pacific, and Latin America and Caribbean. The IRI data library is a freely accessible data repository and analysis tool. IRI allows users to view, manipulate, and download climate-related data sets through a standard web browser.",
"homepage": "https://iri.columbia.edu/resources/data-library/",
"name": "The International Research Institute for Climate and Society",
"prefix": "r3d100010854",
"synonyms": [
"IRI Data Library",
"IRI/LDEO Climate Data Library"
]
},
"r3d100010855": {
"description": "The Registry of Open Data on AWS provides a centralized repository of public data sets that can be seamlessly integrated into AWS cloud-based applications. AWS is hosting the public data sets at no charge to their users. Anyone can access these data sets from their Amazon Elastic Compute Cloud (Amazon EC2) instances and start computing on the data within minutes. Users can also leverage the entire AWS ecosystem and easily collaborate with other AWS users.",
"homepage": "https://registry.opendata.aws/",
"name": "Registry of Open Data on AWS",
"prefix": "r3d100010855",
"synonyms": [
"Registry of Open Data on Amazon Web Services"
],
"xrefs": {
"nlx": "152013",
"scr": "006318"
}
},
"r3d100010856": {
"description": "Gramene is a platform for comparative genomic analysis of agriculturally important grasses, including maize, rice, sorghum, wheat and barley. Relationships between cereals are queried and displayed using controlled vocabularies (Gene, Plant, Trait, Environment, and Gramene Taxonomy) and web-based displays, including the Genes and Quantitative Trait Loci (QTL) modules.",
"homepage": "https://www.gramene.org/",
"name": "Gramene",
"prefix": "r3d100010856",
"xrefs": {
"fairsharing": "fairsharing.zjdfxz",
"nif": "0000-02926",
"scr": "002829"
}
},
"r3d100010857": {
"description": "<<>>!!!>>>",
"homepage": "https://www.ionomicshub.org/home/PiiMS",
"name": "IonomicHub",
"prefix": "r3d100010857",
"synonyms": [
"Collaborative international network for ionomics",
"iHUB"
]
},
"r3d100010858": {
"description": "The JPL Tropical Cyclone Information System (TCIS) was developed to support hurricane research. There are three components to TCIS; a global archive of multi-satellite hurricane observations 1999-2010 (Tropical Cyclone Data Archive), North Atlantic Hurricane Watch and ASA Convective Processes Experiment (CPEX) aircraft campaign. Together, data and visualizations from the real time system and data archive can be used to study hurricane process, validate and improve models, and assist in developing new algorithms and data assimilation techniques.",
"homepage": "https://tropicalcyclone.jpl.nasa.gov/",
"name": "Tropical Cyclone Information System",
"prefix": "r3d100010858",
"synonyms": [
"JPL Tropical Cyclone Information System",
"TCIS"
]
},
"r3d100010859": {
"description": "The World Register of Marine Species (WoRMS) integrates approximately 100 marine datbases to provide an authoritative and comprehensive list of marine organisms. WoRMS has an editorial system where taxonomic groups are managed by experts responsible for the quality of the information. WorMS register of marine species emerged from the European Register of Marine Species (ERMS) and the Flanders Marine Institute (VLIZ). WoRMS is a contribution to Lifewatch, Catalogue of Life, Encyclopedia of Life,\nGlobal Biodiversity Information Facility and the Census of Marine Life.",
"homepage": "https://www.marinespecies.org/index.php",
"name": "World Register of Marine Species",
"prefix": "r3d100010859",
"synonyms": [
"ERMS",
"European Register of Marine Species",
"WoRMS"
],
"xrefs": {
"fairsharing": "fairsharing.7g1bzj",
"nlx": "156921",
"scr": "013312"
}
},
"r3d100010860": {
"description": "The Multi-angle Imaging SpectroRadiometer (MISR) measurements are designed to improve understanding of the Earthβs environment and climate. MISR provides radiometrically and geometrically calibrated images in four spectral bands at each of nine widely-spaced angles. Spatial sampling of 275 and 1100 meters is provided on a global basis. All MISR data products are available in HDF-EOS format, and select products are available in netCDF format.",
"homepage": "https://misr.jpl.nasa.gov/",
"name": "JPL Multi-angle Imaging SpectroRadiometer",
"prefix": "r3d100010860",
"synonyms": [
"MISR",
"Multi-angle Imaging SpectroRadiometer"
]
},
"r3d100010861": {
"description": "Reactome is a manually curated, peer-reviewed pathway database, annotated by expert biologists and cross-referenced to bioinformatics databases. Its aim is to share information in the visual representations of biological pathways in a computationally accessible format. Pathway annotations are authored by expert biologists, in collaboration with Reactome editorial staff and cross-referenced to many bioinformatics databases. These include NCBI Gene, Ensembl and UniProt databases, the UCSC and HapMap Genome Browsers, the KEGG Compound and ChEBI small molecule databases, PubMed, and Gene Ontology.",
"homepage": "https://reactome.org/",
"name": "Reactome",
"prefix": "r3d100010861",
"synonyms": [
"a curated pathway database"
],
"xrefs": {
"fairsharing": "FAIRsharing.tf6kj8",
"miriam": "00000018",
"nif": "0000-03390",
"omics": "02771",
"scr": "003485"
}
},
"r3d100010862": {
"description": "The Health and Retirement Study (HRS) is a longitudinal panel study that surveys a representative sample of more than 26,000 Americans over the age of 50 every two years. The study has collected information about income, work, assets, pension plans, health insurance, disability, physical health and functioning, cognitive functioning, genetic information and health care expenditures.",
"homepage": "https://hrsonline.isr.umich.edu/",
"name": "Health and Retirement Study",
"prefix": "r3d100010862",
"synonyms": [
"HRS"
],
"xrefs": {
"nlx": "151830",
"scr": "008930"
}
},
"r3d100010863": {
"description": "FLOSSmole is a collaborative collection of free, libre, and open source software (FLOSS) data. FLOSSmole contains nearly 1 TB of data covering the period 2004 until now, about more than 500,000 different open source projects.",
"homepage": "https://flossmole.org/",
"name": "FLOSSmole",
"prefix": "r3d100010863"
},
"r3d100010864": {
"description": "The Griffith University Research Data Repository makes the collections and datasets produced by Griffith researchers accessible and searchable.",
"homepage": "https://research-repository.griffith.edu.au/handle/10072/392601",
"name": "Griffith University Research Data Repository",
"prefix": "r3d100010864",
"synonyms": [
"GRO",
"Griffith Research Online"
]
},
"r3d100010865": {
"description": "The Clouds and the Earthβs Radiant Energy System (CERES) is a key component of the Earth Observing System (EOS) program. CERES instruments provide radiometric measurements of the Earthβs atmosphere from three broadband channels. CERES products include both solar-reflected and Earth-emitted radiation from the top of the atmosphere to the Earth's surface.",
"homepage": "https://ceres.larc.nasa.gov/",
"name": "Clouds and the Earth's Radiant Energy System",
"prefix": "r3d100010865",
"synonyms": [
"CERES Data Products",
"CERES Data and Information",
"NASA CERES"
]
},
"r3d100010866": {
"description": "Kenya Open Data offers visualizations tools, data downloads, and easy access for software developers. Kenya Open Data provides core government development, demographic, statistical and expenditure data available for researchers, policymakers, developers and the general public. Kenya is the first developing country to have an open government data portal, the first in sub-Saharan Africa and second on the continent after Morocco. The initiative has been widely acclaimed globally as one of the most significant steps Kenya has made to improve governance and implement the new Constitutionβs provisions on access to information.",
"homepage": "https://www.opendata.go.ke/",
"name": "Kenya Open Data",
"prefix": "r3d100010866"
},
"r3d100010867": {
"description": "<<>>!!!>>>\nTRMM is a research satellite designed to improve our understanding of the distribution and variability of precipitation within the tropics as part of the water cycle in the current climate system. By covering the tropical and sub-tropical regions of the Earth, TRMM provides much needed information on rainfall and its associated heat release that helps to power the global atmospheric circulation that shapes both weather and climate. In coordination with other satellites in NASA's Earth Observing System, TRMM provides important precipitation information using several space-borne instruments to increase our understanding of the interactions between water vapor, clouds, and precipitation, that are central to regulating Earth's climate.\nThe TRMM mission ended in 2015 and final TRMM multi-satellite precipitation analyses (TMPA, product 3B42/3B43) data processing will end December 31st, 2019. As a result, this TRMM webpage is in the process of being retired and some TRMM imagery may not be displaying correctly. Some of the content will be moved to the Precipitation Measurement Missions website https://gpm.nasa.gov/ and our team is exploring ways to provide some of the real-time products using GPM data. Please contact us if you have any additional questions.",
"homepage": "https://trmm.gsfc.nasa.gov/",
"name": "Tropical Rainfall Measuring Mission",
"prefix": "r3d100010867",
"synonyms": [
"TRMM"
]
},
"r3d100010868": {
"description": "Data.gov.au provides public access, download, and reuse to raw data from the Australian Government, state and territory governments. Data.gov.au encourages user feedback and suggestions. Site upgrades and new features will be made over time.",
"homepage": "https://data.gov.au/",
"name": "Data.gov.au",
"prefix": "r3d100010868"
},
"r3d100010869": {
"description": "The Canada Open Data Project provides Government of Canada data to the public as potential driver for economic innovation. Searchable and browsable raw data is available for download, and the public can recommend specific data be made available.",
"homepage": "https://open.canada.ca/en/open-data",
"name": "Open Government Canada - Open Data",
"prefix": "r3d100010869",
"synonyms": [
"Gouvernement Ouvert Canada - donnΓ©es ouvertes"
]
},
"r3d100010870": {
"description": "The Africa Health Research Institute (AHRI) has published its updated analytical datasets for 2016.\nThe datasets cover socio-economic, education and employment information for individuals and households in AHRIβs population research area in rural northern KwaZulu-Natal. The datasets also include details on the migration patterns of the individuals and households who migrated into and out of the surveillance area as well as data on probable causes of death for individuals who passed away. Data collection for the 2016 individual interviews β which involves a dried blood spot sample being taken β is still in progress, and therefore datasets on HIV status and General Health only go up to 2015 for now.\nOver the past 16 years researchers have developed an extensive longitudinal database of demographic, social, economic, clinical and laboratory information about people over the age of 15 living in the AHRI population research area. During this time researchers have followed more than 160 000 people, of which 92 000 are still in the programme.",
"homepage": "https://data.ahri.org/index.php/home",
"name": "AHRI Data Repository",
"prefix": "r3d100010870",
"synonyms": [
"Africa Health Research Institute Data Repository"
]
},
"r3d100010871": {
"description": "The IUCN Red List of Threatened Species provides taxonomic, conservation status and distribution data on plants and animals that are critically endangered, endangered and vulnerable. Data are available in Esri File Geodatabase format, Esri Shapefile format, and Excel format.",
"homepage": "https://www.iucnredlist.org/",
"name": "IUCN Red List of Threatened Species",
"prefix": "r3d100010871",
"xrefs": {
"nlx": "156898",
"scr": "012758"
}
},
"r3d100010872": {
"description": "UNAVCO promotes research by providing access to data that our community of geodetic scientists uses for quantifying the motions of rock, ice and water that are monitored by a variety of sensor types at or near the Earth's surface. After processing, these data enable millimeter-scale surface motion detection and monitoring at discrete points, and high-resolution strain imagery over areas of tens of square meters to hundreds of square kilometers. The data types include GPS/GNSS, imaging data such as from SAR and TLS, strain and seismic borehole data, and meteorological data. Most of these can be accessed via web services. In addition, GPS/GNSS datasets, TLS datasets, and InSAR products are assigned digital object identifiers.",
"homepage": "https://www.unavco.org/data/data.html",
"name": "GAGE",
"prefix": "r3d100010872",
"synonyms": [
"Geodetic Facility for the Advancement of Geoscience",
"NSF GAGE FACILITY",
"formerly: UNAVCO"
],
"xrefs": {
"nlx": "154719",
"scr": "006706"
}
},
"r3d100010873": {
"description": "As a department of the United States Department of Agriculture (USDA) the National Agricultural Statistics Service (NASS) continually surveys and reports on U.S. agriculture. NASS reports include production and supplies of food and fiber, prices paid and received by farmers, farm labor and wages, farm finances, chemical use, and changes in the demographics of U.S. producers. NASS provides objective and unbiased statistics of states and counties, while safeguarding the privacy of farmers and ranchers.",
"homepage": "https://www.nass.usda.gov/",
"name": "National Agricultural Statistics Service",
"prefix": "r3d100010873",
"synonyms": [
"NASS"
]
},
"r3d100010874": {
"description": "XNAT CENTRAL is a publicly accessible datasharing portal at Washinton University Medical School using XNAT software. XNAT provides neuroimaging data through a web interface and a customizable open source platform. XNAT facilitates data uploads and downloads for data sharing, processing and organization.\nNOTICE: Central XNAT will be decommissioned on October 15, 2023. New project creation is no longer permitted.",
"homepage": "https://central.xnat.org/",
"name": "XNAT CENTRAL",
"prefix": "r3d100010874",
"xrefs": {
"nif": "0000-04375",
"scr": "006235"
}
},
"r3d100010875": {
"description": "Swiss Institute of Bioinformatics (SIB) coordinates research and education in bioinformatics throughout Switzerland and provides bioinformatics services to the national and international research community. ExPASy gives access to numerous repositories and databases of SIB. For example: array map, MetaNetX, SWISS-MODEL and World-2DPAGE, and many others see a list here http://www.expasy.org/resources",
"homepage": "https://www.expasy.org/",
"name": "ExPASy Bioinformatics Resource Portal",
"prefix": "r3d100010875",
"synonyms": [
"Expert Protein Analysis System",
"SIB Bioinformatics Resource Portal"
],
"xrefs": {
"nif": "0000-30108",
"scr": "012880"
}
},
"r3d100010876": {
"description": "The U.S. Bureau of Labor Statistics collects, analyzes, and publishes reliable information on many aspects of the United States economy and society. They measure employment, compensation, worker safety, productivity, and price movements. This information is used by jobseekers, workers, business leaders, and others to assist them in making sound decisions at work and at home. Statistical data covers a wide range of topics about the labor market, economy and society in the U.S.; subject areas include: Inflation & Prices, Employment, Unemployment, Pay & Benefits, Spending & Time Use, Productivity, Workplace Injuries, International, and Regional Resources. Data is available in multiple formats including charts and tables as well as Bureau of Labor Statistics publications.",
"homepage": "https://www.bls.gov/data/",
"name": "U.S. Department of Labor, Bureau of Labor Statistics",
"prefix": "r3d100010876",
"synonyms": [
"United States Department of Labor, Bureau of Labor Statistics"
]
},
"r3d100010877": {
"description": "<<>>!!!>>> 2019-03-29: no more access to ROAR Isolate Database",
"homepage": "http://www.roarproject.org/ROAR/html/index.htm",
"name": "ROAR Isolate Database",
"prefix": "r3d100010877",
"synonyms": [
"Reservoirs of Antibiotic Resistance Network"
]
},
"r3d100010878": {
"description": "ComBase is a resource for quantitative and predictive food microbiology. ComBase includes a database of observed microbial responses to a variety of food-related environments and a collection of predictive models.",
"homepage": "https://www.combase.cc/index.php/en/",
"name": "ComBase",
"prefix": "r3d100010878",
"xrefs": {
"nif": "0000-21095",
"scr": "008181"
}
},
"r3d100010879": {
"description": "The Gateway to Global Aging Data is a platform for population survey data on aging around the world. This site offers a digital library of survey questions, a search engine for finding comparable questions across surveys, and identically defined variables for cross-country analysis. The Survey Meta Data Repository provides Health and Retirement Study metadata of family surveys. Survey Meta Data Repository primarily provides access to survey metadata so researchers can compare survey formats, types and identically defined variables. Additional resources include tools for cross-country analysis, general statistics by country and year, survey question library, and tools for comparing questions across the surveys. Datasets are in Stata format; users must register and request datasets.",
"homepage": "https://g2aging.org/home",
"name": "Gateway to Global Aging Data",
"prefix": "r3d100010879",
"synonyms": [
"RAND Survey Meta Data Repository"
]
},
"r3d100010880": {
"description": "VectorBase provides data on arthropod vectors of human pathogens. Sequence data, gene expression data, images, population data, and insecticide resistance data for arthropod vectors are available for download. VectorBase also offers genome browser, gene expression and microarray repository, and BLAST searches for all VectorBase genomes. VectorBase Genomes include Aedes aegypti, Anopheles gambiae, Culex quinquefasciatus, Ixodes scapularis, Pediculus humanus, Rhodnius prolixus. VectorBase is one the Bioinformatics Resource Centers (BRC) projects which is funded by National Institute of Allergy and Infectious Diseases (NAID).",
"homepage": "https://vectorbase.org/vectorbase/app",
"name": "VectorBase",
"prefix": "r3d100010880",
"synonyms": [
"Bioinformatics Resource for Invertebrate Vectors of Human Pathogens"
],
"xrefs": {
"fairsharing": "FAIRsharing.3etvdn",
"miriam": "00000232",
"nif": "0000-03624",
"omics": "03146"
}
},
"r3d100010881": {
"description": "<<>>!!!>>>\n The dbMHC database provides an open, publicly accessible platform for DNA and clinical data related to the human Major Histocompatibility Complex (MHC). The dbMHC provides access to human leukocyte antigen (HLA) sequences, HLA allele and haplotype frequencies, and clinical datasets.",
"homepage": "https://www.ncbi.nlm.nih.gov/gv/mhc/",
"name": "NCBI dbMHC",
"prefix": "r3d100010881",
"synonyms": [
"MHC",
"Major histocompatibility Complex database"
],
"xrefs": {
"nif": "0000-02729"
}
},
"r3d100010882": {
"description": "Cryo electron microscopy enables the determination of 3D structures of macromolecular complexes and cells from 2 to 100 Γ
resolution. EMDataResource is the unified global portal for one-stop deposition and retrieval of 3DEM density maps, atomic models and associated metadata, and is a joint effort among investigators of the Stanford/SLAC CryoEM Facility and the Research Collaboratory for Structural Bioinformatics (RCSB) at Rutgers, in collaboration with the EMDB team at the European Bioinformatics Institute. EMDataResource also serves as a resource for news, events, software tools, data standards, and validation methods for the 3DEM community.\nThe major goal of the EMDataResource project in the current funding period is to work with the 3DEM community to (1) establish data-validation methods that can be used in the process of structure determination, (2) define the key indicators of a well-determined structure that should accompany every deposition, and (3) implement appropriate validation procedures for maps and map-derived models into a 3DEM validation pipeline.",
"homepage": "https://www.emdataresource.org/",
"name": "EMDataResource",
"prefix": "r3d100010882",
"synonyms": [
"formerly: EMDataBank"
],
"xrefs": {
"fairsharing": "FAIRsharing.04fcf5",
"nif": "0000-30776",
"scr": "003207"
}
},
"r3d100010883": {
"description": "The Global Proteome Machine (GPM) is a protein identification database. This data repository allows users to post and compare results. GPM's data is provided by contributors like The Informatics Factory, University of Michigan, and Pacific Northwestern National Laboratories. The GPM searchable databases are: GPMDB, pSYT, SNAP, MRM, PEPTIDE and HOT.",
"homepage": "https://www.thegpm.org/index.html",
"name": "The Global Proteome Machine",
"prefix": "r3d100010883",
"synonyms": [
"GPM",
"Proteomics data analysis, reuse and validation for biological and biomedical research",
"gpmDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.fhcmwq",
"nif": "0000-10455",
"scr": "006617"
}
},
"r3d100010884": {
"description": "A premier source for United States cancer statistics, SEER gathers information related to incidence, prevalence, and survival from specific geographic areas that represent 28 percent of the population, as well as compiles related reports and reports on the national cancer mortality rates. Their aim is to provide information related to cancer statistics and decrease the burden of cancer in the national population. SEER has been collecting data from cancer cases since 1973.",
"homepage": "https://seer.cancer.gov/",
"name": "Surveillance Epidemiology and End Results",
"prefix": "r3d100010884",
"synonyms": [
"SEER"
],
"xrefs": {
"nif": "0000-21366",
"scr": "006902"
}
},
"r3d100010886": {
"description": "MEASURE DHS is advancing global understanding of health and population trends in developing countries through nationally-representative household surveys that provide data for a wide range of monitoring and impact evaluation indicators in the areas of population, health, HIV, and nutrition. The database collects, analyzes, and disseminates data from more than 300 surveys in over 90 countries. MEASURE DHS distributes, at no cost, survey data files for legitimate academic research.",
"homepage": "https://dhsprogram.com/",
"name": "Demographic and Health Surveys",
"prefix": "r3d100010886",
"synonyms": [
"MEASURE DHS",
"The DHS Program"
]
},
"r3d100010887": {
"description": "TalkBank provides transcripts, audio and video of communicative interactions for research in human and animal communication.",
"homepage": "https://www.talkbank.org/",
"name": "TalkBank",
"prefix": "r3d100010887",
"xrefs": {
"nif": "0000-00626",
"scr": "003242"
}
},
"r3d100010888": {
"description": "The Lunar Orbiter Photographic Atlas of the Moon by Bowker and Hughes (NASA SP-206) is considered the definitive reference manual to the global photographic coverage of the Moon. The images contained within the atlas are excellent for studying lunar morphology because they were obtained at low to moderate Sun angles. The digital Lunar Orbiter Atlas of the Moon is a reproduction of the 675 plates contained in Bowker and Hughes. The digital archive, however, offers many improvements upon its original hardbound predecessor. Multiple search capabilities were added to the database to expedite locating images and features of interest. For accuracy and usability, surface feature information has been updated and improved. Lastly, to aid in feature identification, a companion image containing feature annotation has been included. The symbols on the annotated overlays, however, should only be used as locators and not for precise measurements. More detailed information about the digital archive process can be read in abstracts presented at the 30th and 31st Lunar and Planetary Science Conferences.",
"homepage": "https://www.lpi.usra.edu/resources/lunar_orbiter/",
"name": "Digital Lunar Orbiter Photographic Atlas of the Moon",
"prefix": "r3d100010888",
"synonyms": [
"LPI"
]
},
"r3d100010889": {
"description": "The PeptideAtlas validates expressed proteins to provide eukaryotic genome data. Peptide Atlas provides data to advance biological discoveries in humans. The PeptideAtlas accepts proteomic data from high-throughput processes and encourages data submission.",
"homepage": "http://www.peptideatlas.org/",
"name": "PeptideAtlas",
"prefix": "r3d100010889",
"xrefs": {
"fairsharing": "FAIRsharing.dvyrsz",
"miriam": "00000053",
"nif": "0000-03266",
"omics": "02454",
"scr": "006783"
}
},
"r3d100010890": {
"description": "The Protein Circular Dichroism Data Bank (PCDDB) provides and accepts a circular dichroism spectra data. The PCDDB and it's parent organization, the Institute of Structural and Molecular Biology (ISMB), investigate molecular structure using techniques such as biomolecular nuclear magnetic resonance, X-ray crystallography and computational structure prediction, as methods for protein production and biological characterization.",
"homepage": "https://pcddb.cryst.bbk.ac.uk/",
"name": "Protein Circular Dichroism Data Bank",
"prefix": "r3d100010890",
"synonyms": [
"PCDDB",
"Protein Circular Dichroism Data Base"
],
"xrefs": {
"fairsharing": "FAIRsharing.65yfxp",
"scr": "017428"
}
},
"r3d100010891": {
"description": "Rhea is a freely available and comprehensive resource of expert-curated biochemical reactions. It has been designed to provide a non-redundant set of chemical transformations for applications such as the functional annotation of enzymes, pathway inference and metabolic network reconstruction. There are three types of reaction participants (reactants and products): Small molecules, Rhea polymers, Generic compounds.\nAll three types of reaction participants are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both mass and charge balance of the reactions. We have populated the database with the reactions found in the enzyme classification (i.e. in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalysed reactions, other biochemical reactions (including those that are often termed \"spontaneous\") also are included.",
"homepage": "https://www.rhea-db.org/",
"name": "Rhea",
"prefix": "r3d100010891",
"xrefs": {
"fairsharing": "FAIRsharing.pn1sr5",
"miriam": "00000082",
"nlx": "70986",
"omics": "06093"
}
},
"r3d100010892": {
"description": ">>>!!!<<< the url is no longer responsive <<>> South Australia has considerable potential for petroleum and geothermal energy. The Energy Resources Division provides geoscientific and engineering information and data to support industry exploration and development.",
"name": "DMITRE Petroleum",
"prefix": "r3d100010892"
},
"r3d100010894": {
"description": "The International Satellite Cloud Climatology Project (ISCCP) is a database of intended for researchers to share information about cloud radiative properties. The data sets focus on the effects of clouds on the climate, the radiation budget, and the long-term hydrologic cycle. Within the data sets the data entries are broken down into entries of specific characteristics based on temporal resolution, spatial resolution, or temporal coverage.",
"homepage": "https://asdc.larc.nasa.gov/project/ISCCP",
"name": "International Satellite Cloud Climatology Project",
"prefix": "r3d100010894",
"synonyms": [
"ISCCP"
]
},
"r3d100010895": {
"description": ">>>!!!<<< Data originally published in the JCB DataViewer has been moved BioStudies. Please note that while the majority of data were moved, some authors opted to remove their data completely. >>>!!!<<< Migrated data can be found at https://www.ebi.ac.uk/biostudies/JCB/studies. Screen data are available in the Image Data Resource repository. http://idr.openmicroscopy.org/webclient/?experimenter=-1 >>>!!!<<< The DataViewer was decommissioned in 2018 as the journal evolved to an all-encompassing archive policy towards original source data and as new data repositories that go beyond archiving data and allow investigators to make new connections between datasets, potentially driving discovery, emerged. JCB authors are encouraged to make available all datasets included in the manuscript from the date of online publication either in a publicly available database or as supplemental materials hosted on the journal website. We recommend that our authors store and share their data in appropriate publicly available databases based on data type and/or community standard. >>>!!!<<<",
"homepage": "https://rupress.org/jcb/pages/history",
"name": "Journal of Cell Biology - JCB DataViewer",
"prefix": "r3d100010895",
"xrefs": {
"nlx": "156057",
"scr": "002633"
}
},
"r3d100010896": {
"description": "The EVIA Digital Archive Project is a repository of ethnographic video recordings and an infrastructure of tools and systems supporting scholars in the ethnographic disciplines. The project focuses on the fields of ethnomusicology, folklore, anthropology, and dance ethnology.",
"homepage": "http://eviada.webhost.iu.edu/Scripts/mainCat.cfm?mc=7",
"name": "EVIA Digital Archive Project",
"prefix": "r3d100010896",
"synonyms": [
"EVIADA"
]
},
"r3d100010897": {
"description": "Agri-environmental Research Data collection is part of the University of Guelph Research Data Repositories (University of Guelph Dataverse). The purpose of this collection is to provide access to, and long-term stewardship of, agricultural and environmental data created at or in cooperation with the University of Guelph.",
"homepage": "https://borealisdata.ca/dataverse/ugardr",
"name": "Agri-environmental Research Data Dataverse",
"prefix": "r3d100010897",
"synonyms": [
"University of Guelph Dataverse"
],
"xrefs": {
"scr": "006317"
}
},
"r3d100010898": {
"description": "The CDHA assists researchers to create, document, and distribute public use microdata on health and aging for secondary analysis. Major research themes include: midlife development and aging; economics of population aging; inequalities in health and aging; international comparative studies of health and aging; and the investigation of linkages between social-demographic and biomedical research in population aging. The CDHA is one of fourteen demography centers on aging sponsored by the National Institute on Aging.",
"homepage": "https://cdha.wisc.edu/",
"name": "Center for Demography of Health and Aging",
"prefix": "r3d100010898",
"synonyms": [
"CDHA"
]
},
"r3d100010899": {
"description": "Measurements Of Pollution In The Troposphere (MOPITT) was launched into sun-synchronous polar orbit on December 18, 1999, aboard TERRA, a NASA satellite orbiting 705 km above the Earth. MOPITT monitors changes in pollution patterns and the effects on Earthβs troposphere. MOPITT uses near-infrared radiation at 2.3 Β΅m and thermal-infrared radiation at 4.7 Β΅m to calculate atmospheric profiles of CO.",
"homepage": "https://asdc.larc.nasa.gov/project/MOPITT",
"name": "Measurements Of Pollution In The Troposphere",
"prefix": "r3d100010899",
"synonyms": [
"MOPITT"
]
},
"r3d100010900": {
"description": "IRMA (Integrated Resource Management Applications) provides natural and cultural resources data from the National Park Service. Most entries are in the form of peer-reviewed publications, but some are raw data sets based on in-park research projects.",
"homepage": "https://irma.nps.gov/Portal",
"name": "IRMA Portal",
"prefix": "r3d100010900",
"synonyms": [
"Integrated Resource Management Applications Portal"
]
},
"r3d100010901": {
"description": "The HUGO Gene Nomenclature Committee (HGNC) assigned unique gene symbols and names to over 35,000 human loci, of which around 19,000 are protein coding. This curated online repository of HGNC-approved gene nomenclature and associated resources includes links to genomic, proteomic and phenotypic information, as well as dedicated gene family pages.",
"homepage": "https://www.genenames.org/",
"name": "HUGO Gene Nomenclature Committee",
"prefix": "r3d100010901",
"synonyms": [
"HGNC"
],
"xrefs": {
"fairsharing": "FAIRsharing.29we0s",
"nif": "0000-02955",
"omics": "06180",
"scr": "002827"
}
},
"r3d100010902": {
"description": "The Australian National Corpus collates and provides access to assorted examples of Australian English text, transcriptions, audio and audio-visual materials. Text analysis tools are embedded in the interface allowing analysis and downloads in *.CSV format.",
"homepage": "https://researchdata.edu.au/australian-national-corpus/2018",
"name": "Australian National Corpus",
"prefix": "r3d100010902",
"synonyms": [
"AusNC"
]
},
"r3d100010903": {
"description": "The IMLS conducts annual surveys of public and state libraries in the US that have response rates near 100%. Data is compiled for states, library systems, and individual library branches and includes statistics for circulation, visits, staff, expenditures, and more. Data is available in two formats: MS Access and flat file, plain text. Data for museums is now included.",
"homepage": "https://www.imls.gov/research-tools/data-collection",
"name": "Institute of Museum and Library Services Data Collection",
"prefix": "r3d100010903",
"synonyms": [
"IMLS"
]
},
"r3d100010904": {
"description": "The Informatics Research Data Repository is a Japanese data repository that collects data on disciplines within informatics. Such sub-categories are things like consumerism and information diffusion. The primary data within these data sets is from experiments run by IDR on how one group is linked to another.",
"homepage": "https://www.nii.ac.jp/dsc/idr/en/index.html",
"name": "Informatics Research Data Repository",
"prefix": "r3d100010904",
"synonyms": [
"IDR"
]
},
"r3d100010905": {
"description": "<<>>!!!>>>",
"homepage": "https://www.ncbi.nlm.nih.gov/Traces/trace.cgi",
"name": "NCBI Trace Archive",
"prefix": "r3d100010905",
"xrefs": {
"fairsharing": "FAIRsharing.abwvhp",
"omics": "05337",
"scr": "013788"
}
},
"r3d100010906": {
"description": "The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to Europe researchers.",
"homepage": "https://arabidopsis.info/",
"name": "NASC",
"prefix": "r3d100010906",
"synonyms": [
"Nottingham Arabidopsis Stock Centre",
"The European Arabidopsis Stock Centre"
],
"xrefs": {
"fairsharing": "FAIRsharing.2sqcxs",
"nlx": "56885",
"omics": "28815",
"scr": "004576"
}
},
"r3d100010907": {
"description": "The British Columbia Conservation Data Centre (CDC) collects and disseminates information on plants, animals and ecosystems at risk in British Columbia. The \" BC Species and Ecosystems Explorer\" is a source for authoritative conservation information on approximately 7400 plants and animals, and over 600 ecological communities (ecosystems)in British Columbia. Information includes conservation status, legal designation, and ecosection values for ecological communities.",
"homepage": "https://www2.gov.bc.ca/gov/content/environment/plants-animals-ecosystems/conservation-data-centre",
"name": "B.C. Conservation Data Centre",
"prefix": "r3d100010907",
"synonyms": [
"CDC"
]
},
"r3d100010908": {
"description": "The Atlantic Canada Conservation Data Centre (ACCDC) maintains comprehensive lists of plant and animal species. The Atlantic CDC has geo-located records of species occurrences and records of extremely rare to uncommon species in the Atlantic region, including New Brunswick, Nova Scotia, Prince Edward Island, Newfoundland, and Labrador. The Atlantic CDC also maintains biological and other types of data in a variety of linked databases.",
"homepage": "http://www.accdc.com/",
"name": "Atlantic Canada Conservation Data Centre",
"prefix": "r3d100010908",
"synonyms": [
"AC CDC",
"CDC CA",
"Centre de donnΓ©es sur la conservation du Canada atlantique"
],
"xrefs": {
"fairsharing": "FAIRsharing.7b9a7a",
"nlx": "152014",
"scr": "006061"
}
},
"r3d100010909": {
"description": "<<>>!!!>>> The CBIF provides primary data on biological species of interest to Canadians. CBIF supports a wide range of social and economic decisions including efforts to conserve our biodiversity in healthy ecosystems, use our biological resources in sustainable ways, and monitor and control pests and diseases. Tools provided by the CBIF include the Integrated Taxonomic Information System (ITIS), Species Access Network, Online Mapping, and the SpeciesBank, including Butterflies of Canada. The CBIF is a member of the Global Biodiversity Information Facility (GBIF).",
"homepage": "http://www.cbif.gc.ca/eng/home/?id=1370403266262",
"name": "Canadian Biodiversity Information Facility",
"prefix": "r3d100010909",
"synonyms": [
"CBIF",
"SCIB",
"Système canadien d'information sur la biodiversité"
],
"xrefs": {
"biodbcore": "001664"
}
},
"r3d100010910": {
"description": "PDBj (Protein Data Bank Japan) provides a centralized PDB archive of macromolecular structures, integrated tools for data retrieval, visualization, and functional characterization. PDBj is supported by JST-NBDC and Osaka University.",
"homepage": "https://pdbj.org/",
"name": "PDBj",
"prefix": "r3d100010910",
"synonyms": [
"Protein Data Bank Japan"
],
"xrefs": {
"fairsharing": "FAIRsharing.rs2815",
"nlx": "151484",
"scr": "008912"
}
},
"r3d100010912": {
"description": "Fishbase is a global species database and encyclopedia of over 30,000 species and subspecies of fishes that is searchable by common name, genus, species, geography, family, ecosystem, references literature, tools, etc. Links to other, related databases such as the Catalog of Fishes, GenBack, and LarvalBase. Associated with a partner journal, Acta Ichthyologica et Piscatoria. With mirror sites in English, German, French Spanish, Portuguese, French, Swedish, Chinese and Arabian language.",
"homepage": "https://www.fishbase.se/home.php",
"name": "Fishbase",
"prefix": "r3d100010912",
"xrefs": {
"nlx": "39009",
"scr": "004376"
}
},
"r3d100010913": {
"description": "<<>>!!!>>>\nStore.Synchrotron is a fully functional, cloud computing based solution to raw X-ray data archival and dissemination at the Australian Synchrotron, largest stand-alone piece of scientific infrastructure in the southern hemisphere. Store.Synchrotron represents the logical extension of a long-standing effort in the macromolecular crystallography community to ensure that satisfactory evidence is provided to support the interpretation of structural experiments.",
"homepage": "https://store.synchrotron.org.au/",
"name": "Store.Synchrotron Data Store",
"prefix": "r3d100010913",
"synonyms": [
"TARDIS",
"The Australian Repositories for Diffraction ImageS",
"myTARDIS Diffraction Image Repository"
]
},
"r3d100010914": {
"description": "Australian Ocean Data Network (AODN) provides data collected by the Australian marine community. AODN's data is searchable via map interface and metadata catalogue. AODN is Australia's exhaustive repository for marine and climate data. AODN has merged with IMOS eMarine Information Infrastructure (eMII) Facility in May 2016. IMOS is a multi-institutional collaboration with a focus on open data access. It is ideally placed to manage the AODN on behalf of the Australian marine and climate community.",
"homepage": "https://portal.aodn.org.au",
"name": "Australian Ocean Data Network Portal",
"prefix": "r3d100010914",
"synonyms": [
"AODN",
"Open access to ocean data"
],
"xrefs": {
"fairsharing": "FAIRsharing.j5eden",
"omics": "14335"
}
},
"r3d100010915": {
"description": "<<>>!!!>>>",
"homepage": "http://hds.essex.ac.uk/",
"name": "History Data Service",
"prefix": "r3d100010915",
"synonyms": [
"HDS"
]
},
"r3d100010916": {
"description": "The British Geological Survey (BGS), the worldβs oldest national geological survey, has over 400 datasets including environmental monitoring data, digital databases, physical collections (borehole core, rocks, minerals and fossils), records and archives.",
"homepage": "http://www.bgs.ac.uk/",
"name": "British Geological Survey",
"prefix": "r3d100010916"
},
"r3d100010917": {
"description": "Geoscience Australia provides geosciences data on Australia's onshore and offshore natural resources discovery, sustainable energy opportunities, and potential impacts on population, economy and environment.",
"homepage": "https://www.ga.gov.au/",
"name": "Geoscience Australia",
"prefix": "r3d100010917",
"xrefs": {
"fairsharing": "FAIRsharing.d29cd4"
}
},
"r3d100010918": {
"description": "The Atlas of Living Australia (ALA) combines and provides scientifically collected data from a wide range of sources such as museums, herbaria, community groups, government departments, individuals and universities. Data records consist of images, literature, molecular DNA data, identification keys, species interaction data, species profile data, nomenclature, source data, conservation indicators, and spatial data.",
"homepage": "https://www.ala.org.au/",
"name": "Atlas of Living Australia",
"prefix": "r3d100010918",
"synonyms": [
"ALA"
],
"xrefs": {
"fairsharing": "FAIRsharing.2f66da",
"nlx": "152016",
"scr": "006467"
}
},
"r3d100010919": {
"description": "TERN provides open data, research and management tools, data infrastructure and site-based research equipment.\nThe open access ecosystem data is provided by TERN Data Discovery Portal , see https://www.re3data.org/repository/r3d100012013",
"homepage": "https://www.tern.org.au/",
"name": "Terrestrial Ecosystem Research Network",
"prefix": "r3d100010919",
"synonyms": [
"TERN"
]
},
"r3d100010920": {
"description": "OzFlux provides micro-meteorological measurements from over 500 stations to provide data for atmospheric model testing specific to exchanges of carbon, water vapor and energy between terrestrial ecosystems and the atmosphere.",
"homepage": "https://data.ozflux.org.au/portal/home.jspx",
"name": "OzFlux",
"prefix": "r3d100010920",
"synonyms": [
"Australian and New Zealand Flux Research and Monitoring"
]
},
"r3d100010921": {
"description": "<<>>!!!>>>",
"homepage": "http://beetlebase.org/",
"name": "BeetleBase",
"prefix": "r3d100010921",
"xrefs": {
"fairsharing": "FAIRsharing.h5f091",
"nif": "0000-02599",
"omics": "03118"
}
},
"r3d100010922": {
"description": "MozAtlas provides gene expression data of adult male and female mosquitoes as tables, expressions, trees and models. MozAtlas also provides sequence orthology relationships with data provided by FlyBase, Vectorbase, Beetlebase, BeeBase, and WormBase.",
"homepage": "https://mozatlas.gen.cam.ac.uk/mozatlas/",
"name": "MozAtlas",
"prefix": "r3d100010922"
},
"r3d100010923": {
"description": "The Australian Breast Cancer Tissue Bank (ABCTB) provides data contributed by an Australian network of cancer clinicians, researchers, and patients. ABCTB privacy protection policy ensures patients' identities are not revealed and cancer researchers are the only individuals with open access to data.",
"homepage": "https://www.abctb.org.au/abctbNew2/default.aspx",
"name": "Australian Breast Cancer Tissue Bank",
"prefix": "r3d100010923",
"synonyms": [
"ABCTB",
"BCTB",
"Breast Cancer Tissue Bank"
],
"xrefs": {
"nlx": "54620",
"scr": "000926"
}
},
"r3d100010924": {
"description": "The OpenNeuro project (formerly known as the OpenfMRI project) was established in 2010 to provide a resource for researchers interested in making their neuroimaging data openly available to the research community. It is managed by Russ Poldrack and Chris Gorgolewski of the Center for Reproducible Neuroscience at Stanford University. The project has been developed with funding from the National Science Foundation, National Institute of Drug Abuse, and the Laura and John Arnold Foundation.",
"homepage": "https://openneuro.org/",
"name": "OpenNeuro",
"prefix": "r3d100010924",
"synonyms": [
"formerly: OpenfMRI"
],
"xrefs": {
"fairsharing": "FAIRsharing.s1r9bw",
"nlx": "144048",
"scr": "005031"
}
},
"r3d100010925": {
"description": "The Hymenoptera Genome Database is a genome informatics resource that supports the research of insects of the order Hymenoptera (e.g. bees, wasps, ants). HGD provides tools for data mining (HymenopteraMine), sequence searching (BLAST), genome browsing (JBrowse), genome annotation (Apollo) and data download.\nAvailable through the navigation bar on the HGD Home page are the archives Ant Genomes Portal, BeeBase, and NasoniaBase which will not be updated.",
"homepage": "https://hymenoptera.elsiklab.missouri.edu/",
"name": "Hymenoptera Genome Database",
"prefix": "r3d100010925",
"synonyms": [
"HGD"
],
"xrefs": {
"fairsharing": "FAIRsharing.250fc8",
"nlx": "152034",
"scr": "008966"
}
},
"r3d100010926": {
"description": "The Organelle Genome Megasequencing Program (OGMP) provides mitochondrial, chloroplast, and mitochondrial plasmid genome data. OGMP tools allow direct comparison of OGMP and NCBI validated records. Includes GOBASE, a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts.",
"homepage": "https://megasun.bch.umontreal.ca/ogmp/",
"name": "Organelle Genome Megasequencing Program",
"prefix": "r3d100010926",
"synonyms": [
"OGMP",
"Organelle Genomics"
],
"xrefs": {
"nif": "0000-20928",
"omics": "28737",
"scr": "002137"
}
},
"r3d100010927": {
"description": "The Barcode of Life Data Systems (BOLD) provides DNA barcode data. BOLD's online workbench supports data validation, annotation, and publication for specimen, distributional, and molecular data. The platform consists of four main modules: a data portal, a database of barcode clusters, an educational portal, and a data collection workbench.\nBOLD is the go-to site for DNA-based identification. As the central informatics platform for DNA barcoding, BOLD plays a crucial role in assimilating and organizing data gathered by the international barcode research community. Two iBOL (International Barcode of Life) Working Groups are supporting the ongoing development of BOLD.",
"homepage": "https://www.boldsystems.org/",
"name": "Barcode of Life Data Systems",
"prefix": "r3d100010927",
"synonyms": [
"BOLD Systems",
"The Barcode Library"
],
"xrefs": {
"fairsharing": "FAIRsharing.en9npn",
"nlx": "29236",
"omics": "17578",
"scr": "004278"
}
},
"r3d100010928": {
"description": "British Antarctic Survey (BAS) has, for over 60 years, undertaken the majority of Britain's scientific research on and around the Antarctic continent. Atmospheric, biosphere, cryosphere, geosphere, hydrosphere, and Sun-Earth interactions metadata and data are available. Geographic information and collections are highlighted as well. Information and mapping services include a Discovery Metadata System, Data Access System, the Antarctic Digital Database (ADD), Geophysics Data Portal (BAS-GDP), ICEMAR, a fossil database, and the Antarctic Plant Database.",
"homepage": "https://www.bas.ac.uk/data/our-data/",
"name": "British Antarctic Survey",
"prefix": "r3d100010928",
"synonyms": [
"BAS"
]
},
"r3d100010929": {
"description": "The Institute of Ocean Sciences (IOS)/Ocean Sciences Division (OSD) data archive contains the holdings of oceanographic data generated by the IOS and other agencies and laboratories, including the Institute of Oceanography at the University of British Columbia and the Pacific Biological Station. The contents include data from B.C. coastal waters and inlets, B.C. continental shelf waters, open ocean North Pacific waters, Beaufort Sea and the Arctic Archipelago.",
"homepage": "https://www.pac.dfo-mpo.gc.ca/science/oceans/data-donnees/index-eng.html",
"name": "Fisheries and Oceans Canada Pacific Region Data Archive",
"prefix": "r3d100010929",
"synonyms": [
"IOS/OSD data archive",
"Le catalogue de donnΓ©es de l'ISM/DSO",
"PΓͺches et OcΓ©ans Canada Region Pacifique Cataloge de donnΓ©es"
],
"xrefs": {
"fairsharing": "FAIRsharing.8b7a2f"
}
},
"r3d100010930": {
"description": "<<>>!!!<<<",
"homepage": "https://www.tbdb.org/",
"name": "TB Database",
"prefix": "r3d100010930",
"synonyms": [
"TBDB",
"TBDatabase",
"Tuberculosis Database"
],
"xrefs": {
"nif": "0000-03537",
"omics": "03220",
"scr": "006619"
}
},
"r3d100010931": {
"description": "The Swedish Human Protein Atlas project has been set up to allow for a systematic exploration of the human proteome using Antibody-Based Proteomics. This is accomplished by combining high-throughput generation of affinity-purified antibodies with protein profiling in a multitude of tissues and cells assembled in tissue microarrays. Confocal microscopy analysis using human cell lines is performed for more detailed protein localization. The program hosts the Human Protein Atlas portal with expression profiles of human proteins in tissues and cells. The main objective of the resource centre is to produce specific antibodies to human target proteins using a high-throughput production method involving the cloning and protein expression of Protein Epitope Signature Tags (PrESTs). After purification, the antibodies are used to study expression profiles in cells and tissues and for functional analysis of the corresponding proteins in a wide range of platforms.",
"homepage": "https://www.proteinatlas.org/",
"name": "The Human Protein Atlas",
"prefix": "r3d100010931",
"synonyms": [
"HPA"
],
"xrefs": {
"fairsharing": "FAIRsharing.j0t0pe",
"miriam": "00000336",
"nif": "0000-00204",
"scr": "006710"
}
},
"r3d100010932": {
"description": "The GENSAT project aims to map the expression of genes in the central nervous system of the mouse. It is a collection of pictorial gene expression maps of the brain and spinal cord of the mouse.",
"homepage": "http://www.gensat.org/index.html",
"name": "Gene Expression Nervous System Atlas",
"prefix": "r3d100010932",
"synonyms": [
"GENSAT"
],
"xrefs": {
"nif": "0000-00130",
"omics": "03318",
"scr": "002721"
}
},
"r3d100010933": {
"description": "The Australian Institute of Marine Science (AIMS) is a tropical marine research centre. The AIMS Data Repository preserves experimental and survey data, sensor data, research analyses and other types of data collected by projects conducted by the Australian Institute of Marine Science (AIMS). Contributors to the repository are primarily AIMS researchers from various science disciplines including ecology, biology, environmental sciences, microbiology, geosciences and oceanography, geochemistry, biodiversity conservation, evolutionary environmental studies, climate and oceanic change, fisheries, biochemistry and molecular biology, limnology and functions of inland waters, genetics and hereditary, observing network",
"homepage": "https://www.aims.gov.au/data",
"name": "AIMS Data Repository",
"prefix": "r3d100010933",
"synonyms": [
"formerly: AIMS Data Catalogue",
"formerly: AIMS Data Centre"
],
"xrefs": {
"nlx": "157748",
"scr": "010475"
}
},
"r3d100010934": {
"description": "State of the Salmon provides data on abundance, diversity, and ecosystem health of wild salmon populations specific to the Pacific Ocean, North Western North America, and Asia. Data downloads are available using two geographic frameworks: Salmon Ecoregions or Hydro 1K.",
"homepage": "http://www.stateofthesalmon.org/resources/",
"name": "State of the Salmon",
"prefix": "r3d100010934",
"synonyms": [
"Knowledge across borders",
"SoS",
"ΠΠ·ΡΡΠ΅Π½ΠΈΠ΅ ΡΡΠ°ΡΡΡΠ° Π»ΠΎΡΠΎΡΡ",
"γΉγγ€γγ»γͺγγ»γΆγ»γ΅γΌγ’γ³"
]
},
"r3d100010935": {
"description": "The TropFlux provides surface heat and momentum flux data of tropical oceans (30Β°N-30Β°S) between January 1979 and September 2011. The TropFlux data is produced under a collaboration between Laboratoire dβOcΓ©anographie: ExpΓ©rimentation et Approches NumΓ©riques (LOCEAN) from Institut Pierre Simon Laplace (IPSL, Paris, France) and National Institute of Oceanography/CSIR (NIO, Goa, India), and supported by Institut de Recherche pour le DΓ©veloppement (IRD, France). TropFlux relies on data provided by the ECMWF Re-Analysis interim (ERA-I) and ISCCP projects. Since 2014 located at Indian National Centre for Ocean Information Services.",
"homepage": "https://incois.gov.in/tropflux/index.jsp",
"name": "TropFlux",
"prefix": "r3d100010935",
"synonyms": [
"Air-sea fluxes for the global tropical oceans"
]
},
"r3d100010937": {
"description": "MedEffect Canadaβs Adverse Reaction Online Database contains information on suspected adverse reaction reports related to marketed health products that were submitted to Health Canada by consumers and health professionals, who submit reports voluntarily, as well as by Market Authorization Holders (manufacturers and distributors), who are required to submit reports according to the Next link will take you to another Web site Food and Drugs Regulations.",
"homepage": "https://www.canada.ca/en/health-canada/services/drugs-health-products/medeffect-canada.html",
"name": "MedEffect Canada - Adverse Reaction Database",
"prefix": "r3d100010937",
"synonyms": [
"Base de donnΓ©es en ligne des effets indΓ©sirables de Canada Vigilance",
"Canada Vigilance Adverse Reaction Online Database",
"MedEffet Canada - Base de donnΓ©es des effets indΓ©sirables"
],
"xrefs": {
"fairsharing": "FAIRsharing.ea591a"
}
},
"r3d100010938": {
"description": "Statistics Greenland collects, processes, and publicizes statistical material concerning social issues in Greenland. Information is published in English, Greenlandic, and Danish, although not all information has been translated.",
"homepage": "https://stat.gl/default.asp?Lang=en",
"name": "Statistics Greenland",
"prefix": "r3d100010938",
"synonyms": [
"Gronlands Statistik",
"Kalaallit Nunaanni Naatsorsueqqissaartarfik"
]
},
"r3d100010939": {
"description": "The resource section of the Foundation for Child Development is a collection of reports, research, papers, and other materials published primarily by FCD and its grantees. The resource section contains materials relating to FCDβs current programs: PreK-3rd Education, Young Scholars Program, and Child Well-Being Index (CWI). FCD archives from 1909 - 2000 are located at the Rockefeller Archive Center. To view a description of the collection visit FCD at the Rockefeller Archive Center 1904 -2001 https://dimes.rockarch.org/collections/SFRdoaE5i8W4kksvS8TzuB?category=&limit=40&query=fcd",
"homepage": "https://www.fcd-us.org/",
"name": "Foundation for Child Development Resources",
"prefix": "r3d100010939",
"synonyms": [
"including: Pre-Kindergarten through Third Grade Archive Data",
"including: PreK-3rd Data"
]
},
"r3d100010940": {
"description": "<<>>!!!>>> \nAll GeoBase products are available on the Open Government of Canada portal: https://open.canada.ca/data/en/dataset?q=geobase&organization=nrcan-rncan\nGeoBase initiative provides geospatial data of the entire Canadian landmass for government, business, and/or personal assessments of sustainable resource development, public safety, sanitation, and environmental protection. Data is available for download as ESRI Shapefile, FGDB, KML, and GML.",
"homepage": "http://www.geobase.ca/",
"name": "GeoBase",
"prefix": "r3d100010940",
"synonyms": [
"GΓ©oBase"
]
},
"r3d100010941": {
"description": "<<>>!!!<<< \nTPDRC is part of NACJD",
"homepage": "http://www.icpsr.umich.edu/icpsrweb/content/NACJD/guides/tpdrc.html",
"name": "National Archive of Criminal Justice Data, Terrorism and Preparedness Data Resource Center",
"prefix": "r3d100010941",
"synonyms": [
"NACJD, TPDRC"
]
},
"r3d100010942": {
"description": "Western Regional Climate Center (WRCC) provides historical and current climate data for the western United States. WRCC is one of six regional climate centers partnering with NOAA research institutes to promote climate research and data stewardship.",
"homepage": "https://wrcc.dri.edu/",
"name": "Western Regional Climate Center",
"prefix": "r3d100010942",
"synonyms": [
"WRCC"
],
"xrefs": {
"fairsharing": "FAIRsharing.aa1f93"
}
},
"r3d100010943": {
"description": "Protectedplanet.net combines crowd sourcing and authoritative sources to enrich and provide data for protected areas around the world. Data are provided in partnership with the World Database on Protected Areas (WDPA). The data include the location, designation type, status year, and size of the protected areas, as well as species information.",
"homepage": "https://www.protectedplanet.net/en",
"name": "Protected Planet",
"prefix": "r3d100010943",
"synonyms": [
"WDPA",
"World Database on Protected Areas"
]
},
"r3d100010944": {
"description": "The IRI/LDEO Climate Data Library is a collection of climate data sets with the focus of climate change monitoring and mitigation. Browse data by category and source, navigate and analyze datasets using maps, and the Ingrid Data Analysis Language. The IRI/LDEO also includes web tutorials.",
"homepage": "https://iridl.ldeo.columbia.edu/",
"name": "IRI/LDEO Climate Data Library",
"prefix": "r3d100010944"
},
"r3d100010945": {
"description": "<<>>!!!>>>\nThe National Coastal Data Development Center, a division of the National Oceanographic Data Center, is dedicated to building the long-term coastal data record to support environmental prediction, scientific analysis, and formulation of public policy.",
"homepage": "https://www.ncddc.noaa.gov/",
"name": "NOAA National Centers for Environmental Information - formerly: National Coastal Data Development Center",
"prefix": "r3d100010945",
"synonyms": [
"NCDDC",
"formerly: NOAA - NCDDC",
"formerly: National Oceanic Atmospheric Administration - National Coastal Data Development Center"
]
},
"r3d100010946": {
"description": "diversitydata.org is an online tool for exploring quality of life data across metropolitan areas for people of different racial/ethnic groups in the United States. It provides values and rankings for the largest U.S. metropolitan areas on different indicators in 8 areas of life (domains), including demographics, education, economic opportunity, housing, neighborhoods, and health. It also provides a simple mapping utility, showing the range of indicator values for metros across the U.S. \nData from 1999 indicators is archives in the companion Diversity Data Archive (https://diversitydata-archive.org/). For a wider selection of data on child wellbeing, visit our partner site, diversitydatakids.org (https://www.diversitydatakids.org/).\ndiversitydata.org has been named a Health Data All Star by the Health Data Consortium. The list was compiled in consultation with leading health researchers, government officials, entrepreneurs, advocates and others to identify the health data resources that matter most.",
"homepage": "http://diversitydata.org",
"name": "diversitydata.org",
"prefix": "r3d100010946"
},
"r3d100010947": {
"description": "PISCO researchers collect biological, chemical, and physical data about ocean ecosystems in the nearshore portions of the California Current Large Marine Ecosystem. Data are archived and used to create summaries and graphics, in order to ensure that the data can be used and understood by a diverse audience of managers, policy makers, scientists and the general public.",
"homepage": "https://www.piscoweb.org/",
"name": "Partnership for Interdisciplinary Studies of Coastal Oceans",
"prefix": "r3d100010947",
"synonyms": [
"PISCO"
]
},
"r3d100010949": {
"description": "The Numeric Data Services Dataverse provides access to the Cross National Time Series (Banks data), the ITERATE database, and selected survey data. The DataVerse of the Harvard's Numeric Data Services houses a curated collection of datasets to meet the research and instructional needs of the Harvard community, which are also openly accessible. Primarily social sciences.",
"homepage": "https://dataverse.harvard.edu/dataverse/nds",
"name": "Harvard Numeric Data Services Dataverse",
"prefix": "r3d100010949",
"synonyms": [
"Numeric Data Services Dataverse"
]
},
"r3d100010950": {
"description": "The Artstor Digital Library is a nonprofit resource that provides more than one million digital images in the arts, architecture, humanities, and sciences with an accessible suite of software tools for teaching and research. Its community-built collections comprise contributions from outstanding international museums, photographers, libraries, scholars, photo archives, and artists and artists' estates.",
"homepage": "https://www.artstor.org/",
"name": "Artstor",
"prefix": "r3d100010950"
},
"r3d100010951": {
"description": "The Purdue University Research Repository (PURR) provides a virtual research environment and data publication and archiving platform for its campuses. Also supports the publication and online execution of software tools with DataCite DOIs.",
"homepage": "https://purr.purdue.edu/",
"name": "Purdue University Research Repository",
"prefix": "r3d100010951",
"synonyms": [
"PURR"
],
"xrefs": {
"fairsharing": "FAIRsharing.785d2f"
}
},
"r3d100010953": {
"description": "The Polar Data Catalogue is an online database of metadata and data that describes, indexes and provides access to diverse data sets generated by polar researchers. These records cover a wide range of disciplines from natural sciences and policy, to health, social sciences, and more.",
"homepage": "https://www.polardata.ca/",
"name": "Polar Data Catalogue",
"prefix": "r3d100010953",
"synonyms": [
"PDC"
]
},
"r3d100010954": {
"description": "The Alaska Climate Research Center archives and provides digital climate records, climate statistics, and monthly weather summaries on Alaska and the polar regions. The Alaska Climate Research Center is part of the Geophysical Institute at the University of Alaska Fairbanks.",
"homepage": "https://akclimate.org/",
"name": "Alaska Climate Research Center",
"prefix": "r3d100010954",
"xrefs": {
"nlx": "157755",
"scr": "000913"
}
},
"r3d100010955": {
"description": "<<>>!!!>>>",
"homepage": "https://psl.noaa.gov/iasoa/",
"name": "International Arctic Systems for Observing the Atmosphere",
"prefix": "r3d100010955",
"synonyms": [
"IASOA Data Portal"
]
},
"r3d100010956": {
"description": "The Portal is intended to be used as catalog of datasets published by ministries/ department/ organizations of Government of India for public use, in order to enhance transparency in the functioning of the Government as well as to make innovative visualization of dataset. This National Data Portal is being updated frequently to make it as accessible as possible and completely accessible to all irrespective of physical challenges or technology.",
"homepage": "https://data.gov.in/",
"name": "Open Government Data Platform India",
"prefix": "r3d100010956",
"synonyms": [
"OGD",
"data.govin"
],
"xrefs": {
"fairsharing": "FAIRsharing.f778c3"
}
},
"r3d100010957": {
"description": "The Polar Data Center (PDC) manages the Science Database among other repositories for Japanese polar research. The Science Database is the destination repository for all Japanese Antarctic Research Expedition (JARE) data as well as the Japanese contribution to the International Polar Year (IPY) 2007-2008. Metadata are in English and Japanese, and metadata records are shared with the Global Change Master Directory.",
"homepage": "https://scidbase.nipr.ac.jp/?ml_lang=en",
"name": "National Institute of Polar Research Science Database",
"prefix": "r3d100010957",
"synonyms": [
"Polar Data Center Science Database"
]
},
"r3d100010958": {
"description": "The Yeast Resource Center Public Image Repository is a database of fluorescent microscopy images and their associated metadata/experimental parameters. The images depict the localization, co-localization and FRET (fluorescence energy transfer) of proteins in cells, particularly in the budding yeast Saccharomyces cerevisiae as a model organism. Users may download the entire datasets to improve their research.",
"homepage": "https://images.yeastrc.org/imagerepo/searchImageRepoInit.do",
"name": "Yeast Resource Center Public Image Repository",
"prefix": "r3d100010958",
"synonyms": [
"YRC Public Image Repository"
]
},
"r3d100010959": {
"description": "Social Computing Data Repository hosts data from a collection of many different social media sites, most of which have blogging capacity. Some of the prominent social media sites included in this repository are BlogCatalog, Twitter, MyBlogLog, Digg, StumbleUpon, del.icio.us, MySpace, LiveJournal, The Unofficial Apple Weblog (TUAW), Reddit, etc. The repository contains various facets of blog data including blog site metadata like, user defined tags, predefined categories, blog site description; blog post level metadata like, user defined tags, date and time of posting; blog posts; blog post mood (which is defined as the blogger's emotions when (s)he wrote the blog post); blogger name; blog post comments; and blogger social network.",
"homepage": "http://datasets.syr.edu/pages/home.html",
"name": "Social Computing Data Repository",
"prefix": "r3d100010959"
},
"r3d100010960": {
"description": "The UCI Machine Learning Repository is a collection of databases, domain theories, and data generators that are used by the machine learning community for the empirical analysis of machine learning algorithms. It is used by students, educators, and researchers all over the world as a primary source of machine learning data sets. As an indication of the impact of the archive, it has been cited over 1000 times.",
"homepage": "https://archive.ics.uci.edu/",
"name": "UC Irvine Machine Learning Repository",
"prefix": "r3d100010960",
"synonyms": [
"UCI Machine Learning Repository"
]
},
"r3d100010961": {
"description": "The National Park Service Gaseous Pollutant Monitoring Program Database provides gaseous air pollutant and meteorological data as *.csv files. Queries allow filtering by location of ozone, wind speed, wind direction, ambient temperature, relative humidity, solar radiation, wetness data.",
"homepage": "https://ard-request.air-resource.com/",
"name": "NPS Gaseous Pollutant and Meteorological Data Access Page",
"prefix": "r3d100010961",
"synonyms": [
"Access to Gaseous Pollutant and Meteorological Data"
]
},
"r3d100010962": {
"description": "Alaska Ocean Observing System (AOOS) provides ocean and coastal observations data. The AOOS is governed by the Integrated Ocean Observing System (IOOS) which is a partnership among federal, regional, academic and private sector groups.\nThe Ocean Data Explorer contains scientific and management information including real-time sensor feeds, operational oceanographic and atmospheric models, satellite observations and GIS data sets that describe the biological, chemical and physical characteristics of Alaska and its surrounding waters. This map offers many new updated features that build upon the existing data system.",
"homepage": "https://aoos.org/",
"name": "Alaska Ocean Observing System",
"prefix": "r3d100010962",
"synonyms": [
"AOOS"
],
"xrefs": {
"nlx": "157756",
"scr": "010481"
}
},
"r3d100010963": {
"description": "The National Science Foundation (NSF) Ultraviolet (UV) Monitoring Network provides data on ozone depletion and the associated effects on terrestrial and marine systems. Data are collected from 7 sites in Antarctica, Argentina, United States, and Greenland. The network is providing data to researchers studying the effects of ozone depletion on terrestrial and marine biological systems. Network data is also used for the validation of satellite observations and for the verification of models describing the transfer of radiation through the atmosphere.",
"homepage": "https://gml.noaa.gov/grad/antuv/#:~:text=NOAA%20Antarctic%20UV%20Monitoring%20Network&text=Antarctic%20Ultraviolet%20(UV)%20Monitoring%20Network,ozone%20depletion%20reported%20in%20Antarctica.",
"name": "NOAA Antarctic UV Monitoring Network",
"prefix": "r3d100010963",
"synonyms": [
"National Oceanic and Atmospheric Administration Antarctic UV Monitoring Network",
"formerly: NSF UV Monitoring Network",
"formerly: National Science Foundation Polar Programs UV Monitoring Network",
"formerly: UVSIMN"
]
},
"r3d100010964": {
"description": ">>>>!!!<<<>>>!!!<<<<\nACADIS is a repository for Arctic research data to provide data archival, preservation and access for all projects funded by NSF's Arctic Science Program (ARC). Data include long-term observational timeseries, local, regional, and system-scale research from many diverse domains. The Advanced Cooperative Arctic Data and Information Service (ACADIS) program includes data management services.",
"homepage": "https://arcticdata.io/",
"name": "Advanced Cooperative Arctic Data and Information Service",
"prefix": "r3d100010964",
"synonyms": [
"ACADIS Gateway",
"Advanced CADIS",
"an artic data repository"
],
"xrefs": {
"nlx": "157746",
"scr": "010473"
}
},
"r3d100010965": {
"description": ">>>>>> !!! <<<<<< This website ceased operation on Sept. 30, 2020, as the website is no longer funded >>>>> !!!!! <<<<",
"name": "Integrated Fertility Survey Series",
"prefix": "r3d100010965",
"synonyms": [
"IFSS"
]
},
"r3d100010966": {
"description": "Earth System Research Laboratory (ESRL) Global Monitoring Division (GMD) provides data relating to climate change forces and models, ozone depletion and rehabilitation, and baseline air quality. Data are freely available so the public, policy makers, and scientists stay current with long-term atmospheric trends.",
"homepage": "https://gml.noaa.gov/dv/data/",
"name": "Earth System Research Laboratory - Global Monitoring Laboratory",
"prefix": "r3d100010966",
"synonyms": [
"ESRL GML",
"formerly: ESRL GMD",
"formerly: Earth System Research Laboratory - Global Monitoring Division"
]
},
"r3d100010967": {
"description": "The Ocean Date and Information System provides information on physical, chemical, biological and geological parameters of ocean and coasts on spatial and temporal domains that is vital for both research and operational oceanography. In-situ and remote sensing data are included. The Ocean Information Bank is supported by the data received from Ocean Observing Systems in the Indian Ocean (both the in-situ platforms and satellites) as well as by a chain of Marine Data Centres. Ocean and coastal measurements are available. Data products are accessible through various portals on the site and are largely available by data type (in situ or remote sensing) and then by parameter.",
"homepage": "https://odis.incois.gov.in/portal/datainfo/datainfohome.jsp",
"name": "Indian National Centre for Ocean Information Services",
"prefix": "r3d100010967",
"synonyms": [
"ESSO - INCOIS",
"ESSO - Indian National Centre for Ocean Information Services",
"INCOIS",
"formerly: Ocean Date and Information System",
"formerly: ODIS",
"ΰ€ΰ€ΰ€Έΰ€ΰ€Έΰ€ -ΰ€ΰ€Ύΰ€°ΰ€€ΰ₯ΰ€― ΰ€°ΰ€Ύΰ€·ΰ₯ΰ€ΰ₯ΰ€°ΰ₯ΰ€― ΰ€ΰ€Ήΰ€Ύΰ€Έΰ€Ύΰ€ΰ€° ΰ€Έΰ₯ΰ€ΰ€¨ΰ€Ύ ΰ€Έΰ₯ΰ€΅ΰ€Ύ ΰ€ΰ₯ΰ€¨ΰ₯ΰ€¦ΰ₯ΰ€°"
],
"xrefs": {
"ror": "04xbqmj23"
}
},
"r3d100010968": {
"description": "NASA's Prognostics Center of Excellence hosts the Prognostics Data Repository to provide data used in the development of prognostic algorithms, and time series of nominal to failed states. Data are donated from universities, agencies, or companies on an ongoing process.",
"homepage": "https://www.nasa.gov/content/prognostics-center-of-excellence-data-set-repository",
"name": "Prognostics Center of Excellence Data Set Repository",
"prefix": "r3d100010968",
"synonyms": [
"NASA Prognostics Data Repository",
"PCoE Datasets"
]
},
"r3d100010969": {
"description": "Greenland Environmental Observatory (GEOSummit) provides long term year round data on core atmospheric measurements, spatial phenomena, ice sheets, and the Arctic Environment. These data are available to researchers through the National Science Foundation's Science Coordination Office (SCO) which coordinates all research at GEOSummit. Currently there is not a central platform for multi-collaborator data distribution. For specific information related to research it is recommended to contact investigators directly.",
"homepage": "https://www.geosummit.org/",
"name": "Greenland Environmental Observatory at Summit Station",
"prefix": "r3d100010969",
"synonyms": [
"GEO Summit",
"Summit Station"
]
},
"r3d100010970": {
"description": "<<>>!!!>>>\nIndian Genetic Disease Database (IGDD) is an initiative of CSIR Indian Institute of Chemical Biology. It is supported by Council of Scientific and Industrial Research (CSIR) and Department of Biotechnology (DBT) of India. \nThe Indian people represent one-sixth of the world population and consists of a ethnically, geographically, and genetically diverse population. In some communities the ratio of genetic disorder is relatively high due to consanguineous marriage practiced in the community. This database has been created to keep track of mutations in the causal genes for genetic diseases common in India and help the physicians, geneticists, and other professionals retrieve and use the information for the benefit of the public. The database includes scientific information about these genetic diseases and disabilities, but also statistical information about these diseases in today's society. Data is categorized by body part affected and then by title of the disease.",
"homepage": "http://www.igdd.iicb.res.in/home.htm",
"name": "Indian Genetic Disease Database",
"prefix": "r3d100010970",
"synonyms": [
"IGDD"
]
},
"r3d100010971": {
"description": "<<>>!!!>>>\nMarine Microbial Database of India is an initiative of CSIR National Institute of Oceanography (NIO). It is supported by Council of Scientific and Industrial Research (CSIR) and managed by Biodiversity Informatics Group (BIG), Bioinformatics Centre of the NIO. It contains records about 1,814 marine microbes. Each record provides information on microbeβs location, habitat, importance (of the organism), threats (to the organism). The database also provides a Taxonomic Hierarchy and Scientific Name Index.",
"homepage": "http://www.biosearch.in/microbes/",
"name": "Marine Microbial Database of India",
"prefix": "r3d100010971",
"synonyms": [
"bioSearch"
]
},
"r3d100010972": {
"description": "<<>>!!!>>>\n ACEpepDB is a database ran by the Central Food Technological Research Institute. It contains records of about 865 peptides. Each record provides information on the food source, preparation, purification and any other additional information. Each record includes the reference(s). The database provides a search and browsing option for a more personalized research experience.",
"homepage": "http://www.cftri.com/pepdb/",
"name": "ACEpepDB: Peptide Database",
"prefix": "r3d100010972",
"synonyms": [
"Peptide Database of Central Food Technological Research Institute"
],
"xrefs": {
"nlx": "157747",
"scr": "010474"
}
},
"r3d100010973": {
"description": "<<>>!!!>>> TBNet India is an initiative by the Department of Biotechnology, Govt of India with special focus on Indian contributions on research and various issues related to tuberculosis. Around 13 institutions across India are apart of this initiative. TB Net India focuses to gather clinical, epidemiological and molecular data and make it available to the biomedical community.",
"homepage": "http://tbnetindia.ibioinformatics.org/index_html",
"name": "TBNet India",
"prefix": "r3d100010973",
"synonyms": [
"A National Portal for Tuberculosis Initiative",
"Protocols Reference Database"
]
},
"r3d100010975": {
"description": "The Yeast Resource Center provides access to data about mass spectrometry, yeast two-hybrid arrays, deconvolution florescence microscopy, protein structure prediction and computational biology. These services are provided to further the goal of a complete understanding of the chemical interactions required for the maintenance and faithful reproduction of a living cell. The observation that the fundamental biological processes of yeast are conserved among all eukaryotes ensures that this knowledge will shape and advance our understanding of living systems.",
"homepage": "http://depts.washington.edu/yeastrc/",
"name": "Yeast Resource Center",
"prefix": "r3d100010975",
"synonyms": [
"Yeast Resource Center Public Data Repository"
],
"xrefs": {
"fairsharing": "FAIRsharing.karvzj",
"nif": "0000-03650",
"scr": "007942"
}
},
"r3d100010976": {
"description": "ForestPlots.net is a web-accessible secure repository for forest plot inventories in South America, Africa and Asia. The database includes plot geographical information; location, taxonomic information and diameter measurements of trees inside each plot; and participants in plot establishment and re-measurement, including principal investigators, field assistants, students.",
"homepage": "https://forestplots.net/",
"name": "ForestPlots.net",
"prefix": "r3d100010976",
"synonyms": [
"FP"
]
},
"r3d100010977": {
"description": "HIstome: The Histone Infobase is a database of human histones, their post-translational modifications and modifying enzymes. HIstome is a combined effort of researchers from two institutions, Advanced Center for Treatment, Research and Education in Cancer (ACTREC), Navi Mumbai and Center of Excellence in Epigenetics, Indian Institute of Science Education and Research (IISER), Pune.",
"homepage": "http://www3.iiserpune.ac.in/~coee/histome/",
"name": "HIstome",
"prefix": "r3d100010977",
"synonyms": [
"The Histone Infobase"
],
"xrefs": {
"fairsharing": "FAIRsharing.g56qnp",
"nlx": "151419",
"omics": "03500",
"scr": "006972"
}
},
"r3d100010978": {
"description": "Human Protein Reference Database (HPRD) has been established by a team of biologists, bioinformaticists and software engineers. This is a joint project between the PandeyLab at Johns Hopkins University, and Institute of Bioinformatics, Bangalore. HPRD is a definitive repository of human proteins. This database should serve as a ready reckoner for researchers in their quest for drug discovery, identification of disease markers and promote biomedical research in general.\nHuman Proteinpedia (www.humanproteinpedia.org) is its associated data portal.",
"homepage": "http://www.hprd.org",
"name": "Human Protein Reference Database",
"prefix": "r3d100010978",
"synonyms": [
"HPRD"
],
"xrefs": {
"fairsharing": "FAIRsharing.y2qws7",
"nif": "0000-00137",
"omics": "02439",
"scr": "007027"
}
},
"r3d100010979": {
"description": "The India Biodiversity Portal is an educational tool to help educate the citizens of India on India's biodiversity. The IBP has multiple overlapping databases of images and scientific information about the variety of animals, plants, and environments found in India. These images and information can also be accessed via the IBP's maps and checklists features that encourage pursuit of ecological education for all ages.",
"homepage": "https://indiabiodiversity.org/",
"name": "India Biodiversity Portal",
"prefix": "r3d100010979",
"synonyms": [
"IBP"
]
},
"r3d100010980": {
"description": "CTRI is a free, online public record system for registration of clinical trials being conducted in India since 2007. Initiated as a voluntary measure, since 2009 trial registration in the CTRI has been made mandatory by the Drugs Controller General of India (DCGI). While this register is meant primarily for trials conducted in India, the CTRI will also accept registration of trials conducted in other countries in the region, which do not have a Primary Registry of its own. Registered trials on CTRI are freely searchable from the WHO's search portal and the ICTRP, as well as from the CTRI site.",
"homepage": "https://ctri.nic.in/Clinicaltrials/login.php",
"name": "Clinical Trials Registry - India",
"prefix": "r3d100010980",
"synonyms": [
"CTRI"
],
"xrefs": {
"nlx": "151507",
"scr": "000679"
}
},
"r3d100010981": {
"description": "The DMC is designed to provide registered users with access to non-confidential petroleum exploration and production data from offshore Nova Scotia, subject to certain conditions. The DMC is housed in the CNSOPB's Geoscience Research Centre located in Dartmouth, Nova Scotia. Initially, the DMC will manage and distribute the following digital petroleum data: well data (i.e. logs and reports), seismic image files (e.g. TIFF, PDF), and production data. In the future the DMC could be expanded to include operational, safety, environmental, fisheries data, etc.",
"homepage": "https://cnsopbdigitaldata.ca/geoviewer/dmc",
"name": "Canada-Nova Scotia Offshore Petroleum Board Data Management Centre",
"prefix": "r3d100010981",
"synonyms": [
"CNSOPB DMC"
]
},
"r3d100010982": {
"description": "The Mutopia Project offers sheet music editions of classical music for free download. These are based on editions in the public domain, and include works by Bach, Beethoven, Chopin, Handel, Mozart, and many others. A team of volunteers are involved in typesetting the music by computer using the LilyPond software. \nA growing number of modern editions, arrangements and new music are also available for download. The respective editors, arrangers and composers have chosen to make these works freely available.",
"homepage": "https://www.mutopiaproject.org/",
"name": "Mutopia Project",
"prefix": "r3d100010982",
"synonyms": [
"Free sheet music for everyone"
]
},
"r3d100010983": {
"description": "Export Import Data Bank - Tradestat is an initiative of Department of Commerce, Ministry of Commerce & Industry, Government of India. This databank provides international trade figures for imports, exports and total trade, based on data published by the Directorate General of Commercial Intelligence and Statistics (DGCI&S), Kolkata. It also provides commodity-wise, country-wise, and region-wise trade figures for exports and imports.",
"homepage": "https://tradestat.commerce.gov.in/eidb/default.asp",
"name": "Export Import Data Bank",
"prefix": "r3d100010983",
"synonyms": [
"Tradestat"
]
},
"r3d100010985": {
"description": "Human Proteinpedia is a community portal for sharing and integration of human protein data. This is a joint project between Pandey at Johns Hopkins University, and Institute of Bioinformatics, Bangalore. This portal allows research laboratories around the world to contribute and maintain protein annotations. Human Protein Reference Database (HPRD) integrates data, that is deposited in Human Proteinpedia along with the existing literature curated information in the context of an individual protein. All the public data contributed to Human Proteinpedia can be queried, viewed and downloaded.\nData pertaining to post-translational modifications, protein interactions, tissue expression, expression in cell lines, subcellular localization and enzyme substrate relationships may be deposited.",
"homepage": "http://www.humanproteinpedia.org",
"name": "Human Proteinpedia",
"prefix": "r3d100010985",
"xrefs": {
"fairsharing": "FAIRsharing.xxdxtv",
"nif": "0000-02999"
}
},
"r3d100010986": {
"description": "A small genotype data repository containing data used in recent papers from the Estonian Biocentre. Most of the data pertains to human population genetics. PDF files of the papers are also freely available.",
"homepage": "https://evolbio.ut.ee/",
"name": "Estonian Biocentre Free Data",
"prefix": "r3d100010986"
},
"r3d100010987": {
"description": "<<>>!!!>>>",
"homepage": "http://www.summitcamp.org/",
"name": "Summit Station",
"prefix": "r3d100010987"
},
"r3d100010988": {
"description": "Indian Space Science Programme has the primary goal of promoting and establishing space science and technology programme. The ISSDC is the primary data center to be retrieved from Indian space science missions. This center is responsible for the collections of payload data and related ancillary data for space science missions such as Chandrayaan, Astrosat, Youthsat, etc. The payload data sets can include a range of information including satellite images, X-ray spectrometer readings, and other space observations.",
"homepage": "https://www.issdc.gov.in/",
"name": "Indian Space Science Data Center",
"prefix": "r3d100010988",
"synonyms": [
"ISDA",
"ISRO Science Data Archive",
"ISSDC"
]
},
"r3d100010989": {
"description": "<<>>!!!>>>",
"homepage": "http://rodadas.anp.gov.br/en/concession-of-exploratory-blocks/brazil-round-3/bdep-round-3",
"name": "Exploration and Production Data Bank",
"prefix": "r3d100010989",
"synonyms": [
"BDEP",
"Banco de Dados de Exploracao e Producao"
]
},
"r3d100010990": {
"description": "HCUPnet is a free, on-line query system based on data from the healthcare cost and utilization project (HCUP). It provides access to health statistics and information on hospital inpatient and emergency departments. HCUP is used to identify, track, analyze, and compare hospital statistics at the national, regional, and state levels.",
"homepage": "https://hcup-us.ahrq.gov/",
"name": "HCUPnet",
"prefix": "r3d100010990",
"synonyms": [
"Healthcare Cost and Utilization Project"
]
},
"r3d100010991": {
"description": "A databank on the economy, agriculture, tourism, infrastructure, industry, and natural resources of the North Eastern Region of India; comprises seven states namely Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland, Sikkim, Tripura (popularly known as Seven Sisters of India). The region (holds 7.9% of the total land space of the country) is of strategic importance for the country on account of the fact that nearly 90% of its borders form India's international boundaries. Thus information about population distribution, migration of peoples, vast natural resources, literacy rate, infrastructure development, cultural diversity, economy, etc. of this region are quite different from rest of the country.NER databank intends to provide information on multifarious activities of North Eastern states of India, thereby make it accessible to social commons. The North East Databank is a web portal created to provide a regional resource database for the North Eastern Region (NER).",
"homepage": "https://databank.nedfi.com/",
"name": "NER Databank",
"prefix": "r3d100010991",
"synonyms": [
"NEDFi Databank",
"North East Databank"
]
},
"r3d100010992": {
"description": "DBIE is a data warehouse of the Department of Statistics and Information Management (DSIM), under the Reserve Bank of India. It disseminates data on various aspects of the Indian Economy through several of its publications, by means of itβs three parts β namely has mainly three parts Home, Statistics and Time-series Publications. Again, Home is divided into two parts viz. Important Economic Indicators & Economy at a Glance through dashboards. The entire statistics have been presented in seven subject areas - Real Sector, Corporate Sector, Financial Sector, Financial Market, External Sector, Public Finance, Socio-Economic Indicators. Sectors have different sub-sectors and reports under the sub-sectors have been organized on periodicity wise. Downloading of data can be possible into Excel, CSV, PDF formats. User can use the data for their research work with courtesy to the Database on Indian Economy, Reserve Bank of India.",
"homepage": "https://cimsdbie.rbi.org.in/DBIE/#/dbie/home?site=home",
"name": "Database on Indian Economy",
"prefix": "r3d100010992",
"synonyms": [
"DBIE",
"RBI's Data Warehouse",
"ΰ€ΰ€Ύΰ€°ΰ€€ΰ₯ΰ€― ΰ€
ΰ€°ΰ₯ΰ€₯ΰ€΅ΰ₯ΰ€―ΰ€΅ΰ€Έΰ₯ΰ€₯ΰ€Ύ ΰ€ͺΰ€° ΰ€‘ΰ₯ΰ€ΰ€Ύΰ€¬ΰ₯ΰ€Έ"
]
},
"r3d100010994": {
"description": "<<>>!!!>>> \nJapan Space Systems (J-spacesystems) aims to contribute to the advancement of Japanese industry, space systems technology, conservation of the earth environment, utilization of the space environment, and other research and development efforts. The system provides access to data from unmanned space missions and remote sensing instruments.",
"homepage": "https://www.jspacesystems.or.jp/en/",
"name": "Japan Space Systems",
"prefix": "r3d100010994"
},
"r3d100010995": {
"description": "The Web-enabled Landsat data (WELD) project combines geophysical and biophysical Landstat data for the purposes of long-term preservation and monitoring of national, regional, and local data. WELD products are already \"terrain-corrected and radiometrically calibrated\" so as to be more easily accessible to researchers.",
"homepage": "https://www.usgs.gov/landsat-missions/data",
"name": "Landsat Missions",
"prefix": "r3d100010995",
"synonyms": [
"formerly: Web-enabled Landsat data"
]
},
"r3d100010996": {
"description": "CLASS is a data repository for environmental data collected by NOAA. Products include data from polar orbiting satellites, meteorological satellites, sea surface temperature (SST) data, sea surface height data, and more.",
"homepage": "https://www.avl.class.noaa.gov/saa/products/welcome",
"name": "Comprehensive Large Array-data Stewardship System",
"prefix": "r3d100010996",
"synonyms": [
"CLASS"
]
},
"r3d100010997": {
"description": "<<>>!!!>>>",
"homepage": "https://ncbiinsights.ncbi.nlm.nih.gov/?s=clone+db",
"name": "NCBI Clone DB",
"prefix": "r3d100010997",
"synonyms": [
"NCBI clone registry"
]
},
"r3d100011000": {
"description": "<<>>!!!>>>\nThe transfer of records from the Environment Climate Data Sweden (ECDS) database to the Swedish National Dataservice (SND) https://www.re3data.org/repository/r3d100010146 was completed in 2019. SND is a national research infrastructure with a primary function to support the accessibility, preservation, and re-use of research data and related materials.\nYou can search the SND research data portal specifically for Natural Science or Agricultural and Veterinary Sciences datasets.\nData descriptions with associated datasets, or a direct reference/URL to data, have been migrated from the ECDS portal to the SND research data portal. Previous links to these data are now automatically directed to an SND catalogue entry. Records in the ECDS catalogue that only contained metadata (ie information that data could be accessed through another portal, e.g. Pangea), now link directly to the portal in question. If you want to make one of those data descriptions searchable in SNDβs catalogue, please contact SND on snd@snd.gu.se.\n A small number of records were neither migrated to SND nor redirected to external providers, and they redirect.\nContact SND on snd@snd.gu.se if you want more information about the closing of the ECDS portal and the migration of data descriptions to SNDβs research data catalogue.",
"homepage": "https://snd.se/en/information-about-ecds",
"name": "Environment Climate Data Sweden",
"prefix": "r3d100011000",
"synonyms": [
"ECDS",
"SND-KM (formerly)",
"formerly: Swedish National Data Service for Climate and Environment"
]
},
"r3d100011001": {
"description": "<<>>!!!>>>",
"homepage": "https://nesstar.ssc.wisc.edu/index.html",
"name": "Better Access to Data for Global Interdisciplinary Research",
"prefix": "r3d100011001",
"synonyms": [
"BADGIR"
]
},
"r3d100011002": {
"description": "This site contains active weather alerts, warnings, watches, and advisories concerning the US State of Alaska and the surrounding waters. Near-real time data are available as are historical records. Links to the National Data Buoy Center are provided for coastal and ocean conditions around Alaska.",
"homepage": "https://www.weather.gov/arh/",
"name": "National Weather Service, Alaska Region Headquarters",
"prefix": "r3d100011002",
"synonyms": [
"NWS ARHQ",
"NWS Alaska Region HQ"
]
},
"r3d100011003": {
"description": "The National Weather Service, Fairbanks provides weather data relating to and observed in the Fairbanks, AK area. Data includes current, past, and future weather. Databases are organized primarily by the type of data (e.g. weather data, climate data, hydrology, warning/hazard alerts) and then are searchable by research location.",
"homepage": "https://www.weather.gov/afg/",
"name": "National Weather Service, Fairbanks, Alaska Region",
"prefix": "r3d100011003",
"synonyms": [
"NWS, Fairbanks AK"
]
},
"r3d100011004": {
"description": "This resource allows users to search for and compare influenza virus genomes and gene sequences taken from GenBank. It also provides a virus sequence annotation tool and links to other influenza resources: NIAID project, JCVI Flu, Influenza research database, CDC Flu, Vaccine Selection and WHO Flu.\nNOTE: In Fall 2024, NCBI plans to redirect the Influenza Virus Resource to NCBI Virus, possibly as soon as September. For most up-to-date and accurate virus data, see NCBI Virus https://www.re3data.org/repository/r3d100014322",
"homepage": "https://www.ncbi.nlm.nih.gov/genomes/FLU/Database/nph-select.cgi?go=database",
"name": "NCBI Influenza Virus Resource",
"prefix": "r3d100011004",
"synonyms": [
"Influenza Virus Database",
"NCBI Flu"
],
"xrefs": {
"fairsharing": "FAIRsharing.13cdzp",
"nif": "0000-03023",
"scr": "002984"
}
},
"r3d100011005": {
"description": "<<>>!!!>>>\n\nNCBI Virus Variation is a specialized database which collects tools to provide searchable resources in the fields of Influenza virus, Dengue virus, and West Nile virus. Specific BLAST databases are listed. Their new publications are also available in their site. Rotavirus database will be added in their site soon.",
"homepage": "https://www.ncbi.nlm.nih.gov/genome/viruses/variation/",
"name": "NCBI Virus Variation",
"prefix": "r3d100011005",
"synonyms": [
"Dengue Virus Database",
"Influenza Virus Database",
"NCBI Virus",
"Rotavirus Database",
"West Nile Virus Database"
],
"xrefs": {
"scr": "013790"
}
},
"r3d100011006": {
"description": "The World Data Centre for Geomagnetism, Mumbai is the part of the Indian Institute of Geomagnetism, an autonomous research institute under the Department of Science and Technology, Government of India. This Centre is a part of ICSU World Data Centre System operated since 1971. This Centre has collected a comprehensive set of analog and digital geomagnetic data as well as indices of geomagnetic activity supplied from a worldwide network of magnetic observatories.",
"homepage": "http://wdciig.res.in/WebUI/Home.aspx",
"name": "World Data Centre for Geomagnetism, Mumbai",
"prefix": "r3d100011006",
"synonyms": [
"WDC - Geomagnetism, Mumbai",
"WDC Mumbai"
]
},
"r3d100011007": {
"description": "Oral Cancer Gene Database is an initiative of the Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai. The present database, version II, consists of 374 genes. It is developed as a user friendly site that would provide the scientist, information and external links from one place. The database is accessed through a list of all genes, and Keyword Search using gene name or gene symbol, chromosomal location, CGH (in %), and molecular weight. Interaction Network shows the interaction between genes for particular biological processes and molecular functions.",
"homepage": "https://www.actrec.gov.in/OCDB/index.htm",
"name": "Oral Cancer Gene Database",
"prefix": "r3d100011007",
"synonyms": [
"OrCGDB"
]
},
"r3d100011008": {
"description": "The Evidence-based Practice Center (EPC) at Tufts Medical Center, with support from the Agency for Healthcare Research and Quality (AHRQ), has developed the Systematic Review Data Repository (SRDR), which is a Web-based tool for data extraction and storage of systematic review data. Potential users include patients, policy makers/stakeholders, independent researchers, research centers, and funders of research.",
"homepage": "https://srdrplus.ahrq.gov/",
"name": "Systematic Review Data Repository",
"prefix": "r3d100011008",
"synonyms": [
"SRDR",
"SRDR+"
]
},
"r3d100011009": {
"description": "TPA is a database that contains sequences built from the existing primary sequence data in GenBank. TPA records are retrieved through the Nucleotide Database and feature information on the sequence, how it was cataloged, and proper way to cite the sequence information.",
"homepage": "https://www.ncbi.nlm.nih.gov/genbank/tpa/",
"name": "NCBI Third Party Annotation",
"prefix": "r3d100011009",
"synonyms": [
"TPA"
],
"xrefs": {
"nlx": "157738",
"scr": "003593"
}
},
"r3d100011010": {
"description": "The Greenland Climate Network provides year-round data on the climate of Greenland's ice sheet. These data are available to researchers by request through the Greenland Climate Network Data Request Web page. \nGC-Net data, previously hosted by CIRES, have now been moved to WSLβs Envidat data repository.\nThe Geological Survey of Denmark and Greenland (GEUS) in Copenhagen, has been appointed to the continuation of climate monitoring at the GC-Net sites (https://eng.geus.dk/about/news/news-archive/2020/december/geus-takes-over-american-climate-stations-on-the-greenland-ice-sheet). The new GC-Net data will be distributed through the PROMICE website (https://www.promice.org/).",
"homepage": "https://cires1.colorado.edu/science/groups/steffen/gcnet/",
"name": "Greenland Climate Network",
"prefix": "r3d100011010",
"synonyms": [
"GC-NET"
]
},
"r3d100011011": {
"description": "The PPEPDR contains information regarding the availability and security of sustainable supply of oil and gas for economic development and strategic requirements of Pakistan and to coordinate development of natural resources of energy and minerals.",
"homepage": "http://www.ppepdr.net/",
"name": "Pakistan Petroleum Exploration & Production Data Repository",
"prefix": "r3d100011011",
"synonyms": [
"PPEPDR",
"PetroBank"
],
"xrefs": {
"fairsharing": "FAIRsharing.2948d9"
}
},
"r3d100011012": {
"description": "The India Environment Portal provides open access to information about environmental and developmental issues in India. The Portal aggregates and presents data from research institutions, government bodies, NGOs, universities, the mass media, and experts across various issues of environmental management.",
"homepage": "http://www.indiaenvironmentportal.org.in/",
"name": "India Environment Portal",
"prefix": "r3d100011012",
"xrefs": {
"fairsharing": "FAIRsharing.b850f9"
}
},
"r3d100011013": {
"description": "SprΓ₯kbanken was established in 1975 as a national center located in the Faculty of Arts, University of Gothenburg. AllΓ©n's groundbreaking corpus linguistic research resulted in the creation of one of the first large electronic text corpora in another language than English, with one million words of newspaper text. The task of SprΓ₯kbanken is to collect, develop, and store (Swedish) text corpora, and to make linguistic data extracted from the corpora available to researchers and to the public.",
"homepage": "https://spraakbanken.gu.se/en",
"name": "SprΓ₯kbanken Text",
"prefix": "r3d100011013",
"synonyms": [
"SprΓ₯kbanken",
"SprΓ₯kbankenText"
]
},
"r3d100011014": {
"description": "The Norwegian Meteorological Institute supplies climate observations and weather data and forecasts for the country and surrounding waters (including the Arctic). In addition commercial services are provided to fit customers requirements. \n\nData are served through a number of subsystems (information provided in repository link) and cover data from internal services of the institute, from external services operated by the institute and research projects where the institute participates. Further information is provided in the landing page which also contains entry points some of the data portals operated.",
"homepage": "https://www.met.no/en/free-meteorological-data",
"name": "Norwegian Meteorological Institute, Free Meteorological Data",
"prefix": "r3d100011014",
"synonyms": [
"MET Norway",
"Meteorologisk institutt"
]
},
"r3d100011015": {
"description": "The Internet Archive includes texts, audio, moving images, software, and archived web pages.",
"homepage": "https://archive.org/",
"name": "Internet Archive",
"prefix": "r3d100011015",
"xrefs": {
"nif": "0000-10172",
"scr": "001682"
}
},
"r3d100011016": {
"description": "The National Geothermal Data System (NGDS) is a distributed data system that provides access to information related to geothermal energy from a network of data providers, including academic researchers, private industry, and state and federal agencies.",
"homepage": "https://data.geothermaldata.org/",
"name": "National Geothermal Data System",
"prefix": "r3d100011016",
"synonyms": [
"NGDS"
],
"xrefs": {
"nlx": "155574",
"scr": "006545"
}
},
"r3d100011017": {
"description": "This database contains individual-based life history data that have been collected from wild primate populations by nine working group participants over a minimum of 19 years.",
"homepage": "https://plhdb.org/",
"name": "Primate Life Histories database",
"prefix": "r3d100011017",
"synonyms": [
"PLHDB"
]
},
"r3d100011018": {
"description": "<<>>!!!<<< NARSTO is dedicated to improving management of air quality in North America. Additionally, NARSTO is working to improve collaboration between the air-quality and health-sciences research communities, to advance understanding of the scientific issues involved in effecting a multi-pollutant/multi-media approach to air quality management, and to increase understanding of the linkages between air quality and climate change. NARSTO is represented by private and public organizations in Canada, Mexico, and the United States.\nNARSTO was terminated as of December 31, 2010. While data remain available via the original NARSTO Data Archive, the permanent data archive is maintained by the NASA Langley Research Center Atmospheric Science Data Center",
"homepage": "https://www.mce2.org/narsto-home",
"name": "NARSTO",
"prefix": "r3d100011018",
"synonyms": [
"Better air quality for North America",
"North American Research Strategy for Tropospheric Ozone"
],
"xrefs": {
"biodbcore": "001537"
}
},
"r3d100011019": {
"description": "PSLC DataShop houses datasets in the areas of learning science and educational software. The site also provides online tools for analyzing and reporting the data.",
"homepage": "https://pslcdatashop.web.cmu.edu/index.jsp",
"name": "PSLC DataShop",
"prefix": "r3d100011019",
"synonyms": [
"Learnlab DataShop",
"Pittsburgh Science of Learning Center DataShop"
]
},
"r3d100011020": {
"description": "The Barrow, Alaska Observatory (BRW) archives and provides digital access to their findings related to climate change, ozone depletion and baseline air quality. The BRW is part of the National Oceanic and Atmospheric Administration and Earth System Research Laboratory Global Monitoring Division.",
"homepage": "https://gml.noaa.gov/obop/brw/",
"name": "Barrow Atmospheric Baseline Observatory",
"prefix": "r3d100011020",
"synonyms": [
"BRW",
"Barrow, Alaska Observatory (formerly)"
]
},
"r3d100011021": {
"description": "<<>>!!!>>>",
"homepage": "http://www.eip.gov.eg/Default.aspx",
"name": "Egypt's Information Portal",
"prefix": "r3d100011021",
"synonyms": [
"EIP"
]
},
"r3d100011022": {
"description": "<<>>!!!>>>\nHIV and AIDS Costs and Use is the first major research effort to collect information on a nationally representative sample of people in care for HIV infection. Also called the HIV Cost and Services Utilization Study (HCSUS), the core study is meant to help policymakers in the U.S. make informed decisions on the subject. The study describes the type of therapies available and costs of health care services for people with HIV/AIDS, as well as quality of care, social support, and non-medical services HIV/AIDS patients receive. Supplemental studies examine HIV care delivery in rural areas, prevalence of mental and substance abuse disorders, and other health issues of HIV/AIDS patients.",
"homepage": "https://archive.ahrq.gov/research/findings/factsheets/costs/hcsus/index.html",
"name": "HIV & AIDS Costs & Use",
"prefix": "r3d100011022",
"synonyms": [
"HCSUS"
]
},
"r3d100011023": {
"description": "Databrary is a data library for researchers to share research data and analytical tools with other investigators. It is a web-based repository for open sharing and preservation of video data and associated metadata in the area of behavioral sciences. The project aims to increase the openness in scientific research and dedicated to transforming the culture of science through building a community of researchers empowering them with an unprecedented set of tools for discovery. Databrary is complemented by Datavyu (an open source video-coding software).",
"homepage": "https://nyu.databrary.org/",
"name": "Databrary",
"prefix": "r3d100011023",
"xrefs": {
"fairsharing": "FAIRsharing.0a42a6",
"nlx": "157733",
"scr": "010471"
}
},
"r3d100011024": {
"description": "<<>>!!!>>> The portal provides an understanding of energy resources and related data to establish an understanding of the sector in terms of developmental activities and best practices are being carried out in India in the energy sector. Thus it is sharing information on various aspects of energy in a comprehensive manner to a variety of stakeholders to enable effective consolidation and assimilation of knowledge. IEP provides access to energy statistics, case studies, national policies, sectoral overviews.",
"homepage": "http://www.indiaenergyportal.org",
"name": "India Energy Portal",
"prefix": "r3d100011024",
"synonyms": [
"IEP"
]
},
"r3d100011025": {
"description": "The USDA Economics, Statistics and Market Information System contains reports and datasets of multiple agencies within the United States Department of Agriculture, including the Agricultural Marketing Service, the Economic Research Service, the Foreign Agricultural Service, the National Agricultural Statistics Service, and the World Agricultural Outlook Board. Historical and current reports and datasets are included.",
"homepage": "https://usda.library.cornell.edu/",
"name": "USDA Economics, Statistics and Market Information System",
"prefix": "r3d100011025",
"synonyms": [
"ESMIS"
]
},
"r3d100011026": {
"description": "<<>>!!!>>>",
"homepage": "https://dr-dn.cisti-icist.nrc-cnrc.gc.ca/eng/view/object/?id=ba38501b-15cd-4b94-acf7-a3dc0753a66b",
"name": "Global Pesticides Release Data",
"prefix": "r3d100011026",
"synonyms": [
"BDMoRP",
"GloPeRD",
"la Base de donnΓ©es mondiale sur les rejets de pesticides"
]
},
"r3d100011027": {
"description": "It is a statistical system developed for collection, computerization, analysis and use of educational and allied data for planning, management, monitoring and feedback. So, DISE is an initiative of the Department of Educational Management Information System (EMIS) of NUEPA for developing and strengthening the educational management information system in India. The initiative is coordinated from district level to state and extended up to national level are being constantly collected and disseminated. It provides information on vital parameters relating to students, teachers and infrastructure at all levels of education in India. Presently DISE has three modules U-DISE, DISE, and SEMIS. DISE also provides several other derivative statistical products, such as, District Report Cards, State Report Cards, School Report Cards, Flash Statistics, Analytical Reports, Rural/Urban Statistics, etc.",
"homepage": "https://udiseplus.gov.in/#/home",
"name": "Unified-District Information System for Education Plus",
"prefix": "r3d100011027",
"synonyms": [
"UDISE+",
"formerly: DISE",
"formerly: District Information System for Education",
"formerly: U-DISE",
"formerly: Unified-District Information System for Education"
]
},
"r3d100011028": {
"description": "<<>>!!!>>>",
"homepage": "http://archiv.ivt.ethz.ch/vpl/publications/ethtda/index_EN.html",
"name": "ETH Travel Data Archive",
"prefix": "r3d100011028",
"synonyms": [
"ETHTDA"
]
},
"r3d100011029": {
"description": "The Barrow area on the North Slope of Alaska is one of the most intensely sampled locations in the Arctic with research sites dating back to the 1940s. The Barrow Area Information Database (BAID) is a resource for learning about the types of data collection activities in the region. The BAID team collaborates with scientists and the local community to compile and share this information via online web mapping applications.",
"homepage": "https://barrowmapped.org/",
"name": "Barrow Area Information Database",
"prefix": "r3d100011029",
"synonyms": [
"BAID"
]
},
"r3d100011030": {
"description": "The Center for Operational Oceanographic Products and Services (CO-OPS) site offers operational data in near-real time and historic contexts. Focus is on tides and currents but also includes information on harmful algal blooms and weather, etc. Data access is made possible through geopspatial web interfaces as well as OPeNDAP services, etc.",
"homepage": "https://tidesandcurrents.noaa.gov/",
"name": "Center for Operational Oceanographic Products and Services",
"prefix": "r3d100011030",
"synonyms": [
"CO-OPS",
"Tides and Currents"
],
"xrefs": {
"fairsharing.legacy": "2996"
}
},
"r3d100011031": {
"description": "The MG-RAST server is an open source system for annotation and comparative analysis of metagenomes. Users can upload raw sequence data in fasta format; the sequences will be normalized and processed and summaries automatically generated. The server provides several methods to access the different data types, including phylogenetic and metabolic reconstructions, and the ability to compare the metabolism and annotations of one or more metagenomes and genomes. In addition, the server offers a comprehensive search capability. Access to the data is password protected, and all data generated by the automated pipeline is available for download in a variety of common formats. MG-RAST has become an unofficial repository for metagenomic data, providing a means to make your data public so that it is available for download and viewing of the analysis without registration, as well as a static link that you can use in publications. It also requires that you include experimental metadata about your sample when it is made public to increase the usefulness to the community.",
"homepage": "https://www.mg-rast.org/",
"name": "MG-RAST",
"prefix": "r3d100011031",
"synonyms": [
"Metagenomics analysis server"
],
"xrefs": {
"scr": "004814"
}
},
"r3d100011032": {
"description": "The NASA Earth Exchange (NEX) represents a platform for the Earth science community that provides a mechanism for scientific collaboration and knowledge sharing. NEX combines supercomputing, Earth system modeling, workflow management, NASA remote sensing data feeds, and a knowledge sharing platform to deliver a complete work environment in which users can explore and analyze large datasets, run modeling codes, collaborate on new or existing projects, and quickly share results among the Earth Science communities. Includes some local data collections as well as links to data on other sites.\n On January 31st, 2019, the NEX portal will be down-scoped; member logins will be suspended and the portal contents transitioned to a static set of archives. New projects and resources will no longer be possible after this occurs.",
"homepage": "https://www.nasa.gov/nasa-earth-exchange-nex/",
"name": "NASA Earth Exchange",
"prefix": "r3d100011032",
"synonyms": [
"NEX"
]
},
"r3d100011033": {
"description": "<<>>!!!>>>\nThis retirement includes the representation of BioSystems records in the NCBI Entrez system and viewers of BioSystems content. \nNCBI now provides metabolic pathway and other biosystems data through the regularly updated PubChem Pathways resource (https://pubchemdocs.ncbi.nlm.nih.gov/pathways) that offers a fresh, extended, and more modern interface.",
"homepage": "https://www.ncbi.nlm.nih.gov/biosystems/",
"name": "NCBI BioSystems Database",
"prefix": "r3d100011033",
"synonyms": [
"NCBI BioSystems"
],
"xrefs": {
"fairsharing": "FAIRsharing.w2eeqr",
"miriam": "00000097",
"nlx": "69646",
"scr": "004690"
}
},
"r3d100011034": {
"description": "The IFRI research network examines how governance arrangements affect forests and the people who depend on them. It is comprised of 14 Collaborating Research Centers located around the globe. Researchers use a common data collection method to ensure that sites can be compared across space and time. The IFRI database contains information about biodiversity, livelihoods, institutions, and forest carbon for over 250 sites in 15 countries between 1992 and the present.",
"homepage": "http://ifri.forgov.org/",
"name": "International Forestry Resources and Institutions",
"prefix": "r3d100011034",
"synonyms": [
"IFRI"
]
},
"r3d100011035": {
"description": "Central data management of the USGS for water data that provides access to water-resources data collected at approximately 1.5 million sites in all 50 States, the District of Columbia, Puerto Rico, the Virgin Islands, Guam, American Samoa and the Commonwealth of the Northern Mariana Islands. Includes data on water use and quality, groundwater, and surface water.",
"homepage": "https://waterdata.usgs.gov/nwis",
"name": "USGS National Water Information System",
"prefix": "r3d100011035",
"synonyms": [
"NWIS",
"USGS Water Data for the Nation"
]
},
"r3d100011036": {
"description": "The National Data Archive on Child Abuse and Neglect (NDACAN) promotes scholarly exchange among researchers in the child maltreatment field. NDACAN acquires microdata from leading researchers and national data collection efforts and makes these datasets available to the research community for secondary analysis.",
"homepage": "https://www.ndacan.acf.hhs.gov/",
"name": "National Data Archive on Child Abuse and Neglect",
"prefix": "r3d100011036",
"synonyms": [
"NDACAN"
]
},
"r3d100011037": {
"description": "SureChemOpen is a free resource for researchers who want to search, view and link to patent chemistry. For end-users with professional search and analysis needs, we offer the fully-featured SureChemPro. For enterprise users, SureChemDirect provides all our patent chemistry via an API or a data feed. The SureChem family of products is built upon the ClaimsΒ Global Patent Database, a comprehensive international patent collection provided by IFI ClaimsΒ. This state of the art database is normalized and curated to provide unprecedented consistency and quality.",
"homepage": "https://www.surechembl.org/",
"name": "SureChEMBL",
"prefix": "r3d100011037",
"synonyms": [
"Open Patent Data",
"SureCHEM"
],
"xrefs": {
"fairsharing": "FAIRsharing.q2n5wk"
}
},
"r3d100011038": {
"description": "The Qualitative Data Repository (QDR) is a dedicated archive for storing and sharing digital data (and accompanying documentation) generated or collected through qualitative and multi-method research in the social sciences. QDR provides data management consulting services and actively curates all data projects, maintaining the value and usefulness of the data over time, and ensuring their availability and findability for re-use.",
"homepage": "https://qdr.syr.edu/",
"name": "Qualitative Data Repository",
"prefix": "r3d100011038",
"synonyms": [
"QDR"
],
"xrefs": {
"fairsharing": "FAIRsharing.bmz5ap"
}
},
"r3d100011040": {
"description": "<<>>!!!>>>\nThe MultiDark database provides results from cosmological simulations performed within the MultiDark project. This database can be queried by entering SQL statements directly into the Query Form. The access to that form and thus access to the public & private databases is password protected.",
"homepage": "http://www.multidark.org//",
"name": "MultiDark Database",
"prefix": "r3d100011040",
"synonyms": [
"Multimessenger Approach for Dark Matter Detection"
]
},
"r3d100011041": {
"description": "The Fungal Genetics Stock Center has preserved and distributed strains of genetically characterized fungi since 1960. The collection includes over 20,000 accessioned strains of classical and genetically engineered mutants of key model, human, and plant pathogenic fungi. These materials are distributed as living stocks to researchers around the world.",
"homepage": "https://www.fgsc.net/",
"name": "Fungal Genetics Stock Center",
"prefix": "r3d100011041",
"synonyms": [
"FGSC"
],
"xrefs": {
"nif": "0000-20977",
"scr": "008143"
}
},
"r3d100011042": {
"description": "The ClinicalCodes repository aims to hold code lists for all published electronic medical record studies, irrespective of code type (e.g. Read, ICD9-10, SNOMED) and database (CPRD, QResearch, THIN etc.). Once deposited, code lists will be freely available, with no login needed to download codes.",
"homepage": "https://clinicalcodes.rss.mhs.man.ac.uk/",
"name": "ClinicalCodes.org",
"prefix": "r3d100011042",
"synonyms": [
"ClinicalCodes repository"
]
},
"r3d100011043": {
"description": "Academic Torrents is a distributed data repository.\nThe academic torrents network is built for researchers, by researchers. Its distributed peer-to-peer library system automatically replicates your datasets on many servers, so you don't have to worry about managing your own servers or file availability. Everyone who has data becomes a mirror for those data so the system is fault-tolerant.",
"homepage": "https://academictorrents.com/",
"name": "Academic Torrents",
"prefix": "r3d100011043"
},
"r3d100011045": {
"description": "The Index to Marine and Lacustrine Geological Samples is a tool to help scientists locate and obtain geologic material from sea floor and lakebed cores, grabs, and dredges archived by participating institutions around the world. Data and images related to the samples are prepared and contributed by the institutions for access via the IMLGS and long-term archive at NGDC. Before proposing research on any sample, please contact the curator for sample condition and availability. A consortium of Curators guides the IMLGS, maintained on behalf of the group by NGDC, since 1977.",
"homepage": "https://www.ngdc.noaa.gov/mgg/curator/curator.html",
"name": "Index to Marine & Lacustrine Geological Samples",
"prefix": "r3d100011045",
"synonyms": [
"Access to rock and sediment cores, dredges, and grabs from the ocean floor and lakebeds",
"IMLGS"
],
"xrefs": {
"doi": "10.7289/V5H41PB8",
"nlx": "154736",
"scr": "009430"
}
},
"r3d100011046": {
"description": "The Golm Metabolome Database (GMD) facilitates the search for and dissemination of reference mass spectra from biologically active metabolites quantified using gas chromatography (GC) coupled to mass spectrometry (MS)",
"homepage": "http://gmd.mpimp-golm.mpg.de/",
"name": "Golm Metabolome Database",
"prefix": "r3d100011046",
"synonyms": [
"GMD"
],
"xrefs": {
"fairsharing": "FAIRsharing.jykmkw",
"miriam": "00000274",
"nif": "0000-21180",
"scr": "006625"
}
},
"r3d100011047": {
"description": "prometheus is a digital image archive for Art and Cultural Sciences. prometheus enables the convenient search for images on a common user interface within different image archives, variable databases from institutes, research facilities and museums.",
"homepage": "https://www.prometheus-bildarchiv.de/",
"name": "prometheus",
"prefix": "r3d100011047",
"synonyms": [
"Das verteilte digitale Bildarchiv fΓΌr Forschung & Lehre"
]
},
"r3d100011048": {
"description": "As part of the Copernicus Space Component programme, ESA manages the coordinated access to the data procured from the various Contributing Missions and the Sentinels, in response to the Copernicus users requirements. The Data Access Portfolio documents the data offer and the access rights per user category. The CSCDA portal is the access point to all data, including Sentinel missions, for Copernicus Core Users as defined in the EU Copernicus Programme Regulation (e.g. Copernicus Services).The Copernicus Space Component (CSC) Data Access system is the interface for accessing the Earth Observation products from the Copernicus Space Component. The system overall space capacity relies on several EO missions contributing to Copernicus, and it is continuously evolving, with new missions becoming available along time and others ending and/or being replaced.",
"homepage": "https://spacedata.copernicus.eu/",
"name": "Copernicus Contributing Missions Online",
"prefix": "r3d100011048",
"xrefs": {
"biodbcore": "001312"
}
},
"r3d100011049": {
"description": "STOREDB is a platform for the archiving and sharing of primary data and outputs of all kinds, including epidemiological and experimental data, from research on the effects of radiation. It also provides a directory of bioresources and databases containing information and materials that investigators are willing to share. STORE supports the creation of a radiation research commons.",
"homepage": "https://www.storedb.org/store_v3/",
"name": "STOREDB",
"prefix": "r3d100011049",
"synonyms": [
"STORE",
"Sustaining access to Tissues and data frOm Radiobiological Experiments"
],
"xrefs": {
"fairsharing": "FAIRsharing.6h8d2r",
"miriam": "00000577",
"scr": "023207"
}
},
"r3d100011052": {
"description": "The SABIO-RK is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. It aims to support modellers in the setting-up of models of biochemical networks, but it is also useful for experimentalists or researchers with interest in biochemical reactions and their kinetics. All the data are manually curated and annotated by biological experts, supported by automated consistency checks.",
"homepage": "https://sabiork.h-its.org/",
"name": "SABIO-RK",
"prefix": "r3d100011052",
"synonyms": [
"Biochemical reation kinetics database",
"System for the Analysis of Biochemical Pathways - Reaction Kinetics"
],
"xrefs": {
"fairsharing": "FAIRsharing.cwx04e",
"nif": "0000-20912",
"scr": "002122"
}
},
"r3d100011056": {
"description": "The Cornell Center for Social Sciences (CCSS) houses an extensive collection of research data files in the social sciences with particular emphasis on data that matches the interests of Cornell University researchers. CCSS intentionally uses a broad definition of social sciences in recognition of the interdisciplinary nature of Cornell research. CCSS collects and maintains digital research data files in the social sciences, with a current emphasis on Cornell-based social science research, Results Reproduction packages, and potentially at-risk datasets. Our archive historically has focused on a broad range of social science data, including data on demography, economics and labor, political and social behavior, family life, and health. You can search our holdings or browse studies by subject area.",
"homepage": "https://archive.ciser.cornell.edu/",
"name": "CCSS Data & Reproduction Archive",
"prefix": "r3d100011056",
"synonyms": [
"Cornell Center for Social Sciences Data & Reproduction Archive"
]
},
"r3d100011057": {
"description": "Copernicus is a European system for monitoring the Earth.\nCopernicus consists of a complex set of systems which collect data from multiple sources: earth observation satellites and in situ sensors such as ground stations, airborne and sea-borne sensors. It processes these data and provides users with reliable and up-to-date information through a set of services related to environmental and security issues. The services address six thematic areas: land monitoring, marine monitoring, atmosphere monitoring, climate change, emergency management and security.\nThe main users of Copernicus services are policymakers and public authorities who need the information to develop environmental legislation and policies or to take critical decisions in the event of an emergency, such as a natural disaster or a humanitarian crisis.\nBased on the Copernicus services and on the data collected through the Sentinels and the contributing missions , many value-added services can be tailored to specific public or commercial needs, resulting in new business opportunities. In fact, several economic studies have already demonstrated a huge potential for job creation, innovation and growth.",
"homepage": "https://www.copernicus.eu/en",
"name": "Copernicus",
"prefix": "r3d100011057",
"synonyms": [
"The European Earth Observation Pogramme"
]
},
"r3d100011058": {
"description": "VertNet is a NSF-funded collaborative project that makes biodiversity data free and available on the web. VertNet is a tool designed to help people discover, capture, and publish biodiversity data. It is also the core of a collaboration between hundreds of biocollections that contribute biodiversity data and work together to improve it. VertNet is an engine for training current and future professionals to use and build upon best practices in data quality, curation, research, and data publishing. Yet, VertNet is still the aggregate of all of the information that it mobilizes. To us, VertNet is all of these things and more.",
"homepage": "http://vertnet.org/",
"name": "VertNet",
"prefix": "r3d100011058"
},
"r3d100011060": {
"description": "This classic collection of test cases for validation of turbulence models started as an EU / ERCOFTAC project led by Pr. W. Rodi in 1995. It is maintained by Dr. T. Craft at Manchester since 1999. Initialy limited to experimental data, computational results, and results and conclusions drawn from the ERCOFTAC Workshops on Refined Turbulence Modelling (SIG15). At the moment, each case should contain at least a brief description, some data to download, and references to published work. Some cases contain significantly more information than this.",
"homepage": "http://cfd.mace.manchester.ac.uk/ercoftac/doku.php",
"name": "European Research Community on Flow, Turbulence and Combustion Database - Classic Collection",
"prefix": "r3d100011060",
"synonyms": [
"ERCOFTAC Classic Collection"
]
},
"r3d100011061": {
"description": "This website is a portal that enables access to multi-Terabyte turbulence databases. The data reside on several nodes and disks on our database cluster computer and are stored in small 3D subcubes. Positions are indexed using a Z-curve for efficient access.",
"homepage": "http://turbulence.pha.jhu.edu/",
"name": "Johns Hopkins Turbulence Databases",
"prefix": "r3d100011061",
"synonyms": [
"JHTDB"
]
},
"r3d100011062": {
"description": "<<>>!!!>>>",
"homepage": "https://data.gesis.org/sharing/#!Home",
"name": "Archiving BASIS",
"prefix": "r3d100011062",
"synonyms": [
"Archivierung BASIS",
"formerly: GESIS SowiDataNet|datorium"
]
},
"r3d100011063": {
"description": "This site provides access to over 210,000 digitized or born-digital images in the Koç University collections featuring prints, photographs, slides, maps, newspapers, posters, postcards, manuscripts, streaming video, and more. The collections consist of the materials of the Koç University Libraries and Archives (AKMED, ANAMED, SKL, and VEKAM), Koç University Faculty and Departments, and projects carried out in partnership with the Koç University Libraries. It includes the Koç University Institutional Repository (KU-IR).",
"homepage": "https://librarydigitalcollections.ku.edu.tr/en/",
"name": "Koç University Digital Collections",
"prefix": "r3d100011063",
"synonyms": [
"SKL-DL"
]
},
"r3d100011065": {
"description": "The GTN-P database is an object-related database open for a diverse range of data. Because of the complexity of the PAGE21 project, data provided in the GTN-P management system are extremely diverse, ranging from active-layer thickness measurements once per year to flux measurement every second and everthing else in between. The data can be assigned to two broad categories: Quantitative data which is all data that can be measured numerically. Quantitative data comprise all in situ measurements, i.e. permafrost temperatures and active layer thickness (mechanical probing, frost/thaw tubes, soil temperature profiles). Qualitative data (knowledge products) are observations not based on measurements, such as observations on soils, vegetation, relief, etc.",
"homepage": "http://gtnpdatabase.org/",
"name": "Global Terrestrial Network for Permafrost",
"prefix": "r3d100011065",
"synonyms": [
"GTN-P Database"
],
"xrefs": {
"issn": "2410-2385"
}
},
"r3d100011070": {
"description": "Welcome to INTERMAGNET - the global network of observatories, monitoring the Earth's magnetic field. At this site you can find data and information from geomagnetic observatories around the world.\nThe INTERMAGNET programme exists to establish a global network of cooperating digital magnetic observatories, adopting modern standard specifications for measuring and recording equipment, in order to facilitate data exchanges and the production of geomagnetic products in close to real time.",
"homepage": "https://intermagnet.org/",
"name": "Intermagnet",
"prefix": "r3d100011070",
"synonyms": [
"International Real-time Magnetic Observatory Network"
],
"xrefs": {
"issn": "2428-9795"
}
},
"r3d100011071": {
"description": "This project is an open invitation to anyone and everyone to participate in a decentralized effort to explore the opportunities of open science in neuroimaging. We aim to document how much (scientific) value can be generated from a data release β from the publication of scientific findings derived from this dataset, algorithms and methods evaluated on this dataset, and/or extensions of this dataset by acquisition and incorporation of new data.\nThe project involves the processing of acoustic stimuli. In this study, the scientists have demonstrated an audiodescription of classic \"Forrest Gump\" to subjects, while researchers using functional magnetic resonance imaging (fMRI) have captured the brain activity of test candidates in the processing of language, music, emotions, memories and pictorial representations.In collaboration with various labs in Magdeburg we acquired and published what is probably the most comprehensive sample of brain activation patterns of natural language processing.\nVolunteers listened to a two-hour audio movie version of the Hollywood feature film \"Forrest Gump\" in a 7T MRI scanner. High-resolution brain activation patterns and physiological measurements were recorded continuously. These data have been placed into the public domain, and are freely available to the scientific community and the general public.",
"homepage": "https://www.studyforrest.org/",
"name": "studyforrest",
"prefix": "r3d100011071",
"xrefs": {
"nlx": "156710",
"scr": "003112"
}
},
"r3d100011076": {
"description": "DIGITAL.CSIC is the institutional repository of the Spanish National Research Council (CSIC). Designed for organising, archiving, preserving and disseminating via open access the scientific output generated as a product of the CSIC research activities by CSIC researchers",
"homepage": "https://digital.csic.es/?locale=en",
"name": "DIGITAL.CSIC",
"prefix": "r3d100011076",
"xrefs": {
"fairsharing": "FAIRsharing.8d2e5c",
"scr": "011534"
}
},
"r3d100011077": {
"description": "CERN, DESY, Fermilab and SLAC have built the next-generation High Energy Physics (HEP) information system, INSPIRE. It combines the successful SPIRES database content, curated at DESY, Fermilab and SLAC, with the Invenio digital library technology developed at CERN. INSPIRE is run by a collaboration of CERN, DESY, Fermilab, IHEP, IN2P3 and SLAC, and interacts closely with HEP publishers, arXiv.org, NASA-ADS, PDG, HEPDATA and other information resources.\nINSPIRE represents a natural evolution of scholarly communication, built on successful community-based information systems, and provides a vision for information management in other fields of science.",
"homepage": "https://inspirehep.net/?ln=en",
"name": "Inspire-HEP",
"prefix": "r3d100011077",
"synonyms": [
"Inspire-High Energy Physics"
]
},
"r3d100011078": {
"description": "The Research Data Center Qualiservice provides services for archiving and reusing qualitative research data from the social sciences. We advise and accompany research projects in the process of long-term data archiving and data sharing. Data curation is conducted by experts for the social sciences. We also provide research data and relevant context information for reuse in scientific research and teaching. Internationally interoperable metadata ensure that data sets are searchable and findable. Persistent identifiers (DOI) ensure that data and study contexts are citable.\nQualiservice was accredited by the German Data Forum (RatSWD) in 2019 and adheres to its quality assurance criteria. Qualiservice is committed to the German Research Foundationβs (DFG) Guidelines for Safeguarding Good Scientific Practice and takes into account the FAIR Guiding Principles for scientific data management and stewardship as well as the OECD Principles and Guidelines for Access to Research Data from Public Funding. Qualiservice coordinates the networking and further development of scientific infrastructures for archiving and secondary use of qualitative data from social research within the framework of the National Research Data Infrastructure.",
"homepage": "https://www.qualiservice.org/en/",
"name": "Qualiservice",
"prefix": "r3d100011078",
"synonyms": [
"Forschungsdatenzentrum βQualiserviceβ",
"Research Data Center Qualiservice"
]
},
"r3d100011086": {
"description": "The CancerData site is an effort of the Medical Informatics and Knowledge Engineering team (MIKE for short) of Maastro Clinic, Maastricht, The Netherlands. Our activities in the field of medical image analysis and data modelling are visible in a number of projects we are running. CancerData is offering several datasets. They are grouped in collections and can be public or private. You can search for public datasets in the NBIA (National Biomedical Imaging Archive) image archives without logging in.",
"homepage": "https://www.cancerdata.org/",
"name": "CancerData.org",
"prefix": "r3d100011086",
"synonyms": [
"Sharing data for cancer research"
],
"xrefs": {
"fairsharing": "FAIRsharing.s2txbp"
}
},
"r3d100011087": {
"description": "doRiNA is a database of transcriptome-wide binding site data for RNA binding proteins and microRNAs",
"homepage": "https://dorina.mdc-berlin.de/",
"name": "doRiNA",
"prefix": "r3d100011087",
"synonyms": [
"database of RNA interactions in post-transcriptional regulation"
],
"xrefs": {
"fairsharing": "FAIRsharing.z0ea6a",
"nlx": "151321",
"scr": "013222"
}
},
"r3d100011089": {
"description": "GenomeRNAi is a database containing phenotypes from RNA interference (RNAi) screens in Drosophila and Homo sapiens. In addition, the database provides an updated resource of RNAi reagents and their predicted quality.",
"homepage": "http://www.genomernai.org/",
"name": "GenomeRNAi",
"prefix": "r3d100011089",
"xrefs": {
"fairsharing": "FAIRsharing.f55jfq",
"nif": "0000-02901",
"scr": "013088"
}
},
"r3d100011091": {
"description": "DepositOnce is the institutional repository for research data and publications of TU Berlin. In DepositOnce, research results of TU Berlin members and, if applicable, their research partners are archived permanently and made freely accessible on the internet.",
"homepage": "https://depositonce.tu-berlin.de/",
"name": "DepositOnce",
"prefix": "r3d100011091",
"synonyms": [
"Repositorium fΓΌr Forschungsdaten und -publikationen",
"Repository for Research Data and Publications"
],
"xrefs": {
"opendoar": "793",
"roar": "8289"
}
},
"r3d100011094": {
"description": "Ocean Networks Canada maintains several observatories installed in three different regions in the world's oceans. All three observatories are cabled systems that can provide power and high bandwidth communiction paths to sensors in the ocean. The infrastructure supports near real-time observations from multiple instruments and locations distributed across the Arctic, NEPTUNE and VENUS observatory networks.\nThese observatories collect data on physical, chemical, biological, and geological aspects of the ocean over long time periods, supporting research on complex Earth processes in ways not previously possible.",
"homepage": "https://www.oceannetworks.ca/",
"name": "Ocean Networks Canada",
"prefix": "r3d100011094",
"xrefs": {
"fairsharing": "FAIRsharing.1e2ced"
}
},
"r3d100011095": {
"description": "The ODIN Portal hosts scientific databases in the domains of structural materials and hydrogen research and is operated on behalf of the European energy research community by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union. \nODIN contains engineering databases (Mat-Database, Hiad-Database, Nesshy-Database, HTR-Fuel-Database, HTR-Graphit-Database) and document management sites and other information related to European research in the area of nuclear and conventional energy.",
"homepage": "https://odin.jrc.ec.europa.eu/alcor/",
"name": "ODIN",
"prefix": "r3d100011095",
"synonyms": [
"ODIN Portal",
"Online Data & Information Network for Energy"
]
},
"r3d100011098": {
"description": "OpenML is an open ecosystem for machine learning. By organizing all resources and results online, research becomes more efficient, useful and fun.\nOpenML is a platform to share detailed experimental results with the community at large and organize them for future reuse. Moreover, it will be directly integrated in todayβs most popular data mining tools (for now: R, KNIME, RapidMiner and WEKA). Such an easy and free exchange of experiments has tremendous potential to speed up machine learning research, to engender larger, more detailed studies and to offer accurate advice to practitioners. Finally, it will also be a valuable resource for education in machine learning and data mining.",
"homepage": "https://www.openml.org/",
"name": "OpenML",
"prefix": "r3d100011098",
"synonyms": [
"Open Machine Learning"
],
"xrefs": {
"biodbcore": "001316",
"fairsharing": "FAIRsharing.d36c2c"
}
},
"r3d100011099": {
"description": "The data.bris Research Data Repository is an online digital repository of multi-disciplinary research datasets produced at the University of Bristol.",
"homepage": "https://data.bris.ac.uk/data/",
"name": "data.bris Research Data Repository",
"prefix": "r3d100011099"
},
"r3d100011100": {
"description": "<<>>!!!>>> This portal provides access to the GLUES Geodata Infrastructure (Glues GDI). The infrastructure is the common data and service platform for the international research program 'Sustainable Land Management'.",
"homepage": "http://geoportal-glues.ufz.de/index.php",
"name": "GLUES Geoportal",
"prefix": "r3d100011100",
"synonyms": [
"Global Assessment of Land Use Dynamics, Greenhouse Gas Emissions and Ecosystem Services : Geoportal",
"Sustainable Land Management"
],
"xrefs": {
"biodbcore": "001749"
}
},
"r3d100011104": {
"description": "The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. The data contained in the archive include atomic coordinates, crystallographic structure factors and NMR experimental data. Aside from coordinates, each deposition also includes the names of molecules, primary and secondary structure information, sequence database references, where appropriate, and ligand and biological assembly information, details about data collection and structure solution, and bibliographic citations. The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). The wwPDB's mission is to maintain a single PDB archive of macromolecular structural data that is freely and publicly available to the global community.",
"homepage": "https://www.wwpdb.org/",
"name": "Worldwide Protein Data Bank",
"prefix": "r3d100011104",
"synonyms": [
"PDB",
"wwPDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.mckkb4",
"nif": "0000-23903",
"scr": "006555"
}
},
"r3d100011105": {
"description": "The EZRC at KIT houses the largest experimental fish facility in Europe with a capacity of more than 300,000 fish. Zebrafish stocks are maintained mostly as frozen sperm. Frequently requested lines are also kept alive as well as a selection of wildtype strains. Several thousand mutations in protein coding genes generated by TILLING in the Stemple lab of the Sanger Centre, Hinxton, UK and lines generated by ENU mutagenesis by the NΓΌsslein-Volhard lab in addition to transgenic lines and mutants generated by KIT groups or brought in through collaborations. We also accept submissions on an individual basis and ship fish upon request to PIs in Europe and elsewhere. EZRC also provides screening services and technologies such as imaging and high-throughput sequencing. Key areas include automation of embryo handling and automated image acquisition and processing. Our platform also involves the development of novel microscopy techniques (e.g. SPIM, DSLM, robotic macroscope) to permit high-resolution, real-time imaging in 4D. By association with the ComPlat platform, we can support also chemical screens and offer libraries with up to 20,000 compounds in total for external users. As another service to the community the EZRC provides plasmids (cDNAs, transgenes, Talen, Crispr/cas9) maintained by the Helmholtz repository of Bioparts (HERBI) to the scientific community. In addition the fish facility keeps a range of medaka stocks, maintained by the Loosli group.",
"homepage": "https://www.ezrc.kit.edu/index.php",
"name": "European Zebrafish Resource Center",
"prefix": "r3d100011105",
"synonyms": [
"EZRC"
]
},
"r3d100011107": {
"description": "Space-based measurement and modeling of surface water for research, humanitarian, and water management application. \nThe Observatory detects, maps, and measures major flood events world-wide using satellite remote sensing.",
"homepage": "https://floodobservatory.colorado.edu/index.html",
"name": "Dartmouth Flood Observatory",
"prefix": "r3d100011107",
"synonyms": [
"DFO",
"Space-based Measurement and Modeling fo Surface Water"
]
},
"r3d100011108": {
"description": "heiDATA is Heidelberg Universityβs research data repository. It is managed by the Research Data Unit, a joint institution of the University Library and the Computing Centre. All researchers affiliated with Heidelberg University can use this service for archiving and publishing their data.",
"homepage": "https://heidata.uni-heidelberg.de",
"name": "heiDATA",
"prefix": "r3d100011108",
"synonyms": [
"heiDATA Institutional Repository for Research Data of Heidelberg University"
],
"xrefs": {
"fairsharing": "FAIRsharing.zABkyi"
}
},
"r3d100011109": {
"description": "ISDC's online service portal is an access point for all manner of geoscientific geodata, its corresponding metadata, scientific documentation and software tools. The majority of the data and information, the portal currently offers to the public, are global geomonitoring products such as satellite orbit and Earth gravity field data as well as geomagnetic and atmospheric data for the exploration. These products for Earths changing system are provided via state-of-the art retrieval techniques. The projects hosted are: CHAMP, GGP, GRACE, GNSS, GGSP, GGOS, GPS-PDR, ICGEM, TerraSAR-x (TSX-TOR) and TanDEM-X.",
"homepage": "https://isdc.gfz-potsdam.de/homepage/",
"name": "Information System and Data Center for geoscientific data",
"prefix": "r3d100011109",
"synonyms": [
"Global Earth Science Data",
"ISDC"
]
},
"r3d100011110": {
"description": "CHAMP (CHAllenging Minisatellite Payload) is a German small satellite mission for geoscientific and atmospheric research and applications, managed by GFZ. With its highly precise, multifunctional and complementary payload elements (magnetometer, accelerometer, star sensor, GPS receiver, laser retro reflector, ion drift meter) and its orbit characteristics (near polar, low altitude, long duration) CHAMP will generate for the first time simultaneously highly precise gravity and magnetic field measurements over a 5 years period. This will allow to detect besides the spatial variations of both fields also their variability with time. The CHAMP mission had opened a new era in geopotential research and had become a significant contributor to the Decade of Geopotentials. In addition with the radio occultation measurements onboard the spacecraft and the infrastructure developed on ground, CHAMP had become a pilot mission for the pre-operational use of space-borne GPS observations for atmospheric and ionospheric research and applications in weather prediction and space weather monitoring. End of the mission of CHAMP was at September 19 2010, after ten years, two month and four days, after 58277 orbits.",
"homepage": "https://www.gfz-potsdam.de/en/section/geomagnetism/infrastructure/gfz-satellite-mission-champ",
"name": "CHAMP",
"prefix": "r3d100011110",
"synonyms": [
"Challenging Minisatellite Payload"
]
},
"r3d100011111": {
"description": "The twin GRACE satellites were launched on March 17, 2002. Since that time, the GRACE Science Data System (SDS) has produced and distributed estimates of the Earth gravity field on an ongoing basis. These estimates, in conjunction with other data and models, have provided observations of terrestrial water storage changes, ice-mass variations, ocean bottom pressure changes and sea-level variations. This portal, together with PODAAC, is responsible for the distribution of the data and documentation for the GRACE project.",
"homepage": "https://isdc.gfz-potsdam.de/grace-isdc/",
"name": "GRACE ISDC",
"prefix": "r3d100011111",
"synonyms": [
"Gravity Recovery and Climate Experiment"
]
},
"r3d100011112": {
"description": "The term GNSS (Global Navigation Satellite Systems) comprises the different navigation satellite systems like GPS, GLONAS and the future Galileo as well as rawdata from GNSS microwave receivers and processed or derived higher level products and required auxiliary data. The results of the GZF GNSS technology based projects are used as contribution for maintaining and studying the Earth rotational behavior and the global terrestial reference frame, for studying neotectonic processes along plate boundaries and the interior of plates and as input to short term weather forecasting and atmosphere/climate research. Currently only selected products like observation data, navigation data (ephemeriden), meteorological data as well as quality data with a limited spatial coverage are provided by the GNSS ISDC.",
"homepage": "https://www.gfz-potsdam.de/en/section/space-geodetic-techniques/infrastructure/gnss-station-network/",
"name": "GNSS - ISDC",
"prefix": "r3d100011112",
"synonyms": [
"Global Navigation Satellite Systems - Information System and Data Center"
]
},
"r3d100011113": {
"description": "The main function of the GGSP (Galileo Geodetic Service Provider) is to provide a terrestrial reference frame, in the broadest sense of the word, to both the Galileo Core System (GCS) as well as to the Galileo User Segment (all Galileo users). This implies that the GGSP should enable all users of the Galileo System, including the most demanding ones, to access and realise the GTRF with the precision required for their specific application. Furthermore, the GGSP must ensure the proper interfaces to all users of the GTRF, especially the geodetic and scientific user groups. In addition the GGSP must ensure the adherence to the defined standards of all its products. Last but not least the GGSP will play a key role to create awareness of the GTRF and educate users in the usage and realisation of the GTRF.",
"homepage": "https://www.gfz-potsdam.de/en/section/space-geodetic-techniques/projects/grsp/",
"name": "GGSP - ISDC",
"prefix": "r3d100011113",
"synonyms": [
"Galileo Geodetic Service Provider - Information System and Data Center",
"Geodetic Reference Service Provider (GRSP) for Galileo"
]
},
"r3d100011114": {
"description": "<<>>!!!>>> \nGGOS is the Global Geodetic Observing System of the International Association of Geodesy (IAG). It provides observations of the three fundamental geodetic observables and their variations, that is, the Earth's shape, the Earth's gravity field and the Earth's rotational motion. GGOS integrates different geodetic techniques, different models, different approaches in order to ensure a long-term, precise monitoring of the geodetic observables in agreement with the Integrated Global Observing Strategy (IGOS). GGOS provides the observational basis to maintain a stable, accurate and global reference frame and in this function is crucial for all Earth observation and many practical applications.",
"homepage": "http://icgem.gfz-potsdam.de/home",
"name": "GGOS ICGEM",
"prefix": "r3d100011114",
"synonyms": [
"Global Geodetic Observing System at GFZ International Center for Global Gravity Field Models"
]
},
"r3d100011115": {
"description": "<<>>!!!>>> Due to the changes at the individual IGS analysis centers during these years the resulting time series of global geodetic parameters are inhomogeneous and inconsistent. A geophysical interpretation of these long series and the realization of a high-accuracy global reference frame are therefore difficult and questionable. The GPS reprocessing project GPS-PDR (Potsdam Dresden Reprocessing), initiated by TU MΓΌnchen and TU Dresden and continued by GFZ Potsdam and TU Dresden, provides selected products of a homogeneously reprocessed global GPS network such as GPS satellite orbits and Earth rotation parameters.",
"homepage": "http://isdc-old.gfz-potsdam.de/index.php?module=pagesetter&func=viewpub&tid=1&pid=46",
"name": "GPS-PDR ISDC",
"prefix": "r3d100011115",
"synonyms": [
"GPS Potsdam Dresden Reprocessing"
]
},
"r3d100011116": {
"description": "The International Center for Global Earth Models collects and distributes historical and actual global gravity\nfield models of the Earth and offers calculation service for derived quantities. In particular the tasks include: collecting and archiving of all existing global gravity field models, web interface for getting access to global gravity field models, web based visualization of the gravity field models their differences and their time variation, web based service for calculating different functionals of the gravity field models, web site for tutorials on spherical harmonics and the theory of the calculation service. As new service since 2016, ICGEM is providing a Digital Object Identifier (DOI) for the data set of the model (the coefficients).",
"homepage": "http://icgem.gfz-potsdam.de/home",
"name": "ICGEM",
"prefix": "r3d100011116",
"synonyms": [
"International Centre for Global Earth Models"
]
},
"r3d100011117": {
"description": "TerraSAR-X is a German satellite for Earth Observation, which was launched on July 14, 2007. The mission duration was foreseen to be 5 years. TerraSAR-X carries an innovative high resolution x-band sensor for imaging with resolution up to 1 m.\nTerraSAR-X carries as secondary payload an IGOR GPS receiver with GPS RO capability. GFZ provided the IGOR and is responsible for the related TOR experiment (Tracking, Occultation and Ranging). TerraSAR-X provides continuously atmospheric GPS data in near-real time. These data from GFZ are continuously assimilated in parallel with those from GRACE-A by the world-leading weather centers to improve their global forecasts. TerraSAR-X, together with TanDEM-X also forms a twin-satellite constellation for atmosphere sounding and generates an unique data set for the evaluation of the accuracy of the GPS-RO technique.",
"homepage": "https://www.dlr.de/de/forschung-und-transfer/projekte-und-missionen/terrasar-x",
"name": "TerraSAR-X TOR",
"prefix": "r3d100011117",
"synonyms": [
"TSX Tracking Occultation and Ranging"
]
},
"r3d100011118": {
"description": "<<>>!!!>>>",
"homepage": "http://isdc-old.gfz-potsdam.de/index.php?module=pagesetter&func=viewpub&tid=1&pid=21#tandemX",
"name": "TanDEM-X ISDC",
"prefix": "r3d100011118"
},
"r3d100011119": {
"description": "ScholarsArchive@OSU is Oregon State University's digital service for gathering, indexing, making available and storing the scholarly work of the Oregon State University community. It also includes materials from outside the institution in support of the university's land, sun, sea and space grant missions and other research interests.",
"homepage": "https://ir.library.oregonstate.edu",
"name": "ScholarsArchive@OSU",
"prefix": "r3d100011119"
},
"r3d100011121": {
"description": "cIRcle is an open access digital repository for published and unpublished material created by the UBC community and its partners. In BIRS there are thousands of mathematics videos, which are primary research data. Our repository is the largest source of mathematics data with more than 10TB of primary research by the best mathematicians in the world, coming from more than 600 institutions.",
"homepage": "https://circle.ubc.ca/",
"name": "cIRcle",
"prefix": "r3d100011121",
"synonyms": [
"BIRS",
"Banff International Research Station for Mathematical Innovation and Discovery"
]
},
"r3d100011122": {
"description": "<<>>!!!>>>",
"homepage": "http://hustedt.awi.de/default.aspx#ViewID=Home",
"name": "Hustedt Diatom Collection Database",
"prefix": "r3d100011122",
"synonyms": [
"Friedrich Hustedt Diatom Study Centre Database",
"Hustedt Sammlungsdatenbank"
],
"xrefs": {
"fairsharing": "FAIRsharing.e8e24f"
}
},
"r3d100011123": {
"description": "GeoReM is a Max Planck Institute database for reference materials of geological and environmental interest, such as rock powders, synthetic and natural glasses as well as mineral, isotopic, biological, river water and seawater reference materials. GeoReM contains published analytical data and compilation values (major and trace element concentrations and mass fractions, radiogenic and stable isotope ratios). GeoReM contains all important metadata about the analytical values such as uncertainty, analytical method and laboratory. Sample information and references are also included. GeoReM complements the three earthchem databases: GEOROC, NAVDAT and PETDB.",
"homepage": "http://georem.mpch-mainz.gwdg.de/",
"name": "GeoReM",
"prefix": "r3d100011123",
"synonyms": [
"Geological and Environmental Reference Materials"
],
"xrefs": {
"fairsharing": "FAIRsharing.219aec"
}
},
"r3d100011124": {
"description": "mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. The aggregated data forms an interactome which includes many organisms. mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions. Protein interaction databases archive protein-protein interaction (PPI) information from published articles. However, no database alone has sufficient literature coverage to offer a complete resource to investigate \"the interactome\".\nmentha's approach generates every week a consistent interactome (graph). Most importantly, the procedure assigns to each interaction a reliability score that takes into account all the supporting evidence. mentha offers eight interactomes (Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli K12, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae) plus a global network that comprises every organism, including those not mentioned. The website and the graphical application are designed to make the data stored in mentha accessible and analysable to all users. Source databases are: MINT, IntAct, DIP, MatrixDB and BioGRID.",
"homepage": "https://mentha.uniroma2.it/",
"name": "mentha",
"prefix": "r3d100011124",
"synonyms": [
"the interactome browser"
],
"xrefs": {
"fairsharing": "FAIRsharing.j1eyq2",
"omics": "05022",
"scr": "016148"
}
},
"r3d100011125": {
"description": "<<>>!!!>>>",
"homepage": "https://www.science3d.org/",
"name": "Science3D",
"prefix": "r3d100011125",
"synonyms": [
"Open Access tomography database",
"Science 3D"
]
},
"r3d100011126": {
"description": "The National Resource for Advancing Digitization of Biodiversity Collections (ADBC) funded by the National Science Foundation. Through ADBC, data and images for millions of biological specimens are being made available in electronic format for the research community, government agencies, students, educators, and the general public",
"homepage": "https://www.idigbio.org/",
"name": "Integrated Digitized Biocollections",
"prefix": "r3d100011126",
"synonyms": [
"iDigBio"
],
"xrefs": {
"fairsharing": "FAIRsharing.d21jc4",
"scr": "014336"
}
},
"r3d100011128": {
"description": "The National Vegetation Survey (NVS) Databank is a physical archive and electronic databank containing records of over 121,000 vegetation survey plots - including data from over 25,000 permanent plots in New Zealand. The data can be explored online and requested for download. The NVS Databank provides data spanning more than 60 years of indigenous and exotic plant plot records from throughout New Zealand's terrestrial ecosystems. The physical archive includes plot sheets, maps, and photographs from many years of vegetation surveys. Purpose-built software for entering, validating and summarising data is available. NVS is accorded the status of a Nationally Significant database and upkeep and maintenance is supported by Core funding for Crown Research Institutes from the NZ Ministry of Business, Innovation and Employment.",
"homepage": "https://nvs.landcareresearch.co.nz/",
"name": "National Vegetation Survey Databank",
"prefix": "r3d100011128",
"synonyms": [
"NVS",
"New Zealand National Vegetation Survey Databank"
],
"xrefs": {
"fairsharing": "FAIRsharing.LSUZRp"
}
},
"r3d100011129": {
"description": "<<>>!!!>>>",
"homepage": "https://nanomaterialregistry.net/Default.aspx",
"name": "Nanomaterial Registry",
"prefix": "r3d100011129",
"synonyms": [
"NanomaterialRegistry"
],
"xrefs": {
"fairsharing": "FAIRsharing.an0y9t",
"scr": "013793"
}
},
"r3d100011130": {
"description": "!!! <<< this record is no longer maintained, please use https://www.re3data.org/repository/r3d100011876 or https://www.re3data.org/repository/r3d100011647 >>> !!!: e!DAL stands for electronic Data Archive Library. It is a lightweight open source software software framework for publishing and sharing research data. e!DAL was developed based on experiences coming from decades of research data management and has grown towards being a general data archiving and publication infrastructure [https://doi.org/10.1186/1471-2105-15-214]. First research data repository is \"Plant Genomics and Phenomics Research Data Repository\" [https://doi.org/10.1093/database/baw033].",
"homepage": "https://edal.ipk-gatersleben.de/",
"name": "e!DAL - electronic Data Archive Library",
"prefix": "r3d100011130"
},
"r3d100011131": {
"description": "A national study on socioeconomics and family health over lifetimes and across generations funded by National Science Foundation (NSF). It is the longest running longitudinal household survey in the world, started in 1968 with a nationally representative sample of over 18,000 individuals living in 5,000 families in the United States. It is recognizing the importance of the socioeconomic data, available on this website without cost to researchers and analysts.",
"homepage": "https://psidonline.isr.umich.edu/",
"name": "Panel Study on Income Dynamics",
"prefix": "r3d100011131",
"synonyms": [
"PSID"
],
"xrefs": {
"fairsharing.legacy": "3031",
"nlx": "152067",
"scr": "008976"
}
},
"r3d100011132": {
"description": "The Research Documentation Centre of the Centre for Social Sciences at the Hungarian Academy of Sciences provides information on and access to research conducted at the Centre. The metadata and many of the documents of the Research Documentation Centre (RDC) are available to all visitors. External researchers may ask for access to restricted collections",
"homepage": "https://openarchive.tk.mta.hu/",
"name": "Social Scientific Research Documentation Centre Repository",
"prefix": "r3d100011132",
"synonyms": [
"KDK",
"KutatΓ‘si DokumentΓ‘ciΓ³s KΓΆzpont",
"RDC Repository"
]
},
"r3d100011135": {
"description": "IPUMS is the world's largest accessible collection of individual-level data on population, and is a collaboration of over 100 national statistical agencies.",
"homepage": "https://international.ipums.org/international/",
"name": "Integrated Public Use Microdata Series - International",
"prefix": "r3d100011135",
"synonyms": [
"IPUMS-I"
],
"xrefs": {
"fairsharing.legacy": "3267"
}
},
"r3d100011136": {
"description": "<<>>!!!>>>",
"homepage": "https://www.vecnet.org/",
"name": "VecNet",
"prefix": "r3d100011136",
"synonyms": [
"Vector-Borne Disease Network"
],
"xrefs": {
"omics": "22585"
}
},
"r3d100011137": {
"description": "The Open Science Framework (OSF) is part network of research materials, part version control system, and part collaboration software. The purpose of the software is to support the scientist's workflow and help increase the alignment between scientific values and scientific practices.\nDocument and archive studies. Move the organization and management of study materials from the desktop into the cloud. Labs can organize, share, and archive study materials among team members. Web-based project management reduces the likelihood of losing study materials due to computer malfunction, changing personnel, or just forgetting where you put the damn thing.\nShare and find materials. With a click, make study materials public so that other researchers can find, use and cite them. Find materials by other researchers to avoid reinventing something that already exists.\nDetail individual contribution. Assign citable, contributor credit to any research material - tools, analysis scripts, methods, measures, data.\nIncrease transparency. Make as much of the scientific workflow public as desired - as it is developed or after publication of reports. Find public projects here.\nRegistration. Registering materials can certify what was done in advance of data analysis, or confirm the exact state of the project at important points of the lifecycle such as manuscript submission or at the onset of data collection. Discover public registrations here.\nManage scientific workflow. A structured, flexible system can provide efficiency gain to workflow and clarity to project objectives, as pictured.",
"homepage": "https://osf.io/",
"name": "Open Science Framework",
"prefix": "r3d100011137",
"synonyms": [
"OSF"
],
"xrefs": {
"fairsharing": "FAIRsharing.g4z879",
"nlx": "157292",
"scr": "003238"
}
},
"r3d100011138": {
"description": "NWS/NCEP/Climate Prediction Center delivers climate prediction, monitoring, and diagnostic products for timescales from weeks to years to the Nation and the global community for the protection of life and property and the enhancement of the economy. The goal of the CPC website is to provide easy and comprehensive access to data and products that serve our mission. We serve a broad audience ranging from government to non-government entities like academia, NGOΓ’ΒΒs, and the public and private sectors. Specific sectors include agriculture, energy, health, transportation, emergency managers, etc.",
"homepage": "https://www.cpc.ncep.noaa.gov/",
"name": "National Weather Service, Climate Prediction Center",
"prefix": "r3d100011138",
"synonyms": [
"NWS, CPC"
]
},
"r3d100011139": {
"description": "NIST Data Gateway - provides easy access to many of the NIST scientific and technical databases. These databases cover a broad range of substances and properties from many different scientific disciplines. The Gateway includes links to free online NIST data systems as well as to information on NIST PC databases available for purchase.",
"homepage": "https://www.nist.gov/srd",
"name": "NIST Standard Reference Data",
"prefix": "r3d100011139",
"synonyms": [
"NIST Data Gateway",
"SRD"
],
"xrefs": {
"nlx": "144072",
"scr": "006452"
}
},
"r3d100011140": {
"description": "<<>>!!!>>>",
"homepage": "https://ccafs.cgiar.org/resources/tools/agtrials",
"name": "The Global Agricultural Trial Repository and Database",
"prefix": "r3d100011140",
"synonyms": [
"AgTrials"
],
"xrefs": {
"biodbcore": "001783"
}
},
"r3d100011141": {
"description": "China Meteorological Data Service Center, an upgraded system of the meteorological data sharing network, is an important component of the underlying national science and technology platform and a main portal application system of meteorological cloud. It is an authoritative and unified shared service platform for China Meteorological Administration to open its meteorological data resources to domestic and global users, and a data supporting platform for China to open its meteorological service market and promote the sharing and efficient application of meteorological information resources as a new meteorological service system.\nThe comprehensive meteorological database provide online and offline shared services, the existing data types including global upper-air sounding data, surface observations, ocean observations, numerical forecast products, agro-meteorological data of ground observation data encryption, aircraft soundings, numerical weather prediction analysis field data, GPS-Met, Storm 2 No, GOES-9 satellite data, soil moisture, aircraft reported sandstorm monitoring, TOVS, ATOVS, wind profilers, satellite detection information.",
"homepage": "http://data.cma.cn/en",
"name": "China Meteorological Data Service Center",
"prefix": "r3d100011141",
"synonyms": [
"CMDC",
"China Meteorological Data Sharing System"
]
},
"r3d100011147": {
"description": "The Forest Service Research Data Archive is an actively curated repository for the long-term preservation and distribution of citable research data sets that are broadly relevant to forest and grassland ecology, and the economic and social interactions of humans with these ecosystems. Most data sets were created by U.S. Forest Service scientists or by scientists funded through the U.S. Forest Service or the U.S. Joint Fire Science Program.",
"homepage": "https://www.fs.usda.gov/rds/archive/",
"name": "Forest Service Research Data Archive",
"prefix": "r3d100011147",
"synonyms": [
"FSRDA"
],
"xrefs": {
"fairsharing": "FAIRsharing.NzKTvN"
}
},
"r3d100011148": {
"description": "Plants of TAIWAN includes digitized plant specimens and historical botanical literature of Taiwan, and a database of plant names and information for about 5000 species in Taiwan.",
"homepage": "https://tai2.ntu.edu.tw/",
"name": "Plants of TAIWAN",
"prefix": "r3d100011148",
"synonyms": [
"ε°η£ζ€η©θ³θ¨ζ΄εζ₯θ©’η³»η΅±"
]
},
"r3d100011149": {
"description": "Chinese Crop Germplasm Resources Information System provides germplasm resources and genetic information for crops including grains, fruits, vegetables, oilseeds, and fibers. The data includes crop fingerprint and DNA sequence data.",
"homepage": "https://www.cgris.net/cgris_english.html",
"name": "Chinese Crop Germplasm Resources Information System",
"prefix": "r3d100011149",
"synonyms": [
"CGRIS"
]
},
"r3d100011150": {
"description": "DARECLIMED data repository consists of three kind of data: (a) climate, (b) water resources, and (c) energy related data. The first part, climate datasets, will include atmospheric and indirect atmospheric data, proxies and reconstructions, terrestrial and oceanic data. Land use, population, economy and development data will be added as well. Datasets can be handled and analyzed by connecting to the Live Access Server (LAS), which enables to visualize data with on-the-fly graphics, request custom subsets of variables in a choice of file formats, access background reference material about the data (metadata), and compare (difference) variables from distributed locations. Access to server is granted upon request by emailing the data repository manager.",
"homepage": "https://www.cyi.ac.cy/index.php/dareclimed-data-repository.html",
"name": "DARECLIMED",
"prefix": "r3d100011150",
"synonyms": [
"Cyprus Institute Data Repository",
"Data Repositories and Computational infrastructure for environmental and Climate studies in eastern MEDiterranean"
]
},
"r3d100011153": {
"description": "The national data provide the monthly, quarterly and annual, census regions, departments and international social and economic statistic data. It Offers a variety of file output, watchmaking, drawing, Indicators, visualization charts and geographic information data.\nTo speed up the construction of modern service-oriented statistics, and to better serve the community, on the basis of \"China Statistical Database\" created in 2008, the National Bureau of Statistics(NBS) established a new statistical database in 2013.",
"homepage": "https://data.stats.gov.cn/english/",
"name": "National Data",
"prefix": "r3d100011153",
"synonyms": [
"China Statistical Database",
"ε½εΆζ°ζ"
]
},
"r3d100011154": {
"description": "China Earthquake Data Center provides Seismic data, geomagnetic data, geoelectric data, terrain data and underground fluid change data. It is only open in the Seismological Bureau.",
"homepage": "https://data.earthquake.cn/index.html",
"name": "China Earthquake Data Center",
"prefix": "r3d100011154",
"synonyms": [
"formerly: World Data Center for Seismology, Beijing",
"δΈε½ε°ιζ°ζδΈεΏ"
]
},
"r3d100011157": {
"description": "Datatang is a professional data pre-processing company. We are engaged in data collecting, annotating, and customizing to meet our clientsβ various needs. We assist our clients from university research labs and company R&D departments to waive trivial yet necessary data processing procedure and make their approach to the highest-value data in a more efficient way.",
"homepage": "https://www.datatang.ai/",
"name": "Datatang",
"prefix": "r3d100011157",
"synonyms": [
"ζ°ζε "
]
},
"r3d100011158": {
"description": "The National Earth System Science Data Sharing Service Platform is one of the 23 national science and technology infrastructure platforms identified by the Ministry of Science and Technology and the Ministry of Finance as the first batch of platforms. The platform is led by the Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences. Since its construction in 2003, more than 40 domestic and overseas units have participated in the platform construction. National Earth System Science Data Sharing Service Platform main development course:\nThe overall goal of the platform is to integrate and integrate the data resources generated by data center groups, universities, research institutes and scientists in China and abroad, to import international data resources and to receive the data resources generated by major national scientific research projects. Based on this, Processing data products. We will improve standards and operational mechanisms and provide data support for Earth system science research and sustainable socio-economic development through the Earth System Scientific Data Sharing Network Platform and professional service teams. The recent consolidation of data resources required to share the research on land surface systems and human-land relations.",
"homepage": "http://www.geodata.cn/",
"name": "Data Sharing Infrastructure of Earth System Science",
"prefix": "r3d100011158",
"synonyms": [
"ε½εΆε°ηη³»η»η§ε¦ζ°ζε
±δΊ«ζε‘εΉ³ε°"
]
},
"r3d100011159": {
"description": "The Earth System Grid Federation (ESGF) is an international collaboration with a current focus on serving the World Climate Research Programme's (WCRP) Coupled Model Intercomparison Project (CMIP) and supporting climate and environmental science in general.\nData is searchable and available for download at the Federated ESGF-CoG Nodes https://esgf.llnl.gov/nodes.html",
"homepage": "https://esgf.llnl.gov/index.html",
"name": "Earth System Grid Federation",
"prefix": "r3d100011159",
"synonyms": [
"ESGF"
]
},
"r3d100011164": {
"description": "The Australian New Zealand Clinical Trials Registry (ANZCTR) is an online register of clinical trials being undertaken in Australia, New Zealand and elsewhere. The ANZCTR includes trials from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies.",
"homepage": "http://www.anzctr.org.au/",
"name": "Australian New Zealand Clinical Trials Registry",
"prefix": "r3d100011164",
"synonyms": [
"ANZCTR"
],
"xrefs": {
"biodbcore": "001430",
"fairsharing": "FAIRsharing.7f07dd"
}
},
"r3d100011165": {
"description": "The Basis Set Exchange (BSE) provides a web-based user interface for downloading and uploading Gaussian-type (GTO) basis sets, including effective core potentials (ECPs), from the EMSL Basis Set Library. It provides an improved user interface and capabilities over its predecessor, the EMSL Basis Set Order Form, for exploring the contents of the EMSL Basis Set Library. The popular Basis Set Order Form and underlying Basis Set Library were originally developed by Dr. David Feller and have been available from the EMSL webpages since 1994.",
"homepage": "https://www.basissetexchange.org/",
"name": "Basis Set Exchange",
"prefix": "r3d100011165",
"synonyms": [
"BSE",
"EMSL Basis Set Exchange"
]
},
"r3d100011166": {
"description": "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate QM calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods.",
"homepage": "http://www.begdb.org/",
"name": "Benchmark Energy & Geometry Database",
"prefix": "r3d100011166",
"synonyms": [
"BEGDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.nbe4fq"
}
},
"r3d100011169": {
"description": "The program \"Humanist Virtual Libraries\" distributes heritage documents and pursues research associating skills in human sciences and computer science. It aggregates several types of digital documents:\nA selection of facsimiles of Renaissance works digitized in the Central Region and in partner institutions, the Epistemon Textual Database, which offers digital editions in XML-TEI, and Transcripts or analyzes of notarial minutes and manuscripts",
"homepage": "https://www.bvh.univ-tours.fr/",
"name": "Bibliothèques Virtuelles Humanistes",
"prefix": "r3d100011169",
"synonyms": [
"BVH",
"Humanistic Virtual Libraries"
]
},
"r3d100011170": {
"description": "This site offers an enormous collection of photographs of wild species and natural history objects. It covers most groups of organisms with the exception of birds and other vertebrates. The photographs are presented to illustrate biodiversity and as an aid to identification. The criterion for inclusion of a species is that it must have been, or might be expected to be, found in Britain or Ireland. BioImages follows the biological classification. Biota is a hierarchical system with species grouped in genera, genera in families, families in orders and so on up to kingdoms and superkingdoms. The datasets are linked to bioinfo: food webs and species interactions in the Biodiversity of UK and Ireland.",
"homepage": "https://www.bioimages.org.uk/",
"name": "BioImages - Virtual Field-Guide",
"prefix": "r3d100011170",
"synonyms": [
"Virtual Field-Guide to UK Biodiversity"
]
},
"r3d100011172": {
"description": "Lab Notes Online presents historic scientific data from the Caltech Archives' collections in digital facsimile. Beginning in the fall of 2008, the first publication in the series is Robert A. Millikan's notebooks for his oil drop experiments to measure the charge of the electron, dating from October 1911 to April 1912. Other laboratory, field, or research notes will be added to the archive over time.",
"homepage": "https://caltechln.library.caltech.edu/",
"name": "CaltechLabNotes",
"prefix": "r3d100011172",
"synonyms": [
"California Institute of Technology LabNotes",
"California Institute of Technology, Collection of Open Digital Archives",
"CaltechCODA"
]
},
"r3d100011173": {
"description": "The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes.\nThe Data Coordinating Center (DCC) is the central provider of TCGA data. The DCC standardizes data formats and validates submitted data.",
"homepage": "https://cancergenome.nih.gov/",
"name": "Cancer GenomeAtlas Data Portal",
"prefix": "r3d100011173",
"synonyms": [
"Cancer Genome Atlas Data Portal",
"TCGA Data Portal"
],
"xrefs": {
"fairsharing": "FAIRsharing.m8wewa",
"nlx": "156913",
"scr": "003193"
}
},
"r3d100011174": {
"description": ">>>>!!!!<<<< The Cancer Genomics Hub mission is now completed.\n\nThe Cancer Genomics Hub was established in August 2011 to provide a repository to The Cancer Genome Atlas, the childhood cancer initiative Therapeutically Applicable Research to Generate Effective Treatments and the Cancer Genome Characterization Initiative.\n\nCGHub rapidly grew to be the largest database of cancer genomes in the world, storing more than 2.5 petabytes of data and serving downloads of nearly 3 petabytes per month.\n\nAs the central repository for the foundational genome files, CGHub streamlined team science efforts as data became as easy to obtain as downloading from a hard drive.\n\nThe convenient access to Big Data, and the collaborations that CGHub made possible, are now essential to cancer research. That work continues at the NCI's Genomic Data Commons. All files previously stored at CGHub can be found there.\nThe Website for the Genomic Data Commons is here: https://gdc.nci.nih.gov/ >>>>!!!!<<<<\nThe Cancer Genomics Hub (CGHub) is a secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects.\nAccess to CGHub Data: All researchers using CGHub must meet the access and use criteria established by the National Institutes of Health (NIH) to ensure the privacy, security, and integrity of participant data. CGHub also hosts some publicly available data, in particular data from the Cancer Cell Line Encyclopedia. All metadata is publicly available and the catalog of metadata and associated BAMs can be explored using the CGHub Data Browser.",
"homepage": "https://cghub.ucsc.edu/",
"name": "Cancer Genomics Hub",
"prefix": "r3d100011174",
"synonyms": [
"CGHub"
],
"xrefs": {
"nlx": "156095",
"scr": "002657"
}
},
"r3d100011175": {
"description": "<<>>!!!>>>",
"homepage": "https://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?CCRIS",
"name": "Chemical Carcinogenesis Research Information System",
"prefix": "r3d100011175",
"synonyms": [
"CCRIS",
"a toxnet database"
],
"xrefs": {
"nif": "0000-21077",
"scr": "008178"
}
},
"r3d100011176": {
"description": "CURATOR (Chiba University's Repository for Access to Outcomes from Research) captures, preserves and makes publicly available intellectual digital materials from research activities on Chiba University campuses, including peer-reviewed articles, theses, preprints, statistical and experimental data, course materials and softwares. CURATOR is intended to function as the portal for the outcomes from Chiba University's research activities. The University Library is responsible for building and operating CURATOR under the guidance of the Faculty Committee for Improved Scholarly Information Availability, which commissioned by the Library Board of Faculty Representatives to systematically promote and arrange disseminative activities by the University.",
"homepage": "https://opac.ll.chiba-u.jp/da/curator/?lang=1",
"name": "CURATOR",
"prefix": "r3d100011176",
"synonyms": [
"Chiba University Repository for Access To Outcomes from Research"
]
},
"r3d100011177": {
"description": "The Claremont Colleges Digital Library (CCDL) provides access to digitized and born-digital historical and visual resources collections created both by and for The Claremont Colleges community.",
"homepage": "https://ccdl.claremont.edu/digital/",
"name": "Claremont Colleges Digital Library",
"prefix": "r3d100011177",
"synonyms": [
"CCDL"
],
"xrefs": {
"biodbcore": "001515"
}
},
"r3d100011181": {
"description": "Digital Case is Case Western Reserve University's digital library, institutional repository and digital archive. Digital Case stores, disseminates, and preserves the intellectual output of Case faculty, departments and research centers in digital formats (both \"born digital\" items as well as materials of historical interest that have been digitized). Kelvin Smith Library manages Digital Case on behalf of the university. With Digital Case, KSL assumes an active role in the scholarly communication process, providing expertise in the form of a set of services (metadata creation, secure environment, preservation over time) for access and distribution of the universityβs collective intellectual product.",
"homepage": "https://digital.case.edu/",
"name": "Digital Case",
"prefix": "r3d100011181"
},
"r3d100011182": {
"description": "The UA Campus Repository is an institutional repository that facilitates access to the research, creative works, publications and teaching materials of the University by collecting, sharing and archiving content selected and deposited by faculty, researchers, staff and affiliated contributors.",
"homepage": "https://repository.arizona.edu/arizona/",
"name": "UA Campus Repository",
"prefix": "r3d100011182",
"synonyms": [
"University of Arizona Campus Repository"
]
},
"r3d100011183": {
"description": "Digital documents and collections hosted by the University Library - both freely available on the internet and access-restricted - can be found here.",
"homepage": "https://sammlungen.ub.uni-frankfurt.de/",
"name": "Digitale Sammlungen, Goethe-UniversitΓ€t Frankfurt am Main",
"prefix": "r3d100011183"
},
"r3d100011188": {
"description": "The Digital South Asia Library provides digital materials for reference and research on South Asia to scholars, public officials, business leaders, and other users. This program builds upon a two-year pilot project funded by the Association of Research Libraries' Global Resources Program with support from the Andrew W. Mellon Foundation.",
"homepage": "https://dsal.uchicago.edu/",
"name": "Digital South Asia Library",
"prefix": "r3d100011188",
"synonyms": [
"DSAL"
]
},
"r3d100011189": {
"description": "PRISM is a digital archive of the University of Calgary's intellectual output. Established and maintained by Libraries and Cultural Resources to manage, preserve and make available the academic works of faculty, students and research groups. The collection includes faculty publications, masters and doctoral theses, and research output from across Southern Alberta. PRISM is updated regularly, with new works added daily.",
"homepage": "https://prism.ucalgary.ca/",
"name": "PRISM: University of Calgary's Digital Repository",
"prefix": "r3d100011189",
"xrefs": {
"opendoar": "7771"
}
},
"r3d100011191": {
"description": "Earth-Prints is an open archive created and maintained by Istituto Nazionale di Geofisica e Vulcanologia. This digital collection allows users to browse, search and access manuscripts, journal articles, theses, conference materials, books, book-chapters, web products.\nThe goal of our repository is to collect, capture, disseminate and preserve the results of research in the fields of Atmosphere, Cryosphere, Hydrosphere and Solid Earth. Earth-prints is young and growing rapidly.",
"homepage": "https://www.earth-prints.org/",
"name": "Earth-prints Repository",
"prefix": "r3d100011191"
},
"r3d100011192": {
"description": "MGnify (formerly: EBI Metagenomics) offers an automated pipeline for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.",
"homepage": "https://www.ebi.ac.uk/metagenomics",
"name": "MGnify",
"prefix": "r3d100011192",
"synonyms": [
"formerly: EBI Metagenomics"
],
"xrefs": {
"fairsharing": "FAIRsharing.dxj07r"
}
},
"r3d100011193": {
"description": "The Digital Collections repository is a service that provides free and open access to the scholarship and creative works produced and owned by the Texas State University community. The Wittliff Collections, located on the seventh floor of the Albert B. Alkek Library at Texas State University, was founded by William D. Wittliff in 1987. The Wittliff Collections include 2 collections. 1. The Southwestern Writers Collection: These Collection holds the papers of numerous 20th century writers and the Southwestern & Mexican Photography Collection. The film holdings contain over 500 film and television screenplays as well as complete production archives for several popular films, including the television miniseries Lonesome Dove. The music holdings represent the breadth and scope of popular Texas sounds. 2. Mexican Photography Collection: The Southwestern & Mexican Photography Collection assembles a broad range of photographic work from the Southwestern United States and Mexico, from the 19th-century to the present day.",
"homepage": "https://dc.library.txstate.edu/",
"name": "Wittliff Collections - Digital Collections",
"prefix": "r3d100011193"
},
"r3d100011195": {
"description": "This site provides access to complete, annotated genomes from bacteria and archaea (present in the European Nucleotide Archive) through the Ensembl graphical user interface (genome browser). Ensembl Bacteria contains genomes from annotated INSDC records that are loaded into Ensembl multi-species databases, using the INSDC annotation import pipeline.",
"homepage": "https://bacteria.ensembl.org/index.html",
"name": "Ensembl Bacteria",
"prefix": "r3d100011195",
"synonyms": [
"e!EnsemblBacteria"
],
"xrefs": {
"fairsharing": "FAIRsharing.zsgmvd",
"miriam": "00000202",
"nif": "0000-33711",
"scr": "008679"
}
},
"r3d100011196": {
"description": "EnsemblFungi is a genome-centric portal for fungal species. It is a project to maintain annotation on selected genomes.",
"homepage": "http://fungi.ensembl.org/index.html",
"name": "Ensembl Fungi",
"prefix": "r3d100011196",
"synonyms": [
"e!EnsemblFungi"
],
"xrefs": {
"fairsharing": "FAIRsharing.bg5xqs",
"miriam": "00000206",
"nif": "0000-33718",
"scr": "008681"
}
},
"r3d100011197": {
"description": "The Ensembl genome annotation system, developed jointly by the EBI and the Wellcome Trust Sanger Institute, has been used for the annotation, analysis and display of vertebrate genomes since 2000.\nSince 2009, the Ensembl site has been complemented by the creation of five new sites, for bacteria, protists, fungi, plants and invertebrate metazoa, enabling users to use a single collection of (interactive and programatic) interfaces for accessing and comparing genome-scale data from species of scientific interest from across the taxonomy.\nIn each domain, we aim to bring the integrative power of Ensembl tools for comparative analysis, data mining and visualisation across genomes of scientific interest, working in collaboration with scientific communities to improve and deepen genome annotation and interpretation.",
"homepage": "https://ensemblgenomes.org/",
"name": "Ensembl Genomes",
"prefix": "r3d100011197",
"synonyms": [
"e!EnsemblGenomes"
],
"xrefs": {
"fairsharing": "FAIRsharing.923a0p",
"nlx": "65207",
"omics": "01648",
"scr": "006773"
}
},
"r3d100011198": {
"description": "Ensembl Metazoa is a genome-centric portal for metazoan species of scientific interest.",
"homepage": "https://metazoa.ensembl.org/index.html",
"name": "Ensembl Metazoa",
"prefix": "r3d100011198",
"synonyms": [
"e!EnsemblMetazoa"
],
"xrefs": {
"fairsharing": "FAIRsharing.c23cqq",
"miriam": "00000204",
"nif": "0000-33714",
"scr": "000800"
}
},
"r3d100011199": {
"description": "EnsemblPlants is a genome-centric portal for plant species. Ensembl Plants is developed in coordination with other plant genomics and bioinformatics groups via the EBI's role in the transPLANT consortium.",
"homepage": "http://plants.ensembl.org/index.html",
"name": "Ensembl Plants",
"prefix": "r3d100011199",
"synonyms": [
"e!EnsemblPlants"
],
"xrefs": {
"fairsharing": "FAIRsharing.j8g2cv",
"miriam": "00000205",
"nif": "0000-33715",
"scr": "008680"
}
},
"r3d100011200": {
"description": "EnsemblProtists is a genome-centric portal for protists species.",
"homepage": "http://protists.ensembl.org/index.html",
"name": "Ensembl Protists",
"prefix": "r3d100011200",
"synonyms": [
"e!EnsemblProtists"
],
"xrefs": {
"fairsharing": "FAIRsharing.ad1zae",
"nif": "0000-33712",
"scr": "013154"
}
},
"r3d100011201": {
"description": "Online storage, sharing and registration of research data, during the research period and after its completion. DataverseNL is a shared service provided by participating institutions and DANS.",
"homepage": "https://dataverse.nl/",
"name": "DataverseNL",
"prefix": "r3d100011201",
"xrefs": {
"fairsharing": "FAIRsharing.denvnv"
}
},
"r3d100011202": {
"description": "Open Research Exeter (ORE) is the University of Exeter's repository for all types of research, including research papers, research data and theses. Research in ORE can be viewed and downloaded freely by anyone, anywhere: researchers, students, industry, business and the wider public.\nORE's content includes journal articles, conference papers, working papers, reports, book chapters, videos, audio, images, multimedia research project outputs, raw data and analysed data. ORE's content is securely stored, managed and preserved to ensure free, permanent access.",
"homepage": "https://ore.exeter.ac.uk/repository/",
"name": "Open Research Exeter",
"prefix": "r3d100011202",
"synonyms": [
"ORE"
],
"xrefs": {
"opendoar": "956"
}
},
"r3d100011203": {
"description": "Flytrap is an interactive database for displaying gene expression patterns, in particular P[GAL4] patterns, via an intuitive WWW based interface. This development consists of two components, the first being the html interface to the database and the second, a tool-kit for constructing and maintaining the database.",
"homepage": "https://www.fly-trap.org/",
"name": "Flytrap",
"prefix": "r3d100011203",
"xrefs": {
"nif": "0000-00051",
"scr": "003075"
}
},
"r3d100011206": {
"description": "The database GEOROC (Geochemistry of Rocks of the Oceans and Continents) is a comprehensive collection of published analyses of igneous and metamorphic rocks and minerals. It contains major and trace element concentrations, radiogenic and nonradiogenic isotope ratios as well as analytical ages for whole rocks, glasses, minerals and inclusions. Metadata include geospatial and other sample information, analytical details and references. The database was established by the Max Plank Institute for Chemistry, Mainz. It is now maintained by the Digital Geochemical Data Infrastructure (DIGIS) project at GΓΆttingen University.",
"homepage": "https://georoc.eu/georoc/new-start.asp",
"name": "GEOROC",
"prefix": "r3d100011206",
"synonyms": [
"Geochemie der Gesteine von Ozeanen und Kontinenten",
"Geochemistry of Rocks of the Oceans and Continents"
],
"xrefs": {
"fairsharing.legacy": "3164"
}
},
"r3d100011207": {
"description": "GloPAD is a multimedia, multilingual, web-accessible database containing digital images, texts, video clips, sound recordings, and complex media objects (such as 3-D images) related to the performing arts from around the world. \nGloPAD (Global Performing Arts Database) records include authoritative, detailed, multilingual descriptions of digital images, texts, video clips, sound recordings, and complex media objects related to the performing arts around the world, plus information about related pieces, productions, performers, and creators.\nGloPAC is an international organization of institutions and individuals committed to using innovative digital technologies to create easily accessible, multimedia, and multilingual information resources for the study and preservation of the performing arts.",
"homepage": "http://www.glopad.org/pi/en/",
"name": "GloPAD",
"prefix": "r3d100011207",
"synonyms": [
"Datenbank der globalen darstellenden KΓΌnste",
"Global Performing Arts Database"
]
},
"r3d100011208": {
"description": "<<>>!!!>>>",
"homepage": "https://web.archive.org/web/20170206082130/http://hardinmd.lib.uiowa.edu/",
"name": "Hardin.MD",
"prefix": "r3d100011208",
"synonyms": [
"Hardin MD",
"Hardin Mate Directory",
"Medical Picture Gallery"
],
"xrefs": {
"nif": "0000-21186",
"scr": "002364"
}
},
"r3d100011209": {
"description": "<<>>!!!>>>The information is accessible through PubChem:https://pubchem.ncbi.nlm.nih.gov/. Help for HSDB Users in PubChem PDF: https://www.nlm.nih.gov/toxnet/Accessing_HSDB_Content_from_PubChem.pdf Help for HSDB Users in PubChem Web Page: https://www.nlm.nih.gov/toxnet/Accessing_HSDB_Content_from_PubChem.html <<>>",
"homepage": "https://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?HSDB",
"name": "Hazardous Substance Data Bank",
"prefix": "r3d100011209",
"synonyms": [
"A TOXNET database",
"HSDB"
],
"xrefs": {
"nif": "0000-21201",
"scr": "002374"
}
},
"r3d100011210": {
"description": "<<>>!!!>>>",
"homepage": "http://www.hon.ch/HONmedia/",
"name": "HONmedia",
"prefix": "r3d100011210",
"synonyms": [
"Health On The Net Foundation",
"Health on the Net media"
]
},
"r3d100011213": {
"description": "Here you will find authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world.",
"homepage": "https://www.itis.gov/",
"name": "ITIS",
"prefix": "r3d100011213",
"synonyms": [
"Integrated Taxonomic Information System"
]
},
"r3d100011216": {
"description": "KU ScholarWorks is the digital repository of the University of Kansas. It contains scholarly work created by KU faculty, staff and students, as well as material from the University Archives. KU ScholarWorks makes important research and historical items available to a wider audience and helps assure their long-term preservation.",
"homepage": "https://kuscholarworks.ku.edu/",
"name": "KU ScholarWorks",
"prefix": "r3d100011216"
},
"r3d100011218": {
"description": "LSE Research Online is the institutional repository for the London School of Economics and Political Science. LSE Research Online contains research produced by LSE staff, including journal articles, book chapters, books, working papers, conference papers and more.",
"homepage": "https://eprints.lse.ac.uk/",
"name": "LSE Research Online",
"prefix": "r3d100011218",
"synonyms": [
"London School of Economics and Political Science Research Online"
]
},
"r3d100011219": {
"description": "The Metropolitan Travel Survey Archive (MTSA) includes travel surveys from numerous public agencies across the United States.\nThe Transportation Secure Data Center has archived these surveys to ensure their continued public availability. The survey data have been converted to a standard file format and cleansed to remove personally identifiable information, including any detailed spatial data regarding individual trips.",
"homepage": "https://www.nrel.gov/transportation/secure-transportation-data/tsdc-metropolitan-travel-survey-archive.html/",
"name": "Metropolitan Travel Survey Archive",
"prefix": "r3d100011219",
"synonyms": [
"MTSA"
]
},
"r3d100011220": {
"description": "MINDS@UW is designed to gather, distribute, and preserve digital materials related to the University of Wisconsin's research and instructional mission. Content, which is deposited directly by UW faculty and staff, may include research papers and reports, pre-prints and post-prints, datasets and other primary research materials, learning objects, theses, student projects, conference papers and presentations, and other born-digital or digitized research and instructional materials.",
"homepage": "https://minds.wisconsin.edu/",
"name": "MINDS@UW",
"prefix": "r3d100011220",
"synonyms": [
"Minds @ University of Wisconsin"
],
"xrefs": {
"opendoar": "214"
}
},
"r3d100011221": {
"description": "<<>>!!!>>>",
"homepage": "https://www.monash.edu/library/researchers/repository",
"name": "Monash University Research Repository",
"prefix": "r3d100011221",
"synonyms": [
"ARROW (formerly)"
]
},
"r3d100011222": {
"description": "MycoBank is an on-line database aimed as a service to the mycological and scientific society by documenting mycological nomenclatural novelties (new names and combinations) and associated data, for example descriptions and illustrations. The nomenclatural novelties will each be allocated a unique MycoBank number that can be cited in the publication where the nomenclatural novelty is introduced. These numbers will also be used by the nomenclatural database Index Fungorum, with which MycoBank is associated.",
"homepage": "https://www.mycobank.org/",
"name": "MycoBank",
"prefix": "r3d100011222",
"synonyms": [
"Fungal databases, nomenclature and species banks"
],
"xrefs": {
"fairsharing": "FAIRsharing.v8se8r",
"nlx": "91803",
"scr": "004950"
}
},
"r3d100011223": {
"description": "The National Trauma Data BankΒ (NTDB) is the largest aggregation of trauma registry data ever assembled. The goal of the NTDB is to inform the medical community, the public, and decision makers about a wide variety of issues that characterize the current state of care for injured persons. Registry data that is collected from the NTDB is compiled annually and disseminated in the forms of hospital benchmark reports, data quality reports, and research data sets. Research data sets that can be used by researchers. To gain access to NTDB data, researchers must submit requests through our online application process",
"homepage": "https://www.facs.org/quality-programs/trauma/quality/national-trauma-data-bank/",
"name": "National Trauma Data Bank",
"prefix": "r3d100011223",
"synonyms": [
"American College of Surgeons National Trauma Data Bank",
"NTDB"
]
},
"r3d100011226": {
"description": "Physical Reference Data compiles physical data and biblographic sources: Physical constants, atomic spectroscopy data, molecular spectroscopic data, X-Ray and Gamma-Ray data, nuclear physics data etc.",
"homepage": "https://www.nist.gov/pml/productsservices/physical-reference-data",
"name": "NIST Physical reference data",
"prefix": "r3d100011226",
"synonyms": [
"National Institute of Standards and Technology, Physical Measurement Laboratory",
"Physical reference data"
]
},
"r3d100011230": {
"description": "ORA (Oxford University Research Archive) is the institutional repository for the University of Oxford. ORA was established in 2007 as a permanent and secure online archive of research materials produced by members of the University of Oxford.\nORA aims to provide access to the full text of as much of Oxford's academic research as possible. This includes articles, conference papers, theses, research data, working papers, posters and more.\nMaking materials open access removes barriers that restrict access to research, allowing for free dissemination of full text content, available to anyone with Internet access. ORA promotes and encourages the sharing of the scholarly output produced by the members of the University of Oxford that have been published under open access conditions, whilst additionally supporting University compliance with research funder policy and assessment.",
"homepage": "https://ora.ox.ac.uk/",
"name": "Oxford University Research Archive",
"prefix": "r3d100011230",
"synonyms": [
"ORA"
],
"xrefs": {
"fairsharing": "FAIRsharing.rkwr6y"
}
},
"r3d100011232": {
"description": "<<>>!!!>>> PANDIT is a collection of multiple sequence alignments and phylogenetic trees. It contains corresponding amino acid and nucleotide sequence alignments, with trees inferred from each alignment. PANDIT is based on the Pfam database (Protein families database of alignments and HMMs), and includes the seed amino acid alignments of most families in the Pfam-A database. DNA sequences for as many members of each family as possible are extracted from the EMBL Nucleotide Sequence Database and aligned according to the amino acid alignment. PANDIT also contains a further copy of the amino acid alignments, restricted to the sequences for which DNA sequences were found.",
"homepage": "https://www.ebi.ac.uk/research/goldman/software/pandit",
"name": "PANDIT",
"prefix": "r3d100011232",
"synonyms": [
"Protein and Associated Nucleotide Domains with Inferred Trees"
],
"xrefs": {
"nif": "0000-03241",
"scr": "003321"
}
},
"r3d100011234": {
"description": "These pages contain more than 150 clinical, intraoperative and radiologic images related to pediatric surgery. This \"virtual atlas\" is intended to help students, residents and fellows in their understanding of surgical conditions of the infant and child. These images can be used for personal (not commercial) use, but a reference to their origin would be appreciated. WARNING: Some of the clinical images are graphic in nature and may not be suitable for viewing by everyone.",
"homepage": "https://med.brown.edu/pedisurg/Brown/IBCategories.html",
"name": "Pediatric Surgery @ Brown",
"prefix": "r3d100011234",
"synonyms": [
"The Image Bank"
]
},
"r3d100011235": {
"description": "PetDB, the Petrological Database, is a web-based data management system that provides on-line access to geochemical and petrological data. PetDB is a global synthesis of chemical, isotopic, and mineralogical data for rocks, minerals, and melt inclusions. PetDB's current content focuses on data for igneous and metamorphic rocks from the ocean floor, specifically mid-ocean ridge basalts and abyssal peridotites and xenolith samples from the Earth's mantle and lower crust. PetDB is maintained and continuously updated as part of the EarthChem data collections.",
"homepage": "https://search.earthchem.org/",
"name": "PetDB",
"prefix": "r3d100011235",
"synonyms": [
"the petrological Database"
],
"xrefs": {
"nlx": "154723",
"scr": "002209"
}
},
"r3d100011236": {
"description": "PhysioBank is a large and growing archive of well-characterized digital recordings of physiologic signals and related data for use by the biomedical research community.",
"homepage": "https://archive.physionet.org/physiobank/physiobank-intro.shtml#records",
"name": "PhysioBank Archive",
"prefix": "r3d100011236",
"xrefs": {
"nlx": "48903",
"scr": "006949"
}
},
"r3d100011237": {
"description": "<<>>!!!<<< >>>!!!>>> publicdata.eu portal is superseded by European data portal https://www.re3data.org/repository/r3d100012199 >>>!!!<<<",
"homepage": "https://okfn.org/projects/lod2/",
"name": "Publicdata.eu",
"prefix": "r3d100011237",
"synonyms": [
"Europe's Public Data"
]
},
"r3d100011239": {
"description": "The RIT DML captures, distributes and preserves RIT's digital products. Here you can find articles, working papers, preprints, technical reports, conference papers and data sets in various digital formats.",
"homepage": "https://digitalarchive.rit.edu/xmlui/",
"name": "RIT Digital Media Library Repository",
"prefix": "r3d100011239",
"synonyms": [
"RIT DML",
"Rochester Institute of Technology's Digital Media Library"
],
"xrefs": {
"opendoar": "648",
"roar": "1126"
}
},
"r3d100011240": {
"description": "Science Photo Library (SPL) provides creative professionals with striking specialist imagery, unrivalled in quality, accuracy and depth of information. We have more than 600,000 images and 40,000 clips to choose from, with hundreds of new submissions uploaded to the website each week.",
"homepage": "https://www.sciencephoto.com/",
"name": "Science Photo Library",
"prefix": "r3d100011240",
"synonyms": [
"SPL"
]
},
"r3d100011241": {
"description": "The Catalogue of Life is the most comprehensive and authoritative global index of species currently available. It consists of a single integrated species checklist and taxonomic hierarchy. The Catalogue holds essential information on the names, relationships and distributions of over 1.8 million species. This figure continues to rise as information is compiled from diverse sources around the world.",
"homepage": "https://www.catalogueoflife.org/",
"name": "Catalogue of Life",
"prefix": "r3d100011241",
"xrefs": {
"fairsharing": "FAIRsharing.9b63c9",
"nlx": "153875",
"scr": "006701"
}
},
"r3d100011242": {
"description": "The European Genome-phenome Archive (EGA) is designed to be a repository for all types of sequence and genotype experiments, including case-control, population, and family studies. We will include SNP and CNV genotypes from array based methods and genotyping done with re-sequencing methods. \nThe EGA will serve as a permanent archive that will archive several levels of data including the raw data (which could, for example, be re-analysed in the future by other algorithms) as well as the genotype calls provided by the submitters. We are developing data mining and access tools for the database.\nFor controlled access data, the EGA will provide the necessary security required to control access, and maintain patient confidentiality, while providing access to those researchers and clinicians authorised to view the data. In all cases, data access decisions will be made by the appropriate data access-granting organisation (DAO) and not by the EGA. The DAO will normally be the same organisation that approved and monitored the initial study protocol or a designate of this approving organisation. The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).",
"homepage": "https://ega-archive.org/",
"name": "The European Genome-phenome Archive",
"prefix": "r3d100011242",
"synonyms": [
"EGA"
],
"xrefs": {
"fairsharing": "FAIRsharing.mya1ff",
"miriam": "00000512",
"nlx": "91316",
"scr": "004944"
}
},
"r3d100011243": {
"description": "Trove helps you find and use resources relating to Australia. Itβs more than a search engine. Trove brings together content from libraries, museums, archives and other research organisations and gives you tools to explore and build.",
"homepage": "https://trove.nla.gov.au/",
"name": "TROVE",
"prefix": "r3d100011243"
},
"r3d100011244": {
"description": "The UniProtKB Sequence/Annotation Version Archive (UniSave) has the mission of providing freely to the scientific community a repository containing every version of every Swiss-Prot/TrEMBL entry in the UniProt Knowledge Base (UniProtKB). This is achieved by archiving, every release, the entry versions within the current release. The primary usage of this service is to provide open access to all entry versions of all entries. In addition to viewing their content, one can also filter, download and compare versions.",
"homepage": "https://www.ebi.ac.uk/uniprot/unisave/app/#/",
"name": "UniSave",
"prefix": "r3d100011244",
"synonyms": [
"UniProtKB Sequence/Annotation Version Archive"
],
"xrefs": {
"nlx": "91568",
"scr": "004946"
}
},
"r3d100011245": {
"description": "ePrints Soton is the University's Research Repository. It contains journal articles, books, PhD theses, conference papers, data, reports, working papers, art exhibitions and more. Where possible, journal articles, conference proceedings and research data made open access.",
"homepage": "https://eprints.soton.ac.uk/",
"name": "University of Southampton Institutional Research Repository",
"prefix": "r3d100011245",
"synonyms": [
"ePrints Soton"
]
},
"r3d100011249": {
"description": "York Digital Library (YODL) is a University-wide Digital Library service for multimedia resources used in or created through teaching, research and study at the University of York. YODL complements the University's research publications, held in White Rose Research Online and PURE, and the digital teaching materials in the University's Yorkshare Virtual Learning Environment.\nYODL contains a range of collections, including images, past exam papers, masters dissertations and audio. Some of these are available only to members of the University of York, whilst other material is available to the public. YODL is expanding with more content being added all the time",
"homepage": "https://dlib.york.ac.uk/yodl/app/home/index",
"name": "York Digital Library",
"prefix": "r3d100011249",
"synonyms": [
"YODL"
]
},
"r3d100011250": {
"description": "Wellcome Images is one of the Wellcome Library's major visual collections and also forms part of Wellcome Collection. Wellcome Images is one of the world's richest and most unique collections, with themes ranging from medical and social history to contemporary healthcare and biomedical science. This unrivalled collection contains historical images from the Wellcome Library collections, Tibetan Buddhist paintings, ancient Sanskrit manuscripts written on palm leaves, beautifully illuminated Persian books and much more.",
"homepage": "https://wellcomecollection.org/collections",
"name": "Wellcome Collections - Images",
"prefix": "r3d100011250",
"synonyms": [
"formerly: Wellcome Images"
],
"xrefs": {
"nlx": "143611",
"scr": "004181"
}
},
"r3d100011251": {
"description": "AfricaRice is a leading pan-African rice research organization committed to improving livelihoods in Africa through strong science and effective partnerships. AfricaRice dataverse makes studies in rice research open availabe. With the focus on agronomy, breeding, entomoloy, grain quality, pathology, physiology and socio-economics of rice.",
"homepage": "https://dataverse.harvard.edu/dataverse/africarice",
"name": "AfricaRice Dataverse",
"prefix": "r3d100011251",
"synonyms": [
"Rice science at the service of Africa",
"la science rizicole au service de l'Afrique"
]
},
"r3d100011252": {
"description": "The AMIGA project (Analysis of the interstellar Medium of Isolated GAlaxies) involves the identification and study of a statistically significant sample of the most isolated galaxies in the local Universe. Our goal is to quantify the properties of different phases of the interstellar medium in these galaxies which are likely to be least affected by their external environment.",
"homepage": "https://amiga.iaa.csic.es/",
"name": "Analysis of the Interstellar Medium of Isolated Galaxies",
"prefix": "r3d100011252",
"synonyms": [
"AMIGA"
]
},
"r3d100011253": {
"description": "<<>>>!!!!>>>",
"homepage": "http://www.aspergillusgenome.org/",
"name": "AspGD",
"prefix": "r3d100011253",
"synonyms": [
"Aspergillus Genome Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.9k7at4",
"nif": "0000-02577",
"scr": "001880"
}
},
"r3d100011254": {
"description": "The Astronomy data repository at Harvard is currently open to all scientific data from astronomical institutions worldwide. Incorporating Astroinformatics of galaxies and quasars Dataverse. The Astronomy Dataverse is connected to the indexing services provided by the SAO/NASA Astrophysical Data Service (ADS).",
"homepage": "https://dataverse.harvard.edu/dataverse/cfa",
"name": "CfA Dataverses",
"prefix": "r3d100011254",
"synonyms": [
"The Astronomy Dataverse Network"
]
},
"r3d100011255": {
"description": "All observations obtained with the Parkes radio telescope are made available to the general community after an embargo period. Usually this embargo period is set to 18 months after the observation. The catalogue includes all published rotation-powered pulsars, including those detected only at high energies. It also includes Anomalous X-ray Pulsars (AXPs) and Soft Gamma-ray Repeaters (SGRs) for which coherent pulsations have been detected. However, it excludes accretion-powered pulsars such as Her X-1 and the recently discovered X-ray millisecond pulsars.\nATNF Pulsar catalogue contains information on all published pulsars, with complete bibliographic information. For professional astronomers, a more detailed \"Expert\" web interface is available allowing access to parameters of specialist interest. The catalogue can also be accessed using a command-line interface on unix or linux systems.",
"homepage": "https://www.atnf.csiro.au/research/pulsar/psrcat/",
"name": "ATNF Pulsar Catalogue",
"prefix": "r3d100011255",
"synonyms": [
"Psrcat"
]
},
"r3d100011256": {
"description": "ALSPAC is a longitudinal birth cohort study which enrolled pregnant women who were resident in one of three Bristol-based health districts in the former County of Avon with an expected delivery date between 1st April 1991 and 31st December 1992. Around 14,000 pregnant women were initially recruited. Detailed information has been collected on these women, their partners and subsequent children using self-completion questionnaires, data extraction from medical notes, linkage to routine information systems and from hands-on research clinics.\nAdditional cohorts of participants have since been enrolled in their own right including fathers, siblings, children of the children and grandparents of the children.\nEthical approval for the study was obtained from the ALSPAC Ethics and Law Committee (IRB00003312) and Local Research Ethics.",
"homepage": "https://www.bristol.ac.uk/alspac/",
"name": "Avon Longitudinal Study of Parents and Children",
"prefix": "r3d100011256",
"synonyms": [
"ALSPAC",
"Avon Longitudinal Study of Pregnancy and Childhood",
"Children of the 90s"
],
"xrefs": {
"nif": "0000-30224",
"scr": "007260"
}
},
"r3d100011257": {
"description": ">>>!!!>>>Bacterial (BCSDB) and Plant&Fungal (PFCSDB) carbohydrate structure databases have been merged into a single database, CSDB<<>>!!!<<< The NCI Cancer Models Database, caMOD, was retired on December 24, 2015. Information about many of the mouse models hosted in caMOD was obtained from the Jackson Laboratory Mouse Tumor Biology (MTB) Database and can be accessed through that resource http://tumor.informatics.jax.org/mtbwi/index.do . See caMOD Retirement Announcement https://wiki.nci.nih.gov/display/caMOD/caMOD+Retirement+Announcement >>>>!!<<< Query the Cancer Models database for models submitted by fellow researchers. Retrieve information about the making of models, their genetic description, histopathology, derived cell lines, associated images, carcinogenic agents, and therapeutic trials. Links to associated publications and other resources are provided.",
"homepage": "https://wiki.nci.nih.gov/display/caMOD/caMOD",
"name": "Cancer Models Database",
"prefix": "r3d100011264",
"synonyms": [
"caMOD"
]
},
"r3d100011266": {
"description": "The aim of CfA Library Datasets Dataverse is creating a better information system to respond to the changing needs of astronomers not only at the CfA, but worldwide as well. As part of this growing partnership with the ADS, the CfA Library is expanding its metadata and data curation services, and in the process, creating datasets that the astronomy community may find useful. The CfA Library Datasets Dataverse has been created to share these datasets with the greater community with the hope that some members may find it useful. Please remember to acknowledge the CfA Library and the ADS and cite the work using the \"Data Citation\" presented under each study's \"Cataloging Information\" section.",
"homepage": "https://dataverse.harvard.edu/dataverse/cfalibrary",
"name": "CfA Library Datasets Dataverse",
"prefix": "r3d100011266"
},
"r3d100011267": {
"description": "The CGIAR Research Program No. 6 (CRP6): Forests, Trees and Agroforestry: Livelihoods, Landscapes and Governance aims to enhance the management and use of forests, agroforestry and tree genetic resources across the landscape, from farms to forests.",
"homepage": "https://dataverse.harvard.edu/dataverse/crp6",
"name": "CGIAR Research Program on Forests, Trees and Agroforestry Dataverse",
"prefix": "r3d100011267",
"synonyms": [
"Harvard Dataverse Network"
]
},
"r3d100011268": {
"description": "CHILDES is the child language component of the TalkBank system. TalkBank is a system for sharing and studying conversational interactions.",
"homepage": "https://childes.talkbank.org/",
"name": "Child Language Data Exchange System",
"prefix": "r3d100011268",
"synonyms": [
"CHILDES"
],
"xrefs": {
"nif": "0000-00624",
"scr": "003241"
}
},
"r3d100011269": {
"description": "This website makes data available from the first round of data sharing projects that were supported by the CRCNS funding program. To enable concerted efforts in understanding the brain experimental data and other resources such as stimuli and analysis tools should be widely shared by researchers all over the world. To serve this purpose, this website provides a marketplace and discussion forum for sharing tools and data in neuroscience. To date we host experimental data sets of high quality that will be valuable for testing computational models of the brain and new analysis methods. The data include physiological recordings from sensory and memory systems, as well as eye movement data.",
"homepage": "https://crcns.org/",
"name": "Collaborative Research in Computational Neuroscience",
"prefix": "r3d100011269",
"synonyms": [
"CRCNS"
],
"xrefs": {
"nif": "0000-00255",
"scr": "005608"
}
},
"r3d100011270": {
"description": "This repository record is no longer valid.\n<<>>!!!>>>",
"homepage": "https://rda.ucar.edu/",
"name": "Computational and Information Systems Laboratory Research Data Archive",
"prefix": "r3d100011270",
"synonyms": [
"CISL RDA"
]
},
"r3d100011271": {
"description": "The COordinated Molecular Probe Line Extinction Thermal Emission Survey of Star Forming Regions (COMPLETE) provides a range of data complementary to the Spitzer Legacy Program \"From Molecular Cores to Planet Forming Disks\" (c2d) for the Perseus, Ophiuchus and Serpens regions. In combination with the Spitzer observations, COMPLETE will allow for detailed analysis and understanding of the physics of star formation on scales from 500 A.U. to 10 pc.",
"homepage": "https://dataverse.harvard.edu/dataverse/complete",
"name": "COMPLETE Dataverse",
"prefix": "r3d100011271",
"synonyms": [
"COordinated Molecular Probe Line Extinction Thermal Emission Survey of Star Forming Regions Dataverse"
]
},
"r3d100011272": {
"description": "CORUM is a manually curated dataset of mammalian protein complexes. Annotation of protein complexes includes protein complex composition and other valuable information such as method of purification, cellular function of complexes or involvement in diseases.",
"homepage": "https://mips.helmholtz-muenchen.de/corum/",
"name": "The Comprehensive Resource of Mammalian protein complexes",
"prefix": "r3d100011272",
"synonyms": [
"CORUM"
],
"xrefs": {
"nif": "0000-02688",
"omics": "01904",
"scr": "002254"
}
},
"r3d100011273": {
"description": "This database provides structural information on all of the Zeolite Framework Types that have been approved by the Structure Commission of the International Zeolite Association (IZA-SC).",
"homepage": "https://www.iza-structure.org/databases/",
"name": "Database of Zeolite Structures",
"prefix": "r3d100011273"
},
"r3d100011274": {
"description": "DRO is Deakin University's research repository, providing digital curation by describing and preserving the University's research output and enabling worldwide discovery.",
"homepage": "https://dro.deakin.edu.au/",
"name": "Deakin Research Online",
"prefix": "r3d100011274",
"synonyms": [
"DRO"
]
},
"r3d100011275": {
"description": "DEG hosts records of currently available essential genomic elements, such as protein-coding genes and non-coding RNAs, among bacteria, archaea and eukaryotes. Essential genes in a bacterium constitute a minimal genome, forming a set of functional modules, which play key roles in the emerging field, synthetic biology.",
"homepage": "http://origin.tubic.org/deg/public/index.php/browse/archaea",
"name": "DEG",
"prefix": "r3d100011275",
"synonyms": [
"Database of Essential Genes"
],
"xrefs": {
"nif": "0000-02745",
"omics": "08725",
"scr": "012929"
}
},
"r3d100011277": {
"description": "EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.",
"homepage": "https://ecocyc.org/",
"name": "EcoCyc Database",
"prefix": "r3d100011277",
"synonyms": [
"EcoCyc E. coli Database",
"Encyclopedia of E. coli Genes and Metabolism"
],
"xrefs": {
"fairsharing": "FAIRsharing.65dmtr",
"nif": "0000-02783",
"scr": "002433"
}
},
"r3d100011278": {
"description": "The English Lexicon Project (supported by the National Science Foundation) affords access to a large set of lexical characteristics, along with behavioral data from visual lexical decision and naming studies of 40,481 words and 40,481 nonwords.",
"homepage": "https://elexicon.wustl.edu/",
"name": "English Lexicon Project",
"prefix": "r3d100011278",
"synonyms": [
"ELP"
]
},
"r3d100011279": {
"description": "A European network of population-based registries for the epidemiologic surveillance of congenital anomalies.",
"homepage": "https://eu-rd-platform.jrc.ec.europa.eu/eurocat_en",
"name": "EUROCAT",
"prefix": "r3d100011279",
"synonyms": [
"European Surveillance of Congenital Anomalies"
]
},
"r3d100011280": {
"description": "FlowRepository is a web-based application accessible from a web browser that serves as an online database of flow cytometry experiments where users can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field. FlowRepository is funded by the International Society for Advancement of Cytometry (ISAC) and powered by the Cytobank engine specifically extended for the purposes of this repository. FlowRepository has been developed by forking and extending Cytobank in 2011.",
"homepage": "http://flowrepository.org/",
"name": "FlowRepository",
"prefix": "r3d100011280",
"xrefs": {
"fairsharing": "FAIRsharing.veg2d6",
"scr": "013779"
}
},
"r3d100011281": {
"description": "The centerpiece of the Global Trade Analysis Project is a global data base describing bilateral trade patterns, production, consumption and intermediate use of commodities and services. The GTAP Data Base consists of bilateral trade, transport, and protection matrices that link individual country/regional economic data bases. The regional data bases are derived from individual country input-output tables, from varying years.",
"homepage": "https://www.gtap.agecon.purdue.edu/databases/default.asp",
"name": "Global Trade Analysis Project",
"prefix": "r3d100011281",
"synonyms": [
"The GTAP Data Base"
]
},
"r3d100011282": {
"description": "THIN is a medical data collection scheme that collects anonymised patient data from its members through the healthcare software Vision. The UK Primary Care database contains longitudinal patient records for approximately 6% of the UK Population. The anonymised data collection, which goes back to 1994, is nationally representative of the UK population.",
"homepage": "https://www.the-health-improvement-network.com/",
"name": "The Health Improvement Network",
"prefix": "r3d100011282",
"synonyms": [
"THIN"
]
},
"r3d100011283": {
"description": "<<>>!!!>>>",
"homepage": "https://hydra.hull.ac.uk/resources?utf8=%E2%9C%93&search_field=all_fields&q=hmap",
"name": "History of Marine Animal Populations",
"prefix": "r3d100011283",
"synonyms": [
"HMAP Data Pages"
]
},
"r3d100011284": {
"description": "The Household, Income and Labour Dynamics in Australia (HILDA) Survey is a household-based panel study that collects valuable information about economic and personal well-being, labour market dynamics and family life.",
"homepage": "https://melbourneinstitute.unimelb.edu.au/hilda",
"name": "HILDA Survey",
"prefix": "r3d100011284",
"synonyms": [
"Household, Income and Labour Dynamics in Australia Survey"
]
},
"r3d100011285": {
"description": "The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education.",
"homepage": "https://hmdb.ca/",
"name": "Human Metabolome Database",
"prefix": "r3d100011285",
"synonyms": [
"HMDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.sye5js",
"nlx": "152721",
"scr": "013647"
}
},
"r3d100011286": {
"description": "HumanCyc provides an encyclopedic reference on human metabolic pathways. It provides a zoomable human metabolic map diagram, and it has been used to generate a steady-state quantitative model of human metabolism.\n2016: Subscriptions are now required to access HumanCyc. For more information on obtaining a subscription, click here: https://biocyc.org/subscription-faq.shtml.",
"homepage": "https://humancyc.org/",
"name": "HumanCyc",
"prefix": "r3d100011286",
"synonyms": [
"Encyclopedia of Human Genes and Metabolism"
],
"xrefs": {
"fairsharing": "FAIRsharing.zaa7w",
"nif": "0000-21206",
"omics": "02704",
"scr": "007050"
}
},
"r3d100011287": {
"description": "INTEGRALL is a web-based platform dedicated to compile information on integrons and designed to organize all the data available for these genetic structures. INTEGRALL provides a public genetic repository for sequence data and nomenclature and offers to scientists an easy and interactive access to integron's DNA sequences, their molecular arrangements as well as their genetic contexts.",
"homepage": "http://integrall.bio.ua.pt/",
"name": "INTEGRALL",
"prefix": "r3d100011287",
"synonyms": [
"The Integron Database"
]
},
"r3d100011288": {
"description": "ICES is an intergovernmental organization whose main objective is to increase the scientific knowledge of the marine environment and its living resources and to use this knowledge to provide unbiased, non-political advice to competent authorities.",
"homepage": "https://www.ices.dk/data/data-portals/Pages/default.aspx",
"name": "ICES data portal",
"prefix": "r3d100011288",
"synonyms": [
"International Council for the Exploration of the Sea dataset collections"
]
},
"r3d100011289": {
"description": "ISG' activities are on educational, research, and data distribution sides: principal purposes of ISG are the collection and distribution of geoid models, the collection and distribution of software for geoid computation, and the organization of technical schools on geoid determinations. ISG collects and disseminates worldwide local and regional geoid models estimated by geodetic Institutions and researchers of many countries. \nMore than 30 countries are represented, listed in alphabetic order or localized on a map",
"homepage": "https://www.isgeoid.polimi.it/",
"name": "International Service for the Geoid",
"prefix": "r3d100011289",
"synonyms": [
"IGeS",
"ISG",
"International Geoid Service"
]
},
"r3d100011290": {
"description": "The London Datastore is an initiative by the Greater London Authority (GLA) to release as much of the data that it holds as possible.",
"homepage": "https://data.london.gov.uk/",
"name": "London Datastore",
"prefix": "r3d100011290"
},
"r3d100011291": {
"description": "The Population Health Research Data Repository housed at MCHP is a comprehensive collection of administrative, registry, survey, and other data primarily relating to residents of Manitoba. It was developed to describe and explain patterns of health care and profiles of health and illness, facilitating inter-sectoral research in areas such as health care, education, and social services.",
"homepage": "http://mchp-appserv.cpe.umanitoba.ca/dataList.php",
"name": "Manitoba Population Research Data Repository",
"prefix": "r3d100011291",
"synonyms": [
"MCHP Data Repository",
"formerly: Population Health Research Data Repository"
]
},
"r3d100011293": {
"description": "The Medical Expenditure Panel Survey (MEPS) is a set of large-scale surveys of families and individuals, their medical providers, and employers across the United States. MEPS is the most complete source of data on the cost and use of health care and health insurance coverage.",
"homepage": "https://meps.ahrq.gov/mepsweb/",
"name": "Medical Expenditure Panel Survey",
"prefix": "r3d100011293",
"synonyms": [
"MEPS"
]
},
"r3d100011294": {
"description": "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. \nMetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.\nMetaCyc applications include: Online encyclopedia of metabolism, Prediction of metabolic pathways in sequenced genomes, Support metabolic engineering via enzyme database, Metabolite database aids. metabolomics research.",
"homepage": "https://metacyc.org/",
"name": "MetaCyc",
"prefix": "r3d100011294",
"synonyms": [
"Metabolic Pathway Database",
"a member of the BioCyc database collection"
],
"xrefs": {
"fairsharing": "FAIRsharing.yytevr",
"nif": "0000-03114",
"omics": "02718",
"scr": "007778"
}
},
"r3d100011295": {
"description": "In its 10-year tenure, NCED has made major contributions to the growth of Earth-Surface Dynamics (ESD) through direct research in three Integrated Programs (IP) of Streams, Watersheds and Deltas. These contributions include:\nEstablishment of experimental geomorphology and stratigraphy as a major source of insight in ESD, \nIntegration of quantitative methods from engineering, physics, and applied math into ESD,\nAdvances in the coupling of life, especially vegetation, and landscape dynamics,\nIntegration of a variety of novel methods from stochastic hydrology, including nonlocal transport and multifractal spatial signatures, into ESD,\nAdvances in providing the scientific basis for restoring streams, and\nIntegration of subsurface structure and stratigraphic records into understanding present-day delta dynamics.\nAll data created or compiled by NCED-funded scientists is archived here.",
"homepage": "https://repository.nced.umn.edu/",
"name": "National Center for Earth-Surface Dynamics Data Repository",
"prefix": "r3d100011295",
"synonyms": [
"NCED Data Repository"
],
"xrefs": {
"nlx": "154715",
"scr": "002195"
}
},
"r3d100011296": {
"description": "The Atomic Spectra Database (ASD) contains data for radiative transitions and energy levels in atoms and atomic ions. Data are included for observed transitions and energy levels of most of the known chemical elements. ASD contains data on spectral lines with wavelengths from about 0.2 Γ
(Γ₯ngstrΓΆms) to 60 m (meters). For many lines, ASD includes radiative transition probabilities. The energy level data include the ground states and ionization energies for all spectra. Except where noted, the data have been critically evaluated by NIST.\nFor most spectra, wavelengths, transition probabilities, relative intensities, and energy levels are integrated, so that all the available information for a given transition is incorporated under a single listing. For classified lines, in addition to the observed wavelength, ASD includes the Ritz wavelength, which is the wavelength derived from the energy levels. The Ritz wavelengths are usually more precise than the observed ones.\nLine lists containing classified lines can be ordered by either multiplet (for a given spectrum) or wavelength. For some spectra, ASD includes lists of prominent lines with wavelengths and relative intensities but without energy-level classifications.",
"homepage": "https://www.nist.gov/pml/atomic-spectra-database",
"name": "NIST Atomic Spectra Database",
"prefix": "r3d100011296",
"synonyms": [
"ASD",
"NIST Standard Reference Database 78",
"Spectral Data for the Chandra X-Ray Observatory (former database / discontinued)"
],
"xrefs": {
"fairsharing": "FAIRsharing.401958"
}
},
"r3d100011297": {
"description": "The TrΓΈndelag Health Study (The HUNT Study) is one of the largest health studies ever performed. It is a unique database of questionnaire data, clinical measurements and samples from a countyβs inhabitants from 1984 onwards.\nThe HUNT Study is well-known in the county of TrΓΈndelag, and its inhabitants have a generally positive attitude to participation and health research resulting from the study. HUNT has high participation rates, providing a good base for further health surveys in the county and an excellent research environment.\nToday, HUNT Research Centre has a database with information on 230,000 people. Approximately 300 national and international research projects are currently using the samples and data from HUNTs collection.",
"homepage": "https://hunt-db.medisin.ntnu.no/hunt-db/",
"name": "Nord-Trondelag Health Study",
"prefix": "r3d100011297",
"synonyms": [
"HUNT Databank",
"HUNT Study",
"Helseundersokelsen i Nord-Trondelag"
],
"xrefs": {
"nlx": "57833",
"scr": "010626"
}
},
"r3d100011298": {
"description": ">>> !!! the repository is offline !!! <<< \nMore information see: https://dknet.org/about/NURSA_Archive\nAll NURSA-biocurated transcriptomic datasets have been preserved for data mining in SPP through an enhanced and expanded version of Transcriptomine named Ominer. To access these datasets, dkNET provides users with the information of 527 transcriptomic datasets that contain data related to nuclear receptors and nuclear receptor coregulators in the NURSA Datasets table view and redirects users to the current SPP dataset page. Once users find the specific dataset of research interest, users can download the dataset by clicking DOI and then clicking the Download Dataset button at the Signaling Pathways Project webpage. See https://www.re3data.org/repository/r3d100013650",
"homepage": "http://www.nursa.org/nursa/index.jsf",
"name": "Nuclear Receptor Signaling Atlas",
"prefix": "r3d100011298",
"synonyms": [
"NURSA Hub"
],
"xrefs": {
"fairsharing": "FAIRsharing.vszknv",
"nif": "0000-03208",
"scr": "003287"
}
},
"r3d100011299": {
"description": "<<>>!!!>>>",
"homepage": "http://csdb.glycoscience.ru/plant_fungal/",
"name": "Plant and Fungal Carbohydrate Structure Database",
"prefix": "r3d100011299",
"synonyms": [
"PFCSDB",
"Plant & Fungal CSDB"
]
},
"r3d100011300": {
"description": "<<>>!!!>>>\nThe Plant Organelles Database Version 3 (PODB3) is a specialized database project to promote a comprehensive understanding of organelle dynamics, including organelle function, biogenesis, differentiation, movement, and interactions with other organelles.\nThis database consists of 6 individual parts, 'The Electron Micrograph Database', 'The Perceptive Organelles Database', 'The Organelles Movie Database', 'The Organellome Database', 'The Functional Analysis Database', and 'External Links to other databases and Web pages'. All the data and protocols in these databases are populated by direct submission of experimentally determined data from plant researchers.",
"homepage": "http://podb.nibb.ac.jp/Organellome/",
"name": "Plant Organelles Database 3",
"prefix": "r3d100011300",
"synonyms": [
"PODB3"
],
"xrefs": {
"nlx": "151998",
"scr": "006520"
}
},
"r3d100011301": {
"description": "Species included in PlantTFDB 4.0 covers the main lineages of green plants. Therefore, PlantTFDB provides genomic TF repertoires across Viridiplantae. To provide comprehensive information for the TF family, a brief introduction and key references are presented for each family. Comprehensive annotations are made for each identified TF, including functional domains, 3D structures, gene ontology (GO), plant ontology (PO), expression information, expert-curated functional description, regulation information, interaction, conserved elements, references, and annotations in various databases such as UniProt, RefSeq, TransFac, STRING, and VISTA.\nBy inferring orthologous groups and constructing phylogenetic trees, evolutionary relationships among identified TFs were inferred. In addition, PlantTFDB has a simple and user-friendly interface to allow users to query based on combined conditions or make sequence similarity search using BLAST.\nThe new version PlantTFDB 5.0 has been incorporated into PlantRegMap http://plantregmap.gao-lab.org/.",
"homepage": "http://planttfdb.gao-lab.org/",
"name": "Plant Transcription Factor Database",
"prefix": "r3d100011301",
"synonyms": [
"PlantTFDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.ex3fqk",
"nif": "0000-03311",
"omics": "00560",
"scr": "003362"
}
},
"r3d100011302": {
"description": "The Polinsky Language Sciences Lab at Harvard University is a linguistics lab that examines questions of language structure and its effect on the ways in which people use and process language in real time. We engage in linguistic and interdisciplinary research projects ourselves; offer linguistic research capabilities for undergraduate and graduate students, faculty, and visitors; and build relationships with the linguistic communities in which we do our research.\nWe are interested in a broad range of issues pertaining to syntax, interfaces, and cross-linguistic variation. We place a particular emphasis on novel experimental evidence that facilitates the construction of linguistic theory. We have a strong cross-linguistic focus, drawing upon English, Russian, Chinese, Korean, Mayan languages, Basque, Austronesian languages, languages of the Caucasus, and others. We believe that challenging existing theories with data from as broad a range of languages as possible is a crucial component of the successful development of linguistic theory.\nWe investigate both fluent speakers and heritage speakersβthose who grew up hearing or speaking a particular language but who are now more fluent in a different, societally dominant language. Heritage languages, a novel field of linguistic inquiry, are important because they provide new insights into processes of linguistic development and attrition in general, thus increasing our understanding of the human capacity to maintain and acquire language. Understanding language use and processing in real time and how children acquire language helps us improve language study and pedagogy, which in turn improves communication across the globe. Although our lab does not specialize in language acquisition, we have conducted some studies of acquisition of lesser-studied languages and heritage languages, with the purpose of comparing heritage speakers to adults.",
"homepage": "https://dataverse.harvard.edu/dataverse/polinsky",
"name": "The Polinsky Language Sciences Lab Dataverse",
"prefix": "r3d100011302"
},
"r3d100011303": {
"description": "PSI is a global health organization dedicated to improving the health of people in the developing world by focusing on serious challenges like a lack of family planning, HIV and AIDS, barriers to maternal health, and the greatest threats to children under five, including malaria, diarrhea, pneumonia and malnutrition.\nA hallmark of PSI is a commitment to the principle that health services and products are most effective when they are accompanied by robust communications and distribution efforts that help ensure wide acceptance and proper use.\nPSI works in partnership with local governments, ministries of health and local organizations to create health solutions that are built to last. We use original data to monitor and evaluate our programs, generate consumer insight, estimate the impact of our solutions, and evaluate the health of the markets we work to strengthen.",
"homepage": "https://dataverse.harvard.edu/dataverse/PSI",
"name": "Population Services International Dataverse",
"prefix": "r3d100011303",
"synonyms": [
"PSI Dataverse"
]
},
"r3d100011304": {
"description": "The PRISM Climate Group gathers climate observations from a wide range of monitoring networks, applies sophisticated quality control measures, and develops spatial climate datasets to reveal short- and long-term climate patterns. The resulting datasets incorporate a variety of modeling techniques and are available at multiple spatial/temporal resolutions, covering the period from 1895 to the present. Whenever possible, we offer these datasets to the public, either free of charge or for a fee (depending on dataset size/complexity and funding available for the activity).",
"homepage": "http://www.prism.oregonstate.edu/",
"name": "PRISM Climate Data",
"prefix": "r3d100011304",
"synonyms": [
"Parameter-elevation Regressions on Independent Slopes Model Climate Data"
]
},
"r3d100011305": {
"description": "<<>>!!!>>>",
"homepage": "http://recode.ucc.ie/",
"name": "Recode",
"prefix": "r3d100011305",
"synonyms": [
"Database of translational recoding events"
],
"xrefs": {
"nif": "0000-03392",
"scr": "007887"
}
},
"r3d100011306": {
"description": "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.",
"homepage": "https://proteininformationresource.org/resid/resid.shtml",
"name": "RESID Database of Protein Modifications",
"prefix": "r3d100011306",
"xrefs": {
"fairsharing": "FAIRsharing.qaszjp",
"nif": "0000-03400",
"omics": "02422",
"scr": "003505"
}
},
"r3d100011307": {
"description": "The mission of the GDC is to curate and provide access to oceanographic data, especially from Scripps expeditions, making them accessible for scientific and educational use worldwide. Originally launched by Bill Menard, the GDC has been in operation for more than 40 years. While many historic physical artifacts are carefully preserved, the current emphasis is on digital archiving, in coordination with other national and international programs.",
"homepage": "https://gdc.ucsd.edu/",
"name": "Geological Data Center at Scripps Institution of Oceanography",
"prefix": "r3d100011307",
"synonyms": [
"GDC",
"University of California San Diego, Scripps Institution of Oceanography, Geological Data Center"
]
},
"r3d100011308": {
"description": "Dataverse to host followup observations of galaxy clusters identified in South Pole Telescope SZ Surveys. This includes: 1) GMOS spectroscopy of low to moderate redshift galaxy clusters taken as a part of NOAO Large Survey Program 11A-0034 (PI: Christopher Stubbs).",
"homepage": "https://dataverse.harvard.edu/dataverse/SPT_Clusters",
"name": "SPT Galaxy Cluster Followup Dataverse",
"prefix": "r3d100011308",
"synonyms": [
"South Pole Telescope Galaxy Cluster Followup Dataverse"
]
},
"r3d100011309": {
"description": "The SHIP studyΒ΄s main aims include the investigation of health in all its aspects and complexity involving the collection and assessment of data relevant to the prevalence and incidence of common, population-relevant diseases and their risk factors.",
"homepage": "http://www2.medizin.uni-greifswald.de/cm/fv/ship/",
"name": "Study of Health in Pomerania",
"prefix": "r3d100011309",
"synonyms": [
"SHIP"
]
},
"r3d100011310": {
"description": "\"TaiBIF\" stands for Taiwan Biodiversity Information Facility. It is the Taiwan portal of GBIF, and is in charge of integrating Taiwan's biodiversity information, including lists of species and local experts, illustrations of species, introduction of endemic species and invasive species, Taiwan's terrestrial and marine organisms, biodiversity literature, geographical and environmental information, information about relevant institutions, organizations, projects, and observation spots, the Catalog of Life (a list of Taiwanese endemic species), and publications.",
"homepage": "https://portal.taibif.tw/",
"name": "Taiwan Biodiversity Information Facility",
"prefix": "r3d100011310",
"synonyms": [
"TaiBIF"
],
"xrefs": {
"fairsharing": "FAIRsharing.y2vm4r"
}
},
"r3d100011311": {
"description": "The TFRI focuses its work on conserving forest resources, restoring rare animals and plants, improving silvicultural techniques, managing natural forests and providing nature education among other activities. The TRFIβs data catalog contains research data from the various divisions and projects spanning forests, plants, ecology and herbariums throughout the country.",
"homepage": "https://metacat.tfri.gov.tw/tfri",
"name": "Taiwan Forestry Research Institute Data Catalog",
"prefix": "r3d100011311",
"synonyms": [
"TFRI Data Catalog",
"ζ ζ₯ 試 ι© ζ η η©Ά θ³ ζ η ι"
],
"xrefs": {
"biodbcore": "001743",
"fairsharing": "FAIRsharing.1bb2c9"
}
},
"r3d100011312": {
"description": "Data from selected studies from the Abdul Latif Jameel Poverty Action Lab (J-PAL), povertyactionlab.org. A number of other studies from J-PAL have data posted on the MacArthur Dataverse: http://dvn.iq.harvard.edu/dvn/dv/macarthur.",
"homepage": "https://dataverse.harvard.edu/dataverse/jpal",
"name": "The Abdul Latif Jameel Poverty Action Lab",
"prefix": "r3d100011312",
"synonyms": [
"J-PAL Dataverse"
]
},
"r3d100011313": {
"description": "The Census Bureau releases TIGER/Line shapefiles and metadata each year to the public. \nTIGER/Line shapefiles are spatial extracts from the Census Bureauβs MAF/TIGER database. They contain features such as roads, railroads, hydrographic features and legal and statistical boundaries.",
"homepage": "https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html",
"name": "U.S. Census Bureau TIGER/Line Shapefiles and TIGER/LineΒ Files",
"prefix": "r3d100011313",
"synonyms": [
"TIGER/LineΒ Shapefiles and TIGER/LineΒ Files"
],
"xrefs": {
"fairsharing": "FAIRsharing.33f91a"
}
},
"r3d100011314": {
"description": "Welcome to the UCLA Phonetics Lab Archive. For over half a century, the UCLA Phonetics Laboratory has collected recordings of hundreds of languages from around the world, providing source materials for phonetic and phonological research, of value to scholars, speakers of the languages, and language learners alike. The materials on this site comprise audio recordings illustrating phonetic structures from over 200 languages with phonetic transcriptions, plus scans of original field notes where relevant.",
"homepage": "http://archive.phonetics.ucla.edu/",
"name": "UCLA Phonetics Lab Archive",
"prefix": "r3d100011314"
},
"r3d100011315": {
"description": "The Social Science Data Archive is still active and maintained as part of the UCLA Library Data Science Center. SSDA Dataverse is one of the archiving opportunities of SSDA, the others are: Data can be archived by SSDA itself or by ICPSR or by UCLA Library or by California Digital Library. The Social Science Data Archives serves the UCLA campus as an archive of faculty and graduate student survey research. We provide long term storage of data files and documentation. We ensure that the data are useable in the future by migrating files to new operating systems. We follow government standards and archival best practices. The mission of the Social Science Data Archive has been and continues to be to provide a foundation for social science research with faculty support throughout an entire research project involving original data collection or the reuse of publicly available studies. Data Archive staff and researchers work as partners throughout all stages of the research process, beginning when a hypothesis or area of study is being developed, during grant and funding activities, while data collection and/or analysis is ongoing, and finally in long term preservation of research results. Our role is to provide a collaborative environment where the focus is on understanding the nature and scope of research approach and management of research output throughout the entire life cycle of the project. Instructional support, especially support that links research with instruction is also a mainstay of operations.",
"homepage": "https://dataverse.ucla.edu/dataverse/ssda_ucla",
"name": "UCLA Social Science Data Archive",
"prefix": "r3d100011315",
"synonyms": [
"SSDA Dataverse"
]
},
"r3d100011316": {
"description": "UNITE provides unified way how you delimit, identify, communicate and work with DNA based Species Hypotheses (SH).",
"homepage": "https://unite.ut.ee",
"name": "UNITE",
"prefix": "r3d100011316",
"synonyms": [
"UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes",
"Unified system for the DNA based fungal species linked to the classification"
],
"xrefs": {
"fairsharing": "FAIRsharing.cnwx8c",
"nlx": "61947",
"omics": "23522",
"scr": "006518"
}
},
"r3d100011317": {
"description": "This database contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the EAWAG-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology.",
"homepage": "http://eawag-bbd.ethz.ch/",
"name": "University of Minnesota Biocatalysis/Biodegradation Database",
"prefix": "r3d100011317",
"synonyms": [
"EAWAG Biocatalysis/Biodegradation Database",
"EAWAG-BBD",
"UM-BBD"
],
"xrefs": {
"nif": "0000-03607",
"omics": "21934",
"scr": "005787"
}
},
"r3d100011318": {
"description": "The gift of the Stowell Datasets, a digital archive of psychographic data, to the College of Liberal Arts (and continued gift of new datasets) provide a unique opportunity for WSU to facilitate access to a valuable research resource.\nThe datasets include over 350 individual major media market surveys (CATI, Random Digit Dialing telephone surveys) collected over the period 1989-2001 and feature approximately n=1,000+ respondents for each market for each year.",
"homepage": "https://dataverse.harvard.edu/dataverse.xhtml?alias=wsu",
"name": "Washington State University Data Center Dataverse",
"prefix": "r3d100011318"
},
"r3d100011319": {
"description": "The Centreβs vision is a rural transformation in the developing world as smallholder households strategically increase their use of trees in agricultural landscapes to improve their food security, nutrition, income, health, shelter, social cohesion, energy resources and environmental sustainability.\nThe Centreβs mission is to generate science-based knowledge about the diverse roles that trees play in agricultural landscapes, and to use its research to advance policies and practices, and their implementation, that benefit the poor and the environment.",
"homepage": "https://data.worldagroforestry.org/",
"name": "World Agroforestry Centre - ICRAF Dataverse",
"prefix": "r3d100011319"
},
"r3d100011321": {
"description": "The National Archives and Records Administration (NARA) is the nation's record keeper. Of all documents and materials created in the course of business conducted by the United States Federal government, only 1%-3% are so important for legal or historical reasons that they are kept by us forever.\nThose valuable records are preserved and are available to you, whether you want to see if they contain clues about your familyβs history, need to prove a veteranβs military service, or are researching an historical topic that interests you.",
"homepage": "https://dataverse.harvard.edu/dataverse/nara",
"name": "U.S. National Archives and Records Administration Dataverse",
"prefix": "r3d100011321",
"synonyms": [
"NARA Dataverse"
]
},
"r3d100011322": {
"description": "The Radio Telescope Data Center (RTDC) reduces, archives, and makes available on its web site data from SMA and the CfA Millimeter-wave Telescope. The whole-Galaxy CO survey presented in Dame et al. (2001) is a composite of 37 separate surveys. The data from most of these surveys can be accessed. Larger composites of these surveys are available separately.",
"homepage": "https://dataverse.harvard.edu/dataverse/rtdc",
"name": "1.2 Meter CO Survey Dataverse",
"prefix": "r3d100011322"
},
"r3d100011323": {
"description": "SILVA is a comprehensive, quality-controlled web resource for up-to-date aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains alongside supplementary online services. In addition to data products, SILVA provides various online tools such as alignment and classification, phylogenetic tree calculation and viewer, probe/primer matching, and an amplicon analysis pipeline. With every full release a curated guide tree is provided that contains the latest taxonomy and nomenclature based on multiple references. SILVA is an ELIXIR Core Data Resource.",
"homepage": "https://www.arb-silva.de/",
"name": "SILVA",
"prefix": "r3d100011323",
"synonyms": [
"A comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data."
],
"xrefs": {
"fairsharing": "FAIRsharing.5vtYGG",
"nif": "0000-03464",
"omics": "01514",
"rid": "000103",
"ror": "027z9pz32",
"scr": "006423"
}
},
"r3d100011324": {
"description": "<<>>!!!>>>",
"homepage": "https://mb3is.megx.net/",
"name": "megx.net",
"prefix": "r3d100011324",
"synonyms": [
"Marine Ecological GenomiX"
],
"xrefs": {
"nif": "0000-03109",
"omics": "15635",
"scr": "000738"
}
},
"r3d100011326": {
"description": "GEOFON seeks to facilitate cooperation in seismological research and earthquake and tsunami hazard mitigation by providing rapid transnational access to seismological data and source parameters of large earthquakes, and keeping these data accessible in the long term.\nIt pursues these aims by operating and maintaining a global network of permanent broadband stations in cooperation with local partners, facilitating real time access to data from this network and those of many partner networks and plate boundary observatories, providing a permanent and secure archive for seismological data. It also archives and makes accessible data from temporary experiments carried out by scientists at German universities and institutions, thereby fostering cooperation and encouraging the full exploitation of all acquired data and serving as the permanent archive for the Geophysical Instrument Pool at Potsdam (GIPP). It also organises the data exchange of real-time and archived data with partner institutions and international centres.",
"homepage": "https://geofon.gfz-potsdam.de/",
"name": "GEOFON",
"prefix": "r3d100011326",
"synonyms": [
"GEOFOrschungsNetz",
"GFZ Seismological Data Archive"
],
"xrefs": {
"doi": "10.14470/TR560404",
"fairsharing": "FAIRsharing.J3YyP9"
}
},
"r3d100011327": {
"description": "In early 2010 we updated the site to facilitate more rapid transfer of our data to the public database and focus our efforts on the core mission of providing expression pattern images to the research community. The original database https://www.fruitfly.org/index.html reproduced functions available on FlyBase, complicating our updates by the requirement to re-synchronize with FlyBase updates. Our expression reports on the new site still link to FlyBase gene reports, but we no longer reproduce FlyBase functions and therefore can update expression data on an ongoing basis instead of more infrequent major releases. All the functions relating to the expression patterns remain and we soon will add an option to search expression patterns by image similarity, in addition to annotation term searches. In a transitional phase we will leave both the old and the new sites up, but the newer data (post Release 2) will appear only on the new website. We welcome any feedback or requests for additional features. - The goals of the Drosophila Genome Center are to finish the sequence of the euchromatic genome of Drosophila melanogaster to high quality and to generate and maintain biological annotations of this sequence. In addition to genomic sequencing, the BDGP is \n1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; \n2) characterizing the sequence and expression of cDNAs; and \n3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community.",
"homepage": "https://insitu.fruitfly.org/cgi-bin/ex/insitu.pl",
"name": "Berkeley Drosophila Genome Project insitu",
"prefix": "r3d100011327",
"synonyms": [
"BDGP insitu homepage",
"Patterns of gene expression in Drosophila embryogenesis"
],
"xrefs": {
"nif": "0000-25550",
"scr": "002868"
}
},
"r3d100011328": {
"description": "Created in 2005 by the CNRS, CNRTL unites in a single portal, a set of linguistic resources and tools for language processing. The CNRTL includes the identification, documentation (metadata), standardization, storage, enhancement and dissemination of resources. The sustainability of the service and the data is guaranteed by the backing of the UMR ATILF (CNRS - UniversitΓ© Nancy), support of the CNRS and its integration in the excellence equipment project ORTOLANG .",
"homepage": "https://www.cnrtl.fr/",
"name": "Centre National de Ressources Textuelles et Lexicales",
"prefix": "r3d100011328",
"synonyms": [
"CNRTL"
]
},
"r3d100011329": {
"description": "ORTOLANG is an EQUIPEX project accepted in February 2012 in the framework of investissements dβavenir. Its aim is to construct a network infrastructure including a repository of language data (corpora, lexicons, dictionaries etc.) and readily available, well-documented tools for its processing. Expected outcomes comprize:\npromoting research on analysis, modelling and automatic processing of our language to their highest international levels thanks to effective resource pooling;\nfacilitating the use and transfer of resources and tools set up within public laboratories to industrial partners, notably SMEs which often cannot develop such resources and tools for language processing given the cost of investment;\npromoting French language and the regional languages of France by sharing expertise acquired by public laboratories.\nORTOLANG is a service for the language, which is complementary to the service offered by Huma-Num (trΓ¨s grande infrastructure de recherche). Ortolang gives access to SLDR for speech, and CNRTL for text resources.",
"homepage": "https://www.ortolang.fr/en/home/",
"name": "Ortolang",
"prefix": "r3d100011329",
"synonyms": [
"Open Resources and TOols for LanGuage",
"Outils et Ressources pour un Traitement OptimisΓ© de la LANGue"
],
"xrefs": {
"issn": "2417-7482"
}
},
"r3d100011330": {
"description": "ModelDB is a curated database of published models in the broad domain of computational neuroscience. It addresses the need for access to such models in order to evaluate their validity and extend their use. It can handle computational models expressed in any textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment. The model source code doesn't even have to reside inside ModelDB; it just has to be available from some publicly accessible online repository or WWW site.",
"homepage": "https://modeldb.science/",
"name": "ModelDB",
"prefix": "r3d100011330",
"xrefs": {
"fairsharing": "FAIRsharing.5rb3fk",
"miriam": "00000131",
"nif": "0000-00004",
"scr": "007271"
}
},
"r3d100011331": {
"description": "Xenbase's mission is to provide the international research community with a comprehensive, integrated and easy to use web based resource that gives access the diverse and rich genomic, expression and functional data available from Xenopus research. Xenbase also provides a critical data sharing infrastructure for many other NIH-funded projects, and is a focal point for the Xenopus community. In addition to our primary goal of supporting Xenopus researchers, Xenbase enhances the availability and visibility of Xenopus data to the broader biomedical research community.",
"homepage": "https://www.xenbase.org/xenbase/",
"name": "Xenbase",
"prefix": "r3d100011331",
"synonyms": [
"Xenopus Genomics Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.jrv6wj",
"miriam": "00000186",
"nif": "0000-01286",
"scr": "003280"
}
},
"r3d100011332": {
"description": "The focus of CLARIN INT Portal is on resources that are relevant to the lexicological study of the Dutch language and on resources relevant for research in and development of language and speech technology. For Example: lexicons, lexical databases, text corpora, speech corpora, language and speech technology tools, etc. The resources are: Cornetto-LMF (Lexicon Markup Framework), Corpus of Contemporary Dutch (Corpus Hedendaags Nederlands), Corpus Gysseling, Corpus VU-DNC (VU University Diachronic News text Corpus), Dictionary of the Frisian Language (Woordenboek der Friese Taal), DuELME-LMF (Lexicon Markup Framework), Language Portal (Taalportaal), Namescape, NERD (Named Entity Recognition and Disambiguation) and TICCLops (Text-Induced Corpus Clean-up online processing system).",
"homepage": "https://portal.clarin.inl.nl/",
"name": "CLARIN INT Portal",
"prefix": "r3d100011332",
"synonyms": [
"CLARIN INT Center",
"CLARIN IvdNT-portaal"
]
},
"r3d100011333": {
"description": ">>>!!!<<<>>!!!<<<",
"name": "CLARIN Centre Vienna",
"prefix": "r3d100011333",
"synonyms": [
"CCV",
"CLARIN-AT",
"LRP",
"Language Resources Portal"
]
},
"r3d100011334": {
"description": "Currently the institute has more than 700 collections consisting of (digital) research data, digitized material, archival collections, printed material, handwritten questionnaires, maps and pictures. The focus is on resources relevant for the study of function, meaning and coherence of cultural expressions and resources relevant for the structural, dialectological and sociolinguistic study of language variation within the Dutch language. An overview is here https://meertens.knaw.nl/en/datasets/",
"homepage": "https://meertens.knaw.nl/en/collections/",
"name": "Meertens Instituut Collecties",
"prefix": "r3d100011334",
"synonyms": [
"De Digitale Koepel",
"Meertens Institute Collections"
]
},
"r3d100011335": {
"description": "The DNB Household Survey (DHS) supplies longitudinal data to the international academic community, with a focus on the psychological and economic aspects of financial behavior. The study comprises information on work, pensions, housing, mortgages, income, assets, loans, health, economic and psychological concepts, and personal characteristics. The DHS data are collected from 2,000 households participating in the CentERpanel. The CentERpanel is an Internet panel that reflects the composition of the Dutch-speaking population in the Netherlands. Both the DHS as well as the CentERpanel, in which the study in conducted, are run by CentERdata",
"homepage": "https://www.dhsdata.nl/site/users/login",
"name": "DHS Data Access",
"prefix": "r3d100011335",
"synonyms": [
"DNB Household Survey"
]
},
"r3d100011336": {
"description": "eLaborate is an online work environment in which scholars can upload scans, transcribe and annotate text, and publish the results as on online text edition which is freely available to all users. Short information about and a link to already published editions is presented on the page Editions under Published. Information about editions currently being prepared is posted on the page Ongoing projects.\nThe eLaborate work environment for the creation and publication of online digital editions is developed by the Huygens Institute for the History of the Netherlands of the Royal Netherlands Academy of Arts and Sciences. Although the institute considers itself primarily a research facility and does not maintain a public collection profile, Huygens ING actively maintains almost 200 digitally available resource collections.",
"homepage": "https://elaborate.huygens.knaw.nl/",
"name": "eLaborate",
"prefix": "r3d100011336",
"synonyms": [
"Huygens ING: eLaborate",
"e-laborate"
]
},
"r3d100011337": {
"description": "Currently, the IMS repository focuses on resources provided by the Institute for Natural Language Processing in Stuttgart (IMS) and other CLARIN-D related institutions such as the local Collaborative Research Centre 732 (SFB 732) as well as institutions and/or organizations that belong to the CLARIN-D extended scientific community. Comprehensive guidelines and workflows for submission by external contributors are being compiled based on the experiences in archiving such in-house resources.",
"homepage": "http://clarin04.ims.uni-stuttgart.de/repo/",
"name": "IMS UniversitΓ€t Stuttgart Repository",
"prefix": "r3d100011337",
"synonyms": [
"IMS Fedora Repository",
"Repository of the CLARIN-D Centre at IMS Stuttgart"
]
},
"r3d100011338": {
"description": "TRAILS is a prospective cohort study, which started in 2001 with population cohort and 2004 with a clinical cohort (CC). Since then, a group of 2500 young people from the Northern part of the Netherlands has been closely monitored in order to chart and explain their mental, physical, and social development. These TRAILS participants have been measured every two to three years, by means of questionnaires, interviews, and all kinds of tests. By now, we have collected information that spans the total period from preadolescence up until young adulthood. One of the main goals of TRAILS is to contribute to the knowledge of the development of emotional and behavioral problems and the (social) functioning of preadolescents into adulthood, their determinants, and underlying mechanisms.",
"homepage": "https://www.trails.nl/",
"name": "TRAILS",
"prefix": "r3d100011338",
"synonyms": [
"Tracking Adolescents' Individual Lives Survey"
]
},
"r3d100011339": {
"description": "GAMS is an OAIS compliant asset management system for the management, publication and long-term archiving of digital resources from the Humanities. It enables scholars, researchers and students to manage and publish resources from projects with permanent identification and enriched with metadata.",
"homepage": "https://gams.uni-graz.at",
"name": "GAMS",
"prefix": "r3d100011339",
"synonyms": [
"Geisteswissenschaftliches Asset Management System",
"Humanities' Asset Management System"
]
},
"r3d100011340": {
"description": "Network Repository is the first interactive data repository for graph and network data. It hosts graph and network datasets, containing hundreds of real-world networks and benchmark datasets. Unlike other data repositories, Network Repository provides interactive analysis and visualization capabilities to allow researchers to explore, compare, and investigate graph data in real-time on the web.",
"homepage": "https://networkrepository.com/",
"name": "Network Repository",
"prefix": "r3d100011340",
"synonyms": [
"Network Data Repository, Graph Data, Social Networks"
]
},
"r3d100011343": {
"description": "The Biological Collection Access Service for Europe, BioCASE, is a transnational network of biological collections of all kinds. BioCASE enables widespread unified access to distributed and heterogeneous European collection and observational databases using open-source, system-independent software and open data standards and protocols.",
"homepage": "https://www.biocase.org/",
"name": "Biological Collection Access Service for Europe",
"prefix": "r3d100011343",
"synonyms": [
"BioCASe"
],
"xrefs": {
"fairsharing.legacy": "4209"
}
},
"r3d100011344": {
"description": "<<>>!!!>>> C3-Grid is an ALREADY FINISHED project within D-Grid, the initiative to promote a grid-based e-Science framework in Germany. The goal of C3-Grid is to support the workflow of Earth system researchers. A grid infrastructure will be implemented that allows efficient distributed data processing and inter-institutional data exchange. Aim of the effort was to develop an infrastructure for uniform access to heterogeneous data and distributed data processing. The work was structured in two projects funded by the Federal Ministry of Education and Research. The first project was part of the D-Grid initiative and explored the potential of grid technology for climate research and developed a prototype infrastructure. Details about the C3Grid architecture are described in βEarth System Modelling β Volume 6β. In the second phase \"C3Grid - INAD: Towards an Infrastructure for General Access to Climate Data\" this infrastructure was improved especially with respect to interoperability to Earth System Grid Federation (ESGF). Further the portfolio of available diagnostic workflows was expanded.\nThese workflows can be re-used now in adjacent infrastructures MiKlip Evaluation Tool (http://www.fona-miklip.de/en/index.php) and as Web Processes within the Birdhouse Framework (http://bird-house.github.io/).\nThe Birdhouse Framework is now funded as part of the European Copernicus Climate Change Service (https://climate.copernicus.eu/) managed by ECMWF and will be extended to provide scalable processing services for ESGF hosted data at DKRZ as well as IPSL and BADC.",
"homepage": "https://www.dkrz.de/en/projects-and-partners/projects-1/c3-inad?set_language=en",
"name": "Collaborative Climate Community Data and Processing Grid",
"prefix": "r3d100011344",
"synonyms": [
"C3Grid"
],
"xrefs": {
"biodbcore": "001538"
}
},
"r3d100011345": {
"description": "The DARIAH-DE repository is a digital long-term archive for human and cultural-scientific research data. Each object described and stored in the DARIAH-DE Repository has a unique and lasting Persistent Identifier (DOI), with which it is permanently referenced, cited, and kept available for the long term. In addition, the DARIAH-DE Repository enables the sustainable and secure archiving of data collections.\nThe DARIAH-DE Repository is not only to DARIAH-DE associated research projects, but also to individual researchers as well as research projects that want to save their research data persistently, referenceable and long-term archived and make it available to third parties. The main focus is the simple and user-oriented access to long-term storage of research data. To ensure its long term sustainability, the DARIAH-DE Repository is operated by the Humanities Data Centre.",
"homepage": "https://de.dariah.eu/repository",
"name": "DARIAH-DE Repository",
"prefix": "r3d100011345"
},
"r3d100011347": {
"description": "The DRKS is an open access online register for clinical trials conducted in Germany, which allows all users to search, register and share information on clinical trials.",
"homepage": "https://www.drks.de/drks_web/",
"name": "Deutsches Register Klinischer Studien",
"prefix": "r3d100011347",
"synonyms": [
"DRKS",
"German Clinical Trials Register"
]
},
"r3d100011349": {
"description": "EGO examines 500 years of modern European history by transcending national, disciplinary and methodological boundaries. Ten thematic threads tie together processes of intercultural exchange whose influence extended beyond national and cultural borders. These range from religion, politics, science and law to art and music, as well as to the economy, technology and the military. EGO employs the newest research to present European transfer processes comprehensively in a way that is easy to understand. The articles link to images, sources, statistics, animated and interactive maps, and audio and visual clips. EGO thereby takes full advantage of the Internet's multi-media potential.",
"homepage": "http://ieg-ego.eu/",
"name": "EuropΓ€ische Geschichte Online",
"prefix": "r3d100011349",
"synonyms": [
"EGO",
"European History Online"
]
},
"r3d100011352": {
"description": "GEOMAR Helmholtz Centre for Ocean Research Kiel is one of the leading marine science institutions in Europe. GEOMAR investigates the chemical, physical, biological, and geological processes in the oceans, as well as their interactions with the seafloor and the atmosphere.\nOceanRep is an open access digital collection containing the research output of GEOMAR staff and students. Included are journal articles, conference papers, book chapters, theses and more, - with fulltext, if available. Research data are linked to the publications entries.",
"homepage": "https://oceanrep.geomar.de/",
"name": "OceanRep GEOMAR Repository",
"prefix": "r3d100011352",
"synonyms": [
"GEOMAR Helmholtz Centre for Ocean Research Kiel",
"GEOMAR Helmholtz-Zentrum fΓΌr Ozeanforschung Kiel"
]
},
"r3d100011355": {
"description": "The JΓΌlich Observatory for Cloud Evolution (JOYCE) operates ground-based active and passive remote sensing instruments for cloud and precipitation observations. βJOYCE is based on a long-term successful collaboration between the University of Cologne, the University of Bonn and the Research Centre JΓΌlich.\nSince 2017 JOYCE is transformed into a Core Facility (JOYCE - CF) funded by the DFG (Deutsche Forschungsgemeinschaft) with the aim of high quality radar and passive microwave observations of the atmosphere. JOYCE will serve as a reference center for best practices in data acquisition, storage and distribution.\nJOYCE instrumentation aims to observe spatial and temporal variability of atmospheric water cycle variables.",
"homepage": "http://cpex-lab.de/cpex-lab/EN/Home/JOYCE-CF/JOYCE-CF_node.html",
"name": "JΓΌlich ObservatorY for Cloud Evolution - Core Facility",
"prefix": "r3d100011355",
"synonyms": [
"JOYCE - CF",
"formerly: JOYCE"
]
},
"r3d100011360": {
"description": "The mission of the platform is to enable access for academic projects towards experiments in high-throughput without loss of IP and on a cost basis, which does not restrict access towards HTS usage. The FMP hosts the central open access technology platform of EU-OPENSCREEN, the ChemBioNet and theHelmholtz-Initiative fΓΌr Wirkstoffforschung, the Screening Unit. The Unit serves for systematic screening of large compound or genome-wide RNAi libraries with state-of-the-art equipment like automated microscopes and microfluidic systems. The Screening Unit is part of the Chemical Biology Platform of the FMP also supported by the MDC.\nSee also: https://www.mdc-berlin.de/screening-unit",
"homepage": "https://leibniz-fmp.de/research/research-section/chemical-biology/jens-peter-von-kries",
"name": "Screening Unit Berlin-Buch",
"prefix": "r3d100011360",
"synonyms": [
"Screening Unit Jens Peter von Kries"
]
},
"r3d100011361": {
"description": "The European Chemical Biology Database (ECBD) is a prototype database, currently being developed for EU-OPENSCREEN. The purpose of ECBD is to store and integrate screening data from EU-OPENSCREEN partners and contributors.",
"homepage": "https://ecbd.eu/",
"name": "European Chemical Biology Database",
"prefix": "r3d100011361",
"synonyms": [
"ECBD",
"EU-Openscreen's database"
]
},
"r3d100011363": {
"description": "The project of the Stadt- und UniversitΓ€tsbibliothek Frankfurt am Main encompasses safety filming of 50.000 to 70.000 historical photographs from the German colonial history. Public access to the pictures is via a research database on the internet.",
"homepage": "https://sammlungen.ub.uni-frankfurt.de/kolonialesbildarchiv/nav/index/all",
"name": "Der Bildbestand der Deutschen Kolonialgesellschaft in der UniversitΓ€tsbibliothek Frankfurt am Main",
"prefix": "r3d100011363"
},
"r3d100011364": {
"description": "Since January 2012, two previously independent resources called \"ViFaArt β Virtual Library for Contemporary Art\" and \"arthistoricum.net β Virtual Library for Art History\" have been joint together, forming a new service called arthistoricum.net. This unique union makes it now possible to research the whole subject spectrum belonging to Art History. The special interest collection of Art History focuses on Medieval and Early European Art History, including art influenced by Europe in the USA, Canada and Australia, continuing chronologically from the Early Christian era until 1945. The special interest collection of Contemporary Art continues the art historical subject spectrum to include European and North American Art History from 1945.\narthistoricum.net contains text and image resources as well as comprehensive, academically relevant information dealing with all media from the Middle Ages up to the present. arthistoricum.net pools the resources and know-how of the responsible partner institutions, thus making this portal an essential forum for research and teaching.",
"homepage": "https://www.arthistoricum.net/",
"name": "arthistoricum.net",
"prefix": "r3d100011364",
"synonyms": [
"Fachinformationsdienst Kunst - Fotografie - Design",
"Specialized Information Service Art - Photography - Design"
]
},
"r3d100011365": {
"description": "The TextGrid Repository is a digital preservation archive for human sciences research data. It offers an extensive searchable and adaptable corpus of XML/TEI encoded texts, pictures and databases. Amongst the continuously growing corpus is the Digital Library of TextGrid, which consists of works of more than 600 authors of fiction (prose verse and drama) as well as nonfiction from the beginning of the printing press to the early 20th century written in or translated into German. The files are saved in different output formats (XML, ePub, PDF), published and made searchable. Different tools e.g. viewing or quantitative text-analysis tools can be used for visualization or to further research the text.\nThe TextGrid Repository is part of the virtual research environment TextGrid, which besides offering digital preservation also offers open-source software for collaborative creations and publications of e.g. digital editions that are based on XML/TEI.",
"homepage": "https://www.textgridrep.org/",
"name": "TextGrid Repository",
"prefix": "r3d100011365",
"synonyms": [
"Virtual research environment for the Humanities",
"Virtuelle Forschungsumgebung fΓΌr die Geisteswissenschaften"
]
},
"r3d100011366": {
"description": "The Animal Sound Archive at the Museum fΓΌr Naturkunde in Berlin is one of the oldest and largest collections of animal sounds. Presently, the collection consists of about 120,000 bioacoustical recordings comprising almost all groups of animals:\n1.800 bird species\n580 mammalian species\nmore then150 species of invertebrates;\nsome fishes, amphibians and reptiles",
"homepage": "https://www.tierstimmenarchiv.de/",
"name": "Tierstimmenarchiv - Museum fΓΌr Naturkunde Berlin",
"prefix": "r3d100011366",
"synonyms": [
"Animal Sound Archive - Museum fΓΌr Naturkunde Berlin"
]
},
"r3d100011367": {
"description": "Human biomaterial banks (short: biobanks) are collections of human body substances (i.e. blood, DNA, urine or tissue) connected with disease specific information. This allow for research of relations between deseases and underlying (molecular) modifications and paves the way for developing target-oriented therapies (\"personalized medicine\").\nThe biobank material arises from samples taken for therapeutical or diagnostic reasons or is extracted in the context of clinical trials. An approval for usage by the patient is always needed prior to any research activities.",
"homepage": "https://biobank.charite.de/",
"name": "Zentrale Biomaterialbank der CharitΓ©",
"prefix": "r3d100011367",
"synonyms": [
"Central Biomaterial Bank CharitΓ©",
"ZeBanC"
]
},
"r3d100011368": {
"description": "The Centre for Clinical Trials Cologne (KΓΆln ZKS) aims to support all processes of clinical trials and the quality of patient-oriented clinical research in an academic environment. It supports doctors of University Hospital of Cologne, other clinics, study groups and professional associations in the design and conduct of clinical trials. For the pharmaceutical industry and contract research organizations, the ZKS KΓΆln is a clinic near partner for medical research projects.",
"homepage": "https://zks.uni-koeln.de/index.php?s=studien&c=studien_klinische-studien",
"name": "Zentrum fΓΌr Klinische Studien der UniversitΓ€t zu KΓΆln",
"prefix": "r3d100011368",
"synonyms": [
"CTCC",
"Clinical Trials Center Cologne",
"ZKS KΓΆln"
]
},
"r3d100011369": {
"description": "An online web application developed by DMITRE Resources and Energy Group enabling users to search, view and download information relating to minerals, petroleum and geothermal exploration in South Australia.",
"homepage": "https://map.sarig.sa.gov.au/",
"name": "South Australian Resources Information Geoserver",
"prefix": "r3d100011369",
"synonyms": [
"SARIG"
],
"xrefs": {
"fairsharing": "FAIRsharing.764c73"
}
},
"r3d100011371": {
"description": "<<>>!!!>>>",
"homepage": "https://www.nlm.nih.gov/toxnet/index.html",
"name": "TOXNET",
"prefix": "r3d100011371",
"synonyms": [
"Toxicology Data Network"
]
},
"r3d100011372": {
"description": "<<>>!!!>>>\nPhytoPath is a new bioinformatics resource that integrates genome-scale data from important plant pathogen species with literature-curated information about the phenotypes of host infection. Using the Ensembl Genomes browser, it provides access to complete genome assembly and gene models of priority crop and model-fungal, oomycete and bacterial phytopathogens. PhytoPath also links genes to disease progression using data from the curated PHI-base resource. PhytoPath portal is a joint project bringing together Ensembl Genomes with PHI-base, a community-curated resource describing the role of genes in pathogenic infection. PhytoPath provides access to genomic and phentoypic data from fungal and oomycete plant pathogens, and has enabled a considerable increase in the coverage of phytopathogen genomes in Ensembl Fungi and Ensembl Protists.\nPhytoPath also provides enhanced searching of the PHI-base resource as well as the fungi and protists in Ensembl Genomes.",
"homepage": "http://www.phytopathdb.org/",
"name": "PhytoPath",
"prefix": "r3d100011372",
"xrefs": {
"omics": "10268"
}
},
"r3d100011373": {
"description": "Virtual Fly Brain (VFB) - an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster CNS.",
"homepage": "https://virtualflybrain.org/",
"name": "Virtual Fly Brain",
"prefix": "r3d100011373",
"synonyms": [
"VFB",
"VFB Drosophila melanogaster fly brain atlas"
],
"xrefs": {
"fairsharing": "FAIRsharing.nzaz6z",
"nlx": "143644",
"scr": "004229"
}
},
"r3d100011375": {
"description": "Academic Commons provides open, persistent access to the scholarship produced by researchers at Columbia University, Barnard College, Jewish Theological Seminary, Teachers College, and Union Theological Seminary. Academic Commons is a program of the Columbia University Libraries. Academic Commons accepts articles, dissertations, research data, presentations, working papers, videos, and more.",
"homepage": "https://academiccommons.columbia.edu/",
"name": "Columbia University Academic Commons",
"prefix": "r3d100011375"
},
"r3d100011376": {
"description": "The PLANKTON*NET data provider at the Alfred Wegener Institute for Polar and Marine Research is an open access repository for plankton-related information. It covers all types of phytoplankton and zooplankton from marine and freshwater areas. PLANKTON*NET's greatest strength is its comprehensiveness as for the different taxa image information as well as taxonomic descriptions can be archived. PLANKTON*NET also contains a glossary with accompanying images to illustrate the term definitions. PLANKTON*NET therefore presents a vital tool for the preservation of historic data sets as well as the archival of current research results.\nBecause interoperability with international biodiversity data providers (e.g. GBIF) is one of our aims, the architecture behind the new planktonnet@awi repository is observation centric and allows for mulitple assignment of assets (images, references, animations, etc) to any given observation. In addition, images can be grouped in sets and/or assigned tags to satisfy user-specific needs . Sets (and respective images) of relevance to the scientific community and/or general public have been assigned a persistant digital object identifier (DOI) for the purpose of long-term preservation (e.g. set \"\"Plankton*Net celebrates 50 years of Roman Treaties\"\", handle: 10013/de.awi.planktonnet.set.495)\"",
"homepage": "https://planktonnet.awi.de/",
"name": "plankton*net",
"prefix": "r3d100011376"
},
"r3d100011378": {
"description": "MatDB is a database application for experimentally measured engineering materials data. It supports open, registered, and restricted access. It presently hosts more than 20.000 unique data sets coming mainly from European and Member State research programmes. It supports web interfaces for entering, browsing, and retrieving data. MatDB is also enabled for innovative services, including data citation and interoperability standards. The data citation service relies on DataCite DOIs. The historic data sets are being enabled for citation. For all new projects where MatDB is used for managing project data, end-users are encouraged to request DataCite DOIs. There is though no obligation as regards the access level as it is considered sufficient simply that the data sets are made discoverable through data citation. The service that relies on interoperability standards leverages the outputs from a series of CEN Workshops that aim to deliver Standards-compliant data formats for engineering materials data. In this context, MatDB is used to validate and demonstrate said formats with a view to promoting their adoption.\nMatDB is part of the ODIN Portal https://odin.jrc.ec.europa.eu/alcor/",
"homepage": "https://odin.jrc.ec.europa.eu/alcor/PortalController?query=Select&action=Refresh",
"name": "MatDB",
"prefix": "r3d100011378",
"synonyms": [
"Mat-Database",
"MatDatabase"
]
},
"r3d100011379": {
"description": "ScienceBase provides access to aggregated information derived from many data and information domains, including feeds from existing data systems, metadata catalogs, and scientists contributing new and original content. ScienceBase architecture is designed to help science teams and data practitioners centralize their data and information resources to create a foundation needed for their work. ScienceBase, both original software and engineered components, is released as an open source project to promote involvement from the larger scientific programming community both inside and outside the USGS.",
"homepage": "https://www.sciencebase.gov/about/",
"name": "ScienceBase USGS",
"prefix": "r3d100011379",
"synonyms": [
"ScienceBase catalog"
]
},
"r3d100011380": {
"description": "Chinese National Arctic & Antarctic Data Center(CN-NADC) is a national facility within the Polar research institute of China (PRIC), which is a research institute under the State Oceanic Administration (SOA) of China. CN-NADC was established in response to Chinese participation in the Article III.1.c of Antarctic Treaty System - (ATS β http://www.ats.aq) and Chinese Polar Data Policy(http://www.chinare.org.cn/standardDetail/?id=477).\nCN-NADC serves as the only authorized institution in China to capture, standard manage and long-term preserve the data and samples information, and to provide sustainable polar data service. In 2003, CN-NADC became one of the nodes of βNational Data Sharing Infrastructure of Earth Scienceβ (GEODATA,http://www2.geodata.cn/), whichβs one of the Platforms of the National Science and Technology Infrastructures (NSTI, http://www.escience.org.cn//) supported by the Ministry of Science and Technology (MOST) and the Ministry of Finance of Peopleβs Republic of China.",
"homepage": "https://www.chinare.org.cn/en/",
"name": "National Arctic and Antarctic Data Center",
"prefix": "r3d100011380",
"synonyms": [
"CN-NADC"
]
},
"r3d100011381": {
"description": "The CERN Open Data portal is the access point to a growing range of data produced through the research performed at CERN. It disseminates the preserved output from various research activities, including accompanying software and documentation which is needed to understand and analyze the data being shared.",
"homepage": "http://opendata.cern.ch/",
"name": "CERN Open Data",
"prefix": "r3d100011381"
},
"r3d100011382": {
"description": "The Queen's Research Data Centre is a member of the Canadian Research Data Centre Network (CRDCN) that provides researchers with access to microdata 'masterfiles' from population and health surveys. Access to the RDC is limited to those with projects approved by Statistics Canada. Before applying to an RDC, you will have to show that your research cannot be conducted using Public Use Microdata Files (PUMFs) available through the Data Liberation Initiative (DLI). Access to DLI PUMFS at Queen's is available through the Social Science Data Centre, using the ODESI data portal.",
"homepage": "https://www.queensu.ca/qrdc/",
"name": "Queen's Research Data Centre",
"prefix": "r3d100011382",
"synonyms": [
"QRDC"
]
},
"r3d100011384": {
"description": "<<>>!!!>>>\nThe Duanaire project borrows the Irish word for song-book or anthology (loosely, a 'treasury'), to convey the sense of a rich, varied corpus handed down and explored anew. This project, led by Dr Aidan Kane (economics at NUI Galway), will open up a wealth of Irish economic history data, and in particular, Irish fiscal history data, by making accessible online a range of datasets in flexible forms to diverse audiences. The project is constructing a unique infrastructure for the imaginative curation, exploration, and sharing of significant tranches of Irish economic history data.",
"homepage": "http://www.duanaire.ie/",
"name": "Duanaire",
"prefix": "r3d100011384",
"synonyms": [
"A treasury of digital data for Irish economic history"
]
},
"r3d100011386": {
"description": "The Digital Averroes Research Environment (DARE) collects and edits the works of the Andalusian Philosopher Averroes or AbΕ« l-WalΔ«d MuαΈ₯ammad Ibn AαΈ₯mad Ibn RuΕ‘d, born in Cordoba in 1126, died in Marrakesh in 1198.\nDARE makes accessible online digital editions of Averroes's works, and images of all textual witnesses, including manuscripts, incunabula, and early prints. Averroes's writings and the scholarly literature are documented in a bibliographical database.\nAt the same time, DARE is a research platform, giving scholars who work on Averroes the opportunity to present their research and to discuss questions related to Averroes's thought in the Forum. A collaborative, evolving, and open-ended project hosted by DARE is the Averroes Encyclopaedia, designed to document Averroes's philosophical, scientific and technical vocabulary.",
"homepage": "https://dare.uni-koeln.de/",
"name": "Digital Averroes Research Environment",
"prefix": "r3d100011386",
"synonyms": [
"Averroes-Database",
"DARE"
]
},
"r3d100011387": {
"description": "Edmond is the institutional repository of the Max Planck Society for public research data. \nIt enables Max Planck scientists to create citable scientific assets by describing, enriching, sharing, exposing, linking, publishing and archiving research data of all kinds. Further on, all objects within Edmond have a unique identifier and therefore can be clearly referenced in publications or reused in other contexts.",
"homepage": "https://edmond.mpg.de",
"name": "Edmond",
"prefix": "r3d100011387",
"synonyms": [
"The Open Research Data Repository of the Max Planck Society"
]
},
"r3d100011389": {
"description": "<<>>!!!<<<",
"homepage": "http://www.bundesbank.de/Navigation/EN/Bundesbank/Research/Research_centre/research_centre.html",
"name": "Research Centre of the Bundesbank",
"prefix": "r3d100011389",
"synonyms": [
"Forschungszentrum der Deutschen Bundesbank"
]
},
"r3d100011390": {
"description": "The Comparative Study of Electoral Systems (CSES) is a collaborative, cross-national program of comparative electoral behavior among over 60 election study teams from around the world. The CSES allows examination into how societal, political, economic and structural contexts shape citizen behavior and condition democratic choice; the nature of political and social divisions; and how citizens in different political systems evaluate democratic institutions and processes. Participating countries include a common module of survey questions in their post-election studies. The resulting data are deposited along with voting, demographic, district and macro variables. The studies are then merged into a single, free, public dataset for use in comparative study and cross-level analysis. The research agenda, questionnaires, and study design are developed by an international committee of leading scholars of electoral politics and political science. The design is implemented in each country by their foremost social scientists.",
"homepage": "https://cses.org/",
"name": "Comparative Study of Electoral Systems",
"prefix": "r3d100011390",
"synonyms": [
"CSES"
]
},
"r3d100011391": {
"description": "The HSRC Research Data Service provides a digital repository facility for the HSRC's research data in support of evidence based human and social development in South Africa and the broader region. It includes both quantitative and qualitative data. Access to data is dependent on ethical requirements for protecting research participants, as well as on legal agreements with the owners, funders or in the case of data owned by the HSRC, the requirements of the depositors of the data.",
"homepage": "http://datacuration.hsrc.ac.za/",
"name": "HSRC Research Data Service",
"prefix": "r3d100011391",
"synonyms": [
"Human Sciences Research Council Research Data Service"
]
},
"r3d100011392": {
"description": "INDEPTH is a global network of research centres that conduct longitudinal health and demographic evaluation of populations in low- and middle-income countries (LMICs). INDEPTH aims to strengthen global capacity for Health and Demographic Surveillance Systems (HDSSs), and to mount multi-site research to guide health priorities and policies in LMICs, based on up-to-date scientific evidence. The data collected by the INDEPTH Network members constitute a valuable resource of population and health data for LMIC countries. This repository aims to make well documented anonymised longitudinal microdata from these Centres available to data users.",
"homepage": "https://www.indepth-ishare.org/index.php/home",
"name": "INDEPTH Data Repository",
"prefix": "r3d100011392",
"synonyms": [
"International Network for the Demographic Evaluation of Populations and Their Health Data Repository",
"iSHARE Repository"
]
},
"r3d100011393": {
"description": "Open access repository for digital research created at the University of Minnesota. U of M researchers may deposit data to the Librariesβ Data Repository for U of M (DRUM), subject to our collection policies. All data is publicly accessible. Data sets submitted to the Data Repository are reviewed by data curation staff to ensure that data is in a format and structure that best facilitates long-term access, discovery, and reuse.",
"homepage": "https://conservancy.umn.edu/handle/11299/166578",
"name": "Data Repository for the University of Minnesota",
"prefix": "r3d100011393",
"synonyms": [
"DRUM",
"Data Repository for U of M"
],
"xrefs": {
"hdl": "11299/166578"
}
},
"r3d100011394": {
"description": "B2SHARE is a user-friendly, reliable and trustworthy way for researchers, scientific communities and citizen scientists to store and share small-scale research data from diverse contexts and disciplines. B2SHARE is able to add value to your research data via (domain tailored) metadata, and assigning citable Persistent Identifiers PIDs (Handles) to ensure long-lasting access and references. B2SHARE is one of the B2 services developed via EUDAT and long tail data deposits do not cost money. Special arrangements such as branding and special metadata elements can be made on request.",
"homepage": "https://b2share.eudat.eu/",
"name": "B2SHARE",
"prefix": "r3d100011394",
"xrefs": {
"fairsharing": "FAIRsharing.da9307"
}
},
"r3d100011395": {
"description": "The EUDAT project aims to contribute to the production of a Collaborative Data Infrastructure (CDI). The projectΒ΄s target is to provide a pan-European solution to the challenge of data proliferation in Europe's scientific and research communities. \nThe EUDAT vision is to support a Collaborative Data Infrastructure which will allow researchers to share data within and between communities and enable them to carry out their research effectively. EUDAT aims to provide a solution that will be affordable, trustworthy, robust, persistent and easy to use.\nEUDAT comprises 26 European partners, including data centres, technology providers, research communities and funding agencies from 13 countries.\nB2FIND is the EUDAT metadata service allowing users to discover what kind of data is stored through the B2SAFE and B2SHARE services which collect a large number of datasets from various disciplines. EUDAT will also harvest metadata from communities that have stable metadata providers to create a comprehensive joint catalogue to help researchers find interesting data objects and collections.",
"homepage": "https://www.eudat.eu/",
"name": "EUDAT",
"prefix": "r3d100011395",
"synonyms": [
"European Data Infrastructure"
]
},
"r3d100011396": {
"description": "<<>>!!!>>> A collection of open content name datasets for Information Centric Networking. The \"Content Name Collection\" (CNC) lists and hosts open datasets of content names. These datasets are either derived from URL link databases or web traces. The names are typically used for research on Information Centric Networking (ICN), for example to measure cache hit/miss ratios in simulations.",
"name": "The Content Name Collection",
"prefix": "r3d100011396",
"synonyms": [
"CNC"
]
},
"r3d100011397": {
"description": "TERN's AEKOS data portal is the original gateway to Australian ecology data. It is a βdata and research methodsβ data portal for Australiaβs land-dwelling plants, animals and their environments. The primary focus of data content is raw co-located βspecies and environmentβ ecological survey data that has been collected at the βplotβ level to describe biodiversity, its patterns and ecological processes. It is openly accessible with standard discovery metadata and user-oriented, contextual metadata critical for data reuse. Our services support the ecosystem science community, land managers and governments seeking to publish under COPE publishing ethics and the FAIR data publishing principles. AEKOS is registered with Thomson & Reuters Data Citation Index and is a recommended repository of Nature Publishingβs Scientific Data. There are currently 97,037 sites covering mostly plant biodiversity and co-located environmental data of Australia. The AEKOS initiative is supported by TERN (tern.org.au), hosted by The University of Adelaide and funded by the Australian Governmentβs National Research Infrastructure for Australia.",
"homepage": "http://www.aekos.org.au/index.html#/home",
"name": "AEKOS Data Portal",
"prefix": "r3d100011397",
"synonyms": [
"Advanced Ecological and Knowledge Observation System Data Portal"
]
},
"r3d100011398": {
"description": "B2SAFE is a robust, safe and highly available service which allows community and departmental repositories to implement data management policies on their research data across multiple administrative domains in a trustworthy manner.\nA solution to: provide an abstraction layer which virtualizes large-scale data resources, guard against data loss in long-term archiving and preservation, optimize access for users from different regions, bring data closer to powerful computers for compute-intensive analysis",
"homepage": "https://www.eudat.eu/b2safe",
"name": "B2SAFE",
"prefix": "r3d100011398"
},
"r3d100011399": {
"description": "The Research Data Repository of the University of Mannheim invites all researchers and faculty of the University of Mannheim to archive their research data here in order to make it accessible through the Internet. All archived data sets receive DOIs (Digital Object Identifier) to make them accessible and citable. Using this repository is free of charge.",
"homepage": "https://madata.bib.uni-mannheim.de/",
"name": "MADATA - Mannheim research data repository",
"prefix": "r3d100011399",
"synonyms": [
"MADATA - Forschungsdatenrepositorium der UniversitΓ€t Mannheim"
],
"xrefs": {
"opendoar": " 6084"
}
},
"r3d100011400": {
"description": "Catena, the Digital Archive of Historic Gardens and Landscapes, is a collection of historic and contemporary images, including plans, engravings, and photographs, intended to support research and teaching in the fields of garden history and landscape studies. Created through the collaborative efforts of landscape historians and institutions, the initial offering of images is focused on the Villas as a Landscape Type.",
"homepage": "http://catena.bgc.bard.edu/",
"name": "Catena",
"prefix": "r3d100011400",
"synonyms": [
"Digital Archive of Historic Gardens and Landscapes"
]
},
"r3d100011405": {
"description": "<<>>!!!>>>",
"homepage": "http://www.modencode.org/",
"name": "modENCODE",
"prefix": "r3d100011405",
"synonyms": [
"Model Organism ENCyclopedia of DNA Elements"
],
"xrefs": {
"nlx": "151752",
"omics": "03816",
"scr": "006206"
}
},
"r3d100011407": {
"description": "Arachne is the central object-database of the German Archaeological Institute (DAI). In 2004 the DAI and the Research Archive for Ancient Sculpture at the University of Cologne (FA) joined the effort to support Arachne as a tool for free internet-based research.\nArachne's database design uses a model that builds on one of the most basic assumptions one can make about archaeology, classical archaeology or art history: all activities in these areas can most generally be described as contextualizing objects. Arachne tries to avoid the basic mistakes of earlier databases, which limited their object modeling to specific project-oriented aspects, thus creating separated containers of only a small number of objects. All objects inside Arachne share a general part of their object model, to which a more class-specific part is added that describes the specialised properties of a category of material like architecture or topography. Seen on the level of the general part, a powerful pool of material can be used for general information retrieval, whereas on the level of categories and properties, very specific structures can be displayed.",
"homepage": "https://arachne.dainst.org/",
"name": "ARACHNE IDAI.objects",
"prefix": "r3d100011407"
},
"r3d100011413": {
"description": "In the WolfenbΓΌttel Digital Library the Herzog August Bibliothek presents in digital facsimile selected items from its collections which are rare, outstanding, frequently used, or currently most relevant for research. All digitized titles may be accessed not only here, but also via the PICA-OPAC as long as they are monographs. The OPAC allows you to search for digitized books separately by limiting the search options within the database using the term Online Resources.\nProjects which provide additional indexing comprise a project-specific database, an inventory of digitized titles, information about tools and techniques, and references to literature. Here the main objective is to provide search facilities outside the scope of usual bibliographic description, such as page-related indexing.",
"homepage": "https://www.hab.de/digitale-bibliothek-wdb/",
"name": "WolfenbΓΌtteler Digital Library",
"prefix": "r3d100011413",
"synonyms": [
"WDB",
"WolfenbΓΌtteler Digitale Bibliothek"
]
},
"r3d100011414": {
"description": "Zvdd aims to record all digital surrogates of printed works, which are available from the internet and meet certain quality criteria. This comprised all types of printed works, such as newspapers, journals, printed music, flying leaves as well as monographs or serials.",
"homepage": "https://www.zvdd.de/startseite/",
"name": "ZVDD",
"prefix": "r3d100011414",
"synonyms": [
"Zentrales Verzeichnis Digitalisierter Drucke"
]
},
"r3d100011415": {
"description": "The database contains numerical data on atomic and molecular collisions, radiative processes and various other material properties of specific use in fusion and plasma research. Searching the database produces bibliographic results linking to the research paper containing the data of interest. Searches can be performed based on a variety of parameters including reactants, surface of interest, data type; or by date, journal or author.",
"homepage": "https://amdis.iaea.org/db/ambdas/",
"name": "AMBDAS Bibliographic Database",
"prefix": "r3d100011415",
"synonyms": [
"Atomic and Molecular Bibliographic Data System"
]
},
"r3d100011416": {
"description": "<<>>!!!>>>",
"homepage": "https://www-amdis.iaea.org/GENIE/",
"name": "GENIE",
"prefix": "r3d100011416",
"synonyms": [
"GENIE Atomic Data Search Engine",
"General Internet Search Engine for Atomic Data"
]
},
"r3d100011417": {
"description": "This database contains references to publications that include numerical data, general information, comments, and reviews on atomic line broadening and shifts, and is part of the collection of the NIST Atomic Spectroscopy Data Center https://www.nist.gov/pml/quantum-measurement/atomic-spectroscopy/atomic-spectroscopy-data-center-contacts.",
"homepage": "https://physics.nist.gov/cgi-bin/ASBib1/LineBroadBib.cgi",
"name": "NIST Atomic Spectral Line Broadening Bibliographic Database",
"prefix": "r3d100011417"
},
"r3d100011418": {
"description": "FLYCHK provides a capability to generate atomic level populations and charge state distributions for low-Z to mid-Z elements under NLTE conditions.",
"homepage": "https://nlte.nist.gov/FLY/",
"name": "NIST FLYCHK",
"prefix": "r3d100011418",
"synonyms": [
"Collisional-Radiative Code",
"NIST Standard Reference Database 160"
]
},
"r3d100011419": {
"description": "This database contains benchmark results for simulation of plasma population kinetics and emission spectra. The data were contributed by the participants of the 3rd Non-LTE Code Comparison Workshop who have unrestricted access to the database.",
"homepage": "https://nlte.nist.gov/SAHA/",
"name": "NIST Saha Plasma Population Kinetics Modeling Database",
"prefix": "r3d100011419",
"synonyms": [
"SAHA Plasma Population Kinetics Database"
]
},
"r3d100011420": {
"description": "This database contains references to publications that include numerical data, comments, and reviews on atomic transition probabilities (oscillator strengths, line strengths, or radiative lifetimes), and is part of the collection of the NIST Atomic Spectroscopy Data Center http://physics.nist.gov/PhysRefData/datarefs/datarefs_search_form.html",
"homepage": "https://physics.nist.gov/cgi-bin/ASBib1/TransProbBib.cgi",
"name": "NIST Atomic Transition Probability Bibliographic Database",
"prefix": "r3d100011420",
"synonyms": [
"Atomic Transition Probabilities Bibliographic Database"
]
},
"r3d100011421": {
"description": "In February 1986 the NIST measurements were communicated to appropriate astronomers for use in ground-based testing and calibration programs for the GHRS, and in 1990 the NIST group published the new wavelengths for about 3000 lines in the Supplement Series of the Astrophysical Journal. The full report on the NIST measurements in the form of a complete and detailed atlas of the platinum/neon spectrum presented in this special issue of the Journal of Research of NIST will be highly useful to a wide range of scientists.",
"homepage": "https://www.nist.gov/pml/ultraviolet-spectrum-platinum-lamp",
"name": "NIST Ultraviolet Spectrum of Platinum Lamp",
"prefix": "r3d100011421",
"synonyms": [
"Spectrum of Platinum",
"formerly: NIST Atlas of the Spectrum of a Platinum/Hollow-Cathode Lamp in the region 1130-4330 Γ
"
]
},
"r3d100011423": {
"description": "This handbook is designed to provide a selection of the most important and frequently used atomic spectroscopic data in an easily accessible format. The compilation includes data for the neutral and singly-ionized atoms of all elements hydrogen through einsteinium (Z = 1-99).",
"homepage": "https://www.nist.gov/pml/handbook-basic-atomic-spectroscopic-data",
"name": "Handbook of Basic Atomic Spectroscopic Data",
"prefix": "r3d100011423",
"synonyms": [
"NIST Standard Reference Database 108"
]
},
"r3d100011424": {
"description": "This database gives values of the basic constants and conversion factors of physics and chemistry resulting from the 2002 least-squares adjustment of the fundamental physical constants as published by the CODATA Task Group on Fundamental Constants and recommended for international use by CODATA.",
"homepage": "https://physics.nist.gov/cuu/Constants/index.html",
"name": "The NIST Reference on Constants, Units, and Uncertainty",
"prefix": "r3d100011424",
"synonyms": [
"NIST Reference on Constants, Units, and Uncertainty",
"Values of Fundamental Physical Constants"
]
},
"r3d100011426": {
"description": "This site provides up-to-date public access to Robert L. Kurucz data and programs: Vita and bibliography, papers, atoms, molecules, linelists, opacities, grids of model atmospheres, sun, stars, programs, CD-ROMs.",
"homepage": "http://kurucz.harvard.edu/",
"name": "Robert L. Kurucz",
"prefix": "r3d100011426"
},
"r3d100011427": {
"description": "This facility permits selective searches of some atomic data files compiled by R. L. Kurucz (Harvard-Smithsonian Center for Astrophysics). The data provided are: - vacuum wavelength (in nm) [above 200 nm calculated using Edlen, Metrologia, Vol. 2, No. 2, 1966]- air wavelength (in nm) above 200 nm- log(gf), - E [in cm-1], j, parity, and configuration for the levels (lower, upper), - information regarding the source of the data.\nCD-ROM 18 contains the spectrum synthesis programs ATLAS7V, SYNTHE, SPECTRV, ROTATE, BROADEN, PLOTSYN, etc. and sample runs found in directory PROGRAMS; Atomic line data files BELLHEAVY.DAT, BELLLIGHT.DAT, GFIRONLAB.DAT, GULLIVER.DAT, NLTELINES.DAT, GFIRONQ.DAT, obsolete, merged into GFALL, found in directory LINELISTS: Molecular line data files C2AX.ASC, C2BA.ASC, C2DA.ASC, C2EA.ASC, CNAX.ASC, CNBX.ASC, COAX.ASC, COXX.ASC, H2.ASC, HYDRIDES.ASC, SIOAX.ASC, SIOEX.ASC, SIOXX.ASC, found in directory LINELISTS; and my solar flux atlas for test calculations SOLARFLUX.ASC.",
"homepage": "https://lweb.cfa.harvard.edu/amp/ampdata/databases.html",
"name": "R. L. Kurucz atomic linelist",
"prefix": "r3d100011427",
"synonyms": [
"CD-ROM 18 and CD-ROM 23"
]
},
"r3d100011428": {
"description": "<<>>!!!<<< \nPlease use https://www.cfa.harvard.edu/amp/ampdata/kurucz23/sekur.html\nThe atomic line data used in this database are taken from Bob Kurucz' CD-ROM 23 of spectroscopic line calculations. The database contains all lines of the file \"gfall.dat\" with the following items for each line: Wavelength; loggf; element code; lower level: energy, J, configuration; upper level: energy, J, configuration; gamma r; gamma s; gamma w; reference code.\nCD-ROM 23 has all the atomic line data with good wavelengths in one large file and in one file for each species. The big file is also divided into 10 nm and 100 nm sections for convenience. Also given are hyperfine line lists for neutral Sc, V, Mn, and Co that were produced by splitting all the energy levels for which laboratory data are available (only a small fraction).",
"homepage": "http://www.pmp.uni-hannover.de/cgi-bin/ssi/test/kurucz/sekur.html",
"name": "European mirror of Kurucz CD-ROM 23 database",
"prefix": "r3d100011428",
"synonyms": [
"Atomic spectral line database from CD-ROM 23 of Robert L. Kurucz"
]
},
"r3d100011429": {
"description": "Atomic and Ionic UV/VUV Linelist . This facility permits selective searches of some atomic data compliled by R. L. Kelly. The data provided are:\n - vacuum wavelength [in nm], \n - intensity estimate, \n - E [in cm-1], j, and configuration for lower and upper levels, \n - multiplet (where available), \n - reference numbers of the sources of the data.",
"homepage": "https://www.cfa.harvard.edu/ampcgi/kelly.pl",
"name": "R.L.Kelly atomic and ionic linelist",
"prefix": "r3d100011429"
},
"r3d100011430": {
"description": "AtomDB is an atomic database useful for X-ray plasma spectral modeling. The current version of AtomDB is primarly used for modeing collisional plasmas, those where hot electrons colliding with astrophysically abundant elements and ions create X-ray emission. However, AtomDB is also useful when modeling absorption by elements and ions or even photoionized plasmas, where X-ray photons (often from a simple power-law source) interacting with elements and ions create complex spectra.",
"homepage": "http://www.atomdb.org/",
"name": "ATOMDB",
"prefix": "r3d100011430"
},
"r3d100011431": {
"description": "This database provides theoretical values of energy levels of hydrogen and deuterium for principle quantum numbers n = 1 to 200 and all allowed orbital angular momenta l and total angular momenta j. The values are based on current knowledge of the revelant theoretical contributions including relativistic, quantum electrodynamic, recoil, and nuclear size effects.",
"homepage": "https://www.nist.gov/pml/energy-levels-hydrogen-and-deuterium",
"name": "NIST Energy Levels of Hydrogen and Deuterium",
"prefix": "r3d100011431",
"synonyms": [
"Energy Levels of Hydrogen and Deuterium",
"NIST Standard Reference Database 142"
]
},
"r3d100011432": {
"description": "<<>>!!!>>>\nPresented here are excitation cross sections measured for a select number of transitions using the Merged Electron-Ion Beams Energy Loss (MEIBEL) experiment. This is a collaboration of JILA and the Multicharged Ion Research Facility (MIRF) at Oak Ridge National Laboratory (ORNL), where the apparatus is located. Since there exist a nearly infinite number of transitions in multicharged ions we have chosen a few that serve as benchmarks for theoretical efforts. Of particular interest are forbidden transitions which are often dominated by dielectronic resonances whose positions and magnitudes are difficult to predict theoretically.",
"homepage": "http://www.cfadc.phy.ornl.gov/meibel/home.html",
"name": "Electron-Impact Excitation of Multicharged Ions using MEIBEL",
"prefix": "r3d100011432",
"synonyms": [
"Electron-Impact Excitation of Multicharged Ions using Merged Electron-Ion Beams Energy Loss"
]
},
"r3d100011433": {
"description": ">>>!!!<<< 2019-12-04: The repository is no longer available >>>!!!<<< \nPresented here are experimental ionization cross sections measured using the Electron-Ion Crossed Beams apparatus in the Multicharged Ion Research Facility (MIRF) at the Physics Division of Oak Ridge National Laboratory (ORNL). The data are given in both graphical and tabular form along with the reference to the original publication of the experimental results. Also presented in the figures are theoretical cross sections supporting the experiments.",
"homepage": "http://www.cfadc.phy.ornl.gov/xbeam/xbmintro.html",
"name": "Electron-Impact Ionization of Multicharged Ions at ORNL",
"prefix": "r3d100011433"
},
"r3d100011434": {
"description": "The Atomic Data for Astrophysics server provides links to basic atomic data required for calculation of the ionization state of astrophysical plasmas and for quantitative spectroscopy.",
"homepage": "https://www.pa.uky.edu/~verner/atom.html",
"name": "Atomic Data for Astrophysics",
"prefix": "r3d100011434"
},
"r3d100011444": {
"description": "This is a compilation of approximately 923,000 allowed, intercombination and forbidden atomic transitions with wavelengths in the range from 0.5 Γ
to 1000 Β΅m. It's primary intention is to allow the identification of observed atomic absorption or emission features. The wavelengths in this list are all calculated from the difference between the energy of the upper and lower level of the transition. No attempt has been made to include observed wavelengths. Most of the atomic energy level data have been taken from the Atomic Spectra Database provided by the National Institute of Standards and Technology (NIST).",
"homepage": "https://linelist.pa.uky.edu/atomic/",
"name": "The Atomic Line List",
"prefix": "r3d100011444",
"synonyms": [
"The Atomic Line List v2.04"
]
},
"r3d100011446": {
"description": "STARK-B is a database of calculated widths and shifts of isolated lines of atoms and ions due to electron and ion collisions. This database is devoted to modeling and spectroscopic diagnostics of stellar atmospheres and envelopes. In addition, it is also devoted to laboratory plasmas, laser equipments and technological plasmas. So, the domain of temperatures and densities covered by the tables is wide and depends on the ionization degree of the considered ion. The temperature can vary from several thousands for neutral atoms to several hundred thousands of Kelvin for highly charged ions. The electron or ion density can vary from 1012 (case of stellar atmospheres) to several 1019cm-3 (some white dwarfs and some laboratory plasmas).",
"homepage": "https://stark-b.obspm.fr/",
"name": "STARK-B",
"prefix": "r3d100011446",
"xrefs": {
"issn": "2429-6465"
}
},
"r3d100011447": {
"description": "<<>>!!!>>>",
"homepage": "https://griem.obspm.fr/index.php?page=accueil.php",
"name": "Stark Broadening Parameters for Neutral and Singly Charged Ions",
"prefix": "r3d100011447",
"synonyms": [
"Paramètres d'élargissement Stark des éléments neutres et une fois ionisés"
]
},
"r3d100011448": {
"description": "The Vienna Atomic Line Database (VALD) is a collection of atomic and molecular transition parameters of astronomical interest. VALD offers tools for selecting subsets of lines for typical astrophysical applications: line identification, preparing for spectroscopic observations, chemical composition and radial velocity measurements, model atmosphere calculations etc.",
"homepage": "http://vald.astro.uu.se/",
"name": "Vienna Atomic Line Database",
"prefix": "r3d100011448",
"synonyms": [
"VALD"
]
},
"r3d100011449": {
"description": "The MCHF/MCDHF database contains collections of transition data from different relativistic theories by different computational methods. For a few collections the LandΓ© gJ factor is provided.",
"homepage": "https://nlte.nist.gov/MCHF/",
"name": "MCHF/MCDHF Database",
"prefix": "r3d100011449",
"synonyms": [
"Multiconfiguration Hartree-Fock and Multiconfiguration Dirac-Hartree-Focbasek Data"
]
},
"r3d100011450": {
"description": "CHIANTI consists of a critically evaluated set of up-to-date atomic data, together with user-friendly programs written in Interactive Data Language (IDL) and Python to calculate the spectra from astrophysical plasmas.",
"homepage": "https://www.chiantidatabase.org/",
"name": "CHIANTI",
"prefix": "r3d100011450",
"synonyms": [
"An Atomic Database for Spectroscopic Diagnostics of Astrophysical Plasmas"
]
},
"r3d100011452": {
"description": ">>>!!!<<< 2018-01-18: no data nor programs can be found >>>!!!<<< These archives contain public domain programs for calculations in physics and other programs that we suppose about will help during work with computer. Physical constants and experimental or theoretical data as cross sections, rate constants, swarm parameters, etc., that are necessary for physical calculations are stored here, too. Programs are mainly dedicated to computers compatible with PC IBM. If programs do not use graphic units it is possible to use them on other computers, too. It is necessary to reprogram the graphic parts of programs in the other cases.",
"homepage": "http://www.sci.muni.cz/~physics/info.htm",
"name": "Archives of programs and data for physics",
"prefix": "r3d100011452",
"synonyms": [
"Archives for physics"
]
},
"r3d100011454": {
"description": "Portal to Los Alamos Opacity Codes is your gateway to the set of opacity codes developed at the Los Alamos National Laboratory.\nThe TOPS code has been developed to calculate multigroup opacities that can be written in a variety of formats for use in radiation transport codes. Arbitrary mixture of any elements for which OPLIB data exist is supported. Opacities of special mixtures that are important in astrophysical applications are also available as a separate option (Astrophysical opacities).",
"homepage": "https://aphysics2.lanl.gov/apps/",
"name": "Portal to Los Alamos Opacity Codes",
"prefix": "r3d100011454",
"synonyms": [
"Astrophysical opacities",
"TOPS opacities"
]
},
"r3d100011455": {
"description": "Interface to Los Alamos Atomic Physics Codes is your gateway to the set of atomic physics codes developed at the Los Alamos National Laboratory.\n The well known Hartree-Fock method of R.D. Cowan, developed at Group home page of the Los Alamos National Laboratory, is used for the atomic structure calculations. Electron impact excitation cross sections are calculated using either the distorted wave approximation (DWA) or the first order many body theory (FOMBT). Electron impact ionization cross sections can be calculated using the scaled hydrogenic method developed by Sampson and co-workers, the binary encounter method or the distorted wave method. Photoionization cross sections and, where appropriate, autoionizations are also calculated.",
"homepage": "http://aphysics2.lanl.gov/tempweb/lanl/",
"name": "Interface to Los Alamos Atomic Physics Codes",
"prefix": "r3d100011455"
},
"r3d100011456": {
"description": "The CCC method yields accurate excitation and ionisation cross sections for atomic and ionic targets which are well-modelled by one or two valence electrons above a Hartree-Fock core. Inner core ionisation can be a major contributor to the total ionisation cross section. Such contributions can be estimated using various forms of Born-based approximations.",
"homepage": "https://atom.curtin.edu.au/CCC-WWW/index.html",
"name": "CCC Data Base",
"prefix": "r3d100011456",
"synonyms": [
"Convergent Close-Coupling Data Base"
]
},
"r3d100011457": {
"description": "<<>>!!!>>>",
"homepage": "http://atom.kaeri.re.kr/",
"name": "AMODS",
"prefix": "r3d100011457",
"synonyms": [
"Atomic Molecular and Optical Database Systems"
]
},
"r3d100011460": {
"description": "The information accumulated in the SPECTR-W3 ADB contains over 450,000 records and includes factual experimental and theoretical data on ionization potentials, energy levels, wavelengths, radiation transition probabilities, oscillator strengths, and (optionally) the parameters of analytical approximations of electron-collisional cross-sections and rates for atoms and ions. Those data were extracted from publications in physical journals, proceedings of the related conferences, special-purpose publications on atomic data, and provided directly by authors. The information is supplied with references to the original sources and comments, elucidating the details of experimental measurements or calculations, where necessary and available. To date, the SPECTR-W3 ADB is the largest factual database in the world containing the information on spectral properties of multicharged ions.",
"homepage": "http://spectr-w3.snz.ru/index.phtml",
"name": "SPECTR-W3",
"prefix": "r3d100011460",
"synonyms": [
"Atomic Database Spectr-W3 for Plasma Spectroscopy and other Applications",
"SPECTR-W3 Database on spectroscopic properties of atoms and ions"
]
},
"r3d100011461": {
"description": "Welcome to our Atomic & Molecular Database in the Institute of Applied Physics and Computational Mathematics (IAPCM). The database is intended to collect, assess and compile atomic and molecular data for various elementary processes, and especially data needed in plasma simulation and diagnosis. Part data came from the old version of the SPECTR database(by A.Ya Faenov et al).",
"homepage": "http://www.camdb.ac.cn/e/",
"name": "Atomic & Molecular Database",
"prefix": "r3d100011461",
"synonyms": [
"CAMDB",
"Chinese Atomic & Molecular Database",
"εεεεζ°ζεΊ"
]
},
"r3d100011462": {
"description": "<<>>!!!>>>\nThe aim of the present volume is the compilation of experimental data. The Tables of energy levels are presented in a way similar to the \"Atomic Energy levels the Rare Earth Elements\", and incorporate additionnal data: isotope shifts and hyperfine structures. For each spectrum, they are separated in two lists of odd and even levels, the parity of the ground level being given first.",
"homepage": "http://web2.lac.u-psud.fr/lac/Database/Contents.html",
"name": "Selected constants energy levels and atomic spectra of actinides",
"prefix": "r3d100011462",
"synonyms": [
"Constantes selectionnees niveaux d'energie et spectres atomiques des actinides"
],
"xrefs": {
"issn": "2428-257X"
}
},
"r3d100011464": {
"description": "At the heart of the Plasma Data Exchange Project is LXcat (pronounced \"elecscat\"), an open-access website for collecting, displaying, and downloading electron and ion scattering cross sections, swarm parameters (mobility, diffusion coefficient, etc.), reaction rates, energy distribution functions, etc. and other data required for modeling low temperature plasmas. The available data bases have been contributed by members of the community and are indicated by the contributor's chosen title.",
"homepage": "https://fr.lxcat.net/home/",
"name": "LXcat",
"prefix": "r3d100011464",
"synonyms": [
"ICECat",
"electron scattering database",
"ion scattering database"
]
},
"r3d100011466": {
"description": "Hourly \"Near-Earth\" solar wind magnetic field and plasma data, energetic proton fluxes (>1 to >60 MeV), and geomagnetic and solar activity indices. OMNIWeb is part of \"Space Physics Data Facility\" (https://www.re3data.org/repository/r3d100010168 ).",
"homepage": "https://omniweb.gsfc.nasa.gov/ow.html",
"name": "OMNIWeb",
"prefix": "r3d100011466"
},
"r3d100011468": {
"description": "<<>>!!!>>>\nThis page is not longer active, please use www.marine-data.de instead.\nOur data portal data.awi.de offers an integrative one-stop shop framework for discovering AWI research platforms including devices and sensors, tracklines, field reports, peer-reviewed publications, GIS products and mostly important data and data products archived in PANGAEA.",
"homepage": "https://data.awi.de/?site=home",
"name": "Data Portal of the Alfred Wegener Institute",
"prefix": "r3d100011468",
"synonyms": [
"including: AWI EXPEDITION"
],
"xrefs": {
"biodbcore": "001661"
}
},
"r3d100011469": {
"description": "This portal provides an overview of GIS-products at AWI. maps@awi stores and shares public access GIS data created by AWI projects.",
"homepage": "https://maps.awi.de/awimaps/catalog/",
"name": "GIS Maps Portal at AWI",
"prefix": "r3d100011469",
"synonyms": [
"maps@awi"
],
"xrefs": {
"biodbcore": "001511"
}
},
"r3d100011470": {
"description": "The Marine Data Portal is a product of the βUnderwayβ- Data initiative of the German Marine Research Alliance (Deutsche Allianz Meeresforschung - DAM) and is supported by the marine science centers AWI, GEOMAR and Hereon of the Helmholtz Association. This initiative aims to improve and standardize the systematic data collection and data evaluation for expeditions with German research vessels and marine observation. It supports scientists in their data management duties and fosters (data) science through FAIR and open access to marine research data. AWI, GEOMAR and Hereon develop this marine data hub (Marehub) to build a decentralized data infrastructure for processing, long-term archiving and dissemination of marine observation and model data and data products. \nThe Marine Data Portal provides user-friendly, centralized access to marine research data, reports and publications from a wide range of data repositories and libraries in the context of German marine research and its international collaboration. \nThe Marine Data Portal is developed by scientists for scientists in order to facilitate Findability and Access of marine research data for Reuse. It supports machine-readable and data driven science. Please note that the quality of the data may vary depending on the purpose for which it was originally collected.",
"homepage": "https://marine-data.de/",
"name": "Marine Data Portal",
"prefix": "r3d100011470",
"synonyms": [
"formerly name: Data Portal German Marine Research"
],
"xrefs": {
"fairsharing": "FAIRsharing.dac16a"
}
},
"r3d100011471": {
"description": "This portal applicaton brings together the data collected and published via OGC Web-services from the individual observatories and provides access of the data to the public. Therefore, it serves as a database node to provide scientists and decision makers with reliable and well accessible data and data products.",
"homepage": "https://ddp.tereno.net/ddp/",
"name": "TERENO Data Discovery Portal",
"prefix": "r3d100011471",
"synonyms": [
"Terrestrial Environmental Observatories Data Discovery Portal"
]
},
"r3d100011472": {
"description": "Our system consists of a portal (portal.geomar.de), providing access to several projects with personal password. The portal offers document exchange, common or individual blogs and fora and implementation of external webpages and -services. Moreover, you can access the expedition database, that organizes data description and exchange of cruises and expeditions for each project. Expeditions are linked to KML-files (Google-Earth compatible), allowing a visualization of all stations of a cruise/expedition.\nWe established the linkage to the publications database /repository OceanRep (EPrints), as well as the description of model-output and linkage to paper publications.",
"homepage": "https://portal.geomar.de/osis",
"name": "Ocean Science Information System",
"prefix": "r3d100011472",
"synonyms": [
"OSIS",
"Ocean Science Information System"
]
},
"r3d100011473": {
"description": "Thousands of circular RNAs (circRNAs) have recently been shown to be expressed in eukaryotic cells [Salzman et al. 2012, Jeck et al. 2013, Memczak et al. 2013, Salzman et al. 2013]. Here you can explore public circRNA datasets and download the custom python scripts needed to discover circRNAs in your own (ribominus) RNA-seq data.",
"homepage": "http://www.circbase.org/",
"name": "circBase",
"prefix": "r3d100011473"
},
"r3d100011474": {
"description": "database of pSILAC data β information about changes in mRNA levels and protein synthesis following microRNA misexpression in HeLa cells",
"homepage": "https://psilac.mdc-berlin.de/",
"name": "pSILAC",
"prefix": "r3d100011474",
"synonyms": [
"pulsed SILAC"
]
},
"r3d100011475": {
"description": "<<>>!!!>>> A human interactome map. The sequencing of the human genome has provided a surprisingly small number of genes, indicating that the complex organization of life is not reflected in the gene number but, rather, in the gene products β that is, in the proteins. These macromolecules regulate the vast majority of cellular processes by their ability to communicate with each other and to assemble into larger functional units. Therefore, the systematic analysis of protein-protein interactions is fundamental for the understanding of protein function, cellular processes and, ultimately, the complexity of life. Moreover, interactome maps are particularly needed to link new proteins to disease pathways and the identification of novel drug targets.",
"homepage": "http://artemis.mdc-berlin.de/y2h_network/ppi_search.php",
"name": "Human protein-protein interaction network database search",
"prefix": "r3d100011475"
},
"r3d100011476": {
"description": "<<>>!!!>>> The main objective of our work is to understand the pathomechanisms of late onset neurodegenerative disorders such as Huntington's, Parkinson's, Alzheimer's and Machado Joseph disease and to develop causal therapies for them. The disease causing proteins of these illnesses have been identified, but their functions in the unaffected organism are mostly unknown. Here, we have developed a strategy combining library and matrix yeast two-hybrid screens to generate a highly connected PPI network for Huntington's disease (HD).",
"homepage": "http://artemis.mdc-berlin.de/huntington/eingabe.php",
"name": "Huntingtin Interaction Network",
"prefix": "r3d100011476"
},
"r3d100011477": {
"description": "RELMIN collects, studies and publishes legal texts defining the status of religious minorities in medieval Europe. The corpus of texts is rich and varied, spanning ten centuries over a broad geographical area; these texts, in Latin, Arabic, Greek, Hebrew and Aramaic (and also in Medieval Spanish, Portuguese, and other European vernaculars), are dispersed in libraries and archives across Europe. The texts are now gathered in the RELMIN Database in their original language, with translations and commentaries. They are made available to scholars, students and citizens at large. Access is unlimited, free and perennial. and to contribute to the work of compilation. RELMIN is is buil\nding a digital database of legal, judicial and normative sources defining the status of religious\nminorities from the 5th to the 15th century.",
"homepage": "http://telma.irht.cnrs.fr/outils/relmin/index/",
"name": "RELMIN",
"prefix": "r3d100011477",
"synonyms": [
"Le statut lΓ©gal des minoritΓ©s religieuses dans lβespace euro-mΓ©diterranΓ©en (VΓ¨me βXVΓ¨me siΓ¨cles)",
"The legal status of religious minorities in the Euro-Mediterranean world (5th -15th centuries"
],
"xrefs": {
"issn": "2428-4661"
}
},
"r3d100011478": {
"description": "PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets.",
"homepage": "https://www.pombase.org/",
"name": "Pombase",
"prefix": "r3d100011478",
"synonyms": [
"The scientific resource for fission yeast"
],
"xrefs": {
"fairsharing": "FAIRsharing.8jsya3",
"miriam": "00000335",
"nlx": "144356",
"omics": "06183",
"scr": "006586"
}
},
"r3d100011479": {
"description": "TriTrypDB is an integrated genomic and functional genomic database for pathogens of the family Trypanosomatidae, including organisms in both Leishmania and Trypanosoma genera. TriTrypDB and its continued development are possible through the collaborative efforts between EuPathDB, GeneDB and colleagues at the Seattle Biomedical Research Institute (SBRI).",
"homepage": "https://tritrypdb.org/tritrypdb/app",
"name": "TriTrypDB",
"prefix": "r3d100011479",
"synonyms": [
"kinetoplastid genomics resource"
],
"xrefs": {
"fairsharing": "FAIRsharing.fs1z27",
"miriam": "00000155",
"nlx": "152064",
"omics": "03144",
"scr": "007043"
}
},
"r3d100011480": {
"description": "<<>>!!!<<<\nArchived page of Taenia solium genome project see https://web.archive.org/web/20160309194611/http://www.taeniasolium.unam.mx/taenia",
"homepage": "http://www.taeniasolium.unam.mx/taenia/",
"name": "The Taenia solium Genome Project",
"prefix": "r3d100011480",
"synonyms": [
"T. solium Genome Project"
]
},
"r3d100011481": {
"description": "Cranach.net is the research database of the Cranach Research Institute (CRI), a project of the Department of History of Art of the Stuttgart State Academy of Art and Design, which is dedicated to the digitization and indexing of the complete works of Lucas Cranach the Elder and his workshop.",
"homepage": "https://cranach.ub.uni-heidelberg.de/wiki/index.php/Hauptseite",
"name": "cranach.net",
"prefix": "r3d100011481",
"synonyms": [
"das Forschungs-Wiki zu Lucas Cranach, seinen SΓΆhnen und seiner Werkstatt"
]
},
"r3d100011482": {
"description": "Bildarchiv Foto Marburg is Germany's documentation center for art history. Its mission is to collect, index and make available photographs related to European art and architecture, as well as to conduct research on the history, practice and theory of how visual cultural assets are passed on, especially the accompanying transformation process as it relates to the media, the conditions of storing knowledge in visual form, and the significance to society of remembering visual culture. The inventory of Bildarchiv Foto Marburg, the greater part of which is digitally processed, and the inventories of further cultural organizations can be viewed on the internet from the image database: Image Index of Art and Architecture: https://www.bildindex.de/",
"homepage": "https://www.uni-marburg.de/de/fotomarburg",
"name": "Deutsches Dokumentationszentrum fΓΌr Kunstgeschichte, Bildarchiv Foto Marburg",
"prefix": "r3d100011482",
"synonyms": [
"Bildarchiv Foto Marburg",
"Documentation Center for Art History, Bildarchiv Foto Marburg"
]
},
"r3d100011483": {
"description": "!!! We will terminate ASTER Products Distribution Service in March 2016 although we have been providing ASTER Products since November 20, 2000. !!!\nASTER (Advanced Spaceborne Thermal Emission and Reflection radiometer) is the high efficiency optical imager which covers a wide spectral region from the visible to the thermal infra-red by 14 spectral bands. ASTER acquires data which can be used in various fields in earth science. ASTER was launched from Vandenberg Air Force Base in California, USA in 1999 aboard the Terra, which is the first satellite of the EOS Project. The purpose of ASTER project is to make contributions to extend the understanding of local and regional phenomena on the Earth surface and its atmosphere. The followings are ASTER related information, which includes ASTER instrument, ASTER Ground Data System, ASTER Science Activities, ASTER Data Distribution and so on. ASTER Search provides services to search and order ASTER data products on the website.",
"homepage": "http://www.jspacesystems.or.jp/en_project_aster/",
"name": "ASTER j-spacesystems",
"prefix": "r3d100011483",
"synonyms": [
"Advanced Spaceborne Thermal Emission and Reflection Radiometer Ground Data Systems"
]
},
"r3d100011484": {
"description": "The geophysical database, GERDA, is a strong tool for data storage, handling and QC. Data are uploaded to and downloaded from the GERDA database through this website. GERDA is the Danish national database on shallow geophysical data. Since its establishment in 1998-2000, the database has been continuously developed. The database is hosted by the Geological Survey of Denmark and Greenland (GEUS).",
"homepage": "https://eng.geus.dk/products-services-facilities/data-and-maps/national-geophysical-database-gerda/",
"name": "GERDA",
"prefix": "r3d100011484",
"synonyms": [
"GEofysisk Relationel DAtabase",
"GEophysical Relational DAtabase",
"National Geophysical Database",
"National geofysisk database"
],
"xrefs": {
"biodbcore": "001625",
"fairsharing": "FAIRsharing.893fc2"
}
},
"r3d100011485": {
"description": "The Bremen Core Repository - BCR, for International Ocean Discovery Program (IODP), Integrated Ocean Discovery Program (IODP), Ocean Drilling Program (ODP), and Deep Sea Drilling Project (DSDP) cores from the Atlantic Ocean, Mediterranean and Black Seas and Arctic Ocean is operated at University of Bremen within the framework of the German participation in IODP. It is one of three IODP repositories (beside Gulf Coast Repository (GCR) in College Station, TX, and Kochi Core Center (KCC), Japan). One of the scientific goals of IODP is to research the deep biosphere and the subseafloor ocean. IODP has deep-frozen microbiological samples from the subseafloor available for interested researchers and will continue to collect and preserve geomicrobiology samples for future research.",
"homepage": "https://www.marum.de/en/Research/IODP-Bremen-Core-Repository.html",
"name": "IODP Bremen Core Repository",
"prefix": "r3d100011485",
"synonyms": [
"BCR"
]
},
"r3d100011486": {
"description": "The International Ocean Discovery Programβs (IODP) Gulf Coast Repository (GCR) is located in the Research Park on the Texas A&M University campus in College Station, Texas. This repository stores DSDP, ODP, and IODP cores from the Pacific Ocean, the Caribbean Sea and Gulf of Mexico, and the Southern Ocean. A satellite repository at Rutgers University houses New Jersey/Delaware land cores 150X and 174AX.",
"homepage": "https://iodp.tamu.edu/curation/gcr/",
"name": "Gulf Coast Repository",
"prefix": "r3d100011486",
"synonyms": [
"GCR"
]
},
"r3d100011487": {
"description": "Welcome to the home page of the Rutgers/New Jersey Geological and Water Survey Core Repository. We are an official repository of the International Ocean Discovery Program (IODP), hosting Legs 150X and 174AX onshore cores drilled as part of the NJ/Mid-Atlantic Transect, and the New Jersey Geological and Water Survey (NJGWS). Cores from other ODP/IODP repositories are available through ODP.\nIn addition to ODP/IODP cores, we are the repository for:\n1. 6668 m of Newark Basin Drilling Project Triassic cores (e.g., Olsen, Kent, et al. 1996)\n2. More than 10,000 m of the Army Corps of Engineers Passaic Tunnel Project Triassic and Jurassic cores\n3. 1947 m of core from the Chesapeake Bay Impact Structure Deep Hole\n 4. Cores obtained from the Northern North Atlantic as part of the IODP Expedition 303/306\n5. Cores from various rift and drift basins on the eastern and Gulf Coasts of the U.S.\n6. Geological samples from the New Jersey Geological and Water Survey (NJGWS) and United States Geological Survey (USGS) including 304 m of continuous NJGWS/USGS NJ coastal plain cores.",
"homepage": "https://geology.rutgers.edu/rutgers-core-repository",
"name": "Rutgers/New Jersey Geological and Water Survey Core Repository",
"prefix": "r3d100011487",
"synonyms": [
"NJGS"
]
},
"r3d100011488": {
"description": "Kochi Core Center (KCC) houses one of the 3 Inernationational Ocean Discovery Program (IODP) core repositories, accompanied by images and x-ray CT scanning data viewable by the Virtual Core Library. And it hosts Japan Agency for Marine-Earth Science and Technology (JAMSTEC) marine core samples and associated analytical data for general scientific or educational uses, after 2 years have passed since collection of core samples.",
"homepage": "http://www.kochi-core.jp/en/",
"name": "Kochi Core Center",
"prefix": "r3d100011488",
"synonyms": [
"KCC"
]
},
"r3d100011489": {
"description": "The EXFOR library contains an extensive compilation of experimental nuclear reaction data. Neutron reactions have been compiled systematically since the discovery of the neutron, while charged particle and photon reactions have been covered less extensively.",
"homepage": "https://www-nds.iaea.org/exfor/exfor.htm",
"name": "Experimental Nuclear Reaction Data",
"prefix": "r3d100011489",
"synonyms": [
"EXFOR"
]
},
"r3d100011490": {
"description": "The International Network of Nuclear Reaction Data Centres (NRDC) constitutes a worldwide cooperation of nuclear data centres under the auspices of the International Atomic Energy Agency. The Network was established to coordinate the world-wide collection, compilation and dissemination of nuclear reaction data.",
"homepage": "https://www-nds.iaea.org/nrdc/",
"name": "International Network of Nuclear Reaction Data Centres",
"prefix": "r3d100011490",
"synonyms": [
"NRDC"
]
},
"r3d100011492": {
"description": "Core nuclear reaction database contain recommended, evaluated cross sections, spectra, angular distributions, fission product yields, photo-atomic and thermal scattering law data, with emphasis on neutron induced reactions. The data were analyzed by experienced nuclear physicists to produce recommended libraries for one of the national nuclear data projects (USA, Europe, Japan, Russia and China). All data are stored in the internationally-adopted ENDF-6 format maintained by CSEWG.",
"homepage": "https://www-nds.iaea.org/exfor/endf.htm",
"name": "Evaluated Nuclear Data File",
"prefix": "r3d100011492",
"synonyms": [
"ENDF"
]
},
"r3d100011496": {
"description": "CorrDB has data of cattle, relating to meat production, milk production, growth, health, and others. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies.",
"homepage": "https://www.animalgenome.org/cgi-bin/CorrDB/index",
"name": "CorrDB",
"prefix": "r3d100011496",
"synonyms": [
"Animal Trait Correlation Database"
]
},
"r3d100011497": {
"description": "Genome track alignments using GBrowse on this site are featured with: (1) Annotated and predicted genes and transcripts; (2) QTL / SNP Association tracks; (3) OMIA genes; (4) Various SNP Chip tracks; (5) Other mapping fetures or elements that are available.",
"homepage": "https://www.animalgenome.org/gbrowse/",
"name": "Animal Genome Tracks on GBrowse",
"prefix": "r3d100011497"
},
"r3d100011498": {
"description": "This is a animal and human genome database that uses the BioMart software.",
"homepage": "https://www.animalgenome.org/",
"name": "AnimalGenome.ORG",
"prefix": "r3d100011498",
"synonyms": [
"BioMart AnimalGenome.ORG"
],
"xrefs": {
"nlx": "149170",
"scr": "006564"
}
},
"r3d100011503": {
"description": "The DNA Bank Network was established in spring 2007 and was funded until 2011 by the German Research Foundation (DFG). The network was initiated by GBIF Germany (Global Biodiversity Information Facility). It offers a worldwide unique concept. DNA bank databases of all partners are linked and are accessible via a central web portal, providing DNA samples of complementary collections (microorganisms, protists, plants, algae, fungi and animals).\nThe DNA Bank Network was one of the founders of the Global Genome Biodiversity Network (GGBN) and is fully merged with GGBN today. GGBN agreed on using the data model proposed by the DNA Bank Network. The Botanic Garden and Botanical Museum Berlin-Dahlem (BGBM) hosts the technical secretariat of GGBN and its virtual infrastructure. \nThe main focus of the DNA Bank Network is to enhance taxonomic, systematic, genetic, conservation and evolutionary studies by providing:\nβ’ high quality, long-term storage of DNA material on which molecular studies have been performed, so that results can be verified, extended, and complemented,\nβ’ complete on-line documentation of each sample, including the provenance of the original material, the place of voucher deposit, information about DNA quality and extraction methodology, digital images of vouchers and links to published molecular data if available.",
"homepage": "https://data.ggbn.org/ggbn_portal/",
"name": "Global Genome Biodiversity Network",
"prefix": "r3d100011503",
"synonyms": [
"DNA Bank Network (formerly)",
"GGBN"
],
"xrefs": {
"omics": "19241"
}
},
"r3d100011504": {
"description": "The project brings together national key players providing environmentally related biological data and services to develop the βGerman Federation for Biological Data' (GFBio). The overall goal is to provide a sustainable, service oriented, national data infrastructure facilitating data sharing and stimulating data intensive science in the fields of biological and environmental research.",
"homepage": "https://www.gfbio.org/",
"name": "German Federation for Biological Data",
"prefix": "r3d100011504",
"synonyms": [
"GFBio"
]
},
"r3d100011505": {
"description": "The \"Flora of Bavaria\" initiative with its data portal (14 million occurrence data) and Wiki representation is primarily a citizen science project.\nEfforts to describe and monitor the flora of Bavaria have been ongoing for 100 years.\nThe goal of these efforts is to record all vascular plants, including newcomers, and to document threatened or former local occurrences. Being geographically largest state of Germany with a broad range of habitats, Bavaria has a special responsibility for documenting and maintaining its plant diversity . About 85% of all German vascular plant species occur in Bavaria, and in addition it has about 50 endemic taxa, only known from Bavaria (most of them occur in the Alps). The Wiki is collaboration of volunteers and local and regional Bavarian botanical societies.\nEverybody is welcome to contribute, especially with photos or reports of local changes in the flora. The Flora of Bavaria project is providing access to a research data repository for occurrence data powered by the Diversity Workbench database framework.",
"homepage": "https://bayernflora.de/web/Hauptseite",
"name": "Flora von Bayern: Wiki and Data Portal",
"prefix": "r3d100011505"
},
"r3d100011506": {
"description": "Vast networks of meteorological sensors ring the globe measuring atmospheric state variables, like temperature, humidity, wind speed, rainfall, and atmospheric carbon dioxide, on a continuous basis. These measurements serve earth system science by providing inputs into models that predict weather, climate and the cycling of carbon and water. And, they provide information that allows researchers to detect the trends in climate, greenhouse gases, and air pollution. The eddy covariance method is currently the standard method used by biometeorologists to measure fluxes of trace gases between ecosystems and atmosphere.",
"homepage": "https://fluxnet.org/data/",
"name": "Fluxnet - Fluxdata",
"prefix": "r3d100011506",
"synonyms": [
"FLUXNET (formerly)"
],
"xrefs": {
"fairsharing": "FAIRsharing.yfk79s"
}
},
"r3d100011507": {
"description": "Results from time-series analysis of Landsat images in characterizing global forest extent and change from 2000 through 2016.",
"homepage": "https://glad.earthengine.app/view/global-forest-change#dl=1;old=off;bl=off;lon=20;lat=10;zoom=3;",
"name": "Global Forest Change",
"prefix": "r3d100011507"
},
"r3d100011509": {
"description": "This guide aims to provide a starting point to locating Geographic Information System (GIS) information both through the University of Sydney library catalogue and on the World Wide Web.",
"homepage": "https://libguides.library.usyd.edu.au/geospatial",
"name": "Geospatial Data",
"prefix": "r3d100011509"
},
"r3d100011511": {
"description": "The Digital Morphology library, part of the National Science Foundation Digital Libraries Initiative, is a dynamic archive of information on digital morphology and high-resolution X-ray computed tomography of biological specimens. Digital Morphology, part of the National Science Foundation Digital Libraries Initiative, develops and serves unique 2D and 3D visualizations of the internal and external structure of living and extinct vertebrates, and a growing number of 'invertebrates.' The Digital Morphology library contains nearly a terabyte of imagery of natural history specimens that are important to education and central to ongoing cutting-edge research efforts.",
"homepage": "http://www.digimorph.org/index.phtml",
"name": "DigiMorph",
"prefix": "r3d100011511",
"synonyms": [
"Digital Morphology"
],
"xrefs": {
"nlx": "143746",
"scr": "004416"
}
},
"r3d100011512": {
"description": "EarthStat.org serves geographic data sets with the purpose of solving the grand challenge of feeding a growing global population while reducing agricultureβs impact on the environment.",
"homepage": "http://www.earthstat.org/",
"name": "EarthStat",
"prefix": "r3d100011512"
},
"r3d100011514": {
"description": "!!!! <<<< The Community Data Portal (CDP) has been retired after nearly 15 years of service and is no longer available. Data can now be found here: DASH Search: https://data.ucar.edu/ . Please contact us with questions or concerns: datahelp@ucar.edu >>>> !!!! The Community Data Portal (CDP) is a collection of earth science datasets from NCAR, UCAR, UOP, and participating organizations.",
"homepage": "http://cdp.ucar.edu/",
"name": "Community Data Portal",
"prefix": "r3d100011514",
"synonyms": [
"CDP"
]
},
"r3d100011515": {
"description": "Neuroimaging Tools and Resources Collaboratory (NITRC) is currently a free one-stop-shop environment for science researchers that need resources such as neuroimaging analysis software, publicly available data sets, and computing power. Since its debut in 2007, NITRC has helped the neuroscience community to use software and data produced from research that, before NITRC, was routinely lost or disregarded, to make further discoveries. NITRC provides free access to data and enables pay-per-use cloud-based access to unlimited computing power, enabling worldwide scientific collaboration with minimal startup and cost. With NITRC and its componentsβthe Resources Registry (NITRC-R), Image Repository (NITRC-IR), and Computational Environment (NITRC-CE)βa researcher can obtain pilot or proof-of-concept data to validate a hypothesis for a few dollars.",
"homepage": "https://www.nitrc.org/",
"name": "NITRC",
"prefix": "r3d100011515",
"synonyms": [
"Neuroimaging Informatics Tools and Resources Clearinghouse"
],
"xrefs": {
"fairsharing": "FAIRsharing.6b9re3",
"nif": "0000-00202",
"scr": "003430"
}
},
"r3d100011516": {
"description": "<<>>!!!>>> >>>>!!!! <<<< 13.12.2018: PLEXdb is now a static site after funding stopped from NSF. We have stopped registration of new users; but past users who have data can login when needed and interact with the site. You can download data using the authentication provided at the download page. >>>>!!!!<<<<\n PLEXdb is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data.",
"name": "PLEXdb",
"prefix": "r3d100011516",
"synonyms": [
"Plant Expression Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.8pjgwx",
"nlx": "149236",
"omics": "03225",
"scr": "006963"
}
},
"r3d100011517": {
"description": "The ERS mission is to inform and enhance public and private decision making on economic and policy issues related to agriculture, food, the environment, and rural development.",
"homepage": "https://www.ers.usda.gov/data-products.aspx",
"name": "United States Department of Agriculture, Economic Research Service, Data Products",
"prefix": "r3d100011517",
"synonyms": [
"USDA ERS Data Products"
]
},
"r3d100011518": {
"description": "The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.",
"homepage": "https://www.uniprot.org/help/uniref",
"name": "UniRef",
"prefix": "r3d100011518",
"synonyms": [
"UniProt Reference Clusters"
],
"xrefs": {
"nlx": "66133",
"omics": "03879",
"scr": "010646"
}
},
"r3d100011519": {
"description": "The UniProt Archive (UniParc) is a comprehensive and non-redundant database that contains most of the publicly available protein sequences in the world.",
"homepage": "https://www.uniprot.org/help/uniparc",
"name": "UniParc",
"prefix": "r3d100011519",
"synonyms": [
"UniProt Archive"
],
"xrefs": {
"nlx": "76940",
"scr": "004769"
}
},
"r3d100011520": {
"description": "<<>>!!!>>> The UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data. We provide UniMES clusters in order to obtain complete coverage of sequence space at different resolutions.",
"homepage": "https://www.uniprot.org/help/unimes",
"name": "UniMES",
"prefix": "r3d100011520",
"synonyms": [
"UniProt Metagenomic and Environmental Sequences"
],
"xrefs": {
"omics": "03881"
}
},
"r3d100011521": {
"description": "The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data. The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). The UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data. The UniProt Knowledgebase,is an expertly and richly curated protein database, consisting of two sections called UniProtKB/Swiss-Prot and UniProtKB/TrEMBL.",
"homepage": "https://www.uniprot.org/uniprotkb/",
"name": "UniProtKB",
"prefix": "r3d100011521",
"synonyms": [
"UniProtKnowledgebase",
"Universal Protein Knowledgebase"
],
"xrefs": {
"fairsharing": "FAIRsharing.s1ne3g",
"nlx": "53981",
"scr": "004426"
}
},
"r3d100011522": {
"description": "<<>>!!!>>>",
"homepage": "https://sofia.usgs.gov/",
"name": "SOFIA",
"prefix": "r3d100011522",
"synonyms": [
"South Florida Information Access"
]
},
"r3d100011524": {
"description": "The GeoPlatform provides shared and trusted geospatial data, services, and applications for use by the public and by government agencies and partners to meet their mission needs.",
"homepage": "https://www.geoplatform.gov/",
"name": "GeoPlatform",
"prefix": "r3d100011524"
},
"r3d100011525": {
"description": "<<>>!!!>>> Hydra is a repository for digital materials at the University of Hull. It can hold and manage any type of digital material, and is being developed in response to the growth in the amount of digital material that is generated through the research, education and administrative activities within the University. Hydra contains different collections of datasets from University of Hull research projects as: ARCdoc, domesday dataset, History of Marine animal Populations (HMAP) and others.",
"homepage": "https://hydra.hull.ac.uk/",
"name": "Hydra",
"prefix": "r3d100011525",
"synonyms": [
"Hull's digital repository"
],
"xrefs": {
"roar": "4242"
}
},
"r3d100011527": {
"description": "<<>>!!!>>>\nWith the new database, GlycomeDB, it is possible to get an overview of all carbohydrate structures in the different databases and to crosslink common structures in the different databases. Scientists are now able to search for a particular structure in the meta database and get information about the occurrence of this structure in the five carbohydrate structure databases.",
"homepage": "http://www.glycome-db.org/",
"name": "GlycomeDB",
"prefix": "r3d100011527",
"synonyms": [
"A carbohydrate structure metadatabase"
],
"xrefs": {
"nlx": "149174",
"scr": "005717"
}
},
"r3d100011528": {
"description": "<<>>!!!>>> Selected TOXMAP data can be accesse from the following sites:\nU.S. EPA Toxics Release Program (TRI) (https://www.epa.gov/toxics-release-inventory-tri-program)\nU.S. EPA Superfund Program (https://www.epa.gov/superfund)\nU.S. EPA Facilities Registry System (FRS) (https://www.epa.gov/frs)\nU.S. EPA Clean Air Markets Program (https://www.epa.gov/airmarkets)\nU.S. EPA Geospatial Applications (https://www.epa.gov/geospatial/epa-geospatial-applications)\nU.S. NIH NCI Surveillance, Epidemiology, and End Results Program (SEER) (https://seer.cancer.gov/)\nGovernment of Canada National Pollutant Release Inventory (NPRI) (https://www.canada.ca/en/services/environment/pollution-waste-management/national-pollutant-release-inventory.html)\nU.S. Census Bureau (https://www.census.gov/)\nU.S. Nuclear Regulatory Commission (NRC) (https://www.nrc.gov/) >>>!!!>>>",
"homepage": "https://toxmap.nlm.nih.gov/toxmap/",
"name": "TOXMAP",
"prefix": "r3d100011528"
},
"r3d100011529": {
"description": "<<>>!!!>>>\nAs part of a broader NLM reorganization, most of NLM's toxicology information services have been integrated into other NLM products and services.",
"homepage": "https://toxnet.nlm.nih.gov/newtoxnet/tri.htm",
"name": "Toxics Release Inventory",
"prefix": "r3d100011529",
"synonyms": [
"TRI"
],
"xrefs": {
"nif": "0000-21401",
"scr": "008245"
}
},
"r3d100011530": {
"description": "CTD is a robust, publicly available database that aims to advance understanding about how environmental exposures affect human health. It provides manually curated information about chemicalβgene/protein interactions, chemicalβdisease and geneβdisease relationships. These data are integrated with functional and pathway data to aid in development of hypotheses about the mechanisms underlying environmentally influenced diseases.\nWe also have additional ongoing projects involving manual curation of exposome data and chemicalβphenotype relationships to help identify preβdisease biomarkers resulting from environmental exposures.\nThe initial release of CTD was on November 12, 2004. Weβre grateful to our strong community support and encourage you to give us feedback so we can continue to evolve with your research needs.",
"homepage": "https://ctdbase.org/",
"name": "Comparative Toxicogenomics Database",
"prefix": "r3d100011530",
"synonyms": [
"CTD"
],
"xrefs": {
"fairsharing": "FAIRsharing.h3tjtr",
"nif": "0000-02683",
"omics": "01578",
"scr": "006530"
}
},
"r3d100011531": {
"description": "<<>>!!!>>>",
"homepage": "http://toxnet.nlm.nih.gov/newtoxnet/iris.htm",
"name": "Integrated Risk Information System",
"prefix": "r3d100011531",
"synonyms": [
"IRIS"
],
"xrefs": {
"nif": "0000-21221",
"scr": "013005"
}
},
"r3d100011532": {
"description": "ITER is an Internet database of human health risk values and cancer classifications for over 680 chemicals of environmental concern from multiple organizations wordwide. ITER is the only database that presents risk data in a tabular format for easy comparison, along with a synopsis explaining differences in data and a link to each organization for more information.",
"homepage": "https://iter.tera.org/db.html",
"name": "ITER Database",
"prefix": "r3d100011532",
"synonyms": [
"International Toxicity Estimates for Risk Assessment",
"formerly: TOXNET database"
],
"xrefs": {
"nif": "0000-21225",
"scr": "008196"
}
},
"r3d100011533": {
"description": "<<>>!!!>>>",
"homepage": "https://toxnet.nlm.nih.gov/newtoxnet/cpdb.htm",
"name": "Carcinogenic Potency Database",
"prefix": "r3d100011533",
"synonyms": [
"CPDB"
],
"xrefs": {
"omics": "03986"
}
},
"r3d100011534": {
"description": "<<>>!!!>>> SedDB complements current geological data systems (PetDB, EarthChem, NavDat and GEOROC) with an integrated compilation of geochemistry of marine and continental sediments.\nNotice: Content of SedDB has been static since 2014 and will not be updated until further notice.",
"homepage": "http://www.earthchem.org/seddb",
"name": "SedDB",
"prefix": "r3d100011534",
"synonyms": [
"Integrated Data Management for Sediment Geochemistry"
],
"xrefs": {
"nlx": "154724",
"scr": "002210"
}
},
"r3d100011536": {
"description": "<<>>!!!>>> 2021-06-17; VentDB data collections now housed in the EarthChem Library \nVentDB is an effort funded by the US National Science Foundation to build and operate a data management system for hydrothermal spring geochemistry that will host and serve the full range of compositional data acquired on seafloor hydrothermal vents from all tectonic settings. VentDB supports the preservation and dissemination of analytical data on hydrothermal springs and plumes.\nVentDB complements existing geochemical data collections such as SedDB and PetDB. VentDB can accommodate published historical data as well as legacy and new data that investigators contribute.\nContent of VentDB is static and will not be updated until further notice.",
"homepage": "http://www.earthchem.org/ventdb",
"name": "VentDB",
"prefix": "r3d100011536",
"synonyms": [
"Geochemical Database for Seafloor Hydrothermal Springs"
],
"xrefs": {
"nlx": "154725",
"scr": "001632"
}
},
"r3d100011537": {
"description": "Geochron is a global database that hosts geochronologic and thermochronologic information from detrital minerals. Information included with each sample consists of a table with the essential isotopic information and ages, a table with basic geologic metadata (e.g., location, collector, publication, etc.), a Pb/U Concordia diagram, and a relative age probability diagram. This information can be accessed and viewed with any web browser, and depending on the level of access desired, can be designated as either private or public. Loading information into Geochron requires the use of U-Pb_Redux, a Java-based program that also provides enhanced capabilities for data reduction, plotting, and analysis.\nInstructions are provided for three different levels of interaction with Geochron:\n1. Accessing samples that are already in the Geochron database.\n2. Preparation of information for new samples, and then transfer to Arizona LaserChron Center personnel for uploading to Geochron.\n3. Preparation of information and uploading to Geochron using U-Pb_Redux.",
"homepage": "https://www.geochron.org/",
"name": "Geochron",
"prefix": "r3d100011537",
"xrefs": {
"fairsharing": "FAIRsharing.9db34d"
}
},
"r3d100011538": {
"description": "The EarthChem Library is a data repository that archives, publishes and makes accessible data and other digital content from geoscience research (analytical data, data syntheses, models, technical reports, etc.)",
"homepage": "https://earthchem.org/ecl/",
"name": "EarthChem Library",
"prefix": "r3d100011538",
"xrefs": {
"fairsharing": "FAIRsharing.ne5dn7",
"scr": "002207"
}
},
"r3d100011539": {
"description": "The North American Volcanic and Intrusive Rock Database (NAVDAT) is intended as a web-accessible repository for age, chemical and isotopic data from Mesozoic and younger igneous rocks in western North America. \nPlease note: Although this site is fully functional, the content of NAVDAT has been static since 2014 and will not be updated until further notice. All data is still available via the EarthChem Portal http://portal.earthchem.org/",
"homepage": "https://www.navdat.org/",
"name": "NAVDAT",
"prefix": "r3d100011539",
"synonyms": [
"The North American Volcanic and Intrusive Rock Database",
"The Western North American Volcanic and Intrusive Rock Database"
]
},
"r3d100011541": {
"description": "We conduct integrated earth resource evaluation that incorporates sustainable economic vitality and environmental and public health protection.",
"homepage": "https://gis-modnr.opendata.arcgis.com/pages/dnr-missouri-geological-survey",
"name": "Missouri Geological Survey Program",
"prefix": "r3d100011541",
"synonyms": [
"GeoSTRAT"
]
},
"r3d100011543": {
"description": "The Site Survey Data Bank (SSDB) is a repository for site survey data submitted in support of International Ocean Discovery Program (IODP) proposals and expeditions. SSDB serves different roles for different sets of users.",
"homepage": "https://ssdb.iodp.org/",
"name": "Site Survey Data Bank",
"prefix": "r3d100011543",
"synonyms": [
"SSDB"
],
"xrefs": {
"fairsharing.legacy": "3103"
}
},
"r3d100011545": {
"description": "<<>>!!!>>>\nBiobanks are a key prerequisite for modern medical research. By linking samples and clinical data they make it possible to clarify the causes and the course of diseases. The German Biobank Registry pools the medically relevant biobanks in Germany. The German Biobank Registry provides an overview of the medical biobanks in Germany; increases the international visibility of German biobanks; facilitates the networking of biobanks; promotes an exchange of information and samples between research teams; supports the use of existing resources; provides information for investments in biobanks and promotes transparency and trust in research where human samples are used. Searching for samples in all biobanks is possible at the project portal (P2B2) https://p2b2.fraunhofer.de/ after registration.",
"homepage": "https://www.toolpool-gesundheitsforschung.de/produkte/deutsches-biobanken-register",
"name": "Deutsches BioBanken-Register",
"prefix": "r3d100011545",
"synonyms": [
"German Biobank Registry"
],
"xrefs": {
"nlx": "143997",
"scr": "004991"
}
},
"r3d100011547": {
"description": "<<>>!!!>>> The Senate Commission on Oceanography planned and coordinated the activities of the DFG in the field of marine research from 1959 until 2017. Most notably, it advised on matters pertaining to the research vessels METEOR and (from 2006 onwards) MARIA S. MERIAN, which are co-funded by the DFG. The focus was on the review process and evaluation of proposed voyages for these two ships. The Expert Research Vessel Panel (GPF) appointed by the BMBF and DFG, which is responsible for the review process for proposed voyages for all global, oceanic and regional German research vessels within the framework of a joint procedure developed by the BMBF, DFG and HGF, was constituted on 7 March 2018 and thus took on this task concerning METEOR and MARIA S. MERIAN from the Senate Commission on Oceanography. More information on the new review process can be found on the German Research Vessels Portal. https://www.portal-forschungsschiffe.de/index.php?index=53.",
"homepage": "http://dfg-ozean.de1.cc/berichte/berichte.php",
"name": "DFG Senatskommission fΓΌr Ozeanographie - METEOR- und MARIA S. MERIAN-Berichte",
"prefix": "r3d100011547"
},
"r3d100011548": {
"description": "<<>>!!!>>>\nHalOcAt brings together global oceanic and atmospheric data of mainly short-lived brominated and iodinated trace gases.",
"homepage": "https://halocat.geomar.de/home",
"name": "Halocarbons in the Ocean and Atmosphere database project",
"prefix": "r3d100011548",
"synonyms": [
"HalOcAt"
]
},
"r3d100011549": {
"description": "MEMENTO aims to become a valuable tool for identifying regions of the world ocean that should be targeted in future work to improve the quality of air-sea flux estimates.",
"homepage": "https://memento.geomar.de/",
"name": "MEMENTO",
"prefix": "r3d100011549",
"synonyms": [
"MarinE MethanE and NiTrous Oxide",
"Marine CHβ - NβO database"
],
"xrefs": {
"fairsharing": "FAIRsharing.pPOQZf"
}
},
"r3d100011550": {
"description": "<<>>!!!>>>",
"homepage": "http://www.openphacts.org/index.php",
"name": "Open PHACTS",
"prefix": "r3d100011550",
"synonyms": [
"OPS",
"Open Pharmacological Space"
],
"xrefs": {
"nlx": "144033",
"scr": "005050"
}
},
"r3d100011551": {
"description": "The eAtlas is a website, mapping system and set of data visualisation tools for presenting research data in an accessible form that promotes greater use of this information. The eAtlas will serve as the primary data and knowledge repository for all NERP Tropical Ecosystems Hub projects, which focus on the on the Great Barrier Reef, Wet Tropics rainforest and Torres Strait. The eAtlas will capture and record research outcomes and make them available to research-users in a timely, readily accessible manner. It will host meta-data records and provide an enduring repository for raw data. It will also develop and host web visualisations to view information using a simple and intuitive interface. This will assist scientists with data discovery and allow environmental managers to access and investigate research data.",
"homepage": "https://eatlas.org.au/home",
"name": "e-Atlas",
"prefix": "r3d100011551",
"synonyms": [
"Australia's Tropical Land and Seas"
],
"xrefs": {
"fairsharing": "FAIRsharing.e775fd"
}
},
"r3d100011552": {
"description": "The Ningaloo Atlas was created in response to the need for more comprehensive and accessible information on environmental and socio-economic data on the greater Ningaloo region. As such, the Ningaloo Atlas is a web portal to not only access and share information, but to celebrate and promote the biodiversity, heritage, value, and way of life of the greater Ningaloo region.",
"homepage": "https://ningaloo-atlas.org.au/welcome",
"name": "Ningaloo Atlas",
"prefix": "r3d100011552",
"xrefs": {
"fairsharing": "FAIRsharing.2fa60d"
}
},
"r3d100011553": {
"description": "The European Variation Archive is an open-access database of all types of genetic variation data from all species. The EVA provides access to highly detailed, granular, raw variant data from human, with other species to follow. As of September 2017, EMBL-EBI will maintain reliable accessions for non-human genetic variation data through the European Variation Archive (EVA). NCBI's dbSNP database will continue to maintain stable identifiers for human genetic variation data only. This change will enable a more rapid turnaround for data sharing in this burgeoning field.",
"homepage": "https://www.ebi.ac.uk/eva/?Home",
"name": "European Variation Archive",
"prefix": "r3d100011553",
"synonyms": [
"EVA"
],
"xrefs": {
"fairsharing": "FAIRsharing.6824pv",
"omics": "19707"
}
},
"r3d100011554": {
"description": "Welcome to the Coherent X-ray Imaging Data Bank (CXIDB), a new database which offers scientists from all over the world a unique opportunity to access data from Coherent X-ray Imaging (CXI) experiments. CXIDB is dedicated to further the goal of making data from Coherent X-ray Imaging (CXI) experiments available to all, as well as archiving it.",
"homepage": "https://cxidb.org/",
"name": "Coherent X-ray Imaging Data Bank",
"prefix": "r3d100011554",
"synonyms": [
"CXIDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.y6w78m",
"scr": "014722"
}
},
"r3d100011555": {
"description": "INDI was formed as a next generation FCP effort. INDI aims to provide a model for the broader imaging community while simultaneously creating a public dataset capable of dwarfing those that most groups could obtain individually.",
"homepage": "http://fcon_1000.projects.nitrc.org/",
"name": "International Neuroimaging Data-sharing Initiative",
"prefix": "r3d100011555",
"synonyms": [
"INDI"
],
"xrefs": {
"fairsharing": "FAIRsharing.ajpk6x",
"nlx": "144428",
"scr": "015771"
}
},
"r3d100011556": {
"description": "MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments.",
"homepage": "https://www.ebi.ac.uk/metabolights/",
"name": "MetaboLights",
"prefix": "r3d100011556",
"xrefs": {
"fairsharing": "FAIRsharing.kkdpxe",
"miriam": "00000380",
"omics": "02535",
"scr": "014663"
}
},
"r3d100011557": {
"description": "EuPathDB (formerly ApiDB) is an integrated database covering the eukaryotic pathogens in the genera Acanthamoeba, Annacaliia, Babesia, Crithidia, Cryptosporidium, Edhazardia, Eimeria, Encephalitozoon, Endotrypanum, Entamoeba, Enterocytozoon, Giardia, Gregarina, Hamiltosporidium, Leishmania, Nematocida, Neospora, Nosema, Plasmodium, Theileria, Toxoplasma, Trichomonas, Trypanosoma and Vavraia, Vittaforma). While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all of these resources, and the opportunity to leverage orthology for searches across genera.",
"homepage": "https://veupathdb.org/veupathdb/app",
"name": "VEuPathDB",
"prefix": "r3d100011557",
"synonyms": [
"Eukaryotic Pathogen, Vector and Host Informatics Resource",
"formerly: EuPathDB",
"formerly: Eukaryotic Pathogen Database Resources"
],
"xrefs": {
"fairsharing": "FAIRsharing.f94905",
"nlx": "49652",
"omics": "03154",
"scr": "004512"
}
},
"r3d100011558": {
"description": "<<>>!!!>>>",
"homepage": "https://www.fludb.org/brc/home.spg?decorator=influenza",
"name": "Influenza Research Database",
"prefix": "r3d100011558",
"synonyms": [
"IRD"
],
"xrefs": {
"fairsharing": "FAIRsharing.ws7cgw",
"miriam": "00000172",
"nif": "0000-21222",
"omics": "04512",
"scr": "006641"
}
},
"r3d100011559": {
"description": "TCIA is a service which de-identifies and hosts a large archive of medical images of cancer accessible for public download. The data are organized as βcollectionsβ; typically patientsβ imaging related by a common disease (e.g. lung cancer), image modality or type (MRI, CT, digital histopathology, etc) or research focus. Supporting data related to the images such as patient outcomes, treatment details, genomics and expert analyses are also provided when available.",
"homepage": "https://www.cancerimagingarchive.net/",
"name": "The Cancer Imaging Archive",
"prefix": "r3d100011559",
"synonyms": [
"TCIA"
],
"xrefs": {
"fairsharing": "FAIRsharing.jrfd8y",
"issn": "2474-4638",
"nlx": "151749",
"scr": "008927"
}
},
"r3d100011560": {
"description": "The SICAS Medical Image Repository is a freely accessible repository containing medical research data including medical images, surface models, clinical data, genomics data and statistical shape models. The data can freely be organized and shared on SMIR and made publicly accessible with a DOI. Dedicated data sets are organized as collections of anatomical regions (e.g Cochlea). The data can be filtered using a modular search and accessed on the web or through the SMIR API.",
"homepage": "https://www.smir.ch",
"name": "Sicas Medical Image Repository",
"prefix": "r3d100011560",
"synonyms": [
"SMIR",
"formerly: Virtual Skeleton Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.vcmz9h",
"scr": "017420"
}
},
"r3d100011561": {
"description": "Modern signal processing and machine learning methods have exciting potential to generate new knowledge that will impact both physiological understanding and clinical care. Access to data - particularly detailed clinical data - is often a bottleneck to progress. The overarching goal of PhysioNet is to accelerate research progress by freely providing rich archives of clinical and physiological data for analysis.\nThe PhysioNet resource has three closely interdependent components: An extensive archive (\"PhysioBank\"), a large and growing library of software (\"PhysioToolkit\"), and a collection of popular tutorials and educational materials",
"homepage": "https://physionet.org/",
"name": "PhysioNet",
"prefix": "r3d100011561",
"xrefs": {
"fairsharing": "FAIRsharing.bemzxg",
"nif": "0000-00250",
"omics": "25293",
"scr": "007345"
}
},
"r3d100011562": {
"description": "KiMoSys, a web application for quantitative KInetic MOdels of biological SYStems. Kinetic models, with the aim to understand and subsequently design the metabolism of organism of interest are constructed iteratively and require accurate experimental data for both the generation and verification of hypotheses. Therefore, there is a growing requirement for exchanging experimental data and models between the systems biology community, and to automate as much as possible the kinetic model building, editing, simulation and analysis steps.",
"homepage": "https://kimosys.org/",
"name": "Kinetic models of biological systems",
"prefix": "r3d100011562",
"synonyms": [
"KiMoSys"
],
"xrefs": {
"fairsharing": "FAIRsharing.6erywc",
"scr": "017423"
}
},
"r3d100011563": {
"description": "<<>>!!!<<<",
"homepage": "https://www.bundesbank.de/en/bundesbank/research/panel-on-household-finances",
"name": "Panel on household finances",
"prefix": "r3d100011563",
"synonyms": [
"Haushaltsstudie",
"PHF",
"Studie zur wirtschaftlichen Lage privater Haushalte"
]
},
"r3d100011564": {
"description": ">>>!!!<<< The repository is no longer available. >>>!!!<<< The eagle-i National Network and eagle-i resource search at www.eagle-.net was retired on November 4, 2021.!!! Groundbreaking biomedical research requires access to cutting edge scientific resources; however such resources are often invisible beyond the laboratories or universities where they were developed. eagle-i is a discovery platform that helps biomedical scientists find previously invisible, but highly valuable, resources.",
"homepage": "https://open.catalyst.harvard.edu/products/eagle-i/",
"name": "eagle-i",
"prefix": "r3d100011564",
"xrefs": {
"nlx": "143592",
"scr": "013153"
}
},
"r3d100011565": {
"description": "The FCP entailed the aggregation and public release (via www.nitrc.org) of over 1200 resting state fMRI (R-fMRI) datasets collected from 33 sites around the world.",
"homepage": "https://fcon_1000.projects.nitrc.org/fcpClassic/FcpTable.html",
"name": "1000 Functional Connectomes Project",
"prefix": "r3d100011565",
"xrefs": {
"nlx": "144428",
"scr": "015771"
}
},
"r3d100011566": {
"description": "Within WASCAL a large number of heterogeneous data are collected. These data are mainly coming from different initiated research activities within WASCAL (Core Research Program, Graduate School Program) from the hydrological-meteorological, remote sensing, biodiversity and socio economic observation networks within WASCAL, and from the activities of the WASCAL Competence Center in Ouagadougou, Burkina-Faso.",
"homepage": "https://wascal-dataportal.org/wascal_searchportal2/",
"name": "WASCAL Data Discovery Portal",
"prefix": "r3d100011566",
"synonyms": [
"WADI - Data Portal",
"WASCAL SDI",
"WASCAL spatial data infrastructure",
"West African Science Service Center on Climate Change and Adapted Land Use Data Discovery Portal"
]
},
"r3d100011567": {
"description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.",
"homepage": "http://bigg.ucsd.edu/",
"name": "BIGG Database",
"prefix": "r3d100011567",
"synonyms": [
"Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions"
],
"xrefs": {
"fairsharing": "FAIRsharing.va62ke",
"nlx": "149299",
"scr": "005809"
}
},
"r3d100011568": {
"description": "<<>>!!!>>> Introduction of genome-scale metabolic network:\nThe completion of genome sequencing and subsequent functional annotation for a great number of species enables the reconstruction of genome-scale metabolic networks. These networks, together with in silico network analysis methods such as the constraint based methods (CBM) and graph theory methods, can provide us systems level understanding of cellular metabolism. Further more, they can be applied to many predictions of real biological application such as: gene essentiality analysis, drug target discovery and metabolic engineering",
"name": "Genome-Scale Metabolic Network DataBase",
"prefix": "r3d100011568",
"synonyms": [
"GSMNDB"
]
},
"r3d100011569": {
"description": "PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.",
"homepage": "https://plasmodb.org/plasmo/app/",
"name": "PlasmoDB",
"prefix": "r3d100011569",
"synonyms": [
"Plasmodium Genomics Resource"
],
"xrefs": {
"fairsharing": "FAIRsharing.g4n8sw",
"miriam": "00000150",
"nif": "0000-03314",
"omics": "02765",
"scr": "013331"
}
},
"r3d100011570": {
"description": "KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies",
"homepage": "https://www.genome.jp/kegg/",
"name": "Kyoto Encyclopedia of Genes and Genomes",
"prefix": "r3d100011570",
"synonyms": [
"KEGG"
],
"xrefs": {
"fairsharing": "FAIRsharing.327nbg",
"miriam": "00000578",
"nif": "0000-21234",
"nlx": "31015",
"scr": "001120"
}
},
"r3d100011571": {
"description": "The Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC) is a team of researchers, data specialists and computer system developers who are supporting the development of a data management system to store scientific data generated by Gulf of Mexico researchers. The Master Research Agreement between BP and the Gulf of Mexico Alliance that established the Gulf of Mexico Research Initiative (GoMRI) included provisions that all data collected or generated through the agreement must be made available to the public. The Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC) is the vehicle through which GoMRI is fulfilling this requirement. The mission of GRIIDC is to ensure a data and information legacy that promotes continual scientific discovery and public awareness of the Gulf of Mexico Ecosystem.",
"homepage": "https://data.gulfresearchinitiative.org/",
"name": "Gulf of Mexico Research Initiative Information and Data Cooperative",
"prefix": "r3d100011571",
"synonyms": [
"GRIIDC"
]
},
"r3d100011575": {
"description": "The Southern California Earthquake Data Center (SCEDC) operates at the Seismological Laboratory at Caltech and is the primary archive of seismological data for southern California. The 1932-to-present Caltech/USGS catalog maintained by the SCEDC is the most complete archive of seismic data for any region in the United States. Our mission is to maintain an easily accessible, well-organized, high-quality, searchable archive for research in seismology and earthquake engineering.",
"homepage": "https://scedc.caltech.edu/",
"name": "Southern California Earthquake Data Center",
"prefix": "r3d100011575",
"synonyms": [
"SCEDC"
],
"xrefs": {
"fairsharing": "FAIRsharing.2c2cd7",
"nlx": "154718",
"scr": "000663"
}
},
"r3d100011577": {
"description": "The UC San Diego Library Digital Collections website gathers two categories of content managed by the Library: library collections (including digitized versions of selected collections covering topics such as art, film, music, history and anthropology) and research data collections (including research data generated by UC San Diego researchers).",
"homepage": "https://library.ucsd.edu/dc/",
"name": "UC San Diego Library Digital Collections",
"prefix": "r3d100011577"
},
"r3d100011578": {
"description": "Europeana is the trusted source of cultural heritage brought to you by the Europeana Foundation and a large number of European cultural institutions, projects and partners. Itβs a real piece of team work.\nIdeas and inspiration can be found within the millions of items on Europeana. These objects include:\n Images - paintings, drawings, maps, photos and pictures of museum objects\n Texts - books, newspapers, letters, diaries and archival papers\n Sounds - music and spoken word from cylinders, tapes, discs and radio broadcasts\n Videos - films, newsreels and TV broadcasts\nAll texts are CC BY-SA, images and media licensed individually.",
"homepage": "https://www.europeana.eu/de",
"name": "Europeana collections",
"prefix": "r3d100011578"
},
"r3d100011579": {
"description": "<<>>!!!>>>\nIn 2016, NSIDC partnered with the United States Antarctic Program - Data Center (USAP-DC) at Columbia University to consolidate NSF glaciology data into a central USAP Project Catalog and a Data Repository for research datasets derived from these projects. From 2016 to 2018, the AGDC data sets were transferred to USAP-DC. All AGDC data previously archived with NSIDC are now available via the USAP-DC https://www.re3data.org/repository/r3d100010660.",
"homepage": "http://nsidc.org/data/agdc/",
"name": "Antarctic Glaciological Data Center at NSIDC",
"prefix": "r3d100011579",
"synonyms": [
"AGDC"
],
"xrefs": {
"nlx": "154741",
"scr": "002219"
}
},
"r3d100011580": {
"description": "The World Ocean Database (WOD) is a collection of scientifically quality-controlled ocean profile and plankton data that includes measurements of temperature, salinity, oxygen, phosphate, nitrate, silicate, chlorophyll, alkalinity, pH, pCO2, TCO2, Tritium, Ξ13Carbon, Ξ14Carbon, Ξ18Oxygen, Freon, Helium, Ξ3Helium, Neon, and plankton.\nWOD contains all data of \"World Data Service Oceanography\" (WDS-Oceanography).",
"homepage": "https://www.nodc.noaa.gov/OC5/WOD/pr_wod.html",
"name": "World Ocean Database",
"prefix": "r3d100011580",
"synonyms": [
"WOD"
],
"xrefs": {
"fairsharing": "FAIRsharing.73ea53"
}
},
"r3d100011581": {
"description": "<<>>!!!>>>\nThe National Oceanographic Data Center includes the National Coastal Data Development Center (NCDDC) and the NOAA Central Library, which are integrated to provide access to the world's most comprehensive sources of marine environmental data and information. NODC maintains and updates a national ocean archive with environmental data acquired from domestic and foreign activities and produces products and research from these data which help monitor global environmental changes. These data include physical, biological and chemical measurements derived from in situ oceanographic observations, satellite remote sensing of the oceans, and ocean model simulations.",
"homepage": "https://www.nodc.noaa.gov/",
"name": "NOAA National Centers for Environmental Information - formerly: National Oceanographic Data Center",
"prefix": "r3d100011581",
"synonyms": [
"NODC"
]
},
"r3d100011582": {
"description": "The Abacus Data Network is a data repository collaboration involving Libraries at Simon Fraser University (SFU), the University of British Columbia (UBC), the University of Northern British Columbia (UNBC) and the University of Victoria (UVic).",
"homepage": "https://abacus.library.ubc.ca//",
"name": "Abacus Data Network",
"prefix": "r3d100011582",
"synonyms": [
"Abacus Dataverse Network"
]
},
"r3d100011583": {
"description": "The NOMAD Repository and Archive stands for open access of scientific materials data. It enables the confirmatory analysis of materials data, their reuse, and repurposing. All data is available in their raw format as produced by the underlying code (Repository) and in a common, machine-processable, and well-defined data format (Archive).",
"homepage": "https://nomad-lab.eu/services/repo-arch",
"name": "NoMaD Repository & Archive",
"prefix": "r3d100011583",
"synonyms": [
"Novel Materials Discovery"
],
"xrefs": {
"fairsharing": "FAIRsharing.aq20qn"
}
},
"r3d100011584": {
"description": "<<>>!!!>>>\n\nThe MyTARDIS repository at ANSTO is used to:\n* Store metadata for all experiments conducted at ANSTO\n* Provide access and download of metadata and data to authorised users of experiments\n* Provide search, access and download of public metadata and data to the general scientific community",
"homepage": "https://tardis.nbi.ansto.gov.au/",
"name": "MyTARDIS @ ANSTO",
"prefix": "r3d100011584",
"synonyms": [
"Australian Nuclear Science and Technology Organisation (ANSTO)"
]
},
"r3d100011585": {
"description": "<<>>!!!<<< Background: Many studies have been conducted to detect quantitative trait loci (QTL) in dairy cattle. However, these studies are diverse in terms of their differing resource populations, marker maps, phenotypes, etc, and one of the challenges is to be able to synthesise this diverse information. This web page has been constructed to provide an accessible database of studies, providing a summary of each study, facilitating an easier comparison across studies. However, it also highlights the need for uniform reporting of results of studies, to facilitate more direct comparisons being made.\nDescription: Studies recorded in this database include complete and partial genome scans, single chromosome scans, as well as fine mapping studies, and contain all known reports that were published in peer-reviewed journals and readily available conference proceedings, initially up to April 2005. However, this data base is being added to, as indicated by the last web update. Note that some duplication of results will occur, in that there may be a number of reports on the same resource population, but utilising different marker densities or different statistical methodologies. The traits recorded in this map are milk yield, milk composition (protein yield, protein %, fat yield, fat %), and somatic cell score (SCS).",
"homepage": "http://firefly.vetsci.usyd.edu.au/CMS/reprogen/QTL_Map/index.php?Page=QTL+Map",
"name": "Combined QTL Map of Dairy Cattle Traits",
"prefix": "r3d100011585"
},
"r3d100011586": {
"description": "Research data management is a general term covering how you organize, structure, store, and care for the information used or generated during a research project.\nThe University of Oxford policy mandates the preservation of research data and records for a minimum of 3 years after publication.\nA place to securely hold digital research materials (data) of any sort along with documentation that helps explain what they are and how to use them (metadata). The application of consistent archiving policies, preservation techniques and discovery tools, further increases the long term availability and usefulness of the data. This is the main difference between storage and archiving of data. ORA-Data is the University of Oxfordβs research data archive https://www.re3data.org/repository/r3d100011230",
"homepage": "https://researchdata.ox.ac.uk/",
"name": "Research Data Oxford",
"prefix": "r3d100011586"
},
"r3d100011587": {
"description": "NKN is now Research Computing and Data Services (RCDS)!\nWe provide data management support for UI researchers and their regional, national, and international collaborators. This support keeps researchers at the cutting-edge of science and increases our institution's competitiveness for external research grants. Quality data and metadata developed in research projects and curated by RCDS (formerly NKN) is a valuable, long-term asset upon which to develop and build new research and science.",
"homepage": "https://www.hpc.uidaho.edu/",
"name": "Research Computing and Data Services",
"prefix": "r3d100011587",
"synonyms": [
"RCDS",
"formerly name: NKN",
"formerly name: Northwest Knowledge Network"
]
},
"r3d100011589": {
"description": "In order to meet the needs of research data management for Peking University. The PKU library cooperate with the NSFC-PKU data center for management science, PKU science and research department, PKU social sciences department to jointly launch the Peking University Open Research Data Platform. PKU Open research data provides preservation, management and distribution services for research data. It encourage data owner to share data and data users to reuse data.",
"homepage": "https://opendata.pku.edu.cn/dataverse/pku",
"name": "Peking University Open Research Data",
"prefix": "r3d100011589",
"synonyms": [
"PKU-Opendata"
]
},
"r3d100011591": {
"description": "The Brain Transcriptome Database (BrainTx) project aims to create an integrated platform to visualize and analyze our original transcriptome data and publicly accessible transcriptome data related to the genetics that underlie the development, function, and dysfunction stages and states of the brain.",
"homepage": "https://www.cdtdb.neuroinf.jp/CDT/Top.jsp",
"name": "Brain Transcriptome Database",
"prefix": "r3d100011591",
"synonyms": [
"BrainTx",
"formerly: CDT-DB",
"formerly: Cerebellar Development Transcriptome Database"
],
"xrefs": {
"scr": "014457"
}
},
"r3d100011592": {
"description": "The Analytical Geomagnetic Data Center of the Trans-Regional INTERMAGNET Segment is operated by the Geophysical Center of the Russian Academy of Sciences (GC RAS). Geomagnetic data are transmitted from observatories and stations located in Russia and near-abroad countries. The Center also provides access to spaceborne data products. The MAGNUS hardware-software system underlies the operation of the Center. Its particular feature is the automated real-time recognition of artificial (anthropogenic) disturbances in incoming data. Being based on fuzzy logic approach, this quality control service facilitates the preparation of the definitive magnetograms from preliminary records carried out by data experts manually. The MAGNUS system also performs on-the-fly multi-criteria estimation of geomagnetic activity using several indicators and provides online tools for modeling electromagnetic parameters in the near-Earth space.\nThe collected geomagnetic data are stored using relational database management system. The geomagnetic database is intended for storing both 1-minute and 1-second data. The results of anthropogenic and natural disturbance recognition are also stored in the database.",
"homepage": "http://geomag.gcras.ru/",
"name": "Russian-Ukrainian Geomagnetic Data Center",
"prefix": "r3d100011592"
},
"r3d100011593": {
"description": "The Andrews Forest is a place of inquiry. Our mission is to support research on forests, streams, and watersheds, and to foster strong collaboration among ecosystem science, education, natural resource management, and the humanities.\nOur place and our work are administered cooperatively by the USDA Forest Service's Pacific Northwest Research Station, Oregon State University, and the Willamette National Forest.\nFirst established in 1948 as an US Forest Service Experimental Forest, the H.J. Andrews is a 16,000-acre ecological research site in Oregon's beautiful western Cascades Mountains. The landscape is home to iconic Pacific Northwest old-growth forests of Cedar and Hemlock, and moss-draped ancient Douglas Firs; steep terrain; and fast, cold-running streams. In 1980 the Andrews became a charter member of the National Science Foundation's Long-Term Ecological Research (LTER) Program.",
"homepage": "https://andrewsforest.oregonstate.edu/",
"name": "HJ Andrews Experimental Forest",
"prefix": "r3d100011593",
"synonyms": [
"HJA"
]
},
"r3d100011594": {
"description": "As with most biomedical databases, the first step is to identify relevant data from the research community. The Monarch Initiative is focused primarily on phenotype-related resources. We bring in data associated with those phenotypes so that our users can begin to make connections among other biological entities of interest. We import data from a variety of data sources. With many resources integrated into a single database, we can join across the various data sources to produce integrated views. We have started with the big players including ClinVar and OMIM, but are equally interested in boutique databases. You can learn more about the sources of data that populate our system from our data sources page https://monarchinitiative.org/about/sources.",
"homepage": "https://monarchinitiative.org/",
"name": "The Monarch Initiative",
"prefix": "r3d100011594",
"synonyms": [
"Monarch",
"Monarch Initiative"
],
"xrefs": {
"nlx": "152525",
"omics": "14548",
"scr": "001373"
}
},
"r3d100011596": {
"description": "The PhenoGen website shares experimental data with a worldwide community of investigators and provides a flexible, integrated, multi-resolution repository of neuroscience transcriptomic genetic data for collaborative research on genomic disorders. The main development focus is on providing Hybrid Rat Diversity Panel transcriptomic data (sequencing, genome coverage, reconstructed totalRNA/smallRNA transcriptomes, quanification of the transcriptome, eQTLs, and WGCNA) and integrating additional tools to provide platform for visualization and analysis of HRDP transcriptome data.",
"homepage": "https://phenogen.org/",
"name": "PhenoGen Informatics",
"prefix": "r3d100011596",
"synonyms": [
"PhenoGen"
],
"xrefs": {
"nlx": "153879",
"rid": "000093",
"scr": "001613"
}
},
"r3d100011597": {
"description": "The Leicester Database and Archive Service (LEDAS) is an easy to use on-line astronomical database and archive access service, dealing mainly with data from high energy astrophysics missions, but also providing full database functionality for over 200 astronomical catalogues from ground-based observations and space missions. The LEDAS also allows access to images, spectra and light curves in graphics, HDS and FITS formats, as well as access to raw and processed event data. LEDAS provides the primary means of access for the UK astronomical community to the ROSAT Public Data Archive, the ASCA Public Data Archive and the Ginga Products Archive by its Archive Network Interface ARNIE.",
"homepage": "https://www.ledas.ac.uk/",
"name": "LEDAS",
"prefix": "r3d100011597",
"synonyms": [
"LEicester Database and Archive Service"
]
},
"r3d100011598": {
"description": "Research Data Centres offer a secure access to detailed microdata from Statistics Canada's surveys, and to Canadian censuses' data, as well as to an increasing number of administrative data sets. The search engine was designed to help you find out more easily which dataset among all the surveys available in the RDCs best suits your research needs.",
"homepage": "https://crdcn.ca/publications-data/data/",
"name": "Canadian Research Data Centre Network",
"prefix": "r3d100011598",
"synonyms": [
"CRDCN",
"RCCDR",
"RΓ©seau canadien des Centres de donnΓ©es de recherche"
]
},
"r3d100011601": {
"description": "Open access to macromolecular X-ray diffraction and MicroED datasets. The repository complements the Worldwide Protein Data Bank. SBDG also hosts reference collection of biomedical datasets contributed by members of SBGrid, Harvard and pilot communities.",
"homepage": "https://data.sbgrid.org/",
"name": "SBGrid Data Bank",
"prefix": "r3d100011601",
"synonyms": [
"Structural Biology Data Grid"
],
"xrefs": {
"fairsharing": "FAIRsharing.1hqd55",
"nif": "0000-37641",
"omics": "21660",
"scr": "003511"
}
},
"r3d100011602": {
"description": "The EELS database is a public interactive consultable web repository of outer-shell and inner-shell excitation spectra from Electron Energy Loss Spectroscopy and X-Ray experiments, which forms a reference catalog of fine structures for materials. Each spectrum is available with a full set of recording parameters providing a complete overview of the working conditions. The database must also be seen as a research tool for EEL spectroscopists, theoreticians, students, or private firms and a central βlocationβ for the growing EELS community.",
"homepage": "https://eelsdb.eu/",
"name": "EELS Data Base",
"prefix": "r3d100011602",
"synonyms": [
"Electron energy loss spectroscopy Data Base",
"Inner & Outer Shell Excitation Spectrum Repository"
],
"xrefs": {
"issn": "2430-3593"
}
},
"r3d100011604": {
"description": "The Astronomical Data Archives Center (ADAC) provides access to astronomical data from all over the world with links to online data catalogs, journal archives, imaging services and data archives. Users can access the VizieR catalogue service as well as the Hubble Ultra Deep Field Data by requesting password access. ADAC also provides access to the SMOKA public science data obtained through the Subaru Telescope in Hawaii as well as Schmidt Telescope at the University of Tokyo & MITSuME and KANATA Telescope at Higashi-Hiroshima Observatory. Users may need to contact the ADAC for password access or create user accounts for the various data services accessible through the ADAC site.",
"homepage": "http://dbc.nao.ac.jp/",
"name": "Astronomical Data Archives Center",
"prefix": "r3d100011604",
"synonyms": [
"ADAC",
"ADC",
"Astronomy Data Center"
]
},
"r3d100011609": {
"description": "The PLANTS Database provides standardized information about the vascular plants, mosses, liverworts, hornworts, and lichens of the U.S. and its territories. It includes names, plant symbols, checklists, distributional data, species abstracts, characteristics, images, crop information, automated tools, onward Web links, and references. This information primarily promotes land conservation in the United States and its territories, but academic, educational, and general use is encouraged. PLANTS reduces government spending by minimizing duplication and making information exchange possible across agencies and disciplines.",
"homepage": "https://plants.usda.gov/home",
"name": "PLANTS Database",
"prefix": "r3d100011609",
"synonyms": [
"PlantsList of Accepted Nomenclature, Taxoomy and Symbols Database"
]
},
"r3d100011611": {
"description": "Stanford Network Analysis Platform (SNAP) is a general purpose network analysis and graph mining library. It is written in C++ and easily scales to massive networks with hundreds of millions of nodes, and billions of edges. It efficiently manipulates large graphs, calculates structural properties, generates regular and random graphs, and supports attributes on nodes and edges. SNAP is also available through the NodeXL which is a graphical front-end that integrates network analysis into Microsoft Office and Excel. The SNAP library is being actively developed since 2004 and is organically growing as a result of our research pursuits in analysis of large social and information networks. Largest network we analyzed so far using the library was the Microsoft Instant Messenger network from 2006 with 240 million nodes and 1.3 billion edges.\nThe datasets available on the website were mostly collected (scraped) for the purposes of our research.\nThe website was launched in July 2009.",
"homepage": "http://snap.stanford.edu/index.html",
"name": "Stanford Network Analysis Project",
"prefix": "r3d100011611",
"synonyms": [
"SNAP",
"Stanford Large Network Dataset Collection"
]
},
"r3d100011612": {
"description": "This is the KONECT project, a project in the area of network science with the goal to collect network datasets, analyse them, and make available all analyses online. KONECT stands for Koblenz Network Collection, as the project has roots at the University of KoblenzβLandau in Germany. All source code is made available as Free Software, and includes a network analysis toolbox for GNU Octave, a network extraction library, as well as code to generate these web pages, including all statistics and plots.\nKONECT contains over a hundred network datasets of various types, including directed, undirected, bipartite, weighted, unweighted, signed and rating networks. The networks of KONECT are collected from many diverse areas such as social networks, hyperlink networks, authorship networks, physical networks, interaction networks and communication networks. The KONECT project has developed network analysis tools which are used to compute network statistics, to draw plots and to implement various link prediction algorithms. The result of these analyses are presented on these pages. Whenever we are allowed to do so, we provide a download of the networks.",
"homepage": "http://konect.cc/",
"name": "KONECT",
"prefix": "r3d100011612",
"synonyms": [
"Koblenz Network Collection"
]
},
"r3d100011623": {
"description": "The TromsΓΈ Repository of Language and Linguistics (TROLLing) is a FAIR-aligned repository of linguistic data and statistical code. The archive is open access, which means that all information is available to everyone. All data are accompanied by searchable metadata that identify the researchers, the languages and linguistic phenomena involved, the statistical methods applied, and scholarly publications based on the data (where relevant). Linguists worldwide are invited to deposit data and statistical code used in their linguistic research.\n\nTROLLing is a special collection within DataverseNO (https://doi.org/10.17616/R3TV17), and C Centre within CLARIN (Common Language Resources and Technology Infrastructure, a networked federation of European data repositories; https://www.clarin.eu/), and harvested by their Virtual Language Observatory (VLO; https://vlo.clarin.eu/).",
"homepage": "https://dataverse.no/dataverse/trolling",
"name": "TROLLing",
"prefix": "r3d100011623",
"synonyms": [
"TromsΓΈ Repository of Language and Linguistics"
],
"xrefs": {
"fairsharing": "FAIRsharing.JGEjCW"
}
},
"r3d100011625": {
"description": "IATI is a voluntary, multi-stakeholder initiative that seeks to improve the transparency of aid, development, and humanitarian resources in order to increase their effectiveness in tackling poverty. IATI brings together donor and recipient countries, civil society organisations, and other experts in aid information who are committed to working together to increase the transparency and openness of aid. - See more at: https://iatistandard.org/en/about/#sthash.BYPZ6NPt.dpuf",
"homepage": "https://iatistandard.org/en/",
"name": "International Aid Transparency Initiative",
"prefix": "r3d100011625",
"synonyms": [
"IATI",
"IITA",
"Initiative internationale pour la transparence de lβaide"
]
},
"r3d100011626": {
"description": "ETH Data Archive is ETH Zurich's long-term preservation solution for digital information such as research data, digitised content, archival records, or images. It serves as the backbone of data curation and for most of its content, it is a βdark archiveβ without public access.\nIn this capacity, the ETH Data Archive also archives the content of ETH Zurichβs Research Collection which is the primary repository for members of the university and the first point of contact for publication of data at ETH Zurich. All data that was produced in the context of research at the ETH Zurich, can be published and archived in the Research Collection. An automated connection to the ETH Data Archive in the background ensures the medium to long-term preservation of all publications and research data.\nDirect access to the ETH Data Archive is intended only for customers who need to deposit software source code within the framework of ETH transfer Software Registration. Open Source code packages and other content from legacy workflows can be accessed via ETH Library @ swisscovery (https://library.ethz.ch/en/).",
"homepage": "https://go.data-archive.ethz.ch/",
"name": "ETH Data Archive",
"prefix": "r3d100011626"
},
"r3d100011627": {
"description": "The Polar Rock Repository (PRR) at the Byrd Polar and Climate Research Center (BPCRC) at Ohio State University is an NSF-OPP funded facility that provides access to rock, terrestrial drill core, glacial deposits and marine dredge samples from Antarctica and the Southern Ocean. The polar rock collection and database includes field notes, photos, maps, cores, powder and mineral residues, thin sections, and residues. Rock samples may be borrowed for research by university scientists. Samples may also be borrowed for educational or museum use in the United States.",
"homepage": "https://prr.osu.edu/",
"name": "Polar Rock Repository Database",
"prefix": "r3d100011627",
"synonyms": [
"PRR"
],
"xrefs": {
"doi": "10.7289/V5RF5S18",
"nlx": "154740",
"scr": "002212"
}
},
"r3d100011630": {
"description": "The Australian Drosophila Ecology and Evolution Resource (ADEER) from the Hoffmann lab and other contributors is a nationally significant life science collection. \nThe Drosophila Clinal Data Collection contains data on populations along the eastern coast of Australia. It remains an excellent resource for understanding past and future evolutionary responses to climate change.\nThe Drosophila Genomic Data Collection hosts Drosophila genomes sequenced as part of the Genomic Basis for Adaptation to Climate Change Project. 23 genomes have been sequenced as part of this project. Currently assemblies and annotations are available for Drosophila birchii, D. bunnanda, D. hydei, and D. repleta. \nThe Drosophila Species Distribution Data Collection contains distribution data of nine drosophilid species that have been collected in Australia by the Hoffmann lab and other research groups between 1924 and 2005. More than 300 drosophilid species have been identified in the tropical and temperate forests located on the east coast of Australia. Many species are restricted to the tropics, a few are temperate specialists, and some have broad distributions across climatic regions. Their varied distribution along the tropical - temperate cline provide a powerful tool for studying climate adaptation and species distribution limits.",
"homepage": "https://adeer.esrc.info/",
"name": "Australian Drosophila Ecology and Evolution Resource",
"prefix": "r3d100011630",
"synonyms": [
"ADEER"
]
},
"r3d100011631": {
"description": "The UniSA Data Access Portal showcases a range of Open Access research collections and datasets developed or collected by the University of South Australia. The UniSA Data Access Portal also highlights research projects and publications related to the available collections and datasets, and facilitates a variety of searches by researcher, organisation, discipline and keyword.\nResearch collections and datasets available in Open Access can be freely downloaded and used to support your research in line with the terms of the licence under which they are made available.",
"homepage": "https://data.unisa.edu.au/dap/",
"name": "UniSA Research Data Access Portal",
"prefix": "r3d100011631",
"synonyms": [
"University of South Australia Research Data Access Portal"
]
},
"r3d100011632": {
"description": "<<>>!!!>>>",
"homepage": "https://www.adelaide.edu.au/acad/research-strengths/oagr-online-ancient-genome-repository",
"name": "OAGR",
"prefix": "r3d100011632",
"synonyms": [
"Online Ancient Genome Repository"
]
},
"r3d100011633": {
"description": "The Institute for Marine and Antarctic Studies (IMAS) pursues multidisciplinary and interdisciplinary work to advance understanding of temperate marine, Southern Ocean, and Antarctic environments.\nIMAS research is characterised as innovative, relevant, and globally distinctive. Education at IMAS delivers world class programs, resulting in highly trained graduates who serve the needs of academic institutions, industry, government, and the community. IMAS is naturally advantaged by its Southern Ocean location proximal to Antarctica, and hosts one of the world's largest critical masses of marine and Antarctic researchers.\nIMAS also operate facilities and host data sets of national and global interest and to the benefit of the community. The guiding framework of IMAS is that all data that are not commercial-in-confidence or restricted by legislation or agreement are owned by the University on behalf of the community or Commonwealth, are hosted by an organisation, and are shared with researchers for analysis and interpretation. IMAS is committed to the concept of Open Data.\nThe IMAS Data Portal is an online interface showcasing the IMAS metadata catalogue and all available IMAS data. The portal aims to make IMAS data freely and openly available for the benefit of Australian marine and environmental science as a whole.",
"homepage": "https://data.imas.utas.edu.au/static/landing.html",
"name": "IMAS Data Portal",
"prefix": "r3d100011633",
"synonyms": [
"Institute for Marine and Antarctic Studies Data Portal"
],
"xrefs": {
"fairsharing": "FAIRsharing.qwzEsc"
}
},
"r3d100011634": {
"description": "This study assessed differences in avian biodiversity across different forest age-classes, including mature stands (> 100 years), in a managed, mixed-species eucalypt forest located in Gippsland, south-eastern Australia. Avian surveys and detailed habitat measurements were initially carried out in 50 two hectare stands ranging in age from 100 years. Extensive wildfire which occurred during the study reduced the number of sites to 28 (seven in each of four age classes) upon which analyses and inferences were made. Mature vegetation (> 100 years) had the greatest richness, abundance and biomass of birds. Key ecological resources, such as tree-hollows for nesting, generally occurred mostly in stands > 60 years. There were quantum increases in all measures of avian biodiversity in mature stands (> 100 years). The visualisation of the survey data is part of an interoperable web-GIS maintained by the Centre for eResearch and Digital Innovation (CeRDI) at Federation University Australia (FedUni).",
"homepage": "https://data.cerdi.edu.au/gippsland_birds.php",
"name": "Boola Boola Forest bird study",
"prefix": "r3d100011634"
},
"r3d100011635": {
"description": "EarthByte is an internationally leading eGeoscience collaboration between several Australian Universities, international centres of excellence and industry partners. One of the fundamental aims of the EarthByte Group is geodata synthesis through space and time, assimilating the wealth of disparate geological and geophysical data into a four-dimensional Earth model including tectonics, geodynamics and surface processes. The EarthByte Group is pursuing open innovation via collaborative software development, high performance and distributed computing, βbig dataβ analysis and by making open access digital data collections available to the community.",
"homepage": "https://www.earthbyte.org/",
"name": "EarthByte",
"prefix": "r3d100011635"
},
"r3d100011636": {
"description": "In a changing climate, water raises increasingly complex challenges: concerning its quantity, quality, availability, allocation, use and significance as a habitat, resource and cultural medium. Dharmae, a βData Hub of Australian Research on Marine and Aquatic Ecoculturesβ brings together multi-disciplinary research data relating to water in all these forms.\nThe term βecocultureβ guides the development of this collection and its approach to data discovery. Ecoculture recognizes that, since nature and culture are inextricably linked, there is a corresponding need for greater interconnectedness of the different knowledge systems applied to them.",
"homepage": "https://dharmae.research.uts.edu.au/",
"name": "dharmae",
"prefix": "r3d100011636",
"synonyms": [
"Data Hub of Australian Research on Marine & Aquatic Ecocultures"
]
},
"r3d100011637": {
"description": "<<>>!!!>>>",
"homepage": "https://crop-pal.org/",
"name": "cropPAL",
"prefix": "r3d100011637",
"synonyms": [
"Compendium of crop Proteins with Annotated Locations"
],
"xrefs": {
"fairsharing": "FAIRsharing.p7btsb"
}
},
"r3d100011638": {
"description": "University of Southern Queensland Research Data Collection in Research Data Australia cover 123 subjects areas including Agricultural and Veterinary Sciences, Environmental Sciences and Engineering.",
"homepage": "https://researchdata.edu.au/contributors/university-of-southern-queensland",
"name": "University of Southern Queensland research data collection",
"prefix": "r3d100011638"
},
"r3d100011639": {
"description": "Australian Waterbird Surveys (AWS) is an information source of waterbird communities around Australia, based on surveys of their diversity and numbers. It relies on rigorous data collection protocols and includes more than 50 waterbird species and up to 30 years of survey data. This open source also includes the extent of flooding of thousands of wetlands observed during our surveys. As a group, waterbirds can be sentinels of the ecological health of our wetlands and rivers. We hope this free information system will help track long-term changes in the environment, provide an assessment tool for individual species, report on our national and international responsibilities and help improve the way we manage our rivers and wetlands. It has been developed with the support of research and government partners.",
"homepage": "https://aws.ecosystem.unsw.edu.au/",
"name": "Australian Waterbird Surveys",
"prefix": "r3d100011639",
"synonyms": [
"AWS"
]
},
"r3d100011640": {
"description": "The UniSC Research Bank is the institutional research repository for the University of the Sunshine Coast. It provides an open access showcase of the University's scholarly research output ensuring that research is made available to the local, national and international communities. UniSC Research Bank is harvested by search engines, and is also indexed by the National Library of Australia's TROVE. By making research easily accessible, it also facilitates collaboration between researchers. Where possible, access to the full text of the publication is made available, in line with copyright permissions for each output. To access relevant research, use the Browse function, or specific records can be searched for by using the search box. Find research data by filtering by resource type 'Research Dataset'.",
"homepage": "https://research.usc.edu.au/esploro/",
"name": "UniSC Research Bank research data",
"prefix": "r3d100011640",
"synonyms": [
"University of the Sunshine Coast Research Bank research data"
]
},
"r3d100011643": {
"description": "The Polar Geospatial Center provides geospatial support, mapping, and GIS/remote sensing solutions to researchers and logistics groups in the polar science community.",
"homepage": "https://www.pgc.umn.edu/",
"name": "Polar Geospatial Center",
"prefix": "r3d100011643",
"synonyms": [
"PGC"
],
"xrefs": {
"fairsharing.legacy": "3216",
"nlx": "154743",
"scr": "000402"
}
},
"r3d100011646": {
"description": "EchoBase is a database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655.",
"homepage": "https://www.york.ac.uk/res/thomas/index.cfm",
"name": "EchoBase",
"prefix": "r3d100011646",
"synonyms": [
"an integrated post-genomic database for E.coli"
],
"xrefs": {
"miriam": "00000200",
"nif": "0000-02781",
"scr": "002430"
}
},
"r3d100011647": {
"description": "The IPK stores a large volume of research results and information in various databases.\nThe Institute of Plant Genetics and Crop Plant Research IPK Gatersleben, is a nonprofit research institution for crop genetics and molecular biology, and is part of the Leibniz Association. The mission of the IPK Gatersleben is to conduct basic and applied research in the area of plant genetics and crop plant research. The results of this work are not only of significant benefit to plant breeders and the agricultural industry, but also to the food, feed, and chemical industry. An additional research area, the use of renewable raw materials, is increasingly gaining in importance.",
"homepage": "https://www.ipk-gatersleben.de/en/services",
"name": "IPK Gatersleben",
"prefix": "r3d100011647",
"synonyms": [
"Leibniz Institute of Plant Genetics and Crop Plant Research",
"Leibniz-Institut fΓΌr Pflanzengenetik und Kulturpflanzenforschung"
],
"xrefs": {
"scr": "011341"
}
},
"r3d100011648": {
"description": "AHEAD, the European Archive of Historical Earthquake Data 1000-1899, is a distributed archive aiming at preserving, inventorying and making available, to investigators and other users, data sources on the earthquake history of Europe, such as papers, reports, Macroseismic Data Points (MDPs), parametric catalogues, and so on.",
"homepage": "https://www.emidius.eu/AHEAD/",
"name": "AHEAD",
"prefix": "r3d100011648",
"synonyms": [
"European Archive of Historical EArthquake Data"
],
"xrefs": {
"doi": "10.6092/INGV.IT-AHEAD",
"fairsharing.legacy": "3219"
}
},
"r3d100011650": {
"description": "Argo is an international programme using autonomous floats to collect temperature, salinity and current data in the ice-free oceans. It is teamed with the Jason ocean satellite series. Argo will soon reach its target of 3000 floats delivering data within 24 hours to researchers and operational centres worldwide. 23 countries contribute floats to Argo and many others help with float deployments. Argo has revolutionized the collection of information \nfrom inside the oceans. ARGO Project is organized in regional and national Centers with a Project Office, an Information Center (AIC) and 2 Global Data Centers (GDAC), at the United States and at France. Each DAC submits regularly all its new files to both USGODAE and Coriolis GDACs.The whole Argo data set is available in real time and delayed mode from the global data centres (GDACs).\nThe internet addresses are: https://nrlgodae1.nrlmry.navy.mil/ and http://www.argodatamgt.org",
"homepage": "http://www.argo.net/",
"name": "International Argo Project",
"prefix": "r3d100011650",
"synonyms": [
"Argo.net"
]
},
"r3d100011651": {
"description": "The aim of the Freshwater Biodiversity Data Portal is to integrate and provide open and free access to freshwater biodiversity data from all possible sources. To this end, we offer tools and support for scientists interested in documenting/advertising their dataset in the metadatabase, in submitting or publishing their primary biodiversity data (i.e. species occurrence records) or having their dataset linked to the Freshwater Biodiversity Data Portal. This information portal serves as a data discovery tool, and allows scientists and managers to complement, integrate, and analyse distribution data to elucidate patterns in freshwater biodiversity. The Freshwater Biodiversity Data Portal was initiated under the EU FP7 BioFresh project and continued through the Freshwater Information Platform (http://www.freshwaterplatform.eu). To ensure the broad availability of biodiversity data and integration in the global GBIF index, we strongly encourages scientists to submit any primary biodiversity data published in a scientific paper to national nodes of GBIF or to thematic initiatives such as the Freshwater Biodiversity Data Portal.",
"homepage": "https://data.freshwaterbiodiversity.eu/",
"name": "Freshwater Biodiversity Data Portal",
"prefix": "r3d100011651",
"synonyms": [
"BIOFRESH"
]
},
"r3d100011652": {
"description": "BLLAST is a research programme aimed at exploring the late afternoon transition of the atmospheric boundary layer.\nThe late afternoon period of the diurnal cycle of the boundary layer is poorly understood. This is yet an important transition period that impacts the transport and dillution of water vapour and trace species. The main questions adressed by the project are:\n- How the turbulence activity fades when heating by the surface decreases?\n- What is the impact on the transport of chemical species?\n- How relevant processes can be represented in numerical models?\nTo answer all these questions, a field campaign was carried out during the summer of 2011 (from June 14 to July 8). Many observation systems were then deployed and operated by research teams coming from France and abroad. They were spanning a large spectrum of space and time scales in order to achieve a comprehensive description of the boundary layer processes. The observation strategy consisted in intensifying the operations in the late afternoon with tethered balloons, resarch aircrafts and UAVs.",
"homepage": "https://bllast.aeris-data.fr/",
"name": "Boundary Layer Late Afternoon and Sunset Turbulence",
"prefix": "r3d100011652",
"synonyms": [
"BLLAST"
],
"xrefs": {
"issn": "2430-3518"
}
},
"r3d100011653": {
"description": "<<>>!!!>>>",
"homepage": "https://databank.ora.ox.ac.uk/",
"name": "DataBank, Bodleian Libraries, University of Oxford",
"prefix": "r3d100011653"
},
"r3d100011654": {
"description": "The Brown Digital Repository (BDR) is a place to gather, index, store, preserve, and make available digital assets produced via the scholarly, instructional, research, and administrative activities at Brown.",
"homepage": "https://repository.library.brown.edu/studio/",
"name": "Brown Digital Repository",
"prefix": "r3d100011654",
"synonyms": [
"BDR"
]
},
"r3d100011655": {
"description": "The California Coastal Atlas is an experiment in the creation of a new information resource for the description, analysis and understanding of natural and human processes affecting the coast of California.",
"homepage": "https://californiacoastalatlas.net/",
"name": "California Coastal Atlas",
"prefix": "r3d100011655",
"synonyms": [
"CCA"
]
},
"r3d100011656": {
"description": "The Common Cold Project began in 2011 with the aim of creating, documenting, and archiving a database that combines final research data from 5 prospective viral-challenge studies that were conducted over the preceding 25 years: the British Cold Study (BCS); the three Pittsburgh Cold Studies (PCS1, PCS2, and PCS3); and the Pittsburgh Mind-Body Center Cold Study (PMBC). These unique studies assessed predictor (and hypothesized mediating) variables in healthy adults aged 18 to 55 years, experimentally exposed them to a virus that causes the common cold, and then monitored them for development of infection and signs and symptoms of illness.",
"homepage": "https://www.cmu.edu/common-cold-project/data/index.html",
"name": "Common Cold Project Data Sets",
"prefix": "r3d100011656",
"synonyms": [
"Carnegie Mellon University Digital Collections"
]
},
"r3d100011657": {
"description": "The objective of this database is to stimulate the exchange of information and the collaboration between researchers within the ChArMEx community. However, this community is not exclusive and researchers not directly involved in ChArMEx, but who wish to contribute to the achievements of ChArMEx scientific and/or educational goals are welcome to join-in.\nThe database is a depository for all the data collected during the various projects that contribute to ChArMEx coordinated program. It aims at documenting, storing and distributing the data produced or used by the project community. However, it is also intended to host datasets that were produced outside the ChArMEx program but which are meaningful to ChArMEx scientific and/or educational goals. Any data owner who wishes to add or link his dataset to ChArMEx database is welcome to contact the database manager in order to get help and support. The ChArMEx database includes past and recent geophysical in situ observations, satellite products and model outputs. The database organizes the data management and provides data services to end-users of ChArMEx data.\nThe database system provides a detailed description of the products and uses standardized formats whenever it is possible. It defines the access rules to the data and details the mutual rights and obligations of data providers and users (see ChArMEx data and publication policy). The database is being developed jointly by : SEDOO, OMP Toulouse , ICARE, Lille and ESPRI, IPSL Paris",
"homepage": "https://mistrals.sedoo.fr/ChArMEx/",
"name": "ChArMEx database",
"prefix": "r3d100011657",
"synonyms": [
"Chemistry-Aerosol Mediterranean Experiment"
],
"xrefs": {
"issn": "2495-9650"
}
},
"r3d100011658": {
"description": "<<>>!!!>>>",
"homepage": "https://toolkit.cit-ec.uni-bielefeld.de/",
"name": "CITK",
"prefix": "r3d100011658",
"synonyms": [
"Cognitive Interaction Toolkit"
]
},
"r3d100011659": {
"description": "The Satellite Application Facility on Climate Monitoring (CM SAF) develops, produces, archives and disseminates satellite-data-based products in support to climate monitoring. The product suite mainly covers parameters related to the energy & water cycle and addresses many of the Essential Climate Variables as defined by GCOS (GCOS 138). The CM SAF produces both Enviromental Data Records and Climate Data Records.",
"homepage": "https://www.cmsaf.eu/EN/Home/home_node.html",
"name": "Satellite Application Facility on Climate Monitoring",
"prefix": "r3d100011659",
"synonyms": [
"CM SAF"
],
"xrefs": {
"biodbcore": "001544",
"fairsharing": "FAIRsharing.5b85dc"
}
},
"r3d100011660": {
"description": "The CRC806-Database platform is the Research Data Management infrastructure of the SFB / CRC 806. The infrastructure is implemented using Open Source software, and implements Open Science, Open Access and Open Data principles.\nThe Collaborative Research Centre (CRC; βSonderforschungsbereichβ or SFB) is designed to capture the complex nature of chronology, regional structure, climatic, environmental and socio-cultural contexts of major intercontinental and transcontinental events of dispersal of Modern Man from Africa to Western Eurasia, and particularly to Europe (Cited from introductory text on: www.sfb806.de).",
"homepage": "https://crc806db.uni-koeln.de/",
"name": "Collaborative Research Centre 806 Database",
"prefix": "r3d100011660",
"synonyms": [
"CRC 806",
"SFB 806",
"Sonderforschungsbereich 806"
]
},
"r3d100011661": {
"description": "The CZO Multiscale TROPIcal CatchmentS (M-TROPICS) consists in the merging, in 2016, of two previously-existing CZOs: BVET (India and Cameroon) and MSEC (Laos and Vietnam).\nThe CZO Multiscale TROPIcal CatchmentS (M-TROPICS) provides the international scientific community with unique decennial time series of meteorological, hydrological, geochemical, and ecological variables in tropical environments. The CZO M-TROPICS involves academic and governmental partners in tropical countries (Cameroun, India, Lao PDR, and Vietnam) and is included in the Research Infrastructure OZCAR, the French contribution to the international CZO initiative.",
"homepage": "https://mtropics.obs-mip.fr/",
"name": "M-TROPICS",
"prefix": "r3d100011661",
"synonyms": [
"Multiscale TROPIcal CatchmentS",
"formerly: Bassins Versants ExpΓ©rimentaux Tropicaux",
"formerly: Experimental Tropical Watersheds"
]
},
"r3d100011662": {
"description": "The Landcare Research DataStore ('the DataStore') is the general data catalogue and repository for Environmental Research Data from Landcare Research.\nMuch of Landcare Researchβs research data is available through specific web pages, but many datasets sit outside these areas. This data repository provides a mechanism for our staff to deposit and document this wider range of datasets so that they may be discovered and potentially re-used.",
"homepage": "https://datastore.landcareresearch.co.nz/",
"name": "Manaaki Whenua - Landcare Research Data Store",
"prefix": "r3d100011662"
},
"r3d100011663": {
"description": "EOLβs platforms and instruments collect large and often unique data sets that must be validated, archived and made available to the research community. The goal of EOL data services is to advance science through delivering high-quality project data and metadata in ways that are as transparent, secure, and easily accessible as possible - today and into the future. By adhering to accepted standards in data formats and data services, EOL provides infrastructure to facilitate discovery and direct access to data and software from state-of-the-art commercial and locally-developed applications. EOLβs data services are committed to the highest standard of data stewardship from collection to validation to archival.",
"homepage": "https://www.eol.ucar.edu/",
"name": "EOL",
"prefix": "r3d100011663",
"synonyms": [
"Earth Observing Laboratory"
]
},
"r3d100011664": {
"description": "Through our decades of hydrological and ecological practices and the activities on the waterways of the German Federal a valuable inventory of hydrological information has emerged in the stuck our experience and knowledge base. Almost all environmental information have a direct or indirect spatial reference. This inventory of spatial data continues to grow. He is both the basis and results of our scientific work. With GGInA, the hydrological Geographical Information and Analysis System of BfG, you can research yourself in this inventory. Much of the information and data is accessed directly on the Metadata Catalog Search and specialist applications. The Geoportal also opens up databases of our partners in the transport and environment. At the same selected data can also be integrated into other environmental portals.",
"homepage": "https://geoportal.bafg.de/ggina-portal/",
"name": "Geoportal der BFG",
"prefix": "r3d100011664",
"synonyms": [
"GEOPORTAL @ BfG",
"GGInA",
"Geopaortal der Bundesanstalt fΓΌr GewΓ€sserkunde",
"GewΓ€sserkundliches Geografisches Informations- und Analysesystem der BfG"
]
},
"r3d100011665": {
"description": "GLOBE (Global Collaboration Engine) is an online collaborative environment that enables land change researchers to share, compare and integrate local and regional studies with global data to assess the global relevance of their work.",
"homepage": "http://globe.umbc.edu/",
"name": "GLOBE",
"prefix": "r3d100011665",
"synonyms": [
"Global Collaboration Engine"
]
},
"r3d100011667": {
"description": "HYdrological cycle in the Mediterranean EXperiemnt. Considering the science and societal issues motivating HyMeX, the programme aims to : improve our understanding of the water cycle, with emphasis on extreme events, by monitoring and modelling the Mediterranean atmosphere-land-ocean coupled system, its variability from the event to the seasonal and interannual scales, and its characteristics over one decade (2010-2020) in the context of global change, assess the social and economic vulnerability to extreme events and adaptation capacity.The multidisciplinary research and the database developed within HyMeX should contribute to: improve observational and modelling systems, especially for coupled systems, better predict extreme events, simulate the long-term water-cycle more accurately, provide guidelines for adaptation measures, especially in the context of global change.",
"homepage": "https://mistrals.sedoo.fr/HyMeX/",
"name": "HyMeX",
"prefix": "r3d100011667",
"synonyms": [
"HYdrological cycle in the Mediterranean EXperiemnt"
],
"xrefs": {
"issn": "2491-1887"
}
},
"r3d100011668": {
"description": "IDEALS is an institutional repository that collects, disseminates, and provides persistent and reliable access to the research and scholarship of faculty, staff, and students at the University of Illinois at Urbana-Champaign. Faculty, staff, graduate students, and in some cases undergraduate students, can deposit their research and scholarship directly into IDEALS. Departments can use IDEALS to distribute their working papers, technical reports, or other research material. Contact us at https://www.ideals.illinois.edu/feedback for more information.",
"homepage": "https://www.ideals.illinois.edu/",
"name": "IDEALS",
"prefix": "r3d100011668",
"synonyms": [
"Illinois Digital Environment for Access to Learning and Scholarship"
]
},
"r3d100011669": {
"description": "The Water Survey has flourished for more than a century by anticipating and responding to new challenges and opportunities to serve the citizens of Illinois. Today, the ISWS continues to demonstrate flexibility and adaptability by developing new programs, while continuing to provide long-standing services upon which Illinoisans have come to rely. The Scientific Surveys of the University of Illinois at Urbana-Champaign are the primary agencies in Illinois responsible for producing and disseminating scientific and technological information, services, and products related to the environment, economic development, and quality of life. To achieve this mission, the Scientific Surveys conduct state-of-the-art research and collect, analyze, archive, and disseminate high-quality, objective data and technical information. The information, services, and products provide a sound technical basis for the citizens and policymakers of Illinois and the nation to make wise social, economic, and environmental decisions.",
"homepage": "https://www.isws.illinois.edu/",
"name": "Illinois State Water Survey",
"prefix": "r3d100011669",
"synonyms": [
"ISWS"
]
},
"r3d100011670": {
"description": "!!! >>> intrepidbio.com expired <<< !!!! Intrepid Bioinformatics serves as a community for genetic researchers and scientific programmers who need to achieve meaningful use of their genetic research data β but canβt spend tremendous amounts of time or money in the process. The Intrepid Bioinformatics system automates time consuming manual processes, shortens workflow, and eliminates the threat of lost data in a faster, cheaper, and better environment than existing solutions.\nThe system also provides the functionality and community features needed to analyze the large volumes of Next Generation Sequencing and Single Nucleotide Polymorphism data, which is generated for a wide range of purposes from disease tracking and animal breeding to medical diagnosis and treatment.",
"homepage": "http://www.intrepidbio.com/",
"name": "INTREPID bioinformatics",
"prefix": "r3d100011670",
"xrefs": {
"sciex": "574",
"scr": "012625"
}
},
"r3d100011671": {
"description": "MERMex is focused on the biogeochemical changes that will take place in the Mediterranean Sea due to natural changes as well as the socio-economic impacts, and how they will affect marine ecosystems and biodiversity.",
"homepage": "https://mistrals.sedoo.fr/MERMeX/",
"name": "MERMeX",
"prefix": "r3d100011671",
"synonyms": [
"Marine Ecosystems Response in the Mediterranean Experiment"
]
},
"r3d100011672": {
"description": "<<>>!!!>>>\nHere you will find a collection of atomic microstructures that have been built by the atomic modeling community. Feel free to download any of these and use them in your own scientific explorations.The focus of this cyberinfrastructure is to advance the field of atomic-scale modeling of materials by acting as a forum for disseminating new atomistic scale methodologies, educating non-experts and the next generation of computational materials scientists, and serving as a bridge between the atomistic and complementary (electronic structure, mesoscale) modeling communities.",
"homepage": "http://cams.mse.ufl.edu/microstructures",
"name": "Microstructure Database",
"prefix": "r3d100011672",
"synonyms": [
"CAMS microstructure library"
]
},
"r3d100011673": {
"description": "MISTRALS database is a distributed system, that enables users to access datasets produced by all the projects (ChArMEx, HyMeX, MERMex, TerMex, CORSiCA, EMSO and MOOSE) and stored in different data centres. MISTRALS (Mediterranean Integrated STudies at Regional And Local Scales) is a decennial program for systematic observations and research dedicated to the understanding of the Mediterranean Basin environmental process under the planet global change.\n\nIt aims to coordinate, across the Mediterranean Basin, interdisciplinary research on atmosphere, hydrosphere, lithosphere and paleo-climate, including environmental ecology and social sciences. The objective is to achieve a better understanding of the mechanisms shaping and influencing landscape, environment and human impact of this eco-region.",
"homepage": "https://mistrals.sedoo.fr/en/homepage/",
"name": "MISTRALS database",
"prefix": "r3d100011673",
"synonyms": [
"MISTRALS data portal",
"Mediterranean Integrated STudies at Regional And Local Scales"
],
"xrefs": {
"fairsharing": "FAIRsharing.bece4c",
"issn": "2495-9693"
}
},
"r3d100011674": {
"description": "This hub supports the geospatial modeling, data analysis and visualization needs of the broad research and education communities through hosting of groups, datasets, tools, training materials, and educational contents.",
"homepage": "https://mygeohub.org/",
"name": "My Geo Hub",
"prefix": "r3d100011674"
},
"r3d100011675": {
"description": "The Museum is committed to open access and open science, and has launched the Data Portal to make its research and collections datasets available online. It allows anyone to explore, download and reuse the data for their own research. Our natural history collection is one of the most important in the world, documenting 4.5 billion years of life, the Earth and the solar system. Almost all animal, plant, mineral and fossil groups are represented. These datasets will increase exponentially. Under the Museum's ambitious digital collections programme we aim to have 20 million specimens digitised in the next five years.",
"homepage": "https://data.nhm.ac.uk/",
"name": "Natural History Museum, Data Portal",
"prefix": "r3d100011675",
"synonyms": [
"Explore and download the Natural History Museumβs research and collections data"
],
"xrefs": {
"fairsharing": "FAIRsharing.88ea35"
}
},
"r3d100011676": {
"description": "The goal of NGEEβArctic is to reduce uncertainty in projections of future climate by developing and validating a model representation of permafrost ecosystems and incorporating that representation into Earth system models. The new modeling capabilities will improve our confidence in model projections and will enable scientist to better respond to questions about processes and interactions now and in the future. It also will allow them to better communicate important results concerning climate change to decision makers and the general public. And let's not forget about summer in the Antarctic, which happens during our winter months.",
"homepage": "https://ngee-arctic.ornl.gov/",
"name": "NGEE Arctic",
"prefix": "r3d100011676",
"synonyms": [
"Next-Generation Ecosystem Experiments"
]
},
"r3d100011678": {
"description": "The NIRD Research Data Archive is a repository that provides long-term storage for research data and is compliant with the Open Archival Information System (OAIS) reference model . The aim of the archive is to provide (public) access to published research data and to promote cross-disciplinary studies. \nThe NIRD Research Data Archive (NIRD Archive) is in full production. The NIRD Archive will operate on a βsubject to approvalβ basis and will accept any type of research data from Norwegian academically funded projects that is no longer considered proprietary.",
"homepage": "https://archive.sigma2.no/",
"name": "NIRD Research Data Archive",
"prefix": "r3d100011678",
"synonyms": [
"NIRD Archive",
"formerly: NorStore Research Data Archive"
]
},
"r3d100011679": {
"description": "The Northern California Earthquake Data Center (NCEDC) is a permanent archive and distribution center primarily for multiple types of digital data relating to earthquakes in central and northern California. The NCEDC is located at the Berkeley Seismological Laboratory, and has been accessible to users via the Internet since mid-1992. The NCEDC was formed as a joint project of the Berkeley Seismological Laboratory (BSL) and the U.S. Geological Survey (USGS) at Menlo Park in 1991, and current USGS funding is provided under a cooperative agreement for seismic network operations.",
"homepage": "https://ncedc.org/",
"name": "Northern California Earthquake Data Center",
"prefix": "r3d100011679",
"synonyms": [
"NCEDC"
],
"xrefs": {
"doi": "10.7932/NCEDC",
"fairsharing": "FAIRsharing.248eda"
}
},
"r3d100011680": {
"description": "The Ozone Mapping and Profiler Suite measures the ozone layer in our upper atmosphereβtracking the status of global ozone distributions, including the βozone hole.β It also monitors ozone levels in the troposphere, the lowest layer of our atmosphere. OMPS extends out 40-year long record ozone layer measurements while also providing improved vertical resolution compared to previous operational instruments. Closer to the ground, OMPSβs measurements of harmful ozone improve air quality monitoring and when combined with cloud predictions; help to create the Ultraviolet Index, a guide to safe levels of sunlight exposure. OMPS has two sensors, both new designs, composed of three advanced hyperspectralimaging spectrometers.The three spectrometers: a downward-looking nadir mapper, nadir profiler and limb profiler. The entire OMPS suite currently fly on board the Suomi NPP spacecraft and are scheduled to fly on the JPSS-2 satellite mission. NASA will provide the OMPS-Limb profiler.",
"homepage": "https://ozoneaq.gsfc.nasa.gov/omps/",
"name": "Ozone Mapping and Profiler Suite",
"prefix": "r3d100011680",
"synonyms": [
"Measuring global ozone, aerosols, and reflectivity",
"OMPS"
],
"xrefs": {
"fairsharing.legacy": "3032"
}
},
"r3d100011681": {
"description": "The Precipitation Processing System (PPS) evolved from the Tropical Rainfall Measuring Mission (TRMM) Science Data and Information System (TSDIS). The purpose of the PPS is to process, analyze and archive data from the Global Precipitation Measurement (GPM) mission, partner satellites and the TRMM mission. The PPS also supports TRMM by providing validation products from TRMM ground radar sites. All GPM, TRMM and Partner public data products are available to the science community and the general public from the TRMM/GPM FTP Data Archive. Please note that you need to register to be able to access this data. Registered users can also search for GPM, partner and TRMM data, order custom subsets and set up subscriptions using our PPS Data Products Ordering Interface (STORM)",
"homepage": "https://arthurhou.pps.eosdis.nasa.gov/",
"name": "Precipitation Processing System",
"prefix": "r3d100011681",
"synonyms": [
"PPS"
]
},
"r3d100011682": {
"description": "Scholars' Bank is the open access repository for the intellectual work of faculty, students and staff at the University of Oregon and partner institution collections.",
"homepage": "https://scholarsbank.uoregon.edu/xmlui/",
"name": "Scholar's Bank",
"prefix": "r3d100011682",
"xrefs": {
"fairsharing": "FAIRsharing.86123d"
}
},
"r3d100011683": {
"description": "SeaBASS, the publicly shared archive of in situ oceanographic and atmospheric data maintained by the NASA Ocean Biology Processing Group (OBPG). High quality in situ measurements are prerequisite for satellite data product validation, algorithm development, and many climate-related inquiries. As such, the NASA Ocean Biology Processing Group (OBPG) maintains a local repository of in situ oceanographic and atmospheric data to support their regular scientific analyses. The SeaWiFS Project originally developed this system, SeaBASS, to catalog radiometric and phytoplankton pigment data used their calibration and validation activities. To facilitate the assembly of a global data set, SeaBASS was expanded with oceanographic and atmospheric data collected by participants in the SIMBIOS Program, under NASA Research Announcements NRA-96 and NRA-99, which has aided considerably in minimizing spatial bias and maximizing data acquisition rates. Archived data include measurements of apparent and inherent optical properties, phytoplankton pigment concentrations, and other related oceanographic and atmospheric data, such as water temperature, salinity, stimulated fluorescence, and aerosol optical thickness. Data are collected using a number of different instrument packages, such as profilers, buoys, and hand-held instruments, and manufacturers on a variety of platforms, including ships and moorings.",
"homepage": "https://seabass.gsfc.nasa.gov/",
"name": "SeaBASS",
"prefix": "r3d100011683"
},
"r3d100011684": {
"description": "SHARE - Stations at High Altitude for Research on the Environment - is an integrated Project for environmental monitoring and research in the mountain areas of Europe, Asia, Africa and South America responding to the call for improving environmental research and policies for adaptation to the effects of climate changes, as requested by International and Intergovernmental institutions.",
"homepage": "http://share.evk2cnr.org/",
"name": "SHARE Geonetwork",
"prefix": "r3d100011684",
"synonyms": [
"Stations at High Altitude for Research on the Environment"
]
},
"r3d100011686": {
"description": "The TerMEx program addresses, within the framework of circum-Mediterranean cooperation, two sets of major challenges: (1) the scientific challenges of the Mediterranean deep Earth dynamics, its basin deposits and its interactions with climate, and (2) the societal challenges associated with natural hazards, resources and climate change.\nThe database aims at documenting, storing and distributing the data produced or used by the TerMEx community. This community is not exclusive and we encourage researchers of associated and related programs in the Mediterranean (e.g. Actions Marges and ESF-TopoMed) to join-in the community.",
"homepage": "http://mistrals.sedoo.fr/TerMEx/",
"name": "TerMEx",
"prefix": "r3d100011686"
},
"r3d100011687": {
"description": "The Global Precipitation Climatology Centre (GPCC) provides global precipitation analyses for monitoring and research of the earth's climate. The centre is a German contribution to the World Climate Research Programme (WCRP) and to the Global Climate Observing System (GCOS).",
"homepage": "https://www.dwd.de/EN/ourservices/gpcc/gpcc.html",
"name": "Global Precipitation Climatology Centre",
"prefix": "r3d100011687",
"synonyms": [
"GPCC",
"WZN",
"Weltzentrum fΓΌr Niederschlagsklimatologie"
]
},
"r3d100011688": {
"description": "In the framework of the Collaborative Research Centre/Transregio 32 βPatterns in Soil-Vegetation-Atmosphere Systems: Monitoring, Modelling, and Data Assimilationβ (CRC/TR32, www.tr32.de), funded by the German Research Foundation from 2007 to 2018, a RDM system was self-designed and implemented. The so-called CRC/TR32 project database (TR32DB, www.tr32db.de) is operating online since early 2008. The TR32DB handles all data including metadata, which are created by the involved project participants from several institutions (e.g. Universities of Cologne, Bonn, Aachen, and the Research Centre JΓΌlich) and research fields (e.g. soil and plant sciences, hydrology, geography, geophysics, meteorology, remote sensing). The data is resulting from several field measurement campaigns, meteorological monitoring, remote sensing, laboratory studies and modelling approaches. Furthermore, outcomes of the scientists such as publications, conference contributions, PhD reports and corresponding images are collected in the TR32DB.",
"homepage": "https://www.tr32db.uni-koeln.de/site/index.php",
"name": "Collaborative Research Centre Transregio 32 Database",
"prefix": "r3d100011688",
"synonyms": [
"CRC/Transregio 32 \"Patterns in Soil-Vegetation-Atmosphere Systems\"",
"SFB/Transregio 32 \"Muster und Strukturen in Boden-Pflanzen-AtmosphΓ€ren-Systemen",
"TR32DB"
]
},
"r3d100011690": {
"description": "<<>>!!!>>>",
"homepage": "http://www.signaling-gateway.org/molecule/",
"name": "UCSD Signaling gateway",
"prefix": "r3d100011690",
"xrefs": {
"fairsharing": "FAIRsharing.zf8s5t",
"nif": "0000-03604",
"scr": "006907"
}
},
"r3d100011691": {
"description": "The ACTRIS DC is designed to assist scientists with discovering and accessing atmospheric data and contains an up-to-date catalogue of available datasets in a number of databases distributed throughout the world. A site like this can never be complete, but we have aimed at including datasets from the most relevant databases to the ACTRIS project, also building on the work and experiences achieved in the EU FP6 research project Global Earth Observation and Monitoring. The focus of the web portal is validated data, but it is also possible to browse the ACTRIS data server for preliminary data (rapid delivery data) through this site.\nThe web site allows you to search in a local metadata catalogue that contains information on actual datasets that are archived in external archives. It is set up so that you can search for data by selecting the chemical/physical variable, the data location, the database that holds the data, the type of data, the data acquisition platform, and the data matrix",
"homepage": "https://actris.nilu.no/",
"name": "ACTRIS Data Centre",
"prefix": "r3d100011691",
"synonyms": [
"ACTRIS DC"
],
"xrefs": {
"fairsharing": "FAIRsharing.47ac3e"
}
},
"r3d100011692": {
"description": "!!! <<< the repository is offline, please use: https://www.re3data.org/repository/r3d100011650 >>> !!! The USGODAE Project consists of United States academic, government and military researchers working to improve assimilative ocean modeling as part of the International GODAE Project. GODAE hopes to develop a global system of observations, communications, modeling and assimilation, that will deliver regular, comprehensive information on the state of the oceans, in a way that will promote and engender wide utility and availability of this resource for maximum benefit to the community.\nThe USGODAE Argo GDAC is currently operational, serving daily data from the following national DACs: Australia (CSIRO), Canada (MEDS), China (2: CSIO and NMDIS), France (Coriolis), India (INCOIS), Japan (JMA), Korea (2: KMA and Kordi), UK (BODC), and US (AOML).",
"name": "USGODAE Argo GDAC Data Browser",
"prefix": "r3d100011692",
"synonyms": [
"US Global Ocean Data Assimilation Experiment Argo Global Data Assembly Center Data Browser"
]
},
"r3d100011693": {
"description": "The Avian Knowledge Network (AKN) is an international network of governmental and non-governmental institutions and individuals linking avian conservation, monitoring and science through efficient data management and coordinated development of useful solutions using best-science practices based on the data.",
"homepage": "https://avianknowledge.net/",
"name": "Avian Knowledge Network",
"prefix": "r3d100011693",
"synonyms": [
"AKN"
]
},
"r3d100011694": {
"description": "AVISO stands for \"Archiving, Validation and Interpretation of Satellite Oceanographic data\". \nHere, you will find data, articles, news and tools to help you discover or improve your skills in the altimetry domain through four key themes: ocean, coast, hydrology and ice.\nAltimetry is a technique for measuring height. Satellite altimetry measures the time taken by a radar pulse to travel from the satellite antenna to the surface and back to the satellite receiver. Combined with precise satellite location data, altimetry measurements yield sea-surface heights.",
"homepage": "https://www.aviso.altimetry.fr/en/home.html",
"name": "AVISO+",
"prefix": "r3d100011694",
"synonyms": [
"Satellite Altimetry Data"
],
"xrefs": {
"issn": "2496-0144"
}
},
"r3d100011696": {
"description": "Antarctic marine and terrestrial biodiversity data is widely scattered, patchy and often not readily accessible. In many cases the data is in danger of being irretrievably lost. Biodiversity.aq establishes and supports a distributed system of interoperable databases, giving easy access through a single internet portal to a set of resources relevant to research, conservation and management pertaining to Antarctic biodiversity.\nbiodiversity.aq provides access to both marine and terrestrial Antarctic biodiversity data.",
"homepage": "https://www.biodiversity.aq/",
"name": "biodiversity.aq",
"prefix": "r3d100011696",
"synonyms": [
"ANTABIF dataportal",
"SCAR Antarctic Biodiversity Portal"
]
},
"r3d100011697": {
"description": "<<>>!!!>>>\nBioVeL is a virtual e-laboratory that supports research on biodiversity issues using large amounts of data from cross-disciplinary sources. BioVeL supports the development and use of workflows to process data. It offers the possibility to either use already made workflows or create own.\nBioVeL workflows are stored in MyExperiment - Biovel Group http://www.myexperiment.org/groups/643/content. They are underpinned by a range of analytical and data processing functions (generally provided as Web Services or R scripts) to support common biodiversity analysis tasks. You can find the Web Services catalogued in the BiodiversityCatalogue.",
"homepage": "https://www.biovel.eu/",
"name": "BioVel",
"prefix": "r3d100011697",
"synonyms": [
"Biodiversity Virtual e-Laboratory"
]
},
"r3d100011698": {
"description": "Birdata is your gateway to BirdLife Australia data including the Atlas of Australian Birds and Nest record scheme. You can use Birdata to draw bird distribution maps and generate bird lists for any part of the country. You can also join in the Atlas and submit survey information to this important environmental database. Birdata is a partnership between Birds Australia and the Tony and Lisette Lewis Foundation's WildlifeLink program to collect and make Birds Australia data available online.",
"homepage": "https://birdata.birdlife.org.au/",
"name": "Birdata",
"prefix": "r3d100011698",
"synonyms": [
"BirdLife Australia",
"Royal Australasian Ornithologists Union RAOU"
]
},
"r3d100011699": {
"description": "The main objective of the Bolin Centre Database is to ensure the preservation, interoperability and open access of climate research data for members of the Bolin Centre for Climate Research. The Bolin Centre Database also provides expert advice and guidance on data management. The Bolin Centre itself is a multi-disciplinary consortium in Sweden that conducts research and graduate education related to the EarthΒ΄s climate, in collaboration between Stockholm University, The Swedish Meteorological and Hydrological Institute (SMHI) and the KTH Royal Institute of Technology.",
"homepage": "https://bolin.su.se/data/",
"name": "Bolin Centre Database",
"prefix": "r3d100011699",
"synonyms": [
"Bolin Centre for Climate Research"
],
"xrefs": {
"fairsharing": "FAIRsharing.3356e8"
}
},
"r3d100011700": {
"description": "BSRN is a project of the Radiation Panel (now the Data and Assessment Panel) from the Global Energy and Water Cycle Experiment (GEWEX) under the umbrella of the World Climate Research Programme (WCRP). It is the global baseline network for surface radiation for the Global limate Observing System (GCOS), contributing to the Global Atmospheric Watch (GAW), and forming a ooperative network with the Network for the Detection of Atmospheric Composition Change NDACC).",
"homepage": "https://www.bsrn.awi.de/",
"name": "WRMC-BSRN",
"prefix": "r3d100011700",
"synonyms": [
"Baseline Surface Radiation Network",
"World Radiation Monitoring Center, Baseline Surface Radiation Network"
],
"xrefs": {
"fairsharing": "FAIRsharing.6029a3,"
}
},
"r3d100011701": {
"description": "CDAAC is responsible for processing the science data received from COSMIC. This data is currently being processed not long after the data is received, i.e. approximately eighty percent of radio occultation profiles are delivered to operational weather centers within 3 hours of observation as well as in a more accurate post-processed mode (within 8 weeks of observation).",
"homepage": "https://cdaac-www.cosmic.ucar.edu",
"name": "COSMIC Data Analysis and Archive Center",
"prefix": "r3d100011701",
"synonyms": [
"CDAAC",
"Constellation Observing System for Meteorology Ionosphere and Climate, Data Analysis and Archive Center"
]
},
"r3d100011702": {
"description": "The CDAWeb data system enables improved display and coordinated analysis of multi-instrument, multimission data bases of the kind whose analysis is critical to meeting the science objectives of the ISTP program and the InterAgency Consultative Group (IACG) Solar-Terrestrial Science Initiative. The system combines the client-server user interface technology of the World Wide Web with a powerful set of customized IDL routines to leverage the data format standards (CDF) and guidelines for implementation adopted by ISTP and the IACG. The system can be used with any collection of data granules following the extended set of ISTP/IACG standards. CDAWeb is being used both to support coordinated analysis of public and proprietary data and better functional access to specific public data such as the ISTP-precursor CDAW 9 data base that is formatted to the ISTP/IACG standards. \nMany data sets are available through the Coordinated Data Analysis Web (CDAWeb) service and the data coverage continues to grow. These are largely, but not exclusively, magnetospheric data and nearby solar wind data of the ISTP era (1992-present) at time resolutions of approximately a minute. The CDAWeb service provides graphical browsing, data subsetting, screen listings, file creations and downloads (ASCII or CDF). \nPublic data from current (1992-present) space physics missions (including Cluster, IMAGE, ISTP, FAST, IMP-8, SAMPEX and others). Public data from missions before 1992 (including IMP-8, ISIS1/2, Alouette2, Hawkeye and others). Public data from all current and past space physics missions.\nCDAWeb ist part of \"Space Physics Data Facility\" (https://www.re3data.org/repository/r3d100010168).",
"homepage": "https://cdaweb.gsfc.nasa.gov/index.html",
"name": "CDAWeb",
"prefix": "r3d100011702",
"synonyms": [
"Heliophysics Coordinated Data Analysis Web"
]
},
"r3d100011703": {
"description": "This interface provides access to several types of data related to the Chesapeake Bay. Bay Program databases can be queried based upon user-defined inputs such as geographic region and date range. Each query results in a downloadable, tab- or comma-delimited text file that can be imported to any program (e.g., SAS, Excel, Access) for further analysis. Comments regarding the interface are encouraged. Questions in reference to the data should be addressed to the contact provided on subsequent pages.",
"homepage": "https://www.chesapeakebay.net/what/data",
"name": "Chesapeake Bay Data Hub",
"prefix": "r3d100011703",
"synonyms": [
"CPB",
"Chesapeake Bay Program"
]
},
"r3d100011704": {
"description": "Climate Data Online (CDO) provides free access to NCDC's archive of global historical weather and climate data in addition to station history information. These data include quality controlled daily, monthly, seasonal, and yearly measurements of temperature, precipitation, wind, and degree days as well as radar data and 30-year Climate Normals",
"homepage": "https://www.ncdc.noaa.gov/cdo-web/",
"name": "Climate Data Online",
"prefix": "r3d100011704",
"synonyms": [
"CDO"
],
"xrefs": {
"fairsharing": "FAIRsharing.a00142"
}
},
"r3d100011705": {
"description": "Under the World Climate Research Programme (WCRP) the Working Group on Coupled Modelling (WGCM) established the Coupled Model Intercomparison Project (CMIP) as a standard experimental protocol for studying the output of coupled atmosphere-ocean general circulation models (AOGCMs). CMIP provides a community-based infrastructure in support of climate model diagnosis, validation, intercomparison, documentation and data access. This framework enables a diverse community of scientists to analyze GCMs in a systematic fashion, a process which serves to facilitate model improvement. Virtually the entire international climate modeling community has participated in this project since its inception in 1995. The Program for Climate Model Diagnosis and Intercomparison (PCMDI) archives much of the CMIP data and provides other support for CMIP. \nWe are now beginning the process towards the IPCC Fifth Assessment Report and with it the CMIP5 intercomparison activity. The CMIP5 (CMIP Phase 5) experiment design has been finalized with the following suites of experiments:\nI Decadal Hindcasts and Predictions simulations,\nII \"long-term\" simulations,\nIII \"atmosphere-only\" (prescribed SST) simulations for especially computationally-demanding models.\nThe new ESGF peer-to-peer (P2P) enterprise system (http://pcmdi9.llnl.gov) is now the official site for CMIP5 model output. The old gateway (http://pcmdi3.llnl.gov) is deprecated and now shut down permanently.",
"homepage": "https://pcmdi.llnl.gov/mips/cmip5/index.html",
"name": "Coupled Model Intercomparison Project",
"prefix": "r3d100011705",
"synonyms": [
"CMIP"
]
},
"r3d100011707": {
"description": "The Genomic Observatories Meta-Database (GEOME) is a web-based database that captures the who, what, where, and when of biological samples and associated genetic sequences. GEOME helps users with the following goals: ensure the metadata from your biological samples is findable, accessible, interoperable, and reusable; improve the quality of your data and comply with global data standards; and integrate with R, ease publication to NCBI's sequence read archive, and work with an associated LIMS. The initial use case for GEOME came from the Diversity of the Indo-Pacific Network (DIPnet) resource.",
"homepage": "https://geome-db.org/",
"name": "Genomic Observatories MetaDatabase",
"prefix": "r3d100011707",
"synonyms": [
"GEOME"
]
},
"r3d100011708": {
"description": "The ASTER Project consists of two parts, each having a Japanese and a U.S. component. Mission operations are split between Japan Space Systems (J-spacesystems) and the Jet Propulsion Laboratory (JPL) in the U.S. J-spacesystems oversees monitoring instrument performance and health, developing the daily schedule command sequence, processing Level 0 data to Level 1, and providing higher level data processing, archiving, and distribution. The JPL ASTER project provides scheduling support for U.S. investigators, calibration and validation of the instrument and data products, coordinating the U.S. Science Team, and maintaining the science algorithms. The joint Japan/U.S. ASTER Science Team has about 40 scientists and researchers. Data access via NASA Reverb, ASTER Japan site, earth explorer, GloVis,GDEx and LP DAAC. See here https://asterweb.jpl.nasa.gov/data.asp. In Addition data are availabe through the newly implemented ASTER Volcano archive (AVA) https://ava.jpl.nasa.gov/ .",
"homepage": "https://asterweb.jpl.nasa.gov/index.asp",
"name": "ASTER JPL",
"prefix": "r3d100011708",
"synonyms": [
"Advanced Spaceborne Thermal Emission and Reflection Radiometer"
],
"xrefs": {
"fairsharing": "FAIRsharing.00dfd8",
"nlx": "157751",
"scr": "010478"
}
},
"r3d100011709": {
"description": "Complete Genomics provides free public access to a variety of whole human genome data sets generated from Complete Genomicsβ sequencing service. The research community can explore and familiarize themselves with the quality of these data sets, review the data formats provided from our sequencing service, and augment their own research with additional summaries of genomic variation across a panel of diverse individuals. The quality of these data sets is representative of what a customer can expect to receive for their own samples.\nThis public genome repository comprises genome results from both our Standard Sequencing Service (69 standard, non-diseased samples) and the Cancer Sequencing Service (two matched tumor and normal sample pairs).\nIn March 2013 Complete Genomics was acquired by BGI-Shenzhen , the worldβs largest genomics services company. BGI is a company headquartered in Shenzhen, China that provides comprehensive sequencing and bioinformatics services for commercial science, medical, agricultural and environmental applications. Complete Genomics is now focused on building a new generation of high-throughput sequencing technology and developing new and exciting research, clinical and consumer applications.",
"homepage": "https://completegenomics.com/",
"name": "Complete Genomics",
"prefix": "r3d100011709"
},
"r3d100011710": {
"description": "The Coriolis Data Centre handles operational oceanography measurements made in situ, complementing the measurement of the ocean surface made using instruments aboard satellites.\nThis work is realised through the establishment of permanent networks with data collected by ships or autonomous systems that are either fixed or drifting.\nThis data can be used to construct a snapshot of water mass structure and current intensity.",
"homepage": "https://www.coriolis.eu.org/",
"name": "Coriolis",
"prefix": "r3d100011710",
"synonyms": [
"Operational Oceanography"
],
"xrefs": {
"issn": "2495-8956"
}
},
"r3d100011713": {
"description": "DBpedia is a crowd-sourced community effort to extract structured information from Wikipedia and make this information available on the Web. DBpedia allows you to ask sophisticated queries against Wikipedia, and to link the different data sets on the Web to Wikipedia data. We hope that this work will make it easier for the huge amount of information in Wikipedia to be used in some new interesting ways. Furthermore, it might inspire new mechanisms for navigating, linking, and improving the encyclopedia itself.",
"homepage": "https://www.dbpedia.org/",
"name": "DBpedia",
"prefix": "r3d100011713",
"xrefs": {
"nlx": "157815",
"scr": "003661"
}
},
"r3d100011714": {
"description": "The Earth Orientation Centre is responsible for monitoring of long-term earth orientation parameters, publications for time dissemination and leap second announcements.",
"homepage": "https://hpiers.obspm.fr/eop-pc/index.php?index=mission&lang=en",
"name": "Earth Orientation Center",
"prefix": "r3d100011714",
"synonyms": [
"IERS EOP PC"
]
},
"r3d100011716": {
"description": "EartH2Observe brings together the findings from European FP projects DEWFORA, GLOWASIS, WATCH, GEOWOW and others. It will integrate available global earth observations (EO), in-situ datasets and models and will construct a global water resources re-analysis dataset of significant length (several decades). The resulting data will allow for improved insights on the full extent of available water and existing pressures on global water resources in all parts of the water cycle. The project will support efficient and globally consistent water management and decision making by providing comprehensive multi-scale (regional, continental and global) water resources observations. It will test new EO data sources, extend existing processing algorithms and combine data from multiple satellite missions in order to improve the overall resolution and reliability of EO data included in the re-analysis dataset. The resulting datasets will be made available through an open Water Cycle Integrator data portal https://wci.earth2observe.eu/ : the European contribution to the GEOSS/WCI approach. The datasets will be downscaled for application in case-studies at regional and local levels, and optimized based on identified European and local needs supporting water management and decision making . Actual data access: https://wci.earth2observe.eu/data/group/earth2observe",
"homepage": "http://www.earth2observe.eu/",
"name": "eartH2Observe",
"prefix": "r3d100011716",
"synonyms": [
"Global Earth Observation for Integrated Water Resource Assessment"
]
},
"r3d100011717": {
"description": "The Emissions Database for Global Atmospheric Research (EDGAR) provides independent estimates of the global anthropogenic emissions and emission trends, based on publicly available statistics, for the atmospheric modeling community as well as for policy makers. This scientific independent emission inventory is characterized by a coherent world historical trend from 1970 to year x-3, including emissions of all greenhouse gases, air pollutants and aerosols. Data are presented for all countries, with emissions provided per main source category, and spatially allocated on a 0.1x0.1 grid over the globe.",
"homepage": "https://edgar.jrc.ec.europa.eu/",
"name": "EDGAR",
"prefix": "r3d100011717",
"synonyms": [
"Emissions Database for Global Atmospheric Research"
]
},
"r3d100011718": {
"description": "EIDA, an initiative within ORFEUS, is a distributed data centre established to (a) securely archive seismic waveform data and related metadata, gathered by European research infrastructures, and (b) provide transparent access to the archives by the geosciences research communities.\nEIDA nodes are data centres which collect and archive data from seismic networks deploying broad-band sensors, short period sensors, accelerometers, infrasound sensors and other geophysical instruments. Networks contributing data to EIDA are listed in the ORFEUS EIDA networklist (http://www.orfeus-eu.org/data/eida/networks/). Data from the ORFEUS Data Center (ODC), hosted by KNMI, are available through EIDA. \nTechnically, EIDA is based on an underlying architecture developed by GFZ to provide transparent access to all nodes' data. Data within the distributed archives are accessible via the ArcLink protocol (http://www.seiscomp3.org/wiki/doc/applications/arclink).",
"homepage": "https://www.orfeus-eu.org/data/eida/",
"name": "EIDA",
"prefix": "r3d100011718",
"synonyms": [
"European Integrated Data Archive",
"European Integrated waveform Data Archive"
],
"xrefs": {
"fairsharing": "FAIRsharing.vmq5yj"
}
},
"r3d100011719": {
"description": ">>>!!!<<< As stated 2021-06-28 eklima is no longer available >>>!!!<<<",
"homepage": "http://sharki.oslo.dnmi.no/portal/page?_pageid=73,39035,73_39049&_dad=portal&_schema=PORTAL",
"name": "eKlima",
"prefix": "r3d100011719"
},
"r3d100011720": {
"description": "The European Monitoring and Evaluation Programme (EMEP) is a scientifically based and policy driven programme under the Convention on Long-range Transboundary Air Pollution (CLRTAP) for international co-operation to solve transboundary air pollution problems.",
"homepage": "https://www.emep.int/",
"name": "EMEP",
"prefix": "r3d100011720",
"synonyms": [
"The European Monitoring and Evaluation Programme"
]
},
"r3d100011721": {
"description": "The Environmental Change Network is the UKβs long-term environmental monitoring and research (LTER) programme. We make regular measurements of plant and animal communities and their physical and chemical environment. Our long-term datasets are used to increase understanding of the effects of climate change, air pollution and other environmental pressures on UK ecosystems.",
"homepage": "https://ecn.ac.uk/",
"name": "Environmental Change Network",
"prefix": "r3d100011721",
"synonyms": [
"ECN",
"ECN Data Centre",
"UK Environmental Change Network"
]
},
"r3d100011722": {
"description": "ERDDAP is a data server that gives you a simple, consistent way to download subsets of gridded and tabular scientific datasets in common file formats and make graphs and maps. This particular ERDDAP installation has oceanographic data (for example, data from satellites and buoys).",
"homepage": "https://coastwatch.pfeg.noaa.gov/erddap/index.html",
"name": "ERDDAP",
"prefix": "r3d100011722",
"synonyms": [
"Environmental Research Division's Data Access Program"
]
},
"r3d100011723": {
"description": "<<>>!!!>>>",
"homepage": "https://edg.epa.gov/metadata/catalog/main/home.page",
"name": "Environmental Dataset Gateway",
"prefix": "r3d100011723",
"synonyms": [
"EDG",
"EPA's official open data catalog"
],
"xrefs": {
"biodbcore": "001615"
}
},
"r3d100011724": {
"description": "The EPN (or EUREF Permanent Network) is a voluntary organization of several European agencies and universities that pool resources and permanent GNSS station data to generate precise GNSS products. The EPN has been created under the umbrella of the International Association Geodesy and more precisely by its sub-commission EUREF. \nThe European Terrestrial Reference System 89 (ETRS89) is used as the standard precise GPS coordinate system throughout Europe. Supported by EuroGeographics and endorsed by the EU, this reference system forms the backbone for all geographic and geodynamic projects on the European territory both on a national as on an international level.",
"homepage": "https://www.epncb.oma.be/",
"name": "EUREF Permanent GNSS Network",
"prefix": "r3d100011724",
"synonyms": [
"EPN CB",
"EUREF Permanent Network Central Bureau"
]
},
"r3d100011725": {
"description": "Public Opinion in the European Union. Our surveys address major topics concerning European citizenship. The Standard Eurobarometer was established in 1973. Since 1973, the European Commission has been monitoring the evolution of public opinion in the Member States, thus helping the preparation of texts, decision-making and the evaluation of its work. Our surveys and studies address major topics concerning European citizenship: enlargement, social situation, health, culture, information technology, environment, the Euro, defence, etc. Each survey consists of approximately 1000 face-to-face interviews per country. Reports are published twice yearly. Reproduction is authorised, except for commercial purposes, provided the source is acknowledged.\nSpecial Eurobarometer reports are based on in-depth thematic studies carried out for various services of the European Commission or other EU Institutions and integrated in the Standard Eurobarometer's polling waves. Reproduction is authorised, except for commercial purposes, provided the source is acknowledged.\nFlash Eurobarometers are ad hoc thematic telephone interviews conducted at the request of any service of the European Commission. Flash surveys enable the Commission to obtain results relatively quickly and to focus on specific target groups, as and when required. Reproduction is authorised, except for commercial purposes, provided the source is acknowledged.\nThe qualitative studies investigate in-depth the motivations, feelings and reactions of selected social groups towards a given subject or concept, by listening to and analysing their way of expressing themselves in discussion groups or with non-directive interviews.",
"homepage": "https://europa.eu/eurobarometer/screen/home",
"name": "Eurobarometer",
"prefix": "r3d100011725",
"synonyms": [
"Eurobaromètre"
]
},
"r3d100011726": {
"description": "The European Centre for Medium-Range Weather Forecasts (ECMWF) is an independent intergovernmental organisation supported by 34 states.\nECMWF is both a research institute and a 24/7 operational service, producing and disseminating numerical weather predictions to its Member States. This data is fully available to the national meteorological services in the Member States. The Centre also offers a catalogue of forecast data that can be purchased by businesses worldwide and other commercial customers\nForecasts, analyses, climate re-analyses, reforecasts and multi-model data are available from our archive (MARS) or via dedicated data servers or via point-to-point dissemination",
"homepage": "https://www.ecmwf.int/",
"name": "European Centre for Medium-Range Weather Forecasts",
"prefix": "r3d100011726",
"synonyms": [
"CEPMMT",
"Centre europΓ©en pour les prΓ©visions mΓ©tΓ©orologiques Γ moyen terme",
"ECMWF",
"EZMW",
"EuropΓ€isches Zentrum fΓΌr mittelfristige Wettervorhersage"
]
},
"r3d100011728": {
"description": "The European Union Open Data Portal is the single point of access to a growing range of data from the institutions and other bodies of the European Union (EU). Data are free for you to use and reuse for commercial or non-commercial purposes.\nBy providing easy and free access to data, the portal aims to promote their innovative use and unleash their economic potential. It also aims to help foster the transparency and the accountability of the institutions and other bodies of the EU.\nThe EU Open Data Portal is managed by the Publications Office of the European Union. Implementation of the EU's open data policy is the responsibility of the Directorate-General for Communications Networks, Content and Technology of the European Commission.",
"homepage": "https://data.europa.eu/data/datasets",
"name": "European Union Open Data Portal",
"prefix": "r3d100011728",
"synonyms": [
"EU ODP",
"EU Open Data Portal"
],
"xrefs": {
"fairsharing": "FAIRsharing.d7b57d",
"issn": "2315-3091"
}
},
"r3d100011729": {
"description": "EMSC collects real time parametric data (source parmaters and phase pickings) provided by 65 seismological networks of the Euro-Med region. These data are provided to the EMSC either by email or via QWIDS (Quake Watch Information Distribution System, developped by ISTI). The collected data are automatically archived in a database, made available via an autoDRM, and displayed on the web site. The collected data are automatically merged to produce automatic locations which are sent to several seismological institutes in order to perform quick moment tensors determination.",
"homepage": "https://www.emsc-csem.org/#2",
"name": "European-Mediterranean Seismological Centre",
"prefix": "r3d100011729",
"synonyms": [
"CSEM",
"Centre Sismologique Euro-MΓ©diterranΓ©en",
"EMSC"
],
"xrefs": {
"issn": "2495-9324"
}
},
"r3d100011730": {
"description": "This website provides access to an extensive database of environmental data and an integrated suite of online tools and resources to help Federal Land Managers assess and analyze the air quality and visibility in Federally-protected lands such as National Parks, National Forests, and Wilderness Areas",
"homepage": "https://views.cira.colostate.edu/fed/",
"name": "Federal Land Manager Environmental database",
"prefix": "r3d100011730",
"synonyms": [
"FED"
]
},
"r3d100011732": {
"description": "Galaxies, made up of billions of stars like our Sun, are the beacons that light up the structure of even the most distant regions in space. Not all galaxies are alike, however. They come in very different shapes and have very different properties; they may be large or small, old or young, red or blue, regular or confused, luminous or faint, dusty or gas-poor, rotating or static, round or disky, and they live either in splendid isolation or in clusters. In other words, the universe contains a very colourful and diverse zoo of galaxies. For almost a century, astronomers have been discussing how galaxies should be classified and how they relate to each other in an attempt to attack the big question of how galaxies form. Galaxy Zoo (Lintott et al. 2008, 2011) pioneered a novel method for performing large-scale visual classifications of survey datasets. This webpage allows anyone to download the resulting GZ classifications of galaxies in the project.",
"homepage": "https://www.zooniverse.org/projects/zookeeper/galaxy-zoo/",
"name": "Galaxy Zoo",
"prefix": "r3d100011732"
},
"r3d100011733": {
"description": "GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project.\nThe GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-coding genes within the ENCODE regions (approx. 1% of Human genome). Given the initial success of the project, GENCODE now aims to build an βEncyclopedia of genes and genes variantsβ by identifying all gene features in the human and mouse genome using a combination of computational analysis, manual annotation, and experimental validation, and annotating all evidence-based gene features in the entire human genome at a high accuracy.",
"homepage": "https://www.gencodegenes.org/",
"name": "GENCODE",
"prefix": "r3d100011733",
"xrefs": {
"fairsharing": "FAIRsharing.7416f8",
"scr": "014966"
}
},
"r3d100011734": {
"description": "The GEOSS Portal provides an entry point to access Earth Observation information and services. It will connect to a system of existing portals, addressing the GEO Societal Benefit Areas globally and provide national to regional perspective to achieve synergy and leverage.",
"homepage": "https://www.geoportal.org/?f:dataSource=dab",
"name": "GEOSS Portal",
"prefix": "r3d100011734",
"synonyms": [
"The Global Earth Observation System of Systems Portal"
]
},
"r3d100011738": {
"description": "<<>>>!!!<<<",
"homepage": "http://data.geocomm.com/",
"name": "GIS Data Depot",
"prefix": "r3d100011738"
},
"r3d100011739": {
"description": "Surface air temperature change is a primary measure of global climate change. The GISTEMP project started in the late 1970s to provide an estimate of the changing global surface air temperature which could be compared with the estimates obtained from climate models simulating the effect of changes in atmospheric carbon dioxide, volcanic aerosols, and solar irradiance. The continuing analysis updates global temperature change from the late 1800s to the present.",
"homepage": "https://data.giss.nasa.gov/gistemp/",
"name": "GISTEMP",
"prefix": "r3d100011739",
"synonyms": [
"GISS Surface Temperature Analysis",
"Goddard Institute for Space Studies Surface Temperature Analysis"
]
},
"r3d100011740": {
"description": "<<>>!!!>>> The Global Land Cover Facility (GLCF) provides earth science data and products to help everyone to better understand global environmental systems. In particular, the GLCF develops and distributes remotely sensed satellite data and products that explain land cover from the local to global scales.",
"name": "Global Land Cover Facility",
"prefix": "r3d100011740",
"synonyms": [
"GLCF"
]
},
"r3d100011741": {
"description": "The Global Carbon Atlas is an online platform to explore, visualize and interpret global and regional carbon data arising from both human activities and natural processes. The graphics and data sources are made available in the belief that their wide dissemination will lead to new knowledge and better-informed decisions to limit and cope with human-induced climate change.\nThe Global Carbon Atlas is a community effort under the umbrella of the Global Carbon Project based on the contributions of many research institutions and individual scientists around the world who make available observations, models, and interpretation skills.",
"homepage": "https://globalcarbonatlas.org/",
"name": "Global carbon atlas",
"prefix": "r3d100011741",
"xrefs": {
"fairsharing": "FAIRsharing.66b58b"
}
},
"r3d100011742": {
"description": "The AERONET (AErosol RObotic NETwork) program is a federation of ground-based remote sensing aerosol networks established by NASA and PHOTONS (PHOtomΓ©trie pour le Traitement OpΓ©rationnel de Normalisation Satellitaire; Univ. of Lille 1, CNES, and CNRS-INSU) and is greatly expanded by networks (e.g., RIMA, AeroSpan, AEROCAN, and CARSNET) and collaborators from national agencies, institutes, universities, individual scientists, and partners. The program provides a long-term, continuous and readily accessible public domain database of aerosol optical, microphysical and radiative properties for aerosol research and characterization, validation of satellite retrievals, and synergism with other databases. The network imposes standardization of instruments, calibration, processing and distribution.",
"homepage": "https://aeronet.gsfc.nasa.gov/",
"name": "AERONET",
"prefix": "r3d100011742",
"synonyms": [
"AErosol RObotic NETwork"
],
"xrefs": {
"fairsharing.legacy": "3170"
}
},
"r3d100011743": {
"description": "The GOES Space Environment Monitor archive is an important component of the National Space Weather Program --a interagency program to provide timely and reliable space environment observations and forecasts. GOES satellites carry onboard a Space Environment Monitor subsystem that measures X-rays, Energetic Particles and Magnetic Field at the Spacecraft.",
"homepage": "https://www.ngdc.noaa.gov/stp/satellite/goes/",
"name": "GOES Space Environment Monitor",
"prefix": "r3d100011743",
"synonyms": [
"GOES SEM",
"Geostationary Operational Environmental Satellites SEM"
]
},
"r3d100011747": {
"description": "iNaturalist is a citizen science project and online social network of naturalists, citizen scientists, and biologists built on the concept of mapping and sharing observations of biodiversity across the globe. iNat is a platform for biodiversity research, where anyone can start up their own science project with a specific purpose and collaborate with other observers.",
"homepage": "https://www.inaturalist.org/",
"name": "iNaturalist.org",
"prefix": "r3d100011747",
"synonyms": [
"iNat"
]
},
"r3d100011748": {
"description": "TropicosΒ was originally created for internal research but has since been made available to the worldβs scientific community. All of the nomenclatural, bibliographic, and specimen data accumulated in MBGβs electronic databases during the past 30 years are publicly available here.",
"homepage": "https://www.tropicos.org/home",
"name": "TropicosΒ",
"prefix": "r3d100011748",
"synonyms": [
"wΒ³Tropicos"
]
},
"r3d100011749": {
"description": ">>>!!!<<< duplicate >>>!!!<<< see https://www.re3data.org/repository/r3d100010914\nAt 2016-05-29 sees the official merger of the IMOS eMarine Information Infrastructure (eMII) Facility and the Australian Ocean Data Network (AODN) into a single entity. The marine information Facility of IMOS is now the AODN. Enabling open access to marine data is core business for IMOS. The IMOS data will continue to be discoverable alongside a wider collection of Australian marine and climate data via the new-look AODN Portal. Visit the AODN Portal at https://portal.aodn.org.au/. - \nAll IMOS data is open access and can be discovered, accessed and downloaded via the Australian Ocean Data Network (AODN) Portal.",
"homepage": "https://portal.aodn.org.au/",
"name": "Integrated Marine Observing System Ocean Data Portal",
"prefix": "r3d100011749",
"synonyms": [
"Australian Ocean Data Network Portal",
"IMOS Ocean Portal",
"IMOS data Portal"
]
},
"r3d100011750": {
"description": "The Ministry for the Environment, Land and Sea has promoted the project \"Environment 2010\" which plays a strong team move to support the National Strategy for Biodiversity . The crux of the system is the National Biodiversity Network (NNB), a network of Centers of Excellence (CoE) and National Focal Point (FP), accredited to international and national level for the management, sharing and information about data on biodiversity.",
"homepage": "https://www.nnb.isprambiente.it/en",
"name": "Italian National Biodiversity Network",
"prefix": "r3d100011750",
"synonyms": [
"NNB",
"Network Nazionale BiodiversitΓ "
]
},
"r3d100011751": {
"description": "MycoCosm, the DOE JGIβs web-based fungal genomics resource, which integrates fungal genomics data and analytical tools for fungal biologists. It provides navigation through sequenced genomes, genome analysis in context of comparative genomics and genome-centric view. MycoCosm promotes user community participation in data submission, annotation and analysis.",
"homepage": "https://mycocosm.jgi.doe.gov/mycocosm/home",
"name": "JGI MycoCosm",
"prefix": "r3d100011751",
"synonyms": [
"MycoCosm - the fungal genomics resource"
],
"xrefs": {
"nlx": "144366",
"omics": "01657",
"scr": "005312"
}
},
"r3d100011752": {
"description": "The European Soil Data Centre (ESDAC) is the thematic centre for soil related data in Europe. Its ambition is to be the single reference point for and to host all relevant soil data and information at European level. It contains a number of resources that are organized and presented in various ways: datasets, services/applications, maps, documents, events, projects and external links.",
"homepage": "https://esdac.jrc.ec.europa.eu/",
"name": "European Soil Data Centre",
"prefix": "r3d100011752",
"synonyms": [
"ESDAC",
"European Soil Data Centre Portal"
]
},
"r3d100011753": {
"description": "Junar provides a cloud-based open data platform that enables innovative organizations worldwide to quickly, easily and affordably make their data accessible to all. In just a few weeks, your initial datasets can be published, providing greater transparency, encouraging collaboration and citizen engagement, and freeing up precious staff resources.",
"homepage": "https://junar.com/?lang=en",
"name": "Junar",
"prefix": "r3d100011753",
"synonyms": [
"Junar Open Data Platform"
]
},
"r3d100011754": {
"description": "Knoema is a knowledge platform. The basic idea is to connect data with analytical and presentation tools. As a result, we end with one uniformed platform for users to access, present and share data-driven content.\nWithin Knoema, we capture most aspects of a typical data use cycle: accessing data from multiple sources, bringing relevant indicators into a common space, visualizing figures, applying analytical functions, creating a set of dashboards, and presenting the outcome.",
"homepage": "https://knoema.de/",
"name": "Knoema",
"prefix": "r3d100011754"
},
"r3d100011756": {
"description": "The primary function of this database is to provide authoritative information about meteorite names. The correct spelling, complete with punctuation and diacritical marks, of all known meteorites recognized by the Meteoritical Society may be found in this compilation. Official abbreviations for many meteorites are documented here as well. The database also contains status information for meteorites with provisional names, and listings for specimens of doubtful origin and pseudometeorites.\nA seconday purpose of this database is to provide an interface to map services for the display of geographic information about meteorites. Two are currently implemented here. If the user has installed the free NASA program World Wind, links are provided for each meteorite to zoom the program to the find location. The database also provides links to the Google Maps service for the display of find locations.",
"homepage": "https://www.lpi.usra.edu/meteor/",
"name": "Meteoritical bulletin database",
"prefix": "r3d100011756"
},
"r3d100011757": {
"description": "MODIS (or Moderate Resolution Imaging Spectroradiometer) is a key instrument aboard the Terra (originally known as EOS AM-1) and Aqua (originally known as EOS PM-1) satellites. Terra's orbit around the Earth is timed so that it passes from north to south across the equator in the morning, while Aqua passes south to north over the equator in the afternoon. Terra MODIS and Aqua MODIS are viewing the entire Earth's surface every 1 to 2 days, acquiring data in 36 spectral bands, or groups of wavelengths (see MODIS Technical Specifications). These data will improve our understanding of global dynamics and processes occurring on the land, in the oceans, and in the lower atmosphere. MODIS is playing a vital role in the development of validated, global, interactive Earth system models able to predict global change accurately enough to assist policy makers in making sound decisions concerning the protection of our environment.",
"homepage": "https://modis.gsfc.nasa.gov/",
"name": "Moderate Resolution Imaging Spectroradiometer",
"prefix": "r3d100011757",
"synonyms": [
"MODIS"
]
},
"r3d100011758": {
"description": "DATA.NASA.GOV is NASA's clearinghouse site for open-data provided to the public.\nTens of thousands of datasets are available for you.\nThis site is a continually growing catalog of publicly available NASA Datasets, APIs, Visualizations, and more.",
"homepage": "https://data.nasa.gov/",
"name": "Nasa's Data Portal",
"prefix": "r3d100011758"
},
"r3d100011759": {
"description": "NCEP delivers national and global weather, water, climate and space weather guidance, forecasts, warnings and analyses to its Partners and External User Communities. The National Centers for Environmental Prediction (NCEP), an arm of the NOAA's National Weather Service (NWS), is comprised of nine distinct Centers, and the Office of the Director, which provide a wide variety of national and international weather guidance products to National Weather Service field offices, government agencies, emergency managers, private sector meteorologists, and meteorological organizations and societies throughout the world. NCEP is a critical national resource in national and global weather prediction. NCEP is the starting point for nearly all weather forecasts in the United States. The Centers are: Aviation Weather Center (AWC), Climate Prediction Center (CPC), Environmental Modeling Center (EMC), NCEP Central Operations (NCO), National Hurricane Center (NHC), Ocean Prediction Center (OPC), Storm Prediction Center (SPC), Space Weather Prediction Center (SWPC), Weather Prediction Center (WPC)",
"homepage": "https://www.weather.gov/ncep/",
"name": "National Weather Service, National Centers for Environmental Prediction",
"prefix": "r3d100011759",
"synonyms": [
"NCEP",
"National Centers for Environmental Prediction"
]
},
"r3d100011760": {
"description": "The NCEP/NCAR Reanalysis Project is a joint project between the National Centers for Environmental Prediction (NCEP, formerly \"NMC\") and the National Center for Atmospheric Research (NCAR). The goal of this joint effort is to produce new atmospheric analyses using historical data (1948 onwards) and as well to produce analyses of the current atmospheric state (Climate Data Assimilation System, CDAS).",
"homepage": "https://psl.noaa.gov/data/reanalysis/reanalysis.shtml",
"name": "NCEP/NCAR Reanalysis Project",
"prefix": "r3d100011760"
},
"r3d100011761": {
"description": "Neotoma is a multiproxy paleoecological database that covers the Pliocene-Quaternary, including modern microfossil samples. The database is an international collaborative effort among individuals from 19 institutions, representing multiple constituent databases.\nThere are over 20 data-types within the Neotoma Paleoecological Database, including pollen microfossils, plant macrofossils, vertebrate fauna, diatoms, charcoal, biomarkers, ostracodes, physical sedimentology and water chemistry.\nNeotoma provides an underlying cyberinfrastructure that enables the development of common software tools for data ingest, discovery, display, analysis, and distribution, while giving domain scientists control over critical taxonomic and other data quality issues.",
"homepage": "https://www.neotomadb.org/",
"name": "Neotoma Paleoecology Database",
"prefix": "r3d100011761",
"synonyms": [
"Neotoma"
],
"xrefs": {
"fairsharing": "FAIRsharing.3wwc0m",
"nlx": "154700",
"scr": "002190"
}
},
"r3d100011763": {
"description": "The NOAA/ESRL Physical Sciences Division (PSD) conducts weather and climate research to observe and understand Earth's physical environment, and to improve weather and climate predictions on global-to-local scales. PSD archives a wide range of data ranging from gridded climate datasets extending hundreds of years to real-time wind profiler data at a single location. The data or products derived from this data, organized by type, are available to scientists and the general public .",
"homepage": "https://psl.noaa.gov/data/",
"name": "PSD Climate and Weather Data",
"prefix": "r3d100011763",
"synonyms": [
"NOAA, ESRL, PSD, CWD",
"National Oceanic & Atmospheric Administration, Earth System Research Laboratory, Physical Sciences Division, Climate and Weather Data"
]
},
"r3d100011764": {
"description": "Climate Data Record (CDR) is a time series of measurements of sufficient length, consistency and continuity to determine climate variability and change. The fundamental CDRs include sensor data, such as calibrated radiances and brightness temperatures, that scientists have improved and quality-controlled along with the data used to calibrate them. The thematic CDRs include geophysical variables derived from the fundamental CDRs, such as sea surface temperature and sea ice concentration, and they are specific to various disciplines.",
"homepage": "https://www.ncei.noaa.gov/products/climate-data-records",
"name": "NOAA's climate data record program",
"prefix": "r3d100011764",
"synonyms": [
"Climate data record program"
]
},
"r3d100011765": {
"description": "Web Soil Survey (WSS) provides soil data and information produced by the National Cooperative Soil Survey. It is operated by the USDA Natural Resources Conservation Service (NRCS) and provides access to the largest natural resource information system in the world. NRCS has soil maps and data available online for more than 95 percent of the nationβs counties and anticipates having 100 percent in the near future. The site is updated and maintained online as the single authoritative source of soil survey information.",
"homepage": "https://www.nrcs.usda.gov/wps/portal/nrcs/main/soils/survey/",
"name": "Web Soil Survey",
"prefix": "r3d100011765",
"synonyms": [
"NRCS Web Soil Survey",
"SSURGO",
"STATSGO2",
"Soil Survey Geographic Database",
"State Soil Geographic2",
"WSS"
]
},
"r3d100011767": {
"description": "The tree of life links all biodiversity through a shared evolutionary history. This project will produce the first online, comprehensive first-draft tree of all 1.8 million named species, accessible to both the public and scientific communities. Assembly of the tree will incorporate previously-published results, with strong collaborations between computational and empirical biologists to develop, test and improve methods of data synthesis. This initial tree of life will not be static; instead, we will develop tools for scientists to update and revise the tree as new data come in. Early release of the tree and tools will motivate data sharing and facilitate ongoing synthesis of knowledge.",
"homepage": "https://tree.opentreeoflife.org/opentree/argus/opentree13.4@ott93302",
"name": "Open Tree of Life",
"prefix": "r3d100011767",
"synonyms": [
"Tree of Life - Evolution"
]
},
"r3d100011768": {
"description": "OpenWorm aims to build the first comprehensive computational model of the Caenorhabditis elegans (C. elegans), a microscopic roundworm. With only a thousand cells, it solves basic problems such as feeding, mate-finding and predator avoidance. Despite being extremely well studied in biology, this organism still eludes a deep, principled understanding of its biology. \n\nWe are using a bottom-up approach, aimed at observing the worm behaviour emerge from a simulation of data derived from scientific experiments carried out over the past decade. To do so we are incorporating the data available in the scientific community into software models. We are engineering Geppetto and Sibernetic, open-source simulation platforms, to be able to run these different models in concert. We are also forging new collaborations with universities and research institutes to collect data that fill in the gaps\n\nAll the code we produce in the OpenWorm project is Open Source and available on GitHub.",
"homepage": "http://www.openworm.org/",
"name": "OpenWorm",
"prefix": "r3d100011768"
},
"r3d100011769": {
"description": "PAGER (Prompt Assessment of Global Earthquakes for Response) is an automated system that produces content concerning the impact of significant earthquakes around the world, informing emergency responders, government and aid agencies, and the media of the scope of the potential disaster. PAGER rapidly assesses earthquake impacts by comparing the population exposed to each level of shaking intensity with models of economic and fatality losses based on past earthquakes in each country or region of the world. Earthquake alerts β which were formerly sent based only on event magnitude and location, or population exposure to shaking β now will also be generated based on the estimated range of fatalities and economic losses. \nPAGER uses these earthquake parameters to calculate estimates of ground shaking by using the methodology and software developed for ShakeMaps. ShakeMap sites provide near-real-time maps of ground motion and shaking intensity following significant earthquakes. These maps are used by federal, state, and local organizations, both public and private, for post-earthquake response and recovery, public and scientific information, as well as for preparedness exercises and disaster planning.",
"homepage": "https://earthquake.usgs.gov/data/pager/",
"name": "Prompt Assessment of Global Earthquakes for Response",
"prefix": "r3d100011769",
"synonyms": [
"PAGER"
]
},
"r3d100011772": {
"description": "The Information Marketplace for Policy and Analysis of Cyber-risk & Trust (IMPACT) program supports global cyber risk research & development by coordinating, enhancing and developing real world data, analytics and information sharing capabilities, tools, models, and methodologies. In order to accelerate solutions around cyber risk issues and infrastructure security, IMPACT makes these data sharing components broadly available as national and international resources to support the three-way partnership among cyber security researchers, technology developers and policymakers in academia, industry and the government.",
"homepage": "https://www.impactcybertrust.org/home#",
"name": "IMPACT",
"prefix": "r3d100011772",
"synonyms": [
"IMPACT Cyber Trust",
"Information Marketplace for Policy and Analysis of Cyber-Risk & Trust"
]
},
"r3d100011773": {
"description": "Remote Sensing Systems is a world leader in processing and analyzing microwave data from satellite microwave sensors. We specialize in algorithm development, instrument calibration, ocean product development, and product validation. We have worked with more than 30 satellite microwave radiometer, sounder, and scatterometer instruments over the past 40 years. Currently, we operationally produce satellite retrievals for SSMIS, AMSR2, WindSat, and ASCAT. The geophysical retrievals obtained from these sensors are made available in near-real-time (NRT) to the global scientific community and general public via FTP and this web site.",
"homepage": "https://www.remss.com/",
"name": "Remote Sensing Systems",
"prefix": "r3d100011773",
"synonyms": [
"RSS"
]
},
"r3d100011774": {
"description": "data.eaufrance.fr is an information system on water (EIS); it is registered in the National Plan for Water Data (NELS) and will be integrated into the data dissemination web pattern.\n\nIt also complies with the European Directive 2003/98 / EC of November 2003 on the reuse of public sector information.\n\ndata.eaufrance.fr is a public data distribution platform open for reuse in the terms and conditions of the Licence Open / Open License.\nOpendata SIE is coordinated by the National Office for Water and Aquatic Environments (Onema); it was developed by the BRGM and the International Office for Water (IOW).",
"homepage": "https://data.eaufrance.fr/",
"name": "data.eaufrance.fr",
"prefix": "r3d100011774",
"synonyms": [
"RΓ©pertoire des donnΓ©es publiques sur l'eau"
]
},
"r3d100011775": {
"description": "The company RapidEye AG of Brandenburg brought on 29 August 2008 five satellites into orbit that can be aligned within a day to any point on Earth. The data are interesting for a number of large and small companies for applications from harvest planning to assessment of insurance claims case of natural disasters.\nVia the Rapid Eye Science Archive (RESA) science users can receive, free of charge, optical image data of the RapidEye satellite fleet. Imagery is allocated based on a proposal to be submitted via the RESA Portal which will be evaluated by independent experts.",
"homepage": "https://www.planet.com/resa/",
"name": "RESA",
"prefix": "r3d100011775",
"synonyms": [
"Rapid eye science archive"
]
},
"r3d100011776": {
"description": "SMHI's observation stations collect large quantities of data, including temperature, precipitation, wind, air pressure, lightning, solar radiation and ozone. Satellites and radar installations are also important sources. Data is presented continuously on smhi.se and used in SMHI's various weather services.\nIn the Explorer SMHIβs data ( http://opendata-catalog.smhi.se/explore/ ) you find data available with open access (in Swedish). Information in English on Oceanographic observations, Model data (HIROMB BS01), Machine to machine β feeds, and Conditions of use.",
"homepage": "https://www.smhi.se/data/utforskaren-oppna-data/",
"name": "Swedish Meteorological and Hydrological Institute open data",
"prefix": "r3d100011776",
"synonyms": [
"SMHI open data",
"SMHI Γppna data"
]
},
"r3d100011777": {
"description": ">>>!!!<<< This site is going away on April 1, 2021. General access to the site has been disabled and community users will see an error upon login. >>>!!!<<<\nSocrataβs cloud-based solution allows government organizations to put their data online, make data-driven decisions, operate more efficiently, and share insights with citizens.",
"homepage": "https://opendata.socrata.com/",
"name": "Open Data by Socrata",
"prefix": "r3d100011777",
"synonyms": [
"Blist",
"Socrata"
]
},
"r3d100011778": {
"description": "SOHO, the Solar & Heliospheric Observatory, is a project of international collaboration between ESA and NASA to study the Sun from its deep core to the outer corona and the solar wind.\n\nSOHO was launched on December 2, 1995. The SOHO spacecraft was built in Europe by an industry team led by prime contractor Matra Marconi Space (now EADS Astrium) under overall management by ESA. The twelve instruments on board SOHO were provided by European and American scientists.",
"homepage": "https://soho.nascom.nasa.gov/",
"name": "Solar and Heliospheric Observatory",
"prefix": "r3d100011778",
"synonyms": [
"SOHO"
]
},
"r3d100011780": {
"description": "SuperDARN is an international HF radar network designed to measure global-scale magnetospheric convection by observing plasma motion in the Earthβs upper atmosphere. This network consists of more than 20 radars operating on frequencies between 8 and 20 MHz that look into the polar regions of Earth. These radars can measure the position and velocity of charged particles in our ionosphere, the highest layer of the Earth's atmosphere, and provide scientists with information regarding Earth's interaction with the space environment.",
"homepage": "https://superdarn.ca/",
"name": "SuperDARN",
"prefix": "r3d100011780",
"synonyms": [
"Super Dual Auroral Radar Network"
]
},
"r3d100011781": {
"description": "To understand the global surface energy budget is to understand climate. Because it is impractical to cover the earth with monitoring stations, the answer to global coverage lies in reliable satellite-based estimates. Efforts are underway at NASA and universities to develop algorithms to do this, but such projects are in their infancy. In concert with these ambitious efforts, accurate and precise ground-based measurements in differing climatic regions are essential to refine and verify the satellite-based estimates, as well as to support specialized research.\nTo fill this niche, the Surface Radiation Budget Network (SURFRAD) was established in 1993 through the support of NOAA's Office of Global Programs.",
"homepage": "https://gml.noaa.gov/grad/surfrad/",
"name": "SURFRAD",
"prefix": "r3d100011781",
"synonyms": [
"Surface Radiation",
"Surface Radiation Budget Network"
]
},
"r3d100011782": {
"description": "As one of the cornerstones of the U.S. Geological Survey's (USGS) National Geospatial Program, The National Map is a collaborative effort among the USGS and other Federal, State, and local partners to improve and deliver topographic information for the Nation. It has many uses ranging from recreation to scientific analysis to emergency response. The National Map is easily accessible for display on the Web, as products and services, and as downloadable data. The geographic information available from The National Map includes orthoimagery (aerial photographs), elevation, geographic names, hydrography, boundaries, transportation, structures, and land cover. Other types of geographic information can be added within the viewer or brought in with The National Map data into a Geographic Information System to create specific types of maps or map views.",
"homepage": "https://www.usgs.gov/programs/national-geospatial-program/national-map",
"name": "The National Map",
"prefix": "r3d100011782",
"synonyms": [
"TNM",
"Your Source for Topographic Information"
]
},
"r3d100011783": {
"description": "The OpenMadrigal project seeks to develop and support an on-line database for geospace data. The project has been led by MIT Haystack Observatory since 1980, but now has active support from Jicamarca Observatory and other community members. Madrigal is a robust, World Wide Web based system capable of managing and serving archival and real-time data, in a variety of formats, from a wide range of ground-based instruments. Madrigal is installed at a number of sites around the world. Data at each Madrigal site is locally controlled and can be updated at any time, but shared metadata between Madrigal sites allow searching of all Madrigal sites at once from any Madrigal site. Data is local; metadata is shared.",
"homepage": "http://cedar.openmadrigal.org/",
"name": "Madrigal Database",
"prefix": "r3d100011783",
"synonyms": [
"Cedar Madrigal"
]
},
"r3d100011784": {
"description": "The THEMIS mission is a five-satellite Explorer mission whose primary objective is to understand the onset and macroscale evolution of magnetospheric substorms. The five small satellites were launched together on a Delta II rocket and they carry identical sets of instruments including an electric field instrument (EFI), a flux gate magnetometer (FGM), a search coil magnetometer (SCM), a electro-static analyzer, and solid state telescopes (SST). The mission consists of several phases. In the first phase, the spacecraft will all orbit as a tight cluster in the same orbital plane with apogee at 15.4 Earth radii (RE). In the second phase, also called the Dawn Phase, the satellites will be placed in their orbits and during this time their apogees will be on the dawn side of the magnetosphere. During the third phase (also known as the Tail Science Phase) the apogees will be in the magnetotail. The fourth phase is called the Dusk Phase or Radiation Belt Science Phase, with all apogees on the dusk side. In the fifth and final phase, the apogees will shift to the sunward side (Dayside Science Phase). The satellite data will be combined with observations of the aurora from a network of 20 ground observatories across the North American continent. \nThe THEMIS-B (THEMIS-P1) and THEMIS-C (THEMIS-P2) were repurposed to study the lunar environment in 2009. The spacecraft were renamed ARTEMIS (Acceleration, Reconnection, Turbulence and Electrodynamics of the Moonβs Interaction with the Sun), with the P1 and P2 designations maintained.",
"homepage": "https://themis.ssl.berkeley.edu/index.shtml",
"name": "THEMIS",
"prefix": "r3d100011784",
"synonyms": [
"ARTEMIS",
"Acceleration, Reconnection, Turbulence and Electrodynamics of the Moonβs Interaction with the Sun",
"Time History of Events and Macroscale Interactions during Substorms"
]
},
"r3d100011785": {
"description": "Real-time data from moored ocean buoys for improved detection, understanding and prediction of El NiΓ±o and La NiΓ±a.",
"homepage": "https://www.pmel.noaa.gov/tao/drupal/disdel/",
"name": "Tropical Atmosphere Ocean Project",
"prefix": "r3d100011785",
"synonyms": [
"TAO array",
"TAO/TRITON array"
]
},
"r3d100011786": {
"description": "TurtleSAT is a new website where communities are mapping the location of freshwater turtles in waterways and wetlands across the country. Australia's unique freshwater turtles are in crisis - their numbers are declining and your help is needed to record where you see turtles in your local area.",
"homepage": "https://www.turtlesat.org.au/turtlesat/default.aspx",
"name": "TurtleSAT",
"prefix": "r3d100011786"
},
"r3d100011788": {
"description": "U.S. IOOS is a vital tool for tracking, predicting, managing, and adapting to changes in our ocean, coastal and Great Lakes environment. \nA primary focus of U.S. IOOS is integration of, and expedited access to, ocean observation data for improved decision making. The Data Management and Communication (DMAC) subsystem of U.S. IOOS serves as a central mechanism for integrating all existing and projected data sources.",
"homepage": "https://ioos.noaa.gov/",
"name": "IOOSΒ",
"prefix": "r3d100011788",
"synonyms": [
"U.S. Integrated Ocean Observing System"
],
"xrefs": {
"nlx": "157745",
"scr": "003598"
}
},
"r3d100011790": {
"description": "<<>>!!!>>>",
"homepage": "http://www.eu-watch.org/",
"name": "WATCH",
"prefix": "r3d100011790",
"synonyms": [
"WATer and Global CHange"
]
},
"r3d100011791": {
"description": "WorldClim is a set of global climate layers (climate grids) with a spatial resolution of about 1 square kilometer. The data can be used for mapping and spatial modeling in a GIS or with other computer programs.",
"homepage": "https://worldclim.org/",
"name": "WorldClim - Global Climate Data",
"prefix": "r3d100011791",
"xrefs": {
"nlx": "156877",
"scr": "010244"
}
},
"r3d100011792": {
"description": "XSEDE is a single virtual system that scientists can use to interactively share computing resources, data and expertise. People around the world use these resources and services β things like supercomputers, collections of data and new tools β to improve our planet.\nThe Extreme Science and Engineering Discovery Environment (XSEDE) is the most advanced, powerful, and robust collection of integrated advanced digital resources and services in the world. It is a single virtual system that scientists can use to interactively share computing resources, data, and expertise.",
"homepage": "https://www.xsede.org/",
"name": "XSEDE",
"prefix": "r3d100011792",
"synonyms": [
"Extreme Science and Engineering Discovery Environment"
],
"xrefs": {
"nlx": "151554",
"scr": "006091"
}
},
"r3d100011793": {
"description": "The ASTER Volcano Archive (AVA) is the worlds largest specialty archive of volcano data. For 1,549 recently active volcanos listed by the Smithsonian Global Volcanism Program, the AVA has collected the entirety of high-resolution multispectral ASTER data and made it available to the public. Also included are digital elevation maps, NOAA ash advisories, alteration zone imagery, and thermal anomaly reports. LANDSAT7 data are also being processed.",
"homepage": "https://ava.jpl.nasa.gov/",
"name": "ASTER Volcano Archive",
"prefix": "r3d100011793",
"synonyms": [
"AVA"
],
"xrefs": {
"biodbcore": "001299",
"fairsharing": "FAIRsharing.c44966"
}
},
"r3d100011795": {
"description": "The euHCVdb is mainly oriented towards protein sequence, structure and function analyses and structural biology of HCV.",
"homepage": "https://euhcvdb.lyon.inserm.fr/euHCVdb/jsp/index.jsp",
"name": "euHCVdb",
"prefix": "r3d100011795",
"synonyms": [
"european Hepatitis C Virus database",
"european hepatitis C virus sequences database"
],
"xrefs": {
"fairsharing": "FAIRsharing.bwctv",
"issn": "2429-9022",
"nif": "0000-02819",
"scr": "007645"
}
},
"r3d100011796": {
"description": "The VDC is a public, web-based search engine for accessing worldwide earthquake strong ground motion data. While the primary focus of the VDC is on data of engineering interest, it is also an interactive resource for scientific research and government and emergency response professionals.",
"homepage": "https://www.strongmotioncenter.org/vdc/scripts/default.plx",
"name": "Strong Motion Virtual Data Center",
"prefix": "r3d100011796",
"synonyms": [
"Global component of the Center for Engeinnering Strong Motion Data",
"Strong Motion VDC"
],
"xrefs": {
"fairsharing": "FAIRsharing.9eee19"
}
},
"r3d100011797": {
"description": "Strong-motion data of engineering and scientific importance from the United States and other seismically active \ncountries are served through the Center for Engineering Strong Motion Data(CESMD). The CESMD now automatically posts strong-motion data from an increasing number of seismic stations in California within a few minutes following an earthquake as an InternetQuick Report(IQR). As appropriate,IQRs are updated by more comprehensive Internet Data Reports that include reviewed versions of the data and maps showing, for example, the finite fault rupture along with the distribution of recording stations. Automated processing of strong-motion data will be extended to post the strong-motion records of the regional seismic networks of the Advanced National Seismic System (ANSS) outside California.",
"homepage": "https://www.strongmotioncenter.org/",
"name": "Center for Engineering Strong Motion Data",
"prefix": "r3d100011797",
"synonyms": [
"CESMD"
]
},
"r3d100011798": {
"description": "The goal of the NeuroElectro Project is to extract information about the electrophysiological properties (e.g. resting membrane potentials and membrane time constants) of diverse neuron types from the existing literature and place it into a centralized database.",
"homepage": "https://neuroelectro.org/",
"name": "NeuroElectro",
"prefix": "r3d100011798",
"synonyms": [
"organizing information on cellular neurophysiology"
],
"xrefs": {
"nlx": "151885",
"scr": "006274"
}
},
"r3d100011800": {
"description": "LSHTM Data Compass is a curated digital repository of research outputs that have been produced by staff and students at the London School of Hygiene & Tropical Medicine and their collaborators. It is used to share outputs intended for reuse, including: qualitative and quantitative data, software code and scripts, search strategies, and data collection tools.",
"homepage": "https://datacompass.lshtm.ac.uk/",
"name": "LSHTM Data Compass",
"prefix": "r3d100011800"
},
"r3d100011801": {
"description": "NOAA's National Centers for Environmental Information (NCEI) are responsible for hosting and providing public access to one of the most significant archives for environmental data on Earth with over 20 petabytes of comprehensive atmospheric, coastal, oceanic, and geophysical data. NCEI headquarters are located in Asheville, North Carolina. Most employees work in the four main locations, but apart from those locations, NCEI has employees strategically located throughout the United States. The main locations are Cooperative Institute for Climate and SatellitesβNorth Carolina (CICS-NC) at Asheville, North Carolina, Cooperative Institute for Research in Environmental Sciences (CIRES) at Boulder Colorado, Cooperative Institute for Climate and SatellitesβMaryland (CICS-MD) at Silver Spring Maryland and Stennis Space Center, Mississippi.",
"homepage": "https://www.ncei.noaa.gov/",
"name": "NCEI",
"prefix": "r3d100011801",
"synonyms": [
"NOAA National Centers for Environmental Information"
],
"xrefs": {
"doi": "10.25504/FAIRsharing.kjncvg"
}
},
"r3d100011802": {
"description": "Polish CLARIN node β CLARIN-PL Language Technology Centre β is being built at WrocΕaw University of Technology. The LTC is addressed to scholars in the humanities and social sciences. Registered users are granted free access to digital language resources and advanced tools to explore them. They can also archive and share their own language data (in written, spoken, video or multimodal form).",
"homepage": "https://clarin-pl.eu/dspace/",
"name": "CLARIN-PL",
"prefix": "r3d100011802",
"synonyms": [
"Centrum Technologii Jezykowiych",
"Language Technology Centre"
]
},
"r3d100011803": {
"description": "The International Maize and Wheat Improvement Center (CIMMYT) provides a free, open access repository of research software, studies, and datasets produced and developed by CIMMYT scientists as well as the results of the Seeds of Discovery project, which makes available genetic profiles of wheat and maize, two of mankind's three major cereal crops.",
"homepage": "https://data.cimmyt.org/dataverse/root",
"name": "CIMMYT Research Data & Software Repository Network",
"prefix": "r3d100011803",
"synonyms": [
"Centro Internacional de Mejoramiento de MaΓz y Trigo",
"International Maize and Wheat Improvement Center"
]
},
"r3d100011804": {
"description": "RU-Economicas is the repository of the Institute of Economic Research (IIEc) of the UNAM, created to manage, promote and preserve, in digital format, the intellectual production of Institute of Economic Research.\nThe objective of this repository is to promote scholarly communication and increase the visibility and use of the content produced at the Institute. It houses various materials, which may have been arbitrated or not, including books, journals, articles, lectures, presentations, databases, audiovisual, and so on.\nThe RU-Economics provides the general public, students, teachers and researchers, a search service and online consultation of digital resources produced by the academic community of the Institute of Economic Research.\nOur repository is part of our university's Digital Archives Network (RAD-UNAM) which aims to create a network of university repositories to support university departments in the management and dissemination of their digital resources. Thus, the Institute for Economic Research adds to the efforts of the UNAM for better management of and access to intellectual products of the university community in the digital environment.",
"homepage": "https://ru.iiec.unam.mx/",
"name": "RU-IIEc",
"prefix": "r3d100011804",
"synonyms": [
"RU-Economicas",
"Repositorio Universitario Instituto de Investigaciones EconΓ³micas"
]
},
"r3d100011805": {
"description": "The Digital Repository of Ireland (DRI) is a national trusted digital repository (TDR) for Irelandβs social and cultural data. We preserve, curate, and provide sustained access to a wealth of Irelandβs humanities and social sciences data through a single online portal. The repository houses unique and important collections from a variety of organisations including higher education institutions, cultural institutions, government agencies, and specialist archives. DRI has staff members from a wide variety of backgrounds, including software engineers, designers, digital archivists and librarians, data curators, policy and requirements specialists, educators, project managers, social scientists and humanities scholars. DRI is certified by the CoreTrustSeal, the current TDR standard widely recommended for best practice in Open Science. In addition to providing trusted digital repository services, the DRI is also Irelandβs research centre for best practices in digital archiving, repository infrastructures, preservation policy, research data management and advocacy at the national and European levels. DRI contributes to policy making nationally (e.g. via the National Open Research Forum and the IRC), and internationally, including European Commission expert groups, the DPC, RDA and the OECD.",
"homepage": "https://dri.ie/",
"name": "Digital Repository of Ireland",
"prefix": "r3d100011805",
"synonyms": [
"DRI",
"Taisclann Dhigiteach na hΓireann"
],
"xrefs": {
"fairsharing": "FAIRsharing.wL29nJ",
"ror": "034d7ma87"
}
},
"r3d100011806": {
"description": "Founded in 1556, the SLUB today houses a variety of collections. The Library collects most comprehensively media from and about Saxony (Saxonica) and β commissioned by the German Research Foundation β literature on contemporary art, photography, industrial design and commercial art, and history of technology. In addition, also the music and the map collection have a special rank. These and other valuable materials are summarized in the special collections department. Finally the Deutsche Fotothek as one of the most important photo archives in Germany has a prominent role.",
"homepage": "https://digital.slub-dresden.de/en/digital-collections/",
"name": "SLUB Sammlungen",
"prefix": "r3d100011806",
"synonyms": [
"SLUB Collections",
"SLUBArchiv.digital"
]
},
"r3d100011807": {
"description": "The Language Bank features text and speech corpora with different kinds of annotations in over 60 languages. There is also a selection of tools for working with them, from linguistic analyzers to programming environments. Corpora are also available via web interfaces, and users can be allowed to download some of them. The IP holders can monitor the use of their resources and view user statistics.",
"homepage": "https://www.kielipankki.fi/language-bank/",
"name": "Kielipankki",
"prefix": "r3d100011807",
"synonyms": [
"The Language Bank of Finland"
]
},
"r3d100011808": {
"description": "nanoHUB.org is the premier place for computational nanotechnology research, education, and collaboration. Our site hosts a rapidly growing collection of Simulation Programs for nanoscale phenomena that run in the cloud and are accessible through a web browser. In addition to simulation devices, nanoHUB provides Online Presentations, Courses, Learning Modules, Podcasts, Animations, Teaching Materials, and more. These resources help users learn about our simulation programs and about nanotechnology in general. Our site offers researchers a venue to explore, collaborate, and publish content, as well. Much of these collaborative efforts occur via Workspaces and User groups.",
"homepage": "https://nanohub.org/",
"name": "nanoHUB",
"prefix": "r3d100011808",
"synonyms": [
"nanoHUB.org"
],
"xrefs": {
"omics": "27120",
"scr": "013963"
}
},
"r3d100011810": {
"description": "<<>>!!!>>> Our lab investigates how cognition manifests in, and is influenced by, the social contexts in which it occurs. We focus: 1) on how conversational interactions can reshape memory, by promoting shared remembering and shared forgetting, and 2) on how socio-cognitive processes affect the formation of collective memories and beliefs, and the dynamics of collective decisions. In exploring these issues, while maintaining high ecological validity, our lab integrates a wide range of methodologies, including laboratory experiments, field studies, social network analysis, and agent-based simulations.",
"homepage": "http://www.princeton.edu/~acoman/Home.html",
"name": "Socio Cognitive Processes Lab data",
"prefix": "r3d100011810",
"synonyms": [
"Infectious cognition data"
]
},
"r3d100011811": {
"description": "Nordicana series D is a formatted, online data report series archived at CEN. It is produced only in \nelectronic form and is freely and openly accessible\n to CEN researchers and to other users. Each issue \nis \npublished in French and in English, and is indexed \nvia an assigned digital object identifier (DOI). An\n issue may be \nupdated, for example with new data, as a new version number, but will retain the same DOI. Each issue \ncontains data sets and extensive metadata that explain the origin of the data, the format of the data,\n the \nhistory of updates via different version numbers, and the format that should be adopted to cite the data.",
"homepage": "https://nordicana.cen.ulaval.ca/",
"name": "Nordicana D",
"prefix": "r3d100011811",
"synonyms": [
"La collection Nordicana D",
"Nordicana D collection"
]
},
"r3d100011812": {
"description": "More than a quarter of a million people β one in 10 NSW men and women aged over 45 β have been recruited to our 45 and Up Study, the largest ongoing study of healthy ageing in the Southern Hemisphere. The baseline information collected from all of our participants is available in the Studyβs Data Book. This information, which researchers use as the basis for their analyses, contains information on key variables such as height, weight, smoking status, family history of disease and levels of physical activity.\nBy following such a large group of people over the long term, we are developing a world-class research resource that can be used to boost our understanding of how Australians are ageing.\nThis will answer important health and quality-of-life questions and help manage and prevent illness through improved knowledge of conditions such as cancer, heart disease, depression, obesity and diabetes.",
"homepage": "https://www.saxinstitute.org.au/solutions/45-and-up-study/",
"name": "45 and Up Study",
"prefix": "r3d100011812"
},
"r3d100011813": {
"description": "The University has followed all of the children born in Aberdeen in 1921, 1936, and 1950-1956 as they grow and age.\nCollectively these groups are known as the ABERDEEN BIRTH COHORTS, and are a jewel in the crown of Scottish health research and have helped to advance our understanding of aging well.\nThe Children of the 1950s study is a population-based resource for the study of biological and social influences on health across the life-course and between generations.",
"homepage": "https://www.abdn.ac.uk/achds/environment/birth-cohorts/",
"name": "Aberdeen Birth Cohorts",
"prefix": "r3d100011813",
"synonyms": [
"1921 Birth Cohort, 1936 Birth Cohort, Children of the 1950s"
]
},
"r3d100011815": {
"description": "<<>>!!!>>>",
"homepage": "http://doi.nbis.se/",
"name": "NBIS DOI repository",
"prefix": "r3d100011815",
"synonyms": [
"BILS DOI Repository (formerly)",
"Bioinformatics Infrastructure for Life Sciences DOI Repository (formerly)",
"National Bioinformatics Infrastructure Sweden DOI repository"
]
},
"r3d100011817": {
"description": "BeiDare2 is currently at beta version. All new users should try the new service as we no longer provide training for the classic BioDare. -\nBioDare stands for Biological Data Repository, its main focus is data from circadian experiments.\nBioDare is an online facility to share, store, analyse and disseminate timeseries data, focussing on circadian clock data, with browser and web service interfaces. Toolbox features include an improved, speedier FFT-NLLs routine and ROBuSTβs Spectrum Resampling tool that will analyse rhythmic time series data.",
"homepage": "https://biodare2.ed.ac.uk/welcome",
"name": "BioDare2",
"prefix": "r3d100011817",
"synonyms": [
"BioDare (formerly)",
"Biological Data Repository"
]
},
"r3d100011818": {
"description": "Born in Bradford is one of the biggest and most important medical research studies undertaken in the UK. The project started in 2007 and is looking to answer questions about our health by tracking the lives of 13,500 babies and their families and will provide information for studies across the UK and around the world.\nThe aim of Born in Bradford is to find out more about the causes of childhood illness by studying children from all cultures and backgrounds as their lives unfold.",
"homepage": "https://borninbradford.nhs.uk/",
"name": "Born in Bradford",
"prefix": "r3d100011818",
"synonyms": [
"BiB"
]
},
"r3d100011819": {
"description": "The Cancer Cell Line Encyclopedia project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.",
"homepage": "https://sites.broadinstitute.org/ccle",
"name": "Cancer Cell Line Encyclopedia",
"prefix": "r3d100011819",
"synonyms": [
"CCLE"
],
"xrefs": {
"omics": "03988",
"scr": "013836"
}
},
"r3d100011820": {
"description": "CaPSUREβ’ is a longitudinal, observational study of approximately 15,000 men with all stages of biopsy-proven prostate cancer. Patients have enrolled at 43 community urology practices, academic medical centers, and VA hospitals throughout the United States since 1995.\nCEASAR stands for Comparative Effectiveness Analysis of Surgery and Radiation. The ongoing goal of CEASAR is to help learn more about what prostate cancer treatments work best, for which patients, in whose hands.\nThere are currently about 3,600 men with a prostate cancer diagnosis participating in CEASAR. Three rounds of surveys have been completed, with the first carried out in the spring of 2010. We are currently in the process of conducting our fourth survey with the same group of men in our study. This survey, our Three Year Follow-up, will occur throughout the summer of 2014.",
"homepage": "https://urology.ucsf.edu/research/cancer/capsure",
"name": "CaPSURE",
"prefix": "r3d100011820",
"synonyms": [
"Cancer of the Prostate Strategic Urologic Research Endeavor"
]
},
"r3d100011821": {
"description": "The Chickpea Transcriptome Database (CTDB) has been developed with the view to provide most comprehensive information about the chickpea transcriptome, the most relevant part of the genome. The database contains various information and tools for transcriptome sequence, functional annotation, conserved domain(s), transcription factor families, molecular markers (microsatellites and single nucleotide polymorphisms), Comprehensive gene expression and comparative genomics with other legumes. The database is a freely available resource, which provides user scientists/breeders a portal to search, browse and query the data to facilitate functional and applied genomics research in chickpea and other legumes.\nThe current release of database provides transcriptome sequence from cultivated (Cicer arietinum desi (ICC4958) and kabuli (ICCV2)) and wild (Cicer reticulatum, PI489777) chickpea genotypes.",
"homepage": "http://223.31.159.7/ctdb/",
"name": "Chickpea Transcriptome Database",
"prefix": "r3d100011821",
"synonyms": [
"CTDB"
]
},
"r3d100011822": {
"description": "The Cognitive Function and Ageing Studies (CFAS) are population based studies of individuals aged 65 years and over living in the community, including institutions, which is the only large multi-centred population-based study in the UK that has reached sufficient maturity. There are three main studies within the CFAS group. MRC CFAS, the original study began in 1989, with three of its sites providing a parent subset for the comparison two decades later with CFAS II (2008 onwards). Subsequently another CFAS study, CFAS Wales began in 2011.",
"homepage": "https://www.cfas.ac.uk/",
"name": "Cognitive Function and Ageing Study",
"prefix": "r3d100011822",
"synonyms": [
"CFAS"
]
},
"r3d100011823": {
"description": "The Dallas Heart Study (DHS) is a multi-ethnic, population-based probability sample of Dallas County designed to define the social and the biological variables contributingto ethnic differences in cardiovascular health at the community level and to support hypothesis-driven research aimed at determining the underlying mechanisms contributing to differences in cardiovascular risk. The initial data collection from the population was performed in three sequential stages over a two year period(2000-2002) and included the collection of detailed socioeconomic, biomarker and imaging data from each participant. The underlying assumption of the study is that successful identification of new risk factors for cardiovascular disease will require the availability of an exquisitely phenotyped, multiethnic population in close proximity to the Center.",
"homepage": "https://www.utsouthwestern.edu/research/translational-medicine/doing-research/dallas-heart/",
"name": "Dallas Heart Study",
"prefix": "r3d100011823",
"synonyms": [
"DHS",
"DHS cohort"
]
},
"r3d100011824": {
"description": "Exposures in the period from conception to early childhood - including fetal growth, cell division, and organ functioning - may have long-lasting impact on health and disease susceptibility.\nTo investigate these issues the Danish National Birth Cohort (Better health in generations) was established.\nA large cohort of pregnant women with long-term follow-up of the offspring was the obvious choice because many of the exposures of interest cannot be reconstructed with suffcient validity back in time. The study needed to be large, and the aim was to recruit 100,000 women early in pregnancy, and to continue follow-up for decades. \nExposure information was collected by computer-assisted telephone interviews with the women twice during pregnancy and when their children were six and 18 months old. Participants were also asked to fill in a self-administered food frequency questionnaire in mid-pregnancy. Furthermore, a biological bank has been set up with blood taken from the mother twice during pregnancy and blood from theumbilical cord taken shortly after birth.",
"homepage": "https://www.dnbc.dk/",
"name": "Danish National Birth Cohort",
"prefix": "r3d100011824",
"synonyms": [
"Bedre sundhet i generationer",
"DNBC"
]
},
"r3d100011825": {
"description": "<<>>!!!>>>\n\nThe Diabetes Study of Northern California (DISTANCE) conducts epidemiological and health services research in diabetes among a large, multiethnic cohort of patients in a large, integrated health care delivery system.",
"homepage": "https://divisionofresearch.kaiserpermanente.org/projects/distance/",
"name": "Diabetes Study of Northern California",
"prefix": "r3d100011825",
"synonyms": [
"DISTANCE"
]
},
"r3d100011826": {
"description": "The Drosophila Genetic Reference Panel (DGRP) is a population consisting of more than 200 inbred lines derived from the Raleigh, USA population. The DGRP is a living library of common polymorphisms affecting complex traits, and a community resource for whole genome association mapping of quantitative trait loci.",
"homepage": "http://dgrp.gnets.ncsu.edu/",
"name": "Drosophila Genetic Reference Panel 2",
"prefix": "r3d100011826",
"synonyms": [
"DGRP2"
]
},
"r3d100011827": {
"description": "The Drosophila Synthetic Population Resource (DSPR) consists of a new panel of over 1700 recombinant inbred lines (RILs) of Drosophila melanogaster, derived from two highly recombined synthetic populations, each created by intercrossing a different set of 8 inbred founder lines (with one founder line common to both populations). Complete genome sequence data for the founder lines are available, and in addition, there is a high resolution genetic map for each RIL. The DSPR has been developed as a community resource for high-resolution QTL mapping and is intended to be used widely by the Drosophila community.",
"homepage": "https://wfitch.bio.uci.edu/~dspr/index.html",
"name": "DSPR",
"prefix": "r3d100011827",
"synonyms": [
"The Drosophila Synthetic Population Resource"
]
},
"r3d100011828": {
"description": "The Fragile Families and Child Wellbeing Study changed its name to The Future of Families and Child Wellbeing Study (FFCWS). Note that all documentation issued prior to January 2023 contains the studyβs former name. Any further reference to FFCWS should kindly observe this name change.\nThe Fragile Families & Child Wellbeing Study is following a cohort of nearly 5,000 children born in large U.S. cities between 1998 and 2000 (roughly three-quarters of whom were born to unmarried parents). We refer to unmarried parents and their children as βfragile familiesβ to underscore that they are families and that they are at greater risk of breaking up and living in poverty than more traditional families.\nThe core Study was originally designed to primarily address four questions of great interest to researchers and policy makers: (1) What are the conditions and capabilities of unmarried parents, especially fathers?; (2) What is the nature of the relationships between unmarried parents?; (3) How do children born into these families fare?; and (4) How do policies and environmental conditions affect families and children?",
"homepage": "https://ffcws.princeton.edu/FFdata",
"name": "Future of Families and Child Wellbeing Study",
"prefix": "r3d100011828",
"synonyms": [
"FFCWS",
"formerly: Fragile Families and Child Wellbeing Study"
]
},
"r3d100011829": {
"description": "GAZEL is an open epidemiologic laboratory. Like major scientific instruments (telescopes or particle accelerators, for example, or genotyping laboratories equipped with sequencers), GAZEL was not constructed to answer a specific question. Instead it was designed to help analyze a wide range of scientific problems and is accessible to the community of researchers specializing in epidemiology.\nIn accordance with its purpose as a scientific research platform, the GAZEL cohort is permanently open to epidemiologic research teams. Today, more than 50 projects on very diversified themes have been set up in GAZEL by some 20 teams, French, belonging to different bodies, and foreign (Germany, Belgium, Canada, Great Britain, Sweden, Finland, and USA).",
"homepage": "https://www.gazel.inserm.fr/en/gazel-cohort",
"name": "Gazel",
"prefix": "r3d100011829",
"synonyms": [
"The Gazel cohort"
],
"xrefs": {
"nlx": "151989",
"scr": "008962"
}
},
"r3d100011830": {
"description": "KiGGS is a long-term study conducted by the Robert Koch Institute (RKI) on the health of children and adolescents in Germany. The study repeatedly supplies data, representative of the country as a whole, on the health of under 18-year-olds. In addition, the children and adolescents of the first KiGGS study are repeatedly invited, and they continue to be monitored right into their adulthood.",
"homepage": "https://www.rki.de/DE/Content/Gesundheitsmonitoring/Studien/Kiggs/kiggs_node.html",
"name": "Studie zur Gesundheit von Kindern und Jugendlichen in Deutschland",
"prefix": "r3d100011830",
"synonyms": [
"German Health Interview and Examination Survey for Children and Adolescents",
"KiGGS"
]
},
"r3d100011831": {
"description": "<<>>!!!>>>\nsee https://beta.ukdataservice.ac.uk/datacatalogue/studies/study?id=7021#!/details and\nhttps://ota.bodleian.ox.ac.uk/repository/xmlui/discover?query=germanc&submit=Search&filtertype_1=title&filter_relational_operator_1=contains&filter_1=&query=germanc",
"homepage": "https://www.alc.manchester.ac.uk/modern-languages/research/german-studies/germanc/",
"name": "GerManC project",
"prefix": "r3d100011831",
"synonyms": [
"A representative historical corpus of German 1650-1800"
]
},
"r3d100011832": {
"description": "The Growing Up Today Study is a collaborative study between clinicians, researchers, and thousands of participants across the US and beyond. The aim of this study is to gain a deeper understanding of the factors that affect health throughout life. \nTogether we are working to building one of the most powerful resources for fighting cancer, obesity, heart disease, depression, and so much more.",
"homepage": "https://gutsweb.org/",
"name": "Growing Up Today Study",
"prefix": "r3d100011832",
"synonyms": [
"GUTS"
]
},
"r3d100011833": {
"description": "The Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.",
"homepage": "https://lincs.hms.harvard.edu/db/",
"name": "Harvard Medical School, Library of Integrated Network-Based Cellular Signatures Database",
"prefix": "r3d100011833",
"synonyms": [
"HMS, LINCS database"
],
"xrefs": {
"nlx": "156062",
"scr": "006454"
}
},
"r3d100011834": {
"description": "<<>>!!!>>>",
"homepage": "http://inchiantistudy.net/wp/",
"name": "InCHIANTI",
"prefix": "r3d100011834",
"synonyms": [
"Invecchiare nel Chianti",
"The InCHIANTI Study"
]
},
"r3d100011835": {
"description": "<<>>!!!>>>\nA recent computer security audit has revealed security flaws in the legacy HapMap site that require NCBI to take it down immediately. We regret the inconvenience, but we are required to do this. That said, NCBI was planning to decommission this site in the near future anyway (although not quite so suddenly), as the 1,000 genomes (1KG) project has established itself as a research standard for population genetics and genomics. NCBI has observed a decline in usage of the HapMap dataset and website with its available resources over the past five years and it has come to the end of its useful life. \nThe International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings. Using the information in the HapMap, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. The Project is a collaboration among scientists and funding agencies from Japan, the United Kingdom, Canada, China, Nigeria, and the United States. All of the information generated by the Project will be released into the public domain.\nThe goal of the International HapMap Project is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. By making this information freely available, the Project will help biomedical researchers find genes involved in disease and responses to therapeutic drugs. In the initial phase of the Project, genetic data are being gathered from four populations with African, Asian, and European ancestry. Ongoing interactions with members of these populations are addressing potential ethical issues and providing valuable experience in conducting research with identified populations.\nPublic and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. The Project officially started with a meeting in October 2002 (https://www.genome.gov/10005336/) and is expected to take about three years.",
"homepage": "https://www.ncbi.nlm.nih.gov/variation/news/NCBI_retiring_HapMap/",
"name": "International HapMap Project",
"prefix": "r3d100011835",
"synonyms": [
"Asepα» HapMap ti Gbogbo Agbaye",
"Le projet international HapMap",
"ε½ι
δΊΊη±»εΊε η»εδ½εεΎθ‘ε",
"ε½ι HapMap θ¨η»"
],
"xrefs": {
"nif": "0000-02940",
"omics": "00273",
"scr": "002846"
}
},
"r3d100011836": {
"description": "The Johns Hopkins Research Data Repository is an open access repository for Johns Hopkins University researchers to share their research data.\nThe Repository is administered by professional curators at JHU Data Services, who will work with depositors to enable future discovery and reuse of your data, and ensure your data is Findable, Accessible, Interoperable and Reusable (FAIR). More information about the benefits of archiving data can be found here: https://dataservices.library.jhu.edu/",
"homepage": "https://archive.data.jhu.edu/",
"name": "Johns Hopkins Research Data Repository",
"prefix": "r3d100011836",
"synonyms": [
"formerly: JHU Data Archive",
"formerly: Johns Hopkins Data Archive Dataverse Network"
]
},
"r3d100011838": {
"description": "The Malaria Atlas Project (MAP) brings together researchers based around the world with expertise in a wide range of disciplines from public health to mathematics, geography and epidemiology. We work together to generate new and innovative methods of mapping malaria risk. Ultimately our goal is to produce a comprehensive range of maps and estimates that will support effective planning of malaria control at national and international scales.",
"homepage": "https://malariaatlas.org/",
"name": "Malaria Atlas Project",
"prefix": "r3d100011838",
"synonyms": [
"MAP"
]
},
"r3d100011839": {
"description": "Database of mass spectra of known, unknown and provisionally identified substances. MassBank is the first public repository of mass spectral data for sharing them among scientific research community. MassBank data are useful for the chemical identification and structure elucidation of chemical compounds detected by mass spectrometry.",
"homepage": "https://massbank.eu/MassBank/",
"name": "MassBank Europe",
"prefix": "r3d100011839",
"synonyms": [
"High Resolution Mass Spectral Database",
"MassBank",
"NORMAN MassBank"
],
"xrefs": {
"fairsharing": "FAIRsharing.dk451a",
"miriam": "00000273"
}
},
"r3d100011840": {
"description": "The Mexican Health and Aging Study (MHAS) started as a prospective panel study of health and aging in Mexico. \nMHAS is nationally representative of the 13 million Mexicans born prior to 1951. The survey has national and urban/rural representation. The baseline survey, in 2001, included a nationally representative sample of Mexicans aged 50 and over and their spouse/partners regardless of their age. A direct interview was sought with each individual and proxy interviews were obtained when poor health or temporary absence precluded a direct interview. \nThe sample was distributed in all 32 states of the country in urban and rural areas. Households in the six states which account for 40% of all migrants to the U.S. were over-sampled. A sub-sample was selected to obtain anthropometric measures.",
"homepage": "https://www.mhasweb.org/Home/index.aspx",
"name": "Mexican Health and Aging Study",
"prefix": "r3d100011840",
"synonyms": [
"ENASEM",
"Estudio Nacional de Salud y Envejecimiento en MΓ©xico",
"MHAS"
],
"xrefs": {
"fairsharing": "FAIRsharing.n8qft8",
"nlx": "151859",
"scr": "000818"
}
},
"r3d100011841": {
"description": "The MRC National Survey of Health and Development 1946 (NSHD) was the first ever British birth cohort study. It has collected information from birth to the current day on the health and life circumstances of five and a half thousand men and women born during a week in March 1946 throughout England, Wales, and Scotland. The study explores differences in child development by factors like social class, biological factors, health and education. Due to the length of the study it has developed into a study of ageing.",
"homepage": "https://nshd.mrc.ac.uk/",
"name": "MRC National Survey of Health and Development",
"prefix": "r3d100011841",
"synonyms": [
"NSHD",
"National Survey of Health and Development"
]
},
"r3d100011843": {
"description": "The Osteoarthritis Initiative (OAI) is a multi-center, longitudinal, prospective observational study of knee osteoarthritis (OA). The overall aim of the OAI is to develop a public domain research resource to facilitate the scientific evaluation of biomarkers for osteoarthritis as potential surrogate endpoints for disease onset and progression.",
"homepage": "https://nda.nih.gov/oai",
"name": "OsteoArthritis Initiative",
"prefix": "r3d100011843",
"synonyms": [
"OAI"
],
"xrefs": {
"fairsharing": "FAIRsharing.D5iouq"
}
},
"r3d100011844": {
"description": "The Pacific Islands Families (PIF) Study is an ongoing longitudinal birth cohort study that has been tracking the health and development of 1,398 Pacific children and their parents since the children were born at Middlemore Hospital in South Auckland in the year 2000. It is the only prospective study specifically of Pacific peoples in the world.",
"homepage": "https://phrc.aut.ac.nz/our-research/pacific-islands-families-study",
"name": "Pacific Islands Families Study",
"prefix": "r3d100011844",
"synonyms": [
"PIF Study"
]
},
"r3d100011845": {
"description": "Project Achilles is a systematic effort aimed at identifying and cataloging genetic vulnerabilities across hundreds of genomically characterized cancer cell lines. The project uses genome-wide genetic perturbation reagents (shRNAs or Cas9/sgRNAs) to silence or knock-out individual genes and identify those genes that affect cell survival. Large-scale functional screening of cancer cell lines provides a complementary approach to those studies that aim to characterize the molecular alterations (e.g. mutations, copy number alterations) of primary tumors, such as The Cancer Genome Atlas (TCGA). The overall goal of the project is to identify cancer genetic dependencies and link them to molecular characteristics in order to prioritize targets for therapeutic development and identify the patient population that might benefit from such targets.\nProject Achilles data is hosted on the Cancer Dependency Map Portal (DepMap) where it has been harmonized with our genomics and cellular models data. You can access the latest and all past datasets here: https://depmap.org/portal/download/all/",
"homepage": "https://depmap.org/portal/achilles/",
"name": "Project Achilles",
"prefix": "r3d100011845"
},
"r3d100011846": {
"description": "Cell phones have become an important platform for the understanding of social dynamics and influence, because of their pervasiveness, sensing capabilities, and computational power. Many applications have emerged in recent years in mobile health, mobile banking, location based services, media democracy, and social movements. With these new capabilities, we can potentially be able to identify exact points and times of infection for diseases, determine who most influences us to gain weight or become healthier, know exactly how information flows among employees and productivity emerges in our work spaces, and understand how rumors spread.\nIn an attempt to address these challenges, we release several mobile data sets here in \"Reality Commons\" that contain the dynamics of several communities of about 100 people each. We invite researchers to propose and submit their own applications of the data to demonstrate the scientific and business values of these data sets, suggest how to meaningfully extend these experiments to larger populations, and develop the math that fits agent-based models or systems dynamics models to larger populations. \nThese data sets were collected with tools developed in the MIT Human Dynamics Lab and are now available as open source projects or at cost.",
"homepage": "http://realitycommons.media.mit.edu/",
"name": "Reality Commons",
"prefix": "r3d100011846"
},
"r3d100011847": {
"description": "REGARDS is an observational study of risk factors for stroke in adults 45 years or older. 30,239 participants were recruited between January 2003 and October 2007. They completed a telephone interview followed by an in-home physical exam. Measurements included traditional risk factors such as blood pressure and cholesterol levels, and an echocardiogram of the heart. At six month intervals, participants are contacted by phone to ask about stroke symptoms, hospitalizations and general health status. The study is ongoing and will follow participants for many years.",
"homepage": "https://www.uab.edu/soph/regardsstudy/",
"name": "REasons for Geographic and Racial Differences in Stroke Study",
"prefix": "r3d100011847",
"synonyms": [
"REGARDS"
],
"xrefs": {
"nif": "0000-01878",
"scr": "007228"
}
},
"r3d100011848": {
"description": "The Manchester Romani Project is part of an international network of scholarly projects devoted to research on Romani language and linguistics, coordinated in partnership with Dieter Halwachs (Institute of Linguistics, Graz University and Romani-Projekt Graz), and Peter Bakker (Institute of Linguistics, Aarhus University).\nThe project explores the linguistic features of the dialects of the Romani language, and their distribution in geographical space. An interactive web application is being designed, which will allow users to search and locate on a map different dialectal variants, and to explore how variants cluster in particular regions. Examples sentences and words with sound files will also be made available, to give impressions of dialectal variation within Romani. From the distribution of linguistic forms among the dialects it will be possible to make infeences about social-historical contacts among the Romani communities, and about migration patterns.",
"homepage": "https://romani.humanities.manchester.ac.uk//rms/",
"name": "Romani Morpho-Syntax Database",
"prefix": "r3d100011848",
"synonyms": [
"RMS"
]
},
"r3d100011849": {
"description": "Stemformatics is a collaboration between the stem cell and bioinformatics community.\nWe were motivated by the plethora of exciting cell models in the public and private domains, and the realisation that for many biologists these were mostly inaccessible. We wanted a fast way to find and visualise interesting genes in these exemplar stem cell datasets. We'd like you to explore. You'll find data from leading stem cell laboratories in a format that is easy to search, easy to visualise and easy to export.",
"homepage": "https://www.stemformatics.org/",
"name": "Stemformatics",
"prefix": "r3d100011849",
"xrefs": {
"scr": "017002"
}
},
"r3d100011850": {
"description": "The Swiss HIV Cohort Study (SHCS), established in 1988, is a systematic longitudinal study enrolling HIV-infected individuals in Switzerland. It is a collaboration of all Swiss University Hospital infectious disease outpatient clinics, two large cantonal hospitals, all with affiliated laboratories, and with affiliated smaller hospitals and private physicians carrying for HIV patients. \nThe Swiss Mother and Child HIV Cohort Study (MoCHiV) is integrated into the SHCS. It aims at preventing mother to child transmission and enrolls HIV-infected pregnant women and their children.\nThe SHCS involves practically all researchers being active in patient-oriented HIV research in Switzerland.\nThe clinics can delegate recruitment of participants and follow-up visits to other outpatient clinics or to specialized private physicians, provided that the requirements of the protocol can be entirely fulfilled and controlled. The laboratories can contract other laboratories for some of the analyses.",
"homepage": "https://www.shcs.ch/",
"name": "Swiss HIV Cohort Study & Swiss Mother and Child HIV Cohort Study",
"prefix": "r3d100011850",
"synonyms": [
"SHCS & MoCHIV"
]
},
"r3d100011851": {
"description": "The TwinsUK resource is the biggest UK adult twin registry of 14.000 twins used to study the genetic and environmental aetiology of age related complex traits and diseases.",
"homepage": "https://twinsuk.ac.uk/",
"name": "TwinsUK",
"prefix": "r3d100011851"
},
"r3d100011852": {
"description": "UQ eSpace is the single authoritative source for the research outputs of the staff and students of the University of Queensland and is the archival home of UQ Research Higher Degree digital theses. UQ eSpace raises the visibility and accessibility of UQ publications to the wider world and provides data for mandatory Government reporting requirements such as the Higher Education Research Data Collection (HERDC) and Excellence in Research for Australia (ERA) as well as for the internal UQ systems such as the Q-Index. It also operates as an institutional repository for open access publications, research datasets and other digitised materials created by staff of the University such as print materials, photographs, audio materials, videos, manuscripts and other original works.",
"homepage": "https://espace.library.uq.edu.au/DataCollections",
"name": "UQ eSpace, Research Data Collections",
"prefix": "r3d100011852"
},
"r3d100011853": {
"description": "The Twenty-07 Study was set up in 1986 in order to investigate the reasons for differences in health by socio-economic circumstances, gender, area of residence, age, ethnic group, and family type.\n\n4510 people are being followed for 20 years. The initial wave of data collection took place in 1987/8, when respondents were aged 15, 35 and 55. The final wave of data collection took place in 2007/08 when respondents were aged 35, 55 and 75.\n\nIn this way the Twenty-07 Study provides us with unique opportunities to investigate both the changes in people's lives over 20 years and how they affect their health, and the differences in people's experiences at the same ages 20 years apart, and how these have different effects on their health.",
"homepage": "http://2007study.sphsu.mrc.ac.uk/",
"name": "West of Scotland Twenty-07 Study",
"prefix": "r3d100011853"
},
"r3d100011854": {
"description": "The Whitehall II study was established to explore the relationship between socio-economic status, stress and cardiovascular disease. A cohort of 10,308 participants aged 35-55, of whom 3,413 were women and 6,895 men, was recruited from the British Civil Service in 1985. Since this first wave of data collection, self-completion questionnaires and clinical data have been collected from the cohort every two to five years with a high level of participation. Data collection is intended to continue until 2030.",
"homepage": "https://www.ucl.ac.uk/whitehallII",
"name": "Whitehall II Study",
"prefix": "r3d100011854",
"synonyms": [
"Stress and Health Study",
"WII"
]
},
"r3d100011855": {
"description": "WHIP is a database of individual work histories, based on Inps administrative archives.\nThe reference population is made up by all the people β Italian and foreign β who have worked in Italy even only for only a part of their working career. A large representative sample has been extracted from this population: in the standard file the sampling coefficient is about 1: 180, for a dynamic population of about 370,000 people (figures will be doubled in the full edition).\nFor each of these people the main episodes of their working careers are observed. The complete list of observations includes: private employee working contracts, atypical contracts, self-employment activities as artisan, trader and some activities as freelancer, retirement spells, as well as non-working spells in which the individual received social benefits, like unemployment subsidies or mobility benefits. The workers for whom activity is not observed in WHIP are those who worked in the public sector or as freelancers (lawyers or notaries) β who have an autonomous security fund.\nThe WHIP section concerning employee contracts is a Linked Employer Employee Database: in addition to the data about the contract, thanks to a linkage with the Inps Firm Observatory, data concerning the firm in which the worker is employed is also available.",
"homepage": "https://www.laboratoriorevelli.it/whip/whip_datahouse.php",
"name": "Work Histories Italian Panel",
"prefix": "r3d100011855",
"synonyms": [
"WHIP"
]
},
"r3d100011856": {
"description": "Contraceptive prevalence and the unmet need for family planning are key indicators for measuring improvements in access to reproductive health as asserted in the 2030 Agenda for Sustainable Development under target 3.7. \"By 2030, ensure universal access to sexual and reproductive health-care services, including for family planning, information and education, and the integration of reproductive health into national strategies and programmes\".",
"homepage": "https://population.un.org/dataportal/home",
"name": "World Contraceptive Use",
"prefix": "r3d100011856",
"synonyms": [
"Estimates and Projections of Family Planning Indicators"
]
},
"r3d100011857": {
"description": "The version 1.0 of the open database contains 1,151,268 brain signals of 2 seconds each, captured with the stimulus of seeing a digit (from 0 to 9) and thinking about it, over the course of almost 2 years between 2014 & 2015, from a single Test Subject David Vivancos.\nAll the signals have been captured using commercial EEGs (not medical grade), NeuroSky MindWave, Emotiv EPOC, Interaxon Muse & Emotiv Insight, covering a total of 19 Brain (10/20) locations.\nIn 2014 started capturing brain signals and released the first versions of the \"MNIST\" of brain digits, and in 2018 released another open dataset with a subset of the \"IMAGENET\" of The Brain.\nVersion 0.05 (last update 09/28/2021) of the open database contains 24,000 brain signals of 2 seconds each, captured with the stimulus of seeing a real MNIST digit (from 0 to 9) 6,000 so far and thinking about it, + the same amout of signals with another 2 seconds of seeing a black screen, shown in between the digits, from a single Test Subject David Vivancos in a controlled still experiment to reduce noise from EMG & avoiding blinks.",
"homepage": "http://www.mindbigdata.com/",
"name": "MindBigData",
"prefix": "r3d100011857",
"synonyms": [
"The \"MNIST\" of Brain Digits"
]
},
"r3d100011858": {
"description": "<<>>!!!>>>\nPATRIC will go offline by mid-December2022. Here is what you need to know.\nAs announced previously, PATRIC, the bacterial BRC, and IRD / ViPR, the viral BRCs, are being merged into the new Bacterial and Viral Bioinformatics Resource Center (BV-BRC). BV-BRC combines the data, tools, and technologies from these BRCs to provide an integrated resource for bacterial and viral genomics-based infectious disease research.",
"homepage": "https://www.patricbrc.org/portal/portal/patric/Home",
"name": "PATRIC",
"prefix": "r3d100011858",
"synonyms": [
"Pathosystems Resource Integration Center"
],
"xrefs": {
"nlx": "17476",
"omics": "01658",
"scr": "004154"
}
},
"r3d100011859": {
"description": "The nationally recognized National Cancer Database (NCDB)βjointly sponsored by the American College of Surgeons and the American Cancer Societyβis a clinical oncology database sourced from hospital registry data that are collected in more than 1,500 Commission on Cancer (CoC)-accredited facilities. NCDB data are used to analyze and track patients with malignant neoplastic diseases, their treatments, and outcomes. Data represent more than 70 percent of newly diagnosed cancer cases nationwide and more than 34 million historical records.",
"homepage": "https://www.facs.org/quality-programs/cancer/ncdb",
"name": "National Cancer Data Base",
"prefix": "r3d100011859",
"synonyms": [
"NCDB"
]
},
"r3d100011860": {
"description": "<<>>!!!>>>\nBe advised that DataFerrett was decommissioned June 30, 2020; see https://www.census.gov/data/data-tools/dataferrett.html",
"homepage": "https://thedataweb.rm.census.gov/",
"name": "TheDataWeb",
"prefix": "r3d100011860",
"synonyms": [
"DataFerrett"
],
"xrefs": {
"scr": "003197"
}
},
"r3d100011861": {
"description": "The National Sleep Research Resource (NSRR) is an NHLBI-supported repository for sharing large amounts of sleep data (polysomnography, actigraphy and questionnaire-based) from multiple cohorts, clinical trials, and other data sources. Launched in April 2014, the mission of the NSRR is to advance sleep and circadian science by supporting secondary data analysis, algorithmic development, and signal processing through the sharing of high-quality data sets.",
"homepage": "https://sleepdata.org/",
"name": "National Sleep Research Resource",
"prefix": "r3d100011861",
"synonyms": [
"NSRR",
"SleepData"
],
"xrefs": {
"fairsharing": "FAIRsharing.crjxwd",
"scr": "016576"
}
},
"r3d100011864": {
"description": "OpenKIM is an online suite of open source tools for molecular simulation of materials. These tools help to make molecular simulation more accessible and more reliable. Within OpenKIM, you will find an online resource for standardized testing and long-term warehousing of interatomic models and data, and an application programming interface (API) standard for coupling atomistic simulation codes and interatomic potential subroutines.",
"homepage": "https://openkim.org/",
"name": "OpenKIM",
"prefix": "r3d100011864",
"synonyms": [
"Knowledgebase of Interatomic Models"
]
},
"r3d100011865": {
"description": "The Astrophysics Source Code Library (ASCL) is a free online registry for source codes of interest to astronomers and astrophysicists and lists codes that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001).",
"homepage": "https://ascl.net/",
"name": "Astrophysics Source Code Library",
"prefix": "r3d100011865",
"synonyms": [
"ASCL",
"ASCL.net Astrophysics Source Code Library"
],
"xrefs": {
"fairsharing": "FAIRsharing.wb0txg",
"issn": "2381-2028"
}
},
"r3d100011867": {
"description": "\"Seanoe (SEA scieNtific Open data Edition) is a publisher of scientific data in the field of marine sciences. It is operated by Ifremer (http://wwz.ifremer.fr/). Data published by SEANOE are available free. They can be used in accordance with the terms of the Creative Commons license selected by the author of data. Seance contributes to Open Access / Open Science movement for a free access for everyone to all scientific data financed by public funds for the benefit of research. An embargo limited to 2 years on a set of data is possible; for example to restrict access to data of a publication under scientific review. Each data set published by SEANOE has a DOI which enables it to be cited in a publication in a reliable and sustainable way. The long-term preservation of data filed in SEANOE is ensured by Ifremer infrastructure. \"",
"homepage": "https://www.seanoe.org/",
"name": "SEANOE",
"prefix": "r3d100011867",
"synonyms": [
"Publication de donnΓ©es scientifiques marines",
"Sea scientific open data publication"
],
"xrefs": {
"fairsharing": "FAIRsharing.bb5rna",
"issn": "2491-1836"
}
},
"r3d100011868": {
"description": "For datasets big and small; Store your research data online. Quickly and easily upload files of any type and we will host your research data for you. Your experimental research data will have a permanent home on the web that you can refer to.",
"homepage": "https://data.mendeley.com/",
"name": "Mendeley Data",
"prefix": "r3d100011868",
"xrefs": {
"fairsharing": "FAIRsharing.3epmpp",
"scr": "015671"
}
},
"r3d100011869": {
"description": "PSMSL is the global data bank for long term sea level change information from tide gauges and bottom pressure recorders.",
"homepage": "https://psmsl.org/",
"name": "Permanent Service for Mean Sea Level",
"prefix": "r3d100011869",
"synonyms": [
"PSMSL"
],
"xrefs": {
"fairsharing": "FAIRsharing.711500"
}
},
"r3d100011870": {
"description": "\"IndExs\" is a database comprising information on exsiccatae (=exsiccatal series) with titles, abbreviations, bibliography and provides a unique and persistent Exsiccata ID for each series. Exsiccatae are defined as \"published, uniform, numbered sets of preserved specimens distributed with printed labels\" (Pfister 1985). Please note that there are two similar latin terms: \"exsiccata, ae\" is feminine and used for a set of dried specimens as defined above, whereas the term \"exsiccatum, i\" is neutral and used for dried specimens in general. If available, images of one or more examplary labels are added to give layout information.",
"homepage": "http://indexs.botanischestaatssammlung.de",
"name": "IndExs β Index of Exsiccatae",
"prefix": "r3d100011870",
"synonyms": [
"Index of Exsiccatae"
]
},
"r3d100011871": {
"description": "The Human Ageing Genomic Resources (HAGR) is a collection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses.",
"homepage": "https://genomics.senescence.info/",
"name": "HAGR",
"prefix": "r3d100011871",
"synonyms": [
"Human Ageing Genomic Resources"
],
"xrefs": {
"fairsharing": "FAIRsharing.bw1e90",
"nif": "0000-02938",
"scr": "007700"
}
},
"r3d100011872": {
"description": "LIAS is a global information system for Lichenized and Non-Lichenized Ascomycetes. It includes several interoperable data repositories.\nIn recent years, the two core components βLIAS namesβ and βLIAS lightβ have been much enlarged.\nLIAS light is storing phenotypic trait data. They includes > 10,700 descriptions (about 2/3 of all known lichen species), each with up to 75 descriptors comprising 2,000 traits (descriptor states and values), including 800 secondary metabolites. 500 traits may have biological functions and more than 1,000 may have phylogenetic relevance. LIAS is thus one of the most comprehensive trait databases in organismal biology. The online interactive identification key for more than 10,700 lichens is powered by the Java applet NaviKey and has been translated into 19 languages (besides English) in cooperation with lichenologists worldwide.\nThe component βLIAS namesβ is a platform for managing taxonomic names and classifications with currently >50,000 names, including the c. 12,000 accepted species and recognized synonyms.\nThe LIAS portal contents, interfaces, and databases run on servers of the IT Center of the Bavarian Natural History Collections and are maintained there. 'LIAS names' and βLIAS lightβ also deliver content data to the Catalogue of Life, acting as the Global Species Database (GSD) for lichens. LIAS gtm is a database for visualising the geographic distribution of lichen traits. LIAS is powered by the Diversity Workbench database framework with several interfaces for data management and publication. The LIAS long-term project was initiated in the early 1990s and has since been continued with funding from the DFG, the BMBF, and the EU.",
"homepage": "http://www.lias.net/",
"name": "LIAS",
"prefix": "r3d100011872",
"synonyms": [
"A Global Information System for Lichenized and Non-Lichenized Ascomycetes"
]
},
"r3d100011873": {
"description": "The Bavarian Natural History Collections (Staatliche Naturwissenschaftliche Sammlungen Bayerns, SNSB) are a research institution for natural history in Bavaria. They encompass five State Collections (zoology, botany, paleontology and geology, mineralogy, anthropology and paleoanatomy), the Botanical Garden Munich-Nymphenburg and eight museums with public exhibitions in Munich, Bamberg, Bayreuth, EichstΓ€tt and NΓΆrdlingen. Our research focuses mainly on the past and present bio- and geodiversity and the evolution of animals and plants. To achieve this we have large scientific collections (almost 35,000,000 specimens), see \"joint projects\".",
"homepage": "https://www.snsb.de/index.php/en/",
"name": "Staatliche Naturwissenschaftliche Sammlungen Bayerns",
"prefix": "r3d100011873",
"synonyms": [
"Bavarian Natural History Collections",
"SNSB"
]
},
"r3d100011874": {
"description": "A database of optical constants of materials",
"homepage": "https://refractiveindex.info/",
"name": "RefractiveIndex.INFO",
"prefix": "r3d100011874",
"synonyms": [
"Refractive index Database",
"refractiveindex.info database"
],
"xrefs": {
"fairsharing": "FAIRsharing.60127f"
}
},
"r3d100011876": {
"description": "The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) and German Plant Phenotyping Network (DPPN) has jointly initiated the Plant Genomics and Phenomics Research Data Repository (PGP) as infrastructure to comprehensively publish plant research data. This covers in particular cross-domain datasets that are not being published in central repositories because of its volume or unsupported data scope, like image collections from plant phenotyping and microscopy, unfinished genomes, genotyping data, visualizations of morphological plant models, data from mass spectrometry as well as software and documents.",
"homepage": "https://edal-pgp.ipk-gatersleben.de/",
"name": "Plant Genomics and Phenomics Research Data Repository",
"prefix": "r3d100011876",
"synonyms": [
"PGP Repository"
],
"xrefs": {
"fairsharing": "FAIRsharing.rf3m4g",
"omics": "13414"
}
},
"r3d100011879": {
"description": "KDP has replaced the KNMI Data Centre (KDC), which was turned off on the 27th of July 2020. Not only a change of name, but also a transition to new technologies. Initially, the KDP will be more primitive than KDC. To fulfill future ambitions, a digital KNMI transformation has been initiated. Part of this transition is the development of a new KDP as a successor of the KDC. All data on the KNMI Data Platform is free to use. For some datasets a service agreement is available, which is indicated on the page of the dataset. \nThe KNMI Data platform provides access to KNMI data on weather, climate and seismology. Here you will find KNMI data on various subjects such as the most recent 10-minute observations, historical series, data about meteorological measuring stations, model calculations, earthquake data and satellite products. In addition to KNMI datasets, we also make datasets from other parties available, such as ECMWF, ECOMET, EUMETSAT and WMO.",
"homepage": "https://dataplatform.knmi.nl/",
"name": "KNMI Data Platform",
"prefix": "r3d100011879",
"synonyms": [
"KDP",
"formerly: KDC",
"formerly: KNMI Data Centre"
]
},
"r3d100011880": {
"description": "The International Center for Tropical Agriculture (CIAT), a member of the CGIAR Consortium, believes that open access contributes to its mission of reducing hunger and poverty, and improving human nutrition in the tropics through research aimed at increasing the eco-efficiency of agriculture. Research data produced by CIAT and its Partners is distributed freely whenever possible. Kindly note that these datasets require proper citation and citation information is included with the metadata for each dataset.",
"homepage": "https://dataverse.harvard.edu/dataverse/CIAT",
"name": "CIAT Dataverse",
"prefix": "r3d100011880",
"synonyms": [
"CIAT - International Center for Tropical Agriculture Dataverse",
"CIAT Research Online"
]
},
"r3d100011883": {
"description": "The Open Exoplanet Catalogue is a catalogue of all discovered extra-solar planets. It is a new kind of astronomical database. It is decentralized and completely open. We welcome contributions and corrections from both professional astronomers and the general public.",
"homepage": "http://www.openexoplanetcatalogue.com/",
"name": "Open Exoplanet Catalogue",
"prefix": "r3d100011883"
},
"r3d100011890": {
"description": "Ag Data Commons provides access to a wide variety of open data relevant to agricultural research. We are a centralized repository for data already on the web, as well as for new data being published for the first time. While compliance with the U.S. Federal public access and open data directives is important, we aim to surpass them. Our goal is to foster innovative data re-use, integration, and visualization to support bigger, better science and policy.",
"homepage": "https://data.nal.usda.gov",
"name": "Ag Data Commons",
"prefix": "r3d100011890",
"synonyms": [
"USDAβs Open Research Data"
],
"xrefs": {
"fairsharing": "FAIRsharing.83wDfe"
}
},
"r3d100011891": {
"description": "Here you can find out more about Lancasterβs world-class research activities, view details of publications, outputs and awards and make contact with our researchers.",
"homepage": "http://www.research.lancs.ac.uk/portal/",
"name": "Lancaster University Research Directory",
"prefix": "r3d100011891"
},
"r3d100011894": {
"description": "Synapse is an open source software platform that clinical and biological data scientists can use to carry out, track, and communicate their research in real time. Synapse enables co-location of scientific content (data, code, results) and narrative descriptions of that work.",
"homepage": "https://www.synapse.org",
"name": "Synapse",
"prefix": "r3d100011894",
"xrefs": {
"fairsharing": "FAIRsharing.dnxzmk",
"nlx": "151983",
"scr": "006307"
}
},
"r3d100011896": {
"description": "THEREDA (Thermodynamic Reference Database) is a joint project dedicated to the creation of a comprehensive, internally consistent thermodynamic reference database, to be used with suitable codes for the geochemical modeling of aqueous electrolyte solutions up to high concentrations.",
"homepage": "https://www.thereda.de/en",
"name": "THEREDA",
"prefix": "r3d100011896",
"synonyms": [
"Thermodynamic Reference Database",
"Thermodynamische Referenz-Datenbasis"
]
},
"r3d100011898": {
"description": "The UWA Profiles and Research Repository contains research publications, research datasets, theses, equipment, grants and activities created by researchers and postgraduates affiliated with the University of Western Australia (UWA). It is managed by the University Library and provides access to research datasets held at UWA. The information about each dataset has been provided by UWA research groups. Dataset metadata is harvested into Research Data Australia (RDA) https://researchdata.edu.au/.",
"homepage": "https://research-repository.uwa.edu.au/",
"name": "UWA Profiles and Research Repository",
"prefix": "r3d100011898",
"synonyms": [
"UWA Research Repository",
"formerly: RDO",
"formerly: Research Data Online"
]
},
"r3d100011900": {
"description": "The Research Data Center PIAAC (RDC PIAAC) has been accredited by the German Data Forum (RatSWD). The RDC PIAAC makes research data accessible to the scientific community and offers advice to the users. The RDC PIAAC provides German and international datasets in the educational field focusing on the adult population, especially on the Programme for the International Assessment of Adult Competencies (PIAAC).",
"homepage": "https://www.gesis.org/en/piaac/rdc/",
"name": "Research Data Center PIAAC at GESIS",
"prefix": "r3d100011900",
"synonyms": [
"FDZ PIAAC",
"Forschungsdatenzentrum PIAAC bei GESIS",
"PIAAC",
"Programme for the International Assessment of Adult Competencies",
"RDC PIAAC"
],
"xrefs": {
"doi": "10.4232/1.12660"
}
},
"r3d100011901": {
"description": "The German Youth Institute is a leading non-university research institute. Since 1988, empirical studies about the growing up of children and young people and to life situations of adults and families were regularly conducted. The Research Data Centre is part of the department \"Social Monitoring.\" It processes the data and provides data access for secondary analysis.",
"homepage": "https://surveys.dji.de",
"name": "Forschungsdatenzentrum des Deutschen Jugendinstituts",
"prefix": "r3d100011901",
"synonyms": [
"DJI Forschungsdatenbank",
"FDZ DJI",
"Research Data Center of the German Youth Institute"
]
},
"r3d100011902": {
"description": "<<>>!!!>>> The Research Data Center (RDC) of the Collaborative Research Center 882 \"From heterogeneities to inequalities\" at Bielefeld University provides external scientists access to the research data generated in the CRC 882. It provides access to both qualitative and quantitative data from the field of inequality research. The CRC 882 RDC supports external researchers who are reusing the data, as well as gives advice on data documentation and anonymization procedures to the researchers of the CRC to ensure high data quality.\n\nThe datasets include, for example, a panel on youth crime, different series of interviews on ethnicity, paternal life and recalls of employees, as well as other panels, interview data and experimental data. In the further course of the Collaborative Research Center the database will be expanded with the data of future projects. External scientists can make an application for the scientific use of CRC 882 Research Data. In accordance with data privacy requirements, the access will be organized via controlled remote data access or via on-site use. For this purpose, the RDC provides workplaces for guest researchers.",
"homepage": "https://sfb882.uni-bielefeld.de/de/fdz-sfb882.html",
"name": "SFB 882 Forschungsdatenzentrum",
"prefix": "r3d100011902",
"synonyms": [
"CRC 882 RDC",
"FDZ SFB882 \"Von HeterogenitΓ€ten zu Ungleichheiten\"",
"Research Data Centre of the Collaborative Research Centre SFB 882 \"From heterogeneities to inequalities\""
]
},
"r3d100011903": {
"description": "RepOD is a general-purpose repository for open research data, offering all members of the academic community in Poland the possibility to deposit their work. It is intended for scientific data from all disciplines of knowledge and in all formats. The purpose of RepOD is to create a place where research data can be safely stored and openly shared with others.",
"homepage": "https://repod.icm.edu.pl/",
"name": "Repository for Open Data (RepOD)",
"prefix": "r3d100011903",
"synonyms": [
"Repository for Open Data",
"Repozytorium Otwartych Danych"
],
"xrefs": {
"fairsharing": "FAIRsharing.be560c",
"scr": "014697"
}
},
"r3d100011904": {
"description": "The Allele Frequency Net Database (AFND) is a public database which contains frequency information of several immune genes such as Human Leukocyte Antigens (HLA), Killer-cell Immunoglobulin-like Receptors (KIR), Major histocompatibility complex class I chain-related (MIC) genes, and a number of cytokine gene polymorphisms. The Allele Frequency Net Database (AFND) provides a central source, freely available to all, for the storage of allele frequencies from different polymorphic areas in the Human Genome. Users can contribute the results of their work into one common database and can perform database searches on information already available.\nWe have currently collected data in allele, haplotype and genotype format. However, the success of this website will depend on you to contribute your data.",
"homepage": "http://www.allelefrequencies.net/",
"name": "Allele Frequency Net Database",
"prefix": "r3d100011904",
"synonyms": [
"AFND",
"Allele Frequencies in Worldwide populations"
],
"xrefs": {
"fairsharing": "FAIRsharing.2cfr4z",
"nif": "0000-30079",
"omics": "20466",
"scr": "007259"
}
},
"r3d100011905": {
"description": "LOVD portal provides LOVD software and access to a list of worldwide LOVD applications through Locus Specific Database list and List of Public LOVD installations. The LOVD installations that have indicated to be included in the global LOVD listing are included in the overall LOVD querying service, which is based on an API.",
"homepage": "https://www.lovd.nl/3.0/home",
"name": "Leiden Open Variation Database",
"prefix": "r3d100011905",
"synonyms": [
"LOVD"
],
"xrefs": {
"fairsharing": "FAIRsharing.21tjj7",
"nif": "0000-02998",
"omics": "00275",
"scr": "006566"
}
},
"r3d100011906": {
"description": "FungiDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for the kingdom Fungi. FungiDB was first released in early 2011 as a collaborative project between EuPathDB and the group of Jason Stajich (University of California, Riverside). At the end of 2015, FungiDB was integrated into the EuPathDB bioinformatic resource center. FungiDB integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining.",
"homepage": "https://fungidb.org/fungidb/app",
"name": "FungiDB",
"prefix": "r3d100011906",
"synonyms": [
"The Fungal and Oomycete Genomics Resource"
],
"xrefs": {
"fairsharing": "FAIRsharing.xf30yc",
"nlx": "151401",
"omics": "03103",
"scr": "006013"
}
},
"r3d100011907": {
"description": "The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to:\nInformation on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, Information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, Information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors, Tumor pathology reports and images, References, supporting MTB data and Links to other online resources for cancer.",
"homepage": "https://tumor.informatics.jax.org/mtbwi/index.do",
"name": "Mouse Models of Human Cancer database",
"prefix": "r3d100011907",
"synonyms": [
"MMHCdb",
"formerly: MTB Database",
"formerly: Mouse Tumor Biology Database"
],
"xrefs": {
"scr": "017516"
}
},
"r3d100011908": {
"description": "A machine learning data repository with interactive visual analytic techniques. This project is the first to combine the notion of a data repository with real-time visual analytics for interactive data mining and exploratory analysis on the web. State-of-the-art statistical techniques are combined with real-time data visualization giving the ability for researchers to seamlessly find, explore, understand, and discover key insights in a large number of public donated data sets. This large comprehensive collection of data is useful for making significant research findings as well as benchmark data sets for a wide variety of applications and domains and includes relational, attributed, heterogeneous, streaming, spatial, and time series data as well as non-relational machine learning data. All data sets are easily downloaded into a standard consistent format. We also have built a multi-level interactive visual analytics engine that allows users to visualize and interactively explore the data in a free-flowing manner.",
"homepage": "http://mlvis.com/",
"name": "Scientific Data Repository",
"prefix": "r3d100011908",
"synonyms": [
"Data Repository. Interactive Analytics, Exploration & Visualization.",
"MLVIS"
]
},
"r3d100011909": {
"description": "The Sheffield Hallam University Research Data Repository (SHURDA) is an institutional catalogue of digital and non-digital datasets that are produced by researchers at SHU and preserved at the University or elsewhere.",
"homepage": "https://shurda.shu.ac.uk/",
"name": "Sheffield Hallam University Research Data Archive",
"prefix": "r3d100011909",
"synonyms": [
"SHU Research Data Archive",
"SHURDA"
]
},
"r3d100011910": {
"description": "The Magnetics Information Consortium (MagIC) improves research capacity in the Earth and Ocean sciences by maintaining an open community digital data archive for rock magnetic, geomagnetic, archeomagnetic (archaeomagnetic) and paleomagnetic (palaeomagnetic) data. Different parts of the website allow users access to archive, search, visualize, and download these data. MagIC supports the international rock magnetism, geomagnetism, archeomagnetism (archaeomagnetism), and paleomagnetism (palaeomagnetism) research and endeavors to bring data out of private archives, making them accessible to all and (re-)useable for new, creative, collaborative scientific and educational activities. The data in MagIC is used for many types of studies including tectonic plate reconstructions, geomagnetic field models, paleomagnetic field reversal studies, magnetohydrodynamical studies of the Earth's core, magnetostratigraphy, and archeology. \n\nMagIC is a domain-specific data repository and directed by PIs who are both producers and consumers of rock, geo, and paleomagnetic data. Funded by NSF since 2003, MagIC forms a major part of https://earthref.org which integrates four independent cyber-initiatives rooted in various parts of the Earth, Ocean and Life sciences and education.",
"homepage": "https://www2.earthref.org/MagIC",
"name": "Magnetics Information Consortium",
"prefix": "r3d100011910",
"synonyms": [
"MagIC"
],
"xrefs": {
"biodbcore": "001155",
"nlx": "154712",
"scires": "000151",
"scr": "007098"
}
},
"r3d100011913": {
"description": "The PAIN Repository is a recently funded NIH initiative, which has two components: an archive for already collected imaging data (Archived Repository), and a repository for structural and functional brain images and metadata acquired prospectively using standardized acquisition parameters (Standardized Repository) in healthy control subjects and patients with different types of chronic pain. The PAIN Repository provides the infrastructure for storage of standardized resting state functional, diffusion tensor imaging and structural brain imaging data and associated biological, physiological and behavioral metadata from multiple scanning sites, and provides tools to facilitate analysis of the resulting comprehensive data sets.",
"homepage": "https://www.painrepository.org/repositories/",
"name": "PAIN repository",
"prefix": "r3d100011913",
"synonyms": [
"Pain and Interoception Imaging Network Repository"
],
"xrefs": {
"fairsharing": "FAIRsharing.9fmyc7"
}
},
"r3d100011914": {
"description": "Welcome to the largest bibliographic database dedicated to Economics and available freely on the Internet. This site is part of a large volunteer effort to enhance the free dissemination of research in Economics, RePEc, which includes bibliographic metadata from over 1,800 participating archives, including all the major publishers and research outlets. IDEAS is just one of several services that use RePEc data. \nAuthors are invited to register with RePEc to create an online profile. Then, anyone finding some of your research here can find your latest contact details and a listing of your other research. You will also receive a monthly mailing about the popularity of your works, your ranking and newly found citations.\nBesides that IDEAS provides software and public accessible data from Federal Reserve Bank.",
"homepage": "https://ideas.repec.org/",
"name": "IDEAS",
"prefix": "r3d100011914"
},
"r3d100011915": {
"description": "The GDR is the submission point for all data collected from researchers funded by the U.S. Department of Energy's Geothermal Technologies Office. It was established to receive, manage, and make available all geothermal-relevant data generated from projects funded by the DOE Geothermal Technologies Office. This includes data from GTO-funded projects associated with any portion of the geothermal project life-cycle (exploration, development, operation), as well as data produced by GTO-funded research.",
"homepage": "https://gdr.openei.org/",
"name": "Geothermal Data Repository",
"prefix": "r3d100011915",
"synonyms": [
"DOE Geothermal Data Repository",
"GDR"
]
},
"r3d100011922": {
"description": "CLARIN.SI is the Slovenian node of the European CLARIN (Common Language Resources and Technology Infrastructure) Centers. The CLARIN.SI repository is hosted at the JoΕΎef Stefan Institute and offers long-term preservation of deposited linguistic resources, along with their descriptive metadata. The integration of the repository with the CLARIN infrastructure gives the deposited resources wide exposure, so that they can be known, used and further developed beyond the lifetime of the projects in which they were produced. Among the resources currently available in the CLARIN.SI repository are the multilingual MULTEXT-East resources, the CC version of Slovenian reference corpus Gigafida, the morphological lexicon Sloleks, the IMP corpora and lexicons of historical Slovenian, as well as many other resources for a variety of languages. Furthermore, several REST-based web services are provided for different corpus-linguistic and NLP tasks.",
"homepage": "https://www.clarin.si/repository/xmlui/",
"name": "CLARIN.SI repository",
"prefix": "r3d100011922",
"synonyms": [
"Slovenian CLARIN repository"
]
},
"r3d100011923": {
"description": "The vehicle routing problem repository (VRP-REP) is an open data platform for sharing instances and solutions for vehicle routing problems.",
"homepage": "http://www.vrp-rep.org",
"name": "VRP-REP",
"prefix": "r3d100011923",
"synonyms": [
"Vehicle routing problem repository"
]
},
"r3d100011924": {
"description": "The WorldWide Antimalarial Resistance Network (WWARN) is a collaborative platform generating innovative resources and reliable evidence to inform the malaria community on the factors affecting the efficacy of antimalarial medicines. Access to data is provided through diverse Tools and Resources: WWARN Explorer, Molecular Surveyor K13 Methodology, Molecular Surveyor pfmdr1 & pfcrt, Molecular Surveyor dhfr & dhps.",
"homepage": "http://www.wwarn.org/",
"name": "WorldWide Antimalarial Resistance Network",
"prefix": "r3d100011924",
"synonyms": [
"WWARN"
]
},
"r3d100011927": {
"description": "The ECHO initiative aims to create an infrastructure to bring cultural heritage on the Internet, and builds up a network of institutions, research projects and other users which provide content and technology for the common infrastructure, with the aim to enrich the \"agora\" and to create a future Web of Culture and Science.",
"homepage": "https://echo.mpiwg-berlin.mpg.de/home",
"name": "ECHO β Cultural Heritage Online",
"prefix": "r3d100011927",
"synonyms": [
"Open Access Infrastructure for a Future Web of Culture and Science"
]
},
"r3d100011928": {
"description": "The FAIRDOMHub is built upon the SEEK software suite, which is an open source web platform for sharing scientific research assets, processes and outcomes. FAIRDOM (Web Site) will establish a support and service network for European Systems Biology. It will serve projects in standardizing, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable. \nFAIRDOM is an initiative to develop a community, and establish an internationally sustained Data and Model Management service to the European Systems Biology community. FAIRDOM is a joint action of ERA-Net EraSysAPP and European Research Infrastructure ISBE.",
"homepage": "https://fairdomhub.org/",
"name": "FAIRDOMHub",
"prefix": "r3d100011928",
"synonyms": [
"The SEEK datafiles"
],
"xrefs": {
"fairsharing": "fairsharing.nnvcr9",
"scr": "021119"
}
},
"r3d100011929": {
"description": "The African Development Bank Group (AfDB) is committed to supporting statistical development in Africa as a sound basis for designing and managing effective development policies for reducing poverty on the continent. Reliable and timely data is critical to setting goals and targets as well as evaluating project impact. Reliable data constitutes the single most convincing way of getting the people involved in what their leaders and institutions are doing. It also helps them to get involved in the development process, thus giving them a sense of ownership of the entire development process.\nThe AfDB has a large team of researchers who focus on the production of statistical data on economic and social situations. The data produced by the institutionβs statistics department constitutes the background information in the Bankβs flagship development publications. Besides its own publication, the AfDB also finances studies in collaboration with its partners.\nThe Statistics Department aims to stand as the primary source of relevant, reliable and timely data on African development processes, starting with the data generated from its current management of the Africa component of the International Comparison Program (ICP-Africa). The Department discharges its responsibilities through two divisions: The Economic and Social Statistics Division (ESTA1); The Statistical Capacity Building Division (ESTA2)",
"homepage": "https://dataportal.opendataforafrica.org/",
"name": "AfDB Statistical Data Portal",
"prefix": "r3d100011929",
"synonyms": [
"Africa Information Highway",
"African Development Bank Data Portal",
"African Information Highway Portal",
"formerly: Open data for Africa"
]
},
"r3d100011931": {
"description": "<<>>!!!>>>\nMigration of the data, tools, and services from IRD and ViPR to BV-BRC is complete! We are now in the sunsetting phase of the transition. Starting on October 31, 2022, launching the IRD or ViPR home pages will redirect you to the new BV-BRC home page. The current plan is to completely shut down IRD and ViPR by the end of this calendar year. Although it will still be possible to use those sites until shutdown, we strongly encourage you to start using BV-BRC now.",
"homepage": "https://www.viprbrc.org/brc/home.spg?decorator=vipr",
"name": "Virus Pathogen Resource",
"prefix": "r3d100011931",
"synonyms": [
"ViPR"
],
"xrefs": {
"fairsharing": "FAIRsharing.2qx8n8",
"miriam": "00000407",
"nif": "0000-25312",
"scr": "012983"
}
},
"r3d100011932": {
"description": "Pathogen Portal is a repository linking to the Bioinformatics Resource Centers (BRCs) sponsored by the National Institute of Allergy and Infectious Diseases (NIAID) and maintained by The Virginia Bioinformatics Institute. The BRCs are providing web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases. \nThe Pathogen Portal supports and links to five Bioinformatics Resource Centers (BRCs). Each BRC specializes in a different group of pathogens, focusing on, but not limited to, pathogens causing (Re-)Emerging Infectious Diseases, and those in the NIAID Category A-C Priority Pathogen lists for biodefense research. The scope of the BRCs also includes Invertebrate Vectors of Human Disease.\nPathogen Portal covers EuPathDB, IRD, PATRIC, VectorBase and ViPR.",
"homepage": "https://github.com/cidvbi/PathogenPortal/wiki",
"name": "Pathogen Portal",
"prefix": "r3d100011932",
"synonyms": [
"the Bioinformatics Resource Centers Portal"
],
"xrefs": {
"scr": "014603"
}
},
"r3d100011933": {
"description": "Kinsources is an open and interactive platform to archive, share, analyze and compare kinship data used in scientific research. Kinsources is not just another genealogy website, but a peer-reviewed repository designed for comparative and collaborative research. The aim of Kinsources is to provide kinship studies with a large and solid empirical base.\nKinsources combines the functionality of communal data repository with a toolbox providing researchers with advanced software for analyzing kinship data. The software Puck (Program for the Use and Computation of Kinship data) is integrated in the statistical package and the search engine of the Kinsources website.\nKinsources is part of a research perspective that seeks to understand the interaction between genealogy, terminology and space in the emergence of kinship structures. Hosted by the TGIR HumaNum, the platform ensures both security and free access to the scientific data is validated by the research community.",
"homepage": "https://www.kinsources.net/",
"name": "Kinsources.net",
"prefix": "r3d100011933",
"xrefs": {
"issn": "2495-9480"
}
},
"r3d100011934": {
"description": "Soils is part of the National Cooperative Soil Survey, an effort of Federal and State agencies, universities, and professional societies to deliver science-based soil information.",
"homepage": "https://www.nrcs.usda.gov/wps/portal/nrcs/site/soils/home/",
"name": "Natural Resources Conservation Service Soils",
"prefix": "r3d100011934",
"synonyms": [
"USDA NRCS Soils",
"United States Department of Agriculture, Natural Resources Conservation Service Soils"
]
},
"r3d100011936": {
"description": "DEPOD - the human DEPhOsphorylation Database (version 1.1) is a manually curated database collecting human active phosphatases, their experimentally verified protein and non-protein substrates and dephosphorylation site information, and pathways in which they are involved. It also provides links to popular kinase databases and protein-protein interaction databases for these phosphatases and substrates. DEPOD aims to be a valuable resource for studying human phosphatases and their substrate specificities and molecular mechanisms; phosphatase-targeted drug discovery and development; connecting phosphatases with kinases through their common substrates; completing the human phosphorylation/dephosphorylation network.",
"homepage": "https://depod.bioss.uni-freiburg.de/",
"name": "DEPOD",
"prefix": "r3d100011936",
"synonyms": [
"DEPhOsphorylation Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.q9j2e3",
"miriam": "00000428"
}
},
"r3d100011937": {
"description": "The Biodiversity Research Program (PPBio) was created in 2004 with the aims of furthering biodiversity studies in Brazil, decentralizing scientific production from already-developed academic centers, integrating research activities and disseminating results across a variety of purposes, including environmental management and education.\nPPBio contributes its data to the DataONE network as a member node: https://search.dataone.org/#profile/PPBIO",
"homepage": "https://ppbio.inpa.gov.br/en/repository",
"name": "PPBio Data Repository",
"prefix": "r3d100011937",
"synonyms": [
"Programa de Pesquisa em Biodiversidade Repositorio de Dados",
"RepositΓ³rio de Dados de Levantamentos BiolΓ³gicos"
]
},
"r3d100011939": {
"description": "<<< openresearchdata.ch has been discontinued !!! >>> Openresearchdata.ch (ORD@CH) has been developed as a publication platform for open research data in Switzerland. It currently offers a metadata catalogue of the data available at the participating institutions (ETH Zurich Scientific IT Services, FORS Lausanne, Digital Humanities Lab at the University of Basel). In addition, metadata from other institutions is continuously added, with the goal to develop a comprehensive metadata infrastructure for open research data in Switzerland.\nThe ORD@CH project is part of the program βScientific information: access, processing and safeguardingβ, initiated by the Rectorsβ Conference of Swiss Universities (Program SUC 2013-2016 P-2). The portal is currently hosted and developed by ETH Zurich Scientific IT Services.",
"homepage": "https://sis.id.ethz.ch/researchdatamanagement/service-ordch.html",
"name": "Openresearchdata, Platform Switzerland",
"prefix": "r3d100011939",
"synonyms": [
"ORD@CH"
]
},
"r3d100011940": {
"description": "The Linguistic Data Consortium (LDC) is an open consortium of universities, libraries, corporations and government research laboratories. It was formed in 1992 to address the critical data shortage then facing language technology research and development. \nInitially, LDC's primary role was as a repository and distribution point for language resources. Since that time, and with the help of its members, LDC has grown into an organization that creates and distributes a wide array of language resources. LDC also supports sponsored research programs and language-based technology evaluations by providing resources and contributing organizational expertise.\nLDC is hosted by the University of Pennsylvania and is a center within the Universityβs School of Arts and Sciences.",
"homepage": "https://www.ldc.upenn.edu/",
"name": "Linguistic Data Consortium",
"prefix": "r3d100011940",
"synonyms": [
"LDC"
]
},
"r3d100011941": {
"description": "The goal of the Center of Estonian Language Resources (CELR) is to create and manage an infrastructure to make the Estonian language digital resources (dictionaries, corpora β both text and speech β, various language databases) and language technology tools (software) available to everyone working with digital language materials. CELR coordinates and organises the documentation and archiving of the resources as well as develops language technology standards and draws up necessary legal contracts and licences for different types of users (public, academic, commercial, etc.). In addition to collecting language resources, a system will be launched for introducing the resources to, informing and educating the potential users.\nThe main users of CELR are researchers from Estonian R&D institutions and Social Sciences and Humanities researchers all over the world via the CLARIN ERIC network of similar centers in Europe.\nAccess to data is provided through different sites: \nPublic Repository https://entu.keeleressursid.ee/public-document, \nLanguage resources https://keeleressursid.ee/en/resources/corpora, \nand MetaShare CELR https://metashare.ut.ee/.",
"homepage": "https://keeleressursid.ee/en/resources",
"name": "Center of Estonian Language Resources",
"prefix": "r3d100011941",
"synonyms": [
"CELR META-SHARE",
"Eesti Keeleressursside Keskus"
]
},
"r3d100011942": {
"description": "PalDat provides a large amount of data from a variety of plant families. Each data entry ideally includes a detailed description of the pollen grain, images of each pollen grain (LM, SEM and TEM), images of the plant/inflorescence/flower and relevant literature.",
"homepage": "https://www.paldat.org/",
"name": "Palynological Database",
"prefix": "r3d100011942",
"synonyms": [
"PalDat",
"an online publication on recent pollen"
]
},
"r3d100011943": {
"description": "META-SHARE, the open language resource exchange facility, is devoted to the sustainable sharing and dissemination of language resources (LRs) and aims at increasing access to such resources in a global scale.\nMETA-SHARE is an open, integrated, secure and interoperable sharing and exchange facility for LRs (datasets and tools) for the Human Language Technologies domain and other applicative domains where language plays a critical role.\nMETA-SHARE is implemented in the framework of the META-NET Network of Excellence. It is designed as a network of distributed repositories of LRs, including language data and basic language processing tools (e.g., morphological analysers, PoS taggers, speech recognisers, etc.).\nData and tools can be both open and with restricted access rights, free and for-a-fee.",
"homepage": "http://metashare.elda.org/",
"name": "META-SHARE",
"prefix": "r3d100011943"
},
"r3d100011945": {
"description": "Research Data Leeds is the institutional research data repository for the University of Leeds. The service aims to facilitate data discovery and data sharing. The repository houses data generated by researchers at the University of Leeds.",
"homepage": "https://archive.researchdata.leeds.ac.uk/",
"name": "Research Data Leeds Repository",
"prefix": "r3d100011945",
"synonyms": [
"Leeds Repository",
"RDL Repository"
],
"xrefs": {
"fairsharing": "FAIRsharing.nhVgNw"
}
},
"r3d100011947": {
"description": "The University of Bath Research Data Archive was established in 2015 to make data supporting our research discoverable and accessible.",
"homepage": "https://researchdata.bath.ac.uk/",
"name": "University of Bath Research Data Archive",
"prefix": "r3d100011947",
"xrefs": {
"opendoar": "4997"
}
},
"r3d100011948": {
"description": "Project Tycho is a repository for global health, particularly disease surveillance data. Project Tycho currently includes data for 92 notifiable disease conditions in the US, and up to three dengue-related conditions for 99 countries. Project Tycho has compiled data from reputable sources such as the US Centers for Disease Control, the World Health Organization, and National health agencies for countries around the world. Project Tycho datasets are highly standardized and have rich metadata to improve access, interoperability, and reuse of global health data for research and innovation.",
"homepage": "https://www.tycho.pitt.edu/",
"name": "Project Tycho: Data for Health",
"prefix": "r3d100011948",
"xrefs": {
"fairsharing": "FAIRsharing.jnzrt",
"nlx": "157982",
"scr": "010489"
}
},
"r3d100011950": {
"description": "<<>>!!!>>>",
"homepage": "https://seek.virtual-liver.de/data_files",
"name": "Virtual Liver Network",
"prefix": "r3d100011950",
"synonyms": [
"Netzwerk Virtuelle Leber",
"VLN"
]
},
"r3d100011951": {
"description": "MorphΒ·DΒ·Base has been developed to serve scientific research and education. It provides a platform for storing the detailed documentation of all material, methods, procedures, and concepts applied, together with the specific parameters, values, techniques, and instruments used during morphological data production. In other words, it's purpose is to provide a publicly available resource for recording and documenting morphological metadata. Moreover, it is also a repository for different types of media files that can be uploaded in order to serve as support and empirical substantiation of the results of morphological investigations.\nOur long-term perspective with MorphΒ·DΒ·Base is to provide an instrument that will enable a highly formalized and standardized way of generating morphological descriptions using a morphological ontology that will be based on the web ontology language (OWL - http://www.w3.org/TR/owl-features/). This, however, represents a project that is still in development.",
"homepage": "https://www.morphdbase.de/",
"name": "MorphΒ·DΒ·Base",
"prefix": "r3d100011951",
"synonyms": [
"MDB",
"Morph D Base",
"MorphDBase",
"Morphological Description Data Base"
]
},
"r3d100011956": {
"description": "CARIBIC is an innovative scientific project to study and monitor important chemical and physical processes in the EarthΒ΄s atmosphere. Detailed and extensive measurements are made during long distance flights. We deploy an airfreight container with automated scientific apparatus which are connected to an air and particle (aerosol) inlet underneath the aircraft. We use an Airbus A340-600 from Lufthansa since December 2004.",
"homepage": "https://www.caribic-atmospheric.com/",
"name": "CARIBIC",
"prefix": "r3d100011956",
"synonyms": [
"Civil Aircraft for the Regular Investigation of the atmosphere Based on an Instrument Container"
],
"xrefs": {
"fairsharing.legacy": "2806"
}
},
"r3d100011957": {
"description": "The Network for the Detection of Atmospheric Composition Change (NDACC), a major contributor to the worldwide atmospheric research effort, consists of a set of globally distributed research stations providing consistent, standardized, long-term measurements of atmospheric trace gases, particles, spectral UV radiation reaching the Earth's surface, and physical parameters, centered around the following priorities.",
"homepage": "https://ndacc.larc.nasa.gov/",
"name": "Network for the Detection of Atmospheric Composition Change",
"prefix": "r3d100011957",
"synonyms": [
"NDACC"
],
"xrefs": {
"fairsharing": "FAIRsharing.298d50"
}
},
"r3d100011958": {
"description": "HALO-DB is the web platform of a data retrieval and long-term archive system.\nThe system was established to hold and to manage a wide range of data based on observations of the HALO research aircraft and data which are related to HALO observations. \nHALO (High-Altitude and LOng-range aircraft) is the new German research aircraft (German Science Community (DFG)). The aircraft, a Gulfstream GV-550 Business-Jet, is strongly modified for the application as a research platform.\nHALO offers several advantages for scientific campaigns, such as its high range of more than 10000 km, a high maximum altitude of more than 15 km, as well as a relatively high payload.",
"homepage": "https://halo-db.pa.op.dlr.de/",
"name": "HALO database",
"prefix": "r3d100011958",
"synonyms": [
"HALO-DB",
"High Altitude and LOng Range database"
],
"xrefs": {
"fairsharing": "FAIRsharing.e0b9db"
}
},
"r3d100011959": {
"description": "The main focus of tambora.org is Historical Climatology. Years of meticulous work in this field in research groups around the world have resulted in large data collections on climatic parameters such as temperature, precipitation, storms, floods, etc. with different regional, temporal and thematic foci. \ntambora.org enables researchers to collaboratively interpret the information derived from historical sources. It provides a database for original text quotations together with bibliographic references and the extracted places, dates and coded climate and environmental information.",
"homepage": "https://www.tambora.org/",
"name": "TAMBORA",
"prefix": "r3d100011959",
"synonyms": [
"The climAte and environMental history collaBOrative ReseArch environment",
"tambora.org"
],
"xrefs": {
"doi": "10.6094/tambora.org"
}
},
"r3d100011961": {
"description": "The POES satellite system offers the advantage of daily global coverage, by making nearly polar orbits 14 times per day approximately 520 miles above the surface of the Earth. The Earth's rotation allows the satellite to see a different view with each orbit, and each satellite provides two complete views of weather around the world each day. NOAA partners with the European Organisation for the Exploitation of Meteorological Satellites (EUMETSAT) to constantly operate two polar-orbiting satellites β one POES and one European polar-orbiting satellite called Metop.\nNOAA's Polar Orbiting Environmental Satellites (POES) carry a suite of instruments that measure the flux of energetic ions and electrons at the altitude of the satellite. This environment varies as a result of solar and geomagnetic activity. Beginning with the NOAA-15 satellite, an upgraded version of the Space Environment Monitor (SEM-2) has been flown.",
"homepage": "https://www.ngdc.noaa.gov/stp/satellite/poes/index.html",
"name": "POES Space Environment Monitor",
"prefix": "r3d100011961",
"synonyms": [
"POES/MetOp SEM",
"Polar Orbiting Environmental Satellites"
]
},
"r3d100011962": {
"description": "DataStorre is an online digital repository of multi-disciplinary research datasets produced at the University of Stirling.\nUniversity of Stirling researchers who have produced research data associated with an existing or forthcoming publication, or which has potential use for other researchers, are invited to upload their dataset for sharing and safekeeping. A persistent identifier and suggested citation will be provided.",
"homepage": "https://datastorre.stir.ac.uk/",
"name": "DataSTORRE",
"prefix": "r3d100011962",
"synonyms": [
"Stirling Online Repository for Research Data"
]
},
"r3d100011965": {
"description": "A lightweight digital repository for data based on the concepts of collections of filesets. Both the collection and the fileset are assigned a DOI by the DataCite organisation which can be quoted in articles",
"homepage": "https://data.hpc.imperial.ac.uk/",
"name": "Imperial College Research Computing Service Data Repository",
"prefix": "r3d100011965",
"xrefs": {
"fairsharing": "FAIRsharing.LEtKjT"
}
},
"r3d100011966": {
"description": "coastDat is a model based data bank developed mainly for the assessment of long-term changes in data sparse regions. A sequence of numerical models is employed to reconstruct all aspects of marine climate (such as storms, waves, surges etc.) over many decades of years relying only on large-scale information such as large-scale atmospheric conditions or bathymetry.",
"homepage": "https://www.coastdat.de/",
"name": "coastDat",
"prefix": "r3d100011966"
},
"r3d100011967": {
"description": "The repository contains all digital data such as images, 3d models and analysis which were acquired in the Ancient Sundials Project.",
"homepage": "http://repository.edition-topoi.org/collection/BSDP",
"name": "Ancient Sundials",
"prefix": "r3d100011967",
"synonyms": [
"BSDP"
],
"xrefs": {
"doi": "10.17171/1-1"
}
},
"r3d100011968": {
"description": "It is the objective of our motion capture database HDM05 to supply free motion capture data for research purposes. HDM05 contains more than three hours of systematically recorded and well-documented motion capture data in the C3D as well as in the ASF/AMC data format. Furthermore, HDM05 contains for more than 70 motion classes in 10 to 50 realizations executed by various actors.",
"homepage": "http://resources.mpi-inf.mpg.de/HDM05/index.html",
"name": "Motion Capture Database HDM05",
"prefix": "r3d100011968",
"synonyms": [
"Mocap database HDM05"
]
},
"r3d100011969": {
"description": "The European Prospective Investigation into Cancer and Nutrition (EPIC) study is one of the largest cohort studies in the world, with more than half a million (521 000) participants recruited across 10 European countries and followed for almost 15 years.\n\nEPIC was designed to investigate the relationships between diet, nutritional status, lifestyle and environmental factors, and the incidence of cancer and other chronic diseases. EPIC investigators are active in all fields of epidemiology, and important contributions have been made in nutritional epidemiology using biomarker analysis and questionnaire information, as well as genetic and lifestyle investigations.",
"homepage": "https://epic.iarc.fr/index.php",
"name": "EPIC study",
"prefix": "r3d100011969",
"synonyms": [
"European Prospective Investigation into Cancer and Nutrition Study"
]
},
"r3d100011971": {
"description": "The UBIRA eData repository is a multidisciplinary online service for the registration, preservation and publication of research datasets produced or collected at the University of Birmingham. It is part of the University of Birmingham Research Archive (UBIRA).",
"homepage": "https://edata.bham.ac.uk/",
"name": "UBIRA eData",
"prefix": "r3d100011971",
"synonyms": [
"University of Birmingham eData Repository"
]
},
"r3d100011972": {
"description": "The Data Catalogue is a service that allows University of Liverpool Researchers to create records of information about their finalised research data, and save those data in a secure online environment. The Data Catalogue provides a good means of making that data available in a structured way, in a form that can be discovered by both general search engines and academic search tools. There are two types of record that can be created in the Data Catalogue:\nA discovery-only record β in these cases, the research data may be held somewhere else but a record is provided to help people find it. A record is created that alerts users to the existence of the data, and provides a link to where those data are held.\nA discovery and data record β in these cases, a record is created to help people discover the data exist, and the data themselves are deposited into the Data Catalogue. This process creates a unique Digital Object identifier (DOI) which can be used in citations to the data.",
"homepage": "https://datacat.liverpool.ac.uk/",
"name": "University of Liverpool Research Data Catalogue",
"prefix": "r3d100011972",
"synonyms": [
"University of Liverpool DataCat"
]
},
"r3d100011973": {
"description": "The Arctic Data Center is the primary data and software repository for the Arctic section of NSF Polar Programs. The Center helps the research community to reproducibly preserve and discover all products of NSF-funded research in the Arctic, including data, metadata, software, documents, and provenance that links these together. The repository is open to contributions from NSF Arctic investigators, and data are released under an open license (CC-BY, CC0, depending on the choice of the contributor). All science, engineering, and education research supported by the NSF Arctic research program are included, such as Natural Sciences (Geoscience, Earth Science, Oceanography, Ecology, Atmospheric Science, Biology, etc.) and Social Sciences (Archeology, Anthropology, Social Science, etc.). Key to the initiative is the partnership between NCEAS at UC Santa Barbara, DataONE, and NOAAβs NCEI, each of which bring critical capabilities to the Center. Infrastructure from the successful NSF-sponsored DataONE federation of data repositories enables data replication to NCEI, providing both offsite and institutional diversity that are critical to long term preservation.",
"homepage": "https://arcticdata.io/",
"name": "NSF Arctic Data Center",
"prefix": "r3d100011973",
"xrefs": {
"fairsharing": "FAIRsharing.6QPjtA"
}
},
"r3d100011975": {
"description": "Various information, such as xylarium data with wood specimens collected since 1944, atmospheric observation data using the MU radar and other instruments, space-plasma data observed with GEOTAIL satellite, are now combined as Database of Humanosphere and served for public use. Proposals for scientific and technological use are always welcome.",
"homepage": "http://www.rish.kyoto-u.ac.jp/organization_e/databases/",
"name": "Research Institute for Sustainable Humanosphere databases",
"prefix": "r3d100011975",
"synonyms": [
"Database for the humanosphere",
"RISH databases"
]
},
"r3d100011977": {
"description": "The Babylonian astronomical diaries comprise a group of cuneiform texts which record natural events in time spans from months to a whole year",
"homepage": "http://repository.edition-topoi.org/collection/BDIA",
"name": "Babylonian Diaries",
"prefix": "r3d100011977",
"synonyms": [
"BDIA"
],
"xrefs": {
"doi": "10.17171/1-3"
}
},
"r3d100011978": {
"description": "In addition to the common documentation methods of cylinder seals by rolled impression and photography, this collection also offers 3D-models and digital impressions. The 3D-scans can be performed without impacting the objects, thus reducing the risks. This method allows even the most fragile of seals to be documented, including those too delicate to be used for a rolled impression. These scans offer a true-to-scale reproduction of the seals.",
"homepage": "http://repository.edition-topoi.org/collection/VMRS",
"name": "Cylinder Seals",
"prefix": "r3d100011978",
"synonyms": [
"VMRS"
]
},
"r3d100011979": {
"description": "Results of the complete scan of the Pantheon.",
"homepage": "http://repository.edition-topoi.org/collection/BDPP",
"name": "Digital Pantheon",
"prefix": "r3d100011979",
"synonyms": [
"BDPP",
"Bern Digital Pantheon project"
]
},
"r3d100011980": {
"description": "Planetary phaenomena in early Medieval manuscripts",
"homepage": "http://repository.edition-topoi.org/collection/MAPD",
"name": "Medieval Diagrams",
"prefix": "r3d100011980",
"synonyms": [
"MAPD"
],
"xrefs": {
"doi": "10.17171/1-2"
}
},
"r3d100011981": {
"description": "The Canadian Environmental Sustainability Indicators (CESI) program provides data and information to track Canadaβs performance on key environmental sustainability issues including climate change and air quality, water quality and availability, and protected nature. The CESI website ensures that national, regional, local and international trends are readily accessible and transparently presented to all Canadians through the use of graphics, explanatory text, interactive maps and downloadable data.",
"homepage": "https://www.canada.ca/en/environment-climate-change/services/environmental-indicators.html",
"name": "Canadian Environmental Sustainability Indicators",
"prefix": "r3d100011981",
"synonyms": [
"CESI",
"ICDE",
"Indicateurs canadiens de durabilitΓ© de l'environnement"
]
},
"r3d100011982": {
"description": "The Canine Inherited Disorders Database (CIDD) is a joint initiative of the Sir James Dunn Animal Welfare Centre at the Atlantic Veterinary College, University of Prince Edward Island, and the Canadian Veterinary Medical Association. The goals of the database are to reduce the incidence of inherited disorders in dogs by providing information to owners and breeders, and to facilitate the best management possible of these conditions by providing current information to veterinarians.",
"homepage": "https://cidd.discoveryspace.ca/",
"name": "Canine Inherited Disorders Database",
"prefix": "r3d100011982",
"synonyms": [
"CIDD"
]
},
"r3d100011983": {
"description": "Biodiversity Maps provides access to high quality information on Ireland's biological diversity. Use the system to find out what is known about the different species that occur in Ireland, where our protected and threatened species occur, and who is recoding biodiversity. Also find out what is known about the biodiversity of your locality.\nThe National Biodiversity Data Centre endeavours to provide high quality information through this data portal.",
"homepage": "https://maps.biodiversityireland.ie/Home",
"name": "National Biodiversity Data Centre - Biodiversity Maps",
"prefix": "r3d100011983",
"synonyms": [
"MApping Ireland's Wildlife"
]
},
"r3d100011984": {
"description": "The Canadian Ice Service (CIS), a division of the Meteorological Service of Canada (MSC), is the leading authority for information about ice in Canada's navigable waters. The Canadian Ice Service Archive (CISA) allows online access to the following collections: Daily ice analysis charts (since 1999), Regional ice analysis charts, and Weekly ice thickness and on-ice snow depth measurements for Canadian stations.",
"homepage": "https://www.canada.ca/en/environment-climate-change/services/ice-forecasts-observations/latest-conditions/archive-overview.html",
"name": "Canadian Ice Service Archive",
"prefix": "r3d100011984",
"synonyms": [
"Archives du Service canadien des glaces",
"CISA"
]
},
"r3d100011985": {
"description": "<<>>!!!>>>",
"homepage": "http://www.ec.gc.ca/scitech/default.asp?lang=en&n=9ED7FDEC-1",
"name": "Great Lakes Precipitation Network",
"prefix": "r3d100011985",
"synonyms": [
"GLPN",
"RPGL",
"RΓ©seau des prΓ©cipitations des Grands Lacs"
]
},
"r3d100011986": {
"description": "IISD Experimental Lakes Area is one of the worldβs most influential freshwater research facilities. It features a collection of 58 small lakes and their watersheds in Northwestern Ontario, Canada, as well as a facility with accommodations and laboratories for up to 60 personnel.",
"homepage": "http://www.iisd.org/ela/",
"name": "Experimental Lakes Area",
"prefix": "r3d100011986",
"synonyms": [
"IISD - ELA"
]
},
"r3d100011987": {
"description": "The Joint Information Systems Committee (JISC) funded Landmap service which ran from 2001 to July 2014 collected, modified and hosted a large amount of earth observation data for the majority of the UK, including imagery from ERS satellites, ENVISAT and ALOS, high-resolution Digital Elevation Models (DEMs) and Digital Terrain Models (DTMs) and aerial photography dating back to 1930. After removal of JISC funding in 2013, the Landmap service is no longer operational, with the data now held at the NEODC.\nAside from the thermal imagery data which stands alone, the data reside in four collections: optical, elevation, radar and feature.",
"homepage": "http://catalogue.ceda.ac.uk/uuid/7f1280cf215da6f8001eae5c2f019fe8",
"name": "Landmap",
"prefix": "r3d100011987"
},
"r3d100011989": {
"description": "This web site is provided by the United States Geological Surveyβs (USGS) Earthquake Hazards Program as part of our effort to reduce earthquake hazard in the United States. We are part of the USGS Hazards Mission Area and are the USGS component of the congressionally established, multi-agency National Earthquake Hazards Reduction Program (NEHRP).",
"homepage": "https://earthquake.usgs.gov/earthquakes/search/",
"name": "USGS Earthquake Hazards Program Catalog",
"prefix": "r3d100011989",
"synonyms": [
"United States Geological Survey Earthquake Hazards Program Catalog"
]
},
"r3d100011990": {
"description": "The Geoscience Data Repository (GDR) is a collection of Earth Sciences Sector geoscience databases that is managed and accessed by a series of Information Services (GDRIS). This site allows you to discover, view and download information using these services. About 27 data resources are listed and many are also listed in the GeoConnections Discovery Portal.",
"homepage": "http://gdr.agg.nrcan.gc.ca/gdrdap/dap/search-eng.php",
"name": "Geoscience Data Repository for Geophysical Data",
"prefix": "r3d100011990",
"synonyms": [
"EntrepΓ΄t de donnΓ©es gΓ©oscientifiques pour les donnΓ©es gΓ©ophysiques",
"GDR"
]
},
"r3d100011991": {
"description": "GRIN-CA taxonomic data provide the structure and nomenclature for the accessions of the Canadian National Plant Germplasm System (NPGS). Many plants are included in GRIN-CA taxonomy, especially economic plants.",
"homepage": "https://pgrc-rpc.agr.gc.ca/gringlobal/landing",
"name": "GRIN-CA Taxonomy",
"prefix": "r3d100011991",
"synonyms": [
"Genetic Resource Information Network - Canadian Version Taxonomy",
"Plant Gene Resources of Canada: GRIN-CA Taxonomy",
"Ressources PhytogΓ©nΓ©tiques du Canada: Taxonomie de RIRGC (GRIN-CA)"
]
},
"r3d100011992": {
"description": "The NSDB is the set of computer readable files which contain soil, landscape, and climatic data for all of Canada. It serves as the national archive for land resources information that was collected by federal and provincial field surveys, or created by land data analysis projects. The NSDB includes GIS coverages at a variety of scales, and the characteristics of each named soil series. The principal types of NSDB data holdings (ordered by scale) are as follows: National Ecological Framework (EcoZones, EcoRegions, and EcoDistricts); Soil Map of Canada / Land Potential DataBase (LPDB); Agroecological Resource Areas (ARAs); Soil Landscapes of Canada (SLC); Canada Land Inventory (CLI); Detailed Soil Surveys.",
"homepage": "https://sis.agr.gc.ca/cansis/nsdb/index.html",
"name": "The National Soil DataBase",
"prefix": "r3d100011992",
"synonyms": [
"BNDS",
"Base nationale de donnΓ©es sur les sols",
"NSDB"
]
},
"r3d100011993": {
"description": "CDC WONDER, developed by the Centers for Disease Control and Prevention (CDC), is an integrated information and communication system for public health. It allows you to access wide-ranging online data for epidemiologic research.",
"homepage": "https://wonder.cdc.gov/",
"name": "CDC WONDER",
"prefix": "r3d100011993",
"synonyms": [
"Centers for Disease Control and Prevention, Wide-ranging OnLine Data for Epidemiologic Research"
]
},
"r3d100011994": {
"description": "SCISAT, also known as the Atmospheric Chemistry Experiment (ACE), is a Canadian Space Agency small satellite mission for remote sensing of the Earth's atmosphere using solar occultation. The satellite was launched on 12 August 2003 and continues to function perfectly. The primary mission goal is to improve our understanding of the chemical and dynamical processes that control the distribution of ozone in the stratosphere and upper troposphere, particularly in the Arctic. The high precision and accuracy of solar occultation makes SCISAT useful for monitoring changes in atmospheric composition and the validation of other satellite instruments. The satellite carries two instruments. A high resolution (0.02 cm-ΒΉ) infrared Fourier transform spectrometer (FTS) operating from 2 to 13 microns (750-4400 cm-ΒΉ) is measuring the vertical distribution of trace gases, particles and temperature. This provides vertical profiles of atmospheric constituents including essentially all of the major species associated with ozone chemistry. Aerosols and clouds are monitored using the extinction of solar radiation at 1.02 and 0.525 microns as measured by two filtered imagers. The vertical resolution of the FTS is about 3-4 km from the cloud tops up to about 150 km. Peter Bernath of the University of Waterloo is the principal investigator. A dual optical spectrograph called MAESTRO (Measurement of Aerosol Extinction in the Stratosphere and Troposphere Retrieved by Occultation) covers the 400-1030 nm spectral region and measures primarily ozone, nitrogen dioxide and aerosol/cloud extinction. It has a vertical resolution of about 1-2 km. Tom McElroy of Environment and Climate Change Canada is the principal investigator. ACE data are freely available from the University of Waterloo website. SCISAT was designated an ESA Third Party Mission in 2005. ACE data are freely available through an ESA portal.",
"homepage": "http://www.ace.uwaterloo.ca/",
"name": "Atmospheric Chemistry Experiment",
"prefix": "r3d100011994",
"synonyms": [
"ACE",
"SCISAT"
]
},
"r3d100011995": {
"description": "Launched in November 1995, RADARSAT-1 provided Canada and the world with an operational radar satellite system capable of timely delivery of large amounts of data. Equipped with a powerful synthetic aperture radar (SAR) instrument, it acquired images of the Earth day or night, in all weather and through cloud cover, smoke and haze.\nRADARSAT-1 was a Canadian-led project involving the Canadian federal government, the Canadian provinces, the United States, and the private sector. It provided useful information to both commercial and scientific users in such fields as disaster management, interferometry, agriculture, cartography, hydrology, forestry, oceanography, ice studies and coastal monitoring.\nIn 2007, RADARSAT-2 was launched, producing over 75,000 images per year since. In 2019, the RADARSAT Constellation Mission was deployed, using its three-satellite configuration for all-condition coverage. More information about RADARSAT-2 see https://mda.space/en/geo-intelligence/ RADARSAT-2 PORTAL see https://gsiportal.mda.space/gc_cp/#/map",
"homepage": "https://www.asc-csa.gc.ca/eng/satellites/radarsat1/default.asp",
"name": "RADARSAT-1",
"prefix": "r3d100011995",
"synonyms": [
"Canada's Earth Observation Satellite"
]
},
"r3d100011996": {
"description": "<<>>!!!>>> The Canadian Poisonous Plants Information System presents data on plants that cause poisoning in livestock, pets, and humans. The plants include native, introduced, and cultivated outdoor plants as well as indoor plants that are found in Canada. Some food and herbal plants that may cause potential poisoning problems are also included.",
"homepage": "http://www.cbif.gc.ca/eng/species-bank/canadian-poisonous-plants-information-system/?id=1370403265036",
"name": "Canadian Poisonous Plants Information System",
"prefix": "r3d100011996",
"synonyms": [
"Système canadien d'information sur les plantes toxiques"
]
},
"r3d100011997": {
"description": "The National Earthquake Database (NEDB) comprises a number of separate databases that together act as the national repository for all raw seismograph data, measurements, and derived parameters arising from the Canadian National Seismograph Network (CNSN), the Yellowknife Seismological Array (YKA), previous regional telemetered networks in eastern and western Canada (ECTN, WCTN), local telemetered networks (CLTN, SLTN), the Regional Analogue Network, and the former Standard Seismograph Network (CSN). It supports the efforts of Earthquakes Canada in Canadian seismicity monitoring, global seismic monitoring, verification of the Comprehensive nuclear Test Ban Treaty, and international data exchange. It also supports the Nuclear Explosion Monitoring project.",
"homepage": "https://www.earthquakescanada.nrcan.gc.ca/stndon/NEDB-BNDS/index-en.php",
"name": "National Earthquake DataBase",
"prefix": "r3d100011997",
"synonyms": [
"BNDS",
"Base Nationale de DonnΓ©es Sismologiques",
"NEDB"
]
},
"r3d100011999": {
"description": "Surveys provide annual information on the total, seasonal and spatial harvest of ducks, geese and other game birds in Canada, on the ecological characteristics of waterfowl harvested in Canada and the hunter activity associated with that harvest. The survey covers all of Canada divided into 23 zones and has been carried out annually since 1966. The bilingual database currently contains 9,000,000+ records.",
"homepage": "https://www.canada.ca/en/environment-climate-change/services/bird-surveys/waterfowl/national-harvest.html",
"name": "National Harvest Survey",
"prefix": "r3d100011999",
"synonyms": [
"EnquΓͺte nationale sur les prises",
"NHS"
]
},
"r3d100012000": {
"description": "Real time and archival databases containing Canadian water information. These data include, archived hydrometric data, water level and streamflow statistics, daily and monthly mean flow, water level and sediment concentration for monitoring station across Canada.\nThe Water Survey of Canada (WSC) is the national authority responsible for the collection, interpretation and dissemination of standardized water resource data and information in Canada. In partnership with the provinces, territories and other agencies, WSC operates over 2800 active hydrometric gauges across the country.",
"homepage": "https://www.canada.ca/en/environment-climate-change/services/water-overview/quantity/monitoring/survey.html",
"name": "Water Survey of Canada",
"prefix": "r3d100012000",
"synonyms": [
"RHC",
"RelevΓ©s hydrologiques du Canada",
"WSC"
]
},
"r3d100012001": {
"description": "The Illinois Data Bank is a public access data repository that collects, disseminates, and provides persistent and reliable access to the research data of faculty, staff, and students at the University of Illinois at Urbana-Champaign. Faculty, staff, graduate students can deposit their research data directly into the Illinois Data Bank and receive a DOI for citation purposes.",
"homepage": "https://databank.illinois.edu/",
"name": "Illinois Data Bank",
"prefix": "r3d100012001"
},
"r3d100012002": {
"description": "The International Plant Names Index (IPNI) is a database of the names and associated basic bibliographical details of seed plants, ferns and lycophytes. Its goal is to eliminate the need for repeated reference to primary sources for basic bibliographic information about plant names. The data are freely available and are gradually being standardized and checked. IPNI is a dynamic resource, depending on direct contributions by all members of the botanical community.\nIPNI is the product of a collaboration between The Royal Botanic Gardens, Kew, The Harvard University Herbaria, and the Australian National Herbarium.",
"homepage": "https://www.ipni.org/",
"name": "International Plant Names Index",
"prefix": "r3d100012002",
"synonyms": [
"IPNI"
],
"xrefs": {
"fairsharing": "FAIRsharing.45c8c8"
}
},
"r3d100012003": {
"description": "The UMIN case data repository system was implemented by adding a function to the UMIN Clinical Trials Registry System. The aim of this system is to keep anonymized case data from clinical research conducted by individual researchers at the UMIN center, and to guarantee the content of the data to third parties. This system enables other researchers to inspect case data or to repeat statistical analyses",
"homepage": "https://www.umin.ac.jp/ctr/index.htm",
"name": "University Hospital Medical Information Network Individual Case Data Repository",
"prefix": "r3d100012003",
"synonyms": [
"UMIN CTR",
"UMIN Clinical Trials Registry",
"UMIN-CTR",
"UMIN-ICDR"
],
"xrefs": {
"fairsharing": "FAIRsharing.802961"
}
},
"r3d100012005": {
"description": "The Innsbruck Dissociative Electron Attachment (DEA) DataBase node holds relative cross sections for dissociative electron attachment processes of the form: AB + eβ β> Aβ + B, where AB is a molecule. It hence supports querying by various identifiers for molecules and atoms, such as chemical names, stoichiometric formulae, InChI (-keys) and CAS registry numbers. These identifiers are searched both in products and reactants of the processes. It then returns XSAMS files describing the processes found including numeric values for the relative cross sections of the processes. Alternatively, cross sections can be exported as plain ASCII files.",
"homepage": "http://ideadb.uibk.ac.at",
"name": "IDEADB",
"prefix": "r3d100012005",
"synonyms": [
"Innsbruck Dissociative Electron Attachment Database"
]
},
"r3d100012008": {
"description": "The Mindboggle-101 data consist of three data sets: (1) individually labeled human brain surfaces and volumes, (2) templates (unlabeled images combining the individual brains, used for registration), and (3) atlases (anatomical labels combining the individual brains, used for labeling).",
"homepage": "https://dataverse.harvard.edu/dataverse/mindboggle101",
"name": "Mindboggle-101",
"prefix": "r3d100012008",
"xrefs": {
"nlx": "155814",
"scr": "002439"
}
},
"r3d100012009": {
"description": "By stimulating inspiring research and producing innovative tools, Huygens ING intends to open up old and inaccessible sources, and to understand them better. Huygens INGβs focus is on Digital Humanities, History, History of Science, and Textual Scholarship. Huygens ING pursues research in the fields of History, Literary Studies, the History of Science and Digital Humanities. Huygens ING aims to publish digital sources and data responsibly and with care. Innovative tools are made as widely available as possible. We strive to share the available knowledge at the institute with both academic peers and the wider public.",
"homepage": "https://www.huygens.knaw.nl/?lang=en",
"name": "Huygens ING",
"prefix": "r3d100012009",
"synonyms": [
"Huygens Institute for the History of the Netherlands",
"Huygens Instituut voor Nederlandse Geschiedenis"
]
},
"r3d100012010": {
"description": "<<>>!!!>>>",
"homepage": "https://www.supersites.net.au/knb/",
"name": "Australian SuperSite Network Data Portal",
"prefix": "r3d100012010",
"synonyms": [
"SupeSites Data Portal"
]
},
"r3d100012011": {
"description": "The Consortium of Pacific Herbaria (CPH) supports the enhancement of research cyberinfrastructure within Hawai'i and the Pacific basin for implementing shared specimen data hosting of plant specimens. The CPH network is a regional node of the US Virtual Herbarium.",
"homepage": "https://serv.biokic.asu.edu/pacific/portal/collections/index.php",
"name": "Consortium of Pacific Herbaria",
"prefix": "r3d100012011",
"synonyms": [
"Supporting regional databases, digitization and data sharing of plant specimens"
]
},
"r3d100012013": {
"description": "The TERN Data Discovery Portal (TDDP) is a gateway to search and access all the datasets published by the Australian Terrestrial Ecosystem Research Network. In the TERN data discovery portal, users can conduct textual and graphical searches on the metadata catalogue using a web interface with temporal, spatial, and eco science related controlled vocabulary keywords. Requests to download data discovered through different data services associated with TERN. Downloading, using and sharing data will be subjected to the TERN data licensing framework (https://www.tern.org.au/datalicence/).",
"homepage": "https://portal.tern.org.au",
"name": "TERN Data Discovery Portal",
"prefix": "r3d100012013",
"synonyms": [
"TDDP",
"Terrestrial Ecosystem Research Network Data Discovery Portal"
],
"xrefs": {
"fairsharing": "FAIRsharing.e77632"
}
},
"r3d100012014": {
"description": "HyperLeda is an information system for astronomy: It consists in a database and tools to process that data according to the user's requirements. The scientific goal which motivates the development of HyperLeda is the study of the physics and evolution of galaxies. LEDA was created more than 20 years ago, in 1983, and became HyperLeda after the merging with Hypercat in 2000",
"homepage": "https://leda.univ-lyon1.fr/",
"name": "HyperLeda",
"prefix": "r3d100012014",
"synonyms": [
"Database for physics of galaxies",
"Leda",
"Lyon-Meudon Extragalactic Database"
],
"xrefs": {
"issn": "2497-5486"
}
},
"r3d100012015": {
"description": "GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.",
"homepage": "https://www.genecards.org/",
"name": "GeneCards",
"prefix": "r3d100012015",
"synonyms": [
"The Human Gene Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.g7jbvn",
"nif": "0000-02879",
"omics": "01652",
"scr": "002773"
}
},
"r3d100012016": {
"description": "Volare is the repository of the Vorarlberger Landesbibliothek (Vorarlberg State Library). Digital Objects are made end-user-friendly available and they are secured in a long term. Pupils, students, patrimonial researchers but also the general public can use the imagery for various purposes. Volare facilitates access to regional, social and cultural history research. Volare encourages those who rediscover their native place or their holiday desination or just generally want to browse in the past.",
"homepage": "https://www.vorarlberg.at/volare",
"name": "volare",
"prefix": "r3d100012016",
"synonyms": [
"Vorarlberger Landesrepositorium"
]
},
"r3d100012017": {
"description": "LifeMap DiscoveryΒ is a compendium of embryonic development for stem cell research and regenerative medicine, constructed by integrating extensive molecular, cellular, anatomical and medical data curated from scientific literature and high-throughput data sources.",
"homepage": "https://discovery.lifemapsc.com/",
"name": "LifeMap Discovery",
"prefix": "r3d100012017",
"synonyms": [
"Embryonic development & stem cell Compendium"
]
},
"r3d100012018": {
"description": "MalaCards is an integrated database of human maladies and their annotations, modeled on the architecture and richness of the popular GeneCards database of human genes. MalaCards mines and merges varied web data sources to generate a computerized web card for each human disease. Each MalaCard contains disease specific prioritized annotative information, as well as links between associated diseases, leveraging the GeneCards relational database, search engine, and GeneDecks set-distillation tool. As proofs of concept of the search/distill/infer pipeline we find expected elucidations, as well as potentially novel ones.",
"homepage": "https://www.malacards.org/",
"name": "MalaCards",
"prefix": "r3d100012018",
"synonyms": [
"Human disease Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.e4r5nj",
"nlx": "149314",
"omics": "04647",
"scr": "005817"
}
},
"r3d100012019": {
"description": "Repository of research data sets created under the auspices of the University of Central Lancashire",
"homepage": "https://uclandata.uclan.ac.uk/",
"name": "UCLanData",
"prefix": "r3d100012019"
},
"r3d100012020": {
"description": "CLARINO Bergen Center repository is the repository of CLARINO, the Norwegian infrastructure project . Its goal is to implement the Norwegian part of CLARIN. The ultimate aim is to make existing and future language resources easily accessible for researchers and to bring eScience to humanities disciplines.\nThe repository includes INESS the Norwegian Infrastructure for the Exploration of Syntax and Semantics. This infrastructure provides access to treebanks, which are databases of syntactically and semantically annotated sentences.",
"homepage": "https://repo.clarino.uib.no/xmlui/",
"name": "CLARINO Bergen Center repository",
"prefix": "r3d100012020"
},
"r3d100012021": {
"description": "Cocoon \"COllections de COrpus Oraux NumΓ©riques\" is a technical platform that accompanies the oral resource producers, create, organize and archive their corpus; a corpus can consist of records (usually audio) possibly accompanied by annotations of these records.\nThe resources registered are first cataloged and stored while, and then, secondly archived in the archive of the TGIR Huma-Num. The author and his institution are responsible for filings and may benefit from a restricted and secure access to their data for a defined period, if the content of the information is considered sensitive.\nThe COCOON platform is jointly operated by two joint research units: Laboratoire de Langues et civilisations Γ tradition orale (LACITO - UMR7107 - UniversitΓ© Paris3 / INALCO / CNRS) and Laboratoire LigΓ©rien de Linguistique (LLL - UMR7270 - UniversitΓ©s d'OrlΓ©ans et de Tours, BnF, CNRS).",
"homepage": "https://cocoon.huma-num.fr/exist/crdo/?lang=en",
"name": "CoCoON",
"prefix": "r3d100012021",
"synonyms": [
"COllections de COrpus Oraux NumΓ©riques",
"Digital Oral Corpus COllections"
],
"xrefs": {
"issn": "2495-943X",
"opendoar": "2787",
"roar": "7296"
}
},
"r3d100012023": {
"description": "PathCards is an integrated database of human biological pathways and their annotations. Human pathways were clustered into SuperPaths based on gene content similarity. Each PathCard provides information on one SuperPath which represents one or more human pathways.",
"homepage": "https://pathcards.genecards.org/",
"name": "PathCards",
"prefix": "r3d100012023",
"synonyms": [
"Pathway Unification Database"
],
"xrefs": {
"omics": "07645"
}
},
"r3d100012025": {
"description": "This website provides a collection of all troposphere models published by TU Wien as well as all related data files.",
"homepage": "https://vmf.geo.tuwien.ac.at/",
"name": "VMF Data Server",
"prefix": "r3d100012025",
"synonyms": [
"Vienna Mapping Functions Open Access Data"
]
},
"r3d100012029": {
"description": "EMS is the BC Ministry of Environment's primary monitoring data repository. The system was designed to capture data covering physical/chemical and biological analyses performed on water, air, solid waste discharges and ambient monitoring sites throughout the province. \nIt also contains related quality assurance data. Samples are collected by either ministry staff or permittees under the Environmental Management Act and then analyzed in public or private sector laboratories. The majority of such monitoring data is entered into EMS electronically via Electronic Data Transfer (EDT). \nEMS data is typically available in formatted hard copy reports or electronically in comma delimited (e.g., .csv) files as: \nMonitoring location-related data, \nSample and results-related data.\nDirect access to EMS is restricted to ministry staff, however public access is available upon request through EMS Web Reporting.",
"homepage": "https://www2.gov.bc.ca/gov/content/environment/research-monitoring-reporting/monitoring/environmental-monitoring-system",
"name": "Environmental Monitoring System",
"prefix": "r3d100012029",
"synonyms": [
"British Columbia Environmental Monitoring System",
"EMS",
"Environmental Monitoring Databases"
]
},
"r3d100012030": {
"description": "FactSage is a fully integrated Canadian thermochemical database system which couples proven software with self-consistent critically assessed thermodynamic data. It currently contains data on over 5000 chemical substances as well as solution databases representing over 1000 non-ideal multicomponent solutions (oxides, salts, sulfides, alloys, aqueous, etc.). FactSage is available for use with Windows.",
"homepage": "https://www.factsage.com/",
"name": "FactSage",
"prefix": "r3d100012030"
},
"r3d100012031": {
"description": ">>>!!!<<< 2021-03-19: The repository is no longer available >>>!!!<<<\nThe National Contaminants Information System was begun as part of the Department's Green Plan. The NCIS is a computerized warehouse of information on toxic chemicals in fish, other aquatic life and their habitats. It was built to help manage the growing base of data and information.",
"name": "National Contaminants Information System",
"prefix": "r3d100012031",
"synonyms": [
"NCIS",
"SNIC",
"Système National d'Information sur les Contaminants"
]
},
"r3d100012032": {
"description": "OGSEarth provides geoscience data, collected by the Mines and Minerals division, which can be viewed using user-friendly geographic information programs such as Google Earthβ’. OSGEarth provides data on Mining claims, Geology, Index maps, Administrative boundaries and Abandoned mines.",
"homepage": "https://www.geologyontario.mndm.gov.on.ca/ogsearth.html",
"name": "OGSEarth",
"prefix": "r3d100012032"
},
"r3d100012033": {
"description": "Digital Rocks is a data portal for fast storage and retrieval of images of varied porous micro-structures. It has the purpose of enhancing research resources for modeling/prediction of porous material properties in the fields of Petroleum, Civil and Environmental Engineering as well as Geology.\nThis platform allows managing and preserving available images of porous materials and experiments performed on them, and any accompanying measurements (porosity, capillary pressure, permeability, electrical, NMR and elastic properties, etc.) required for both validation on modeling approaches and the upscaling and building of larger (hydro)geological models.\nStarting September 2021 we charge fees for publishing larger projects; projects < 2GB remain free: see user agreement https://www.digitalrocksportal.org/user-agreement/",
"homepage": "https://www.digitalrocksportal.org/",
"name": "Digital Rocks Portal",
"prefix": "r3d100012033",
"synonyms": [
"DRP"
]
},
"r3d100012034": {
"description": "The Ontario Natural Heritage Information Centre (NHIC) compiles, maintains and provides information on rare, threatened and endangered species and spaces in Ontario. This information is stored in a central repository composed of computerized databases, map files and an information library, which are accessible for conservation applications, land use development planning, park management, etc. Ministry of Natural Resources, Ontario.",
"homepage": "https://www.ontario.ca/page/natural-heritage-information-centre",
"name": "Natural Heritage Information Centre",
"prefix": "r3d100012034",
"synonyms": [
"CIPN",
"Centre d'information sur le patrimoine naturel",
"NHIC"
]
},
"r3d100012036": {
"description": "<<>>!!!>>>",
"homepage": "https://www.phy.ornl.gov/groups/atomic/atomic.html",
"name": "Controlled Fusion Atomic Data Center",
"prefix": "r3d100012036",
"synonyms": [
"Atomic Data for Fusion",
"CFADC"
]
},
"r3d100012037": {
"description": "The BBS is a cooperative effort between the U.S. Geological Survey's Patuxent Wildlife Research Center and Environment Canada's Canadian Wildlife Service to monitor the status and trends of North American bird populations. Following a rigorous protocol, BBS data are collected by thousands of dedicated participants along thousands of randomly established roadside routes throughout the continent. Professional BBS coordinators and data managers work closely with researchers and statisticians to compile and deliver these population data and population trend analyses on more than 400 bird species, for use by conservation managers, scientists, and the general public.",
"homepage": "https://www.pwrc.usgs.gov/bbs/index.cfm",
"name": "North American Breeding Bird Survey",
"prefix": "r3d100012037",
"synonyms": [
"BBS",
"NABBS"
]
},
"r3d100012038": {
"description": "Androgen Receptor Gene Mutations Database is for all who are interested in mutations of the Androgen Receptor Gene. In light of the difficulty in getting new AR mutations published the curator will now accept new mutations that have not been published, provided that it is from a reputable research or clinical laboratory. The curator also strongly suggests that where possible, particularly in the case of new unique mutations that an attempt be made to at least confirm the pathogenicity of the putatative mutation, by showing that the mutation when transfected into a suitable expression system produces a mutant androgen receptor protein.",
"homepage": "https://www.androgendb.mcgill.ca/",
"name": "Androgen Receptor Mutations Database",
"prefix": "r3d100012038",
"synonyms": [
"AR Gene Mutations Database"
],
"xrefs": {
"nif": "0000-02547",
"scr": "006887"
}
},
"r3d100012039": {
"description": "Databases maintained by Ocean Sciences at the Bedford Institute of Oceanography, including temperature-salinity profiles for the NW Atlantic, sea-surface temperature and chlorophyll from satellite, monthly statistics of ocean currents and other moored instruments, and daily temperature observations from coastal thermographs.",
"homepage": "https://www.bio.gc.ca/science/data-donnees/base/index-en.php",
"name": "Bedford Institute of Oceanography - Oceanographic Databases",
"prefix": "r3d100012039",
"synonyms": [
"Institut ocΓ©anographique de Bedford - Bases de donnΓ©es ocΓ©anographiques"
]
},
"r3d100012040": {
"description": "<<>>!!!>>> \nMessage since 2018-06: This virtual host is being reconstructed.",
"homepage": "http://www.casrdb.mcgill.ca",
"name": "CASRdb",
"prefix": "r3d100012040",
"synonyms": [
"Calcium Sensing Receptor Database"
],
"xrefs": {
"nif": "0000-02638",
"scr": "007581"
}
},
"r3d100012041": {
"description": "The Canadian Disaster Database (CDD) contains detailed disaster information on more than 1000 natural, technological and conflict events (excluding war) that have happened since 1900 at home or abroad and that have directly affected Canadians.\nMessage since 2022-01: The Canadian Disaster Database geospatial view is temporarily out of service. We apologize for the inconvenience. The standard view of the database is still available.",
"homepage": "https://www.publicsafety.gc.ca/cnt/rsrcs/cndn-dsstr-dtbs/index-en.aspx",
"name": "Canadian Disaster Database",
"prefix": "r3d100012041",
"synonyms": [
"BDC",
"Base de donnΓ©es canadienne sur les catastrophes",
"CDD"
],
"xrefs": {
"fairsharing": "FAIRsharing.ea287c"
}
},
"r3d100012043": {
"description": "CANSIM is Statistics Canada's key socioeconomic database. Updated daily, CANSIM provides fast and easy access to a large range of the latest statistics available in Canada.\nBefore June 2018, the Data Tables collection was called CANSIM. That name was retired, but the content is still available. CANSIM tables have been given new numbers, but you can still search the Data Tables using the old CANSIM table and vector numbers (or use this Concordance to look up the new table number).",
"homepage": "https://www150.statcan.gc.ca/n1/en/type/data",
"name": "Statistics Canada Data Tables",
"prefix": "r3d100012043",
"synonyms": [
"Statcan Data Tables",
"Statistics Canadaβs main socioeconomic time series database",
"formerly: CANSIM",
"formerly: Canadian Socio-economic Information Management System"
]
},
"r3d100012044": {
"description": "Access analytical research reports and statistical information on citizenship and immigration trends. Research for Citizenship and Immigration Canadaβs strategic research program furthers our understanding of the impact of immigration on Canadian society. Citizenship and Immigration Canadaβs statistical publications provide information on permanent and temporary residents as well as immigration and citizenship programs. Older Research and Statistics reports from Library and Archives Canada. Key findings of external and internal projects related to public opinion.",
"homepage": "https://www.canada.ca/en/immigration-refugees-citizenship/corporate/reports-statistics.html",
"name": "Immigration, Refugees and Citizenship Canada Research and Statistics",
"prefix": "r3d100012044",
"synonyms": [
"CitoyennetΓ© et Immigration Canada Recherche et Statistiques",
"IRCC",
"Immigration, RΓ©fugiΓ©s et CitoyennetΓ© Canada Recherche et Statistiques",
"formerly: Citizenship and Immigration Canada Research and Statistics",
"formerly: CIC"
]
},
"r3d100012045": {
"description": "Databank of Official Statistics on QuΓ©bec. A collaborative effort involving partner departments and agencies under the coordination of the Institut de la statistique du QuΓ©bec.",
"homepage": "https://bdso.gouv.qc.ca/pls/ken/Ken211_Page_Accu.page_accu",
"name": "Databank of Official Statistics on Quebec",
"prefix": "r3d100012045",
"synonyms": [
"BDSO",
"Banque de donnΓ©es des statistiques officielles sur le QuΓ©bec"
]
},
"r3d100012046": {
"description": "The name Earth Online derives from ESA's Earthnet programme. Earthnet prepares and attracts new ESA Earth Observation missions by setting the international cooperation scheme, preparing the basic infrastructure, building the scientific and application Community and competency in Europe to define and set-up own European Programmes in consultation with member states.\nEarth Online is the entry point for scientific-technical information on Earth Observation activities by the European Space Agency (ESA). The web portal provides a vast amount of content, grown and collected over more than a decade:\nDetailed technical information on Earth Observation (EO) missions;\nSatellites and sensors; EO data products & services;\nOnline resources such as catalogues and library;\nApplications of satellite data;\nAccess to promotional satellite imagery.\nAfter 10 years of operations on distinct sites, the two principal portals of ESA Earth Observation - Earth Online (earth.esa.int) and the Principal Investigator's Portal (eopi.esa.int) have moved to a new platform. ESA's technical and scientific earth observation user communities will from now on be served from a single portal, providing a modern and easy-to-use interface to our services and data.",
"homepage": "https://earth.esa.int/eogateway/",
"name": "ESA Earth Online",
"prefix": "r3d100012046",
"synonyms": [
"EO Data",
"Earth Online"
]
},
"r3d100012051": {
"description": "This database and dataset collection is part of the Institutional Repository of San Ignacio de Loyola University.\nThe institutional repository of the Universidad San Ignacio de Loyola houses the academic papers of our study center and allows free access to them by researchers and the community in general, in addition to the exchange of information with all entities that produce Similar contents. Books, magazines, teaching materials, theses, files and databases, among others, are combined in a single space freely available.",
"homepage": "https://repositorio.usil.edu.pe/home",
"name": "Repositorio Institucional USIL",
"prefix": "r3d100012051",
"synonyms": [
"Archivos de Datos y Programas",
"Repositorio de la Universidad San Ignacio de Loyola"
],
"xrefs": {
"opendoar": "3128",
"roar": "11444"
}
},
"r3d100012052": {
"description": "The Cancer Immunome Database (TCIA) provides results of comprehensive immunogenomic analyses of next generation sequencing data (NGS) data for 20 solid cancers from The Cancer Genome Atlas (TCGA) and other datasource. The Cancer Immunome Atlas (TCIA) was developed and is maintained at the Division of Bioinformatics (ICBI). The database can be queried for the gene expression of specific immune-related gene sets, cellular composition of immune infiltrates (characterized using gene set enrichment analyses and deconvolution), neoantigens and cancer-germline antigens, HLA types, and tumor heterogeneity (estimated from cancer cell fractions). Moreover it provides survival analyses for different types immunological parameters.\nTCIA will be constantly updated with new data and results.",
"homepage": "https://tcia.at/home",
"name": "The Cancer Immunome Atlas",
"prefix": "r3d100012052",
"synonyms": [
"TCIA",
"The Cancer Immunome Database",
"The Cancer Immunome Database"
],
"xrefs": {
"scr": "014508"
}
},
"r3d100012053": {
"description": "<<>>!!!>>>",
"homepage": "http://opendata.uit.no/",
"name": "UiT Open Research Data Dataverse",
"prefix": "r3d100012053"
},
"r3d100012054": {
"description": "The Berlin-Brandenburg Academy of Sciences and Humanities (BBAW) is a CLARIN partner institution and has been an officially certified CLARIN service center since June 20th, 2013. The CLARIN center at the BBAW focuses on historical text corpora (predominantly provided by the 'Deutsches Textarchiv'/German Text Archive, DTA) as well as on lexical resources (e.g. dictionaries provided by the 'Digitales WΓΆrterbuch der Deutschen Sprache'/Digital Dictionary of the German Language, DWDS).",
"homepage": "https://clarin.bbaw.de",
"name": "CLARIN service center of the Zentrum Sprache at the BBAW",
"prefix": "r3d100012054",
"synonyms": [
"CLARIN Center BBAW",
"CLARIN-Servicezentrum am Zentrum Sprache der BBAW"
]
},
"r3d100012058": {
"description": "BExIS is the online data repository and information system of the Biodiversity Exploratories Project (BE). The BE is a German network of biodiversity related working groups from areas such as vegetation and soil science, zoology and forestry. Up to three years after data acquisition, the data use is restricted to members of the BE. Thereafter, the data is usually public available (https://www.bexis.uni-jena.de/ddm/publicsearch/index).",
"homepage": "https://www.bexis.uni-jena.de/",
"name": "Biodiversity Exploratories Information System",
"prefix": "r3d100012058",
"synonyms": [
"BExIS"
],
"xrefs": {
"fairsharing": "FAIRsharing.6AmTXC"
}
},
"r3d100012059": {
"description": "In response to emerging pathogens, LabKey launched the Open Research Portal in 2016 to help facilitate collaborative research. It was initially created as a platform for investigators to make Zika research data, commentary and results publicly available in real-time. It now includes other viruses like SARS-CoV-2 where there is a compelling need for real-time data sharing.\nProjects are freely available to researchers. If you are interested in sharing real-time data through the portal, please contact LabKey to get started.",
"homepage": "https://openresearch.labkey.com/project/home/begin.view",
"name": "LabKey Open Research Portal",
"prefix": "r3d100012059",
"synonyms": [
"formerly: Zika Open-Research Portal"
]
},
"r3d100012060": {
"description": "The Wilson Center Digital Archive contains once-secret documents from governments all across the globe, uncovering new sources and providing fresh insights into the history of international relations and diplomacy. It contains newly declassified historical materials from archives around the worldβmuch of it in translation and including diplomatic cables, high level correspondence, meeting minutes and more. It collects the research of three Wilson Center projects which focus on the interrelated histories of the Cold War, Korea, and Nuclear Proliferation.",
"homepage": "https://digitalarchive.wilsoncenter.org/",
"name": "Wilson Center Digital Archive",
"prefix": "r3d100012060"
},
"r3d100012061": {
"description": "The NCI's Genomic Data Commons (GDC) provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine. \nThe GDC obtains validated datasets from NCI programs in which the strategies for tissue collection couples quantity with high quality.\nTools are provided to guide data submissions by researchers and institutions.",
"homepage": "https://portal.gdc.cancer.gov/",
"name": "Genomic Data Commons",
"prefix": "r3d100012061",
"synonyms": [
"GDC",
"Genomic Data Commons Data Portal"
],
"xrefs": {
"fairsharing": "FAIRsharing.RyVjoS",
"scr": "014514"
}
},
"r3d100012062": {
"description": "SAGE is a data and research platform that enables the secondary use of data related to child and youth development, health and well-being. It currently contains research data, and at a later stage we aim to also house administrative and community service delivery data. Technical infrastructure and governance processes are in place to ensure ethical use and the privacy of participants. \nThis dataverse provides metadata for the various data holdings available in SAGE (Secondary Analysis to Generate Evidence), a research data repository based in Edmonton Alberta and an intiative of PolicyWise for Children & Families. In general, SAGE contains data holdings too sensitive for open access. Each study lists a security level which indicates the procedure required to access the data.",
"homepage": "https://borealisdata.ca/dataverse/SAGE",
"name": "Secondary Analysis to Generate Evidence (SAGE) Dataverse",
"prefix": "r3d100012062",
"synonyms": [
"SAGE",
"Secondary Analysis to Generate Evidence"
]
},
"r3d100012064": {
"description": "The University of Reading Research Data Archive (the Archive) is a multidisciplinary online service for the registration, preservation and publication of research datasets produced or collected at the University of Reading.",
"homepage": "https://researchdata.reading.ac.uk/",
"name": "University of Reading Research Data Archive",
"prefix": "r3d100012064"
},
"r3d100012065": {
"description": "The data in the U of Mβs Clinical Data Repository comes from the electronic health records (EHRs) of more than 2 million patients seen at 8 hospitals and more than 40 clinics. For each patient, data is available regarding the patient's demographics (age, gender, language, etc.), medical history, problem list, allergies, immunizations, outpatient vitals, diagnoses, procedures, medications, lab tests, visit locations, providers, provider specialties, and more.",
"homepage": "https://www.ctsi.umn.edu/researcher-resources/clinical-data-repository",
"name": "Clinical data repository",
"prefix": "r3d100012065",
"synonyms": [
"CDR",
"CDW",
"Clinical Data Warehouse"
]
},
"r3d100012066": {
"description": "The Shuttle Radar Topography Mission, which flew aboard NASA's Space Shuttle Endeavour during an 11-day mission in 2000, made the first near-global topographical map of Earth, collecting data on nearly 80 percent of Earth's land surfaces. \n\n The instrument's design was essentially a modified version of the earlier Shuttle Imaging Radar instruments with a second antenna added to allow for topographic mapping using a technique similar to stereo photography.",
"homepage": "https://www.earthdata.nasa.gov/sensors/srtm",
"name": "Shuttle Radar Topography Mission",
"prefix": "r3d100012066",
"synonyms": [
"SRTM"
]
},
"r3d100012067": {
"description": "AlgaeBase is a database of information on algae that includes terrestrial, marine and freshwater organisms. At present, the data for the marine algae, particularly seaweeds, are the most complete.",
"homepage": "https://www.algaebase.org/",
"name": "AlgaeBase",
"prefix": "r3d100012067"
},
"r3d100012068": {
"description": "CORD is Cranfield University's research data repository, for secure preservation of institutional research data outputs. Cranfield is an exclusively postgraduate university that is a global leader for transformational research in technology and management. We are focused on the specialist themes of aerospace, defence and security, energy and power, environment and agrifood, manufacturing, transport systems, and water. The Cranfield School of Management is world leader in management education and research.",
"homepage": "https://cord.cranfield.ac.uk/",
"name": "Cranfield Online Research Data",
"prefix": "r3d100012068",
"synonyms": [
"CORD"
]
},
"r3d100012069": {
"description": "This database will provide a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets. Top-down proteomics is a method of protein identification that uses an ion trapping mass spectrometer to store an isolated protein ion for mass measurement and tandem mass spectrometry analysis.",
"homepage": "http://repository.topdownproteomics.org/",
"name": "Top Down Proteomics Repository",
"prefix": "r3d100012069",
"synonyms": [
"Proteoform Atlas",
"TDPR"
]
},
"r3d100012071": {
"description": "Open Core Data is a data infrastructure focused on making data from scientific continental and ocean drilling projects semantically discoverable, persistent, citable, and approachable to maximize their utility to present and future geoscience researchers.",
"homepage": "https://opencoredata.org/",
"name": "Open Core Data",
"prefix": "r3d100012071",
"synonyms": [
"OCD"
]
},
"r3d100012072": {
"description": "In order to control access to the experimental data obtained at the ILL in a coherent and secure fashion, the ILL has recently developed a single portal for consulting, downloading and managing your data. Here βdataβ is understood to mean raw data (i.e. numor files), processed data, and meta-data (e.g. log files or βlogsβ).",
"homepage": "https://www.ill.eu/users/user-guide/after-your-experiment/data-management#c8867",
"name": "ILL Data Portal",
"prefix": "r3d100012072",
"synonyms": [
"Institut Laue-Langevin Data Portal"
]
},
"r3d100012074": {
"description": "BindingDB is a public, web-accessible knowledgebase of measured binding affinities, focusing chiefly on the interactions of proteins considered to be candidate drug-targets with ligands that are small, drug-like molecules. BindingDB supports medicinal chemistry and drug discovery via literature awareness and development of structure-activity relations (SAR and QSAR); validation of computational chemistry and molecular modeling approaches such as docking, scoring and free energy methods; chemical biology and chemical genomics; and basic studies of the physical chemistry of molecular recognition. BindingDB also includes a small collection of host-guest binding data of interest to chemists studying supramolecular systems.\nThe data collection derives from a variety of measurement techniques, including enzyme inhibition and kinetics, isothermal titration calorimetry, NMR, and radioligand and competition assays. BindingDB includes data extracted from the literature and from US Patents by the BindingDB project, selected PubChem confirmatory BioAssays, and ChEMBL entries for which a well defined protein target (\"TARGET_TYPE='PROTEIN'\") is provided.",
"homepage": "https://bindingdb.org/bind/index.jsp",
"name": "BindingDB",
"prefix": "r3d100012074",
"synonyms": [
"BDB",
"The Binding Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.3b36hk",
"nif": "0000-02603",
"scr": "000390"
}
},
"r3d100012075": {
"description": "D-PLACE contains cultural, linguistic, environmental and geographic information for over 1400 human βsocietiesβ. A βsocietyβ in D-PLACE represents a group of people in a particular locality, who often share a language and cultural identity. All cultural descriptions are tagged with the date to which they refer and with the ethnographic sources that provided the descriptions. The majority of the cultural descriptions in D-PLACE are based on ethnographic work carried out in the 19th and early-20th centuries (pre-1950).",
"homepage": "https://d-place.org",
"name": "D-PLACE",
"prefix": "r3d100012075",
"synonyms": [
"Database of Places, Language, Culture and Environment"
]
},
"r3d100012076": {
"description": "MaxQB stores and displays collections of large proteomics projects and allows joint analysis and comparison. As a first dataset is contains proteome data of 11 different human cell lines. The 11 cell line proteomes together identify proteins expressed from more than half of all human genes. For each protein of interest, expression levels estimated by label-free quantification can be visualized across the cell lines. Similarly, the expression rank order and estimated amount of each protein within each proteome are plotted.",
"homepage": "http://maxqb.biochem.mpg.de/mxdb/",
"name": "The MaxQuant DataBase",
"prefix": "r3d100012076",
"synonyms": [
"MaxQB"
]
},
"r3d100012077": {
"description": "Citrination is the premier open database and analytics platform for the world's material and chemical information. Here you can find tabulated materials property data, that users have contributed or Citrine has automatically extracted from literature.",
"homepage": "https://www.citrination.com/",
"name": "Citrination",
"prefix": "r3d100012077",
"xrefs": {
"fairsharing": "FAIRsharing.x6y19r"
}
},
"r3d100012078": {
"description": "The Sol Genomics Network (SGN) is a clade-oriented database dedicated to the biology of the Solanaceae family which includes a large number of closely related and many agronomically important species such as tomato, potato, tobacco, eggplant, pepper, and the ornamental Petunia hybrida.\nSGN is part of the International Solanaceae Initiative (SOL), which has the long-term goal of creating a network of resources and information to address key questions in plant adaptation and diversification",
"homepage": "https://solgenomics.net/",
"name": "SOL Genomics Network",
"prefix": "r3d100012078",
"synonyms": [
"SGN",
"Solanaceae Genomics Network"
],
"xrefs": {
"fairsharing": "FAIRsharing.3zqvaf",
"nlx": "89764",
"scr": "004933"
}
},
"r3d100012079": {
"description": "The CPTAC Data Portal is the centralized repository for the dissemination of proteomic data collected by the Proteome Characterization Centers (PCCs) for the CPTAC program. The portal also hosts analyses of the mass spectrometry data (mapping of spectra to peptide sequences and protein identification) from the PCCs and from a CPTAC-sponsored common data analysis pipeline (CDAP).",
"homepage": "https://cptac-data-portal.georgetown.edu/cptac/aboutData/show?scope=about",
"name": "Clinical Proteomic Tumor Analysis Consortium Data Portal",
"prefix": "r3d100012079",
"synonyms": [
"CPTAC Data Portal"
]
},
"r3d100012080": {
"description": "The Materials Data Facility (MDF) is set of data services built specifically to support materials science researchers. MDF consists of two synergistic services, data publication and data discovery (in development). The production-ready data publication service offers a scalable repository where materials scientists can publish, preserve, and share research data. The repository provides a focal point for the materials community, enabling publication and discovery of materials data of all sizes.",
"homepage": "https://www.materialsdatafacility.org/",
"name": "Materials Data Facility",
"prefix": "r3d100012080",
"synonyms": [
"MDF"
]
},
"r3d100012081": {
"description": "<<>>!!!>>> GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts. GOBASE is currently expanding to include information on representative bacteria that are thought to be specifically related to the bacterial ancestors of mitochondria and chloroplasts",
"name": "GOBASE",
"prefix": "r3d100012081",
"synonyms": [
"The Organelle Genome Database"
],
"xrefs": {
"nif": "0000-02917",
"scr": "007692"
}
},
"r3d100012083": {
"description": "Ocean Tracking Network (OTN) deploys Canadian, state of the art acoustic receivers and oceanographic monitoring equipment in key ocean locations. These are being used to document the movements and survival of marine animals carrying acoustic tags and to document how both are influenced by oceanographic conditions.",
"homepage": "https://oceantrackingnetwork.org/",
"name": "Ocean Tracking Network",
"prefix": "r3d100012083",
"synonyms": [
"OTN"
]
},
"r3d100012084": {
"description": "<<>>!!!>>>",
"homepage": "https://www.pahdb.mcgill.ca",
"name": "Phenylalanine Hydroxylase Locus Knowledgebase",
"prefix": "r3d100012084",
"synonyms": [
"PAHdb"
],
"xrefs": {
"scr": "013381"
}
},
"r3d100012085": {
"description": "<<>>!!!>>>\nhttps://megasun.bch.umontreal.ca/pepdb/pepdb.html",
"name": "Protist EST Program Database",
"prefix": "r3d100012085",
"synonyms": [
"PEP Database",
"PEPdb",
"TBestDB"
],
"xrefs": {
"scr": "007962"
}
},
"r3d100012086": {
"description": "The Pseudomonas Genome Database collaborates with an international panel of expert Pseudomonas researchers to provide high quality updates to the PAO1 genome annotation and make cutting edge genome analysis data available.",
"homepage": "https://www.pseudomonas.com/",
"name": "Pseudomonas Genome DB",
"prefix": "r3d100012086",
"synonyms": [
"PGD",
"Pseudocap",
"Pseudomonas Genome Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.mn5m1p",
"miriam": "00000180",
"nif": "0000-03369",
"scr": "006590"
}
},
"r3d100012087": {
"description": "A primary source for cross-nationally comparable statistics on education, science and technology, culture, and communication for more than 200 countries and territories.",
"homepage": "http://data.uis.unesco.org/",
"name": "UNESCO Institute for Statistics, Data Centre",
"prefix": "r3d100012087",
"synonyms": [
"ISU Centre de donnΓ©es",
"Institut de statistique de l'UNESCO, Centre de donnΓ©es",
"UIS Data Centre",
"UIS.stat"
]
},
"r3d100012088": {
"description": "Databases of viral genomic information (genes, gene families, and genomes), and software to perform comparative genomics analyses",
"homepage": "https://4virology.net/",
"name": "Viral Bioinformatics Resource Center",
"prefix": "r3d100012088",
"synonyms": [
"VBRC"
],
"xrefs": {
"nif": "0000-03632",
"scr": "005971"
}
},
"r3d100012089": {
"description": "CCCma has developed a number of climate models. These are used to study climate change and variability, and to understand the various processes which govern the climate system. They are also used to make quantitative projections of future long-term climate change (given various greenhouse gas and aerosol forcing scenarios), and increasingly to make initialized climate predictions on time scales ranging from seasons to decades. A brief description of these models and their corresponding references can be found: https://www.canada.ca/en/environment-climate-change/services/climate-change/science-research-data/modeling-projections-analysis/centre-modelling-analysis/models.html",
"homepage": "https://www.canada.ca/en/environment-climate-change/services/climate-change/science-research-data/modeling-projections-analysis/centre-modelling-analysis.html",
"name": "Canadian Centre for Climate Modelling and Analysis",
"prefix": "r3d100012089",
"synonyms": [
"CCCma",
"CCmaC",
"Centre canadien de la modΓ©lisation et de l'analyse climatique"
]
},
"r3d100012090": {
"description": "The CCDS is an interface for distributing climate change information. The goals of CCDS are to: Support climate change impact and adaptation research in Canada and other countries; Support stakeholders requiring scenario information for decision making and policy development. Provide access to Canadian research on the development of scenarios and adaptation research.",
"homepage": "https://climate-scenarios.canada.ca/?page=main",
"name": "Canadian Climate Data and Scenarios",
"prefix": "r3d100012090",
"synonyms": [
"CCDS",
"DSCC",
"DonnΓ©es et scΓ©narios climatiques canadiens"
]
},
"r3d100012092": {
"description": "The Autism Chromosome Rearrangement Database is a collection of hand curated breakpoints and other genomic features, related to autism, taken from publicly available literature: databases and unpublished data. The database is continuously updated with information from in-house experimental data as well as data from published research studies.",
"homepage": "http://projects.tcag.ca/autism/",
"name": "Autism Chromosome Rearrangement Database",
"prefix": "r3d100012092",
"synonyms": [
"ACRD"
],
"xrefs": {
"fairsharing": "FAIRsharing.ac329k",
"nif": "0000-00239",
"scr": "006474"
}
},
"r3d100012093": {
"description": "The Cystic Fibrosis Mutation Database (CFTR1) was initiated by the Cystic Fibrosis Genetic Analysis Consortium in 1989 to increase and facilitate communications among CF researchers, and is maintained by the Cystic Fibrosis Centre at the Hospital for Sick Children in Toronto. The specific aim of the database is to provide up to date information about individual mutations in the CFTR gene. In a major upgrade in 2010, all known CFTR mutations and sequence variants have been converted to the standard nomenclature recommended by the Human Genome Variation Society.",
"homepage": "http://www.genet.sickkids.on.ca/cftr/app",
"name": "Cystic Fibrosis Mutation Database",
"prefix": "r3d100012093",
"synonyms": [
"CFMDB",
"CFTR1"
],
"xrefs": {
"nif": "0000-21105",
"scr": "000685"
}
},
"r3d100012094": {
"description": "This web site provides adjusted and homogenized climate data for many climatological stations in Canada. These data were created for use in climate research including climate change studies. They incorporate a number of adjustments applied to the original station data to address shifts due to changes in instruments and in observing procedures. Sometimes the observations from several stations were joined to generate a long time series. The adjusted and homogenized data are provided for four climate elements: surface air temperature, precipitation, surface pressure, and surface wind speed.",
"homepage": "https://www.canada.ca/en/environment-climate-change/services/climate-change/science-research-data/climate-trends-variability/adjusted-homogenized-canadian-data.html",
"name": "Adjusted and Homogenized Canadian Climate Data",
"prefix": "r3d100012094",
"synonyms": [
"AHCCD",
"DCCAH",
"DonnΓ©es Climatiques Canadiennes AjustΓ©es et HomogΓ©nΓ©isΓ©es"
]
},
"r3d100012095": {
"description": "The RAM Legacy Stock Assessment Database is a compilation of stock assessment results for commercially exploited marine populations from around the world. The recently updated database offers many graphical and analytic tools to explore the data, as well as new data sets including; assessments from N.W. Africa, assessments from the Mediterranean Sea, assessments from Chile, data sets on Pacific salmon. The database is seeking collaborators to cover parts of the world that we are missing.",
"homepage": "http://ramlegacy.org/",
"name": "RAM Legacy Stock Assessment Database",
"prefix": "r3d100012095"
},
"r3d100012097": {
"description": "The Large Fire Database (LFDB) is a compilation of forest fire data from all Canadian agencies, including provinces, territories, and Parks Canada. The data set includes only fires greater than 200 hectares in final size; these represent only a few percent of all fires but account for most of the area burned (usually more than 97%). Therefore, the LFDB can be used for spatial and temporal analyses of landscape-scale fire impacts. For information on smaller fires (up to 200 ha in final size), please contact individual fire agencies. Links to other agencies can be found through the Canadian Interagency Forest Fire Centre (CIFFC).",
"homepage": "https://cwfis.cfs.nrcan.gc.ca/home",
"name": "Canadian Wildland Fire Information System",
"prefix": "r3d100012097",
"synonyms": [
"CWFIS",
"SCIFV",
"Système canadien d'information sur les feux de végétation"
]
},
"r3d100012100": {
"description": "<<>>!!!>>>",
"homepage": "http://ec.gc.ca/eau-water/default.asp?lang=En&n=ED7C2D33-1",
"name": "Water use data",
"prefix": "r3d100012100",
"synonyms": [
"EnquΓͺte sur l'eau potable et les eaux usΓ©es des municipalitΓ©s",
"Municipal Water and Wastewater Survey",
"Utilisation municipale de l'eau",
"WMMS"
]
},
"r3d100012101": {
"description": "The University Information System RUSSIA (UIS RUSSIA) is a mutual project of Research Computing Center and Economic Faculty at Lomonosov Moscow State University. It was introduced in 2000 and has been designed as a digital library for research and educational purposes, primarily in the fields of economic and social sciences. Since then it was maintained to meet the growing interest and challenges of the Russian universities and educational community.\nStarting from 2003 our development team concentrated on statistical databases to build an infrastructure for educational courses, to assist broad Russian social and economic studies from regional to local and down to household level. Today profound knowledge of statistical data and ability to implement advanced modern methods of applied analysis are expected from successful university graduates and are in high demand among new specialists, particularly in economics, public administration and related areas.",
"homepage": "https://uisrussia.msu.ru/",
"name": "University Information System RUSSIA",
"prefix": "r3d100012101",
"synonyms": [
"Databases and analytical publications",
"UIS RUSSIA"
]
},
"r3d100012102": {
"description": "NAKALA is a repository dedicated to SSH research data in France. Given its generalist and multi-disciplinary nature, all types of data are accepted, although certain formats are recommended to ensure longterm data preservation. It has been developed and is hosted by Huma-Num, the French national research infrastructure for digital humanities.",
"homepage": "https://www.nakala.fr",
"name": "NAKALA",
"prefix": "r3d100012102",
"xrefs": {
"issn": "2495-8972"
}
},
"r3d100012103": {
"description": "The National Collaborative on Childhood Obesity Research (NCCOR) brings together four of the nation's leading research funders β the Centers for Disease Control and Prevention (CDC), the National Institutes of Health (NIH), the Robert Wood Johnson Foundation (RWJF), and the U.S. Department of Agriculture (USDA) β to address the problem of childhood obesity in America.\nThe Tools of the NCCOR are: Catalogue of Surveillance Systems, Measures Registry and Registry of Studies.",
"homepage": "https://www.nccor.org/",
"name": "NCCOR",
"prefix": "r3d100012103",
"synonyms": [
"National Collaborative on Childhood Obesity Research"
],
"xrefs": {
"scr": "019150"
}
},
"r3d100012104": {
"description": "One of the worldβs largest banks of biological, psychosocial and clinical data on people suffering from mental health problems. The Signature center systematically collects biological, psychosocial and clinical indicators from patients admitted to the psychiatric emergency and at four points throughout their journey in the hospital: upon arrival to the emergency room (state of crisis), at the end of their hospital stay, as well as at the beginning and the end of outpatient treatment. For all hospital clients who agree to participate, blood specimens are collected for the purpose of measuring metabolic, genetic, toxic and infectious biomarkers, while saliva samples are collected to measure sex hormones and hair samples are collected to measure stress hormones. Questionnaire has been selected to cover important dimensional aspects of mental illness such as Behaviour and Cognition (Psychosis, Depression, Anxiety, Impulsiveness, Aggression, Suicide, Addiction, Sleep),Socio-demographic Profile (Spiritual beliefs, Social functioning, Childhood experiences, Demographic, Family background) and Medical Data (Medication, Diagnosis, Long-term health, RAMQ data).\nOn 2016, May there are more than 1150 participants and 400 for the longitudinal Follow-Up",
"homepage": "https://www.banquesignature.ca/en/",
"name": "Signature Bank",
"prefix": "r3d100012104",
"synonyms": [
"Banque Signature"
]
},
"r3d100012108": {
"description": "mdw Repository provides researchers with a robust infrastructure for research data management and ensures accessibility of research data during and after completion of research projects, thus, providing a quality boost to contemporary and future research.",
"homepage": "https://www.mdw.ac.at/repository/",
"name": "mdw Repository",
"prefix": "r3d100012108",
"xrefs": {
"roar": "11574"
}
},
"r3d100012109": {
"description": "<<>>!!!>>> The Amsterdam cohort study (ACS) on human immunodeficiency virus (HIV) infection and AIDS among homosexual men started in 1984 and was expanded to include drug users in 1985. Thus far, about 2100 homosexual men and 1630 (injecting) drug users have been included of whom approximately 700 homosexual men and 550 drug users are still in active follow-up. Every 3-6 months participants complete a standardized questionnaire to obtain medical, epidemiological and social scientific information and undergo a medical examination. In addition, they have blood drawn for virological and immunological tests and storage.",
"homepage": "https://www.cohortstudies.nl/",
"name": "Amsterdam Cohort Studies on HIV infection and AIDS",
"prefix": "r3d100012109",
"synonyms": [
"ACS"
]
},
"r3d100012110": {
"description": "The FigShare service for University of Auckland, New Zealand was launched in January 2015 and allows researchers to store, share and publish research data. It helps the research data to be accessible by storing Metadata alongside datasets. Additionally, every uploaded item recieves a Digital Object identifier (DOI), which allows the data to be cited. If there are any ethical or copyright concerns about publishing a certain dataset, it is possible to publish the metadata associated with the dataset to help discoverability while sharing the data itself via a private channel through manual approval.",
"homepage": "https://auckland.figshare.com/",
"name": "University of Auckland Data Repository",
"prefix": "r3d100012110"
},
"r3d100012112": {
"description": "The Cellular Phenotype database stores data derived from high-throughput phenotypic studies and it is being developed as part of the Systems Microscopy Network of Excellence project.\nThe aim of the Cellular Phenotype database is to provide easy access to phenotypic data and facilitate the integration of independent phenotypic studies.\nThrough its interface, users can search for a gene of interest, or a collection of genes, and retrieve the loss-of-function phenotypes observed, in human cells, by suppressing the expression of the selected gene(s), through RNA interference (RNAi), across independent phenotypic studies.\nSimilarly, users can search for a phenotype of interest and retrieve the RNAi reagents that have caused such phenotype and the associated target genes. Information about specific RNAi reagents can also be obtained when searching for a reagent ID.",
"homepage": "https://www.ebi.ac.uk/fg/sym",
"name": "Cellular Phenotype database",
"prefix": "r3d100012112"
},
"r3d100012113": {
"description": "Using a combination of remote sensing data and ground observations as inputs, CHC scientists have developed rainfall estimation techniques and other resources to support drought monitoring and predict crop performance in parts of the world vulnerable to crop failure. Policymakers within governments and non-governmental organizations rely on CHC decision-support products to make critical resource allocation decisions. The CHC's scientific focus is \"geospatial hydroclimatology,\" with an emphasis on the early detection and forecasting of hydroclimatic hazards related to food-security droughts and floods. Basic research seeks an improved understanding of the climatic processes that govern drought and flood hazards in FEWS NET countries (https://fews.net/). The CHC develops better techniques, algorithms, and modeling applications in order to use remote sensing and other geospatial data for hazards early warning.",
"homepage": "https://chc.ucsb.edu/data",
"name": "Climate Hazards Center Data Archive",
"prefix": "r3d100012113",
"synonyms": [
"CHC Data Archive"
]
},
"r3d100012114": {
"description": "Chapman University Digital Commons is an open access digital repository and publication platform designed to collect, store, index, and provide access to the scholarly and creative output of Chapman University faculty, students, staff, and affiliates. In it are faculty research papers and books, data sets, outstanding student work, audiovisual materials, images, special collections, and more, all created by members of or owned by Chapman University. The datasets are listed in a separate collection.",
"homepage": "https://digitalcommons.chapman.edu/data.html",
"name": "Chapman University Digital Commons Datasets",
"prefix": "r3d100012114",
"xrefs": {
"issn": "2572-1496"
}
},
"r3d100012115": {
"description": "Satellite observations of sea ice concentration in the Arctic and the Antarctic are the backbone of www.meereisportal.de since its launch in April 2013. Since then, daily maps and data sets are published on the information and data portal. Time series and trends are updated daily, representing the status of the sea ice cover on hemispheres.\nmeereisportal.de/seaiceportal.de was laid out as an open portal and shall serve scientific groups performing research on sea ice as a platform for communicating the results of their research.",
"homepage": "https://www.meereisportal.de/en/",
"name": "Meereis Portal",
"prefix": "r3d100012115",
"synonyms": [
"Sea Ice Portal"
]
},
"r3d100012116": {
"description": "The Comparative Welfare Entitlements Project (CWEP) collects data on institutional features of social insurance programs in 33 countries dating back to the early 1970s. The project extends and updates information collected and published online as CWED by Lyle Scruggs and CWED 2 by Lyle Scruggs, Detlef Jahn, and Kati Kuitto. Data is currently provided for unemployment and sickness insurance benefits as well as for standard and minimum pensions and covers income replacement rates of cash benefits, eligibility criteria and coverage of the programs. Replacement rates are available for ten household types, making CWEP one of the most comprehensive datasets on replacement rates for social insurance programs.",
"homepage": "https://www.cwep.us/",
"name": "Comparative Welfare Entitlements Project Dataset",
"prefix": "r3d100012116",
"synonyms": [
"CWED",
"CWEP"
]
},
"r3d100012117": {
"description": "BrainMaps.org, launched in May 2005, is an interactive multiresolution next-generation brain atlas that is based on over 20 million megapixels of sub-micron resolution, annotated, scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet.\nCurrently featured are complete brain atlas datasets for various species, including Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegicus, and Tyto alba.",
"homepage": "http://www.brainmaps.org/index.php",
"name": "BrainMaps.org",
"prefix": "r3d100012117",
"xrefs": {
"nif": "0000-00093",
"scr": "006878"
}
},
"r3d100012118": {
"description": "eBird is among the worldβs largest biodiversity-related science projects, with more than 1 billion records, more than 100 million bird sightings contributed annually by eBirders around the world, and an average participation growth rate of approximately 20% year over year. A collaborative enterprise with hundreds of partner organizations, thousands of regional experts, and hundreds of thousands of users, eBird is managed by the Cornell Lab of Ornithology.\n\neBird data document bird distribution, abundance, habitat use, and trends through checklist data collected within a simple, scientific framework. Birders enter when, where, and how they went birding, and then fill out a checklist of all the birds seen and heard during the outing. Data can be accessed from the Science tab on the website.",
"homepage": "https://ebird.org/home",
"name": "eBird",
"prefix": "r3d100012118"
},
"r3d100012119": {
"description": "The Online Data Portal (ODP) is an evolving project to support collaborative river restoration projects, such as the TRRP. The goal is to provide a centralized clearing house of documents and data for program partners, stakeholders, and the public.\nThe functionality and data holdings will continue to be expanded over the next few years. The ability to store Data Packages is new as of Fall 2011 and holdings should expand substantially in the months afterward. A project to scan many older documents also began in December 2011. Simple time-series datasets have long been stored in the ODP, but holdings of these data are likely to increase as TRRP implements an upcoming Data Management and Utility Plan. Major upgrades to the Interactive Map are expected to start in winter and spring of 2012. The long term vision is that many data resources will be accessible both by text searches and via the Interactive Map.\nThe ODP will be available for use by other river restoration programs.\nODP is followed by TRRP DataPort.",
"homepage": "https://www.trrp.net/dataport/",
"name": "Trinity River Restoration Program DataPort",
"prefix": "r3d100012119",
"synonyms": [
"TRRP DataPort",
"formerly: TRRP ODP",
"formerly: Trinity River Restoration Program Online Data Portal"
]
},
"r3d100012120": {
"description": "The Allen Brain Atlas provides a unique online public resource integrating extensive gene expression data, connectivity data and neuroanatomical information with powerful search and viewing tools for the adult and developing brain in mouse, human and non-human primate",
"homepage": "https://portal.brain-map.org/",
"name": "Allen Brain Map",
"prefix": "r3d100012120",
"synonyms": [
"Allen Brain Atlas",
"Data Portal"
],
"xrefs": {
"fairsharing": "FAIRsharing.618298",
"scr": "017001"
}
},
"r3d100012121": {
"description": "The Square Kilometre Array (SKA) is a radio telescope with around one million square metres of collecting area, designed to study the Universe with unprecedented speed and sensitivity.\nThe SKA is not a single telescope, but a collection of various types of antennas, called an array, to be spread over long distances.\nThe SKA will be used to answer fundamental questions of science and about the laws of nature, such as: how did the Universe, and the stars and galaxies contained in it, form and evolve? Was Einsteinβs theory of relativity correct? What is the nature of βdark matterβ and βdark energyβ? What is the origin of cosmic magnetism? Is there life somewhere else in the Universe?",
"homepage": "https://www.skatelescope.org/ska-site-raw-data/",
"name": "Square Kilometre Array Telescope",
"prefix": "r3d100012121",
"synonyms": [
"SKA Telescope"
]
},
"r3d100012122": {
"description": "<<>>!!!>>>",
"homepage": "http://exac.broadinstitute.org/",
"name": "ExAC Browser",
"prefix": "r3d100012122",
"synonyms": [
"Exome Aggregation Consortium Browser"
],
"xrefs": {
"biodbcore": "001219",
"nlx": "158505",
"omics": "14216",
"scr": "004068"
}
},
"r3d100012123": {
"description": "Bridges is Monash University's repository for research data, collections, and research activity outputs. It is also the home of the University's online archive of PhD and Masters by Research theses.",
"homepage": "https://bridges.monash.edu/",
"name": "Monash Bridges",
"prefix": "r3d100012123",
"synonyms": [
"monash.figshare (formerly)"
]
},
"r3d100012124": {
"description": "The figshare service for the University of Sheffield allows researchers to store, share and publish research data. It helps the research data to be accessible by storing Metadata alongside datasets. Additionally, every uploaded item receives a Digital Object identifier (DOI), which allows the data to be citable and sustainable. If there are any ethical or copyright concerns about publishing a certain dataset, it is possible to publish the metadata associated with the dataset to help discoverability while sharing the data itself via a private channel through manual approval.",
"homepage": "https://orda.shef.ac.uk/",
"name": "ORDA - The University of Sheffield Research Data Catalogue and Repository",
"prefix": "r3d100012124",
"synonyms": [
"Discover research from The University of Sheffield"
]
},
"r3d100012125": {
"description": "WISER is a self-service platform for data of the Global Networks of Isotopes in Precipitation (GNIP) and Rivers (GNIR), hosted within the IAEA's repository for technical resources (NUCLEUS).\nGNIP in WISER currently contains over 130,000 records, and stable isotopes are current to the end of 2013, and will be updated as verified data comes in. Parts of the GNIR water isotope data is online as well (synoptic/time series), although we are still in process of verifying and completing GNIR data uploads and for other isotopic parameters over the next year. Check back occasionally for GNIR updates. Tritium data after 2009 is in the process of being updated in the next year.\nWhen accessing WISER through the URL https://nucleus.iaea.org/wiser, you will be forwarded to the NUCLEUS log-in page. After entering your user credentials and validation, you will be forwarded to the WISER landing page.",
"homepage": "https://nucleus.iaea.org/wiser",
"name": "Water Isotope System for Data Analysis, Visualization and Electronic Retrieval",
"prefix": "r3d100012125",
"synonyms": [
"WISER"
]
},
"r3d100012129": {
"description": "<<>>!!!>>>",
"homepage": "http://www.jbldesign.com/jmogil/enter.html",
"name": "Pain Genes Database",
"prefix": "r3d100012129",
"synonyms": [
"Pain Genes DB",
"PainGenesdb"
],
"xrefs": {
"nlx": "77039",
"scr": "004771"
}
},
"r3d100012131": {
"description": "The Northern Ontario Plant Database (NOPD) is a website that provides free public access to records of herbarium specimens housed in northern Ontario educational and government institutions. A herbarium is an archival collection of plants that have been pressed, dried, mounted, and labelled. It also provides up-to-date and accurate information on the flora of northern Ontario.",
"homepage": "http://www.northernontarioflora.ca/",
"name": "Northern Ontario Plant Database",
"prefix": "r3d100012131",
"synonyms": [
"NOPD"
]
},
"r3d100012132": {
"description": "Reptiles and amphibians are collectively known as herpetofauna and are a unique part of Ontarioβs biodiversity. An earlier atlas, called the Ontario Herpetofaunal Summary Atlas, provided extensive information about where many of the provinceβs reptiles and amphibians occurred.\nThe Atlas is transitioning into a new era, with Ontario Nature wrapping-up the data collection phase of this project as of December 1, 2019. Now that we have discontinued our app and online form, we encourage you to continue submitting any future observations through the βHerps of Ontarioβ project (https://www.inaturalist.org/projects/herps-of-ontario) on iNaturalist or directly to the Natural Heritage Information Centre (nhicrequests@ontario.ca) for species at risk. To learn more about the transition, read our blog (https://ontarionature.org/ontario-reptile-and-amphibian-atlas-changes-blog/)",
"homepage": "https://ontarionature.org/programs/community-science/reptile-amphibian-atlas/",
"name": "Ontario Reptile and Amphibian Atlas",
"prefix": "r3d100012132"
},
"r3d100012133": {
"description": "The goals of FMGP are to: \n(i) sequence complete mitochondrial genomes from all major fungal lineages, \n(ii) infer a robust fungal phylogeny, \n(iii) define the origin of the fungi, their protistan ancestors, and their specific phylogenetic link to the animals, \n(iv) investigate mitochondrial gene expression, introns, RNAse P RNA structures, mobile elements.",
"homepage": "https://megasun.bch.umontreal.ca/People/lang/FMGP/FMGP.html",
"name": "Fungal Mitochondrial Genome Project",
"prefix": "r3d100012133",
"synonyms": [
"FMGP"
]
},
"r3d100012135": {
"description": "A curated database of mutations and polymorphisms associated with Lafora Progressive Myoclonus Epilepsy. The Lafora progressive myoclonus epilepsy mutation and polymorphism database is a collection of hand curated mutation and polymorphism data for the EPM2A and EPM2B (NHLRC1) from publicly available literature: databases and unpublished data. The database is continuously updated with information from in-house experimental data as well as data from published research studies.",
"homepage": "http://projects.tcag.ca/lafora",
"name": "The Lafora Progressive Myoclonus Epilepsy Mutation and Polymorphism Database",
"prefix": "r3d100012135",
"synonyms": [
"The Lafora Database"
]
},
"r3d100012136": {
"description": "<<>>!!!>>>",
"homepage": "http://www.chr7.org/",
"name": "The Chromosome 7 Annotation Project",
"prefix": "r3d100012136",
"xrefs": {
"fairsharing": "FAIRsharing.rkq0vj",
"nif": "0000-03550",
"scr": "007134"
}
},
"r3d100012138": {
"description": "On February 24, 2000, Terra began collecting what will ultimately become a new, 15-year global data set on which to base scientific investigations about our complex home planet. Together with the entire fleet of EOS spacecraft, Terra is helping scientists unravel the mysteries of climate and environmental change. TERRA's data collection instruments include: \nAdvanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER), \nClouds and the Earth's Radiant Energy System (CERES), \nMulti-angle Imaging Spectro-Radiometer (MISR), \nModerate-resolution Imaging Spectroradiometer (MODIS), \nMeasurement of Pollution in the Troposphere (MOPITT)",
"homepage": "https://terra.nasa.gov/",
"name": "TERRA",
"prefix": "r3d100012138",
"synonyms": [
"Terra: The EOS Flagship"
]
},
"r3d100012139": {
"description": "The Centre for Applied Genomics hosts a variety of databases related to ongoing supported projects. Curation of these databases is performed in-house by TCAG Bioinformatics staff. The Autism Chromosome Rearrangement Database, The Cystic Fibrosis Mutation Database, TThe Lafora Progressive Myoclonus Epilepsy Mutation and Polymorphism Database are included. Large Scale Genomics Research resources include, the Database of Genomic Variants, The Chromosome 7 Annotation Project, The Human Genome Segmental Duplication Database, and the Non-Human Segmental Duplication Database",
"homepage": "https://www.tcag.ca/databases/index.html",
"name": "The Centre for Applied Genomics Databases",
"prefix": "r3d100012139",
"synonyms": [
"TCAG Databases"
]
},
"r3d100012140": {
"description": "Brunel Figshare (brunel.figshare.com) is a Data Repository where Brunelβs researchers can deposit their digital Research Data, to make it available in a citable, shareable and discoverable manner.",
"homepage": "https://brunel.figshare.com/",
"name": "Brunel figshare",
"prefix": "r3d100012140",
"synonyms": [
"Brunel research data repository & registry"
]
},
"r3d100012141": {
"description": "Climate4impact: a dedicated interface to ESGF for the climate impact community\nThe portal Climate4impact, part of the ENES Data Infrastructure, provides access to data and quick looks of global and regional climate models and downscaled higher resolution climate data. The portal provides data transformation tooling and mapping & plotting capabilities, guidance, documentation, FAQ and examples.\nThe Climate4Impact portal will be further developed during the IS-ENES3 project (2019-2023)and moved to a different environment. Meanwhile the portal at https://climate4impact.eu will remain available, but no new information or processing options will be included. When the new portal will become available this will be announced on https://is.enes.org/.",
"homepage": "https://climate4impact.eu/impactportal/general/index.jsp",
"name": "climate4impact",
"prefix": "r3d100012141",
"xrefs": {
"fairsharing": "FAIRsharing.30f068"
}
},
"r3d100012143": {
"description": "Loughborough Research Repository is the institutional repository of Loughborough University powered by figshare.",
"homepage": "https://repository.lboro.ac.uk/",
"name": "Loughborough Research Repository",
"prefix": "r3d100012143",
"synonyms": [
"Loughborough University Research Repository",
"formerly: Loughborough Data Repository"
]
},
"r3d100012144": {
"description": "Figshare is the University of Salford Data Repository for archiving and publishing research data, in accordance with EPSRC expectations, and to increase the impact of the research.",
"homepage": "https://salford.figshare.com/",
"name": "University of Salford Data Repository",
"prefix": "r3d100012144"
},
"r3d100012145": {
"description": "melbourne.figshare.com is a specialised service that has been tailored according to specific needs and requirements of the University and our community of researchers. The service offered at the University is free to use, provides 100GB of data, and stores all data on the University's storage system.",
"homepage": "https://melbourne.figshare.com/",
"name": "University of Melbourne data repository",
"prefix": "r3d100012145",
"synonyms": [
"melbourne.figshare.com"
]
},
"r3d100012146": {
"description": "Additionally to the institutional repository, current St. Edward's faculty have the option of uploading their work directly to their own SEU accounts on stedwards.figshare.com. Projects created on Figshare will automatically be published on this website as well. For more information, please see documentation",
"homepage": "https://stedwards.figshare.com/",
"name": "St. Edward's University institutional repository",
"prefix": "r3d100012146",
"synonyms": [
"St. Edwardβs University Figshare"
]
},
"r3d100012147": {
"description": "Researchers at Stockholm University have access to a repository for data through the Figshare Services via su.figshare.com.",
"homepage": "https://su.figshare.com/",
"name": "Stockholm University Figshare Repository",
"prefix": "r3d100012147",
"xrefs": {
"opendoar": "9925"
}
},
"r3d100012148": {
"description": "The University research data repository β BathSPAdata β enables staff to upload their research data into a secure space, and to share this data publicly where appropriate, or where funders or publishers require this as part of their conditions. Resources and toolkits for external use can be made available through this forum, and can be used by Schools, policy makers, business and industry, and the cultural sector.",
"homepage": "https://data.bathspa.ac.uk/",
"name": "Bath Spa University figshare",
"prefix": "r3d100012148",
"synonyms": [
"BathSPAdata"
]
},
"r3d100012149": {
"description": "This site is now made possible by University of Canterbury, New Zealand, and serves as historical repository of collections of files once housed at datacenterhub (without the interactive tools that were available on that site). \nFormer description: \nWe offer a public platform to help researchers organize, share, and explore their research data.\nDataCenterHub provides a simple, standardized yet flexible platform to preserve and share data. In the future, this platform will offer data visualization tools and the ability to compare directly data from different sources.",
"homepage": "https://datacenterhub.org/",
"name": "DataHub",
"prefix": "r3d100012149",
"synonyms": [
"DEEDS DataHub",
"DataCenterHub",
"Digital Environment for Enabling Data-Driven Science DataHub"
]
},
"r3d100012151": {
"description": "GroupLens is a research lab in the Department of Computer Science and Engineering at the University of Minnesota, Twin Cities specializing in recommender systems, online communities, mobile and ubiquitous technologies, digital libraries, and local geographic information systems.",
"homepage": "https://grouplens.org/datasets/",
"name": "Grouplens Datasets",
"prefix": "r3d100012151"
},
"r3d100012152": {
"description": "FooDB is the worldβs largest and most comprehensive resource on food constituents, chemistry and biology. It provides information on both macronutrients and micronutrients, including many of the constituents that give foods their flavor, color, taste, texture and aroma.",
"homepage": "https://foodb.ca/",
"name": "FooDB",
"prefix": "r3d100012152",
"synonyms": [
"Food Database"
]
},
"r3d100012153": {
"description": "Exposome-Explorer is the first database dedicated to biomarkers of exposure to environmental risk factors for diseases. It contains detailed information on the nature of biomarkers, populations and subjects where measured, samples analyzed, methods used for biomarker analyses, concentrations in biospecimens, correlations with external exposure measurements, and biological reproducibility over time.",
"homepage": "http://exposome-explorer.iarc.fr/",
"name": "Exposome-Explorer",
"prefix": "r3d100012153",
"synonyms": [
"Exposome-Explorer database"
]
},
"r3d100012155": {
"description": "ACU Research Bank is the Australian Catholic University's institutional research repository. It serves to collect, preserve, and showcase the research publications and outputs of ACU staff and higher degree students. Where possible and permissible, a full text version of a research output is available as open access.",
"homepage": "https://acuresearchbank.acu.edu.au/",
"name": "ACU Research Bank",
"prefix": "r3d100012155",
"synonyms": [
"Australian Catholic University Research Bank"
]
},
"r3d100012156": {
"description": "The figshare service for The Open University was launched in 2016 and allows researchers to store, share and publish research data. It helps the research data to be accessible by storing metadata alongside datasets. Additionally, every uploaded item receives a Digital Object Identifier (DOI), which allows the data to be citable and sustainable. If there are any ethical or copyright concerns about publishing a certain dataset, it is possible to publish the metadata associated with the dataset to help discoverability while sharing the data itself via a private channel through manual approval.",
"homepage": "https://ordo.open.ac.uk/",
"name": "Open Research Data Online",
"prefix": "r3d100012156",
"synonyms": [
"ORDO",
"The Open University Data Repository"
],
"xrefs": {
"biodbcore": "001689"
}
},
"r3d100012157": {
"description": "Fairdata IDA is a research data storage service that provides secure storage for research data.\nThe Fairdata services are a group of nationally developed Finnish ICT services for managing research data, especially in the later phases of the research life cycle (sharing, publishing, and preserving). Development of research data management infrastructure has been identified as an important step in enabling implementation of the FAIR principles.\nThe Fairdata services are funded by the Finnish Ministry of Education and Culture, and developed and maintained by CSC IT Center for Science. The services consist of the following service components: IDA β Research Data Storage; Etsin β Research Data Finder; Qvain β Research Dataset Metadata Tool; Metax β Metadata Warehouse; AVAA β Dynamic Data Publishing Platform and the Digital Preservation Service for Research Data (including management and packaging). The services also provide means for applying for and granting permits to use restricted access datasets.\nThe service is offered free of charge for its users. The services are available to the research community in accordance with the applicable usage policy. Minedu offers access to research data storage service IDA to Finnish higher education institutions, state research institutes and projects funded by the Academy of Finland. Minedu may also grant separate access or storage capacity to the service. Finnish higher education institutions and research institutes may distribute IDA storage capacity to actors within the Finnish research system, within the limits of their usage shares.\nThe service is intended for storing research data and materials related to it. The data stored in the service is available to all project users. The users mark their data to be persistently stored (βFrozenβ) in the service. All project members may make the βFrozenβ data and related metadata publicly accessible by using the other aforementioned Fairdata services. The data in the service is stored in Finland.\nIDA service stores the data stored by organisations projects continuously or until itβs transferred to digital preservation, provided that the Terms of Use are met. The owners of the data decide on the openness and usage policies for their own data.\nUser organisations are offered support and guidance on using the service.",
"homepage": "https://ida.fairdata.fi/login",
"name": "Fairdata IDA Research Data Storage Service",
"prefix": "r3d100012157",
"synonyms": [
"Fairdata IDA - Tutkimusdatan sΓ€ilytyspalvelu",
"IDA Research Data Storage Service"
]
},
"r3d100012158": {
"description": "Etsin is a research data finder that contains descriptive information β that is, metadata β on research datasets. In the service you can search and find data from various fields of research. A researcher, research group or organisation can use Etsin to publish information on their datasets and offer them for wider use. The metadata contained in Etsin makes it easy for anyone to discover the datasets. Etsin assigns a permanent URN identifier to datasets, making it possible to link to the dataset and gather merit through its publication and use.\nThe metadata enables users to search for datasets and evaluate the potential for reuse. Etsin includes a description of the dataset, keywords and various dataset identifiers. The dataset information includes, for example, its subject, language, author, owner and how it is licensed for reuse. Good description of data plays an important role in its discoverability and visibility. Etsin encourages comprehensive descriptions by adapting a common set of discipline independent metadata fields and by making it easy to enter metadata.\nEtsin only collects metadata on datasets, not the data themselves. Anyone may browse and read the metadata. Etsin can be used with a browser or through an open interface (API). The service is discipline independent and free to use. \nEtsin is a service provided by the Ministry of Education and Culture to actors in the Finnish research system. The service is produced by CSC β IT Center for Science (CSC). Customer service contacts and feedback is available through servicedesk@csc.fi. The service maintenance window is on the fourth Monday of every month between 4 and 6 PM (EET). During that time, the service will be out of use.",
"homepage": "https://etsin.fairdata.fi/",
"name": "Etsin Research Data Finder",
"prefix": "r3d100012158",
"synonyms": [
"Etsin - tutkimusaineistojen hakupalvelu"
]
},
"r3d100012160": {
"description": "The ChemBio Hub vision is to provide the tools that will make it easier for Oxford University scientists to connect with colleagues to improve their research, to satisfy funders that the data they have paid for is being managed according to their policies, and to make new alliances with pharma and biotech partners.\nFunding and development of the ChemBio Hub was ending on the 30th June 2016. Please be reassured that the ChemBio Hub system and all your data will continue to be secured on the SGC servers for the foreseeable future. You can continue to use the services as normal.",
"homepage": "https://www.chembiohub.com/",
"name": "ChemBio Hub",
"prefix": "r3d100012160"
},
"r3d100012161": {
"description": "This data server provides access to the GTC Public Archive. GTC data become public once the proprietary (1 year) is over. The Gran Telescopio CANARIAS (GTC), is a 10.4m telescope with a segmented primary mirror.",
"homepage": "https://gtc.sdc.cab.inta-csic.es/gtc/",
"name": "Gran Telescopio CANARIAS Public Archive",
"prefix": "r3d100012161",
"synonyms": [
"GRANTECAN Archivo de datos",
"GTC Public Archive",
"Gran Telescopio CANARIAS Archivo de datos"
]
},
"r3d100012162": {
"description": "LibraData is a place for UVA researchers to share data publicly. It is UVA's local instance of Dataverse. LibraData is part of the Libra Scholarly Repository suite of services which includes works of UVA scholarship such as articles, books, theses, and data.",
"homepage": "https://dataverse.lib.virginia.edu/",
"name": "LibraData",
"prefix": "r3d100012162",
"synonyms": [
"UVA Dataverse",
"University of Virginia Dataverse"
]
},
"r3d100012163": {
"description": "NASAβs Precipitation Measurement Missions β TRMM and GPM β provide advanced information on rain and snow characteristics and detailed three-dimensional knowledge of precipitation structure within the atmosphere, which help scientists study and understand Earth's water cycle, weather and climate.",
"homepage": "https://gpm.nasa.gov/",
"name": "Precipitation Measurement Missions",
"prefix": "r3d100012163",
"synonyms": [
"NASA Global Precipitation Measurement Missions",
"PMM"
]
},
"r3d100012164": {
"description": "The Global Precipitation Measurement (GPM) mission is an international network of satellites that provide the next-generation global observations of rain and snow. Building upon the success of the Tropical Rainfall Measuring Mission (TRMM), the GPM concept centers on the deployment of a βCoreβ satellite carrying an advanced radar / radiometer system to measure precipitation from space and serve as a reference standard to unify precipitation measurements from a constellation of research and operational satellites.",
"homepage": "https://gpm.nasa.gov/missions/GPM",
"name": "Global Precipitation Measurement",
"prefix": "r3d100012164",
"synonyms": [
"GPM"
]
},
"r3d100012165": {
"description": "The Database explores the interactions of chemicals and proteins. It integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins.",
"homepage": "http://stitch.embl.de/",
"name": "STITCH",
"prefix": "r3d100012165",
"synonyms": [
"Search Tool for Interactions of Chemicals"
],
"xrefs": {
"fairsharing": "FAIRsharing.zhwa8x",
"nif": "0000-03499",
"scr": "007947"
}
},
"r3d100012166": {
"description": "The Database for Hydrological Time Series of Inland Waters (DAHITI) was developed by the Deutsches GeodΓ€tisches Forschungsinstitut der Technischen UniversitΓ€t MΓΌnchen (DGFI-TUM) in 2013. DAHITI provides water level time series of lakes, reservoirs, rivers, and wetlands derived from multi-mission satellite altimetry for hydrological applications. All water level time series are free available for the user community after a short registration process.",
"homepage": "https://dahiti.dgfi.tum.de/en/",
"name": "Database for Hydrological Time Series of Inland Waters",
"prefix": "r3d100012166",
"synonyms": [
"DAHITI"
]
},
"r3d100012167": {
"description": "Sound and Vision has one of the largest audiovisual archives in Europe. The institute manages over 70 percent of the Dutch audiovisual heritage. The collection contains more than a million hours of television, radio, music and film from the beginning in 1898 until today. All programs of the Dutch public broadcasters come in digitally every day. Individuals and institutions entrust their collection to Sound and Vision as well. The institute ensures that the material is optimally preserved for (re)use. Broadcasters, producers and editors use the archive for the creation of new programs. The collection is also used to develop products and services for a wide audience, such as exhibitions, iPhone applications, DVD boxes and various websites.\nThe collection of Sound and Vision contains the complete radio and television archives of the Dutch public broadcasters; films of virtually every leading Dutch documentary maker; newsreels; the national music depot; various audiovisual corporate collections; advertising, radio and video material of cultural and social organizations, of scientific institutes and of all kinds of educational institutions. There are also collections of images and articles from the history of Dutch broadcasting itself, like the elaborate collection of historical television sets.",
"homepage": "https://www.beeldengeluid.nl/en",
"name": "Sound and Vision",
"prefix": "r3d100012167",
"synonyms": [
"Beeld en Geluid"
]
},
"r3d100012168": {
"description": "Patient Reported Outcomes Following Initial treatment and Long term Evaluation of Survivorship (PROFILES)β is a registry for the study of the physical and psychosocial impact of cancer and its treatment from a dynamic, growing population-based cohort of both short and long-term cancer survivors. Researchers from the Netherlands Comprehensive Cancer Centre and Tilburg University in Tilburg, The Netherlands, work together with medical specialists from national hospitals in order to setup different PROFILES studies, collect the necessary data, and present the results in scientific journals and (inter)national conferences.",
"homepage": "https://www.profilesregistry.nl/",
"name": "PROFILES Registry",
"prefix": "r3d100012168"
},
"r3d100012169": {
"description": "NONCODE is an integrated knowledge database dedicated to non-coding RNAs (excluding tRNAs and rRNAs). Now, there are 16 species in NONCODE(human, mouse, cow, rat, chicken, fruitfly, zebrafish, celegans, yeast, Arabidopsis, chimpanzee, gorilla, orangutan, rhesus macaque, opossum and platypus).The source of NONCODE includes literature and other public databases. We searched PubMed using key words βncrnaβ, βnoncodingβ, βnon-codingβ,βno codeβ, βnon-codeβ, βlncrnaβ or βlincrna. We retrieved the new identified lncRNAs and their annotation from the Supplementary Material or web site of these articles. Together with the newest data from Ensembl , RefSeq, lncRNAdb and GENCODE were processed through a standard pipeline for each species.",
"homepage": "http://www.noncode.org/index.php",
"name": "NONCODE",
"prefix": "r3d100012169",
"xrefs": {
"fairsharing": "FAIRsharing.hmb1f4",
"nif": "0000-03195",
"scr": "007822"
}
},
"r3d100012171": {
"description": "The Restriction Enzyme Database is a collection of information about restriction enzymes, methylases, the microorganisms from which they have been isolated, recognition sequences, cleavage sites, methylation specificity, the commercial availability of the enzymes, and references - both published and unpublished observations (dating back to 1952). REBASE is updated daily and is constantly expanding.",
"homepage": "http://rebase.neb.com/rebase/rebase.html",
"name": "REBASE",
"prefix": "r3d100012171",
"synonyms": [
"The Restriction Enzyme Database"
],
"xrefs": {
"nif": "0000-03391",
"scr": "007886"
}
},
"r3d100012173": {
"description": "FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain. The FlyCircuit Database currently contains about 30,000 high resolution 3D brain neural images of the drosophila fruit fly brain that are combined into a neural circuitry network that researchers can use as a blueprint to further explore how the brain of a fruit fly processes external sensory signals (i.e. how vision, hearing, and smell are transmitted to the central nerve system).",
"homepage": "http://www.flycircuit.tw/",
"name": "FlyCircuit",
"prefix": "r3d100012173",
"synonyms": [
"A Database of Drosophila Brain Neurons"
],
"xrefs": {
"nif": "0000-07738",
"scr": "006375"
}
},
"r3d100012174": {
"description": "The GeoPortal.rlp allows the central search and visualization of geo data. \nInside the geo data infrastructure of Rhineland-Palatinate the GeoPortal.rlp inherit the central duty a service orientated branch exchange between user and offerer of geo data. The GeoPortal.rlp establishes the access to geo data over the electronic network.\nThe GeoPortal.rlp was brought on line on January, 8th 2007 for the first time, on February, 2nd 2011 it occured a site-relaunch.",
"homepage": "https://www.geoportal.rlp.de/",
"name": "GeoPortal.rlp",
"prefix": "r3d100012174"
},
"r3d100012176": {
"description": "iDog, an integrated resource for domestic dog (Canis lupus familiaris) and wild canids, provides the worldwide dog research community a variety of data services. This includes Genes, Genomes, SNPs, Breed/Disease Traits, Gene Expressions, Single Cell, Dog-Human Homolog Diseases and Literatures. In addition, iDog provides Online tools for performing genomic data visualization and analyses.",
"homepage": "https://ngdc.cncb.ac.cn/idog/",
"name": "iDog",
"prefix": "r3d100012176",
"synonyms": [
"DoGSD",
"Dog Genome SNP Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.exc0vp"
}
},
"r3d100012177": {
"description": "The JenAge Ageing Factor Database AgeFactDB is aimed at the collection and integration of ageing phenotype and lifespan data. Ageing factors are genes, chemical compounds or other factors such as dietary restriction, for example.\nIn a first step ageing-related data are primarily taken from existing databases. In addition, new ageing-related information is included both by manual and automatic information extraction from the scientific literature.\nBased on a homology analysis, AgeFactDB also includes genes that are homologous to known ageing-related genes. These homologs are considered as candidate or putative ageing-related genes.",
"homepage": "http://agefactdb.jenage.de/",
"name": "JenAge Ageing Factor Database",
"prefix": "r3d100012177",
"synonyms": [
"AgeFactDB"
]
},
"r3d100012178": {
"description": "<<>>!!!>>>",
"homepage": "https://cgap.nci.nih.gov/cgap_mitelman_retire_notice.html",
"name": "Cancer Genome Anatomy Project",
"prefix": "r3d100012178",
"synonyms": [
"CGAP"
],
"xrefs": {
"nif": "0000-30468",
"scr": "003072"
}
},
"r3d100012179": {
"description": "Ag-Analytics is an online open source database of various economic and environmental data. It automates the collection, formatting, and processing of several different commonly used datasets, such as the National Agricultural Statistics Service (NASS), the Agricultural Marketing Service (AMS), Risk Management agency (RMA), the PRISM weather database, and the U.S. Commodity Futures Trading Commission (CFTC). All the data have been cleaned and well-documented to save users the inconvenience of scraping and cleaning the data themselves.",
"homepage": "https://www.analytics.ag/",
"name": "Ag-Analytics",
"prefix": "r3d100012179"
},
"r3d100012181": {
"description": "Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders.",
"homepage": "https://www.braincode.ca/",
"name": "Brain-CODE",
"prefix": "r3d100012181",
"synonyms": [
"Brain-Centre for Ontario Data Exploration"
],
"xrefs": {
"fairsharing": "FAIRsharing.f12f67",
"scr": "015877"
}
},
"r3d100012182": {
"description": "OASIS-3 is the latest release in the Open Access Series of Imaging Studies (OASIS) that aimed at making neuroimaging datasets freely available to the scientific community. By compiling and freely distributing this multi-modal dataset, we hope to facilitate future discoveries in basic and clinical neuroscience. Previously released data for OASIS-Cross-sectional (Marcus et al, 2007) and OASIS-Longitudinal (Marcus et al, 2010) have been utilized for hypothesis driven data analyses, development of neuroanatomical atlases, and development of segmentation algorithms. OASIS-3 is a longitudinal neuroimaging, clinical, cognitive, and biomarker dataset for normal aging and Alzheimerβs Disease.\nThe OASIS datasets hosted by central.xnat.org provide the community with open access to a significant database of neuroimaging and processed imaging data across a broad demographic, cognitive, and genetic spectrum an easily accessible platform for use in neuroimaging, clinical, and cognitive research on normal aging and cognitive decline. All data is available via www.oasis-brains.org.",
"homepage": "https://www.oasis-brains.org/",
"name": "OASIS",
"prefix": "r3d100012182",
"synonyms": [
"Open Access Series of Imaging Studies"
],
"xrefs": {
"nif": "0000-00387",
"scr": "007385"
}
},
"r3d100012183": {
"description": "Collection of various motion capture recordings (walking, dancing, sports, and others) performed by over 140 subjects. The database contains free motions which you can download and use. There is a zip file of all asf/amc's on the FAQs page.",
"homepage": "http://mocap.cs.cmu.edu/",
"name": "CMU Graphics Lab Motion Capture Database",
"prefix": "r3d100012183",
"synonyms": [
"Carnegie Mellon University Motion Capture Database"
]
},
"r3d100012184": {
"description": "With the KIT Whole-Body Human Motion Database, we aim to provide a simple way of sharing high-quality motion capture recordings of human whole-body motion. In addition, with the Motion Annotation Tool (https://motion-annotation.humanoids.kit.edu/ ), we aim to collect a comprehensive set of whole-body motions along with natural language descriptions of these motions (https://motion-annotation.humanoids.kit.edu/dataset/).",
"homepage": "https://motion-database.humanoids.kit.edu/",
"name": "KIT Whole-Body Human Motion Database",
"prefix": "r3d100012184"
},
"r3d100012185": {
"description": "BiRD is a pilot service, run by the library. It allows all researchers at Birkbeck to upload data, and get a DOI. It allows long term storage of Birkbeck's high quality research data, supporting publications.",
"homepage": "https://researchdata.bbk.ac.uk",
"name": "Birkbeck Research Data",
"prefix": "r3d100012185",
"synonyms": [
"BiRD",
"Birkbeck Data Repository"
]
},
"r3d100012186": {
"description": "Silkworm Pathogen Database (SilkPathDB) is a comprehensive resource for studying on pathogens of silkworm, including microsporidia, fungi, bacteria and virus. SilkPathDB provides access to not only genomic data including functional annotation of genes and gene products, but also extensive biological information for gene expression data and corresponding researches. SilkPathDB will be help with researches on pathogens of silkworm as well as other Lepidoptera insects.",
"homepage": "https://silkpathdb.swu.edu.cn/",
"name": "SilkPathDB",
"prefix": "r3d100012186",
"synonyms": [
"A Comprehensive Resource for Silkworm Pathogens",
"Silkworm Pathogen Database"
],
"xrefs": {
"fairsharing": "AIRsharing.801eea"
}
},
"r3d100012187": {
"description": "SilkDB is a database of the integrated genome resource for the silkworm, Bombyx mori. This database provides access to not only genomic data including functional annotation of genes, gene products and chromosomal mapping, but also extensive biological information such as microarray expression data, ESTs and corresponding references. SilkDB will be useful for the silkworm research community as well as comparative genomics",
"homepage": "https://silkdb.bioinfotoolkits.net/",
"name": "SilkDB 3.0",
"prefix": "r3d100012187",
"synonyms": [
"SilkWorm",
"Silkworm Genome Database"
],
"xrefs": {
"nif": "0000-03462",
"scr": "007926"
}
},
"r3d100012188": {
"description": "The Johanna Mestorf Academy provides data from several archaeology related projects. JMA supports open access/open data and open formats. \nThe JMA promotes research and education pertaining to the field of βSocietal, Environmental, Cultural Changeβ (Kiel SECC), which is one of the four research foci of CAU.",
"homepage": "https://www.jma.uni-kiel.de/en/research-projects/data-exchange-platform",
"name": "Research Data Exchange Platform - Johanna Mestorf Academy",
"prefix": "r3d100012188",
"synonyms": [
"Research Data Exchange Platform - JMA"
]
},
"r3d100012189": {
"description": "The Toxin and Toxin Target Database is a unique bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. The focus of the T3DB is on providing mechanisms of toxicity and target proteins for each toxin. This dual nature of the T3DB, in which toxin and toxin target records are interactively linked in both directions, makes it unique from existing databases.",
"homepage": "http://www.t3db.ca/",
"name": "T3DB",
"prefix": "r3d100012189",
"synonyms": [
"Toxic Exposome Database",
"Toxin and Toxin Target Database"
],
"xrefs": {
"nif": "0000-22933",
"omics": "01592",
"scr": "002672"
}
},
"r3d100012190": {
"description": "The ZBW Journal Data Archive is a service for editors of journals in economics and management. The Journal Data Archive offers the possibility for journal authors of papers that contain empirical work, simulations or experimental work to store the data, programs, and other details of computations, to make these files publicly available and to support confirmability and replicability of their published research papers.",
"homepage": "https://journaldata.zbw.eu/",
"name": "ZBW Journal Data Archive",
"prefix": "r3d100012190",
"synonyms": [
"Leibniz Information Centre for Economics Journal Data Archive",
"ZBW JDA"
],
"xrefs": {
"fairsharing": "FAIRsharing.Z1Y4J2"
}
},
"r3d100012191": {
"description": "The CMU Multi-Modal Activity Database (CMU-MMAC) database contains multimodal measures of the human activity of subjects performing the tasks involved in cooking and food preparation. The CMU-MMAC database was collected in Carnegie Mellon's Motion Capture Lab. A kitchen was built and to date twenty-five subjects have been recorded cooking five different recipes: brownies, pizza, sandwich, salad, and scrambled eggs.",
"homepage": "http://kitchen.cs.cmu.edu/",
"name": "Grand Challenge Data Collection",
"prefix": "r3d100012191",
"synonyms": [
"CMU-MMAC Database",
"Carnegie Mellon University Multi-Modal Activity Database"
]
},
"r3d100012192": {
"description": "This Web resource provides data and information relevant to SARS coronavirus. It includes links to the most recent sequence data and publications, to other SARS related resources, and a pre-computed alignment of genome sequences from various isolates. \nIn order to provide free and easy access to genome and protein sequences and associated metadata from the SARS-CoV-2, we created a dedicated Severe acute respiratory syndrome coronavirus 2 data hub.\nYou can access the Results Table on SARS-CoV-2 data hub, by pressing \"RefSeq genomes\", \"nucleotide\" or \"protein\" links on announcement banner located on NCBI home page, in \"Find data\" navigation menu or using \"Up-to-date SARS-CoV-2\" shortcut button in \"Search by virus\" form. \nSARS-CoV-2 sequences is part of NCBI Virus https://www.re3data.org/repository/r3d100014322",
"homepage": "https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Severe%20acute%20respiratory%20syndrome-related%20coronavirus,%20taxid:694009",
"name": "SARS-CoV-2 Data Hub",
"prefix": "r3d100012192",
"synonyms": [
"NCBI SARS-CoV",
"SARS-CoV",
"Severe Acute Respiratory Syndrome Coronavirus"
]
},
"r3d100012193": {
"description": "The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research. The key components are: (1) a molecular atlas of gene expression for the developing organs of the GenitoUrinary (GU) tract; (2) a high resolution molecular anatomy that highlights development of the GU system; (3) mouse strains to facilitate developmental and functional studies within the GU system; (4) tutorials describing GU organogenesis; and (5) rapid access to primary data via the GUDMAP database.",
"homepage": "https://www.gudmap.org/index.html",
"name": "GUDMAP",
"prefix": "r3d100012193",
"synonyms": [
"GenitoUrinary Development Molecular Anatomy Project"
],
"xrefs": {
"nif": "0000-33426",
"nlx": "152871",
"scr": "001554"
}
},
"r3d100012194": {
"description": "IoT Lab is a research platform exploring the potential of crowdsourcing and Internet of Things for multidisciplinary research with more end-user interactions. \nIoT Lab is a European Research project which aims at researching the potential of crowdsourcing to extend IoT testbed infrastructure for multidisciplinary experiments with more end-user interactions. It addresses topics such as:\n- Crowdsourcing mechanisms and tools;\n- βCrowdsourcing-driven researchβ;\n- Virtualization of crowdsourcing and testbeds;\n- Ubiquitous Interconnection and Cloudification of testbeds;\n- Testbed as a Service platform;\n- Multidisciplinary experiments;\n- End-user and societal value creation;\n- Privacy and personal data protection.",
"homepage": "http://ckan.iotlab.eu/",
"name": "CKAN @ IoT Lab",
"prefix": "r3d100012194"
},
"r3d100012195": {
"description": "<<>>!!!>>>",
"homepage": "http://bioinformatics.charite.de/supertarget/",
"name": "SuperTarget",
"prefix": "r3d100012195",
"xrefs": {
"fairsharing": "FAIRsharing.se4zhk",
"nif": "0000-00416",
"omics": "01591",
"scr": "002696"
}
},
"r3d100012196": {
"description": "The iBeetle-Base stores gene related information for all genes of the official gene set (red box). Among others, RNA and protein sequences can be downloaded and links lead to the respective annotation in the genome browser. Further, the Drosophila orthologs are displayed including links to FlyBase. Wherever available, the phenotypic data gathered in the iBeetle screen is displayed below the gene information in separate sections for the pupal and larval screening parts (yellow box).",
"homepage": "https://ibeetle-base.uni-goettingen.de/",
"name": "ibeetle",
"prefix": "r3d100012196",
"synonyms": [
"A database of Tribolium RNAi phenotypes"
]
},
"r3d100012197": {
"description": "Phenol-Explorer is the first comprehensive database on polyphenol content in foods",
"homepage": "http://phenol-explorer.eu/",
"name": "Phenol-Explorer",
"prefix": "r3d100012197",
"synonyms": [
"Database on Polyphenol Content in Foods"
],
"xrefs": {
"nif": "0000-32996",
"scr": "008647"
}
},
"r3d100012198": {
"description": "sciencedata.dk is a research data store provided by DTU, the Danish Technical University, specifically aimed at researchers and scientists at Danish academic institutions.\nThe service is intended for working with and sharing active research data as well as for safekeeping of large datasets. The data can be accessed and manipulated via a web interface, synchronization clients, file transfer clients or the command line. The service is built on and with open-source software from the ground up: FreeBSD, ZFS, Apache, PHP, ownCloud/Nextcloud. DTU is actively engaged in community efforts on developing research-specific functionality for data stores. Our servers are attached directly to the 10-Gigabit backbone of \"Forskningsnettet\" (the National Research and Education Network of Denmark) - implying that up and download speed from Danish academic institutions is in principle comparable to those of an external USB hard drive. Data store for research data allowing private sharing and sharing via links / persistent URLs.",
"homepage": "https://sciencedata.dk",
"name": "ScienceData",
"prefix": "r3d100012198",
"synonyms": [
"Data store by DTU - the Technical University of Denmark",
"DeiC data (formerly)"
]
},
"r3d100012199": {
"description": "The European Data Portal harvests the metadata of Public Sector Information available on public data portals across European countries. Information regarding the provision of data and the benefits of re-using data is also included.",
"homepage": "https://data.europa.eu/en",
"name": "European Data Portal",
"prefix": "r3d100012199",
"synonyms": [
"EDP",
"EuropΓ€isches Datenportal",
"Portail europΓ©en de donnΓ©es",
"formerly: publicdata.eu"
],
"xrefs": {
"fairsharing.legacy": "2940"
}
},
"r3d100012200": {
"description": "IBICT is providing a research data repository that takes care of long-term preservation and archiving of good practices, so that researchers can share, maintain control and get recognition for your data. The repository supports research data sharing with Quote persistent data, allowing them to be played. The Dataverse is a large open data repository of all disciplines, created by the Institute for Quantitative Social Science at Harvard University. IBICT the Dataverse repository provides a means available for free to deposit and find specific data sets stored by employees of the institutions participating in the Cariniana network.",
"homepage": "https://repositoriopesquisas.ibict.br/",
"name": "IBICT Cariniana Dataverse Network",
"prefix": "r3d100012200",
"synonyms": [
"Instituto Brasileiro de Informação em CiΓͺncia e Tecnologia Cariniana Dataverse Network"
]
},
"r3d100012201": {
"description": "The Historical Atlas of Sydney contains digital versions of maps and associated documents.",
"homepage": "https://archives.cityofsydney.nsw.gov.au/pages/historicalatlas",
"name": "Historical Atlas of Sydney",
"prefix": "r3d100012201",
"synonyms": [
"City of Sydney - Archives & History Ressources"
]
},
"r3d100012203": {
"description": "ICOS Carbon Portal is the data portal of the Integrated Carbon Observation System. It provides observational data from the state of the carbon cycle in Europe and the world.\nThe Carbon Portal is the data center of the ICOS infrastructure. ICOS will collect greenhouse gas concentration and fluxes observations from three separate networks, all these observations are carried out to support research to help us understand how the Earthβs greenhouse gas balance works, because there are still many and large uncertainties!",
"homepage": "https://data.icos-cp.eu/portal/",
"name": "ICOS Carbon Portal",
"prefix": "r3d100012203",
"synonyms": [
"Integrated Carbon Observation System"
],
"xrefs": {
"fairsharing": "FAIRsharing.p9SgT0"
}
},
"r3d100012204": {
"description": "<<>>!!!>>> - eir fields, maintained by the FlyReactome staff.",
"homepage": "https://fly.reactome.org/",
"name": "FlyReactome",
"prefix": "r3d100012204",
"synonyms": [
"a curated knowledgebase of drosophila melanogaster pathways"
],
"xrefs": {
"omics": "02692"
}
},
"r3d100012205": {
"description": "HITRAN is an acronym for high-resolution transmission molecular absorption database. \nThe HITRAN compilation of the SAO (HIgh resolution TRANmission molecular absorption database) is used for predicting and simulating transmission and emission of light in atmospheres. It is the world-standard database in molecular spectroscopy. The journal article describing it is the most cited reference in the geosciences. There are presently about 5000 HITRAN users world-wide.\nIts associated database HITEMP (high-temperature spectroscopic absorption parameters) is accessible by the HITRAN website.",
"homepage": "https://hitran.org/",
"name": "HITRAN online",
"prefix": "r3d100012205",
"synonyms": [
"HITRAN database",
"HIgh resolution TRANsmission molecular absorption database"
]
},
"r3d100012206": {
"description": "The ICTWSS database covers four key elements of modern political economies: trade unionism, wage setting, state intervention and social pacts. The database contains annual data for all OECD and EU member states - Australia; Austria; Belgium; Bulgaria; Canada; Chile, Cyprus, the Czech Republic; Denmark; Estonia; Germany; Greece; Finland; France; Hungary; Iceland; Ireland; Israel, Italy; Japan; Korea, Latvia; Lithuania; Luxembourg; Malta; Mexico; the Netherlands; New Zealand; Norway; Poland; Portugal; Romania; Spain; Slovakia; Slovenia; Sweden; Switzerland; Turkey; the United Kingdom; and the United States β with some additional data for emerging economies Brazil; China; India; Indonesia; Russia; and South Africa; and it runs from 1960 till 2014.",
"homepage": "http://uva-aias.net/en/ictwss",
"name": "ICTWSS database",
"prefix": "r3d100012206",
"synonyms": [
"Database on Institutional Characteristics of Trade Unions, Wage Setting, State Intervention and Social Pacts in 51 countries between 1960 and 2014"
]
},
"r3d100012207": {
"description": "The vision of the JaLTER is to provide scientific knowledge which contributes to conservation, advancement and sustainability of environment, ecosystem services, productivity and biodiversity for a society by conducting long-term and interdisciplinary research in ecological science including human dimensions. The JaLTER is closely linked with the International Long-Term Ecological Research Network (ILTER Network).",
"homepage": "https://db.cger.nies.go.jp/JaLTER/",
"name": "JaLTER MetaCat Service",
"prefix": "r3d100012207",
"synonyms": [
"JaLTER Database Systems",
"Japan Long-Term Ecological Research Network MetaCat Service"
]
},
"r3d100012208": {
"description": "KLIPS (Korean Labor & Income Panel Study) is a longitudinal survey of the labor market / income activities of households and individuals residing in urban areas. The 1st Wave of the KLIPS was launched by the KLI (Korea Labor Institute) in 1998, amid an unprecedented economic crisis and labor market turmoil.",
"homepage": "https://www.kli.re.kr/klips_eng#secondPage",
"name": "Korean Labor & Income Panel Study",
"prefix": "r3d100012208",
"synonyms": [
"KLIPS"
]
},
"r3d100012211": {
"description": "Sydney has a constantly updated bank of information for historians, researchers and demographers.",
"homepage": "https://www.cityofsydney.nsw.gov.au/learn/research-and-statistics",
"name": "City of Sydney - Research and statistics",
"prefix": "r3d100012211"
},
"r3d100012212": {
"description": "Sydneyβs history is all around us. Discover the rich, vivid history of Sydney from early Aboriginal life through to the modern global city. Our history and archives teams are here to help.",
"homepage": "https://www.cityofsydney.nsw.gov.au/library-information-services/access-open-data",
"name": "City of Sydney - Historians and archivists",
"prefix": "r3d100012212"
},
"r3d100012213": {
"description": "The FREEBIRD website aims to facilitate data sharing in the area of injury and emergency research in a timely and responsible manner. It has been launched by providing open access to anonymised data on over 30,000 injured patients (the CRASH-1 and CRASH-2 trials).",
"homepage": "https://freebird.lshtm.ac.uk/home/",
"name": "freeBIRD",
"prefix": "r3d100012213",
"synonyms": [
"free Bank of Injury and Emergency Research Data"
]
},
"r3d100012214": {
"description": "MTD is focused on mammalian transcriptomes with a current version that contains data from humans, mice, rats and pigs. Regarding the core features, the MTD browses genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exons, transcripts, and genes by integrating them into a genome browser. We developed a novel nomenclature for each transcript that considers its genomic position and transcriptional features.",
"homepage": "https://ngdc.cncb.ac.cn/mtd/index.php",
"name": "Mammalian Transcriptomic Database",
"prefix": "r3d100012214",
"synonyms": [
"MTD"
],
"xrefs": {
"fairsharing.legacy": "2909",
"omics": "11215"
}
},
"r3d100012215": {
"description": "The PRO-ACT platform houses the largest ALS clinical trials dataset ever created. It is a powerful tool for biomedical researchers, statisticians, clinicians, or anyone else interested in \"Big Data.\" PRO-ACT merges data from existing public and private clinical trials, generating an invaluable resource for the design of future ALS clinical trials. The database will also contribute to the identification of unique observations, novel correlations, and patterns of ALS disease progression, as well as a variety of still unconsidered analyses. More than 600,000 people around them world are battling ALS. The disease strikes indiscriminately, and typically patients will die within 2-5 years following diagnosis. Currently, there are no effective treatments or a cure for ALS. Users of PRO-ACT are helping to accelerate the discovery, development, and delivery of ALS treatments, which will provide hope to patients and their families.",
"homepage": "https://ncri1.partners.org/ProACT/",
"name": "PRO-ACT",
"prefix": "r3d100012215",
"synonyms": [
"Pooled Resource Open-Access ALS Clinical Trials Database"
]
},
"r3d100012216": {
"description": "<<>>!!!>>>",
"homepage": "http://pr.cs.cornell.edu/humanactivities/data.php",
"name": "Cornell Activity Datasets: CAD-60 & CAD-120",
"prefix": "r3d100012216"
},
"r3d100012217": {
"description": "Among the basic tasks of WDC for Geophysics, Beijing there is collection, handling and storage of science data and giving access to it for usage both in science research and study process. That includes remote access to own information resources for the scientists from the universities and institutions.",
"homepage": "http://www.geophys.ac.cn/",
"name": "WDC for geophysics, Beijing",
"prefix": "r3d100012217",
"synonyms": [
"WDCδΈε½ε°ηη©ηε¦η§δΈεΏ"
]
},
"r3d100012218": {
"description": "Global Change Research Data Publishing and Repository (GCdataPR) is an open data infrastructure on earth science, particular on the global environmental changes. The GCdataPRβ management policies following the international common understanding to the data sharing principles and guidelines is the key to make the qualified data publishing and sharing smoothly and successfully. The data management policies including dataset submission for publishing policy, peer review policy data quality control policy data long-term preservation policy, data sharing policy, 10% rule for identify original dataset policy, claim discovery with both data and paper policy, and data service statistics policy.",
"homepage": "https://www.geodoi.ac.cn/WebEn/Default.aspx",
"name": "Global Change Research Data Publishing and Repository",
"prefix": "r3d100012218",
"synonyms": [
"GCdataPR",
"PRdataGC"
]
},
"r3d100012220": {
"description": "The USGS Alaska Region has the largest geographic extent of the seven regional units within the USGS and represents a dynamic landscape of great natural wonder. It is a transforming landscape shaped by volcanoes, earthquakes, major rivers, and glaciers and a strategic landscape of yet untapped mineral and energy resources. The Region conducts research to help inform management of the extensive national parks and wildlife refuges of the far north and the international birds, fish, and marine mammals that migrate to these lands and waters; informs national Arctic energy policy through research on the National Petroleum Reserve-Alaska and the U.S. Outer Continental Shelf; and provides science to understand, help respond to and mitigate impacts from natural hazards.\nThis work is accomplished in part by the Region's two Science Centers headquartered in Anchorage, the Alaska Science Center and the Volcano Science Center.",
"homepage": "https://www.usgs.gov/centers/alaska-science-center",
"name": "Alaska Science Center",
"prefix": "r3d100012220",
"synonyms": [
"ASC"
]
},
"r3d100012221": {
"description": "The Cross-National Time-Series Data Archive (CNTS) was initiated by Arthur S. Banks in 1968 with the aim of assembling, in machine readable, longitudinal format, certain of the aggregate data resources of The Statesmanβs Yearbook. The CNTS offers a listing of international and national country-data facts. The dataset contains statistical information on a range of countries, with data entries ranging from 1815 to the present.",
"homepage": "https://www.cntsdata.com/",
"name": "Cross-National Time-Series Data Archive",
"prefix": "r3d100012221",
"synonyms": [
"CNTS Data Archive"
],
"xrefs": {
"issn": "2412-8082"
}
},
"r3d100012222": {
"description": "The RΓ©sif-EPOS Seismic data repository hosts and distributes seismological data from permanent and temporary seismic networks operated all over the world by French research institutions and international partners, to support research on source processes and imaging of the Earth's interior at all scales. RΓ©sif-EPOS (French seismologic and geodetic network) is a French national equipment for the observation and understanding of the solid Earth.",
"homepage": "https://seismology.resif.fr/",
"name": "RΓ©sif Seismological Data Portal",
"prefix": "r3d100012222",
"synonyms": [
"RΓ©seau sismologique et gΓ©odΓ©sique francais"
],
"xrefs": {
"fairsharing": "FAIRsharing.3a9142"
}
},
"r3d100012223": {
"description": "Over 1000 detailed, fully referenced and verified datasets for steels, aluminium and titanium alloys, cast irons/steels, weld metals. Materials can be searched according to a number of different criteria. Initial search results are presented in the form of a table from which they can be selected for presentation in form of detailed report or for comparison overview (up to 5 materials). In addition to material information and values of properties/parameters, images of microstructure, specimens and those of stress-strain, stress- and strain-life curves (if available) can be reviewed as well.",
"homepage": "https://www.matdat.com/",
"name": "MatDat.com",
"prefix": "r3d100012223",
"synonyms": [
"Material Properties Database and Estimation Tools"
]
},
"r3d100012224": {
"description": "MorphoSource is a data repository specialized for 3D representing physical objects used in research in education (e.g., from museum or laboratory collections). It allows researchers and museum collection staff to store and organize, share, and distribute their own 3d data. Furthermore any registered user can immediately search for and download 3d morphological data sets that have been made accessible through the consent of data authors.",
"homepage": "https://www.morphosource.org/",
"name": "MorphoSource",
"prefix": "r3d100012224",
"xrefs": {
"fairsharing": "FAIRsharing.7mFpMg"
}
},
"r3d100012225": {
"description": "The aim of the EPPO Global Database is to provide in a single portal for all pest-specific information that has been produced or collected by EPPO. The full database is available via the Internet, but when no Internet connection is available a subset of the database called βEPPO GD Desktopβ can be run as a software (now replacing PQR).",
"homepage": "https://gd.eppo.int/",
"name": "EPPO Global Database",
"prefix": "r3d100012225",
"synonyms": [
"European and Mediterranean Plant Protection Organization Global Database",
"containing \"Pitt Quantum Repository\""
]
},
"r3d100012226": {
"description": "EM-DAT is a global database on natural and technological disasters, containing essential core data on the occurrence and effects of more than 26,000 disasters in the world, from 1900 to present. EM-DAT provides geographical, temporal, human and economic information on disasters at the country level. The database is compiled from various sources, including UN agencies, non-governmental organisations, insurance companies, research institutes and press agencies.",
"homepage": "https://www.emdat.be/",
"name": "EM-DAT",
"prefix": "r3d100012226",
"synonyms": [
"Emergency Events Database",
"The International Disaster Database"
]
},
"r3d100012227": {
"description": "ResearchGate is a network where 15+ million scientists and researchers worldwide connect to share their work. Researchers can upload data of any type and receive DOIs, detailed statistics and real-time feedback.\nIn Data discovery Section of ResearchGate you can explore the added datasets.",
"homepage": "https://www.researchgate.net/search/data",
"name": "ResearchGate Data",
"prefix": "r3d100012227",
"xrefs": {
"nlx": "143849",
"scr": "006505"
}
},
"r3d100012228": {
"description": "<<>>!!!>>> The current successor is https://www.lovd.nl/USH1C. <<< The database contains all the variants published as pathogenic mutations in the international literature up to November 2007. In addition, unpublished Usher mutations and non-pathogenic variants from the laboratory of Montpellier have been included.",
"homepage": "http://www.umd.be/USH1C/",
"name": "The USH1C mutations database",
"prefix": "r3d100012228"
},
"r3d100012230": {
"description": "<<>>!!!<<<",
"homepage": "https://reactome.org/content/detail/R-GGA-70171",
"name": "GallusReactome",
"prefix": "r3d100012230"
},
"r3d100012231": {
"description": "The main objective of our research is to address the theoretical and empirical problem of how political institutions of high quality can be created and maintained. A second objective is to study the effects of Quality of Government on a number of policy areas, such as health, the environment, social policy, and poverty.",
"homepage": "https://www.gu.se/en/quality-government/qog-data",
"name": "Quality of Government Institute's Data",
"prefix": "r3d100012231",
"synonyms": [
"QoG Institute's data"
]
},
"r3d100012232": {
"description": "Surrey Research Insight (SRI) is an open access resource that hosts, preserves and disseminates the full text of scholarly papers produced by members of the University of Surrey. Its main purpose is to help Surrey authors make their research more widely known; their ideas and findings readily accessible; and their papers more frequently read and cited.\nSurrey Research Insight (formerly Surrey Scholarship Online) was developed in line with the Open Access Initiative, promoting free access to scholarship for the benefit of authors and scholars. It is one of many open access repositories around the world that operate on agreed standards to ensure wide and timely dissemination of research.",
"homepage": "https://openresearch.surrey.ac.uk/esploro/",
"name": "Surrey Research Insight",
"prefix": "r3d100012232",
"synonyms": [
"SRI",
"University of Surrey Open Research repository"
],
"xrefs": {
"opendoar": "305",
"roar": "1240"
}
},
"r3d100012233": {
"description": "Here you will find data on the estimated stock of social capital in each US county for the years 1990, 1997, 2005, 2009, and 2014\nPLEASE NOTE: The data are presented \"as is\" without any implied guarantees for accuracy, and that there are slight differences between 1990/1997 and 2005 as a result of the switch from the SIC to the NAICS codes.",
"homepage": "https://aese.psu.edu/nercrd/community/social-capital-resources",
"name": "County-level measure of social capital",
"prefix": "r3d100012233"
},
"r3d100012234": {
"description": "High spatial resolution, contemporary data on human population distributions are a prerequisite for the accurate measurement of the impacts of population growth, for monitoring changes and for planning interventions. The WorldPop project aims to meet these needs through the provision of detailed and open access population distribution datasets built using transparent approaches.\nThe WorldPop project was initiated in October 2013 to combine the AfriPop, AsiaPop and AmeriPop population mapping projects. It aims to provide an open access archive of spatial demographic datasets for Central and South America, Africa and Asia to support development, disaster response and health applications. The methods used are designed with full open access and operational application in mind, using transparent, fully documented and peer-reviewed methods to produce easily updatable maps with accompanying metadata and measures of uncertainty.",
"homepage": "https://www.worldpop.org/",
"name": "Worldpop",
"prefix": "r3d100012234"
},
"r3d100012235": {
"description": "The YODA Project is an effort by a group of academically-based clinical researchers to facilitate access to participant-level clinical research data and/or comprehensive reports of clinical research, such as full Clinical Study Reports (CSRs), a level of detail not customarily found in journal publications, with the aim of promoting scientific research that may advance science or lead to improvements in individual and public health and healthcare delivery. The YODA Project is guided by the following core principles, which reflect the overall mission of the project to promote open science by:\nPromoting the sharing of clinical research data to advance science and improve public health and healthcare,\nPromoting the responsible conduct of research,\nEnsuring good stewardship of clinical research data, and\nProtecting the rights of research participants",
"homepage": "https://yoda.yale.edu/",
"name": "YODA Project",
"prefix": "r3d100012235",
"synonyms": [
"Yale University Open Data Access"
],
"xrefs": {
"fairsharing": "FAIRsharing.b6b091",
"scr": "022761"
}
},
"r3d100012236": {
"description": "The Agricultural and Environmental Data Archive (AEDA) is the direct result of a project managed by the Freshwater Biological Association in partnership with the Centre for e-Research at King's College London, and funded by the Department for the Environment, Food & Rural Affairs (Defra). This project ran from January 2011 until December 2014 and was called the DTC Archive Project, because it was initially related to the Demonstration Test Catchments Platform developed by Defra. The archive was also designed to hold data from the GHG R&D Platform (www.ghgplatform.org.uk). After the DTC Archive Project was completed the finished archive was renamed as AEDA to reflect it's broader remit to archive data from any and all agricultural and environmental research activities.",
"homepage": "http://www.environmentdata.org/",
"name": "Agricultural and Environmental Data Archive",
"prefix": "r3d100012236",
"synonyms": [
"AEDA"
]
},
"r3d100012238": {
"description": "Maddison's work contains the Project Dataset with estimates of GDP per capita for all countries in the world between 1820 and 2010 in a format amenable to analysis in R. \nThe database was last updated in January 2013. The update incorporates much of the latest research in the field, and presents new estimates of economic growth in the world economic between AD 1 and 2010\nThe Maddison Project database presented builts on Angus Maddison's original dataset. The original estimates are kept intact, and only revised or adjusted when there is more and better information available. Angus Maddison's unaltered final dataset remains available on the Original Maddison Homepage https://www.rug.nl/ggdc/historicaldevelopment/maddison/original-maddison",
"homepage": "https://www.rug.nl/ggdc/historicaldevelopment/maddison/",
"name": "Maddison Project",
"prefix": "r3d100012238",
"synonyms": [
"Maddison Historical Statistics"
]
},
"r3d100012239": {
"description": "The Supreme Court Database is the definitive source for researchers, students, journalists, and citizens interested in the U.S. Supreme Court. The Database contains over two hundred pieces of information about each case decided by the Court between the 1791 and 2015 terms. Examples include the identity of the court whose decision the Supreme Court reviewed, the parties to the suit, the legal provisions considered in the case, and the votes of the Justices. The project started with Spaeth's original database. \nThe analysis tools allow you to select and summarize cases from the Modern or Legacy Database based on your needs.",
"homepage": "http://supremecourtdatabase.org/",
"name": "Supreme Court Database",
"prefix": "r3d100012239",
"synonyms": [
"SCDB",
"U.S. Supreme Court Database"
]
},
"r3d100012240": {
"description": "The World Christian Database provides comprehensive statistical information on world religions, Christian denominations, and people groups.\nThe World Christian Database transforms current religious statistics into a real-time analysis tool that takes just minutes to perform even detailed research. This comprehensive database brings together a fully updated and cohesive religious data set with a world-class database architecture. The result is a simple, yet powerful database tool that enables users to customize reports and download data for in use in charts, tables, and graphs",
"homepage": "https://worldchristiandatabase.org/",
"name": "World Christian Database",
"prefix": "r3d100012240",
"synonyms": [
"WCD"
],
"xrefs": {
"issn": "1874-6551"
}
},
"r3d100012241": {
"description": "The World Religion Database (WRD) contains detailed statistics on religious affiliation for every country of the world. It provides source material, including censuses and surveys, as well as best estimates for every religion to offer a definitive picture of international religious demography. It offers best estimates at multiple dates for each of the worldβs religions for the period 1900 to 2050.",
"homepage": "https://worldreligiondatabase.org/",
"name": "World Religion Database",
"prefix": "r3d100012241",
"synonyms": [
"WRD"
],
"xrefs": {
"issn": "1876-1410"
}
},
"r3d100012242": {
"description": "The Worldwide Governance Indicators, reporting estimates of six dimensions of governance for over 200 countries based on close to 40 data sources produced by over 30 organizations worldwide between 1996 and 2019, have become widely used among policymakers and academics. The six dimensions of governance: Voice and Accountability - Political Stability and Absence of Violence - Government Effectiveness - Regulatory Quality - Rule of Law - Control of Corruption.",
"homepage": "https://www.worldbank.org/en/publication/worldwide-governance-indicators#home",
"name": "Worldwide Governance Indicators Project",
"prefix": "r3d100012242",
"synonyms": [
"WGI Project"
]
},
"r3d100012244": {
"description": "OHSU Digital Commons is a repository for the scholarly and creative work of Oregon Health & Science University. Developed by the OHSU Library, Digital Commons provides the university community with a platform for publishing and accessing content produced by students, faculty, and staff. OHSU Digital Commons documents the history and growth of the university, as well as current progress in education, research, and health care.",
"homepage": "https://digitalcollections.ohsu.edu/",
"name": "OHSU Digital Commons",
"prefix": "r3d100012244",
"synonyms": [
"OHSU Digital Collections"
]
},
"r3d100012246": {
"description": "PWT version 10.1 is a database with information on relative levels of income, output, input and productivity, covering 183 countries between 1950 and 2019.",
"homepage": "https://www.rug.nl/ggdc/productivity/pwt/",
"name": "Penn World Table",
"prefix": "r3d100012246",
"synonyms": [
"PWT"
],
"xrefs": {
"doi": "10.15141/S5J01T"
}
},
"r3d100012247": {
"description": "J-GLOBAL is a service based on the concept of Linking, Expanding, and Sparking, linking science and technology information which hitherto stood alone to support the generation of ideas.\nBy linking the information entered, we provide opportunities to make unexpected discoveries and obtain knowledge from dissimilar fields from high-quality science and technology information within and outside JST.",
"homepage": "https://jglobal.jst.go.jp/en",
"name": "J-Global",
"prefix": "r3d100012247",
"synonyms": [
"JCSD",
"formerly: Japan Chemical Substance Dictionary Nikkaji"
],
"xrefs": {
"fairsharing": "FAIRsharing.vd25jp",
"miriam": "00000241"
}
},
"r3d100012248": {
"description": "The Comparative Political Data Set 1960-2018 (CPDS) is a collection of political and institutional data which have been assembled in the context of the research projects βDie HandlungsspielrΓ€ume des Nationalstaatesβ and βCritical junctures. An international comparisonβ directed by Klaus Armingeon and funded by the Swiss National Science Foundation. This data set consists of (mostly) annual data for 36 democratic OECD and/or EU-member coun-tries for the period of 1960 to 2018. In all countries, political data were collected only for the democratic periods. The data set is suited for cross-national, longitudinal and pooled time-series analyses.",
"homepage": "https://www.cpds-data.org/index.php",
"name": "Comparative Political Data Set",
"prefix": "r3d100012248",
"synonyms": [
"CPDS"
]
},
"r3d100012249": {
"description": "The Constituency-Level Elections Archive (CLEA) is a repository of detailed election results at the constituency level for lower house legislative elections from around the world. Our motivation is to preserve and consolidate these valuable data in one comprehensive and reliable resource that is ready for analysis and publicly available at no cost. This public good is expected to be of use to a range of audiences for research, education, and policy-making.",
"homepage": "https://electiondataarchive.org/",
"name": "Constituency-Level Elections Archive",
"prefix": "r3d100012249",
"synonyms": [
"CLEA"
]
},
"r3d100012250": {
"description": "COW seeks to facilitate the collection, dissemination, and use of accurate and reliable quantitative data in international relations. Key principles of the project include a commitment to standard scientific principles of replication, data reliability, documentation, review, and the transparency of data collection procedures. More specifically, we are committed to the free public release of data sets to the research community, to release data in a timely manner after data collection is completed, to provide version numbers for data set and replication tracking, to provide appropriate dataset documentation, and to attempt to update, document, and distribute follow-on versions of datasets where possible. We intend to use our website as the center of our data distribution efforts, to serve as central site for collection of possible error information and questions, to provide a forum for interaction with users of Correlates of War data, and as a way for the international relations community to contribute to the continuing development of the project.",
"homepage": "https://correlatesofwar.org/",
"name": "Correlates of War Project",
"prefix": "r3d100012250",
"synonyms": [
"COW"
]
},
"r3d100012251": {
"description": "The RAMEDIS system is a platform independent, web-based information system for rare metabolic diseases based on filed case reports. It was developed in close cooperation with clinical partners to allow them to collect information on rare metabolic diseases with extensive details, e.g. about occurring symptoms, laboratory findings, therapy and molecular data.",
"homepage": "https://agbi.techfak.uni-bielefeld.de/ramedis/htdocs/eng/index.php",
"name": "RAMEDIS",
"prefix": "r3d100012251",
"synonyms": [
"Rare Metabolic Diseases Database"
]
},
"r3d100012252": {
"description": "The RDSC provides researchers access to selected microdata from the Bundesbank's data records for independent and non-commercial scientific research projects on basis of the legal requirements. The RDSC is the mediator between the Bundesbankβs wide range of different micro data in various departments and β on the other side β researchers or analysts. In connection with this, the RDSC is responsible for the methodological improvement, the access of and the comprehensive documentation of the high-quality microdata. It also offers additional consultancy and support services to existing and prospective data users and satisfies data protection requirements.\nEnglish version see: https://www.bundesbank.de/en/bundesbank/research/rdsc/research-data-and-service-centre-rdsc--869492",
"homepage": "https://www.bundesbank.de/de/bundesbank/forschung/fdsz",
"name": "Forschungsdaten- und Servicezentrum der Bundesbank",
"prefix": "r3d100012252",
"synonyms": [
"FDSZ Bundesbank",
"RDSC Deutsche Bundesbank",
"Research Data and Service Centre Deutsche Bundesbank"
]
},
"r3d100012253": {
"description": "The IWH Research Data Centre provides external scientists with data for non-commercial research. The research data centre of the IWH was accredited by RatSWD.",
"homepage": "https://www.iwh-halle.de/en/research/data-and-analysis/research-data-centre/",
"name": "Forschungsdatenzentrum IWH",
"prefix": "r3d100012253",
"synonyms": [
"FDZ-IWH",
"Forschungsdatenzentrum des Leibniz-Instituts fΓΌr Wirtschaftsforschung Halle",
"Research Data Centre Halle Institute for Economic Research",
"Research Data Centre IWH"
]
},
"r3d100012254": {
"description": "Lithuania became a full member of CLARIN ERIC in January of 2015 and soon CLARIN-LT consortium was founded by three partner universities: Vytautas Magnus University, Kaunas Technology University and Vilnius University. The main goal of the consortium is to become a CLARIN B centre, which will be able to serve language users in Lithuania and Europe for storing and accessing language resources.",
"homepage": "http://clarin-lt.lt/?lang=en",
"name": "CLARIN-LT",
"prefix": "r3d100012254",
"synonyms": [
"CLARIN-LT Repository"
]
},
"r3d100012256": {
"description": "SprΓ₯kbanken is a collection of Norwegian language technology resources, and a national infrastructure for language technology and research. Our mandate is to collect and develop language resources, and to make these available for researchers, students and the ICT industry which works with the development of language-based ICT solutions.\nSprΓ₯kbanken was established as a language policy initiative, designed to ensure that language technology solutions based on the Norwegian language will be developed, and thereby prevent domain loss of Norwegian in technology-dependent areas, cf. MΓ₯l og meining (Report 35, 2007 β 2008).\nAs of today the collection contains resources in both Norwegian BokmΓ₯l and Nynorsk, as well as in Swedish, Danish and Norwegian Sign Language (NTS).",
"homepage": "https://www.nb.no/sprakbanken/en/sprakbanken/",
"name": "National Library of Norway | SprΓ₯kbanken",
"prefix": "r3d100012256",
"synonyms": [
"Speech & Language Data Bank",
"SprΓ₯kbankens ressurskatalog",
"The Norwegian Language Bank"
]
},
"r3d100012257": {
"description": "The focus of PolMine is on texts published by public institutions in Germany. Corpora of parliamentary protocols are at the heart of the project: Parliamentary proceedings are available for long stretches of time, cover a broad set of public policies and are in the public domain, making them a valuable text resource for political science.\nThe project develops repositories of textual data in a sustainable fashion to suit the research needs of political science. Concerning data, the focus is on converting text issued by public institutions into a sustainable digital format (TEI/XML).",
"homepage": "https://polmine.github.io/",
"name": "PolMine",
"prefix": "r3d100012257",
"synonyms": [
"PolMine Project"
]
},
"r3d100012258": {
"description": "Competence Centre IULA-UPF-CC CLARIN manages, disseminates and facilitates this catalogue, which provides access to reference information on the use of language technology projects and studies in different disciplines, especially with regard to Humanities and Social Sciences.\nThe Catalog relates information that is organized by Γreas, (disciplines and research topics), Projects (of research that use or have used language technologies), Tasks (that make the tools), Tools (of language technology), Documentation (articles regarding the tools and how they are used) and resources such as Corpora (collections of annotated texts) and Lexica (collections of words for different uses).",
"homepage": "http://www.clarin-es-lab.org/index-en.html",
"name": "Spanish CLARIN K-Centre",
"prefix": "r3d100012258",
"synonyms": [
"Centro-K CLARIN",
"Spanish CLARIN Knowledge Centre"
]
},
"r3d100012259": {
"description": "The CLARIN-D Centre CEDIFOR provides a repository for long-term storage of resources and meta-data. Resources hosted in the repository stem from research of members as well as associated research projects of CEDIFOR. This includes software and web-services as well as corpora of text, lexicons, images and other data.",
"homepage": "https://www.cedifor.de/",
"name": "Repository CLARIN-D Centre CEDIFOR",
"prefix": "r3d100012259",
"synonyms": [
"Centre for the Digital Foundation of Research in the Humanities, Social, and Educational Sciences",
"Centrum fΓΌr Digitale Forschung in den Geistes-, Sozial- und Bildungswissenschaften"
]
},
"r3d100012260": {
"description": "The Text Laboratory provides assistance with databases, word lists, corpora and tailored solutions for language technology.\nWe also work on research and development projects alone or in cooperation with others - locally, nationally and internationally.\nServices and tools: Word and frequency lists, Written corpora, Speech corpora, Multilingual corpora, Databases, Glossa Search Tool, The Oslo-Bergen Tagger, GREI grammar games, Audio files: dialects from Norway and America etc., Nordic Atlas of Language Structures (NALS) Journal, Norwegian in America, NEALT, Ethiopian Language Technology, Access to Corpora",
"homepage": "https://www.hf.uio.no/iln/english/about/organization/text-laboratory/",
"name": "Tekstlaboratoriet",
"prefix": "r3d100012260",
"synonyms": [
"The Text Laboratory",
"tekstlab"
]
},
"r3d100012262": {
"description": "ILC-CNR for CLARIN-IT repository is a library for linguistic data and tools. Including: Text Processing and Computational Philology; Natural Language Processing and Knowledge Extraction; Resources, Standards and Infrastructures; Computational Models of Language Usage. The studies carried out within each area are highly interdisciplinary and involve different professional skills and expertises that extend across the disciplines of Linguistics, Computational Linguistics, Computer Science and Bio-Engineering.",
"homepage": "https://dspace-clarin-it.ilc.cnr.it/repository/xmlui/",
"name": "ILC-CNR for CLARIN-IT repository",
"prefix": "r3d100012262",
"synonyms": [
"CLARIN-IT Repository",
"ILC4CLARIN"
]
},
"r3d100012263": {
"description": "This database host for fungi data related to new classification with morphology, molecular and other important data.\nThis fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens.",
"homepage": "https://www.facesoffungi.org/",
"name": "Faces Of Fungi database",
"prefix": "r3d100012263",
"synonyms": [
"Facesoffungi",
"FoF"
],
"xrefs": {
"fairsharing": "FAIRsharing.jr31ex"
}
},
"r3d100012265": {
"description": "CryptoDB is an integrated genomic and functional genomic database for the parasite Cryptosporidium and other related genera. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining.",
"homepage": "https://cryptodb.org/cryptodb/app",
"name": "CryptoDB",
"prefix": "r3d100012265",
"xrefs": {
"fairsharing": "FAIRsharing.t3nprm",
"miriam": "00000149",
"scr": "013455"
}
},
"r3d100012266": {
"description": "ToxoDB is a genome database for the genus Toxoplasma, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including toxoplasmosis.",
"homepage": "https://toxodb.org/toxo/app",
"name": "ToxoDB",
"prefix": "r3d100012266",
"xrefs": {
"fairsharing": "FAIRsharing.a08mtc",
"miriam": "00000153",
"nif": "0000-03572",
"omics": "03168",
"scr": "013453"
}
},
"r3d100012267": {
"description": "The Cross-National Equivalent File (CNEF) contains population panel data from Australia, Canada, Germany, Great Britain, Korea, Russia, Switzerland and the United States. Each of these countries undertakes a longitudinal household economic survey. The data are made equivalent, providing a reference dataset which cross-links each of the individual studies and allowing cross-national comparisons.",
"homepage": "https://www.cnefdata.org/",
"name": "Cross-national Equivalent File",
"prefix": "r3d100012267",
"synonyms": [
"CNEF"
],
"xrefs": {
"nlx": "151820",
"scr": "008935"
}
},
"r3d100012268": {
"description": "Curtin University has 2758 data records in Research Data Australia, which cover 527 subjects areas including EARTH SCIENCES, GEOLOGY and MINERAL EXPLORATION and involve 64 group(s).",
"homepage": "https://researchdata.edu.au/contributors/curtin-university",
"name": "Curtin University Research Data Collection",
"prefix": "r3d100012268"
},
"r3d100012269": {
"description": "The Integrated Resource for Reproducibility in Macromolecular Crystallography includes a repository system and website designed to make the raw data of protein crystallography more widely available. Our focus is on identifying, cataloging and providing the metadata related to datasets, which could be used to reprocess the original diffraction data. The intent behind this project is to make the resulting three dimensional structures more reproducible and easier to modify and improve as processing methods advance.",
"homepage": "https://proteindiffraction.org/",
"name": "Integrated Resource for Reproducibility in Macromolecular Crystallography",
"prefix": "r3d100012269",
"synonyms": [
"IRRMC"
],
"xrefs": {
"fairsharing": "FAIRsharing.kqbg3s"
}
},
"r3d100012270": {
"description": "The LINZ Data Service provides free online access to New Zealandβs most up-to-date land and seabed data. The data can be searched, browsed and downloaded. The LINZ web services can be also integrated into other applications.",
"homepage": "https://data.linz.govt.nz/",
"name": "Land Information New Zealand Data Service",
"prefix": "r3d100012270",
"synonyms": [
"LINZ Data Service"
]
},
"r3d100012273": {
"description": "Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm.\nSASBDB is a fully searchable curated repository of freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data.",
"homepage": "https://www.sasbdb.org/",
"name": "SASBDB",
"prefix": "r3d100012273",
"synonyms": [
"Small Angle Scattering Biological Data Bank"
],
"xrefs": {
"fairsharing": "FAIRsharing.i1F3Hb"
}
},
"r3d100012274": {
"description": "The Smithsonian Repository is a digital service that collects, preserves, and disseminates research materials via several communities including Research Data Sets. It preserves and protects the organization's legacy...",
"homepage": "https://repository.si.edu/",
"name": "Smithsonian Research Online",
"prefix": "r3d100012274",
"synonyms": [
"SRO"
],
"xrefs": {
"hdl": "10088/27849",
"opendoar": "1122",
"roar": "6428"
}
},
"r3d100012275": {
"description": "BIOS is a system designed to enable the management, visualization, and analysis of biogeographic data collected by the California Department of Fish and Wildlife and its partner organizations. BIOS integrates GIS, relational database management, and ESRI's ArcGIS Server technology to create a statewide, integrated information management tool that can be used on any computer with access to the Internet.",
"homepage": "https://wildlife.ca.gov/Data/BIOS",
"name": "Biogeographic Information and Observation System",
"prefix": "r3d100012275",
"synonyms": [
"BIOS"
]
},
"r3d100012276": {
"description": "RUresearch Data Portal is a subset of RUcore (Rutgers University Community Repository), provides a platform for Rutgers researchers to share their research data and supplementary resources with the global scholarly community. This data portal leverages all the capabilities of RUcore with additional tools and services specific to research data. It provides data in different clusters (research-genre) with excellent search facility; such as experimental data, multivariate data, discrete data, continuous data, time series data, etc. However it facilitates individual research portals that include the Video Mosaic Collaborative (VMC), an NSF-funded collection of mathematics education videos for Teaching and Research.\nIts' mission is to maintain the significant intellectual property of Rutgers University; thereby intended to provide open access and the greatest possible impact for digital data collections in a responsible manner to promote research and learning.",
"homepage": "https://rucore.libraries.rutgers.edu/research/",
"name": "RUresearch Data Portal",
"prefix": "r3d100012276",
"synonyms": [
"RUcore",
"Rutgers University Research Data Portal"
],
"xrefs": {
"nlx": "152163",
"scr": "006382"
}
},
"r3d100012277": {
"description": "SWATHAtlas is a repository of mass spectrometry data of the human proteome. The repository provides open access to libraries of SWATH-MS (Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra) datasets. SWATH-MS is a method which combines both data-independent acquisition (DIA) and targeted data analysis techniques for the collection and storage of fragmentation spectra of peptides. Compared to techniques of selected reaction monitoring (SRM), SWATH-MS allows for a more extensive throughput of proteins in a sample to be targeted. The spectra collected in SWATHAtlas can be interpreted with the help of software such as OpenSWATH or Peakview.",
"homepage": "http://www.swathatlas.org/",
"name": "SWATHAtlas",
"prefix": "r3d100012277",
"synonyms": [
"SWATH Atlas"
],
"xrefs": {
"omics": "19910"
}
},
"r3d100012278": {
"description": "The database MORPHYLL contains quantitative and qualitative morphometric data of fossil angiosperm leaves from the Paleogene. The data are compiled from different fossil sites housed in various European Natural History Museums.",
"homepage": "https://www.morphyll.naturkundemuseum-bw.de/",
"name": "MORPHYLL",
"prefix": "r3d100012278",
"synonyms": [
"Database for acquisition of ecophysiologically relevant morphometric data of fossil leaves"
],
"xrefs": {
"biodbcore": "001724",
"fairsharing.legacy": "3211"
}
},
"r3d100012281": {
"description": "The UWE Research Data Repository holds research data and metadata associated with existing or forthcoming EPSRC-funded publications, produced by UWE Bristol researchers.",
"homepage": "https://www.uwe.ac.uk/study/library/research-support/research-data-repository",
"name": "UWE Research Data Repository",
"prefix": "r3d100012281",
"synonyms": [
"University of West England Research Data Repository"
]
},
"r3d100012282": {
"description": "4DGenome is a public database that archives and disseminates chromatin interaction data. Currently, 4DGenome contains over 8,038,247 interactions curated from both experimental studies (high throughput and individual studies) and computational predictions. It covers five organisms, Homo sapiens, Mus musculus, Drosophila melanogaster, Plasmodium falciparum, and Saccharomyces cerevisiae.",
"homepage": "https://4dgenome.research.chop.edu/",
"name": "4DGenome",
"prefix": "r3d100012282",
"synonyms": [
"Chromatin Interaction Database"
]
},
"r3d100012284": {
"description": "<<>>!!!>>>",
"homepage": "http://www.carmen.org.uk/",
"name": "CARMEN",
"prefix": "r3d100012284",
"synonyms": [
"Code analysis, repository & modelling for e-neuroscience"
],
"xrefs": {
"nif": "0000-00442",
"scr": "002795"
}
},
"r3d100012285": {
"description": "Aston Data Explorer is Aston University's repository for our research datasets. It is one of three services providing information about Aston Universityβs research. Aston Publications Explorer holds Aston's Open Access publications and Aston Research Explorer has broader information about Aston's research work including research staff, awards and activities, projects and research groups.",
"homepage": "https://researchdata.aston.ac.uk/",
"name": "Aston Data Explorer",
"prefix": "r3d100012285"
},
"r3d100012287": {
"description": "Based on Bowerman & Pedersonβs Topological Relations Picture Series (TRPS), the author has researched the semantic space of static spatial prepositions of Hieroglyphic Ancient Egyptian (Egyptian, Afro-Asiatic), Arabic, English, French, German, Hebrew, Italian, Russian, and Spanish. This repository publication publishes the raw data.",
"homepage": "http://repository.edition-topoi.org/collection/TRPS",
"name": "BowPed TRPS Data",
"prefix": "r3d100012287",
"xrefs": {
"doi": "10.17171/2-5"
}
},
"r3d100012288": {
"description": "The Climate Change Centre Austria - Data Centre provides the central national archive for climate data and information.\nThe data made accessible includes observation and measurement data, scenario data, quantitative and qualitative data, as well as the measurement data and findings of research projects.",
"homepage": "https://data.ccca.ac.at/",
"name": "CCCA Data Server",
"prefix": "r3d100012288",
"synonyms": [
"Climate Change Centre Austria Data Centre"
]
},
"r3d100012290": {
"description": "The Media Repository is a web-based digital asset management system to store, organize and share digital media files. Not only images and documents are directly supported β audio and video content is supported as well. The data can be re-used in other systems. The system manages a variety of file formats and metadata schemes. It stores and organizes media data and helps to manage workflows with them.\nPublic web presentations are possible as well as collaborative work in restricted groups. The Media Repository helps both small teams and larger research projects in the management of media assets and their long-term storage.",
"homepage": "https://media.hu-berlin.de/",
"name": "Media Repository Humboldt-UniversitΓ€t zu Berlin",
"prefix": "r3d100012290",
"synonyms": [
"Medien-Repositorium Humboldt-UniversitΓ€t zu Berlin"
]
},
"r3d100012291": {
"description": "The Norwegian Polar Institute is a governmental institution for scientific research, mapping and environmental monitoring in the Arctic and the Antarctic. The instituteβs Polar Data Centre (NPDC) manages and provides access to scientific data, environmental monitoring data, and topographic and geological map data from the polar regions. The scientific datasets are ranging from human field observations, through in situ and moving sensor data, to remote sensing products. The institute's data holdings also include photographic images, audio and video records.",
"homepage": "https://data.npolar.no/dataset",
"name": "Norwegian Polar Data Centre",
"prefix": "r3d100012291",
"synonyms": [
"NPDC"
],
"xrefs": {
"fairsharing": "FAIRsharing.4dbb9e"
}
},
"r3d100012295": {
"description": "The Alaska Native Language Archive houses documentation of the various Native languages of Alaska and helps to preserve and cultivate this unique heritage for future generations. As the premier repository worldwide for information relating to the Native languages of Alaska, the Archive serves researchers, teachers and students, as well as members of the broader community. The collection includes both published and unpublished materials in or on all of the Alaska Native languages and related languages. The collection has enduring cultural, historic, and intellectual value, particularly for Alaska Native language speakers and their descendants",
"homepage": "https://www.uaf.edu/anla/",
"name": "Alaska Native Language Archive",
"prefix": "r3d100012295",
"synonyms": [
"ANLA",
"Michael E. Krauss Alaska Native Language Archive"
]
},
"r3d100012296": {
"description": "FDAT is a research data repository hosted by the University of TΓΌbingen, designed to facilitate long-term archiving and publication of research data. Managed by the Information, Communication and Media Center (IKM), it primarily caters to the humanities and social sciences, while welcoming researchers from all scientific disciplines at the university. Committed to high-quality data management, FDAT emphasizes the importance of adhering to the FAIR Data Principles, promoting findability, accessibility, interoperability, and reusability of the research data it contains.",
"homepage": "https://fdat.uni-tuebingen.de",
"name": "Research Data Repository FDAT",
"prefix": "r3d100012296",
"synonyms": [
"Research Data Repository of the University of Tuebingen"
]
},
"r3d100012297": {
"description": "<<>>!!!>>>",
"homepage": "http://gesdb.nhri.org.tw/",
"name": "GESDB",
"prefix": "r3d100012297",
"synonyms": [
"Genetic Epidemiology Simulation Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.rbba3x",
"omics": "11980"
}
},
"r3d100012298": {
"description": "<<>>!!!>>>",
"homepage": "http://www.chorotree.de",
"name": "Chorotree",
"prefix": "r3d100012298",
"synonyms": [
"database for chorology of trees and shrubs"
]
},
"r3d100012300": {
"description": "<<>>!!!>>>",
"homepage": "https://www.cbil.upenn.edu/ErythronDB/",
"name": "ErythronDB",
"prefix": "r3d100012300",
"synonyms": [
"Erythron Database"
]
},
"r3d100012302": {
"description": "The PSDS is an EPSRC-funded National Research Facility provided by the University of Southampton, and Science and Technology Facilities Council. Its purpose is to provide a common access point to data resources within the Physical Sciences to all staff, students and other members of UK academic institutions. By providing a common point of access, free at the point of use, the service aims to provide benefit to the research community by maximising the use of resources via common acedemic licencing, and adding value as a common hub for aggregating and integrating data resources for the Physical Sciences.",
"homepage": "https://www.psds.ac.uk/",
"name": "Physical Sciences Data-Science Service",
"prefix": "r3d100012302",
"synonyms": [
"PSDS",
"formerly name: CDS National Chemical Database Service"
]
},
"r3d100012304": {
"description": "The Universitat de Barcelona Digital Repository is an institutional resource containing open-access digital versions of publications related to the teaching, research and institutional activities of the UB's teaching staff and other members of the university community, including research data.",
"homepage": "https://diposit.ub.edu/dspace/handle/2445/56364",
"name": "DipΓ²sit Digital de la Universitat de Barcelona Dades",
"prefix": "r3d100012304",
"synonyms": [
"DD DipΓ²sit Digital"
]
},
"r3d100012305": {
"description": "The Centre for Environmental Data Analysis (CEDA) serves the environmental science community through managing data centres, data analysis environments, and participation in a host of relevant research projects.\nWe aim to support environmental science, further environmental data archival practices, and develop and deploy new technologies to enhance access to data. Additionally we provide services to aid large scale data analysis.\nThe CEDA Archive operates the atmospheric and earth observation data centre functions on behalf of NERC for the UK atmospheric science and earth observation communities. It covers climate, composition, observations and NWP data as well as various earth observation datasets, including airborne and satellite data and imagery. Prior to November 2016 these functions were operted by CEDA under the titles of the British Atmospheric Data Centre (BADC) and the NERC Earth Observation Data Centre (NEODC).\nCEDA also operates the UK Solar System Data Centre (UKSSDC), which curates and provides access to archives of data from the upper atmosphere, ionosphere and Earth's solar environment.",
"homepage": "https://www.ceda.ac.uk/",
"name": "Centre for Environmental Data Analysis",
"prefix": "r3d100012305",
"synonyms": [
"CEDA",
"formerly: Centre for Environmental Data Archival"
]
},
"r3d100012307": {
"description": "<<>>!!!>>>",
"homepage": "http://radar.luke.fi/catalog/search/search.page",
"name": "RADAR Luke",
"prefix": "r3d100012307",
"synonyms": [
"Luke research data descriptions",
"Luonnonvarakeskuksen tutkimusaineistokuvausten hakupalvelu",
"Research data descriptions discovery service of Natural Resources Institute Finland"
]
},
"r3d100012308": {
"description": "The DesignSafe Data Depot Repository (DDR) is the platform for curation and publication of datasets generated in the course of natural hazards research. The DDR is an open access data repository that enables data producers to safely store, share, organize, and describe research data, towards permanent publication, distribution, and impact evaluation. The DDR allows data consumers to discover, search for, access, and reuse published data in an effort to accelerate research discovery. It is a component of the DesignSafe cyberinfrastructure, which represents a comprehensive research environment that provides cloud-based tools to manage, analyze, curate, and publish critical data for research to understand the impacts of natural hazards. DesignSafe is part of the NSF-supported Natural Hazards Engineering Research Infrastructure (NHERI), and aligns with its mission to provide the natural hazards research community with open access, shared-use scholarship, education, and community resources aimed at supporting civil and social infrastructure prior to, during, and following natural disasters. It serves a broad national and international audience of natural hazard researchers (both engineers and social scientists), students, practitioners, policy makers, as well as the general public. It has been in operation since 2016, and also provides access to legacy data dating from about 2005. These legacy data were generated as part of the NSF-supported Network for Earthquake Engineering Simulation (NEES), a predecessor to NHERI. Legacy data and metadata belonging to NEES were transferred to the DDR for continuous preservation and access.",
"homepage": "https://www.designsafe-ci.org/",
"name": "DesignSafe-CI Data Depot Repository",
"prefix": "r3d100012308",
"synonyms": [
"A Repository Infrastructure for Natural Hazards Datasets",
"DDR"
],
"xrefs": {
"fairsharing": "FAIRsharing.6a3ef8"
}
},
"r3d100012309": {
"description": "CORE is a full-text, interdisciplinary, non-profit social repository designed to increase the impact of work in the Humanities.\nCommons Open Repository Exchange, a library-quality repository for sharing, discovering, retrieving, and archiving digital work. CORE provides Humanities Commons members with a permanent, open access storage facility for their scholarly output, facilitating maximum discoverability and encouraging peer feedback.",
"homepage": "https://hcommons.org/core/",
"name": "Humanities Commons",
"prefix": "r3d100012309",
"synonyms": [
"CORE, Open Access for the Humanities",
"Commons Open Repository Exchange"
]
},
"r3d100012310": {
"description": "The Humanities Data Centre (HDC) project is developing a design study for a data center for the long-term availability and reusability of humanities research data.",
"homepage": "https://humanities-data-centre.de/",
"name": "Humanities Data Centre",
"prefix": "r3d100012310",
"synonyms": [
"HDC"
]
},
"r3d100012311": {
"description": "METLIN represents the largest MS/MS collection of data with the database generated at multiple collision energies and in positive and negative ionization modes. The data is generated on multiple instrument types including SCIEX, Agilent, Bruker and Waters QTOF mass spectrometers.",
"homepage": "https://metlin.scripps.edu/landing_page.php?pgcontent=mainPage",
"name": "Metlin",
"prefix": "r3d100012311",
"synonyms": [
"The original and most comprehensive MS/MS metabolite database"
],
"xrefs": {
"nlx": "158116",
"omics": "02633",
"scr": "010500"
}
},
"r3d100012313": {
"description": "mzCloud is an extensively curated database of high-resolution tandem mass spectra that are arranged into spectral trees. MS/MS and multi-stage MSn spectra were acquired at various collision energies, precursor m/z, and isolation widths using Collision-induced dissociation (CID) and Higher-energy collisional dissociation (HCD). Each raw mass spectrum was filtered and recalibrated giving rise to additional filtered and recalibrated spectral trees that are fully searchable. Besides the experimental and processed data, each database record contains the compound name with synonyms, the chemical structure, computationally and manually annotated fragments (peaks), identified adducts and multiply charged ions, molecular formulas, predicted precursor structures, detailed experimental information, peak accuracies, mass resolution, InChi, InChiKey, and other identifiers. mzCloud is a fully searchable library that allows spectra searches, tree searches, structure and substructure searches, monoisotopic mass searches, peak (m/z) searches, precursor searches, and name searches. mzCloud is free and available for public use online.",
"homepage": "https://www.mzcloud.org/",
"name": "mzCloud",
"prefix": "r3d100012313",
"synonyms": [
"Advanced mass spectral database"
],
"xrefs": {
"omics": "14329",
"scr": "014669"
}
},
"r3d100012314": {
"description": "With the creation of the Metabolomics Data Repository managed by Data Repository and Coordination Center (DRCC), the NIH acknowledges the importance of data sharing for metabolomics. Metabolomics represents the systematic study of low molecular weight molecules found in a biological sample, providing a \"snapshot\" of the current and actual state of the cell or organism at a specific point in time. Thus, the metabolome represents the functional activity of biological systems. As with other βomicsβ, metabolites are conserved across animals, plants and microbial species, facilitating the extrapolation of research findings in laboratory animals to humans. Common technologies for measuring the metabolome include mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR), which can measure hundreds to thousands of unique chemical entities.\nData sharing in metabolomics will include primary raw data and the biological and analytical meta-data necessary to interpret these data. Through cooperation between investigators, metabolomics laboratories and data coordinating centers, these data sets should provide a rich resource for the research community to enhance preclinical, clinical and translational research.",
"homepage": "https://www.metabolomicsworkbench.org/",
"name": "UCSD Metabolomics Workbench",
"prefix": "r3d100012314",
"synonyms": [
"Metabolomics Workbench"
],
"xrefs": {
"fairsharing": "FAIRsharing.xfrgsf",
"scr": "013794"
}
},
"r3d100012315": {
"description": "Tthe Lipidomics Gateway - a free, comprehensive website for researchers interested in lipid biology, provided by the LIPID MAPS (Lipid Metabolites and Pathways Strategy) Consortium. The LIPID MAPS Lipidomics Gateway provides a rich collection of information and resources to help you stay abreast of the latest developments in this rapidly expanding field. LIPID Metabolites And Pathways Strategy (LIPID MAPSΒ) is a multi-institutional effort created in 2003 to identify and quantitate, using a systems biology approach and sophisticated mass spectrometers, all of the major β and many minor β lipid species in mammalian cells, as well as to quantitate the changes in these species in response to perturbation.\nThe ultimate goal of our research is to better understand lipid metabolism and the active role lipids play in diabetes, stroke, cancer, arthritis, Alzheimer's and other lipid-based diseases in order to facilitate development of more effective treatments.\nSince our inception, we have made great strides toward defining the \"lipidome\" (an inventory of the thousands of individual lipid molecular species) in the mouse macrophage. We have also worked to make lipid analysis easier and more accessible for the broader scientific community and to advance a robust research infrastructure for the international research community. We share new lipidomics findings and methods, hold annual meetings open to all interested investigators, and are exploring joint efforts to extend the use of these powerful new methods to new applications",
"homepage": "https://www.lipidmaps.org/",
"name": "LIPID MAPS",
"prefix": "r3d100012315",
"synonyms": [
"LIPID MAPS Lipidomics Gateway",
"LIPID Metabolites And Pathways Strategy"
],
"xrefs": {
"fairsharing": "FAIRsharing.cpneh8",
"nif": "0000-00368",
"omics": "02529",
"scr": "006579"
}
},
"r3d100012316": {
"description": "e-cienciaDatos is a multidisciplinary data repository that houses the scientific datasets of researchers from the public universities of the Community of Madrid and the UNED, members of the Consorcio MadroΓ±o, in order to give visibility to these data, to ensure its preservation And facilitate their access and reuse.\ne-cienciaDatos is structured as a system constituted by different communities that collects datasets of each of the individual universities.\ne-cienciaDatos offers the deposit and publication of datasets, assigning a digital object identifier DOI to each of them. The association of a dataset with a DOI will facilitate data verification, dissemination, reuse, impact and long-term access.\nIn addition, the repository provides a standardized citation for each dataset, which contains sufficient information so that it can be identified and located, including the DOI.",
"homepage": "https://edatos.consorciomadrono.es",
"name": "e-cienciaDatos",
"prefix": "r3d100012316",
"synonyms": [
"cienciaDatos"
],
"xrefs": {
"fairsharing": "FAIRsharing.lone3g"
}
},
"r3d100012318": {
"description": "MassBank of North America (MoNA) is a metadata-centric, auto-curating repository designed for efficient storage and querying of mass spectral records. It intends to serve as a the framework for a centralized, collaborative database of metabolite mass spectra, metadata and associated compounds. MoNA currently contains over 200,000 mass spectral records from experimental and in-silico libraries as well as from user contributions.",
"homepage": "https://mona.fiehnlab.ucdavis.edu/",
"name": "MoNA",
"prefix": "r3d100012318",
"synonyms": [
"MassBank of North America"
],
"xrefs": {
"omics": "13585",
"scr": "015536"
}
},
"r3d100012319": {
"description": "The vocabulary of forenames is a simple, multilingual vocabulary (i.e. without hierarchies etc.) in which the forenames of the project partnersβ persons and the forenamesβ spelling variants, both historical and dialectal, are documented with references or passages. As a rule, each forename is assigned one or more persons bearing that name. There is a hit list of the most frequent forenames between 200 BC and AD 2016 as well as a visualisation in word clouds and the occurrences in a timeline.",
"homepage": "https://data.histhub.ch/",
"name": "Forenames_histHub",
"prefix": "r3d100012319",
"synonyms": [
"Dal 200 a.C. al 2016: piΓΉ di 2200 anni di prenomi in Svizzera",
"De 200 av. J.-C. Γ 2016 : Plus de 2200 ans de prΓ©noms en Suisse",
"From 200 BC to 2016: Over 2200 years of first names in Switzerland",
"Von 200 v. Chr. bis 2016: Γber 2200 Jahre Vornamen der Schweiz",
"histHub"
]
},
"r3d100012320": {
"description": "Since 1898 the Swiss Lawyers Society edits a collection of law sources which had been created on Swiss territory up to 1798, the Collection of Swiss Law Sources. The Collection contains material from the early middle ages until early modern times (1798). Over 100 volumes, or more than 70,000 pages of source material and comments from all language regions of Switzerland have been published so far.",
"homepage": "https://www.ssrq-sds-fds.ch/projekte/ssrq-online/",
"name": "Sammlung Schweizerischer Rechtsquellen online",
"prefix": "r3d100012320",
"synonyms": [
"Collana Fonti del diritto svizzero online",
"Collection des sources du droit suisse online",
"FDS-online",
"SDS-online",
"SSRQ-online"
]
},
"r3d100012321": {
"description": "CAZy is a specialist database dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description.",
"homepage": "http://www.cazy.org/",
"name": "Carbohydrate-Active enZYmes Database",
"prefix": "r3d100012321",
"synonyms": [
"CAZy"
],
"xrefs": {
"fairsharing": "FAIRsharing.ntyq70",
"nif": "0000-02642",
"omics": "01677",
"scr": "012909"
}
},
"r3d100012322": {
"description": "eCommons is a service of the Cornell University Library that provides long-term access to a broad range of Cornell-related digital content of enduring value. eCommons accepts both educational and research-oriented content, including pre- and post-publication papers, datasets, technical reports, theses and dissertations, books, lectures, presentations and more.",
"homepage": "https://ecommons.cornell.edu/home",
"name": "eCommons - Cornell's digital repository",
"prefix": "r3d100012322",
"xrefs": {
"fairsharing": "FAIRsharing.N0nNXm",
"opendoar": "69",
"roar": "477"
}
},
"r3d100012325": {
"description": "PharmGKB is a comprehensive resource that curates knowledge about the impact of genetic variation on drug response for clinicians and researchers. PharmGKB brings together the relevant data in a single place and adds value by combining disparate data on the same relationship, making it easier to search and easier to view the key aspects and by interpreting the data.PharmGKB provide clinical interpretations of this data, curated pathways and VIP summaries which are not found elsewhere.",
"homepage": "https://www.pharmgkb.org/",
"name": "PharmGKB",
"prefix": "r3d100012325",
"synonyms": [
"Pharmacogenomics Knowledgebase"
],
"xrefs": {
"fairsharing": "FAIRsharing.t7yckc",
"nif": "0000-00414",
"omics": "01586",
"scr": "002689"
}
},
"r3d100012326": {
"description": ">>>!!!<<< 08.11.2019: SowidataNet has moved ; you can now access the SowiDataNet service at https://data.gesis.org/sharing/#!Home >>>!!!<<<",
"name": "SowiDataNet",
"prefix": "r3d100012326"
},
"r3d100012327": {
"description": "SIP-Archiv is an Internet based archive and database for petrophysical data derived by Spectral Induced Polarization (SIP) measurements on sediments and consolidated rocks, building materials, man-made materials and wood. It is open for all SIP related working Groups, and the usage is free of charge for scientific purposes. Nevertheless, a simple registration is needed for both, the users and the user's institution. More details can be found on the website.",
"homepage": "https://www.sip-archiv.de/",
"name": "SIP-Archiv",
"prefix": "r3d100012327",
"synonyms": [
"SIP Archive",
"das Archiv fΓΌr Spektral Induzierte Polarisation"
]
},
"r3d100012328": {
"description": "Real-Time Database for high-resolution Neutron Monitor measurements.\nNMDB provides access to Neutron Monitor measurements from stations around the world. The goal of NMDB is to provide easy access to all Neutron Monitor measurements through an easy to use interface. NMDB provides access to real-time as well as historical data.",
"homepage": "https://www.nmdb.eu",
"name": "NMDB",
"prefix": "r3d100012328",
"synonyms": [
"Neutron Monitor Database"
]
},
"r3d100012329": {
"description": "STRENDA DB is a storage and search platform supported by the Beilstein-Institut that incorporates the STRENDA Guidelines in a user-friendly, web-based system. If you are an author who is preparing a manuscript containing functional enzymology data, STRENDA DB provides you the means to ensure that your data sets are complete and valid before you submit them as part of a publication to a journal. \n Data entered in the STRENDA DB submission form are automatically checked for compliance with the STRENDA Guidelines; users receive warnings informing them when necessary information is missing.",
"homepage": "https://www.beilstein-strenda-db.org/strenda/",
"name": "STRENDA DB",
"prefix": "r3d100012329",
"synonyms": [
"Standards for Reporting Enzymology Data"
],
"xrefs": {
"fairsharing": "FAIRsharing.ekj9zx",
"scr": "017422"
}
},
"r3d100012330": {
"description": "RADAR offers researchers at publicly funded universities and non-academic research institutions in Germany a customized and user-friendly repository for archiving and publication of research data independent of discipline and format. The administration of the service, the individual workflows for uploading, organising and annotating the research data with metadata as well as the curation of the datasets and optional quality assurance through peer review are the responsibility of the using institution. For data archiving, data providers can flexibly choose retention periods (5, 10, 15 years) and define access rights. Published datasets are kept for at least 25 years, they are always assigned a DOI via DataCite and can thus be internationally identified and cited. RADAR is operated exclusively on servers in Germany. The data are stored in three copies at two locations. All contracts are subject to German law.",
"homepage": "https://www.radar-service.eu/en",
"name": "RADAR",
"prefix": "r3d100012330",
"synonyms": [
"Research Data Repository"
]
},
"r3d100012332": {
"description": "Clinical Genomic Database (CGD) is a manually curated database of conditions with known genetic causes, focusing on medically significant genetic data with available interventions.",
"homepage": "https://research.nhgri.nih.gov/CGD/",
"name": "Clinical Genomic Database",
"prefix": "r3d100012332",
"synonyms": [
"CGD"
],
"xrefs": {
"nlx": "152872",
"scr": "006427"
}
},
"r3d100012333": {
"description": "DataDOI is an institutional research data repository managed by University of Tartu Library. DataDOI gathers all fields of research data and stands for encouraging open science and FAIR (Findable, Accessible, Interoperable, Reusable) principles. DataDOI is made for long-term preservation of research data. Each dataset is given a DOI (Digital Object Identifier) through DataCite Estonia Concortium.",
"homepage": "https://datadoi.ee",
"name": "DataDOI",
"prefix": "r3d100012333"
},
"r3d100012335": {
"description": "GFZ Data Services is a repository for research data and scientific software across the Earth System Sciences, hosted at GFZ. The curated data are archived, persistently accessible and published with digital object identifier (DOI). They range from large dynamic datasets from global monitoring networks with real-time aquisition, to international services in geodesy and geophysics, to the full suite of small and highly heterogeneous datasets collected by individual researchers or small teams (\"long-tail data\"). In addition to the DOI registration and data archiving itself, GFZ Data Services team offers comprehensive consultation by domain scientists and IT specialists. Among others, GFZ Data Services is data publisher for the IAG Services ICGEM, IGETS and ISG (IAG = Int. Association for Geodesy; ICGEM = Int. Center for Global Earth Models; IGETS = Int. Geodynamics and Earth Tide Service; ISG = Int. Service for the Geoid), the World Stress Map, INTERMAGNET, GEOFON, the Geophysical Instrument Pool Potsdam GIPP, TERENO, EnMAP Flight Campaigns, the Potsdam Institute for Climate Impact Research PIK, the Specialised Information Service for Solid Earth Geosciences (FID GEO) and hosts the GFZ Catalogue for the International Generic Sample Number IGSN.",
"homepage": "https://dataservices-cms.gfz-potsdam.de/",
"name": "GFZ Data Services",
"prefix": "r3d100012335",
"xrefs": {
"fairsharing": "FAIRsharing.e0d571"
}
},
"r3d100012336": {
"description": "EBAS is a database hosting observation data of atmospheric chemical composition and physical properties. EBAS hosts data submitted by data originators in support of a number of national and international programs ranging from monitoring activities to research projects. EBAS is developed and operated by the Norwegian Institute for Air Research (NILU). We hope the information found on the web-site is self explanatory, and we would particularly ask you to consider the text found in the data disclaimer and in the βinfoβ pages associated to the filter criteria.",
"homepage": "https://ebas.nilu.no/",
"name": "EBAS",
"prefix": "r3d100012336",
"xrefs": {
"fairsharing.legacy": "3066"
}
},
"r3d100012338": {
"description": "The DBCP is an international program coordinating the use of autonomous data buoys to observe atmospheric and oceanographic conditions, over ocean areas where few other measurements are taken.",
"homepage": "https://www.ocean-ops.org/dbcp/",
"name": "Data Buoy Cooperation Panel",
"prefix": "r3d100012338",
"synonyms": [
"DBCP"
]
},
"r3d100012339": {
"description": "APID Interactomes is a database that provides a comprehensive collection of protein interactomes for more than 400 organisms based in the integration of known experimentally validated protein-protein physical interactions (PPIs). Construction of the interactomes is done with a methodological approach to report quality levels and coverage over the proteomes for each organism included. In this way, APID provides interactomes from specific organisms that in 25 cases have more than 500 proteins. As a whole APID includes a comprehensive compendium of 90,379 distinct proteins and 678,441 singular interactions. The analytical and integrative effort done in APID unifies PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. In this way, 8,388 structures have been analyzed to find specific protein-protein interactions reported with details of their molecular interfaces. APID also includes a new data visualization web-tool that allows the construction of sub-interactomes using query lists of proteins of interest and the visual exploration of the corresponding networks, including an interactive selection of the properties of the interactions (i.e. the reliability of the \"edges\" in the network) and an interactive mapping of the functional environment of the proteins (i.e. the functional annotations of the \"nodes\" in the network).",
"homepage": "http://cicblade.dep.usal.es:8080/APID/init.action",
"name": "APID",
"prefix": "r3d100012339",
"synonyms": [
"APID Interactomes",
"Agile Protein Interactomes DataServer"
],
"xrefs": {
"fairsharing": "fairsharing.8ye60e",
"nlx": "149321",
"scr": "008871"
}
},
"r3d100012340": {
"description": "SAHFOS is an internationally funded independent research non-profit organisation responsible for the operation of the Continuous Plankton Recorder (CPR) Survey. As a large-scale global survey, it provides the scientific and policy communities with a basin-wide and long-term measure of the ecological health of marine plankton. Established in 1931, the CPR Survey is the longest running, most geographically extensive marine ecological survey in the world. It has a considerable database of marine plankton and associated metadata that is used by researchers and policy makers to examine strategically important science pillars such as climate change, human health, fisheries, biodiversity, pathogens, invasive species, ocean acidification and natural capital.\nThe Continuous Plankton Recorder (CPR) Survey has merged with the Marine Biological Association. Today the Survey is operated by the Marine Biological Association, based in Plymouth, UK.",
"homepage": "https://www.cprsurvey.org/about-us/sir-alister-hardy-and-the-continuous-plankton-recorder-cpr-survey/",
"name": "SAHFOS",
"prefix": "r3d100012340",
"synonyms": [
"CPR Survey",
"Continuous Plankton Recorder Survey",
"Sir Alister Hardy Foundation for Ocean Science"
],
"xrefs": {
"fairsharing": "FAIRsharing.e2cbef"
}
},
"r3d100012341": {
"description": "CODEX is a database of NGS mouse and human experiments. Although, the main focus of CODEX is Haematopoiesis and Embryonic systems, the database includes a large variety of cell types. In addition to the publically available data, CODEX also includes a private site hosting non-published data. CODEX provides access to processed and curated NGS experiments. To use CODEX: (i) select a specialized repository (HAEMCODE or ESCODE) or choose the whole compendium (CODEX), then (ii) filter by organism and (iii) choose how to explore the database.",
"homepage": "http://codex.stemcells.cam.ac.uk/",
"name": "Codex",
"prefix": "r3d100012341",
"synonyms": [
"A comprehensive and functional compendium of Next Generation Sequencing experiments."
],
"xrefs": {
"omics": "05871"
}
},
"r3d100012342": {
"description": "GSA is a data repository specialized for archiving raw sequence reads. It supports data generated from a variety of sequencing platforms ranging from Sanger sequencing machines to single-cell sequencing machines and provides data storing and sharing services free of charge for worldwide scientific communities. In addition to raw sequencing data, GSA also accommodates secondary analyzed files in acceptable formats (like BAM, VCF). Its user-friendly web interfaces simplify data entry and submitted data are roughly organized as two parts, viz., Metadata and File, where the former can be further assorted into BioProject, BioSample, Experiment and Run, and the latter contains raw sequence reads.",
"homepage": "https://ngdc.cncb.ac.cn/gsa/",
"name": "Genome Sequence Archive",
"prefix": "r3d100012342",
"synonyms": [
"GSA"
],
"xrefs": {
"fairsharing": "FAIRsharing.tdhkc6"
}
},
"r3d100012343": {
"description": "The Service Centre of the Federal Government for Geo-Information and Geodesy (Dienstleistungszentrum des Bundes fΓΌr Geoinformation und GeodΓ€sie - DLZ) provides geodetic and geo-topographic reference data of the Federal Government centrally to federal institutions, public administrations, economy, science and citizens. The establishment of the Service Centre is based on the Federal Geographic Reference Data Act (Bundesgeoreferenzdatengesetz β BGeoRG), which came into effect on 1 November 2012. This act regulates use, quality and technology of the geodetic and geo-topographic reference systems, networks and data.",
"homepage": "https://gdz.bkg.bund.de/",
"name": "Service Centre of the Federal Government for Geo-Information and Geodesy - Open Data",
"prefix": "r3d100012343",
"synonyms": [
"Dienstleistungszentrum des Bundes fΓΌr Geoinformation und GeodΓ€sie"
]
},
"r3d100012344": {
"description": "BioPortal is an open repository of biomedical ontologies, a service that provides access to those ontologies, and a set of tools for working with them. BioPortal provides a wide range of such tools, either directly via the BioPortal web site, or using the BioPortal web service REST API. BioPortal also includes community features for adding notes, reviews, and even mappings to specific ontologies.\nBioPortal has four major product components: the web application; the API services; widgets, or applets, that can be installed on your own site; and a Virtual Appliance version that is available for download or through Amazon Web Services machine instance (AMI). There is also a beta release SPARQL endpoint.",
"homepage": "https://bioportal.bioontology.org/",
"name": "BioPortal",
"prefix": "r3d100012344",
"xrefs": {
"fairsharing": "FAIRsharing.4m97ah",
"miriam": "00000187",
"nif": "0000-23346",
"scr": "002713"
}
},
"r3d100012345": {
"description": "SAMD is a repository for Standardized Atmospheric Measurement Data:\nCentral Europe is a region with one of the most comprehensive networks for cloud and precipitation observations worldwide. To unify these observations, establish the infrastructure to store it and make it accessible to the research community is the goal of SAMD. SAMD is one result of the project \"High Definition of Clouds and Precipitation in advancing Climate Prediction\" (HD(CP)Β²).",
"homepage": "https://www.cen.uni-hamburg.de/en/icdc/research/samd.html",
"name": "SAMD",
"prefix": "r3d100012345",
"synonyms": [
"Archive for Standardized Atmospheric Measurement Data",
"Standardized Atmospheric Measurement Data"
]
},
"r3d100012347": {
"description": "As Germanyβs first disciplinary repository in the field of international and interdisciplinary legal scholarship Β²Dok offers to all academic scholars currently affiliated with a university, college or research institute the opportunity to self-archive their quality-assured research data, research papers, pre-prints and previously published articles by means of open access. The disciplinary repository Β²Dok is a service offer provided by the Scientific Information Service for International and Interdisciplinary Legal Research (Fachinformationsdienst fΓΌr internationale und interdisziplinΓ€re Rechtsforschung) established at Berlin State Library (Staatsbibliothek zu Berlin) and funded by the German Research Foundation (Deutsche Forschungsgemeinschaft).",
"homepage": "https://intr2dok.vifa-recht.de/content/index.xml",
"name": "Β²Dok[Β§]",
"prefix": "r3d100012347",
"synonyms": [
"Inter-Zwei-Dok"
]
},
"r3d100012348": {
"description": "ANPERSANA is the digital library of IKER (UMR 5478), a research centre specialized in Basque language and texts. The online library platform receives and disseminates primary sources of data issued from research in Basque language and culture. As of today, two corpora of documents have been published. The first one, is a collection of private letters written in an 18th century variety of Basque, documented in and transcribed to modern standard Basque. The discovery of the collection, named Le Dauphin, has enabled the emerging of new questions about the history and sociology of writing in the domain of minority languages, not only in France, but also among the whole Atlantic Arc. The second of the two corpora is a selection of sound recordings about monodic chant in the Basque Country. The documents were collected as part of a PhD thesis research work that took place between 2003 and 2012. It's a total of 50 hours of interviews with francophone and bascophone cultural representatives carried out at either their workplace of the informers or in public areas. ANPERSANA is bundled with an advanced search engine. The documents have been indexed and geo-localized on an interactive map. The platform is engaged with open access and all the resources can be uploaded freely under the different Creative Commons (CC) licenses.",
"homepage": "https://anpersana.iker.univ-pau.fr",
"name": "ANPERSANA",
"prefix": "r3d100012348",
"synonyms": [
"bibliothèque numérique"
]
},
"r3d100012349": {
"description": "jPOSTrepo (Japan ProteOme STandard Repository) is a repository of sharing MS raw/processed data. It consists of a high-speed file upload process, flexible file management system and easy-to-use interfaces. Users can release their \"raw/processed\" data via this site with a unique identifier number for the paper publication. Users also can suspend (or \"embargo\") their data until their paper is published. The file transfer from usersβ computer to our repository server is very fast (roughly ten times faster than usual file transfer) and uses only web browsers β it does not require installing any additional software.",
"homepage": "https://repository.jpostdb.org/",
"name": "jPOSTrepo",
"prefix": "r3d100012349",
"synonyms": [
"Japan ProteOme STandard Repository/Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.p899f7"
}
},
"r3d100012350": {
"description": "<<>>!!!>>>",
"homepage": "https://forsbase.unil.ch/",
"name": "FORSbase",
"prefix": "r3d100012350",
"synonyms": [
"Fondation suisse pour la recherche en sciences sociales base",
"Your research information and data access portal in Switzerland"
]
},
"r3d100012351": {
"description": "This database serves forest tree scientists by providing online access to hardwood tree genomic and genetic data, including assembled reference genomes, transcriptomes, and genetic mapping information. The web site also provides access to tools for mining and visualization of these data sets, including BLAST for comparing sequences, Jbrowse for browsing genomes, Apollo for community annotation and Expression Analysis to build gene expression heatmaps.",
"homepage": "https://www.hardwoodgenomics.org/",
"name": "Hardwood Genomics Project",
"prefix": "r3d100012351",
"synonyms": [
"Genomic resources for hardwood trees",
"HWG"
],
"xrefs": {
"fairsharing": "FAIRsharing.srgkaf"
}
},
"r3d100012352": {
"description": "TreeGenes is a genomic, phenotypic, and environmental data resource for forest tree species. The TreeGenes database and Dendrome project provide custom informatics tools to manage the flood of information.The database contains several curated modules that support the storage of data and provide the foundation for web-based searches and visualization tools. GMOD GUI tools such as CMAP for genetic maps and GBrowse for genome and transcriptome assemblies are implemented here. A sample tracking system, known as the Forest Tree Genetic Stock Center, sits at the forefront of most large-scale projects. Barcode identifiers assigned to the trees during sample collection are maintained in the database to identify an individual through DNA extraction, resequencing, genotyping and phenotyping. DiversiTree, a user-friendly desktop-style interface, queries the TreeGenes database and is designed for bulk retrieval of resequencing data. CartograTree combines geo-referenced individuals with relevant ecological and trait databases in a user-friendly map-based interface. ---- The Conifer Genome Network (CGN) is a virtual nexus for researchers working in conifer genomics. The CGN web site is maintained by the Dendrome Project at the University of California, Davis.",
"homepage": "https://treegenesdb.org/",
"name": "TreeGenes",
"prefix": "r3d100012352",
"synonyms": [
"A forest tree genome database",
"Dendrome"
],
"xrefs": {
"fairsharing": "FAIRsharing.lCVfCv"
}
},
"r3d100012353": {
"description": "CAD INASAN was established in 1980 as a branch regional center of the Centre de Donnes Stellaire (CDS). Since that time, the CAD has been working to distribute, create and store astronomical data according to the requirements of time, specifics of techniques and requests of the Russian astronomical community. At present, the staff of the CAD is maintaining mirrors of several major astronomical data resources, keeping a record of Russian astronomical data resources, and is working to create new astronomical data resources. Since 2002, we are the important part of the Russian Virtual Observatory project (member of the International Virtual Observatory Alliance - IVOA). The CAD archive is based on astronomical catalogues received from Strasbourg since 1980. Several well known astronomical archives and databases are also stored at INASAN (e.g. VizieR, ADS, INES, VALD). At present CAD coordinates work on the Russian Virtual Observatory (RVO) project",
"homepage": "http://www.inasan.ru/en/divisions/dpss/cad/",
"name": "Centre for Astronomical Data of the Institute of Astronomy of the Russian Academy of Sciences",
"prefix": "r3d100012353",
"synonyms": [
"CAD INASAN"
]
},
"r3d100012354": {
"description": "DNASU is a central repository for plasmid clones and collections. Currently we store and distribute over 200,000 plasmids including 75,000 human and mouse plasmids, full genome collections, the protein expression plasmids from the Protein Structure Initiative as the PSI: Biology Material Repository (PSI : Biology-MR), and both small and large collections from individual researchers. We are also a founding member and distributor of the ORFeome Collaboration plasmid collection.",
"homepage": "https://dnasu.org/DNASU/Home.do",
"name": "DNASU plasmid repository",
"prefix": "r3d100012354",
"synonyms": [
"DNASU"
],
"xrefs": {
"fairsharing": "FAIRsharing.qqc7zw",
"sciex": "10298",
"scr": "012185"
}
},
"r3d100012355": {
"description": "PeanutBase is a peanut community resource providing genetic, genomic, gene function, and germplasm data to support peanut breeding and molecular research. This includes molecular markers, genetic maps, QTL data, genome assemblies, germplasm records, and traits. Data is curated from literature and submitted directly by researchers. Funding for PeanutBase is provided by the Peanut Foundation with in-kind contributions from the USDA-ARS.",
"homepage": "https://peanutbase.org",
"name": "PeanutBase",
"prefix": "r3d100012355",
"synonyms": [
"Genetic and genomic data to enable more rapid crop improvement in peanut"
],
"xrefs": {
"fairsharing": "FAIRsharing.fYFurb"
}
},
"r3d100012356": {
"description": "EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload, download and reprocess the thousands of raw, 2D images used to build a 3D structure. \nThe purpose of EMPIAR is to provide an easy access to the state-of-the-art raw data to facilitate methods development and validation, which will lead to better 3D structures. It complements the Electron Microscopy Data Bank (EMDB), where 3D images are stored, and uses the fault-tolerant Aspera platform for data transfers",
"homepage": "https://www.ebi.ac.uk/empiar/",
"name": "Electron Microscopy Public Image Archive",
"prefix": "r3d100012356",
"synonyms": [
"EMDB Public Image Archive",
"EMPIAR",
"Electron Microscopy Data Bank Public Image Archive",
"formerly: Electron Microscopy Pilot Image ARchive"
],
"xrefs": {
"fairsharing": "FAIRsharing.dff3ef"
}
},
"r3d100012358": {
"description": "The Australian Marine Mammal Centre has developed database applications to support marine mammal conservation and policy initiatives.",
"homepage": "https://data.marinemammals.gov.au/",
"name": "National Marine Mammal Data Portal",
"prefix": "r3d100012358",
"synonyms": [
"NMMDB"
]
},
"r3d100012359": {
"description": "The Intermediate Filament Database will function as a continuously updated review of the intermediate filament field and it is hoped that users will contribute to the development and expansion of the database on a regular basis. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants. Suggestions on ways to improve the database are also welcome.",
"homepage": "http://www.interfil.org/index.php",
"name": "Human Intermediate Filament Database",
"prefix": "r3d100012359",
"synonyms": [
"HIFD"
],
"xrefs": {
"nif": "0000-03034",
"scr": "007744"
}
},
"r3d100012360": {
"description": "The project aims to examine and index the genomic diversity through the generation of complete mitochondrial and nuclear genome sequences of sharks and rays of the Pacific Rim. There is a huge diversity of elasmobranch fishes in this region, but many species are under threat because of poor management and conservation measures in many countries. It is absolutely critical that speciesβ identities are correct for conservation and fisheries management purposes. This project will provide this clarity of identity for both charismatic and commercially important species through the inclusion of βgenetypesβ (ie., BioVouchers) and the application of genetic tools that utilize whole mitochondrial and nuclear genome sequences.",
"homepage": "https://www.molecularfisherieslaboratory.com.au/efish/",
"name": "eFish",
"prefix": "r3d100012360",
"synonyms": [
"Genomic Database Repository"
]
},
"r3d100012361": {
"description": "IANUS is a DFG-funded project to set up a national research data center for archeology and ancient science in Germany.",
"homepage": "http://datenportal.ianus-fdz.de/",
"name": "IANUS Datenportal",
"prefix": "r3d100012361",
"synonyms": [
"Digitale Forschungsdaten aus ArchΓ€ologie & Altertumswissenschaften"
]
},
"r3d100012362": {
"description": "VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools.",
"homepage": "https://viperdb.org/",
"name": "VIPERdb",
"prefix": "r3d100012362",
"synonyms": [
"Virus Particle Explorer database"
],
"xrefs": {
"fairsharing": "FAIRsharing.45e0f5",
"nif": "0000-03630",
"scr": "007970"
}
},
"r3d100012363": {
"description": "GrainGenes is a digital platform that serves small grains research communities as their central data repository and as a facilitator for community activities.",
"homepage": "https://wheat.pw.usda.gov/GG3/",
"name": "GrainGenes",
"prefix": "r3d100012363",
"synonyms": [
"A Database for Triticeae and Avena"
],
"xrefs": {
"fairsharing": "FAIRsharing.pcs58g",
"nif": "0000-02925",
"scr": "007696"
}
},
"r3d100012366": {
"description": "The Comparative RNA Web (CRW) Site disseminates information about RNA structure and evolution that has been determined using comparative sequence analysis. We present both raw (sequences, structure models, metadata) and processed (analyses, evolution, accuracy) data, organized into four main sections.",
"homepage": "https://crw-site.chemistry.gatech.edu/",
"name": "Comparative RNA Web",
"prefix": "r3d100012366",
"synonyms": [
"CRW"
]
},
"r3d100012368": {
"description": "The Life Science Database Archive maintains and stores the datasets generated by life scientists in Japan in a long-term and stable state as national public goods. The Archive makes it easier for many people to search datasets by metadata (description of datasets) in a unified format, and to access and download the datasets with clear terms of use.\nIn addition, the Archive provides datasets in forms friendly to different types of users in public and private institutions, and thereby supports further contribution of each research to life science.",
"homepage": "https://dbarchive.biosciencedbc.jp/index-e.html",
"name": "Life Science Database Archive",
"prefix": "r3d100012368",
"synonyms": [
"LSDB Archive"
],
"xrefs": {
"fairsharing": "FAIRsharing.dq46p7"
}
},
"r3d100012369": {
"description": "Code Ocean is a cloud-based computational reproducibility platform that provides researchers an easy way to share, discover and run code published in academic journals and conferences.",
"homepage": "https://codeocean.com/",
"name": "Code Ocean",
"prefix": "r3d100012369",
"synonyms": [
"CO"
],
"xrefs": {
"fairsharing": "FAIRsharing.thskvr",
"scr": "015532"
}
},
"r3d100012372": {
"description": "<<>>!!!>>>",
"homepage": "http://rdp.cme.msu.edu/index.jsp",
"name": "RDP",
"prefix": "r3d100012372",
"synonyms": [
"Ribosomal Database Project"
],
"xrefs": {
"nif": "0000-03404",
"omics": "01513",
"scr": "006633"
}
},
"r3d100012374": {
"description": "DaSCH is the trusted platform and partner for open research data in the Humanities.\nDaSCH develops and operates a FAIR long-term repository and a generic virtual research environment for open research data in the humanities in Switzerland. We provide long-term direct access to the data, enable their continuous editing and allow for precise citation of single objects within a dataset. We ensure interoperability with tools used by the Humanities and Cultural Sciences communities and foster the use of standards. The development of our platform happens in close cooperation with these communities. We provide training and advice in the area of research data management, promote open data and the use of standards.\nDaSCH is the coordinating institution and representative of Switzerland in the European Research Infrastructure Consortium βDigital Research Infrastructure for the Arts and Humanitiesβ (DARIAH ERIC). Within this mandate, we actively engage in community building within Switzerland and abroad.\nDaSCH cooperates with national and international organizations and initiatives in order to provide services that are fit for purpose within the broader Swiss open research data landscape and that are coordinated with other institutions such as FORS.\nWe base our actions on the values reliability, flexibility, appreciation, curiosity, and persistence.\nFurthermore, DARIAHβs activities in Switzerland are coordinated by DaSCH and DaSCH is acting as DARIAH-CH Coordination Office.",
"homepage": "https://admin.dasch.swiss/",
"name": "Swiss National Data and Service Center for the Humanities",
"prefix": "r3d100012374",
"synonyms": [
"DaSCH"
],
"xrefs": {
"fairsharing": "FAIRsharing.095469"
}
},
"r3d100012375": {
"description": "The CosmoSim database provides results from cosmological simulations performed within different projects: the MultiDark and Bolshoi project, and the CLUES project. \nThe CosmoSim webpage provides access to several cosmological simulations, with a separate database for each simulation. Simulations overview: https://www.cosmosim.org/cms/simulations/simulations-overview/ .\nCosmoSim is a contribution to the German Astrophysical Virtual Observatory.",
"homepage": "https://www.cosmosim.org/",
"name": "CosmoSim",
"prefix": "r3d100012375",
"synonyms": [
"CosmoSim database"
]
},
"r3d100012376": {
"description": "An open digital archive of scholarly, intellectual and research outputs of the University of South Africa. The UnisaIR contains and preserves theses and dissertations, research articles, conference papers, rare and special materials and many other digital assets. With special collections from the Documentation Center for African Studies including manuscripts, photos, political posters and other archival materials about the history of South Africa.",
"homepage": "https://uir.unisa.ac.za/",
"name": "Unisa Institutional Repository",
"prefix": "r3d100012376",
"synonyms": [
"UnisaIR",
"University of South Africa Institutional Repository"
],
"xrefs": {
"roar": "3911"
}
},
"r3d100012377": {
"description": "B2FIND is a discovery service based on metadata steadily harvested from research data collections from EUDAT data centres and other repositories. The service offers faceted browsing and it allows in particular to discover data that is stored through the B2SAFE and B2SHARE services. The B2FIND service includes metadata that is harvested from many different community repositories.",
"homepage": "https://b2find.eudat.eu/",
"name": "B2FIND",
"prefix": "r3d100012377"
},
"r3d100012378": {
"description": "The Analysis & Policy Observatory is an award-winning research collection and information service curating key resources to support evidence-informed policy and practice. Open access public policy and practice repository for grey literature and data.",
"homepage": "https://apo.org.au/",
"name": "Analysis and Policy Observatory",
"prefix": "r3d100012378",
"synonyms": [
"APO"
]
},
"r3d100012379": {
"description": "This is the (meta) data catalog of Senckenberg Nature Research Society.",
"homepage": "https://dataportal.senckenberg.de/",
"name": "Senckenberg (meta) data portal",
"prefix": "r3d100012379",
"synonyms": [
"Senckenberg (meta) data catalog"
]
},
"r3d100012380": {
"description": "<<>>!!!>>>",
"homepage": "http://iid.ophid.utoronto.ca/",
"name": "Integrated Interactions Database",
"prefix": "r3d100012380",
"synonyms": [
"IID"
],
"xrefs": {
"fairsharing": "FAIRsharing.536d54"
}
},
"r3d100012381": {
"description": "HPIDB is a public resource, which integrates experimental PPIs from various databases into a single database. The Host-Pathogen Interaction Database (HPIDB) is a genomics resource devoted to understanding molecular interactions between key organisms and the pathogens to which they are susceptible.",
"homepage": "https://hpidb.igbb.msstate.edu/",
"name": "Host - Pathogen Interaction Database",
"prefix": "r3d100012381",
"synonyms": [
"HPIDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.fk0z49"
}
},
"r3d100012383": {
"description": "OceanSITES is a worldwide system of long-term, deepwater reference stations measuring dozens of variables and monitoring the full depth of the ocean from air-sea interactions down to 5,000 meters.\n\nSince 1999, the international OceanSITES science team has shared both data and costs in order to capitalize on the enormous potential of these moorings. The growing network now consists of about 30 surface and 30 subsurface arrays. Satellite telemetry enables near real-time access to OceanSITES data by scientists and the public.\n\nOceanSITES moorings are an integral part of the Global Ocean Observing System. They complement satellite imagery and ARGO float data by adding the dimensions of time and depth.",
"homepage": "http://www.oceansites.org/index.html",
"name": "OceanSITES",
"prefix": "r3d100012383",
"synonyms": [
"Taking the pulse of the global ocean"
]
},
"r3d100012384": {
"description": "CaltechDATA is an institutional data repository for Caltech. Caltech library runs the repository to preserve the accomplishments of Caltech researchers and share their results with the world. Caltech-associated researchers can upload data, link data with their publications, and assign a permanent DOI so that others can reference the data set. The repository also preserves software and has automatic Github integration. All files present in the repository are open access or embargoed, and all metadata is always available to the public.",
"homepage": "https://data.caltech.edu",
"name": "CaltechDATA",
"prefix": "r3d100012384",
"synonyms": [
"California Institute of Technology Research Data Repository"
],
"xrefs": {
"fairsharing": "FAIRsharing.S09se7"
}
},
"r3d100012385": {
"description": "The Texas Data Repository is a platform for publishing and archiving datasets (and other data products) created by faculty, staff, and students at Texas higher education institutions. The repository is built in an open-source application called Dataverse, developed and used by Harvard University.\nThe repository is hosted by the Texas Digital Library, a consortium of academic libraries in Texas with a proven history of providing shared technology services that support secure, reliable access to digital collections of research and scholarship. For a list of TDL participating institutions, please visit: https://www.tdl.org/members/.",
"homepage": "https://dataverse.tdl.org/",
"name": "Texas Data Repository",
"prefix": "r3d100012385",
"synonyms": [
"TDR"
],
"xrefs": {
"fairsharing": "FAIRsharing.wqsxtg"
}
},
"r3d100012386": {
"description": "<<>>!!!>>>",
"homepage": "https://www.ub.edu/sior/",
"name": "SIOR",
"prefix": "r3d100012386",
"synonyms": [
"Social Impact of Science"
]
},
"r3d100012388": {
"description": "GlyTouCan is the international glycan structure repository. This repository is a freely available, uncurated registry for glycan structures that assigns globally unique accession numbers to any glycan independent of the level of information provided by the experimental method used to identify the structure(s). Any glycan structure, ranging in resolution from monosaccharide composition to fully defined structures can be registered as long as there are no inconsistencies in the structure.",
"homepage": "https://glytoucan.org/",
"name": "GlyTouCan",
"prefix": "r3d100012388",
"synonyms": [
"International Glycan Repository"
],
"xrefs": {
"fairsharing": "FAIRsharing.5Pze7l"
}
},
"r3d100012389": {
"description": "The repository contains all digital data such as images, 3d models and analysis which were acquired in the Ancient Steelyards Project.",
"homepage": "http://repository.edition-topoi.org/collection/BSYP",
"name": "Ancient Steelyards",
"prefix": "r3d100012389",
"synonyms": [
"BSYP"
],
"xrefs": {
"doi": "10.17171/1-6"
}
},
"r3d100012390": {
"description": "Methods of digital architectural documentation/polychromy (pilot project). Three architectural fragments were recorded with photography, architectural drawings by hand, different techniques of 3D scanning, and Reflectance Transformation Imaging (RTI).",
"homepage": "http://repository.edition-topoi.org/collection/MAGN",
"name": "Architectural Fragments from Magnesia on the Maeander",
"prefix": "r3d100012390",
"synonyms": [
"MAGN"
],
"xrefs": {
"doi": "10.17171/2-3"
}
},
"r3d100012391": {
"description": "The repository contains the complete model of the Bern campaign; only the upper part of the vault could not be measured due to renovation works carried out on the dome at the time of the campaign.",
"homepage": "http://repository.edition-topoi.org/collection/HASO",
"name": "Hagia Sophia 3D",
"prefix": "r3d100012391",
"synonyms": [
"HASO",
"Sancta Sophia"
],
"xrefs": {
"doi": "10.17171/2-6"
}
},
"r3d100012392": {
"description": "A digital collection of Early Christian Greek Inscriptions from Asia Minor and Greece.",
"homepage": "http://repository.edition-topoi.org/collection/ICG",
"name": "Inscriptiones Christianae Graecae",
"prefix": "r3d100012392",
"synonyms": [
"ICG"
],
"xrefs": {
"doi": "10.17171/1-8"
}
},
"r3d100012393": {
"description": "Published data is based on the drawings from three books published by WΓ€fler and Marschall.\nRock paintings in Indonesia were recorded during three short excursions by Markus WΓ€fler and Wolfgang Marschall. Threatened by environmental changes and human interventions and activities, these rock paintings represent the latest specimen of early drawings in that region.",
"homepage": "http://repository.edition-topoi.org/collection/PIND",
"name": "Rock Paintings in Indonesia",
"prefix": "r3d100012393",
"synonyms": [
"PIND"
],
"xrefs": {
"doi": "10.17171/1-7"
}
},
"r3d100012394": {
"description": "ISTA Research Explorer is an online digital repository of multi-disciplinary research datasets as well as publications produced at IST Austria, hosted by the Library. ISTA researchers who have produced research data associated with an existing or forthcoming publication, or which has potential use for other researches, are invited to upload their dataset for sharing and safekeeping. A persistent identifier and suggested citation will be provided.",
"homepage": "https://research-explorer.ista.ac.at/",
"name": "ISTA Research Explorer",
"prefix": "r3d100012394",
"synonyms": [
"ISTA REx"
]
},
"r3d100012396": {
"description": "A database for plant breeders and researchers to combine, visualize, and interrogate the wealth of phenotype and genotype data generated by the Triticeae Coordinated Agricultural Project (TCAP).",
"homepage": "https://triticeaetoolbox.org",
"name": "Triticeae Toolbox",
"prefix": "r3d100012396",
"synonyms": [
"T3"
],
"xrefs": {
"fairsharing": "FAIRsharing.55ev2y"
}
},
"r3d100012397": {
"description": "Brainlife promotes engagement and education in reproducible neuroscience. We do this by providing an online platform where users can publish code (Apps), Data, and make it \"alive\" by integragrate various HPC and cloud computing resources to run those Apps. Brainlife also provide mechanisms to publish all research assets associated with a scientific project (data and analyses) embedded in a cloud computing environment and referenced by a single digital-object-identifier (DOI). The platform is unique because of its focus on supporting scientific reproducibility beyond open code and open data, by providing fundamental smart mechanisms for what we refer to as βOpen Services.β",
"homepage": "https://brainlife.io",
"name": "brainlife",
"prefix": "r3d100012397",
"synonyms": [
"brain life",
"brainlife.io"
],
"xrefs": {
"fairsharing": "FAIRsharing.by3p8p",
"scr": "020940"
}
},
"r3d100012398": {
"description": "The aim of the research project TOPOI II A-2-4 was to re-evaluate archaeological records and finds resulting from earlier investigations within the context of recent and ongoing research across the region.",
"homepage": "http://repository.edition-topoi.org/collection/MRMD",
"name": "The Neolithic in the Nile Delta",
"prefix": "r3d100012398",
"synonyms": [
"MRMD"
],
"xrefs": {
"doi": "10.17171/1-9"
}
},
"r3d100012399": {
"description": "DIGIBUG aims to collect, compile and organise the scientific, teaching and institutional digital documents produced by the University of Granada to support research, teaching and learning.",
"homepage": "https://digibug.ugr.es/",
"name": "Digibug: Repositorio Institucional de la Universidad de Granada",
"prefix": "r3d100012399",
"synonyms": [
"University of Granada Institutional Repository"
],
"xrefs": {
"roar": "437"
}
},
"r3d100012400": {
"description": "Collections of digital resources to ancient columns",
"homepage": "http://repository.edition-topoi.org/collection/CLMN/",
"name": "Ancient Columns",
"prefix": "r3d100012400",
"synonyms": [
"CLMN"
],
"xrefs": {
"doi": "10.17171/2-2"
}
},
"r3d100012402": {
"description": "BioGPS is a gene portal built with two guiding principles in mind -- customizability and extensibility. It is a complete resource for learning about gene and protein function. A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function.",
"homepage": "http://biogps.org/#goto=welcome",
"name": "BioGPS",
"prefix": "r3d100012402",
"synonyms": [
"Biological Gene Portal Services"
],
"xrefs": {
"nif": "0000-10168",
"omics": "03291",
"scr": "006433"
}
},
"r3d100012403": {
"description": "TCCON is a network of ground-based Fourier Transform Spectrometers recording direct solar spectra in the near-infrared spectral region. From these spectra, accurate and precise column-averaged abundance of CO2, CH4, N2O, HF, CO, H2O, and HDO are retrieved.",
"homepage": "https://tccondata.org",
"name": "TCCON Data Archive",
"prefix": "r3d100012403",
"synonyms": [
"Total Carbon Column Observing Network Data Archive"
]
},
"r3d100012404": {
"description": "The Research Data Center for Higher Education Research and Science Studies (FDZ-DZHW) at the German Centre for Higher Education Research and Science Studies (DZHW) in Hannover provides the scientific community with quantitative and qualitative research data from the field of higher education and science studies for research and teaching purposes. The data pool of the Research Data Centre is based on two sources: Firstly, it contains the current surveys of the panels conducted in-house (especially DZHW Graduate Panel, Social Survey, DZHW Panel Study of School Leavers with a Higher Education Entrance Qualification, DZHW Scientists Survey), which are integrated by default. Secondly, the Research Data Centre constantly processes, documents and integrates inventory data of the DZHW and its prior organisations. External data from the research area is also integrated into the FDZ data pool.",
"homepage": "https://fdz.dzhw.eu/en/",
"name": "FDZ-DZHW",
"prefix": "r3d100012404",
"synonyms": [
"Forschungsdatenzentrum fΓΌr Hochschul- und Wissenschaftsforschung",
"Research Data Centre for Higher Education Research and Science Studies"
]
},
"r3d100012405": {
"description": "The Research Data Repository is the University of Essex's online data repository where research data resulting from research taking place within the university can be deposited, published and made accessible to the research community.",
"homepage": "https://researchdata.essex.ac.uk/",
"name": "Research Data at Essex",
"prefix": "r3d100012405",
"synonyms": [
"University of Essex Research Data Repository"
]
},
"r3d100012406": {
"description": "The Spiral Digital Repository is the Imperial College London institutional open access repository. This system allows you, as an author, to make your research documents open access without incurring additional publication costs.\nWhen you self-archive a research document in Spiral it becomes free for anyone to read. You can upload copies of your publications to Spiral using Symplectic Elements. All deposited content becomes searchable online.",
"homepage": "https://spiral.imperial.ac.uk/",
"name": "Spiral",
"prefix": "r3d100012406",
"synonyms": [
"Spiral digital repository"
]
},
"r3d100012407": {
"description": "The University of Lincoln's Institutional Repository is for the permanent deposit of research outputs produced by the University. Repository content can be browsed or searched through this website or through searching the internet. Wherever possible, repository content is freely available for download and use according to our Copyright and Use Notice.",
"homepage": "https://eprints.lincoln.ac.uk/",
"name": "Lincoln repository",
"prefix": "r3d100012407",
"xrefs": {
"opendoar": "5",
"roar": "1392"
}
},
"r3d100012408": {
"description": "A digital repository for Newcastle Universityβs research data.",
"homepage": "https://data.ncl.ac.uk/",
"name": "NCL Data",
"prefix": "r3d100012408",
"synonyms": [
"Newcastle University Data",
"data.ncl"
]
},
"r3d100012409": {
"description": "The online digital research data repository of multi-disciplinary research datasets produced at the University of Nottingham, hosted by Information Services and managed and curated by Libraries, Research & Learning Resources.\nUniversity of Nottingham researchers who have produced research data associated with an existing or forthcoming publication, or which has potential use for other researchers, are invited to upload their dataset.",
"homepage": "https://rdmc.nottingham.ac.uk/",
"name": "Nottingham Research Data Management Repository",
"prefix": "r3d100012409",
"xrefs": {
"opendoar": "3902"
}
},
"r3d100012410": {
"description": "eData is a data repository where QMU researchers can store finished project data that, where appropriate, can be accessed and potentially re-used by other researchers.",
"homepage": "https://eresearch.qmu.ac.uk/handle/20.500.12289/4",
"name": "QMU eData Repository",
"prefix": "r3d100012410",
"synonyms": [
"Queen Margaret University eData Repository"
]
},
"r3d100012411": {
"description": "The St Andrews research portal features the research activities within the University of St Andrews.",
"homepage": "https://risweb.st-andrews.ac.uk/portal/en/datasets/index.html",
"name": "St Andrews Research portal - Research Data",
"prefix": "r3d100012411"
},
"r3d100012412": {
"description": "The KnowledgeBase of the University of Strathclyde includes research data from the staff and students of the university.",
"homepage": "https://pureportal.strath.ac.uk/en/datasets/",
"name": "University of Strathclyde KnowledgeBase Datasets",
"prefix": "r3d100012412"
},
"r3d100012413": {
"description": "This Repository holds research data for all research projects where there is a need to store and share the supporting research.\n\nAccording to current Research Data Policy these records will include all data from projects funded by RCUK funders and in particular the AHRC.",
"homepage": "https://ualresearchonline.arts.ac.uk/",
"name": "UAL Research Online",
"prefix": "r3d100012413",
"synonyms": [
"University of the Arts London Data Repository"
]
},
"r3d100012414": {
"description": "UEL Research Repository: the institutional repository of open access publications and research data at the University of East London. As a research archive, it preserves and disseminates scholarly work created by members of the University of East London.",
"homepage": "https://repository.uel.ac.uk",
"name": "UEL Research Repository",
"prefix": "r3d100012414",
"synonyms": [
"formerly: data.uel"
]
},
"r3d100012415": {
"description": "The Warwick Research Archive Portal (WRAP) is the home of the University's full text, open access research content and contains, journal articles, Warwick doctoral dissertations, book chapters, conference papers, working papers and more.",
"homepage": "https://wrap.warwick.ac.uk/",
"name": "WRAP",
"prefix": "r3d100012415",
"synonyms": [
"Warwick Research Archive Portal"
],
"xrefs": {
"opendoar": "1288",
"roar": "1496"
}
},
"r3d100012417": {
"description": "UCL Discovery is UCL's open access repository, showcasing and providing access to UCL research publications. UCL Discovery accepts small scale datasets associated with publications.",
"homepage": "https://discovery.ucl.ac.uk/",
"name": "UCL Discovery",
"prefix": "r3d100012417"
},
"r3d100012418": {
"description": "<<>>!!!>>> The Detection of Archaeological Residues using Remote-sensing Techniques (DART) project was initiated in 2010 in order to investigate the ability of various sensors to detect archaeological features in βdifficultβ circumstances. Concluding in September 2013, DART had the overall aim of developing analytical methods for identifying and quantifying gradual changes and dynamics in sensor responses associated with surface and near-surface archaeological features under different environmental and land-management conditions.",
"homepage": "http://dartportal.leeds.ac.uk/",
"name": "DART Data",
"prefix": "r3d100012418",
"synonyms": [
"Detection of Archaeological Residues using Remote-sensing Techniques"
],
"xrefs": {
"biodbcore": "001554"
}
},
"r3d100012419": {
"description": "DIAS aims at collecting and storing earth observation data; analyzing such data in combination with socio-economic data, and converting data into information useful for crisis management with respect to global-scale environmental disasters, and other threats; and to make this information available within Japan and overseas.",
"homepage": "https://diasjp.net/en/",
"name": "DIAS",
"prefix": "r3d100012419",
"synonyms": [
"Data Integration and Analysis System"
]
},
"r3d100012420": {
"description": "<<>>!!!>>> \nSeedMe is a result of a decade of onerous experience in preparing and sharing visualization results from supercomputing simulations with many researchers at different geographic locations using different operating systems. Itβs been a laborβintensive process, unsupported by useful tools and procedures for sharing information. SeedMe provides a secure and easy-to-use functionality for efficiently and conveniently sharing results that aims to create transformative impact across many scientific domains.",
"homepage": "https://www.seedme.org/",
"name": "SeedMe",
"prefix": "r3d100012420",
"synonyms": [
"Stream, Encode, Explore and Disseminate My Experiments"
]
},
"r3d100012421": {
"description": "LINCS Data Portal provides access to LINCS data from various sources. The program has six Data and Signature Generation Centers: Drug Toxicity Signature Generation Center, HMS LINCS Center, LINCS Center for Transcriptomics, LINCS Proteomic Characterization Center for Signaling and Epigenetics, MEP LINCS Center, and NeuroLINCS Center.",
"homepage": "https://lincsportal.ccs.miami.edu/dcic-portal/",
"name": "LINCS Data Portal",
"prefix": "r3d100012421",
"synonyms": [
"Library of Integrated Network-based Signatures Data Portal"
],
"xrefs": {
"fairsharing": "FAIRsharing.fb0r2g",
"scr": "014939"
}
},
"r3d100012422": {
"description": "The Tropospheric Ozone Assessment Report (TOAR) database of global surface observations is the world's most extensive collection of surface ozone measurements and includes also data on other air pollutants and on weather for some regions. Measurements from 1970 to 2019 (Version 1) have been collected in a relational database, and are made available via a graphical web interface, a REST service (https://toar-data.fz-juelich.de/api/v1) and as aggregated products on PANGAEA (https://doi.pangaea.de/10.1594/PANGAEA.876108). Measurements from 1970 to present (Version 2) are being collected in a relational database, and are made available via a REST service (https://toar-data.fz-juelich.de/api/v2).",
"homepage": "https://toar-data.fz-juelich.de/",
"name": "TOAR Surface Observation Database",
"prefix": "r3d100012422",
"synonyms": [
"Surface station data from JΓΌlich database",
"TOAR Surface Observation Database Version 1",
"TOAR Surface Observation Database Version 2",
"TOAR Surface Stations Database",
"Tropospheric Ozone Assessment Report database of global surface observations"
]
},
"r3d100012426": {
"description": ">>>!!!<<< OMICtools is no longer online >>>!!!<<< \nWe founded OMICtools in 2012 with the vision to drive progress in life science. We wanted to empower life science practitioners all over the world to achieve breakthroughs by getting data to talk. While we made tremendous progress over the past three years, developing a bioinformatics database of software and dynamic protocols, attracting more than 1.5M visitors a year, we lacked the financial support we needed to continue. We certainly gave it our all. We'd like to thank everyone who believed in us and supported us on this journey: all our users, our community, our friends, families and employees (who we consider as our extended family!).\nomicX will probably shut down its operations within the next few weeks. The team and I remain firmly committed to our vision, particularly at this very difficult time. It is now, more than ever before, that researchers need access to a resource that pools collective scientific intelligence. We have accumulated an awful lot of experience which we are keen to share. If your institution would be interested in taking over our website and database, to provide researchers with continued access to the platform, or you simply want to stay in touch with the omicX team, contact us at contact@omictools.com or at carine.toutain@fhbx.eu.",
"homepage": "https://omictools.com/",
"name": "OMICtools",
"prefix": "r3d100012426",
"xrefs": {
"nlx": "155571",
"scr": "002250"
}
},
"r3d100012427": {
"description": "AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products. Our long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models.",
"homepage": "https://agbase.arizona.edu/",
"name": "AgBase",
"prefix": "r3d100012427",
"xrefs": {
"fairsharing": "FAIRsharing.kn4ycg",
"nif": "0000-02537",
"omics": "03223",
"scr": "007547"
}
},
"r3d100012429": {
"description": "<<>>!!!>>>\nThe sequencing of several bird genomes and the anticipated sequencing of many more provided the impetus to develop a model organism database devoted to the taxonomic class: Aves. Birds provide model organisms important to the study of neurobiology, immunology, genetics, development, oncology, virology, cardiovascular biology, evolution and a variety of other life sciences. Many bird species are also important to agriculture, providing an enormous worldwide food source worldwide. Genomic approaches are proving invaluable to studying traits that affect meat yield, disease resistance, behavior, and bone development along with many other factors affecting productivity. In this context, BirdBase will serve both biomedical and agricultural researchers.",
"homepage": "http://birdbase.arizona.edu/birdbase/",
"name": "Birdbase",
"prefix": "r3d100012429",
"synonyms": [
"A database of avian genes & genomes"
]
},
"r3d100012430": {
"description": "This data repository provides access to gravity wave observations of the Atmospheric Infrared Sounder (AIRS) aboard NASA's Aqua satellite. Information on stratospheric gravity wave activity is derived from radiance measurements in the 4.3 and 15 micron CO2 fundamental bands. The repository provides browse images and netCDF data files for the years 2002 to 2017 and is frequently updated.",
"homepage": "https://datapub.fz-juelich.de/slcs/airs/gravity_waves/",
"name": "AIRS/Aqua Observations of Gravity Waves",
"prefix": "r3d100012430",
"synonyms": [
"Atmospheric Infrared Sounder / Aqua Observations of Gravity Waves"
]
},
"r3d100012431": {
"description": "AIRS moves climate research and weather prediction into the 21st century. AIRS is one of six instruments on board the Aqua satellite, part of the NASA Earth Observing System. AIRS along with its partner microwave instrument the Advanced Microwave Sounding Unit AMSU-A, represents the most advanced atmospheric sounding system ever deployed in space. Together these instruments observe the global water and energy cycles, climate variation and trends, and the response of the climate system to increased greenhouse gases.",
"homepage": "https://airs.jpl.nasa.gov/data/about-the-data/processing/",
"name": "Atmospheric Infrared Sounder",
"prefix": "r3d100012431",
"synonyms": [
"AIRS"
],
"xrefs": {
"biodbcore": "001556"
}
},
"r3d100012432": {
"description": "GABI, acronym for \"Genomanalyse im biologischen System Pflanze\", is the name of a large collaborative network of different plant genomic research projects. Plant data from different βomicsβ fronts representing more than 10 different model or crop species are integrated in GabiPD.",
"homepage": "https://www.gabipd.org/",
"name": "GabiPD",
"prefix": "r3d100012432",
"synonyms": [
"GABI Primary Database",
"Genomanalyse im biologischen System Pflanze",
"Genome Analysis of the Plant Biological System"
],
"xrefs": {
"miriam": "00000164",
"nif": "0000-02866",
"omics": "03230",
"scr": "002755"
}
},
"r3d100012433": {
"description": "The Human Genetic Variation Database (HGVD) aims to provide a central resource to archive and display Japanese genetic variation and association between the variation and transcription level of genes. The database currently contains genetic variations determined by exome sequencing of 1,208 individuals and genotyping data of common variations obtained from a cohort of 3,248 individuals.",
"homepage": "https://www.hgvd.genome.med.kyoto-u.ac.jp/index.html",
"name": "Human Genetic Variation Repository",
"prefix": "r3d100012433",
"synonyms": [
"HGVD"
],
"xrefs": {
"fairsharing": "FAIRsharing.c7edd8",
"omics": "11833"
}
},
"r3d100012435": {
"description": "The IDR makes datasets that have never previously been accessible publicly available, allowing the community to search, view, mine and even process and analyze large, complex, multidimensional life sciences image data. Sharing data promotes the validation of experimental methods and scientific conclusions, the comparison with new data obtained by the global scientific community, and enables data reuse by developers of new analysis and processing tools.",
"homepage": "https://idr.openmicroscopy.org/about/",
"name": "Image Data Resource",
"prefix": "r3d100012435",
"synonyms": [
"IDR"
],
"xrefs": {
"fairsharing": "FAIRsharing.6wf1zw",
"omics": "13850",
"scr": "017421"
}
},
"r3d100012436": {
"description": "With its βBlood Donor BIOBANKβ, the Bavarian Red Cross (BRK) Blood Donor Service offers a unique and innovative resource for biomarker research: the worldβs first blood donor based biobank. Biobanks as collections of biological material together with associated medical data open new possibilities for the development of new targeted diagnostics and therapies. The BRK Blood Donor Service maintains a unique collection of over 3 million blood samples, making it one of the largest sample collections worldwide. Every working day 2,000 new samples are added to the collection.",
"homepage": "https://www.bio-bank.de/de/index.php",
"name": "Biobank of blood donors",
"prefix": "r3d100012436",
"synonyms": [
"Biobank der Blutspender",
"Blood Donor BIOBANK"
]
},
"r3d100012437": {
"description": "The German National Cohort (NAKO) has been inviting men and women aged between 20 and 69 to 18 study centers throughout Germany since 2014. The participants are medically examined and questioned about their living conditions. The GNCβs aim is to investigate the causes of chronic diseases, such as cancer, diabetes, cardiovascular diseases, rheumatism, infectious diseases, and dementia in order to improve prevention, early diagnoses and treatment of these very widely spread diseases.",
"homepage": "https://nako.de/",
"name": "Nationale Kohorte",
"prefix": "r3d100012437",
"synonyms": [
"GNC",
"German National Cohort",
"Gesundheitsstudie",
"NAKO"
]
},
"r3d100012438": {
"description": "Historic Environment Scotland was formed in October 2015 following the merger between Historic Scotland and The Royal Commission on the Ancient and Historical Monuments of Scotland. Historic Environment Scotland is the lead public body established to investigate, care for and promote Scotlandβs historic environment. We lead and enable Scotlandβs first historic environment strategy Our Place in Time, which sets out how our historic environment will be managed. It ensures our historic environment is cared for, valued and enhanced, both now and for future generations.",
"homepage": "https://www.historicenvironment.scot/archives-and-research/archives-and-collections/",
"name": "Historic Environment Scotland",
"prefix": "r3d100012438",
"synonyms": [
"Arainneadchd eachdraidheil alba",
"HES",
"Historic Scotland (formerly)",
"Royal Commission on the Ancient and Historical Monuments of Scotland (formerly)",
"The National Record of the Historic Environment"
]
},
"r3d100012439": {
"description": "The German Neuroinformatics Node's data infrastructure (GIN) services provide a platform for comprehensive and reproducible management and sharing of neuroscience data. Building on well established versioning technology, GIN offers the power of a web based repository management service combined with a distributed file storage. The service addresses the range of research data workflows starting from data analysis on the local workstation to remote collaboration and data publication.",
"homepage": "https://gin.g-node.org/",
"name": "GIN",
"prefix": "r3d100012439",
"synonyms": [
"G-Node Data Infrastructure Services"
],
"xrefs": {
"fairsharing": "FAIRsharing.nv6mrg",
"scr": "015864"
}
},
"r3d100012440": {
"description": "DR-NTU (Data) is the institutional open access research data repository for Nanyang Technological University (NTU), Singapore. NTU researchers are encouraged to use DR-NTU (Data) to deposit, publish and archive their final research data in order to make their research data discoverable, accessible and reusable.",
"homepage": "https://researchdata.ntu.edu.sg/",
"name": "DR-NTU (Data)",
"prefix": "r3d100012440",
"synonyms": [
"Data repository - Nanyang Technological University"
],
"xrefs": {
"fairsharing": "FAIRsharing.08f055",
"opendoar": "3925",
"roar": "13092"
}
},
"r3d100012441": {
"description": "<<>>!!!>>>",
"homepage": "http://www.molgen.vib-ua.be/ADMutations/",
"name": "Alzheimer Disease & Frontotemporal Dementia Mutation Database",
"prefix": "r3d100012441",
"synonyms": [
"AD & FTD Mutation Database"
],
"xrefs": {
"nif": "0000-23934",
"omics": "16526",
"scr": "008286"
}
},
"r3d100012442": {
"description": "The Environmental Information Platform provides enhanced access to CEH's key data holdings via web-based tools, programming interfaces and a data catalogue. It enables you to visualise and interrogate some of the diverse environmental datasets held by CEH.",
"homepage": "https://eip.ceh.ac.uk/",
"name": "Environmental Information Platform",
"prefix": "r3d100012442",
"synonyms": [
"CEH-EIP",
"Centre for Ecology & Hydrology - Environmental Information Platform"
]
},
"r3d100012443": {
"description": "The aim of this repository is for it to be a location from which a wide variety of well analysed IFC-based data files can be sourced. It is planned that over time the number of data files will expand to provide significant coverage of the major aspects that would need to be tested for interoperability.",
"homepage": "https://openifcmodel.cs.auckland.ac.nz/",
"name": "Open IFC Model Repository",
"prefix": "r3d100012443"
},
"r3d100012444": {
"description": "Psi Open Data is an open repository for parapsychology research data, operated by the Society for Psychical Research. The datasets may be freely used, modified, and shared by anyone β subject, at most, to the requirement to attribute and/or share-alike (see the license attached to each dataset for details).",
"homepage": "https://open-data.spr.ac.uk/",
"name": "Psi Open Data",
"prefix": "r3d100012444"
},
"r3d100012445": {
"description": "The Rotterdam Ophthalmic Data Repository (ROD-Rep) contains data sets related to ophthalmology that the Rotterdam Ophthalmic Institute has made freely available for researchers worldwide. This portal is an initiative of the Rotterdam Ophthalmic Institute, which is the research institute of the Rotterdam Eye Hospital. It provides the datasets from ophthalmic research (includes measurements such as visual fields and various imaging modalities, grades, etc.) for sharing and re-use to accelerate multi-disciplinary research, resulting in better ophthalmic care. The portal is the successor of the ORGIDS (or Open Rotterdam Glaucoma Imaging Data Sets site); which was an initiative of Koen Vermeer, Hans Lemij and Netty Dorrestijn and initial financial support was provided by Stichting Glaucoomfonds (The Netherlands).",
"homepage": "http://www.rodrep.com/",
"name": "Rotterdam Ophthalmic Data Repository",
"prefix": "r3d100012445",
"synonyms": [
"ROD-REP"
]
},
"r3d100012447": {
"description": "MIDAS is a national research data repository. The aim of MIDAS is to collect, process, store and analyse research data and other relevant information in all fields of knowledge, enabling free, easy and convenient access to the data via the Internet. MIDAS provides services for registered and unregistered users: students, listeners, academics, researchers, scientists, research administrators, other actors of the research and studies ecosystem, and all individuals interested in research data. MIDAS consists of the MIDAS portal and MIDAS user account. The MIDAS portal is a public space accessible to anyone interested in discovering and viewing published research Data and their metadata, whereas MIDAS user account is available to registered users only. MIDAS is managed by Vilnius University.",
"homepage": "https://www.midas.lt/public-app.html#/midas?lang=en",
"name": "MIDAS",
"prefix": "r3d100012447",
"synonyms": [
"Nacionalinis atviros prieigos moksliniΕ³ tyrimΕ³ duomenΕ³ archyvas",
"National Open Access Research Data Archive"
]
},
"r3d100012448": {
"description": "Online materials database (known as PAULING FILE project) with nearly 2 million entries: physical properties, crystal structures, phase diagrams, available via API, ready for modern data-intensive applications. The source of these entries are about 0.5M peer-reviewed publications in materials science, processed during the last 30 years by an international team of PhD editors. The results are presented online with a quick search interface. The basic access is provided for free.",
"homepage": "https://mpds.io",
"name": "MPDS",
"prefix": "r3d100012448",
"synonyms": [
"Materials Platform for Data Science",
"PAULING FILE"
]
},
"r3d100012449": {
"description": "This data repository provides access to the climatology of polar stratospheric clouds (PSC) observations of Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) onboard the Envisat satellite of the European Space Agency (ESA). The MIPAS instrument operated from July 2002 until April 2012. The infrared limb emission measurements provide a unique dataset of day and night observations of polar stratospheric clouds (PSCs) up to both poles.",
"homepage": "https://datapub.fz-juelich.de/slcs/mipas/psc/",
"name": "MIPAS/Envisat Observations of Polar Stratospheric Clouds",
"prefix": "r3d100012449"
},
"r3d100012451": {
"description": "Originally established in 1989 at the University of Essex to house the British Household Panel Survey (BHPS), ISER has grown into a leading centre for the production and analysis of longitudinal studies. It encompasses the ESRC Research Centre on Micro-Social Change and the successor to the BHPS, Understanding Society. As well as providing unrivalled postgraduate study opportunities, ISER also houses an internationally-renowned Microsimulation Unit which develops and runs the tax and benefit model, EUROMOD.",
"homepage": "https://www.iser.essex.ac.uk/",
"name": "ISER Centres and Surveys",
"prefix": "r3d100012451",
"synonyms": [
"Institute for Social and Economic Research"
]
},
"r3d100012455": {
"description": "clarin:el is the Greek national network of language resources, a nation-wide Research Infrastructure devoted to the sustainable storage, sharing, dissemination and preservation of language resources.\nCLARIN EL infrastructure, which is a Greek nation-wide Research Infrastructure devoted to the sustainable storage, sharing, dissemination and preservation of language resources (LRs) and aims at increasing access to and augmentation of such resources at a national scale and beyond. It is an open, integrated, secure and interoperable storage, sharing and processing infrastructure for LRs (datasets, tools and processing services) for all domains domains and disciplines where language plays a critical role, notably. CLARIN EL is implemented in the framework of the CLARIN Attiki, national project in support of ESFRI/2006 Research Infrastructures.",
"homepage": "https://inventory.clarin.gr/",
"name": "clarin:el Central inventory of language resources and services",
"prefix": "r3d100012455"
},
"r3d100012457": {
"description": "AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first iteration (released in early 2010), AmoebaDB contains the genomes of three Entamoeba species (see below). AmoebaDB integrates whole genome sequence and annotation and will rapidly expand to include experimental data and environmental isolate sequences provided by community researchers . The database includes supplemental bioinformatics analyses and a web interface for data-mining.",
"homepage": "https://amoebadb.org/amoeba/app",
"name": "AmoebaDB",
"prefix": "r3d100012457",
"xrefs": {
"fairsharing": "FAIRsharing.swbypy",
"miriam": "00000148"
}
},
"r3d100012458": {
"description": "Giardia lamblia is a significant, environmentally transmitted, human pathogen and an amitochondriate protist. It is a major contributor to the enormous worldwide burden of human diarrheal diseases, yet the basic biology of this parasite is not well understood. No virulence factor has been identified. The Giardia lamblia genome contains only 12 million base pairs distributed onto five chromosomes. Its analysis promises to provide insights about the origins of nuclear genome organization, the metabolic pathways used by parasitic protists, and the cellular biology of host interaction and avoidance of host immune systems.\nSince the divergence of Giardia lamblia lies close to the transition between eukaryotes and prokaryotes in universal ribosomal RNA phylogenies, it is a valuable, if not unique, model for gaining basic insights into genetic innovations that led to formation of eukaryotic cells. In evolutionary terms, the divergence of this organism is at least twice as ancient as the common ancestor for yeast and man. A detailed study of its genome will provide insights into an early evolutionary stage of eukaryotic chromosome organization as well as other aspects of the prokaryotic / eukaryotic divergence.",
"homepage": "https://giardiadb.org/giardiadb/app",
"name": "GiardiaDB",
"prefix": "r3d100012458",
"xrefs": {
"fairsharing": "FAIRsharing.e7skwg",
"miriam": "00000151",
"nif": "0000-02908",
"omics": "03161",
"scr": "013377"
}
},
"r3d100012459": {
"description": "MicrosporidiaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for the phylum Microsporidia. In its first iteration (released in early 2010), MicrosporidiaDB contains the genomes of two Encephalitozoon species (see below). MicrosporidiaDB integrates whole genome sequence and annotation and will rapidly expand to include experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining.",
"homepage": "https://microsporidiadb.org/micro/app",
"name": "MicrosporidiaDB",
"prefix": "r3d100012459",
"xrefs": {
"fairsharing": "FAIRsharing.vk0ax6",
"miriam": "00000152",
"omics": "03153"
}
},
"r3d100012460": {
"description": "A genome database for the genus Piroplasma. PiroplasmaDB is a member of pathogen-databases that are housed under the NIAID-funded EuPathDB Bioinformatics Resource Center (BRC) umbrella.",
"homepage": "https://piroplasmadb.org/piro/app",
"name": "PiroplasmaDB",
"prefix": "r3d100012460",
"xrefs": {
"fairsharing": "FAIRsharing.a5a0af",
"miriam": "00000351",
"omics": "06546"
}
},
"r3d100012461": {
"description": "TrichDB integrated genomic resources for the eukaryotic protist pathogens Trichomonas vaginalis.",
"homepage": "https://trichdb.org/trichdb/app",
"name": "TrichDB",
"prefix": "r3d100012461",
"synonyms": [
"Trichomonas vaginalis Sequence Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.pv0ezt",
"miriam": "00100199",
"omics": "03162"
}
},
"r3d100012462": {
"description": "OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species/genomes, but also groups representing species-specific gene expansion families. So it serves as an important utility for automated eukaryotic genome annotation. OrthoMCL starts with reciprocal best hits within each genome as potential in-paralog/recent paralog pairs and reciprocal best hits across any two genomes as potential ortholog pairs. Related proteins are interlinked in a similarity graph. Then MCL (Markov Clustering algorithm,Van Dongen 2000; www.micans.org/mcl) is invoked to split mega-clusters. This process is analogous to the manual review in COG construction. MCL clustering is based on weights between each pair of proteins, so to correct for differences in evolutionary distance the weights are normalized before running MCL.",
"homepage": "https://orthomcl.org/orthomcl/app",
"name": "OrthoMCL",
"prefix": "r3d100012462",
"synonyms": [
"Ortholog Groups of Protein Sequences"
],
"xrefs": {
"fairsharing": "FAIRsharing.283caf",
"nif": "0000-03230",
"scr": "007839"
}
},
"r3d100012463": {
"description": "The arctic data archive system (ADS) collects observation data and modeling products obtained by various Japanese research projects and gives researchers to access the results. By centrally managing a wide variety of Arctic observation data, we promote the use of data across multiple disciplines. Researchers use these integrated databases to clarify the mechanisms of environmental change in the atmosphere, ocean, land-surface and cryosphere. That ADS will be provide an opportunity of collaboration between modelers and field scientists, can be expected.",
"homepage": "https://ads.nipr.ac.jp/",
"name": "ADS",
"prefix": "r3d100012463",
"synonyms": [
"Arctic Data archive System"
],
"xrefs": {
"fairsharing": "FAIRsharing.WDGf1A"
}
},
"r3d100012464": {
"description": "GeneWeaver combines cross-species data and gene entity integration, scalable hierarchical analysis of user data with a community-built and curated data archive of gene sets and gene networks, and tools for data driven comparison of user-defined biological, behavioral and disease concepts. Gene Weaver allows users to integrate gene sets across species, tissue and experimental platform. It differs from conventional gene set over-representation analysis tools in that it allows users to evaluate intersections among all combinations of a collection of gene sets, including, but not limited to annotations to controlled vocabularies. There are numerous applications of this approach. Sets can be stored, shared and compared privately, among user defined groups of investigators, and across all users.",
"homepage": "https://www.geneweaver.org",
"name": "GeneWeaver.org",
"prefix": "r3d100012464",
"synonyms": [
"ODE",
"The Ontological Discovery Environment"
],
"xrefs": {
"fairsharing": "FAIRsharing.1y79y9",
"nif": "0000-00517",
"omics": "02232",
"scr": "003009"
}
},
"r3d100012465": {
"description": "The European Space Agency's Planetary Science Archive (PSA) is the central repository for all scientific and engineering data returned by ESA's Solar System missions: currently including Giotto, Huygens, Mars Express, Venus Express, Rosetta, SMART-1 and ExoMars 16, as well as several ground-based cometary observations. Future missions hosted by the PSA will be Bepi Colombo, ExoMars Rover and Surface Platform and Juice.",
"homepage": "https://archives.esac.esa.int/psa/#!Home%20View",
"name": "ESA Planetary Science Archive",
"prefix": "r3d100012465",
"synonyms": [
"PSA"
]
},
"r3d100012467": {
"description": "OpenAgrar is an open access repository which publishes, stores, archives and distributes publications, publication references and research data. Its resources can be searched and used by everyone. It contains amongst others theses, reports, conference proceedings, journal articles, books, institutional documents, research datasets, videos and interviews.",
"homepage": "https://www.openagrar.de/content/index.xml?lang=en",
"name": "OpenAgrar",
"prefix": "r3d100012467",
"synonyms": [
"OA",
"Open Agrar"
],
"xrefs": {
"opendoar": "4173"
}
},
"r3d100012468": {
"description": "In the digital collections, you can take a look at the digitized prints from the holdings of the ULB DΓΌsseldorf free of cost. In special collections, the ULB unites rare, valuable and unique parts of holdings that are installed as an ensemble. Deposita, unpublished works, donations, acquisition of rare books etc. were and are an important source for the constant growth of the library. These treasures and specialties - beyond their academic value - also contribute substantially to the profile of the ULB.",
"homepage": "https://digital.ub.uni-duesseldorf.de/?lang=en",
"name": "Digital Collections ULB DΓΌsseldorf",
"prefix": "r3d100012468",
"synonyms": [
"Digitale Sammlungen Heinrich Heine UniversitΓ€t DΓΌsseldorf"
]
},
"r3d100012469": {
"description": "To target the multidisciplinary, broad scale nature of empirical educational research in the Federal Republic of Germany, a networked research data infrastructure is required which brings together disparate services from different research data providers, delivering services to researchers in a usable, needs-oriented way. The Verbund Forschungsdaten Bildung (Educational Research Data Alliance, VFDB) therefore aims to cooperate with relevant actors from science, politics and research funding institutes to set up a powerful infrastructure for empirical educational research. This service is meant to adequately capture specific needs of the scientific communities and support empirical educational research in carrying out excellent research.",
"homepage": "https://www.forschungsdaten-bildung.de",
"name": "Verbund Forschungsdaten Bildung",
"prefix": "r3d100012469",
"synonyms": [
"German Network for Educational Research Data",
"VerbundFDB"
]
},
"r3d100012470": {
"description": "The Edition Topoi research platform is an innovative, reliable information infrastructure. It serves the publication of citable research data such as 3D models, high-resolution pictures, data and databases. The content and its meta data are subject to peer review and made available on an Open Access basis. The published or publishable combination of citable research content and its technical and contextually relevant meta data is defined as Citable. The public data are generated via a cloud and can be directly connected with the individual computing environment.",
"homepage": "http://repository.edition-topoi.org/",
"name": "Edition Topoi Repository",
"prefix": "r3d100012470",
"synonyms": [
"edition|topoi"
]
},
"r3d100012471": {
"description": "A data repository and social network so that researchers can interact and collaborate, also offers tutorials and datasets for data science learning.\n\"data.world is designed for data and the people who work with data. From professional projects to open data, data.world helps you host and share your data, collaborate with your team, and capture context and conclusions as you work.\"",
"homepage": "https://data.world/",
"name": "data.world",
"prefix": "r3d100012471",
"xrefs": {
"fairsharing": "FAIRsharing.pP4ALT"
}
},
"r3d100012473": {
"description": "The Map Collection at the Faculty of Science CU (formerly the State Map Collection) belongs to one of the most extensive university map collections in Central and East Europe. The map collection is digitized as part of the Czech Ministry of Culture's project NAKI.",
"homepage": "https://www.natur.cuni.cz/geography/map-collection?set_language=en",
"name": "Map collection Charles University Faculty of Science",
"prefix": "r3d100012473",
"synonyms": [
"DigitΓ‘lni mapovΓ‘ sbirka",
"MapovΓ‘ sbΓrka PΕΓrodovΔdeckΓ© fakulty UK"
]
},
"r3d100012474": {
"description": "<<>>!!!>>>",
"homepage": "http://www.molgen.vib-ua.be/PDMutDB/",
"name": "Parkinson Disease Mutation Database",
"prefix": "r3d100012474",
"synonyms": [
"PDmutDB"
]
},
"r3d100012476": {
"description": "BioGrid Australia Limited operates a federated data sharing platform for collaborative translational health and medical research providing a secure infrastructure that advances health research by linking privacy-protected and ethically approved data among a wide network of health collaborators. BioGrid links real-time de-identified health data across institutions, jurisdictions and diseases to assist researchers and clinicians improve their research and clinical outcomes. The web-based infrastructure provides ethical access while protecting both privacy and intellectual property.",
"homepage": "https://www.biogrid.org.au/",
"name": "Biogrid Australia",
"prefix": "r3d100012476",
"xrefs": {
"nlx": "152036",
"scr": "006334"
}
},
"r3d100012477": {
"description": "<<>>!!!>>>",
"homepage": "http://www.biosearch.in/",
"name": "Biosearch",
"prefix": "r3d100012477",
"synonyms": [
"Marine Biodiversity Database of India"
]
},
"r3d100012478": {
"description": "The following databases are maintained at IAA-ULB: Nuclear Database (BRUSLIB - A collection of nuclear data (masses, fission barriers, E1 strength functions, nuclear level densities, partition functions, reaction rates) of interest for nuclear astrophysics, stellar evolution and nucleosynthesis), Nuclear Network Generator NetGen (A tool for generating nuclear-reaction rates on user-defined networks), NACRE II (An update of the Nuclear Astrophysics Compilation of Reaction Rates (NACRE) including the evaluation of 34 reactions on stable targets with mass numbers A<16), The Ninth Catalogue of Orbits of Spectroscopic Binaries (SB9), The Henize sample of S stars, The radial-velocity monitoring of barium and S stars, Molecular linelist (Molecular linelists for stellar spectra), and Stellar models (Pre-main-sequence and super-AGB phases).",
"homepage": "http://www.astro.ulb.ac.be/pmwiki/IAA/Databases",
"name": "Institut d'Astronomie et d'Astrophysique Databases",
"prefix": "r3d100012478",
"synonyms": [
"Institut d'Astronomie et d'Astrophysique Bases de DonnΓ©es"
]
},
"r3d100012479": {
"description": "<<>>!!!>>> \nThe website is archived: https://web.archive.org/web/20161118010932/http:/ourocean.jpl.nasa.gov/ You can follow links to navigate further into archived content from that site.",
"homepage": "https://ourocean.jpl.nasa.gov/",
"name": "JPL OurOcean Portal",
"prefix": "r3d100012479",
"synonyms": [
"JET Propulsion Laboratory OurOcean Portal"
]
},
"r3d100012480": {
"description": "NASA Life Sciences Portal is the next generation of the Life Sciences Data Archive for Human, Animal and Plant Research\nNASA's Human Research Program (HRP) conducts research and develops technologies that allow humans to travel safely and productively in space. The Program uses evidence from data collected on astronauts, as well as other supporting studies. These data are stored in the research data repository, Life Sciences Data Archive (LSDA).",
"homepage": "https://nlsp.nasa.gov",
"name": "NASA Life Sciences Portal",
"prefix": "r3d100012480",
"synonyms": [
"NLSP",
"formerly: LSDA",
"formerly: NASA Life Sciences Data Archive"
],
"xrefs": {
"fairsharing": "FAIRsharing.581df9"
}
},
"r3d100012481": {
"description": "!!! >>> integrated in https://www.re3data.org/repository/r3d100012653 <<< !!! The National Database for Clinical Trials Related to Mental Illness (NDCT) is an informatics platform for the sharing of human subjects data from all clinical trials funded by the National Institute of Mental Health (NIMH).",
"homepage": "https://data-archive.nimh.nih.gov/ndct/",
"name": "National Database for Clinical Trials Related to Mental Illness",
"prefix": "r3d100012481",
"synonyms": [
"NDCT"
],
"xrefs": {
"fairsharing": "FAIRsharing.1h7t5t",
"scr": "013795"
}
},
"r3d100012482": {
"description": "National Genomic Resources Repository is established as an institutional framework for methodical and centralized efforts to collect, generate, conserve and distribute genomic resources for agricultural research.",
"homepage": "http://www.nbpgr.ernet.in:8080/repository/home.htm",
"name": "National Genomic Resources Repository",
"prefix": "r3d100012482"
},
"r3d100012483": {
"description": "The I&M GIS group of NPS manages the collection, analysis, and distribution of I&M, NPS, and related geospatial data to I&M networks, the NPS, and the public. Develops, collects, and shares helpful GIS tools, extensions, and applications with I&M networks, the NPS, and the public.",
"homepage": "https://www.nps.gov/gis/index.html",
"name": "National Park Service Geographic Information Systems",
"prefix": "r3d100012483",
"synonyms": [
"I&M GIS",
"Inventory & Monitoring Geopgraphic Information Systems"
]
},
"r3d100012485": {
"description": "Natural Resources Canada (NRCan) seeks to enhance the responsible development and use of Canadaβs natural resources and the competitiveness of Canadaβs natural resources products. We are an established leader in science and technology in the fields of energy, forests, and minerals and metals and use our expertise in earth sciences to build and maintain an up-to-date knowledge base of our landmass.",
"homepage": "https://www.nrcan.gc.ca/earth-sciences/earth-sciences-resources/earth-sciences-tools-applications/10790",
"name": "Natural Resources Canada Earth Sciences Data",
"prefix": "r3d100012485",
"synonyms": [
"Ressources naturelles Canada DonnΓ©es Sciences de la Terre"
]
},
"r3d100012486": {
"description": "SimTK is a free project-hosting platform for the biomedical computation community that enables researchers to easily share their software, data, and models and provides the infrastructure so they can support and grow a community around their projects.\nIt has over 126.656 members, hosts 1.648 projects from researchers around the world, and has had more than 2.095.783 files downloaded from it. Individuals have created SimTK projects to meet publisher and funding agenciesβ software and data sharing requirements, run scientific challenges, create a collection of their communityβs resources, and much more.",
"homepage": "https://simtk.org",
"name": "SimTK",
"prefix": "r3d100012486",
"xrefs": {
"nif": "0000-23302",
"scr": "002680"
}
},
"r3d100012487": {
"description": "The South African Environmental Observation Network (SAEON) Open Data Platform (ODP) is a metadata repository that facilitates the publication, discovery, dissemination, and preservation of earth observation and environmental data in South Africa. SAEON is a long-term environmental observation and research facility of the National Research Foundation (NRF).",
"homepage": "https://catalogue.saeon.ac.za/",
"name": "South African Environmental Observation Network Data Portal",
"prefix": "r3d100012487",
"synonyms": [
"SAEON Data Portal"
],
"xrefs": {
"fairsharing": "FAIRsharing.387a4a"
}
},
"r3d100012488": {
"description": "WBG Finances is a World Bank Group digital platform that provides our clients and partners access to public financial data and portfolio information from across all Group entities in one place.\nWBG Finances simplifies the presentation of financial information in an βeasy to consumeβ and in the context of Country and Portfolio across WBG.\nOpen Finances makes World Bank Groupβs financials available for everybody to explore. All the data presented is available to everybody to analyze, visualize, and share with others. We invite you to explore the numerous tools, build your own visualizations or download the data in multiple formats. If you are a developer, connect to it through the APIs associated with all the datasets.",
"homepage": "https://finances.worldbank.org/",
"name": "WBG Open Finances",
"prefix": "r3d100012488",
"synonyms": [
"World Bank Group Finances Open Finances"
]
},
"r3d100012489": {
"description": "<<>>!!!>>>",
"homepage": "http://data.gov.ru/?language=en",
"name": "Open Data Portal Russia",
"prefix": "r3d100012489",
"synonyms": [
"Open Data Portal of the Russian Federation",
"Open Data Russia"
]
},
"r3d100012490": {
"description": "The CALIPSO satellite provides new insight into the role that clouds and atmospheric aerosols play in regulating Earth's weather, climate, and air quality.\nCALIPSO combines an active lidar instrument with passive infrared and visible imagers to probe the vertical structure and properties of thin clouds and aerosols over the globe. CALIPSO was launched on April 28, 2006, with the CloudSat satellite.\nCALIPSO and CloudSat are highly complementary and together provide new, never-before-seen 3D perspectives of how clouds and aerosols form, evolve, and affect weather and climate. CALIPSO and CloudSat fly in formation with three other satellites in the A-train constellation to enable an even greater understanding of our climate system.",
"homepage": "https://www-calipso.larc.nasa.gov/",
"name": "Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations",
"prefix": "r3d100012490",
"synonyms": [
"CALIPSO"
],
"xrefs": {
"fairsharing": "FAIRsharing.50d4cd"
}
},
"r3d100012491": {
"description": "The NASA/GEWEX SRB project is a major component of the GEWEX radiation research. The objective of the NASA/GEWEX SRB project is to determine surface, top-of-atmosphere (TOA), and atmospheric shortwave (SW) and longwave (LW) radiative fluxes with the precision needed to predict transient climate variations and decadal-to-centennial climate trends.",
"homepage": "https://asdc.larc.nasa.gov/project/SRB",
"name": "NASA GEWEX Surface Radiation Budget",
"prefix": "r3d100012491",
"synonyms": [
"NASA GEWEX SRB"
]
},
"r3d100012492": {
"description": "The mission of NCHS is to provide statistical information that will guide actions and policies to improve the health of the American people. As the Nation's principal health statistics agency, NCHS is responsible for collecting accurate, relevant, and timely data. NCHS' mission, and those of its counterparts in the Federal statistics system, focuses on the collection, analysis, and dissemination of information that is of use to a broad range of us.",
"homepage": "https://www.cdc.gov/nchs/index.htm",
"name": "National Center for Health Statistics",
"prefix": "r3d100012492",
"synonyms": [
"NCHS"
],
"xrefs": {
"nlx": "151844",
"scr": "001078"
}
},
"r3d100012493": {
"description": "The Project on Human Development in Chicago Neighborhoods (PHDCN) is a large-scale, interdisciplinary study of how families, schools, and neighborhoods affect child and adolescent development. It was designed to advance the understanding of the developmental pathways of both positive and negative human social behaviors. In particular, the project examined the causes and pathways of juvenile delinquency, adult crime, substance abuse, and violence. At the same time, the project also provided a detailed look at the environments in which these social behaviors take place by collecting substantial amounts of data about urban Chicago, including its people, institutions, and resources.\nNearly all PHDCN data require an individual application with supporting materials to obtain the data. Applications are handled by the the National Archive of Criminal Justice Data (NACJD). Further instructions will appear on the study home page (linked from search results), where relevant.",
"homepage": "https://www.icpsr.umich.edu/web/pages/NACJD/guides/phdcn/index.html",
"name": "Project on Human Development in Chicago Neighborhoods",
"prefix": "r3d100012493",
"synonyms": [
"PHDCN"
]
},
"r3d100012494": {
"description": "TES is the first satellite instrument to provide simultaneous concentrations of carbon monoxide, ozone, water vapor and methane throughout Earthβs lower atmosphere. This lower atmosphere (the troposphere) is situated between the surface and the height at which aircraft fly, and is an important part of the atmosphere that we often impact with our activities.",
"homepage": "https://www.jpl.nasa.gov/missions/tropospheric-emission-spectrometer-tes",
"name": "Tropospheric Emission Spectrometer",
"prefix": "r3d100012494",
"synonyms": [
"TES"
],
"xrefs": {
"biodbcore": "001533"
}
},
"r3d100012495": {
"description": "The LJMU Research Data Repository is the University's institutional repository where researchers can safely deposit and store research data on an Open Access basis.\nData stored in the LJMU Research Data Repository can be made freely available to anyone online and located by users of web search engines.",
"homepage": "http://opendata.ljmu.ac.uk/",
"name": "Liverpool John Moores University Research Data Repository",
"prefix": "r3d100012495",
"synonyms": [
"LJMU Data Repository",
"LJMU Research Data Repository"
]
},
"r3d100012496": {
"description": "GESIS preserves (mainly quantitative) social research data to make it available to the scientific research community. The data is described in a standardized way, secured for the long term, provided with a permanent identifier (DOI), and can be easily found and reused through browser-optimized catalogs (https://search.gesis.org/).",
"homepage": "https://www.gesis.org/en/data-services/share-data",
"name": "GESIS Data Archive",
"prefix": "r3d100012496",
"synonyms": [
"GESIS Langzeitarchivierung",
"GESIS Long-term digital preservation"
]
},
"r3d100012497": {
"description": "EOS-EarthData provides free, customized Earth Science data. All data are freely available. \nEOS-WEBSTER has been replaced by EOS-Earthdata. EOS-Earthdata offers much simpler access to data, and does not require you to register or login.",
"homepage": "https://eos-earthdata.sr.unh.edu/",
"name": "EOS-EarthData",
"prefix": "r3d100012497"
},
"r3d100012498": {
"description": "CESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states.",
"homepage": "https://www.cesm.ucar.edu/experiments/",
"name": "CESM Experiments",
"prefix": "r3d100012498",
"synonyms": [
"Comnunity Earth System Model Experiments"
]
},
"r3d100012499": {
"description": "The CAS Data Catalog contains a variety of atmospheric and oceanic energy budget calculations derived from satellites and Reanalysis products.\nThe CAS Data Catalog has been archived in favor of the Climate Data Guide https://www.re3data.org/repository/r3d100012500.\nPlease visit that website for your climate data needs and to view datasets from the CAS Data Catalog refer to the Climate Analysis Section (CAS) Data Catalog tag (https://climatedataguide.ucar.edu/collections/climate-analysis-section-cas-data-catalog) on the Climate Data Guide website.",
"homepage": "https://www.cgd.ucar.edu/cas/catalog",
"name": "NCAR Climate Analysis Section Data Catalog",
"prefix": "r3d100012499",
"synonyms": [
"CAS Data Catalog"
]
},
"r3d100012500": {
"description": "Search and access 201 data sets covering the Atmosphere, Ocean, Land and more. Explore climate indices, reanalyses and satellite data and understand their application to climate model metrics. This is the only data portal that combines data discovery, metadata, figures and world-class expertise on the strengths, limitations and applications of climate data.",
"homepage": "https://climatedataguide.ucar.edu/",
"name": "NCAR UCAR Climate Data Guide",
"prefix": "r3d100012500",
"xrefs": {
"fairsharing": "FAIRsharing.4vsxkr"
}
},
"r3d100012501": {
"description": "A catalog of NASA images and animations of our home planet.",
"homepage": "https://visibleearth.nasa.gov/",
"name": "Visible earth",
"prefix": "r3d100012501"
},
"r3d100012502": {
"description": "The Gateway to Astronaut Photography of Earth hosts the best and most complete online collection of astronaut photographs of the Earth from 1961 through the present. This service is provided by the International Space Station program and the JSC Earth Science & Remote Sensing Unit, ARES Division, Exploration Integration Science Directorate.",
"homepage": "https://eol.jsc.nasa.gov/",
"name": "Gateway to Astronaut Photography of earth",
"prefix": "r3d100012502"
},
"r3d100012503": {
"description": "NASA officially has launched a new resource to help the public search and download out-of-this-world images, videos and audio files by keyword and metadata searches from NASA.gov. The NASA Image and Video Library website consolidates imagery spread across more than 60 collections into one searchable location. NASA Image and Video Library allows users to search, discover and download a treasure trove of more than 140,000 NASA images, videos and audio files from across the agencyβs many missions in aeronautics, astrophysics, Earth science, human spaceflight, and more. Users can browse the agencyβs most recently uploaded files, as well as discover historic and the most popularly searched images, audio files and videos. Other features include:\nAutomatically scales the interface for mobile phones and tablets\nDisplays the EXIF/camera data that includes exposure, lens used, and other information, when available from the original image\nAllows for easy public access to high resolution files\nAll video includes a downloadable caption file\nNASA Image and Video Libraryβs Application Programmers Interface (API) allows automation of imagery uploads for NASA, and gives members of the public the ability to embed content in their own sites and applications. This public site runs on NASAβs cloud native βinfrastructure-as-a-codeβ technology enabling on-demand use in the cloud.",
"homepage": "https://images.nasa.gov/",
"name": "NASA Image and Video Library",
"prefix": "r3d100012503"
},
"r3d100012504": {
"description": "NASA funded OpenAltimetry facilitates the advanced discovery, processing, and visualization services for ICESat and ICESat-2 altimeter data.",
"homepage": "https://www.openaltimetry.org",
"name": "OpenAltimetry",
"prefix": "r3d100012504",
"xrefs": {
"fairsharing": "FAIRsharing.M2wo0O"
}
},
"r3d100012505": {
"description": "ORDaR is a data repository for research data in geoscience.",
"homepage": "https://ordar.otelo.univ-lorraine.fr/accueil",
"name": "ORDaR",
"prefix": "r3d100012505",
"synonyms": [
"OTELo Research Data Repository",
"Observatory Earth Environnemment of Lorraine Research Data Repository"
]
},
"r3d100012506": {
"description": "<<>>!!!<<< Data.DURAARK provides a unique collection of real world datasets from the architectural profession. The repository is unique, as it provides several different datatypes, such as 3d scans, 3d models and classifying Metadata and Geodata, to real world physical buildings.domain. Many of the datasets stem from architectural stakeholders and provide the community in this way with insights into the range of working methods, which the practice employs on large and complex building data.",
"homepage": "http://data.duraark.eu/",
"name": "DURAARK datasets",
"prefix": "r3d100012506",
"synonyms": [
"DURAARK",
"Data.DURAARK (formerly)",
"Durable Architectural Knowledge"
]
},
"r3d100012509": {
"description": "GEISHA is the online repository of in situ hybridization and corresponding metadata for genes expressed in the chicken embryo during the first six days of development.",
"homepage": "http://geisha.arizona.edu/geisha/index.jsp",
"name": "GEISHA",
"prefix": "r3d100012509",
"synonyms": [
"Gallus Expression in Situ Hybridization Analysis"
],
"xrefs": {
"nif": "0000-01251",
"omics": "03312",
"scr": "007440"
}
},
"r3d100012511": {
"description": "The IOER Monitor is a research data infrastructure of the Leibniz Institute of Ecological Urban and Regional Development (IOER). It provides various information on land use structure and its development as well as on landscape quality for the Federal Republic of Germany.",
"homepage": "https://www.ioer-monitor.de",
"name": "Monitor of Settlement and Open Space Development",
"prefix": "r3d100012511",
"synonyms": [
"IΓR-Monitor",
"Monitor der Siedlungs- und Freiraumentwicklung"
]
},
"r3d100012512": {
"description": "<<>>!!!>>>",
"homepage": "https://researchdata.sfu.ca/node/6",
"name": "SFU Radar",
"prefix": "r3d100012512",
"synonyms": [
"SFU's Research Data Repository",
"Simon Fraser University's research data repository"
]
},
"r3d100012513": {
"description": "DataSpace is a digital repository meant for both archiving and publicly disseminating digital data which are the result of research, academic, or administrative work performed by members of the Princeton University community. DataSpace will promote awareness of the data and address concerns for ensuring the long-term availability of data in the repository.",
"homepage": "https://dataspace.princeton.edu/jspui/",
"name": "DataSpace",
"prefix": "r3d100012513",
"synonyms": [
"DataSpace at Princeton University"
]
},
"r3d100012514": {
"description": "<<>>!!!>>>",
"homepage": "http://metpetdb.com/",
"name": "MetPetDB",
"prefix": "r3d100012514",
"synonyms": [
"MPD"
],
"xrefs": {
"nlx": "154722",
"omics": "02721",
"scr": "002208"
}
},
"r3d100012515": {
"description": "ResearchWorks Archive is the University of Washingtonβs digital repository (also known as βinstitutional repositoryβ) for disseminating and preserving scholarly work. ResearchWorks Archive can accept any digital file format or content (examples include numerical datasets, photographs and diagrams, working papers, technical reports, pre-prints and post-prints of published articles).",
"homepage": "https://digital.lib.washington.edu/researchworks/",
"name": "ResearchWorks Archive University of Washington",
"prefix": "r3d100012515",
"xrefs": {
"opendoar": "359"
}
},
"r3d100012516": {
"description": "<<>>!!!>>>",
"homepage": "https://plasmid.med.harvard.edu/PLASMID/Home.xhtml",
"name": "PlasmID",
"prefix": "r3d100012516",
"synonyms": [
"Plasmid Information Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.k9ptv7",
"omics": "08730"
}
},
"r3d100012517": {
"description": "Welcome to the Animal Genome Size Database, Release 2.0, a comprehensive catalogue of animal genome size data.",
"homepage": "https://www.genomesize.com/",
"name": "Animal Genome Size Database",
"prefix": "r3d100012517",
"xrefs": {
"fairsharing": "FAIRsharing.efp5v2",
"nif": "0000-02548",
"omics": "16749",
"scr": "007551"
}
},
"r3d100012518": {
"description": "AmphibiaWeb is an online system enabling any user to search and retrieve information relating to amphibian biology and conservation. This site was motivated by the global declines of amphibians, the study of which has been hindered by the lack of multidisplinary studies and a lack of coordination in monitoring, in field studies, and in lab studies. We hope AmphibiaWeb will encourage a shared vision to collaboratively face the challenge of global amphibian declines and the conservation of remaining amphibians and their habitats.",
"homepage": "https://amphibiaweb.org/index.html",
"name": "AmphibiaWeb",
"prefix": "r3d100012518",
"xrefs": {
"nlx": "153878",
"omics": "14883",
"scr": "001612"
}
},
"r3d100012519": {
"description": "Avibase is an extensive database information system about all birds of the world, containing over 60 million records about 10,000 species and 22,000 subspecies of birds, including distribution information, taxonomy, synonyms in several languages and more. This site is managed by Denis Lepage and hosted by Bird Studies Canada, the Canadian copartner of Birdlife International. Avibase has been a work in progress since 1992 and I am now pleased to offer it as a service to the bird-watching and scientific community.",
"homepage": "https://avibase.bsc-eoc.org/avibase.jsp?lang=EN&pg=home",
"name": "Avibase",
"prefix": "r3d100012519",
"synonyms": [
"the world bird database"
]
},
"r3d100012521": {
"description": "HunCLARIN is a strategic research infrastructure of Hungaryβs leading knowledge centres involved in R&D in speech- and language processing. It contains linguistic resources and tools that form the basis of research. The infrastructure has obtained an βSKIβ qualification (Strategic Research Infrastructure) in 2010, and has been significantly expanded since. Currently comprising 36 members, the infrastructure includes several general- and specific-purpose text corpora, different language processing tools and analysers, linguistic databases as well as ontologies. RIL HAS was a co-founder of the European CLARIN project, which aims at supporting humanities and social sciences research with the help of language technology and by making digital linguistic resources more easily available. In accordance with these goals HunClarin makes the research infrastructures developed by the respective centres directly accessible for researchers through a common network entry point. A general goal of the infrastructure is to realise the interoperability of the collected research infrastructures and to enable comparing the performance of the respective alternatives and to coordinate different foci in R&D. The coordinator and contact person of the infrastructure is TamΓ‘s VΓ‘radi, RIL HAS.",
"homepage": "https://clarin.hu/content/hunclarin-tagjai",
"name": "HunCLARIN",
"prefix": "r3d100012521"
},
"r3d100012522": {
"description": "CLARIN-UK is a consortium of centres of expertise involved in research and resource creation involving digital language data and tools. The consortium includes the national library, and academic departments and university centres in linguistics, languages, literature and computer science.",
"homepage": "https://www.clarin.ac.uk/",
"name": "CLARIN-UK",
"prefix": "r3d100012522"
},
"r3d100012523": {
"description": "ARCHE (A Resource Centre for the HumanitiEs) is a service aimed at offering stable and persistent hosting as well as dissemination of digital research data and resources for the Austrian humanities community. ARCHE welcomes data from all humanities fields.\nARCHE is the successor of the Language Resources Portal (LRP) and acts as Austriaβs connection point to the European network of CLARIN Centres for language resources.",
"homepage": "https://arche.acdh.oeaw.ac.at/browser/",
"name": "ARCHE",
"prefix": "r3d100012523",
"synonyms": [
"A Resource Centre for the HumanitiEs"
]
},
"r3d100012525": {
"description": "As a member of SWE-CLARIN, the Humanities Lab will provide tools and expertise related to language archiving, corpus and (meta)data management, with a continued emphasis on multimodal corpora, many of which contain Swedish resources, but also other (often endangered) languages, multilingual or learner corpora. As a CLARIN K-centre we provide advice on multimodal and sensor-based methods, including EEG, eye-tracking, articulography, virtual reality, motion capture, av-recording.\nCurrent work targets automatic data retrieval from multimodal data sets, as well as the linking of measurement data (e.g. EEG, fMRI) or geo-demographic data (GIS, GPS) to language data (audio, video, text, annotations). We also provide assistance with speech and language technology related matters to various projects.\nA primary resource in the Lab is The Humanities Lab corpus server, containing a varied set of multimodal language corpora with standardised metadata and linked layers of annotations and other resources.",
"homepage": "https://archive.humlab.lu.se",
"name": "Lund University Humanities Lab Archive",
"prefix": "r3d100012525",
"synonyms": [
"LU Humanities Lab Archive",
"formerly: Lund University Humanities Lab corpus server"
]
},
"r3d100012526": {
"description": "A place of living memory, the Phonotheque of the MMSH aims to bring together recordings of the sound heritage that have the value of ethnological, linguistic, historical, musicological or literary information on the Mediterranean area. It documents fields little covered by conventional sources, or completes them with the point of view of actors or witnesses.\nThe collection holds more than 8000 hours of audio archives recorded since the late 1950s concerning all the humanities sciences.",
"homepage": "http://phonotheque.mmsh.huma-num.fr/",
"name": "Maison méditerranéenne des sciences de l'homme, Phonothèque",
"prefix": "r3d100012526",
"synonyms": [
"MMSH Phonothèque",
"Mediterranean Research Centre for the Humanities"
]
},
"r3d100012527": {
"description": "The Phonogrammarchiv is a multi-disciplinary research sound and video archive, covering holdings from all continents. Since its foundation in 1899 the Phonogrammarchiv has been building up its holdings by cooperating with Austrian scholars and archiving their collected material, or by fieldwork conducted by staff members on special topics exploring new fields of methods and contents. The main tasks comprise the production, annotation, cataloguing and long-term preservation of audio-visual field recordings, making the cultural heritage available for future generations and enabling the dissemination of the recordings as well as technical developments in the field of AV recording and storage. Thus the Phonogrammarchiv adds to infrastructural performance valuable to both the scholarly community and the public at large.",
"homepage": "https://www.oeaw.ac.at/phonogrammarchiv/",
"name": "Phonogrammarchiv",
"prefix": "r3d100012527",
"synonyms": [
"PhA"
]
},
"r3d100012528": {
"description": "The Canadian Open Genetics Repository is a collaborative effort for the collection, storage, sharing and robust analysis of variants reported by medical diagnostics laboratories across Canada. As clinical laboratories adopt modern genomics technologies, the need for this type of collaborative framework is increasingly important. If you want to join COGR project and get data please send an email at cogr@opengenetics.ca and the introduction to the project will be arranged.",
"homepage": "https://opengenetics.ca/",
"name": "Canadian Open Genetics Repository",
"prefix": "r3d100012528",
"synonyms": [
"COGR"
]
},
"r3d100012529": {
"description": "The Immunology Database and Analysis Portal (ImmPort) archives clinical study and trial data generated by NIAID/DAIT-funded investigators. Data types housed in ImmPort include subject assessments i.e., medical history, concomitant medications and adverse events as well as mechanistic assay data such as flow cytometry, ELISA, ELISPOT, etc. --- You won't need an ImmPort account to search for compelling studies, peruse study demographics, interventions and mechanistic assays. But why stop there? What you really want to do is download the study, look at each experiment in detail including individual ELISA results and flow cytometry files. Perhaps you want to take those flow cytometry files for a test drive using FLOCK in the ImmPort flow cytometry module. To download all that interesting data you will need to register for ImmPort access.",
"homepage": "https://www.immport.org/shared/home",
"name": "ImmPort",
"prefix": "r3d100012529",
"synonyms": [
"Immunology Database and Analysis Portal"
],
"xrefs": {
"fairsharing": "FAIRsharing.bpkzqp",
"nlx": "152691",
"omics": "16756",
"scr": "012804"
}
},
"r3d100012530": {
"description": "The University of Amsterdam (UvA) and the Amsterdam University of Applied Sciences (AUAS/HvA) cooperate to connect academic research with the insights and experiences from professional practice, and together the UvA and AUAS offer students a wide range of education pathways.",
"homepage": "https://uvaauas.figshare.com/",
"name": "University of Amsterdam / Amsterdam University of Applied Sciences figshare",
"prefix": "r3d100012530",
"synonyms": [
"UvA / AUAS figshare"
]
},
"r3d100012531": {
"description": "Figshare has been chosen as the University of Adelaide's official data and digital object repository with unlimited local storage.\nAll current staff and HDR students can access and publish research data and digital objects on the University of Adelaide's Figshare site. Because Figshare is cloud-based, you can access it anywhere and at any time.",
"homepage": "https://adelaide.figshare.com/",
"name": "University of Adelaide figshare",
"prefix": "r3d100012531"
},
"r3d100012532": {
"description": "Provided by the University Libraries, KiltHub is the comprehensive institutional repository and research collaboration platform for research data and scholarly outputs produced by members of Carnegie Mellon University and their collaborators. KiltHub collects, preserves, and provides stable, long-term global open access to a wide range of research data and scholarly outputs created by faculty, staff, and student members of Carnegie Mellon University in the course of their research and teaching.",
"homepage": "https://kilthub.figshare.com/",
"name": "kilthub figshare",
"prefix": "r3d100012532"
},
"r3d100012534": {
"description": "IMGTΒ is a pioneering international information system in immunogenetics and immunoinformatics. It provides databases and tools based on the IMGT-ONTOLOGY to the scientific community for in-depth exploration of the adaptive immune response. IMGTΒ is dedicated to advancing scientific knowledge through its three main axes of research and development.",
"homepage": "https://www.imgt.org/IMGTindex/LIGM-DB.php",
"name": "IMGT/LIGM-DBI",
"prefix": "r3d100012534",
"synonyms": [
"IMGT, the international ImMunoGeneTics information system"
],
"xrefs": {
"fairsharing": "FAIRsharing.8d3ka8",
"nif": "0000-03015",
"scr": "006931"
}
},
"r3d100012535": {
"description": "The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR).",
"homepage": "https://www.imgt.org/IMGTPrimerDB/",
"name": "IMGT/PRIMER-DB",
"prefix": "r3d100012535",
"synonyms": [
"ImMunoGeneTics/PRIMER-DB",
"International ImMunoGeneTics information system/PRIMER-Database"
]
},
"r3d100012536": {
"description": "IMGT/GENE-DB is the IMGT genome database for IG and TR genes from human, mouse and other vertebrates. IMGT/GENE-DB provides a full characterization of the genes and of their alleles: IMGT gene name and definition, chromosomal localization, number of alleles, and for each allele, the IMGT allele functionality, and the IMGT reference sequences and other sequences from the literature. IMGT/GENE-DB allele reference sequences are available in FASTA format (nucleotide and amino acid sequences with IMGT gaps according to the IMGT unique numbering, or without gaps).",
"homepage": "https://www.imgt.org/genedb/",
"name": "IMGT/GENE-DB",
"prefix": "r3d100012536",
"synonyms": [
"ImMunoGeneTics / Gene-DB",
"International ImMunoGeneTics information system/Gene-DB"
],
"xrefs": {
"nif": "0000-03012",
"scr": "006964"
}
},
"r3d100012537": {
"description": "<<>>!!!>>>\nDash is an open data publication platform for upload, access, and re-use of research data. Submissions to Dash may be from researchers at participating UC campuses, researchers in earth science and ecology (DataONE), and researchers submitting to the UC Press journals Elementa and Collabra. Self-service depositing of research data through Dash fulfills publisher, funder, and data management plan requirements regarding data sharing and preservation. When researchers publish their datasets through Dash, their datasets are issued a DOI (DataCite) to optimize citability, and are publicly available for download and re-use under a CC BY 4.0 or CC-0 license. Deposited data are preserved in Merritt, California Digital Libraryβs preservation repository.",
"homepage": "https://cdlib.org/services/uc3/",
"name": "Dash",
"prefix": "r3d100012537",
"xrefs": {
"fairsharing": "FAIRsharing.v1knrj"
}
},
"r3d100012538": {
"description": "DataverseNO is a curated, FAIR-aligned national generic repository for open research data from all academic disciplines. DataverseNO commits to facilitate that published data remain accessible and (re)usable in a long-term perspective. The repository is owned and operated by UiT The Arctic University of Norway. DataverseNO accepts submissions from researchers primarily from Norwegian research institutions. Datasets in DataverseNO are grouped into institutional collections as well as special collections. The technical infrastructure of the repository is based on the open source application Dataverse (https://dataverse.org), which is developed by an international developer and user community led by Harvard University.",
"homepage": "https://dataverse.no/",
"name": "DataverseNO",
"prefix": "r3d100012538",
"xrefs": {
"fairsharing": "FAIRsharing.5O9YTT"
}
},
"r3d100012539": {
"description": "IMGT/3Dstructure-DB is the IMGT three-dimensional (3D) structure database.",
"homepage": "https://www.imgt.org/3Dstructure-DB/",
"name": "IMGT/3Dstructure-DB and IMGT/2Dstructure-DB",
"prefix": "r3d100012539",
"synonyms": [
"ImMunoGeneTics/3Dstructure-DB and IMGT/2Dstructure-DB",
"International ImMunoGeneTics information system/3Dstructure-DB and IMGT/2Dstructure-DB"
],
"xrefs": {
"nif": "0000-03013",
"scr": "007734"
}
},
"r3d100012540": {
"description": "IMGT/mAb-DB provides a unique expertised resource on monoclonal antibodies (mAbs) with diagnostic or therapeutic indications, fusion proteins for immune applications (FPIA), composite proteins for clinical applications (CPCA) and relative proteins of the immune system (RPI) with clinical indications.",
"homepage": "https://www.imgt.org/mAb-DB/",
"name": "IMGT/mAb-DB",
"prefix": "r3d100012540",
"synonyms": [
"ImMunoGeneTics/MAB-DB",
"International ImMunoGeneTics information system/mAB-DB"
]
},
"r3d100012542": {
"description": "RC content presented through one of our portals is peer reviewed, while the remaining expositions and other information are quality controlled by the individual author(s) themselves. As a result, the RC is highly inclusive.\nThe open source status of the RC is essential to its nature and serves its function as a connective and transitional layer between academic discourse and artistic practice, thereby constituting a discursive field for artistic research.",
"homepage": "https://www.researchcatalogue.net",
"name": "Research Catalogue - Society for Artistic Research",
"prefix": "r3d100012542",
"synonyms": [
"RC - an International Database for Artistic Research"
]
},
"r3d100012543": {
"description": "The Antarctic Research Facility is a national repository for geological materials collected in polar regions. The Facility houses the largest such Southern Ocean collection in the world. These materials have been acquired from over 90 USAP research vessel cruises.",
"homepage": "http://arf.fsu.edu/",
"name": "Antarctic Marine Geology Research Facility",
"prefix": "r3d100012543",
"synonyms": [
"AMGRF"
],
"xrefs": {
"nlx": "154735",
"scr": "002213"
}
},
"r3d100012544": {
"description": "CSDMS is a virtual home for a vibrant and growing community of about 1,000 international modeling experts and students who study the dynamic interactions of lithosphere, hydrosphere, cryosphere, and atmosphere at Earthβs surface. Participating in cross-disciplinary groups, members develop integrated software modules that predict the movement of water, sediment, and nutrients across landscapes and into the ocean. We share an open library of models, software, and access to high-performance computing. We also share knowledge that helps create higher-resolution simulations, often involving higher complexity algorithms. Together, we support the discovery, use, and conservation of natural resources; mitigation of natural hazards; geotechnical support of commercial and infrastructure development; environmental stewardship; and terrestrial surveillance for global security.",
"homepage": "https://csdms.colorado.edu/wiki/Main_Page",
"name": "Community Surface Dynamics Modeling System",
"prefix": "r3d100012544",
"synonyms": [
"CSDMS"
],
"xrefs": {
"nlx": "154705",
"scr": "002196"
}
},
"r3d100012545": {
"description": "The NSF-supported Program serves the international scientific community through research, infrastructure, data, and models. We focus on how components of the Critical Zone interact, shape Earth's surface, and support life.\nARCHIVED CONTENT: In December 2020, the CZO program was succeeded by the Critical Zone Collaborative Network (CZ Net) https://criticalzone.org/",
"homepage": "https://czo-archive.criticalzone.org/national/data/",
"name": "Critical Zone Observatories data",
"prefix": "r3d100012545",
"synonyms": [
"CZO data"
]
},
"r3d100012547": {
"description": "The Lamont-Doherty Core Repository (LDCR) contains one of the worldβs most unique and important collection of scientific samples from the deep sea. Sediment cores from every major ocean and sea are archived at the Core Repository. The collection contains approximately 72,000 meters of core composed of 9,700 piston cores; 7,000 trigger weight cores; and 2,000 other cores such as box, kasten, and large diameter gravity cores. We also hold 4,000 dredge and grab samples, including a large collection of manganese nodules, many of which were recovered by submersibles. Over 100,000 residues are stored and are available for sampling where core material is expended. In addition to physical samples, a database of the Lamont core collection has been maintained for nearly 50 years and contains information on the geographic location of each collection site, core length, mineralogy and paleontology, lithology, and structure, and more recently, the full text of megascopic descriptions.",
"homepage": "https://corerepository.ldeo.columbia.edu/",
"name": "Lamont-Doherty Core Repository",
"prefix": "r3d100012547",
"synonyms": [
"LDCR"
],
"xrefs": {
"nlx": "154738",
"scr": "002216"
}
},
"r3d100012548": {
"description": "LEPR is a database of results of published experimental studies involving liquid-solid phase equilibria relevant to natural magmatic systems. TraceDs is a database of experimental studies involving trace element distribution between liquid, solid and fluid phases.",
"homepage": "https://lepr.earthchem.org/access_user/login.php",
"name": "LEPR - Library of Experimental Phase Relations",
"prefix": "r3d100012548",
"synonyms": [
"Library of Experimental Phase Relations and Trace element Distribution experimental database"
],
"xrefs": {
"fairsharing": "FAIRsharing.fc0f58",
"nlx": "154711",
"scr": "002202"
}
},
"r3d100012549": {
"description": "The MGDS MediaBank contains high quality images, illustrations, animations and video clips that are organized into galleries. Media can be sorted by category, and keyword and map-based search options are provided. Each item in the MediaBank is accompanied by metadata that provides access into our cruise catalog and data repository.",
"homepage": "http://media.marine-geo.org/",
"name": "MediaBank",
"prefix": "r3d100012549",
"synonyms": [
"Image galleries",
"MGDS MediaBank",
"Marine Geoscience Data System"
],
"xrefs": {
"nlx": "154726",
"scr": "006875"
}
},
"r3d100012550": {
"description": "The NCMA maintains the largest and most diverse collection of publically available marine algal strains in the world. The algal strains in the collection have been obtained from all over the world, from polar to tropical waters, marine, freshwater, brackish, and hyper-saline environments. New strains (50 - 100 per year) are added largely through the accession of strains deposited by scientists in the community. A stringent accession policy is required to help populate the collection with a diverse range of strains.",
"homepage": "https://ncma.bigelow.org/",
"name": "Bigelow National Center for Algae and Microbiota",
"prefix": "r3d100012550",
"synonyms": [
"NCMA",
"formerly: CCMP"
],
"xrefs": {
"nlx": "154729",
"scr": "002120"
}
},
"r3d100012553": {
"description": "ioChem-BD is a Digital Repository to manage Computational Chemistry and Material Science digital assets. The platform follows the philosophy of Crystallographic databases, the principles and needs of open access, and solves reproducibility and traceability issues.",
"homepage": "https://www.iochem-bd.org/",
"name": "ioChem-BD",
"prefix": "r3d100012553",
"xrefs": {
"doi": "10.19061/iochem-bd-find",
"fairsharing": "FAIRsharing.lwW6a1"
}
},
"r3d100012554": {
"description": "The National River Flow Archive is the primary archive of daily and peak river flows for the United Kingdom. The archive incorporates daily, monthly and flood peak data from over 1500 gauging stations. The NRFA holds a wide range of hydrological information to assist in the understanding and interpretation of measured river flows. In addition to time series of gauged river flow, the data centre maintains hydrometric information relating to the gauging stations and the catchments they command and data quantifying other parts of the hydrological cycle.",
"homepage": "https://nrfa.ceh.ac.uk/",
"name": "National River Flow Archive",
"prefix": "r3d100012554",
"synonyms": [
"NRFA"
],
"xrefs": {
"fairsharing": "FAIRsharing.63pjQU"
}
},
"r3d100012555": {
"description": "Supported by the DFG, the project βMO|RE dataβ assembles a public eResearch-Infrastructure for motor research data until 2016. It focuses on selected standardized motor tests of wide acceptance. Furthermore MO|RE data generates quality authority control and publishes accompanying material for motor tests.",
"homepage": "https://motor-research-data.de/",
"name": "MO|RE data",
"prefix": "r3d100012555",
"synonyms": [
"Motor Research data"
]
},
"r3d100012557": {
"description": "The Research Collection is ETH Zurich's publication platform. It unites the functions of a university bibliography, an open access repository and a research data repository within one platform. Researchers who are affiliated with ETH Zurich, the Swiss Federal Institute of Technology, may deposit research data from all domains. They can publish data as a standalone publication, publish it as supplementary material for an article, dissertation or another text, share it with colleagues or a research group, or deposit it for archiving purposes. Research-data-specific features include flexible access rights settings, DOI registration and a DOI preview workflow, content previews for zip- and tar-containers, as well as download statistics and altmetrics for published data. All data uploaded to the Research Collection are also transferred to the ETH Data Archive, ETH Zurichβs long-term archive.",
"homepage": "https://www.research-collection.ethz.ch",
"name": "ETH ZΓΌrich Research Collection",
"prefix": "r3d100012557",
"xrefs": {
"fairsharing": "FAIRsharing.fNXAq5"
}
},
"r3d100012558": {
"description": "<<>>!!!>>>\n\nNetPath is currently one of the largest open-source repository of human signaling pathways that is all set to become a community standard to meet the challenges in functional genomics and systems biology. Signaling networks are the key to deciphering many of the complex networks that govern the machinery inside the cell. Several signaling molecules play an important role in disease processes that are a direct result of their altered functioning and are now recognized as potential therapeutic targets. Understanding how to restore the proper functioning of these pathways that have become deregulated in disease, is needed for accelerating biomedical research. This resource is aimed at demystifying the biological pathways and highlights the key relationships and connections between them. Apart from this, pathways provide a way of reducing the dimensionality of high throughput data, by grouping thousands of genes, proteins and metabolites at functional level into just several hundreds of pathways for an experiment. Identifying the active pathways that differ between two conditions can have more explanatory power than just a simple list of differentially expressed genes and proteins.",
"homepage": "http://www.netpath.org/",
"name": "NetPath",
"prefix": "r3d100012558",
"xrefs": {
"nlx": "157701",
"omics": "14109",
"scr": "003567"
}
},
"r3d100012561": {
"description": "DEEMY is collecting descriptive data on ectomycorrhizae, including extant character descriptions and definitions. Ectomycorrhizae are mutualistic structures formed by fungi and the roots of forest trees. They are predominantly found in the temperate and boreal climate zones but occur also in humid tropic regions, as well as in soils of poor nutrition. Without mycorrhizae, trees would not be able to take up water and minerals. Ectomycorrhizae show a wide range of anatomical diversity which represents their possible function in tree nutrition and ecology. Their anatomical data, in general, allow a quick determination and provide at the same time ecologically important information about possible functions for tree nutrition.",
"homepage": "http://www.deemy.de/",
"name": "DEEMY",
"prefix": "r3d100012561",
"synonyms": [
"Determination of Ectomycorrhizae"
]
},
"r3d100012562": {
"description": "The FishNet network is a collaborative effort among fish collections around the world to share and distribute data on specimen holdings. There is an open invitation for any institution with a fish collection to join.",
"homepage": "http://www.fishnet2.net/",
"name": "Fishnet2",
"prefix": "r3d100012562",
"xrefs": {
"nif": "0000-25778",
"scr": "013191"
}
},
"r3d100012563": {
"description": "HADb provides a complete and an up-to-date list of human genes and proteins involved directly or indirectly in autophagy as described in literature.",
"homepage": "http://autophagy.lu/index.html",
"name": "Human Autophagy Database",
"prefix": "r3d100012563",
"synonyms": [
"HADb"
]
},
"r3d100012564": {
"description": "ScholarBank@NUS is the university's Institutional Repository (IR). Its goals are to collect, preserve and showcase the research output including research data of NUS researchers and departments.",
"homepage": "https://scholarbank.nus.edu.sg/",
"name": "ScholarBank@NUS",
"prefix": "r3d100012564"
},
"r3d100012565": {
"description": "The goal of the Autophagy Database is to provide up-to-date relevant information including protein structure data to researchers of autophagy, and to disseminate important findings to a wider audience so that their ramifications can be appreciated. For this purpose, we strive to make the database to contain as much pertinent information as possible and to make the contents freely available in a user-friendly format.",
"homepage": "http://www.tanpaku.org/autophagy/index.html",
"name": "Autophagy Database",
"prefix": "r3d100012565",
"xrefs": {
"omics": "03306",
"scr": "002671"
}
},
"r3d100012567": {
"description": "SWE-CLARIN is a national node in European Language and Technology Infrastructure (CLARIN) - an ESFRI initiative to build an infrastructure for e-science in the humanities and social sciences.\nSWE-CLARIN makes language-based materials available as research data using advanced processing tools and other resources. One basic idea is that the increasing amount of text and speech - contemporary and historical - as digital research material enables new forms of e-science and new ways to tackle old research issues.",
"homepage": "https://sweclarin.se/eng/home",
"name": "SWE-CLARIN",
"prefix": "r3d100012567"
},
"r3d100012568": {
"description": "TAED is a database of phylogenetically indexed gene families. It contains multiple sequence alignments from MAFFT1, maximum likelihood phylogenetic trees from PhyML2, bootstrap values for each node, dN/dS ratios for each lineage from the free ratios model in PAML3, and labels for each node of speciation or duplication from gene tree/species tree reconciliation using SoftParsMap4. The phylogenetic indexing enables simultaneous viewing of lineages with high dN/dS that occurred along the same species tree branches. Resources from the Protein Data Bank (PDB) and the Kyoto Encyclopedia of Genes and Genomes (KEGG)5, have been incorporated into the TAED analysis to detect substitutions along each branch within the phylogenetic tree and to assess selection within pathways.",
"homepage": "https://liberles.cst.temple.edu/TAED/index.html",
"name": "The Adaptive Evolution Database",
"prefix": "r3d100012568",
"synonyms": [
"TAED"
],
"xrefs": {
"nif": "0000-03533",
"scr": "006930"
}
},
"r3d100012569": {
"description": "IEEE DataPortβ’ is a universally accessible online data repository created, owned, and supported by IEEE, the worldβs largest technical professional organization. It enables all researchers and data owners to upload their dataset without cost. IEEE DataPort makes data available in three ways: standard datasets, open access datasets, and data competition datasets. By default, all \"standard\" datasets that are uploaded are accessible to paid IEEE DataPort subscribers. Data owners have an option to pay a fee to make their dataset βopen accessβ, so it is available to all IEEE DataPort users (no subscription required). The third option is to host a \"data competition\" and make a dataset accessible for free for a specific duration with instructions for the data competition and how to participate. IEEE DataPort provides workflows for uploading data, searching, and accessing data, and initiating or participating in data competitions. All datasets are stored on Amazon AWS S3, and each dataset uploaded by an individual can be up to 2TB in size. Institutional subscriptions are available to the platform to make it easy for all members of a given institution to utilize the platform and upload datasets.",
"homepage": "https://ieee-dataport.org",
"name": "IEEE DataPort",
"prefix": "r3d100012569",
"synonyms": [
"DataPort"
],
"xrefs": {
"fairsharing": "FAIRsharing.0f24d5"
}
},
"r3d100012570": {
"description": "The University of GΓΆttingen preserves one of the most important collections of scientific collections. At more than 30 distributed locations on the GΓΆttingen Campus, the collections reflect its disciplinary diversity: the spectrum ranges from archeology to zoology, from astrophysical instruments to the living cell cultures of the algae collection. Historical legacy dating back to the Age of Enlightenment: The founding holdings of the Royal Academic Museum of Georgia Augusta are largely preserved. Research and teaching to date access to the collection objects and increase the stocks. Get to know our collections in this portal, which have been used to create knowledge for three centuries.",
"homepage": "https://sammlungen.uni-goettingen.de/index/",
"name": "Sammlungsportal Georg-August-UniversitΓ€t GΓΆttingen",
"prefix": "r3d100012570",
"synonyms": [
"Akademische Kabinette der UniversitΓ€t GΓΆttingen",
"Wissenschaftliche Sammlungen der Georg-August-UniversitΓ€t GΓΆttingen"
]
},
"r3d100012571": {
"description": "The CiardRING is a global directory of web-based information services and datasets for agricultural research for development (ARD). It is the principal tool created through the CIARD initiative to allow information providers to register their services and datasets in various categories and so facilitate the discovery of sources of agriculture-related information across the world.\nThe RING aims to provide an infrastructure to improve the accessibility of the outputs of agricultural research and of information relevant to agriculture.",
"homepage": "https://ring.ciard.info/",
"name": "CIARD Ring",
"prefix": "r3d100012571",
"synonyms": [
"CIARDRING",
"Coherence Information for Agricultural Research for Development - Routemap to Information Nodes and Gateways",
"RING"
],
"xrefs": {
"fairsharing.legacy": "2666"
}
},
"r3d100012574": {
"description": "The Energy Data eXchange (EDX) is an online collection of capabilities and resources that advance research and customize energy-related needs. EDX is developed and maintained by NETL-RIC researchers and technical computing teams to support private collaboration for ongoing research efforts, and tech transfer of finalized DOE NETL research products. EDX supports NETL-affiliated research by:\nCoordinating historical and current data and information from a wide variety of sources to facilitate access to research that crosscuts multiple NETL projects/programs;\nProviding external access to technical products and data published by NETL-affiliated research teams;\nCollaborating with a variety of organizations and institutions in a secure environment through EDXβs ;Collaborative Workspaces",
"homepage": "https://edx.netl.doe.gov",
"name": "Energy Data eXchange",
"prefix": "r3d100012574",
"synonyms": [
"EDX"
],
"xrefs": {
"fairsharing": "FAIRsharing.ltYWUS"
}
},
"r3d100012575": {
"description": "A repository for high-quality gene models produced by the manual annotation of vertebrate genomes. The final update of Vega, version 68, was released in February 2017 and is now archived at vega.archive.ensembl.org. We plan to maintain this resource until Feb 2020.",
"homepage": "http://vega.archive.ensembl.org/index.html",
"name": "Vega",
"prefix": "r3d100012575",
"synonyms": [
"Vertebrate Genome Annotation database"
],
"xrefs": {
"fairsharing": "FAIRsharing.mr293q",
"nif": "0000-03626",
"scr": "007907"
}
},
"r3d100012576": {
"description": "data.public.lu is Luxembourg's central and official platform for data from the public sector, from research institutes and the private sector.",
"homepage": "https://data.public.lu/en/",
"name": "data.public.lu",
"prefix": "r3d100012576"
},
"r3d100012578": {
"description": "The repository KITopen is a key infrastructure service at KIT. Immediately KITopen not only allows the publication and archiving of publications, but also on research data from all disciplines and data types. The focus is on research data from publication projects that are specifically prepared for re-use.",
"homepage": "https://www.bibliothek.kit.edu/kitopen.php",
"name": "KITopen",
"prefix": "r3d100012578",
"synonyms": [
"KITopen repository"
]
},
"r3d100012580": {
"description": "ISIDORE is a international search engine and a discovery platform for open science allowing the access to digital materials from social sciences and humanities (SSH). Open to all and especially to teachers, researchers, PhD students, and students, it relies on the principles of Web of data and provides access to data in free access (open access). By its vocation, ISIDORE will foster access to open access data produced by research and higher education institutions, laboratories and research teams: digital publication, documentary databases, digitized collections of research libraries, research notebooks and scientific event announcements.\nISIDORE collects, enriches and highlights digital data and documents from the Humanities and Social Sciences while providing unified access to them. More information see: https://isidore.science/about",
"homepage": "https://isidore.science",
"name": "ISIDORE",
"prefix": "r3d100012580",
"synonyms": [
"Integration Services, interconnection of Data of the Research and Education"
]
},
"r3d100012581": {
"description": "The βICSSR Data Serviceβ is culmination of signing of Memorandum of Understanding (MoU) between Indian Council of Social Science Research (ICSSR) and Ministry of Statistics and Programme Implementation (MoSPI). The MoU provides for setting-up of βICSSR Data Service: Social Science Data Repositoryβ and host NSS and ASI datasets generated by MoSPI. Under the initiative, social science research institutes, NGOs, individuals and others dealing with social science research are also being approached to deposit / provide their research datasets for hosting into the repository of ICSSR Data Service. The ICSSR Data Service includes social science and statistical datasets of various national-level surveys on debt & investment, domestic tourism, enterprise survey, employment and unemployment, housing condition, household consumer expenditure, health care, etc., into its repository.\n\nICSSR Data Service aims to facilitate data sharing, preservation, accessibility and reuse of social science research data collected from entire social science community in India & abroad. The Information and Library Network (INFLIBNET) Centre, Gandhinagar has been assigned the task of setting-up the data repository.",
"homepage": "http://www.icssrdataservice.in/",
"name": "ICSSR Data Service: Social Science Data Repository",
"prefix": "r3d100012581",
"synonyms": [
"ICSSR Data Service: Indian Social Science Data Repository",
"Social Science Data Repository"
]
},
"r3d100012582": {
"description": "The Scientific Database of the Federal University of ParanΓ‘ aims to gather the scientific data used in the researches that were published by the UFPR community in theses, dissertations, journal articles, and other bibliographic materials.\nBDC joins RDI / UFPR as an innovative service that tracks the worldwide trend in research planning, management, production, organization, storage, dissemination and reuse. The availability of research data contributes to the transparency and optimization of scientific production through the reuse of data sets and the possibility of new analyzes and approaches",
"homepage": "https://bdc.c3sl.ufpr.br/",
"name": "Base de Dados CientΓficos da Universidade Federal do ParanΓ‘",
"prefix": "r3d100012582",
"synonyms": [
"BDC Universidade Federal do ParanΓ‘",
"Scientific Database of the Federal University of ParanΓ‘"
]
},
"r3d100012585": {
"description": "The NCAR Climate Data Gateway provides data discovery and access services for global and regional climate model data, knowledge, and software. The NCAR Climate Data Gateway supports community access to data products from many of NCAR's community modeling efforts, including the IPCC, PCM, AMPS, CESM, NARCCAP, and NMME activities.\nData products are generally open and available, however, download access may require a login.",
"homepage": "https://www.earthsystemgrid.org/",
"name": "Climate Data Gateway at NCAR",
"prefix": "r3d100012585",
"synonyms": [
"Climate Data at the National Center for Atmospheric Research",
"NCAR Climate Data Gateway"
],
"xrefs": {
"fairsharing": "FAIRsharing.w13xsb"
}
},
"r3d100012586": {
"description": "The global scientific community, international partners, the private sector, civil society, and other relevant stakeholders establish a voluntary platform to link clinical trials registers in order to ensure a single point of access and the unambiguous identification of trials with a view to enhancing access to information by patients, families, patient groups and others.",
"homepage": "https://www.who.int/clinical-trials-registry-platform",
"name": "International Clinical Trials Registry Platform",
"prefix": "r3d100012586",
"synonyms": [
"ICTRP",
"WHO ICTRP"
],
"xrefs": {
"fairsharing": "FAIRsharing.5a3bc5",
"nlx": "143764",
"scr": "004475"
}
},
"r3d100012587": {
"description": "With the Program EnviDat we develop a unified and managed access portal for WSL's rich reservoir of environmental monitoring and research data. EnviDat is designed as a portal to publish, connect and search across existing data but is not intended to become a large data centre hosting original data. While sharing of data is centrally facilitated, data management remains decentralised and the know-how and responsibility to curate research data remains with the original data providers.",
"homepage": "https://www.envidat.ch/",
"name": "EnviDat",
"prefix": "r3d100012587",
"synonyms": [
"Environmental Data Portal"
]
},
"r3d100012588": {
"description": "Our Frozen ZooΒ is the largest and most diverse collection of its kind in the world. It contains over 10,000 living cell cultures, oocytes, sperm, and embryos representing nearly 1,000 taxa, including one extinct species, the poβouli. Located at the Beckman Center for Conservation Research, the collection is also duplicated for safekeeping at a second site. The irreplaceable living cell lines, gametes, and embryos stored in the Frozen ZooΒ provide an invaluable resource for conservation, assisted reproduction, evolutionary biology, and wildlife medicine.",
"homepage": "https://science.sandiegozoo.org/resources/frozen-zoo%C2%AE",
"name": "Frozen ZooΒ",
"prefix": "r3d100012588"
},
"r3d100012592": {
"description": "VAMDC aims to be an interoperable e-infrastructure that provides the international research community with access to a broad range of atomic and molecular (A&M) data compiled within a set of A&M databases accessible through the provision of this portal and of user software. Furthermore VAMDC aims to provide A&M data providers and compilers with a large dissemination platform for their work.\nVAMDC infrastructure was established to provide a service to a wide international research community and has been developed in conjunction with consultations and advice from the A&M user community.",
"homepage": "https://portal.vamdc.eu/vamdc_portal/home.seam",
"name": "VAMDC Portal",
"prefix": "r3d100012592",
"synonyms": [
"Virtual Atomic and Molecular Data Centre Portal"
]
},
"r3d100012593": {
"description": "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union.",
"homepage": "https://data.jrc.ec.europa.eu/",
"name": "JRC Data Catalogue",
"prefix": "r3d100012593",
"synonyms": [
"EC's Joint Research Centre Data Catalogue"
],
"xrefs": {
"fairsharing": "FAIRsharing.4e2z82",
"miriam": "00100849"
}
},
"r3d100012594": {
"description": "TemperateReefBase is a resource for temperate reef researchers worldwide to use and contribute data. Unique in its role as a one-stop-shop for global temperate reef data, TemperateReefBase was initially established by IMAS in collaboration with the Kelp Ecology Ecosystem Network (KEEN).\nKEEN was instigated through a National Centre for Ecological Analysis and Synthesis (NCEAS) working group which assembled experts from around the world to examine the impacts of global change on kelp-bed ecosystem worldwide. The group has assembled significant global data for kelps, other seaweeds and associated species including fishes, and has embarked on unprecedented global experiments and surveys in which identical experiments and surveys are being conducted at sites in kelp beds around the world to determine global trends and examine the capacity of kelps to respond to disturbance in the face of climate change and other anthropogenic stressors.\nThe TemperateReefBase Data Portal is an online discovery interface showcasing temperate reef data collected from around the globe. The portal aims to make this data freely and openly available for the benefit of marine and environmental science as a whole.\nThe TemperateReefBase Data Portal is hosted and maintained by the Institute for Marine and Antarctic Studies at the University of Tasmania, Australia.",
"homepage": "https://temperatereefbase.imas.utas.edu.au/static/landing.html",
"name": "Temperate Reef Base",
"prefix": "r3d100012594",
"synonyms": [
"Temperate Reef Base Portal",
"TemperateReefBase Data Portal"
]
},
"r3d100012596": {
"description": "DBT is the institutional repository of the FSU Jena, the TU Ilmenau and the University of Erfurt as well as members of the other Thuringian universities and colleges can publish scientific documents in the DBT. In individual cases, land users (via the ThULB Jena) can also archive documents in the DBT.",
"homepage": "https://www.db-thueringen.de/servlets/solr/find?fq=mods.genre:research_data",
"name": "Digitale Bibliothek ThΓΌringen",
"prefix": "r3d100012596",
"synonyms": [
"DBT"
],
"xrefs": {
"opendoar": "650",
"roar": "349"
}
},
"r3d100012600": {
"description": "The Alberta Food Composition Database (AFCDB) is the first comprehensive resource on food constituents, chemistry and biology dedicated to major Alberta-grown produce. It provides information on both macronutrients and micronutrients, including many of the constituents that give foods their flavor, color, taste, texture and aroma. Users can view the contents of the AFCDB from the βFoodViewβ (listing foods by their chemical composition) or the βChemViewβ (listing chemicals by their food sources).",
"homepage": "https://afcdb.ca/",
"name": "Alberta Food Composition Database",
"prefix": "r3d100012600",
"synonyms": [
"AFCDB"
]
},
"r3d100012601": {
"description": "The purpose of the Virginia Tech Data Repository is to highlight, preserve, and provide access to research products (e.g. datasets) of the Virginia Tech community, and in doing so help to disseminate the intellectual output of the university in its land-grant mission. The Virginia Tech Data Repository and Virginia Tech serve the Commonwealth of Virginia, the nation, and the worldβs community through the discovery and dissemination of new knowledge.",
"homepage": "https://data.lib.vt.edu/",
"name": "Virginia Tech Data Repository",
"prefix": "r3d100012601",
"xrefs": {
"fairsharing": "FAIRsharing.Ff6HHc"
}
},
"r3d100012603": {
"description": "SwissLipids is an expert curated resource that provides a framework for the integration of lipid and lipidomic data with biological knowledge and models.",
"homepage": "https://www.swisslipids.org/#/",
"name": "SwissLipids",
"prefix": "r3d100012603",
"synonyms": [
"A knowledge resource for lipids and their biology",
"Swiss+Lipids"
],
"xrefs": {
"fairsharing": "FAIRsharing.pxr7x2",
"miriam": "00100727",
"omics": "08652"
}
},
"r3d100012604": {
"description": "AMS Acta is the institutional open access repository which enables the researchers of the Alma Mater Studiorum - University of Bologna to share, preserve and showcase their scientific results making them easily accessible, citable and reusable. The repository collects and disseminates scientific publications, research data and preprints.\nAMS Acta is the archiving infrastructure for the University of Bolognaβs researchers participating in the European programme H2020 that requires open access and the mandatory deposit of all funded peer-reviewed publications in a repository. AMS Acta collects both publications and research data so it is also a suitable archiving solution for the funded projects participating in the H2020 Open Research Data Pilot.",
"homepage": "https://amsacta.unibo.it/",
"name": "AMS Acta",
"prefix": "r3d100012604",
"synonyms": [
"AMSActa",
"Alma Mater Studorium Acta",
"Insitutional Research Repository"
],
"xrefs": {
"issn": "2038-7954",
"opendoar": "3",
"roar": "5509"
}
},
"r3d100012607": {
"description": "Research Data UPC hosts research data linked to a publication (magazine article, etc.) or to a research project (H2020, etc.).",
"homepage": "https://upcommons.upc.edu/dades",
"name": "UPCommons - Research Data",
"prefix": "r3d100012607",
"synonyms": [
"UPCommons. Global access to UPC knowledge - Research Data",
"UPCommons. Portal de acceso abierto al conocimiento de la UPC - Dades de Recerca",
"UPCommons. Portal del coneixement obert de la UPC - Dades de Recerca"
],
"xrefs": {
"opendoar": "3484",
"roar": "10326"
}
},
"r3d100012611": {
"description": "FAIR & long-term storage of research data from computational materials science, or from experimental materials science that is of relevance to simulations. Complementary tools available to explore the full provenance of the calculations and to perform simulations or data analytics in the cloud.",
"homepage": "https://archive.materialscloud.org/",
"name": "Materials Cloud Archive",
"prefix": "r3d100012611",
"synonyms": [
"Materials Cloud"
],
"xrefs": {
"fairsharing": "FAIRsharing.tlbUpj"
}
},
"r3d100012613": {
"description": "RADAM portal is an interface to the network of RADAM (RADiation DAMage) Databases collecting data on interactions of ions, electrons, positrons and photons with biomolecular systems, on radiobiological effects and relevant phenomena occurring at different time, spatial and energy scales in irradiated targets during and after the irradiation. This networking system has been created by the Consortium of COST Action MP1002 (Nano-IBCT: Nano-scale insights into Ion Beam Cancer Therapy) during 2011-2014 using the Virtual Atomic and Molecular Data Center (VAMDC) standards.",
"homepage": "https://radamdb.mbnresearch.com/#",
"name": "RADAM database portal",
"prefix": "r3d100012613",
"synonyms": [
"RADiation DAMage database"
]
},
"r3d100012617": {
"description": "Library Open Access Repository (LOAR) is an open data repository established in 2016 as a service for storing and providing access to Danish research data.\nThe service has the following key goals: Make data accessible to review for publications. Enable researchers to meet requirements for Danish and European grants. Ensure data privacy and removal of data as appropriate. Enable reuse of data where appropriate\nResearchers who upload data are expected to share the data using Creative Commons licenses.",
"homepage": "https://loar.kb.dk/home",
"name": "LOAR",
"prefix": "r3d100012617",
"synonyms": [
"Library Open Access Repository"
]
},
"r3d100012621": {
"description": "DISS is a georeferenced repository of tectonic, fault, and paleoseismological information expressly devoted, but not limited, to potential applications in the assessment of seismic hazard at regional and national scale.",
"homepage": "https://diss.ingv.it",
"name": "Database of Individual Seismogenic Sources",
"prefix": "r3d100012621",
"synonyms": [
"DISS"
],
"xrefs": {
"doi": "10.13127/diss3.3.0",
"fairsharing": "FAIRsharing.733c3f"
}
},
"r3d100012622": {
"description": "The European Database of Seismogenic Faults (EDSF) was compiled in the framework of the EU Project SHARE, Work Package 3, Task 3.2. EDSF includes only faults that are deemed to be capable of generating earthquakes of magnitude equal to or larger than 5.5 and aims at ensuring a homogeneous input for use in ground-shaking hazard assessment in the Euro-Mediterranean area. Several research institutions participated in this effort with the contribution of many scientists (see the Database section for a full list). The EDSF database and website are hosted and maintained by INGV.",
"homepage": "https://edsf13.ingv.it/",
"name": "The European Database of Seismogenic Faults",
"prefix": "r3d100012622",
"synonyms": [
"EDSF"
],
"xrefs": {
"doi": "10.6092/ingv.it-share-edsf",
"fairsharing": "FAIRsharing.a1c2cd"
}
},
"r3d100012623": {
"description": "Yoda publishes research data on behalf of researchers that are affiliated with Utrecht University, its research institutes and consortia where it acts as a coordinating body.\nData packages are not limited to a particular field of research or license.\nYoda publishes data packages via Datacite. To find data publications use: https://public.yoda.uu.nl/, or the Datacite search engine: https://commons.datacite.org/doi.org?query=client.uid:delft.uu",
"homepage": "https://www.uu.nl/en/research/yoda",
"name": "Yoda",
"prefix": "r3d100012623",
"synonyms": [
"Universiteit Utrecht, Your Data - Yoda"
]
},
"r3d100012625": {
"description": "HydroShare is a system operated by The Consortium of Universities for the Advancement of Hydrologic Science Inc. (CUAHSI) that enables users to share and publish data and models in a variety of flexible formats, and to make this information available in a citable, shareable and discoverable manner. HydroShare includes a repository for data and models, and tools (web apps) that can act on content in HydroShare providing users with a gateway to high performance computing and computing in the cloud.\nWith HydroShare you can: share data and models with colleagues; manage access to shared content; share, access, visualize, and manipulate a broad set of hydrologic data types and models; publish data and models and obtain a citable digital object identifier (DOI); aggregate resources into collections; discover and access data and models published by others; use the web services application programming interface (API) to programmatically access resources; and use integrated web applications to visualize, analyze and run models with data in HydroShare.",
"homepage": "https://www.hydroshare.org/",
"name": "HydroShare",
"prefix": "r3d100012625",
"xrefs": {
"fairsharing": "FAIRsharing.ZvHsiN"
}
},
"r3d100012626": {
"description": "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of 'small molecular entities'. The term 'molecular entity' encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms (either deliberately, as for drugs, or unintentionally', as for chemicals in the environment). The qualifier 'small' implies the exclusion of entities directly encoded by the genome, and thus as a rule nucleic acids, proteins and peptides derived from proteins by cleavage are not included.",
"homepage": "https://www.ebi.ac.uk/chebi/",
"name": "ChEBI",
"prefix": "r3d100012626",
"synonyms": [
"Chemical Entities of Biological Interest"
],
"xrefs": {
"fairsharing": "FAIRsharing.62qk8w",
"miriam": "00000002",
"nif": "0000-02655",
"omics": "02752",
"scr": "002088"
}
},
"r3d100012627": {
"description": "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database accepts submissions via an online tool, or in a simple tab-delimited format. It also enables authors to submit supplementary information and link to it from the publication.",
"homepage": "https://www.ebi.ac.uk/biostudies/",
"name": "BioStudies",
"prefix": "r3d100012627",
"xrefs": {
"fairsharing": "FAIRsharing.mtjvme"
}
},
"r3d100012628": {
"description": "BioSamples stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. Samples are either 'reference' samples (e.g. from 1000 Genomes, HipSci, FAANG) or have been used in an assay database such as the European Nucleotide Archive (ENA) or ArrayExpress.",
"homepage": "https://www.ebi.ac.uk/biosamples/",
"name": "Biosamples",
"prefix": "r3d100012628",
"synonyms": [
"Biosample Database at EBI"
],
"xrefs": {
"fairsharing": "FAIRsharing.ewjdq6",
"miriam": "00100447",
"nlx": "143930",
"scr": "004856"
}
},
"r3d100012629": {
"description": "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in the CATH hierarchy; Class, Architecture, Topology and Homologous superfamily.",
"homepage": "https://www.cathdb.info/",
"name": "CATH",
"prefix": "r3d100012629",
"synonyms": [
"CATH-Gene3D",
"Class Architecture Topology Homologous superfamily"
],
"xrefs": {
"fairsharing": "FAIRsharing.xgcyyn",
"miriam": "00000210",
"nif": "0000-02640",
"scr": "007583"
}
},
"r3d100012630": {
"description": "arrayMap is a repository of cancer genome profiling data. Original) from primary repositories (e.g. NCBI GEO, EBI ArrayExpress, TCGA) is re-processed and annotated for metadata. Unique visualization of the processed data allows critical evaluation of data quality and genome information. Structured metadata provides easy access to summary statistics, with a focus on copy number aberrations in cancer entities.",
"homepage": "https://progenetix.org/progenetix-cohorts/arraymap/",
"name": "arrayMap",
"prefix": "r3d100012630",
"xrefs": {
"fairsharing": "FAIRsharing.1fbc5y"
}
},
"r3d100012633": {
"description": "The University of Cape Town (UCT) uses Figshare for institutions for their data repository, which was launched in 2017 and is called ZivaHub: Open Data UCT. ZivaHub serves principal investigators at the University of Cape Town who are in need of a repository to store and openly disseminate the data that support their published research findings. The repository service is provided in terms of the UCT Research Data Management Policy. It provides open access to supplementary research data files and links to their respective scholarly publications (e.g. theses, dissertations, papers et al) hosted on other platforms, such as OpenUCT.",
"homepage": "https://zivahub.uct.ac.za/",
"name": "ZivaHub",
"prefix": "r3d100012633",
"synonyms": [
"Open Data UCT",
"UCT IDR",
"UCT Institutional Data Repository",
"University of Cape Town data repository",
"University of Cape Town figshare repository"
]
},
"r3d100012634": {
"description": "KRISHI Portal is an initiative of Indian Council of Agricultural Research (ICAR) to bring its knowledge resources to all stakeholders at one place. The portal is being developed as a centralized data repository system of ICAR consisting of Technology, Data generated through Experiments/ Surveys/ Observational studies, Geo-spatial data, Publications, Learning Resources etc. \nFor implementation of research data management electronically in ICAR Institutes and digitization of agricultural research, KRISHI (Knowledge based Resources Information Systems Hub for Innovations in Agriculture) Portal has been developed as ICAR Research Data Repository for knowledge management. Data Inventory Repository aims at creating Meta Data Inventory through information related to data availability at Institute level. The portal consists of six repositories viz. technology, publication, experimental data, observational data survey data and geo-portal. The portal can be accessed at http://krishi.icar.gov.in. During the period of 2016-17, input data on latitude and longitude of all KVKs under this Zone was submitted to the concerned authority to put them in geo-portal. One brainstorming session was organized at this institute for all scientists on its use and uploading information in portal. As per guidelines of the council, various kinds of publications pertaining to this institute were also uploaded in this portal.",
"homepage": "https://krishi.icar.gov.in/",
"name": "KRISHI - Knowledge based Resources Information Systems Hub for Innovations in Agriculture",
"prefix": "r3d100012634",
"synonyms": [
"Agricultural Data Repository in India",
"ICAR Research Data Repository for Knowledge Management",
"KRISHI"
]
},
"r3d100012636": {
"description": "Repository for New Mexico Experimental Program to Stimulate Competitive Research Data Collection.\nProvides access to data generated by the Energize New Mexico project as well as data gathered in our previous project that focused on Climate Change Impacts (RII 3). NM EPSCoR contributes its data to the DataONE network as a member node: https://search.dataone.org/#profile/NMEPSCOR\nDigital Repository NM EPSCoR is part of UNM Digital Repository https://digitalrepository.unm.edu/\nsee also: https://data.nmepscor.org/",
"homepage": "https://digitalrepository.unm.edu/nmepscor/",
"name": "Digital Repository NM EPSCoR",
"prefix": "r3d100012636",
"synonyms": [
"Energize NM Data Portal",
"Formerly:NM EPSCoR Data Portal",
"New Mexico Experimental Program to Stimulate Competitive Research Data Collection Data Portal"
]
},
"r3d100012638": {
"description": "India Votes is India's largest public elections resource. It covers all Lok Sabha elections since 1952 and all State elections since 1977. IndiaVotes already has data on over 200 national as well as state elections and will be enriched with inputs from users.\nEven though election data is available online, it is not easily searchable or cannot be consumed in structured formats necessary for analysis. IndiaVotes aims to become the open-source equivalent and Wikipedia of election information in India.",
"homepage": "https://www.indiavotes.com/",
"name": "IndiaVotes",
"prefix": "r3d100012638",
"synonyms": [
"India Votes",
"India's Largest Election Database"
]
},
"r3d100012639": {
"description": "The Centre conducts real-time data collection on all ongoing and incoming General and Assembly Elections, and diffuses data-driven analysis through print and electronic media. The coverage includes the analysis, contextualization, and visualisation of results and the profiling of main parties candidates.\nFor each election, we assemble a team of field researchers and scholars to complete and expand existing data. Besides the ECI results data, we collect information on the socio-demographic profile of main partiesβ candidates and on the sociological profile of constituencies.",
"homepage": "https://lokdhaba.ashoka.edu.in/",
"name": "Lok Dhaba",
"prefix": "r3d100012639",
"synonyms": [
"Lok Dhaba Food For Political Thought",
"Trivedi Centre for Political Data"
]
},
"r3d100012641": {
"description": "The European VLBI Network (EVN) is an interferometric array of radio telescopes located primarily in Europe and Asia, with additional telescopes in South Africa and Puerto Rico. The EVN performs high-resolution observations of cosmic radio sources at wavelenghts from 92cm to 7mm. The EVN Data Archive contains, among other things, the correlated data from EVN observations plus pipeline output, including the initial calibration tables to apply to the correlated data and preliminary images. In general, the correlated data and some pipeline results are proprietary for one year following distribution to the PI of the final epoch of observations resulting from a proposal after which the data enters the public domain; more details are in the \"EVN Data Access Policy\" linked via the archive-introduction page.",
"homepage": "http://www.jive.eu/select-experiment",
"name": "European VLBI Network Data Archive",
"prefix": "r3d100012641",
"synonyms": [
"EVN Data Archive",
"EVN Data Archive at JIVE"
]
},
"r3d100012643": {
"description": "The Deep Blue Data repository is a means for University of Michigan researchers to make their research data openly accessible to anyone in the world, provided they meet collections criteria. Submitted data sets undergo a curation review by librarians to support discovery, understanding, and reuse of the data.",
"homepage": "https://deepblue.lib.umich.edu/data",
"name": "Deep Blue Data",
"prefix": "r3d100012643"
},
"r3d100012644": {
"description": "The EuMMCR (European Mouse Mutant cell Repository) is the mouse ES cell distribution unit in Europe. The EuMMCR unit distributes targeting vectors and mutant ES cell lines produced in the EUCOMM and EUCOMMTOOLS consortia.",
"homepage": "https://www.eummcr.info/",
"name": "European Mouse Mutant Cell Repository",
"prefix": "r3d100012644",
"synonyms": [
"EuMMCR"
],
"xrefs": {
"nlx": "152805",
"scr": "001506"
}
},
"r3d100012645": {
"description": "<<>>!!!>>>",
"homepage": "http://www.herbi.kit.edu/",
"name": "HeRBi",
"prefix": "r3d100012645",
"synonyms": [
"Helmholtz Repository of Bioparts"
]
},
"r3d100012646": {
"description": "The Federated Research Data Repository (FRDR) is a bilingual publishing platform for sharing and preserving Canadian research data. It is a curated, general-purpose repository, custom built for large datasets.",
"homepage": "https://www.frdr-dfdr.ca/repo/",
"name": "Federated Research Data Repository",
"prefix": "r3d100012646",
"synonyms": [
"DFDR",
"DΓ©pΓ΄t fΓ©dΓ©rΓ© de donnΓ©es de recherche",
"FRDR"
],
"xrefs": {
"fairsharing": "FAIRsharing.EnRBIa",
"scr": "019218"
}
},
"r3d100012647": {
"description": "GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, markers, polymorphisms, germplasms, phenotypes and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Research Institute for Agriculture, Food and Environment. It is regularly improved and released several times per year. GnpIS is accessible through a web portal and allows to browse different types of data either independently through dedicated interfaces or simultaneously using a quick search ('google like search') or advanced search (Biomart, Galaxy, Intermine) tools.",
"homepage": "https://urgi.versailles.inrae.fr/gnpis",
"name": "GnpIS",
"prefix": "r3d100012647",
"synonyms": [
"Genetic and Genomic Information System"
],
"xrefs": {
"fairsharing": "fairsharing.dw22y3",
"miriam": "00100831",
"omics": "11988"
}
},
"r3d100012648": {
"description": "coastMap offers campaign data, model analysis and thematic maps predominantly in the Biogeosciences. Spotlights explain in a nutshell important topics of the research conducted for the interested public. The portal offers applications to visualise and download field and laboratory work and to connect the information with interactive maps. Filter functions allow the user to search for general topics like a marine field of interest or single criteria, for example a specific ship campaign or one of 1000 measured parameters.",
"homepage": "https://www.hereon.de/institutes/carbon_cycles/data_coastal_research/coastmap/index.php.en",
"name": "coastMap",
"prefix": "r3d100012648",
"synonyms": [
"marine Geoportal der Hereon Institute fΓΌr Kohlenstoff-KreislΓ€ufe und Umweltchemie des KΓΌstenraumes",
"marine Geoportal of the Hereon Institute of Carbon Cycles and Hereon Institute of Coastal Environmental Chemistry"
],
"xrefs": {
"fairsharing": "FAIRsharing.278768"
}
},
"r3d100012650": {
"description": "<< Search Radiology Portal menu item. The NBIA software is now maintained on GitHub, and can be built and deployed with the latest improvements and fixes that have been completed for TCIA. >>>!!!>>>",
"homepage": "https://imaging.nci.nih.gov/ncia/login.jsf",
"name": "National Biomedical Imaging Archive",
"prefix": "r3d100012650",
"synonyms": [
"NBIA"
]
},
"r3d100012652": {
"description": "The Health Atlas is an alliance of medical ontologists, medical systems biologists and clinical trials groups to design and implement a multi-functional and quality-assured atlas. It provides models, data and metadata on specific use cases from medical research projects from the partner institutions.",
"homepage": "https://www.health-atlas.de/",
"name": "Health Atlas",
"prefix": "r3d100012652",
"synonyms": [
"LHA",
"Leipzig Health Atlas"
]
},
"r3d100012653": {
"description": "The National Institute of Mental Health Data Archive (NDA) makes available human subjects data collected from hundreds of research projects across many scientific domains. The NDA provides infrastructure for sharing research data, tools, methods, and analyses enabling collaborative science and discovery. De-identified human subjects data, harmonized to a common standard, are available to qualified researchers. Summary data is available to all.\nThe primary point of entry to the NDA is currently through the National Database for Autism Research (NDAR) website, which serves the autism research community. All NDA repositories can be accessed through this website for data contribution and querying with other scientific communities, allowing for aggregation and secondary analysis of data.",
"homepage": "https://nda.nih.gov/",
"name": "National Institute of Mental Health Data Archive",
"prefix": "r3d100012653",
"synonyms": [
"NDA",
"NIMH Data Archive"
]
},
"r3d100012654": {
"description": "!!! >>> merged with https://www.re3data.org/repository/r3d100012653 <<< !!! RDoCdb is an informatics platform for the sharing of human subjects data generated by investigators as part of the NIMH's Research Domain Criteria initiative, and to support this initiative's aims. It also accepts and shares appropriate data related to mental health from other sources.",
"homepage": "https://data-archive.nimh.nih.gov/rdocdb/",
"name": "Research Domain Criteria Database",
"prefix": "r3d100012654",
"synonyms": [
"RDoCdb"
],
"xrefs": {
"fairsharing": "FAIRsharing.af3j4h",
"omics": "15206",
"scr": "013796"
}
},
"r3d100012655": {
"description": "<<>>!!!>>>",
"homepage": "https://pediatricmri.nih.gov/nihpd/info/index.html",
"name": "Pediatric MRI Data Repository",
"prefix": "r3d100012655",
"synonyms": [
"NIH Pediatric MRI Repository",
"PedsMRI"
],
"xrefs": {
"nif": "0000-00201",
"omics": "15204",
"scr": "003394"
}
},
"r3d100012656": {
"description": "The ABCD Data Repository houses all data generated by the Adolescent Brain Cognitive Development (ABCD) Study. The ABCD Study is supported by NIH partners (the National Institute on Drug Abuse, the National Institute on Alcohol Abuse and Alcoholism, the National Cancer Institute, the Eunice Kennedy Shriver National Institute of Child Health and Human Development, the National Institute of Mental Health, the National Institute on Minority Health and Health Disparities, the National Institute of Neurological Disorders and Stroke, the NIH Office of Behavioral and Social Sciences Research, and the NIH Office of Research on Womenβs Health), as well as the Centers for Disease Control and Prevention β Division of Adolescent and School Health. This repository will store data generated by ABCD investigators, serve as a collaborative platform for harmonizing these data, and share those data with qualified researchers.",
"homepage": "https://nda.nih.gov/abcd",
"name": "ABCD Data Repository",
"prefix": "r3d100012656",
"synonyms": [
"Adolescent Brain Cognitive Development"
]
},
"r3d100012657": {
"description": "The Connectome Coordination Facility (CCF) houses and distributes public research data for a series of studies that focus on the connections within the human brain. These are known as Human Connectome Projects. he Connectome Coordination Facility (CCF) was chartered to help coordinate myriad research projects, harmonize their data, and facilitate the dissemination of results.",
"homepage": "https://nda.nih.gov/ccf",
"name": "CCF",
"prefix": "r3d100012657",
"synonyms": [
"Connectome Coordination Facility"
]
},
"r3d100012661": {
"description": "The Open Data Platform supports the 'Open Data Policy' of the Government of Telangana. The portal will be the central repository of all the datasets of the Government of Telangana that should be in the public domain. The portal will house datasets form the various departments and organizations of the Government of Telangana.\nThe portal could be used by a variety of stakeholders and will enhance transparency in the working of the government apart from triggering innovative solutions to various problems.",
"homepage": "https://public.tableau.com/app/profile/open.data.telangana",
"name": "Telangana Open Data Portal",
"prefix": "r3d100012661",
"synonyms": [
"Open Data Telangana"
]
},
"r3d100012662": {
"description": "Open Government Data Portal of Sikkimβsikkim.data.gov.in - is a platform for supporting Open Data initiative of Government of Sikkim. The portal is intended to be used by Departments/Organizations of Government of Sikkim to publish datasets, documents, services, tools and applications collected by them for public use. It intends to increase transparency in the functioning of the state Government and also open avenues for many more innovative uses of Government Data to give different perspective.\nOpen Government Data Portal of Sikkim is designed and developed by the Open Government Data Division of National Informatics Centre (NIC), Department of Electronics and Information Technology (DeitY), Government of India. The portal has been created under Software as A Service (SaaS) model of Open Government Data (OGD) Platform India of NIC.\nThe data available in the portal are owned by various Departments/Organization of Government of Sikkim.\nOpen Government Data Portal of Sikkim has following modules:\nData Management System (DMS) β Module for contributing data catalogs by various state government agencies for making those available on the front end website after a due approval process through a defined workflow.\nContent Management System (CMS) β Module for managing and updating various functionalities and content types of Open Government Data Portal of Sikkim.\nVisitor Relationship Management (VRM) β Module for collating and disseminating viewer feedback on various data catalogs.\nCommunities β Module for community users to interact and share their zeal and views with others, who share common interests as that of theirs.",
"homepage": "https://sikkim.data.gov.in/",
"name": "Open Government Data Portal of Sikkim",
"prefix": "r3d100012662"
},
"r3d100012663": {
"description": "Open Data DK has established a governance model to ensure that the members perceive the association as open, equal and result-creating. Open Data DK is a union with a board and teams. The Board is the general and strategic forum and consists of a chairman and five board members. The General Assembly is the Association's decision-making body and highest authority. The individual teams coordinate efforts within specific focus areas.\nGovernance model with teams must support the need to coordinate the work as well as possible while taking into account the autonomy that the individual teams have in terms of the democratic basic element on which the association is based. The gain of using this form of organization is a joint work across the members of the association.",
"homepage": "https://www.opendata.dk/",
"name": "Open Data DK",
"prefix": "r3d100012663"
},
"r3d100012664": {
"description": "βB-Clearβ stands for Bloomington Clear, or Be Clear about what weβre up to.\nB-Clear is a one-stop place to build an ever-growing assembly of useful data. Weβre organizing it as open, accessible data so everyone can see and use it and manipulate it.",
"homepage": "https://data.bloomington.in.gov/",
"name": "B-Clear",
"prefix": "r3d100012664",
"synonyms": [
"Bloomington Clear",
"City of Bloomington Data Portal"
]
},
"r3d100012665": {
"description": "The Portal aims to serve as a unique access point to timely, comprehensive migration statistics and reliable information about migration data globally. The site is designed to help policy makers, national statistics officers, journalists and the general public interested in the field of migration to navigate the increasingly complex landscape of international migration data, currently scattered across different organisations and agencies. \nEspecially in critical times, such as those faced today, it is essential to ensure that responses to migration are based on sound facts and accurate analysis. By making the evidence about migration issues accessible and easy to understand, the Portal aims to contribute to a more informed public debate.\nThe Portal was launched in December 2017 and is managed and developed by IOMβs Global Migration Data Analysis Centre (GMDAC), with the guidance of its Advisory Board, and was supported in its conception by the Economist Intelligence Unit (EIU). The Portal is supported financially by the Governments of Germany, the United States of America and the UK Department for International Development (DFID).",
"homepage": "https://migrationdataportal.org/?i=stock_abs_&t=2017",
"name": "Migration data portal",
"prefix": "r3d100012665",
"synonyms": [
"IOM's Global Migration Data Portal"
]
},
"r3d100012666": {
"description": "Genome resource samples of wild animals, particularly those of endangered mammalian and avian species, are very difficult to collect. In Korea, many of these animals such as tigers, leopards, bears, wolves, foxes, gorals, and river otters, are either already extinct, long before the Korean biologists had the opportunity to study them, or are near extinction. Therefore, proposal for a systematic collection and preservation of genetic samples of these precious animals was adopted by Korea Science & Engineering Foundation (KOSEF). As an outcome, Conservation Genome Resource Bank for Korean Wildlife (CGRB; www.cgrb.org) was established in 2002 at the College of Veterinary Medicine, Seoul National University as one of the Special Research Materials Bank supported by the Scientific and Research Infrastructure Building Program of KOSEF. CGRB operates in collaboration with Seoul Grand Park Zoo managed by Seoul Metropolitan Government, and has offices and laboratories at both Seoul National University and Seoul Grand Park, where duplicate samples are maintained, thereby assuring a long-term, safe preservation of the samples. Thus, CGRB is the first example of the collaborative scientific infrastructure program between university and zoo in Korea.",
"homepage": "http://www.cgrb.org/",
"name": "Conservation Genome Resource Bank for Korean Wildlife",
"prefix": "r3d100012666",
"synonyms": [
"CGRB"
]
},
"r3d100012667": {
"description": "<<>>!!!>>>\n\nDatabase platform for cotton expressed sequence tag (EST)-related information, covering assembled contigs, function annotation, analysis of GO and KEGG, SNP, miRNA, SSR-related marker information.",
"homepage": "http://150.216.56.64/index.php",
"name": "Cotton EST database",
"prefix": "r3d100012667",
"xrefs": {
"scr": "003301"
}
},
"r3d100012668": {
"description": "CottonGen is a new cotton community genomics, genetics and breeding database being developed to enable basic, translational and applied research in cotton. It is being built using the open-source Tripal database infrastructure. CottonGen consolidates and expands the data from CottonDB and the Cotton Marker Database, providing enhanced tools for easy querying, visualizing and downloading research data.",
"homepage": "https://www.cottongen.org/",
"name": "CottonGen",
"prefix": "r3d100012668",
"synonyms": [
"Cotton Database Resources"
],
"xrefs": {
"fairsharing": "FAIRsharing.2f668a"
}
},
"r3d100012669": {
"description": "Cotton Functional Genomics Database (CottonFGD) integrates with modern genomic/transcriptomic data and earch/analysis/visualization modules. It aims at providing an easy, quick and visualized data analysis platform for cotton (Gossypium spp) researchers and other functional genomic researches.",
"homepage": "https://cottonfgd.net/",
"name": "Cotton Functional Genomics Database",
"prefix": "r3d100012669",
"synonyms": [
"CottonFGD"
]
},
"r3d100012670": {
"description": "The USDA Agricultural Marketing Service (AMS) Cotton Program maintains a National Database (NDB) in Memphis, Tennessee for owner access to cotton classification data.\nThe NDB is computerized telecommunications system which allows owners or authorized agents of owners to retrieve classing data from the current crop and/or the previous four crops.\nThe NDB stores classing information from all 10 regional classing offices.",
"homepage": "https://www.ams.usda.gov/datasets/national-cotton-database",
"name": "National Cotton Database",
"prefix": "r3d100012670",
"synonyms": [
"USDA AMS Cotton Program NDB"
]
},
"r3d100012671": {
"description": "This interactive database provides complete access to statistics on seasonal cotton supply and use for each country and each region in the world, from 1920/21 to date. This project is part of ICACβs efforts to improve the transparency of world cotton statistics.",
"homepage": "https://icac.gen10.net/",
"name": "ICAC World Cotton Database",
"prefix": "r3d100012671",
"synonyms": [
"International Cotton Advisory Committee World Cotton Database"
]
},
"r3d100012672": {
"description": "The Wolfram Data Repository is a public resource that hosts an expanding collection of computable datasets, curated and structured to be suitable for immediate use in computation, visualization, analysis and more.\nBuilding on the Wolfram Data Framework and the Wolfram Language, the Wolfram Data Repository provides a uniform system for storing data and making it immediately computable and useful. With datasets of many types and from many sources, the Wolfram Data Repository is built to be a global resource for public data and data-backed publication.",
"homepage": "https://datarepository.wolframcloud.com/",
"name": "Wolfram Data Repository",
"prefix": "r3d100012672"
},
"r3d100012673": {
"description": "INRAE is the worldβs first organisation specialized on agricultural, food and environmental sciences. Data INRAE is offered by INRAE as part of its mission to open the results of its research.\nData INRAE will share research data in relation with food, nutrition, agriculture and environment. It includes experimental, simulation and observation data, omic data, survey and text data.\nOnly data produced by or in collaboration with INRAE will be hosted in the repository, but anyone can access the metadata and the open data.",
"homepage": "https://entrepot.recherche.data.gouv.fr/dataverse/inrae",
"name": "Data INRAE",
"prefix": "r3d100012673",
"synonyms": [
"Data Institut national de recherche pour l'agriculture, l'alimentation et l'environnement",
"EntrepΓ΄t de donnΓ©es dβINRAE",
"INRAE data repository"
],
"xrefs": {
"fairsharing": "fairsharing.178bmt"
}
},
"r3d100012674": {
"description": "OGS is recognised as the Italian National Oceanographic Data Centre (OGS-NODC) within the International Oceanographic Data Exchange System of the UNESCO Intergovernmental Oceanographic Commission (IOC) since 27/6/2002.\nOGS is also listed in EurOcean (Marine Research Infrastructures Database) and in EDMO (European Directory of Marine Organisations).\nOGS as part of the IOC's network of National Oceanographic Data Centres has designated responsibility for the coordination of data and information management at national level. The oceanographic database covers the fields of marine physics, chemical, biological, underway geophysics and general information on Italian oceanographic cruises and data sets.\nThe main objectives are (revision IODE-XXII, March 2013):\n-Facilitate and promote the discovery, exchange of, and access to, marine data and information including metadata, products and information in real-time, near real time and delayed mode, through the use of international standards, and in compliance with the IOC Oceanographic Data Exchange Policy for the ocean research and observation community and other stakeholders;\n- Encourage the long term archival, preservation, documentation, management and services of all marine data, data products, and information;\n- Develop or use existing best practices for the discovery, management, exchange of, and access to marine data and information, including international standards, quality control and appropriate information technology;\n- Assist Member States to acquire the necessary capacity to manage marine research and observation data and information and become partners in the IODE network;\n- Support international scientific and operational marine programmes, including the Framework for Ocean Observing for the benefit of a wide range.",
"homepage": "https://nodc.ogs.it/",
"name": "NODC Italian Oceanographic Data Centre",
"prefix": "r3d100012674",
"synonyms": [
"NODC-OGS",
"National Oceanographic Data Centre at OGS"
]
},
"r3d100012676": {
"description": "In keeping with the open data policies of the U.S. Agency for International Development (USAID) and Bill & Melinda Gates Foundation, the Cereal Systems Initiative for South Asia (CSISA) has launched the CSISA Data Repository to ensure public accessibility to key data sets, including crop cut data- directly observed, crop yield estimates, on-station and on-farm research trial data and socioeconomic surveys.\nCSISA is a science-driven and impact-oriented regional initiative for increasing the productivity of cereal-based cropping systems in Bangladesh, India and Nepal, thus improving food security and farmersβ livelihoods. CSISA generates data that is of value and interest to a diverse audience of researchers, policymakers and the public.\nCSISAβs data repository is hosted on Dataverse, an open source web application developed at Harvard University to share, preserve, cite, explore and analyze research data. CSISAβs repository contains rich datasets, including on-station trial data from 2009β17 about crop and resource management practices for sustainable future cereal-based cropping systems. Collection of this data occurred during the long-term, on-station research trials conducted at the Indian Council of Agricultural Research β Research Complex for the Eastern Region in Bihar, India. The data include information on agronomic management for the sustainable intensification of cropping systems, mechanization, diversification, futuristic approaches to sustainable intensification, long-term effects of conservation agriculture practices on soil health and the pest spectrum.\nAdditional trial data in the repository includes nutrient omission plot technique trials from Bihar, eastern Uttar Pradesh and Odisha, India, covering 2012β15, which help determine the indigenous nutrient supplying ability of the soil. This data helps develop precision nutrient management approaches that would be most effective in different types of soils.\nCSISAβs most popular dataset thus far includes crop cut data on maize in Odisha, India and rice in Nepal. Crop cut datasets provide ground-truthed yield estimates, as well as valuable information on relevant agronomic and socioeconomic practices affecting production practices and yield. A variety of research data on wheat systems are also available from Bangladesh and India. Additional crop cut data will also be coming online soon.\nCropping system-related data and socioeconomic data are in the repository, some of which are cross-listed with a Dataverse run by the International Food Policy Research Institute. The socioeconomic datasets contain baseline information that is crucial for technology targeting, as well as to assess the adoption and performance of CSISA-supported technologies under smallholder farmersβ constrained conditions, representing the ultimate litmus test of their potential for change at scale. Other highly interesting datasets include farm composition and productive trajectory information, based on a 20-year panel dataset, and numerous wheat crop cut and maize nutrient omission trial data from across Bangladesh.",
"homepage": "https://data.cimmyt.org/dataverse/csisadvn",
"name": "CSISA Data Repository",
"prefix": "r3d100012676",
"synonyms": [
"Cereal Systems Initiative for South Asia (CSISA) Research Data"
]
},
"r3d100012677": {
"description": "The Indian Census is the largest single source of a variety of statistical information on different characteristics of the people of India. With a history of more than 130 years, this reliable, time tested exercise has been bringing out a veritable wealth of statistics every 10 years, beginning from 1872 when the first census was conducted in India non-synchronously in different parts. To scholars and researchers in demography, economics, anthropology, sociology, statistics and many other disciplines, the Indian Census has been a fascinating source of data. The rich diversity of the people of India is truly brought out by the decennial census which has become one of the tools to understand and study India\n\n\nThe responsibility of conducting the decennial Census rests with the Office of the Registrar General and Census Commissioner, India under Ministry of Home Affairs, Government of India. It may be of historical interest that though the population census of India is a major administrative function; the Census Organisation was set up on an ad-hoc basis for each Census till the 1951 Census. The Census Act was enacted in 1948 to provide for the scheme of conducting population census with duties and responsibilities of census officers. The Government of India decided in May 1949 to initiate steps for developing systematic collection of statistics on the size of population, its growth, etc., and established an organisation in the Ministry of Home Affairs under Registrar General and ex-Officio Census Commissioner, India. This organisation was made responsible for generating data on population statistics including Vital Statistics and Census. Later, this office was also entrusted with the responsibility of implementation of Registration of Births and Deaths Act, 1969 in the country.",
"homepage": "https://censusindia.gov.in/census.website/data/census-tables",
"name": "Censusindia",
"prefix": "r3d100012677",
"synonyms": [
"Census India"
]
},
"r3d100012678": {
"description": "Survey of India, The National Survey and Mapping Organization of the country under the Department of Science & Technology, is the OLDEST SCIENTIFIC DEPARTMENT OF THE GOVT. OF INDIA. It was set up in 1767 and has evolved rich traditions over the years. In its assigned role as the nation's Principal Mapping Agency, Survey of India bears a special responsibility to ensure that the country's domain is explored and mapped suitably, provide base maps for expeditious and integrated development and ensure that all resources contribute with their full measure to the progress, prosperity and security of our country now and for generations to come.\nThe history of the Survey of India dates back to the 18th Century. Forerunners of army of the East India Company and Surveyors had an onerous task of exploring the unknown. Bit by bit the tapestry of Indian terrain was completed by the painstaking efforts of a distinguished line of Surveyors such as Mr. Lambton and Sir George Everest. It is a tribute to the foresight of such Surveyors that at the time of independence the country inherited a survey network built on scientific principles. The great Trigonometric series spanning the country from North to South East to West are some of the best geodetic control series available in the world. The scientific principles of surveying have since been augmented by the latest technology to meet the multidisciplinary requirement of data from planners and scientists.\nOrganized into only 5 Directorates in 1950, mainly to look after the mapping needs of Defense Forces in North West and North East, the Department has now grown into 22 Directorates spread in approx. all parts (states) of the country to provide the basic map coverage required for the development of the country. Its technology, latest in the world, has been oriented to meet the needs of defense forces, planners and scientists in the field of geo-sciences, land and resource management. Its expert advice is being utilized by various Ministries and undertakings of Govt. of India in many sensitive areas including settlement of International borders, State boundaries and in assisting planned development of hitherto under developed areas.\nFaced with the requirement of digital topographical data, the department has created three Digital Centers during late eighties to generate Digital Topographical Data Base for the entire country for use in various planning processes and creation of geographic information system. Its specialized Directorates such as Geodetic and Research Branch, and Indian Institute of Surveying & Mapping (erstwhile Survey Training Institute) have been further strengthened to meet the growing requirement of user community. The department is also assisting in many scientific programs of the Nation related to the field of geo-physics, remote sensing and digital data transfers.",
"homepage": "https://surveyofindia.gov.in/",
"name": "Survey of India",
"prefix": "r3d100012678"
},
"r3d100012679": {
"description": "It is a platform (designed and developed by the National Informatics Centre (NIC), Government of India) for supporting Open Data initiative of Surat Municipal Corporation, intended to publish government datasets for public use. The portal has been created under Software as A Service (SaaS) model of Open Government Data (OGD) Platform, thus gives avenues for resuing datasets of the City in different perspective.\nThis Portal has numerious modules; (a) Data Management System (DMS) for contributing data catalogs by various departments for making those available on the front end website after a due approval process through a defined workflow; (b) Content Management System (CMS) for managing and updating various functionalities and content types of Open Government Data Portal of Surat City; (c) Visitor Relationship Management (VRM) for collating and disseminating viewer feedback on various data catalogs; and (d) Communities module for community users to interact and share their zeal and views with others, who share common interests as that of theirs.",
"homepage": "https://surat.data.gov.in/",
"name": "Open Government Data Portal of Surat City",
"prefix": "r3d100012679",
"synonyms": [
"Surat Municipal Corporation Open Data Initiative"
]
},
"r3d100012680": {
"description": "This data platform initiated by Government of Maharastra (India) maintained by Mastek Ltd. (for Directorate of Economics and Statistics, Planning Department) to consolidate and collate data sets available with the various state departments. Objectively it creates a decision support system which will also serve as a knowledge repository for various information seekers such as researchers, academicians and general public.",
"homepage": "https://mahasdb.maharashtra.gov.in/home.do",
"name": "Maharashtra State Data Bank",
"prefix": "r3d100012680"
},
"r3d100012681": {
"description": "It collects, processes, and generates a large amount of data made available publicly in an open format to facilitate use, reuse and redistribute for social, economic and developmental purposes. This data portal of the Pune Municipal Corporation (designed and developed by the Benchmark IT Solutions) is free from any license or any other mechanism of control; thus opening up of government data (municipal level) would enhance transparency and accountability while encouraging public engagement. \n\nKeeping the need of seamless data availability and efficient sharing of data among intra-governmental agencies along with data standards and interoperable systems; Pune DataStore endorses government of Indiaβs Open Government Data (OGD) Platform in which supports Open Data initiative of Government of India.",
"homepage": "http://opendata.punecorporation.org/Citizen/User/Index",
"name": "Pune Datastore",
"prefix": "r3d100012681",
"synonyms": [
"PMC Open Data Store",
"Pune Municipal Corporation Open Data Store"
]
},
"r3d100012682": {
"description": "Open Government Data Portal of Tamil Nadu is a platform (designed by the National Informatics Centre), for Open Data initiative of the Government of Tamil Nadu. The portal is intended to publish datasets collected by the Tamil Nadu Government for public uses in different perspective. It has been created under Software as A Service (SaaS) model of Open Government Data (OGD) and publishes dataset in open formats like CSV, XLS, ODS/OTS, XML, RDF, KML, GML, etc. \nThis data portal has following modules, namely (a) Data Management System (DMS) for contributing data catalogs by various state government agencies for making those available on the front end website after a due approval process through a defined workflow; (b) Content Management System (CMS) for managing and updating various functionalities and content types; (c) Visitor Relationship Management (VRM) for collating and disseminating viewer feedback on various data catalogs; and (d) Communities module for community users to interact and share their views and common interests with others.\nIt includes different types of datasets generated both in geospatial and non-spatial data classified as shareable data and non-shareable data. Geospatial data consists primarily of satellite data, maps, etc.; and non-spatial data derived from national accounts statistics, price index, census and surveys produced by a statistical mechanism. It follows the principle of data sharing and accessibility via Openness, Flexibility, Transparency, Quality, Security and Machine-readable.",
"homepage": "https://tn.data.gov.in/",
"name": "Open Government Data Portal of Tamil Nadu",
"prefix": "r3d100012682",
"xrefs": {
"fairsharing": "FAIRsharing.15514b"
}
},
"r3d100012683": {
"description": "National Data Repository (NDR) is a reliable and integrated data repository of Exploration and Production (E&P) data of Indian sedimentary basins. It offers a unique platform to all concerns of E&P with provisions for seamless access to reliable geo-scientific data for India. Streamlining all associated procedures, policies and workflows pertaining to data submission, data management, data retrieval for all concerned pertaining to government agencies, academia and research communities with restrictions. NDR is owned by the Government of India, hosted at Directorate General of Hydrocarbons (DGH), Ministry of Petroleum and Natural Gas (MoPNG). Objectively it operates with geological data, petrophysical data, natural gas, seismic data, well & log data, spatial data, Reservoir data, Gravity & Magnetic data. NDR maintains and preserve hydrocarbon exploration & production data in a standard and reusable manner, but can't made available to entitled users freely. One cannot get access independently.",
"homepage": "https://www.ndrdgh.gov.in/NDR/",
"name": "National Data Repository",
"prefix": "r3d100012683",
"synonyms": [
"NDR - National Data Repository India",
"National Data Repository India"
]
},
"r3d100012684": {
"description": "It is a platform for supporting Open Data initiative of Government of Odisha, intends to publish datasets collected by them for public use. It also supports widely used file formats that are suitable for machine processing, thus gives avenues for many more innovative uses of Government Data in different perspective. This portal has been created under Software as A Service (SaaS) model of Open Government Data (OGD) Platform India of NIC. The data available in the portal are owned by various Departments/Organization of Government of Odisha. It follows principles on which data sharing and accessibility need to be based include: Openness, Flexibility, Transparency, Quality, Security and Machine-readable.",
"homepage": "https://odisha.data.gov.in/",
"name": "Open Government Data Portal of Odisha",
"prefix": "r3d100012684",
"synonyms": [
"Odisha Open Government Data Portal"
]
},
"r3d100012685": {
"description": "The Cotton Database is provided by the Central Institute for Cotton Research in India. The database includes data on cotton production, protection, improvement, economy, and industry.",
"homepage": "http://www.cicr.org.in/Database.html",
"name": "Cotton Database",
"prefix": "r3d100012685"
},
"r3d100012687": {
"description": "The ord.fkp.jku.at portal offers a Data Repository of the JKUs Magnetic Oxides Group and provides access to the latest research data of the Magnetic Oxide research group of the Johannes Kepler University in Linz, Austria. The Repository contains Datasets in the following research areas: Dilute magnetic semiconductors and oxides, Ferromagnetic thin films and nanoparticles, X-ray absorption spectroscopy, Element-selective structure and magnetism, Functional heterostructures and interfaces, and Frequency-dependent magnetic resonance.",
"homepage": "https://ord.fkp.jku.at/",
"name": "JKU Magnetic Oxides Data Repository",
"prefix": "r3d100012687",
"synonyms": [
"Johannes Kepler University Magnetic Oxides Data Repository"
]
},
"r3d100012688": {
"description": "<<>>!!!>>>\n\n\nA database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data.",
"homepage": "https://www.ncbi.nlm.nih.gov/assembly",
"name": "NCBI Assembly",
"prefix": "r3d100012688",
"xrefs": {
"omics": "10736"
}
},
"r3d100012689": {
"description": "The Japanese Genotype-phenotype Archive (JGA) is a service for permanent archiving and sharing of all types of individual-level genetic and de-identified phenotypic data resulting from biomedical research projects. The JGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the JGA. Once processed, all data are encrypted. Users can contact the JGA team from here.\nJGA services are provided in collaboration with National Bioscience Database Center (NBDC) of Japan Science and Technology Agency.",
"homepage": "https://www.ddbj.nig.ac.jp/jga/index-e.html",
"name": "Japanese Genotype-phenotype Archive",
"prefix": "r3d100012689",
"synonyms": [
"JGA"
],
"xrefs": {
"fairsharing": "FAIRsharing.pwgf4p",
"nlx": "156741",
"scr": "003118"
}
},
"r3d100012690": {
"description": "The NDEx Project provides an open-source framework where scientists and organizations can share, store, manipulate, and publish biological network knowledge.\nThe NDEx Project maintains a free, public website; alternatively, users can also decide to run their own copies of the NDEx Server software in cases where the stored networks must be kept in a highly secure environment (such as for HIPAA compliance) or where high application load is incompatible with a shared public resource.",
"homepage": "https://home.ndexbio.org/index/",
"name": "Network Data Exchange",
"prefix": "r3d100012690",
"synonyms": [
"NDEx"
],
"xrefs": {
"fairsharing": "FAIRsharing.8nq9t6",
"nlx": "158334",
"scr": "003943"
}
},
"r3d100012691": {
"description": "TiU Dataverse is the central online repository for research data at Tilburg University. The TiU Dataverse is managed by the Research Data Office (RDO) at Library and IT Services (LIS).\nTiU Dataverse takes part of the DataverseNL network. DataverseNL is a shared data service of several Dutch universities and institutions. The data management is in the hands of the member organizations, while the national organization Data Archiving and Networked Services (DANS) manages the network",
"homepage": "https://dataverse.nl/dataverse/tiu",
"name": "Tilburg University Dataverse",
"prefix": "r3d100012691"
},
"r3d100012692": {
"description": "Scholars' Mine is an online collection of scholarly and creative works produced by the faculty, staff, and students of the Missouri University of Science and Technology.",
"homepage": "https://scholarsmine.mst.edu/",
"name": "Scholars' Mine",
"prefix": "r3d100012692",
"xrefs": {
"fairsharing": "FAIRsharing.SWMYY2"
}
},
"r3d100012693": {
"description": "A service of the Inter-university Consortium for Political and Social Research (ICPSR), openICPSR is a self-publishing repository for social, behavioral, and health sciences research data. openICPSR is particularly well-suited for the deposit of replication data sets for researchers who need to publish their raw data associated with a journal article so that other researchers can replicate their findings.",
"homepage": "https://www.openicpsr.org/openicpsr/",
"name": "openICPSR",
"prefix": "r3d100012693",
"xrefs": {
"fairsharing": "FAIRsharing.nvwz0x"
}
},
"r3d100012694": {
"description": "<<>>!!!>>>",
"homepage": "http://www.alsgene.org/",
"name": "ALSGENE",
"prefix": "r3d100012694",
"xrefs": {
"omics": "04618"
}
},
"r3d100012695": {
"description": "ALSoD is a freely available database that has been transformed from a single gene storage facility recording mutations in the SOD1 gene to a multigene ALS bioinformatics repository and analytical instrument combining genotype, phenotype, and geographical information with associated analysis tools. These include a comparison tool to evaluate genes side by side or jointly with user configurable features, a pathogenicity prediction tool using a combination of computational approaches to distinguish variants with nonfunctional characteristics from disease-associated mutations with more dangerous consequences, and a credibility tool to enable ALS researchers to objectively assess the evidence for gene causation in ALS. Furthermore, integration of external tools, systems for feedback, annotation by users, and two-way links to collaborators hosting complementary databases further enhance the functionality of ALSoD.",
"homepage": "https://alsod.ac.uk/",
"name": "ALSoD",
"prefix": "r3d100012695",
"synonyms": [
"ALS Online Database",
"Amyotrophic Lateral Sclerosis Online genetics Database"
],
"xrefs": {
"scr": "018075"
}
},
"r3d100012696": {
"description": "Iowa State Universityβs DataShare is an open access repository for sharing and publishing research data created by Iowa State University scholars and researchers.",
"homepage": "https://iastate.figshare.com/",
"name": "DataShare: the Open Data Repository of Iowa State University",
"prefix": "r3d100012696",
"synonyms": [
"DataShare",
"ISU's Open Data Repository",
"Iowa State Universityβs DataShare"
],
"xrefs": {
"fairsharing": "FAIRsharing.yOKiQs"
}
},
"r3d100012698": {
"description": "The Repository stores in digital format all the academic and scientific documentation (Theses, Articles, Papers) generated by the institution. Its main objectives are to promote open access to the scientific-technological production generated by the Institution. It is organized by collections: Thesis and Final Works, Research, Institutional History and Photographic Archive.",
"homepage": "https://bibliotecas.ucasal.edu.ar/opac_css/index.php?lvl=cmspage&pageid=16",
"name": "Repositorio Institucional UCASAL",
"prefix": "r3d100012698"
},
"r3d100012700": {
"description": "We are working on a new version of ALFRED web interface. The current web interface will not be available from December 15th, 2023. There will be a period where a public web interface is not available for viewing ALFRED data. Expected date for the deployment of the new ALFRED web interface with minimum functions is March 1st, 2024 \n---------------------------------------------\nALFRED is a free, web-accessible, curated compilation of allele frequency data on DNA sequence polymorphisms in anthropologically defined human populations. ALFRED is distinct from such databases as dbSNP, which catalogs sequence variation.",
"homepage": "https://alfred.med.yale.edu/alfred/index.asp",
"name": "ALlele FREquency Database",
"prefix": "r3d100012700",
"synonyms": [
"ALFRED"
],
"xrefs": {
"fairsharing": "FAIRsharing.y2yct1",
"nif": "0000-02541",
"omics": "20460",
"scr": "001730"
}
},
"r3d100012701": {
"description": "<<>>!!!>>>\nThe repository of the Donders Institute for Brain, Cognition and Behaviour at the Radboud University was used to manage, share and publish neuroscience and neuroimaging data, including MRI, EEG, MEG and other types of research data.",
"homepage": "https://data.donders.ru.nl/",
"name": "Donders Repository",
"prefix": "r3d100012701",
"xrefs": {
"fairsharing": "FAIRsharing.1sfhp3"
}
},
"r3d100012702": {
"description": "IEDB offers easy searching of experimental data characterizing antibody and T cell epitopes studied in humans, non-human primates, and other animal species. Epitopes involved in infectious disease, allergy, autoimmunity, and transplant are included.\nThe IEDB also hosts tools to assist in the prediction and analysis of B cell and T cell epitopes.",
"homepage": "https://www.iedb.org/",
"name": "Immune Epitope Database",
"prefix": "r3d100012702",
"synonyms": [
"IEDB",
"Immune Epitope Database and Analysis Resource"
],
"xrefs": {
" nif": "0000-03017",
"fairsharing": "FAIRsharing.c886cd",
"scr": "006604"
}
},
"r3d100012704": {
"description": "Arquivo.pt is a research infrastructure that preserves millions of files collected from the web since 1996 and provides a public search service over this information. It contains information in several languages. Periodically it collects and stores information published on the web. Then, it processes the collect data to make it searchable, providing a βGoogle-likeβ service that enables searching the past web (English user interface available at https://arquivo.pt/?l=en). This preservation workflow is performed through a large-scale distributed information system and can also accessed through API (https://arquivo.pt/api).",
"homepage": "https://arquivo.pt/",
"name": "Arquivo.pt - the Portuguese web-archive",
"prefix": "r3d100012704",
"synonyms": [
"Arquivo.pt - pesquise pΓ‘ginas do passado"
]
},
"r3d100012705": {
"description": "Kaggle is a platform for predictive modelling and analytics competitions in which statisticians and data miners compete to produce the best models for predicting and describing the datasets uploaded by companies and users. This crowdsourcing approach relies on the fact that there are countless strategies that can be applied to any predictive modelling task and it is impossible to know beforehand which technique or analyst will be most effective.",
"homepage": "https://www.kaggle.com/datasets",
"name": "Kaggle",
"prefix": "r3d100012705",
"synonyms": [
"Your home for data science"
],
"xrefs": {
"fairsharing": "FAIRsharing.mjq9vj"
}
},
"r3d100012708": {
"description": "The Land Portal is the leading online resource for land governance issues. It collects metadata from statistical datasets relating to land, peer-reviewed articles and other research reports, national laws and policies, grey literature but also news, blogs and organization profiles.",
"homepage": "https://www.landportal.org",
"name": "Land Portal",
"prefix": "r3d100012708",
"synonyms": [
"Land Portal Foundation"
]
},
"r3d100012712": {
"description": "Epidat provides the inventory, documentation, editions and presentation of epigraphical collections.",
"homepage": "http://www.steinheim-institut.de/cgi-bin/epidat?lang=de",
"name": "Epidat",
"prefix": "r3d100012712",
"synonyms": [
"Datenbank zur jΓΌdischen Grabsteinepigraphik",
"The Database of Jewish epigraphy"
]
},
"r3d100012713": {
"description": "Alzforum is an independent research project to develop an online community resource to manage scientific knowledge, information, and data about Alzheimer disease (AD).",
"homepage": "https://www.alzforum.org/",
"name": "Alzforum",
"prefix": "r3d100012713",
"synonyms": [
"Networking for a cure"
],
"xrefs": {
"nif": "0000-00095",
"scr": "006416"
}
},
"r3d100012714": {
"description": "Here you find our web GIS. It was developed in close cooperation with the Institute for Geoinformatics of the WWU MΓΌnster. Here, the raw data of the survey project βWadi Abu Dom Itineraryβ are presented to the public.\nAt the moment, this presentation platform is shared with the research project βDolicheβ of the research center Asia Minor at the WWU MΓΌnster. In future, the integration of other research projects is planned.",
"homepage": "http://en.wadi-abu-dom.de/webgis/",
"name": "W.A.D.I. Wadi Abu Dom Investigations",
"prefix": "r3d100012714",
"synonyms": [
"WebGIS UniversitΓ€t MΓΌnster"
]
},
"r3d100012715": {
"description": "enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products.",
"homepage": "https://envipath.org/",
"name": "enviPath",
"prefix": "r3d100012715",
"synonyms": [
"The enironmental contaminant biotransormation pathway resource",
"including: Biocatalysis/Biodegradation Database EAWAG PPS Rules"
],
"xrefs": {
"fairsharing": "FAIRsharing.g0c5qn",
"omics": "11129"
}
},
"r3d100012716": {
"description": "The Portal de datos de Biodiversidad is the biodiversity data portal of the National System of Biological Data (Sistema Nacional de Datos BiolΓ³gicos, SNDB). It provides georeferenced data, published data sets, and information about biodiversity collections of the SNDB.",
"homepage": "http://datos.sndb.mincyt.gob.ar/",
"name": "Portal de datos de Biodiversidad",
"prefix": "r3d100012716",
"synonyms": [
"Sistema Nacional de Datos BiolΓ³gicos - Portal de datos"
]
},
"r3d100012717": {
"description": "<<>>!!!>>>",
"homepage": "http://portal.mincyt.gob.ar/portal/",
"name": "Portal de Datos del Mar - SNDM",
"prefix": "r3d100012717",
"synonyms": [
"Ocean Data Portal",
"Portal Argentino de Datos del Mar"
]
},
"r3d100012718": {
"description": "Fondo Antiguo is part of UVaDOC Repositorio Documental de la Universidad de Valladolid. It contains ancient printed documents.",
"homepage": "https://uvadoc.uva.es/handle/10324/150",
"name": "UvaDOC - Fonda Antiguo",
"prefix": "r3d100012718",
"synonyms": [
"University of Valladolid Documentary Repository - Fonda Antiguo"
]
},
"r3d100012721": {
"description": "TopFIND is a protein-centric database for the annotation of protein termini currently in its third version. Non-canonical protein termini can be the result of multiple different biological processes, including pre-translational processes such as alternative splicing and alternative translation initiation or post-translational protein processing by proteases that cleave proteases as part of protein maturation or as a regulatory modification. Accordingly, protein termini evidence in TopFIND is inferred from other databases such as ENSEMBL transcripts, TISdb for alternative translation initiation, MEROPS for protein cleavage by proteases, and UniProt for canonical and protein isoform start sites.",
"homepage": "https://topfind.clip.msl.ubc.ca/",
"name": "TopFIND",
"prefix": "r3d100012721",
"synonyms": [
"The public knowledgebase for protein termini and protease processing"
],
"xrefs": {
"fairsharing": "FAIRsharing.rkpmhn",
"nlx": "151607",
"omics": "10578",
"scr": "008918"
}
},
"r3d100012722": {
"description": "<<>>!!!>>>",
"homepage": "http://phenom.ccbr.utoronto.ca/",
"name": "PhenoM",
"prefix": "r3d100012722",
"synonyms": [
"Phenomics of yeast Mutants"
],
"xrefs": {
"fairsharing": "FAIRsharing.bp5hpt",
"nlx": "151489",
"omics": "03109",
"scr": "006970"
}
},
"r3d100012723": {
"description": "Database for identification and cataloguing of group II introns. All bacterial introns listed are full-length and appear to be functional, based on intron RNA and IEP characteristics. The database names the full-length introns, and provides information on their boundaries, host genes, and secondary structures. In addition, the website provides tools for analysis that may be useful to researchers who encounter group II introns in DNA sequences. Intron data can be downloaded in FASTA format.",
"homepage": "http://webapps2.ucalgary.ca/~groupii/",
"name": "Database for Bacterial Group II Introns",
"prefix": "r3d100012723",
"synonyms": [
"Group II introns database"
],
"xrefs": {
"fairsharing": "FAIRsharing.710xh8"
}
},
"r3d100012724": {
"description": "BacMap is a picture atlas of annotated bacterial genomes. It is an interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes.",
"homepage": "http://bacmap.wishartlab.com/",
"name": "BacMap",
"prefix": "r3d100012724",
"synonyms": [
"BacMap Genome Atlas"
],
"xrefs": {
"fairsharing": "FAIRsharing.z6rbe3",
"miriam": "00100539",
"nif": "0000-02591",
"omics": "20942",
"scr": "006988"
}
},
"r3d100012725": {
"description": "iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID.",
"homepage": "https://wodaklab.org/iRefWeb/",
"name": "iRefWeb",
"prefix": "r3d100012725",
"synonyms": [
"Interaction Reference Index Web Interface"
],
"xrefs": {
"fairsharing": "FAIRsharing.t31wcb",
"nif": "0000-20861",
"omics": "02922",
"scr": "008118"
}
},
"r3d100012726": {
"description": "Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase.",
"homepage": "https://compsysbio.org/bacteriome/",
"name": "Bacteriome.org",
"prefix": "r3d100012726",
"synonyms": [
"Bacterial Protein Interaction Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.mx5cxe",
"nif": "0000-02592",
"scr": "001934"
}
},
"r3d100012727": {
"description": "A bioinformatic database of antimicrobial resistance genes, their products and associated phenotypes.",
"homepage": "https://card.mcmaster.ca/",
"name": "Comprehensive Antibiotic Resistance Database",
"prefix": "r3d100012727",
"synonyms": [
"CARD"
],
"xrefs": {
"fairsharing": "FAIRsharing.9dbmwg"
}
},
"r3d100012728": {
"description": "OrtholugeDB contains Ortholuge-based orthology predictions for completely sequenced bacterial and archaeal genomes. It is also a resource for reciprocal best BLAST-based ortholog predictions, in-paralog predictions (recently duplicated genes) and ortholog groups in Bacteria and Archaea. The Ortholuge method improves the specificity of high-throughput orthology prediction.",
"homepage": "https://ortholugedb.ca/",
"name": "OrtholugeDB",
"prefix": "r3d100012728",
"synonyms": [
"The Ortholog Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.675y92"
}
},
"r3d100012729": {
"description": "<<>>!!!>>>\nFormerly known as mycoCLAP, CLAE is a curated database of Characterized Lignocellulose-Active Enzymes",
"homepage": "https://clae.fungalgenomics.ca/",
"name": "CLAE",
"prefix": "r3d100012729",
"synonyms": [
"Characterized Lignocellulose-Active Proteins of Fungal Origin",
"formerly: mycoCLAP"
],
"xrefs": {
"fairsharing": "FAIRsharing.ezp87",
"omics": "07832"
}
},
"r3d100012730": {
"description": "SCRIPDB is a chemical structure database designed to make patent metadata accessible. We index public-domain chemical information contained in U.S. patents, and provide the full patent text, reactions, and relationships described within any individual patent, as well as the original CDX, MOL, and TIFF files.",
"homepage": "http://dcv.uhnres.utoronto.ca/SCRIPDB",
"name": "SCRIPDB",
"prefix": "r3d100012730",
"synonyms": [
"Syntheses, Chemicals, and Reactions In Patents"
],
"xrefs": {
"fairsharing": "FAIRsharing.sncr74",
"nlx": "151638",
"omics": "10794",
"scr": "008922"
}
},
"r3d100012731": {
"description": "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. The data is freely available under the license terms of each contributing database.",
"homepage": "https://www.pathwaycommons.org/",
"name": "Pathway Commons",
"prefix": "r3d100012731",
"xrefs": {
"fairsharing": "FAIRsharing.5y3gdd",
"nif": "0000-20884",
"omics": "02761",
"scr": "002103"
}
},
"r3d100012732": {
"description": "A data repository for the storage and sharing of Adaptive Immune Receptor Repertoire data. Primary public repository for the iReceptor Platform and Scientific Gateway. Further URL for the repository: http://www.ireceptor.org",
"homepage": "http://ireceptor.irmacs.sfu.ca/",
"name": "iReceptor",
"prefix": "r3d100012732",
"xrefs": {
"fairsharing": "FAIRsharing.ekdqe5"
}
},
"r3d100012733": {
"description": "The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Bakerβs yeast and Brewerβs yeast). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions and other electronic databases.",
"homepage": "https://www.ymdb.ca/",
"name": "The Yeast Metabolome Database",
"prefix": "r3d100012733",
"synonyms": [
"YMDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.tawpg2",
"scr": "005890"
}
},
"r3d100012747": {
"description": "Gemma is a database for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. Users can search, access and visualize co-expression and differential expression results.",
"homepage": "https://gemma.msl.ubc.ca/home.html",
"name": "Gemma",
"prefix": "r3d100012747",
"synonyms": [
"Tools and database for meta-analysis of functional genomics data"
],
"xrefs": {
"fairsharing": "FAIRsharing.t98nav",
"nif": "0000-08127",
"omics": "27257",
"scr": "008007"
}
},
"r3d100012752": {
"description": "BenchSci is a free platform designed to help biomedical research scientists quickly and easily identify validated antibodies from publications. Using various filters including techniques, tissue, cell lines, and more, scientists can find out published data along with the antibody that match specific experimental contexts within seconds. Free registration & access for academic research scientists.",
"homepage": "https://www.benchsci.com/",
"name": "BenchSCI",
"prefix": "r3d100012752",
"synonyms": [
"A.I. Driven Antibody Search"
],
"xrefs": {
"fairsharing": "fairsharing.fwg0qf"
}
},
"r3d100012753": {
"description": "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.",
"homepage": "https://smpdb.ca/",
"name": "Small Molecule Pathway Database",
"prefix": "r3d100012753",
"synonyms": [
"SMPDB",
"formerly: PathBank"
],
"xrefs": {
"fairsharing": "fairsharing.y1zyaq",
"miriam": "00000104",
"nlx": "143926",
"scr": "004844"
}
},
"r3d100012754": {
"description": "The Health Canada Drug Product Database contains product specific information on drugs approved for use in Canada. The database is managed by Health Canada and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. It contains approximately 15,000 products which companies have notified Health Canada as being marketed.",
"homepage": "https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/drug-product-database.html",
"name": "Health Canada Drug Product Database",
"prefix": "r3d100012754",
"synonyms": [
"BDPP",
"Base de donnΓ©es sur les produits pharmaceutiques",
"DPD",
"Drug Product Database",
"HC DPD"
],
"xrefs": {
"fairsharing": "fairsharing.tyyn81",
"miriam": "00100351"
}
},
"r3d100012755": {
"description": "BACTIBASE contains calculated or predicted physicochemical properties of bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships structure/function and target organisms of these peptides and therefore better exploitation of their biological activity in both the medical and food sectors.",
"homepage": "http://bactibase.hammamilab.org/main.php",
"name": "BACTIBASE",
"prefix": "r3d100012755",
"synonyms": [
"a database dedicated to bacteriocins"
],
"xrefs": {
"fairsharing": "FAIRsharing.5f5mfm",
"nlx": "54530",
"omics": "05726",
"scr": "006694"
}
},
"r3d100012756": {
"description": "The Chemical Probes Portal is an online open access catalog of annotated small molecule inhibitors, agonists and other chemical tools for biological research and preclinical drug discovery. Annotations for are extensive and distinguish between activity in cells and model organisms.",
"homepage": "https://new.chemicalprobes.org/",
"name": "The Chemical Probes Portal",
"prefix": "r3d100012756",
"xrefs": {
"fairsharing": "FAIRsharing.yrkkbt"
}
},
"r3d100012757": {
"description": "Rodare is the institutional research data repository at HZDR (Helmholtz-Zentrum Dresden-Rossendorf). Rodare allows HZDR researchers to upload their research software and data and enrich those with metadata to make them findable, accessible, interoperable and retrievable (FAIR). By publishing all associated research software and data via Rodare research reproducibility can be improved. Uploads receive a Digital Object Identfier (DOI) and can be harvested via a OAI-PMH interface.",
"homepage": "https://rodare.hzdr.de/",
"name": "RODARE",
"prefix": "r3d100012757",
"synonyms": [
"Rossendorf Data Repository"
]
},
"r3d100012760": {
"description": "The Centro de Documentação e Pesquisa Digital de Pesquisa (CEDAP) of the Universidade Federal do Rio Grande do Sul (UFRGS) aims to gather the scientific data used in research, classified as long syllable, in the various areas of knowledge. The Scientific Data Repository of Research of CEDAP aims to gather the scientific data used in the researches, with the provision of documentation, in order to provide an environment of study of methodologies of use and reuse of research data. Maintained in partnership with the Data Processing Center (CPD) of UFRGS for the development of policies, planning, management, description, evaluation, storage, dissemination and reuse of research data. Created in June 2017, the Research Data Repository meets the sharing needs in Brazil.",
"homepage": "https://cedap.ufrgs.br/jspui/handle/2050011959/90",
"name": "CEDAP Research Data Repository - research data",
"prefix": "r3d100012760",
"synonyms": [
"Centro de Documentação e Acervo Digital da Pesquisa - Dados de Pesquisa"
]
},
"r3d100012761": {
"description": "The collection contains computed images (ortho-photos), camera photos, and wall plans of the textual witness of the Egyptian Netherworld Book, \"Book of Caverns\", in the tomb of Petamenophis in the necropolis of Thebes in Egypt (TT 33).",
"homepage": "http://repository.edition-topoi.org/collection/BOCA",
"name": "The Book of Caverns in Theban Tomb 33: Arbeitsphotos",
"prefix": "r3d100012761",
"synonyms": [
"BOCA"
],
"xrefs": {
"doi": "10.17171/2-8"
}
},
"r3d100012762": {
"description": "Database of ancient sources concerning Roman Water Law. Specific legal sources, e.g. from the Corpus Iuris Civilis or the Codex Theodosianus, and literary sources, for example from Cicero, Frontinus, Hyginus, Siculus Flaccus or Vitruvius, were collected to give an overview of water related legal problems in ancient Rome. Furthermore, the aim of the database is to classify these sources into different legal topics, in order to facilitate the research for sources concerning specific questions regarding Roman Water Law.",
"homepage": "http://repository.edition-topoi.org/collection/RMWR",
"name": "Roman Water Law",
"prefix": "r3d100012762",
"synonyms": [
"RMWR"
],
"xrefs": {
"doi": "10.17171/1-10"
}
},
"r3d100012763": {
"description": "OpenStreetMap (https://www.openstreetmap.org/export#map=6/51.324/10.426) is built by a community of mappers that contribute and maintain data about roads, trails, cafΓ©s, railway stations, and much more, all over the world. Planet.osm is the OpenStreetMap data in one file.",
"homepage": "https://planet.openstreetmap.org/",
"name": "OpenStreetMap",
"prefix": "r3d100012763",
"synonyms": [
"OSM",
"Planet.osm"
]
},
"r3d100012765": {
"description": "Ecosounds is a repository of environmental audio recordings. This website facilitates the management, access, visualization, and analysis of environmental acoustic data. It uses the Acoustic Workbench software which is open source and available from GitHub.\nThe website is run by the QUT Ecoacoustics Research Group to support bioacoustics and ecoacoustics research.",
"homepage": "https://www.ecosounds.org/",
"name": "Ecosounds",
"prefix": "r3d100012765",
"synonyms": [
"Queensland University of Technology"
]
},
"r3d100012766": {
"description": "NetSlim is a resource of high-confidence signaling pathway maps derived from NetPath pathway reactions. 40-60% of the molecules and their reactions in NetPath pathways are available in NetSlim.",
"homepage": "http://www.netpath.org/netslim/",
"name": "NetSlim",
"prefix": "r3d100012766"
},
"r3d100012768": {
"description": "The portal \"Wissenschaftliche Sammlungen\" is a project of the Coordination Office for Academic University Collections in Germany in cooperation with the Academic University and University Collections.\nTogether we create a platform that makes information on scientific collections, activities and actors as well as metadata and digitised objects visible, searchable and scientifically usable via a web portal. The data will be freely and openly accessible via technical interfaces in standard formats and fed into national reference systems such as the German Digital Library.",
"homepage": "https://portal.wissenschaftliche-sammlungen.de/",
"name": "Wissenschaftliche Sammlungen",
"prefix": "r3d100012768",
"synonyms": [
"Wissenschaftliche Sammlungen in Deutschland und ihre Digitalisierung"
]
},
"r3d100012769": {
"description": "The French Center for Socio-Political Data over 390 surveys and studies through its data bank (Banque de donnΓ©es), based on the Dataverse open solution. Accessing the data requires creating an account, accepting of General Terms of Use, and manual approval of the request by data managers. Election results and metadata, which are openly available, do not fall under these prerequisites.",
"homepage": "https://data.sciencespo.fr/dataverse/cdsp",
"name": "Banque de donnΓ©es du CDSP",
"prefix": "r3d100012769",
"synonyms": [
"Banque de donnΓ©es du Centre de donnΓ©es socio-politiques"
]
},
"r3d100012770": {
"description": "The range of CIRAD's research has given rise to numerous datasets and databases associating various types of data: primary (collected), secondary (analysed, aggregated, used for scientific articles, etc), qualitative and quantitative. These \"collections\" of research data are used for comparisons, to study processes and analyse change. They include: genetics and genomics data, data generated by trials and measurements (using laboratory instruments), data generated by modelling (interpolations, predictive models), long-term observation data (remote sensing, observatories, etc), data from surveys, cohorts, interviews with players.",
"homepage": "https://dataverse.cirad.fr/",
"name": "CIRAD Dataverse",
"prefix": "r3d100012770",
"synonyms": [
"DonnΓ©es de recherche du CIRAD"
],
"xrefs": {
"doi": "10.18167/infrastructure/00003",
"fairsharing": "FAIRsharingβ§b52cce"
}
},
"r3d100012771": {
"description": "The Center for International Forestry Research (CIFOR) envisions a more equitable world where forestry and landscapes enhance the environment and well-being for all. The Center for International Forestry Research (CIFOR) is committed to advancing human well-being, equity and environmental integrity by conducting innovative research, developing partnersβ capacity and actively engaging in dialogue with all stakeholders to inform policies and practices that affect forests and people.",
"homepage": "https://dataverse.harvard.edu/dataverse/cifor_harvested",
"name": "CIFOR Harvested Dataverse",
"prefix": "r3d100012771",
"synonyms": [
"Center for International Forestry Research Harvested Dataverse"
]
},
"r3d100012773": {
"description": "Created and managed by the Library, DataSpace@HKUST is the data repository and workspace service for HKUST research community. Faculty members and research postgraduate students can use the platform to store, share, organize, preserve and publish research data. It is built on Dataverse, an open source web application developed at Harvardβs Institute for Quantitative Social Science. Using Dataverse architecture, the repository hosts multiple \"dataverses\". Each dataverse contains datasets; while each dataset may contain multiple data files and the corresponding descriptive metadata.",
"homepage": "https://dataspace.hkust.edu.hk/",
"name": "DataSpace@HKUST",
"prefix": "r3d100012773"
},
"r3d100012775": {
"description": "Open for Fudan University affiliated researchers to deposit data.",
"homepage": "https://dvn.fudan.edu.cn/dataverse.xhtml",
"name": "Fudan University Social Science Data Repository",
"prefix": "r3d100012775",
"synonyms": [
"ε€ζ¦ε€§ε¦η€ΎδΌη§ε¦ Dataverse"
]
},
"r3d100012777": {
"description": "The Repositori Ilmiah Nasional (RIN) is a means for storing, preserving, citing, analyzing and sharing research data. RIN acts as an online media in managing, storing and sharing research data. Researchers, data writers, publishers, data distributors, and affiliated institutions all receive academic credit and web visibility. Researchers, agencies, and funders have full control over research data.",
"homepage": "https://rin.brin.go.id/",
"name": "RIN Data Repository",
"prefix": "r3d100012777",
"synonyms": [
"BRIN Dataverse",
"Badan Riset dan Inovasi Nasional Dataverse",
"RIN Dataverse",
"Repositori Ilmiah Nasional",
"formerly: Lembaga Ilmu Pengetahuan Indonesia (LIPI) Dataverse"
]
},
"r3d100012778": {
"description": "The Maine Dataverse Network is a cloud-based data repository intended to act as a long-term archive and to facilitate data sharing among the research community in accordance with NSF, NIH, NASA and other granting authority data management plan requirements. The Maine Dataverse Network offers a convenient and secure method of sharing and archiving data and is made available to the Maine research community at no cost.",
"homepage": "http://dataverse.acg.maine.edu/dvn/",
"name": "Maine Dataverse Network",
"prefix": "r3d100012778"
},
"r3d100012783": {
"description": "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.",
"homepage": "https://www.ebi.ac.uk/merops/",
"name": "MEROPS",
"prefix": "r3d100012783",
"xrefs": {
"fairsharing": "/FAIRsharing.2s4n8r",
"nif": "0000-03112",
"scr": "007777"
}
},
"r3d100012785": {
"description": "The New York Brain Bank (NYBB) at Columbia University was established to collect postmortem human brains to meet the needs of neuroscientists investigating specific psychiatric and neurological disorders.",
"homepage": "http://www.columbianeuroresearch.org/taub/res-investigation.html",
"name": "New York Brain Bank",
"prefix": "r3d100012785",
"synonyms": [
"NYBB"
],
"xrefs": {
"nlx": "43593",
"scr": "007142"
}
},
"r3d100012786": {
"description": "The Language Archive Cologne (LAC) is a research data repository for the linguistics and all humanities disciplines working with audiovisual data. The archive forms a cluster of the Data Center for Humanities in cooperation with the Institute of Linguistics of the University of Cologne. The LAC is an archive for language resources, which is freely available via a web-based access. In addition, concrete technical and methodological advice is offered in the research data cycle - from the collection of the data, their preparation and archiving, to publication and reuse.",
"homepage": "https://lac.uni-koeln.de",
"name": "Language Archive Cologne",
"prefix": "r3d100012786",
"synonyms": [
"KAΒ³ Language Archive Cologne",
"LAC"
]
},
"r3d100012787": {
"description": "Gambling Research Exchange Ontario (GREO) is a knowledge translation and exchange organization that aims to eliminate harm from gambling. Our goal is to support evidence-informed decision making in responsible gambling policies, standards and practices. In line with this mandate, datasets curated in this archive relate to gambling and reducing gambling related harms.",
"homepage": "https://borealisdata.ca/dataverse/GREO",
"name": "Gambling Research Exchange Dataverse",
"prefix": "r3d100012787",
"synonyms": [
"GREO"
]
},
"r3d100012788": {
"description": "<<>>!!!>>>",
"homepage": "http://www.thearkdb.org/arkdb/",
"name": "ArkDB",
"prefix": "r3d100012788",
"xrefs": {
"nif": "0000-02568",
"omics": "20036",
"scr": "001838"
}
},
"r3d100012789": {
"description": "Wiki-Pi is a wiki resource centered on human protein-protein interactions. Wiki-Pi's intuitive search functionality allows you to retrieve and discover interactions effectively.",
"homepage": "http://severus.dbmi.pitt.edu/wiki-pi/",
"name": "Wiki-Pi",
"prefix": "r3d100012789"
},
"r3d100012790": {
"description": "<<>>!!!<<<",
"homepage": "http://prof.pusan.ac.kr/user/indexSub.action?codyMenuSeq=9872&siteId=uc",
"name": "Future Network & Communication Repository",
"prefix": "r3d100012790"
},
"r3d100012791": {
"description": "SIDER contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect frequency, drug and side effect classifications as well as links to further information, for example drugβtarget relations.",
"homepage": "http://sideeffects.embl.de/",
"name": "SIDER",
"prefix": "r3d100012791",
"synonyms": [
"Side Effect Resource"
],
"xrefs": {
"fairsharing": "FAIRsharing.zzaykv",
"nlx": "33359",
"scr": "004321"
}
},
"r3d100012793": {
"description": "Brock University Dataverse, housed under the Ontario Council of University Librariesβ Scholars Portal Dataverse, is the central online repository for research data at Brock University.",
"homepage": "https://borealisdata.ca/dataverse/brock",
"name": "Brock University Dataverse",
"prefix": "r3d100012793"
},
"r3d100012794": {
"description": "The Carleton University Data Repository Dataverse is the research data repository for Carleton University. It is managed by the Data Services in the MacOdrum Library. The repository also houses the MacOdrum Library Dataverse Collection which contains numerous public opinion polls.",
"homepage": "https://borealisdata.ca/dataverse/carleton",
"name": "Carleton University Dataverse Collection",
"prefix": "r3d100012794"
},
"r3d100012795": {
"description": "Lakehead University Dataverse is the central online repository for research data at Lakehead University.",
"homepage": "https://borealisdata.ca/dataverse/lakehead",
"name": "Lakehead University Dataverse",
"prefix": "r3d100012795"
},
"r3d100012796": {
"description": "Laurentian University Dataverse is an institutional research data repository for research data produced at Laurentian University.",
"homepage": "https://borealisdata.ca/dataverse/laurentian",
"name": "Laurentian University Dataverse",
"prefix": "r3d100012796"
},
"r3d100012797": {
"description": "The McMaster University Dataverse is a central location for research at McMaster University and a service of the Ontario Council of University Libraries.",
"homepage": "https://borealisdata.ca/dataverse/mcmaster",
"name": "McMaster University Dataverse",
"prefix": "r3d100012797"
},
"r3d100012800": {
"description": "Queen's University Dataverse is the institutional open access research data repository for Queen's University, featuring Queen's University Biological Station (QUBS) which includes research related to ecology, evolution, resource management and conservation, GIS, climate data, and environmental science.",
"homepage": "https://borealisdata.ca/dataverse/queens",
"name": "Queen's University Dataverse",
"prefix": "r3d100012800"
},
"r3d100012801": {
"description": "A data repository for researchers affiliated with Toronto Metropolitan University. This resource is part of Borealis which is a service provided by the Ontario Council of University Libraries.",
"homepage": "https://borealisdata.ca/dataverse/tmu",
"name": "Toronto Metropolitan University Dataverse",
"prefix": "r3d100012801"
},
"r3d100012802": {
"description": "Trent University Dataverse is a research data repository for our faculty, students and staff. Files are held in a secure environment on Canadian servers. The platform makes it possible for researchers to deposit data, create appropriate metadata, and version documents as they work. Researchers can choose to make content available publicly, to specific individuals, or to keep it locked.",
"homepage": "https://borealisdata.ca/dataverse/trent",
"name": "Trent University Dataverse",
"prefix": "r3d100012802"
},
"r3d100012803": {
"description": "The University of Guelph Research Data Repositories provide long-term stewardship of research data created at or in cooperation with the University of Guelph. The Data Repositories are guided by the FAIR Guiding Principles for scientific data management and stewardship which aim to improve the Findability, Accessibility, Interoperability and Reuse of research data. The Data Repositories is composed of two main collections: the Agri-environmental Research Data collection which houses agricultural and environmental research data, and the Cross-disciplinary Research Data collection which houses all other disciplinary research data.",
"homepage": "https://borealisdata.ca/dataverse/guelph",
"name": "University of Guelph Research Data Repositories",
"prefix": "r3d100012803",
"synonyms": [
"University of Guelph Dataverse"
]
},
"r3d100012805": {
"description": "Data deposit is supported for University of Ottawa faculty, students, and affiliated researchers. The repository is multidisciplinary and hosted on Canadian servers. It includes features such as permanent links (DOIs) which encourage citation of your dataset and help you set terms for access and reuse of your data. uOttawa Dataverse is currently optimal for small to medium datasets.",
"homepage": "https://borealisdata.ca/dataverse/ottawa",
"name": "University of Ottawa Dataverse",
"prefix": "r3d100012805",
"synonyms": [
"uOttawa Dataverse"
]
},
"r3d100012806": {
"description": "The University of Toronto Dataverse is a research data repository for our faculty, students, and staff. Files are held in a secure environment on Canadian servers. Researchers can choose to make content available publicly, to specific individuals, or to restrict access.",
"homepage": "https://borealisdata.ca/dataverse/toronto",
"name": "University of Toronto Dataverse",
"prefix": "r3d100012806"
},
"r3d100012807": {
"description": "Dataverse is a free and secure data repository that supports the deposit and sharing of University of Windsor research data. This service has been established by the Academic Data Centre (ADC) at Leddy Library.",
"homepage": "https://borealisdata.ca/dataverse/windsor",
"name": "University of Windsor Dataverse",
"prefix": "r3d100012807"
},
"r3d100012808": {
"description": "The University of Waterloo Dataverse is a data repository for research outputs of our faculty, students, and staff. Files are held in a secure environment on Canadian servers. Researchers can choose to make content available to the public, to specific individuals, or to keep it private.",
"homepage": "https://borealisdata.ca/dataverse/waterloo",
"name": "University of Waterloo Dataverse",
"prefix": "r3d100012808"
},
"r3d100012809": {
"description": "Western University's Dataverse is a research data repository for our faculty, students, and staff. Files are held in a secure environment on Canadian servers. Researchers can choose to make content available publicly, to specific individuals, or to keep it locked.",
"homepage": "https://borealisdata.ca/dataverse/westernu",
"name": "Western University Dataverse",
"prefix": "r3d100012809"
},
"r3d100012810": {
"description": "The Wilfrid Laurier University Dataverse is a research data repository for our faculty, students, and staff. Files are held in a secure environment on Canadian servers.",
"homepage": "https://borealisdata.ca/dataverse/laurier",
"name": "Wilfrid Laurier University Dataverse",
"prefix": "r3d100012810",
"synonyms": [
"WLU Dataverse"
]
},
"r3d100012811": {
"description": "The University of Regina Library offers our institution's researchers the opportunity to store (and share, if appropriate) their research data in our University of Regina Dataverse.",
"homepage": "https://borealisdata.ca/dataverse/regina",
"name": "University of Regina Dataverse",
"prefix": "r3d100012811"
},
"r3d100012812": {
"description": "York University Libraries makes available Borealis for despositing data . Borealis is a an instance of Dataverse hosted by The Ontario Council of University Libraries, of which York University Libraries is a member.",
"homepage": "https://borealisdata.ca/dataverse/york",
"name": "York University Dataverse",
"prefix": "r3d100012812"
},
"r3d100012813": {
"description": "The Dalhousie University Dataverse is a research data repository for our faculty, students, and staff. Files are held in a secure environment on Canadian servers, hosted by Borealis.",
"homepage": "https://borealisdata.ca/dataverse/dal",
"name": "Dalhousie University Dataverse @ Borealis",
"prefix": "r3d100012813"
},
"r3d100012814": {
"description": "University of Alberta Dataverse is a service provided by the University of Albert Library to help researchers publish, analyze, distribute, and preserve data and datasets. Open for University of Alberta-affiliated researchers to deposit data.",
"homepage": "https://borealisdata.ca/dataverse/ualberta",
"name": "University of Alberta Dataverse",
"prefix": "r3d100012814",
"xrefs": {
"doi": "10.7939/dvn"
}
},
"r3d100012815": {
"description": "UNB Dataverse is repository for research data collected by researchers and organizations primarily affiliated with the University of New Brunswick. The repository allows researchers to deposit, share, analyze, cite, and explore data. Dataverse is an open source application developed by the Institute for Quantitative Social Science (IQSS) at Harvard University.",
"homepage": "https://dataverse.lib.unb.ca/",
"name": "UNB Libraries Dataverse Research Data Repository",
"prefix": "r3d100012815",
"synonyms": [
"University of New Brunswick Libraries Dataverse Research Data Repository"
]
},
"r3d100012816": {
"description": "UM Dataverse is part of the Dataverse Project conceived of by Harvard University. It is an open source repository to assist researchers in the creation, management and dissemination of their research data. UM Dataverse allows for the creation of multiple collaborative environments containing datasets, metadata and digital objects. UM Dataverse provides formal scholarly data citations and can help with data requirements from publishers and funders.",
"homepage": "https://borealisdata.ca/dataverse/manitoba",
"name": "University of Manitoba Dataverse",
"prefix": "r3d100012816",
"synonyms": [
"University of Manitoba Libraries Dataverse"
]
},
"r3d100012818": {
"description": "Spectrum, Concordia University's open access research repository, provides access to and preserves research created at Concordia. By depositing in Spectrum, Concordia scholars provide free and immediate access to their work and thus increase the visibility of both their own research and their university's intellectual output. Open access leads to the increased research profile and impact of scholars by bringing about greater levels of readership and citation of their publications.",
"homepage": "https://spectrum.library.concordia.ca/",
"name": "Spectrum Research Repository",
"prefix": "r3d100012818"
},
"r3d100012820": {
"description": "The Progenetix database provides an overview of copy number abnormalities in human cancer from currently 32548 array and chromosomal Comparative Genomic Hybridization (CGH) experiments, as well as Whole Genome or Whole Exome Sequencing (WGS, WES) studies. The cancer profile data in Progenetix was curated from 1031 articles and represents 366 different cancer types, according to the International classification of Diseases in Oncology (ICD-O).",
"homepage": "https://www.progenetix.org/",
"name": "Progenetix",
"prefix": "r3d100012820",
"xrefs": {
"fairsharing": "FAIRsharing.65tdnz",
"miriam": "00000600",
"omics": "02591"
}
},
"r3d100012822": {
"description": "ConsensusPathDB integrates interaction networks in humans (and in the model organisms - yeast and mouse) including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions, as well as biochemical pathways. Data originate from public resources for interactions and interactions curated from the literature. The interaction data are integrated in a complementary manner to avoid redundancies.",
"homepage": "http://cpdb.molgen.mpg.de/CPDB",
"name": "ConsensusPathDB",
"prefix": "r3d100012822",
"synonyms": [
"CPDB"
],
"xrefs": {
"omics": "01903",
"scr": "002231"
}
},
"r3d100012823": {
"description": "Vivli is a non-profit organization working to advance human health through the insights and discoveries gained by sharing and analyzing data. It is home to an independent global data-sharing and analytics platform which serves all elements of the international research community. The platform includes a data repository, in-depth search engine and cloud-based analytics, and harmonizes governance, policy and processes to make sharing data easier. Vivli acts as a neutral broker between data contributor and data user and the wider data sharing community.",
"homepage": "https://vivli.org/",
"name": "Vivli",
"prefix": "r3d100012823",
"synonyms": [
"A global clinical research data sharing platform"
],
"xrefs": {
"fairsharing": "FAIRsharing.uovQrT",
"omics": "18399",
"scr": "018080"
}
},
"r3d100012824": {
"description": "The Repositorio de datos del Ministerio de EducaciΓ³n del PerΓΊ provides the scientific community with a series of data sets for its reuse. The MINEDU Data Repository is integrated into the Digital National Repository of Science, Technology and Innovation of Open Access - ALICIA (http://alicia.concytec.gob.pe) managed and administrated by CONCYTEC.",
"homepage": "https://datos.minedu.gob.pe/",
"name": "Repositorio de datos del Ministerio de EducaciΓ³n del PerΓΊ",
"prefix": "r3d100012824",
"synonyms": [
"Repository of Open Data of the Ministry of Education"
]
},
"r3d100012825": {
"description": "Researcher of the Leibniz UniversitΓ€t Hannover can publish and archive research related data in this repository.",
"homepage": "https://data.uni-hannover.de",
"name": "Forschungsdaten-Repositorium der LUH",
"prefix": "r3d100012825",
"synonyms": [
"Research Data Repository"
]
},
"r3d100012827": {
"description": "BEI Resources was established by the National Institute of Allergy and Infectious Diseases (NIAID) to provide reagents, tools and information for studying Category A, B, and C priority pathogens, emerging infectious disease agents, non-pathogenic microbes and other microbiological materials of relevance to the research community. BEI Resources acquires authenticates, and produces reagents that scientists need to carry out basic research and develop improved diagnostic tests, vaccines, and therapies. By centralizing these functions within BEI Resources, access to and use of these materials in the scientific community is monitored and quality control of the reagents is assured",
"homepage": "https://www.beiresources.org/",
"name": "BEI Resource",
"prefix": "r3d100012827",
"synonyms": [
"BEI Resource Repository",
"Biodefense & Emerging Infections Research Resources Repository",
"supporting infectious disease research"
],
"xrefs": {
"fairsharing": "FAIRsharing.gcxmpf",
"scr": "013698"
}
},
"r3d100012828": {
"description": "The BioSample database contains descriptions of biological source materials used in experimental assays.",
"homepage": "https://www.ncbi.nlm.nih.gov/biosample/",
"name": "BioSample",
"prefix": "r3d100012828",
"synonyms": [
"BioSample at the NCBI"
],
"xrefs": {
"fairsharing": "FAIRsharing.qr6pqk",
"nlx": "143929",
"scr": "004854"
}
},
"r3d100012832": {
"description": "The Community Coordinated Modeling Center (CCMC) is a multi-agency partnership based at the NASA Goddard Space Flight Center in Greenbelt, Maryland and a component of the National Space Weather Program. The CCMC provides, to the international research community, access to modern space science simulations. In addition, the CCMC supports the transition to space weather operations of modern space research models.",
"homepage": "https://ccmc.gsfc.nasa.gov/",
"name": "Community Coordinated Modeling Center",
"prefix": "r3d100012832",
"synonyms": [
"CCMC"
]
},
"r3d100012834": {
"description": "<<>>!!!>>>The Deep Carbon Observatory (DCO) is a global community of multi-disciplinary scientists unlocking the inner secrets of Earth through investigations into life, energy, and the fundamentally unique chemistry of carbon. Deep Carbon Observatory Digital Object Registry (βDCO-VIVOβ) is a centrally-managed digital object identification, object registration and metadata management service for the DCO. Digital object registration includes DCO-ID generation based on the global Handle System infrastructure and metadata collection using VIVO. Users will be able to deposit their data into the DCO Data Repository and have that data discoverable and accessible by others.",
"homepage": "https://info.deepcarbon.net/vivo/",
"name": "Deep Carbon Observatory Data Portal",
"prefix": "r3d100012834",
"synonyms": [
"DCO Data Portal",
"DCO-VIVO"
],
"xrefs": {
"biodbcore": "001654"
}
},
"r3d100012835": {
"description": "The Seamount Catalog is a digital archive for bathymetric seamount maps from all the oceans that can be viewed and downloaded in various formats. This catalog contains morphological data, sample information, related grid and multibeam data files, as well as user-contributed files that all can be downloaded.",
"homepage": "https://earthref.org/SC/",
"name": "Seamount Catalog",
"prefix": "r3d100012835",
"synonyms": [
"SC"
],
"xrefs": {
"biodbcore": "001612"
}
},
"r3d100012836": {
"description": "The eyeGENEΒ Research Resource is open for approved research studies. Application details here Researchers and clinicians are actively developing gene-based therapies to treat ophthalmic genetic diseases that were once considered untreatable.",
"homepage": "https://eyegene.nih.gov/",
"name": "EyeGENE",
"prefix": "r3d100012836",
"synonyms": [
"The National Ophthalmic Genotyping and Phenotyping Network"
],
"xrefs": {
"fairsharing": "/FAIRsharing.5nnxqn",
"nif": "0000-00229",
"omics": "05773",
"scr": "004523"
}
},
"r3d100012837": {
"description": "The Federal Interagency Traumatic Brain Injury Research (FITBIR) informatics system was developed to share data across the entire TBI research field and to facilitate collaboration between laboratories, as well as interconnectivity with other informatics platforms. Sharing data, methodologies, and associated tools, rather than summaries or interpretations of this information, can accelerate research progress by allowing re-analysis of data, as well as re-aggregation, integration, and rigorous comparison with other data, tools, and methods. This community-wide sharing requires common data definitions and standards, as well as comprehensive and coherent informatics approaches.",
"homepage": "https://fitbir.nih.gov/",
"name": "Federal Interagency Traumatic Brain Injury Research Informatics System",
"prefix": "r3d100012837",
"synonyms": [
"FITBIR"
],
"xrefs": {
"fairsharing": "fairsharing.rz7h29",
"nlx": "151755",
"scr": "006856"
}
},
"r3d100012840": {
"description": "LONIβs Image and Data Archive (IDA) is a secure data archiving system. The IDA uses a robust infrastructure to provide researchers with a flexible and simple interface for de-identifying, searching, retrieving, converting, and disseminating their biomedical data. With thousands of investigators across the globe and more than 21 million data downloads to data, the IDA guarantees reliability with a fault-tolerant network comprising multiple switches, routers, and Internet connections to prevent system failure.",
"homepage": "https://ida.loni.usc.edu/login.jsp",
"name": "Laboratory of Neuroimaging Image & Data Archive",
"prefix": "r3d100012840",
"synonyms": [
"IDA",
"LONI Image & Data Archive",
"Laboratory of Neuroimaging Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.r4ph5f",
"nif": "0000-10494",
"scr": "001922"
}
},
"r3d100012841": {
"description": "Archiving data and housing geological collections is an important role the Bureau of Geology plays in improving our understanding of the geology of New Mexico. Aside from our numerous publications, several datasets are available to the public. Data in this repository supplements published papers in our publications. Please refer to both the published material and the repository documentation before using this data. Please cite repository data as shown in each repository listing.",
"homepage": "https://geoinfo.nmt.edu/repository/",
"name": "New Mexico Bureau of Geology & Mineral Resources Data Repository",
"prefix": "r3d100012841",
"xrefs": {
"biodbcore": "001596",
"fairsharing": "FAIRsharing.e4ac97"
}
},
"r3d100012842": {
"description": "A place where researchers can publicly store and share unthresholded statistical maps, parcellations, and atlases produced by MRI and PET studies.",
"homepage": "https://neurovault.org/",
"name": "NeuroVault",
"prefix": "r3d100012842",
"xrefs": {
"fairsharing": "FAIRsharing.rm14bx"
}
},
"r3d100012845": {
"description": "The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK).",
"homepage": "https://dknet.org/",
"name": "NIDDK Information Network",
"prefix": "r3d100012845",
"synonyms": [
"National Institute of Diabetes and Digestive and Kidney Disease Information Network",
"dkNET"
],
"xrefs": {
"fairsharing": "FAIRsharing.1mapgk",
"nlx": "153866",
"scr": "001606"
}
},
"r3d100012849": {
"description": "The CardioVascular Research Grid (CVRG) project is creating an infrastructure for secure seamless access to study data and analysis tools.\nCVRG tools are developed using the Software as a Service model, allowing users to access tools through their browser, thus eliminating the need to install and maintain complex software.",
"homepage": "https://www.cvrgrid.org/",
"name": "Cardiovascular Research Grid",
"prefix": "r3d100012849",
"synonyms": [
"CVRG"
],
"xrefs": {
"fairsharing": "FAIRsharing.x80z26",
"nlx": "143758",
"omics": "20739",
"scr": "004472"
}
},
"r3d100012850": {
"description": "<<>>!!!>>>",
"homepage": "http://pfam.xfam.org/",
"name": "Pfam Protein Families",
"prefix": "r3d100012850",
"synonyms": [
"Pfam"
],
"xrefs": {
"fairsharing": "FAIRsharing.y3scf6",
"omics": "01696",
"scr": "004726"
}
},
"r3d100012851": {
"description": "Originally named the Radiation Belt Storm Probes (RBSP), the mission was re-named the Van Allen Probes, following successful launch and commissioning. For simplicity and continuity, the RBSP short-form has been retained for existing documentation, file naming, and data product identification purposes. The RBSPICE investigation including the RBSPICE Instrument SOC maintains compliance with requirements levied in all applicable mission control documents.",
"homepage": "https://rbspice.ftecs.com/Data.html",
"name": "Radiation Belt Storm Probes Ion Composition Experiment",
"prefix": "r3d100012851",
"synonyms": [
"RBSPICE",
"Van Allen Probes Radiation Belt Storm Probes Ion Composition Experiment"
]
},
"r3d100012857": {
"description": "The Media Archive of the Zurich University of the Arts is the platform for collaborative work, sharing and archiving of media at the ZHdK. It is available to students, lecturers, reserarchers and staff. The areas of application of the media archive are mainly focused on teaching and research, but the ZHdK departments archive and university communication also benefit. The media archive manages a wide range of visual and audiovisual content and supports collaborative forms of working. It serves as an instutional repository for research data management and as a platform for hybrid publications.",
"homepage": "https://medienarchiv.zhdk.ch/",
"name": "Medienarchiv der ZΓΌrcher Hochschule der KΓΌnste",
"prefix": "r3d100012857"
},
"r3d100012858": {
"description": "MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. MassIVE datasets can be assigned ProteomeXchange accessions to satisfy publication requirements.",
"homepage": "https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp",
"name": "Mass Spectrometry Interactive Virtual Environment",
"prefix": "r3d100012858",
"synonyms": [
"MassIVE"
],
"xrefs": {
"fairsharing": "FAIRsharing.LYsiMd",
"scr": "013665"
}
},
"r3d100012860": {
"description": "The Eurac Research CLARIN Centre (ERCC) is a dedicated repository for language data. It is hosted by the Institute for Applied Linguistics (IAL) at Eurac Research, a private research centre based in Bolzano, South Tyrol. The Centre is part of the Europe-wide CLARIN infrastructure, which means that it follows well-defined international standards for (meta)data and procedures and is well-embedded in the wider European Linguistics infrastructure. The repository hosts data collected at the IAL, but is also open for data deposits from external collaborators.",
"homepage": "https://clarin.eurac.edu/",
"name": "Eurac Research CLARIN Centre",
"prefix": "r3d100012860",
"synonyms": [
"ERCC"
]
},
"r3d100012861": {
"description": "This repository contains about 500 medieval codices and manuscripts (dated from 8th to 18th century), which were a part of the BMBF-funded project eCodicology. The collection and database contains descriptional data about the manuscripts in TEI conformant XML format as well as digitized images of every codex page.",
"homepage": "https://stmatthias.uni-trier.de/",
"name": "Virtuelles Skriptorium St. Matthias",
"prefix": "r3d100012861"
},
"r3d100012862": {
"description": "This is CSDB version 1 merged from Bacterial (BCSDB) and Plant&Fungal (PFCSDB) databases. This database aims at provision of structural, bibliographic, taxonomic, NMR spectroscopic and other information on glycan and glycoconjugate structures of prokaryotic, plant and fungal origin. It has been merged from the Bacterial and Plant&Fungal Carbohydrate Structure Databases (BCSDB+PFCSDB). The key points of this service are:\n High coverage. The coverage for bacteria (up to 2016) and archaea (up to 2016) is above 80%. Similar coverage for plants and fungi is expected in the future. The database is close to complete up to 1998 for plants, and up to 2006 for fungi.\nData quality. High data quality is achieved by manual curation using original publications which is assisted by multiple automatic procedures for error control. Errors present in publications are reported and corrected, when possible. Data from other databases are verified on import.\nDetailed annotations. Structural data are supplied with extended bibliography, assigned NMR spectra, taxon identification including strains and serogroups, and other information if available in the original publication.\nServices. CSDB serves as a platform for a number of computational services tuned for glycobiology, such as NMR simulation, automated structure elucidation, taxon clustering, 3D molecular modeling, statistical processing of data etc.\nIntegration. CSDB is cross-linked to other glycoinformatics projects and NCBI databases. The data are exportable in various formats, including most widespread encoding schemes and records using GlycoRDF ontology.\nFree web access. Users can access the database for free via its web interface (see Help). \nThe main source of data is retrospective literature analysis. About 20% of data were imported from CCSD (Carbbank, University of Georgia, Athens; structures published before 1996) with subsequent manual curation and approval. The current coverage is displayed in red on the top of the left menu. The time lag between the publication of new data and their deposition into CSDB is ca. 1 year.\nIn the scope of bacterial carbohydrates, CSDB covers nearly all structures of this origin published up to 2016. Prokaryotic, plant and fungal means that a glycan was found in the organism(s) belonging to these taxonomic domains or was obtained by modification of those found in them. Carbohydrate means a structure composed of any residues linked by glycosidic, ester, amidic, ketal, phospho- or sulpho-diester bonds in which at least one residue is a sugar or its derivative.",
"homepage": "http://csdb.glycoscience.ru/database/",
"name": "Carbohydrate Structure Database",
"prefix": "r3d100012862",
"synonyms": [
"CSDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.dkbt9j",
"omics": "09727"
}
},
"r3d100012863": {
"description": "The human pluripotent stem cell registry (hPSCreg) is a public registry and data portal for human embryonic and induced pluripotent stem cell lines (hESC and hiPSC). The Registry provides comprehensive and standardized biological and legal information as well as tools to search and compare information from multiple hPSC sources and hence addresses a translational research need. To facilitate unambiguous identification over different resources, hPSCreg automatically creates a unique standardized name (identifier) for each cell line registered. In addition to biological information, hPSCreg stores extensive data about ethical standards regarding cell sourcing and conditions for application and privacy protection. hPSCreg is the first global registry that holds both, manually validated scientific and ethical information on hPSC lines, and provides access by means of a user-friendly, mobile-ready web application.",
"homepage": "https://hpscreg.eu/",
"name": "hPSCreg",
"prefix": "r3d100012863",
"synonyms": [
"human Pluripotent Stem Cell registry"
],
"xrefs": {
"fairsharing": "FAIRsharing.7C0aVE",
"miriam": "00100898"
}
},
"r3d100012864": {
"description": "The Department of Energy Systems Biology Knowledgebase (KBase) is a software and data platform designed to meet the grand challenge of systems biology: predicting and designing biological function. KBase integrates data and tools in a unified graphical interface so users do not need to access them from numerous sources or learn multiple systems in order to create and run sophisticated systems biology workflows. Users can perform large-scale analyses and combine multiple lines of evidence to model plant and microbial physiology and community dynamics.\nKBase is the first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase aims to provide a knowledgebase: an integrated environment where knowledge and insights are created and multiplied.",
"homepage": "https://www.kbase.us/",
"name": "KBase",
"prefix": "r3d100012864",
"synonyms": [
"KBase: The U.S. Department of Energy Systems Biology Knowledgebase"
],
"xrefs": {
"fairsharing": "FAIRsharing.jsxqrk",
"omics": "13621"
}
},
"r3d100012866": {
"description": "CU Scholar is an open access institutional repository supporting the research and teaching mission of the University of Colorado Boulder. It is intended to serve as a platform for preserving the research activities of members of the CU Boulder community and for providing public access to that research. CU Scholar is maintained by the University Libraries.",
"homepage": "https://scholar.colorado.edu/",
"name": "CU Scholar",
"prefix": "r3d100012866",
"synonyms": [
"University of Colorado Boulder's institutional repository"
],
"xrefs": {
"opendoar": "3721",
"roar": "9057"
}
},
"r3d100012867": {
"description": "The EBiSC Catalogue is a collection of human iPS cells being made available to academic and commercial researchers for use in disease modelling and other forms of preclinical research.\nThe initial collection has been generated from a wide range of donors representing specific disease backgrounds and healthy controls. As the collection grows, more isogenic control lines will become available which will add further to the collectionβs appeal.",
"homepage": "https://cells.ebisc.org/",
"name": "EBiSC catalogue",
"prefix": "r3d100012867",
"synonyms": [
"European Bank for induced pluripotent Stem Cells catalogue"
]
},
"r3d100012868": {
"description": "Digital resources of the excavations campaigns since 2015.",
"homepage": "http://repository.edition-topoi.org/collection/SORR/",
"name": "Roman Villa of Capo di Sorrento",
"prefix": "r3d100012868",
"xrefs": {
"doi": "10.17171/2-4"
}
},
"r3d100012869": {
"description": "The Maya Image Archive is intended to host research materials provided by various scholars, such as Karl Herbert Mayer, Berthold Riese, Stephan Merk and the members of the project among others. Comprising image collections with photographs, drawings, notes and manuscripts, the Maya Image Archive allows the user to browse through the results of several decades of research trips through the entire Maya region.",
"homepage": "https://classicmayan.kor.de.dariah.eu/",
"name": "Maya Image Archive",
"prefix": "r3d100012869"
},
"r3d100012870": {
"description": "EarthWorks is a discovery tool for geospatial (a.k.a. GIS) data. It allows users to search and browse the GIS collections owned by Stanford University Libraries, as well as data collections from many other institutions. Data can be searched spatially, by manipulating a map; by keyword search; by selecting search limiting facets (e.g., limit to a given format type); or by combining these options.",
"homepage": "https://earthworks.stanford.edu/",
"name": "EarthWorks",
"prefix": "r3d100012870"
},
"r3d100012871": {
"description": "<<>>!!!>>>",
"homepage": "http://datos.sndg.mincyt.gob.ar/",
"name": "Portal de Datos GenΓ³micos del SNDG",
"prefix": "r3d100012871",
"synonyms": [
"Sistema Nacional de Datos GenΓ³micos - Portal de datos"
]
},
"r3d100012872": {
"description": "The USN Research Data Archive is an institutional archive where research data produced and collected by University of South-East Norway's reseachers can be stored, made visible and accessible. The researcher can apply the necessary licenses and possibly put embargo and access restrictions on the research data.",
"homepage": "https://usn.figshare.com/",
"name": "USN Research Data Archive",
"prefix": "r3d100012872",
"synonyms": [
"USN RDA",
"University of South-Eastern Norway Figshare"
]
},
"r3d100012873": {
"description": "The Norwegian Marine Data Centre (NMD) at the Institute of Marine Research was established as a national data centre dedicated to the professional processing and long-term storage of marine environmental and fisheries data and production of data products.\nThe Institute of Marine Research continuously collects large amounts of data from all Norwegian seas. Data are collected using vessels, observation buoys, manual measurements, gliders β amongst others.\nNMD maintains the largest collection of marine environmental and fisheries data in Norway.",
"homepage": "https://www.hi.no/en/hi/forskning/research-groups-1/the-norwegian-marine-data-centre-nmd",
"name": "Norwegian Marine Data Center",
"prefix": "r3d100012873",
"synonyms": [
"NMD",
"Norsk marint datasenter"
]
},
"r3d100012874": {
"description": "US National Science Foundation (NSF) facility to support drilling and coring in continental locations worldwide. Drill core metadata and data, borehole survey data, geophysical site survey data, drilling metadata, software code. The CSD Facility offers repositories with samples, data, publications and reference collections from scientific drilling and coring.",
"homepage": "https://cse.umn.edu/csd",
"name": "Continental Scientific Drilling Facility",
"prefix": "r3d100012874",
"synonyms": [
"CSD Facility",
"formerly: NSF Facilities for Continental Scientific & Drilling & Coring"
]
},
"r3d100012875": {
"description": "RESPECT aims to unveil for the mountain rain forest in South Ecuador how major ecosystem functions, (i) ecosystem biomass production, and (ii) water fluxes, are affected by ongoing and future environmental changes through alterations in response and effect traits of relevant biota. The research question is addressed with two approaches: (i) A newest generation Land Surface Model (LSM) and (ii) a statistical responseβeffect framework (REF). By including (i) specific Plant Functional Types (PFTs) for the megadiverse biodiversity hotspot, (ii) introducing trait diversity, (iii) new modules for tree hydraulics and (iv) new modules of focal biological processes (seed dispersal and PFT establishment, herbivory) we will conduct a biodiversification of LSMs.",
"homepage": "https://vhrz669.hrz.uni-marburg.de/tmf_respect/data_pre.do",
"name": "RESPECT",
"prefix": "r3d100012875",
"synonyms": [
"Environmental changes in biodiverstiy hotspot ecosystems of South Ecuador: RESPonse and feedback effECTs"
]
},
"r3d100012879": {
"description": "The Tropical Data Hub (TDH) Research Data repository makes data collections and datasets generated by James Cook University researchers searchable and accessible. This increases their visibility and facilitates sharing and collaboration both within JCU and externally. Services provided include archival storage, access controls (open access preferred), metadata review and DOI minting.",
"homepage": "https://research.jcu.edu.au/researchdata",
"name": "Research Data JCU",
"prefix": "r3d100012879",
"synonyms": [
"James Cook University Research Data repository",
"formerly name: Tropical Data Hub Research Data repository"
]
},
"r3d100012880": {
"description": "<<>>!!!>>> LacCore curates cores and samples from continental coring and drilling expeditions around the world, and also archives metadata and contact information for cores stored at other institutions.LacCore curates cores and samples from continental coring and drilling expeditions around the world, and also archives metadata and contact information for cores stored at other institutions.",
"homepage": "http://lrc.geo.umn.edu/laccore/index.html",
"name": "LacCore",
"prefix": "r3d100012880",
"synonyms": [
"National Lacustrine Core Facility"
],
"xrefs": {
"nlx": "154737",
"scr": "002215"
}
},
"r3d100012882": {
"description": "DIAMM (the Digital Image Archive of Medieval Music) is a leading resource for the study of medieval manuscripts. We present images and metadata for thousands of manuscripts on this website. We also provide a home for scholarly resources and editions, undertake digital restoration of damaged manuscripts and documents, publish high-quality facsimiles, and offer our expertise as consultants.",
"homepage": "https://www.diamm.ac.uk/",
"name": "DIAMM",
"prefix": "r3d100012882",
"synonyms": [
"Digital Image Archive of Medieval Music"
]
},
"r3d100012883": {
"description": "IITA conducts research on the following thematic areas: Biotechnology and genetic improvement, Natural resource management, Social science and agribusiness, and Plant production and plant health.",
"homepage": "https://data.iita.org/",
"name": "International Institute of Tropical Agriculture datasets",
"prefix": "r3d100012883",
"synonyms": [
"IITA",
"International Institute of Tropical Agriculture CKAN repository"
]
},
"r3d100012884": {
"description": "The Kinder Institute Urban Data Platform is a secure data repository and an analytical computing environment that provides research-ready urban data for the Greater Houston Area. The UDP facilitates cross-disciplinary research and community studies to advance knowledge and information about Houston's people, government, and built environment.",
"homepage": "https://www.kinderudp.org/#/",
"name": "Kinder Institute Urban Data Platform",
"prefix": "r3d100012884",
"synonyms": [
"Data Science for Urban Solutions",
"UDP"
]
},
"r3d100012888": {
"description": "O2 is the UOC's institutional repository. \nSection 'Dades' contains primary data accompanying documents published in the Research and Institutional communities.",
"homepage": "https://openaccess.uoc.edu/",
"name": "O2 Repositori UOC - Dades",
"prefix": "r3d100012888",
"xrefs": {
"opendoar": " 1732"
}
},
"r3d100012889": {
"description": "The edoc-Server, start 1998, is the Institutional Repository of the Humboldt-UniversitΓ€t zu Berlin and offers the posibility of text- and data-publications. Every item is published for Open-Access with an optional embargo period of up to five years. Data publications since 01.01.2018.",
"homepage": "https://edoc.hu-berlin.de/handle/18452/19149",
"name": "edoc-Server - Forschungsdaten",
"prefix": "r3d100012889",
"synonyms": [
"Open-Access-Publikationsserver der Humboldt-UniversitΓ€t zu Berlin",
"edoc-Server Open-Access Institutional Repository of the Humboldt-UniversitΓ€t zu Berlin"
]
},
"r3d100012890": {
"description": "The World Ocean Atlas (WOA) contains objectively analyzed climatological fields of in situ temperature, salinity, oxygen, and other measured variables at standard depth levels for various compositing periods for the world ocean. Regional climatologies were created from the Atlas, providing a set of high resolution mean fields for temperature and salinity.\nA new version of the WOA is released in conjunction with each major update to the WOD, the largest collection of publicly available, uniformly formatted, quality controlled subsurface ocean profile data in the world.",
"homepage": "https://www.ncei.noaa.gov/products/world-ocean-atlas",
"name": "World Ocean Atlas",
"prefix": "r3d100012890",
"synonyms": [
"WOA"
],
"xrefs": {
"fairsharing": "FAIRsharing.566048"
}
},
"r3d100012891": {
"description": "German astronomical observatories own considerable collection of photographic plates. While these observations lead to significant discoveries in the past, they are also of interest for scientists today and in the future. In particular, for the study of long-term variability of many types of stars, these measurements are of immense scientific value.\nThere are about 85000 plates in the archives of Hamburger Sternwarte, Dr. Karl Remeis-Sternwarte Bamberg, and Leibniz-Institut fΓΌr Astrophysik Potsdam (AIP). The plates are digitized with high-resolution flatbed scanners. In addition, the corresponding plate envelopes and observation logbooks are digitized, and further metadata are entered into the database. The work is carried out within the project βDigitalisierung astronomischer Fotoplatten und ihre Integration in das internationale Virtual Observatoryβ, which is funded by the DFG.",
"homepage": "https://www.plate-archive.org/applause/",
"name": "APPLAUSE",
"prefix": "r3d100012891",
"synonyms": [
"Archives of Photographic PLates for Astronomical USE"
]
},
"r3d100012892": {
"description": "The projects include airborne, ground-based and ocean measurements, social science surveys, satellite data use, modelling studies and value-added product development. Therefore, the BAOBAB data portal enables to access a great amount and a large variety of data: - 250 local observation datasets, that have been collected by operational networks since 1850, long term monitoring research networks and intensive scientific campaigns; - 1350 outputs of a socio-economics questionnaire; - 60 operational satellite products and several research products; - 10 output sets of meteorological and ocean operational models and 15 of research simulations. Data documentation complies with metadata international standards, and data are delivered into standard formats. The data request interface takes full advantage of the database relational structure and enables users to elaborate multicriteria requests (period, area, propertyβ¦).",
"homepage": "https://baobab.sedoo.fr/catalogue/",
"name": "BAOBAB",
"prefix": "r3d100012892",
"synonyms": [
"Base Afrique de l'Ouest Beyond AMMA Base"
]
},
"r3d100012893": {
"description": "Database and data handling portal for vegetation data from Germany.",
"homepage": "https://www.vegetweb.de/#!startseite",
"name": "vegetweb",
"prefix": "r3d100012893",
"synonyms": [
"das Vegetationsportal fΓΌr Deutschland"
]
},
"r3d100012894": {
"description": "LinkedEarth is an EarthCube-funded project aiming to better organize and share Earth Science data, especially paleoclimate data.\nLinkedEarth facilitates the work of scientists by empowering them to curate their own data and to build new tools centered around those.",
"homepage": "https://wiki.linked.earth/Main_Page",
"name": "LinkedEarth Wiki",
"prefix": "r3d100012894",
"xrefs": {
"fairsharing": "FAIRsharing.430b4f"
}
},
"r3d100012898": {
"description": "The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with comprehensive information oΒn the approximately 700 prokaryote species that are present in the human oral cavity. Approximately 49% are officially named, 17% unnamed (but cultivated) and 34% are known oΒnly as uncultivated phylotypes. The HOMD presents a provisional naming scheme for the currently unnamed species so that strain, clone, and probe data from any laboratory can be directly linked to a stably named reference scheme. The HOMD links sequence data with phenotypic, phylogenetic, clinical, and bibliographic information. Genome sequences for oral bacteria determined as part of this project, the Human Microbiome Project, and other sequencing projects are being added to the HOMD as they become available. Genomes for 315 oral taxa (46% of taxa oΒn HOMD) are currently available oΒn HOMD. The HOMD site offers easy to use tools for viewing all publically available oral bacterial genomes.",
"homepage": "https://www.homd.org/",
"name": "eHOMD",
"prefix": "r3d100012898",
"synonyms": [
"expanded Human Oral Microbiome Database"
],
"xrefs": {
"fairsharing": "FAIRsharing.v3jf2q",
"nlx": "22198",
"omics": "29834",
"scr": "012770"
}
},
"r3d100012899": {
"description": "MODES focuses on the representation of the inertio-gravity circulation in numerical weather prediction models, reanalyses, ensemble prediction systems and climate simulations. The project methodology relies on the decomposition of global circulation in terms of 3D orthogonal normal-mode functions. It allows quantification of the role of inertio-gravity waves in atmospheric varibility across the whole spectrum of resolved spatial and temporal scales.\n\nMODES is compiled by using gfortran although other options have been succesfully tested. The application requires the use of the netcdf and (optionally) grib-api libraries.",
"homepage": "http://modes.fmf.uni-lj.si",
"name": "MODES",
"prefix": "r3d100012899",
"synonyms": [
"Modal view of atmospheric circulation"
]
},
"r3d100012900": {
"description": "BaAMPs is the first database dedicated to antimicrobial peptides (AMPs) specifically tested against microbial biofilms. The aim of this project is to provide useful resources for the study of AMPs against biofilms to microbiologist, bioinformatics researcher and medical scientist working in this field in an open-access framework.",
"homepage": "https://www.baamps.it/",
"name": "Biofilm-active AMPs database",
"prefix": "r3d100012900",
"synonyms": [
"BaAMPs"
],
"xrefs": {
"omics": "10516"
}
},
"r3d100012901": {
"description": "The Antimicrobial Peptide Database (APD) was originally created by a graduate student, Zhe Wang, as his master's thesis in the laboratory of Dr. Guangshun Wang. The project was initiated in 2002 and the first version of the database was open to the public in August 2003. It contained 525 peptide entries, which can be searched in multiple ways, including APD ID, peptide name, amino acid sequence, original location, PDB ID, structure, methods for structural determination, peptide length, charge, hydrophobic content, antibacterial, antifungal, antiviral, anticancer, and hemolytic activity. Some results of this bioinformatics tool were reported in the 2004 database paper. The peptide data stored in the APD were gleaned from the literature (PubMed, PDB, Google, and Swiss-Prot) manually in over a decade.",
"homepage": "https://aps.unmc.edu/database",
"name": "Antimicrobial Peptide Database",
"prefix": "r3d100012901",
"synonyms": [
"AMP Database",
"APD"
],
"xrefs": {
"fairsharing": "FAIRsharing.ctwd7b",
"nif": "0000-02553",
"omics": "05706",
"scr": "006606"
}
},
"r3d100012902": {
"description": "ArachnoServer is a manually curated database containing information on the sequence, three-dimensional structure, and biological activity of protein toxins derived from spider venom. Spiders are the largest group of venomous animals and they are predicted to contain by far the largest number of pharmacologically active peptide toxins (Escoubas et al., 2006). ArachnoServer has been custom-built so that a wide range of biological scientists, including neuroscientists, pharmacologists, and toxinologists, can readily access key data relevant to their discipline without being overwhelmed by extraneous information.",
"homepage": "https://arachnoserver.qfab.org/mainMenu.html",
"name": "ArachnoServer",
"prefix": "r3d100012902",
"xrefs": {
"fairsharing": "FAIRsharing.c54ywe",
"miriam": "00000193",
"omics": "03117"
}
},
"r3d100012903": {
"description": "The database aims to bridge the gap between agent repositories and studies documenting the effect of antimicrobial combination therapies. Most notably, our primary aim is to compile data on the combination of antimicrobial agents, namely natural products such as AMP. To meet this purpose, we have developed a data curation workflow that combines text mining, manual expert curation and graph analysis and supports the reconstruction of AMP-Drug combinations.",
"homepage": "https://www.sing-group.org/antimicrobialCombination/networks/view",
"name": "Antimicrobial Combination Networks",
"prefix": "r3d100012903",
"xrefs": {
"omics": "14444"
}
},
"r3d100012909": {
"description": "The BCDC serves the research data obtained, and the data syntheses assembled, by researchers within the Bjerknes Centre for Climate Research. Furthermore it is open for all interested scientists independent of institution.\nAll data from the different disciplines (e.g. geology, oceanography, biology, model community) will be archived in a long-term repository, interconnected and made publicly available by the BCDC. BCDC has collaborations with many international data repositories and actively archives metadata and data at those ensuring quality and FAIRness. BCDC has it's main focus on services for data management for external and internal funded projects in the field of climate research, provides data management plans and ensures that data is archived accordingly according to the best practices in the field. The data management services rank from project work for small external funded project to top-of-the-art data management services for research infrastructures on the ESFRI roadmap (e.g. RI ICOS β Integrated Carbon Observation System) and for provides products and services for Copernicus Marine Environmental Monitoring Services. In addition BCDC is advising various communities on data management services e.g. IOC UNESCO, OECD, IAEA and various funding agencies. BCDC will become an Associated Data Unit (ADU) under IODE, International Oceanographic Data and Information Exchange, a worldwide network that operates under the auspices of the Intergovernmental Oceanographic Commission of UNESCO and aims at becoming a part of ICSU World Data System.",
"homepage": "https://www.bcdc.no/",
"name": "Bjerknes Climate Data Centre",
"prefix": "r3d100012909",
"synonyms": [
"BCDC"
],
"xrefs": {
"fairsharing": "FAIRsharing.b2017d"
}
},
"r3d100012910": {
"description": "DEIMS-SDR (Dynamic Ecological Information Management System - Site and dataset registry) is an information management system that allows you to discover long-term ecosystem research sites around the globe, along with the data gathered at those sites and the people and networks associated with them. DEIMS-SDR describes a wide range of sites, providing a wealth of information, including each siteβs location, ecosystems, facilities, parameters measured and research themes. It is also possible to access a growing number of datasets and data products associated with the sites. All sites and dataset records can be referenced using unique identifiers that are generated by DEIMS-SDR. It is possible to search for sites via keyword, predefined filters or a map search. By including accurate, up to date information in DEIMS, site managers benefit from greater visibility for their LTER site, LTSER platform and datasets, which can help attract funding to support site investments. The aim of DEIMS-SDR is to be the globally most comprehensive catalogue of environmental research and monitoring facilities, featuring foremost but not exclusively information about all LTER sites on the globe and providing that information to science, politics and the public in general.",
"homepage": "https://deims.org",
"name": "DEIMS-SDR",
"prefix": "r3d100012910",
"synonyms": [
"Dynamic Ecological Information Management System - Site and Dataset Registry"
],
"xrefs": {
"fairsharing": "FAIRsharing.SrP8P7"
}
},
"r3d100012911": {
"description": "RWTH Publications Research Data offers all RWTH Aachen University affiliates the organizational and technical means to electronically document and publish research data at this institutional repository. Certainly, researchers are encouraged to prefer a subject specific repository whenever appropriate and available. RWTH Aachen University is the largest technical university in Germany and one of nine 'German Universities of Excellence' (elite university). The University library Aachen operates the repository as a member of the join community.",
"homepage": "https://publications.rwth-aachen.de/collection/ResearchData?ln=de",
"name": "RWTH Publications Research Data",
"prefix": "r3d100012911",
"synonyms": [
"RWTH Publications Forschungsdaten"
]
},
"r3d100012912": {
"description": "The NCIS is a national database of information on every death reported to a coroner in Australia and New Zealand. It contains demographic information on the deceased, contextual information on the nature of the fatality and medico-legal documents including the coroner's finding, autopsy and toxicology reports and the police notification of death report.",
"homepage": "https://www.ncis.org.au/",
"name": "National Coronial Information System",
"prefix": "r3d100012912",
"synonyms": [
"NCIS"
],
"xrefs": {
"fairsharing": "FAIRsharing.U9GXhB"
}
},
"r3d100012915": {
"description": "The Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Data and Specimen Hub (DASH) is a centralized resource that allows researchers to share and access de-identified data from studies funded by NICHD. DASH also serves as a portal for requesting biospecimens from selected DASH studies.",
"homepage": "https://dash.nichd.nih.gov/",
"name": "Data and Specimen Hub",
"prefix": "r3d100012915",
"synonyms": [
"DASH",
"NICHD DASH"
],
"xrefs": {
"fairsharing": "FAIRsharing.dYSI4O",
"scr": "016314"
}
},
"r3d100012917": {
"description": "The China National GeneBank database (CNGBdb) is a unified platform for biological big data sharing and application services. CNGBdb has now integrated a large amount of internal and external biological data from resources such as CNGB, NCBI, and the EBI. There are several sub-databases in CNGBdb, including literature, variation, gene, genome, protein, sequence, organism, project, sample, experiment, run, and assembly. Based on underlying big data and cloud computing technologies, it provides various data services, including archive, analysis, knowledge search, and management authorization of biological data. CNGBdb adopts data structures and standards of international omics, health, and medicine, such as The International Nucleotide Sequence Database Collaboration (INSDC), The Global Alliance for Genomics and Health GA4GH (GA4GH), Global Genome Biodiversity Network (GGBN), American College of Medical Genetics and Genomics (ACMG), and constructs standardized data and structures with wide compatibility. All public data and services provided by CNGBdb are freely available to all users worldwide.\nCNGB Sequence Archive (CNSA) is the bionomics data repository of CNGBdb.\nCNGB Sequence Archive (CNSA) is a convenient and efficient archiving system of multi-omics data in life science, which provides archiving services for raw sequencing reads and further analyzed results. CNSA follows the international data standards for omics data, and supports online and batch submission of multiple data types such as Project, Sample, Experiment/Run, Assembly, Variation, Metabolism, Single cell, and Sequence. Moreover, CNSA has achieved the correlation of sample entities, sample information, and analyzed data on some projects. Its data submission service can be used as a supplement to the literature publishing process to support early data sharing.CNGB Sequence Archive (CNSA) is a convenient and efficient archiving system of multi-omics data in the life science of CNGBdb, which provides archiving services for raw sequencing reads and further analyzed results. CNSA follows the international data standards for omics data, and supports online and batch submission of multiple data types such as Project, Sample, Experiment/Run, Assembly, Variation, Metabolism, Single cell, Sequence. Its data submission service can be used as a supplement to the literature publishing process to support early data sharing.",
"homepage": "https://db.cngb.org/",
"name": "China National GeneBank DataBase",
"prefix": "r3d100012917",
"synonyms": [
"CNGBdb",
"ε½εΆεΊε εΊηε½ε€§ζ°ζεΉ³ε°"
],
"xrefs": {
"fairsharing": "/FAIRsharing.9btRvC"
}
},
"r3d100012918": {
"description": "This data repository hosts source and replication datasets for the Kemri Wellcome Trust Research Programme (KWTRP).",
"homepage": "https://dataverse.harvard.edu/dataverse/kwtrp",
"name": "KWTRP Research Data Repository Dataverse",
"prefix": "r3d100012918",
"synonyms": [
"KWTRP Research Data Repository",
"Kemri Wellcome Trust Research Programme Research Data Repository Dataverse",
"Kenya medical Research Institute Wellcome Trust Research Programme Research Data Repository Dataverse"
]
},
"r3d100012920": {
"description": "The Water Quality Portal (WQP) is a cooperative service sponsored by the United States Geological Survey (USGS), the Environmental Protection Agency (EPA) and the National Water Quality Monitoring Council (NWQMC) that integrates publicly available water quality data from the USGS National Water Information System (NWIS) the EPA STOrage and RETrieval (STORET) Data Warehouse, and the USDA ARS Sustaining The Earthβs Watersheds - Agricultural Research Database System (STEWARDS) . It serves water quality data collected by over 400 state, federal, tribal, and local agencies in the United States. As of July 2015, over 265 million results from over 2.2 million monitoring locations are currently accessible through the portal. The portal reports samples and results collected from each location since the beginning of the databases.",
"homepage": "https://www.waterqualitydata.us/",
"name": "Water Quality Portal",
"prefix": "r3d100012920",
"synonyms": [
"WQP"
],
"xrefs": {
"fairsharing": "FAIRsharing.e6766c"
}
},
"r3d100012922": {
"description": "A number of sociological research institutions have worked together with partners from IT and the information sciences to establish a new research data infrastructure for qualitative research, the interdisciplinary center for qualitative research data from the sociology of work (eLabour). The infrastructure will be fully operational in early 2019. In addition, the center will expand its qualitative data pool and open up to external scientists. At the same time, IT-based processes and tools for qualitative data management are being developed to establish a competence center for professional qualitative research data management, which can provide support and services for a variety of scientific user groups.\nResearch data are available as Scientific Use Files (SUF) and Campus Files (CF).\nList of available research data at 'Projects' page: http://elabour.de/auswaehlen-und-nutzen/forschungsdaten/",
"homepage": "http://elabour.de/",
"name": "eLabour",
"prefix": "r3d100012922",
"synonyms": [
"FDZ eLabour",
"Interdisciplinary center for qualitative research data from the sociology of work (eLabour)",
"InterdisziplinΓ€res Zentrum fΓΌr qualitative arbeitssoziologische Forschungsdaten (FDZ eLabour)"
]
},
"r3d100012923": {
"description": "Data Publication Server Forschungszentrum Juelich is a web server for providing large data sets to the general public. It's main application is publishing data belonging to scientific publications.",
"homepage": "https://datapub.fz-juelich.de/",
"name": "Data Publication Server Forschungszentrum JΓΌlich",
"prefix": "r3d100012923",
"synonyms": [
"Data Server",
"DataPub Server"
]
},
"r3d100012924": {
"description": "The Cancer in Young People in Canada (CYP-C) surveillance program collects in-depth data concerning risk factors, health outcomes, quality and accessibility of care, and late effects among children and youth with cancer. CYP-C represents a collaboration involving the C17 Council, Canadian Partnerships Against Cancer (CPAC), Public Health Agency of Canada (PHAC), provincial and territorial cancer registries, Statistics Canada and non-governmental organizations.",
"homepage": "https://www.c17.ca/committees/CYP-C",
"name": "Cancer in Young People in Canada",
"prefix": "r3d100012924",
"synonyms": [
"CCJC",
"CYP-C",
"Cancer Chez les Jeunes au Canada"
]
},
"r3d100012925": {
"description": "Arch is an open access repository for the research and scholarly output of Northwestern University. Log in with your NetID to deposit, describe, and organize your research for public access and long-term preservation. We'll use our expertise to help you curate, share, and preserve your work.",
"homepage": "https://arch.library.northwestern.edu/",
"name": "Arch",
"prefix": "r3d100012925",
"synonyms": [
"Research and Data Repository"
],
"xrefs": {
"issn": "2572-5653",
"opendoar": "4726",
"roar": "13020"
}
},
"r3d100012926": {
"description": "The Korea Polar Data Center (KPDC) is an organization dedicated for managing different types of data acquired during scientific research that South Korea carries out in Antarctic and Arctic regions. South Korea, as an Antarctic Treaty Consultative Party (ATCP) and an accredited member of the Scientific Committee on Antarctic Research (SCAR) established the Center in 2003 as part of its effort to joint international Antarctic research.",
"homepage": "https://kpdc.kopri.re.kr/",
"name": "Korea Polar Data Center",
"prefix": "r3d100012926",
"synonyms": [
"KPDC"
]
},
"r3d100012927": {
"description": "The datacommons@psu was developed in 2005 to provide a resource for data sharing, discovery, and archiving for the Penn State research and teaching community. Access to information is vital to the research, teaching, and outreach conducted at Penn State. The datacommons@psu serves as a data discovery tool, a data archive for research data created by PSU for projects funded by agencies like the National Science Foundation, as well as a portal to data, applications, and resources throughout the university. The datacommons@psu facilitates interdisciplinary cooperation and collaboration by connecting people and resources and by:\n\n Acquiring, storing, documenting, and providing discovery tools for Penn State based research data, final reports, instruments, models and applications.\n Highlighting existing resources developed or housed by Penn State.\n Supporting access to project/program partners via collaborative map or web services.\n Providing metadata development citation information, Digital Object Identifiers (DOIs) and links to related publications and project websites.\n\nMembers of the Penn State research community and their affiliates can easily share and house their data through the datacommons@psu. The datacommons@psu will also develop metadata for your data and provide information to support your NSF, NIH, or other agency data management plan.",
"homepage": "https://www.datacommons.psu.edu/default.html",
"name": "datacommons@psu",
"prefix": "r3d100012927",
"synonyms": [
"Penn State Data Commons",
"datacommons@psu"
]
},
"r3d100012928": {
"description": "The MicroScope platform is an informatics infrastructure dedicated to the annotation and comparative analysis of microbial genomes and metagenomes.",
"homepage": "https://mage.genoscope.cns.fr/microscope/home/index.php",
"name": "MicroScope",
"prefix": "r3d100012928",
"synonyms": [
"Microbial Genome Annotation & Analysis Platform"
],
"xrefs": {
"fairsharing": "/FAIRsharing.3t5qc3"
}
},
"r3d100012929": {
"description": "RADAR (Research And Digital Assets Repository) is the institutional repository of Oxford Brookes University. The role of RADAR is to share the intellectual product of Oxford Brookes freely and openly with the staff and students of Oxford Brookes or with the global academic and public community.\nβRADAR has a variety of research collections (primarily containing original research publications) and teaching collections (primarily containing resources that support teaching at Oxford Brookes University). Some of the collectionsβ and resources on RADAR are freely accessible to the general public and other collectionsβ and resources are only accessible by current Oxford Brookes staff and students.",
"homepage": "https://radar.brookes.ac.uk/radar",
"name": "Oxford Brookes University: RADAR",
"prefix": "r3d100012929",
"xrefs": {
"opendoar": "1680",
"roar": "2287"
}
},
"r3d100012930": {
"description": "Sinmin contains texts of different genres and styles of the modern and old Sinhala language. The main sources of electronic copies of texts for the corpus are online Sinhala newspapers, online Sinhala news sites, Sinhala school textbooks available in online, online Sinhala magazines, Sinhala Wikipedia, Sinhala fictions available in online, Mahawansa, Sinhala Blogs, Sinhala subtitles and Sri lankan gazette.",
"homepage": "https://osf.io/a5quv/",
"name": "SinMin",
"prefix": "r3d100012930"
},
"r3d100012931": {
"description": "The IISH Dataverse contains micro-, meso-, and macro-level datasets on social and economic history.",
"homepage": "https://datasets.iisg.amsterdam/",
"name": "IISH Dataverse",
"prefix": "r3d100012931",
"synonyms": [
"International Institute of Social History Dataverse"
]
},
"r3d100012932": {
"description": "<<>>!!!>>>",
"homepage": "https://dare.iiasa.ac.at/",
"name": "IIASA DARE",
"prefix": "r3d100012932",
"synonyms": [
"Data Repository of the International Institute of Applied Systems Analysis"
],
"xrefs": {
"opendoar": "4236",
"roar": "14320"
}
},
"r3d100012934": {
"description": "Our research focuses mainly on the past and present bio- and geodiversity and the evolution of animals and plants. The Information Technology Center of the Staatliche Naturwissenschaftliche Sammlungen Bayerns is the institutional repository for scientific data of the SNSB. Its major tasks focus on the management of bio- and geodiversity data using different kinds of information technological structures. The facility guarantees a sustainable curation, storage, archiving and provision of such data.",
"homepage": "https://www.snsb.info/dwb_biocase.html",
"name": "DWB BioCASe Data Publication pipeline and RDF service",
"prefix": "r3d100012934",
"synonyms": [
"Bavarian Natural History Collections - occurrence data",
"SNSB"
]
},
"r3d100012935": {
"description": "Applying the Terrestrial Systems Modeling Platform, TerrSysMP, this dataset consists of the first simulated long-term (1989-2018), high-resolution (~12.5km) terrestrial system climatology over Europe, which comprises variables from groundwater across the land surface to the top of atmosphere (G2A). This data set constitutes a near-natural realization of the European terrestrial system, which cannot be obtained from observations, and can, thus, serve as a reference for global change simulations including human water use and climate change.",
"homepage": "https://datapub.fz-juelich.de/slts/cordex/index.html",
"name": "EURO-CORDEX 1989-2018 using TerrSysMP",
"prefix": "r3d100012935",
"synonyms": [
"EUR-11 evaluation simulations with TerrSysMP"
]
},
"r3d100012936": {
"description": "The IOWDB was designed for the particular requirements of the Leibniz Institute for Baltic Sea Research. It is aimed at the management of historical and recent measurement of the IOW (to some extend of other data, too) and to provide them in a user-friendly way via the research tool ODIN (Oceanographic Database research with Interactive Navigation).",
"homepage": "https://www.io-warnemuende.de/en_iowdb.html",
"name": "IOWDB",
"prefix": "r3d100012936",
"synonyms": [
"Die ozeanographische Datenbank des IOW",
"The Oceanographic Database of IOW"
]
},
"r3d100012937": {
"description": "Data are the key to successful scientific work. A sophisticated data management will guarantee the long-term availability of observational data and metadata, and will allow for an easy data search and retrieval, to supplement the international data exchange and to provide data products for scientific, political, industrial and public stakeholders.",
"homepage": "https://www.io-warnemuende.de/data-portal.html",
"name": "IOW Data Portal",
"prefix": "r3d100012937",
"synonyms": [
"IOW Datenportal"
],
"xrefs": {
"fairsharing": "FAIRsharing.6738fd"
}
},
"r3d100012938": {
"description": "Making government data easier to access for individuals, businesses, and researchers.",
"homepage": "https://data.novascotia.ca/",
"name": "Nova Scotia Government's Open Data Portal",
"prefix": "r3d100012938"
},
"r3d100012939": {
"description": "Making government data available, accessible, and re-usable.",
"homepage": "https://data.princeedwardisland.ca/",
"name": "Prince Edward Island Government Open Data Portal",
"prefix": "r3d100012939"
},
"r3d100012940": {
"description": "The Newfoundland and Labrador Open Data repository increases access to government information and data.",
"homepage": "https://opendata.gov.nl.ca/",
"name": "Newfoundland and Labrador Open Data",
"prefix": "r3d100012940"
},
"r3d100012941": {
"description": "An open data sharing platform resulting from collaboration between cities and the Government of Quebec.",
"homepage": "https://www.donneesquebec.ca/recherche/fr/dataset",
"name": "DonnΓ©es QuΓ©bec",
"prefix": "r3d100012941"
},
"r3d100012943": {
"description": "This purpose of this repository is to share Ontario's government data sets online to increase transparency and accountability. We're adding to the hundreds of records weβve released so far to create an inventory of known government data. Data will either be open, restricted, under review or in the process of being made open, depending on the sensitivity of the information.",
"homepage": "https://data.ontario.ca/",
"name": "Ontario Open Government Data",
"prefix": "r3d100012943"
},
"r3d100012944": {
"description": "The open government portal is a collection of datasets and publications by government departments and agencies. The public can use and access this data freely to learn more about how government works, carry out research or build web apps. The portal functions as both a library for current publications and as an archive for old publications which have historic value.",
"homepage": "https://open.alberta.ca/opendata",
"name": "Government of Alberta Open Datasets",
"prefix": "r3d100012944",
"synonyms": [
"Alberta Open Data"
]
},
"r3d100012945": {
"description": "The B.C. Data Catalogue provides the easiest access to government's data holdings, as well as applications and web services. Thousands of the datasets discoverable in the Catalogue are available under the Open Government License - British Columbia.",
"homepage": "https://catalogue.data.gov.bc.ca/",
"name": "DataBC",
"prefix": "r3d100012945",
"synonyms": [
"British Columbia Data Catalogue"
]
},
"r3d100012946": {
"description": "A collection of high quality multiple sequence alignments for objective, comparative studies of alignment algorithms. The alignments are constructed based on 3D structure superposition and manually refined to ensure alignment of important functional residues. A number of subsets are defined covering many of the most important problems encountered when aligning real sets of proteins. It is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The first release provided sets of reference alignments dealing with the problems of high variability, unequal repartition and large N/C-terminal extensions and internal insertions. Version 2.0 of the database incorporates three new reference sets of alignments containing structural repeats, trans-membrane sequences and circular permutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences.\nWithin the resource, users can look at a list of all the alignments, download the whole database by ftp, get the \"c\" program to compare a test alignment with the BAliBASE reference (The source code for the program is freely available), or look at the results of a comparison study of several multiple alignment programs, using BAliBASE reference sets.",
"homepage": "https://lbgi.fr/balibase/",
"name": "BAliBASE",
"prefix": "r3d100012946",
"synonyms": [
"Benchmark Alignment dataBASE"
],
"xrefs": {
"fairsharing": "FAIRsharing.sed5tq",
"nif": "0000-02594",
"scr": "001940"
}
},
"r3d100012948": {
"description": "As part of Halifax Regional Municipalityβs commitment to improving citizen engagement and enhancing transparency and accountability to its residents, the municipality is pleased to provide public access to its data. Open Data is a permanent service provided to citizens and businesses to access data free of charge in machine readable format.",
"homepage": "https://data-hrm.hub.arcgis.com/pages/open-data-catalogue",
"name": "Halifax Open Data",
"prefix": "r3d100012948",
"synonyms": [
"Halifax Data, Mapping & Analytics Hub Open Data"
]
},
"r3d100012949": {
"description": "Explore the City of Toronto's open data catalogue, including datasets from a wide range of City divisions.",
"homepage": "https://open.toronto.ca/",
"name": "City of Toronto Open Data Portal",
"prefix": "r3d100012949"
},
"r3d100012950": {
"description": "This website is a source of data released by the City of Ottawa for free use by the public.",
"homepage": "https://open.ottawa.ca",
"name": "Open Data Ottawa",
"prefix": "r3d100012950"
},
"r3d100012951": {
"description": "By opening its data to everyone, Ville de MontrΓ©al allows it to be reused for various purposes, including commercial ones. The results of this reuse can then be shared in the community, creating a multiplier effect. The data released and reused thus generate benefits in the economic, cultural, social and technological spheres.",
"homepage": "https://donnees.montreal.ca/",
"name": "MontrΓ©al Portail Donnees Ouvertes",
"prefix": "r3d100012951"
},
"r3d100012952": {
"description": "Free access to open data and information from the City of Winnipeg.",
"homepage": "https://data.winnipeg.ca/",
"name": "City of Winnipeg Open Data Portal",
"prefix": "r3d100012952"
},
"r3d100012953": {
"description": "Open Data reflects a commitment to open, accountable and transparent government. Open Data is a practice that makes data/information freely available to everyone to use and republish.",
"homepage": "https://open.regina.ca/dataset",
"name": "City of Regina Open Data",
"prefix": "r3d100012953"
},
"r3d100012954": {
"description": "This data, from across the city's departments and branches is freely available here in a single place - the Open Data Portal.",
"homepage": "https://data.edmonton.ca/browse",
"name": "Edmonton Open Data",
"prefix": "r3d100012954",
"synonyms": [
"City of Edmonton Open Data"
]
},
"r3d100012955": {
"description": "Research Data Unipd is a data archive and supports research produced by the members of the University of Padova. The service aims to facilitate data discovery, data sharing, and reuse, as required by funding institutions (eg. European Commission). Datasets published in the archive have a set of metadata that ensure proper description and discoverability.",
"homepage": "https://researchdata.cab.unipd.it/",
"name": "Research Data Unipd",
"prefix": "r3d100012955",
"xrefs": {
"doi": "10.25430/researchdataunipd",
"fairsharing": "FAIRsharing.984218"
}
},
"r3d100012961": {
"description": "Patients-derived tumor xenograft (PDX) mouse models are an important oncology research platform to study tumor evolution, drug response and personalised medicine approaches.\nWe have expanded to organoids and cell lines and are now called CancerModels.Org",
"homepage": "https://www.cancermodels.org/",
"name": "CancerModels.Org",
"prefix": "r3d100012961",
"synonyms": [
"formerly: PDX Finder",
"formerly; Patients-derived tumor xenograft finder"
],
"xrefs": {
"fairsharing": "FAIRsharing.738b9c"
}
},
"r3d100012962": {
"description": "Phaidra (Permanent Hosting, Archiving and Indexing of Digital Resources and Assets) is the University of Padua Library Systemβs platform for long-term archiving of digital collections.\nPhaidra hosts various types of digital objects (antiquarian books, manuscripts, photographs, wallcharts, maps, learning objects, films, archive material and museum objects). Phaidra offers a search facility to identify specific objects, and each object can be viewed, downloaded, used and reused to the extent permitted by law and by its associated licences.\nThe objects in the digital collections on the Phaidra platform are sourced from libraries (in large part due to the digitisation projects promoted by the Library System itself), museums and archives at the University of Padua and other institutions, including the Caβ Foscari University and the UniversitΓ Iuav in Venice.",
"homepage": "https://phaidra.cab.unipd.it/",
"name": "PHAIDRA - University of Padua",
"prefix": "r3d100012962",
"synonyms": [
"Digital collections of the University of Padua"
],
"xrefs": {
"doi": "10.25430/phaidra",
"fairsharing": "FAIRsharing.692301"
}
},
"r3d100012965": {
"description": "SISMER (Scientific Information Systems for the Sea) is Ifremer's service in charge of managing numerous marine databases and information systems which Ifremer is responsible for implementing. The information systems managed by SISMER range from CATDS (SMOS satellite data) to geoscience data (bathymetry, seismics, geological samples), not forgetting water column data (physics and chemistry, data for operational oceanography β Coriolis - Copernicus CMEMS), fisheries data (Harmonie), coastal environment data (Quadrige 2) and deep-sea environment data (ArchimΓ¨de).\nSISMER therefore plays a pivotal role in marine database management both for Ifremer and for many national, European and international projects.",
"homepage": "https://data.ifremer.fr/",
"name": "IFREMER-SISMER Portail de donnΓ©es marines",
"prefix": "r3d100012965",
"synonyms": [
"French Research Institute for Exploitation of the Sea - Scientific Information Systems for the Sea, Oceanographic Data",
"Institut franΓ§ais de recherche pour l'exploitation de la mer - SystΓ¨mes dβinformations scientifiques de la Mer, Portail des donnΓ©es marines"
]
},
"r3d100012966": {
"description": "OpARA (Open Access Repository and Archive) is the repository for digital research data of the TU Dresden (TUD) and the TU Bergakademie Freiberg (TUBAF). It offers researchers the possibility of archiving their digital research data and optionally making it accessible to third parties under an Open Access license.",
"homepage": "https://opara.zih.tu-dresden.de/xmlui/",
"name": "OpARA",
"prefix": "r3d100012966",
"synonyms": [
"Open Access Repository and Archive"
]
},
"r3d100012967": {
"description": "The City of Victoriaβs Open Data Portal allows you to explore and download open data, discover and analyze datasets using maps, and develop new web and mobile applications.",
"homepage": "https://opendata.victoria.ca/",
"name": "City of Victoria Open Data Portal",
"prefix": "r3d100012967"
},
"r3d100012968": {
"description": "The City of Calgaryβs Open Data Catalogue provides public access to information and data managed by The City. The Open Data Catalogue contains hundreds of datasets which are available in multiple file formats and can be downloaded for free. The data may be used for any purpose subject to the Open Data Catalogue Terms of Use. By providing public access to City data, we are not only promoting transparency in government, but also innovation within our community.",
"homepage": "https://data.calgary.ca/browse",
"name": "Open Calgary",
"prefix": "r3d100012968"
},
"r3d100012969": {
"description": "Open data for the City of Hamilton. Open Hamilton is designed to enable the community to better explore, visualize and download City data.",
"homepage": "https://open.hamilton.ca/",
"name": "Open Hamilton",
"prefix": "r3d100012969"
},
"r3d100012970": {
"description": "The City of Kitchener is committed to supporting citizen engagement and enhancing transparency and accountability to its residents by providing public access to its data.",
"homepage": "https://open-kitchenergis.opendata.arcgis.com/",
"name": "Kitchener GeoHub",
"prefix": "r3d100012970",
"synonyms": [
"City of Kitchener Open Data"
]
},
"r3d100012971": {
"description": "Public access to open data from the Regional Municipality of Waterloo (the cities of Kitchener, Cambridge, and Waterloo, and the townships of Wellesley, Woolwich, Wilmot, and North Dumfries).",
"homepage": "https://rowopendata-rmw.opendata.arcgis.com/",
"name": "Region of Waterloo - Open Data",
"prefix": "r3d100012971",
"xrefs": {
"biodbcore": "001579"
}
},
"r3d100012972": {
"description": "The Open Data Kingston Portal provides access to the City's open datasets.",
"homepage": "https://opendatakingston.cityofkingston.ca/pages/welcome/",
"name": "Open Data Kingston",
"prefix": "r3d100012972"
},
"r3d100012973": {
"description": "This Open GIS Data Portal provides residents, visitors, business owners and investors a means to easily find, access and view information through the use of maps and mapping technology.",
"homepage": "https://public-barrie.opendata.arcgis.com/",
"name": "City of Barrie Open GIS Data Portal",
"prefix": "r3d100012973",
"synonyms": [
"Cityβs Open GIS Data Portal"
]
},
"r3d100012974": {
"description": "Searchable public data from the City of Guelph.",
"homepage": "http://data.open.guelph.ca/",
"name": "Guelph Open Data Portal",
"prefix": "r3d100012974"
},
"r3d100012975": {
"description": "Find open data for the City of Saint John via their Open Data catalogue.",
"homepage": "https://catalogue-saintjohn.opendata.arcgis.com/",
"name": "The City of Saint John Open Data",
"prefix": "r3d100012975"
},
"r3d100012976": {
"description": "Free and open data from the City of Lethbridge.",
"homepage": "https://opendata.lethbridge.ca/",
"name": "Open Data Catalogue - City of Lethbridge",
"prefix": "r3d100012976"
},
"r3d100012977": {
"description": "This is Kelowna's Open Data Portal. This is the community's public platform for exploring and downloading open data, discovering and building apps. You can analyze and combine Open Datasets using maps, as well as develop new web and mobile applications. Search and download open datasets at no cost.",
"homepage": "https://opendata.kelowna.ca/",
"name": "Open Data Portal - City of Kelowna",
"prefix": "r3d100012977"
},
"r3d100012978": {
"description": "Search and explore the City of Burlington's open data. The Open Data service makes raw city data available for public use and new application development. The Open Data service is just one of the innovative ways we are evolving our customer service practices using online technology.",
"homepage": "https://navburl-burlington.opendata.arcgis.com/pages/data",
"name": "City of Burlington's Open Data Catalogue",
"prefix": "r3d100012978",
"synonyms": [
"Navigate Burlington data"
]
},
"r3d100012979": {
"description": "This portal provides access to available open data from the City of Greater Sudbury.",
"homepage": "https://opendata.greatersudbury.ca/",
"name": "City of Greater Sudbury Open Data Portal",
"prefix": "r3d100012979"
},
"r3d100012980": {
"description": "This Open Data catalogue allows users to search, explore, and download the City of Oshawa's available open data.",
"homepage": "https://city-oshawa.opendata.arcgis.com/",
"name": "City of Oshawa Open Data",
"prefix": "r3d100012980"
},
"r3d100012981": {
"description": "Access and download datasets of information from the City of Niagara.",
"homepage": "https://niagaraopendata.ca/",
"name": "Niagara Open Data",
"prefix": "r3d100012981"
},
"r3d100012986": {
"description": "This website provides access to published open map data from the City of Cambridge.",
"homepage": "https://geohub.cambridge.ca/",
"name": "City of Cambridge GeoHub",
"prefix": "r3d100012986"
},
"r3d100012987": {
"description": "Freely explore the City of Surrey's datasets via their Open Data website.\nData.surrey.ca provides one-stop access to the City of Surreyβs searchable open data and open information, together with open dialogue, as part of Surreyβs commitment to enhance transparency and accountability. We encourage the participation of all citizens to make data.surrey.ca better.",
"homepage": "https://data.surrey.ca/",
"name": "City of Surrey Open Data",
"prefix": "r3d100012987",
"synonyms": [
"data.surrey.ca"
]
},
"r3d100012989": {
"description": "This catalogue allows users to search, browse, and download open data about the City of Brantford.",
"homepage": "https://data-brantford.opendata.arcgis.com/",
"name": "City of Brantford Open Data Catalogue",
"prefix": "r3d100012989"
},
"r3d100012990": {
"description": "Easy access to open information about the City of Nanaimo.",
"homepage": "https://www.nanaimo.ca/open-data-catalogue/",
"name": "Nanaimo Data Catalogue",
"prefix": "r3d100012990"
},
"r3d100012991": {
"description": "This Open Data portal provides access to data and information about the city of Prince George.",
"homepage": "https://data-cityofpg.opendata.arcgis.com/",
"name": "Open Data Prince George",
"prefix": "r3d100012991"
},
"r3d100012992": {
"description": "Public access to the City of Grand Prairie`s open data catalogue.",
"homepage": "https://opendata-cityofgp.hub.arcgis.com/",
"name": "City of Grand Prairie Open Data Catalogue",
"prefix": "r3d100012992"
},
"r3d100012993": {
"description": "This catalogue provides public access to open data managed by the City of Kamloops.",
"homepage": "https://mydata-kamloops.opendata.arcgis.com/?agree=0",
"name": "City of Kamloops Open Data Catalog",
"prefix": "r3d100012993"
},
"r3d100012994": {
"description": "Dataverse UNIMI is the institutional data repository of the University of Milan. The service aims at facilitating data discovery, data sharing, and reuse, as required by funding institutions (eg. European Commission). Datasets published in the archive have a set of metadata that ensure proper description and discoverability.",
"homepage": "https://dataverse.unimi.it/",
"name": "Dataverse UNIMI",
"prefix": "r3d100012994",
"synonyms": [
"Dataverse UniversitΓ degli Studi di Milano"
],
"xrefs": {
"opendoar": " 4578"
}
},
"r3d100012997": {
"description": "Open Data Strathcona is designed to allow the public to explore and access open City data.",
"homepage": "https://opendata-strathconacounty.hub.arcgis.com/",
"name": "Strathcona County's Open Data",
"prefix": "r3d100012997"
},
"r3d100012998": {
"description": "The open data catalogue for the City of Brandon.",
"homepage": "https://opengov.brandon.ca/catalog.php",
"name": "City of Brandon Open Data",
"prefix": "r3d100012998"
},
"r3d100012999": {
"description": "Open data portal for the town of Oakville allows users to search, explore, and download open data.",
"homepage": "https://portal-exploreoakville.opendata.arcgis.com/",
"name": "Town of Oakville Open Data",
"prefix": "r3d100012999"
},
"r3d100013000": {
"description": "Open datasets from the City of New Westminster.",
"homepage": "https://opendata.newwestcity.ca/",
"name": "New Westminster Open Data",
"prefix": "r3d100013000"
},
"r3d100013001": {
"description": "Access to the York Region open data catalogue. Explore, combine, and download open data from York Region.",
"homepage": "https://insights-york.opendata.arcgis.com/",
"name": "York Region Open Data",
"prefix": "r3d100013001"
},
"r3d100013002": {
"description": "This Open Data catalogue is the public platform for the City of Niagara Falls.",
"homepage": "https://open.niagarafalls.ca/",
"name": "Niagara Falls Open Data",
"prefix": "r3d100013002"
},
"r3d100013003": {
"description": "Discover, analyze, and download Brampton's Open Data via this portal.",
"homepage": "https://geohub.brampton.ca/pages/data/",
"name": "City of Brampton Open Data",
"prefix": "r3d100013003"
},
"r3d100013004": {
"description": "This portal provides open data sourced directly from the Township of Langley.",
"homepage": "https://data-tol.opendata.arcgis.com/",
"name": "Township of Langley Open Data Portal",
"prefix": "r3d100013004"
},
"r3d100013005": {
"description": "Town of Canmore Open Data Catalogue is a publicly available data sharing in ArcGIS Online portal where anyone can access and utilize data relating to the Town of Canmore, Alberta, Canada. You can browse, search, preview, and download a variety of municipal geospatial datasets.",
"homepage": "https://opendata-canmore.opendata.arcgis.com/",
"name": "Town of Canmore Open Data",
"prefix": "r3d100013005"
},
"r3d100013006": {
"description": "The County of Grande Prairie public platform for exploring and downloading open data, discovering and building apps, and engaging to solve important local issues. You can analyze and combine Open Datasets using maps, as well as develop new web and mobile applications.",
"homepage": "https://opendata.countygp.ab.ca/",
"name": "County of Grande Prairie Open Data",
"prefix": "r3d100013006"
},
"r3d100013007": {
"description": "This catalogue provides access to published open data from the District of Squamish.",
"homepage": "https://data.squamish.ca/",
"name": "Squamish Open Data",
"prefix": "r3d100013007"
},
"r3d100013008": {
"description": "Open data (including maps and applications) for the Town of Huntsville.",
"homepage": "https://huntsville-muskoka.opendata.arcgis.com/",
"name": "Town of Huntsville Open Data",
"prefix": "r3d100013008"
},
"r3d100013009": {
"description": "This is Grey's public hub for exploring and Downloading Open Data, Learning about Grey's Stories and Analyzing and Combining Open Datasets to tell your own story.",
"homepage": "https://maps.grey.ca/pages/open-data",
"name": "Grey County Open Data",
"prefix": "r3d100013009"
},
"r3d100013010": {
"description": "This is Haldimand County's public platform for exploring and downloading open data, discovering and building apps, and engaging to solve important local issues. You can analyze and combine Open Datasets using maps, as well as develop new web and mobile applications.",
"homepage": "https://opendata-haldimand.hub.arcgis.com/",
"name": "Haldimand County Open Data",
"prefix": "r3d100013010"
},
"r3d100013011": {
"description": "Free and open access to data from the Town of Ajax. This website includes downloadable data, interactive maps, and more.",
"homepage": "https://opendata.ajax.ca/",
"name": "Town of Ajax Open Data",
"prefix": "r3d100013011",
"synonyms": [
"Ajax Open Data"
]
},
"r3d100013012": {
"description": "<<>>!!!>>>",
"homepage": "https://sensor.awi.de",
"name": "SENSOR",
"prefix": "r3d100013012",
"synonyms": [
"SENSOR.awi.de"
]
},
"r3d100013014": {
"description": "This is an institutional repository which hosts the publications and research outputs (including data sets) of higher and further education institutions in Sachsen-Anhalt, Germany. The interface of the repository is available in German and English. Most of the content is in German.",
"homepage": "https://opendata.uni-halle.de",
"name": "Share_it",
"prefix": "r3d100013014",
"synonyms": [
"Open Access und Forschungsdaten-Repositorium der Hochschulbibliotheken in Sachsen-Anhalt"
]
},
"r3d100013015": {
"description": "Project Data Sphere, LLC, operates a free digital library-laboratory where the research community can broadly share, integrate and analyze historical, de-identified, patient-level data from academic and industry cancer Phase II-III clinical trials. These patient-level datasets are available through the Project Data Sphere platform to researchers affiliated with life science companies, hospitals and institutions, as well as independent researchers, at no cost and without requiring a research proposal.",
"homepage": "https://data.projectdatasphere.org/projectdatasphere/html/home",
"name": "Project Data Sphere",
"prefix": "r3d100013015",
"synonyms": [
"PDS"
],
"xrefs": {
"nlx": "157911",
"scr": "003726"
}
},
"r3d100013016": {
"description": "This catalogue provides access to open government data for the sub-region of West Parry Sound.",
"homepage": "https://data-wpsgn.opendata.arcgis.com/",
"name": "West Parry Sound Geography Network",
"prefix": "r3d100013016"
},
"r3d100013017": {
"description": "Open data sourced from the City of Airdrie.",
"homepage": "https://data-airdrie.opendata.arcgis.com/",
"name": "City of Airdrie Open Data",
"prefix": "r3d100013017"
},
"r3d100013018": {
"description": "The Alberta Geological Survey (AGS) Open Data Portal features a subset of GIS data related to the geology of the province of Alberta and published by the AGS. The AGS delivers geoscience in several key areas; including surficial mapping, bedrock mapping, geological modelling, resource evaluation (hydrocarbons, minerals), groundwater, and geological hazards.",
"homepage": "https://geology-ags-aer.opendata.arcgis.com/",
"name": "Alberta Geological Survey Open Data Portal",
"prefix": "r3d100013018",
"synonyms": [
"AGS Open Data Portal"
],
"xrefs": {
"fairsharing": "FAIRsharing.027f17"
}
},
"r3d100013019": {
"description": "This open data portal provides access to the geospatial datasets of the Sunshine Coast Regional District (SCRD).",
"homepage": "https://data-myscrd.opendata.arcgis.com/",
"name": "Sunshine Coast Regional District Open Data",
"prefix": "r3d100013019",
"synonyms": [
"SCRD Open Data"
]
},
"r3d100013020": {
"description": "Search, explore, and download open datasets sourced from the District of Peachland.",
"homepage": "https://peachland2017-01-16t194902237z-rdco.opendata.arcgis.com/",
"name": "District of Peachland Open Data",
"prefix": "r3d100013020"
},
"r3d100013021": {
"description": "This open data portal includes datasets related to Westbank First Nation.",
"homepage": "https://wfn-open-data-rdco.opendata.arcgis.com/",
"name": "Westbank First Nation Open Data",
"prefix": "r3d100013021",
"synonyms": [
"WFN Open Data"
]
},
"r3d100013022": {
"description": "Explore and download open data from the Central Lake Ontario Conservation (CLOCA) Open Data Portal.",
"homepage": "https://cloca-camaps.opendata.arcgis.com/",
"name": "Central Lake Ontario Conservation Open Data Portal",
"prefix": "r3d100013022",
"synonyms": [
"CLOCA Open Data Portal"
]
},
"r3d100013023": {
"description": "Free access to open GIS data from the city of Quinte West.",
"homepage": "https://geodata-quintewest.opendata.arcgis.com/",
"name": "Quinte West Open GIS Data Portal",
"prefix": "r3d100013023",
"xrefs": {
"fairsharing": "FAIRsharing.809b50"
}
},
"r3d100013025": {
"description": "This portal provides free access to GIS data from the Municipality of East Hants, Nova Scotia.",
"homepage": "https://newdata-easthants.opendata.arcgis.com/",
"name": "East Hants Open Data",
"prefix": "r3d100013025"
},
"r3d100013027": {
"description": "The DPUK Data Portal brings together records of over 2 million people in a free-to-access resource. Researchers can identify which cohorts are relevant to them, apply for access to the data and then analyse it in a secure, remote environment with a complete data linkage and analysis package.",
"homepage": "https://portal.dementiasplatform.uk/",
"name": "Dementias Platform UK Data Portal",
"prefix": "r3d100013027",
"synonyms": [
"DPUK Data Portal"
]
},
"r3d100013028": {
"description": "BBMRI-ERIC is a European research infrastructure for biobanking. We bring together all the main players from the biobanking field β researchers, biobankers, industry, and patients β to boost biomedical research. To that end, we offer quality management services, support with ethical, legal and societal issues, and a number of online tools and software solutions. Ultimately, our goal is to make new treatments possible. The Directory is a tool to share aggregate information about the biobanks that are willing external collaboration. It is based on the MIABIS 2.0 standard, which describes the samples and data in the biobanks at an aggregated level.",
"homepage": "https://directory.bbmri-eric.eu/menu/main/app-molgenis-app-biobank-explorer/biobankexplorer#/catalogue",
"name": "BBMRI-ERIC Directory",
"prefix": "r3d100013028",
"synonyms": [
"Biobanking and BioMolecular resources Research Infrastructure - European Research Infrastructure Consortium Directory",
"Directory of Biobanks"
],
"xrefs": {
"fairsharing": "FAIRsharing.q9VUYM"
}
},
"r3d100013029": {
"description": "TUdatalib is the institutional repository of the TU Darmstadt for research data. It enables the structured storage of research data and descriptive metadata, long-term archiving (at least 10 years) and, if desired, the publication of data including DOI assignment. In addition there is a fine granular rights and role management.",
"homepage": "https://tudatalib.ulb.tu-darmstadt.de/",
"name": "TUdatalib",
"prefix": "r3d100013029",
"synonyms": [
"TUdatalib Repositorium",
"TUdatalib Repository"
]
},
"r3d100013030": {
"description": "RiuNet is intended to save the University community's production, personal or institutional, in collections. These can be made up of different types of documents such as Objects of learning (Polimedia, virtual labs and educational articles), theses, journal articles, maps, scholary works, creative works, institutional heritage, multimedia, teaching material, institutional production, electronic journals, conference proceedings and research data.",
"homepage": "https://riunet.upv.es/handle/10251/55048",
"name": "RiuNet",
"prefix": "r3d100013030",
"synonyms": [
"Repositorio Institucional UPV",
"Repositorio Institucional de la Universitat Politècnica de València"
],
"xrefs": {
"hdl": "10251/55048",
"opendoar": "1560",
"roar": "1127"
}
},
"r3d100013031": {
"description": "The AIDA data hub is a place where researchers can collaboratively gather, annotate, share and enrich large volumes of research data for machine learning in medical imaging diagnostics.",
"homepage": "https://datahub.aida.scilifelab.se/",
"name": "AIDA Data Hub",
"prefix": "r3d100013031",
"synonyms": [
"AIDA Dataset Register",
"Analytic Imaging Diagnostics Arena Data Hub"
]
},
"r3d100013033": {
"description": "The measured values of the panel form the basis for a 3D reconstruction of the panel, which was calculated using photos taken by Gerd GraΓhoff and Joanna Pruszynska with kind support of the Museum Warmii in autumn 2016. This repository contains the photos, the models, and the research data derived from them.",
"homepage": "http://repository.edition-topoi.org/collection/COPS",
"name": "Copernicus' Heliograph",
"prefix": "r3d100013033",
"synonyms": [
"COPS"
],
"xrefs": {
"doi": "10.17171/2-7"
}
},
"r3d100013034": {
"description": "In the Hellenistic and Roman period, many buildings and material objects were constructed using structural geometrical specifications. Ancient sundials were built using basic geometrical forms of very few construction types taking also into account the astronomical dimensions. In architectural drawings, comparable proportions can be found. The tower of the winds merges all these geometrical principles of construction. The construction drawings of this collection comprise geometrical drafts used for the construction of buildings. They differ from simple geometrical forms in that they present the general layout of the lines indicating objects and geometrical areas. Their geometrical dimensions are constructed according to the principles of proportional relations and were implemented in β sometimes very complex β work processes in which artefacts of the original objects were constructed. Construction drawings from the pillars of Didyma, which were discovered by Lothar Haselberger, serve as a paradigmatic model for these architectural drawings.",
"homepage": "http://repository.edition-topoi.org/collection/ACDC",
"name": "Construction Drawings",
"prefix": "r3d100013034",
"synonyms": [
"ACDC"
]
},
"r3d100013035": {
"description": "CMO is a long-term project for the critical edition of Near Eastern music manuscripts. The project focusing on manuscripts of Ottoman music written in Hampartsum and staff notations during the nineteenth century, is funded by the German Research Foundation (DFG).\nThis platform provides access to the online versions of both music and text editions, as well as the source catalogue, which is a comprehensive database of printed, manuscript and online sources.",
"homepage": "https://corpus-musicae-ottomanicae.de/content/index.xml",
"name": "CMO Editionen und Quellen-Katalog",
"prefix": "r3d100013035",
"synonyms": [
"CMO EdisyonlarΔ± ve Kaynak KataloΔu",
"CMO Editions and Catalogue",
"Corpus Musicae Ottomanicae Editionen und Quellen-Katalog"
]
},
"r3d100013036": {
"description": "LIVIVO is an interdisciplinary search engine for literature and information in the field of life sciences. It is run by ZB MED β Information Centre for Life Sciences. LIVIVO automatically searches for the terms you enter in a central index of all the databases.\nThe ZB MED Searchportal already provides a large amount of research data from DataCite data centres (e.g. Beijing Genomics Institute, Natural Environment Research Council) in the field of life sciences. These can be searched directly using the \"Documenttype=research data\" filter. A further integration of data from life science data repositories is planned.",
"homepage": "https://www.livivo.de",
"name": "LIVIVO",
"prefix": "r3d100013036",
"synonyms": [
"ZB MED Suchportal Lebenswissenschaften",
"ZB MED Search Portal for Life Sciences"
]
},
"r3d100013037": {
"description": "Phaidra Vetmeduni Vienna is the Universitys platform for long-term archiving of digital collections such as Thesis and Research Data. In two years we would enlarge the collection for archive materials such as fotos, books an dias f.e.",
"homepage": "https://phaidra.vetmeduni.ac.at/",
"name": "Phaidra Vetmeduni Vienna",
"prefix": "r3d100013037"
},
"r3d100013039": {
"description": "This online portal provides access to open data sourced from the Toronto Police Service.",
"homepage": "https://data.torontopolice.on.ca/pages/open-data",
"name": "Toronto Police Service Public Safety Data Portal",
"prefix": "r3d100013039",
"synonyms": [
"Toronto Police Service Open Data Portal"
]
},
"r3d100013040": {
"description": "<<>>!!!>>>",
"homepage": "http://www.eo-geohub.com/",
"name": "Employment Ontario Geo Hub",
"prefix": "r3d100013040"
},
"r3d100013043": {
"description": "<<>>!!!>>>",
"homepage": "https://undatacatalog.org/",
"name": "UN Data Catalog",
"prefix": "r3d100013043",
"synonyms": [
"United Nations System Data Catalog"
]
},
"r3d100013044": {
"description": "The ILO Department of Statistics is the focal point to the United Nations on labour statistics. They develop international standards for better measurement of labour issues and enhanced international comparability; provide relevant, timely and comparable labour statistics; and help Member States develop and improve their labour statistics.",
"homepage": "https://ilostat.ilo.org/",
"name": "ILOSTAT",
"prefix": "r3d100013044",
"synonyms": [
"International Labour Organization Statistics"
]
},
"r3d100013045": {
"description": "The aim of the project is systematic mapping of Czech and other languages in comparison with Czech. CNC corpora are accessible to everybody interested in studying the language after free registration.",
"homepage": "https://korpus.cz/",
"name": "Czech National Corpus",
"prefix": "r3d100013045",
"synonyms": [
"CNC",
"CNK",
"ΔeskΓ½ nΓ‘rodnΓ korpus"
]
},
"r3d100013046": {
"description": "PORTULAN CLARIN Research Infrastructure for the Science and Technology of Language, belonging to the Portuguese National Roadmap of Research Infrastructures of Strategic Relevance, and part of the international research infrastructure CLARIN ERIC",
"homepage": "https://portulanclarin.net/",
"name": "PORTULAN CLARIN repository",
"prefix": "r3d100013046"
},
"r3d100013047": {
"description": "The South African Centre for Digital Language Resources (SADiLaR) is a national centre supported by the Department of Science and Technology (DST). SADiLaR has an enabling function, with a focus on all official languages of South Africa, supporting research and development in the domains of language technologies and language-related studies in the humanities and social sciences.",
"homepage": "https://sadilar.org/en/",
"name": "South African Centre for Digital Language Resources",
"prefix": "r3d100013047",
"synonyms": [
"SADiLaR"
]
},
"r3d100013048": {
"description": "The knowledge centre is an information service offering advice on the use of digital language resources and tools for Swedish and other languages in Sweden, as well as other parts of the intangible cultural heritage of Sweden.",
"homepage": "https://sweclarin.se/eng/centers/sprakradet",
"name": "CLARIN Knowledge Centre for the Languages of Sweden",
"prefix": "r3d100013048",
"synonyms": [
"Clarin kunskapscentrum",
"SWELANG"
]
},
"r3d100013049": {
"description": "Data from high-alpine mountain permafrost research sites.",
"homepage": "http://data.permasense.ch",
"name": "PermaSense High-Alpine Permafrost Data",
"prefix": "r3d100013049"
},
"r3d100013050": {
"description": "The Tree Atlas Project is focused on the trees and shrubs of Namibia. The project gathered and recorded information about the distribution, abundance and general biology of woody plants, which are an important resource in Namibia. The information was collected over 6 years (October 1997-December 2003) and entered into a database housed at the National Botanical Research Institute.\nThis web site was made possible, and remains online, through the continued kind support of the Namibian Tree Atlas Project.\nOnline version active since paper version launch date, 2005. This page last modified on: 11 February 2018, at 08:42 am (Namibian time).\nSite design, layout and coding by John Irish.",
"homepage": "https://treeatlas.biodiversity.org.na/index.php",
"name": "Tree Atlas Project",
"prefix": "r3d100013050",
"synonyms": [
"NBRI Tree Atlas Project",
"Namibian Tree Atlas",
"National Botanical Research Institute Tree Atlas Project"
]
},
"r3d100013051": {
"description": "The ENCODE Encyclopedia organizes the most salient analysis products into annotations, and provides tools to search and visualize them. The Encyclopedia has two levels of annotations:\nIntegrative-level annotations integrate multiple types of experimental data and ground level annotations. \nGround-level annotations are derived directly from the experimental data, typically produced by uniform processing pipelines.",
"homepage": "https://www.encodeproject.org/",
"name": "ENCODE",
"prefix": "r3d100013051",
"synonyms": [
"ENCODE Encyclopedia",
"Encyclopedia of DNA Elements"
],
"xrefs": {
"fairsharing": "FAIRsharing.7ykpy5",
"miriam": "00000662",
"omics": "00532",
"scr": "015482"
}
},
"r3d100013052": {
"description": "A substance database for nanomaterial safety information",
"homepage": "https://data.enanomapper.net/",
"name": "data.enanomapper",
"prefix": "r3d100013052",
"synonyms": [
"eNanoMapper prototype database"
],
"xrefs": {
"fairsharing": "FAIRsharing.r18yt0"
}
},
"r3d100013053": {
"description": "Research Data Repository of the UniversitΓ€t Hamburg",
"homepage": "https://www.fdr.uni-hamburg.de/",
"name": "ZFDM repository",
"prefix": "r3d100013053",
"synonyms": [
"Center for Sustainable Research Data Management Research Data Repository",
"FDR@UHH",
"Zentrum fΓΌr nachhaltiges Forschungsdatenmanagement Forschungsdatenrepositorium"
]
},
"r3d100013057": {
"description": "The Open Data Repository of the H2020/CIVITAS/SUITS Project (https://www.suits-project.eu/) is used to store large volumes of crowdsourced traffic data, useful for SUMP implementations by local authorities of small-medium cities.",
"homepage": "https://dare.suits-project.eu",
"name": "SUITS Data Repository",
"prefix": "r3d100013057",
"synonyms": [
"S-ODR",
"SUITS DaRe",
"SUITS Open Data Repository"
]
},
"r3d100013058": {
"description": "The Data Repository of the H2020/TINNGO Project (https://www.tinngo.eu/) is used to store large volumes of gendered innovation related data, acquired from 10 national hubs of a pan-European Gender Observatory, Living Labs and other sources.",
"homepage": "https://tinngo.sboing.net/#repository",
"name": "Gendered Innovation Open Data Repository",
"prefix": "r3d100013058",
"synonyms": [
"formerly: Gender Observatory Data Repository (GO-DaRe)",
"formerly: TInnGO ODR (T-ODR)"
]
},
"r3d100013060": {
"description": "BacDive is a bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity. The database is a resource for different kind of phenotypic data like taxonomy, morphology, physiology, environment and molecular-biology. The majority of data is manually annotated and curated. With the release in April 2019 BacDive offers information for 80,584 strains. The database is hosted by the Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH and is part of de.NBI the German Network for Bioinformatics Infrastructure.",
"homepage": "https://bacdive.dsmz.de/",
"name": "BacDive",
"prefix": "r3d100013060",
"synonyms": [
"Bacterial Diversity Metadatabase"
],
"xrefs": {
"fairsharing": "FAIRsharing.aSszvY",
"miriam": "00000676",
"omics": "10161"
}
},
"r3d100013062": {
"description": "Data Univ Gustave Eiffel is an institutional repository for research data of university Gustave Eiffel : it catalogues multidisciplinary research data.",
"homepage": "https://data.univ-gustave-eiffel.fr/",
"name": "Data Univ Gustave Eiffel",
"prefix": "r3d100013062",
"synonyms": [
"DonnΓ©es de recherche de l'UniversitΓ© Gustave Eiffel",
"UniversitΓ© Gustave Eiffel Dataverse"
]
},
"r3d100013064": {
"description": "Scicat allows users to access the metadata of raw and derived data which is taken at experiment facilities. Scientific datasets are linked to proposals and samples. Scientific datasets are can be linked to publications (DOI, PID). SciCat helps keeping track of data provenance (i.e. the steps leading to the final results). Scicat allows users to find data based on the metadata (both your own data and other peoplesβ public data). In the long term, SciCat will help to automate scientific analysis workflows.",
"homepage": "https://scicat.ess.eu/",
"name": "SciCat",
"prefix": "r3d100013064",
"synonyms": [
"SciCat Data Catalog System",
"SciCat ESS",
"SciCat European Spallation Source"
]
},
"r3d100013068": {
"description": "The Freshwater Research and Environmental Database is the central data repository for IGB. It is where we store and share environmental data from observations of lakes, rivers, peatlands and other freshwater habitats. In FRED you can find continuous data collected over several decades from our long-term research programme at the lakes MΓΌggelsee, Stechlinsee, Arendsee and the river Spree, as well as environmental data derived from short-term projects in aquatic ecosystems. All data include detailed metadata descriptions in text form to allow reuse of the data. The database can be searched for a range of aspects, such as ecosystem types or abiotic and biotic variables. Data use, where not freely accessible, shall be granted after consulting with the contact person given in the database, and is subject to the IGB Data Policy.",
"homepage": "https://fred.igb-berlin.de",
"name": "Freshwater Research and Environmental Database",
"prefix": "r3d100013068",
"synonyms": [
"FRED"
]
},
"r3d100013071": {
"description": "The NCI National Research Data Collection is Australiaβs largest collection of research data, encompassing more than 10 PB of nationally and internationally significant datasets.",
"homepage": "https://geonetwork.nci.org.au/geonetwork/srv/ger/catalog.search",
"name": "NCI Data Portal",
"prefix": "r3d100013071",
"synonyms": [
"NCI Catalogue"
]
},
"r3d100013072": {
"description": "Data products developed and distributed by the National Institute of Standards and Technology span multiple disciplines of research and are widely used in research and development programs by industry and academia.\nNIST's publicly available data sets showcase its committment to providing accurate, well-curated measurements of physical properties, exemplified by the Standard Reference Data program, as well as its committment to advancing basic research.\nIn accordance with U.S. Government Open Data Policy and the NIST Plan for providing public access to the results of federally funded research data, NIST maintains a publicly accessible listing of available data, the NIST Public Dataset List (json). Additionally, these data are assigned a Digital Object Identifier (DOI) to increase the discovery and access to research output; these DOIs are registered with DataCite and provide globally unique persistent identifiers. The NIST Science Data Portal provides a user-friendly discovery and exploration tool for publically available datasets at NIST.\nThis portal is designed and developed with data.gov Project Open Data standards and principles. The portal software is hosted in the usnistgov github repository.",
"homepage": "https://data.nist.gov/sdp/#/",
"name": "NIST Data Discovery",
"prefix": "r3d100013072",
"synonyms": [
"NIST PDR",
"NIST Public Data Repository",
"NIST Science Data Portal"
]
},
"r3d100013073": {
"description": "GTS AI is an Artificial Intelligence Company that offers excellent services to its clients. We use high definition images and use high quality data to analyze and help in Machine Learning Company . We are a dataset provider and we collect data in regards to artificial intelligence.",
"homepage": "https://gts.ai/",
"name": "GTS AI Data Collection",
"prefix": "r3d100013073"
},
"r3d100013076": {
"description": "Research Data TUHH is the institutional repository for research data of Hamburg University of Technology (TUHH)",
"homepage": "https://tore.tuhh.de/handle/11420/2023",
"name": "TUHH Open Research - Research Data TUHH",
"prefix": "r3d100013076",
"synonyms": [
"TORE - Research Data TUHH"
],
"xrefs": {
"hdl": "11420/2023"
}
},
"r3d100013077": {
"description": "Within this project the spatial and visual characteristics of circular enclosures of the early 5th millennium BC in Germany are being investigated.\nThe here presented ever-expanding repository comprises a database of all circular enclosures under investigation. The database entries include the coordinates and a thorough description of each enclosure. Additionally, several resources like skyline and viewshed maps, files of input parameters and plots of astronomical features are deposited.",
"homepage": "http://repository.edition-topoi.org/collection/KGAL",
"name": "The Kreisgraben-Phenomenon",
"prefix": "r3d100013077",
"synonyms": [
"KGAL"
],
"xrefs": {
"doi": " 10.17171/2-9"
}
},
"r3d100013078": {
"description": "The Digital Atlas of Innovations presents the oldest evidence for innovations over a long time period. This collection presents the data/information at the basis of the atlas in stable and citable manner.",
"homepage": "https://repository.edition-topoi.org/collection/BAOI",
"name": "Atlas of Innovations",
"prefix": "r3d100013078",
"synonyms": [
"BAOI"
],
"xrefs": {
"doi": "10.17171/2-11"
}
},
"r3d100013079": {
"description": "data.isric.org is our central location for searching and downloading soil data bases/layers from around the world. ISRIC - World Soil Infomation (WDC-Soils) is a regular member of the ICS World Data System (WDS). We support Open Data whenever possible, respecting inherited rights (licences).",
"homepage": "https://data.isric.org",
"name": "ISRIC Soil Metadata Catalogue",
"prefix": "r3d100013079",
"synonyms": [
"data.isric.org"
],
"xrefs": {
"fairsharing": "FAIRsharing.bLMnnR"
}
},
"r3d100013080": {
"description": "DataStream is an open access platform for sharing information on freshwater health. It currently allows users to access, visualize, and download full water quality datasets collected by Indigenous Nations, community groups, researchers and governments throughout five regional hubs: Atlantic Canada, the Great Lakes and Saint Lawrence region, the Lake Winnipeg Basin, the Mackenzie River Basin and the Pacific region. DataStream was developed by The Gordon Foundation and is carried out in collaboration with regional monitoring networks.",
"homepage": "https://datastream.org/en-ca/platform",
"name": "DataStream",
"prefix": "r3d100013080",
"xrefs": {
"fairsharing": "FAIRsharing.EEDgWH"
}
},
"r3d100013082": {
"description": "Numerous studies on gender relations and gender equality policy in academia regularly produce research data that could be useful for a secondary analysis and for other research topics. At present, only a small amount of research data that was explicitly collected on gender relations in academia is archived. Long-term surveys such as graduate studies or social surveys on students are also available to be used in gender-specific studies.\nCEWS would like to support researchers in their search for research data and at the same time motivate them to archive data from their own projects and thus make them accessible to other researchers by providing search options at GESIS and other data-providing institutions as well as basic information on data archiving.",
"homepage": "https://www.gesis.org/en/cews/portfolio/digital-services/research-data",
"name": "Research Data On Gender Relations In Academia",
"prefix": "r3d100013082",
"synonyms": [
"CEWS Forschungsdaten",
"CEWS Research Data",
"Forschungsdaten Geschlecht und Wissenschaft"
]
},
"r3d100013083": {
"description": "Fox DEN provides investigators with a tool to explore, download and apply statistical models on aggregated data collected for the Fox Insight online clinical study. The Fox Insight study collects patient-reported outcomes and genetic data from people with Parkinson's disease and their loved ones.",
"homepage": "https://foxden.michaeljfox.org/insight/explore/insight.jsp",
"name": "Fox Insight Date Exploration Network",
"prefix": "r3d100013083",
"synonyms": [
"Fox DEN"
],
"xrefs": {
"scr": "022321"
}
},
"r3d100013084": {
"description": "The SURF Data Repository is a user-friendly web-based data publication platform that allows researchers to store, annotate and publish research datasets of any size to ensure long-term preservation and availability of their data. The service allows any dataset to be stored, independent of volume, number of files and structure. A published dataset is enriched with complex metadata, unique identifiers are added and the data is preserved for an agreed-upon period of time. The service is domain-agnostic and supports multiple communities with different policy and metadata requirements.",
"homepage": "https://repository.surfsara.nl",
"name": "SURF Data Repository",
"prefix": "r3d100013084",
"xrefs": {
"fairsharing": "FAIRsharing.7ccc58"
}
},
"r3d100013086": {
"description": "The sources of the data sets include data sets donated by researchers, surveys carried out by SRDA, as well as by government department and other academic organizations. Prior to the release of data sets, the confidentiality and sensitivity of every survey data set are evaluated. Standard data management and cleaning procedures are applied to ensure data accuracy and completeness. In addition, metadata and relevant supplement files are also edited and attached.",
"homepage": "https://srda.sinica.edu.tw/index_en.php",
"name": "Survey Research Data Archive",
"prefix": "r3d100013086",
"synonyms": [
"SRDA"
]
},
"r3d100013090": {
"description": "The UCL Research Data Repository is the institutional data repository of University College London. Based on Figshare, it accepts data deposits from UCL staff and doctoral students from all disciplines. Depositors are encouraged to use CC0 licences to make their data available to the widest possible range of users and the widest range of uses.",
"homepage": "https://rdr.ucl.ac.uk/",
"name": "UCL Research Data Repository",
"prefix": "r3d100013090"
},
"r3d100013095": {
"description": "The information system Graffiti in Germany (INGRID) is a cooperation project between the linguistics department at the University of Paderborn and the art history department at the Karlsruhe Institute of Technology (KIT). As part of the joint project, graffiti image collections will be compiled, stored in an image database and made available for scientific use. At present, more than 100,000 graffiti from the years 1983 to 2018 from major German cities are recorded, including Cologne, Mannheim and Munich.",
"homepage": "https://www.uni-paderborn.de/forschungsprojekte/ingrid/",
"name": "Informationssystem Graffiti in Deutschland (INGRID)",
"prefix": "r3d100013095",
"synonyms": [
"INGRID"
]
},
"r3d100013100": {
"description": "An interactive database hosted by Collaborative Drug Discovery for antibiotic susceptibility data (MIC and IC50). Data is extracted from journal articles and/or contributed by different organizations and individuals. In some cases, the data has not previously been published. Access to the database is open to everyone and can be requested at pewtrusts.org/spark-antibiotic-discovery.\nEffective November 18, 2021, Pew transferred all SPARK data to The University of Queenslandβs Community for Open Antimicrobial Drug Discovery (CO-ADD). Please visit spark.co-add.org https://co-add.org/.",
"homepage": "https://www.pewtrusts.org/en/research-and-analysis/articles/2018/09/21/the-shared-platform-for-antibiotic-research-and-knowledge",
"name": "Shared Platform for Antibiotic Research and Knowledge",
"prefix": "r3d100013100",
"synonyms": [
"SPARK"
],
"xrefs": {
"fairsharing": "FAIRsharing.50cFTB"
}
},
"r3d100013102": {
"description": "mediaTUM β the media and publications repository of the Technical University of Munich:\nmediaTUM supports the publication of digital documents and research data as well as the use of multimedia content in research and teaching.",
"homepage": "https://mediatum.ub.tum.de/?change_language=en",
"name": "mediaTUM",
"prefix": "r3d100013102"
},
"r3d100013103": {
"description": "The Colombian Biodiversity Information Facility (SiB Colombia) is a national initiative established in early 2000 and coordinated by Instituto Humboldt to facilitate free and open access to biodiversity data. It comprises a network of more than 100 organizations (including universities, biological collections, research institutes, environmental authorities and NGOs among others) that work together to ensure that biodiversity data is available to support further research, education, policy making and incentive measures for the conservation and sustainable use of biodiversity.\nSiB Colombiaβs mission is to facilitate the management of biodiversity data by bringing together users, publishers and data producers to support research, education and decision making related to knowledge, conservation and sustainable use of biodiversity and ecosystem services.\nSiB Colombia aims to consolidate the collaborative platform that facilitates the generation, use and democratization of knowledge on the biodiversity of Colombia. Thus, SiB Colombia contributes to a vision of a society that knows and values the biodiversity in which it is immersed, and uses such knowledge for its development.",
"homepage": "https://biodiversidad.co/",
"name": "SiB Colombia Portal de Datos",
"prefix": "r3d100013103",
"synonyms": [
"GBIF Colombia"
]
},
"r3d100013106": {
"description": "The National Archives of the Netherlands (Nationaal Archief), which is situated in The Hague, holds over 3.5 million records that have been created by the central government, organisations and individuals and are of national significance. Many records relate to the colonial and trading history of the Netherlands in the period from 1600 to 1975. The Dutch presence in countries in North and South America, Africa and Asia is reflected within these collections.",
"homepage": "https://www.nationaalarchief.nl",
"name": "e-Depot of the National Archives of the Netherlands",
"prefix": "r3d100013106"
},
"r3d100013107": {
"description": "PsychArchives is a disciplinary repository for psychological science and neighboring disciplines. Accommodating 20 different digital research object (DRO) types, including articles, preprints, research data, code, supplements, preregistrations, tests and multimedia objects, PsychArchives provides a digital space that integrates all research-related content relevant to psychology. PsychArchives is committed to the FAIR principles, facilitating the findability, accessibility, interoperability and reusability of research and research data.",
"homepage": "https://www.psycharchives.org/",
"name": "PsychArchives",
"prefix": "r3d100013107",
"xrefs": {
"fairsharing.legacy": "4726"
}
},
"r3d100013108": {
"description": "The University of Chile Research Data Repository preserves, disseminates and provides access to the research data generated by its academics and researchers, in order to give visibility, guarantee its preservation and facilitate its access and reuse.",
"homepage": "https://datos.uchile.cl/",
"name": "Repositorio de Datos de InvestigaciΓ³n de la Universidad de Chile",
"prefix": "r3d100013108"
},
"r3d100013111": {
"description": "The CRC1211DB is the project-database of the Collaborative Research Centre 1211 \"Earth -Evolution at the dry limit\" (CRC1211, https://sfb1211.uni-koeln.de/) funded by the German Research Foundation (DFG, German Research Foundation β Projektnummer 268236062). The project-database is a new implementation of the TR32DB and online since 2016. It handles all data including metadata, which are created by the involved project participants from several institutions (e.g. Universities of Cologne, Bonn, Aachen, and the Research Centre JΓΌlich) and research fields (e.g. soil and plant sciences, biology, geography, geology, meteorology and remote sensing). The data is resulting from several field measurement campaigns, meteorological monitoring, remote sensing, laboratory studies and modelling approaches. Furthermore, outcomes of the scientists such as publications, conference contributions, PhD reports and corresponding images are collected.",
"homepage": "https://www.crc1211db.uni-koeln.de/site/index.php",
"name": "Collaborative Research Centre 1211 Database",
"prefix": "r3d100013111",
"synonyms": [
"CRC1211DB"
]
},
"r3d100013113": {
"description": "PTB is the national metrology institute of the Federal Republic of Germany. The Open Access Repository of the Physikalisch-Technische Bundesanstalt grants free access to a number of factual datasets and documents that were elaborated at PTB. This includes publications such as the \"PTB-Mitteilungen\", the metrological expert journal of PTB, and numerous of documents from the field of legal metrology.",
"homepage": "https://oar.ptb.de/",
"name": "PTB-OAR",
"prefix": "r3d100013113",
"synonyms": [
"PTB Open Access Repository"
]
},
"r3d100013116": {
"description": "University repository containing publication data and datasets.",
"homepage": "https://uhra.herts.ac.uk/",
"name": "University of Hertfordshire Research Archive",
"prefix": "r3d100013116",
"synonyms": [
"UHRA"
],
"xrefs": {
"opendoar": "882",
"roar": "1386"
}
},
"r3d100013118": {
"description": "B2SHARE allows publishing research data and belonging metadata. It supports different research communities with specific metadata schemas. This server is provided for researchers of the Research Centre Juelich and related communities.",
"homepage": "https://b2share.fz-juelich.de/",
"name": "B2SHARE Server Forschungszentrum JΓΌlich",
"prefix": "r3d100013118",
"xrefs": {
"fairsharing": "FAIRsharing.f1e88c"
}
},
"r3d100013120": {
"description": "The interdisciplinary data platform INPTDAT provides easy access to research data and information from all fields of applied plasma physics and plasma medicine. It aims to support the findability, accessibility, interoperability and re-use of data for the low-temperature plasma physics community.",
"homepage": "https://www.inptdat.de",
"name": "INPTDAT",
"prefix": "r3d100013120",
"synonyms": [
"The Data Platform for Plasma Technology"
],
"xrefs": {
"fairsharing": "FAIRsharing.2VADoR",
"scr": "022167"
}
},
"r3d100013121": {
"description": "DMU Figshare is De Montfort University's institutional research data management platform. It showcases research from staff at the university.",
"homepage": "https://figshare.dmu.ac.uk/",
"name": "DMU Figshare",
"prefix": "r3d100013121",
"synonyms": [
"De Montfort University Data Repository"
]
},
"r3d100013130": {
"description": "PhenoCam is a cooperative network that archives and distributes imagery and derived data products from digital cameras deployed at research sites across North America and around the world.",
"homepage": "https://phenocam.nau.edu/webcam/",
"name": "PhenoCam",
"prefix": "r3d100013130"
},
"r3d100013132": {
"description": "<<>>!!!>>>\nChina Seismic Array Data Management Center(DOI:10.12001/ChinArray.Data) provides ChinArray data, China Air Gunshot experiment data, and China seismic networks data.",
"homepage": "http://www.chinarraydmc.cn/",
"name": "China Seismic Array Data Management Center",
"prefix": "r3d100013132",
"synonyms": [
"δΈε½ε°ιη§ε¦ζ’ζ΅ε°ι΅ζ°ζδΈεΏ"
],
"xrefs": {
"doi": "10.12001/ChinArray.Data"
}
},
"r3d100013133": {
"description": "This Open Data Portal provides access to a wide range of research data and data for research from various institutes, departments, faculties, research projects, libraries, archives, and individuals of the Pontifical Catholic University of Peru. It serves the entire university community, offering an extensive repository of datasets to support academic research and collaboration.",
"homepage": "https://datos.pucp.edu.pe/",
"name": "Portal de Datos Abiertos de la Pontificia Universidad CatΓ³lica del PerΓΊ",
"prefix": "r3d100013133"
},
"r3d100013134": {
"description": "The DataSuds data warehouse provides IRD scientists and their partners with a service to disseminate, preserve and enhance their research data by facilitating their identification and citation. It is one of the elements of the open science system for the South promoted by the IRD.",
"homepage": "https://dataverse.ird.fr/",
"name": "DataSuds",
"prefix": "r3d100013134",
"synonyms": [
"Des donnΓ©es ouvertes pour une science durable au Sud"
]
},
"r3d100013135": {
"description": "Fordatis is the institutional research data repository of the Fraunhofer-Gesellschaft. Fraunhofer-Gesellschaft based in Germany is Europes largest research and technology organization. Fordatis contains research data created by researcher at Fraunhofer. These are data from the engineering, natural sciences and social sciences.",
"homepage": "https://fordatis.fraunhofer.de",
"name": "Fordatis",
"prefix": "r3d100013135",
"synonyms": [
"Forschungsdaten-Repositorium der Fraunhofer-Gesellschaft",
"Research Data Repository of Fraunhofer-Gesellschaft"
]
},
"r3d100013138": {
"description": "Three parts of a database provide published and unpublished chemical analysis results of archaeological ceramics. These are the results of forty years of applying WD-XRF and other mineralogical and physical laboratory methods to the analysis of sherds from excavations and museums. Drawing on some 30,000 analyses from research projects in Europe, Turkey, the near East, and Sudan, the part published here covers the results of three long-term projects: Early pottery in Thessaly, Greece (1,305 records), Firmalampen and other Roman lamps (1,666 records), and Roman and other pottery produced in Central Europe (4,043 records). This collated information provides an opportunity to work directly on published and unpublished data. These can be used as chemical reference groups for comparison for fine ware classification and in provenance studies.",
"homepage": "http://repository.edition-topoi.org/collection/CRMC",
"name": "Chemical composition of ancient ceramics",
"prefix": "r3d100013138",
"synonyms": [
"CRMC"
],
"xrefs": {
"doi": "10.17171/1-11"
}
},
"r3d100013139": {
"description": "Collection of ancient waterclocks including descriptions, images and 3D scans.",
"homepage": "http://repository.edition-topoi.org/collection/BWCP/overview",
"name": "Berlin Waterclock Project",
"prefix": "r3d100013139",
"synonyms": [
"BWCP"
],
"xrefs": {
"doi": "10.17171/2-10"
}
},
"r3d100013140": {
"description": "The architecture of the Myus Temple (Ionian coast) is preserved only in a few very fragmented parts. These components, currently housed in the Staatlichen Museen zu Berlin - Antikensammlung, were digitalized and will be used in the reconstruction of a column from a temple likely dedicated to Dionysos.",
"homepage": "http://repository.edition-topoi.org/collection/MYUS",
"name": "Architectural Fragments of Myus",
"prefix": "r3d100013140",
"synonyms": [
"MYUS"
],
"xrefs": {
"doi": "10.17171/2-14"
}
},
"r3d100013141": {
"description": "The collection contains stature-related and other anthropometric data of 7686 skeletal individuals (including aggregated information for several individuals) from the prehistory of Southwest Asia and Europe. While the focus period of our collection is the Holocene ca. 10 000 to 1000 BC, the data collection also includes older specimens of anatomically modern humans (dating as early as 110 k BP in the case of Qafzeh). The upper date range in some cases extends to around 100 AD, although the great majority of datasets date no later than 600 BC. Correctness and completeness were pursued for all information relevant to stature, i.e. basic information such as sex (after SjΓΈvold 1988) and age (after SzilvΓ‘ssy 1988) as well as the long bone measurements, whereas other measurements were merely inherited from the two integrated older data bases and not explicitly checked. All measurements conform to the definitions given by Martin 1928. To grasp common publication practice in the literature, not only left and right body side, but also mean values from both sides as well as measurements with unknown siding have their own separate fields for the stature-related long bone measurements.",
"homepage": "http://repository.edition-topoi.org/collection/LIVE/overview",
"name": "LiVES Collection of Osteological Anthropometry Digest",
"prefix": "r3d100013141",
"synonyms": [
"LiVES COstA Digest"
],
"xrefs": {
"doi": "10.17171/2-12"
}
},
"r3d100013142": {
"description": "Atlas of the early iron age kurgans (burial mounds) of the Saks in the Land of Seven Rivers between the river Ili and the foothills of the Transili-Alatau as well as in the mountain valleys of the northern Tien-Shans.",
"homepage": "http://repository.edition-topoi.org/collection/KUSS",
"name": "Pyramids of the Steppe / Kazakhstan, Land of Seven Rivers",
"prefix": "r3d100013142",
"synonyms": [
"KUSS"
],
"xrefs": {
"doi": "10.17171/2-13"
}
},
"r3d100013143": {
"description": "Cobalt was commonly used as a colourant in the Egyptian glass industries of the 18th dynasty, dark blue glass being a regular find at palatial and settlement sites, including Amarna and Malqata. The main source of cobalt ore used during this period has been identified in the Egyptian Western Desert, around the oases of Kharga and Dakhla. The data presented here was obtained in order to better understand the chaΓne opΓ©ratoire of Late Bronze Age glass production and -working, in particular with regard to cobalt ore. For this purpose, chemical analysis by portable X-Ray fluorescence (pXRF) was carried out in the field on contextualised archaeological material excavated at the site of Amarna, which cannot be exported from Egypt for analysis. In addition, glass and other vitreous materials from the same site, but without a more precise archaeological context, were analysed in the Egyptian Museum and Papyrus Collection, Berlin. The results of this study demonstrate how cobalt ore from various sub-sources was used in the known workshop sites at Amarna, resulting in a deeper understanding of raw materials use and exchange across this settlemen",
"homepage": "http://repository.edition-topoi.org/collection/KBLT",
"name": "Portable X-Ray fluorescence analysis of Late Bronze Age glass from Amarna",
"prefix": "r3d100013143",
"synonyms": [
"KBLT"
],
"xrefs": {
"doi": " 10.17171/2-15"
}
},
"r3d100013144": {
"description": "The small digitized archive comprises drawings and photos made by Hans J. Nissen, many of which were not included in the book, The Uruk Countryside. Most of the material consists of pottery, but other ceramic artifacts, stone and metal objects as well as inscribed bricks were also documented. All materials were recorded in the field.\nThe goal of this website is to provide online access to this remaining archival documentation of the Uruk-Warka survey.",
"homepage": "http://repository.edition-topoi.org/collection/URUK",
"name": "The Uruk-Warka Survey",
"prefix": "r3d100013144",
"synonyms": [
"URUK"
],
"xrefs": {
"doi": " 10.17171/1-12"
}
},
"r3d100013148": {
"description": "The Pennsieve platform is a cloud-based scientific data management platform focused on integrating complex datasets, fostering collaboration and publishing scientific data according to all FAIR principles of data sharing.\nThe platform is developed to enable individual labs, consortiums, or inter-institutional projects to manage, share and curate data in a secure cloud-based environment and to integrate complex metadata associated with scientific files into a high-quality interconnected data ecosystem. The platform is used as the backend for a number of public repositories including the NIH SPARC Portal and Pennsieve Discover repositories. It supports flexible metadata schemas and a large number of scientific file-formats and modalities.",
"homepage": "https://discover.pennsieve.io/",
"name": "Pennsieve Discover",
"prefix": "r3d100013148",
"synonyms": [
"formerly: Blackfynn Discover"
],
"xrefs": {
"scr": "021677"
}
},
"r3d100013152": {
"description": "Data repository of a meteorological experiment conducted in PerdigΓ£o, Portugal between December 15, 2016 to June 15, 2017.\nThe Perdigao field project is part of a larger joint US/European multi-year program in Portugal. The project is partially funded by the European Union (EU) ERANET+ to provide the wind energy sector with more detailed resource mapping capabilities in the form of a new digital EU wind atlas. A major goal of the PerdigΓ£o field project is to quantify errors of wind resource models against a benchmark dataset collected in complex terrain. The US participation will complement this activity by identifying physical and numerical weaknesses of models and developing new knowledge and methods to overcome such deficiencies.",
"homepage": "https://perdigao.fe.up.pt/",
"name": "Perdigao Field Experiment",
"prefix": "r3d100013152"
},
"r3d100013153": {
"description": "Meteorology, atmospheric science and oceanography, forecasts, current and historical observations for weather, water, space weather data; data analyses and reports.",
"homepage": "http://www.bom.gov.au/metadata/catalogue/index.shtml",
"name": "Australian Bureau of Meteorology data catalogue",
"prefix": "r3d100013153"
},
"r3d100013154": {
"description": "The Duke Research Data Repository is a service of the Duke University Libraries that provides curation, access, and preservation of research data produced by the Duke community. Duke's RDR is a discipline agnostic institutional data repository that is intended to preserve and make public data related to the teaching and research mission of Duke University including data linked to a publication, research project, and/or class, as well as supplementary software code and documentation used to provide context for the data.",
"homepage": "https://research.repository.duke.edu/",
"name": "Duke Research Data Repository",
"prefix": "r3d100013154",
"synonyms": [
"Duke RDR"
],
"xrefs": {
"fairsharing": "FAIRsharing.sbikSF"
}
},
"r3d100013155": {
"description": "ROSA P is the United States Department of Transportation (US DOT) National Transportation Library's (NTL) Repository and Open Science Access Portal (ROSA P). The name ROSA P was chosen to honor the role public transportation played in the civil rights movement, along with one of the important figures, Rosa Parks. To meet the requirements outlined in its legislative mandate, NTL collects research and resources across all modes of transportation and related disciplines, with specific focus on research, data, statistics, and information produced by USDOT, state DOTs, and other transportation organizations. Content types found in ROSA P include textual works, datasets, still image works, moving image works, other multimedia, and maps. These resources have value to federal, state, and local transportation decision makers, transportation analysts, and researchers.",
"homepage": "https://rosap.ntl.bts.gov/",
"name": "ROSA P",
"prefix": "r3d100013155",
"synonyms": [
"NTL Repository",
"Repository & Open Science Access Portal"
],
"xrefs": {
"doi": "10.21949/1398953",
"fairsharing": "FAIRsharing.GbmifP"
}
},
"r3d100013156": {
"description": "Collection of maps showing reconstructions of routes and paths through Rome described in Renaissance guidebooks and antiquarian literature.",
"homepage": "http://repository.edition-topoi.org/collection/WGRM",
"name": "Paths through Rome",
"prefix": "r3d100013156",
"synonyms": [
"WGRM"
],
"xrefs": {
"doi": "10.17171/2-16"
}
},
"r3d100013157": {
"description": "The research project βTextile Revolutionβ integrates studies on the introduction and spread of the woolly sheep and wool usage from different scientific fields. Wool production is closely connected to the domesticated sheep and specifically to those animals that carry a woolly coat. With the keeping of woolly sheep, not only did the economy of prehistoric communities change, but also the textile technology, meaning both, the tools and the techniques for thread and textile making.",
"homepage": "http://repository.edition-topoi.org/collection/WOLL",
"name": "The Textile Revolution",
"prefix": "r3d100013157",
"synonyms": [
"WOLL"
],
"xrefs": {
"doi": "10.17171/2-17"
}
},
"r3d100013158": {
"description": "The research data of the last 6000 years were produced using global and regional climate simulations. Climate models of the present and future climate are applied as background for the simulations. The global climate was simulated in a high spatial resolution by using the so-called time slice approach for chosen periods in the past 6000 years.",
"homepage": "http://repository.edition-topoi.org/collection/ANCM",
"name": "Climate Models",
"prefix": "r3d100013158",
"synonyms": [
"ANCM"
]
},
"r3d100013159": {
"description": "The Digital Collections present selected pieces of all historical collections of the WΓΌrttembergische Landesbibliothek. The aim is to offer digital reproductions of objects which are created within the framework of cataloguing and research projects.",
"homepage": "http://digital.wlb-stuttgart.de/start/",
"name": "Digitale Sammlungen der WΓΌrttembergischen Landesbibliothek",
"prefix": "r3d100013159"
},
"r3d100013160": {
"description": "BioGRID ORCS is an open repository of CRISPR screens compiled through comprehensive curation efforts. The current index is version 1.0.3 and searches more than 49 publications and 58,161 genes to return more than 895 CRISPR screens from 3 major model organism species and 629 cell lines. All screen data are freely provided through our search index and available via download in a wide variety of standardized formats.",
"homepage": "https://orcs.thebiogrid.org",
"name": "BioGRID ORCS",
"prefix": "r3d100013160",
"synonyms": [
"BioGRID Open Repository of CRISPR Screens"
],
"xrefs": {
"fairsharing": "FAIRsharing.lKaOme"
}
},
"r3d100013162": {
"description": "The Gotha Research Library of the University of Erfurt and the Erfurt University Library preserve unique collections of manuscripts, old prints and maps. The Digital Historical Library Erfurt/Gotha provides research-relevant, particularly valuable or frequently used parts of the historical holdings.",
"homepage": "https://dhb.thulb.uni-jena.de/templates/master/template_dhb/index.xml",
"name": "Digitale Historische Bibliothek Erfurt/Gotha",
"prefix": "r3d100013162",
"synonyms": [
"Digital Historical Library Erfurt/Gotha"
]
},
"r3d100013164": {
"description": "The Geoscience Data Exchange (GDEX) mission is to provide public access to data and other digital research assets related to the Earth and its atmosphere, oceans, and space environment. GDEX fulfills federal and scientific publication requirements for open data access by:\nProviding long-term curation and stewardship of research assets;\nEnabling scientific transparency and traceability of research findings in digital formats;\nComplementing existing NCAR community data management and archiving capabilities;\nFacilitating openness and accessibility for the public to leverage the research assets and thereby benefit from NCAR's historical and ongoing scientific research.\nThis mission intentionally supports and aligns with those of NCAR and its sponsor, the National Science Foundation (NSF).",
"homepage": "https://gdex.ucar.edu/",
"name": "Geoscience Data Exchange",
"prefix": "r3d100013164",
"synonyms": [
"GDEX",
"NCAR UCAR Geoscience Data Exchange",
"formerly: DASH Repository"
]
},
"r3d100013165": {
"description": "SUNScholarData is an institutional research data repository which can be used for the registration, archival storage, sharing and dissemination of research data produced or collected in relation to research conducted under the auspices of Stellenbosch University. The repository has a public interface which can be used for finding content. It also has private user accounts which can be used by Stellenbosch University users in order to upload, share or publish their research data. In addition to this Stellenbosch University researchers can also use SUNScholarData in order to collaborate with researchers from other institutions whilst working on their research projects. The repository creates a medium through which Stellenbosch Universityβs research data can be made findable and accessible. It also facilitates the interoperability and re-usability of the universityβs research data.",
"homepage": "https://scholardata.sun.ac.za/",
"name": "SUNScholarData",
"prefix": "r3d100013165",
"xrefs": {
"fairsharing": "FAIRsharing.085e23"
}
},
"r3d100013166": {
"description": "The research data centre at the Federal Motor Transport Authority provides anonymised microdata on driver, vehicles, and road freight transport free of charge for non-commercial and independent scientific research.",
"homepage": "https://www.kba.de/DE/Statistik/Forschungsdatenzentrum/forschungsdatenzentrum_node.html",
"name": "Forschungsdatenzentrum im Kraftfahrt-Bundesamt",
"prefix": "r3d100013166",
"synonyms": [
"FDZ im KBA",
"Research Data Centre at the Federal Motor Transport Authority"
]
},
"r3d100013167": {
"description": "The WSI-Datenzentrum is a service provided by the Institute for Social and Economic Research (WSI). It collects and presents primary and secondary data on e.g. working conditions, co-determination or social policy. Primary data collected are primarily the WSI works councils surveys. Interested academics can use the works councils surveys collected from 2005 to 2011. The records are available to everyone and free of charge after contacting the repository owner and signing a data usage statement.",
"homepage": "https://www.wsi.de/de/wsi-datenzentrum-23411.htm",
"name": "WSI-Datenzentrum",
"prefix": "r3d100013167",
"synonyms": [
"The Institute of Economic and Social Research Data Center",
"WSI Data Center",
"Wirtschafts- und Sozialwissenschaftliches Institut Datenzentrum"
]
},
"r3d100013168": {
"description": "The Research Data Center DeZIM.fdz at the German Center for Integration and Migration Research consists of four interconnected modules: (1) data archive, (2) support for staff and users, (3) online access panel and (4) metadatabase.\nIt offers interested researchers the opportunity to access research data collected in the course of projects carried out at the DeZIM Institute and at the institutes of the DeZIM Research Association. In addition to the access to the data, the DeZIM.fdz organizes an extensive support for the individual data sets in its data offer as well as for various methodological key topics. The regularly conducted surveys within the framework of the Online Access Panel enable scientists at the DeZIM Institute, at the institutes of the DeZIM Research Association, external scientists and the staff of the BMFSFJ to access a pool of potential interviewees. Furthermore, DeZIM.fdz offers an extensive information database, which enables research on studies - both internally and externally archived - that deal with the topics of integration and migration.",
"homepage": "https://fdz.dezim-institut.de/en",
"name": "DeZIM Research Data Center",
"prefix": "r3d100013168",
"synonyms": [
"DSFZ",
"DeZIM-Forschungsdatenzentrum",
"DeZIM.fdz"
]
},
"r3d100013169": {
"description": "European XFEL Data Portal is provided by myMdC, allowing users to access the metadata of scientific data taken at the European XFEL facility. Datasets are linked to experiment proposals, annotated by data collection types, samples and are assigned DOIs to be referenced in publications.\nmyMdC helps data management activities and allows users to find open and own proposals data based on the metadata.",
"homepage": "https://in.xfel.eu/metadata",
"name": "European XFEL Data Portal",
"prefix": "r3d100013169",
"synonyms": [
"European X-Ray Free-Electron Laser Data Management Portal",
"European XFEL Metadata Catalogue"
]
},
"r3d100013171": {
"description": "DaRUS, the data repository of the University of Stuttgart, offers a secure location for research data and codes, be it for the administration of own data, for exchange within a research group, for sharing with selected partners or for publishing.",
"homepage": "https://darus.uni-stuttgart.de",
"name": "DaRUS",
"prefix": "r3d100013171",
"synonyms": [
"Data Repository of the University of Stuttgart",
"Datenrepositorium der UniversitΓ€t Stuttgart"
]
},
"r3d100013173": {
"description": "Data Repository of the University of Minho. Share, publish and manage data from University of Minho research units.",
"homepage": "https://datarepositorium.uminho.pt/",
"name": "DataRepositoriUM",
"prefix": "r3d100013173",
"synonyms": [
"RepositΓ³rio de Dados da Universidade do Minho"
]
},
"r3d100013176": {
"description": "The platform hosts the critical edition of the letters written to Jacob Burckhardt, reconstructing in open access one of the most important European correspondences of the 19th century. Save a few exceptions, these letters are all unpublished. On a later stage, the project aims to publish also Jacob Burckhardtβs letters.\nThe editing process has been carried out using Muruca semantic digital library framework. The Muruca framework has been modified over the project, as the requirements of the philological researchers emerged more clearly. The results are stored in and accessible from the front-end of the platform.",
"homepage": "https://burckhardtsource.org/",
"name": "burckhardtsource.org",
"prefix": "r3d100013176",
"synonyms": [
"Burckhardt Source",
"The European correspondence to Jacob Burckhardt"
]
},
"r3d100013177": {
"description": "Science Data Bank is an open generalist data repository developed and maintained by the Chinese Academy of Sciences Computing and Network Information Center (CNIC). It promotes the publication and reuse of scientific data. Researchers and journal publishers can use it to store, manage and share science data.",
"homepage": "https://www.scidb.cn/en",
"name": "ScienceDB",
"prefix": "r3d100013177",
"synonyms": [
"Science Data Bank",
"scidb"
],
"xrefs": {
"doi": "10.11922/sciencedb.0",
"fairsharing": "fairsharing.tb0bkn"
}
},
"r3d100013178": {
"description": "GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. GNPS aids in identification and discovery throughout the entire life cycle of data; from initial data acquisition/analysis to post publication.",
"homepage": "https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp",
"name": "GNPS: Global Natural Products Social Molecular Networking",
"prefix": "r3d100013178",
"xrefs": {
"fairsharing": "FAIRsharing.8b203d"
}
},
"r3d100013179": {
"description": "CERIC Data Portal allows users to consult and manage data related to experiments carried out at CERIC (Central European Research Infrastructure Consortium) partner facilities. Data made available includes scientific datasets collected during experiments, experiment proposals, samples used and publications if any. Users can search for data based on related metadata (both their own data and other peoples' public data).",
"homepage": "https://data.ceric-eric.eu",
"name": "CERIC Data Portal",
"prefix": "r3d100013179",
"synonyms": [
"CERIC Metadata Catalogue",
"Central European Research Infrastructure Consortium Data Portal"
]
},
"r3d100013180": {
"description": "The UK Government Web Archive captures, preserves, and makes accessible UK central government information published on the web. The web archive includes videos, tweets, images and websites dating from 1996 to present.",
"homepage": "https://www.nationalarchives.gov.uk/webarchive/",
"name": "UK Government Web Archive",
"prefix": "r3d100013180",
"synonyms": [
"UKGWA"
]
},
"r3d100013182": {
"description": "The GIGA (German Institute of Global and Area Studies) researchers generate a large number of qualitative and quantitative research data. On this page you will find descriptions of this research data (\"metadata\") as well as information about the available access options. To facilitate its reuse, and to enhance research transparency, a large part of the GIGA research data is published in datorium, a repository hosted by the GESIS Leibniz Institute for the Social Sciences: https://www.re3data.org/repository/r3d100011062\nOur objective is to offer free access to as much of our data as possible, to guarantee the possibility of its citation, and to secure its safe storage. Metadata of research data that cannot be published open access due to its sensitivity is also shown on this page.",
"homepage": "https://www.giga-hamburg.de/en/publications/research-datasets",
"name": "GIGA Research Data",
"prefix": "r3d100013182",
"synonyms": [
"GIGA Metadata Database"
]
},
"r3d100013187": {
"description": "Genomic Expression Archive (GEA) is a public database of functional genomics data such as gene expression, epigenetics and genotyping SNP array. Both microarray- and sequence-based data are accepted in the MAGE-TAB format in compliance with MIAME and MINSEQE guidelines, respectively. GEA issues accession numbers, E-GEAD-n to experiment and A-GEAD-n to array design.\nData exchange between GEA and EBI ArrayExpress is planned.",
"homepage": "https://www.ddbj.nig.ac.jp/gea/index-e.html",
"name": "Genomic Expression Archive",
"prefix": "r3d100013187",
"synonyms": [
"GEA"
],
"xrefs": {
"fairsharing": "FAIRsharing.hESBcy"
}
},
"r3d100013188": {
"description": "The Marine Data Archive (MDA) is an online repository specifically developed to independently archive data files in a fully documented manner. The MDA can serve individuals, consortia, working groups and institutes to manage data files and file versions for a specific context (project, report, analysis, monitoring campaign), as a personal or institutional archive or back-up system and as an open repository for data publication.",
"homepage": "https://marinedataarchive.org/",
"name": "Marine Data Archive",
"prefix": "r3d100013188",
"synonyms": [
"MDA"
]
},
"r3d100013189": {
"description": "The DRH is a quantitative and qualitative encyclopedia of religious history. It consists of a variety of entry types including religious group and religious place. Scholars contribute entries on their area of expertise by answering questions in standardised polls. Answers are initially coded in the binary format Yes/No or categorically, with comment boxes for qualitative comments, references and links. Experts are able to answer both Yes and No to the same question, enabling nuanced answers for specific circumstances. Media, such as photos, can also be attached to either individual questions or whole entries. The DRH captures scholarly disagreement, through fine-grained records and multiple temporally and spatially overlapping entries. Users can visualise changes in answers to questions over time and the extent of scholarly consensus or disagreement.",
"homepage": "https://religiondatabase.org/landing/",
"name": "Database of Religious History",
"prefix": "r3d100013189",
"synonyms": [
"DRH"
]
},
"r3d100013190": {
"description": "The RΓ©pertoire International des Sources Musicales (RISM) - International Inventory of Musical Sources - is an international, non-profit organization that aims to comprehensively document extant musical sources worldwide. These primary sources are music manuscripts or printed music editions, writings on music theory, and libretti. They are preserved in libraries, archives, churches, schools and private collections.\n\nRISM was founded in Paris in 1952 and is the largest and only international organization that documents written musical sources. RISM records what exists and where it can be found. As a result, by virtue of being cataloged in a comprehensive inventory, music traditions are protected while also being made available to musicologists and musicians alike. Such work is thus not an end in itself, but leads directly to practical applications.",
"homepage": "https://rism.online",
"name": "RΓ©pertoire International des Sources Musicales (RISM)",
"prefix": "r3d100013190",
"synonyms": [
"International Inventory of Music Sources",
"Internationales Quellenlexikon der Musik",
"MiΔdzynarodowy Katalog ΕΉrΓ³deΕ Muzycznych",
"Repertorio Internacional de las Fuentes Musicales",
"Repertorio internazionale delle fonti musicali"
]
},
"r3d100013193": {
"description": "The Humanitarian Data Exchange (HDX) is an open platform for sharing data across crises and organisations. Launched in July 2014, the goal of HDX is to make humanitarian data easy to find and use for analysis. \nHDX is managed by OCHA's Centre for Humanitarian Data, which is located in The Hague. OCHA is part of the United Nations Secretariat and is responsible for bringing together humanitarian actors to ensure a coherent response to emergencies. The HDX team includes OCHA staff and a number of consultants who are based in North America, Europe and Africa.",
"homepage": "https://data.humdata.org/",
"name": "Humanitarian Data Exchange",
"prefix": "r3d100013193",
"synonyms": [
"HDX"
],
"xrefs": {
"fairsharing": "FAIRsharing.81c0a5"
}
},
"r3d100013195": {
"description": "The ZBW Digital Long-Term Archive is a dark archive whose sole purpose is to guarantee the long term availability of the objects stored in it. The storage for the ZBWβs digital objects and their representation platforms is maintained by the ZBW division IT-Infrastructures and is not part of the tasks of the group Digital Preservation. The content that the ZBW provides is accessible via special representation platforms. The special representation platforms are: \nEconStor: an open access publication server for literature on business and economics. ZBW DIGITAL ARCHIVE: it contains born digital material from the domains of business and economics. The content of this archive is accessible in open access via EconBiz, the subject portal for business and economics of the ZBW. National and Alliance Licenses: the ZBW negotiates and curates licenses for electronic products on a national level. This is processed under the framework of the German Research Foundation as well as the Alliance of Science Associations, partly with third party funding, partly solely funded by the ZBW. A part of these electronic products is already hosted by the ZBW and counts among the items that are preserved in the digital archive. 20th Century Press Archive: a portal with access to archival material consisting of press clippings from newspapers covering the time period from the beginning of the 20th century to the year 1949.",
"homepage": "https://www.zbw.eu/de/",
"name": "ZBW Digital Long-Term Archive",
"prefix": "r3d100013195"
},
"r3d100013198": {
"description": "The National Data Archive has been disseminating microdata from surveys and censuses primarily under the Ministry of Statistics and Programme Implementation (MoSPI), Government of India. The archive is powered by the National Data Archive (NADA, ver. 4.3) software with DDI Metadata standard. It serves as a portal for researchers to browse, search, and download relevant datasets freely; even with related documentation (viz. survey methodology, sampling procedures, questionnaires, instructions, survey reports, classifications, code directories, etc). A few data files require the user to apply for approval to access with no charge. Currently, the archive holds more than 144 datasets of the National Sample Surveys (NSS), Annual Survey of Industries (ASI), and the Economic Census as available with the Ministry. However, efforts are being made to include metadata of surveys conducted by the State Governments and other government agencies.",
"homepage": "https://microdata.gov.in/nada43/index.php/home",
"name": "National Data Archive: An Online Microdata Library",
"prefix": "r3d100013198"
},
"r3d100013199": {
"description": "The National Population Health Data Center (NPHDC) is one of the 20 national science data center approved by the Ministry of Science and Technology and the Ministry of Finance. The Population Health Data Archive (PHDA) is developed by NPHDC relying on the Institute of Medical Information, Chinese Academy of Medical Sciences. PHDA mainly receives scientific data from science and technology projects supported by the national budget, and also collects data from other multiple sources such as medical and health institutions, research institutions and social individuals, which is oriented to the national big data strategy and the healthy China strategy. The data resources cover basic medicine, clinical medicine, public health, traditional Chinese medicine and pharmacy, pharmacy, population and reproduction. PHDA supports data collection, archiving, processing, storage, curation, verification, certification and release in the field of population health. Provide multiple types of data sharing and application services for different hierarchy users and help them find, access, interoperate and reuse the data in a safe and controlled environment. PHDA provides important support for promoting the open sharing of scientific data of population health and domestic and foreign cooperation.",
"homepage": "https://www.ncmi.cn/",
"name": "Population Health Data Archive",
"prefix": "r3d100013199",
"synonyms": [
"PHDA",
"δΊΊε£ε₯εΊ·η§ε¦ζ°ζδ»ε¨"
],
"xrefs": {
"fairsharing": "FAIRsharing.xb3lbl"
}
},
"r3d100013200": {
"description": "PRISM Dataverse is the institutional data repository of the University of Calgary, which has its purpose in digital archiving and sharing of research data from researchers. PRISM Dataverse is a data repository hosted through Borealis, a service of the Ontario Council of University Libraries and supported by University of Calgary's Libraries and Cultural Resources. PRISM Dataverse enables scholars to easily deposit data, create data-specific metadata for searchability and publish their datasets.",
"homepage": "https://borealisdata.ca/dataverse/calgary",
"name": "PRISM Dataverse",
"prefix": "r3d100013200",
"synonyms": [
"University of Calgary Data Repository"
]
},
"r3d100013201": {
"description": "This data repository provides access to tropopause parameters estimated from meteorological reanalyses. The tropopause data sets provided on this web site have been created using meteorological reanalyses distributed by the European Centre for Medium-Range Weather Forecasts (ECMWF), the National Aeronautics and Space Administration (NASA), the National Center for Atmospheric Research (NCAR), and the National Centers for Atmospheric Prediction (NCEP). Currently, the repository covers ERA-Interim, MERRA-2, and the NCEP/NCAR Reanalysis 1 for the time period from 2000 to 2018 and ERA5 from 2009 to 2018. The tropopause data files provide geopotential height, pressure, temperature, and water vapor volume mixing ratio for the WMO 1st and 2nd tropopause, the cold point, and the dynamical tropopause.",
"homepage": "https://datapub.fz-juelich.de/slcs/tropopause",
"name": "Reanalysis Tropopause Data Repository",
"prefix": "r3d100013201",
"xrefs": {
"biodbcore": "001613",
"fairsharing": "FAIRsharing.c7bf1b"
}
},
"r3d100013202": {
"description": "Primate Cell Type Database, a publicly available web-accessible archive of intracellular patch clamp recordings and highly detailed three-dimensional digital reconstructions of neuronal morphology.",
"homepage": "https://primatedatabase.com/",
"name": "Primate Cell Type Database",
"prefix": "r3d100013202",
"synonyms": [
"PCTD"
],
"xrefs": {
"fairsharing": "FAIRsharing.7IQk4a"
}
},
"r3d100013204": {
"description": "The University of Victoria Dataverse is a research data repository for our faculty, researchers, and students. It is a general repository, suitable for all disciplines, and accepts a wide range of data types and formats. All deposited files are held in a secure environment on Canadian servers, and depositors can choose to make content available publicly, to specific individuals, or to keep it locked.",
"homepage": "https://borealisdata.ca/dataverse/uvic",
"name": "University of Victoria Dataverse",
"prefix": "r3d100013204",
"synonyms": [
"UVic Dataverse"
]
},
"r3d100013205": {
"description": "The Libraries offer members of the UniversitΓ© de MontrΓ©al community the opportunity to publish their research data in a Dataverse repository space",
"homepage": "https://borealisdata.ca/dataverse/montreal",
"name": "UniversitΓ© de MontrΓ©al β Dataverse",
"prefix": "r3d100013205",
"synonyms": [
"Dataverse UdeM"
]
},
"r3d100013207": {
"description": "LITTERBASE summarises results from 2,046 scientific studies in understandable global maps and figures and opens scientific knowledge on marine litter to the public.\nIn LITTERBASE, we compile information from 2,046 scientific publications on marine litter in a comprehensive data base. This forms the basis of continuously updated maps and figures for policy makers, authorities, scientists, media and the general public on the global amount, distribution and composition of marine litter and its impacts on aquatic life. The portal conveys a broad, fact-based understanding of this environmental problem.",
"homepage": "https://litterbase.awi.de/",
"name": "Litterbase",
"prefix": "r3d100013207",
"synonyms": [
"Online Portal for Marine Litter"
],
"xrefs": {
"biodbcore": "001663",
"fairsharing": "FAIRsharing.1547e3,"
}
},
"r3d100013208": {
"description": "depositar β taking the term from the Portuguese/Spanish verb for to deposit β is an online repository for research data. The site is built by the researchers for the researchers. You are free to deposit, discover, and reuse datasets on depositar for all your research purposes.",
"homepage": "https://data.depositar.io/en/",
"name": "depositar",
"prefix": "r3d100013208",
"synonyms": [
"η η©Άθ³ζε―εζ"
],
"xrefs": {
"fairsharing": "FAIRsharing.58a42b",
"wikidata": "Q98433008"
}
},
"r3d100013209": {
"description": "An increasing number of Language Resources (LT) in the various fields of Human Language Technology (HLT) are distributed on behalf of ELRA via its operational body ELDA, thanks to the contribution of various players of the HLT community. Our aim is to provide Language Resources, by means of this repository, so as to prevent researchers and developers from investing efforts to rebuild resources which already exist as well as help them identify and access those resources.",
"homepage": "https://catalog.elra.info/en-us/",
"name": "ELRA Catalogue of Language Resources",
"prefix": "r3d100013209",
"synonyms": [
"ELRA Catalogue",
"European Language Resources Association Catalogue of Language Resources"
]
},
"r3d100013210": {
"description": "The speaking language atlas gives a multimedia impression of the dialects of the state Baden-WΓΌrttemberg in Germany. The maps of the Speaking Language Atlas of Baden-WΓΌrttemberg are based on two databases:\nSΓΌdwestdeutschen Sprachatlas (SSA) and the Sprachatlas von Nord Baden-WΓΌrttemberg (SNBW). The dialect recordings that form the basis for the maps were carried out at the SSA between 1974 and 1986, but at the SNBW between 2009 and 2012. For the southern part, this means that the maps may present a state of affairs that is no longer valid today.",
"homepage": "https://dh-center.uni-tuebingen.de/escience/sprachatlas/#8/48.676/8.990",
"name": "Sprachatlas Baden-WΓΌrttemberg",
"prefix": "r3d100013210",
"synonyms": [
"Die Dialekte Baden-WΓΌrttembergs",
"Sprachatlas BW",
"Sprechender Sprachatlas"
]
},
"r3d100013212": {
"description": "The Universidad del Rosario Research data repository is an institutional iniciative launched in 2019 to preserve, provide access and promote the use of data resulting from Universidad del Rosario research projects. The Repository aims to consolidate an online, collaborative working space and data-sharing platform to support Universidad del Rosario researchers and their collaborators, and to ensure that research data is available to the community, in order to support further research and contribute to the democratization of knowledge.\n\nThe Research data repository is the heart of an institutional strategy that seeks to ensure the generation of Findable, Accessible, Interoperable and Reusable (FAIR) data, with the aim of increasing its impact and visibility. This strategy follows the international philosophy of making research data βas open as possible and as closed as necessaryβ, in order to foster the expansion, valuation, acceleration and reusability of scientific research, but at the same time, safeguard the privacy of the subjects.\nThe platform storage, preserves and facilitates the management of research data from all disciplines, generated by the researchers of all the schools and faculties of the University, that work together to ensure research with the highest standards of quality and scientific integrity, encouraging innovation for the benefit of society.",
"homepage": "https://research-data.urosario.edu.co/",
"name": "Repositorio de datos de investigaciΓ³n de la Universidad del Rosario",
"prefix": "r3d100013212",
"synonyms": [
"Research data repository of Universidad del Rosario"
]
},
"r3d100013213": {
"description": "<<>>!!!<<< Domestic and foreign research data information in one place It is a national research data portal.",
"name": "KORD Repository",
"prefix": "r3d100013213"
},
"r3d100013215": {
"description": "eData is an institutional repository where STFC staff can deposit data and software that underpin journal articles and other published research.",
"homepage": "https://edata.stfc.ac.uk/",
"name": "eData: the STFC Research Data Repository",
"prefix": "r3d100013215",
"xrefs": {
"opendoar": "10037"
}
},
"r3d100013216": {
"description": "The research data repository of the RUB Research Department Plasmas with Complex Interactions provides access to the data associated with the scientific publications of the PIs.",
"homepage": "https://rdpcidat.rub.de/",
"name": "RDPCIDAT",
"prefix": "r3d100013216",
"synonyms": [
"RUB Research Department Plasmas with Complex Interactions",
"Research Data Repository - Research Department Plasmas with Complex Interactions"
]
},
"r3d100013217": {
"description": "Explore, search, and download data and metadata from your experiments and from public Open Data.\nThe ESRF data repository is intended to store and archive data from photon science experiments done at the ESRF and to store digital material like documents and scientific results which need a DOI and long term preservation. Data are made public after an embargo period of maximum 3 years.",
"homepage": "https://data.esrf.fr",
"name": "ESRF Portal",
"prefix": "r3d100013217",
"synonyms": [
"European Synchrotron Radiation Facility Data Repository"
]
},
"r3d100013218": {
"description": "California Digital Library (CDL) seeks to be a catalyst for deeply collaborative solutions providing a rich, intuitive and seamless environment for publishing, sharing and preserving our scholarsβ increasingly diverse outputs, as well as for acquiring and accessing information critical to the University of Californiaβs scholarly enterprise. University of California Curation Center (UC3) is the digital curation program within CDL. The mission of UC3 is to provide transformative preservation, curation, and research data management systems, services, and initiatives that sustain and promote open scholarship.",
"homepage": "https://cdlib.org/",
"name": "California Digital Library",
"prefix": "r3d100013218",
"synonyms": [
"CDL"
],
"xrefs": {
"nlx": "156041",
"ror": "03yrm5c26",
"scr": "006481"
}
},
"r3d100013219": {
"description": "The European Vitis Database is being meintained since 2007 by the Julius-KΓΌhn-Institut to ensure the long-term and efficient use of grape genetic resources.",
"homepage": "http://www.eu-vitis.de/index.php",
"name": "European Vitis Database",
"prefix": "r3d100013219",
"synonyms": [
"Genetic resources of grapes"
]
},
"r3d100013220": {
"description": "In order to ensure the long-term and efficient use of grape genetic resources in Germany and to guarantee their availability, the Deutsche Genbank Reben was founded in 2010 as a gene bank network. The Deutsche Genbank Reben consists of vine conservation facilities and is thus an essential instrument for securing vine genetic resources in Germany.",
"homepage": "https://www.deutsche-genbank-reben.julius-kuehn.de/",
"name": "Deutsche Genbank Reben",
"prefix": "r3d100013220",
"synonyms": [
"DGR"
]
},
"r3d100013221": {
"description": "In 1984 the establishment of the Vitis International Variety Catalogue (VIVC) took place at the Institute for Grapevine Breeding Geilweilerhof. The concept of a database on grapevine genetic resources was supported by IBPGR (today called Bioversity) and the International Organisation of Vine and Wine (OIV). Today VIVC is an encyclopedic database with around 23000 cultivars, breeding lines and Vitis species, existing in grapevine repositories and/or described in bibliography. It is an information source for breeders, researchers, curators of germplasm repositories and interested wine enthusiasts. Besides cultivar specific passport data, SSR-marker data, comprehensive bibliography and photos are to be found.",
"homepage": "https://www.vivc.de/",
"name": "Vitis International Variety Catalogue",
"prefix": "r3d100013221",
"synonyms": [
"VIVC"
]
},
"r3d100013223": {
"description": ">>>!!!<<< duplicate >>>!!!<<< see https://www.re3data.org/repository/r3d100012397",
"homepage": "https://brainlife.io/",
"name": "Brainlife",
"prefix": "r3d100013223",
"synonyms": [
"brain life"
],
"xrefs": {
"fairsharing": "FAIRsharing.by3p8p"
}
},
"r3d100013224": {
"description": "Born of the desire to systematize analyses from The Cancer Genome Atlas pilot and scale their execution to the dozens of remaining diseases to be studied, GDAC Firehose now sits atop terabytes of analysis-ready TCGA data and reliably executes thousands of pipelines per month. More information: https://broadinstitute.atlassian.net/wiki/spaces/GDAC/",
"homepage": "https://gdac.broadinstitute.org/",
"name": "Broad GDAC Firehose",
"prefix": "r3d100013224",
"synonyms": [
"Genome Data Analysis Center"
]
},
"r3d100013225": {
"description": "The Digital Repository at the University of Maryland (DRUM) collects, preserves, and provides public access to the scholarly output of the university. Faculty and researchers can upload research products for rapid dissemination, global visibility and impact, and long-term preservation.",
"homepage": "https://drum.lib.umd.edu/",
"name": "Digital Repository at the University of Maryland",
"prefix": "r3d100013225",
"synonyms": [
"DRUM"
]
},
"r3d100013226": {
"description": "Finding planets orbiting nearby stars has been a holy grail in astronomy for more than 400 years. We began working on this problem 30 years ago, at a time when there were no known extrasolar planets. In late 1995 we began routinely finding planets around the nearest stars. Since then we have found several hundred planets, including the first sub-saturn mass planet, the first neptune mass planet, the first terrestrial mass planet, the first multiple planet system, and the first transiting planet.",
"homepage": "https://ebps.carnegiescience.edu/",
"name": "The Earthbound Planet Search",
"prefix": "r3d100013226",
"synonyms": [
"EBPS"
]
},
"r3d100013227": {
"description": "Hakai Data stores and shares research information associated with Hakai Institute. The Hakai Institute is a scientific research institution that advances long-term research at remote locations on the coastal margin of British Columbia, Canada. Hakai Data Systems: Data Catalogue, Sensor Network, Geospatial Data, Weather Stations and Webcams, ERDDAP Data Server",
"homepage": "https://data.hakai.org/",
"name": "Hakai Data",
"prefix": "r3d100013227",
"synonyms": [
"Hakai Institute Data Systems"
]
},
"r3d100013228": {
"description": "The worldβs largest collection of TCR and BCR sequences. Easily incorporate millions of sequences worth of public data into your next papers and projects using immunoSEQ Analyzer. Construct your own projects, draw your own conclusions, and freely publish new discoveries.",
"homepage": "https://clients.adaptivebiotech.com/immuneaccess",
"name": "immuneACCESS",
"prefix": "r3d100013228",
"synonyms": [
"immune ACCESS"
]
},
"r3d100013230": {
"description": "The Million Song Dataset is a freely-available collection of audio features and metadata for a million contemporary popular music tracks.\nThe core of the dataset is the feature analysis and metadata for one million songs, provided by The Echo Nest. The dataset does not include any audio, only the derived features. Note, however, that sample audio can be fetched from services like 7digital, using code we provide.",
"homepage": "http://millionsongdataset.com/",
"name": "Million Song Dataset",
"prefix": "r3d100013230",
"synonyms": [
"MSD"
]
},
"r3d100013232": {
"description": "<<>>!!!>>>",
"homepage": "https://dataportal.cmcc.it/home",
"name": "CMCC Data Portal",
"prefix": "r3d100013232"
},
"r3d100013233": {
"description": "PQR is an online database of molecular properties predicted from quantum mechanics with integrated capabilities for molecular visualization and data sharing. ased on the number of molecules, PQR is currently the largest open database of molecular quantum calculations. PQR features interactive high-quality rendering of molecular structures and properties on computers, tablets, and cell phones and allows to efficiently share data via digital object identifiers (DOI) and scannable QR barcodes.",
"homepage": "https://pqr.pitt.edu/",
"name": "Pitt Quantum Repository",
"prefix": "r3d100013233",
"synonyms": [
"PQR"
]
},
"r3d100013235": {
"description": "Institutional research data repository of Riga Technical University (RTU). The aim is to collect and store scientific research data and other relevant information in all fields of knowledge of RTU, enabling free, easy and convenient access to it.",
"homepage": "https://ortus.rtu.lv/science/en/datamodule/search",
"name": "RTU research data repository",
"prefix": "r3d100013235",
"synonyms": [
"ORTUS",
"Riga Technical University Research Outputs and Resources",
"RΔ«gas TehniskΔ universitΔte ZinΔtniskΔs darbΔ«bas rezultΔti un resursi"
]
},
"r3d100013236": {
"description": "The Social Science Japan Data Archive (SSJDA) collects, maintains, and provides access to the academic community, a vast archive of social science data (quantitative data obtained from social surveys) for secondary analyses.",
"homepage": "https://csrda.iss.u-tokyo.ac.jp/english/infrastructure/",
"name": "Social Science Japan Data Archive",
"prefix": "r3d100013236",
"synonyms": [
"SSJ Data Archive",
"SSJDA"
]
},
"r3d100013237": {
"description": "The Balearic Islands Coastal Observing and Forecasting System (ICTS SOCIB) is a multi-platform distributed and integrated system that provides streams of oceanographic data products, and modelling services. It supports operational oceanography in a Spanish, European, and international framework and contributes to the needs of marine and coastal research in a global change context. ICTS SOCIB coordinates the deployment and data management of a wide range of equipment and models from eight facilities. It also manages data from external international institutions and collaborates with international aggregators for the dissemination of ocean data.",
"homepage": "https://www.socib.es/data/",
"name": "ICTS SOCIB Data Repository",
"prefix": "r3d100013237",
"synonyms": [
"Balearic Islands Coastal Observing and Forecasting System Data Repository",
"ICTS SOCIB Data Repository",
"Repositori de Dades del Sistema d'ObservaciΓ³ i PredicciΓ³ Costaner de les Illes Balears",
"Repositorio de Datos del Sistema de ObservaciΓ³n y PredicciΓ³n Costero de las Islas Baleares"
]
},
"r3d100013238": {
"description": "Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.",
"homepage": "https://www.bioconductor.org/",
"name": "Bioconductor",
"prefix": "r3d100013238",
"synonyms": [
"Open Source Software for Bioinformatics"
],
"xrefs": {
"fairsharing": "FAIRsharing.81ettx",
"nif": "0000-10445",
"omics": "01759",
"scr": "006442"
}
},
"r3d100013239": {
"description": "Built on the Islandora digital repository framework, the UPEI hosted Published and Archived Data (data.upei.ca) service provides researchers with a place to securely publish or archive their research datasets.",
"homepage": "https://data.upei.ca/",
"name": "University of Prince Edward Island Data (Beta)",
"prefix": "r3d100013239"
},
"r3d100013240": {
"description": "The UTM Data Centre is responsible for managing spatial data acquired during oceanographic cruises on board CSIC research vessels (RV Sarmiento de Gamboa, RV GarcΓa del Cid) and RV HespΓ©rides.\nThe aim is, on the one hand, to disseminate which data exist and where, how and when they have been acquired. And on the other hand, to provide access to as much of the interoperable data as possible, following the FAIR principles, so that they can be used and reused.\n\nFor this purpose, the UTM has a Spatial Data Infrastructure at a national level that consists of several services:\n\nOceanographic Cruise and Data Catalogue\nIncluding metadata from more than 600 cruises carried out since 1991, with links to documentation associated to the cruise, navigation maps and datasets\n\nGeoportal\nGeospatial data mapping interface\n\nUnderway Plot & QC\nVisualization, Quality Control and conversion to standard format of meteorological data and temperature and salinity of surface water\n\nAt an international level, the UTM is a National Oceanographic Data Centre (NODC) of the Distributed European Marine Data Infrastructure SeaDataNet, to which the UTM provides metadata published in the Cruise Summary Report Catalog and in the data catalog Common Data Index Catalog, as well as public data to be shared.",
"homepage": "http://data.utm.csic.es",
"name": "UTM-CSIC Data Centre",
"prefix": "r3d100013240",
"synonyms": [
"Centro de Datos de la Unidad de TecnologΓa Marina",
"Marine Technology Unit Data Centre"
]
},
"r3d100013241": {
"description": "Welcome to the York Research Database, where you can find all our research staff, projects, publications and organisational units, and explore the connections between them all. The university of York is a member of the Russell Group of research-intensive universities.",
"homepage": "https://pure.york.ac.uk/portal/",
"name": "York Research Database",
"prefix": "r3d100013241",
"synonyms": [
"YRD"
]
},
"r3d100013242": {
"description": "Institutional Repository of the University of Antioquia coordinated by the Libraries System. Here you can consult and download full text documents of the scientific, academic and cultural production of our university community.",
"homepage": "https://bibliotecadigital.udea.edu.co/",
"name": "Repositorio Institucional Universidad de Antioquia",
"prefix": "r3d100013242"
},
"r3d100013243": {
"description": "Welcome to Smithsonian Open Access, where you can download, share, and reuse millions of the Smithsonianβs imagesβright now, without asking. With new platforms and tools, you have easier access to nearly 3 million 2D and 3D digital items from our collectionsβwith many more to come. This includes images and data from across the Smithsonianβs 19 museums, nine research centers, libraries, archives, and the National Zoo.",
"homepage": "https://www.si.edu/openaccess",
"name": "Smithsonian Open Access",
"prefix": "r3d100013243"
},
"r3d100013248": {
"description": "The Migrant Integration Policy Index (MIPEX) is a unique tool that measures policies to integrate migrants in all EU Member States, Australia, Canada, Iceland, Japan, South Korea, New Zealand, Norway, Switzerland, Turkey and the USA. 167 policy indicators have been developed to create a rich, multi-dimensional picture of migrantsβ opportunities to participate in society. The index is a useful tool to evaluate and compare what governments are doing to promote the integration of migrants in all the countries analysed.",
"homepage": "https://www.mipex.eu/",
"name": "Migrant Integration Policy Index",
"prefix": "r3d100013248",
"synonyms": [
"MIPEX"
]
},
"r3d100013257": {
"description": "<<>>!!!>>>\n\nThe Historical Data Centre Saxony-Anhalt was founded in 2008. Its main tasks are the computer-aided provision, processing and evaluation of historical research data, the development of theoretically consolidated normative data and vocabularies as well as the further development of methods in the context of digital humanities, research data management and quality assurance.\nThe \"Historical Data Centre Saxony-Anhalt\" sees itself as a central institution for the data service of historical data in the federal state of Saxony-Anhalt and is thus part of a nationally and internationally linked infrastructure for long-term data storage and use. The Centre primarily acquires individual-specific microdata for the analysis of life courses, employment biographies and biographies (primarily quantitative, but also qualitative data), which offer a broad interdisciplinary and international analytical framework and meet clearly defined methodological and technical requirements. The studies are processed, archived and - in compliance with data protection and copyright conditions - made available to the scientifically interested public in accordance with internationally recognized standards. The degree of preparation depends on the type and quality of the study and on demand. Reference studies and studies in high demand are comprehensively documented - often in cooperation with primary researchers or experts - and summarized in data collections. \nThe Historical Data Centre supports researchers in meeting the high demands of research data management. This includes the advisory support of the entire life cycle of data, starting with data production, documentation, analysis, evaluation, publication, long-term archiving and finally the subsequent use of data. In cooperation with other infrastructure facilities of the state of Saxony-Anhalt as well as national and international, interdisciplinary data repositories, the Data Centre provides tools and infrastructures for the publication and long-term archiving of research data. Together with the University and State Library of Saxony-Anhalt, the Data Centre operates its own data repository as well as special workstations for the digitisation and analysis of data.\nThe Historical Data Centre aims to be a contact point for very different users of historical sources. We collect data relating to historical persons, events and historical territorial units.",
"homepage": "https://www.geschichte.uni-halle.de/struktur/hist-data/daten/",
"name": "Historical Data Centre Saxony-Anhalt",
"prefix": "r3d100013257",
"synonyms": [
"Historisches Datenzentrum Sachsen-Anhalt"
]
},
"r3d100013258": {
"description": "Research Data @PUC-Rio is an aggregator to make it easier to access Resarch Data among many other digital contents on the Maxwell Repository. All datasets must be licensed under a CC License (as stated on the homepage of the aggregator) to be made available on the Maxwell System (https:\\\\www.maxwell.vrac.puc-rio.br). All interfaces and metadata shown on the aggregator are in English though all contents are described in Portuguese too.",
"homepage": "https://www.maxwell.vrac.puc-rio.br/projetosEspeciais/ResearchData/index.php?b=1",
"name": "Open Research Data @PUC-Rio",
"prefix": "r3d100013258"
},
"r3d100013260": {
"description": "AmeriFlux is a network of PI-managed sites measuring ecosystem CO2, water, and energy fluxes in North, Central and South America. It was established to connect research on field sites representing major climate and ecological biomes, including tundra, grasslands, savanna, crops, and conifer, deciduous, and tropical forests. As a grassroots, investigator-driven network, the AmeriFlux community has tailored instrumentation to suit each unique ecosystem. This βcoalition of the willingβ is diverse in its interests, use of technologies and collaborative approaches. As a result, the AmeriFlux Network continually pioneers new ground.",
"homepage": "https://ameriflux.lbl.gov/",
"name": "AmeriFlux",
"prefix": "r3d100013260",
"synonyms": [
"Measuring carbon, water and energy flux across the Americas"
],
"xrefs": {
"fairsharing": "FAIRsharing.a784f5"
}
},
"r3d100013261": {
"description": "Smithsonian figshare is best for sharing data that need a DOI including those that underlie peer-reviewed publications; bounded datasets of mixed formats; or data that is periodically updated and needs to be versioned. See the Figshare Confluence site for more information.",
"homepage": "https://smithsonian.figshare.com/ResearchData",
"name": "Smithsonian figshare",
"prefix": "r3d100013261",
"synonyms": [
"Smithsonian Research Data",
"The Smithsonian research repository"
]
},
"r3d100013262": {
"description": "Institutional repository of Universidad TecnolΓ³gica de BolΓvar. Containing historical Photo collection.",
"homepage": "https://repositorio.utb.edu.co/",
"name": "Repositorio Digital UTB",
"prefix": "r3d100013262",
"xrefs": {
"opendoar": " 9623"
}
},
"r3d100013263": {
"description": "FaceBase is a collaborative NIDCR-funded project that houses comprehensive data in support of advancing research into craniofacial development and malformation. It serves as a community resource by curating large datasets of a variety of types from the craniofacial research community and sharing them via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this project is to facilitate cooperation and collaboration between the central coordinating center (ie, the Hub) and the craniofacial research community.",
"homepage": "https://www.facebase.org",
"name": "FaceBase",
"prefix": "r3d100013263",
"xrefs": {
"fairsharing": "FAIRsharing.mqvqde",
"nlx": "151372",
"scr": "005998"
}
},
"r3d100013265": {
"description": "An open resource for intermolecular interactions",
"homepage": "https://suprabank.org/",
"name": "SupraBank",
"prefix": "r3d100013265",
"xrefs": {
"fairsharing": "FAIRsharing.vjWUT7"
}
},
"r3d100013266": {
"description": "With Open Science OVGU the Otto-von-Guericke University provides its scientists with a research data repository. Measurement data, laboratory values, survey data, methodical test procedures, etc. can be archived in Open Science OVGU and made available to the scientific community via Open Access.",
"homepage": "https://open-science.ub.ovgu.de/home",
"name": "Open Science OVGU",
"prefix": "r3d100013266",
"synonyms": [
"Repository for Research Data and Publications of OVGU"
]
},
"r3d100013268": {
"description": "JHU has stopped collecting data as of 03/10/2023\nAfter three years of around-the-clock tracking of COVID-19 data from around the world, Johns Hopkins has discontinued the Coronavirus Resource Centerβs operations. The siteβs two raw data repositories will remain accessible for information collected from 1/22/20 to 3/10/23 on cases, deaths, vaccines, testing and demographics.\n\nCoronavirus COVID-19 Global Cases by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU). Johns Hopkins experts in global public health, infectious disease, and emergency preparedness have been at the forefront of the international response to COVID-19. This website is a resource to help advance the understanding of the virus, inform the public, and brief policymakers in order to guide a response, improve care, and save lives. All data collected and displayed are made freely available through a GitHub repository https://github.com/CSSEGISandData/COVID-19, along with the feature layers of the dashboard, which are now included in the ESRI Living Atlas: https://livingatlas.arcgis.com/en/home/",
"homepage": "https://coronavirus.jhu.edu/map.html",
"name": "COVID-19 Interactive Map",
"prefix": "r3d100013268",
"synonyms": [
"Johns Hopkins Coronavirus Resource Center"
],
"xrefs": {
"fairsharing": "FAIRsharing.5824e1"
}
},
"r3d100013271": {
"description": "Launched in February 2020, data.sciencespo is a repository that offers visibility, sharing and preservation of data collected, curated and processed at Sciences Po. The repository is based on the Dataverse open-source software and organised into collections:\nCDSP Collection \nThis collection managed by the Centre des donnΓ©es socio-politiques (CDSP) includes the catalogue of surveys, in the social science and humanities, processed and curated by CDSP engineers since 2005. This catalogue brings together surveys produced at Sciences Po and other French and international institutions. \n- Sciences Po collection (self-deposit)\nThis collection, which is managed by the Direction des ressources et de l'information scientifique (DRIS), is intended to host data produced by researchers affiliated with Sciences Po, following the self-deposit process assisted by the Library's staff.",
"homepage": "https://data.sciencespo.fr",
"name": "data.sciencespo",
"prefix": "r3d100013271",
"synonyms": [
"Research data repository of Sciences Po"
]
},
"r3d100013272": {
"description": "ReefTEMPS is a temperature, pressure, salinity and other observables sensor network in coastal area of South, West and South West of Pacific ocean, driven by UMR ENTROPIE. It is an observatory service from the French national research infrastructure ILICO for βcoastal environmentsβ. Some of the networkβs sensors have been deployed since 1958. Nearly hundred sensors are actually deployed in 14 countries covering an area of more than 8000 km from East to West. The data are acquired at different rates (from 1sec to 30 mn) depending on sensors and sites. They are processed and described using Climate and Forecast Metadata Convention at the end of oceanographic campaigns organized for sensors replacement every 6 months to 2 years.",
"homepage": "https://www.reeftemps.science/en/home/",
"name": "ReefTEMPS",
"prefix": "r3d100013272",
"synonyms": [
"Portail d'information du réseau Réseau d'observation des eaux côtières du Pacifique insulaire"
],
"xrefs": {
"fairsharing": "FAIRsharing.5ftlhl"
}
},
"r3d100013273": {
"description": "RosDok is the platform of the University of Rostock for online publication and permanent archiving of digital documents.",
"homepage": "https://rosdok.uni-rostock.de/",
"name": "RosDok",
"prefix": "r3d100013273",
"synonyms": [
"RosDok - Rostocker Dokumentenserver",
"RosDok β Publikationsserver der UniversitΓ€t Rostock",
"RosDok β Rostock University Publication Server"
]
},
"r3d100013275": {
"description": "GRO.data is a research data repository for the GΓΆttingen Campus. Belonging researchers can use it for free. It serves different purposes such as: to simply preserve datasets, to keep track of changes across several versions, to share data with colleagues, to make data itself publicly available, to receive a persistent identifier upon publications.",
"homepage": "https://data.goettingen-research-online.de/",
"name": "GRO.data",
"prefix": "r3d100013275",
"synonyms": [
"GΓΆttingen Research Online"
]
},
"r3d100013276": {
"description": "The Arctic Permafrost Geospatial Centre (APGC) is an Open Access Circum-Arctic Geospatial Data Portal that promotes, describes and visualizes geospatial permafrost data. A data catalogue and a WebGIS application allow to easily discover and view data and metadata. Data can be downloaded directly via link to the publishing data repository.",
"homepage": "https://apgc.awi.de/",
"name": "Arctic Permafrost Geospatial Centre",
"prefix": "r3d100013276",
"synonyms": [
"APGC"
],
"xrefs": {
"fairsharing": "FAIRsharing.hrM7RP"
}
},
"r3d100013280": {
"description": "ArcGIS 'Living Atlas of the World is a unique collection of worldwide geographic information. It contains maps, apps and data layers that support you in your work.\nCorona Virus resources https://coronavirus-resources.esri.com/",
"homepage": "https://livingatlas.arcgis.com/",
"name": "Living Atlas of the World",
"prefix": "r3d100013280",
"synonyms": [
"ArcGIS Living Atlas of the World"
]
},
"r3d100013283": {
"description": "FactGrid is a Wikibase instance designed to be used by historians with a focus on international projects. The database is hosted by the University of Erfurt and coordinated at the Gotha Research Centre. Partners in joint ventures are Wikimedia Germany as the software provider and the German National Library in a project to open the GND to international research.",
"homepage": "https://database.factgrid.de/wiki/Main_Page",
"name": "FactGrid",
"prefix": "r3d100013283",
"synonyms": [
"FactGrid: Eine Datenbank fΓΌr die Geschichtswissenschaften",
"FactGrid: una base de datos para estudios histΓ³ricos",
"FactGridΒ : Une base de donnΓ©es pour les Γ©tudes historiques",
"a database for historians"
]
},
"r3d100013285": {
"description": "The National Tibetan Plateau/Third Pole Environment Data Center (TPDC) is one of a first group of 20 national data centers approved by the Ministry of Science and Technology of China in 2019. It possesses the most comprehensive scientific data on the Tibetan Plateau and surrounding regions of any data centers in China. TPDC provides online and offline data download services according to TPDC data Sharing Protocol with bilingual of Chinese and English (https://data.tpdc.ac.cn/). There are more than 2400 datasets, covering geography, atmospheric science, cryospheric science, hydrology, ecology, geology, geophysics, natural resource science, social economy, and other fields. There are more than 30000 registered users. TPDC complies with the principle of βFindable, Accessible, Interoperable, and Reusable (FAIR)β, and has adopted a series of measures to protect the intellectual property by giving credit to data providers. Digital Object Identifiers (DOI) are used for scientific data access, tracking, and citation. The Creative Commons 4.0 protocol is used for data re-distribution and re-use. Data users are required to cite the datasets and provide necessary acknowledgement in order to give credit to data authors as journal papers. The data citation references are provided on the TPDC landing page of each dataset.",
"homepage": "https://data.tpdc.ac.cn/home",
"name": "National Tibetan Plateau/Third Pole Environment Data Center",
"prefix": "r3d100013285",
"synonyms": [
"TPDC"
],
"xrefs": {
"fairsharing": "FAIRsharing.YzTIE8"
}
},
"r3d100013286": {
"description": "For many years, the Badische Landesbibliothek has been digitising outstanding holdings from its cultural fundus in order to make them available to interested parties worldwide free of charge. This heritage includes medieval manuscripts and valuable music as well as copyright-free sources, reference works and important individual writings on Baden and its history.",
"homepage": "https://digital.blb-karlsruhe.de/",
"name": "BLB Digitale Sammlungen",
"prefix": "r3d100013286",
"synonyms": [
"BLB Digital Collections"
]
},
"r3d100013287": {
"description": "Ktisis is an open access institutional repository gathering any digital material relating to the various activities of the Cyprus University of Technology, especially original research material produced by the members of the University. Defined in this framework, Ktisis demonstrates the intellectual life and the research activities of the University, preserving, spreading and promoting the scientific research to the local and international community. Ktisis was named after the symbol of the Cyprus University of Technology depicting Ktisis, the spirit of creation.",
"homepage": "https://ktisis.cut.ac.cy",
"name": "KTISIS",
"prefix": "r3d100013287",
"synonyms": [
"Institutional repository Cyprus University of Technology",
"ΞΞ€ΞΞ£ΞΞ£"
],
"xrefs": {
"opendoar": "1540",
"roar": "776"
}
},
"r3d100013291": {
"description": "The MOSES Data Discovery Portal is the central component of the MOSES data management infrastructure. It holds the metadata of MOSES campaigns, sensors and data and enables high-performance data searches. In addition, it provides access to the decentral data repositories and infrastructures of the participating Helmholtz centers where MOSES data is stored.",
"homepage": "https://moses-data.gfz-potsdam.de/onestop/#/",
"name": "MOSES Data Discovery Portal",
"prefix": "r3d100013291",
"synonyms": [
"Modular Observation Solutions for Earth Systems Data Discovery Portal"
],
"xrefs": {
"fairsharing": "FAIRsharing.36b459"
}
},
"r3d100013292": {
"description": "The COVID-19 Data Portal was launched in April 2020 to bring together relevant datasets for sharing and analysis in an effort to accelerate coronavirus research. It enables researchers to upload, access and analyse COVID-19 related reference data and specialist datasets as part of the wider European COVID-19 Data Platform.",
"homepage": "https://www.covid19dataportal.org/",
"name": "COVID-19 Data Portal",
"prefix": "r3d100013292",
"xrefs": {
"fairsharing": "FAIRsharing.f3b7a9"
}
},
"r3d100013293": {
"description": "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines, Naturally immortal cell lines (example: stem cell lines), Finite life cell lines when those are distributed and used widely, Vertebrate cell line with an emphasis on human, mouse and rat cell lines, Invertebrate (insects and ticks) cell lines. Its scope does not include: Primary cell lines (with the exception of the finite life cell lines described above), Plant cell lines. Cellosaurus was initiated to be used as a cell line controlled vocabulary in the context of the neXtProt knowledgebase, but it quickly become apparent that there was a need for a cell line knowledge resource that would serve the needs of individual researchers, cell line distributors and bioinformatic resources. This leads to an increase of the scope and depth of the content of the Cellosaurus. The Cellosaurus is a participant of the Resource Identification Initiative and contributes actively to the work of the International Cell Line Authentication Committee (ICLAC). It is a Global Core Biodata Resource, an ELIXIR Core Data Resource and an IRDiRC Recognized Resource.",
"homepage": "https://www.cellosaurus.org/",
"name": "Cellosaurus",
"prefix": "r3d100013293",
"synonyms": [
"Cellosaurus - a knowledge resource on cell lines"
],
"xrefs": {
"fairsharing": "FAIRsharing.hkk309",
"scr": "013869"
}
},
"r3d100013294": {
"description": "The mission of ChiCTR is to βunite clinicians, clinical epidemiologists, biostatisticians, epidemiologists and healthcare managers both at home and abroad, to manage clinical trials in a strict and scientific manner, and to promote their quality in China, so as to provide reliable evidence from clinical trials for health care workers, consumers and medical policy decision makers, and also to use medical resources more effectively to provide better service for Chinese people and all human beings.",
"homepage": "https://www.chictr.org.cn",
"name": "Chinese Clinical Trial Register",
"prefix": "r3d100013294",
"synonyms": [
"ChiCTR"
],
"xrefs": {
"biodbcore": "001438",
"fairsharing": "FAIRsharing.4ca1fb"
}
},
"r3d100013295": {
"description": "The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms, entered into the IntAct molecular interaction database (https://www.ebi.ac.uk/intact/). Data includes protein-only complexes as well as protein-small molecule and protein-nucleic acid complexes. All complexes are derived from physical molecular interaction evidences extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background. All complexes are tagged with Evidence and Conclusion Ontology codes to indicate the type of evidence available for each entry.",
"homepage": "https://www.ebi.ac.uk/complexportal/home",
"name": "Complex Portal",
"prefix": "r3d100013295",
"synonyms": [
"CP"
],
"xrefs": {
"fairsharing": "FAIRsharing.wP3t2"
}
},
"r3d100013297": {
"description": "The ERGβ (Exploration of energization and Radiation in Geospace) project is a mission to elucidate acceleration and loss mechanisms of relativistic electrons around Earth during geospace storms. The project consists of the satellite observation team, the ground-based network observation team, and the integrated data analysis/simulation team. The science center archives data related to the ERG project, releases the data to the public, develops integrated analysis tools for the data, and promotes studies related to the ERGβ project.",
"homepage": "https://ergsc.isee.nagoya-u.ac.jp/",
"name": "ERG-Science Center",
"prefix": "r3d100013297",
"synonyms": [
"ERG-SC",
"Exploration of energization and Radiation in Geospace Science Center"
]
},
"r3d100013298": {
"description": "The Coronavirus Antiviral Research Database is designed to expedite the development of SARS-CoV-2 antiviral therapy. It will benefit global coronavirus drug development efforts by (1) promoting uniform reporting of experimental results to facilitate comparisons between different candidate antiviral compounds; (2) identifying gaps in coronavirus antiviral drug development research; (3) helping scientists, clinical investigators, public health officials, and funding agencies prioritize the most promising compounds and repurposed drugs for further development; (4) providing an objective, evidenced-based, source of information for the public; and (5) creating a hub for the exchange of ideas among coronavirus researchers whose feedback is sought and welcomed. By comprehensively reviewing all published laboratory, animal model, and clinical data on potential coronavirus therapies, the Database makes it unlikely that promising treatment approaches will be overlooked. In addition, by making it possible to compare the underlying data associated with competing treatment strategies, stakeholders will be better positioned to prioritize the most promising anti-coronavirus compounds for further development.",
"homepage": "https://covdb.stanford.edu/",
"name": "Coronavirus Antiviral Research Database",
"prefix": "r3d100013298",
"synonyms": [
"COVDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.ec45c4"
}
},
"r3d100013299": {
"description": "The COVID-19 pandemic has affected every country in the world. It is well documented that those most susceptible to the worst outcomes of COVID-19 are the immunocompromised and those with underlying comorbidities. Therefore, patients requiring treatment for COVID-19 will also be on additional medication, posing a risk for drug-drug interactions (DDIs). In order to address this, the Liverpool Drug Interactions website team developed this freely available drug interactions resource to provide information on the likelihood of interactions between the experimental agents used for the treatment of COVID-19 and commonly prescribed co-medications.",
"homepage": "https://www.covid19-druginteractions.org/",
"name": "Liverpool COVID-19 Drug Interactions",
"prefix": "r3d100013299",
"xrefs": {
"fairsharing": "FAIRsharing.37b795"
}
},
"r3d100013300": {
"description": "<<>>!!!>>>",
"homepage": "https://covid19.elsevierpure.com/",
"name": "COVID-19 Research Collaborations",
"prefix": "r3d100013300",
"xrefs": {
"fairsharing.legacy": "2926"
}
},
"r3d100013301": {
"description": "DisGeNET is a discovery platform containing one of the largest publicly available collections of genes and variants associated to human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models and the scientific literature. DisGeNET data are homogeneously annotated with controlled vocabularies and community-driven ontologies. Additionally, several original metrics are provided to assist the prioritization of genotypeβphenotype relationships.",
"homepage": "https://www.disgenet.org/",
"name": "DisGeNET",
"prefix": "r3d100013301",
"synonyms": [
"A knowledge base for disease genomics"
],
"xrefs": {
"fairsharing": "FAIRsharing.fssydn",
"nlx": "151710",
"scr": "006178"
}
},
"r3d100013302": {
"description": "The European Union Clinical Trials Register allows you to search for protocol and results information on interventional clinical trials that are conducted in the European Union (EU) and the European Economic Area (EEA) and clinical trials conducted outside the EU / EEA that are linked to European paediatric-medicine development. The EU Clinical Trials Register is part of EudraPharm, which is the community database of authorised medicinal products. The website provides public access to information extracted from the European Union Drug Regulating Authorities Clinical Trials Database, EudraCT.",
"homepage": "https://www.clinicaltrialsregister.eu/",
"name": "EU Clinical Trial Register",
"prefix": "r3d100013302",
"synonyms": [
"EUCTR",
"European Union Clinical Trials Register"
],
"xrefs": {
"fairsharing": "FAIRsharing.566n8c"
}
},
"r3d100013303": {
"description": "Risklayer Explorer is a collaboration between Risklayer GmbH and the Karlsruhe Institute of Technology's Center for Disaster Risk Management and Risk Reduction Technology (CEDIM). This website is still under development, but we are going live with it already, because we want to present data on the Novel Coronavirus (COVID-19) to help inform the public of the current situation.\nYou will be able to track disaster events and read about our analysis here. Our work is a continuation of a new style of disaster research started by CEDIM in 2011 to analyze disasters immediately after their occurrence, assess the impacts, and retrace the temporal development of disaster events. We are already analyzing damaging earthquakes globally, providing you with event characteristics, earthquake's intensity footprints, as well as the population affected by earthquakes. In addition to earthquake events, we expect to be tracking and analyzing tropical cyclone, volcano and extreme weather events in 2020.",
"homepage": "https://www.risklayer-explorer.com/",
"name": "Risklayer Explorer",
"prefix": "r3d100013303"
},
"r3d100013304": {
"description": "ECDC is an EU agency aimed at strengthening Europe's defences against infectious diseases. The core functions cover a wide spectrum of activities: surveillance, epidemic intelligence, response, scientific advice, microbiology, preparedness, public health training, international relations, health communication, and the scientific journal Eurosurveillance.\nWithin the field of its mission, the Centre shall: search for, collect, collate, evaluate and disseminate relevant scientific and technical data; provide scientific opinions and scientific and technical assistance including training; provide timely information to the Commission, the Member States, Community agencies and international organisations active within the field of public health; coordinate the European networking of bodies operating in the fields within the Centre's mission, including networks that emerge from public health activities supported by the Commission and operating the dedicated surveillance networks; exchange information, expertise and best practices, and facilitate the development and implementation of joint actions.",
"homepage": "https://www.ecdc.europa.eu/en",
"name": "European Centre for Disease Prevention and Control",
"prefix": "r3d100013304",
"xrefs": {
"fairsharing": "FAIRsharing.7ceb60"
}
},
"r3d100013305": {
"description": "To help flattening the COVID-19 curve public health systems need better information on whether preventive measures are working and how the virus may spread. Facebook Data for Good offer maps on population movement that researchers and nonprofits are already using to understand the coronavirus crisis, using aggregated data to protect peopleβs privacy.",
"homepage": "https://dataforgood.facebook.com/",
"name": "Facebook Data for Good",
"prefix": "r3d100013305",
"xrefs": {
"fairsharing": "FAIRsharing.355cdf"
}
},
"r3d100013307": {
"description": "The ISRCTN registry is a primary clinical trial registry recognised by WHO and ICMJE that accepts all clinical research studies (whether proposed, ongoing or completed), providing content validation and curation and the unique identification number necessary for publication. All study records in the database are freely accessible and searchable.\nISRCTN supports transparency in clinical research, helps reduce selective reporting of results and ensures an unbiased and complete evidence base.\nISRCTN accepts all studies involving human subjects or populations with outcome measures assessing effects on human health and well-being, including studies in healthcare, social care, education, workplace safety and economic development.",
"homepage": "https://www.isrctn.com/",
"name": "ISRCTN Registry",
"prefix": "r3d100013307",
"synonyms": [
"International Standard Randomised Controlled Trial Number Registry"
],
"xrefs": {
"biodbcore": "001431"
}
},
"r3d100013308": {
"description": "The International Union of Basic and Clinical Pharmacology (IUPHAR) / British Pharmacological Society (BPS) Guide to PHARMACOLOGY is an expert-curated resource of ligand-activity-target relationships, the majority of which come from high-quality pharmacological and medicinal chemistry literature. It is intended as a βone-stop shopβ portal to pharmacological information and its main aim is to provide a searchable database with quantitative information on drug targets and the prescription medicines and experimental drugs that act on them. In future versions we plan to add resources for education and training in pharmacological principles and techniques along with research guidelines and overviews of key topics. We hope that the IUPHAR/BPS Guide to PHARMACOLOGY (abbreviated as GtoPdb) will be useful for researchers and students in pharmacology and drug discovery and provide the general public with accurate information on the basic science underlying drug action.",
"homepage": "https://www.guidetopharmacology.org",
"name": "IUPHAR/BPS Guide to Pharmacology",
"prefix": "r3d100013308",
"synonyms": [
"GtoPdb",
"Guide to Pharmacology"
],
"xrefs": {
"fairsharing": "FAIRsharing.f1dv0"
}
},
"r3d100013309": {
"description": "The Lens is building an open platform for Innovation Cartography. Specifically, the Lens serves nearly all of the patent documents in the world as open, annotatable digital public goods that are integrated with scholarly and technical literature along with regulatory and business data.",
"homepage": "https://www.lens.org/",
"name": "The Lens",
"prefix": "r3d100013309",
"synonyms": [
"Lens COVID-19 Datasets"
],
"xrefs": {
"fairsharing": "FAIRsharing.4ff837"
}
},
"r3d100013311": {
"description": "The Dutch Trial Register (LTR) is a register in which a part of the clinical studies in The Netherlands are registered. This currently includes all data from the former National Trial Register (NTR).",
"homepage": "https://onderzoekmetmensen.nl/en",
"name": "Dutch Trial Register",
"prefix": "r3d100013311",
"synonyms": [
"LTR",
"Landelijk Trial Register",
"formerly: NTR",
"formerly: Netherlands Trial Register"
],
"xrefs": {
"fairsharing.legacy": "2932",
"nlx": "156848",
"scr": "010234"
}
},
"r3d100013312": {
"description": "Novartis provides the technical results and trial summaries for patients from Phase 1 through 4 interventional trials for innovative products within one year of trial completion. A trial summary for patients is a trial result written in easier to understand language than the technical results.",
"homepage": "https://www.novartis.com/clinicaltrials",
"name": "Novartis Clinical Trial Results Database",
"prefix": "r3d100013312",
"xrefs": {
"fairsharing": "FAIRsharing.58ee0e"
}
},
"r3d100013313": {
"description": "Surveillance Epidemiology of Coronavirus (COVID19) Under Research Exclusion is an international, pediatric and adult database to monitor and report on outcomes of COVID-19 occurring in IBD patients.",
"homepage": "https://covidibd.org/",
"name": "Surveillance Epidemiology of Coronavirus (COVID19) Under Research Exclusion",
"prefix": "r3d100013313",
"synonyms": [
"SECURE-IBD"
],
"xrefs": {
"fairsharing": "FAIRsharing.88637f"
}
},
"r3d100013314": {
"description": "ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries.",
"homepage": "https://viralzone.expasy.org/",
"name": "ViralZone",
"prefix": "r3d100013314",
"xrefs": {
"fairsharing": "FAIRsharing.tppk10",
"nlx": "144372",
"scr": "006563"
}
},
"r3d100013315": {
"description": "VirHostNet is a bioinformatic information system dedidacted to the biocuration, data integration, reproducible systems-level analysis and visualisation of Virus / Host protein-protein interactions Network based on graph theory. VirHostNet is an open and gold standard knowledgebase shared in PSI MITAB 2.5 format using the PSICQUIC webservice and distributed through the NDEx platform. VirHostNet is FAIR and is recognized as a COVID-19 ressource by Elixir bio.tools, the European Virus Bioinformatics Center and FAIRsharing.org.",
"homepage": "https://virhostnet.prabi.fr/",
"name": "VirHostNet",
"prefix": "r3d100013315",
"xrefs": {
"fairsharing": "FAIRsharing.m3316t"
}
},
"r3d100013316": {
"description": "WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. Building on the same MediaWiki software that powers Wikipedia, we added a custom graphical pathway editing tool and integrated databases covering major gene, protein, and small-molecule systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.",
"homepage": "https://www.wikipathways.org/",
"name": "WikiPathways",
"prefix": "r3d100013316",
"xrefs": {
"fairsharing": "FAIRsharing.1x53qk",
"nif": "0000-20925",
"scr": "002134"
}
},
"r3d100013317": {
"description": "As 3D and reality capture strategies for heritage documentation become more widespread and available, there has emerged a growing need to assist with guiding and facilitating accessibility to data, while maintaining scientific rigor, cultural and ethical sensitivity, discoverability, and archival standards. In response to these areas of need, The Open Heritage 3D Alliance (OHA) has developed as an advisory group governing the Open Heritage 3D initiative. This collaborative advisory group are among some of the earliest adopters of 3D heritage documentation technologies, and offer first-hand guidance for best practices in data management, sharing, and dissemination approaches for 3D cultural heritage projects.\nThe founding members of the OHA, consist of experts and organizational leaders from CyArk, Historic Environment Scotland, and the University of South Florida Libraries, who together have significant repositories of legacy and on-going 3D research and documentation projects. These groups offer unique insight into not only the best practices for 3D data capture and sharing, but also have come together around concerns dealing with standards, formats, approach, ethics, and archive commitment. Together, the OHA has begun the journey to provide open access to cultural heritage 3D data, while maintaining integrity, security, and standards relating to discoverable dissemination. Together, the OHA will work to provide democratized access to primary heritage 3D data submitted from donors and organizations, and will help to facilitate an operation platform, archive, and organization of resources into the future.",
"homepage": "https://openheritage3d.org/",
"name": "OpenHeritage 3D",
"prefix": "r3d100013317"
},
"r3d100013319": {
"description": "<<>>!!!>>>",
"homepage": "http://dkan.isp.uni-luebeck.de",
"name": "COEMS Open Data",
"prefix": "r3d100013319",
"synonyms": [
"COEMS Open Data Portal",
"Continuous Observation of Embedded Multicore Systems Data"
]
},
"r3d100013320": {
"description": "The Materials Project produces one of the world's foremost databases of computed information about inorganic, crystalline materials, along with providing powerful web-based apps to help analyze this information to help the design of novel materials. Access is provided free-of-charge with an API available and under a permissive license.",
"homepage": "https://materialsproject.org",
"name": "Materials Project",
"prefix": "r3d100013320"
},
"r3d100013322": {
"description": "The UNAM opens the door to share millions of open data for the benefit of education and research. With this portal (www.datosabiertos.unam.mx) the university shares records of digital collections, academic research projects, repositories and publications to generate new knowledge. This way, it works as an online access point to search university collections authorized for their use, reuse and free redistribution by anyone, without copyright restrictions, patents or other control mechanisms, as long as the Terms of Free Use for UNAM Open Data are respected. \nThe UNAM Open Data Portal contains data, digital objects and geospatial layers of biological collections, artistic work, music, veterinary medicine, university projects, among others. It allows databases to be consulted and downloaded in open and structured formats. One of the most outstanding collections is the National Herbarium of Mexico (MEXU), with almost two million records and high resolution images of plants around the world, mainly collected in Mexico. MEXU is the largest herbarium in the country and in Latin America; itβs among one of the ten most active herbariums in the world.",
"homepage": "https://datosabiertos.unam.mx/",
"name": "Portal de Datos Abiertos UNAM, Colecciones Universitarias",
"prefix": "r3d100013322",
"synonyms": [
"UNAM Open Data Portal"
]
},
"r3d100013323": {
"description": "WorldData.AI comes with a built-in workspace β the next-generation hyper-computing platform powered by a library of 3.3 billion curated external trends.\nWorldData.AI allows you to save your models in its βMy Models Trainedβ section.\nYou can make your models public and share them on social media with interesting images, model features, summary statistics, and feature comparisons. Empower others to leverage your models.\nFor example, if you have discovered a previously unknown impact of interest rates on new-housing demand, you may want to share it through βMy Models Trained.β \nUpload your data and combine it with external trends to build, train, and deploy predictive models with one click!\nWorldData.AI inspects your raw data, applies feature processors, chooses the best set of algorithms, trains and tunes multiple models, and then ranks model performance.",
"homepage": "https://worlddata.ai/",
"name": "WorldData.AI",
"prefix": "r3d100013323"
},
"r3d100013325": {
"description": "EBRAINS offers one of the most comprehensive platforms for sharing brain research data ranging in type as well as spatial and temporal scale. We provide the guidance and tools needed to overcome the hurdles associated with sharing data. The EBRAINS data curation service ensures that your dataset will be shared with maximum impact, visibility, reusability, and longevity, hhttps://www.ebrains.eu/data/find-data/. Find data - the user interface of the EBRAINS Knowledge Graph - allows you to easily find data of interest. EBRAINS hosts a wide range of data types and models from different species. All data are well described and can be accessed immediately for further analysis.",
"homepage": "https://www.ebrains.eu/",
"name": "EBRAINS",
"prefix": "r3d100013325",
"xrefs": {
"fairsharing": "FAIRsharing.XO6ppp",
"scr": "019260"
}
},
"r3d100013328": {
"description": "The long term goal of the Software Heritage initiative is to collect all publicly available software in source code form together with its development history, replicate it massively to ensure its preservation, and share it with everyone who needs it. The Software Heritage archive is growing over time as we crawl new source code from software projects and development forges.",
"homepage": "https://archive.softwareheritage.org/",
"name": "Software Heritage Archive",
"prefix": "r3d100013328",
"xrefs": {
"biodbcore": "001832",
"fairsharing": "FAIRsharing.6ffb92"
}
},
"r3d100013329": {
"description": "The NanoTox Knowlege Base provides access to Nanomaterials, their physico-chemical characterisations, toxicological assays and environmental data as well as computational model based descriptors.",
"homepage": "https://www.nanocommons.eu/nanocommons-knowledge-base/",
"name": "NanoCommons Knowledge Base",
"prefix": "r3d100013329",
"synonyms": [
"NanoSolveIT Knowledge Base",
"formerly: NanoTox Knowledge Base"
]
},
"r3d100013330": {
"description": "The BioProject database is a searcheable collection of complete and incomplete (in-progress) large-scale molecular projects including genome sequencing and assembly, transcriptome, metagenomic, annotation, expression and mapping projects. BioProject provides a central point to link to all data associated with a project in the NCBI molecular and literature databases.",
"homepage": "https://www.ncbi.nlm.nih.gov/bioproject/",
"name": "BioProject",
"prefix": "r3d100013330",
"xrefs": {
"fairsharing": "FAIRsharing.aqhv1y",
"nlx": "143909",
"scr": "004801"
}
},
"r3d100013331": {
"description": "ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works in collaboration with interested organizations to meet the needs of the medical genetics community as efficiently and effectively as possible",
"homepage": "https://www.ncbi.nlm.nih.gov/clinvar/",
"name": "ClinVar",
"prefix": "r3d100013331",
"xrefs": {
"fairsharing": "FAIRsharing.wx5r6f",
"nlx": "151671",
"scr": "006169"
}
},
"r3d100013333": {
"description": "BIRD is a digital service that collects, preserves, and distributes digital material. Repositories are important tools for preserving an organization's legacy; they facilitate digital preservation and scholarly communication.",
"homepage": "https://bird.unit.no/",
"name": "BIRD",
"prefix": "r3d100013333",
"synonyms": [
"lagre og dele forskningsdata",
"store and share research data"
]
},
"r3d100013336": {
"description": "The Heritage Centre represents the four keepers of historical collections of the municipality of Zutphen: Archeology, Monuments, Museum Zutphen, Regional Archive Zutphen (includes the municipalities of Brummen and Lochem)\nThis portal means to be the online gateway to the municipal heritage in Zutphen and wants to provide you with the opportunity to search all their collections at once.",
"homepage": "https://erfgoedcentrumzutphen.nl/",
"name": "Regionaal Archief Zutphen (part of Gemeente Zutphen)",
"prefix": "r3d100013336",
"synonyms": [
"RAZ",
"Regional Archives of Zutphen"
]
},
"r3d100013337": {
"description": "Paris Astronomical Data Centre aims at providing VO access to its data collections, at participating to international standards developments, at implementing VO compliant simulation codes, data visualization and analysis software.\nThis centre hosts high level permanent activities for tools and data distribution under the format of reference services. These sustainable services are recognized at the national level as CNRS labeled services.\nThe various activities are organised as portals whose functions are to provide visibility and information on the projects and to encourage collaboration.",
"homepage": "https://padc.obspm.fr/",
"name": "Paris Astronomical Data Centre",
"prefix": "r3d100013337",
"synonyms": [
"PADC"
]
},
"r3d100013339": {
"description": "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.",
"homepage": "https://datanator.info/",
"name": "Datanator",
"prefix": "r3d100013339",
"xrefs": {
"fairsharing": "FAIRsharing.NmIgg9"
}
},
"r3d100013342": {
"description": "Phaidra is the Institutional Repository and Digital Asset Management System of the St. PΓΆlten University of Applied Sciences. The researchers and students at the University can use it to secure and archive their digital objects such as data, Open Access Publications and dissertations long-term as well as make them widely available to the public. Phaidra provides access to the objects using metadata in English and German. The Repository plays an important part in knowledge transfer in Austria and worldwide.",
"homepage": "https://phaidra.fhstp.ac.at/",
"name": "FHSTP Phaidra",
"prefix": "r3d100013342",
"synonyms": [
"Phaidra"
],
"xrefs": {
"opendoar": "4231"
}
},
"r3d100013343": {
"description": "ReDATA is the research data repository for the University of Arizona and a sister repository to the UA Campus Repository (which is intended for document-based materials). The UA Research Data Repository (ReDATA) serves as the institutional repository for non-traditional scholarly outputs resulting from research activities by University of Arizona researchers. Depositing research materials (datasets, code, images, videos, etc.) associated with published articles and/or completed grants and research projects, into ReDATA helps UA researchers ensure compliance with funder and journal data sharing policies as well as University data retention policies. ReDATA is designed for materials intended for public availability.",
"homepage": "https://arizona.figshare.com",
"name": "ReDATA",
"prefix": "r3d100013343",
"synonyms": [
"UA Data Repository",
"University of Arizona Research Data Repository"
],
"xrefs": {
"fairsharing": "FAIRsharing.Q0Ytmr"
}
},
"r3d100013344": {
"description": "βPeekβ is a digital archive system to provide access to digitized data of Research Resource Archive, Kyoto University (KURRA). It includes various materials that were made within educational and research activities in Kyoto University. A central feature of KURRA is that it treats materials other than books and specimens: photographs, films, recordings, field books, records of research meetings, lecture notes, and manuscripts, from primary sources.",
"homepage": "https://peek.rra.museum.kyoto-u.ac.jp/app/?ln=en",
"name": "Peek",
"prefix": "r3d100013344",
"synonyms": [
"KUDAS",
"Kyoto University Digital Archive System",
"δΊ¬ι½ε€§ε¦γγΈγΏγ«γ’γΌγ«γ€γγ·γΉγγ "
]
},
"r3d100013347": {
"description": "This repository accepts data from life science researchers and service units in Sweden. The repository is operated by SciLifeLab, which is the national infrastructure for life science and environmental research in Sweden. This repository replaces NBIS DOI repository: https://doi.org/10.17616/R3CW52",
"homepage": "https://figshare.scilifelab.se/",
"name": "SciLifeLab Data Repository",
"prefix": "r3d100013347",
"synonyms": [
"SciLifeLab figshare",
"Science for Life Laboratory research repository"
]
},
"r3d100013348": {
"description": "Humadoc is a digital service that collects, preserves and distributes digital material corresponding to the intellectual production of the Faculty of Humanities of the National University of Mar del Plata. Repositories are important tools for preserving an institution's legacy; they facilitate digital preservation and academic communication.",
"homepage": "http://humadoc.mdp.edu.ar/site/",
"name": "Humadoc repositorio",
"prefix": "r3d100013348",
"xrefs": {
"opendoar": "9625",
"roar": "11835"
}
},
"r3d100013351": {
"description": "Accredited through the MEDIN partnership, and core-funded by the Department for the Environment, Food and Rural Affairs (Defra) and the Scottish Government, DASSH provides tools and services for the long-term curation, management and publication of marine species and habitats data, within the UK and internationally. Working closely with partners and data providers we are committed to the FAIR Data Principles, to make marine biodiversity data Findable, Accessible, Interoperable and Reusable. DASSH is a flagship initiative of the Marine Biological Association (MBA), and builds on the MBA's historic role in marine science. Through partnerships with other UK and European data centres DASSH contributes to data portals including the NBN Atlas, EMODnet, EurOBIS and GBIF. On an international scale DASSH is also the UK node of the Ocean Biogeographic Information System (OBIS), and an Associated Data Unit of the International Oceanographic Data and Information Exchange (IODE), giving the Data Archive Centre global recognition.",
"homepage": "https://www.dassh.ac.uk",
"name": "DASSH - The Archive for Marine Species and Habitats Data",
"prefix": "r3d100013351",
"synonyms": [
"Data Archive for Seabed Species and Habitats"
]
},
"r3d100013352": {
"description": "Bilkent University Institutional Repository (BUIR), a service of Bilkent University Libraries, collects, preserves, and distributes the intellectual output of Bilkent University. Faculty, staff, and students are invited to deposit their research and scholarship. Departments, administrative units, programs, and centers are invited to use the Institutional Repository to distribute their working papers, technical reports, conference proceedings, and other research material.",
"homepage": "https://repository.bilkent.edu.tr/home",
"name": "Bilkent University Institutional Repository",
"prefix": "r3d100013352",
"synonyms": [
"BUIR",
"DSpace@Bilkent"
],
"xrefs": {
"opendoar": "3533",
"roar": "10776"
}
},
"r3d100013353": {
"description": "TIBβs core task is to provide science and industry with both elementary and highly technical specialist and researchinformation. TIB has globally unique collections in the subject areas of science and technology, as well as architecture,chemistry, computer science, mathematics and physics. Besides textual materials, the libraryβs collections also includeknowledge objects such as research data, 3D models and audiovisual media.\nThe TIB has assumed responsibility for the long-term preservation and availability of the digital materials it collects and documents, as well as their interpretability for use by different target groups. To this end, it has created the necessary infrastructure and guarantees the permanent provision of both material and human resources.\nSearch for research data search at: https://www.tib.eu/en/search-discover/research-data",
"homepage": "https://www.tib.eu/en/publishing-archiving/digital-preservation",
"name": "TIB Digital Long-Term Archive",
"prefix": "r3d100013353",
"synonyms": [
"Digital Preservation at TIB"
]
},
"r3d100013354": {
"description": "Open Power System Data is a free-of-charge data platform dedicated to electricity system researchers. We collect, check, process, document, and publish data that are publicly available but currently inconvenient to use. The project is a service provider to the modeling community: a supplier of a public good. Learn more about its background or just go ahead and explore the data platform.",
"homepage": "https://open-power-system-data.org/",
"name": "Open Power System Data",
"prefix": "r3d100013354",
"synonyms": [
"OPSD"
]
},
"r3d100013355": {
"description": "Since 2004, the Leibniz Institute for Prevention Research and Epidemiology β BIPS has been working on the establishment and maintenance of the project-based German Pharmacoepidemiological Research Database (short GePaRD). GePaRD is based on claims data from statutory health insurance (SHI) providers and currently includes information on about 20 million persons who have been insured with one of the participating providers since 2004. Per data year, there is information on approximately 17% of the general population from all geographical regions of Germany.",
"homepage": "https://www.bips-institut.de/forschung/forschungsinfrastrukturen/gepard.html",
"name": "GePaRD",
"prefix": "r3d100013355",
"synonyms": [
"German Pharmacoepidemiological Research Database"
]
},
"r3d100013356": {
"description": "Research on German and European financial markets suffers from a lack of pan-European data sets. Also, existing sets do not provide a standard identification of, for example, companies. Therefore, researchers often utilize data from the United States where the integration of different databases is more advanced. As a consequence, empirical analyses are mostly based on non-European data. Because of the institutional differences, political recommendations that result from these analyses cannot β or only in a limited scope β be transferred to Europe.\nAgainst this background, the SAFE Research Data Center not only draws on the usual international data sources but also creates new European data sets, brings existing data together and processes them. The aim is to place the central research areas of SAFE on a common European data footing.\nData access is provided by 'SAFE data sources' https://datacenter.safefrankfurt.de/datacenter/_databases/ and 'FiF - Repositorium fΓΌr Forschungsdaten aus dem Finanzbereich (Preview version)' https://fif.safe-frankfurt.de/xmlui/",
"homepage": "https://safe-frankfurt.de/de/data-center.html",
"name": "Data Center - SAFE",
"prefix": "r3d100013356",
"synonyms": [
"Data Center - Sustainable Architecture for Finance in Europe",
"SAFE-FDZ"
]
},
"r3d100013358": {
"description": "The Infectious Diseases Data Observatory (IDDO) assembles clinical, laboratory and epidemiological data on a collaborative platform to be shared with the research and humanitarian communities. The data are analysed to generate reliable evidence and innovative resources that enable research-driven responses to the major challenges of emerging and neglected infections. Access is available to individual patient data held for malaria and Ebola virus disease. Resources for visceral leishmaniasis, schistosomiasis and soil transmitted helminths, Chagas disease and COVID-19 are under development.\nIDDO contains the following repositories : COVID-19 Data Platform, Chagas Data Platform, Schistosomiasis & Soil Transmitted Helminths Data Platform, Visceral Leishmaniasis Data Platform, Ebola Data Platform, WorldWide Antimalarial Resistance Network (WWARN)",
"homepage": "https://www.iddo.org/",
"name": "Infectious Diseases Data Observatory",
"prefix": "r3d100013358",
"synonyms": [
"IDDO"
],
"xrefs": {
"fairsharing": "FAIRsharing.cF5x1V",
"ror": "04tp3cz81"
}
},
"r3d100013359": {
"description": "KORDS is a research data repository service providing long term storage and public access for datasets that support published research and/or have long term value.",
"homepage": "https://kcl.figshare.com/",
"name": "KORDS",
"prefix": "r3d100013359",
"synonyms": [
"King's College London Open Research Data System"
]
},
"r3d100013361": {
"description": "BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and simulation tools (e.g., COPASI, libRoadRunner/tellurium, NFSim, VCell). BioSimulations aims to help researchers discover published models that might be useful for their research and quickly try them via a simple web-based interface.",
"homepage": "https://biosimulations.org/",
"name": "BioSimulations",
"prefix": "r3d100013361",
"xrefs": {
"fairsharing.legacy": "3208",
"scr": "018733"
}
},
"r3d100013362": {
"description": "Mountain Scholar is an open access repository service that collects, preserves, and provides access to digitized library collections and other scholarly and creative works from several academic entities within the state of Colorado. Colorado State University research data from the fall of 2022 and forward is available in Dryad; CSU legacy research data prior to fall 2022 is in Mountain Scholar.",
"homepage": "https://mountainscholar.org/",
"name": "Mountain Scholar",
"prefix": "r3d100013362",
"synonyms": [
"Digital Collections of Colorado"
],
"xrefs": {
"opendoar": "1267"
}
},
"r3d100013364": {
"description": "This repository stores and links the openly available power-grid frequency recordings across the globe.\nThis database is comprised of open data existent across three dimensions: - TSO data: Transmission System's Operator (TSO) recordings made public; - Research projects: Open-data database research projects; - Independent Gatherings: Industrial, private, or personal recordings that were made publicly available.",
"homepage": "https://osf.io/m43tg/",
"name": "Open Access Power-Grid Frequency Database",
"prefix": "r3d100013364",
"synonyms": [
"OSF repository Open Access Power-Grid Frequency Database"
]
},
"r3d100013365": {
"description": "IAGOS aims to provide long-term, regular and spatially resolved in situ observations of the atmospheric composition. The observation systems are deployed on a fleet of 10 to 15 commercial aircraft measuring atmospheric chemistry concentrations and meteorological fields.\nThe IAGOS Data Centre manages and gives access to all the data produced within the project.",
"homepage": "https://iagos.aeris-data.fr/",
"name": "IAGOS Data Centre",
"prefix": "r3d100013365",
"synonyms": [
"IAGOS Data Center",
"IAGOS Data Portal",
"In-service Aircraft for a Global Observing System"
],
"xrefs": {
"fairsharing": "FAIRsharing.caOJPM"
}
},
"r3d100013366": {
"description": "The nature of the βBridge of Dataβ project is to design and build a platform that allows collecting, searching, analyzing and sharing open research data and to provide it with unique data collected from the three most important Pomeranian universities: GdaΕsk University of Technology, Medical University of GdaΕsk and the University of GdaΕsk. These data will be made available free of charge to the scientific community, entrepreneurs and the public. A bridge will be built to allow reuse of Open Research Data.\n\nThe available research data will be described by standards developed by dedicated, experienced scientific teams. The metadata will allow other external computer systems to interpret the collected data. ORD descriptions will also include data reuse or reduction scenarios to facilitate further processing.",
"homepage": "https://mostwiedzy.pl/en/open-research-data/",
"name": "Most Wiedzy Open Research Data Catalog",
"prefix": "r3d100013366",
"synonyms": [
"Bridge of Knowledge",
"Most Wiedzy Katalog Danych Badawczych"
],
"xrefs": {
"fairsharing": "FAIRsharing.ac4e2b"
}
},
"r3d100013369": {
"description": "The Scientific Data Repository Hosting Service (SARDC) intends to provide a platform for free access to data created and used in the scope of the research work of national institutions.\nIt is characterized by the availability of a repository platform ( DSpace ) and support for the entire data maintenance component, such as backups, monitoring, updating, security, etc., thus keeping researchers out of the concern of these tasks. Finally, the SARDC service intends to make the data deposited in the repository available through the RCAAP Portal.",
"homepage": "https://dados.rcaap.pt/?locale=en",
"name": "RepositΓ³rio de Dados CientΓficos",
"prefix": "r3d100013369"
},
"r3d100013370": {
"description": "This data archive of experiments studying the dynamics of pedestrians is build up by the Institute for Advanced Simulation 7: Civil Safety Research of Forschungszentrum JΓΌlich. \nThe landing page provides our own data of experiments. Data of research colleagues are listed within the data archive at https://ped.fz-juelich.de/extda\nFor most of the experiments, the video recordings, as well as the resulting trajectories of single pedestrians, are available. The experiments were performed under laboratory conditions to focus on the influence of a single variable. \nYou are very welcome to use our data for further research, as long as you name the source of the data. If you have further questions feel free to contact Maik Boltes.",
"homepage": "https://ped.fz-juelich.de/da/",
"name": "Pedestrian Dynamics Data Archive",
"prefix": "r3d100013370",
"synonyms": [
"Data archive of experimental data from studies about pedestrian dynamics"
]
},
"r3d100013372": {
"description": "Global environmental (climate, vegetation, soils, land degradation, hydrology, land cover) layers representing the land mask. Hosted by the OpenGeoHub foundation\nOpenLandMap.org is a data portal to the world's environmental data representing land mask (land cover, vegetation, soil, climate, terrain data and similar). OpenLandMap.org is the web-mapping component of the LandGIS (Geographic Information System for land data).",
"homepage": "https://openlandmap.org",
"name": "OpenLandMap.org",
"prefix": "r3d100013372",
"synonyms": [
"LandGIS"
]
},
"r3d100013374": {
"description": "The Rhodes Research Data repository is the offical repository at Rhodes University for storing and sharing research data and open educational resources.",
"homepage": "https://researchdata.ru.ac.za/",
"name": "Rhodes University Research Data",
"prefix": "r3d100013374",
"synonyms": [
"Rhodes University research repository"
]
},
"r3d100013377": {
"description": "data_UMR is the institutional repository of the University of Marburg for research data of all kinds that has been generated in the context of research activities at the University of Marburg.",
"homepage": "https://data.uni-marburg.de/",
"name": "data_UMR",
"prefix": "r3d100013377"
},
"r3d100013378": {
"description": "All ADNI data are shared without embargo through the LONI Image and Data Archive (IDA), a secure research data repository. Interested scientists may obtain access to ADNI imaging, clinical, genomic, and biomarker data for the purposes of scientific investigation, teaching, or planning clinical research studies.\n\"The Alzheimerβs Disease Neuroimaging Initiative (ADNI) unites researchers with study data as they work to define the progression of Alzheimerβs disease (AD). ADNI researchers collect, validate and utilize data, including MRI and PET images, genetics, cognitive tests, CSF and blood biomarkers as predictors of the disease. Study resources and data from the North American ADNI study are available through this website, including Alzheimerβs disease patients, mild cognitive impairment subjects, and elderly controls. \"",
"homepage": "https://adni.loni.usc.edu/",
"name": "Alzheimer's Disease Neuroimaging Initiative Image and Data Archive",
"prefix": "r3d100013378",
"synonyms": [
"ADNI Image and Data Archive",
"IDA",
"LONI Image and Data Archive"
]
},
"r3d100013382": {
"description": "Intellectum is the Institutional Repository of the University of La Sabana, has been created to manage, preserve and disseminate the intellectual, scientific, cultural and historical production of the university community.",
"homepage": "https://intellectum.unisabana.edu.co/",
"name": "intellectum",
"prefix": "r3d100013382",
"synonyms": [
"RII",
"Repositorio Institucional Intellectum",
"Repository of the University of La Sabana"
],
"xrefs": {
"opendoar": "2587",
"roar": "9637"
}
},
"r3d100013383": {
"description": "IsoArcH is an open access isotope web-database for bioarchaeological samples from prehistoric and historical periods all over the world. With 40,000+ isotope related data obtained on 13,000+ specimens (i.e., humans, animals, plants and organic residues) coming from 500+ archaeological sites, IsoArcH is now one of the world's largest repositories for isotopic data and metadata deriving from archaeological contexts. IsoArcH allows to initiate big data initiatives but also highlights research lacks in certain regions or time periods. Among others, it supports the creation of sound baselines, the undertaking of multi-scale analysis, and the realization of extensive studies and syntheses on various research issues such as paleodiet, food production, resource management, migrations, paleoclimate and paleoenvironmental changes.",
"homepage": "https://isoarch.eu/",
"name": "IsoArcH",
"prefix": "r3d100013383",
"xrefs": {
"fairsharing": "FAIRsharing.a79fcf"
}
},
"r3d100013385": {
"description": "Provided by the University Libraries, DataHub is the comprehensive institutional repository for research data and scholarly outputs produced by the researchers and students in the University of Hong Kong and their collaborators.",
"homepage": "https://datahub.hku.hk/",
"name": "DataHub Figshare",
"prefix": "r3d100013385",
"synonyms": [
"University of Hong Kong Data Repository"
],
"xrefs": {
"fairsharing": "FAIRsharing.rafti9"
}
},
"r3d100013386": {
"description": "The ACEnano Knowledge Infrastructure facilitates access and sharing of methodology applied in nanosafety, starting with nanomaterials characterisation protocols developed or optimised within the ACEnano project.",
"homepage": "https://acenano.douglasconnect.com/",
"name": "ACEnano",
"prefix": "r3d100013386",
"synonyms": [
"ACEnano Knowledge Infrastructure",
"Analytical and Characterisation Excellence in nanomaterial risk assessment"
]
},
"r3d100013387": {
"description": "Earth science data visualization and data delivery application.",
"homepage": "https://argovis.colorado.edu",
"name": "Argovis",
"prefix": "r3d100013387",
"synonyms": [
"A Web Application for Fast Delivery, Visualization, and Analysis of Argo Data"
]
},
"r3d100013391": {
"description": "The University of Pittsburgh English Language Institute Corpus (PELIC) is a 4.2-million-word learner corpus of written texts. These texts were collected in an English for Academic Purposes (EAP) context over seven years in the University of Pittsburghβs Intensive English Program, and were produced by over 1100 students with a wide range of linguistic backgrounds and proficiency levels. PELIC is longitudinal, offering greater opportunities for tracking development in a natural classroom setting.",
"homepage": "https://eli-data-mining-group.github.io/Pitt-ELI-Corpus/",
"name": "The University of Pittsburgh English Language Institute Corpus",
"prefix": "r3d100013391",
"synonyms": [
"PELIC"
]
},
"r3d100013392": {
"description": "Geoscientific Data & Discovery Publishing Center (GDD) is based on the geological scientific data generated globally, establishing policies and systems for the scientific data publishing, absorbing the concepts and methods of international open data, and joint Digital Object Unique Identifier-DOI registration agencies to provide standard data reference formats and permanent access address for data references, doing publishing through the Internet platform, which combines innovation and advance.\nGDD mainly includes data descriptor and entity data publishing. The data papers describe entity data and corresponding metadata information. The entity data includes common shared data such as geographic information, geologic maps, and databases, and also includes multiple data types, such as documents, archive records, data forms and other multimedia formed during geological work, various data-centric applications, database interface services, and typical data services.",
"homepage": "http://geodb.cgs.gov.cn/en",
"name": "Geoscientific Data & Discovery Publishing Center",
"prefix": "r3d100013392",
"synonyms": [
"GDD",
"ε°θ΄¨η§ε¦ζ°ζεΊηδΈεΏ"
]
},
"r3d100013393": {
"description": "The information in the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer relates cytogenetic changes and their genomic consequences, in particular gene fusions, to tumor characteristics, based either on individual cases or associations. All the data have been manually culled from the literature by Felix Mitelman in collaboration with Bertil Johansson and Fredrik Mertens.",
"homepage": "https://mitelmandatabase.isb-cgc.org/",
"name": "Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer",
"prefix": "r3d100013393"
},
"r3d100013394": {
"description": "LeoPARD is the institutional repository of the Technical University of Braunschweig and is operated by the University Library. It is used for the publication of research results and documentation by scientists of the TU Braunschweig.",
"homepage": "https://leopard.tu-braunschweig.de/content/index.xml",
"name": "LeoPARD - TU Braunschweig Publications And Research Data",
"prefix": "r3d100013394",
"synonyms": [
"formerly name: Digitale Bibliothek - Der Publikationsserver der TU Braunschweig"
],
"xrefs": {
"opendoar": "719"
}
},
"r3d100013395": {
"description": "Research Data Repository of the Instituto Federal Goiano - Campus UrutaΓ, a Brazilian public institution of the Ministry of Education. The project is an initiative of the Directorate of Post-Graduate Studies, Research and Innovation of the Federal Institute of GoiΓ‘s - Campus UrutaΓ, which follows the philosophy of Open Science, for expansion and valuation of scientific research, aiming to provide data from technical-scientific observations and experimentation, ensuring that its authors, researchers and students receive all the credit they deserve as agents generating data. At the same time, the appropriate reuse of data is envisaged, whether in didactic-pedagogical activities or in new research.",
"homepage": "https://dataverse.harvard.edu/dataverse/pesquisa-urt/",
"name": "Dados Abertos De Pesquisas",
"prefix": "r3d100013395",
"synonyms": [
"RepositΓ³rio de Dados de Pesquisas do Instituto Federal Goiano β Campus UrutaΓ",
"Research Data Repository of the Federal Institute of Goiania"
]
},
"r3d100013399": {
"description": "The Institutional Repository of the Universidad Santo TomΓ‘s manages, preserves, stores, disseminates and provides access to digital objects, the product of all academic and administrative production.",
"homepage": "https://repository.usta.edu.co",
"name": "Repositorio Institucional Universidad Santo TomΓ‘s",
"prefix": "r3d100013399",
"synonyms": [
"Institutional Repository of the Saint Thomas Aquinas University"
],
"xrefs": {
"opendoar": "3896"
}
},
"r3d100013400": {
"description": "Tethys is an Open Access Research Data Repository of the GeoSphere Austria, which publishes and distributes georeferenced geoscientific research data generated at and in cooperation with the GeoSphere Austria. The research data publications and the associated metadata are predominantly provided in German or in English. The abstracts are provided in both languages. Tethys aims to provide published data sets as open data and in accordance with the FAIR Data Principles, findable, accessible, interoperable and reusable.",
"homepage": "https://www.tethys.at/",
"name": "Tethys",
"prefix": "r3d100013400",
"synonyms": [
"Tethys RDR"
]
},
"r3d100013404": {
"description": "The Copernicus Marine Environment Monitoring Service (CMEMS) provides regular and systematic reference information on the physical and biogeochemical state, variability and dynamics of the ocean and marine ecosystems for the global ocean and the European regional seas.\n\nThe observations and forecasts produced by the service support all marine applications, including:\n\n Marine safety;\n Marine resources;\n Coastal and marine environment;\n Weather, seasonal forecasting and climate.\n\nFor instance, the provision of data on currents, winds and sea ice help to improve ship routing services, offshore operations or search and rescue operations, thus contributing to marine safety.\n\nThe service also contributes to the protection and the sustainable management of living marine resources in particular for aquaculture, sustainable fisheries management or regional fishery organisations decision-making process.\n\nPhysical and marine biogeochemical components are useful for water quality monitoring and pollution control. Sea level rise is a key indicator of climate change and helps to assess coastal erosion. Sea surface temperature elevation has direct consequences on marine ecosystems and appearance of tropical cyclones. As a result of this, the service supports a wide range of coastal and marine environment applications.\n\nMany of the data delivered by the service (e.g. temperature, salinity, sea level, currents, wind and sea ice) also play a crucial role in the domain of weather, climate and seasonal forecasting.",
"homepage": "https://marine.copernicus.eu/",
"name": "Copernicus Marine Environment Monitoring Service",
"prefix": "r3d100013404",
"synonyms": [
"CMEMS"
]
},
"r3d100013405": {
"description": "Launched in December 2013, Gaia is destined to create the most accurate map yet of the Milky Way. By making accurate measurements of the positions and motions of stars in the Milky Way, it will answer questions about the origin and evolution of our home galaxy. The first data release (2016) contains three-dimensional positions and two-dimensional motions of a subset of two million stars. The second data release (2018) increases that number to over 1.6 Billion. Gaiaβs measurements are as precise as planned, paving the way to a better understanding of our galaxy and its neighborhood.\nThe AIP hosts the Gaia data as one of the external data centers along with the main Gaia archive maintained by ESAC and provides access to the Gaia data releases as part of Gaia Data Processing and Analysis Consortium (DPAC).",
"homepage": "https://gaia.aip.de/",
"name": "Gaia@AIP",
"prefix": "r3d100013405",
"synonyms": [
"Gaia@AIP Services"
]
},
"r3d100013407": {
"description": "CosmoHub is a web application based on Hadoop to perform interactive exploration and distribution of massive cosmological datasets",
"homepage": "https://cosmohub.pic.es",
"name": "CosmoHub",
"prefix": "r3d100013407"
},
"r3d100013408": {
"description": "ProteomicsDB started as a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. The data types and contents grew over time to include RNA-Seq expression data, drug-target interactions and cell line viability data.",
"homepage": "https://www.proteomicsdb.org/",
"name": "ProteomicsDB",
"prefix": "r3d100013408",
"synonyms": [
"PrDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.6y9h91"
}
},
"r3d100013413": {
"description": "Sciflection accepts structured data directly uploaded from Electronic Laboratory Notebooks (open enventory, Sciformation ELN, open for others) in JSON format. Searchable by chemical structure, text parts, numeric parameters, etc.",
"homepage": "https://sciflection.com",
"name": "Sciflection",
"prefix": "r3d100013413",
"xrefs": {
"fairsharing": "FAIRsharing.NKUobC"
}
},
"r3d100013414": {
"description": "Germania Sacra is a long-term research project ongoing at the GΓΆttingen Academy of Sciences and Humanities. The project has a long-standing tradition of researching the history of dioceses, monasteries, collegiate churches, and convents within the Holy Roman Empire. The results of this work are published in reference books, the digital editions of these reference books along with two databases are the core components of Germania Sacraβs Online Portal. One of these databases is the βDigital Index of Personsβ, which provides access to biographical and prosopographical information about the clerical staff affiliated to the institutions researched. This includes information about the bishops of a diocese, the canons or canonesses of individual collegiate churches, the monks and nuns of numerous monasteries, etc. The second primary feature of the online portal is the βDatabase of Monasteries, Collegiate Churches, and Convents of the Holy Roman Empireβ.",
"homepage": "https://adw-goe.de/germania-sacra/",
"name": "Germania Sacra Online",
"prefix": "r3d100013414"
},
"r3d100013415": {
"description": "For datasets from individual researchers or research groups affiliated with Stockholm University, who do not want set up a separate Dataverse for a project or institution. Metadata provisions for Geospatial, Social Science, Humanities, Astronomy, Astrophysics, Life Sciences and Journals (all optional, by choice) are included. Data curation help from Stockholm University Library possible on request.",
"homepage": "https://dataverse.harvard.edu/dataverse/StockholmUniversityLibrary",
"name": "Stockholm University Library Dataverse",
"prefix": "r3d100013415"
},
"r3d100013418": {
"description": "Contains data on patients who have been tested for COVID-19 (whether positive or negative) in participating health institutions in Brazil. This initiative makes available three kinds of pseudonymized data: demographics (gender, year of birth, and region of residency), clinical and laboratory exams. Additional hospitalization information - such as data on transfers and outcomes - is provided when available. Clinical, lab, and hospitalization information is not limited to COVID-19 data, but covers all health events for these individuals, starting November 1st 2019, to allow for comorbidity studies. Data are deposited periodically, so that health information for a given individual is continuously updated to time of new version upload.",
"homepage": "https://repositoriodatasharingfapesp.uspdigital.usp.br/",
"name": "FAPESP COVID-19 Data Sharing/BR",
"prefix": "r3d100013418"
},
"r3d100013419": {
"description": "ROAD is spatio-temporal database targeting a systemic understanding of human activities and expansions 3 Ma β 20 ka in Africa and Eurasia. The database contains cultural, anthropological, environmental and geographical information about archaeological sites and assemblages. After registration, the database offers access through a SQL query tool, an interactive web map (called \"Map Module\") as well as \"Summary Factsheets\", which present information about single localities in a PDF file.",
"homepage": "https://www.roceeh.uni-tuebingen.de/roadweb/smarty_road_simple_search.php",
"name": "ROCEEH Out of Africa Database",
"prefix": "r3d100013419",
"synonyms": [
"ROAD",
"The Role of Culture in Early Expansions of Humans Out of Africa Database"
]
},
"r3d100013420": {
"description": "The Portuguese Archive of Social Information (APIS) is a scientific infrastructure acting on the domain of preservation and dissemination of social science data. Based at Instituto de CiΓͺncias Sociais, University of Lisbon, the archive works towards the acquisition and sharing of digital data for the purposes of public consultation, secondary analysis and pedagogical use. The archive comprises a range of datasets provided by research projects of the national scientific community.",
"homepage": "https://dados.rcaap.pt/handle/10400.20/1",
"name": "APIS",
"prefix": "r3d100013420",
"synonyms": [
"Arquivo PortuguΓͺs de Informação Social",
"Portuguese Archive of Social Information"
]
},
"r3d100013421": {
"description": "ERIC/open is the institutional repository where Eawag scientists publish their research data. Research data is organized in Packages which contain one or more Resources. Resources are usually files containing research data proper or ancillary information such as a README-file. A URL pointing to external information might also constitute a Resource.",
"homepage": "https://opendata.eawag.ch/",
"name": "ERIC/open",
"prefix": "r3d100013421",
"synonyms": [
"The Eawag Research Data Institutional Repository"
],
"xrefs": {
"fairsharing": "FAIRsharing.1a0bbf"
}
},
"r3d100013422": {
"description": "The N3C Data Enclave is a secure portal containing a very large and extensive set of harmonized COVID-19 clinical electronic health record (EHR) data. The data can be accessed through a secure cloud Enclave hosted by NCATS and cannot be downloaded due to regulatory control. Broad access is available to investigators at institutions that sign a Data Use Agreements and via Data Use Requests by investigators. The N3C is a unique open, reproducible, transparent, collaborative team science initiative to leverage sensitive clinical data to expedite COVID-19 discoveries and improve health outcomes.",
"homepage": "https://ncats.nih.gov/n3c",
"name": "National COVID Cohort Collaborative",
"prefix": "r3d100013422",
"synonyms": [
"N3C",
"National COVID Cohort Collaborative Data Enclave"
],
"xrefs": {
"scr": "018757"
}
},
"r3d100013423": {
"description": "Yareta is a repository service built on digital solutions for archiving, preserving and sharing research data that enable researchers and institutions of any disciplines to share and showcase their research results. The solution was developed as part of a larger project focusing on Data Life Cycle Management (dlcm.ch) that aims to develop various services for research data management. Thanks to its highly modular architecture, Yareta can be adapted both to small institutions that need a \"turnkey\" solution and to larger ones that can rely on Yareta to complement what they have already implemented. Yareta is compatible with all formats in use in the different scientific disciplines and is based on modern technology that interconnects with researchers' environments (such as Electronic Laboratory Notebooks or Laboratory Information Management Systems).",
"homepage": "https://yareta.unige.ch/",
"name": "Yareta",
"prefix": "r3d100013423",
"synonyms": [
"Le Data Repository des chercheurs et chercheuses des hautes Γ©coles genevoises",
"The Research Data Repository of Geneva's Higher Education Institutions, Switzerland",
"Yareta Service"
]
},
"r3d100013425": {
"description": "DAIS - Digital Archive of the Serbian Academy of Sciences and Arts is a joint digital repository of the Serbian Academy of Sciences and Arts (SASA) and the research institutes under the auspices of SASA. The aim of the repository is to provide open access to publications and other research outputs resulting from the projects implemented by the SASA and its institutes. The repository uses a DSpace-based software platform developed and maintained by the Belgrade University Computer Centre (RCUB).",
"homepage": "https://dais.sanu.ac.rs/?locale-attribute=en",
"name": "DAIS",
"prefix": "r3d100013425",
"synonyms": [
"Digital Archive of the Serbian Academy of Sciences and Arts",
"Digitalni arhiv izdanja SANU"
]
},
"r3d100013426": {
"description": "A space for managing, preserving and disseminating the intellectual, scientific, cultural and historical production of the university community. It allows access to documents produced by the different UNAB members as a result of research, teaching and extension activities.",
"homepage": "https://repository.unab.edu.co/",
"name": "Autonomous University of Bucaramanga Repository",
"prefix": "r3d100013426",
"synonyms": [
"Repositorio Institucional UNAB",
"Repositorio Universidad AutΓ³noma de Bucaramanga"
]
},
"r3d100013427": {
"description": "The Institutional Repository of the University of Burgos is based on the digital collections that include the documents generated by the members of the university community in their academic activities. These are accessible via the Internet, in accordance with the University's Open Access Institutional Policy.",
"homepage": "https://riubu.ubu.es/",
"name": "Repositorio Institucional de la Universidad de Burgos",
"prefix": "r3d100013427",
"synonyms": [
"Institutional Repository of the University of Burgos",
"RIUBU"
],
"xrefs": {
"opendoar": "1527",
"roar": "9559"
}
},
"r3d100013428": {
"description": "The Genome Warehouse (GWH) is a public repository housing genome-scale data for a wide range of species and delivering a series of web services for genome data submission, storage, release and sharing.",
"homepage": "https://bigd.big.ac.cn/gwh/",
"name": "Genome Warehouse",
"prefix": "r3d100013428",
"synonyms": [
"GWH"
],
"xrefs": {
"fairsharing": "/FAIRsharing.7qBaJ0"
}
},
"r3d100013429": {
"description": "The Astromaterials Data System (AstroMat) is a data infrastructure to store, curate, and provide access to laboratory data acquired on samples curated in the Astromaterials Collection of the Johnson Space Center. AstroMat is developed and operated at the Lamont-Doherty Earth Observatory of Columbia University and funded by NASA.",
"homepage": "https://www.astromat.org",
"name": "Astromaterials Data System",
"prefix": "r3d100013429",
"synonyms": [
"AstroMat",
"AstroRepo",
"Astromaterials Data System Repository"
],
"xrefs": {
"fairsharing": "FAIRsharing.tYYt1o"
}
},
"r3d100013430": {
"description": "Provides quick, uncluttered access to information about Heliophysics research data that have been described with SPASE resource descriptions.",
"homepage": "https://hpde.io/",
"name": "HPDE.io",
"prefix": "r3d100013430",
"synonyms": [
"HPDE Registry",
"Heliophysics Data Environment Registry"
]
},
"r3d100013431": {
"description": "Ever growing search and retrieval site for a comprehensive set of Heliophysics data from NASA and other spacecraft and ground-based observatories.",
"homepage": "https://heliophysicsdata.gsfc.nasa.gov/websearch/dispatcher",
"name": "NASA Heliophysics Data Portal",
"prefix": "r3d100013431",
"synonyms": [
"HP Data Portal"
]
},
"r3d100013432": {
"description": "BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms, and modeling formats) needed for specific modeling projects.",
"homepage": "https://biosimulators.org",
"name": "BioSimulators",
"prefix": "r3d100013432",
"xrefs": {
"fairsharing": "FAIRsharing.pwEima"
}
},
"r3d100013433": {
"description": "BOARD (Bicocca Open Archive Research Data) is the institutional data repository of the University of Milano-Bicocca. \nBOARD is an open, free-to-use research data repository, which enables members of University of Milano-Bicocca to make their research data publicly available. \nBy depositing their research data in BOARD researchers can: \n- Make their research data citable \n- Share their data privately or publicly\n- Ensure long-term storage for their data\n- Keep access to all versions\n- Link their article to their data",
"homepage": "https://board.unimib.it/research-data/",
"name": "Bicocca Open Archive Research Data",
"prefix": "r3d100013433",
"synonyms": [
"BOARD"
],
"xrefs": {
"fairsharing": "FAIRsharing.DDotIl"
}
},
"r3d100013438": {
"description": "The URV's institutional repository is a deposit of digital documents that contains the teaching and research output of the members of the URV university community: for example, articles that have not yet been published (preprints), published articles (postprints), research data, end-of-degree projects, bachelor's degree theses, doctoral theses, teaching material and other documents that may be useful for generating knowledge. It is available to all the institutions that are part of the Campus of International Excellence Southern Catalonia and who wish to use it in cooperation with others.",
"homepage": "https://www.crai.urv.cat/en/information-resources/repository/",
"name": "Repositori Institucional Universitat Rovira i Virgili",
"prefix": "r3d100013438",
"synonyms": [
"Rovira i Virgily Institutional Repository"
],
"xrefs": {
"opendoar": "3351",
"roar": "11366"
}
},
"r3d100013439": {
"description": "DataON is Korea's National Research Data Platform. It provides integrated search of metadata for KISTI's research data and domestic and international research data and links to raw data. DataON allows users (researchers, policy makers, etc.) to perform the following tasks: Easily search for various types of research data in all scientific fields. By registering research results, research data can be posted and cited. Build a community among researchers and enable collaborative research. It provides a data analysis environment that allows one-stop analysis of discovered research data.",
"homepage": "https://dataon.kisti.re.kr",
"name": "DataON Repository",
"prefix": "r3d100013439",
"synonyms": [
"previous name: KORD",
"previous name: Korea Open Research Data"
]
},
"r3d100013440": {
"description": "Breeding, molecular, genetics and genomics data on cassava (Manihot esculenta) and wild relatives",
"homepage": "https://cassavabase.org",
"name": "Cassavabase",
"prefix": "r3d100013440",
"xrefs": {
"fairsharing": "FAIRsharing.ejofJI"
}
},
"r3d100013441": {
"description": "The Repository of Psychological Instruments in Serbian (REPOPSI), run by the Laboratory for Research of Individual Differences at the University of Belgrade and hosted on the Open Science Framework, is an open-access repository of psychological instruments. REPOPSI is a collection of psychological measures, scales, tests, and other research instruments commonly used in social and behavioral science research. Documented are Serbian, English and multilingual instruments, which can be used free of charge for non-commercial purposes (e.g., academic research or education).",
"homepage": "https://www.repopsi.f.bg.ac.rs/en/",
"name": "Repository of Psychological Instruments in Serbian",
"prefix": "r3d100013441",
"synonyms": [
"REPOPSI",
"Repozitorijum psiholoΕ‘kih instrumenata na srpskom jeziku"
],
"xrefs": {
"doi": "10.17605/OSF.IO/5ZB8P"
}
},
"r3d100013442": {
"description": "A collection that brings together the scientific and academic production generated by the university's teachers and researchers.\nObjectives\n* Bring together the academic and scientific production generated by the university.\nβ Preserve and disseminate documents produced at the UCC\nβ To provide greater visibility and increase the impact of publications.\nβ Ensure free and open access to the university's scientific and academic production.\nβ Ensure long-term preservation.",
"homepage": "https://pa.bibdigital.uccor.edu.ar/",
"name": "ProducciΓ³n AcadΓ©mica UCC",
"prefix": "r3d100013442",
"xrefs": {
"opendoar": "2718",
"roar": "6686"
}
},
"r3d100013444": {
"description": "Aperta is the open access repository of The Scientific and Technological Research Council of Turkey (TΓBΔ°TAK). The publications produced from the projects supported by TUBITAK must be uploaded to TUBITAK Open Archive Aperta. It is recommended that the research data of these publications should be open access.",
"homepage": "https://aperta.ulakbim.gov.tr/",
"name": "Aperta TΓBΔ°TAK Open Archive",
"prefix": "r3d100013444",
"synonyms": [
"Aperta - TΓBΔ°TAK AΓ§Δ±k ArΕivi"
]
},
"r3d100013445": {
"description": "SEDICI [Intellectual Creation Diffusion Service] is the institutional repository of the Universidad Nacional de La Plata (UNLP), a public university located at Argentina. Its goal is to index, preserve and grant open access to all kind of academic work produced at this institution including thesis, scientific articles, datasets, books, conference objects, and more.",
"homepage": "https://sedici.unlp.edu.ar/",
"name": "SEDICI",
"prefix": "r3d100013445",
"synonyms": [
"Institutional Repository of the UNLP",
"Servicio de DifusiΓ³n de la CreaciΓ³n Intelectual"
]
},
"r3d100013449": {
"description": "A database of fugitives from North American slavery. Freedom on the Move is a citizen science (crowdsourcing) project operated by the Cornell Institute for Social and Economic Research (CISER) at Cornell University, in collaboration with several other institutions which support digital humanities research. The project involves members of the public in transcribing and responding to questions regarding historical newspaper advertisements placed by enslavers who wanted to recapture self-liberating Africans and African Americans. The database created is intended to be an invaluable research aid, pedagogical tool, and resource for genealogists.",
"homepage": "https://freedomonthemove.org/",
"name": "Freedom on the Move",
"prefix": "r3d100013449",
"synonyms": [
"FOTM project"
]
},
"r3d100013450": {
"description": "Preserves and enables easy and open access to all types of digital content including text, images, moving images, mpegs and data sets of Autonomous University of Manizales.",
"homepage": "https://repositorio.autonoma.edu.co",
"name": "Repositorio Institucional-Universidad AutΓ³noma de Manizales",
"prefix": "r3d100013450",
"synonyms": [
"Institutional Repository - Autonomous University of Manizales",
"REPOUAM"
],
"xrefs": {
"opendoar": "4706"
}
},
"r3d100013451": {
"description": "QSAR DataBank (QsarDB) is repository for (Quantitative) Structure-Activity Relationships ((Q)SAR) data and models. It also provides open domain-specific digital data exchange standards and associated tools that enable research groups, project teams and institutions to share and represent predictive in silico models.",
"homepage": "https://qsardb.org/",
"name": "QsarDB",
"prefix": "r3d100013451",
"synonyms": [
"QSAR Data Base"
]
},
"r3d100013453": {
"description": "Iceland joined CLARIN ERIC on February 1st, 2020, after having been an observer since November 2018. The Ministry of Education, Science and Culture assigned The Γrni MagnΓΊsson Institute for Icelandic Studies the role of leading partner in the Icelandic National Consortium and appointed Professor Emeritus EirΓkur RΓΆgnvaldsson as National Coordinator, later replaced by StarkaΓ°ur Barkarson, a project manager at The Γrni MagnΓΊsson Institute. Most of the relevant institutions participate in the CLARIN-IS National Consortium. \nThe Γrni MagnΓΊsson Institute has already established a Metadata Providing Centre (CLARIN C-Centre) which hosts metadata for Icelandic language resources and makes them available through the Virtual Language Observatory. The aim is to establish a Service Providing Centre (CLARIN B-Centre) which will provide both service and access to resources and knowledge.",
"homepage": "https://clarin.is/",
"name": "CLARIN-IS",
"prefix": "r3d100013453",
"synonyms": [
"CLARIN Γ‘ Γslandi"
]
},
"r3d100013455": {
"description": "WorldViews is a multilingual, digital resource for primary source material, containing digitised excerpts from textbooks from around the world on topics that are of global, transnational and interregional relevance.",
"homepage": "https://worldviews.gei.de/",
"name": "Worldviews",
"prefix": "r3d100013455"
},
"r3d100013456": {
"description": "Podlasie digital repository of natural science data",
"homepage": "https://dataverse.openforestdata.pl/",
"name": "Open Forest Data",
"prefix": "r3d100013456",
"synonyms": [
"e-Puszcza"
]
},
"r3d100013458": {
"description": "UBC Dataverse Collection is a free research data repository for our faculty, students and staff. The platform makes it possible for researchers to deposit data, create appropriate metadata, obtain DOIs for permanent links, and maintain version control of their datasets. All files are held in a secure environment on Canadian servers. Researchers are encouraged to make their data available publicly, but can choose to restrict access to their data if they wish.",
"homepage": "https://borealisdata.ca/dataverse/ubc",
"name": "UBC Dataverse Collection",
"prefix": "r3d100013458",
"synonyms": [
"formerly name: University of British Columbia Dataverse Collection"
]
},
"r3d100013459": {
"description": "The Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) onboard the ENVISAT satellite provided atmospheric infrared limb emission spectra. From these, profiles of temperature and atmospheric trace gases were retrieved using the research data processor developed at the Institut fΓΌr Meteorologie und Klimaforschung (IMK), which is complemented by the component of non-local thermodynamic equilibrium (non-LTE) treatment from the Instituto de AstrofΓsica de AndalucΓa (IAA). The MIPAS data products on this server are commonly known as IMK/IAA MIPAS Level2 data products. The MIPAS instrument measured during two time frames: from 2002 to 2004 in full spectral resolution (high resolution = HR aka full resolution = FR), and from 2005 to 2012 in reduced spectral, but improved spatial resolution (reduced resolution = RR aka optimized resolution = OR). For this reason, there are different version numbers covering the full MIPAS mission period: xx for the HR/FR period, and 2xx for the RR/OR period (example: 61 for HR/FR, 261 for RR/OR). Beyond this, measurements were conducted in different modes covering different altitude ranges during the RR period: Nominal (6 β 70 km), MA (18 β 102 km), NLC (39 β 102 km), UA (42 β 172 km), UTLS-1 (5.5 β 19 km), UTLS-2 (12 β 42 km), AE (7 β 38 km). The non-nominal modes are identified by the following version numbers: MA = 5xx, NLC = 7xx, UA = 6xx, UTLS-1/2 = 1xx (no retrievals for AE mode).",
"homepage": "https://www.imk-asf.kit.edu/english/308.php",
"name": "IMK/IAA generated MIPAS/Envisat data",
"prefix": "r3d100013459"
},
"r3d100013461": {
"description": "The CONP portal is a web interface for the Canadian Open Neuroscience Platform (CONP) to facilitate open science in the neuroscience community. CONP simplifies global researcher access and sharing of datasets and tools. The portal internalizes the cycle of a typical research project: starting with data acquisition, followed by processing using already existing/published tools, and ultimately publication of the obtained results including a link to the original dataset. \nFrom more information on CONP, please visit https://conp.ca",
"homepage": "https://portal.conp.ca",
"name": "Canadian Open Neuroscience Platform Portal",
"prefix": "r3d100013461",
"synonyms": [
"CONP",
"Canadian Open Neuroscience Platform",
"PCNO",
"Plateforme Canadienne de Neuroscience Ouverte"
],
"xrefs": {
"fairsharing": "FAIRsharing.7qwrhY",
"scr": "016433"
}
},
"r3d100013465": {
"description": "The DDD, the UAB Digital Repository of Documents, is the tool that collects, manages, disseminates and preserves the scientific, educational and institutional production of the University. It also gathers digital documents that are part of or complement UAB libraries collections. The DDD repository shows an organized, open access and interoperable collection.\nThe Universitat AutΓ²noma de Barcelona (UAB) acknowledges the importance of research data and the need for a policy aimed at promoting its visibility and reuse. This policy was drawn up by the Open Access Commission and was approved by the University Governing Council on 11 March 2020.",
"homepage": "https://ddd.uab.cat/?ln=en",
"name": "DipΓ²sit Digital de Documents de la UAB",
"prefix": "r3d100013465",
"synonyms": [
"DDD",
"DepΓ³sito Digital de Documentos de la UAB",
"UAB Digital Repository of Documents"
],
"xrefs": {
"opendoar": "1404",
"roar": "10452"
}
},
"r3d100013466": {
"description": "RADAR4KIT enables KIT researchers to manage, archive, share in project teams and publish their research data in a repository. It allows users to compile research data from completed scientific studies and projects into data packages, describe them with metadata, store them permanently and archive them or make them publicly accessible if required. Published data are given a persistent identifier (DOI) and can thus be found internationally and are also referenced in KITopen. The operator is the Karlsruhe Institute of Technology (KIT). RADAR4KIT is based on the RADAR service offered by FIZ Karlsruhe. The data is stored exclusively on the KIT IT infrastructure at the Steinbuch Centre for Computing (SCC).",
"homepage": "https://radar.kit.edu/",
"name": "RADAR4KIT",
"prefix": "r3d100013466",
"synonyms": [
"Research Data Repository for KIT"
]
},
"r3d100013468": {
"description": "The Arizona State University (ASU) Research Data Repository provides a platform for ASU-affiliated researchers to share, preserve, cite, and make research data accessible and discoverable. The ASU Research Data Repository provides a permanent digital identifier for research data, which complies with data sharing policies. The repository is powered by the Dataverse open-source application, developed and used by Harvard University. Both the ASU Research Data Repository and the KEEP Institutional Repository are managed by the ASU Library to ensure research produced at Arizona State University is discoverable and accessible to the global community.",
"homepage": "https://dataverse.asu.edu",
"name": "ASU Library Research Data Repository",
"prefix": "r3d100013468",
"synonyms": [
"Arizona State University Dataverse",
"Arizona State University Library Research Data Repository"
]
},
"r3d100013469": {
"description": "The EarthEnv project is a collaborative project of biodiversity scientists and remote sensing experts to develop near-global standardized, 1km resolution layers for monitoring and modeling biodiversity, ecosystems, and climate. The work is supported by NCEAS, NASA, NSF, and Yale University.",
"homepage": "https://www.earthenv.org/",
"name": "EarthEnv",
"prefix": "r3d100013469"
},
"r3d100013470": {
"description": "The BonaRes Repository stores, manage and publishes soil and agricultural research data from research projects, agricultural long-term field experiments and soil profiles which contribute significantly to the analysis of changes of soil and soil functions over the long term. Research data are described by the metadata following the BonaRes Metadata Schema (DOI: 10.20387/bonares-5pgg-8yrp) which combines international recognized standards for the description of geospatial data (INSPIRE Directive) and research data (DataCite 4.0). Metadata includes AGROVOC keywords. Within the BonaRes Repository research data is provided for free reuse under the CC License and can be discovered by advanced text and map search via a number of criteria.",
"homepage": "https://www.bonares.de/research-data",
"name": "BonaRes Repository",
"prefix": "r3d100013470",
"synonyms": [
"Publishing research data from agricultural domain"
],
"xrefs": {
"fairsharing": "FAIRsharing.2cw3HU"
}
},
"r3d100013471": {
"description": "Welcome to the transparency portal of the city of Karlsruhe, your central contact point for open data and documents of the city of Karlsruhe.\nOn this portal you will find documents and reports as well as machine-readable data sets (\"open data\"). You may - under a few conditions - distribute, edit and also commercially use this information free of charge. We are happy if interesting projects arise from this - and if you tell us about your project. The information offered is constantly being expanded.",
"homepage": "https://transparenz.karlsruhe.de/",
"name": "Transparenzportal der Stadt Karlsruhe",
"prefix": "r3d100013471",
"xrefs": {
"wikidata": "Q63433716"
}
},
"r3d100013475": {
"description": "Bioinformatics.org serves the scientific and educational needs of bioinformatic practitioners and the general public. We develop and maintain computational resources to facilitate world-wide communications and collaborations between people of all educational and professional levels. We provide and promote open access to the materials and methods required for, and derived from, research, development and education.",
"homepage": "https://www.bioinformatics.org/",
"name": "Bioinformatics.org",
"prefix": "r3d100013475",
"xrefs": {
"scr": "012008"
}
},
"r3d100013478": {
"description": "Bitbucket is a web-based version control repository hosting service owned by Atlassian, for source code and development projects that use either Mercurial or Git revision control systems.",
"homepage": "https://bitbucket.org/",
"name": "Bitbucket",
"prefix": "r3d100013478",
"synonyms": [
"Atlassian Bitbucket"
],
"xrefs": {
"fairsharing": "FAIRsharing.fc3431",
"nlx": "158615",
"scr": "000502"
}
},
"r3d100013484": {
"description": "The WashU Research Data repository accepts any publishable research data set, including textual, tabular, geospatial, imagery, computer code, or 3D data files, from researchers affiliated with Washington University in St. Louis. Datasets include metadata and are curated and assigned a DOI to align with FAIR data principles.",
"homepage": "https://data.library.wustl.edu/",
"name": "Washington University Research Data",
"prefix": "r3d100013484",
"synonyms": [
"WURD",
"WashU Research Data",
"Washington University Digital Materials Research Repository"
]
},
"r3d100013486": {
"description": "The Oxford COVID-19 Government Response Tracker (OxCGRT) systematically collects information on several different common policy responses that governments have taken to respond to the pandemic on 18 indicators such as school closures and travel restrictions. It now has data from more than 180 countries.",
"homepage": "https://www.bsg.ox.ac.uk/research/covid-19-government-response-tracker",
"name": "Coronavirus Government Response Tracker",
"prefix": "r3d100013486",
"synonyms": [
"OxCGRT"
]
},
"r3d100013487": {
"description": "Polish Platform of Medical Research (PPM) is a digital platform presenting the scientific achievements and research potential of 8 Polish medical universities from Bialystok, Gdansk, Katowice, Lublin, Szczecin, Warsaw, Wroclaw, the Nofer Institute of Occupational Medicine in Lodz and the Jagiellonian University Medical College in Cracow that form a partnership for the PPM Project. It incorporates the features of a Current Research Information System and a consortium repository and uses OMEGA-PSIR software. It provides open access to full texts of publications, doctoral theses, research data and other documents. PPM is a central platform that aggregates data from the local platforms of the PPM Project Partners. PPM is accessible for any Internet user.",
"homepage": "https://ppm.edu.pl/index.seam",
"name": "Polish Platform of Medical Research",
"prefix": "r3d100013487",
"synonyms": [
"PPM",
"Polska Platforma Medyczna"
]
},
"r3d100013488": {
"description": "Institutional data repository built on the Figshare platform. Contains research data from the Technical University of Denmark",
"homepage": "https://data.dtu.dk/",
"name": "DTU Data",
"prefix": "r3d100013488",
"synonyms": [
"Technical University of Denmark Data"
]
},
"r3d100013494": {
"description": "DATICE was established in late 2018 and is funded by the University of Iceland's (UI) School of Social Sciences, with a contribution from the university's Centennial Fund. DATICE is the appointed service provider for the Consortium of European Social Science Data Archives (CESSDA ERIC) in Iceland and is located within the UI Social Science Research Institute (SSRI). The main goal of the data service is to ensure open and free access to high quality research data for the research community as well as the general public.",
"homepage": "https://dataverse.rhi.hi.is",
"name": "DATICE",
"prefix": "r3d100013494",
"synonyms": [
"GAGNΓS",
"GagnaΓΎjΓ³nusta fΓ©lagsvΓsinda Γ‘ Γslandi",
"The Icelandic Social Science Data Service"
]
},
"r3d100013497": {
"description": "The Cape Peninsula University of Technology uses Figshare for institutions for their data repository and it is called eSango. The repository's Designated community are academics at the university who produce outputs for funded research. It fits with the University's ambition to increase the visibility, reach, and impact of its research. The Designated Community consists of researchers from all the discipline areas researched at CPUT Figshare (as evidenced by https://cput.figshare.com)",
"homepage": "https://esango.cput.ac.za/",
"name": "eSango",
"prefix": "r3d100013497",
"synonyms": [
"CPUT Data Repository",
"Cape Peninsula University of Technology Figshare"
]
},
"r3d100013499": {
"description": "MDR is a data repository to collect and store papers, presentation materials, and related materials data to accumulate and release them in a form suitable for the promotion of materials research and materials informatics. Users can search the documents and the data from information (metadata) such as sample, instrument, method, and from the full text of the deposited data, to browse and download them freely. User registration is not required and there is no charge for use.",
"homepage": "https://mdr.nims.go.jp",
"name": "Materials Data Repository",
"prefix": "r3d100013499",
"synonyms": [
"MDR",
"NIMS Materials Data Repository",
"ζζγγΌγΏγͺγγΈγγͺ"
],
"xrefs": {
"opendoar": "9713"
}
},
"r3d100013500": {
"description": "OLOS is a Swiss-based data management portal tailored for researchers and institutions. Powerful yet easy to use, OLOS works with most tools and formats across all scientific disciplines to help researchers safely manage, publish and preserve their data. The solution was developed as part of a larger project focusing on Data Life Cycle Management (dlcm.ch) that aims to develop various services for research data management. Thanks to its highly modular architecture, OLOS can be adapted both to small institutions that need a \"turnkey\" solution and to larger ones that can rely on OLOS to complement what they have already implemented. OLOS is compatible with all formats in use in the different scientific disciplines and is based on modern technology that interconnects with researchers' environments (such as Electronic Laboratory Notebooks or Laboratory Information Management Systems).",
"homepage": "https://olos.swiss",
"name": "OLOS",
"prefix": "r3d100013500",
"synonyms": [
"Long-term preservation and publication of research data at the level of Switzerland"
]
},
"r3d100013503": {
"description": "arthistoricum.net@heiDATA is the research data repository of arthistoricum.net (Specialized Information Service Art - Photography - Design). It provides art historians with the opportunity to permanently publish and archive research data in the field of art history in connection with an open access online publication (e.g. article, ejournal, ebook) hosted by Heidelberg University Library. All research data e.g. images, videos, audio files, tables, graphics etc. receive a DOI (Digital Object Identifier). The data publications can be cited, viewed and permanently linked to as distinct academic output.",
"homepage": "https://heidata.uni-heidelberg.de/dataverse/arthistoricum",
"name": "arthistoricum.net@heiDATA",
"prefix": "r3d100013503"
},
"r3d100013504": {
"description": "PSI Open Data Provider allows users to consult open data related to experiments carried out at PSI. Data made available includes scientific datasets collected during experiments and publications if any. Users can search for data based on related metadata (both their own data and other people's public data).",
"homepage": "https://doi.psi.ch/",
"name": "PSI Open Data Provider",
"prefix": "r3d100013504",
"synonyms": [
"PSI Public Data Repository"
]
},
"r3d100013505": {
"description": "The Health Data Research Innovation Gateway (the βGatewayβ) provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access.\nThe Gateway includes the ability to search for research projects, publications and health data tools, such as those related to COVID-19. New interactive features provide a community forum for researchers to collaborate and connect and the ability to add research projects.\nThe Innovation Gateway does not hold or store any datasets or patient or health data but rather acts as a portal to allow discovery of datasets and to request access to them for health research. A dataset is a collection of related individual pieces of data but in the case of health data, identifiable information (e.g. name or NHS number) is removed and data is de-identified where possible. When you access the Gateway you will not be able to view or extract the data itself. Instead, you will be able to see information that describes what the different datasets are (e.g. where the dataset has come from, a description of the dataset, the time period and the geographical areas the dataset covers).",
"homepage": "https://www.healthdatagateway.org/",
"name": "Health Data Research Innovation Gateway",
"prefix": "r3d100013505",
"synonyms": [
"HDRUK Innovation Gateway"
]
},
"r3d100013506": {
"description": "The Center for Remote Sensing of Ice Sheets radar data repository containing data products from the Greenland Ice Sheet, the Antarctic Ice Sheet, sea ice, and land snow.",
"homepage": "https://data.cresis.ku.edu/",
"name": "Center for Remote Sensing of Ice Sheets",
"prefix": "r3d100013506",
"synonyms": [
"CReSIS"
]
},
"r3d100013507": {
"description": "Additional to the the e-publishing offer for articles, books and journals, Propylaeum provides classical scholars with the opportunity to archive the respective research data permanently. These can be linked directly to online publications hosted on the Heidelberg publishing platforms. All research data β e.g. images, videos, audio files, tables, graphics etc. β receive a DOI (Digital Object Identifiyer). Thus, they can be cited, viewed and permanently linked to as distinct academic output.",
"homepage": "https://heidata.uni-heidelberg.de/dataverse/propylaeum",
"name": "Propylaeum@heiDATA",
"prefix": "r3d100013507",
"synonyms": [
"Data publications of the Specialized Information Service Classics",
"Datenpublikationen des Fachinformationsdienst (FID) Altertumswissenschaften"
],
"xrefs": {
"fairsharing": "FAIRsharing.xFI5ob"
}
},
"r3d100013508": {
"description": "DASS-BiH (Data Archive for Social Sciences in Bosnia and Herzegovina) is the national service whose role is to ensure long-term preservation and dissemination of social science research data. The purpose of the data archive is to provide a vital research data resource for researchers, teachers, students, and all other interested users.",
"homepage": "https://dass.credi.ba/",
"name": "DASS-BiH",
"prefix": "r3d100013508",
"synonyms": [
"Data Archive for Social Sciences in Bosnia and Herzegovina"
]
},
"r3d100013510": {
"description": "DABAR (Digital Academic Archives and Repositories) is the key component of the Croatian e-infrastructureβs data layer. It provides technological solutions that facilitate maintenance of higher education and science institutions' digital assets, i.e., various digital objects produced by the institutions and their employees.",
"homepage": "https://dabar.srce.hr/en",
"name": "DABAR",
"prefix": "r3d100013510",
"synonyms": [
"Digital Academic Archives and Repositories"
]
},
"r3d100013511": {
"description": "The REA-IAPH aims to manage and disseminate the graphic collection of the institution as well as the scientific production and technical documentation resulting from its projects and activities of research and innovation, documentation, intervention, communication and dissemination in the field of Cultural Heritage.",
"homepage": "https://repositorio.iaph.es/",
"name": "Repositorio de Activos Digitales",
"prefix": "r3d100013511",
"synonyms": [
"Repositorio de Activos Digitales del Instituto Andaluz de Patrimonio HistΓ³rico"
]
},
"r3d100013512": {
"description": "The Open Energy Family aims to ensure quality, transparency and reproducibility in energy system research. It is a collection of various tools and information and that help working with energy related data. It is a collaborative community effort, everything is openly developed and therefore constantly evolving.\nThe main module is the Open Energy Platform (OEP), a web interface to access most of the modules, especially the community database. It provides a way to publish data with proper documentation (metadata), and link it to source code and underlying assumptions.\nOpen Energy Database is an open community database for energy, climate and modelling data.",
"homepage": "https://openenergyplatform.org/",
"name": "Open Energy Platform",
"prefix": "r3d100013512",
"synonyms": [
"Open Energy Database",
"Open Energy Family"
],
"xrefs": {
"fairsharing": "FAIRsharing.457642"
}
},
"r3d100013513": {
"description": "The KiezDeutsch-Korpus (KiDKo) has been developed by project B6 (PI: Heike Wiese) of the collaborative research centre Information Structure (SFB 632) at the University of Potsdam from 2008 to 2015. KiDKo is a multi-modal digital corpus of spontaneous discourse data from informal, oral peer group situations in multi- and monoethnic speech communities.\nKiDKo contains audio data from self-recordings, with aligned transcriptions (i.e., at every point in a transcript, one can access the corresponding area in the audio file). The corpus provides parts-of-speech tags as well as an orthographically normalised layer (Rehbein & Schalowski 2013). Another annotation level provides information on syntactic chunks and topological fields.\nThere are several complementary corpora:\nKiDKo/E (Einstellungen - \"attitudes\") captures spontaneous data from the public discussion on Kiezdeutsch: it assembles emails and readers' comments posted in reaction to media reports on Kiezdeutsch. By doing so, KiDKo/E provides data on language attitudes, language perceptions, and language ideologies, which became apparent in the context of the debate on Kiezdeutsch, but which frequently related to such broader domains as multilingualism, standard language, language prestige, and social class.\nKiDKo/LL (\"Linguistic Landscape\") assembles photos of written language productions in public space from the context of Kiezdeutsch, for instance love notes on walls, park benches, and playgrounds, graffiti in house entrances, and scribbled messages on toilet walls.\nContains materials in following languages: Spanish, Italian, Greek, Kurdish, Swedish, French, Croatian, Arabic, Turkish.",
"homepage": "https://www.linguistik.hu-berlin.de/de/institut/professuren/multilinguale-kontexte/korpora/kiezdeutschkorpus/",
"name": "Kiezdeutschkorpus KiDKo",
"prefix": "r3d100013513",
"synonyms": [
"KiDKo"
]
},
"r3d100013514": {
"description": "The Bach portal is a database for researchers and practical musicians interested in Johann Sebastian Bach and the whole Bach family. It contains detailed, fully searchable findings from research into Bach and high-resolution scans of works and sources.",
"homepage": "https://www.bach-digital.de/content/index.xed",
"name": "Bach digital",
"prefix": "r3d100013514"
},
"r3d100013516": {
"description": "\"The Digital Mozart Edition (DME) aims at making accessible the oeuvre of Wolfgang AmadΓ© Mozart (1756β1791) in digital formats. Access is free of charge for everybody.\"",
"homepage": "https://mozarteum.at/digitale-mozart-edition#info",
"name": "Digitale Mozart-Edition",
"prefix": "r3d100013516",
"synonyms": [
"DME",
"Digital Mozart Edition"
]
},
"r3d100013517": {
"description": "IMSLP is a subscription-based project for the creation of a virtual library of public-domain music scores.",
"homepage": "https://imslp.org/wiki/Main_Page",
"name": "International Music Score Library Project",
"prefix": "r3d100013517",
"synonyms": [
"MSLP",
"Petrucci Music Library"
]
},
"r3d100013518": {
"description": "SODHA is the federal Belgian data archive for social sciences and the digital humanities. SODHA is a new service of the State Archives of Belgium and acts as the Belgian service provider for the Consortium of European Social Science Data Archives (CESSDA).",
"homepage": "https://www.sodha.be/",
"name": "Social Sciences and Digital Humanities Archive",
"prefix": "r3d100013518",
"synonyms": [
"SODHA"
]
},
"r3d100013519": {
"description": "The institutional repository Refubium is a service of the University Library of Freie UniversitΓ€t. All the university members (research staff/scientists, students and other authors currently affiliated with Freie UnivesitΓ€t) are encouraged to deposit their scientific papers, master and bachelor thesis, as well as research data.",
"homepage": "https://refubium.fu-berlin.de/?locale-attribute=en",
"name": "Refubium",
"prefix": "r3d100013519",
"xrefs": {
"opendoar": "4732"
}
},
"r3d100013520": {
"description": "The TRR170-DB was set up to manage data products of the collaborative research center TRR 170 'Late Accretion onto Terrestrial Planets' (https://www.trr170-lateaccretion.de/). However, meanwhile the repository also stores data by other institutions and researchers. Data include laboratory and other instrumental data on planetary samples, remote sensing data, geological maps and model simulations.",
"homepage": "https://planetary-data-portal.org/",
"name": "TRR170-DB",
"prefix": "r3d100013520",
"synonyms": [
"Late Accretion Onto Terrestrial Planets"
]
},
"r3d100013522": {
"description": "Being both, a demand as well as a chance of the present age of information technology for cultural preservation and continuation, public databases possess an immense importance for providing a comprehensive access to cultural material as far as their contents and also their clientele of users are concerned. Therefore, an exemplary completely preserved stock of primary sources as the one of the Weimar theatre is no less than an invaluable piece of luck, possibly just due to the manageable local conditions of this small (former courtly) town in the middle of German language area. In this English version, first this rare cultural-historical phenomenon and its sources are described. Furthermore, the data- and metadata-contents within the Weimar theatre- and music-ephemera database are presented. Finally, the principal opportunities of searching this (meta-)data pool are explained, where presumed to be necessary supported by screenshot images from the internet platform.",
"homepage": "http://theaterzettel-weimar.de/home.html",
"name": "Theater und Musik in Weimar 1754 - 1990",
"prefix": "r3d100013522"
},
"r3d100013523": {
"description": "ZB MED's Repository for Life Sciences offers authors the chance to publish their scientific texts and research data from the fields of medicine, health, nutritional, environmental and agricultural sciences. In accordance with the principles of Open Access, these publications can be accessed over the Internet without restrictions.\nThere is no charge to publish, archive or use the documents.",
"homepage": "https://repository.publisso.de/",
"name": "PUBLISSO-Fachrepositorium Lebenswissenschaften",
"prefix": "r3d100013523",
"synonyms": [
"PUBLISSO-Repository for Life Sciences"
]
},
"r3d100013524": {
"description": "SMU Research Data Repository (SMU RDR) is a tool and service for researchers from Singapore Management University (SMU) to store, share and publish their research data. SMU RDR accepts a wide range of research data and outputs generated from research projects.",
"homepage": "https://researchdata.smu.edu.sg/",
"name": "SMU Research Data Repository",
"prefix": "r3d100013524",
"synonyms": [
"SMU RDR",
"Singapore Management University Research Data Repository"
]
},
"r3d100013525": {
"description": "Data@Lincoln is the research data repository for Lincoln University (New Zealand). Datasets may stand alone, or may consist of appendices to theses, or figures or other supplementary material to journal articles and other publications.",
"homepage": "https://data.lincoln.ac.nz/",
"name": "Data@Lincoln",
"prefix": "r3d100013525",
"xrefs": {
"opendoar": "4872"
}
},
"r3d100013526": {
"description": "The Universal Multimedia Electronic Library (UrMEL) is the central access platform for multimedia offers of the Thuringian University and State Library Jena (ThULB) and other partners. It provides access to scholarly information and cultural resources from the region of Thuringia and beyond.\nUrMEL cooperates with numerous archives, libraries, museums and scientific institutions.",
"homepage": "http://www.urmel-dl.de/",
"name": "UrMEL",
"prefix": "r3d100013526",
"synonyms": [
"Universal Multimedia Electronic Library"
]
},
"r3d100013527": {
"description": "St. Jude Cloud, an initiative of St. Jude Children's Research Hospital, provides data and analysis resources to the global research community. Our goal is to empower researchers across the world to advance cures for pediatric cancer and other pediatric catastrophic diseases.",
"homepage": "https://www.stjude.cloud/",
"name": "St. Jude Cloud",
"prefix": "r3d100013527"
},
"r3d100013528": {
"description": "The goal of e-codices is to provide free access to all medieval and a selection of modern manuscripts of Switzerland by means of a virtual library.",
"homepage": "https://www.e-codices.unifr.ch/en",
"name": "e-codices",
"prefix": "r3d100013528"
},
"r3d100013529": {
"description": "FULIR Data is a research data repository that gathers, permanently stores and allows open access to primary data produced by researchers based at RuΔer BoΕ‘koviΔ Institute. Researchers deposit datasets by themselves (self-archiving) with the support given by the Centre for Scientific Information and their RDM experts.",
"homepage": "https://data.fulir.irb.hr/",
"name": "FULIR Data",
"prefix": "r3d100013529",
"synonyms": [
"Repozitorij istraΕΎivaΔkih podataka Instituta RuΔer BoΕ‘koviΔ",
"RuΔer BoΕ‘koviΔ institute Data Repository"
]
},
"r3d100013531": {
"description": "<<>>!!!>>>",
"homepage": "https://dataverse.yale-nus.edu.sg/",
"name": "Yale-NUS Dataverse",
"prefix": "r3d100013531"
},
"r3d100013532": {
"description": "LaMBDa is the Research Data Portal of the Leibniz Institute for East and Southeast European Studies (IOS).",
"homepage": "https://lambda.ios-regensburg.de/",
"name": "IOS Regensburg Research Data Respository",
"prefix": "r3d100013532",
"synonyms": [
"LaMBDa IOS Research Data Respository",
"Labour, Migration and Biographical Data"
]
},
"r3d100013533": {
"description": "The University of the Western Cape (UWC) uses Figshare for Institutions for their institutional research data repository. It is called Kikapu, and serves as a repository for storing and disseminating research data.",
"homepage": "https://kikapu.uwc.ac.za/",
"name": "Kikapu",
"prefix": "r3d100013533",
"synonyms": [
"UWC Data Repository",
"UWC Figshare Repository",
"UWC IDR",
"University of the Western Cape Institutional Research Data Respository"
]
},
"r3d100013535": {
"description": "The BCMT data portal offers access magnetic data and indices of the French network of ground observatories, operated all over the world by French research institutions and international partners.",
"homepage": "http://www.bcmt.fr",
"name": "Bureau Central de MagnΓ©tisme Terrestre",
"prefix": "r3d100013535",
"synonyms": [
"BCMT"
]
},
"r3d100013536": {
"description": "The TRR228DB is the project-database of the Collaborative Research Centre 228 \"Future Rural Africa: Future-making and social-ecological transformation\" (CRC/Transregio 228, https://www.crc228.de) funded by the German Research Foundation (DFG, German Research Foundation β Project number 328966760). The project-database is a new implementation of the TR32DB and online since 2018. It handles all data including metadata, which are created by the involved project participants from several institutions (e.g. Universities of Cologne and Bonn) and research fields (e.g. anthropology, agroeconomics, ecology, ethnology, geography, politics and soil sciences). The data is resulting from several field campaigns, interviews, surveys, remote sensing, laboratory studies and modelling approaches. Furthermore, outcomes of the scientists such as publications, conference contributions, PhD reports and corresponding images are collected.",
"homepage": "https://www.trr228db.uni-koeln.de",
"name": "Collaborative Research Centre Transregio 228 Database",
"prefix": "r3d100013536",
"synonyms": [
"CRC/Transregio 228: Future Rural Africa: Future-making and social-ecological transformation",
"TRR228DB"
]
},
"r3d100013537": {
"description": "UCrea offers electronic access to documents generated by UC members in their academic, learning or research activity. The aim is to give greater visibility to academic production, increase impact and ensure preservation. UCrea supports documentation in various electronic formats and can include academic papers, research projects, preprints, articles, conference papers, etc.",
"homepage": "https://repositorio.unican.es/",
"name": "UCREA",
"prefix": "r3d100013537",
"synonyms": [
"Repositorio Abierto de la Universidad de Cantabria",
"Repository of the University of Cantabria"
],
"xrefs": {
"roar": "5212"
}
},
"r3d100013538": {
"description": "The Jurisdictional Ocean Information Sharing System (JOISS) is a research activity to promote joint utilization of marine R&D projects and marine scientific materials at home and abroad.\nAs a representative research activity, data curation activities are continuously carried out in accordance with the data life cycle to expand the utilization of the JOISS portal system.\nIn order to provide integrated and standardized marine information, we are conducting standardization research for the distribution of marine geographic information metadata by referring to international standards and domestic and international marine data centers.\nIn addition, we provide information and guidance for marine education and research, and strive to strengthen the exchange of data between marine research data repositories.",
"homepage": "https://joiss.kr/joiss/",
"name": "Jurisdictional Ocean Information Sharing System",
"prefix": "r3d100013538",
"synonyms": [
"JOISS",
"κ΄ν ν΄μν΄μμ 보 곡λνμ©μμ€ν
"
]
},
"r3d100013539": {
"description": "RETOPEA investigates the different ways in which religious coexistence is thought of in different environments and how religious peace treaties have been established in the past. The idea is to use the insights gained to inform thinking about present-day peaceful religious co-existence\nThe dataset contains the contents and the metadata of the resources (i.e., clippings) published on the RETOPEA website (retopea.eu).",
"homepage": "https://www.retopea.eu/",
"name": "RETOPEA",
"prefix": "r3d100013539",
"synonyms": [
"Religious Toleration and Peace"
]
},
"r3d100013541": {
"description": "Harmonia universalis is a prosopographical database gathering data on the actors of the mesmerist movement at the end of the 18th century.\nThe Harmonia Universalis database is designed as a space for exchange and sharing between researchers and enthusiasts. Any interested person can participate in its realization by contacting the administrators of the database. They will then be able to enter directly on line the information they wish to introduce. These will be integrated into the database after confirmation by the administrators.",
"homepage": "https://harmoniauniversalis.univ-paris1.fr/",
"name": "Harmonia Universalis",
"prefix": "r3d100013541"
},
"r3d100013542": {
"description": "The long-term vision of the NMDC is to support microbiome data exploration through a sustainable data discovery platform that promotes open science and shared-ownership across a broad and diverse community of researchers, funders, publishers, and societies. The NMDC is developing a distributed data infrastructure while engaging with the research community to enable multidisciplinary and FAIR microbiome data.",
"homepage": "https://microbiomedata.org/",
"name": "National Microbiome Data Collaborative",
"prefix": "r3d100013542",
"synonyms": [
"NMDC"
],
"xrefs": {
"biodbcore": "001563"
}
},
"r3d100013544": {
"description": "The ZFMK Biodiversity Data Center is aimed at hosting, archiving, publishing and distributing data from biodiversity research and zoological collections. The Biodiversity Data Center handles and curates data on:\n- The specimens of the institutes collection, including provenance, distribution, habitat, and taxonomic data.\n- Observations, recordings and measurements from field research, monitoring and ecological inventories.\n- Morphological measurements, descriptions on specimens, as well as\n- Genetic barcode libraries, and\n- Genetic and molecular research data associated with specimens or environmental samples.\nFor this purpose, suitable software and hardware systems are operated and the required infrastructure is further developed.\nCore components of the software architecture are:\n The DiversityWorkbench suite for managing all collection-related information.\n The Digital Asset Management system easyDB for multimedia assets.\n The description database MorphΒ·DΒ·Base for morphological data sets and character matrices.",
"homepage": "https://www.zfmk.de/en/research/research-centres-and-groups/datacenter",
"name": "ZFMK Biodiversity Data Center",
"prefix": "r3d100013544",
"synonyms": [
"ZFMK\nNatural History Collections - occurrence data",
"ZFMK Datenzentrum"
]
},
"r3d100013546": {
"description": "ScholarWorks offers long-term storage and public access to the data and datasets produced by labs and researchers at UMass Amherst.",
"homepage": "https://scholarworks.umass.edu/data/",
"name": "ScholarWorks@UMassAmherst",
"prefix": "r3d100013546",
"synonyms": [
"ScholarWorks",
"ScholarWorks@UMassAmherst Data Repository"
]
},
"r3d100013547": {
"description": "LiceBase is a database for sea lice genomics. LiceBase provides the genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, Blast functionality and access to related high-thoughput genomics data.",
"homepage": "https://licebase.org/",
"name": "LiceBase",
"prefix": "r3d100013547",
"xrefs": {
"fairsharing": "FAIRsharing.c7w81a"
}
},
"r3d100013548": {
"description": "CLARIN-LV is a national node of Clarin ERIC (Common Language Resources and Technology Infrastructure). The mission of the repository is to ensure the availability and longΒ term preservation of language resources. The data stored in the repository are being actively used and cited in scientific publications.",
"homepage": "https://repository.clarin.lv",
"name": "CLARIN-LV repository",
"prefix": "r3d100013548",
"synonyms": [
"CLARIN Latvia repository"
]
},
"r3d100013549": {
"description": "We present the MUSE-Wide survey, a blind, 3D spectroscopic survey in the CANDELS/GOODS-S and CANDELS/COSMOS regions. Each MUSE-Wide pointing has a depth of 1 hour and hence targets more extreme and more luminous objects over 10 times the area of the MUSE-Deep fields (Bacon et al. 2017). The legacy value of MUSE-Wide lies in providing \"spectroscopy of everything\" without photometric pre-selection. We describe the data reduction, post-processing and PSF characterization of the first 44 CANDELS/GOODS-S MUSE-Wide pointings released with this publication. Using a 3D matched filtering approach we detected 1,602 emission line sources, including 479 Lyman-Ξ± (Lya) emitting galaxies with redshifts 2.9β²zβ²6.3. We cross-match the emission line sources to existing photometric catalogs, finding almost complete agreement in redshifts and stellar masses for our low redshift (z < 1.5) emitters. At high redshift, we only find ~55% matches to photometric catalogs. We encounter a higher outlier rate and a systematic offset of Ξzβ0.2 when comparing our MUSE redshifts with photometric redshifts. Cross-matching the emission line sources with X-ray catalogs from the Chandra Deep Field South, we find 127 matches, including 10 objects with no prior spectroscopic identification. Stacking X-ray images centered on our Lya emitters yielded no signal; the Lya population is not dominated by even low luminosity AGN. A total of 9,205 photometrically selected objects from the CANDELS survey lie in the MUSE-Wide footprint, which we provide optimally extracted 1D spectra of. We are able to determine the spectroscopic redshift of 98% of 772 photometrically selected galaxies brighter than 24th F775W magnitude. All the data in the first data release - datacubes, catalogs, extracted spectra, maps - are available at the website.",
"homepage": "https://musewide.aip.de/",
"name": "MUSE-Wide",
"prefix": "r3d100013549",
"synonyms": [
"MUSE-Wide archive",
"Multi Unit Spectroscopic Explorer Wide"
]
},
"r3d100013550": {
"description": "RΔ«ga StradiΕΕ‘ University (RSU) Dataverse is created for RSU researchers to deposit their data there after the end of research projects or other research activities, especially in cases when there are no trusted field specific repositories.",
"homepage": "https://dataverse.rsu.lv/dataverse/rsu",
"name": "Riga Stradins University dataverse",
"prefix": "r3d100013550",
"synonyms": [
"RSU data repository",
"RΔ«ga StradiΕΕ‘ University Institutional Repository Dataverse"
]
},
"r3d100013553": {
"description": "The German National Library offers free access to its bibliographic data and several collections of digital objects. As the central access point for presenting, accessing and reusing digital resources, DNBLab allows users to access our data, object files and full texts. The access is available by download and through various interfaces.",
"homepage": "https://www.dnb.de/librarylab",
"name": "DNBLab",
"prefix": "r3d100013553"
},
"r3d100013555": {
"description": "FinBIF is an integral part of the global biodiversity informatics framework, dedicated to managing species information. Its mission encompasses a wide array of services, including the generation of digital data through various processes, as well as the sourcing, collation, integration, and distribution of existing digital data. Key initiatives under FinBIF include the digitization of collections, the development of data systems for collections Kotka (https://biss.pensoft.net/article/37179/) and observations (https://biss.pensoft.net/article/39150/), and the establishment of a national DNA barcode reference library. \n\nFinBIF manages data types such as verbal species descriptions (which include drawings, pictures, and other media types), biological taxonomy, scientific collection specimens, opportunistic systematic and event-based observations, and DNA barcodes. It employs a unified IT architecture to manage data flows, delivers services through a single online portal, fosters collaboration under a cohesive umbrella concept, and articulates development visions under a unified brand. The portal Laji.fi serves as the entry point to this harmonized open data ecosystem. FinBIF's portal is accessible in Finnish, Swedish, and English. Data intended for restricted use are made available to authorities through a separate portal, while open data are also shared with international systems, such as GBIF.",
"homepage": "https://laji.fi/en",
"name": "Finnish Biodiversity Information Facility",
"prefix": "r3d100013555",
"synonyms": [
"FinBIF",
"Finlands Artdatacenter",
"Laji.fi",
"Suomen Lajitietokeskus"
],
"xrefs": {
"fairsharing": "FAIRsharing.58bd67",
"ror": "01c0yey93"
}
},
"r3d100013556": {
"description": "JΓΌlich DATA is a registry service to index all research data created at or in the context of Forschungszentrum JΓΌlich. As an institutionial repository, it may also be used for data and software publications.",
"homepage": "https://data.fz-juelich.de/",
"name": "JΓΌlich DATA",
"prefix": "r3d100013556"
},
"r3d100013557": {
"description": "TU Wien Research Data is an institutional repository of TU Wien to enable storing, sharing and publishing of digital objects, in particular research data. It facilitates the funders' requirements for open access to research data and the FAIR principles by making research output findable, accessible, interoperable, and reusable. A DOI is assigned to each dataset published in TU Wien Research Data. This service is developed by the TU Wien Center for Research Data Management and hosted by TU.it.",
"homepage": "https://researchdata.tuwien.at/",
"name": "TU Wien Research Data",
"prefix": "r3d100013557",
"xrefs": {
"fairsharing": "FAIRsharing.88d503"
}
},
"r3d100013559": {
"description": "The CORA. Repositori de dades de Recerca is a repository of open, curated and FAIR data that covers all academic disciplines. CORA. Repositori de dades de Recerca is a shared service provided by participating Catalan institutions (Universities and CERCA Research Centers). The repository is managed by the CSUC and technical infrastructure is based on the Dataverse application, developed by international developers and users led by Harvard University (https://dataverse.org).",
"homepage": "https://dataverse.csuc.cat/",
"name": "CORA. Repositori de Dades de Recerca",
"prefix": "r3d100013559",
"xrefs": {
"fairsharing": "FAIRsharing.av9fsp"
}
},
"r3d100013562": {
"description": "Movebank is an online platform that helps researchers and wildlife managers worldwide manage, share, analyze and archive animal movement data. Movebank's database is designed for locations of individual animals over time, commonly referred to as tracking data, and measurements collected by other sensors attached to animals, as well as information about related animals, tags and deployments. The platform supports public and controlled-access sharing, and offers services for working with data from initial collection through publication, discovery and re-use.",
"homepage": "https://www.movebank.org/",
"name": "Movebank",
"prefix": "r3d100013562"
},
"r3d100013563": {
"description": "The data publishing portal of Marine Scotland, the directorate of the Scottish Government responsible for the management of Scotland's seas.",
"homepage": "https://data.marine.gov.scot/",
"name": "Marine Scotland Data",
"prefix": "r3d100013563"
},
"r3d100013564": {
"description": "The JACQ System is a combined metadata and digital images platform and repository that contains data from botanical object collections.",
"homepage": "https://www.jacq.org",
"name": "JACQ - Virtual Herbaria",
"prefix": "r3d100013564",
"synonyms": [
"JACQ"
],
"xrefs": {
"fairsharing": "FAIRsharing.e28856"
}
},
"r3d100013565": {
"description": "An institutional repository at Graz University of Technology to enable storing, sharing and publishing research data, publications and open educational resources. It provides open access services and follows the FAIR principles.",
"homepage": "https://repository.tugraz.at/",
"name": "TU Graz Repository",
"prefix": "r3d100013565"
},
"r3d100013567": {
"description": "The Digital German Women's Archive (DDF) is an interactive specialist portal on the history of women's movements in Germany. It invites you to get to know topics, actors and networks of the women's movements from two centuries. For this purpose, the lesbian / women's archives, libraries and documentation centers, which are linked in the i.d.a. umbrella organization, present selected digital copies and further information from their holdings.",
"homepage": "https://www.digitales-deutsches-frauenarchiv.de",
"name": "Digitales Deutsches Frauenarchiv",
"prefix": "r3d100013567",
"synonyms": [
"DDF"
]
},
"r3d100013569": {
"description": "The purpose of the Social Data Repository (RDS) is to make available in the Internet social data, consisting of data sets and accompanying technical or methodological documentation. The use of Repository is open for everyone.\n\nThe repository is operated by the University of Warsaw (Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw). Individual collections in the Social Data Repository are subject to editorial review by University of Warsaw or collection administrators, under separate rules for a given collection. In particular, the supervising editor for the collection βArchive of Quantitative Social Dataβ is the Team of the Archive of Quantitative Social Data.",
"homepage": "https://rds.icm.edu.pl/",
"name": "Social Data Repository (RDS)",
"prefix": "r3d100013569",
"synonyms": [
"Repozytorium Danych SpoΕecznych (RDS)"
]
},
"r3d100013570": {
"description": "MD-SOAR is a shared digital repository platform for eleven colleges and universities in Maryland. It is currently funded by the University System of Maryland and Affiliated Institutions (USMAI) Library Consortium (usmai.org) and other participating partner institutions. MD-SOAR is jointly governed by all participating libraries, who have agreed to share policies and practices that are necessary and appropriate for the shared platform. Within this broad framework, each library provides customized repository services and collections that meet local institutional needs. Please follow the links below to learn more about each library's repository services and collections.",
"homepage": "https://mdsoar.org/",
"name": "MD-SOAR",
"prefix": "r3d100013570",
"synonyms": [
"Maryland Shared Open Access Repository"
]
},
"r3d100013571": {
"description": "The NF Data Portal is designed to help openly explore and share NF datasets, analysis tools, resources, and publications related to neurofibromatosis. Anyone can join the NF Open Science Initiative (NF-OSI) to participate! We welcome contributions from anyone in the neurofibromatosis and schwannomatosis research community, such as original datasets generated by the community or analyses of data from the NF Data Portal.",
"homepage": "https://nf.synapse.org",
"name": "NF Data Portal",
"prefix": "r3d100013571",
"xrefs": {
"scr": "021683"
}
},
"r3d100013574": {
"description": "Macromolecular Xtallography Raw Data Repository (MX-RDR) is a domain-specific digital repository of crystallographic open research data. The use of Repository is open for everyone.",
"homepage": "https://mxrdr.icm.edu.pl/",
"name": "Macromolecular Xtallography Raw Data Repository",
"prefix": "r3d100013574",
"synonyms": [
"MX-RDR"
]
},
"r3d100013575": {
"description": "Open At LaTrobe (OPAL) is La Trobe Universityβs official repository for Open Access materials generated by academic and professional staff and HDR students. These include publications and other research outputs, theses, open data, and educational resources. OPAL enables the storage, sharing, and selective publication of files and the assignment of a persistent DOI. Users maintain control over who can see their private files and all uploads are stored in La Trobe University approved storage. Access is via La Trobe University login credentials.\nLa Trobe produces a wide range of useful datasets including supplementary data associated with publications and stand-alone datasets and collections.",
"homepage": "https://opal.latrobe.edu.au/Open_Data",
"name": "OPAL",
"prefix": "r3d100013575",
"synonyms": [
"Open At La Trobe"
]
},
"r3d100013576": {
"description": "The Archaeological Map of the Czech Republic (AMCR) is a repository designed for information on archaeological investigations, sites and finds, operated by the Archaeological Institutes of the CAS in Prague and Brno. The archives of these institutions contain documentation of archaeological fieldwork on the territory of the Czech Republic from 1919 to the present day, and they continue to enrich their collections. The AMCR database and related documents form the largest collection of archaeological data concerning the Czech Republic and are therefore an important part of our cultural heritage. The AMCR digital archive contains various types of records - individual archaeological documents (texts, field photographs, aerial photographs, maps and plans, digital data), projects, fieldwork events, archaeological sites, records of individual finds and a library of 3D models. Data and descriptive information are continuously taken from the AMCR and presented in the the AMCR Digital Archive interface.",
"homepage": "https://digiarchiv.aiscr.cz/",
"name": "Archaeological Map of the Czech Republic",
"prefix": "r3d100013576",
"synonyms": [
"AMCR Digital Archive",
"ArcheologickΓ‘ mapa ΔeskΓ© republiky",
"DigitΓ‘lnΓ archiv AMΔR"
],
"xrefs": {
"fairsharing": "FAIRsharing.4160e0"
}
},
"r3d100013577": {
"description": "Diamond Light Source is the UKβs national synchrotron, located at the Harwell Science and Innovation Campus in Oxfordshire. It works like a giant microscope, harnessing the power of electrons to produce bright light that scientists can use to study anything from fossils to jet engines to viruses and vaccines. ICAT allows you to browse and download archived data from instrument experiments at Diamond Light Source.",
"homepage": "https://icat.diamond.ac.uk/datagateway",
"name": "Diamond data catalogue",
"prefix": "r3d100013577",
"synonyms": [
"Diamond Light Source data catalogue",
"ICAT"
]
},
"r3d100013578": {
"description": "The European Mouse Mutant Archive β EMMA is a non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant mouse strains essential for basic biomedical research. The laboratory mouse is the most important mammalian model for studying genetic and multi-factorial diseases in man. The comprehensive physical and data resources of EMMA support basic biomedical and preclinical research, and the available research tools and mouse models of human disease offer the opportunity to develop a better understanding of molecular disease mechanisms and may provide the foundation for the development of diagnostic, prognostic and therapeutic strategies.",
"homepage": "https://www.infrafrontier.eu/emma/",
"name": "European Mouse Mutant Archive",
"prefix": "r3d100013578",
"synonyms": [
"EMMA"
],
"xrefs": {
"fairsharing": "FAIRsharing.g2fjt2",
"nlx": "151625",
"scr": "006136"
}
},
"r3d100013579": {
"description": "The Linguistic Linked Open Data cloud is a collaborative effort pursued by several members of the OWLG, with the general goal to develop a Linked Open Data (sub-)cloud of linguistic resources. The diagram is inspired by the Linking Open Data cloud diagram by Richard Cyganiak and Anja Jentzsch, and the resources included are chosen according to the same criteria of openness, availability and interlinking. Although not all resources are already available, we actively work towards this goal, and subsequent versions of this diagram will be restricted to openly available resources. Until that point, please refer to the diagram explicitly as a \"draft\".",
"homepage": "https://linguistic-lod.org/",
"name": "Linguistic Linked Open Data",
"prefix": "r3d100013579",
"synonyms": [
"LLOD"
]
},
"r3d100013580": {
"description": "ScholarWorks preserves and provides access to the research and creative scholarship created by Brandeis faculty, students, and staff. The research papers, theses, dissertations, books, reports, interviews, data and multimedia here represent Brandeisβs rich intellectual and cultural community.",
"homepage": "https://scholarworks.brandeis.edu/",
"name": "Brandeis ScholarWorks",
"prefix": "r3d100013580"
},
"r3d100013582": {
"description": "Finnish Meteorological Institute (FMI) research data repository METIS is provided by EUDAT and enables the institute data to be preserved, discovered, and accessed. FMI covers a wide range of research on weather, sea, climate and space. According to the FMI's Research Data policy , publicly funded research data must be made available to the widest possible audience (under CC BY license, at the minimum), as the best way to maximize the data impact but also to do justice to all the hard labor put into collecting, cleaning, and analyzing the data.",
"homepage": "https://fmi.b2share.csc.fi",
"name": "METIS",
"prefix": "r3d100013582",
"synonyms": [
"FMIβs Research Data Repository",
"Finnish Meteorological Institute's Research Data Repository"
]
},
"r3d100013583": {
"description": "The Endangered Languages Archive (ELAR) is a digital repository for preserving multimedia collections of endangered languages from all over the world, making them available for future generations.\nIn ELARβs collections you can find recordings of every-day conversations, instructions on how to build fish traps or boats, explanations of kinship systems and the use of medicinal plants, and learn about art forms like string figures and sand drawings. ELARβs collections are unique records of local knowledge systems encoded in their languages, described by the holders of the knowledge themselves.",
"homepage": "https://www.elararchive.org/",
"name": "Endangered Languages Archive",
"prefix": "r3d100013583",
"synonyms": [
"ELAR"
]
},
"r3d100013584": {
"description": "aviDa is the RDC for audio-visual data of empirical qualitative social research at the Department of General Sociology at the Technische UniversitΓ€t Berlin, developed in cooperation between the Technische UniversitΓ€t Berlin and the University of Bayreuth. aviDa aims at opening and sharing videographic research data since 2018.",
"homepage": "https://depositonce.tu-berlin.de/collections/583fdd9c-3d05-4e09-9959-08ab7d74c1f0",
"name": "aviDa",
"prefix": "r3d100013584",
"synonyms": [
"FDZ-aviDa",
"Forschungsdateninfrastruktur fΓΌr audio-visuelle Forschungsdaten der empirischen qualitativen Sozialforschung",
"RDC-aviDa",
"Research Data Centre for audio-visual data of qualitative social research"
]
},
"r3d100013585": {
"description": "The BAMF-FDZ is part of the BAMF Research Centre. The establishment of the Research Data Centre is, among others, the result of an amendment to the German Act on the Central Register of Foreigners (AuslΓ€nderzentralregistergesetz, AZRG). The data service is free of charge.",
"homepage": "https://www.bamf.de/DE/Themen/Forschung/Forschungsdatenzentrum/forschungsdatenzentrum-node.html",
"name": "Forschungsdatenzentrum des Bundesamtes fΓΌr Migration und FlΓΌchtlinge",
"prefix": "r3d100013585",
"synonyms": [
"BAMF-FDZ"
]
},
"r3d100013586": {
"description": "The ACSS Dataverse is a repository of interdisciplinary social science research data produced in and on the Arab region. The ACSS Dataverse, part of an initiative of the Arab Council for the Social Sciences in collaboration with the Odum Institute for Research in Social Science at the University of North Carolina at Chapel Hill, preserves and facilitates access to social science datasets in and on the Arab region and is open to relevant research data deposits.",
"homepage": "https://dataverse.theacss.org/",
"name": "ACSS Dataverse",
"prefix": "r3d100013586",
"synonyms": [
"Arab Council for the Social Sciences Dataverse",
"Conseil Arabe pour les Sciences Sociales Dataverse"
]
},
"r3d100013589": {
"description": "The National Library of Scotland was formally constituted by an Act of Parliament in 1925 and is one of six libraries covered by the UK legal deposit system.\nThe Library is Scotland's national archive for published and other literary heritage materials. One of our primary responsibilities is to safeguard the collections for future generations.\nOur collections care facility is recognised nationally and internationally as a centre of excellence for the preservation and conservation of library materials.\nNLS includes \"Data Foundry\", data collections from the National Library of Scotland.",
"homepage": "https://www.nls.uk/",
"name": "National Library of Scotland",
"prefix": "r3d100013589",
"synonyms": [
"Leabharlann NΓ iseanta na h-Alba"
]
},
"r3d100013590": {
"description": "The University selected figshare as a general purpose research data repository to enable researchers to share research data, facilitate open research practices and meet the evolving requirements of research funders and academic publishers. This is a public-facing platform for researchers to share their data and build, over time, a comprehensive representation of the research done at the University across all faculties and disciplines.",
"homepage": "https://figshare.manchester.ac.uk/",
"name": "University of Manchester figshare",
"prefix": "r3d100013590"
},
"r3d100013591": {
"description": "National ecosystem data bank (EcoDB) is a public professional scientific data repository supported by the National Ecosystem Science Data Center (NESDC) for researchers in ecology and related fields, which provides long-term preservation, publication, sharing and access services of scientific data. EcoDB provides services for both individual researchers and scientific journals. Individuals can use this repository to store, manage and publish scientific data, get feedback from others on the data, and discover scientific data shared by others through this repository. Journals can use the repository to gather, manage and review the supporting data of submitted paper. At the same time, journals can timely publish these supporting data according to their own data policies.",
"homepage": "http://ecodb.cern.ac.cn",
"name": "National Ecosystem Data Bank",
"prefix": "r3d100013591",
"synonyms": [
"EcoDB",
"ε½εΆηζη§ε¦ζ°ζεε¨εΊ"
],
"xrefs": {
"fairsharing": "FAIRsharing.ad7575"
}
},
"r3d100013592": {
"description": "IDOC-DATA is a department of IDOC \nIDOC (Integrated Data & Operation Center) has existed since 2003 as a satellite operations center and data center for the Institute of Space Astrophysics (IAS) in Orsay, France. Since then, it has operated within the OSUPS (Observatoire des Sciences de l'Univers de l'UniversitΓ© Paris-Saclay - first french university in shanghai ranking), which includes three institutes: IAS, AIM (Astrophysique, InterprΓ©tation, ModΓ©lisation - IRFU, CEA) and GEOPS (Geosciences Paris-Saclay) . \nIDOC participates in the space missions of OSUPS and its partners, from mission design to long-term scientific data archiving. For each phase of the missions, IDOC offers three kinds of services in the scientific themes of OSUPS and therefore IDOC's activities are divided into three departments: \n IDOC-INSTR: instrument design and testing, \n IDOC-OPE: instrument operations, \n IDOC-DATA: data management and data value chain: to produce the different levels of data constructed from observations of these instruments and make them available to users for ergonomic and efficient scientific interpretation (IDOC-DATA). It includes the responsibility: \n - To build access to these datasets. \n - To offer the corresponding services such as catalogue management, visualization tools, software pipeline automation, etc. \n - To preserve the availability and reliability of this hardware and software infrastructure, its confidentiality where applicable and its security.",
"homepage": "https://idoc.osups.universite-paris-saclay.fr/",
"name": "IDOC-DATA",
"prefix": "r3d100013592",
"synonyms": [
"Integrated Data and Operation Center repository"
]
},
"r3d100013594": {
"description": "Cary Institute data repository allows researchers to store, share and publish their research data, supplementary information and associated metadata. Each published item is assigned a Digital Object identifier (DOI), which allows the data to be citable and sustainable. This repository is a member node of DataOne.",
"homepage": "https://caryinstitute.figshare.com/",
"name": "Cary Institute of Ecosystem Studies figshare",
"prefix": "r3d100013594"
},
"r3d100013596": {
"description": "The German Central Health Study Hub is a platform that serves two different kinds of users. First, it allows scientists and data holding organizations (data producers) to publish their project characteristics, documents and data related to their research endeavour in a FAIR manner. Obviously, patient-level data cannot be shared publicly, however, metadata describing the patient-level data along with information about data access can be shared via the platform (preservation description information). The other kind of user is a scientist or researcher (data consumer) that likes to find information about past and ongoing studies and is interested in reusing existing patient-level data for their project. To summarize, the platforms connect data providers with data consumers in the domain of clinical, public health and epidemiologic health research to foster reuse. \nThe platform aggregates and harmonizes information already entered in various public repositories such as DRKS, clinicaltrials.gov, WHO ICTRP to provide a holistic view of the German research landscape in the aforementioned research areas. In addition, data stewards actively collect available information from (public) resources such as websites that cannot be automatically integrated.\nThe service started during the COVID-19 pandemic.",
"homepage": "https://csh.nfdi4health.de/",
"name": "German Central Health Study Hub",
"prefix": "r3d100013596"
},
"r3d100013602": {
"description": "The University of Tasmania Research Data Portal (RDP) enables UTAS researchers to securely store and publish their datasets. Datasets published in RDP are publicly available through the Research Data Australia Search Portal (https://researchdata.edu.au/).",
"homepage": "https://rdp.utas.edu.au",
"name": "University of Tasmania Research Data Portal",
"prefix": "r3d100013602",
"synonyms": [
"UTAS RDP"
],
"xrefs": {
"fairsharing": "FAIRsharing.l3u60T"
}
},
"r3d100013603": {
"description": "TIWβs Warehouse is a centralized, electronic database holding the most current details on the official, or βgold,β record for virtually all cleared and bilateral credit default swap (CDS) contracts outstanding in the global marketplace. The Warehouse contains more than 50,000 accounts representing derivatives counterparties across 95 countries.",
"homepage": "https://www.dtcc.com/repository-otc-data",
"name": "Depository Trust & Clearing Corporation Data Services",
"prefix": "r3d100013603",
"synonyms": [
"DTCC Data Services"
]
},
"r3d100013604": {
"description": "A consolidated feed from 35 million instruments provides sophisticated normalized data, streamlining analysis and decisions from front office to operations. And with flexible delivery options including cloud and API, timely accurate data enables the enterprise to capture opportunities, evaluate risk and ensure compliance in fast-moving markets.",
"homepage": "https://www.bloomberg.com/professional/product/market-data/",
"name": "Bloomberg",
"prefix": "r3d100013604",
"synonyms": [
"Bloomberg Market Data"
]
},
"r3d100013606": {
"description": "In 2018, the Ministry of Higher Education, Research and Innovation has included in its roadmap the creation of a new infrastructure called the National Biodiversity Data Centre (PNDB). The PNDB's missions are part of a FAIR (Easy to Find, Accessible, Interoperable, Reusable) approach, and consist in\n- providing access to datasets and metadata, associated services and products derived from the analyses\n- promoting scientific leadership to identify gaps and foster the emergence of community-driven systems of users and producers\n- facilitate the sharing of practices with other research communities, encourage the sharing of data and their reuse, and be part of the reflection on the future Earth System infrastructure.\n- promote coherence with national, European and international efforts concerning access to and use of biodiversity research data and the promotion of products and services.\nThe PNDB is supported by the MusΓ©um national d'Histoire naturelle, more specifically by the UMS 2006 PatriNat, a MNHN CNRS and AFB unit. The project is closely linked with the FRB and several of its founding institutions (AFB, BRGM, CIRAD, CNRS, Ifremer, INERIS, INRA, IRD, IRSTEA, MNHN, Univ. Montpellier).",
"homepage": "https://data.pndb.fr/",
"name": "PΓ΄le National de DonnΓ©es de BiodiversitΓ©",
"prefix": "r3d100013606",
"synonyms": [
"National Biodiversity Data Center",
"PNDB"
],
"xrefs": {
"fairsharing": "FAIRsharing.SfXDoZ"
}
},
"r3d100013607": {
"description": "The Radboud Data Repository (RDR) is an institutional repository for archiving and sharing of data collected, processed, or analyzed by researchers working at or affiliated with the Radboud University (Nijmegen, the Netherlands). The repository allows safe long-term (at least 10 years) storage of large datasets. The RDR promotes findability of datasets by providing a DOI and rich metadata fields and allows researchers to easily manage data access.",
"homepage": "https://data.ru.nl",
"name": "Radboud Data Repository",
"prefix": "r3d100013607",
"synonyms": [
"RDR"
],
"xrefs": {
"fairsharing": "FAIRsharing.559bc5"
}
},
"r3d100013608": {
"description": "DaKS is the institutional repository of the University of Kassel for research data. It offers structured storage of research data alongside with descriptive metadata, long-term archiving for at least 10 years and β if requested β the publication of the dataset with a DOI.",
"homepage": "https://daks.uni-kassel.de",
"name": "DaKS",
"prefix": "r3d100013608",
"synonyms": [
"Datarepository of the University of Kassel",
"Datenrepositorium Kassel",
"Datenrepository der UniversitΓ€t Kassel"
]
},
"r3d100013609": {
"description": "The Royal Library of the Netherlands (Dutch: Koninklijke Bibliotheek or KB; Royal Library) is the national library of the Netherlands. The KB collects everything that is published in and concerning the Netherlands, from medieval literature to today's publications. The e-Depot contains\nthe Dutch National Library Collection of born-digital publications from, and about, the Netherlands, and international\npublications consisting of born-digital scholarly articles included in journals produced by publishers originally based in the\nNetherlands",
"homepage": "https://www.kb.nl/",
"name": "National Library of the Netherlands e-depot",
"prefix": "r3d100013609",
"synonyms": [
"Koninklijke Bibliotheek - KB"
]
},
"r3d100013612": {
"description": "Atmosphere to Electrons (A2e) is a new, multi-year, multi-stakeholder U.S. Department of Energy (DOE) research and development initiative tasked with improving wind plant performance and mitigating risk and uncertainty to achieve substantial reduction in the cost of wind energy production.\nThe A2e strategic vision will enable a new generation of wind plant technology, in which smart wind plants are designed to achieve optimized performance stemming from more complete knowledge of the inflow wind resource and complex flow through the wind plant.",
"homepage": "https://a2e.energy.gov/data",
"name": "Atmosphere to Electrons, Data Archive and Portal",
"prefix": "r3d100013612",
"synonyms": [
"A2e, DAP"
]
},
"r3d100013613": {
"description": "The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) is a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab). All data generated by the DOE Joint Genome Institute is available through this repository once the data are published or public.",
"homepage": "https://data.jgi.doe.gov",
"name": "Joint Genome Institute Data Portal",
"prefix": "r3d100013613",
"synonyms": [
"JGI Data Portal"
]
},
"r3d100013615": {
"description": "AlphaFold DB provides open access to protein structure predictions for the human proteome and 20 other key organisms to accelerate scientific research.",
"homepage": "https://alphafold.ebi.ac.uk/",
"name": "AlphaFold",
"prefix": "r3d100013615",
"synonyms": [
"AlphaFold Protein Structure Database"
]
},
"r3d100013617": {
"description": "Data catalogue and repository for New Zealand's Biological Heritage National Science Challenge",
"homepage": "https://data.bioheritage.nz/",
"name": "New Zealand's Biological Heritage National Science Challenge Data Repository",
"prefix": "r3d100013617",
"synonyms": [
"NZ BioHeritage National Science Challenge Data Repository"
],
"xrefs": {
"scr": "023141"
}
},
"r3d100013623": {
"description": "The MHKDR is the repository for all data collected using funds from the Water Power Technologies Office (WPTO) of the U.S. Department of Energy (DOE). It was established to receive, manage, and make available all water power relevant data generated from projects funded by the DOE Water Power Technologies Office. This includes data from WPTO-funded projects associated with any portion of the water power project life-cycle (exploration, development, operation), as well as data produced by WPTO-funded research.",
"homepage": "https://mhkdr.openei.org/",
"name": "MHKDR",
"prefix": "r3d100013623",
"synonyms": [
"Marine and Hydrokinetic Data Repository"
]
},
"r3d100013624": {
"description": "Water DAMS (Water Data Analysis and Management System) provides access to foundational water treatment technology data that enable researchers and decision-makers to identify and quantify opportunities for technology innovations to reduce the cost and energy intensity of desalination. It is the submission point for all data generated by research conducted by the National Alliance for Water Innovation (NAWI) and is designed to be used by the broader water research community.\nWith publicly accessible contributions from a variety of academic and industrial partners, Water DAMS seeks to enable data discoverability, improve accessibility, and accelerate collaboration that contributes to pipe parity and innovation in water treatment technologies.",
"homepage": "https://nawi.openei.org/",
"name": "NAWI Water DAMS",
"prefix": "r3d100013624",
"synonyms": [
"National Alliance for Water Innovation Water Data Analysis and Management System"
]
},
"r3d100013625": {
"description": "OEDI is a centralized repository of high-value energy research datasets aggregated from the U.S. Department of Energyβs Programs, Offices, and National Laboratories. Built to enable data discoverability, OEDI facilitates access to a broad network of findings, including the data available in technology-specific catalogs like the Geothermal Data Repository and Marine Hydrokinetic Data Repository.",
"homepage": "https://data.openei.org/home",
"name": "OEDI",
"prefix": "r3d100013625",
"synonyms": [
"OEDI Data Lake",
"Open Energy Data Initiative"
]
},
"r3d100013626": {
"description": "ArkeoGIS is a unified scientific data publishing platform. It is a multilingual Geographic Information System (GIS), initially developed in order to mutualize archaeological and paleoenvironmental data of the Rhine Valley. Today, it allows the pooling of spatialized scientific data concerning the past, from prehistory to the present day. The databases come from the work of institutional researchers, doctoral students, master students, private companies and archaeological services. They are stored on the TGIR Huma-Num service grid and archived as part of the Huma-Num/CINES long-term archiving service. Because of their sensitive nature, which could lead to the looting of archaeological deposits, access to the tool is reserved to archaeological professionals, from research institutions or non-profit organizations. Each user can query online all or part of the available databases and export the results of his query to other tools.",
"homepage": "https://arkeogis.org/",
"name": "ArkeoGIS",
"prefix": "r3d100013626",
"synonyms": [
"ArkeoGIS"
]
},
"r3d100013628": {
"description": "The purpose of the Dataset Catalogue is to enhance discovery of GNS Science datasets. At a minimum, users will be able to determine whether a dataset on a specific topic exists and then whether it pertains to a specific place and/or a specific date or period.\n\nSome datasets include a web link to an online resource. In addition, contact details are provided for the custodian of each dataset as well as conditions of use.",
"homepage": "https://data.gns.cri.nz/metadata/srv/eng/catalog.search#/home",
"name": "GNS Science Dataset Catalogue",
"prefix": "r3d100013628"
},
"r3d100013630": {
"description": "Discovery is the digital repository of research, and related activities, undertaken at the University of Dundee.\nThe content held in Discovery is varied and ranges from traditional research outputs such as peer-reviewed articles and conference papers, books, chapters and post-graduate research theses and data to records for artefacts, exhibitions, multimedia and software. Where possible Discovery provides full-text access to a version of the research.\nDiscovery is the data catalogue for datasets resulting from research undertaken at the University of Dundee and in some instances the publisher of research data.",
"homepage": "https://discovery.dundee.ac.uk/",
"name": "Discovery",
"prefix": "r3d100013630",
"synonyms": [
"The University of Dundee Research Portal"
]
},
"r3d100013631": {
"description": "Varieties of Democracy (V-Dem) is a new approach to conceptualizing and measuring democracy. We provide a multidimensional and disaggregated dataset that reflects the complexity of the concept of democracy as a system of rule that goes beyond the simple presence of elections. The V-Dem project distinguishes between five high-level principles of democracy: electoral, liberal, participatory, deliberative, and egalitarian, and collects data to measure these principles.",
"homepage": "https://www.v-dem.net/en/",
"name": "Varieties of Democracy",
"prefix": "r3d100013631",
"synonyms": [
"V-Dem: Global Standards, Local Knowledge"
]
},
"r3d100013633": {
"description": "Scholar@UC enables the UC community to share research and scholarly works with a worldwide audience. The University of Cincinnati Libraries and IT@UC, with support from the Office of Research, are partnering to support Scholar@UC.",
"homepage": "https://scholar.uc.edu/",
"name": "Scholar@UC",
"prefix": "r3d100013633"
},
"r3d100013634": {
"description": "Constellation is a digital object identifier (DOI) based science network for supercomputing data. Constellation makes it possible for OLCF researchers to obtain DOIs for large data collections by tying them together with the associated resources and processes that went into the production of the data (e.g., jobs, collaborators, projects), using a scalable database. It also allows the annotation of the scientific conduct with rich metadata, and enables the cataloging and publishing of the artifacts for open access, aiding in scalable data discovery. OLCF users can use the DOI service to publish datasets even before the publication of the paper, and retain key data even after project expiration. From a center standpoint, DOIs enable the stewardship of data, and better management of the scratch and archival storage.",
"homepage": "https://doi.ccs.ornl.gov/",
"name": "Oak Ridge Leadership Computing Facility Constellation Portal",
"prefix": "r3d100013634",
"synonyms": [
"OLCF"
]
},
"r3d100013635": {
"description": "The NREL Data Catalog is where descriptive information (i.e., metadata) is maintained about public data resulting from federally funded research conducted by the National Renewable Energy Laboratory (NREL) researchers and analysts.\nOur Goal: Making Federally Funded Data Publicly Available\n\nNREL's mission is to develop clean energy and energy efficiency technologies and practices, advance related science and engineering, and provide knowledge and innovations to integrate energy systems at all scales. The NREL Data Catalog helps accomplish this by ensuring the data behind the science and engineering are well-documented and useful to the scientific community at large.",
"homepage": "https://data.nrel.gov/",
"name": "NREL Data Catalog",
"prefix": "r3d100013635"
},
"r3d100013636": {
"description": "The future of tropical forests matter to future climate.\nNGEE-Tropics is advancing model predictions of tropical forest carbon cycle responses to a changing climate over the 21st Century.",
"homepage": "https://ngee-tropics.lbl.gov/",
"name": "NGEE Tropics",
"prefix": "r3d100013636",
"synonyms": [
"Next-Generation Ecosystem Experiments - Tropics"
]
},
"r3d100013637": {
"description": "Addis Ababa University Research Data Repository holds multi disciplinary datasets produced by members of the university.",
"homepage": "https://rdm.aau.edu.et",
"name": "Addis Ababa University Research Data Repository",
"prefix": "r3d100013637",
"synonyms": [
"AAU-Research Data Repository"
]
},
"r3d100013638": {
"description": "The US BRAIN Initiative archive for publishing and sharing neurophysiology data including electrophysiology, optophysiology, and behavioral time-series, and images from immunostaining experiments.",
"homepage": "https://dandiarchive.org/",
"name": "DANDI",
"prefix": "r3d100013638",
"synonyms": [
"DANDI Archive",
"Distributed Archives for Neurophysiology Data Integration"
],
"xrefs": {
"fairsharing": "FAIRsharing.f2c119",
"scr": "017571"
}
},
"r3d100013639": {
"description": "The Buildings Data Platform mission is to collect and curate high-resolution, well-calibrated time series of building operational and indoor/outdoor environmental data, which are crucial to understanding and optimizing building energy efficiency performance and demand flexibility capabilities as well as benchmarking energy algorithms.",
"homepage": "https://bbd.labworks.org/",
"name": "Buildings Data Platform",
"prefix": "r3d100013639",
"synonyms": [
"Benchmark Datasets of Building Environmental Conditions and Occupancy Parameters"
]
},
"r3d100013640": {
"description": "The objective of the PDRC is to construct and collect a well-designed and large-scale panel data set and provide rigorous empirical studies based on these data sets. The data will enable us (i) to provide international comparisons and fact-findings on the household income changes, social mobility, changes in employment status and the investment activities; (ii) to verify the hypotheses related to the dynamics of economic behavior derived from economic theory; and (iii) to evaluate important policy changes in the tax system and social security program, which might have lagged effects.",
"homepage": "https://www.pdrc.keio.ac.jp/en/paneldata/datasets/",
"name": "Panel Data Research Center at Keio University Data",
"prefix": "r3d100013640",
"synonyms": [
"PDRC Data"
]
},
"r3d100013641": {
"description": "The International Soil Carbon Network (ISCN) is a science-based network that facilitates data sharing, assembles databases, identifies gaps in data coverage, and enables spatially explicit assessments of soil carbon in context of landscape, climate, land use, and biotic variables. \nThe ISCN Database is an evolving data resource. Because it is too large to present in one file, it is available as a set of documents, reports, and tables; because it changes over time, it is important to note the version date stamped in the upper-left corner of any dataset that you access.",
"homepage": "https://iscn.fluxdata.org/",
"name": "International Soil Carbon Network",
"prefix": "r3d100013641",
"synonyms": [
"ISCN"
]
},
"r3d100013642": {
"description": "HepSim is a public repository with Monte Carlo simulations for particle-collision experiments. It contains predictions from leading-order (LO) parton shower models, next-to-leading order (NLO) and NLO with matched parton showers. It also includes Monte Carlo events after fast (\"parametric\") and full (Geant4) detector simulations and event reconstruction.",
"homepage": "https://atlaswww.hep.anl.gov/hepsim/",
"name": "HepSim",
"prefix": "r3d100013642"
},
"r3d100013645": {
"description": "Reference anatomies of the brain and corresponding atlases play a central role in experimental neuroimaging workflows and are the foundation for reporting standardized results. The choice of such references βi.e., templatesβ and atlases is one relevant source of methodological variability across studies, which has recently been brought to attention as an important challenge to reproducibility in neuroscience. TemplateFlow is a publicly available framework for human and nonhuman brain models. The framework combines an open database with software for access, management, and vetting, allowing scientists to distribute their resources under FAIR βfindable, accessible, interoperable, reusableβ principles. TemplateFlow supports a multifaceted insight into brains across species, and enables multiverse analyses testing whether results generalize across standard references, scales, and in the long term, species, thereby contributing to increasing the reliability of neuroimaging results.",
"homepage": "https://templateflow.org",
"name": "TemplateFlow",
"prefix": "r3d100013645",
"xrefs": {
"opendoar": "10204"
}
},
"r3d100013646": {
"description": "Brain Analysis Library of Spatial maps and Atlases (BALSA) is a database for hosting and sharing neuroimaging and neuroanatomical datasets for human and primate species. BALSA houses curated, user-created Study datasets, extensively analyzed neuroimaging data associated with published figures and Reference datasets mapped to brain atlas surfaces and volumes in human and nonhuman primates as a general resource (e.g., published cortical parcellations).",
"homepage": "https://balsa.wustl.edu",
"name": "Brain Analysis Library of Spatial maps and Atlases",
"prefix": "r3d100013646",
"synonyms": [
"BALSA"
],
"xrefs": {
"fairsharing": "FAIRsharing.11c072",
"scr": "022960"
}
},
"r3d100013647": {
"description": "<<>>!!!>>>",
"homepage": "https://cloudflame.kaust.edu.sa",
"name": "CloudFlame",
"prefix": "r3d100013647",
"xrefs": {
"fairsharing": "FAIRsharing.agwgmc"
}
},
"r3d100013648": {
"description": "The Radiocarbon Palaeolithic Europe Database stores available radiometric data taken from literature and from other more restricted databases. Data is collected by continuous checking of newly published articles in hundreds of international and regional scientific journals and in collections or books dealing with a particular period or a specific Paleolithic site. User submissions are also accepted. Please note that this database is only available for download and local use via Microsoft Access or, in a more limited way, via Excel. As such, its accessibility is limited.",
"homepage": "https://ees.kuleuven.be/geography/projects/14c-palaeolithic/download/index.html",
"name": "Radiocarbon Palaeolithic Europe Database",
"prefix": "r3d100013648",
"xrefs": {
"biodbcore": "001836"
}
},
"r3d100013649": {
"description": "WOVOdat is a comprehensive global database on volcanic unrest aimed at understanding pre-eruptive processes and improving eruption forecasts. WOVOdat is brought to you by WOVO (World Organization of Volcano Observatories) and presently hosted at the Earth Observatory of Singapore.",
"homepage": "https://www.wovodat.org/",
"name": "WOVOdat",
"prefix": "r3d100013649",
"synonyms": [
"Database of Volcanic Unrest"
],
"xrefs": {
"biodbcore": "001855"
}
},
"r3d100013650": {
"description": "The goal of the Signaling Pathways Project knowledgebase is to allow bench researchers to routinely ask sophisticated questions of the universe of multi-omics data points generated by the cellular signaling community.\nSPP is dedicated to helping researchers to make sense of the often overwhelming volume of multi-omics information in the field of cellular signaling.",
"homepage": "https://www.signalingpathways.org/datasets/index.jsf",
"name": "Signaling Pathways Project",
"prefix": "r3d100013650",
"synonyms": [
"SSP"
],
"xrefs": {
"fairsharing": "FAIRsharing.WxI96O",
"scr": "018412"
}
},
"r3d100013652": {
"description": "The web service correspSearch aggregates metadata of letters from printed and digital scholarly editions and publications. It offers the aggregated correspondence metadata both via a feature-rich interface and via an API. The letter metadata are provided by scholarly projects of different institutions in a standardised, TEI-XML-based exchange format and and by using IDs from authority files (GeoNames, GND, VIAF etc.). The web service itself does not set a spatial or temporal collection focus. Currently, the time frame of the aggregated correspondence data ranges from 1500 to the 20th century.",
"homepage": "https://correspsearch.net/en/home.html",
"name": "correspSearch - Search scholarly editions of letters",
"prefix": "r3d100013652",
"synonyms": [
"correspSearch - Briefeditionen vernetzen"
]
},
"r3d100013656": {
"description": "IIT Dataverse is the institutional research data repository of the Istituto Italiano di Tecnologia. IIT Dataverse has been operative since May 2021 and is currently open to IIT-affiliated researchers for research data deposition and sharing.",
"homepage": "https://dataverse.iit.it/",
"name": "IIT Dataverse",
"prefix": "r3d100013656",
"synonyms": [
"Italian Institute of Technology Dataverse"
]
},
"r3d100013658": {
"description": "SciELO Data is a multidisciplinary repository for deposition, preservation and dissemination of research data from articles submitted and approved for publication, already published in SciELO Network journals or deposited in SciELO Preprints.",
"homepage": "https://data.scielo.org/",
"name": "SciELO Data",
"prefix": "r3d100013658",
"synonyms": [
"Scientific Electronic Library Online Data"
],
"xrefs": {
"fairsharing": "FAIRsharing.4adbf7"
}
},
"r3d100013660": {
"description": "Research Data Repository for Middlesex University, London, UK",
"homepage": "https://mdx.figshare.com/",
"name": "Middlesex University Research Data Repository",
"prefix": "r3d100013660",
"synonyms": [
"Middlesex University Figshare"
]
},
"r3d100013661": {
"description": "The CUHK Research Data Repository serves as an institutional research data repository for The Chinese University of Hong Kong (CUHK). It facilitates CUHK researchers to deposit, publish, and curate their research data and for the worldwide to discover, access, and reuse the research data outputs at CUHK.",
"homepage": "https://researchdata.cuhk.edu.hk",
"name": "CUHK Research Data Repository",
"prefix": "r3d100013661"
},
"r3d100013663": {
"description": "The MDR harvests metadata on data objects from a variety of sources within clinical research (e.g. trial registries, data repositories) and brings that together in a single searchable portal. The metadata is concerned with discoverability, access and provenance of the data objects (which because the data may be sensitive will often be available under a controlled access regime). At the moment (01/2021) the MDR obtains study data from: Clinical Trials.gov (CTG), The European Clinical Trials Registry (EUCTR), ISRCTN, The WHO ICTRP",
"homepage": "https://newmdr.ecrin.org/",
"name": "Clinical Research Metadata Repository",
"prefix": "r3d100013663",
"synonyms": [
"ECRIN MDR"
],
"xrefs": {
"biodbcore": "001575"
}
},
"r3d100013664": {
"description": "The Research Data Center of the Federal Institute for Occupational Safety and Health (FDZ-BAuA) provides selected data from BAuA research. The Public Use Files can be used by scientists as well as by the interested public.",
"homepage": "https://www.baua.de/DE/Angebote/Forschungsdaten/Forschungsdaten_node.html",
"name": "ForschungsdatenΒzentrum der Bundesanstalt fΓΌr Arbeitsschutz und Arbeitsmedizin",
"prefix": "r3d100013664",
"synonyms": [
"Data Centre of the Federal Institute for Occupational Safety and Health",
"FDZ-BAuA"
]
},
"r3d100013665": {
"description": "DUGiDocs is the institutional repository of the Universitat de Girona. Its aim is to preserve, spread and make visible the intellectual production issued from research and teaching lead at the UdG, such as degree final reports, master reports and doctorate research reports by university students as well as articles in scientific periodicals. Moreover it includes indexing and content description tools, makes visualization from many other internet sites easier (interoperability) and it also includes open access.",
"homepage": "https://dugi-doc.udg.edu/",
"name": "UdG Digital Repository",
"prefix": "r3d100013665",
"synonyms": [
"DUGiDocs",
"Repositori Digital de la UdG",
"Repositorio Digital de la UdG"
],
"xrefs": {
"opendoar": "5533",
"roar": "309"
}
},
"r3d100013666": {
"description": "NeuGRID is a secure data archiving and HPC processing system. The neuGRID platform uses a robust infrastructure to provide researchers with a simple interface for analysing, searching, retrieving and disseminating their biomedical data. With hundreds of investigators across the globe and more than 10 million of downloadable attributes, neuGRID aims to become a widespread resource for brain analyses. NeuGRID platform guarantees reliability with a fault-tolerant network to prevent system failure.",
"homepage": "https://neugrid2.eu",
"name": "neuGRID",
"prefix": "r3d100013666"
},
"r3d100013667": {
"description": "The BCCM/GeneCorner Plasmid Collection accepts plasmids from and distributes plasmids to researchers worldwide. Funding by the Belgian Science Policy (Belspo) allowed BCCM/GeneCorner to evolve into a unique plasmid repository in Europe.",
"homepage": "https://bccm.belspo.be/about-us/bccm-genecorner",
"name": "GeneCorner Plasmid Collection",
"prefix": "r3d100013667",
"synonyms": [
"BCCM/GeneCorner Plasmid Collection",
"Belgian CoOrdinated Collections Of MicroOrganisms/GeneCorner Plasmid Collection"
],
"xrefs": {
"fairsharing": "fairsharing.k4yzh",
"nif": "0000-30146",
"scr": "007193"
}
},
"r3d100013668": {
"description": "bio.tools is a software registry for bioinformatics and the life sciences.",
"homepage": "https://bio.tools",
"name": "bio.tools",
"prefix": "r3d100013668",
"xrefs": {
"biodbcore": "001815"
}
},
"r3d100013670": {
"description": "GPOβs govinfo system is an ISO 16363 certified Trustworthy Digital Repository that ensures free online access to current and historical information from all three branches of the United States Federal Government today and into the future.",
"homepage": "https://www.govinfo.gov",
"name": "govinfo",
"prefix": "r3d100013670",
"synonyms": [
"U.S. Government Information"
]
},
"r3d100013671": {
"description": "Database of forestry research installations in Canada with a focus on tree-level datasets (dendrometry, physical properties, dendrochronology, phenology, etc.).",
"homepage": "https://treesource.rncan.gc.ca/en",
"name": "TreeSource",
"prefix": "r3d100013671"
},
"r3d100013672": {
"description": "AUB ScholarWorks is a digital service that collects, preserves, and distributes digital material. AUB ScholarWorks hosts not only articles, but any other kind of research output, such as research data.",
"homepage": "https://scholarworks.aub.edu.lb/",
"name": "AUBScholarWorks",
"prefix": "r3d100013672",
"synonyms": [
"American University of Beirut ScholarWorks"
]
},
"r3d100013673": {
"description": "The Centre for the Environment, Fisheries and Aquaculture Science (Cefas), as one of the world's longest-established marine research organisations, has provided advice on the sustainable exploitation of marine resources since 1902. Today Cefas works in support of a healthy environment and a growing blue economy providing innovative solutions for the aquatic environment, biodiversity and food security. The Cefas Data Hub provides access to over 2080 metadata records, with over 5500 data sets available to download and connect to in support of commitments to Open Science through the Data Portal. Datasets available are increasingly diverse and include many legacy datasets including those from fish, shellfish and plankton surveys from the 1980's to the present day. Other increasingly international datasets made available include species migration data from tagging activities and data on habitat and sediment, ecosystem change, human activities including marine litter, otolith sampling and fish stomach contents, oceanography, acoustics, health and water quality. Data is provided under Open Government License by default where feasible.",
"homepage": "https://data.cefas.co.uk/",
"name": "Cefas Data Hub",
"prefix": "r3d100013673",
"synonyms": [
"Cefas Data Portal",
"Centre for Environment Fisheries and Aquaculture Science Data Portal"
]
},
"r3d100013674": {
"description": "The data repository of the Helmholtz Centre for Environmental Research.\nThe Data Investigation Portal (DRP) provides the opportunity to publicly access the administered data in the Data Management Portal and search them. The presentation is here limited to metadata and non-restricted information. DRP users can thus gain an overview of the data sets and, if necessary, contact the author to gain access to the data.",
"homepage": "https://www.ufz.de/drp/en/",
"name": "Datenrechercheportal UFZ",
"prefix": "r3d100013674",
"synonyms": [
"DRP UFZ",
"Data Investigation Portal Helmholtz Centre for Environmental Research",
"Data Investigation Portal UFZ",
"Datenrechercheportal Helmholtz-Zentrums fΓΌr Umweltforschung GmbH"
]
},
"r3d100013676": {
"description": "Institutional repository of the University of Bern. BORIS Portal allows researchers at the University of Bern to archive and manage research data as well as project and funding information, to make it accessible and clearly identifiable.",
"homepage": "https://boris-portal.unibe.ch",
"name": "BORIS Portal",
"prefix": "r3d100013676",
"synonyms": [
"Bern Open Repository and Information System"
]
},
"r3d100013677": {
"description": "J-STAGE Data is a data repository developed and managed by the Japan Science and Technology Agency (JST). J-STAGE Data supports the publication and distribution of data related to J-STAGE articles with the aim of contributing to the promotion of open science in Japan.\nJournals published on J-STAGE can use J-STAGE Data to publish data related to their own articles. DOI is automatically assigned to the data published in J-STAGE Data, and data is distributed worldwide as open access (anyone can access it for free, and the conditions for secondary use are clarified state), so anyone can use data under the conditions specified by the copyright holder, such as citing, sharing, and reusing.",
"homepage": "https://jstagedata.jst.go.jp/",
"name": "J-STAGE Data",
"prefix": "r3d100013677"
},
"r3d100013678": {
"description": "Dataverse for faculty, researchers, and students at St. Francis Xavier University or affiliated institutions. Hosted by Borealis.",
"homepage": "https://borealisdata.ca/dataverse/stfx",
"name": "St. Francis Xavier University Dataverse",
"prefix": "r3d100013678",
"synonyms": [
"StFX Dataverse"
]
},
"r3d100013679": {
"description": "Discover provides access to research data from projects related to LMU Munich, which are stored and preserved in repositories of the University Library LMU.",
"homepage": "https://discover.ub.uni-muenchen.de/",
"name": "Discover",
"prefix": "r3d100013679",
"synonyms": [
"Discover @ UB LMU",
"UB Discover"
]
},
"r3d100013680": {
"description": "GeneLab is an interactive, open-access resource where scientists can upload, download, store, search, share, transfer, and analyze omics data from spaceflight and corresponding analogue experiments. Users can explore GeneLab datasets in the Data Repository, analyze data using the Analysis Platform, and create collaborative projects using the Collaborative Workspace. GeneLab promises to facilitate and improve information sharing, foster innovation, and increase the pace of scientific discovery from extremely rare and valuable space biology experiments. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.\nGeneLab helps scientists understand how the fundamental building blocks of life itself β DNA, RNA, proteins, and metabolites β change from exposure to microgravity, radiation, and other aspects of the space environment. GeneLab does so by providing fully coordinated epigenomics, genomics, transcriptomics, proteomics, and metabolomics data alongside essential metadata describing each spaceflight and space-relevant experiment. By carefully curating and implementing best practices for data standards, users can combine individual GeneLab datasets to gain new, comprehensive insights about the effects of spaceflight on biology. In this way, GeneLab extends the scientific knowledge gained from each biological experiment conducted in space, allowing scientists from around the world to make novel discoveries and develop new hypotheses from these priceless data.",
"homepage": "https://genelab.nasa.gov",
"name": "GeneLab",
"prefix": "r3d100013680",
"xrefs": {
"scr": "017658"
}
},
"r3d100013681": {
"description": "KonDATA is the research data repository of the University of Konstanz. This service offered by KIM provides you with the simple and convenient option of publishing your research data in a way that is visible and citable in the long term",
"homepage": "https://kondata.uni-konstanz.de/",
"name": "KonDATA",
"prefix": "r3d100013681"
},
"r3d100013683": {
"description": "The Netherlands Polar Data Center (NPDC) is part of the Netherlands Polar Program (NPP). NPDC archives and provides access to the data of Polar Research by researchers funded by Dutch Research Council (NWO) or otherwise carried out by researchers from Dutch universities and research institutions. The repository provides: 1) An overview of current and completed projects from the Netherlands Polar Programme (NPP) and other Dutch projects in the Polar Regions; 2) Access to the data of research carried out by Dutch researchers in the Polar Regions; and, 3) Links to external sources of Polar research data. For more information about the NPDC and the services it may offer to the Dutch Polar research community see https://npdc.nl/npdc.",
"homepage": "https://npdc.nl",
"name": "Netherlands Polar Data Center",
"prefix": "r3d100013683",
"synonyms": [
"NPDC"
]
},
"r3d100013688": {
"description": "The institutional data repository DOREL - DOnnΓ©es de REcherche Lorraines - is a tool for referencing the scientific production of the University of Lorraine as well as a space for publishing data sets produced within its research units.\nIt is a multidisciplinary repository, developed with the Dataverse software.",
"homepage": "https://dorel.univ-lorraine.fr",
"name": "DOREL",
"prefix": "r3d100013688",
"synonyms": [
"DOnnΓ©es de la REcherche Lorraines"
]
},
"r3d100013689": {
"description": "RIULL is the Institutional Repository of the University of La Laguna, created with the aim of gathering, preserving and disseminating in open access the scientific and academic production of the University of La Laguna. It is managed by the University Library.",
"homepage": "https://riull.ull.es/xmlui/",
"name": "RIULL",
"prefix": "r3d100013689",
"synonyms": [
"Repositorio Institucional de la Universidad de La Laguna"
]
},
"r3d100013691": {
"description": "The main mission of IPGP Data Center is to manage and to distribute geophysical data from the Institut de physique du globe de Paris to support the geophysical research community.",
"homepage": "http://datacenter.ipgp.fr/data.php",
"name": "IPGP Data Center",
"prefix": "r3d100013691",
"synonyms": [
"Centre de DonnΓ©es IPGP"
]
},
"r3d100013693": {
"description": "LuleΓ₯ University of Technology offers the opportunity to publish research data in the university's publication database DiVA. Choose the publication type \"Dataset\"",
"homepage": "http://urn.kb.se/resolve?urn=urn:nbn:se:ltu:diva-70730",
"name": "LuleΓ₯ University of Technology research data in the university's publication database DiVA",
"prefix": "r3d100013693"
},
"r3d100013696": {
"description": "DDBJ Sequence Read Archive (DRA) is the public archive of high throughput sequencing data. DRA stores raw sequencing data and alignment information to enhance reproducibility and facilitate new discoveries through data analysis. DRA is a member of the International Nucleotide Sequence Database Collaboration (INSDC) and archiving the data in a close collaboration with NCBI Sequence Read Archive (SRA) and EBI Sequence Read Archive (ERA).",
"homepage": "https://www.ddbj.nig.ac.jp/dra/index-e.html",
"name": "DRA",
"prefix": "r3d100013696",
"synonyms": [
"DDBJ Sequence Read Archive"
],
"xrefs": {
"biodbcore": "001521",
"nlx": "152515",
"scr": "001370"
}
},
"r3d100013698": {
"description": "Pandora is an open data platform devoted to the study of the human story. Data may be deposited from various disciplines and research topics that investigate humans from their early beginnings until present in addition to their environmental context (e.g. archeology, anthropology history, ancient DNA, isotopes, zooarchaeology, archaeobotany, and paleoenvironmental and paleoclimatic studies, etc.).\nPandora allows autonomous data communities to self-manage their webspace and community membership. Data communities self-curate their data plus other supporting resources. Datasets may be assigned a new DOI and a schema markup is employed to improve data findability.\nPandora also allows for links to datasets stored externally and having previously assigned DOIs. Through this, it becomes possible to establish data networks devoted to specific topics that may combine a mix of datasets stored either within Pandora or externally.",
"homepage": "https://pandora.earth/",
"name": "Pandora",
"prefix": "r3d100013698"
},
"r3d100013701": {
"description": "PubData is Leuphana's instituΒtional research data reposiΒtory for the long-term preserΒvation, documenΒtation and publiΒcation of research data from scientiΒfic projects. \nPubData is mainΒtained by Leuphana's Media and InforΒmation Centre (MIZ) and is free of charge. The service is primarily aimed at Leuphana emΒployees and additionally at reΒsearchers from coopeΒration partners conΒtractually assoΒciated with Leuphana.",
"homepage": "https://pubdata.leuphana.de/",
"name": "PubData",
"prefix": "r3d100013701",
"synonyms": [
"Das Forschungsdaten-Repositorium der Leuphana UniversitΓ€t LΓΌneburg",
"Research Data Repository Leuphana University LΓΌneburg"
]
},
"r3d100013702": {
"description": "OCTOPUS is an Open Geospatial Consortium (OGC) compliant web-enabled database that allows users to visualise, query, and download cosmogenic 10Be and 26Al, luminescence, and radiocarbon ages and denudation rates associated with erosional landscapes, Quaternary depositional landforms and archaeological records, along with associated geospatial (vector and raster) data layers.",
"homepage": "https://octopusdata.org",
"name": "OCTOPUS database",
"prefix": "r3d100013702",
"synonyms": [
"An open cosmogenic isotope and luminescence database"
],
"xrefs": {
"doi": "10.25900/32de-mj32"
}
},
"r3d100013704": {
"description": "Regionaal Archief Tilburg (RA Tilburg) is one of the four institutions of foundation Mommerskwartier and is based in Tilburg, the Netherlands. \nThe statutory task (Public Records Act https://bit.ly/3iCTI7f) of RA Tilburg is to function as a repository for decentralized, local government organizations such as municipalities, communal schemes, and Water Authorities. RA Tilburg also manages private archives, and archives of organizations, institutes, or the public in general.",
"homepage": "https://www.regionaalarchieftilburg.nl/",
"name": "Regionaal Archief Tilburg",
"prefix": "r3d100013704",
"synonyms": [
"RA Tilburg"
]
},
"r3d100013705": {
"description": "A secure platform for developing and sharing reproducible methods. A research protocol is a document that describes the background, rationale, objectives, design, methodology, statistical considerations, and organization of a clinical research project.",
"homepage": "https://www.protocols.io/",
"name": "protocols.io",
"prefix": "r3d100013705",
"xrefs": {
"fairsharing.legacy": "3758",
"issn": "2473-1838",
"nlx": "158033",
"scr": "010490"
}
},
"r3d100013707": {
"description": "The Harvard Dataverse Repository is a free data repository open to all researchers from any discipline, both inside and outside of the Harvard community, where you can share, archive, cite, access, and explore research data. Each individual Dataverse collection is a customizable collection of datasets (or a virtual repository) for organizing, managing, and showcasing datasets.",
"homepage": "https://dataverse.harvard.edu/dataverse/openhealthdata",
"name": "Open Health Data Dataverse",
"prefix": "r3d100013707"
},
"r3d100013708": {
"description": "The NORPERM permafrost database provides information on ground temperatures from boreholes and from the near-surface using miniloggers (MTDs). The database was established during the International Polar Year as one of the main goals of the project TSP Norway - \"A Contribution to the Thermal State of Permafrost in Norway and Svalbard\".",
"homepage": "https://geo.ngu.no/kart/permafrost_mobil/",
"name": "NORPERM",
"prefix": "r3d100013708",
"synonyms": [
"Norwegian Permafrost Database"
]
},
"r3d100013711": {
"description": "Bioresources, often referred to as biological resources, are essential experimental research materials for life science and bioindustry. Under the three principles of βTrustβ, βSustainabilityβ and βLeadershipβ, RIKEN BRC is committed to receiving deposition/donation of bioresources from the research community, confirming the authenticity of bioresources by rigorous quality examination, preserving, and distributing them back to the research community. f you wish to search quickly or to search multiple bioresources (mouse, cell, plant, microorganism, gene) simultaneously, we recommend to search from the Top Page. At the Top page, bioresource search and Google-based site search are available.",
"homepage": "https://web.brc.riken.jp/en/",
"name": "RIKEN Bioresource Research Center",
"prefix": "r3d100013711",
"synonyms": [
"RIKEN BRC",
"RIKEN Bioresource Center",
"ηεε¦η η©Άζγγγ€γͺγͺγ½γΌγΉη η©Άγ»γ³γΏγΌ"
]
},
"r3d100013713": {
"description": "CHERRY, ie CHEmistry RepositoRY is a joint digital repository of the all departments in University of Belgrade - Faculty of Chemistry. CHERRY provides open access to the publications, as well as to other outputs of the research projects implemented in this institution.\nThe software platform meets the current requirements that apply to the dissemination of scholarly publications and it is compatible with relevant international infrastructures.",
"homepage": "https://cherry.chem.bg.ac.rs",
"name": "CHERRY",
"prefix": "r3d100013713",
"synonyms": [
"CHEmistry RepositoRY"
]
},
"r3d100013715": {
"description": "The MMRRC is the nationβs premier national public repository system for mutant mice. Funded by the NIH continuously since 1999, the MMRRC archives and distributes scientifically valuable spontaneous and induced mutant mouse strains and ES cell lines for use by the biomedical research community. The MMRRC consists of a national network of breeding and distribution repositories and an Informatics Coordination and Service Center located at 4 major academic centers across the nation. The MMRRC is committed to upholding the highest standards of experimental design and quality control to optimize the reproducibility of research studies using mutant mice.",
"homepage": "https://www.mmrrc.org",
"name": "Mutant Mouse Resource & Research Centers",
"prefix": "r3d100013715",
"synonyms": [
"MMRRC"
],
"xrefs": {
"fairsharing": "FAIRsharing.9dpd18",
"nif": "0000-00045",
"scr": "002953"
}
},
"r3d100013717": {
"description": "Institutional repository intended to gather, preserve and disseminate, through open access, in accordance with the principles of the OAI open archives movement, the documents resulting from the academic, scientific and teaching activity, as well as the institutional publications of the Saint Paul Universities -CEU, Cardenal Herrera-CEU, Abat Oliba CEU and its dependent Academic Centers.",
"homepage": "https://repositorioinstitucional.ceu.es",
"name": "CEU Institutional Repository",
"prefix": "r3d100013717",
"synonyms": [
"CEU Repositorio Institucional"
],
"xrefs": {
"opendoar": "6284",
"roar": "2560"
}
},
"r3d100013719": {
"description": "The overall vision for the SPARC Portal is to accelerate autonomic neuroscience research and device development by providing access to digital resources that can be shared, cited, visualized, computed, and used for virtual experimentation.",
"homepage": "https://sparc.science",
"name": "SPARC Portal",
"prefix": "r3d100013719",
"synonyms": [
"Stimulating Peripheral Activity to Relieve Conditions"
],
"xrefs": {
"fairsharing": "FAIRsharing.d0307c",
"scr": "017041"
}
},
"r3d100013720": {
"description": "The European Xenopus Resource Centre (EXRC) is situated in Portsmouth, United Kingdom and provides tools and services to support researchers using Xenopus models. The EXRC depends on researchers to obtain and deposit Xenopus transgenic and mutant lines, Xenopus in-situ hybridization clones, Xenopus specific antibodies and other resources with the centre. EXRC staff perform quality assurance testing on these reagents and then makes them available to the community at cost. EXRC also supplies wild type Xenopus, embryos, oocytes, egg extracts, X.tropicalis Fosmids, X.laevis BACs and ORFeomes.",
"homepage": "https://xenopusresource.org",
"name": "European Xenopus Resource Center",
"prefix": "r3d100013720",
"synonyms": [
"EXRC"
]
},
"r3d100013722": {
"description": "The repository stores resources generated by this University. It is organized into five collections: theses and dissertations; teaching material to support online training courses; OA publications from the university press; and historical documentation (includes academic journals and monographs in Spanish (1875-1940) and original material on local educational institutions (16th-20th centuries).",
"homepage": "https://dspace.unia.es/",
"name": "Repositorio Abierto",
"prefix": "r3d100013722",
"synonyms": [
"Repositorio Abierto de la Universidad Internacional de AndalucΓa",
"UNIA Open Repository"
],
"xrefs": {
"roar": "5792"
}
},
"r3d100013727": {
"description": "Database and knowledgebase of authenticated microbial genomics data with full data provenance to physical materials held within American Type Culture Collection's (ATCC) biorepository and culture collections. Data includes whole genome sequencing data for bacterial, viral and fungal strains at ATCC, their genome assemblies, metadata, drug susceptibility data, and more. All data is freely available for non-commercial research use only (RUO) applications via the web portal interface or via a REST-API. The goal is to provide the research community with provenance information and authentication between the biological source materials and reference genome assemblies derived from them.",
"homepage": "https://genomes.atcc.org",
"name": "ATCC Genome Portal",
"prefix": "r3d100013727",
"xrefs": {
"scr": "021330"
}
},
"r3d100013732": {
"description": "The Biofilms Structural Database contains information on different protein structures involved in biofilm formation, development, and virulence.",
"homepage": "https://biofilms.biosim.pt",
"name": "Biofilms Structural Database",
"prefix": "r3d100013732"
},
"r3d100013733": {
"description": "The UNESP Institucional Repository aims to store, preserv, disseminate and provide open access to scientific, academic, artistic and technical documentation, as well as data and plan management, produced by researchers and students at UNESP.",
"homepage": "https://repositorio.unesp.br/handle/11449/183294",
"name": "UNESP Institutional Repository",
"prefix": "r3d100013733",
"synonyms": [
"RepositΓ³rio Institucional UNESP"
]
},
"r3d100013735": {
"description": "A world database on Legionella outbreaks. It is based on a metadata analysis of peer-reviewed manuscripts from PubMed and SCOPUS. LegionellaDB is dynamic and extensible, allowing users to search for specific outbreaks, suggest additional information to be included after curation, visualize statistical representations on specific outbreaks, and download selected data.",
"homepage": "https://legionelladb.biosim.pt",
"name": "LegionellaDB",
"prefix": "r3d100013735"
},
"r3d100013736": {
"description": "The Perovskite Database Project aims at making all perovskite device data, both past and future, available in a form adherent to the FAIR data principles, i.e. findable, accessible, interoperable, and reusable.",
"homepage": "https://www.perovskitedatabase.com/",
"name": "The Perovskite Database Project",
"prefix": "r3d100013736"
},
"r3d100013737": {
"description": "The NIH 3D Print Exchange (the βExchangeβ) is an open, comprehensive, and interactive website for searching, browsing, downloading, and sharing biomedical 3D print files, modeling tutorials, and educational material. \"Biomedical\" includes models of cells, bacteria, or viruses, molecules like proteins or DNA, and anatomical models of organs, tissue, and body parts. \nThe NIH 3D Print Exchange provides models in formats that are readily compatible with 3D printers, and offers a unique set of tools to create and share 3D-printable models related to biomedical science.",
"homepage": "https://3dprint.nih.gov/",
"name": "NIH 3D Print Exchange",
"prefix": "r3d100013737",
"xrefs": {
"fairsharing": "FAIRsharing.tjf1jg,"
}
},
"r3d100013738": {
"description": "Datasets repository for the data papers published in the Journal of Open Archaeology Data (JOAD).",
"homepage": "https://dataverse.harvard.edu/dataverse/JOAD",
"name": "JOAD Dataverse",
"prefix": "r3d100013738",
"synonyms": [
"Journal of Open Archaeology Data Dataverse"
]
},
"r3d100013739": {
"description": "Savannah hosts the majority of GNU software and some non-GNU software. Savannah's focus is on hosting for free software projects. To ensure that only free software is hosted, Savannah implements very strict hosting policies, including a ban against the use of non-free formats (such as Macromedia Flash).",
"homepage": "http://savannah.gnu.org/",
"name": "Savannah",
"prefix": "r3d100013739",
"xrefs": {
"fairsharing": "FAIRsharing.3f074b"
}
},
"r3d100013740": {
"description": "MetabolomeXchange.org delivers the mechanisms needed for disseminating the data to the metabolomics community at large (both metabolomics researchers and databases). The main objective is to make it easier for metabolomics researchers to become aware of newly released, publicly available, metabolomics datasets that may be useful for their research.\nMetabolomeXchange contains datasets from different data providers: MetaboLights, Metabolomic Repository Bordeaux, Metabolomics Workbench, and Metabolonote",
"homepage": "http://www.metabolomexchange.org/site/",
"name": "MetabolomeXchange",
"prefix": "r3d100013740",
"xrefs": {
"scr": "014664"
}
},
"r3d100013741": {
"description": "The MAPPA Open Data archaeological archive (MOD) is an archaeological digital archive that publishes the archaeological documentation (Dataset) and gray literature (Reports) produced in the course of archaeological investigations.",
"homepage": "http://mappaproject.arch.unipi.it/mod/Index.php",
"name": "Mappa",
"prefix": "r3d100013741",
"synonyms": [
"MOD",
"Metodologie Applicate alla PredittivitΓ‘ del potenziale Archeologico",
"Open Data Archaeological Archive"
]
},
"r3d100013743": {
"description": "The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), advances life & health sciences by providing open access to a suite of resources, with the aim to translate big data into big discoveries and support worldwide activities in both academia and industry.",
"homepage": "https://ngdc.cncb.ac.cn/",
"name": "National Genomics Data Center",
"prefix": "r3d100013743",
"synonyms": [
"BIG Data Center",
"Beijing Institute of Genomics Data Center",
"NGDC",
"ε½εΆεΊε η»η§ε¦ζ°ζδΈεΏ"
]
},
"r3d100013744": {
"description": "The data repository aims to store, preserve and make available research data generated by the academic community, in open access - as open as possible, as closed as necessary.",
"homepage": "https://dados.ipb.pt/",
"name": "DadosIPB",
"prefix": "r3d100013744",
"synonyms": [
"RepositΓ³rio de dados cientΓficos do Instituto PolitΓ©cnico de BraganΓ§a"
]
},
"r3d100013745": {
"description": "SLAPIS is an integrated Flood Early Warning System that aims to promote decision-making and behavioral changes from reactive to proactive at several levels, from the community to the administration, for the reduction of flood risk in the Communes of the Sirba (main tributary of the Niger River and cause of the main floods in the region)",
"homepage": "https://www.slapis-niger.org/fr",
"name": "SLAPIS",
"prefix": "r3d100013745",
"synonyms": [
"SLAPIS Early Warning System",
"SystΓ¨me Local dβAlerte PrΓ©coce pour les Inondations de la Sirba"
]
},
"r3d100013746": {
"description": "SWISSUbase is a national cross-disciplinary solution for Swiss universities and other research organisations in need of local institutional data repositories for their researchers. SWISSUbase offers to the Swiss research institutions a tool for the curation, preservation, and dissemination of scientific research data and for the storage of information on ongoing and completed research projects in the country. The platform relies on international archiving standards and processes to ensure that data are preserved and accessible in the long-term. Datasets are curated by Data Service Units (DSU).\nDSU LaRS β Language Repository of Switzerland: https://www.lars.uzh.ch/en.html",
"homepage": "https://www.swissubase.ch/en/",
"name": "SWISSUbase",
"prefix": "r3d100013746"
},
"r3d100013747": {
"description": "The National Microbial Data Center (NMDC) is jointly constructed by the Institute of Microbiology of the Chinese Academy of Sciences (IMS), the Institute of Oceanography of the Chinese Academy of Sciences, the Institute of Infectious Diseases of the Chinese Center for Disease Control and Prevention, the Institute of Plant Physiology and Ecology of the Chinese Academy of Sciences, and the Computer Network Information Centre of the Chinese Academy of Sciences. The General Office of the Chinese Academy of Sciences is the parent department. The data resources covering the whole life cycle of microbiological research, including microbiological resources, microbiological and cross-technological methods, research processes and engineering, microbiomics, microbiological technologies, as well as microbiological literature, patents, experts and results. The Centre focuses on promoting the convergence and integration of scientific and technological resources in the field of microbiology to the national platform, strengthening the development, application and analysis of microbiological resources, enhancing the effective use of microbiological resources and the ability to support scientific and technological innovation, and providing high-quality scientific and technological resource sharing services for scientific research, technological progress and social development.",
"homepage": "https://nmdc.cn/en",
"name": "National Microbiology Data Center",
"prefix": "r3d100013747",
"synonyms": [
"NMDC",
"ε½εΆεΎηη©η§ε¦ζ°ζδΈεΏ"
]
},
"r3d100013748": {
"description": "The National Earth Observation Science Data Center, whose predecessor was the National Integrated Earth Observation Data Sharing Platform, has formed a sustainable, cross-agency, one-stop data sharing service capability after years of construction, and it is also the main channel for international exchange of remote sensing data in China. In the future, it will manage and coordinate scientific data resources in the field of earth observation on behalf of the country, and build a national-level earth observation big data infrastructure. Coordinate various industry data centers, scientific research institutions and enterprises in the field of Earth observation in China to cooperate in building a national strategic, fundamental, scientific, internationalized, and independent and controllable scientific big data environment in the field of Earth observation. On the basis of the already formed data ecology and cooperation mechanism, data sharing services, and international data cooperation, we will actively expand to the whole life cycle management of data and carry out data management work such as the collection, management, analysis and mining, and sharing services of national scientific data resources for Earth observation. Form a unified technical support system and data sharing service environment for Earth observation data in China. Maintain and enhance its international influence and become a domestic and international first-class scientific data center for Earth observation!",
"homepage": "https://www.chinageoss.cn/en/",
"name": "National Earth Observation Data Center",
"prefix": "r3d100013748",
"synonyms": [
"National Earth Observation Data Center",
"ε½εΆε―Ήε°θ§ζ΅η§ε¦ζ°ζδΈεΏ"
]
},
"r3d100013750": {
"description": "The Diccionario del EspaΓ±ol Medieval electrΓ³nico (DEMel) provides a lemmatised and semantically pre-structured electronic data archive on medieval Spanish. The basis of the data collection is the digitised material archived in card indexes of the Diccionario del EspaΓ±ol Medieval (DEM), which was discontinued at the end of 2007 for financial reasons. The DEM covers the history of the development of Spanish vocabulary between the 10th and the beginning of the 15th century on the basis of far more than 600 literary and non-literary works or collections of texts and documents.",
"homepage": "https://demel.uni-rostock.de/?lang=en",
"name": "DEMel",
"prefix": "r3d100013750",
"synonyms": [
"Diccionario del EspaΓ±ol Medieval electrΓ³nico"
]
},
"r3d100013752": {
"description": "National Materials Corrosion and Protection Scientific Data Center, the competent department is the Ministry of Education, the supporting unit is the University of Science and Technology Beijing, is a long-standing base for material environmental corrosion data accumulation and experimental research, an authoritative institution for material corrosion testing, testing and analysis, as well as a platform for basic scientific research and personnel training in material corrosion. At present, the integration of the completion of the national materials corrosion and protection experimental research base composed of 32 national test stations and materials corrosion platform center, the construction of the national materials corrosion and environmental data science center, the center fully use of modern information technology, effective integration of scientific and technological resources, for scientific research, technology research and development, enterprise innovation and major engineering construction to provide information technology, network technology support services.",
"homepage": "https://www.corrdata.org.cn/index_en.php",
"name": "National Materials Corrosion and Protection Data Center",
"prefix": "r3d100013752",
"synonyms": [
"ε½εΆζζθ
θδΈι²ζ€η§ε¦ζ°ζδΈεΏ"
]
},
"r3d100013753": {
"description": "A Research Data Management Tool for the Vrije Universiteit Amsterdam Research Community.",
"homepage": "https://osf.vu.nl/",
"name": "OSF - Vrije Universiteit Amsterdam",
"prefix": "r3d100013753"
},
"r3d100013754": {
"description": "The National Cryosphere Desert Data Center (hereinafter referred to as NCDC) is supported by the Institute of environment and Engineering in the cold and dry areas of the Chinese Academy of Sciences, in cooperation with Xinjiang Institute of ecology and geography of the Chinese Academy of Sciences, Chengdu Institute of mountain land disaster and environment of the Ministry of water resources of the Chinese Academy of Sciences, Qinghai Salt Lake Research Institute of the Chinese Academy of Sciences and Qinghai Gao of the Chinese Academy of Sciences The Institute of protobiology and other units were jointly established. The supporting units of glacier permafrost desert data center have formed a scientific research and support system of seven research laboratories and three research systems, highlighting the research characteristics of glacier, permafrost, desert, atmosphere, water and soil, ecology, environment, resources, engineering and sustainable development in the dry areas of cold regions.",
"homepage": "http://www.ncdc.ac.cn",
"name": "National Cryosphere Desert Data Center",
"prefix": "r3d100013754",
"synonyms": [
"NCDC",
"ε½εΆε°ε·ε»εζ²ζΌ η§ε¦ζ°ζδΈεΏ"
]
},
"r3d100013755": {
"description": "The National Important Wild Plant Germplasm Repository has ten types of resources and data such as seeds, DNA, isolated materials, dried leaves, etc. totaling about 180,000 copies",
"homepage": "https://seed.iflora.cn/Home/English",
"name": "National Wild Seed Resource Center",
"prefix": "r3d100013755",
"synonyms": [
"National Wild Plant Germplasm Resource Center",
"ε½εΆιθ¦ιηζ€η©η§θ΄¨θ΅ζΊεΊ"
]
},
"r3d100013756": {
"description": "The Organic Chemistry Portal offers an overview of recent topics, interesting reactions, and information on important chemicals for organic chemists. \nSearchable index of citations, chemical synthesis and chemical products. We publish 1000 additional citations per year. \nGerman version see https://www.organische-chemie.ch/",
"homepage": "https://www.organic-chemistry.org/synthesis/",
"name": "Organic Synthesis Search",
"prefix": "r3d100013756",
"synonyms": [
"Organic Chemistry Portal",
"Portal fΓΌr Organische Chemie"
]
},
"r3d100013757": {
"description": "The National Tropical Plant Germplasm Repository, supported by the Institute of Tropical Crop Variety Resources of the Chinese Academy of Tropical Agricultural Sciences (CATAS) and jointly constructed by 11 units including the Institute of Fruit Tree Research of the Guangdong Academy of Agricultural Sciences and Hainan University, aims to provide information and physical support for scientific and technological innovation in tropical crop seed industry, increase the income of farmers in hot regions, alleviate poverty, the \"One Belt One Road\" initiative and the National Tropical Agricultural Science Centre. The National Centre for Tropical Agricultural Sciences (NCTAS) provides information and physical support for tropical crop germplasm resources. The National Tropical Plant Germplasm Repository consists of a national medium-term tropical crop germplasm preservation repository, a medium-term tropical forage preservation repository and 12 national nurseries, covering 24 crops in nine categories, including rubber trees, tropical forage, tropical fruit trees, tropical oilseeds, tropical aromatic beverages, southern medicine, tropical grains, tropical flowers and tropical special vegetables, with more than 26,000 copies of resources, accounting for more than 90% of the total tropical crop germplasm resources in China. The resources account for more than 90% of the total amount of tropical crop germplasm resources in China. It has built an efficient management system and a stable human resources team, a conservation system that combines centralized conservation in germplasm banks and moderate distribution in germplasm nurseries, a technical specification system for the unified description of germplasm resources of major tropical crops, and an integrated system for the conservation and utilization of China's tropical crop germplasm resource information network, ensuring the efficient operation and sustainable development of the national tropical crop germplasm resource bank.",
"homepage": "http://ctcgris.cn/",
"name": "China Tropical Crop Germplasm Resources Information Network",
"prefix": "r3d100013757",
"synonyms": [
"National Tropical Crop Germplasm Resource Center",
"εΆηεΈ¦ζ€η©η§θ΄¨θ΅ζΊεΊ"
]
},
"r3d100013758": {
"description": "NODE (The National Omics Data Encyclopedia) provides an integrated, compatible, comparable, and scalable multi-omics resource platform that supports flexible data management and effective data release. NODE uses a hierarchical data architecture to support storage of muti-omics data including sequencing data, MS based proteomics data, MS or NMR based metabolomics data, and fluorescence imaging data.\nLaunched in early 2017, NODE has collected and published over 900 terabytes of omics data for researchers from China and all over the world in last three years, 22% of which contains multiple omics data. NODE provides functions around the whole life cycle of omics data, from data archive, data requests/responses to data sharing, data analysis, data review and publish.",
"homepage": "https://www.biosino.org/node/",
"name": "National Omics Data Encyclopedia",
"prefix": "r3d100013758",
"synonyms": [
"NODE"
],
"xrefs": {
"fairsharing": "/FAIRsharing.EivZJw"
}
},
"r3d100013759": {
"description": "Multidisciplinary research data repository, hosted by DTU, the Danish Technical University.",
"homepage": "https://sciencerepository.dk",
"name": "ScienceRepository",
"prefix": "r3d100013759"
},
"r3d100013762": {
"description": "The National Center for Forestry and Grassland Genetic Resources (Forestry and Grassland Repository) consists of a series of in situ and ex situ repositories and ex situ repositories, including 15 in situ repositories, 137 ex situ repositories and 3 facility repositories (attached), all of which are recognized by the Seedling Department of the State Forestry and Grassland Administration or the National Forestry Germplasm Resource Platform to collect and preserve forest, grass, flower, bamboo and rattan germplasm resources, and to establish a big data system through standardization, digitization. The purpose of the Forestry and Grassland Resource Bank is to strengthen the germplasm resources of forests, grasses, flowers, bamboos and rattan. The purpose of the Forestry and Grass Resource Bank is to strengthen the collection and preservation of forestry germplasm resources and open sharing, and to promote sustainable use; the objective is to use ultra-low temperature freezing, genomics, artificial intelligence and other high technology to carry out long-term preservation, accurate identification and in-depth exploration of germplasm resources, and to achieve safe preservation and efficient use of germplasm resources. The Forestry and Grassland Resource Bank undertakes the rendezvous of scientific and technological projects in the forestry germplasm resource category. By building an integrated sharing service platform for germplasm resource production, academia and research, it improves the innovation and exploitation capacity of forestry germplasm resources, supports major national needs in scientific research, ecological construction and economic development, promotes the docking of resources and needs, and facilitates the use of resources and the transformation of results. It realizes information and physical sharing, so that forest germplasm resources can be safely preserved and scientifically utilized.",
"homepage": "http://www.nfgrp.cn",
"name": "National Center for Forestry and Grassland Genetic Resources",
"prefix": "r3d100013762",
"synonyms": [
"NFGRP",
"ε½εΆζδΈεθεη§θ΄¨θ΅ζΊεΊ"
]
},
"r3d100013763": {
"description": "National Aquatic Biological Resource Center (NABRC), established in June 2019, is a member of National Science and Technology Resource Platform supported by the Ministry of Science and Technology and the Ministry of Finance. The NABRC consists of 6 sub-platforms. In summary, these six sub-platforms have reached leading levels at home and abroad in terms of the resource richness, the resource digitization, as well as the amount and quality of resource services. Right now, these platforms are in strong support of basic biology, basic medicine, aquatic economics, water environmental protection and other areas in China. It is an essential way to practice the \"Great Yangtze River Protection\" and promote the construction of ecological civilization in the Yangtze River. In the future, the platforms will further integrate different types of resources, optimize the resource configuration and improve the service systems, so as to build a high standard resource sharing platform on a global scale and promote international communication and cooperation.",
"homepage": "http://www.nabrc.org.cn/",
"name": "National Aquatic Biological Resource Center",
"prefix": "r3d100013763",
"synonyms": [
"NABRC",
"National Aquatic Germplasm Bank",
"ε½εΆζ°΄ηηη©η§θ΄¨θ΅ζΊεΊ"
]
},
"r3d100013764": {
"description": "The construction goal of the national marine aquatic germplasm resource bank: by 2025, promote the national marine aquatic germplasm resource bank to become an international marine aquatic germplasm resource collection and preservation center with rich species, wide coverage, and 200,000 preserved copies. The transformation of resources from decentralized management to centralized integration, from focusing on collection and preservation to focusing on both preservation and development, provides a material basis for promoting the sustainable development of the national economy, building a society in which humans and nature coexist in harmony, and promoting my country's transformation from marine aquatic species to species. The transformation from a country with large quality resources to a country with strong resources.",
"homepage": "http://marine.fishinfo.cn",
"name": "National Marine Aquatic Germplasm Resource Bank",
"prefix": "r3d100013764",
"synonyms": [
"ε½εΆζ΅·ζ΄ζ°΄ηηη©η§θ΄¨θ΅ζΊεΊ"
]
},
"r3d100013765": {
"description": "National freshwater aquatic germplasm repository, competent department: Ministry of Agriculture and Rural Affairs, relying unit: China Academy of Fisheries Science. By the Heilongjiang Fisheries Research Institute, Yangtze River Fisheries Research Institute, Freshwater Fisheries Research Center, Pearl River Fisheries Research Institute, Fisheries Machinery and Instruments Research Institute and Shanghai Ocean University 6 units. Relying on the unit's outstanding ability to informatization of resources, the establishment of an advanced system, functional, stable operation, high visibility in the field of portal, can carry out deep mining and digital processing of freshwater aquatic germplasm resources information. The co-construction unit has relatively complete functional laboratory, preservation library and base facilities, with the hardware conditions to provide knowledge-based and professional services of freshwater aquatic germplasm resources. The participants have many years of experience in the collection and integration of freshwater aquatic germplasm resources, with solid professional background and outstanding business ability, which can improve the depth and breadth of integration and utilization of freshwater aquatic germplasm resources.",
"homepage": "http://freshwater.fishinfo.cn",
"name": "National Freshwater Genetic Resource Center",
"prefix": "r3d100013765",
"synonyms": [
"National Freshwater Aquatic Germplasm Repository",
"National Freshwater Aquatic Germplasm Resource Bank",
"ε½εΆζ·‘ζ°΄ζ°΄δΊ§η§θ΄¨θ΅ζΊεΊ"
]
},
"r3d100013766": {
"description": "Plastics are widely used in our economy and each year, at least 350-400 million tons are being produced at a global level. Due to poor recycling and low circular use, tens of millions of tons accumulate annually in marine and terrestrial environments. While it has become obvious that micro and macroplastics contaminate our environments recent research has identified few bacteria and fungi actively degrading plastics by enzymatic reactions. In general these are promiscuous enzymes (hydrolases) acting on low crystaline and mostly low density polymers of PET, ester-based PUR and oligomers of PA. Notably today, no enzymes have been characterized on a biochemical level for polymeric and crystaline PE, ether-based PUR, PS, PVC, PP. While many publications report on plastic degradation often, no convincing biochemical data have been published. Therefore the PAZy database lists exclusively biochemically characterized plastic-active enzymes. Predicted and putative enzymes that were not characterized on a biochemical, functional or structural level are not included in the PAZy database. The entries are manually curated.",
"homepage": "https://pazy.eu/doku.php",
"name": "The Plastics-Active Enzymes Database",
"prefix": "r3d100013766",
"synonyms": [
"PAZy"
]
},
"r3d100013770": {
"description": "The institutional research data repository of the UniversitΓ€t Innsbruck is a service to enable storing, sharing and publishing of research data according to the FAIR principles for its employees and project partners.",
"homepage": "https://researchdata.uibk.ac.at/",
"name": "Research data repository of the UniversitΓ€t Innsbruck",
"prefix": "r3d100013770",
"synonyms": [
"UIBK Data Repository"
]
},
"r3d100013771": {
"description": "From 2005 to 2008, with the support of the Ministry of Science and Technology (MOST), the construction of parasite germplasm repositories has spread to 20 conservation institutions in 15 provinces (cities) nationwide, with 3 physical exhibition halls; 3 live parasite conservation centers. A total of 1115 species/117814 pieces of parasitic germplasm resources of 23 orders in 11 phyla have been integrated into the physical library and database, including human parasites and vectors, animal parasites, plant nematodes, medical insects, trematodes, and parasitic snails, and the resources are combined with moderate distribution, medium- and long-term support, and off-site duplicates. The number of resources accounts for 39.27% of the national total. Through 10 years of accumulation, we have built the largest and only parasite species resource database in the field of parasites in China, and created a sharing platform of parasite germplasm resource center.",
"homepage": "https://www.tdrc.org.cn/",
"name": "National Parasite Resource Center",
"prefix": "r3d100013771",
"synonyms": [
"National Parasite Germplasm Resources Service Platform",
"ε½εΆε―ηθ«θ΅ζΊεΊ"
]
},
"r3d100013772": {
"description": "The National Microbial Resource Center (NMRC) is an important part of the national science and technology resources sharing service platform, responsible for the research, conservation, management and sharing of national microbial strain resources, ensuring the strategic security and sustainable use of microbial strain resources, and providing support for scientific and technological innovation, industrial development and social progress. The main tasks of the NMRC are: to collect, organize and preserve microbial strain resources around national needs and scientific research; to undertake the task of remitting, organizing and preserving strain resources resulting from the implementation of science and technology projects; to be responsible for the development and improvement of microbial strain resource standards, and to standardize and guide the development of microbial strain resources in various fields. The company is responsible for the development and improvement of microbial strain resource standards, standardizing and guiding the protection and utilization of microbial strain resources in various fields; building and maintaining the national strain resource online service system, and carrying out social sharing of physical and information resources of strains; developing key common technologies, creating new resources, and carrying out customized services according to innovative needs; carrying out scientific popularization for the society; carrying out international exchange and cooperation on strain resources, participating in relevant international academic organizations, and safeguarding national interests and Security",
"homepage": "http://www.nimr.org.cn/",
"name": "National Microbial Resource Platform",
"prefix": "r3d100013772",
"synonyms": [
"ε½εΆθη§θ΅ζΊεΊ"
]
},
"r3d100013775": {
"description": "National Human Brain Bank for Development and Function was originally established in 2012 by the Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences as a public interest institution dedicated to the preservation and research of human brain tissues based on the volunteer donor station of Peking Union Medical College. In 2019, it was officially recognised by the Ministry of Science and Technology as a national science and technology resource platform: National Human Brain Bank for Development and Function.\nSince its establishment, the Concordia Brain Bank has accepted and preserved more than two hundred and seventy whole brain tissue samples. While conducting its own research on the standardisation of brain banks, neuropathology and various histologies related to human brain ageing and dementia, it has also developed and published the Standardised Operational Protocol for Human Brain Tissue Banks in China for more than ten universities in China, and has provided valuable human brain tissue samples for a number of research groups in our own institutions and other units in China, which has strongly supported brain science and brain disease research in China.\nAs a national resource platform, we will continue to aim to support and lead brain science research in China and make positive contributions to maintaining brain health and defeating brain diseases.",
"homepage": "http://anatomy.sbm.pumc.edu.cn/brainbank",
"name": "National Human Brain Bank for Development and Function",
"prefix": "r3d100013775",
"synonyms": [
"ε½εΆεθ²εεθ½δΊΊθη»η»θ΅ζΊεΊ"
]
},
"r3d100013776": {
"description": "AgroSpace is the institutional digital repository of the University of Belgrade, Faculty of Agriculture. It provides open access to publications and other research outputs resulting from the projects implemented by the Faculty of Agriculture.\nThe software platform of the repository is adapted to the modern standards applied in the dissemination of scientific publications and is compatible with international infrastructure in this field.",
"homepage": "http://aspace.agrif.bg.ac.rs/",
"name": "AgroSpace",
"prefix": "r3d100013776",
"synonyms": [
"Repozitorijum Poljoprivrednog fakulteta (Univerzitet u Beogradu)"
]
},
"r3d100013777": {
"description": "BCCM/ITM is a collection of well documented mycobacteria, characterized by phenotypic and/or genotypic tests. While having an emphasis on (drug-resistant) M. tuberculosis complex, BCCM/ITM comprises more than 90 mycobacterial species from human, animal and environmental origin from all continents.",
"homepage": "https://bccm.belspo.be/about-us/bccm-itm",
"name": "BCCM/ITM Mycobacteria Collection",
"prefix": "r3d100013777",
"synonyms": [
"Belgian Co-Ordinated Collections Of Micro-Organisms/ITM Mycobacteria Collection"
],
"xrefs": {
"fairsharing": "FAIRsharing.5ckyx7"
}
},
"r3d100013778": {
"description": "The National Human Brain Tissue Bank for Health and Disease (the Brain Bank) was built to meet the needs of scientific research by integrating experts and forces from neuroscience, human anatomy, pathology and other related disciplines. The Brain Bank collects and stores post-mortem brain tissue donated by patients with various neuropsychiatric disorders and normal controls, as well as their life histories, in accordance with international standards, and provides a detailed and accurate neuropathological diagnosis of these brain tissue samples (also known as the \"final diagnosis\"). The aim is to discover and elucidate the causes of human neuropsychiatric diseases such as Alzheimer's disease, Parkinson's disease, depression, schizophrenia and other human diseases, and to provide scientists with the most direct and effective means of finding the relevant pathogenesis and establishing effective treatments. The National Brain Tissue Resource for Health and Disease The goal of the National Human Brain Tissue Repository for Health and Disease is to integrate collection, diagnosis, storage and utilisation, and to build a first-class human resource preservation infrastructure in China that is in line with international standards and provides support for neuroscience research. In 2020, the National Brain Bank has established three branches of the National Brain Bank in Hefei, Anhui, Nanjing, Jiangsu, and Shanghai. major cities.",
"homepage": "http://zjubrainbank.zju.edu.cn/",
"name": "National Health and Disease Human Brain Tissue Resource Center",
"prefix": "r3d100013778",
"synonyms": [
"National Human Brain Bank For Health And Disease",
"ε½εΆε₯εΊ·εηΎη
δΊΊθη»η»θ΅ζΊεΊ"
]
},
"r3d100013779": {
"description": "BCCM/ULC is a small and dedicated public collection, currently containing one of the largest collections of documented (sub)polar cyanobacteria worldwide. The BCCM/ULC collection is hosted by the In-Bios research unit of the University of Liège. The host Unit is very active in research projects concerning the cyanobacterial diversity and biogeography, with a focus on polar biotopes. The participation to field expeditions in the Antarctic and Arctic has enabled to collect samples in many locations. Moreover, taxonomic research is carried out by the host Unit to improve the classification of the cyanobacterial phylum.",
"homepage": "https://bccm.belspo.be/about-us/bccm-ulc",
"name": "ULC Cyanobacteria Collection",
"prefix": "r3d100013779",
"synonyms": [
"BCCM/ULC Cyanobacteria Collection",
"Belgian CoOrdinated Collections Of MicroOrganisms/ULC Cyanobacteria Collection"
],
"xrefs": {
"fairsharing": "FAIRsharing.1z88ee"
}
},
"r3d100013780": {
"description": "The National Stem Cell Resource Bank (formerly Beijing Stem Cell Bank) was established in 2007 and is a service platform approved by the Ministry of Science and Technology and the Ministry of Finance for the exchange of scientific and technological resources at the national level scientific and technological innovation base of basic supply and state guarantee.",
"homepage": "http://www.bjscb.cn/dms",
"name": "National Stem Cell Resource Bank",
"prefix": "r3d100013780",
"synonyms": [
"ε½εΆεΉ²η»θθ΅ζΊεΊ"
]
},
"r3d100013781": {
"description": "The National Stem Cell Translational Resource Bank (NSCTRB) contains various stem cell resources of both clinical and research grade, especially a sub-bank composed with HLA high-frequency iPSC lines in which the HLA types could match more than 60% of the Chinese population. It can not only provide services to stem cell clinical researches and translation applications, but also provide effective resources for scientific research to the Universities, research institutes, companies, etc. The bank has complete standards, specifications and relevant management systems, and has more than 200 perfessonals in the field of stem cells.",
"homepage": "http://nsctrc.tongji.edu.cn",
"name": "National Stem Cell Translational Resource Center",
"prefix": "r3d100013781",
"synonyms": [
"NSCTRB",
"ε½εΆεΉ²η»θ转εθ΅ζΊεΊ"
]
},
"r3d100013782": {
"description": "BCCM/IHEM is a fungal culture collection specialized in medical and veterinary mycology. About 16.000 strains of yeasts and moulds are available from all over the world: pathogens, allergenic species, strains producing mycotoxins, reference strains, teaching material, etc. It also comprises the Raymond Vanbreuseghem collection and the collection of Janssen Pharmaceutica. The BCCM/IHEM collection makes strains or their genomic DNA publicly available for medical, pharmaceutical and biological research, as well as for method validation, testing or educational purposes. Deposits of strains for public access are free of charge for the depositor. The collection also accept safe and patent deposits, and offers a range of services including trainings in mycology and identifications of strains. Moreover, BCCM/IHEM has expertise in fungal taxonomy, in MALDI-TOF MS identification of moulds and yeasts as well as in genomics (whole genome sequencing of fungal strains, phylogenomics, phylogenetics).",
"homepage": "https://bccm.belspo.be/about-us/bccm-ihem",
"name": "IHEM Fungi Collection: Human & Animal Health",
"prefix": "r3d100013782",
"synonyms": [
"BCCM/IHEM Fungi Collection: Human & Animal Health",
"Belgian Co-Ordinated Collections Of Micro-Organisms/IHEM Fungi Collection: Human & Animal Health"
],
"xrefs": {
"fairsharing": "FAIRsharing.etwpd5"
}
},
"r3d100013783": {
"description": "BCCM/MUCL is a generalist fungal culture collection of over 30000 filamentous fungi, yeasts and arbuscular mycorrhizal fungi including type, reference and test strains. It provides curated documentation and information on these bioresourced in its database. The collections activities include the distribution of its holdings, the accession of new material in its public, safe and patent domains, and services valorising its holdings and/or expertise to cultivate, isolate and identify fungal diversity in natural and anthropological ecosystems, agro-food (food and feed transformation and spoilage), and fungal-plant interactions.",
"homepage": "https://bccm.belspo.be/about-us/bccm-mucl",
"name": "MUCL Agro-food & Environmental Fungal Collection",
"prefix": "r3d100013783",
"synonyms": [
"BCCM/MUCL Agro-food & Environmental Fungal Collection",
"Belgian Co-Ordinated Collections Of Micro-Organisms/MUCL Agro-food & Environmental Fungal Collection"
],
"xrefs": {
"fairsharing": "FAIRsharing.4njvzy"
}
},
"r3d100013784": {
"description": "The BCCM/DCG public collection is the only culture collection worldwide specialized in diatoms, the most species-rich and ecologically important group of algae. However, other microalgae interesting from a scientific or applied perspective are also included in this collection. Strains can be kept as safe deposits or public deposits. These latter are available worldwide as research or reference material for both, scientific institutions and companies.",
"homepage": "https://bccm.belspo.be/about-us/bccm-dcg",
"name": "BCCM/DCG Diatoms Collection",
"prefix": "r3d100013784",
"synonyms": [
"Belgian Co-Ordinated Collections Of Micro-Organisms/DCG Diatoms Collection"
],
"xrefs": {
"fairsharing": "FAIRsharing.yxs0d0"
}
},
"r3d100013785": {
"description": "BCCM/LMG is a bacterial culture collection currently comprising over 26.000 well-characterized strains. The biological origin of our collection is very broad, including bacterial isolates from food, clinical, veterinary, agricultural, aquatic and other environmental sources. This way, the biological resources of BCCM/LMG may serve the needs of various R&D sectors, including green, red, blue and white biotechnology.",
"homepage": "https://bccm.belspo.be/about-us/bccm-lmg",
"name": "LMG Bacteria Collection",
"prefix": "r3d100013785",
"synonyms": [
"BCCM/LMG Bacteria Collection",
"Belgian CoOrdinated Collections Of MicroOrganisms/LMG Bacteria Collection"
],
"xrefs": {
"fairsharing": "FAIRsharing.zfdxet"
}
},
"r3d100013787": {
"description": "Chinese Virtual Herbarium is online access to herbarium specimens and botanical information in China.",
"homepage": "https://www.cvh.ac.cn",
"name": "Chinese Virtual Herbarium",
"prefix": "r3d100013787",
"synonyms": [
"ε½εΆζ€η©ζ ζ¬θ΅ζΊεΊ"
]
},
"r3d100013789": {
"description": "Koszalin University of Technology is the only technical university in Central Pomerania. It is located in a town of 100 thousand inhabitants, about 10 km from the Baltic Sea. Central Pomerania is a region with well-developed tourism, agriculture, food-processing and electronics industries. Koszalin University \nof Technology conducts teaching and scientific-research activities in disciplines related primarily to the directions of development of the region.\nKoszalin University of Technology is authorized to confer doctoral degrees. \nThe doctoral degree is conferred by the Doctoral School operating at Koszalin University of Technology. It educates students on I st and II nd degree studies, \nin stationary and non-stationary mode. \nThe Repository is to be used for collecting, storing (archiving), presenting (making available) and retrieving information on the scientific and popular scientific achievement of employees, doctoral students and students,\n as well as on their professional achievements and activities that create \nthe university's output and shaping its image among other scientific institutions in the country and in the world.",
"homepage": "https://sdr.tu.koszalin.pl/",
"name": "Science Direct Repository Koszalin University of Technology",
"prefix": "r3d100013789",
"synonyms": [
"Konstelacja Wiedzy"
],
"xrefs": {
"opendoar": "10404"
}
},
"r3d100013791": {
"description": "eLMSG (eLibrary of Microbial Systematics and Genomics) is a web microbial library that integrates not only taxonomic information, but also genomic information and phenotypic information (including morphology, physiology, biochemistry and enzymology). The taxonomic system of eLMSG is manually curated and composed of all validly and some effectively published taxa. For each taxon, the Latin name, taxon ID (NCBI taxonomy), etymology, rank, lineage, the dates of effective and/or valid publication, feature descriptions, nomenclature type and references for the proposal and emendations during the history of the taxon are presented. Besides these data, the species taxa contain information about 16S rRNA gene and/or genome sequences. All publicly available genome data of each type species including both type and non-type strains were collected, and if needed, re-annotated using the standardized analysis pipeline. Furthermore, pan-genomic data analyses were conducted for species with β₯5 genome sequences available. Finally, for all type species, taxonomically relevant phenotypic data were extracted and curated from literatures, which were further indexed into eLMSG as searchable and analyzable data records. Taken together, eLMSG is a comprehensive web platform for studying mi- crobial systematics and genomics, potentially useful for better understanding microbial taxonomy, natural evolutionary processes and ecological relationships.",
"homepage": "https://www.biosino.org/elmsg/index",
"name": "eLibrary of Microbial Systematics and Genomics",
"prefix": "r3d100013791",
"synonyms": [
"eLMSG"
],
"xrefs": {
"fairsharing": "FAIRsharing.3254c6"
}
},
"r3d100013792": {
"description": "NIMRF offers state-owned specimens with scientific values, including minerals, rocks and fossils. As a data provider, it is our mission to advance the understanding of geo-resources and to provide services for academia, education and scientific popularization in the field of geoscience through collecting, organizing, and sharing specimen resources as well as attaching links to rock-mineral-fossil websites worldwide.",
"homepage": "http://www.nimrf.net.cn/en/english",
"name": "National Infrastructure of Mineral Rock and Fossil Resources for Science and Technology",
"prefix": "r3d100013792",
"synonyms": [
"NIMRF",
"ε½εΆε²©ηΏεη³ζ ζ¬θ΅ζΊεΊ"
]
},
"r3d100013793": {
"description": "Standard, reference material is used for measurement process control and reliability evaluation of measurement results, and plays a key role in important fields such as food safety, international and domestic trade, medicine and health, and environmental monitoring.\nIn order to realize the efficient use and sharing of reference material resources in the whole society, the Institute of Chemistry of China Institute of Metrology (formerly the National Reference Material Research Center), with the support of the Ministry of Science and Technology, launched the \"National Reference Material Information Service\" at the end of 2003.",
"homepage": "http://www.ncrm.org.cn",
"name": "National Sharing Platform for Reference Materials",
"prefix": "r3d100013793",
"synonyms": [
"NCRM",
"ε½εΆζ εη©θ΄¨θ΅ζΊεΊ"
]
},
"r3d100013794": {
"description": "The center is a national-level cell bank that is in line with international standards, has complete collections, and is rich in data. The center mainly collects and preserves various types of cells related to medical and biological research and provides technical services. In addition, it also conducts collaborative research and technical training of personnel.",
"homepage": "http://www.cellresource.cn",
"name": "National Infrastructure of Cell line Resources BMCR; NICR",
"prefix": "r3d100013794",
"synonyms": [
"ε½εΆηη©ε»ε¦ειͺη»θθ΅ζΊεΊ"
]
},
"r3d100013799": {
"description": "Cell Bank/Stem Cell Bank is a nonprofit biological resource center, which includes two divisions named as cell bank and stem cell bank. It is affiliated to Shanghai Institute of Biochemistry and Cell Biology (SIBCB), a nation-renowned biomedical research institution with worldwide reputation. Our mission focuses on collection, authentication, production, preservation, development and distribution of standard reference cell lines in the life sciences.",
"homepage": "http://www.cellbank.org.cn/",
"name": "National Collection of Authenticated Cell Cultures",
"prefix": "r3d100013799",
"synonyms": [
"Cell Bank of the Chinese Academy of Sciences",
"ε½εΆζ¨‘εΌδΈηΉθ²ειͺη»θθ΅ζΊεΊ"
]
},
"r3d100013800": {
"description": "Based on the needs of national scientific and technological innovation for laboratory animal resources, we use various methods such as foreign introduction, domestic collection, independent research and development, and protocol conservation to collect, integrate, and optimize laboratory animal resources. The resource library now preserves more than 200 varieties and strains in four categories, including mice, rats, guinea pigs, and rabbits, including routine laboratory animals, genetically modified animal models, and animal models for disease.\nThe predecessor of the resource bank was the National Rodent Laboratory Animal Seed Center (Guoke Cai Zi [1998] No. 010), established in 1998 and based on the Laboratory Animal Resources Research Institute of the Chinese National Academy of Food and Drug Administration.",
"homepage": "http://nrla.nifdc.org.cn",
"name": "National Rodent Laboratory Animal Resource Bank",
"prefix": "r3d100013800",
"synonyms": [
"ε½εΆει½Ώε¨η©ειͺε€ε¨η©θ΅ζΊεΊ"
]
},
"r3d100013802": {
"description": "Sharing and preserving data are central to protecting the integrity of science. DataHub, a Research Computing endeavor, provides tools and services to meet scientific data challenges at Pacific Northwest National Laboratory (PNNL).\nDataHub helps researchers address the full data life cycle for their institutional projects and provides a path to creating findable, accessible, interoperable, and reusable (FAIR) data products. Although open science data is a crucial focus of DataHubβs core services, we are interested in working with evidence-based data throughout the PNNL research community.",
"homepage": "https://data.pnnl.gov/",
"name": "Pacific Northwest National Laboratory DataHub: Scientific Data Repository",
"prefix": "r3d100013802",
"synonyms": [
"PNNL DataHub",
"PNNL2"
],
"xrefs": {
"doi": "10.25584/PNNL.DataHub/1812943",
"fairsharing": "FAIRsharing.45bf5b"
}
},
"r3d100013804": {
"description": "AdattΓ‘r stores research data associated with the University of Debrecen, and provides services such as data transfer, storage and sharing. As a result, research data is easily accessible and more visible to the scientific community in each field, following disciplinary standards. AdattaΜr aims to foster best practices of findability and accessibility of research data, and will provide guidance regarding issues of access, privacy, and copyright. AdattaΜr aims to be a widely used, inter-disciplinary, trusted platform for managing, sharing, and archiving research data created by the researchers associated with the university.",
"homepage": "https://adattar.unideb.hu/",
"name": "Debreceni Egyetem AdattΓ‘r",
"prefix": "r3d100013804",
"synonyms": [
"University of Debrecen Dataverse"
],
"xrefs": {
"fairsharing.legacy": "3815"
}
},
"r3d100013805": {
"description": "The non-human primate laboratory animal resource bank conducts external services and research through professional preservation institutions, mainly including: research, formulation and improvement of genetic material preservation, breeding technical regulations, innovative technology research, etc.; implementation of information sharing, development of Laboratory technical training, sharing information and technology with scientific research institutions, enterprises and other personnel inside and outside the platform, using network retrieval, telephone consultation, on-site guidance and other forms of communication. The service targets are enterprises, public institutions, social groups, and international organizations engaged in non-human primate genetics and breeding, production, scientific research, and teaching.",
"homepage": "http://nhp.kiz.ac.cn/",
"name": "National Non-Human Primate Laboratory Animal Resource Bank",
"prefix": "r3d100013805",
"synonyms": [
"ε½εΆιδΊΊη΅ιΏη±»ειͺε¨η©θ΅ζΊεΊ"
]
},
"r3d100013806": {
"description": "The National Science and Technology Resource Sharing Service Platform belongs to the national science and technology innovation base of basic support and condition guarantee. Facing the needs of scientific and technological innovation, economic and social development, innovative social governance, and building a safe China, it strengthens the effective integration of high-quality scientific and technological resources and improves the efficiency of scientific and technological resources. Scientific research, technological progress and social development provide networked and socialized scientific and technological resource sharing services.",
"homepage": "http://pla.caas.cn/web/index.html",
"name": "National Avian Laboratory Animal Resource Bank",
"prefix": "r3d100013806",
"synonyms": [
"National Poultry Laboratory Animal Resource Bank",
"ε½εΆη¦½η±»ειͺε¨η©θ΅ζΊεΊ"
]
},
"r3d100013808": {
"description": "Veterinar β Electronic Repository of Research and Scientific Papers is the institutional digital repository of the University of Belgrade - Faculty of Veterinary Medicine. It provides open access to publications and other research outputs resulting from the projects implemented by the Faculty of Veterinary Medicine. The software platform of the repository is adapted to the modern standards applied in the dissemination of scientific publications and is compatible with international infrastructure in this field.",
"homepage": "https://vet-erinar.vet.bg.ac.rs",
"name": "Veterinar - Electronic Repository of Research and Scientific Papers",
"prefix": "r3d100013808",
"synonyms": [
"Veterinar - Elektronski repozitorijum istraΕΎivaΔkih i nauΔnih radova",
"Veterinar - Repository of the Faculty of Veterinary Medicine"
],
"xrefs": {
"opendoar": "9677",
"roar": "16087"
}
},
"r3d100013809": {
"description": "RIVeC - Repository of the Institute for Vegetable Crops is the institutional digital repository of the Institute for Vegetable Crops. The aim of the repository is to provide open access to publications and other research outputs resulting from the projects implemented by the Institute for Vegetable Crops. The repository uses a DSpace-based software platform developed and maintained by the Belgrade University Computer Centre (RCUB).",
"homepage": "https://rivec.institut-palanka.rs/?locale-attribute=en",
"name": "RIVeC",
"prefix": "r3d100013809",
"synonyms": [
"Repository of the Institute for Vegetable Crops",
"Repozitorijum Instituta za povrtarstvo Smederevska Palanka"
],
"xrefs": {
"opendoar": "10160",
"roar": "17220"
}
},
"r3d100013811": {
"description": "CeR β Central Repository is the institutional digital repository of the Institute of Chemistry, Technology and Metallurgy, University of Belgrade. The aim of the repository is to provide open access to publications and other research outputs resulting from the projects implemented by the Institute of Chemistry, Technology and Metallurgy. The repository uses a DSpace-based software platform developed and maintained by the Belgrade University Computer Centre (RCUB).",
"homepage": "https://cer.ihtm.bg.ac.rs",
"name": "CeR β Central Repository ICTM",
"prefix": "r3d100013811",
"synonyms": [
"CeR β Central Repository of the Institute of Chemistry, Technology and Metallurgy, University of Belgrade",
"CeR β Centralni repozitorijum Instituta za hemiju, tehnologiju i metalurgiju Univerziteta u Beogradu"
]
},
"r3d100013812": {
"description": "The GEOROC data repository hosts research data within the scope of the GEOROC database: geochemical compositions of rocks, glasses, minerals and inclusions from all geological settings on Earth. The repository is curated by the Digital Geochemical Data Infrastructure (DIGIS) project at GΓΆttingen University.",
"homepage": "https://data.goettingen-research-online.de/dataverse/digis",
"name": "GEOROC Data Repository",
"prefix": "r3d100013812",
"synonyms": [
"Geochemistry of Rocks of the Oceans and Continents Data Repository"
]
},
"r3d100013814": {
"description": "The RIAA's primary functions are to collect, organize, preserve, manage, and provide electronic access to information and quality content produced with public funds.",
"homepage": "https://repositorioinstitucional.buap.mx/",
"name": "Repositorio de Acceso Abierto BUAP",
"prefix": "r3d100013814",
"synonyms": [
"BUAP Open Access Repository",
"RIAA",
"Repositorio Institucional de Acceso Abierto"
],
"xrefs": {
"opendoar": "4773"
}
},
"r3d100013815": {
"description": "FishSounds presents a compilation of acoustic recordings and published information on sound production across all extant fish species globally. We hope this information can be used to advance research into fish behavior, passive acoustic monitoring, and human impacts on underwater soundscapes as well as serve as a public resource for anyone interested in learning more about fish sounds. This work is the product of an international collaboration between researchers and developers from five organizations. We have taken a cross-disciplinary approach, combining expertise in fish ecology, bioacoustics, and data management to produce a website that we hope will serve the wider marine research community. All versions of the FishSounds website and associated publications and products are stored in a long-term Dataverse dataset as a permanent repository (https://doi.org/10.5683/SP2/TACOUX).",
"homepage": "https://fishsounds.net/index.js",
"name": "FishSounds",
"prefix": "r3d100013815"
},
"r3d100013816": {
"description": "MDM-Portal (Medical Data Models) is a meta-data registry for creating, analyzing, sharing and reusing medical forms. It serves as an infrastructure for academic (non-commercial) medical research to contribute a solution to this problem. It contains forms in the system-independent CDISC Operational Data Model (ODM) format with more than 500,000 data-elements. The Portal provides numerous core data sets, common data elements or data standards, code lists and value sets. This enables researchers to view, discuss, download and export forms in most common technical formats such as PDF, CSV, Excel, SQL, SPSS, R, etc.",
"homepage": "https://medical-data-models.org/",
"name": "Portal of Medical Data Models",
"prefix": "r3d100013816",
"synonyms": [
"MDM Portal"
],
"xrefs": {
"fairsharing": "FAIRsharing.wnk2eq"
}
},
"r3d100013817": {
"description": "Within the RESIF-EPOS observation research infrastructure and the Action SpΓ©cifique RESIF-GNSS action, the Reseau National GNSS permanent (RENAG) is the network of GNSS observation stations of French universities and research organizations. It is currently composed of 85 GNSS stations (Global Navigation Satellite System such as GPS, GLONASS, Galileo). The scientific objectives of RESIF-RENAG range from the quantification of the slow deformation in France to the sounding of the atmosphere (troposphere and ionosphere), through the measurement of sea-level variations and the characterization of transient movements related to overloads. \nData production is carried out in a distributed way by the laboratories and organizations that manage the stations. 12 teams are specifically in charge of station maintenance and of accurately filling in the metadata files. A single data center, RENAG-DC, hosted at the Observatoire de la CΓ΄te d'Azur (OCA) within the Geoazur laboratory, is in charge of data management, from their collection to their distribution in the standard RINEX format (http://renag.resif.fr).",
"homepage": "http://renag.resif.fr/en",
"name": "RENAG-DC",
"prefix": "r3d100013817",
"synonyms": [
"REseau NAtional GNSS permanent",
"Renag data center",
"RΓ©sif-RENAG"
],
"xrefs": {
"doi": "10.15778/resif.rg"
}
},
"r3d100013818": {
"description": "The center's main task is to introduce, collect and preserve dog laboratory animal varieties, strains, develop and maintain new technologies, cultivate new varieties and strains, and provide standard experimental seeds. In 2019, the Ministry of Science and Technology and the Ministry of Finance, for the purpose of improving the scientific and technological resources sharing service system, promoted the opening and sharing of scientific and technological resources to society, and carried out the optimization and adjustment of the national platform. The National Canine Laboratory Animal Seed Center was successfully approved as the only \"National Canine Laboratory Animal Resource Center\".",
"homepage": "https://www.nclarc.org.cn/",
"name": "National Canine Laboratory Animal Resource Center",
"prefix": "r3d100013818",
"synonyms": [
"ε½εΆη¬η±»ειͺε¨η©θ΅ζΊδΈεΏ"
]
},
"r3d100013819": {
"description": "NRCMM is a service platform that integrates preservation and supply of resources of model mice, creation and development of disease model, experimental animal personnel training as a whole. The mission of NRCMM is two-fold: to provide preservation, production, supply, information consultation that aim to benifit human health, and to provide multiple training for graduate students as well as scientists on using the model animals. Resource center also provide service for experimental animal research and cooperation throughout China that will promote leading position of our country in the related field and the development of related disciplines, such as life science, medical science and pharmacy.",
"homepage": "http://www.nrcmm.cn/",
"name": "Model Animal Resource Information Platform",
"prefix": "r3d100013819",
"synonyms": [
"ε½εΆιδΌ ε·₯η¨ε°ιΌ θ΅ζΊεΊ"
]
},
"r3d100013820": {
"description": "The National Human Disease Animal Model Resource Bank is supported by the Institute of Medical Laboratory Animals, Chinese Academy of Medical Sciences. The institute is a professional institute engaged in the scientific research and teaching of experimental zoology and comparative medicine. The research unit is the undertaking unit of the national-level laboratory animal technology resource bank for infectious diseases and new drug creation research. In 2015, it established the Key Laboratory of Animal Model Research for Infectious Diseases, the Beijing Engineering Technology Research Center for Laboratory Animal Models of Human Diseases, and established the Human Disease Animal Model Resource Center of the Chinese Academy of Medical Sciences in 2015. The institute has passed CNAS measurement certification, national laboratory accreditation and international AAALAC certification.",
"homepage": "https://www.namr.org.cn/",
"name": "National Human Disease Animal Model Resource Center",
"prefix": "r3d100013820",
"synonyms": [
"ε½εΆδΊΊη±»ηΎη
ε¨η©ζ¨‘εθ΅ζΊεΊ"
]
},
"r3d100013821": {
"description": "Lexique is a database that provides various information for 140,000 words in the French language. For example, it will give in particular the frequencies of occurrences in different corpora, the phonological representation, the associated lemmas, the number of syllables, the grammatical category, and many other information.\nOpenlexicon brings together several lexical databases, including the Lexicon database, but also other databases providing information such as age of acquisition, reading times or concreteness, for example.",
"homepage": "http://www.lexique.org/",
"name": "Lexique",
"prefix": "r3d100013821"
},
"r3d100013822": {
"description": "Museum explorers travel to ocean depths, the peaks of the Andes, Africa's Rift Valley, the rainforests of South America, and the deserts of Central Asia. Perhaps even to a field site or research institution in your own state, territory or country. In each area, researchers collect specimens: fossils, minerals, and rocks, plants and animals, tools and artworks. Collections care professionals have meticulously preserved, labeled, cataloged, and organized items of this kind for more than 150 years. \nTaken together, the NMNH collections form the largest, most comprehensive natural history collection in the world. By comparing items gathered in different eras and regions, scientists learn how our world has varied across time and space.",
"homepage": "https://collections.nmnh.si.edu/search/",
"name": "Smithsonian National Museum of Natural History",
"prefix": "r3d100013822",
"xrefs": {
"ror": "00cz47042"
}
},
"r3d100013824": {
"description": "KU Leuven RDR (pronounced \"RaDaR\") is KU Leuven's Research Data Repository, built on Dataverse.org - open source repository software built by Harvard University. RDR gives KU Leuven researchers a one-stop platform to upload, describe, and share their research data, conveniently and with support from university staff.",
"homepage": "https://rdr.kuleuven.be/",
"name": "KU Leuven RDR",
"prefix": "r3d100013824",
"synonyms": [
"KU Leuven Research Data Repository"
]
},
"r3d100013827": {
"description": "The ESCAPE Open-source Scientific Software and Service Repository (OSSR) is a sustainable open-access repository to share scientific software, services and datasets to the astro-particle-physics-related communities and enable open science. It is built as a curated Zenodo community (https://zenodo.org/communities/escape2020) integrated with several tools to enable a complete software life-cycle. The ESCAPE Zenodo community welcomes entries that support the software and service projects in the OSSR such as user-support documentation, tutorials, presentations and training activities. It also encourages the archival of documents and material that disseminate and support the goals of ESCAPE.",
"homepage": "http://purl.org/escape/ossr",
"name": "Open-source Scientific Software and Service Repository",
"prefix": "r3d100013827",
"synonyms": [
"ESCAPE OSSR",
"OSSR",
"The European Science Cluster of Astronomy & Particle Physics Open-source Scientific Software and Service Repository"
]
},
"r3d100013830": {
"description": "HELIX DATA is an integral component of the Hellenic Data Service \"HELIX\" supporting knowledge management and scholarly communication in Greece.\nHELIX DATA is the data catalogue and repository, with a dual role to store and preserve data that are self-deposited by researchers as well as to harvest data records from other national data sources and catalogues.",
"homepage": "https://data.hellenicdataservice.gr/",
"name": "HELIX DATA",
"prefix": "r3d100013830",
"synonyms": [
"ΞΟΞΏΞΈΞ΅ΟΞΟΞΉΞΏ ΞΡδομΞΞ½ΟΞ½ \"HELIX\""
]
},
"r3d100013831": {
"description": "UNSWorks is the UNSW Open Access institutional repository which enables UNSW researchers to make their research outputs freely available and accessible.",
"homepage": "https://unsworks.unsw.edu.au/",
"name": "UNSWorks",
"prefix": "r3d100013831",
"synonyms": [
"University of New South Wales Institutional Repository"
],
"xrefs": {
"opendoar": "17",
"roar": "3116"
}
},
"r3d100013832": {
"description": "ROHub is a holistic solution for the storage, lifecycle management and preservation of scientific investigations, campaigns and operational processes via research objects. It makes these resources available to others, allows to publish and release them through a DOI, and allows to discover and reuse pre-existing scientific knowledge. Built entirely around the research object concept and inspired by sustainable software management principles, ROHub is the reference platform implementing natively the full research object model and paradigm, which provides the backbone to a wealth of RO-centric applications and interfaces across different scientific communities.",
"homepage": "https://reliance.rohub.org/",
"name": "ROHub",
"prefix": "r3d100013832",
"synonyms": [
"Research Object Hub Platform"
]
},
"r3d100013833": {
"description": "osnaData, the institutional research data repository of the OsnabrΓΌck University, offers all members of the university the opportunity to publish their scientific research data free of charge and thus share it with the public in accordance with open science. Research data of all types and formats can be published and provided with appropriate licenses. osnaData assigns DOIs to datasets as persistent identifiers.",
"homepage": "https://osnadata.ub.uni-osnabrueck.de/",
"name": "osnaData",
"prefix": "r3d100013833",
"synonyms": [
"Das Forschungsdatenrepositorium der UniversitΓ€t OsnabrΓΌck"
]
},
"r3d100013834": {
"description": "The EUR Data Repository [EDR] is the institutional data repository from the Erasmus University Rotterdam. The EUR Data Repository is an online platform where you showcase your research and make it findable, citable, and reusable for others.",
"homepage": "https://datarepository.eur.nl/",
"name": "EUR Data Repository",
"prefix": "r3d100013834",
"synonyms": [
"EDR",
"Erasmus University Rotterdam Data Repository"
]
},
"r3d100013835": {
"description": "Macquarie University's Institutional Research Data Repository (RDR) allows researchers to upload, publish, search and download research data. The RDR promotes collaboration, data sharing and discovery amongst researchers globally according to FAIR data principles.\nThe RDR is based on Figshare for Institutions, which has been specifically tailored to suit the needs of the Macquarie University research community.",
"homepage": "https://figshare.mq.edu.au/data",
"name": "Macquarie University Research Data Repository",
"prefix": "r3d100013835",
"synonyms": [
"Macquarie University RDR"
]
},
"r3d100013836": {
"description": "The Netherlands Cancer Registry is the national registration since 1989, providing statistics on cancer in the Netherlands. The registry is maintained by the Netherlands Comprehensive Cancer Organisation (IKNL). Data on incidence, prevalence, survival, mortality can be viewed in NCR data & figures on the IKNL website.",
"homepage": "https://iknl.nl/en/ncr",
"name": "Netherlands Cancer Registry",
"prefix": "r3d100013836",
"synonyms": [
"NCR",
"NKR",
"Nederlandse Kankerregistratie"
]
},
"r3d100013837": {
"description": "HilData is registered by Hildesheim University Library, \nThe access is via registration to the data and to the repository. Research data is with regards to educational science. Research data are sensitive and cannot be made fully open. HILDE Online is integrated in HilData: https://www.uni-hildesheim.de/celeb/projekte/fallarchiv-hilde/hildeonline-streaming-server/ HilData is working on its metadata (exposing metadata via interfaces) w.r.t. the FAIR principles and data citation. HilData and HILDE Online provide long-term storage and access to research data. \nThe research data repository provides restricted access to its data. \nThe research data repository uses DOI to make its provided data persistent, unique and citable.",
"homepage": "https://hildata.uni-hildesheim.de/",
"name": "HilData",
"prefix": "r3d100013837",
"synonyms": [
"HILDEonline"
]
},
"r3d100013843": {
"description": "ITESO's Institutional Repository (ReI) is a digital repository that integrates the university's academic production, which manages, preserves and makes available in open access mode the works of researchers, professors and students of this university.",
"homepage": "https://rei.iteso.mx/",
"name": "Repositorio Institucional del ITESO",
"prefix": "r3d100013843",
"synonyms": [
"Rel"
],
"xrefs": {
"opendoar": "2660"
}
},
"r3d100013844": {
"description": "Maenduar in Tupi means \"to remember\". The Maenduar repository, created by LARHUD is an institutional repository (IBICT) dedicated to research data in Digital Humanities and Humanities. The repository encompasses the production of LARHUD members and partners and extends to the public space as a public deposit repository.\nResearchers, professors, students linked to any institutions will be able to deposit their research data, understanding that Maenduar becomes, from this action, a public, national repository, dedicated to the production of knowledge in the Humanities in the face of the development of digital culture in all areas of the world. social world.",
"homepage": "https://zenodo.org/communities/larhud/",
"name": "Maenduar",
"prefix": "r3d100013844"
},
"r3d100013881": {
"description": "This platform aims to realize data storage, data management, data analysis, data sharing and data citation traceability of various data sets in the field of Humanities and Social Sciences of East China Normal University.",
"homepage": "http://sdsp.ecnu.edu.cn/sdp",
"name": "East China Normal University Social Data Sharing Platform",
"prefix": "r3d100013881",
"synonyms": [
"εδΈεΈθ倧ε¦δΊΊζη€Ύη§ε€§ζ°ζεΉ³ε°"
]
},
"r3d100013882": {
"description": "The Data Repository of the Department of Statistical Sciences of the University of Padova is a research data archive with the objective of sharing datasets collected within the Department. The service aims to facilitate data discovery, data sharing, and reuse.",
"homepage": "https://datarepository.stat.unipd.it/",
"name": "Department of Statistical Sciences Data Repository - Unipd",
"prefix": "r3d100013882",
"xrefs": {
"doi": "10.25430/datarepository-statisticalsciences"
}
},
"r3d100013884": {
"description": "REDU is the institutional open research data repository of the University of Campinas, Brazil. It contains research data produced by all research groups of the University, in a wide range of scientific domains, which are indexed by DataCite DOI. Created at the end of 2020, it is coordinated by a scientific and technical committee composed by data librarians, IT professionals, and scientists representing user groups. Implemented on top of Dataverse, it exports metadata using OAIS. Files with sensitive content (due to ethics or legal constraints) are not stored therein - rather, only their metadata is recorded in REDU, as well as contact information so that interested researchers can contact the persons responsible for the files for conditional subsequent access. It is being little by little populated, following the University's Open Science policies.",
"homepage": "https://redu.unicamp.br",
"name": "REDU - Unicamp Institutional Research Data Repository",
"prefix": "r3d100013884",
"synonyms": [
"Repositorio de Dados de Pesquisa da Unicamp"
]
},
"r3d100013885": {
"description": "Work With Data functions as a data library, collecting data from multiple reliable sources and merging them altogether into one database. It focuses on access through insights, datasets and api.",
"homepage": "https://www.workwithdata.com/",
"name": "Work With Data",
"prefix": "r3d100013885",
"synonyms": [
"The Data Library"
]
},
"r3d100013886": {
"description": "Open access database for rodent cognition data integration and sharing",
"homepage": "https://mousebytes.ca/home",
"name": "Mousebytes",
"prefix": "r3d100013886",
"xrefs": {
"scr": "021598"
}
},
"r3d100013887": {
"description": "CanWIN is the data centre for the Centre for Earth Observation Science (CEOS). We support research and education, and inform management, policy and evidence based decision-making from the Nelson River Watershed to the Arctic.",
"homepage": "https://canwin-datahub.ad.umanitoba.ca/",
"name": "Canadian Watershed Information Network",
"prefix": "r3d100013887",
"synonyms": [
"CanWin Data Hub"
]
},
"r3d100013888": {
"description": "The CBU Dataverse is a research data repository for Cape Breton University. Files are held securely on Canadian servers, and can be made openly accessible to further research, gain citations and promote our world class research.",
"homepage": "https://borealisdata.ca/dataverse/capebreton",
"name": "Cape Breton University Dataverse",
"prefix": "r3d100013888"
},
"r3d100013889": {
"description": "The Extreme Light Infrastructure (ELI) is the world's most advanced laser-based research infrastructure. The ELI Facilities provide access to a broad range of world-class high-power, high repetition-rate laser systems and secondary sources. This enables cutting-edge research and new regimes of high intensity physics in physical, chemical, medical, and materials sciences.",
"homepage": "https://data.eli-laser.eu/",
"name": "ELI ERIC Open Data Repository",
"prefix": "r3d100013889",
"synonyms": [
"ELI ERIC Open Data Portal",
"Extreme Light Infrastructure"
]
},
"r3d100013891": {
"description": "In HilReDa, researchers can permanently secure their research data and make it publicly available (publish) in open access in a sustainable and quality-appropriate manner. The research data is given a persistent identifier when it is published.",
"homepage": "https://www.uni-hildesheim.de/bibliothek/forschen-publizieren/forschungsdatenmanagement/hilreda/",
"name": "HilReDa",
"prefix": "r3d100013891",
"synonyms": [
"Forschungsdatenrepositorium der UniversitΓ€t Hildesheim"
]
},
"r3d100013892": {
"description": "Provides free and open access to over 155 city datasets with new ones added regularly. Open data is anonymized (not personally identifiable), free, and available to everyone in one or more open and accessible formats.",
"homepage": "https://opendata.vancouver.ca/pages/home/",
"name": "City of Vancouver Open Data Portal",
"prefix": "r3d100013892"
},
"r3d100013893": {
"description": "The Concordia University Dataverse is a research data repository for Concordia faculty, students, and staff. Files are held in a secure environment on Canadian servers.",
"homepage": "https://borealisdata.ca/dataverse/concordia",
"name": "Concordia University Dataverse",
"prefix": "r3d100013893"
},
"r3d100013894": {
"description": "Government of Yukon open data provides an easy way to find, access and reuse the government's public datasets. This service brings all of the government's data together in one searchable website. Our datasets are created and managed by different government departments. We cannot guarantee the quality or timeliness of all data. If you have any feedback you can get in touch with the department that produced the dataset. This is a pilot project. We are in the process of adding a quality framework to make it easier for you to access high quality, reliable data.",
"homepage": "https://open.yukon.ca/data",
"name": "Yukon Open Data",
"prefix": "r3d100013894"
},
"r3d100013895": {
"description": "This collection is the institutional data repository reserved for the entire research community of the Institut national de la recherche scientifique (INRS).",
"homepage": "https://borealisdata.ca/dataverse/inrs",
"name": "Dataverse de l'Institut national de la recherche scientifique",
"prefix": "r3d100013895",
"synonyms": [
"Dataverse de l'INRS"
]
},
"r3d100013896": {
"description": "This Dataverse is an institutional data repository reserved for the Laval University community.",
"homepage": "https://borealisdata.ca/dataverse/laval",
"name": "Dataverse de l'UniversitΓ© Laval",
"prefix": "r3d100013896"
},
"r3d100013897": {
"description": "GCRIS Database is a research and performance evaluation information system that enables searching and discovering all research outputs within the Izmir Institute of Technology research ecosystem, associating these outputs with researchers, providing advanced reporting with different metrics, and supporting corporate strategic decisions. Besides, it is an institutional repository at international standards that brings together and organizes all kinds of academic outputs related to research activities and allows sharing with the whole scientific world by providing long-term preservation.",
"homepage": "https://gcris.iyte.edu.tr/",
"name": "IZTECH GCRIS",
"prefix": "r3d100013897",
"synonyms": [
"Δ°YTE GCRIS"
],
"xrefs": {
"hdl": "11147",
"opendoar": "2661"
}
},
"r3d100013898": {
"description": "This Dataverse is the institutional data repository reserved for the entire research community of the UniversitΓ© TΓLUQ.",
"homepage": "https://borealisdata.ca/dataverse/teluq",
"name": "Dataverse de l'UniversitΓ© TΓLUQ",
"prefix": "r3d100013898"
},
"r3d100013899": {
"description": "This dataverse is the institutional data repository reserved for the entire research community of for UQAC researchers.",
"homepage": "https://dataverse.scholarsportal.info/dataverse/uqac",
"name": "Dataverse de l'UniversitΓ© du QuΓ©bec Γ Chicoutimi",
"prefix": "r3d100013899",
"synonyms": [
"Dataverse de l'UQAC"
]
},
"r3d100013900": {
"description": "This collection is the institutional data repository reserved for the entire research community of UQAM.",
"homepage": "https://dataverse.scholarsportal.info/dataverse/uqam",
"name": "UQAM - Dataverse",
"prefix": "r3d100013900",
"synonyms": [
"UniversitΓ© du QuΓ©bec Γ MontrΓ©al - Dataverse"
]
},
"r3d100013901": {
"description": "This Dataverse is the institutional data repository reserved for the entire research community of the Université du Québec à Trois-Rivières.",
"homepage": "https://borealisdata.ca/dataverse/uqtr",
"name": "Université du Québec à Trois-Rivières - Borealis",
"prefix": "r3d100013901",
"synonyms": [
"Collection UQTR de Borealis",
"UQTR Dataverse"
]
},
"r3d100013902": {
"description": "This collection is the institutional data repository reserved for the entire research community of HEC MontrΓ©al .",
"homepage": "https://borealisdata.ca/dataverse/hec",
"name": "HEC MontrΓ©al Dataverse",
"prefix": "r3d100013902",
"synonyms": [
"Γcole des Hautes Γtudes commerciales dataverse"
]
},
"r3d100013903": {
"description": "The MacEwan University Data Repository provides a place to store, share, and explore data and supports the teaching and scholarly activity of MacEwan University.",
"homepage": "https://borealisdata.ca/dataverse/macewan",
"name": "MacEwan University Data Repository",
"prefix": "r3d100013903"
},
"r3d100013904": {
"description": "Arca Data is Fiocruz's official repository for archiving, publishing, disseminating, preserving and sharing digital research data produced by the Fiocruz community or in partnership with other research institutes or bodies, with the aim of promoting new research, ensuring the reproducibility or replicability of existing research and promoting an Open and Citizen Science. Its objective is to stimulate the wide circulation of scientific knowledge, strengthening the institutional commitment to Open Science and free access to health information, in addition to providing transparency and fostering collaboration between researchers, educators, academics, managers and graduate students, to the advancement of knowledge and the creation of solutions that meet the demands of society.",
"homepage": "https://arcadados.fiocruz.br/",
"name": "Arca Dados",
"prefix": "r3d100013904",
"synonyms": [
"Arca Data",
"Arca de datos"
],
"xrefs": {
"doi": "10.35078"
}
},
"r3d100013905": {
"description": "The McGill University Dataverse is a research data repository for McGill faculty, students, and staff. Files are held in a secure environment on Canadian servers.",
"homepage": "https://borealisdata.ca/dataverse/mcgill",
"name": "McGill University Dataverse",
"prefix": "r3d100013905"
},
"r3d100013906": {
"description": "The Memorial University Dataverse is a research data repository for our faculty, students, and staff. Files are held in a secure environment on Canadian servers. Researchers can choose to make content available to the public, to specific individuals, or to keep it locked.",
"homepage": "https://borealisdata.ca/dataverse/memorial",
"name": "Memorial University Dataverse",
"prefix": "r3d100013906",
"synonyms": [
"Memorial University of Newfoundland Dataverse"
]
},
"r3d100013907": {
"description": "This collection is the institutional data repository reserved for the entire research community of Mount Royal University",
"homepage": "https://dataverse.scholarsportal.info/dataverse/mru",
"name": "Mount Royal University Dataverse",
"prefix": "r3d100013907",
"synonyms": [
"MRU Dataverse"
]
},
"r3d100013908": {
"description": "The SMU Dataverse is a research data repository for our faculty, students, and staff. Files are held in a secure environment on Canadian servers. Researchers can choose to make content available publicly, to specific individuals, or to keep it locked.",
"homepage": "https://borealisdata.ca/dataverse/smu",
"name": "Saint Mary's University Dataverse",
"prefix": "r3d100013908",
"synonyms": [
"SMU Dataverse"
]
},
"r3d100013909": {
"description": "The University of Northern British Columbia Dataverse is a research data repository for research data from UNBC researchers. Files are held in a secure environment on Canadian servers. The platform makes it possible for researchers to deposit data, create appropriate metadata, and version documents as they work. Researchers can choose to make content available publicly, to specific individuals, or to keep it locked.",
"homepage": "https://borealisdata.ca/dataverse/unbc",
"name": "University of Northern British Columbia Dataverse",
"prefix": "r3d100013909",
"synonyms": [
"UNBC"
]
},
"r3d100013910": {
"description": "UWinnipeg Research Data Repository accepts research data and datasets that have been created by researchers and research groups at the University of Winnipeg. Files are held in a secure environment on Canadian servers. The UWinnipeg Data Repository accepts finalized datasets that are ready for publication and sharing.",
"homepage": "https://borealisdata.ca/dataverse/uwinnipeg",
"name": "University of Winnipeg Research Data Repository",
"prefix": "r3d100013910",
"synonyms": [
"UWinnipeg Research Data Repository"
]
},
"r3d100013911": {
"description": "The Vancouver Island University Dataverse is part of Borealis, the Canadian Dataverse Repository, and is a research data repository for VIU faculty, students, and staff. Files are held in a secure environment on Canadian servers. Researchers can choose to make content available to the public, to specific individuals, or to keep it locked.",
"homepage": "https://borealisdata.ca/dataverse/viu",
"name": "Vancouver Island University Dataverse",
"prefix": "r3d100013911",
"synonyms": [
"VIU Dataverse"
]
},
"r3d100013913": {
"description": "Established in 1998, we have been the authoritative source of spatial data and imagery in Alberta for over 20 years.\nWe have a joint venture agreement with Alberta Data Partnerships Ltd. (ADP) and are responsible for the day-to-day management and distribution of the digital data sets they manage. As the agent for ADP, we are responsible for making mapping products available, accessible, accurate and affordable. We are the leading data management, maintenance, and distribution company in Alberta, and ensure the continued updating, re-engineering, storage, distribution, value-added redistribution, and general management of primary provincial mapping datasets.\nOur webstore, Altalis.com, enables customers to explore, view, and acquire spatial data products both paid and open data with the click of a button. We take pride in providing exceptional customer service and building long-term relationships with our clients. Our experienced customer service team are available to answer any questions you may have about finding the right data to meet your needs.",
"homepage": "https://www.altalis.com/",
"name": "Altalis",
"prefix": "r3d100013913"
},
"r3d100013914": {
"description": "The Canadian Integrated Ocean Observing System (CIOOS) Data Catalogue is an online open-access data catalogue designed for sharing reliable and high-quality.\nCIOOS is a collaboration between institutional, governmental, and non-governmental partners located in the Pacific, the St. Lawrence, and the Atlantic. These Regional Associations (RAs) work closely with local organizations to meet end-user needs and develop place-based solutions for a diverse country.",
"homepage": "https://catalogue.cioos.ca/",
"name": "Canadian Integrated Ocean Observing System Data Catalogue",
"prefix": "r3d100013914",
"synonyms": [
"CIOOS Data Catalogue",
"Catalogue de donnΓ©es du SIOOC",
"Catalogue de données du Système Intégré d'Observation des Oceans du Canada"
],
"xrefs": {
"fairsharing.legacy": "3260"
}
},
"r3d100013916": {
"description": "The digital edition provides the complete correspondence of the German author Jean Paul (1763-1825) as well as some letters from contemporaries from his circle.",
"homepage": "https://www.jeanpaul-edition.de/",
"name": "Jean Paul β SΓ€mtliche Briefe digital",
"prefix": "r3d100013916",
"xrefs": {
"zenodo": "4155301"
}
},
"r3d100013917": {
"description": "The Better Outcomes Registry & Network (BORN) is Ontario's prescribed perinatal, newborn and child registry with the role of facilitating quality care for families across the province. BORN collects, interprets, shares and rigorously protects high-quality data essential to making Ontario the safest place in the world to have a baby.",
"homepage": "https://www.bornontario.ca/en/index.aspx",
"name": "BORN Ontario",
"prefix": "r3d100013917",
"synonyms": [
"Better Outcomes Registry & Network",
"Le Registre et réseau des bons résultats dès la naissance"
],
"xrefs": {
"fairsharing.legacy": "4061"
}
},
"r3d100013918": {
"description": "Covalent DNA modifications have been found in numerous organisms and more are continually being discovered and characterized, as detection methods improve. Many of these modifications can affect the conformation of the DNA double helix, often resulting in downstream effects upon transcription factor binding. Some of these modifications have been demonstrated to be stable, while others are viewed as merely transient. DNAmod catalogues information on known DNA modifications, of which the well-known 5-methylcytosine is only one. It aims to profile modifications' properties, building upon data contained within the Chemical Entities of Biological Interest (ChEBI) database. It also provides literature citations and includes curated annotations on mapping techniques and natural occurrence information.",
"homepage": "https://dnamod.hoffmanlab.org/index.html",
"name": "DNAmod",
"prefix": "r3d100013918",
"synonyms": [
"DNA modification database"
],
"xrefs": {
"fairsharing": "FAIRsharing.qgMKai"
}
},
"r3d100013919": {
"description": "This database documents the expression and localization patterns of Drosophila mRNAs at the cellular and subcellular level during early embryogenesis and third instar larval tissues. A high-resolution, high-throughput fluorescence detection method is used to detect expressed mRNAs. The data can be accessed by searching the localization categories, searching for specific genes or browsing the list of tested genes.",
"homepage": "http://fly-fish.ccbr.utoronto.ca/",
"name": "Fly-FISH",
"prefix": "r3d100013919",
"xrefs": {
"fairsharing": "FAIRsharing.14c4ca"
}
},
"r3d100013920": {
"description": "Satellog is a database to identify and dynamically prioritize repeats by using various characteristics, for example, repeat unit, repeat length percentile rank, class, period, total length, genomic coordinates, UniGene polymorphism profile, proximity to or presence within gene regions, such as CDS, UTR, location upstream.",
"homepage": "http://satellog.bcgsc.ca/index.php",
"name": "Satellog",
"prefix": "r3d100013920",
"xrefs": {
"fairsharing": "FAIRsharing.fa9ccb"
}
},
"r3d100013921": {
"description": "The National Forest Inventory (NFI) is a collaborative effort involving federal, provincial and territorial government agencies. They monitor a network of twenty thousand sampling points across Canada on an ongoing basis to provide information on the state of Canada's forests and a continuous record of forest change. They provide data and products to forest science researchers, forest policy decision-makers and interested stakeholders.",
"homepage": "https://nfi.nfis.org/en",
"name": "Canada's National Forest Inventory",
"prefix": "r3d100013921",
"synonyms": [
"IFN",
"Inventaire forestier national du Canada",
"NFI",
"National Forest Inventory"
]
},
"r3d100013922": {
"description": "The South African Weather Service (SAWS) is a Section 3(a) public entity under the Ministry of Environmental Affairs and is governed by a Board. It is an authoritative voice for weather and climate forecasting in South Africa and as a member of the World Meteorological Organization (WMO) it complies with international meteorological standards. \nThe South African Weather Service has a variety of weather products and services which can be customized.",
"homepage": "https://www.weathersa.co.za/",
"name": "South African Weather Service",
"prefix": "r3d100013922",
"synonyms": [
"SAWS"
]
},
"r3d100013924": {
"description": "Through its Blood4Research Program based in Vancouver, the Centre for Innovation collects blood from committed donors who have been deferred from donating blood for patient use. The collected blood is processed and provided to investigators to facilitate research that promotes advances in the fields of transfusion, cellular therapies, and transplantation medicine.\nThrough its Cord Blood for Research Program, Canadian Blood Servicesβ Cord Blood Bank provides investigators with cord blood products to facilitate research that promotes advances in the fields of transfusion, cellular therapies, and transplantation medicine.β\nThe Cord Blood for Research Program distributes cord blood products that do not meet the criteria for storage in the cord blood bank but still contain enough cells for meaningful research and for which mothersβ research consent has been obtained.",
"homepage": "https://www.blood.ca/en/research/products-and-services-researchers/products-research#datasets",
"name": "Canadia Blood Services Data4Research Program",
"prefix": "r3d100013924"
},
"r3d100013925": {
"description": "NIAIDβs TB Portals Program is a multi-national collaboration for TB data sharing and analysis to advance TB research. \n As a global consortium of clinicians, scientists, and IT professionals from 40 sites in 16 countries throughout eastern Europe, Asia, and sub-Saharan Africa, the TB Portals Program is a web-based, open-access repository of multi-domain TB data and tools for its analysis. Researchers can find linked socioeconomic/geographic, clinical, laboratory, radiological, and genomic data from overβ―7,500 international published TB patient cases with an emphasis on drug-resistant tuberculosis.",
"homepage": "https://tbportals.niaid.nih.gov",
"name": "TB Portals",
"prefix": "r3d100013925",
"synonyms": [
"Tuberculosis data science"
],
"xrefs": {
"scr": "016594"
}
},
"r3d100013927": {
"description": "The Canadian Institute for Health Information (CIHI) provides comparable and actionable data and information that are used to accelerate improvements in health care, health system performance and population health across Canada.",
"homepage": "https://www.cihi.ca/en/access-data-and-reports",
"name": "Canadian Institute for Health Information Repository",
"prefix": "r3d100013927",
"synonyms": [
"CIHI's Repository"
]
},
"r3d100013928": {
"description": "The Canadian Laboratory Initiative on Pediatric Reference Intervals (CALIPER) is a nation-wide health initiative to improve the diagnosis and monitoring of children and adolescents with medical concerns. Our main objective is to establish a comprehensive database of reference intervals for blood test results in children and adolescents. CALIPER is designed to fill the gaps that currently exist in accurately interpreting blood test results with the ultimate goal of improving the care of children at SickKids and other childrenβs hospitals around the world.",
"homepage": "https://caliperdatabase.org/#/",
"name": "Canadian Laboratory Initiative on Pediatric Reference Intervals",
"prefix": "r3d100013928",
"synonyms": [
"CALIPER"
]
},
"r3d100013929": {
"description": "The Pennington/Louisiana NORC Biorepository is a collection of de-identified data from studies of human subjects conducted at Pennington Biomedical Research Center since 1980. The repository includes data from trials centered around obesity and nutrition and those funded by the National Institutes of Health, Department of Defense, United States Department of Agriculture, American Heart Association, American Diabetes Association and other government and non-profit organizations.",
"homepage": "https://my.pbrc.edu/NORC",
"name": "Pennington/Louisiana NORC Biorepository",
"prefix": "r3d100013929",
"synonyms": [
"Pennington Nutrition Obesity Data Repository",
"Pennington/Louisiana Nutrition Obesity Research Center Biorepository"
]
},
"r3d100013931": {
"description": "The Research Data Gouv platform is the French national federated platform for open and shared research data serving the national scientific community. This platform was an integral part of the Second National Plan for Open Science (PNSO) and offers a multidisciplinary data repository, a registry which reports data hosted in other repositories and a web portal. The multidisciplinary repository is a sovereign publishing solution for sharing and opening up data for communities which are yet to set up their own recognised thematic repository.",
"homepage": "https://recherche.data.gouv.fr/en",
"name": "Recherche Data Gouv France",
"prefix": "r3d100013931",
"synonyms": [
"French Research Data Gouv Platform"
]
},
"r3d100013932": {
"description": "A Research Data Repository (RDR) for researchers in India. Any registered researchers of Indian Universities can manage their research data on eSHODHMANTHAN-RDR free of cost. This research data repository is configured to provide free of cost research data management services to existing and forthcoming researchers throughout their research life. eSHODHMANTHAN-RDR is powered by Dataverse project of Harvard University",
"homepage": "https://dataverse.harvard.edu/dataverse/RDR",
"name": "eSHODHMANTHAN",
"prefix": "r3d100013932",
"synonyms": [
"eSHODHMANTHAN Research Data Repository of India",
"eSHODHMANTHAN-RDR",
"eSRDR",
"ΰ€ΰ€Άΰ₯ΰ€§ΰ€ΰ€ΰ€₯ΰ€¨"
]
},
"r3d100013933": {
"description": "CanPath is Canadaβs largest population health cohort and a national platform for population-level health research.It is a unique Canadian platform allowing scientists to explore the complex factors that contribute to disease. It is a deeply characterized cohort of individuals who have provided broad consent and now include two per cent of all Canadians between 30 and 74 years of age. CanPath can save researchers time β sometimes up to a decade β associated with arranging and measuring their own population samples.\nResearchers around the world can readily integrate CanPath data into their own studies. The standardization and harmonization of data across CanPathβs regional cohorts has been facilitated by Maelstrom Research.",
"homepage": "https://portal.canpath.ca/",
"name": "CanPath Portal",
"prefix": "r3d100013933",
"synonyms": [
"Canadian Partnership for Tomorrowβs Health Portal"
]
},
"r3d100013935": {
"description": "The Community Data Program (CDP) is a membership-based community development initiative open to any Canadian public, non-profit or community sector organization with a local service delivery or public policy mandate. The program facilitates access to the evidence needed to tell our stories and inform effective and responsive policy and program design and implementation. The CDP makes data accessible and useful for all members with training and capacity building resources. Through its vibrant network, the CDP facilitates and supports dialogue and the sharing of best practices in the use of community data. The CDP has emerged as a unique Canada-wide platform for generating information, convening and collaborating.",
"homepage": "https://communitydata.ca/",
"name": "Community Data Program",
"prefix": "r3d100013935",
"synonyms": [
"CDP"
]
},
"r3d100013936": {
"description": "ICARUS is an open access, searchable, web-based infrastructure for storing, sharing, and utilizing atmospheric simulation chamber data. Atmospheric simulation chambers (sometimes called \"smog chambers\", environmental chambers, flow tubes, and continuously stirred reactors) are indispensable tools for atmospheric chemistry and physics research. The fundamental kinetic, mechanistic, or physical results from atmospheric chambers integrate into chemical transport models and inform scientific decision making. The data available in ICARUS are highly curated, uniform, and freely available to researchers, policy makers, and the general public worldwide.",
"homepage": "https://icarus.ucdavis.edu/",
"name": "ICARUS",
"prefix": "r3d100013936",
"synonyms": [
"Integrated Chamber Atmospheric data Repository for Unified Science"
]
},
"r3d100013938": {
"description": "REPOSIT is the institutional repository for research data of Hamburg University of Applied Sciences.",
"homepage": "https://reposit.haw-hamburg.de/",
"name": "REPOSIT",
"prefix": "r3d100013938"
},
"r3d100013939": {
"description": "The Institutional Repository of the Universidad Francisco JosΓ© de Caldas RIUD is a tool where digital objects corresponding to the intellectual production of the University are deposited to protect, preserve, and disseminate.",
"homepage": "https://repository.udistrital.edu.co/",
"name": "Repositorio Institucional de la Universidad Distrital Francisco JosΓ© de Caldas",
"prefix": "r3d100013939",
"synonyms": [
"RIUD",
"Repositorio Institucional Universidad Distrital"
]
},
"r3d100013940": {
"description": "Health Data Nova Scotia (HDNS), is a data repository based in the Faculty of Medicine's, Department of Community Health and Epidemiology at Dalhousie University, focused on supporting data driven research for a healthier Nova Scotia. HDNS facilitates research and innovation in Nova Scotia by providing access to linkable administrative health data and analysis for research and health service assessment purposes in a secure, controlled environment, while respecting the privacy and confidentiality of Nova Scotians.",
"homepage": "https://medicine.dal.ca/departments/department-sites/community-health/research/hdns.html",
"name": "Health Data Nova Scotia",
"prefix": "r3d100013940",
"synonyms": [
"HDNS"
]
},
"r3d100013942": {
"description": "The Wildlife Management Information System (WMIS) is the Government of Northwest Territories (GNWT) online, geo-referenced wildlife database. WMIS provides a central repository for government staff, industry, researchers and public to store and access standardized wildlife observation data to support the conservation and management of wild species and their habitat in the Northwest Territories (NWT).",
"homepage": "https://www.enr.gov.nt.ca/en/services/research-and-data-nwt/wildlife-management-information-system",
"name": "Wildlife Management Information System",
"prefix": "r3d100013942",
"synonyms": [
"WMIS"
]
},
"r3d100013943": {
"description": "NB-IRDT is expanding research potential through pseudonymised, linkable data sets. Our repository includes a growing collection to meet diverse research needs. We only host pseudonymous data in the NB-IRDT repository. NB-IRDT also offers public use data sets, which consist of de-identified data that is publicly accessible. All our data can be accessed in the NB-IRDT lab spaces.",
"homepage": "https://www.unb.ca/nbirdt/data/",
"name": "NB Institute for Research, Data and Training",
"prefix": "r3d100013943",
"synonyms": [
"NB-IRDT",
"New Brunswick Institute for Research, Data and Training"
]
},
"r3d100013944": {
"description": "With more than 60 years of experience, Toronto and Region Conservation Authority (TRCA) is one of 36 Conservation Authorities in Ontario, created to safeguard and enhance the health and well-being of watershed communities through the protection and restoration of the natural environment and the ecological services the environment provides.\nAt TRCA, we are working towards providing free and open access to our data and information, in both accessible and machine readable formats, to ensure itβs available and easy to consume. Improving access to TRCAβs data and information will provide transparency into the decision making process and will improve accountability while increasing the publicβs understanding and engagement with the organization.",
"homepage": "https://data.trca.ca/",
"name": "Toronto and Region Conservation Authority Open Data",
"prefix": "r3d100013944",
"synonyms": [
"TRCA Open Data"
]
},
"r3d100013945": {
"description": "An open access data, tools, and compute resource for assessing and processing human NeuroElectroMagnetic data shared by its authors thru OpenNeuro.org.",
"homepage": "https://nemar.org/",
"name": "NEMAR",
"prefix": "r3d100013945",
"synonyms": [
"NeuroElectroMagnetic data Archive and tools Resource"
],
"xrefs": {
"scr": "019100"
}
},
"r3d100013946": {
"description": "Open data portal for the Government of New Brunswick",
"homepage": "https://gnb.socrata.com/",
"name": "Open Data New Brunswick",
"prefix": "r3d100013946"
},
"r3d100013947": {
"description": "Population Data BC (PopData) is a multi-university, data and education resource facilitating interdisciplinary research on the determinants of human health, well-being and development.\nProviding a range of services to researchers and data providers, PopData strives to ensure that researchers have timely access to the data and training they need to address research questions on population health. Research using these data informs policy-making and leads to healthier communities.",
"homepage": "https://www.popdata.bc.ca/",
"name": "Population Data BC",
"prefix": "r3d100013947",
"synonyms": [
"PopData",
"populationdata BC"
]
},
"r3d100013948": {
"description": "The British Columbia Centre for Disease Control's (BCCDC) data dashboards and reports provide quick access to a selection of statistics on diseases in BC and on the health of the province's populations and communities. Additional data can be made available upon request.",
"homepage": "http://www.bccdc.ca/health-professionals/data-reports",
"name": "BCCDC Data",
"prefix": "r3d100013948",
"synonyms": [
"British Columbia Centre for Disease Control Data"
]
},
"r3d100013949": {
"description": "The BioImage Archive stores and distributes life sciences imaging datasets. It supports deposition of biological imaging data associated with publications for the whole research community, as well as reference imaging datasets. All data deposited to the BioImage Archive is made openly accessible to the scientific community.",
"homepage": "https://www.ebi.ac.uk/bioimage-archive/",
"name": "BioImage Archive",
"prefix": "r3d100013949",
"synonyms": [
"BIA"
],
"xrefs": {
"fairsharing": "FAIRsharing.x38D2k"
}
},
"r3d100013950": {
"description": "The BigBrain Project repository contains data from BigBrain: A high-resolution, 3D model of a human post-mortem brain, which was obtained in accordance with ethical requirements of the University of DΓΌsseldorf. The brain of a 65-year-old body donor was sectioned, stained for cell bodies, scanned at very high resolution, and then digitally reconstructed in 3D. The full dataset of images, volumes, and surfaces are available for download on the project's ftp site, while a subset of files offering different spatial resolutions can be accessed via LORIS. The web-based 3D interactive atlas viewer is capable of displaying very large brain volumes, including oblique slicing, a whole brain overview, surface meshes, and maps. It enables navigating the BigBrain in 3D, exploring the growing set of highly detailed maps for cortical layers and cytoarchitectonic areas, and finding related neuroscience data.",
"homepage": "https://bigbrain.loris.ca/main.php",
"name": "BigBrain Database",
"prefix": "r3d100013950",
"synonyms": [
"Big Brain"
],
"xrefs": {
"nlx": "153840",
"scr": "001593"
}
},
"r3d100013951": {
"description": "DDE DPR is a repository of geoscience data established with the support of Deep-time Digital Earth international big science program (DDE), which is committed to building a resource base for long-term data sharing and data release. Users can provide their research results to consumers in a discoverable, shareable and referential way, provide long-term preservation, sharing and acquisition services for scientific data, and promote the findability, accessibility, interoperability and reusability (FAIR) of data on the basis of protecting the rights and interests of data authors, so as to promote the sharing of geoscience data.",
"homepage": "https://repository.deep-time.org/",
"name": "DDE Data Publisher & Repository",
"prefix": "r3d100013951",
"synonyms": [
"DDE DPR",
"Deep-time Digital Earth Data Publisher & Repository"
],
"xrefs": {
"fairsharing": "FAIRsharing.5f3df5"
}
},
"r3d100013952": {
"description": "The Open Archive for Miscellaneous Data (OMIX) database is a data repository developed and maintained by the National Genomics Data Center (NGDC). The database specializes in descriptions of biological studies, including genomic, proteomic, and metabolomic, as well as data that do not fit in the structured archives at other databases in NGDC. It can accept various types of studies described via a simple format and enables researchers to upload supplementary information and link to it from the publication.",
"homepage": "https://ngdc.cncb.ac.cn/omix/",
"name": "Open Archive for Miscellaneous Data",
"prefix": "r3d100013952",
"synonyms": [
"OMIX",
"ε€ε
ζ°ζε½ζ‘£εΊ"
]
},
"r3d100013953": {
"description": "E-RA provides a permanent managed repository and knowledgebase for secure storage of metadata and data from Rothamsted's Long-term Experiments, the oldest, continuous agronomic experiments in the world. Together with the accompanying meteorological records, associated documentation and sample archive, it is a unique historical record of experiments that have been measured continuously since 1843. e-RA provides comprehensive descriptions of Rothamsted's long-term experiments including Broadbalk Wheat, Park Grass Hay, Hoosfield Barley, Rothamsted and Woburn Ley Arables, and Long-term Liming. e-RA maintains long-term routine data collections including crop yields, quality traits, agronomic management, soil chemistry, disease, and botanical diversity. The experiments are available as a research infrastructure to scientists and scientists are encouraged to deposit any new data generated with e-RA.",
"homepage": "http://www.era.rothamsted.ac.uk/",
"name": "Rothamsted Long-term Experiments Electronic Archive",
"prefix": "r3d100013953",
"synonyms": [
"e-RA"
]
},
"r3d100013955": {
"description": "The Canadian VirusSeq Data Portal (CVDP) is an open-access data portal funded by Genome Canada. It is intended to facilitate access to Canadian SARS-CoV-2 sequences and associated non-sensitive metadata adhering to the FAIR Data principles. Limited contextual metadata and viral genome sequences can be shared among Canadian public health labs, researchers and other groups interested in accessing the data for surveillance, research, and innovation purposes. The CVDP will harmonize, validate, and automate submission to international databases and enable the creation of real-time dashboards that summarize the Canadian data contributions while facilitating exploration and access. Sequences or metadata submitted to the CVDP may not include data that could reveal the personal identity of the source. Its is part of Canadian COVID Genomics Network (CanCOGeN).",
"homepage": "https://virusseq-dataportal.ca/",
"name": "Canadian VirusSeq Data Portal",
"prefix": "r3d100013955",
"synonyms": [
"CVDP"
],
"xrefs": {
"fairsharing": "FAIRsharing.802704"
}
},
"r3d100013956": {
"description": "Brain Image Library (BIL) is an NIH-funded public resource serving the neuroscience community by providing a persistent centralized repository for brain microscopy data. Data scope of the BIL archive includes whole brain microscopy image datasets and their accompanying secondary data such as neuron morphologies, targeted microscope-enabled experiments including connectivity between cells and spatial transcriptomics, and other historical collections of value to the community. The BIL Analysis Ecosystem provides an integrated computational and visualization system to explore, visualize, and access BIL data without having to download it.",
"homepage": "https://www.brainimagelibrary.org/",
"name": "Brain Image Library",
"prefix": "r3d100013956",
"synonyms": [
"BIL"
],
"xrefs": {
"scr": "017272"
}
},
"r3d100013957": {
"description": "CANJEM (CANadian Job-Exposure Matrix) is a large source of retrospective information on job-based exposure for a given occupation and time period. Covering most occupations and many agents, it provides information on the probability, frequency and intensity of exposure from a list of 258 occupational risk factors.\n\nCANJEM was built from past individual expert evaluations of occupational exposures in a series of four case control studies of various cancers conducted since the mid-1980s up to 2010 in the greater Montreal area. During these studies over 30 000 jobs from 1930 to 2005 held by close to 10 000 subjects were evaluated by experts who assigned exposures based on descriptions of tasks, processes, work environment, and exposure control measures.\"",
"homepage": "http://www.canjem.ca/",
"name": "CANJEM",
"prefix": "r3d100013957",
"synonyms": [
"Canadian Job-Exposure Matrix",
"Occupational exposure information system"
]
},
"r3d100013959": {
"description": "PSnpBind is a large database of proteinβligand complexes covering a wide range of binding pocket mutations and small moleculesβ landscape. This database can be used as a source of data for different types of studies, for example, developing machine learning algorithms to predict proteinβligand affinity or mutation's effect on it which requires an extensive amount of data with a wide coverage of mutation types and small molecules. Also, studies of protein-ligand interactions and conformer orientation changes across different mutated versions of a protein can be established using data from PSnpBind.",
"homepage": "https://psnpbind.org",
"name": "PSnpBind",
"prefix": "r3d100013959"
},
"r3d100013960": {
"description": "The Academic Data Repository of the National University of Rosario (RDA- UNR) allows for sharing, storing, accessing, exploring, and citing research data managed by UNR professors, researchers and students so as to make these data visible and promote its use and reutilization, ensuring its long-term preservation. It is a self-publishing repository, i.e. users upload, organize, describe and publish their own data with the assistance of a team of curators, user guides and training sessions.",
"homepage": "https://dataverse.unr.edu.ar/",
"name": "Repositorio de Datos AcadΓ©micos Universidad Nacional de Rosario",
"prefix": "r3d100013960",
"synonyms": [
"Academic Data Repository National University of Rosario",
"RDA UNR"
],
"xrefs": {
"doi": "10.57715/UNR/"
}
},
"r3d100013961": {
"description": "The National Biodiversity Information System (SNIB) of Mexico by the National Commission for the Knowledge and Use of Biodiversity (CONABIO).\nThe SNIB is of strategic importance in a megadiversity country like Mexico, making it clear to CONABIO from the beginning that the SNIB should rely on the work of the multiplicity of institutions and national and foreign experts that for years have been dedicated to the study of biodiversity of Mexico. The creation of this system was expressed as a mandate for CONABIO in the General Law of Ecological Balance and Environmental Protection (LGEEPA Art. 80 fraction V).\nThe participation of specialists in the generation of data and information for the SNIB is one of the various ways in which they collaborate with this system, since having an information system that allows the country to make informed decisions regarding its biodiversity requires that it be made up of data and information supported by a broad network of experts.",
"homepage": "https://snib.mx/",
"name": "National Biodiversity Information System of Mexico",
"prefix": "r3d100013961",
"synonyms": [
"SNIB",
"Sistema Nacional de InformaciΓ³n sobre Biodiversidad de MΓ©xico"
]
},
"r3d100013962": {
"description": "Sextant is a marine and coastal geographic data infrastructure. It is operated by Scientific Information Systems for the Sea (SISMER) of Ifremer (https://www.ifremer.fr/). \nSextant aims to document, disseminate and promote a catalog of data related to the marine environment. For Ifremer's laboratories and partners, as well as for national and European actors working in the marine and coastal field, Sextant provides tools that promote and facilitate the archiving, consultation and availability of these geographical data. \nData published by Sextant are available free or restricted. They can be used in accordance with the terms of the Creative Commons license selected by the author of data. Sextant infrastructure and the technologies used are in line with the implementation of the INSPIRE Directive and make it possible to follow the Open Data approach.\nSome data set published by Sextant has a DOI which enables it to be cited in a publication in a reliable and sustainable way. The long-term preservation of data filed in Sextant is ensured by Ifremer infrastructure.",
"homepage": "https://sextant.ifremer.fr/eng",
"name": "Sextant",
"prefix": "r3d100013962",
"synonyms": [
"Infrastructure de DonnΓ©es GΓ©ographiques (IDG) marines et littorales"
],
"xrefs": {
"fairsharing": "FAIRsharing.85b457"
}
},
"r3d100013963": {
"description": "Canadian Urban Environmental Health Research Consortium (CANUE) collates and generates standard measures of environmental factors and provides these data to a wide range of health data organizations who pre-link and distribute them to the Canadian research community. Exposure metrics currently distributed by CANUE include air quality (nitrogen dioxide, sulfur dioxide, ozone, and fine particulate matter concentrations), green and blue spaces (Landsat, MODIS, and AVHRR normalized difference vegetation indices), neighborhood factors (access to employment, material and social deprivation indices, marginalization indices, nighttime light, and active living environments), and weather and climate (weather indicators, local climate zones, and water balance).",
"homepage": "https://www.canuedata.ca/",
"name": "Canue Data Portal",
"prefix": "r3d100013963",
"synonyms": [
"Canadian Urban Environmental Health Research Consortium Data Portal"
]
},
"r3d100013965": {
"description": "The CSIRO National Collections and Marine Infrastructure (NCMI) Information and Data Centre has managed marine data for Australia's government research organisation for over 30 years. They have an enduring archive of marine and climate research data, and regularly publish data (including physical, chemical, bathymetric and biological data) collected on board RV Investigator as part of the Marine National Facility. Data from the MNF is freely and publicly available.",
"homepage": "https://marlin.csiro.au/",
"name": "Marlin Metadata Catalogue",
"prefix": "r3d100013965",
"synonyms": [
"CSIRO NCMI Information and Data Centre"
]
},
"r3d100013966": {
"description": "The INAH Media Library is the open access repository of the National Institute of Anthropology and History of Mexico. Its objective is to preserve and make accessible the digital representation of the historical and cultural heritage under its custody, as well as the scientific knowledge it generates through its education and research centres.",
"homepage": "https://mediateca.inah.gob.mx/islandora_74/",
"name": "Mediateca INAH",
"prefix": "r3d100013966",
"xrefs": {
"opendoar": "9666",
"roar": "13382"
}
},
"r3d100013967": {
"description": "TheCellVision.org is a freely available and web-accessible image visualization and data browsing tool that serves as a central repository for fluorescence microscopy images and associated quantitative data produced by high-content screening experiments. Currently, TheCellVision.org hosts images and associated analysis results from two published high- content screening (HCS) projects focused on the budding yeast Saccharomyces cerevisiae.\nTheCellVision.org allows users to access, visualize and explore fluorescence microscopy images, and to search, compare, and extract data related to subcellular compartment morphology, protein abundance, and localization. Each dataset can be queried independently or as part of a search across multiple datasets using the advanced search option. The website also hosts computational tools associated with the available datasets, which can be applied to other projects and cell systems, a feature we demonstrate using published images of mammalian cells. Providing access to HCS data through websites such as TheCellVision.org enables new discovery and independent re-analyses of imaging data.\"",
"homepage": "https://thecellvision.org",
"name": "The Cell Vision",
"prefix": "r3d100013967"
},
"r3d100013968": {
"description": "The CHILDdb platform provides access to data produced by the CHILD project, a longitudinal birth cohort study of children from pregnancy to 8 years of age, across four Canadian provinces. This study analyzes the participants' home environment including physical, chemical, viral, bacterial, nutritional and psychosocial exposures. This data is expected to further knowledge of the genetic and environmental determinants of atopic diseases including asthma, allergy, allergic rhinitis, and eczema. \nResearchers can create an account to view meta and aggregate data; access demographic data summaries based on selected variables; and submit a scientific Concept Proposal for approval to access individual-level study data.",
"homepage": "https://childstudy.ca/childdb/",
"name": "CHILDdb",
"prefix": "r3d100013968",
"synonyms": [
"CHILD Cohort Study",
"CHILD database"
]
},
"r3d100013969": {
"description": "The Canadian Longitudinal Study on Aging (CLSA) is a large, national, long-term study of more than 50,000 individuals who were between the ages of 45 and 85 when recruited. These participants will be followed until 2033 or death. The aim of the CLSA is to find ways to help us live long and live well, and understand why some people age in healthy fashion while others do not.",
"homepage": "https://www.clsa-elcv.ca/",
"name": "Canadian Longitudinal Study on Aging",
"prefix": "r3d100013969",
"synonyms": [
"CLSA",
"ELCV",
"Γtude longitudinale canadienne sur le vieillissement"
]
},
"r3d100013970": {
"description": "TheCellMap.org serves as a central repository for storing and analyzing quantitative genetic interaction data produced by genome-scale Synthetic Genetic Array (SGA) experiments with the budding yeast Saccharomyces cerevisiae. In particular, TheCellMap.org allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize subnetworks, using data-driven network layouts in an intuitive and interactive manner.",
"homepage": "https://thecellmap.org/",
"name": "The Cell Map",
"prefix": "r3d100013970",
"synonyms": [
"TheCellMap"
]
},
"r3d100013971": {
"description": "The Catalog of Inferred Sequence Binding Preferences (CIS-BP) is a library of transcription factor (TF) DNA binding motifs and specificities. The data are organized in a user friendly manner for ease of searching, browsing, and downloading. CIS-BP also includes built-in web tools for scanning DNA sequences for putative TF binding sites, predicting the DNA binding motif of a given TF, and identifying a TF that might recognize a given DNA motif.",
"homepage": "http://cisbp.ccbr.utoronto.ca/",
"name": "CIS-BP",
"prefix": "r3d100013971",
"synonyms": [
"Catalog of Inferred Sequence Binding Preferences"
],
"xrefs": {
"scr": "017236"
}
},
"r3d100013972": {
"description": "CAPE began as a collection of UK local governments' Climate Action Plans, and has expanded to include a number of useful datapoints around climate, carbon emissions and local government.\nThe Climate Action Plan Explorer collects UK Council Climate Action Plans in a single database, alongside some data on area emissions estimates within the scope of influence of councils. It allows anyone to quickly and easily find out if their council has a plan, and put those plans into context.",
"homepage": "https://data.climateemergency.uk/",
"name": "Climate Action Plan Explorer",
"prefix": "r3d100013972",
"synonyms": [
"CAPE"
]
},
"r3d100013973": {
"description": "The Data Access Support Hub (DASH) is a one-stop data access service portal for researchers requiring multi-regional data in Canada.\nDASH services are provided by a multi-centre coordination team from various provincial/territorial data centres and pan-Canadian organizations, including the Canadian Institute for Health Information (CIHI) and Statistics Canada.",
"homepage": "https://www.hdrn.ca/en/dash",
"name": "Data Access Support Hub",
"prefix": "r3d100013973",
"synonyms": [
"DASH"
]
},
"r3d100013975": {
"description": "ScholarWorks is a collection of services designed to capture and showcase all scholarly output by the Boise State University community.",
"homepage": "https://scholarworks.boisestate.edu/",
"name": "ScholarWorks Boise State University",
"prefix": "r3d100013975",
"xrefs": {
"opendoar": "1558"
}
},
"r3d100013977": {
"description": "citaREA is the institutional repository of the Centro de InvestigaciΓ³n y TecnologΓa Agroalimentaria de AragΓ³n (CITA), a public research organization under the Ministry of Industry and Innovation of the Government of Aragon.",
"homepage": "https://citarea.cita-aragon.es/citarea/",
"name": "citaREA",
"prefix": "r3d100013977",
"xrefs": {
"opendoar": "2165"
}
},
"r3d100013978": {
"description": "GeneMANI helps you predict the function of your favourite genes and gene sets. GeneMania, a real-time multiple association network integration algorithm for predicting gene function.",
"homepage": "https://genemania.org/",
"name": "GeneMANIA",
"prefix": "r3d100013978",
"xrefs": {
"nlx": "149159",
"scr": "005709"
}
},
"r3d100013979": {
"description": "The British Ocean Sediment Core Research Facility (BOSCORF) is based at the Southampton site of the National Oceanography Centre and is Britainβs national deep-sea core repository.\nBOSCORF is responsible for long-term storage and curation of sediment cores collected through UKRI-NERC research programmes. We promote secondary usage of sediment core samples and analytical data relating to the sample collection.",
"homepage": "https://boscorf.org/",
"name": "BOSCORF",
"prefix": "r3d100013979",
"synonyms": [
"British Ocean Sediment Core Research Facility"
]
},
"r3d100013980": {
"description": "'Redape' is a digital repository that aims to preserve and disseminate research data produced by the Brazilian Agricultural Research Corporation - Embrapa. It allows the organization, management and publication of data in accordance with the FAIR principles.",
"homepage": "https://www.redape.dados.embrapa.br/",
"name": "Redape",
"prefix": "r3d100013980",
"synonyms": [
"Embrapa Research Data Repository",
"RepositΓ³rio de Dados de Pesquisa da Embrapa"
]
},
"r3d100013981": {
"description": "The INFRA-ART Spectral Library is an open-access integrated spectral library of artist paint materials that was designed as a digital support tool for research specialists and other heritage-related professionals that work with non- or minimally invasive spectroscopic techniques.",
"homepage": "https://infraart.inoe.ro/",
"name": "INFRA-ART Spectral Library",
"prefix": "r3d100013981",
"synonyms": [
"INFRA-ART Spectral Database"
]
},
"r3d100013982": {
"description": "Institutional Open Access Repository for National University of Colombia. It manages, preserves and publishes on-line academic digital works produced by the universiy along its history, including books, teaching resources, thesis and dissertations, among others.",
"homepage": "https://repositorio.unal.edu.co/",
"name": "Repositorio Institucional Universidad Nacional de Colombia",
"prefix": "r3d100013982",
"synonyms": [
"Institutional Repository of National University of Colombia",
"Repositorio Institucional UNAL"
],
"xrefs": {
"opendoar": "1326"
}
},
"r3d100013983": {
"description": "The INGV Data Registry collects the metadata describing the Research Data that are the result of the scientific production of INGV and/or managed and/or published by INGV, regardless of whether these data are static or dynamic, and regardless of the procedures followed for their creation. The Data Registry is publicly accessible through INGVβs institutional Web portal https://data.ingv.it/, and use thereof aims at satisfying needs within INGV, but also the needs of outside users.",
"homepage": "https://data.ingv.it",
"name": "INGV Open Data Registry",
"prefix": "r3d100013983",
"synonyms": [
"Registro Dati INGV",
"Registro Dati Istituto Nazionale di Geofisica e Vulcanologia"
],
"xrefs": {
"doi": "10.13127/data-registry"
}
},
"r3d100013984": {
"description": "Discuss Data is an open repository for storing, sharing and discussing research data on Eastern Europe, the South Caucasus and Central Asia. The platform, launched in September 2020, is funded by the German Research Foundation (DFG) and operated by the Research Centre for East European Studies at the University of Bremen (FSO) and the GΓΆttingen State and University Library (SUB). Discuss Data goes beyond ordinary repositories and offers an interactive online platform for the discussion and quality assessment of research data. Our aim is to create a space for academic communication and for the community-specific publication, curation, annotation and discussion of research data.",
"homepage": "https://discuss-data.net",
"name": "Discuss Data",
"prefix": "r3d100013984"
},
"r3d100013986": {
"description": "DUnAs is the institutional research data repository of the University of Aveiro. This repository is intended to share, archive, preserve, cite, access, and explore research data produced in the university scientific research activities.",
"homepage": "https://dunas.ua.pt/",
"name": "DUnAs",
"prefix": "r3d100013986",
"synonyms": [
"Institutional research data repository of the University of Aveiro",
"Repositório de dados de investigação da Universidade de Aveiro"
]
},
"r3d100013987": {
"description": "An open data repository for scientists from the Geological Survey of Denmark and Greenland (GEUS) to share and preserve their research data.",
"homepage": "https://dataverse.geus.dk/",
"name": "GEUS Dataverse",
"prefix": "r3d100013987",
"synonyms": [
"Geological Survey of Denmark and Greenland Dataverse"
]
},
"r3d100013989": {
"description": "The INESC TEC data repository showcases datasets produced or used by INESC TEC researchers and their partners. The repository is organized in four groups (institutional clusters). Computer Science, Power and Energy, Network and Intelligent Systems and Power and Energy.",
"homepage": "https://rdm.inesctec.pt/",
"name": "INESC TEC Research Data Repository",
"prefix": "r3d100013989"
},
"r3d100013991": {
"description": "The International Human Epigenome Consortium (IHEC) makes available comprehensive sets of reference epigenomes relevant to health and disease. The IHEC Data Portal can be used to view, search and download the data already released by the different IHEC-associated projects.",
"homepage": "https://epigenomesportal.ca/ihec/",
"name": "IHEC Data Portal",
"prefix": "r3d100013991",
"synonyms": [
"International Human Epigenome Consortium Data Portal"
],
"xrefs": {
"fairsharing": "FAIRsharing.6f54c5",
"scr": "014625"
}
},
"r3d100013992": {
"description": "The ICES Data Repository consists of record-level, coded and linkable health data sets. It encompasses much of the publicly funded administrative health services records for the Ontario population eligible for universal health coverage since 1986 and is capable of integrating research-specific data, registries and surveys. Currently, the repository includes health service records for as many as 13 million people.\nFiles in the ICES Data Repository are described in the Data Dictionary. This includes ICES General Use Data, as well as ICES Controlled Use Data. Datasets obtained by ICES for specific project(s) (project-specific data) are not described in the Data Dictionary.\nThe ICES Data Dictionary is an essential resource for anyone doing research at ICES. The information in this Data Dictionary is almost entirely based on the metadata belonging to the datasets described.",
"homepage": "https://datadictionary.ices.on.ca/Applications/DataDictionary/Default.aspx",
"name": "ICES Data Repository",
"prefix": "r3d100013992",
"synonyms": [
"ICES Data Dictionary"
]
},
"r3d100013993": {
"description": "Policy-relevant observational studies for population health equity and responsible development.\nHigh-quality statistical information adult and children's health from the UN's Demographic and Health Surveys (DHS) program and UNICEF's Multiple Indicator Cluster Surveys (MICS). These datasets contain longitudinal information dating back to 1995 or 1999 for a series of social policies in up to 193 UN countries. DHS data variables include fertility, family planning and nutritional status for women aged 15-49 and young children, as well as demographic information on household structure, employment, education, wealth, and place of residence. MICS data includes information on nutritional status and child mortality, medical care during the antenatal and postnatal periods, and sibling maternal mortality, among others.",
"homepage": "https://www.prosperedproject.com/database-descriptions",
"name": "Prospered Project",
"prefix": "r3d100013993"
},
"r3d100013995": {
"description": "The Maelstrom Catalogue provides a user-friendly solution for data discovery. It contains comprehensive information about epidemiological research networks and studies, and the data they have collected. It also provides information about harmonized data generated by these research networks.",
"homepage": "https://www.maelstrom-research.org/page/catalogue",
"name": "Maelstrom Catalogue",
"prefix": "r3d100013995"
},
"r3d100013996": {
"description": "The BC Oil and Gas Commission (Commission) is an independent, single-window regulatory agency with responsibilities for overseeing oil and gas operations in British Columbia, including exploration, development, pipeline transportation and reclamation. Spatial and non-spatial data is collected from various sources to support oil and gas operations in the province and is used widely within the Commission. As part of its commitment to improving citizen access and involvement, enhancing transparency and understanding, the Commission is pleased to provide interactive public access to this data. Users are encouraged to explore the site and select and download the datasets that are of interest to them.",
"homepage": "https://data-bcogc.opendata.arcgis.com/",
"name": "BC Oil and Gas Commission Open Data Portal",
"prefix": "r3d100013996",
"synonyms": [
"BCOGC Open Data Portal"
]
},
"r3d100013997": {
"description": "It's a multidisciplinary repository that collect and diseminate research, academic, institutional and learning results from Universitat Jaume I. It also includes digitised documentary material on the province of CastellΓ³ and other information resources from different institutions, like Spain-European Union Digital Archive (SEDAS).",
"homepage": "http://repositori.uji.es/",
"name": "Repositori de la Universitat Jaume I",
"prefix": "r3d100013997",
"synonyms": [
"Repositori UJI"
],
"xrefs": {
"opendoar": "1500",
"roar": "1066"
}
},
"r3d100013998": {
"description": "The Ocean Observatories Initiative (OOI) is a science-driven ocean observing network that delivers real-time data from more than 800 instruments to address critical science questions regarding the worldβs ocean. OOI data are freely available online to anyone with an Internet connection.",
"homepage": "https://oceanobservatories.org/",
"name": "Ocean Observatories Initiative Data",
"prefix": "r3d100013998",
"synonyms": [
"OOI Data",
"Ocean Observatories Initiative Data Portal"
],
"xrefs": {
"fairsharing": "/FAIRsharing.909afd"
}
},
"r3d100014000": {
"description": "AusGeochem is an easy-to-use platform for uploading, visualising, analysing and discovering georeferenced sample information and data produced by various geoscience research institutions such as universities, geological survey agencies and museums. With respect to analytical research laboratories, AusGeochem provides a centralised repository allowing laboratories to upload, archive, disseminate and publish their datasets. The intuitive user interface (UI) allows users to access national publicly funded data quickly through the ability to view an area of interest, synthesise a variety of geochemical data in real-time, and extract the required data, gaining novel scientific insights through multi-method data collation. Lithodat Pty Ltd has integrated built-in data synthesis functions into the platform, such as cumulative age histograms, age vs elevation plots, and step-heating diagrams, allowing for rapid inter-study comparisons. Data can be extracted in multiple formats for re-use in a variety of software systems, allowing for the integration of regional datasets into machine learning and AI systems.",
"homepage": "https://ausgeochem.auscope.org.au./#/",
"name": "AusGeochem",
"prefix": "r3d100014000"
},
"r3d100014001": {
"description": "The data page makes the data that PCIC collects and produces publicly available with an open license. The page presently provides access to BC Station Data, High-Resolution Climatology, Downscaled Climate Scenarios and VIC Hydrologic Model Output and Extreme Indices calculated from CMIP5.",
"homepage": "https://www.pacificclimate.org/data",
"name": "Pacific Climate Impacts Consortium Data Portal",
"prefix": "r3d100014001",
"synonyms": [
"PCIC Data Portal"
]
},
"r3d100014002": {
"description": "Port Moody's Open Data Portal gives access to data, statistics, and information about your city government. By making data accessible, we aim to promote public collaboration, increase government transparency, and spark innovation. This information will be used to inform local decision-making and will help us better plan for the future. Our data portal contains a lot of information. You can search through past and current permit, licence, and business applications. Review demographic information about program registration, find information about the location of businesses within Port Moody and filter the business directory by the type of business or service.",
"homepage": "https://data.portmoody.ca/",
"name": "Port Moody's Open Data Portal",
"prefix": "r3d100014002"
},
"r3d100014003": {
"description": "We aim to provide a βone-stop shopβ for data. To this end, we provide information on Strait of Georgia data that can be found within this Data Centre, as well as in other existing databases and locations. Clicking on the different categories in our Marine Data BC open data portal will allow you information on 1) all the data that is within this SoG Data Centre, 2) links to custodians that can provide other data sets that cannot be directly downloaded from our Data Centre, as well as 3) links to other existing data search engines where data can be immediately downloaded.",
"homepage": "https://soggy2.zoology.ubc.ca/geonetwork/srv/eng/catalog.search#/home",
"name": "Marine Data BC",
"prefix": "r3d100014003",
"synonyms": [
"Strait of Georgia Data Centre Marine Data BC Open Data Portal"
]
},
"r3d100014004": {
"description": "Welcome to the District of North Vancouverβs Open Data portal. Here you have access to many free datasets which you can use in your printed products or online services β completely free of charge. Our datasets are updated automatically and refreshed each week. Every dataset comes with its own metadata providing valuable information on the origin, history, accuracy and completeness of the dataset.",
"homepage": "https://geoweb.dnv.org/data/",
"name": "District of North Vancouverβs Open Data portal",
"prefix": "r3d100014004",
"synonyms": [
"District of North Vancouverβs GEOweb"
]
},
"r3d100014005": {
"description": "A domain-specific repository for Archaeology and related data, primarily aimed at the Netherlands, but not exclusively.",
"homepage": "https://archaeology.datastations.nl/",
"name": "DANS: Data Station Archaeology",
"prefix": "r3d100014005",
"synonyms": [
"DANS Archaeology"
]
},
"r3d100014006": {
"description": "The City of Burnaby maintains a wide range of data. As part of our commitment to engagement, transparency and accountability, we want to share our data with you. Please explore this site and use Burnabyβs data to analyze information, build apps, combine open datasets using maps, develop new web and mobile applications, and to meet your specific data needs. Together, using open data, weβll make our great community even better!",
"homepage": "https://data.burnaby.ca/",
"name": "Burnaby's Open Data Portal",
"prefix": "r3d100014006"
},
"r3d100014007": {
"description": "The data download section intent is to increase the availability of Digital Data Sets produced by the Regional District of North Okanagan to outside users. The Digital Data download options will be provided as CSV, KML, Shapefile, GeoJSON.",
"homepage": "https://regional-district-of-north-okanagan-gis-open-data-site-rdnogis.hub.arcgis.com/",
"name": "Regional District of North Okanagan GIS Open Data Site",
"prefix": "r3d100014007",
"synonyms": [
"RDNO GIS Open Data Site"
]
},
"r3d100014008": {
"description": "Kadi4Mat instance for use at the Karlsruhe Institute of Technology (KIT) and for cooperations, including the Cluster of Competence for Solid-state Batteries (FestBatt), the Battery Competence Cluster Analytics/Quality Assurance (AQua), and more.\n Kadi4Mat is the Karlsruhe Data Infrastructure for Materials Science, an open source software for managing research data. It is being developed as part of several research projects at the Institute for Applied Materials - Microstructure Modelling and Simulation (IAM-MMS) of the Karlsruhe Institute of Technology (KIT).\nThe goal of this project is to combine the ability to manage and exchange data, the repository , with the possibility to analyze, visualize and transform said data, the electronic lab notebook (ELN). Kadi4Mat supports a close cooperation between experimenters, theorists and simulators, especially in materials science, to enable the acquisition of new knowledge and the development of novel materials. This is made possible by employing a modular and generic architecture, which allows to cover the specific needs of different scientists, each utilizing unique workflows. At the same time, this opens up the possibility of covering other research disciplines as well.",
"homepage": "https://kadi.iam.kit.edu/",
"name": "Kadi4Mat",
"prefix": "r3d100014008",
"synonyms": [
"Kadi4Mat instance KIT+",
"Karlsruhe Data Infrastructure for Materials Sciences"
]
},
"r3d100014009": {
"description": "This website constitutes a repository of tools and resources for researchers and teachers that are interested in second language speech acquisition and pronunciation teaching in diverse educational contexts.\nIf you are a RESEARCHER in the field of second language acquisition (SLA), here you will find a wide range of validated tools that may be useful for your individual differences, SLA or L2 speech studies.\nIf you are a passionate second language pronunciation TEACHER interested in communicative methods, here you will be able to download several carefully designed explicit instruction, communicative form-focused activities and pronunciation-based tasks that are ready to be used in your classroom",
"homepage": "http://sla-speech-tools.com/",
"name": "Tools for Second Language Speech Research and Teaching",
"prefix": "r3d100014009",
"synonyms": [
"SLA Speech Tools"
]
},
"r3d100014010": {
"description": "RADAR4Chem is a low-threshold and easy-to use service for sustainable publication and preservation of research data from all disciplines of chemistry. It offers free publication for any data type and format according to the FAIR principles, independent of the researcherΒ΄s institutional affiliation. Through persistent identifiers (DOI) and a guaranteed retention period of at least 25 years, the research data remain available, citable and findable long-term.\nCurrently, the offer is aimed exclusively at researchers in the field of chemistry at publicly funded research institutions and universities in Germany. No contract is required and no data publication fees are charged. The researchers are responsible for the upload, organisation, annotation and curation of research data as well as the peer-review process (as an optional step) and finally their publication.",
"homepage": "https://radar4chem.radar-service.eu/radar/en/home",
"name": "RADAR4Chem",
"prefix": "r3d100014010"
},
"r3d100014011": {
"description": "RADAR4Culture is a low-threshold and easy-to use service for sustainable publication and preservation of cultural heritage research data. It offers free publication for any data type and format according to the FAIR principles, independent of the researcherΒ΄s institutional affiliation. Through persistent identifiers (DOI) and a guaranteed retention period of at least 25 years, the research data remain available, citable and findable long-term. Currently, the offer is aimed exclusively at researchers at publicly funded research institutions and (art) universities as well as non-commercial academies, galleries, libraries, archives and museums in Germany. No contract is required and no data publication fees are charged. The researchers are responsible for the upload, organisation, annotation and curation of research data as well as the peer-review process (as an optional step) and finally their publication.",
"homepage": "https://radar4culture.radar-service.eu/radar/en/home",
"name": "RADAR4Culture",
"prefix": "r3d100014011"
},
"r3d100014012": {
"description": "Welcome to the City of White Rock GIS Hub! This is the place for exploring GIS maps, apps, and data. Our goal is to inform and inspire our community, and to promote the use of GIS to address important issues. We encourage our community to utilize the available technologies to combine, visualize and analyze spatial datasets using maps",
"homepage": "https://data.whiterockcity.ca/",
"name": "White Rock Open Data Portal",
"prefix": "r3d100014012",
"synonyms": [
"City of White Rock GIS Hub"
]
},
"r3d100014013": {
"description": "Coquitlamβs Open Data Portal is available to everyone without restrictions with the goal of empowering citizens, helping small businesses, supporting the development community and enhancing service delivery. Search for data or explore popular data categories to preview, analyze and download datasets. Using the available APIs, you can interact with data directly through your own maps, tables and charts. You can also download city-wide data packages, LiDAR, aerial photographs, terrain and 3D digital elevation models.",
"homepage": "https://data.coquitlam.ca/",
"name": "Coquitlam Open Data",
"prefix": "r3d100014013"
},
"r3d100014014": {
"description": "Anyone can use open data from the Maple Ridge Open Data Portal at no cost. Download raw data and share your insights with your community or build new applications that serve specific users",
"homepage": "https://opengov.mapleridge.ca/",
"name": "Maple Ridge Open Government Portal",
"prefix": "r3d100014014",
"synonyms": [
"Maple Ridge OGP",
"OGP"
]
},
"r3d100014015": {
"description": "Welcome to the City of Penticton's Open Data Hub. Browse by category, preview the data, analyze on the fly before downloading! The information available for download is subject to the terms and conditions of our Open Government Licence. Third parties who use this information and data to make decisions, produce applications, or produce public information accept any errors and omissions",
"homepage": "https://open.penticton.ca/",
"name": "Open Penticton",
"prefix": "r3d100014015",
"synonyms": [
"City of Penticton's Open Data Hub"
]
},
"r3d100014016": {
"description": "Data can help you identify problems, perform forecasting, monitor change, set priorities, manage and respond to events and understand trends. Our City of Abbotsford Data Hub is the platform for exploring and downloading data, discovering and building apps, and engaging others to solve important issues. You can analyze and combine datasets using maps, as well as develop new web and mobile applications. The city is committed to supporting community engagement, enhancing transparency and accountability to our residents by providing public access to our data. Let's work together to achieve our goals!",
"homepage": "https://opendata-abbotsford.hub.arcgis.com/",
"name": "City of Abbotsford's Open Data Hub",
"prefix": "r3d100014016"
},
"r3d100014017": {
"description": "LidarBC's Open LiDAR Data Portal is an initiative to provide open public access to LiDAR and associated datasets collected by the Province of British Columbia. LiDAR is a rich data type with very large file sizes. LidarBC has divided datasets covering large areas into smaller blocks to provide file sizes that will not overload browsers. This Portal uses a provincial map to allow users to identify datasets for their area of interest.",
"homepage": "https://governmentofbc.maps.arcgis.com/apps/MapSeries/index.html?appid=d06b37979b0c4709b7fcf2a1ed458e03",
"name": "LidarBC",
"prefix": "r3d100014017",
"synonyms": [
"Open LiDAR Data Portal",
"Open Light Detection And Ranging Data Portal"
]
},
"r3d100014018": {
"description": "Datasets from six key areas across Alberta is available for no cost. These include earth observation, remote sensing, geospatial data, environmental data, and social and economic datasets from private industry and government",
"homepage": "https://www.opendataareas.ca/",
"name": "Open Data Areas Alberta",
"prefix": "r3d100014018",
"synonyms": [
"ODAA"
]
},
"r3d100014019": {
"description": "Data Download section provides easy access to the ABMIβs data and innovative data products ranging from raw field data, to species habitat associations, to remote sensing and geospatial products, to animal camera trap data, and more.",
"homepage": "https://abmi.ca/home/data-analytics.html",
"name": "Alberta Biodiversity Monitoring Institute Data & Analytics Portal",
"prefix": "r3d100014019",
"synonyms": [
"ABMI Data & Analytics Portal"
]
},
"r3d100014020": {
"description": "WildTrax is an online platform for storing, managing, and sharing environmental sensor Data. WildTrax was created through a partnership between the University of Alberta, Dr. Erin Bayne and the Bioacoustic Unit, the Alberta Biodiversity Monitoring Institute (ABMI), and Environment and Climate Change Canada\n(ECCC)",
"homepage": "https://www.wildtrax.ca/home.html",
"name": "Wildtrax",
"prefix": "r3d100014020"
},
"r3d100014021": {
"description": "Open data for the Manitoba Government.",
"homepage": "https://geoportal.gov.mb.ca/",
"name": "Data MB",
"prefix": "r3d100014021",
"synonyms": [
"OpenMB"
]
},
"r3d100014022": {
"description": "The Manitoba Collaborative Data Portal (MBCDP) aspires to be a single place for Manitobans to find the data they need to support their work in communities. On the MBCDP, community and government organizations and agencies can easily find a wide range of neighborhood and local-level information. The information can be used to support programs and policies, engage the public, conduct further analyses, and better understand our province and the people in it.",
"homepage": "http://www.mbcdp.ca/",
"name": "Manitoba Collaborative Data Portal",
"prefix": "r3d100014022",
"synonyms": [
"MBCDP"
]
},
"r3d100014023": {
"description": "GeoNB is the Province of New Brunswickβs gateway to geographic information and related value-added applications.",
"homepage": "http://www.snb.ca/geonb1/e/dc/catalogue-E.asp",
"name": "GeoNB",
"prefix": "r3d100014023"
},
"r3d100014024": {
"description": "In the digital collections, you can take a look at the digitized prints from the holdings of the GWLB Hannover free of cost. In special collections, the GWLB unites rare, valuable and unique parts of holdings that are installed as an ensemble. Deposita, unpublished works, donations, acquisition of rare books etc. were and are an important source for the constant growth of the library. These treasures and specialties - beyond their academic value - also contribute substantially to the profile of the GWLB.",
"homepage": "https://digitale-sammlungen.gwlb.de/start",
"name": "Digitale Sammlungen der GWLB Hannover",
"prefix": "r3d100014024",
"synonyms": [
"Digital Collections GWLB Hanover",
"Digitale Sammlungen der Gottfried Wilhelm Leibniz Bibliothek"
]
},
"r3d100014025": {
"description": "The Geo Big Data Open Platform of the Korea Institute of Geological Resources is a data-based repository that allows anyone to easily access the latest geological resource information scattered in Korea. It was established for the purpose of quickly organizing and providing domestic and foreign geological resource research information pouring out of a super-gap society to utilize the solution of national social problems and create an open science research ecosystem in the geological resource field.",
"homepage": "https://data.kigam.re.kr/",
"name": "Geo Big Data Open Platform",
"prefix": "r3d100014025",
"synonyms": [
"μ§μ€λΉ
λ°μ΄ν° μ€ννλ«νΌ"
]
},
"r3d100014027": {
"description": "This is the City of Frederictonβs public platform for exploring and downloading open data, discovering and building apps, and engaging in solutions important to local issues. Our site is built on the Esriβ’ Open Data portal platform. The site in includes various data sets and over 20 apps.",
"homepage": "https://data-fredericton.opendata.arcgis.com/",
"name": "Fredericton Open Data",
"prefix": "r3d100014027",
"synonyms": [
"DonnΓ©es ouvertes de Fredericton"
]
},
"r3d100014028": {
"description": "This is the community's public platform for exploring and downloading open data and information documents, discovering and building apps, and engaging to solve important local issues. You can analyze and combine open datasets using maps, as well as develop new web and mobile applications.",
"homepage": "https://open.moncton.ca/",
"name": "Open Data Moncton",
"prefix": "r3d100014028",
"synonyms": [
"DonnΓ©es ouvertes Moncton"
]
},
"r3d100014029": {
"description": "Open GIS Data and Applications from the Government of Newfoundland and Labrador's Department of Fisheries, Forestry and Agriculture (FFA). Includes datasets on Agriculture, Forestry, Wildlife, Fisheries, Aquaculture, Crown Lands and Land Management.",
"homepage": "https://geohub-gnl.hub.arcgis.com/",
"name": "Newfoundland and Labrador Fisheries, Forestry and Agriculture GeoHub",
"prefix": "r3d100014029",
"synonyms": [
"FFA GeoHUB",
"Newfoundland and Labrador FFA GeoHub"
]
},
"r3d100014030": {
"description": "The NWT Centre for Geomatics is a GNWT-wide corporate service that provides custom maps, geospatial data creation, analysis and maintenance, data centralization, geospatial web applications, earth observation and software management.",
"homepage": "https://www.geomatics.gov.nt.ca/en/resources/field_resource_category/data-3",
"name": "NWT Centre for Geomatics",
"prefix": "r3d100014030",
"synonyms": [
"Centre de gΓ©omatique des TNO",
"NortwestTerritories Centre for Geomatics"
]
},
"r3d100014031": {
"description": "Northwest Territories Geological Survey (NTGS) Open Data presents a collection of geoscience information for the Northwest Territories. The information is grouped thematically and is ready for use in Excel, ArcMap or Google Earth",
"homepage": "https://ntgs-open-data-ntgs.hub.arcgis.com/",
"name": "Northwest Territories Geological Survey Open Data",
"prefix": "r3d100014031",
"synonyms": [
"NTGS Open Data"
]
},
"r3d100014032": {
"description": "The ASEP Data Repository is an institutional multidisciplinary on-line repository that stores scientific outputs - bibliographic records, full texts and datasets of the institutional authors from The Czech Academy of Sciences. The repository is hosted by Library of the Czech Academy of Sciences. Data that are stored in database are accessible in the on-line catalogue. Each dataset has its own description and metadata according to international standards.",
"homepage": "https://asep-portal.lib.cas.cz/basic-information/dataset-repository/",
"name": "ASEP Repository",
"prefix": "r3d100014032",
"synonyms": [
"Repository of Czech Academy of Sciences",
"RepozitΓ‘Ε ASEP"
]
},
"r3d100014033": {
"description": "The NWT Discovery Portal is the most comprehensive online source for environmental monitoring knowledge in the Northwest Territories. It is administered by the NWT Cumulative Impact Monitoring Program. The Portal is a search tool that allows users to access data, metadata and reports. It is also a share tool that allows users to contribute by uploading research and monitoring information.",
"homepage": "https://nwtdiscoveryportal.enr.gov.nt.ca/geoportal/catalog/main/home.page",
"name": "NWT Discovery Portal",
"prefix": "r3d100014033",
"synonyms": [
"Northwest Territories Discovery Portal"
]
},
"r3d100014034": {
"description": "The authoritative source for Ontario's geospatial data.",
"homepage": "https://geohub.lio.gov.on.ca/",
"name": "Ontario GeoHub",
"prefix": "r3d100014034"
},
"r3d100014035": {
"description": "The Northwest Territories (NWT) Species Infobase is a searchable catalogue of referenced information on NWT species. It includes the information on habitat, distribution, population numbers, trends and threats used to rank the general status of NWT species.",
"homepage": "https://www.enr.gov.nt.ca/species-search/",
"name": "NWT Species Infobase",
"prefix": "r3d100014035",
"synonyms": [
"Northwest Territories Species Infobase"
]
},
"r3d100014036": {
"description": "PHO's data inventory lists all PHO data sets and identifies whether a data set is currently open, in the process of being opened or exempt from being released.",
"homepage": "https://www.publichealthontario.ca/en/data-and-analysis/using-data/open-data",
"name": "Public Health Ontario Open Data",
"prefix": "r3d100014036",
"synonyms": [
"PHO",
"SantΓ© publique Ontario DonnΓ©es ouvertes"
]
},
"r3d100014037": {
"description": "Essex County Open Data is afree and open data sharing portal where anyone can access and use data relating to the County of Essex and its local municipalities of Amherstburg, Essex, Kingsville, Lakeshore, LaSalle, Leamington, Tecumseh.",
"homepage": "https://opendata.countyofessex.ca/",
"name": "Essex County Open Data",
"prefix": "r3d100014037"
},
"r3d100014038": {
"description": "Town is embracing the Open Data information movement and releasing data for free to the public.",
"homepage": "https://navigate-newmarket.hub.arcgis.com/pages/open-data",
"name": "Navigate Newmarket",
"prefix": "r3d100014038"
},
"r3d100014039": {
"description": "Open data allows the public to access the Region's data more easily and encourages innovation in the community.",
"homepage": "https://opendata.durham.ca/",
"name": "Open Data Region of Durham",
"prefix": "r3d100014039"
},
"r3d100014040": {
"description": "San Raffaele Open Research Data Repository (ORDR) is an institutional platform which allows to safely store, preserve and share research data. ORDR is endowed with the essential characteristics of trusted repositories, as it ensures: a) open or restricted access to contents, with persistent unique identifiers to enable referencing and citation; b) a comprehensive set of Metadata fields to enable discovery and reuse; c) provisions to safeguard integrity, authenticity and long-term preservation of deposited data.",
"homepage": "https://ordr.hsr.it/research-data/",
"name": "San Raffaele Open Research Data Repository",
"prefix": "r3d100014040",
"synonyms": [
"ORDR"
]
},
"r3d100014041": {
"description": "Harmonized, indexed, searchable large-scale human FG data collection with extensive metadata. Provides scalable, unified way to easily access massive functional genomics (FG) and annotation data collections curated from large-scale genomic studies. Direct integration (API) with custom / high-throughput genetic and genomic analysis workflows.",
"homepage": "https://lisanwanglab.org/FILER",
"name": "FILER: Functional genomics repository",
"prefix": "r3d100014041"
},
"r3d100014042": {
"description": "Users can explore, download open data, discover web maps and engaging communities\nto solve important local issues. This Open Data Hub contains data from various Ontario Conservation Authority sites.",
"homepage": "https://co-opendata-camaps.hub.arcgis.com/",
"name": "Conservation Ontario Open Data Hub",
"prefix": "r3d100014042"
},
"r3d100014043": {
"description": "This City of London open data platform serves to be a one stop shop for information for residents, students, non-profits and businesses throughout the city. Anyone can use open data from the City of London at no cost. Download raw data and share your insights with the rest of your community or build new applications that serve specific users.",
"homepage": "https://opendata.london.ca/",
"name": "City of London Open Data",
"prefix": "r3d100014043"
},
"r3d100014045": {
"description": "Our open data portal allows the public to access Pickering's data more easily and encourages collaboration and innovation in the community",
"homepage": "https://opendata.pickering.ca/",
"name": "City of Pickering Open Data Portal",
"prefix": "r3d100014045"
},
"r3d100014046": {
"description": "This is the County of Huron's public platform for exploring and downloading open data, discovering and building apps, and engaging to solve important local issues. You can analyze and combine Open Datasets using maps, as well as develop new web and mobile applications.",
"homepage": "https://data-huron.opendata.arcgis.com/",
"name": "Huron County Open Data",
"prefix": "r3d100014046"
},
"r3d100014047": {
"description": "The Region of Peel Data Portal provides a central place to access data about Peel Region. We have information on topics such as demographics, population, housing, economic activity, and the operations of the Region.",
"homepage": "https://data.peelregion.ca/",
"name": "Region of Peel Data Portal",
"prefix": "r3d100014047"
},
"r3d100014048": {
"description": "Search from over 100 variety of datasets such as census results, city public WiFi locations, licensed eateries and more",
"homepage": "https://data.mississauga.ca/",
"name": "City of Mississauga Open Data Catalogue",
"prefix": "r3d100014048"
},
"r3d100014049": {
"description": "The Open Data Portal provides a number of datasets in formats such as spreadsheets, pdf, KML, and shapefiles. You can search for individual datasets or browse datasets by category.",
"homepage": "https://data-ptbo.opendata.arcgis.com/",
"name": "City of Peterborough Open Data Portal",
"prefix": "r3d100014049"
},
"r3d100014050": {
"description": "The Alcohol and Gaming Commission of Ontarioβs Data Inventory lists all of the agencyβs data sets and identifies whether a data set is currently open, in the process of being opened or exempt from being released as open data due to legal, security, privacy, confidentiality or commercially-sensitive reasons.",
"homepage": "https://www.agco.ca/data-inventory",
"name": "Alcohol and Gaming Commission of Ontario Data Inventory",
"prefix": "r3d100014050",
"synonyms": [
"AGCO Data Inventory"
]
},
"r3d100014051": {
"description": "You can freely access and use local data that has been collected by the City anytime and anywhere at no cost to you",
"homepage": "https://opendata.thunderbay.ca/",
"name": "Thunder Bay Open Data Portal",
"prefix": "r3d100014051"
},
"r3d100014052": {
"description": "The national information site on seismicity in France provides real-time information on seismic events in or near France, based on recordings from the monitoring stations of the French seismological and geodesic network RΓ©sif, from research or monitoring project stations, from stations in the networks of bordering countries (Germany, United Kingdom, Belgium, Spain, Italy, Luxembourg, Switzerland) and from stations in the global networks.",
"homepage": "https://api.franceseisme.fr/en/search",
"name": "Bureau Central Sismologique Français - Réseau National de Surveillance Sismique",
"prefix": "r3d100014052",
"synonyms": [
"BCSF-RΓ©NaSS",
"Bureau Central Sismologique Français",
"French National Network of Seismic Survey"
]
},
"r3d100014053": {
"description": "The Swedish Infrastructure for Ecosystem Science (SITES) is a national infrastructure for terrestrial and limnological field research. SITES aims to promote high-quality research through long-term field measurements and field experiments, and by making data available. Quality-controlled monitoring data from SITES is freely available on the SITES Data Portal from all participating stations and thematic programs. New datasets are continuously being uploaded.",
"homepage": "https://data.fieldsites.se/portal/",
"name": "SITES Data Portal",
"prefix": "r3d100014053",
"synonyms": [
"Swedish Infrastructure for Ecosystem Science"
]
},
"r3d100014054": {
"description": "A free and open data-sharing portal providing access to the definitive source of geographic and other data relating to the City of Markham.",
"homepage": "https://data-markham.opendata.arcgis.com/",
"name": "Open Data Markham",
"prefix": "r3d100014054",
"synonyms": [
"Markham Open Data Portal"
]
},
"r3d100014055": {
"description": "Welcome to Conservation Halton's platform for exploring and downloading open data, discovering web maps, and engaging communities to solve important local issues",
"homepage": "https://conservationhalton-camaps.opendata.arcgis.com/",
"name": "Conservation Halton Open Data Hub",
"prefix": "r3d100014055",
"synonyms": [
"Conservation Halton's platform for open data"
]
},
"r3d100014060": {
"description": "This open data portal has been created to allow everyone access to a diverse range of information about the Ottawa River watershed. It is a platform designed to facilitate the exploration and discovery of the many reports and data available about the Ottawa River and its tributaries from a wide variety of sources.",
"homepage": "https://ottawa-riverkeeper-open-data-ork-so.hub.arcgis.com/",
"name": "Ottawa Riverkeeper Open Data",
"prefix": "r3d100014060",
"synonyms": [
"Garde-rivière des Outaouais Données ouvertes"
]
},
"r3d100014061": {
"description": "The Whitby GeoHub is a place to discover, explore, search and download apps, maps and location based data about the Town.",
"homepage": "https://geohub-whitby.hub.arcgis.com/",
"name": "Whitby GeoHub",
"prefix": "r3d100014061",
"synonyms": [
"Whitby Open Data"
]
},
"r3d100014062": {
"description": "Geospatial data portal from the Government of Saskatchewan",
"homepage": "https://geohub.saskatchewan.ca/",
"name": "Saskatchewan GeoHub",
"prefix": "r3d100014062"
},
"r3d100014063": {
"description": "The SKCDC collects information on wild species and relies on submissions of observations from across the province of Saskatchewan. This data is used to inform biodiversity conservation efforts.\nThe Saskatchewan Conservation Data Centre manages observation records for plants, animals, insects and special features of biodiversity.",
"homepage": "http://biodiversity.sk.ca/OnlineRep.htm",
"name": "Saskatchewan Conservation Data Centre",
"prefix": "r3d100014063",
"synonyms": [
"SKCDC"
]
},
"r3d100014064": {
"description": "Beta open data catalogue for the City of Saskatoon.",
"homepage": "http://opendata-saskatoon.cloudapp.net/",
"name": "City of Saskatoon Open Data Catalogue",
"prefix": "r3d100014064"
},
"r3d100014065": {
"description": "Technology has allowed Concordia to collect large amounts of data and information on a variety of topics, which the university feels should be accessible to all. Concordiaβs open data makes machine-readable data easy to access from a single point and free to reuse without copyright, patents or other restrictions.",
"homepage": "https://www.concordia.ca/web/open-data.html",
"name": "Concordia's Open Data",
"prefix": "r3d100014065"
},
"r3d100014066": {
"description": "The open data movement has become an important trend in the space of a few years. Governments, companies and communities integrate open data into their innovation efforts. This project aims to enable others to further utilize Hydro-Quebec data in order to actively contribute to the energy transition.",
"homepage": "https://www.hydroquebec.com/documents-data/open-data/",
"name": "Hydro-QuΓ©bec Open Data",
"prefix": "r3d100014066",
"synonyms": [
"DonnΓ©es ouvertes Hydro-QuΓ©bec"
]
},
"r3d100014067": {
"description": "Γlections QuΓ©bec's Open Data is available on this website is accessible to everyone, but is mostly used by media, IT developers and researchers. It is used, among other things, on websites, for applications and in studies.",
"homepage": "https://dgeq.org/en/",
"name": "Γlections QuΓ©bec's Open Data",
"prefix": "r3d100014067",
"synonyms": [
"DonnΓ©es ouvertes d'Γlections QuΓ©bec"
]
},
"r3d100014068": {
"description": "The Biobanque quΓ©bΓ©coise de la COVID-19 (BQC19) is a pan-provincial initiative that collects, stores and shares data and blood samples from COVID-19 patients, both severe and non-severe cases and control cases, in an effort to respond effectively to the public health challenges posed by the pandemic. BQC19 believes that better understanding the disease will help society in returning to social activities and in preparing for future pandemics. It sees access to high-quality samples and data as essential in fulfilling research and works to bring about national and international research collaborations.",
"homepage": "https://en.quebeccovidbiobank.ca/",
"name": "Biobanque quΓ©bΓ©coise de la COVID-19",
"prefix": "r3d100014068",
"synonyms": [
"BQC19"
]
},
"r3d100014069": {
"description": "An Open Science resource that promotes scientific research and discovery in neurological diseases and accelerates the development of new treatments. It includes a growing collection of biospecimens, longitudinal clinical and neuropsychiatric information, imaging and genetic data from patients with neurological disease as well as healthy controls.",
"homepage": "https://cbigr-open.loris.ca/",
"name": "The Neuro C-BIG Repository Data Portal (Beta)",
"prefix": "r3d100014069",
"synonyms": [
"C-BIG Repository Data Portal - Beta Version"
]
},
"r3d100014070": {
"description": "NORMAN SusDat is a \"living database\" compiling information provided by NORMAN network members and external contributors via the NORMAN Suspect List Exchange (NORMAN-SLE). NORMAN SusDat merges the many chemical lists on the SLE into a common format and includes all data suitable for screening purposes, along with selected identifiers and predicted values as a service for NORMAN members and beyond. SusDat is undergoing constant development and improvement to expand the coverage, together with contributors and cheminformatics experts. The original lists on the NORMAN-SLE should be consulted to verify chemical information if necessary.",
"homepage": "https://www.norman-network.com/nds/susdat/",
"name": "NORMAN Substance Database",
"prefix": "r3d100014070",
"synonyms": [
"NORMAN SusDat"
],
"xrefs": {
"fairsharing": "FAIRsharing.9ATgeT"
}
},
"r3d100014071": {
"description": "A community platform to Share Data, Publish Data with a DOI, and get Citations. Advancing Spinal Cord Injury research through sharing of data from basic and clinical research.",
"homepage": "https://odc-sci.org/",
"name": "Open Data Commons for Spinal Cord Injury",
"prefix": "r3d100014071",
"synonyms": [
"ODC-SCI"
],
"xrefs": {
"fairsharing": "FAIRsharing.M6Ruz3"
}
},
"r3d100014072": {
"description": "COViMS (COVID-19 Infections in MS & Related Diseases) is a joint effort of the National MS Society, Consortium of MS Centers and Multiple Sclerosis Society of Canada to capture information on outcomes of people with MS and other CNS demyelinating diseases (Neuromyelitis Optica, or MOG antibody disease) who have developed COVID-19.",
"homepage": "https://www.covims.org/current-data",
"name": "COViMS",
"prefix": "r3d100014072",
"synonyms": [
"COVID-19 Infections in MS & Related Diseases"
],
"xrefs": {
"fairsharing": "FAIRsharing.MtkkWk"
}
},
"r3d100014073": {
"description": "Welcome to the National Yang Ming Chiao Tung University Dataverse research data knowledge management website, where you can learn how to obtain, upload, cite and explore research data in the National Yang Ming Chiao Tung University Dataverse.",
"homepage": "https://dataverse.lib.nycu.edu.tw/",
"name": "NYCU Dataverse",
"prefix": "r3d100014073"
},
"r3d100014074": {
"description": "NCI Imaging Data Commons (IDC) is a cloud-based repository of publicly available cancer imaging data co-located with the analysis and exploration tools and resources. IDC is a node within the broader NCI Cancer Research Data Commons (CRDC) infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data.",
"homepage": "https://imaging.datacommons.cancer.gov/",
"name": "NCI Imaging Data Commons",
"prefix": "r3d100014074",
"synonyms": [
"NCI IDC",
"National Cancer Institute Imaging Data Commons"
],
"xrefs": {
"fairsharing.legacy": "4504",
"scr": "019127"
}
},
"r3d100014075": {
"description": "The BAW is a research institute for the Federal Ministry of Transport and acts as an advisor to the federal government for issues of waterway engineering. In this role the BAW consumes and produces large volumes of data and information. As part of the implementation of Open Data legislation and in support of Open Data and Open Access principles, the BAW provides access to scientific data together with their metadata.\nThe BAW-Datenrepository was developed as a point of access for hydraulic engineering experts, contractors and customers of the BAW as well as the general public. It is a source for quality-assured information and provides standardised, long-term access to waterway engineering data. The BAW-Datenrepository supports the targeted search for information and data and gives direct access to them.\nBy publishing its scientific data, the BAW promotes transparency in public discourse as well as accountability of public administration enabling the data to create value beyond the BAW.",
"homepage": "https://datenrepository.baw.de",
"name": "BAW-Datenrepository",
"prefix": "r3d100014075"
},
"r3d100014076": {
"description": "ClimateData.ca enables Canadians to access, visualize, and analyze climate data, and provides related information and tools to support adaptation planning and decision-making. Our collaborative approach to providing climate services to Canadians aims to foster the development of a network of national and regional climate services providers which will support the ongoing provision of specialized information tailored to specific industry sectors.",
"homepage": "https://climatedata.ca/",
"name": "ClimateData.ca",
"prefix": "r3d100014076",
"synonyms": [
"Climate Data Canada",
"DonnΓ©esClimatiques.ca"
]
},
"r3d100014078": {
"description": "The Open Science and Data Platform provides access to science, data, publications and information about development activities across the country that can be used to understand the cumulative effects of human activities to support better decisions in the future.",
"homepage": "https://osdp-psdo.canada.ca/dp/en",
"name": "Open Science and Data Platform",
"prefix": "r3d100014078",
"synonyms": [
"OSDP",
"PSDO",
"Plateforme de science et de donnΓ©es ouvertes"
]
},
"r3d100014079": {
"description": "Various data and information available from space-related missions and activities.",
"homepage": "https://donnees-data.asc-csa.gc.ca/dataset",
"name": "Open data and information Portal Canadian Space Agency",
"prefix": "r3d100014079",
"synonyms": [
"Portail de donnΓ©es et information ouvertes Agence spatiale canadienne"
]
},
"r3d100014080": {
"description": "Resources available on ECCCβs Data Catalogue are the same as those on the Open Governmental Portal, although they are meant for ECCC employees to access the information on their departmental platform.",
"homepage": "https://catalogue.ec.gc.ca/geonetwork/srv/eng/catalog.search#/home",
"name": "Environment and Climate Change Canada Data Catalogue",
"prefix": "r3d100014080",
"synonyms": [
"Catalogue de donnΓ©es d'Environnement et Changement climatique Canada",
"ECCC Catalogue de donnΓ©es",
"ECCC Data Catalogue"
]
},
"r3d100014081": {
"description": "The Environment Canada Data Catalogue provides a one-stop solution to describing, publishing and discovering EC's environmental and scientific data.",
"homepage": "https://data-donnees.ec.gc.ca/data/?lang=en",
"name": "Environment Canada Data Catalogue",
"prefix": "r3d100014081",
"synonyms": [
"Catalogue de donnees d'Environnement Canada"
]
},
"r3d100014082": {
"description": "BioChem is an archive of marine biological and chemical data maintained by Fisheries and Oceans Canada (DFO). It holds biological and chemical data that are: from department research initiatives and collected in areas of Canadian interest",
"homepage": "https://www.dfo-mpo.gc.ca/science/data-donnees/biochem/index-eng.html",
"name": "BioChem database",
"prefix": "r3d100014082",
"synonyms": [
"Base de donnΓ©es BioChem",
"Biological and chemical marine data",
"DonnΓ©es biologiques et chimiques marines"
]
},
"r3d100014083": {
"description": "The Canadian tide and water level data archive presently holds water level observations reported from over a thousand stations, with the earliest dating back to 1848. The number of observations spans on average 6 years per station, with 60 stations measuring water levels for over 50 years.",
"homepage": "https://www.isdm-gdsi.gc.ca/isdm-gdsi/twl-mne/index-eng.htm",
"name": "Canadian Tides and Water Levels Data Archive",
"prefix": "r3d100014083",
"synonyms": [
"Archives canadiennes des donnΓ©es sur les marΓ©es et niveaux dβeau"
]
},
"r3d100014084": {
"description": "The Forest Climate Change Data Catalogue is a collection of data sets that are relevant to the Canadian forest sector under a changing climate. Created by Canadian Forest Service scientists, these data sets include static maps, raw data, and interactive maps that cover all of Canada. Data themes include drought, fire, climate and tree distribution; multiple climate scenarios are projected to the year 2100. The data sets will be periodically updated as new information becomes available.",
"homepage": "https://cfs.nrcan.gc.ca/fc-data-catalogue",
"name": "Forest Change Data Catalogue",
"prefix": "r3d100014084",
"synonyms": [
"Catalogue de donnΓ©es de changements forestiers"
]
},
"r3d100014085": {
"description": "The Canadian Centre for Energy Information (CCEI) is a convenient one-stop virtual shop for independent and trusted information on energy in Canada. It houses resources on all things energy-related, including production, consumption, international trade and much more.",
"homepage": "https://energy-information.canada.ca/en",
"name": "Canadian Centre for Energy Information",
"prefix": "r3d100014085",
"synonyms": [
"CCEI",
"Centre canadien d'information sur l'Γ©nergie"
]
},
"r3d100014086": {
"description": "This website is the public interface to the \"Canadian Database of Geochemical Surveys\". The database has two long-term goals. Firstly, it aims to catalogue all of the regional geochemical surveys that have been carried out across Canada, beginning in the 1950s. Secondly, it aims to make the raw data from those surveys available in a standardised format. Over 1,500 surveys have been catalogued. Approximately 500 are considered to be of long-term strategic value for mineral exploration and environmental baseline studies. Work is progressing on standardising the data for these 500 surveys. To date over 250 datasets have been converted.",
"homepage": "https://geochem.nrcan.gc.ca/cdogs/content/main/home_en.htm",
"name": "Canadian Database of Geochemical Surveys",
"prefix": "r3d100014086",
"synonyms": [
"Banque de donnΓ©es de levΓ©s gΓ©ochimiques du Canada",
"CDoGS"
]
},
"r3d100014087": {
"description": "The Groundwater Information Network is developed to improve knowledge of groundwater systems, and enhance groundwater management, through increased access to groundwater information. GIN connects a variety of groundwater information from authoritative sources, such as water well databases, water monitoring data, aquifer and geology maps, and related publications. Provincial and territorial collaborators include British Columbia, Alberta, Saskatchewan, Manitoba, Ontario, QuΓ©bec, Nova Scotia, Yukon and Newfoundland and Labrador; international collaborators include the USGS and others.",
"homepage": "https://gin.gw-info.net/service/api_ngwds:gin2/en/gin.html",
"name": "Groundwater Information Network",
"prefix": "r3d100014087",
"synonyms": [
"GIN",
"RIES",
"RΓ©seau dβinformation sur les eaux souterraines"
]
},
"r3d100014088": {
"description": "The National 3D Data Repository is a safe and secure place to store, expose and publish any 3D model produced in the humanities and social sciences through publicly funded projects. Each 3D model is referenced by a DOI",
"homepage": "https://3d.humanities.science",
"name": "National 3D Data Repository",
"prefix": "r3d100014088",
"synonyms": [
"CND3D",
"Conservatoire National des DonnΓ©es 3D"
]
},
"r3d100014089": {
"description": "The Permafrost Information Network (PIN) is being developed to improve knowledge of permafrost conditions and contribute pertinent information to government, northern, and research stakeholders. PIN connects borehole stratigraphic, geotechnical, ground thermal, and surficial geology data from a variety of data sources. Currently, PIN includes geotechnical and ground thermal data from published Geological Survey of Canada databases. However, the goal is to collaborate with Territorial data holders to connect their collections through the PIN application.",
"homepage": "https://pin.geosciences.ca/en",
"name": "Permafrost Information Network",
"prefix": "r3d100014089",
"synonyms": [
"PIN",
"RIP",
"RΓ©seau d'information sur le pergΓ©lisol"
]
},
"r3d100014090": {
"description": "The Canadian Coast Guard is a special operating agency within Fisheries and Oceans Canada. The Canadian Coast Guard aids to navigation, environmental response, fees, icebreaking, communications, security, waterways management and search and rescue.",
"homepage": "https://e-navigation.canada.ca/gn/index-en",
"name": "Canadian Coast Guard Data Catalogue",
"prefix": "r3d100014090",
"synonyms": [
"CCG Data Catalogue",
"GCC Catalogue de donnΓ©es",
"Garde côtière canadienne : Catalogue de données",
"Portail e-Navigation",
"e-Navigation Portal"
]
},
"r3d100014091": {
"description": "The purpose of the Biobank is to accelerate future research projects and build health monitoring opportunities on a nationally-representative sample of Canadians. The Biobank receives samples from surveys like CHMS or CCAHS that collect dried blood spot, blood, urine, and saliva samples from consenting participants. These samples are stored in a secure location for future health studies. To obtain approval for the use of these samples, research projects undergo a thorough scientific, ethical, and security review process.",
"homepage": "https://www.statcan.gc.ca/en/microdata/biobank",
"name": "Statistics Canada Biobank",
"prefix": "r3d100014091",
"synonyms": [
"Biobanque de l'EnquΓͺte canadienne de mesures de santΓ©",
"Biobanque du Statistique Canada",
"Canadian Health Measures Survey Biobank"
]
},
"r3d100014092": {
"description": "OpenAQ is an open, real-time and historical air quality platform, aggregating government-measured and research-grade data, as well as low-cost sensor data. Its goal is to help the worldwide air quality community work with these data to fight air inequality - the unequal access to clean air.",
"homepage": "https://openaq.org/#/",
"name": "OpenAQ",
"prefix": "r3d100014092"
},
"r3d100014093": {
"description": "eMaapΓ΅u is a window to geological information in Estonia, proving direct search functionality to the data hosted in the geoscience data platform SARV, and links to external resources and applications.",
"homepage": "https://geoloogia.info/en",
"name": "eMaapΓ΅u",
"prefix": "r3d100014093"
},
"r3d100014095": {
"description": "Scholars Portal Dataverse is a secure and publicly searchable Canadian data repository, though researchers who deposit their data here can choose how openly available to make their data, from freely accessible to mediated access to inaccessible. Managed by the Ontario Council of University Libraries (OCUL), Dataverse has contributors and adopters from across Canada. Researchers can use Dataverse to search for secondary data, deposit their own data, store metadata, and visualize and explore data.",
"homepage": "https://dataverse.scholarsportal.info/dataverse/rru",
"name": "Royal Roads University Dataverse",
"prefix": "r3d100014095"
},
"r3d100014097": {
"description": "Loyalist Migrations is a partnership between the United Empire Loyalist Association of Canada (UELAC), Huron University Collegeβs Community History Centre, and Western Librariesβ Map and Data Centre.\nOur researchers use the genealogical records of the UELAC as well as other archival sources to reconstruct the migrations of thousands of exiles, refugees, economic migrants, settlers, and soldiers from all walks of life who fled the American Revolution. Not all migrants called themselves Loyalists and it is not the intention of this project to ascribe political motivations for their journeys. The migrations included a diverse array of settlers, Indigenous people, and African Americans who embarked on their journeys, willingly or forced, in search of safety and security in lands claimed by the British Empire.",
"homepage": "https://loyalistmigrations-westernu.opendata.arcgis.com/",
"name": "Loyalist Migrations",
"prefix": "r3d100014097",
"synonyms": [
"Loyalist Migrations Project"
]
},
"r3d100014099": {
"description": "Repository of the Faculty of Science is institutional repository that gathers, permanently stores and allows access to the results of scientific and intellectual property of the Faculty of Science, University of Zagreb. The objects that can be stored in the repository are research data, scientific articles, conference papers, theses, dissertations, books, teaching materials, images, video and audio files, and presentations. To improve searchability, all materials are described with predetermined set of metadata.",
"homepage": "https://repozitorij.pmf.unizg.hr/en",
"name": "Repository of the Faculty of Science",
"prefix": "r3d100014099",
"synonyms": [
"Repository of the Faculty of Science of the University of Zagreb"
]
},
"r3d100014100": {
"description": "The Bacterial and Viral Bioinformatics Resource Center (BV-BRC) is an information system designed to support research on bacterial and viral infectious diseases. BV-BRC combines two long-running BRCs: PATRIC, the bacterial system, and IRD/ViPR, the viral systems.",
"homepage": "https://www.bv-brc.org/",
"name": "Bacterial and Viral Bioinformatics Resource Center",
"prefix": "r3d100014100",
"synonyms": [
"BV-BRC"
]
},
"r3d100014101": {
"description": "Portal ZarzΔ
dzania WiedzΔ
UJ CM is a knowledge and research potential management platform of medical information.\nEasy data localization will be possible thanks to DOI and URL addresses given by administrators of the Knowledge Management Platform JU MC. The data will be stored in 2 copies for 10 years.",
"homepage": "https://portalwiedzy.cm-uj.krakow.pl/",
"name": "Portal ZarzΔ
dzania WiedzΔ
UJ CM",
"prefix": "r3d100014101",
"synonyms": [
"Knowledge Management Platform of Jagiellonian University Medical College",
"PZW UJ CM"
]
},
"r3d100014102": {
"description": "RADaR - Digital Repository of Archived Publications of the Institute for Biological Research βSiniΕ‘a StankoviΔβ is the institutional digital repository of the Institute for Biological Research βSiniΕ‘a StankoviΔβ β National Institute of Republic of Serbia, University of Belgrade.\nThe aim of the repository is to provide open access to publications and other research outputs resulting from the projects implemented by the Institute for Biological Research βSiniΕ‘a StankoviΔβ.\nThe repository uses a DSpace-based software platform developed and maintained by the Belgrade University Computer Centre (RCUB).",
"homepage": "https://radar.ibiss.bg.ac.rs/?locale-attribute=en",
"name": "RADaR - Digital Repository of Archived Publications of the Institute for Biological Research βSiniΕ‘a StankoviΔβ",
"prefix": "r3d100014102",
"synonyms": [
"Π ΠΠΠ°Π - Π Π΅ΠΏΠΎΠ·ΠΈΡΠΎΡΠΈΡΡΠΌ ΠΡΡ
ΠΈΠ²ΠΈΡΠ°Π½ΠΈΡ
ΠΠΈΠ³ΠΈΡΠ°Π»Π½ΠΈΡ
Π Π°Π΄ΠΎΠ²Π° ΠΠ½ΡΡΠΈΡΡΡΠ° Π·Π° Π±ΠΈΠΎΠ»ΠΎΡΠΊΠ° ΠΈΡΡΡΠ°ΠΆΠΈΠ²Π°ΡΠ° βΠ‘ΠΈΠ½ΠΈΡΠ° Π‘ΡΠ°Π½ΠΊΠΎΠ²ΠΈΡβ"
],
"xrefs": {
"opendoar": "4035",
"roar": "14159"
}
},
"r3d100014103": {
"description": "ResearchDataGov is a web portal for discovering and requesting access to restricted microdata from US federal statistical agencies.",
"homepage": "https://www.researchdatagov.org",
"name": "ResearchDataGov.org",
"prefix": "r3d100014103",
"synonyms": [
"Research Data Gov"
]
},
"r3d100014104": {
"description": "Mondragon Unibertsitateaβs open access repository provides you with full text access to the documents produced by University members, as result of the academic, research and institutional activity. Its purpose is to increase the visibility of UniversityΒ΄s scientific and teaching production, to spread its impact and to assure its preservation.\nYou can find PhD theses, Bachelor theses, didactic material, University publications, working papers, preprints, post-prints, articles, proceedings, institutional documentation, etc.",
"homepage": "https://ebiltegia.mondragon.edu",
"name": "eBiltegia",
"prefix": "r3d100014104",
"synonyms": [
"Digital repository of Mondragon Unibertsitatea"
],
"xrefs": {
"opendoar": "4435"
}
},
"r3d100014109": {
"description": "This repository supports the researchers of the EΓΆtvΓΆs LorΓ‘nd Research Network (elkh.org), and to some extent the Hungarian scientists in general.",
"homepage": "https://repo.researchdata.hu/",
"name": "ARP Research Data Repository",
"prefix": "r3d100014109",
"synonyms": [
"HUN-REN ARP",
"HUN-REN Data Repository Platform"
],
"xrefs": {
"fairsharing": "FAIRsharing.b7f3ff"
}
},
"r3d100014110": {
"description": "AURIN is a collaborative national network of leading researchers and data providers across the academic, government, and private sectors. We provide a one-stop online workbench with access to thousands of multidisciplinary datasets, from over 100 different data sources.",
"homepage": "https://aurin.org.au/",
"name": "Australian Urban Research Infrastructure Network",
"prefix": "r3d100014110",
"synonyms": [
"AURIN"
]
},
"r3d100014111": {
"description": "Phaidra (Permanent Hosting, Archiving and Indexing of Digital Resources and Assets) is the University of Applied Arts Vienna Systemβs platform for long-term archiving of digital collections.",
"homepage": "https://phaidra.bibliothek.uni-ak.ac.at/",
"name": "Angewandte Repository",
"prefix": "r3d100014111",
"synonyms": [
"Angewandte Repositorium"
]
},
"r3d100014112": {
"description": "A planetary-scale platform for Earth science data & analysis.\nGoogle Earth Engine combines a multi-petabyte catalog of satellite imagery and geospatial datasets with planetary-scale analysis capabilities. Scientists, researchers, and developers use Earth Engine to detect changes, map trends, and quantify differences on the Earth's surface.",
"homepage": "https://developers.google.com/earth-engine/datasets/catalog",
"name": "Earth Engine Data Catalog",
"prefix": "r3d100014112",
"synonyms": [
"Google Earth Engine"
]
},
"r3d100014113": {
"description": "DOOR is the open institutional repository of the University for Continuing Education Krems, formerly known as Danube University Krems. DOOR runs on the fedora Software and is a partner repository of Phaidra Vienna and other fedora users in Austria. We provide access to OA publications, scientific data and much more for interested users and support our scientists and co-workers in their publication processis.",
"homepage": "https://door.donau-uni.ac.at/",
"name": "DOOR",
"prefix": "r3d100014113",
"synonyms": [
"DOOR University for Continuing Education Krems",
"DOOR UniversitΓ€t fΓΌr Weiterbildung Krems",
"Danube University Open Online Repository"
]
},
"r3d100014114": {
"description": "The GRSF, the Global Record of Stocks and Fisheries, integrates data from three authoritative sources: FIRMS (Fisheries and Resources Monitoring System), RAM (RAM Legacy Stock Assessment Database) and FishSource (Program of the Sustainable Fisheries Partnership).\nThe GRSF content publicly disseminated through this catalogue is distributed as a beta version to test the logic to generate unique identifiers for stocks and fisheries. The access to and review of collated stock and fishery data is restricted to selected users. This beta release can contain errors and we welcome feedback on content and software performance, as well as the overall usability.\nBeta users are advised that information on this site is provided on an \"as is\" and \"as available\" basis. The accuracy, completeness or authenticity of the information on the GRSF catalogue is not guaranteed. It is reserved the right to alter, limit or discontinue any part of this service at its discretion. Under no circumstances shall the GRSF be liable for any loss, damage, liability or expense suffered that is claimed to result from the use of information posted on this site, including without limitation, any fault, error, omission, interruption or delay.\nThe GRSF is an active database, updates and additions will continue after the beta release. For further information, or for using the GRSF unique identifiers as a beta tester please contact FIRMS-Secretariat@fao.org.",
"homepage": "https://i-marine.d4science.org/web/grsf/data-catalogue",
"name": "Global Record of Stocks and Fisheries",
"prefix": "r3d100014114",
"synonyms": [
"GRSF"
]
},
"r3d100014115": {
"description": "This data repository contains the experimental data produced at the ISIS Neutron and Muon Source (https://www.isis.stfc.ac.uk/Pages/home.aspx/) in the UK Science and Technology Facilities Council (STFC, https://www.ukri.org/councils/stfc/). The repository contains the open data as well as the data under embargoed that can be accessed by the data producers.",
"homepage": "https://data.isis.stfc.ac.uk/datagateway",
"name": "ISIS DataGateway",
"prefix": "r3d100014115",
"synonyms": [
"ISIS Neutron and Muon Source Data Repository"
]
},
"r3d100014116": {
"description": "HI HOPES aims is to provide free home based support and information without bias to every family with an infant or toddler with hearing loss. Through an early intervention framework of care, support, information and partnership in a culturally sensitive, community based manner to allow we aim to empower the family in their home environment and help the baby with a hearing loss to reach her/his full potential.",
"homepage": "https://www.hihopes.co.za/",
"name": "HI HOPES",
"prefix": "r3d100014116"
},
"r3d100014118": {
"description": "The UK Hydrographic Office (UKHO) is a world-leading centre for hydrography, specialising in marine geospatial data to support safe, secure and thriving oceans.\nUK Hydrographic Office Bathymetry Data Archive Centre (UKHO DAC) is the UK national repository for bathymetry data.\nIt is provided by the UK Hydrographic Office (UKHO) as part of the wider Marine Environmental Data and Information\nNetwork (MEDIN) https://medin.org.uk/. The UKHO DAC holds bathymetry data assets from a wide range of sources β Government funded, commercial, environmental and defence.\nThe ADMIRALTY Marine Data Portal https://www.gov.uk/guidance/inspire-portal-and-medin-bathymetry-data-archive-centre provides access to marine data sets held by the UK Hydrographic Office within the UK Exclusive Economic Zone (EEZ).",
"homepage": "https://www.gov.uk/government/organisations/uk-hydrographic-office",
"name": "UK Hydrographic Office",
"prefix": "r3d100014118",
"synonyms": [
"UKHO"
]
},
"r3d100014119": {
"description": "Regionaal Archief Alkmaar (RAA) is a joint arrangement that operates within a large region in the province of\nNoord-Holland. The first purpose of this arrangement is to fulfill the function of a regional knowledge and information center through the acquisition and preservation of a broad collection of historical sources. The second purpose is to make these sources actively available. It does so according to the Dutch Public Records Act (Archiefwet 1995).\nAt the time of writing, the joint arrangement services include 9 municipalities, namely: Alkmaar, Bergen, Castricum, Den Helder, Heiloo, Hollands Kroon, Schagen, Dijk en Waard and Texel. The arrangement also includes other joint arrangements. These are the GGD Hollands Noorden and Veiligheidsregio Noord-Holland Noord. Also, the RAA keeps the archives of the water authority Hoogheemraadschap Hollands Noorderkwartier and its predecessors. This is being done on the basis of a service agreement.\nFinally many archives of families, persons of interest, companies and non-governmental organizations are being collected and managed. This is a secondary task of the RAA, but these archives are also being managed on the ground of the Dutch Public Records Act.",
"homepage": "https://www.regionaalarchiefalkmaar.nl/",
"name": "Regionaal Archief Alkmaar",
"prefix": "r3d100014119",
"synonyms": [
"Regional Archive Alkmaar"
]
},
"r3d100014120": {
"description": "Regionaal Archief Nijmegen (RAN) is part of the municipality of Nijmegen. RAN has been designated as the repository for the municipality of Nijmegen, neighboring municipalities (Berg en Dal, Beuningen, Druten, Heumen, Lingewaard, Wijchen, Mook and Middelaar, West Maas and Waal), a regional water authority (Waterschap Rivierenland) and a number of joint arrangements (cooperative ventures between different public authorities). According to the 1995 Public Records Act we have a legal duty to manage government archives, make them accessible and available to the public. We also manage archives of individuals and private organizations in Nijmegen and the region, audiovisual material and a library.",
"homepage": "https://regionaalarchiefnijmegen.nl/",
"name": "Regionaal Archief Nijmegen (Gemeente Nijmegen)",
"prefix": "r3d100014120",
"synonyms": [
"RAN"
]
},
"r3d100014121": {
"description": "Thai National Research Repository (TNRR) is a central database of science, research, and innovation of Thailand managed by the National Research Council of Thailand (NRCT) under the Ministry of Higher Education, Science, Research and Innovation (MHESI) Act B.E. 2562 (2019). The TNRR system serves and disseminates an extensive collection of information to the public as open access to research and innovation knowledge. The goal is to be the system that provides information services on Thailand's research findings. This information is collected from academic institutes and information-oriented government agencies in Thailand. In other words, the data in the TNRR system is accumulated from 3 national databases including 1. National Research Innovation and Information System (NRIIS), 2. Research agencies within Thailandβs research and innovation ecosystem that have agreed to share their data; including research projects, research results, bodies of knowledge, theses, as well as various inventions and innovations; and 3. Other related databases of agencies that have shared their data for audit purposes and to improve the operation of the central database, such as the Department of Provincial Administration, the Department of Intellectual Property, and the Department of Business Development, etc.\nThai National Research Repository (TNRR) also provides open data of research findings via API which can be accessed at https://tnrr.nriis.go.th/#/service/opendata and https://opendata.nrct.go.th/en/",
"homepage": "https://tnrr.nriis.go.th",
"name": "Thai National Research Repository",
"prefix": "r3d100014121",
"synonyms": [
"TNRR",
"Thai Research Archives",
"ΰΈ£ΰΈ°ΰΈΰΈΰΈΰΈ₯ΰΈ±ΰΈΰΈΰΉΰΈΰΈ‘ΰΈΉΰΈ₯ΰΈΰΈ²ΰΈΰΈ§ΰΈ΄ΰΈΰΈ±ΰΈ’ΰΉΰΈΰΈ’"
]
},
"r3d100014123": {
"description": "As a research data hub for social and economic history, Emporion enables the free and standards-compliant publication of time series, historical statistical and panel data, georeferenced vector data, text mining analyses and data papers. Emporion is also open to contributions from the fields of business and environmental history and the history of technology. Emporion's supporting institutions are the DFG Priority Programme 1859 'Experience and Expectations. Historical Foundations of Economic Behavior' and the Gesellschaft fΓΌr Sozial- und Wirtschaftsgeschichte in conjunction with the Staatsbibliothek zu Berlin β PreuΓischer Kulturbesitz.",
"homepage": "https://emporion.gswg.info/",
"name": "Emporion",
"prefix": "r3d100014123",
"synonyms": [
"Forschungsdaten-Hub fΓΌr die Sozial- & Wirtschaftsgeschichte",
"Research Data Hub for Social and Economic History"
]
},
"r3d100014124": {
"description": "ODC-TBI is a community platform to Share Data, Publish Data with a DOI, and get Citations. Advancing Traumatic Brain Injury research through sharing of data from basic and clinical research.",
"homepage": "https://odc-tbi.org/",
"name": "Open Data Commons for Traumatic Brain Injury",
"prefix": "r3d100014124",
"synonyms": [
"ODC-TBI"
],
"xrefs": {
"fairsharing.legacy": "3338",
"scr": "021736"
}
},
"r3d100014127": {
"description": "The Virtual Research Environment (VRE) is an open-source data management platform that enables medical researchers to store, process and share data in compliance with the European Union (EU) General Data Protection Regulation (GDPR). The VRE addresses the present lack of digital research data infrastructures fulfilling the need for (a) data protection for sensitive data, (b) capability to process complex data such as radiologic imaging, (c) flexibility for creating own processing workflows, (d) access to high performance computing. The platform promotes FAIR data principles and reduces barriers to biomedical research and innovation. The VRE offers a web portal with graphical and command-line interfaces, segregated data zones and organizational measures for lawful data onboarding, isolated computing environments where large teams can collaboratively process sensitive data privately, analytics workbench tools for processing, analyzing, and visualizing large datasets, automated ingestion of hospital data sources, project-specific data warehouses for structured storage and retrieval, graph databases to capture and query ontology-based metadata, provenance tracking, version control, and support for automated data extraction and indexing. The VRE is based on a modular and extendable state-of-the art cloud computing framework, a RESTful API, open developer meetings, hackathons, and comprehensive documentation for users, developers, and administrators. The VRE with its concerted technical and organizational measures can be adopted by other research communities and thus facilitates the development of a co-evolving interoperable platform ecosystem with an active research community.",
"homepage": "https://www.bihealth.org/en/translation/network/digital-medicine/bihcharite-virtual-research-environment",
"name": "BIH / CharitΓ© Virtual Research Environment",
"prefix": "r3d100014127",
"synonyms": [
"BIH / VRE",
"Berlin Institute of Health / CharitΓ© Virtual Research Environment"
]
},
"r3d100014129": {
"description": "With the support of TELOTA, the Library of the Berlin-Brandenburg Academy of Sciences and Humanities (BBAW) operates an institutional repository for the first and second publication of scholarly publications authored or edited by members or staff of the BBAW and its predecessor institutions. The edoc server makes the publications available to the worldwide scholarly community in open access and ensures their long-term archiving. The edoc server is thus part of the implementation of the Academy's Open Science mission statement. Since 11/2022 the edoc-server of the academy is as well accepting research data and is thus the institutional research data repository of the academy.",
"homepage": "https://edoc.bbaw.de/solrsearch",
"name": "edoc server der Berlin-Brandenburgischen Akademie der Wissenschaften",
"prefix": "r3d100014129",
"synonyms": [
"edoc-Server BBAW"
]
},
"r3d100014130": {
"description": "This Dataverse is the research data repository for the Polytechnique MontrΓ©al community.",
"homepage": "https://borealisdata.ca/dataverse/polymtl",
"name": "Dataverse de Polytechnique MontrΓ©al",
"prefix": "r3d100014130"
},
"r3d100014131": {
"description": "The public MorpheusML model repository collects, curates, documents and tests computational models for multi-scale and multicellular biological systems. Model must be encoded in the model description language MorpheusML. Subsections of the repository distinguish published models from contributed non-published and example models. New models are simulated in Morpheus or Artistoo independently from the authors and results are compared to published results. Successful reproduction is documented on the model's webpage. Models in this repository are included into the CI and test pipelines for each release of the model simulator Morpheus to check and guarantee reproducibility of results across future simulator updates. The modelβs webpage provides a History-link to all past model versions and edits that are automatically tracked via Git. Each model is registered with a unique and persistent ID of the format M..... The model description page (incl. the biological context and key results of that model), the modelβs XML file, the associated paper, and all further files (often simulation result videos) connected with that model can be retrieved via a persistent URL of the format https://identifiers.org/morpheus/M.....\n- for technical details on the citable ModelID please see https://registry.identifiers.org/registry/morpheus\n- for the model definition standard MorpheusML please see https://doi.org/10.25504/FAIRsharing.78b6a6\n- for the model simulator Morpheus please see https://morpheus.gitlab.io\n- for the model simulator Artistoo please see https://artistoo.net/converter.html",
"homepage": "https://morpheus.gitlab.io/model/",
"name": "MorpheusML model repository",
"prefix": "r3d100014131",
"synonyms": [
"Morpheus model repository"
],
"xrefs": {
"fairsharing": "FAIRsharing.b83dd9",
"miriam": "00000725"
}
},
"r3d100014132": {
"description": "VinaR is the digital repository of the VinΔa Institute of Nuclear Sciences, University of Belgrade. VinaR provides open access to the publications, as well as to other outputs of the research projects implemented in these institutions.\nThe software platform meets the current requirements that apply to the dissemination of scholarly publications and it is compatible with relevant international infrastructures.",
"homepage": "https://vinar.vin.bg.ac.rs/",
"name": "VinaR - Repository of the VinΔa Nuclear Institute",
"prefix": "r3d100014132",
"synonyms": [
"VinaR - Repozitorijum Instituta za nuklearne nauke βVinΔaβ",
"VinaR Repository"
]
},
"r3d100014135": {
"description": "The BHIC is an archive repository in 's-Hertogenbosch. It is the Regional Historical Centre (RHC) of the province of North Brabant and was created by a merger in 2005 of the former state archives and several regional archives in Northeast Brabant. It currently comprises nine municipalities, two water boards, the province of North Brabant and several joint arrangements (GRs). The BHIC has the legal task of managing (digital) archives in good, orderly and accessible condition for the above-mentioned decentralised authorities. In addition, the BHIC also manages private archives.",
"homepage": "https://www.bhic.nl",
"name": "Brabants Historisch Informatie Centrum",
"prefix": "r3d100014135",
"synonyms": [
"BHIC"
]
},
"r3d100014136": {
"description": "idUS is the digital archive that gives access to full text of the scientific production of the University of Seville and their datasets. Its objective is to gather, preserve and disseminate the documents and data resulting from the scientific activity of the University, making the documents visible, accessible, recoverable, usable and preservable for any user.",
"homepage": "https://idus.us.es/",
"name": "idUS",
"prefix": "r3d100014136",
"synonyms": [
"DepΓ³sito de InvestigaciΓ³n Universidad de Sevilla"
],
"xrefs": {
"roar": " 9631"
}
},
"r3d100014138": {
"description": "HHU ResearchData enables researchers of Heinrich Heine University DΓΌsseldorf to make their research data available to the scientific community.",
"homepage": "https://researchdata.hhu.de/",
"name": "HHU ResearchData",
"prefix": "r3d100014138",
"synonyms": [
"Heinrich-Heine-University DΓΌsseldorf ResearchData"
]
},
"r3d100014139": {
"description": "This repository is a data publication platform for members of the Faculty of Physics at the LMU Munich and is designed to hold very large datasets. The repository is a collaboration between the Faculty of Physics, the University Library of LMU, and the Leibniz Supercomputing Centre (LRZ). Data publications follow the FAIR principles, including the assignment of DOIs via DataCite.",
"homepage": "https://opendata.physik.lmu.de",
"name": "Open Data LMU - Physics",
"prefix": "r3d100014139"
},
"r3d100014140": {
"description": "NIE Data Repository is the institutional research data repository for National Institute of Education, Nanyang Technological University (NIE NTU), Singapore. The Repository is open to NIE researchers and staff to archive, publish and share their final research data related to publications.",
"homepage": "https://researchdata.nie.edu.sg/",
"name": "NIE Data Repository",
"prefix": "r3d100014140"
},
"r3d100014141": {
"description": "Open Data repository focused on dataset publication by INGV OE - Osservatorio Etneo. \nThe Catania-Osservatorio Etneo Section is a public scientific institution of the National Institute of Geophysics and Volcanology (INGV) which carries out research, monitoring and surveillance activities in the fields of geophysics and volcanology.",
"homepage": "https://oedatarep.ct.ingv.it",
"name": "OEDataRep",
"prefix": "r3d100014141",
"synonyms": [
"INGV - Osservatorio Etneo Open Data repository"
]
},
"r3d100014142": {
"description": "The Research Data Repository of FID move is a digital long-term repository for open data from the field of transport and mobility research. All datasets are provided with an open licence and are assigned a persistent DataCite DOI (Digital Object Identifier). Both data search and archiving are free. \nThe Specialised Information Service for Mobility and Transport Research (FID move) has been set up by the Saxon State and University Library Dresden (SLUB) and the German TIB β Leibniz Information Centre for Science and Technology as part of the DFG funding programme \"Specialised Information Services\".",
"homepage": "https://data.fid-move.de/en/",
"name": "FID move",
"prefix": "r3d100014142",
"synonyms": [
"Forschungsdaten-Repositorium des Fachinformationsdienstes MobilitΓ€ts- und Verkehrsforschung",
"Repository for Research Data from Mobility and Transport Research"
]
},
"r3d100014143": {
"description": "data.InDoRES is a repositery for research data in biodiversity, environment and societies.",
"homepage": "https://data.indores.fr/",
"name": "data.InDoRES",
"prefix": "r3d100014143",
"synonyms": [
"Inventaire des DonnΓ©es de la Recherche en Environnement et SociΓ©tΓ©s",
"Inventory of Data from Research in Environment and Societies"
]
},
"r3d100014148": {
"description": "A central source for NEI biomedical digital objects including data sets, software and analytical workflow, metadata, standards, publications and more.",
"homepage": "https://neidatacommons.nei.nih.gov/",
"name": "National Eye Institute Data Commons",
"prefix": "r3d100014148",
"synonyms": [
"NEI Data Commons"
]
},
"r3d100014150": {
"description": "The purpose of the Canadian Urban Data Repository (CUDR) is to provide a βhomeβ for urban datasets. While primarily focused on datasets created by academe, it will also contain datasets created by NGOs, governments, citizens, and industry. Datasets stored in the repository will be open-access and will not contain personally identifiable information.\nThe purpose of the Canadian Urban Data Catalogue (CUDC) is to enhance the awareness of urban datasets that exist across Canada by providing a catalogue of Canadian and Canadian-created urban datasets. It will catalogue datasets available in CUDR and external datasets available on other platforms and as web services. These external datasets may be open or closed. CUDC uses a rich metadata model that supports the documentation and search for datasets relevant to a userβs needs. Catalogue entry metadata may be exported and imported from/to CUDC.",
"homepage": "https://data.urbandatacentre.ca/",
"name": "Canadian Urban Data Repository",
"prefix": "r3d100014150",
"synonyms": [
"CUDR"
]
},
"r3d100014151": {
"description": "The Society of American Archivists (SAA) Dataverse is an SAA data service that was established to support the needs and interests of SAAβs members and the broader archives community. The SAA Dataverse supports the reuse of datasets for purposes of fostering knowledge, insights, and a deeper understanding of archival organizations, the status of archivists, and the impact of archives and archival work on the broader society. Deposited datasets should be βactionableβ in that they should support direct analysis and interpretation. The SAA Dataverse welcomes deposits of collections of quantitative or qualitative data and associated documentation. SAA membership is not required to deposit or use data in the SAA Dataverse.",
"homepage": "https://dataverse.unc.edu/dataverse/saa",
"name": "Society of American Archivists Dataverse",
"prefix": "r3d100014151"
},
"r3d100014155": {
"description": "An open database of parent reports on young children's vocabulary development, alongside a variety of visualization tools.",
"homepage": "http://wordbank.stanford.edu",
"name": "Wordbank",
"prefix": "r3d100014155"
},
"r3d100014156": {
"description": "The TecnolΓ³gico de Monterrey's Data Hub offers Open Data generated by our researchers and other initiatives. This initiative is sponsored by both the Living Lab & Data Hub of the Institute for the Future of Education (IFE and the Tecnologico de Monterrey's Research Office.\nThis repository is organized by Institutes and Schools.",
"homepage": "https://datahub.tec.mx",
"name": "TecnolΓ³gico de Monterrey Data Hub",
"prefix": "r3d100014156",
"synonyms": [
"TecnolΓ³gico de Monterrey"
]
},
"r3d100014160": {
"description": "A research data repository for the education and developmental sciences.",
"homepage": "https://www.ldbase.org",
"name": "LDbase",
"prefix": "r3d100014160",
"xrefs": {
"fairsharing": "FAIRsharing.9c5ec2"
}
},
"r3d100014161": {
"description": "RODBUK Cracow Open Research Data Repository is co-created by six Cracow universities: AGH University of Science and Technology, University of Physical Education in Krakow, Cracow University of Technology, Krakow University of Economics, Jagiellonian University in KrakΓ³w, Pedagogical University of Krakow. The purpose of RODBUK is to collect, develop, archive and make available in open access all types of research data created by researchers, PhD candidates and students in the course of scientific activity. RODBUK aims to implement the Open Science policy by creating a publicly available platform for depositing research datasets enabling: getting acquainted with the research conducted in Cracow's scientific centers, storage of various types of research data obtaining a permanent Digital Object Identifier (DOI) for each dataset, standardized data citation, choosing a data usage license agreement (Creative Commons or other. RODBUK allows to collect and share open research data from various disciplines and in all file formats. RODBUK applies the FAIR Principles, which means the data is findable, accessible, interoperable, reusable.",
"homepage": "https://rodbuk.pl",
"name": "RODBUK Cracow Open Research Data Repository",
"prefix": "r3d100014161",
"synonyms": [
"RODBUK",
"Repozytorium Otwartych Danych Badawczych Uczelni Krakowskich"
]
},
"r3d100014165": {
"description": "The mission of the GO Consortium is to develop a comprehensive, computational model of biological systems, ranging from the molecular to the organism level, across the multiplicity of species in the tree of life.\nThe Gene Ontology (GO) knowledgebase is the worldβs largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research.",
"homepage": "http://geneontology.org",
"name": "Gene Ontology",
"prefix": "r3d100014165",
"synonyms": [
"GO"
],
"xrefs": {
"fairsharing": "FAIRsharing.6xq0ee"
}
},
"r3d100014169": {
"description": "The HCDC data portal offers data from the research field Earth and Environment for download. You can find for example climate model results, biogeochemical measurements in water and sediment and sensor data from the extensive Hereon sensor network. Discover the data by using the free text search bar.",
"homepage": "https://hcdc.hereon.de/datasearch/",
"name": "HCDC datasearch",
"prefix": "r3d100014169",
"synonyms": [
"HCDC data portal"
]
},
"r3d100014172": {
"description": "The George Mason University Dataverse is available for George Mason faculty, staff, and students to publish, share, and preserve their research data of enduring value. It is a companion to the Mason Archival Repository Service (https://mars.gmu.edu).",
"homepage": "https://dataverse.orc.gmu.edu",
"name": "George Mason University Dataverse",
"prefix": "r3d100014172"
},
"r3d100014173": {
"description": "The team have established the CardiacAI Data Repository that brings large amounts of Australian healthcare data together in a secure environment with strict conditions for use of these data with an appropriate level of oversight of research activities.\nThe CardiacAI Data Repository collects de-identified EMR data about cardiovascular patients who are admitted to a group of urban and regional hospitals in NSW and links this with state-wide hospital and emergency deparment visit and mortality data and mobile-health remote monitoring data.",
"homepage": "https://cardiacai.com.au/data/",
"name": "CardiacAI Data Repository",
"prefix": "r3d100014173",
"synonyms": [
"Cardiac Analaytics and Innovation Data Repository"
]
},
"r3d100014174": {
"description": "GlobeData is a repository for archiving and publishing research data at the Leipzig Research Centre Global Dynamics (ReCentGlobe). It is furthermore open to researchers worldwide in the interdisciplinary fields of global and area studies and will engage in systematic data collection.",
"homepage": "https://globedata.uni-leipzig.de/",
"name": "GlobeData",
"prefix": "r3d100014174"
},
"r3d100014175": {
"description": "SISSA Open Data is the Sissa repository for the research data managment. It is an institutional repository that captures, stores, preserves, and redistributes the data of the SISSA scientific community in digital form. SISSA Open Data is managed by the SISSA Library as a service to the SISSA scientific community.",
"homepage": "https://opendata.sissa.it/",
"name": "SISSA Open Data",
"prefix": "r3d100014175",
"synonyms": [
"Scuola Internazionale Superiore di Studi Avanzati Open Data"
]
},
"r3d100014176": {
"description": "Research Data Repository is the institutional repository of the University of Bamberg to enable storing, sharing and publishing of research data.",
"homepage": "https://fd-repo.uni-bamberg.de",
"name": "Forschungsdatenrepositorium der Otto-Friedrich-UniversitΓ€t Bamberg",
"prefix": "r3d100014176",
"synonyms": [
"Research Data Repository of the University of Bamberg"
]
},
"r3d100014177": {
"description": "The National Nuclear Data Center (NNDC) collects, evaluates, and disseminates nuclear physics data for basic nuclear research and applied nuclear technologies. The NNDC is a worldwide resource for nuclear data. The information available to the users of NNDC services is the product of the combined efforts of the NNDC and cooperating data centers and other interested groups, both in the United States and worldwide.\nThe NNDC specializes in the following areas:\n- Nuclear structure and low-energy nuclear reactions\n- Nuclear databases and information technology\n- Nuclear data compilation and evaluation",
"homepage": "https://www.nndc.bnl.gov/databases/",
"name": "National Nuclear Data Center",
"prefix": "r3d100014177",
"synonyms": [
"NNDC"
]
},
"r3d100014178": {
"description": "opendata@uni-kiel is the open research data repository of Kiel University for FAIR data.",
"homepage": "https://opendata.uni-kiel.de/",
"name": "opendata@uni-kiel",
"prefix": "r3d100014178",
"synonyms": [
"Forschungsdatenrepositorium der CAU",
"Kiel University Research Data Repository"
]
},
"r3d100014179": {
"description": "The Upper Austrian Regional Library views itself as keeper of the Upper Austrian heritage and does so by digitizing the so called \"OBDERENNSIA\", reginally releveant (mainly historical) literature from the 16th to the 20th century as well as medieval manuscripts and autographs.",
"homepage": "https://digi.landesbibliothek.at/viewer/index/",
"name": "digital Upper Austrian Regional Library",
"prefix": "r3d100014179",
"synonyms": [
"Digitale Landesbibliothek OberΓΆsterreich"
]
},
"r3d100014184": {
"description": "The Biodiversity Information System of Ecuador, SiB-Ec, is a technological tool that will become the core of the national information exchange network that promotes and facilitates interoperability, standardisation and implementation of guidelines for the management of data and information on biodiversity, through the National Catalogue of Biological Objects (CNOB), so that this information is available with different levels of access, and is used for the benefit of conservation, sustainable use of biodiversity, decision making and generation of public policy. SiB-Ec also makes it possible to manage the information generated on the country's Natural Heritage and to coordinate the efforts of the actors involved in the generation, management, publication and use of national biodiversity data and information. SiB-Ec also makes it possible to manage the information generated on the country's Natural Heritage and to coordinate the efforts of the actors involved in the generation, management, publication and use of national biodiversity data and information. Within SIB-Ec there is an IPT (The Integrated Publishing Toolkit) which is connected to GBIF for the exchange of biodiversity data in this network.",
"homepage": "http://patrimonio.ambiente.gob.ec/iptmae",
"name": "Sistema de InformaciΓ³n de Biodiversidad de Ecuador SiB-Ec",
"prefix": "r3d100014184",
"synonyms": [
"GBIF Ecuador - MAATE"
],
"xrefs": {
"fairsharing.legacy": "4721"
}
},
"r3d100014185": {
"description": "The UMCG Research Data Catalogue is a manually filled catalogue for large data collections (i.e. Databanks and Biobanks) of the University medical center Groningen. Currently you can find more than 60 resources in this catalogue, however this catalogue is still in development. In the future we hope to share all re-usable research data of the UMCG in this catalogue.",
"homepage": "https://umcgresearchdatacatalogue.nl/UMCG/ssr-catalogue/",
"name": "UMCG Research Data Catalogue",
"prefix": "r3d100014185",
"synonyms": [
"University Medical Centre Groningen Data Catalogue"
]
},
"r3d100014186": {
"description": "TUL Open Research Data Repository (RDB.open) is a service addressed to the scientific and research community of the Lodz University of Technology. The main purpose of RDB.open is to collect, share and store the open research data, both during the research and after its completion, at least for the minimum period indicated by the funder or the scientists. The RDB.open is a place where research data can be openly shared, accessed and then reused by others.",
"homepage": "https://rdb.p.lodz.pl",
"name": "Open Research Data at TUL",
"prefix": "r3d100014186",
"synonyms": [
"Open Research Data Repository of the Lodz University of Technology",
"RDB.open",
"Repozytorium Otwartych Danych Badawczych Politechniki ΕΓ³dzkiej"
]
},
"r3d100014187": {
"description": "RIVMdata is a metadata catalog. This catalog is filled with the metadata of RIVM datasets. ISO 19115 and DCAT standards are used as the metadata standards. The catalog consists of an internal site, which is only accessible to RIVM employees, and an external site, in which the metadata is accessible to the general public.",
"homepage": "https://data.rivm.nl/meta/srv/eng/catalog.search#/home",
"name": "RIVMdata",
"prefix": "r3d100014187",
"synonyms": [
"Dutch National Institute for Public Health and the Environment Data Catalog",
"RIVM Data Catalogus",
"Rijksinstituut voor Volksgezondheid en Milieu Data Catalogus"
],
"xrefs": {
"fairsharing": "FAIRsharing.bd4fb1"
}
},
"r3d100014188": {
"description": "The repository of the Institute of Nuclear Physics Polish Academy of Sciences collects, stores and shares documents that are the result of research work of the Institute's employees and doctoral students. Its purpose is to disseminate the scientific achievements of employees and promote scientific research conducted at the Institute.",
"homepage": "https://rifj.ifj.edu.pl/",
"name": "Repozytorium IFJ PAN",
"prefix": "r3d100014188",
"synonyms": [
"The Repository of the Institute of Nuclear Physics Polish Academy of Sciences"
]
},
"r3d100014189": {
"description": "The purpose of the JKU Repository is to record and archive the academic and scientific output of all scholars at Jan Kochanowski University, as well as making the data available, thus ensuring unrestricted access to knowledge and maintaining the principle of transparency.",
"homepage": "https://repozytorium.ujk.edu.pl/",
"name": "Repository of the Jan Kochanowski University",
"prefix": "r3d100014189",
"synonyms": [
"Repozytorium Uniwersytetu Jana Kochanowskiego"
]
},
"r3d100014190": {
"description": "The institutional Repository of IMDEA Nanociencia is the digital archive that collects the scientific production of the institute, with the aim of preserving and disseminating research results in open access.",
"homepage": "https://repositorio.imdeananociencia.org/",
"name": "Institutional Repository of IMDEA Nanociencia",
"prefix": "r3d100014190",
"synonyms": [
"IMDEA Nanociencia",
"Repositorio Institucional del Instituto MadrileΓ±o de Estudios Avanzados en Nanociencia",
"Repositorio de IMDEA Nanociencia"
],
"xrefs": {
"opendoar": ":10070"
}
},
"r3d100014191": {
"description": "Repository of research data produced by the different departments and faculties of the Universidad del PacΓfico",
"homepage": "https://datasets.up.edu.pe/",
"name": "Repositorio de datos de investigaciΓ³n de la Universidad del PacΓfico",
"prefix": "r3d100014191",
"synonyms": [
"Repositorio de datos UP"
]
},
"r3d100014193": {
"description": "RepoMed is the institutional repository of the Hannover Medical School (MHH) and is operated by the MHH Library. It serves to publish research results and scientific publications by researchers at Hannover Medical School.",
"homepage": "https://mhh-publikationsserver.gbv.de/content/index.xml",
"name": "RepoMed",
"prefix": "r3d100014193",
"xrefs": {
"opendoar": "10430"
}
},
"r3d100014194": {
"description": "Tallinn University of Technology Data Repository (TalTechData) is a storage space for researchers to deposit data sets associated with their research.\nThe main goal of TalTechData is to gather all fields of research data and encouraging open science and FAIR principles (Findable, Accessible, Interoperable and Reusable).\nThrough preserving open research data TalTechData enriches academic quality and collaboration, supports innovative developments and supports overall use of scientific materials.",
"homepage": "https://data.taltech.ee/",
"name": "TalTech Data",
"prefix": "r3d100014194",
"synonyms": [
"TalTechData repository"
]
},
"r3d100014195": {
"description": "A domain-specific repository for Social Sciences and Humanities data, primarily aimed at the Netherlands, but not exclusively.",
"homepage": "https://ssh.datastations.nl/",
"name": "DANS Data Station Social Sciences and Humanities",
"prefix": "r3d100014195"
},
"r3d100014197": {
"description": "Yabelana is a data repository of the University of KwaZulu-Natal (UKZN) which was developed to preserve, manage and share UKZN-Researchers research data; which include figures, datasets, software/code, images, videos, posters presentations.",
"homepage": "https://yabelana.ukzn.ac.za/",
"name": "Yabelana",
"prefix": "r3d100014197",
"synonyms": [
"University of KwaZulu-Natal research repository"
]
},
"r3d100014199": {
"description": "SRUC is currently on a transformational journey as we move towards becoming a unique, market-led and mission diverse 21st Century rural university, driving the future needs of a dynamic, innovative and competitive rural sector in Scotland, and working with our collaborators and partners worldwide to solve the biggest global agrifood challenges. Our researchers already carry out strategic and applied research on global and local food security issues, and actively support the translation of research results into practice. Our research ethos is strongly collaborative, and we have a long history of industrial, NGO and academic partnerships locally and internationally. As well as having longstanding disciplinary strengths in several key areas, we actively promote interdisciplinary research, especially linking natural and social sciences. We have a particular interest in research that helps inform policy, with Scottish and UK Government rural affairs and environment departments and the EU as key research clients.",
"homepage": "https://sruc.figshare.com/",
"name": "Scotland's Rural College Research Data Repository",
"prefix": "r3d100014199",
"synonyms": [
"SRUC research data"
]
},
"r3d100014203": {
"description": "The CNRS Research Data institutional repository offers CNRS scientists and their collaborators a solution for sharing data when there is no thematic or institutional repository adapted to their research field. CNRS Research Data provides a space in which depositors can share and promote data (legally disseminable, completed, documented and reusable) produced or co-produced as part of research work supported by the CNRS.",
"homepage": "https://entrepot.recherche.data.gouv.fr/dataverse/cnrs",
"name": "CNRS Research Data",
"prefix": "r3d100014203"
},
"r3d100014208": {
"description": "RIUMA is the Institutional Repository of the University of Malaga whose objective is to facilitate and improve the visibility of the scientific and academic production of the University of Malaga, allowing open access to its contents and guaranteeing the preservation and conservation of this production. The collection includes articles, research data, scientific papers, teaching material, digitized old collection and other documents in different digital formats.",
"homepage": "https://riuma.uma.es",
"name": "RIUMA",
"prefix": "r3d100014208",
"synonyms": [
"Repositorio Institucional de la Universidad de MΓ‘laga"
],
"xrefs": {
"opendoar": "1785"
}
},
"r3d100014209": {
"description": "The GWAS Catalog is an open access repository of all human genome wide association studies. It is considered the βgo-toβ resource for genetic evidence of associations between common genetic variation and diseases or phenotypes, is accessed by scientists, clinicians and other users worldwide, and is integrated with numerous other resources. Association data and metadata are identified and extracted from the scientific literature by expert data curators. Submissions of full genome wide summary data can be made directly by authors, either before or after journal publication.",
"homepage": "https://www.ebi.ac.uk/gwas",
"name": "GWAS Catalog",
"prefix": "r3d100014209",
"synonyms": [
"NHGRI-EBI GWAS Catalog"
],
"xrefs": {
"nif": "0000-06666",
"scr": "012745"
}
},
"r3d100014211": {
"description": "nmrXiv is an open, FAIR and consensus-driven NMR spectroscopy data repository and analysis platform. We archive raw and processed NMR data, providing support for browsing, search, analysis, and dissemination of NMR data worldwide.",
"homepage": "https://nmrxiv.org/",
"name": "nmrXiv",
"prefix": "r3d100014211"
},
"r3d100014212": {
"description": "The Preclinical Image DAtaset Repository (PIDAR) is a public repository of metadata information of preclinical image datasets from any imaging modality associated to peer-review publications. The metadata information are organized in a proper schema to create a standard metadata model for preclinical imaging.",
"homepage": "https://pidar.hpc4ai.unito.it/",
"name": "Preclinical Image DAtaset Repository",
"prefix": "r3d100014212",
"synonyms": [
"PIDAR"
],
"xrefs": {
"fairsharing": "FAIRsharing.f64055"
}
},
"r3d100014214": {
"description": "The Research Data Repository is a technological infrastructure that allows the preservation and access to research data produced at Universidad AndrΓ©s Bello (Chile). The repository complies with international standards for the deposit and access of data, highlighting the FAIR principles. These principles guarantee that the data will be Findable, Accessible, Interoperable and Reusable.",
"homepage": "https://repositoriodedatos.unab.cl/",
"name": "Repositorio de Datos de InvestigaciΓ³n Universidad AndrΓ©s Bello",
"prefix": "r3d100014214",
"synonyms": [
"Repositorio de Datos UNAB"
]
},
"r3d100014216": {
"description": "e-space is Manchester Metropolitan Universityβs research repository. It provides a permanent record of the intellectual outputs of the University, and where possible, makes a full text of the publication freely available to download. e-space is managed by the Library Service.",
"homepage": "https://e-space.mmu.ac.uk/",
"name": "e-space",
"prefix": "r3d100014216"
},
"r3d100014218": {
"description": "Teesside University Research Data Repository links to the University's Research Portal and enables your datasets to be linked to your staff profile. It helps prevent data loss by storing it in a safe secure environment and enables your research data to be open access. https://researchdata.tees.ac.uk/about.",
"homepage": "https://researchdata.tees.ac.uk/research-data/",
"name": "Teesside University Research Data Repository",
"prefix": "r3d100014218",
"synonyms": [
"TU Research Data Repository"
]
},
"r3d100014219": {
"description": "Consortium data repository for institutions in Colombia.",
"homepage": "https://papyrus-datos.co/",
"name": "Papyrus",
"prefix": "r3d100014219"
},
"r3d100014220": {
"description": "The USACH research data repository provides a platform for researchers affiliated to the University to share, manage and preserve research data. So that they are accessible and detectable, both for the internal and external community, bringing the knowledge generated closer to the population.",
"homepage": "https://datos.usach.cl/",
"name": "Repositorio de Datos de InvestigaciΓ³n Universidad de Santiago de Chile",
"prefix": "r3d100014220",
"synonyms": [
"Repositorio de datos de investigaciΓ³n USACH",
"USACH Dataverse"
]
},
"r3d100014221": {
"description": "MathRepo is a repository of the Max Planck Institute for Mathematics in the Sciences in Leipzig, dedicated to mathematical research data. Research data are all digital objects that arise during the process of doing research or are a result thereof. In particular, the purpose of this repository is to collect scripts and code, to explain applications of mathematical software, to showcase additional examples to paper publications, and more generally to host supplementary material developed for research projects or discussed in workshops.",
"homepage": "https://mathrepo.mis.mpg.de",
"name": "MathRepo",
"prefix": "r3d100014221",
"synonyms": [
"Mathematical Research-Data Repository"
]
},
"r3d100014222": {
"description": "bonndata is the institutional, FAIR-aligned and curated, cross-disciplinary research data repository for the publication of research data for all researchers at the University of Bonn. The repository is fully embedded into the University IT and Data Center and curated by the Research Data Service Center (https://www.forschungsdaten.uni-bonn.de/en).\nThe software that bonndata is based on is the open source software Dataverse (https://dataverse.org)",
"homepage": "https://bonndata.uni-bonn.de/",
"name": "bonndata",
"prefix": "r3d100014222",
"xrefs": {
"fairsharing": "FAIRsharing.af119c",
"opendoar": "10835"
}
},
"r3d100014225": {
"description": "The ANID Repository (Chile) is a stable digital information service that disseminates, manages and preserves the scientific production obtained by the different instruments funded by the National Agency for Research and Development, ANID, facilitating its access and availability to the public, as all resources are in open access.",
"homepage": "https://repositorio.anid.cl/home",
"name": "Repositorio ANID",
"prefix": "r3d100014225",
"synonyms": [
"Repositorio Agencia Nacional de InvestigaciΓ³n y Desarrollo"
],
"xrefs": {
"opendoar": "2220"
}
},
"r3d100014226": {
"description": "A web-based Interface for searching and accessing a vast treasure trove of Australian geoscientific data, information, imagery, services and applications. Its main purpose is to provide access to datasets produced by Australia's geoscience research community.",
"homepage": "https://portal.auscope.org.au/",
"name": "AuScope Discovery Portal",
"prefix": "r3d100014226"
},
"r3d100014227": {
"description": "The purpose of this central repository is to gather all the research data created by Greek researchers and academics from Greek Universities, and make them available in the most open and secure way possible.\n HARDMIN has been developed with the open software CKAN and, along with HELIX, constitutes the national digital research infrastructure (eInfrastructure) software for cataloguing services and research data repository, part of the Open Access infrastructure of Heal-Link. The repository provides the capability to connect to already established repositories and extract data from existing collections.",
"homepage": "https://hardmin.heal-link.gr",
"name": "Hellenic Academic Research Data Repository",
"prefix": "r3d100014227"
},
"r3d100014228": {
"description": "The Leibniz Data Manager (LDM) is a scientific repository for research data from the fields of science and technology.\nThe service supports a better re-usability of research data for scientific projects. The LDM fosters the management and access to heterogeneous research data publications and assists researchers in the selection of relevant data sets for their respective disciplines.\nThe LDM currently offers the following functions for the visualization of research data:\nΒ· Supports data collections and publications with different formats.\nΒ· Different views on the same data set (2D and 3D support).\nΒ· Visualization of Auto CAD files.\nΒ· Jupyter Notes for demonstrating live code.\nΒ· RDF Description of data collections.",
"homepage": "https://service.tib.eu/ldmservice/",
"name": "Leibniz Data Manager",
"prefix": "r3d100014228",
"synonyms": [
"LDM-TIB"
]
},
"r3d100014229": {
"description": "UltraViolet is part of a suite of repositories at New York University that provide a home for research materials, operated as a partnership of the Division of Libraries and NYU IT's Research and Instruction Technology. UltraViolet provides faculty, students, and researchers within our university community with a place to deposit scholarly materials for open access and long-term preservation. UltraViolet also houses some NYU Libraries collections, including proprietary data collections.",
"homepage": "https://ultraviolet.library.nyu.edu/",
"name": "UltraViolet",
"prefix": "r3d100014229"
},
"r3d100014231": {
"description": "The South African Marine Information Management System (MIMS) is an Open Archival Information System (OAIS) repository that plays a multifaceted role in archiving, publishing, and preserving marine-related datasets. As an IODE-accredited Associate Data Unit (ADU), MIMS serves as a national node for the IODE of the IOC of UNESCO. It archives and publishes collections and subsets of marine-related datasets for the National Department of Forestry, Fisheries, and the Environment (DFFE) and its regional partners.\nAs an IOC member organization, DFFE is committed to supporting the long-term preservation and archival of marine and coastal data for South Africa and its regional partners, promoting open access to data, and encouraging scientific collaboration. Tasked with the long-term preservation of South Africa's marine and coastal data, MIMS functions as an institutional data repository. It provides primary access to all data collected by the DFFE Oceans and Coastal Research Directorate and acts as a trusted broker of scientific marine data for a wide range of South African institutions.\nMIMS hosts the IODE AFROBIS Node, an OBIS Node that coordinates and collates data management activities within the sub-Saharan African region. As part of the OBIS Steering Group, MIMS represents sub-Saharan Africa on issues around biological (biodiversity) data standards. It also facilitates data and metadata publishing for the region through the GBIF and OBIS networks. \nOperating on the Findable, Accessible, Interoperable, and Reusable (FAIR) data principles, MIMS aligns its practices to maximize ocean data exchange and use while respecting the conditions stipulated by the Data Provider. By integrating various functions and commitments, MIMS stands as a vital component in the marine and coastal data landscape, fostering collaboration, standardization, and accessibility in alignment with international standards and regional needs.",
"homepage": "https://data.ocean.gov.za/",
"name": "Marine Information Management System (MIMS)",
"prefix": "r3d100014231",
"synonyms": [
"MIMS",
"South Africa's oceans and coastal data archive"
]
},
"r3d100014234": {
"description": "IMAGINE is the institutional digital repository of the Institute of molecular genetics and genetic engineering. It provides open access to publications and other research outputs resulting from the projects implemented by this institution. The software platform of the repository is adapted to the modern standards applied in the dissemination of scientific publications and is compatible with international infrastructure in this field.",
"homepage": "https://imagine.imgge.bg.ac.rs/",
"name": "IMAGINE",
"prefix": "r3d100014234",
"synonyms": [
"IMAGINE - Repository of the Institute of molecular genetics and genetic engineering",
"IMAGINE - Repozitorijum Institut za molekularnu genetiku i genetiΔko inΕΎenjerstvo"
]
},
"r3d100014235": {
"description": "Repository \"Open Science Resource Atlas 2.0\" aims to increase the accessibility, improve the quality and extend the reusability of science resources. Repository focuses on the digital sharing of resources of great importance to the field of science and economy. These include publications, scripts, lectures, 3D models, audio and video recordings, photos, input and output files of various computer programs, databases collecting data from various fields, machines, systems, language corpora and many others. The target group, apart from academics, students and doctoral students, is everyone interested, including entrepreneurs and, what is important and unique - disabled, blind, visually impaired and deaf people.",
"homepage": "https://zasobynauki.pl/",
"name": "Open Science Resource Atlas 2.0 (AZON)",
"prefix": "r3d100014235",
"synonyms": [
"Atlas ZasobΓ³w Otwartej Nauki 2.0 (AZON)"
]
},
"r3d100014236": {
"description": "The University of Lodz Repository is an institutional repository whose purpose is to disseminate the scholarly output of its staff and promote research conducted at the UL. It is an archive of its own electronic documents β each deposited publication or collection of research data is given a permanent identifier (handle), enabling the document to be cited and indexed in scientific databases.\nThe University of Lodz Repository operates as an institutional repository based on Regulation No. 51 of the Rector of the University of Lodz of 31 March 2015.",
"homepage": "https://repozytorium.uni.lodz.pl/",
"name": "Repozytorium Uniwersytetu ΕΓ³dzkiego",
"prefix": "r3d100014236",
"synonyms": [
"RUΕ",
"Repozytorium UΕ",
"University of Lodz Repository"
],
"xrefs": {
"hdl": "11089"
}
},
"r3d100014238": {
"description": "The Aleia Repository is Ibict's official digital repository for archiving, publishing, disseminating, preserving and sharing digital research data produced by the Ibict scientific community, with the mission of promoting, supporting and facilitating the adoption of open access to research data, fostering new research and promoting Open Science. For the purposes of this document, the institutional scientific community is made up of its staff, visiting researchers, fellows and postgraduate program students.",
"homepage": "https://aleia.ibict.br/",
"name": "Aleia",
"prefix": "r3d100014238",
"synonyms": [
"RepositΓ³rio de Dados de Pesquisa do Instituto Brasileiro de Informação em CiΓͺncia e Tecnologia (Ibict)"
]
},
"r3d100014239": {
"description": "The data repository of the University of ConcepciΓ³n houses research data with open access characteristics.",
"homepage": "https://datav.udec.cl",
"name": "Repositorio de datos - UdeC",
"prefix": "r3d100014239",
"synonyms": [
"Repository of the University of ConcepciΓ³n"
]
},
"r3d100014240": {
"description": "WueData is the institutional research data repository of the University of WΓΌrzburg. This service offered by the IT Center and the University Library enables scientists to publish their digital research data in accordance with the FAIR principles.",
"homepage": "https://wuedata.uni-wuerzburg.de",
"name": "WueData",
"prefix": "r3d100014240",
"synonyms": [
"Forschungsdatenrepositorium der JMU",
"Forschungsdatenrepositorium der Julius-Maximilians-UniversitΓ€t WΓΌrzburg",
"Research Data Repository of the University of WΓΌrzburg"
]
},
"r3d100014241": {
"description": "Data Repository of the Universidad SimΓ³n BolΓvar",
"homepage": "https://unisimon.digitalcommonsdata.com/research-data/",
"name": "Research Data Universidad SimΓ³n BolΓvar",
"prefix": "r3d100014241",
"synonyms": [
"Research Data University Simon Bolivar"
]
},
"r3d100014244": {
"description": "Base of Knowledge WrocΕaw University of Environmental and Life Sciences / Research Data Repository is an institutional open research data repository, offering the possibility to deposit datasets (as well as publications) created by researchers, PhD candidates and students of WrocΕaw University of Environmental and Life Sciences. It is intended for scientific data from the disciplines related to the Universityβs profile. It is a platform where research data can be safely collected, stored and openly shared with others, obtaining a permanent Digital Object Identifier (DOI) for each dataset and choosing a data usage license. Research Data Repository applies the FAIR Principles (data is findable, accessible, interoperable and reusable).",
"homepage": "https://bazawiedzy.upwr.edu.pl",
"name": "Repozytorium Uniwersytetu Przyrodniczego we WrocΕawiu",
"prefix": "r3d100014244",
"synonyms": [
"Base of Knowledge",
"Repository of WrocΕaw University of Environmental and Life Sciences",
"Repozytorium UPWr"
]
},
"r3d100014247": {
"description": "Research Data and E-publishing repository of the Specialised Information Services Asiaβ (FID Asien), hosted by the East Asia Department of the Staatsbibliothek zu Berlin , was funded by the German Research Foundation (DFG)",
"homepage": "https://repository.crossasia.org/content/index.xml",
"name": "CrossAsia Open Access Repository",
"prefix": "r3d100014247"
},
"r3d100014249": {
"description": "The Energy Data Centre holds information relating to energy research, focused on the UK. It has a research data catalogue, information on publications resulting from the UK Energy Research Centre and the Energy Technologies Institute and energy research related grants.",
"homepage": "https://ukerc.rl.ac.uk/",
"name": "Energy Data Centre",
"prefix": "r3d100014249"
},
"r3d100014250": {
"description": "The Repository of University of Wroclaw is an institutional repository, which archives and makes available scientific as well as research and development materials, that were created by the employees, postgraduate students, and (in the selection) by the students of the University of Wroclaw or issued at the University of Wroclaw. These materials include, inter alia, dissertations, postdoctoral thesis, selected undergraduateβs and postgraduateβs thesis, research articles, conference papers, monographs or their chapters, didactic materials, posters, and also research data. Repository is organized by fields of knowledge, in accordance with the areas represented at the University in the frameworks of its organizational units, such as departments, institutes and other interfaculty units, and its structure is hierarchical, based on groups of subjects, covering a variety of collections.",
"homepage": "https://www.repozytorium.uni.wroc.pl",
"name": "Repository of University of Wroclaw",
"prefix": "r3d100014250",
"synonyms": [
"Repozytorium Uniwersytetu WrocΕawskiego"
],
"xrefs": {
"opendoar": "10140"
}
},
"r3d100014251": {
"description": "Arias Montano, Institutional Repository of the University of Huelva is a repository of digital documents, whose aim is to publicize the scientific and teaching production of the University community, and ensure the preservation of their productions in digital format, as well as those institutions with which the University of Huelva has established agreements for this purpose.\nIn order to collect the data management plans of the research projects carried out by the research groups and centers of the University of Huelva, the collection \"Research data: complementary information\" was created in Arias Montano, Institutional Repository of Investigations https://rabida.uhu.es/dspace/handle/10272/14868",
"homepage": "https://rabida.uhu.es/dspace/",
"name": "Arias Montano",
"prefix": "r3d100014251",
"synonyms": [
"DΓ©pΓ΄t Institutionnel de l'UniversitΓ© de Huelva",
"Institutional Repository of the University of Huelva",
"Repositorio Institucional de la Universidad de Huelva",
"RepositΓ³rio Institucional da Universidade de Huelva"
],
"xrefs": {
"opendoar": "1388"
}
},
"r3d100014252": {
"description": "The main objective of the project is to digitize the data collected by the Maritime Administration and make it available for reuse by digitizing analog resources, integrating and harmonizing data and building a digital repository, and disseminating information about the resources collected in the system. \nThe aim of the project is to make maritime administration data sets available on the Internet.",
"homepage": "https://sipam.gov.pl/",
"name": "SIPAM",
"prefix": "r3d100014252",
"synonyms": [
"Spatial Information System of the Maritime Administration",
"System Informacji Przestrzennej Administracji Morskiej"
]
},
"r3d100014253": {
"description": "The purpose of the Repository of the University of Life Sciences in Lublin is to disseminate the academic achievements of the University' employees and to promote research conducted at the University. The repository contains resources from various fields of life sciences. Only the community of the University is allowed to upload new records.",
"homepage": "https://repozytorium.up.lublin.pl/en",
"name": "Repository of the University of Life Sciences in Lublin",
"prefix": "r3d100014253",
"synonyms": [
"Repozytorium Uniwersytetu Przyrodniczego w Lublinie",
"University of Life Sciences in Lublin Repository"
]
},
"r3d100014254": {
"description": "Discover the data on entrepreneurship projects, innovation plans, digital transformation proposals, consumers, and financial markets. Also, explore research on business, management, and entrepreneurship research development at our Business school.",
"homepage": "https://opendata.cesa.edu.co/",
"name": "CESA | Repositorio de datos acadΓ©micos",
"prefix": "r3d100014254"
},
"r3d100014255": {
"description": "University of Warsaw Research Data Repository aims to collect, archive, preserve and make available all types of research data. Storing and making data available is possible for users affiliated with the University of Warsaw, Poland, or those involved in projects carried out in partnership with the University of Warsaw. Browsing and downloading publicly available research data is open to all interested.",
"homepage": "https://danebadawcze.uw.edu.pl/",
"name": "University of Warsaw Research Data Repository",
"prefix": "r3d100014255",
"synonyms": [
"Dane Badawcze UW. Repozytorium",
"Dane Badawcze Uniwersytetu Warszawskiego. Repozytorium"
]
},
"r3d100014256": {
"description": "figshare is the RDM system at the University. It is a cloud-based data repository that supports multiple file formats. Research data in the form of datasets, code, audio, images and more can be disseminated via the University's figshare. Citations can be traced for datasets (not just the final research output/article) and analytics will show who is looking at our research data around the world.\nfigshare enables researchers to store research data in a secure way. The system is user-friendly, with easy access, and shareable with colleagues and collaborators on research projects. Where appropriate it enables researchers to make research data openly accessible.",
"homepage": "https://ufs.figshare.com/",
"name": "UFS Figshare",
"prefix": "r3d100014256",
"synonyms": [
"University of the Free State Figshare"
]
},
"r3d100014257": {
"description": "Nightingale helps researchers safely access, use, and share health data, particularly high-dimensional data such as medical imaging and waveforms linked to ground truth outcomes.",
"homepage": "https://www.ngsci.org/",
"name": "Nightingale Open Science",
"prefix": "r3d100014257",
"synonyms": [
"NGSCI",
"Nightingale OS"
],
"xrefs": {
"scr": "024598"
}
},
"r3d100014262": {
"description": "The Central Neuroimaging Data Archive (CNDA) allows for sharing of complex imaging data to investigators around the world, through a simple web portal.\nThe CNDA is an imaging informatics platform that provides secure data management services for Washington University investigators, including source DICOM imaging data sharing to external investigators through a web portal, cnda.wustl.edu. The CNDAβs services include automated archiving of imaging studies from all of the Universityβs research scanners, automated quality control and image processing routines, and secure web-based access to acquired and post-processed data for data sharing, in compliance with NIH data sharing guidelines. The CNDA is currently accepting datasets only from Washington University affiliated investigators. Through this platform, the data is available for broad sharing with researchers both internal and external to Washington University.. The CNDA overlaps with data in oasis-brains.org https://www.re3data.org/repository/r3d100012182, but CNDA is a larger data set.",
"homepage": "https://cnda.wustl.edu",
"name": "Central Neuroimaging Data Archive",
"prefix": "r3d100014262",
"synonyms": [
"CNDA"
]
},
"r3d100014264": {
"description": "This collection is the institutional data repository reserved for the entire research community of the UniversitΓ© du QuΓ©bec Γ Rimouski (UQAR).",
"homepage": "https://borealisdata.ca/dataverse/uqar",
"name": "UniversitΓ© du QuΓ©bec Γ Rimouski - Borealis",
"prefix": "r3d100014264",
"synonyms": [
"UQAR - Dataverse"
]
},
"r3d100014267": {
"description": "The Forensic Linguistic Databank (FoLD) is a permanent, controlled access online repository for forensic linguistic data, including malicious communication data, investigative interview data, and forensic evidence validation data for both speech and text.\nWe broadly understand forensic linguistics as any academic research with a potential to improve the delivery of justice through the analysis of language. FoLD thus comprises a wide range of datasets with relevance to forensic linguistics and language and law, including commercial extortion letters, investigative interviews in police and other contexts, legal documents, forum posts from far-right online groups, and comment threads from political blogs.\nThe intention for the databank is to not only further academic research into forensic linguistics by developing new methods and approaches but also to directly contribute to impact in assisting the delivery of justice. Therefore, research projects using this data will validate methods for forensic analysis, further the effectiveness of interviewing techniques used by British police, and help tackle internet crime and abuse on behalf of law enforcement beneficiaries, such as the National Crime Agency.",
"homepage": "https://fold.aston.ac.uk/",
"name": "The Forensic Linguistic Databank",
"prefix": "r3d100014267",
"synonyms": [
"FoLD"
]
},
"r3d100014269": {
"description": "Institutional Repository of the University of Agriculture in Krakow (Poland). It includes the scientific achievements of the university's staff and students, including raw research data, as well as full texts of journals published by the University of Agriculture in Krakow.",
"homepage": "https://repo.ur.krakow.pl/",
"name": "Base of Scientific Achievements University of Agriculture in Krakow",
"prefix": "r3d100014269",
"synonyms": [
"Baza Dorobku Naukowego Uniwersytetu Rolniczego w Krakowie"
]
},
"r3d100014270": {
"description": "EaSy Data (for Earth System Data) is the French data repository for the environmental domain. It allows researchers in the Environmental and Earth sciences to publish their data and obtain a DOI. Submissions must comply with the scope defined by the communities. Data are moderated by community scientists before validation. Metadata are based on community standards (ISO 19115) and are exposed via standard API (CSW and OGC API)",
"homepage": "https://www.easydata.earth",
"name": "EaSy Data",
"prefix": "r3d100014270",
"synonyms": [
"Earth System Data Repository"
]
},
"r3d100014271": {
"description": "The Research Data Repository of the National University of La Plata is an online platform dedicated to the organization and dissemination of research data for the entire academic community of the UNLP. The objective of this platform is to gather and provide access to data generated from all areas of the UNLP to ensure its preservation, encourage reuse and maximize its impact.",
"homepage": "https://datos.unlp.edu.ar",
"name": "Repositorio de Datos de InvestigaciΓ³n de la Universidad Nacional de La Plata",
"prefix": "r3d100014271",
"synonyms": [
"Repositorio de Datos de InvestigaciΓ³n UNLP"
]
},
"r3d100014272": {
"description": "The NOAA Repository is a digital library of scientific literature and research produced by the National Oceanic and Atmospheric Administration. The repository contains NOAA publications, as defined in the NOAA Publications Policy, dating from NOAAβs formation in 1970 to present and NOAA-authored and -funded journal articles from 2015 forward.",
"homepage": "https://repository.library.noaa.gov/welcome",
"name": "NOAA Institutional Repository",
"prefix": "r3d100014272"
},
"r3d100014273": {
"description": "The Common Research Data Repository (Deposita Dados) is a database for archiving, publishing, disseminating, preserving and sharing digital research data and its mission is to promote, support and facilitate the adoption of open access to the datasets of Brazilian researchers linked to scientific institutions that do not yet have their own research data repositories and/or of Brazilian researchers who have executed their datasets through scientific collaboration in foreign teaching and research institutions.",
"homepage": "https://depositadados.ibict.br/",
"name": "Deposita Dados",
"prefix": "r3d100014273",
"synonyms": [
"RepositΓ³rio Comum de Dados de Pesquisa"
]
},
"r3d100014274": {
"description": "CLOSER Discovery is a research tool for locating the variables that best suit your research interests and testing their robustness.\nMetadata repository for Longitudinal Population Studies in the United Kingdom",
"homepage": "https://discovery.closer.ac.uk",
"name": "CLOSER Discovery",
"prefix": "r3d100014274",
"synonyms": [
"Cohort & Longitudinal Studies Enhancement Resources"
]
},
"r3d100014275": {
"description": "SSHADE is an interoperable Solid Spectroscopy database infrastructure (www.sshade.eu) providing spectral and photometric data obtained by various spectroscopic techniques over the whole electromagnetic spectrum from gamma to radio wavelengths, through X, UV, Vis, IR, and mm ranges. The measured samples include ices, minerals, rocks, organic and carbonaceous materials... and also liquids. They are either synthesized in the laboratory, natural terrestrial analogs collected or measured in the field, or extraterrestrial samples collected on Earth or on planetary bodies: (micro-)meteorites, IDPs, lunar soils... \nSSHADE contains a set of specialized databases from various research groups, mostly from Europe. It is developed under the H2020 European programs* \"Europlanet 2020 RI\" and now \"Europlanet 2024 RI\" with the help of OSUG, CNRS/INSU, IPAG, and CNES. It is hosted by the OSUG data center / UniversitΓ© Grenoble Alpes, France. It can also be searched through the Virtual European Solar and Planetary Access (VESPA) virtual observatory.",
"homepage": "https://www.sshade.eu/",
"name": "SSHADE",
"prefix": "r3d100014275",
"synonyms": [
"Solid Spectroscopy Hosting Architecture of Databases and Expertise"
]
},
"r3d100014276": {
"description": "The Penn Integrated Neurodegenerative Disease Database (INDD) contains data from individuals with Alzheimer's disease, Parkinson's disease, frontotemporal dementia, and amyotrophic lateral sclerosis, who have been followed in research studies at the University of Pennsylvania. The database has been periodically described in publications (https://pubmed.ncbi.nlm.nih.gov/23978324/), with updates on the website. Researchers can request biosamples as well as clinical and biomarker data. Scientists work collaboratively to analyze the Integrative Neurodegenerative Disease Database (INDD) from the Center for Neurodegenerative Disease Research (CNDR) that tracks ~11,000 patients who attended one of four neurodegenerative disease centers at Penn.",
"homepage": "https://www.med.upenn.edu/cndr/datasharing.html",
"name": "Integrated Neurodegenerative Disease Database",
"prefix": "r3d100014276",
"synonyms": [
"INDD"
]
},
"r3d100014277": {
"description": "IRIS is a free and public collection of instruments, materials, stimuli, data, and data coding and analysis tools used for research into languages, including first, second-, and beyond, and signed language learning, multilingualism, language education, language use, and language processing. Materials are freely accessible and searchable, easy to upload (for contributions) and download (for use).\n\nFor materials or data to be held on IRIS, it must have been used for an accepted peer-reviewed journal article, book chapter, conference proceeding or an approved PhD thesis. \n\nMaterials and data are given a DOI and reference at the point of submission. \n\nBy default, uploaders assigned a https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode.en",
"homepage": "https://iris-database.org/",
"name": "IRIS",
"prefix": "r3d100014277",
"synonyms": [
"Instruments and data for research in language studies"
],
"xrefs": {
"fairsharing": "FAIRsharing.e20b79"
}
},
"r3d100014280": {
"description": "An online data management workbench and computing service provider for biology and related disciplines.",
"homepage": "https://plutof.ut.ee",
"name": "PlutoF",
"prefix": "r3d100014280",
"xrefs": {
"fairsharing": "FAIRsharing.23ac74"
}
},
"r3d100014283": {
"description": "MIDRC aims to develop a high-quality repository for medical images related to COVID-19 and associated clinical data, and develop and foster medical image-based artificial intelligence (AI) for use in the detection, diagnosis, prognosis, and monitoring of COVID-19.",
"homepage": "https://data.midrc.org/",
"name": "Medical Imaging and Data Research Center",
"prefix": "r3d100014283",
"synonyms": [
"MIDRC"
],
"xrefs": {
"fairsharing": "FAIRsharing.33dccb"
}
},
"r3d100014286": {
"description": "The FRIS Research Portal offers a unique view of publicly funded research in Flanders. The portal is a source of inspiration for reporting, analysis and statistics.",
"homepage": "https://researchportal.be/nl",
"name": "FRIS",
"prefix": "r3d100014286",
"synonyms": [
"FRIS Onderzoeksportaal",
"FRIS Research Portal",
"Flanders Research Information Space",
"Onderzoeksinformatie Vlaanderen"
]
},
"r3d100014288": {
"description": "InTOR is the institutional digital repository of the Institute of Virology, Vaccines and Sera βTorlakβ. It provides open access to publications and other research outputs resulting from the projects implemented by the Institute of Virology, Vaccines and Sera βTorlakβ.\n\nThe software platform of the repository is adapted to the modern standards applied in the dissemination of scientific publications and is compatible with international infrastructure in this field.",
"homepage": "https://intor.torlakinstitut.com/",
"name": "InTOR - Electronic Repository of Research and Scientific Papers",
"prefix": "r3d100014288",
"synonyms": [
"InTOR - Repository of the Institute βTorlakβ",
"InTor - Elektronski repozitorijum istraΕΎivaΔkih i nauΔnih radova"
],
"xrefs": {
"opendoar": "10088",
"roar": "16964"
}
},
"r3d100014291": {
"description": "The Integrated Catalogue (InK) of Mediathek of the Basel Academy of Art and Design (Hochschule fΓΌr Gestaltung und Kunst Basel, HGK) hosts, collects, archives and makes available digital resources of HGK and its digital, special collections. It is available both to members of the Academy of Applied Sciences of Northwestern Switzerland (Fachhochschule Nordwestschweiz, FHNW) to which the HGK belongs and to the general public. In addition to data for internal university use (login area), there is a large amount of unrestricted, freely accessible content. \nThe thematic focus is on contemporary art and design, art and design research, and topics related to the HGK. The sources cover a wide range of media: in addition to thesis and PDFs based documents, there are cluster objects, which assign several images, videos, audio and/or text files to a defined data set. \nThe InK serves as an institutional repository for research data management and as a platform for hybrid publications.",
"homepage": "https://mediathek.hgk.fhnw.ch/amp/search",
"name": "Integrierter Katalog (InK) der Mediathek HGK Basel FHNW",
"prefix": "r3d100014291",
"synonyms": [
"Integrated Catalogue (InK) of Mediathek HGK Basel FHNW"
]
},
"r3d100014298": {
"description": "NCBI Datasets is a continually evolving platform designed to provide easy and intuitive access to NCBIβs sequence data and metadata. NCBI Datasets is part of theβ―NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analysesβ―for all eukaryotic organisms through an NCBI Toolkit and community collaboration.",
"homepage": "https://www.ncbi.nlm.nih.gov/datasets/",
"name": "NCBI Datasets",
"prefix": "r3d100014298"
},
"r3d100014299": {
"description": "UniversitΓ© CΓ΄te d'Azur has its own institutional space on the EntrepΓ΄t Recherche Data Gouv. \nThis is a multidisciplinary dissemination space.",
"homepage": "https://entrepot.recherche.data.gouv.fr/dataverse/univ-cotedazur/",
"name": "UniversitΓ© CΓ΄te d'Azur - espace institutionnel EntrepΓ΄t Recherche Data Gouv",
"prefix": "r3d100014299"
},
"r3d100014304": {
"description": "A domain-specific repository for the Life Sciences, covering the health, medical as well as the green life sciences. The repository services are primarily aimed at the Netherlands, but not exclusively.",
"homepage": "https://lifesciences.datastations.nl/",
"name": "DANS Data Station Life Sciences",
"prefix": "r3d100014304",
"xrefs": {
"opendoar": "10851"
}
},
"r3d100014306": {
"description": "From April 2020 to March 2023, the Covid-19 Immunity Task Force (CITF) supported 120 studies to generate knowledge about immunity to SARS-CoV-2. The subjects addressed by these studies include the extent of SARS-CoV-2 infection in Canada, the nature of immunity, vaccine effectiveness and safety, and the need for booster shots among different communities and priority populations in Canada. The CITF Databank was developed to further enhance the impact of CITF funded studies by allowing additional research using the data collected from CITF-supported studies. The CITF Databank centralizes and harmonizes individual-level data from CITF-funded studies that have met all ethical requirements to deposit data in the CITF Databank and have completed a data sharing agreement. The CITF Databank is an internationally unique resource for sharing epidemiological and laboratory data from studies about SARS-CoV-2 immunity in different populations. The types of research that are possible with data from the CITF Databank include observational epidemiological studies, mathematical modelling research, and comparative evaluation of surveillance and laboratory methods.",
"homepage": "https://portal.citf.mcgill.ca/",
"name": "Covid-19 Immunity Task Force Databank",
"prefix": "r3d100014306",
"synonyms": [
"Banque de DonnΓ©es du GTIC",
"CITF",
"CITF Data Portal",
"GTIC",
"Groupe de Travail sur l'ImmunitΓ© face Γ la COVID-19"
]
},
"r3d100014308": {
"description": "The Hive is the University of Utah's institutional data repository. All datasets are associated with a U of Utah current or past faculty member or student. They are also all freely available under creative commons licenses. The repository spans disciplines and has over 80 datasets at this time.",
"homepage": "https://hive.utah.edu",
"name": "The Hive",
"prefix": "r3d100014308",
"synonyms": [
"Research Data Repository of the University of Utah"
]
},
"r3d100014310": {
"description": "ARAMOB is a German project aiming at consolidating and mobilising data from systematic studies on the ecology of spiders in Germany through this online portal. The underlying data management is done with the modularized database system Diversity Workbench. This framework was enhanced as a virtual research environment for arachnology by including lists, thesaury and trans-modular functions and tools helpful for data management in studies of spider taxonomy and ecology. The ARAMOB database will serve as repository for ecological data on spiders from Germany, provided by the Arachnologische Gesellschaft (AraGes) in the sense of the German Federation for Biological Data (GFBio). Through the portal or direct use of the database with Diversity Workbench data will be available to members of the AraGes for ecological analyses of spider species and assemblages, e.g. occurence and distribution, phenology, habitat preferences, ecological preferences, indication of habitat quality, a.o.",
"homepage": "https://aramob.de/en/home/",
"name": "ARAMOB - Mobilizing Spider Data for Research",
"prefix": "r3d100014310",
"synonyms": [
"ARAMOB - Γkologische Daten fΓΌr die Forschung",
"Data Portal of the Arachnologische Gesellschaft",
"Datenportal der Arachnologischen Gesellschaft"
]
},
"r3d100014312": {
"description": "Lingnan Data Repository serves as an institutional research data repository for Lingnan University in Hong Kong. It provides a secure platform for the Lingnan research community to deposit, share, and publish their research datasets, and supports data reuse by the global research community.",
"homepage": "https://dataverse.ln.edu.hk/",
"name": "Lingnan Data Repository",
"prefix": "r3d100014312"
},
"r3d100014314": {
"description": "The AMUReD Institutional Research Data Repository of the Adam Mickiewicz University in Poznan (UAM) collects and provides access to digital versions of research data collected, processed or produced as part of the scientific research or developmental work of UAM employees.The AMUReD Repository is part of the AMU Research Portal, with University Library in Poznan as the operating unit. \nDepositing data is possible after logging into the AMU Research Portal, according to the attached instructions.\nThe AMUReD repository is open, and research data are made available in three models: open (Open Access), embargo (Embargo) and closed (Restricted Access).\nThe detailed rules of the AMUReD repository are defined in the Regulations.\nThe AMUReD repository complies with the FAIR Principles.\nEach dataset is given a unique DOI identifier.\nThe AMUReD repository complies with the FAIR Principles. \nEach dataset is given a unique DOI identifier. The prefix for DOIs is doi:10.60629.\nIt is possible to choose a Creative Commons license for shared datasets.",
"homepage": "https://researchportal.amu.edu.pl/globalResultList.seam?r=researchdata&tab=RESEARCHDATA&lang=pl",
"name": "AMU Research Portal",
"prefix": "r3d100014314",
"synonyms": [
"AMUReD Repozytorium danych badawczych Uniwersytetu im. Adama Mickiewicza w Poznaniu",
"AMUReD Research Data Repository of Adam Mickiewicz University"
]
},
"r3d100014317": {
"description": "The National High Energy Physics Science Data Center (NHEPSDC) is a repository for high-energy physics. In 2019, it was designated as a scientific data center at the national level by the Ministry of Science and Technology of China (MOST). NHEPSDC is constructed and operated by the Institute of High Energy Physics (IHEP) of the Chinese Academy of Sciences (CAS). NHEPSDC consists of a main data center in Beijing, a branch center in Guangdong-Hong Kong-Macao Greater Bay Area, and a branch center in Huairou District of Beijing. The mission of NHEPSDC is to provide the services of data collection, archiving, long-term preservation, access and sharing, software tools, and data analysis. The services of NHEPSDC are mainly for high-energy physics and related scientific research activities. The data collected can be roughly divided into the following two categories: one is the raw data from large scientific facilities, and the other is data generated from general scientific and technological projects (usually supported by government funding), hereafter referred to as generic data. More than 70 people work in NHEPSDC now, with 18 in high-energy physics, 17 in computer science, 15 in software engineering, 20 in data management and some other operation engineers. NHEPSDC is equipped with a hierarchical storage system, high-performance computing power, high bandwidth domestic and international network links, and a professional service support system. In the past three years, the average data increment is about 10 PB per year. By integrating data resources with the IT environment, a state-of-art data process platform is provided to users for scientific research, the volume of data accessed every year is more than 400 PB with more than 10 million visits.",
"homepage": "https://www.nhepsdc.cn/",
"name": "National High Energy Physics Science Data Center",
"prefix": "r3d100014317",
"synonyms": [
"NHEPSDC",
"ε½εΆι«θ½η©ηη§ε¦ζ°ζδΈεΏ"
]
},
"r3d100014318": {
"description": "With its 15 collections and four institutes, the Staatliche Museen zu Berlin (National Museums in Berlin) are a universal museum for preserving, researching, and transferring knowledge about art and cultural treasures from the entire history of humankind. The museum has grown over generations and its collections encompass the artistic fields of European and non-European art, archeology, and ethnology from almost all nations, cultures, and eras.",
"homepage": "https://sammlung.smb.museum/",
"name": "Collections-Online - Sammlungsportal der Staatlichen Museen zu Berlin",
"prefix": "r3d100014318",
"synonyms": [
"Sammlungen Online - Sammlungsportal der Staatlichen Museen zu Berlin"
]
},
"r3d100014320": {
"description": "media/rep/ is the disciplinary repository for German-language media studies. It offers free and open access to publications and research data in media studies and related disciplines.",
"homepage": "https://mediarep.org/home",
"name": "media/rep/",
"prefix": "r3d100014320",
"synonyms": [
"MEDIAREP"
],
"xrefs": {
"opendoar": "4272",
"roar": "14063",
"wikidata": "Q116847936"
}
},
"r3d100014321": {
"description": "The ColabFit Exchange is an online resource for the discovery, exploration and submission of datasets for data-driven interatomic potential (DDIP) development for materials science and chemistry applications. ColabFit's goal is to increase the Findability, Accessibility, Interoperability, and Reusability (FAIR) of DDIP data by providing convenient access to well-curated and standardized first-principles and experimental datasets. Content on the ColabFit Exchange is open source and freely available.",
"homepage": "https://materials.colabfit.org/",
"name": "ColabFit Exchange",
"prefix": "r3d100014321"
},
"r3d100014322": {
"description": "NCBI Virus is a community portal for viral sequence data from RefSeq, GenBank and other NCBI repositories. To find, retrieve and analyze data, choose one of the offered options.",
"homepage": "https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/",
"name": "NCBI Virus",
"prefix": "r3d100014322",
"xrefs": {
"fairsharing": "FAIRsharing.d38075"
}
},
"r3d100014324": {
"description": "This website was developed by Iranian National Center for Ocean Data (INCOD) to provide useful services in the field of oceanographic data and information management for marine researchers and organizations. The INCOD website is used as a discovery service. Its goal is to improve marine research by facilitating the exchange of oceanographic data and information between national marine organizations. This website provides a gateway and access point to INCOD products containing data, information, websites, tools, applications, atlases, data catalogues and user manuals to public users.",
"homepage": "http://incod.inio.ac.ir/",
"name": "INCOD",
"prefix": "r3d100014324",
"synonyms": [
"Iranian National Center for Ocean Data"
]
},
"r3d100014328": {
"description": "datastore is the cross-domain research data repository of the University MΓΌnster (Germany). In datastore, scientific members of the University MΓΌnster can publish their research data following the FAIR principles, including the assignment of a DOI for each dataset as a persistent identifier.",
"homepage": "https://datastore.uni-muenster.de",
"name": "datastore by UniversitΓ€t MΓΌnster",
"prefix": "r3d100014328"
},
"r3d100014333": {
"description": "The Unifesp Research Data Repository is a platform for storing, preserving and accessing research data for the institution's academic community.",
"homepage": "https://repositoriodedados.unifesp.br/",
"name": "RepositΓ³rio de Dados de Pesquisa Unifesp",
"prefix": "r3d100014333",
"synonyms": [
"Unifesp Data Repository"
]
},
"r3d100014335": {
"description": "Coscine is a web-based RDM platform for all kind of generic research data that was developed at RWTH Aachen University. It enables the storage, management and archiving for ten years of research and metadata generated in the context of research projects. The platform also promotes cooperation across organizational boundaries, as researchers can log in either via their organization via SSO or via ORCID. To enable meaningful metadata management for all research areas, Coscine allows flexible description with metadata based on established technologies (SHACL/RDF). The platform is designed to make warm/used/active data FAIR.",
"homepage": "https://www.coscine.de",
"name": "Coscine",
"prefix": "r3d100014335"
},
"r3d100014336": {
"description": "TechnoRep is the institutional digital repository of the University of Belgrade - Faculty of Technology and Metallurgy. It provides open access to publications and other research outputs resulting from the projects implemented by the Faculty of Technology and Metallurgy.\nThe software platform of the repository is adapted to the modern standards applied in the dissemination of scientific publications and is compatible with international infrastructure in this field.",
"homepage": "https://technorep.tmf.bg.ac.rs/",
"name": "TechnoRep - Electronic Repository of Research and Scientific Papers",
"prefix": "r3d100014336",
"synonyms": [
"TechnoRep - Faculty of Technology and Metallurgy Repository",
"TechnoRep - Repozitorijum TehnoloΕ‘ko-metalurΕ‘kog fakulteta"
],
"xrefs": {
"opendoar": "10093"
}
},
"r3d100014340": {
"description": "FreiData is the publication platform of the University of Fribourg for research data and other digital objects from research. FreiData can be used by all members and affiliates of the university with an account .",
"homepage": "https://freidata.uni-freiburg.de/",
"name": "FreiData",
"prefix": "r3d100014340"
},
"r3d100014344": {
"description": "IGS PAS Data Portal is an open data repository of Institute of Geological Sciences Polish Academy of Sciences. This portal is used to collect and share data, taking into account access to the data from external repositories.\nIGS PAS data are open and provided for free use for non-commercial purposes under applicable laws on data sharing public and publicly funded. In the case of using data by external entities, the data source must be cited following the guidelines (information on how to cite data is included in the Cite Dataset field).",
"homepage": "https://dataportal.ing.pan.pl/",
"name": "IGS PAS Data Portal",
"prefix": "r3d100014344",
"synonyms": [
"Institute of Geological Sciences Polish Academy of Sciences Data Portal"
]
},
"r3d100014345": {
"description": "DaYta Ya Rona is the research data repository of the North-West University to store, share, and explore research data, making it accessible, citable, and shareable",
"homepage": "https://dayta.nwu.ac.za/",
"name": "DaYta Ya Rona",
"prefix": "r3d100014345",
"synonyms": [
"DaYta Ya Rona Figshare"
]
},
"r3d100014346": {
"description": "GeoNetwork portal for the Observatoire des Sciences de l'Univers Nantes Atlantique (Osuna)",
"homepage": "https://ids.osuna.univ-nantes.fr/geonetwork/srv/fre/catalog.search#/home",
"name": "GΓ©Osuna",
"prefix": "r3d100014346"
},
"r3d100014351": {
"description": "The transfer unit for data and biomaterials at the interface between Community Medicine and Molecular Medicine at the Medical Faculty of the University Medicine Greifswald enables the use of data from the studies of the research association Community Medicine (FVCM), e.g. the \"Study of Health in Pomerania\" (SHIP), \"Study of Neonates in Pomerania\" (SNiP), or \"Greifswald Approach to Individualized Medicine\" (GANI_MED), coordinated with regard to application, provision and documentation.",
"homepage": "https://transfer.ship-med.uni-greifswald.de/FAIRequest/?lang=en",
"name": "FAIRequest - transfer unit for data and biomaterials",
"prefix": "r3d100014351"
},
"r3d100014353": {
"description": "GenBase is a genetic sequence database that accepts user submissions (mRNA, genomic DNAs, ncRNA, or small genomes such as organelles, viruses, plasmids, phages from any organism) and integrates data from INSDC.",
"homepage": "https://ngdc.cncb.ac.cn/genbase/?lang=en",
"name": "GenBase",
"prefix": "r3d100014353"
},
"r3d100014355": {
"description": "The Austrian NeuroCloud (ANC) is a FAIR-enabling platform for sustainable research data management in Cognitive Neuroscience. \nMost of the offered research data is restricted, the publicly available datasets can be seen under https://data.anc.plus.ac.at/explore\nThe ANC offers tools and services to archive, manage, and share neurocognitive data flexibly and according to community standards. Scientists have full control over what they share (e.g., full original datasets or data derivatives), how they share it (by choosing from a selection of licensing models), and with whom (e.g., by using the ANCβs adjustable User Agreement templates).\nThe ANC provides persistent DOIs for data releases and operates in accordance with European GDPR. Moreover, the ANC fully supports the mission of the EOSC and is committed to the EUβs open science policy, legal standards, and best open science practices. Accordingly, the ANC aspires to facilitate FAIR data operations along the entire data lifecycle, actively supporting the ongoing shift in research culture towards increased transparency, data reusability, and result reproducibility.",
"homepage": "https://anc.plus.ac.at",
"name": "Austrian NeuroCloud",
"prefix": "r3d100014355",
"synonyms": [
"ANC"
]
},
"r3d100014356": {
"description": "The Weizenbaum Library is the open access repository of the Weizenbaum Institute. It makes the open research results (publications and research data) of the Institute permanently accessible worldwide.",
"homepage": "https://www.weizenbaum-library.de",
"name": "Weizenbaum Library",
"prefix": "r3d100014356",
"xrefs": {
"opendoar": "10845"
}
},
"r3d100014357": {
"description": "ReSpecTh is a joint reaction kinetics, spectroscopy, and thermochemistry information system maintained by the MTA-ELTE Complex Chemical Systems Research Group, the Laboratory of Molecular Structure and Dynamics, and the Chemical Kinetics Laboratory research laboratories of the Institute of Chemistry, EΓΆtvΓΆs LorΓ‘nd University, Budapest, Hungary.\nReSpecTh has three branches, Re for reaction kinetics related data, Spec for specthroscopy related data and Th for thermodynamics related data.",
"homepage": "https://respecth.elte.hu/",
"name": "ReSpecTh",
"prefix": "r3d100014357"
},
"r3d100014358": {
"description": "The W1M3A observing system is one of the most important infrastructures of the National Research Council of Italy and it is part of the network of deep ocean European observatories, and the two ERICs EMSO and ICOS. The open sea laboratory is moored in the middle of the Ligurian Sea, inside the area known as the \"Cetaceans Sanctuary\" on the route between Genoa and Cape Corse, about 80 Km off the coast of Liguria where the water depth is about 1200 m. The observatory helps to monitor the conditions and the sea state of the Ligurian basin by continuously acquiring meteorological, physical, bio-geochemical and wave measurements. The collected data are transmitted in near real time to the station ashore to be used by national and international agencies and institutions.\nThe buoy can be also imagined as a \"miniature island\" able to offer a substrate for the development of a rich biological community. Many organisms settle and develop on the buoy, colonising its entire underwater surface.",
"homepage": "http://erddap.w1m3a.cnr.it/erddap/index.html",
"name": "ERDDAP of the W1M3A research facility",
"prefix": "r3d100014358"
},
"r3d100014359": {
"description": "The Goethe University Data Repository (GUDe) provides a platform for its members to electronically archive, share, and publish their research data. GUDe is jointly operated by the University Library and the University Data Center of the Goethe University. The metadata of all public content is freely available and indexed by search engines as well as scientific web services. GUDe follows the FAIR principles for long-term accessibility (minimum 10 years), allows for reliable citation via DOIs as well as cooperative access to non-public data and operates on DSpace-CRIS v7.\n\nIf you have any questions regarding the use of GUDe, please consult the user documentation.",
"homepage": "https://gude.uni-frankfurt.de/home",
"name": "Goethe University Data Repository - GUDe",
"prefix": "r3d100014359",
"synonyms": [
"Repositorium fΓΌr Forschungsdaten an der Goethe-UniversitΓ€t Frankfurt"
]
},
"r3d100014360": {
"description": "Data portal of the Royal Belgian Institute for Space Aeronomy.",
"homepage": "https://data.aeronomie.be/dataset/",
"name": "Repository of BIRA-IASB",
"prefix": "r3d100014360",
"synonyms": [
"Repository of the Royal Belgian Institute for Space Aeronomy"
]
},
"r3d100014363": {
"description": "The AuScope Data Repository preserves and offers continued access to data from Australiaβs geoscience community working on fundamental geoscience questions and grand challenges, including climate change, natural resources security and natural hazards.",
"homepage": "https://repository.data.auscope.org.au/",
"name": "AuScope Data Repository",
"prefix": "r3d100014363"
},
"r3d100014365": {
"description": "The Geodatenkatalog.de is the metadata information system of the Geodateninfrastruktur Deutschland (GDI-DE) and forms the data basis for Geoportal.de. With the help of this central component, metadata for geodata sets, geodata services, and other IT-supported geodata applications are collected and can be researched and retrieved via Geoportal.de.",
"homepage": "https://gdk.gdi-de.org/gdi-de/srv/eng/catalog.search#/home",
"name": "Geodatenkatalog",
"prefix": "r3d100014365",
"synonyms": [
"Geodatenkatalog.de"
]
},
"r3d100014366": {
"description": "The Repositorio de Datos de InvestigaciΓ³n del Consejo Nacional de Investigaciones CientΓficas y TΓ©cnicas is a plataform of open access centralized in the storage, preservation and difusion of research data, which facilitates the access and reutilization of the scientific information created and self-archived by organism's researchers, fellowships and support staff.",
"homepage": "https://datosdeinvestigacion.conicet.gov.ar/",
"name": "Repositorio de Datos de InvestigaciΓ³n CONICET",
"prefix": "r3d100014366",
"synonyms": [
"CONICET Digital Research Data Repository"
]
},
"r3d100014367": {
"description": "The objective of the Research Data Repository of the University of Rzeszow is to store and provide access to data collected or produced as material in the course of analysis in the course of scientific research by employees, doctoral students and students of the University of Rzeszow in accordance with the policy of Open Access, i.e. making publicly funded scientific publications and research results available in digital form on the Internet in order to enable their free use by researchers, students, businesses and society at large. The University of Rzeszow Repository operates as an institutional repository based on Regulation No. ZR/96/2023 of the Rector of the University of Rzeszow of 28 July 2023.",
"homepage": "https://rdb.ur.edu.pl",
"name": "Repozytorium Danych Badawczych Uniwersytetu Rzeszowskiego",
"prefix": "r3d100014367",
"synonyms": [
"RDB"
]
},
"r3d100014368": {
"description": "Welcome to the GALENOS Data Repository. The GALENOS Data Repository provides access to all the research data produced by the Global Alliance for Living Evidence on aNxiety, depressiOn and pSychosis (GALENOS). If you're interested in learning more about GALENOS, please visit the website at https://galenos.org.uk.",
"homepage": "https://galenos-data.aliveevidence.org/",
"name": "GALENOS Data Repository",
"prefix": "r3d100014368",
"synonyms": [
"Global Alliance for Living Evidence on aNxiety, depressiOn and pSychosis Data Repository"
]
},
"r3d100014369": {
"description": "The GeoSphere Austria Data Hub is a national data repository that provides high-quality data from the fields of weather, climate, environment, and geophysics from GeoSphere Austria and other Austrian research-performing organizations. The datasets are described with rich metadata and canΒ be accessedΒ via different data access services (API, bulk download, THREDDS data service). By offering high-qualityΒ dataΒ the GeoSphere Austria Data Hub aims to promote FAIR and open research and encourageΒ innovation by making data easily accessible across different disciplines.",
"homepage": "https://data.hub.geosphere.at/",
"name": "GeoSphere Austria Data Hub",
"prefix": "r3d100014369"
},
"r3d100014370": {
"description": "The Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) is a community-driven climate impact modeling initiative that aims to contribute to a quantitative and cross-sectoral synthesis of the various impacts of climate change, including associated uncertainties. It is designed as a continuous model intercomparison and improvement process for climate impact models and is supported by the international climate impact research community. ISIMIP is organized into simulation rounds, for which a simulation protocol specifies a set of common experiments. The protocol further describes a set of climate and direct human forcing data to be used as input data for all ISIMIP simulations. Based on this information, modelling groups from different sectors (e.g. agriculture, biomes, water) perform simulations using various climate impact models.\nAfter the simulations are performed, the data is collected by the ISIMIP data team, quality controlled and eventually published on the ISIMIP Repository. From there, it can be freely accessed for further research and analyses. The data is widely used within academia, but also by companies and civil society. ISIMIP was initiated by the Potsdam Institute for Climate Impact Research (PIK) and the International Institute for Applied Systems Analysis\n(IIASA).",
"homepage": "https://data.isimip.org",
"name": "ISIMIP Repository",
"prefix": "r3d100014370",
"synonyms": [
"Inter-Sectoral Impact Model Intercomparison Project Repository"
]
},
"r3d100014372": {
"description": "Federation.figshare is a collaborative digital repository for Federation researchers, professional staff and Higher Degree by Research students to store, share and publish their digital files. It accepts all forms of digital research outputs including audio, video, PDF, images, code, datasets, presentations and more.",
"homepage": "https://federation.figshare.com/",
"name": "Federation.figshare",
"prefix": "r3d100014372",
"synonyms": [
"Federation University Australia figshare"
]
},
"r3d100014373": {
"description": "Repository of the Institute of Law Studies of the Polish Academy of Sciences. It provides access to publications by our academic staff (both final versions and manuscripts), as well as researchers' data resulted projects carried out by academics. The institutional repository is also a place for making available publications issued by the Institute's Publishing House (both books and scientific journal), as well as digitized library materials. Materials protected by copyright are made available online only to authorized users (employees) or other users - in the reading room of the IlS PAS Library.",
"homepage": "https://e-bp.inp.pan.pl/",
"name": "e-Biblioteka Prawnicza",
"prefix": "r3d100014373",
"synonyms": [
"e-Law Library"
],
"xrefs": {
"opendoar": "10786"
}
},
"r3d100014375": {
"description": "The National Health Research and Studies Portal (NHRSP) is an initiative to build a national digital research data infrastructure, that provides data for health-related research, to meet tomorrow's health challenges. NHRSP aims to make health research more sustainable, efficient and responsive to health challenges, through research data sharing and re-cycling, in accordance with the ethical standards of scientific research.",
"homepage": "https://nhrsp.shc.gov.sa/",
"name": "National Health Research and Studies Portal",
"prefix": "r3d100014375",
"synonyms": [
"NHRSP",
"NahrSab"
]
},
"r3d100014377": {
"description": "The Research Data Center at LIfBi (Forschungsdatenzentrum, FDZ-LIfBi) is primarily responsible for the user-friendly preparation of survey and test data of the National Educational Panel Study (NEPS) and its provision to researchers in the form of Scientific Use Files. Data from other panel studies such as ReGES are also part of the research data infrastructure. The FDZ-LIfBi offers comprehensive documentation of the data material in German and English. It ensures secure and flexible data access via several options (download, remote, on-site). Further services are contract and authorization management, regular data trainings and workshops, annual user conferences, the semi-annual newsletter \"LIfBi data\", a collection of video tutorials, an online discussion forum and several other tools. The FDZ-LIfBi became accredited by the German Data Forum (RatSWD) in 2012 and has since been actively involved in the Committee for Data Access (FDI Ausschuss). As part of the quality assurance, it demonstrates compliance with the criteria of FAIR data provision and data access in an annual monitoring.",
"homepage": "https://www.lifbi.de/en-us/Start/Data-Services",
"name": "Forschungsdatenzentrum des LIfBi",
"prefix": "r3d100014377",
"synonyms": [
"FDZ-LIfBi",
"Forschungsdatenzentrum des Leibniz-Instituts fΓΌr BildungsverlΓ€ufe",
"Research Data Center at the Leibniz Institute for Educational Trajectories"
]
},
"r3d100014378": {
"description": "The Research Data Center of the Research Institute Social Cohesion (RDC-RISC) supports the scientific community by establishing a portal to available data relevant for empirical analysis on issues of social cohesion. This data portal includes data collected within the Research Institute Social Cohesion (RISC) as well as external data. The RDC-RISC also fulfills central tasks of documenting, archiving and providing the quantitative data collected at the RISC for secondary scientific use.",
"homepage": "https://fgz-risc-data.de/en/",
"name": "Research Data Centre of the Research Institute Social Cohesion",
"prefix": "r3d100014378",
"synonyms": [
"FDZ-FGZ",
"Forschungsdatenzentrum des Forschungsinstitut Gesellschaftlicher Zusammenhalt",
"RDC-RISC"
]
},
"r3d100014379": {
"description": "The Research Data Centre of the Leibniz Institute of Ecological Urban and Regional Development (IOER) provides high-resolution data, methods, indicators, models, tools and scenarios for cross-disciplinary, spatial sustainability research. The IOER RDC focuses, among others, on the topics of settlement and open space development, ecosystems of Germany and the built environment. The data and information offered are addressed to scientists, public administrators as well as the general public.",
"homepage": "https://ioer-fdz.de/en",
"name": "Research Data Centre of the Leibniz Institute of Ecological Urban and Regional Development",
"prefix": "r3d100014379",
"synonyms": [
"Forschungsdatenzentrum am Leibniz-Institut fΓΌr ΓΆkologische Raumentwicklung",
"IOER RDC",
"IΓR-FDZ"
]
},
"r3d100014380": {
"description": "The Research Open Data Repository of Uruguay (Redata) seeks to encourage the publication and reuse of national research data results in any area or discipline.\nIt is a project of the National Agency for Research and Innovation (ANII) of Uruguay and has the following objectives:\nFacilitate the identification, verification and reuse of research results.\nMinimize duplication of efforts in data collection.\nDevelop capacities at the national level for data management subject to international standards and best practices.\nContribute to the development of infrastructures for open science, in line with international recommendations and trends.",
"homepage": "https://redata.anii.org.uy",
"name": "Redata",
"prefix": "r3d100014380",
"synonyms": [
"Repositorio de datos abiertos de investigaciΓ³n de Uruguay"
]
},
"r3d100014382": {
"description": "The portal that allows you, in a centralized way, to search and access all the primary research data sets available in open access through the institutional digital repositories that make up the Sistema Nacional de Repositorios Digitales (SNRD)",
"homepage": "https://dacytar.mincyt.gob.ar/",
"name": "DACyTAr",
"prefix": "r3d100014382"
},
"r3d100014383": {
"description": "Observatorio Medioambiental La Plata is a joint initiative between CONICET, UNLP and CICPBA, which seeks to assist in the survey and development of proposals to address environmental problems in the Greater La Plata region and other regions of the province of Buenos Aires, Argentina.",
"homepage": "http://omlp.sedici.unlp.edu.ar/",
"name": "Observatorio Medioambiental La Plata",
"prefix": "r3d100014383"
},
"r3d100014384": {
"description": "In accordance with National Law No. 26,899 on the Creation of Open Access Institutional Digital Repositories, INTA Digital (Repositorio Institucional-Biblioteca Digital) was founded to provide public, open and free access to scientific and technological production, to agricultural dissemination and extension, to all forms of knowledge transfer and the experiences carried out by researchers, professionals, technicians, and INTA agents.",
"homepage": "https://repositorio.inta.gob.ar/xmlui/discover?filtertype_1=dc.subtype&filter_relational_operator_1=contains&filter_1=dato",
"name": "INTA Digital - Repositorio institucional",
"prefix": "r3d100014384",
"synonyms": [
"Repositorio Institucional-Biblioteca Digital"
]
},
"r3d100014385": {
"description": "Soil open data portal of the province of CΓ³rdoba, Argentina.",
"homepage": "https://sueloscordoba-agrounc.opendata.arcgis.com/",
"name": "Suelos de CΓ³rdoba",
"prefix": "r3d100014385"
},
"r3d100014387": {
"description": "RIO, Olavide Institutional Repository, aims to guarantee the preservation, access and open dissemination of the scientific, teaching and institutional production of the Pablo de Olavide University of Seville.",
"homepage": "https://rio.upo.es",
"name": "Repositorio Institucional Olavide",
"prefix": "r3d100014387",
"synonyms": [
"RIO"
],
"xrefs": {
"opendoar": " 3034"
}
},
"r3d100014388": {
"description": "Institutional Repository of the Pontificia Universidad CatΓ³lica Argentina",
"homepage": "https://repositorio.uca.edu.ar/?locale=es",
"name": "Repositorio Institucional UCA",
"prefix": "r3d100014388",
"synonyms": [
"Repositorio Institucional Pontificia Univesida CatΓ³lica Argentina"
]
},
"r3d100014389": {
"description": "The Italian Archive of Historical Earthquake Data ASMI (Archivio Storico Macrosismico Italiano) provides access to data on more than 6500 Italian earthquakes in the period 461 b.C to 2020, deriving from more than 430 seismological studies. For each earthquake, different kinds of studies are accessible, giving a wide perspective on the multiplicity of the available information.",
"homepage": "https://emidius.mi.ingv.it/ASMI/index_en.php",
"name": "Archivio Storico Macrosismico Italiano",
"prefix": "r3d100014389",
"synonyms": [
"ASMI",
"Italian Archive of Historical Earthquake Data"
],
"xrefs": {
"doi": "10.13127/asmi"
}
},
"r3d100014390": {
"description": "The BULERIA Institutional Repository is an open access digital archive that houses the full text of documents generated by members of the University of LeΓ³n in the development of their academic and research activity. The repository also holds the University's institutional documentation. In accordance with the principles of the Open Science movement, the aim is to facilitate the recovery, reuse and preservation of research results, in addition to promoting the dissemination and visibility of the scientific production of the Institution, effectively guaranteeing the advancement of science.",
"homepage": "https://buleria.unileon.es/",
"name": "BULERIA",
"prefix": "r3d100014390",
"xrefs": {
"opendoar": "2010",
"roar": "3739"
}
},
"r3d100014392": {
"description": "The Amazon Tall Tower Observatory (ATTO) is a joint German-Brazilian project launched in 2009. ATTO is with its tall tower, the associated research infrastructure and scientific plots a unique interdisciplinary scientific platform in a region of global significance. Its core objective is to obtain a detailed understanding of the biogeochemical cycles and energy fluxes at the geo-, bio-, atmosphere interface in the Amazon, and to integrate this knowledge into diverse climate and Earth system models to improve our prognostic abilities regarding climatic and ecological processes as well as our understanding of the various effects of global climate change.\nThe ATTO Data Portal is a data management platform, built for storing, sharing, exchanging and publishing data of the ATTO research consortium scientists.",
"homepage": "https://www.attodata.org/",
"name": "ATTO data portal",
"prefix": "r3d100014392",
"synonyms": [
"Amazon Tall Tower Observatory data portal"
]
},
"r3d100014394": {
"description": "IG PAS Data Portal is an open data platform for Institute of Geophysics Polish Academy of Sciences. This Portal is used to collect and share IG PAS data, taking into account access to the data from external repositories.\nIG PAS data are open and provided for free, use in non-commercial purpose under applicable laws on data sharing public and publicly-funded. In the case of using data by external entities, the data source must be cited following the IG PAS guidelines contained in the metadata of the IG PAS Data Portal (information on how to cite data is included in the Dataset Citation field).\nThis Data Portal is currently a work in progress, and we will be adding much more data of IG PAS in the coming months as well as developing a host of new interactive features where users can explore the data in several ways.",
"homepage": "https://dataportal.igf.edu.pl/",
"name": "IG PAS Data Portal",
"prefix": "r3d100014394",
"synonyms": [
"Institute of Geophysics Polish Academy of Sciences Data Portal",
"Instytut Geofizyki Polskiej Akademii Nauk Data Portal"
]
},
"r3d100014396": {
"description": "repOS is the institutional repository of HafenCity University Hamburg. It's open access and supports the publication of scientific publications and research data.",
"homepage": "https://repos.hcu-hamburg.de/",
"name": "repOS : The Open Science Repository of the HCU",
"prefix": "r3d100014396",
"synonyms": [
"repOS : Das Open Science Repository der HCU"
]
},
"r3d100014397": {
"description": "DidΟmena is the platform that enables EHESS research units to organize, share and perpetuate the data used or produced as part of their work. Data are described according to scientific and technical information standards. The DidΟmena publication is primarily intended to illustrate or support published results; but it also makes it possible to reuse of data in other research projects and, more generally access to data for all those interested in social science research.",
"homepage": "https://didomena.ehess.fr/",
"name": "DidΓ³mena",
"prefix": "r3d100014397",
"synonyms": [
"Didomena",
"EHESS research data repository"
]
},
"r3d100014398": {
"description": "Redivis is a data platform for academic research. It provides research organizations with a central hub where researchers can easily discover, access, and analyze their data.",
"homepage": "https://redivis.com",
"name": "Redivis",
"prefix": "r3d100014398",
"xrefs": {
"scr": "023111"
}
}
} ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9739666
bioregistry-0.11.12/src/bioregistry/external/rrid/ 0000755 0001751 0000177 00000000000 14655546227 021556 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/rrid/__init__.py 0000644 0001751 0000177 00000007164 14655542206 023670 0 ustar 00runner docker """A source for the SciCrunch Registry (SCR).
The SciCrunch static data was suggested by Anita Bandrowski in
https://github.com/biopragmatics/bioregistry/issues/949#issuecomment-1747702117.
Based on the name, it was likely exported on August 24th, 2023. It can be accessed at
https://docs.google.com/spreadsheets/d/1BEPZXZsENhK7592AR83xUwbPbR2J-GVQ/edit?\
usp=sharing&ouid=107737386203376389514&rtpof=true&sd=true.
"""
import csv
from pathlib import Path
from typing import Mapping
from bioregistry.constants import RAW_DIRECTORY
from bioregistry.external.alignment_utils import Aligner
__all__ = [
"get_rrid",
"RRIDAligner",
]
HERE = Path(__file__).parent.resolve()
PATH = RAW_DIRECTORY.joinpath("rrid.tsv")
COLUMN_RENAMES = {"Resource_Name": "name"}
skip = {"RIN", "Resource Information Network"}
#: FIXME - see https://github.com/biopragmatics/bioregistry/issues/954
UNCURATABLE = {
"XEP": "could not find an example entity number",
"CWRU": "could not find evidence that this is an identifier resource",
"XGSC": "could not find evidence that this is an identifier resource",
"SSCLBR": "dead resource",
"EXRC": "resource does not have stable/referencable identifiers for entities",
"IMSR": "meta-site that seems to wrap other IMSR sites",
"IMSR_CARD": "dead website",
"IMSR_CMMR": "just a wrapper around MGI",
"IMSR_CRL": "Massive site, too cryptic, can't find",
"IMSR_GPT": "actual URLs don't match accession numbers",
"IMSR_HAR": "could not find evidence that this is an identifier resource",
"IMSR_NM-KI": "multiple conflicting identifiers - actual URLs don't match accession numbers",
"IMSR_NIG": "could not find evidence that this is an identifier resource",
"IMSR_TIGM": "could not find evidence that this is an identifier resource",
}
def get_rrid(force_download: bool = False) -> Mapping[str, Mapping[str, str]]:
"""Get RRIDs."""
rv = {}
with PATH.open() as file:
reader = csv.DictReader(file, delimiter="\t")
for record in reader:
rrid_pattern = record.get("RRID_Identifier_Pattern")
if not rrid_pattern or not rrid_pattern.startswith("RRID:"):
continue
prefix = rrid_pattern[len("RRID:") :].rstrip("_")
ddd = {
"name": record["Resource_Name"],
"homepage": record["Resource_URL"],
"scr": record["scr_id"][len("SCR_") :],
# "uri_format": f"https://scicrunch.org/resolver/RRID:{prefix}_$1",
}
pubmeds = [
x[len("PMID:") :]
for x in _split(record["Defining_Citation"])
if x.startswith("PMID:")
]
if pubmeds:
ddd["pubmeds"] = pubmeds
keywords = sorted(set(_split(record["Keywords"])).difference(skip))
if keywords:
ddd["keywords"] = keywords
abbreviation = record["Abbreviation"]
if abbreviation and abbreviation != prefix:
ddd["abbreviation"] = abbreviation
twitter = record["Twitter_Handle"]
if twitter:
ddd["twitter"] = twitter.lstrip("@")
# could get license
rv[prefix] = ddd
return rv
def _split(s: str):
return [c.strip() for c in s.split(",")]
class RRIDAligner(Aligner):
"""Aligner for the RRID."""
key = "rrid"
getter = get_rrid
alt_key_match = "abbreviation"
curation_header = ("name", "homepage")
def get_skip(self) -> Mapping[str, str]:
"""Get prefixes to skip."""
return UNCURATABLE
if __name__ == "__main__":
RRIDAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1723255958.9739666
bioregistry-0.11.12/src/bioregistry/external/togoid/ 0000755 0001751 0000177 00000000000 14655546227 022103 5 ustar 00runner docker ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/togoid/__init__.py 0000644 0001751 0000177 00000005105 14655542206 024206 0 ustar 00runner docker # -*- coding: utf-8 -*-
"""Download TogoID."""
import json
from pathlib import Path
from typing import Dict
import requests
import yaml
from bioregistry.constants import RAW_DIRECTORY, URI_FORMAT_KEY
from bioregistry.external.alignment_utils import Aligner
__all__ = [
"get_togoid",
"TogoIDAligner",
]
DIRECTORY = Path(__file__).parent.resolve()
RAW_PATH = RAW_DIRECTORY / "togoid.json"
PROCESSED_PATH = DIRECTORY / "processed.json"
ONTOLOGY_URL = (
"https://raw.githubusercontent.com/togoid/togoid-config/main/ontology/togoid-ontology.ttl"
)
DATASET_URL = "https://raw.githubusercontent.com/togoid/togoid-config/main/config/dataset.yaml"
def _get_ontology() -> Dict[str, str]:
import rdflib
graph = rdflib.Graph()
graph.parse(ONTOLOGY_URL, format="turtle")
rows = graph.query("SELECT ?namespace ?prefix WHERE { ?namespace dcterms:identifier ?prefix }")
return {
str(prefix): namespace.removeprefix("http://togoid.dbcls.jp/ontology#")
for namespace, prefix in rows
}
def _get_dataset():
data = yaml.safe_load(requests.get(DATASET_URL).text)
rv = {}
for prefix, record in data.items():
name = record.get("label")
if not name:
continue
rr = {
"name": name,
"pattern": record["regex"].replace("", ""),
URI_FORMAT_KEY: record["prefix"] + "$1", # this is right, they named it weird
}
examples_lists = record.get("examples", [])
if examples_lists:
rr["examples"] = examples_lists[0]
category = record.get("category")
if category:
rr["keywords"] = [category]
integbio_catalog_id = record.get("catalog")
if integbio_catalog_id and integbio_catalog_id != "FIXME":
rr["catalog"] = integbio_catalog_id
rv[prefix] = rr
return rv
def get_togoid(*, force_download: bool = False, force_refresh: bool = False):
"""Get the TogoID data."""
if PROCESSED_PATH.exists() and not force_refresh:
with PROCESSED_PATH.open() as file:
return json.load(file)
key_to_prefix = _get_ontology()
records = _get_dataset()
rv = {
key_to_prefix[key]: record | {"prefix": key_to_prefix[key]}
for key, record in records.items()
}
with PROCESSED_PATH.open("w") as file:
json.dump(rv, file, indent=2, sort_keys=True)
return rv
class TogoIDAligner(Aligner):
"""Aligner for TogoID."""
key = "togoid"
getter = get_togoid
curation_header = ("name", "uri_format")
if __name__ == "__main__":
TogoIDAligner.cli()
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/external/togoid/processed.json 0000644 0001751 0000177 00000136232 14655542206 024765 0 ustar 00runner docker {
"AffyProbeset": {
"examples": [
"1553582_a_at",
"211531_x_at",
"202573_at",
"201640_x_at",
"205117_at",
"201017_at",
"205099_s_at",
"200614_at",
"201895_at",
"202666_s_at"
],
"keywords": [
"Probe"
],
"name": "Affymetrix probeset",
"pattern": "^(?\\d{3,}(?:_[a-z])?_at)$",
"prefix": "AffyProbeset",
"uri_format": "http://identifiers.org/affy.probeset/$1"
},
"AssemblyInsdc": {
"examples": [
"GCA_000001215",
"GCA_000001405",
"GCA_000001545",
"GCA_000001635",
"GCA_000001735",
"GCA_000001765",
"GCA_000001895",
"GCA_000001905",
"GCA_000001985",
"GCA_000002035"
],
"keywords": [
"Genome"
],
"name": "Assembly INSDC",
"pattern": "^(?GCA_\\d{9})(\\.\\d+)?$",
"prefix": "AssemblyInsdc",
"uri_format": "http://identifiers.org/insdc.gca/$1"
},
"AssemblyRefseq": {
"examples": [
"GCF_000002035",
"GCF_009870125",
"GCF_000840205",
"GCF_000004195",
"GCF_000475195",
"GCF_000296755",
"GCF_000151885",
"GCF_000715135",
"GCF_001039355",
"GCF_000331145"
],
"keywords": [
"Genome"
],
"name": "Assembly RefSeq",
"pattern": "^(?GCF_\\d{9})(\\.\\d+)?$",
"prefix": "AssemblyRefseq",
"uri_format": "http://identifiers.org/insdc.gca/$1"
},
"Atc": {
"examples": [
"J01DD11",
"B02BA02",
"A03AD30",
"R03AC17",
"J01CA05",
"D07AB07",
"D07XB03",
"G04CA01",
"S01BC11",
"G03DB05"
],
"keywords": [
"Drug"
],
"name": "ATC classification",
"pattern": "^(?[A-Z]\\d{2}[A-Z]{2}\\d{2})$",
"prefix": "Atc",
"uri_format": "http://identifiers.org/atc/$1"
},
"Bioproject": {
"catalog": "nbdc00476",
"examples": [
"PRJDB575",
"PRJDB1880",
"PRJDB478",
"PRJDA45949",
"PRJEB6285",
"PRJEA28961",
"PRJEB2222",
"PRJNA30641",
"PRJNA68235",
"PRJNA42549"
],
"keywords": [
"Project"
],
"name": "BioProject",
"pattern": "^(?PRJ[DEN][A-Z]\\d+)$",
"prefix": "Bioproject",
"uri_format": "http://identifiers.org/bioproject/$1"
},
"BioprojectUmbrella": {
"catalog": "nbdc00476",
"examples": [
"PRJDB10770",
"PRJDB14691",
"PRJEB55721",
"PRJEB56110",
"PRJNA388429",
"PRJNA510115",
"PRJNA834739",
"PRJNA561326",
"PRJNA672702",
"PRJNA248220"
],
"keywords": [
"Project"
],
"name": "BioProject umbrella",
"pattern": "^(?PRJ[DEN][A-Z]\\d+)$",
"prefix": "BioprojectUmbrella",
"uri_format": "http://identifiers.org/bioproject/$1"
},
"Biosample": {
"catalog": "nbdc01983",
"examples": [
"SAMD00003683",
"SAMD00006315",
"SAMD00003741",
"SAMD00011226",
"SAMN13091859",
"SAMN05877962",
"SAMN05877838",
"SAMEA104232303",
"SAMEA4760552",
"SAMEA1572228"
],
"keywords": [
"Sample"
],
"name": "BioSample",
"pattern": "^(?SAM[NED]\\w?\\d+)$",
"prefix": "Biosample",
"uri_format": "http://identifiers.org/biosample/$1"
},
"Ccds": {
"catalog": "nbdc00023",
"examples": [
"CCDS1471",
"CCDS10913",
"CCDS14790",
"CCDS35175",
"CCDS2395",
"CCDS58412",
"CCDS55555",
"CCDS34401",
"CCDS41889",
"CCDS9052"
],
"keywords": [
"Gene"
],
"name": "Consensus CDS",
"pattern": "^(?CCDS\\d+)(?:\\.\\d+)?$",
"prefix": "Ccds",
"uri_format": "http://identifiers.org/ccds/$1"
},
"Cellosaurus": {
"catalog": "nbdc02180",
"examples": [
"CVCL:7T24",
"CVCL:SE45",
"CVCL:XG73",
"CVCL:B6HT",
"CVCL:WM34",
"CVCL:7891",
"CVCL:FV52",
"CVCL:0367",
"CVCL:9Z18",
"CVCL:CG19"
],
"keywords": [
"CellLine"
],
"name": "Cellosaurus",
"pattern": "^CVCL[:_](?[A-Z0-9]{4})$",
"prefix": "Cellosaurus",
"uri_format": "http://www.cellosaurus.org/CVCL_$1"
},
"Chebi": {
"catalog": "nbdc00027",
"examples": [
"84824",
"40167",
"32807",
"87666",
"57524",
"64860",
"94440",
"18005",
"4806",
"50158"
],
"keywords": [
"Compound"
],
"name": "ChEBI compound",
"pattern": "^(?:CHEBI[:_])?(?\\d+)$",
"prefix": "Chebi",
"uri_format": "http://purl.obolibrary.org/obo/CHEBI_$1"
},
"ChemblCompound": {
"catalog": "nbdc02555",
"examples": [
"CHEMBL121649",
"CHEMBL190334",
"CHEMBL3103282",
"CHEMBL69329",
"CHEMBL2105131",
"CHEMBL2177390",
"CHEMBL3091820",
"CHEMBL1200335",
"CHEMBL3094412",
"CHEMBL67367"
],
"keywords": [
"Compound"
],
"name": "ChEMBL compound",
"pattern": "^(?CHEMBL\\d+)$",
"prefix": "ChemblCompound",
"uri_format": "http://identifiers.org/chembl.compound/$1"
},
"ChemblTarget": {
"catalog": "nbdc02555",
"examples": [
"CHEMBL2788",
"CHEMBL3091264",
"CHEMBL3831324",
"CHEMBL5524",
"CHEMBL5597",
"CHEMBL3983",
"CHEMBL4187",
"CHEMBL3391681",
"CHEMBL5135",
"CHEMBL1255130"
],
"keywords": [
"Protein"
],
"name": "ChEMBL target",
"pattern": "^(?CHEMBL\\d+)$",
"prefix": "ChemblTarget",
"uri_format": "http://identifiers.org/chembl.target/$1"
},
"Clinvar": {
"catalog": "nbdc01514",
"examples": [
"658761",
"619209",
"745342",
"11955",
"731668",
"724289",
"725734",
"743127",
"789913",
"5302"
],
"keywords": [
"Variant"
],
"name": "ClinVar variant",
"pattern": "^(VCV0*)?(?(\\d{1,9}))$",
"prefix": "Clinvar",
"uri_format": "http://identifiers.org/clinvar/$1"
},
"Cog": {
"catalog": "nbdc00397",
"examples": [
"COG0130",
"COG0663",
"COG0762",
"COG1186",
"COG1285",
"COG1390",
"COG3079",
"COG3354",
"COG4957",
"COG5379"
],
"keywords": [
"Ortholog"
],
"name": "COG",
"pattern": "^(?COG\\d{4})$",
"prefix": "Cog",
"uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1"
},
"Dbsnp": {
"catalog": "nbdc00206",
"examples": [
"rs746303788",
"rs1407020249",
"rs374003162",
"rs4647297",
"rs549539526",
"rs1387864740",
"rs1177577242",
"rs769848663",
"rs16961655",
"rs79135400"
],
"keywords": [
"Variant"
],
"name": "dbSNP",
"pattern": "^(?rs\\d+)$",
"prefix": "Dbsnp",
"uri_format": "http://identifiers.org/dbsnp/$1"
},
"Doid": {
"catalog": "nbdc00261",
"examples": [
"DO:9036",
"DO:3159",
"DO:10964",
"DO:12698",
"DO:0060459",
"DO:11840",
"DO:11339",
"DO:914",
"DO:9945",
"DO:1407"
],
"keywords": [
"Phenotype"
],
"name": "Disease ontology",
"pattern": "^DO(?:ID)?[:_](?\\d+)$",
"prefix": "Doid",
"uri_format": "http://purl.obolibrary.org/obo/DOID_$1"
},
"Drugbank": {
"catalog": "nbdc01071",
"examples": [
"DB15589",
"DB13471",
"DB05830",
"DB07423",
"DB07074",
"DB08912",
"DB02908",
"DB05088",
"DB05229",
"DB08910"
],
"keywords": [
"Drug"
],
"name": "DrugBank",
"pattern": "^(?DB\\d{5})$",
"prefix": "Drugbank",
"uri_format": "http://identifiers.org/drugbank/$1"
},
"Ec": {
"catalog": "nbdc01883",
"examples": [
"1.6.3.1",
"2.4.1.353",
"1.1.1.288",
"1.5.1.2",
"3.1.1.71",
"1.3.1.31",
"3.5.1.29",
"1.16.1.1",
"3.1.3.48",
"2.3.1.138"
],
"keywords": [
"Function"
],
"name": "Enzyme nomenclature",
"pattern": "^(?:EC:)?(?\\d+\\.(?:(?:-\\.-\\.-)|\\d+\\.(?:(?:-\\.-)|\\d+\\.(?:-|n?\\d+))))$",
"prefix": "Ec",
"uri_format": "http://identifiers.org/ec-code/$1"
},
"EnsemblGene": {
"catalog": "nbdc00054",
"examples": [
"ENSG00000186283",
"ENSAMEG00000018238",
"ENSG00000167916",
"ENSG00000213417",
"ENSG00000133328",
"ENSG00000274404",
"ENSG00000184363",
"FBgn0021742",
"FBgn0030057",
"FBgn0265139"
],
"keywords": [
"Gene"
],
"name": "Ensembl gene",
"pattern": "^(?:(?:(?ENS[A-Z]*G\\d{11})(?:\\.\\d+)?)|(?FBgn\\d{7})|(?:(?MGP_[A-Za-z0-9]+_G\\d{7})(?:\\.\\d+)?)|(?LRG_\\d+)|(?WBGene\\d{8})|(?Y[A-Z]{2}\\d{3}[A-Z](?:-[A-Z])?)|(?Q\\d{4})|(?[A-Z]{3}\\d{1,3}(?:-\\d)?)|(?snR\\d+-?[A-Za-z]?)|(?t[A-Z]\\([ACGUX]{3}\\)[A-Z]\\d?))$",
"prefix": "EnsemblGene",
"uri_format": "http://identifiers.org/ensembl/$1"
},
"EnsemblProtein": {
"catalog": "nbdc00054",
"examples": [
"ENSP00000365411",
"ENSP00000420674",
"ENSAZOP00000020796",
"FBpp0070277",
"FBpp0070535",
"ENSAZOP00000019433",
"ENSP00000372042",
"ENSAZOP00000017910",
"ENSP00000370977",
"ENSP00000481894"
],
"keywords": [
"Protein"
],
"name": "Ensembl protein",
"pattern": "^(?:(?:(?ENS[A-Z]*P\\d{11})(?:\\.\\d+)?)|(?FBpp\\d{7})|(?:(?MGP_[A-Za-z0-9]+_P\\d{7})(?:\\.\\d+)?)|(?LRG_\\d+p\\d+(?:-\\d)?)|(?(?:[A-Za-z0-9][A-Za-z0-9_]+)\\.t?\\d+[a-z]?(?:\\.\\d+)?)|(?Y[A-Z]{2}\\d{3}[A-Z](?:-[A-Z])?)|(?Q\\d{4}))$",
"prefix": "EnsemblProtein",
"uri_format": "http://identifiers.org/ensembl/$1"
},
"EnsemblTranscript": {
"catalog": "nbdc00054",
"examples": [
"ENST00000638000",
"ENST00000307864",
"ENSTRUT00000006732",
"ENSAMET00000021072",
"ENSAZOT00000021040",
"ENST00000622541",
"ENST00000462612",
"ENSBTAT00000072441",
"ENSAZOT00000005048",
"ENST00000475822"
],
"keywords": [
"Transcript"
],
"name": "Ensembl transcript",
"pattern": "^(?:(?:(?ENS[A-Z]*T\\d{11})(?:\\.\\d+)?)|(?FBtr\\d{7})|(?:(?MGP_[A-Za-z0-9]+_T\\d{7})(?:\\.\\d+)?)|(?LRG_\\d+t\\d+(?:-\\d)?)|(?(?:[A-Za-z0-9][A-Za-z0-9_]+)\\.t?\\d+[a-z]?(?:\\.\\d+)?)|(?Y[A-Z]{2}\\d{3}[A-Z](?:-[A-Z])?(?:_[a-z]{1,3}RNA)?)|(?Q\\d{4}_[a-z]{1,3}RNA)|(?[A-Z]{3}\\d{1,3}(?:-\\d)?_[a-z]{1,3}RNA)|(?snR\\d+-?[A-Za-z]?_sno?RNA)|(?
{% for term in terms %}
{% endfor %}
{% endblock %}
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1723253894.0
bioregistry-0.11.12/src/bioregistry/app/templates/meta/summary.html 0000644 0001751 0000177 00000045557 14655542206 025074 0 ustar 00runner docker {% extends "prose.html" %}
{% block title %}Bioregistry Summary{% endblock %}
{% block content %}
